# 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/Halopiger_xanaduensis_SH_6_uid68105/NC_015666.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/Halopiger_xanaduensis_SH_6_uid68105/NC_015666.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Halopiger_xanaduensis_SH_6_uid68105/NC_015666.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|336252097|ref|YP_004595204.1|  [L=65]
Description: hypothetical protein Halxa_0686 [Halopiger xanaduensis SH-6]
Scores for 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   12.9   0.1       0.12   12.8   0.1    1.2  1  APC_u15   Unstructured region on APC between APC_crr regions 


Domain annotation for each model (and alignments):
>> APC_u15  Unstructured region on APC between APC_crr regions 5 and 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   6.8e-06      0.12       1      29 [.       6      34 ..       6      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.8e-06
                           APC_u15  1 FDDDdvDlSrEKAELrKgKeeKeaeaket 29
                                      FDDD vD+  E  E r ++e  e  ++++
  gi|336252097|ref|YP_004595204.1|  6 FDDDGVDVVYEGTEFRLERELIEEATEKS 34
                                      9******************9766555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.37u 0.99s 00:00:01.36 Elapsed: 00:00:03.41
# Mc/sec: 57.87
//
Query:       gi|336252098|ref|YP_004595205.1|  [L=534]
Description: methyl-accepting chemotaxis sensory transducer [Halopiger xanaduensis SH-6]
Scores for complete 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-37  129.0  22.7    1.6e-37  129.0  22.7    4.6  4  MCPsignal     Methyl-accepting chemotaxis protein (MCP) signa
    0.00075   19.7  36.1     0.0037   17.5   2.8    5.2  5  DUF948        Bacterial protein of unknown function (DUF948)
      0.002   16.9   7.7      0.002   16.9   7.7    2.6  2  AAA_13        AAA domain
     0.0061   16.7   0.1     0.0061   16.7   0.1    3.7  4  UPF0242       Uncharacterised protein family (UPF0242) N-term
     0.0063   16.6  24.6       0.26   11.3   2.1    4.7  4  DUF1664       Protein of unknown function (DUF1664)
  ------ inclusion threshold ------
      0.029   14.2   1.1      0.029   14.2   1.1    4.2  4  Phage_GP20    Phage minor structural protein GP20
      0.043   14.2   1.5      0.043   14.2   1.5    4.6  4  HAMP          HAMP domain
      0.077   13.1   0.3      0.077   13.1   0.3    5.1  6  COG2          COG (conserved oligomeric Golgi) complex compon
       0.11   11.9  19.1       0.33   10.4   2.7    3.1  3  Mce4_CUP1     Cholesterol uptake porter CUP1 of Mce4, putativ
       0.23   11.5  35.6        0.1   12.6   0.8    5.1  5  Laminin_II    Laminin Domain II
       0.33   10.9   0.1       0.33   10.9   0.1    3.5  3  ApoO          Apolipoprotein O
       0.43   10.5   6.7         13    5.7   0.1    3.8  3  DUF1759       Protein of unknown function (DUF1759)
       0.59   10.5  25.1        9.4    6.6   2.2    5.1  5  BLOC1_2       Biogenesis of lysosome-related organelles compl
        0.6   10.5  18.4         12    6.4   0.5    5.9  5  FlaC_arch     Flagella accessory protein C (FlaC)
       0.97    8.9  12.9       0.44   10.0   1.5    2.7  2  Allexi_40kDa  Allexivirus 40kDa protein
        1.8    8.7  14.4        2.3    8.4   2.5    3.9  4  Fib_alpha     Fibrinogen alpha/beta chain family
        2.9    7.7  11.3       0.87    9.4   0.1    4.7  5  DASH_Duo1     DASH complex subunit Duo1
          3    8.0   8.4        4.2    7.5   0.1    4.5  4  Med9          RNA polymerase II transcription mediator comple
        3.7    7.5  10.5       0.27   11.2   0.3    3.7  5  BORCS8        BLOC-1-related complex sub-unit 8
        3.9    6.9   8.9        2.6    7.5   0.5    3.3  3  DUF2452       Protein of unknown function (DUF2452)
        5.1    4.9  12.8          5    5.0   2.0    2.2  2  Prominin      Prominin
        7.7    6.7  25.4       0.33   11.1   3.9    4.4  4  IFT20         Intraflagellar transport complex B, subunit 20


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   5.7      0.59   4.8e+02      80     138 ..     115     173 ..     100     204 .. 0.66
   2 !    8.1  11.7    0.0026       2.1      96     162 ..     223     289 ..     205     294 .. 0.60
   3 !  129.0  22.7   1.9e-40   1.6e-37       6     168 ..     301     463 ..     296     467 .. 0.94
   4 ?    4.8   4.0     0.028        23     130     168 ..     460     498 ..     457     503 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.59
                                       HHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHH CS
                         MCPsignal  80 LAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveava 138
                                        A+r  + a+  +a  +e  ++ +d+ ++ e++++++e  +e  ++t++++k   ea+a
  gi|336252098|ref|YP_004595205.1| 115 AADRRREEAEASRAEAEESRRDAEDARSVAESSKREAEALTESLQRTATDFKGTMEAAA 173
                                       45555555555556666778888999999999999999999999999999998777654 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0026
                                       ..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  96 ieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevn 162
                                       +++++   d+ ++ +++ + v++ +++ +e +++l+++++++++++++++e+a++++  +++++e +
  gi|336252098|ref|YP_004595205.1| 223 TAVTESASDVERASQQVSESVQSIATTNAEQTRSLQTVADEMGDLSATIEEVASSADGVASTATEAA 289
                                       2334444444444455555555555555555567778888888888888888888777777777655 PP

  == domain 3  score: 129.0 bits;  conditional E-value: 1.9e-40
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHH CS
                         MCPsignal   6 easeeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkLAe 82 
                                       +a +   +  ++ +++v+++e++++   ei +i++ id iadQTNlLALNA+iEAA AG +G GFaVVAdE+++LA 
  gi|336252098|ref|YP_004595205.1| 301 DAADAMADIRQTSEETVAKVEALDEDIGEIIEIVDLIDRIADQTNLLALNASIEAATAGSAGSGFAVVADEIKSLAG 377
                                       444444455677899************************************************************** PP

                                       HHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  83 rsaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasie 159
                                       ++ +a++ ie+ i+++   + ++v+ ++  r +v  g++++e + +al++i+++v+ v  ++qe+++a+++q+as++
  gi|336252098|ref|YP_004595205.1| 378 EASEATQRIESQIANVRSSTTETVDEIQGMRDQVTDGVTTIEGSIDALEDITDHVETVHMSIQEVNRATDQQAASAQ 454
                                       ***************************************************************************** PP

                                       HHHHHHHHH CS
                         MCPsignal 160 evnqaveev 168
                                       ev + ve v
  gi|336252098|ref|YP_004595205.1| 455 EVVSMVEDV 463
                                       **9999876 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 130 lkeiveavaevadlvqeiaaaseeqsasieevnqaveev 168
                                       ++++v a ++ +d+ q ++aa+eeq+asi +v+++ ++ 
  gi|336252098|ref|YP_004595205.1| 460 VEDVVGASERTEDETQSVSAAAEEQTASIAQVSESTDAF 498
                                       56789999999**********************998765 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 ?   -0.1   0.1       1.4   1.1e+03      36      68 ..     138     170 ..     125     180 .. 0.66
   2 !   12.1   5.6   0.00022      0.18       4      88 ..     191     275 ..     189     276 .. 0.87
   3 ?    3.4   0.2      0.12        95      35      71 ..     299     335 ..     281     348 .. 0.73
   4 !   17.5   2.8   4.5e-06    0.0037      25      88 ..     380     443 ..     363     444 .. 0.62
   5 ?    2.9   5.4      0.16   1.3e+02      28      85 ..     439     496 ..     434     512 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.4
                            DUF948  36 eelekqvdpilkevedllakvnelledvnekle 68 
                                       e+ ++ +++  +e+e+l++  ++++ d ++ +e
  gi|336252098|ref|YP_004595205.1| 138 EDARSVAESSKREAEALTESLQRTATDFKGTME 170
                                       555555566666777777777777777666555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00022
                            DUF948   4 lIaAiAFvvLviflivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadl 80 
                                         +A AF ++ + l +++l+l+   +e+a+  + +++ +  + + ++++ + v+ ++    e++ +++++ ++++dl
  gi|336252098|ref|YP_004595205.1| 191 TAIATAFNAMLADLERTMLELRAFSTEVATESTAVTESASDVERASQQVSESVQSIATTNAEQTRSLQTVADEMGDL 267
                                       56899999999999999999999999999999999999999999999999999999999999*************** PP

                            DUF948  81 gesvseln 88 
                                       +++++e+ 
  gi|336252098|ref|YP_004595205.1| 268 SATIEEVA 275
                                       ****9986 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.12
                            DUF948  35 ieelekqvdpilkevedllakvnelledvneklekvd 71 
                                        ++  + +  i + +e+++akv++l ed+ e +e vd
  gi|336252098|ref|YP_004595205.1| 299 ARDAADAMADIRQTSEETVAKVEALDEDIGEIIEIVD 335
                                       5566667777777778888888888888777666666 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 4.5e-06
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       ++  ++++++i+++++ ++++++e++++ ++v + +  +++ +++++ +t++v+++  s++e+n
  gi|336252098|ref|YP_004595205.1| 380 SEATQRIESQIANVRSSTTETVDEIQGMRDQVTDGVTTIEGSIDALEDITDHVETVHMSIQEVN 443
                                       3444555566666666666666666666666666666666677777777777777777777766 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.16
                            DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                       ++e++++ ++    +++++  ved++  ++++ ++ ++ +++ ++ t+++a+++es  
  gi|336252098|ref|YP_004595205.1| 439 IQEVNRATDQQAASAQEVVSMVEDVVGASERTEDETQSVSAAAEEQTASIAQVSESTD 496
                                       6777777777777788888888888888888888888888888888888888888765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0  10.8    0.0023       1.9     280     463 ..     146     337 ..     132     350 .. 0.65
   2 !   16.9   7.7   2.5e-06     0.002     285     454 ..     343     510 ..     337     515 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0023
                            AAA_13 280 efeekqerLekliekveskkselleklkavsdeasensafeed.keelkaeaealeeqLkglqraleaKrkepfksv 355
                                       +++++ e+L + +++ +++ +  +e  +a+  + ++++++e++    + ++++a+ + L+  + +l a  +e++++ 
  gi|336252098|ref|YP_004595205.1| 146 SSKREAEALTESLQRTATDFKGTMEAAAAGDLTRRLDPESESEaMTAIATAFNAMLADLERTMLELRAFSTEVATES 222
                                       45566666666677666666666667777777777777766662566666779999999999999**********77 PP

                            AAA_13 356 e.lesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseld....eykkkykklekaiek 427
                                       + ++++++++e+++++v+e  ++ia  N+  ++  + +++   +l +  +ee+ s  d    + +++ ++ e+   +
  gi|336252098|ref|YP_004595205.1| 223 TaVTESASDVERASQQVSESVQSIATTNAEQTRSLQTVADEMGDLSA-TIEEVASSADgvasTATEAAERGEAGRAN 298
                                       74699999********************8766666666666666665.33334444441112333444444544444 PP

                            AAA_13 428 lekelke...eeaelkkleeeikeLekqlrdekpaaeei 463
                                       + +++++   + +  ++  +++++L + + ++ ++++ i
  gi|336252098|ref|YP_004595205.1| 299 ARDAADAmadIRQTSEETVAKVEALDEDIGEIIEIVDLI 337
                                       444444400044444444444556666666555555555 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.5e-06
                            AAA_13 285 qerLekliekveskksellek.lkavsde.asensafeedkeelkaeaealeeqLkglqraleaKrkepfksve.le 358
                                       q +L  l +++e +++  + + ++ v+de +s+  ++ e+++ +++++ +++++ ++  ++++  r+++   v+ +e
  gi|336252098|ref|YP_004595205.1| 343 QTNLLALNASIEAATAGSAGSgFAVVADEiKSLAGEASEATQRIESQIANVRSSTTETVDEIQGMRDQVTDGVTtIE 419
                                       55566666666666666555534444443466667788889999999999999999999999999999999666368 PP

                            AAA_13 359 svkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkee 435
                                        + + +e i++ v+++  +i++ N+ +++ +++++e+ + +e  + ++      + +++ +++++a+e+ ++++++ 
  gi|336252098|ref|YP_004595205.1| 420 GSIDALEDITDHVETVHMSIQEVNRATDQQAASAQEVVSMVEDVVGASE-----RTEDETQSVSAAAEEQTASIAQV 491
                                       899999***********************************99776633.....3457889999999999******* PP

                            AAA_13 436 eaelkkleeeikeLekqlr 454
                                       ++ + + ++++ eLe +l 
  gi|336252098|ref|YP_004595205.1| 492 SESTDAFAAQATELEDRLD 510
                                       **************98875 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 !   16.7   0.1   7.4e-06    0.0061      32     135 ..      65     167 ..      53     175 .. 0.93
   2 ?    2.0   0.5      0.24   1.9e+02     121     166 ..     227     272 ..     179     279 .. 0.49
   3 ?    2.2   1.2      0.21   1.7e+02      79     149 ..     252     322 ..     207     353 .. 0.55
   4 ?   -0.1   4.9         1   8.3e+02      82     170 ..     426     510 ..     370     517 .. 0.44

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.4e-06
                           UPF0242  32 sWsllsiGlllaaaGsLlllllllkwekalkeklekskleekeaklteldeglktkeealeelqeeeeeLkeeldak 108
                                        W lls+ ll +  G   ++ +   ++  +++k e   +e+  +  ++ +e  +  +e+ e +++e ee ++  +  
  gi|336252098|ref|YP_004595205.1|  65 FWDLLSLILLGITTGVF-AITSTGSLSAVVDLKRERRSVEASRREAVAAKEAADRRREEAEASRAEAEESRRDAEDA 140
                                       6******9999999987.99999****************************************************** PP

                           UPF0242 109 eeelerlkeenqqLqekleaiaedfee 135
                                        +  e  k+e + L e l+ +a df+ 
  gi|336252098|ref|YP_004595205.1| 141 RSVAESSKREAEALTESLQRTATDFKG 167
                                       ************************985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.24
                           UPF0242 121 qLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvle 166
                                       +  +  e ++++++e+ + +  + ae++  lq+ + ++ ++ +++e
  gi|336252098|ref|YP_004595205.1| 227 ESASDVERASQQVSESVQSIATTNAEQTRSLQTVADEMGDLSATIE 272
                                       2223334444455555555555555555555555555544444444 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.21
                           UPF0242  79 eldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqe 149
                                       e+  +l+t ++++ +l +  ee +   d   ++  +  e+ +  +  + ++a  +++ ++ +ee++a+ + 
  gi|336252098|ref|YP_004595205.1| 252 EQTRSLQTVADEMGDLSATIEEVASSADGVASTATEAAERGEAGRANARDAADAMADIRQTSEETVAKVEA 322
                                       11234444444555555555555555666666666666666666666666666777777777777766554 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1
                           UPF0242  82 eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqeti 158
                                       e+++ + e++  + +e ++  ++++a  +e+  + e+    +e++e+   + + ++ ++eeq a    +++e+   +
  gi|336252098|ref|YP_004595205.1| 426 EDITDHVETVHMSIQEVNRATDQQAASAQEVVSMVEDVVGASERTED---ETQSVSAAAEEQTAS-IAQVSESTDAF 498
                                       22222233333333333333333333333333333333333333333...444444444444332.23455566666 PP

                           UPF0242 159 eeqrsvlekrqd 170
                                         q  +le r d
  gi|336252098|ref|YP_004595205.1| 499 AAQATELEDRLD 510
                                       666666666655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.8    0.0019       1.5      52     115 ..     185     248 ..     166     255 .. 0.85
   2 ?    4.5   0.6     0.041        34      57     120 ..     267     330 ..     248     345 .. 0.59
   3 !   11.3   2.1   0.00032      0.26      43     120 ..     365     442 ..     355     444 .. 0.81
   4 !    8.1   3.9    0.0031       2.5      55     121 ..     426     492 ..     413     495 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0019
                           DUF1664  52 qvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       + se+++a    +++ ++ +++++ e  + s+e++ e t+v e  s++++ +++v+e v+++++
  gi|336252098|ref|YP_004595205.1| 185 SESEAMTAIATAFNAMLADLERTMLELRAFSTEVATESTAVTESASDVERASQQVSESVQSIAT 248
                                       345788888999999********************************************99876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.041
                           DUF1664  57 laatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       l+at ++ +s  d v ++  e +e  ++ +++  ++ + +++i++ +e+  + ve l++ + +i
  gi|336252098|ref|YP_004595205.1| 267 LSATIEEVASSADGVASTATEAAERGEAGRANARDAADAMADIRQTSEETVAKVEALDEDIGEI 330
                                       3344445555555555555555555555556666666666666666666666666666665554 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00032
                           DUF1664  43 vesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                        + v+ +++++  + +++ ++++s+i++v ++  e+ + ++ ++++vt+    ++   + +e + + ve++ +++++
  gi|336252098|ref|YP_004595205.1| 365 FAVVADEIKSLAGEASEATQRIESQIANVRSSTTETVDEIQGMRDQVTDGVTTIEGSIDALEDITDHVETVHMSIQE 441
                                       67788999999999999999999*****9999988888888888888888777777777888888888888888777 PP

                           DUF1664 120 i 120
                                       +
  gi|336252098|ref|YP_004595205.1| 442 V 442
                                       6 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0031
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       e++++  +     i++v++  d+q++ ++e+ + v++v +  ++++++ +sv++a e+  +++++++
  gi|336252098|ref|YP_004595205.1| 426 EDITDHVETVHMSIQEVNRATDQQAASAQEVVSMVEDVVGASERTEDETQSVSAAAEEQTASIAQVS 492
                                       4566666677889*****************************************9999999888876 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 ?   -0.9   1.3       1.6   1.3e+03      23      79 ..     102     158 ..      89     176 .. 0.53
   2 ?    0.2   2.4      0.72   5.9e+02      19      67 ..     231     280 ..     215     333 .. 0.53
   3 ?   14.2   1.1   3.5e-05     0.029      16      77 ..     397     458 ..     368     464 .. 0.86
   4 ?   -0.5   0.2       1.2   9.7e+02      18      45 ..     486     513 ..     461     524 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.6
                        Phage_GP20  23 veeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadl 79 
                                       ve+ r +     +++d   e+ +++  ++ee  ++ e+    ++ +k e+ea  + l
  gi|336252098|ref|YP_004595205.1| 102 VEASRREAVAAKEAADRRREEAEASRAEAEESRRDAEDARSVAESSKREAEALTESL 158
                                       444444444444444444455555555555555555555555555555555544444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.72
                        Phage_GP20  19 kldeveeerdt.lkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkk 67 
                                       +++++ +++ + +++  +++ +q   L+++a +  +L ++iee+   ++ 
  gi|336252098|ref|YP_004595205.1| 231 DVERASQQVSEsVQSIATTNAEQTRSLQTVADEMGDLSATIEEVASSADG 280
                                       33333333322022222344455555555555556666666555544443 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 3.5e-05
                        Phage_GP20  16 tkakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakia 77 
                                       t + +de++  rd++++ +++ +++++ L++ +  +e++   i+e++ + +++ a +++ ++
  gi|336252098|ref|YP_004595205.1| 397 TTETVDEIQGMRDQVTDGVTTIEGSIDALEDITDHVETVHMSIQEVNRATDQQAASAQEVVS 458
                                       477899**********************************************9998887665 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.2
                        Phage_GP20  18 akldeveeerdtlkeqlkdrdkqLedLk 45 
                                       a++++v e  d +  q ++ +  L+ ++
  gi|336252098|ref|YP_004595205.1| 486 ASIAQVSESTDAFAAQATELEDRLDAFE 513
                                       3445555555555556555555555554 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.9   1.5e+03      28      49 ..     141     163 ..     113     167 .. 0.74
   2 ?   14.2   1.5   5.2e-05     0.043      16      52 ..     168     205 ..     163     206 .. 0.91
   3 ?    5.2   0.1     0.035        29      12      48 ..     238     275 ..     236     280 .. 0.67
   4 ?   -2.5   0.0       8.7   7.1e+03       7      28 ..     485     508 ..     484     511 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.9
                                       T.CCTTSSSHHHHHHHHHHHHHH CS
                              HAMP  28 r.lpvsgrDEiGeLarafNaMld 49 
                                       r + +s++ E  +L +++ + ++
  gi|336252098|ref|YP_004595205.1| 141 RsVAESSKREAEALTESLQRTAT 163
                                       35889999999999999988775 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.2e-05
                                       HHHHHTTTBTSSTCCTTSSSH.HHHHHHHHHHHHHHHH CS
                              HAMP  16 aarriaaGdldtrlpvsgrDE.iGeLarafNaMldrLr 52 
                                       ++++ aaGdl+ rl++++  E + ++a afNaMl  L+
  gi|336252098|ref|YP_004595205.1| 168 TMEAAAAGDLTRRLDPESESEaMTAIATAFNAMLADLE 205
                                       79999***********9999978***********9997 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.035
                                       HHHHHHHHHTTT.BTSSTCCTTSSSHHHHHHHHHHHHH CS
                              HAMP  12 rLaraarriaaG.dldtrlpvsgrDEiGeLarafNaMl 48 
                                       ++++++++ia      tr   +  DE+G+L +++++ +
  gi|336252098|ref|YP_004595205.1| 238 QVSESVQSIATTnAEQTRSLQTVADEMGDLSATIEEVA 275
                                       566777777765233333444678*******9999876 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 8.7
                                       HHHHHHHHHHHHHHTTT..BTSST CS
                              HAMP   7 lrPLrrLaraarriaaG..dldtr 28 
                                       ++++ ++++++++ aa   +l+ r
  gi|336252098|ref|YP_004595205.1| 485 TASIAQVSESTDAFAAQatELEDR 508
                                       578899999999999643355555 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 ?   -2.1   3.1       4.6   3.7e+03      75     113 ..      99     137 ..      88     162 .. 0.53
   2 ?    5.2   2.1     0.025        21      70     128 ..     210     273 ..     187     278 .. 0.71
   3 ?    0.9   0.3      0.55   4.5e+02      77     132 ..     266     323 ..     252     324 .. 0.51
   4 ?   -1.5   0.0         3   2.5e+03      70      92 ..     305     327 ..     294     344 .. 0.59
   5 ?   13.1   0.3   9.4e-05     0.077      67     117 ..     386     436 ..     378     453 .. 0.86
   6 ?    0.8   1.8      0.57   4.7e+02      83     114 ..     454     487 ..     437     513 .. 0.43

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.6
                              COG2  75 esplaaarkkvesvreklsereeeveskleeakeleekr 113
                                       + +++a r++  +++e+ ++r+ee e+  +ea+e ++  
  gi|336252098|ref|YP_004595205.1|  99 RRSVEASRREAVAAKEAADRRREEAEASRAEAEESRRDA 137
                                       344444455555555555555555555444444444433 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.025
                              COG2  70 eleevesplaaarkkvesvreklsereeeveskleeakeleekr.....ellklllkldevvek 128
                                       el+ +++++a+  + v++  + +++++++v++ ++  +  ++++      + + + +l++++e+
  gi|336252098|ref|YP_004595205.1| 210 ELRAFSTEVATESTAVTESASDVERASQQVSESVQSIATTNAEQtrslqTVADEMGDLSATIEE 273
                                       6788888999999999999999999999999998865444444432444555555555555555 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.55
                              COG2  77 plaaarkkvesvreklsereeeveskleeakeleekr.....ellklllkldevvekleal 132
                                       +l+a+ ++v s  + ++ + +e  ++ e+ ++          ++ ++ +  +e+v k+eal
  gi|336252098|ref|YP_004595205.1| 266 DLSATIEEVASSADGVASTATEAAERGEAGRAN---ArdaadAMADIRQTSEETVAKVEAL 323
                                       344444555555554444444443333322222...1233457777777778888888876 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 3
                              COG2  70 eleevesplaaarkkvesvrekl 92 
                                       ++  +++  ++++ kve++ e +
  gi|336252098|ref|YP_004595205.1| 305 AMADIRQTSEETVAKVEALDEDI 327
                                       44444444444444444444444 PP

  == domain 5  score: 13.1 bits;  conditional E-value: 9.4e-05
                              COG2  67 lqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellk 117
                                       +++++ +v+s+ ++++++++ +r+++ +  +++e+ +++ ++++++ e + 
  gi|336252098|ref|YP_004595205.1| 386 IESQIANVRSSTTETVDEIQGMRDQVTDGVTTIEGSIDALEDITDHVETVH 436
                                       7899**************************************999875544 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 0.57
                              COG2  83 kkvesvreklsereeeveskleeakeleekr..e 114
                                       ++v s++e +  ++e+ e++ +  ++++e++   
  gi|336252098|ref|YP_004595205.1| 454 QEVVSMVEDVVGASERTEDETQSVSAAAEEQtaS 487
                                       3333333333333333333333333333333221 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 ?    7.5   6.7    0.0031       2.6       6     113 ..     177     284 ..     174     309 .. 0.91
   2 ?   -1.1   0.1       1.2     1e+03      70     106 ..     297     333 ..     283     358 .. 0.72
   3 ?   10.4   2.7   0.00041      0.33      37     108 ..     418     490 ..     406     517 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0031
                         Mce4_CUP1   6 lleavdPakLnatLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdna 82 
                                       l ++ dP+  ++ ++A+a+A++     l +++ +l ++ +e+ ++   ++e  ++++++++  +++ + + ++ ++ 
  gi|336252098|ref|YP_004595205.1| 177 LTRRLDPESESEAMTAIATAFNAMLADLERTMLELRAFSTEVATESTAVTESASDVERASQQVSESVQSIATTNAEQ 253
                                       6788999999******************************************************************* PP

                         Mce4_CUP1  83 vttsrTiveqqaeLdalllaavglsntgadl 113
                                       ++  +T++++  +L+a + ++++ ++ +a+ 
  gi|336252098|ref|YP_004595205.1| 254 TRSLQTVADEMGDLSATIEEVASSADGVAST 284
                                       ******************9999988877665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                         Mce4_CUP1  70 daapdlldaLdnavttsrTiveqqaeLdalllaavgl 106
                                       + a d  da++++++ts+  v++ ++Ld+ + +++++
  gi|336252098|ref|YP_004595205.1| 297 ANARDAADAMADIRQTSEETVAKVEALDEDIGEIIEI 333
                                       6788888888888888888888888888766666554 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00041
                         Mce4_CUP1  37 ltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaav.glsn 108
                                       ++   + L+++ +++++++  i+e+++++d  a++a++++++++++v  s+  +++ ++++a+  + + ++++
  gi|336252098|ref|YP_004595205.1| 418 IEGSIDALEDITDHVETVHMSIQEVNRATDQQAASAQEVVSMVEDVVGASERTEDETQSVSAAAEEQTaSIAQ 490
                                       55556789******************************************99999999999887654413333 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.7       1.2   9.5e+02      30      69 ..     120     159 ..     103     175 .. 0.65
   2 ?    2.3   2.0       0.2   1.6e+02      12      63 ..     194     245 ..     184     253 .. 0.52
   3 ?   12.1   1.8   0.00018      0.14       8      84 ..     253     329 ..     247     358 .. 0.84
   4 ?   12.6   0.8   0.00012       0.1       2      68 ..     373     439 ..     372     445 .. 0.92
   5 ?    4.1   3.7     0.052        42      10      69 ..     451     510 ..     441     521 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.2
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
                        Laminin_II  30 keklseinrsveetnekvkdankairdArrsvkkLeklap 69 
                                       +e+++  ++++ee   +++da  + ++ +r+   L++ ++
  gi|336252098|ref|YP_004595205.1| 120 REEAEASRAEAEESRRDAEDARSVAESSKREAEALTESLQ 159
                                       4555555555556666666666666666666666666554 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.2
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkk 63 
                                       a++  + la+l+  + ++++   e++++   ++e ++d  +a +++++sv+ 
  gi|336252098|ref|YP_004595205.1| 194 ATAFNAMLADLERTMLELRAFSTEVATESTAVTESASDVERASQQVSESVQS 245
                                       4444444555555555555555555555555555555555555555555544 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II   8 anetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                          +++ v + + +ls+ +e++ +++ ++++++ e  e  ++     rdA +++ ++ ++ ++ ++k++ l++   +
  gi|336252098|ref|YP_004595205.1| 253 QTRSLQTVADEMGDLSATIEEVASSADGVASTATEAAERGEAGRANARDAADAMADIRQTSEETVAKVEALDEDIGE 329
                                       4567899************************************************************8888765444 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TT CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekla 68 
                                       k+la ea+e ++ +++q+a++   + +t +++++++++v      ++ +  a++d  + v ++ + +
  gi|336252098|ref|YP_004595205.1| 373 KSLAGEASEATQRIESQIANVRSSTTETVDEIQGMRDQVTDGVTTIEGSIDALEDITDHVETVHMSI 439
                                       8899**********************************99999999999999999999999888766 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.052
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
                        Laminin_II  10 etakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklap 69 
                                        +a+ev + ++++    e+t+++ +++ + +ee ++ + + ++ ++    +  +Le  ++
  gi|336252098|ref|YP_004595205.1| 451 ASAQEVVSMVEDVVGASERTEDETQSVSAAAEEQTASIAQVSESTDAFAAQATELEDRLD 510
                                       567888888888888888888888888888777777777777777766666666666555 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.5      0.72   5.9e+02      22      63 ..     210     250 ..     199     273 .. 0.65
   2 ?   10.9   0.1    0.0004      0.33      10      51 ..     380     421 ..     366     436 .. 0.86
   3 ?    0.1   0.2      0.87   7.1e+02      15      55 ..     434     474 ..     421     494 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.72
                              ApoO  22 slRkslepytsavqdelnkvkskvetaeqsvtdtiasLkepp 63 
                                       +lR + ++ +++ + ++++  s ve a q+v+++++s++  +
  gi|336252098|ref|YP_004595205.1| 210 ELRAFSTEVATEST-AVTESASDVERASQQVSESVQSIATTN 250
                                       55555554444433.344455567777777777777776654 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0004
                              ApoO  10 eeptdrLeegvrslRkslepytsavqdelnkvkskvetaeqs 51 
                                       +e t+r+e++++++R s++++++++q   ++v+++v t e s
  gi|336252098|ref|YP_004595205.1| 380 SEATQRIESQIANVRSSTTETVDEIQGMRDQVTDGVTTIEGS 421
                                       67899**********************999999999888765 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.87
                              ApoO  15 rLeegvrslRkslepytsavqdelnkvkskvetaeqsvtdt 55 
                                       ++  +++++ +++ ++++ +q+ ++ v++ v  +e++  +t
  gi|336252098|ref|YP_004595205.1| 434 TVHMSIQEVNRATDQQAASAQEVVSMVEDVVGASERTEDET 474
                                       56667788888888888888888888887777776654333 PP

>> DUF1759  Protein of unknown function (DUF1759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1       0.1        82      77     119 ..     239     281 ..     223     291 .. 0.82
   2 ?    5.7   0.1     0.017        13      46     119 ..     271     344 ..     264     354 .. 0.83
   3 ?    4.3   0.2     0.044        36      87     119 ..     417     449 ..     380     477 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.1
                           DUF1759  77 llnelmklpslkeedasqlrrivdavneivralealgeeadky 119
                                         ++++++  ++ e+++ l+++ d++  +  ++e+++  ad +
  gi|336252098|ref|YP_004595205.1| 239 VSESVQSIATTNAEQTRSLQTVADEMGDLSATIEEVASSADGV 281
                                       5677889999999999999999999999999999999888765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.017
                           DUF1759  46 vahlalseenYeaaveaLkkrYdnkrkiirellnelmklpslkeedasqlrrivdavneivralealgeeadky 119
                                       ++ +a s++   ++ +   +r +  r   r+  +++ ++++++ee +++++++ + + ei+ +++ + + ad+ 
  gi|336252098|ref|YP_004595205.1| 271 IEEVASSADGVASTATEAAERGEAGRANARDAADAMADIRQTSEETVAKVEALDEDIGEIIEIVDLIDRIADQT 344
                                       56666677777777778888888889999999********************************9999988855 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.044
                           DUF1759  87 lkeedasqlrrivdavneivralealgeeadky 119
                                       + e + + l+ i+d v++++  ++++++ +d+ 
  gi|336252098|ref|YP_004595205.1| 417 TIEGSIDALEDITDHVETVHMSIQEVNRATDQQ 449
                                       445567788899999999999999998888764 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 ?   -2.4   0.1       7.7   6.3e+03      44      64 ..     138     158 ..     121     173 .. 0.55
   2 ?    5.5   1.3     0.025        20      39      92 ..     218     272 ..     187     277 .. 0.76
   3 ?    6.3   0.3     0.014        12      48      88 ..     301     341 ..     284     345 .. 0.61
   4 ?    5.8   0.2     0.021        17      34      86 ..     381     434 ..     367     441 .. 0.56
   5 ?    6.6   2.2     0.011       9.4      19      91 ..     439     512 ..     433     515 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.7
                           BLOC1_2  44 aslekkleklnekyeelqpyl 64 
                                       +++++ +e  +++ e+l + l
  gi|336252098|ref|YP_004595205.1| 138 EDARSVAESSKREAEALTESL 158
                                       444444444444444443333 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                           BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqie.kqvteLeeavseLDeyskeLE 92 
                                       ++++   ++++++++++ ++++++ +q+i   + +q+++L+++++e+   s  +E
  gi|336252098|ref|YP_004595205.1| 218 VATESTAVTESASDVERASQQVSESVQSIATTNaEQTRSLQTVADEMGDLSATIE 272
                                       5566667777788888888888888888877753577788888888877777776 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.014
                           BLOC1_2  48 kkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                       + ++++    ++ ++ + +++++++++ e+ e+v+ +D + 
  gi|336252098|ref|YP_004595205.1| 301 DAADAMADIRQTSEETVAKVEALDEDIGEIIEIVDLIDRIA 341
                                       33333333334666677777777777777777777777654 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.021
                           BLOC1_2  34 ekykklkdvaaslekklek.lnekyeelqpylqqidqiekqvteLeeavseLDe 86 
                                       e  + +++++a+++++  + ++e +   ++  + +  ie +++ Le++ +++++
  gi|336252098|ref|YP_004595205.1| 381 EATQRIESQIANVRSSTTEtVDEIQGMRDQVTDGVTTIEGSIDALEDITDHVET 434
                                       444444555555544433303333334444555667777777777777766654 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.011
                           BLOC1_2  19 vedyklLeklNeaasekykklkdvaasl.ekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                        ++++  +    a+++++ ++ + + ++ e++ +++++ +++ +++  +i q+ ++++ + + + eL+    + 
  gi|336252098|ref|YP_004595205.1| 439 IQEVNRATDQQAASAQEVVSMVEDVVGAsERTEDETQSVSAAAEEQTASIAQVSESTDAFAAQATELEDRLDAF 512
                                       55555555555556666655554444440444455666677888899999999999999999999988776655 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 ?    2.1   0.4      0.33   2.7e+02      15      34 ..     228     247 ..     209     252 .. 0.71
   2 ?    2.3   0.1      0.28   2.3e+02      15      34 ..     256     275 ..     248     281 .. 0.84
   3 ?    6.0   0.1      0.02        16      16      52 ..     306     345 ..     300     345 .. 0.80
   4 ?    6.4   0.5     0.015        12      10      39 ..     384     413 ..     378     418 .. 0.91
   5 ?    2.2   0.4      0.31   2.5e+02      23      40 ..     425     442 ..     414     465 .. 0.46

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.33
                         FlaC_arch  15 eletvkkeneelsksveelk 34 
                                       + + v++  +++s+sv+ + 
  gi|336252098|ref|YP_004595205.1| 228 SASDVERASQQVSESVQSIA 247
                                       55667888888888888775 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.28
                         FlaC_arch  15 eletvkkeneelsksveelk 34 
                                       +l+tv +e+ +ls ++ee+ 
  gi|336252098|ref|YP_004595205.1| 256 SLQTVADEMGDLSATIEEVA 275
                                       79999999999999999985 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.02
                         FlaC_arch  16 letvkkeneelsksveelkenV...kdllsLYEvVsnqvN 52 
                                       ++ ++++ ee   +ve l+e++    ++++L + +++q N
  gi|336252098|ref|YP_004595205.1| 306 MADIRQTSEETVAKVEALDEDIgeiIEIVDLIDRIADQTN 345
                                       7889999***************666666677777777766 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.015
                         FlaC_arch  10 sklsteletvkkeneelsksveelkenVkd 39 
                                       +++++++++v+++  e  ++++ + ++V d
  gi|336252098|ref|YP_004595205.1| 384 QRIESQIANVRSSTTETVDEIQGMRDQVTD 413
                                       689***********************9975 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.31
                         FlaC_arch  23 neelsksveelkenVkdl 40 
                                       +e++ + ve++  +++++
  gi|336252098|ref|YP_004595205.1| 425 LEDITDHVETVHMSIQEV 442
                                       333333333333333332 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.5   0.00054      0.44      52     153 ..     188     290 ..     184     307 .. 0.76
   2 ?    4.6   1.9     0.024        20      75     149 ..     382     454 ..     365     479 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00054
                      Allexi_40kDa  52 eWLthishdvdsiinklnpvsllsqttlLselrdalrtltklldklksvekklelsaetas..dskllkklesiets 126
                                       e +t i+   + ++ +l+ + +l   +  +e+ ++++++t+   ++++ ++++++s +++   + + +++l+++  +
  gi|336252098|ref|YP_004595205.1| 188 EAMTAIATAFNAMLADLERT-MLELRAFSTEVATESTAVTESASDVERASQQVSESVQSIAttNAEQTRSLQTVADE 263
                                       56788888889999999888.45555666789999999999999999999999999887651145667899999999 PP

                      Allexi_40kDa 127 leelhakldelsssetsesegPssspt 153
                                       + +l a ++e++ss++   ++ + + +
  gi|336252098|ref|YP_004595205.1| 264 MGDLSATIEEVASSADGVASTATEAAE 290
                                       99******9999998877766554444 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.024
                      Allexi_40kDa  75 sqttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelsssetsesegPs 149
                                       +++   s++ +     t+++d+++ + +++++  +t++ s   + le i  ++e++h+ ++e+ ++++++ ++ +
  gi|336252098|ref|YP_004595205.1| 382 ATQRIESQIANVRSSTTETVDEIQGMRDQVTDGVTTIEGSI--DALEDITDHVETVHMSIQEVNRATDQQAASAQ 454
                                       44444456666666677888888888888887777776654..67888888899999999888877776655533 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 ?    4.4   0.6     0.047        38      28      87 ..     192     251 ..     187     275 .. 0.56
   2 ?    0.8   0.1      0.61   4.9e+02      31     103 ..     258     329 ..     253     354 .. 0.62
   3 ?    8.4   2.5    0.0028       2.3      27     113 ..     373     459 ..     367     464 .. 0.70
   4 ?    7.5   2.9    0.0053       4.3      29     122 ..     407     506 ..     396     515 .. 0.52

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.047
                                       CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskele 87 
                                          + ++  l++le+++ e++  ++e+ + ++++++s  + ++ +++ ++ +++++++  
  gi|336252098|ref|YP_004595205.1| 192 AIATAFNAMLADLERTMLELRAFSTEVATESTAVTESASDVERASQQVSESVQSIATTNA 251
                                       555666666777777777777777777666666666666666666654444444443333 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.61
                                       CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesn 103
                                       ++v +++ +l  ++ee+++s   + ++ +e  +  ++  ++++d   ++ +++++ ee +++++  +d+ + +
  gi|336252098|ref|YP_004595205.1| 258 QTVADEMGDLSATIEEVASSADGVASTATEAAERGEAGRANARDAADAMADIRQTSEETVAKVE-ALDEDIGE 329
                                       5667777777777777777777777777777777777666666666666666666664444443.23444433 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0028
                                       CCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHH CS
                         Fib_alpha  27 lkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesn 103
                                       ++   + ++  +++e++++++++st+e+ + ++ ++d++++  ++ +++  +++++++++e+ ++ ++e   a+ ++
  gi|336252098|ref|YP_004595205.1| 373 KSLAGEASEATQRIESQIANVRSSTTETVDEIQGMRDQVTDGVTTIEGSIDALEDITDHVETVHMSIQEVNRATDQQ 449
                                       55555666677788888888888888888888888888888888888888888888888887777777665555577 PP

                                       HHHHHHHHHH CS
                         Fib_alpha 104 irvLqnvles 113
                                           q+v++ 
  gi|336252098|ref|YP_004595205.1| 450 AASAQEVVSM 459
                                       7666666655 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0053
                                       CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHCCCHHHHHHH CS
                         Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.......dnvikksskeleeeilrlketid 98 
                                       ++ +v++ ++++e +++ +++ t ++e++  +i+++ r++ ++++         + v+  s+++ + e + + +   
  gi|336252098|ref|YP_004595205.1| 407 MRDQVTDGVTTIEGSIDALEDITDHVETVHMSIQEVNRATDQQAASAqevvsmvEDVVGASERTED-ETQSVSAAAE 482
                                       455555555556655555555555555555555555555555555440000001444444433333.5666666666 PP

                                       CCHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  99 aqesnirvLqnvlesneqkiqkLe 122
                                       +q  +i +  +  ++   + ++Le
  gi|336252098|ref|YP_004595205.1| 483 EQTASIAQVSESTDAFAAQATELE 506
                                       666666666666666555555555 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1       0.3   2.5e+02       4      39 ..     185     220 ..     184     227 .. 0.87
   2 ?   -0.4   0.1       1.2   9.7e+02       7      39 ..     241     273 ..     237     280 .. 0.79
   3 ?   -2.8   0.0       7.1   5.7e+03      16      38 ..     320     342 ..     305     348 .. 0.50
   4 ?    9.4   0.1    0.0011      0.87       8      42 ..     410     444 ..     403     449 .. 0.87
   5 ?   -0.8   0.0       1.7   1.4e+03      10      38 ..     454     482 ..     447     489 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.3
                         DASH_Duo1   4 kEleqLrkinevienviesLkkaksniervketves 39 
                                        E e ++ i ++++++ ++L+++  ++  +++ v +
  gi|336252098|ref|YP_004595205.1| 185 SESEAMTAIATAFNAMLADLERTMLELRAFSTEVAT 220
                                       799999*****************9999999888765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                         DASH_Duo1   7 eqLrkinevienviesLkkaksniervketves 39 
                                       e++++i ++    + sL+++ +++  ++ t+e+
  gi|336252098|ref|YP_004595205.1| 241 ESVQSIATTNAEQTRSLQTVADEMGDLSATIEE 273
                                       677788888888888999999999888888876 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.1
                         DASH_Duo1  16 ienviesLkkaksniervketve 38 
                                       +e+++e++ ++ + ++ + +  +
  gi|336252098|ref|YP_004595205.1| 320 VEALDEDIGEIIEIVDLIDRIAD 342
                                       33444444444444443444333 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0011
                         DASH_Duo1   8 qLrkinevienviesLkkaksniervketvestnt 42 
                                       q+++  ++ie++i++L+++++++e+v+ +++++n+
  gi|336252098|ref|YP_004595205.1| 410 QVTDGVTTIEGSIDALEDITDHVETVHMSIQEVNR 444
                                       66666789**********************99986 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 1.7
                         DASH_Duo1  10 rkinevienviesLkkaksniervketve 38 
                                       +++ +++e+v+++ +++++++++v+ + e
  gi|336252098|ref|YP_004595205.1| 454 QEVVSMVEDVVGASERTEDETQSVSAAAE 482
                                       67889999999999999999999987766 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.4   1.1e+03      44      66 ..     242     264 ..     225     276 .. 0.60
   2 ?    7.5   0.1    0.0051       4.2      37      66 ..     298     327 ..     297     340 .. 0.92
   3 ?    1.0   0.2      0.57   4.6e+02      33      65 ..     388     410 ..     369     460 .. 0.70
   4 ?   -0.1   0.2       1.3     1e+03      57      57 ..     472     472 ..     417     508 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.4
                              Med9  44 elpgidrsveeqeaeieeleeql 66 
                                       +++ i  + +eq + +++  +++
  gi|336252098|ref|YP_004595205.1| 242 SVQSIATTNAEQTRSLQTVADEM 264
                                       34445555555555555544444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0051
                              Med9  37 karelirelpgidrsveeqeaeieeleeql 66 
                                       +ar + + + +i  + ee  a++e+l+e +
  gi|336252098|ref|YP_004595205.1| 298 NARDAADAMADIRQTSEETVAKVEALDEDI 327
                                       89************************9987 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.57
                              Med9  33 hkLkkarelirelpgidrsveeqeaeieeleeq 65 
                                        ++ +          +  s+ e  +ei+ +++q
  gi|336252098|ref|YP_004595205.1| 388 SQIAN----------VRSSTTETVDEIQGMRDQ 410
                                       44444..........444444444444444444 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.3
                              Med9  57 a 57 
                                       +
  gi|336252098|ref|YP_004595205.1| 472 D 472
                                       2 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 ?   -1.5   0.1       2.9   2.3e+03      47      79 ..     119     151 ..     111     171 .. 0.70
   2 ?    0.7   0.1      0.58   4.7e+02       5      23 ..     229     247 ..     206     276 .. 0.60
   3 ?   -3.1   0.0       8.8   7.2e+03       3      20 ..     315     332 ..     299     341 .. 0.58
   4 ?   11.2   0.3   0.00033      0.27      15      87 ..     368     441 ..     364     462 .. 0.87
   5 ?   -0.3   0.2       1.2   9.7e+02      37      77 ..     442     482 ..     438     508 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.9
                            BORCS8  47 kkkevkeleeelqgacydveyaisavksikese 79 
                                       +++e ++ + e +++  d+e+a s   s k   
  gi|336252098|ref|YP_004595205.1| 119 RREEAEASRAEAEESRRDAEDARSVAESSKREA 151
                                       566777777788888888888877666655444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.58
                            BORCS8   5 eekvkkasekisenihila 23 
                                       ++ v++as+++se+++ +a
  gi|336252098|ref|YP_004595205.1| 229 ASDVERASQQVSESVQSIA 247
                                       2223333333333333332 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 8.8
                            BORCS8   3 eleekvkkasekisenih 20 
                                       e++ kv+   e i e i+
  gi|336252098|ref|YP_004595205.1| 315 ETVAKVEALDEDIGEIIE 332
                                       344444444444444444 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00033
                            BORCS8  15 isenihilaNePSlalYrlQeHvrkalPelvekkkevkeleeelqgacydveyaisavksikesessf.eniqe 87 
                                       +++ i+ la e S a  r+   + ++     e  +e++ ++ ++++ + ++e +i a+  i++  +++  +iqe
  gi|336252098|ref|YP_004595205.1| 368 VADEIKSLAGEASEATQRIESQIANVRSSTTETVDEIQGMRDQVTDGVTTIEGSIDALEDITDHVETVhMSIQE 441
                                       6799*******************************************************999988888445554 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 1.2
                            BORCS8  37 vrkalPelvekkkevkeleeelqgacydveyaisavksike 77 
                                       v +a  + +   +ev ++ e++ ga++  e+ ++ v +  e
  gi|336252098|ref|YP_004595205.1| 442 VNRATDQQAASAQEVVSMVEDVVGASERTEDETQSVSAAAE 482
                                       55666666666666666666666666666666666654433 PP

>> DUF2452  Protein of unknown function (DUF2452)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.5    0.0032       2.6      25      68 ..     220     263 ..     205     283 .. 0.61
   2 ?    3.0   0.0     0.079        64      19      68 ..     335     381 ..     317     392 .. 0.77
   3 ?   -0.8   0.7       1.2   9.5e+02      13      49 ..     439     475 ..     425     506 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0032
                           DUF2452  25 sdaeDlvelakevqkadefvkanacnkLkviaeqikaLqeqark 68 
                                       ++++ + e a++v++a+++v  ++ +  ++ aeq + Lq+ a +
  gi|336252098|ref|YP_004595205.1| 220 TESTAVTESASDVERASQQVSESVQSIATTNAEQTRSLQTVADE 263
                                       34445556666666666666666666666666666666665544 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.079
                           DUF2452  19 ervarksdaeDlvelakevqkadefvkanacnkLkviaeqikaLqeqark 68 
                                       + + r +d+++l++l + ++ a   +  +a++   v+a+ ik L  +a++
  gi|336252098|ref|YP_004595205.1| 335 DLIDRIADQTNLLALNASIEAA---TAGSAGSGFAVVADEIKSLAGEASE 381
                                       5567788899999999999876...5689999************998876 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.2
                           DUF2452  13 vqlvspervarksdaeDlvelakevqkadefvkanac 49 
                                       +q v+ ++ ++ ++a+++v+++++v  a+e ++ ++ 
  gi|336252098|ref|YP_004595205.1| 439 IQEVNRATDQQAASAQEVVSMVEDVVGASERTEDETQ 475
                                       4444555555555555666666665555555544443 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   2.0    0.0061         5     623     701 ..     201     278 ..     184     321 .. 0.63
   2 ?    4.9   3.0    0.0063       5.1     192     305 ..     368     483 ..     364     516 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0061
                          Prominin 623 kvnletlaekleelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksvkklde...ensdlqesikk 696
                                         +le ++ +l+++++e+ ++    +++++++a+d+++  q+  + ++s++ +  +++++l++   e  dl+++i++
  gi|336252098|ref|YP_004595205.1| 201 LADLERTMLELRAFSTEVATE----STAVTESASDVERASQQVSESVQSIATTNAEQTRSLQTvadEMGDLSATIEE 273
                                       457777777778888777666....4444555555555555555555555444444444444444455555555555 PP

                          Prominin 697 llaav 701
                                       + +++
  gi|336252098|ref|YP_004595205.1| 274 VASSA 278
                                       55444 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0063
                          Prominin 192 vpqhidhvlvqnyeelekhvsddLddagkhlgldlad..tlesnvlpaLaelerllenlkeakeqLeqvnklekeLr 266
                                       v+++i++++ +  +e+ +++++++ ++ ++  +++ +   ++++v+  ++++e  +++l+++ ++ e+v+ + +e+ 
  gi|336252098|ref|YP_004595205.1| 368 VADEIKSLAGE-ASEATQRIESQIANVRSSTTETVDEiqGMRDQVTDGVTTIEGSIDALEDITDHVETVHMSIQEVN 443
                                       66777777777.45555577777777776666655532246666677777777777777777777777777777777 PP

                          Prominin 267 ksgsqLrdglrgvkrdlnqalsn.lCqseeCskilsslei 305
                                         ++q  ++ ++v   +++++   + ++ e+++++  +e 
  gi|336252098|ref|YP_004595205.1| 444 RATDQQAASAQEVVSMVEDVVGAsERTEDETQSVSAAAEE 483
                                       7777777777777777777766644333444444433333 PP

>> IFT20  Intraflagellar transport complex B, subunit 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   3.2       2.7   2.2e+03      53      89 ..      99     135 ..      86     164 .. 0.60
   2 ?    1.1   0.5      0.53   4.3e+02      44      90 ..     227     252 ..     186     282 .. 0.50
   3 ?    7.4   0.1     0.006       4.9      14      65 ..     299     350 ..     293     360 .. 0.87
   4 ?   11.1   3.9   0.00041      0.33      17     118 ..     393     490 ..     370     491 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.7
                             IFT20  53 akkvekeKlkAigarnllkseakqreaeqqqlqalia 89 
                                        ++ve  + +A++a+ + +  +++ ea +++ ++  +
  gi|336252098|ref|YP_004595205.1|  99 RRSVEASRREAVAAKEAADRRREEAEASRAEAEESRR 135
                                       5678888888888888777666666555555444332 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.53
                             IFT20  44 elievleelakkvekeKlkAigarnllkseakqreaeqqqlqaliae 90 
                                       e  + +e+ +++v                      +  q + ++ ae
  gi|336252098|ref|YP_004595205.1| 227 ESASDVERASQQV---------------------SESVQSIATTNAE 252
                                       2222222222222.....................2222222222222 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.006
                             IFT20  14 dpevaeeteelkeeckeFvkkinefqklvkelievleelakkvekeKlkAig 65 
                                       + ++a+  ++++++++e v k++ +++ ++e+ie+++ + +  ++  l A+ 
  gi|336252098|ref|YP_004595205.1| 299 ARDAADAMADIRQTSEETVAKVEALDEDIGEIIEIVDLIDRIADQTNLLALN 350
                                       56889999****************************9988888888777765 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00041
                             IFT20  17 vaeeteelkeeckeFvkkinefqklvkelievleelakkvekeKlkAigarnllkseakqreaeqqqlqaliaekka 93 
                                       v ++t+e  +e +   +++++  +++++ i+ le++ ++ve+  +  i     ++ +++q+ a  q++ +++++   
  gi|336252098|ref|YP_004595205.1| 393 VRSSTTETVDEIQGMRDQVTDGVTTIEGSIDALEDITDHVETVHMS-I---QEVNRATDQQAASAQEVVSMVEDVVG 465
                                       5677888888888899999999999****************99984.4...457789999***************** PP

                             IFT20  94 eleRlrvelesLqkveqeqkeliek 118
                                         eR + e +s++ + +eq++ i++
  gi|336252098|ref|YP_004595205.1| 466 ASERTEDETQSVSAAAEEQTASIAQ 490
                                       ********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2812  (0.156841); expected 358.6 (0.02)
Passed bias filter:                      826  (0.0460706); expected 358.6 (0.02)
Passed Vit filter:                       136  (0.00758548); 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):              22  [number of targets reported over threshold]
# CPU time: 1.91u 0.79s 00:00:02.70 Elapsed: 00:00:03.23
# Mc/sec: 501.28
//
Query:       gi|336252099|ref|YP_004595206.1|  [L=120]
Description: hypothetical protein Halxa_0688 [Halopiger xanaduensis SH-6]
Scores for 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  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); 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:                         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 0.82s 00:00:01.28 Elapsed: 00:00:01.21
# Mc/sec: 298.84
//
Query:       gi|336252100|ref|YP_004595207.1|  [L=156]
Description: hypothetical protein Halxa_0689 [Halopiger xanaduensis SH-6]
Scores for 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:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      132  (0.00736237); 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: 0.44u 0.59s 00:00:01.03 Elapsed: 00:00:00.57
# Mc/sec: 826.82
//
Query:       gi|336252101|ref|YP_004595208.1|  [L=269]
Description: cyclase/dehydrase [Halopiger xanaduensis SH-6]
Scores for complete 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   31.8   1.0    2.3e-07   31.2   1.0    1.3  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    2.1e-07   30.8   0.2    3.6e-07   30.1   0.2    1.3  1  DUF2892          Protein of unknown function (DUF2892)
    1.4e-05   25.3   0.0      2e-05   24.8   0.0    1.2  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   1.0   3.8e-11   2.3e-07       3     125 ..     110     228 ..     108     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 3.8e-11
                                       EEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCS..SEEEEEEEEEETTTTEEEE CS
                   Polyketide_cyc2   3 kvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggr..gtvreelvevdpegrllsy 77 
                                       +v +s+++  ++++  a+ +d++ ++r   e a+   + +gg+  g +++v+  g   +t ++e   v++++  l++
  gi|336252101|ref|YP_004595208.1| 110 TVDRSITVGEDADELPAYWRDPDRLSRIVGEFAEISDV-PGGD--GHRWRVQ--GPldRTFEWETRLVEDDEEQLRW 181
                                       7999**************************99977544.5888..6656666..444499*********99****** PP

                                       EEE...SSS-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHH CS
                   Polyketide_cyc2  78 riv..kpvpvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaak 125
                                       +++  + vp + y  +++ +p g gt vt ++e+++  +gg + ++a+++
  gi|336252101|ref|YP_004595208.1| 182 EARegASVPHE-YAISFEPEPGGRGTIVTLEVEYEP--PGGAVGDAAMDR 228
                                       **656667766.6666666666667**********5..777775555544 PP

>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.2     6e-11   3.6e-07       4      62 ..      35      95 ..      32      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 6e-11
                           DUF2892  4 NvgtldRilrivvGlvllllallglsggwgwllglvGavllltgltgfCplyallg...int 62
                                      Nvg+ +R++++++G +l++ +l ++s g g  ++l+G++l+ +g+tg   ly+ll    ++t
  gi|336252101|ref|YP_004595208.1| 35 NVGRGERVASVALGGLLVARGLRRGSFG-GAATALAGGALVYRGITGRSRLYRLLEsspVDT 95
                                      ************************9655.999***********************6355555 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   3.4e-09     2e-05       5     114 ..     121     225 ..     117     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.4e-09
                                       HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...EEEEC.STTSSCEEEEEEEEEEETTTEEECTTCCCCCEEEEE CS
                    Polyketide_cyc   5 adqvyalvadvesypeflphcssvevleeaesglsadlev.gfggltesftarvtldppeeitfklvegdfkslegk 80 
                                       ad++ a+++d +++++++ +  + + +   + +   +++v g    t ++++r ++d +e+++ + +eg    +e +
  gi|336252101|ref|YP_004595208.1| 121 ADELPAYWRDPDRLSRIVGEFAEISDVPGGDGH---RWRVqGPLDRTFEWETRLVEDDEEQLRWEAREGASVPHEYA 194
                                       6677799****************6666666653...55551455667889999999999997777777777777777 PP

                                       EEECTECCEEECEEEEEEEEEEEE-SSCHHHHHH CS
                    Polyketide_cyc  81 Wtieslppnsggtrtkvalevdfkfaspllgalv 114
                                        ++e+ p    g +t v+lev++++ ++++g+++
  gi|336252101|ref|YP_004595208.1| 195 ISFEPEPG---GRGTIVTLEVEYEPPGGAVGDAA 225
                                       77777776...99999999999998888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); 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: 0.46u 0.37s 00:00:00.83 Elapsed: 00:00:00.57
# Mc/sec: 1414.36
//
Query:       gi|336252102|ref|YP_004595209.1|  [L=386]
Description: Saccharopine dehydrogenase [Halopiger xanaduensis SH-6]
Scores for complete 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   37.9   0.0    2.8e-09   37.3   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> 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 !   37.3   0.0   1.6e-13   2.8e-09       1     128 [.       4     129 ..       4     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.6e-13
                                       EEEE--.SHHHHHHHHHHHCTCCT-G...EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEE CS
                   Sacchrp_dh_NADP   1 vliiGa.GsvGqavaellarhfdvda...eitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlv 73 
                                       vl+ G+ G+vG  +a++  ++ +  +   ++ +a+r+ ++l++ ++++ ++   ++  d++ +++ L+++  e+d v
  gi|336252102|ref|YP_004595209.1|   4 VLLYGSyGFVGNLMAREAIDRIEDGDadfDLLLAGRNGDRLREQVDDLERPGYRFALEDPDTVAEALERA--EADCV 78 
                                       7899999*********9998888766799***************************99****99999995..99*** PP

                                       EE-SSGG..GHHHHHHHHHHHT-EEEE.....SS-BCGCCSCHCCSHHHHHTHHHHHHCTSE CS
                   Sacchrp_dh_NADP  74 vnlsppi..ssldvlkaCietgvhyvd.....tsiskeertnyalreavlklkekakeagvt 128
                                       +n+++p+   + ++++ C++tg++yvd     ++i           e + + +++ ++agvt
  gi|336252102|ref|YP_004595209.1|  79 LNCAGPFsnTAGPLVEGCVRTGTDYVDitgeiPVI-----------ESIADRDADGADAGVT 129
                                       *******66667***************75443333...........5555555555556666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); 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: 0.51u 0.53s 00:00:01.04 Elapsed: 00:00:00.60
# Mc/sec: 1923.41
//
Query:       gi|336252103|ref|YP_004595210.1|  [L=175]
Description: hypothetical protein Halxa_0692 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.03   14.4   0.2      0.045   13.9   0.2    1.4  1  RecA_dep_nuc  Recombination enhancement, RecA-dependent nucle
      0.033   14.1   2.8      0.038   13.9   0.3    2.1  2  C1_1          Phorbol esters/diacylglycerol binding domain (C
      0.051   13.7   0.1      0.097   12.8   0.1    1.4  1  DUF2387       Probable metal-binding protein (DUF2387)
      0.059   13.5   3.9       0.11   12.8   3.9    1.4  1  HNH           HNH endonuclease


Domain annotation for each model (and alignments):
>> RecA_dep_nuc  Recombination enhancement, RecA-dependent nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2     1e-05     0.045      29      61 ..      96     133 ..      76     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                                       -...EEEEES..S-SSSTTGGGSEEEEEHHHHT----H CS
                      RecA_dep_nuc  29 e...velhhi..agrtkpdahkktlpLcawhhqaaapa 61 
                                       e    e hh+  +  ++  +h+ t+ Lc+w h ++   
  gi|336252103|ref|YP_004595210.1|  96 ErplLEEHHLsyDRDGETLSHEITIYLCRWCHAKVHNS 133
                                       25558899993345688899************998765 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 ?   -0.2   0.1      0.22   9.7e+02       2      18 ..      71      85 ..      71      97 .. 0.75
   2 ?   13.9   0.3   8.5e-06     0.038      24      41 ..     116     133 ..     102     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.22
                                      -EEEE--SS--B-TTT- CS
                              C1_1  2 hwvhrnfkqptfCkhCg 18
                                      h++ rn  +   C  Cg
  gi|336252103|ref|YP_004595210.1| 71 HFRSRN--HDRECVRCG 85
                                      566666..677788776 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.5e-06
                                       SSS-EEEETTT--EE-CC CS
                              C1_1  24 kekqglkCswCkllvHkk 41 
                                       +e++++ C+wC+ +vH++
  gi|336252103|ref|YP_004595210.1| 116 HEITIYLCRWCHAKVHNS 133
                                       678999**********95 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.2e-05     0.097      29      65 ..      77     113 ..      67     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                           DUF2387  29 eyrECvsCgftdelsekgqsvakelktrvnkdeekea 65 
                                       + rECv Cg  +++ +++ + +  ++ ++  d+  e+
  gi|336252103|ref|YP_004595210.1|  77 HDRECVRCGLEEKRMAHDDERPLLEEHHLSYDRDGET 113
                                       569**************99999999999988876544 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.9   2.3e-05      0.11       1      46 [.      81     132 ..      81     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                               HNH   1 CeyCgrkfhks......ealevdHiipisqggaddieNlqllCksCHnkkhd 46 
                                       C +Cg + +        + le +H     +g +++ e  + lC+ CH k h+
  gi|336252103|ref|YP_004595210.1|  81 CVRCGLEEKRMahdderPLLEEHHLSYDRDGETLSHEITIYLCRWCHAKVHN 132
                                       99*****98889*************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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: 0.43u 0.56s 00:00:00.99 Elapsed: 00:00:00.60
# Mc/sec: 878.36
//
Query:       gi|336252104|ref|YP_004595211.1|  [L=876]
Description: methyl-accepting chemotaxis sensory transducer [Halopiger xanaduensis SH-6]
Scores for 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-31  107.4  56.6    2.6e-30  105.5  24.2    4.2  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
      9e-12   45.2  11.5    1.4e-08   34.9   0.1    5.2  4  HAMP             HAMP domain
    8.5e-05   22.6  31.7      0.011   15.7   1.8    5.3  5  DUF1664          Protein of unknown function (DUF1664)
     0.0011   19.0  38.0      0.021   14.8   1.5    5.1  5  Laminin_II       Laminin Domain II
     0.0037   17.5  40.0      0.014   15.7   0.9    7.3  3  DUF948           Bacterial protein of unknown function (DUF94
     0.0056   16.3   3.1     0.0056   16.3   3.1    4.1  4  HAUS-augmin3     HAUS augmin-like complex subunit 3
  ------ inclusion threshold ------
      0.021   15.0  22.8       0.68   10.1   1.0    4.6  5  Fib_alpha        Fibrinogen alpha/beta chain family
      0.038   14.2  35.3       0.14   12.4   1.2    5.7  5  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.047   12.7  25.8      0.026   13.5   5.1    4.1  3  IFT57            Intra-flagellar transport protein 57
      0.073   13.1  27.7      0.075   13.1   3.6    4.1  5  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.19   12.1  14.7         14    6.2   2.4    4.7  3  Syntaxin_2       Syntaxin-like protein
       0.23   11.9   0.1       0.23   11.9   0.1    5.3  5  TSNAXIP1_N       Translin-associated factor X-interacting N-t
       0.23   12.0  31.6       0.22   12.0   1.0    6.0  6  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.82   10.4  13.1        4.1    8.2   0.0    5.2  6  Occludin_ELL     Occludin homology domain
        1.2    9.5   8.0       0.91    9.9   0.1    3.7  4  DUF2935          Domain of unknown function (DUF2935)
        1.9    8.2   4.6         10    5.8   0.0    3.2  3  Vac_Fusion       Chordopoxvirus multifunctional envelope prot
          2    8.4   7.5          4    7.5   0.4    3.5  3  DUF730           Protein of unknown function (DUF730)
          3    7.3  17.7       0.05   13.1   1.2    3.3  4  Allexi_40kDa     Allexivirus 40kDa protein
        3.3    7.5  14.3         24    4.8   0.2    5.3  6  DASH_Duo1        DASH complex subunit Duo1
        4.3    6.1  42.8        0.3    9.9   4.9    4.1  4  Spc7             Spc7 kinetochore protein
        4.6    6.9   6.8         47    3.6   0.2    3.2  3  DCB              Dimerisation and cyclophilin-binding domain 
        4.8    6.2  12.6        1.2    8.1   1.3    2.9  2  FH2              Formin Homology 2 Domain
        4.9    7.3  10.0         20    5.3   0.0    5.0  6  DUF2730          Protein of unknown function (DUF2730)
        5.7    6.2  24.5        1.4    8.2   4.8    3.6  3  CorA             CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  16.5     0.027        20      42     138 ..     433     529 ..     377     545 .. 0.56
   2 !  105.5  24.2   3.5e-33   2.6e-30       6     171 ..     544     711 ..     532     712 .. 0.93
   3 !    7.5   6.8    0.0042       3.2     109     169 ..     698     758 ..     696     761 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHHHHHHHHHHTCCC..CHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHH CS
                         MCPsignal  42 ideiadQTNlLALNAaiEAARAGeq..GrGFaVVAdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrv 116
                                       ++ei++  N  A+ A +EA  AG +      a   +EV +  e+ + a++e+++ ++ei  + ++  +sl++  +++
  gi|336252104|ref|YP_004595211.1| 433 LTEIGEEFN--AMLADLEATVAGLNqfATDVATASEEVTASSEEVQRASREVSESVQEISDGADRQHQSLQSIDSEM 507
                                       555665555..555666666666554455666666777777777777777777777666655555555555444444 PP

                                       HHHHHHHHHHCCHHHHHHHHHH CS
                         MCPsignal 117 eegselveetgealkeiveava 138
                                       ++ s+++ee + + +++++ +a
  gi|336252104|ref|YP_004595211.1| 508 NTLSTTTEEIAASSNDVADVAA 529
                                       4444444433333333333332 PP

  == domain 2  score: 105.5 bits;  conditional E-value: 3.5e-33
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT..CCCCHHHHHHHHHHHHH CS
                         MCPsignal   6 easeeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARA..GeqGrGFaVVAdEVrkL 80 
                                        a +  ++ + e ++vv++ e+++++ ++i+ +++ i eiadQTN+LALNA iEA R   G   +GF+ VA+EV++L
  gi|336252104|ref|YP_004595211.1| 544 AAIDAFDDLEAEYEDVVAEFEQLRNQINQIESLTDTIAEIADQTNMLALNANIEASRSadGADAEGFTAVASEVKQL 620
                                       3444444558999********************************************8345669************* PP

                                       HHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  81 Aersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsas 157
                                        + +++aa ei++ + ++q ++++s+++++ t +++e   +lv +   +l +i+e +ae +d vqei++a+eeq+a+
  gi|336252104|ref|YP_004595211.1| 621 SADTKEAAAEIDERLDALQSQTEESADVVDRTSEEIERVNDLVTDVVASLDDIAEYAAETNDGVQEISSATEEQAAA 697
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHH CS
                         MCPsignal 158 ieevnqaveevakv 171
                                        +ev   v+eva++
  gi|336252104|ref|YP_004595211.1| 698 TQEVVAMVDEVASI 711
                                       *********99987 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0042
                                       .HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 109 leetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveeva 169
                                        +e++  v+e +++ eet+ + +++++a++e ++++qe++a+++ +s+ ++  + a+++ +
  gi|336252104|ref|YP_004595211.1| 698 TQEVVAMVDEVASISEETTAEAQTVAAAAEEQTSSMQEVSASADRLSHQATRLSGALDRFE 758
                                       57899999999*************************************9999999988765 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   1.9e-11   1.4e-08       1      53 []     323     375 ..     323     375 .. 0.96
   2 !   11.9   1.0   0.00029      0.22      15      52 ..     410     448 ..     409     449 .. 0.92
   3 ?   -0.7   0.0       2.6   1.9e+03      12      26 ..     481     496 ..     477     537 .. 0.64
   4 ?    1.0   0.1      0.76   5.7e+02       4      28 ..     567     595 ..     566     603 .. 0.71

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.9e-11
                                       HHHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHHH CS
                              HAMP   1 llarrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLre 53 
                                       +l r++++++ rL++ a+++ +Gdld++l++++ D iG+L   f+ M+ +Lre
  gi|336252104|ref|YP_004595211.1| 323 VLGRNTSKSIDRLKSKAAAMEDGDLDVDLETKRIDSIGRLYDGFDSMRVALRE 375
                                       588*********************************************99985 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00029
                                       HHHHHHTTTBTSSTCCTTSSSH.HHHHHHHHHHHHHHHH CS
                              HAMP  15 raarriaaGdldtrlpvsgrDE.iGeLarafNaMldrLr 52 
                                       ++++  a+Gdl++r ++++ +E + e+++ fNaMl  L+
  gi|336252104|ref|YP_004595211.1| 410 AVMQDAADGDLTVRMEPESENEaLTEIGEEFNAMLADLE 448
                                       689999***********9999989***********9987 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.6
                                       HHHHHHHHHTTT.BTS CS
                              HAMP  12 rLaraarriaaG.dld 26 
                                       ++++++++i++G d  
  gi|336252104|ref|YP_004595211.1| 481 EVSESVQEISDGaDRQ 496
                                       5666667777665332 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.76
                                       HTTHHHHHHHHHHHHHHTTT....BTSST CS
                              HAMP   4 rrilrPLrrLaraarriaaG....dldtr 28 
                                       r+ ++ ++ L++++++ia+      l++ 
  gi|336252104|ref|YP_004595211.1| 567 RNQINQIESLTDTIAEIADQtnmlALNAN 595
                                       667788999********974445555555 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.076        57      65     118 ..     353     406 ..     328     411 .. 0.92
   2 !   15.7   1.8   1.5e-05     0.011      40     109 ..     458     527 ..     430     534 .. 0.78
   3 ?    1.4   0.2      0.41     3e+02      50      84 ..     552     586 ..     539     598 .. 0.53
   4 !   14.9   3.0   2.6e-05      0.02      43     121 ..     610     688 ..     607     691 .. 0.92
   5 ?    4.5   2.2     0.044        33      56     119 ..     686     749 ..     680     753 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.076
                           DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                       ++rid++++  d    +  +++e++++++   +e +++ e v+++  +le+k +
  gi|336252104|ref|YP_004595211.1| 353 TKRIDSIGRLYDGFDSMRVALREQIEDAEAAREEAERERERVERMNDHLEAKAD 406
                                       689******************************************999999976 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.5e-05
                           DUF1664  40 sdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkea 109
                                       +  v++ s++++  se+++++ r+ s+ ++++ +  d q +  ++i++e+++++  ++ei   ++ v ++
  gi|336252104|ref|YP_004595211.1| 458 ATDVATASEEVTASSEEVQRASREVSESVQEISDGADRQHQSLQSIDSEMNTLSTTTEEIAASSNDVADV 527
                                       3334455666777789999999999999999999999999999999999999999999999888888765 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.41
                           DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiske 84 
                                       le  +e++ a  ++L ++i+++++  d  +ei+ +
  gi|336252104|ref|YP_004595211.1| 552 LEAEYEDVVAEFEQLRNQINQIESLTDTIAEIADQ 586
                                       33334444444444444444444444444444444 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 2.6e-05
                           DUF1664  43 vesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                        + v+++++q+s++ +++  ++ +r+d ++++ +e++++   ++ee+++v++ ++++   ++ + e   + +  +++
  gi|336252104|ref|YP_004595211.1| 610 FTAVASEVKQLSADTKEAAAEIDERLDALQSQTEESADVVDRTSEEIERVNDLVTDVVASLDDIAEYAAETNDGVQE 686
                                       578999*********************************************************99999888888887 PP

                           DUF1664 120 ie 121
                                       i+
  gi|336252104|ref|YP_004595211.1| 687 IS 688
                                       76 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.044
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       +++++ ++ ++  ++v + +de++ is+e+++e ++v    +e  + +++v++    l ++ +r
  gi|336252104|ref|YP_004595211.1| 686 EISSATEEQAAATQEVVAMVDEVASISEETTAEAQTVAAAAEEQTSSMQEVSASADRLSHQATR 749
                                       4555666666666777777777777777777777777777777777777777777777666555 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.4     1e+03       6      38 ..     381     413 ..     367     427 .. 0.53
   2 !   10.8   1.0   0.00049      0.37       7      63 ..     428     484 ..     422     495 .. 0.91
   3 !   14.8   1.5   2.9e-05     0.021       9      97 ..     497     585 ..     491     595 .. 0.94
   4 !    9.9   3.0   0.00091      0.68       1      61 [.     624     684 ..     617     688 .. 0.83
   5 ?    3.2   7.0      0.11        83       3      77 ..     675     749 ..     668     762 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.4
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinr 38 
                                       ++a e a+   e ++ ++  le   +++s + +
  gi|336252104|ref|YP_004595211.1| 381 EAAREEAERERERVERMNDHLEAKADEYSAVMQ 413
                                       333333333344444444444444444443333 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00049
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkk 63 
                                       + ne ++e+ e  +++ ++le t + l++++++v+   e+v ++++ ++ A+r+v++
  gi|336252104|ref|YP_004595211.1| 428 SENEALTEIGEEFNAMLADLEATVAGLNQFATDVATASEEVTASSEEVQRASREVSE 484
                                       5689999**********************************************9986 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 2.9e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH. CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeas 85 
                                        ++++++ + ++ ls+ +e++ ++ + +++ +++t e  +   ++ + A ++  +Le + +++++ +++l+++ ++ 
  gi|336252104|ref|YP_004595211.1| 497 HQSLQSIDSEMNTLSTTTEEIAASSNDVADVAARTAETGRGGRETAEAAIDAFDDLEAEYEDVVAEFEQLRNQINQI 573
                                       67899999********************************************************************* PP

                                       ..HHHHHHHHHH CS
                        Laminin_II  86 sslsdniseike 97 
                                       +sl d i ei  
  gi|336252104|ref|YP_004595211.1| 574 ESLTDTIAEIAD 585
                                       *******99965 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00091
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   1 skelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsv 61 
                                       +ke aae++e + + ++q+++ +  +++t+e+++++n+ v  + + ++d  +  ++ ++ v
  gi|336252104|ref|YP_004595211.1| 624 TKEAAAEIDERLDALQSQTEESADVVDRTSEEIERVNDLVTDVVASLDDIAEYAAETNDGV 684
                                       5899999999999999999999999999999999999998888888888777766666655 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHH CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklke 77 
                                       e aae n+ ++e+ + +++ ++ ++++ + + e+++  eet+++++    a ++  +s++++   a++L  +  +
  gi|336252104|ref|YP_004595211.1| 675 EYAAETNDGVQEISSATEEQAAATQEVVAMVDEVASISEETTAEAQTVAAAAEEQTSSMQEVSASADRLSHQATR 749
                                       446666666666666666666777777777777777777777777777777777788888888888888777555 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 ?    0.3   0.1       1.2   8.8e+02      28      79 ..     366     417 ..     310     424 .. 0.77
   2 !   15.7   0.9   1.8e-05     0.014      32      86 ..     430     484 ..     420     491 .. 0.94
   3 ?    1.9   5.3      0.35   2.6e+02      29      67 ..     494     531 ..     485     591 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.2
                            DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavad 79 
                                       +d+++ +++e  +++++  +e+e+  + v+++ + ++ k ++  ++++ +ad
  gi|336252104|ref|YP_004595211.1| 366 FDSMRVALREQIEDAEAAREEAERERERVERMNDHLEAKADEYSAVMQDAAD 417
                                       5555555555567777777788888888888888888888888888888776 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.8e-05
                            DUF948  32 aatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       +++++e++++ +++l ++e+++a  n+ + dv   +e+v +  e+v+ +++ vse
  gi|336252104|ref|YP_004595211.1| 430 NEALTEIGEEFNAMLADLEATVAGLNQFATDVATASEEVTASSEEVQRASREVSE 484
                                       78899********************************************999986 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.35
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvnekl 67 
                                       d+  ++++++ ++++ +++ +e++ a +n+ ++dv  ++
  gi|336252104|ref|YP_004595211.1| 494 DRQHQSLQSIDSEMNTLSTTTEEIAASSND-VADVAART 531
                                       556667777777777777777777777777.55554433 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   3.1   7.5e-06    0.0056      31     162 ..     330     466 ..     322     475 .. 0.81
   2 ?   -0.9   4.1       1.3     1e+03      70     127 ..     469     526 ..     460     575 .. 0.50
   3 ?    1.1   5.1      0.33   2.4e+02      69     163 ..     552     651 ..     531     681 .. 0.67
   4 ?   -2.0   9.4       2.9   2.1e+03      49     159 ..     631     745 ..     628     751 .. 0.46

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.5e-06
                      HAUS-augmin3  31 qayeeLkksGkpiLegeaLeeaLktie.psdlkq.....edvellevileeeeesleaLeqelqeLqkekalklkrl 101
                                       +  + Lk +    +e+ +L+  L+t   +s +       + + +l++++e+ e++ e+ e+e +  ++++++++ + 
  gi|336252104|ref|YP_004595211.1| 330 KSIDRLKSKAA-AMEDGDLDVDLETKRiDSIGRLydgfdSMRVALREQIEDAEAAREEAERERERVERMNDHLEAKA 405
                                       55666766666.7777777777777666232222245555666789999999************************* PP

                      HAUS-augmin3 102 nkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaetnavLqqlteeakqlaeyfe 162
                                       +++ +++ ++++++ ++  e ++ ++ l+e+ ee++a  a+++a    l++ a+ +a   e
  gi|336252104|ref|YP_004595211.1| 406 DEYSAVMQDAADGDLTVRMEPESENEALTEIGEEFNAMLADLEATVAGLNQFATDVATASE 466
                                       *******************************************999999998888776555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                      HAUS-augmin3  70 evileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakk 127
                                       +++ ee + + ++  + +qe     +++ + l+ ++  +++l+ + ++ +++++ ++ 
  gi|336252104|ref|YP_004595211.1| 469 TASSEEVQRASREVSESVQEISDGADRQHQSLQSIDSEMNTLSTTTEEIAASSNDVAD 526
                                       4444444444444444555555444444444444444444444444444444443333 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.33
                      HAUS-augmin3  69 levileeeeesleaLeqelqe...LqkekalklkrlnkLqvqaaslqqelrkleeee..keakkklkeaqeelraen 140
                                       le++ e+  +  e+L++++++   L  + a +  + n+L + a+  ++++ + +++e  ++++ ++k++ ++++++ 
  gi|336252104|ref|YP_004595211.1| 552 LEAEYEDVVAEFEQLRNQINQiesLTDTIAEIADQTNMLALNANIEASRSADGADAEgfTAVASEVKQLSADTKEAA 628
                                       45555555555666665544400045555566677777777776666666555555433677788888888888888 PP

                      HAUS-augmin3 141 aetnavLqqlteeakqlaeyfee 163
                                       ae+++ L+ l++++++ a   + 
  gi|336252104|ref|YP_004595211.1| 629 AEIDERLDALQSQTEESADVVDR 651
                                       88888888888888777665554 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2.9
                      HAUS-augmin3  49 LeeaLktie.psdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeeke 124
                                       ++e L+ ++ +++++ + v+ +++++e  ++ + +  + l++  ++ a  +   +++  ++ +++   +++ +  +e
  gi|336252104|ref|YP_004595211.1| 631 IDERLDALQsQTEESADVVDRTSEEIERVNDLVTDVVASLDDIAEYAAETNDGVQEISSATEEQAAATQEVVAMVDE 707
                                       55666666633333335556666666666666666666666666655555555555555544444444433333333 PP

                      HAUS-augmin3 125 a...kkklkeaqeelraenaetnavLqqlteeakqlae 159
                                       +   +++ +   + ++a+  e ++ +q+++++a +l++
  gi|336252104|ref|YP_004595211.1| 708 VasiSEETTAEAQTVAAAAEEQTSSMQEVSASADRLSH 745
                                       30003333333333444444444555555555555554 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 ?   -2.9   0.1       9.1   6.8e+03      54      88 ..     387     403 ..     365     416 .. 0.44
   2 ?   10.1   1.0   0.00091      0.68      25     111 ..     432     517 ..     430     526 .. 0.81
   3 ?    9.5   1.2    0.0014       1.1      31     125 ..     501     596 ..     498     602 .. 0.83
   4 ?    6.7   0.6     0.011       7.8      46     104 ..     616     673 ..     606     675 .. 0.85
   5 ?    8.0   3.0    0.0041         3      33     122 ..     652     737 ..     648     751 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  54 aeelvkeikdslrekqkskkdndnvikksskelee 88 
                                       ae+                    + +++++++le 
  gi|336252104|ref|YP_004595211.1| 387 AERE------------------RERVERMNDHLEA 403
                                       2221..................2222333333332 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00091
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe 101
                                       +l++  ++++  l++le +++ +++  +++ + ++e++ s +e q+ +++ ++ ++++s+  +++++ l ++id+++
  gi|336252104|ref|YP_004595211.1| 432 ALTEIGEEFNAMLADLEATVAGLNQFATDVATASEEVTASSEEVQRASREVSESVQEISDGADRQHQSL-QSIDSEM 507
                                       577778899999999999999999999999999999999999999999999999999999999666665.5688888 PP

                                       HHHHHHHHHH CS
                         Fib_alpha 102 snirvLqnvl 111
                                       +++   ++ +
  gi|336252104|ref|YP_004595211.1| 508 NTLSTTTEEI 517
                                       7776655555 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0014
                                       CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvL 107
                                       ++++ ++++l  + eei+ s++++ ++  ++ ++ r   ++++    ++ +++ e e +++   e++ +q+++i+ L
  gi|336252104|ref|YP_004595211.1| 501 QSIDSEMNTLSTTTEEIAASSNDVADVAARTAETGRGGRETAEAAIDAFDDLEAEYE-DVVAEFEQLRNQINQIESL 576
                                       67899999*****************************99999999999*********.5555556789********* PP

                                       HHHHHHHH..HHHHHHHHHH CS
                         Fib_alpha 108 qnvlesne..qkiqkLeqdi 125
                                       ++++ +     ++  L+ +i
  gi|336252104|ref|YP_004595211.1| 577 TDTIAEIAdqTNMLALNANI 596
                                       **999875114555555555 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.011
                                       CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHH CS
                         Fib_alpha  46 eisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesni 104
                                       e+++ + +++e   ei++ l + q++++++  v+ + s+e+e ++++l   ++a    i
  gi|336252104|ref|YP_004595211.1| 616 EVKQLSADTKEAAAEIDERLDALQSQTEESADVVDRTSEEIE-RVNDLVTDVVASLDDI 673
                                       67888999999999999999999999999999*********9.9998888888776665 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.0041
                                       CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHH CS
                         Fib_alpha  33 vkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqn 109
                                       +++++e++++ ++++  s  ++ e+  e++d ++e  + ++++  +++++  +++ e++ + e+ +a+ +++ +   
  gi|336252104|ref|YP_004595211.1| 652 TSEEIERVNDLVTDVVASLDDIAEYAAETNDGVQEISSATEEQAAATQEVVAMVD-EVASISEETTAEAQTVAA--- 724
                                       5677888888888888888888888888888888888888888888888888888.888887777776666543... PP

                                       HHHHHHHHHHHHH CS
                         Fib_alpha 110 vlesneqkiqkLe 122
                                         e++ +++q+  
  gi|336252104|ref|YP_004595211.1| 725 AAEEQTSSMQEVS 737
                                       4445555555544 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 ?    4.5   3.3     0.055        41      18      95 ..     335     413 ..     324     417 .. 0.75
   2 ?    7.1   1.6    0.0084       6.3      18     101 ..     420     507 ..     412     517 .. 0.67
   3 ?   12.4   1.2   0.00019      0.14      28     100 ..     497     573 ..     487     575 .. 0.91
   4 ?    8.1   4.4    0.0041       3.1      21      99 ..     539     637 ..     533     646 .. 0.73
   5 ?    5.2   3.7     0.032        24      25     103 ..     653     735 ..     640     740 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.055
                                       HCCCTCCCHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  18 lkkRgedkadvdelleldekrrelqvel.eelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkel 93 
                                       lk++ ++ +d d  ++l++kr   + +l + + + r +l ++I+ a ++ e+ae+ +++v+ +++ l+a+ +e +++
  gi|336252104|ref|YP_004595211.1| 335 LKSKAAAMEDGDLDVDLETKRIDSIGRLyDGFDSMRVALREQIEDAEAAREEAERERERVERMNDHLEAKADEYSAV 411
                                       55555555555555666666665555543667778888999***************************999998887 PP

                                       HH CS
                      Seryl_tRNA_N  94 ea 95 
                                        +
  gi|336252104|ref|YP_004595211.1| 412 MQ 413
                                       65 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0084
                                       HCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  18 lkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleael 90 
                                       l  R e +++ ++l e+ e+  ++ ++le+  a  N+ +  ++ a+++     e+ ++   ev+e  +e+++  +++
  gi|336252104|ref|YP_004595211.1| 420 LTVRMEPESENEALTEIGEEFNAMLADLEATVAGLNQFATDVATASEEVtassEEVQRASREVSESVQEISDGADRQ 496
                                       55677778888899999999999999999999999999999999998777777555555555554444444444444 PP

                                       HHHHHHHHHHH CS
                      Seryl_tRNA_N  91 keleaelekll 101
                                        +  + +++ +
  gi|336252104|ref|YP_004595211.1| 497 HQSLQSIDSEM 507
                                       33333333333 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  28 vdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekl 100
                                        ++l ++d+++ +l +++ee+ a +N ++   ++  + +    e ae+ i+  ++l +e +++ ae ++l+++++++
  gi|336252104|ref|YP_004595211.1| 497 HQSLQSIDSEMNTLSTTTEEIAASSNDVADVAARTAETGrggrETAEAAIDAFDDLEAEYEDVVAEFEQLRNQINQI 573
                                       5678899*********************99999999999999*******************************9986 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0041
                                       CTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHCCCCCCTT.................S-TCCCCCCCH CS
                      Seryl_tRNA_N  21 RgedkadvdelleldekrrelqveleelqaerNel...skeIgkakkkk.................edaeeliaevk 77 
                                       R+ ++a +d++ +l+++ + + +e+e+l+++ N++   + +I+++ ++                  +dae   a ++
  gi|336252104|ref|YP_004595211.1| 539 RETAEAAIDAFDDLEAEYEDVVAEFEQLRNQINQIeslTDTIAEIADQTnmlalnanieasrsadgADAEGFTAVAS 615
                                       66788999*************************87222578999988888888887777776666655555555555 PP

                                       HHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  78 elkeelkaleaelkeleaelek 99 
                                       e+k+  ++++++ +e++++l++
  gi|336252104|ref|YP_004595211.1| 616 EVKQLSADTKEAAAEIDERLDA 637
                                       5555555555555555555554 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.032
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  25 kadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleael 97 
                                       +++++++ +l +   +   ++ e  ae N   +eI++a +++    ++  ++++ev++++ee+ a  ++++++ +e+
  gi|336252104|ref|YP_004595211.1| 653 SEEIERVNDLVTDVVASLDDIAEYAAETNDGVQEISSATEEQaaatQEVVAMVDEVASISEETTAEAQTVAAAAEEQ 729
                                       56778888888888888888899999999999999999999998888999999999999999999999999999998 PP

                                       HHHHCT CS
                      Seryl_tRNA_N  98 ekllla 103
                                       ++ +++
  gi|336252104|ref|YP_004595211.1| 730 TSSMQE 735
                                       887765 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   5.1   3.4e-05     0.026     187     324 ..     374     510 ..     332     529 .. 0.79
   2 ?    2.4   0.6     0.085        63     272     333 ..     549     606 ..     539     626 .. 0.58
   3 ?   -0.3   0.2      0.54   4.1e+02     274     322 ..     714     762 ..     708     765 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.4e-05
                             IFT57 187 eeeiieskvdaaeWklEleRvlpqLkvtikadakdWrahleqmkkhkksieeslpetksqlkklhedisktlekies 263
                                       +e+i  ++   +e + E eRv+ +++ +++a+a ++ a ++   +   +++ + ++ +++l+++ e+++ +l  +e+
  gi|336252104|ref|YP_004595211.1| 374 REQIEDAEAAREEAERERERVE-RMNDHLEAKADEYSAVMQDAADGDLTVRMEPESENEALTEIGEEFNAMLADLEA 449
                                       5666677777788888888886.567788888889999999999999999999999999999999999999999999 PP

                             IFT57 264 rEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeer 324
                                           ln+   +  +  +e+ ++ +ev++  +++se+v+e ++  ++  + l+++ +em+  
  gi|336252104|ref|YP_004595211.1| 450 TVAGLNQFATDVATASEEVTASSEEVQRASREVSESVQEISDGADRQHQSLQSIDSEMNTL 510
                                       9999998888888888888888888888888888888888777777777777777777654 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.085
                             IFT57 272 leellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDgsp 333
                                       +++l +ey+++ +e+++++++++q    +++lt++ aei ++ + +  + +   s+ +Dg+ 
  gi|336252104|ref|YP_004595211.1| 549 FDDLEAEYEDVVAEFEQLRNQINQ----IESLTDTIAEIADQTNMLALNANIEASRSADGAD 606
                                       444555666666666666655554....5677778888888877776666666666666554 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.54
                             IFT57 274 ellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqeme 322
                                       e+++e +++ +  +e++ +++++s++   l+++ +++s  l++ ++++e
  gi|336252104|ref|YP_004595211.1| 714 ETTAEAQTVAAAAEEQTSSMQEVSASADRLSHQATRLSGALDRFETDVE 762
                                       5556666777788888999999999999999999999999998887766 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.6    0.0001     0.075      17      99 ..     439     519 ..     430     533 .. 0.69
   2 ?    2.6   1.2      0.18   1.3e+02      56      81 ..     558     585 ..     540     602 .. 0.41
   3 ?    4.2  11.0     0.055        41       4     105 ..     570     674 ..     568     713 .. 0.55
   4 ?    5.3   7.6     0.024        18       2      93 ..     615     701 ..     614     743 .. 0.65
   5 ?    0.9   1.0      0.59   4.4e+02      23      81 ..     706     759 ..     681     772 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                      Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsi 93 
                                       +++ +L+++ +  + + +q at++++  ++++a se++++++ e+++ +++ ++  +++ ++lq ++++e+++l + 
  gi|336252104|ref|YP_004595211.1| 439 EFNAMLADLEATVAGL-NQFATDVATASEEVTASSEEVQRASREVSESVQEISDGADRQHQSLQ-SIDSEMNTLSTT 513
                                       6778888885555555.88888888888888888888888888888888888888888888887.455555554444 PP

                      Baculo_PEP_C  94 ltnLls 99 
                                         ++++
  gi|336252104|ref|YP_004595211.1| 514 TEEIAA 519
                                       444333 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.18
                      Baculo_PEP_C  56 sllaeldt...rldtlltnLtdalnalqd 81 
                                       +++ae+++   +++ +++ Ltd++++++d
  gi|336252104|ref|YP_004595211.1| 558 DVVAEFEQlrnQIN-QIESLTDTIAEIAD 585
                                       22222222221111.12233333333332 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.055
                      Baculo_PEP_C   4 vqqL.nggggnqfldLtnvLnairlqnvqilaqlatl......ldaietqLnalsedlksllaeldtrldtlltnLt 73 
                                       ++q+ +++ +    ++ ++ n + ++n++i a  +++      ++a+++++++ls+d k++ ae+d+rld+l ++ +
  gi|336252104|ref|YP_004595211.1| 570 INQIeSLTDTI--AEIADQTNML-ALNANIEASRSADgadaegFTAVASEVKQLSADTKEAAAEIDERLDALQSQTE 643
                                       55665555543..2333333333.34444444333330000004555555666666666666666666666555533 PP

                      Baculo_PEP_C  74 dalnalqdtlrneLtnlnsiltnLlssvtNin 105
                                       +  + + d  ++e++ +n  +t+ ++s+  i 
  gi|336252104|ref|YP_004595211.1| 644 E-SADVVDRTSEEIERVNDLVTDVVASLDDIA 674
                                       3.345557888899999999999988877665 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.024
                      Baculo_PEP_C   2 advqqLnggggnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalna 78 
                                       ++v+qL+  +     ++ + L+a+++q+ + +  + ++ ++ie+ +n+l +d+ ++l ++++     +++ +d +++
  gi|336252104|ref|YP_004595211.1| 615 SEVKQLSADTKEAAAEIDERLDALQSQTEESADVVDRTSEEIER-VNDLVTDVVASLDDIAE----YAAETNDGVQE 686
                                       57999999999999999999999999999997777777777776.88888888887775554....44444555555 PP

                      Baculo_PEP_C  79 lqdtlrneLtnlnsi 93 
                                       ++ + +++  +++ +
  gi|336252104|ref|YP_004595211.1| 687 ISSATEEQAAATQEV 701
                                       554444444444333 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.59
                      Baculo_PEP_C  23 nairlqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqd 81 
                                       + +        a +++  +a ++++ a +e+ +s+++e+++   rl++++t+L+ al ++++
  gi|336252104|ref|YP_004595211.1| 706 DEV--------ASISEETTAEAQTVAAAAEEQTSSMQEVSAsadRLSHQATRLSGALDRFET 759
                                       333........444444444444444444444444444444444666666666666666653 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.4     0.018        14      35      97 ..     468     574 ..     438     577 .. 0.51
   2 ?    4.6   1.7     0.056        42       7      63 ..     565     645 ..     559     654 .. 0.72
   3 ?    4.3   3.4     0.071        53      14      70 ..     630     687 ..     614     759 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.018
                        Syntaxin_2  35 lhelieeinelikktnellkklsqldnsssds............................................q 67 
                                       +  + ee+++ +++++e+++++s  ++ +++s                                            +
  gi|336252104|ref|YP_004595211.1| 468 VTASSEEVQRASREVSESVQEISDGADRQHQSlqsidsemntlsttteeiaassndvadvaartaetgrggretaeA 544
                                       44444444444444444444444444443333322322222222234444444444455555555556677777643 PP

                        Syntaxin_2  68 qklqkekLkkdfkealqeFqkiqrqyaeke 97 
                                        + + + L  ++++++ eF+++ +q+++ e
  gi|336252104|ref|YP_004595211.1| 545 AIDAFDDLEAEYEDVVAEFEQLRNQINQIE 574
                                       333778888888888888888888887766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.056
                        Syntaxin_2   7 kinsnvstleklvkqLgtkkdteelr........................eklhelieeinelikktnellkklsql 59 
                                       ++ ++++++e+l++++    d++++                         +++++l  +++e + ++ e+l  l++ 
  gi|336252104|ref|YP_004595211.1| 565 QLRNQINQIESLTDTIAEIADQTNMLalnanieasrsadgadaegftavaSEVKQLSADTKEAAAEIDERLDALQSQ 641
                                       66777777777777777777766555566666677788888887777777888888888888888888888888877 PP

                        Syntaxin_2  60 dnss 63 
                                       ++ s
  gi|336252104|ref|YP_004595211.1| 642 TEES 645
                                       7665 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.071
                        Syntaxin_2  14 tleklvkqLgtkk.dteelreklhelieeinelikktnellkklsqldnsssdsqqkl 70 
                                       ++++ ++ L++++ ++ ++ ++  e ie++n+l++++ ++l ++++++  ++d  q +
  gi|336252104|ref|YP_004595211.1| 630 EIDERLDALQSQTeESADVVDRTSEEIERVNDLVTDVVASLDDIAEYAAETNDGVQEI 687
                                       5666777777775358888888888888888888888888888888888877763333 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3      0.75   5.6e+02      51      99 ..     366     414 ..     360     420 .. 0.80
   2 ?   11.9   0.1    0.0003      0.23      43     101 ..     432     490 ..     430     501 .. 0.84
   3 ?    1.0   1.9       0.7   5.2e+02      48     108 ..     553     632 ..     546     635 .. 0.58
   4 ?    2.1   0.5      0.32   2.4e+02      69     108 ..     614     650 ..     605     663 .. 0.73
   5 ?   -1.2   2.5       3.5   2.6e+03      63     100 ..     699     737 ..     685     751 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.75
                        TSNAXIP1_N  51 Yelyiahllesqreaqylkaklktlsessdkraleleekreelraleke 99 
                                       ++ +  +l+e++++a++ +++ +   e+ ++  + le k +e +a+ ++
  gi|336252104|ref|YP_004595211.1| 366 FDSMRVALREQIEDAEAAREEAERERERVERMNDHLEAKADEYSAVMQD 414
                                       6777788999999999999999888888888888999987777776665 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0003
                        TSNAXIP1_N  43 lLseIKkEYelyiahllesqreaqylkaklktlsessdkraleleekreelralekesk 101
                                        L+eI +E+ +++a l+ +   ++  ++ ++t+se+ + +  e++++ +e+++ ++e +
  gi|336252104|ref|YP_004595211.1| 432 ALTEIGEEFNAMLADLEATVAGLNQFATDVATASEEVTASSEEVQRASREVSESVQEIS 490
                                       599********************************************777766666554 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.7
                        TSNAXIP1_N  48 KkEYelyiah...llesqreaqylkaklktlsessd................kraleleekreelralekeskalle 105
                                        +EYe+++a+   l++++++ + l  ++++++++++                  a  ++    e+++l +++k++ +
  gi|336252104|ref|YP_004595211.1| 553 EAEYEDVVAEfeqLRNQINQIESLTDTIAEIADQTNmlalnanieasrsadgADAEGFTAVASEVKQLSADTKEAAA 629
                                       57888887661114455555555566667777777655555555555555554444555555666666666666666 PP

                        TSNAXIP1_N 106 eid 108
                                       eid
  gi|336252104|ref|YP_004595211.1| 630 EID 632
                                       665 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.32
                        TSNAXIP1_N  69 kaklktlsessdkraleleekreelralekeskalleeid 108
                                       ++++k ls+++++ a e++e+   l al++++++  + +d
  gi|336252104|ref|YP_004595211.1| 614 ASEVKQLSADTKEAAAEIDER---LDALQSQTEESADVVD 650
                                       567778888888777777777...7777777776665544 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 3.5
                        TSNAXIP1_N  63 reaqylkaklktlsessdkraleleek.reelralekes 100
                                       +e  +   +++++se+++ +a+++  + +e+ +++++ s
  gi|336252104|ref|YP_004595211.1| 699 QEVVAMVDEVASISEETTAEAQTVAAAaEEQTSSMQEVS 737
                                       333334566688888888777777777444444443333 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1         2   1.5e+03      28      53 ..     385     410 ..     369     456 .. 0.67
   2 ?   12.0   1.0   0.00029      0.22       7      61 ..     455     510 ..     450     521 .. 0.86
   3 ?    5.4   1.0     0.033        25      26      63 ..     548     585 ..     542     597 .. 0.82
   4 ?    5.1   0.8     0.041        31      21      55 ..     611     646 ..     608     654 .. 0.78
   5 ?    2.4   8.0       0.3   2.2e+02      11      50 ..     654     676 ..     625     719 .. 0.45
   6 ?    0.4   0.3       1.2   9.2e+02      11      57 ..     706     753 ..     699     763 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2
                           NPV_P10  28 ddvqenlpdvtelnekLdaqsaqLae 53 
                                       ++ + + + v+ +n++L+a +++  +
  gi|336252104|ref|YP_004595211.1| 385 EEAERERERVERMNDHLEAKADEYSA 410
                                       55555666677777777776665444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00029
                           NPV_P10   7 lvIradikavddkVdalqqqvddvqenl.pdvtelnekLdaqsaqLaeletkvenI 61 
                                        +  +d++  ++ V+a +++v++ + ++ + v+e+++  d+q ++L+++++++++ 
  gi|336252104|ref|YP_004595211.1| 455 NQFATDVATASEEVTASSEEVQRASREVsESVQEISDGADRQHQSLQSIDSEMNTL 510
                                       566789***************9998775267*******************988765 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.033
                           NPV_P10  26 qvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       + dd++++ +dv    e+L +q +q+++l +++ +I d
  gi|336252104|ref|YP_004595211.1| 548 AFDDLEAEYEDVVAEFEQLRNQINQIESLTDTIAEIAD 585
                                       56899999999888888999999999999999999976 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.041
                           NPV_P10  21 dalqqqvddvqenlpdv.telnekLdaqsaqLaele 55 
                                       +a+ ++v++++++ ++   e+ e+Lda++ q +e  
  gi|336252104|ref|YP_004595211.1| 611 TAVASEVKQLSADTKEAaAEIDERLDALQSQTEESA 646
                                       788999999999998752699999999998877655 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.3
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaq 50 
                                       ++i+ v+d V+ + +++dd++e                  
  gi|336252104|ref|YP_004595211.1| 654 EEIERVNDLVTDVVASLDDIAE-----------------Y 676
                                       2333444444444444433332.................2 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1.2
                           NPV_P10  11 adikavddkVdalqqqv.ddvqenlpdvtelnekLdaqsaqLaeletk 57 
                                       ++++ +++  +a  q v +  +e+   ++e+++  d++s q + l+ +
  gi|336252104|ref|YP_004595211.1| 706 DEVASISEETTAEAQTVaAAAEEQTSSMQEVSASADRLSHQATRLSGA 753
                                       455566666666555552334555666666666666666666666554 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2       4.3   3.2e+03      37      62 ..     376     401 ..     361     416 .. 0.46
   2 ?    3.2   0.1       0.2   1.5e+02      23      76 ..     439     496 ..     431     508 .. 0.63
   3 ?    0.0   0.0       1.9   1.4e+03      28      60 ..     497     529 ..     493     534 .. 0.71
   4 ?    8.2   0.0    0.0055       4.1      23      61 ..     548     586 ..     542     599 .. 0.86
   5 ?    1.0   0.1      0.93     7e+02      32      68 ..     622     658 ..     608     667 .. 0.65
   6 ?    1.8   0.1      0.52   3.9e+02       5      61 ..     668     725 ..     664     756 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.3
                      Occludin_ELL  37 kfseLerelkelkegskeykkieeei 62 
                                       ++++ e+  +e+++++++++++++++
  gi|336252104|ref|YP_004595211.1| 376 QIEDAEAAREEAERERERVERMNDHL 401
                                       33333333344444443333333332 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.2
                      Occludin_ELL  23 eYkelhaeleevskkfseLerelkelkegsk....eykkieeeilqeykklkkdpeyq 76 
                                       e++++ a+le++ + ++++ +++ +++e+ +    e++++ +e+ ++ ++++  ++ q
  gi|336252104|ref|YP_004595211.1| 439 EFNAMLADLEATVAGLNQFATDVATASEEVTasseEVQRASREVSESVQEISDGADRQ 496
                                       4555555555665556555555544444433333489999999998888887744433 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.9
                      Occludin_ELL  28 haeleevskkfseLerelkelkegskeykkiee 60 
                                       h++l+++ ++++ L++ ++e + +s+ ++++++
  gi|336252104|ref|YP_004595211.1| 497 HQSLQSIDSEMNTLSTTTEEIAASSNDVADVAA 529
                                       677777888888888777777777777766665 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0055
                      Occludin_ELL  23 eYkelhaeleevskkfseLerelkelkegskeykkieee 61 
                                        + +l+ae e+v ++f++L++++++ +  ++++++i+++
  gi|336252104|ref|YP_004595211.1| 548 AFDDLEAEYEDVVAEFEQLRNQINQIESLTDTIAEIADQ 586
                                       5788999*****************999999999999888 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.93
                      Occludin_ELL  32 eevskkfseLerelkelkegskeykkieeeilqeykk 68 
                                       +++++  +e++++l++l+ +++e ++++++  +e ++
  gi|336252104|ref|YP_004595211.1| 622 ADTKEAAAEIDERLDALQSQTEESADVVDRTSEEIER 658
                                       3445555666677777777777777777776666555 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.52
                      Occludin_ELL   5 ksaeqrerYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegsk.eykkieee 61 
                                        s ++  +Y ae n+  +e ++  +e +++++++  + +e+ + +e+++ e +++++ 
  gi|336252104|ref|YP_004595211.1| 668 ASLDDIAEYAAETNDGVQEISSATEEQAAATQEVVAMVDEVASISEETTaEAQTVAAA 725
                                       5677788899999999999999999999999999999888888888877555555544 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.2   9.3e+02      32      63 ..     433     473 ..     374     514 .. 0.58
   2 ?    0.9   0.1      0.72   5.4e+02      35      71 ..     548     583 ..     532     599 .. 0.45
   3 ?    9.9   0.1    0.0012      0.91      26      95 ..     618     686 ..     610     692 .. 0.89
   4 ?   -1.3   0.0       3.6   2.7e+03      45      87 ..     714     759 ..     686     771 .. 0.49

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.2
                           DUF2935  32 likeakefkkeFekllaeavelseglv.........rasse 63 
                                       l ++ +ef+  + +l+a +  l++  +         +asse
  gi|336252104|ref|YP_004595211.1| 433 LTEIGEEFNAMLADLEATVAGLNQFATdvataseevTASSE 473
                                       33333444444444444443333333233333332222222 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.72
                           DUF2935  35 eakefkkeFekllaeavelseglvrasseleeavakL 71 
                                         ++++ e+e++ ae ++l + +  + ++l++ +a++
  gi|336252104|ref|YP_004595211.1| 548 AFDDLEAEYEDVVAEFEQLRNQI-NQIESLTDTIAEI 583
                                       33333333344444443333333.2222222222222 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0012
                           DUF2935  26 dpkekdlikeakefkkeFekllaeavelseglvrasseleeavakLneealkltreliqFkkellekvls 95 
                                       ++  +d  + a e+ +++++l ++++e ++++   +se+ e+v++L +++++ ++ + ++++e+ ++v++
  gi|336252104|ref|YP_004595211.1| 618 KQLSADTKEAAAEIDERLDALQSQTEESADVV-DRTSEEIERVNDLVTDVVASLDDIAEYAAETNDGVQE 686
                                       5666788999*****************99999.999***************************9999876 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.6
                           DUF2935  45 kllaeavelseglv...rasseleeavakLneealkltreliqFkk 87 
                                       +++aea+ ++       +  +e   +  +L ++a +l+ +l +F +
  gi|336252104|ref|YP_004595211.1| 714 ETTAEAQTVAAAAEeqtSSMQEVSASADRLSHQATRLSGALDRFET 759
                                       3333332222222122133344444445555555555555555555 PP

>> Vac_Fusion  Chordopoxvirus multifunctional envelope protein A27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.0       5.3     4e+03      24      38 ..     388     402 ..     379     403 .. 0.83
   2 ?    5.8   0.0     0.014        10      12      51 ..     552     596 ..     545     598 .. 0.82
   3 ?    2.4   0.0      0.16   1.2e+02       4      33 ..     630     659 ..     627     661 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.3
                                       HHHHHHHHHHH-XXX CS
                        Vac_Fusion  24 krvnealkRlEnHle 38 
                                        r  e+++R+  Hle
  gi|336252104|ref|YP_004595211.1| 388 ERERERVERMNDHLE 402
                                       67789999*****98 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHH-XXXXX.....XXXXXXXXXXX CS
                        Vac_Fusion  12 lekdfqlvikcckrvnealkRlEnHleTl.....RkamlaLakKI 51 
                                       le ++++v+ ++ +  ++++ +E  ++T+       +mlaL+  I
  gi|336252104|ref|YP_004595211.1| 552 LEAEYEDVVAEFEQLRNQINQIESLTDTIaeiadQTNMLALNANI 596
                                       899*************************94444445788777666 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        Vac_Fusion   4 dleerllvlekdfqlvikcckrvnealkRl 33 
                                       ++ erl  l+ + +++++   r++e ++R+
  gi|336252104|ref|YP_004595211.1| 630 EIDERLDALQSQTEESADVVDRTSEEIERV 659
                                       6889*************************8 PP

>> DUF730  Protein of unknown function (DUF730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.4    0.0053         4      68     118 ..     361     411 ..     342     415 .. 0.89
   2 ?   -2.7   0.0       7.7   5.7e+03      75      92 ..     435     452 ..     431     481 .. 0.76
   3 ?    3.5   0.1     0.091        68      65      96 ..     700     731 ..     664     748 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0053
                            DUF730  68 alcdefdkikeektemkkdleaakkrvesqaekiflmekkfetlekkyesl 118
                                        l d fd ++    e  +d eaa+++ e + e++  m+ ++e+   +y ++
  gi|336252104|ref|YP_004595211.1| 361 RLYDGFDSMRVALREQIEDAEAAREEAERERERVERMNDHLEAKADEYSAV 411
                                       4889**************************************999999876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.7
                            DUF730  75 kikeektemkkdleaakk 92 
                                        i ee + m  dlea+  
  gi|336252104|ref|YP_004595211.1| 435 EIGEEFNAMLADLEATVA 452
                                       678899999999998754 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.091
                            DUF730  65 wtvalcdefdkikeektemkkdleaakkrves 96 
                                         va+ de   i ee+t   + + aa ++  s
  gi|336252104|ref|YP_004595211.1| 700 EVVAMVDEVASISEETTAEAQTVAAAAEEQTS 731
                                       4699************9999988887744333 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.2   6.7e-05      0.05      52     152 ..     431     532 ..     427     554 .. 0.76
   2 ?    1.1   0.8      0.32   2.4e+02      81     145 ..     564     635 ..     539     650 .. 0.49
   3 ?    3.3   1.1     0.067        50      82     162 ..     623     698 ..     606     713 .. 0.60
   4 ?    1.1   3.4      0.31   2.3e+02      77     155 ..     653     726 ..     628     758 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-05
                      Allexi_40kDa  52 eWLthishdvdsiinklnpvsllsqttlLselrdalrtltklldklksvekklelsaetasd..skllkklesiets 126
                                       e Lt i+++ + ++ +l+++ +   ++  +++ +a++++t   +++++ ++++++s +++sd   +  ++l+si+ +
  gi|336252104|ref|YP_004595211.1| 431 EALTEIGEEFNAMLADLEAT-VAGLNQFATDVATASEEVTASSEEVQRASREVSESVQEISDgaDRQHQSLQSIDSE 506
                                       789**************988.6667777778888888888888888888877777777766522334679******* PP

                      Allexi_40kDa 127 leelhakldelsssetsesegPsssp 152
                                       +++l +  +e+++s+++  +    + 
  gi|336252104|ref|YP_004595211.1| 507 MNTLSTTTEEIAASSNDVADVAARTA 532
                                       ***********999998877654443 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.32
                      Allexi_40kDa  81 selrdalrtltklldklksvek.......klelsaetasdskllkklesietsleelhakldelsssetses 145
                                        +lr++++++++l d+++++ +       + +++a++  d   ++ ++++  ++++l a  +e +++ ++  
  gi|336252104|ref|YP_004595211.1| 564 EQLRNQINQIESLTDTIAEIADqtnmlalNANIEASRSADGADAEGFTAVASEVKQLSADTKEAAAEIDERL 635
                                       333333333333333333333300000003333444444444556666666666666666655555444444 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.067
                      Allexi_40kDa  82 elrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelsssetsesegPsssptkassa 158
                                       + ++a  ++++ ld l+   +++e+sa+  + +   +++e ++  + ++ a ld++++ ++++++g +  ++ ++ +
  gi|336252104|ref|YP_004595211.1| 623 DTKEAAAEIDERLDALQ---SQTEESADVVDRT--SEEIERVNDLVTDVVASLDDIAEYAAETNDGVQEISSATEEQ 694
                                       23344444444444443...3444444433333..467888999999999999999999999999866555544443 PP

                      Allexi_40kDa 159 eaaa 162
                                        aa+
  gi|336252104|ref|YP_004595211.1| 695 AAAT 698
                                       3333 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.31
                      Allexi_40kDa  77 ttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelsssetsesegPssspt 153
                                       + ++ ++ d ++ +   ld++++   ++++  +++s+       ++     +e+ a +de++s +++++++ ++   
  gi|336252104|ref|YP_004595211.1| 653 SEEIERVNDLVTDVVASLDDIAEYAAETNDGVQEISSATEE--QAA-A--TQEVVAMVDEVASISEETTAEAQTVAA 724
                                       34455666666666666666666666666666555554422..222.2..244445555555444444444333322 PP

                      Allexi_40kDa 154 ka 155
                                        a
  gi|336252104|ref|YP_004595211.1| 725 AA 726
                                       22 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         6   4.5e+03       3      18 ..     388     403 ..     386     411 .. 0.85
   2 ?    3.0   0.1      0.12        89       4      41 ..     428     465 ..     427     466 .. 0.93
   3 ?    3.6   0.2     0.074        55       7      39 ..     484     516 ..     480     531 .. 0.87
   4 ?    4.8   0.2     0.032        24       4      30 ..     561     587 ..     546     599 .. 0.65
   5 ?    1.6   0.0      0.31   2.3e+02       6      39 ..     653     686 ..     649     690 .. 0.82
   6 ?   -2.5   0.0         6   4.5e+03      26      45 ..     726     745 ..     704     750 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6
                         DASH_Duo1   3 ekEleqLrkinevien 18 
                                       e+E e ++++n+ +e+
  gi|336252104|ref|YP_004595211.1| 388 ERERERVERMNDHLEA 403
                                       6899999999999886 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.12
                         DASH_Duo1   4 kEleqLrkinevienviesLkkaksniervketvestn 41 
                                        E e L++i e ++++ ++L+++   ++++++ v +++
  gi|336252104|ref|YP_004595211.1| 428 SENEALTEIGEEFNAMLADLEATVAGLNQFATDVATAS 465
                                       799****************************9999887 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.074
                         DASH_Duo1   7 eqLrkinevienviesLkkaksniervketves 39 
                                       e++++i +  +  ++sL+++ s+++++++t+e+
  gi|336252104|ref|YP_004595211.1| 484 ESVQEISDGADRQHQSLQSIDSEMNTLSTTTEE 516
                                       677778888888899***************997 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.032
                         DASH_Duo1   4 kEleqLrkinevienviesLkkaksni 30 
                                       +E eqLr+ ++ ie++++++ ++ +++
  gi|336252104|ref|YP_004595211.1| 561 AEFEQLRNQINQIESLTDTIAEIADQT 587
                                       456666666666666666666555333 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.31
                         DASH_Duo1   6 leqLrkinevienviesLkkaksniervketves 39 
                                        e+++++n+ + +v++sL+++ ++  + +  v++
  gi|336252104|ref|YP_004595211.1| 653 SEEIERVNDLVTDVVASLDDIAEYAAETNDGVQE 686
                                       578999*************999888877777665 PP

  == domain 6  score: -2.5 bits;  conditional E-value: 6
                         DASH_Duo1  26 aksniervketvestntLLd 45 
                                       a++++++++e   s+++L +
  gi|336252104|ref|YP_004595211.1| 726 AEEQTSSMQEVSASADRLSH 745
                                       33666666666666666655 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   5.1      0.17   1.3e+02     203     280 ..     368     445 ..     364     456 .. 0.71
   2 ?    9.9   4.9    0.0004       0.3     161     254 ..     429     521 ..     423     533 .. 0.62
   3 ?    8.2   8.4    0.0013      0.99     170     277 ..     550     658 ..     539     666 .. 0.40
   4 ?    5.9  12.4     0.007       5.2     179     288 ..     613     721 ..     604     753 .. 0.49

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.17
                              Spc7 203 elreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkale 279
                                       ++r +l+e+ ++ e+ ++e ++ +e++e+ ++ +e+ ++++s ++++ a  + +++++ +++++ + ++ ee++a+ 
  gi|336252104|ref|YP_004595211.1| 368 SMRVALREQIEDAEAAREEAERERERVERMNDHLEAKADEYSAVMQDAADGDLTVRMEPESENEALTEIGEEFNAML 444
                                       56777888888888888888888888888888888888888888888777777777777777777777777776665 PP

                              Spc7 280 e 280
                                        
  gi|336252104|ref|YP_004595211.1| 445 A 445
                                       5 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0004
                              Spc7 161 qeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekie 237
                                       ++e l+e+ +e+++  a+le++++ l+++a+++++  +ee+ +  ee+++++ e++e  +e+++  ++  ++ ++i+
  gi|336252104|ref|YP_004595211.1| 429 ENEALTEIGEEFNAMLADLEATVAGLNQFATDVAT-ASEEVTASSEEVQRASREVSESVQEISDGADRQHQSLQSID 504
                                       45566666666666666666666666666666544.56666666667776666666666666666666666666666 PP

                              Spc7 238 elkeqkseleeeiaeae 254
                                       +  +  s++ eeia++ 
  gi|336252104|ref|YP_004595211.1| 505 SEMNTLSTTTEEIAASS 521
                                       66666666666666554 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0013
                              Spc7 170 peleeekaeleeeleklqeaaeeles........idkeeLeelreelaelkaeieekkkelaelqeqleeleekiee 238
                                       ++le+e++++ +e+e+l+++ +++es         d++++ +l  ++++        +       e  +++++++++
  gi|336252104|ref|YP_004595211.1| 550 DDLEAEYEDVVAEFEQLRNQINQIESltdtiaeiADQTNMLALNANIEAS-------RSADGADAEGFTAVASEVKQ 619
                                       55555555555555555555555555322222222344443333333333.......33333333333333333333 PP

                              Spc7 239 lkeqkseleeeiaeaervleeckgwsesevsrlkeevka 277
                                       l++  +e+ +ei e  + l+ + + s++ v+r  ee ++
  gi|336252104|ref|YP_004595211.1| 620 LSADTKEAAAEIDERLDALQSQTEESADVVDRTSEEIER 658
                                       333333333333333333333333333333333333332 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.007
                              Spc7 179 leeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaer 255
                                       + +e+++l +  +e ++   e+L +l+++ +e    +++ ++e++++++ ++++ +++++++e  +e+++ ++e  +
  gi|336252104|ref|YP_004595211.1| 613 VASEVKQLSADTKEAAAEIDERLDALQSQTEESADVVDRTSEEIERVNDLVTDVVASLDDIAEYAAETNDGVQEISS 689
                                       44444555554444444445555555555555555555555555555555555555555555555555555555444 PP

                              Spc7 256 vleeckgwsesevsrlkeevkaleeltgwkivs 288
                                        +ee+    ++ev ++ +ev ++ e+t  +  +
  gi|336252104|ref|YP_004595211.1| 690 ATEEQA-AATQEVVAMVDEVASISEETTAEAQT 721
                                       444332.33344444444444444444433322 PP

>> DCB  Dimerisation and cyclophilin-binding domain of Mon2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3      0.27     2e+02       9      56 ..     456     503 ..     450     519 .. 0.81
   2 ?    3.5   0.1     0.067        50      14      59 ..     610     655 ..     601     671 .. 0.78
   3 ?    3.6   0.2     0.063        47       8      49 ..     702     743 ..     695     757 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.27
                               DCB   9 alqsdlkalsseskrkhskvkeasekgilkLktikssseeeeqslaea 56 
                                       +  +d  + s+e    +++v+ as +++  +++i++  ++++qsl++ 
  gi|336252104|ref|YP_004595211.1| 456 QFATDVATASEEVTASSEEVQRASREVSESVQEISDGADRQHQSLQSI 503
                                       566788888899999999999999999999999999998889988876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.067
                               DCB  14 lkalsseskrkhskvkeasekgilkLktikssseeeeqslaeasee 59 
                                       + a++se k+ +++ kea+ ++  +L  ++s++ee+   + ++see
  gi|336252104|ref|YP_004595211.1| 610 FTAVASEVKQLSADTKEAAAEIDERLDALQSQTEESADVVDRTSEE 655
                                       7788999999999999999999999999999995555555444443 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.063
                               DCB   8 ealqsdlkalsseskrkhskvkeasekgilkLktikssseee 49 
                                        a++ +  ++s+e+    ++v++a+e++ + ++++++s ++ 
  gi|336252104|ref|YP_004595211.1| 702 VAMVDEVASISEETTAEAQTVAAAAEEQTSSMQEVSASADRL 743
                                       56778899**************************99998443 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.8     0.029        21     276     343 ..     445     513 ..     427     523 .. 0.86
   2 ?    8.1   1.3    0.0016       1.2     244     353 ..     575     682 ..     558     692 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.029
                                       S-HHHHHHHHHHHHHHHHHHHHHHHHCCT.TSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FH2 276 vnleslekevkklekglkklekelessek.keepsdkflevlkeflkeaeeklkkleeelkeakelvke 343
                                        +le+ ++ ++++ ++++ +++e+++s++  +  s +++e+++e+ + a+++ ++l++  +e+++l ++
  gi|336252104|ref|YP_004595211.1| 445 ADLEATVAGLNQFATDVATASEEVTASSEeVQRASREVSESVQEISDGADRQHQSLQSIDSEMNTLSTT 513
                                       6889999999999999999999999999888899999*******************9999999987665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
                                       BHHHHHHHHHHTTSGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHH CS
                               FH2 244 tLLHylvkiireklpevldfsseLknvkkaakvnleslekevkklekglkklekelessekkeepsdkflevlkefl 320
                                       +L +++++i +   + +l ++  +++ ++a   + e +++  +++++  +++++ + + ++  +  +  +e   +++
  gi|336252104|ref|YP_004595211.1| 575 SLTDTIAEIAD--QTNMLALNANIEASRSADGADAEGFTAVASEVKQLSADTKEAAAEIDERLDALQSQTEESADVV 649
                                       55555555533..345566666666666666666665555555555555555555555555555999999******* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTT--TT CS
                               FH2 321 keaeeklkkleeelkeakelvkelveYfgedkk 353
                                       ++++e++++++++ +++ + +++++eY  e ++
  gi|336252104|ref|YP_004595211.1| 650 DRTSEEIERVNDLVTDVVASLDDIAEYAAETND 682
                                       ***************************877655 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       7.9   5.9e+03      28      52 ..      56      80 ..      36     113 .. 0.80
   2 ?    1.8   0.1      0.35   2.6e+02      31      87 ..     426     483 ..     419     494 .. 0.71
   3 ?    1.5   0.1      0.41   3.1e+02      35      82 ..     486     534 ..     480     540 .. 0.80
   4 ?    5.3   0.0     0.027        20      65      95 ..     549     579 ..     545     583 .. 0.89
   5 ?    0.9   0.1      0.65   4.8e+02      39      79 ..     625     670 ..     610     692 .. 0.65
   6 ?   -2.2   0.1         6   4.5e+03      72      93 ..     726     747 ..     695     752 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.9
                           DUF2730 28 kYakredleklaekveendkrltel 52
                                        + r++ + l e v+e+++ l+++
  gi|336252104|ref|YP_004595211.1| 56 ESTARQEASALDEWVAEHERFLSST 80
                                      5567999999999999999877765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.35
                           DUF2730  31 kredleklaekveendkrlteletkvenLPt.akdlekLkllladlrgelkaleaevr 87 
                                       + ++ e l+e+ ee +  l++le++v+ L   a d+++ + +++    e++ +++ev+
  gi|336252104|ref|YP_004595211.1| 426 PESENEALTEIGEEFNAMLADLEATVAGLNQfATDVATASEEVTASSEEVQRASREVS 483
                                       56788999999999999**********9976467888777777655555554444443 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.41
                           DUF2730  35 leklaekveendkrlteletkvenLPt.akdlekLkllladlrgelkal 82 
                                       ++++ + ++++++ l+++++++++L t ++++++ + ++ad+ +++ ++
  gi|336252104|ref|YP_004595211.1| 486 VQEISDGADRQHQSLQSIDSEMNTLSTtTEEIAASSNDVADVAARTAET 534
                                       6677778888889999999999999862567999999999999998877 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.027
                           DUF2730  65 lekLkllladlrgelkaleaevrqlshqvdL 95 
                                       +++L+ + +d+ +e+++l+++++q++ ++d 
  gi|336252104|ref|YP_004595211.1| 549 FDDLEAEYEDVVAEFEQLRNQINQIESLTDT 579
                                       67899*********************99985 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.65
                           DUF2730  39 aekveendkrlteletkvenLP.....takdlekLkllladlrgel 79 
                                       +e ++e+d+rl++l+++ e+       t +++e+++ l++d+ + l
  gi|336252104|ref|YP_004595211.1| 625 KEAAAEIDERLDALQSQTEESAdvvdrTSEEIERVNDLVTDVVASL 670
                                       4667788888888877766532111224555555555555555555 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 6
                           DUF2730  72 ladlrgelkaleaevrqlshqv 93 
                                        ++    +++++a+ ++lshq+
  gi|336252104|ref|YP_004595211.1| 726 AEEQTSSMQEVSASADRLSHQA 747
                                       4444555666666666666665 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.4      0.02        15     188     227 ..     367     406 ..     338     413 .. 0.84
   2 ?    8.2   4.8    0.0019       1.4     121     224 ..     473     579 ..     468     597 .. 0.72
   3 ?    1.9   6.3      0.15   1.2e+02     124     219 ..     625     726 ..     586     756 .. 0.48

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.02
                              CorA 188 dedkeylrdlldelerllemlealrerleslqdtysslls 227
                                       d ++  lr+ ++++e + e++e  rer+e+++d + +  +
  gi|336252104|ref|YP_004595211.1| 367 DSMRVALREQIEDAEAAREEAERERERVERMNDHLEAKAD 406
                                       4455568899999999999999999999999999887665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0019
                              CorA 121 drlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkey.l 194
                                       +++ ++ ++++e ++e++d    ++++ ++i +e+ +l ++  ++  + ++  +v  r  ++++++++++e++   +
  gi|336252104|ref|YP_004595211.1| 473 EEVQRASREVSESVQEISDGAdrQHQSLQSIDSEMNTLSTTTEEIAASSNDVADVAARTAETGRGGRETAEAAIDaF 549
                                       67788999*************95555555666667779999***************999998888888888754446 PP

                              CorA 195 rdlldelerllemlealrerleslqdtyss 224
                                       +dl+ e e ++ + e+lr++++++ ++  +
  gi|336252104|ref|YP_004595211.1| 550 DDLEAEYEDVVAEFEQLRNQINQIESLTDT 579
                                       666666666666666666666655554433 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.15
                              CorA 124 fellekleeeldeledeledstkkeilrelaq.lrrrlvklrralapnrevlk..........rllakaddklldde 189
                                        e+  +++e+ld l+++   +++++ ++++++ ++r    + +++a + ++ +          ++ + +++     +
  gi|336252104|ref|YP_004595211.1| 625 KEAAAEIDERLDALQSQT--EESADVVDRTSEeIERVNDLVTDVVASLDDIAEyaaetndgvqEISSATEEQAAATQ 699
                                       333444444444444444..344444444444333333333444444444442100000000022221111111111 PP

                              CorA 190 dkeylrdlldelerllemlealrerleslq 219
                                       +      + de+++++e+++a ++ +    
  gi|336252104|ref|YP_004595211.1| 700 E---VVAMVDEVASISEETTAEAQTVAAAA 726
                                       1...34444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (876 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1985  (0.110714); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                       149  (0.00831056); expected 17.9 (0.001)
Passed Fwd filter:                        97  (0.00541023); 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: 2.02u 0.50s 00:00:02.52 Elapsed: 00:00:00.93
# Mc/sec: 2849.88
//
Query:       gi|336252105|ref|YP_004595212.1|  [L=120]
Description: hypothetical protein Halxa_0694 [Halopiger xanaduensis SH-6]
Scores for 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-21   75.7   0.0    2.6e-21   75.6   0.0    1.0  1  DUF192    Uncharacterized ACR, COG1430


Domain annotation for each model (and alignments):
>> DUF192  Uncharacterized ACR, COG1430
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.0   1.5e-25   2.6e-21       2      94 ..      18     112 ..      17     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 1.5e-25
                                       EEEEE-SHHHHHHTTTT-----TTEEEEEEECCEEEEEE--TT--S-EEEEEE-TTSBEEEEEEEE-TT......-E CS
                            DUF192   2 tvevAdteeerarGLmgreslpedegmlfvfdkerehsfwMkntripLdiifldadgriveieealkpq......sv 72 
                                       tv +Ad+  ++ rGLm+r+s+p+d+++ f+fd+ +++ ++M ++ +p+d+++l  d +++++e+ l+p+      ++
  gi|336252105|ref|YP_004595212.1|  18 TVDFADSVLSQLRGLMFRRSIPDDYALAFRFDSVETQDVHMLFVFFPIDVVWL-VDDTVQRVER-LRPWlgfkraEA 92 
                                       799**************************************************.9********6.77**88776558 PP

                                       CEEEEEETTHHHHHT--TT-EE CS
                            DUF192  73 ryvLElpaGaakklgikpGdrl 94 
                                       + ++ElpaG+a+  +++pGdrl
  gi|336252105|ref|YP_004595212.1|  93 DTIVELPAGTAD--DVEPGDRL 112
                                       88*********8..9*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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 0.41s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 772.29
//
Query:       gi|336252106|ref|YP_004595213.1|  [L=523]
Description: (R)-citramalate synthase [Halopiger xanaduensis SH-6]
Scores for 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-67  226.3   3.1      1e-66  225.2   3.1    1.5  1  HMGL-like   HMGL-like
    2.5e-30  105.1   3.0    5.8e-30  103.9   3.0    1.7  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 !  225.2   3.1   1.1e-70     1e-66       2     264 .]      30     284 ..      29     284 .. 0.99

  Alignments for each domain:
  == domain 1  score: 225.2 bits;  conditional E-value: 1.1e-70
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       v+++dttLRDGeqa++++ls +ek++ia+ L++agv++iE+g +  + ++++++  + +   +ar+++ +r  e+di
  gi|336252106|ref|YP_004595213.1|  30 VRLLDTTLRDGEQAPGVSLSPDEKVEIARSLERAGVAVIEAGSACTGAGERQAISRVTDLDLDARVTSFCRGLEHDI 106
                                       899************************************************************************** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       + a e    + ++ vh+++++s+ h++ k++ +re+ ++ ++e+v++a+++   ve+  ed sr+dl++l e++e+a
  gi|336252106|ref|YP_004595213.1| 107 DLALE----CDVDGVHIVVPASDRHVEEKVGTSREDNLEATAELVEYATDHDLWVEVIGEDGSRADLDYLEELMETA 179
                                       *****....******************************************************************** PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                        +aGa+r  +aDtvG + P+  ae +s+l+e  +    +s H+H+dlGl+v n++aAv  Gad v +tvnGlGeraG
  gi|336252106|ref|YP_004595213.1| 180 LDAGADRTCFADTVGHTGPERTAEAVSRLAELGP----VSAHTHDDLGLGVTNAIAAVASGADLVHCTVNGLGERAG 252
                                       *****************************99888....*************************************** PP

                                       B-BHHHHHHHHHHTT-B----HHHHHHHHHHH CS
                         HMGL-like 233 naaleelvaalealgvdtgldlqklrsiaalv 264
                                       n+alee+++al +      l+l++l+++a++v
  gi|336252106|ref|YP_004595213.1| 253 NVALEEVAIALSHVYDVETLELEQLYDLAQVV 284
                                       *************998899*********9987 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   3.0   6.5e-34   5.8e-30       2     133 .]     380     511 ..     379     511 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 6.5e-34
                                       XXXXXXXXXXXXXXXXXX.--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH..T CS
                        LeuA_dimer   2 vtdedlealvkdelleae.erlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv..d 75 
                                       vtd+dl a+++d++++ + + ++l++l+ +sg + ++ta+++lev +gee++as++G+GpvdA++ A+r+alg+  d
  gi|336252106|ref|YP_004595213.1| 380 VTDADLLAIAEDVTGDDReRVVELLDLNATSGGS-VPTASIRLEV-EGEERVASGTGSGPVDAAVSAVREALGSmaD 454
                                       9***************987999**********97.**********.9***************************999 PP

                                       -EEEEEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHHS CS
                        LeuA_dimer  76 ikLldYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrll 133
                                       ++L++Y+v+a+t+gtda ++v V++  +d+++v+    ++di++AS++A+++al+rll
  gi|336252106|ref|YP_004595213.1| 455 AELESYHVDAVTGGTDAVVTVEVTMA-RDDRSVTVARSEADITRASVEAMVDALDRLL 511
                                       9*************************.77776999999****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.57u 0.75s 00:00:01.31 Elapsed: 00:00:00.78
# Mc/sec: 2035.31
//
Query:       gi|336252107|ref|YP_004595214.1|  [L=65]
Description: hypothetical protein Halxa_0696 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0085   15.7   6.2      0.011   15.3   6.2    1.1  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 !   15.3   6.2   6.1e-07     0.011     137     182 ..       6      50 ..       2      52 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.1e-07
                            DUF998 137 lvggvallllvaalvwllaaaldgslllGlaerllvlaitawllal 182
                                       ++ + +++++va+l+++ ++ ldgsl++Gl+ rl+v++++++l+a+
  gi|336252107|ref|YP_004595214.1|   6 RIVVGTIWIAVAGLMATTLE-LDGSLSAGLIARLVVILVALFLAAV 50 
                                       44455556666666666666.**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.94s 00:00:01.35 Elapsed: 00:00:00.88
# Mc/sec: 222.21
//
Query:       gi|336252108|ref|YP_004595215.1|  [L=477]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-33  113.1   7.7    4.7e-33  113.1   7.7    2.5  2  Ferredoxin_N  N-terminal region of 4Fe-4S ferredoxin iron-sul
    1.3e-14   54.5  19.4    1.4e-07   32.0   5.7    3.4  3  Fer4_7        4Fe-4S dicluster domain
    1.4e-11   44.4   4.2    1.4e-11   44.4   4.2    2.7  3  Fer4_11       4Fe-4S dicluster domain
    8.1e-09   35.5  23.4    5.8e-06   26.3   3.3    3.8  4  Fer4_10       4Fe-4S dicluster domain
    3.4e-08   33.0  30.3     0.0001   21.9   3.5    4.4  4  Fer4          4Fe-4S binding domain
    7.6e-08   32.1  30.7     0.0012   18.8   2.9    4.3  4  Fer4_6        4Fe-4S binding domain
    1.3e-06   28.4  25.0     0.0079   16.3   7.7    3.5  3  Fer4_9        4Fe-4S dicluster domain
    1.7e-06   27.8  31.6    0.00028   20.8   1.9    4.3  4  Fer4_2        4Fe-4S binding domain
     0.0015   19.3  38.9       0.39   11.7   0.2    4.3  4  Fer4_3        4Fe-4S binding domain
     0.0022   18.5  20.4      0.063   13.8   2.2    4.2  5  Fer4_17       4Fe-4S dicluster domain
     0.0037   17.7  25.0      0.039   14.4   5.5    4.1  4  Fer4_8        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.017   16.1   5.2      0.017   16.1   5.2    4.4  3  Fer4_16       4Fe-4S double cluster binding domain
      0.046   13.8  24.7        2.3    8.4   1.5    3.7  4  Fer4_21       4Fe-4S dicluster domain
      0.049   14.4  12.4       0.25   12.1   0.5    4.1  3  Fer4_15       4Fe-4S single cluster domain
       0.05   14.1  26.6        0.1   13.1   3.0    4.3  4  Fer4_4        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Ferredoxin_N  N-terminal region of 4Fe-4S ferredoxin iron-sulfur binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1   7.7   3.9e-36   4.7e-33       1      65 []      14      78 ..      14      78 .. 0.99
   2 ?   -1.5   1.4       2.3   2.8e+03      18      44 ..     392     419 ..     375     429 .. 0.69

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 3.9e-36
                      Ferredoxin_N  1 hplgeeweeeleemLddteYDaeLGlemarDAvrvtkGeLseaeFhekYheaVlaEFgeDeRPta 65
                                      hplge++eee+e+mL+dteYDaeLG+emarDA+rvtkGeLs+++F+++Yhe+V++EFgeD+RP+a
  gi|336252108|ref|YP_004595215.1| 14 HPLGEAAEEEFEKMLEDTEYDAELGMEMARDAMRVTKGELSDEAFYDRYHEDVMEEFGEDSRPMA 78
                                      89*************************************************************95 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.3
                      Ferredoxin_N  18 teYDaeLGlemar.DAvrvtkGeLseae 44 
                                        + D e G  m++  A ++ +Ge+ +a+
  gi|336252108|ref|YP_004595215.1| 392 EPADEEGGDGMTEeEASQLLAGEFGDAD 419
                                       3467888888875269999999998876 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   6.4   1.5e-08   1.8e-05       1      52 []     173     244 ..     168     244 .. 0.73
   2 !   32.0   5.7   1.2e-10   1.4e-07       2      52 .]     261     344 ..     260     344 .. 0.64
   3 !   12.7   0.1   0.00012      0.15       3      27 ..     331     355 ..     329     379 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.5e-08
                            Fer4_7   1 rCigCgaCvaaC..................pvkaieldeeenekgtekveidpekClgCga..CvavCPtga 52 
                                       +C gC  Cv+aC                    +++e +e ++ + t++ ++  + C++C+   C++vCPt a
  gi|336252108|ref|YP_004595215.1| 173 SCDGCLSCVVACnaehnwdeganwmyvlayEDGTVESPEPDDFESTRDFNYIVRPCQHCTDapCEKVCPTTA 244
                                       5***********88777777555444444433333333333444668889999*******999******986 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 1.2e-10
                            Fer4_7   2 CigCgaCvaaCpvkaield..eeenek..........gtekv.........eidpekCl...............gCg 42 
                                       CigC++C++aCp+++ +++  e ++++          +             +++++kC+               g++
  gi|336252108|ref|YP_004595215.1| 261 CIGCRYCQVACPYGVNYFQwnEPNVDAeeldeemmydQ---RdrwvsgrgpRGVMQKCVfdparqdgqmgedlvGTT 334
                                       ************88777663343333333443333331...0333555555999*****55555555555555559* PP

                            Fer4_7  43 aCvavCPtga 52 
                                       aC+++CP ga
  gi|336252108|ref|YP_004595215.1| 335 ACEQACPPGA 344
                                       *******987 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00012
                            Fer4_7   3 igCgaCvaaCpvkaieldeeenekg 27 
                                       +g+ aC++aCp +ai++ + ++++ 
  gi|336252108|ref|YP_004595215.1| 331 VGTTACEQACPPGAIQFGDMNDPES 355
                                       6899*************98877653 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.4         9   1.1e+04      10      21 ..     174     183 ..     168     194 .. 0.57
   2 !   44.4   4.2   1.2e-14   1.4e-11       3      67 ..     221     284 ..     219     291 .. 0.93
   3 ?    5.4   0.1     0.016        19      66      99 ..     310     349 ..     304     350 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9
                           Fer4_11  10 CrhCleppCvas 21 
                                       C  Cl  +Cv +
  gi|336252108|ref|YP_004595215.1| 174 CDGCL--SCVVA 183
                                       44443..23333 PP

  == domain 2  score: 44.4 bits;  conditional E-value: 1.2e-14
                           Fer4_11   3 wlflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgk 67 
                                       ++++ + C+hC+++pC +++p++a + +++ G+Vl+d + +  ++r ++ acPy + + ++++ +
  gi|336252108|ref|YP_004595215.1| 221 FNYIVRPCQHCTDAPCEKVCPTTARHTRDQGGLVLTDYDVCI-GCRYCQVACPYGVNYFQWNEPN 284
                                       679999***********************************7.***************9998765 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.016
                           Fer4_11  66 gkvekCdmcldrveaGl......lpacvescptgalnfgd 99 
                                       g+++kC +  +r++  +      ++ac ++cp ga++fgd
  gi|336252108|ref|YP_004595215.1| 310 GVMQKCVFDPARQDGQMgedlvgTTACEQACPPGAIQFGD 349
                                       67899999888876322224344689************98 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9  12.9   0.00064      0.76       2      56 .]     167     241 ..     166     241 .. 0.82
   2 !   18.3  12.5   1.5e-06    0.0018       7      56 .]     226     272 ..     220     272 .. 0.94
   3 !   26.3   3.3   4.9e-09   5.8e-06       3      56 .]     255     341 ..     253     341 .. 0.88
   4 ?    4.0   0.3     0.045        53      13      36 ..     334     352 ..     331     375 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00064
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl...................tsvgakgeaseeeavrk.kvekCtgcg..aCveaCP 56 
                                       + id d+C +C  Cv aC  ++                   t  + ++ + e+ ++    v  C++c+   C ++CP
  gi|336252108|ref|YP_004595215.1| 167 MAIDLDSCDGCLSCVVAC--NAehnwdeganwmyvlayedgTVESPEPDDFESTRDFNyIVRPCQHCTdaPCEKVCP 241
                                       579***************..6667**************987555555555555555445899*****888******9 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.5e-06
                           Fer4_10   7 dtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                         C +C+   C k+CP+      a+  +++++ v ++++ C+gc +C+ aCP
  gi|336252108|ref|YP_004595215.1| 226 RPCQHCTdaPCEKVCPT-----TARHTRDQGGLVLTDYDVCIGCRYCQVACP 272
                                       56****9999*******.....*****************************9 PP

  == domain 3  score: 26.3 bits;  conditional E-value: 4.9e-09
                           Fer4_10   3 vidddtCirCgkCvkaCPadl..................tsvgakgeaseeeavrkkvekCtg.............. 47 
                                         d d Ci+C+ C+ aCP+ +                   ++++++    +   r++++kC +              
  gi|336252108|ref|YP_004595215.1| 255 LTDYDVCIGCRYCQVACPYGVnyfqwnepnvdaeeldeeMMYDQRDRWVSGRGPRGVMQKCVFdparqdgqmgedlv 331
                                       6799***************99***************99777777777788888889*******99999999888886 PP

                           Fer4_10  48 .cgaCveaCP 56 
                                         +aC +aCP
  gi|336252108|ref|YP_004595215.1| 332 gTTACEQACP 341
                                       668******9 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.045
                           Fer4_10  13 gkCvkaCPadltsvgakgeaseee 36 
                                       ++C +aCP      ga+++ + ++
  gi|336252108|ref|YP_004595215.1| 334 TACEQACPP-----GAIQFGDMND 352
                                       679999998.....5555555554 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   4.4   6.6e-05     0.078       2      18 ..     168     184 ..     167     184 .. 0.94
   2 ?    4.7   0.5     0.024        29      14      22 ..     236     244 ..     235     246 .. 0.87
   3 !   21.9   3.5   8.7e-08    0.0001       4      21 ..     257     274 ..     254     275 .. 0.91
   4 !    9.2   1.0   0.00091       1.1      13      24 .]     335     346 ..     334     346 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.6e-05
                                       EEETTTSSS-THHHHHS CS
                              Fer4   2 videekCigCGaCvevC 18 
                                        id + C gC  Cv +C
  gi|336252108|ref|YP_004595215.1| 168 AIDLDSCDGCLSCVVAC 184
                                       59*************** PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                                       HHHHSTTTE CS
                              Fer4  14 CvevCPvgA 22 
                                       C++vCP+ A
  gi|336252108|ref|YP_004595215.1| 236 CEKVCPTTA 244
                                       ******965 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 8.7e-08
                                       ETTTSSS-THHHHHSTTT CS
                              Fer4   4 deekCigCGaCvevCPvg 21 
                                       d++ CigC +C  +CP+g
  gi|336252108|ref|YP_004595215.1| 257 DYDVCIGCRYCQVACPYG 274
                                       99**************99 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.00091
                                       HHHHHSTTTEEE CS
                              Fer4  13 aCvevCPvgAIt 24 
                                       aC+++CP gAI+
  gi|336252108|ref|YP_004595215.1| 335 ACEQACPPGAIQ 346
                                       7*********95 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.9   6.6e-06    0.0079       3      21 ..     168     186 ..     167     194 .. 0.90
   2 !    9.0   3.9    0.0013       1.5       8      21 ..     227     242 ..     224     245 .. 0.90
   3 !   18.8   2.9     1e-06    0.0012       5      23 ..     257     275 ..     254     276 .. 0.91
   4 ?    3.9   0.5     0.051        61      14      24 .]     335     345 ..     332     345 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.6e-06
                            Fer4_6   3 eidpdkCigCgdCvrvCPe 21 
                                       +id d+C+gC  Cv++C +
  gi|336252108|ref|YP_004595215.1| 168 AIDLDSCDGCLSCVVACNA 186
                                       69***************75 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                            Fer4_6   8 kCigCgd..CvrvCPe 21 
                                       +C +C d  C++vCP+
  gi|336252108|ref|YP_004595215.1| 227 PCQHCTDapCEKVCPT 242
                                       6****999*******7 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 1e-06
                            Fer4_6   5 dpdkCigCgdCvrvCPega 23 
                                       d+d CigC+ C ++CP+g+
  gi|336252108|ref|YP_004595215.1| 257 DYDVCIGCRYCQVACPYGV 275
                                       8899*************97 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.051
                            Fer4_6  14 dCvrvCPegai 24 
                                       +C+ +CP gai
  gi|336252108|ref|YP_004595215.1| 335 ACEQACPPGAI 345
                                       7******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 !   14.7   9.7   2.1e-05     0.026       2      49 ..     174     243 ..     173     245 .. 0.79
   2 !   16.3   7.7   6.6e-06    0.0079       2      51 .]     261     345 ..     260     345 .. 0.84
   3 ?    4.8   0.3     0.027        33      41      51 .]     335     345 ..     331     352 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase.....................eaCigCga..CveaCpkg 49 
                                       C gC +Cv aC+a+++ ++ +++ + + a+++                       C +C +  C+++Cp++
  gi|336252108|ref|YP_004595215.1| 174 CDGCLSCVVACNAEHNWDE-GANWMYVLAYEDgtvespepddfestrdfnyivRPCQHCTDapCEKVCPTT 243
                                       ***********88765444.4444444444455788888888999999999*989**************97 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 6.6e-06
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase....................eaCigCga...............Cv 43 
                                       C+gC++C+ aCp+gv+  +++e  +  ++ +e                    ++C++  a               C+
  gi|336252108|ref|YP_004595215.1| 261 CIGCRYCQVACPYGVNYFQWNEPNVDAEELDEemmydqrdrwvsgrgprgvmQKCVFDPArqdgqmgedlvgttaCE 337
                                       ***************999999999998888889999999999**********66764433566777777777777** PP

                            Fer4_9  44 eaCpkgai 51 
                                       +aCp gai
  gi|336252108|ref|YP_004595215.1| 338 QACPPGAI 345
                                       ****9987 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.027
                            Fer4_9  41 aCveaCpkgai 51 
                                       aC++aCp gai
  gi|336252108|ref|YP_004595215.1| 335 ACEQACPPGAI 345
                                       46666665554 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.7   2.3e-06    0.0028       3      22 .]     167     186 ..     165     186 .. 0.89
   2 ?    4.6   4.9     0.034        40      10      22 .]     228     242 ..     223     242 .. 0.75
   3 !   20.8   1.9   2.4e-07   0.00028       4      22 .]     255     273 ..     252     273 .. 0.89
   4 ?    1.4   1.1      0.34   4.1e+02      15      21 ..     335     341 ..     332     342 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.3e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       +++d d+C gC +Cv aC a
  gi|336252108|ref|YP_004595215.1| 167 MAIDLDSCDGCLSCVVACNA 186
                                       789***************65 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.034
                            Fer4_2  10 CigCg..aCvsaCPa 22 
                                       C +C   +C ++CP+
  gi|336252108|ref|YP_004595215.1| 228 CQHCTdaPCEKVCPT 242
                                       7777556*******7 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 2.4e-07
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                         d d CigC+ C+ aCP+
  gi|336252108|ref|YP_004595215.1| 255 LTDYDVCIGCRYCQVACPY 273
                                       5699**************5 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.34
                            Fer4_2  15 aCvsaCP 21 
                                       aC +aCP
  gi|336252108|ref|YP_004595215.1| 335 ACEQACP 341
                                       7*****9 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   7.2      0.31   3.8e+02       1      11 [.     174     184 ..     174     184 .. 0.96
   2 !    9.7   5.3    0.0014       1.7       1      13 [.     228     242 ..     228     244 .. 0.84
   3 !   11.1   5.1   0.00052      0.62       1      14 [.     261     274 ..     261     275 .. 0.95
   4 !   11.7   0.2   0.00033      0.39       6      15 .]     335     344 ..     326     344 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.31
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C+gC  Cv++C
  gi|336252108|ref|YP_004595215.1| 174 CDGCLSCVVAC 184
                                       ****88***** PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                            Fer4_3   1 CtgCg..aCvevCPv 13 
                                       C++C   +C++vCP+
  gi|336252108|ref|YP_004595215.1| 228 CQHCTdaPCEKVCPT 242
                                       ****6668******7 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00052
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+gC+ C ++CP+g
  gi|336252108|ref|YP_004595215.1| 261 CIGCRYCQVACPYG 274
                                       ****99******98 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00033
                            Fer4_3   6 aCvevCPvgA 15 
                                       aC+++CP+gA
  gi|336252108|ref|YP_004595215.1| 335 ACEQACPPGA 344
                                       9********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 ?    3.9   1.9     0.064        77      42      58 ..     170     186 ..     137     189 .. 0.77
   2 ?    2.6  10.2      0.17     2e+02       2      58 ..     174     242 ..     173     245 .. 0.68
   3 !    6.7  10.5    0.0088        11       2      61 .]     228     276 ..     227     276 .. 0.74
   4 !   13.8   2.2   5.3e-05     0.063       2      18 ..     261     277 ..     260     318 .. 0.64
   5 ?    3.1   0.0      0.11   1.4e+02       6      36 ..     334     371 ..     331     386 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.064
                           Fer4_17  42 kaslCieCgeCerkCPq 58 
                                         ++C +C  C+ +C +
  gi|336252108|ref|YP_004595215.1| 170 DLDSCDGCLSCVVACNA 186
                                       56889999999999965 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.17
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraakl..........glleeaeke.ekaslCieCge..CerkCPq 58 
                                       C +C  C+ +C    + d+  +++++ +++           ++e + +    +  C +C    Ce++CP 
  gi|336252108|ref|YP_004595215.1| 174 CDGCLSCVVACNAEHNWDE-GANWMYVLAYedgtvespepDDFESTRDFnYIVRPCQHCTDapCEKVCPT 242
                                       9999999999998776554.5666666666555555544455665544334678999997555******6 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0088
                           Fer4_17   2 CiqCgy..ClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgld 61 
                                       C++C    C+++Cp+ +++  ++  l+                 + Ci+C+ C+ +CP+g++
  gi|336252108|ref|YP_004595215.1| 228 CQHCTDapCEKVCPTTARHTRDQGGLVLT-------------DYDVCIGCRYCQVACPYGVN 276
                                       77777666777777777777766666555.............3578************9985 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 5.3e-05
                           Fer4_17   2 CiqCgyClpeCpsyeay 18 
                                       Ci+C+yC  +Cp++ +y
  gi|336252108|ref|YP_004595215.1| 261 CIGCRYCQVACPYGVNY 277
                                       99999999999987774 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.11
                           Fer4_17   6 gyClpeCpsyea....ydn...epkkllraaklgllee 36 
                                        +C+++Cp +++    +++   +p+++++++ l++ ++
  gi|336252108|ref|YP_004595215.1| 334 TACEQACPPGAIqfgdMNDpesDPQQYVENVPLARARN 371
                                       46889999655544443332225777777776643333 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   2.6    0.0028       3.4      44      63 ..     151     186 ..     125     189 .. 0.66
   2 ?    5.5   9.8      0.02        24       2      63 ..     171     242 ..     170     244 .. 0.63
   3 !   14.4   5.5   3.3e-05     0.039       3      62 ..     259     341 ..     257     344 .. 0.56
   4 ?    1.8   0.4      0.28   3.3e+02       9      19 ..     334     344 ..     331     391 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0028
                            Fer4_8  44 e................eealwsCttcgaCtevCpv 63 
                                       +                +  l+sC +c +C+++C  
  gi|336252108|ref|YP_004595215.1| 151 SggegeghggdetqwgmAIDLDSCDGCLSCVVACNA 186
                                       133334444444555668899*************75 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.02
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaae.........dvqeeqvlee.......eealwsCttcga..Ctev 60 
                                       l++C +C  C  aC + +++++  +  +  a e         d        +       ++++  C++c    C++v
  gi|336252108|ref|YP_004595215.1| 171 LDSCDGCLSCVVACNAEHNWDEGANWMYVLAYEdgtvespepD--------DfestrdfNYIVRPCQHCTDapCEKV 239
                                       789***********75555443333333333332222223321........13334455899********999**** PP

                            Fer4_8  61 Cpv 63 
                                       Cp+
  gi|336252108|ref|YP_004595215.1| 240 CPT 242
                                       **7 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 3.3e-05
                            Fer4_8   3 ekCieCgaCqsaCp...vlrrtkkhlldargeaae..dvqeeqvlee.....................eealwsCtt 53 
                                       + Ci+C +Cq aCp    + ++++ + da++  +e  ++q+++                          ++ +  ++
  gi|336252108|ref|YP_004595215.1| 259 DVCIGCRYCQVACPygvNYFQWNEPNVDAEELDEEmmYDQRDR---WvsgrgprgvmqkcvfdparqdGQMGEDLVG 332
                                       56***********966644444444444444444444222222...1233555444444444444444555666678 PP

                            Fer4_8  54 cgaCtevCp 62 
                                       + aC+++Cp
  gi|336252108|ref|YP_004595215.1| 333 TTACEQACP 341
                                       888888888 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.28
                            Fer4_8   9 gaCqsaCpvlr 19 
                                        aC++aCp   
  gi|336252108|ref|YP_004595215.1| 334 TACEQACPPGA 344
                                       46777777433 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 ?    3.0   5.3      0.17   2.1e+02       2      16 ..     228     244 ..     227     251 .. 0.86
   2 ?   16.1   5.2   1.4e-05     0.017       2      65 ..     261     341 ..     260     343 .. 0.83
   3 ?    9.7   0.2    0.0014       1.6       6      34 ..     334     366 ..     331     389 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.17
                           Fer4_16   2 CgtCgk..CaevCPtna 16 
                                       C+ C+   C +vCPt a
  gi|336252108|ref|YP_004595215.1| 228 CQHCTDapCEKVCPTTA 244
                                       99**9999*******98 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.4e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikek.kekeiearecisy................ntaekkdlaedeekckkqeaitgCdiCq 61 
                                       C++C+ C  +CP ++   + +e++++a+e  ++                 + +k  + + ++  +++e++ g  +C+
  gi|336252108|ref|YP_004595215.1| 261 CIGCRYCQVACPYGVNYFQwNEPNVDAEELDEEmmydqrdrwvsgrgprGVMQKCVFDPARQDGQMGEDLVGTTACE 337
                                       *************997766678999888844445558889999999997777777888888888899********** PP

                           Fer4_16  62 dvCP 65 
                                       ++CP
  gi|336252108|ref|YP_004595215.1| 338 QACP 341
                                       ***9 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0014
                           Fer4_16   6 gkCaevCPtnaikek..kekeiearecisy..n 34 
                                       ++C ++CP +ai+    +++e ++++ +++   
  gi|336252108|ref|YP_004595215.1| 334 TACEQACPPGAIQFGdmNDPESDPQQYVENvpL 366
                                       68***********88333444444433333542 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.5     0.002       2.3       3      20 ..     169     186 ..     167     195 .. 0.87
   2 ?    0.2   3.0       0.7   8.4e+02      37      53 ..     224     242 ..     214     247 .. 0.66
   3 ?    6.7  12.0    0.0065       7.8       8      52 ..     228     272 ..     222     277 .. 0.69
   4 ?    5.2   0.1     0.019        23      27      58 ..     316     346 ..     308     347 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.002
                           Fer4_21   3 idedkCigCgkCliaCed 20 
                                       id d+C gC +C++aC+ 
  gi|336252108|ref|YP_004595215.1| 169 IDLDSCDGCLSCVVACNA 186
                                       89999***********84 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.7
                           Fer4_21  37 vedeCvGCn..lCssvCPv 53 
                                       +   C  C+   C +vCP+
  gi|336252108|ref|YP_004595215.1| 224 IVRPCQHCTdaPCEKVCPT 242
                                       5556777752259999996 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0065
                           Fer4_21   8 CigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                       C +C+   C ++C++t+      d+   + +  d C+GC  C   CP
  gi|336252108|ref|YP_004595215.1| 228 CQHCTDapCEKVCPTTARHT--RDQGGLVLTDYDVCIGCRYCQVACP 272
                                       66665433777777554443..3344455566899************ PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.019
                           Fer4_21  27 eidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                        +d++++   + ++ vG + C + CP  ++i+
  gi|336252108|ref|YP_004595215.1| 316 VFDPARQDGQMGEDLVGTTACEQACP-PGAIQ 346
                                       566777777788999***********.68886 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 ?   12.1   0.5   0.00021      0.25       3      35 ..     169     200 ..     167     219 .. 0.68
   2 ?    8.1   0.5    0.0037       4.4       2      19 ..     255     272 ..     254     300 .. 0.78
   3 ?   -1.0   0.0       2.6   3.1e+03      57      65 ..     338     346 ..     320     347 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                           Fer4_15   3 vDrdaCigcglCvaeapevfeldedglasvlld 35 
                                       +D d C+gc  Cv ++     + ++g + + + 
  gi|336252108|ref|YP_004595215.1| 169 IDLDSCDGCLSCVVACN-AEHNWDEGANWMYVL 200
                                       9**************95.555555666555544 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0037
                           Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                         D d Cigc  C  ++p
  gi|336252108|ref|YP_004595215.1| 255 LTDYDVCIGCRYCQVACP 272
                                       5699*************7 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.6
                           Fer4_15  57 raCPvdAIr 65 
                                       +aCP +AI+
  gi|336252108|ref|YP_004595215.1| 338 QACPPGAIQ 346
                                       589999996 PP

>> Fer4_4  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    0.0051       6.1       2      14 ..     172     184 ..     171     187 .. 0.89
   2 ?    4.2   2.0     0.064        76       4      16 ..     228     242 ..     222     249 .. 0.89
   3 ?   13.1   3.0   8.7e-05       0.1       2      17 .]     259     274 ..     258     276 .. 0.92
   4 ?    2.3   0.1      0.26   3.1e+02       9      15 ..     335     341 ..     313     355 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0051
                            Fer4_4   2 erCigCgsCvaaC 14 
                                       ++C gC sCv aC
  gi|336252108|ref|YP_004595215.1| 172 DSCDGCLSCVVAC 184
                                       89*********** PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.064
                            Fer4_4   4 CigCgs..CvaaCPq 16 
                                       C++C    C+ +CP+
  gi|336252108|ref|YP_004595215.1| 228 CQHCTDapCEKVCPT 242
                                       99999678******6 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 8.7e-05
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       + CigC+ C  aCP+g
  gi|336252108|ref|YP_004595215.1| 259 DVCIGCRYCQVACPYG 274
                                       88************86 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.26
                            Fer4_4   9 sCvaaCP 15 
                                       +C+ aCP
  gi|336252108|ref|YP_004595215.1| 335 ACEQACP 341
                                       6*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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):              15  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2856.84
//
Query:       gi|336252109|ref|YP_004595216.1|  [L=316]
Description: ATPase [Halopiger xanaduensis SH-6]
Scores for 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-67  223.8   0.3    1.3e-66  222.4   0.1    1.7  2  AAA_3            ATPase family associated with various cellul
    3.6e-20   71.6   0.6    6.9e-20   70.7   0.6    1.5  1  AAA_lid_2        AAA lid domain
    2.9e-15   56.5   0.0    2.3e-14   53.5   0.0    2.0  2  AAA_5            AAA domain (dynein-related subfamily)
    1.2e-06   29.0   0.0    3.4e-06   27.5   0.0    1.8  2  AAA              ATPase family associated with various cellul
    3.2e-05   23.7   0.0     0.0017   18.1   0.0    2.1  2  Sigma54_activat  Sigma-54 interaction domain
     0.0057   15.8   0.0     0.0089   15.2   0.0    1.3  1  MCM              MCM P-loop domain
     0.0057   16.4   0.0       0.09   12.5   0.0    2.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.009   15.4   0.1        2.4    7.5   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.035   14.2   0.0      0.074   13.2   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)


Domain annotation for each model (and alignments):
>> 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 !  222.4   0.1   6.3e-70   1.3e-66       1     131 []      40     170 ..      40     170 .. 0.99
   2 ?   -1.5   0.0       1.1   2.2e+03      28      48 ..     284     304 ..     274     310 .. 0.81

  Alignments for each domain:
  == domain 1  score: 222.4 bits;  conditional E-value: 6.3e-70
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       hvlle+vPG++ktl+++++a+al+l+f+riqftpdllP+d++Gt+vf+e+e++fef++Gp+fan++ladeinrappk
  gi|336252109|ref|YP_004595216.1|  40 HVLLEDVPGTGKTLTARSVADALGLSFSRIQFTPDLLPADVTGTHVFNERERKFEFNEGPIFANIVLADEINRAPPK 116
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                       tq+alleamee qvtv+get++lp+pf+v+atqnP+eqeGt+plpeaq+drfl+
  gi|336252109|ref|YP_004595216.1| 117 TQAALLEAMEEGQVTVDGETRQLPDPFFVIATQNPVEQEGTFPLPEAQVDRFLV 170
                                       ****************************************************95 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                             AAA_3  28 kriqftpdllPsdilGtevfe 48 
                                       +r+ +tpd    d+  ++v++
  gi|336252109|ref|YP_004595216.1| 284 HRLVLTPDATVNDVQKSQVVD 304
                                       789999999999998888876 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.6   3.4e-23   6.9e-20       2      71 ..     234     304 ..     233     306 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 3.4e-23
                         AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeive 71 
                                       +tr++ ++ +gvs+r +++ l +aArA+A + gr+yVtp+D+k++a++VLaHRl+  +++  ++++++++v+
  gi|336252109|ref|YP_004595216.1| 234 ETRTDGRVDVGVSPR-GTQRLFEAARAYATIVGREYVTPDDIKRVAEPVLAHRLVltPDATVNDVQKSQVVD 304
                                       899************.***************************************99999999998888876 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 !   53.5   0.0   1.2e-17   2.3e-14       1     138 []      40     168 ..      40     168 .. 0.94
   2 ?    0.5   0.0      0.27   5.4e+02      24      68 ..     257     302 ..     249     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.2e-17
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       +vlL   pGtgK+  a+++a al+ ++  +q+t d+ ++d++g   ++  +++ ++ ++p+      + i++ DE++
  gi|336252109|ref|YP_004595216.1|  40 HVLLEDVPGTGKTLTARSVADALGLSFSRIQFTPDLLPADVTGTHVFNerERKFEFNEGPIF-----ANIVLADEIN 111
                                       6888889*****************************************99999999******.....9********* PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra+++++++Ll  +ee ++   +g +++  ++      f viat np++  +  +l +a ++Rf
  gi|336252109|ref|YP_004595216.1| 112 RAPPKTQAALLEAMEEGQVT-VDGETRQLPDP------FFVIATQNPVEqEGTFPLPEAQVDRF 168
                                       *******************9.77777777777......9**********889999999999998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.27
                                       S--EEEEE--TT--HHHHH--B--..........--------G-SE CS
                             AAA_5  24 nreveyvqltrdtteedlkgrreik.ngttslvdsplvraaregei 68 
                                        r + ++ ++++ t++d+k   e+    + +l++ + v+ ++++++
  gi|336252109|ref|YP_004595216.1| 257 ARAYATIVGREYVTPDDIKRVAEPVlAHRLVLTPDATVNDVQKSQV 302
                                       5678899999999****99999988888888888888888888877 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 !   27.5   0.0   1.7e-09   3.4e-06       2     112 ..      42     152 ..      41     176 .. 0.71
   2 ?   -2.8   0.0       3.9   7.8e+03      39      57 ..     243     261 ..     227     265 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.7e-09
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SS.....STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGH CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisg.sell.sk.....yvgesekkirelfkeakeka.kpsilfiDEidal 70 
                                       ll   pGtGKTl+a++va  lg +f +i+  ++ll  +     ++ e+e+k++  f+e         i++ DEi + 
  gi|336252109|ref|YP_004595216.1|  42 LLEDVPGTGKTLTARSVADALGLSFSRIQFtPDLLpADvtgthVFNERERKFE--FNEG---PiFANIVLADEINRA 113
                                       67778********************9999626777333444444444444444..2222...23338********** PP

                                       HHHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESSG CS
                               AAA  71 aksrsgseseeeervvnqLlteldgvkkk........eskvivigatnrp 112
                                        ++            +++Ll+++++ +           ++++vi++ n +
  gi|336252109|ref|YP_004595216.1| 114 PPKT-----------QAALLEAMEEGQVTvdgetrqlPDPFFVIATQNPV 152
                                       9999...........*********99999999999986668888887763 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.9
                                       TTHHHHHHHHHHHHHHHTS CS
                               AAA  39 vgesekkirelfkeakeka 57 
                                       vg s++ ++ lf++a++ a
  gi|336252109|ref|YP_004595216.1| 243 VGVSPRGTQRLFEAARAYA 261
                                       7888999999999988766 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.027        55      22      43 ..      38      59 ..      25      73 .. 0.83
   2 !   18.1   0.0   8.5e-07    0.0017      96     145 ..     104     152 ..      79     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.027
                                      SS-EEEECSTTSSHHHHHHHHH CS
                   Sigma54_activat 22 dlsvlitGesGtGKellaraih 43
                                      + +vl++   GtGK+l ar++ 
  gi|336252109|ref|YP_004595216.1| 38 RGHVLLEDVPGTGKTLTARSVA 59
                                      56899999**********9875 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 8.5e-07
                                       EEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-H CS
                   Sigma54_activat  96 tlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedl 145
                                       +++ Dei++ p+++Q+ Ll++++eg+v+  G++++ +  + +i at++ +
  gi|336252109|ref|YP_004595216.1| 104 IVLADEINRAPPKTQAALLEAMEEGQVTVDGETRQLPDPFFVI-ATQNPV 152
                                       5667****************************99998766655.555555 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.4e-06    0.0089      95     174 ..      78     152 ..      30     161 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.4e-06
                                       SHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE CS
                               MCM  95 agLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAa 171
                                       a+ t + v +e++++f ++ G +      +++ De+++   +++ al+EamE+ ++++   G + +L+    v+a  
  gi|336252109|ref|YP_004595216.1|  78 ADVTGTHVFNERERKFEFNEGPIFA---NIVLADEINRAPPKTQAALLEAMEEGQVTVD--GETRQLPDPFFVIATQ 149
                                       5666666666666667777776654...3999************************997..4457888888888888 PP

                                       --S CS
                               MCM 172 npk 174
                                       np+
  gi|336252109|ref|YP_004595216.1| 150 NPV 152
                                       886 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 !   12.5   0.0   4.5e-05      0.09      34     113 ..      39     130 ..      29     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-05
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlekagdlaa..lltnleek..........dvlfideihrls 97 
                                        hvll   PG Gkt  a+ +a+ lg ++ +i  +P l  ++d+++  ++++ e+k          ++++ dei r  
  gi|336252109|ref|YP_004595216.1|  39 GHVLLEDVPGTGKTLTARSVADALGLSFsRIQFTPDLL-PADVTGthVFNERERKfefnegpifaNIVLADEINRAP 114
                                       7************************9873566677765.44554411333222211122223333677889999999 PP

                            RuvB_N  98 raveevlysamedfrl 113
                                       ++++  l  ame+ ++
  gi|336252109|ref|YP_004595216.1| 115 PKTQAALLEAMEEGQV 130
                                       9999999999998776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0012       2.4      17      44 ..      33      60 ..      20      68 .. 0.81
   2 !    5.7   0.0    0.0044       8.8     109     159 ..     104     152 ..     101     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0012
                      Mg_chelatase 17 iaaaGgHnlllvGppGsGKtmlakrlps 44
                                      + +  + ++ll   pG+GKt+ a+ ++ 
  gi|336252109|ref|YP_004595216.1| 33 VGVVARGHVLLEDVPGTGKTLTARSVAD 60
                                      555666789**************98876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0044
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                       +++ DE+     k+  +L e +e+g+vt+   +++   p  f ++a+ Np 
  gi|336252109|ref|YP_004595216.1| 104 IVLADEINRAPPKTQAALLEAMEEGQVTVDGETRQ--LPDPFFVIATQNPV 152
                                       56779************************987765..58889999999996 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.7e-05     0.074       6     113 ..      41     135 ..      37     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-05
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHH.TTS.....EEEEET CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgae.egG.....ivllDE 76 
                                       +ll +  g+Gkt++a+++a+ l +    ++ r+  +  l        v+   + ++   ++e ++G     ivl DE
  gi|336252109|ref|YP_004595216.1|  41 VLLEDVPGTGKTLTARSVADALGL----SFSRIQFTPDLL----PADVTGTHVFNERERKFEfNEGpifanIVLADE 109
                                       677778899999999999999998....999999988888....333333333333333333223347777****** PP

                                       GGG-------------HHHHHHHHHHHH--EE----- CS
                             AAA_2  77 idKihpkessgadvSregVqrdLLqileggtltdkqg 113
                                       i ++ p             q +LL  +e+g++t   +
  gi|336252109|ref|YP_004595216.1| 110 INRAPP-----------KTQAALLEAMEEGQVTVDGE 135
                                       ******...........99*************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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: 0.52u 0.57s 00:00:01.08 Elapsed: 00:00:00.57
# Mc/sec: 1659.74
//
Query:       gi|336252110|ref|YP_004595217.1|  [L=103]
Description: hypothetical protein Halxa_0699 [Halopiger xanaduensis SH-6]
Scores for 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   18.0   2.7     0.0024   17.2   2.7    1.5  1  zf-ribbon_3     zinc-ribbon domain
     0.0031   17.5   0.1     0.0034   17.4   0.1    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.011   15.4   1.4       0.11   12.2   0.0    2.2  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.026   14.7   0.0      0.026   14.7   0.0    1.6  2  zf-RING_7       C4-type zinc ribbon domain
       0.13   12.1   4.3        0.4   10.5   0.6    1.9  2  zinc_ribbon_2   zinc-ribbon domain
       0.22   11.5   2.0       0.66   10.0   2.0    1.8  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        0.3   11.4   0.6       0.43   10.9   0.6    1.2  1  Ribosomal_L32p  Ribosomal L32p protein family
       0.32   11.1   4.0       0.45   10.7   0.2    2.1  2  Zn-ribbon_8     Zinc ribbon domain
       0.41   10.8   4.6        2.7    8.2   0.5    2.2  2  UPF0547         Uncharacterised protein family UPF0547
          7    6.7   6.0       0.55   10.3   0.6    1.8  2  Ogr_Delta       Ogr/Delta-like zinc 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 !   17.2   2.7   1.3e-06    0.0024       3      24 ..      79     100 ..      77     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                       zf-ribbon_3   3 vrCPnCGaplssddnvCpyCGt 24 
                                       +rCP+CGap  +d ++C  CG+
  gi|336252110|ref|YP_004595217.1|  79 IRCPHCGAPTLADGSACLECGH 100
                                       8*******99999999***997 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.9e-06    0.0034      28      49 .]      78      99 ..      46     103 .] 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.9e-06
                               DZR 28 edrCpsCgekvdpearfCpeCG 49
                                       +rCp+Cg+++ ++ + C eCG
  gi|336252110|ref|YP_004595217.1| 78 VIRCPHCGAPTLADGSACLECG 99
                                      5677777777777777777776 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   0.0   6.3e-05      0.11      14      25 ..      75      86 ..      68      89 .. 0.85
   2 ?    2.0   0.4     0.092   1.6e+02      20      25 ..      95     100 ..      94     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.3e-05
                                      SSS----SSS-- CS
                    DNA_RNApol_7kD 14 kgdpiRCkeCGh 25
                                       g +iRC +CG 
  gi|336252110|ref|YP_004595217.1| 75 DGSVIRCPHCGA 86
                                      6889*******6 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.092
                                       -SSS-- CS
                    DNA_RNApol_7kD  20 CkeCGh 25 
                                       C eCGh
  gi|336252110|ref|YP_004595217.1|  95 CLECGH 100
                                       889998 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 ?   14.7   0.0   1.5e-05     0.026      10      31 ..      65      86 ..      63      86 .. 0.75
   2 ?   -3.1   0.3       5.4   9.6e+03      26      30 ..      95      99 ..      94      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                      -CCHHHHHCCSTB-EE-TTT-- CS
                         zf-RING_7 10 ppqvlselragdevvtCpeCGR 31
                                      p + +s   + + v++Cp+CG+
  gi|336252110|ref|YP_004595217.1| 65 PGEAESSAFGDGSVIRCPHCGA 86
                                      5566666667789*******96 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.4
                                      -TTT- CS
                         zf-RING_7 26 CpeCG 30
                                      C eCG
  gi|336252110|ref|YP_004595217.1| 95 CLECG 99
                                      77898 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.6   0.00022       0.4       2      22 ..      81      87 ..      75      89 .. 0.65
   2 ?    9.7   4.5   0.00039       0.7       1      21 [.      80     100 ..      80     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      Cp+CGa              p
  gi|336252110|ref|YP_004595217.1| 81 CPHCGA--------------P 87
                                      555555..............4 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00039
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGt 21 
                                       +Cp+CGa+   +   C +CG+
  gi|336252110|ref|YP_004595217.1|  80 RCPHCGAPTLADGSACLECGH 100
                                       6******99999999999998 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 ?   10.0   2.0   0.00037      0.66      12      29 ..      70      89 ..      68     101 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                     Zn_Tnp_IS1595 12 alrWpng..fvCPhCgsrka 29
                                      +  +++g   +CPhCg  ++
  gi|336252110|ref|YP_004595217.1| 70 SSAFGDGsvIRCPHCGAPTL 89
                                      56688887667*****4444 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.6   0.00024      0.43      26      48 ..      78     101 ..      74     103 .] 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                                       EEEETTTCCEECT.TC-BTTTTBS CS
                    Ribosomal_L32p  26 lvecpncgelklp.HrvcpscGyY 48 
                                       + +cp cg+++l+  ++c +cG+ 
  gi|336252110|ref|YP_004595217.1|  78 VIRCPHCGAPTLAdGSACLECGHS 101
                                       679********98479*****985 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00025      0.45      22      35 ..      73      88 ..      66      91 .. 0.72
   2 ?    1.4   0.4       0.2   3.7e+02       8      13 ..      95     100 ..      94     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                       Zn-ribbon_8 22 s.dapltaCPeCgs.e 35
                                      + d + + CP+Cg+ +
  gi|336252110|ref|YP_004595217.1| 73 FgDGSVIRCPHCGApT 88
                                      44777888*****944 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.2
                       Zn-ribbon_8   8 CeeCgh 13 
                                       C eCgh
  gi|336252110|ref|YP_004595217.1|  95 CLECGH 100
                                       999998 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.5    0.0015       2.7      14      21 ..      78      85 ..      77      86 .. 0.86
   2 ?    4.1   0.3     0.028        50      16      23 ..      94     101 ..      90     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                           UPF0547 14 aqfCphCG 21
                                      + +CphCG
  gi|336252110|ref|YP_004595217.1| 78 VIRCPHCG 85
                                      679****9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.028
                           UPF0547  16 fCphCGyv 23 
                                       +C +CG++
  gi|336252110|ref|YP_004595217.1|  94 ACLECGHS 101
                                       6999**97 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 ?   10.3   0.6   0.00031      0.55       1       9 [.      80      88 ..      80      93 .. 0.86
   2 ?   -1.5   0.6       1.5   2.6e+03      32      35 ..      97     100 ..      94     101 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                         Ogr_Delta  1 rCPhCgapa 9 
                                      rCPhCgap 
  gi|336252110|ref|YP_004595217.1| 80 RCPHCGAPT 88
                                      7******95 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                         Ogr_Delta  32 eCga 35 
                                       eCg+
  gi|336252110|ref|YP_004595217.1|  97 ECGH 100
                                       6776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.89
# Mc/sec: 348.44
//
Query:       gi|336252111|ref|YP_004595218.1|  [L=896]
Description: phosphoenolpyruvate carboxylase [Halopiger xanaduensis SH-6]
Scores for complete 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  800.8   0.8   1.6e-239  797.1   0.0    2.1  2  PEPcase         Phosphoenolpyruvate carboxylase
    0.00084   18.0   0.0     0.0016   17.1   0.0    1.4  1  PEPcase_2       Phosphoenolpyruvate carboxylase
  ------ inclusion threshold ------
      0.083   12.7   1.5       0.55   10.1   0.1    2.7  3  Activator-TraM  Transcriptional activator TraM
       0.16   12.0   0.5        3.1    7.9   0.1    2.7  2  SchA_CurD       SchA/CurD like domain
        1.6    8.7   5.8       0.36   10.8   0.4    2.6  3  Peptidase_M16   Insulinase (Peptidase family M16)


Domain annotation for each model (and alignments):
>> PEPcase  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.01        38     280     348 ..       1      71 [.       1      87 [. 0.87
   2 !  797.1   0.0  4.5e-243  1.6e-239       3     795 .]     130     896 .]     128     896 .] 0.95

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.01
                                       TTSSEEEEEEEHHHHHHHHHHHHHHTTS.--GGGS-HHHHHHH..HHHHHH-SS--S-TT----HHHHHHH CS
                           PEPcase 280 lhLaklDiRqeserheealaeileylglekdYaelseeervel..LlreLeskrplipkelelseeteevl 348
                                       ++L++ D+Rq+ ++  + l +++e     k++++++  +r ++   + e++s++pli++  +ls++ ++++
  gi|336252111|ref|YP_004595218.1|   1 MQLHNRDVRQDVRELGALLGDVIEEQTSRKSFETVESCRRAAIdyRSGEIDSRQPLISELENLSPHQQRIV 71 
                                       578899*****************************99999775116679**********999999988876 PP

  == domain 2  score: 797.1 bits;  conditional E-value: 4.5e-243
                                       -EEEEE---TT--SSS--HHHHHHHHHHHHHHT-SS--HHHHHHHHHHHHHHHHHHHH---B-SS---HHHHHHHHH CS
                           PEPcase   3 eielVlTAHPteivRrtilkkqrriaelleqldeaelteeereeleeqleeeiallwrtdelrqekptvldEvengl 79 
                                        ie+ +TAHPte++R+t+ +k r+i++ le+lde+ lt++e++++ +++ +e+++lw+t ++r+++p++ dE++n  
  gi|336252111|ref|YP_004595218.1| 130 LIEPTFTAHPTEARRKTVKSKLRAISTDLETLDERLLTDKEKSQVWRDVDAEVTSLWQTPQVRNRQPEPEDEARNVQ 206
                                       5899************************************************************************* PP

                                       HHHHHTHHHHHHHHHHHHHHHHHHHTS.----T---EEEEE-TTTB-TT-TT--HHHHHHHHHHHHHHHHHHHHHHH CS
                           PEPcase  80 syfeevlfeavPellreleealkesfpelelpaasflrfgsWiGgDRDGNpnVtaevtrevlllqrelalekylkev 156
                                       +y+e++lf++v e+++el +a++e++   +++ +++++f sW G+DRDGNp Vt+evt ++l  qr+++le+y  ++
  gi|336252111|ref|YP_004595218.1| 207 WYLENTLFDVVGEVYDELADAIDEEVD-GDIDIPKLFEFRSWAGSDRDGNPYVTPEVTANTLERQRSVILEQYRLQL 282
                                       ***********************9998.8899999****************************************** PP

                                       HHHHHH---....----HHHHHTT-SSS..............TTSHHHHHHHHHHHHHHHHHHHHHHHHHT-.---- CS
                           PEPcase 157 eeLieeLslslelvevseellesleedkekleevyeelaerykeepYRlklaelrkrLentrerleelaekeeeele 233
                                       ++L   Ls   + +e+++++++sle+d+e+l+  +++ +ery +epYR kl+ +r+rL +      +          
  gi|336252111|ref|YP_004595218.1| 283 KRLSGVLSQDGSRIETDSAFEASLERDRERLPGSARTAEERYPDEPYRQKLKLMRERLDRVG----DVRPG------ 349
                                       *********************************************************97543....33444...... PP

                                       -TT---SHHHHHHHHHHHHHHHHHTT-HHHHTTHHHHHHHHHHHTTTTSSEEEEEEEHHHHHHHHHHHHHHTTS.-- CS
                           PEPcase 234 eeeayesaeelledLelikesLketgaklladgeledlirqvevfGlhLaklDiRqeserheealaeileylglekd 310
                                           y++a+elledLe+i+e+L+++ga+++ d++++ + r+v++fG++La+lD+R++ ++h++a+ae le  g+  d
  gi|336252111|ref|YP_004595218.1| 350 ---GYDDADELLEDLEIIAETLRDNGAESVVDAHVDPIRRRVATFGFSLASLDLRDHQQKHTDAIAEALESEGI--D 421
                                       ...5999*******************************************************************..* PP

                                       GGGS-HHHHHHHHHHHHH-SS--S..-TT----HHHHHHHHHHHHHHHS.-...TTSEEEEEEET--SHHHHHHHHH CS
                           PEPcase 311 YaelseeervelLlreLeskrpli..pkelelseeteevldvlrviaelqeefgkeiietyviSmaeeasdvLevll 385
                                       Y+++seeer e+L++ + ++ p+i  +++ +ls++ ++vl +++ +ae q+e+g e+i+ty iSm++e+s+vLevl+
  gi|336252111|ref|YP_004595218.1| 422 YHAMSEEERAEWLTDAVLQDEPVIdlSDTEDLSDDSARVLRLFDNLAEWQTEYGVEAIDTYCISMTDEPSHVLEVLF 498
                                       **********************962256679********************************************** PP

                                       HHHHTT-..-....S---EEEEE-SHHHHHHHHHHHHHHHHSHHHHHHTTT...EEEEEE-HHHHHHHH-HHHHHHH CS
                           PEPcase 386 LakeaglldkaegaaelrvvPLfEtvedLknapevleellslplyrelvkksgelqevMlGYSDSnKdaGfltsnWe 462
                                       La +ag+++  e ++ +++vPL+Et   L+ a +++ +l+++++y ++++++g++qe+MlGYSDSnK+ Gfl++nW+
  gi|336252111|ref|YP_004595218.1| 499 LADQAGVVSLPE-HCGIDIVPLLETEYALSGARRIMGSLFENEAYSQALEARGQTQEIMLGYSDSNKENGFLAANWS 574
                                       *******88776.9*************************************************************** PP

                                       HHHHHHHHHHHHHHHT-EEEEEE-SSTGGGS-HHHHHHHHHTS-TTTTTT-EEEEE-GGGHHHHHSSHHHHHHHHHH CS
                           PEPcase 463 lykaqealvkvaeeagvklrlFHGrGGsvgRGGgpayeailaqPpgtvngrikiTeQGEviaskyslpelalrnLel 539
                                       lyk q++l +++++++v++rlFHGrGGs++RGGgp +ea+la P++tv+g++k+TeQGE ia+ky++p +a rn+e+
  gi|336252111|ref|YP_004595218.1| 575 LYKNQRRLGEICDDFDVTMRLFHGRGGSISRGGGPMNEALLALPNSTVTGQVKFTEQGEAIAEKYANPRIAERNIEQ 651
                                       ***************************************************************************** PP

                                       HHHHHHHHHHS------....HHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHS-HHHHHHSS-SSS------- CS
                           PEPcase 540 vtaavleaslleeaeekk...eeweeimeelsevsreaYrklvyeepdfveyFreaTPieeiskLnigSRPakRkkk 613
                                       +++a l+a  ++ +++++   eew ++me++++++r++Yr+l+ e+++fv+yF++aTPi+ i++Ln+gSRPa+R+ +
  gi|336252111|ref|YP_004595218.1| 652 MLNAQLRARHNAIHQPEEdvpEEWMDAMETMADAARQEYRDLL-ESDGFVQYFEQATPITVIEDLNLGSRPASRSGE 727
                                       ******987544444433346*********************9.9******************************** PP

                                       --GGSS-HHHHHHHHHHTT--GGGTTTHHHHHHHH..HTTTTHHHHHHHHHH-HHHHHHHHHHHHHHHH--HHHHHH CS
                           PEPcase 614 kglesLRAIPWvFsWtqsRlllpaWyGvgtalkevlekeeeklelLremykkwpffrtliskvemvlaKadleiake 690
                                       +++e+LRAIPWvFsWtqsR++lp+Wy++ t+++++  ++ + +e+L++my++wpff+t+++++ + l++++leia++
  gi|336252111|ref|YP_004595218.1| 728 RTVEDLRAIPWVFSWTQSRCILPGWYAIATGVDAY-LEDGGDVETLQQMYEDWPFFQTTLDNAALSLSRTELEIAEQ 803
                                       **********************************8.577899*********************************** PP

                                       HHHHHS-GG.GHHHHHHHHHHHHHHHHHHHHHHT-SSTTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.. CS
                           PEPcase 691 YvqllvdkelrerlfeeireelertvelvleitgqkelldknpvlqrsvelRnayidPlnllQvelLkrlRqaeeek 767
                                       Y++l+ d+elre++f ++++e+er+ elv +i  q++ l+++ +l +++e Rn+y+dPlnllQ  lL ++ +++   
  gi|336252111|ref|YP_004595218.1| 804 YADLA-DEELREQFFPRLTDEYERAAELVKTIG-QRDQLHTRDWLGENLERRNPYVDPLNLLQTYLLDQTHRTDV-- 876
                                       *9876.5666999**************999985.566678899************************87655544.. PP

                                       TT----HHHHHHHHHHHHHHHHHH---- CS
                           PEPcase 768 seeeeeellrdallltinGiaaGlrntG 795
                                                +++l lt++GiaaG++ntG
  gi|336252111|ref|YP_004595218.1| 877 --------EERTLRLTVKGIAAGMKNTG 896
                                       ........368999*************9 PP

>> PEPcase_2  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.3e-07    0.0016     170     320 ..     513     676 ..     484     700 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.3e-07
                                       SSEEEEEE-SHHHHHTHHHHHHHHH......HHT...--SEEEEEEESHHHHHHH-HHHHHHHHHHHHHHHHHHHHH CS
                         PEPcase_2 170 sievIPLiEdkesllnideiveeyv......kek...klkelRvflarSDpAlnyGlisavllvkvAlselykleee 237
                                        i ++PL+E++ +l  +++i+  ++      + +   + + + ++l+ SD+  + G+++a  +      +l ++ ++
  gi|336252111|ref|YP_004595218.1| 513 GIDIVPLLETEYALSGARRIMGSLFeneaysQ-AleaRGQTQEIMLGYSDSNKENGFLAANWSLYKNQRRLGEICDD 588
                                       599********************997655541.1455778899********************************** PP

                                       HT-EEEEEEE-BSSGGGT-..--TTGHHHHHHHTTT-SEEEE-H...HHHHTTHHHHHHHHHHHHHHGGG------- CS
                         PEPcase_2 238 lgvkiyPilGvGslpfRGh..lspenveevleeYagvkTfTvQS...afkYdyeeeevkeairkineaevkkprels 309
                                        +v++    G G +  RG+  +++  ++   ++  g   fT Q    a kY  ++ + ++  + +n + + + + ++
  gi|336252111|ref|YP_004595218.1| 589 FDVTMRLFHGRGGSISRGGgpMNEALLALPNSTVTGQVKFTEQGeaiAEKYANPRIAERNIEQMLNAQLRARHNAIH 665
                                       **********9999999764588888888888888888888886444668877765555555555544444444444 PP

                                       HHHHHHHHHHH CS
                         PEPcase_2 310 eeeeelllevi 320
                                       + ee++ +e++
  gi|336252111|ref|YP_004595218.1| 666 QPEEDVPEEWM 676
                                       44444433333 PP

>> Activator-TraM  Transcriptional activator TraM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.21   7.4e+02      52      78 ..     105     131 ..      96     169 .. 0.73
   2 ?   -2.5   0.0       1.1     4e+03      28      43 ..     158     173 ..     152     179 .. 0.90
   3 ?   10.1   0.1   0.00015      0.55      48     111 ..     626     691 ..     609     711 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.21
                    Activator-TraM  52 eeleaiasrWgddakekaervlnaala 78 
                                       + le+ a++ g+d  e  e+vl+  l 
  gi|336252111|ref|YP_004595218.1| 105 DSLETAAEQLGEDDVETVEQVLDDVLI 131
                                       678999999999999999999988775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                    Activator-TraM  28 lqtinerllqdsakaq 43 
                                       l t++erll d  k+q
  gi|336252111|ref|YP_004595218.1| 158 LETLDERLLTDKEKSQ 173
                                       789********99988 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00015
                    Activator-TraM  48 dqfkeeleaiasrWgdd..akekaervlnaalaaskealvkllqegakeaaevvrkeveaalarlk 111
                                       ++f e+ eaia+++ +   a    e++lna l a ++a+ +  ++  +e  +++ +  +aa  + +
  gi|336252111|ref|YP_004595218.1| 626 VKFTEQGEAIAEKYANPriAERNIEQMLNAQLRARHNAIHQPEEDVPEEWMDAMETMADAARQEYR 691
                                       6899**********996558999*****************99999999999999888888876655 PP

>> SchA_CurD  SchA/CurD like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1   0.00086       3.1      57     116 ..      94     156 ..      84     158 .. 0.83
   2 ?    1.1   0.0      0.12   4.1e+02      90     110 ..     687     707 ..     659     714 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00086
                         SchA_CurD  57 vRfieveGdleavlrhvarq...pevravEealkpyLeedRdletpesarafFkraalravsq 116
                                       +R+   eG+le+ l   a+q   ++v++vE+ l++ L e+  +  p  ar+   ++ lra+s+
  gi|336252111|ref|YP_004595218.1|  94 IRTESQEGTLEDSLETAAEQlgeDDVETVEQVLDDVLIEPTFTAHPTEARRKTVKSKLRAIST 156
                                       33334569******99999955457**********************************9985 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.12
                         SchA_CurD  90 LeedRdletpesarafFkraa 110
                                        +e Rdl + +++ ++F++a+
  gi|336252111|ref|YP_004595218.1| 687 RQEYRDLLESDGFVQYFEQAT 707
                                       5788**************997 PP

>> Peptidase_M16  Insulinase (Peptidase family M16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4    0.0001      0.36      80     129 ..     115     163 ..     108     181 .. 0.80
   2 ?   -1.3   0.0      0.54   1.9e+03      50      73 ..     407     431 ..     403     441 .. 0.82
   3 ?   -2.8   0.3       1.5   5.5e+03      91     133 ..     635     677 ..     632     689 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                                       EGGGHHHHHHHHHHHHHSBTTSHHHHHHHHHHHHHHHHHHCCHHHHHHHH CS
                     Peptidase_M16  80 lskdlekaldvladvfkaplleesevererkvvekeveavdaepekvvee 129
                                        ++d+e++ +vl dv+++p+++ + +e+ rk+v+ ++ a+++   + + e
  gi|336252111|ref|YP_004595218.1| 115 GEDDVETVEQVLDDVLIEPTFTAHPTEARRKTVKSKLRAISTDL-ETLDE 163
                                       578899999*****************************999988.33333 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.54
                                       H.HHHHHHHHHTTCEEEEEEESSEE CS
                     Peptidase_M16  50 s.nklaeeleklGgslnAttsrent 73 
                                       + +++ae le++G  + A +++e+ 
  gi|336252111|ref|YP_004595218.1| 407 HtDAIAEALESEGIDYHAMSEEERA 431
                                       348999************9999976 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.5
                                       HHHHHHSBTTSHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH CS
                     Peptidase_M16  91 ladvfkaplleesevererkvvekeveavdaepekvveenlha 133
                                       +a+  ++p++ e ++e+  ++ ++ +  +  +pe+ v+e+ + 
  gi|336252111|ref|YP_004595218.1| 635 IAEKYANPRIAERNIEQMLNAQLRARHNAIHQPEEDVPEEWMD 677
                                       6777788888888888866644444444444444555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (896 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.67u 0.91s 00:00:01.58 Elapsed: 00:00:00.72
# Mc/sec: 3764.24
//
Query:       gi|336252112|ref|YP_004595219.1|  [L=82]
Description: hypothetical protein Halxa_0701 [Halopiger xanaduensis SH-6]
Scores for 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   15.0   1.4      0.029   14.0   1.4    1.5  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.031   14.4   0.7      0.064   13.4   0.7    1.5  1  Zn-ribbon_8     Zinc ribbon domain
      0.036   14.1   0.8      0.043   13.8   0.8    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.14   12.1   2.4       0.33   10.9   1.4    1.9  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.26   11.0   5.0        1.9    8.2   5.0    2.3  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        1.4    8.6   4.0        6.7    6.4   0.3    2.0  2  FlhC            Flagellar transcriptional activator (FlhC)


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 ?   14.0   1.4   9.8e-06     0.029       3      24 ..      56      77 ..      55      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.8e-06
                                      -SSS--B----SSS----SSS- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCG 24
                                      C +Cg +  l ++   RC  CG
  gi|336252112|ref|YP_004595219.1| 56 CSRCGRSYVLVASNTMRCPACG 77
                                      *********************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 ?   13.4   0.7   2.1e-05     0.064       8      34 ..      56      78 ..      55      81 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                       Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgs 34
                                      C +Cg +  vl+++    +t  CP+Cg 
  gi|336252112|ref|YP_004595219.1| 56 CSRCG-RSYVLVAS----NTMrCPACGD 78
                                      *****.55566643....5566****96 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 ?   13.8   0.8   1.4e-05     0.043      69      94 ..      52      78 ..      17      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                                      -EEEETTTS-EEECHHH.HHS-TTTSS CS
                              HypA 69 vkvrCreCgkefeleek.alrCpkCgs 94
                                      +   C++Cg+++ l ++ ++rCp+Cg 
  gi|336252112|ref|YP_004595219.1| 52 IGGPCSRCGRSYVLVASnTMRCPACGD 78
                                      4457*********7664599*****97 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   0.0      0.34     1e+03      36      54 ..      25      44 ..      22      51 .. 0.72
   2 ?   10.9   1.4   0.00011      0.33      31      53 ..      56      77 ..      53      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.34
                    OrfB_Zn_ribbon 36 sknke.alsgrtfkCpnCgf 54
                                      +++++ ++++r+++ + C  
  gi|336252112|ref|YP_004595219.1| 25 ARVTRlEREQRLLRTTTCAI 44
                                      55566667888888888865 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00011
                    OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCg 53
                                      Cs+Cg+     ++++t++Cp+Cg
  gi|336252112|ref|YP_004595219.1| 56 CSRCGRSYVL-VASNTMRCPACG 77
                                      *******999.***********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 ?    8.2   5.0   0.00063       1.9       6      28 ..      56      77 ..      56      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00063
                     zf-NADH-PPase  6 CgrCGaptepaeggwarvCpaCg 28
                                      C+rCG   ++++    ++CpaCg
  gi|336252112|ref|YP_004595219.1| 56 CSRCGRSYVLVAS-NTMRCPACG 77
                                      ***********99.7899****9 PP

>> FlhC  Flagellar transcriptional activator (FlhC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3    0.0022       6.7      14      41 ..      15      42 ..       9      51 .. 0.80
   2 ?    4.2   0.4     0.011        33     135     157 ..      54      76 ..      43      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0022
                              FlhC 14 qlAielielGARlqvlesetslsrerli 41
                                      + A+ + +lGAR+  le+e +l r+   
  gi|336252112|ref|YP_004595219.1| 15 ETAAAIDALGARVTRLEREQRLLRTTTC 42
                                      56777889***********999887655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.011
                              FlhC 135 asCkrCkgefvthaedlesefvC 157
                                         C+rC+ ++v  a+++ +   C
  gi|336252112|ref|YP_004595219.1|  54 GPCSRCGRSYVLVASNTMRCPAC 76 
                                       57*********999877665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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: 0.45u 0.78s 00:00:01.23 Elapsed: 00:00:00.86
# Mc/sec: 287.58
//
Query:       gi|336252113|ref|YP_004595220.1|  [L=337]
Description: short-chain dehydrogenase/reductase SDR [Halopiger xanaduensis SH-6]
Scores for complete 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-46  158.0   0.1    2.6e-46  157.6   0.1    1.1  1  adh_short        short chain dehydrogenase
    2.1e-34  119.1   0.7    2.7e-34  118.7   0.7    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    5.2e-12   46.1   0.2    8.4e-12   45.4   0.2    1.4  1  KR               KR domain
      0.004   16.6   0.1     0.0074   15.8   0.1    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0047   16.9   0.8      0.009   16.0   0.8    1.4  1  ADH_zinc_N       Zinc-binding dehydrogenase
  ------ inclusion threshold ------
       0.01   15.0   0.0      0.012   14.7   0.0    1.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      0.016   15.0   0.4       0.03   14.2   0.4    1.4  1  DFP              DNA / pantothenate metabolism flavoprotein
      0.078   12.8   0.1       0.16   11.8   0.1    1.4  1  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 
      0.088   13.5   0.1       0.23   12.2   0.1    1.8  1  Methyltransf_25  Methyltransferase domain
       0.11   12.9   0.4       0.26   11.8   0.4    1.6  1  NAD_binding_7    Putative NAD(P)-binding
       0.15   11.9   0.2       0.29   11.0   0.2    1.5  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


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 !  157.6   0.1   1.6e-49   2.6e-46       1     190 [.      11     202 ..      11     206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 157.6 bits;  conditional E-value: 1.6e-49
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       +v+++tGassGIG+a+a++ a +Ga+vv+++rse++l+e+ +e++++g +a ++ +Dv+dr++v+++ + a++  g+
  gi|336252113|ref|YP_004595220.1|  11 QVIVITGASSGIGLATARTAADRGARVVLAARSEDALREATEEIRADGGDAEYVVADVSDRDDVREIARVAEETDGG 87 
                                       69*********************************************************************9999** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                        d  vn+A+++  g+ +++  e++++ ++vN+ g++  + ++++++ +  +Gr +n++S+++  +v+ + +YsAsK+
  gi|336252113|ref|YP_004595220.1|  88 FDTWVNGAAVSIYGTLEDVPVEDMREQFDVNVWGLLYGSLEAVDHFRETGGGRLINIGSIVSDRAVILQGSYSASKH 164
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHGGGT..EEEEEEEESSBSSHHHHHH CS
                         adh_short 155 avagltrslakelaptg..irvnavaPGlvdTdmakel 190
                                       av+g+t++l++el+++g  ++v+ v P ++dT++a+ +
  gi|336252113|ref|YP_004595220.1| 165 AVKGFTDTLRMELEEEGapVSVTLVKPSAIDTPFAEHA 202
                                       *********************************98765 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 !  118.7   0.7   1.7e-37   2.7e-34       1     212 [.      17     227 ..      17     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 1.7e-37
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvn 75 
                                       Ga sgIG a+A+++a++Ga+vvl+ ++e+a ++++ee+ +++g + ++ +DV+d+++v+++++ ++e+ g++D  vn
  gi|336252113|ref|YP_004595220.1|  17 GASSGIGLATARTAADRGARVVLAARSEDAlREATEEIRADGGDAeYVVADVSDRDDVREIARVAEETDGGFDTWVN 93 
                                       899**************************************996659****************************** PP

                                       -----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHH CS
                      adh_short_C2  76 nagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalea 150
                                        a+++    g +++++ e++++ +dvn+ +l++ + +a+ +++e+  g+++n+ s+ + r+v  +  y+a+K+a+++
  gi|336252113|ref|YP_004595220.1|  94 GAAVSIY--GTLEDVPVEDMREQFDVNVWGLLYGSLEAVDHFRETggGRLINIGSIVSDRAVILQGSYSASKHAVKG 168
                                       *******..*******************************8887778****************************** PP

                                       HHHHHHHHHGGGT..EEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHH CS
                      adh_short_C2 151 ltrylAvelgpkg..iRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaal 212
                                       +t +l +el ++g  + v  v p++i+T+ a+++k+   + e++   ap+     pe va+++l
  gi|336252113|ref|YP_004595220.1| 169 FTDTLRMELEEEGapVSVTLVKPSAIDTPFAEHAKN--YMDEAATLPAPVY---APETVARTIL 227
                                       ***********884467889***********99983..3333333333332...4666666665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.2   5.2e-15   8.4e-12       3     161 ..      13     171 ..      11     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 5.2e-15
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        +itG+  g+Gl++ar+ a++gar +vl +Rs   +++ ++ ++e++a g + e+v aDvsd+d+v+++ + +++++
  gi|336252113|ref|YP_004595220.1|  13 IVITGASSGIGLATARTAADRGAR-VVLAARS---EDALREATEEIRADGGDAEYVVADVSDRDDVREIARVAEETD 85 
                                       68********************97.7899999...45556689********************************** PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHH..HH..HHTTTS--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawn..Lh..elledesldffvlfSSiagllgsagqanYaaa 152
                                       +     ++ A v+  ++le++  ed+++ +   v G+    L+    ++++    ++ + Si +      q++Y+a 
  gi|336252113|ref|YP_004595220.1|  86 GGFDTWVNGAAVSIYGTLEDVPVEDMREQFDVNVWGLLYgsLEavDHFRETGGGRLINIGSIVSDRAVILQGSYSAS 162
                                       ********************************999875322431134556677777777888777777777777777 PP

                                       HHHHHHHHH CS
                                KR 153 NaflDalae 161
                                        + + ++ +
  gi|336252113|ref|YP_004595220.1| 163 KHAVKGFTD 171
                                       665555554 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   4.5e-06    0.0074       1      75 [.      13      98 ..      13     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.5e-06
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHH...HH..T-SEE CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfk...ee..qpdav 68
                                      i++tGa+  iG a+++  +++g +v+  +r ++a ++a +e        e v +d+ dr++++++ +   e+  ++d+ 
  gi|336252113|ref|YP_004595220.1| 13 IVITGASSGIGLATARTAADRGARVVLAARSEDALREATEEIRadggdaEYVVADVSDRDDVREIARvaeETdgGFDTW 91
                                      89**********************999999988877777665599***************8877643111333455666 PP

                                      EE--S-- CS
                         Epimerase 69 ihlAavg 75
                                      ++ Aav+
  gi|336252113|ref|YP_004595220.1| 92 VNGAAVS 98
                                      6666655 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.8   5.6e-06     0.009       1      64 [.      21      93 ..      21     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.6e-06
                                      HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHT.....T.ESEEEET...TTC.HHHHHHHHHTTTSSEEEEEE CS
                        ADH_zinc_N  1 gvGlaavqlAkalGaeviavdsseeklelakkl.....G.adeviny...kea.dlverikeltggegvdvvfe 64
                                      g+Gla+   A+  Ga+v+ +++se+ l+ a +      G a++v+     +++ +  +r++e t ++g+d  ++
  gi|336252113|ref|YP_004595220.1| 21 GIGLATARTAADRGARVVLAARSEDALREATEEiradgGdAEYVVADvsdRDDvREIARVAEET-DGGFDTWVN 93
                                      8**************************9999855999867999999976544345677788888.448887655 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   7.5e-06     0.012       1     100 [.      13     110 ..      13     187 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.5e-06
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT... CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel. 76 
                                       +++tGa+  iG +  r+ +++  ++++l  r+E +l e ++e++++  + ++      v++dv d++ ++++ +   
  gi|336252113|ref|YP_004595220.1|  13 IVITGASSGIGLATARTAADRG-ARVVLAARSEDALREATEEIRADGGDAEY------VVADVSDRDDVREIARVAe 82 
                                       79**********9998877765.68999**************9877777544......5777777777776654221 PP

                                       ....T-SEEEE------HHHHHHSHHHH CS
                   Polysacc_synt_2  77 ....kvdvvfhaAAlKhVPlveenplea 100
                                           + d+ ++ AA+    ++e  p+e 
  gi|336252113|ref|YP_004595220.1|  83 etdgGFDTWVNGAAVSIYGTLEDVPVED 110
                                       1111567777777777666666666554 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   1.8e-05      0.03      19      93 ..      11      98 ..       2     111 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                                      TTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-.SS--..........-TT-EEEE--SHHHHHHHHH...HHHTT- CS
                               DFP 19 pVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpv.slet..........pegvevvkvesaeemleave...ealkea 83
                                      +V +i+  SSG  G+a A+ aa+rGa+V l + +  +l++           +++ v +v++ ++ +e ++   e+    
  gi|336252113|ref|YP_004595220.1| 11 QVIVITGASSG-IGLATARTAADRGARVVLAARSEdALREateeiradggDAEYVVADVSDRDDVREIARvaeETDGGF 88
                                      6789*******.6*****************9877535543333444443323344445555555544433110222333 PP

                                      SEEEE---S- CS
                               DFP 84 divimaAAva 93
                                      d+ +  AAv+
  gi|336252113|ref|YP_004595220.1| 89 DTWVNGAAVS 98
                                      7777777776 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   9.6e-05      0.16      41      61 ..      11      31 ..       2      39 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.6e-05
                                      SEEEEESTSSHHHHHHHHHHH CS
                   Eno-Rase_NADH_b 41 kkvLviGaStGYGLAsriaaa 61
                                      + + + GaS+G GLA+  +aa
  gi|336252113|ref|YP_004595220.1| 11 QVIVITGASSGIGLATARTAA 31
                                      556677*********855544 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.23       6      58 ..      20      71 ..      15     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                      -TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGB CS
                   Methyltransf_25  6 cGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedl 58
                                       G G  t++ a+  g a+v+    se++l++a e+++++g ++e+v++d++d 
  gi|336252113|ref|YP_004595220.1| 20 SGIGLATARTAADRG-ARVVLAARSEDALREATEEIRADGGDAEYVVADVSDR 71
                                      467776666665545.*********************************9763 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 ?   11.8   0.4   0.00016      0.26       6      84 ..       9      83 ..       5      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                     NAD_binding_7  6 kgkkvlvvGgG.evAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatddrelneriaeaak 83
                                      +++ +++ G+   +++  +r+ ++ ga+v++ a       e+ ++ a ee+++d  +a+ v+a ++dr+  ++ia+ a+
  gi|336252113|ref|YP_004595220.1|  9 EEQVIVITGASsGIGLATARTAADRGARVVLAARS-----EDALREATEEIRADGGDAEYVVADVSDRDDVREIARVAE 82
                                      556666677642599999************99999.....6788889999************************99987 PP

                     NAD_binding_7 84 a 84
                                      +
  gi|336252113|ref|YP_004595220.1| 83 E 83
                                      5 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 ?   11.0   0.2   0.00018      0.29      10      44 ..      22      56 ..      12      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                      CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N 10 mGagiaavfasagleVvlvdiseealekalekiek 44
                                      +G   a  +a +g +Vvl  +se+al++a+e+i++
  gi|336252113|ref|YP_004595220.1| 22 IGLATARTAADRGARVVLAARSEDALREATEEIRA 56
                                      7999999*************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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 0.70s 00:00:01.24 Elapsed: 00:00:01.18
# Mc/sec: 867.27
//
Query:       gi|336252114|ref|YP_004595221.1|  [L=479]
Description: hypothetical protein Halxa_0703 [Halopiger xanaduensis SH-6]
Scores for 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   22.0   0.0    0.00021   21.0   0.0    1.5  1  HTH_IclR   IclR helix-turn-helix domain
    0.00041   19.9   0.0    0.00072   19.1   0.0    1.4  1  HTH_24     Winged helix-turn-helix DNA-binding
    0.00054   19.8   0.0     0.0013   18.6   0.0    1.5  1  MarR_2     MarR family
     0.0062   16.4   0.0     0.0098   15.7   0.0    1.3  1  HTH_5      Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.079   13.0   0.1       0.14   12.1   0.1    1.4  1  HTH_Crp_2  Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   5.8e-08   0.00021       8      49 ..     412     453 ..     411     456 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.8e-08
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                       + ++++e +++++   + ++tg++kS+v+ lL+ ++  G++ 
  gi|336252114|ref|YP_004595221.1| 412 VVKLIRENGGRMKQVNIVEETGWSKSKVSMLLSDMEDDGLIS 453
                                       678999*********************************986 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 !   19.1   0.0     2e-07   0.00072       8      47 ..     412     452 ..     411     453 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2e-07
                            HTH_24   8 ILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       + +l+++n++ + q  + e++g S+s v+  l  +e++GlI
  gi|336252114|ref|YP_004595221.1| 412 VVKLIRENGGrMKQVNIVEETGWSKSKVSMLLSDMEDDGLI 452
                                       66899**9999*****************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   3.5e-07    0.0013      13      53 ..     415     454 ..     410     460 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.5e-07
                                       HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53 
                                        ++ ++gr + +  +++++g sks vs +l ++++ GL+ +
  gi|336252114|ref|YP_004595221.1| 415 LIRENGGR-MKQVNIVEETGWSKSKVSMLLSDMEDDGLISK 454
                                       46666665.9****************************965 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 !   15.7   0.0   2.7e-06    0.0098       8      47 .]     413     454 ..     411     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.7e-06
                                       HHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5   8 LklLae..gelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                       +kl +e  g ++   ++ee+g s+s+vS+ L+ +++ GL++k
  gi|336252114|ref|YP_004595221.1| 413 VKLIREngGRMKQVNIVEETGWSKSKVSMLLSDMEDDGLISK 454
                                       5666666666777789************************97 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 ?   12.1   0.1     4e-05      0.14      29      61 ..     430     466 ..     406     467 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4e-05
                                       HHTTSSHHHHHHHHHHHHHTTSEE..E.TEE.EEES- CS
                         HTH_Crp_2  29 smlGltretvsrilseLkreglis..r.grr.irild 61 
                                       +  G + + vs +ls+++++glis  r gr+ i+ ld
  gi|336252114|ref|YP_004595221.1| 430 EETGWSKSKVSMLLSDMEDDGLISklRvGREnIISLD 466
                                       66789999****************7434454676665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 3185.18
//
Query:       gi|336252115|ref|YP_004595222.1|  [L=195]
Description: beta-lactamase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-17   62.0   8.8    8.7e-16   58.5   8.8    2.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00012   21.7   1.6     0.0002   20.9   1.6    1.6  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.18   11.8   0.1       0.67   10.0   0.1    1.9  2  TTRAP          Putative tranposon-transfer assisting protein


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 !   58.5   8.8   1.5e-19   8.7e-16       4     197 .]      12     173 ..       9     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1.5e-19
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       + +n++l+e +++++L+D+G   +  +       +   + d +av+lTH H+DH+ +l+ +++a+dv v+ + ++ +
  gi|336252115|ref|YP_004595222.1|  12 FTSNVFLVE-GERTVLVDAGANFDVVDRI-----RSNLDGDFEAVVLTHTHPDHVDNLEAVTDAFDVEVWGYDAAIE 82 
                                       679999995.9****************98.....8**********************************99999988 PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS.SHH CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall.age 156
                                           +++                      + ++ +  +g++++++ ++pgh  +h+++++++  +lf+GD+++ +g+
  gi|336252115|ref|YP_004595222.1|  83 GVAIDHE----------------------IADEGTVQLGDHEYVALHTPGHKDDHLCFYAPEPEILFAGDLVFqNGS 137
                                       8888888......................778889999***********************************8888 PP

                                       CCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 157 tgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                        gr+dl     e +d++   +++d++l++++ +   l +gH
  gi|336252115|ref|YP_004595222.1| 138 FGRTDL-----EEGDRATLIESIDRVLERIDEDLTALHAGH 173
                                       888888.....***************999998888888777 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 !   20.9   1.6   3.4e-08    0.0002       1      65 [.      23      79 ..      23     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.4e-08
                                      SEEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHH CS
                     Lactamase_B_2  1 rriLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkg 65
                                      r +L+Dag ++     r +   + +d   + +aV+lth H DH+ +l  +   +   ++++++ + 
  gi|336252115|ref|YP_004595222.1| 23 RTVLVDAGANFDVV-DRIR---SNLDG--DFEAVVLTHTHPDHVDNLEAVTDaF---DVEVWGYDA 79
                                      789*****997666.5554...24667..9**************9998887732...367776544 PP

>> TTRAP  Putative tranposon-transfer assisting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       0.9   5.4e+03      49      58 ..      97     106 ..      97     108 .. 0.81
   2 ?   10.0   0.1   0.00011      0.67      14      39 ..     145     169 ..     143     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.9
                                       T--HHHHHHH CS
                             TTRAP  49 altDaefael 58 
                                       +l D+e+ +l
  gi|336252115|ref|YP_004595222.1|  97 QLGDHEYVAL 106
                                       6889**9877 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00011
                                       -SHHHHHHHHHHHSTTTS.-HHHHHH CS
                             TTRAP  14 egtRkelieelkaalkyleddelreL 39 
                                       eg+R+ lie+++ +l+ + d++l +L
  gi|336252115|ref|YP_004595222.1| 145 EGDRATLIESIDRVLERI-DEDLTAL 169
                                       89****************.***9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); 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: 0.54u 1.12s 00:00:01.66 Elapsed: 00:00:00.70
# Mc/sec: 842.93
//
Query:       gi|336252116|ref|YP_004595223.1|  [L=377]
Description: polyamine-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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-33  116.1   0.0    2.8e-33  115.3   0.0    1.4  1  ABC_tran     ABC transporter
    1.1e-09   38.5   0.2    2.1e-05   24.5   0.1    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    6.6e-06   26.2   0.3    6.6e-06   26.2   0.3    2.5  2  TOBE_2       TOBE domain
    7.5e-05   23.0   0.1    0.00028   21.2   0.1    1.8  1  AAA_22       AAA domain
     0.0016   17.9   0.0       0.14   11.5   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0053   17.1   0.9       0.02   15.3   0.9    1.9  1  AAA_16       AAA ATPase domain
     0.0089   16.5   0.2       0.07   13.6   0.1    2.2  2  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.031   14.2   0.0    1.3  1  Rad17        Rad17 P-loop domain
      0.017   15.4   1.6      0.032   14.5   0.1    2.3  2  TOBE         TOBE domain
      0.031   14.0   0.1      0.083   12.6   0.1    1.8  1  AAA_30       AAA domain
      0.053   13.1   0.3       0.23   11.0   0.3    2.1  1  AAA_25       AAA domain
      0.099   12.8   0.4       0.43   10.7   0.4    2.0  1  AAA_33       AAA domain
       0.11   11.3   0.6       0.44    9.3   0.0    2.2  2  ABC_ATPase   Predicted ATPase of the ABC class
       0.14   12.1   0.0       0.25   11.2   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
       0.18   12.0   0.4        1.7    8.9   0.4    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
        0.2   12.1   0.1       0.35   11.4   0.1    1.3  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 !  115.3   0.0   2.5e-36   2.8e-33       1     136 [.      27     170 ..      27     171 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 2.5e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++v+l+++ ge   +vG++G+GK+t l+++ag + pt+G+i +dg++++    +  ++ +g+++q   lfp+++v+
  gi|336252116|ref|YP_004595223.1|  27 LRDVDLTVRDGEFFTLVGPSGCGKTTTLRTIAGFEAPTAGRIAFDGESTTG--VPPEERDVGIVFQSYALFPHMSVA 101
                                       689***********************************************9..9999******************** PP

                                       HH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en              + de+++++l+ ++l+++ d+       +LSgGq+qrvalaral+ +p+llllDEp+
  gi|336252116|ref|YP_004595223.1| 102 ENvgyglqfreppedtTTDERVADLLELVDLEGMGDRSP----DQLSGGQQQRVALARALAPEPDLLLLDEPM 170
                                       *************99888999999999999999888887....*****************************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 !   12.0   0.0   0.00012      0.13       1      22 [.      39      60 ..      39      91 .. 0.78
   2 !   24.5   0.1   1.8e-08   2.1e-05     223     298 ..     129     202 ..      94     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      +  l+Gp g+GK++ L+++ ++
  gi|336252116|ref|YP_004595223.1| 39 FFTLVGPSGCGKTTTLRTIAGF 60
                                      5689***************876 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.8e-08
                            AAA_21 223 flengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHS 298
                                       +++ ++ +++++++lS G+++  al+ al+  +   +lll+DEp + L+ +l ++l  +l+++ s+ g+  + +TH+
  gi|336252116|ref|YP_004595223.1| 129 LVDLEGMGDRSPDQLSGGQQQRVALARALAPEP---DLLLLDEPMSALDAQLRESLRrQLVRIQSELGITTVYVTHD 202
                                       5555666789999********999999999888...9********************8999***************9 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.1   9.1e+03      52      66 ..     200     215 ..     186     219 .. 0.56
   2 !   26.2   0.3   5.9e-09   6.6e-06       2      75 ..     306     371 ..     305     372 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.1
                            TOBE_2  52 adr.dsalapGdtVel 66 
                                       +++ ++ala+ d+V++
  gi|336252116|ref|YP_004595223.1| 200 THDqAEALAISDRVAV 215
                                       2222346666666655 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 5.9e-09
                            TOBE_2   2 aiRPEklrlaaagg.anglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavv 75 
                                       ++RP +l+    +  +n+ls tVe  e+lG+++r++    + ++v+   ++      +++G+++++++ p+da+v
  gi|336252116|ref|YP_004595223.1| 306 CVRPGALSR---ELeRNRLSVTVETAEFLGEQVRVHGCWNDVPIVLR-LAD-----VPDEGSELTVGFAPEDAHV 371
                                       799999998...44359*******************99999988443.333.....357***************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   2.5e-07   0.00028       5     112 ..      37     181 ..      34     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.5e-07
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..................................erpevv.... 43 
                                         + +++G+sG+GKTt+lr+++     ++ a +                                  e    v    
  gi|336252116|ref|YP_004595223.1|  37 GEFFTLVGPSGCGKTTTLRTIAGFE--APTAGRiafdgesttgvppeerdvgivfqsyalfphmsvaE---NVgygl 108
                                       67889*****************997..3444447799***********************97664432...336668 PP

                            AAA_22  44 .fvtlpsstsskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lrseealeeL 112
                                        f ++p++t+ ++   +ll+ ++le+ +   s ++l   + ++ + ara    + ll++DE    l  +++ e L
  gi|336252116|ref|YP_004595223.1| 109 qFREPPEDTTTDERVADLLELVDLEGMG-DRSPDQLSgGQQQRVALARALapePDLLLLDEPMSaL-DAQLRESL 181
                                       899999999****************999.66666666566666666666688999*****965556.33333334 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 ?    4.1   0.0     0.025        28      25      44 ..      38      57 ..      27      61 .. 0.83
   2 !   11.5   0.0   0.00013      0.14     128     190 ..     134     192 ..      99     221 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.025
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                      +f  +vGp G+GK+  l  i
  gi|336252116|ref|YP_004595223.1| 38 EFFTLVGPSGCGKTTTLRTI 57
                                      68899********9887766 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00013
                                       HCTT-STTCS-HHHHHHHHHHHHHHHHCCS--S.EEEECTTTTTS-HHHHHHHHHHHHHHCTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 128 esagiskelLSgGektLvalaLlfAiqkvkpap.lyllDeidaaLDeknvkkvaellkekskna 190
                                        + + s+++LSgG+++ vala  +A     p+p l llDe  +aLD++ ++ + + l + +++ 
  gi|336252116|ref|YP_004595223.1| 134 GMGDRSPDQLSGGQQQRVALARALA-----PEPdLLLLDEPMSALDAQLRESLRRQLVRIQSEL 192
                                       33334577**********9998766.....555499************9999987766555454 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.9   1.8e-05      0.02      18      46 ..      33      59 ..      21     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellr 46
                                      +vr+g  e   l+G+sG+GK++ +r+++ 
  gi|336252116|ref|YP_004595223.1| 33 TVRDG--EFFTLVGPSGCGKTTTLRTIAG 59
                                      56666..6899**************9984 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 !   13.6   0.1   6.2e-05      0.07       3      20 ..      42      59 ..      40      92 .. 0.89
   2 ?    0.3   0.0      0.76   8.5e+02      47      74 ..     148     176 ..     117     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.2e-05
                                      EESSTTSSHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavak 20
                                      l+Gp G+GKT++ + +a 
  gi|336252116|ref|YP_004595223.1| 42 LVGPSGCGKTTTLRTIAG 59
                                      89************9996 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.76
                                       HHHHHHHHHTS.TSEEEEEETGGGHHHHH CS
                               AAA  47 relfkeakeka.kpsilfiDEidalaksr 74 
                                       ++ ++ a++ a +p  l++DE  +   ++
  gi|336252116|ref|YP_004595223.1| 148 QQRVALARALApEPDLLLLDEPMSALDAQ 176
                                       45555566666779999999976666666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-05     0.031      46      66 ..      38      58 ..      22      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                             Rad17 46 riLLisGPsGCgkstvvkvLs 66
                                      +   + GPsGCgk+t+++ ++
  gi|336252116|ref|YP_004595223.1| 38 EFFTLVGPSGCGKTTTLRTIA 58
                                      567799***********9886 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.5     5e+03      30      47 ..     193     209 ..     183     213 .. 0.66
   2 ?   14.5   0.1   2.9e-05     0.032       4      64 .]     318     371 ..     317     371 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.5
                              TOBE  30 gatLtArvtrrsaeeLgL 47 
                                       g   t+ vt ++ae+L++
  gi|336252116|ref|YP_004595223.1| 193 GI-TTVYVTHDQAEALAI 209
                                       44.567788888888665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.9e-05
                              TOBE   4 rNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                       rN+l +tV+  e+lg +v+V+   ++ + ++ r+  + +++     G+e+++ + +++ h+
  gi|336252116|ref|YP_004595223.1| 318 RNRLSVTVETAEFLGEQVRVHGCWNDVP-IVLRL--ADVPD----EGSELTVGFAPEDAHV 371
                                       9***************************.****9..78888....8******999999886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   7.4e-05     0.083      17      45 ..      37      64 ..      29     197 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.4e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa 45
                                      g  + +l+Gp G GKtt+l++++   +  
  gi|336252116|ref|YP_004595223.1| 37 G-EFFTLVGPSGCGKTTTLRTIAGFEAPT 64
                                      3.48899**************98765555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3    0.0002      0.23      30      61 ..      34      67 ..      27     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava..tGk 61
                                      ++ ge+  l+G++g+GKtt +  +a   a   G+
  gi|336252116|ref|YP_004595223.1| 34 VRDGEFFTLVGPSGCGKTTTLRTIAGFEAptAGR 67
                                      56799**************998888777765444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4   0.00038      0.43       4      20 ..      42      58 ..      40     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                            AAA_33  4 lvGlpGsGKstlaerll 20
                                      lvG++G+GK+t ++ ++
  gi|336252116|ref|YP_004595223.1| 42 LVGPSGCGKTTTLRTIA 58
                                      79**********99985 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 ?   -2.4   0.1       1.3   1.5e+03     242     264 ..      34      57 ..      32      59 .. 0.83
   2 ?    9.3   0.0   0.00039      0.44     324     420 ..     144     225 ..     135     241 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                                       E-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAl 264
                                       ++ G  +++vG+   GK+T L+ +
  gi|336252116|ref|YP_004595223.1|  34 VRDGeFFTLVGPSGCGKTTTLRTI 57 
                                       6667778999**********9988 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00039
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GC CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgd 400
                                       SG   q +++++al  + +llL+DE  sA    +r ++ ++lv               ++ ++lg++t+ v+    +
  gi|336252116|ref|YP_004595223.1| 144 SGGQQQRVALARALAPEPDLLLLDEPMSALDAQLRESLRRQLV---------------RIQSELGITTVYVTHDQAE 205
                                       7777777777777777777777777777777777776666666...............3334577777777777777 PP

                                       CTTT-SEEEEEETTEEEE-H CS
                        ABC_ATPase 401 yldvAdtvilmeeykpkdvt 420
                                        l+++d+v +m++ ++++v 
  gi|336252116|ref|YP_004595223.1| 206 ALAISDRVAVMRDGRVEQVG 225
                                       77777777777777777665 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   0.00023      0.25      91     122 ..      28      60 ..      11      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       +++   ++d ++ +lvG+SG GK+t + ++++ 
  gi|336252116|ref|YP_004595223.1|  28 RDVDLTVRDgEFFTLVGPSGCGKTTTLRTIAGF 60 
                                       5556666666999*************9999875 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 ?    8.9   0.4    0.0015       1.7      54      85 ..     157     182 ..     130     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0015
                           SbcCD_C  54 yssaegrepalrlvfLDEAFsklDeesiatll 85 
                                       +       p ++l++LDE  s lD++ +++l 
  gi|336252116|ref|YP_004595223.1| 157 L------APEPDLLLLDEPMSALDAQLRESLR 182
                                       2......46799*************9998875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00031      0.35      18      39 ..      36      57 ..      21      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                            AAA_23 18 skgltlItGpNGaGKTTildAi 39
                                      +  ++ ++Gp G+GKTT l+ i
  gi|336252116|ref|YP_004595223.1| 36 DGEFFTLVGPSGCGKTTTLRTI 57
                                      557899***********99877 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:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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 0.49s 00:00:01.05 Elapsed: 00:00:00.54
# Mc/sec: 2093.65
//
Query:       gi|336252117|ref|YP_004595224.1|  [L=642]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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  102.3  41.4    1.9e-16   60.4  11.2    3.0  3  BPD_transp_1     Binding-protein-dependent transport system i
  ------ inclusion threshold ------
       0.38   10.5   6.3          7    6.4   0.1    2.8  2  DUF3464          Photosynthesis affected mutant 68
       0.55   10.9  11.4         43    4.8   0.0    4.7  3  Sm_multidrug_ex  Putative small multi-drug export protein


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 ?   -2.3   0.2      0.52   3.1e+03      56      71 ..      37      52 ..      23      59 .. 0.49
   2 !   60.4  11.2   3.1e-20   1.9e-16       1     162 [.     159     336 ..     155     358 .. 0.86
   3 !   54.1  14.3   2.7e-18   1.6e-14       2     179 ..     453     636 ..     452     641 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.52
                      BPD_transp_1 56 viillllsaapyvrli 71
                                      ++il+++ ++p+ +++
  gi|336252117|ref|YP_004595224.1| 37 AAILAVMLYVPVGVVF 52
                                      3333333333333333 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 3.1e-20
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf...............vilsilghlilp.viilll 61 
                                       g+++++++a n+ + +++ lr l+i+++ lP + +a+ ++++f                 +  +    l+ v+++ +
  gi|336252117|ref|YP_004595224.1| 159 GLPAAYVLA-NYEFYGRRTLRSLTILPFVLPGIMVAVGFYAMFgragtlngllglvdvGPIPFIEANPLAiVVVAHA 234
                                       566666777.***********************************************9444456677888799**** PP

                      BPD_transp_1  62 lsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.. 136
                                       +++ap+v +++ aa +s++   ve+ar lGa++++ fr vv+P+++p ++tg++l+f++ +  + +++ lg   G  
  gi|336252117|ref|YP_004595224.1| 235 FYNAPLVARLTVAAWESVDVRAVETARSLGAGPRRAFRDVVVPQLAPAVLTGALLTFVFTFMTFPIVLALG---Glq 308
                                       ***********************************************************************...755 PP

                      BPD_transp_1 137 ...lgtllleailgydyseisnggvlalv 162
                                          +  ++ + i++ dy+e++ ++++  +
  gi|336252117|ref|YP_004595224.1| 309 latVEVWIYDRIQQLDYAEAA-TLAILET 336
                                       577888888888888888887.3333322 PP

  == domain 3  score: 54.1 bits;  conditional E-value: 2.7e-18
                      BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf........vilsilghlilpviillllsaapyv 68 
                                       +++G+++   + r ++l  ++++l  ++l++  +v++i l+  +          +    ++ ++++++ ++ a p+v
  gi|336252117|ref|YP_004595224.1| 453 VPMGVVISvlTVRAGRLGTAIDTLAMLPLAVSGVVFGIGLLQGLvfglslpgG-WRLQLTGPIAIVVAHAVAAYPFV 528
                                       67788887777788889999999999999999999666655333558888743.43444688889************ PP

                      BPD_transp_1  69 rlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleai 145
                                       +++++  l+sl++  ve aralGasr + ++ v lP++++ i++g+++af++++g+++ + +l+s++  ++++  a 
  gi|336252117|ref|YP_004595224.1| 529 TRNVSPLLSSLDSAMVESARALGASRLRALVDVELPLVATGIVAGAAFAFAISIGEFSSTVILASGS-ESYTMPVAV 604
                                       ****************************************************************888.778888888 PP

                      BPD_transp_1 146 lgydyseisnggvlalviavlllnlvadilqrll 179
                                       + y     s g+++a++ ++ll++++++++++ +
  gi|336252117|ref|YP_004595224.1| 605 ERYLGR-RS-GPAIAMGTLLLLVTAASFVVVDRV 636
                                       877777.77.899999999999999998888766 PP

>> DUF3464  Photosynthesis affected mutant 68
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0012         7      41      79 ..       6      44 ..       1      80 [. 0.55
   2 ?    4.5   2.6    0.0044        26      65     115 ..     449     499 ..     433     512 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0012
                           DUF3464 41 kdkeekeeaaiPevVskRmirRvalfsGiPlalGlatfv 79
                                      +d+ +++ +++P+ Vs+R+ rR + ++ + +a+ la++ 
  gi|336252117|ref|YP_004595224.1|  6 DDRISAALERVPDSVSDRLERRALSLAALVTAAILAVML 44
                                      4555666778************98777766654443332 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0044
                           DUF3464  65 lfsGiPlalGlatfvvfylivskelvdlptwvvllvslvlFglgvl.GlsYG 115
                                       l++ +P+ + ++++ v  +   ++++d  ++++l+vs v+Fg+g+l Gl +G
  gi|336252117|ref|YP_004595224.1| 449 LAVAVPMGVVISVLTVR-AGRLGTAIDTLAMLPLAVSGVVFGIGLLqGLVFG 499
                                       56778887777766654.456678899999**************99899888 PP

>> Sm_multidrug_ex  Putative small multi-drug export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.081   4.8e+02      16      43 ..      31      58 ..      26      74 .. 0.71
   2 ?    4.8   0.0    0.0071        43      12      82 ..     321     396 ..     299     407 .. 0.76
   3 ?    4.0   5.3     0.012        74      80     114 ..     560     594 ..     449     599 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.081
                   Sm_multidrug_ex 16 pllallvsvlgnllpvplillflrklle 43
                                      ++  + +++l+ +l vp+ ++f++ ++e
  gi|336252117|ref|YP_004595224.1| 31 LAALVTAAILAVMLYVPVGVVFVNAVVE 58
                                      5556667777779999999999999888 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0071
                   Sm_multidrug_ex  12 lgldpllallvsvlgnllpvplillf..lrkllellkkkkl...lkklfekleekaekksekiekygflGLllFva 82 
                                        +ld+++a  +++l  +l++ l + +   ++    +++++     + lf  l+++   ++  i  yg+++L++Fv+
  gi|336252117|ref|YP_004595224.1| 321 QQLDYAEAATLAILETALSLGLTYAYlrYESAQAGFSQTASppsKEPLFPDLRTTLTGRRLAIVAYGLVALVVFVG 396
                                       4789999999999999888777775523556555444433335688999999999999999999***********7 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.012
                   Sm_multidrug_ex  80 FvaiPLpgTGawtGsliasllglkkkkallaillG 114
                                        v +PL  TG + G++ a+ + +   +++++++ G
  gi|336252117|ref|YP_004595224.1| 560 DVELPLVATGIVAGAAFAFAISIGEFSSTVILASG 594
                                       5889*******************999999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3970.51
//
Query:       gi|336252118|ref|YP_004595225.1|  [L=393]
Description: ThiB subfamily ABC transporter periplasmic binding protein [Halopiger xanaduensis SH-6]
Scores for 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-24   84.7   0.0    9.2e-24   84.2   0.0    1.1  1  SBP_bac_6   Bacterial extracellular solute-binding protein
      2e-17   64.0   0.4    2.4e-17   63.6   0.4    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    1.4e-08   35.1   3.1      3e-08   34.0   3.1    1.5  1  SBP_bac_1   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.099   12.4   0.0       0.14   11.9   0.0    1.3  1  SBP_bac_11  Bacterial extracellular solute-binding protein
        0.3   11.0   2.9       0.45   10.4   2.9    1.3  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0   2.6e-27   9.2e-24      21     228 ..     146     357 ..     133     367 .. 0.90

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 2.6e-27
                         SBP_bac_6  21 eglfqpldpanlpnvnkdfaeeglkdpdgkyypygvgplvlavnkdrlkgrpvPksWaDLldPeykgkvalpgnngs 97 
                                        glf  l+ + l++ ++  +  ++ dp  +  py++g++++++++ ++ ++  P++++DL++P y++     +   s
  gi|336252118|ref|YP_004595225.1| 146 GGLFGELERDGLEHADRVRDGLDVGDPHDRVLPYDTGYISIVYDENEV-DE--PQTFEDLTEPPYEDALLAQNAQAS 219
                                       5888889999999999888899*************************9.56..9*****************99999* PP

                         SBP_bac_6  98 dlfealllalykdfgedgvkkllrnlkanlhpaq...mvkaagslesgepavsvvpyffadilpekkkgk....nlk 167
                                       d+ +a+ll +   fgedg+ +++r+l +n+  +    ++ + g+  +ge   ++v+ +++d++ +++ ++    + +
  gi|336252118|ref|YP_004595225.1| 220 DPGQAFLLWTIDAFGEDGYLDYWRELDDNGVRILddwTESYSGAYMEGE--RPMVVSYSTDQVYANE-YDydfsRHQ 293
                                       *******************************998888************..*********9988886.44479*999 PP

                         SBP_bac_6 168 vvwPedGalvspifmlvkkg.kkkelakafidfllspevqailakaggvfPvv..tnpavlnel 228
                                       v   +d ++++p+ m++  g ++++la+af df ls+e qa +a  + +fP+v  + +++++e+
  gi|336252118|ref|YP_004595225.1| 294 VAFLNDQGYANPEGMAIFEGsENADLAEAFFDFVLSNEPQAEIAQRNVQFPAVadEYVDLDEEF 357
                                       ******99********************************************844444444443 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.4   6.8e-21   2.4e-17       2     281 ..      87     364 ..      86     365 .. 0.80

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 6.8e-21
                                       HHHHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT-.--SEE.EEE-HHHHHHHHH....TTSB--GG..GSTTHHH CS
                         SBP_bac_8   2 lakefekkt.gvkvnvvtaasndleqklkaalaagt.apdidvvwanedalatlae....eglladls..dldnldd 70 
                                       l ++fe+++ +v+++ +  ++++++  +  a+++ +  pd+  +  n d+l   ++     gl+ +l+   l+ +d 
  gi|336252118|ref|YP_004595225.1|  87 LKDAFEAEYpDVTLEWTRLPDQGINYYIERAAQDVEiEPDV-YLGLNVDDLVLVDDnlgdGGLFGELErdGLEHADR 162
                                       5689*****99******999999988888888877734554.45555666654444677799*****9655577777 PP

                                       -HHHHHTT--TS.----EEEEEEE-EEEEEHHHHHHS.---BHHHHHHHHHHHHHH-.SEGG---GGGGGGTHHETT CS
                         SBP_bac_8  71 ltdalaavgydgklygvPyasetpyvliynkdllekaedpktwdellaaakklkgkf.glpdpasgwlqaallakdg 146
                                       + d l+  +  +    +Py+++    ++y++  ++    p+t+++l++  + ++ +  ++ ++as+ +qa+ll    
  gi|336252118|ref|YP_004595225.1| 163 VRDGLDVGDPHD--RVLPYDTGY-ISIVYDENEVD---EPQTFEDLTE--PPYEDALlAQNAQASDPGQAFLLW-TI 230
                                       777777656655..89******8.9**********...6*********..999544422223445555555555.54 PP

                                       EE---H..HHH.HHHHHHHHHHHHTT-.EE-S...--SSTTTTTSBSEEEE-TTHHHHHH-TTT...SEEEE--S-- CS
                         SBP_bac_8 147 ksldddggkdglkealellkklkdngk.tydtg.adavsefanGevaftingswdiaaaqkagk...klgaivpkqg 218
                                       + + +d        +l+++++l dng+ ++d++ +++  ++ +Ge  +++++s d   a++ +    + ++++++++
  gi|336252118|ref|YP_004595225.1| 231 DAFGED-------GYLDYWRELDDNGVrILDDWtESYSGAYMEGERPMVVSYSTDQVYANEYDYdfsRHQVAFLNDQ 300
                                       456554.......699**********8455777478888****************999997764235778999**** PP

                                       EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHH.HH---BS-S-TTT.HHHHHH-HHH. CS
                         SBP_bac_8 219 sfaggkglavpknaknedlaAldFlkwltspenqaalae.ktgyipvnksaal.spevkkdpalp 281
                                         a+ +g+a++ +++n+dl A +F  +++s+e qa+ a+ + +++ v ++  + ++e+ +++++p
  gi|336252118|ref|YP_004595225.1| 301 GYANPEGMAIFEGSENADL-AEAFFDFVLSNEPQAEIAQrNVQFPAVADEYVDlDEEFDQYAHVP 364
                                       ******************9.*******************999********998799999999887 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   3.1   8.2e-12     3e-08      16     315 .]      89     334 ..      78     334 .. 0.67

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 8.2e-12
                                       HHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTS.SSCSEEEE.CGGHHH....HHHHTTSBECCHHHHHHTTECTT CS
                         SBP_bac_1  16 kafekehpgikVeiesvgsgslaqkltlaiaaGd.gpaDviav.dndwia....rlakaglllpldpyvkaylapgv 86 
                                       +afe+e+p+++ e++  + ++    +  a +     p Dv  + + d++      l ++gl+ +l            
  gi|336252118|ref|YP_004595225.1|  89 DAFEAEYPDVTLEWTRLPDQGINYYIERAAQDVEiEP-DVYLGlNVDDLVlvddNLGDGGLFGEL------------ 152
                                       56999************99999996666666666666.999996655555333334444555555............ PP

                                       CCTEEEEHHHHTHHHHCEEE..ES.EEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCE CS
                         SBP_bac_1  87 kdaadklsssvlpkildskv..ly.vPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkpiggargg 159
                                        +       + + + ld ++     +P+++ +  ++Y     ++ ++d+p t+++l+e+  +      +      ++
  gi|336252118|ref|YP_004595225.1| 153 -ERDGLEHADRVRDGLDVGDphDRvLPYDTgYISIVY-----DENEVDEPQTFEDLTEPPYEDALLAQNA-----QA 218
                                       .3333333334444444333676779***77******.....5555555778888876544444333333.....33 PP

                                       EHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHH.TTSC CS
                         SBP_bac_1 160 sasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfe.aGea 235
                                       s+ g+a++++                          +++++ +  + +++ +   + +    d+++ ++  + +Ge 
  gi|336252118|ref|YP_004595225.1| 219 SDPGQAFLLW--------------------------TIDAFGEDGYLDYWRELDDNGVRILDDWTESYSGAYmEGER 269
                                       4444444443..........................3333333334667888889999999999999999999**** PP

                                       SEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHH CS
                         SBP_bac_1 236 amaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspe 312
                                       +m ++++++         +v +++ + ++  +  ++      + ++   +  g+ai+ gs n + A++F+df+ls+e
  gi|336252118|ref|YP_004595225.1| 270 PMVVSYSTD---------QVYANEYDYDFSRHQVAFL----NDQGY--ANPEGMAIFEGSENADLAEAFFDFVLSNE 331
                                       *******99.........6666666666666666665....22222..49*************************** PP

                                       HHH CS
                         SBP_bac_1 313 aqa 315
                                       +qa
  gi|336252118|ref|YP_004595225.1| 332 PQA 334
                                       996 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.8e-05      0.14      81     225 ..     184     337 ..      87     340 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                                       EEEEESTT-TT---SHHHHHHSS-..-EEEE--T-TTTTHH.H.HHHGGG--...HHHHHHHHHTEEEEESSHHHHH CS
                        SBP_bac_11  81 lviavpkgnpkkikgwadLlkpgl..klavadPttspsGlaal.alleaaga...qellkalekkvvklgessrqll 151
                                       + i++ ++  + +++++dL+ p     l   + ++s  G+a l  +++a g     +++++l ++ v+  ++ +  +
  gi|336252118|ref|YP_004595225.1| 184 ISIVYDENEVDEPQTFEDLTEPPYedALLAQNAQASDPGQAFLlWTIDAFGEdgyLDYWRELDDNGVRILDDWTESY 260
                                       66788888899999*******96644455556666666664333666666555558899******888888777777 PP

                                       HH.HHTTT-SEEEEEHH.HHH.....HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHH CS
                        SBP_bac_11 152 ta.veageadagivyes.eakaa...engdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaqai 223
                                       +   ++ge  ++++y + +++a+       + ++  l ++ ++   + ++a+  ++ ++  A+aF +f++s e qa 
  gi|336252118|ref|YP_004595225.1| 261 SGaYMEGERPMVVSYSTdQVYANeydYDFSRHQVAFLNDQGYA--NPEGMAIFEGSENADLAEAFFDFVLSNEPQAE 335
                                       7668999*99999999845555554324446666677777775..57899**********************99986 PP

                                       HH CS
                        SBP_bac_11 224 lr 225
                                       ++
  gi|336252118|ref|YP_004595225.1| 336 IA 337
                                       65 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.9   0.00013      0.45       4      25 ..       3      23 ..       1      24 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                        TAT_signal  4 RRdFLKgsAAaaAAaa.lggcaa 25
                                      RR+FL   A+++A a+ ++gc++
  gi|336252118|ref|YP_004595225.1|  3 RRTFLG--AVGGASAVgVAGCLT 23
                                      ******..999977777999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2827.14
//
Query:       gi|336252119|ref|YP_004595226.1|  [L=281]
Description: P-loop ATPase/GTPase-like protein [Halopiger xanaduensis SH-6]
Scores for 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  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.50
# Mc/sec: 1677.53
//
Query:       gi|336252120|ref|YP_004595227.1|  [L=99]
Description: hypothetical protein Halxa_0709 [Halopiger xanaduensis SH-6]
Scores for 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:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 764.09
//
Query:       gi|336252121|ref|YP_004595228.1|  [L=595]
Description: multi-sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for complete 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-44  152.7  20.1      2e-44  152.3  20.1    1.1  1  HisKA_7TM    N-terminal 7TM region of histidine kinase
    1.1e-14   54.9   0.0    2.1e-14   54.0   0.0    1.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    3.1e-13   49.5   1.3    2.7e-12   46.6   0.2    2.3  2  HisKA        His Kinase A (phospho-acceptor) domain
    2.3e-11   43.9   0.3    1.4e-10   41.4   0.2    2.5  2  PAS_4        PAS fold
    4.7e-08   33.2   0.2    1.1e-07   32.1   0.0    1.7  2  PAS_9        PAS domain
    1.5e-05   25.0   0.0    4.2e-05   23.5   0.0    1.8  1  PAS          PAS fold
    2.2e-05   24.4   0.3    0.00015   21.7   0.2    2.4  2  PAS_8        PAS domain
    3.6e-05   23.9   0.1    0.00053   20.1   0.1    2.4  1  PAS_7        PAS fold
     0.0001   22.1   0.6     0.0023   17.6   0.0    2.3  2  dCache_3     Double sensory domain of two-component sensor ki
  ------ inclusion threshold ------
      0.015   14.6   0.1        0.3   10.3   0.0    2.3  2  L-fibroin    Fibroin light chain (L-fibroin)
      0.016   15.2   0.1      0.034   14.1   0.1    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
       0.02   15.5   0.1      0.041   14.5   0.1    1.5  1  PAS_10       PAS domain


Domain annotation for each model (and alignments):
>> HisKA_7TM  N-terminal 7TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.3  20.1   1.3e-47     2e-44       3     220 .]      13     230 ..      11     230 .. 0.95

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 1.3e-47
                         HisKA_7TM   3 lisallslvlaiyawrrrskpgaraflllllavalwslgyalellattleakllwaklqylgivfipvlwllfaley 79 
                                       +++++++lvl  ++wr+r+++ga ++++ l+a+a+w+++ +++ +a++++   ++ ++ y+g+  ++++ llfaley
  gi|336252121|ref|YP_004595228.1|  13 AVATIVALVLSGVVWRHRDAAGAVPLTASLVAAAVWAGSLFVATFAESYAVSSFALRILYVGVGGTVLGSLLFALEY 89 
                                       799************************************************************************** PP

                         HisKA_7TM  80 tgkrrwltrrrlallllvpvltlilvltnplhhlfy...vsagsfvvlefehGplfwvhlaysyllliagvvllira 153
                                       +g++r++trr++all+++pvl+l+l++ np + +f     + + ++ +++e+G +f +hl+ysyll++++++++++ 
  gi|336252121|ref|YP_004595228.1|  90 AGRERFVTRRLVALLSIEPVLVLALAFWNPGNTFFTvlePDPTALTGIAVEFGTAFDAHLVYSYLLVLISTAVILEL 166
                                       ******************************88887567777778888888******88******************* PP

                         HisKA_7TM 154 lirssglyrrqalllligllvPwlanllyllglsplpgidltplafaltglllaiaifryrlldivP 220
                                       l +s+ lyr qa++l  +llvP+ an+ly++g   l g+d tp++f+++g l+aiai+ry+l divP
  gi|336252121|ref|YP_004595228.1| 167 LYNSRALYRGQAAALTGALLVPLPANALYTFG---LVGFDTTPIGFIVAGGLYAIAIVRYQLTDIVP 230
                                       ******************************96...3488***************************9 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 !   54.0   0.0   1.4e-17   2.1e-14       2     107 ..     448     573 ..     447     577 .. 0.79

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 1.4e-17
                                       HHHHHHHHHHHHHHHHHHH......................HSTTTEEEEEEEEEETEEEEE...EEESSSSSTTHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkf......................atkageieveikaseddlvis...veDnGiGipked 53 
                                       d +r ++++ nl  Na+++                      a  ++ ie+++ +  ++  i+   veD+G+Gip + 
  gi|336252121|ref|YP_004595228.1| 448 DADRTTRLFENLFRNAIEHgrpssspapkpvdgageaddpaADGSNAIEITVGTIGGEGAIEgfyVEDDGRGIPSDR 524
                                       78999**************9999988887777765555432223334455555422455554444************ PP

                                       HTGTCS.TTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  54 lkklfe.kfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgrGttftft 107
                                       ++++fe  ++       +g gtGlGlsiv++++e +g ++  ++++ +G +f +t
  gi|336252121|ref|YP_004595228.1| 525 RERIFEsGYTG------DGDGTGLGLSIVERIAEAHGWTVAATESEAGGARFEVT 573
                                       ******66666......799**********************9999*****9875 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.2   1.8e-15   2.7e-12       2      65 ..     350     408 ..     349     410 .. 0.94
   2 ?    1.4   0.0      0.22   3.3e+02      34      59 ..     435     460 ..     418     466 .. 0.78

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.8e-15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                       l rf+++v+H+Lr+PLs+  g++++ ++           le++ ++ +r++ +++d+L l+r +
  gi|336252121|ref|YP_004595228.1| 350 LDRFASMVSHDLRNPLSVADGYVSLARE-----TGDTSHLEDAARSLERMETIIDDVLALTRDG 408
                                       78***********************999.....788999*********************9987 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.22
                                       HSSCHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  34 teelkeyletiesearrldhlvedlL 59 
                                        e   ++ +ti+  a+r ++l e+l 
  gi|336252121|ref|YP_004595228.1| 435 AELTVDATATIRADADRTTRLFENLF 460
                                       466667899**************994 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         9   1.3e+04      75      89 ..      90     104 ..      78     112 .. 0.77
   2 !   41.4   0.2   9.5e-14   1.4e-10       1     110 []     237     338 ..     237     338 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 9
                             PAS_4  75 pgeerhyelrllPlr 89 
                                        g+er++  rl+ l+
  gi|336252121|ref|YP_004595228.1|  90 AGRERFVTRRLVALL 104
                                       789999999998885 PP

  == domain 2  score: 41.4 bits;  conditional E-value: 9.5e-14
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ld + ++++v+d+d r +++N+++++ +  ++e+++G++ ++l+++    +  + ++ + + ++  + +  +++   
  gi|336252121|ref|YP_004595228.1| 237 LDTIAEGVFVIDRDDRLVDVNPSGRRFIDNDDEAIVGRSIESLFSP----AAIDLYETLTAVRDKSRGVLSVND--- 306
                                       677889*************************************998....666777777777777788886666... PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                         +y++r++P++d++ + +g++v++ DiTer+r
  gi|336252121|ref|YP_004595228.1| 307 -SYYDVRVTPIDDSRNRHVGWIVVASDITERKR 338
                                       .******************************97 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   7.1e-11   1.1e-07       2     104 .]     242     335 ..     241     335 .. 0.93
   2 ?   -3.5   0.0       8.3   1.2e+04      45      74 ..     382     409 ..     376     412 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 7.1e-11
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       +g+++++ d r++++N++ +r++  + e+++g+si+ lf   + a+ +l + l + r   +++ v  ++++    ++
  gi|336252121|ref|YP_004595228.1| 242 EGVFVIDRDDRLVDVNPSGRRFIDNDDEAIVGRSIESLF---SPAAIDLYETLTAVR--DKSRGVLSVNDS----YY 309
                                       78999889999*************99*************...***************..788888888876....48 PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                       +++++p+ d+ ++ vg+iv+  Dite
  gi|336252121|ref|YP_004595228.1| 310 DVRVTPIDDSRNRHVGWIVVASDITE 335
                                       9******999***************8 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.3
                             PAS_9  45 eanerlraaleqgrkkerevevvlirknge 74 
                                       ++ e+ ++ le+++     ++v   +++g 
  gi|336252121|ref|YP_004595228.1| 382 SHLEDAARSLERME--TIIDDVLALTRDGD 409
                                       55667777788888..88888888888886 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.8e-08   4.2e-05       4     113 .]     234     333 ..     232     333 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.8e-08
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       +++l+++++++fv+D+d r + vN++ +++   + e ++g+s+  l+++       +l+e+l +++ +sr++    +
  gi|336252121|ref|YP_004595228.1| 234 HRVLDTIAEGVFVIDRDDRLVDVNPSGRRFIDNDDEAIVGRSIESLFSPA----AIDLYETLTAVRDKSRGVLSVND 306
                                       689*****************************************999997....55555555555555555544333 PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                              + +vr++p+ d   ++ g+++v+ di
  gi|336252121|ref|YP_004595228.1| 307 S------YYDVRVTPIDDSRNRHVGWIVVASDI 333
                                       3......77799999999999999999999997 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   9.7e-08   0.00015       5      57 ..     235     284 ..     233     296 .. 0.79
   2 ?   -1.4   0.0       1.8   2.6e+03      18      33 ..     296     311 ..     283     343 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 9.7e-08
                             PAS_8   5 alfesspdgiavvdlgdrivdvNqaalellGysadlkgellgqllpvlrplle 57 
                                        +++++++g++v+d++dr+vdvN++  ++   +  ++++ +g+ ++ l ++ +
  gi|336252121|ref|YP_004595228.1| 235 RVLDTIAEGVFVIDRDDRLVDVNPSGRRFID-N--DDEAIVGRSIESLFSPAA 284
                                       589***********9999**********996.3..677777777777666655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                             PAS_8  18 d.lgdrivdvNqaalel 33 
                                       d   + ++ vN+++++ 
  gi|336252121|ref|YP_004595228.1| 296 DkSRG-VLSVNDSYYDV 311
                                       43445.99999999876 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   3.5e-07   0.00053       1     114 [.     237     340 ..     237     341 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.5e-07
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphs 77 
                                       l+ + +G+ v+D+d+rLv +N   ++  d  +e + vg+++e+l+    +   ++      +++++ +  +++   s
  gi|336252121|ref|YP_004595228.1| 237 LDTIAEGVFVIDRDDRLVDVNPSGRRFIDNDDEAI-VGRSIESLFSPA-AIDLYE------TLTAVRD--KSRGVLS 303
                                       7899*******************************.*******99765.334444......2222222..2334456 PP

                             PAS_7  78 fererpdgrvievrgnplpdgGfVttytDiTerrrae 114
                                       ++ +  d rv  +  ++  + G++++ +DiTer+r+e
  gi|336252121|ref|YP_004595228.1| 304 VNDSYYDVRVTPIDDSRNRHVGWIVVASDITERKRHE 340
                                       777778889**************************98 PP

>> dCache_3  Double sensory domain of two-component sensor kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.5e-06    0.0023     182     237 ..     282     335 ..     263     336 .. 0.87
   2 ?    2.5   0.3     0.066        99      16      79 ..     340     413 ..     337     462 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                          dCache_3 182 pidrellkelkeqqtlgklfreleidgrsylvvllpLkdysgeligvlvigldvta 237
                                       p   +l+++l++  +  k+ ++l++++  y v + p++d++++++g +v+++d+t+
  gi|336252121|ref|YP_004595228.1| 282 PAAIDLYETLTAVRD--KSRGVLSVNDSYYDVRVTPIDDSRNRHVGWIVVASDITE 335
                                       667789999999999..************************************986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.066
                          dCache_3  16 enlleqeedqllallelvasspg.........vaeaisegdreqlerlldsiwndlg..leqivlldadgtvilr 79 
                                       e++le+++++l +++ +v+ + +         v+ a ++gd++ le+  +s+  +++  ++ + +l++dg  + +
  gi|336252121|ref|YP_004595228.1| 340 ERKLERQNERLDRFASMVSHDLRnplsvadgyVSLARETGDTSHLEDAARSLE-RMEtiIDDVLALTRDGDEVTD 413
                                       5678899999999999999999999999999999999*********9988876.888899999999999887666 PP

>> L-fibroin  Fibroin light chain (L-fibroin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0002       0.3     128     202 ..     117     191 ..     108     201 .. 0.86
   2 ?    1.6   0.1     0.098   1.5e+02      23      42 ..     420     439 ..     406     452 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                         L-fibroin 128 inpgqlrysvgpalgcagggriydfeaawdailassdssflneeycivkrlynsrnsqsnniaayitahllppva 202
                                        npg+  ++v      a  g   +f +a+da l  s   +l    +i+  lynsr     + aa   a l+p  a
  gi|336252121|ref|YP_004595228.1| 117 WNPGNTFFTVLEPDPTALTGIAVEFGTAFDAHLVYSYLLVLISTAVILELLYNSRALYRGQAAALTGALLVPLPA 191
                                       58899889888888889999999*********************************9999988888887777555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.098
                         L-fibroin  23 ssvisrawdyvddtdksiai 42 
                                        s++ rawd+vd +   +++
  gi|336252121|ref|YP_004595228.1| 420 ESLVERAWDHVDSAAAELTV 439
                                       6899********98776665 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.3e-05     0.034      39     111 ..     459     553 ..     422     566 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                       HATPase_c_2  39 actNavehayleapegpvevr........lesdeealtve..............vaDsGpgfdpetlpdpteeepke 93 
                                       ++ Na+eh++++ + +p  v         + ++++a++++              v+D+G+g +   +++  e ++++
  gi|336252121|ref|YP_004595228.1| 459 LFRNAIEHGRPSSSPAPKPVDgageaddpAADGSNAIEITvgtiggegaiegfyVEDDGRGIPSDRRERIFESGYTG 535
                                       689*********997666555558888998888888999888999999999999*******99999999999999** PP

                       HATPase_c_2  94 slkegGrGlalikglvDe 111
                                       +++  G+Gl +++++++ 
  gi|336252121|ref|YP_004595228.1| 536 DGDGTGLGLSIVERIAEA 553
                                       *************99876 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.7e-05     0.041       7     106 .]     239     334 ..     234     334 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.7e-05
                            PAS_10   7 stpieltflDdnlqirrFtpaakklfkli.padvGrpladihpkkavknveeviealrtgekdevevvvpkngkwvl 82 
                                       +++ ++  +D+++++   +p+ +++++   +a vGr+++++ ++ a++   e + a+r++ + +     ++n+ ++ 
  gi|336252121|ref|YP_004595228.1| 239 TIAEGVFVIDRDDRLVDVNPSGRRFIDNDdEAIVGRSIESLFSPAAIDL-YETLTAVRDKSRGVL----SVNDSYYD 310
                                       5555666678888888888877777765415679*******88888764.455667787777755....599***** PP

                            PAS_10  83 vrylpyrdedgeiaGvvetfvDit 106
                                       vr+ p+ d  ++  G +++  Dit
  gi|336252121|ref|YP_004595228.1| 311 VRVTPIDDSRNRHVGWIVVASDIT 334
                                       **********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 4126.56
//
Query:       gi|336252122|ref|YP_004595229.1|  [L=1016]
Description: D-lactate dehydrogenase (cytochrome) [Halopiger xanaduensis SH-6]
Scores for 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  199.7   0.1      1e-58  198.9   0.1    1.4  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
      3e-42  143.7   0.3    7.5e-42  142.4   0.3    1.7  1  FAD_binding_4  FAD binding domain
    8.3e-11   42.2   4.6    1.9e-10   41.0   4.6    1.6  1  Fer4_8         4Fe-4S dicluster domain
    2.5e-10   40.7   4.4    4.7e-10   39.9   4.4    1.5  1  Fer4_17        4Fe-4S dicluster domain
    0.00028   21.4   4.1    0.00077   20.0   4.1    1.8  1  Fer4_7         4Fe-4S dicluster domain
    0.00069   19.7   8.6      0.029   14.5  10.3    2.3  2  Fer4_10        4Fe-4S dicluster domain
      0.001   19.1   9.7       0.15   12.2   1.2    2.6  2  Fer4_2         4Fe-4S binding domain
     0.0041   16.9  11.5      0.055   13.3   3.2    2.6  2  Fer4           4Fe-4S binding domain
  ------ inclusion threshold ------
       0.01   16.0   7.1      0.062   13.5   7.5    2.1  2  Fer4_9         4Fe-4S dicluster domain
      0.013   15.7   3.1       0.18   11.9   0.2    2.6  2  Fer4_21        4Fe-4S dicluster domain
       0.02   15.1   0.1       0.82    9.9   0.0    3.1  3  CCG            Cysteine-rich domain
       0.11   13.5   4.2        0.3   12.1   4.2    1.8  1  Fer4_16        4Fe-4S double cluster binding domain
       0.12   12.6   0.1       0.31   11.2   0.1    1.7  1  Fer4_18        4Fe-4S dicluster domain
       0.14   12.7  12.3       0.25   11.9   2.5    2.5  2  Fer4_4         4Fe-4S binding domain
       0.34   11.0  12.1       0.46   10.7   2.6    2.5  2  Fer4_6         4Fe-4S 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 !  198.9   0.1   8.6e-62     1e-58       2     250 .]     305     554 ..     304     554 .. 0.99

  Alignments for each domain:
  == domain 1  score: 198.9 bits;  conditional E-value: 8.6e-62
                                       -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SS...TTS-TTT-EEEEEEEEE-HHHH CS
                     FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgak...kglpdeeealllvefegddeee 75 
                                       pe++a++++ ++++ +a++av+++ +     +a+elmd++ ++l+++ ++ +   +++pd+++a+l++ef++   e 
  gi|336252122|ref|YP_004595229.1| 305 PEETALVVCCYDELLEALAAVPDALDL--EASAVELMDEEVFRLAANSQEYAeyaAPIPDGTAAALMLEFDSEVYED 379
                                       99***********************99..**********************99************************ PP

                                       HHHHHHHHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHH CS
                     FAD-oxidase_C  76 aeeelealveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikal 152
                                       +  ++e++ ++++++++a d   a ++a++++lwk+Rkaa+p+l ++ +++++++++eD svP+++la++v  ++++
  gi|336252122|ref|YP_004595229.1| 380 LPDAVEDARAHLVDEGAAFDSIEAFSPAKRDRLWKLRKAAIPLLMSMEGDPKPYPFVEDASVPPEELAAYVDGFQDI 456
                                       ******999999999999999******************************************************** PP

                                       HHHHHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THH CS
                     FAD-oxidase_C 153 ldkyglevvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeegl 229
                                       l+++++++++f+Hag g lh+++ ++l+ e+++e+++ ++d+v+dl++e+ Gs sgEHG Gl++ ++ ++ +g++++
  gi|336252122|ref|YP_004595229.1| 457 LEAHDTTAAYFAHAGVGTLHIRPVLNLKEEDDVEKVRSIADDVTDLVLEHEGSFSGEHGDGLARTEFNPKLYGPDLW 533
                                       ***************************************************************************** PP

                                       HHHHHHHHHH-TT--BSTT-- CS
                     FAD-oxidase_C 230 almrriKaalDPkgiLNPgkv 250
                                       ++++ +K+a+DP++ LNPgkv
  gi|336252122|ref|YP_004595229.1| 534 QAFKDVKSAFDPDWRLNPGKV 554
                                       ********************8 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.4   0.3   6.3e-45   7.5e-42       1     138 [.      72     210 ..      72     211 .. 0.99

  Alignments for each domain:
  == domain 1  score: 142.4 bits;  conditional E-value: 6.3e-45
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETT.S--EEEEETTTTEEEEETTSBHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsr.lnrileideeegtatveaGvtlgd 76 
                                       pa+vv p+++++v+aa+r+a+e+g+pvl+rG+Gssl+gqav  g+vvldlsr +n i+eid++e++a+v++Gv+ + 
  gi|336252122|ref|YP_004595229.1|  72 PAGVVLPRDTDDVRAAVRVAAEHGAPVLPRGAGSSLAGQAVGPGCVVLDLSRhMNEIREIDPDEQRAVVQPGVVQDH 148
                                       799*************************************99*********99************************ PP

                                       HHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                     FAD_binding_4  77 lvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                       l+ al+ +gl + ++p+s +++t+GG i +n+ G +s +yG +  +v++ +vvladG+++r+
  gi|336252122|ref|YP_004595229.1| 149 LDDALDSHGLKFAPDPASSNRATIGGGIGNNSTGAHSVRYGITDAYVEECRVVLADGSLIRT 210
                                       ***********************************************************997 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   4.6   1.6e-13   1.9e-10       4      65 .]     597     673 ..     595     673 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.6e-13
                            Fer4_8   4 kCieCgaCq.....saCpvlrrtkkhlldargeaae...........dvqeeqvlee.......eealwsCttcgaC 57 
                                        C++Cg C+      +Cp++r+t +++ ++rg+a+            +        e       ee l+ C +c+ C
  gi|336252122|ref|YP_004595229.1| 597 LCNGCGTCRqtdsdVMCPTYRATEEEIATTRGRANLlraaisgdlepE--------ErfserfqEEVLDLCIGCKGC 665
                                       6********9998888*****************999888777755432........033335569************ PP

                            Fer4_8  58 tevCpvgi 65 
                                       ++ Cp+g+
  gi|336252122|ref|YP_004595229.1| 666 QSDCPTGV 673
                                       *****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 !   39.9   4.4   3.9e-13   4.7e-10       2      61 .]     598     674 ..     597     674 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 3.9e-13
                           Fer4_17   2 CiqCgyClp.....eCpsyeaydnepkkllraakl............glleeaekeekaslCieCgeCerkCPqgld 61 
                                       C++Cg C++     +Cp+y+a+++e ++++ +a+l            +++ e  +ee+ +lCi+C++C+++CP g+d
  gi|336252122|ref|YP_004595229.1| 598 CNGCGTCRQtdsdvMCPTYRATEEEIATTRGRANLlraaisgdlepeERFSERFQEEVLDLCIGCKGCQSDCPTGVD 674
                                       *********************999866666666555555555444443444444458*****************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 !   20.0   4.1   6.4e-07   0.00077       2      52 .]     598     673 ..     597     673 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.4e-07
                            Fer4_7   2 CigCgaCv.....aaCpvkaieldeeenekgtekv....................eidpekClgCgaCvavCPtga 52 
                                       C gCg C      ++Cp++  + +e +  +g++ +                    e + + C+gC+ C++ CPtg+
  gi|336252122|ref|YP_004595229.1| 598 CNGCGTCRqtdsdVMCPTYRATEEEIATTRGRANLlraaisgdlepeerfserfqEEVLDLCIGCKGCQSDCPTGV 673
                                       *******855555679988888776555554422233333444444444455444556789*************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 !   14.5  10.3   2.5e-05     0.029       7      56 .]     596     670 ..     592     670 .. 0.93
   2 !   14.3   1.4   2.7e-05     0.032       7      27 ..     657     674 ..     652     693 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                           Fer4_10   7 dtCirCgkCvk.....aCPadl....................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       + C +Cg+C++     +CP++                     +++   +e+  e  ++++++ C+gc  C++ CP
  gi|336252122|ref|YP_004595229.1| 596 ELCNGCGTCRQtdsdvMCPTYRateeeiattrgranllraaiSGDLEPEERFSERFQEEVLDLCIGCKGCQSDCP 670
                                       67*************88***99*******************888888888888888889***************9 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.7e-05
                           Fer4_10   7 dtCirCgkCvkaCPadltsvg 27 
                                       d Ci+C+ C++ CP+ +   +
  gi|336252122|ref|YP_004595229.1| 657 DLCIGCKGCQSDCPTGV---D 674
                                       79*************43...2 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   1.8   0.00035      0.42       8      22 .]     596     615 ..     591     615 .. 0.74
   2 !   12.2   1.2   0.00013      0.15       7      22 .]     656     671 ..     650     671 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                            Fer4_2   8 drCigCgaCv....sa.CPa 22 
                                       + C+gCg+C+    ++ CP+
  gi|336252122|ref|YP_004595229.1| 596 ELCNGCGTCRqtdsDVmCPT 615
                                       78*******74444667775 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                        d CigC+ C+s CP+
  gi|336252122|ref|YP_004595229.1| 656 LDLCIGCKGCQSDCPT 671
                                       589****99******7 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   1.2    0.0026       3.1       6      14 ..     596     604 ..     594     607 .. 0.89
   2 !   13.3   3.2   4.6e-05     0.055       6      21 ..     657     672 ..     655     673 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0026
                                       TTSSS-THH CS
                              Fer4   6 ekCigCGaC 14 
                                       e+C gCG+C
  gi|336252122|ref|YP_004595229.1| 596 ELCNGCGTC 604
                                       89******* PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.6e-05
                                       TTSSS-THHHHHSTTT CS
                              Fer4   6 ekCigCGaCvevCPvg 21 
                                       ++CigC+ C + CP+g
  gi|336252122|ref|YP_004595229.1| 657 DLCIGCKGCQSDCPTG 672
                                       89*************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 ?    3.9   1.0     0.049        59      33      44 ..     588     606 ..     567     607 .. 0.67
   2 ?   13.5   7.5   5.2e-05     0.062       2      49 ..     598     672 ..     597     674 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.049
                            Fer4_9  33 e.......eaCigCgaCve 44 
                                       e       e C gCg+C +
  gi|336252122|ref|YP_004595229.1| 588 EggfshlvELCNGCGTCRQ 606
                                       1455556677888888865 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.2e-05
                            Fer4_9   2 CtgCgaC.....veaCpagvvvedaaerkarlraase........................eaCigCgaCveaCpkg 49 
                                       C+gCg+C       +Cp+  ++e++ ++++   +                           + CigC+ C   Cp+g
  gi|336252122|ref|YP_004595229.1| 598 CNGCGTCrqtdsDVMCPTYRATEEEIATTRGRAN--LlraaisgdlepeerfserfqeevlDLCIGCKGCQSDCPTG 672
                                       *******665544458777776666655544322..145689999******************************98 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3      0.08        95      29      49 ..     586     606 ..     579     620 .. 0.71
   2 ?   11.9   0.2   0.00015      0.18      35      53 ..     653     671 ..     636     678 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.08
                           Fer4_21  29 daktvlkvvedeCvGCnlCss 49 
                                       d++  + ++ + C GC  C +
  gi|336252122|ref|YP_004595229.1| 586 DEEGGFSHLVELCNGCGTCRQ 606
                                       556666777899999999975 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00015
                           Fer4_21  35 kvvedeCvGCnlCssvCPv 53 
                                       + v d C+GC+ C s CP+
  gi|336252122|ref|YP_004595229.1| 653 EEVLDLCIGCKGCQSDCPT 671
                                       556789***********96 PP

>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.7   4.4e+03      62      81 ..     582     602 ..     575     604 .. 0.77
   2 ?    1.0   0.0      0.42     5e+02      10      35 ..     777     802 ..     771     836 .. 0.79
   3 ?    9.9   0.0   0.00069      0.82      14      84 ..     911     994 ..     901     995 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.7
                               CCG  62 vetaeet.gadaivtacpgCl 81 
                                       ++ ++e+ g   +v  c+gC 
  gi|336252122|ref|YP_004595229.1| 582 AQDFDEEgGFSHLVELCNGCG 602
                                       6677777678999999***97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.42
                               CCG  10 lraaypevrkalkkllealgveleel 35 
                                        ++++pe++ka  ++lea+ v + ++
  gi|336252122|ref|YP_004595229.1| 777 TNYSNPEPGKAAVEVLEAADVYVAVP 802
                                       5788**************99887765 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00069
                               CCG  14 ypevrkalkkllealgveleelekesCCGagggrsgkee...lae...alakrnvetaeetg........adaivta 76 
                                       ++  ++    +l+++g  +++  ++ CCG +g +  + +   l++   +l ++++e++e t            +v++
  gi|336252122|ref|YP_004595229.1| 911 ARGADHHAVGVLRRAGYRVDPV-DSGCCGMAGSFGYEADhydLSRaigDLLREQLEALETTAdgdndaadEPTVVAP 986
                                       4455555667889999999988.***********9998877766633455555555555542345555434456666 PP

                               CCG  77 cpgCllql 84 
                                         +C +q+
  gi|336252122|ref|YP_004595229.1| 987 GTSCRTQI 994
                                       66666665 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 ?   12.1   4.2   0.00025       0.3       2      66 ..     598     671 ..     597     672 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                           Fer4_16   2 CgtCgkCae.....vCPtnaikekkekeiearecisy.....ntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       C +Cg C +     +CPt   +e++ ++ + r++          + +++++e+ +++     ++gC+ Cq  CP 
  gi|336252122|ref|YP_004595229.1| 598 CNGCGTCRQtdsdvMCPTYRATEEEIATTRGRANLLRaaisgDLEPEERFSERFQEEV-LDLCIGCKGCQSDCPT 671
                                       999999997444446***9888884444444443333444445555666666666665.6778***********6 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00026      0.31      50      78 ..     648     676 ..     622     681 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                           Fer4_18  50 keerkekgagdcidcescvkvcPtgidir 78 
                                       +e+ +e+    ci c+ c + cPtg+d+ 
  gi|336252122|ref|YP_004595229.1| 648 SERFQEEVLDLCIGCKGCQSDCPTGVDLA 676
                                       45556666677****************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 ?    5.4   2.4     0.027        32       2      11 ..     596     605 ..     596     616 .. 0.79
   2 ?   11.9   2.5   0.00021      0.25       2      17 .]     657     672 ..     656     672 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.027
                            Fer4_4   2 erCigCgsCv 11 
                                       e C+gCg C+
  gi|336252122|ref|YP_004595229.1| 596 ELCNGCGTCR 605
                                       57*******7 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00021
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       + CigC+ C + CP+g
  gi|336252122|ref|YP_004595229.1| 657 DLCIGCKGCQSDCPTG 672
                                       78************86 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   2.1     0.025        29       7      21 ..     596     615 ..     595     618 .. 0.73
   2 ?   10.7   2.6   0.00038      0.46       7      23 ..     657     673 ..     656     673 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.025
                            Fer4_6   7 dkCigCgdC....vrv.CPe 21 
                                       ++C+gCg C     +v CP+
  gi|336252122|ref|YP_004595229.1| 596 ELCNGCGTCrqtdSDVmCPT 615
                                       79*******66555556665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00038
                            Fer4_6   7 dkCigCgdCvrvCPega 23 
                                       d+CigC  C + CP+g+
  gi|336252122|ref|YP_004595229.1| 657 DLCIGCKGCQSDCPTGV 673
                                       89************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1016 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.69u 0.44s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 6027.90
//
Query:       gi|336252123|ref|YP_004595230.1|  [L=200]
Description: Manganese/iron superoxide dismutase [Halopiger xanaduensis SH-6]
Scores for 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-30  104.1   0.6    8.1e-30  103.1   0.6    1.5  1  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin
    1.2e-28   99.2   0.0    1.8e-28   98.7   0.0    1.3  1  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do


Domain annotation for each model (and alignments):
>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.1   0.6     9e-34   8.1e-30       2      82 .]       4      84 ..       3      84 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 9e-34
                                      ------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCHHHHCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                          Sod_Fe_N  2 yeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekleeakkkleelvlkklekalrnnagghvnHslfwkn 80
                                      +eLp+LpY+ydaLeP is+++l++Hhd+Hh++Yvn+lN+a+e+l+e++++ +  ++ ++ k++++n+ gh +H+lfw+n
  gi|336252123|ref|YP_004595230.1|  4 HELPPLPYDYDALEPSISEQVLTWHHDTHHQGYVNGLNSAEETLAENREEGDYGSTPGALKDVTHNGCGHYLHTLFWEN 82
                                      9****************************************************************************** PP

                                      B- CS
                          Sod_Fe_N 81 ls 82
                                      +s
  gi|336252123|ref|YP_004595230.1| 83 MS 84
                                      96 PP

>> Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.0     2e-32   1.8e-28       1     101 [.      91     190 ..      91     191 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 2e-32
                                       --HHHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTH CS
                          Sod_Fe_C   1 psgelaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYy 76 
                                       p+ge+a++ieedfgs+e +k ef++aa a  + Gwa+Lv+d+  k+L+ + ++++d+   ++a+p+LalDvweh+Yy
  gi|336252123|ref|YP_004595230.1|  91 PEGEVADRIEEDFGSYEGWKGEFQKAAGA--AGGWALLVYDPVaKQLRNLAVDKHDQGALWGAHPILALDVWEHSYY 165
                                       899**********************9998..89********98689******************************* PP

                                       HHHTT-HHHHHHHHGGGBBHHHHHH CS
                          Sod_Fe_C  77 ldyqnkradYieafwnvvnWkevee 101
                                        dy  +r ++i+af++vvnW+ vee
  gi|336252123|ref|YP_004595230.1| 166 YDYGPDRGEFIDAFFDVVNWDSVEE 190
                                       ***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1457.63
//
Query:       gi|336252124|ref|YP_004595231.1|  [L=145]
Description: hypothetical protein Halxa_0713 [Halopiger xanaduensis SH-6]
Scores for 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   15.6   2.2      0.017   15.2   2.2    1.1  1  Podoplanin  Podoplanin


Domain annotation for each model (and alignments):
>> Podoplanin  Podoplanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   2.2   9.4e-07     0.017      48     103 ..      34      91 ..      30     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.4e-07
                                       XXXXXXXXXXXXXX.XXXXXXXXX.XXXX-----GGG-XXXXXXXXXXXXXXXXXXXX CS
                        Podoplanin  48 dnvvttgaseepye.sglttlvpt.stesvtdlrledlptaestvkakeesqstttln 103
                                       d v ttg+ +++    ++ tl +  +tes+++ ++e ++t++stv+ + es+s++t++
  gi|336252124|ref|YP_004595231.1|  34 DGVATTGDLTDHVAeLEMRTLEAEgDTESISEPEIEAESTPDSTVESGSESESASTAS 91 
                                       67889999888876688888877779***************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1131.49
//
Query:       gi|336252125|ref|YP_004595232.1|  [L=154]
Description: Nucleoside diphosphate kinase [Halopiger xanaduensis SH-6]
Scores for 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-53  178.4   0.0    7.2e-53  178.2   0.0    1.0  1  NDK       Nucleoside diphosphate kinase
  ------ inclusion threshold ------
       0.15   12.7   0.1       0.31   11.7   0.1    1.6  1  DUF2285   Uncharacterized conserved protein (DUF2285)


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 !  178.2   0.0     8e-57   7.2e-53       1     134 [.       5     140 ..       5     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 178.2 bits;  conditional E-value: 8e-57
                                       EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEEST CS
                               NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlege 77 
                                       ert+v++KPda +rgl+ge+isrle++glk+va+k+ ++ +e+aeehY eh++kpf+++lv+f+tsgpvv +v+eg+
  gi|336252125|ref|YP_004595232.1|   5 ERTFVMVKPDAFARGLVGEVISRLEDRGLKLVAIKVENMPRERAEEHYGEHEDKPFYDDLVDFITSGPVVPMVWEGQ 81 
                                       89*************************************************************************** PP

                                       THHHHHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHH..HHHHHHHHHSTGGG CS
                               NDK  78 daiekvreliGatnpaeaapgtiRadfgvslgeNlvHgSdsee..saereiklfFkeee 134
                                       da+++vr++iG+t+p ea+pgtiR+d++++lg+N+vH++d+e+  + erei++ F+++e
  gi|336252125|ref|YP_004595232.1|  82 DATRQVRQMIGETDPLEAEPGTIRGDYALDLGRNVVHAADHEDegANEREIAIHFDDDE 140
                                       ****************************************998334789******9987 PP

>> DUF2285  Uncharacterized conserved protein (DUF2285)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.5e-05      0.31      17      72 ..      85     141 ..      72     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.5e-05
                           DUF2285  17 rlarala.grapgplaralaltpqqrrrllhlLqalDarlagaslreiAevlfgaer 72 
                                       r  r++  +++p ++   + + +++ ++ +++ +a+D + +ga  reiA    ++e 
  gi|336252125|ref|YP_004595232.1|  85 RQVRQMIgETDPLEAEPGTIRGDYALDLGRNVVHAADHEDEGANEREIAIHFDDDEL 141
                                       444444436666777777788889999999*******************98766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1210.01
//
Query:       gi|336252126|ref|YP_004595233.1|  [L=111]
Description: 50S ribosomal protein L24e [Halopiger xanaduensis SH-6]
Scores for 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   0.0    3.3e-21   75.3   0.0    1.1  1  Ribosomal_L24e  Ribosomal protein L24e


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 !   75.3   0.0   1.8e-25   3.3e-21       4      61 ..       5      62 ..       2      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 1.8e-25
                                      -B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTT-XXXXX CS
                    Ribosomal_L24e  4 ekCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrnPrklkWTkayRrahkk 61
                                      ++C+++g++i+PG+G+++v+nDg+v++F++sK+ek++k  r+Pr+l+WT   R  ++ 
  gi|336252126|ref|YP_004595233.1|  5 RTCDYTGEEIEPGTGIMYVKNDGTVLHFVDSKAEKNYKLGREPRDLEWTAEGRAGKGP 62
                                      79**************************************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 851.59
//
Query:       gi|336252127|ref|YP_004595234.1|  [L=74]
Description: 30S ribosomal protein S28e [Halopiger xanaduensis SH-6]
Scores for complete 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-28   98.7   0.8    1.5e-28   98.5   0.8    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 !   98.5   0.8   8.6e-33   1.5e-28       4      63 ..      11      70 ..       8      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 8.6e-33
                                      EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT- CS
                    Ribosomal_S28e  4 klAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArr 63
                                      ++AeVi+++g+tG++Ge++qV++++ eg+++grii+Rn+ GPvreGD+L L+Et+rEA  
  gi|336252127|ref|YP_004595234.1| 11 TPAEVIEIVGKTGMHGEAMQVKCRIQEGENQGRIITRNCLGPVREGDVLQLRETAREADS 70
                                      79********************************************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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 0.33s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 496.77
//
Query:       gi|336252128|ref|YP_004595235.1|  [L=120]
Description: 50S ribosomal protein L7Ae [Halopiger xanaduensis SH-6]
Scores for 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   84.5   0.0    3.9e-24   84.2   0.0    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
    1.9e-05   24.5   0.0    2.5e-05   24.1   0.0    1.2  1  PELOTA_1        PELOTA RNA binding domain
  ------ inclusion threshold ------
      0.083   13.4   0.1       0.14   12.7   0.1    1.5  1  eRF1_3          eRF1 domain 3
       0.28   11.5   2.0         11    6.4   0.0    2.1  2  DUF1269         Protein of unknown function (DUF1269)


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 !   84.2   0.0   8.6e-28   3.9e-24       3      91 ..      17     105 ..      15     108 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 8.6e-28
                                       HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSE CS
                    Ribosomal_L7Ae   3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrp 79 
                                       + e+l++a+++g++++G++e+tka+erg+a+lv +Aedv+pee++ +l+ l+ ek++p+v+++ + + G+++g+++ 
  gi|336252128|ref|YP_004595235.1|  17 ALEALEVARDTGRVKKGTNETTKAIERGNAELVYVAEDVSPEEIVMHLPDLADEKGIPVVFIETQDDVGHAAGLEVG 93 
                                       56899************************************************************************ PP

                                       CSEEEEEESTTT CS
                    Ribosomal_L7Ae  80 vsalaikdegds 91 
                                       ++a+ai+d+g++
  gi|336252128|ref|YP_004595235.1|  94 SAAAAIVDAGEA 105
                                       *********987 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   5.5e-09   2.5e-05      17      70 ..      25      80 ..      13      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.5e-09
                          PELOTA_1 17 edinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpd 70
                                      +d+ ++K g  E+T+++ R   e v v+++ +  + + hl  La+ekg+pv+ +++
  gi|336252128|ref|YP_004595235.1| 25 RDTGRVKKGTNETTKAIERGNAELVYVAEDVSpeEIVMHLPDLADEKGIPVVFIET 80
                                      6899*************************888335589*************87654 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     3e-05      0.14      14      54 ..      22      62 ..      12     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                                      HHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHH CS
                            eRF1_3 14 elakdtgkavYGveevlkalemgAvetLLvseelersrdtl 54
                                      e+a+dtg++  G +e+ ka+e g  e + v e++  ++ ++
  gi|336252128|ref|YP_004595235.1| 22 EVARDTGRVKKGTNETTKAIERGNAELVYVAEDVSPEEIVM 62
                                      7899*****************************99887554 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0024        11      42      77 ..      31      66 ..      17      81 .. 0.83
   2 ?    4.6   1.0    0.0085        38      20      53 ..      84     117 ..      71     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0024
                           DUF1269 42 ddflkelgeklkpgtsalfllvekatvdkvlealak 77
                                      ++  +e  +++++g++ l+ ++e++ +++++ +l +
  gi|336252128|ref|YP_004595235.1| 31 KKGTNETTKAIERGNAELVYVAEDVSPEEIVMHLPD 66
                                      556678899*********************988755 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0085
                           DUF1269  20 lGaavGAaaGAlvgalsdvgidddflkelgeklk 53 
                                       +G a+G  +G++++a+ d+g  ++ ++++++k++
  gi|336252128|ref|YP_004595235.1|  84 VGHAAGLEVGSAAAAIVDAGEASGDVEDIADKVE 117
                                       6899****************99999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 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:                        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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 895.81
//
Query:       gi|336252129|ref|YP_004595236.1|  [L=109]
Description: hypothetical protein Halxa_0718 [Halopiger xanaduensis SH-6]
Scores for complete 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  118.8   2.5    1.6e-34  118.6   2.5    1.0  1  YbjQ_1      Putative heavy-metal-binding
  ------ inclusion threshold ------
      0.012   15.9   0.1      0.025   14.9   0.0    1.6  2  DUF4156     Domain of unknown function (DUF4156)
      0.029   14.2   0.1      0.035   13.9   0.1    1.1  1  Pan_kinase  Type III pantothenate kinase


Domain annotation for each model (and alignments):
>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   2.5   2.7e-38   1.6e-34       2     103 ..       5     105 ..       4     106 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 2.7e-38
                            YbjQ_1   2 ivtttesiegkeivevlgivtgetvrsrnvlkdilaglrslvGGelkayeeeleeareeAlerlkeeAeelGAnAvv 78 
                                        +ttt+ +eg+e+ve++g+v+ge+v+++nv++di+ag+r++vGG++++ye+++e+ reeA+++l+++AeelGA+Avv
  gi|336252129|ref|YP_004595236.1|   5 TITTTDGLEGREVVEYCGVVSGEAVIGANVVSDIAAGIRDVVGGRSGSYEKKIETGREEAIADLRADAEELGADAVV 81 
                                       79*************************************************************************** PP

                            YbjQ_1  79 gvrldtseigekgmlevlayGTAVk 103
                                       g  +d++e+ge gml v  +GTAVk
  gi|336252129|ref|YP_004595236.1|  82 GATFDYEEMGE-GMLWVNLSGTAVK 105
                                       *********99.************8 PP

>> DUF4156  Domain of unknown function (DUF4156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.85   5.1e+03      59      66 ..      29      36 ..      25      43 .. 0.80
   2 ?   14.9   0.0   4.2e-06     0.025      46      71 ..      61      86 ..      42     105 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.85
                           DUF4156 59 alGgntiv 66
                                       +G+n++ 
  gi|336252129|ref|YP_004595236.1| 29 VIGANVVS 36
                                      58999985 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.2e-06
                           DUF4156 46 vrgaandLrneAaalGgntivlvtst 71
                                       ++a+ dLr  A++lG++ +v++t  
  gi|336252129|ref|YP_004595236.1| 61 REEAIADLRADAEELGADAVVGATFD 86
                                      46799****************99866 PP

>> Pan_kinase  Type III pantothenate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.8e-06     0.035      54     133 ..      25     104 ..       7     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-06
                                       C.EEEEEEESSCHHHHHHHHHHHHHHSS-EEEES.CSSECTCEE-SSSGGGS-HHHHHHHHHHHHHCTTSEEEEEEE CS
                        Pan_kinase  54 i.eaviissVvpaavaalleallkyfkveplvvrssaaklgltngydnpkelGaDRwvaavaarellpgkpllvvdf 129
                                         eavi ++Vv++++a +++++  + +     ++ ++ +  +    ++ +elGaD +v+a   +e   g+ +l v++
  gi|336252129|ref|YP_004595236.1|  25 SgEAVIGANVVSDIAAGIRDVVGGRSGSYEKKIE-TGREEAIADLRADAEELGADAVVGATFDYEEM-GEGMLWVNL 99 
                                       24789********************887666677.666666666666789***************77.777888876 PP

                                       .SSEE CS
                        Pan_kinase 130 .GTAt 133
                                        GTA+
  gi|336252129|ref|YP_004595236.1| 100 sGTAV 104
                                       69998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 823.38
//
Query:       gi|336252130|ref|YP_004595237.1|  [L=765]
Description: hypothetical protein Halxa_0719 [Halopiger xanaduensis SH-6]
Scores for 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-50  170.7   0.0    4.5e-50  169.9   0.0    1.4  1  Helicase_RecD    Helicase
    3.9e-44  150.8   0.0    1.4e-27   96.6   0.0    2.2  2  GNAT_acetyltr_2  GNAT acetyltransferase 2
    3.4e-28   97.4   0.0    8.1e-26   89.8   0.0    2.9  2  DUF1726          Domain of unknown function (DUF1726)
    2.4e-08   34.0   2.1    8.4e-08   32.2   1.2    2.2  2  AAA_30           AAA domain
     0.0018   18.7   0.0      0.005   17.2   0.0    1.8  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0054   16.7   0.0      0.012   15.6   0.0    1.6  1  Acetyltransf_13  ESCO1/2 acetyl-transferase
  ------ inclusion threshold ------
      0.038   13.9   0.0      0.074   13.0   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.9   0.0   1.8e-53   4.5e-50       1     177 []     232     403 ..     232     403 .. 0.91

  Alignments for each domain:
  == domain 1  score: 169.9 bits;  conditional E-value: 1.8e-53
                     Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglkeeekkkkaekaelrvrkqrie 77 
                                       vl AdRGRGKS+a+Gla+ a++a+g  ++lvtap+ +n++++fe++++ +e+l+  + + +++++    ++ + r++
  gi|336252130|ref|YP_004595237.1| 232 VLEADRGRGKSSAAGLAAGAFAADGL-DVLVTAPNARNAAEVFERARELCERLEDVDVTAADSRR--LETTTGGRVR 305
                                       799**************999999975.***********************999866544443333..2334499*** PP

                     Helicase_RecD  78 yiapdellklkeqadllvvDEAAaiplpllkkllekfkrvvlatTvhGYEGtGrgfslkflkqlkkekkrelrelel 154
                                       +++p e++++ e+ad++vvDEAAa+p++ l+++l + +rv++atT+hGYEG+Grgfs++f ++l ++++ ++++ +l
  gi|336252130|ref|YP_004595237.1| 306 FHEPAEAVDRLETADIVVVDEAAALPVSRLEAFL-AADRVAFATTIHGYEGAGRGFSVRFRDRLAESDH-DVTDRTL 380
                                       **********************************.999**************************98877.******* PP

                     Helicase_RecD 155 eepiRyaegdplEkwlndlLlLd 177
                                        epiRya+gdp+E w +++LlLd
  gi|336252130|ref|YP_004595237.1| 381 VEPIRYAAGDPVEVWAFRALLLD 403
                                       *********************97 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.0   5.3e-31   1.4e-27       3     124 ..     441     554 ..     439     557 .. 0.93
   2 !   54.6   0.0   3.8e-18   9.7e-15     172     225 ..     550     603 ..     546     605 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 5.3e-31
                   GNAT_acetyltr_2   3 vallvssHYknsPnDLqllsDaPahklfvLlapkkekkklpevlcvvqvalEGkiskesvknslsrgkrasGdlipw 79 
                                       ++llv +HY+++PnDL+ l DaP+ +  +L+++        +v++v  +a EG+++  + + ++++g r +G+++p+
  gi|336252130|ref|YP_004595237.1| 441 FGLLVLAHYRTEPNDLARLLDAPNLEARALVHEG-------HVVSVALLAREGNLDPATRTMMYEGG-RVRGNMLPD 509
                                       789*****************************55.......6**************99777776666.********* PP

                   GNAT_acetyltr_2  80 tlsqqfqdeefaslsGaRivRiAvhpelqkmGYGsralellekyy 124
                                       +l++q +de++++ +G+R+vRiA+h+e++++G Gsr le +++++
  gi|336252130|ref|YP_004595237.1| 510 VLTSQLRDESAGEPAGLRVVRIATHHEARSRGLGSRLLECVREEF 554
                                       ***************************************998876 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 3.8e-18
                   GNAT_acetyltr_2 172 lseekpekldylgvsfGltseLlkFWkragfspvylrqtaneltGEhsaimlrs 225
                                       ++ee +++ld+lg++fG ts Ll+FW+ +g+++v+l++t+n+++GE+sa+ml +
  gi|336252130|ref|YP_004595237.1| 550 VREEFADELDWLGTGFGATSGLLEFWRANGYRTVHLSTTRNDASGEYSALMLAP 603
                                       5678899********************************************987 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.0   3.2e-29   8.1e-26       3      93 .]      70     161 ..      68     161 .. 0.97
   2 ?    4.3   0.0     0.015        37       6      33 ..     435     461 ..     432     463 .. 0.84

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 3.2e-29
                           DUF1726   3 esekvLGqtydllvldlfealtPnalgrlvetVrGGGliilllppleelkqlytdfhkklvveplt.eevkkrfnkr 78 
                                       ++ ++LG+t ++++ld++e l+Pnalg++v++V+GGGl++ll+pple +++ + +f ++l+v+p++ +ev++rf++r
  gi|336252130|ref|YP_004595237.1|  70 NAGELLGTTREVVILDAHEGLRPNALGKVVGAVDGGGLLVLLTPPLEAWSDRRGAFDESLAVPPFQlSEVTGRFRRR 146
                                       56789************************************************************************ PP

                           DUF1726  79 firklkehegilivd 93 
                                       ++++l++h+gi ivd
  gi|336252130|ref|YP_004595237.1| 147 LVETLRAHRGISIVD 161
                                       ************998 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.015
                           DUF1726   6 kvLGqtydllvldlfealtPnalgrlve 33 
                                        +L +t++llvl  +   +Pn+l+rl +
  gi|336252130|ref|YP_004595237.1| 435 TLLRETFGLLVLA-HYRTEPNDLARLLD 461
                                       67889******95.6789*******987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   1.2   3.3e-11   8.4e-08      15     111 ..     225     341 ..     218     353 .. 0.86
   2 ?   -0.8   0.0      0.41     1e+03      46      64 ..     591     613 ..     567     642 .. 0.66

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 3.3e-11
                            AAA_30  15 tsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa..........eelgieastiakllkrlk 81 
                                       + +++ +vl++  G GK+ a + ++ a++a+g +v++ Ap+++ A+++           e+++++a+   +l ++++
  gi|336252130|ref|YP_004595237.1| 225 GADRQAVVLEADRGRGKSSAAGLAAGAFAADGLDVLVTAPNARNAAEVFerarelcerlEDVDVTAADSRRLETTTG 301
                                       5677899***********************************99988774666666555588899999999998888 PP

                            AAA_30  82 ..........grarlepgtllivDEagmvdtkqlaallka 111
                                                 +  rle++++++vDEa+ +  + l+a+l+a
  gi|336252130|ref|YP_004595237.1| 302 grvrfhepaeAVDRLETADIVVVDEAAALPVSRLEAFLAA 341
                                       99*******9668999*************99999999865 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.41
                            AAA_30  46 g....grviglAptgkaAkvLae 64 
                                            ++ ++lApt+ a ++L +
  gi|336252130|ref|YP_004595237.1| 591 DasgeYSALMLAPTSDAGRDLHD 613
                                       03334667777777777777764 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     2e-06     0.005      26      75 ..     527     581 ..     504     582 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2e-06
                                       CTEEEEE-GGGTTSSHHHHHHHH.......TTSEEEEEEEEE.....THHHHHHHHHHTTEE CS
                    Acetyltransf_7  26 eitrlaVdpeyrgkGiGraLlea.......aekgiileqlel.....naekaikfYeklGFe 75 
                                          r+a++ e+r +G+G++Lle+       +     l   +l     +++  ++f++ +G++
  gi|336252130|ref|YP_004595237.1| 527 RVVRIATHHEARSRGLGSRLLECvreefadE-----LD--WLgtgfgATSGLLEFWRANGYR 581
                                       3456******************733222210.....11..2321211111335588888886 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.7e-06     0.012       4      34 ..     525     555 ..     522     560 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.7e-06
                   Acetyltransf_13   4 lcGisriWvssshRrkgiAtkLldaarenfi 34 
                                        + + ri +++++R++g+ ++Ll+++re+f 
  gi|336252130|ref|YP_004595237.1| 525 GLRVVRIATHHEARSRGLGSRLLECVREEFA 555
                                       566889**********************996 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.9e-05     0.074      53     116 ..     527     590 ..     512     594 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
                   Acetyltransf_10  53 hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnaspyavpfYeklGFkavgeeqeen 116
                                       ++ +++ ++e+r++G+g++Lle v+ee+  d++    +   a++   +f +  G+++v   +++n
  gi|336252130|ref|YP_004595237.1| 527 RVVRIATHHEARSRGLGSRLLECVREEF-ADELDWlGTGFGATSGLLEFWRANGYRTVHLSTTRN 590
                                       67899**********************7.455555599999999***********9997776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (765 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.67u 0.72s 00:00:01.39 Elapsed: 00:00:00.61
# Mc/sec: 3793.06
//
Query:       gi|336252131|ref|YP_004595238.1|  [L=62]
Description: hypothetical protein Halxa_0720 [Halopiger xanaduensis SH-6]
Scores for 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   11.5   0.5       0.18   11.5   0.5    1.8  2  GBP_PSP   Paralytic/GBP/PSP peptide


Domain annotation for each model (and alignments):
>> GBP_PSP  Paralytic/GBP/PSP peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.21   3.8e+03      13      15 ..       5       7 ..       4      10 .. 0.66
   2 ?   11.5   0.5   9.9e-06      0.18       6      18 ..      22      32 ..      19      34 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.21
                                      E-T CS
                           GBP_PSP 13 RTa 15
                                      RT+
  gi|336252131|ref|YP_004595238.1|  5 RTP 7 
                                      898 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.9e-06
                                      ---TTEEE-TTS- CS
                           GBP_PSP  6 GCaTGyKRTaDGR 18
                                      GC+  + RTaDGR
  gi|336252131|ref|YP_004595238.1| 22 GCS--FERTADGR 32
                                      787..9******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 474.77
//
Query:       gi|336252132|ref|YP_004595239.1|  [L=245]
Description: short-chain dehydrogenase/reductase SDR [Halopiger xanaduensis SH-6]
Scores for 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-32  112.3   0.0    2.5e-32  111.9   0.0    1.1  1  adh_short       short chain dehydrogenase
    9.4e-24   84.3   0.2    1.2e-23   83.9   0.2    1.1  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    3.3e-07   30.4   0.2    6.2e-07   29.5   0.2    1.4  1  KR              KR domain
    3.1e-06   26.9   0.2    8.3e-06   25.4   0.2    1.7  1  Epimerase       NAD dependent epimerase/dehydratase family
    6.3e-06   26.2   0.4    1.1e-05   25.4   0.4    1.6  1  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.074   12.1   0.1       0.11   11.5   0.1    1.2  1  RmlD_sub_bind   RmlD substrate binding domain
       0.17   11.7   0.0       0.29   10.9   0.0    1.3  1  DFP             DNA / pantothenate metabolism flavoprotein


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 !  111.9   0.0   9.9e-36   2.5e-32       3     188 ..       5     193 ..       3     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 9.9e-36
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkld 79 
                                       ++++GassGIG a+a+ela eG+++ +++r+ e+++++ +el  +    +++++D+ d e++++ + + ++ +  +d
  gi|336252132|ref|YP_004595239.1|   5 AIIVGASSGIGAALARELADEGYQIGLAARRTERMRQIGSELPTK---SYVATMDLLDPEDAREGFFELAEAMPAVD 78 
                                       89*****************************************85...89*************************** PP

                                       EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH......HCTTEEEEEEEEGGGTSB-TTBHHHH CS
                         adh_short  80 vLvnNAGitgsgpfselseeewervievNltgvflltravlpaml......kqssGrIvnvsSvagkvpvagvaaYs 150
                                       ++v  AG++ ++p  +l+ ++ +r+i+vN+ g   ++ a+l+++       ++  G+ v +sSva++ +  g+ aY 
  gi|336252132|ref|YP_004595239.1|  79 LVVISAGVAAMNP--DLEWDAERRTIDVNVRGFTAIATAALEYFEnypdhaSEADGHLVGISSVAAHLGTGGTQAYN 153
                                       ********65555..56666668*********************9999999999*********************** PP

                                       HHHHHHHHHHHHHHHHHGGGT..EEEEEEEESSBSSHHHH CS
                         adh_short 151 AsKaavagltrslakelaptg..irvnavaPGlvdTdmak 188
                                       AsKa v  + + l++  + +   ++++++ PG+vdTd+ +
  gi|336252132|ref|YP_004595239.1| 154 ASKAYVSRYLEGLRHRQQHRDadVTITTIEPGFVDTDLSM 193
                                       *************9876666666**************976 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 !   83.9   0.2   4.6e-27   1.2e-23       1     180 [.       9     193 ..       9     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 4.6e-27
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE..EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae..vlecDVtdeeqvealveevvekfgklDilvn 75 
                                       Ga sgIG+a+A++la+eG+++ l+ ++ e+   ++++ +el+++  v  +D  d+e+ ++ + e++e +  +D +v 
  gi|336252132|ref|YP_004595239.1|   9 GASSGIGAALARELADEGYQIGLAARRTER---MRQIGSELPTKsyVATMDLLDPEDAREGFFELAEAMPAVDLVVI 82 
                                       899*********************999998...99999999977656****************************** PP

                                       -----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC........CEEEEEEEGGGTSBSTTTTHHHHH CS
                      adh_short_C2  76 nagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg........gsivnlssvgaervvpnynaygaa 144
                                       +ag+a    +p  +++++  +r++dvn+++++++a aal+++++         g +v +ssv+a+ ++ +++ay+a+
  gi|336252132|ref|YP_004595239.1|  83 SAGVAAM--NP--DLEWDAERRTIDVNVRGFTAIATAALEYFENYpdhaseadGHLVGISSVAAHLGTGGTQAYNAS 155
                                       ******9..66..9999999********************8877666778889************************ PP

                                       HHHHHHHHHHHHHHHGG..GTEEEEEEEE--BHCTGGG CS
                      adh_short_C2 145 KaalealtrylAvelgp..kgiRvNavspgpikTlaas 180
                                       Ka +      l +   +    +++ ++ pg+++T+++ 
  gi|336252132|ref|YP_004595239.1| 156 KAYVSRYLEGLRHRQQHrdADVTITTIEPGFVDTDLSM 193
                                       *****999999765444227899***********9854 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.2   2.4e-10   6.2e-07       4     167 ..       6     171 ..       4     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 2.4e-10
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       +i+G+  g+G +lar la++g  ++ l +R+   +e++++  +el    ++  v+ +D+ d+++ ++ + e+ + +p
  gi|336252132|ref|YP_004595239.1|   6 IIVGASSGIGAALARELADEGY-QIGLAARR---TERMRQIGSEL---PTKSYVATMDLLDPEDAREGFFELAEAMP 75 
                                       79*******************7.69999999...34444444444...557778999******************** PP

                                       ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT..........S--SEEEEEEEHHHHH--TT-H CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled..........esldffvlfSSiagllgsagqa 147
                                       ++  v+ +Agv++ ++  e   ++ ++ +   v+G   + ++  +          e   ++v +SS+a+ lg+ g  
  gi|336252132|ref|YP_004595239.1|  76 AVDLVVISAGVAAMNPDLE--WDAERRTIDVNVRGFTAIATAALEyfenypdhasEADGHLVGISSVAAHLGTGGTQ 150
                                       ************9998555..5555788999999999888776666666777774444589**************** PP

                                       HHHHHHHHHHHHHHH.HHHHH CS
                                KR 148 nYaaaNaflDalaey.rrsqg 167
                                       +Y a  a++  + e  r++q+
  gi|336252132|ref|YP_004595239.1| 151 AYNASKAYVSRYLEGlRHRQQ 171
                                       *****9999877653133333 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.2   3.2e-09   8.3e-06       2     105 ..       6     119 ..       5     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.2e-09
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HH.......HHHHHHHHH.T-S CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl....elveldltdrs.......alerlfkee.qpd 66 
                                       +++Ga+  iG+al+++l+++gy++   +r++++ ++    +l     + ++dl+d++       +l+++     ++d
  gi|336252132|ref|YP_004595239.1|   6 IIVGASSGIGAALARELADEGYQIGLAARRTERMRQI-GSELptksYVATMDLLDPEdaregffELAEA---MpAVD 78 
                                       79*********************98888885554433.3333678899999***999533333333333...24789 PP

                                       EEEE--S..---HHHHHHSHHHHHHHHTHHHHHHHHHHHHH CS
                         Epimerase  67 avihlAa..vggvaassedpadfieknlqgtlnlleaarka 105
                                        v+  A+    +++ +++   ++i+ n++g + ++ aa ++
  gi|336252132|ref|YP_004595239.1|  79 LVVISAGvaAMNPDLEWDAERRTIDVNVRGFTAIATAALEY 119
                                       999999854456788999999**************999865 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 !   25.4   0.4   4.4e-09   1.1e-05       1      78 [.       9     113 ..       9     203 .. 0.64

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 4.4e-09
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCT..TTCEEEE--TT-CC.......HHHHHHTT-SEEEES- CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleae..eglevvegdvtdve.......dlaealkgadaVvsal 68 
                                       GA+ ++G +l++el+++ g+++ + +R++e++ ++ +e   +  v ++d++d+e       +laea+  +d Vv+++
  gi|336252132|ref|YP_004595239.1|   9 GASSGIGAALARELADE-GYQIGLAARRTERMRQIGSElpTKSYVATMDLLDPEdaregffELAEAMPAVDLVVISA 84 
                                       9****************.5**************99865545667888999999845555556899999***766555 PP

                                       --TCC........HHHH.............H CS
                    NAD_binding_10  69 ggggk........deeg.............a 78 
                                       g  +         +                a
  gi|336252132|ref|YP_004595239.1|  85 GVAAMnpdlewdaE--RrtidvnvrgftaiA 113
                                       43333244444321..133444444444441 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 ?   11.5   0.1   4.5e-05      0.11       4      91 ..       6     118 ..       3     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                                       EEESTTSHHHHHHHHHCTTTSEEEEEE-TT..................T--TTSHHHHHHHH...HHH--S...EEE CS
                     RmlD_sub_bind   4 lvtGanGqlGseLakqlaeeglevlaltre..................eldltdaeavaell...keakpd...vvv 56 
                                       +++Ga+  +G +La++la eg+++    r+                  ++dl d+e ++e +   +ea p+   vv+
  gi|336252132|ref|YP_004595239.1|   6 IIVGASSGIGAALARELADEGYQIGLAARRtermrqigselptksyvaTMDLLDPEDAREGFfelAEAMPAvdlVVI 82 
                                       689******************998655555699*************************9987555455554454455 PP

                                       E--.----HHHHHHSHHHHHHHHTHHHHHHHHHHHH CS
                     RmlD_sub_bind  57 naA.AytavDkaEseeeaayavnaeavealAeaaaa 91 
                                       +a+ A  + D   + e++   vn+++  a+A aa +
  gi|336252132|ref|YP_004595239.1|  83 SAGvAAMNPDLEWDAERRTIDVNVRGFTAIATAALE 118
                                       55423444555555688999************9965 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.29      26      97 ..      10      91 ..       6     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                      ----HHHHHHHHHHHHTT-EEEEEE-S-S........S--...-TT-EEEE--SHHHHHHHHHHHHTT-SEEEE---S- CS
                               DFP 26 rSSGkmGyalAeaaaarGaeVtlvsgpvs........let...pegvevvkvesaeemleaveealkeadivimaAAva 93
                                       SSG  G+alA+++a++G ++ l +  ++        l+t    +++++++ e+a+e   ++ ea+++ d+v+ +A va
  gi|336252132|ref|YP_004595239.1| 10 ASSG-IGAALARELADEGYQIGLAARRTErmrqigseLPTksyVATMDLLDPEDAREGFFELAEAMPAVDLVVISAGVA 87
                                      6888.6******************999753444433333322222356677788888888999999999*********9 PP

                                      -EEE CS
                               DFP 94 Dyrp 97
                                        +p
  gi|336252132|ref|YP_004595239.1| 88 AMNP 91
                                      7766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1728.36
//
Query:       gi|336252133|ref|YP_004595240.1|  [L=161]
Description: hypothetical protein Halxa_0722 [Halopiger xanaduensis SH-6]
Scores for 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-25   88.9  24.9    3.5e-25   88.9  24.9    1.5  1  DUF456    Protein of unknown function (DUF456)
  ------ inclusion threshold ------
        7.1    6.5   9.9       0.17   11.7   2.2    2.3  2  DUF2976   Protein of unknown function (DUF2976)


Domain annotation for each model (and alignments):
>> DUF456  Protein of unknown function (DUF456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9  24.9   3.9e-29   3.5e-25       2     139 .]      22     158 ..      21     158 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 3.9e-29
                            DUF456   2 vPvLPGtllilaglllyalltgfaelgwlflavllvlallglvldylapalgakraGaskrgligaivGaivGffll 78 
                                       +P++PG  l+lag++ly++++gf++ g +++a+l++l +++lv++++ + ++a++ Gas++++++a+v +i+ +++ 
  gi|336252133|ref|YP_004595240.1|  22 LPLVPGGALSLAGVFLYWWHSGFTDPGAITVAALTILGAIALVVELFGGSIAARAGGASWATTAAAAVVGIALMIVT 98 
                                       79************************************************************************999 PP

                            DUF456  79 pplGlllgpflgaflgEllrarkdlreAlkaalgalvGfllgtlvklvlallmlvlflvav 139
                                       +plGll+g f+++f+ E+ r+r ++++++++a+++++G+l++t+v+++l+  +l+ fl+av
  gi|336252133|ref|YP_004595240.1|  99 GPLGLLAGLFGTVFVLEFARER-TFDHSARSAIYTTIGVLASTAVEALLTASVLFGFLIAV 158
                                       9****************99999.**********************************9985 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.0      0.31   2.7e+03      67      76 ..       5      14 ..       1      22 [. 0.53
   2 ?   11.7   2.2   1.9e-05      0.17      31      78 ..      48      98 ..      29     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.31
                           DUF2976 67 tlvvGvvllv 76
                                      + vv+v llv
  gi|336252133|ref|YP_004595240.1|  5 ITVVAVALLV 14
                                      3444444443 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.9e-05
                           DUF2976 31 lgLvlaavaflaVakaalkkfnei...segkaewgkfgltlvvGvvllvvv 78
                                      +++ +aa+ +l  +  +++ f      + g a+w+  ++++vvG+ l++v+
  gi|336252133|ref|YP_004595240.1| 48 GAITVAALTILGAIALVVELFGGSiaaRAGGASWATTAAAAVVGIALMIVT 98
                                      67888999999999999999976445599******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1093.92
//
Query:       gi|336252134|ref|YP_004595241.1|  [L=298]
Description: PEGA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-26   91.0  16.8    1.1e-15   57.7   3.0    3.0  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    3.8e-16   58.8   0.9    7.4e-07   29.1   0.2    2.3  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
    5.4e-13   48.6   0.3    0.00012   22.0   0.1    3.4  3  PEGA             PEGA domain
    9.1e-06   25.8   0.0       0.16   12.1   0.0    2.2  2  DUF2012          Protein of unknown function (DUF2012)
    2.9e-05   24.0   0.0     0.0032   17.5   0.0    2.4  2  CooC_C           CS1-pili formation C-terminal
    5.1e-05   23.5  11.0     0.0057   16.9   1.5    4.0  3  Big_6            Bacterial Ig domain
    0.00085   19.5   2.1     0.0022   18.2   0.6    2.2  2  SdrD_B           SdrD B-like domain
     0.0024   17.6   5.0      0.023   14.5   0.7    2.6  2  fn3_3            Polysaccharide lyase family 4, domain II
     0.0038   17.2   2.2       0.58   10.2   0.6    2.5  2  phage_tail_N     Prophage tail fibre N-terminal
      0.004   17.0   6.9       0.54   10.2   0.1    3.3  3  DUF1416          Protein of unknown function (DUF1416)
     0.0063   16.8   6.4      0.028   14.7   0.7    2.5  2  SpaA             Prealbumin-like fold domain
  ------ inclusion threshold ------
      0.021   15.1   2.7       0.55   10.5   0.3    2.4  2  MetallophosN     N terminal of Calcineurin-like phosphoestera
      0.025   15.0   6.8       0.37   11.2   0.6    2.7  2  DUF3869          Domain of unknown function (DUF3869)
      0.026   14.4   0.1          1    9.3   0.0    2.8  2  DUF1533          Protein of unknown function (DUF1533)
      0.028   14.5   1.5       0.34   11.0   0.0    3.0  4  BiPBP_C          Penicillin-Binding Protein C-terminus Family
      0.029   14.9   4.7       0.69   10.5   0.2    3.2  2  Cadherin-like    Cadherin-like beta sandwich 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 !   57.7   3.0   9.6e-19   1.1e-15       2      82 .]      39     114 ..      38     114 .. 0.94
   2 ?   -0.8   0.0       1.7     2e+03      48      81 ..     173     206 ..     166     207 .. 0.67
   3 !   39.2   4.0   5.4e-13   6.1e-10       3      81 ..     225     295 ..     223     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 9.6e-19
                   CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttld 78 
                                       i G++td  g p+a atVt++  d+   +++ttd+dG++ ++ l+pgty  tv+a+Gy+ at+  v+++a+++tt +
  gi|336252134|ref|YP_004595241.1|  39 IDGTITD-FGVPVADATVTLA--DGIDAHTATTDEDGSYEID-LEPGTYYHTVTADGYRGATS-VVDVAADDPTTAN 110
                                       7899998.9************..67789*************7.*******************6.7************ PP

                   CarboxypepD_reg  79 itLe 82 
                                       + Le
  gi|336252134|ref|YP_004595241.1| 111 VSLE 114
                                       *996 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                   CarboxypepD_reg  48 gtysvtv.sapGyatatreevtltagqtttlditL 81 
                                       g  +v+v  a+Gy+    +   ++a++t+   ++L
  gi|336252134|ref|YP_004595241.1| 173 GWWEVRVtNAEGYDDGYGK-AYVAADETAVAVVEL 206
                                       5666777567888888864.667777777666655 PP

  == domain 3  score: 39.2 bits;  conditional E-value: 5.4e-13
                   CarboxypepD_reg   3 sGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttldi 79 
                                       +G+V+  + +pi  atV++        ++++t +dG+f ++ l+ g+++vtv apGy++a+  +v+++  ++tt ++
  gi|336252134|ref|YP_004595241.1| 225 TGTVVGNDEEPIGDATVRAD------GTRVRTTEDGTFEVE-LEHGRHTVTVDAPGYESAAA-TVEVRFARETTGTV 293
                                       8*******************......7899*********97.*******************8.59999888887776 PP

                   CarboxypepD_reg  80 tL 81 
                                        L
  gi|336252134|ref|YP_004595241.1| 294 SL 295
                                       66 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.2e-09   1.3e-06       1      77 [.      39     114 ..      39     117 .. 0.84
   2 !   29.1   0.2   6.6e-10   7.4e-07       2      67 ..     225     286 ..     224     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.2e-09
                   CarbopepD_reg_2   1 isGtVvdketkeplpgatVyvkgt.k.kgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnil 75 
                                       i Gt++d +   p++ atV++ +      ++Tde+G++e++ l++g+y  +v++ Gy+ ++  v+v+ +  ++ n++
  gi|336252134|ref|YP_004595241.1|  39 IDGTITDFG--VPVADATVTLADGiDaHTATTDEDGSYEID-LEPGTYYHTVTADGYRGATSVVDVAADDPTTANVS 112
                                       689999975..6*********76424256679********5.************************99887777776 PP

                   CarbopepD_reg_2  76 lk 77 
                                       l+
  gi|336252134|ref|YP_004595241.1| 113 LE 114
                                       65 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 6.6e-10
                   CarbopepD_reg_2   2 sGtVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvske 67 
                                       +GtVv ++ +ep+  atV   gt++   T e+G+Fe++ l++g++t++v + Gy+++  +v+v   
  gi|336252134|ref|YP_004595241.1| 225 TGTVVGND-EEPIGDATVRADGTRVR--TTEDGTFEVE-LEHGRHTVTVDAPGYESAAATVEVRFA 286
                                       7****876.59********9999876..5699*****6.******************999999733 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.9e-06    0.0066      28      68 ..      75     115 ..      73     116 .. 0.94
   2 !    6.5   0.0     0.007       7.8      31      67 ..     170     207 ..     165     210 .. 0.84
   3 !   22.0   0.1     1e-07   0.00012      28      60 ..     257     290 ..     238     296 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.9e-06
                              PEGA  28 tlsleaGnyslrvekeGYedlektvtvtagetvklnltLek 68 
                                       ++ le+G+y  +v ++GY+ ++  v+v a++ +++n+ Le+
  gi|336252134|ref|YP_004595241.1|  75 EIDLEPGTYYHTVTADGYRGATSVVDVAADDPTTANVSLER 115
                                       6789*********************************9997 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.007
                              PEGA  31 leaGnyslrv.ekeGYedlektvtvtagetvklnltLe 67 
                                       +++G  ++rv ++eGY d + + +v a+et  + ++L+
  gi|336252134|ref|YP_004595241.1| 170 VAEGWWEVRVtNAEGYDDGYGKAYVAADETAVAVVELR 207
                                       7788899999558****************988877776 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 1e-07
                              PEGA  28 tlsleaGnyslrvekeGYedlektvtvt.agetv 60 
                                       +++le G+++++v ++GYe + +tv+v+ a et+
  gi|336252134|ref|YP_004595241.1| 257 EVELEHGRHTVTVDAPGYESAAATVEVRfARETT 290
                                       6889************************766665 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00014      0.16       8      78 ..      51     121 ..      47     130 .. 0.87
   2 !   11.5   0.0   0.00021      0.24      23      61 ..     247     284 ..     230     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                           DUF2012   8 antrvlLdsgqqrkfkalvrrDGsFifrdlpegsYlLevespeyvFepyrVdvk..dkgkakasklrivetae 78 
                                       a+++v+L  g     +a + +DGs+ + dl++g+Y+  v + +y  ++  Vdv+  d+ +a+ s  r + ++e
  gi|336252134|ref|YP_004595241.1|  51 ADATVTLADGID-AHTATTDEDGSYEI-DLEPGTYYHTVTADGYRGATSVVDVAadDPTTANVSLERAWGPGE 121
                                       7899***99988.778999*******9.9*************************8888888888777777665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00021
                           DUF2012  23 kalvrrDGsFifrdlpegsYlLevespeyvFepyrVdvk 61 
                                       ++ +++DG+F + +l+ g++++ v++p+y+ +   V+v+
  gi|336252134|ref|YP_004595241.1| 247 RVRTTEDGTFEV-ELEHGRHTVTVDAPGYESAAATVEVR 284
                                       6899*******9.5*****************99999998 PP

>> CooC_C  CS1-pili formation C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.042        47      40      68 ..      63      91 ..      34     105 .. 0.81
   2 !   17.5   0.0   2.9e-06    0.0032      19      69 ..     224     274 ..     220     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.042
                            CooC_C 40 agvavteedGvFtlevdakapsltvengd 68
                                      a +a t+edG + ++++ +  + tv++++
  gi|336252134|ref|YP_004595241.1| 63 AHTATTDEDGSYEIDLEPGTYYHTVTADG 91
                                      45678899*********999999999886 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.9e-06
                            CooC_C  19 viGrlvdedgqplanakilnhagvavteedGvFtlevdakapsltvengdt 69 
                                       + G +v +d +p+ +a++  ++ + +t edG F +e++++  + tv + + 
  gi|336252134|ref|YP_004595241.1| 224 FTGTVVGNDEEPIGDATVRADGTRVRTTEDGTFEVELEHGRHTVTVDAPGY 274
                                       5799999***********************************999987654 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.5   5.1e-06    0.0057       2      56 ..      28      82 ..      27     105 .. 0.78
   2 ?   -0.2   0.0       1.1   1.3e+03      32      56 ..     159     183 ..     137     202 .. 0.76
   3 !    9.3   1.0    0.0012       1.4      30      81 ..     242     283 ..     225     285 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.1e-06
                             Big_6  2 PeaptdlavsedgttltGkaeagatVtvkdadgtvlgtgtadadGeFsvtlepaq 56
                                      P+a    +  + + t+t  + + a  tv+ adg    t+t d+dG+++++lep  
  gi|336252134|ref|YP_004595241.1| 28 PAAADSATAGHIDGTITDFGVPVADATVTLADGIDAHTATTDEDGSYEIDLEPGT 82
                                      6666666667777789999999999999***********************9843 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                             Big_6  32 adgtvlgtgtadadGeFsvtlepaq 56 
                                       +dg+    g a a+G ++v +++a+
  gi|336252134|ref|YP_004595241.1| 159 PDGERWNAGFAVAEGWWEVRVTNAE 183
                                       5677777788888888888887765 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0012
                             Big_6  30 kdadgtvlgtgtadadGeFsvtlepaqangetlsvvatDaagntSdaatvta 81 
                                       + adgt +     ++dG+F+v+le         + v +Da g +S+aatv +
  gi|336252134|ref|YP_004595241.1| 242 R-ADGTRVR---TTEDGTFEVELEHG------RHTVTVDAPGYESAAATVEV 283
                                       2.3333333...37899999999753......355667**********9987 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.6     2e-06    0.0022      22      86 ..      48     110 ..      37     118 .. 0.77
   2 ?   -0.3   0.0       1.1   1.2e+03      43      67 ..     249     272 ..     227     287 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-06
                            SdrD_B  22 kgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagy..tvtakkaGsddaldSd 86 
                                         +++ tVtL  a+g  ++t tTd++G+Y+ + l+pG+Y+ ++ta  gy  +++  + ++dd + ++
  gi|336252134|ref|YP_004595241.1|  48 VPVADATVTL--ADGIDAHTATTDEDGSYEID-LEPGTYYHTVTAD-GYrgATSVVDVAADDPTTAN 110
                                       5789999**9..88888899**********97.******9988764.44346666777777766555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                            SdrD_B  43 tTdasGkYkFtnltpGeYkVeftap 67 
                                        T ++G+++ + l++G+ +V++ ap
  gi|336252134|ref|YP_004595241.1| 249 RTTEDGTFEVE-LEHGRHTVTVDAP 272
                                       44566666653.7777777777666 PP

>> fn3_3  Polysaccharide lyase family 4, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.7     2e-05     0.023      28      74 ..      65     108 ..      48     109 .. 0.91
   2 ?    4.5   0.2     0.026        29      30      73 ..     249     290 ..     222     292 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
                             fn3_3  28 wteadssgsftipnVkpGtYrltvYadglfgdykqdsvtVtagkttt 74 
                                       ++++d++gs++i+   pGtY  tv adg+ g++  + v V+a   tt
  gi|336252134|ref|YP_004595241.1|  65 TATTDEDGSYEID-LEPGTYYHTVTADGYRGAT--SVVDVAADDPTT 108
                                       5899********6.8******************..*****9987776 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.026
                             fn3_3  30 eadssgsftipnVkpGtYrltvYadglfgdykqdsvtVt.agktt 73 
                                       +++++g+f+++    G++++tv a+g++ +   ++v+V  a +tt
  gi|336252134|ref|YP_004595241.1| 249 RTTEDGTFEVE-LEHGRHTVTVDAPGYESAA--ATVEVRfARETT 290
                                       67788888885.799*************999..*****9666665 PP

>> phage_tail_N  Prophage tail fibre N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.6   0.00052      0.58      41      71 ..      66      96 ..      36     113 .. 0.75
   2 !    6.1   0.0    0.0095        11      40      73 ..     247     280 ..     237     294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00052
                      phage_tail_N 41 enpdeaGrysldvetGkysvilkvdgfpesh 71
                                       ++de+G y +d e G y  ++  dg+    
  gi|336252134|ref|YP_004595241.1| 66 ATTDEDGSYEIDLEPGTYYHTVTADGYRGAT 96
                                      579***********************97543 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0095
                      phage_tail_N  40 senpdeaGrysldvetGkysvilkvdgfpeshaG 73 
                                        + + e+G + ++ e+G+++v++   g++   a 
  gi|336252134|ref|YP_004595241.1| 247 RVRTTEDGTFEVELEHGRHTVTVDAPGYESAAAT 280
                                       57899*******************9999876554 PP

>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00048      0.54      11      74 ..      28      89 ..      20     114 .. 0.74
   2 !    6.3   0.1    0.0077       8.7      59      90 ..     166     201 ..     145     207 .. 0.65
   3 ?    2.9   0.2     0.091     1e+02      23      70 ..     225     267 ..     222     293 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00048
                           DUF1416 11 pagvdvekeaviqGkvtrdgepvggayvRLLdssgeFtaevvtsaeGefrFfaapGeWtvRala 74
                                      pa++d ++   i G++t+ g pv+ a v L d+ +  ta  +t ++G++     pG++   + a
  gi|336252134|ref|YP_004595241.1| 28 PAAADSATAGHIDGTITDFGVPVADATVTLADGIDAHTA--TTDEDGSYEIDLEPGTYYHTVTA 89
                                      67788889999***************************9..58899999999999987544433 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0077
                           DUF1416  59 frFfaapGeWtvRalarkgn....gdaeveaesggv 90 
                                         F  a+G W vR+ +++g     g+a v a+++ v
  gi|336252134|ref|YP_004595241.1| 166 AGFAVAEGWWEVRVTNAEGYddgyGKAYVAADETAV 201
                                       557889*********999872111344455554444 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.091
                           DUF1416  23 qGkvtr.dgepvggayvRLLdssgeFtaevvtsaeGefrFfaapGeWtv 70 
                                       +G+v+  d+ep+g a vR  d+     + v t+++G+f      G+ tv
  gi|336252134|ref|YP_004595241.1| 225 TGTVVGnDEEPIGDATVRA-DG-----TRVRTTEDGTFEVELEHGRHTV 267
                                       7888887999999999994.22.....3466666666666666665555 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.7   2.5e-05     0.028      30      68 ..      58      93 ..      28     107 .. 0.73
   2 ?    4.9   0.6      0.03        34      35      76 ..     236     283 ..     165     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-05
                                      TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEE CS
                              SpaA 30 ktgtevttlttdenGkatfegLplGtYllvEtkaPegYv 68
                                      ++g ++ t+ttde+G  +++ L++GtY+ +   + +gY+
  gi|336252134|ref|YP_004595241.1| 58 ADGIDAHTATTDEDGSYEID-LEPGTYYHT--VTADGYR 93
                                      3455679************9.******964..5566665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.03
                                       E.........SEEE-BTTSEEEEEEEESEEEEEEEEE-STTEEE-SSEEEE CS
                              SpaA  35 v.........ttlttdenGkatfegLplGtYllvEtkaPegYvldkepfev 76 
                                       +         t++ t e+G++++e L+ G  +++ + a  gY+  ++++ev
  gi|336252134|ref|YP_004595241.1| 236 IgdatvradgTRVRTTEDGTFEVE-LEHGRHTVT-VDA-PGYESAAATVEV 283
                                       0333333333778899*******9.999998886.334.477776666666 PP

>> MetallophosN  N terminal of Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00049      0.55       1      34 [.      41      78 ..      41      93 .. 0.75
   2 ?    4.4   0.1      0.04        44       1      49 [.     226     274 ..     226     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                      MetallophosN  1 GkVtskgkgvag..VvVsDGvn..vtkTdakGrYeLks 34
                                      G++t  g +va+  V+  DG++  +++Td++G Ye++ 
  gi|336252134|ref|YP_004595241.1| 41 GTITDFGVPVADatVTLADGIDahTATTDEDGSYEIDL 78
                                      677888888876225566**9632689********984 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.04
                      MetallophosN   1 GkVt.skgkgvagVvVs.DGvnvtkTdakGrYeLksdkkakfVyistPagy 49 
                                       G+V  ++++++ + +V  DG+  ++T ++G++e + ++  + V +  P gy
  gi|336252134|ref|YP_004595241.1| 226 GTVVgNDEEPIGDATVRaDGT-RVRTTEDGTFEVELEHGRHTVTVDAP-GY 274
                                       667768888998888852565.5677899****998888888988888.44 PP

>> DUF3869  Domain of unknown function (DUF3869)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.9     0.012        14      23      83 ..      39     103 ..      25     113 .. 0.53
   2 ?   11.2   0.6   0.00033      0.37      25      83 ..     226     287 ..     223     297 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                                       EEEEE..EETTTTEE-CGCCEEC..........CCCCSSEEEECCSCT-EEEEEEECTETTEEEEEEEE-- CS
                           DUF3869  23 isgtvldieattgtdvtdkatis..........tssgtatfkggaelaakavkisatGYegiktatVsvaa 83 
                                       i gt+  +++  g+ v+  at++          t     +++ + e + +  +++a+GY g++   V vaa
  gi|336252134|ref|YP_004595241.1|  39 IDGTI--TDF--GVPVA-DATVTladgidahtaTTDEDGSYEIDLEPGTYYHTVTADGYRGAT-SVVDVAA 103
                                       55555..332..33333.333442233221111111122333333356666678888*****9.7777765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00033
                                       EEE..EETTTTEE-C...GCCEECCCCCSSEEEECCSCT-EEEEEEECTETTEE.EEEEEE-- CS
                           DUF3869  25 gtvldieattgtdvt...dkatistssgtatfkggaelaakavkisatGYegik.tatVsvaa 83 
                                       gtv+  +++   d+t   d + + t +   tf+ + e + + v++ a GYe +  t++V  a+
  gi|336252134|ref|YP_004595241.1| 226 GTVVGNDEEPIGDATvraDGTRVRTTE-DGTFEVELEHGRHTVTVDAPGYESAAaTVEVRFAR 287
                                       666666666666777564455565555.689999999999*************9555555555 PP

>> DUF1533  Protein of unknown function (DUF1533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.19   2.1e+02      41      57 ..      80      96 ..      39      99 .. 0.81
   2 ?    9.3   0.0    0.0009         1      40      59 ..     261     280 ..     258     281 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.19
                           DUF1533 41 aGentIvIkakGYeDvt 57
                                       G++  ++ a+GY+ +t
  gi|336252134|ref|YP_004595241.1| 80 PGTYYHTVTADGYRGAT 96
                                      56666688888888776 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0009
                           DUF1533  40 kaGentIvIkakGYeDvtit 59 
                                       + G +t++++a GYe ++ t
  gi|336252134|ref|YP_004595241.1| 261 EHGRHTVTVDAPGYESAAAT 280
                                       679************88766 PP

>> BiPBP_C  Penicillin-Binding Protein C-terminus Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.2   1.4e+03      56      78 ..      66      88 ..      56     101 .. 0.72
   2 ?   -3.1   0.0       7.7   8.6e+03      64      77 ..     115     126 ..     103     132 .. 0.59
   3 ?    0.2   0.1      0.72   8.1e+02      54      83 ..     154     185 ..     152     188 .. 0.78
   4 ?   11.0   0.0    0.0003      0.34      45      84 ..     238     275 ..     215     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                           BiPBP_C 56 aetkrgrelawqpepGrhrLtvv 78
                                      a+t+ + + ++++epG++  tv+
  gi|336252134|ref|YP_004595241.1| 66 ATTDEDGSYEIDLEPGTYYHTVT 88
                                      47888888999999998765553 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.7
                           BiPBP_C  64 lawqpepGrhrLtv 77 
                                        aw   pG+ +L+v
  gi|336252134|ref|YP_004595241.1| 115 RAWG--PGEGELEV 126
                                       3444..55555544 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.72
                           BiPBP_C  54 plaetkrgrelawqp..epGrhrLtvvDaaGr 83 
                                       pl+++ +g+++   +   +G ++++v++a+G 
  gi|336252134|ref|YP_004595241.1| 154 PLGSVPDGERWNAGFavAEGWWEVRVTNAEGY 185
                                       6667777777776666799**********995 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.0003
                           BiPBP_C  45 plrWlldgeplaetkrgrelawqpepGrhrLtvvDaaGrv 84 
                                         + + dg+ +  t+ + ++++++e Grh++tv Da G  
  gi|336252134|ref|YP_004595241.1| 238 DATVRADGTRV-RTTEDGTFEVELEHGRHTVTV-DAPGYE 275
                                       567899*****.888999**************9.988865 PP

>> Cadherin-like  Cadherin-like beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.6     0.036        41      30      64 ..      75     116 ..      33     153 .. 0.78
   2 ?   10.5   0.2   0.00062      0.69      39      72 ..     238     271 ..     227     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.036
                     Cadherin-like  30 titataedsvatvtvngvaveeg.......stetkdvsLneG 64 
                                        i+ ++  +++tvt +g ++ ++       +++t++vsL+ +
  gi|336252134|ref|YP_004595241.1|  75 EIDLEPGTYYHTVTADGYRGATSvvdvaadDPTTANVSLERA 116
                                       455555577889999999998888999988899999999743 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00062
                     Cadherin-like  39 vatvtvngvaveegstetkdvsLneGrnkieikv 72 
                                       +atv+ +g++v++ +++t++v+L+ Gr ++++  
  gi|336252134|ref|YP_004595241.1| 238 DATVRADGTRVRTTEDGTFEVELEHGRHTVTVDA 271
                                       69************************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2201.49
//
Query:       gi|336252135|ref|YP_004595242.1|  [L=270]
Description: blue (type 1) copper domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   35.5   1.0    2.3e-08   34.4   0.0    2.0  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    2.3e-06   27.2   0.3    3.3e-06   26.7   0.3    1.3  1  TAT_signal    TAT (twin-arginine translocation) pathway signa


Domain annotation for each model (and alignments):
>> 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 ?   -1.2   0.3      0.33   2.9e+03      28      57 ..      63      94 ..      55     128 .. 0.51
   2 !   34.4   0.0   2.6e-12   2.3e-08      24      99 .]     144     214 ..     133     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.33
                                      EEEEESSSSBEEEEET..TSSTTTGGGTTSCT CS
                       Copper-bind 28 tfvnlavmgHNvvldk..dgvpagvdkdkvka 57
                                      t++  +  g N   ++  d+++++ ++++++ 
  gi|336252135|ref|YP_004595242.1| 63 TTTDETETGDNETETEpgDEAENETEDNETDN 94
                                      44444555555444444433333333333333 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 2.6e-12
                                       TEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE..SSEEEEEEETTTTTTTSEEEEEE CS
                       Copper-bind  24 gekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfd..eagtYkffCsPHaaagMkgkvtv 98 
                                       +  +t+ n ++  HN+v+  d+ ++ vd+ ++++     +  +Ge+ ++++d  +++  +++C+PH++  M+g +++
  gi|336252135|ref|YP_004595242.1| 144 SYDITWENADGAQHNLVIWDDS-DEIVDDYETDM-----VSEEGETATLEIDevTSEMAQYVCEPHSST-MVGDIEL 213
                                       55789*************9988.56677766666.....5556*********765666*********99.****998 PP

                                       E CS
                       Copper-bind  99 e 99 
                                       e
  gi|336252135|ref|YP_004595242.1| 214 E 214
                                       5 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.3   3.7e-10   3.3e-06       2      25 ..      23      46 ..      22      47 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.7e-10
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      ++RR+ LK +++a+  +al+gc++
  gi|336252135|ref|YP_004595242.1| 23 ITRRTVLKITGVAGVTTALAGCGG 46
                                      89********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.44
# Mc/sec: 1859.98
//
Query:       gi|336252136|ref|YP_004595243.1|  [L=575]
Description: glutamyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-61  205.6   0.0    1.1e-60  205.2   0.0    1.2  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    1.5e-19   70.5   0.0    4.9e-19   68.9   0.0    1.9  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 !  205.2   0.0   1.2e-64   1.1e-60       1     312 [.     107     415 ..     107     417 .. 0.93

  Alignments for each domain:
  == domain 1  score: 205.2 bits;  conditional E-value: 1.2e-64
                                       S-EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--H..HHHHHHHHHHHHTT---SSEEEEGG CS
                      tRNA-synt_1c   1 kVrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdpereke..eaeesiledlkwlgikwdekptyqs 75 
                                       +Vr R aP+P+G  H+Gha+   +   +  +++G f++R++DTdpe + +  +a ++iledl++lg+++d  ++++s
  gi|336252136|ref|YP_004595243.1| 107 EVRMRVAPNPNGPWHVGHARMPAVIGTYKERYDGWFCVRFDDTDPETKRPdlDAYDAILEDLEYLGFEPD-DVYRAS 182
                                       69******************************************986665226899*************5.5***** PP

                                       GGHHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBT CS
                      tRNA-synt_1c  76 drfdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkide 152
                                       dr++++++ a eLi+   AY c c+ +e  e++++    ++++rd+  e   + f e m +g++e++++v+R+k d 
  gi|336252136|ref|YP_004595243.1| 183 DRLETYYDHARELIELDGAYTCSCSGDEFSELKNS--GEACPHRDKDAETVKEEF-EAMVDGEYESGEMVLRVKTDI 256
                                       *********************************99..89999*************.9*******************9 PP

                                       TSS.GGGSSTEEEEEEESGGGSBTT.TBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S. CS
                      tRNA-synt_1c 153 ess.vefrDlvrgriklepqeihdl.vivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglev 227
                                       e++  ++rD v+ r+  +p   h++   + ++  P+ df   idD+l +ith++r+ + +d+ +++  +++++g++ 
  gi|336252136|ref|YP_004595243.1| 257 EHKnPALRDWVAFRMIDTP---HPReEASEYRCWPMLDFQSGIDDHLIGITHIIRGIDLQDSAKRQQFVYDYFGWDY 330
                                       9999**********99999...6651678999********************************************9 PP

                                       -EEE.EEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHH CS
                      tRNA-synt_1c 228 ppfi.heylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresks 303
                                       p+++ +  + l + + k+S   +s l++e ++++wdd+r ++++ lrr+G+  e++ + + + + ++s+ ++  ++s
  gi|336252136|ref|YP_004595243.1| 331 PEVVhWGHVQLDAYDVKMSTSTISELIEEGELDGWDDPRAPTIKSLRRRGIRGEAIVDAMVELGTSTSD-VDLAMSS 406
                                       776515678899999**************************************************9999.9999999 PP

                                       HHHHHHHHH CS
                      tRNA-synt_1c 304 leafdrkkL 312
                                       + a +r+ +
  gi|336252136|ref|YP_004595243.1| 407 IYANNRDLI 415
                                       988887765 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 !   68.9   0.0   5.4e-23   4.9e-19       2     174 .]     420     561 ..     419     561 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 5.4e-23
                    tRNA-synt_1c_C   2 pRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereD.akrlkpgeevrLkelynikveev 77 
                                       +R++ V++  +v + +   + + e++ plhp+++++g r++p+++++++e eD  ++ +++++v Lk+l+++++++ 
  gi|336252136|ref|YP_004595243.1| 420 DRRFLVREGNQVPLAG---DPPAEANPPLHPDHEDRGVREIPVGDSVLLEPEDlPDDDAEDRRVWLKGLGCFRFDDG 493
                                       6999999999999994...4589******************************55777889*************887 PP

                    tRNA-synt_1c_C  78 ekdesgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepa 153
                                       +           ley +++++  r +   +ihWv+aee+v++                 + + d++    +g aepa
  gi|336252136|ref|YP_004595243.1| 494 V-----------LEYTDDDIDVVRDEGVdVIHWVPAEESVPV----------------RMRTMDGDV---RGRAEPA 540
                                       4...........889999**999999999*************................899999993...8****** PP

                    tRNA-synt_1c_C 154 lanlkkgdivQfeRiGyfrvd 174
                                       + +l+++++vQfeR G++r+d
  gi|336252136|ref|YP_004595243.1| 541 VGDLEADEMVQFERVGFVRID 561
                                       *******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3878.60
//
Query:       gi|336252137|ref|YP_004595244.1|  [L=161]
Description: TspO and MBR like protein [Halopiger xanaduensis SH-6]
Scores for 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-40  136.0  17.4    9.1e-40  135.8  17.4    1.0  1  TspO_MBR         TspO/MBR family
     0.0035   16.7   2.9     0.0041   16.4   2.9    1.1  1  CcmF_C           Cytochrome c-type biogenesis protein CcmF C-
  ------ inclusion threshold ------
        4.3    7.8   0.0        4.3    7.8   0.0    3.1  3  FeoB_associated  FeoB-associated Cys-rich membrane protein


Domain annotation for each model (and alignments):
>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8  17.4   1.5e-43   9.1e-40       2     134 ..      19     158 ..      15     159 .. 0.95

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 1.5e-43
                                       HHHHHHHHHHHHHHHHHCCHHHHHHS---TTS--HHHHTTHHHHHHHHHHHHHHHHHHH..........HHHHHHHH CS
                          TspO_MBR   2 alalpllvgllgglftkseeewykslrkPpwaPpdwvfppvWtvlyilmgvaaylvwka..........lalyavql 68 
                                       +++ + ++g+l ++f  s+++w   +++P+++Pp+++fp+vWt+l++lmg+a+y++w++          la++++q+
  gi|336252137|ref|YP_004595244.1|  19 FVLGVNALGALPSVFIGSDTSW---IDRPWFYPPSILFPIVWTLLFTLMGLALYRIWRRgpsrqavrvaLAAFGIQF 92 
                                       4566677888888888888888...8*******************************************99****** PP

                                       HHHHTSGGCTTTTTSGGGHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHCHHHHHHHHHHHHHHHHH CS
                          TspO_MBR  69 vlnllwsplffglkspvlalvdivallglvvalilafskvdklaallllpyllWllfatylnasiw 134
                                       +lnl+w+p+ffgl++p l++++i+al++++v +i+af +vd+laa+ll+pyl+W++fa++ln++i+
  gi|336252137|ref|YP_004595244.1|  93 ALNLAWTPAFFGLQRPDLGIAVIAALWIAIVGTIVAFDRVDRLAAALLVPYLGWVSFAAVLNYAIY 158
                                       ***************************************************************997 PP

>> CcmF_C  Cytochrome c-type biogenesis protein CcmF C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.9   6.9e-07    0.0041      78     160 ..      51     134 ..      30     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.9e-07
                            CcmF_C  78 avfvplmvplllllgvGpllrWkraklaellkrllvalvlalvlall.lalllgelkvlaalglalavwvvlaalae 153
                                        +f ++ ++l+ l+g++ +  W+r+  +++++  l+a+ + ++l+l+ +++++g  +    +++++a+w+++  ++ 
  gi|336252137|ref|YP_004595244.1|  51 ILFPIVWTLLFTLMGLALYRIWRRGPSRQAVRVALAAFGIQFALNLAwTPAFFGLQRPDLGIAVIAALWIAIVGTIV 127
                                       456667778889******************99999999999999999434455555688999999*****9999999 PP

                            CcmF_C 154 laerlra 160
                                        ++r+++
  gi|336252137|ref|YP_004595244.1| 128 AFDRVDR 134
                                       9999843 PP

>> 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 ?   -2.2   0.3      0.99   5.9e+03       4      10 ..      14      20 ..      12      26 .. 0.51
   2 ?    7.8   0.0   0.00071       4.3       4      23 ..      55      74 ..      51      79 .. 0.91
   3 ?   -2.7   4.0       1.4   8.5e+03       8      18 ..     113     123 ..     110     129 .. 0.47

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.99
                   FeoB_associated  4 IVgliia 10
                                      IV+l+ +
  gi|336252137|ref|YP_004595244.1| 14 IVALAFV 20
                                      3333332 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00071
                   FeoB_associated  4 IVgliiaaavafvirrlikk 23
                                      IV  +++ +++++++r++++
  gi|336252137|ref|YP_004595244.1| 55 IVWTLLFTLMGLALYRIWRR 74
                                      99****************97 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.4
                   FeoB_associated   8 iiaaavafvir 18 
                                       +++aa++ +i+
  gi|336252137|ref|YP_004595244.1| 113 AVIAALWIAIV 123
                                       44444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); 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:                         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: 00:00:00.41
# Mc/sec: 1183.23
//
Query:       gi|336252138|ref|YP_004595245.1|  [L=365]
Description: polyprenyl synthetase [Halopiger xanaduensis SH-6]
Scores for 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-65  218.3   0.1    1.1e-64  218.0   0.1    1.1  1  polyprenyl_synt  Polyprenyl synthetase


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 !  218.0   0.1   6.2e-69   1.1e-64       2     229 ..      36     292 ..      35     317 .. 0.87

  Alignments for each domain:
  == domain 1  score: 218.0 bits;  conditional E-value: 6.2e-69
                                       HHHHHHHHHHHHSSS--HHHHHHHHHHHHHSCG.......H.......................HHHHHHHHHHHHH CS
                   polyprenyl_synt   2 elleealeylveagGKrlRpllvllaaealkee.......e.......................eelekaavlawiv 48 
                                       e l+ea++yl++agGKrlRp+++l a e l +        +                       +   ++ ++a+ v
  gi|336252138|ref|YP_004595245.1|  36 ERLYEASRYLLDAGGKRLRPTVLLTAGESLVDAepltadyRefptlygageidgvsssdgadgpD-AIDLMDAAVSV 111
                                       57999**************************3334666550566666777777777888887754.455899***** PP

                                       HHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHHHHHHHHHHHHHHHHHHHHH...STTHHHHHHHHHHHHHHHHH CS
                   polyprenyl_synt  49 ellhaasLvhDDimDdsetRRGqpcahrlvGnklAindgdfllarafellaklf...ekslellelfsevllqtveG 122
                                       e++++++L+hDDimDd+++RRG p++hr+++ ++Ai++gd l+++afe++ ++    e+ +e+l+++++++++++eG
  gi|336252138|ref|YP_004595245.1| 112 EVIQSFTLIHDDIMDDDDLRRGVPAVHREYDLETAILAGDTLYSKAFEIMLETGaapERAVEALDILATTCTKICEG 188
                                       ***************************************************998886777***************** PP

                                       HHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS- CS
                   polyprenyl_synt 123 qlldleeekdddlskfsleeyleivkyKTaylfalpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgd 199
                                       q ld+  e+++d++    +eyle+v++KTa+l+a+++ l a+l ga+de+++al+ +gl +G aFQiqDD+lDl+  
  gi|336252138|ref|YP_004595245.1| 189 QSLDVTFEERTDVT---PDEYLEMVEQKTAVLYAASACLPAVLLGADDETIDALYGYGLDIGRAFQIQDDVLDLTVP 262
                                       *****999999999...************************************************************ PP

                                       HHHHSS-TSHHHHTT---HHHHHHHHCT-H CS
                   polyprenyl_synt 200 pevlgKpagtDiqegkctlpilkalelasp 229
                                       +e+lgK+ g+D+ e+k tl++++a e+  +
  gi|336252138|ref|YP_004595245.1| 263 SEKLGKQRGSDLVENKQTLITVHAREQGVD 292
                                       ************************995443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2699.46
//
Query:       gi|336252139|ref|YP_004595246.1|  [L=450]
Description: RNA-metabolising metallo-beta-lactamase [Halopiger xanaduensis SH-6]
Scores for 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-09   35.4   2.8      3e-07   30.2   0.2    2.6  3  Lactamase_B_2  Beta-lactamase superfamily domain
    3.1e-07   30.6   1.7      1e-06   28.9   1.7    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
      2e-05   24.5   0.2    0.00079   19.3   0.0    2.7  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity


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 ?   -2.7   0.0       0.6   3.6e+03     138     167 ..       6      35 ..       4      52 .. 0.75
   2 !   30.2   0.2     5e-11     3e-07      30     114 ..      73     155 ..      58     195 .. 0.83
   3 !    4.9   0.1    0.0027        16     147     200 ..     362     413 ..     323     414 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.6
                                       EEESS-S---HHHHHHHCT-SEEEEE-S-S CS
                     Lactamase_B_2 138 yyigDtgyipeeigerlggadllllditay 167
                                       + ig+ +++  ++ +  +g d++++d+++ 
  gi|336252139|ref|YP_004595246.1|   6 ATIGGYEEVGRQMTAVRAGDDVVIFDMGLN 35 
                                       567788888888888888899999999875 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 5e-11
                                       SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEE.CSTTEEE CS
                     Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfel.gdgglei 105
                                       +++a++ th+H DH+  +  l+++++  +p++a++ +++ +++++  +++    + ++ ++d+ge++++ ++g++e+
  gi|336252139|ref|YP_004595246.1|  73 DVQAIVPTHGHLDHIGAISKLAHRYN--APVVATPFTIELVKQQIEGEQKFGV-ENDLIKMDAGETMSIgDSGQVEL 146
                                       79*************99999999655..8***************988888777.99*************54456888 PP

                                       EEEEE-EE- CS
                     Lactamase_B_2 106 tatparhks 114
                                       +++ + h+ 
  gi|336252139|ref|YP_004595246.1| 147 EFVNVTHSI 155
                                       888888875 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0027
                                       -HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 147 peeigerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                       p   g+r++  +ll +++ +  dd      gHl +e+  e++++l+++ +++ H
  gi|336252139|ref|YP_004595246.1| 362 PTNEGQRYQAEKLLGMQGARIYDDIH--VSGHLCQEGHYEMLDALQPQHVIPAH 413
                                       55667888888888888776666553..68**********************99 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   1.7   1.7e-10     1e-06       9      84 ..      19     113 ..      12     181 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.7e-10
                                       EEEEETTCEEEES--SCHHHHHHHH...................HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTT CS
                       Lactamase_B   9 yliegdggviLiDtGtsteaaraal...................elaalglkpkdvdavilTHlHlDHiGglgglve 66 
                                       + ++ +++v+++D G+  ++ ++ +                   + +       dv a++ TH+HlDHiG+  +l++
  gi|336252139|ref|YP_004595246.1|  19 TAVRAGDDVVIFDMGLNLSQVLIHDnvetermhsldlidmgaipDDRIMSDLEGDVQAIVPTHGHLDHIGAISKLAH 95 
                                       5566666666666666666666655666666666666666665555555666789********************** PP

                                       HHCCEETCCEHHHHCCHC CS
                       Lactamase_B  67 atdvpvgavaeeapalfm 84 
                                       ++++pv+a + + +  + 
  gi|336252139|ref|YP_004595246.1|  96 RYNAPVVATPFTIELVKQ 113
                                       ******987766665555 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 ?    1.9   0.0     0.035   2.1e+02      34      54 ..      77      96 ..      72     123 .. 0.84
   2 !   19.3   0.0   1.3e-07   0.00079       9      51 ..     384     426 ..     380     433 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.035
                             RMMBL 34 vilvHGeeeatsalarllkee 54
                                      +++ HG+ +++ a  +l+   
  gi|336252139|ref|YP_004595246.1| 77 IVPTHGHLDHIGAISKLA-HR 96
                                      99**********999998.44 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.3e-07
                             RMMBL   9 eeidfSgHadknellelirklkprnvilvHGeeeatsalarll 51 
                                       ++i++SgH  ++++ e++  l+p++vi+ H +    s++ +l+
  gi|336252139|ref|YP_004595246.1| 384 DDIHVSGHLCQEGHYEMLDALQPQHVIPAHQDLSGFSSYVNLC 426
                                       5799**************************6666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); 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:                         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 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3193.88
//
Query:       gi|336252140|ref|YP_004595247.1|  [L=251]
Description: 3-oxoacyl-(acyl-carrier-protein) reductase [Halopiger xanaduensis SH-6]
Scores for 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-69  233.2   0.8    3.4e-69  233.0   0.8    1.0  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    1.7e-57  194.1   0.3      2e-57  193.8   0.3    1.1  1  adh_short      short chain dehydrogenase
    3.7e-12   46.5   0.4    5.1e-12   46.1   0.4    1.2  1  KR             KR domain
     0.0036   17.1   0.1     0.0085   15.9   0.1    1.5  1  HTH_Tnp_Tc3_1  Tc3 transposase
  ------ inclusion threshold ------
      0.013   15.0   0.2        0.1   12.1   0.2    2.0  1  Epimerase      NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> 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 !  233.0   0.8   9.6e-73   3.4e-69       4     233 ..      16     248 ..      11     249 .. 0.97

  Alignments for each domain:
  == domain 1  score: 233.0 bits;  conditional E-value: 9.6e-73
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                       sgIG+++A ++ae+Ga+vv++dl+ ++ + +v+++++++g ++ +e+DV+d+e+ +a+v+++v+++g+lD+++nnag
  gi|336252140|ref|YP_004595247.1|  16 SGIGQETALEFAERGANVVVADLDVDGgEGTVDSIEDAGGDAIfVETDVADPESAAAMVDAAVDEYGSLDCAFNNAG 92 
                                       8*************************************999955********************************* PP

                                       --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC...CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalplmkeg...gsivnlssvgaervvpnynaygaaKaalealt 152
                                       i  + ++p+ e   e++ +++dvnl ++f+++ka l+ mk++   g+ivn ss+ ++++++  +ay+aaK+++ +lt
  gi|336252140|ref|YP_004595247.1|  93 IGGE-RAPVDEYAPEDWSQVIDVNLVGVFNCMKAELERMKDQesgGAIVNNSSILGKVGFATSSAYSAAKHGVLGLT 168
                                       ****.**********************************998899******************************** PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEE CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvv 229
                                       +++A e g+ g+R+N+v+pg+i+T++ ++   +de ++++e ++ ++rlgtpeeva+a+++L+sdeas++tG+ + v
  gi|336252140|ref|YP_004595247.1| 169 KSAALENGETGVRINSVCPGFIETPLIEESL-SDEERAQIEGMHAMNRLGTPEEVAAAVVWLCSDEASFVTGEGFGV 244
                                       **************************88776.68889**************************************** PP

                                       STTG CS
                      adh_short_C2 230 DgGl 233
                                        gG+
  gi|336252140|ref|YP_004595247.1| 245 EGGY 248
                                       ***8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.8   0.3   5.7e-61     2e-57       2     193 ..       8     201 ..       7     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 193.8 bits;  conditional E-value: 5.7e-61
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                       +++vtG++sGIG+++a e+a++Ga+vvv+d   +  e ++++++++g +a+++++Dv+d e++ a+v++av+++g+l
  gi|336252140|ref|YP_004595247.1|   8 TAVVTGGGSGIGQETALEFAERGANVVVADLDVDGGEGTVDSIEDAGGDAIFVETDVADPESAAAMVDAAVDEYGSL 84 
                                       79*************************************************************************** PP

                                       SEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                         adh_short  79 dvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                       d+  nNAGi  +++p+ e+  e+w +vi+vNl+gvf++++a l+ m+ ++s+G+Ivn sS+ gkv++a  +aYsA+K
  gi|336252140|ref|YP_004595247.1|  85 DCAFNNAGIgGERAPVDEYAPEDWSQVIDVNLVGVFNCMKAELERMKdQESGGAIVNNSSILGKVGFATSSAYSAAK 161
                                       *********98999*********************************777899************************ PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmakelrek 193
                                       ++v glt+s+a e  +tg+r+n+v+PG+++T++ +e+ ++
  gi|336252140|ref|YP_004595247.1| 162 HGVLGLTKSAALENGETGVRINSVCPGFIETPLIEESLSD 201
                                       ********************************99887666 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.4   1.4e-15   5.1e-12       1     154 [.       7     162 ..       7     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1.4e-15
                                       SEEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                                KR   1 gtylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeika 77 
                                       +t ++tGG  g+G+e+a   ae+ga+ +v    +    +  + +++++e+ g +  +v+ Dv+d+++ +a+++++ +
  gi|336252140|ref|YP_004595247.1|   7 ATAVVTGGGSGIGQETALEFAERGANVVVAD-LD---VDGGEGTVDSIEDAGGDAIFVETDVADPESAAAMVDAAVD 79 
                                       5789********************9866653.33...3455669********************************* PP

                                       HSS---EEEE------.---TTT--HHHHHHHHTTTTHHHHH.....HHHHTTTS--SEEEEEEEHHHHH--TT-HH CS
                                KR  78 eeppikGvihaAgvlr.dklleemtaedleqvlapKvkGawn.....LhelledesldffvlfSSiagllgsagqan 148
                                       e +++   ++ Ag+    ++++e   ed+ qv+   + G+ n     L+++  +es   +v  SSi g +g a+ ++
  gi|336252140|ref|YP_004595247.1|  80 EYGSLDCAFNNAGIGGeRAPVDEYAPEDWSQVIDVNLVGVFNcmkaeLERMKDQESGGAIVNNSSILGKVGFATSSA 156
                                       **************873789*******************98832222455555589999****************** PP

                                       HHHHHH CS
                                KR 149 YaaaNa 154
                                       Y+aa +
  gi|336252140|ref|YP_004595247.1| 157 YSAAKH 162
                                       ***975 PP

>> HTH_Tnp_Tc3_1  Tc3 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.4e-06    0.0085       4      20 ..     198     214 ..     197     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-06
                                       ---HHHHHHHHHHHHTT CS
                     HTH_Tnp_Tc3_1   4 aLSDtEraillvmklln 20 
                                       +LSD Era++++m+ +n
  gi|336252140|ref|YP_004595247.1| 198 SLSDEERAQIEGMHAMN 214
                                       8*************987 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   2.8e-05       0.1       2     102 ..      10     126 ..       9     187 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.8e-05
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HH....HHHHHHHHH.T-S CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrs....alerlfkee.qpd 66 
                                       +VtG+   iG+ ++ +++e+g +v++ d + ++++   +  +        +ve d+ d++     ++++++e+   d
  gi|336252140|ref|YP_004595247.1|  10 VVTGGGSGIGQETALEFAERGANVVVADLDVDGGEGTVDS-IedaggdaIFVETDVADPEsaaaMVDAAVDEYgSLD 85 
                                       8********************9988888776655543332.2466*************9976666788888889999 PP

                                       EEEE--S---HHHHH.....HSHHHHHHHHTHHHHHHHHHH CS
                         Epimerase  67 avihlAavggvaass.....edpadfieknlqgtlnlleaa 102
                                       + ++ A++gg +a +     ed +++i+ nl+g+ n ++a 
  gi|336252140|ref|YP_004595247.1|  86 CAFNNAGIGGERAPVdeyapEDWSQVIDVNLVGVFNCMKAE 126
                                       99999998887665411111233455666666666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1932.63
//
Query:       gi|336252141|ref|YP_004595248.1|  [L=251]
Description: aspartate/glutamate/uridylate kinase [Halopiger xanaduensis SH-6]
Scores for 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-36  126.8   4.6    1.3e-36  126.4   4.6    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 !  126.4   4.6   7.1e-41   1.3e-36       2     227 ..       1     219 [.       1     222 [. 0.91

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 7.1e-41
                                       EEEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHT...TEEEEEE--HHHHHHHHHHTCCCCCHHHC....E. CS
                         AA_kinase   2 rvVvKlGGssltdkee......aslrrlaeqiaalkesg...nklvvVhGggsftdgllalksglssgelaaglrst 69 
                                       ++V+KlGGs++tdke+      ++l r+a+ i+a+  +g   ++lv+VhGggsf+++ +++ +g++    +      
  gi|336252141|ref|YP_004595248.1|   1 MIVLKLGGSAITDKERpetldgDALGRAADAISAA-LDGgdaEDLVIVHGGGSFGHHNASE-HGVTTAAGT------ 69 
                                       59*********************************.444599*******************.***999987...... PP

                                       .HHHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESE CS
                         AA_kinase  70 leeagevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgf 146
                                        ++++ +  + a+ +l++ ++++ll+  ++av+++++++  ++a+           + + +ie++l++g+vpvl+g+
  gi|336252141|ref|YP_004595248.1|  70 RDAEAVADIHGAMKTLNQFVLQRLLERDVNAVPVHPFSTARRDADG-------ALALPTGQIETMLAEGFVPVLHGD 139
                                       6888999999*********************************999.......99999******************9 PP

                                       EEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEE.EHHHCHH....CSSS.TTTH CS
                         AA_kinase 147 igldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpei.svdeaee....saselatgG 218
                                        ++    + +++s+D + a+lA  l+Ad++ +++ V+GV+d++      a+ ++ i s++++e+    s+++++tgG
  gi|336252141|ref|YP_004595248.1| 140 LVAHAGAGATVVSGDELVAALARDLEADRVGLCSTVPGVLDDED-----AV-IDCItSFEDVEAvlgaSDATDVTGG 210
                                       966666669*******************************9964.....43.444436777777779********** PP

                                       HHHCHHHHH CS
                         AA_kinase 219 mkvkhpaal 227
                                       m  k++  l
  gi|336252141|ref|YP_004595248.1| 211 MAGKVRTLL 219
                                       ****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1863.17
//
Query:       gi|336252142|ref|YP_004595249.1|  [L=328]
Description: mevalonate kinase [Halopiger xanaduensis SH-6]
Scores for 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-16   59.8   0.8    5.5e-16   58.6   0.8    1.7  1  GHMP_kinases_N   GHMP kinases N terminal domain
    2.3e-15   56.7   1.6    1.2e-14   54.4   0.1    2.3  2  GHMP_kinases_C   GHMP kinases C terminal
    0.00028   20.4   0.1    0.00062   19.3   0.1    1.6  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 !   58.6   0.8   9.2e-20   5.5e-16       1      66 []     104     172 ..     104     172 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 9.2e-20
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerlaqggngsggDvaasvyGg 66 
                                       d++i+s+iP+gaGLGSSAA++va++ A+++ lg+sle    a+ a++ e+++q g  s  D ++s+ Gg
  gi|336252142|ref|YP_004595249.1| 104 DVTIESDIPLGAGLGSSAAVVVAAIDAAARELGVSLEAdeiAERAYRTEHEVQDGQASRADTFCSATGG 172
                                       699********************************944458*************************998 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 ?    0.9   0.1     0.099   5.9e+02      55      76 ..     114     132 ..     113     150 .. 0.74
   2 !   54.4   0.1   2.1e-18   1.2e-14       3      70 ..     235     300 ..     234     307 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.099
                    GHMP_kinases_C  55 GaGgGptvfalfkdkdeaeqva 76 
                                       GaG+G++ ++++   ++ +++a
  gi|336252142|ref|YP_004595249.1| 114 GAGLGSSAAVVV---AAIDAAA 132
                                       999999999998...3433343 PP

  == domain 2  score: 54.4 bits;  conditional E-value: 2.1e-18
                    GHMP_kinases_C   3 ealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkd 70 
                                       eal  gdle+lg+l+n ++   l+  +g+++++l++++ a+++++a+gakl+GaGgG++++al ++++
  gi|336252142|ref|YP_004595249.1| 235 EALADGDLEELGRLMNFNHG--LLSALGVSSRSLDTMVWAARDADAYGAKLTGAGGGGCIVALDPTPE 300
                                       78999***************..899**************************************75554 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 !   19.3   0.1     1e-07   0.00062      13      45 ..       3      35 ..       2      39 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1e-07
                                      EEEEEEEEEEE--S-TTTT-EEEEEEEEEEEEE CS
                   GalKase_gal_bdg 13 vasAPGRvnLiGEHtDYngGfVlpmAieqdiyi 45
                                      v sAPG v L GEH    g    p+Aie++  +
  gi|336252142|ref|YP_004595249.1|  3 VSSAPGKVYLFGEHAVVYGEPAVPCAIERRARV 35
                                      789*************************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2599.05
//
Query:       gi|336252143|ref|YP_004595250.1|  [L=307]
Description: XRE family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-52  177.0   0.3    3.1e-52  176.5   0.3    1.2  1  ThiP_synth      Thiamine-phosphate synthase
    1.2e-05   25.3   0.1    3.2e-05   23.9   0.1    1.7  1  HTH_3           Helix-turn-helix
    2.2e-05   24.2   0.3    0.00057   19.7   0.1    2.7  2  MarR_2          MarR family
    9.5e-05   22.1   0.0    0.00044   20.0   0.0    2.2  1  HTH_23          Homeodomain-like domain
    0.00026   21.2   3.0    0.00052   20.3   0.4    2.8  2  HTH_31          Helix-turn-helix domain
     0.0013   18.2   0.1     0.0052   16.3   0.0    2.0  2  Sigma70_r4      Sigma-70, region 4
     0.0013   18.3   0.0     0.0028   17.2   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0021   18.0   0.0     0.0051   16.7   0.0    1.6  1  HTH_37          Helix-turn-helix domain
     0.0027   17.7   0.0      0.017   15.1   0.0    2.1  2  HTH_19          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.026   14.4   0.0    1.7  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.013   15.3   0.1      0.051   13.3   0.0    2.0  2  HTH_38          Helix-turn-helix domain
      0.018   15.1   0.0       0.21   11.8   0.0    2.5  2  HTH_28          Helix-turn-helix domain
      0.024   14.3   0.1      0.055   13.1   0.1    1.6  1  Sigma70_r4_2    Sigma-70, region 4
      0.046   13.8   0.0      0.086   12.9   0.0    1.4  1  RepB            RepB plasmid partitioning protein
      0.049   13.5   0.0        0.1   12.5   0.0    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
       0.12   12.1   0.9       0.36   10.7   0.1    2.2  2  TetR_N          Bacterial regulatory proteins, tetR family
       0.16   12.0   0.0       0.33   10.9   0.0    1.5  1  HTH_11          HTH domain
       0.18   11.4   0.0       0.46   10.1   0.0    1.7  1  Kelch_1         Kelch motif
        0.2   11.8   0.1       0.56   10.4   0.1    1.7  1  Trp_repressor   Trp repressor protein
       0.28   11.1   0.7       0.63    9.9   0.1    1.9  1  P22_Cro         DNA-binding transcriptional regulator Cro


Domain annotation for each model (and alignments):
>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.5   0.3   3.4e-55   3.1e-52       1     163 [.     141     298 ..     141     300 .. 0.98

  Alignments for each domain:
  == domain 1  score: 176.5 bits;  conditional E-value: 3.4e-55
                                       HHHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC CS
                        ThiP_synth   1 eleralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkf 77 
                                       ++++a+++l++++++a++iP+vg+N+++alpdA ++ DvaavpGRI+ ++gr++++++pefgas+hva+++laa ++
  gi|336252143|ref|YP_004595250.1| 141 NVRTAARTLASIPGMAQYIPNVGTNVGMALPDAHDETDVAAVPGRIYAMGGRIEIPANPEFGASKHVATAVLAASDA 217
                                       599************************************************************************** PP

                                       -TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EEEEEE CS
                        ThiP_synth  78 dpevraainirydekilealeelglkvvefdreeepeevgstmewgvaeaieel.evpdviydeGgvGkEpmiyvlg 153
                                       dpe+r aini++d+++l+a++e g++  efd+++e ++      ++ ++ ++e+ +vp+v y++G++G+Ep++yv+g
  gi|336252143|ref|YP_004595250.1| 218 DPEIRGAINIATDDALLDAAREHGIDPLEFDADYEDRG------EHLRDRFAERgDVPRVAYHQGAFGIEPTTYVFG 288
                                       **************************************......789999999989********************* PP

                                       SSHHHHHHHH CS
                        ThiP_synth 154 kdaeevvekv 163
                                       ++a++++e+v
  gi|336252143|ref|YP_004595250.1| 289 ATAVDAAERV 298
                                       ********98 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   3.6e-08   3.2e-05       5      30 ..      26      51 ..      22      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.6e-08
                                      HHHTTHHHHHHHHHHTSSHHHHHHHH CS
                             HTH_3  5 RkqlglsqeeLAeklGvsrstisriE 30
                                      + ++gl+q+e+A++lGv+++++s++ 
  gi|336252143|ref|YP_004595250.1| 26 LAERGLTQREIAAELGVTQAAVSKYV 51
                                      569*********************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   6.3e-07   0.00057       9      42 ..      21      51 ..      14      52 .. 0.77
   2 ?    1.2   0.0      0.37   3.3e+02       5      19 ..     133     147 ..     127     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.3e-07
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHH CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsril 42
                                      ++  +L+ r+   lt++e+a++lg++++avs+ +
  gi|336252143|ref|YP_004595250.1| 21 MLATELAERG---LTQREIAAELGVTQAAVSKYV 51
                                      3333477777...9*****************865 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHHCTTT CS
                            MarR_2   5 paqarvLaaLgrrpg 19 
                                       +a+++vLa+++ + +
  gi|336252143|ref|YP_004595250.1| 133 RAERDVLANVRTAAR 147
                                       699*******98874 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   4.9e-07   0.00044       7      38 ..      19      51 ..      16      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.9e-07
                            HTH_23  7 Rlrillllae.GlsvreIAreLgvsrrTvyrwl 38
                                      R+  +  lae Gl++reIA+eLgv++  v++++
  gi|336252143|ref|YP_004595250.1| 19 RAMLATELAErGLTQREIAAELGVTQAAVSKYV 51
                                      66666677778******************9876 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.4   5.8e-07   0.00052      12      54 ..      28      78 ..      18      84 .. 0.86
   2 ?   -0.6   0.1       1.9   1.7e+03      37      60 ..     223     246 ..     191     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.8e-07
                            HTH_31 12 raGLsqeevAerlgvsestlsrlEqGrrgrp.........spavlealaral 54
                                      ++GL+q+e A+ lgv+++ +s++  G+ g           + a++e++a++l
  gi|336252143|ref|YP_004595250.1| 28 ERGLTQREIAAELGVTQAAVSKYVGGEGG-GdarfrddpeTVATVERIADGL 78
                                      78***********************8887.3367788888888999999887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.9
                            HTH_31  37 Grrgrpspavlealaralgldpae 60 
                                       G++++ + ++l  +ar +g dp e
  gi|336252143|ref|YP_004595250.1| 223 GAINIATDDALLDAAREHGIDPLE 246
                                       555556677777777777777665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.8e-06    0.0052      18      38 ..      28      48 ..       7      50 .. 0.78
   2 ?   -2.0   0.0       2.9   2.6e+03       9      26 ..     135     152 ..     133     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.8e-06
                                      TTT--HHHHHHHHTS-HHHHH CS
                        Sigma70_r4 18 geglTleEIgerlgiSrerVr 38
                                      ++glT+ EI+++lg+++ +V+
  gi|336252143|ref|YP_004595250.1| 28 ERGLTQREIAAELGVTQAAVS 48
                                      89***************9998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.9
                                       HHHHHHHHHTTT--HHHH CS
                        Sigma70_r4   9 erevlelrfgeglTleEI 26 
                                       er+vl  ++   +Tl+ I
  gi|336252143|ref|YP_004595250.1| 135 ERDVLANVRTAARTLASI 152
                                       999999999999998866 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 !   17.2   0.0   3.1e-06    0.0028      15      38 ..      28      51 ..      22      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.1e-06
                            HTH_24 15 nprisqreLAerlglSpstvnrrl 38
                                      + +++qre+A +lg+++++v++++
  gi|336252143|ref|YP_004595250.1| 28 ERGLTQREIAAELGVTQAAVSKYV 51
                                      568*******************98 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.7e-06    0.0051      22      50 ..      21      49 ..      17      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.7e-06
                                      HHHHHHHHCT--HHHHHHHHT--HHHHHH CS
                            HTH_37 22 aiaeliekrelsqseaaqllgiaqPkvsr 50
                                      ++a  +++r+l+q+e+a+ lg++q+ vs+
  gi|336252143|ref|YP_004595250.1| 21 MLATELAERGLTQREIAAELGVTQAAVSK 49
                                      5888999********************97 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.9e-05     0.017      10      35 ..      28      53 ..      23      74 .. 0.92
   2 ?   -0.7   0.0       1.7   1.5e+03      40      56 ..     228     244 ..     222     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                            HTH_19 10 elgltqeelaerlgisrskisaiEng 35
                                      e+gltq+e+a +lg++++  s++ +g
  gi|336252143|ref|YP_004595250.1| 28 ERGLTQREIAAELGVTQAAVSKYVGG 53
                                      89*********************998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                            HTH_19  40 psaelllkiaealgidl 56 
                                       ++ + ll++a++ gid+
  gi|336252143|ref|YP_004595250.1| 228 ATDDALLDAAREHGIDP 244
                                       56678999*******96 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 ?   14.4   0.0     3e-05     0.026      10      37 ..      32      59 ..      27      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3e-05
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqvpa 37
                                      +q++ A +lgv+q+aVs+ + g+++ +a
  gi|336252143|ref|YP_004595250.1| 32 TQREIAAELGVTQAAVSKYVGGEGGGDA 59
                                      5999****************99888444 PP

>> HTH_38  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   5.7e-05     0.051      16      39 ..      26      49 ..      19      51 .. 0.84
   2 ?   -2.0   0.0       3.5   3.2e+03       6      21 ..      98     113 ..      98     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.7e-05
                            HTH_38 16 llaeGlslreIArrLgrspsTIsR 39
                                      l ++Gl++reIA +Lg+    +s+
  gi|336252143|ref|YP_004595250.1| 26 LAERGLTQREIAAELGVTQAAVSK 49
                                      6689************99877775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                            HTH_38   6 sleeReeIerllaeGl 21 
                                       sle+R  I  l++e +
  gi|336252143|ref|YP_004595250.1|  98 SLEDRGPICELHEEEM 113
                                       799**99999999977 PP

>> HTH_28  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   0.00023      0.21       9      33 ..      26      51 ..      19      65 .. 0.78
   2 ?   -0.1   0.0       1.2   1.1e+03      17      26 ..     235     244 ..     229     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                            HTH_28  9 la.aGhsvreaArelgisrrtvyrWi 33
                                      la +G ++re+A+elg+++  v++ +
  gi|336252143|ref|YP_004595250.1| 26 LAeRGLTQREIAAELGVTQAAVSKYV 51
                                      552677*************9998755 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                            HTH_28  17 eaArelgisr 26 
                                       +aAre+gi++
  gi|336252143|ref|YP_004595250.1| 235 DAAREHGIDP 244
                                       5888888875 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 ?   13.1   0.1   6.2e-05     0.055      25      46 ..      29      50 ..      25      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.2e-05
                                      S---HHHHHHHHT--HHHHHHH CS
                      Sigma70_r4_2 25 eglsykEIAellgisegtVksr 46
                                       gl+++EIA++lg++ ++V ++
  gi|336252143|ref|YP_004595250.1| 29 RGLTQREIAAELGVTQAAVSKY 50
                                      59*****************887 PP

>> RepB  RepB plasmid partitioning protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.6e-05     0.086      10      43 ..      19      52 ..      13      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.6e-05
                              RepB 10 rarfaarleerGvdreeiasalgldkqtvskmva 43
                                      ra+ a  l erG++++eia+ lg+++++vsk+v+
  gi|336252143|ref|YP_004595250.1| 19 RAMLATELAERGLTQREIAAELGVTQAAVSKYVG 52
                                      6788999************************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 ?   12.5   0.0   0.00011       0.1      11      34 ..      26      49 ..      18      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                      HTTSSEEHHHHHHHHTS-HHHHHH CS
                             HTH_5 11 LaegelcvcelaeelglsqstvSh 34
                                      Lae+ l+  e+a+elg++q++vS 
  gi|336252143|ref|YP_004595250.1| 26 LAERGLTQREIAAELGVTQAAVSK 49
                                      89999999**************96 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 ?   10.7   0.1    0.0004      0.36      16      36 ..      30      50 ..      23      51 .. 0.88
   2 ?   -3.1   0.0       7.9   7.1e+03       1       7 [.     233     239 ..     233     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                                      T--HHHHHHHHTSSHHHHHHH CS
                            TetR_N 16 attvreIAkrAGvskgalYry 36
                                      ++t reIA+++Gv+++a+ +y
  gi|336252143|ref|YP_004595250.1| 30 GLTQREIAAELGVTQAAVSKY 50
                                      56789************9877 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.9
                                       HHHHHHH CS
                            TetR_N   1 IldaAre 7  
                                       +ldaAre
  gi|336252143|ref|YP_004595250.1| 233 LLDAARE 239
                                       79***97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00037      0.33      11      36 ..      27      51 ..      19      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
                            HTH_11 11 eargpisgeeLAeeLnvSrrtvrrdI 36
                                      ++rg ++  e+A eL+v+ ++v +++
  gi|336252143|ref|YP_004595250.1| 27 AERG-LTQREIAAELGVTQAAVSKYV 51
                                      5555.9*****************996 PP

>> Kelch_1  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00052      0.46       7      22 ..     179     194 ..     177     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00052
                                       EEEETTEEEEEEEBCS CS
                           Kelch_1   7 avvvggkiYviGGsdg 22 
                                       +++v g+iY++GG+ +
  gi|336252143|ref|YP_004595250.1| 179 VAAVPGRIYAMGGRIE 194
                                       799**********976 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00063      0.56      38      67 ..      19      48 ..      17      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00063
                     Trp_repressor 38 RlqvvkeLLkeelsqreIaeelgvSiAtIt 67
                                      R   + eL + +l+qreIa+elgv  A ++
  gi|336252143|ref|YP_004595250.1| 19 RAMLATELAERGLTQREIAAELGVTQAAVS 48
                                      667788999***************999876 PP

>> P22_Cro  DNA-binding transcriptional regulator Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00071      0.63      12      29 ..      33      50 ..      32      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00071
                                      HHHHHHHHTS-HHHHHHH CS
                           P22_Cro 12 vekvAkalgvtksAVsqW 29
                                      ++ +A+ lgvt++AVs+ 
  gi|336252143|ref|YP_004595250.1| 33 QREIAAELGVTQAAVSKY 50
                                      7889************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2225.96
//
Query:       gi|336252144|ref|YP_004595251.1|  [L=41]
Description: hypothetical protein Halxa_0733 [Halopiger xanaduensis SH-6]
Scores for 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:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 345.16
//
Query:       gi|336252145|ref|YP_004595252.1|  [L=272]
Description: 30S ribosomal protein S2 [Halopiger xanaduensis SH-6]
Scores for 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   0.5    5.9e-14   51.8   1.0    2.1  2  Ribosomal_S2     Ribosomal protein S2
  ------ inclusion threshold ------
      0.074   14.0   3.4      0.073   14.0   1.9    1.7  2  tRNA_synt_1c_R2  Glutaminyl-tRNA synthetase, non-specific RNA


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 !   31.7   0.0   9.4e-12   8.5e-08       2      96 ..      91     182 ..      90     188 .. 0.90
   2 !   51.8   1.0   6.6e-18   5.9e-14     148     212 ..     189     253 ..     184     255 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 9.4e-12
                      Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIyger.ngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaak 77 
                                       L agvh+G q++  + +m+++I+ +r +g +++d+ kt + +r+a++++ +   + ++il  ++++  +   ++ a+
  gi|336252145|ref|YP_004595252.1|  91 LGAGVHIGTQQK--TADMERFIHRVRtDGLYVLDVSKTDQRIRTAADFLANY--DPEQILVTSSRQYGRFPAEKFAE 163
                                       679*****7666..899******999569********************875..67899999999999999999*** PP

                      Ribosomal_S2  78 rangyyvnerWlgGtLTNf 96 
                                        +++   + r+++GtLTN 
  gi|336252145|ref|YP_004595252.1| 164 AVGARARTGRFIPGTLTNP 182
                                       ******************6 PP

  == domain 2  score: 51.8 bits;  conditional E-value: 6.6e-18
                      Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladai 212
                                        Pd+vvv+dp  +  avkEa ++gipvia++D+n + ++vd ++p N++  +++++++ +la+ +
  gi|336252145|ref|YP_004595252.1| 189 EPDVVVVTDPIGDAQAVKEAITVGIPVIAMCDSNNQVSNVDLVVPTNNKGRKALSVVYWLLANEV 253
                                       59********************************************************9999876 PP

>> tRNA_synt_1c_R2  Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.9   8.1e-06     0.073       3      70 ..      16      83 ..      15     106 .. 0.74
   2 ?   -3.0   0.0       1.6   1.4e+04      76      83 ..     181     188 ..     179     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.1e-06
                   tRNA_synt_1c_R2  3 nevDaqllelLGPKteaDnlkpkkkkkkkkkkkeekkkaakkakkekeeeesegaetieel.egellkf 70
                                      +e+D++ +e  GP  e+D ++p+++++++++++e+++ a+ ++++++ee e++g +  +++   e++++
  gi|336252145|ref|YP_004595252.1| 16 EEIDEEPAEGAGPAAEED-VEPVDEQSADAAADEAEADAEVAEETDAEEAEDAGPTLDDDVmSDEEADL 83
                                      699***************.9**99999998888888877777666666655555555555425555555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.6
                   tRNA_synt_1c_R2  76 Nfktdgyv 83 
                                       N+k dgy+
  gi|336252145|ref|YP_004595252.1| 181 NPKYDGYI 188
                                       99*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2076.41
//
Query:       gi|336252146|ref|YP_004595253.1|  [L=403]
Description: Enolase [Halopiger xanaduensis SH-6]
Scores for complete 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-77  261.0   1.0    1.7e-77  260.6   1.0    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    7.5e-35  120.0   1.5    2.1e-34  118.5   0.2    2.4  2  Enolase_N  Enolase, N-terminal domain
    7.8e-11   42.0   0.1    1.5e-10   41.0   0.1    1.5  1  MR_MLE_C   Enolase C-terminal domain-like
    0.00034   19.9   0.1    0.00068   18.9   0.1    1.4  1  MAAL_C     Methylaspartate ammonia-lyase C-terminus


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 !  260.6   1.0   3.8e-81   1.7e-77       4     280 ..     133     401 ..     131     403 .] 0.94

  Alignments for each domain:
  == domain 1  score: 260.6 bits;  conditional E-value: 3.8e-81
                                       E-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHH CS
                         Enolase_C   4 lPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnk 80 
                                       +P P+ nv+ GG+ha ++ ++qef+ +Pvga+s+++a+   a v+ +++++l++++  + +  GdeG +aP++++ +
  gi|336252146|ref|YP_004595253.1| 133 FPTPLGNVVGGGEHAADATDIQEFLAAPVGAPSVEDAVFANAAVHAEVADLLEERG--HPSGKGDEGAWAPSIDD-A 206
                                       699****************************************************9..78889**********86.6 PP

                                       HHHHHHHHHHHHCT-TC..TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEE CS
                         Enolase_C  81 ealdliveaiekaGykg..kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsie 155
                                       ea++++ ea++    +   ++  +ldva++e+y+++ ++y+ +  + + d      +e+  ++  +lv++y +v +e
  gi|336252146|ref|YP_004595253.1| 207 EAFEIVDEAVSTVQDEVgfNIGFGLDVAAAEMYDADSETYEYESAGISRD------TEEQIEYIADLVEEYDLVYVE 277
                                       8*********9887776668999******************999994444......344568999************ PP

                                       S-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEE CS
                         Enolase_C 156 dpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvv 232
                                       dpldedd++a++ lt+e+gd+  i Gddl+vtn++rl ++i+++aan++l+k nqiG+lt++++a++la+++gy  v
  gi|336252146|ref|YP_004595253.1| 278 DPLDEDDYDAFADLTDEVGDQTLICGDDLFVTNTDRLVDGIDRGAANSILIKPNQIGTLTDAFDAIELATQNGYDSV 354
                                       ***************************************************************************** PP

                                       EE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHH CS
                         Enolase_C 233 vshrsGetedttiadlavglsaGqiktGaparserlakynqllrieee 280
                                       +shrsGetedttia+lav++ a  iktGa+   er ak+n+l+ri ++
  gi|336252146|ref|YP_004595253.1| 355 ISHRSGETEDTTIAHLAVATDAPFIKTGAVG-GERTAKLNELIRIADD 401
                                       *****************************86.8************886 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.5   0.2   4.7e-38   2.1e-34       1     131 []       4     124 ..       4     124 .. 0.96
   2 ?   -1.3   0.1      0.51   2.3e+03      81      81 ..     233     233 ..     174     274 .. 0.67

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 4.7e-38
                                       EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHT CS
                         Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapali 77 
                                       I++++ r ildSrGnpTve++v+te+g +graa+psGaStge+ea+e           +  ++a+++++e+  p+l+
  gi|336252146|ref|YP_004595253.1|   4 ITDIRLRRILDSRGNPTVEADVVTESGGFGRAAAPSGASTGEYEAVE-----------RPPTEAIAAAREHAVPRLV 69 
                                       899*******************************************4...........45679************** PP

                                       T.SBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                         Enolase_N  78 g.ldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                       g   + +q+e+D++l ++Dgt++ s++GaN+++a+S+A+aka+A+ ++ pl+++l
  gi|336252146|ref|YP_004595253.1|  70 GeAYAGNQREVDSILRAADGTDDFSEIGANSAVAISMAAAKAGADVLGAPLFQHL 124
                                       747799***********************************************97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.51
                                       T CS
                         Enolase_N  81 v 81 
                                       v
  gi|336252146|ref|YP_004595253.1| 233 V 233
                                       2 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 !   41.0   0.1   3.4e-14   1.5e-10      32     174 ..     214     377 ..     175     395 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 3.4e-14
                                       HHHHHHHHHHTTTSTSEEEEE-TTT..S................BHHHHHHHHHHH.GGGTESEEESSSSTTTHHHH CS
                          MR_MLE_C  32 ervravreavgpgddvdlmvDanqa..w................dlatAirvarel.eeldllwlEEPvppeddleg 89 
                                       e v  v+++v  g ++ + +D+ +a  +                d+++ i+++  l ee+dl ++E+P+   dd+++
  gi|336252146|ref|YP_004595253.1| 214 EAVSTVQDEV--GFNIGFGLDVAAAemYdadsetyeyesagisrDTEEQIEYIADLvEEYDLVYVEDPLDE-DDYDA 287
                                       4566666666..44556666666663337777778888888888999999999999677***********9.78*** PP

                                       HHHHHH.HH.SSEEEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-E.EEEBSCS.SHH CS
                          MR_MLE_C  90 laelra.ra.sipiaagEslys.radfrelleagavdivqpdvsrvgGitearkvaalaeafgvp.vapHsgs.ggl 161
                                        a+l++    ++ i+++    +   ++ + +++ga+  + ++++++g +t a + ++la ++g++ v+ H  + +  
  gi|336252146|ref|YP_004595253.1| 288 FADLTDeVGdQTLICGDDLFVTnTDRLVDGIDRGAANSILIKPNQIGTLTDAFDAIELATQNGYDsVISHRSGeTED 364
                                       *****963367888888876665999**************************************9444444322455 PP

                                       HHHHHHHHHHTTT CS
                          MR_MLE_C 162 glaaslhlaaaip 174
                                       +++a+l +a+ +p
  gi|336252146|ref|YP_004595253.1| 365 TTIAHLAVATDAP 377
                                       5555555555444 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.5e-07   0.00068      85     219 ..     253     377 ..     238     388 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.5e-07
                            MAAL_C  85 fdddeervadylakleeaaapyklliegPldagskeeqierlaelreklkekgikvelvaDeW.cntledirefvda 160
                                       ++ d+e+ ++y+a+l e+     +++e+Pld+++     +++a l++++   g +  +  D+    +++ + + +d+
  gi|336252146|ref|YP_004595253.1| 253 ISRDTEEQIEYIADLVEEYD--LVYVEDPLDEDDY----DAFADLTDEV---GDQTLICGDDLfVTNTDRLVDGIDR 320
                                       66789999999999987654..3689****98764....5667777665...555667777751555566999**** PP

                            MAAL_C 161 eaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvsarvsvhvalatrpa 219
                                       +aa+ + ik   +G+++++ +a+  + ++g  + +   + et+ +  +++h+a+at++ 
  gi|336252146|ref|YP_004595253.1| 321 GAANSILIKPNQIGTLTDAFDAIELATQNGYDSVISHRSGETEDT--TIAHLAVATDAP 377
                                       *****************************************9975..689999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2961.59
//
Query:       gi|336252147|ref|YP_004595254.1|  [L=59]
Description: DNA-directed RNA polymerase subunit K [Halopiger xanaduensis SH-6]
Scores for 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    3.2e-11   43.0   0.0    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 !   43.0   0.0   1.8e-15   3.2e-11       7      49 .]       6      52 ..       2      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.8e-15
                                      --HHHHHHHHHHHHHHH....HT........SS-SSSSTTCHHHHTT-S-- CS
                      RNA_pol_Rpb6  7 ltrYelvriaakRArQieegesl........etqkpvviAlrEiaegkipi 49
                                       +rYe++ri+++RA+Q     s         + + p+ iA +E ++g +p+
  gi|336252147|ref|YP_004595254.1|  6 HNRYEKARILGARALQV----SYgapvlietDQTQPILIAAEEYDAGVLPF 52
                                      69***************....6666666743245***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 430.57
//
Query:       gi|336252148|ref|YP_004595255.1|  [L=64]
Description: DNA-directed RNA polymerase subunit N [Halopiger xanaduensis SH-6]
Scores for 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   99.5   0.2      1e-28   99.4   0.2    1.0  1  RNA_pol_N  RNA polymerases N / 8 kDa subunit


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 !   99.4   0.2   5.8e-33     1e-28       1      57 [.       1      58 [.       1      60 [. 0.96

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 5.8e-33
                                      ----SS-TTT--B-STHHHHHHHHHHTT.--HHHHHHHHT--SHHHHHHHHTB--THH CS
                         RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekg.eepkdaLdaLglkryCCrrmllthvdlie 57
                                      M++PVrCFtCG+v+ge+wee+ e+ ++g e+p+++Ld+Lg++ryCCrrml++h+dl++
  gi|336252148|ref|YP_004595255.1|  1 MMVPVRCFTCGNVVGEHWEEFDERANEGdEDPEKVLDELGVDRYCCRRMLVSHTDLVD 58
                                      9************************777699*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 497.55
//
Query:       gi|336252149|ref|YP_004595256.1|  [L=132]
Description: 30S ribosomal protein S9P [Halopiger xanaduensis SH-6]
Scores for 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-33  114.0   0.1    6.5e-33  113.8   0.1    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 !  113.8   0.1   3.6e-37   6.5e-33       1     121 []       7     132 .]       7     132 .] 0.92

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 3.6e-37
                                       EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSS..SEEEEEEEESS-HHHHHHHHHHHHH CS
                      Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllg..kfdvfvkvkgGGlsgqaeAirlgia 75 
                                       G++K++vAr+++++g+g++++n+k++e  ++ e++r k+lep++++g+    ++d+ v+v+gGG+sgqa+A+r++ia
  gi|336252149|ref|YP_004595256.1|   7 GKKKTAVARATVRDGEGRVRINSKPVEL-VEPEMSRLKMLEPFRIAGEDLrsEMDIDVRVEGGGISGQADAVRTAIA 82 
                                       89*************************9.877*************99744447************************ PP

                                       HHHHHHHHHHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                      Ribosomal_S9  76 raLvalekeekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                       r++v++++    eL+      +++ll++D R+ E+kK g ++AR++yq+s+R
  gi|336252149|ref|YP_004595256.1|  83 RGIVQHTN--DAELRdafmefDRSLLVNDVRQSEPKKWGGPGARARYQKSYR 132
                                       *****988..467775555888****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 992.33
//
Query:       gi|336252150|ref|YP_004595257.1|  [L=149]
Description: 50S ribosomal protein L13 [Halopiger xanaduensis SH-6]
Scores for 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-10   39.6   0.1    2.6e-06   27.7   0.0    2.4  2  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 !   10.4   0.0   3.3e-05       0.6       3      22 ..      12      31 ..      12      37 .. 0.86
   2 !   27.7   0.0   1.5e-10   2.6e-06      38     121 ..      35     115 ..      30     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.3e-05
                                      EEEEETTSBHHHHHHHHHHH CS
                     Ribosomal_L13  3 yviDAegqvlgrlaskiakv 22
                                      +v+DA++ +lgr+as++a++
  gi|336252150|ref|YP_004595257.1| 12 VVVDARDCILGRVASEVAQR 31
                                      58***************974 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 1.5e-10
                                       S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHHCCSHHHHHHHHHHCCS-.SSHHHHHHGCTEEEES CS
                     Ribosomal_L13  38 GdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakellekkpeeilekaVkgmLp.knklgrrrlkrLkvya 113
                                       G+ v v+nae+  +tg+k +    yr     g+           k+p+ i+++ ++gmLp k+  gr+ +++++vy 
  gi|336252150|ref|YP_004595257.1|  35 GERVAVVNAEDAIITGDKEDIFETYRTRLQLGSD----SGPYYPKRPDTIFKRSIRGMLPyKKPRGREAFENVRVYV 107
                                       8899**************9876666665555543....44567899**************5566899999******* PP

                                       SSTTSGGG CS
                     Ribosomal_L13 114 geehphea 121
                                       g+  ++e+
  gi|336252150|ref|YP_004595257.1| 108 GNPYEDEQ 115
                                       *9877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1187.48
//
Query:       gi|336252151|ref|YP_004595258.1|  [L=117]
Description: 50S ribosomal protein L18e [Halopiger xanaduensis SH-6]
Scores for 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    2.1e-08   33.8   0.0    1.0  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    2.2e-06   28.3   0.3    7.7e-06   26.6   0.3    1.7  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> 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 !   33.8   0.0   2.3e-12   2.1e-08      21     135 ..       6     113 ..       1     117 [] 0.88

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.3e-12
                     Ribosomal_L18  21 nvylklLvklyrfLarRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPkl 97 
                                       n+ l+ L+   +  +r td++  + +  rL + r+ ++ + l r+ ++ ++    ++++vv g+v+    l++   +
  gi|336252151|ref|YP_004595258.1|   6 NPRLTDLIAELKSTSRETDADVWRDIADRLEKPRRTHAEVNLGRIERYARE----EETVVVPGKVLGSGALQK--SV 76 
                                       566666666667889*******************************99985....58***********99997..69 PP

                     Ribosomal_L18  98 svaALrftetararilkaGGeiltlDqLalraPtGknt 135
                                       +vaA+ f+++a ++i + G e + l+qL  ++P+G+++
  gi|336252151|ref|YP_004595258.1|  77 TVAAVDFSSSAETKIDQVG-ETVQLEQLLEENPEGSDV 113
                                       ***************9885.889************987 PP

>> 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 !   26.6   0.3   8.5e-10   7.7e-06      71     127 ..      41      99 ..      26     100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 8.5e-10
                                       ---EEEGGGTTTTSSS......SE..EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A  71 eaeeidleelaeaglikk..kdgv..KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                       +++e++l ++ +     +  +  v  Kvlg+g l+k ++v a  fS++A+ kI ++G +v+
  gi|336252151|ref|YP_004595258.1|  41 THAEVNLGRIERYAR--EeeTVVVpgKVLGSGALQKSVTVAAVDFSSSAETKIDQVGETVQ 99 
                                       445777777733332..234334446*******************************8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 859.64
//
Query:       gi|336252152|ref|YP_004595259.1|  [L=249]
Description: DNA-directed RNA polymerase subunit D [Halopiger xanaduensis SH-6]
Scores for 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-21   74.6   0.0    3.8e-20   72.3   0.0    2.1  2  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    4.5e-17   61.2   0.0    5.8e-17   60.9   0.0    1.1  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain


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 !   72.3   0.0   4.3e-24   3.8e-20       1     111 [.      48     144 ..      48     145 .. 0.95
   2 ?   -2.2   0.0       0.6   5.4e+03      18      33 ..     171     185 ..     161     236 .. 0.63

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 4.3e-24
                                       EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBESSSSCE CS
                     RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkledadve 77 
                                       V++ en+sv+ DE +a rlgl+pl++ +++e              + e+ +v+l+++v+gp + ++gdl+++d+ v+
  gi|336252152|ref|YP_004595259.1|  48 VRFVENSSVMFDEQLALRLGLVPLTTPPEDE--------------FGEDATVTLSIDVEGPATAYSGDLESSDELVQ 110
                                       7899*********************888666..............688889************************** PP

                                       ESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT CS
                     RNA_pol_A_bac  78 ivnpdilIakLrkgqeleleakvkkGiGkehakf 111
                                       +++++++I++L+++q+le ea ++ ++Gk+hak+
  gi|336252152|ref|YP_004595259.1| 111 PADENVPIIELKDDQRLEAEADAVLDRGKDHAKH 144
                                       ********************************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.6
                                       HHHCSTCBSSCHHHHH CS
                     RNA_pol_A_bac  18 rlgliplvsedvleil 33 
                                       + + +++v ed+ e l
  gi|336252152|ref|YP_004595259.1| 171 EAQIVRGVVEDDGE-L 185
                                       55566666666666.2 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 !   60.9   0.0   6.5e-21   5.8e-17       1      67 [.      18     238 ..      18     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 6.5e-21
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
                         RNA_pol_L   1 efllrgvdhtlgNaLRrillsevpgvaiea............................................... 30 
                                       +fl+rgv+++++N +Rr +l++vp++ai++                                               
  gi|336252152|ref|YP_004595259.1|  18 RFLVRGVTPAFANGIRRAMLADVPTMAIDTvrfvenssvmfdeqlalrlglvplttppedefgedatvtlsidvegp 94 
                                       59**************************************************9999999999999999999999999 PP

                                       ................................................................xx........... RF
                         RNA_pol_L  31 ................................................................pv........... 32 
                                                                                                        v           
  gi|336252152|ref|YP_004595259.1|  95 ataysgdlessdelvqpadenvpiielkddqrleaeadavldrgkdhakhqgavavgyrhlqrvVVeddlpefeese 171
                                       99888888888888888888887777777777777777666666666666666655555555550055555555555 PP

                                       ................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  33 ................................vkvntdkdklilevetdgslkPeealkeAlkiLke 67 
                                                                       v+v+++++ +++ vetdgs ++ee++++A++ +++
  gi|336252152|ref|YP_004595259.1| 172 aqivrgvveddgelvptsefdhdlsnrypdkqVSVEDVPNAFVFHVETDGSFTVEELVTRAAETIES 238
                                       566666666666666667777777777777777888***************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 00:00:00.44
# Mc/sec: 1695.34
//
Query:       gi|336252153|ref|YP_004595260.1|  [L=129]
Description: 30S ribosomal protein S11P [Halopiger xanaduensis SH-6]
Scores for 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-47  159.2   2.5    4.9e-47  158.9   2.5    1.1  1  Ribosomal_S11   Ribosomal protein S11
  ------ inclusion threshold ------
      0.016   15.6   0.1      0.022   15.1   0.1    1.2  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


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 !  158.9   2.5   5.4e-51   4.9e-47       1     109 [.       9     126 ..       9     127 .. 0.99

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 5.4e-51
                     Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg...... 70 
                                       G+ah++asfnnt++t+tdl+Gae+++ks+Gg+ vk++r ++sPyaa+++ae++ae+v+  Gi+ ++v+v+g      
  gi|336252153|ref|YP_004595260.1|   9 GIAHVHASFNNTVMTVTDLTGAETIAKSSGGTAVKQNRdEASPYAAMQMAESVAEEVKAAGITGLHVRVRGpggnlq 85 
                                       9**************************************************************************** PP

                     Ribosomal_S11  71 ..pGpGreaalralaraGlkigriedvtPiPhdgirrpkkr 109
                                         pGpG++a++ralar+G++igriedvtPiPhdg r+pk++
  gi|336252153|ref|YP_004595260.1|  86 ksPGPGAQATIRALARSGIEIGRIEDVTPIPHDGSRAPKGK 126
                                       **************************************975 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 ?   15.1   0.1   2.5e-06     0.022      28      87 ..      12      71 ..       4      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-06
                                      EEEE-SS-EEEEEE-TTT--EEEEECS-SCCCTS-SSSCHHHHHHHHHHHHHHHCHHCHT CS
                    Ribosomal_L18p 28 vvfrsnrhiyaQviddvkgktlasastlekelklkstknkeaakkvgeliAerakekgie 87
                                       v+ s ++ +  v d +  +t+a++s+  +  + + + +  aa +++e +Ae+ k++gi+
  gi|336252153|ref|YP_004595260.1| 12 HVHASFNNTVMTVTDLTGAETIAKSSGGTAVKQNRDEASPYAAMQMAESVAEEVKAAGIT 71
                                      588899999999************99987777788899999*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1018.99
//
Query:       gi|336252154|ref|YP_004595261.1|  [L=173]
Description: 30S ribosomal protein S4 [Halopiger xanaduensis SH-6]
Scores for 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-14   51.8   1.9    5.7e-14   51.6   0.3    1.9  2  S4            S4 domain
    0.00084   20.2   1.6     0.0011   19.8   1.0    1.6  2  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal 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 ?   -1.0   0.1      0.17   1.5e+03      16      22 ..      51      57 ..      44      60 .. 0.84
   2 !   51.6   0.3   6.3e-18   5.7e-14       1      47 [.     104     150 ..     104     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.17
                                      HHHHHHH CS
                                S4 16 rreArql 22
                                      rreAr+l
  gi|336252154|ref|YP_004595261.1| 51 RREARDL 57
                                      9****98 PP

  == domain 2  score: 51.6 bits;  conditional E-value: 6.3e-18
                                       EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCE CS
                                S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDv 47 
                                       rRL++v++r+gla +  +Arq+I hG++ V+G++ + psy V++ ++
  gi|336252154|ref|YP_004595261.1| 104 RRLQTVVYRKGLANTTQQARQFITHGHIVVDGQRHRVPSYVVDVDEE 150
                                       8*****************************************97654 PP

>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.0   1.3e-07    0.0011      29      80 ..       6      59 ..       1     103 [. 0.82
   2 ?   -1.3   0.0      0.47   4.2e+03      11      22 ..     104     123 ..      68     151 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.3e-07
                                      TTTS.-----CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHHH CS
                      Ribosomal_S4 29 hgkr.rkklseYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLlq 80
                                      + k+ ++   +Y+  ++ +++ l+ rYgl+ +++++r+++e+r++r + ++ Ll 
  gi|336252154|ref|YP_004595261.1|  6 KTKQyETPNHPYQGeRIANEHSLIDRYGLKnKEELWRAQSELRSYR-REARDLLG 59
                                      444445666799999*******************************.99999985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.47
                                       CHCTS-STSSS........S CS
                      Ribosomal_S4  11 Rrvgfklflkg........r 22 
                                       Rr+++ ++ kg        r
  gi|336252154|ref|YP_004595261.1| 104 RRLQTVVYRKGlanttqqaR 123
                                       55555555555544433332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1405.58
//
Query:       gi|336252155|ref|YP_004595262.1|  [L=173]
Description: 30S ribosomal protein S13P [Halopiger xanaduensis SH-6]
Scores for 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-45  153.9   3.1    3.4e-45  153.6   3.1    1.1  1  Ribosomal_S13  Ribosomal protein S13/S18
  ------ inclusion threshold ------
      0.013   14.3   0.0      0.013   14.3   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA


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 !  153.6   3.1   3.8e-49   3.4e-45       1     128 []      20     147 ..      20     147 .. 0.98

  Alignments for each domain:
  == domain 1  score: 153.6 bits;  conditional E-value: 3.8e-49
                     Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdi 76 
                                       Ri +td+dg+k+ve +lt+++GiG+r+a+ii+++a+vd+++ +g l+++ i++++e+ven   +++p+w+ nr +d+
  gi|336252155|ref|YP_004595262.1|  20 RIGQTDLDGTKSVERSLTEMNGIGHRTARIIAQEAGVDRTATFGRLDDDVIDEVVELVEN-YADEVPDWLnNRPEDF 95 
                                       99**********************************************************.7788899988****** PP

                     Ribosomal_S13  77 kdGkdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                        +G+++h++ ndl+ ++++di+R+k+i+sy+G+RHkrG+kvRGQrTk+tgRt
  gi|336252155|ref|YP_004595262.1|  96 YTGETTHEIGNDLELTRQHDINRMKMIDSYKGVRHKRGQKVRGQRTKSTGRT 147
                                       ***************************************************8 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 ?   14.3   0.0   1.5e-06     0.013     184     257 ..      24     100 ..       2     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-06
                                       H...S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHTXXX.....XXEE..... CS
                              FbpA 184 k...kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqelleelee.ekfepqlvlkee 256
                                       +    +k++++  +++++G++  +a+ ++++ag+d++ +   l+++ ++++ e ++++ +e+    + +p+ +++ e
  gi|336252155|ref|YP_004595262.1|  24 TdldGTKSVERS-LTEMNGIGHRTARIIAQEAGVDRTATFGRLDDDVIDEVVELVENYADEVPDwLNNRPEDFYTGE 99 
                                       255344444454.56779******************************************99854455555555554 PP

                                       X CS
                              FbpA 257 k 257
                                       +
  gi|336252155|ref|YP_004595262.1| 100 T 100
                                       3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1428.34
//
Query:       gi|336252156|ref|YP_004595263.1|  [L=327]
Description: hypothetical protein Halxa_0745 [Halopiger xanaduensis SH-6]
Scores for 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   37.2   2.3    2.7e-09   37.2   2.3    2.2  2  DUF4129          Domain of unknown function (DUF4129)
    0.00022   21.3   0.2    0.00066   19.7   0.1    1.7  2  MARVEL           Membrane-associating domain
    0.00043   19.8   0.2    0.00061   19.3   0.2    1.3  1  Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
  ------ inclusion threshold ------
      0.014   14.8   0.7      0.014   14.8   0.7    1.4  2  Glucos_trans_II  Glucosyl transferase GtrII
       0.06   13.8   3.9        1.9    8.9   4.4    2.2  2  DUF983           Protein of unknown function (DUF983)
       0.26    9.5   0.3       0.39    8.9   0.3    1.2  1  DUF2070          Predicted membrane protein (DUF2070)
       0.55   10.0   4.4        6.9    6.4   4.1    2.4  3  DUF2157          Predicted membrane protein (DUF2157)
       0.58    9.0   6.9       0.14   11.0   0.7    2.3  3  MFS_1            Major Facilitator Superfamily
       0.67    9.6   4.1       0.42   10.2   1.7    1.9  3  DUF4131          Domain of unknown function (DUF4131)
       0.98    7.7   2.6        1.5    7.0   2.6    1.2  1  PTPS_related     6-pyruvoyl-tetrahydropterin synthase related
        1.2    8.8   6.6       0.23   11.1   0.7    2.2  2  Oxidored_q2      NADH-ubiquinone/plastoquinone oxidoreductase
          2    8.9   6.8       0.11   12.9   0.9    1.9  3  DUF2569          Protein of unknown function (DUF2569)
        2.6    7.7   6.6         27    4.4   7.6    1.8  2  Wzy_C            O-Antigen ligase


Domain annotation for each model (and alignments):
>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.9   2.6e+03      23      47 ..     197     221 ..     187     226 .. 0.59
   2 !   37.2   2.3   1.9e-12   2.7e-09       5      68 ..     227     291 ..     224     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.9
                           DUF4129  23 rEyarrv.riapspaaalaalaelfe 47 
                                       +E a +v  +a+ +a++++ +a+ ++
  gi|336252156|ref|YP_004595263.1| 197 TEAA-AVgSAAGRAADRIDGAATDVD 221
                                       4444.445666667777777776665 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 1.9e-12
                           DUF4129   5 llraLaer.gldrrpgeTprEyarrvriapspaaalaalaelfeearYGgrpasaeeyrrlveal 68 
                                       +++ +++   +dr+ + TprE+a+++ +a+ +++ + +l++lfee+rYG+ + + e   r+v+ l
  gi|336252156|ref|YP_004595263.1| 227 AWKEMTALlEVDRPDSSTPREFATAAVEAGIDREYVGELTRLFEEVRYGDVETTSEMETRAVDVL 291
                                       34444444479***************77788************************9999999876 PP

>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   4.8e-07   0.00066       7      95 ..       6     118 ..       1     137 [. 0.87
   2 ?   -1.3   0.0       1.5     2e+03      10      20 ..     158     168 ..     141     189 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.8e-07
                            MARVEL   7 gilrilqlvfaiiilgliaslia.........................kldqllgspssalnfavfvavfsflyalf 58 
                                        ++r+l  v ai +++l+a++i                          ++    g++++ l++ v +  + +++al+
  gi|336252156|ref|YP_004595263.1|   6 RLVRLLAAVSAIAAIALAAATIEnpletggsegvgpgegggpgqqpmpTQPVAGGDAPPFLEYLVYAVLIIIAVALV 82 
                                       589******************************************99977667788899999988888888888888 PP

                            MARVEL  59 llvlylfknsaftsilwplidlivdalaallwlvafi 95 
                                       + +l +++++a+  i+  l++++v al++ + + +f+
  gi|336252156|ref|YP_004595263.1|  83 WYLL-AYRRDAVKMIAVVLAVCLVGALLFAFLFQGFS 118
                                       8888.33488889999999999999999999998886 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                            MARVEL  10 rilqlvfaiii 20 
                                        +l+++ ai++
  gi|336252156|ref|YP_004595263.1| 158 FVLSVITAIFV 168
                                       22333333333 PP

>> Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   4.4e-07   0.00061     188     263 ..       7     119 ..       2     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.4e-07
                   Cyt_bd_oxida_II 188 arrlalvlalvllvllvvvllwtll.....................................lvllllavlalllav 227
                                       + rl ++++++++++l+++++  +l                                     lv ++l ++a++l++
  gi|336252156|ref|YP_004595263.1|   7 LVRLLAAVSAIAAIALAAATIENPLetggsegvgpgegggpgqqpmptqpvaggdappfleyLVYAVLIIIAVALVW 83 
                                       44444444444444444444444447777777777788888888888888888888888887677788888889999 PP

                   Cyt_bd_oxida_II 228 lllrkkreglaflasaltvllvvlllavslfPyllp 263
                                        ll+ +r+++ ++a++l+v lv +ll++ lf  + p
  gi|336252156|ref|YP_004595263.1|  84 YLLAYRRDAVKMIAVVLAVCLVGALLFAFLFQGFSP 119
                                       888889999999999999999988888888654444 PP

>> Glucos_trans_II  Glucosyl transferase GtrII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.7     1e-05     0.014     227     272 ..      65     113 ..      58     130 .. 0.80
   2 ?   -4.1   0.1       5.8     8e+03     233     240 ..     159     166 ..     150     177 .. 0.44

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                   Glucos_trans_II 227 pkklllililliliilllalllkkkkkkkksll...llllllllllpfa 272
                                       +  +l++++l+i++++l+++ll  ++   k ++   +++l+++ll+ f+
  gi|336252156|ref|YP_004595263.1|  65 FLEYLVYAVLIIIAVALVWYLLAYRRDAVKMIAvvlAVCLVGALLFAFL 113
                                       6789************************999997655566666666665 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 5.8
                   Glucos_trans_II 233 ilillili 240
                                       +l ++++i
  gi|336252156|ref|YP_004595263.1| 159 VLSVITAI 166
                                       22222222 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.4    0.0014       1.9      22      72 ..      58     110 ..      52     117 .. 0.76
   2 ?    1.8   0.0      0.24   3.3e+02      25      45 ..     153     173 ..     145     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0014
                            DUF983  22 raddgPayfvilivghlvvpla..llvevayepplwvhlliwlpltlllslll 72 
                                         +d+P+++ +l+ ++l+++++  ++  +ay+ +   +++++l ++l+ +ll+
  gi|336252156|ref|YP_004595263.1|  58 AGGDAPPFLEYLVYAVLIIIAValVWYLLAYRRDAVKMIAVVLAVCLVGALLF 110
                                       4679***9988876555444433399999999999999999999999988875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.24
                            DUF983  25 dgPayfvilivghlvvplall 45 
                                        gP  fv+ ++++++v+ +l+
  gi|336252156|ref|YP_004595263.1| 153 TGPLLFVLSVITAIFVGGLLV 173
                                       699999999999999998876 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3   0.00029      0.39     100     164 ..      65     166 ..      53     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00029
                           DUF2070 100 vllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly............................ 148
                                       +l +lv ++ +++a+ l+ +++  +++  k+++++l+  l+++ll+ ++                            
  gi|336252156|ref|YP_004595263.1|  65 FLEYLVYAVLIIIAVALVWYLLAYRRDAVKMIAVVLAVCLVGALLFAFLfqgfspeldaqpieepatvnnssgggdf 141
                                       66788999999999999999999999999999999999999998888887888888888888888888888888888 PP

                           DUF2070 149 .........fspesfllllllslif 164
                                                fs+   l++l ++ ++
  gi|336252156|ref|YP_004595263.1| 142 gsgegetdsFSTGPLLFVLSVITAI 166
                                       8888777554333333333333333 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.35   4.9e+02      63      83 ..       6      26 ..       2      51 .. 0.77
   2 ?    6.4   4.1     0.005       6.9      65     111 ..      66     110 ..      60     115 .. 0.83
   3 ?   -1.5   0.0       1.4   1.9e+03      69      86 ..     158     175 ..     151     234 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.35
                           DUF2157 63 rlvkfllllvllllslllgav 83
                                      rlv++l +++++++ +l++a 
  gi|336252156|ref|YP_004595263.1|  6 RLVRLLAAVSAIAAIALAAAT 26
                                      667777777777777766654 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.005
                           DUF2157  65 vkfllllvllllslllgavlwrdrrvpprlgeallllaalllgaaia 111
                                       +  l+ +vl++++++l+++l+    +++++  ++++la++l+ga+++
  gi|336252156|ref|YP_004595263.1|  66 LEYLVYAVLIIIAVALVWYLLA--YRRDAVKMIAVVLAVCLVGALLF 110
                                       5566777888888888899999..678*****************987 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.4
                           DUF2157  69 lllvllllslllgavlwr 86 
                                        +l+++ + +++g+++ r
  gi|336252156|ref|YP_004595263.1| 158 FVLSVITAIFVGGLLVSR 175
                                       445555555555544444 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.7   2.3e+03     158     290 ..      12      23 ..       6      41 .. 0.51
   2 ?   11.0   0.7    0.0001      0.14     230     297 ..      52     116 ..      48     125 .. 0.81
   3 ?    1.2   0.1       0.1   1.4e+02     244     272 ..     151     177 ..     135     181 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                             MFS_1 158 aivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplyl 234
                                       a+vs++a++                                                                    
  gi|336252156|ref|YP_004595263.1|  12 AAVSAIAAI-------------------------------------------------------------------- 20 
                                       333333333.................................................................... PP

                             MFS_1 235 qevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalg 290
                                                                                            al+
  gi|336252156|ref|YP_004595263.1|  21 -----------------------------------------------------ALA 23 
                                       .....................................................222 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0001
                             MFS_1 230 lplylqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt 297
                                       +p+  q v g +   +l +l++a+l +++++l  ++  l+ r  + +++ + l+++l++al++a+l   
  gi|336252156|ref|YP_004595263.1|  52 MPT--QPVAGGDaPPFLEYLVYAVLIIIAVAL--VWYLLAYRRDAVKMIAVVLAVCLVGALLFAFLFQG 116
                                       566..777777773466776788888888766..******99899******************999765 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.1
                             MFS_1 244 llaglllallalvgailallagrlsdrlg 272
                                       +++g ll +l++++ai+  ++g l+ r g
  gi|336252156|ref|YP_004595263.1| 151 FSTGPLLFVLSVITAIF--VGGLLVSRRG 177
                                       66676666666666666..7777776655 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       3.9   5.4e+03      35      46 ..      13      24 ..       5      33 .. 0.44
   2 ?   10.2   1.7   0.00031      0.42       6      49 ..      71     112 ..      64     134 .. 0.51
   3 ?   -2.8   0.0       3.2   4.4e+03      35      48 ..     159     172 ..     152     195 .. 0.52

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.9
                           DUF4131 35 llllllllallg 46
                                      ++++++++al+ 
  gi|336252156|ref|YP_004595263.1| 13 AVSAIAAIALAA 24
                                      222222222222 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00031
                           DUF4131   6 alvllalllllllllllllrrrprrrvllllllllllallgfal 49 
                                       ++vl++++++l  +ll++   r   ++++++l+++l+++l fa+
  gi|336252156|ref|YP_004595263.1|  71 YAVLIIIAVALVWYLLAYR--RDAVKMIAVVLAVCLVGALLFAF 112
                                       2333333333333333333..55555555555555555555544 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.2
                           DUF4131  35 llllllllallgfa 48 
                                       +l+++ +++++g++
  gi|336252156|ref|YP_004595263.1| 159 VLSVITAIFVGGLL 172
                                       22222222222222 PP

>> PTPS_related  6-pyruvoyl-tetrahydropterin synthase related domain; membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   2.6    0.0011       1.5      23      60 ..      65     103 ..      62     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0011
                      PTPS_related  23 ivafklvvllivfvgalgwylllrregr.rlvavvaavL 60 
                                       +  + ++ +li++ +al wyll +r+   +++avv+av 
  gi|336252156|ref|YP_004595263.1|  65 FLEYLVYAVLIIIAVALVWYLLAYRRDAvKMIAVVLAVC 103
                                       566889999999999999**9999999989999998875 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 ?    0.3   0.6      0.37   5.1e+02      58      80 ..       4      26 ..       1      28 [. 0.84
   2 ?   11.1   0.7   0.00017      0.23       2      55 ..      71     144 ..      70     173 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.37
                                      ....TTSCGGHHHHHHHHHHHHH CS
                       Oxidored_q2 58 atefadplpqalvLtaivigaae 80
                                      +t+ + +l+ + ++ ai+++aa+
  gi|336252156|ref|YP_004595263.1|  4 NTRLVRLLAAVSAIAAIALAAAT 26
                                      67788899999999999999998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHHHHHHHSSCCHHHH.HHHHHHHHHHHHHHHHHHHHC............................. CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvl.iglelisnavnlllvlagvftegtlvi......................t 55 
                                       +++li++++++  y++ +rr+++k++ + l + + ++ l+ +l+  f+ +   +                       
  gi|336252156|ref|YP_004595263.1|  71 YAVLIIIAVALVWYLLAYRRDAVKMIaVVLAVCLVGALLFAFLFQGFSPE---LdaqpieepatvnnssgggdfgsG 144
                                       7889999*****************9967899999**********999833...233355666666666666666662 PP

>> DUF2569  Protein of unknown function (DUF2569)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       9.1   1.3e+04      48      66 ..       7      25 ..       2      27 .. 0.55
   2 ?   12.9   0.9   8.3e-05      0.11      55     116 ..      66     127 ..      63     131 .. 0.84
   3 ?   -2.6   0.0       4.8   6.6e+03      60      77 ..     158     175 ..     152     177 .. 0.58

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.1
                           DUF2569 48 lltlllileiitnialvaf 66
                                      l++ll++++ i +ial+a 
  gi|336252156|ref|YP_004595263.1|  7 LVRLLAAVSAIAAIALAAA 25
                                      5555666666666655555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.3e-05
                           DUF2569  55 leiitnialvafsilllvlffkrrksfPklyiifllanlvlalidalllspifekldaqair 116
                                       le+++ ++l+++++ l+++++  r+   k++ ++l + lv al+ a+l++ ++++ldaq i+
  gi|336252156|ref|YP_004595263.1|  66 LEYLVYAVLIIIAVALVWYLLAYRRDAVKMIAVVLAVCLVGALLFAFLFQGFSPELDAQPIE 127
                                       67888999999999999999988888888888888999999999899999988888888776 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.8
                           DUF2569  60 nialvafsilllvlffkr 77 
                                       ++++v+ +i+++ l+++r
  gi|336252156|ref|YP_004595263.1| 158 FVLSVITAIFVGGLLVSR 175
                                       455555555555555555 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.3   1.8e+03      42      62 ..      10      30 ..       3      37 .. 0.48
   2 ?    4.4   7.6      0.02        27      19      58 ..      74     111 ..      70     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                             Wzy_C 42 lllgilvgvilliilfvlstn 62
                                      ll+++ ++++++++ +++++ 
  gi|336252156|ref|YP_004595263.1| 10 LLAAVSAIAAIALAAATIENP 30
                                      333344444444444445555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.02
                             Wzy_C  19 iigllvalivlliifykrripfllllgilvgvilliilfv 58 
                                       +i ++val+++l+++ +  +  ++++++l++ +++++lf+
  gi|336252156|ref|YP_004595263.1|  74 LIIIAVALVWYLLAYRRDAV--KMIAVVLAVCLVGALLFA 111
                                       57789999999999999999..777776666665555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      831  (0.0463495); expected 358.6 (0.02)
Passed Vit filter:                       132  (0.00736237); 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):              13  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.39
# Mc/sec: 2536.25
//
Query:       gi|336252157|ref|YP_004595264.1|  [L=664]
Description: hypothetical protein Halxa_0746 [Halopiger xanaduensis SH-6]
Scores for 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   69.6   0.4    6.2e-19   68.1   0.2    1.9  2  DUF58            Protein of unknown function DUF58
    1.2e-09   38.4   0.0    6.6e-09   36.0   0.0    2.2  2  DUF11            Domain of unknown function DUF11
  ------ inclusion threshold ------
       0.05   13.6   0.1       0.16   12.0   0.1    1.8  1  Glyco_transf_4   Glycosyltransferase Family 4
       0.64   10.1  11.0      0.047   13.7   3.5    2.6  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        1.9    8.5  14.0       0.17   11.9   7.5    2.3  2  Sensor           Putative sensor
        7.6    6.5  11.1       0.46   10.3   2.0    3.4  2  VPDSG-CTERM      VPDSG-CTERM motif


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.2   2.1e-22   6.2e-19       1      86 []     420     507 ..     420     507 .. 0.96
   2 ?   -3.3   0.0       3.8   1.1e+04      70      85 ..     591     606 ..     589     607 .. 0.85

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 2.1e-22
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstg..dekletavsaaaslar 75 
                                       g+ f+++ReY++gDpl+r+dW+  A+tgel + ef++era++v++++d+++ + l+ ++    +++++v+aa  +a+
  gi|336252157|ref|YP_004595264.1| 420 GTTFHSVREYRAGDPLSRVDWNRRAKTGELATLEFHEERAARVVVLIDARKAAFLAPDPdgTHAVDRSVAAAGRIAA 496
                                       578**************************************************9998888899************** PP

                             DUF58  76 qlldegdrvgl 86 
                                       +ll+ gd vgl
  gi|336252157|ref|YP_004595264.1| 497 SLLADGDTVGL 507
                                       *********97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.8
                             DUF58  70 aaslarqlldegdrvg 85 
                                       a+++ar+l ++g++v 
  gi|336252157|ref|YP_004595264.1| 591 AVTIARRLESRGHPVT 606
                                       78999******99996 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.6   4.9e+03      40      40 ..     138     138 ..      72     187 .. 0.48
   2 !   36.0   0.0   2.2e-12   6.6e-09       6      82 ..     289     357 ..     284     360 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
                             DUF11  40 P 40 
                                        
  gi|336252157|ref|YP_004595264.1| 138 A 138
                                       1 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 2.2e-12
                             DUF11   6 dksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrta 82 
                                       +  ++ pGd++++t+t tN +++  +++++ D +P+gla +++s + gta        L + es  l++tv v+r +
  gi|336252157|ref|YP_004595264.1| 289 SDDDPEPGDEIDVTVTITNESGRFVPDLRLVDGVPPGLAVIEGSNRLGTA--------LRPHESVALEYTVAVRRGT 357
                                       556789****************************************6666........*************999865 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.4e-05      0.16       8      47 ..     591     629 ..     589     653 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.4e-05
                    Glyco_transf_4   8 vleLaraLarrGheVtvvtpgddgpleeevelvvrvprvp 47 
                                       ++++ar+L  rGh Vtvv+p++  +       + +v r+ 
  gi|336252157|ref|YP_004595264.1| 591 AVTIARRLESRGHPVTVVSPDPTADRTAG-HQLASVARRV 629
                                       5789**************99877665555.2233333332 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 ?   13.7   3.5   1.6e-05     0.047      39      99 ..       9      69 ..       2      72 .. 0.74
   2 ?   -0.5   0.8      0.42   1.3e+03      44      58 ..     240     254 ..     232     277 .. 0.46

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                   Phage_holin_3_6 39 llgaagvlallalllllval.alalaalwlaalivaavllvlagvlalvglkklkkakp.lpe 99
                                      l+++ gv+a+++++++++++ a+ l    +  l+v+++   +++v++++ +   ++a++ +pe
  gi|336252157|ref|YP_004595264.1|  9 LALVLGVVAFVGAIAISAGVvAVPL--DGWVVLVVGLLATGIGVVAVFRRRGVRRQAETpTPE 69
                                      6778899999999999999944555..999999999999999988887766644444443666 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.42
                   Phage_holin_3_6  44 gvlallalllllval 58 
                                       gv+al+a+++  +a 
  gi|336252157|ref|YP_004595264.1| 240 GVVALFAVGIGALAE 254
                                       333333333332222 PP

>> Sensor  Putative sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   7.5   5.9e-05      0.17       4      73 ..       9      80 ..       8      94 .. 0.64
   2 ?   -0.8   0.4      0.48   1.4e+03     129     145 ..     241     257 ..     229     285 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                            Sensor  4 lglplgvaafvllvtglslglgllvllvGlplLa.lalllarglaaveRrr.arlllglpvprph.rapep.pg 73
                                      l+l+lgv+afv +++ +s+g++ ++l  G+++L+ ++l+ + g+ av Rrr +r+   +p p+ + + p+p ++
  gi|336252157|ref|YP_004595264.1|  9 LALVLGVVAFVGAIA-ISAGVVAVPL-DGWVVLVvGLLATGIGVVAVFRRRgVRRQAETPTPEHRtPVPAPgAT 80
                                      689**********99.9999988665.57766651555556666555555516766666666555444443433 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.48
                            Sensor 129 allvavlGlllllvllw 145
                                       +++++++G+++l+ ++ 
  gi|336252157|ref|YP_004595264.1| 241 VVALFAVGIGALAESPG 257
                                       22222333333222222 PP

>> VPDSG-CTERM  VPDSG-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.0   0.00016      0.46       9      25 ..      41      57 ..      41      57 .. 0.95
   2 ?   -1.5   1.9      0.79   2.4e+03       9      20 ..     242     253 ..     242     253 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00016
                       VPDSG-CTERM  9 laLLglgLlgLlglRRr 25
                                      ++LL++g+++++++RRr
  gi|336252157|ref|YP_004595264.1| 41 VGLLATGIGVVAVFRRR 57
                                      68**************9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.79
                       VPDSG-CTERM   9 laLLglgLlgLl 20 
                                       +aL++ g+++L+
  gi|336252157|ref|YP_004595264.1| 242 VALFAVGIGALA 253
                                       79********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (664 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.23s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 4998.88
//
Query:       gi|336252158|ref|YP_004595265.1|  [L=221]
Description: hypothetical protein Halxa_0747 [Halopiger xanaduensis SH-6]
Scores for 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  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); 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:                        12  (0.000669307); 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 0.23s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 1750.46
//
Query:       gi|336252159|ref|YP_004595266.1|  [L=344]
Description: molybdenum cofactor biosynthesis protein A [Halopiger xanaduensis SH-6]
Scores for 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-24   85.2   0.0    1.2e-23   84.3   0.0    1.5  1  Radical_SAM  Radical SAM superfamily
    2.6e-15   56.5   0.1    1.1e-14   54.5   0.1    2.0  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    1.7e-07   31.6   0.0    3.5e-07   30.6   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
    1.5e-06   28.4   0.0    3.6e-06   27.1   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.039   14.2   0.0    1.7  1  PAS_3        PAS fold
       0.22   12.7   1.0         14    6.9   0.0    3.1  3  Cytochrom_C  Cytochrome c


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 !   84.3   0.0   3.9e-27   1.2e-23       2     153 ..      16     164 ..      15     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 3.9e-27
                                       EEESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla 74 
                                       + t  Cn++C++C++       + + +   +++++++++ ++ + ae +v+ v ++ggep+l+ d++e++er     
  gi|336252159|ref|YP_004595266.1|  16 SLTDRCNFDCVYCHNEGLgdtrGPMDPQDDEMDTDDVVRFLEVA-AEFDVDAVKFTGGEPMLRQDLEEIIERTPD-- 89 
                                       6799************99**************************.6778*****************999999999.. PP

                                       CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivg 151
                                          ++++++tngt + +  +e l+++g+ rv+++ +a+d+ ++ +++ + + +e+vle+++++ eag+++v+ ++v+
  gi|336252159|ref|YP_004595266.1|  90 --QMEVSLTTNGTFL-PGRAEDLVDAGLERVNVSQDALDPADFAEIT-KSGAYEKVLEGVDAALEAGLDPVKLNMVV 162
                                       ..5************.*******************************.88*************************** PP

                                       BT CS
                                       xx RF
                       Radical_SAM 152 lp 153
                                       ++
  gi|336252159|ref|YP_004595266.1| 163 FK 164
                                       98 PP

>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.1   3.6e-18   1.1e-14       2     126 ..     184     319 ..     183     321 .. 0.66

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 3.6e-18
                                       EEEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE--SS..........T-SSEEEEE....TTT-.-EEEE CS
                       Mob_synth_C   2 elrfIElmpvgegeewrekkvvsadeilerieerlalleakket..........kgpakryki....kdgk.geigl 63 
                                       +l++IE+mp  +g+  ++ ++ + ++ le+ + +++ +e ++++          ++ a  +++     + + g +++
  gi|336252159|ref|YP_004595266.1| 184 QLQLIEYMPELTGKPEWNIDIERVHNWLEERAVEVEHREMHDRRrywiaegavdDEDAGDVTLeaadRS-ElGMVEI 259
                                       789999999877766555444444444444333332222221111233333333444444544664333.3589*** PP

                                       E-TTTS-.-GGG--EEEE-TTSEEESSSS-SS-EEHHHHHHTT--HHHHHHHHHHHHHT----H CS
                       Mob_synth_C  64 Iapvsep.FCasCnRlRltadGklktCLfaeeeidlrdllregaseeeLkelikealarkkekh 126
                                       ++pv++p FCa+C R+R+t +G lk CL ++++++ +  + +++    ++e+++e++a++ +++
  gi|336252159|ref|YP_004595266.1| 260 VDPVENPtFCANCHRVRVTHEGYLKGCLNRNDDLKSMGEMTKPE----IREAFREVVANRVPYY 319
                                       ********************************988888887774....8899999999887765 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 !   30.6   0.0   1.2e-10   3.5e-07       5      93 ..      12      99 ..       9     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.2e-10
                           Fer4_12  5 GvrlslfvsgCnlsCkgCfnketwsfk.....sgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvke 78
                                      Gvr+sl + +Cn+ C +C+n+ + + +     + +e++++   + +e +++  ++ + ++GGEP+l   +++l e++++
  gi|336252159|ref|YP_004595266.1| 12 GVRVSL-TDRCNFDCVYCHNEGLGDTRgpmdpQDDEMDTDDVVRFLEVAAEFDVDAVKFTGGEPML---RQDLEEIIER 86
                                      677775.799**************999777778888888888999999888889************...8889999988 PP

                           Fer4_12 79 vkeekpekdiwlytg 93
                                         +    + + ++g
  gi|336252159|ref|YP_004595266.1| 87 TPDQME--VSLTTNG 99
                                      877765..4555555 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 !   27.1   0.0   1.2e-09   3.6e-06       5      91 ..      18     101 ..      15     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.2e-09
                           Fer4_14   5 lsgCnlsCkgCdnketwks..elgkpqteelleqilk.dlkkseikiqglvltGGePLhyenkkellklvkrlkeey 78 
                                       + +Cn+ C+ C n+   +    + ++++e + +++++    + e++ + + +tGGeP++    ++l ++++r  +++
  gi|336252159|ref|YP_004595266.1|  18 TDRCNFDCVYCHNEGLGDTrgPMDPQDDEMDTDDVVRfLEVAAEFDVDAVKFTGGEPMLR---QDLEEIIERTPDQM 91 
                                       579*********9986555224566666667777777656678899999*********55...66666666666666 PP

                           Fer4_14  79 pekkiwletngtl 91 
                                          ++ l tngt+
  gi|336252159|ref|YP_004595266.1|  92 ---EVSLTTNGTF 101
                                       ...9999999986 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.3e-05     0.039      36      69 ..     302     335 ..     296     342 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                             PAS_3  36 ervrealqealkkgepyegeyRirrkdGeyrwve 69 
                                       +++rea+ e+++++ py gey +++ dGe++  +
  gi|336252159|ref|YP_004595266.1| 302 PEIREAFREVVANRVPYYGEYMVKNDDGEWVVND 335
                                       6899**************************9755 PP

>> Cytochrom_C  Cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.093   2.8e+02      11      28 ..      24      48 ..      12     133 .. 0.69
   2 ?   -0.6   0.0         1     3e+03      28      57 ..     191     220 ..     172     245 .. 0.58
   3 ?    6.9   0.0    0.0048        14      11      36 ..     268     298 ..     265     328 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.093
                                      TGGGTB-SSSBSSS............ CS
                       Cytochrom_C 11 nCaaCHgvegggakqgg........g 28
                                      +C+ CH  + g +  g+         
  gi|336252159|ref|YP_004595266.1| 24 DCVYCHNEGLGDTR-GPmdpqddemD 48
                                      69999965555443.43233333330 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                                       .--HHHHHHHTTT-HHHHHHHHTTSS--SS CS
                       Cytochrom_C  28 gptlsgaaerasaasigasvanpaavsapr 57 
                                        p l+g  e++   + + ++ + +av+   
  gi|336252159|ref|YP_004595266.1| 191 MPELTGKPEWNIDIERVHNWLEERAVEVEH 220
                                       378888888888888888888777666542 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0048
                                       TGGGTB-SSSBSSS.........--HHHHHH CS
                       Cytochrom_C  11 nCaaCHgvegggakqgg.....gptlsgaae 36 
                                        Ca+CH+v+ +  ++ +     + +l+ ++e
  gi|336252159|ref|YP_004595266.1| 268 FCANCHRVRVTHEGYLKgclnrNDDLKSMGE 298
                                       5******998887766666666555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); 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:                         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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2418.10
//
Query:       gi|336252160|ref|YP_004595267.1|  [L=222]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   62.9   0.1    3.4e-17   62.0   0.1    1.5  1  HTH_10    HTH DNA binding domain
    2.4e-11   43.8   2.6    3.5e-11   43.2   2.6    1.2  1  BAT       GAF and HTH_10 associated domain
  ------ inclusion threshold ------
      0.022   14.6   0.1      0.084   12.8   0.0    2.0  2  MarR_2    MarR family
      0.099   12.5   0.0       0.17   11.8   0.0    1.3  1  DUF1463   Protein of unknown function (DUF1463)


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 !   62.0   0.1   7.6e-21   3.4e-17       1      53 []     158     210 ..     158     210 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 7.6e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LTd+q+e+l +A+e GY++ PR+++++ L++elG+s ++lse+Lr+a ++l+e
  gi|336252160|ref|YP_004595267.1| 158 LTDAQYETLVAALERGYYEIPRDMDMEHLSNELGVSHQALSERLRRAHRTLVE 210
                                       9************************************************9985 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   2.6   7.7e-15   3.5e-11      19     154 ..      19     158 ..       6     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 7.7e-15
                               BAT  19 alaaeldcrveleglvprsdgevlvfftvdgad..peevrdaaedldavedvrvvseeddgtlleltvsgpslas.. 91 
                                       +l +  d  ve+e++v+ + + v+ +++ +g++     v+d +e+ ++ve  +++++ dd+ l+++ + +++ +   
  gi|336252160|ref|YP_004595267.1|  19 TLEESGDVDVEIERVVAYDPDHVMPYVWFSGDEstLSVVADRLEADPSVEAFELLTDLDDERLYRMNWVDDVTVMir 95 
                                       678888999**********************66224459****************************8877766555 PP

                               BAT  92 tlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrref 154
                                        l+e  +tv +a +e+++++++v +P+++ + +v+e  +++  +v+    + +e++++ r ++
  gi|336252160|ref|YP_004595267.1|  96 LLTEEKATVLDAWVEGTQWQFRVLFPERESLSNVYEFATDEGISVSIQKIHRVEEDRHNRYDL 158
                                       9*******************************************************9998776 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      0.99   4.4e+03      36      47 ..      52      63 ..      49      68 .. 0.57
   2 ?   12.8   0.0   1.9e-05     0.084       3      46 ..     158     205 ..     156     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.99
                                      HHHHHHHHHHHH CS
                            MarR_2 36 savsrilkrLva 47
                                      s++s + +rL+a
  gi|336252160|ref|YP_004595267.1| 52 STLSVVADRLEA 63
                                      455555555554 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.9e-05
                                       --HHHHHHHHHHHCTTTS....EEEHHHHHHHHTSSHHHHHHHHHHHH CS
                            MarR_2   3 ltpaqarvLaaLgrrpgr....dltvgelarrlglsksavsrilkrLv 46 
                                       lt aq+  L a   r+ +    d+ +  l  +lg+s++a+s +l+r+ 
  gi|336252160|ref|YP_004595267.1| 158 LTDAQYETLVAALERGYYeiprDMDMEHLSNELGVSHQALSERLRRAH 205
                                       6666666666655555336777999********************985 PP

>> DUF1463  Protein of unknown function (DUF1463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.7e-05      0.17      14      93 ..      19      98 ..      11     105 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                           DUF1463 14 tlldsgklelsseptvrakissedknlpvislr.dpktvvyvfd.levskgsldyklltklsdeqfyeld.vrkedklk 89
                                      tl +sg +++  e   r ++   d+ +p + +  d  t+  v d le       + llt+l de++y ++ v     + 
  gi|336252160|ref|YP_004595267.1| 19 TLEESGDVDVEIE---RVVAYDPDHVMPYVWFSgDESTLSVVADrLEADPSVEAFELLTDLDDERLYRMNwVDDVTVMI 94
                                      5555555555444...45667789999988885378888888775888888899***************9445555666 PP

                           DUF1463 90 dlvf 93
                                      +l+ 
  gi|336252160|ref|YP_004595267.1| 95 RLLT 98
                                      6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1705.91
//
Query:       gi|336252161|ref|YP_004595268.1|  [L=74]
Description: hypothetical protein Halxa_0750 [Halopiger xanaduensis SH-6]
Scores for 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  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 543.67
//
Query:       gi|336252162|ref|YP_004595269.1|  [L=488]
Description: hypothetical protein Halxa_0751 [Halopiger xanaduensis SH-6]
Scores for 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-157  524.5   0.1   2.4e-157  524.4   0.1    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 !  524.4   0.1  1.3e-161  2.4e-157       1     412 []      53     488 .]      53     488 .] 0.98

  Alignments for each domain:
  == domain 1  score: 524.4 bits;  conditional E-value: 1.3e-161
                                       HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvke 73 
                                       qlkn+++lpgi++++++mPD H+G+g+p+G+V a++   g+i+P+aVG+DI CGvr+++tnlt++el+++ +elv++
  gi|336252162|ref|YP_004595269.1|  53 QLKNTTHLPGITNYAICMPDGHQGYGFPVGGVGALDaenGCISPGAVGYDInCGVRMMRTNLTYDELQGREEELVDS 129
                                       89*************************************************************************** PP

                                       HHHHS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB  74 lekavpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlG 150
                                       l++++p+glg  + v+   +++ee+le+g++wa+e+g + eedl ++e+eg  ++ad++kvs+kak+r+++q+G+lG
  gi|336252162|ref|YP_004595269.1| 130 LFANIPSGLGGGGIVEAGVDTVEEILERGVDWALENGHAVEEDLLHCEDEGMRAGADADKVSQKAKDRGKNQIGSLG 206
                                       **********99****999********************************************************** PP

                                       STT-EEEEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 151 sGNHFiEvqlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagse 227
                                       sGNHF+Evq v++++d+++ +a+glee+q+vv++H+GSRglGhq ++dyl++++++ +    +lpd++La++pags+
  gi|336252162|ref|YP_004595269.1| 207 SGNHFLEVQRVTDVFDDDVGEAFGLEEDQIVVLIHCGSRGLGHQTCNDYLRKIEQQHQGLLNQLPDKELAAAPAGSQ 283
                                       ******************************************************99998888*************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxx RF
                              RtcB 228 egqaYlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAt 300
                                        +++Y++am+aa n+A++NRq+i++r+r+++e+v++++ e+++++l++dvaHNiakkE+h+ d   ++++VhRKGAt
  gi|336252162|ref|YP_004595269.1| 284 LAEDYYAAMNAAINFAWVNRQLIMHRTRQVFERVFDRSWEEMDMHLLYDVAHNIAKKETHTvDgeeRELYVHRKGAT 360
                                       ***********************************99999*********************956789********** PP

                                       E-.............TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCC CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 301 rA.............kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeq 362
                                       rA             +vgqpviipGsmg++Sy+++G +n++  +fgSt+HGAGRlmsR++ak++f++ +v+++leeq
  gi|336252162|ref|YP_004595269.1| 361 RAfpaghpevpkayrDVGQPVIIPGSMGAGSYVLRGGENSMdlTFGSTAHGAGRLMSRTQAKNEFWGGDVQQQLEEQ 437
                                       **************************************************************************665 PP

                                       .T-EEEE------------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 363 .gigvearkkegvleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                         i+v+a++ ++v+eEap+ YKd+deVv++ ++ g+ ++var  pv+++kg
  gi|336252162|ref|YP_004595269.1| 438 dRIYVKAQSGATVAEEAPGVYKDVDEVVRVSDALGIGDKVARTFPVCNIKG 488
                                       2799*********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3360.36
//
Query:       gi|336252163|ref|YP_004595270.1|  [L=355]
Description: DoxX family protein [Halopiger xanaduensis SH-6]
Scores for 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   32.6   9.9    9.2e-08   32.6   9.9    3.9  3  DoxX      DoxX
     0.0048   16.8   9.4      0.045   13.6   1.2    3.5  3  DoxD      TQO small subunit DoxD
  ------ inclusion threshold ------
      0.041   13.5   5.6        1.9    8.1   2.6    2.6  2  Wzy_C     O-Antigen ligase
      0.074   12.9   1.3       0.22   11.4   1.3    1.9  1  DUF4321   Domain of unknown function (DUF4321)
        6.7    7.4  18.8        4.4    8.0   5.6    2.9  2  DoxX_3    DoxX-like family


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.3         5   1.8e+04      44      55 ..      49      60 ..      39      64 .. 0.56
   2 !    8.0  11.9    0.0012       4.3      50      78 ..     118     146 ..      86     154 .. 0.92
   3 !   32.6   9.9   2.6e-11   9.2e-08       3      82 ..     218     301 ..     216     310 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 5
                              DoxX 44 laylaalvElvg 55
                                      l  + a++ lvg
  gi|336252163|ref|YP_004595270.1| 49 LGGALAVLALVG 60
                                      344444444444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0012
                              DoxX  50 lvElvgglllllGlltRlaAlalavtllv 78 
                                       l+++++g lll+Gl+tRl+Al+ +v  lv
  gi|336252163|ref|YP_004595270.1| 118 LLQVALGFLLLFGLATRLVALIGLVAYLV 146
                                       6899*****************98887665 PP

  == domain 3  score: 32.6 bits;  conditional E-value: 2.6e-11
                              DoxX   3 lllRlllgvlfiahGl.qkltgfglegtaasla...alglpppellaylaalvElvgglllllGlltRlaAlalavt 75 
                                       ++ R+ lg++f++ G+ qkl  +g++ ++ ++    a+ + +pel+++ a+l+E ++gl+l+lGl+tR  A+  + +
  gi|336252163|ref|YP_004595270.1| 218 TITRVGLGATFVVLGVgQKLLRPGIALAVVERYdltAVVPVAPELWVLGAGLAETALGLALILGLFTRATAVTAIGM 294
                                       789*********999857999665555555544555677777**************************777777766 PP

                              DoxX  76 llvatlt 82 
                                          + ++
  gi|336252163|ref|YP_004595270.1| 295 FTLTLFA 301
                                       6655554 PP

>> DoxD  TQO small subunit DoxD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.6    0.0042        15      74      97 ..     119     142 ..     112     186 .. 0.78
   2 ?    0.6   0.0      0.13   4.6e+02       1      26 [.     216     241 ..     216     250 .. 0.91
   3 !   13.6   1.2   1.3e-05     0.045      72     149 ..     268     339 ..     252     347 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0042
                              DoxD  74 vEiivGlllliGlltRlsslvafa 97 
                                       + + +G lll Gl tRl++l  ++
  gi|336252163|ref|YP_004595270.1| 119 LQVALGFLLLFGLATRLVALIGLV 142
                                       56789************9975443 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                              DoxD   1 fllilRlalgliflsagirkkvlkpa 26 
                                       f++i R+ lg +f+  g+ +k+l+p+
  gi|336252163|ref|YP_004595270.1| 216 FPTITRVGLGATFVVLGVGQKLLRPG 241
                                       67899******************997 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 1.3e-05
                              DoxD  72 tlvEiivGlllliGlltRlsslvafalalg..ialsayWlgstcedEyqiglllvaaelvliltgsgklslDylllk 146
                                       +l E  +Gl l++Gl+tR +++ a+ +     +al+   + +       +gl  +a   vl++tgsg +++D +l  
  gi|336252163|ref|YP_004595270.1| 268 GLAETALGLALILGLFTRATAVTAIGMFTLtlFALPDDPVLA------HVGLFGMA--SVLLITGSGPYAVDEYLET 336
                                       56799**************99999887433013334333333......45555554..4678899999999999876 PP

                              DoxD 147 klk 149
                                        ++
  gi|336252163|ref|YP_004595270.1| 337 LMG 339
                                       665 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.6   0.00052       1.9       3      72 ..     121     204 ..     119     247 .. 0.66
   2 ?    5.7   0.1    0.0029        10       3      66 ..     272     337 ..     270     348 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00052
                             Wzy_C   3 lllsllalflstsRsgiigllvalivlliifykrripfllllgilvgvilliilfv...................ls 60 
                                       ++l++l+lf+  +R   +   ++l+++l+ ++++    lll + +vg +++i+l+                    + 
  gi|336252163|ref|YP_004595270.1| 121 VALGFLLLFGLATRLVAL---IGLVAYLVGLIRWPT--LLLQLEFVGGLAAIALVGsgkpsadhvlqqvagtsgtVY 192
                                       579999********9554...455555555555555..555555555555555555444445666666666555555 PP

                             Wzy_C  61 tnletlknitka 72 
                                       +++  ++++ +a
  gi|336252163|ref|YP_004595270.1| 193 RQFDPVHRRAQA 204
                                       555555555555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0029
                             Wzy_C   3 lllsllalflstsRsgiigllvalivlliifykrri.pfllllg.ilvgvilliilfvlstnletl 66 
                                       ++l+l+++++  +R+  +++++++ + l++++   + ++++l g + v++i++  + ++++ letl
  gi|336252163|ref|YP_004595270.1| 272 TALGLALILGLFTRATAVTAIGMFTLTLFALPDDPVlAHVGLFGmASVLLITGSGPYAVDEYLETL 337
                                       679999**************9999999999999888667777777888888888888888888887 PP

>> DUF4321  Domain of unknown function (DUF4321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.3   6.2e-05      0.22      12      48 .]     107     144 ..      97     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.2e-05
                           DUF4321  12 lssPl.tlDLgvlkltFglsfkinlasiiGiilAiliY 48 
                                       + sP+ ++DL  l++++g+ + + la+ +  +++++ Y
  gi|336252163|ref|YP_004595270.1| 107 FISPAvEVDLRLLQVALGFLLLFGLATRLVALIGLVAY 144
                                       556877***************************99988 PP

>> DoxX_3  DoxX-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   4.8     0.013        46      22      84 ..      97     156 ..      82     171 .. 0.63
   2 ?    8.0   5.6    0.0012       4.4      35      74 ..     261     300 ..     238     310 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.013
                            DoxX_3  22 allaaaglgealasllliaggladialGlllllrrkrrlalllqialllayllaatlllpelw 84 
                                        l++a + g+ + +++ + + l+++alG lll++ ++rl++l+    l+ayl++++ ++  l+
  gi|336252163|ref|YP_004595270.1|  97 PLIGAGFSGYFISPAVEVDLRLLQVALGFLLLFGLATRLVALI---GLVAYLVGLIRWPTLLL 156
                                       555554444444444445566899************9976655...55566666666655555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0012
                            DoxX_3  35 sllliaggladialGlllllrrkrrlalllqialllayll 74 
                                       +l ++++gla+ alGl+l+l+  +r++++++i++ ++ l+
  gi|336252163|ref|YP_004595270.1| 261 ELWVLGAGLAETALGLALILGLFTRATAVTAIGMFTLTLF 300
                                       5678999*************99999888888876655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2447.69
//
Query:       gi|336252164|ref|YP_004595271.1|  [L=93]
Description: hypothetical protein Halxa_0753 [Halopiger xanaduensis SH-6]
Scores for 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  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 748.23
//
Query:       gi|336252165|ref|YP_004595272.1|  [L=153]
Description: hypothetical protein Halxa_0754 [Halopiger xanaduensis SH-6]
Scores for 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-37  127.6   0.1    4.2e-37  127.5   0.1    1.0  1  Archease  Archease protein family (MTH1598/TM1083)


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 !  127.5   0.1   2.4e-41   4.2e-37       1     138 []       3     153 .]       3     153 .] 0.88

  Alignments for each domain:
  == domain 1  score: 127.5 bits;  conditional E-value: 2.4e-41
                                       EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS-.-TT---S-EE.....EEEEEESSSHHHHHHHHHHHHHHHH CS
                          Archease   1 yeyldhtADviieawGksleeafesaalalfeymtd.lskvepkeek.....eieveaedledlLfdfLdellylfd 71 
                                       ye++dhtADv+++a+G+slee+f+s+a++l+++++d +   +++e+      +++v+ae++++lLfd+Lde++yl+d
  gi|336252165|ref|YP_004595272.1|   3 YELRDHTADVAVAATGDSLEEVFASVADGLAAASCDeIPAADADEDGsgdrfSFAVAAENRDALLFDYLDEVIYLRD 79 
                                       9***********************************5555555544478889************************* PP

                                       HT--S----EE..........EE.E-SSSEEEEEEEE----.-TT----.----B--S---EEEEETTEEEEEEEEE CS
                          Archease  72 teyfvfkevkv..........deeeeeeeleleaeargekfdkekhevq.tevKAvTyhelrieeeddgweayvvvD 137
                                       ++  +  + +v          d+e+++++++lea+arg+++     e++ +evKAvTy+e+++e++ddgw ayvv+D
  gi|336252165|ref|YP_004595272.1|  80 VRAELPVDHRVeairepgeatDDETDDDRWSLEATARGVPL----GEIDaREVKAVTYSEMELERRDDGWGAYVVFD 152
                                       **66666666677888998875568899*************....235559************************** PP

                                       - CS
                          Archease 138 i 138
                                       +
  gi|336252165|ref|YP_004595272.1| 153 V 153
                                       8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1289.24
//
Query:       gi|336252166|ref|YP_004595273.1|  [L=158]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-15   56.5   0.1    4.6e-15   55.8   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.7e-15   56.0   0.1    4.5e-15   55.7   0.1    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.9e-14   52.9   0.2    5.5e-14   52.4   0.2    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    7.9e-10   38.6   0.0    1.2e-09   38.0   0.0    1.3  1  FR47             FR47-like protein
    0.00061   20.0   0.1     0.0012   19.0   0.1    1.7  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00081   19.6   0.1     0.0014   18.8   0.1    1.5  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
     0.0025   17.9   0.0     0.0083   16.2   0.0    1.9  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0038   17.3   0.0     0.0065   16.6   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.055   13.3   0.0       0.12   12.2   0.0    1.5  1  Acetyltransf_18  Acetyltransferase (GNAT) domain
        2.9    8.3   5.5        1.8    9.1   3.3    1.7  2  NTS_2            N-terminal segments of P. falciparum erythro


Domain annotation for each model (and alignments):
>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.1   2.5e-18   4.6e-15       3      75 ..      51     122 ..      47     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 2.5e-18
                                       EEEEEEEETTEEEEEEEEEEESTCTEEEEE-GGGTTSSHHHHHHH.HTT.SEEEEE.EEEETHHHHHHHHHHTTEE CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslldaeitrlaVdpeyrgkGiGraLle.aae.kgiile.qlelnaekaikfYeklGFe 75 
                                        +++V  +dg  +Gf+a+ +++ +i +laVdp+yrg GiG++L++ +ae +  +++ ++++++e+a++fYe+lGFe
  gi|336252166|ref|YP_004595273.1|  51 VHCYV--QDGDLIGFAAVRRDG-YILFLAVDPAYRGEGIGKRLVArVAEdHD-TITcHARTSNENALQFYEHLGFE 122
                                       46664..579999****99997.9999*****************85323433.2355666755689*********8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.1   2.5e-18   4.5e-15      31     109 ..      49     124 ..      17     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.5e-18
                   Acetyltransf_10  31 alllvaeeggkivGvielrdgshisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnasp.yavpfYeklGF 106
                                        +++ + ++g ++G++++r++++i  l+Vdp+yrg Gigk+L+ +v e  ++     + +++ s+ +a +fYe+lGF
  gi|336252166|ref|YP_004595273.1|  49 SKVHCYVQDGDLIGFAAVRRDGYILFLAVDPAYRGEGIGKRLVARVAEDHDTI----TCHARTSNeNALQFYEHLGF 121
                                       45666777899***********************************9996433....677777889*********** PP

                   Acetyltransf_10 107 kav 109
                                       +  
  gi|336252166|ref|YP_004595273.1| 122 EIK 124
                                       966 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.2   3.1e-17   5.5e-14       8     117 .]      21     121 ..      15     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 3.1e-17
                                       HHHHTHHHHHHHHHHH.HHHH....HHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHH CS
                    Acetyltransf_1   8 lvesffppnedaseee.fees....fsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGs 79 
                                       ++e ++  ne++ +   ++++     ++   +++v   dg liGf+    + d     +yi +laV+p+yrg G+G+
  gi|336252166|ref|YP_004595273.1|  21 AWELKERINEEEGVLKqRRKFftdaYRRSKVHCYV--QDGDLIGFAA--VRRD-----GYILFLAVDPAYRGEGIGK 88 
                                       34444433444444444444422224444446666..*********4..4455.....78***************** PP

                                       HHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  80 aLlealeerareegikkivlaveedndaairlYeklGF 117
                                       +L+  ++e   ++  + i ++ + +n+ a  +Ye lGF
  gi|336252166|ref|YP_004595273.1|  89 RLVARVAE---DH--DTITCHARTSNENALQFYEHLGF 121
                                       ***99998...44..5689999999********99**9 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   6.8e-13   1.2e-09      12      80 ..      60     124 ..      53     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 6.8e-13
                                       EEEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  12 laawilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                       l++    + +g++  l v+p  r++G g+rlv+ +    ae  +t++ ++++sN+++ ++ye lGfe  
  gi|336252166|ref|YP_004595273.1|  60 LIGFAAVRRDGYILFLAVDPAYRGEGIGKRLVARV----AEDHDTITCHARTSNENALQFYEHLGFEIK 124
                                       5556666789*********************9866....5679***********************965 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   6.9e-07    0.0012     121     151 ..      97     138 ..      15     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.9e-07
                    Acetyltransf_4 121 p...........nensiqfhkalGFelvgifkkcikkngrwi 151
                                       +           nen+ qf+++lGFe+ ++ +++++++g  +
  gi|336252166|ref|YP_004595273.1|  97 DhdtitchartsNENALQFYEHLGFEIKRRIDDYYEDGGDAY 138
                                       433333333345999*********************999766 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   7.8e-07    0.0014      21     122 ..       8      97 ..       4     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.8e-07
                    Acetyltransf_6  21 rfrvatdpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrldgrpvAvalglrsgdrlyy 97 
                                       r+++  +++ +e ++el+++  ++  +v     +r+f++d++++        +++   dg ++++a++ r+g   y 
  gi|336252166|ref|YP_004595273.1|   8 RVVTPGSDDYVEDAWELKERINEEE-GVL--KQRRKFFTDAYRRS------KVHCYVQDGDLIGFAAVRRDG---YI 72 
                                       56667789999**********9999.999..7899*********9......8**************998887...99 PP

                    Acetyltransf_6  98 wlggydpelaklspgllllwelied 122
                                       ++ ++dp++++ ++g+ l+++++ed
  gi|336252166|ref|YP_004595273.1|  73 LFLAVDPAYRGEGIGKRLVARVAED 97 
                                       9********************9987 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) 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    0.0083      54     127 ..      48     123 ..      10     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.6e-06
                                       EEEEEEEEEEEEETT.EEEEE.EEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--..SSHHHHHTTT-E CS
                    Acetyltransf_9  54 vgqlallplelnvpG.ktlka.agvtgVavapehrgrgvlskLlaraleemreegqplsllfP..ssipiYrrfGye 126
                                        ++++++ ++  + G + ++  +++   av+p +rg+g+ ++L+ar+ e+ +   ++    +    + ++Y+++G+e
  gi|336252166|ref|YP_004595273.1|  48 RSKVHCYVQDGDLIGfAAVRRdGYILFLAVDPAYRGEGIGKRLVARVAEDHDT--ITCHARTSneNALQFYEHLGFE 122
                                       577788888888888744444499***********************999887..6666666655557899999988 PP

                                       E CS
                    Acetyltransf_9 127 i 127
                                       i
  gi|336252166|ref|YP_004595273.1| 123 I 123
                                       6 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 !   16.6   0.0   3.6e-06    0.0065      30      52 ..      75      97 ..      50     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.6e-06
                   Acetyltransf_CG 30 TeVpeelrGkGiAkkLvkaaldd 52
                                        V++++rG+Gi+k+Lv ++ +d
  gi|336252166|ref|YP_004595273.1| 75 LAVDPAYRGEGIGKRLVARVAED 97
                                      579***************99876 PP

>> Acetyltransf_18  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.7e-05      0.12      12     101 ..      37     123 ..      31     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                   Acetyltransf_18  12 dRskfLkrrlkqaeqklvvveedgeivGyglarktrkglk..iGPlvAeneeiAeaLlkalvanaegkkvridvpee 86 
                                       +R+kf+++  + ++    ++ +dg + G++ +r+    l   + P + + e i ++L+++++++++   ++ +  ++
  gi|336252166|ref|YP_004595273.1|  37 QRRKFFTDAYRRSKV--HCYVQDGDLIGFAAVRRDGYILFlaVDPAY-RGEGIGKRLVARVAEDHDT--ITCHARTS 108
                                       799999999887666..888889999*******99876652255765.6678899999999988887..79999999 PP

                   Acetyltransf_18  87 nkalielleklgfke 101
                                       n+++ ++ e lgf+ 
  gi|336252166|ref|YP_004595273.1| 109 NENALQFYEHLGFEI 123
                                       ***********9985 PP

>> NTS_2  N-terminal segments of P. falciparum erythrocyte membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         8   1.4e+04      33      42 ..      49      58 ..      49      59 .. 0.51
   2 ?    9.1   3.3   0.00098       1.8      36      48 ..     129     141 ..     126     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8
                             NTS_2 33 SevqYYrsGG 42
                                      S+v  Y   G
  gi|336252166|ref|YP_004595273.1| 49 SKVHCYVQDG 58
                                      5566565555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00098
                             NTS_2  36 qYYrsGGDGdYLk 48 
                                       +YY+ GGD +YLk
  gi|336252166|ref|YP_004595273.1| 129 DYYEDGGDAYYLK 141
                                       7***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1202.22
//
Query:       gi|336252167|ref|YP_004595274.1|  [L=185]
Description: regulatory protein ArsR [Halopiger xanaduensis SH-6]
Scores for complete 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   47.5   1.2    3.2e-12   46.3   1.2    1.6  1  HTH_20       Helix-turn-helix domain
      4e-06   26.6   0.3    5.4e-05   23.0   0.3    2.3  1  HTH_5        Bacterial regulatory protein, arsR family
     0.0026   17.7   0.4     0.0048   16.8   0.4    1.5  1  HTH_12       Ribonuclease R winged-helix domain
     0.0026   17.7   0.2     0.0051   16.7   0.2    1.5  1  PadR         Transcriptional regulator PadR-like family
     0.0031   17.3   0.0      0.005   16.7   0.0    1.4  1  TFIIE_alpha  TFIIE alpha subunit
     0.0048   17.2   1.9       0.33   11.3   0.0    2.6  2  PqqD         Coenzyme PQQ synthesis protein D (PqqD)
  ------ inclusion threshold ------
       0.04   13.8   0.0        0.1   12.5   0.0    1.7  1  TrmB         Sugar-specific transcriptional regulator TrmB
        0.1   12.6   0.1        0.2   11.6   0.1    1.5  1  Cdc6_C       CDC6, C terminal winged helix domain
       0.17   11.5   0.1       0.44   10.1   0.0    1.8  2  HTH_24       Winged helix-turn-helix DNA-binding


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 !   46.3   1.2   1.6e-15   3.2e-12       3      58 ..      20      79 ..      18      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1.6e-15
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHH.....TS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerl.....dlskntlsyHLrvLeeagLvevvr 58
                                      + +A+++P R+++l++L  ++++++++l+e+l     d ++nt+++H+++L++agLve  r
  gi|336252167|ref|YP_004595274.1| 20 VSSAVDEPIRAMLLDML-AEGERSVADLDEALaergyDRTRNTVRHHVNELRDAGLVEIAR 79
                                      679**************.**************999888*******************9776 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 !   23.0   0.3   2.7e-08   5.4e-05       2      46 ..      27      76 ..      26      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.7e-08
                                      HHHHHHHHHHTTSSEEHHHHHHHH.....TS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeel.....glsqstvShHLkkLreaGLVe 46
                                      p R  +L +Laege++v +l e+l     + ++ tv+hH + Lr+aGLVe
  gi|336252167|ref|YP_004595274.1| 27 PIRAMLLDMLAEGERSVADLDEALaergyDRTRNTVRHHVNELRDAGLVE 76
                                      89******************9999777667899****************6 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 !   16.8   0.4   2.4e-06    0.0048       2      49 ..      31      76 ..      30      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.4e-06
                            HTH_12  2 eILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltr 49
                                      + L++lae ++  +   + e L +rgyd    +vR +   l + gl++
  gi|336252167|ref|YP_004595274.1| 31 MLLDMLAEGER--SVADLDEALAERGYDRTRNTVRHHVNELRDAGLVE 76
                                      68999***999..7789****************************997 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   2.6e-06    0.0051       1      66 [.      32      94 ..      32      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.6e-06
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEES CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlT 66
                                      +L +l+e+++   ++ ++l+e+  g ++    ++    ++L++ glve  + e++ g+++kyYr +
  gi|336252167|ref|YP_004595274.1| 32 LLDMLAEGERSVADLDEALAER--G-YDRTRNTVRHHVNELRDAGLVEIARLEEQGGGTTKYYRAN 94
                                      68999*****************..9.899999*******************************975 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.5e-06     0.005      39      75 ..      57      92 ..      21     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.5e-06
                                      S-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEE CS
                       TFIIE_alpha 39 idlnelrklLnrLyearlvkykrrrdeekswykyywr 75
                                        +n +r+ +n+L++a+lv++ r  +++ ++ kyy r
  gi|336252167|ref|YP_004595274.1| 57 RTRNTVRHHVNELRDAGLVEIARLEEQGGGTTKYY-R 92
                                      45799*******************99999988876.4 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00017      0.33      22      67 .]      32      75 ..      29      75 .. 0.85
   2 ?    4.7   0.4     0.019        37      31      61 ..     108     139 ..     101     144 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                      HHHH-.SSSS-HHHHHHHHHHHC.T--HHHHHHHHHHHHHHHHCTT-- CS
                              PqqD 22 iWkll.dgersveeivaalaeey.dvdeeeaeadvlafldqLrekgli 67
                                      ++++l +gersv+++ +alae+  d      ++ v+  +++Lr++gl+
  gi|336252167|ref|YP_004595274.1| 32 LLDMLaEGERSVADLDEALAERGyDR----TRNTVRHHVNELRDAGLV 75
                                      6788889*************775264....6799*********99997 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.019
                                       -.HHHHHHHHHHHC.T--HHHHHHHHHHHHHHH CS
                              PqqD  31 s.veeivaalaeey.dvdeeeaeadvlafldqL 61 
                                         vee ++ala    d   +++ead  +++d+ 
  gi|336252167|ref|YP_004595274.1| 108 AdVEEMATALAPDVaDLV-ATLEADYGETIDEI 139
                                       457777777776664554.67777777777665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.1e-05       0.1      15      64 ..      33      93 ..      30      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-05
                                      HHHHHHCCCHHCHHCCCT.....TSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE CS
                              TrmB 15 laLlklgpatadeiaeel.....gvprskvYevLrsLedkGlVerekgr......pklYra 64
                                      l +l++g+ ++ ++ e+l     ++ r++v   +++L d+GlVe+ + +      +k+Yra
  gi|336252167|ref|YP_004595274.1| 33 LDMLAEGERSVADLDEALaergyDRTRNTVRHHVNELRDAGLVEIARLEeqgggtTKYYRA 93
                                      56777788888777776544444799******************99855578886667776 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 ?   11.6   0.1    0.0001       0.2      37      73 ..      57      92 ..      50     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                      --HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEE CS
                            Cdc6_C 37 ltqrevsdllseLemlgileleksskGrregrtrkis 73
                                      +t+++v+++++eL + g++e+++  + +++g t++++
  gi|336252167|ref|YP_004595274.1| 57 RTRNTVRHHVNELRDAGLVEIARLEE-QGGGTTKYYR 92
                                      7999*****************96544.3457777776 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 ?   10.1   0.0   0.00022      0.44      30      48 .]      58      76 ..      56      76 .. 0.92
   2 ?   -2.9   0.0       2.7   5.4e+03      38      45 ..      77      84 ..      77      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                            HTH_24 30 SpstvnrrlkrLeeeGlIk 48
                                      +++tv+ ++++L ++Gl++
  gi|336252167|ref|YP_004595274.1| 58 TRNTVRHHVNELRDAGLVE 76
                                      679**************96 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.7
                            HTH_24 38 lkrLeeeG 45
                                      + rLee+G
  gi|336252167|ref|YP_004595274.1| 77 IARLEEQG 84
                                      679**998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1502.68
//
Query:       gi|336252168|ref|YP_004595275.1|  [L=70]
Description: Heavy metal transport/detoxification protein [Halopiger xanaduensis SH-6]
Scores for complete 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   47.8   0.1    1.6e-12   47.7   0.1    1.0  1  HMA            Heavy-metal-associated domain
      0.001   19.1   0.0     0.0011   19.1   0.0    1.0  1  Tox-PL-2       Papain fold toxin 2
     0.0037   17.4   0.0     0.0039   17.4   0.0    1.0  1  Thioredoxin_4  Thioredoxin


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 !   47.7   0.1   2.6e-16   1.6e-12       2      62 .]       6      66 ..       5      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 2.6e-16
                               HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                      +rv + +C  Ca+ ve++L + +gVe++ v + t++v++e+d+++++ +++ +ai k gy+
  gi|336252168|ref|YP_004595275.1|  6 YRVTDFDCPTCASNVERALTKTDGVEDAAVHFTTGRVEIEYDETAVDAETLENAITKQGYT 66
                                      688899***************************************999*********9995 PP

>> Tox-PL-2  Papain fold toxin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.8e-07    0.0011       7      69 ..       2      65 ..       1      70 [] 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.8e-07
                          Tox-PL-2  7 geivkrfklleCveCAaalekyLke.qgisGkrlklktksaedaasfilserlekqaaisenGr 69
                                      ++i  r+++++C +CA+++e++L +  g++   ++ +t+  e +++  + +    ++ai++ G+
  gi|336252168|ref|YP_004595275.1|  2 TQIEYRVTDFDCPTCASNVERALTKtDGVEDAAVHFTTGRVEIEYDETAVDAETLENAITKQGY 65
                                      7888999***************965279**********99887776666666555657**9998 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.6e-07    0.0039      21      80 ..       9      65 ..       2      70 .] 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.6e-07
                                      E-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE-..---STTTHHHHHHHTT--TTHHH CS
                     Thioredoxin_4 21 edlrCphCakfeeeveklleeyidtGkvkfiirdfpldkekeslkaamaarcageespea 80
                                      +d++Cp+Ca   e    ++++ +++  v f+ + + ++ ++ +++a ++ ++  +++  +
  gi|336252168|ref|YP_004595275.1|  9 TDFDCPTCASNVERA-LTKTDGVEDAAVHFTTGRVEIEYDETAVDAETLENAITKQG--Y 65
                                      7********854444.578999*************9999999*********999987..4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 582.81
//
Query:       gi|336252169|ref|YP_004595276.1|  [L=632]
Description: heavy metal translocating P-type ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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  155.1   2.0    1.3e-45  155.1   2.0    1.9  2  E1-E2_ATPase  E1-E2 ATPase
    7.2e-40  137.5   6.5    7.2e-40  137.5   6.5    1.7  2  Hydrolase     haloacid dehalogenase-like hydrolase
    0.00082   19.8   0.4    0.00082   19.8   0.4    2.6  3  HAD           haloacid dehalogenase-like hydrolase
     0.0013   18.5   1.4       0.13   12.0   1.3    2.3  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
      0.003   17.6   0.8      0.019   15.1   0.0    2.7  4  Hydrolase_6   Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.04   14.4   0.2       0.18   12.3   0.0    2.3  2  CBS           CBS domain


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 !  155.1   2.0   4.5e-49   1.3e-45       1     180 [.     119     290 ..     119     291 .. 0.98
   2 ?   -3.4   0.2         2   5.9e+03     119     131 ..     588     600 ..     566     623 .. 0.49

  Alignments for each domain:
  == domain 1  score: 155.1 bits;  conditional E-value: 4.5e-49
                                       SSS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEE CS
                      E1-E2_ATPase   1 kllpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvv 77 
                                       +++p+ta v+r g+e+e++a++++ G  v++k+g +vp+Dg++ +g++ +d+s +TGEs pv+k++gd+v++Gt++ 
  gi|336252169|ref|YP_004595276.1| 119 EMTPDTAIVRRHGEEVEVPARDVEAGETVVVKPGAKVPVDGEVTDGESAIDQSPVTGESAPVHKDAGDEVYAGTINQ 195
                                       5899************************************************************************* PP

                                       E-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHH CS
                      E1-E2_ATPase  78 sgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralal 154
                                       +g +++v+t tg+dt+l++i+r veea+++k+p++ ++++++ +++p+++++a+ +++++           + al+l
  gi|336252169|ref|YP_004595276.1| 196 EGALEVVATGTGRDTTLERIIRRVEEAQEAKAPTETIIERFATYYTPAIVALAAGAYAVT--------GDAVMALTL 264
                                       ***********************************************************8........7899***** PP

                                       HHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 155 lvaaiPcaLplavplalalgarrlak 180
                                       lv+ +P aL++  p++++ +++++a+
  gi|336252169|ref|YP_004595276.1| 265 LVIGCPGALVIGPPVSIVSAIGSAAR 290
                                       ***********************998 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHH CS
                      E1-E2_ATPase 119 gkvlvpvvllial 131
                                       +  +++v+ll+a 
  gi|336252169|ref|YP_004595276.1| 588 AIAVATVGLLLAG 600
                                       2222222222222 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.5   4.3e+03     132     170 ..     195     235 ..     157     259 .. 0.59
   2 !  137.5   6.5   2.4e-43   7.2e-40       1     210 []     307     540 ..     307     540 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                                       HTTEEEEEEESSEH.HHHHHHHHHTT.GGGESEEEEHHCES CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxx RF
                         Hydrolase 132 aagievvlltgdnp.etaeraanqlG.ddyfdaviasdiet 170
                                       + g   v++tg  + +t er+++++  ++  +a  +++ie 
  gi|336252169|ref|YP_004595276.1| 195 QEGALEVVATGTGRdTTLERIIRRVEeAQEAKAPTETIIER 235
                                       34442333333333133335555555433334444444444 PP

  == domain 2  score: 137.5 bits;  conditional E-value: 2.4e-43
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHH.................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx.................. RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakar.................. 53 
                                       i++v+fDk+GTLt+ge  v dv     ++ +++l+t+      seh+++ a+ +aa ++                  
  gi|336252169|ref|YP_004595276.1| 307 IDLVAFDKTGTLTKGETTVADVEGFG-VDDREVLRTAaiaekrSEHHLADAILEAARDLggesngayatdgglvler 382
                                       799*************9999999999.8888888888888889****************777776666666666655 PP

                                       .HHHH.HHHHHETTTE........HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHT CS
                                       .xxxx.xxxxxxxxxx........xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                         Hydrolase  54 .sgal.tgfatfigrg........ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadp 116
                                         +   ++f++++g+g        ++ +g++ +l++   + p+++ a   + ++ g+t++++  + ++++v+ + d+
  gi|336252169|ref|YP_004595276.1| 383 rIP-DpDEFEVVPGKGvvarhdgrVIVVGNRSLLAERgvELPEQVAAYARKREENGETAVYVvrDEEVVGVVSLRDE 458
                                       222.246666688888*********************************************99999*********** PP

                                       HHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 117 lkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeev 193
                                         ++++aa++va+L++ag+++v+ltgdn++ta+++a+ +G          +++  a  +pe k+ ai+ +q+ ++ v
  gi|336252169|ref|YP_004595276.1| 459 --LREDAADVVAALQDAGVRTVMLTGDNERTARAVAETVG----------IDDYRAAMLPEEKQDAIQSFQAAGHVV 523
                                       ..**************************************..........6666*********************** PP

                                       EEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxx RF
                         Hydrolase 194 amVGDgvnDaaalaaAg 210
                                       amVGDg+nDa+ la A+
  gi|336252169|ref|YP_004595276.1| 524 AMVGDGINDAPSLATAD 540
                                       **************997 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.6   7.7e+03      31      84 ..      87     138 ..      81     153 .. 0.53
   2 ?   -2.5   0.0       1.9   5.7e+03       2      27 ..     311     335 ..     310     364 .. 0.58
   3 !   19.8   0.4   2.8e-07   0.00082      86     186 ..     459     535 ..     412     537 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.6
                               HAD  31 wralreklllalfrellrldraglaelleallagls.eelaaelerfvaevirpk 84 
                                       w+a+++++l al   +++l+ +   +  +al + l+  ++ a ++r ++ev  p+
  gi|336252169|ref|YP_004595276.1|  87 WEAAAVFFLFAL---GSYLEARTMGKTRSALEELLEmTPDTAIVRRHGEEVEVPA 138
                                       555555555555...4444444444444444444444445555666666556665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                               HAD   2 lfDfDgTLldgdslelllrfllrrga 27 
                                        fD  gTL+ g++  + ++   ++++
  gi|336252169|ref|YP_004595276.1| 311 AFDKTGTLTKGETTVADVE-GFGVDD 335
                                       5777789999988876666.333222 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 2.8e-07
                               HAD  86 ldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewl 162
                                       l+++a +++aa ++aG+r+v+++g +++ ++++++ +g    ++        + +           e+k +a+++  
  gi|336252169|ref|YP_004595276.1| 459 LREDAADVVAALQDAGVRTVMLTGDNERTARAVAETVG----IDD-------YRAA-------MLPEEKQDAIQS-- 515
                                       5589******9***************************....888.......4444.......344455567777.. PP

                               HAD 163 aaegegidleevvayGDspsDlpl 186
                                       +++  +     v  +GD+++D p 
  gi|336252169|ref|YP_004595276.1| 516 FQAAGH----VVAMVGDGINDAPS 535
                                       333322....25555888888776 PP

>> Hydrolase_3  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      0.01        31      16      57 ..     459     500 ..     453     505 .. 0.89
   2 !   12.0   1.3   4.3e-05      0.13     198     240 ..     515     558 ..     508     565 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.01
                                       --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSE CS
                       Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgldlp 57 
                                       + e ++++++ l+++g+  v  TG + r+++ v+e +g+d +
  gi|336252169|ref|YP_004595276.1| 459 LREDAADVVAALQDAGVRTVMLTGDNERTARAVAETVGIDDY 500
                                       66788999******************************9976 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.3e-05
                                       HCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS.-HHHHHHSS CS
                       Hydrolase_3 198 elnisleeviafGDgeNDieMLeaaglgvAmgna.seevkkaAd 240
                                        ++     v+ +GDg ND + L  a++g+Amg a ++++++ Ad
  gi|336252169|ref|YP_004595276.1| 515 SFQAAGHVVAMVGDGINDAPSLATADVGIAMGAAgTDTAIETAD 558
                                       566666778999*******************9863677777776 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.6   7.6e+03       7      21 ..     292     306 ..     291     307 .. 0.87
   2 ?   -1.5   0.0      0.91   2.7e+03       1      19 [.     310     328 ..     310     331 .. 0.85
   3 ?   -3.7   0.0       4.3   1.3e+04      78      92 ..     401     415 ..     396     417 .. 0.77
   4 !   15.1   0.0   6.3e-06     0.019       6      72 ..     450     521 ..     429     530 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.6
                                       TTSEETTEE-TTHHH CS
                       Hydrolase_6   7 GvLwrgdkaipgaae 21 
                                       GvL++g++ ++ a +
  gi|336252169|ref|YP_004595276.1| 292 GVLMKGGEHLETAGK 306
                                       9*******9999876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.91
                                       EEEESTTTSEETTEE-TTH CS
                       Hydrolase_6   1 flfDidGvLwrgdkaipga 19 
                                       ++fD  G+L +g++ +  +
  gi|336252169|ref|YP_004595276.1| 310 VAFDKTGTLTKGETTVADV 328
                                       579*********9988776 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.3
                                       SXXXEEEEESXHHHH CS
                       Hydrolase_6  78 kadkkvlvigeeglr 92 
                                       ++d++v v+g+  l+
  gi|336252169|ref|YP_004595276.1| 401 RHDGRVIVVGNRSLL 415
                                       578899999988776 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 6.3e-06
                                       TTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHH.....HHTT----GGGEEEHHHHHHH CS
                       Hydrolase_6   6 dGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkl.....eklgvditeeqvvtsataaae 72 
                                        Gv+   d++ + aa+++ al++ag+++v+lT  + ++ +++a+ +     ++  ++ ++++ ++s +aa +
  gi|336252169|ref|YP_004595276.1| 450 VGVVSLRDELREDAADVVAALQDAGVRTVMLTGDNERTARAVAETVgiddyRAAMLPEEKQDAIQSFQAAGH 521
                                       6999999***********************************998732111222333455777777777665 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         3   8.9e+03      15      26 ..     209     220 ..     208     223 .. 0.81
   2 ?   12.3   0.0   5.9e-05      0.18      30      50 ..     438     457 ..     425     464 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3
                                       TSBHHHHHHHHH CS
                               CBS  15 dttleealelmr 26 
                                       dttle ++++ +
  gi|336252169|ref|YP_004595276.1| 209 DTTLERIIRRVE 220
                                       899999999984 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.9e-05
                                       SSEEEEEETTTBEEEEEEHHH CS
                               CBS  30 vsrlPVVdedgklvGivtlrD 50 
                                        ++++VV  d+++vG+v+lrD
  gi|336252169|ref|YP_004595276.1| 438 ETAVYVV-RDEEVVGVVSLRD 457
                                       4599***.5667********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.24s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4351.98
//
Query:       gi|336252170|ref|YP_004595277.1|  [L=212]
Description: hypothetical protein Halxa_0759 [Halopiger xanaduensis SH-6]
Scores for 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-05   23.7   0.0    9.5e-05   22.5   0.0    1.6  1  FmdE      FmdE, Molybdenum formylmethanofuran dehydrogenase o


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 !   22.5   0.0   5.3e-09   9.5e-05       3     125 ..      53     203 ..      51     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.3e-09
                                       SS--CHHHHHHHHHHHHHHCC....-TT.SSSEEEEES-S..................TCHHHHHHHHCS--TTTTS CS
                              FmdE   3 GHlCpglvlGyrmakaalkelgpkeeeg.deelvaivetd..................sCldDAiqvltgctlGkgn 60 
                                       GH Cp ++  yr+ak  l+ l p +e   + e+ +++ +                   +   D++  l +   G++n
  gi|336252170|ref|YP_004595277.1|  53 GHSCPTAAGAYRIAKDGLEALYPGDELPvRGEIAVLAGDPrddsaygvtarllsyitgAAGEDGFGGLADGHGGRRN 129
                                       9********************996554476666666666688888888888999999*******************9 PP

                                       EEE--...SS-SEEEEEETTT-EEEEEEE-.......CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHHHHHS CS
                              FmdE  61 livmd...ygkkaltfkkrktgkavrlklk.......eelpelreklakgkakeekeeeeleeeleeaikkilna 125
                                       l        +  a+ + +++t ++vr+++          +     kl++g+a+++ e++++ + ++  +++iln 
  gi|336252170|ref|YP_004595277.1| 130 LLRYGaigADGVAVELTRTDTDETVRVTYHvedvpagGPATSTLPKLIDGTATDA-ERAAFADDWHGRVAAILNG 203
                                       976665557777889****************999999667777788888888777.7889999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1689.61
//
Query:       gi|336252171|ref|YP_004595278.1|  [L=391]
Description: DNA primase small subunit [Halopiger xanaduensis SH-6]
Scores for 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-23   83.3   0.0    4.8e-23   82.1   0.0    1.6  1  DNA_primase_S  DNA primase small subunit


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 !   82.1   0.0   2.7e-27   4.8e-23       1     171 [.      97     319 ..      97     323 .. 0.78

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 2.7e-27
                                       EEEEEETTT-...TT--HHHHHHHHHHHHHHHHHHHH-----GGGEEEEE--SEEEEEEE--TTEEES-HHHHHHHH CS
                     DNA_primase_S   1 FDiDmddydd..cseatvcekcwkfvsvavkvldellredfgfkdilwvfsgrrGfHcwvsdkdarpltdeeraaiv 75 
                                       FD+D+d++++    e+++ e+++k  +   ++ld +l+ df f+++ +vfsg+rG+H++v+d ++ +l +e+r++iv
  gi|336252171|ref|YP_004595278.1|  97 FDLDADHLPNvtLGEDSYAEMLAKCKDALLRLLD-FLENDFAFQNMEIVFSGGRGYHVHVRDANVLELEREHRREIV 172
                                       9********************************8.889*************************************** PP

                                       H.H..........................................................HCHHHHCT-------- CS
                     DNA_primase_S  76 n.ylnly..............rplhpflsrsmlkivkpvveeiileeqdpf..........eikkllrllpdkslre 127
                                       +   +++                             k+  e  +l+ q+ +          +++ ll++  d++l +
  gi|336252171|ref|YP_004595278.1| 173 DyVRGIGldfeelietetvagL------------GRKTPTERRMLQIQGGWgkrihahfmdFVDDLLAMEEDAALER 237
                                       *555566655443333222221............4444455558999999999977774443333333333333333 PP

                                       ..........................................................-----------------.. CS
                     DNA_primase_S 128 kkkw........................................eakedivlvllyprldeqvtkgikhllkapfci 164
                                          +                                            +  +++    +de+vt+++++l+++p+++
  gi|336252171|ref|YP_004595278.1| 238 ---LqefdgigegkaqatlnaarnnregldsgnvtvhtaveqlaQRFAERAVERDNAPIDEPVTTDTNRLIRLPGSL 311
                                       ...24447778888888999999999999***********988844445556677788******************* PP

                                       ..---.-- CS
                     DNA_primase_S 165 hgktg.nv 171
                                       hg++g ++
  gi|336252171|ref|YP_004595278.1| 312 HGGSGlKT 319
                                       ***99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3085.62
//
Query:       gi|336252172|ref|YP_004595279.1|  [L=345]
Description: hypothetical protein Halxa_0761 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00042   20.8   0.1    0.00067   20.1   0.1    1.3  1  Sld5      GINS complex protein
  ------ inclusion threshold ------
       0.15   11.3   1.0       0.26   10.6   0.6    1.5  2  CorA      CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   7.5e-08   0.00067      25     108 ..       1     104 [.       1     105 [. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.5e-08
                                       HCHHHHHHCCCHHTTSSSSTTTTTTHH.HHHHHHHHHHT........................HCHHHHHHHHHHHH CS
                              Sld5  25 lspesleailedetkssdlpslpphfl.elavkllelard.......................ldelkrllrdllev 77 
                                       ++ ++l++++++e+++  l++l p f+ e+++++ +l+ +                       ++  k +++++ e 
  gi|336252172|ref|YP_004595279.1|   1 MNLDELRSVQSKERQKDSLQNLRPSFYqEVGEYIADLEDErdrvaeqaedpfsspevgrltdeIETAKDVVEAIYER 77 
                                       57899***********888888777663799*******655588888888999999999988999999********* PP

                                       HHHHHHHTHCHHHHHHHTS-TCCHCCS-HHH CS
                              Sld5  78 RlakirkfaenledaagggggellsglseeE 108
                                       R+ k+ k+a+  ++        +++gl++eE
  gi|336252172|ref|YP_004595279.1|  78 RMGKLVKQASLAAAGM----PADDEGLTAEE 104
                                       **********999999....77888999998 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6   2.9e-05      0.26     121     206 ..      28     120 ..      13     133 .. 0.76
   2 ?   -2.1   0.0      0.21   1.9e+03     148     194 ..     294     344 ..     286     345 .] 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.9e-05
                              CorA 121 drlfellekleeeldeledeledstkkeilrelaq.lr..rrlvkl..rralapnrevlkrlla...kaddklldde 189
                                       +++ e++ +le+e+d++ ++ ed  + +++++l++ ++  +++v+   +r +  + +   +l a    add+ l++e
  gi|336252172|ref|YP_004595279.1|  28 QEVGEYIADLEDERDRVAEQAEDPFSSPEVGRLTDeIEtaKDVVEAiyERRMGKLVKQA-SLAAagmPADDEGLTAE 103
                                       567799***************99999999999987544447777766744444444444.455556899******** PP

                              CorA 190 dkeylrdlldelerlle 206
                                       ++++++dl d++e+   
  gi|336252172|ref|YP_004595279.1| 104 EADLFDDLVDRIESNKS 120
                                       ************98444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.21
                              CorA 148 eilrelaqlrrrlvkl.....rralapnrevlkrllakaddkllddedkeyl 194
                                       +  r+++++ r+++ +     r++ + + +++ +l +++ d+l++++++e+l
  gi|336252172|ref|YP_004595279.1| 294 DVDRTTVRITRDVGSIlgiddREYTLSTDDIV-TLPEQNADPLVEQDAAERL 344
                                       55667778888888888888899999999999.9999999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2497.65
//
Query:       gi|336252173|ref|YP_004595280.1|  [L=163]
Description: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen [Halopiger xanaduensis SH-6]
Scores for 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-34  116.8   0.0    6.4e-34  116.5   0.0    1.1  1  AhpC-TSA   AhpC/TSA family
    4.3e-17   62.2   0.0    5.1e-17   61.9   0.0    1.0  1  Redoxin    Redoxin
    7.5e-07   29.1   0.0      1e-06   28.7   0.0    1.3  1  SCO1-SenC  SCO1/SenC
     0.0016   18.0   0.0     0.0018   17.8   0.0    1.1  1  DUF899     Bacterial protein of unknown function (DUF899)


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 !  116.5   0.0   1.4e-37   6.4e-34       1     123 [.       4     132 ..       4     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 1.4e-37
                                       TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfi 77 
                                       vg++ap+fel n++getv+lsd++g+ +v++fyp++++++Ctte++ + +++e+f+ +   v+g+s+d++++++ f+
  gi|336252173|ref|YP_004595280.1|   4 VGEAAPEFELSNQHGETVRLSDFEGRRLVVYFYPRANTEGCTTEACGFDDVLEQFETLETAVVGISDDPVDDLETFA 80 
                                       79*************************************************************************** PP

                                       HH-H.SSEEEE-TTSHHHHHTT-EETT......TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  78 ekeslnfpllsDeegkvakaygvlkee......kglalratfvidkegkiry 123
                                       ++++l f+llsDe g+va+ y+ + e+        +  r t+v+ ++g i++
  gi|336252173|ref|YP_004595280.1|  81 DDYDLSFDLLSDELGEVATLYDSYGEKqmfgntFDGVFRNTYVVGPDGRIEA 132
                                       *******************************99999*************986 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0   1.1e-20   5.1e-17       2     145 ..       4     145 ..       3     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 1.1e-20
                                       TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHH CS
                           Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvke 78 
                                       +g++aP+f+l   +++g++v ls+f+g+++vv+f+p+a +  C++e++ ++++ e++++    vv+++ d  +    
  gi|336252173|ref|YP_004595280.1|   4 VGEAAPEFEL--SNQHGETVRLSDFEGRRLVVYFYPRANTEGCTTEACGFDDVLEQFETLETAVVGISDDPVDDLET 78 
                                       7999*****8..56**********************************88888788799998887777666666*** PP

                                       HHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG.....EEE-EEEEEEETTEEEEEEESSSCHTSTTSHHH CS
                           Redoxin  79 fwgkeglkfpvlsDgsaaftkalGlrleedaseg.....lrtpryavidedgkvvylevepepeteesnaea 145
                                       f+++++l+f +lsD+ ++++  ++ + e++   +        + + v+  dg++ +++  ++p +    aea
  gi|336252173|ref|YP_004595280.1|  79 FADDYDLSFDLLSDELGEVATLYDSYGEKQM--FgntfdGVFRNTYVVGPDGRIEAVFEDVSPDG---HAEA 145
                                       **************66666655554432222..123466899*******************9944...4433 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   2.3e-10     1e-06       2     107 ..       9     108 ..       8     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.3e-10
                         SCO1-SenC   2 gpFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkey 78 
                                        +Fel +q+ge+v+ +d+eg+  +v+f     ++ C+t+    ++vl++++    +  ++ i+ DP    +++l+++
  gi|336252173|ref|YP_004595280.1|   9 PEFELSNQHGETVRLSDFEGRRLVVYFYPRANTEGCTTEACGFDDVLEQFETL--ETAVVGISDDP----VDDLETF 79 
                                       58************************************************998..66777777676....5679999 PP

                         SCO1-SenC  79 leafdpriigltGskeeiakaakefrvyv 107
                                       ++ +d ++  l+++  e+a+++++++ ++
  gi|336252173|ref|YP_004595280.1|  80 ADDYDLSFDLLSDELGEVATLYDSYGEKQ 108
                                       9999999999*999999999999997654 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     4e-07    0.0018      48     152 ..      10     108 ..       2     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4e-07
                            DUF899  48 eyrfdgeeGkvsLadlFegrsqLivyhfmfgpdaeegCpgCslladhvdgalahLeardvtlavvsraplekleayk 124
                                       e+++  ++G++  +  Fegr+ L+vy   f p   ++ +gC++ a  +d  l+++e+ +++++ +s  p+++le++ 
  gi|336252173|ref|YP_004595280.1|  10 EFELSNQHGETVRLSDFEGRR-LVVY---FYPR--ANTEGCTTEACGFDDVLEQFETLETAVVGISDDPVDDLETFA 80 
                                       566667777765555588885.7776...4444..3457899999999999************************** PP

                            DUF899 125 rrmGwtlpwvssaesdfnrdfnvsleee 152
                                       ++   ++++ s+   ++ + +    e++
  gi|336252173|ref|YP_004595280.1|  81 DDYDLSFDLLSDELGEVATLYDSYGEKQ 108
                                       ************9999998888544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1189.26
//
Query:       gi|336252174|ref|YP_004595281.1|  [L=166]
Description: AsnC family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-13   48.8   0.1    5.7e-13   48.2   0.1    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
    4.8e-12   45.5   0.9    8.9e-12   44.6   0.9    1.5  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    0.00011   22.0   0.1    0.00029   20.7   0.0    1.7  2  MarR_2           MarR family
     0.0002   21.4   0.0    0.00035   20.6   0.0    1.4  1  HTH_20           Helix-turn-helix domain
    0.00022   21.1   1.8    0.00041   20.3   1.8    1.3  1  BAT              GAF and HTH_10 associated domain
     0.0013   18.6   0.1     0.0035   17.2   0.0    1.6  2  HTH_11           HTH domain
     0.0015   18.1   0.3     0.0034   16.9   0.3    1.6  1  HTH_CodY         CodY helix-turn-helix domain
      0.005   16.7   0.0        4.2    7.3   0.0    2.4  2  TrmB             Sugar-specific transcriptional regulator Trm
     0.0068   16.3   0.0      0.016   15.1   0.0    1.6  2  MarR             MarR family
     0.0094   15.9   0.0      0.023   14.7   0.0    1.7  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0097   16.4   0.1      0.028   14.9   0.0    1.8  2  HTH_27           Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.018   14.8   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
      0.017   14.6   0.0      0.023   14.1   0.0    1.2  1  Glyco_hydro_101  Endo-alpha-N-acetylgalactosaminidase
      0.022   14.8   0.3      0.094   12.8   0.0    1.9  2  P2               P2 response regulator binding domain
      0.041   13.7   0.0       0.13   12.1   0.0    1.8  2  HTH_23           Homeodomain-like domain
      0.043   14.0   0.0      0.092   12.9   0.0    1.6  1  AsnC_trans_reg2  AsnC-like ligand binding domain
      0.045   13.9   0.3       0.13   12.4   0.1    1.8  2  DprA_WH          DprA winged helix domain
      0.085   13.1   0.6       0.15   12.3   0.6    1.4  1  ALS_ss_C         Small subunit of acetolactate synthase
       0.17   11.7   0.0       0.29   10.9   0.0    1.4  1  LexA_DNA_bind    LexA DNA binding domain


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 !   48.2   0.1   6.1e-16   5.7e-13       1      48 []      13      61 ..      13      61 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 6.1e-16
                            HTH_24  1 ldetdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ld+td +IL +Lq+++r i+   + +r+gl  stv  r+ +Lee+G+I+
  gi|336252174|ref|YP_004595281.1| 13 LDRTDMAILHVLQDDARnITTEAIGDRVGLAASTVANRIANLEESGVIE 61
                                      79**********************************************7 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 !   44.6   0.9   9.4e-15   8.9e-12       1      42 []      13      55 ..      13      55 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 9.4e-15
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaR.isyaeLAervGlSestvlrRvrrLe 42
                                      LD++D +IL+ Lq daR i+ +++++rvGl++stv++R++ Le
  gi|336252174|ref|YP_004595281.1| 13 LDRTDMAILHVLQDDARnITTEAIGDRVGLAASTVANRIANLE 55
                                      8**************8879*********************998 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   3.1e-07   0.00029       2      52 ..      12      61 ..      11      65 .. 0.94
   2 ?   -3.2   0.0       8.9   8.4e+03      16      27 ..      86      99 ..      76     101 .. 0.52

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.1e-07
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +l++++  +L++L +  + ++t  ++ +r gl  s+v ++++ L++ G +e
  gi|336252174|ref|YP_004595281.1| 12 DLDRTDMAILHVLQDDAR-NITTEAIGDRVGLAASTVANRIANLEESGVIE 61
                                      78999*********9996.59***************************998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.9
                                      CTTTS...EEEHHHH CS
                            MarR_2 16 rrpgr...dltvgel 27
                                      ++++    d +v+e+
  gi|336252174|ref|YP_004595281.1| 86 DADRDavvD-RVSEI 99
                                      444323333.66666 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.7e-07   0.00035       9      56 ..      14      62 ..       9      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.7e-07
                                      -HHHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  9 hPvRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +++ ++il  L  +a+  t +++ +r++l+ +t+ ++++ Lee g +e+
  gi|336252174|ref|YP_004595281.1| 14 DRTDMAILHVLqDDARNITTEAIGDRVGLAASTVANRIANLEESGVIEG 62
                                      678899*****9999999*****************************96 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   1.8   4.3e-07   0.00041      39      95 ..      76     132 ..      66     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.3e-07
                               BAT  39 gevlvfftvdgadpeevrdaaedldavedvrvvseeddgtlleltvsgpslastlae 95 
                                        + l+ +t+++ad ++v+d ++++++v +v+v+  ++d   +el  ++++ a+++a+
  gi|336252174|ref|YP_004595281.1|  76 HRMLLVGTIEDADRDAVVDRVSEIENVVSVTVLMVDEDNVYVELVSRSQDRAERVAD 132
                                       578999***************************************999999999986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.7e-06    0.0035       4      44 ..      19      59 ..      17      64 .. 0.90
   2 ?   -2.5   0.0       5.5   5.2e+03      38      48 ..     133     143 ..     129     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-06
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      +il+ L +   +i+ e + ++ ++  +tv ++I+ Lee+gv
  gi|336252174|ref|YP_004595281.1| 19 AILHVLQDDARNITTEAIGDRVGLAASTVANRIANLEESGV 59
                                      69999*777777****************************4 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.5
                            HTH_11  38 aLeelgvpIes 48 
                                       +L+++g++I +
  gi|336252174|ref|YP_004595281.1| 133 ELNDIGIEISK 143
                                       78889988865 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 !   16.9   0.3   3.6e-06    0.0034       5      35 ..      31      61 ..      28      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.6e-06
                          HTH_CodY  5 LtaskiaDriGitrsvivnaLrkLesaGiie 35
                                      +t   i Dr+G++ s + n +  Le +G+ie
  gi|336252174|ref|YP_004595281.1| 31 ITTEAIGDRVGLAASTVANRIANLEESGVIE 61
                                      57789*************************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 !    7.2   0.0     0.005       4.7      20      53 ..      28      61 ..      10      63 .. 0.83
   2 !    7.3   0.0    0.0044       4.2      10      33 ..     112     135 ..     108     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.005
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                        + t++ i  ++g+  s+v + + +Le+ G++e
  gi|336252174|ref|YP_004595281.1| 28 ARNITTEAIGDRVGLAASTVANRIANLEESGVIE 61
                                      567899*************************997 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0044
                                       CCCHCHHHHHHCCCHHCHHCCCTT CS
                              TrmB  10 EakvYlaLlklgpatadeiaeelg 33 
                                       E  vY+ L+++ + +a+ +a el+
  gi|336252174|ref|YP_004595281.1| 112 EDNVYVELVSRSQDRAERVADELN 135
                                       778*****************9986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.7e-05     0.016       4      48 ..      16      61 ..      13      63 .. 0.84
   2 ?   -3.0   0.0       7.9   7.4e+03      45      52 ..     118     125 ..     118     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                                      HHHHHHHHHH.HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  4 tqfviLrily.eqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      t + iL+ l  +  +++   +++++g+  stv + +  Le+ G ie
  gi|336252174|ref|YP_004595281.1| 16 TDMAILHVLQdDARNITTEAIGDRVGLAASTVANRIANLEESGVIE 61
                                      666777777514667999*************************997 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.9
                                       TSEEEEEE CS
                              MarR  45 GlieRsks 52 
                                       +l++Rs++
  gi|336252174|ref|YP_004595281.1| 118 ELVSRSQD 125
                                       68999997 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 !   14.7   0.0   2.4e-05     0.023      20      52 ..      29      61 ..      10      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglis 52
                                       ++t e +++++Gl  +tv   ++ L++ g+i+
  gi|336252174|ref|YP_004595281.1| 29 RNITTEAIGDRVGLAASTVANRIANLEESGVIE 61
                                      479*****************************8 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 !   14.9   0.0   2.9e-05     0.028       3      49 ..      15      61 ..      13      65 .. 0.90
   2 ?   -2.4   0.0       7.6   7.2e+03      10      24 ..     118     130 ..     112     135 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-05
                            HTH_27  3 rqqalvLhlirhrrrrkkl.adlcgrlnvedshisyslkkLtekGLve 49
                                      r + ++Lh+++  ++r++  +++ +r+ + +s++++ +  L+e G++e
  gi|336252174|ref|YP_004595281.1| 15 RTDMAILHVLQ-DDARNITtEAIGDRVGLAASTVANRIANLEESGVIE 61
                                      66889******.88888888*************************994 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.6
                            HTH_27  10 hlirhrrrrkkladl 24 
                                       +l+   r +++++++
  gi|336252174|ref|YP_004595281.1| 118 ELVS--RSQDRAERV 130
                                       4444..444444444 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 ?   14.8   0.0   1.9e-05     0.018       6      49 ..      18      61 ..      13      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +aiL  l   ++  t   + +r gl+ Stv + ++ L+e G +e
  gi|336252174|ref|YP_004595281.1| 18 MAILHVLQDDARNITTEAIGDRVGLAASTVANRIANLEESGVIE 61
                                      69*************************************99876 PP

>> Glyco_hydro_101  Endo-alpha-N-acetylgalactosaminidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.4e-05     0.023     143     216 ..      81     159 ..      64     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                                       B-HHHHHHTT.HHHHHHHHHHHH-......T--EEEEESTSTTSHHHHHHHHHHHCTT-EEEES-TTS-TTT-SBBH CS
                   Glyco_hydro_101 143 idsreDlasgkllkRfkelreelge.....eldfiYvDvyresgwaskklskelnkqGwrvasewaealeedstwsh 214
                                       + ++eD    ++++R++e+++ ++      + d +Yv+   +s  +++++++eln+ G+++++    + ++d  ++h
  gi|336252174|ref|YP_004595281.1|  81 VGTIEDADRDAVVDRVSEIENVVSVtvlmvDEDNVYVELVSRSQDRAERVADELNDIGIEISKTGVITEQRDRPFNH 157
                                       5677899999999999999999988777667799****************************999999999999999 PP

                                       HH CS
                   Glyco_hydro_101 215 Wa 216
                                        +
  gi|336252174|ref|YP_004595281.1| 158 LG 159
                                       76 PP

>> P2  P2 response regulator binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.9e-05     0.094      23      77 ..      51     105 ..      41     108 .. 0.74
   2 ?   -0.4   0.1       1.3   1.2e+03      52      75 ..     118     142 ..     110     147 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.9e-05
                                       HHHHHHTTEEEEEES-HHHHHTT-SSSEEEEEE...EESS-HHHHHHHHHTSSS-SEE CS
                                P2  23 fkaLeelgeiiksiPsvedieeekfdegfevvl...ltkeskeeikealasiseiesv 77 
                                       + +Lee g i  + P    i+ e+ +++ +++l   + + + + + +++++i  + sv
  gi|336252174|ref|YP_004595281.1|  51 IANLEESGVIEGYMP---MIDHENAGFEHRMLLvgtIEDADRDAVVDRVSEIENVVSV 105
                                       679************...7778888*******93333455556666655555555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
                                       EEEEEESS-HHHHHHHHHT.SSS-S CS
                                P2  52 evvlltkeskeeikealas.iseie 75 
                                       e+v  ++  +e++ ++l++   ei+
  gi|336252174|ref|YP_004595281.1| 118 ELVSRSQDRAERVADELNDiGIEIS 142
                                       4555678888888888877555665 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   0.00014      0.13      10      46 ..      19      60 ..      18      62 .. 0.84
   2 ?   -1.9   0.0       3.4   3.2e+03      17      28 ..     124     135 ..     117     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                            HTH_23 10 illllae....GlsvreIAreLgvsrrTvyrwlkryreeG.l 46
                                      ++l++++     +++++I ++ g   +Tv + +   +e+G +
  gi|336252174|ref|YP_004595281.1| 19 AILHVLQddarNITTEAIGDRVGLAASTVANRIANLEESGvI 60
                                      566666667889******************999999999955 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.4
                            HTH_23  17 GlsvreIAreLg 28 
                                        ++ +++A+eL+
  gi|336252174|ref|YP_004595281.1| 124 QDRAERVADELN 135
                                       567788999986 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 ?   12.9   0.0   9.8e-05     0.092       2      65 ..      72     136 ..      71     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.8e-05
                   AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpe.vtHcYeRewpynlyfmvharseeeveevlaeiaa 65 
                                       +Gf++  l +  +++++ ++v  +v+e+++ v+  ++   + n+y+ +  rs+++ e+v++e+++
  gi|336252174|ref|YP_004595281.1|  72 AGFEHRMLLVGTIEDADRDAVVDRVSEIENvVSVTVLMVDEDNVYVELVSRSQDRAERVADELND 136
                                       8*************************98762688899999*********************9975 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00014      0.13       2      56 ..       5      61 ..       4      63 .. 0.87
   2 ?   -2.4   0.0       5.7   5.4e+03      11      22 ..      86      97 ..      84     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                           DprA_WH  2 pappaepplddlerrvLaaLgpePv..hvDqLvrrtglpaaevsaaLleLELaGlve 56
                                      p p a  +ld +  ++L  L+ +++  + +++  r+gl a++v+    +LE +G +e
  gi|336252174|ref|YP_004595281.1|  5 PDPGADVDLDRTDMAILHVLQDDARniTTEAIGDRVGLAASTVANRIANLEESGVIE 61
                                      56777888999999******988654599**********************888886 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.7
                           DprA_WH 11 ddlerrvLaaLg 22
                                      d+++++v+++++
  gi|336252174|ref|YP_004595281.1| 86 DADRDAVVDRVS 97
                                      788999998877 PP

>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   0.00016      0.15      17      70 ..      95     148 ..      83     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                       HHHHHHHHTT-EEEEEETTEEEEEEEE.-HHHHHHHHHHS-GGGEEEEEEEEEEE CS
                          ALS_ss_C  17 eileiaeifrakivdvspdsliieltg.teekidaliellkpfgilevvRtGrvA 70 
                                        + ei ++ ++ ++ v +d + +el+  ++++ + + ++l+++gi e+++tG++ 
  gi|336252174|ref|YP_004595281.1|  95 RVSEIENVVSVTVLMVDEDNVYVELVSrSQDRAERVADELNDIGI-EISKTGVIT 148
                                       578899999***************875167899**********96.9*****985 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 ?   10.9   0.0   0.00031      0.29      29      57 ..      34      61 ..      20      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                                      HHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                     LexA_DNA_bind 29 reiaralglkSpsaveehLkaLerKGyie 57
                                        i++++gl+ +s+v+++ + Le  G+ie
  gi|336252174|ref|YP_004595281.1| 34 EAIGDRVGLA-ASTVANRIANLEESGVIE 61
                                      569*******.9****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1337.79
//
Query:       gi|336252175|ref|YP_004595282.1|  [L=123]
Description: hypothetical protein Halxa_0764 [Halopiger xanaduensis SH-6]
Scores for 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-20   73.8   0.2    1.4e-20   73.4   0.2    1.2  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.2   7.6e-25   1.4e-20       1      75 []      22      93 ..      22      93 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 7.6e-25
                            HalOD1  1 deespstaVveavaavegvdptel.epLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75
                                      ++e++++++ve+vaa+++ +p el  pLy+a+DpdAL +L +s    +++++ +v+F yeg+ Vt++++g + V+p
  gi|336252175|ref|YP_004595282.1| 22 SSERLVQRIVETVAATRESSPSELsTPLYEAVDPDALGRLQQS----SDDSSLRVQFAYEGCVVTIDGSGAVSVSP 93
                                      5899********************888****************....67889**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1047.21
//
Query:       gi|336252176|ref|YP_004595283.1|  [L=753]
Description: AAA family ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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-100  332.6   0.0    3.1e-49  166.8   0.0    2.4  2  AAA              ATPase family associated with various cellul
    3.8e-29  100.2   2.9    4.1e-16   58.5   0.2    2.9  2  AAA_lid_3        AAA+ lid domain
    2.2e-24   85.4   0.1    1.8e-23   82.5   0.1    2.5  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    8.6e-17   61.8   0.1    4.5e-08   33.4   0.0    2.5  2  AAA_2            AAA domain (Cdc48 subfamily)
    3.2e-16   59.5   0.0    7.3e-08   32.3   0.0    2.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    4.4e-15   55.2   0.2    1.5e-14   53.5   0.2    1.9  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    2.2e-13   50.9   0.5      1e-05   26.0   0.1    3.7  2  AAA_16           AAA ATPase domain
    2.2e-11   44.1   0.0    0.00012   22.2   0.0    2.9  2  AAA_33           AAA domain
    1.3e-10   41.4   1.4     0.0006   19.8   0.1    4.6  2  AAA_5            AAA domain (dynein-related subfamily)
    1.3e-10   41.7   1.2     0.0026   18.1   0.0    4.0  4  AAA_22           AAA domain
      3e-10   39.9   0.0    0.00027   20.3   0.0    2.3  2  TIP49            TIP49 P-loop domain
    4.1e-09   36.6   0.0     0.0012   18.9   0.0    2.6  2  AAA_14           AAA domain
    2.6e-08   34.2   0.0     0.0054   17.1   0.0    2.7  2  RNA_helicase     RNA helicase
    1.1e-07   31.8   0.0     0.0046   16.7   0.0    2.3  2  IstB_IS21        IstB-like ATP binding protein
    1.8e-07   30.9   0.0      0.022   14.3   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    3.5e-07   29.6   0.0     0.0022   17.2   0.0    2.8  2  DUF815           Protein of unknown function (DUF815)
    4.4e-07   29.5   0.5      0.013   14.8   0.1    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    8.7e-07   28.7   0.8       0.38   10.3   0.1    4.0  4  AAA_25           AAA domain
    1.5e-06   28.1   0.0      0.016   15.0   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    2.1e-06   28.1   0.0      0.043   14.1   0.0    2.8  2  AAA_28           AAA domain
    2.8e-06   27.4   0.0       0.11   12.5   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    4.2e-06   26.6   0.1       0.12   12.1   0.0    3.4  3  Sigma54_activat  Sigma-54 interaction domain
    5.1e-06   27.1   0.0        0.2   12.2   0.0    3.1  2  AAA_18           AAA domain
    5.2e-06   27.0   0.0       0.11   13.0   0.0    2.6  2  ABC_tran         ABC transporter
    1.2e-05   25.2   0.0       0.13   12.1   0.0    2.4  2  AAA_11           AAA domain
    1.8e-05   24.3   0.1      0.065   12.7   0.0    2.4  2  PhoH             PhoH-like protein
    1.9e-05   24.6   0.3       0.89    9.5   0.0    4.0  3  NACHT            NACHT domain
      2e-05   24.1   0.2       0.23   10.8   0.0    3.4  3  ATPase           KaiC
    2.1e-05   24.4   0.1       0.15   11.8   0.1    2.9  2  AAA_24           AAA domain
    2.8e-05   23.9   0.1       0.15   11.8   0.0    2.5  2  AAA_30           AAA domain
    3.5e-05   23.1   0.0        0.2   10.8   0.0    2.6  2  NB-ARC           NB-ARC domain
    5.6e-05   22.5   0.1       0.18   11.1   0.0    2.5  2  Zeta_toxin       Zeta toxin
    8.1e-05   22.0   0.0       0.27   10.4   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00017   21.5   0.1       0.25   11.3   0.0    2.7  2  Vps4_C           Vps4 C terminal oligomerisation domain
    0.00018   21.5   0.0        1.1    9.2   0.0    3.6  4  ATPase_2         ATPase domain predominantly from Archaea
    0.00033   20.6   0.0       0.16   11.8   0.0    2.5  2  Bac_DnaA         Bacterial dnaA  protein
    0.00039   19.6   0.1       0.55    9.3   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00095   19.6   0.0        2.8    8.4   0.0    2.8  2  AAA_17           AAA domain
    0.00095   19.5   0.3        2.5    8.4   0.2    2.7  2  AAA_19           AAA domain
    0.00098   19.3   0.0          3    8.0   0.0    3.0  3  Sigma54_activ_2  Sigma-54 interaction domain
      0.001   19.0   0.5        1.9    8.4   0.0    3.7  2  NTPase_1         NTPase
     0.0063   16.5   0.0        5.4    6.9   0.0    3.0  3  Rad17            Rad17 P-loop domain
     0.0064   15.6   0.0        1.5    7.8   0.0    2.3  2  T2SSE            Type II/IV secretion system protein
     0.0078   16.2   0.1        3.3    7.7   0.0    2.9  2  ResIII           Type III restriction enzyme, res subunit
     0.0078   15.1   0.0        2.9    6.7   0.0    2.5  2  AFG1_ATPase      AFG1-like ATPase
  ------ inclusion threshold ------
      0.012   15.3   0.0       0.58    9.8   0.0    2.6  2  Zot              Zonular occludens toxin (Zot)
      0.025   14.3   0.1         10    5.8   0.0    2.9  3  Cytidylate_kin   Cytidylate kinase
      0.029   14.4   0.3      0.068   13.2   0.3    1.6  1  HJURP_C          Holliday junction regulator protein family C
      0.043   13.2   0.1         20    4.5   0.0    3.5  4  TniB             Bacterial TniB protein
      0.086   12.9   0.0        5.9    7.0   0.0    2.5  2  Torsin           Torsin
      0.093   12.3   0.1         56    3.3   0.0    3.3  3  cobW             CobW/HypB/UreG, nucleotide-binding domain
        0.1   13.2   0.0         22    5.7   0.0    3.0  2  DnaG_DnaB_bind   DNA primase DnaG DnaB-binding
       0.12   12.1   0.0         22    4.9   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
       0.15   11.2   0.0          8    5.5   0.0    2.5  2  PIF1             PIF1-like helicase
       0.21   11.3   0.0         16    5.2   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.37   10.0   1.1        6.7    5.8   0.0    2.6  3  COOH-NH2_lig     Phage phiEco32-like COOH.NH2 ligase-type 2


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 !  163.7   0.0   8.7e-51   2.8e-48       1     131 [.     228     357 ..     228     358 .. 0.98
   2 !  166.8   0.0   9.8e-52   3.1e-49       1     131 [.     501     632 ..     501     633 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 8.7e-51
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+GppGtGKTl+akava+e++++f +isg+e++sky gese+++re+f+ea+e+a p i+fiDE+d++a +r+++
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEIDAHFETISGPEIMSKYYGESEEQLREVFEEAEENA-PAIIFIDELDSIAAKREDA 303
                                       79******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                         ++e+rvv+qLl+ +dg++++ ++v+vi+atnr+d++dpal+r gRfdr+iei+
  gi|336252176|ref|YP_004595283.1| 304 GGDVERRVVAQLLSLMDGLEER-GRVTVIAATNRIDDIDPALRRgGRFDREIEIG 357
                                       *********************7.77***************************996 PP

  == domain 2  score: 166.8 bits;  conditional E-value: 9.8e-52
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..T CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..s 75 
                                       vl+yGppGtGKTllakava+e++++f++i+g+ell+kyvgesek +re+f++a+++a p+++f+DEid++a++r  +
  gi|336252176|ref|YP_004595283.1| 501 VLMYGPPGTGKTLLAKAVANEAQSNFISIKGPELLNKYVGESEKGVREVFEKARSNA-PTVIFFDEIDSIAGQRgrQ 576
                                       79******************************************************9.****************988 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       +++s+++ervv+qLlteldg+++ e+ v+vi++tnrpd +d+allr gR+dr+++++
  gi|336252176|ref|YP_004595283.1| 577 QGDSGVGERVVSQLLTELDGLEELED-VVVIATTNRPDLIDQALLRpGRLDRHVHVP 632
                                       99*********************755.**************************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 !   41.3   0.2   2.9e-13   9.4e-11       2      34 ..     381     425 ..     380     441 .. 0.73
   2 !   58.5   0.2   1.3e-18   4.1e-16       1      41 [.     655     695 ..     655     723 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 2.9e-13
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrr............g 34 
                                       +dl++ Ae T+G++GADl++l re a++Alrr            +
  gi|336252176|ref|YP_004595283.1| 381 IDLDQYAESTHGFVGADLESLAREGAMNALRRirpdldleedeiD 425
                                       8*******************************5555555444440 PP

  == domain 2  score: 58.5 bits;  conditional E-value: 1.3e-18
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitme 41 
                                       +vdl++LAe+TeGy+GAD++a+creA+++A r+ i +++ e
  gi|336252176|ref|YP_004595283.1| 655 SVDLDWLAEETEGYVGADIEAVCREASMAASREFINSVDPE 695
                                       69*******************************88877655 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 !   82.5   0.1   5.7e-26   1.8e-23       1      84 [.       2      87 ..       2      88 .. 0.95
   2 ?   -1.2   0.0       7.5   2.4e+03      20      39 ..     213     232 ..     212     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 5.7e-26
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEEC..CCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveieg..krkTvaivwpaepedegkgiIrmdgvtRknagvsiGdk 77
                                      +L+V+ ++q+d+grg ++id+  m+el+le+gd++ ieg  + ++va vwp++pedeg+giIr+dg +R+ a+v+i+d 
  gi|336252176|ref|YP_004595283.1|  2 KLTVKPLKQKDAGRGLAAIDRVSMRELDLENGDYIVIEGsgDGQAVARVWPGYPEDEGRGIIRIDGRLRQEADVGIDDN 80
                                      5899**********************************964555*********************************** PP

                                      EEEEEE- CS
                           CDC48_N 78 VtVrkae 84
                                      V+V++a+
  gi|336252176|ref|YP_004595283.1| 81 VSVEPAD 87
                                      ****997 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 7.5
                                       -HHHHHHHTS-TTSEEEEEC CS
                           CDC48_N  20 dpedmeelglepgdvveieg 39 
                                       +pe +++lg+ep + v ++g
  gi|336252176|ref|YP_004595283.1| 213 HPELFQQLGIEPPKGVLLHG 232
                                       6899********99999887 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   1.4e-10   4.5e-08       6     105 ..     228     321 ..     224     332 .. 0.93
   2 !   25.7   0.0   3.3e-08   1.1e-05       6     104 ..     501     595 ..     497     602 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.4e-10
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++aka+a+ +++    ++ ++   e++     + + +++++ ++   +aee+   i+++DE+d i
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEIDA----HFETISGPEIMS----KYYGESEEQLREVFEEAEENApaIIFIDELDSI 296
                                       6889******************96....************....********************99*********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       ++k e +g dv r  V+  LL +++g
  gi|336252176|ref|YP_004595283.1| 297 AAKrEDAGGDVERR-VVAQLLSLMDG 321
                                       ***99******997.66668888887 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 3.3e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +l+ gp g+Gkt+laka+a+  +    +++i +   ell     + + ++++g ++   +a  +   ++++DEid i
  gi|336252176|ref|YP_004595283.1| 501 VLMYGPPGTGKTLLAKAVANEAQ----SNFISIKGPELLN----KYVGESEKGVREVFEKARSNAptVIFFDEIDSI 569
                                       6899****************998....5************....88889999999999999999899********** PP

                                       ---..---------HHHHHHHHHHHH CS
                             AAA_2  81 hpk..essgadvSregVqrdLLqile 104
                                       + +  +++g    +e V+  LL  l+
  gi|336252176|ref|YP_004595283.1| 570 AGQrgRQQGDSGVGERVVSQLLTELD 595
                                       **976455555557888888887666 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 !   32.3   0.0   2.3e-10   7.3e-08      34     101 ..     226     301 ..     218     304 .. 0.81
   2 !   24.0   0.0     8e-08   2.6e-05      31      71 ..     496     536 ..     476     572 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 2.3e-10
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsrave 101
                                         vll+GpPG Gkt +ak +a+e+++++++ sgP +      e + +l  ++ + ee+   ++fide+  ++ + e
  gi|336252176|ref|YP_004595283.1| 226 KGVLLHGPPGTGKTLMAKAVANEIDAHFETISGPEImskyygESEEQLREVFEEAEENapAIIFIDELDSIAAKRE 301
                                       569*******************************99443333345778888888877633699****998877655 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 8e-08
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlek 71 
                                       +a   vl+yGpPG Gkt lak +a+e ++++ +  gP l +
  gi|336252176|ref|YP_004595283.1| 496 QAAKGVLMYGPPGTGKTLLAKAVANEAQSNFISIKGPELLN 536
                                       566789******************************98743 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 !   53.5   0.2   4.6e-17   1.5e-14       1      63 [.     103     172 ..     103     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 4.6e-17
                                       ..SCCCCH.HHHCCCTTEEE-TTEEEEECCT.......CCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                           CDC48_2   1 ridgdema.ylkrqFlgrpvtkGdlvvfefk.......gqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                       ri+gd +   +++++ g++vt+G++v+f+ +       gq ++l+++st+P+g+v+it++T i++++ p+e
  gi|336252176|ref|YP_004595283.1| 103 RIRGD-IGpLVRDKLSGQAVTEGQTVPFSLSfgpmassGQSVPLKIASTSPSGTVVITDSTTIDISETPAE 172
                                       68899.6669******************9977888999****************************99987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   3.1e-08     1e-05      24     139 ..     216     331 ..     195     345 .. 0.61
   2 !   19.6   0.0   2.9e-06   0.00092      16      63 ..     490     534 ..     488     606 .. 0.64

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.1e-08
                            AAA_16  24 p.........elvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysalaqalareellrqlldea 89 
                                                   vll+G++G+GK+ +++++++++ ++   f  ++g    +     y    ++l r e++++ +++ 
  gi|336252176|ref|YP_004595283.1| 216 LfqqlgieppKGVLLHGPPGTGKTLMAKAVANEIDAH---FetISGPEIMS---KYYGESEEQL-R-EVFEEAEEN- 283
                                       345555555699********************99977...62244444444...2232245555.4.444444444. PP

                            AAA_16  90 esaeleawrekleealaavpelagaea.srllellkrllallsrderplvl 139
                                          +++      ++++aa +e+ag +  +r+ ++l +l++ l++++r +v+
  gi|336252176|ref|YP_004595283.1| 284 ---APAIIFIDELDSIAAKREDAGGDVeRRVVAQLLSLMDGLEERGRVTVI 331
                                       ...444444444444444555555555699999999999999987875444 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.9e-06
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                       +e+  ++    vl +G++G+GK+ l+++++++++ +   f++ k  +l
  gi|336252176|ref|YP_004595283.1| 490 FEQMDMQAAKGVLMYGPPGTGKTLLAKAVANEAQSN---FISIKGPEL 534
                                       56666677789********************99999...665555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   3.9e-07   0.00012       2      54 ..     228     283 ..     228     346 .. 0.74
   2 !   18.6   0.0     5e-06    0.0016       2      46 ..     501     547 ..     501     656 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.9e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdytr.vldr 54 
                                       vll+G+pG+GK+  a+ ++++ +  ++++s ++++++++g+ ++++++  + ++++
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEIDahFETISGPEIMSKYYGESEEQLREVFEeAEEN 283
                                       799****************99999****************8887777433322222 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 5e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                                       vl+ G+pG+GK+ la+ ++++ +  ++ +  ++l+++++g+ ++  +
  gi|336252176|ref|YP_004595283.1| 501 VLMYGPPGTGKTLLAKAVANEAQsnFISIKGPELLNKYVGESEKGVR 547
                                       79*****************9999999999999999999885444333 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 !   19.8   0.1   1.9e-06    0.0006       1      77 [.     227     296 ..     227     347 .. 0.61
   2 !   14.6   0.1   7.4e-05     0.024       1      33 [.     500     532 ..     500     622 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.9e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ +a+ +a  + + +e++ +++ +++            + + +  ++ ++a+   ++i+++DE++
  gi|336252176|ref|YP_004595283.1| 227 GVLLHGPPGTGKTLMAKAVANEIDAHFETISGPEIMSKYYG---------ESEEQLREVFEEAEenAPAIIFIDELD 294
                                       59*****************************9997765322.........222233445555554566777777777 PP

                                       G- CS
                             AAA_5  76 ra 77 
                                        +
  gi|336252176|ref|YP_004595283.1| 295 SI 296
                                       54 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7.4e-05
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE-- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqlt 33 
                                       +vl+ GppGtgK+ la+ +a   ++++  + ++
  gi|336252176|ref|YP_004595283.1| 500 GVLMYGPPGTGKTLLAKAVANEAQSNFISIKGP 532
                                       59****************998887777666555 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     8e-06    0.0026       8      58 ..     228     278 ..     223     283 .. 0.73
   2 ?    3.7   0.1      0.22        71      73     119 ..     268     323 ..     258     340 .. 0.68
   3 !   17.0   0.0   1.7e-05    0.0054       8      45 ..     501     538 ..     494     559 .. 0.68
   4 ?   -1.6   0.0       9.3     3e+03      85     104 ..     552     570 ..     535     595 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllr 58 
                                       ++++G++GtGKT+ ++ ++++ d++ +    +pe++ +++  s++ ++++++
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEIDAHFETIS-GPEIMsKYYGESEEQLREVFE 278
                                       689******************987655444.555555666666666666665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.22
                            AAA_22  73 lsseellealeqalraravielliiDEaqhlr...s.......eealeeLrsllnl.s 119
                                        s+e+l+e +e+a +++ +  ++ iDE + +    +        +++ +L sl++  +
  gi|336252176|ref|YP_004595283.1| 268 ESEEQLREVFEEAEENAPA--IIFIDELDSIAakrEdaggdveRRVVAQLLSLMDGlE 323
                                       5667777777777777766..*********9876515566677888888888887663 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 1.7e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fv 45 
                                       ++ +G++GtGKT+l++ ++++++  +++  ++pe++ ++
  gi|336252176|ref|YP_004595283.1| 501 VLMYGPPGTGKTLLAKAVANEAQS-NFISIKGPELLnKY 538
                                       6789*****************943.33333555555544 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 9.3
                            AAA_22  85 alraravielliiDEaqhlr 104
                                        +r+ a   ++  DE++ + 
  gi|336252176|ref|YP_004595283.1| 552 KARSNAP-TVIFFDEIDSIA 570
                                       3344444.79999**99985 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   8.3e-07   0.00027      51      97 ..     226     270 ..     218     281 .. 0.86
   2 !   17.1   0.0   7.9e-06    0.0025      49      97 ..     497     543 ..     489     555 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.3e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       ++vLl Gp+gtGkt +a a+++e+    +f ++sg e+ s     +e
  gi|336252176|ref|YP_004595283.1| 226 KGVLLHGPPGTGKTLMAKAVANEID--AHFETISGPEIMSKYYGESE 270
                                       89**********************7..89*********998766554 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 7.9e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  49 aGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       a ++vL+ Gp+gtGkt la a+++e      f++++g e+    v  +e
  gi|336252176|ref|YP_004595283.1| 497 AAKGVLMYGPPGTGKTLLAKAVANEAQ--SNFISIKGPELLNKYVGESE 543
                                       679*********************976..6899**99999877666665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   6.9e-05     0.022       5      76 ..     228     296 ..     225     337 .. 0.74
   2 !   18.9   0.0   3.7e-06    0.0012       5      76 ..     501     569 ..     497     608 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.9e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT ++k +++e      ++  i+  +   k + ++e+ l++++e+++e+   ++f+DE   +
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEID---AHFETISGPEIMSKYYGESEEQLREVFEEAEENAPAIIFIDELDSI 296
                                       7899**********999997766...899999998888877776664555555555556999******9877 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 3.7e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT l+k +++e     ++++ i+  +  +k   ++ek  ++++ek++++  t++f+DEi  +
  gi|336252176|ref|YP_004595283.1| 501 VLMYGPPGTGKTLLAKAVANEAQ---SNFISIKGPELLNKYVGESEKGVREVFEKARSNAPTVIFFDEIDSI 569
                                       7889***************8888...99999999998888777777777777777655699********987 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.7e-05    0.0054       1      36 [.     228     263 ..     228     284 .. 0.88
   2 !   14.5   0.0   0.00011     0.036       1      27 [.     501     530 ..     501     611 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                       ++l+Gp+g+GK+++ak +a+++  ++++++ ++++s
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEIDAHFETISGPEIMS 263
                                       689**********************98888777766 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 0.00011
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl...k 27 
                                       +++yGp+g+GK++lak +a++ ++++   k
  gi|336252176|ref|YP_004595283.1| 501 VLMYGPPGTGKTLLAKAVANEAQSNFisiK 530
                                       679**************9999987774442 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 !   12.6   0.0   0.00027     0.087      44      70 ..     222     248 ..     202     256 .. 0.86
   2 !   16.7   0.0   1.4e-05    0.0046      45      75 ..     496     526 ..     489     566 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00027
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgve 70 
                                       ie  ++++l Gp+G+GK+ +a a++ e
  gi|336252176|ref|YP_004595283.1| 222 IEPPKGVLLHGPPGTGKTLMAKAVANE 248
                                       5666889****************9876 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.4e-05
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavrag 75 
                                       ++++++++ Gp+G+GK+ la a++ ea  + 
  gi|336252176|ref|YP_004595283.1| 496 QAAKGVLMYGPPGTGKTLLAKAVANEAQSNF 526
                                       567899******************9997665 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 !   13.7   0.0   0.00011     0.034      30      62 ..     222     253 ..     213     300 .. 0.86
   2 !   14.3   0.0   6.9e-05     0.022      29      63 ..     494     527 ..     487     532 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkeky 62 
                                       ++  k vll Gp GtGKt+++k + +++d  ++
  gi|336252176|ref|YP_004595283.1| 222 IEPPKGVLLHGPPGTGKTLMAKAVANEID-AHF 253
                                       666789*******************9999.444 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.9e-05
                             AAA_7  29 llknkkpvllvGptGtGKtviikdllkkldkekyl 63 
                                        +++ k vl++Gp GtGKt+++k + ++ + ++++
  gi|336252176|ref|YP_004595283.1| 494 DMQAAKGVLMYGPPGTGKTLLAKAVANEAQ-SNFI 527
                                       578999******************999988.5554 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0022      0.69      52     116 ..     224     293 ..     188     336 .. 0.73
   2 !   17.2   0.0   6.9e-06    0.0022      24     157 ..     460     617 ..     440     630 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0022
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlke....lpklvellrerperfilfvDDL 116
                                       p + vLL G  GtGK  + ka+ ne+ ++   +   e+  +   e    l +++e+  e++   i+f+D L
  gi|336252176|ref|YP_004595283.1| 224 PPKGVLLHGPPGTGKTLMAKAVANEIDAHFetISGPEIMSKYYGEseeqLREVFEEA-EENAPAIIFIDEL 293
                                       6678*********************98876445555665554443000044444432.3455678888877 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 6.9e-06
                            DUF815  24 evklddLvgidkqkealvente.........qfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlievek 89 
                                        v++dd+ g+++ ke+l e ++         + ++ ++a+ vL++G  GtGK  l ka+ ne++++   ++  e+ +
  gi|336252176|ref|YP_004595283.1| 460 DVTWDDVGGLEDTKERLRETIQwpldypevfEQMDMQAAKGVLMYGPPGTGKTLLAKAVANEAQSNFisIKGPELLN 536
                                       56666777777777777665542222222113467789**************************9984444457777 PP

                            DUF815  90 edlkelpklvellr...erperfilfvDDL...sFeeeeeey.........ksLksvLeGsleakpenvliyaTsNr 151
                                       + + e +k v+++    +++   ++f D +   + +++ ++           +L + L+G   ++ e+v++ aT+Nr
  gi|336252176|ref|YP_004595283.1| 537 KYVGESEKGVREVFekaRSNAPTVIFFDEIdsiAGQRGRQQGdsgvgervvSQLLTELDGL--EELEDVVVIATTNR 611
                                       7776666555555312233445677777653112222222113333554445666667763..44567777888888 PP

                            DUF815 152 RhLlpe 157
                                        +L+ +
  gi|336252176|ref|YP_004595283.1| 612 PDLIDQ 617
                                       888776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00026     0.084      25      43 ..     228     246 ..     224     263 .. 0.90
   2 !   14.8   0.1   4.2e-05     0.013      24      42 ..     500     518 ..     492     523 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll GppG+GKt++ak+++
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVA 246
                                       79*************9975 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.2e-05
                      Mg_chelatase  24 nlllvGppGsGKtmlakrl 42 
                                        +l++GppG+GKt+lak++
  gi|336252176|ref|YP_004595283.1| 500 GVLMYGPPGTGKTLLAKAV 518
                                       58**************987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0      0.02       6.4      36      53 ..     228     245 ..     217     249 .. 0.87
   2 !   10.3   0.1    0.0012      0.38     128     176 ..     271     319 ..     260     333 .. 0.83
   3 ?    7.1   0.0     0.012       3.7      36      52 ..     501     517 ..     478     523 .. 0.85
   4 ?   -0.9   0.0       3.2     1e+03     130     172 ..     546     590 ..     536     608 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.02
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll G+pgtGKt +a  +
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAV 245
                                       689**********99665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0012
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                       ++++++ +++ee + ++ + iD l+++ +  e++  dv +++v++l ++ 
  gi|336252176|ref|YP_004595283.1| 271 EQLREVFEEAEE-NAPAIIFIDELDSIAAKREDAGGDVeRRVVAQLLSLM 319
                                       566778888888.66**********************9999999987765 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.012
                            AAA_25  36 allaGapgtGKttlald 52 
                                       +l +G+pgtGKt la  
  gi|336252176|ref|YP_004595283.1| 501 VLMYGPPGTGKTLLAKA 517
                                       789**********9965 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 3.2
                            AAA_25 130 vdaleaaieevegvrlvviDplsralgg..densnsdv.galveal 172
                                       v+++ +++++ + + ++ +D ++++ g     + +s v +++v++l
  gi|336252176|ref|YP_004595283.1| 546 VREVFEKARS-NAPTVIFFDEIDSIAGQrgRQQGDSGVgERVVSQL 590
                                       6777888888.6799*********9999655555555556666655 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 !   15.0   0.0   5.1e-05     0.016       2      30 ..     228     256 ..     227     298 .. 0.93
   2 !   10.6   0.0    0.0012       0.4       2      37 ..     501     535 ..     500     629 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.1e-05
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll+g PG++ktl++ka+a+ +d++f+ i
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEIDAHFETI 256
                                       89************************988 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0012
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdll 37 
                                       vl+ g PG++ktll+ka+a+  + +f  i+  p+ll
  gi|336252176|ref|YP_004595283.1| 501 VLMYGPPGTGKTLLAKAVANEAQSNFISIK-GPELL 535
                                       7999*******************9998886.45555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   0.00013     0.043       2      49 ..     228     280 ..     227     310 .. 0.76
   2 !   11.0   0.0    0.0012      0.39       2      35 ..     501     539 ..     500     566 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00013
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakgedalpwv 49 
                                       + + G+++tGKT +++a a++    ++++  pE++ +++ e  ++ ++  +++
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEidaHFETIsgPEIMSKYYGESEEQLREVFEEA 280
                                       6799***************7777778888899*99999988887777766665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0012
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareil 35 
                                       + + G+++tGKT l++a a++   ++  +  pE   +++
  gi|336252176|ref|YP_004595283.1| 501 VLMYGPPGTGKTLLAKAVANEaqsNFISIkgPELLNKYV 539
                                       5789***************66545443334666666665 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   0.00033      0.11      19      59 ..     225     265 ..     201     276 .. 0.74
   2 !   12.3   0.0    0.0004      0.13      16      60 ..     495     539 ..     474     549 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00033
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEE CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeY 59 
                                        + +lL+G+ G+GKT +++++a++++ +  +++ P   ++++Y
  gi|336252176|ref|YP_004595283.1| 225 PKGVLLHGPPGTGKTLMAKAVANEIDAHfeTISGP--EIMSKY 265
                                       4559********************98877567666..455555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0004
                                       HCHTEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEEE CS
                              TsaE  16 kalgdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeYe 60 
                                        ++++ +l++G+ G+GKT l++++a++ + +  ++k P   l+++Y 
  gi|336252176|ref|YP_004595283.1| 495 MQAAKGVLMYGPPGTGKTLLAKAVANEAQSNfiSIKGP--ELLNKYV 539
                                       3335569********************99887788888..5666665 PP

>> Sigma54_activat  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    0.0017      0.54      23      46 ..     226     249 ..     212     261 .. 0.85
   2 !   12.1   0.0   0.00037      0.12      21      55 ..     497     528 ..     485     572 .. 0.83
   3 ?   -1.0   0.0         4   1.3e+03      28      55 ..     577     604 ..     576     620 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0017
                                       S-EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheas 46 
                                         vl++G  GtGK+l+a+a+ ++ 
  gi|336252176|ref|YP_004595283.1| 226 KGVLLHGPPGTGKTLMAKAVANEI 249
                                       679***************998765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00037
                                       SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEE CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpfva 55 
                                           vl+ G  GtGK+lla+a+ ++ +   ++f++
  gi|336252176|ref|YP_004595283.1| 497 AAKGVLMYGPPGTGKTLLAKAVANEAQ---SNFIS 528
                                       44679****************987654...45555 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 4
                                       ECSTTSSHHHHHHHHHHHSTTTTS-EEE CS
                   Sigma54_activat  28 tGesGtGKellaraiheaskrkekpfva 55 
                                       +G+sG+G  ++++++ e    +e + v 
  gi|336252176|ref|YP_004595283.1| 577 QGDSGVGERVVSQLLTELDGLEELEDVV 604
                                       699*****99999998865554444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00062       0.2       1      43 [.     228     272 ..     228     327 .. 0.63
   2 !   11.0   0.0    0.0015      0.49       2      23 ..     502     524 ..     501     565 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00062
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..gvnlrdvakenglllevdp 43 
                                       +ll G+pG+GKt +ak+++++      ++++  +  +++ +++++
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEIDAhfETISGPEIMSKYYGESEEQ 272
                                       7899**************998522243333333333333333333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0015
                            AAA_18   2 lltGtpGvGKttlakeLskrl.g 23 
                                       l  G+pG+GKt lak+++++   
  gi|336252176|ref|YP_004595283.1| 502 LMYGPPGTGKTLLAKAVANEAqS 524
                                       678**************888622 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0    0.0013       0.4       6      67 ..     220     279 ..     218     341 .. 0.76
   2 !   13.0   0.0   0.00033      0.11       6      71 ..     493     556 ..     491     610 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0013
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                       l +++ + v + G+ G+GK+ ++k++a++ +   ++i   g ++ ++   +++++++ +++e
  gi|336252176|ref|YP_004595283.1| 220 LGIEPPKGVLLHGPPGTGKTLMAKAVANEIDAHFETI--SGPEIMSKYYGESEEQLREVFEE 279
                                       6778888999*********************999999..55555554455555555555555 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00033
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlf 71 
                                       +++++ + v + G+ G+GK+ L+k++a++ +  +  i ++g +l ++   +++k ++ ++++++ +
  gi|336252176|ref|YP_004595283.1| 493 MDMQAAKGVLMYGPPGTGKTLLAKAVANEAQ--SNFISIKGPELLNKYVGESEKGVREVFEKARSN 556
                                       56788888999*****************975..789999999999999999999999999985544 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0    0.0004      0.13      19      42 ..     227     250 ..     211     286 .. 0.78
   2 !   10.6   0.0    0.0011      0.37      20      42 ..     501     523 ..     490     560 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0004
                            AAA_11  19 itliqGPPGtgKTktivellsqll 42 
                                        +l++GPPGtgKT +  ++ +++ 
  gi|336252176|ref|YP_004595283.1| 227 GVLLHGPPGTGKTLMAKAVANEID 250
                                       479**********88888877774 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0011
                            AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                       +l+ GPPGtgKT    ++ +++ 
  gi|336252176|ref|YP_004595283.1| 501 VLMYGPPGTGKTLLAKAVANEAQ 523
                                       79**********88888888874 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0027      0.86      22      41 ..     228     247 ..     218     259 .. 0.86
   2 !   12.7   0.0    0.0002     0.065      18      43 ..     497     522 ..     488     529 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0027
                                       EEEE--TTSSTTHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalav 41 
                                       v   Gp GtGKt++a a+a 
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVAN 247
                                       6789***********99985 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0002
                                       H-SEEEEE--TTSSTTHHHHHHHHHH CS
                              PhoH  18 kndivfaiGpaGtGKtylavalavea 43 
                                       + + v + Gp GtGKt+la a+a ea
  gi|336252176|ref|YP_004595283.1| 497 AAKGVLMYGPPGTGKTLLAKAVANEA 522
                                       5667899**************99776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0049       1.6       3      24 ..     228     249 ..     226     349 .. 0.96
   2 !    9.5   0.0    0.0028      0.89       3      26 ..     501     524 ..     499     528 .. 0.90
   3 ?   -1.3   0.0       5.6   1.8e+03      83     112 ..     559     594 ..     533     632 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0049
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       v+l+G++G GKT +++ +a ++
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEI 249
                                       799*************999886 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0028
                                       EEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawae 26 
                                       v++ G++G GKT L++ +a ++++
  gi|336252176|ref|YP_004595283.1| 501 VLMYGPPGTGKTLLAKAVANEAQS 524
                                       7899**************999876 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 5.6
                                       EEEEEE-STT-SS-TCH...............HHHH CS
                             NACHT  83 lLlilDglDelvtdlgq......kekqpvrtlLsel 112
                                       +++ +D +D ++ + g        +++ v +lL+el
  gi|336252176|ref|YP_004595283.1| 559 TVIFFDEIDSIAGQRGRqqgdsgVGERVVSQLLTEL 594
                                       445577777777666655544444444444444444 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00072      0.23      13      37 ..     219     243 ..     192     250 .. 0.80
   2 ?    0.4   0.0       1.1   3.4e+02     105     154 ..     271     322 ..     249     336 .. 0.61
   3 !    8.2   0.0    0.0045       1.4      19      38 ..     498     517 ..     488     529 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00072
                            ATPase  13 kgGipegrvvlitGepGtGKtifal 37 
                                       + Gi   + vl+ G pGtGKt++a+
  gi|336252176|ref|YP_004595283.1| 219 QLGIEPPKGVLLHGPPGTGKTLMAK 243
                                       368888999**************97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                            ATPase 105 eelieelaeaikeikakrvviDsitgl.ayeeke..avaReilrqlvrvlkkl 154
                                       e+l e ++ea  e     + iD ++++ a++e++  +v R+ + ql++ + +l
  gi|336252176|ref|YP_004595283.1| 271 EQLREVFEEAE-ENAPAIIFIDELDSIaAKREDAggDVERRVVAQLLSLMDGL 322
                                       33333333332.22335677887777743333322267899999999888654 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0045
                            ATPase  19 grvvlitGepGtGKtifalq 38 
                                       ++ vl++G pGtGKt++a+ 
  gi|336252176|ref|YP_004595283.1| 498 AKGVLMYGPPGTGKTLLAKA 517
                                       56799************975 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0026      0.82       5      75 ..     228     294 ..     225     303 .. 0.60
   2 !   11.8   0.1   0.00046      0.15       4      22 ..     500     518 ..     497     613 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0026
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie......swedfldevvelaaeladyktlviDtid 75 
                                       +l+ Gp+g+GKT +ak    + +   +e     +    +p+i       s e++++ ++e +++ +   +++iD +d
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAV-ANEIDAHFET----IS---GPEIMskyygeSEEQLREVFEEAEENAP--AIIFIDELD 294
                                       799************999.4444333333....22...2222222233366666666666655555..567777666 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00046
                            AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                        +l+yGp+g+GKT lak  
  gi|336252176|ref|YP_004595283.1| 500 GVLMYGPPGTGKTLLAKAV 518
                                       5899************988 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00046      0.15      21      45 ..     228     252 ..     215     262 .. 0.81
   2 !    9.3   0.0    0.0027      0.87      16      43 ..     496     523 ..     488     531 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00046
                            AAA_30  21 avltGpAGtGKttalkalreaweaa 45 
                                       ++l+Gp+GtGKt + ka+++ ++a+
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEIDAH 252
                                       789**************98877665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0027
                            AAA_30  16 sgdrvavltGpAGtGKttalkalreawe 43 
                                       + ++ +++ Gp+GtGKt + ka+++ ++
  gi|336252176|ref|YP_004595283.1| 496 QAAKGVLMYGPPGTGKTLLAKAVANEAQ 523
                                       555667899************9977655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00061       0.2      23      54 ..     228     256 ..     215     279 .. 0.85
   2 !    9.3   0.0    0.0018      0.56      22      45 ..     500     523 ..     486     529 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00061
                                       EEEEESTTSSHHHHHHHHCCSHCCCCCCBTEE CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksdevegrFdsv 54 
                                       v l+G +G GKt +ak + n+   ++ +F+ +
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANE---IDAHFETI 256
                                       789**********99999999...88888865 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0018
                                       EEEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksd 45 
                                        v ++G +G GKt lak + n+ +
  gi|336252176|ref|YP_004595283.1| 500 GVLMYGPPGTGKTLLAKAVANEAQ 523
                                       5889***************99943 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0029      0.94      14      42 ..     223     251 ..     215     257 .. 0.88
   2 !   11.1   0.0   0.00056      0.18      17      51 ..     499     531 ..     488     540 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0029
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdeler 42 
                                       e Pk +ll G pG GK+ +a+++++e+++
  gi|336252176|ref|YP_004595283.1| 223 EPPKGVLLHGPPGTGKTLMAKAVANEIDA 251
                                       56999********************9874 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00056
                        Zeta_toxin  17 klillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       k +l+ G pG GK+ la+++++e   q+n++ +++
  gi|336252176|ref|YP_004595283.1| 499 KGVLMYGPPGTGKTLLAKAVANEA--QSNFISIKG 531
                                       6699*******************8..99*999976 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00085      0.27       4      26 ..     228     254 ..     225     303 .. 0.76
   2 !    9.3   0.0    0.0018      0.59       4      25 ..     501     522 ..     499     565 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00085
                           DUF2075   4 vlVtGvaGtGKtvvllnllael....e 26 
                                       vl +G +GtGKt+++ ++++e+    e
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEIdahfE 254
                                       6889*****************944431 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0018
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       vl  G +GtGKt+++ ++++e+
  gi|336252176|ref|YP_004595283.1| 501 VLMYGPPGTGKTLLAKAVANEA 522
                                       6789***************998 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 ?    7.3   0.0     0.015       4.7      18      44 ..     423     449 ..     417     453 .. 0.85
   2 !   11.3   0.0    0.0008      0.25      21      56 ..     698     733 ..     677     737 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.015
                            Vps4_C  18 dipsdkllePpvtlkDflkalkkarpt 44 
                                       +i+++ l   +vt +Df++alk  +p+
  gi|336252176|ref|YP_004595283.1| 423 EIDAEVLESLQVTERDFKEALKGIQPS 449
                                       6777777777************99998 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0008
                            Vps4_C  21 sdkllePpvtlkDflkalkkarptVskeDLekheeF 56 
                                       +d + +  ++ ++f+ al+++ p+V++e  e++ee 
  gi|336252176|ref|YP_004595283.1| 698 ADTIGNVRISKEHFEHALEEVNPSVTPETREQYEEI 733
                                       577778899*******************99999985 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 ?    2.7   0.0      0.31        99      18      44 ..     223     249 ..     215     257 .. 0.77
   2 ?    4.5   0.0     0.091        29     101     163 ..     268     332 ..     250     336 .. 0.66
   3 !    9.2   0.0    0.0033       1.1      16      46 ..     494     524 ..     487     570 .. 0.78
   4 ?   -1.2   0.0         5   1.6e+03     106     136 ..     546     573 ..     523     611 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.31
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienl 44 
                                       ep + +++ Gp g GKt + k ++++ 
  gi|336252176|ref|YP_004595283.1| 223 EPPKGVLLHGPPGTGKTLMAKAVANEI 249
                                       566678899********8888888776 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.091
                          ATPase_2 101 lvfkaielllekikkkgkkiiiiiDelqkli....dlglngaellvkeLlnliesltkekhlcvvic 163
                                       + ++++ +++e+ ++++   ii+iDel  +     d g + ++ +v++Ll+l++ l ++ +++v+ +
  gi|336252176|ref|YP_004595283.1| 268 ESEEQLREVFEEAEENAP-AIIFIDELDSIAakreDAGGDVERRVVAQLLSLMDGLEERGRVTVI-A 332
                                       446666777777666644.7899****99872222445558899999999999997666665554.3 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0033
                          ATPase_2  16 erepneiyfiYGpegsGKtaLlkeiienled 46 
                                       +++ ++ ++ YGp g GKt L k ++++ ++
  gi|336252176|ref|YP_004595283.1| 494 DMQAAKGVLMYGPPGTGKTLLAKAVANEAQS 524
                                       5666677899*********999999998744 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 5
                          ATPase_2 106 ielllekikkkgkk...iiiiiDelqklidlgln 136
                                       + +++ek +         +i++De+  +   g +
  gi|336252176|ref|YP_004595283.1| 546 VREVFEKAR----SnapTVIFFDEIDSIA--GQR 573
                                       344444433....2344899999999887..544 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.023       7.3      37      63 ..     228     254 ..     223     369 .. 0.88
   2 !   11.8   0.0    0.0005      0.16      34      66 ..     498     530 ..     488     617 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.023
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenap 63 
                                       ++++g+ G Gkt + ka++ne+ ++++
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEIDAHFE 254
                                       79*******************988765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0005
                                       S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS- CS
                          Bac_DnaA  34 ynPlfiygevGlGktHLlkaignevlenapelr 66 
                                          +++yg+ G Gkt L ka++ne+++n+ + +
  gi|336252176|ref|YP_004595283.1| 498 AKGVLMYGPPGTGKTLLAKAVANEAQSNFISIK 530
                                       56799********************99986544 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 !    8.0   0.0    0.0042       1.3     117     138 ..     228     249 ..     222     252 .. 0.89
   2 !    9.3   0.0    0.0017      0.55     117     136 ..     501     520 ..     492     525 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0042
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                       v+++Gp+ tGkt +a+a a+ +
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEI 249
                                       899***************9976 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0017
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v++yGp+ tGkt la+a a+
  gi|336252176|ref|YP_004595283.1| 501 VLMYGPPGTGKTLLAKAVAN 520
                                       899**************997 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0096       3.1       2      47 ..     232     278 ..     231     310 .. 0.69
   2 !    8.4   0.0    0.0088       2.8       1      26 [.     504     529 ..     504     579 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0096
                                       E-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTTTSHSSHHHHC CS
                            AAA_17   2 GgPGsGKgtqceklveky..gfthlsaGdllreeakrgglakardemr 47 
                                       G+PG GK+ +++ ++ ++  +f+ +s  +++ +   +++ ++ r+ ++
  gi|336252176|ref|YP_004595283.1| 232 GPPGTGKTLMAKAVANEIdaHFETISGPEIMSKYYGESE-EQLREVFE 278
                                       9**************998667888997777765543333.23344444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0088
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                       +G+PG GK+ +++ ++ + +  ++s 
  gi|336252176|ref|YP_004595283.1| 504 YGPPGTGKTLLAKAVANEAQSNFISI 529
                                       7**************99987666654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2    0.0079       2.5      11      34 ..     226     249 ..     219     287 .. 0.80
   2 ?    8.0   0.0      0.01       3.4      10      35 ..     498     523 ..     492     568 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0079
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivall 34 
                                       k +l+ ++pGtGKT + k++ +++
  gi|336252176|ref|YP_004595283.1| 226 KGVLLHGPPGTGKTLMAKAVANEI 249
                                       56899*********9988877665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.01
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallv 35 
                                       +k +l+ ++pGtGKT + k++ ++++
  gi|336252176|ref|YP_004595283.1| 498 AKGVLMYGPPGTGKTLLAKAVANEAQ 523
                                       5678999********98887776655 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 ?    7.2   0.0     0.016         5      24      45 ..     228     249 ..     222     301 .. 0.63
   2 !    8.0   0.0    0.0094         3      20      48 ..     497     525 ..     489     573 .. 0.65
   3 ?   -1.0   0.0       5.4   1.7e+03      28      47 ..     578     597 ..     577     621 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.016
                                       EEEEEETT--HHHHHHCC--TT CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhkns 45 
                                       v+l G++G+gk+l+A++ +++ 
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEI 249
                                       9***************998753 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0094
                                       -SS-EEEEEETT--HHHHHHCC--TTS-E CS
                   Sigma54_activ_2  20 sklpvfltGekGsgkelvArlLhknsgpw 48 
                                       +   v++ G++G+gk+l A++ +++++ +
  gi|336252176|ref|YP_004595283.1| 497 AAKGVLMYGPPGTGKTLLAKAVANEAQSN 525
                                       56679****************99987663 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 5.4
                                       EETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  28 GekGsgkelvArlLhknsgp 47 
                                       G+ G g  +v++lL + +g 
  gi|336252176|ref|YP_004595283.1| 578 GDSGVGERVVSQLLTELDGL 597
                                       889***********998765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.021       6.8       2      25 ..     228     251 ..     227     263 .. 0.85
   2 !    8.4   0.0    0.0058       1.9       3      32 ..     502     531 ..     500     615 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.021
                                       EEEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellks 25 
                                       v++ GppG+GKt + k v+++++ 
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEIDA 251
                                       6789***************99965 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0058
                                       EEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       ++ GppG+GKt l k v+++ +s+ ++++G
  gi|336252176|ref|YP_004595283.1| 502 LMYGPPGTGKTLLAKAVANEAQSNFISIKG 531
                                       567******************999999988 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.038        12      48      99 ..     228     280 ..     216     309 .. 0.69
   2 ?    6.9   0.0     0.017       5.4      43     112 ..     496     566 ..     473     588 .. 0.78
   3 ?   -1.5   0.0       6.2     2e+03      65      99 ..     706     740 ..     700     746 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.038
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkglteke 99 
                                       +L+ GP+G gk+ + k ++ e   +++  + p  + +     +++++ ++e  
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEIDAHFETISGPEIMSKYYGeSEEQLREVFEEA 280
                                       6899***************9998888777766553322222445555555555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.017
                             Rad17  43 rkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqiesfkel 112
                                       +  + +L+ GP+G gk+   k ++ e   +++    p +l++     ++ ++ ++ek  +  + +  f e+
  gi|336252176|ref|YP_004595283.1| 496 QAAKGVLMYGPPGTGKTLLAKAVANEAQSNFISIKGPELLNKYVGeSEKGVREVFEKARSNAPTVIFFDEI 566
                                       444567999*****************999999999888876544337777888888888778888878777 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 6.2
                             Rad17  65 Lskelgiklrewlnpvslkepdnqksdfkglteke 99 
                                       +ske+  +  e +np    e+  q +++  ++++ 
  gi|336252176|ref|YP_004595283.1| 706 ISKEHFEHALEEVNPSVTPETREQYEEIEEQFDTA 740
                                       69*************99999999999888877765 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 !    7.8   0.0    0.0047       1.5     130     160 ..     226     256 ..     202     261 .. 0.88
   2 ?    5.3   0.0     0.028       8.9     127     155 ..     496     524 ..     450     532 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0047
                             T2SSE 130 glilvsGgTgsGKttllyallkeinksderi 160
                                       + +l+ G+ g+GKt ++ a+ +ei+++ e i
  gi|336252176|ref|YP_004595283.1| 226 KGVLLHGPPGTGKTLMAKAVANEIDAHFETI 256
                                       56899*******************9996655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.028
                             T2SSE 127 rerglilvsGgTgsGKttllyallkeink 155
                                       ++ + +l+ G+ g+GKt l+ a+ +e ++
  gi|336252176|ref|YP_004595283.1| 496 QAAKGVLMYGPPGTGKTLLAKAVANEAQS 524
                                       45678999*************99988766 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 ?    7.7   0.0      0.01       3.3      21      49 ..     222     250 ..     199     257 .. 0.80
   2 ?    4.9   0.0     0.072        23      17      50 ..     491     524 ..     468     530 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.01
                                       ..TTSEEEEEESTTSTHHHHHHHHHHHH- CS
                            ResIII  21 skrdkrglikmaTGtGKTlvaaklierll 49 
                                       ++  k +l++ + GtGKTl+a +++ ++ 
  gi|336252176|ref|YP_004595283.1| 222 IEPPKGVLLHGPPGTGKTLMAKAVANEID 250
                                       46778999************988877765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.072
                                       ......TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                            ResIII  17 eklkskrdkrglikmaTGtGKTlvaaklierllk 50 
                                       e+++ +  k +l+  + GtGKTl+a +++ + ++
  gi|336252176|ref|YP_004595283.1| 491 EQMDMQAAKGVLMYGPPGTGKTLLAKAVANEAQS 524
                                       444446677888999*********9888877665 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0     0.009       2.9      58      79 ..     221     242 ..     182     294 .. 0.82
   2 ?    5.6   0.0     0.019       6.1      57      79 ..     493     515 ..     480     524 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.009
                       AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                         ep++g+ l+G+ G GKt + 
  gi|336252176|ref|YP_004595283.1| 221 GIEPPKGVLLHGPPGTGKTLMA 242
                                       468****************764 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.019
                       AFG1_ATPase  57 ksvepvrglYlwGgvGrGKtylm 79 
                                        + ++++g+ ++G+ G GKt l 
  gi|336252176|ref|YP_004595283.1| 493 MDMQAAKGVLMYGPPGTGKTLLA 515
                                       4789****************985 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0018      0.58       4      65 ..     229     295 ..     228     307 .. 0.83
   2 ?    2.5   0.0      0.31        99       4      23 ..     502     523 ..     500     573 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0018
                               Zot   4 lvtGapGsgKts..gavkkdllpalk..egRkiitnidGlrlerieqvlgekvs.tarliridnpeg 65 
                                       l +G+pG+gKt+  +av +++       +g +i+ +  G   e+++ v++e+ + ++ +i+id+ ++
  gi|336252176|ref|YP_004595283.1| 229 LLHGPPGTGKTLmaKAVANEIDAHFEtiSGPEIMSKYYGESEEQLREVFEEAEEnAPAIIFIDELDS 295
                                       789********722579999998655447**********************9999999****95554 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.31
                               Zot   4 lvtGapGsgKts..gavkkdll 23 
                                       l +G+pG+gKt+  +av ++++
  gi|336252176|ref|YP_004595283.1| 502 LMYGPPGTGKTLlaKAVANEAQ 523
                                       789********72245666555 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.031        10       3      26 ..     230     253 ..     228     258 .. 0.89
   2 ?    5.2   0.0     0.048        15       5      28 ..     505     528 ..     501     530 .. 0.90
   3 ?   -2.3   0.0       9.7   3.1e+03      31      75 ..     675     719 ..     666     733 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.031
                                       EE-STTSSHHHHHHHHHHHHT-EE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglky 26 
                                       + GP g+GK  +a+a+a+++++++
  gi|336252176|ref|YP_004595283.1| 230 LHGPPGTGKTLMAKAVANEIDAHF 253
                                       68*****************99876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.048
                                       -STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   5 GPagsGKssvaralaeklglkyld 28 
                                       GP g+GK  +a+a+a++ + ++++
  gi|336252176|ref|YP_004595283.1| 505 GPPGTGKTLLAKAVANEAQSNFIS 528
                                       9****************9998875 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 9.7
                                       HHHHHHHHHHHHTT--TT-HHHHHHHHHT--EEEEEEEEEETTEE CS
                    Cytidylate_kin  31 alYRalalaalrrkvdlldeaalvelakevelsfeaekvllnged 75 
                                       a+ R  ++aa r+ ++ +d +++++ + +v++s e+ +  l++ +
  gi|336252176|ref|YP_004595283.1| 675 AVCREASMAASREFINSVDPEEMADTIGNVRISKEHFEHALEEVN 719
                                       567888899999999999999999999999999999888887765 PP

>> HJURP_C  Holliday junction regulator protein family C-terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   0.00021     0.068      16      32 ..     722     738 ..     716     739 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00021
                           HJURP_C  16 ltprtenkYreIkeeFD 32 
                                        tp+t++ Y eI+e+FD
  gi|336252176|ref|YP_004595283.1| 722 VTPETREQYEEIEEQFD 738
                                       49**************9 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.13        43      26      57 ..     216     247 ..     205     258 .. 0.81
   2 ?   -0.7   0.0       2.5     8e+02     108     135 ..     273     300 ..     253     323 .. 0.68
   3 ?    4.5   0.0     0.062        20      29      59 ..     492     522 ..     474     530 .. 0.80
   4 ?   -1.3   0.0       3.8   1.2e+03     111     139 ..     549     577 ..     528     579 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
                              TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFar 57 
                                       L++    + ++ +ll+G++ +GKt +++  a+
  gi|336252176|ref|YP_004595283.1| 216 LFQQLGIEPPKGVLLHGPPGTGKTLMAKAVAN 247
                                       666666677789************99887665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.5
                              TniB 108 eqqvlrllrelkvrvLiiDEihnllags 135
                                        ++v +  +e  + ++ iDE++++ a +
  gi|336252176|ref|YP_004595283.1| 273 LREVFEEAEENAPAIIFIDELDSIAAKR 300
                                       3344444455668899******998755 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.062
                              TniB  29 ypkrkrmpnlllvGdsnnGKtmivekFarlh 59 
                                         + +  + +l++G++ +GKt +++  a++ 
  gi|336252176|ref|YP_004595283.1| 492 QMDMQAAKGVLMYGPPGTGKTLLAKAVANEA 522
                                       4455666899*************99877665 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.8
                              TniB 111 vlrllrelkvrvLiiDEihnllagsarkq 139
                                       v +  r+  + v+ +DEi+++   + r+q
  gi|336252176|ref|YP_004595283.1| 549 VFEKARSNAPTVIFFDEIDSIAGQRGRQQ 577
                                       33333445678999*****9985555555 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.019       5.9      56      77 ..     228     249 ..     219     257 .. 0.88
   2 ?    3.1   0.0      0.31        98      57      76 ..     502     521 ..     489     539 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.019
                                       EEEEE-TTSSHHHHHHHHHHHH CS
                            Torsin  56 lsfhGwtGtGknfvaeiiaenl 77 
                                       + +hG +GtGk  +a+ +a+++
  gi|336252176|ref|YP_004595283.1| 228 VLLHGPPGTGKTLMAKAVANEI 249
                                       458***************9976 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.31
                                       EEEE-TTSSHHHHHHHHHHH CS
                            Torsin  57 sfhGwtGtGknfvaeiiaen 76 
                                        ++G +GtGk  +a+ +a++
  gi|336252176|ref|YP_004595283.1| 502 LMYGPPGTGKTLLAKAVANE 521
                                       5789************9987 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 ?    2.7   0.0      0.25        80      75      96 ..      19      46 ..       8      67 .. 0.70
   2 ?    1.7   0.0      0.55   1.7e+02       4      21 ..     229     246 ..     227     256 .. 0.78
   3 ?    3.3   0.0      0.17        56       5      26 ..     503     524 ..     500     530 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.25
                                      HHHHHH......TT-SEEEEEECTTTTH CS
                              cobW 75 aleere......erldviliEttGlaeP 96
                                      a+ + +      e+ d+i+iE +G  ++
  gi|336252176|ref|YP_004595283.1| 19 AIDRVSmreldlENGDYIVIEGSGDGQA 46
                                      444444444677789*********6555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.55
                                       EEEESTTCCHHHHHHHHH CS
                              cobW   4 vltGflGsGKTtLlnhll 21 
                                       +l G++G+GKT + +++ 
  gi|336252176|ref|YP_004595283.1| 229 LLHGPPGTGKTLMAKAVA 246
                                       689*******98766654 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.17
                                       EEESTTCCHHHHHHHHHCT--S CS
                              cobW   5 ltGflGsGKTtLlnhllenrag 26 
                                       + G++G+GKT L +++ +++++
  gi|336252176|ref|YP_004595283.1| 503 MYGPPGTGKTLLAKAVANEAQS 524
                                       679******9888877766554 PP

>> DnaG_DnaB_bind  DNA primase DnaG DnaB-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.22        69       1      59 [.     203     267 ..     203     324 .. 0.68
   2 ?    5.7   0.0     0.068        22       2      62 ..     477     546 ..     476     561 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.22
                    DnaG_DnaB_bind   1 vrealallLqhPelagelpdalaleaf.edp...glallrelieal..aaepelntaaLlerlrg 59 
                                       vre++ l + hPel+++l  +++     + p   g  l++++++    a+ + +++++++ ++ g
  gi|336252176|ref|YP_004595283.1| 203 VREMIELPMRHPELFQQLGIEPPKGVLlHGPpgtGKTLMAKAVANEidAHFETISGPEIMSKYYG 267
                                       69**************9964444332223334556666666665554322255566665555555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.068
                    DnaG_DnaB_bind   2 realallLqhPelagelpdalale..afedp..glallreliealaaepel..ntaaLlerlrg.tp..e 62 
                                       re +++ L +Pe +++++ + a        p  g  ll+++++  a+++++  ++++Ll ++ g ++   
  gi|336252176|ref|YP_004595283.1| 477 RETIQWPLDYPEVFEQMDMQAAKGvlMYGPPgtGKTLLAKAVANEAQSNFIsiKGPELLNKYVGeSEkgV 546
                                       999**************9666655545566677999******9998888887788889999988455444 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 ?    4.5   0.0     0.092        29      21      38 ..     225     241 ..     215     248 .. 0.74
   2 ?    4.9   0.0     0.068        22      16      39 ..     492     515 ..     486     520 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.092
                            AAA_29  21 lkgatlltGpsGsGKSTl 38 
                                       +kg +ll Gp G+GK+ +
  gi|336252176|ref|YP_004595283.1| 225 PKG-VLLHGPPGTGKTLM 241
                                       356.9**********755 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.068
                            AAA_29  16 tieidlkgatlltGpsGsGKSTll 39 
                                       +++++ +  +l+ Gp G+GK+ l 
  gi|336252176|ref|YP_004595283.1| 492 QMDMQAAKGVLMYGPPGTGKTLLA 515
                                       445554455***********8765 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.17        55      22      48 ..     225     251 ..     216     257 .. 0.84
   2 ?    5.5   0.0     0.025         8      12      48 ..     488     524 ..     485     529 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.17
                                       TS-EEEEESTTSSCHHHHHHHHHHCHC CS
                              PIF1  22 gklfFvtGsgGtgKtflwkallkklrs 48 
                                       +k + ++G  GtgKt + ka+ + + +
  gi|336252176|ref|YP_004595283.1| 225 PKGVLLHGPPGTGKTLMAKAVANEIDA 251
                                       5667789**************999876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                                       HH......HCTS-EEEEESTTSSCHHHHHHHHHHCHC CS
                              PIF1  12 aiieavlnekgklfFvtGsgGtgKtflwkallkklrs 48 
                                       ++ e++  + +k + ++G  GtgKt l ka+ +  +s
  gi|336252176|ref|YP_004595283.1| 488 EVFEQMDMQAAKGVLMYGPPGTGKTLLAKAVANEAQS 524
                                       5667778888899999*************99987665 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      0.12        38       2      24 ..     229     252 ..     228     294 .. 0.68
   2 ?    5.2   0.0     0.049        16       4      71 ..     504     566 ..     501     572 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.12
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts.li 24 
                                       + hG pG GK+ + + ++++   +
  gi|336252176|ref|YP_004595283.1| 229 LLHGPPGTGKTLMAKAVANEIdAH 252
                                       68**************99994433 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.049
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                        G pG GK+ l + ++++   ++ +++   ell++ + ++++   + ++++ +++       ++++DE+
  gi|336252176|ref|YP_004595283.1| 504 YGPPGTGKTLLAKAVANEAqSNFISIKG-PELLNKYVGESEKGVREVFEKARSNA-----PTVIFFDEI 566
                                       588***************8877777777.88999888666555444444444443.....348999997 PP

>> COOH-NH2_lig  Phage phiEco32-like COOH.NH2 ligase-type 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.9   1.2e+03     174     213 ..     244     282 ..     237     287 .. 0.73
   2 ?    5.8   0.0     0.021       6.7      24      74 ..     389     439 ..     382     448 .. 0.89
   3 ?    1.6   0.1      0.43   1.4e+02       2      73 ..     670     743 ..     669     748 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.9
                      COOH-NH2_lig 174 lvareyeelekrpleseelqeAfYegdkealrelleelle 213
                                        va+e ++ + ++++ +e+ + +Y   +e+lre++ee  e
  gi|336252176|ref|YP_004595283.1| 244 AVANEIDA-HFETISGPEIMSKYYGESEEQLREVFEEAEE 282
                                       45544443.3456778999999***********9998765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.021
                      COOH-NH2_lig  24 erdGavGcDarslereekelplaElRPapaedpaelleelrkllqeaaeli 74 
                                       +++G vG+D  sl re  + +l  +RP+ + + +e+ +e+ ++lq +++  
  gi|336252176|ref|YP_004595283.1| 389 STHGFVGADLESLAREGAMNALRRIRPDLDLEEDEIDAEVLESLQVTERDF 439
                                       578********************************9999999999887765 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.43
                      COOH-NH2_lig   2 GaDpEfllrkktgklvpasrfl.erdGavGcDar...slereekelplaElRPapaedpaelleelrkllqeaael 73 
                                       GaD+E + r  +  ++ + +f+ ++d +  +D++   ++ +e+ e++l E+ P+ + +++e  ee+++ + +a+ +
  gi|336252176|ref|YP_004595283.1| 670 GADIEAVCR--EASMAASREFInSVDPEEMADTIgnvRISKEHFEHALEEVNPSVTPETREQYEEIEEQFDTAEPQ 743
                                       778887776..45566666776323333344443111466677799**********************99999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (753 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        56  (0.00312343); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              56  [number of targets reported over threshold]
# CPU time: 0.77u 0.26s 00:00:01.03 Elapsed: 00:00:00.39
# Mc/sec: 5731.34
//
Query:       gi|336252177|ref|YP_004595284.1|  [L=82]
Description: hypothetical protein Halxa_0766 [Halopiger xanaduensis SH-6]
Scores for 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   12.9   1.5       0.15   12.5   0.9    1.6  2  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 ?   12.5   0.9   8.4e-06      0.15      24      48 ..      31      55 ..      26      70 .. 0.90
   2 ?   -1.4   0.0      0.19   3.4e+03      34      43 ..      70      79 ..      60      82 .] 0.61

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-06
                               HMA 24 pgVesvkvdlatktvtVegdaestk 48
                                      +gV +++vdl+ +tv V +d+e+ +
  gi|336252177|ref|YP_004595284.1| 31 TGVADASVDLVDDTVIVIVDDEQYE 55
                                      69*******************9955 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.19
                               HMA 34 atktvtVegd 43
                                      +++ +tVe++
  gi|336252177|ref|YP_004595284.1| 70 KNGVLTVELE 79
                                      4555666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 639.01
//
Query:       gi|336252178|ref|YP_004595285.1|  [L=284]
Description: TatD-related deoxyribonuclease [Halopiger xanaduensis SH-6]
Scores for 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-17   61.8   0.1    2.4e-14   53.3   0.0    2.0  2  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 !   53.3   0.0   1.3e-18   2.4e-14       2     162 ..      10     199 ..       9     208 .. 0.86
   2 !    6.7   0.0   0.00023       4.1     196     233 ..     218     253 ..     202     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1.3e-18
                                       EEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSG..................GGHHHHHHHHTT.TTTEEEEE- CS
                        TatD_DNase   2 DaHcHldskefeedreeileraeeagvaavvvvgtss..................kdskavlelakkypnkvyavlG 60 
                                       D+H Hld ++  +   ++++ +++ g+++++vv+  s                   +++ v+e ++  +++ ++vlG
  gi|336252178|ref|YP_004595285.1|  10 DNHLHLDPDN--HRGIDAVRDFARLGGTHLLVVNKPSwhlgveaeagedfryvfeRTIEIVEEASEVLEGRAWPVLG 84 
                                       9*******44..5788889************9999999*********999988733555555555559999****** PP

                                       --GGGGGC..........C.CCHH.HHHHHH.HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTE CS
                        TatD_DNase  61 iHPnevde..........asedll.eelkel.anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelkl 125
                                       +HP  + +          +  dl+ + l+ + ++v++ ++ a+ + G+++y+++++ +ea ++v+++ ++   +l++
  gi|336252178|ref|YP_004595285.1|  85 VHPGLISRlvddrgfepaEARDLMqAGLDVAaEYVADGEALAL-KSGRPHYDVSDAVWEASNDVMRHAFEHGGDLDC 160
                                       ***9999988899998863334446889999999*********.********************************* PP

                                       EEEEEEES-HH..HHHHHHHHCGGCCSEEEETT--S-HH CS
                        TatD_DNase 126 plviHlrkaee..dlleilkeaaeakakvvlHsfsgsae 162
                                       ++++H++++ee  ++ e  ++a+ ++++vv H   g+ e
  gi|336252178|ref|YP_004595285.1| 161 AVQLHTEASEEmtTVAEWGEDAGMERHQVVKHYAAGRLE 199
                                       ********7765578888888888888*****9999876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00023
                                       -GGGEEE---TTSSEECCCTT.SE--GGGHHHHHHHHHH CS
                        TatD_DNase 196 pldrlLiETDaPyltpkpyrg.krnepanvayvveklae 233
                                         + +L+ETD  y ++ p r+ ++  p++v++ v+ l e
  gi|336252178|ref|YP_004595285.1| 218 RGEPFLMETD--YVDD-PDRPgAVLGPKTVPRRVRWLLE 253
                                       56779*****..8999.99999**********9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2031.48
//
Query:       gi|336252179|ref|YP_004595286.1|  [L=193]
Description: hypothetical protein Halxa_0768 [Halopiger xanaduensis SH-6]
Scores for 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-72  241.1   7.8    9.8e-72  240.9   7.8    1.0  1  DUF2150   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
        9.6    6.5   6.8        2.1    8.7   0.2    3.0  3  zf-HC2    Putative zinc-finger


Domain annotation for each model (and alignments):
>> DUF2150  Uncharacterized protein conserved in archaea (DUF2150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.9   7.8   1.1e-75   9.8e-72       1     188 []       7     191 ..       7     191 .. 0.98

  Alignments for each domain:
  == domain 1  score: 240.9 bits;  conditional E-value: 1.1e-75
                           DUF2150   1 eFYteeRwqNWlnrvkeedldle.edseeleaavllnlqdDvilavlkiikaveeeelskeeAleeleevreivlee 76 
                                       eFY+eeRwqNW++r+k+ed+d+e e+s    a++llnlqdD+++av+ki++a++++el++eeAl+e+e+vreivl e
  gi|336252179|ref|YP_004595286.1|   7 EFYSEERWQNWIDRIKDEDIDPEdESS----ARLLLNLQDDTAIAVAKIVSAYDDGELEQEEALSEIEDVREIVLGE 79 
                                       7*********************95555....********************************************** PP

                           DUF2150  77 veeddeekeeliesvqtsllvvfaaaeeyieggvakekdieelvkaaaeaeaeedleaaleivaqiGakvidgeklp 153
                                       v+++deek  l+++vqtsl++vf aaeeyi++g a++ ++ +++ aaa+aeaeedl+aal+++aq+G+ +idge+l+
  gi|336252179|ref|YP_004595286.1|  80 VDIEDEEKLILVDGVQTSLVCVFFAAEEYIANGPAEDGSVGDYLGAAADAEAEEDLDAALGYAAQAGTLIIDGEELD 156
                                       ***************************************************************************** PP

                           DUF2150 154 ekvledleyglvaewldgidslaaamsssesveee 188
                                       ++v+e leyglv+ew++g+dsl++ams++e+vee+
  gi|336252179|ref|YP_004595286.1| 157 MEVAEGLEYGLVTEWINGLDSLQSAMSDPEVVEED 191
                                       *********************************97 PP

>> zf-HC2  Putative zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.4   1.2e+04      13      20 ..      23      30 ..      13      32 .. 0.70
   2 ?    8.7   0.2   0.00023       2.1       8      22 ..      52      66 ..      47      71 .. 0.83
   3 ?    0.1   0.7      0.11     1e+03       5      23 ..     120     138 ..     118     140 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.4
                                      CCT-SCCC CS
                            zf-HC2 13 DGeLspee 20
                                      D +++pe+
  gi|336252179|ref|YP_004595286.1| 23 DEDIDPED 30
                                      66678887 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00023
                                      HHHHHCCT-SCCCHC CS
                            zf-HC2  8 LsaYlDGeLspeera 22
                                      +saY DGeL  ee+ 
  gi|336252179|ref|YP_004595286.1| 52 VSAYDDGELEQEEAL 66
                                      89**********986 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.11
                                       HHHHHHHHCCT-SCCCHCC CS
                            zf-HC2   5 relLsaYlDGeLspeerar 23 
                                        ++L a +D e  ++ +a+
  gi|336252179|ref|YP_004595286.1| 120 GDYLGAAADAEAEEDLDAA 138
                                       4667777777766655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 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:                        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: 1435.64
//
Query:       gi|336252180|ref|YP_004595287.1|  [L=764]
Description: hypothetical protein Halxa_0769 [Halopiger xanaduensis SH-6]
Scores for 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  (764 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.40
# Mc/sec: 5676.85
//
Query:       gi|336252181|ref|YP_004595288.1|  [L=445]
Description: hydroxymethylglutaryl-CoA synthase [Halopiger xanaduensis SH-6]
Scores for 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-26   93.9   0.0    1.7e-26   93.2   0.0    1.4  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
    2.4e-24   86.4   0.0    3.9e-24   85.8   0.0    1.2  1  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
  ------ inclusion threshold ------
      0.069   13.0   0.2       0.16   11.8   0.2    1.5  1  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
      0.098   12.4   0.0          1    9.0   0.0    2.1  2  MAF_flag10      Protein of unknown function DUF115


Domain annotation for each model (and alignments):
>> 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 !   93.2   0.0   3.7e-30   1.7e-26       4     171 ..       3     175 ..       1     178 [. 0.89

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 3.7e-30
                    HMG_CoA_synt_N   4 dvgilaleiylpaqyvdqa.elekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrle 79 
                                        vgi a+ei+     +d    +   +g +  kyt glg    +f +  edi ++     ++l+er+ l+ d igr++
  gi|336252181|ref|YP_004595288.1|   3 AVGIDAIEIWTGNLKLDLPgTFAPQKGEDPEKYTKGLGLNASSFPDSYEDIVTMGANAAHRLMERKGLEPDDIGRID 79 
                                       5899999999998888864156777889999********************************************** PP

                    HMG_CoA_synt_N  80 vgtetiidksksvksvlmqlfeesgntdiegi...dtlnacyggtaalfnavnwiessawdgryalvvagdiaiyds 153
                                       v te+  d+sk v + +   +e+  + d       +   ac  gt++l +a nwi +    gr alv+a d a+y++
  gi|336252181|ref|YP_004595288.1|  80 VATESSFDNSKPVSTYVAGCLEQVYDGDFHHAnkgERKFACIAGTQSLDDAYNWIRAGRNRGRSALVIATDTALYAR 156
                                       ***************999999998888887651115678************************************** PP

                    HMG_CoA_synt_N 154 gna.rptggagavalligp 171
                                       g+a   t gagava+li  
  gi|336252181|ref|YP_004595288.1| 157 GDAgEATQGAGAVAMLISE 175
                                       *883689*********975 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 !   85.8   0.0   8.7e-28   3.9e-24      17     244 ..     195     413 ..     188     433 .. 0.83

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 8.7e-28
                                       SEE---TT-S--EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH------GGG-SEEEE--SSHHHHHHHHHHHHHH CS
                    HMG_CoA_synt_C  17 DFykPdlaseYPvvDGklslscYlkaldrcYksyskkvkkitkdadkeftlddfdyvifhsPfcklvqkslarllyn 93 
                                       DF kP+    +P vDGk s++ Yl  ++++ + y +           +  lddf y  fh+Pf  +v+k+ a l y 
  gi|336252181|ref|YP_004595288.1| 195 DFLKPN--QQFPSVDGKRSVQVYLARMREAVEDYESVA--------GDVHLDDFAYAPFHTPFPGMVRKA-ALLAYR 260
                                       9****8..57************************9874........5667*******************8.99**** PP

                                       HHHH.S-HHHHHHH-GGGGGG...TT--GGGGGT-..HHHHHHHHHH..HHHHHHHHTGGGGHHHHHH---GGGHHH CS
                    HMG_CoA_synt_C  94 Dflanassdkeeevkekleek...ddlkldesltd..kdlekallki..akelfkkkvkpsllvptevGnmYtasly 163
                                          +n+s   eee+ +++ ++   ++++ de++ d  +d   +l +    +e + + ++p+l +++evGn Yt s++
  gi|336252181|ref|YP_004595288.1| 261 HVIRNTS--VEEELADEIGRQpraEAFDTDEAYRDalRDYMDSLKETdrYREWYAEAIDPTLSISREVGNWYTGSVH 335
                                       ****999..456777777655445789999999985555555555441157899*********************** PP

                                       HHHHHHHHHS-HH..HHTT-EEEEEEEETTTEEEEEEEEE-S--STTSHHHHHTTTTHHHHHHTSEEE-HHHHHHHH CS
                    HMG_CoA_synt_C 164 aalasllskvsad..elagkriglfsYGsGlaaslfslrvkqdvsedsildiakvldlkkkLdsRkevtPeefeeal 238
                                        a as l+++ +d  +++++r+++ sYGsG  a +++ +v++  ++    +i ++ +++++L++R  +  e++ee+ 
  gi|336252181|ref|YP_004595288.1| 336 IARASALKEALEDgrDMTDERLLVGSYGSGAQAEIHAETVQDGWEK----EIEAL-NVDEQLAERYDMDWEDYEEIH 407
                                       *******99877655899**********************999888....67665.******************987 PP

                                       HHHHHH CS
                    HMG_CoA_synt_C 239 elreka 244
                                       +  ++ 
  gi|336252181|ref|YP_004595288.1| 408 DAHNHE 413
                                       665443 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 ?   11.8   0.2   3.6e-05      0.16       6      65 ..     119     177 ..     116     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                                       GGGHHHHHHHHHHHHHHTT..S-SEEEEEEEEEGGGCS-TTTHHHHTTB-EEEEEEEEEEES CS
                       ACP_syn_III   6 aCsgfvyalsvAdaliesg..aakrvLvigaetlskilDwkdrstavlfGDGAgAvvlease 65 
                                       aC + ++ l+ A + i++g  + + +Lvi+++t  +    +  +   + G GA A++++++ 
  gi|336252181|ref|YP_004595288.1| 119 ACIAGTQSLDDAYNWIRAGrnRGRSALVIATDTALY---ARGDAGEATQGAGAVAMLISEDP 177
                                       7999999************87899*********544...5556667799*********9974 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 ?    0.8   0.0     0.076   3.4e+02      49      87 ..      51      90 ..      42     100 .. 0.82
   2 ?    9.0   0.0   0.00023         1      18      62 ..     108     155 ..      99     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.076
                        MAF_flag10 49 dkaviiaadtalkaLlkegIkPDivvslDp.qeasyevfk 87
                                      +++v + a++a + ++ +g++PD +  +D  +e+s++ +k
  gi|336252181|ref|YP_004595288.1| 51 EDIVTMGANAAHRLMERKGLEPDDIGRIDVaTESSFDNSK 90
                                      567778899999*************999996777777655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00023
                        MAF_flag10  18 llnkfkgnkpaiivgaGPSLeknlellkelr...dkaviiaadtalka 62 
                                       +++ +kg++++  +++  SL++ ++++++ r    +a++ia dtal a
  gi|336252181|ref|YP_004595288.1| 108 FHHANKGERKFACIAGTQSLDDAYNWIRAGRnrgRSALVIATDTALYA 155
                                       556667777777788889*********877767899*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3552.08
//
Query:       gi|336252182|ref|YP_004595289.1|  [L=119]
Description: hypothetical protein Halxa_0771 [Halopiger xanaduensis SH-6]
Scores for 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  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 942.13
//
Query:       gi|336252183|ref|YP_004595290.1|  [L=275]
Description: hypothetical protein Halxa_0772 [Halopiger xanaduensis SH-6]
Scores for 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-51  173.3  12.8    6.8e-51  173.1  12.8    1.1  1  DsbD_2    Cytochrome C biogenesis protein transmembrane regio
  ------ inclusion threshold ------
       0.17   11.4   1.5       0.28   10.8   0.3    1.9  2  PIRT      Phosphoinositide-interacting protein family


Domain annotation for each model (and alignments):
>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.1  12.8   7.5e-55   6.8e-51       2     198 ..      14     237 ..      13     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 173.1 bits;  conditional E-value: 7.5e-55
                            DsbD_2   2 afllgLlgslhClgmCggivlalslsk................pkra......l.alllynlGRilsYallGalvgl 55 
                                       ++++gLlg++hC+gmCg++v+ +++++                +  +      + +++l+nlGR++sY+llGal+g+
  gi|336252183|ref|YP_004595290.1|  14 FLVIGLLGGAHCIGMCGPLVTVYASRMdgaatdggqrhrdrgrE--ShlttyeVrQHALFNLGRTASYTLLGALFGA 88 
                                       789*********************99988887777655543321..0223333436********************* PP

                            DsbD_2  56 lgsvlqlagel.....eglrallgvllgllllllglklllkkkllk..lerlgkllsrllkklakklkslasalllG 125
                                       lgsvl++++++     e +r+ +g+++g ++++ g+++ll+++     l  l++++srl+  + + l++ +++++lG
  gi|336252183|ref|YP_004595290.1|  89 LGSVLFVTTDAltpvlETVRGGVGLVIGGFVIATGVYYLLGRTTGGiqLPGLERVVSRLTAHVDR-LANGPGIVGLG 164
                                       *****9998876777788********************976665541156677888877777765.79********* PP

                            DsbD_2 126 llnGllpCglvysalllalasgsaleGalvmlaFgLGTlpalllfglllgllskklrkkllrlagvllillgl 198
                                       +l+GllpC+++y+a+l+a+a+gs+++Gal+++a+g+GT+pa++++g+++  +  + r++++rl+gv++++lg+
  gi|336252183|ref|YP_004595290.1| 165 ALHGLLPCPILYPAFLYAFATGSPAGGALALAALGIGTIPAVFAYGTVIDAVDVAHRRRVHRLLGVAFVVLGY 237
                                       ************************************************************************8 PP

>> PIRT  Phosphoinositide-interacting protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.18   1.6e+03      80     107 ..      76     103 ..      59     127 .. 0.61
   2 ?   10.8   0.3   3.1e-05      0.28      57     105 ..     204     247 ..     194     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.18
                              PIRT  80 kevfklsGpaflslGlmllvcGlvwvpi 107
                                       +  + l G  f +lG +l+v      p+
  gi|336252183|ref|YP_004595290.1|  76 TASYTLLGALFGALGSVLFVTTDALTPV 103
                                       4455666666666666666554444444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 3.1e-05
                              PIRT  57 gavfllGvvittlsrnstlknkdkevfklsGpaflslGlmllvcGlvwv 105
                                        avf +G+vi ++        + ++v++l G af+ lG +ll  Gl+ +
  gi|336252183|ref|YP_004595290.1| 204 PAVFAYGTVIDAV-----DVAHRRRVHRLLGVAFVVLGYVLLAHGLMSL 247
                                       489******9999.....344567899******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1838.30
//
Query:       gi|336252184|ref|YP_004595291.1|  [L=834]
Description: heavy metal translocating P-type ATPase [Halopiger xanaduensis SH-6]
Scores for 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-43  147.0   4.6    4.2e-43  147.0   4.6    2.6  3  E1-E2_ATPase   E1-E2 ATPase
    4.7e-33  115.3   8.7    8.9e-33  114.3   8.7    1.5  1  Hydrolase      haloacid dehalogenase-like hydrolase
    4.6e-12   46.2   0.0    2.3e-11   44.0   0.0    2.3  1  HMA            Heavy-metal-associated domain
     0.0042   16.9   0.8      0.008   15.9   0.8    1.4  1  Hydrolase_3    haloacid dehalogenase-like hydrolase
     0.0067   17.1   0.9      0.013   16.2   0.2    1.8  1  ATPase-cat_bd  Putative metal-binding domain of cation transp
  ------ inclusion threshold ------
      0.029   14.2   2.3       0.11   12.3   2.3    2.1  1  DUF5612        Domain of unknown function (DUF5612)


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 ?   -1.2   0.8      0.41   1.2e+03     121     146 ..     201     233 ..     157     266 .. 0.67
   2 !  147.0   4.6   1.4e-46   4.2e-43       5     179 ..     304     478 ..     300     480 .. 0.95
   3 ?   -2.6   0.1       1.1   3.3e+03      22      40 ..     506     524 ..     493     526 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHHHS-STTTSSTT.......H CS
                      E1-E2_ATPase 121 vlvpvvlliallvflialllgksla.......e 146
                                         +p+ l+ia+l+ +i+ ++gk++        +
  gi|336252184|ref|YP_004595291.1| 201 LATPFYLMIAALTTIILGVTGKPILqgayvsaK 233
                                       456777777777777777777776655555442 PP

  == domain 2  score: 147.0 bits;  conditional E-value: 1.4e-46
                                       -EEEEE.-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-E CS
                      E1-E2_ATPase   5 ptakvi.rdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsge 80 
                                       ++a+++ +dg+ e+++ +el   D vl++ag+r+p+Dg +veg+a vde+++TGEslpv+k++gd v +G++v +g 
  gi|336252184|ref|YP_004595291.1| 304 DSARRVgEDGSHEDVALEELSASDRVLVRAGERIPVDGAVVEGEAAVDEAVVTGESLPVTKDAGDAVVGGSMVADGA 380
                                       5677777********************************************************************** PP

                                       EEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHH CS
                      E1-E2_ATPase  81 akavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallva 157
                                       ++++V + + ++ l++i++lv + +s +  +qk +dkl+ ++vpvvl++a++v ++ l lg ++  all +l++l++
  gi|336252184|ref|YP_004595291.1| 381 VTVEVGEDA-TSSLDRITELVWDLQSGTHGIQKLADKLATIFVPVVLALAVVVTVARLALGAPIEGALLTGLTVLIV 456
                                       ****98876.5679*************************************************************** PP

                                       HS-TTHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 158 aiPcaLplavplalalgarrla 179
                                       ++PcaL+la+pla+a+g+r + 
  gi|336252184|ref|YP_004595291.1| 457 SCPCALGLATPLAVAAGIRDAL 478
                                       ******************9875 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.1
                                       G--TTSEEEEETT-B--SE CS
                      E1-E2_ATPase  22 elvpGDivllkagdrvpaD 40 
                                        l +GD+ +++a   v aD
  gi|336252184|ref|YP_004595291.1| 506 TLTTGDMTVVEADTDVDAD 524
                                       3555666666666666665 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   8.7     3e-36   8.9e-33       2     210 .]     497     742 ..     496     742 .. 0.92

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 3e-36
                                       SEEEEESBTTTBCHHHHHHHHHHHH...CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH..HHHHHETTTE...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx...... RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa...alalaaaletgsehpigkalvaaakarsgal..tgfatfigrg...... 67 
                                       +tvvfDk+GTLttg + v+++   +    l +aa+le  s hp g+a++a a + sg+   tg +t+++ g      
  gi|336252184|ref|YP_004595291.1| 497 DTVVFDKTGTLTTGDMTVVEADTDVdadLLGRAAILEGRSAHPVGQAIAAMAGGSSGDGadTGSGTVADGGtvetag 573
                                       79*************999997666666678999999999****************5555447777777777788888 PP

                                       ...................................HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TT CS
                                       ...................................xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xx RF
                         Hydrolase  68 ...................................ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qa 105
                                                                          ++ +g p+++++   d+p+ + ++++++ + gr  + +  ++
  gi|336252184|ref|YP_004595291.1| 574 aetsvatddagetgdgrlesfesyrngvagvvdgeEIVVGHPDLFRDRgwDVPEAVAKQVEAHRETGRVPVAVgrDG 650
                                       9999999999999************************************************************99** PP

                                       HHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH.TTGGGESEEEEHHCESSTTTSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 106 ralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq.lGddyfdaviasdietvakpspegkva 181
                                        a +v+ + d+  +++e  e+v ++ + g evv+ltgd+ + a+r  ++ +            + ++a++ pegk +
  gi|336252184|ref|YP_004595291.1| 651 TAAGVIVVGDE--LREEWGETVTAIADSGAEVVVLTGDDAKAADRFREHgAV-----------DRVFAGVPPEGKAE 714
                                       ***********..*******************************99998555...........777*********** PP

                                       HHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 182 aireLqgkpeevamVGDgvnDaaalaaAg 210
                                       ++++L+g + +++m+GDg nDa+alaaA+
  gi|336252184|ref|YP_004595291.1| 715 TVERLKGTG-RTVMIGDGTNDAPALAAAD 742
                                       *****9999.9*****************8 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   7.6e-15   2.3e-11       3      61 ..      77     135 ..      76     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 7.6e-15
                               HMA   3 rvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61 
                                        v+gmhCa C+a +e+v  e +gV+ ++ +++t+tv +++d++s++  ++ +ai+ +gy
  gi|336252184|ref|YP_004595291.1|  77 EVDGMHCATCEAFIESVATETEGVSGASASYVTDTVRIDHDPDSVSQDDLAAAISGLGY 135
                                       69******************************************88899*********9 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.8   2.7e-06     0.008     205     242 ..     724     761 ..     716     773 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-06
                                       GEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEE CS
                       Hydrolase_3 205 eviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyv 242
                                       +++ +GDg ND + L aa+lg+A+g ++  +  aAd  
  gi|336252184|ref|YP_004595291.1| 724 RTVMIGDGTNDAPALAAADLGIALGGGTAMAADAADVA 761
                                       6899*************************999999975 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 !   16.2   0.2   4.3e-06     0.013       1      64 [.      10      69 ..      10      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.3e-06
                     ATPase-cat_bd  1 aCyHCglpveesaklkaeiegeerefCCkGCqavaqliveaglesyYklrtekakkaeelllpe 64
                                      +C+ C lpve s     ++++e ++fCC GC+ v +++ + +  +  + r+++++++e+++lp+
  gi|336252184|ref|YP_004595291.1| 10 QCTLCDLPVEGS----DVTDDEGNRFCCVGCRDVSDALGDVDEVDADDVRNAREDDSEDRELPD 69
                                      599999999876....67889999*************998877777777776666666655555 PP

>> DUF5612  Domain of unknown function (DUF5612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.3   3.6e-05      0.11      22      86 ..     316     385 ..     307     441 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHHHHHHHHCT.SS-EEEEEEE--SHHHHHHHHHHGGGSTTEE...EEEEESSB-.-THHHHHH CS
                           DUF5612  22 aqvalGaiseadrhnir.GerisvdtiplvGeeelaeaveavsrlprvk...vlvlaGslm.GGkiteav 86 
                                        +val  +s +dr  +r Geri vd   + Ge ++ eav + + lp +k     v+ Gs++  G++t +v
  gi|336252184|ref|YP_004595291.1| 316 EDVALEELSASDRVLVRaGERIPVDGAVVEGEAAVDEAVVTGESLPVTKdagDAVVGGSMVaDGAVTVEV 385
                                       5799999*********989********************9988888654111567777765246666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (834 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.25s 00:00:00.97 Elapsed: 00:00:00.44
# Mc/sec: 5750.65
//
Query:       gi|336252185|ref|YP_004595292.1|  [L=437]
Description: hypothetical protein Halxa_0774 [Halopiger xanaduensis SH-6]
Scores for 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-34  117.9  32.3    6.5e-34  117.6  32.3    1.1  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6  32.3   3.6e-38   6.5e-34       5     325 ..      32     346 ..      28     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 3.6e-38
                   AI-2E_transport   5 lvllllllalypfiselllplliAlvlayllnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvplliaqltq 81 
                                       l+  + +l+ ++++ ++l  +l+++vlay+l p  ++L ++ v+ + a+l++++++++ ++l++ +++ +++  + +
  gi|336252185|ref|YP_004595292.1|  32 LAV-VSALLGLFVVLPYLQYVLLGVVLAYVLMPAQRRL-ETYVRPITAALVLVAVAILTIILPLSYVLAVALREALN 106
                                       333.333333344446999*******************.99999999***9999**************999999999 PP

                   AI-2E_transport  82 lvkslpayidslqnilnelpslleelenliqalkqslskilsnilssilnsllsllasllglilslvlvllllffll 158
                                       +++ ++     + +i + l+s+       + ++ q++++ ++  l+ +++s ++l++ ++gl++ l ++l++lf ll
  gi|336252185|ref|YP_004595292.1| 107 ILDAVEGGDLNVGAIESRLESNGYAV--DLTEMYQAYQEPIETGLQGLATSGIELVSGVPGLLIGLTVTLFVLFALL 181
                                       99999966666666666666665555..478999999**************************************** PP

                   AI-2E_transport 159 ldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvglanliP 235
                                       +dg  l+  + ++lp +  + ++++  e+++ +++ + g+v va i++v++++gl++l vp   +l++ +++++l+P
  gi|336252185|ref|YP_004595292.1| 182 RDGGALVAWFHRILPIE-DDILDELQAEIDQLMWASVVGNVAVAGIQAVMLGVGLVLLDVPAVVFLTVATFVLALLP 257
                                       *****************.99********************************************************* PP

                   AI-2E_transport 236 yiGavivlipiaiialltggikevlivlivvllvqliegnilePklmgkrlglhplvillsllaggklfGlvGlila 312
                                       ++Ga+ v++p+a++++ +g++  + i++++  lv++ +  +l+P l+g++   + ++i++ +++g+ +fG vGl+++
  gi|336252185|ref|YP_004595292.1| 258 LVGAFGVWVPVAVYLIAVGQFVPAAILVAYGSLVSASD-TYLRPALIGRTSAFNSAIIVVGIFGGIVVFGGVGLFIG 333
                                       ****************************9999999877.89************************************ PP

                   AI-2E_transport 313 vpltavikailea 325
                                       +++++ +k +l++
  gi|336252185|ref|YP_004595292.1| 334 PVVLGGAKITLDV 346
                                       ****999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 3260.40
//
Query:       gi|336252186|ref|YP_004595293.1|  [L=239]
Description: hypothetical protein Halxa_0775 [Halopiger xanaduensis SH-6]
Scores for complete 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-68  229.7   1.7    2.2e-68  229.5   1.7    1.0  1  DUF2270       Predicted integral membrane protein (DUF2270)
  ------ inclusion threshold ------
      0.011   15.3   3.8      0.015   14.9   0.9    2.0  2  DUF998        Protein of unknown function (DUF998)
       0.12   12.0   0.0       0.23   11.1   0.0    1.5  1  CPP1-like     Protein CHAPERONE-LIKE PROTEIN OF POR1-like
       0.13   12.5   0.1       0.13   12.5   0.1    1.8  2  DUF2516       Protein of unknown function (DUF2516)
       0.21   11.3   0.1       0.21   11.3   0.1    2.2  2  FtsK_4TM      4TM region of DNA translocase FtsK/SpoIIIE
       0.41   10.3   6.6        6.2    6.4   3.2    2.2  2  DUF4131       Domain of unknown function (DUF4131)
       0.41   10.4   3.2        1.1    9.0   1.1    2.2  2  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr
        3.6    8.0   6.7         18    5.7   0.2    2.2  2  DUF4199       Protein of unknown function (DUF4199)


Domain annotation for each model (and alignments):
>> DUF2270  Predicted integral membrane protein (DUF2270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.5   1.7   9.9e-72   2.2e-68       2     183 ..      36     212 ..      35     213 .. 0.99

  Alignments for each domain:
  == domain 1  score: 229.5 bits;  conditional E-value: 9.9e-72
                           DUF2270   2 hlYRgeveratawreRlDrttnWavvvtaallsvalsspeashavlllgmllvlvfLliearryrfydvwrsrvrll 78 
                                       h+YRgev++a++ ++R+Drtt+Wa++++aalls+++ss+e+++++ll+g++++++fL++e+rryrfyd wr+rvr++
  gi|336252186|ref|YP_004595293.1|  36 HFYRGEVSQANSAQDRIDRTTDWAITLMAALLSLVFSSQEMPAFLLLIGLFVLCIFLFFEVRRYRFYDHWRARVRFI 112
                                       9**************************************************************************** PP

                           DUF2270  79 eenffaealdpeegaeeeeWreeLaedlrkPtlkislleAlgrRLrrnYlwlllvlllawllkitlfkkeeesleel 155
                                       +en+fa+al+p  g+e++ WreeL++dlr+Pt+k+s leAl+rR+rr+Y  l++v+ +aw++k++lf++e+    ++
  gi|336252186|ref|YP_004595293.1| 113 QENVFANALEPV-GVEHPYWREELSDDLRNPTFKVSNLEALSRRIRRVYGLLFAVVGIAWIFKVSLFTPEQ----QW 184
                                       ***********9.999******************************************************9....79 PP

                           DUF2270 156 lerAavgplpGelvllvvalfylallvl 183
                                       +e+A+++ ++G +v++++ lfy+a++vl
  gi|336252186|ref|YP_004595293.1| 185 AEAAELPGVHGYYVAGMLGLFYAAVVVL 212
                                       ************************9987 PP

>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.13     3e+02     164     174 ..      77      87 ..      41     109 .. 0.53
   2 ?   14.9   0.9   6.8e-06     0.015      65     131 ..     153     221 ..     146     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.13
                            DUF998 164 lGlaerllvla 174
                                       ++++  +++++
  gi|336252186|ref|YP_004595293.1|  77 PAFLLLIGLFV 87 
                                       22222222222 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.8e-06
                            DUF998  65 rgragragrlllavaglg.lvlagvfptdpgggspslsglvHglasavaflalavavllla.saarrra 131
                                       ++r++r+ +ll+av g++  + + +f   +  + +     vHg+  a ++ ++ +av++l+ ++  rra
  gi|336252186|ref|YP_004595293.1| 153 SRRIRRVYGLLFAVVGIAwIFKVSLFTPEQQWAEAAELPGVHGYYVAGMLGLFYAAVVVLTlWPSSRRA 221
                                       68999********9999966667777555555555577779********************86666665 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 ?   11.1   0.0    0.0001      0.23      97     134 ..      55      92 ..      17     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                         CPP1-like  97 liraavflvlavltlvapaesvpalllalglgasiyfl 134
                                       ++  a+ l+ a+l+lv++++++pa+ll +gl++  +fl
  gi|336252186|ref|YP_004595293.1|  55 TTDWAITLMAALLSLVFSSQEMPAFLLLIGLFVLCIFL 92 
                                       4566788899999******************9998887 PP

>> DUF2516  Protein of unknown function (DUF2516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.9e-05      0.13      36      80 ..      48      93 ..      41      98 .. 0.78
   2 ?   -2.3   0.7       2.4   5.4e+03      60      60 ..     198     198 ..     159     215 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-05
                           DUF2516 36 aagkrtKpf.WlailgvallvlllglfgalsllgliavvaalvYlv 80
                                      a ++  +++ W++ l++all l+++ + +  +l li++ + +++l+
  gi|336252186|ref|YP_004595293.1| 48 AQDRIDRTTdWAITLMAALLSLVFSSQEMPAFLLLIGLFVLCIFLF 93
                                      455555443299888888888888999999**************85 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                           DUF2516  60 l 60 
                                       +
  gi|336252186|ref|YP_004595293.1| 198 V 198
                                       1 PP

>> FtsK_4TM  4TM region of DNA translocase FtsK/SpoIIIE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   2.2      0.28   6.2e+02      73     114 ..      62     101 ..      55     110 .. 0.50
   2 ?   11.3   0.1   9.4e-05      0.21      84     135 ..     150     203 ..     131     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.28
                          FtsK_4TM  73 llawglrllrrkslerrllrllgalllllasaalfalrlasl 114
                                       l+a+ l+l++++++     +ll + l++l++  +f++r +++
  gi|336252186|ref|YP_004595293.1|  62 LMAALLSLVFSSQEM--PAFLLLIGLFVLCIFLFFEVRRYRF 101
                                       444445555544332..3344444445555555555555554 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.4e-05
                          FtsK_4TM  84 kslerrllrllgalllllasaalf..alrlasledelpggaGGvlGrllaaals 135
                                       + l+rr++r+ g+l++++ +a +f  +l++++ +++ ++++ Gv G+ +a++l 
  gi|336252186|ref|YP_004595293.1| 150 EALSRRIRRVYGLLFAVVGIAWIFkvSLFTPEQQWAEAAELPGVHGYYVAGMLG 203
                                       567799999**************94455666669999999*********99874 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.2    0.0028       6.2      12      53 ..      61     100 ..      57     109 .. 0.75
   2 ?    4.9   0.1    0.0082        18      10      60 ..     160     226 ..     156     232 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0028
                           DUF4131  12 lllllllllllllrrrprrrvllllllllllallgfalrapq 53 
                                       +l+++ll l++ +  +  + +lll++l+ l+++l+f +r ++
  gi|336252186|ref|YP_004595293.1|  61 TLMAALLSLVFSS--QEMPAFLLLIGLFVLCIFLFFEVRRYR 100
                                       3444455555554..899***************999888765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0082
                           DUF4131  10 lalllllllllllllrr................rprrrvllllllllllallgfalrapqpnandls 60 
                                        +ll+++  ++++++ +                   + v+++l+l+++++++  ++++ ++++ +++
  gi|336252186|ref|YP_004595293.1| 160 YGLLFAVVGIAWIFKVSlftpeqqwaeaaelpgVHGYYVAGMLGLFYAAVVVLTLWPSSRRAKGEIH 226
                                       5677777777777766688777777777666666666669999999999999999999999887776 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 ?    0.6   0.0      0.19   4.2e+02     104     131 ..      43      70 ..      19      74 .. 0.61
   2 ?    9.0   1.1    0.0005       1.1      61     102 ..     151     191 ..     147     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.19
                      Trp_oprn_chp 104 tgvasaaaave.ltawpvlalaggvllll 131
                                       ++++sa+ +++ +t+w++  l++++l l+
  gi|336252186|ref|YP_004595293.1|  43 SQANSAQDRIDrTTDWAIT-LMAALLSLV 70 
                                       3345556666645556555.555555443 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0005
                      Trp_oprn_chp  61 avrglgrrvvgvllalagagaavaalslltdpadaaraaaaa 102
                                       a+ + +rrv g+l a++g++ ++  +sl+t +++ a+aa+  
  gi|336252186|ref|YP_004595293.1| 151 ALSRRIRRVYGLLFAVVGIAWIFK-VSLFTPEQQWAEAAELP 191
                                       78899**************99886.67778877777777733 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.7     0.015        33      14      56 ..      61     100 ..      58     107 .. 0.53
   2 ?    5.7   0.2    0.0081        18       2      51 ..     160     213 ..     159     228 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                           DUF4199  14 fllilyllglhqi.lstg.pllgllallllllvpflvylalkkyr 56 
                                       +l +++ll+l  + ++ + ++l l++   l++  +++++ +++yr
  gi|336252186|ref|YP_004595293.1|  61 TL-MAALLSL-VFsSQEMpAFLLLIG---LFVLCIFLFFEVRRYR 100
                                       33.4455555.332333323333333...33334569*****998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0081
                           DUF4199   2 fGlilglvwilifll.ilyllglh.qilstg....pllglla.llllllvpflvyla 51 
                                       +Gl++++v+i++++   l+   ++    +      +  g+ +  +l l+  ++v+l 
  gi|336252186|ref|YP_004595293.1| 160 YGLLFAVVGIAWIFKvSLFTPEQQwA--EAAelpgV-HGYYVaGMLGLFYAAVVVLT 213
                                       8*************644444444322..22223221.22222233333334444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); 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):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 1779.88
//
Query:       gi|336252187|ref|YP_004595294.1|  [L=448]
Description: glycine dehydrogenase [Halopiger xanaduensis SH-6]
Scores for complete 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-98  330.7   0.0    1.5e-98  330.5   0.0    1.0  1  GDC-P            Glycine cleavage system P-protein
    0.00043   19.3   0.0    0.00068   18.7   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.037   12.6   0.0      0.051   12.1   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.5   0.0  2.5e-102   1.5e-98       3     374 ..      12     389 ..      10     429 .. 0.91

  Alignments for each domain:
  == domain 1  score: 330.5 bits;  conditional E-value: 2.5e-102
                                       H-SS-HHHHHHHHHHHT-SSHHHHHHHHS-GGGB--S---------HHHHHHHHHHHHTTB---EE--BTTB----- CS
                             GDC-P   3 higpsekdqkemLetlGlkslddliekavPkeiklkkelkleapksEeellaelekiasknkvvksfiGaGyydtil 79 
                                       + +++++d+  mLe++G++++ +l+  ++P+ +++  e+ ++ + +E+e ++ +++i  +n  +++ +G G y  ++
  gi|336252187|ref|YP_004595294.1|  12 YAPHTDEDRAAMLEAVGAETVAELF--DIPEPVRFDDEFGID-ARTERETRRLVRSILGRNDDLTELLGRGHYGYYV 85 
                                       77999********************..9********999986.579******************************* PP

                                       -HHHHHHTTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SSS--E CS
                             GDC-P  80 PaviqrnilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskkkakk 156
                                       P+ +++ + +++e++t+Yt Yq+E+sqG L+al+++q+l+++ltGl+ian s++D +tA++EA++la r+      +
  gi|336252187|ref|YP_004595294.1|  86 PSLVDH-LADRSEFLTSYTQYQPEVSQGFLQALFEYQSLLVELTGLEIANCSMYDAATALGEAATLADRVRDVTGYR 161
                                       ******.********************************************************************** PP

                                       EEEETT..S-HHHHHHHHHHHGGGT-EEEEE-GGG--S-.........S-EEEEEEEES-TTSB---.-HHHHHHHH CS
                             GDC-P 157 vvvdkk..vhpqtlevlktrakglgieivevdlteekvtd......kekevagvlvqypnteGried.lkelvekak 224
                                       v+v ++  + ++ +++l+ +  g+++ei+  ++++ +v+       + +ev  v    p + G+ie+ l ++ e a 
  gi|336252187|ref|YP_004595294.1| 162 VLVPEAdlLREERRRTLENYVAGTDLEIESYPTADGNVDLealeqtVDEEVVMVYAENPTVRGTIEEgLAAIGELAD 238
                                       **9653337788999***************9977777665888888999****************9989******** PP

                                       HTT-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GGGGGG--S-EEEEEEBTTS-EEE CS
                             GDC-P 225 kkkslvvvaadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkeklkRkiPGRlvGvskDaegkral 301
                                        +++l+++ +d++aL+ll+ P ++gaD+vvG+a  +G+P +yG    g fA++e++ R++PGRlvG s+Da+++ra+
  gi|336252187|ref|YP_004595294.1| 239 ANDALFTLGSDPVALALLERPVDVGADVVVGDASVLGLPTSYGM-GLGLFATREDYLRQVPGRLVGASEDATDRRAF 314
                                       ******************************************85.589***************************** PP

                                       EEE-CCGSHHCCHHHCS-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT...T-EE--SS CS
                             GDC-P 302 rlalqtREqHirRdkAtsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkk..leeelkkkk 374
                                       +l+lqtREqHirR++AtsniCt+qa +A+ +a++a ++G++g+ ++a+r  ++++ la+ l     ++  +++++
  gi|336252187|ref|YP_004595294.1| 315 TLTLQTREQHIRRERATSNICTNQAWVALRTAIHAAALGPTGMVDLANRGVRRAADLAERLDDLtgVKAPVHDRH 389
                                       ***********************************************************9988743333344433 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.1e-07   0.00068     119     340 ..     192     422 ..     180     431 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-07
                                       EEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE.B--HHHHHHHHHHTT-EEEE..E-.TTTTTTS---HHHHT CS
                       Aminotran_5 119 ipldeegeldldelekllnektklvaithvsnvtGt.iqpveeigklakkkgalvlv..Da.aqavghipidvkklg 191
                                       +p +++g++dl++le++++e++ +v ++ + +v Gt  + +++ig+la +++al+ +  D  a a++ +p+dv +  
  gi|336252187|ref|YP_004595294.1| 192 YP-TADGNVDLEALEQTVDEEVVMV-YAENPTVRGTiEEGLAAIGELADANDALFTLgsDPvALALLERPVDVGADV 266
                                       44.599************9887655.7899******44569*************99844542668999***995432 PP

                                       E..SEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STT..SEEEEET.TEEEEHCTTGGGS.SS--HH...HHHH CS
                       Aminotran_5 192 v..DflafsghKllgPtGiGvlyvrkellekleplllgge..mveevsl.eettfaeapskfeaGTpnva...giig 260
                                       v  D  +++    +g  G+G+   r+++l +++  l+g +    ++  +  + +++e+  + e  T n+    ++++
  gi|336252187|ref|YP_004595294.1| 267 VvgDASVLGLPTSYG-MGLGLFATREDYLRQVPGRLVGASedATDRRAFtLTLQTREQHIRRERATSNICtnqAWVA 342
                                       223666666666666.5***************777777541145555554555588999999999***964448*** PP

                                       HHHHHHHH..HCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEET.TCSHHHHHHHHHHTTEE CS
                       Aminotran_5 261 lgaaleyl..eeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfk.gvhaedvatlLdeegIa 334
                                       l++a+       +g+   +++  + a+ l erl++l gv+  +    + r+++  f+ + +  a  +a  L+++g a
  gi|336252187|ref|YP_004595294.1| 343 LRTAIHAAalGPTGMVDLANRGVRRAADLAERLDDLTGVKAPV----HDRHHLREFVARvDQPAGAIAEDLERRGFA 415
                                       ****98764478999999*********************9933....555556555554033346778888888888 PP

                                       EEE.E-T CS
                       Aminotran_5 335 vrs.Ghh 340
                                       v+  G h
  gi|336252187|ref|YP_004595294.1| 416 VHVvGDH 422
                                       8877777 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 ?   12.1   0.0   8.6e-06     0.051     125     194 ..     199     269 ..     132     274 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.6e-06
                                       TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEE.GTTTHTTTS-GGGGT-SEEEE CS
                   Cys_Met_Meta_PP 125 sdleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvD.ntfaspllqrplklgaDivvh 194
                                        dle+le+ ++e++ +vy E pt        +++i +la ++++l  +    +a  ll rp++ gaD+vv 
  gi|336252187|ref|YP_004595294.1| 199 VDLEALEQTVDEEVVMVYAENPTVRGTIEEGLAAIGELADANDALFTLGsDPVALALLERPVDVGADVVVG 269
                                       5789********************99999*************976666514566679************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.82
# Mc/sec: 1648.69
//
Query:       gi|336252188|ref|YP_004595295.1|  [L=518]
Description: class V aminotransferase [Halopiger xanaduensis SH-6]
Scores for 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-10   38.6   0.0    9.4e-10   38.0   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    5.7e-05   22.5   0.0    9.3e-05   21.8   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
    5.8e-05   22.1   0.0     0.0016   17.4   0.0    2.1  2  GDC-P            Glycine cleavage system P-protein
  ------ inclusion threshold ------
       0.21   10.1   0.0       0.35    9.3   0.0    1.2  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 !   38.0   0.0   2.1e-13   9.4e-10      84     207 ..     187     309 ..     172     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.1e-13
                                       C.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE.B--H CS
                       Aminotran_5  84 s.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt.iqpv 158
                                       +   +++e+++ e+ h  n+ + ++     g++v+ +p de+g++dl++le++l+e+t+++++t   n++G    ++
  gi|336252188|ref|YP_004595295.1| 187 NgEGHRNEVIIPESAHGTNF-ASAA---LGGYDVVSLPSDEDGRVDLEALESALSENTAALMLTN-PNTLGLfERDI 258
                                       35667899***********9.4444...56*******************************9985.678899799** PP

                                       HHHHHHHHHTT-EEEEE-TT.TTTTS---HHHHTESEEEEETTT.TTSSTT CS
                       Aminotran_5 159 eeigklakkkgalvlvDaaq.avghipidvkklgvDflafsghK.llgPtG 207
                                       +ei+++++++g l+  D+a  +++  +    ++g D++    hK +  P G
  gi|336252188|ref|YP_004595295.1| 259 AEIAEMVHDVGGLLYYDGANlNALLGRARPGDMGFDVMHYNVHKtFATPHG 309
                                       *******************857888999999*************7777877 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.1e-08   9.3e-05      31     169 ..     143     277 ..     122     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.1e-08
                                       -HHHHHHHHHHHHHTT-SEEEEES.-HHHHHHHHHHHH--TTEEEEEETT........-HHHHSSTTHHHHCC--EE CS
                   Beta_elim_lyase  31 dktvnrLedavaelfgkeaalfvp.qGtaAnsillkillqrgeevivtep........ahihfdetgaiaelagvkl 98 
                                        + ++rL+d++ ++ g++a+   p  G a++ + +++ +  +e    +++        ah+    + a a+l+g  +
  gi|336252188|ref|YP_004595295.1| 143 LELMYRLQDYLGRIGGMDAVTLQPpAGAAGEFVGIRVAAAYHEHNGEGHRneviipesAHGT---NFASAALGGYDV 216
                                       567899************98765438*********887755555555555233332225543...34667789**** PP

                                       EEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase  99 rdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                       + l+++e+G +dle+le+a+ e      ++++++lt+ n    G  +    ++e+a+++++ g  l +DgA
  gi|336252188|ref|YP_004595295.1| 217 VSLPSDEDGRVDLEALESALSE------NTAALMLTNPNTL--G--LFERDIAEIAEMVHDVGGLLYYDGA 277
                                       *********************9......799******9998..5..67889*******************9 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 !   17.4   0.0   3.5e-07    0.0016     106     286 ..     140     330 ..     134     352 .. 0.72
   2 ?    2.6   0.0     0.011        48     330     374 ..     373     417 ..     367     471 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.5e-07
                                       HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SSS......--EEEEETTS-HHHHHHHHHHHG CS
                             GDC-P 106 qGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskkk......akkvvvdkkvhpqtlevlktrak 176
                                       qG+Le +   q  +  + G+d     l   + Aa+E v + ++a+ ++      +++v++ ++ h  + +     a 
  gi|336252188|ref|YP_004595295.1| 140 QGTLELMYRLQDYLGRIGGMDA--VTLQPPAGAAGEFVGIRVAAAYHEhngeghRNEVIIPESAHGTNFA----SAA 210
                                       7888888888888888888875..4577777788886655444332221001113444444444443332....344 PP

                                       GGT-EEEEE-GGG--S-..........S-EEEEEEEES-TTSB--.--HHHHHHHHHTT-EEEE.EE-TTGGGTB-- CS
                             GDC-P 177 glgieivevdlteekvtd.......kekevagvlvqypnteGrie.dlkelvekakkkkslvvv.aadllaLtllkp 244
                                         g ++v  ++ e++  d        ++++a++++  pnt G  e d+ e++e +++   l+    a+l aL   + 
  gi|336252188|ref|YP_004595295.1| 211 LGGYDVVSLPSDEDGRVDlealesaLSENTAALMLTNPNTLGLFErDIAEIAEMVHDVGGLLYYdGANLNALLGRAR 287
                                       45667777777777777777777777899*************98747**********98777652789999999999 PP

                                       HHHHT-SEEEEE.-TTTT---GGG----EEEEE-GGGGGG--S CS
                             GDC-P 245 PgelgaDivvGs.aqrfGvPlgyGGPhagffAvkeklkRkiPG 286
                                       Pg++g D++  +  + f  P g GGP ag + v ++l+  +P 
  gi|336252188|ref|YP_004595295.1| 288 PGDMGFDVMHYNvHKTFATPHGGGGPGAGPVGVVDELAPFLPA 330
                                       ********97661578*************99999999877775 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T-EE--SS CS
                             GDC-P 330 nlaalyavyhGkeglkeiarrihkkteilakelkkkleeelkkkk 374
                                       + a  y+  +G egl + + +   ++++la++++ ++     +++
  gi|336252188|ref|YP_004595295.1| 373 VKAFAYIARLGDEGLADASAKAVLNANYLASQIEYDVPYGPFHHE 417
                                       556779999***********************9887544433333 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 ?    9.3   0.0   7.8e-05      0.35     126     192 ..     228     296 ..     214     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 7.8e-05
                                       SHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTT..S-GGGGT-SEE CS
                   Cys_Met_Meta_PP 126 dleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspll..qrplklgaDiv 192
                                       dle+le+a++ent ++ l  p    l   Di++ia++++++g l+  D + +  ll   rp ++g D+ 
  gi|336252188|ref|YP_004595295.1| 228 DLEALESALSENTAALMLTNPNTLGLFERDIAEIAEMVHDVGGLLYYDGANLNALLgrARPGDMGFDVM 296
                                       7899**************************************999999988887763345667777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3461.99
//
Query:       gi|336252189|ref|YP_004595296.1|  [L=57]
Description: hypothetical protein Halxa_0778 [Halopiger xanaduensis SH-6]
Scores for 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-05   23.6   2.8      0.013   15.9   0.3    2.1  2  zf-H2C2_2        Zinc-finger double domain
    0.00034   20.6   1.3       0.47   10.5   0.2    2.2  2  Rubredoxin       Rubredoxin
    0.00071   19.9   2.2       0.17   12.4   0.1    2.2  2  zf-C2H2          Zinc finger, C2H2 type
    0.00087   19.2   0.7     0.0013   18.7   0.7    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0015   18.7   0.3       0.12   12.6   0.0    2.2  2  zinc_ribbon_9    zinc-ribbon
     0.0027   18.1   0.8     0.0034   17.7   0.8    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.009   15.4   3.0       0.39   10.2   0.5    2.2  2  zf-ribbon_3      zinc-ribbon domain
  ------ inclusion threshold ------
      0.012   16.1   2.2       0.23   11.9   0.2    2.0  2  DUF983           Protein of unknown function (DUF983)
      0.017   15.0   2.4        1.1    9.2   0.3    2.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.02   14.4   1.1       0.15   11.6   0.1    2.1  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.026   13.9   0.2       0.32   10.4   0.0    2.0  2  zf_Rg            Reverse gyrase zinc finger
      0.028   14.3   2.4      0.098   12.5   0.2    2.1  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.029   14.1   3.5       0.94    9.3   0.2    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
      0.032   14.5   0.8       0.69   10.2   0.1    2.1  2  zf-LITAF-like    LITAF-like zinc ribbon domain
      0.037   14.1   2.2        1.7    8.8   0.5    2.2  2  DUF1272          Protein of unknown function (DUF1272)
      0.052   13.3   1.1       0.45   10.2   0.0    2.0  2  Ribosomal_S27e   Ribosomal protein S27
      0.056   13.8   0.2      0.059   13.7   0.2    1.1  1  DUF3268          zinc-finger-containing domain
       0.12   12.3   2.3       0.12   12.3   2.3    2.2  2  DUF1610          Domain of unknown function (DUF1610)
       0.12   12.4   0.4       0.18   11.8   0.4    1.4  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.13   12.9   4.3       0.94   10.2   0.2    2.1  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.15   12.1   2.5         12    5.9   2.5    2.1  1  CpXC             CpXC protein
        0.2   11.7   3.3        6.2    6.9   0.1    2.2  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
       0.36   11.0   4.6        2.7    8.2   0.7    2.1  2  Zn-ribbon_8      Zinc ribbon domain
        0.4   10.5   3.0        4.9    7.0   0.3    2.2  2  zinc_ribbon_5    zinc-ribbon domain
          1    9.3   5.8         16    5.4   2.0    2.7  3  DUF3797          Domain of unknown function (DUF3797)


Domain annotation for each model (and alignments):
>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0044       3.2      15      24 ..       7      18 ..       3      20 .. 0.80
   2 !   15.9   0.3   1.8e-05     0.013       9      25 ..      27      44 ..      24      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0044
                         zf-H2C2_2 15 yeCplCd..kaF 24
                                      +eCp C+  k+F
  gi|336252189|ref|YP_004595296.1|  7 HECPNCGeeKTF 18
                                      9*****966666 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.8e-05
                         zf-H2C2_2  9 Htgekp.yeCplCdkaFk 25
                                      H g k+ ++Cp Cd+ F+
  gi|336252189|ref|YP_004595296.1| 27 HLGTKIkWHCPDCDYGFV 44
                                      9999988**********8 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0014         1      34      45 ..       6      17 ..       2      19 .. 0.84
   2 !   10.5   0.2   0.00066      0.47      34      42 ..      33      41 ..      29      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0014
                                      T-BBTTTB-BGG CS
                        Rubredoxin 34 dWvCPdCgveke 45
                                      d +CP+Cg ek+
  gi|336252189|ref|YP_004595296.1|  6 DHECPNCGEEKT 17
                                      789*****9997 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00066
                                      T-BBTTTB- CS
                        Rubredoxin 34 dWvCPdCgv 42
                                      +W+CPdC+ 
  gi|336252189|ref|YP_004595296.1| 33 KWHCPDCDY 41
                                      6******85 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   0.00024      0.17       1      20 [.       7      28 ..       7      30 .. 0.91
   2 !    7.7   0.2    0.0073       5.3       3      11 ..      36      44 ..      34      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                                      EEETTTT..EEESSHHHHHHHH CS
                           zf-C2H2  1 ykCpdCg..ksFkrksnLkrHi 20
                                      ++Cp Cg  k+F r  + + H+
  gi|336252189|ref|YP_004595296.1|  7 HECPNCGeeKTFYRAASTTLHL 28
                                      78************99999996 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0073
                                      ETTTTEEES CS
                           zf-C2H2  3 CpdCgksFk 11
                                      CpdC++ F 
  gi|336252189|ref|YP_004595296.1| 36 CPDCDYGFV 44
                                      ******996 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 !   18.7   0.7   1.7e-06    0.0013      20      45 ..       8      41 ..       4      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                     Zn_Tnp_IS1595 20 vCPhCgsr.kayrikt.......rglfqCkeCrk 45
                                       CP+Cg + ++yr ++         +++C +C +
  gi|336252189|ref|YP_004595296.1|  8 ECPNCGEEkTFYRAASttlhlgtKIKWHCPDCDY 41
                                      6*******9999999999**************76 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.056        40      24      29 ..       9      14 ..       2      17 .. 0.80
   2 !   12.6   0.0   0.00017      0.12      23      33 ..      35      45 ..      22      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.056
                     zinc_ribbon_9 24 CPhCgg 29
                                      CP+Cg 
  gi|336252189|ref|YP_004595296.1|  9 CPNCGE 14
                                      ****95 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00017
                     zinc_ribbon_9 23 lCPhCgggFVE 33
                                       CP+C+ gFV 
  gi|336252189|ref|YP_004595296.1| 35 HCPDCDYGFVK 45
                                      5********95 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 !   17.7   0.8   4.8e-06    0.0034       5      54 ..       8      57 .]       6      57 .] 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.8e-06
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigq..cvyCadCgastpwfkiaedeaeaekea 54
                                       CP Cg++++  r+ +++ + g+    +C dC +    +ki++++  +++ea
  gi|336252189|ref|YP_004595296.1|  8 ECPNCGEEKTFYRAASTTLHLGTkiKWHCPDCDY--GFVKIDDAVDSSAAEA 57
                                      7****************9998889999*******..6777777777766665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.5   0.00054      0.39       4      10 ..       8      14 ..       7      17 .. 0.76
   2 ?    5.7   0.1     0.014       9.9       4      16 ..      35      48 ..      33      50 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00054
                       zf-ribbon_3  4 rCPnCGa 10
                                      +CPnCG+
  gi|336252189|ref|YP_004595296.1|  8 ECPNCGE 14
                                      6888887 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.014
                       zf-ribbon_3  4 rCPnCGa.plssdd 16
                                      +CP C+   ++ dd
  gi|336252189|ref|YP_004595296.1| 35 HCPDCDYgFVKIDD 48
                                      68888877777776 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00032      0.23       6      26 ..       4      24 ..       2      31 .. 0.85
   2 ?    4.6   0.2     0.062        44       6      24 ..      31      49 ..      29      55 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00032
                            DUF983  6 kvadaCeaCgldlsharaddg 26
                                      ++ ++C++Cg++ +++ra+ +
  gi|336252189|ref|YP_004595296.1|  4 ELDHECPNCGEEKTFYRAAST 24
                                      67899************9876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.062
                            DUF983  6 kvadaCeaCgldlsharad 24
                                      k++ +C+ C+  + +++ +
  gi|336252189|ref|YP_004595296.1| 31 KIKWHCPDCDYGFVKIDDA 49
                                      7888*****8877666554 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 ?    6.2   0.1     0.014       9.7       6      13 ..       8      15 ..       6      24 .. 0.80
   2 ?    9.2   0.3    0.0015       1.1       2      12 ..      31      41 ..      30      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                    Zn_ribbon_SprT  6 rCtgCgre 13
                                       C++Cg+e
  gi|336252189|ref|YP_004595296.1|  8 ECPNCGEE 15
                                      6*****87 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0015
                    Zn_ribbon_SprT  2 kyvYrCtgCgr 12
                                      k +++C++C+ 
  gi|336252189|ref|YP_004595296.1| 31 KIKWHCPDCDY 41
                                      779******93 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00021      0.15       2      17 ..       8      23 ..       7      26 .. 0.74
   2 ?    1.9   0.1      0.23   1.6e+02       3       6 ..      36      39 ..      35      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                                      EETTTTCEECHEETST CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDper 17
                                       CPnCg +++ + +++
  gi|336252189|ref|YP_004595296.1|  8 ECPNCGEEKTFYRAAS 23
                                      6******997766655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.23
                                      ETTT CS
                      TF_Zn_Ribbon  3 CPnC 6 
                                      CP+C
  gi|336252189|ref|YP_004595296.1| 36 CPDC 39
                                      7777 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00045      0.32       8      22 ..       7      21 ..       3      24 .. 0.83
   2 ?    1.6   0.0      0.26   1.9e+02       9      14 ..      35      40 ..      31      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00045
                             zf_Rg  8 klCPNCgGdisdeRl 22
                                      + CPNCg + + +R+
  gi|336252189|ref|YP_004595296.1|  7 HECPNCGEEKTFYRA 21
                                      67*****99888886 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.26
                             zf_Rg  9 lCPNCg 14
                                       CP C+
  gi|336252189|ref|YP_004595296.1| 35 HCPDCD 40
                                      7****6 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 ?   12.5   0.2   0.00014     0.098       1      15 [.       7      21 ..       7      24 .. 0.87
   2 ?    2.1   0.2      0.25   1.8e+02       3      35 ..      36      40 ..      29      44 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                           TFIIS_C  1 akCpkCgsreayffq 15
                                      ++Cp+Cg++++++  
  gi|336252189|ref|YP_004595296.1|  7 HECPNCGEEKTFYRA 21
                                      69*********9975 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.25
                           TFIIS_C  3 CpkCgsreayffqlQtRsaDEpmtvfykCtkCg 35
                                      Cp C                             
  gi|336252189|ref|YP_004595296.1| 36 CPDC----------------------------D 40
                                      5555............................4 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3     0.012       8.9      17      22 ..       9      14 ..       7      18 .. 0.69
   2 ?    9.3   0.2    0.0013      0.94      12      20 ..      31      39 ..      27      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp+Cg+
  gi|336252189|ref|YP_004595296.1|  9 CPNCGE 14
                                      677764 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0013
                      Rubredoxin_2 12 kwfGrCpsC 20
                                      k  ++Cp+C
  gi|336252189|ref|YP_004595296.1| 31 KIKWHCPDC 39
                                      566****** 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 ?   10.2   0.1   0.00097      0.69      54      65 ..       4      15 ..       1      20 [. 0.78
   2 ?    3.4   0.1      0.13        94      55      63 ..      32      40 ..      26      45 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00097
                     zf-LITAF-like 54 dvehyCpnCgal 65
                                      + +h CpnCg+ 
  gi|336252189|ref|YP_004595296.1|  4 ELDHECPNCGEE 15
                                      678******976 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.13
                     zf-LITAF-like 55 vehyCpnCg 63
                                      ++ +Cp C 
  gi|336252189|ref|YP_004595296.1| 32 IKWHCPDCD 40
                                      667788885 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.5    0.0024       1.7      39      50 ..       4      15 ..       1      22 [. 0.84
   2 ?    5.8   0.0      0.02        14      39      52 ..      31      44 ..      15      46 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0024
                           DUF1272 39 vlenvCPncgGe 50
                                       l++ CPncg e
  gi|336252189|ref|YP_004595296.1|  4 ELDHECPNCGEE 15
                                      57999****965 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.02
                           DUF1272 39 vlenvCPncgGelv 52
                                      +++ +CP+c  ++v
  gi|336252189|ref|YP_004595296.1| 31 KIKWHCPDCDYGFV 44
                                      45789****98887 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00063      0.45       7      26 ..       6      25 ..       3      30 .. 0.86
   2 ?    2.3   0.3       0.2   1.4e+02       9      14 ..      35      40 ..      29      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00063
                                      EEE-TTTS-EEEEESS-SS- CS
                    Ribosomal_S27e  7 dvkCpdCenetvvFshaatv 26
                                      d  Cp+C++e++ +  a+t 
  gi|336252189|ref|YP_004595296.1|  6 DHECPNCGEEKTFYRAASTT 25
                                      568*********99999986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.2
                                      E-TTTS CS
                    Ribosomal_S27e  9 kCpdCe 14
                                       CpdC 
  gi|336252189|ref|YP_004595296.1| 35 HCPDCD 40
                                      6****6 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   8.3e-05     0.059       3      38 ..       7      41 ..       5      54 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.3e-05
                           DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkCda 38
                                      + Cp CGe+ ++ +a++    +   k+ + Cp+Cd 
  gi|336252189|ref|YP_004595296.1|  7 HECPNCGEEKTFYRAASTT-LHLGTKIKWHCPDCDY 41
                                      57*****987776666655.46777899******93 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.3   0.00017      0.12      17      24 .]       7      14 ..       6      14 .. 0.89
   2 ?    2.5   0.3       0.2   1.4e+02      18      22 ..      35      39 ..      32      39 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                           DUF1610 17 FpCPNCGE 24
                                      + CPNCGE
  gi|336252189|ref|YP_004595296.1|  7 HECPNCGE 14
                                      77*****9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.2
                           DUF1610 18 pCPNC 22
                                       CP C
  gi|336252189|ref|YP_004595296.1| 35 HCPDC 39
                                      6**** 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 ?   11.8   0.4   0.00026      0.18      68      99 ..       4      46 ..       1      54 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                                      --EEEETTTS-EEECHHHHH...........S-TTTSSS-EEE CS
                              HypA 68 pvkvrCreCgkefeleekal...........rCpkCgsadvei 99
                                      ++  +C +Cg+e +  ++a            +Cp+C+   v+i
  gi|336252189|ref|YP_004595296.1|  4 ELDHECPNCGEEKTFYRAASttlhlgtkikwHCPDCDYGFVKI 46
                                      56779*****998855431235788999999*****9877766 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 ?   10.2   0.2    0.0013      0.94       3      14 ..       7      19 ..       6      28 .. 0.74
   2 ?    5.2   0.4     0.047        34      35      47 .]      26      39 ..      19      39 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0013
                           zf-ISL3  3 hrCPnCgsk.tvv 14
                                      h CPnCg+  t +
  gi|336252189|ref|YP_004595296.1|  7 HECPNCGEEkTFY 19
                                      78*****994444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.047
                           zf-ISL3 35 Lrlr.krRyrCkeC 47
                                      L+l  k +++C++C
  gi|336252189|ref|YP_004595296.1| 26 LHLGtKIKWHCPDC 39
                                      55555778999999 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.5     0.017        12       3      45 ..       9      41 ..       7      48 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.017
                              CpXC  3 CpaCgkefeaeiwtsidadedpelkeklldgslfeatCpkCga 45
                                      Cp+Cg+e ++    s            l  g+  +++Cp+C++
  gi|336252189|ref|YP_004595296.1|  9 CPNCGEEKTFYRAAS----------TTLHLGTKIKWHCPDCDY 41
                                      555555444433222..........223345555666666665 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 ?    5.2   0.9     0.029        21       1       7 [.       8      14 ..       8      15 .. 0.84
   2 ?    6.9   0.1    0.0086       6.2       1       6 [.      35      40 ..      35      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.029
                    DNA_ligase_ZBD  1 hCPvCGs 7 
                                      +CP CG 
  gi|336252189|ref|YP_004595296.1|  8 ECPNCGE 14
                                      5*****7 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0086
                    DNA_ligase_ZBD  1 hCPvCG 6 
                                      hCP C+
  gi|336252189|ref|YP_004595296.1| 35 HCPDCD 40
                                      9****7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.7    0.0038       2.7      28      34 ..       7      14 ..       1      21 [. 0.70
   2 ?    6.5   4.9     0.012       8.8       7      32 ..       8      39 ..       6      55 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0038
                       Zn-ribbon_8 28 a.CPeCgs 34
                                      + CP+Cg+
  gi|336252189|ref|YP_004595296.1|  7 HeCPNCGE 14
                                      44999997 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.012
                       Zn-ribbon_8  7 rCeeCghefevlqsisdap.....lta.CPeC 32
                                      +C +Cg+e +  +++s         +  CP+C
  gi|336252189|ref|YP_004595296.1|  8 ECPNCGEEKTFYRAASTTLhlgtkIKWhCPDC 39
                                      79999988884443332112444444568888 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.037        27       4      10 ..       8      14 ..       5      34 .. 0.58
   2 ?    7.0   0.3    0.0068       4.9       4      12 ..      35      43 ..      32      53 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.037
                     zinc_ribbon_5  4 rCpdCdt 10
                                       Cp+C+ 
  gi|336252189|ref|YP_004595296.1|  8 ECPNCGE 14
                                      6****73 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0068
                     zinc_ribbon_5  4 rCpdCdtkF 12
                                       CpdCd  F
  gi|336252189|ref|YP_004595296.1| 35 HCPDCDYGF 43
                                      6*****888 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.0     0.023        16      15      23 ..       8      16 ..       2      22 .. 0.84
   2 ?    2.4   0.0      0.21   1.5e+02      34      45 ..      14      25 ..      14      28 .. 0.80
   3 ?    4.9   0.1     0.035        25       6      20 ..      25      40 ..      22      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.023
                           DUF3797 15 qCPeCgNnk 23
                                       CP+Cg +k
  gi|336252189|ref|YP_004595296.1|  8 ECPNCGEEK 16
                                      6*****887 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.21
                           DUF3797 34 eddtfyreCkCg 45
                                      e+ tfyr  + +
  gi|336252189|ref|YP_004595296.1| 14 EEKTFYRAASTT 25
                                      689****98766 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.035
                           DUF3797  6 ivkLdek.YvqCPeCg 20
                                      +++L+ k    CP+C 
  gi|336252189|ref|YP_004595296.1| 25 TLHLGTKiKWHCPDCD 40
                                      67788887779****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 418.62
//
Query:       gi|336252190|ref|YP_004595297.1|  [L=177]
Description: ATP/cobalamin adenosyltransferase [Halopiger xanaduensis SH-6]
Scores for 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  192.1   0.0    8.1e-57  191.9   0.0    1.0  1  Cob_adeno_trans  Cobalamin adenosyltransferase
  ------ inclusion threshold ------
       0.19   12.4   7.4       0.57   10.9   7.3    1.8  1  ABATE            Putative stress-induced transcription regula


Domain annotation for each model (and alignments):
>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.9   0.0     9e-61   8.1e-57       1     164 []       3     164 ..       3     164 .. 0.97

  Alignments for each domain:
  == domain 1  score: 191.9 bits;  conditional E-value: 9e-61
                                       XXXXXXXXXXXXXXXX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BT CS
                   Cob_adeno_trans   1 iyTrtGDkGtTslvggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekk 77 
                                       iyT +GD+G+T+l +++rvsK++pr+eayGtvDeln+++g +r   ++ +++++++L+ +qn+L+ ++a++a+p+ +
  gi|336252190|ref|YP_004595297.1|   3 IYTGRGDDGKTDLRDMTRVSKSSPRIEAYGTVDELNALVGTIR---PTGHDDIDDRLQTVQNHLHVVQADFANPDPD 76 
                                       9******************************************...556889**********************999 PP

                                       CCG-S--HHHHHHHHHHHHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS..HHHHHHHHHHH CS
                   Cob_adeno_trans  78 kekkkiteeeveelekeideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee.veeevlkylNRL 153
                                       +++ +i++++ve++e++ide+++el+pl+sf+lp+gs + a+lh+aRtvcRraER++v+la +e ++e++++ylNRL
  gi|336252190|ref|YP_004595297.1|  77 EDDPAIRADHVETVEDWIDEYDEELEPLTSFVLPTGSDSGARLHHARTVCRRAERRAVDLATAEeINEQAVQYLNRL 153
                                       9999********************************************************9977899********** PP

                                       HHHHHHHHHHH CS
                   Cob_adeno_trans 154 SDlLfvlarvv 164
                                       SD Lf+ arvv
  gi|336252190|ref|YP_004595297.1| 154 SDGLFTFARVV 164
                                       ********985 PP

>> ABATE  Putative stress-induced transcription regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   7.3   6.4e-05      0.57       6     106 ..      69     174 ..      35     177 .] 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.4e-05
                                       HHHHH----HHHHHHHTTT-HHHHHH--TTHHHHHH......................................... CS
                             ABATE   6 dlvNTrargggrraDlLttpadLaaWleaagllpagtaaagada................................e 50 
                                       d++N                              ++ ++++a +                                +
  gi|336252190|ref|YP_004595297.1|  69 DFANP-----------------------------DPDEDDPAIRadhvetvedwideydeelepltsfvlptgsdsG 116
                                       44444.............................33333333334444444444444444444444444445***84 PP

                                       .HHHHHHHHHHHHHHTHHHH............HHHHHHHHHS----EEEE-TTS-E... CS
                             ABATE  51 lararaLRealrallaaaaag...dpppaaalaalnallaaappaprLvrhddgpvdra 106
                                        ar+++ R++ r+  ++a++    ++  ++a++ ln+l +   + +r v+  dg++++a
  gi|336252190|ref|YP_004595297.1| 117 -ARLHHARTVCRRAERRAVDLataEEINEQAVQYLNRLSDGLFTFARVVNKRDGEPEEA 174
                                       .6666666666666664442222278999*********999999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1252.00
//
Query:       gi|336252191|ref|YP_004595298.1|  [L=102]
Description: hypothetical protein Halxa_0780 [Halopiger xanaduensis SH-6]
Scores for 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   22.2   0.9    0.00068   19.6   0.9    2.0  1  HTH_20    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 !   19.6   0.9   3.8e-08   0.00068       2      44 ..       9      51 ..       8      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.8e-08
                                      HHHHHHS-HHHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHH CS
                            HTH_20  2 qiaeALahPvRrrilraL.araegltaselaerldlskntlsyH 44
                                       ++eALa+  Rrr++++L  r++ + +++ +++l + ++++s++
  gi|336252191|ref|YP_004595298.1|  9 LLFEALADGHRRRLCAYLaDRDGTVEFADACATL-CERSQCSRR 51
                                      689***************9889999999999999.777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 811.83
//
Query:       gi|336252192|ref|YP_004595299.1|  [L=213]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-17   60.5   0.0    1.7e-16   59.7   0.0    1.4  1  HTH_10         HTH DNA binding domain
    5.1e-12   45.9   3.1    8.1e-12   45.3   3.1    1.3  1  BAT            GAF and HTH_10 associated domain
    8.7e-05   22.0   0.3    0.00017   21.0   0.3    1.5  1  Sigma70_r4     Sigma-70, region 4
    0.00029   20.3   0.5    0.00087   18.8   0.2    1.9  2  HTH_24         Winged helix-turn-helix DNA-binding
    0.00095   19.0   0.0     0.0026   17.6   0.0    1.7  1  MarR_2         MarR family
     0.0026   17.5   0.9     0.0026   17.5   0.9    2.1  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   14.8   0.2       0.15   11.8   0.2    2.4  1  Sigma70_r4_2   Sigma-70, region 4
      0.017   15.1   0.0       0.13   12.3   0.0    2.3  2  HTH_Crp_2      Crp-like helix-turn-helix domain
       0.11   12.6   0.3       0.46   10.6   0.1    2.2  3  HTH_3          Helix-turn-helix


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 !   59.7   0.0   8.8e-20   1.7e-16       1      53 []     156     208 ..     156     208 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 8.8e-20
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       L++ q+ +l  Aye+GYF+ PRr++ +eL  elGIs++++se+Lr+a s l+e
  gi|336252192|ref|YP_004595299.1| 156 LSPSQRDALVSAYELGYFEIPRRISQEELGVELGISAQSVSERLRRAVSSLVE 208
                                       7889*********************************************9985 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   3.1   4.1e-15   8.1e-12      14     127 ..      10     128 ..       3     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 4.1e-15
                               BAT  14 ddvlv.alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtlleltvsgpsl 89 
                                       ++vl+ +l+a  d r+++e    + dg+v++ff+++g+dp+++++++e+ ++v+++r ++++d+++l+++ ++ +  
  gi|336252192|ref|YP_004595299.1|  10 AAVLQrTLSAFPDIRLTHEAQYLTADGTVRLFFRMAGVDPATFESTLESDPTVTNARRIDRTDSTALYRVDFTVEGR 86 
                                       445554899999*****************************************************998888764444 PP

                               BAT  90 as....tlaehGgtvrsaeaedgrarlvvevPpgadvRsvve 127
                                       a     + a  ++++ +a+ +++++r++++vP+++ + +  e
  gi|336252192|ref|YP_004595299.1|  87 AKstfpRWAIDDVVLLEATGTPDGWRIRMRVPDRETLLEYRE 128
                                       44445588888**********************987766555 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.3   8.8e-08   0.00017       5      48 ..     156     206 ..     155     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 8.8e-08
                                       S-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   5 Lpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       L++ +r+ l+  +        +  ++eE+g +lgiS   V+ +++rA+  L
  gi|336252192|ref|YP_004595299.1| 156 LSPSQRDALVSAYelgyfeiPRRISQEELGVELGISAQSVSERLRRAVSSL 206
                                       899999999999999999988999***********************9876 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 ?   -1.7   0.0       1.1   2.2e+03      24      38 ..      65      79 ..      55      80 .. 0.67
   2 !   18.8   0.2   4.4e-07   0.00087      17      42 ..     178     203 ..     176     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                            HTH_24 24 AerlglSpstvnrrl 38
                                      A+r++ + st ++r+
  gi|336252192|ref|YP_004595299.1| 65 ARRIDRTDSTALYRV 79
                                      566666667777766 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 4.4e-07
                            HTH_24  17 risqreLAerlglSpstvnrrlkrLe 42 
                                       risq eL  +lg+S + v++rl+r +
  gi|336252192|ref|YP_004595299.1| 178 RISQEELGVELGISAQSVSERLRRAV 203
                                       7**********************976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.3e-06    0.0026      19      47 ..     176     204 ..     154     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                                       TSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2  19 grdltvgelarrlglsksavsrilkrLva 47 
                                       +r++++ el  +lg+s ++vs +l+r+v+
  gi|336252192|ref|YP_004595299.1| 176 PRRISQEELGVELGISAQSVSERLRRAVS 204
                                       3389**********************997 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 ?   -1.9   0.1       1.5     3e+03      24      38 ..      65      79 ..      63      80 .. 0.66
   2 !   17.5   0.9   1.3e-06    0.0026      17      40 ..     178     201 ..     177     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                     HTH_AsnC-type 24 AervGlSestvlrRv 38
                                      A+r+  + st+l Rv
  gi|336252192|ref|YP_004595299.1| 65 ARRIDRTDSTALYRV 79
                                      566666667777776 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.3e-06
                     HTH_AsnC-type  17 RisyaeLAervGlSestvlrRvrr 40 
                                       Ris +eL+ ++G+S++ v +R+rr
  gi|336252192|ref|YP_004595299.1| 178 RISQEELGVELGISAQSVSERLRR 201
                                       9**********************9 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 ?   11.8   0.2   7.4e-05      0.15      11      52 ..     156     204 ..     154     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.4e-05
                                       S-HHHHHHHHHHHTS--.......-HHHHHHHHT--HHHHHHHHHHHHH CS
                      Sigma70_r4_2  11 Lperqreifllrylegl.......sykEIAellgisegtVksrlsRArk 52 
                                       L++ qr +++  y+ g+       s++E   +lgis ++V  rl+RA  
  gi|336252192|ref|YP_004595299.1| 156 LSPSQRDALVSAYELGYfeiprriSQEELGVELGISAQSVSERLRRAVS 204
                                       77777777777777776666666699*********************76 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 ?   -0.5   0.0       0.6   1.2e+03      55      67 ..     114     125 ..     102     126 .. 0.78
   2 ?   12.3   0.0   6.3e-05      0.13      16      44 ..     171     201 ..     151     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.6
                                       EEEEES-HHHHHH CS
                         HTH_Crp_2  55 rririldleaLra 67 
                                       r +r++d+e L +
  gi|336252192|ref|YP_004595299.1| 114 R-MRVPDRETLLE 125
                                       4.99*****9977 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6.3e-05
                                       C..EEEEEHHHHHHHHHTTSSHHHHHHHHHH CS
                         HTH_Crp_2  16 g..eielpltqeelAsmlGltretvsrilse 44 
                                       g  ei  +++qeel+  lG++ ++vs  l++
  gi|336252192|ref|YP_004595299.1| 171 GyfEIPRRISQEELGVELGISAQSVSERLRR 201
                                       23567779******************98875 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.6   1.1e+04      34      44 ..      58      68 ..      57      70 .. 0.79
   2 ?   -2.4   0.0       2.6   5.2e+03      26      36 ..     165     175 ..     164     178 .. 0.83
   3 ?   10.6   0.1   0.00023      0.46       9      28 ..     178     197 ..     173     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.6
                                      SCSBHHHHHHH CS
                             HTH_3 34 rnPsletlkkl 44
                                      + P+++++ ++
  gi|336252192|ref|YP_004595299.1| 58 SDPTVTNARRI 68
                                      78999999887 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                                       HHHHHTTSSCS CS
                             HTH_3  26 isriEnGernP 36 
                                       +s++E G+ ++
  gi|336252192|ref|YP_004595299.1| 165 VSAYELGYFEI 175
                                       799**998765 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00023
                                       THHHHHHHHHHTSSHHHHHH CS
                             HTH_3   9 glsqeeLAeklGvsrstisr 28 
                                        +sqeeL  +lG+s +++s 
  gi|336252192|ref|YP_004595299.1| 178 RISQEELGVELGISAQSVSE 197
                                       59****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1768.51
//
Query:       gi|336252193|ref|YP_004595300.1|  [L=91]
Description: hypothetical protein Halxa_0782 [Halopiger xanaduensis SH-6]
Scores for 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   15.7   2.4      0.047   13.6   1.7    1.9  2  Apolipoprotein   Apolipoprotein A1/A4/E domain
       0.15   12.6   2.9       0.42   11.2   0.7    2.0  2  DUF883           Bacterial protein of unknown function (DUF88
       0.16   12.0   2.0       0.26   11.3   1.5    1.5  1  Exotox-A_target  Exotoxin A, targeting
       0.35   11.0   3.8       0.67   10.1   0.2    2.1  2  DUF1490          Protein of unknown function (DUF1490)


Domain annotation for each model (and alignments):
>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.015        66     115     131 ..      23      39 ..       8      44 .. 0.59
   2 ?   13.6   1.7     1e-05     0.047      73     129 ..      25      86 ..      21      90 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.015
                                       HHHHHCHHHHHHHHHHH CS
                    Apolipoprotein 115 lkarlapyveelrqkla 131
                                       + ++lap ++++r++l+
  gi|336252193|ref|YP_004595300.1|  23 IAETLAPVTDRIRDRLG 39 
                                       34444444444444443 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1e-05
                                       HHCCHHHHHHHHHHHH.....CHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHH CS
                    Apolipoprotein  73 qrlapyteelrerlaa.....daeelqeqlavyaeelrerlerhvealkarlapyveelrqk 129
                                       ++lap t+++r+rl +     + e   ++l+++ ee+ +++++++++ ++r+++y+ e+ + 
  gi|336252193|ref|YP_004595300.1|  25 ETLAPVTDRIRDRLGRsepepEPESELDRLETVREEVASQAREAIGTARERVTAYRGEASAT 86 
                                       55666666666666552111124555578888888888888888888888888888887765 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 ?    2.0   0.1     0.072   3.2e+02      38      71 ..       3      36 ..       1      41 [. 0.66
   2 ?   11.2   0.7   9.5e-05      0.42       8      45 ..      48      85 ..      41      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.072
                            DUF883 38 erlerarerlrdaeeavaerakeaaeaaddyVre 71
                                      ++++++r  l++a+e+++  + e  + + d +r+
  gi|336252193|ref|YP_004595300.1|  3 KHFHDSRYYLTRAAEHARLGIAETLAPVTDRIRD 36
                                      5667777777777777777666666666666655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.5e-05
                            DUF883  8 eslladleellkeaadeageeaeelRerleerlerare 45
                                      es l+ le + +e a++a+e + ++Rer++++  +a +
  gi|336252193|ref|YP_004595300.1| 48 ESELDRLETVREEVASQAREAIGTARERVTAYRGEASA 85
                                      5567889999999999***********99999887765 PP

>> Exotox-A_target  Exotoxin A, targeting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.5   5.8e-05      0.26      61     116 ..      30      88 ..      18      90 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.8e-05
                                       HHHHHHS.TTTT.......HHHH..HHHHHS.HHHHHHHHHHHHHHHHHHHCC-TT--H CS
                   Exotox-A_target  61 vddllasrpvsGaqdpealadlG..eavret.peqarealaeaearleayvangaGade 116
                                       v d +  r +    +pe  ++l   e+vre+   qarea+  a  r+ ay+ + + +de
  gi|336252193|ref|YP_004595300.1|  30 VTDRIRDRLGRSEPEPEPESELDrlETVREEvASQAREAIGTARERVTAYRGEASATDE 88 
                                       5556666655555555554444322788875278*****************99887776 PP

>> DUF1490  Protein of unknown function (DUF1490)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00015      0.67      56      77 ..      14      35 ..       8      50 .. 0.78
   2 ?    2.1   0.9     0.045     2e+02      61      79 ..      52      72 ..      40      80 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                           DUF1490 56 eaaEsarLkvaDvvaeAreriG 77
                                      +aaE+arL +a+ +a   +ri 
  gi|336252193|ref|YP_004595300.1| 14 RAAEHARLGIAETLAPVTDRIR 35
                                      68***********998877763 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.045
                           DUF1490 61 arLkva..DvvaeAreriGee 79
                                       rL++   +v ++Are iG  
  gi|336252193|ref|YP_004595300.1| 52 DRLETVreEVASQAREAIGTA 72
                                      555543226888999999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 792.93
//
Query:       gi|336252194|ref|YP_004595301.1|  [L=277]
Description: hypothetical protein Halxa_0783 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0082   16.2   8.5       0.17   11.9   1.5    2.3  2  Sensor    Putative sensor


Domain annotation for each model (and alignments):
>> Sensor  Putative sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   1.5   9.5e-06      0.17      72     146 ..      58     129 ..      33     143 .. 0.63
   2 !    8.3   0.8   0.00012       2.2       4      39 ..     176     210 ..     174     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.5e-06
                            Sensor  72 pgllarlrallrdpatwrdllylllhfplglvlfvvavvllalalalltaPlwtlpeallvavlGlllllvllwv 146
                                       +  ++ +r++l++  t+r +   l+ ++ ++   +va++++alal++l +P++  ++ +++av+ l+   ++   
  gi|336252194|ref|YP_004595301.1|  58 QEYITSIRSRLHSSPTYRGVDDRLVAGVGAM---IVAIAVVALALTALRLPAAEGMATIGLAVATLAGGSAAELA 129
                                       6678889999999999999988888888877...88888888888888888864334444444444444333333 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00012
                            Sensor   4 lglplgvaafvllvtglslglgllvllvGlplLala 39 
                                        g +l++++f++l++++   +gllvl+ G   Lala
  gi|336252194|ref|YP_004595301.1| 176 GGGLLATVSFLWLLAAIGPLAGLLVLVAGGG-LALA 210
                                       67789********************999977.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1989.66
//
Query:       gi|336252195|ref|YP_004595302.1|  [L=36]
Description: hypothetical protein Halxa_0784 [Halopiger xanaduensis SH-6]
Scores for 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:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 278.61
//
Query:       gi|336252196|ref|YP_004595303.1|  [L=46]
Description: hypothetical protein Halxa_0785 [Halopiger xanaduensis SH-6]
Scores for 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:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 360.99
//
Query:       gi|336252197|ref|YP_004595304.1|  [L=136]
Description: hypothetical protein Halxa_0786 [Halopiger xanaduensis SH-6]
Scores for 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:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 925.83
//
Query:       gi|336252198|ref|YP_004595305.1|  [L=197]
Description: ribonuclease H [Halopiger xanaduensis SH-6]
Scores for complete 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-26   92.6   0.0    2.1e-26   92.1   0.0    1.2  1  RVT_3        Reverse transcriptase-like
    2.5e-11   43.9   0.0    7.5e-11   42.4   0.0    1.8  1  RNase_H      RNase H
  ------ inclusion threshold ------
      0.074   13.4   0.0       0.13   12.6   0.0    1.4  1  Radical_SAM  Radical SAM superfamily


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 !   92.1   0.0   3.6e-30   2.1e-26       2     124 .]      73     193 ..      72     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 3.6e-30
                             RVT_3   2 fdgafkkksgaggagvvirdsnGevllagaeklqgkasveeAElqALlrGLqlalklgirrlvvegDsktvvqllng 78 
                                       fdg  + + g +g+g+vi++ +G v  ag++   g+a++ +AE++AL+ +L++a ++g+ +++v gDs+ +v++++g
  gi|336252198|ref|YP_004595305.1|  73 FDGGSRGNPGPAGIGWVIVTGDGIVAEAGERI--GRATNNQAEYEALIAALEAARDYGFDEVHVRGDSELIVKQVRG 147
                                       7999999****************999999966..999**************************************** PP

                             RVT_3  79 rekvksselanlldeirkllksfesvsvehipReqNrvAdalAkra 124
                                       + + +++el+     + +ll sf++ ++eh+pRe N  Ad lA++a
  gi|336252198|ref|YP_004595305.1| 148 EYDTNNPELRERRVTVHELLGSFDEWTLEHVPREVNDRADGLANEA 193
                                       *******************************************986 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   1.2e-14   7.5e-11       5      79 ..      70     147 ..      67     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.2e-14
                                       EEEEEEEEECTTTCEEEEEEE.CTT...EEEEEEECCCCHHHHHHHHHHHHHHHTT.SC..SEEEEEES-HHHHHHH CS
                           RNase_H   5 vvYtDGsclgnpgeggagavl.ykeg.arnisapleeaqtnnraELsAvieaLkalksd..ekvniytDSkYvvkgi 77 
                                        vY DG ++gnpg++g+g v+  ++g   +  +++ ++ tnn+aE +A+i+aL+a++     +v+++ DS+ +vk +
  gi|336252198|ref|YP_004595305.1|  70 HVYFDGGSRGNPGPAGIGWVIvTGDGiVAEAGERI-GRATNNQAEYEALIAALEAARDYgfDEVHVRGDSELIVKQV 145
                                       69*****************6636664222444444.7*****************64433689*********999955 PP

                                       HC CS
                           RNase_H  78 tq 79 
                                         
  gi|336252198|ref|YP_004595305.1| 146 RG 147
                                       43 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.3e-05      0.13      94     145 ..      58     134 ..      38     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                                       HHHHHHTT-SEEEEEEBSSSHH.......................HHHHHHTCTSHHHHHHHHHHHHHHTTSET..E CS
                                       xxxxxxxxxxxxxxxxxxxxxx.......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                       Radical_SAM  94 lerllelgvdrvslgleaadde.......................kvlklmnrghtfeevlealeklreagikr..v 145
                                       +e++l+ +  r ++  + ++                         ++ + +n + ++e++++ale++r++g+++  v
  gi|336252198|ref|YP_004595305.1|  58 IEAILREEGGRAHVYFDGGSRGnpgpagigwvivtgdgivaeageRIGRATNNQAEYEALIAALEAARDYGFDEvhV 134
                                       5555555556666666666666666666666666666666667778**************************98440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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 0.20s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1572.40
//
Query:       gi|336252199|ref|YP_004595306.1|  [L=320]
Description: transcription initiation factor IIB [Halopiger xanaduensis SH-6]
Scores for 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-47  156.9   2.9    8.4e-26   89.8   0.2    2.3  2  TFIIB            Transcription factor TFIIB repeat
    4.3e-19   67.7   3.4    8.6e-19   66.8   3.4    1.5  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0036   17.0   0.5     0.0082   15.8   0.5    1.6  1  A2L_zn_ribbon    A2L zinc ribbon domain
  ------ inclusion threshold ------
      0.011   16.1   0.1       0.52   10.7   0.1    2.4  2  HARE-HTH         HB1, ASXL, restriction endonuclease HTH doma
      0.039   13.9   2.1      0.084   12.8   2.1    1.5  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.058   13.5   0.0       0.56   10.3   0.0    2.1  2  Cyclin_C         Cyclin, C-terminal domain
      0.076   12.5   2.9       0.37   10.3   0.1    3.4  4  Sigma70_r4       Sigma-70, region 4
      0.078   13.0   0.0        1.7    8.6   0.0    2.3  2  RB_B             Retinoblastoma-associated protein B domain
      0.079   13.0   0.1       0.18   11.8   0.1    1.6  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.095   13.1   1.3       0.17   12.3   0.4    1.9  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.096   12.5   0.8        0.7    9.8   0.1    2.8  3  HTH_23           Homeodomain-like domain
       0.12   12.9   0.0       0.29   11.7   0.0    1.8  1  RPA_interact_C   Replication protein A interacting C-terminal
       0.87    9.8   3.4        6.6    6.9   0.4    2.5  2  Zn-ribbon_8      Zinc ribbon domain


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 !   67.6   0.2   5.3e-22   7.3e-19       1      71 []     141     211 ..     141     211 .. 0.98
   2 !   89.8   0.2   6.1e-29   8.4e-26       1      71 []     235     305 ..     235     305 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 5.3e-22
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i r+a+al+ p  V++ A  ++++al+e+++ Grs +g+a ++ly Acrke+  r+++eis+v++V+ k+i
  gi|336252199|ref|YP_004595306.1| 141 IDRMASALGVPRSVREVASVIYRRALKEDLIRGRSIEGVATSALYAACRKEGIPRSLEEISEVSRVERKEI 211
                                       789****************************************************************9997 PP

  == domain 2  score: 89.8 bits;  conditional E-value: 6.1e-29
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rf+++leL+e+V+ +A+e++++++ee++l+G+sp+g+aAA++y A++++++k+tq+e+++v+qV+e+ti
  gi|336252199|ref|YP_004595306.1| 235 VPRFCSELELSEEVQTKANEIIEKTAEEGLLSGKSPTGYAAAAIYAASLLCNEKKTQREVADVAQVTEVTI 305
                                       689******************************************************************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 !   66.8   3.4   6.2e-22   8.6e-19       2      43 .]      25      66 ..      24      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 6.2e-22
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                       CP+C s+nlv D +rgel+C+dCGlV+e++ id+gpewr+f
  gi|336252199|ref|YP_004595306.1| 25 ACPECESDNLVKDSDRGELICEDCGLVVEEEKIDPGPEWRAF 66
                                      5***************************************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 !   15.8   0.5   5.9e-06    0.0082       6      30 ..      26      51 ..      23      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.9e-06
                     A2L_zn_ribbon  6 CsvCggngiln.seqgylvCieCgas 30
                                      C  C +++++  s++g+l+C +Cg++
  gi|336252199|ref|YP_004595306.1| 26 CPECESDNLVKdSDRGELICEDCGLV 51
                                      888*********************86 PP

>> HARE-HTH  HB1, ASXL, restriction endonuclease HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.11   1.6e+02      19      53 ..     153     189 ..     146     203 .. 0.78
   2 ?   10.7   0.1   0.00038      0.52      19      51 ..     251     281 ..     242     291 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.11
                                       EHHHHHHHHHHHTTS-....GGHHGCHHH.HHHHHHH CS
                          HARE-HTH  19 tvkeIwekiqekgliklt..gktpeatlaaqlytdik 53 
                                       +v+e++ +i ++ l++    g++ e    ++ly+ ++
  gi|336252199|ref|YP_004595306.1| 153 SVREVASVIYRRALKEDLirGRSIEGVATSALYAACR 189
                                       56777777777777766666*************9998 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00038
                                       EHHHHHHHHHHHTTS-..GGHHGCHHH.HHHHH CS
                          HARE-HTH  19 tvkeIwekiqekglikltgktpeatlaaqlytd 51 
                                       +++eI ek  e+gl++  gk+p    aa++y+ 
  gi|336252199|ref|YP_004595306.1| 251 KANEIIEKTAEEGLLS--GKSPTGYAAAAIYAA 281
                                       689*************..***********9975 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.1   6.1e-05     0.084       4      26 ..      25      49 ..      24      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                    PhnA_Zn_Ribbon  4 kCplCaSeytY..edgallvCpeCa 26
                                      +Cp+C S++     d+  l+C++C+
  gi|336252199|ref|YP_004595306.1| 25 ACPECESDNLVkdSDRGELICEDCG 49
                                      5*******877999999*******7 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.44   6.1e+02      47      86 ..     179     218 ..     177     227 .. 0.78
   2 ?   10.3   0.0   0.00041      0.56       4      86 ..     232     312 ..     229     318 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.44
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcveli 86 
                                       +A++al++a++  + p   e++ ++++++ +++   ++ i
  gi|336252199|ref|YP_004595306.1| 179 VATSALYAACRKEGIPRSLEEISEVSRVERKEIGRTYRYI 218
                                       799******9997777777888888877777777666655 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00041
                                       HHHHHHH.HCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHH CS
                          Cyclin_C   4 lsFlrrf.lkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgyskedl 79 
                                         ++ rf +    + ++ e++t a+ ++e t+ +  + + +p   Aaaa+++a+   n+++ ++++  + ++++  +
  gi|336252199|ref|YP_004595306.1| 232 KKYVPRFcSEL--ELSE-EVQTKANEIIEKTAEEGLLSGKSPTGYAAAAIYAASLLCNEKKTQREVADVAQVTEVTI 305
                                       56666775555..4456.9999999999999999999999******************************9999999 PP

                                       HHHHHHH CS
                          Cyclin_C  80 kpcveli 86 
                                       ++ ++  
  gi|336252199|ref|YP_004595306.1| 306 RNRYQEQ 312
                                       8877765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.7   2.3e+03      34      46 ..     155     167 ..     145     168 .. 0.64
   2 ?   -0.5   0.0      0.68   9.4e+02      20      29 ..     194     203 ..     187     211 .. 0.80
   3 ?   -1.4   0.0       1.3   1.8e+03      18      32 ..     210     224 ..     206     224 .. 0.74
   4 ?   10.3   0.1   0.00027      0.37      18      42 ..     286     310 ..     277     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHH CS
                        Sigma70_r4  34 rerVrqiekrAlr 46 
                                       re ++ i +rAl+
  gi|336252199|ref|YP_004595306.1| 155 REVASVIYRRALK 167
                                       4556777777776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.68
                                       T--HHHHHHH CS
                        Sigma70_r4  20 glTleEIger 29 
                                       +++leEI+e+
  gi|336252199|ref|YP_004595306.1| 194 PRSLEEISEV 203
                                       7899***986 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.3
                                       TTT--HHHHHHHHTS CS
                        Sigma70_r4  18 geglTleEIgerlgi 32 
                                       + g+T+  I+++lg+
  gi|336252199|ref|YP_004595306.1| 210 EIGRTYRYISQELGL 224
                                       557888889999885 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00027
                                       TTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiek 42 
                                        e+ T+ E++++ ++++ ++r +  
  gi|336252199|ref|YP_004595306.1| 286 NEKKTQREVADVAQVTEVTIRNRYQ 310
                                       5899*****************9976 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 ?    8.6   0.0    0.0013       1.7      11      96 ..     135     218 ..     131     225 .. 0.84
   2 ?    1.8   0.0      0.16   2.3e+02      19      43 ..     237     261 ..     232     312 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0013
                              RB_B  11 klaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpq 87 
                                       + a + + ++ + L + +++re +  + +++l  +++l++ R ++ +  +a+Y+ ++ +   +s++ei +  r + +
  gi|336252199|ref|YP_004595306.1| 135 QFALSEIDRMASALGVPRSVREVASVIYRRAL--KEDLIRGRSIEGVATSALYAACRKEGIPRSLEEISEVSRVERK 209
                                       66777888888888888888777776666666..568********************************99999999 PP

                              RB_B  88 asskvyrsv 96 
                                       +  ++yr +
  gi|336252199|ref|YP_004595306.1| 210 EIGRTYRYI 218
                                       998888876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.16
                              RB_B  19 dLcerLklsselrekiwtlfehvlv 43 
                                       + c++L+ls+e+++k+ +++e++  
  gi|336252199|ref|YP_004595306.1| 237 RFCSELELSEEVQTKANEIIEKTAE 261
                                       6799**********99999998753 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 ?   11.8   0.1   0.00013      0.18      19      44 ..      24      49 ..      19      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCr 44
                                      + CP C+s+ + + ++rg + C++C+
  gi|336252199|ref|YP_004595306.1| 24 RACPECESDNLVKDSDRGELICEDCG 49
                                      55***********************7 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   0.4   0.00012      0.17       4      37 ..      24      59 ..      21      77 .. 0.74
   2 ?   -2.1   0.0       3.9   5.3e+03      17      36 ..     247     287 ..     238     306 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCga........s 37
                                        CP C +++ ++ s r+        +C+dCg          
  gi|336252199|ref|YP_004595306.1| 24 RACPECESDNLVKDSDRGE------LICEDCGLvveeekidP 59
                                      68*************9995......8******9554444441 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.9
                   Lar_restr_allev  17 rsqrvvaeigq...................cvyCad..Cga 36 
                                       + q +++ei +                    +y a   C+ 
  gi|336252199|ref|YP_004595306.1| 247 EVQTKANEIIEktaeegllsgksptgyaaaAIYAASllCNE 287
                                       44444444443444444444444444444444444444554 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       8.3   1.1e+04      24      32 ..     145     153 ..     145     153 .. 0.84
   2 ?   -1.3   0.0       1.5     2e+03      16      28 ..     210     223 ..     204     227 .. 0.70
   3 ?    9.8   0.1   0.00051       0.7      12      47 ..     283     314 ..     275     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.3
                            HTH_23  24 AreLgvsrr 32 
                                       A +Lgv+r+
  gi|336252199|ref|YP_004595306.1| 145 ASALGVPRS 153
                                       679***997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                            HTH_23  16 e.GlsvreIAreLg 28 
                                       e G ++r I++eLg
  gi|336252199|ref|YP_004595306.1| 210 EiGRTYRYISQELG 223
                                       35777777888887 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00051
                            HTH_23  12 lllaeGlsvreIAreLgvsrrTvyrwlkryreeGle 47 
                                       ll+ e++++re+A+   v++ T++   +ry +e++e
  gi|336252199|ref|YP_004595306.1| 283 LLCNEKKTQREVADVAQVTEVTIR---NRY-QEQIE 314
                                       56667******************9...667.56665 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 ?   11.7   0.0   0.00021      0.29       2      27 ..      26      54 ..      25     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                    RPA_interact_C  2 CPvCkkrklkets..evifCe.Cglrlet 27
                                      CP C++++l ++s    ++Ce Cgl +e 
  gi|336252199|ref|YP_004595306.1| 26 CPECESDNLVKDSdrGELICEdCGLVVEE 54
                                      *********99664567*******98887 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   0.4    0.0048       6.6      26      38 ..      22      36 ..       9      38 .. 0.75
   2 ?    2.7   0.2       0.1   1.4e+02       7      17 ..      44      54 ..      42      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0048
                       Zn-ribbon_8 26 lta.CPeCgs.evrr 38
                                       +  CPeC s ++ +
  gi|336252199|ref|YP_004595306.1| 22 GVRaCPECESdNLVK 36
                                      4445******99877 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.1
                       Zn-ribbon_8  7 rCeeCghefev 17
                                       Ce+Cg + e+
  gi|336252199|ref|YP_004595306.1| 44 ICEDCGLVVEE 54
                                      69999988885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2553.51
//
Query:       gi|336252200|ref|YP_004595307.1|  [L=215]
Description: PyrE-like protein [Halopiger xanaduensis SH-6]
Scores for 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-15   56.1   0.0    5.3e-15   55.3   0.0    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00014   21.5   0.0     0.0023   17.6   0.0    2.2  2  HTH_23        Homeodomain-like domain
     0.0026   17.8   0.0     0.0056   16.7   0.0    1.5  1  HTH_7         Helix-turn-helix domain of resolvase
  ------ inclusion threshold ------
      0.011   15.5   0.3       0.38   10.6   0.0    2.9  3  HTH_38        Helix-turn-helix domain
      0.012   15.5   0.2      0.091   12.7   0.1    2.3  2  HTH_11        HTH domain
      0.024   14.1   0.1      0.048   13.2   0.1    1.5  1  Sigma70_r4    Sigma-70, region 4
      0.027   14.0   0.0       0.11   12.1   0.0    2.0  2  HTH_24        Winged helix-turn-helix DNA-binding
      0.053   13.4   0.0       0.31   11.0   0.0    2.1  2  MarR_2        MarR family
      0.074   12.5   0.0       0.14   11.7   0.0    1.4  1  PRTase_2      Phosphoribosyl transferase
       0.12   12.0   0.0       0.26   10.8   0.0    1.5  1  GerE          Bacterial regulatory proteins, luxR family
       0.15   11.5   0.0       0.22   10.9   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
       0.16   11.6   0.2        0.5   10.0   0.0    1.8  2  CENP-B_N      CENP-B N-terminal DNA-binding domain
       0.16   11.9   0.0       0.38   10.7   0.0    1.6  1  HTH_Crp_2     Crp-like helix-turn-helix domain
       0.17   12.0   0.1       0.64   10.1   0.0    1.9  2  HTH_3         Helix-turn-helix


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 !   55.3   0.0   4.1e-18   5.3e-15       9     141 ..      75     206 ..      67     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 4.1e-18
                                       --EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHS..TT-.EE-EEEEEE-TTT--EE........EE- CS
                      Pribosyltran   9 paildavarlaaeileeyngkpdvvvgiargGvpfakiladeL..evp.layvrkvkyrpdgseeaargssdesrll 82 
                                        + ++++  ++a++l + ++  d+ +gi++ G p+a+ +a+eL  ++  ++   +++ ++d  e+   ++s   r+ 
  gi|336252200|ref|YP_004595307.1|  75 SKRMEHISAAMADLLAKHGEDVDLTIGIEKAGGPIATLIARELgtDLGtYTPAKHQWEEGD-IEDLGGTFS---RNF 147
                                       556667777777777777777**********************552221344444443333.233333333...59* PP

                                       ---TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS. CS
                      Pribosyltran  83 edpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvf 141
                                       + ++++ + +VDD +++G+T+++++e+++++g e + ++vl+dk   ee +   +++++
  gi|336252200|ref|YP_004595307.1| 148 AGIRDRECYVVDDTITSGTTMRETIEAIRAEGGEPLACVVLADKQGIEELDGVPVYSLL 206
                                       *******************************************9987777766666655 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.8e-06    0.0023      11      35 ..      12      36 ..       9      43 .. 0.84
   2 ?    1.3   0.0      0.26   3.3e+02      23      49 ..     113     139 ..     113     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.8e-06
                            HTH_23 11 llllaeGlsvreIAreLgvsrrTvy 35
                                      + l+ +Gls+ eIA+eL+vsr T +
  gi|336252200|ref|YP_004595307.1| 12 AELAERGLSKGEIADELNVSRETAS 36
                                      456666*****************86 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.26
                            HTH_23  23 IAreLgvsrrTvyrwlkryreeG.legl 49 
                                       IAreLg    T+   ++ + eeG +e+l
  gi|336252200|ref|YP_004595307.1| 113 IARELGTDLGTYTPAKHQW-EEGdIEDL 139
                                       8999999999999999999.55548876 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 !   16.7   0.0   4.4e-06    0.0056      11      37 ..       8      34 ..       2      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.4e-06
                                      HGGGGSSTTTT--STTTSSSS---SSS CS
                             HTH_7 11 inrvvkLleeGisiskIAkevnisRsT 37
                                      i+++ +L e G s+ +IA+e+n+sR+T
  gi|336252200|ref|YP_004595307.1|  8 IESAAELAERGLSKGEIADELNVSRET 34
                                      78899********************99 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00029      0.38      14      36 ..      12      34 ..       7      41 .. 0.88
   2 ?    0.6   0.0      0.38   4.9e+02      26      33 ..     113     120 ..     105     123 .. 0.81
   3 ?   -0.0   0.0       0.6   7.6e+02      10      21 ..     169     181 ..     167     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                            HTH_38 14 erllaeGlslreIArrLgrspsT 36
                                      + l ++Gls  eIA +L++s+ T
  gi|336252200|ref|YP_004595307.1| 12 AELAERGLSKGEIADELNVSRET 34
                                      67899****************99 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.38
                            HTH_38  26 IArrLgrs 33 
                                       IAr+Lg +
  gi|336252200|ref|YP_004595307.1| 113 IARELGTD 120
                                       89999976 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.6
                            HTH_38  10 ReeIerllaeG.l 21 
                                       Re+Ie+ +aeG +
  gi|336252200|ref|YP_004595307.1| 169 RETIEAIRAEGgE 181
                                       9*******99955 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.1e-05     0.091      12      32 ..      16      35 ..      10      36 .. 0.84
   2 ?   -0.6   0.0         1   1.3e+03      28      44 ..     164     185 ..     162     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.1e-05
                            HTH_11 12 argpisgeeLAeeLnvSrrtv 32
                                      +rg +s  e+A+eLnvSr t 
  gi|336252200|ref|YP_004595307.1| 16 ERG-LSKGEIADELNVSRETA 35
                                      444.8999**********995 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                            HTH_11  28 SrrtvrrdIkaLeelg.....v 44 
                                       S +t r  I+a+++ g     +
  gi|336252200|ref|YP_004595307.1| 164 SGTTMRETIEAIRAEGgeplaC 185
                                       6788899999999998655543 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.7e-05     0.048      19      39 ..      17      37 ..       8      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-05
                                      TT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 19 eglTleEIgerlgiSrerVrq 39
                                      +gl+  EI+++l++Sre+++ 
  gi|336252200|ref|YP_004595307.1| 17 RGLSKGEIADELNVSRETASW 37
                                      788889************985 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 ?   12.1   0.0   8.2e-05      0.11      15      40 ..      16      41 ..      11      41 .. 0.90
   2 ?   -2.5   0.0       3.2   4.1e+03      23      33 ..     113     123 ..     111     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.2e-05
                            HTH_24 15 nprisqreLAerlglSpstvnrrlkr 40
                                      + ++s  e+A++l++S+ t ++ ++r
  gi|336252200|ref|YP_004595307.1| 16 ERGLSKGEIADELNVSRETASWLVER 41
                                      5689*****************99876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.2
                            HTH_24  23 LAerlglSpst 33 
                                       +A++lg  ++t
  gi|336252200|ref|YP_004595307.1| 113 IARELGTDLGT 123
                                       89999988887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00024      0.31      13      44 ..      13      41 ..      11      41 .. 0.87
   2 ?   -1.1   0.0       1.4   1.8e+03      23      34 ..     109     120 ..      97     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkr 44
                                      +L+ r+   l+ ge+a++l++s+ ++s +++r
  gi|336252200|ref|YP_004595307.1| 13 ELAERG---LSKGEIADELNVSRETASWLVER 41
                                      677777...9***************9988876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                                       EHHHHHHHHTSS CS
                            MarR_2  23 tvgelarrlgls 34 
                                        ++ +ar+lg +
  gi|336252200|ref|YP_004595307.1| 109 IATLIARELGTD 120
                                       677899999976 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.14     122     149 ..     153     180 ..     144     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                          PRTase_2 122 kelvLvDDEistGktalnliralqeklp 149
                                       +e  +vDD i++G+t+ ++i+a++++  
  gi|336252200|ref|YP_004595307.1| 153 RECYVVDDTITSGTTMRETIEAIRAEGG 180
                                       56678******************98754 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00021      0.26      13      33 ..      14      34 ..      11      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                                      HHCTTS-HHHHHHHHTS-HHH CS
                              GerE 13 llaeGksnkeIAeelniSekT 33
                                      l   G+s  eIA+eln+S +T
  gi|336252200|ref|YP_004595307.1| 14 LAERGLSKGEIADELNVSRET 34
                                      56689*************999 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00017      0.22     119     169 ..     150     197 ..     143     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                           UPRTase 119 iaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrl 169
                                       i++r+ +++D +i +G ++ + i+ ++ +g +    l + vla ++g+++l
  gi|336252200|ref|YP_004595307.1| 150 IRDRECYVVDDTITSGTTMRETIEAIRAEGGEP---LACVVLADKQGIEEL 197
                                       578999**********************88653...677788999999876 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00039       0.5      19      40 ..      15      36 ..      11      41 .. 0.88
   2 ?   -2.1   0.1       2.5   3.2e+03       8      17 ..     167     176 ..     167     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00039
                                      HHCTT-HHHHHHHHT--CCHHH CS
                          CENP-B_N 19 leegeSkaelarrfnvpestls 40
                                       e+g Sk+e+a ++nv + t+s
  gi|336252200|ref|YP_004595307.1| 15 AERGLSKGEIADELNVSRETAS 36
                                      69999***************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.5
                                       -HHHHHHHHH CS
                          CENP-B_N   8 TlreKievIq 17 
                                       T+re ie+I+
  gi|336252200|ref|YP_004595307.1| 167 TMRETIEAIR 176
                                       89999**998 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    0.0003      0.38      21      39 ..      18      36 ..       6      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                                      EHHHHHHHHHTTSSHHHHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvs 39
                                       l++ e+A+ l+++ret s
  gi|336252200|ref|YP_004595307.1| 18 GLSKGEIADELNVSRETAS 36
                                      589**************98 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0005      0.64       5      27 ..      14      36 ..      11      36 .. 0.87
   2 ?   -2.4   0.0       3.9     5e+03      42      52 ..     111     121 ..     107     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0005
                                      HHHTTHHHHHHHHHHTSSHHHHH CS
                             HTH_3  5 RkqlglsqeeLAeklGvsrstis 27
                                      + ++gls+ e+A++l+vsr t s
  gi|336252200|ref|YP_004595307.1| 14 LAERGLSKGEIADELNVSRETAS 36
                                      5699***************9965 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.9
                                       HHHHHHHTSEH CS
                             HTH_3  42 kklakaLgvsl 52 
                                        ++a+ Lg++l
  gi|336252200|ref|YP_004595307.1| 111 TLIARELGTDL 121
                                       57899999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.42u 0.19s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1767.61
//
Query:       gi|336252201|ref|YP_004595308.1|  [L=429]
Description: Haloacid dehalogenase domain-containing protein hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-11   44.0   0.0    9.4e-05   22.3   0.0    2.2  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
     0.0019   18.6   4.2        2.1    8.7   0.1    3.6  3  HAD          haloacid dehalogenase-like hydrolase
     0.0089   16.3   0.1      0.032   14.5   0.1    1.9  1  Hydrolase    haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.6e-08   9.4e-05       1      49 [.      94     145 ..      94     188 .. 0.88
   2 !   19.7   0.0   9.3e-08   0.00055     147     223 ..     300     375 ..     246     397 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.6e-08
                                       EEEEIIIIIS-...TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHH CS
                       Hydrolase_3   1 ialDlDGTLln...sdkkisektkeaikklkekgikvviATGRslravlpvl 49 
                                       ++lD+D TL +    d++i+ +t +++ +++e+g+ +vi+TG  l++v+ ++
  gi|336252201|ref|YP_004595308.1|  94 LVLDVDETLRSaggTDNEIPRETLHVLTEFHEAGVPIVICTGQTLENVKGFA 145
                                       589******887778899**************************99998765 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 9.3e-08
                                       EES-HHHHHHHHHHHHHHCTTTEEEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSS CS
                       Hydrolase_3 147 ilkdkekldelekelksklnklltitssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaag 223
                                        ++ + + de+ ++l++ l+  +++  ++    ei + + +K  ++++    l+i+    +++GD++ D+  +e+++
  gi|336252201|ref|YP_004595308.1| 300 GVYPDRDADEVPAQLADTLER-IDVAYYEADAAEIGSLELNKVVGVERAFDVLGIDDPFALVMGDSKSDLRVMEWVE 375
                                       556677888888889998865.6****************************************************93 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1   0.00036       2.1      89     129 ..     115     156 ..      38     180 .. 0.71
   2 ?    1.0   0.0     0.083   4.9e+02      65      96 ..     182     212 ..     176     222 .. 0.74
   3 !    8.3   0.2   0.00048       2.9     124     188 .]     307     372 ..     286     372 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00036
                               HAD  89 galellaahraaGdrvvvvSgglrplvepll.aelgadevla 129
                                       + l +l + ++aG+++v+++g   ++v+ ++ + lg++ v +
  gi|336252201|ref|YP_004595308.1| 115 ETLHVLTEFHEAGVPIVICTGQTLENVKGFAiQGLGSEIVHS 156
                                       6666667667*********************99999444422 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.083
                               HAD  65 lseelaaelerfvaevirpklldpgalella.a 96 
                                       l+e+l++e+++ +++v+ +  l p+a + l+  
  gi|336252201|ref|YP_004595308.1| 182 LYEDLDEEIRAVFDDVRSRV-L-PEAPDELRrG 212
                                       66899999999998888765.5.9**9999963 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00048
                               HAD 124 adev...latelevdd..rltgelglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                       adev   la  le+ d  ++ +     +  + + +kv  +++  a    gid +   + GDs sDl  ++
  gi|336252201|ref|YP_004595308.1| 307 ADEVpaqLADTLERIDvaYYEAD--AAEIGSLELNKVVGVER--AFDVLGIDDPFALVMGDSKSDLRVME 372
                                       56665557778888888889999..8899999999*******..9999999999999*********9885 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   5.3e-06     0.032     113     160 ..     107     154 ..      39     196 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.3e-06
                                       HHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH.TTGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                         Hydrolase 113 iadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq.lGddyf 160
                                         d+ ++  e+ +++ ++++ag+++v++tg+  e+++  a q lG +++
  gi|336252201|ref|YP_004595308.1| 107 GTDN-EIPRETLHVLTEFHEAGVPIVICTGQTLENVKGFAIQgLGSEIV 154
                                       3344.4556677*************************999888**3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 3490.11
//
Query:       gi|336252202|ref|YP_004595309.1|  [L=225]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   67.9   0.2    8.6e-19   67.1   0.2    1.4  1  HTH_10      HTH DNA binding domain
    3.4e-08   33.5   7.6    5.5e-08   32.8   7.6    1.4  1  BAT         GAF and HTH_10 associated domain
     0.0014   18.8   0.0     0.0031   17.7   0.0    1.5  1  UPF0122     Putative helix-turn-helix protein, YlxM / p13 lik
     0.0022   17.5   0.3     0.0056   16.2   0.3    1.7  1  Sigma70_r4  Sigma-70, region 4
  ------ inclusion threshold ------
      0.021   14.7   0.2       0.07   13.0   0.0    2.0  2  MarR_2      MarR family
      0.021   14.6   0.1       0.31   10.9   0.1    2.6  3  HTH_30      PucR C-terminal helix-turn-helix domain
      0.022   14.3   0.2      0.051   13.1   0.1    1.7  2  HTH_24      Winged helix-turn-helix DNA-binding
      0.028   14.5   1.1      0.028   14.5   1.1    2.0  2  Sigma70_r3  Sigma-70 region 3
      0.053   13.5   0.1       0.69    9.9   0.0    2.5  2  HTH_11      HTH domain
      0.065   13.3   0.3       0.24   11.5   0.0    2.1  2  HTH_20      Helix-turn-helix domain
       0.18   11.8   0.4       0.88    9.6   0.1    2.3  3  DUF4250     Domain of unknown function (DUF4250)


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 !   67.1   0.2   5.3e-22   8.6e-19       1      51 [.     160     210 ..     160     212 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 5.3e-22
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskl 51 
                                       LT+ q e++++Ay++GY+d+PR+++l+eLA+el+Is ++lse+Lr+a + l
  gi|336252202|ref|YP_004595309.1| 160 LTEPQKEAIAEAYRQGYYDVPREISLEELANELDISHQALSERLRRANRVL 210
                                       9**********************************************9866 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   7.6   3.3e-11   5.5e-08       7     138 ..       6     142 ..       3     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.3e-11
                               BAT   7 eleirdeddvlv.alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaae.dldavedvrvvseeddg...t 78 
                                       el+++ ++++l+ +  +   ++v++e++v+ + g+++ +++ + +d +e+ +++  d   ve  ++++++ddg    
  gi|336252202|ref|YP_004595309.1|   6 ELSVSTDEFALAeTFRQLPSMEVRVESVVAEGPGRTTPLVWFSNVDSDELDETLRaDSTVVEHQQLLEDTDDGelfY 82 
                                       5555666666663555666899******************************9986777788999999999996666 PP

                               BAT  79 lleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveL 138
                                       +le   + +s+ +++ +h+gtv  a++ d +++l+v +P ++ +   v+ +ee   +v++
  gi|336252202|ref|YP_004595309.1|  83 RLEYSEDVSSICRAIYAHDGTVLGAQVADNQWTLRVLFPHREGLSDAVSDIEELGVRVDV 142
                                       6788888899999***********************************999997666655 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.9e-06    0.0031      25      62 ..     172     211 ..     157     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
                           UPF0122  25 ylelyya..dDlSlsEiAeefnvsrqavydnikrteklle 62 
                                       y + yy+   ++Sl+E+A+e ++s+qa+++ ++r++++l 
  gi|336252202|ref|YP_004595309.1| 172 YRQGYYDvpREISLEELANELDISHQALSERLRRANRVLA 211
                                       444566533578************************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 !   16.2   0.3   3.4e-06    0.0056       4      48 ..     159     210 ..     158     211 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.4e-06
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                        L+e ++e +   +        ++ +leE++++l+iS  + + +++rA r L
  gi|336252202|ref|YP_004595309.1| 159 ALTEPQKEAIAEAYrqgyydvPREISLEELANELDISHQALSERLRRANRVL 210
                                       799999999999999999999899************************8766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         4   6.5e+03      42      49 ..     142     149 ..     142     149 .. 0.91
   2 ?   13.0   0.0   4.3e-05      0.07      20      45 ..     181     206 ..     160     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4
                                       HHHHHHTT CS
                            MarR_2  42 lkrLvaaG 49 
                                       +kr+v+aG
  gi|336252202|ref|YP_004595309.1| 142 VKRMVEAG 149
                                       89****98 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.3e-05
                                       SEEEHHHHHHHHTSSHHHHHHHHHHH CS
                            MarR_2  20 rdltvgelarrlglsksavsrilkrL 45 
                                       r+++  ela +l++s++a+s +l+r+
  gi|336252202|ref|YP_004595309.1| 181 REISLEELANELDISHQALSERLRRA 206
                                       468999******************97 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 ?   -0.5   0.0      0.68   1.1e+03       9      29 ..      84     104 ..      82     105 .. 0.86
   2 ?   -1.7   0.0       1.6   2.6e+03      21      39 ..     118     136 ..     115     140 .. 0.74
   3 ?   10.9   0.1   0.00019      0.31      14      41 ..     184     211 ..     181     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.68
                                       HHTTT-HHHHHHHHTS-HHHH CS
                            HTH_30   9 lenggnisatAkaLhvHrnTl 29 
                                       le + ++s  ++a + H  T+
  gi|336252202|ref|YP_004595309.1|  84 LEYSEDVSSICRAIYAHDGTV 104
                                       67788999999****999887 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.6
                                       HHTS-HHHHHHHHHHHHHH CS
                            HTH_30  21 aLhvHrnTlryRLrrieel 39 
                                        L+ Hr  l+  +  ieel
  gi|336252202|ref|YP_004595309.1| 118 VLFPHREGLSDAVSDIEEL 136
                                       4777888887777777776 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00019
                                       -HHHHHHHHTS-HHHHHHHHHHHHHHHS CS
                            HTH_30  14 nisatAkaLhvHrnTlryRLrrieellg 41 
                                       ++++ A++L ++ + l+ RLrr++++l 
  gi|336252202|ref|YP_004595309.1| 184 SLEELANELDISHQALSERLRRANRVLA 211
                                       67899******************99986 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 ?   -3.3   0.0       4.1   6.8e+03      38      45 ..     142     149 ..     142     149 .. 0.90
   2 ?   13.1   0.1   3.1e-05     0.051      18      40 ..     183     205 ..     180     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.1
                            HTH_24  38 lkrLeeeG 45 
                                       +kr++e+G
  gi|336252202|ref|YP_004595309.1| 142 VKRMVEAG 149
                                       79***998 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.1e-05
                            HTH_24  18 isqreLAerlglSpstvnrrlkr 40 
                                       is  eLA +l++S +++++rl+r
  gi|336252202|ref|YP_004595309.1| 183 ISLEELANELDISHQALSERLRR 205
                                       999******************98 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.6   4.3e+03      43      52 ..      61      70 ..      48      81 .. 0.45
   2 ?   14.5   1.1   1.7e-05     0.028       6      51 ..     168     213 ..     164     221 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.6
                                      HHXXXEETTX CS
                        Sigma70_r3 43 aarepvSldl 52
                                      a   +v  ++
  gi|336252202|ref|YP_004595309.1| 61 ADSTVVEHQQ 70
                                      4333333333 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHHSSXXXHHHHHHHHTXXHHHHHHHHHHHXXXEETT CS
                        Sigma70_r3   6 ikraqreLeqelgrePtpeEiAeeLglseekVrevleaarepvSld 51 
                                       i++a r+ + +  re + eE+A+eL++s + + e l+ a+++++ +
  gi|336252202|ref|YP_004595309.1| 168 IAEAYRQGYYDVPREISLEELANELDISHQALSERLRRANRVLASE 213
                                       88899999999999***************************99876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.38   6.2e+02      36      50 ..     130     144 ..     123     149 .. 0.84
   2 ?    9.9   0.0   0.00043      0.69      15      36 ..     182     203 ..     178     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.38
                            HTH_11  36 IkaLeelgvpIesep 50 
                                       + ++eelgv+++ ++
  gi|336252202|ref|YP_004595309.1| 130 VSDIEELGVRVDVKR 144
                                       7899****9999876 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00043
                            HTH_11  15 pisgeeLAeeLnvSrrtvrrdI 36 
                                        is eeLA eL++S ++   ++
  gi|336252202|ref|YP_004595309.1| 182 EISLEELANELDISHQALSERL 203
                                       39************99987666 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.2   5.3e+03      29      49 ..      54      73 ..      52      76 .. 0.69
   2 ?   11.5   0.0   0.00015      0.24      23      46 ..     181     204 ..     157     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.2
                                      HHHHHHTS-HHHHHHHHHHHH CS
                            HTH_20 29 elaerldlskntlsyHLrvLe 49
                                      el+e+l  +++t+  H + Le
  gi|336252202|ref|YP_004595309.1| 54 ELDETL-RADSTVVEHQQLLE 73
                                      788888.77777766666666 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00015
                                       TTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  23 egltaselaerldlskntlsyHLr 46 
                                       ++ +++ela +ld+s + ls +Lr
  gi|336252202|ref|YP_004595309.1| 181 REISLEELANELDISHQALSERLR 204
                                       6789******************98 PP

>> DUF4250  Domain of unknown function (DUF4250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.8   4.6e+03      31      42 ..      49      60 ..      45      62 .. 0.82
   2 ?   -3.6   0.0       6.9   1.1e+04      17      29 ..      83      96 ..      83      99 .. 0.74
   3 ?    9.6   0.1   0.00054      0.88      22      44 ..     184     206 ..     181     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.8
                           DUF4250 31 didkeeleekLa 42
                                      ++d +el e+L 
  gi|336252202|ref|YP_004595309.1| 49 NVDSDELDETLR 60
                                      689999999886 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.9
                           DUF4250 17 RDey.ssldelced 29
                                      R ey ++++++c++
  gi|336252202|ref|YP_004595309.1| 83 RLEYsEDVSSICRA 96
                                      77787788888875 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00054
                           DUF4250  22 sldelcedldidkeeleekLasi 44 
                                       sl+el+++ldi+ ++l e+L  +
  gi|336252202|ref|YP_004595309.1| 184 SLEELANELDISHQALSERLRRA 206
                                       9*******************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1733.29
//
Query:       gi|336252203|ref|YP_004595310.1|  [L=183]
Description: HAD-superfamily hydrolase [Halopiger xanaduensis SH-6]
Scores for complete 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   74.3   0.0    4.3e-19   69.3   0.0    2.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    8.7e-12   45.8   1.6    2.3e-08   34.6   0.2    2.2  2  Hydrolase       haloacid dehalogenase-like hydrolase
    7.8e-07   29.7   0.5    1.1e-06   29.3   0.5    1.2  1  HAD             haloacid dehalogenase-like hydrolase
    1.2e-06   28.5   0.0    2.6e-06   27.4   0.0    1.6  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
       0.03   14.2   0.0       0.28   11.0   0.0    2.1  1  Acid_PPase      Acid 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 !   69.3   0.0   1.2e-22   4.3e-19       1     175 [.      11     173 ..      11     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 1.2e-22
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkke 77 
                                       +++DlDgTl+d e  +++a++ + e y+            +++++ el + l+   +  ++++++ ++  +++ +  
  gi|336252203|ref|YP_004595310.1|  11 VVYDLDGTLVDLEVDWADAARAVREVYET---------AGVEPPSTELWDMLEA-ADDAGLLADVESTLADRERE-G 76 
                                       789*****************999988855.........2333333333333333.23344555555555555555.5 PP

                             HAD_2  78 vkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkee 154
                                        +  + +  + e L e+ + +g+ + + ++a +  le++g+ +  d +v+ ++v  +KPdpe++++a+++l++++e+
  gi|336252203|ref|YP_004595310.1|  77 ARAAPRLTRADELL-ERTVPVGVCSLNCEAACRIALEKHGLADAVDIVVGRDTVATQKPDPEPLLEAVRELGVDPEN 152
                                       55566555553333.678*********************************************************** PP

                             HAD_2 155 viyvGDsptDieaakkagikv 175
                                       +++vGDs +D  +a +ag+ +
  gi|336252203|ref|YP_004595310.1| 153 AVFVGDSRRDELTAERAGVAF 173
                                       ******************976 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00015      0.53       2      37 ..       9      40 ..       8      56 .. 0.72
   2 !   34.6   0.2   6.5e-12   2.3e-08     137     210 .]      96     170 ..      46     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                                      SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  2 ktvvfDkdGTLttgepsvedvivsaalalaaaletg 37
                                      ++vv D+dGTL++ e    d+     +a +++ et+
  gi|336252203|ref|YP_004595310.1|  9 EAVVYDLDGTLVDLEVDWADAA----RAVREVYETA 40
                                      79**********9993333333....5557777766 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 6.5e-12
                                       EEEEESSEHHHHHHHHHH.TT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 137 vvlltgdnpetaeraanq.lG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       v++++ +  e a r+a +  G +d++d+v+++d+++  kp+pe +++a+reL+++pe+ ++VGD+  D   +++Ag
  gi|336252203|ref|YP_004595310.1|  96 VGVCSLNC-EAACRIALEkHGlADAVDIVVGRDTVATQKPDPEPLLEAVRELGVDPENAVFVGDSRRDELTAERAG 170
                                       55555333.33446777769999999******************************************99999997 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.5   2.9e-10   1.1e-06       1     183 [.      11     162 ..      11     167 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.9e-10
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrl.draglaelleallaglseelaaelerf 76 
                                       +++D+DgTL+d + +  ++++ +++  ++ ++++ +++    ++++l+  d+agl + +e++la+ +       ++ 
  gi|336252203|ref|YP_004595310.1|  11 VVYDLDGTLVDLEVD--WADAARAV--REVYETAGVEPPSTELWDMLEAaDDAGLLADVESTLADRE-------REG 76 
                                       79*********9644..44422222..2339999999777776666666044444444444444444.......333 PP

                               HAD  77 vaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgeg 153
                                           ++p+l    a ell+    + ++v v+S + +   ++ l+++g    la        ++    +++++  ++ 
  gi|336252203|ref|YP_004595310.1|  77 A--RAAPRL--TRADELLE----RTVPVGVCSLNCEAACRIALEKHG----LAD------AVDIV-VGRDTVATQKP 134
                                       3..122442..36666666....779*********************....999......66666.66677888878 PP

                               HAD 154 kvaalrewlaaegegidleevvayGDspsD 183
                                       ++  l e  a ++ g d+e+ v++GDs+ D
  gi|336252203|ref|YP_004595310.1| 135 DPEPLLE--AVRELGVDPENAVFVGDSRRD 162
                                       8888888..8888***************99 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   7.2e-10   2.6e-06       3      51 ..     132     179 ..     130     182 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 7.2e-10
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSS CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltG 51 
                                        KP pe + +a+++lg+dpe+ +++GD+ + D + A +aG+ +  V +G
  gi|336252203|ref|YP_004595310.1| 132 QKPDPEPLLEAVRELGVDPENAVFVGDS-RRDELTAERAGVAFEYVGSG 179
                                       6***************************.************99888887 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.8e-05      0.28       5      59 ..      10      74 ..       7     182 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.8e-05
                                      EEEE-STTTSSSS-TTTS..............S-S-EEE-TTS.-EEETT--EE---TTHHHHHHHHHH CS
                        Acid_PPase  5 livFDLDyTLWpfevdtl..............vsaplkkeskksevvDrrgeelklypdveeileelks 59
                                      ++v+DLD TL ++evd                v++p ++  + +e  D       l  dve+ l++ ++
  gi|336252203|ref|YP_004595310.1| 10 AVVYDLDGTLVDLEVDWAdaaravrevyetagVEPPSTELWDMLEAAD----DAGLLADVESTLADRER 74
                                      79**************98655555554433333333333333333333....34455666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1407.82
//
Query:       gi|336252204|ref|YP_004595311.1|  [L=80]
Description: hypothetical protein Halxa_0793 [Halopiger xanaduensis SH-6]
Scores for 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:                       563  (0.0314016); 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:                         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: 583.24
//
Query:       gi|336252205|ref|YP_004595312.1|  [L=270]
Description: 3-methyl-2-oxobutanoate hydroxymethyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-104  347.8   0.9   4.3e-104  347.5   0.9    1.0  1  Pantoate_transf  Ketopantoate hydroxymethyltransferase
    9.4e-06   25.2   1.8    1.4e-05   24.6   1.6    1.4  1  PEP_mutase       Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> Pantoate_transf  Ketopantoate hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.5   0.9  4.8e-108  4.3e-104       3     258 ..       3     256 ..       2     257 .. 0.98

  Alignments for each domain:
  == domain 1  score: 347.5 bits;  conditional E-value: 4.8e-108
                   Pantoate_transf   3 tvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralv 79 
                                       tv+dl+++  e e+i+mlTayda+tA++vd+a+vdviLVGDs+g+  lgye+tlpvt+++m++h+ aV+r++++alv
  gi|336252205|ref|YP_004595312.1|   3 TVRDLTAKAGE-EPITMLTAYDAPTAEIVDDADVDVILVGDSVGNASLGYETTLPVTVDDMARHVGAVSRATEDALV 78 
                                       67788776655.***************************************************************** PP

                   Pantoate_transf  80 vadlPfgsyeaskeqalenAarllkeggadavKleggaevaetvkalveagipVmgHiGltPqsvnalggykvqgkt 156
                                       vad+Pf+s+ +++ +++enA+r+lke+ga+avKle g +++++ +++v+ gipVm+H+GltPq+vn++ggy  qg +
  gi|336252205|ref|YP_004595312.1|  79 VADMPFLSFGVDEGESIENAGRMLKEEGAHAVKLESGPHTVDLTEKMVQLGIPVMAHLGLTPQHVNQYGGYPRQGTD 155
                                       ***************************************************************************** PP

                   Pantoate_transf 157 eeeaeklledakaleeaGafalvlEavpaelakeiteklsiptIGIGAGaacdGqvlvlhDllgltekfkpkfvkky 233
                                       e++ae++++ a a e aGaf+lvlE+vp++la+++te+++iptIGIGAG++cdGqvlv++D++gl+ + +p+f+k++
  gi|336252205|ref|YP_004595312.1| 156 EAAAERIVDLAAAHEVAGAFSLVLEHVPSNLAAAVTEAIDIPTIGIGAGPDCDGQVLVVDDAVGLS-EWSPSFAKQF 231
                                       *****************************************************************9.779******* PP

                   Pantoate_transf 234 aelaesieeavkaYaeevkegsFPa 258
                                        +++e++e+av++Y+e+v++g+FPa
  gi|336252205|ref|YP_004595312.1| 232 GNVREEMESAVADYVEAVESGAFPA 256
                                       ************************8 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   1.6   1.6e-09   1.4e-05       6     111 ..      11     120 ..       5     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.6e-09
                        PEP_mutase   6 akgeplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevv.slPlivDl...ed 78 
                                       a++ep+ ++ a+Da +a+iv +a ++ + ++     aslG++ +  ++++ + ++v a+ +++ +  + +D+     
  gi|336252205|ref|YP_004595312.1|  11 AGEEPITMLTAYDAPTAEIVDDADVDVILVGDSVGNASLGYETTLPVTVDDMARHVGAVSRATeDALVVADMpflSF 87 
                                       5668***********************************************************55666777622134 PP

                        PEP_mutase  79 GygespeevaetvrrliaaGvvgvniEDkkkn.d 111
                                       G  ++ e+++++ r l + G+ +v +E   +  d
  gi|336252205|ref|YP_004595312.1|  88 G-VDEGESIENAGRMLKEEGAHAVKLESGPHTvD 120
                                       4.35568888888999999*******98833323 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1981.52
//
Query:       gi|336252206|ref|YP_004595313.1|  [L=69]
Description: hypothetical protein Halxa_0795 [Halopiger xanaduensis SH-6]
Scores for 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   13.6   1.7      0.046   13.4   1.7    1.0  1  DUF2244      Integral membrane protein (DUF2244)
      0.089   12.5   1.3       0.12   12.1   1.3    1.3  1  Tetraspanin  Tetraspanin family
        3.7    7.6   6.6          7    6.7   2.5    2.0  2  DUF4342      Domain of unknown function (DUF4342)


Domain annotation for each model (and alignments):
>> DUF2244  Integral membrane protein (DUF2244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.7   7.7e-06     0.046      15      67 ..      13      66 ..       6      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.7e-06
                           DUF2244 15 lllalalvslvialafl.laGawpvlpFaglevlalalafrvsarhardrEeit 67
                                       +++l++v+l ++la + l    ++ +F ++ + + + ++++++r  ++ Eei 
  gi|336252206|ref|YP_004595313.1| 13 SVGILVTVVLSVSLAYAlLTANILLWVFGVVSIGVSGGVLYLFYRLVTAVEEIA 66
                                      578999999999999995666777789999999999***************995 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.3     2e-05      0.12       2      29 ..      27      59 ..      26      69 .] 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                                      XXXXXXXXXXXXXXXXXXXXXX...XXXXX..X CS
                                      xxxxxxxxxxxxxxxxxxxxxx...xxxxx..x RF
                       Tetraspanin  2 kyllfffnllfwligivllavG...vwlrl..k 29
                                       y l+  n+l+w++g+v ++v+   ++l +   
  gi|336252206|ref|YP_004595313.1| 27 AYALLTANILLWVFGVVSIGVSggvLYLFYrlV 59
                                      6999*****************545555533442 PP

>> DUF4342  Domain of unknown function (DUF4342)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.5    0.0012         7      42      65 ..       9      32 ..       7      43 .. 0.72
   2 ?    3.2   0.2     0.015        88      45      68 ..      43      65 ..      41      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0012
                           DUF4342 42 eiPltaGvvggviavllapllaal 65
                                      e+P ++G++++v++++ +++ ++ 
  gi|336252206|ref|YP_004595313.1|  9 ELPTSVGILVTVVLSVSLAYALLT 32
                                      99********77776655554443 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.015
                           DUF4342 45 ltaGvvggviavllapllaalgai 68
                                      +++Gv ggv+  l++ l++a+  i
  gi|336252206|ref|YP_004595313.1| 43 VSIGVSGGVLY-LFYRLVTAVEEI 65
                                      67899997777.999999998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 534.83
//
Query:       gi|336252207|ref|YP_004595314.1|  [L=113]
Description: hypothetical protein Halxa_0796 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.001   18.4   0.8     0.0012   18.2   0.8    1.0  1  UbiA             UbiA prenyltransferase family
  ------ inclusion threshold ------
      0.034   14.2   1.2      0.052   13.6   1.2    1.3  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


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 !   18.2   0.8   1.4e-07    0.0012     184     246 ..      12      72 ..       7      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-07
                              UbiA 184 Grkaarillalllavlllallllllalllllylllalllaalallraarlvrrrdakkaakff 246
                                       G ++a++ +++l+++l  a +l+ll+l + l++++++l+++l+l+  + l+++++++ +++++
  gi|336252207|ref|YP_004595314.1|  12 GVQVAFYAYVALTCALT-A-GLWLLGLPTELTVVAFVLIGGLLLIPFWPLFTDQHPEHDEATV 72 
                                       66778874554555444.4.6************************************999887 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 ?   13.6   1.2   5.8e-06     0.052      41      85 ..      10      54 ..       5      74 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.8e-06
                   Phage_holin_3_6 41 gaagvlallalllllvalalalaa.lwlaalivaavllvlagvlal 85
                                      ++++ +a++a ++l++al ++l + l l + ++ +++++++g+l++
  gi|336252207|ref|YP_004595314.1| 10 FGGVQVAFYAYVALTCALTAGL-WlLGLPTELTVVAFVLIGGLLLI 54
                                      5677899999999999997677.33444555545555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 851.50
//
Query:       gi|336252208|ref|YP_004595315.1|  [L=260]
Description: alpha/beta hydrolase fold protein [Halopiger xanaduensis SH-6]
Scores for 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-20   72.2   9.1    1.1e-19   71.9   9.1    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
    5.5e-14   52.4   1.1    1.5e-07   31.3   0.4    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    3.1e-12   46.3   0.7    6.6e-12   45.2   0.7    1.5  1  Hydrolase_4    Serine aminopeptidase, S33
    0.00027   21.0   0.0    0.00063   19.8   0.0    1.7  1  Abhydrolase_4  TAP-like protein
  ------ inclusion threshold ------
      0.036   13.7   0.0      0.079   12.6   0.0    1.7  1  Esterase       Putative esterase
      0.065   13.4   0.0       0.12   12.5   0.0    1.6  1  NitrOD2        Nitrososphaera output domain 2
      0.082   13.0   0.0       0.15   12.2   0.0    1.4  1  Thioesterase   Thioesterase domain
      0.083   12.6   0.2       0.47   10.2   0.1    1.9  2  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   9.1   4.9e-23   1.1e-19       4     220 .]      28     250 ..      27     250 .. 0.69

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 4.9e-23
                                       E--GC.....GC.HHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH.CHHHHHHHCCTT.....TTSEEEEEETCH CS
                     Abhydrolase_6   4 lHGagssassWl.vapLaallaagvhvlapDlpGhGrsdpppldled.ladlaalldelaa...gggpvvlvGHSlG 75 
                                       +HG+g+s+++W  + +L    a++  v+a+Dl GhG+s  ++ d ++ +a+l+a++d+++a    +++ vlvG+SlG
  gi|336252208|ref|YP_004595315.1|  28 VHGSGGSRHVWKsQHRL----ADRTPVVALDLSGHGDS--DDIDASAgYATLSAYADDVIAvaeATDATVLVGNSLG 98 
                                       8**********545599....999888*********44..44333333455555555555544335667******** PP

                                       HHHHHH.HHHCC......EEEEES-..----TTTS----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHHC.CCCHCH CS
                     Abhydrolase_6  76 Galala.aapla....lvvgvlldppptalpagllaaalelllallallrllawlsreplprlfladeda.daawra 146
                                       Ga++l+ ++  a    +++ vl  +   ++++g l ++l++l++  ++++ +       ++r f+++e++ +++  +
  gi|336252208|ref|YP_004595315.1|  99 GAVVLHiLLERAnefdPDAVVLTGA---GARLGVLEDLLQWLEHDFDRAVEFLHG----DDRFFHDPEPElRERSKE 168
                                       **99996555557875444466666...888888999999999888877774444....665666655523333333 PP

                                       CCCGHH......HHCCHHC.....HTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH..STTEEETCE...SSS-H CS
                     Abhydrolase_6 147 rlarla......allaglg.....llpaaawadlpvpllvl.ggeDplvprllerlla..qagarlpvvlpgaGHlp 209
                                       r+ +        +     +     +  ++ +  + +p+l + g+ D+l p+++ ++la  +++  l   +++a Hl 
  gi|336252208|ref|YP_004595315.1| 169 RFHECGqavtnrD-----FqtchtFDVRDQLGEIDAPVLAVyGEYDQLTPPWFHEFLAdeIEDSYL-AGIEDAAHLA 239
                                       3322222222222.....1222224458899999999988867***************98777777.99******** PP

                                       HHHSHHHHHHH CS
                     Abhydrolase_6 210 hleepdevaea 220
                                       +le+pd++++a
  gi|336252208|ref|YP_004595315.1| 240 MLEQPDAFNDA 250
                                       ********986 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.4   6.6e-11   1.5e-07       1     106 [.      23     123 ..      23     159 .. 0.78
   2 !   20.3   0.0   1.6e-07   0.00036     192     256 ..     182     243 ..     141     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 6.6e-11
                                       SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEE. CS
                     Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddklt. 76 
                                       p+++++hG +gs +vw     +  La+ +  v++lDl G+g S+   a+    y t  + ++ d + +       t 
  gi|336252208|ref|YP_004595315.1|  23 PTVCYVHGSGGSRHVWKS---QHRLAD-RTPVVALDLSGHGDSDDIDAS--AGYAT--LSAYADDVIAVAEATDATv 91 
                                       6899**********9888...667776.*******************99..88888..7777775544444444555 PP

                                       EEEETHHHHHHHHHHHHH.....GGGEEEEEEESE CS
                     Abhydrolase_1  77 lvGhSmGGmialayaaey.....perVkalvllga 106
                                       lvG S+GG+++l+ ++e      p+   a+vl+ga
  gi|336252208|ref|YP_004595315.1|  92 LVGNSLGGAVVLHILLERanefdPD---AVVLTGA 123
                                       9************999885443333...5566555 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.6e-07
                                       HHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                     Abhydrolase_1 192 wpttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafleg 256
                                       ++t +++ + ++l+e   + ap+l ++g++D+l+pp   e+la+ + +++l  i+da Hla le 
  gi|336252208|ref|YP_004595315.1| 182 FQTCHTFDVRDQLGE---IDAPVLAVYGEYDQLTPPWFHEFLADEIEDSYLAGIEDAAHLAMLEQ 243
                                       455556666666665...888****************************************9986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.7   2.9e-15   6.6e-12      27     238 ..      44     243 ..      22     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 2.9e-15
                       Hydrolase_4  27 LaaqGfavyalDhrGhGrse..gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkv 101
                                       La++   v+alD  GhG s+   + +  + ++ y dD+ a+ e+          +l+G S+GG+++l++ll++++++
  gi|336252208|ref|YP_004595315.1|  44 LADR-TPVVALDLSGHGDSDdiDASAGYATLSAYADDVIAVAEATD------ATVLVGNSLGGAVVLHILLERANEF 113
                                       4433.579************997888899*********99976666......689***************9999977 PP

                       Hydrolase_4 102 a..glilsaPalkikaklkappllklllkllgkllpklqvsnnlkadslsrdpevva.ayeadplvhgkitvrllle 175
                                       +  +++l+++  ++     +  ll++l   + +++  l+     +  +   +pe ++ + e+ + +++++t+r +++
  gi|336252208|ref|YP_004595315.1| 114 DpdAVVLTGAGARLGV---LEDLLQWLEHDFDRAVEFLHG---DDRFFHDPEPELRErSKERFHECGQAVTNRDFQT 184
                                       7779******998873...566666666666666555555...3333333334444424566777899999999988 PP

                       Hydrolase_4 176 lldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnEp 238
                                       +++   +++++  +i++P+l ++Ge D++++p  ++ l++++   d  l+ ++ + H  + E+
  gi|336252208|ref|YP_004595315.1| 185 CHT--FDVRDQLGEIDAPVLAVYGEYDQLTPPWFHEFLADEIE--DSYLAGIEDAAHLAMLEQ 243
                                       875..59**********************************99..899999999999988886 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.8e-07   0.00063      32      94 ..     196     258 ..     166     260 .] 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.8e-07
                     Abhydrolase_4  32 kgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLltG 94 
                                       + +apvL + +e+D  TP++ ++ la++++++ l   e++ H a+ ++ ++ ++av ++L++ 
  gi|336252208|ref|YP_004595315.1| 196 EIDAPVLAVYGEYDQLTPPWFHEFLADEIEDSYLAGIEDAAHLAMLEQPDAFNDAVLEFLDET 258
                                       2368********************************************************875 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.5e-05     0.079     113     140 ..      86     113 ..      13     119 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                                       ECCCEEEEEETHHHHHHHHHHHCSTTTC CS
                          Esterase 113 apdgravaGqSmGGlgALilalkhpdrF 140
                                       a+d+++++G S+GG + L++ l++ ++F
  gi|336252208|ref|YP_004595315.1|  86 ATDATVLVGNSLGGAVVLHILLERANEF 113
                                       45569******************99988 PP

>> NitrOD2  Nitrososphaera output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.5e-05      0.12      20      63 ..     212     257 ..     189     260 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-05
                           NitrOD2  20 Gpevfd.almeliaedylggemd.vrtailqrpdlferalvellGe 63 
                                        p+ f+  l++ i + yl g  d +  a+l++pd f+ a++e+l e
  gi|336252208|ref|YP_004595315.1| 212 TPPWFHeFLADEIEDSYLAGIEDaAHLAMLEQPDAFNDAVLEFLDE 257
                                       4455541678889999**886662678***************9987 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.5e-05      0.15       2      79 ..      24     101 ..      23     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.5e-05
                                       EEEEE--TTCCSGGGHHHHHHCTTCEEEEEEECSTTST..SHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHH CS
                      Thioesterase   2 pLflfppagGsasvfrslasklsdpvvevlavqlpgre..rdepplesieelaaeyaealrqiqpegPyalfGhSlG 76 
                                       +++ ++++gGs +v +s ++  +++   v+a+ l g++  +d  +  + ++l a+  + +      + ++l+G SlG
  gi|336252208|ref|YP_004595315.1|  24 TVCYVHGSGGSRHVWKSQHRLADRT--PVVALDLSGHGdsDDIDASAGYATLSAYADDVIAVAEATDATVLVGNSLG 98 
                                       6899*************88777776..8999999999886777888888888888888888888888********** PP

                                       HHH CS
                      Thioesterase  77 gll 79 
                                       g++
  gi|336252208|ref|YP_004595315.1|  99 GAV 101
                                       *98 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.29   6.5e+02      36      70 ..      36      75 ..      27      78 .. 0.73
   2 ?   10.2   0.1   0.00021      0.47      36      81 ..      92     134 ..      74     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.29
                                      EESTTC.....SCCEEEEEETTS--EEEEETTTTEEEEET CS
                     FAD_binding_4 36 llgqav.....atggvvldlsrlnrileideeegtatvea 70
                                       + +++     +t  v ldls   +  +id+++g+at+ a
  gi|336252208|ref|YP_004595315.1| 36 HVWKSQhrladRTPVVALDLSGHGDSDDIDASAGYATLSA 75
                                      4444433455667889999988888899999999999865 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00021
                                       EESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHHH CS
                     FAD_binding_4  36 llgqavatggvvldlsrlnrileideeegtatveaGvtlgdlveal 81 
                                       l+g+++  g+vvl++  l+r  e+d+ + ++  +aG++lg l+  l
  gi|336252208|ref|YP_004595315.1|  92 LVGNSL-GGAVVLHI-LLERANEFDP-DAVVLTGAGARLGVLEDLL 134
                                       448997.999*****.8*********.9************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1969.92
//
Query:       gi|336252209|ref|YP_004595316.1|  [L=154]
Description: hypothetical protein Halxa_0798 [Halopiger xanaduensis SH-6]
Scores for complete 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-18   67.3   0.0    2.2e-18   67.1   0.0    1.0  1  NYN            NYN domain
  ------ inclusion threshold ------
       0.06   13.8   0.1        4.9    7.7   0.0    2.0  2  CoA_binding_2  CoA binding domain
       0.13   12.3   0.3       0.26   11.2   0.3    1.6  1  ADH_zinc_N     Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   3.7e-22   2.2e-18       2     147 .]      21     153 ..      20     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 3.7e-22
                               NYN   2 vavfiDgenlpvpakgkevdyrklleeirskgelvraraygnwedeeqnkfqdalsstgikvkhkplkkrggsgkka 78 
                                       v++f+Dg n++   ++ +vd++ l++++r  g++ ++r y++  + +  ++ +a ++ g++v +           ++
  gi|336252209|ref|YP_004595316.1|  21 VGLFVDGPNVFR--DEFDVDLNDLRDAARDLGRVGVIRLYLD--EHATPGLIQAAEARGFEVIVT---------SGD 84 
                                       899*********..6678************************..44456777999*****88664.........589 PP

                               NYN  79 vDvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaadefisle 147
                                       vDv+lavda+ l    ++d++ + s+D DF p++e++   g++++ ++  +   s++L++aad+ i+++
  gi|336252209|ref|YP_004595316.1|  85 VDVKLAVDATALGSAGTIDRLAIASRDTDFKPVLEHAGTVGIETIAIAPGSYGRSDALQNAADQAITID 153
                                       ******************************************999999766699**********99875 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0051        31      53      85 ..      49      81 ..      25      99 .. 0.77
   2 ?    7.7   0.0   0.00083       4.9      52     101 ..      98     148 ..      80     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0051
                                      ..T--EEEE-S-HHHHGGGHHHHHHH--SEEEE CS
                     CoA_binding_2 53 pepvdlvdvftppeatpeivkealalgakavwl 85
                                       + v ++ +++  +atp ++++a+a+g ++++ 
  gi|336252209|ref|YP_004595316.1| 49 LGRVGVIRLYLDEHATPGLIQAAEARGFEVIVT 81
                                      44566999*******************998875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00083
                                       ...T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT..---HHHHHHHHHT CS
                     CoA_binding_2  52 dpepvdlvdvftppeatpeivkealalgakavwlqpg..sedeeaaelaeea 101
                                       + +++d + ++ + ++  ++++ a+++g++++ + pg   +++++ ++a+ +
  gi|336252209|ref|YP_004595316.1|  98 SAGTIDRLAIASRDTDFKPVLEHAGTVGIETIAIAPGsyGRSDALQNAAD-Q 148
                                       468999999****************************5444444444444.3 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   4.4e-05      0.26       6      60 ..      67     127 ..      66     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHTT-EEEEEESSHH.HHHH.HHHTTESEEEET....TTC.HHHHHHHHHTTTSSEE CS
                        ADH_zinc_N   6 avqlAkalGaeviavdssee.klel.akklGadeviny....kea.dlverikeltggegvd 60 
                                       ++q+A a G+evi+++++ + kl+  a  lG   +i++    +++ d++  ++ +  + g+ 
  gi|336252209|ref|YP_004595316.1|  67 LIQAAEARGFEVIVTSGDVDvKLAVdATALGSAGTIDRlaiaSRDtDFKPVLEHAG-TVGIE 127
                                       69*************99987566542566899999999888855447776665554.44555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); 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:                         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: 00:00:00.40
# Mc/sec: 1158.44
//
Query:       gi|336252210|ref|YP_004595317.1|  [L=683]
Description: Thermitase [Halopiger xanaduensis SH-6]
Scores for complete 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-48  165.5  11.7    2.6e-48  164.8  11.7    1.3  1  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.8  11.7   1.4e-52   2.6e-48       3     298 .]     161     408 ..     159     408 .. 0.93

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 1.4e-52
                                       T-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   3 gvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanapee 79 
                                       +v+++++D G++++hp l ++      ++d+ ++ g  f+g  s+++ +  +++       HGthv Giaa+++++ 
  gi|336252210|ref|YP_004595317.1| 161 DVTISIVDQGIQYDHPALADN------MDDSVSNHGDVFTGYGSDPYPVAGDEQ-------HGTHVGGIAAGGTDDG 224
                                       79*****************55......77888889999*********9998877.......************7777 PP

                                       SSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.CCT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  80 gekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsiealainravnkkgv 156
                                        +  g+  ++++ls+++ld sg+ +   +++++ai++++  ++d++n+slg +ts   t rs    a+++a  ++gv
  gi|336252210|ref|YP_004595317.1| 225 TGHAGIS-NCSLLSARALDRSGQGAL--SDIADAIQWSVDAGADIVNLSLG-ATSGYYTLRS----ACDYAA-NNGV 292
                                       7777775.**************9985..9**********************.8888888876....9*****.89** PP

                                       EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 157 lvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgnivstwsrqsn 233
                                       l+v ++GN+g          +v +p+ ++ v++v a+t+++++a+fS++G+ +      di+apG++i+s +++++ 
  gi|336252210|ref|YP_004595317.1| 293 LLVGATGNSG--------ANSVAYPAAYDDVMAVTAVTSNDSLASFSNTGSRV------DITAPGTQILSAVPWDD- 354
                                       **********........7899*****************************98......6****************. PP

                                       HHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 234 nsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdlgkadniesfaqGaG 298
                                              y  msGTSmA+P+++g+a l+lsa+p+l+  ++r+ l  tA d+      +s+aqGaG
  gi|336252210|ref|YP_004595317.1| 355 -------YGRMSGTSMAAPVVSGVAGLVLSAYPDLSGGELRQHLKDTAVDV----GLSSYAQGAG 408
                                       .......*****************************************665....6889999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (683 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.23s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 5075.74
//
Query:       gi|336252211|ref|YP_004595318.1|  [L=383]
Description: Aminomethyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-80  270.9   0.0    1.3e-80  270.5   0.0    1.2  1  GCV_T     Aminomethyltransferase folate-binding domain
    1.5e-21   76.1   0.1      3e-21   75.1   0.1    1.5  1  GCV_T_C   Glycine cleavage T-protein C-terminal barrel domain
  ------ inclusion threshold ------
       0.16   12.1   0.4        3.8    7.7   0.1    2.2  2  SoxG      Sarcosine oxidase, gamma subunit family


Domain annotation for each model (and alignments):
>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.5   0.0   2.2e-84   1.3e-80       4     256 ..      11     278 ..       8     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: 270.5 bits;  conditional E-value: 2.2e-84
                             GCV_T   4 rhkalgakfvefagwemPvqYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgkaty 80 
                                        h ++gakf+ef+gw+mPv++  +si+ eh avre++g+fDvShmg+i+v+Gpda++l+qrl+tnd+s+l +g+a+y
  gi|336252211|ref|YP_004595318.1|  11 THDERGAKFTEFGGWDMPVEF--DSIRTEHAAVREDVGIFDVSHMGQIHVTGPDATELMQRLTTNDVSRLGVGDAQY 85 
                                       699******************..****************************************************** PP

                             GCV_T  81 tlllnedGgvidDlivarld.............edefllvvnaankekdl.awlekaaekkdldvevedvteelall 143
                                       +++++edG +idD++++rl              e ++l++ na++ e  + +w+ +++e +dl+++v+++t+e+a++
  gi|336252211|ref|YP_004595318.1|  86 AAITDEDGTIIDDTVIYRLPdegetpqgsredgEATYLFIPNAGTDESTHeRWIGYRNE-WDLEATVDNRTDEYAMF 161
                                       ********************7777777777654469***********999899999555.***************** PP

                             GCV_T 144 alqGPkarevlskll.........gadlselkffsfaevelaggkkvlvsRtgytGedGfeiyipaeeaeelweaLl 211
                                       a+qGP+a++++ +++         + ++++l+ f+++e +++ g++++ +RtgytGedGfe+++p+ eae++w a  
  gi|336252211|ref|YP_004595318.1| 162 AVQGPNAADLVGDVVdvadtadaiDGSVTDLSRFEATESTID-GVDCWTARTGYTGEDGFELIVPWPEAERIWSAF- 236
                                       ***************998877644444**************9.********************************9. PP

                             GCV_T 212 eagkeegvkpaGlgArdtlRlEaglrlyghdldee...ttPleaglgw 256
                                             +++p+GlgArdtlR+Eagl l g+d+d+e    tP+eag+g+
  gi|336252211|ref|YP_004595318.1| 237 ------DCQPCGLGARDTLRIEAGLLLAGQDFDPEdnpRTPYEAGIGF 278
                                       ......79***************************9999******987 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.1   5.1e-25     3e-21       3      80 .]     304     381 ..     303     381 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 5.1e-25
                           GCV_T_C   3 lvgleld.dgapllrggepilr.dgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaevvkkp 77 
                                       lvg++l  +g  ++r+g+ i + + +v+G+vTSg++sptl+++i+l+yv+ e+a++gt+++v vrg+  +a+v ++p
  gi|336252211|ref|YP_004595318.1| 304 LVGFQLIdRG--VPRHGYDITNpESRVIGTVTSGTMSPTLEQAIGLGYVPVEYADPGTTLQVVVRGQSKKARVEQTP 378
                                       9*****7355..88******96588999************************************************* PP

                           GCV_T_C  78 fyD 80 
                                       f D
  gi|336252211|ref|YP_004595318.1| 379 FID 381
                                       *98 PP

>> SoxG  Sarcosine oxidase, gamma subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00063       3.8      65     112 ..      46      90 ..      31     100 .. 0.78
   2 ?    2.4   0.0     0.027   1.6e+02     105     140 ..     197     235 ..     149     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00063
                              SoxG  65 svvdlShgrvlisisGakaeavlakltaiDlsadaFpvGaaaatilgk 112
                                        + d+Sh   +i+++G+ a +++++lt+ D+s     vG a+ +++ +
  gi|336252211|ref|YP_004595318.1|  46 GIFDVSHMG-QIHVTGPDATELMQRLTTNDVSR--LGVGDAQYAAITD 90 
                                       567899964.79******************974..6788887776665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.027
                              SoxG 105 aaatilgkvevvil...rtgsdafevlvfrsFaeslwka 140
                                       a+++ ++ v +       tg+d fe++v    ae +w+a
  gi|336252211|ref|YP_004595318.1| 197 ATESTIDGVDCWTArtgYTGEDGFELIVPWPEAERIWSA 235
                                       555566666666662224789*******99999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2807.14
//
Query:       gi|336252212|ref|YP_004595319.1|  [L=127]
Description: glycine cleavage system H protein [Halopiger xanaduensis SH-6]
Scores for 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-44  148.8   0.0    6.7e-44  148.7   0.0    1.0  1  GCV_H          Glycine cleavage H-protein
     0.0071   16.1   0.2      0.013   15.3   0.2    1.4  1  Biotin_lipoyl  Biotin-requiring enzyme
  ------ inclusion threshold ------
       0.16   12.0   0.0       0.23   11.5   0.0    1.2  1  RnfC_N         RnfC Barrel sandwich hybrid domain


Domain annotation for each model (and alignments):
>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.7   0.0   1.1e-47   6.7e-44       1     118 [.       9     125 ..       9     127 .] 0.97

  Alignments for each domain:
  == domain 1  score: 148.7 bits;  conditional E-value: 1.1e-47
                                       -EE-TTSEEEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GG CS
                             GCV_H   1 lyytkehewvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNek 77 
                                       ++y ++hew  +  dgv++vGitdfaq+elgdvvfvelp++g+ v+++ ++++vEs Ka+s++yapvsGevv vNe+
  gi|336252212|ref|YP_004595319.1|   9 RRYLESHEWALE-TDGVVRVGITDFAQDELGDVVFVELPDEGDDVDQETEFGVVESIKAVSDLYAPVSGEVVSVNED 84 
                                       58*******987.678************************************************************* PP

                                       GTT-TTHHHH-TTTTT--EEEEES-GGGGGGSEEHHHHHHH CS
                             GCV_H  78 leeepeliNkdpyeegWliklklsnleeleeLlsaeeyekl 118
                                       l + pel+N+dp++egW++ +++++  ele Llsa+eye+ 
  gi|336252212|ref|YP_004595319.1|  85 LFDAPELVNEDPFGEGWMLEIEPDDIGELEALLSADEYEDQ 125
                                       **************************************976 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   2.2e-06     0.013      22      57 ..      47      82 ..      36      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-06
                                      STTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEES CS
                     Biotin_lipoyl 22 kvGdkVkagqvlaeveamKmemeieapkaGvvkeil 57
                                       +Gd V ++    +ve+ K++ ++ ap++G v+++ 
  gi|336252212|ref|YP_004595319.1| 47 DEGDDVDQETEFGVVESIKAVSDLYAPVSGEVVSVN 82
                                      58******************************9985 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 ?   11.5   0.0   3.8e-05      0.23      48      87 ..      48      88 ..      42      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                            RnfC_N 48 vgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlvah 87
                                      +gd V +    +  e+    +  +a+vsG+V+++++ l   
  gi|336252212|ref|YP_004595319.1| 48 EGDDVDQETEFGVVESiKAVSDLYAPVSGEVVSVNEDLFDA 88
                                      6888888888888887445679************9877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 982.46
//
Query:       gi|336252213|ref|YP_004595320.1|  [L=358]
Description: hypothetical protein Halxa_0802 [Halopiger xanaduensis SH-6]
Scores for 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-10   39.3   0.0    7.2e-10   38.5   0.0    1.3  1  GIDE      E3 Ubiquitin ligase


Domain annotation for each model (and alignments):
>> GIDE  E3 Ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0     4e-14   7.2e-10      26     107 ..     205     291 ..     195     321 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 4e-14
                              GIDE  26 ersvpFvlrDdtgrVlVdpegaeielttvldefepaea.srvtlllgffsldl....ek..tlGyryeEkvLpvgkr 95 
                                        r++pF+lrDdtgrVlVdp++a++ l+ +  +  p+ a +r+  +++   ++     ++   ++  y E  L +g+ 
  gi|336252213|ref|YP_004595320.1| 205 DRRQPFWLRDDTGRVLVDPDRAKLRLERTASR--PVAAdERPAEAIATRLREAiddaDErrDRARVYHEAALEPGTA 279
                                       5899***************************9..6666666666666666665654311469*************** PP

                              GIDE  96 vtvvGeaqsded 107
                                       v v+G+a+  ed
  gi|336252213|ref|YP_004595320.1| 280 VSVLGVAVVPED 291
                                       *****9965555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2836.72
//
Query:       gi|336252214|ref|YP_004595321.1|  [L=51]
Description: hypothetical protein Halxa_0803 [Halopiger xanaduensis SH-6]
Scores for 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:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 387.96
//
Query:       gi|336252215|ref|YP_004595322.1|  [L=236]
Description: XRE family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for complete 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-09   38.0   0.2    3.9e-09   36.7   0.2    1.6  1  HTH_31          Helix-turn-helix domain
    1.2e-08   34.8   0.0    3.3e-08   33.4   0.0    1.7  2  HTH_3           Helix-turn-helix
    3.1e-06   27.1   0.0    7.8e-06   25.8   0.0    1.7  1  HTH_19          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.024   14.2   0.0       0.12   11.9   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.032   14.1   0.0       0.08   12.8   0.0    1.7  1  MarR_2          MarR family
      0.067   13.2   0.0       0.19   11.7   0.0    1.8  1  HTH_11          HTH domain
       0.07   13.0   0.0       0.17   11.7   0.0    1.6  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.085   13.3   0.0       0.21   12.1   0.0    1.7  1  HTH_26          Cro/C1-type HTH DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.2   1.7e-12   3.9e-09       3      55 ..      25      77 ..      25      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.7e-12
                            HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55
                                      Ga+Lr +R+   +sq+++Ae lgvs s +s++E+Grr  p  +v+ +l+++l 
  gi|336252215|ref|YP_004595322.1| 25 GATLRKWRTDFDVSQTDLAEELGVSSSVISDYESGRRESPGIGVVGRLVEGLL 77
                                      899*********************************************99875 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.9   8.7e+03      13      19 ..       8      14 ..       3      15 .. 0.65
   2 !   33.4   0.0   1.5e-11   3.3e-08       1      46 [.      28      74 ..      28      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.9
                                      HHHHHHH CS
                             HTH_3 13 eeLAekl 19
                                      +eLAek+
  gi|336252215|ref|YP_004595322.1|  8 RELAEKI 14
                                      5677664 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 1.5e-11
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklak 46
                                      l+++R   + sq++LAe+lGvs s is++E+G + +P + ++ +l +
  gi|336252215|ref|YP_004595322.1| 28 LRKWRTDFDVSQTDLAEELGVSSSVISDYESGrRESPGIGVVGRLVE 74
                                      799*****************************877788888877766 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   3.5e-09   7.8e-06       1      50 [.      25      74 ..      25      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.5e-09
                            HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiae 50
                                      G  L++ R  +  +q +lae+lg+s s is +E+g+++ p+++++ +++e
  gi|336252215|ref|YP_004595322.1| 25 GATLRKWRTDFDVSQTDLAEELGVSSSVISDYESGRRESPGIGVVGRLVE 74
                                      567999***********************************888844433 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 ?   -2.0   0.0       1.3   2.8e+03      21      27 ..       8      14 ..       6      15 .. 0.83
   2 ?   11.9   0.0   5.4e-05      0.12      18      36 ..      37      55 ..      36      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.3
                            HTH_24 21 reLAerl 27
                                      reLAe++
  gi|336252215|ref|YP_004595322.1|  8 RELAEKI 14
                                      8****97 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.4e-05
                            HTH_24 18 isqreLAerlglSpstvnr 36
                                       sq++LAe+lg+S+s ++ 
  gi|336252215|ref|YP_004595322.1| 37 VSQTDLAEELGVSSSVISD 55
                                      69*************9886 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.6e-05      0.08      15      39 ..      21      54 ..      14      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-05
                                      HCTTTS.........EEEHHHHHHHHTSSHHHHH CS
                            MarR_2 15 grrpgr.........dltvgelarrlglsksavs 39
                                       + pg          d+++++la++lg+s s +s
  gi|336252215|ref|YP_004595322.1| 21 SDDPGAtlrkwrtdfDVSQTDLAEELGVSSSVIS 54
                                      44444488888888899**************998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.4e-05      0.19      14      33 ..      35      54 ..      29      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.4e-05
                            HTH_11 14 gpisgeeLAeeLnvSrrtvr 33
                                       ++s  +LAeeL+vS +++ 
  gi|336252215|ref|YP_004595322.1| 35 FDVSQTDLAEELGVSSSVIS 54
                                      459************99985 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 ?   11.7   0.0   7.8e-05      0.17      10      34 ..      38      62 ..      37      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.8e-05
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkq 34
                                      +q+ LAe+lgvs++ +s+  +g+++
  gi|336252215|ref|YP_004595322.1| 38 SQTDLAEELGVSSSVISDYESGRRE 62
                                      79***************99888776 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 ?   12.1   0.0   9.2e-05      0.21       2      38 ..      28      64 ..      27      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.2e-05
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkperv 38
                                      Lr++  d ++++++La+ +g+s++ +s + +g+ e++
  gi|336252215|ref|YP_004595322.1| 28 LRKWRTDFDVSQTDLAEELGVSSSVISDYESGRRESP 64
                                      888889999*********************9986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1729.15
//
Query:       gi|336252216|ref|YP_004595323.1|  [L=259]
Description: molybdopterin binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-29  102.4   0.1    2.5e-29  101.8   0.1    1.3  1  MoCF_biosynth  Probable molybdopterin binding domain
  ------ inclusion threshold ------
        6.3    7.0   7.7         15    5.8   0.9    3.2  3  DUF5132        Protein of unknown function (DUF5132)


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8   0.1   2.8e-33   2.5e-29       1     137 [.       4     168 ..       4     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 2.8e-33
                                       EEEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHH CS
                     MoCF_biosynth   1 avitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpea 77 
                                       a+++vGdell+g++++tn+++la +l+e+g +v+++ ++pDd +ei++ + ++ +e d++i+tGG+G tpdD+t+ea
  gi|336252216|ref|YP_004595323.1|   4 AIVSVGDELLAGTTTNTNAAWLAGRLTERGSTVHRILTIPDDRAEIADYVGRWRDEFDAVIVTGGIGGTPDDMTVEA 80 
                                       79************************************************9997888******************** PP

                                       HHHHHSEE-HHHHHHHHHHHHHHCC.................................TTSHGGGGGGE.EETTEEE CS
                     MoCF_biosynth  78 laklfekelegfeeafrrvslkpgk.................................pvgvapgailsravgktii 121
                                        a+ +++ l+ +e + + ++ k  +                                 +   apg+i++     +++
  gi|336252216|ref|YP_004595323.1|  81 AAEGLDRDLVVHERIYDDLREKAAEfreenpemvaeydleldleaaaslpegatpivvDEAWAPGCIVE-----NVY 152
                                       **********************988************************77777555544455665555.....69* PP

                                       EE-SSHHHHHHHHHHH CS
                     MoCF_biosynth 122 gLPGspkavkealeei 137
                                       +  G p ++k++++e+
  gi|336252216|ref|YP_004595323.1| 153 VFAGIPEEMKAMFREV 168
                                       *************987 PP

>> DUF5132  Protein of unknown function (DUF5132)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.015   1.4e+02      32      41 ..      74      83 ..      68      86 .. 0.85
   2 ?    5.8   0.9    0.0017        15      16      41 ..      95     120 ..      94     127 .. 0.89
   3 ?    0.7   0.1     0.065   5.8e+02      28      44 ..     158     174 ..     154     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.015
                           DUF5132 32 eDlvAEvkAE 41
                                      +D++ E++AE
  gi|336252216|ref|YP_004595323.1| 74 DDMTVEAAAE 83
                                      7********9 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0017
                           DUF5132  16 lyeearkaaaevGEeLeDlvAEvkAE 41 
                                       +y  +r+ aae+ Ee   +vAE   E
  gi|336252216|ref|YP_004595323.1|  95 IYDDLREKAAEFREENPEMVAEYDLE 120
                                       7889******************7665 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.065
                           DUF5132  28 GEeLeDlvAEvkAEllA 44 
                                        Ee++ +  Ev+AE  +
  gi|336252216|ref|YP_004595323.1| 158 PEEMKAMFREVEAEFRG 174
                                       589999999*****765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2064.11
//
Query:       gi|336252217|ref|YP_004595324.1|  [L=391]
Description: family 1 extracellular solute-binding protein [Halopiger xanaduensis SH-6]
Scores for 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   57.3   0.1    2.8e-15   56.9   0.1    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    1.2e-13   51.1   0.0    1.7e-13   50.6   0.0    1.2  1  SBP_bac_6   Bacterial extracellular solute-binding protein
    8.1e-11   42.4   0.2    1.2e-10   41.9   0.2    1.2  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    4.5e-08   33.1   0.0    6.9e-08   32.5   0.0    1.3  1  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.1   6.3e-19   2.8e-15       6     259 ..      92     336 ..      87     350 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 6.3e-19
                                       HHHH-TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG..GSTTHHH-HHHHHTT-- CS
                         SBP_bac_8   6 fekktgvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladls..dldnlddltdalaavgy 80 
                                       +e+++gv+v++   ++nd+   ++   ++g+ p  dv++a++++     +egl++++    ++nld+  d ++    
  gi|336252217|ref|YP_004595324.1|  92 YEDEYGVDVRL-HGGWNDILVDIRQ--SSGEPP-YDVTVADGYFYHVGRQEGLFEPVRtdNVPNLDGAIDHYTEIRT 164
                                       89999*****9.67899*9999999..699977.69****9999999999*****9987566999997676777766 PP

                                       TS.----EEEEEEE-EEEEEHHHHHHS.---BHHHHHHHHHHHHHH-SEGG---GGGGGGTHH....ETTEE---H. CS
                         SBP_bac_8  81 dgklygvPyasetpyvliynkdllekaedpktwdellaaakklkgkfglpdpasgwlqaalla....kdgksldddg 153
                                           ygvP++ + p  +iy++d+ +    p+tw++l a  + + + +g+  ++ +w++  + a    +d +   + +
  gi|336252217|ref|YP_004595324.1| 165 TE--YGVPVD-GAPCNIIYREDM-DF--EPETWADLGA--DPVDNSTGIGIDTGFWWFPVHAAavgmDDRELAGELY 233
                                       66..******.6689*****999.54..7*********..***99***99999889888888866665555555553 PP

                                       .HHH..HHHHHHHHHHHHTT-EE-S..--SSTTTTTSBSEEE.E-TTHHHHHH-TTTSEEEE--S--EEEEE.EEEE CS
                         SBP_bac_8 154 gkdgl.kealellkklkdngktydtgadavsefanGevafti.ngswdiaaaqkagkklgaivpkqgsfagg.kgla 227
                                        ++ l + +++ l++++ n  + ++g d++++f +G++  ++ ++++ + ++++  + l+ ++p +   +g+ ++++
  gi|336252217|ref|YP_004595324.1| 234 -EESLhDSVFDQLRSWNINS-WASSGQDIWQAFDDGTIDVAQwYFEQTAYDIDD-HDGLTHTLPEE--TTGYlNNWC 305
                                       .333359*********9666.568999**************9556666777666.67789999987..5666257** PP

                                       EBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH CS
                         SBP_bac_8 228 vpknaknedlaAldFlkwltspenqaalaekt 259
                                       v ++++ +d+ A +Fl +l+s+e q+ ++e +
  gi|336252217|ref|YP_004595324.1| 306 VVNGTERRDQ-AEEFLDFLLSAETQTTWSESS 336
                                       *********9.*****************9965 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   3.7e-17   1.7e-13       2     220 ..     120     351 ..     119     375 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 3.7e-17
                         SBP_bac_6   2 plpdlilsfdkdflekfieeglfqpldpanlpnvnkdfa.eeglkdpdgkyypygvgplvlavnkdrlkgrpvPksW 77 
                                       p +d+++  d +f+    +eglf+p+ ++n+pn++  ++ +++++    + +p++  p  +++ +d  + +  P++W
  gi|336252217|ref|YP_004595324.1| 120 PPYDVTV-ADGYFYHVGRQEGLFEPVRTDNVPNLDGAIDhYTEIRTT-EYGVPVDGAPCNIIYREDM-DFE--PETW 191
                                       7899999.99*************************999776666664.5556*************99.566..**** PP

                         SBP_bac_6  78 aDLldPeykgkvalpgnng..sdlfealllalyk.........dfgedgvkkllrnlkanlhpaqmvkaagslesge 143
                                       aDL  +   ++ ++  + g    + +a+++ +           +   d v + lr++  n   + +++++++ + g+
  gi|336252217|ref|YP_004595324.1| 192 ADLGADPVDNSTGIGIDTGfwWFPVHAAAVGMDDrelagelyeESLHDSVFDQLRSWNINSWASSGQDIWQAFDDGT 268
                                       ****9999******99999555555555555555*****88844448888888888888888888************ PP

                         SBP_bac_6 144 pavsvvpyffadilpekkkgknlkvvwPedGalvspifmlvkkg.kkkelakafidfllspevqailakaggvfPvv 219
                                         ++v+ ++f +++   ++ + l  + Pe+ ++ + + ++v++g +++++a++f+dflls+e+q+ +++++   P+ 
  gi|336252217|ref|YP_004595324.1| 269 --IDVAQWYFEQTAYDIDDHDGLTHTLPEE-TTGYLNNWCVVNGtERRDQAEEFLDFLLSAETQTTWSESS---PAL 339
                                       ..****************************.777777777777778***********************98...554 PP

                         SBP_bac_6 220 ...........t 220
                                                  +
  gi|336252217|ref|YP_004595324.1| 340 fcnaemeyandL 351
                                       444444433322 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.2   2.6e-14   1.2e-10       9     314 ..      83     329 ..      77     330 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 2.6e-14
                                       HHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHT.TSBECCHHHHHHTTEC CS
                         SBP_bac_1   9 alqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlaka.glllpldpyvkaylap 84 
                                        +++ v+  +e  ++g++V++   g+++      ++ ++G +p+Dv   d++++ +  ++ gl++p+ ++ +++l  
  gi|336252217|ref|YP_004595324.1|  83 RFEESVVPLYED-EYGVDVRLHG-GWNDILV--DIRQSSGEPPYDVTVADGYFY-HVGRQeGLFEPVRTDNVPNLDG 154
                                       577777777877.78******87.5888877..66666666********65555.455566********99999543 PP

                                       TTCCTEEEEHHHHTHHHHCEEE...ES.EEEEE.EEEEEEETTTHHCTTGGG.SHBHHHHHHHHHHHHHHCTCTHCC CS
                         SBP_bac_1  85 gvkdaadklsssvlpkildskv...ly.vPlya.argliYNkdlfekagldp.pwtWdelveaakklkekgkkpigg 155
                                         +           +++ +       y vP+++ +  +iY       +++d  p+tW +l +  +     ++++   
  gi|336252217|ref|YP_004595324.1| 155 AID-----------HYT-E--IrttEYgVPVDGaPCNIIY------REDMDFePETWADLGADPV-----DNST--- 203
                                       322...........222.1..1235699****74777777......566666799***9994443.....4444... PP

                                       HCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHT CS
                         SBP_bac_1 156 arggsasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfea 232
                                          g + +t+++++   a+  g            ++       y + l++ ++++    + +++ ++g++  ++f  
  gi|336252217|ref|YP_004595324.1| 204 ---GIGIDTGFWWFPVHAAAVG-----------MDDRELAGELYEESLHDSVFDQLRSWNINSWASSGQDIWQAFDD 266
                                       ...6788999999998888899...........6777777999********************************** PP

                                       TSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHT CS
                         SBP_bac_1 233 GeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfll 309
                                       G++++a  +  +           a+++d+++   ++    lP +++g     +  ++ +++g+  +++A++Fldfll
  gi|336252217|ref|YP_004595324.1| 267 GTIDVAQWYFEQ----------TAYDIDDHDGLTHT----LPEETTG-----YLNNWCVVNGTERRDQAEEFLDFLL 324
                                       *****8766544..........44444444444433....6888888.....9999********************* PP

                                       SHHHH CS
                         SBP_bac_1 310 speaq 314
                                       s+e q
  gi|336252217|ref|YP_004595324.1| 325 SAETQ 329
                                       ***98 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   1.5e-11   6.9e-08      16     225 ..      88     333 ..      75     335 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.5e-11
                                       HHHHHHHHH---EEEEESSHHHHHHHHHHH.....-SEEEESSH.HHHHHHHHGGGGG................... CS
                        SBP_bac_11  16 laaaFeahtgvkvevsaggsgklarqiadga...rpDvwipassawlellaaaglvqa................... 70 
                                       +++ +e ++gv+v++ +g    l++ i++++   ++Dv +++        +++gl  +                   
  gi|336252217|ref|YP_004595324.1|  88 VVPLYEDEYGVDVRLHGGWNDILVD-IRQSSgepPYDVTVADGY-FYHVGRQEGLFEPvrtdnvpnldgaidhytei 162
                                       6677777788888876555444444.433322378888888765.44667888888888888888888888889999 PP

                                       ...GG-EEEEEEEEEEEESTT-TT---SHHHHHHS....................S--EEEE--T-TTTTHH.HHHH CS
                        SBP_bac_11  71 ...esavplassplviavpkgnpkkikgwadLlkp....................glklavadPttspsGlaalall 124
                                          e +vp+ ++p  i++++++   + +wadL+++                       +++ d  ++ +G   ++ l
  gi|336252217|ref|YP_004595324.1| 163 rttEYGVPVDGAPCNIIYREDMDFEPETWADLGADpvdnstgigidtgfwwfpvhAAAVGMDD--RELAGELYEESL 237
                                       99999*****************99**********86888777766554433322222333333..344444444555 PP

                                       GGG--HHHHHHHHHT.EEEEESSHHHHHHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE CS
                        SBP_bac_11 125 eaagaqellkalekk.vvklgessrqlltaveageadagivyeseakaaengdkleavylpeglnldpldypaavlk 200
                                       +       +++l+++ +  ++ s  ++ +a+++g +d++  y  ++++    +++   +lpe++   +l    +v++
  gi|336252217|ref|YP_004595324.1| 238 HD----SVFDQLRSWnINSWASSGQDIWQAFDDGTIDVAQWYFEQTAYDIDDHDGLTHTLPEETTG-YL-NNWCVVN 308
                                       54....58999999878889999999************9977555555656667778899999986.45.4799*** PP

                                       -TT--HHHHHHHHHTTSHHHHHHHH CS
                        SBP_bac_11 201 kaakreaAraFlafLrspeaqailr 225
                                       ++ +r  A++Fl+fL+s+e+q+++ 
  gi|336252217|ref|YP_004595324.1| 309 GTERRDQAEEFLDFLLSAETQTTWS 333
                                       *********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.49u 0.20s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3196.61
//
Query:       gi|336252218|ref|YP_004595325.1|  [L=378]
Description: polyamine-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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  119.5   0.0    2.6e-34  118.7   0.0    1.4  1  ABC_tran     ABC transporter
    1.8e-15   56.8   2.3    1.6e-14   53.8   0.2    3.0  2  TOBE_2       TOBE domain
    2.2e-07   31.0   0.2     0.0015   18.4   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0056   17.1   0.1     0.0099   16.3   0.1    1.6  1  AAA_16       AAA ATPase domain
     0.0057   16.9   0.8      0.028   14.7   0.7    2.0  1  AAA_22       AAA domain
     0.0059   16.1   0.0       0.34   10.3   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.022   14.6   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.015   15.1   0.0      0.035   13.8   0.0    1.6  1  AAA_29       P-loop containing region of AAA domain
      0.028   13.6   0.0      0.033   13.4   0.0    1.2  1  G-alpha      G-protein alpha subunit
      0.059   13.1   0.4        0.2   11.4   0.0    2.0  3  AAA_30       AAA domain
      0.094   12.4   0.0       0.16   11.7   0.0    1.3  1  AAA_24       AAA domain
      0.098   12.8   0.1       0.21   11.8   0.1    1.7  1  AAA_33       AAA domain
       0.11   13.1   0.1       0.31   11.6   0.1    2.1  1  AAA_18       AAA domain
       0.11   12.9   1.0        1.3    9.5   1.0    2.2  1  AAA          ATPase family associated with various cellular a
       0.18   11.7   0.1       0.31   11.0   0.1    1.3  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 !  118.7   0.0   2.2e-37   2.6e-34       2     136 ..      20     161 ..      19     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 2.2e-37
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++vs ++  ge++ ++G++G+GKSt l+++agl++pt G i++ ++d+++   + ++++ ++++q+  lfp++tv e
  gi|336252218|ref|YP_004595325.1|  20 EDVSATIADGELLCLLGPSGSGKSTTLRMIAGLESPTDGGIHVGDEDVTD--QPAYERNTATVFQDWALFPHKTVLE 94 
                                       799**********************************************9..99*********************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e++e+++k+l+++++ +  d+      ++LSgGqkqrvalar+l+ +p++lllDEp 
  gi|336252218|ref|YP_004595325.1|  95 NvafglkmhgvpkeERRERAQKMLERVEMGDYGDQDP----TNLSGGQKQRVALARSLAVEPDVLLLDEPL 161
                                       ***********98888888999999999999888777....*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0021       2.5      49      72 ..     263     284 ..     233     287 .. 0.62
   2 !   53.8   0.2   1.3e-17   1.6e-14       1      76 []     278     367 ..     278     367 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0021
                            TOBE_2  49 qpnadrdsalapGdtVelswdpdd 72 
                                         ++d  ++l++G++V+ls++p+ 
  gi|336252218|ref|YP_004595325.1| 263 EISTD--ETLDEGEQVTLSLRPEV 284
                                       22233..589***********996 PP

  == domain 2  score: 53.8 bits;  conditional E-value: 1.3e-17
                            TOBE_2   1 laiRPEklrla...............aagg.anglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapG 61 
                                       l++RPE l+++               a+gg ++++ Gt+e+v+y+Gs++ry v+++g +l +v++++ad +  +++G
  gi|336252218|ref|YP_004595325.1| 278 LSLRPEVLSIEpapdatpvaneaqpiADGGsQTATVGTIENVIYRGSTVRYAVDVDGSSL-FVERSVAD-AGSFDAG 352
                                       79***************999999888777756799***********************99.99*****9.679**** PP

                            TOBE_2  62 dtVelswdpddavvl 76 
                                       d+++++wd  d++++
  gi|336252218|ref|YP_004595325.1| 353 DEIRIEWDETDVLAF 367
                                       ***********9987 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 !   11.1   0.0   0.00022      0.26       3      24 ..      33      54 ..      31      95 .. 0.82
   2 !   18.4   0.0   1.3e-06    0.0015     219     274 ..     110     168 ..      57     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                            AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                      +l Gp gsGKS+ L+ + +l +
  gi|336252218|ref|YP_004595325.1| 33 CLLGPSGSGKSTTLRMIAGLES 54
                                      799**************99944 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.3e-06
                            AAA_21 219 r......gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkl 274
                                       r       +  +e+gd+++ ++++lS G+k+  al+ +l+  +   ++ll+DEp ++L+ +l
  gi|336252218|ref|YP_004595325.1| 110 RreraqkMLERVEMGDYGDQDPTNLSGGQKQRVALARSLAVEP---DVLLLDEPLSNLDKRL 168
                                       033344478899********************9*******999...************9876 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   0.1   8.3e-06    0.0099      23      46 ..      28      51 ..      16     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.3e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellr 46
                                      ++el+ l G+sG+GKs+ +r+++ 
  gi|336252218|ref|YP_004595325.1| 28 DGELLCLLGPSGSGKSTTLRMIAG 51
                                      338999**************9984 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.7   2.4e-05     0.028       6      70 ..      30     102 ..      26     192 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee................erpevvfvtlpsstsskdl.lrellralg 65 
                                        +l++ G+sG+GK+t+lr+++        +++                e     + t+++  +++ +  + +l+++ 
  gi|336252218|ref|YP_004595325.1|  30 ELLCLLGPSGSGKSTTLRMIAGLES----PTDggihvgdedvtdqpayE-----RNTATVFQDWALFpHKTVLENVA 97 
                                       57999**************998753....22245567777775333331.....44444444444444444444444 PP

                            AAA_22  66 lelka 70 
                                        +lk 
  gi|336252218|ref|YP_004595325.1|  98 FGLKM 102
                                       33333 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 ?    3.6   0.0     0.033        39      26      41 ..      31      46 ..      17      51 .. 0.81
   2 !   10.3   0.0   0.00028      0.34     134     200 ..     131     195 ..      74     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.033
                                      EEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnll 41
                                      + +++Gp GSGKs  l
  gi|336252218|ref|YP_004595325.1| 31 LLCLLGPSGSGKSTTL 46
                                      56899********866 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00028
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislree 200
                                       +++LSgG+k+ vala  +A++   p  + llDe  ++LD++  + +   l+e +++  + f+ ++++++
  gi|336252218|ref|YP_004595325.1| 131 PTNLSGGQKQRVALARSLAVE---PD-VLLLDEPLSNLDKRLSEDMQIELREIHEDveTTFVHVTHDQD 195
                                       449************999975...55.5689********999988888777666553355666666554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.9e-05     0.022      85     121 ..      14      51 ..       1      70 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                                       TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                        ++ ++e++++ ++d ++ +l+G+SG GKSt + ++++
  gi|336252218|ref|YP_004595325.1|  14 GDTLAVEDVSATIADgELLCLLGPSGSGKSTTLRMIAG 51 
                                       5556788999999998***************9999887 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 ?   13.8   0.0     3e-05     0.035      18      39 ..      25      46 ..      18      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-05
                            AAA_29 18 eidlkg.atlltGpsGsGKSTll 39
                                      +i   g    l GpsGsGKST l
  gi|336252218|ref|YP_004595325.1| 25 TIAD-GeLLCLLGPSGSGKSTTL 46
                                      5553.447889**********76 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.7e-05     0.033      26      51 ..      32      67 ..      15     224 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-05
                                      EEEEESTTSSHHHHHHHHHHHCS--..........- CS
                           G-alpha 26 llllGqseSGKsTilkqlkllykkg..........f 51
                                      l llG s+SGKsT+l+ +  l+ ++          +
  gi|336252218|ref|YP_004595325.1| 32 LCLLGPSGSGKSTTLRMIAGLESPTdggihvgdedV 67
                                      789***************999988777776555442 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   0.00016       0.2      12      40 ..      24      51 ..      19      62 .. 0.81
   2 ?   -2.9   0.0       3.8   4.5e+03      38      70 ..     176     208 ..     172     210 .. 0.83
   3 ?   -3.0   0.1       4.1   4.9e+03      52      72 ..     248     268 ..     242     277 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                            AAA_30 12 alltsgdrvavltGpAGtGKttalkalre 40
                                      a++++g+ + +l Gp G+GK+t+l+ ++ 
  gi|336252218|ref|YP_004595325.1| 24 ATIADGE-LLCLLGPSGSGKSTTLRMIAG 51
                                      4556665.9999*************9875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.8
                            AAA_30  38 lreaweaaggrviglAptgkaAkvLaeelgiea 70 
                                       lre++e+ + + + +++ +  A +La+ +gi a
  gi|336252218|ref|YP_004595325.1| 176 LREIHEDVETTFVHVTHDQDEAFTLADRIGIMA 208
                                       688888888899999999999999999999877 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.1
                            AAA_30  52 lAptgkaAkvLaeelgieast 72 
                                        A   ++A +L+e+l+i ++ 
  gi|336252218|ref|YP_004595325.1| 248 TANGVRVATELEEALEISTDE 268
                                       577778999999999987764 PP

>> AAA_24  AAA domain
   #    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       5      44 ..      32      69 ..      29     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                            AAA_24  5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfp 44
                                      +++ Gpsg+GK+t+++++    l   t++G +  d d  +
  gi|336252218|ref|YP_004595325.1| 32 LCLLGPSGSGKSTTLRMI--AGLESPTDGGIHVGDEDVTD 69
                                      699*************99..78888888888665555544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00017      0.21       2      33 ..      32      80 ..      31     204 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                            AAA_33  2 vllvGlpGsGKstlaerllkklg....avllssdt.............l 33
                                      + l G++GsGKst ++ ++  +     ++++   +             +
  gi|336252218|ref|YP_004595325.1| 32 LCLLGPSGSGKSTTLRMIAGLESptdgGIHVGDEDvtdqpayerntatV 80
                                      6789**********99885333345778888777734444443333330 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00026      0.31       2      42 ..      33      76 ..      32     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf....gvnlrdvakenglllevd 42
                                      +l G++G+GK+t  + ++ ++ +    g++++d    +++ +e++
  gi|336252218|ref|YP_004595325.1| 33 CLLGPSGSGKSTTLRMIAGLE-SptdgGIHVGDEDVTDQPAYERN 76
                                      799************998774.55688888888777777666665 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 ?    9.5   1.0    0.0011       1.3       1      21 [.      32      52 ..      32     207 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                                      EEEESSTTSSHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavake 21
                                      ++l Gp G GK+++ + +a  
  gi|336252218|ref|YP_004595325.1| 32 LCLLGPSGSGKSTTLRMIAGL 52
                                      589***************986 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00026      0.31      46      66 ..      30      50 ..      17      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                             Rad17 46 riLLisGPsGCgkstvvkvLs 66
                                      ++L + GPsG gkst++++++
  gi|336252218|ref|YP_004595325.1| 30 ELLCLLGPSGSGKSTTLRMIA 50
                                      58999************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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: 0.54u 0.21s 00:00:00.75 Elapsed: 00:00:00.36
# Mc/sec: 3127.08
//
Query:       gi|336252219|ref|YP_004595326.1|  [L=315]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for complete 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   51.3  15.7    1.1e-13   51.3  15.7    2.1  2  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 ?   -0.9   4.4     0.066   1.2e+03     109     174 ..      53     115 ..      29     123 .. 0.59
   2 !   51.3  15.7   6.1e-18   1.1e-13       3     178 ..     112     304 ..     110     308 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.066
                      BPD_transp_1 109 piitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadi 174
                                       ++  +++l++ ++ g++++++  g+w+ l       ++g   + i+  +++a+++av ++++++ +
  gi|336252219|ref|YP_004595326.1|  53 VVPFLMLLRISFAEGATAAAYQPGTWS-LEAYAGVLESGLAWDVIQ--YSFAIGAAVTVITIALGL 115
                                       444455566666666666666666666.666666666666666666..444444444444444433 PP

  == domain 2  score: 51.3 bits;  conditional E-value: 6.1e-18
                      BPD_transp_1   3 llGilaalnrnkkldkllrpliivllslPsfvlaillvlvf....................vilsilghlilpviil 59 
                                        lG+  a +  ++ d +++ +  +   lP +  +++ +++f                    +   ++  +  ++ii 
  gi|336252219|ref|YP_004595326.1| 112 ALGLCYA-YAIWRADGVVQSILLFAVVLPLLTTLVVKTYAFrplltpegtlndvlmglhviSEPVSIVPGTAGAIIG 187
                                       6777777.777899**********************99999*****************9885555556678889*** PP

                      BPD_transp_1  60 lllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG 136
                                        ++  +py++l +++++ +++ +lveaar lGasr + +  vv+P a+p ii   +++f++++g+++++ +l+++  
  gi|336252219|ref|YP_004595326.1| 188 QVYIVLPYAVLAIYSVMATMDWQLVEAARDLGASRPRSVLEVVVPRAMPGIIVATVISFAWSVGAYAAPFLLAGGDI 264
                                       ************************************************************************95543 PP

                      BPD_transp_1 137 lgtllleailgydyseisnggvlalviavlllnlvadilqrl 178
                                          +++e +l +++++    +++  vi+++l+++++ +++ +
  gi|336252219|ref|YP_004595326.1| 265 SFAVRVEKQLLQNFQWPE--ATALSVIMIVLMLASIAAIVGA 304
                                       555555555555555433..4444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2326.84
//
Query:       gi|336252220|ref|YP_004595327.1|  [L=269]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for complete 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   60.6  15.9    1.6e-16   60.6  15.9    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.042   13.8   0.3      0.092   12.7   0.3    1.6  1  DUF3439       Domain of unknown function (DUF3439)
       0.64    9.5   4.4          1    8.8   0.1    2.4  2  DUF1129       Protein of unknown function (DUF1129)


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 ?   -1.7   4.4      0.34     2e+03      33      74 ..      23      89 ..       7      99 .. 0.52
   2 !   60.6  15.9   2.7e-20   1.6e-16       3     176 ..      83     255 ..      81     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.34
                      BPD_transp_1 33 fvlaillvlvf.........................vilsilghlilpviillllsaapyvrlirra 74
                                      f+l++llv+v+                          ++ +l     ++i+ l ++ +++++ +++a
  gi|336252220|ref|YP_004595327.1| 23 FLLLPLLVVVVtsfsassqlvfppesytmasylaffENNAWLEAFDNSLIVGLGTTVVATILGVTAA 89
                                      3344444444444444555555666666666666663333444444444444444444444444444 PP

  == domain 2  score: 60.6 bits;  conditional E-value: 2.7e-20
                      BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraal 76 
                                       +lG+ aa       +   ++l pl+ ++l +P++++++ l++ f  l +l+++ l++i++ +l a+p+v++++r+++
  gi|336252220|ref|YP_004595327.1|  83 ILGVTAAfgqEIDDGAAGRVLVPLVLLPLLIPPVIFGVTLLVYFNEL-GLQDTYLSLILAHTLWATPLVYFVMRSVF 158
                                       6777777766666788899********************99876666.9**************************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       +  + ++  aar lGa++++ f++vvlPn++  i+ g++laf+ +l ++v+++fl +++  + ++  + ++   ++ 
  gi|336252220|ref|YP_004595327.1| 159 SRFDWQQLDAARDLGAGPIRSFVHVVLPNVKHGIFVGALLAFIVSLQEFVMALFLSGDS--TATIPVVAWNTLRDSL 233
                                       ********************************************************774..7777777777777777 PP

                      BPD_transp_1 154 snggvlalviavlllnlvadilq 176
                                          +v ++  +++l+++va +l+
  gi|336252220|ref|YP_004595327.1| 234 D-PIVSVVSTFLILISIVALLLA 255
                                       7.444444444444444444333 PP

>> DUF3439  Domain of unknown function (DUF3439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   1.5e-05     0.092      73     117 ..     106     155 ..      70     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                           DUF3439  73 mvkvp.lvppeafgrvm....nacayfpsyiflhlvhglaavplvylvch 117
                                       +v +p l+pp  fg  +    n+     +y+ l l h+l a plvy+v  
  gi|336252220|ref|YP_004595327.1| 106 LVLLPlLIPPVIFGVTLlvyfNELGLQDTYLSLILAHTLWATPLVYFVMR 155
                                       55566357999999754233388888899*****************9975 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00017         1      75     110 ..      60      98 ..      37     129 .. 0.74
   2 ?    1.6   0.9     0.027   1.6e+02     156     180 ..     239     263 ..     191     268 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00017
                           DUF1129  75 enpwlmalDnsLll...lalfallfgilalfskkkqtas 110
                                       +n+wl a DnsL++   + ++a + g++a+f+++    +
  gi|336252220|ref|YP_004595327.1|  60 NNAWLEAFDNSLIVglgTTVVATILGVTAAFGQEIDDGA 98 
                                       89**********9865578999*********99766555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.027
                           DUF1129 156 llvvwlvlftlvallpaviNpvLpp 180
                                       ++  +l+l+++vall av+   L++
  gi|336252220|ref|YP_004595327.1| 239 VVSTFLILISIVALLLAVVATNLQW 263
                                       3444444455555555555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2163.71
//
Query:       gi|336252221|ref|YP_004595328.1|  [L=137]
Description: hypothetical protein Halxa_0810 [Halopiger xanaduensis SH-6]
Scores for 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-07   29.4  22.8    8.3e-07   29.2  22.8    1.0  1  EamA             EamA-like transporter family
  ------ inclusion threshold ------
      0.017   15.1   4.0      0.017   15.1   4.0    1.4  1  TMEM234          Putative transmembrane family 234
       0.99    9.9  14.5        6.4    7.3   0.3    3.3  3  PNTB_4TM         4TM region of pyridine nucleotide transhydro
        2.3    7.7  11.5        1.5    8.4  10.2    1.4  1  ABC2_membrane_5  ABC-2 family transporter protein


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 !   29.2  22.8   1.9e-10   8.3e-07       3     136 ..       5     136 ..       3     137 .] 0.92

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.9e-10
                              EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlaf 79 
                                       +i lal+  l+++ ++v+++++ r++s + ++ ++++++  l+  +a+l+++++   + +d+++ l  g++  +++ 
  gi|336252221|ref|YP_004595328.1|   5 AIALALATLLLFGGWAVAADVATRSLSAVNAVLLSYVASIGLVGGYAVLSRRPI-AGTSTDIAFALGSGVF-LAAGT 79 
                                       67899*******************************877777788888888888.9999999999999975.66777 PP

                              EamA  80 llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       l+f+ al+++s +++s i  l  v+ ++ +v+++   l+   ++g++l++++v+li 
  gi|336252221|ref|YP_004595328.1|  80 LAFYAALTRGSMAVVSAIAGLYFVVPVLVGVAYFETALSTANVVGFALAVVAVVLIA 136
                                       *******************************************************95 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   4.0   3.8e-06     0.017      56     115 ..      77     135 ..      59     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.8e-06
                           TMEM234  56 sgSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                        g + f+++l++ +++++++ia  l fv+ vl++ +  e  l++  v+g +l vv+++l+
  gi|336252221|ref|YP_004595328.1|  77 AGTLAFYAALTRGSMAVVSAIA-GLYFVVPVLVGVAYFETALSTANVVGFALAVVAVVLI 135
                                       68999***************98.69********************************997 PP

>> PNTB_4TM  4TM region of pyridine nucleotide transhydrogenase, mitoch
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3    0.0021       9.4      55      74 ..       4      23 ..       1      31 [. 0.87
   2 ?    7.3   0.3    0.0014       6.4      50      75 ..      30      55 ..      22      56 .. 0.75
   3 ?    3.4   3.1     0.024   1.1e+02      27      66 ..      90     132 ..      67     136 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0021
                          PNTB_4TM 55 gaiavvlasinvvGGFlvtq 74
                                       aia++la++ ++GG++v  
  gi|336252221|ref|YP_004595328.1|  4 VAIALALATLLLFGGWAVAA 23
                                      5799*************975 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0014
                          PNTB_4TM 50 lakvlgaiavvlasinvvGGFlvtqr 75
                                      l++v +++   +asi +vGG++v +r
  gi|336252221|ref|YP_004595328.1| 30 LSAVNAVLLSYVASIGLVGGYAVLSR 55
                                      4555566666899**********887 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.024
                          PNTB_4TM  27 Lmsvtnaisgiiivgallalg...stlakvlgaiavvlasinv 66 
                                        m+v  ai g+  v  +l+     +t+ ++ ++++ +la++ v
  gi|336252221|ref|YP_004595328.1|  90 SMAVVSAIAGLYFVVPVLVGVayfETALSTANVVGFALAVVAV 132
                                       4888888888876665554443553344444444444444444 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 ?    8.4  10.2   0.00033       1.5      93     192 ..      39     135 ..      25     137 .] 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00033
                   ABC2_membrane_5  93 ailitlllliiavlikgnvtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaifslsk 169
                                       +  + ++ l+ ++ + ++  i  + ++i+++l+ ++++ a +l +y  +   +g ++++ +i+g+ f+++ ++ + +
  gi|336252221|ref|YP_004595328.1|  39 S-YVASIGLVGGYAVLSRRPIAGTSTDIAFALGSGVFLAAGTLAFYAALT--RGSMAVVSAIAGLYFVVPVLVGVAY 112
                                       2.22333333333344444467899999*****************99999..999********************** PP

                   ABC2_membrane_5 170 lelslidlsnyilliillviill 192
                                       +e++l++ + + +++ +++++l+
  gi|336252221|ref|YP_004595328.1| 113 FETALSTANVVGFALAVVAVVLI 135
                                       ***98888877666655555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1018.64
//
Query:       gi|336252222|ref|YP_004595329.1|  [L=644]
Description: KH-domain/beta-lactamase-domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-33  113.3   1.0    2.2e-29  101.2   0.1    2.9  3  KH_7           KH domain
    5.4e-22   78.2   0.0    1.2e-21   77.0   0.0    1.6  1  Beta-Casp      Beta-Casp domain
    7.2e-17   61.1   0.0    1.9e-16   59.7   0.0    1.8  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.6e-14   54.3   3.1    5.8e-14   52.6   3.1    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.9e-12   47.0   0.0    3.4e-12   46.2   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    1.4e-09   37.7   0.1    2.6e-09   36.9   0.1    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.7e-07   31.0   0.1    1.6e-06   27.9   0.0    2.3  2  KH_2           KH domain
    6.1e-05   23.0   0.1    0.00023   21.1   0.0    1.8  2  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.059   13.3   0.1       0.14   12.1   0.1    1.6  1  KH_4           KH domain
      0.084   12.7   0.0       0.32   10.9   0.0    2.0  1  KH_1           KH domain


Domain annotation for each model (and alignments):
>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.2   0.1   1.2e-32   2.2e-29       1      68 []       5      72 ..       5      72 .. 0.98
   2 !    9.8   0.0   0.00041      0.74       5      42 ..      76     115 ..      73     129 .. 0.71
   3 ?   -3.2   0.0       4.7   8.4e+03       5      18 ..     298     311 ..     297     318 .. 0.78

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 1.2e-32
                              KH_7  1 eevleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                                      e++l++l+++i+++lP+++++++v++EGPelV+Yt++pk+fa++gdlir+lA++lrkRi++RpDpsvl
  gi|336252222|ref|YP_004595329.1|  5 EQQLDDLQAEITSELPSDISVSSVKYEGPELVVYTRDPKKFAQQGDLIRQLASKLRKRITVRPDPSVL 72
                                      5899**************************************************************98 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00041
                              KH_7   5 eelkekieeklPkevkitdveFE..GPelViYtknpklfa 42 
                                       ee +e+i++ +P+e+ +td++F     e+Vi ++ p  ++
  gi|336252222|ref|YP_004595329.1|  76 EEAREEIMNVIPEEAGVTDLDFHadTGEVVIEAQKPGMVI 115
                                       899*******************511456777666666665 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.7
                              KH_7   5 eelkekieeklPke 18 
                                       e+++e i++++P e
  gi|336252222|ref|YP_004595329.1| 298 EQVREAIKHTIPLE 311
                                       68999999999965 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0   6.8e-25   1.2e-21       2     110 .]     424     548 ..     423     548 .. 0.84

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 6.8e-25
                                       HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.........................E-SHH....H CS
                         Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae.........................veakslewme 53 
                                       qe++++Lee+++e  ++++++p+ ld+ ++ +at+++++y+e                         +     +  e
  gi|336252222|ref|YP_004595329.1| 424 QEIMLVLEEAMRE--GDIPEMPVHLDG-MIWEATAIHTTYPEylrddlrdrifhedenpfladefnhI-----DGGE 492
                                       9************..547789******.************9999999999998887777765444322.....2223 PP

                                       HHH..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  54 skkeelnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                       +++++   + +p++il++sgm++gG++  +l ++ +dp++t+ +vgyqa+gTlgr++
  gi|336252222|ref|YP_004595329.1| 493 EERQD-VADGEPCIILSTSGMVTGGPIMSWLSHIGPDPDSTLTFVGYQAQGTLGRRI 548
                                       33322.35679********************************************97 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 !   59.7   0.0   1.1e-19   1.9e-16       2      62 .]     572     635 ..     571     635 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.1e-19
                             RMMBL   2 ipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvfiP 62 
                                       +++++++e++d fSgHad+++l +++++++pr+  v  vHG+e++t++l ++l  +++ ++f+P
  gi|336252222|ref|YP_004595329.1| 572 LSLNMHVETVDgFSGHADRAGLENFVKTMNPRPekVLCVHGDERSTQDLSSALYHNYDMRTFAP 635
                                       6899*************************************************99999999987 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   3.1   3.2e-17   5.8e-14       7     176 ..     196     396 ..     191     416 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 3.2e-17
                                       EEEEEEETTCEEEES--SCHHHHHHHH...HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   7 nsyliegdggviLiDtGtsteaaraal...elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                        s+++ ++++ iL+D+G  + a+ ++    ++ a g +p+ +dav+lTH+HlDH +  + l +     ++++ e ++
  gi|336252222|ref|YP_004595329.1| 196 ASFILSTPETRILVDCGDKPGAEGEVPylhAPEAFGAGPETIDAVVLTHAHLDHSAFIPLLFKYGYDGPIYCTEPTR 272
                                       5788889********************************************************************** PP

                                       CCHCHHHHHHHHHCCHH.........TTCHCGCCEEEEETTTEECCCTEEEEE...HECTTSTSCCEEEEEETTCCE CS
                       Lactamase_B  81 alfmeeaddaasrkgll.........lagvsadkpdvdeeeldgnaggrraly...vtggpghghghgvveygggkv 145
                                        l +    d+      +           ++ +++ ++ e ++ ++ ++++ l    + ++ g+  +h+++++g  +v
  gi|336252222|ref|YP_004595329.1| 273 DLMGLLTLDYLDVAAKEgrtppydseQVREAIKHTIPLEYGDVTDIAPDVKLTlhnAGHILGSAVSHFHIGDGLYNV 349
                                       ******999888877779******99444444555555555544444444443111568999999************ PP

                                       EEECTTTSSHHCCCCCC.................TTCEEE-SHCHHH CS
                       Lactamase_B 146 lftGDallagetgridl................tlrgaevrdpsdae 176
                                       +f+GD  ++  ++  +                  +r+ +  d+ d e
  gi|336252222|ref|YP_004595329.1| 350 CFSGDIHYEDTRLFNGAvndfprvetlvlestyGGRNDYQTDQEDSE 396
                                       ********888888777777777777766654444444444444444 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 !   46.2   0.0   1.9e-15   3.4e-12       1     173 [.     199     366 ..     199     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.9e-15
                     Lactamase_B_6   1 lLeldnvkiLlDvGwdes...kvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlp 74 
                                       +L+  +++iL+D+G +     +v + +a +      +t+d+++L+ha l+h + ++ l++    k++ + p+y+t p
  gi|336252222|ref|YP_004595329.1| 199 ILSTPETRILVDCGDKPGaegEVPYLHAPEAFGAGPETIDAVVLTHAHLDHSA-FIPLLF----KYGYDGPIYCTEP 270
                                       5777789*******99651113444444444444569**************87.655554....37889******** PP

                     Lactamase_B_6  75 vvkLGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGti..Wki 149
                                       +  L  +++ld+   +  +g +     + e ++ea ++ ++l Y   +++     ++ +t +naGh lG ++  ++i
  gi|336252222|ref|YP_004595329.1| 271 TRDLMGLLTLDYLDVAAKEGRT--PPYDSEQVREAIKHTIPLEYGDVTDIAP---DVKLTLHNAGHILGSAVshFHI 342
                                       **********999888666654..467889****************999985...799999********97655889 PP

                     Lactamase_B_6 150 skesekivYavdwnhakeshLnga 173
                                        +++ ++ +  d++ +  ++ nga
  gi|336252222|ref|YP_004595329.1| 343 GDGLYNVCFSGDIHYEDTRLFNGA 366
                                       999999999999988877777775 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 !   36.9   0.1   1.5e-12   2.6e-09       1     150 [.     205     362 ..     205     397 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.5e-12
                                       SEEEES--TTHHHH.HTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHH...... CS
                     Lactamase_B_2   1 rriLiDagpdlrqq.alral.qPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvla...... 68 
                                       +riL+D+g    +  + ++l  P +  + ++ idaV+lthaH DH a ++ l + ++  + p+y+++ +++      
  gi|336252222|ref|YP_004595329.1| 205 TRILVDCGDKPGAEgEVPYLhAPEAFGAGPETIDAVVLTHAHLDHSAFIPLLFKyGY--DGPIYCTEPTRDlmgllt 279
                                       79******87444455677757877999999****************9***999443..479****99999888888 PP

                                       .......HCCTTCGHHHCHTT....TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTT CS
                     Lactamase_B_2  69 .......vleanfvylaleee....pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrieggg 134
                                                e ++++  +  e    ++ ++ +l+ g+ ++++ +++++t++ a h  g         +  + i++g 
  gi|336252222|ref|YP_004595329.1| 280 ldyldvaAKEGRTPPYDS--EqvreAIKHTIPLEYGDVTDIA-PDVKLTLHNAGHILGS-------AVSHFHIGDGL 346
                                       887764322223333333..2457888888999999999999.5999999999999999.......89999****** PP

                                       EEEEEESS-S---HHH CS
                     Lactamase_B_2 135 krvyyigDtgyipeei 150
                                        +v+++gD  y + ++
  gi|336252222|ref|YP_004595329.1| 347 YNVCFSGDIHYEDTRL 362
                                       ********99877543 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.4   7.2e+02      43      59 ..      48      64 ..      47      71 .. 0.85
   2 !   27.9   0.0   8.8e-10   1.6e-06       3      67 ..      79     142 ..      77     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.4
                                      GGHHHHHHHHHHHHHHH CS
                              KH_2 43 gGsnikkigkelrkdie 59
                                      +G  i+++ ++lrk+i 
  gi|336252222|ref|YP_004595329.1| 48 QGDLIRQLASKLRKRIT 64
                                      6899***********95 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 8.8e-10
                                       HHHHHHHT.ECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEE CS
                              KH_2   3 peslavei.kkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVk 67 
                                       +e + ++i ++agv +++   +a+  ++vi + +pg+vIG+ Gs++++i+k+++   e+++  +++
  gi|336252222|ref|YP_004595329.1|  79 REEIMNVIpEEAGVTDLDF--HADTGEVVIEAQKPGMVIGRHGSTLREITKNVGWTPEVVRTPPIE 142
                                       788889999**********..5599**************************999887777777766 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 !   21.1   0.0   1.3e-07   0.00023       6      51 ..     194     251 ..     192     262 .. 0.79
   2 ?   -1.6   0.1       1.3   2.3e+03      98     119 ..     339     360 ..     306     368 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                     Lactamase_B_3   6 ghnsflletagarilvDPf............kanlgyeppa.......eeaDlvlisqaledHah 51 
                                       g +sf l+t+++rilvD +            +a       +       e++D+v++++a+ dH +
  gi|336252222|ref|YP_004595329.1| 194 GRASFILSTPETRILVDCGdkpgaegevpylHA-------PeafgagpETIDAVVLTHAHLDHSA 251
                                       89***************9966666555544422.......25555555***************86 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                     Lactamase_B_3  98 gflleqdgltiyhlGhlahels 119
                                        f++ ++ +++++ G++++e +
  gi|336252222|ref|YP_004595329.1| 339 HFHIGDGLYNVCFSGDIHYEDT 360
                                       58888888999*****999754 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.6e-05      0.14      28      52 ..      99     123 ..      78     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.6e-05
                              KH_4  28 eveielnvegedlGrvIGkrGrtld 52 
                                        ++ e+ +e ++ G vIG++G tl+
  gi|336252222|ref|YP_004595329.1|  99 ADTGEVVIEAQKPGMVIGRHGSTLR 123
                                       455677788999***********96 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00018      0.32       5      27 ..     105     127 ..     101     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                                       EEGGGHHHHHHTGGGHHHHHHHH CS
                              KH_1   5 lvPsslvgriIGkgGsnIkeIre 27 
                                        + +++ g +IG+ Gs+++eI +
  gi|336252222|ref|YP_004595329.1| 105 VIEAQKPGMVIGRHGSTLREITK 127
                                       566666799************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 4727.30
//
Query:       gi|336252223|ref|YP_004595330.1|  [L=161]
Description: hypothetical protein Halxa_0812 [Halopiger xanaduensis SH-6]
Scores for 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  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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 0.19s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1361.54
//
Query:       gi|336252224|ref|YP_004595331.1|  [L=195]
Description: hypothetical protein Halxa_0813 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.043   13.4   0.3      0.055   13.1   0.3    1.1  1  SAICAR_synt  SAICAR synthetase
       0.15   11.6  12.9       0.24   11.0  12.9    1.3  1  Spt20        Spt20 family
        1.8    7.3   6.3        2.1    7.0   6.3    1.1  1  Presenilin   Presenilin
        2.6    8.0   8.5       0.15   11.9   2.2    2.0  2  TAT_signal   TAT (twin-arginine translocation) pathway signal
        7.1    6.5  12.3        1.3    8.9   6.9    2.1  2  DivIC        Septum formation initiator


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 ?   13.1   0.3   1.5e-05     0.055     154     246 ..      70     163 ..      52     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                                       T-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTT.EEEEES--.STTTEEEEETTT.....GGGB- CS
                       SAICAR_synt 154 gteeeaeeieelalavyekaaelaaergiilvDtKlEFGldeedg.elvLaDevltpDssRfwdaetyeegkeqesl 229
                                       +++e ++e ++l  +  ++++++a++rgi + D   EFGl + +g +  ++D     D   +++ ++y++  +qe+ 
  gi|336252224|ref|YP_004595331.1|  70 NRTEALDEQQALNEDAVSAFEDTASDRGISVEDSAAEFGLLQVTGdDSAIMDSLRNGDIRGIYPGDQYDAFVQQEQQ 146
                                       356677777778888888999******************988766379999***9999999********55555554 PP

                                       STHHHHTT-STHHHHHH CS
                       SAICAR_synt 230 DKqfvRdwleeveekwk 246
                                         q  R   e+++++ +
  gi|336252224|ref|YP_004595331.1| 147 RAQQQRMIAEQQQQQQE 163
                                       44444444444333333 PP

>> Spt20  Spt20 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0  12.9   6.6e-05      0.24     112     156 ..     143     187 ..     118     195 .] 0.39

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.6e-05
                             Spt20 112 qnqqqqqqqqqqqqqqqqqqeqqqqqnekdsttteekekkskskn 156
                                       q+qq +qqq   + qqqqqqeqq+ ++++ds + + +e  + + +
  gi|336252224|ref|YP_004595331.1| 143 QEQQRAQQQRMIAEQQQQQQEQQSANETNDSDADSGNESDADNTS 187
                                       222222222222222222222222222222222222222222222 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   6.3   0.00059       2.1     270     313 ..      95     185 ..      42     194 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00059
                        Presenilin 270 e...............................................seeeseeesseaessaeesseekeseess 299
                                       +                                               +e+++ ++++  ++++++++e+++++e++
  gi|336252224|ref|YP_004595331.1|  95 DrgisvedsaaefgllqvtgddsaimdslrngdirgiypgdqydafvqQEQQRAQQQRMIAEQQQQQQEQQSANETN 171
                                       13344555566667777777777777777777777777777777776433333333333444444444444433333 PP

                        Presenilin 300 esseeeeeeeeeee 313
                                       +s++++ +e+++++
  gi|336252224|ref|YP_004595331.1| 172 DSDADSGNESDADN 185
                                       33333333333332 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.2   4.3e-05      0.15       2      24 ..       5      26 ..       4      28 .. 0.75
   2 ?   -0.8   0.5      0.43   1.5e+03      11      17 ..      43      49 ..      42      53 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.3e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                       SRR FL  ++ ++  aal+gc+
  gi|336252224|ref|YP_004595331.1|  5 PSRRRFLALTGTGT-TAALAGCS 26
                                      59******777777.55577775 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.43
                        TAT_signal 11 sAAaaAA 17
                                      ++A++ A
  gi|336252224|ref|YP_004595331.1| 43 GGAVTVA 49
                                      4444443 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.17     6e+02      24      50 ..      55      81 ..      47      89 .. 0.66
   2 ?    8.9   6.9   0.00035       1.3      15      45 ..     136     166 ..     131     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                                      HHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC 24 qeiaalqaelaklkaeneeLeaevkdL 50
                                      +e++ l+++l++    + e  +e + L
  gi|336252224|ref|YP_004595331.1| 55 AELESLNEQLQSGELNRTEALDEQQAL 81
                                      666777777777666666666666666 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00035
                                       XXXHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC  15 gllaykqlkqeiaalqaelaklkaeneeLea 45 
                                       ++ a+ q++q++a++q+ +a+++++++e ++
  gi|336252224|ref|YP_004595331.1| 136 QYDAFVQQEQQRAQQQRMIAEQQQQQQEQQS 166
                                       567889******************9999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2845  (0.158681); expected 358.6 (0.02)
Passed bias filter:                     1046  (0.0583412); expected 358.6 (0.02)
Passed Vit filter:                       170  (0.00948185); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 1384.61
//
Query:       gi|336252225|ref|YP_004595332.1|  [L=247]
Description: hypothetical protein Halxa_0814 [Halopiger xanaduensis SH-6]
Scores for 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-70  234.9   0.0    8.4e-70  234.7   0.0    1.0  1  NucS      Endonuclease NucS
     0.0083   16.0   0.0      0.013   15.4   0.0    1.2  1  YhcG_C    YhcG PDDEXK nuclease domain


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.7   0.0   9.3e-74   8.4e-70       3     216 ..      33     247 .]      31     247 .] 0.97

  Alignments for each domain:
  == domain 1  score: 234.7 bits;  conditional E-value: 9.3e-74
                              NucS   3 avlvvlarCkvsyeGraksrLeegerlivikpdGaflvhkdrkvePvnWqppkssltaevedgslilksirrkpeee 79 
                                       a++ v+ rC+v+yeGra srLe+g+r +++kpdGa lvh d  ++PvnWqpp++   ++ ed+ l+l+s+r  p+e+
  gi|336252225|ref|YP_004595332.1|  33 ALVTVFGRCTVDYEGRASSRLEAGDRHVMLKPDGAALVHTDEGQQPVNWQPPGCEHDVYQEDDRLVLESVRSTPDER 109
                                       678899*********************************************************************** PP

                              NucS  80 LkveieevehasayeledveelvldGseaelaeliiehpdLieeGfkpvareyavaiGivdiLgkdeegklvivelk 156
                                       L+v    v ++sa+   d+++l l G+e +l e i+ +pdL+e Gf+p+a e  +++G vdi gkd  +++v+velk
  gi|336252225|ref|YP_004595332.1| 110 LRVSFGTVLQVSAFSGTDENDLALVGTEEDLREHILAEPDLLEPGFTPLATERETPAGAVDIYGKDSAERTVVVELK 186
                                       ***************************************************************************** PP

                              NucS 157 rrkaevdaveqLkryvellkeds.vldkvrGvlvapsittdaekllkeeglefkeldppkd 216
                                       rr+ + dav+qL+ryv+ l++d  + + vrG+lvaps+t  a +ll e+glef  l+pp +
  gi|336252225|ref|YP_004595332.1| 187 RRRVGPDAVSQLRRYVDALERDLhADATVRGILVAPSVTDRADRLLVEHGLEFVSLEPPAE 247
                                       *********************9625679*******************************75 PP

>> YhcG_C  YhcG PDDEXK nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.4e-06     0.013      71     116 ..     178     221 ..     171     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-06
                            YhcG_C  71 kcyvvieLKvgefkpedagklnlYlsaldeelkkeednptiGiilc 116
                                       ++ vv+eLK +++ p+ +++l  Y++al++ l+++   +  Gi+++
  gi|336252225|ref|YP_004595332.1| 178 ERTVVVELKRRRVGPDAVSQLRRYVDALERDLHADA--TVRGILVA 221
                                       5679************************99987654..44466654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1974.08
//
Query:       gi|336252226|ref|YP_004595333.1|  [L=151]
Description: YbhB YbcL family protein [Halopiger xanaduensis SH-6]
Scores for 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  114.9   0.2    3.6e-33  114.7   0.2    1.0  1  PBP           Phosphatidylethanolamine-binding protein
  ------ inclusion threshold ------
        5.5    5.7   8.7        7.2    5.3   8.7    1.2  1  Calreticulin  Calreticulin family


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 !  114.7   0.2     4e-37   3.6e-33       2     132 .]      15     149 ..      14     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 114.7 bits;  conditional E-value: 4e-37
                                       --GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCT.TEEEEEEEEEETTSSEE-TTC.......EE-B-T CS
                               PBP   2 lpkky..egentsPplswsdvpegtksyalvviDpDapkvse.tflHwvvtnipasvtslpega.......vqgkns 68 
                                       +p++y  e +n++Ppl+++d pe+++++al+v DpDa + ++  + Hw+v+n+p ++t++pe+         +++n+
  gi|336252226|ref|YP_004595333.1|  15 IPDRYgyERDNVNPPLEIEDPPEEAETFALIVDDPDAVEPAGkVWEHWIVWNVPSEQTEIPENWdpddagaYEATND 91 
                                       8999877999***************************7555545*****************9667777788****** PP

                                       TSSCCCCS---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                               PBP  69 lgeesesgYlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                       +ge   +gY+gp Pp+++  H+Y f+++al+ + l+l+ +++ +el+ a++ghv+ +atl g Y
  gi|336252226|ref|YP_004595333.1|  92 YGE---TGYGGPKPPDRE--HTYRFTVFALNNT-LELDDDPDADELRDAMEGHVISQATLEGAY 149
                                       ***...************..**********988.589999999*****************9988 PP

>> Calreticulin  Calreticulin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   8.7   0.00081       7.2     226     279 ..      34      89 ..       7      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.00081
                      Calreticulin 226 kPedwdekapekipdpeavkPed..WledepelipdpeaekPedwdeeedgeweap 279
                                        P +  e+    + dp+av+P++  W++ +   +p +++e Pe+wd ++ g +ea+
  gi|336252226|ref|YP_004595333.1|  34 DPPEEAETFALIVDDPDAVEPAGkvWEHWIVWNVPSEQTEIPENWDPDDAGAYEAT 89 
                                       45555566667899*******8777****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1276.04
//
Query:       gi|336252227|ref|YP_004595334.1|  [L=174]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.2   0.2    2.3e-15   56.8   0.2    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.2e-09   37.3   0.1    4.6e-09   36.3   0.1    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    7.9e-09   35.4   0.1    1.3e-08   34.7   0.1    1.2  1  FR47             FR47-like protein
    1.4e-08   35.0   0.0    2.2e-08   34.4   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00027   21.1   0.0    0.00068   19.8   0.0    1.7  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00031   20.8   1.3     0.0019   18.3   1.3    1.9  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.018   15.1   0.0       0.03   14.4   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.022   14.4   1.5      0.074   12.7   0.2    2.1  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 !   56.8   0.2     1e-18   2.3e-15      12     117 .]      32     146 ..      15     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1e-18
                                       THHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEET.........TSTTEEEEEEEEESGGGTTSSHHH CS
                    Acetyltransf_1  12 ffppnedaseeefeesfsleaegllvaeedgeliGfisllkipd.........ekggvayieslaVspeyrgkGlGs 79 
                                       + + ++d+++e+ +e   +  + +lv+e d ++++   +++  d         +    +++ ++ V pe++++G+G+
  gi|336252227|ref|YP_004595334.1|  32 YAEDRPDEDLEAIRETYLEAGGAFLVGEIDARIVAIGAFRPPGDdhylehfvdLPASAVVLTRMRVEPEHQRRGYGQ 108
                                       23667777777755554555558888******************777777777556677777*************** PP

                                       HHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  80 aLlealeerareegikkivlaveedndaairlYeklGF 117
                                       + +eale rar++g+ +ivl++ + ++aa++lYe  GF
  gi|336252227|ref|YP_004595334.1| 109 RIYEALEARARDRGYAAIVLDTMARQTAARGLYEANGF 146
                                       *********************************99999 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.1     2e-12   4.6e-09      52     115 ..      83     155 ..      23     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2e-12
                   Acetyltransf_10  52 s.......hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavgeeqee 115
                                                ++++ V+pe++++G+g+++ ea+e++a+++g++   l   a + +a+++Ye  GF++v +e++e
  gi|336252227|ref|YP_004595334.1|  83 VdlpasavVLTRMRVEPEHQRRGYGQRIYEALEARARDRGYAAiVLDTMARQtAARGLYEANGFEEVRRERVE 155
                                       0555555578999*****************************99776666555**************999876 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.1   5.7e-12   1.3e-08      24      82 ..      92     151 ..      83     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 5.7e-12
                                       EEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEE.EETT-HHHHHHHHHHT-EEEEE CS
                              FR47  24 lgalqvlpehrrrGlgsrlvkalakeiaergktvllv.vvasNtpsirlyeklGfekiee 82 
                                       l  + v+peh+rrG+g+r+ +al ++ + rg+ ++++ + a  t+++ lye+ Gfe+ + 
  gi|336252227|ref|YP_004595334.1|  92 LTRMRVEPEHQRRGYGQRIYEALEARARDRGYAAIVLdTMARQTAARGLYEANGFEEVRR 151
                                       77899**************************99887648899**************9843 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   9.6e-12   2.2e-08      24      76 .]      74     148 ..      51     148 .. 0.60

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 9.6e-12
                                       S...............TCTEEEEE-GGGTTSSHHHHHHHH...TT..SEEEEEEEEE..THH.HHHHHHHHTTEEE CS
                    Acetyltransf_7  24 d...............aeitrlaVdpeyrgkGiGraLlea...ae..kgiileqlel..nae.kaikfYeklGFee 76 
                                       +                 +tr+ V pe++++G+G+++ ea   ++  +g+  ++l +  + + +a+++Ye +GFee
  gi|336252227|ref|YP_004595334.1|  74 GddhylehfvdlpasaVVLTRMRVEPEHQRRGYGQRIYEAleaRArdRGYAAIVLDTmaR-QtAARGLYEANGFEE 148
                                       34444444444444445567799**************99754422567754231222222.237888*******96 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   3.2e+03       7      17 ..      39      49 ..      34      59 .. 0.85
   2 !   19.8   0.0     3e-07   0.00068      82     152 ..      95     162 ..      54     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                    Acetyltransf_4  7 eDakeilaiya 17
                                      eD+++i+++y 
  gi|336252227|ref|YP_004595334.1| 39 EDLEAIRETYL 49
                                      89999999985 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 3e-07
                    Acetyltransf_4  82 vylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiD 152
                                       + + e   + +g+g+ +++ale +++  ++  ++  +++ ++++  +++a GFe v++++   + + +++D
  gi|336252227|ref|YP_004595334.1|  95 MRV-EPEHQRRGYGQRIYEALEARARDRGYAAIVLDTMARQTAARGLYEANGFEEVRRER--VETFEEPFD 162
                                       555.356899**********************************************9887..455555555 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.3   8.4e-07    0.0019       2     127 ..       7     148 ..       6     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.4e-07
                                       EEEE-GGGHHHHHHHHHHHTT----H.......HHHHHHHHHHTTS.EEEEEEETTEEEEEEEEEEE..EEEETT.E CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespl....e.eireyfrkllees.rvlgaedngelvgqlallpl..elnvpG.k 69 
                                       +r+++ +d d v el+++a  d   ++    + ++++  + +le +  +l+ e + ++v+  a+ p   + ++    
  gi|336252227|ref|YP_004595334.1|   7 VRRYRAADRDRVRELHEAAMRDVGAYAedrpDeDLEAIRETYLEAGgAFLVGEIDARIVAIGAFRPPgdDHYLEHfV 83 
                                       69999999999999999999999999988875466566666666643788888899999999998864355665557 PP

                                       EEEEEEE..EEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  70 tlkaagv..tgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                        l+a +v  t   v peh++rg+ +++ +++ +++r++g+  ++l       +++++Y+  G+e 
  gi|336252227|ref|YP_004595334.1|  84 DLPASAVvlTRMRVEPEHQRRGYGQRIYEALEARARDRGYAAIVLDTmarqtAARGLYEANGFEE 148
                                       77776661155689*****************************9955447766678999998886 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 ?   14.4   0.0   1.4e-05      0.03      23      63 ..      88     128 ..      69     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                   Acetyltransf_CG  23 gvldfthTeVpeelrGkGiAkkLvkaalddareeglkvvpt 63 
                                         +++t   V++e++++G+++++ +a    ar++g+  +++
  gi|336252227|ref|YP_004595334.1|  88 SAVVLTRMRVEPEHQRRGYGQRIYEALEARARDRGYAAIVL 128
                                       5789999****************************988775 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.15   3.4e+02      58      81 ..       6      30 ..       4      33 .. 0.82
   2 ?   12.7   0.2   3.3e-05     0.074      88     141 ..      98     150 ..      32     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.15
                                      EEEEEEGG.GCGGGGCS---TT-EE CS
                    Acetyltransf_8 58 yfeiYwak.edelaeyydaepgdrG 81
                                      y+ +Y+a+ +d++ e ++a   d+G
  gi|336252227|ref|YP_004595334.1|  6 YVRRYRAAdRDRVRELHEAAMRDVG 30
                                      7888986527999999999999998 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.3e-05
                                       SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                    Acetyltransf_8  88 eaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                                       e+e+ ++g+++++ +al +++ +d++ + +v++  +r ++a+ l+e+ Gfe+++
  gi|336252227|ref|YP_004595334.1|  98 EPEHQRRGYGQRIYEALEARA-RDRGYAAIVLDTMARQTAARGLYEANGFEEVR 150
                                       7899999****9999988776.566*************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1506.41
//
Query:       gi|336252228|ref|YP_004595335.1|  [L=930]
Description: DNA mismatch repair protein mutS [Halopiger xanaduensis SH-6]
Scores for 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-78  262.7   0.2    3.2e-78  262.1   0.2    1.3  1  MutS_V    MutS domain V
    1.6e-41  142.7   3.0    2.9e-41  141.8   3.0    1.4  1  MutS_III  MutS domain III
    2.9e-36  124.1   0.0    5.8e-36  123.2   0.0    1.5  1  MutS_I    MutS domain I
      2e-32  111.4   0.1    5.8e-32  109.9   0.1    1.9  1  MutS_IV   MutS family domain IV
    3.9e-10   40.2   0.0    2.4e-09   37.6   0.0    2.3  3  MutS_II   MutS domain II
  ------ inclusion threshold ------
      0.015   14.5   0.0      0.038   13.2   0.0    1.6  1  PLU-1     PLU-1-like protein
      0.029   14.4   0.0       0.12   12.5   0.0    2.0  1  AAA_14    AAA domain
      0.082   12.5   0.0       0.18   11.4   0.0    1.5  1  AAA_27    AAA domain
       0.17   12.3   1.2       0.43   11.1   0.0    2.1  2  AAA_23    AAA domain
        0.2   11.4   0.0       0.55   10.0   0.0    1.7  1  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.1   0.2   1.8e-81   3.2e-78       2     185 ..     665     848 ..     664     851 .. 0.99

  Alignments for each domain:
  == domain 1  score: 262.1 bits;  conditional E-value: 1.8e-81
                                       EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TT CS
                            MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatek 78 
                                       +itGpnm+Gksty+rqva ivllaq+Gsfvpa +a++++vd+iftRvgasDd+a g+stFmvEm E+a+il++a e+
  gi|336252228|ref|YP_004595335.1| 665 VITGPNMSGKSTYMRQVAQIVLLAQVGSFVPAGSARLTPVDRIFTRVGASDDIAGGRSTFMVEMDELATILREADER 741
                                       8**************************************************************************** PP

                                       SEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEEEEEEEE CS
                            MutS_V  79 slvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavkeeeedivflykvke 155
                                       slv+lDE+GRGtst+dG+aia+a++e+l++++ a+tlfatH+h lt+la+ le   +lh++v++e+ ++vf +++++
  gi|336252228|ref|YP_004595335.1| 742 SLVLLDEVGRGTSTADGMAIAQAITEHLHDEVGATTLFATHHHPLTELADDLEGAFTLHFEVDQEDGEVVFHHEIAP 818
                                       ***************************************************************************** PP

                                       S--SS--HHHHHHHTT--HHHHHHHHHHHH CS
                            MutS_V 156 gaaeksyGikvaklaglPesvverArevlk 185
                                       gaa+ syG++va+ ag+Pe+vver re ++
  gi|336252228|ref|YP_004595335.1| 819 GAATGSYGVEVATAAGVPEDVVERSRELVA 848
                                       *************************99876 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.8   3.0   1.6e-44   2.9e-41       2     191 .]     309     600 ..     308     600 .. 0.94

  Alignments for each domain:
  == domain 1  score: 141.8 bits;  conditional E-value: 1.6e-44
                                       HHHHTTSSS-.TTS.SSSS-HHHHH---SSHHHHHHHHHHHH--BS-HHHHHHHHHHHHH.T..TT.HHHHHHHHTT CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                          MutS_III   2 TlrnLeilen.lrggskegsLlgvldrTvTamGaRlLrewllqPltdleeInaRldaVee.leneelreelrellrr 76 
                                       +lr+Le++e  + +g ++ +L+gvld+T++a G R Lr wl +Pl+++e+I+aRldaVee  +  ++reel+ellr+
  gi|336252228|ref|YP_004595335.1| 309 ALRSLELFEPrTVHGRDDATLVGVLDETSSALGGRKLRDWLRRPLLEPERIEARLDAVEElTSAVQTREELHELLRE 385
                                       79*****995444446677*****************************************7778899********** PP

                                       ---HHHHHHHHHTT---HHHHHHHHHHHHHHHTTTTT---SSTHHHHH........HHHHHHHHHHB-SS--SSGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III  77 lpDleRllsrislgkakardlkallealkaleelvallekeklaesee........eslaelleeaideeplaleke 145
                                       ++DleRl+ ris ++a+ardl++l+++l  +++++a   + ++++ +          +++el+++a++ +p+ +  e
  gi|336252228|ref|YP_004595335.1| 386 VYDLERLIGRISRERANARDLRSLRDTLAVVPDIRAEIADADCERLRRlhenldplVDVRELIDDAVVADPPIEITE 462
                                       **************************************99998766668766654444449**************** PP

                                       S--B-T....................................................................... CS
                                       xxxxxx....................................................................... RF
                          MutS_III 146 gedlra....................................................................... 151
                                       g+++++                                                                       
  gi|336252228|ref|YP_004595335.1| 463 GGIIAEgydedlddlrstardgeqwidnleererertgidslkvghnsvhgyyievtnpnldsvpedyqrrqtlkns 539
                                       ***************************************************************************** PP

                                       .....................HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH CS
                                       .....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III 152 .....................iealeqelfqelleeveealerlrrlaealaeLDvllSlA 191
                                                            +++le+elf+e+++ev+e++er ++la+ala+LD+l+SlA
  gi|336252228|ref|YP_004595335.1| 540 erfvtpelkeredeivgakqrADDLEYELFREVRREVAEEVERVQHLADALATLDALVSLA 600
                                       *********************99**************999********************9 PP

>> MutS_I  MutS domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.2   0.0   3.2e-39   5.8e-36       1     113 []      19     130 ..      19     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 3.2e-39
                                       HHHHHHHHCCCHH-TTCEEEEEETTEEEEECHHHHHHHHHCSSSSTT.ESSSSC.EEEEEEEHHHHHHHHHHHHHTT CS
                            MutS_I   1 tplmkqylelkkkykdavlffrvGdfYelfgeDAviaareleitltkrkkssekeipmagvPehalekylrkLvekg 77 
                                       tp+m+qy++l ++y+da+++f+vGdfYe+f   A+  ar+le+ lt+r++s+++ +pmag+P  ++e+y+++L+e+g
  gi|336252228|ref|YP_004595335.1|  19 TPMMRQYHDLCERYDDAIVLFQVGDFYETFCGAAERTARVLEVALTSREDSTGE-YPMAGIPIDNAESYIEELLEAG 94 
                                       8***********************************************998888.********************** PP

                                       -EEEEEEE-S-HHHHS.S--EEEEEEEBTTC-TTSC CS
                            MutS_I  78 ykVavveqtetpaekkgvvkrevvrviTpGtltdee 113
                                       y+Vav++q+e+p e++gvv+r v+rviTpGtlt++e
  gi|336252228|ref|YP_004595335.1|  95 YRVAVADQVEEPGETSGVVERAVTRVITPGTLTEDE 130
                                       *********************************985 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.9   0.1   3.2e-35   5.8e-32       1      91 [.     469     559 ..     469     560 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 3.2e-35
                                       TTSHHHHHHHHHHHHHHHHHHHHHCCCCCCCT-TTBEECCCSSSEEEEEE-TCCCTTT--SEEEEEECTCEEEEECC CS
                           MutS_IV   1 gfdeeLdelrdrleelekeleeleekereklgikslkveynkvlGyylevtrseakkvpkefirlqtlknserytta 77 
                                       g+de+Ld lr++ ++ e+++++lee+ere++gi+slkv++n+v+Gyy+evt+ + ++vp+++ r+qtlknser++t+
  gi|336252228|ref|YP_004595335.1| 469 GYDEDLDDLRSTARDGEQWIDNLEERERERTGIDSLKVGHNSVHGYYIEVTNPNLDSVPEDYQRRQTLKNSERFVTP 545
                                       8**************************************************************************** PP

                                       CHHHHHHHHHHHHH CS
                           MutS_IV  78 elkkleaelleaee 91 
                                       elk+ e+e+  a++
  gi|336252228|ref|YP_004595335.1| 546 ELKEREDEIVGAKQ 559
                                       *********99987 PP

>> MutS_II  MutS domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   1.3e-12   2.4e-09       1     127 [.     138     257 ..     138     262 .. 0.86
   2 ?   -3.0   0.0       4.7   8.4e+03      40      54 ..     292     306 ..     289     312 .. 0.82
   3 ?   -2.1   0.1       2.5   4.4e+03      62      88 ..     400     426 ..     368     439 .. 0.66

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.3e-12
                                       -EEEEEEEE.....TTTSE.EEEEEEETTTTEEEEEEEEE-HHHHHHHHHH-ESEEEEESS-SCCCHHHHHHCHCTT CS
                           MutS_II   1 nylaAisek.....regrr.vGlafiDlstgefvvsefedfeeleaeLsrlsPkElllpedlsestaeeessklrel 71 
                                       n++aA+++         ++  +la +D+stg+f  ++++ +e +++e+sr+ P+E ++++d+  +        l + 
  gi|336252228|ref|YP_004595335.1| 138 NFVAAVARGadngdAGPDAeLALALLDVSTGDFLATSSASRESIADEVSRFDPAEAVVGPDAPTD--------LFPA 206
                                       6677766666666534445589***************************************9766........6699 PP

                                       T-EEEEESCCCCSHCCHHHHCHHHB--STTTTTTTGGG-HHHHHHHHHHHHHCCCC CS
                           MutS_II  72 rsrvgvretvefesekaserleedfsvedldgfglekekklalaAlgalisYleet 127
                                          v+ +++  f+ e a e+l+++f++ d    +l    + +++A+gal+sY+e  
  gi|336252228|ref|YP_004595335.1| 207 ECMVTPYDERTFDRERAGEKLATYFRNPD----AL-LAGDAEIRACGALLSYAEYV 257
                                       9************************9999....33.5569*************975 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.7
                                       HHHHHH-ESEEEEES CS
                           MutS_II  40 aeLsrlsPkElllpe 54 
                                       + L+r+ P+E ll +
  gi|336252228|ref|YP_004595335.1| 292 THLTRYDPREYLLLD 306
                                       789*******99855 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.5
                                       HHHHHCHCTTT-EEEEESCCCCSHCCH CS
                           MutS_II  62 eeessklrelrsrvgvretvefeseka 88 
                                       ++    lr+lr+ + v++++  e+++a
  gi|336252228|ref|YP_004595335.1| 400 RANARDLRSLRDTLAVVPDIRAEIADA 426
                                       456788899999999999999988887 PP

>> PLU-1  PLU-1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.1e-05     0.038      82     269 ..     354     552 ..     347     608 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                             PLU-1  82 lsleelekLleeldslpFdlpeieqLkelleeieefqkkarellseesedssieeleklieeGksfnvelpe..lee 156
                                       l++e++e+ l+ ++ l+  ++  e+L ell+e++++++ + ++ +e+ +  +++ l +++     +  e+ +  +e+
  gi|336252228|ref|YP_004595335.1| 354 LEPERIEARLDAVEELTSAVQTREELHELLREVYDLERLIGRISRERANARDLRSLRDTLAVVPDIRAEIADadCER 430
                                       56788888888899999999999*******************9999999999***********999999988779** PP

                             PLU-1 157 LkkvleqlkWleevrevreekkqltleevkeLieeGeelaippekeellaelqelleaaekweekakelLearekls 233
                                       L++  e l  l +vre+ +++  +  +   e+ e G+  +    ++e l+ l++  + +e+w++ ++e  e re+  
  gi|336252228|ref|YP_004595335.1| 431 LRRLHENLDPLVDVRELIDDA--VVADPPIEITEGGIIAEG---YDEDLDDLRSTARDGEQWIDNLEER-E-RERTG 500
                                       *****************9666..999999999997766664...799**********************.5.***** PP

                             PLU-1 234 leeLeallneaq..eipvslpslaaleeilkkarewq..............r 269
                                       +++L+  +n+++   i+v+ p+l+++ e +++ + ++               
  gi|336252228|ref|YP_004595335.1| 501 IDSLKVGHNSVHgyYIEVTNPNLDSVPEDYQRRQTLKnserfvtpelkereD 552
                                       ************9999999999999998888888877554444555544441 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.5e-05      0.12       2      73 ..     661     749 ..     660     757 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.5e-05
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell.......vkkesilyinldderd.....kkladpe.............kll 53 
                                       r++ vitG+  +GK+t+++q+++  l       v++ s     +d+  +     +     +             +l 
  gi|336252228|ref|YP_004595335.1| 661 RRLAVITGPNMSGKSTYMRQVAQIVLlaqvgsfVPAGSARLTPVDRIFTrvgasD-----DiaggrstfmvemdELA 732
                                       5788******************888787777775555555555555444222220.....12222221222221222 PP

                            AAA_14  54 elileklkeekktylflDEi 73 
                                       ++++e    +++++++lDE+
  gi|336252228|ref|YP_004595335.1| 733 TILREA---DERSLVLLDEV 749
                                       333332...57788888887 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0001      0.18      21      48 ..     657     683 ..     649     686 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                            AAA_27  21 fsaeeadlhliyGpNEAGKstalrAisd 48 
                                       f  ++++l +i GpN +GKst +r + +
  gi|336252228|ref|YP_004595335.1| 657 FT-GDRRLAVITGPNMSGKSTYMRQVAQ 683
                                       55.6899****************98766 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   2.6       6.3   1.1e+04     118     118 ..     498     498 ..     356     593 .. 0.59
   2 ?   11.1   0.0   0.00024      0.43      17      36 ..     657     678 ..     648     685 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.3
                            AAA_23 118 e 118
                                       +
  gi|336252228|ref|YP_004595335.1| 498 R 498
                                       0 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00024
                            AAA_23  17 F..skgltlItGpNGaGKTTil 36 
                                       F  ++ l +ItGpN +GK+T +
  gi|336252228|ref|YP_004595335.1| 657 FtgDRRLAVITGPNMSGKSTYM 678
                                       3448899*************77 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 ?   10.0   0.0    0.0003      0.55      24      39 ..     663     678 ..     649     693 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0003
                            AAA_29  24 atlltGpsGsGKSTll 39 
                                         ++tGp+ sGKST +
  gi|336252228|ref|YP_004595335.1| 663 LAVITGPNMSGKSTYM 678
                                       689***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (930 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.75u 0.27s 00:00:01.02 Elapsed: 00:00:00.42
# Mc/sec: 6626.02
//
Query:       gi|336252229|ref|YP_004595336.1|  [L=527]
Description: ArsR family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for complete 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   66.4   4.6    9.9e-10   38.3   1.7    2.5  2  HTH_20           Helix-turn-helix domain
    4.5e-16   58.4   0.0    4.1e-10   39.4   0.0    2.5  2  HTH_5            Bacterial regulatory protein, arsR family
    2.3e-14   52.7   0.0    2.4e-06   27.0   0.0    2.3  2  HTH_24           Winged helix-turn-helix DNA-binding
    2.9e-11   43.1   4.1    1.3e-07   31.3   0.3    2.8  2  MarR_2           MarR family
    7.7e-11   41.8   0.0    1.3e-06   28.2   0.0    2.6  2  MarR             MarR family
    3.6e-09   36.3   0.1    0.00059   19.6   0.0    2.5  2  HTH_IclR         IclR helix-turn-helix domain
    1.2e-07   31.8   0.0    0.00015   21.9   0.0    2.6  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    4.7e-07   30.2   0.0    0.00068   20.0   0.0    2.4  2  Penicillinase_R  Penicillinase repressor
    2.8e-06   27.2   0.0      0.071   13.1   0.0    2.4  2  HTH_11           HTH domain
    9.3e-06   25.4   0.0     0.0017   18.2   0.0    2.4  2  TrmB             Sugar-specific transcriptional regulator Trm
    7.2e-05   22.7   0.4     0.0051   16.8   0.0    2.4  2  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00022   21.1   0.1       0.63   10.0   0.0    2.6  2  HTH_12           Ribonuclease R winged-helix domain
    0.00061   19.5   0.1      0.095   12.5   0.0    2.4  2  HTH_DeoR         DeoR-like helix-turn-helix domain
    0.00086   19.8   0.2      0.066   13.7   0.0    2.4  2  HTH_27           Winged helix DNA-binding domain
     0.0014   18.2   0.1          1    9.0   0.0    2.5  2  GntR             Bacterial regulatory proteins, gntR family
     0.0034   17.1   0.0       0.14   12.0   0.0    2.3  2  HTH_38           Helix-turn-helix domain
     0.0036   17.0   0.1        1.5    8.5   0.0    2.3  2  RP-C             Replication protein C N-terminal domain
     0.0041   17.3   0.0       0.01   16.0   0.0    1.6  1  FUR              Ferric uptake regulator family
     0.0046   17.3   0.0       0.92    9.9   0.0    2.4  2  Rrf2             Transcriptional regulator
     0.0085   16.0   5.5     0.0085   16.0   5.5    1.8  2  Apolipoprotein   Apolipoprotein A1/A4/E domain
  ------ inclusion threshold ------
      0.024   14.7   0.1         10    6.2   0.0    2.6  2  HTH_29           Winged helix-turn helix
      0.036   14.0   0.1        1.1    9.3   0.0    3.0  3  HTH_1            Bacterial regulatory helix-turn-helix protei
      0.037   14.2   0.0        3.3    7.9   0.0    2.4  2  B-block_TFIIIC   B-block binding subunit of TFIIIC
      0.042   14.0   0.0        7.4    6.8   0.0    2.3  2  DUF2250          Uncharacterized protein conserved in archaea
       0.06   13.1   0.0        2.1    8.2   0.0    2.4  2  LexA_DNA_bind    LexA DNA binding domain
      0.071   13.2   0.0       0.88    9.7   0.0    2.2  2  MerR_1           MerR HTH family regulatory protein
      0.082   12.9   6.2       0.48   10.4   0.0    3.3  3  BLACT_WH         Beta-lactamase associated winged helix domai
       0.14   12.2   0.0       0.28   11.3   0.0    1.5  1  DUF2300          Predicted secreted protein (DUF2300)
       0.16   11.9   0.1         23    5.1   0.0    2.4  2  Cdc6_C           CDC6, C terminal winged helix domain
        8.6    6.6  11.9        0.1   12.7   2.0    3.0  2  DprA_WH          DprA winged 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 !   28.2   0.1   2.5e-09   1.5e-06       9      58 ..     366     415 ..     360     416 .. 0.92
   2 !   38.3   1.7   1.7e-12   9.9e-10       3      61 .]     433     491 ..     431     491 .. 0.97

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.5e-09
                                       -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20   9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58 
                                       ++ R +i+++++ + g  +se+ +r d+s +t+++H+rvLee gL+ +v+
  gi|336252229|ref|YP_004595336.1| 366 NERREAIYDLIRAEPGCYLSEVGDRQDVSLSTVRHHVRVLEEEGLIASVT 415
                                       5667789***************************************9986 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 1.7e-12
                                       HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20   3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       ++ ALa+P  r++l aLa+ +++  + la++l+ +++t+s+HL +Le+ gLv ++r gr
  gi|336252229|ref|YP_004595336.1| 433 LHAALAEPAKREVLEALADLGPVNNGRLADELERDPSTVSHHLSALEDDGLVVRERDGR 491
                                       689*****************************************************997 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 !   16.6   0.0   8.6e-06    0.0051       5      46 ..     369     412 ..     366     413 .. 0.76
   2 !   39.4   0.0   6.8e-13   4.1e-10       2      45 ..     440     484 ..     439     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.6e-06
                                       HHHHHHHTT.SS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   5 lkILklLae.ge.lcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       ++ ++ L + ++ ++ +e  +  ++s stv+hH ++L+e+GL+ 
  gi|336252229|ref|YP_004595336.1| 369 REAIYDLIRaEPgCYLSEVGDRQDVSLSTVRHHVRVLEEEGLIA 412
                                       55555566645567777777777899****************96 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 6.8e-13
                                       HHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5   2 ptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45 
                                       p+++++L +La+ g+   + la+el+  +stvShHL++L++ GLV
  gi|336252229|ref|YP_004595336.1| 440 PAKREVLEALADlGPVNNGRLADELERDPSTVSHHLSALEDDGLV 484
                                       899*****************************************9 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 !   27.0   0.0     4e-09   2.4e-06       2      47 ..     366     411 ..     365     412 .. 0.96
   2 !   23.6   0.0   4.6e-08   2.8e-05       5      47 ..     442     484 ..     439     485 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4e-09
                            HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       +e + +I+ l++++p++  +e+ +r ++S+stv+ +++ LeeeGlI
  gi|336252229|ref|YP_004595336.1| 366 NERREAIYDLIRAEPGCYLSEVGDRQDVSLSTVRHHVRVLEEEGLI 411
                                       678889***************************************9 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 4.6e-08
                            HTH_24   5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       +r++Le+L + +  ++  LA++l   pstv+ +l  Le++Gl+
  gi|336252229|ref|YP_004595336.1| 442 KREVLEALADLGPVNNGRLADELERDPSTVSHHLSALEDDGLV 484
                                       6899*************************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1    0.0002      0.12      14      55 ..     376     415 ..     364     421 .. 0.84
   2 !   31.3   0.3   2.2e-10   1.3e-07       4      61 ..     439     491 ..     435     492 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                                       HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       ++++pg  +  +e+ +r ++s s+v  +++ L++ GL+  ++
  gi|336252229|ref|YP_004595336.1| 376 IRAEPG--CYLSEVGDRQDVSLSTVRHHVRVLEEEGLIASVT 415
                                       566676..99****************************8775 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 2.2e-10
                                       -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2   4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61 
                                       +pa + vL aL++ ++  ++ g la++l  ++s+vs +l  L++ GLv+r++   D+R
  gi|336252229|ref|YP_004595336.1| 439 EPAKREVLEALADLGP--VNNGRLADELERDPSTVSHHLSALEDDGLVVRER---DGR 491
                                       7999************..*********************************8...566 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0007      0.42      11      51 ..     375     415 ..     372     422 .. 0.89
   2 !   28.2   0.0   2.2e-09   1.3e-06       7      52 ..     444     489 ..     440     492 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0007
                                       HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                       +++ ++++++se +++  vs stv   ++ Le++Gli +  
  gi|336252229|ref|YP_004595336.1| 375 LIRAEPGCYLSEVGDRQDVSLSTVRHHVRVLEEEGLIASVT 415
                                       5888999******************************8765 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 2.2e-09
                                       HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52 
                                       ++L+ l++ gp ++  La+ l+ ++stv+  l +Le++Gl+ R+++
  gi|336252229|ref|YP_004595336.1| 444 EVLEALADLGPVNNGRLADELERDPSTVSHHLSALEDDGLVVRERD 489
                                       58999**************************************997 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 !   14.1   0.0   5.1e-05      0.03      11      49 ..     375     412 ..     371     414 .. 0.85
   2 !   19.6   0.0   9.8e-07   0.00059       8      51 ..     445     487 ..     444     488 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.1e-05
                                       T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                       +++++p+   lse+ +r +++ Stv+++++ L+e+G++ 
  gi|336252229|ref|YP_004595336.1| 375 LIRAEPG-CYLSEVGDRQDVSLSTVRHHVRVLEEEGLIA 412
                                       4445555.68**************************985 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 9.8e-07
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                       +L+ala  ++ +++  lA+++   +Stv+++L+ L+  G+v ++
  gi|336252229|ref|YP_004595336.1| 445 VLEALADLGP-VNNGRLADELERDPSTVSHHLSALEDDGLVVRE 487
                                       9********9.7*****************************885 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 ?    7.1   0.0     0.011       6.4      11      52 ..     370     411 ..     369     416 .. 0.88
   2 !   21.9   0.0   2.6e-07   0.00015      13      57 ..     445     489 ..     443     492 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress  11 etIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52 
                                       e+IY+l   +     +++  r +vs s+V   ++ Le++G++
  gi|336252229|ref|YP_004595336.1| 370 EAIYDLIRAEPGCYLSEVGDRQDVSLSTVRHHVRVLEEEGLI 411
                                       78999998667777899999********************97 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.6e-07
                                       HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                    Fe_dep_repress  13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyeky 57 
                                       ++++  + ++v + +la +L+  ps+Vs  l+ Le+dG+v+ e +
  gi|336252229|ref|YP_004595336.1| 445 VLEALADLGPVNNGRLADELERDPSTVSHHLSALEDDGLVVRERD 489
                                       5566678899******************************98765 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0076       4.5      25      72 ..     385     432 ..     364     437 .. 0.85
   2 !   20.0   0.0   1.1e-06   0.00068       4      79 ..     441     512 ..     438     519 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0076
                                       HT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXX CS
                   Penicillinase_R  25 eeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeav 72 
                                       +e+ ++++++ sTV+  +r L++ gl+++ +   + +Y  + +e+++ 
  gi|336252229|ref|YP_004595336.1| 385 SEVGDRQDVSLSTVRHHVRVLEEEGLIASVTIDGKRRYFTVEDEDDVA 432
                                       67788999***********************99999999999888865 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.1e-06
                                       S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXXXX CS
                   Penicillinase_R   4 lEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavasavkql 79 
                                       + +ev+e+l ++g+++ + + +ele++    +sTV   l+ L++ gl+ re++gra +   +++ e a+++++++l
  gi|336252229|ref|YP_004595336.1| 441 AKREVLEALADLGPVNNGRLADELERD----PSTVSHHLSALEDDGLVVRERDGRAVVNDLTADTEAAIRGESSEL 512
                                       5689***********************....**************************9999999999988887765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00012     0.071       1      51 [.     368     421 ..     368     423 .. 0.82
   2 !   11.8   0.0    0.0003      0.18       5      46 ..     445     485 ..     442     494 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                            HTH_11   1 RllqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpIesepg 51 
                                       R+++i+ l+ +a++    +e  ++ +vS +tvr +++ Lee g    v I+++++
  gi|336252229|ref|YP_004595336.1| 368 RREAIYDLI-RAEPGCYLSEVGDRQDVSLSTVRHHVRVLEEEGliasVTIDGKRR 421
                                       566666666.444447777888999********************9999999997 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0003
                            HTH_11   5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46 
                                       +le L +  gp++  +LA+eL++  +tv  ++ aLe+ g+ +
  gi|336252229|ref|YP_004595336.1| 445 VLEAL-ADLGPVNNGRLADELERDPSTVSHHLSALEDDGLVV 485
                                       56666.666789999***********************9665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.045        27      26      65 ..     385     425 ..     374     428 .. 0.85
   2 !   18.2   0.0   2.9e-06    0.0017      12      59 ..     444     491 ..     442     497 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.045
                                       CHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE- CS
                              TrmB  26 deiaeelgvprskvYevLrsLedkGlVerekgr.pklYrav 65 
                                       +e+  + +v+ s+v   +r Le+ Gl+  +    +++Y +v
  gi|336252229|ref|YP_004595336.1| 385 SEVGDRQDVSLSTVRHHVRVLEEEGLIASVTIDgKRRYFTV 425
                                       68889999*******************99985557777666 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.9e-06
                                       CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB  12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59 
                                       +v  aL  lgp +   +a el+++ s+v   L+ Led GlV re+  +
  gi|336252229|ref|YP_004595336.1| 444 EVLEALADLGPVNNGRLADELERDPSTVSHHLSALEDDGLVVRERDGR 491
                                       68899**************************************98765 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 ?    3.8   0.1     0.095        57      31      63 ..     391     429 ..     384     432 .. 0.77
   2 !   16.8   0.0   8.5e-06    0.0051      21      63 ..     454     498 ..     432     499 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.095
                                       TTSSHHHHHHHHHHHHHTTSEE..E..T.EE.EEES-HH CS
                         HTH_Crp_2  31 lGltretvsrilseLkreglis..r..g.rr.irildle 63 
                                         ++ +tv    + L++egli   +  g rr +++ d +
  gi|336252229|ref|YP_004595336.1| 391 QDVSLSTVRHHVRVLEEEGLIAsvTidGkRRyFTVEDED 429
                                       56788999999**********986355545678888865 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 8.5e-06
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE.T.EEEEES-HH CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglisr.g.rririldle 63 
                                       p+++  lA+ l   ++tvs  ls+L+++gl+ r + +r +++dl 
  gi|336252229|ref|YP_004595336.1| 454 PVNNGRLADELERDPSTVSHHLSALEDDGLVVReRdGRAVVNDLT 498
                                       899999**************************5233349999975 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 !   10.0   0.0    0.0011      0.63      29      52 ..     392     415 ..     385     421 .. 0.81
   2 !    8.4   0.0    0.0035       2.1      13      56 ..     454     492 ..     443     500 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                            HTH_12  29 digeravRyrLrkleergltrrvg 52 
                                       d++  +vR + r+lee+gl+  v 
  gi|336252229|ref|YP_004595336.1| 392 DVSLSTVRHHVRVLEEEGLIASVT 415
                                       556689*************97665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0035
                            HTH_12  13 pigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagr 56 
                                       p+  +++a+eL+         +v  +L +le++gl+ r + + +
  gi|336252229|ref|YP_004595336.1| 454 PVNNGRLADELERDP-----STVSHHLSALEDDGLVVRERDGRA 492
                                       688888888886532.....45899***********99887654 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 !   12.5   0.0   0.00016     0.095       1      44 [.     368     411 ..     368     414 .. 0.97
   2 ?    4.8   0.0      0.04        24       4      52 ..     444     492 ..     442     498 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                          HTH_DeoR   1 RieqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44 
                                       R+e+i +l++ +  + + e+ ++ +vS  T+R   + Lee+gl+
  gi|336252229|ref|YP_004595336.1| 368 RREAIYDLIRAEPGCYLSEVGDRQDVSLSTVRHHVRVLEEEGLI 411
                                       99****************************************98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.04
                          HTH_DeoR   4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthGGav 52 
                                       + le l++ g ++  +l+++l+  + T+   L+ Le +gl++R + G +
  gi|336252229|ref|YP_004595336.1| 444 EVLEALADLGPVNNGRLADELERDPSTVSHHLSALEDDGLVVRERDGRA 492
                                       67899999999999**************************999885543 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 ?    3.5   0.0      0.17     1e+02      21      52 ..     384     415 ..     376     426 .. 0.82
   2 !   13.7   0.0   0.00011     0.066       7      66 ..     444     499 ..     439     500 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.17
                            HTH_27  21 ladlcgrlnvedshisyslkkLtekGLvertg 52 
                                       l+++ +r +v+ s++   ++ L+e GL+ + +
  gi|336252229|ref|YP_004595336.1| 384 LSEVGDRQDVSLSTVRHHVRVLEEEGLIASVT 415
                                       68999999********************5554 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00011
                            HTH_27   7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTd 66 
                                        vL+ ++  ++++   +l++ l ++ s++s  l++L+  GLv+r+   +d+r++   lT+
  gi|336252229|ref|YP_004595336.1| 444 EVLEALA-DLGPVNNGRLADELERDPSTVSHHLSALEDDGLVVRE---RDGRAVVNDLTA 499
                                       6888888.9999999***************************777...778999888887 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0094       5.6      20      56 ..     380     413 ..     369     418 .. 0.84
   2 !    9.0   0.0    0.0018         1      29      63 ..     459     493 ..     444     494 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0094
                                       TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR  20 pGdkLPsereLaaefgVsrttvReALrrLeaeglver 56 
                                       pG  L   +e+ ++ +Vs +tvR   r Le+egl+ +
  gi|336252229|ref|YP_004595336.1| 380 PGCYL---SEVGDRQDVSLSTVRHHVRVLEEEGLIAS 413
                                       56666...78889999******************976 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                                       HHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEE CS
                              GntR  29 eLaaefgVsrttvReALrrLeaeglverrqgrGtf 63 
                                        La+e++ + +tv   L+ Le +glv+r++ + ++
  gi|336252229|ref|YP_004595336.1| 459 RLADELERDPSTVSHHLSALEDDGLVVRERDGRAV 493
                                       59**************************9876655 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.19   1.1e+02       8      42 ..     367     403 ..     364     403 .. 0.81
   2 !   12.0   0.0   0.00023      0.14       8      41 ..     441     475 ..     439     476 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.19
                            HTH_38   8 eeReeIerll..aeGlslreIArrLgrspsTIsRElk 42 
                                       e Re I++l+  + G+ l+e++ r ++s sT+  +++
  gi|336252229|ref|YP_004595336.1| 367 ERREAIYDLIraEPGCYLSEVGDRQDVSLSTVRHHVR 403
                                       66999****6333579999*************99887 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00023
                            HTH_38   8 eeReeIerllaeG.lslreIArrLgrspsTIsREl 41 
                                       + Re++e+l + G  ++ + A +L r+psT+s +l
  gi|336252229|ref|YP_004595336.1| 441 AKREVLEALADLGpVNNGRLADELERDPSTVSHHL 475
                                       579999999999999999**************987 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 ?    6.1   0.0     0.013         8      81     113 ..     391     423 ..     385     436 .. 0.81
   2 !    8.5   0.0    0.0024       1.5      74     103 ..     457     486 ..     454     492 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                              RP-C  81 lglsestlrrhlaaLveaGliirrDspngkRya 113
                                        ++s st+r+h++ L e Gli+       +Ry 
  gi|336252229|ref|YP_004595336.1| 391 QDVSLSTVRHHVRVLEEEGLIASVTIDGKRRYF 423
                                       56899****************987766666665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0024
                              RP-C  74 NaqLsralglsestlrrhlaaLveaGliir 103
                                       N +L+ +l + +st+++hl+aL + Gl++r
  gi|336252229|ref|YP_004595336.1| 457 NGRLADELERDPSTVSHHLSALEDDGLVVR 486
                                       88999***********************98 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.7e-05      0.01      36      75 ..     389     428 ..     367     436 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                                       TTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSS CS
                               FUR  36 edpeislaTVYrtLklleeaglvkelefedgesryelakk 75 
                                       +++++sl+TV   +++lee+gl+ +++++++++++ ++++
  gi|336252229|ref|YP_004595336.1| 389 DRQDVSLSTVRHHVRVLEEEGLIASVTIDGKRRYFTVEDE 428
                                       6789*************************88888887754 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0015      0.92      26      58 ..     382     414 ..     371     419 .. 0.88
   2 ?    4.8   0.0     0.062        37      21      57 ..     450     486 ..     443     492 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0015
                                       B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2  26 vsseeiaerqnispsylekilakLrkaglvksv 58 
                                       + ++e+ +rq++s s +++ ++ L+++gl+ sv
  gi|336252229|ref|YP_004595336.1| 382 CYLSEVGDRQDVSLSTVRHHVRVLEEEGLIASV 414
                                       5678999***********************997 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.062
                                       STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2  21 eeeepvsseeiaerqnispsylekilakLrkaglvks 57 
                                       ++ +pv+   +a++ +  ps +++ l+ L+  glv  
  gi|336252229|ref|YP_004595336.1| 450 ADLGPVNNGRLADELERDPSTVSHHLSALEDDGLVVR 486
                                       5556788899************************965 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   5.5   1.4e-05    0.0085      15     103 ..      96     183 ..      82     218 .. 0.72
   2 ?   -1.2   0.1       2.6   1.6e+03      15      58 ..     447     502 ..     440     508 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                                       CHHHCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHH CS
                    Apolipoprotein  15 eleeqlaplaqelrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaadae 91 
                                       e+++ l + a++  +    e++++  +l+ +lee +++le+ ++e    l+++  e    l+++t++++e l+  ++
  gi|336252229|ref|YP_004595336.1|  96 ETNDSLDD-ADSSSNDGDTESDDAETELGDDLEERTDSLEDATNETTDSLEDTPNETTDSLENATDDVTEPLEDTTN 171
                                       55555555.34455556678889999999999999999999999999999999999999999999999776666666 PP

                                       CCHHCHCCHCHH CS
                    Apolipoprotein  92 elqeqlavyaee 103
                                       e  + l+  ae+
  gi|336252229|ref|YP_004595336.1| 172 ETADELEDSAED 183
                                       666666554443 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.6
                                       CHHHCHHCHHH.HHHHHHHHHHHHHHHHH...........HHHHHHHHHHCCCCHH CS
                    Apolipoprotein  15 eleeqlaplaq.elrdrlskeleelrarl...........raeleevrarlepyrd 58 
                                       e  + l+p++  +l+d l+ ++  ++  l           +++  +v++ l+++++
  gi|336252229|ref|YP_004595336.1| 447 EALADLGPVNNgRLADELERDPSTVSHHLsaleddglvvrERDGRAVVNDLTADTE 502
                                       55677888877568888888888888888777777777777777777777777766 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.017        10      21      49 ..     390     420 ..     377     422 .. 0.80
   2 ?    5.8   0.0     0.024        14       6      52 ..     447     491 ..     442     503 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.017
                            HTH_29  21 llglsrrtvyrwlkrfeegGlaa..lldrrr 49 
                                       + ++s +tv+++++  ee+Gl a  ++d++r
  gi|336252229|ref|YP_004595336.1| 390 RQDVSLSTVRHHVRVLEEEGLIAsvTIDGKR 420
                                       5689****************77756777443 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.024
                            HTH_29   6 lllaeGvs.tvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgr 52 
                                        +la+ ++ +  ++A  l  +++tv ++l + e +G   l  r r gr
  gi|336252229|ref|YP_004595336.1| 447 EALADLGPvNNGRLADELERDPSTVSHHLSALEDDG---LVVRERDGR 491
                                       55555545688899**********************...666666666 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 ?   -2.3   0.1       7.6   4.5e+03      38      49 ..     119     130 ..     117     134 .. 0.83
   2 ?    0.5   0.0         1   6.1e+02      21      40 ..     389     408 ..     383     409 .. 0.84
   3 ?    9.3   0.0    0.0018       1.1       6      39 ..     445     480 ..     442     496 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.6
                                       HHHHTS-SEEES CS
                             HTH_1  38 EeelgvpLfeRt 49 
                                       E elg++L eRt
  gi|336252229|ref|YP_004595336.1| 119 ETELGDDLEERT 130
                                       899*****9995 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1
                                       HHHTS-HHHHHHHHHHHHHH CS
                             HTH_1  21 eeLglsqpavsrqikrLEee 40 
                                       ++  +s ++v ++++ LEee
  gi|336252229|ref|YP_004595336.1| 389 DRQDVSLSTVRHHVRVLEEE 408
                                       6678999***********96 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0018
                                       HHHHHHHHS..SHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_1   6 lfvavaeeg..sftrAAeeLglsqpavsrqikrLEe 39 
                                       +++a+a+ g  +  r A+eL   +++vs+++++LE+
  gi|336252229|ref|YP_004595336.1| 445 VLEALADLGpvNNGRLADELERDPSTVSHHLSALED 480
                                       67777777733334559******************8 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 ?    3.5   0.0      0.14        81      35      53 ..     398     416 ..     385     424 .. 0.85
   2 ?    7.9   0.0    0.0056       3.3      24      51 ..     460     487 ..     455     490 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.14
                    B-block_TFIIIC  35 lfyrlksLekkgLIvkqsi 53 
                                       + +++++Le+ gLI  ++i
  gi|336252229|ref|YP_004595336.1| 398 VRHHVRVLEEEGLIASVTI 416
                                       6689************999 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0056
                    B-block_TFIIIC  24 LakeskqdprslfyrlksLekkgLIvkq 51 
                                       La e++ dp+ + ++l +Le+ gL+v+ 
  gi|336252229|ref|YP_004595336.1| 460 LADELERDPSTVSHHLSALEDDGLVVRE 487
                                       8999*********************986 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 ?    4.9   0.0     0.048        29      29      56 ..     388     415 ..     366     421 .. 0.87
   2 ?    6.8   0.0     0.012       7.4       8      56 ..     440     488 ..     433     503 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.048
                           DUF2250  29 akeleipleevrellkkLeelGLlerve 56 
                                        ++ +++l+ vr+ ++ Lee GL+  v+
  gi|336252229|ref|YP_004595336.1| 388 GDRQDVSLSTVRHHVRVLEEEGLIASVT 415
                                       5678999*****************9886 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.012
                           DUF2250   8 elalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56 
                                       + + +vl+ l+ +++     +a+ele + + v++ l +Le+ GL+ r  
  gi|336252229|ref|YP_004595336.1| 440 PAKREVLEALADLGPVNNGRLADELERDPSTVSHHLSALEDDGLVVRER 488
                                       5667899999999988888999**********************97754 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 ?    2.1   0.0      0.27   1.6e+02      39      57 ..     394     412 ..     385     421 .. 0.83
   2 ?    8.2   0.0    0.0035       2.1      39      59 ..     467     487 ..     459     492 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.27
                                       .HHHHHHHHHHHHHTTSEE CS
                     LexA_DNA_bind  39 SpsaveehLkaLerKGyie 57 
                                       S s+v +h + Le  G+i 
  gi|336252229|ref|YP_004595336.1| 394 SLSTVRHHVRVLEEEGLIA 412
                                       5789************996 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0035
                                       .HHHHHHHHHHHHHTTSEE-G CS
                     LexA_DNA_bind  39 SpsaveehLkaLerKGyierd 59 
                                        ps+v +hL aLe  G++ r+
  gi|336252229|ref|YP_004595336.1| 467 DPSTVSHHLSALEDDGLVVRE 487
                                       49**************98553 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0         1   6.2e+02      20      42 ..     337     362 ..     336     364 .. 0.93
   2 ?    9.7   0.0    0.0015      0.88      14      47 ..     399     432 ..     386     441 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1
                                       HHHHTT.-S-EE..-TTS-EEEEHHH CS
                            MerR_1  20 wekegl.lkpkr..teggrryYtded 42 
                                       w ++ l l p++  +  g+ +Y+d+d
  gi|336252229|ref|YP_004595336.1| 337 WLRRLLsLAPAEllSVLGYSRYDDSD 362
                                       99********************9987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHTT-S-EE-TTS-EEEEHHHHHHHH CS
                            MerR_1  14 thtlrywekegllkpkrteggrryYtdedierLk 47 
                                        h +r  e+egl+     +g rry+t ed + ++
  gi|336252229|ref|YP_004595336.1| 399 RHHVRVLEEEGLIASVTIDGKRRYFTVEDEDDVA 432
                                       588999******999999*********9977665 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.15        92      24      42 ..     397     415 ..     395     420 .. 0.84
   2 ?    0.2   0.7       1.3   7.9e+02      13      32 ..     433     452 ..     431     453 .. 0.87
   3 ?   10.4   0.0   0.00081      0.48      24      43 ..     470     489 ..     469     492 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.15
                          BLACT_WH  24 gvlahLeKLeeeGkVkreg 42 
                                       +v++h + LeeeG+++++ 
  gi|336252229|ref|YP_004595336.1| 397 TVRHHVRVLEEEGLIASVT 415
                                       6999***********9865 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                          BLACT_WH  13 vpeslhpaAergvlahLeKL 32 
                                       +++ l ++A+r vl  L  L
  gi|336252229|ref|YP_004595336.1| 433 LHAALAEPAKREVLEALADL 452
                                       678899*********99877 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00081
                          BLACT_WH  24 gvlahLeKLeeeGkVkregd 43 
                                       +v +hL  Le++G+V+re d
  gi|336252229|ref|YP_004595336.1| 470 TVSHHLSALEDDGLVVRERD 489
                                       689**************997 PP

>> DUF2300  Predicted secreted protein (DUF2300)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00047      0.28      49     103 ..     327     379 ..     317     401 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00047
                           DUF2300  49 eaWlarqapaWlrelralqgeervsvkalltllaglPaedrerarsvlrdlvsae 103
                                        +Wl+  + +Wlr+l  l++ e  sv    +   + P    ++ r++++dl  ae
  gi|336252229|ref|YP_004595336.1| 327 ANWLNPTQGRWLRRLLSLAPAELLSVLGYSRYDDSDPL--ENERREAIYDLIRAE 379
                                       68************************************..555566666665555 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 ?    4.3   0.0     0.068        41      35      74 ..     391     425 ..     383     435 .. 0.75
   2 ?    5.1   0.0     0.038        23      37      64 ..     466     491 ..     460     503 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.068
                                       ----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEE CS
                            Cdc6_C  35 dpltqrevsdllseLemlgileleksskGrregrtrkisL 74 
                                       + ++ ++v+++++ Le  g++ + +       g+ r++++
  gi|336252229|ref|YP_004595336.1| 391 QDVSLSTVRHHVRVLEEEGLIASVTI-----DGKRRYFTV 425
                                       678999*****************999.....355555555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.038
                                       --HHHHHHHHHHHHHTTSEEEEEEE-CC CS
                            Cdc6_C  37 ltqrevsdllseLemlgileleksskGr 64 
                                       ++ ++vs++ls Le+ g++ +e+   Gr
  gi|336252229|ref|YP_004595336.1| 466 RDPSTVSHHLSALEDDGLVVRERD--GR 491
                                       56799**************99987..33 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.7   2.8e+03      11      55 ..     366     411 ..     359     414 .. 0.58
   2 ?   12.7   2.0   0.00017       0.1      10      59 ..     438     488 ..     429     490 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.7
                           DprA_WH  11 ddlerrvLaaLgpeP.vhvDqLvrrtglpaaevsaaLleLELaGlv 55 
                                        + ++++ +++ +eP + + ++  r  ++ ++v ++   LE +Gl+
  gi|336252229|ref|YP_004595336.1| 366 NERREAIYDLIRAEPgCYLSEVGDRQDVSLSTVRHHVRVLEEEGLI 411
                                       5677888888888862344444444555555555555555555555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00017
                           DprA_WH  10 lddlerrvLaaLgp.ePvhvDqLvrrtglpaaevsaaLleLELaGlverlp 59 
                                       +++ +r vL+aL+   Pv    L+ ++  ++++vs++L+ LE +Glv r  
  gi|336252229|ref|YP_004595336.1| 438 AEPAKREVLEALADlGPVNNGRLADELERDPSTVSHHLSALEDDGLVVRER 488
                                       578999******9889*******************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1436  (0.0800937); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                        48  (0.00267723); 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: 0.82u 0.29s 00:00:01.10 Elapsed: 00:00:00.42
# Mc/sec: 3723.69
//
Query:       gi|336252230|ref|YP_004595337.1|  [L=109]
Description: zinc finger CHY domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-13   48.8   5.7      1e-12   48.3   5.7    1.2  1  zf-CHY    CHY zinc finger
     0.0019   18.5   0.4     0.0019   18.5   0.4    2.4  2  C1_2      C1 domain
     0.0073   16.3   6.9      0.009   16.0   4.3    2.2  1  DZR       Double zinc ribbon
  ------ inclusion threshold ------
        0.1   12.6   0.8        0.1   12.6   0.8    1.8  2  HypA      Hydrogenase/urease nickel incorporation, metallocha
       0.23   11.4   7.8       0.22   11.4   3.6    2.8  2  zf-HIT    HIT zinc finger


Domain annotation for each model (and alignments):
>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   5.7   2.9e-16     1e-12       1      74 [.      17      91 ..      17      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 2.9e-16
                            zf-CHY  1 CkHykra..vvairapcCkklyaCreCHeeledhelerlevkevlcllCeteqekavlCkkCkk.......efaeyfCp 70
                                      C+Hy++   vva+r++cC+ +++C +CHe+l+dhe   +  +++        +e +vlC+ C++         a+y Cp
  gi|336252230|ref|YP_004595337.1| 17 CAHYHTVrdVVAFRFNCCDGYFPCFRCHEALTDHEGVPWPRERF--------DEPSVLCGVCRTeltvpeyLEADYRCP 87
                                      *****9888********************************988........6789******998855544334558** PP

                            zf-CHY 71 iCkl 74
                                       C++
  gi|336252230|ref|YP_004595337.1| 88 ACDA 91
                                      **86 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   6.8         5   1.8e+04      30      46 ..      28      43 ..      12      46 .. 0.74
   2 !   18.5   0.4   5.2e-07    0.0019      13      47 .]      59      98 ..      44      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 5
                              C1_2 30 gffYsCseCd.fslhvrC 46
                                       f+++C  Cd ++ ++rC
  gi|336252230|ref|YP_004595337.1| 28 AFRFNC--CDgYFPCFRC 43
                                      566788..7656666666 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 5.2e-07
                              C1_2 13 edssesfnCsaCgrk..idgff....YsCseCdfslhvrCa 47
                                      + ++ s  C +C+++  + +++    Y+C+ Cd ++   Ca
  gi|336252230|ref|YP_004595337.1| 59 RFDEPSVLCGVCRTEltV-PEYleadYRCPACDAAFNPGCA 98
                                      55667789*******963.4445799*********999997 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   4.3   2.5e-06     0.009       1      42 [.      40      97 ..      40      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.5e-06
                               DZR  1 CpqCgee.............lppdarfCseCgtklkavaa....edrCpsCgekvdpea 42
                                      C +C+e+              ++ +  C+ C+t+l  v++     +rCp+C+++ +p++
  gi|336252230|ref|YP_004595337.1| 40 CFRCHEAltdhegvpwprerFDEPSVLCGVCRTELT-VPEyleaDYRCPACDAAFNPGC 97
                                      777777777777777777777888899*******97.5555999*********998887 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 ?   -0.6   0.3      0.35   1.3e+03      66      79 ..      33      46 ..      13      55 .. 0.57
   2 ?   12.6   0.8   2.9e-05       0.1      68      95 ..      62      92 ..      57     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.35
                                      EE--EEEETTTS-E CS
                              HypA 66 evpvkvrCreCgke 79
                                        +  + C +C++ 
  gi|336252230|ref|YP_004595337.1| 33 CCDGYFPCFRCHEA 46
                                      33444445555544 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.9e-05
                                      --EEEETTTS-EEECHH..H.HHS-TTTSSS CS
                              HypA 68 pvkvrCreCgkefelee..k.alrCpkCgsa 95
                                      + +v C +C++e ++ e  + ++rCp+C++a
  gi|336252230|ref|YP_004595337.1| 62 EPSVLCGVCRTELTVPEylEaDYRCPACDAA 92
                                      57899*********777453689*****975 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.68   2.4e+03      16      20 ..      40      44 ..      38      47 .. 0.67
   2 ?   11.4   3.6     6e-05      0.22       2      21 ..      64      91 ..      63      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.68
                                      -TTT- CS
                            zf-HIT 16 CpkCn 20
                                      C +C+
  gi|336252230|ref|YP_004595337.1| 40 CFRCH 44
                                      66665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6e-05
                                      --B-TTT-S........B-SEE-TTT-- CS
                            zf-HIT  2 rklCgvCgf........pakYkCpkCnt 21
                                      + lCgvC          +a Y+Cp C +
  gi|336252230|ref|YP_004595337.1| 64 SVLCGVCRTeltvpeylEADYRCPACDA 91
                                      679****98888888899********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 959.37
//
Query:       gi|336252231|ref|YP_004595338.1|  [L=190]
Description: Gas vesicle synthesis family protein [Halopiger xanaduensis SH-6]
Scores for complete 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   98.4   1.6    4.1e-28   97.2   1.6    1.6  1  GvpO         Gas vesicle synthesis protein GvpO
  ------ inclusion threshold ------
       0.15   12.2   0.4       0.28   11.3   0.4    1.4  1  zf-SAP30     SAP30 zinc-finger


Domain annotation for each model (and alignments):
>> GvpO  Gas vesicle synthesis protein GvpO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   1.6   4.6e-32   4.1e-28       7      92 ..     100     185 ..      94     187 .. 0.92

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 4.6e-32
                              GvpO   7 eeeesrleaaeaarkareqlaeLlgrelegvssvertedgWrvevevlElervPdttdilasYeveldeegeltgYr 83 
                                       +++e+  ++  ++r+ ++++ eL+gre+++vs++  t+dgWr++vev+E+++vPdt+di+++Ye+el+e+  + gYr
  gi|336252231|ref|YP_004595338.1| 100 TDHEEIEGVLAVRRTVQSSAGELIGREFDAVSEIAPTDDGWRAVVEVVERRAVPDTQDIIGRYEIELNENATVHGYR 176
                                       555666678889999999*********************************************************** PP

                              GvpO  84 rvrRYrRgr 92 
                                       r++RYrRg+
  gi|336252231|ref|YP_004595338.1| 177 RLDRYRRGD 185
                                       ********8 PP

>> zf-SAP30  SAP30 zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   3.1e-05      0.28       2      23 ..      12      33 ..      11      39 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.1e-05
                          zf-SAP30  2 sdqlCcLvddgeRCkrkaGnas 23
                                      +dq+ +L++dgeRC+r+a +  
  gi|336252231|ref|YP_004595338.1| 12 NDQCKALTEDGERCSRPAKDDG 33
                                      578889***********97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1026  (0.0572257); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 1561.47
//
Query:       gi|336252232|ref|YP_004595339.1|  [L=345]
Description: gas vesicle protein GvpN [Halopiger xanaduensis SH-6]
Scores for 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-16   59.2   0.0    1.5e-14   54.2   0.0    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
    2.3e-05   24.1   0.3    7.4e-05   22.4   0.3    1.9  1  AAA_25           AAA domain
    5.3e-05   23.6   0.0    9.8e-05   22.8   0.0    1.7  1  AAA              ATPase family associated with various cellul
    0.00025   20.8   0.0    0.00048   19.9   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0051   16.7   0.0      0.011   15.6   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
     0.0065   16.0   0.0      0.015   14.8   0.0    1.6  1  PhoH             PhoH-like protein
     0.0077   15.9   0.0        1.3    8.7   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.027   14.9   0.0      0.058   13.8   0.0    1.6  1  AAA_16           AAA ATPase domain
       0.03   14.4   0.0      0.068   13.3   0.0    1.6  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.034   13.7   0.0      0.059   12.9   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.035   14.3   0.0       0.11   12.7   0.0    2.0  2  AAA_33           AAA domain
      0.038   13.4   0.0      0.058   12.8   0.0    1.2  1  IPT              Isopentenyl transferase
      0.044   13.1   0.1       0.47    9.7   0.0    2.6  3  Zeta_toxin       Zeta toxin
      0.048   13.6   0.0       0.11   12.4   0.0    1.5  2  ATPase_2         ATPase domain predominantly from Archaea
       0.12   12.9   0.0       0.19   12.3   0.0    1.6  1  ABC_tran         ABC transporter
       0.14   11.2   0.0       0.22   10.6   0.0    1.2  1  AAA_9            ATP-binding dynein motor region


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   1.3e-17   1.5e-14       2     138 .]      82     235 ..      81     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.3e-17
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........................---- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..................ngttslvdsplv 60 
                                       v L+Gp+G+gK+ la + aa  +r+v+ +++ +   ++ l+g                         ++++vd+pl 
  gi|336252232|ref|YP_004595339.1|  82 VHLIGPTGCGKTALALSAAAERGRPVVWINGDEAVDTAALVGDHAGGerykeddrfvsgvskqteIVRERWVDNPLS 158
                                       77****************************************99865777788888888887776677889999999 PP

                                       ----G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHT CS
                             AAA_5  61 raaregeilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrs 136
                                        a+reg++lv +E+ r ++++ n+Lls++ee  l  +  ++  +       ++fr i+t+n+++  +++e++ al++
  gi|336252232|ref|YP_004595339.1| 159 VAVREGATLVYNEFSRSDPAAHNVLLSVFEEGVLERPGKRGDDRSID--VHPEFRAIFTSNDVEyAGVHEQQDALLD 233
                                       9999*******************************777776665544..5566************9*********** PP

                                       T- CS
                             AAA_5 137 Rf 138
                                       Rf
  gi|336252232|ref|YP_004595339.1| 234 RF 235
                                       *9 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.3   6.6e-08   7.4e-05      20      83 ..      66     116 ..      55     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.6e-08
                            AAA_25  20 pprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdse 83 
                                       +++r  + g+l a+  + l+G++g+GKt+lal+ a++  +G+           +V++++++++ 
  gi|336252232|ref|YP_004595339.1|  66 QSLRGRITGWLEADQPVHLIGPTGCGKTALALSAAAE--RGR-----------PVVWINGDEAV 116
                                       678899**************************99986..333...........45555555555 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 !   22.8   0.0   8.8e-08   9.8e-05       2      38 ..      83     121 ..      82     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8.8e-08
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS..S CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk..y 38 
                                        l+Gp G+GKT+la + a e g++++ i+g e ++   +
  gi|336252232|ref|YP_004595339.1|  83 HLIGPTGCGKTALALSAAAERGRPVVWINGDEAVDTaaL 121
                                       699*****************************9965552 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 !   19.9   0.0   4.3e-07   0.00048      31      82 ..      61     111 ..      50     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.3e-07
                         IstB_IS21  31 dkrkvkeL..atlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvr 82 
                                       +  +v++L  + + ++e+ + + l+Gp+G GK+ la +   +a+++g  v+++ 
  gi|336252232|ref|YP_004595339.1|  61 ETDAVQSLrgRITGWLEADQPVHLIGPTGCGKTALALS---AAAERGRPVVWIN 111
                                       56677888333468*******************99876...5667777777775 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 !   15.6   0.0   9.7e-06     0.011      66     130 ..     167     236 ..     159     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.7e-06
                             AAA_3  66 lladeinrappktqsalleameerqvtv.....egethklpepflvlatqnPieqeGtyplpeaqldrfl 130
                                       l+ +e  r+ p ++  ll + ee  +       ++++ +++  f  + t n +e+ G+++  +a ldrf+
  gi|336252232|ref|YP_004595339.1| 167 LVYNEFSRSDPAAHNVLLSVFEEGVLERpgkrgDDRSIDVHPEFRAIFTSNDVEYAGVHEQQDALLDRFV 236
                                       5668999*************9999887522222456788999***************************6 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.3e-05     0.015      16      42 ..      76     102 ..      64     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                                       HHH-SEEEEE--TTSSTTHHHHHHHHH CS
                              PhoH  16 lkkndivfaiGpaGtGKtylavalave 42 
                                       l++ + v  iGp+G+GKt la+++a+e
  gi|336252232|ref|YP_004595339.1|  76 LEADQPVHLIGPTGCGKTALALSAAAE 102
                                       566777899**************9986 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0011       1.3       5      42 ..      62      99 ..      59     122 .. 0.81
   2 ?    5.0   0.0     0.016        18      93     135 ..     163     206 ..     158     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                                      SHHHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHH CS
                   Sigma54_activat  5 sealkelleqikkvaktdlsvlitGesGtGKellarai 42
                                      ++a+++l+ +i+   + d +v + G +G+GK+ la + 
  gi|336252232|ref|YP_004595339.1| 62 TDAVQSLRGRITGWLEADQPVHLIGPTGCGKTALALSA 99
                                      5678888899999999****************999654 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.016
                                       TTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSS.SEEE--E CS
                   Sigma54_activat  93 dgGtlfLDeigelplelQekLlrvlqegevervGss.keikvdv 135
                                       +g tl  +e ++ ++++ + Ll v +eg +er G++ + +++dv
  gi|336252232|ref|YP_004595339.1| 163 EGATLVYNEFSRSDPAAHNVLLSVFEEGVLERPGKRgDDRSIDV 206
                                       7899****************************998633455554 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   5.2e-05     0.058      25      61 ..      80     115 ..      61     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.2e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcd 61 
                                       + v l+G+ G+GK++l+ +++ +  +  +++++g+  
  gi|336252232|ref|YP_004595339.1|  80 QPVHLIGPTGCGKTALALSAAAERGRP-VVWINGDEA 115
                                       56899************7777544444.666776654 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 ?   13.3   0.0   6.1e-05     0.068       4      39 ..      62      97 ..      59     120 .. 0.86
   2 ?   -3.5   0.0       9.1     1e+04      68      90 ..     162     184 ..     140     190 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.1e-05
                                      -HHHHHHHHHHHHHHT-SS-EEEEEETT--HHHHHH CS
                   Sigma54_activ_2  4 saaiqelkerLeqaaqsklpvfltGekGsgkelvAr 39
                                      + a+q l+ r+    ++  pv+l+G+ G+gk+  A 
  gi|336252232|ref|YP_004595339.1| 62 TDAVQSLRGRITGWLEADQPVHLIGPTGCGKTALAL 97
                                      678999*************************99885 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.1
                                       TTTSEEEEEE-TT--HHHHHHHH CS
                   Sigma54_activ_2  68 akggtLylkdiadlskaeqkeLl 90 
                                        +g+tL+ +++   ++a+   Ll
  gi|336252232|ref|YP_004595339.1| 162 REGATLVYNEFSRSDPAAHNVLL 184
                                       47888888888877777666655 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 ?   12.9   0.0   5.2e-05     0.059      14      52 ..      60      98 ..      50     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                             AAA_7 14 VptvdtvrysyllelllknkkpvllvGptGtGKtviikd 52
                                      V+t    +++  ++  l++++pv l+GptG+GKt+++ +
  gi|336252232|ref|YP_004595339.1| 60 VETDAVQSLRGRITGWLEADQPVHLIGPTGCGKTALALS 98
                                      6666666666667778999***************98765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.7e-05      0.11       2      39 ..      82     123 ..      82     209 .. 0.81
   2 ?   -2.7   0.0       5.2   5.8e+03      65      79 ..     257     271 ..     222     297 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.7e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrr..rlfg 39 
                                       v l+G+ G+GK+ la + ++++g  +v ++ d++ +  +l+g
  gi|336252232|ref|YP_004595339.1|  82 VHLIGPTGCGKTALALSAAAERGrpVVWINGDEAVDtaALVG 123
                                       5689******************999999****9888433443 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.2
                            AAA_33  65 kalsagrnvildatn 79 
                                       +   +g  +++dat 
  gi|336252232|ref|YP_004595339.1| 257 ELSDEGVETVVDATR 271
                                       444566666677664 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.2e-05     0.058       6      31 ..      84     109 ..      80     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.2e-05
                               IPT   6 ifGatttGKtaeaiklaketgapviv 31 
                                       + G+t+ GKta a + a e+g pv+ 
  gi|336252232|ref|YP_004595339.1|  84 LIGPTGCGKTALALSAAAERGRPVVW 109
                                       45**********************96 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   0.00042      0.47      21      53 ..      84     114 ..      69     118 .. 0.87
   2 ?   -1.6   0.0       1.2   1.4e+03     160     195 ..     135     170 ..     125     173 .. 0.70
   3 ?   -1.3   0.0         1   1.1e+03      57      76 ..     206     225 ..     200     234 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00042
                        Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrldpDd 53 
                                       l G +G+GK++la  +++e   ++ vv +++D+
  gi|336252232|ref|YP_004595339.1|  84 LIGPTGCGKTALALSAAAER--GRPVVWINGDE 114
                                       5699*********9999996..9********97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                        Zeta_toxin 160 deafeglresvealeeekqldrvkikdrdgktvlyd 195
                                       d+ ++g+++++e++ e+   + ++++ r+g t +y+
  gi|336252232|ref|YP_004595339.1| 135 DRFVSGVSKQTEIVRERWVDNPLSVAVREGATLVYN 170
                                       556677777777777776555566777777777776 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1
                        Zeta_toxin  57 lhPeyeeilkadpkkaselt 76 
                                        hPe+++i+  ++ +++ + 
  gi|336252232|ref|YP_004595339.1| 206 VHPEFRAIFTSNDVEYAGVH 225
                                       7*******998766665543 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 ?   12.4   0.0   9.4e-05      0.11      11      44 ..      72     103 ..      68     153 .. 0.82
   2 ?   -3.1   0.0       5.3   5.9e+03     180     214 ..     231     261 ..     213     271 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.4e-05
                          ATPase_2  11 leeilerepneiyfiYGpegsGKtaLlkeiienl 44 
                                       +  +le   ++++ + Gp g+GKtaL   ++ ++
  gi|336252232|ref|YP_004595339.1|  72 ITGWLEA--DQPVHLIGPTGCGKTALALSAAAER 103
                                       5667766..8899999**********99888776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.3
                          ATPase_2 180 legrhkyilvddldketalnflkegfkeleelske 214
                                       l +r  +++vd  d et +++++       els+e
  gi|336252232|ref|YP_004595339.1| 231 LLDRFVGVHVDYYDDETEREIVRSH----VELSDE 261
                                       4455555555555555555555553....333344 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017      0.19       8      28 ..      76      96 ..      71     272 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                                      EETTSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  8 lkegekvaivGenGaGKStLl 28
                                      l++++ v ++G++G+GK+ L+
  gi|336252232|ref|YP_004595339.1| 76 LEADQPVHLIGPTGCGKTALA 96
                                      788999************996 PP

>> AAA_9  ATP-binding dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019      0.22      57     123 ..     150     218 ..     129     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                                       TTHHHH.HHHHHHTTSEEEESTT.SSHHSTTHHHHTTCCEE....CEEEESSS.E.EE--SSCEEEEEESS CS
                             AAA_9  57 kkflkt.LenairfGkplliedvgeeldpiLepvLekeiikkg..rkliklgd.keieysenFrLylttkl 123
                                       ++++++ L  a+r G +l+ ++  ++ dp+  +vL   + + g  ++  k gd + i+++++Fr ++t+++
  gi|336252232|ref|YP_004595339.1| 150 ERWVDNpLSVAVREGATLVYNEF-SRSDPAAHNVLLSVFEE-GvlERPGKRGDdRSIDVHPEFRAIFTSND 218
                                       4555555999*************.99**********76666.5565566666559*********9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2587.06
//
Query:       gi|336252233|ref|YP_004595340.1|  [L=95]
Description: Gas vesicle structural protein [Halopiger xanaduensis SH-6]
Scores for 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-17   60.8   6.7    1.3e-16   60.4   6.7    1.2  1  Gas_vesicle  Gas vesicle protein


Domain annotation for each model (and alignments):
>> Gas_vesicle  Gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   6.7   7.2e-21   1.3e-16       1      39 []      12      50 ..      12      50 .. 0.99

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 7.2e-21
                       Gas_vesicle  1 sLaDlLDrvLdkGvVIdgditisvagieLltikLrlviA 39
                                      sLa++LDr+LdkGvVId + +isv+gieLlti++r+v+A
  gi|336252233|ref|YP_004595340.1| 12 SLAEVLDRILDKGVVIDVWARISVVGIELLTIEARVVVA 50
                                      8*************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 751.85
//
Query:       gi|336252234|ref|YP_004595341.1|  [L=209]
Description: Gas vesicle synthesis GvpLGvpF [Halopiger xanaduensis SH-6]
Scores for 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  153.7   2.2      1e-25   91.1   0.3    2.0  2  GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF


Domain annotation for each model (and alignments):
>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.3   5.8e-30     1e-25       2     130 ..       4     132 ..       3     135 .. 0.89
   2 !   64.5   0.3   7.7e-22   1.4e-17     171     244 .]     129     202 ..     123     202 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 5.8e-30
                         GvpL_GvpF   2 lYvYgivdadsddseaadtGv.dgepVrlvragglaavvsdvpeeeydaerleqverwllaHqrVvealma...egt 74 
                                       +YvYgivd ++++ e ++  v + ++V++++++ ++avvsd+++ + ++++++     + +H++V++++m+    ++
  gi|336252234|ref|YP_004595341.1|   4 RYVYGIVDGTEEPIEFETDAVgGADRVYTISHRRIGAVVSDIDTTDPEETDED-----AQRHDDVLREVMEydgGRS 75 
                                       8******9999988877766656899***************************.....************6567789 PP

                         GvpL_GvpF  75 vlPlrFgtvlkdeeavrelLeeeadelreaLerlagkvEygvkvlwdeea.lleell 130
                                       ++P++Fg+ ++++++++++L+  +  +r+a+  ++g+ E+g+kv+ d +a +++e++
  gi|336252234|ref|YP_004595341.1|  76 IVPMQFGMAFESDRTLKNVLRGARPAFRRAMNDVEGRFELGLKVVRDADAdVDTEAV 132
                                       ***********************************************9541444444 PP

  == domain 2  score: 64.5 bits;  conditional E-value: 7.7e-22
                         GvpL_GvpF 171 reelaeeleeaLaplaeevrerepqdeemvlnaafLvdrdreeefgeaveelaarldglevrltGPwpPYsFvp 244
                                        e++ e++  +L+p+a+++++++  +++ vln ++L+drd+ e+f+eav++l+++ ++l++r+tGP +PYsFv+
  gi|336252234|ref|YP_004595341.1| 129 TEAVEETVAGELEPIAAQSVPNDLFSDRLVLNRSYLIDRDEREAFDEAVARLEEKREDLTFRYTGPFAPYSFVD 202
                                       6788899************************************************999**************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1520.75
//
Query:       gi|336252235|ref|YP_004595342.1|  [L=84]
Description: gas vesicle G [Halopiger xanaduensis SH-6]
Scores for 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-06   25.8   2.0    9.2e-06   25.6   2.0    1.1  1  GvpG      Gas vesicle protein G
    0.00056   20.2   2.1    0.00064   20.0   2.1    1.1  1  THOC7     Tho complex subunit 7


Domain annotation for each model (and alignments):
>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   2.0     1e-09   9.2e-06       2      68 ..       5      68 ..       4      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1e-09
                              GvpG  2 lllllaPvrgviWiaeqvqeraeeqlddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrLeal 68
                                      ++ll+ Pv g   i++ ++  a  +++d e+l++ L + q+  + Ge +eee+ rr eel   +e  
  gi|336252235|ref|YP_004595342.1|  5 DDLLFRPVVG---IVDTLHTMALDEMYDLEALEADLKENQLLYELGERSEEEYRRRKEELEAEIEFA 68
                                      6777888777...679*******************************************98888844 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   2.1   7.1e-08   0.00064      46      94 ..      27      75 ..      16      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.1e-08
                             THOC7 46 lldfaafelsierlqllakanerereryeaekeeieseieavreeieel 94
                                      + d++a+e  ++  qll +  er  e+y + kee+e+eie +re +e+l
  gi|336252235|ref|YP_004595342.1| 27 MYDLEALEADLKENQLLYELGERSEEEYRRRKEELEAEIEFAREVHERL 75
                                      5699****************************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 654.88
//
Query:       gi|336252236|ref|YP_004595343.1|  [L=205]
Description: hypothetical protein Halxa_0825 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00037   20.6   0.2       0.13   12.4   0.0    2.4  2  HSP20       Hsp20/alpha crystallin family
      0.003   17.1   0.2       0.02   14.4   0.2    2.1  1  ArsA_HSP20  HSP20-like domain found in ArsA


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 !   12.4   0.0   1.4e-05      0.13       6      44 ..     130     167 ..     125     178 .. 0.78
   2 !    6.6   0.0   0.00095       8.5      68      91 ..     173     196 ..     168     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                                       EEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..--- CS
                             HSP20   6 eeefevkldvpglkkeelkvkvednrvlvkgeheeeeed 44 
                                       ++e  v++dv+g++++e++v  ++ +++v    + e e 
  gi|336252236|ref|YP_004595343.1| 130 DDELLVTADVAGVDPDEVTVGFDGSTLVVGVSDR-ELER 167
                                       677889********************99966655.4444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00095
                                       -TTT-EEEEETTEEEEEEEBSS-- CS
                             HSP20  68 dadkvkaslkdGvLtvtvpkkepe 91 
                                       d+ + +a++k+GvL v v  +++ 
  gi|336252236|ref|YP_004595343.1| 173 DDRSAQATIKNGVLAVRVVPESAS 196
                                       6777899**********9877665 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 !   14.4   0.2   2.2e-06      0.02       1      62 [.     130     189 ..     130     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-06
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkignfr.RqitLPsvlarkevtsAkfedgvLeIr 62 
                                       dde  +++d+ +vd++e+ +  +g++L++ + +    ++  P    +++ ++A++++gvL +r
  gi|336252236|ref|YP_004595343.1| 130 DDELLVTADVAGVDPDEVTVGFDGSTLVVGVSDRElERVDVPW---DDRSAQATIKNGVLAVR 189
                                       78999*************************9854314466664...46667899999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1635.36
//
Query:       gi|336252237|ref|YP_004595344.1|  [L=329]
Description: hypothetical protein Halxa_0826 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        6.6    5.5  11.0         10    4.9  11.0    1.2  1  MscS_TM   Mechanosensitive ion channel inner membrane domain 


Domain annotation for each model (and alignments):
>> MscS_TM  Mechanosensitive ion channel inner membrane domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  11.0   0.00056        10     251     286 ..     290     325 ..     280     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.00056
                           MscS_TM 251 lvarRRlayerakekRaaalaqrakeeeeeeekkes 286
                                       ++  RR  +er k++R+++++qr++++ee+ + +++
  gi|336252237|ref|YP_004595344.1| 290 RIYGRRFEIEREKQRRRNQEEQRRRNQEEQRQRTQE 325
                                       5889************************99877554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1691  (0.0943165); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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 0.23s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2454.73
//
Query:       gi|336252238|ref|YP_004595345.1|  [L=196]
Description: gas vesicle protein GVPa [Halopiger xanaduensis SH-6]
Scores for 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-14   51.5   4.4    1.5e-13   50.7   4.4    1.4  1  Gas_vesicle  Gas vesicle protein


Domain annotation for each model (and alignments):
>> Gas_vesicle  Gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   4.4   8.1e-18   1.5e-13       2      39 .]      17      54 ..      16      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 8.1e-18
                       Gas_vesicle  2 LaDlLDrvLdkGvVIdgditisvagieLltikLrlviA 39
                                      La++++++LdkG+VI++di +s+ ++ Ll+++Lr++iA
  gi|336252238|ref|YP_004595345.1| 17 LAEVVEMLLDKGIVINADIAVSIGDTQLLGVQLRAAIA 54
                                      8************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1510.46
//
Query:       gi|336252239|ref|YP_004595346.1|  [L=114]
Description: Gas vesicle K [Halopiger xanaduensis SH-6]
Scores for complete 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-24   85.6   6.8    2.3e-24   85.3   6.8    1.1  1  GvpK           Gas vesicle protein K
     0.0014   18.9   0.7     0.0018   18.6   0.7    1.1  1  Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
  ------ inclusion threshold ------
      0.026   14.6   0.1      0.033   14.3   0.1    1.1  1  DUF2730        Protein of unknown function (DUF2730)
      0.037   14.3   1.1      0.057   13.7   1.1    1.4  1  Glu-tRNAGln    Glu-tRNAGln amidotransferase C subunit
      0.044   13.0   0.3       0.05   12.8   0.3    1.0  1  DLP_helical    Dynamin-like helical domain
      0.046   14.1   0.7      0.069   13.5   0.7    1.3  1  Csm1_N         Csm1 N-terminal domain
      0.059   13.6   1.4      0.073   13.4   1.4    1.1  1  Rx_N           Rx N-terminal domain
      0.061   13.3   0.0      0.074   13.1   0.0    1.2  1  FlxA           FlxA-like protein
      0.099   13.1   0.2       0.21   12.0   0.2    1.6  1  FlaC_arch      Flagella accessory protein C (FlaC)
       0.13   12.6   1.4        0.2   12.0   1.3    1.3  1  TetR_C_24      Tetracyclin repressor-like, C-terminal domain
       0.15   12.6   0.1        0.3   11.6   0.1    1.6  1  MobC           Bacterial mobilisation protein (MobC)


Domain annotation for each model (and alignments):
>> GvpK  Gas vesicle protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   6.8   1.4e-27   2.3e-24       5      82 ..       8      87 ..       4      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 1.4e-27
                              GvpK  5 dpesverglakLvLtvveLlrqllErqaiRRmeagdlsdeeierlgetLmkleeeleelkesfgleee..dLnldLgpl 81
                                      d e++++gl++Lv+tvve+l ++lEr+a+RRme+g+l deeierlge+L ++e+e+e+lke+ g+e+   dL+ dL+ l
  gi|336252239|ref|YP_004595346.1|  8 DGEDARQGLVTLVVTVVEILMDALEREAVRRMESGNLADEEIERLGEQLATIEAEIEQLKEDEGIEDGvdDLRGDLDGL 86
                                      56899*************************************************************9777******988 PP

                              GvpK 82 g 82
                                       
  gi|336252239|ref|YP_004595346.1| 87 V 87
                                      6 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.7   1.1e-06    0.0018      20     100 ..       9      89 ..       4     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                     Jnk-SapK_ap_N  20 geevvkgLmPkvVkvLElLeslasrneeeeael.eelreeleqLeteyerekelrkraeeeleeiedqweeerkelq 95 
                                       ge++ +gL+++vV+v E L  +++r++ +  e  ++  ee+e+L +++    e++ ++ +e e ied +++ r +l+
  gi|336252239|ref|YP_004595346.1|   9 GEDARQGLVTLVVTVVEILMDALEREAVRRMESgNLADEEIERLGEQL-ATIEAEIEQLKEDEGIEDGVDDLRGDLD 84 
                                       8999*************9988888887777775156678999999855.5667777777788888888888888877 PP

                     Jnk-SapK_ap_N  96 ekveq 100
                                         v++
  gi|336252239|ref|YP_004595346.1|  85 GLVND 89 
                                       66655 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     2e-05     0.033      11      88 ..      17      93 ..      14     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                           DUF2730 11 lavisvvvavilllldskYakredleklae.kveendkrlteletkvenLPtakdlekLkllladlrgelkal.eaevr 87
                                      ++++ +vv +++  l++  ++r +  +la+ ++e+  ++l+++e+++e+L      e ++  + dlrg+l+ l +  ++
  gi|336252239|ref|YP_004595346.1| 17 VTLVVTVVEILMDALEREAVRRMESGNLADeEIERLGEQLATIEAEIEQLKED---EGIEDGVDDLRGDLDGLvNDAIE 92
                                      4677888899999999************863799***************9655...55667888888888754144555 PP

                           DUF2730 88 q 88
                                      q
  gi|336252239|ref|YP_004595346.1| 93 Q 93
                                      5 PP

>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.1   3.5e-05     0.057       2      34 ..      45      79 ..      44     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-05
                                      -HHHHHHHHHHHHHHHHHHTTCGCS-.-T.T---- CS
                       Glu-tRNAGln  2 seeEleklakelnsildyveqLqevd.tt.gvepl 34
                                       +eE+e+l ++l  i + +eqL+e + ++ gv+ l
  gi|336252239|ref|YP_004595346.1| 45 ADEEIERLGEQLATIEAEIEQLKEDEgIEdGVDDL 79
                                      69**********************44433355543 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   3.1e-05      0.05      65     136 ..      24      97 ..      11     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                       DLP_helical  65 ksvirdvlerqlpeaeerleelekevekleesakriekelaelkke..ieearielreelkayfsdLilqvkgl 136
                                         ++ d ler+    +e  + +++e+e+l e++++ie+e+++lk++  ie+   +lr  l+ + +d i q++g 
  gi|336252239|ref|YP_004595346.1|  24 VEILMDALEREAVRRMESGNLADEEIERLGEQLATIEAEIEQLKEDegIEDGVDDLRGDLDGLVNDAIEQLHGE 97 
                                       67999*************************************997666**********************9985 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.7   4.2e-05     0.069      25      64 ..      31      70 ..      23      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.2e-05
                            Csm1_N 25 lvhENsvLsqkletkdqeiesLkeqlaeleekvkeleerr 64
                                      l  E +  ++  +  d+eie+L eqla++e+++++l+e++
  gi|336252239|ref|YP_004595346.1| 31 LEREAVRRMESGNLADEEIERLGEQLATIEAEIEQLKEDE 70
                                      555666667777889*********************9976 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.4   4.5e-05     0.073       2      68 ..      20      90 ..      19      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                              Rx_N  2 vsallqkLadllaeea....kllkgvkeeleklkdeLesiqavLedaeerqikdeavkeWlkelrdlayda 68
                                      v ++++ L d l+ ea    ++    +ee+e+l ++L +i+a +e+  e +  ++ v+    +l  l+ da
  gi|336252239|ref|YP_004595346.1| 20 VVTVVEILMDALEREAvrrmESGNLADEEIERLGEQLATIEAEIEQLKEDEGIEDGVDDLRGDLDGLVNDA 90
                                      6678999999999999988777777889**********************999999999999999888886 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.5e-05     0.074       9      40 ..      39      70 ..      34      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                              FlxA  9 sssssgsasqiasLqkQiknlqkqLkelsesd 40
                                      ++s++  +++i++L +Q+++++ ++++l+e++
  gi|336252239|ref|YP_004595346.1| 39 MESGNLADEEIERLGEQLATIEAEIEQLKEDE 70
                                      678899999********************994 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 ?   12.0   0.2   0.00013      0.21       7      40 ..      47      79 ..      43      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                         FlaC_arch  7 nklsklsteletvkkeneelsksveelkenVkdl 40
                                      +++++l  +l+t+++e+e+l+++ e +++ V dl
  gi|336252239|ref|YP_004595346.1| 47 EEIERLGEQLATIEAEIEQLKED-EGIEDGVDDL 79
                                      799*****************987.8888888776 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.3   0.00012       0.2       2      67 ..      10      76 ..       9      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                      SSHHHHHHHHHHHHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHH.HHHHTTS CS
                         TetR_C_24  2 gspaerLralvrahveviaeereeaavllrelraLspehreeiralrreyerllrdlie.eGvaage 67
                                      +++++ L  lv ++ve++++  e+ av   e  +L +e+ e++ ++   +e+ +++l e eG+++g+
  gi|336252239|ref|YP_004595346.1| 10 EDARQGLVTLVVTVVEILMDALEREAVRRMESGNLADEEIERLGEQLATIEAEIEQLKEdEGIEDGV 76
                                      57888899************************************************98636888885 PP

>> MobC  Bacterial mobilisation protein (MobC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00019       0.3      16      45 .]      37      66 ..      35      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                              MobC 16 raaNsgqgsqavlaelkeelaeinkeLdql 45
                                      r++ sg+++++ +++l e+la+i++e++ql
  gi|336252239|ref|YP_004595346.1| 37 RRMESGNLADEEIERLGEQLATIEAEIEQL 66
                                      66678999********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 910.91
//
Query:       gi|336252240|ref|YP_004595347.1|  [L=344]
Description: Gas vesicle synthesis GvpLGvpF [Halopiger xanaduensis SH-6]
Scores for 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-80  269.1   0.7    5.3e-80  268.9   0.7    1.1  1  GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF


Domain annotation for each model (and alignments):
>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.9   0.7     3e-84   5.3e-80       1     244 []      42     321 ..      42     321 .. 0.98

  Alignments for each domain:
  == domain 1  score: 268.9 bits;  conditional E-value: 3e-84
                         GvpL_GvpF   1 glYvYgivdadsddseaad...........tGvdgepVrlvragglaavvsdvpeeeydaerleqverwllaHqrVv 66 
                                       g+Y+Y+iv+ d+d +e+ad           tGvdgepV++v ++g++avv+++ ++ yd+++l+qv+rwl++Hq+Vv
  gi|336252240|ref|YP_004595347.1|  42 GRYLYCIVQVDNDGAEGADseddatatldtTGVDGEPVSVVVEDGIGAVVHAC-DGIYDSADLAQVRRWLVRHQTVV 117
                                       79********999999999**********************************.8********************** PP

                         GvpL_GvpF  67 ealm.aegtvlPlrFgtvlkdeeav.relLeeeadelreaLerlagkvEygvkvlwdeealleelleedpelrelre 141
                                       ++++ a+gt++P++F+t+l+++++  re+L+ee+d+l++aL+ la+++Ey+v+v++ ++ ++++l+e+d++lrel +
  gi|336252240|ref|YP_004595347.1| 118 DEAGqAFGTPIPFQFDTILRGDDERvREWLREERDTLERALSGLADHWEYRVEVVERDPIEDAALIERDERLRELDA 194
                                       ****99**************888877*************************************************** PP

                         GvpL_GvpF 142 eieaasesgtayllrkrlgqrleealeerreelaeeleeaLaplaeevrerepqd...................... 196
                                       +i +++e gta+ll+k+l+qrl+e +++rre+l+++lee+La +a+ev++ e+++                      
  gi|336252240|ref|YP_004595347.1| 195 KIGDSGE-GTAFLLEKKLDQRLNEVRAARRESLTADLEERLADAAREVHSLERSPtaslddavaddsggsgaesdgs 270
                                       *******.9******************************************************************** PP

                         GvpL_GvpF 197 ....eemvlnaafLvdrdreeefgeaveelaarldglevrltGPwpPYsFvp 244
                                           +e+++++++L+++d+e+e+g++++++aa+ dglevr+tGPwpPY+F+p
  gi|336252240|ref|YP_004595347.1| 271 addgGETLCRLTLLAHEDAESEIGSILDDVAAE-DGLEVRFTGPWPPYTFAP 321
                                       *********************************.****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); 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:                         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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2981.10
//
Query:       gi|336252241|ref|YP_004595348.1|  [L=114]
Description: gas vesicle protein GVPa [Halopiger xanaduensis SH-6]
Scores for 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-13   48.5   9.7    8.8e-13   48.2   9.7    1.1  1  Gas_vesicle  Gas vesicle protein


Domain annotation for each model (and alignments):
>> Gas_vesicle  Gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   9.7   4.9e-17   8.8e-13       1      39 []       9      47 ..       9      47 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 4.9e-17
                       Gas_vesicle  1 sLaDlLDrvLdkGvVIdgditisvagieLltikLrlviA 39
                                      +L+D+LD++L  G+++++d+++sva+i+L++ikL ++iA
  gi|336252241|ref|YP_004595348.1|  9 TLVDVLDVLLRDGAILRADVIVSVADIPLVGIKLTAAIA 47
                                      79************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 1014.46
//
Query:       gi|336252242|ref|YP_004595349.1|  [L=71]
Description: hypothetical protein Halxa_0831 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.086   12.7   1.8       0.12   12.2   0.2    1.9  2  zf-CCHC_2        Zinc knuckle
      0.092   12.8   0.2       0.11   12.6   0.2    1.1  1  Kp4              Kp4
       0.11   12.9   1.8          2    8.8   0.1    2.1  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.14   12.3   0.4       0.17   12.0   0.4    1.0  1  MqsA_antitoxin   Antitoxin component of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> zf-CCHC_2  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.25   1.1e+03       6      12 ..       4      10 ..       3      10 .. 0.78
   2 ?   12.2   0.2   2.7e-05      0.12       2      13 ..      33      44 ..      32      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.25
                         zf-CCHC_2  6 ChiCgkk 12
                                      C  C ++
  gi|336252242|ref|YP_004595349.1|  4 CTNCETP 10
                                      9999876 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.7e-05
                         zf-CCHC_2  2 pgYvChiCgkkG 13
                                      ++Y C +Cg+ G
  gi|336252242|ref|YP_004595349.1| 33 ETYECTLCGSTG 44
                                      89*******999 PP

>> Kp4  Kp4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   2.3e-05      0.11      72     114 ..      11      54 ..       2      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                               Kp4  72 aflqktggvsgatiksllqelvd.hgCkvCGsvPllyakgnndv 114
                                        flq t+++   +  ++++e+ + + C+ CGs   ++ +++ d 
  gi|336252242|ref|YP_004595349.1|  11 QFLQITQSRVYFEDGEVINEISEtYECTLCGSTGQYIYDDDHDE 54 
                                       5899888888888899999998659********98766554443 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 ?    4.5   0.1      0.01        46      28      42 ..       1      13 [.       1      26 [. 0.72
   2 ?    8.8   0.1   0.00045         2      15      50 ..      21      55 ..      16      58 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.01
                   Lar_restr_allev 28 cvyCadCgastpwfk 42
                                      +++C++C+   p+f 
  gi|336252242|ref|YP_004595349.1|  1 MITCTNCET--PQFL 13
                                      699****99..4444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00045
                   Lar_restr_allev 15 lersqrvvaeigqcvyCadCgastpwfkiaedeaea 50
                                      +++++ v +ei+++ +C+ Cg  t ++ +++d+ e+
  gi|336252242|ref|YP_004595349.1| 21 YFEDGEVINEISETYECTLCGS-TGQYIYDDDHDEE 55
                                      5566666677777888988998.7777777776654 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 ?   12.0   0.4   3.8e-05      0.17       2      62 ..       3      65 ..       2      68 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                    MqsA_antitoxin  2 kCpvCgkaelvrdtrdvpytykgektvikavtgdf.CarC...Gegvldeeeedrlseellefrk 62
                                       C+ C ++++++ t+  +y   ge  vi++++  + C+ C   G+ ++d++++++ ++  +e+ k
  gi|336252242|ref|YP_004595349.1|  3 TCTNCETPQFLQITQSRVYFEDGE--VINEISETYeCTLCgstGQYIYDDDHDEETVTGDVELTK 65
                                      69*************999988887..667776666666661115679999999988888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 00:00:00.40
# Mc/sec: 539.23
//
Query:       gi|336252243|ref|YP_004595350.1|  [L=106]
Description: hypothetical protein Halxa_0832 [Halopiger xanaduensis SH-6]
Scores for 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:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 856.36
//
Query:       gi|336252244|ref|YP_004595351.1|  [L=57]
Description: hypothetical protein Halxa_0833 [Halopiger xanaduensis SH-6]
Scores for 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:                       507  (0.0282782); 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:                         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: 439.96
//
Query:       gi|336252245|ref|YP_004595352.1|  [L=196]
Description: hypothetical protein Halxa_0834 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0056   17.3   2.3     0.0084   16.8   2.3    1.3  1  ABATE     Putative stress-induced transcription regulator
  ------ inclusion threshold ------
      0.021   14.9   0.3      0.081   13.0   0.6    1.7  2  DUF5346   Family of unknown function (DUF5346)


Domain annotation for each model (and alignments):
>> ABATE  Putative stress-induced transcription regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   2.3   9.4e-07    0.0084      26      85 ..      47     109 ..      42     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.4e-07
                                       HHHHHH--TTHHHHHH.............HHHHHHHHHHHHHHTHHHH.........HHHHHH CS
                             ABATE  26 adLaaWleaagllpagtaaagada...elararaLRealrallaaaaagdpppaaalaalnal 85 
                                       a+ ++W  ++ l  a+  ++++++   e  ++ ++R++++++l++ a+g ++ aaa+ +l+al
  gi|336252245|ref|YP_004595352.1|  47 AWIVRWYYRRTLGVAPDDERRTAEahfERNEFETVRDVVDDVLEQLAEGSDDVAAAVGRLTAL 109
                                       77888887766655555555554468*99*******************************998 PP

>> DUF5346  Family of unknown function (DUF5346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.38   3.5e+03      58      72 ..      10      24 ..       6      39 .. 0.77
   2 ?   13.0   0.6     9e-06     0.081      29      68 ..     149     191 ..     142     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.38
                           DUF5346 58 tygaayrpaapfyny 72
                                      t  a yr ++p y+ 
  gi|336252245|ref|YP_004595352.1| 10 TKAAEYREQEPLYSV 24
                                      778899999999975 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9e-06
                           DUF5346  29 pwpqcppq..sy.cyatnsvdvgpyfccpiwstygaayrpaap 68 
                                       p+p+  p   +y  y   + dv   + c iw+ y a++r ++ 
  gi|336252245|ref|YP_004595352.1| 149 PYPEPEPSidAYeTYLERCRDVCDRYECDIWTLYRALWRCWKE 191
                                       55555554113434566789*******************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1574.46
//
Query:       gi|336252246|ref|YP_004595353.1|  [L=711]
Description: formate dehydrogenase subunit alpha [Halopiger xanaduensis SH-6]
Scores for 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-75  253.8   0.0    3.8e-75  253.5   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    5.6e-29  100.4   0.1    1.3e-28   99.3   0.1    1.6  1  Molydop_binding  Molydopterin dinucleotide binding domain
    3.4e-14   52.6   0.6    8.3e-14   51.3   0.6    1.7  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.5   0.0   6.3e-79   3.8e-75       1     430 [.      64     499 ..      64     501 .. 0.89

  Alignments for each domain:
  == domain 1  score: 253.5 bits;  conditional E-value: 6.3e-79
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rl++P+++   + +G+F+++sW+e +e+i ++l++++++ygpd+  +f+s++ m +e+ ++l+kl++++g    +++
  gi|336252246|ref|YP_004595353.1|  64 RLTDPLIK---E-DGEFREASWEECFEYIVDELERIREEYGPDATGFFGSSKTM-NEENYLLQKLARRYGT---NNV 132
                                       9*******...6.9************************************9999.999999*********9...899 PP

                                       ECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGG.GG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-H CS
                     Molybdopterin  78 dwyadlppasaqqtigsdsrsnyessnpledl.ensdliilwGsNvreerpilnarirkaalkkkakvivigpryae 153
                                       d++ + ++as++ ++ +++  + +++n++ dl e+ dl+ + G+N+ e +pi+n++  ++a  ++a vi ++p  ++
  gi|336252246|ref|YP_004595353.1| 133 DNCTRMCHASTVWALRTSLG-AGAMTNSMRDLrEECDLFWIQGANPGEQHPIANSQYFRQAVLDGATVIQVDPHANK 208
                                       99999999999844444333.445666777775889*****************877665555557************ PP

                                       .......CGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCC.......TCHHHHHHEECHHHCCCCCCCEECCSHHHH CS
                     Molybdopterin 154 .......llkfadewlaikpgtdaalalamghvilqelkv.......dkeflrkytygkeetdmpllvtleeetgkk 216
                                                +  +++l ++pgtd +l++   ++il+   +       d+ef++ +t g++ +++ l+   +e ++++
  gi|336252246|ref|YP_004595353.1| 209 ttrsfqiDDTDRHQHLQLNPGTDIPLLNIVLKTILEHHEEnpedgwiDEEFVEARTEGFDHLQETLEDFDKEAAAEE 285
                                       99976653456789************9999999997654444455559************************88888 PP

                                       HHCCHHHHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHT CS
                     Molybdopterin 217 kevvariarelarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvg 293
                                       ++ + + +  la++ +++a +++i+ G+g+ +++ g ++++  inLal++gn g+ g+g++ l+Gq++++g  ++vg
  gi|336252246|ref|YP_004595353.1| 286 CGLPLEDIE-LAAKKYAEADNAAIFTGMGMSQHACGVDNVQNEINLALITGNLGRAGTGVNPLRGQNNVQG-TCDVG 360
                                       888877765.5555555555599999*********************************************.9**** PP

                                       CCTTCCCCCCCTT...HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSS CS
                     Molybdopterin 294 alpvllsvkslke...ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekld 367
                                       a+p  l+ ++l+     ++++ + +  +++  p+ + ve s+  + + +k ly++g+np+++ +d+n+v +  ++l+
  gi|336252246|ref|YP_004595353.1| 361 AMPNVLPGYQLVDddeARTRVEDVWGFEIPDEPGLTNVEISHQFG-EAVKGLYVMGENPIMSEPDANQVAERIQDLE 436
                                       ***********9998888888888999******************.79999************************** PP

                                       EEEEEESCSSHHHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHH CS
                     Molybdopterin 368 lvvvldgrltstalyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLa 430
                                       + vv d+++t+ta+yaD++LPa+tw E+ +++tn+++r+q+++ + +   + k+d +Il+++ 
  gi|336252246|ref|YP_004595353.1| 437 FMVVQDIFMTETAQYADVVLPATTWAERGGTVTNTDRRVQRMRGVEKVHENTKHDLEILSEVG 499
                                       ***********************************************************9986 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.1   2.1e-32   1.3e-28       1     110 [.     586     691 ..     586     692 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 2.1e-32
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfm 76 
                                       l+L+t r  ++++++t++r+++ l++  p ++v ++p+dA+++Gi+dG++V ++srrG+++v+a+vte++++G+v+ 
  gi|336252246|ref|YP_004595353.1| 586 LILTTARLEEHYNTGTMSRRSPTLNRQTPeNFVDVHPNDAERYGIEDGEKVLLKSRRGEITVEAQVTEDIKEGSVWT 662
                                       79*************************************************************************** PP

                                       ESSHCC.....S-GHCTS--SCSTTT--CSTT-E CS
                   Molydop_binding  77 pfgwweagekggnaNaltddatdplsgtpefksv 110
                                       + ++ +     ++aN+lt+d +d+ s++pe+k++
  gi|336252246|ref|YP_004595353.1| 663 TPHFAA-----ASANRLTNDVLDERSKIPEYKAA 691
                                       ****99.....********************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 !   51.3   0.6   1.4e-17   8.3e-14       2      55 .]       7      61 ..       6      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 1.4e-17
                                      EEEEEE-SSBTT--EEEEEEETTEEE.EEEE-TTSTTTTT---HHHHTCHHCCCB CS
                    Molybdop_Fe4S4  2 kvvktaCpyCgvgCglevhvkdgkiv.kvegdpdhpvnegrlCvKGrtllervyn 55
                                       +vkt+CpyCgvgCg++v    + +  +  ++ ++pvnegr+C+KG ++ e v++
  gi|336252246|ref|YP_004595353.1|  7 DTVKTICPYCGVGCGIQVRQGEEPGDvQFMPWGEAPVNEGRICIKGGAATEVVDH 61
                                      58*****************965555339********************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (711 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); 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:                         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: 00:00:00.39
# Mc/sec: 5434.98
//
Query:       gi|336252247|ref|YP_004595354.1|  [L=64]
Description: cold-shock DNA-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-19   68.0   0.4      5e-19   67.9   0.4    1.0  1  CSD       'Cold-shock' DNA-binding domain
  ------ inclusion threshold ------
      0.081   12.6   2.7       0.11   12.2   2.7    1.3  1  OB_RNB    Ribonuclease B OB domain
       0.15   12.0   1.9       0.36   10.8   1.9    1.7  1  S1-like   S1-like


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.4   8.3e-23     5e-19       2      65 ..       3      63 ..       2      64 .] 0.97

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 8.3e-23
                                      EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                               CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                      +G+V  fn+  g+GFI +ed d+dvF+H+ ++ g++   L+eg e+eF++++  kgp+A+nV++
  gi|336252247|ref|YP_004595354.1|  3 NGKVDFFNDTGGYGFIDTEDADEDVFFHMEDVGGED---LTEGTEIEFDIEQAPKGPRATNVVR 63
                                      79******************************9999...***********************86 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.7   1.8e-05      0.11       8      28 ..      13      33 ..       4      36 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.8e-05
                                      SS-EEEEECT.TEEEEE-HHH CS
                            OB_RNB  8 kGFGFlipdegkeDifippeq 28
                                       G+GF+++++ +eD+f + e+
  gi|336252247|ref|YP_004595354.1| 13 GGYGFIDTEDADEDVFFHMED 33
                                      59**************87766 PP

>> S1-like  S1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.9     6e-05      0.36      14      42 ..      14      47 ..       4      60 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6e-05
                           S1-like 14 tfGfvD.....eevfFqrsvvkGrlpkvgdrVlv 42
                                       +Gf+D     e+vfF+++ v G     g  +++
  gi|336252247|ref|YP_004595354.1| 14 GYGFIDtedadEDVFFHMEDVGGEDLTEGTEIEF 47
                                      6999954444489******999987776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); 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):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 490.55
//
Query:       gi|336252248|ref|YP_004595355.1|  [L=142]
Description: Glyoxalase/bleomycin resistance protein/dioxygenase [Halopiger xanaduensis SH-6]
Scores for complete 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-10   41.3   0.5    3.1e-10   40.4   0.5    1.5  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    1.4e-06   29.0   0.3      2e-06   28.6   0.3    1.2  1  Glyoxalase_6  Glyoxalase-like domain
    0.00046   20.1   0.0     0.0018   18.2   0.0    1.8  1  Glyoxalase_2  Glyoxalase-like domain
     0.0077   16.5   0.1      0.011   16.0   0.1    1.2  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge


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 !   40.4   0.5   6.8e-14   3.1e-10       2     128 .]       4     121 ..       3     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 6.8e-14
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC..TSEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkiee..tvhh 76 
                                       +dh+ + v+dle+s +FY++vL++++ +       + +  +a f++g+++++l+    ++g + +   + +    +h
  gi|336252248|ref|YP_004595355.1|   4 VDHINVDVDDLEASYAFYRDVLDLEVRRPPS----DFKGEHAMFQVGETVVTLAETGRADGWDERG--LAHplDKAH 74 
                                       69************************99999....889999*************999998888887..445677888 PP

                                       EEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  77 vafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       +af ++ +e  ++  d+l  +     +  g + ++  ++fyf DpdG+lle+
  gi|336252248|ref|YP_004595355.1|  75 LAFETDREEY-EALMDELNGQF----PNQGPYDWDEFEGFYFLDPDGNLLEV 121
                                       8888877777.88888887766....444679999999999*********96 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.3   4.4e-10     2e-06       2     106 ..       7     121 ..       6     122 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 4.4e-10
                      Glyoxalase_6   2 vvldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe........paknrvHldlavedld 70 
                                       + +d++d +a  aF++++l++ev+r+++  + ++++   +e+ +tl+   + +        +  ++ Hl +++ d++
  gi|336252248|ref|YP_004595355.1|   7 INVDVDDLEASYAFYRDVLDLEVRRPPSDFKGEHAMFQVGETVVTLAETGRADgwderglaHPLDKAHLAFET-DRE 82 
                                       789************************555555555555555555554444447888888755557*****99.666 PP

                      Glyoxalase_6  71 aevarlvalGArvlreprdgthgr....vlaDPeGneFcv 106
                                       +  a + +l ++   +   + +++     + DP+Gn   v
  gi|336252248|ref|YP_004595355.1|  83 EYEALMDELNGQFPNQGPYD-WDEfegfYFLDPDGNLLEV 121
                                       77778888988877654443.233469*********9887 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     4e-07    0.0018       8     113 ..      11     121 ..       5     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4e-07
                                       ES-HHHHHHHHHHTT---EE...EE-.SSEEEETTS-EEE..EHHHHHH----.---S--SS-EEEEEES..-HHHH CS
                      Glyoxalase_2   8 vkdieeskkFYedvlelkik...ldf.Genvsfetgfalk..edlkelinlde.siaeqsnnfeLyFeve..dvdaf 75 
                                       v+d+e s  FY+dvl+l+++    df Ge+ +f+ g ++    +  +  + de   a+  ++ +L Fe +  + +a+
  gi|336252248|ref|YP_004595355.1|  11 VDDLEASYAFYRDVLDLEVRrppSDFkGEHAMFQVGETVVtlAETGRADGWDErGLAHPLDKAHLAFETDreEYEAL 87 
                                       89*****************833347779*****99998851244455557777566778889999998642267788 PP

                                       HHHH..GGGS-EEEEEEE-TTS-.EEEEEE-TT--EEEE CS
                      Glyoxalase_2  76 lqklkeaeniellhelkekpWgq.rvirfyDpDkhiiEi 113
                                       +++l+ +       +   + W     ++f DpD++++E+
  gi|336252248|ref|YP_004595355.1|  88 MDELNGQ-----FPNQGPYDWDEfEGFYFLDPDGNLLEV 121
                                       8888443.....356678899863679999****99998 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.4e-06     0.011       1      88 [.       5      93 ..       5     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.4e-06
                                      EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTE..EEEEEEETTEEEEEEEESSTT-THHH...TS-EEEEEEE CS
                      Glyoxalase_4  1 dQigivVeDleaavarfsallGvgpwqryrdepqevdl..afallgsgsvqieLieplegpeflae...hgeglhhlay 74
                                      d+i + V+Dlea  a++ ++l+++++++    p++++   a++++g+    + L e+ + + + ++   h     hla+
  gi|336252248|ref|YP_004595355.1|  5 DHINVDVDDLEASYAFYRDVLDLEVRRP----PSDFKGehAMFQVGE--TVVTLAETGRADGWDERglaHPLDKAHLAF 77
                                      699999****************866555....555544116677777..588888888887665559999999****** PP

                                      EES..-HHHHHHHHCT CS
                      Glyoxalase_4 75 wvd..dldaavarlee 88
                                      ++d  +++a +++l  
  gi|336252248|ref|YP_004595355.1| 78 ETDreEYEALMDELNG 93
                                      **75589999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 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:                        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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1143.86
//
Query:       gi|336252249|ref|YP_004595356.1|  [L=334]
Description: NMT1/THI5 like domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-33  114.3   0.0    1.3e-32  113.5   0.0    1.4  1  NMT1            NMT1/THI5 like
    1.7e-06   27.8   0.2    2.4e-06   27.3   0.2    1.4  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
    2.1e-05   24.4   0.1    0.00044   20.0   0.1    2.4  1  NMT1_2          NMT1-like family


Domain annotation for each model (and alignments):
>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.5   0.0   2.2e-36   1.3e-32       4     216 .]      29     242 ..      26     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 2.2e-36
                                       GHHHHHHHHTTHHHHTTEEEEEE--SSTTHHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--EEEEEE CS
                              NMT1   4 haglyvAkekGYFkeeGldVeivepadpsdatelvasgkadfgvsyqesllaarakglpvvsvaallqeplsglivl 80 
                                        a++++A+e+G++++eGl+V++ve+ ++  a e  a+g a+f+++    +l  +++gl+  +vaa+  +++ ++ +l
  gi|336252249|ref|YP_004595356.1|  29 QAPYFLARERGFYADEGLEVRFVEGHGSPFAAEQAAKGRAEFALAGASAVLSVQSRGLEPLAVAAVTGKTPAAIYTL 105
                                       589************************************************************************** PP

                                       CC...C--SSGGGGTTSEEEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHH...HHHCTSSSEEECEETTT CS
                              NMT1  81 kd...sgikspkDLkGkrigyvgspfekallkallakdggdpsdvtlvnvggtslak...alltgkvDaaiggyenw 151
                                       +d   +++++p+ L+G +i+ +   ++++l  +ll+ +g+  ++v+l+ v+   +     +ll+g vDaa+g+++n 
  gi|336252249|ref|YP_004595356.1| 106 RDvfgEPLEEPAQLAGCTIAPSA-TKTRILAAQLLEDAGI-RDEVELLGVDDHTHHRvqhKLLEGDVDAAVGVVTN- 179
                                       *855457*************999.79**************.89999998865543322349**************9. PP

                                       HHHHHHHTT--EEEE-GGGTT-----SEEEEEEHHHHHH-HHHHHHHHHHHHHHHHHHHHSHHHH CS
                              NMT1 152 egvelesegkelrifaladlgvpdyyslvlitnekllkenpelvkkFlrAlkkGyeyalahPeea 216
                                        g+ele+e +++ +++l   +   +y  +++t  ++++enpe+v++Flr +++G+e+a+ +Pe+a
  gi|336252249|ref|YP_004595356.1| 180 -GYELERE-HDRTADELPIGDRLGVYGMTIVTDPAFADENPETVRAFLRGTARGWEAATTDPEAA 242
                                       .9999877.6666666665555567*************************************987 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 !   27.3   0.2   4.1e-10   2.4e-06      40     182 ..      57     194 ..      37     261 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.1e-10
                                       HHHHHHHHTTS-SEEE--HHHHHHHHHHS-EEEEEEEEETT--SEEEEEEEEETT...SS--SHHHHGG-EEEE--T CS
                    Phosphonate-bd  40 aavvealragqvDiaflgplayvqardqagveplatrvrsdGsasyrsviivrad...sdiqsledLkgktiafvsp 113
                                         ++e+ + g++++a++g++a++ ++ + g+epla+     G++   ++i + +d   +++++ ++L+g tia   p
  gi|336252249|ref|YP_004595356.1|  57 PFAAEQAAKGRAEFALAGASAVLSVQSR-GLEPLAVAAV-TGKTP--AAIYTLRDvfgEPLEEPAQLAGCTIA---P 126
                                       55789999**************999976.9********8.88876..44555554222479999999999997...7 PP

                                       T-TTTTHHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEEEEEHHHHHHHHHH-HHHHTTE CS
                    Phosphonate-bd 114 sStsGylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdadaaavsadaledlvaegpedkdel 182
                                       s+t   ++ a+lL ++ag++ e  +  v  ++h  +   +l+gd+daa+   ++ ++l++e+    del
  gi|336252249|ref|YP_004595356.1| 127 SATKTRILAAQLL-EDAGIRDEVELLGVDDHTHHRVQHKLLEGDVDAAVGVVTNGYELEREHDRTADEL 194
                                       8888889999999.9****9887777788899****************965555555555555555555 PP

>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   7.4e-08   0.00044      14     232 ..      25     229 ..      12     248 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.4e-08
                            NMT1_2  14 altdaaplvvakekglfakeGltvelekqaswaelrdkllagelDaahv.ltpapllidlGiggakadmkvlaslnl 89 
                                       ++   ap + a+e+g++a+eGl+v+ ++  + + + ++ ++g+   a++   ++++  ++G+    ++++v+a   +
  gi|336252249|ref|YP_004595356.1|  25 PNGFQAPYFLARERGFYADEGLEVRFVEGHGSPFAAEQAAKGRAEFALAgASAVLSVQSRGL----EPLAVAAVTGK 97 
                                       5666799******************************************8888888888999....9********** PP

                            NMT1_2  90 nGqaitlsnklkdkkvsdakalkdlvakkkaskplkiavtfpgsthdlllrywLaaaGldpeadvklvvvpp.pqmv 165
                                        ++ai   +++  + +++ ++l          ++ +ia       +++l   +L+ aG+  e + + v+ +   ++ 
  gi|336252249|ref|YP_004595356.1|  98 TPAAIYTLRDVFGEPLEEPAQL----------AGCTIAP--SATKTRILAAQLLEDAGIRDEVELLGVDDHThHRVQ 162
                                       *****99877555444333333..........3445554..344556777777777777775555555555545566 PP

                            NMT1_2 166 anlkagtidgfcv..gePwnaqavaegiGvtaltsqelwkdhPekvlgvredfveknpntaralvkall 232
                                        +l +g++d++++  +  ++   +++     +    +l  +  +  +++  +f+++np+t+ra+++  +
  gi|336252249|ref|YP_004595356.1| 163 HKLLEGDVDAAVGvvTNGYELEREHDRTADELPIGDRL--GVYGMTIVTDPAFADENPETVRAFLRGTA 229
                                       67777777777653355554444444444333333333..22344466666777777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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: 00:00:00.40
# Mc/sec: 2488.64
//
Query:       gi|336252250|ref|YP_004595357.1|  [L=331]
Description: ABC transporter periplasmic solute-binding protein [Halopiger xanaduensis SH-6]
Scores for complete 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-08   35.3   0.0    1.7e-08   34.7   0.0    1.3  1  NMT1            NMT1/THI5 like
    0.00071   19.1   0.0     0.0011   18.5   0.0    1.3  1  SBP_bac_3       Bacterial extracellular solute-binding protei
     0.0069   16.0   0.0     0.0096   15.5   0.0    1.3  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub


Domain annotation for each model (and alignments):
>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   2.8e-12   1.7e-08      21     208 ..      53     250 ..      36     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.8e-12
                                       EEEEEE--...SSTTHHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--EEEEEECCC--SSGGGGTTS CS
                              NMT1  21 ldVeivep...adpsdatelvasgkadfgvsyqesllaarakglpvvsvaallqeplsglivlkdsgikspkDLkGk 94 
                                       ldVe+v      + +++++ + +g+ad+   + +s++ +r  g+p+v++  +  +++ gl+v++ds i+ ++DL+  
  gi|336252250|ref|YP_004595357.1|  53 LDVELVSDeleDGLETVEAKLHEGDADLIDIDYISTARERVGGAPIVAFHPYG-RTVGGLVVHEDSAIEGLTDLRDC 128
                                       777777653312334566678899****999999**************98876.99********************* PP

                                       EEEE-S.-TTHHHHHHHHHHHTT-.-GGG-EE.EE-..TT-HHHHHHCTSSSEEECEETTTHHHHHHHTT--EEEE- CS
                              NMT1  95 rigyvg.spfekallkallakdgg.dpsdvtl.vnv.ggtslakalltgkvDaaiggyenwegvelesegkelrifa 167
                                       r+g+v   +++ +l +a +++++  dp+d  + v++ +  +l+  l +g+vDaa+  ++   + e+ + g  +++++
  gi|336252250|ref|YP_004595357.1| 129 RVGVVRrLDKNWILTRAACREYHDfDPEDEAIsVEAgSKVELTRMLRDGEVDAAL-QFWQ-IVPEIVETGPYREALP 203
                                       *****96666777777777665544776633314441456677799********9.9999.4566667777777777 PP

                                       GGGT.....T--.---SEEEEEEHHHHHH-HHHHHHHHHHHHHHHHH CS
                              NMT1 168 ladl.....gvp.dyyslvlitnekllkenpelvkkFlrAlkkGyey 208
                                       +adl     g   ++   ++ t+e++l+e+p++v+ F rA++ ++e 
  gi|336252250|ref|YP_004595357.1| 204 MADLvqrlsGADeTLPISTFLTSEDYLAESPDAVEGFKRAYADAVER 250
                                       77762222244447777899*********************999875 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.8e-07    0.0011      52     171 ..      71     197 ..      52     230 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.8e-07
                                       HHHHTTSSSEEESSEB--HHHHTT.....EEEESESEEEEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  52 palksgkvDiaiaaititpeReek.....vdFsqpyfsagqvllvrkkdaskissiksladLkgkkvgvqagstaee 123
                                       ++l +g +D++    +i+ +Re +     v+F  py ++  +l+v+++  s+i++++   dL + +vgv++      
  gi|336252250|ref|YP_004595357.1|  71 AKLHEGDADLI-DIDYISTARERVggapiVAFH-PYGRTVGGLVVHED--SAIEGLT---DLRDCRVGVVRRLDKNW 140
                                       56667777754.233344444444445547776.9***********65..4677777...**999******977664 PP

                                       HHHHHHHC.........TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHCC CS
                                       xxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 124 llkeelkk.........gaeivefdtleealqaLkngrvdavvadspvlaylvkknp 171
                                       +l++++ +         +a  ve  +  e++++L++g+vda++    ++ ++v++ p
  gi|336252250|ref|YP_004595357.1| 141 ILTRAACReyhdfdpedEAISVEAGSKVELTRMLRDGEVDAALQFWQIVPEIVETGP 197
                                       5555222256778888766667899****************9976666666655555 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 !   15.5   0.0   1.6e-06    0.0096      41     175 ..      68     196 ..      52     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHTTS-SEEE--HHHHHHHHHHS-EEEEEEEEETT--SEEEEEEEEETTSS--SHHHHGG-EEEE--TT-TT CS
                    Phosphonate-bd  41 avvealragqvDiaflgplayvqardqagveplatrvrsdGsasyrsviivradsdiqsledLkgktiafvspsSts 117
                                       +v+  l +g +D+  ++ ++   ar++ g  p+++   ++G++   + ++v++ds+i+ l dL++ ++++v +    
  gi|336252250|ref|YP_004595357.1|  68 TVEAKLHEGDADLIDIDYIS--TARERVGGAPIVAFH-PYGRTV--GGLVVHEDSAIEGLTDLRDCRVGVVRRLDKN 139
                                       56666777777777776544..467778889999998.588776..789*************************988 PP

                                       TTHHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEEEEEHHHHHHHHHH- CS
                    Phosphonate-bd 118 GylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdadaaavsadaledlvaeg 175
                                        +++ +a   + ++ dped   +v +gs  +  + + +g++daa  + +++ + v++g
  gi|336252250|ref|YP_004595357.1| 140 -WILTRAACREYHDFDPEDEAISVEAGSKVELTRMLRDGEVDAALQFWQIVPEIVETG 196
                                       .8888888988899******************************96666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2522.11
//
Query:       gi|336252251|ref|YP_004595358.1|  [L=300]
Description: nitrate/sulfonate/bicarbonate ABC transporter periplasmic protein [Halopiger xanaduensis SH-6]
Scores for 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-11   43.0   0.0    8.3e-09   35.7   0.0    3.1  1  NMT1       NMT1/THI5 like
     0.0017   17.8   0.0     0.0033   16.9   0.0    1.4  1  SBP_bac_3  Bacterial extracellular solute-binding proteins, f
     0.0051   16.6   0.0       0.74    9.5   0.0    2.4  2  NMT1_2     NMT1-like family


Domain annotation for each model (and alignments):
>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   1.4e-12   8.3e-09       9     214 ..      22     222 ..      17     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.4e-12
                                       HHHHTTHHHHTTEEEEEE--SSTTHHHHHH.....HCTS-SE...EEE-HHHHHHHHH.TT--EEEEEEEE-S--EE CS
                              NMT1   9 vAkekGYFkeeGldVeivepadpsdatelv.....asgkadf...gvsyqesllaara.kglpvvsvaallqeplsg 76 
                                       vA+e+GYF+eeGldVe++e   ++   +++      +g++d+    v + esl  + + ++  +v+ +a+    +++
  gi|336252251|ref|YP_004595358.1|  22 VAAERGYFAEEGLDVELLERDRREVDRKYIpadwtLTGDDDVdlyPVCKWESLRRTWSlEDGRIVAHGAFA-DLPYT 97 
                                       9******************96665555544222225666666114444556666555579999***99988.67899 PP

                                       EEEECCC--SSGGGGTTSEEEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHH.HHHCTSSSEEECEETTTH CS
                              NMT1  77 livlkdsgikspkDLkGkrigyvgspfekallkallakdggdpsdvtlvnvggtslak.alltgkvDaaiggyenwe 152
                                       l v+ +s+ ++p+DL+   ++++    ++++  + l++ ++ p+dv+l  +g+      al +g+vDaa+  +  + 
  gi|336252251|ref|YP_004595358.1|  98 LHVRPESNFETPADLANVPVAVNRRTGQEYTAMRALEE-HLPPEDVELEHYGMPTDRLrALRDGEVDAAT-LLDPHS 172
                                       ************************66666666666665.577******99966444335**********9.666644 PP

                                       HHHHHHTT--EEEE-GGGTT-----SEEEEEEHHHHHH-HHHHHHHHHHHHHHHHHHHHSHH CS
                              NMT1 153 gvelesegkelrifaladlgvpdyyslvlitnekllkenpelvkkFlrAlkkGyeyalahPe 214
                                       ++ +++ g e+   ++  +gv         +  + l+   e++ +F+rA+++++e + a+P+
  gi|336252251|ref|YP_004595358.1| 173 TL-ADQLGLERLLEFPNHIGV---------VGAEGLEG--ETLDAFMRAYERAVETINANPD 222
                                       44.489999999999999997.........55555666..89******************98 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.5e-07    0.0033      91     157 ..     100     166 ..      86     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.5e-07
                                       EEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHC.....TSEEEEESSHHHHHHHHHTTSSSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  91 vrkkdaskissiksladLkgkkvgvqagstaeellkeelkk.....gaeivefdtleealqaLkngrvdavv 157
                                       vr +     s+++++adL++  v+v + + +e ++ ++l++     ++e+ ++   ++ l+aL++g+vda+ 
  gi|336252251|ref|YP_004595358.1| 100 VRPE-----SNFETPADLANVPVAVNRRTGQEYTAMRALEEhlppeDVELEHYGMPTDRLRALRDGEVDAAT 166
                                       5522.....5799999************998876555444466679************************86 PP

>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00012      0.74      14      41 ..      13      40 ..       4      45 .. 0.85
   2 !    4.7   0.0    0.0034        21     154     188 ..     142     175 ..     107     232 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
                            NMT1_2 14 altdaaplvvakekglfakeGltvelek 41
                                      + + + p+ va+e+g+fa+eGl+vel +
  gi|336252251|ref|YP_004595358.1| 13 PFSFMLPQRVAAERGYFAEEGLDVELLE 40
                                      556689999***************9975 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0034
                            NMT1_2 154 vklvvvpp.pqmvanlkagtidgfcvgePwnaqava 188
                                       v+l +  +  +  ++l+ g++d+++  +P+    +a
  gi|336252251|ref|YP_004595358.1| 142 VELEHYGMpTDRLRALRDGEVDAATLLDPHS--TLA 175
                                       5554444433445555555555555555552..222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2211.38
//
Query:       gi|336252252|ref|YP_004595359.1|  [L=112]
Description: Cupin 2 barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-21   75.3   0.8      3e-21   74.9   0.8    1.1  1  Cupin_2          Cupin domain
    4.5e-07   29.8   0.1    5.6e-07   29.5   0.1    1.1  1  AraC_binding     AraC-like ligand binding domain
    7.9e-06   25.5   0.0      1e-05   25.1   0.0    1.2  1  Cupin_3          Protein of unknown function (DUF861)
    4.5e-05   23.1   0.0    5.8e-05   22.7   0.0    1.1  1  Cupin_1          Cupin
     0.0027   17.6   0.0     0.0035   17.3   0.0    1.2  1  MannoseP_isomer  Mannose-6-phosphate isomerase
     0.0095   15.8   0.0      0.012   15.5   0.0    1.3  1  Cupin_7          ChrR Cupin-like domain
  ------ inclusion threshold ------
      0.031   14.5   0.0      0.041   14.1   0.0    1.1  1  CENP-C_C         Mif2/CENP-C like
      0.051   13.3   0.0      0.066   13.0   0.0    1.2  1  EutQ             Ethanolamine utilisation protein EutQ
      0.052   13.2   0.1      0.056   13.1   0.1    1.1  1  AraC_binding_2   AraC-binding-like domain
      0.078   12.3   0.0      0.099   12.0   0.0    1.3  1  CDO_I            Cysteine dioxygenase type I


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 !   74.9   0.8   1.6e-24     3e-21       2      68 ..      33      98 ..      32     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1.6e-24
                                      EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEE CS
                           Cupin_2  2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparll 68
                                      +++++pG++ psh H++e +++yVl+G+++ +vdg ev+le+Gd++ fp++++H+ +N++depa+ l
  gi|336252252|ref|YP_004595359.1| 33 YWRVEPGATLPSHEHEHE-QIGYVLQGTLTAIVDGGEVVLEEGDAYRFPSNERHGAENRSDEPAVGL 98
                                      689***************.********************************************9865 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 !   29.5   0.1   3.2e-10   5.6e-07      16      69 ..      42      95 ..      35     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.2e-10
                                      EEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEE CS
                      AraC_binding 16 fpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgw 69
                                       p h h++ +i+yv++Gt +  ++g+++ l++Gd   +p +e H  e  s+++ 
  gi|336252252|ref|YP_004595359.1| 42 LPSHEHEHEQIGYVLQGTLTAIVDGGEVVLEEGDAYRFPSNERHGAENRSDEPA 95
                                      578******************************************999998875 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 !   25.1   0.0   5.6e-09     1e-05       4      59 ..      26      82 ..      23      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 5.6e-09
                                      CTCCEEEEEEEECEEE.EECESSEEEE.EEEECEEEEEETTTEEEEEETTEEEEE-TT CS
                           Cupin_3  4 lgvfswgiwectpGkf.rltyeedEfc.yileGevkvtpeggetvelraGDlvvlpkg 59
                                       ++ s+ +w ++pG   + +  e+E + y+l+G  +  + +g +v l++GD+ ++p +
  gi|336252252|ref|YP_004595359.1| 26 GDRASMKYWRVEPGATlPSHEHEHEQIgYVLQGTLTAIV-DGGEVVLEEGDAYRFPSN 82
                                      6788999*******86255666677778***********.666688**********76 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   3.2e-08   5.8e-05      33     113 ..      29     101 ..      22     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.2e-08
                                       EEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEE CS
                           Cupin_1  33 isaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepava 109
                                        s+   ++epg+ l+ h h   ++i yvlqG+++  +v  g+       +l+eGd+  +P++  h + n  depav 
  gi|336252252|ref|YP_004595359.1|  29 ASMKYWRVEPGATLPSHEH-EHEQIGYVLQGTLT-AIVDGGE------VVLEEGDAYRFPSNERHGAENRSDEPAVG 97 
                                       566667789**********.**************.8888885......67************************997 PP

                                       EEEE CS
                           Cupin_1 110 ivvf 113
                                       + v+
  gi|336252252|ref|YP_004595359.1|  98 LGVL 101
                                       6665 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.9e-06    0.0035      57     126 ..      23      91 ..       8      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.9e-06
                   MannoseP_isomer  57 ldegeryqvkritvkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpG 126
                                       l++g+r  +k   v+Pg++l  + h h    + v++Gt    vd  +++l+e +    p ++ h  en  
  gi|336252252|ref|YP_004595359.1|  23 LSTGDRASMKYWRVEPGATLPSHEHEHEQIGY-VLQGTLTAIVDGGEVVLEEGDAYRFPSNERHGAENRS 91 
                                       7789999******************9998776.689**9999**********************999975 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.5e-06     0.012      23      56 ..      28      61 ..      11      92 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.5e-06
                                      -EEEEEEEE-TTEE---EE-TT-EEEEEEEEEEE CS
                           Cupin_7 23 aratslvryapgsafsahkHpggeeilVLeGvfs 56
                                      + + +  r++pg+ +++h+H+     +VL+G+++
  gi|336252252|ref|YP_004595359.1| 28 RASMKYWRVEPGATLPSHEHEHEQIGYVLQGTLT 61
                                      44667789***********************986 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.3e-05     0.041      28      79 ..      44      95 ..      35      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                                      EE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE-SSS-E CS
                          CENP-C_C 28 knskkatlvFyViqGrvevtvsktsfvigkgsvFqvPagneysieNklnkea 79
                                      ++ +++  + yV+qG++ + v + + v+ +g+ +  P+      eN++++ a
  gi|336252252|ref|YP_004595359.1| 44 SHEHEHEQIGYVLQGTLTAIVDGGEVVLEEGDAYRFPSNERHGAENRSDEPA 95
                                      5556667778************************************999987 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.7e-05     0.066      61     128 ..      16      82 ..       3      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                              EutQ  61 dvvltkdlvtleeskrlgaGlmemkettfdwtlnydeidyvieGrldvlidGrkvvaeaGdviliPkg 128
                                       d v+  dl t++ + ++    +e   t      ++++i yv++G l  ++dG +vv e Gd    P +
  gi|336252252|ref|YP_004595359.1|  16 DGVYLGDLSTGDRA-SMKYWRVEPGATLPSHEHEHEQIGYVLQGTLTAIVDGGEVVLEEGDAYRFPSN 82 
                                       55666677766543.5666666666677777788999***********************98877765 PP

>> AraC_binding_2  AraC-binding-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.1e-05     0.056      26      87 ..      15      81 ..       3      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.1e-05
                    AraC_binding_2 26 lrsarlgdlslgrlrygaavsirpsel.....ddfylvqlplsGraeveqggrevvlgpgdavvldp 87
                                       +++ lgdls g+  +   ++++p++       ++ ++ + l+G+ +  ++g+evvl++gda  + +
  gi|336252252|ref|YP_004595359.1| 15 ADGVYLGDLSTGDRASMKYWRVEPGATlpsheHEHEQIGYVLQGTLTAIVDGGEVVLEEGDAYRFPS 81
                                      566777888888888888889999986677777799*************************976665 PP

>> CDO_I  Cysteine dioxygenase type I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.5e-05     0.099     120     159 ..      66     104 ..      38     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.5e-05
                                       EEEE--TT-EEEE-TTT-EEEEEES-SSS-EEEEEEEES- CS
                             CDO_I 120 dekrllsngtayvndelglHrveNlSsdegAVSlHlYaPP 159
                                       + ++ l++g+ay + +++ H  eN S de+AV l + +PP
  gi|336252252|ref|YP_004595359.1|  66 GGEVVLEEGDAYRFPSNERHGAENRS-DEPAVGLGVLSPP 104
                                       457899********************.************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 828.51
//
Query:       gi|336252253|ref|YP_004595360.1|  [L=311]
Description: hypothetical protein Halxa_0842 [Halopiger xanaduensis SH-6]
Scores for 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:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2424.76
//
Query:       gi|336252254|ref|YP_004595361.1|  [L=388]
Description: NMT1/THI5 like domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-34  118.2   0.0    7.3e-34  117.6   0.0    1.2  1  NMT1        NMT1/THI5 like
     0.0096   15.6   1.2       0.21   11.2   0.2    3.1  2  NMT1_2      NMT1-like family
  ------ inclusion threshold ------
      0.091   12.6   3.4       0.24   11.3   3.4    1.7  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
       0.31   10.4   2.6       0.82    9.1   2.6    1.7  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6   0.0   1.6e-37   7.3e-34       3     216 .]      87     296 ..      85     296 .. 0.94

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 1.6e-37
                                       GGHHHHHHHHTTHHHHTTEE.EEEE--SSTTHHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--EEEE CS
                              NMT1   3 nhaglyvAkekGYFkeeGld.Veivepadpsdatelvasgkadfgvsyqesllaarakglpvvsvaallqeplsgli 78 
                                        ha++++A+e G++ eeG + Vei  + ++  a +  + g+++f+vs++++ll   ++gl  ++v+ ++q++++ ++
  gi|336252254|ref|YP_004595361.1|  87 LHAPYVAAREEGFYDEEGFEtVEIESGDGSDFAANQAGLGNVEFAVSSPDQLLNVNSRGLSPRCVGVVMQRNPNVVF 163
                                       59*****************957*****99999******************************************999 PP

                                       EECCC-..-SSGGGGTTSEEEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHH CS
                              NMT1  79 vlkdsg..ikspkDLkGkrigyvgspfekallkallakdggdpsdvtlvnvggtslakalltgkvDaaiggyenweg 153
                                       + +d+   +++p+ L+  ++g  + +  +++ +a l+++g+  ++v+ v++ g++++++ll+g+vDaa  g+ + ++
  gi|336252254|ref|YP_004595361.1| 164 ATRDGFgeLDDPAQLEDATVGSGP-GMVRQMTQAYLEHHGV-LESVEYVDT-GFDTVQQLLSGEVDAAG-GVFG-DV 235
                                       88886447*************988.89**************.99*******.777779**********8.5556.6* PP

                                       HHHHHTT--EEEE-GGGTT-----SEEEEEEHHHHHH-HHHHHHHHHHHHHHHHHHHHSHHHH CS
                              NMT1 154 velesegkelrifaladlgvpdyyslvlitnekllkenpelvkkFlrAlkkGyeyalahPeea 216
                                       v +e++g e++++++ +  +   y  v++t e ++++n  +v++FlrA+++G+ +a+++Pe+a
  gi|336252254|ref|YP_004595361.1| 236 VDAEHQGAEVDVLSIHEAIP--SYGHVIATDEGFASDNGATVRAFLRATARGAVWATQNPEAA 296
                                       *****************997..9**************************************87 PP

>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.2   4.7e-05      0.21      15     244 ..      85     295 ..      72     303 .. 0.77
   2 ?   -3.7   0.0       1.7   7.5e+03     175     185 ..     337     347 ..     332     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.7e-05
                            NMT1_2  15 ltdaaplvvakekglfakeGlt.velekqaswaelrdkllagelDaahv.ltpapllidlGiggakadmkvlaslnl 89 
                                       +  +ap v+a+e+g++++eG + ve+e   +   + ++   g++  a+   + ++   ++G+     +  v + ++ 
  gi|336252254|ref|YP_004595361.1|  85 NGLHAPYVAAREEGFYDEEGFEtVEIESGDGSDFAANQAGLGNVEFAVSsPDQLLNVNSRGL----SPRCVGVVMQR 157
                                       56699*****************999999999999999999999**99994455555557788....78899999999 PP

                            NMT1_2  90 nGqaitlsnklkdkkvsdakalkdlvakkkas.kplkiavtfpgsthdlllrywLaaaGldpeadvklvvvpppqmv 165
                                       n++ ++++++          ++ +l   ++a+ ++ +++     ++ + +++ +L+ +G+     v+ v++   ++v
  gi|336252254|ref|YP_004595361.1| 158 NPNVVFATRD----------GFGEL--DDPAQlEDATVGS--GPGMVRQMTQAYLEHHGVLE--SVEYVDTG-FDTV 217
                                       9999999874..........33333..3333334445665..45677778888899999876..88888876.5789 PP

                            NMT1_2 166 anlkagtidgfcvgePwnaqavaegiGvtaltsqelwkdhPekvlgvredfveknpntaralvkalleAtkwldakk 242
                                       ++l +g++d++ +     + a+++g+ v +l+  e  +   + v+++ e f+ +n +t+ra+++a ++ + w ++++
  gi|336252254|ref|YP_004595361.1| 218 QQLLSGEVDAAGGVFGDVVDAEHQGAEVDVLSIHEAIPS-YGHVIATDEGFASDNGATVRAFLRATARGAVWATQNP 293
                                       999999999986655457888888888888877766555.5788999999999999999999999999999999765 PP

                            NMT1_2 243 en 244
                                       e+
  gi|336252254|ref|YP_004595361.1| 294 EA 295
                                       54 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.7
                            NMT1_2 175 gfcvgePwnaq 185
                                       g+  +ePw+a+
  gi|336252254|ref|YP_004595361.1| 337 GWSESEPWQAT 347
                                       67778999875 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.4   5.4e-05      0.24       3      22 ..       7      26 ..       6      30 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.4e-05
                        TAT_signal  3 SRRdFLKgsAAaaAAaalgg 22
                                      +RR FL +++ aa A+ lgg
  gi|336252254|ref|YP_004595361.1|  7 TRRRFLAATGTAAVAGCLGG 26
                                      8***************9998 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.6   0.00018      0.82       9      26 ..       6      22 ..       4      24 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00018
                        UCR_Fe-S_N  9 ptRRDFLyiATgavgaVG 26
                                      +tRR+FL +ATg +++ G
  gi|336252254|ref|YP_004595361.1|  6 HTRRRFL-AATGTAAVAG 22
                                      69*****.6666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); 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:                         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 0.21s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3167.13
//
Query:       gi|336252255|ref|YP_004595362.1|  [L=275]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-21   75.4  12.7    4.6e-21   75.4  12.7    1.9  2  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 ?    0.3   0.3     0.028     5e+02      50      89 ..      32      72 ..      23      79 .. 0.75
   2 !   75.4  12.7   2.6e-25   4.6e-21       3     169 ..     100     261 ..      98     270 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.028
                      BPD_transp_1 50 ghlilp.viillllsaapyvrlirraalrslpkdlveaara 89
                                      g  +lp +++l++l aa+ ++++ +++   +  + +e+a+a
  gi|336252255|ref|YP_004595362.1| 32 GRRVLPpAVVLAALLAAWHAVVVAYEIPTLVLPSPREVALA 72
                                      55566668888888888888888888777777777777766 PP

  == domain 2  score: 75.4 bits;  conditional E-value: 2.6e-25
                      BPD_transp_1   3 llGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       ++G+ +a  + ++++ ++ l+p++ +l+  P++++a+ll+       +lg +i + ++l+++ ++++v++   ++lr
  gi|336252255|ref|YP_004595362.1| 100 VVGLALAfaMTHSRTATRTLLPYVVALRIAPVIAVAPLLF------LWLGRGIPARAALVATLTTFPVTIAALDGLR 170
                                       56666666699*****************************......9****************************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                       + p+ +  +a   Gasr ++f  v++P+a+p++++g+ +a+++++ g+v++ef++   Glg +++e+  +  ++e++
  gi|336252255|ref|YP_004595362.1| 171 ETPDAYLDLADSVGASRLETFLFVRVPAAAPSVVAGFKIASALSVVGTVVAEFVTLRAGLGARVFETATYLETAETY 247
                                       ***************************************************************************99 PP

                      BPD_transp_1 155 nggvlalviavllln 169
                                        +++++l  + + + 
  gi|336252255|ref|YP_004595362.1| 248 -AALVVLSGLGIGFY 261
                                       .66655555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); 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):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.19s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 2447.99
//
Query:       gi|336252256|ref|YP_004595363.1|  [L=283]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-18   65.1  10.9    6.5e-18   65.1  10.9    1.5  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.92   10.1   3.2    1.1e+02    3.5   0.2    4.0  4  PC_rep        Proteasome/cyclosome repeat
       0.99    7.6   5.0        2.7    6.2   5.0    1.6  1  DUF2070       Predicted membrane protein (DUF2070)


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 ?   -2.8   0.3      0.77   4.6e+03     163     163 ..      47      47 ..      30      75 .. 0.54
   2 !   65.1  10.9   1.1e-21   6.5e-18       1     184 [.      98     272 ..      98     273 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.77
                      BPD_transp_1 163 i 163
                                       +
  gi|336252256|ref|YP_004595363.1|  47 L 47 
                                       1 PP

  == domain 2  score: 65.1 bits;  conditional E-value: 1.1e-21
                      BPD_transp_1   1 gillGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraa 75 
                                       gi +G+l+a  +++  +++ +++p+  +++ lP +++a+ll+       +lg++   +i+ ++l ++++ +l+++a+
  gi|336252256|ref|YP_004595363.1|  98 GIATGFLLAvlVAYLPWVRTAVYPYLVAVRVLPKIAVAPLLL------IYLGTGTETAIVFVALITFFPLVLNTAAG 168
                                       688889999988899***************************......9**************************** PP

                      BPD_transp_1  76 lrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyse 152
                                       l+  p++++e+ r   a+  +++ +v lP alp +++gl  ++++++ gav+ e+++++ Glg l+l  +++     
  gi|336252256|ref|YP_004595363.1| 169 LDRAPTEHRELLRSVDAGALERIAYVDLPYALPDVFAGLKQSVTLAVVGAVVGEWVIADDGLGFLVLMGSENVRPE- 244
                                       *****************************************************************99999999999. PP

                      BPD_transp_1 153 isnggvlalviavlllnlvadilqrlldprvr 184
                                           ++la++ ++l+l l+++  + l+++ vr
  gi|336252256|ref|YP_004595363.1| 245 ----VMLAALSVLLALGLALYGSVVLVQRGVR 272
                                       ....6778888888888888888888887776 PP

>> PC_rep  Proteasome/cyclosome repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.018   1.1e+02       1      12 [.      39      50 ..      39      57 .. 0.83
   2 ?   -2.2   0.0       1.2   6.9e+03      17      28 ..      83      94 ..      81      98 .. 0.80
   3 ?    3.2   0.0     0.024   1.4e+02       8      19 ..     139     150 ..     139     152 .. 0.90
   4 ?    0.5   0.3      0.17     1e+03       3      10 ..     253     260 ..     251     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.018
                                      HHHHHHHHHCTT CS
                            PC_rep  1 GAllALGlihaG 12
                                      +A+lA+G+++ +
  gi|336252256|ref|YP_004595363.1| 39 AAALAIGVLCWW 50
                                      79******9955 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                      HHHHHHHHHHHH CS
                            PC_rep 17 eaislLkpylsd 28
                                       a+s L+++++ 
  gi|336252256|ref|YP_004595363.1| 83 NALSTLEKVVYG 94
                                      58999*999886 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.024
                                       HHCTTSTCHHHH CS
                            PC_rep   8 lihaGsgneeai 19 
                                       li++G+g+e+ai
  gi|336252256|ref|YP_004595363.1| 139 LIYLGTGTETAI 150
                                       8********886 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.17
                                       HHHHHHHC CS
                            PC_rep   3 llALGlih 10 
                                       llALGl+ 
  gi|336252256|ref|YP_004595363.1| 253 LLALGLAL 260
                                       79****96 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   5.0   0.00046       2.7      96     189 ..     113     281 ..      35     282 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00046
                           DUF2070  96 l...qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly..................... 148
                                           +a++++ +++  +l  + +  +l+++ ++ + +a++ +++++++ ++l ++                      
  gi|336252256|ref|YP_004595363.1| 113 PwvrTAVYPYLVAVR-VLPKIAVAPLLLIYLGTGTETAIVFVALITFFPLVLNTAAgldraptehrellrsvdagal 188
                                       132233333333333.3333333333333333333344444444444444445544577888888888888888888 PP

                           DUF2070 149 ....................................................fspesfllllllslifalavylfiv 173
                                                                                           ++pe +l +l ++l+++la+y  +v
  gi|336252256|ref|YP_004595363.1| 189 eriayvdlpyalpdvfaglkqsvtlavvgavvgewviaddglgflvlmgsenVRPEVMLAALSVLLALGLALYGSVV 265
                                       8888888888888888888888888888888899999**************************************** PP

                           DUF2070 174 vvdrplkrnlgvsald 189
                                       +v+r ++r lg++a+d
  gi|336252256|ref|YP_004595363.1| 266 LVQRGVRRWLGFDATD 281
                                       ***********99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); 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:                         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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2446.15
//
Query:       gi|336252257|ref|YP_004595364.1|  [L=255]
Description: taurine-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-30  104.7   0.0      1e-29  103.8   0.0    1.4  1  ABC_tran     ABC transporter
    2.5e-06   28.0   0.1    4.3e-06   27.2   0.1    1.5  1  AAA_16       AAA ATPase domain
    7.1e-06   26.0   0.0     0.0047   16.8   0.0    2.4  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0003   21.1   0.4     0.0013   19.1   0.4    2.0  1  AAA_22       AAA domain
    0.00058   19.6   0.1     0.0016   18.2   0.1    1.8  2  AAA_30       AAA domain
    0.00074   19.7   0.0     0.0015   18.7   0.0    1.6  1  AAA_33       AAA domain
     0.0037   17.2   0.0     0.0061   16.5   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
     0.0048   15.8   0.1       0.69    8.6   0.0    2.4  2  ABC_ATPase   Predicted ATPase of the ABC class
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.022   14.0   0.0    1.4  1  NB-ARC       NB-ARC domain
      0.014   15.0   0.0      0.038   13.6   0.0    1.7  1  AAA_25       AAA domain
      0.018   15.5   0.1      0.097   13.1   0.1    2.1  2  AAA          ATPase family associated with various cellular a
       0.02   14.8   0.1      0.049   13.6   0.1    1.6  1  NACHT        NACHT domain
      0.023   14.4   0.0      0.042   13.6   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.026   14.4   0.0      0.051   13.5   0.0    1.5  1  ATPase_2     ATPase domain predominantly from Archaea
      0.035   13.5   0.0       0.86    9.0   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
      0.036   14.1   0.0       0.19   11.8   0.0    2.2  2  AAA_14       AAA domain
      0.048   13.9   0.7       0.31   11.3   0.0    2.4  3  AAA_28       AAA domain
      0.058   13.9   0.1       0.09   13.3   0.1    1.2  1  AAA_23       AAA domain
       0.12   12.1   0.0       0.23   11.2   0.0    1.5  2  AAA_24       AAA domain
       0.12   13.0   0.0       0.22   12.2   0.0    1.5  1  PIG-L        GlcNAc-PI de-N-acetylase
       0.14   12.1   0.0       0.22   11.4   0.0    1.2  1  Rad17        Rad17 P-loop domain
       0.21   11.1   0.1       0.34   10.5   0.1    1.3  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.25   10.9   0.0       0.51    9.8   0.0    1.5  1  AAA_7        P-loop containing dynein motor region
       0.25   11.1   0.1       0.43   10.3   0.1    1.3  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.28   11.1   0.7        4.8    7.1   0.2    2.2  2  NTPase_1     NTPase
       0.32   10.7   0.0       0.46   10.1   0.0    1.1  1  AAA_15       AAA ATPase 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 !  103.8   0.0   1.5e-32     1e-29       3     136 ..      19     156 ..      17     157 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 1.5e-32
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                       +++l + ege v +vG++G+GK+tLl+++ gl +pt+G++++dg++       ++ + +g+++q ++l p +t+ en
  gi|336252257|ref|YP_004595364.1|  19 DIDLRIDEGEFVTVVGPSGCGKTTLLRTIGGLQEPTAGRVRIDGRSPAA---AQAAADLGFVFQRHTLLPWKTALEN 92 
                                       799*****************************************99998...99*********************** PP

                                       ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                  + + ++ ++l+++gl++++d +     ++LSgG++qrva+aral   +++ll+DEp+
  gi|336252257|ref|YP_004595364.1|  93 vtflrkladqpANEGDARALLRSMGLEGFEDARP----AELSGGMRQRVAIARALHLGADVLLMDEPF 156
                                       *****99888777777*****************9....*****************************6 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   6.3e-09   4.3e-06      19     121 ..      22     137 ..      11     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6.3e-09
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekd.ggif.lrgkcdql.esa..........ipysalaqalareell 82 
                                       +r +++e v ++G+sG+GK++l+r++   l++   g + + g+     + a           +++++ +al++ ++l
  gi|336252257|ref|YP_004595364.1|  22 LRIDEGEFVTVVGPSGCGKTTLLRTIG-GLQEPtAGRVrIDGRSPAAaQ-AaadlgfvfqrHTLLPWKTALENVTFL 96 
                                       55667799*******************.566663244445555555532.2345555544334478*****999999 PP

                            AAA_16  83 rqlldeaesaeleawrekleeala.......avpelagaeasrlle 121
                                       r+l+d++++   e ++++l+++++         +el+g    r + 
  gi|336252257|ref|YP_004595364.1|  97 RKLADQPAN---EGDARALLRSMGlegfedaRPAELSGG--MRQRV 137
                                       999999444...444444555555555554422222222..33333 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 !   16.8   0.0   6.8e-06    0.0047       2      24 ..      30      52 ..      29      69 .. 0.80
   2 !    6.9   0.0    0.0069       4.8     232     299 ..     124     190 ..      78     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.8e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                        ++Gp g+GK++LL+++ +l+ 
  gi|336252257|ref|YP_004595364.1| 30 VTVVGPSGCGKTTLLRTIGGLQE 52
                                      679***************99973 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0069
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS.p 299
                                         ++elS G+++  a++ al+  +   ++ll DEp   L+     +l   +++l r ++  v+++THS p
  gi|336252257|ref|YP_004595364.1| 124 ARPAELSGGMRQRVAIARALHLGA---DVLLMDEPFGELDEITRDELGVEIRDLWRrERKTVVFVTHSvP 190
                                       456899*****9988888888877...********99999988899999998888888889999999955 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.4   1.8e-06    0.0013       5      38 ..      27      72 ..      23     190 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.8e-06
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee..............e 38
                                        +++v+G+sG+GKTtllr++    +  + a +              +
  gi|336252257|ref|YP_004595364.1| 27 GEFVTVVGPSGCGKTTLLRTIGGLQE--PTAGRvridgrspaaaqaaA 72
                                      6799***************9987653..22222445555555555551 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.3e-06    0.0016      18      67 ..      27      75 ..      19     154 .. 0.81
   2 ?   -2.2   0.0       4.3     3e+03      37      63 ..     170     196 ..     167     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.3e-06
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelg 67
                                        +++++Gp G GKtt+l+++  + e   grv +   + +aA++ a +lg
  gi|336252257|ref|YP_004595364.1| 27 GEFVTVVGPSGCGKTTLLRTIGGLQEPTAGRVRIDGRSPAAAQAAA-DLG 75
                                      45899*********************99878887776666666554.444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.3
                            AAA_30  37 alreaweaaggrviglAptgkaAkvLa 63 
                                       ++r++w+++ ++v+ ++++   A  La
  gi|336252257|ref|YP_004595364.1| 170 EIRDLWRRERKTVVFVTHSVPEAVFLA 196
                                       578999999999999988876666555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.2e-06    0.0015       2      99 ..      30     191 ..      29     205 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-06
                            AAA_33   2 vllvGlpGsGKstlaerl..lkklgavllssdt............................................ 32 
                                       v +vG++G+GK+tl++ +  l++ +a +++ d                                             
  gi|336252257|ref|YP_004595364.1|  30 VTVVGPSGCGKTTLLRTIggLQEPTAGRVRIDGrspaaaqaaadlgfvfqrhtllpwktalenvtflrkladqpane 106
                                       679**************988999999898888888888888888888888888888666666666544444444444 PP

                            AAA_33  33 .....lrrrlfgtdqqskt...........dytrvldrlyqilnelarkalsagrnvil.dat.............. 78 
                                            l                        ++++++  ++q++ ++a +al  g++v+l d +              
  gi|336252257|ref|YP_004595364.1| 107 gdaraL------------LrsmglegfedaRPAELSGGMRQRV-AIA-RALHLGADVLLmDEPfgeldeitrdelgv 169
                                       443332............0444444333335566666677776.444.57888888666677766666666666666 PP

                            AAA_33  79 .nlsrrerarflklarrlgvpv 99 
                                         ++ ++r+r+  ++  ++vp+
  gi|336252257|ref|YP_004595364.1| 170 eIRDLWRRERKTVVFVTHSVPE 191
                                       5555666677777777777764 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.9e-06    0.0061      80     129 ..       7      57 ..       1      64 [. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.9e-06
                                       EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                       ++v  ++ ++++++  ++++ +++++vG+SG GK+tL+ ++ + +e   g 
  gi|336252257|ref|YP_004595364.1|   7 VTVTFDEFTAVADIDLRIDEgEFVTVVGPSGCGKTTLLRTIGGLQEPTAGR 57 
                                       55555666778888888888799****************998866655555 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 ?    4.6   0.0     0.017        11     242     264 ..      24      47 ..       7      69 .. 0.81
   2 !    8.6   0.0     0.001      0.69     324     350 ..     130     156 ..     122     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.017
                                       E-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAl 264
                                       i +G  +++vG+   GK+TLL+ +
  gi|336252257|ref|YP_004595364.1|  24 IDEGeFVTVVGPSGCGKTTLLRTI 47 
                                       667767789************987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.001
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGG CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDt 350
                                       SG + q ++i++al++ga++lL+DE  
  gi|336252257|ref|YP_004595364.1| 130 SGGMRQRVAIARALHLGADVLLMDEPF 156
                                       9************************65 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.2e-05     0.022      17      40 ..      26      47 ..      14      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-05
                                      TSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqi 40
                                      e +  +v++vG  G+GKttl++ i
  gi|336252257|ref|YP_004595364.1| 26 EGE--FVTVVGPSGCGKTTLLRTI 47
                                      555..9**************9987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.5e-05     0.038      29      50 ..      23      44 ..      19      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.5e-05
                            AAA_25 29 llpagelallaGapgtGKttla 50
                                       + +ge++ ++G++g+GKttl+
  gi|336252257|ref|YP_004595364.1| 23 RIDEGEFVTVVGPSGCGKTTLL 44
                                      6899****************97 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 ?   13.1   0.1   0.00014     0.097       2      20 ..      31      49 ..      30      83 .. 0.83
   2 ?   -0.3   0.0         2   1.4e+03      45      66 ..     132     154 ..      99     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                                      EEESSTTSSHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavak 20
                                       ++Gp G+GKT+l + +  
  gi|336252257|ref|YP_004595364.1| 31 TVVGPSGCGKTTLLRTIGG 49
                                      689***********99865 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2
                                       HHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  45 kirelfkeakeka.kpsilfiDE 66 
                                        +r+ ++ a++   +  +l++DE
  gi|336252257|ref|YP_004595364.1| 132 GMRQRVAIARALHlGADVLLMDE 154
                                       45555555555555578999996 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   7.1e-05     0.049       3      20 ..      30      47 ..      28      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.1e-05
                                      EEEEC-TTTCHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkl 20
                                      v + G++G+GKTtLl+ +
  gi|336252257|ref|YP_004595364.1| 30 VTVVGPSGCGKTTLLRTI 47
                                      789************987 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 ?   13.6   0.0   6.1e-05     0.042      16      39 ..      21      44 ..      10      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.1e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                      +++id+ +++ ++GpsG GK+Tll
  gi|336252257|ref|YP_004595364.1| 21 DLRIDEGEFVTVVGPSGCGKTTLL 44
                                      45677555999************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 ?   13.5   0.0   7.3e-05     0.051      19      40 ..      26      47 ..      11      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.3e-05
                          ATPase_2 19 pneiyfiYGpegsGKtaLlkei 40
                                      + e++ + Gp g+GKt+Ll+ i
  gi|336252257|ref|YP_004595364.1| 26 EGEFVTVVGPSGCGKTTLLRTI 47
                                      46788999***********986 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 ?    9.0   0.0    0.0012      0.86      24      44 ..      27      47 ..       7      58 .. 0.78
   2 ?    2.5   0.0      0.12        83     113     184 ..      99     172 ..      78     205 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                                      SSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAi 44
                                       +f  +vGp G+GK+ ll  i
  gi|336252257|ref|YP_004595364.1| 27 GEFVTVVGPSGCGKTTLLRTI 47
                                      35999***********99876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.12
                                       ETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 113 ingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaell 183
                                       + ++ +++ + + ll+s+g++        +LSgG ++ va+a  + +     a + l+De   +LDe  + ++   +
  gi|336252257|ref|YP_004595364.1|  99 LADQPANEGDARALLRSMGLEGFedarpaELSGGMRQRVAIARALHL----GADVLLMDEPFGELDEITRDELGVEI 171
                                       56677777777777777777543444444999999998888754432....33455666666666666666655555 PP

                                       H CS
                                       x RF
                             SMC_N 184 k 184
                                       +
  gi|336252257|ref|YP_004595364.1| 172 R 172
                                       5 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   0.00027      0.19       3      23 ..      28      48 ..      26      80 .. 0.84
   2 ?   -1.1   0.0       2.7   1.8e+03      70     100 ..     159     188 ..     148     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                            AAA_14  3 kilvitGaRrvGKTtllkqli 23
                                      + ++++G+  +GKTtll+++ 
  gi|336252257|ref|YP_004595364.1| 28 EFVTVVGPSGCGKTTLLRTIG 48
                                      6799*************9885 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.7
                            AAA_14  70 lDEiqevpewekalkslvdegknldvivtGS 100
                                       lDEi + +e+   +++l +++++  v+vt S
  gi|336252257|ref|YP_004595364.1| 159 LDEITR-DELGVEIRDLWRRERKTVVFVTHS 188
                                       788876.577888999999998889999877 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00044      0.31       2      20 ..      30      48 ..      29      90 .. 0.89
   2 ?    0.1   0.0       1.2   8.3e+02      63     120 ..     170     191 ..     134     216 .. 0.66
   3 ?   -2.3   0.0       6.6   4.5e+03      46      70 ..     217     241 ..     207     250 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00044
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      + ++G++++GKTtll+ + 
  gi|336252257|ref|YP_004595364.1| 30 VTVVGPSGCGKTTLLRTIG 48
                                      6799***********9865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.2
                            AAA_28  63 qleeeaaaaankvlfcDrglldtlaYarayggeaeaeleaaarekrydlvfllppape 120
                                       +                                    + + +r++r + vf++  +pe
  gi|336252257|ref|YP_004595364.1| 170 E------------------------------------IRDLWRRERKTVVFVTHSVPE 191
                                       3....................................334455555555555554443 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.6
                            AAA_28  46 lpwvedllafaervleeqleeeaaa 70 
                                       lp+ +d+  f +r  +eq+++ +++
  gi|336252257|ref|YP_004595364.1| 217 LPDPRDASVFGSRAFQEQVAQVRET 241
                                       6666677777777777777766655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00013      0.09      15      39 ..      20      47 ..       4      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAi 39
                                      id+   +  ++ ++Gp G+GKTT+l+ i
  gi|336252257|ref|YP_004595364.1| 20 IDLridEGEFVTVVGPSGCGKTTLLRTI 47
                                      5556655567789************876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00033      0.23       5      23 ..      30      50 ..      27     104 .. 0.84
   2 ?   -3.3   0.0       8.7     6e+03     116     131 ..     172     188 ..     164     191 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                            AAA_24  5 iliyGpsgiGKTtlakel..g 23
                                      + ++Gpsg GKTtl++++   
  gi|336252257|ref|YP_004595364.1| 30 VTVVGPSGCGKTTLLRTIggL 50
                                      6799************98551 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.7
                            AAA_24 116 kklqelrk.nvifiahe 131
                                       ++l+     +v+f+ h+
  gi|336252257|ref|YP_004595364.1| 172 RDLWRRERkTVVFVTHS 188
                                       55555444599999986 PP

>> PIG-L  GlcNAc-PI de-N-acetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00032      0.22      52     113 ..     131     189 ..      87     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHHHHHHCTE..EEEEECCCBTT-STTS-CHHHHHHHHHHHHHH--SEEEEE-TT CS
                             PIG-L  52 aeiRekEaraaakhlgvadedvffldfpDgslesydedellddlaklieryrPdvvltldpe 113
                                       + +R++ a a a hlg+   dv  +d p g+l++ ++del  ++ +l +r r++vv++++  
  gi|336252257|ref|YP_004595364.1| 131 GGMRQRVAIARALHLGA---DVLLMDEPFGELDEITRDELGVEIRDLWRRERKTVVFVTHSV 189
                                       34466667777889999...*************************************99865 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00032      0.22      48      65 ..      30      47 ..      17      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                             Rad17 48 LLisGPsGCgkstvvkvL 65
                                      + + GPsGCgk+t ++ +
  gi|336252257|ref|YP_004595364.1| 30 VTVVGPSGCGKTTLLRTI 47
                                      5689*********99875 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 ?   10.5   0.1    0.0005      0.34       3      20 ..      30      47 ..      28      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                                      EEEEESTTCCHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhl 20
                                      + ++G+ G GKTtLl+++
  gi|336252257|ref|YP_004595364.1| 30 VTVVGPSGCGKTTLLRTI 47
                                      5799***********997 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 ?    9.8   0.0   0.00074      0.51      26      52 ..      20      46 ..       4      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00074
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikd 52
                                      ++l ++++  v +vGp+G+GKt+++++
  gi|336252257|ref|YP_004595364.1| 20 IDLRIDEGEFVTVVGPSGCGKTTLLRT 46
                                      67778899999************9876 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00063      0.43       4      23 ..      30      49 ..      28      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00063
                         PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                      + ++G++g+GKttL +++ g
  gi|336252257|ref|YP_004595364.1| 30 VTVVGPSGCGKTTLLRTIGG 49
                                      6789**********999876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2     0.007       4.8       2      19 ..      30      47 ..      29      62 .. 0.85
   2 ?    2.1   0.0      0.23   1.6e+02      91     135 ..     141     189 ..     132     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.007
                                      EEEE--TTSSHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkv 19
                                      v + Gp+G GKtTl++ +
  gi|336252257|ref|YP_004595364.1| 30 VTVVGPSGCGKTTLLRTI 47
                                      5788**********9876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.23
                                       HHH.HHH-EEEE--.-STT.GGG-HHHHHHHHHHHT.TTSEEEEE--SS CS
                          NTPase_1  91 kal.seadviviDE.iGkm.ElkskkfkeaveevLk.sekpvlavihrr 135
                                       +al  +adv+++DE  G++ E +  ++  +++++ + + k v++v h  
  gi|336252257|ref|YP_004595364.1| 141 RALhLGADVLLMDEpFGELdEITRDELGVEIRDLWRrERKTVVFVTHSV 189
                                       4443789*******78999777888999999999998888888888865 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00067      0.46      15      43 ..      18      47 ..       7      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00067
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsileal 43
                                       d+++ ++e  + +++G+ ++GK+++l+ +
  gi|336252257|ref|YP_004595364.1| 18 ADIDLRIDEGeFVTVVGPSGCGKTTLLRTI 47
                                      56666666668****************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.49u 0.20s 00:00:00.69 Elapsed: 00:00:00.35
# Mc/sec: 2201.93
//
Query:       gi|336252258|ref|YP_004595365.1|  [L=455]
Description: NMT1/THI5 like domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-29  101.3   0.0    9.6e-29  100.9   0.0    1.1  1  NMT1            NMT1/THI5 like
    2.1e-06   27.5   0.0    3.4e-06   26.8   0.0    1.4  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
     0.0032   17.3   3.2      0.028   14.3   1.4    2.8  2  MarR_2          MarR family
  ------ inclusion threshold ------
      0.027   14.2   0.0      0.054   13.2   0.0    1.5  1  NMT1_2          NMT1-like family


Domain annotation for each model (and alignments):
>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.0   2.2e-32   9.6e-29       2     211 ..     172     378 ..     171     382 .. 0.92

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 2.2e-32
                                       GGGHHHHHHHHTTHHHHTTEEEEEE--SSTTHHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--EEEE CS
                              NMT1   2 pnhaglyvAkekGYFkeeGldVeivepadpsdatelvasgkadfgvsyqesllaarakglpvvsvaallqeplsgli 78 
                                       + ha++y+A e G+++  G+d+++    ++  a+e v sg+ad+g++   +++ ara++ pvv +a  +q+ ++ l 
  gi|336252258|ref|YP_004595365.1| 172 ALHAPIYAALEAGWYETFGVDLRVDHCDGSRRALERVRSGAADVGIAGAATVVRARAADEPVVPIAVCYQRAMTVLY 248
                                       66*************************************************************************** PP

                                       EECC...C--SSGGGGTTSEEEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTH CS
                              NMT1  79 vlkd...sgikspkDLkGkrigyvgspfekallkallakdggdpsdvtlvnvggtslakalltgkvDaaiggyenwe 152
                                       +l++   ++  s++ L+G+rig+++s  e  ll +l  ++ +  + v +v+++g +  +al +g +D+++g + +  
  gi|336252258|ref|YP_004595365.1| 249 TLREvfgEPFRSVAQLEGRRIGMPPS-SETRLLGRLFLSQTALGDGVRIVDTNGEE-RDALRRGDADVVTGSFSD-- 321
                                       **9744367****************5.66667777776667779********7766.57***********99988.. PP

                                       HHHHHHTT--EEEE-GGGTT-----SEEEEEEHHHHHH-HHHHHHHHHHHHHHHHHHHH CS
                              NMT1 153 gvelesegkelrifaladlgvpdyyslvlitnekllkenpelvkkFlrAlkkGyeyala 211
                                          le++g+++++++lad+ +  +y ++li+ e+  +e++ +++ +l+ +  G+ +a +
  gi|336252258|ref|YP_004595365.1| 322 PRALERRGERVDVLPLADHFP--IYGPTLIVREEAFAERRPALRGMLAGTTAGWVAAQQ 378
                                       77777***************8..*******************************99876 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 !   26.8   0.0   7.5e-10   3.4e-06      25     201 ..     187     353 ..     171     414 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 7.5e-10
                                       HHHSSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS.-EEEEEEEEETT--SEEEEEEEEETT...SS- CS
                    Phosphonate-bd  25 eelGvevelvvatdyaavvealragqvDiaflgplayvqardqa.gveplatrvrsdGsasyrsviivrad...sdi 97 
                                       e  Gv+ ++   +    + e++r+g +D++ +g+ ++v+ar+ +  v+p+a+  +     +  +v+ + ++   ++ 
  gi|336252258|ref|YP_004595365.1| 187 ETFGVDLRVDHCDGSRRALERVRSGAADVGIAGAATVVRARAADePVVPIAVCYQ-----RAMTVLYTLREvfgEPF 258
                                       445888888888999999***********************998689*******8.....44455555554222589 PP

                                       -SHHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEEEEEHHHHHHHHHH CS
                    Phosphonate-bd  98 qsledLkgktiafvspsStsGylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdadaaavsadaledlvae 174
                                       +s+++L+g++i+++ +s t   l+ +  L ++    ++d  + v ++   +  +a+ +gdad+ + s +  + l+++
  gi|336252258|ref|YP_004595365.1| 259 RSVAQLEGRRIGMPPSSETR--LLGRLFL-SQTA--LGDGVRIVDTN--GEERDALRRGDADVVTGSFSDPRALERR 328
                                       *************9988877..*******.5554..45677776444..455667779****998776666666665 PP

                                       -HHHHTTEEEEEEEEEEE--EEEEETT CS
                    Phosphonate-bd 175 gpedkdelrviassppipndpvvvrke 201
                                       g  ++ ++  +a   pi ++++ vr+e
  gi|336252258|ref|YP_004595365.1| 329 G--ERVDVLPLADHFPIYGPTLIVREE 353
                                       5..233444444444555555555555 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.4   6.3e-06     0.028       2      58 ..      23      82 ..      22      86 .. 0.90
   2 ?    1.3   0.0     0.074   3.3e+02      10      45 ..     246     283 ..     242     283 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.3e-06
                                      T--HHHHHHHHHHHCTTTS...EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                            MarR_2  2 gltpaqarvLaaLgrrpgr...dltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                      gl ++ arvLa+L  r +r   + t   l   +g  ++a+s + +rL+a  L+er++  +
  gi|336252258|ref|YP_004595365.1| 23 GLGRTAARVLAYLLLRAEResdPTTTVHLRIGTGCNRPAISDATARLEALDLLERSSVRD 82
                                      8889*********99999999655*******************************96544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.074
                                       HHHHHHCTTTSEE.EHHHHH.HHHTSSHHHHHHHHHHH CS
                            MarR_2  10 vLaaLgrrpgrdl.tvgela.rrlglsksavsrilkrL 45 
                                       vL+ L+   g+++ +v++l+ rr g+++s+ +r+l rL
  gi|336252258|ref|YP_004595365.1| 246 VLYTLREVFGEPFrSVAQLEgRRIGMPPSSETRLLGRL 283
                                       56666666666455888886479**********99987 PP

>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05     0.054       7      67 ..     163     223 ..     157     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                            NMT1_2   7 qlklGfialtdaaplvvakekglfakeGltvelekqaswaelrdkllagelDaahvltpap 67 
                                       +l + + ++  +ap+ +a e+g+++  G+++++    +   +++++ +g  D++++ ++ +
  gi|336252258|ref|YP_004595365.1| 163 TLAVNWRPNALHAPIYAALEAGWYETFGVDLRVDHCDGSRRALERVRSGAADVGIAGAATV 223
                                       56677778889*******************************************9944443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); 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 0.21s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3630.72
//
Query:       gi|336252259|ref|YP_004595366.1|  [L=306]
Description: hypothetical protein Halxa_0848 [Halopiger xanaduensis SH-6]
Scores for 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  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2327.85
//
Query:       gi|336252260|ref|YP_004595367.1|  [L=569]
Description: alcohol dehydrogenase (acceptor) [Halopiger xanaduensis SH-6]
Scores for complete 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-27   94.4   7.3    6.8e-05   22.6   0.1    7.7  7  PQQ       PQQ enzyme repeat
    4.6e-22   78.8   5.5    1.5e-11   44.3   0.0    3.4  3  PQQ_2     PQQ-like domain
    2.8e-10   40.4  30.7      0.001   19.5   0.2    7.6  7  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   2.1e-05      0.12       2      32 ..     116     146 ..     115     148 .. 0.87
   2 !   22.6   0.1   1.1e-08   6.8e-05       1      37 [.     164     200 ..     164     201 .. 0.94
   3 !   17.7   0.0     4e-07    0.0024      10      34 ..     224     248 ..     221     252 .. 0.88
   4 !    9.5   0.0   0.00016      0.94      14      37 ..     301     324 ..     297     325 .. 0.92
   5 ?    2.5   0.0     0.026   1.5e+02       7      21 ..     349     363 ..     343     365 .. 0.77
   6 ?    3.5   0.1     0.013        77      13      25 ..     462     474 ..     456     482 .. 0.87
   7 !   22.4   0.0   1.3e-08   7.8e-05       3      37 ..     497     531 ..     495     532 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                                       EEEEEETTSEEEEEETTTCCEEEEEESSSCG CS
                               PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggpv 32 
                                       v+y +  ++++ A+D + G+vlW++   +p+
  gi|336252260|ref|YP_004595367.1| 116 VMYQTNGPNHIKAIDPREGEVLWSYTYAPPI 146
                                       678888889****************987775 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.1e-08
                                       TEEEEEETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggpvlslpi 37 
                                       ++vy+++ d  + Al+++TG++ W ++t ++  ++++
  gi|336252260|ref|YP_004595367.1| 164 DKVYMTTLDSGVIALNRYTGEEEWYTQTADHQSGYSA 200
                                       68****************************9999875 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 4e-07
                                       SEEEEEETTTCCEEEEEESSSCGSS CS
                               PQQ  10 GylyAlDadTGkvlWrfktggpvls 34 
                                       G + AlDa++G+++W+++t +++ +
  gi|336252260|ref|YP_004595367.1| 224 GFIAALDAESGDMVWQTDTLPEDEW 248
                                       7899**************9888877 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00016
                                       EEETTTCCEEEEEESSSCGSSESE CS
                               PQQ  14 AlDadTGkvlWrfktggpvlslpi 37 
                                        l++++G   W f+ +++++++++
  gi|336252260|ref|YP_004595367.1| 301 TLNLEDGSREWGFQSSPHDVWDYD 324
                                       59*******************986 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.026
                                       ETTSEEEEEETTTCC CS
                               PQQ   7 sadGylyAlDadTGk 21 
                                       ++ G +y lDad+G+
  gi|336252260|ref|YP_004595367.1| 349 DKAGWVYTLDADSGQ 363
                                       666779********7 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.013
                                       EEEETTTCCEEEE CS
                               PQQ  13 yAlDadTGkvlWr 25 
                                        A+D +TG+ +Wr
  gi|336252260|ref|YP_004595367.1| 462 AAVDPSTGERVWR 474
                                       59999*******9 PP

  == domain 7  score: 22.4 bits;  conditional E-value: 1.3e-08
                                       EEEEETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ   3 vylgsadGylyAlDadTGkvlWrfktggpvlslpi 37 
                                       v+ g+ +G+l+A+D ++G+ lW+++ + p+ ++p+
  gi|336252260|ref|YP_004595367.1| 497 VFNGTQNGNLVAYDGESGERLWEYEFDVPISASPM 531
                                       66689********************9999988887 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   2.5e-15   1.5e-11      37     152 ..     115     245 ..      86     274 .. 0.85
   2 !   12.1   0.5   1.8e-05      0.11      48     144 ..     226     364 ..     224     369 .. 0.72
   3 !   31.2   0.4   2.6e-11   1.5e-07       6      72 ..     462     530 ..     455     553 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 2.5e-15
                             PQQ_2  37 gtlfvatgggrlvaldaatGkvlWettlegpvvga.........plvaegrvvvvasdgqlialdaedGkrlWstqq 104
                                        + ++++g + + a+d+  G+vlW++t   p+              v +++v+  + d  +ial+  +G++ W tq 
  gi|336252260|ref|YP_004595367.1| 115 PVMYQTNGPNHIKAIDPREGEVLWSYTYAPPIGVElccddnnrgAAVYGDKVYMTTLDSGVIALNRYTGEEEWYTQT 191
                                       5678899999999*************99777665577778999889999999**********************777 PP

                             PQQ_2 105 rseepaelrssaspavagdtvvvgessgkl......valdpkdGkvlWerel.aa 152
                                       +   +   + + +p+v+++t++ g ++g+       +ald+++G+ +W++    +
  gi|336252260|ref|YP_004595367.1| 192 AD-HQSGYSATWAPVVHDGTIYTGSAGGEYgvlgfiAALDAESGDMVWQTDTlPE 245
                                       77.55556899999999*******9988877778889***********9987555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.8e-05
                             PQQ_2  48 lvaldaatGkvlWettl...egpvvga...........plvaegrvvvva...................sdgqlial 91 
                                       ++alda++G  +W+t+    +++v  +           p+++e+r v+ +                   +    i+l
  gi|336252260|ref|YP_004595367.1| 226 IAALDAESGDMVWQTDTlpeDEWVGMSrehgcgtswmtPTIDEERGVLYSpvanpgpdfdgtvrpgpnfPTCGTITL 302
                                       789*************99966666555999****************999999999999666665544333336667* PP

                             PQQ_2  92 daedGkrlWstqqrseepaelrssaspava..........gdtvvvgessgklvaldpkdGkv 144
                                       + edG r W +q++ +   +   +a+p v            d vv  +  g ++ ld+++G++
  gi|336252260|ref|YP_004595367.1| 303 NLEDGSREWGFQSSPHDVWD-YDAAAPRVLlrdveangesMDMVVSSDKAGWVYTLDADSGQL 364
                                       **********8888854444.333333333223334444455555555588888888888876 PP

  == domain 3  score: 31.2 bits;  conditional E-value: 2.6e-11
                             PQQ_2   6 saldaatGaelWrvdlarp.....lgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgap 72 
                                       +a+d+ tG+++Wr  ++ +     +gg +s+a+   g +f +t  g+lva+d ++G+ lWe+++++p+ ++p
  gi|336252260|ref|YP_004595367.1| 462 AAVDPSTGERVWRDWIESEdefymWGGSMSTAT---GLVFNGTQNGNLVAYDGESGERLWEYEFDVPISASP 530
                                       478889*******93333245666888885555...*******************************99986 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   1.7e-07     0.001       1      38 [.     134     180 ..     134     182 .. 0.80
   2 !   14.3   1.0   7.3e-06     0.043       1      40 []     183     233 ..     183     233 .. 0.74
   3 ?    0.8   0.1      0.13   7.8e+02       1      17 [.     234     251 ..     234     289 .. 0.66
   4 ?   -1.1   0.0      0.52   3.1e+03      29      40 .]     349     361 ..     343     361 .. 0.73
   5 ?   -0.8   0.9       0.4   2.4e+03      29      37 ..     453     462 ..     402     465 .. 0.59
   6 !   17.1   0.1   9.9e-07    0.0059       1      39 [.     469     512 ..     469     513 .. 0.77
   7 !    6.1   0.2    0.0027        16       1      18 [.     514     533 ..     514     555 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.7e-07
                             PQQ_3   1 GevlWsvqlpgpvnssp.........avdgglvyvgtgdGtlyAlDa 38 
                                       GevlWs++   p++  +         av+g++vy++t d ++ Al+ 
  gi|336252260|ref|YP_004595367.1| 134 GEVLWSYTYAPPIGVELccddnnrgaAVYGDKVYMTTLDSGVIALNR 180
                                       9******6666665444666666666******************985 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.3e-06
                             PQQ_3   1 GevlWsvqlpg..pvnssp....avdgglvyvgtg......dGtlyAlDaet 40 
                                       Ge+ W +q+ +   + +s+    +v +g++y+g+        G + AlDae+
  gi|336252260|ref|YP_004595367.1| 183 GEEEWYTQTADhqSG-YSAtwapVVHDGTIYTGSAggeygvLGFIAALDAES 233
                                       666677766555322.3333555************99999999999999986 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.13
                             PQQ_3   1 GevlWsvql.pgpvnssp 17 
                                       G+ +W++++ p++ + ++
  gi|336252260|ref|YP_004595367.1| 234 GDMVWQTDTlPEDEWVGM 251
                                       888999966577776666 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.52
                             PQQ_3  29 g.dGtlyAlDaet 40 
                                       +  G +y lDa++
  gi|336252260|ref|YP_004595367.1| 349 DkAGWVYTLDADS 361
                                       36899*****986 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 0.4
                             PQQ_3  29 g.dGtlyAlD 37 
                                       + +G+++A+ 
  gi|336252260|ref|YP_004595367.1| 453 EwNGNITAFA 462
                                       1466666665 PP

  == domain 6  score: 17.1 bits;  conditional E-value: 9.9e-07
                             PQQ_3   1 GevlWsvqlpg....pvn.sspavdgglvyvgtgdGtlyAlDae 39 
                                       Ge++W+  + +    + + +s+ ++ glv+ gt +G+l+A+D e
  gi|336252260|ref|YP_004595367.1| 469 GERVWRDWIESedefYMWgGSMSTATGLVFNGTQNGNLVAYDGE 512
                                       7788888443333356666999********************76 PP

  == domain 7  score: 6.1 bits;  conditional E-value: 0.0027
                             PQQ_3   1 GevlWsvqlpgpvnssp..a 18 
                                       Ge+lW+++++ p+ +sp   
  gi|336252260|ref|YP_004595367.1| 514 GERLWEYEFDVPISASPmsW 533
                                       9************9999642 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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: 00:00:00.39
# Mc/sec: 4365.61
//
Query:       gi|336252261|ref|YP_004595368.1|  [L=501]
Description: blue (type 1) copper domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   38.0   0.2    6.1e-08   33.0   0.0    2.9  2  Copper-bind  Copper binding proteins, plastocyanin/azurin fam
      0.004   16.9   2.8     0.0073   16.1   2.8    1.4  1  TAT_signal   TAT (twin-arginine translocation) pathway signal
  ------ inclusion threshold ------
      0.014   15.4   5.3      0.014   15.4   5.3    5.9  7  Gp5_C        Gp5 C-terminal repeat (3 copies)
       0.36   10.7   0.0       0.36   10.7   0.0    3.6  5  PEGA         PEGA domain


Domain annotation for each model (and alignments):
>> 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 !   33.0   0.0   1.4e-11   6.1e-08      26      98 ..      90     159 ..      81     160 .. 0.84
   2 ?    2.0   0.1     0.065   2.9e+02      34      78 ..     355     395 ..     322     491 .. 0.67

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.4e-11
                                       EEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEE.EEEEETTTTTTTSEEEEEE CS
                       Copper-bind  26 kvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagt.YkffCsPHaaagMkgkvtv 98 
                                       +v ++n ++  HN  +++++    +d+ +v +   ++++ +Ge +s++f+++++  ++fC PH a+ M+g v++
  gi|336252261|ref|YP_004595368.1|  90 EVIWINGDGSMHNFNITAGSS--VADDVEVLEA-TETVTEQGEYTSIRFTATEEmEEYFCMPHPAQ-MRGPVEL 159
                                       6889999***********984..6677776665.556*************776669********99.***9976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.065
                                       SSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSE CS
                       Copper-bind  34 vmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeag 78 
                                         gHN+ ++++g    +d +    +d t    +G +++v+f +++
  gi|336252261|ref|YP_004595368.1| 355 LPGHNLAIASGGE--TIDWNTFVRSDFT--AEEGATQTVEFVANE 395
                                       5677777777442..3333333333222..333444444443222 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.8   1.6e-06    0.0073       1      24 [.      10      33 ..      10      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-06
                        TAT_signal  1 klSRRdFLKgsAAaaAAaalggca 24
                                      +lSRR  LKg+AA++  aal g a
  gi|336252261|ref|YP_004595368.1| 10 NLSRRGVLKGTAALTGIAALTGEA 33
                                      58*************999998865 PP

>> Gp5_C  Gp5 C-terminal repeat (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.1   4.9e+03       9      23 ..     101     115 ..     100     116 .. 0.81
   2 ?   -2.6   0.1       1.8     8e+03       6      14 ..     117     125 ..     112     125 .. 0.56
   3 ?    1.2   0.3      0.11   5.1e+02      11      20 ..     272     282 ..     271     286 .. 0.76
   4 ?    0.3   0.5      0.21   9.6e+02       8      20 ..     431     443 ..     430     445 .. 0.75
   5 ?   -1.2   0.3      0.65   2.9e+03       2      12 ..     441     451 ..     440     457 .. 0.59
   6 ?   10.5   2.5   0.00013      0.56       9      20 ..     466     477 ..     463     478 .. 0.88
   7 ?   15.4   5.3   3.2e-06     0.014       1      23 [.     479     501 .]     479     501 .] 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                                       S-EEEEESS-EEEEE CS
                             Gp5_C   9 GNrTvtVgGNqTetV 23 
                                        N+++t g +++  V
  gi|336252261|ref|YP_004595368.1| 101 HNFNITAGSSVADDV 115
                                       699***999888776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
                                       EESS-EEEE CS
                             Gp5_C   6 tVkGNrTvt 14 
                                       + ++++Tvt
  gi|336252261|ref|YP_004595368.1| 117 VLEATETVT 125
                                       555666655 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.11
                                       EEEEESS.-EE CS
                             Gp5_C  11 rTvtVgG.NqT 20 
                                       +Tvt++G +++
  gi|336252261|ref|YP_004595368.1| 272 ETVTIDGeDRQ 282
                                       79999998876 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.21
                                       SS-EEEEESS-EE CS
                             Gp5_C   8 kGNrTvtVgGNqT 20 
                                       +GN+Tv  gGN+T
  gi|336252261|ref|YP_004595368.1| 431 NGNATVEEGGNET 443
                                       5888887788877 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 0.65
                                       -EEEEESS-EE CS
                             Gp5_C   2 netetVkGNrT 12 
                                       net +  GN+T
  gi|336252261|ref|YP_004595368.1| 441 NETAIGAGNET 451
                                       55555555555 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.00013
                                       S-EEEEESS-EE CS
                             Gp5_C   9 GNrTvtVgGNqT 20 
                                        N+TvtV+GN+T
  gi|336252261|ref|YP_004595368.1| 466 DNETVTVDGNET 477
                                       69999****999 PP

  == domain 7  score: 15.4 bits;  conditional E-value: 3.2e-06
                                       S-EEEEESS-EEEEESS-EEEEE CS
                             Gp5_C   1 GnetetVkGNrTvtVgGNqTetV 23 
                                       Gnet+  +GN+T+ V+GN+T  V
  gi|336252261|ref|YP_004595368.1| 479 GNETIDAGGNETTAVDGNETDDV 501
                                       9*******************987 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.39   1.8e+03       9      19 ..     178     188 ..     167     191 .. 0.79
   2 ?   10.7   0.0   8.1e-05      0.36      31      67 ..     253     288 ..     248     291 .. 0.83
   3 ?   -2.3   0.0      0.92   4.1e+03      48      64 ..     385     401 ..     383     405 .. 0.70
   4 ?   -3.0   0.1       1.5   6.9e+03      23      35 ..     418     430 ..     412     443 .. 0.75
   5 ?   -1.0   0.1      0.37   1.7e+03      12      21 ..     467     476 ..     464     479 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.39
                              PEGA   9 npeGatVyidG 19 
                                       +p Ga+Vy++ 
  gi|336252261|ref|YP_004595368.1| 178 EPLGAEVYVGD 188
                                       68899999954 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.1e-05
                              PEGA  31 leaGnyslrvekeGYedlektvtvtagetvklnltLe 67 
                                       le+G+y ++v   G+e +++tvt++ ge  +l++tL 
  gi|336252261|ref|YP_004595368.1| 253 LENGEYDIEVWTYGHERVSETVTID-GEDRQLTVTLP 288
                                       89***********************.66666666665 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.92
                              PEGA  48 lektvtvtagetvklnl 64 
                                       +++tv++ a+e++ ++l
  gi|336252261|ref|YP_004595368.1| 385 ATQTVEFVANEEMAVYL 401
                                       56788888888877764 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.5
                              PEGA  23 GkTPvtlsleaGn 35 
                                       G+TP     +aG 
  gi|336252261|ref|YP_004595368.1| 418 GETPAAADAPAGA 430
                                       7999988877775 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.37
                              PEGA  12 GatVyidGky 21 
                                       + tV++dG++
  gi|336252261|ref|YP_004595368.1| 467 NETVTVDGNE 476
                                       6788888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.36
# Mc/sec: 4173.00
//
Query:       gi|336252262|ref|YP_004595369.1|  [L=149]
Description: hypothetical protein Halxa_0851 [Halopiger xanaduensis SH-6]
Scores for 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-34  117.4   0.3      4e-34  117.2   0.3    1.0  1  Haem_degrading  Haem-degrading


Domain annotation for each model (and alignments):
>> Haem_degrading  Haem-degrading
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.3   2.3e-38     4e-34       3     118 ..      17     141 ..      15     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 2.3e-38
                    Haem_degrading   3 ledAkelgaaarakarekgkpvviaivdaggqllffarmdgaspdnedwaerKantaarfgkstaalgeklk..... 74 
                                       le+Ak++++aa+++a e + p+vi++++++g+l++++rmdga+++++d++++Ka+taa++ ++t +l+e +k     
  gi|336252262|ref|YP_004595369.1|  17 LETAKAVIDAAEQRADEIDNPMVITVANSEGNLVAQHRMDGAWLASVDISRNKAYTAAALDMPTDELAEPTKpgesl 93 
                                       79*********************************************************************977555 PP

                    Haem_degrading  75 ...eedya...grv.ilgGGvpirvkggvvGaigvSGlkqeeDhqvavaal 118
                                          +   +   gr+ i+gGG+p+  +g+vvGaigvSG++ ++D++va+ ++
  gi|336252262|ref|YP_004595369.1|  94 yglQ---NtnqGRMvIFGGGYPLERDGEVVGAIGVSGGEVAQDMDVAQSGV 141
                                       5542...05568889********98***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.36u 0.19s 00:00:00.55 Elapsed: 00:00:00.33
# Mc/sec: 1365.00
//
Query:       gi|336252263|ref|YP_004595370.1|  [L=388]
Description: formaldehyde dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-27   95.1   0.3    3.7e-27   94.4   0.3    1.4  1  ADH_N        Alcohol dehydrogenase GroES-like domain
    8.6e-11   41.9   0.0    3.1e-10   40.1   0.0    1.8  2  ADH_zinc_N   Zinc-binding dehydrogenase
    5.5e-10   39.0   0.9    1.5e-09   37.6   0.9    1.8  1  ADH_N_assoc  Alcohol dehydrogenase GroES-associated
     0.0033   16.9   0.0      0.017   14.6   0.0    2.1  2  Glu_dehyd_C  Glucose dehydrogenase C-terminus
     0.0043   15.8   0.1      0.028   13.1   0.1    1.9  2  HI0933_like  HI0933-like protein
     0.0065   15.8   0.0      0.011   15.0   0.0    1.3  1  AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
       0.17   11.1   0.0       0.28   10.4   0.0    1.3  1  Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.3   1.4e-30   3.7e-27       2     102 ..      28     136 ..      27     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 1.4e-30
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-G CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegee 78 
                                       +++++++++++iCgsDlh+++g  ++++ +++++GHE +G+v e+g++v++l+ GdrVv++++++cg C++C++g++
  gi|336252263|ref|YP_004595370.1|  28 NDIIVDITTTAICGSDLHMYEG--RTSADPGIVFGHENMGTVIETGDAVTSLEEGDRVVMPFNVACGFCRNCENGYT 102
                                       799******************9..6999************************************************* PP

                                       GG-.........TTBEETTTS........S-SSSBSEEEEC CS
                             ADH_N  79 nlC.........eeakllgvs........ldGgfaeyvvvp 102
                                        +C                          ++Gg+ae++ vp
  gi|336252263|ref|YP_004595370.1| 103 GFCtnvnpgfagG-------AygyvamgpYKGGQAEKLRVP 136
                                       ***7776664443.......133335668********9998 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   1.2e-13   3.1e-10       1      70 [.     187     256 ..     187     261 .. 0.90
   2 ?   -1.5   0.0      0.88   2.3e+03      71     109 ..     278     329 ..     268     347 .. 0.68

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.2e-13
                                       HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsga 70 
                                       +vGl+a   Ak  Ga e+++vd+ e++lela++    ++in +e d+ve+ik+l g +gvd  +++vG++a
  gi|336252263|ref|YP_004595370.1| 187 PVGLMAAYSAKLQGAsEIYVVDRVESRLELAEDHCDARAINFEERDPVEQIKDLHG-GGVDNGVDAVGYQA 256
                                       7********************************877888888444**********5.5**********665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.88
                                       HHHHHHHCEEEEEEEEECSC..TSSEEE...........EEHHHHHHTT-EE CS
                        ADH_zinc_N  71 tleaalkllkpgGrlvvvGg..gkgeee...........fdlrnlllkeksi 109
                                       +l++ ++ ++p G l v G+  ++++             +d+++l+ k +++
  gi|336252263|ref|YP_004595370.1| 278 VLNQLIQTVRPTGELGVPGLyvPSDPGApdemaaqgrlgIDFGKLFEKGLKV 329
                                       5788999999999999999876333332344666666666666666666665 PP

>> ADH_N_assoc  Alcohol dehydrogenase GroES-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.9   5.8e-13   1.5e-09       1      23 []       3      25 ..       3      25 .. 0.98

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 5.8e-13
                       ADH_N_assoc  1 MKAVTyqGpkdVrVeeVPDPkIe 23
                                      M AV+yqGp+dV+ eeV++P+Ie
  gi|336252263|ref|YP_004595370.1|  3 MDAVVYQGPNDVAIEEVDEPEIE 25
                                      99********************8 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.8e-06     0.017      32      97 ..     178     240 ..     167     260 .. 0.64
   2 ?   -1.0   0.0      0.39     1e+03     157     203 ..     329     375 ..     310     386 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.8e-06
                       Glu_dehyd_C  32 esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlve.elGatYvd.sretpvdeipea 97 
                                       es  v GaG++GL+a+   ++  +g +++yv++r +    +++l e + +a  ++ ++++pv++i + 
  gi|336252263|ref|YP_004595370.1| 178 ESIAVFGAGPVGLMAAYSAKL--QGASEIYVVDRVES---RLELAEdHCDARAINfEERDPVEQIKDL 240
                                       7899***********777665..79999*****8543...3333321334444441234566666655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.39
                       Glu_dehyd_C 157 vGsvNanrrhfeaavdtLaalpeslldelvtkvvdldeleeAfeddd 203
                                       vG+   n+++++  ++++    +   + +v+++vdld++ e +e+ d
  gi|336252263|ref|YP_004595370.1| 329 VGTGQCNVKEYNRELRDMIIEGRADPSWVVSHRVDLDQAPEMYEKFD 375
                                       56666666666666666666556666667888888888888777544 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   1.1e-05     0.028       2      32 ..     179     210 ..     178     215 .. 0.79
   2 ?    0.4   0.0     0.083   2.1e+02      36      60 ..     323     347 ..     317     359 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                                       SEEEE--SHHHHHHHHHHHHTT-.-EEEE-SS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgk.rVllleka 32 
                                       +++v G+G+ GlmaA sa+ +g+ ++ ++++ 
  gi|336252263|ref|YP_004595370.1| 179 SIAVFGAGPVGLMAAYSAKLQGAsEIYVVDRV 210
                                       589***************76664167777765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.083
                                       -HHHHHCGGGT-EEEETT-SGGGEE CS
                       HI0933_like  36 grKilisGgGrcNvTnlseepeell 60 
                                        +K l  G G+cNv  +++e+++++
  gi|336252263|ref|YP_004595370.1| 323 FEKGLKVGTGQCNVKEYNRELRDMI 347
                                       5677778********9999988776 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 !   15.0   0.0   4.3e-06     0.011      30      81 ..     179     232 ..     163     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-06
                                       EEEEESTSHHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHH.TTTCECEEHCHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglga.kVtvlDvrparleqles.lgakfvevlksq 81 
                                        + v+G+G +Gl A+  ak  ga +++v+D  ++rle  e+ + a+ ++  +++
  gi|336252263|ref|YP_004595370.1| 179 SIAVFGAGPVGLMAAYSAKLQGAsEIYVVDRVESRLELAEDhCDARAINFEERD 232
                                       589****************999856**************999999988876655 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 ?   10.4   0.0   0.00011      0.28       2      29 ..     182     209 ..     181     215 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEk 29 
                                       + GaGP Gl aa+ +k  g +++ ++++
  gi|336252263|ref|YP_004595370.1| 182 VFGAGPVGLMAAYSAKLQGASEIYVVDR 209
                                       67***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.34
# Mc/sec: 3372.22
//
Query:       gi|336252264|ref|YP_004595371.1|  [L=721]
Description: multi-sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for 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-30  103.5   0.1    4.3e-29  101.3   0.0    2.1  2  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    1.3e-13   51.1   0.0      4e-13   49.5   0.0    1.9  1  PAS_9            PAS domain
    2.3e-11   44.2   0.1    6.6e-11   42.7   0.0    1.9  1  GAF_3            GAF domain
    7.6e-10   39.0   0.1    2.8e-09   37.2   0.1    2.0  1  PAS_4            PAS fold
    1.1e-09   39.0   0.2    2.8e-09   37.7   0.2    1.7  1  GAF              GAF domain
    3.1e-09   36.8   0.0    1.1e-08   35.1   0.0    2.0  1  PAS              PAS fold
    3.4e-09   37.1   1.1    1.3e-08   35.3   1.1    2.1  1  GAF_2            GAF domain
    4.4e-09   36.3   5.2    1.5e-08   34.5   0.0    3.8  3  HisKA            His Kinase A (phospho-acceptor) domain
    1.4e-07   31.7   0.1    1.3e-05   25.4   0.0    3.2  3  PAS_3            PAS fold
    1.2e-06   28.2   2.6      3e-06   26.9   2.6    1.7  1  HisKA_4TM        Archaeal 4TM region of histidine kinase
    0.00014   21.7   0.0    0.00048   20.0   0.0    1.8  1  HATPase_c_5      GHKL domain
     0.0002   21.3   0.0    0.00052   20.0   0.0    1.7  1  HATPase_c_2      Histidine kinase-like ATPase domain
     0.0017   18.3   3.0       0.28   11.1   0.4    2.3  2  DUF327           Protein of unknown function (DUF327)
  ------ inclusion threshold ------
      0.022   15.3   0.6      0.022   15.3   0.6    2.7  2  Syntaxin-6_N     Syntaxin 6, N-terminal
      0.034   12.9   7.1      0.035   12.9   4.0    2.2  2  Tektin           Tektin family
      0.066   13.4   1.9      0.081   13.1   0.2    2.0  2  RasGAP_C         RasGAP C-terminus
      0.098   12.7   0.1       0.41   10.7   0.1    2.1  1  PAS_8            PAS domain
       0.11   12.6  14.6       0.46   10.6   0.2    3.1  3  bZIP_1           bZIP transcription factor
       0.11   12.3   0.0       0.27   11.1   0.0    1.6  1  HATPase_c_3      Histidine kinase-, DNA gyrase B-, and HSP90-
        0.2   11.9   2.2          9    6.6   0.3    2.3  2  23S_rRNA_IVP     23S rRNA-intervening sequence protein
       0.26   11.2   8.4          4    7.3   3.4    2.5  2  Ax_dynein_light  Axonemal dynein light chain
        0.3   11.5   7.3        5.3    7.5   0.3    2.5  2  Streptin-Immun   Lantibiotic streptin immunity protein
       0.37   10.0   7.0       0.16   11.3   0.2    2.8  3  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.44    9.3   3.8       0.14   11.0   0.7    1.6  2  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
        0.5   10.7  11.6        3.1    8.1   2.3    3.2  3  OmpH             Outer membrane protein (OmpH-like)
       0.51    9.2   8.3       0.18   10.6   2.5    2.4  2  Spc7             Spc7 kinetochore protein
       0.81   10.0   6.7        3.4    8.0   2.3    2.3  2  DUF5082          Domain of unknown function (DUF5082)
        3.7    7.6   9.2       0.58   10.2   4.2    2.2  1  DUF2205          Short coiled-coil protein
          4    7.6   9.8         13    6.0   3.6    2.5  2  Exonuc_VII_S     Exonuclease VII small subunit
        4.9    7.2  12.2       0.76    9.8   0.7    2.6  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
        5.9    6.1  13.1      0.039   13.3   0.5    2.6  2  DUF3450          Protein of unknown function (DUF3450)
        7.8    6.8   7.0        4.2    7.6   1.9    2.5  2  Spc24            Spc24 subunit of Ndc80
        8.7    6.8  12.8        1.1    9.6   2.4    3.1  3  DUF4200          Domain of unknown function (DUF4200)
        9.6    5.6   8.4       0.45    9.9   0.4    2.3  2  HNOBA            Heme NO binding associated
         10    6.6  11.4         26    5.3   4.4    2.4  2  PGBA_C           Plasminogen-binding protein pgbA C-terminal


Domain annotation for each model (and alignments):
>> 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 ?   -1.4   0.0       6.2   3.2e+03      35      57 ..     564     588 ..     529     589 .. 0.64
   2 !  101.3   0.0   8.5e-32   4.3e-29       1     110 [.     590     699 ..     590     701 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.2
                                       E..TEEEEEEEESSSSSTTHHHTGT CS
                         HATPase_c  35 e..ddlvisveDnGiGipkedlkkl 57 
                                       +  d+l+++++ +   i+ e l+++
  gi|336252264|ref|YP_004595371.1| 564 DvrDNLRVKIKETDAEITAESLPRV 588
                                       1346999999999999999998865 PP

  == domain 2  score: 101.3 bits;  conditional E-value: 8.5e-32
                                       EHHHHHHHHHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSH CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGl 76 
                                       gd  +Lrqi++n++ Na+++++ + ++i+v+ ++s  + ++s+ D GiGi++ed++++f+ f++  +++++++gtG+
  gi|336252264|ref|YP_004595371.1| 590 GDRGQLRQIFQNVLANAIQYSGdEPPRIHVSAEQSGRRWTVSIADEGIGIDPEDQDRIFDVFQR-LHSRDTHSGTGI 665
                                       6899****************66677788888886669***************************.8889999***** PP

                                       HHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  77 GlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       Gl++++++ve++gG+iwvesepg+Gtt+ ftlp 
  gi|336252264|ref|YP_004595371.1| 666 GLALCERIVERHGGDIWVESEPGEGTTVSFTLPT 699
                                       *******************************995 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   7.8e-16     4e-13       3     103 ..     191     289 ..     189     290 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 7.8e-16
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwv 78 
                                        + ++ +dg++ ++Ne+++ ++Gys +ev   +  d+f  d+e++e +++al +g +    +ve +l++k+ge++++
  gi|336252264|ref|YP_004595371.1| 191 IFYVIEKDGTLQRWNESLCAVTGYSDAEVASMNAVDFF--DAEDREQIENALVRGFEtGSLQVEAELRTKDGERIPY 265
                                       566778***999**************************..77777777777777777799***************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDit 103
                                       +  as++   +ge+v+ ++i rDi+
  gi|336252264|ref|YP_004595371.1| 266 EYAASTLETPEGEVVL-AGIGRDIS 289
                                       *******999*****5.9******9 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   1.3e-13   6.6e-11       1     129 []     320     461 ..     320     461 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.3e-13
                             GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagw..dgkpalsesld..edsalarralssgevvsepsfa 73 
                                       +ldel+ +++++++ +l+ e++ +l ld+++++l  + g   d + + + ++   e+++ a+++l+++ ++++ + +
  gi|336252264|ref|YP_004595371.1| 320 DLDELMHEAARQVAVVLDNEYCKVLDLDARRDELLLRQGVgwDDGIVGEAAVSavEADSQAAYTLAHDHPIVVEDIE 396
                                       79******************************9988866544888888776666689999*************9988 PP

                             GAF_3  74 eedg......lpdraala.vPLvagr..qviGvlalastkprafdaedlelleslArqiataier 129
                                        e +      l+d+ +   ++ v+g   ++ G+l+ + t+ + f++ed+ +++s+A+++a aier
  gi|336252264|ref|YP_004595371.1| 397 TEARfggpalLRDHDVRSgISTVIGPsdEPWGILGTHDTERKTFTDEDVNFVQSVANVLAEAIER 461
                                       8766666666677666444555554447************999*********************8 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.1   5.5e-12   2.8e-09       1     109 [.     185     292 ..     185     293 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 5.5e-12
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       l+++ d+++v+ +dg+ +++N++ +++ g++++e+  +   +++ +ed++++e+al r  e++  + ++e ++ +ge
  gi|336252264|ref|YP_004595371.1| 185 LNAIHDIFYVIEKDGTLQRWNESLCAVTGYSDAEVASMNAVDFFDAEDREQIENALVRGFETGSLQVEAELRTKDGE 261
                                       678999*********************************************************99999998888*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       + +ye  ++ l+ ++Ge + + +i+rDi++r 
  gi|336252264|ref|YP_004595371.1| 262 RIPYEYAASTLETPEGE-VVLAGIGRDISART 292
                                       *****************.88899******996 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.2   5.4e-12   2.8e-09       1     133 []     320     459 ..     320     459 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 5.4e-12
                                       SHHHHHHHHHHHHHHHHTESEEEEEE..EEETTEEE.CEEEEECC.........EEEETTSHHHH.........HHH CS
                               GAF   1 dleelldtvveelrellgadrvalyl..pdydGlhy.dipqasrw.........lfmkngrgicg.........qvl 56 
                                       dl+el ++++++++ +l+ +++ ++   +      +  + q+  w         +                   ++l
  gi|336252264|ref|YP_004595371.1| 320 DLDELMHEAARQVAVVLDNEYCKVLDldA--RRD-ElLLRQGVGWddgivgeaaV---------SaveadsqaaYTL 384
                                       899*********************76331..222.13488888884444333222.........24444555569** PP

                                       HHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHH CS
                               GAF  57 atgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvava 132
                                       a++ p+v++d+ ++ rf     + ll+ + +rs ++  +   +e wG+l  h++ +  ft+e+++++q++a+ +a a
  gi|336252264|ref|YP_004595371.1| 385 AHDHPIVVEDIETEARFGG---PALLRDHDVRSGISTVIGPSDEPWGILGTHDTERkTFTDEDVNFVQSVANVLAEA 458
                                       *******************...78********999998888************54458**************99988 PP

                                       H CS
                               GAF 133 l 133
                                       +
  gi|336252264|ref|YP_004595371.1| 459 I 459
                                       6 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   2.1e-11   1.1e-08       4     113 .]     182     288 ..     179     288 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.1e-11
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       +++l++++d   v+ +dg    +N++ +  +G+s  ev + + +d++  e    ++e++e++l  g e  + ++  +
  gi|336252264|ref|YP_004595371.1| 182 DHVLNAIHDIFYVIEKDGTLQRWNESLCAVTGYSDAEVASMNAVDFFDAE----DREQIENALVRGFETGSLQVEAE 254
                                       689********************************************988....77888888888777777777666 PP

                                       C..TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 l..rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       l  +dg+ i+ e  as++  ++ge+  + g++rdi
  gi|336252264|ref|YP_004595371.1| 255 LrtKDGERIPYEYAASTLETPEGEV-VLAGIGRDI 288
                                       6669********************9.999999998 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   1.1   2.5e-11   1.3e-08       2     138 .]     319     460 ..     318     460 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.5e-11
                                       HHHHHHHHHHHHHHHH.SS..EEEEEEE-TTS-.EEEE.EEEES-TTSTT-S-B---TT.HHHHHHHHTS-EEES-G CS
                             GAF_2   2 adleelldlvldelve.lgaalgyillvdddgg.lrla.awgeaeeefgaaldrplgeg.lvgealrtgrpvilndl 74 
                                        dl+el+ ++ ++++  l+ +++ +l +d++++ l l+   g +++ +g+a+ +++++   +++ l++  p++++d+
  gi|336252264|ref|YP_004595371.1| 319 DDLDELMHEAARQVAVvLDNEYCKVLDLDARRDeLLLRqGVGWDDGIVGEAAVSAVEADsQAAYTLAHDHPIVVEDI 395
                                       69************885699***999999777743333688888888888888888555369**************9 PP

                                       GG-S-HHHHH.HHHHTT--EEEEEE-T.TS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  75 eedpdkkglp.aghaglrsflavPlis.egrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       e++++  g + ++++++rs+++  + +  +++ G+l+   +++ +f++ed+ +++++a+ +a aie
  gi|336252264|ref|YP_004595371.1| 396 ETEARFGGPAlLRDHDVRSGISTVI-GpSDEPWGILGTHDTERKTFTDEDVNFVQSVANVLAEAIE 460
                                       9988888888899999999999877.55689******98999999*******************98 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       2.5   1.3e+03      32      51 ..     148     167 ..     113     184 .. 0.55
   2 ?    3.3   0.5      0.17        85      23      53 ..     455     484 ..     445     485 .. 0.79
   3 !   34.5   0.0     3e-11   1.5e-08       2      67 .]     482     549 ..     481     549 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.5
                                       T-HSSCHHHHHHHHHHHHHH CS
                             HisKA  32 klteelkeyletiesearrl 51 
                                        +  el+e ++ +e+  +rl
  gi|336252264|ref|YP_004595371.1| 148 VTQSELEETVDELERANERL 167
                                       23345555666666655555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.17
                                       HHHHHHC..T-HSSCHHHHHHHHHHHHHHHH CS
                             HisKA  23 naeaLkregklteelkeyletiesearrldh 53 
                                        aea++r +++  el+ +++++e++ +rl++
  gi|336252264|ref|YP_004595371.1| 455 LAEAIER-QQYQAELETLVADLEESNERLEQ 484
                                       4667777.59999***************986 PP

  == domain 3  score: 34.5 bits;  conditional E-value: 3e-11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       l++f+   +H+L  PL  ++ ++ +++++  ++ + + +e+l+ ++++a+r+++++e lL++sr e+g
  gi|336252264|ref|YP_004595371.1| 482 LEQFAYAASHDLQEPLRMVSSYLRLIENRygDAFDADGEEFLAFAVDGADRMREMIEGLLQYSRVETG 549
                                       789***********************7777999999****************************9987 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   2.4e-08   1.3e-05       4      83 ..     204     280 ..     202     284 .. 0.92
   2 ?   -1.6   0.0       6.8   3.5e+03      34      54 ..     591     611 ..     589     613 .. 0.89
   3 ?    2.1   0.0      0.47   2.4e+02      32      69 ..     641     684 ..     638     686 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.4e-08
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdeng 80 
                                       ++e+ + ++Gys++e+ +   +  d+   eDre++++al + +++g+ +++e  +r+kdGe +  e  a+ +   +g
  gi|336252264|ref|YP_004595371.1| 204 WNESLCAVTGYSDAEVASM--NAVDFFDAEDREQIENALVRGFETGS-LQVEAELRTKDGERIPYEYAASTLETPEG 277
                                       9******************..************************99.999**********9999888888888887 PP

                             PAS_3  81 kpv 83 
                                       ++v
  gi|336252264|ref|YP_004595371.1| 278 EVV 280
                                       776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.8
                             PAS_3  34 Drervrealqealkkgepyeg 54 
                                       Dr ++r+ +q++l++  +y+g
  gi|336252264|ref|YP_004595371.1| 591 DRGQLRQIFQNVLANAIQYSG 611
                                       999**********99998876 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.47
                             PAS_3  32 peDrervrealqealkkgepy.ege.....yRirrkdGeyrwve 69 
                                       peD++r+++ +q++ +++++  +g       Ri+ ++G+ +wve
  gi|336252264|ref|YP_004595371.1| 641 PEDQDRIFDVFQRLHSRDTHSgTGIglalcERIVERHGGDIWVE 684
                                       9***********98865552212223444467777777777776 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   2.6   5.9e-09     3e-06       6     132 ..      19     141 ..      15     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 5.9e-09
                         HisKA_4TM   6 vfGlvlaaaaivhhgaeaaaidsvrGPvlal.aldGllalglvyagyrlastdlpaeqewtvlvwslgGavvvgavi 81 
                                       ++G++++a +  + +a +aa   + G vl + +l   +  +l+y gyrl + d+ ae   ++++w+lgG  ++g+v+
  gi|336252264|ref|YP_004595371.1|  19 ALGAAYVALTTGWAVARTAAETPL-GNVLVIsLLVAGPGFALLYFGYRLPAFDIRAEFYDAIAAWCLGGFGAMGTVL 94 
                                       677777777778887777765544.445444144556899*****************************99998875 PP

                         HisKA_4TM  82 gltvlvrllegrtiaePvfvvlvaaevGavaGllaGylaararadasrakr 132
                                           +v  l+   i +   ++l+ + +G+vaG   G + a a++ ++  ++
  gi|336252264|ref|YP_004595371.1|  95 ----VVYSLQPGEIVDDFSTILILTALGSVAGFAVGLHDAEAKTRTRELEQ 141
                                       ....677888888999999********************999987766555 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   9.3e-07   0.00048       6      91 ..     595     687 ..     591     695 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.3e-07
                       HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ek......kklesskskkeehGiGl 71 
                                       l  i+ n+L NAi+ + + +   + I+++++++ +  ++si  +  g     +       ++l+s+  +++  GiGl
  gi|336252264|ref|YP_004595371.1| 595 LRQIFQNVLANAIQYSGDEP---PRIHVSAEQSGRRWTVSIADEGIGidpedQDrifdvfQRLHSRD-THSGTGIGL 667
                                       7789*********9988755...9*****************99966655555114454456676655.57899**** PP

                       HATPase_c_5  72 ksireivkkykgnlsieaed 91 
                                          ++iv++++g++++e e 
  gi|336252264|ref|YP_004595371.1| 668 ALCERIVERHGGDIWVESEP 687
                                       ***************99886 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     1e-06   0.00052      33     122 ..     596     694 ..     561     697 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1e-06
                       HATPase_c_2  33 rlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep....keslkegGrGlali 105
                                       r   + +++Na+++  +e p  +++v++e+++++ tv++aD+G g dpe++++     +     +     G+Glal 
  gi|336252264|ref|YP_004595371.1| 596 RQIFQNVLANAIQYSGDEPP--RIHVSAEQSGRRWTVSIADEGIGIDPEDQDRIFDVFQrlhsRDTHSGTGIGLALC 670
                                       555666799*******9888..9999*******************9999766544333377777888899******* PP

                       HATPase_c_2 106 kglvDev..ey.....dgegnvvt 122
                                       +++v+    ++      geg++v+
  gi|336252264|ref|YP_004595371.1| 671 ERIVERHggDIwvesePGEGTTVS 694
                                       *99998766444554445566665 PP

>> DUF327  Protein of unknown function (DUF327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.4   0.00055      0.28      29      94 ..     138     203 ..     128     211 .. 0.82
   2 ?    7.0   0.1      0.01       5.2      25      81 ..     450     509 ..     431     518 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00055
                                       HHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHT..---- CS
                            DUF327  29 tlekeeee..eseeelkelleeidkqgerLaesrtiedlkkYkklvkeflkevvknslklkkersldr 94 
                                       +le+ +ee   ++ el+e ++e++++ erLa s   e+l++Y++     l+ + +  + ++k+  l+r
  gi|336252264|ref|YP_004595371.1| 138 ELEQRNEElqVTQSELEETVDELERANERLATSN--EQLEHYREYTDHVLNAIHDIFYVIEKDGTLQR 203
                                       565555555588999***************9876..7899***********99999999998877765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.01
                                       -HHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-..-HHHHHHHHHHHHHHHHHHHH CS
                            DUF327  25 sFsetl.ekeeeeeseeelkelleeidkqgerLaesr..tiedlkkYkklvkeflkevvk 81 
                                       s  ++l e++e++++++el+ l+ +++++ erL++       dl++  ++v+++l+ + +
  gi|336252264|ref|YP_004595371.1| 450 SVANVLaEAIERQQYQAELETLVADLEESNERLEQFAyaASHDLQEPLRMVSSYLRLIEN 509
                                       4456666778889********************986511556788877777777776655 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 ?   15.3   0.6   4.2e-05     0.022      36      97 ..     129     190 ..     108     191 .. 0.89
   2 ?   -0.1   0.1       2.7   1.4e+03      38      62 ..     460     484 ..     439     505 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.2e-05
                      Syntaxin-6_N  36 seeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrrafveevreevke 97 
                                         e +  ++eL++  ++++ + ++Leetv+ +e+ +++   ++++l+  r++ ++v + + +
  gi|336252264|ref|YP_004595371.1| 129 DAEAKTRTRELEQRNEELQVTQSELEETVDELERANERLATSNEQLEHYREYTDHVLNAIHD 190
                                       568888999*************************99***********999999988887765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.7
                      Syntaxin-6_N  38 eldetrteLrkalrsiewdledLee 62 
                                       e ++ + eL++ + ++e+  e Le+
  gi|336252264|ref|YP_004595371.1| 460 ERQQYQAELETLVADLEESNERLEQ 484
                                       5556666666666666666666665 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.0   6.8e-05     0.035      42     101 ..     133     192 ..     127     197 .. 0.89
   2 ?    0.1   0.1      0.53   2.7e+02      68     109 ..     467     512 ..     443     518 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-05
                            Tektin  42 adsnkrLeeRiediefwkeeLekeleelkeeieaLeeekrrlekalealeeplhiaqecl 101
                                       +  +++Le+R e+++  ++eLe++++el++  e L ++ ++le+  e +++ l+ +++  
  gi|336252264|ref|YP_004595371.1| 133 KTRTRELEQRNEELQVTQSELEETVDELERANERLATSNEQLEHYREYTDHVLNAIHDIF 192
                                       567999*****************************************9999998877765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.53
                            Tektin  68 elkeeieaLeeekrrlek....alealeeplhiaqeclelRekRqg 109
                                       el++ + +Lee+ +rle+    a  +l+epl++++  l l e+R g
  gi|336252264|ref|YP_004595371.1| 467 ELETLVADLEESNERLEQfayaASHDLQEPLRMVSSYLRLIENRYG 512
                                       2333345566666666652222456677888888888888777766 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   0.00016     0.081      40      88 ..     134     195 ..     129     276 .. 0.65
   2 ?   -2.2   0.1       8.4   4.3e+03      46      69 ..     462     482 ..     446     494 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                          RasGAP_C  40 nkgrlrekrkeEles....leetlktLseknnyl...esqlesYkayienvleql......k 88 
                                       ++ r  e+r+eEl++    leet+++L+  n+ l   ++qle+Y++y ++vl+ +       
  gi|336252264|ref|YP_004595371.1| 134 TRTRELEQRNEELQVtqseLEETVDELERANERLatsNEQLEHYREYTDHVLNAIhdifyvI 195
                                       556666677777765222245677788777776633379*************9995555550 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.4
                          RasGAP_C  46 ekrkeElesleetlktLseknnyl 69 
                                       ++ ++Ele+    +++L+e n+ l
  gi|336252264|ref|YP_004595371.1| 462 QQYQAELET---LVADLEESNERL 482
                                       333333333...233444444444 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0008      0.41       5      57 ..     183     233 ..     179     245 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0008
                             PAS_8   5 alfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrplle 57 
                                        ++++++d   v+  +g+ +  +N++ +  +Gys a++  +   + ++ ++ + +
  gi|336252264|ref|YP_004595371.1| 183 HVLNAIHDIFYVIEkDGT-LQRWNESLCAVTGYSdAEVASM---NAVDFFDAEDR 233
                                       699**********95666.**************96555442...55555555444 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.9     0.013       6.6      27      60 ..     135     168 ..     132     172 .. 0.68
   2 ?    9.2   3.1    0.0025       1.3      27      55 ..     149     177 ..     141     182 .. 0.89
   3 ?   10.6   0.2    0.0009      0.46      24      46 ..     461     483 ..     460     492 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  27 eieeLerrvkaLekeNksLkseleelkkevekLk 60 
                                       ++ eLe+r ++L+   ++L ++++el+  +e L 
  gi|336252264|ref|YP_004595371.1| 135 RTRELEQRNEELQVTQSELEETVDELERANERLA 168
                                       5667777777777777777777777777777665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  27 eieeLerrvkaLekeNksLkseleelkke 55 
                                        ++eLe+ v++Le  N+ L+  +e+l+  
  gi|336252264|ref|YP_004595371.1| 149 TQSELEETVDELERANERLATSNEQLEHY 177
                                       689***********************875 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0009
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  24 KqaeieeLerrvkaLekeNksLk 46 
                                       +q++++eLe+ v+ Le+ N+ L 
  gi|336252264|ref|YP_004595371.1| 461 RQQYQAELETLVADLEESNERLE 483
                                       79******************886 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 ?   11.1   0.0   0.00052      0.27      22      80 ..     617     668 ..     597     713 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00052
                       HATPase_c_3  22 vkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkGiGlklA 80 
                                       +++++++  g   +++i D+G G+++e+ ++ + + +  ++    +++++  GiGl  A
  gi|336252264|ref|YP_004595371.1| 617 IHVSAEQS-GRRWTVSIADEGIGIDPEDQDRIFDVFQRLHS----RDTHSGTGIGL--A 668
                                       56666654.77899*****************9998877777....67888888984..3 PP

>> 23S_rRNA_IVP  23S rRNA-intervening sequence protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3     0.018         9      46     104 ..     129     188 ..     120     190 .. 0.85
   2 ?    4.7   0.1     0.073        37      27      75 ..     436     484 ..     431     495 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.018
                                       HHHHHTS.SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHH CS
                      23S_rRNA_IVP  46 IaeGsgr.rskkefirflniargslaEletqlelakdlgylseeefeelleeleeiskml 104
                                        ae+  r r   ++   l+  + +l+E+   le a+++   s+e++e+ +e ++++ + +
  gi|336252264|ref|YP_004595371.1| 129 DAEAKTRtRELEQRNEELQVTQSELEETVDELERANERLATSNEQLEHYREYTDHVLNAI 188
                                       58888886666778889********************************99999988766 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.073
                                       GTTTHHHHHHHHHHHHHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHHHH CS
                      23S_rRNA_IVP  27 ekygltsQirraavSipanIaeGsgrrskkefirflniargslaEletq 75 
                                       e+  +t++    + S+ + +ae+ +r+++++ +  l   + +++E   q
  gi|336252264|ref|YP_004595371.1| 436 ERKTFTDEDVNFVQSVANVLAEAIERQQYQAELETLVADLEESNERLEQ 484
                                       67777777788899************77777666666666666654444 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 ?    7.3   3.4    0.0079         4     123     165 ..     131     173 ..     125     189 .. 0.57
   2 ?    5.9   0.2     0.022        11      95     140 ..     439     484 ..     429     510 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0079
                   Ax_dynein_light 123 elekkikeLeeekeelekqvaelkaklealekrekerrqeeek 165
                                       e + + +eLe+++eel+   +el++ +++le+ +++  +++e+
  gi|336252264|ref|YP_004595371.1| 131 EAKTRTRELEQRNEELQVTQSELEETVDELERANERLATSNEQ 173
                                       4444455566666666666666666666655555544444433 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.022
                   Ax_dynein_light  95 tiaayktlyessvaFgmrkalqaeqgkselekkikeLeeekeelek 140
                                       t++  +  + +sva  + +a++++q ++ele  +++Lee +e+le+
  gi|336252264|ref|YP_004595371.1| 439 TFTDEDVNFVQSVANVLAEAIERQQYQAELETLVADLEESNERLEQ 484
                                       5555555566789999999*************************97 PP

>> Streptin-Immun  Lantibiotic streptin immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   1.8     0.023        12      53      84 ..     138     169 ..     131     177 .. 0.87
   2 ?    7.5   0.3      0.01       5.3      30      86 ..     432     486 ..     429     492 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.023
                    Streptin-Immun  53 tleqiekeieklqnelskkideyeelvrkldk 84 
                                        leq ++e++ +q el++++de e +  +l +
  gi|336252264|ref|YP_004595371.1| 138 ELEQRNEELQVTQSELEETVDELERANERLAT 169
                                       68999********************9999976 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.01
                    Streptin-Immun  30 sedeetrrlakydfsklnltesvtleqiekeieklqnelskkideyeelvrkldkfv 86 
                                       ++d+e++ ++  d++ +   ++v  e ie+  ++ q el++ + + ee+  +l++f+
  gi|336252264|ref|YP_004595371.1| 432 THDTERKTFTDEDVNFVQSVANVLAEAIER--QQYQAELETLVADLEESNERLEQFA 486
                                       678888888888888888888888999988..5899*******************97 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 ?   11.3   0.2    0.0003      0.16       9      86 ..     110     185 ..     106     203 .. 0.68
   2 ?   -0.3   0.1      0.97     5e+02      55      99 ..     291     335 ..     260     347 .. 0.71
   3 ?    0.6   0.4      0.53   2.7e+02      49      97 ..     449     498 ..     431     509 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                              HemX   9 llallvala.vgaglyylgqqqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleq 84 
                                       ++ +l al+ v  ++  +g + + e+++++ el+q+ ++l+ +++++e+   + ++  erl++ +e+le+ ++ +++
  gi|336252264|ref|YP_004595371.1| 110 TILILTALGsV--AGFAVGLHDA-EAKTRTRELEQRNEELQVTQSELEETVDELERANERLATSNEQLEHYREYTDH 183
                                       66777777733..4555555553.55677788888888888888887777777777777777777777777766555 PP

                              HemX  85 lq 86 
                                         
  gi|336252264|ref|YP_004595371.1| 184 VL 185
                                       44 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.97
                              HemX  55 eaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskv 99 
                                       ++e+e++ e+ +r qq   +l +l+ e+++l++ ++e ++q++ v
  gi|336252264|ref|YP_004595371.1| 291 RTERERELEQRARQQQVVADLGQLALETDDLDELMHEAARQVAVV 335
                                       444555555556666667777777777777777777777777665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.53
                              HemX  49 qqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqlee.lqqqls 97 
                                       q++a+v ae+ + q+ +++l++l  +le+++++leq + + ++ lq+ l 
  gi|336252264|ref|YP_004595371.1| 449 QSVANVLAEAIERQQYQAELETLVADLEESNERLEQFAYAASHdLQEPLR 498
                                       44455566677777777777777777777777777665444332555555 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7   0.00027      0.14     166     241 ..     129     200 ..     124     245 .. 0.73
   2 ?   -2.6   0.1       3.6   1.8e+03     203     227 ..     461     483 ..     435     512 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                        Fmp27_WPPW 166 ndpervqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkesee 241
                                       +  +++ ++ le+R eel+   ++lee+++ele  +e+    l++  e+le+  + +++ l+ ++++   ++++ +
  gi|336252264|ref|YP_004595371.1| 129 DAEAKTRTRELEQRNEELQVTQSELEETVDELERANER----LATSNEQLEHYREYTDHVLNAIHDIFYVIEKDGT 200
                                       55678899999**********************99999....6777777777777777777777776666655554 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.6
                        Fmp27_WPPW 203 kedeelkeeieelekeikelkekle 227
                                       +  +++++e+e+l  +++e +e+le
  gi|336252264|ref|YP_004595371.1| 461 R--QQYQAELETLVADLEESNERLE 483
                                       2..2333333333333333333322 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.3    0.0061       3.1      25      74 ..     129     176 ..     127     189 .. 0.68
   2 ?    0.8   0.1       1.1   5.7e+02      60     105 ..     293     332 ..     252     355 .. 0.62
   3 ?    6.4   0.2     0.021        11      27      62 ..     460     494 ..     443     538 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0061
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHH.HHHHHHHHHH CS
                              OmpH  25 ekkfkklqaeleakekelqklqeelqkkakklekeekeqe.lqkkeqelqq 74 
                                       ++++k++  ele++++elq  q el++   +    e+++e l++ +++l+ 
  gi|336252264|ref|YP_004595371.1| 129 DAEAKTRTRELEQRNEELQVTQSELEETVDE---LERANErLATSNEQLEH 176
                                       5678888888999999999888888744433...34444446666666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  60 ekeqelqkkeqelqqkqqqka..qelqkkqqellkpildkinkaikev 105
                                       e       +e+el+q+++q++   +l +   e ++ + + +++a ++v
  gi|336252264|ref|YP_004595371.1| 293 E-------RERELEQRARQQQvvADLGQLALE-TDDLDELMHEAARQV 332
                                       3.......334444433333333333333322.222444444444444 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHH CS
                              OmpH  27 kfkklqaeleakekelqklqeelqkkakklekeeke 62 
                                       +++++qaele++ ++l++  e+l++ a ++ + + +
  gi|336252264|ref|YP_004595371.1| 460 ERQQYQAELETLVADLEESNERLEQFAYAA-SHDLQ 494
                                       448899999999999999999998766664.33333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.5   0.00035      0.18     198     251 ..     136     189 ..     126     205 .. 0.48
   2 ?    0.9   0.3      0.33   1.7e+02     173     196 ..     462     485 ..     434     512 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00035
                              Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeia 251
                                         eLe+  eel+  ++e+ee  +el++ +e+l++++e++e+ +e  +++ ++i 
  gi|336252264|ref|YP_004595371.1| 136 TRELEQRNEELQVTQSELEETVDELERANERLATSNEQLEHYREYTDHVLNAIH 189
                                       334444444444444444444444444444444444444444444444444443 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.33
                              Spc7 173 eeekaeleeeleklqeaaeelesi 196
                                       ++++aele  +++l+e +e le+ 
  gi|336252264|ref|YP_004595371.1| 462 QQYQAELETLVADLEESNERLEQF 485
                                       222223333333333333333322 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.3    0.0066       3.4       2      55 ..     133     186 ..     132     190 .. 0.89
   2 ?    3.8   0.1      0.13        67      80     111 ..     462     493 ..     441     502 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0066
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekpln 55 
                                       kt+ ++l+++ +el+ + + lee + +L++a ++l + +e+l++ +++  + ln
  gi|336252264|ref|YP_004595371.1| 133 KTRTRELEQRNEELQVTQSELEETVDELERANERLATSNEQLEHYREYTDHVLN 186
                                       67778999**********************************998888777665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.13
                           DUF5082  80 qtyvdkldelidaieeEIerLenqiseaqgvl 111
                                       q+y+ +l++l++ +ee  erLe+  + a+ +l
  gi|336252264|ref|YP_004595371.1| 462 QQYQAELETLVADLEESNERLEQFAYAASHDL 493
                                       8999*************999999888777766 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.2    0.0011      0.58      17      59 ..     135     177 ..     127     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                           DUF2205  17 arerLqqqakeLqssLqaLaervdeVkeehdKLesenrfLqqY 59 
                                          +L+q+ +eLq +  +L e vde    +++L + n+ L +Y
  gi|336252264|ref|YP_004595371.1| 135 RTRELEQRNEELQVTQSELEETVDELERANERLATSNEQLEHY 177
                                       34579************************************99 PP

>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   3.6     0.025        13       6      46 ..     137     177 ..     134     179 .. 0.89
   2 ?    4.4   0.4     0.075        38       6      24 ..     466     484 ..     463     486 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.025
                      Exonuc_VII_S   6 aeLeeIvekLEsgelsLeeslklyeeGvkLlkeCekkLdea 46 
                                        eLe+  e+L+  + +Lee +++ e++ + l+  +++L+  
  gi|336252264|ref|YP_004595371.1| 137 RELEQRNEELQVTQSELEETVDELERANERLATSNEQLEHY 177
                                       589999999999999****************9999999876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.075
                      Exonuc_VII_S   6 aeLeeIvekLEsgelsLee 24 
                                       aeLe++v+ LE+ +  Le+
  gi|336252264|ref|YP_004595371.1| 466 AELETLVADLEESNERLEQ 484
                                       79*********99998886 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 ?    9.8   0.7    0.0015      0.76      85     155 ..     137     178 ..     111     197 .. 0.53
   2 ?    4.8   0.9     0.053        27      86     140 ..     446     500 ..     431     510 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0015
                           UPF0242  85 ktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyq 155
                                       ++ e+  eelq  + eL+e +d+ e++ erl   n+qL+                             +y+
  gi|336252264|ref|YP_004595371.1| 137 RELEQRNEELQVTQSELEETVDELERANERLATSNEQLE-----------------------------HYR 178
                                       222233333333333333333333333333333333333.............................332 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.053
                           UPF0242  86 tkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklel 140
                                       +  +++ ++ +e  e+++ +++ e++++ l+e n+ L++ + a+++d +e ++ +
  gi|336252264|ref|YP_004595371.1| 446 NFVQSVANVLAEAIERQQYQAELETLVADLEESNERLEQFAYAASHDLQEPLRMV 500
                                       4456788888888888898999999999999999999999999999999876655 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   7.6e-05     0.039      48     102 ..     131     185 ..     112     192 .. 0.74
   2 ?    1.8   0.4      0.24   1.2e+02      48      86 ..     446     484 ..     434     522 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.6e-05
                           DUF3450  48 ellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpll 102
                                       e + + r+l++++e+l+v +++le+ v+++e+  ++l ++ e++e+ ++    +l
  gi|336252264|ref|YP_004595371.1| 131 EAKTRTRELEQRNEELQVTQSELEETVDELERANERLATSNEQLEHYREYTDHVL 185
                                       5566777778888888888888888888888888888887777777776555554 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.24
                           DUF3450  48 ellaeyralkeeleslevyneqlerlvasqeqeiaslee 86 
                                       + ++ + ++ +e+ + + y+++le lva++e++ ++le+
  gi|336252264|ref|YP_004595371.1| 446 NFVQSVANVLAEAIERQQYQAELETLVADLEESNERLEQ 484
                                       455555555555555555666666666666655555554 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.9    0.0083       4.2      12      44 ..     135     170 ..     129     203 .. 0.77
   2 ?    0.7   0.2       1.2   6.1e+02      21      43 ..     462     484 ..     441     506 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0083
                             Spc24  12 elsdleselesleselaelkeeleeleeesee...k 44 
                                         ++le+  e+l+ +++el+e+++ele+ +e+   +
  gi|336252264|ref|YP_004595371.1| 135 RTRELEQRNEELQVTQSELEETVDELERANERlatS 170
                                       568999999999999999999999999988886542 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.2
                             Spc24  21 esleselaelkeeleeleeesee 43 
                                       ++ ++el+ l + lee +e  e+
  gi|336252264|ref|YP_004595371.1| 462 QQYQAELETLVADLEESNERLEQ 484
                                       34445555555555555555444 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.4    0.0022       1.1      21      53 ..     131     163 ..     124     188 .. 0.55
   2 ?   -1.5   0.4       6.1   3.1e+03      34      88 ..     296     317 ..     287     335 .. 0.43
   3 ?    3.4   0.1      0.19        99      68      99 ..     454     485 ..     438     509 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0022
                           DUF4200  21 eiqrleealkqreeelekkeqeleedllkfdkf 53 
                                       e +++ ++l+qr eel+ +++elee++ ++++ 
  gi|336252264|ref|YP_004595371.1| 131 EAKTRTRELEQRNEELQVTQSELEETVDELERA 163
                                       455555555555555555555555555444443 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.1
                           DUF4200  34 eelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkae 88 
                                       +ele                                 +r ++++  a++ +l  e
  gi|336252264|ref|YP_004595371.1| 296 RELE---------------------------------QRARQQQVVADLGQLALE 317
                                       2222.................................222223333444444444 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.19
                           DUF4200  68 aeeerklkkekeaeikklkaeietlkseiekl 99 
                                       +  e+ ++++++ae++ l a++e+ ++++e++
  gi|336252264|ref|YP_004595371.1| 454 VLAEAIERQQYQAELETLVADLEESNERLEQF 485
                                       55688889999999999999999988666654 PP

>> HNOBA  Heme NO binding associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4   0.00087      0.45     154     204 ..     127     173 ..     113     188 .. 0.70
   2 ?    0.3   0.2      0.76   3.9e+02     178     200 ..     462     484 ..     446     488 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00087
                             HNOBA 154 lsDlplhdssrelvlagiqqsaelelaldqleeksaeLeesmkeleeekkr 204
                                       l D     ++rel    +q+++el++++ +lee+ +eLe+++++l   +++
  gi|336252264|ref|YP_004595371.1| 127 LHDAEAKTRTREL----EQRNEELQVTQSELEETVDELERANERLATSNEQ 173
                                       5555566666665....7888888888888888888888888886665555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.76
                             HNOBA 178 elaldqleeksaeLeesmkelee 200
                                       +  + +le+  a+Lees+++le+
  gi|336252264|ref|YP_004595371.1| 462 QQYQAELETLVADLEESNERLEQ 484
                                       22233566677777777777664 PP

>> PGBA_C  Plasminogen-binding protein pgbA C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   4.4     0.051        26      47      80 ..     129     161 ..     127     165 .. 0.83
   2 ?    5.0   0.6     0.062        32      52      65 ..     293     306 ..     287     314 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.051
                            PGBA_C  47 kakaeqrarefeqrarehqerdekeleerrkale 80 
                                        a a+ r+re+eqr  e q   + elee    le
  gi|336252264|ref|YP_004595371.1| 129 DAEAKTRTRELEQRNEELQVT-QSELEETVDELE 161
                                       58899**********999975.679999888777 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.062
                            PGBA_C  52 qrarefeqrarehq 65 
                                       +r re+eqrar+ q
  gi|336252264|ref|YP_004595371.1| 293 ERERELEQRARQQQ 306
                                       599********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1371  (0.0764683); expected 358.6 (0.02)
Passed bias filter:                      881  (0.0491383); expected 358.6 (0.02)
Passed Vit filter:                       149  (0.00831056); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.79u 0.26s 00:00:01.05 Elapsed: 00:00:00.38
# Mc/sec: 5640.80
//
Query:       gi|336252265|ref|YP_004595372.1|  [L=55]
Description: hypothetical protein Halxa_0854 [Halopiger xanaduensis SH-6]
Scores for 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   13.6   0.1      0.062   13.6   0.1    1.1  1  APOC4     Apolipoprotein C4


Domain annotation for each model (and alignments):
>> APOC4  Apolipoprotein C4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.4e-06     0.062      31      72 ..      16      54 ..       4      55 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.4e-06
                             APOC4 31 lvtrtrerwqwfwgPeafqgfvqtyyddhlkdlgprtkawlr 72
                                       v r  ++ +w+   +++  +++  y+dhl+d  pr   wlr
  gi|336252265|ref|YP_004595372.1| 16 AVDRECDHCEWYGVASSYPKLIKR-YQDHLRDEHPR--VWLR 54
                                      5788899999*9999999999986.69*****9998..4776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 421.17
//
Query:       gi|336252266|ref|YP_004595373.1|  [L=52]
Description: hypothetical protein Halxa_0855 [Halopiger xanaduensis SH-6]
Scores for 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:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 432.30
//
Query:       gi|336252267|ref|YP_004595374.1|  [L=378]
Description: cobalamin synthesis protein P47K [Halopiger xanaduensis SH-6]
Scores for complete 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-51  174.3   0.0    2.2e-51  173.9   0.0    1.1  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
    1.3e-28   98.7   0.0    2.4e-28   97.9   0.0    1.5  1  CobW_C       Cobalamin synthesis protein cobW C-terminal doma
    0.00028   20.5   0.0      0.084   12.4   0.0    2.2  2  GTP_EFTU     Elongation factor Tu GTP binding domain
     0.0028   17.6   0.0        0.4   10.6   0.0    2.3  2  RsgA_GTPase  RsgA GTPase
     0.0082   16.5   0.0      0.023   15.1   0.0    1.9  2  AAA_16       AAA ATPase domain
     0.0095   15.0   0.0      0.016   14.3   0.0    1.2  1  T2SSE        Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.085   13.0   0.0       0.18   12.0   0.0    1.5  1  AAA_33       AAA domain
       0.11   12.6   0.0       0.35   11.0   0.0    2.0  1  MMR_HSR1     50S ribosome-binding GTPase
       0.17   11.8   0.1       0.44   10.5   0.1    1.7  1  PfaD_N       Fatty acid synthase subunit PfaD N-terminal doma


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 !  173.9   0.0   1.1e-54   2.2e-51       1     175 [.       8     205 ..       8     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: 173.9 bits;  conditional E-value: 1.1e-54
                                       EEEEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCC..CT.EEEETTTTECCHCTT-HHHHHHH CS
                              cobW   1 pvtvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellret..gveivelenGciCctlredllkelea 75 
                                       pvtv++G+lG+GKTtLln++l+n  ++++avivN++gev++Da+l++++  ++ iv+l+nGciCc l++dll e+++
  gi|336252267|ref|YP_004595374.1|   8 PVTVVSGYLGAGKTTLLNRVLSNPGDRRIAVIVNDMGEVNVDADLIAREneDEGIVDLSNGCICCRLQDDLLTEAAE 84 
                                       79********************************************77733444*********************** PP

                                       HHHHHTT-SEEEEEECTTTTHHHH..HTT......SHHHHHCCCECEEEEEEETTTH................CCHC CS
                              cobW  76 leereerldviliEttGlaePapv..aft......eeelksdltldavvavvDaknl...............eaeee 129
                                       l+e +  +d++l+E++G++eP pv  +ft      + + +++++ld++v+v+D   +                + ++
  gi|336252267|ref|YP_004595374.1|  85 LAESR-AFDYLLVESSGISEPIPVaqVFTegtedsDVDPTNRFRLDTMVTVLDTYGFwkefdagaalpegaqPDTDR 160
                                       *****.9*****************88777899866666678*************888*************9988999 PP

                                       CHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHHTTS-E CS
                              cobW 130 kieekaedqlaaadllvlnKtDlldeeallekleerlrqlnpeakv 175
                                       + ++ + ++++++d+l+lnKtD+++++  le++e++++ql+p+ak 
  gi|336252267|ref|YP_004595374.1| 161 PLSDVLVEGIEFCDVLLLNKTDMVPDDV-LEEIEAVVEQLQPRAKR 205
                                       ***************************5.5************9985 PP

>> CobW_C  Cobalamin synthesis protein cobW C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   0.0   1.2e-31   2.4e-28       1      94 []     268     358 ..     268     358 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 1.2e-31
                            CobW_C   1 issfvfrarrpfdperleelleeelpegilRaKGivwlagkpdalvlqgvggrlrlepagawwaaededrrseLVfI 77 
                                       +ssfvfr++rpf+perl+++lee + ++i+RaKG++++a++++++ ++++g++++ +p g+w ++  +dr+++LVfI
  gi|336252267|ref|YP_004595374.1| 268 VSSFVFRSDRPFHPERLADWLEE-WDGSIVRAKGVCYVANREEVIGVSQAGPSVSAGPIGEWRPD--DDRGTQLVFI 341
                                       68*********************.99************************************999..********** PP

                            CobW_C  78 GrdldkealeeaLdacl 94 
                                       Gr++d+e+++++L+acl
  gi|336252267|ref|YP_004595374.1| 342 GREMDEERIRDELEACL 358
                                       ****************7 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 !    6.2   0.0    0.0033       6.5       5      31 ..       9      35 ..       5      62 .. 0.75
   2 !   12.4   0.0   4.2e-05     0.084     105     158 ..     152     207 ..     125     298 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0033
                                      EEEEEESTTSSHHHHHHHHHHHTTSSC CS
                          GTP_EFTU  5 nigiighvDhGKtTLtdrLlyktgais 31
                                        ++ g + +GKtTL+ r+l + g+ +
  gi|336252267|ref|YP_004595374.1|  9 VTVVSGYLGAGKTTLLNRVLSNPGDRR 35
                                      567889999**********98877655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.2e-05
                                       TBSTHHHHHHHHHHHHTTTE..EEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU 105 eGvepqteevlrlalkegvp..iivfiNKmDrlkaelkeiveevkqklsrkeekle 158
                                       eG +p t + l  +l eg++   ++++NK D++ +++ e +e+v ++l+ + ++l+
  gi|336252267|ref|YP_004595374.1| 152 EGAQPDTDRPLSDVLVEGIEfcDVLLLNKTDMVPDDVLEEIEAVVEQLQPRAKRLR 207
                                       899*****************8889*********77777777777777766644443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0002       0.4     101     123 ..       9      31 ..       3      48 .. 0.80
   2 ?    4.6   0.0     0.014        27      48      76 ..     173     200 ..     149     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                                       EEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpel 123
                                       ++v+ G  G+GK+tL+n++l++ 
  gi|336252267|ref|YP_004595374.1|   9 VTVVSGYLGAGKTTLLNRVLSNP 31 
                                       7999**************99863 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.014
                                       EEEEEEE-GGG--HHHHHHHHHHHHHHTT CS
                       RsgA_GTPase  48 epvivlnKiDlleeeeeleelkeelealg 76 
                                         v++lnK+D++ ++  lee+++ +e+l+
  gi|336252267|ref|YP_004595374.1| 173 CDVLLLNKTDMVPDDV-LEEIEAVVEQLQ 200
                                       3589**********99.888888888875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05     0.023      20      56 ..       3      39 ..       1     129 [. 0.78
   2 ?   -2.4   0.0       2.6   5.2e+03      67     110 ..     160     201 ..     143     233 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekdggifl 56
                                      + +r +++++sG+ G GK++l++++l    ++++ ++
  gi|336252267|ref|YP_004595374.1|  3 SNDRIPVTVVSGYLGAGKTTLLNRVLSNPGDRRIAVI 39
                                      56677999******************87777765553 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                            AAA_16  67 ipysa.laqalareellrqlldeaesaeleawrekleealaavpe 110
                                       +p+s  l++ +   e++  ll ++++  +++  e++e+++++ ++
  gi|336252267|ref|YP_004595374.1| 160 RPLSDvLVEGI---EFCDVLLLNKTDMVPDDVLEEIEAVVEQLQP 201
                                       56655566666...4566666665555666666666665553332 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 !   14.3   0.0   7.8e-06     0.016     133     187 ..      11      64 ..       5      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.8e-06
                             T2SSE 133 lvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnakkakvt 187
                                       +vsG  g GKttll+ +l+   ++ +  v+v D  E++++++   + n++++ v+
  gi|336252267|ref|YP_004595374.1|  11 VVSGYLGAGKTTLLNRVLSNPGDR-RIAVIVNDMGEVNVDADLIARENEDEGIVD 64 
                                       89****************988777.666899*******99887776666655555 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   8.8e-05      0.18       1      26 [.       9      38 ..       9      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg....av 26
                                      ++++ G  G+GK+tl+ r+l + g    av
  gi|336252267|ref|YP_004595374.1|  9 VTVVSGYLGAGKTTLLNRVLSNPGdrriAV 38
                                      67899***************9988665444 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   0.00018      0.35       3      31 ..      11      45 ..       9     209 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                      EEEESTTSSHHHHHHHHHTS......TEEESSSTT CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge......kaivsdkpg 31
                                      ++ G+  +GK+tL+n+ + +      ++iv+d+  
  gi|336252267|ref|YP_004595374.1| 11 VVSGYLGAGKTTLLNRVLSNpgdrriAVIVNDMGE 45
                                      678*************9964333333456666655 PP

>> PfaD_N  Fatty acid synthase subunit PfaD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00022      0.44      26      46 ..     302     322 ..     298     327 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                                       EEEEETTTCEEEES--B---- CS
                            PfaD_N  26 cYiVrseggiGvtnegylvpe 46 
                                       cY+ + e+ iGv++ g  v++
  gi|336252267|ref|YP_004595374.1| 302 CYVANREEVIGVSQAGPSVSA 322
                                       ****************87776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 3003.13
//
Query:       gi|336252268|ref|YP_004595375.1|  [L=98]
Description: regulatory protein ArsR [Halopiger xanaduensis SH-6]
Scores for 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-14   52.5   0.0    7.7e-14   51.3   0.0    1.6  2  HTH_5           Bacterial regulatory protein, arsR family
    9.1e-13   48.1   0.2    1.2e-12   47.7   0.2    1.1  1  HTH_20          Helix-turn-helix domain
    8.4e-06   25.6   0.0    1.1e-05   25.2   0.0    1.3  1  MarR_2          MarR family
    1.4e-05   24.8   0.3    2.4e-05   24.0   0.3    1.5  1  HTH_IclR        IclR helix-turn-helix domain
      9e-05   22.0   0.0    0.00057   19.4   0.0    2.0  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00023   21.0   0.2     0.0012   18.7   0.2    1.9  1  PadR            Transcriptional regulator PadR-like family
    0.00028   20.9   0.1    0.00052   20.1   0.1    1.4  1  DprA_WH         DprA winged helix domain
    0.00099   19.0   0.0     0.0014   18.5   0.0    1.2  1  MarR            MarR family
     0.0016   18.9   0.1     0.0021   18.5   0.1    1.2  1  HTH_27          Winged helix DNA-binding domain
     0.0021   17.9   0.1      0.003   17.4   0.1    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0041   17.2   0.4      0.025   14.7   0.6    1.8  2  DUF2250         Uncharacterized protein conserved in archaea 
  ------ inclusion threshold ------
      0.014   15.4   0.0       0.02   14.9   0.0    1.1  1  HTH_45          Winged helix-turn-helix
      0.032   14.2   0.0      0.044   13.7   0.0    1.3  1  HTH_11          HTH domain
      0.033   14.5   0.0      0.046   14.1   0.0    1.2  1  Rrf2            Transcriptional regulator
      0.034   13.8   0.0      0.046   13.4   0.0    1.2  1  RP-C            Replication protein C N-terminal domain
      0.062   13.5   0.0       0.09   13.0   0.0    1.2  1  PaaX            PaaX-like protein
      0.094   12.9   0.0       0.14   12.3   0.0    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.095   12.7   0.0       0.13   12.3   0.0    1.2  1  HTH_36          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   7.8e-17   7.7e-14       2      46 ..      12      56 ..      11      57 .. 0.97
   2 ?   -1.7   0.0       2.8   2.8e+03      13      27 ..      60      74 ..      59      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 7.8e-17
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       tRl+IL+ L++++++v+elae++g+   t  hHL+ L+eaGLV+
  gi|336252268|ref|YP_004595375.1| 12 GTRLEILRELSREPKYVTELAEATGMDGKTAVHHLSTLEEAGLVD 56
                                      59******************************************6 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.8
                                      TSSEEHHHHHHHHTS CS
                             HTH_5 13 egelcvcelaeelgl 27
                                      +g+++  el+++++l
  gi|336252268|ref|YP_004595375.1| 60 RGNRKYYELTAAVEL 74
                                      578888999999986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.2   1.2e-15   1.2e-12       3      55 ..       5      56 ..       3      61 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.2e-15
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      ++eAL++ +R++ilr+L ++e+  ++elae+ +++ +t+ +HL +LeeagLv+
  gi|336252268|ref|YP_004595375.1|  5 LIEALGNGTRLEILREL-SREPKYVTELAEATGMDGKTAVHHLSTLEEAGLVD 56
                                      78***************.*********************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.1e-08   1.1e-05       5      52 ..      12      56 ..       7      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.1e-08
                                      HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      ++ + +L +L r+p     v+ela+++g++  ++  +l  L++aGLv 
  gi|336252268|ref|YP_004595375.1| 12 GTRLEILRELSREPK---YVTELAEATGMDGKTAVHHLSTLEEAGLVD 56
                                      68889*********9...9****************************6 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 !   24.0   0.3   2.4e-08   2.4e-05       6      49 ..      15      56 ..       2      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.4e-08
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      l+iL+ l+++p    ++elA++tg+   t+ ++L+tL+e G+v 
  gi|336252268|ref|YP_004595375.1| 15 LEILRELSREPKY--VTELAEATGMDGKTAVHHLSTLEEAGLVD 56
                                      5677777777776..***************************95 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 !   19.4   0.0   5.7e-07   0.00057       2      47 ..      11      55 ..      10      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.7e-07
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      + t+++IL++L ++p+   +eLAe++g+   t   +l  Lee+Gl+
  gi|336252268|ref|YP_004595375.1| 11 NGTRLEILRELSREPKY-VTELAEATGMDGKTAVHHLSTLEEAGLV 55
                                      56899********9997.68************************98 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   1.2e-06    0.0012       5      68 ..      21      71 ..      17      77 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                                      HCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHC CS
                              PadR  5 leeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTda 68
                                      l+++p y +e++++      g +++        L++Le+ glv+++++      +rkyY+lT+a
  gi|336252268|ref|YP_004595375.1| 21 LSREPKYVTELAEATGMD--GKTAV------HHLSTLEEAGLVDHYMRG-----NRKYYELTAA 71
                                      555555555555554444..43333......359************885.....8*******97 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   5.2e-07   0.00052      13      56 ..      13      56 ..       4      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.2e-07
                           DprA_WH 13 lerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlve 56
                                      ++  +L  L+ eP  v +L+++tg++  +  ++L+ LE aGlv 
  gi|336252268|ref|YP_004595375.1| 13 TRLEILRELSREPKYVTELAEATGMDGKTAVHHLSTLEEAGLVD 56
                                      6789*************************************996 PP

>> MarR  MarR family
   #    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       4      48 ..      13      56 ..      11      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                                      HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      t+++iLr l++ +p +v+eLa++ g++  t+   l +Le++Gl++
  gi|336252268|ref|YP_004595375.1| 13 TRLEILRELSR-EPKYVTELAEATGMDGKTAVHHLSTLEEAGLVD 56
                                      67788888875.6789***************************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 !   18.5   0.1   2.1e-06    0.0021       8      66 ..      17      70 ..      11      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-06
                            HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTd 66
                                      +L+ +   r++k  ++l++++ ++  +++  l+ L+e+GLv   ++ + + +k ++lT+
  gi|336252268|ref|YP_004595375.1| 17 ILRELS--REPKYVTELAEATGMDGKTAVHHLSTLEEAGLV--DHY-MRGNRKYYELTA 70
                                      555555..777777***************************..333.445569999998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     3e-06     0.003      18      63 ..      21      67 ..      16      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3e-06
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEE CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYr 63
                                      l+++p+ ++e+ae++g +  ++   L+ Le++GlV+    g++k+Y+
  gi|336252268|ref|YP_004595375.1| 21 LSREPKYVTELAEATGMDGKTAVHHLSTLEEAGLVDHYMrGNRKYYE 67
                                      6899*******************************987635566665 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 !   14.7   0.6   2.5e-05     0.025      10      62 ..      14      65 ..       7      70 .. 0.85
   2 ?    2.0   0.1      0.23   2.3e+02      74      88 ..      60      74 ..      58      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-05
                           DUF2250 10 alkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegktikr 62
                                       l++l+ l + ++ Y   +a+ + ++ + + + l  Lee+GL++++ +   k+
  gi|336252268|ref|YP_004595375.1| 14 RLEILRELSR-EPKYVTELAEATGMDGKTAVHHLSTLEEAGLVDHYMRGNRKY 65
                                      6778888765.899******************************998766665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.23
                           DUF2250 74 hkhHtYYrltreGel 88
                                      + + +YY+lt   el
  gi|336252268|ref|YP_004595375.1| 60 RGNRKYYELTAAVEL 74
                                      55789*****87765 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     2e-05      0.02       9      60 ..      15      70 ..      14      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                            HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTe 60
                                      ++IL+ +s++ +  T++  +  ++ k++   L++L e gl+    + + + Y+lT+
  gi|336252268|ref|YP_004595375.1| 15 LEILRELSREPKYVTELAEATGMDGKTAVHHLSTLEEAGLVdhymRGNRKYYELTA 70
                                      58***************************************887666888888885 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.4e-05     0.044       2      43 ..      14      53 ..      13      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      +l il+ L ++ +     eLAe +++  +t + ++ +Lee+g
  gi|336252268|ref|YP_004595375.1| 14 RLEILRELSREPK--YVTELAEATGMDGKTAVHHLSTLEEAG 53
                                      5778999955555..578***********************9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.6e-05     0.046      23      68 ..      23      69 ..      13      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-05
                                      CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE.ETTT-TCEEES CS
                              Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvks.vrGkgGGyrLa 68
                                      +ep  ++e+ae +++  + + + l++L++aglv    rG++  y L+
  gi|336252268|ref|YP_004595375.1| 23 REPKYVTELAEATGMDGKTAVHHLSTLEEAGLVDHyMRGNRKYYELT 69
                                      3445689**************************75267777666665 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 ?   13.4   0.0   4.6e-05     0.046      75     112 ..      29      66 ..      25      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.6e-05
                              RP-C  75 aqLsralglsestlrrhlaaLveaGliirrDspngkRy 112
                                       ++L++a+g+  +t  +hl+ L eaGl+ +    n k y
  gi|336252268|ref|YP_004595375.1|  29 TELAEATGMDGKTAVHHLSTLEEAGLVDHYMRGNRKYY 66 
                                       5799**********************987777776655 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     9e-05      0.09      28      69 ..      30      71 ..      26      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9e-05
                              PaaX 28 rllaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsdk 69
                                      +l ++ G++ ++    ls l++aG+++    g+r +Y+L+++
  gi|336252268|ref|YP_004595375.1| 30 ELAEATGMDGKTAVHHLSTLEEAGLVDHYMRGNRKYYELTAA 71
                                      67888899999999999**********************975 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 ?   12.3   0.0   0.00014      0.14      18      54 ..      20      57 ..      16      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                      H.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress 18 e.ekkvvktkdlaerLnvspssVsemlkkLekdGyvey 54
                                      e ++++  +++lae+ +  + ++   l+ Le++G+v++
  gi|336252268|ref|YP_004595375.1| 20 ElSREPKYVTELAEATGMDGKTAVHHLSTLEEAGLVDH 57
                                      5566677789**************************98 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.13      29      55 .]      29      55 ..      17      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            HTH_36 29 etlakrlglsknTvsraikeLeqlGyi 55
                                        la+++g++ +T++ ++  Le++G++
  gi|336252268|ref|YP_004595375.1| 29 TELAEATGMDGKTAVHHLSTLEEAGLV 55
                                      679**********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); 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:                        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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 817.29
//
Query:       gi|336252269|ref|YP_004595376.1|  [L=100]
Description: hypothetical protein Halxa_0858 [Halopiger xanaduensis SH-6]
Scores for 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:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 852.90
//
Query:       gi|336252270|ref|YP_004595377.1|  [L=295]
Description: hypothetical protein Halxa_0859 [Halopiger xanaduensis SH-6]
Scores for 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  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2404.49
//
Query:       gi|336252271|ref|YP_004595378.1|  [L=213]
Description: hypothetical protein Halxa_0860 [Halopiger xanaduensis SH-6]
Scores for 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  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1628.17
//
Query:       gi|336252272|ref|YP_004595379.1|  [L=121]
Description: transcriptional regulator PadR family protein [Halopiger xanaduensis SH-6]
Scores for 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-17   62.5   1.0    4.1e-17   61.9   1.0    1.2  1  PadR      Transcriptional regulator PadR-like family
    1.3e-05   25.6   0.1    9.6e-05   22.8   0.0    2.0  2  HTH_27    Winged helix DNA-binding domain
    0.00031   21.4   0.0     0.0004   21.0   0.0    1.3  1  RTP       Replication terminator protein
     0.0013   18.5   0.0     0.0019   18.0   0.0    1.4  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
  ------ inclusion threshold ------
      0.028   14.4   0.1      0.046   13.7   0.1    1.4  1  HTH_45    Winged helix-turn-helix


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 !   61.9   1.0   1.1e-20   4.1e-17       1      71 [.      24      88 ..      24      91 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 1.1e-20
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71
                                      iL +l+++p+yG++i++elee++ g +e+++G+lYp+L++L + glve+++ +    ++++ Y lTd+G +
  gi|336252272|ref|YP_004595379.1| 24 ILVILAKEPMYGLAIKRELEEYY-G-TEVNHGRLYPNLDELVELGLVEKSELD----KRTNQYSLTDDGYE 88
                                      899*******************8.6.7***********************998....59**********76 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 !   22.8   0.0   2.7e-08   9.6e-05      18      68 .]      36      86 ..      17      86 .. 0.78
   2 ?    0.8   0.0      0.19     7e+02      11      26 ..     101     116 ..      91     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.7e-08
                            HTH_27 18 rkkladlcgrlnvedshis.y.slkkLtekGLvertgdeadrrekrvrlTdkG 68
                                       +++++l +++ +e  h+  y +l++L+e GLv  +++e d+r+ +++lTd G
  gi|336252272|ref|YP_004595379.1| 36 LAIKRELEEYYGTEVNHGRlYpNLDELVELGLV--EKSELDKRTNQYSLTDDG 86
                                      44558899999999988888449**********..667889**********98 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.19
                            HTH_27  11 lirhrrrrkkladlcg 26 
                                       ++ +++r ++++++++
  gi|336252272|ref|YP_004595379.1| 101 VVTGEDRADEIREIVD 116
                                       3449999999999975 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.1e-07    0.0004      13      89 ..      23      90 ..      14     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.1e-07
                                      HHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHHH CS
                               RTP 13 ylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkeka 89
                                       ++ +++k+++ygl +  el +    +g + nh  +y  l+elve g++++ +  k          Ysltd+G+e++
  gi|336252272|ref|YP_004595379.1| 23 NILVILAKEPMYGLAIKRELEE---YYGTEVNHGRLYPNLDELVELGLVEKSELDK------RTNQYSLTDDGYEAV 90
                                      47889999********999986...5899*******************99876554......455799999999986 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 !   18.0   0.0   5.2e-07    0.0019      50      87 ..      53      90 ..      21      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.2e-07
                           DUF1495 50 gkrynsessLielGLveeeeeseglklYklteeGieiv 87
                                      g  y + + L+elGLve+ e ++ ++ Y+lt+ G e v
  gi|336252272|ref|YP_004595379.1| 53 GRLYPNLDELVELGLVEKSELDKRTNQYSLTDDGYEAV 90
                                      566777889*******99999*************9866 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.3e-05     0.046      27      65 ..      46      89 ..      37      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                            HTH_45 27 ykanLsykllnkYLdmLvekgli.....kkskekYvlTekGlel 65
                                      y  + +  +l   Ld Lve gl+     +k++++Y+lT+ G e 
  gi|336252272|ref|YP_004595379.1| 46 YGTEVNHGRLYPNLDELVELGLVekselDKRTNQYSLTDDGYEA 89
                                      6667788888899*********9888888999*********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 893.75
//
Query:       gi|336252273|ref|YP_004595380.1|  [L=177]
Description: Inorganic pyrophosphatase [Halopiger xanaduensis SH-6]
Scores for complete 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  174.6   1.6    1.4e-51  174.4   1.6    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 !  174.4   1.6     8e-56   1.4e-51       1     159 [.      20     172 ..      20     173 .. 0.98

  Alignments for each domain:
  == domain 1  score: 174.4 bits;  conditional E-value: 8e-56
                                       EEEEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEE CS
                   Pyrophosphatase   1 vvvEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkv 77 
                                       +vvE  +g+++Kye+dk+   ++ldrvl++ ++yp +YGfipq + d     D+DP Dvlvl+e++++pg+v+e+++
  gi|336252273|ref|YP_004595380.1|  20 AVVECLKGERNKYEYDKDVPGVVLDRVLHSNVHYPSDYGFIPQSYYD-----DEDPFDVLVLVEDQTFPGCVIEARP 91 
                                       59*********************************************.....***********999*********** PP

                                       EEEEEEEETTEEEEEEEEEETTSGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHHHH CS
                   Pyrophosphatase  78 lGvlamiDegetDdKiiavpvkdprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekviee 154
                                       +++++m D+ge+DdK+iavp++dpr+++i+d+ed+p++ l+ei++fF tyk+le ++k+v+ ++w+dk++A + ie+
  gi|336252273|ref|YP_004595380.1|  92 VALMKMDDDGEQDDKVIAVPSEDPRYDHIEDLEDIPQQQLDEIDEFFATYKNLE-EGKEVETQGWEDKQAAYDAIEH 167
                                       ******************************************************.66999***************** PP

                                       HHHHH CS
                   Pyrophosphatase 155 ahery 159
                                       a+e y
  gi|336252273|ref|YP_004595380.1| 168 AQELY 172
                                       99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1344.33
//
Query:       gi|336252274|ref|YP_004595381.1|  [L=280]
Description: cobyrinic acid a,c-diamide synthase [Halopiger xanaduensis SH-6]
Scores for 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-31  108.7   0.0      4e-31  108.3   0.0    1.1  1  AAA_31           AAA domain
      2e-18   66.7   0.0    4.4e-18   65.6   0.0    1.6  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    5.7e-09   35.8   0.1    1.3e-08   34.6   0.1    1.6  1  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
    7.7e-09   35.4   0.4    1.8e-08   34.1   0.1    1.7  2  ParA             NUBPL iron-transfer P-loop NTPase
    1.2e-08   34.5   0.3    1.6e-07   30.8   0.3    2.1  1  ArsA_ATPase      Anion-transporting ATPase
    1.4e-07   31.0   0.9     0.0035   16.7   0.2    3.1  3  MipZ             ATPase MipZ
    0.00014   21.4   0.0    0.00026   20.5   0.0    1.4  1  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
    0.00015   21.6   0.0     0.0003   20.6   0.0    1.4  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
     0.0031   16.6   0.1     0.0045   16.0   0.1    1.2  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0049   16.4   0.1       0.01   15.4   0.1    1.5  2  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
  ------ inclusion threshold ------
      0.011   15.4   0.1      0.019   14.6   0.1    1.3  1  SRP54            SRP54-type protein, GTPase domain
      0.014   14.7   0.0      0.022   14.1   0.0    1.2  1  VirC1            VirC1 protein
      0.016   15.2   0.1      0.025   14.6   0.1    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
      0.028   14.1   0.0       0.05   13.3   0.0    1.4  1  Thymidylate_kin  Thymidylate kinase
      0.064   13.7   4.8       0.24   11.8   4.6    1.9  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      0.071   12.6   0.0       0.12   11.8   0.0    1.2  1  adh_short        short chain dehydrogenase
      0.073   13.5   0.2       0.16   12.4   0.2    1.9  1  AAA_16           AAA ATPase domain
       0.12   12.1   0.0        0.4   10.4   0.0    1.7  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.12   12.9   0.0       0.21   12.1   0.0    1.5  1  AAA_18           AAA domain
       0.18   10.7   0.0       0.25   10.2   0.0    1.2  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN


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 !  108.3   0.0   4.4e-34     4e-31       5     157 ..       5     162 ..       1     175 [. 0.88

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 4.4e-34
                            AAA_31   5 aianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgi.ekneiektlyevli..eeknikeaiiktkv 78 
                                       +++ qKGGvGKTT ++nla  la +g+ v lvD+DpQ++at +lg+ +  +++++l +vl   + ++ ++++ +++ 
  gi|336252274|ref|YP_004595381.1|   5 TVMLQKGGVGKTTIATNLADRLAARGHEVVLVDVDPQGSATEALGCgDAYTADTHLAHVLDpdDPSSASDLLRTDT- 80 
                                       6788******************************************778889*******94436677777777444. PP

                            AAA_31  79 enl..dlipssidLaeaeielvelekkeeil.kellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeay 152
                                       e    dl+ps+  L +++  ++++++ e  l ++l++ ++d+YD i++D+pP++g l++ aLva    + p+q ++ 
  gi|336252274|ref|YP_004595381.1|  81 EPWgvDLVPSNAALHQVSATIQTADDGEAKLyRSLVRPLSDRYDWIVFDAPPTIGPLADAALVATRRAVLPMQLSKP 157
                                       33346********************99999878899*************************************9877 PP

                            AAA_31 153 aleGl 157
                                       + + l
  gi|336252274|ref|YP_004595381.1| 158 SADAL 162
                                       76664 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 !   65.6   0.0   4.9e-21   4.4e-18       2     101 ..       5     210 ..       4     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 4.9e-21
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       +++ +kGGvGKTt+a+nLa  la rg++V+lvD+Dpq+++++ l     + +                         
  gi|336252274|ref|YP_004595381.1|   5 TVMLQKGGVGKTTIATNLADRLAARGHEVVLVDVDPQGSATEALGCGDAYTADthlahvldpddpssasdllrtdte 81 
                                       67789*************************************866666666668999999999************** PP

                                       ............................................................................C CS
                                       ............................................................................x RF
                              CbiA  55 ............................................................................d 55 
                                                                                                                   +
  gi|336252274|ref|YP_004595381.1|  82 pwgvdlvpsnaalhqvsatiqtaddgeaklyrslvrplsdrydwivfdapptigpladaalvatrravlpmqlskpS 158
                                       *********************************************************************88888887 PP

                                       CHCCCHHHHHHCHCHHHH........EEEEEEEEESS...-TTCHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  56 lkrllellealgkkkall......lkiagvvlnrvdgeneetllkealeelk 101
                                       ++ l++++ +   ++++       ++i+ +v+nrv+g+nee++  eale+ +
  gi|336252274|ref|YP_004595381.1| 159 ADALVRTVTNQLFPLSDRlpdsdpIEILAIVPNRVKGDNEERRVLEALEDSQ 210
                                       7777777744443444447888**************************9976 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.1   1.5e-11   1.3e-08       5     151 ..       5     161 ..       1     175 [. 0.70

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.5e-11
                          CBP_BcsQ   5 alqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnv..dieqregwaraeldgapwrqaaleyap.. 77 
                                       ++   +GGvG+t++++ La+ l + g++v+++D+ p+   +       +++ ++ +a+ +  + p +++ l  ++  
  gi|336252274|ref|YP_004595381.1|   5 TVMLQKGGVGKTTIATNLADRLAARGHEVVLVDVDPQGSATEALGCgdAYTADTHLAHVLDPDDPSSASDLLRTDte 81 
                                       555568****************************9987766555541044444444444444444444433222234 PP

                          CBP_BcsQ  78 ..gldllPfGelnveekenlqqlaekaeallaa.lkelkeqyrwillDlpagasaltrellaladlv...llvvepd 148
                                         g+dl+P  ++ ++  +++q+ ++ + +l +  ++ l+ +y+wi++D p    +l+ ++l  + +    +++ +p 
  gi|336252274|ref|YP_004595381.1|  82 pwGVDLVPSNAALHQVSATIQTADDGEAKLYRSlVRPLSDRYDWIVFDAPPTIGPLADAALVATRRAvlpMQLSKPS 158
                                       4589*****999999999999988887777666156799*************9999998876554441114555555 PP

                          CBP_BcsQ 149 anc 151
                                       a +
  gi|336252274|ref|YP_004595381.1| 159 ADA 161
                                       555 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 !   34.1   0.1   2.1e-11   1.8e-08       6      46 ..       4      44 ..       1      71 [. 0.86
   2 ?   -1.3   0.0       1.4   1.2e+03     111     124 ..     122     135 ..      93     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.1e-11
                              ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGps 46
                                      ++v+  KGGVGK+t+a+nlA  La++g++v l+D+D  G  
  gi|336252274|ref|YP_004595381.1|  4 LTVMLQKGGVGKTTIATNLADRLAARGHEVVLVDVDPQGSA 44
                                      678999******************************99965 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                              ParA 111 elDyLiiDlPPGtg 124
                                         D+++ D PP  g
  gi|336252274|ref|YP_004595381.1| 122 RYDWIVFDAPPTIG 135
                                       569999****9876 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.3   1.8e-10   1.6e-07       8     135 ..       9     133 ..       4     150 .. 0.65

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.8e-10
                                       ESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS.--BSS-EEETSSEEEEE--HH..HHHHHHHCCHH CS
                       ArsA_ATPase   8 GKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdq.klgkeptkvkeNLsavEidpe..veleeakqevq 81 
                                        KGGVGKtt+++ +a +l+  g++v+l+ +DP  s   ++   ++    t +     a  +dp+    ++   +  +
  gi|336252274|ref|YP_004595381.1|   9 QKGGVGKTTIATNLADRLAARGHEVVLVDVDPQGSATEALGCgDAYTADTHL-----AHVLDPDdpSSASDLLRTDT 80 
                                       59*******************************9999998872222222222.....33355552233333333333 PP

                                       GGGSCCHHHHHHHHHHHHHHTSSTTHH..HHHHHHHHHHHHHCSSSSEEEEESBSC CS
                       ArsA_ATPase  82 keeeallgleeledvlaeelaslPGid..eilsfeellkyvkeeeydvvvlDtaPT 135
                                       +  +  + l   + +l++ +a++   d  e+  + +l++ + ++ yd +v+D +PT
  gi|336252274|ref|YP_004595381.1|  81 EPWG--VDLVPSNAALHQVSATIQTADdgEAKLYRSLVRPL-SDRYDWIVFDAPPT 133
                                       3333..33334445555555555555522455566666655.57788888888888 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   3.9e-06    0.0035       8      40 ..       9      41 ..       4      61 .. 0.88
   2 !    8.9   0.0   0.00095      0.85      70     130 ..      94     153 ..      78     170 .. 0.78
   3 ?    2.5   0.0      0.08        72     211     236 ..     232     257 ..     230     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.9e-06
                                      SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TT CS
                              MipZ  8 ekGGsGksttavhvavaLlkkGarvaaidldlr 40
                                      +kGG Gk+t+a  +a  L+++G++v  +d+d +
  gi|336252274|ref|YP_004595381.1|  9 QKGGVGKTTIATNLADRLAARGHEVVLVDVDPQ 41
                                      7*****************************964 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00095
                                       SSS-HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEE CS
                              MipZ  70 lseaeeaeveeeeeaevaeleelvadleaeldfividtPGsdsalsrlahsladtlvtPln 130
                                       l++  +a+++  ++ e +  + lv+ l+ ++d+iv+d+P +  +l+  a       v P+ 
  gi|336252274|ref|YP_004595381.1|  94 LHQ-VSATIQTADDGEAKLYRSLVRPLSDRYDWIVFDAPPTIGPLADAALVATRRAVLPMQ 153
                                       444.345677777888778899*****************9999999998888888888876 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.08
                                       ---B--GGGTTTGGGT--GGGSSSS- CS
                              MipZ 211 sGlserviyrelfpsGltlldlkelg 236
                                       +G++er+ +r  +  G+ l+  +e++
  gi|336252274|ref|YP_004595381.1| 232 PGIRERIAFRRAYRDGVSLAAHDETV 257
                                       79***************998766654 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 !   20.5   0.0   2.9e-07   0.00026       7      46 ..       9      48 ..       5      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.9e-07
                         Fer4_NifH  7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrll 46
                                       kGG+Gk+t ++nl+  la++g+ v++v  DP+  +t  l
  gi|336252274|ref|YP_004595381.1|  9 QKGGVGKTTIATNLADRLAARGHEVVLVDVDPQGSATEAL 48
                                      69*******************************9999766 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 !   20.6   0.0   3.3e-07    0.0003       4      34 ..      12      42 ..      10      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.3e-07
                            CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDvGq 34
                                       +GK+T+a++L+++++ +g+++v+vD+D+  
  gi|336252274|ref|YP_004595381.1| 12 GVGKTTIATNLADRLAARGHEVVLVDVDPQG 42
                                      59**************************965 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 !   16.0   0.1     5e-06    0.0045      38      72 ..      11      45 ..       3      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5e-06
                                      TTSSHHHHHHHHHHHHHCTT--EEEEEE------- CS
                              MeaB 38 PGaGkstlvealglelrrrGkrvavlavDPsspft 72
                                       G+Gk t+  +l+ +l++rG+ v ++ vDP  + t
  gi|336252274|ref|YP_004595381.1| 11 GGVGKTTIATNLADRLAARGHEVVLVDVDPQGSAT 45
                                      59****************************87766 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 !   15.4   0.1   1.1e-05      0.01       4      85 ..      16      98 ..      12     113 .. 0.77
   2 ?   -3.6   0.0       7.3   6.5e+03     140     159 ..     151     170 ..     141     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                      TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE...EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                      adh_short_C2  4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev...lecDVtdeeqvealveevvekfgklDilvnnag 78
                                        I+  +A +la++G evvl+d++ ++ + ++    +++ a+      +D  d+++  +l ++ +e + ++D +  na+
  gi|336252274|ref|YP_004595381.1| 16 TTIATNLADRLAARGHEVVLVDVDPQGsATEALGCGDAYTADThlaHVLDPDDPSSASDLLRTDTEPW-GVDLVPSNAA 93
                                      679************************77777777788877732357888888888888888877777.6899999999 PP

                                      --EGCSS CS
                      adh_short_C2 79 iapklkg 85
                                        +   +
  gi|336252274|ref|YP_004595381.1| 94 LHQV--S 98
                                      8876..4 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.3
                                       HHHHHHHHHHHHHHHHHHHH CS
                      adh_short_C2 140 aygaaKaalealtrylAvel 159
                                        ++ +K +  al+r++ ++l
  gi|336252274|ref|YP_004595381.1| 151 PMQLSKPSADALVRTVTNQL 170
                                       68889999999999887776 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.1e-05     0.019       9      39 ..      10      40 ..       3      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                                      STTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  9 lqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                        G+GKTt ++ La++l ++g++v+lv +D 
  gi|336252274|ref|YP_004595381.1| 10 KGGVGKTTIATNLADRLAARGHEVVLVDVDP 40
                                      569************************9885 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.4e-05     0.022       1      39 [.       1      39 [.       1      46 [. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                             VirC1  1 mklitfcslkGGaGkttalmglcsalasdgkrvalfead 39
                                      m+ +t+   kGG Gktt    l   la++g+ v l + d
  gi|336252274|ref|YP_004595381.1|  1 MNGLTVMLQKGGVGKTTIATNLADRLAARGHEVVLVDVD 39
                                      777899999***************************998 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.8e-05     0.025       6      37 ..      17      48 ..      11     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
                    Glyco_transf_4  6 rhvleLaraLarrGheVtvvtpgddgpleeev 37
                                      + + +La +La+rGheV++v  +++g + e+ 
  gi|336252274|ref|YP_004595381.1| 17 TIATNLADRLAARGHEVVLVDVDPQGSATEAL 48
                                      6789****************666666555554 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.6e-05      0.05       6      36 ..      12      43 ..      11      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.6e-05
                                      TSSHHHHHHHHHHHHHHTTE..EEEESSSTTS CS
                   Thymidylate_kin  6 GaGKttqaellkerlkeegik.vvltrepggt 36
                                      G+GKtt+a +l++rl ++g++ v++   p+g+
  gi|336252274|ref|YP_004595381.1| 12 GVGKTTIATNLADRLAARGHEvVLVDVDPQGS 43
                                      89*******************77777777766 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 ?   11.8   4.6   0.00026      0.24       4      95 ..      16     145 ..      11     152 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                   Glyco_trans_4_4   4 gryvaelaraLaarGheVtvltpapapg.............................apeleedgvrvhrlpvprrp 51 
                                       ++ + +la +LaarGheV+++  +p+++                             + +l +   + +++++ ++ 
  gi|336252274|ref|YP_004595381.1|  16 TTIATNLADRLAARGHEVVLVDVDPQGSatealgcgdaytadthlahvldpddpssaS-DLLRTDTEPWGVDLVPSN 91 
                                       455699*************998444444222333333333333333333322111110.111111222233333332 PP

                   Glyco_trans_4_4  52 spladlaal........ral.rrllrqrrerpdvvhahs.ptaglaarlarrrr 95 
                                       + l  ++a+        + l r+l+r  + r+d ++    pt+g++a +a +++
  gi|336252274|ref|YP_004595381.1|  92 AALHQVSATiqtaddgeAKLyRSLVRPLSDRYDWIVFDApPTIGPLADAALVAT 145
                                       222233333444444443332444466799999888888557777777666443 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.12      10      96 ..      16     103 ..      12     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                       SHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE- CS
                         adh_short  10 sGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklgkldvLvnN 84 
                                         I  ++a++la++G +vv+vd  ++  ++ a  ++++  +++ la  +D  d +++++l+++  + +g +d++  N
  gi|336252274|ref|YP_004595381.1|  16 TTIATNLADRLAARGHEVVLVDVDPQGSATEALGCGDAytADTHLAHVLDPDDPSSASDLLRTDTEPWG-VDLVPSN 91 
                                       67999********************999999999999987777888899999*******9999887776.9****** PP

                                       --SS--SSGGGC CS
                         adh_short  85 AGitgsgpfsel 96 
                                       A++++++++ ++
  gi|336252274|ref|YP_004595381.1|  92 AALHQVSATIQT 103
                                       **9766655444 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   0.2   0.00018      0.16      33      97 ..      11      75 ..      10     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                            AAA_16 33 sGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleaw 97
                                       GvGK+++++ l+++l ++g  ++  + d  +sa++ +   +a ++++ l+ +ld+++ +++++ 
  gi|336252274|ref|YP_004595381.1| 11 GGVGKTTIATNLADRLAARGHEVVLVDVDPQGSATEALGCGDAYTADTHLAHVLDPDDPSSASDL 75
                                      59*****************8777888888888888888888888777777777777444333332 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 ?   10.4   0.0   0.00044       0.4       6      35 ..      12      41 ..      10      48 .. 0.92
   2 ?   -1.8   0.0       2.4   2.1e+03      62      99 ..      94     131 ..      85     131 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
                        ATP_bind_1  6 GsGKttfvgalseilelrgrsvavvNLDPA 35
                                      G+GKtt+  +l++ l +rg +v +v  DP 
  gi|336252274|ref|YP_004595381.1| 12 GVGKTTIATNLADRLAARGHEVVLVDVDPQ 41
                                      9***************************95 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.4
                        ATP_bind_1  62 lgpngalvvaleflresl.dwldeelekeed..dyllfDtP 99 
                                       l +  a++  ++ ++ +l   l + l   +d  d+++fD P
  gi|336252274|ref|YP_004595381.1|  94 LHQVSATIQTADDGEAKLyRSLVRPL---SDryDWIVFDAP 131
                                       55556777777778888844444444...443699999998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00024      0.21       8      30 ..      12      43 ..      10     103 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                            AAA_18  8 GvGKttlakeLskrlgf.........gvnlrd 30
                                      GvGKtt+a +L++rl+          ++  ++
  gi|336252274|ref|YP_004595381.1| 12 GVGKTTIATNLADRLAArghevvlvdVDPQGS 43
                                      9*************944477555555444444 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 ?   10.2   0.0   0.00028      0.25      24      58 ..      11      47 ..       4      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00028
                     TrwB_AAD_bind 24 tGsGKtqalekllrairargdraivlD..ltGafvsr 58
                                       G GKt+ +++l + + arg+ ++ +D  ++G  +++
  gi|336252274|ref|YP_004595381.1| 11 GGVGKTTIATNLADRLAARGHEVVLVDvdPQGSATEA 47
                                      599********************99762267887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2033.69
//
Query:       gi|336252275|ref|YP_004595382.1|  [L=41]
Description: hypothetical protein Halxa_0864 [Halopiger xanaduensis SH-6]
Scores for 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:                        70  (0.00390429); expected 358.6 (0.02)
Passed bias filter:                       60  (0.00334653); 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: 0.33u 0.19s 00:00:00.52 Elapsed: 00:00:00.36
# Mc/sec: 345.72
//
Query:       gi|336252276|ref|YP_004595383.1|  [L=447]
Description: type I phosphodiesterase/nucleotide pyrophosphatase [Halopiger xanaduensis SH-6]
Scores for complete 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  205.4   0.1    2.1e-60  205.2   0.1    1.0  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
  ------ inclusion threshold ------
      0.039   14.1   0.0      0.083   13.1   0.0    1.5  1  DUF2990       Protein of unknown function (DUF2990)
      0.043   13.2   1.2       0.42    9.9   0.1    2.3  2  Sulfatase     Sulfatase


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.2   0.1   3.6e-64   2.1e-60       1     357 []      15     403 ..      15     403 .. 0.86

  Alignments for each domain:
  == domain 1  score: 205.2 bits;  conditional E-value: 3.6e-64
                                       EEEEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEE CS
                      Phosphodiest   1 vlvislDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgeyv 77 
                                       v +i++DG++ +ll +  +l pn+aa+a+ g+ ++ + +++P+++ +++ sl TG +Pge+G++g  f dr+ g y 
  gi|336252276|ref|YP_004595383.1|  15 VAFIGVDGVPYSLLAENEDLFPNFAAIADDGTAGE-ISSIVPPESSACWPSLTTGVNPGETGVYG--FQDREVGTYD 88 
                                       578*************546****************.*****************************..8899999999 PP

                                       EEETTTTGGGGGCTTS-HHHHHHHTHTTCEEEESETTTTSEBTTCT.SC..........TBHHSBTCT......... CS
                      Phosphodiest  78 vfvtededaprwwqgepiwdtaakarglkaaalfwpgsevdystyyylvs.........etppryled......... 136
                                       ++v+  +d    +q +++wd+++ + g+ a ++++p + ++ ++ +++vs           +p+ +++         
  gi|336252276|ref|YP_004595383.1|  89 TYVPMGRD----VQADRVWDRVQEE-GRQATVMNVPVTFPPERNVQRMVSgflspglekAAHPDDVREylegldyri 160
                                       *****999....9************.************************999999888555555544677785556 PP

                                       .CSTTSCHHHHHHHHHHHHHHHCHTHSHHHHHCT.......SSESEEEEEECCCHHHHHHH.......-TTSHHHHH CS
                      Phosphodiest 137 dfnakvpledkvdkavlqtwldaafakvvlekel.......ekpdlllvyleetDtvgHkf.......Gpdspeved 199
                                       d+n k+++++++++ ++++  ++ +a+ +            +++dl++++++ tD+v H +       G ++ e+ +
  gi|336252276|ref|YP_004595383.1| 161 DVNPKLGHQEDKSE-FIEDAHATVDARFE----AfrhyieeDDWDLFFGVFMTTDRVNHFLfkdyerdGEYKDEFIE 232
                                       66666677777766.55455444544433....23355899******************995555555566888*** PP

                                       HHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEHTTSEEEGGGTSTGGHGEEEEECBHHS.SSE........ CS
                      Phosphodiest 200 alrrvDkaigdLlealderglsaetniilvSDHGmadvsddkvielndlleekgllhlkdegkggakal........ 268
                                        +++vD++ig+L+e+l+e+     +++i++SDHG++++  d+ +++n++l+e+g+l+ k++  +   ++        
  gi|336252276|ref|YP_004595383.1| 233 FYQKVDDYIGRLRESLPED-----VTMIVASDHGFTSL--DYEVHFNEWLRENGWLSFKTDDPEELGDIsddtkays 302
                                       *******************.....**************..**************66666666666666666666677 PP

                                       .....EEEEESTEE.E.CCCTTHHHHHHHHHHTCHHCCHSTHTT..TEEEEEGG.GS-GGGCHSTTS-SEEEEE-TT CS
                      Phosphodiest 269 .....iainpkare.lnrvaeaeaeevyaelkakleelrkkege..alavylke.aipkrlhykkrapdlvlvadpg 336
                                             +in+++re ++ v+e+e++ev+++lk+ l+el  +eg+    +v +ke a+++++   + apdlv++++ g
  gi|336252276|ref|YP_004595383.1| 303 fipgrFYINLEGREpRGSVPEEEYDEVRDQLKSELLELEGPEGRqvVDRVVEKEdAFRGDHD--DIAPDLVAIPNKG 377
                                       77888*****************************9998744777779999999989****99..************* PP

                                       EEEESSTTCS.....SBS-SEE--SS CS
                      Phosphodiest 337 wsitskdkpd.....eyeikgthGyd 357
                                       + + s+ k+d     +    g+h++d
  gi|336252276|ref|YP_004595383.1| 378 FDLKSGFKGDaeifdTGPRNGMHSFD 403
                                       ********998888777777777765 PP

>> DUF2990  Protein of unknown function (DUF2990)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.083      20      44 ..     225     249 ..     220     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                           DUF2990  20 dfsdeLaefygkVskyIeeakdsik 44 
                                       ++ de+ efy+kV+ yI + ++s++
  gi|336252276|ref|YP_004595383.1| 225 EYKDEFIEFYQKVDDYIGRLRESLP 249
                                       699***************9988765 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   7.1e-05      0.42     208     252 ..     208     263 ..     121     285 .. 0.79
   2 ?    2.0   0.1     0.019   1.1e+02     294     309 .]     419     434 ..     403     434 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7.1e-05
                                       H................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSC CS
                         Sulfatase 208 r................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgas 252
                                       +                ++ +++  +   vDd igr+ + L      +++++++ SDhg  
  gi|336252276|ref|YP_004595383.1| 208 TtdrvnhflfkdyerdgEYKDEFIEFYQKVDDYIGRLRESL-----PEDVTMIVASDHGFT 263
                                       044444455555555558889999999**************.....*************65 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.019
                                       EEGGGHHHHHHHHTTE CS
                         Sulfatase 294 vshiDlfptildlagi 309
                                       +++ D++ptildl+++
  gi|336252276|ref|YP_004595383.1| 419 ADLFDITPTILDLMDV 434
                                       5689*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3546.90
//
Query:       gi|336252277|ref|YP_004595384.1|  [L=66]
Description: hypothetical protein Halxa_0866 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.29   11.2   1.1       0.35   10.9   1.0    1.5  1  OppC_N           N-terminal TM domain of oligopeptide transpo
        0.5   10.4   8.5       0.55   10.3   8.5    1.0  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        8.4    5.6   5.8        9.6    5.5   5.8    1.0  1  DUF4407          Domain of unknown function (DUF4407)
        8.7    6.3  10.5        1.6    8.7   1.6    2.4  2  DUF1072          Protein of unknown function (DUF1072)


Domain annotation for each model (and alignments):
>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.0   7.9e-05      0.35      13      36 ..       2      25 ..       1      55 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.9e-05
                            OppC_N 13 NklAvvglvilllllliaifaPli 36
                                      N +Av+g ++ll++l++ +++ l 
  gi|336252277|ref|YP_004595384.1|  2 NDTAVIGGCMLLTMLAAGFVGLLT 25
                                      789*************99887555 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 ?   10.3   8.5   0.00012      0.55      32      86 ..       4      59 ..       2      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                   Phage_holin_3_6 32 ragsgagllgaagvlallalllllvalalala.alwlaalivaavllvlagvlalv 86
                                       a++g+++l+  ++ ++++ll+ + a ++a + +  + +l v++  ++ a+v a++
  gi|336252277|ref|YP_004595384.1|  4 TAVIGGCMLLTMLAAGFVGLLTGSYATVFAGTpVGFAVYLAVGIGNVLGAIVRAFR 59
                                      5899************************9998789999999999999999887765 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   5.8    0.0021       9.6      14      57 ..       5      55 ..       2      63 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0021
                           DUF4407 14 agiGavvlltallAalsgayAlytvlkspll.......lallvGllwgllI 57
                                      a iG+ +llt+l A+++g +  ++++    +       la+ +G + g+++
  gi|336252277|ref|YP_004595384.1|  5 AVIGGCMLLTMLAAGFVGLLTGSYATVFAGTpvgfavyLAVGIGNVLGAIV 55
                                      679************999887666555555222434444444444444444 PP

>> DUF1072  Protein of unknown function (DUF1072)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.6   0.00035       1.6       1      25 [.       1      26 [.       1      27 [. 0.86
   2 ?    2.5   1.9      0.03   1.4e+02      15      24 ..      30      41 ..      28      55 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00035
                           DUF1072  1 MdDLHVIAvCvLalTvlag..igavag 25
                                      M+D  VI  C+L lT la+  +g+  g
  gi|336252277|ref|YP_004595384.1|  1 MNDTAVIGGCML-LTMLAAgfVGLLTG 26
                                      9***********.88998879888665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.03
                           DUF1072 15 Tvlag..igava 24
                                      Tv+ag  +g ++
  gi|336252277|ref|YP_004595384.1| 30 TVFAGtpVGFAV 41
                                      9****8866554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 519.07
//
Query:       gi|336252278|ref|YP_004595385.1|  [L=137]
Description: hypothetical protein Halxa_0867 [Halopiger xanaduensis SH-6]
Scores for complete 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-52  177.0   0.1    1.7e-52  176.9   0.1    1.0  1  DUF371    Domain of unknown function (DUF371)


Domain annotation for each model (and alignments):
>> DUF371  Domain of unknown function (DUF371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.9   0.1   9.6e-57   1.7e-52       1     133 []       5     137 .]       5     137 .] 0.99

  Alignments for each domain:
  == domain 1  score: 176.9 bits;  conditional E-value: 9.6e-57
                                       EEEE--TT-----SSEEEEES-S---TT-TTEEEBS-S--GGGS-HHHHHHHS----EEEEEEE-SS-EEEEEEE-- CS
                            DUF371   1 ikarGHenvkaehksTleitkddeltprgdCIigveadkaaadlseelkealkeeeatitvtlevgeledeitgrGs 77 
                                       i+arGHenv+aeh+sT+e+t+dd+ltp+gdCI+++ead+a+ad++ ++ +a++++eatit+++e+++++d+++grG+
  gi|336252278|ref|YP_004595385.1|   5 IHARGHENVSAEHASTFEVTTDDYLTPAGDCILAIEADRAPADFDPDFIAACQDREATITFEIEADGHRDSVVGRGD 81 
                                       79*************************************************************************** PP

                                       TT-----SSEEEEESSS---TTEEEBS-S--GGGS-HHHHHHHHTT-EEEEEEEEE CS
                            DUF371  78 pkltlenerdlvvRkSdyvddrTllvkadkaaadldrelveaLkkgaeltveleve 133
                                       p+l+++ner++v R+S+yvddrT++  a  aa+ +drelveaL++gae+tv+++ve
  gi|336252278|ref|YP_004595385.1|  82 PDLEFTNERSAVGRTSEYVDDRTIMNGAAFAAEGFDRELVEALADGAEATVTITVE 137
                                       *****************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1019.64
//
Query:       gi|336252279|ref|YP_004595386.1|  [L=61]
Description: hypothetical protein Halxa_0868 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00049   20.0   2.8      0.048   13.6   0.1    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
     0.0012   18.9   1.4     0.0015   18.6   1.4    1.1  1  CpXC            CpXC protein
     0.0051   16.7   0.8       0.18   11.7   0.0    2.1  2  Cys_rich_CPXG   Cysteine-rich CPXCG
     0.0093   15.9   2.8        2.1    8.4   0.3    2.3  2  zinc_ribbon_4   zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   16.0   1.1       0.49   10.7   0.1    2.2  2  zinc_ribbon_9   zinc-ribbon
      0.015   15.2   6.4       0.26   11.2   1.0    2.2  2  zf-C2HC_2       zinc-finger of a C2HC-type
      0.016   14.6   1.9        3.2    7.3   0.2    2.3  2  zf-ribbon_3     zinc-ribbon domain
      0.043   14.7   4.9        2.4    9.2   0.1    2.2  2  zf-C2H2_4       C2H2-type zinc finger
      0.048   13.6   6.5        1.3    9.0   0.4    2.2  2  Nudix_N_2       Nudix N-terminal
      0.061   14.0   8.0       0.22   12.2   0.6    2.1  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
      0.068   13.2   4.5       0.19   11.8   4.5    1.7  1  Elf1            Transcription elongation factor Elf1 like
      0.075   13.5   2.4        4.5    7.9   0.3    2.2  2  zf-H2C2_2       Zinc-finger double domain
      0.079   12.7   4.6       0.83    9.5   0.4    2.3  2  zinc_ribbon_2   zinc-ribbon domain
       0.11   12.8   3.8       0.25   11.7   0.1    2.0  2  GFA             Glutathione-dependent formaldehyde-activating
       0.12   12.3   4.5       0.32   11.0   0.7    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.13   12.2   2.5        1.3    9.0   0.1    2.2  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.13   12.4   2.6        7.2    6.8   0.1    2.3  2  Zn-ribbon_8     Zinc ribbon domain
       0.45   10.2   4.5          2    8.1   0.6    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.47   10.0   5.6        6.6    6.3   5.6    2.1  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.55   10.8   4.4         14    6.4   0.2    2.3  2  zf-C2H2         Zinc finger, C2H2 type
       0.56   10.2   5.0        2.5    8.1   4.9    2.0  1  ADK_lid         Adenylate kinase, active site lid
        1.1    9.6   6.6        0.6   10.4   0.8    2.1  2  zf-LITAF-like   LITAF-like zinc ribbon domain
        5.6    6.9   6.3       0.77    9.7   1.5    1.8  2  RseC_MucC       Positive regulator of sigma(E), RseC/MucC


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 !   13.6   0.1   6.2e-05     0.048      17      34 ..       3      20 ..       2      28 .. 0.82
   2 !    7.3   0.3     0.006       4.7      19      35 ..      40      58 ..      32      61 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.2e-05
                     Zn_Tnp_IS1595 17 ngfvCPhCgsrkayrikt 34
                                      +++vCPhC  +++  i++
  gi|336252279|ref|YP_004595386.1|  3 QRVVCPHCSEKTFVDINR 20
                                      6799*****999999987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.006
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayrikt..r 35
                                       +C +Cg + a+++++  r
  gi|336252279|ref|YP_004595386.1| 40 GTCSKCGEKFACKVADpsR 58
                                      57*****999999888443 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.4   1.9e-06    0.0015       1      49 [.       5      51 ..       5      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                              CpXC  1 ltCpaCgkefeaeiwtsidadedpelkeklldgslfeatCpkCgatakl 49
                                      + Cp+C++++ ++i + ++ +  +  +  l dg  ++ tC kCg++++ 
  gi|336252279|ref|YP_004595386.1|  5 VVCPHCSEKTFVDINRKVQRT--KTEVGTLNDGYDRSGTCSKCGEKFAC 51
                                      67*************988765..667999****************9976 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00023      0.18       2      15 ..       6      19 ..       5      27 .. 0.78
   2 ?    3.8   0.1      0.07        54       2      14 ..      41      53 ..      41      60 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                     Cys_rich_CPXG  2 qCPyCgeeievlvD 15
                                       CP+C e++ v+++
  gi|336252279|ref|YP_004595386.1|  6 VCPHCSEKTFVDIN 19
                                      7******9888776 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.07
                     Cys_rich_CPXG  2 qCPyCgeeievlv 14
                                      +C  Cge++   v
  gi|336252279|ref|YP_004595386.1| 41 TCSKCGEKFACKV 53
                                      5999****98876 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1    0.0035       2.7       2      11 ..       4      13 ..       4      29 .. 0.80
   2 !    8.4   0.3    0.0026       2.1      27      35 ..      41      49 ..      38      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0035
                     zinc_ribbon_4  2 kitCpsCkak 11
                                      +++Cp+C+ k
  gi|336252279|ref|YP_004595386.1|  4 RVVCPHCSEK 13
                                      689****876 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0026
                     zinc_ribbon_4 27 rCskCghvF 35
                                      +CskCg++F
  gi|336252279|ref|YP_004595386.1| 41 TCSKCGEKF 49
                                      699999998 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00063      0.49      20      33 ..       4      17 ..       1      18 [. 0.68
   2 ?    4.6   0.1      0.05        39      22      31 ..      39      49 ..      22      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00063
                     zinc_ribbon_9 20 sdvlCPhCg.ggFVE 33
                                      + v CPhC    FV 
  gi|336252279|ref|YP_004595386.1|  4 RVV-CPHCSeKTFVD 17
                                      445.****6369985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.05
                     zinc_ribbon_9 22 v.lCPhCgggF 31
                                      + +C  Cg  F
  gi|336252279|ref|YP_004595386.1| 39 SgTCSKCGEKF 49
                                      458*****998 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 ?    7.1   0.4    0.0065       5.1       2      10 ..       4      12 ..       3      13 .. 0.81
   2 ?   11.2   1.0   0.00034      0.26       4      15 ..      41      52 ..      40      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0065
                         zf-C2HC_2  2 lvpCpkCgR 10
                                      +v Cp+C+ 
  gi|336252279|ref|YP_004595386.1|  4 RVVCPHCSE 12
                                      789****96 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00034
                         zf-C2HC_2  4 pCpkCgRsFnpd 15
                                       C kCg +F+ +
  gi|336252279|ref|YP_004595386.1| 41 TCSKCGEKFACK 52
                                      5********976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0055       4.3      17      22 ..       5      10 ..       2      14 .. 0.76
   2 ?    7.3   0.2    0.0041       3.2       5      10 ..      42      47 ..      38      50 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0055
                       zf-ribbon_3 17 nvCpyC 22
                                      +vCp+C
  gi|336252279|ref|YP_004595386.1|  5 VVCPHC 10
                                      689998 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0041
                       zf-ribbon_3  5 CPnCGa 10
                                      C++CG+
  gi|336252279|ref|YP_004595386.1| 42 CSKCGE 47
                                      666665 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 ?    9.2   0.1     0.003       2.4       2      14 ..       6      19 ..       5      24 .. 0.82
   2 ?    6.9   1.5     0.017        13       2      14 ..      41      53 ..      41      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.003
                         zf-C2H2_4  2 kCpiC.gksFsskk 14
                                       Cp+C  k+F + +
  gi|336252279|ref|YP_004595386.1|  6 VCPHCsEKTFVDIN 19
                                      6****999998765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.017
                         zf-C2H2_4  2 kCpiCgksFsskk 14
                                      +C+ Cg+ F +k 
  gi|336252279|ref|YP_004595386.1| 41 TCSKCGEKFACKV 53
                                      5********9985 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   0.4    0.0017       1.3      21      29 ..       3      11 ..       1      12 [. 0.88
   2 ?    7.7   1.1    0.0042       3.3       3      17 ..      42      56 ..      42      61 .] 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                                      -EEEETTTT CS
                         Nudix_N_2 21 eRlvCpaCg 29
                                      +R vCp+C+
  gi|336252279|ref|YP_004595386.1|  3 QRVVCPHCS 11
                                      8*******6 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0042
                                      -TTT--B-EEE--TT CS
                         Nudix_N_2  3 CsqCGtpvelripdg 17
                                      Cs+CG++ + ++ d 
  gi|336252279|ref|YP_004595386.1| 42 CSKCGEKFACKVADP 56
                                      *******99999654 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 ?   12.2   0.6   0.00029      0.22       2      22 ..       4      24 ..       3      28 .. 0.80
   2 ?    6.1   1.5     0.022        17       3      18 ..      40      56 ..      38      61 .] 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00029
                           zf-ISL3  2 phrCPnCgsktvvkhgkkerr 22
                                      + +CP+C +kt v+  +k +r
  gi|336252279|ref|YP_004595386.1|  4 RVVCPHCSEKTFVDINRKVQR 24
                                      689*******99887776665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.022
                           zf-ISL3  3 hrCPnCgsk.tvvkhgk 18
                                       +C +Cg+k   ++ + 
  gi|336252279|ref|YP_004595386.1| 40 GTCSKCGEKfACKVADP 56
                                      79*******85555554 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   4.5   0.00024      0.19      21      60 ..       4      54 ..       1      59 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                              Elf1 21 kFdCpfCnheksvevkldkkek...........iaevsCkvCgesfetkvn 60
                                      +  Cp+C++++ v+++ + ++              + +C++Cge+f +kv 
  gi|336252279|ref|YP_004595386.1|  4 RVVCPHCSEKTFVDINRKVQRTktevgtlndgyDRSGTCSKCGEKFACKVA 54
                                      567*******9999987666556687777777656668**********986 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 ?    6.1   0.1      0.02        16      15      24 ..       5      15 ..       2      17 .. 0.80
   2 ?    7.9   0.3    0.0058       4.5      16      25 ..      41      50 ..      21      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.02
                         zf-H2C2_2 15 yeCplCd.kaF 24
                                      + Cp C+ k+F
  gi|336252279|ref|YP_004595386.1|  5 VVCPHCSeKTF 15
                                      67*****7777 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0058
                         zf-H2C2_2 16 eCplCdkaFk 25
                                      +C++C+ +F+
  gi|336252279|ref|YP_004595386.1| 41 TCSKCGEKFA 50
                                      8********7 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   0.3     0.026        20       2       5 ..       7      10 ..       5      13 .. 0.69
   2 ?    9.5   0.4    0.0011      0.83      13      22 ..      39      48 ..      33      49 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.026
                     zinc_ribbon_2  2 CpnC 5 
                                      Cp+C
  gi|336252279|ref|YP_004595386.1|  7 CPHC 10
                                      8888 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                     zinc_ribbon_2 13 akFCpyCGtp 22
                                      +  C++CG++
  gi|336252279|ref|YP_004595386.1| 39 SGTCSKCGEK 48
                                      5568888876 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00031      0.25      48      80 ..       3      35 ..       1      41 [. 0.89
   2 ?    3.1   0.7      0.15   1.2e+02      50      62 ..      40      52 ..      34      60 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00031
                               GFA 48 trsfCpeCgsplyseesaapevvivrvGtlddp 80
                                      +r +Cp+C  + +++ +++ + +  +vGtl+d 
  gi|336252279|ref|YP_004595386.1|  3 QRVVCPHCSEKTFVDINRKVQRTKTEVGTLNDG 35
                                      6799***************99********9985 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.15
                               GFA 50 sfCpeCgsplyse 62
                                        C++Cg ++ ++
  gi|336252279|ref|YP_004595386.1| 40 GTCSKCGEKFACK 52
                                      68*****998875 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 ?    4.6   0.3     0.038        30      45      61 ..       3      19 ..       1      23 [. 0.81
   2 ?   11.0   0.7   0.00041      0.32       8      37 ..      18      48 ..      13      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.038
                    OrfB_Zn_ribbon 45 rtfkCpnCgfeadrDvn 61
                                      ++++Cp+C  +   D+n
  gi|336252279|ref|YP_004595386.1|  3 QRVVCPHCSEKTFVDIN 19
                                      6789****998877776 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00041
                    OrfB_Zn_ribbon  8 leykakeyGikveevnpay.TSktCseCgsk 37
                                      +  k ++   +v + n  y  S tCs+Cg+k
  gi|336252279|ref|YP_004595386.1| 18 INRKVQRTKTEVGTLNDGYdRSGTCSKCGEK 48
                                      567888888999999999999********97 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 ?    9.0   0.1    0.0016       1.3      25      35 ..       4      14 ..       3      16 .. 0.80
   2 ?    3.5   0.3     0.089        69      13      18 ..      41      46 ..      36      48 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                           DUF35_N 25 ravCphCgsdd 35
                                      r vCphC  ++
  gi|336252279|ref|YP_004595386.1|  4 RVVCPHCSEKT 14
                                      789****8766 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.089
                           DUF35_N 13 rCpdCG 18
                                       C++CG
  gi|336252279|ref|YP_004595386.1| 41 TCSKCG 46
                                      466665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0092       7.2      27      34 ..       5      12 ..       1      16 [. 0.69
   2 ?    5.9   0.4     0.017        14       8      16 ..      42      50 ..      36      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0092
                       Zn-ribbon_8 27 taCPeCgs 34
                                      ++CP+C +
  gi|336252279|ref|YP_004595386.1|  5 VVCPHCSE 12
                                      45****76 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.017
                       Zn-ribbon_8  8 CeeCghefe 16
                                      C +Cg++f 
  gi|336252279|ref|YP_004595386.1| 42 CSKCGEKFA 50
                                      999998885 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2      0.05        39       3      10 ..       5      12 ..       3      15 .. 0.83
   2 ?    8.1   0.6    0.0026         2       4      13 ..      41      50 ..      38      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.05
                            zf_UBZ  3 ylCerCgk 10
                                      ++C+ C +
  gi|336252279|ref|YP_004595386.1|  5 VVCPHCSE 12
                                      79****87 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0026
                            zf_UBZ  4 lCerCgkeip 13
                                      +C++Cg+++ 
  gi|336252279|ref|YP_004595386.1| 41 TCSKCGEKFA 50
                                      8******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 ?    6.3   5.6    0.0084       6.6       2      28 ..       6      48 ..       5      61 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0084
                                      EETTTTCEEC................HEE.TSTTCEEESSSSBE CS
                      TF_Zn_Ribbon  2 kCPnCgstnl................veD.pergelvCtdCGlV 28
                                      +CP C+ +++                ++D ++r   +C++CG+ 
  gi|336252279|ref|YP_004595386.1|  6 VCPHCSEKTFvdinrkvqrtktevgtLNDgYDR-SGTCSKCGEK 48
                                      8*****988668999999999998877775444.4479999986 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2     0.018        14       2      11 ..       6      16 ..       5      18 .. 0.84
   2 ?    5.8   0.6     0.027        21       2      10 ..      41      49 ..      41      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.018
                                      EETTTT.EEES CS
                           zf-C2H2  2 kCpdCg.ksFk 11
                                      +Cp+C+ k+F 
  gi|336252279|ref|YP_004595386.1|  6 VCPHCSeKTFV 16
                                      7*****88885 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.027
                                      EETTTTEEE CS
                           zf-C2H2  2 kCpdCgksF 10
                                      +C++Cg++F
  gi|336252279|ref|YP_004595386.1| 41 TCSKCGEKF 49
                                      7******99 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 ?    8.1   4.9    0.0032       2.5       1      30 [.       4      48 ..       4      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0032
                                      EEE-TTT--.EE...ETTTB--S...........STTB-TTT--. CS
                           ADK_lid  1 RrvCpkCGr.sY...hvvfnpPk...........veglCDkCGep 30
                                      R vCp C + ++   +++    k             g C kCGe+
  gi|336252279|ref|YP_004595386.1|  4 RVVCPHCSEkTFvdiNRKVQRTKtevgtlndgydRSGTCSKCGEK 48
                                      99****9988997666444555578888888888*********97 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   0.8   0.00077       0.6       3      25 ..       2      24 ..       1      33 [. 0.79
   2 ?    3.0   0.6      0.16   1.2e+02      55      67 ..      38      50 ..      31      53 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00077
                     zf-LITAF-like  3 ptqvdCpaCqqrvvTsveyksgk 25
                                      +++v Cp+C++++   +++k + 
  gi|336252279|ref|YP_004595386.1|  2 SQRVVCPHCSEKTFVDINRKVQR 24
                                      689********997777777654 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.16
                     zf-LITAF-like 55 vehyCpnCgallg 67
                                         +C++Cg++ +
  gi|336252279|ref|YP_004595386.1| 38 RSGTCSKCGEKFA 50
                                      5568999998765 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.62   4.9e+02      15      26 ..       3      14 ..       1      34 [. 0.74
   2 ?    9.7   1.5   0.00098      0.77      13      34 ..      36      55 ..      22      61 .] 0.78

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.62
                         RseC_MucC 15 rksaCgsCaaks 26
                                      ++  C +C++k 
  gi|336252279|ref|YP_004595386.1|  3 QRVVCPHCSEKT 14
                                      677899999764 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00098
                         RseC_MucC 13 ierksaCgsCaakssCklsale 34
                                      ++r+ +C++C++k +Ck+  ++
  gi|336252279|ref|YP_004595386.1| 36 YDRSGTCSKCGEKFACKV--AD 55
                                      57999***********55..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 487.08
//
Query:       gi|336252280|ref|YP_004595387.1|  [L=274]
Description: HhH-GPD family protein [Halopiger xanaduensis SH-6]
Scores for 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-17   62.7   0.0    7.8e-17   61.7   0.0    1.5  2  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    1.2e-05   25.5   7.4    2.7e-05   24.4   7.4    1.6  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
    4.8e-05   23.0   0.0    0.00014   21.5   0.0    1.8  1  HHH            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.079   13.6   0.1       0.22   12.2   0.0    1.8  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 !   61.7   0.0   1.7e-20   7.8e-17       1     105 [.      58     208 ..      58     211 .. 0.95
   2 ?   -3.9   0.0         4   1.8e+04      42      51 ..     246     255 ..     242     258 .. 0.76

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.7e-20
                                       HHHHHHTTS-HHHHHHHHHHHHHHHS...HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfg...fptpedladadeekLrelirelGfyrrKakyikelArilv........ 66 
                                       v++ilsq+tsd++  ++   l er+       +e+la+a+++ L+e i+++G+y++K + i+++A+ ++        
  gi|336252280|ref|YP_004595387.1|  58 VRTILSQNTSDKASQPAHDALIERYDgegIDLAESLAGAEQSILAETIQPAGLYNQKSEIIIDTAEWVLeafgsaaa 134
                                       799*************************87789******************************************** PP

                                       ....................................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHH CS
                                       ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ....................................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleel 105
                                                                           g+ + +++vD+hv+ri +rl+++ ++ +++ v++ le+ 
  gi|336252280|ref|YP_004595387.1| 135 fdefvkdedpaevretllevrgvgpktadcvllfagGRGG-VFPVDTHVHRIYRRLGIAPADADHEAVRAVLERE 208
                                       ***********************************97655.8899*********************999988765 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4
                                       HHHHTTSTTH CS
                                       xxxxxxxxxx RF
                           HhH-GPD  42 relirelGfy 51 
                                       ++l++++G+y
  gi|336252280|ref|YP_004595387.1| 246 ADLCEQVGVY 255
                                       5788888887 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   7.4     6e-09   2.7e-05       1      17 []     229     249 ..     229     249 .. 0.99

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6e-09
                     EndIII_4Fe-2S   1 CTARkPkC....eaCPLaDlC 17 
                                       C ARkP+C    eaCP+aDlC
  gi|336252280|ref|YP_004595387.1| 229 CSARKPACledpEACPMADLC 249
                                       99******************* PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   3.1e-08   0.00014      10      30 .]     148     168 ..     148     168 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.1e-08
                                       HHHHHTSTT-SHHHHHHHHHH CS
                               HHH  10 reeLlalPGVGpktAeaIlsy 30 
                                       re Ll++ GVGpktA+++l +
  gi|336252280|ref|YP_004595387.1| 148 RETLLEVRGVGPKTADCVLLF 168
                                       799***************976 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1         4   1.8e+04      22      38 ..      86     102 ..      83     104 .. 0.62
   2 ?   12.2   0.0   4.8e-05      0.22      33      53 ..     147     167 ..     120     170 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4
                                       T--SHHHHHHS-HHHHH CS
                             HHH_5  22 GiesvedlaaadveeLa 38 
                                       Gi+  e la a++  La
  gi|336252280|ref|YP_004595387.1|  86 GIDLAESLAGAEQSILA 102
                                       56666677777666555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.8e-05
                                       -HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5  33 dveeLakipGiGkktAeriil 53 
                                        +e+L ++ G+G+ktA+ ++l
  gi|336252280|ref|YP_004595387.1| 147 VRETLLEVRGVGPKTADCVLL 167
                                       346799999999999886665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2109.96
//
Query:       gi|336252281|ref|YP_004595388.1|  [L=645]
Description: GAF sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for complete 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-50  171.1   4.1    1.9e-50  170.8   1.3    2.4  3  MEDS         MEDS: MEthanogen/methylotroph, DcmR Sensory doma
    2.1e-29  102.3   0.0    1.4e-28   99.7   0.0    2.2  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
      1e-08   35.1   3.5    1.9e-08   34.2   0.0    2.8  2  HisKA        His Kinase A (phospho-acceptor) domain
    1.3e-07   31.2   0.1    2.7e-07   30.2   0.1    1.4  1  ATPase       KaiC
      3e-07   30.8   0.8    1.4e-06   28.7   0.0    2.6  3  GAF_2        GAF domain
    1.1e-05   25.8   0.0    2.2e-05   24.8   0.0    1.6  1  GAF_3        GAF domain
    1.4e-05   24.9   0.0    8.6e-05   22.4   0.0    2.1  2  HATPase_c_5  GHKL domain
      2e-05   25.2   0.0    0.00012   22.7   0.0    2.3  2  GAF          GAF domain
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.033   14.1   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain
      0.041   13.7   0.0      0.076   12.8   0.0    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
       0.05   12.9   0.0      0.096   12.0   0.0    1.4  1  HEM4         Uroporphyrinogen-III synthase HemD
       0.19   11.6   0.0       0.95    9.4   0.0    2.0  2  DUF5380      Family of unknown function (DUF5380)


Domain annotation for each model (and alignments):
>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.8   1.3   1.3e-53   1.9e-50       1     161 []      47     206 ..      47     206 .. 0.99
   2 ?   -0.6   0.0      0.68     1e+03      37      84 ..     233     278 ..     213     284 .. 0.49
   3 ?   -3.3   0.0       4.8   7.1e+03      57      93 ..     510     550 ..     503     564 .. 0.45

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 1.3e-53
                              MEDS   1 dHvclfyedeeellealvpfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrggg 77 
                                       dH++l+ye++ee+++a++pf+++gl+r+e++ly++ +++++e++ea+r++g+dvdaal+sgql+++d++etylr+ +
  gi|336252281|ref|YP_004595388.1|  47 DHFALIYESQEEQFAAVIPFLRQGLERNERCLYITAENSREEVLEAMRERGIDVDAALDSGQLSVHDETETYLRNET 123
                                       8**************************************************************************** PP

                              MEDS  78 fdpermlealrralakaladgyaglrvigemtwalrspaereelleyEallneliadepvtalClYdrrrfsaevla 154
                                       fd++++++++ +a+++a+++ y+ lr++gem+ +l++++e eel++ Ea++n l++d + +alC+Y+r+rf+++v++
  gi|336252281|ref|YP_004595388.1| 124 FDADETVAFIDAAIEDATEE-YEALRMAGEMSSVLQEDPEGEELVKCEAKANYLFDDADGIALCQYNRNRFPSDVIH 199
                                       ****************9877.***********9999999************************************** PP

                              MEDS 155 dvlrtHp 161
                                       dv++tHp
  gi|336252281|ref|YP_004595388.1| 200 DVVSTHP 206
                                       ******8 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.68
                              MEDS  37 astldelrealrkagldvdaalesgqleildaeetylrgggfdperml 84 
                                       a+++d+ +ealr++ ++  ++++++  ++l++++  +++ + d e  l
  gi|336252281|ref|YP_004595388.1| 233 AREVDRQLEALRDQTDAKVELQRRE--RFLRESHEITAEPELDFETKL 278
                                       2333333444444444333344444..555555555555555555555 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.8
                              MEDS  57 alesgqleildaeety....lrgggfdpermlealrralak 93 
                                       +le  ql+i da+       l+  + d ++  + l++ l++
  gi|336252281|ref|YP_004595388.1| 510 VLEDLQLRIEDADAEItagdLPRVEGDGNQLRQVLQNLLDN 550
                                       44444444444444441122222222333333344444444 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 ?   -0.7   0.0       1.4     2e+03      29      56 ..     501     532 ..     475     534 .. 0.65
   2 !   99.7   0.0   9.1e-32   1.4e-28       1     110 [.     535     644 ..     535     645 .] 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                                       EEEEE..EE..TEEEEEEEESSSSSTTHHHTG CS
                         HATPase_c  29 veika..se..ddlvisveDnGiGipkedlkk 56 
                                       +e+++  ++  +dl++++eD    i+  dl++
  gi|336252281|ref|YP_004595388.1| 501 IELETvlDDvlEDLQLRIEDADAEITAGDLPR 532
                                       3333333235679********99999999986 PP

  == domain 2  score: 99.7 bits;  conditional E-value: 9.1e-32
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE..EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSS CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveika..seddlvisveDnGiGipkedlkklfekfsqddstkrggggtG 75 
                                       gd  +Lrq+++nl+dNa+ + +  +  +++i+a  ++ + v+sv+D+GiGi +e+++++f+ f++  ++++++ gtG
  gi|336252281|ref|YP_004595388.1| 535 GDGNQLRQVLQNLLDNAITY-GGRSPPRIRIDAtrRKREWVLSVSDDGIGIEPENQDRIFDIFDR-LHSRDEYDGTG 609
                                       68899***************.656666666666435589**************************.899999***** PP

                                       HHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  76 lGlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       +Gl++++++ve++gGe+wvesepg+G+tf ftlp 
  gi|336252281|ref|YP_004595388.1| 610 IGLALCQRVVERHGGEMWVESEPGEGSTFFFTLPA 644
                                       *********************************96 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   1.3e-11   1.9e-08       2      67 .]     427     494 ..     426     494 .. 0.94
   2 ?    0.5   0.3      0.42   6.2e+02      35      60 ..     524     549 ..     505     551 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.3e-11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrieag 67 
                                       l++f+   +H+L  PL  ++ ++ ++  +  ++ + + +e+le ++++a+r++++++ lL +sr e+g
  gi|336252281|ref|YP_004595388.1| 427 LEQFAYAASHDLQEPLRMVSSYLRLIDTQygDAFDADGEEFLEYAVDGADRMREMIDGLLAYSRVETG 494
                                       789***********************5556989999****************************9987 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.42
                                       SSCHHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  35 eelkeyletiesearrldhlvedlLd 60 
                                       e  +  l ++e  +++l++++++lLd
  gi|336252281|ref|YP_004595388.1| 524 EITAGDLPRVEGDGNQLRQVLQNLLD 549
                                       455556778888999*********98 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   1.8e-10   2.7e-07      39     120 ..      66     146 ..      62     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.8e-10
                            ATPase  39 FlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaeesaeekdkedleelieelaeai 115
                                       Fl +g+e+ +e+++++t e + e++ e +++ G+d+++  ++g+l + d +e+  ++++ +  e +  + + +++a 
  gi|336252281|ref|YP_004595388.1|  66 FLRQGLER-NERCLYITAENSREEVLEAMRERGIDVDAALDSGQLSVHDETETYLRNETFDADETVAFIDAAIEDAT 141
                                       999**999.****************************************9999877544455555555666666666 PP

                            ATPase 116 keika 120
                                       +e++a
  gi|336252281|ref|YP_004595388.1| 142 EEYEA 146
                                       66655 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       3.1   4.6e+03       3      42 ..      85     125 ..      83     173 .. 0.60
   2 !   28.7   0.0     9e-10   1.4e-06       3     131 ..     273     405 ..     271     412 .. 0.84
   3 ?   -2.0   0.0       2.6   3.9e+03       4      21 ..     503     522 ..     501     560 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHHHSS....EEEEEEE-TTS-EEEEEEEES CS
                             GAF_2   3 dleelldlvldelvelgaa..lgyillvdddgglrlaawgea 42 
                                       + ee+l+++ ++ ++++aa   g + ++d+ +  +l+  +++
  gi|336252281|ref|YP_004595388.1|  85 SREEVLEAMRERGIDVDAAldSGQLSVHDETET-YLRNETFD 125
                                       567777777777777754334666555554433.23333333 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 9e-10
                                       HHHHHHHHHHHHHHH.SS...EEEEEEE-TTS-EEEE...EEEES-TTSTT-S-B---TT.HHHHHHHHTS-EEES- CS
                             GAF_2   3 dleelldlvldelve.lg.aalgyillvdddgglrla...awgeaeeefgaaldrplgeg.lvgealrtgrpvilnd 73 
                                       d+e+ l+++ld  +e +g  a+g  +l+  d++   +   + g+ ++++ +++  ++geg  + +a+++ +pv  +d
  gi|336252281|ref|YP_004595388.1| 273 DFETKLEELLDLGCEwMGlDAAGLTHLPARDDK--FHnqcTIGYGDGSDEGRT--DPGEGcYCRRAIESDEPVGMAD 345
                                       566667888888888668666899999888888..555577778888888888..88***88*************** PP

                                       GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES........--HHHHHHHHHHHH CS
                             GAF_2  74 leedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppa..fdeedlelLeelae 131
                                       ++  +  + +  +++gl+  l+  ++ +  ++G l++++++p++  f+++++++Le++++
  gi|336252281|ref|YP_004595388.1| 346 VRGTEWEDDEIYREHGLACYLGTKVTNGPTPYGTLWVGSTEPRDreFTDTERTFLELMGQ 405
                                       888777777777***************999*******988888889**********9986 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHH.HHS.S.. CS
                             GAF_2   4 leelldlvldel.vel.gaa 21 
                                       le++ld vl+ l +++ +a+
  gi|336252281|ref|YP_004595388.1| 503 LETVLDDVLEDLqLRIeDAD 522
                                       66666666666655554433 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.5e-08   2.2e-05       3     129 .]     275     413 ..     273     413 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.5e-08
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnkl..qvaagw.dgkpalsesld.edsalarralssgevvsepsfaee 75 
                                       +  le+ll+l+++ +g++++ l  l ++ +k+  q ++g+ dg++      d  + + +rra++s+e+v  ++++++
  gi|336252281|ref|YP_004595388.1| 275 ETKLEELLDLGCEWMGLDAAGLTHLPARDDKFhnQCTIGYgDGSDEGR--TDpGEGCYCRRAIESDEPVGMADVRGT 349
                                       667999************999987777777664678899977777763..4459999***********866666554 PP

                             GAF_3  76 dglpdraa.....la.vPLvagr..qviGvlalastkpra..fdaedlelleslArqiataier 129
                                       +  +d+ +      + +  ++++  +++G+l ++st+pr+  f+++++ +le ++++++ +ier
  gi|336252281|ref|YP_004595388.1| 350 EWEDDEIYrehglACyLGTKVTNgpTPYGTLWVGSTEPRDreFTDTERTFLELMGQWVSYEIER 413
                                       3322322222222222445555566***********999778********************98 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.93   1.4e+03      35      58 ..      71      94 ..      58     127 .. 0.74
   2 !   22.4   0.0   5.7e-08   8.6e-05       5      91 ..     539     632 ..     536     640 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.93
                       HATPase_c_5 35 vrekkksliisieNsyegekkkle 58
                                      ++++++ l+i++eNs e+  + ++
  gi|336252281|ref|YP_004595388.1| 71 LERNERCLYITAENSREEVLEAMR 94
                                      566778888899998887554443 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 5.7e-08
                       HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ek........kklesskskkeehGiG 70 
                                        l  +l nlLdNAi    + +   + Ir+ ++++k+  ++s++    g   e+        ++l+s+  + +  GiG
  gi|336252281|ref|YP_004595388.1| 539 QLRQVLQNLLDNAITYGGRSP---PRIRIDATRRKREWVLSVSDDGIGiepENqdrifdifDRLHSR-DEYDGTGIG 611
                                       67789**********999988...89*****************995554443333445445666664.458899*** PP

                       HATPase_c_5  71 lksireivkkykgnlsieaed 91 
                                       l   +++v++++g++++e e 
  gi|336252281|ref|YP_004595388.1| 612 LALCQRVVERHGGEMWVESEP 632
                                       ****************99886 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.1   3.1e+03      47      95 ..      94     137 ..      47     160 .. 0.63
   2 !   22.7   0.0     8e-08   0.00012       1     133 []     273     411 ..     273     411 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.1
                                       TTSHHHH..HHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEE CS
                               GAF  47 ngrgicg..qvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPl 95 
                                         rg ++  ++l +gq l+++d  +++ +++    +++++ ++++++ +++
  gi|336252281|ref|YP_004595388.1|  94 RERG-IDvdAALDSGQ-LSVHD--ETETYLR---NETFDADETVAFIDAAI 137
                                       2444.44535555444.55554..7777777...56777777777777766 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 8e-08
                                       SHHHHHHHHHHHHHHHHTESEEEE.EEEEETTE.EE....CEEEEECCEEEETTSH.HHHHHHHHSSSEEESTGGTS CS
                               GAF   1 dleelldtvveelrellgadrval.ylpdydGl.hy....dipqasrwlfmkngrg.icgqvlatgqplvipdstpd 70 
                                       d e+ l+++++  +e +g+d + l +lp +d+  h     +  ++s+  ++ +g+g  c +++++++p+  +d++ +
  gi|336252281|ref|YP_004595388.1| 273 DFETKLEELLDLGCEWMGLDAAGLtHLPARDDKfHNqctiGYGDGSDEGRTDPGEGcYCRRAIESDEPVGMADVRGT 349
                                       567889999999999999999888677766775344666666778888888888884466************98644 PP

                                       TTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS...CSHHHHHHHHHHHHHHHHHHH CS
                               GAF  71 prfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp...pftreelellqvladqvaval 133
                                       +   +    ++ +++g   +l+  ++n+   +G+l + ++ p   +ft+ e+ +l+ +++ v+ ++
  gi|336252281|ref|YP_004595388.1| 350 EWEDD----EIYREHGLACYLGTKVTNGPTPYGTLWVGSTEPrdrEFTDTERTFLELMGQWVSYEI 411
                                       44333....56667*************************777779**************9998765 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.2e-05     0.033      31     110 ..     539     620 ..     499     631 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-05
                       HATPase_c_2  31 eirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep......keslkegGrG 101
                                       ++r +++ ++ Na++++ ++ p  ++++ +++++++ +++v+D+G g +pe++++             ++ +  G+G
  gi|336252281|ref|YP_004595388.1| 539 QLRQVLQNLLDNAITYGGRSPP--RIRIDATRRKREWVLSVSDDGIGIEPENQDRIFD--IfdrlhsRDEYDGTGIG 611
                                       67777777889*******9877..***********************99987554322..24567777889999999 PP

                       HATPase_c_2 102 lalikglvD 110
                                       lal +++v+
  gi|336252281|ref|YP_004595388.1| 612 LALCQRVVE 620
                                       999998886 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 ?   12.8   0.0   5.1e-05     0.076       4      62 ..     541     601 ..     538     621 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.1e-05
                       HATPase_c_3   4 ekAlaelvdNsldAdaen...vkievnknrgktgeivieDdGkGmseeelknalrlatsske 62 
                                       +++l  l+dN+++   ++   + i + +++  +  +++ DdG G+++e+ ++ + +    ++
  gi|336252281|ref|YP_004595388.1| 541 RQVLQNLLDNAITYGGRSpprIRIDATRRK-REWVLSVSDDGIGIEPENQDRIFDIFDRLHS 601
                                       6789999****9955444455888888865.789**************99998887655554 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.4e-05     0.096      97     145 ..      53     102 ..      40     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.4e-05
                                       E-..SSSHHHHGGGS-.---E.EEEEE-SS.S--HHHHHHHHHTTEEEEE CS
                              HEM4  97 vpseegtaegLaeelaeslag.krvlllrgeiarddlaegLeergaevde 145
                                       + s+e++ ++++++l++ l   +r l++ +e++r+++ e+ +erg++vd+
  gi|336252281|ref|YP_004595388.1|  53 YESQEEQFAAVIPFLRQGLERnERCLYITAENSREEVLEAMRERGIDVDA 102
                                       6778999999*******88888**************************97 PP

>> DUF5380  Family of unknown function (DUF5380)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.4     2e+03      43      55 ..     122     134 ..     116     161 .. 0.75
   2 ?    9.4   0.0   0.00063      0.95      43      82 ..     165     205 ..     161     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.4
                           DUF5380  43 etfksdksanfls 55 
                                       etf +d ++ f++
  gi|336252281|ref|YP_004595388.1| 122 ETFDADETVAFID 134
                                       9999999999985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00063
                           DUF5380  43 etfksdksanflsdGaGhvvfrqfrrlrl.sdvlqeskkar 82 
                                       e  k +  an+l d a  + + q+ r r+ sdv +++ +++
  gi|336252281|ref|YP_004595388.1| 165 ELVKCEAKANYLFDDADGIALCQYNRNRFpSDVIHDVVSTH 205
                                       56789999********************879***9998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 0.63u 0.24s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 4724.24
//
Query:       gi|336252282|ref|YP_004595389.1|  [L=511]
Description: Replication factor C large subunit [Halopiger xanaduensis SH-6]
Scores for 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-11   42.4   0.0    3.3e-10   40.5   0.0    2.1  1  AAA             ATPase family associated with various cellula
    2.3e-06   27.4   0.0    4.6e-06   26.5   0.0    1.5  1  RuvB_N          Holliday junction DNA helicase RuvB P-loop do
    0.00011   22.5   0.2    0.00038   20.7   0.2    2.0  1  AAA_assoc_2     AAA C-terminal domain
    0.00041   20.0   0.2       0.13   11.8   0.0    2.9  3  AAA_25          AAA domain
    0.00094   19.5   0.0       0.33   11.2   0.0    3.0  1  AAA_22          AAA domain
     0.0017   18.1   0.3     0.0047   16.7   0.3    1.8  1  AAA_30          AAA domain
     0.0029   18.0   0.4      0.018   15.4   0.0    2.4  3  AAA_16          AAA ATPase domain
     0.0061   16.8   0.1      0.023   14.9   0.1    2.1  1  AAA_28          AAA domain
     0.0075   16.2   0.0      0.015   15.3   0.0    1.4  1  Rad17           Rad17 P-loop domain
     0.0077   16.4   0.2      0.028   14.6   0.0    2.1  1  AAA_33          AAA domain
       0.01   15.8   0.0      0.031   14.2   0.0    1.8  2  RsgA_GTPase     RsgA GTPase
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.065   13.2   0.0    1.9  1  AAA_5           AAA domain (dynein-related subfamily)
      0.021   14.1   0.0      0.044   13.1   0.0    1.5  1  Zeta_toxin      Zeta toxin
      0.022   15.0   0.1      0.022   15.0   0.1    2.6  3  Hydin_ADK       Hydin Adenylate kinase-like domain
      0.031   14.0   0.0      0.058   13.1   0.0    1.4  1  IstB_IS21       IstB-like ATP binding protein
      0.035   14.7   0.0       0.18   12.4   0.0    2.3  1  AAA_18          AAA domain
      0.056   13.2   0.0      0.099   12.4   0.0    1.4  1  DNA_pol3_delta  DNA polymerase III, delta subunit
      0.058   13.8   0.0       0.13   12.6   0.0    1.7  1  RNA_helicase    RNA helicase
      0.066   13.0   0.1        5.7    6.7   0.0    3.2  3  Bac_DnaA        Bacterial dnaA  protein
      0.073   12.4   0.0       0.13   11.6   0.0    1.4  1  IPT             Isopentenyl transferase
      0.084   12.6   0.0        8.5    6.1   0.0    2.9  3  DEAD            DEAD/DEAH box helicase
       0.12   11.6   0.9        3.8    6.7   0.0    2.8  3  DUF2075         Uncharacterized conserved protein (DUF2075)
       0.16   11.9   0.0        0.5   10.3   0.0    1.8  1  NACHT           NACHT domain
       0.36   10.5   5.0       0.88    9.2   5.0    1.7  1  TraH_2          TraH_2


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 !   40.5   0.0   4.5e-13   3.3e-10       1      86 [.      40     127 ..      40     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 4.5e-13
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.......TSEEEEEETGGGH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka.......kpsilfiDEidal 70 
                                       v+++G pG+GKT++a+a+a ++g +++e+++s+ +      +++ i+ +  ea+++        +   +++DE+d++
  gi|336252282|ref|YP_004595389.1|  40 VIVHGSPGVGKTSAAHALAADMGWPVMELNASDSR------GADVIERVAGEASKSGtltggesGRRLVILDEADNF 110
                                       689********************************......56666666666555555666654569********** PP

                                       HHHH.TTCCCHHHHHHH CS
                               AAA  71 aksr.sgseseeeervv 86 
                                       +++   g+++e+++ v 
  gi|336252282|ref|YP_004595389.1| 111 HGNAdYGGSREVTRVVK 127
                                       ***95555555555444 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 !   26.5   0.0   6.2e-09   4.6e-06       2      61 ..       9      65 ..       8      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.2e-09
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl 61
                                      rP++l+e  g +k +++l+   e a++ +e+ d v+++G+PG+Gkt+ a+ +a+++g  +
  gi|336252282|ref|YP_004595389.1|  9 RPTTLSEVRGNNKARDQLE---EWAETWDEHRDAVIVHGSPGVGKTSAAHALAADMGWPV 65
                                      9*****************9...6688999***************************9765 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 !   20.7   0.2     5e-07   0.00038       4      41 ..     176     222 ..     173     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5e-07
                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..........X CS
                       AAA_assoc_2   4 klkleddalealaeladGDaRkaLnlLElaaeaaeak.........e 41 
                                        +++e++ale +ae  +GD R+a n L+++ae +e+          +
  gi|336252282|ref|YP_004595389.1| 176 GVEFEEEALEKIAESTSGDLRSAVNDLQAVAEDTERLtvddvvtseR 222
                                       6899***************************9998765555555440 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   0.00018      0.13      12      57 ..      16      61 ..       6      81 .. 0.80
   2 ?    4.9   0.0     0.022        17     143     173 ..      99     130 ..      92     132 .. 0.90
   3 ?   -3.3   0.1       7.8   5.8e+03     126     141 ..     195     210 ..     181     224 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                            AAA_25 12 vadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalav 57
                                      v++ +++  +++ + + +    + +++ G pg+GKt +a  la+++
  gi|336252282|ref|YP_004595389.1| 16 VRGNNKARDQLEEWAETWDEHRDAVIVHGSPGVGKTSAAHALAADM 61
                                      455555666777777778788899*******************997 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.022
                            AAA_25 143 vrlvviDplsralgg.densnsdvgalveale 173
                                        rlv++D  + ++g+ d   +++v+++v++++
  gi|336252282|ref|YP_004595389.1|  99 RRLVILDEADNFHGNaDYGGSREVTRVVKNAN 130
                                       58*************999999999****9987 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 7.8
                            AAA_25 126 ltadvdaleaaieeve 141
                                       l ++v++l+a++e++e
  gi|336252282|ref|YP_004595389.1| 195 LRSAVNDLQAVAEDTE 210
                                       3344444444444443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00045      0.33       4      27 ..      36      59 ..      32     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00045
                            AAA_22  4 tagilvvtGesGtGKTtllrrlle 27
                                      ++  ++v+G +G+GKT  +  l+ 
  gi|336252282|ref|YP_004595389.1| 36 HRDAVIVHGSPGVGKTSAAHALAA 59
                                      778899**********99998876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   6.2e-06    0.0047       5     123 ..      24     137 ..      21     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.2e-06
                            AAA_30   5 eQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrvi.glAptgkaAkvLaeelgieastiakllkrl 80 
                                       +Q +  +++  +++  ++++G +G GKt a  al+   ++ g +v+ + A+ ++ A+v+++ +  eas    l+   
  gi|336252282|ref|YP_004595389.1|  24 DQLEEWAETWDEHRDAVIVHGSPGVGKTSAAHALA---ADMGWPVMeLNASDSRGADVIER-VAGEASKSGTLTGGE 96 
                                       6777777788888899************9766554...45588888466888888988885.555888888888555 PP

                            AAA_30  81 kgrarlepgtllivDEagmv....dtkqlaallkaaekagakvilvG 123
                                        g      ++l+i DEa       d    +++++ +++a+  ++lv 
  gi|336252282|ref|YP_004595389.1|  97 SG------RRLVILDEADNFhgnaDYGGSREVTRVVKNANQPIVLVA 137
                                       54......59******9555444477777777777777777777775 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   2.4e-05     0.018       9      46 ..      23      59 ..      16      83 .. 0.85
   2 ?   -1.4   0.0       3.5   2.6e+03      80     124 ..     166     200 ..     108     237 .. 0.53
   3 ?   -2.8   0.1       9.4     7e+03      96      96 ..     454     454 ..     393     497 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.4e-05
                            AAA_16  9 leqLlsalervrsgrpelvllsGesGvGKsslvrellr 46
                                      ++qL++  e++ ++r  +v+++G +GvGK+s + +l+ 
  gi|336252282|ref|YP_004595389.1| 23 RDQLEEWAETWDEHR-DAVIVHGSPGVGKTSAAHALAA 59
                                      577788888888888.89**************998875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.5
                            AAA_16  80 ellrqlldeaesaeleawrekleealaavpelagaeasrllellk 124
                                        +lr++++++     e++ ek+ e+++           +l+ +++
  gi|336252282|ref|YP_004595389.1| 166 PVLRDICRREGVEFEEEALEKIAESTS----------GDLRSAVN 200
                                       345555555333333333343333333..........22222222 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 9.4
                            AAA_16  96 a 96 
                                       +
  gi|336252282|ref|YP_004595389.1| 454 D 454
                                       1 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   3.1e-05     0.023       2      28 ..      40      67 ..      39      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvvp 28
                                      +++ G ++ GKT+ + aLaa+ g+pv++
  gi|336252282|ref|YP_004595389.1| 40 VIVHGSPGVGKTSAAHALAADmGWPVME 67
                                      8999***************877888864 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     2e-05     0.015       8      75 ..       3      67 ..       1      80 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                             Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre 75
                                       W eky+P ++ e+    k  ++++ew ++    +     +++ G +G gk+ + + L+  +g  + e
  gi|336252282|ref|YP_004595389.1|  3 DWTEKYRPTTLSEVRGNNKARDQLEEWAETWDEHR---DAVIVHGSPGVGKTSAAHALAADMGWPVME 67
                                      6**************************88764333...48899****************999988776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.8e-05     0.028       2      47 ..      40      99 ..      40     171 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.8e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklg...avllssdt....lrrrlfgtdqqskt.......d 47
                                      v+++G pG+GK+  a+ l++  g   ++l +sd+    +++r++g+  +s t       +
  gi|336252282|ref|YP_004595389.1| 40 VIVHGSPGVGKTSAAHALAADMGwpvMELNASDSrgadVIERVAGEASKSGTltggesgR 99
                                      79*****************99997655555555588888888888777766655555540 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.1e-05     0.031      67     138 ..       3      76 ..       1      88 [. 0.88
   2 ?   -3.2   0.0       9.2   6.9e+03     125     146 ..     393     414 ..     387     419 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-05
                                       HHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT..SEEEEECSTTSSHHHHHHHHCTT-----S---------- CS
                       RsgA_GTPase  67 elkeelealgyevllvsaktkegleelkellkd..ktsvlvGqSGvGKStLinallpelelktgevseklgrGk 138
                                       ++ e+++ + ++ +  ++k +++lee +e +++  + +++ G+ GvGK++   al+ ++   + e+ ++++rG 
  gi|336252282|ref|YP_004595389.1|   3 DWTEKYRPTTLSEVRGNNKARDQLEEWAETWDEhrDAVIVHGSPGVGKTSAAHALAADMGWPVMELNASDSRGA 76 
                                       57788888888888889999999999999999866678899*****************************9996 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.2
                                       ---S--------------SEEE CS
                       RsgA_GTPase 125 lktgevseklgrGkhTTtavel 146
                                       l  +evs  +g+Gk T + +++
  gi|336252282|ref|YP_004595389.1| 393 LDEKEVSFVTGSGKDTNKVQSI 414
                                       5667899999999999876665 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   8.7e-05     0.065       2      77 ..      40     110 ..      39     114 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.7e-05
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-.SEEEEESGGG- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraareg.eilvlDEvera 77 
                                       v++ G pG+gK++ a  laa ++++v + +  +d + +d++ r+     +++ + + l+  +++g ++++lDE ++ 
  gi|336252282|ref|YP_004595389.1|  40 VIVHGSPGVGKTSAAHALAADMGWPVMELNA-SDSRGADVIERVA----GEASKSGTLT-GGESGrRLVILDEADNF 110
                                       8999*********************987655.5578888888887....3444455555.55544146667777665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.9e-05     0.044      13      51 ..      34      70 ..      23      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.9e-05
                        Zeta_toxin 13 qerPklillgGqpGAGKselaellkdelerqgnvvrldp 51
                                      +e+ +++++ G+pG GK+++a++l++++  +  v +l++
  gi|336252282|ref|YP_004595389.1| 34 DEHRDAVIVHGSPGVGKTSAAHALAADM--GWPVMELNA 70
                                      57889*********************99..666666665 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 ?   15.0   0.1     3e-05     0.022       1      24 [.      39      62 ..      39      72 .. 0.87
   2 ?   -2.8   0.0       8.9   6.6e+03      24      34 ..     208     218 ..     169     228 .. 0.51
   3 ?   -0.1   2.3       1.3   9.4e+02      48     136 ..     379     468 ..     348     501 .. 0.47

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-05
                         Hydin_ADK  1 aiivhGaPlsGKtatavtLakkYe 24
                                      a+ivhG+P  GKt++a +La   +
  gi|336252282|ref|YP_004595389.1| 39 AVIVHGSPGVGKTSAAHALAADMG 62
                                      89*****************97655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.9
                         Hydin_ADK  24 eaAlltiDsvv 34 
                                       ++  lt+D+vv
  gi|336252282|ref|YP_004595389.1| 208 DTERLTVDDVV 218
                                       23334444444 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.3
                         Hydin_ADK  48 rArelCaeaaieqaekekeeaaeeaekkegqlsvealvkktselssaaeekaasskiskk..kktsvvsgkkkaese 122
                                       + rel +++a   + +eke +  + + k ++  v+ +v++++e  + +  +++ s+++++  +     s+ +  +s+
  gi|336252282|ref|YP_004595389.1| 379 KNRELTVRTAATYELDEKEVSFVTGSGKDTN-KVQSIVEDAEERREKETVEHSGSAFFEAedAGDGAASSDDSDDSD 454
                                       5567776666666655555554444443332.222222222222222221122222111100111222222222222 PP

                         Hydin_ADK 123 gaksqkqkekktse 136
                                       ++ ++  +e+++ +
  gi|336252282|ref|YP_004595389.1| 455 DSDDSDDSENDQAT 468
                                       22222222222222 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 ?   13.1   0.0   7.7e-05     0.058      40      69 ..      30      59 ..      14     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.7e-05
                         IstB_IS21 40 tlsfiekkenivllGpsGvGKshlaialgv 69
                                      +  + e+++++++ G +GvGK+  a al+ 
  gi|336252282|ref|YP_004595389.1| 30 AETWDEHRDAVIVHGSPGVGKTSAAHALAA 59
                                      4579999********************986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00024      0.18       1      22 [.      40      61 ..      40      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                            AAA_18  1 IlltGtpGvGKttlakeLskrl 22
                                      +++ G pGvGKt+ a++L+  +
  gi|336252282|ref|YP_004595389.1| 40 VIVHGSPGVGKTSAAHALAADM 61
                                      7999**************8876 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 ?   12.4   0.0   0.00013     0.099      57     171 ..      98     204 ..      96     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                       SEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHH CS
                    DNA_pol3_delta  57 dkrivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkk 133
                                       ++r+v+l+ + ++    + +     e +++++n ++ +  +l+a+    e   +   L +    +e+  +++  +  
  gi|336252282|ref|YP_004595389.1|  98 GRRLVILDEADNF--HGNADYGGSREVTRVVKNANQPI--VLVAN----EFYDMSNSLRNACETIEFRDVSKRSIVP 166
                                       5666777766666..44445566666666666644443..33445....344466667776678999999999999* PP

                                       HHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHHH CS
                    DNA_pol3_delta 134 wiqkraqelglkiekealelLlelvennlsaikqelek 171
                                        + ++++++g+++e+eale ++e+++++l+ + + l+ 
  gi|336252282|ref|YP_004595389.1| 167 VLRDICRREGVEFEEEALEKIAESTSGDLRSAVNDLQA 204
                                       *******************************9999986 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   0.00018      0.13       1      23 [.      40      62 ..      40     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakall 23
                                      ++++G++g+GK+++a+ La+++ 
  gi|336252282|ref|YP_004595389.1| 40 VIVHGSPGVGKTSAAHALAADMG 62
                                      689****************9997 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0076       5.7      14      56 ..      17      59 ..       5      71 .. 0.84
   2 ?    1.1   0.0       0.4     3e+02     171     215 ..     164     205 ..     138     210 .. 0.75
   3 ?    0.1   0.0      0.81   6.1e+02     167     199 ..     341     376 ..     336     390 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0076
                                      TTTHHHHHHHHHHHHSTTT.S--EEEE-SSSSSHHHHHHHHHH CS
                          Bac_DnaA 14 asnrlAlaaalkvaeapgkkynPlfiygevGlGktHLlkaign 56
                                       +n+ A+    + ae+ +++ + ++++g+ G+Gkt   +a++ 
  gi|336252282|ref|YP_004595389.1| 17 RGNNKARDQLEEWAETWDEHRDAVIVHGSPGVGKTSAAHALAA 59
                                      6788899999999999999****************99998875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHHTT----TTHHHHHHHH--S-HHHHHHHHHHHHHH CS
                          Bac_DnaA 171 rlailkkkieaeklevpeevlefiaervtdnvRelegalnrlkay 215
                                        + +l+   ++e++e  ee+le iae+ + ++R   +a+n l+a+
  gi|336252282|ref|YP_004595389.1| 164 IVPVLRDICRREGVEFEEEALEKIAESTSGDLR---SAVNDLQAV 205
                                       45677777889999************9998766...566666665 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.81
                                       -HHHHHHHHHHHHHHTT--...--TTHHHHHHHH-- CS
                          Bac_DnaA 167 dletrlailkkkieaekle...vpeevlefiaervt 199
                                        ++tr ai ++ +e+e++     ++e+l f++   +
  gi|336252282|ref|YP_004595389.1| 341 KRNTRDAIAERIAEREGTSvgtARREILPFLSAMTH 376
                                       6899**********999996677899*999986543 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00017      0.13       5      32 ..      41      68 ..      37      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                               IPT  5 lifGatttGKtaeaiklaketgapvivl 32
                                      +++G+ ++GKt+ a +la + g+pv+ l
  gi|336252282|ref|YP_004595389.1| 41 IVHGSPGVGKTSAAHALAADMGWPVMEL 68
                                      789**********************977 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.12        89      15      33 ..      38      56 ..      22      63 .. 0.77
   2 ?    6.1   0.0     0.011       8.5     120     149 ..      97     129 ..      70     140 .. 0.79
   3 ?   -1.2   0.0       1.9   1.4e+03      50      91 ..     384     424 ..     365     434 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                                      CEEEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                              DEAD 15 gdvlvaaeTGsGKTlafli 33
                                      + v+v++  G GKT a+  
  gi|336252282|ref|YP_004595389.1| 38 DAVIVHGSPGVGKTSAAHA 56
                                      5799***********9865 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
                                       TTEEEEEEETHHHHHHT...TTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                              DEAD 120 sqvrflVlDEadrlldq...gfsdfinrilnql 149
                                       s  r+++lDEad++  +   g s+++ r++++ 
  gi|336252282|ref|YP_004595389.1|  97 SGRRLVILDEADNFHGNadyGGSREVTRVVKNA 129
                                       55699*********9987666666677766665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.9
                                       EEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  50 alivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardql 91 
                                       ++  + t eL e+ ++ ++ ++k ++ +v++i+++ ++r+++
  gi|336252282|ref|YP_004595389.1| 384 TVRTAATYELDEKEVSFVTGSGKDTN-KVQSIVEDAEERREK 424
                                       44445555555555555555555443.455555544444444 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0051       3.8       3      25 ..      39      61 ..      37      79 .. 0.79
   2 ?   -0.3   0.0      0.65   4.9e+02      91     140 ..     101     151 ..      67     288 .. 0.50
   3 ?    1.5   0.0      0.18   1.4e+02      30      83 ..     394     447 ..     376     474 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0051
                           DUF2075  3 vvlVtGvaGtGKtvvllnllael 25
                                       v+V+G +G GKt  + +l+a++
  gi|336252282|ref|YP_004595389.1| 39 AVIVHGSPGVGKTSAAHALAADM 61
                                      699*************9999987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.65
                           DUF2075  91 vvivDEAhrlltksdqaekqseenqlkelmkrak...vvva..lvDegQelntge 140
                                       +vi DEA         ++++ +  ++++++k+a+   v+va  ++D +  l++  
  gi|336252282|ref|YP_004595389.1| 101 LVILDEADNFHG----NADYGGSREVTRVVKNANqpiVLVAneFYDMSNSLRNAC 151
                                       566666665555....345555555555555544333333333444444444333 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.18
                           DUF2075  30 eertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeek 83 
                                       +e+++ +++++++  +++++ ++  ee+++k+++ +  s+f ++ + ++ a+++
  gi|336252282|ref|YP_004595389.1| 394 DEKEVSFVTGSGKDTNKVQSIVEDAEERREKETVEHSGSAFFEAEDAGDGAASS 447
                                       678899***************999998888888888888898888866444433 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00066       0.5       2      23 ..      39      60 ..      38      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00066
                                      CEEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklala 23
                                       vi++G +G+GKT  ++ la +
  gi|336252282|ref|YP_004595389.1| 39 AVIVHGSPGVGKTSAAHALAAD 60
                                      69***************99976 PP

>> TraH_2  TraH_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   5.0    0.0012      0.88     116     193 ..     402     481 ..     373     497 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                            TraH_2 116 yGnpkeddvlpqifedavea..wktGefeGvsvfqaadpGkvvateealgaededvkekdsaklktadadteleeke 190
                                        G+ k+ + +  i eda e    +t e  G + f+a+d G+  a  ++  ++d++  ++ds++ +++ a +  ++ e
  gi|336252282|ref|YP_004595389.1| 402 TGSGKDTNKVQSIVEDAEERreKETVEHSGSAFFEAEDAGDGAASSDDSDDSDDSDDSDDSENDQATLAASSGTDGE 478
                                       57788888999999999875115688999************999888777766655555555444433333333333 PP

                            TraH_2 191 ddv 193
                                        + 
  gi|336252282|ref|YP_004595389.1| 479 SSS 481
                                       322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1239  (0.0691059); expected 358.6 (0.02)
Passed bias filter:                      776  (0.0432818); expected 358.6 (0.02)
Passed Vit filter:                       134  (0.00747392); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); 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: 0.79u 0.29s 00:00:01.08 Elapsed: 00:00:00.42
# Mc/sec: 3629.17
//
Query:       gi|336252283|ref|YP_004595390.1|  [L=66]
Description: hypothetical protein Halxa_0874 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00021   21.0   0.6    0.00024   20.8   0.6    1.0  1  RNF220     E3 ubiquitin-protein ligase RNF220
      0.002   18.3   0.7     0.0032   17.7   0.5    1.4  1  zf-Di19    Drought induced 19 protein (Di19), zinc-binding
  ------ inclusion threshold ------
      0.028   15.3   0.5      0.061   14.2   0.2    1.7  2  zf-C2H2_4  C2H2-type zinc finger
       0.44   10.4   2.1       0.57   10.0   0.5    1.8  2  GAGA       GAGA factor


Domain annotation for each model (and alignments):
>> RNF220  E3 ubiquitin-protein ligase RNF220
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.6   5.3e-08   0.00024     106     152 ..       2      60 ..       1      64 [. 0.91

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.3e-08
                            RNF220 106 pednvcpvCnkkvl..eeltlhveaclrkse..........sedededdedesidvEge 152
                                       +++++cp+C ++     +l  h+e+  rkse          + + + d+ed+s+ ++ge
  gi|336252283|ref|YP_004595390.1|   2 TDQQRCPLCAEHYAerTDLRIHLEVEHRKSEivselidvrrHLSGEMDEEDDSVAIDGE 60 
                                       5789*******9996779*********************998899999********998 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 !   17.7   0.5   7.2e-07    0.0032       4      28 ..       6      31 ..       3      35 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.2e-07
                           zf-Di19  4 tCPyCgk.eltvkeLveHvedeHrve 28
                                       CP C +   + + L  H+e+eHr++
  gi|336252283|ref|YP_004595390.1|  6 RCPLCAEhYAERTDLRIHLEVEHRKS 31
                                      68888884567777888888888765 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 ?   14.2   0.2   1.4e-05     0.061       2      24 .]       6      28 ..       5      28 .. 0.94
   2 ?   -1.6   0.0       1.6   7.1e+03      16      20 ..      40      44 ..      35      46 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                         zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                                      +Cp+C + +  +++L+ Hl+  H
  gi|336252283|ref|YP_004595390.1|  6 RCPLCAEHYAERTDLRIHLEVEH 28
                                      6******************9887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                         zf-C2H2_4 16 LlrHl 20
                                      ++rHl
  gi|336252283|ref|YP_004595390.1| 40 VRRHL 44
                                      68897 PP

>> GAGA  GAGA factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5   0.00013      0.57      27      50 ..       7      30 ..       3      34 .. 0.91
   2 ?   -0.6   0.0      0.26   1.2e+03      40      44 ..      40      44 ..      36      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
                                      -TTT--EESSHHHHHHHHHHHTTT CS
                              GAGA 27 CPiCqAviRqsRnLRRHLELRHFk 50
                                      CP+C        +LR HLE+ H k
  gi|336252283|ref|YP_004595390.1|  7 CPLCAEHYAERTDLRIHLEVEHRK 30
                                      *******9999*********9965 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.26
                                      HHHHH CS
                              GAGA 40 LRRHL 44
                                      +RRHL
  gi|336252283|ref|YP_004595390.1| 40 VRRHL 44
                                      79**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 521.88
//
Query:       gi|336252284|ref|YP_004595391.1|  [L=404]
Description: 8-amino-7-oxononanoate synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-55  189.2   0.0    1.3e-55  189.0   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0038   15.8   0.0      0.007   15.0   0.0    1.4  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.014   14.7   1.4      0.059   12.7   1.4    1.9  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.036   12.8   0.0      0.068   11.9   0.0    1.4  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
      0.075   12.9   0.1        6.8    6.5   0.0    2.3  2  DUF992           Protein of unknown function (DUF992)
       0.11   11.4   0.0       0.17   10.8   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
       0.15   12.0   0.0        5.3    7.0   0.0    2.4  2  Flg_hook         Flagellar hook-length control protein FliK


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 !  189.0   0.0   5.1e-59   1.3e-55       4     362 ..      55     393 ..      52     394 .. 0.94

  Alignments for each domain:
  == domain 1  score: 189.0 bits;  conditional E-value: 5.1e-59
                                       EESSSSSTTSTTSSHHHHHHHHHHHH..HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   4 inLgsneylgdsgkptlpevakaeke..galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       + ++sn+ylg+++   ++++a++++   g +ag ++  +g++ ++ +le  la+            e+a++++sG+ 
  gi|336252284|ref|YP_004595391.1|  55 LVFASNNYLGLTADRRVQDAARQAAAtvGTGAGASRLVTGDTMVHRDLERLLAETKD--------CERALTFSSGYA 123
                                       679********9996666666666666****************************99........999********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTE...TEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnk...ktkvi 152
                                       a+  ++++l      d+++++++++as ++++rlsg+e v y        h d+ +l  +l+  +e++    ++ +i
  gi|336252284|ref|YP_004595391.1| 124 ANVGTITALEP----DVVFSDELNHASLIDGCRLSGAETVVYD-------HRDVADLRSKLEARAEQDDaadERWLI 189
                                       ****9999996....9***************************.......*************9999999*9***** PP

                                       EEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSS.HTHHHHGGSTTSTTEEEEEESSSTTSSGGG CS
                     Aminotran_1_2 153 lvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsl.davatranveeepnllivgslsKafGlaGe 228
                                       ++ ++++ +Gtva+le +++l   a++ +++++vDea+a++ + +  ++  +  +++++++ + +g+lsKa+++ G 
  gi|336252284|ref|YP_004595391.1| 190 ITDTVFSVDGTVAPLESICDL---AEAFGAWVMVDEAHATGLYVDGgGV-VQAEGLADRIH-VQMGTLSKALASQG- 260
                                       *********************...*******************998444.449********.**************. PP

                                       -EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCS CS
                     Aminotran_1_2 229 RvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsg 305
                                         Gy++g+++++++l + +r+f +s+ l + +aaa+s al    +++++r+rl+++  +lrd+L++ g++  +  s 
  gi|336252284|ref|YP_004595391.1| 261 --GYVAGSDELIECLINDARSFVYSTGLTPPAAAAASEALHL-ARHSDARERLWENVAHLRDGLESMGFDAPGD-SQ 333
                                       ..**********************999999999999998876.59*************************9885.** PP

                                       SEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHHHHHHHH CS
                     Aminotran_1_2 306 mflltdlsaetakelskkLleevgvyvtpgtsftv...pgrlRitv.Aglteeeleelvea 362
                                       ++++ ++++e+a +l++ L+e+  ++  +++++ v   ++r+R+t+ A+++++++   +ea
  gi|336252284|ref|YP_004595391.1| 334 ILPVIVGNREDALALAEGLRER-DIVAPAIRPPAVpegESRIRVTPiATHDKDDIVACLEA 393
                                       **********************.****************************9998766665 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 !   15.0   0.0   2.7e-06     0.007      54     182 ..      99     230 ..      76     232 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHH CS
                   Cys_Met_Meta_PP  54 rsvleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleel 130
                                       ++ le+ +a+ ++ e+al +ssG aA   +i+al     ++v sd+l   +       ++ +g e+ ++d  d+++l
  gi|336252284|ref|YP_004595391.1|  99 HRDLERLLAETKDCERALTFSSGYAANVGTITAL---EPDVVFSDELNHASLID---GCRLSGAETVVYDHRDVADL 169
                                       6789***********************6666665...45788888886655433...33344455555555444444 PP

                                       HHHCCT.........TEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS CS
                   Cys_Met_Meta_PP 131 ekaike.........ntklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllq 182
                                       +++++          +  l+ ++t+ +    v+ +e+i++la + g+ v+vD + a++l++
  gi|336252284|ref|YP_004595391.1| 170 RSKLEAraeqddaadERWLIITDTVFSVDGTVAPLESICDLAEAFGAWVMVDEAHATGLYV 230
                                       4443331111222225568999**********************************99876 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 ?   12.7   1.4   2.3e-05     0.059      26     155 ..     100     232 ..      76     268 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GG CS
                   DegT_DnrJ_EryC1  26 eeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpa 102
                                       +++E+ +a+    + a+++ssG aA+  +++al+ +    V    l+ ++ +   + +ga++v  D         +a
  gi|336252284|ref|YP_004595391.1| 100 RDLERLLAETKDCERALTFSSGYAANVGTITALEPD---VVFSDELNHASLIDGCRLSGAETVVYDHRD------VA 167
                                       567777777777777777777777777777777544...666666777777777777777777776542......11 PP

                                       GCGGG--TTE..............EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT CS
                   DegT_DnrJ_EryC1 103 aieaaitert..............kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg 155
                                       +++++++ r                   +  + G va ++++ ++a++ g +v+ D AhA G  ++g
  gi|336252284|ref|YP_004595391.1| 168 DLRSKLEARAeqddaaderwliitDT--VFSVDGTVAPLESICDLAEAFGAWVMVDEAHATGLYVDG 232
                                       22222221111112223322222122..234569****************************99998 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.7e-05     0.068     156     207 ..     169     225 ..     119     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHSTTTGS...ESEEEEESS-T..TSEEE-HHHHHHHHTTSESEEEEE-TT- CS
                          OKR_DC_1 156 lkekikevpdaka...prlavitnsTY..dGvlynakeivdkleklsdrilfDeAwv 207
                                       l++k+++ +++ +    r+++it + +  dG+++ +++i d++e ++  +++DeA+ 
  gi|336252284|ref|YP_004595391.1| 169 LRSKLEARAEQDDaadERWLIITDTVFsvDGTVAPLESICDLAEAFGAWVMVDEAHA 225
                                       555665555554444477799999876559*************************97 PP

>> DUF992  Protein of unknown function (DUF992)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.016        41      96     114 ..      77      95 ..      61     103 .. 0.91
   2 ?    6.5   0.0    0.0027       6.8      10      46 ..     242     278 ..     235     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.016
                            DUF992  96 sasaavgvGlganvlvggs 114
                                       +a a+vg+G+ga  lv g 
  gi|336252284|ref|YP_004595391.1|  77 QAAATVGTGAGASRLVTGD 95 
                                       799************9985 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0027
                            DUF992  10 aqaekvqvGvLeCeveggvglvvgsskelsCvfrsas 46 
                                       a++ +vq+G+L+ +++++ g+v gs + ++C  ++a+
  gi|336252284|ref|YP_004595391.1| 242 ADRIHVQMGTLSKALASQGGYVAGSDELIECLINDAR 278
                                       557789*************************988764 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.5e-05      0.17     142     180 ..     188     226 ..     150     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.5e-05
                                       EEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTT CS
                       Aminotran_5 142 lvaithvsnvtGtiqpveeigklakkkgalvlvDaaqav 180
                                       l++   v +v Gt+ p+e+i++la + ga+v+vD a a 
  gi|336252284|ref|YP_004595391.1| 188 LIITDTVFSVDGTVAPLESICDLAEAFGAWVMVDEAHAT 226
                                       556667889*************************99876 PP

>> Flg_hook  Flagellar hook-length control protein FliK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.062   1.6e+02      46      68 ..     238     260 ..     235     267 .. 0.83
   2 ?    7.0   0.0    0.0021       5.3      44      70 ..     301     327 ..     297     330 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.062
                                       SCHHHHHHHHTHHHHHHHHHCCT CS
                          Flg_hook  46 npetrelLeqnlprLreaLaaaG 68 
                                        +  +++++ ++++L +aLa++G
  gi|336252284|ref|YP_004595391.1| 238 AEGLADRIHVQMGTLSKALASQG 260
                                       5667889999************9 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0021
                                       E-SCHHHHHHHHTHHHHHHHHHCCTTC CS
                          Flg_hook  44 aenpetrelLeqnlprLreaLaaaGlk 70 
                                       a ++++re+L +n ++Lr+ L+++G+ 
  gi|336252284|ref|YP_004595391.1| 301 ARHSDARERLWENVAHLRDGLESMGFD 327
                                       67899********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2845.64
//
Query:       gi|336252285|ref|YP_004595392.1|  [L=367]
Description: Biotin synthase [Halopiger xanaduensis SH-6]
Scores for 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-16   59.8   0.0    4.3e-16   58.8   0.0    1.5  1  BATS         Biotin and Thiamin Synthesis associated domain
      4e-15   56.6   0.9    2.5e-13   50.8   0.2    2.3  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.19   11.5   0.0       0.41   10.5   0.0    1.5  1  STN          Secretin and TonB N terminus short domain


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 !   58.8   0.0   7.1e-20   4.3e-16       1      86 []     238     330 ..     238     330 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 7.1e-20
                                       E--B----TCCCC............HHHHHHHHHHSTTSE.CCCTCHH-HHHHHH..HHHCCT--EEE-C---TTTG CS
                              BATS   1 siprlrpikdtpl............lkiiaalRlllPkag.illsgResaefrdq..lllklGansisagsktevgg 62 
                                       +++ l+p+++tpl            +k+ia++Rll P+a+ +l +gRe++   d+  l l++Ga+ + +g+      
  gi|336252285|ref|YP_004595392.1| 238 PVNVLNPVPGTPLaergveitteeiVKTIAVYRLLHPEARvRLTGGREANLAPDEqhLPLEAGADGLLTGD------ 308
                                       89**********************************************988765558999***********...... PP

                                       GGSESSTT-TCCCCHHHHHHTT-E CS
                              BATS  63 yaflttdgrsleedvkmleelGle 86 
                                         +ltt+g+s+ +d+k +e++Gle
  gi|336252285|ref|YP_004595392.1| 309 --YLTTEGQSPADDLKIIERAGLE 330
                                       ..********************85 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.2   4.1e-17   2.5e-13       6     163 ..      67     225 ..      65     228 .. 0.90
   2 !    4.1   0.0    0.0091        55      24      72 ..     252     301 ..     245     348 .. 0.75

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 4.1e-17
                                       EESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEE...SSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpet.vrregrgrslsveeileevkelkaekg.vkevilg...ggepllypdfvellerlaklavpg 77 
                                        C+ +C fCa++ +     +++ +l +e+ile +k++ +++g  ++ i++   g     +pd+  +++++++l  ++
  gi|336252285|ref|YP_004595392.1|  67 NCAEDCGFCAQSVHfDTGIDTYDFLGPEKILEAAKRA-ERDGaQRFGIVVaekGVSKERRPDEWAEVLEAIRLVRDK 142
                                       5************************************.9***5555555566666666668888888888888789* PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpG 154
                                         + v ++ + ++ee +e l+  g+ ++++++e+     + +++ ++h+fe+++e+le ++ ag++  + +++++ G
  gi|336252285|ref|YP_004595392.1| 143 CDLEVDASLGILTEEEAEILAAEGIKHYNHNIETSPRY-FPEIV-DTHSFEDRVETLEVAKGAGMD-LCAGVILGMG 216
                                       **************************************.*****.*********************.9999999999 PP

                                       TSHHHHHHH CS
                                       xxxxxxxxx RF
                       Radical_SAM 155 endeeleel 163
                                       e+  +++e 
  gi|336252285|ref|YP_004595392.1| 217 ETPTDRVEA 225
                                       *99888775 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0091
                                       HHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  24 grgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlak 72 
                                       +rg ++++eei++ +  ++  ++ +++ + gg e +l pd++ l +++ +
  gi|336252285|ref|YP_004595392.1| 252 ERGVEITTEEIVKTIAVYRlLHPEARVRLTGGREANLAPDEQHLPLEAGA 301
                                       678899*************8777688888888899999888877666555 PP

>> STN  Secretin and TonB N terminus short domain
   #    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      21      35 ..       6      20 ..       5      24 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.9e-05
                               STN 21 gnvtideaLdeLLkg 35
                                      gn+t+d+aL+++L+g
  gi|336252285|ref|YP_004595392.1|  6 GNETVDDALERVLAG 20
                                      8*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); 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 0.21s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2943.51
//
Query:       gi|336252286|ref|YP_004595393.1|  [L=269]
Description: hypothetical protein Halxa_0877 [Halopiger xanaduensis SH-6]
Scores for 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:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 1960.66
//
Query:       gi|336252287|ref|YP_004595394.1|  [L=290]
Description: succinyl-CoA synthetase subunit alpha [Halopiger xanaduensis SH-6]
Scores for 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-26   91.1   0.8    5.5e-26   91.1   0.8    2.3  2  CoA_binding    CoA binding domain
    2.5e-15   56.6   0.5    5.5e-15   55.5   0.5    1.5  1  Ligase_CoA     CoA-ligase
    5.6e-12   45.6   0.0    8.5e-12   45.0   0.0    1.3  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    2.3e-06   28.1   0.0    1.4e-05   25.5   0.0    2.1  2  CoA_binding_2  CoA binding domain
  ------ inclusion threshold ------
       0.04   13.5   0.1      0.072   12.7   0.1    1.4  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.8   1.5e-29   5.5e-26       2      96 .]       7      99 ..       6      99 .. 0.97
   2 ?   -0.5   0.1      0.57   2.1e+03      25      43 ..     167     186 ..     144     234 .. 0.56

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 1.5e-29
                                      TTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHH CS
                       CoA_binding  2 kdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavd 80
                                       dt+v+v+G++g   +g +h k++++yg+++v+g  p+k+g+ev+g+pvy++v+e++e+ ++d++vi+vP+++a +a+ 
  gi|336252287|ref|YP_004595394.1|  7 DDTRVVVQGITGG--EGKFHAKQMMEYGTNVVAGAVPGKGGQEVDGVPVYDTVHEAVEEENADTSVIFVPPAFAGDAIF 83
                                      79*********99..999*****************************************77****************** PP

                                      HHHHTT-SEEEEESST CS
                       CoA_binding 81 elveagikgiviiteg 96
                                      e++++   ++v+iteg
  gi|336252287|ref|YP_004595394.1| 84 EALDTDLDLAVAITEG 99
                                      **************97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.57
                                       HHHECEEEEEEC-TT.TTTC CS
                       CoA_binding  25 klkygikavfgvnpr.kvgt 43 
                                       ++++g + ++g++++  +gt
  gi|336252287|ref|YP_004595394.1| 167 NRGMGQSTAIGIGGDpIIGT 186
                                       45666666666665533332 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.5   1.5e-18   5.5e-15       1     151 [.     151     271 ..     151     272 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.5e-18
                                       EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEE CS
                        Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvi 77 
                                       ++++GtL+y  +d +++               g +q++ i++G+d            +t++ +al+ + +dpe+++i
  gi|336252287|ref|YP_004595394.1| 151 VSRSGTLTYQVVDNLTNR--------------GMGQSTAIGIGGDPII---------GTDFVDALELFENDPETEAI 204
                                       689***************..............***************7.........******************** PP

                                       EEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHT.TTSSEEE-SSHHHHHHH CS
                        Ligase_CoA  78 lldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakalee.agveiasskaqalraak 151
                                       ++ +++G g+ e++aa++++++ ++       pv  ++aG +a+p++++++a+a+ + +g  +a+sk  al  a+
  gi|336252287|ref|YP_004595394.1| 205 VMCGEIG-GEDEEEAAAYIDEHVDT-------PVAGFIAGRTAPPGKRMGHAGAIVSgSGTGTAESKISALNDAG 271
                                       *******.************98777.......8******************999877368889999999988776 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 !   45.0   0.0   2.4e-15   8.5e-12       1     134 [.     145     284 ..     145     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.4e-15
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsirdgrkflsaa 75 
                                       +G+++l+s SG+l  +++d +++rg+g s+++ +G    + +d+ d le +++dpet++i+++ E  ++ ++ ++a 
  gi|336252287|ref|YP_004595394.1| 145 EGNVGLVSRSGTLTYQVVDNLTNRGMGQSTAIGIGGdpIIGTDFVDALELFENDPETEAIVMCGEIGGEDEEEAAAY 221
                                       59*********************************9455889***********************777755544444 PP

                      Succ_CoA_lig  76 rraarkkpvvvlksGr....seagaraaashtgalagsdavvdaafrqaGvlrvdsleelfda 134
                                          + + pv  + +Gr     ++   a a  +g+ +g  +   +a++ aGv + d+ ee++d 
  gi|336252287|ref|YP_004595394.1| 222 IDEHVDTPVAGFIAGRtappGKRMGHAGAIVSGSGTGTAESKISALNDAGVPVGDTPEEVADH 284
                                       4444589*********43333455556677888899999999999999*99999999999886 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0     4e-09   1.4e-05      37     114 ..      43     128 ..      10     130 .. 0.74
   2 ?   -0.3   0.0       0.4   1.4e+03       6      35 ..     148     178 ..     148     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 4e-09
                                       -..SEETTEES----T......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT....---HHHHHHHHHTT-EE CS
                     CoA_binding_2  37 e..eeilgekvyaslaed..pepvdlvdvftppeatpeivkealalgakavwlqpg....sedeeaaelaeeagirv 105
                                       +  +e++g++vy ++ e+  +e+ d+ ++f+pp+ + + + eal+ +   ++   +       + + +++ e + r+
  gi|336252287|ref|YP_004595394.1|  43 KggQEVDGVPVYDTVHEAveEENADTSVIFVPPAFAGDAIFEALDTDLDLAVAITEgiptQDMARVNKRLTETDTRL 119
                                       2359************94589**********************99987665555444443444445556666***** PP

                                       E.ES-HHHH CS
                     CoA_binding_2 106 vgdrCilve 114
                                       +g++C++++
  gi|336252287|ref|YP_004595394.1| 120 IGPNCPGLI 128
                                       ******986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.4
                                       ET--S-TTSHHHHHHHHHHHHT.--EEEESS CS
                     CoA_binding_2   6 vGasdnpgkfgykvlryllehg.lpvvpVnp 35 
                                       vG+ +++g   y+v+++l ++g  + +++  
  gi|336252287|ref|YP_004595394.1| 148 VGLVSRSGTLTYQVVDNLTNRGmGQSTAIGI 178
                                       7999999999999999999976225555555 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 ?   12.7   0.1     2e-05     0.072       5     121 ..       9     126 ..       5     134 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                                       S-EEEES-.SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEE.EHHHHHH..T-SEEEE-S-HHHHHHHH CS
                              IlvN   5 kkiaviGy.GsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevl.tvaeavk..kadvvmiliPDelqkevy 77 
                                        +++v G  G  G+ +a+++ + g +vv g   g+      + +g+ v+ tv+eav+  +ad  +i +P  +  + +
  gi|336252287|ref|YP_004595394.1|   9 TRVVVQGItGGEGKFHAKQMMEYGTNVVAGAVPGK---GGQEVDGVPVYdTVHEAVEeeNADTSVIFVPPAFAGDAI 82 
                                       67788885499**********************99...455678888873578888522699999999988776665 PP

                                       HHHTGGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-S CS
                              IlvN  78 eeeiepnlkegkalafahGfnihfglikppkdvdvvlvAPkgpG 121
                                        e++   l+   a++ +   +   +  k  ++ d+ l+ P +pG
  gi|336252287|ref|YP_004595394.1|  83 FEALDTDLDLAVAITEGIPTQDMARVNKRLTETDTRLIGPNCPG 126
                                       56666666544333322222222222333355666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2178.73
//
Query:       gi|336252288|ref|YP_004595395.1|  [L=384]
Description: succinyl-CoA ligase (ADP-forming) subunit beta [Halopiger xanaduensis SH-6]
Scores for 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-62  210.0   0.2    4.2e-62  209.3   0.2    1.3  1  ATP-grasp_2      ATP-grasp domain
      7e-20   71.4   3.9    1.3e-18   67.3   3.3    2.5  2  ATP-grasp_5      ATP-grasp domain
    1.7e-13   50.6   0.3    4.7e-13   49.2   0.3    1.6  1  Ligase_CoA       CoA-ligase
    3.3e-13   49.6   0.7      2e-10   40.6   0.4    2.3  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.2e-07   31.5   0.1    2.4e-07   30.5   0.1    1.5  1  ATP-grasp        ATP-grasp domain
      3e-06   27.1   0.2    6.9e-06   26.0   0.2    1.6  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
  ------ inclusion threshold ------
      0.084   12.7   0.0       0.15   11.8   0.0    1.4  1  Succ_CoA_lig     Succinyl-CoA ligase like flavodoxin domain
       0.13   12.8   0.0       0.46   11.0   0.0    1.9  2  DUF4891          Domain of unknown function (DUF4891)
       0.24   10.9   3.8       0.13   11.8   0.7    2.1  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus


Domain annotation for each model (and alignments):
>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.3   0.2   2.1e-65   4.2e-62       1     201 [.       4     196 ..       4     197 .. 0.99

  Alignments for each domain:
  == domain 1  score: 209.3 bits;  conditional E-value: 2.1e-65
                                       BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTT CS
                       ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellg 77 
                                       +lhEyqak+++a+ g+++p +++a++ + + +aa+++g  + +vKaQv++GGRGKagG+kl+++++ea+eaa+++lg
  gi|336252288|ref|YP_004595395.1|   4 KLHEYQAKDVFADAGIPTPASQLASDVDGVIAAAEEIGYPV-AVKAQVQVGGRGKAGGIKLAEDEDEAREAAESILG 79 
                                       69*************************************99.9********************************** PP

                                       SEEE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB- CS
                       ATP-grasp_2  78 kelvtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakgl 154
                                       ++l+       G +v++vlveea+d+  ElY++i++Dr + k+v+++S++GGv+iEeva++ P++i++ +idp+ g+
  gi|336252288|ref|YP_004595395.1|  80 MDLK-------GYRVDQVLVEEAVDFVNELYVGITMDRGEGKPVAMVSTKGGVNIEEVAEEDPDAIAREHIDPSFGM 149
                                       ****.......****************************************************************** PP

                                       -HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEE CS
                       ATP-grasp_2 155 keeqareiakklglekelvkkaakiikklyklfveldatlvEiNPLv 201
                                       +++qar+ + ++g+++++++++++++++ly+l+ ++d   +EiNPL+
  gi|336252288|ref|YP_004595395.1| 150 HPYQARKAVYDAGVDQSVARDVSSVLTTLYDLWDSRDGADAEINPLM 196
                                       **********************************************7 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   3.3   6.4e-22   1.3e-18      10     222 .]       5     212 ..       3     212 .. 0.86
   2 ?    1.6   0.0     0.079   1.6e+02      30      56 ..     322     348 ..     309     381 .. 0.80

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 6.4e-22
                       ATP-grasp_5  10 LteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeile 86 
                                       L e++ak+++++ gip++ ++las+++ +++aaeeigypv++K ++ ++  + ++gG++l  +d++e r+aae+il 
  gi|336252288|ref|YP_004595395.1|   5 LHEYQAKDVFADAGIPTPASQLASDVDGVIAAAEEIGYPVAVKAQV-QVGGRGKAGGIKL-AEDEDEAREAAESILG 79 
                                       89*****************************************996.699**********.9*************99 PP

                       ATP-grasp_5  87 rvkekspeariegvlVqemakrggrElivgvteDpvFG.pvilf.GlGGtavevlkdvavalpplnstlareliert 161
                                             ++ r+++vlV+e ++    El vg+t D   G pv ++   GG+ +e +++   +    ++ +    +   
  gi|336252288|ref|YP_004595395.1|  80 M---DLKGYRVDQVLVEEAVD-FVNELYVGITMDRGEGkPVAMVsTKGGVNIEEVAEEDPDAIAREHIDPSFGMHPY 152
                                       7...45688************.9***************444444256******999999777666666666666666 PP

                       ATP-grasp_5 162 kaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllvee.egvvalDarirl 222
                                       +a k++ +     ++  + ++++l++l +L ++    +  +inPl+v++ ++v+a+Da++++
  gi|336252288|ref|YP_004595395.1| 153 QARKAVYDAGVD-QSVARDVSSVLTTLYDLWDS-RDGADAEINPLMVTSdDEVIAADAVMNI 212
                                       666666665444.6778999999****999987.77799********99455********87 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.079
                       ATP-grasp_5  30 rlassaeeaveaaeeigypvvlKivsp 56 
                                        +a+  +ea+e ++ei  pvv++++  
  gi|336252288|ref|YP_004595395.1| 322 EVARGINEALEQFDEIPKPVVVRLAGT 348
                                       5788999***************98765 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.3   2.4e-16   4.7e-13       3     149 ..     259     374 ..     257     377 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.4e-16
                                       SSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEE CS
                        Ligase_CoA   3 nGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvill 79 
                                       nG++L + ++dl+ +               g+++++++d+G++a            +++ +al  + +d++v+ +++
  gi|336252288|ref|YP_004595395.1| 259 NGAGLVMTTLDLVDHY--------------GGQPANFLDVGGGAK----------AQRIANALDMVFSDDNVDSVVF 311
                                       7999999999999999..............***************..........7********************* PP

                                       EEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHH CS
                        Ligase_CoA  80 divlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalra 149
                                       +i++G+ + +++a ++ +a+++ +    ++pvv+r+aGt+ +     e+ ++l+e  v++ ++ + a++ 
  gi|336252288|ref|YP_004595395.1| 312 NIFGGITRGDEVARGINEALEQFD--EIPKPVVVRLAGTNWE-----EGMEILNEDLVTVEQTLEDAVQR 374
                                       ***********************8..9***************.....9999**99999999988888765 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 !   40.6   0.4   9.8e-14     2e-10       4     102 ..       9     109 ..       7     121 .. 0.89
   2 !    7.0   0.0    0.0019       3.7      22      74 ..     323     375 ..     307     382 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 9.8e-14
                                       HHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTE....EEESSHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   4 sakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGm....rvarneeelaelvkkalaeaka 76 
                                       +ak+  +++++p+  s+ a  ++++ ++a+a+eigyPv +ka + +GG+G     ++a++e+e +e++++ l +   
  gi|336252288|ref|YP_004595395.1|   9 QAKDVFADAGIPTPASQLA--SDVDGVIAAAEEIGYPVAVKAQVQVGGRGKaggiKLAEDEDEAREAAESILGMDLK 83 
                                       67889999*****999999..***************************97433338********************* PP

                                       HHSTS-EEEEE--SSSEEEEEEEEEE CS
                       CPSase_L_D2  77 afgnkqvlvekslkgpkeiEvevlrD 102
                                        +  +qvlve+ ++   e+ v +  D
  gi|336252288|ref|YP_004595395.1|  84 GYRVDQVLVEEAVDFVNELYVGITMD 109
                                       ***********999888887777766 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0019
                                       SSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSH.HHHHHHHHHHHHHH CS
                       CPSase_L_D2  22 apvetleealaiakeigyPviikaafglGGkGmrvarne.eelaelvkkalaea 74 
                                       + ++ ++eal+  +ei  Pv+++ a +   +Gm + +++  +++++++ a++ a
  gi|336252288|ref|YP_004595395.1| 323 V-ARGINEALEQFDEIPKPVVVRLAGTNWEEGMEILNEDlVTVEQTLEDAVQRA 375
                                       3.677899**************************98765234444555555554 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.1   1.2e-10   2.4e-07       3      98 ..      16     121 ..      14     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.2e-10
                                       TTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTT....TEEEECTCCGHHCHHHHC........GTTCEE CS
                         ATP-grasp   3 klglpvprflaveskeeleeaaeelglpvvvKarrlgydGk....Gqsvvrseedleqaleal........keekvi 67 
                                       ++g+p+p  +++++ + + +aaee+g+pv vKa ++   G+    G ++ ++e+++++a+e +        +  +v+
  gi|336252288|ref|YP_004595395.1|  16 DAGIPTPASQLASDVDGVIAAAEEIGYPVAVKA-QVQVGGRgkagGIKLAEDEDEAREAAESIlgmdlkgyRVDQVL 91 
                                       689*****************************5.555556600444467788888888888879****9988999** PP

                                       EEE----SEEEEEEEEEETTC-EEE--EEEE CS
                         ATP-grasp  68 vEefvpfekElsvlvvrsaeGetafypvvet 98 
                                       vEe v+f  El v ++   +Ge + +++v t
  gi|336252288|ref|YP_004595395.1|  92 VEEAVDFVNELYV-GITMDRGEGKPVAMVST 121
                                       **********964.55556665555555554 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 !   26.0   0.2   3.4e-09   6.9e-06       6      90 ..      10      97 ..       6     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.4e-09
                                      HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT....-EEEESSHHHHHHHHHHHCTS-TTCCCC CS
                            GARS_A  6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagK....gvivakseeealkavkeilekkkfGeag 80
                                      akd++++agipt+  +  +d++ + +  ee + ++  vKa+   +g+    g+++a++e+ea +a+++il     G   
  gi|336252288|ref|YP_004595395.1| 10 AKDVFADAGIPTPASQLASDVDGVIAAAEEIGYPV-AVKAQVQVGGRgkagGIKLAEDEDEAREAAESILGMDLKGYRV 87
                                      79*********************************.8899877776522446999************************ PP

                                      SSEEEEE--- CS
                            GARS_A 81 ekvviEelle 90
                                      ++v++Ee ++
  gi|336252288|ref|YP_004595395.1| 88 DQVLVEEAVD 97
                                      *******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 ?   11.8   0.0   7.6e-05      0.15       1      94 [.     251     351 ..     251     376 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.6e-05
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvd.vadlleylaedpetkvill.ylEsirdgrkfls.. 73 
                                       +G++++i    +l+++ ld + + g + ++++ +G  a+ + +a  l+++ +d++++++++  + +i +g++ ++  
  gi|336252288|ref|YP_004595395.1| 251 EGNVGIIGNGAGLVMTTLDLVDHYGGQPANFLDVGGGAKAQrIANALDMVFSDDNVDSVVFnIFGGITRGDEVARgi 327
                                       59*********************************988764389****99999999877661568899976666511 PP

                      Succ_CoA_lig  74 ..aarraark.kpvvvlksGrsea 94 
                                         a+++  +  kpvvv  +G++ +
  gi|336252288|ref|YP_004595395.1| 328 neALEQFDEIpKPVVVRLAGTNWE 351
                                       116666677799999999998654 PP

>> DUF4891  Domain of unknown function (DUF4891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023      0.46      30      77 ..      45      95 ..      31     106 .. 0.84
   2 ?   -2.6   0.0       4.1   8.1e+03      35      57 ..     117     139 ..     114     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                           DUF4891 30 tvKakveikedGk...vkvlsyvkkqslkvekyirkrlkkfrvkkellesg 77
                                       vKa+v++   Gk   +k+ + +++   + e+ +   lk +rv+++l+e++
  gi|336252288|ref|YP_004595395.1| 45 AVKAQVQVGGRGKaggIKLAEDEDEAREAAESILGMDLKGYRVDQVLVEEA 95
                                      79*****9755543339******************************9986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
                           DUF4891  35 veikedGkvkvlsyvkkqslkve 57 
                                       + ++++G v++ + +++ + ++ 
  gi|336252288|ref|YP_004595395.1| 117 AMVSTKGGVNIEEVAEEDPDAIA 139
                                       56788899999988888776664 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 ?   11.8   0.7   6.3e-05      0.13      30      94 ..      35     109 ..      20     207 .. 0.74
   2 ?   -2.5   0.1       1.6   3.1e+03      55      75 ..     362     382 ..     360     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.3e-05
                                       HHHHHC-SSEEEEESSS....STTTTEEEESSGGGHHHHHHHHHTT-......SCEEEEE--.ESEEEEEEEEETS CS
                   Dala_Dala_lig_C  30 kveeelgypvfVKpare....GSSvGvskveseeelkeaieeafkyd......ekvlvEeai.egreievavlgne 94 
                                       +  ee+gypv VK+  +    G   G++ +e e+e +ea e+ + +d       +vlvEea+   +e+ v++   +
  gi|336252288|ref|YP_004595395.1|  35 AAAEEIGYPVAVKAQVQvggrGKAGGIKLAEDEDEAREAAESILGMDlkgyrvDQVLVEEAVdFVNELYVGITM-D 109
                                       56789********986444448999*****************9999944433346*******7799*****976.2 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                                       ESSGGGHHHHHHHHHTT-SCE CS
                   Dala_Dala_lig_C  55 veseeelkeaieeafkydekv 75 
                                       v+ e+ l++a+++a++y  +v
  gi|336252288|ref|YP_004595395.1| 362 VTVEQTLEDAVQRAVEYADEV 382
                                       6778899999*9999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); 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: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2922.22
//
Query:       gi|336252289|ref|YP_004595396.1|  [L=290]
Description: UbiA prenyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-22   79.8  18.7    2.9e-22   79.2  18.7    1.3  1  UbiA      UbiA prenyltransferase family


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 !   79.2  18.7   1.6e-26   2.9e-22      24     226 ..      53     251 ..      29     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 1.6e-26
                              UbiA  24 llllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltallgllal 100
                                       l ++++++a+++++++N+++D e+D +  + p+R+    r   +  l+++  l++++++++ + l ++ a+ +ll +
  gi|336252289|ref|YP_004595396.1|  53 LPIFIVFAATLFVYTINRFLDLEEDEQ--NVPRRAAFVKRYG-RFWLALGSGLYLAAIGVA-VALELPGAGYMLLPV 125
                                       345677899999***************..*****88888888.889999999999999999.99************* PP

                              UbiA 101 llyvvYt.glrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDrkagi 176
                                       +++v+Y+     Kr+ l++++++g+a+g++pl+  +++++  sl +l++a  + ++++  a++ d++d+egDr+ gi
  gi|336252289|ref|YP_004595396.1| 126 AVAVLYSlA-GVKRVFLVKNLFVGLAWGIIPLGVGYYYGQLQSLDILFVAGYITAMITIAAVIFDVKDIEGDREEGI 201
                                       *******87.9*********************99999988779999999999877777777777************* PP

                              UbiA 177 ktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaala 226
                                        t p ++G++++r++ +a+ +av+ ++ ++++++  l+  +l++l++ a+ 
  gi|336252289|ref|YP_004595396.1| 202 ATVPNRYGPATTRRVcQAANVAVAAAV-VAVVALSSLSGRFLVVLAMNAYV 251
                                       **************9855555555544.33444444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2098.37
//
Query:       gi|336252290|ref|YP_004595397.1|  [L=75]
Description: hypothetical protein Halxa_0881 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0031   17.6   0.9      0.024   14.7   0.1    2.1  2  Zn-ribbon_8     Zinc ribbon domain
     0.0098   15.8   0.2      0.013   15.4   0.2    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.025   14.7   0.0      0.029   14.5   0.0    1.1  1  DiS_P_DiS       Bacterial Peptidase A24 N-terminal domain
      0.029   14.8   0.1      0.029   14.8   0.1    1.2  1  DraK_HK_N       DraK Histidine Kinase N-terminal domain


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 !   14.7   0.1   5.5e-06     0.024      22      39 ..      31      49 ..      22      50 .. 0.76
   2 ?    1.6   0.1     0.071   3.2e+02       7      12 ..      63      68 ..      62      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.5e-06
                       Zn-ribbon_8 22 s.dapltaCPeCgsevrrv 39
                                      s ++++ +CP+Cg++v +v
  gi|336252290|ref|YP_004595397.1| 31 SiEEADRECPDCGGNVLKV 49
                                      23778888******99876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.071
                       Zn-ribbon_8  7 rCeeCg 12
                                      +C++C+
  gi|336252290|ref|YP_004595397.1| 63 KCQDCD 68
                                      799997 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 !   15.4   0.2     3e-06     0.013      16      59 ..      23      75 .]      14      75 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3e-06
                    OrfB_Zn_ribbon 16 Gikveevnpay.TSktCseCgsknke.......alsgrtfkCpnCgfe.adrD 59
                                      G +v ev+       +C+ Cg ++ +       +     +kC++C  + adrD
  gi|336252290|ref|YP_004595397.1| 23 GDSVMEVDSIEeADRECPDCGGNVLKvtympsvTELVTGWKCQDCDWSeADRD 75
                                      5667777777777799*****999999999998888999******98879*99 PP

>> DiS_P_DiS  Bacterial Peptidase A24 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.4e-06     0.029      22      59 ..      31      68 ..       4      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.4e-06
                         DiS_P_DiS 22 slvkprSrCpkCghklkwleliPvlSylllrgrCraCk 59
                                      s+ + + +Cp Cg ++  +  +P +  l+++ +C+ C+
  gi|336252290|ref|YP_004595397.1| 31 SIEEADRECPDCGGNVLKVTYMPSVTELVTGWKCQDCD 68
                                      67777889*****************************6 PP

>> DraK_HK_N  DraK Histidine Kinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   6.6e-06     0.029      23      52 ..       3      32 ..       1      59 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.6e-06
                                      HHHHHHTS---HHHHTTT-SS-SEEEEE-T CS
                         DraK_HK_N 23 dsrlaagepitaelLeeqvpgdryvvVrip 52
                                      ++r+ +g+++tae L+e v+gd+   V+  
  gi|336252290|ref|YP_004595397.1|  3 ENRVVQGRMVTAEKLAELVEGDSVMEVDSI 32
                                      89********************98888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 573.79
//
Query:       gi|336252291|ref|YP_004595398.1|  [L=105]
Description: hypothetical protein Halxa_0882 [Halopiger xanaduensis SH-6]
Scores for 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:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 796.67
//
Query:       gi|336252292|ref|YP_004595399.1|  [L=90]
Description: hypothetical protein Halxa_0883 [Halopiger xanaduensis SH-6]
Scores for 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-20   71.2   0.3    7.6e-20   71.0   0.3    1.1  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.3   4.2e-24   7.6e-20       3      68 ..      16      80 ..      14      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 4.2e-24
                            HalOD1  3 espstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsd 68
                                      +++ +++v+ vaa+ g+dptel+pL++a+DpdAL ++f+ +++g  +++g+v+F y+gy++t++ d
  gi|336252292|ref|YP_004595399.1| 16 DRVYERIVTEVAAIDGTDPTELPPLFNAVDPDALLTVFSATESG-VSRSGRVEFPYAGYDITITFD 80
                                      67899***********************************6666.57789*************866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 672.83
//
Query:       gi|336252293|ref|YP_004595400.1|  [L=74]
Description: hypothetical protein Halxa_0884 [Halopiger xanaduensis SH-6]
Scores for 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   14.8   0.0      0.022   14.8   0.0    1.1  1  DUF4567   Domain of unknown function (DUF4567)


Domain annotation for each model (and alignments):
>> DUF4567  Domain of unknown function (DUF4567)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.2e-06     0.022       1      46 [.      14      62 ..      14      74 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-06
                           DUF4567  1 rldesptplglqhhlelgkalamalpplvvegpathh...iaggrladl 46
                                      r++e p+   + h+ elg a   +lp l  +gp +      ag r  dl
  gi|336252293|ref|YP_004595400.1| 14 RIEEVPAESRVCHYDELGEAAKATLPALTNDGPVAVDgsvAAGFRDCDL 62
                                      789999999************************8643221445566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 565.78
//
Query:       gi|336252294|ref|YP_004595401.1|  [L=279]
Description: 2,5-didehydrogluconate reductase [Halopiger xanaduensis SH-6]
Scores for complete 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-54  185.5   0.0    2.2e-52  178.1   0.0    2.0  1  Aldo_ket_red   Aldo/keto reductase family
  ------ inclusion threshold ------
       0.14   11.9   0.0         11    5.7   0.0    2.2  2  FAD_binding_4  FAD binding domain


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 !  178.1   0.0   2.4e-56   2.2e-52       2     293 ..      23     265 ..      22     266 .. 0.97

  Alignments for each domain:
  == domain 1  score: 178.1 bits;  conditional E-value: 2.4e-56
                                       EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTS CS
                      Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeik 78 
                                       lglGtwq ++      ++ +e +r+ale G++++DtA+ Y    +e  +Ge ++++ ++ree+++atKv        
  gi|336252294|ref|YP_004595401.1|  23 LGLGTWQNTG------DQCAESVRTALEMGYRHVDTAQGY---DNEAAVGEGIAQADVDREEIFLATKV------ST 84 
                                       899***7776......8***********************...**************************......** PP

                                       SSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTTT- CS
                      Aldo_ket_red  79 sglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkkkv 155
                                       s+l ++++ e  ++sl rLg+dyvDll++H+p ++++  e +l+a+ +l++ G+i ++GvSnf+ +qle+a      
  gi|336252294|ref|YP_004595401.1|  85 SNLAHDDVLETTRASLDRLGVDYVDLLYVHWPARTYD-PEGTLSAFSKLYDDGLIENVGVSNFQPAQLEEAVDVCDA 160
                                       *************************************.*********************************999999 PP

                                       -EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHH CS
                      Aldo_ket_red 156 kivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeel 232
                                       +i a+q+e+++l  l +e+++e+c+++++ ++ayspl++G                                  +e+
  gi|336252294|ref|YP_004595401.1| 161 PILANQIECHPL--LPQEEVREACEHYDIEVVAYSPLARGGVF-----------------------------DQPEI 206
                                       ************..************************99887.............................3579* PP

                                       HHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHHH CS
                      Aldo_ket_red 233 selakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldell 293
                                       +e+a eh v+  q++l+++   ++++++ip+a+  ++++dn+++l l+l+ e+++++d++ 
  gi|336252294|ref|YP_004595401.1| 207 REIADEHAVTEVQVSLAWLR--EKGITAIPKATGEAHIRDNFESLTLELDREDIDAIDAIQ 265
                                       ********************..************************************985 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0    0.0052        47      22      79 ..      17      73 ..      13      75 .. 0.87
   2 ?    5.7   0.0    0.0012        11      10      66 ..     215     271 ..     211     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0052
                                      HCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHH CS
                     FAD_binding_4 22 eaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlve 79
                                      + g+p+l +G+  ++++q+ ++  + l +  ++++ + +  ++ a v+ G+  +d+++
  gi|336252294|ref|YP_004595401.1| 17 ASGIPMLGLGTWQNTGDQCAESVRTALEM-GYRHVDTAQGYDNEAAVGEGIAQADVDR 73
                                      6799************8887788899999.78988888888999*******9999987 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETT..S--EEEEETTTTEE CS
                     FAD_binding_4  10 eeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsr..lnrileideeegta 66 
                                       + ev+  l++ +e+g++ ++ ++G   ++++  ++ ++l l+r  ++ i  i+e+++t+
  gi|336252294|ref|YP_004595401.1| 215 VTEVQVSLAWLREKGITAIPKATGEAHIRDN--FESLTLELDRedIDAIDAIQETNRTI 271
                                       5799************************999..78888888654677788888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2164.44
//
Query:       gi|336252295|ref|YP_004595402.1|  [L=256]
Description: hypothetical protein Halxa_0886 [Halopiger xanaduensis SH-6]
Scores for 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   13.4   0.1      0.066   12.9   0.1    1.2  1  Glyco_transf_5  Starch synthase catalytic domain
        1.3    9.0   5.0        0.8    9.6   2.2    2.0  2  SLATT_1         SMODS and SLOG-associating 2TM effector domai
        8.4    6.6   6.8        3.8    7.7   2.4    2.2  2  GPHR_N          The Golgi pH Regulator (GPHR) Family N-termin


Domain annotation for each model (and alignments):
>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.1e-05     0.066      13      47 ..     136     170 ..     131     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                    Glyco_transf_5  13 aktGGLadvvgaLpkaLaklghdvrvilPrygaik 47 
                                       a + G+a v++aL+ a ak g +v++++ +y++  
  gi|336252295|ref|YP_004595402.1| 136 AAASGVATVATALAAACAKFGGRVTTVVLAYPFAM 170
                                       6789***************************8765 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 ?    9.6   2.2   0.00013       0.8      11      67 ..      83     142 ..      78     147 .. 0.83
   2 ?   -0.1   0.2      0.14   8.4e+02      33      45 ..     144     156 ..     140     184 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00013
                           SLATT_1  11 dwYrkkaeeneraakrwrlllillellalllaalrafgelsv...dlvgvlaavaaalla 67 
                                       ++Y++k+++ + +  ++ ++ ++l + +ll  a++a++ ++     l  vla++aa+++a
  gi|336252295|ref|YP_004595402.1|  83 RYYAAKLDSTRTRLGIVGVTALALVGWGLLTLAWGAMSYMEQvdiPLNSVLAVAAASGVA 142
                                       7******************99999999999998887766655443788999999999988 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.14
                           SLATT_1  33 llellalllaalr 45 
                                       ++++la+++a ++
  gi|336252295|ref|YP_004595402.1| 144 VATALAAACAKFG 156
                                       3333333333333 PP

>> GPHR_N  The Golgi pH Regulator (GPHR) Family N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.4   0.00064       3.8       8      38 ..      93     122 ..      88     138 .. 0.81
   2 ?    0.0   0.6      0.16   9.3e+02      17      33 ..     133     149 ..     132     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00064
                            GPHR_N   8 lsrvsviGvtlmAiLSGfGavstpyetfslf 38 
                                        +r++++Gvt +A+  G G  + ++ ++s+ 
  gi|336252295|ref|YP_004595402.1|  93 RTRLGIVGVTALAL-VGWGLLTLAWGAMSYM 122
                                       58**********95.5999999999999884 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.16
                            GPHR_N  17 tlmAiLSGfGavstpye 33 
                                         +A+ SG+++v t+  
  gi|336252295|ref|YP_004595402.1| 133 LAVAAASGVATVATALA 149
                                       668888******99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2209.19
//
Query:       gi|336252296|ref|YP_004595403.1|  [L=63]
Description: hypothetical protein Halxa_0887 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.002   17.5   4.6     0.0023   17.3   4.6    1.0  1  SLAC1            Voltage-dependent anion channel
  ------ inclusion threshold ------
      0.028   14.7   2.4      0.032   14.5   2.4    1.1  1  Phage_holin_5_2  Phage holin family Hol44, in holin superfami
       0.38    9.7   1.0       0.41    9.6   1.0    1.0  1  Aconitase        Aconitase family (aconitate hydratase)


Domain annotation for each model (and alignments):
>> SLAC1  Voltage-dependent anion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   4.6   3.9e-07    0.0023     134     182 ..       7      56 ..       4      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.9e-07
                             SLAC1 134 itpawllpvvgllvvallgallaesqnpslqll..gilvvslllwglGlll 182
                                       +t+a +++v++l v +l++a ++++ +        +++v++l+++g+Gll+
  gi|336252296|ref|YP_004595403.1|   7 TTAAAFIAVIALGVGGLIAAPMMTTDTVLMM-VapSMIVFGLIMFGIGLLH 56 
                                       589*******************766333333.2588*************97 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 ?   14.5   2.4   5.4e-06     0.032      19      59 ..       9      52 ..       4      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.4e-06
                   Phage_holin_5_2 19 kdkyIPlilgiiGiilgvvivfta...dfqaedilifgaiiqGi 59
                                      +  +I +i + +G+++++ +++t+   ++ a ++++fg i+ Gi
  gi|336252296|ref|YP_004595403.1|  9 AAAFIAVIALGVGGLIAAPMMTTDtvlMMVAPSMIVFGLIMFGI 52
                                      5689*************9999996699999********888777 PP

>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.0   6.9e-05      0.41     132     167 ..       7      42 ..       4      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 6.9e-05
                         Aconitase 132 TtmigglGvlaiGvGgieaeavllgqplelkipkvv 167
                                       Tt +  ++v+a GvGg  a+ ++++ ++ + +  ++
  gi|336252296|ref|YP_004595403.1|   7 TTAAAFIAVIALGVGGLIAAPMMTTDTVLMMVAPSM 42 
                                       56666689*******************988776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.33
# Mc/sec: 569.62
//
Query:       gi|336252297|ref|YP_004595404.1|  [L=323]
Description: phosphoadenosine phosphosulfate reductase [Halopiger xanaduensis SH-6]
Scores for 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-18   67.1   0.0    1.7e-14   54.2   0.0    3.1  2  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
  ------ inclusion threshold ------
       0.04   13.4   0.0      0.086   12.3   0.0    1.6  2  Diphthami_syn_2  Diphthamide synthase


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 !   54.2   0.0   1.9e-18   1.7e-14       2     146 ..      48     229 ..      47     237 .. 0.86
   2 !    7.4   0.0   0.00045         4     149     172 ..     261     284 ..     254     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.9e-18
                                       EEEE--SSCTCHHHHHHHHHHCTTH.....EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH- CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.....pvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekh 73 
                                       ++v + gGkds+ +l  + ++ + +     p vf+d  ++f+e+ +fvd  +++ +l+++++++e+ ++   +    
  gi|336252297|ref|YP_004595404.1|  48 PAVMWTGGKDSTLTLYFIKEVADRFdlevpPAVFIDHYQHFDEIHDFVDHWADEWDLEVIYARNEDVGEYVDEHGLE 124
                                       78999***********999999997899999***************************9999999987776666666 PP

                                       S-THHHC.............................HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSE CS
                       PAPS_reduct  74 gsslyee.............................aaeriaKveplkkaLekldedalltGaRrdesksraklpiv 121
                                       + ++ e                                +++ K+++l+ aLe++d d +++G+R de+++ra + ++
  gi|336252297|ref|YP_004595404.1| 125 PGDDIEIselsehnqhhvreileyeedtfpflldtyVGNHLLKTVALNDALEEHDIDGVISGVRWDEQEARADETFF 201
                                       6666665667777778888888888888888888776788888888888**************************** PP

                                       EECTTT-S....CEEE-CCCT--HHHHHH CS
                       PAPS_reduct 122 eidedfek....slrvfPllnWteedvwq 146
                                       + + d ++    + r++P+l+++e  vw+
  gi|336252297|ref|YP_004595404.1| 202 SPRHD-PDiyppHDRIQPILQFDEAAVWD 229
                                       *9998.33455699**************7 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00045
                                       HHCT--B-CCCCTT-SS--BCTTB CS
                       PAPS_reduct 149 lrenipynpLydqgfrsiGcvpct 172
                                       ++e++p+ p y++gfrs+G   +t
  gi|336252297|ref|YP_004595404.1| 261 TQEDVPISPKYFAGFRSLGSEVST 284
                                       689****************98777 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.6e-06     0.086       4      22 ..      49      67 ..      46     119 .. 0.81
   2 ?   -2.7   0.0      0.38   3.4e+03      15      31 ..     169     185 ..     167     197 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.6e-06
                   Diphthami_syn_2  4 avlysGGkDsilaLykalk 22
                                      av++ GGkDs+l Ly + +
  gi|336252297|ref|YP_004595404.1| 49 AVMWTGGKDSTLTLYFIKE 67
                                      89*************7543 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.38
                   Diphthami_syn_2  15 laLykalkesevesLvs 31 
                                       +aL  al+e++++ ++s
  gi|336252297|ref|YP_004595404.1| 169 VALNDALEEHDIDGVIS 185
                                       67777777777776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2481.41
//
Query:       gi|336252298|ref|YP_004595405.1|  [L=368]
Description: UDP-N-acetylglucosamine 2-epimerase [Halopiger xanaduensis SH-6]
Scores for 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-107  358.0   0.0   4.8e-107  357.8   0.0    1.0  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
     0.0081   16.6   0.0      0.021   15.2   0.0    1.7  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.031   14.3   1.2      0.078   13.0   0.8    1.9  1  baeRF_family2    Bacterial archaeo-eukaryotic release factor 
       0.15   10.6   0.0       0.22   10.0   0.0    1.2  1  MutL             MutL protein


Domain annotation for each model (and alignments):
>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.8   0.0  1.1e-110  4.8e-107      10     346 ..      28     350 ..      21     351 .. 0.95

  Alignments for each domain:
  == domain 1  score: 357.8 bits;  conditional E-value: 1.1e-110
                                       EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSHHHHHHHHH CS
                       Epimerase_2  10 elqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDtnetlagala 86 
                                       e++lv+tGqH+d+em+d++feel+i++p+y+l+++s++++++t+r++ +le v+eee+pD+vl++GDtn+tlaga++
  gi|336252298|ref|YP_004595405.1|  28 EEVLVHTGQHYDEEMSDVFFEELDIPEPEYNLGVKSDTHGRQTARMIAELEPVVEEEDPDVVLLYGDTNSTLAGAIV 104
                                       689************************************************************************** PP

                                       HHHTT-EEEEET-----S-TT..SHHHHHHHHHHHT-SEEEESSHHHHHHHHHTT--GGGEEE---HHHHHHHHHHH CS
                       Epimerase_2  87 AfklripvaHveAGlRsfdltegmpeEinRhlidklsdlhfapteearenLlkegeeeerifvvGntviDalllske 163
                                       ++k+++ vaHveAGlRs++++  mpeE+nR+l+d+ sdl fap+e+a +nL +eg+  + ++ +G++++Da+l  ++
  gi|336252298|ref|YP_004595405.1| 105 GSKRDVAVAHVEAGLRSGNRE--MPEEVNRILTDHASDLCFAPSEAAVDNLAAEGI-VDGVHWTGDVMYDAVLAARD 178
                                       *********************..*********************************.789***************** PP

                                       HHH...T-HHHHHH..--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHHH..HHHH CS
                       Epimerase_2 164 eieeklkaseilke..lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkrl..leel 236
                                       +++e+    +il++  l+ +++vl+t+Hr++n+de    ++++++l+ la+   ++vv+p+h  prt +rl  ++ +
  gi|336252298|ref|YP_004595405.1| 179 RARENS---TILEDlgLEPDEFVLTTVHRASNTDER---ENLEAILDGLADA-PLPVVFPAH--PRTVNRLqeYDLW 246
                                       **9555...9*99999******************55...8888889999997.799******..*******887788 PP

                                       HH-.TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT-HHHHHHH CS
                       Epimerase_2 237 eel.envtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvnlReeteRpegveagtnvlvgtdkeeIvaa 312
                                       e++ +++ +ieplgyldf++ll +a+ v tdSgG+q+Ea++lg+ +v++Reete+ e+v++g+n lvg++++ I + 
  gi|336252298|ref|YP_004595405.1| 247 ERAtDDLEIIEPLGYLDFVRLLDTAERVATDSGGVQKEAFFLGTRCVTMREETEWTETVDCGWNQLVGPNADLIREG 323
                                       88877***********************************************************************9 PP

                                       HHHHCT-..--......--TT-SS-HHHHHHHHH CS
                       Epimerase_2 313 leklledkkelekmanaknpYgdGkaseriveil 346
                                       l++  e        +++ +pYgdG as+riv +l
  gi|336252298|ref|YP_004595405.1| 324 LTTDWEP-------QSNPQPYGDGSASRRIVGLL 350
                                       9887744.......45589***********9877 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 !   15.2   0.0   4.8e-06     0.021      12     149 ..      21     158 ..      14     164 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.8e-06
                   Glyco_trans_4_4  12 raLaarGheVtvltpapapgape......leedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvhahs. 81 
                                       r  ++ G eV v t + + +++       l+    + ++l v    +++ ++++++ l+ ++  ++e pdvv + + 
  gi|336252298|ref|YP_004595405.1|  21 RKIRDVGEEVLVHTGQHYDEEMSdvffeeLDI-PEPEYNLGVKSDTHGRQTARMIAELEPVV--EEEDPDVVLLYGd 94 
                                       55666677777877666666442222111222.222346677777789999***********..***********97 PP

                   Glyco_trans_4_4  82 ptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrr.adavlvvseaeaeelralgv 149
                                         + la+++   +r++ +  ++ +  lr+     r +  +++r l  +  d+++++sea ++ l+a g+
  gi|336252298|ref|YP_004595405.1|  95 TNSTLAGAIVGSKRDVAV-AHVEAG-LRS---GNREMPEEVNRILTDHaSDLCFAPSEAAVDNLAAEGI 158
                                       88********95555555.555553.233...35556677777777775799*************9986 PP

>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.8   1.7e-05     0.078      57     133 ..      68     139 ..      61     157 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                     baeRF_family2  57 erNaeavAeevdrlvresgaelVvlaGDvrarsllrdeLpervrelvvevegggraagadrealaeevaealaerra 133
                                       +++a+ +A e++ +v+e+++++V+l GD+ +   l+ ++    r+++v   + g  +g  ++++ eev+++l+++++
  gi|336252298|ref|YP_004595405.1|  68 RQTARMIA-ELEPVVEEEDPDVVLLYGDTNS--TLAGAIVGSKRDVAVAHVEAGLRSG--NREMPEEVNRILTDHAS 139
                                       45555555.79*****************975..6888888888887765444444444..58888888888888876 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0     5e-05      0.22     116     179 ..      81     143 ..      61     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5e-05
                              MutL 116 lrelrpdiiLLaGGtDgGnkevllenAellaeaklklpviyAGNkaareeveeiLeeagkelvv 179
                                       ++e  pd++LL G t+     +++   + +a a++++  +  GN+++ eev+ iL+++  +l +
  gi|336252298|ref|YP_004595405.1|  81 VEEEDPDVVLLYGDTNSTLAGAIVGSKRDVAVAHVEAG-LRSGNREMPEEVNRILTDHASDLCF 143
                                       45889****************************99875.79****************9888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); 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:                         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 0.23s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 2949.12
//
Query:       gi|336252299|ref|YP_004595406.1|  [L=370]
Description: hypothetical protein Halxa_0890 [Halopiger xanaduensis SH-6]
Scores for 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-07   30.0   0.0    5.2e-07   29.1   0.0    1.5  1  DUF354           Protein of unknown function (DUF354)
    0.00015   22.3   0.8     0.0017   18.8   0.8    2.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0021   18.0   0.1     0.0042   17.1   0.1    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
      0.074   13.1   0.0       0.25   11.4   0.0    1.9  2  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom


Domain annotation for each model (and alignments):
>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   1.2e-10   5.2e-07       9     277 ..       8     269 ..       4     333 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.2e-10
                            DUF354   9 nap.hvryfrdlikkfekeGievlltardsGdlaklvklynfvfksiGkhGvtlkekliesakrvinlskliaevkp 84 
                                       n+p hv+ +++ ++++e +G +vl+ ar     + l+  ++  +++ G  G +l+  l e     +++ +      p
  gi|336252299|ref|YP_004595406.1|   8 NTPaHVHLYKHTVERLEADGHDVLVLARGDEFTESLLSYHDVPYETYGDRGESLHSLLWELPTHLYEMGRKARAFDP 84 
                                       5554*************************9999******************************************** PP

                            DUF354  85 dvalakhsvelprvafGlnipvvyvldnehaeaankltlpladeiikpividendlkktGadpnrirryeGtsevin 161
                                       dv +          ++  + p++ vld e ++    ++ p+++  + p++ +    k++G +     r+eG  e + 
  gi|336252299|ref|YP_004595406.1|  85 DVIFGIGPYAAYTGTI-TGTPAIAVLDSEPSLD-HVVSRPFVQAFLTPEAFQ----KDLGEK---HYRFEGFKESAY 152
                                       **76554333332222.478*********9885.57899**********986....466776...345888888776 PP

                            DUF354 162 vqs..yeideeilkdlnlkledektilmrpepslasyldad..chkdvltkiveklkdridilviprdeeqkeiyee 234
                                       ++   +e de + +dl+ +  de+  ++r +  +  +  +      +   +++e l +++ i v   de  +  +  
  gi|336252299|ref|YP_004595406.1| 153 LHPdvFEPDESVREDLG-VGPDEPYAIVRLNAFNGHHDVGRegFSLEQRRRLLEALSEHATIFV--SDEGGELDFSS 226
                                       65555************.6677787788888755544333200223445679999999998776..45555566888 PP

                            DUF354 235 vdnviviketvdalsllkrsdlviGaGGtmnreaallGipvvs 277
                                       ++      ++      l ++dl++    tm  eaallG+p++ 
  gi|336252299|ref|YP_004595406.1| 227 LEARPYDLHPARIHDALAEADLLVADTQTMVTEAALLGTPAIR 269
                                       887777788888889999**********************995 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 !   18.8   0.8   3.8e-07    0.0017       9      92 ..      18     102 ..      14     270 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.8e-07
                   Glyco_trans_4_4   9 elaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpsplad.laalralrrll.....rqrrerpdvvha 79 
                                       +++++L+a+Gh+V vl++      +e +e  + +h +p    +++  + ++ l+ l   l     ++r++ pdv+  
  gi|336252299|ref|YP_004595406.1|  18 HTVERLEADGHDVLVLAR-----GDEFTESLLSYHDVPYETYGDRGESlHSLLWELPTHLyemgrKARAFDPDVIFG 89 
                                       789***************.....5568999*******977666533331556677777666666656*********9 PP

                   Glyco_trans_4_4  80 hsptaglaarlar 92 
                                        +p+a++ + +  
  gi|336252299|ref|YP_004595406.1|  90 IGPYAAYTGTITG 102
                                       9999877665544 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   9.5e-07    0.0042      10      88 ..      18      99 ..      13     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.5e-07
                    Glyco_transf_4 10 eLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllr.....slaflrrlrrllkrekpDvvHahspaa 83
                                      + +++L ++Gh+V v+++gd+  +      +++vp+  +  ++  l+      +++l  + r +++++pDv+   +p+a
  gi|336252299|ref|YP_004595406.1| 18 HTVERLEADGHDVLVLARGDEFTESLL--SYHDVPYETYGDRGESLHsllweLPTHLYEMGRKARAFDPDVIFGIGPYA 94
                                      67899************9988777776..67788887776655544411111566777889999********9888888 PP

                    Glyco_transf_4 84 lgaal 88
                                      ++ + 
  gi|336252299|ref|YP_004595406.1| 95 AYTGT 99
                                      76654 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 ?   11.4   0.0   5.5e-05      0.25      11     101 ..      12      96 ..       9     108 .. 0.82
   2 ?   -2.4   0.0      0.99   4.4e+03      14      51 ..     104     145 ..     102     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHHHHHCTT-EEEEEEETCCCHHHHHHCCT-EEEE---GHCTT..CHHHHCCHHHHHHHHHHHHHHHHHH CS
                   Glyco_transf_28  11 hvfPalAlakeLkkegheVrylgtkrgleerlveeaglefepiageklrrklspknlkeilkvlkavvkakkilkea 87 
                                       hv ++   +++L+++gh+V  l+  ++++e l   +++++e+ + +   ++   + l+e+++    + ++ +  + +
  gi|336252299|ref|YP_004595406.1|  12 HVHLYKHTVERLEADGHDVLVLARGDEFTESLLSYHDVPYETYGDR---GESLHSLLWELPTH---LYEMGRKARAF 82 
                                       99999999************************77788888665555...44566777777777...77889999999 PP

                                       HHCCCCCCCCCCCH CS
                   Glyco_transf_28  88 kpdavvgtggyvsl 101
                                        pd+++g g y++ 
  gi|336252299|ref|YP_004595406.1|  83 DPDVIFGIGPYAAY 96 
                                       99999999999876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.99
                                       HHHHHHHHHHCTT-EEE.....EEEETCCCHHHHHHCCT-EEE CS
                   Glyco_transf_28  14 PalAlakeLkkegheVr.....ylgtkrgleerlveeaglefe 51 
                                       Pa+A+ +     +h V+     ++ t++ +++ l  e+++ fe
  gi|336252299|ref|YP_004595406.1| 104 PAIAVLDSEPSLDHVVSrpfvqAFLTPEAFQKDL-GEKHYRFE 145
                                       6777776666667666666666888999999998.66666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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 0.20s 00:00:00.68 Elapsed: 00:00:00.35
# Mc/sec: 3139.95
//
Query:       gi|336252300|ref|YP_004595407.1|  [L=457]
Description: hypothetical protein Halxa_0891 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.03   14.3   0.1      0.065   13.3   0.1    1.5  1  CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit
      0.061   13.4   0.1      0.061   13.4   0.1    2.4  3  HEPN          HEPN domain


Domain annotation for each model (and alignments):
>> CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   7.2e-06     0.065       3      21 ..       5      23 ..       4      35 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.2e-06
                      CytB6-F_Fe-S  3 VPDmsrRqllNlllvGaia 21
                                       P++srRqll+ l +Ga+ 
  gi|336252300|ref|YP_004595407.1|  5 LPSLSRRQLLGGLAGGAAV 23
                                      6**********99999873 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.8e-06     0.061       7      38 ..     102     133 ..      96     134 .. 0.86
   2 ?   -2.9   0.0      0.79   7.1e+03       5      16 ..     235     246 ..     215     259 .. 0.68
   3 ?   -2.6   0.1      0.67     6e+03      83      95 ..     288     300 ..     261     308 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-06
                                       HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                              HEPN   7 rAeedleaAellleegdydlacfhaqqaaeka 38 
                                        A   le+Ae +le+gdy++a+f a + +++a
  gi|336252300|ref|YP_004595407.1| 102 GAGGWLEDAEASLEAGDYNDALFEARYGLQFA 133
                                       57778********************9988765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.79
                                       HHHHHHHHHHHH CS
                              HEPN   5 lrrAeedleaAe 16 
                                       +rrAe   e+Ae
  gi|336252300|ref|YP_004595407.1| 235 IRRAEIAVESAE 246
                                       344444444444 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.67
                                       CCHHCCCTSS--S CS
                              HEPN  83 ayiesrYpdakee 95 
                                         +esrY d++ e
  gi|336252300|ref|YP_004595407.1| 288 DEVESRYVDDDAE 300
                                       3466777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.35
# Mc/sec: 3886.26
//
Query:       gi|336252301|ref|YP_004595408.1|  [L=193]
Description: hypothetical protein Halxa_0892 [Halopiger xanaduensis SH-6]
Scores for 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    9.9   0.1        0.2    9.8   0.1    1.0  1  CRT10     CRT10


Domain annotation for each model (and alignments):
>> CRT10  CRT10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   1.1e-05       0.2     363     436 ..      28     101 ..       8     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 1.1e-05
                             CRT10 363 qsaytkggkikyevvrekkvlvkykvdlddckkekrkntyadeklgkekleedkkkvkekesswqeesglklqe 436
                                       + a  + g+   e +r +++l+ ++v +d+   + +   + +  + + +++e+  + + ++ sw+ee++ +++ 
  gi|336252301|ref|YP_004595408.1|  28 EEAKYPDGIDDVELTRRNNTLILKAVAEDQSVSKYTPTAQLKASVTENRVYEEDPDERRQSFSWDEEEEEEIES 101
                                       34444567778899*************99999999999***************9************99777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.40u 0.19s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 1716.53
//
Query:       gi|336252302|ref|YP_004595409.1|  [L=114]
Description: glutaredoxin [Halopiger xanaduensis SH-6]
Scores for 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-16   59.7   0.0    5.1e-16   58.6   0.0    1.6  2  Glutaredoxin   Glutaredoxin
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.16   11.6   0.0    1.1  1  Abhydrolase_1  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   5.7e-20   5.1e-16       1      60 []      27      92 ..      27      92 .. 0.97
   2 ?   -2.8   0.0      0.88   7.8e+03      31      43 ..      97     109 ..      96     112 .. 0.58

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 5.7e-20
                                      EEEEES.....TSSHHHHHHHHHHHHTTGGEEEEEGCCSH.HHHHHHHHHHTSSSSSEEEETTEEE CS
                      Glutaredoxin  1 vvlftk.....ptCpyCkkakrlLkelgvkfeeidvdkde.eireelkelsgvrtvPqvfidgkhv 60
                                      vvlf+k     p+C+y++ka  l + ++ ++e++dv++   e+r++l e s+++t+Pq f+dg++v
  gi|336252302|ref|YP_004595409.1| 27 VVLFMKgtelmPQCGYSRKALGLIDHHRDEYETVDVLESLdEYRQALSEHSDWETIPQTFVDGEFV 92
                                      89************************************955***********************97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.88
                                       GCCSHHHHHHHHH CS
                      Glutaredoxin  31 vdkdeeireelke 43 
                                       ++++ e+r el e
  gi|336252302|ref|YP_004595409.1|  97 ILEELEERGELAE 109
                                       5555566666655 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.7e-05      0.16      38      71 ..      38      74 ..      37      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.7e-05
                                      TTSTTSSSTTTGB....CHHSHHHHHHHHHHHHHHCT CS
                     Abhydrolase_1 38 rGvgySspapacin...ddygtasvaddldrildalg 71
                                      + +gyS++a+  i+   d+y+t++v ++ld  ++al 
  gi|336252302|ref|YP_004595409.1| 38 PQCGYSRKALGLIDhhrDEYETVDVLESLDEYRQALS 74
                                      789*******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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: 0.36u 0.19s 00:00:00.55 Elapsed: 00:00:00.33
# Mc/sec: 1021.12
//
Query:       gi|336252303|ref|YP_004595410.1|  [L=209]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-21   74.7   0.1    2.1e-20   73.2   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    1.1e-18   67.6   0.1      3e-18   66.3   0.0    1.7  2  Methyltransf_11  Methyltransferase domain
    6.4e-15   55.3   0.0    7.8e-15   55.0   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    8.4e-15   55.0   0.0    1.1e-14   54.6   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.6e-10   41.6   0.0      3e-10   40.7   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    2.2e-07   30.4   0.0      3e-07   30.0   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.2e-06   28.1   0.0    1.4e-06   27.8   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    7.9e-06   25.6   0.0    1.1e-05   25.1   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
    0.00063   19.3   0.0    0.00092   18.8   0.0    1.2  1  MTS              Methyltransferase small domain
    0.00072   19.1   0.0     0.0051   16.3   0.0    2.2  3  CheR             CheR methyltransferase, SAM binding domain
    0.00072   19.5   0.0     0.0015   18.4   0.0    1.6  1  Methyltransf_8   Hypothetical methyltransferase
  ------ inclusion threshold ------
      0.024   13.2   0.0       0.03   12.9   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
      0.052   12.5   0.0      0.058   12.3   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.061   13.0   0.0       0.21   11.2   0.0    1.7  2  TPMT             Thiopurine S-methyltransferase (TPMT)
       0.11   12.4   0.0        0.2   11.6   0.0    1.4  1  DUF5348          Domain of unknown function (DUF5348)
       0.21   11.1   0.0        1.2    8.6   0.0    2.0  1  Methyltransf_4   Putative methyltransferase


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 !   73.2   0.0   1.9e-23   2.1e-20       1      97 []      45     137 ..      45     137 .. 0.94
   2 ?   -1.4   0.0       3.6     4e+03      21      38 ..     163     180 ..     149     202 .. 0.66

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 1.9e-23
                                       EEEET-TTSH.HHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGr.ltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       vLd+GcG+G+ ++++l +  ++ + tgvD+s ++l+ a e a    +nv + qgd+++lp +d+ fD+v+++++l h
  gi|336252303|ref|YP_004595410.1|  45 VLDAGCGQGDpVLRRLDDD-PAVEATGVDFSRQQLRFASEAA----PNVALAQGDITSLPVADSAFDAVTAFHSLIH 116
                                       9********9455666666.79********************....9************************88899* PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                       +++ +++++++e+arvL+pgG
  gi|336252303|ref|YP_004595410.1| 117 VPETQHRAVVDEFARVLRPGG 137
                                       ********************9 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                                       SSEEEEEESSHHHHHHHH CS
                   Methyltransf_25  21 kakvtgvDiseemleaar 38 
                                       +  + g D + e+l+aa 
  gi|336252303|ref|YP_004595410.1| 163 QWYIAGADATREQLRAAG 180
                                       567778888888887775 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   2.7e-21     3e-18       1      95 [.      46     140 ..      46     141 .. 0.89
   2 ?   -1.6   0.0         4   4.5e+03       9      39 ..     151     184 ..     149     197 .. 0.64

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 2.7e-21
                                       EEET-TTSHHHHHHH.HTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-. CS
                   Methyltransf_11   1 LdvGcGtGrlaeala.krg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv. 74 
                                       Ld+GcG+G  +     +    + +gvD+s ++l+ a+e+a++      + ++d+++lp++d+ fD+v+++++l hv 
  gi|336252303|ref|YP_004595410.1|  46 LDAGCGQGDPVLRRLdDDPaVEATGVDFSRQQLRFASEAAPNVA----LAQGDITSLPVADSAFDAVTAFHSLIHVp 118
                                       8*****99866554424447****************99999976....5***************************9 PP

                                       .CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 .edpekalkeiaRvLkpgGllv 95 
                                         +++++++e+aRvL+pgGl +
  gi|336252303|ref|YP_004595410.1| 119 eTQHRAVVDEFARVLRPGGLAL 140
                                       88999**************976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4
                                       HHHHHHHHTT....SEEEEEES-HHHHHHHHHHCC CS
                   Methyltransf_11   9 rlaealakrg....arvvgvDlskemlklakekas 39 
                                       +++ +l+ +g      + g D + e+l++a   ++
  gi|336252303|ref|YP_004595410.1| 151 ANSDWLE-TGvemqWYIAGADATREQLRAAGFTVR 184
                                       5555666.223445778888988888877755444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   6.9e-18   7.8e-15       3     113 ..      41     145 ..      39     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 6.9e-18
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                       +g +vlD+GCG+G+ +++      p  e +G+D+s + +++A e a      nv + qgdi++l+  ++d+ fD ++
  gi|336252303|ref|YP_004595410.1|  41 SGAQVLDAGCGQGDPVLRRL-DDDPAVEATGVDFSRQQLRFASEAAP-----NVALAQGDITSLP--VADSAFDAVT 109
                                       6889***********99999.667899*****************755.....*************..99******** PP

                   Methyltransf_31  80 snevlnaladpd..kileeiervlkpggilliedpr 113
                                       ++  l ++++ +  ++  e  rvl+pgg  l+++  
  gi|336252303|ref|YP_004595410.1| 110 AFHSLIHVPETQhrAVVDEFARVLRPGGLALLTEGT 145
                                       *****9999876337999************999988 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   9.8e-18   1.1e-14      13     162 ..      32     183 ..      18     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 9.8e-18
                   Methyltransf_23  13 lerllpklraggrvLdiGcGtG.illevlrengf.svtgvDlspeaveiae.kakkaqkdqfdeqeaaepqgkfdlI 86 
                                       lerl ++l++g+ vLd GcG G  +l+ l + ++ + tgvD s+++   a+  a++    q d  + ++ +  fd +
  gi|336252303|ref|YP_004595410.1|  32 LERLRERLPSGAQVLDAGCGQGdPVLRRLDDDPAvEATGVDFSRQQLRFASeAAPNVALAQGDITSLPVADSAFDAV 108
                                       678888889*************99*****999888********99888777644555555555558888889***** PP

                   Methyltransf_23  87 vlrevlehvp..dppellrqiatllkpgGylllseplaslk.edrllldw.lylvpagrhisffsarslkelleeaG 159
                                       +++++l hvp   + ++++ +a+ l+pgG++ll+e +a+++ +++   dw +  v++    +   a++ +e+l++aG
  gi|336252303|ref|YP_004595410.1| 109 TAFHSLIHVPetQHRAVVDEFARVLRPGGLALLTEGTADWQgANS---DWlETGVEM--QWYIAGADATREQLRAAG 180
                                       **********655**********************9998652333...442233333..225558899999999999 PP

                   Methyltransf_23 160 lev 162
                                       ++v
  gi|336252303|ref|YP_004595410.1| 181 FTV 183
                                       987 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   2.6e-13     3e-10       1      98 [.      46     138 ..      46     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 2.6e-13
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       L+ GcG G+ + + l++ p +e tgvD+s++++     ++a++ +    nv l + d+ +l+   s+fD+v+a++ l
  gi|336252303|ref|YP_004595410.1|  46 LDAGCGQGDPVLRRLDDDPAVEATGVDFSRQQL-----RFASEAA---PNVALAQGDITSLPVAdSAFDAVTAFHSL 114
                                       89******9988888888***************.....5555553...455555555544443356********999 PP

                   Methyltransf_12  77 hhl..kdirevldnirklLkpgGr 98 
                                        h+   + r+v+d+++++L+pgG 
  gi|336252303|ref|YP_004595410.1| 115 IHVpeTQHRAVVDEFARVLRPGGL 138
                                       999666666**************6 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   2.7e-10     3e-07      45     152 ..      39     142 ..      10     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.7e-10
                                       S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEE CS
                   Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvt 121
                                         +ga+vlD  +G gD  ++ +d  +   + +++D++ + L+ +      e+  n+ + q++   Lp  d +fD vt
  gi|336252303|ref|YP_004595410.1|  39 LPSGAQVLDAGCGQGDPVLRRLDD-DPAVEATGVDFSRQQLRFAS-----EAAPNVALAQGDITSLPVADSAFDAVT 109
                                       45789***********99987776.5778999******9997765.....677899999****************** PP

                                       EES-GGG-S-HH..HHHHHHHHHEEEEEEEEEE CS
                   Ubie_methyltran 122 vsfGlrnvtDkl..kaLkeayrvlkpGGrlvvl 152
                                         + l  v++++   ++ e  rvl+pGG  +  
  gi|336252303|ref|YP_004595410.1| 110 AFHSLIHVPETQhrAVVDEFARVLRPGGLALLT 142
                                       ********9876225899**********86655 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.3e-09   1.4e-06      59     230 ..      38     201 ..      29     209 .] 0.81

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.3e-09
                                       T--TT-EEEEES-TTSHHHHHHH.HHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEE CS
                              CMAS  59 elkpGmtlLdiGcGWGslvrrav.erydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsv 134
                                       +l  G ++Ld GcG G  v r   +   v+  g+ +S++q + a ++  ++ l++  +++       d  +d+v ++
  gi|336252303|ref|YP_004595410.1|  38 RLPSGAQVLDAGCGQGDPVLRRLdDDPAVEATGVDFSRQQLRFASEAAPNVALAQG-DIT--SLPVADSAFDAVTAF 111
                                       5889************977666615567999****************999997654.444..44455679******* PP

                                       S-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTTCCCHHHHHHTSTTS---BHHHHHHHHHHTT-E CS
                              CMAS 135 gafehvgkenydtffkklkkllkedGllllhtitslhkkelaerglklkfidkeiFPgGelpsieeieeeiseagft 211
                                         + hv + ++ + ++++ ++l+++Gl ll   t+  +        ++ ++++ +  + +++  ++  e+ ++agft
  gi|336252303|ref|YP_004595410.1| 112 HSLIHVPETQHRAVVDEFARVLRPGGLALLTEGTADWQG------ANSDWLETGVEMQWYIAGADATREQLRAAGFT 182
                                       **************************9998655544433......44589999999999999999999999999999 PP

                                       EEEEEE-HHHHHHHHHHHH CS
                              CMAS 212 vvdveslrahYakTLkaWa 230
                                       v d + ++ + a     W+
  gi|336252303|ref|YP_004595410.1| 183 VRDERLVGDELADEEASWT 201
                                       9998888777776666665 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   9.7e-09   1.1e-05       7     101 ..      35     132 ..      30     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 9.7e-09
                              MetW   7 iaelikpgsrvldlGcGdGe.llellkeekqvdgrGleldeegvaecvak..Glsviqgdldkdlenfedksfdyvv 80 
                                       + e +++g++vld GcG+G+ +l+ l ++  v++ G++ +++ +  + +    +++ qgd+       +d++fd v 
  gi|336252303|ref|YP_004595410.1|  35 LRERLPSGAQVLDAGCGQGDpVLRRLDDDPAVEATGVDFSRQQLRFASEAapNVALAQGDIT--SLPVADSAFDAVT 109
                                       6677899************8689******************998777655015666677664..456799******9 PP

                              MetW  81 lsqtlqatrnp..kevldellri 101
                                          +l  + ++  + v+de  r+
  gi|336252303|ref|YP_004595410.1| 110 AFHSLIHVPETqhRAVVDEFARV 132
                                       99999888655115689998887 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   8.2e-07   0.00092      16     133 ..      24     137 ..      17     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.2e-07
                                       --HHHHHHHHHCHCC..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STT CS
                               MTS  16 lDkGsklLletlpke..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvl 90 
                                        D G   +le l ++     +vlD GcG G   +  ++  p +e t vd + + l++a e + + +    + + d++
  gi|336252303|ref|YP_004595410.1|  24 PDGGEWRMLERLRERlpSGAQVLDAGCGQGDPVLRRLDDDPAVEATGVDFSRQQLRFASEAAPNVA----LAQGDIT 96 
                                       567777799999999877889************************************998876655....5666666 PP

                                       T.TSTTS-EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEE CS
                               MTS  91 e.eveekkfdlivsNPPfhagkatelavaeeliaeAkeaLkegG 133
                                       +  v++  fd++     fh+  ++ ++  ++++ e +++L++gG
  gi|336252303|ref|YP_004595410.1|  97 SlPVADSAFDAVTA---FHSLIHVPETQHRAVVDEFARVLRPGG 137
                                       62455777888875...888888777777788888888888887 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.55   6.2e+02      31      44 ..      41      54 ..      30      56 .. 0.74
   2 !   16.3   0.0   4.5e-06    0.0051     108     173 ..      76     141 ..      68     166 .. 0.87
   3 ?   -2.0   0.0       1.9   2.1e+03      58      82 ..     157     181 ..     150     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.55
                                      SSEEEEEES-TTTH CS
                              CheR 31 krvriwsagcssGe 44
                                      +  +++ agc++G 
  gi|336252303|ref|YP_004595410.1| 41 SGAQVLDAGCGQGD 54
                                      55789*******95 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 4.5e-06
                                       TCEEE-HHHHTTEEEEE--TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
                              CheR 108 dsykvkkeikelvkFeklnllekksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLll 173
                                       ++ ++ +e   +v  ++ ++++   + + +D +++   li   e++ ++v+++fa+ l+pggl ll
  gi|336252303|ref|YP_004595410.1|  76 QQLRFASEAAPNVALAQGDITSLPVADSAFDAVTAFHSLIHVPETQHRAVVDEFARVLRPGGLALL 141
                                       567899999999**********99999***********************************8665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.9
                                       TTTSSS-EEEEEEESSCHHHHHHHH CS
                              CheR  58 pkaaklkvkilAtDidlkvlekAka 82 
                                       ++ +++++ i + D  ++ l +A  
  gi|336252303|ref|YP_004595410.1| 157 ETGVEMQWYIAGADATREQLRAAGF 181
                                       5667789999999999999988865 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.3e-06    0.0015      97     159 ..      79     144 ..      21     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                                       EEEESS-SSTTEEES-TTS-S--TT-EEEEEEES---S...S-HHHHHHHHHHHEEEEEEEEEEEE CS
                    Methyltransf_8  97 rsfdlvavnervvacdlakvPledesvdvavfclslmg...tnladflkeanrvlkvGGllkvaev 159
                                       r    +a+n  +   d++ +P++d++ d +    sl+    t+ +  + e  rvl++GGl  ++e 
  gi|336252303|ref|YP_004595410.1|  79 RFASEAAPNVALAQGDITSLPVADSAFDAVTAFHSLIHvpeTQHRAVVDEFARVLRPGGLALLTEG 144
                                       444456788889999*************999999998433388999*************9988875 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 ?   12.9   0.0   2.7e-05      0.03     120     218 ..      44     142 ..      31     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                   Methyltransf_29 120 tvlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaLeRgvpailavlgtkrlpyPsrsfdlihCsrCridwte 196
                                       +vlD GCg    +   l+ d  ++  +  D  ++q+ fa e      la    + lp   ++fd +     +i+  e
  gi|336252303|ref|YP_004595410.1|  44 QVLDAGCGQGDPVLRRLDDD-PAVEATGVDFSRQQLRFASEAAPNVALAQGDITSLPVADSAFDAVTAFHSLIHVPE 119
                                       69999**9999888888877.57788889************99888888888999*************999999876 PP

                   Methyltransf_29 197 ed.gilllevdRvlRpgGyfvls 218
                                       ++  +++ e  RvlRpgG  +l+
  gi|336252303|ref|YP_004595410.1| 120 TQhRAVVDEFARVLRPGGLALLT 142
                                       65156778**********87765 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 ?   12.3   0.0   5.2e-05     0.058     105     195 ..      33     123 ..      26     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.2e-05
                                       HHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-S.EEEEE---HHHH.HHHHHHHCCTTTTSSEEEE---GGGS-T CS
                    Methyltransf_9 105 drvlphlsdlkgrtildvGcgnGyhlwrmvgegak.lvvGidPselfl.iqfeavrkllgedqrahllplgieqlpe 179
                                       +r+++ l+   g ++ld Gcg+G  + r + ++++  + G+d s++ l +  ea  ++   +   + lp++   +++
  gi|336252303|ref|YP_004595410.1|  33 ERLRERLP--SGAQVLDAGCGQGDPVLRRLDDDPAvEATGVDFSRQQLrFASEAAPNVALAQGDITSLPVADSAFDA 107
                                       45555553..5789*************999988662689***99877625678888888888888899999988998 PP

                                       ---EEEEEEES-GGG- CS
                    Methyltransf_9 180 leafdtvfsmGvlyhr 195
                                       + af  +  +    hr
  gi|336252303|ref|YP_004595410.1| 108 VTAFHSLIHVPETQHR 123
                                       9888887776666665 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.42   4.7e+02      34      70 ..      38      76 ..      29      83 .. 0.66
   2 ?   11.2   0.0   0.00019      0.21      86     153 ..      76     141 ..      63     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.42
                                      T-S--EEEEEET-TT-HHHHHH-..BTTEEEEEE-S-HH CS
                              TPMT 34 kakaglrvlvPlCGkaldlvwlA..eqgrevvGvelsel 70
                                      ++++g++vl  +CG++  +      ++  e  Gv++s +
  gi|336252303|ref|YP_004595410.1| 38 RLPSGAQVLDAGCGQGDPVLRRLddDPAVEATGVDFSRQ 76
                                      47889999999***9988765430134455577777766 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00019
                                       GGEEEE--...........-TTT---SS-..EEEEEEESSTTTS-GGGHHHHHHHHHHHEEEEEE..E CS
                              TPMT  86 kelsgvkeysageiellcgdvFtlraeelgkfdliydraalvAlppelreryakslaelLkpdgeglL 153
                                       ++l+++ e +a+++ l +gd+  l+ ++   fd++     l+ +p+    + +++ a++L+p+g  lL
  gi|336252303|ref|YP_004595410.1|  76 QQLRFASE-AAPNVALAQGDITSLPVADS-AFDAVTAFHSLIHVPETQHRAVVDEFARVLRPGGLALL 141
                                       56667777.899****************9.9*********************************9887 PP

>> DUF5348  Domain of unknown function (DUF5348)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018       0.2      36      68 ..     153     184 ..     138     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                           DUF5348  36 deWvptriEmdngewYlvg.dg.lklllleglrvr 68 
                                         W++t +Em   +wY+ g d  + +l+  g +vr
  gi|336252303|ref|YP_004595410.1| 153 SDWLETGVEM---QWYIAGaDAtREQLRAAGFTVR 184
                                       48********...8*****8766766666666665 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0     0.001       1.2       4      54 ..      44      89 ..      41     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEE CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlr 54
                                       vl+ GcG+G+ +++   ++P ++  G++ +++ ++ + +++      N++
  gi|336252303|ref|YP_004595410.1| 44 QVLDAGCGQGDPVLRRLDDDPAVEATGVDFSRQQLRFASEAA-----PNVA 89
                                      5899**************************999887665544.....3444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1604.43
//
Query:       gi|336252304|ref|YP_004595411.1|  [L=81]
Description: hypothetical protein Halxa_0895 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.093   12.4   0.3       0.39   10.5   0.2    1.9  2  DUF3948   Protein of unknown function (DUF3948)


Domain annotation for each model (and alignments):
>> DUF3948  Protein of unknown function (DUF3948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0     0.091   1.6e+03       6      20 ..      27      41 ..      26      41 .. 0.77
   2 ?   10.5   0.2   2.2e-05      0.39      16      29 ..      48      61 ..      47      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.091
                           DUF3948  6 VlqvtKsDfiGsasG 20
                                      Vl +t    +G++ G
  gi|336252304|ref|YP_004595411.1| 27 VLAFTAAERLGLLEG 41
                                      788888888888866 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 2.2e-05
                           DUF3948 16 GsasGAvvLTafIl 29
                                      G a GAvv Ta I+
  gi|336252304|ref|YP_004595411.1| 48 GRAYGAVVFTAVIV 61
                                      7788*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 628.66
//
Query:       gi|336252305|ref|YP_004595412.1|  [L=265]
Description: succinylglutamate desuccinylase/aspartoacylase [Halopiger xanaduensis SH-6]
Scores for 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   60.9   0.2    1.8e-16   60.1   0.2    1.4  1  AstE_AspA      Succinylglutamate desuccinylase / Aspartoacyla
     0.0023   17.4   0.0      0.004   16.6   0.0    1.3  1  Peptidase_M99  Carboxypeptidase controlling helical cell shap


Domain annotation for each model (and alignments):
>> AstE_AspA  Succinylglutamate desuccinylase / Aspartoacylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.2     2e-20   1.8e-16       2     277 ..      10     243 ..       9     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 2e-20
                                       S-EEEEEE-SSTT-HHHHHHHHHHHHHHHCCCESCCEEEEEESSHHHHHCTSSSSSTT-S-CTTTTTCCCCCSSTCH CS
                         AstE_AspA   2 gpkvlisAGvHGnElaGvellrqllkqleeadilgeitlvplaNppAiaagsRyipidredLNRaFpgrslgrslde 78 
                                       +p v+++AG+HG+E +Gv ++++ll    e  +  + + +++aN  A++++ R+++   edLNRaFpg+++      
  gi|336252305|ref|YP_004595412.1|  10 TPEVAVVAGIHGDEPCGVRAVERLLD---ERPTVERPVKLIVANEKALERQVRFVD---EDLNRAFPGDPDA----- 75 
                                       589*********************75...5667777899999**************...*************..... PP

                                       HHHHHHHHHHHHHHCHCTCCCGCEEEEEEEESSTBCCSSEEEE---SSHHHHHHHHHHTTTSEEEEEESS--SSHHH CS
                         AstE_AspA  79 alrateaerladalfaaalpeadivlDLHtgtrglkhllfaeadiaeaqlqslallkalglpavllldekesagfle 155
                                           t   +la++l +++  e  + + +H++ ++    +fa+++  ++ +      + +++ +++  ++ e++ f e
  gi|336252305|ref|YP_004595412.1|  76 ---KTHEGQLAHRLVEEL--EGCLTFSMHSTQSHA--EPFAIVNGVNETA------EEIVPQLPV-TAMVETSNFAE 138
                                       ...666667777777666..345899*****9999..7777777755544......555555555.55557776777 PP

                                       HHHHHCTSEEEEEEEES.TTTTCCHHCCHHHHHHHHHHHHCTCHTT-SCC.CEEEEEEEEEEGGSCCCSSCSEEECC CS
                         AstE_AspA 156 taaeelgalaftlElGgagrlgaedisrtakgvlnvlahigvvagqeavepaklyrvlreldeprdiraeeaGlvef 232
                                       +++   ++ ++ +E G++g  ++++++++ ++++++l ++g++ g++  + + +yr ++ +++++          ++
  gi|336252305|ref|YP_004595412.1| 139 GRLF-SEIDTVEVECGMQG--SETAAQNADRLTRAFLTAVGALPGDTMYNDLPVYRLTDVIRKQEA---------DT 203
                                       7764.589999******88..588899*******************6555599********99998.........44 PP

                                       CCSTTTTETCTEEEETTEEEEECTSTEEEEESSSSEEEESCCTSC CS
                         AstE_AspA 233 kvklgddveagellakalvldslggekvelrapqdgvivfineaa 277
                                          +   v++++ ++ +  ++  +g++   +a++++++v+  ++ 
  gi|336252305|ref|YP_004595412.1| 204 YEVF---VDNFAEVEAGESFAAADGDE--QVADESFYPVLMSSNG 243
                                       4324...77777777777777776766..5677778888777665 PP

>> Peptidase_M99  Carboxypeptidase controlling helical cell shape catalytic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.5e-07     0.004      36      97 ..      10      70 ..       4      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.5e-07
                                      S-EEEEE--SSTT-HHHHHHHHHHHHHEEE-SSEEEEES-STHHHHHTT-S-TTS-GGG-SS CS
                     Peptidase_M99 36 aphllllagiqgdepggfnaanlflmhyevkkglvevvpvlnkpsilrnhrglyddmnrkfa 97
                                      +p + ++agi gdep g  a + +l         v+++ v n +++ r+ r + +d+nr f 
  gi|336252305|ref|YP_004595412.1| 10 TPEVAVVAGIHGDEPCGVRAVERLLDERPTVERPVKLI-VANEKALERQVRFVDEDLNRAFP 70
                                      688999*****************999999888889887.569999**************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2128.89
//
Query:       gi|336252306|ref|YP_004595413.1|  [L=163]
Description: hypothetical protein Halxa_0897 [Halopiger xanaduensis SH-6]
Scores for complete 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-14   53.5   0.2    2.4e-14   52.8   0.2    1.4  1  DUF309    Domain of unknown function (DUF309)


Domain annotation for each model (and alignments):
>> DUF309  Domain of unknown function (DUF309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.2   1.3e-18   2.4e-14       3      59 .]      40      99 ..      38      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 1.3e-18
                            DUF309  3 eaielfnegeffeaHEvlEelWkeagep..erkllqglIqlAvAlyh.lrrgnvrgakrl 59
                                      ++++lfn+g ++e H+++E  W ++g++  e  +l+g++q+A++ y+ +  +n +g+++l
  gi|336252306|ref|YP_004595413.1| 40 HGVRLFNDGAYHESHDCFELEWYNYGRGseESAFLHGMVQVAAGAYKhVDFENDDGMRSL 99
                                      79***********************99877999**********999879999*9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1229.56
//
Query:       gi|336252307|ref|YP_004595414.1|  [L=60]
Description: hypothetical protein Halxa_0898 [Halopiger xanaduensis SH-6]
Scores for 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   22.1   1.1    0.00014   21.8   1.1    1.1  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00019   21.2   4.0      0.015   15.1   0.3    2.1  2  zf-HIT          HIT zinc finger
    0.00044   19.7   5.5    0.00074   19.0   5.5    1.6  1  TF_Zn_Ribbon    TFIIB zinc-binding
    0.00057   19.8   0.7    0.00081   19.4   0.7    1.2  1  DZR             Double zinc ribbon
    0.00067   19.0   2.8       0.21   11.1   0.4    2.2  2  zf-ribbon_3     zinc-ribbon domain
     0.0024   17.8   3.0       0.11   12.5   0.2    2.2  2  zinc_ribbon_4   zinc-ribbon domain
     0.0038   16.9   3.7       0.24   11.2   0.4    2.2  2  zinc_ribbon_2   zinc-ribbon domain
     0.0051   17.5   0.2     0.0061   17.2   0.2    1.2  1  FYDLN_acid      Protein of unknown function (FYDLN_acid)
     0.0072   16.1   0.1     0.0073   16.1   0.1    1.1  1  Rep_fac-A_C     Replication factor-A C terminal domain
  ------ inclusion threshold ------
      0.011   15.6   2.3       0.76    9.7   0.1    2.2  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.012   15.5   0.2      0.015   15.3   0.2    1.2  1  zinc-ribbons_6  zinc-ribbons
      0.014   15.1   7.0      0.068   12.9   0.8    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.015   15.2   0.3      0.019   14.8   0.3    1.1  1  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.018   15.0   1.2      0.019   15.0   1.2    1.1  1  DUF4589         Domain of unknown function (DUF4589)
      0.019   13.8   0.8       0.02   13.7   0.8    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
      0.026   14.6   1.1        1.9    8.7   0.2    2.3  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
      0.029   14.4   0.2       0.03   14.3   0.2    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.053   13.2   6.4      0.077   12.7   6.4    1.2  1  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
      0.053   13.5   5.2       0.13   12.2   5.3    1.6  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.059   13.0   4.0       0.99    9.1   0.5    2.2  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.08   13.2   0.5         11    6.3   0.2    2.1  2  zf-LITAF-like   LITAF-like zinc ribbon domain
      0.088   12.4   0.5          9    6.0   0.1    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.11   12.5   6.9        1.4    8.9   1.4    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.11   12.7   1.5       0.14   12.3   1.5    1.2  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.12   12.0   3.1        3.5    7.3   0.3    2.2  2  Sgf11           Sgf11 (transcriptional regulation protein)
       0.13   12.4   4.2        5.6    7.2   0.1    2.3  2  Zn-ribbon_8     Zinc ribbon domain
       0.14   11.8   2.4       0.14   11.8   2.4    1.1  1  NESP55          Neuroendocrine-specific golgi protein P55 (NE
       0.15   11.9   1.7          3    7.7   0.1    2.1  2  zinc_ribbon_5   zinc-ribbon domain
       0.16   12.4   6.3       0.39   11.1   0.3    2.3  2  zf-IS66         zinc-finger binding domain of transposase IS6
       0.23   10.8   3.6       0.63    9.4   3.5    1.7  1  zf-TFIIB        Transcription factor zinc-finger
       0.25   11.4   3.2          3    7.9   0.2    2.1  2  Ogr_Delta       Ogr/Delta-like zinc finger
       0.26   11.1   8.6        6.6    6.6   8.3    2.2  2  zf-RING_4       RING/Ubox like zinc-binding domain
       0.28   11.6   3.5          8    6.9   0.2    2.1  2  DUF983          Protein of unknown function (DUF983)
       0.29   10.7   3.3        8.6    6.0   0.1    2.6  2  zf_C2H2_10      C2H2 type zinc-finger
       0.33   11.0  10.8       0.76    9.8   3.1    2.4  2  DUF1610         Domain of unknown function (DUF1610)
       0.53   11.0   6.5        0.7   10.6   0.4    2.1  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
        1.1    9.1   4.7         38    4.1   0.4    2.2  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
        1.1    8.7   7.4        5.6    6.4   0.5    2.1  2  zf_Rg           Reverse gyrase zinc finger
        4.2    7.5   9.8       0.76    9.9   5.7    1.9  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
          6    7.1   8.6         16    5.8   0.2    2.6  3  zf-RING_7       C4-type zinc ribbon domain
        7.7    6.5   8.1        2.8    7.9   0.8    2.1  2  DUF3797         Domain of unknown function (DUF3797)


Domain annotation for each model (and alignments):
>> 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 !   21.8   1.1   3.1e-07   0.00014      30      59 ..       7      35 ..       6      37 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.1e-07
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfeadrD 59
                                      +C++Cg++++e   +  ++CpnC +++ +D
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGERLYE-HIEGGYRCPNCETQYGAD 35
                                      6**********.99************9998 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.3    0.0078       3.4      15      22 ..       7      14 ..       6      16 .. 0.89
   2 !   15.1   0.3   3.4e-05     0.015      11      23 ..      20      32 ..      17      32 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0078
                                      E-TTT--E CS
                            zf-HIT 15 kCpkCntr 22
                                      +Cp+C++r
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGER 14
                                      8*****98 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.4e-05
                                      B-SEE-TTT--EE CS
                            zf-HIT 11 pakYkCpkCntry 23
                                      ++ Y+Cp+C+t y
  gi|336252307|ref|YP_004595414.1| 20 EGGYRCPNCETQY 32
                                      789********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 !   19.0   5.5   1.7e-06   0.00074       2      34 ..       7      37 ..       6      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-06
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCC CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsi 34
                                      +CPnCg +  ++++ +g ++C++C++    ++ 
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGER--LYEHIEGGYRCPNCETQYGADDL 37
                                      7*****98..9*************987666655 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.7   1.9e-06   0.00081      15      38 ..       8      32 ..       2      37 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.9e-06
                               DZR 15 CseCgtklkavaa.edrCpsCgekv 38
                                      C++Cg++l +  +  +rCp+C+++ 
  gi|336252307|ref|YP_004595414.1|  8 CPNCGERLYEHIEgGYRCPNCETQY 32
                                      ********755449********985 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.4   0.00047      0.21       4      10 ..       7      13 ..       5      15 .. 0.66
   2 !    8.4   0.1    0.0034       1.5       3      10 ..      23      30 ..      21      37 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00047
                       zf-ribbon_3  4 rCPnCGa 10
                                      rCPnCG+
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGE 13
                                      5777775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0034
                       zf-ribbon_3  3 vrCPnCGa 10
                                      +rCPnC +
  gi|336252307|ref|YP_004595414.1| 23 YRCPNCET 30
                                      68999955 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.3     0.027        12      27      33 ..       7      13 ..       7      15 .. 0.65
   2 !   12.5   0.2   0.00025      0.11       4      16 ..      24      36 ..      23      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.027
                     zinc_ribbon_4 27 rCskCgh 33
                                      rC++Cg+
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGE 13
                                      6777764 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00025
                     zinc_ribbon_4  4 tCpsCkakyeidd 16
                                      +Cp+C+++y  dd
  gi|336252307|ref|YP_004595414.1| 24 RCPNCETQYGADD 36
                                      7********7665 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.4   0.00054      0.24       1       9 [.       7      15 ..       7      18 .. 0.71
   2 ?    6.9   0.2     0.012       5.3       1       9 [.      24      32 ..      24      36 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00054
                     zinc_ribbon_2  1 fCpnCGael 9 
                                      +CpnCG+ l
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGERL 15
                                      588888765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
                     zinc_ribbon_2  1 fCpnCGael 9 
                                      +CpnC ++ 
  gi|336252307|ref|YP_004595414.1| 24 RCPNCETQY 32
                                      699998775 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 !   17.2   0.2   1.4e-05    0.0061      12      54 ..       8      51 ..       6      60 .] 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-05
                        FYDLN_acid 12 CpscgakFYDLnkdPivcpkcgeefepeev.lksraaaaeaeea 54
                                      Cp+cg++ Y        cp+c++++  + +    ++ +++++e+
  gi|336252307|ref|YP_004595414.1|  8 CPNCGERLYEHIEGGYRCPNCETQYGADDLdFDLESEVESESEP 51
                                      **************************999953333333333333 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 !   16.1   0.1   1.7e-05    0.0073      17      56 ..       4      41 ..       1      51 [. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-05
                                      EEEB--STT---B-EEETTTEEEETTTTEEESS--EEEEE CS
                       Rep_fac-A_C 17 vYkACpsedCnkKvveeedgewrCekCdkeveepkyryil 56
                                       Y  Cp  +C  ++ e+ +g +rC +C++++   ++ + l
  gi|336252307|ref|YP_004595414.1|  4 PYGRCP--NCGERLYEHIEGGYRCPNCETQYGADDLDFDL 41
                                      5899**..*********************99776666555 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 ?    9.7   0.1    0.0017      0.76      11      21 ..       5      15 ..       4      18 .. 0.79
   2 ?    5.9   0.2     0.027        12      11      20 ..      22      31 ..      22      32 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                           DUF35_N 11 gqrCpdCGtvq 21
                                      ++rCp+CG   
  gi|336252307|ref|YP_004595414.1|  5 YGRCPNCGERL 15
                                      58999999865 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.027
                           DUF35_N 11 gqrCpdCGtv 20
                                      g rCp+C t 
  gi|336252307|ref|YP_004595414.1| 22 GYRCPNCETQ 31
                                      5699999875 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   3.4e-05     0.015       2      27 ..       7      33 ..       6      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.4e-05
                                      --SSS-S--E.E-SSEEE-TTT--EEE CS
                    zinc-ribbons_6  2 kCpeCqqele.krgeqyhCeaCqedlk 27
                                       Cp+C + l  + +  y+C +C++++ 
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGERLYeHIEGGYRCPNCETQYG 33
                                      5*******99777899******99775 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.8   0.00015     0.068      14      22 ..       5      13 ..       2      13 .. 0.88
   2 ?    5.9   0.7     0.024        11       1       8 [.      23      30 ..      23      34 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                      Rubredoxin_2 14 fGrCpsCgs 22
                                      +GrCp+Cg+
  gi|336252307|ref|YP_004595414.1|  5 YGRCPNCGE 13
                                      9******96 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.024
                      Rubredoxin_2  1 YvCsqCGf 8 
                                      Y+C +C  
  gi|336252307|ref|YP_004595414.1| 23 YRCPNCET 30
                                      55555554 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 ?   14.8   0.3   4.4e-05     0.019      12      36 ..       6      30 ..       2      34 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.4e-05
                                      -B-TTT-SB--SSSS-EEEETTT-- CS
                              C1_1 12 tfCkhCgeflwgkekqglkCswCkl 36
                                      ++C  Cge l+++   g++C +C+ 
  gi|336252307|ref|YP_004595414.1|  6 GRCPNCGERLYEHIEGGYRCPNCET 30
                                      68********99***********86 PP

>> DUF4589  Domain of unknown function (DUF4589)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.2   4.3e-05     0.019     147     181 ..      24      58 ..       2      60 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-05
                           DUF4589 147 lCcDddeeedeeeeelhlqeekedeaslkedpeee 181
                                        C+ ++++++ ++ + +l++e e+e++++ +pee+
  gi|336252307|ref|YP_004595414.1|  24 RCPNCETQYGADDLDFDLESEVESESEPDLEPEES 58 
                                       4*****************************99987 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.8   4.7e-05      0.02     503     527 ..       1      30 [.       1      39 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.7e-05
                                       EE--EEEETT.--.EESS....SB-TTT-- CS
                              NRDD 503 inpkidvCnecgy.kgei....ekCpkCgs 527
                                       +n+++ +C++cg    e+    ++Cp+C+ 
  gi|336252307|ref|YP_004595414.1|   1 MNHPYGRCPNCGErLYEHieggYRCPNCET 30 
                                       69**********973333679999****94 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 ?    8.7   0.2    0.0043       1.9       3      12 ..       7      16 ..       7      18 .. 0.88
   2 ?    4.9   0.1     0.063        27       3       9 ..      24      30 ..      23      38 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0043
                            zf-ACC  3 KCpsCgemly 12
                                      +Cp Cge ly
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGERLY 16
                                      6******999 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.063
                            zf-ACC  3 KCpsCge 9 
                                      +Cp C++
  gi|336252307|ref|YP_004595414.1| 24 RCPNCET 30
                                      5888876 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 ?   14.3   0.2   6.9e-05      0.03      70      95 ..       5      31 ..       1      46 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.9e-05
                                      EEEETTTS-EEECHHH.HHS-TTTSSS CS
                              HypA 70 kvrCreCgkefeleek.alrCpkCgsa 95
                                        rC +Cg++  ++ +  +rCp+C+++
  gi|336252307|ref|YP_004595414.1|  5 YGRCPNCGERLYEHIEgGYRCPNCETQ 31
                                      579*****99986655689*****975 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 ?   12.7   6.4   0.00018     0.077       6      32 .]       7      33 ..       6      33 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00018
                           zf-RRN7  6 pCgvCgcrsftlddGfyyCrrChtqeg 32
                                      +C+ Cg r++  ++G y C +C tq g
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGERLYEHIEGGYRCPNCETQYG 33
                                      8******99999**********99976 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 ?   12.2   5.3   0.00031      0.13      20      46 .]       7      31 ..       2      31 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00031
                     Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeCrkq 46
                                      +CP+Cg r +  i++   ++C  C +q
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGERLYEHIEG--GYRCPNCETQ 31
                                      6*****666666665..*******987 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 ?    9.1   0.5    0.0023      0.99      23      32 .]       7      16 ..       7      16 .. 0.90
   2 ?    5.3   0.2     0.036        16      23      30 ..      24      31 ..      20      32 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0023
                     zf-NADH-PPase 23 vCpaCglehY 32
                                      +Cp+Cg++ Y
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGERLY 16
                                      7*****9987 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.036
                     zf-NADH-PPase 23 vCpaCgle 30
                                      +Cp+C + 
  gi|336252307|ref|YP_004595414.1| 24 RCPNCETQ 31
                                      8****976 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 ?    6.3   0.2     0.026        11      58      67 ..       7      16 ..       3      19 .. 0.81
   2 ?    5.6   0.0     0.044        19      58      66 ..      24      32 ..      22      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.026
                     zf-LITAF-like 58 yCpnCgallg 67
                                      +CpnCg++l 
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGERLY 16
                                      6999998886 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.044
                     zf-LITAF-like 58 yCpnCgall 66
                                      +CpnC+++ 
  gi|336252307|ref|YP_004595414.1| 24 RCPNCETQY 32
                                      577777665 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.021         9       5      15 ..       8      18 ..       5      20 .. 0.84
   2 ?    4.9   0.1     0.044        19       2      12 ..      22      32 ..      21      38 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.021
                            zf_UBZ  5 CerCgkeipes 15
                                      C+ Cg+++ e+
  gi|336252307|ref|YP_004595414.1|  8 CPNCGERLYEH 18
                                      ******98776 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.044
                            zf_UBZ  2 tylCerCgkei 12
                                       y C+ C ++ 
  gi|336252307|ref|YP_004595414.1| 22 GYRCPNCETQY 32
                                      699****9876 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 ?    6.9   0.4     0.014         6       6      13 ..       7      14 ..       6      18 .. 0.75
   2 ?    8.9   1.4    0.0031       1.4       5      15 ..      23      33 ..      22      34 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.014
                    Zn_ribbon_SprT  6 rCtgCgre 13
                                      rC++Cg++
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGER 14
                                      89999943 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0031
                    Zn_ribbon_SprT  5 YrCtgCgreyt 15
                                      YrC++C ++y+
  gi|336252307|ref|YP_004595414.1| 23 YRCPNCETQYG 33
                                      9******9996 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 ?   12.3   1.5   0.00033      0.14      18      40 .]       8      29 ..       6      29 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00033
                     Auto_anti-p27 18 CpvCgvPLmrdrkggkvyCvaCd 40
                                      Cp+Cg  L +  +gg   C++C+
  gi|336252307|ref|YP_004595414.1|  8 CPNCGERLYEHIEGGY-RCPNCE 29
                                      **********865555.*****6 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3     0.008       3.5       3      11 ..       4      12 ..       2      14 .. 0.85
   2 ?    5.5   0.2     0.029        13       5      11 ..      23      29 ..      22      33 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.008
                                      -EEE-TTTS CS
                             Sgf11  3 eyvtCpnCg 11
                                      +y +CpnCg
  gi|336252307|ref|YP_004595414.1|  4 PYGRCPNCG 12
                                      7889****8 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.029
                                      EE-TTTS CS
                             Sgf11  5 vtCpnCg 11
                                      ++CpnC+
  gi|336252307|ref|YP_004595414.1| 23 YRCPNCE 29
                                      58****7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.013       5.6      29      35 ..       8      14 ..       2      19 .. 0.72
   2 ?    6.8   0.9     0.016       7.1       6      15 ..      23      32 ..      22      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.013
                       Zn-ribbon_8 29 CPeCgse 35
                                      CP+Cg++
  gi|336252307|ref|YP_004595414.1|  8 CPNCGER 14
                                      8888874 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                       Zn-ribbon_8  6 YrCeeCghef 15
                                      YrC +C +++
  gi|336252307|ref|YP_004595414.1| 23 YRCPNCETQY 32
                                      9999999875 PP

>> NESP55  Neuroendocrine-specific golgi protein P55 (NESP55)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.4   0.00031      0.14      92     130 ..      17      56 ..       7      60 .] 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                            NESP55  92 eevepelarpecl.eydeeeyetetdseteseseiesete 130
                                       e++e     p+c  +y  ++ +++ +se esese + e e
  gi|336252307|ref|YP_004595414.1|  17 EHIEGGYRCPNCEtQYGADDLDFDLESEVESESEPDLEPE 56 
                                       5567777789995379999988888888888877655544 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2      0.13        55       4       9 ..       7      12 ..       6      15 .. 0.82
   2 ?    7.7   0.1    0.0068         3       4      12 ..      24      32 ..      23      38 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.13
                     zinc_ribbon_5  4 rCpdCd 9 
                                      rCp+C+
  gi|336252307|ref|YP_004595414.1|  7 RCPNCG 12
                                      799997 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0068
                     zinc_ribbon_5  4 rCpdCdtkF 12
                                      rCp+C+t++
  gi|336252307|ref|YP_004595414.1| 24 RCPNCETQY 32
                                      8******87 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 ?    4.9   0.9     0.078        34       3       9 ..       7      13 ..       6      17 .. 0.77
   2 ?   11.1   0.3    0.0009      0.39      33      46 .]      16      29 ..      13      29 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.078
                           zf-IS66  3 tCpcCGg 9 
                                       Cp+CG 
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGE 13
                                      6999997 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0009
                           zf-IS66 33 iehirpkyaCpcCe 46
                                       ehi   y+Cp+Ce
  gi|336252307|ref|YP_004595414.1| 16 YEHIEGGYRCPNCE 29
                                      59***********7 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.5    0.0014      0.63       2      26 ..       8      29 ..       7      29 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                          zf-TFIIB  2 CPkCqdeleeserggveidyCpqCr 26
                                      CP+C+  l e+  gg   ++Cp+C+
  gi|336252307|ref|YP_004595414.1|  8 CPNCGERLYEHIEGG---YRCPNCE 29
                                      ***************...99**996 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 ?    7.9   0.2     0.007         3       1       9 [.       7      15 ..       7      17 .. 0.86
   2 ?    4.4   0.3     0.084        37       1       7 [.      24      30 ..      24      34 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.007
                         Ogr_Delta  1 rCPhCgapa 9 
                                      rCP+Cg++ 
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGERL 15
                                      7*****985 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.084
                         Ogr_Delta  1 rCPhCga 7 
                                      rCP+C++
  gi|336252307|ref|YP_004595414.1| 24 RCPNCET 30
                                      7****86 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.6     0.043        19      37      44 ..       5      12 ..       1      16 [. 0.78
   2 ?    6.6   8.3     0.015       6.6      25      47 ..       8      32 ..       5      33 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.043
                         zf-RING_4 37 egrCPaCr 44
                                       grCP+C 
  gi|336252307|ref|YP_004595414.1|  5 YGRCPNCG 12
                                      68*****6 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                         zf-RING_4 25 ClfCyhrile..eeegrCPaCreeY 47
                                      C  C +r+ e  e + rCP+C ++Y
  gi|336252307|ref|YP_004595414.1|  8 CPNCGERLYEhiEGGYRCPNCETQY 32
                                      8889999998666799*******99 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2     0.018         8      10      21 ..       7      18 ..       3      23 .. 0.82
   2 ?    6.3   0.3     0.029        13      10      24 ..      24      38 ..      19      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.018
                            DUF983 10 aCeaCgldlsha 21
                                      +C++Cg++l  +
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGERLYEH 18
                                      8******98766 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.029
                            DUF983 10 aCeaCgldlsharad 24
                                      +C++C++++++ + d
  gi|336252307|ref|YP_004595414.1| 24 RCPNCETQYGADDLD 38
                                      8*********99887 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 ?    5.2   0.2     0.035        15       5      12 ..       8      15 ..       4      16 .. 0.85
   2 ?    6.0   0.1      0.02       8.6       3      16 ..      23      38 ..      22      39 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.035
                        zf_C2H2_10  5 CPKCqekl 12
                                      CP C+e l
  gi|336252307|ref|YP_004595414.1|  8 CPNCGERL 15
                                      *****976 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                        zf_C2H2_10  3 fsCPKC..qeklPDiD 16
                                      + CP C  q+ + D+D
  gi|336252307|ref|YP_004595414.1| 23 YRCPNCetQYGADDLD 38
                                      56****5556678887 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.1    0.0017      0.76      19      24 .]       8      13 ..       7      13 .. 0.94
   2 ?    5.6   0.9     0.036        16      19      22 ..      25      28 ..      22      28 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0017
                           DUF1610 19 CPNCGE 24
                                      CPNCGE
  gi|336252307|ref|YP_004595414.1|  8 CPNCGE 13
                                      *****9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.036
                           DUF1610 19 CPNC 22
                                      CPNC
  gi|336252307|ref|YP_004595414.1| 25 CPNC 28
                                      **** 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 ?   10.6   0.4    0.0016       0.7       3      12 ..       6      16 ..       4      24 .. 0.73
   2 ?    4.1   1.0      0.18        78       4      10 ..      24      30 ..      22      35 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0016
                           zf-ISL3  3 hrCPnCgsk.t 12
                                       rCPnCg++  
  gi|336252307|ref|YP_004595414.1|  6 GRCPNCGERlY 16
                                      79*****9943 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.18
                           zf-ISL3  4 rCPnCgs 10
                                      rCPnC  
  gi|336252307|ref|YP_004595414.1| 24 RCPNCET 30
                                      7999975 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 ?    4.1   0.4     0.087        38      46      52 ..       7      13 ..       5      15 .. 0.87
   2 ?    3.4   4.7      0.14        63      44      52 ..      22      30 ..       8      32 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.087
                    zinc_ribbon_10 46 rCpkCga 52
                                      rCp+Cg+
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGE 13
                                      8****97 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.14
                    zinc_ribbon_10 44 kyrCpkCga 52
                                       yrCp+C +
  gi|336252307|ref|YP_004595414.1| 22 GYRCPNCET 30
                                      69*****86 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   8.7       0.3   1.3e+02       9      31 ..       7      28 ..       5      28 .. 0.80
   2 ?    6.4   0.5     0.013       5.6      10      20 ..      25      35 ..      20      41 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.3
                             zf_Rg  9 lCPNCgGdisdeRlekGLpCkrC 31
                                       CPNCg  +  e +e G  C +C
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGERL-YEHIEGGYRCPNC 28
                                      5****7666.5779999999998 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                             zf_Rg 10 CPNCgGdisde 20
                                      CPNC+ +  ++
  gi|336252307|ref|YP_004595414.1| 25 CPNCETQYGAD 35
                                      ****9766655 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 ?    9.9   5.7    0.0017      0.76       1      22 [.       7      27 ..       7      30 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0017
                    DNA_ligase_ZBD  1 hCPvCGsavvReegeaiyRCtn 22
                                      +CP CG  +     e  yRC+n
  gi|336252307|ref|YP_004595414.1|  7 RCPNCGERLYEHI-EGGYRCPN 27
                                      5*********544.557****9 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 ?    5.3   1.9     0.052        23      25      30 ..       7      12 ..       6      12 .. 0.94
   2 ?    5.8   0.2     0.036        16      24      29 ..      23      28 ..      14      29 .. 0.80
   3 ?   -1.9   0.0       9.3   4.1e+03       9      16 ..      41      48 ..      37      50 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.052
                                      E-TTT- CS
                         zf-RING_7 25 tCpeCG 30
                                      +Cp+CG
  gi|336252307|ref|YP_004595414.1|  7 RCPNCG 12
                                      8****9 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.036
                                      EE-TTT CS
                         zf-RING_7 24 vtCpeC 29
                                       +Cp+C
  gi|336252307|ref|YP_004595414.1| 23 YRCPNC 28
                                      79**** PP

  == domain 3  score: -1.9 bits;  conditional E-value: 9.3
                                      --CCHHHH CS
                         zf-RING_7  9 lppqvlse 16
                                      l ++v+se
  gi|336252307|ref|YP_004595414.1| 41 LESEVESE 48
                                      34555555 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.8    0.0064       2.8      13      21 ..       5      13 ..       1      22 [. 0.83
   2 ?    3.1   1.2       0.2        87      15      22 ..      24      31 ..      19      34 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0064
                           DUF3797 13 YvqCPeCgN 21
                                      Y  CP+Cg 
  gi|336252307|ref|YP_004595414.1|  5 YGRCPNCGE 13
                                      99*****96 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.2
                           DUF3797 15 qCPeCgNn 22
                                       CP+C  +
  gi|336252307|ref|YP_004595414.1| 24 RCPNCETQ 31
                                      6****865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 453.66
//
Query:       gi|336252308|ref|YP_004595415.1|  [L=522]
Description: HTTM domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   47.2   0.0    1.7e-12   46.9   0.0    1.1  1  VKG_Carbox      Vitamin K-dependent gamma-carboxylase
     0.0011   18.4   1.1     0.0027   17.1   0.0    2.2  3  LysR_substrate  LysR substrate binding domain
  ------ inclusion threshold ------
      0.063   13.0   0.0       0.17   11.7   0.0    1.7  1  Flavi_M         Flavivirus envelope glycoprotein M


Domain annotation for each model (and alignments):
>> VKG_Carbox  Vitamin K-dependent gamma-carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   2.8e-16   1.7e-12      36     261 ..      78     321 ..      38     377 .. 0.72

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 2.8e-16
                        VKG_Carbox  36 Fplfewvk..plslew..myllylvmllaalgialGlkYrlsillfvllytyielldktsynNHyYllgllallllf 108
                                       +p fe ++  +ls++     ll+l+ +++a ++ +G++  l++l+ +ll + ++  +  + n    +l  l +l lf
  gi|336252308|ref|YP_004595415.1|  78 YPTFEALSlhALSGSAwaQGLLFLIAGVFAGLLLVGYRTTLATLASALLLASMQARNPYVLNGGDTILLSLLVLGLF 154
                                       6666654411344332246799***************9999999999999999988877777766666666677789 PP

                        VKG_Carbox 109 lpanryfslDalknkkikkk............svprwnllilkfqlfivYfyAglaKlnsd.Wlegaaplklwlfsk 172
                                       lp  + +s+Da+++ +  ++            +v    + ++ + ++ +Y + g+ K  s+ W++g+a+ +++  ++
  gi|336252308|ref|YP_004595415.1| 155 LPLGARWSIDARRRGRCADRdtaadtpatvddRVLSVATATILVHFVTIYAVNGVLKTRSEtWMNGTAVAQIFHLEQ 231
                                       ***********777766555567777777777777888899999999**********98877**********66666 PP

                        VKG_Carbox 173 fkllligelleeeidali.vswfgllfDllivflLllk.ktRilalllvvvFhllnsilFqIGmFPyvmlatlllFf 247
                                       f +  +g+ l+e++ +l+   w+  ++ ++ + lL+++ ++R     + v  +l  ++  ++G FP+vm+a lllFf
  gi|336252308|ref|YP_004595415.1| 232 FIVG-LGPYLAEQTPLLVaANWSWSALLTAAPLLLVCRdRLRFALAGAFVGAQLGLAATMRLGAFPFVMVAALLLFF 307
                                       6666.89966666665550556666665556665555414455555567778899999******************* PP

                        VKG_Carbox 248 saewprkllaklks 261
                                        ++   +l a l++
  gi|336252308|ref|YP_004595415.1| 308 PPRVWDRLEAALER 321
                                       **965666555544 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       1.1   6.5e+03       6      34 ..     108     136 ..     106     137 .. 0.79
   2 ?   -2.6   0.0      0.48   2.9e+03     113     131 ..     309     327 ..     289     335 .. 0.77
   3 !   17.1   0.0   4.6e-07    0.0027     142     202 ..     375     433 ..     366     437 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.1
                                       EEEEEEEECCCHHHHHHHHHHHHHHHSTT CS
                    LysR_substrate   6 grLrigapptlaryllppllarfraryPe 34 
                                       g L +g  +tla+   + lla+ +ar+P 
  gi|336252308|ref|YP_004595415.1| 108 GLLLVGYRTTLATLASALLLASMQARNPY 136
                                       66778888888888889999999999985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.48
                                       STHHHHHHHHHHCTTEECE CS
                    LysR_substrate 113 sglrdlledalreaglkpr 131
                                        + +d+le+al+++gl++r
  gi|336252308|ref|YP_004595415.1| 309 PRVWDRLEAALERTGLERR 327
                                       5678899999999988765 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 4.6e-07
                                       HHHHHHTTS-BEEEEGGGHHCCCHTTTEEEEEESSTTCEEEEEEEEETTCCCHHHHHHHHH CS
                    LysR_substrate 142 llalvaaGlGiallprsavrdeladgrlvalplpepplprelylvyrkgrelspavrafid 202
                                       l+a+ aaGlG+a +p+ +v+d+++d  ++++ +++ p++ +++ ++ ++ e  +++ +++d
  gi|336252308|ref|YP_004595415.1| 375 LIAWQAAGLGVAEMPEEVVEDDVED--VSWAFFAPEPISGTWWYAWEADLESGETIDTLRD 433
                                       78999********************..887777777999********99998888888887 PP

>> Flavi_M  Flavivirus envelope glycoprotein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.8e-05      0.17       8      36 ..     207     234 ..     202     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.8e-05
                           Flavi_M   8 nlGlktrtekWmssegaekqlqkverWal 36 
                                       n  lktr e+Wm +  a  q+  +e++++
  gi|336252308|ref|YP_004595415.1| 207 NGVLKTRSETWMNGT-AVAQIFHLEQFIV 234
                                       6679********996.6789999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3731.21
//
Query:       gi|336252309|ref|YP_004595416.1|  [L=277]
Description: inositol monophosphatase [Halopiger xanaduensis SH-6]
Scores for complete 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-56  192.1   0.7    1.6e-56  191.9   0.7    1.0  1  Inositol_P  Inositol monophosphatase family
  ------ inclusion threshold ------
      0.021   14.3   0.0       0.03   13.8   0.0    1.2  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain


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 !  191.9   0.7   1.7e-60   1.6e-56       4     269 ..      18     273 ..      15     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 191.9 bits;  conditional E-value: 1.7e-60
                                       HHHHHHHHHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT. CS
                        Inositol_P   4 evtkaavelaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekse 80 
                                         +++a+++a + +++ +++f+  +l +e+k   g++d+vt++d+ ++  ++e+++e fp+++i+gee+ a  +   
  gi|336252309|ref|YP_004595416.1|  18 RRASVAISAAEAGAAIAADSFR-GDLEVEQKD--GKTDVVTQVDRNAQTRVIEVIREAFPDDPIVGEEEDALKQ--- 88 
                                       56789999***9999******9.999999888..9*********************************999888... PP

                                       SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEETTEEEEEEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGG CS
                        Inositol_P  81 ltedgltwivDPiDGTknFvrgipqvaVsigllvegkpvlGviaqPllgqlysaakgkGaflngeklplsrappise 157
                                       ++e+g+ wivDPiDGT n+v gi+ ++++i+ +v+g+pv+G+  +P+l+ +y  +  kGaflnge+l++s++++ ++
  gi|336252309|ref|YP_004595416.1|  89 VPEAGPAWIVDPIDGTNNYVDGIRAFGTAIAAVVDGEPVAGATVCPALEDTYR-VGPKGAFLNGEPLSVSDCTDPER 164
                                       9*********************************************9999995.7789***************9999 PP

                                       TEEEEEESSSSSSHHHHCHHHHHHHCCCCCHEEEBESSHHHHHHHHHHTSTSEEEEEC.EBHHHHHHHHHHHHHTTE CS
                        Inositol_P 158 allvtlfavssrkdtseasllekvesavsaegvrsvgssalklaavaeGkadaylefgrekkWDhAAGeaileeaGG 234
                                       a+++ +f+++ +++ + a+  +++  +    +vr++g ++l+l +va+G ++ +++  r ++WD+ AG+a++++aGG
  gi|336252309|ref|YP_004595416.1| 165 AHVCPTFWWDFDQRDQYAAATRALVDRFG--DVRRFGCAQLELGMVASGALEGVVTNLRANPWDTVAGVALIRAAGG 239
                                       999999***98887777555555544444..46*******************9999988****************** PP

                                       EEEESSSCSSSTTSSEEEEESCHHHHHHHHHHHCC CS
                        Inositol_P 235 vvtdakgegrlllargiiaanqkelaellaaavee 269
                                       +vtd++ge++ + +rg++a+n +  ++ l++a++e
  gi|336252309|ref|YP_004595416.1| 240 TVTDLEGERWRHDSRGLVASN-GGVHDELLEAARE 273
                                       ********9999999999999.5556666666665 PP

>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.4e-06      0.03      57     126 ..      50     117 ..      24     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-06
                            FBPase  57 tGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSn.idtnvsvGti 126
                                       + d++ ++D  a+  +ie++++      +v EEe+ l+ +    e++ + ++DP+DG  n +d   + Gt 
  gi|336252309|ref|YP_004595416.1|  50 KTDVVTQVDRNAQTRVIEVIREAFPDDPIVGEEEDALKQV---PEAGPAWIVDPIDGTNNyVDGIRAFGTA 117
                                       4588999********************************9...556666778*****98856777777774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2165.76
//
Query:       gi|336252310|ref|YP_004595417.1|  [L=375]
Description: hypothetical protein Halxa_0901 [Halopiger xanaduensis SH-6]
Scores for 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  117.7  12.0    1.4e-31  110.7   9.1    3.1  2  DUF63     Membrane protein of unknown function DUF63
  ------ inclusion threshold ------
       0.06   12.1   1.1      0.081   11.7   0.3    1.6  1  DUF2206   Predicted membrane protein (DUF2206)


Domain annotation for each model (and alignments):
>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.029   2.6e+02       3      16 ..      39      52 ..      37      59 .. 0.87
   2 !  110.7   9.1   1.5e-35   1.4e-31      17     272 .]      82     375 .]      79     375 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.029
                             DUF63  3 eFiykyYidpivyk 16
                                      eFi++yY+ p+v +
  gi|336252310|ref|YP_004595417.1| 39 EFIWQYYWGPVVAD 52
                                      8*********9976 PP

  == domain 2  score: 110.7 bits;  conditional E-value: 1.5e-35
                             DUF63  17 egYnivntltyaiiLivavyliykllkklkikidekfvlatipyvilgsslRvveDagl..........lkpplsyl 83 
                                        gY+ v    y   Li+ v+ ++ l+k+l+i+  +  ++ + p++++g+ lRvveDa+           ++ p+s +
  gi|336252310|ref|YP_004595417.1|  82 PGYTFVSYAGYIPTLILGVIGVVFLIKRLEIERYRAGFYGLFPFMLFGGALRVVEDANAaayratgtlaIDLPWSGF 158
                                       69*********99*******************************************76422222222336789**** PP

                             DUF63  84 litPliyflvflitlavlliskklekk.lkkdykklyaavGvvlvlvvlllLl...lteevvnlevlll..vlllaa 154
                                       +i+Pliyf+vf++t +++++s+ le++ +++ y+  ++avG+ l++++l+ L    +te   +++ lll  +l+ a+
  gi|336252310|ref|YP_004595417.1| 159 IISPLIYFTVFAVTAVAVVVSVWLERNdYVSGYEYPLFAVGTGLLALTLAHLGytaATEPFSRFYPLLLvtTLVGAT 235
                                       ****************************************************9554455555555554400455577 PP

                             DUF63 155 vltalvllllrklk..lellsdklnlllllahllDasatfvgidl.......lgYvEqHvvpsfLidltGt...... 216
                                       ++tal +  ++ +   ++  ++ + +++++ah +D+ a ++g+d+        + v +H+++++++d+tG+      
  gi|336252310|ref|YP_004595417.1| 236 AATALTWGAIQRFApgINRGTEYMGIVVIWAHAVDGVANVIGLDWatafghsSNLVPKHPINAAIVDWTGSilpanv 312
                                       8889999888888767888899999********************9886655567889*999999998775443333 PP

                             DUF63 217 ......alvmyplkllvlipvlyildkevkeeee.lrnlvklailvlGlaPgiRnllrmvlgv 272
                                             a+ ++ +kl+  + v++i+d++v e++     l++++++++Gl+Pg+R++lr ++gv
  gi|336252310|ref|YP_004595417.1| 313 vavtgeAWPFLLVKLAAAVVVVWIFDETVFEDSPrYAILLMITVVAVGLGPGTRDMLRATFGV 375
                                       3333337778899*************99998887688888889999**************997 PP

>> DUF2206  Predicted membrane protein (DUF2206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3     9e-06     0.081      94     185 ..     139     230 ..     131     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9e-06
                           DUF2206  94 nptttqglavitkqissllhtvskylhliiqfliviGvlsvlflrkkkyrlsieylaivlvllvilvasivlpyfas 170
                                       n  + +++  + ++ +   + +s +++++++++ ++ v+  ++l+++ y  + ey ++++ + ++++++  l y+a 
  gi|336252310|ref|YP_004595417.1| 139 NAAAYRATGTLAIDLPWSGFIISPLIYFTVFAVTAVAVVVSVWLERNDYVSGYEYPLFAVGTGLLALTLAHLGYTAA 215
                                       556667777788888888888999*******9988877776***99******************************9 PP

                           DUF2206 171 alntaRlyqillifl 185
                                           +R y +ll+++
  gi|336252310|ref|YP_004595417.1| 216 TEPFSRFYPLLLVTT 230
                                       9999*******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2697.83
//
Query:       gi|336252311|ref|YP_004595418.1|  [L=789]
Description: amino acid permease-associated protein [Halopiger xanaduensis SH-6]
Scores for 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-45  154.4  42.9      5e-45  154.1  42.9    1.1  1  AA_permease_2   Amino acid permease
      4e-41  141.1  39.0    5.4e-41  140.7  39.0    1.1  1  AA_permease     Amino acid permease
    1.2e-19   71.2  15.4    7.5e-11   42.7   0.7    3.7  3  Usp             Universal stress protein family
    2.4e-05   23.3  11.6    2.4e-05   23.3  11.6    2.3  2  Spore_permease  Spore germination protein
  ------ inclusion threshold ------
       0.14   11.4   6.5       0.33   10.1   6.5    1.6  1  MIG-14_Wnt-bd   Wnt-binding factor required for Wnt secretion
       0.62    9.4   2.9        2.9    7.2   0.0    2.6  3  DUF3810         Protein of unknown function (DUF3810)
        1.1    9.3   7.9        1.1    9.4   4.7    2.7  2  AA_permease_C   C-terminus of AA_permease
        8.5    6.2   8.4       0.26   11.1   2.1    1.6  2  DUF5373         Family of unknown function (DUF5373)


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 !  154.1  42.9   2.2e-48     5e-45       1     400 [.      12     418 ..      12     442 .. 0.86

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 2.2e-48
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       l+llsa+ + ig++ig+gifv +  ++a +gp+++ +++i+ +  +   +l   El++a+p+sgG+y y  +a g++
  gi|336252311|ref|YP_004595418.1|  12 LGLLSAITIGIGTMIGAGIFVLPgtAVADVGPLAAATFVIGGVTAM-FTALSASELGTAMPKSGGAYFYINRALGPL 87 
                                       799********************988888****9999999999985.6888899***99****************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgp...dlqg.ntwltyliaiaililvalinirgikesakiqnilg 148
                                       ++++s+w+nw++ +++ +++++ +++y  +++g     l + + +++  i+ +  +l++++n++g ke++ +q i++
  gi|336252311|ref|YP_004595418.1|  88 FGSISGWANWLGLAFASSFYMYGFGEYVNQLVGApalALGPlTVTAAQTIGLVGAVLFIAVNYVGAKETGGLQIIIV 164
                                       ****************************99998557845442344667778888899******************99 PP

                     AA_permease_2 149 ilkillpliiliilglitvdgggfsslstetdtffpngwpg.vllgllivlwsfdGfesaanvseevkk..kdvpka 222
                                       ++ +  +l+ + ++gl+ +d +  +        ++++g +g vl + + v+ s+ Gf  +++v+ee+k+  +++p+a
  gi|336252311|ref|YP_004595418.1| 165 VTLL-AILAAFTVVGLLNADMDSLQ-------PIVQDGAMGeVLPVTALVFVSYLGFVQITSVAEEIKNpgRNLPLA 233
                                       9999.68899999999999776554.......79*******88999999*****************999989***** PP

                     AA_permease_2 223 ifigllivlvlyllvniaflgvvpddeianlsn.lgsvaalffeavg......gkvvaiivvilialsllgaintav 292
                                        + +++iv+v+y l+ +++l++vp d ++ +++ ++++a+l+f ++       g  + +++ +++ l+ + ++n+ +
  gi|336252311|ref|YP_004595418.1| 234 VIGSVAIVTVVYALFLLVLLAAVPTDLVSGNDTaVVEAAQLLFGQYEvfgynlGLLGWGMLLFGGLLATASSANASI 310
                                       ****************************9877778889999999987665543336666667777789999****** PP

                     AA_permease_2 293 igssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliig 368
                                       ++ssr+++a++r++++    + ++ +fg+p+ +i +t ++  +++llf      ++ +l++++s++++i+y+ll i+
  gi|336252311|ref|YP_004595418.1| 311 LSSSRINFAMGREKIISPSVNEIHpRFGTPFKSILITGTLI-VVFLLFG-----NIELLSTAGSVLHLIVYGLLNIA 381
                                       **************************************996.5555663.....589******************** PP

                     AA_permease_2 369 alilrkkrphlkr.....pgkilvaiigalfllfllv 400
                                       +++ r  +p         p ++ v iiga++++ l++
  gi|336252311|ref|YP_004595418.1| 382 LIVMREAEPADYDpdfevPLYPFVPIIGAISSFALIA 418
                                       *******997644233333335666666666665553 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.7  39.0   2.4e-44   5.4e-41       3     431 ..      18     420 ..      16     459 .. 0.87

  Alignments for each domain:
  == domain 1  score: 140.7 bits;  conditional E-value: 2.4e-44
                       AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviG 79 
                                       + i +g +iG+g+fv  g +++ +Gpl+a   ++++gv  ++++ls +e+ t++pksgg+y+y+ r lgp +G   G
  gi|336252311|ref|YP_004595418.1|  18 ITIGIGTMIGAGIFVLPGTAVADVGPLAA-ATFVIGGVTAMFTALSASELGTAMPKSGGAYFYINRALGPLFGSISG 93 
                                       6799**********************555.*********************************************** PP

                       AA_permease  80 lnylfswitvlaleltaasiliqfwelvtdlpkawvt.............gavflvvlliinlvgvkvygeaefila 143
                                       +         l+l+++ + ++ +f e+v +l  a +              g+v  v+++++n+vg+k  g  ++i+ 
  gi|336252311|ref|YP_004595418.1|  94 WA------NWLGLAFASSFYMYGFGEYVNQLVGAPALalgpltvtaaqtiGLVGAVLFIAVNYVGAKETGGLQIIIV 164
                                       **......5566666677777777777777776666677889999******************************** PP

                       AA_permease 144 likiiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvai 220
                                       + ++ +++af +vg  l+a+ +  +                 ++++      ga+  ++ v + v++++ G+  ++ 
  gi|336252311|ref|YP_004595418.1| 165 VTLLAILAAFTVVG-LLNADMDSLQP----------------IVQD------GAMGEVLPVTALVFVSYLGFVQITS 218
                                       **************.35555555555................5666......68999******************** PP

                       AA_permease 221 iagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasa......aspfvifikesgvsvlapl 291
                                       +a+E+k+P +++P a++  v ++t++Y l+ll++ + vp++   + nd+a++       + +++f+ ++g+ +++ l
  gi|336252311|ref|YP_004595418.1| 219 VAEEIKNPGRNLPLAVIGSVAIVTVVYALFLLVLLAAVPTDL-VSGNDTAVVeaaqllFGQYEVFGYNLGLLGWGML 294
                                       ***************************************987.666777777779********************99 PP

                       AA_permease 292 inaviltaalssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnf 367
                                       +  + l+a+ ssan+s+ s+sR+ +++ +++++  +v + + + g P ++il++  + +++ll  ++ l        
  gi|336252311|ref|YP_004595418.1| 295 LFGG-LLATASSANASILSSSRINFAMGREKIISpSVNEIHPRFGTPFKSILITGTLIVVFLLFGNIELL------- 363
                                       8666.667889*********************988*******************9999999988877777....... PP

                       AA_permease 368 llaisaliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilal 431
                                        +++  +  liv++l +++++++R a   +  ++ +  f+ +l+p+ +i++   +++++li+ +
  gi|336252311|ref|YP_004595418.1| 364 -STAGSVLHLIVYGLLNIALIVMREA---EPADY-DPDFEVPLYPFVPIIGA--ISSFALIAYI 420
                                       .999999******************9...66666.88999999999999764..4444444444 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.7   3.3e-14   7.5e-11       4     139 ..     483     616 ..     482     618 .. 0.92
   2 !   32.0   3.8   6.7e-11   1.5e-07       3     139 ..     625     742 ..     624     744 .. 0.92
   3 ?   -3.1   0.1       4.6     1e+04     111     127 ..     746     761 ..     746     762 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 3.3e-14
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       +++V+v +  +   +le A  laka+++ + ++h+++ +++++  ++ e  ++  +e+++  ++    ++ +   ++
  gi|336252311|ref|YP_004595418.1| 483 TVVVPVSNPRTESDLLELASVLAKANDGVVQAVHIVEVPDQTPLREGSEHIQRIDAESQALMEQVR--EDTETLDVP 557
                                       699***7777777************************************99999999888877665..599****** PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                       +++ +v+++   ee  +va++edad +V+G+   ++ s        + + ++ pc+ lv
  gi|336252311|ref|YP_004595418.1| 558 VEVRTVVSHRSFEEVFDVARREDADTVVMGWGPSRSWSAGRAERPLDELTHNLPCDFLV 616
                                       ********************************988888888999999999999999998 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 6.7e-11
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                       +r+lV++ g ++s+  ++ A  l  + g+e++llhv+d++++ a ++a+ ++  + + le a+ ++d          
  gi|336252311|ref|YP_004595418.1| 625 DRVLVPTAGGPDSDLSADVARYLRDQVGSEITLLHVVDDESDRADGEAFLTEWAADHGLEDATIQLD---------- 691
                                       69*********************999***********************************977655.......... PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                              ++gd  ++i+ +  +   +l+++G++ r+ lsrl+ GS ++ vl+ ++c+V++
  gi|336252311|ref|YP_004595418.1| 692 -------TSGDIEDAIATASAR--HSLVILGATERGLLSRLVRGSLASDVLEDVDCSVIL 742
                                       .......678888877766665..9*********************************96 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4.6
                                       SCCSSTTTTCSSBHHHH CS
                               Usp 111 srgrsglsrlllGSvse 127
                                       s++ ++++++l+GS s+
  gi|336252311|ref|YP_004595418.1| 746 SHD-RSIRQRLFGSSSD 761
                                       577.889999****997 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3  11.6   1.1e-08   2.4e-05       8     248 ..      18     270 ..      12     316 .. 0.78
   2 ?   -0.7   4.3      0.22   4.9e+02     112     177 ..     339     403 ..     337     432 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.1e-08
                    Spore_permease   8 fvlivsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpek.tliellkkilgkwLGsllsi 83 
                                       +++ + +++G+gi +lp+++++  +p +  + +++g+ +++ +l +++l   +p++   + +++  lg + Gs+ + 
  gi|336252311|ref|YP_004595418.1|  18 ITIGIGTMIGAGIFVLPGTAVADVGPLAAATFVIGGVTAMFTALSASELGTAMPKSgGAYFYINRALGPLFGSISGW 94 
                                       5666899*********************************************99862578899******99999999 PP

                    Spore_permease  84 lfilyFlllaafelRefseliqvfl.........ledtplwiiilllllvilYlvvkGieslareflfiivilliil 151
                                       +  l  ++ ++f +  f+e ++  +         l+ t   +i l+  ++++ + + G ++   + ++i+v ll+il
  gi|336252311|ref|YP_004595418.1|  95 ANWLGLAFASSFYMYGFGEYVNQLVgapalalgpLTVTAAQTIGLVGAVLFIAVNYVGAKETGGLQIIIVVTLLAIL 171
                                       88888888888888888886654432222222223344444444444455555555566665535556666666777 PP

                    Spore_permease 152 llillfslklaeiknlrPvlgngik.pvlkslkttslsflgveillllvpflkdkkkvkkaallg.vlistllyllt 226
                                        +++++ l  a+++ l+P++++g + +vl  +  + +s+lg++ ++ + + +k++ + +  a++g v+i+t++y+l 
  gi|336252311|ref|YP_004595418.1| 172 AAFTVVGLLNADMDSLQPIVQDGAMgEVLPVTALVFVSYLGFVQITSVAEEIKNPGRNLPLAVIGsVAIVTVVYALF 248
                                       7788888999***********9965499999************************99998887754899*******9 PP

                    Spore_permease 227 tlivilvlsveqlkkatwptls 248
                                       +l+ +++   + ++    + ++
  gi|336252311|ref|YP_004595418.1| 249 LLVLLAAVPTDLVSGNDTAVVE 270
                                       9999988777766655555555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.22
                    Spore_permease 112 tplwiiilllllvilYlvvkGieslareflfiivilliilllillfslklaeiknlrPvlgngikp 177
                                       tp   i+++  l++++l+++ ie l+     ++  ++  ll i l+++++ae+   +P ++  + p
  gi|336252311|ref|YP_004595418.1| 339 TPFKSILITGTLIVVFLLFGNIELLS-TAGSVLHLIVYGLLNIALIVMREAEPADYDPDFEVPLYP 403
                                       6777888889999999**********.788889999999999999999999999988877765443 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 ?   10.1   6.5   0.00015      0.33     106     284 ..     145     385 ..     137     386 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                     MIG-14_Wnt-bd 106 filellfnswflllldiifqsiFlsvLllFwlvff.....eslrdeqnrrktlsfylpklllvlllwlvllvlalye 177
                                       fi+  ++ ++ +  l+ii+ ++ l++L  F +v +     +sl    ++   +   lp   lv++ +l ++   +  
  gi|336252311|ref|YP_004595418.1| 145 FIAVNYVGAKETGGLQIIIVVTLLAILAAFTVVGLlnadmDSLQPIVQD-GAMGEVLPVTALVFVSYLGFVQ--ITS 218
                                       5555556666666788888899999999998888876555555433333.4555566655555555544443..445 PP

                     MIG-14_Wnt-bd 178 rleqlkdpfysiwssalilkilaiilavlyflyLlylifr..................................... 217
                                         e++k+p  +     l+++  ++i++v+y+l+Ll+l+                                       
  gi|336252311|ref|YP_004595418.1| 219 VAEEIKNPGRNLP---LAVIGSVAIVTVVYALFLLVLLAAvptdlvsgndtavveaaqllfgqyevfgynlgllgwg 292
                                       5568999999886...48888999999**********9999999999999999999999999999999999999999 PP

                     MIG-14_Wnt-bd 218 ............................sfseirskrvkegdiRfkflilltllvlavlvifiilglvselsptsds 266
                                                                      +i s +v e   Rf   +  +l++ +++v+f+++g ++ l      
  gi|336252311|ref|YP_004595418.1| 293 mllfggllatassanasilsssrinfamGREKIISPSVNEIHPRFGTPFKSILITGTLIVVFLLFGNIELL--STAG 367
                                       99999999999888888877777766664455555555566668877666666666666666666664434..4456 PP

                     MIG-14_Wnt-bd 267 saqflgvygllNlyvytl 284
                                       s+  l+vygllN+ ++++
  gi|336252311|ref|YP_004595418.1| 368 SVLHLIVYGLLNIALIVM 385
                                       *************99887 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.3         1   2.3e+03      23      76 ..     125     176 ..     107     186 .. 0.50
   2 ?    1.6   0.3     0.064   1.4e+02      23      77 ..     195     251 ..     193     255 .. 0.81
   3 ?    7.2   0.0    0.0013       2.9      55     111 ..     415     505 ..     355     567 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1
                           DUF3810  23 Svgellivllillvilylvlaiklkkrkkkkkrllkvllrvllvllvvyflftl 76 
                                       ++g l+++++  + ++  vl+i ++  + k++  l+++  ++++ll++++ ft+
  gi|336252311|ref|YP_004595418.1| 125 ALGPLTVTAAQTIGLVGAVLFIAVNYVGAKETGGLQII--IVVTLLAILAAFTV 176
                                       55555555544444444444443344444434444433..33334444444443 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.064
                           DUF3810  23 Svgellivllillvilylvlai..klkkrkkkkkrllkvllrvllvllvvyflftll 77 
                                       ++ge+l v ++++v ++ ++ i  + ++ k+  ++l  +++  +++++vvy+lf+l+
  gi|336252311|ref|YP_004595418.1| 195 AMGEVLPVTALVFVSYLGFVQItsVAEEIKNPGRNLPLAVIGSVAIVTVVYALFLLV 251
                                       578999998888888888888878666777777778888888999999999999875 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0013
                           DUF3810  55 rllkvllrvllvllvvyflftllwglnYyreplserlglk...................................ke 96 
                                       +l+ ++  v++ l++++++f  lw l+Y+r+ ++++  +                                    ++
  gi|336252311|ref|YP_004595418.1| 415 ALIAYIEPVVIGLSAALVVFAGLWYLLYSRTRVENTG-VFanwildrseempdaavtaasaaspandeytvvvpvSN 490
                                       56778888999********************999854.433666666666666666666666666666666666555 PP

                           DUF3810  97 eyseeelaelaeklv 111
                                         +e++l ela+ l+
  gi|336252311|ref|YP_004595418.1| 491 PRTESDLLELASVLA 505
                                       555555555555444 PP

>> AA_permease_C  C-terminus of AA_permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.3   2.8e+03      24      44 ..      12      32 ..      10      36 .. 0.78
   2 ?    9.4   4.7   0.00049       1.1       1      48 [.     397     444 ..     397     447 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.3
                     AA_permease_C 24 LdsltwirfgvwmliglliYf 44
                                      L+ l+ i +g+ ++ig  i++
  gi|336252311|ref|YP_004595418.1| 12 LGLLSAITIGIGTMIGAGIFV 32
                                      556677889999999999887 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00049
                     AA_permease_C   1 FkvPlvPflPalsIlvNiyLmlqLdsltwirfgvwmliglliYflYgi 48 
                                       F+vPl+Pf+P+++ +  + L++ ++     + ++ +++  l Y+lY++
  gi|336252311|ref|YP_004595418.1| 397 FEVPLYPFVPIIGAISSFALIAYIEPVVIGLSAALVVFAGLWYLLYSR 444
                                       99*******************999999888888888888888998876 PP

>> DUF5373  Family of unknown function (DUF5373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.1   0.00012      0.26      32     165 ..     134     276 ..     116     287 .. 0.69
   2 ?   -3.7   0.5       4.1   9.3e+03     101     135 ..     348     383 ..     340     386 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                           DUF5373  32 lqilalvlqiv.....wllaeetskvl.lllkivsivltaftvavfivenkiLmrahyysalifllvplavlvllii 102
                                        q + lv  ++     ++ a+et  +  ++++ ++++l+aftv+  +  +   ++  +  +++  ++p++ lv++ +
  gi|336252311|ref|YP_004595418.1| 134 AQTIGLVGAVLfiavnYVGAKETGGLQiIIVVTLLAILAAFTVVGLLNADMDSLQPIVQDGAMGEVLPVTALVFVSY 210
                                       555544444330001244445666565145566789************999999*********************** PP

                           DUF5373 103 laflkilflnleaielksvlslvvaliilcvyivYltlCrkLvkaldq...qpddlPeldttqglf 165
                                       l f++i+  + e  +    l+l+v   + +v +vY+ +  +L+ a+ +     +d   ++++q lf
  gi|336252311|ref|YP_004595418.1| 211 LGFVQITSVAEEIKNPGRNLPLAVIGSVAIVTVVYALFLLVLLAAVPTdlvSGNDTAVVEAAQLLF 276
                                       ******999955555555557777766777777777766666665532111345555556666555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.1
                           DUF5373 101 iilaflkilflnlea.ielksvlslvvaliilcvyi 135
                                        +l+++ +lf+n e  ++  svl+l+v  ++ +++i
  gi|336252311|ref|YP_004595418.1| 348 GTLIVVFLLFGNIELlSTAGSVLHLIVYGLLNIALI 383
                                       344444455555433133445555555555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (789 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); 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:                        12  (0.000669307); 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: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.43
# Mc/sec: 5487.75
//
Query:       gi|336252312|ref|YP_004595419.1|  [L=769]
Description: amino acid permease-associated protein [Halopiger xanaduensis SH-6]
Scores for 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-45  153.3  43.4    1.1e-44  152.9  43.4    1.1  1  AA_permease_2   Amino acid permease
    4.7e-37  127.7  39.6    6.2e-37  127.3  39.6    1.1  1  AA_permease     Amino acid permease
    9.6e-23   81.3   8.7      3e-10   40.8   3.5    3.2  2  Usp             Universal stress protein family
     0.0074   16.3   3.7     0.0074   16.3   3.7    2.6  3  AA_permease_C   C-terminus of AA_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 !  152.9  43.4   2.5e-48   1.1e-44       1     404 [.      12     430 ..      12     453 .. 0.81

  Alignments for each domain:
  == domain 1  score: 152.9 bits;  conditional E-value: 2.5e-48
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       l+l+sa+a+ ig++ig+gifv +  +a  +gp+++l+++++ +i  +  +++  El++a+p+ gG+y y  +  g++
  gi|336252312|ref|YP_004595419.1|  12 LGLVSALAVGIGTMIGAGIFVLPgvAAQEAGPIVVLSFIVGGMIA-MVNAFTVSELGTAMPKAGGAYYYINRSLGPL 87 
                                       799********************866666***************9.69*********99****************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgn....................twltyliaiaililvali 132
                                       ++++s++  w++ +++ a++++ +++yl+ +l +++ +                     +  + + a +  + ++ +
  gi|336252312|ref|YP_004595419.1|  88 FGSISGMGDWMGLAFASAFYCIGFGGYLADVLEGTVLPVpgvgeiallptvalgplvlsD--IQIGALLAGVAFVGV 162
                                       *******************************98744333666667777778888776543..34456777788999* PP

                     AA_permease_2 133 nirgikesakiqnilgilkillpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaan 209
                                       n++g ke++ +q+++++l + ++l+++ ++g++ +d g+       ++++ p g  ++l g + v+ sf G+  +a 
  gi|336252312|ref|YP_004595419.1| 163 NYMGAKETGGVQTVIVTLLL-GILTVFALFGFFSFDWGTVM----TDGSVAPLGYGQILPGTALVFVSFLGYAKIAT 234
                                       *************9999999.68888888888887444443....2234444455557778888************* PP

                     AA_permease_2 210 vseevkk..kdvpkaifigllivlvlyllvniaflgvvpddeianlsn.lgsvaalffeavggkvvaiivvilials 283
                                       + ee k+  +++p+ai+ +++iv+v+y  +  +++g++p d+i+   + ++ +a+++fe   g v+ + + i++ l+
  gi|336252312|ref|YP_004595419.1| 235 IGEELKNpgRNLPIAIIGSVAIVMVIYAILVGLMVGIIPYDSISDETPmSH-AAGIVFEGNLGAVGIASITIAALLA 310
                                       ****888879*********************************87666344.56665555455999999******** PP

                     AA_permease_2 284 llgaintavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgli 359
                                        + ++n+ +++s+r+++a++rd++  ++++ ++ +f +p+r+i +t     +l++++l+   +++ +l+ ++s++++
  gi|336252312|ref|YP_004595419.1| 311 TASSANASILASARINFAMGRDKIVTDWLNEIHpRFATPYRSIAVTGGMI-LLFIAVLG---NDLEILSKAASVLHL 383
                                       ************************************************96.66666765...58************* PP

                     AA_permease_2 360 isyllliigalilrkk.rphl.kr...pgkilvaiigalfllfllvalff 404
                                       i+y+l+ +++++ r    p++ +    p ++++ i+g++++l l+   +f
  gi|336252312|ref|YP_004595419.1| 384 IVYALINVALVVFREAdVPEYdPDftvPFYPITPILGFVLSLGLI---AF 430
                                       ***********9995515555433444333344444444444333...33 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.3  39.6   1.4e-40   6.2e-37       4     426 ..      19     428 ..      16     458 .. 0.86

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 1.4e-40
                       AA_permease   4 vialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGl 80 
                                          +g +iG+g+fv  gv++++aGp  ++l+++++g++ +  + +++e+ t++pk+gg+y+y+ r+lgp +G   G+
  gi|336252312|ref|YP_004595419.1|  19 AVGIGTMIGAGIFVLPGVAAQEAGP-IVVLSFIVGGMIAMVNAFTVSELGTAMPKAGGAYYYINRSLGPLFGSISGM 94 
                                       5689*********************.678************************************************ PP

                       AA_permease  81 nylfswitvlaleltaasiliqfwelvtdlpkawvt...........................gavflvvlliinlv 130
                                                ++l+++ a ++i+f +++ d+++  v                            +++  v+++++n++
  gi|336252312|ref|YP_004595419.1|  95 G------DWMGLAFASAFYCIGFGGYLADVLEGTVLpvpgvgeiallptvalgplvlsdiqigALLAGVAFVGVNYM 165
                                       *......555666669***************55555**************************88888899******* PP

                       AA_permease 131 gvkvygeaefilalikiiaiiafiivg.iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfv 206
                                       g+k  g +++++  +++ ++  f ++g +++ +g  +++g        +++     l+            +++ + +
  gi|336252312|ref|YP_004595419.1| 166 GAKETGGVQTVIVTLLLGILTVFALFGfFSFDWGTVMTDG--------SVA----PLGY----------GQILPGTA 220
                                       *********9977777777777777776************........444....4444..........59****** PP

                       AA_permease 207 ivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikes 283
                                        v+++f G+  +a+i++E+k+P +++P+ai+  v +++++Y +++ l++ ++p+++ +  +    a    ++f  ++
  gi|336252312|ref|YP_004595419.1| 221 LVFVSFLGYAKIATIGEELKNPGRNLPIAIIGSVAIVMVIYAILVGLMVGIIPYDSISDETPMSHA--AGIVFEGNL 295
                                       *******************************************************98887765555..567777888 PP

                       AA_permease 284 gvsvlaplinaviltaalssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnl 359
                                       g  ++a++ +++ l+a+ ssan+s+ ++ R+ +++ +d++   +  + + +   P+r+i+++  + ll++  a l  
  gi|336252312|ref|YP_004595419.1| 296 GAVGIASI-TIAALLATASSANASILASARINFAMGRDKIVTdWLNEIHPRFATPYRSIAVTGGMILLFI--AVLGN 369
                                       88888875.666677899************************5556678999**********98888888..99999 PP

                       AA_permease 360 aapivfnfllaisaliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiil 426
                                       +     ++l+ ++ +  liv+ li++++++fR a  + +    +  f+ +++p ++il++++ + ++
  gi|336252312|ref|YP_004595419.1| 370 D----LEILSKAASVLHLIVYALINVALVVFREA-DVPEY---DPDFTVPFYPITPILGFVLSLGLI 428
                                       9....99**************************9.33333...568999999999998765544333 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.2   1.2e-13   5.3e-10       4     140 ..     495     629 ..     494     630 .. 0.88
   2 !   40.8   3.5   6.7e-14     3e-10       3     139 ..     637     754 ..     635     756 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.2e-13
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       +++V+v +  +  ++le A  laka+++ + ++h+++ +++++  ++ e  ++  +e+++   +    ++ +   ++
  gi|336252312|ref|YP_004595419.1| 495 TVVVPVANPRTESNLLELASVLAKANDGVVQAVHIVEVPDQTPLQEGSEHIQRIDEESQQLMTQVR--EDTETLDVP 569
                                       589***7777777*****************************999999998876666655444433..479999999 PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       + + +++++   ee  +va++e ad +V+G+   +  s   +  + + +++  pc+ lv 
  gi|336252312|ref|YP_004595419.1| 570 VDVRTIVSHRSFEEVFDVARRERADTVVMGWGPGRPWSAGRVEGTFDELAHDLPCDFLVL 629
                                       9999***************************9988888889999************9985 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 6.7e-14
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                       +r+lV++ g ++s+  +e A +l  + gae++llhv+ ++++ a ++a+ ++  + + l+ a+ +            
  gi|336252312|ref|YP_004595419.1| 637 DRVLVPTAGGPDSDLSAEVARHLRDQVGAEITLLHVVGDESDRADGEAFLTEWADDHGLADAAIR------------ 701
                                       79*********************************************************999664............ PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                            v ++gd  ++i+ +a   d +l+V+G++ r+ lsrll GS +  v++ ++c+V++
  gi|336252312|ref|YP_004595419.1| 702 -----VDVSGDIEDAIAAAAA--DHSLLVLGATERGLLSRLLRGSLAYDVVHDVDCSVIM 754
                                       .....5567777777766655..69*********************************97 PP

>> AA_permease_C  C-terminus of AA_permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.2   5.3e+03      30      45 ..      18      33 ..      11      37 .. 0.75
   2 ?   -3.8   0.9       3.2   1.4e+04      30      38 ..     257     265 ..     251     273 .. 0.51
   3 !   16.3   3.7   1.6e-06    0.0074       1      50 [.     408     457 ..     408     458 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                     AA_permease_C 30 irfgvwmliglliYfl 45
                                      + +g+ ++ig  i++l
  gi|336252312|ref|YP_004595419.1| 18 LAVGIGTMIGAGIFVL 33
                                      5688999999988875 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.2
                     AA_permease_C  30 irfgvwmli 38 
                                       ++++  +l+
  gi|336252312|ref|YP_004595419.1| 257 VMVIYAILV 265
                                       333333344 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 1.6e-06
                     AA_permease_C   1 FkvPlvPflPalsIlvNiyLmlqLdsltwirfgvwmliglliYflYgirh 50 
                                       F vP++P+ P+l+ ++ + L++ +d    ++ ++ ++i ++ Y++Y +++
  gi|336252312|ref|YP_004595419.1| 408 FTVPFYPITPILGFVLSLGLIAFMDRIEVALSLAFVAIAVIWYVVYARHE 457
                                       99********************************************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (769 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.45
# Mc/sec: 5189.34
//
Query:       gi|336252313|ref|YP_004595420.1|  [L=432]
Description: hypothetical protein Halxa_0904 [Halopiger xanaduensis SH-6]
Scores for 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-87  291.4   1.4    1.1e-86  290.6   1.4    1.4  1  BNR_4     BNR repeat-containing family member


Domain annotation for each model (and alignments):
>> BNR_4  BNR repeat-containing family member
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.6   1.4   6.2e-91   1.1e-86       1     273 []      34     307 ..      34     307 .. 0.96

  Alignments for each domain:
  == domain 1  score: 290.6 bits;  conditional E-value: 6.2e-91
                                       EEEEEEE-TTSEEEEEEEET.T--......-EEEEEEEE----.---SEEEEEE-TTS-EEEEEESSSSS--EEEBS CS
                             BNR_4   1 kqYiayydaegsvvvarrdleges......Welleldykqtad.DsHnvislgvdgdgrlhlafdhHsdplvYrrst 70 
                                       +q++a+yda+++++v++r+l + +      W++++l+  ++ + D+Hn+ +l+vd++++lhl++++H +pl+Y+r+ 
  gi|336252313|ref|YP_004595420.1|  34 HQFVAFYDADRNITVGQRELGTDDadeageWTVARLPEDRKIEwDAHNSLALAVDREDYLHLSGNMHVHPLKYYRTR 110
                                       69******************5554667778******86666667********************************* PP

                                       STT---.B-----SS..SSS-SSEEEEEEEE-GGG-EEEEEEE-TTSS-EEEEEEEETTTTEEEEEES-.SB--T.T CS
                             BNR_4  71 apldlsslgeveemlpggekessvTYPrflstedgkLllsyRdgksgngnavlneYdektdkwktlgekqlldgeeg 147
                                       ++ld+++++++ em+  g++es+vTYP+f++ +d++L++ yRdg sg gn ++n Yde+++kw++l e +l+ g  +
  gi|336252313|ref|YP_004595420.1| 111 ESLDVTTFERIDEMV--GTEESQVTYPQFFRGPDDELVFKYRDGYSGGGNWRYNVYDERNHKWNRLLEAPLTYGG-D 184
                                       ***************..9999*****************************************************8.* PP

                                       T-EEEEEE.EE-TTS-EEEEEEEE-SSSGGGEEEEEEEEESSTTSS-B-TTS-B--.SSB-TTT-EE.EE---TTS- CS
                             BNR_4 148 qrnaYlkglsygkdgrihvtwtwretpdaetnhdlyYaysddggrtwenaaGeklaelpikvstagvvvdpipknsg 224
                                       ++naY++g+ +g+ g +h++w+wr++++a+tnhdl+Ya+s+d  r+we+++G++l+ lpi++++ ++ vdp+p+++g
  gi|336252313|ref|YP_004595420.1| 185 AMNAYPHGPVVGPGGDYHCCWVWRDHGGAQTNHDLCYARSPDL-REWETSQGAPLE-LPIDINSGDL-VDPVPPYGG 258
                                       *******************************************.9***********.**********.********* PP

                                       --S.S-EEEE-TT--EEEEEEE--TT-SS-EEEEEEE-SS-EEEEE-S-- CS
                             BNR_4 225 lin.qesvavDkegnpvvlyskfddagatqkyyyrkanggaWekrqvada 273
                                       +in ++++++D++g++v++y+kfd++g+tq y +r a++  We+ +++d+
  gi|336252313|ref|YP_004595420.1| 259 MINnNTKIGFDTAGRVVISYHKFDHEGNTQLYNAR-AEADGWEIYRTSDW 307
                                       ***********************************.89999**9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3426.63
//
Query:       gi|336252314|ref|YP_004595421.1|  [L=51]
Description: hypothetical protein Halxa_0905 [Halopiger xanaduensis SH-6]
Scores for 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:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 389.42
//
Query:       gi|336252315|ref|YP_004595422.1|  [L=218]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-23   81.6   0.2    7.3e-23   81.6   0.2    1.5  2  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 ?   -2.6   0.1       0.4   7.2e+03      57      57 ..      23      23 ..       5      49 .. 0.46
   2 !   81.6   0.2   4.1e-27   7.3e-23       4     141 .]      54     191 ..      52     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.4
                                      H CS
                               Usp 57 e 57
                                      +
  gi|336252315|ref|YP_004595422.1| 23 D 23
                                      1 PP

  == domain 2  score: 81.6 bits;  conditional E-value: 4.1e-27
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHHHCT CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaaeag 78 
                                       r+lV++Dgs+ s  Ale A++l  +  a++++l+++d+++ ++v  + ++   +++ + ++ l  +   a++ ae +
  gi|336252315|ref|YP_004595422.1|  54 RVLVPFDGSDPSCGALEAAFKLFPD--AAVTALTIVDDSTISYVRSPSSDPNASAEGELLRGLPSELerATEIAERR 128
                                       8********************8655..79**********99988877777766666666666555556789999*** PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++  ++  + g++ ++ile++e+e +d +V+Gs  r+g++rll GSv+e v+rh+++pV+v++
  gi|336252315|ref|YP_004595422.1| 129 DERIQTAGRIGSATRGILEYVEREAVDHVVIGSLCRTGIARLLRGSVAETVVRHSSVPVTVIP 191
                                       *************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); 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 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1802.22
//
Query:       gi|336252316|ref|YP_004595423.1|  [L=217]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-17   63.5   0.1    1.9e-17   62.8   0.1    1.4  1  HTH_10          HTH DNA binding domain
    3.5e-11   43.2   0.4    3.5e-11   43.2   0.4    1.8  2  BAT             GAF and HTH_10 associated domain
    0.00022   20.7   0.2    0.00054   19.4   0.2    1.7  1  Sigma70_r4      Sigma-70, region 4
     0.0014   18.5   1.0     0.0044   16.9   0.6    2.0  2  MarR_2          MarR family
  ------ inclusion threshold ------
      0.024   14.5   0.7      0.054   13.3   0.7    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.026   14.1   0.2      0.047   13.3   0.2    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.055   14.0   0.2         14    6.3   0.0    3.1  3  Arg_decarbox_C  Arginine decarboxylase C-terminal helical ext
      0.081   12.6   0.3        6.8    6.5   0.0    2.3  2  Sigma70_r4_2    Sigma-70, region 4
       0.17   12.1   0.0       0.32   11.3   0.0    1.3  1  UPF0122         Putative helix-turn-helix protein, YlxM / p13


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 !   62.8   0.1   9.8e-21   1.9e-17       1      52 [.     154     205 ..     154     206 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 9.8e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       L+++q+ +l +Ay++GYF++PRr+tl eLA++  +s+s+ls++Lr+a++ l+
  gi|336252316|ref|YP_004595423.1| 154 LSPRQRDALLTAYRQGYFEVPRRTTLTELADTVEVSDSALSQRLRRATNALV 205
                                       789*********************************************9987 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.4   1.7e-14   3.5e-11      15     139 ..      14     140 ..       5     145 .. 0.87
   2 ?   -0.8   0.2      0.63   1.3e+03     115     142 ..     172     199 ..     170     209 .. 0.68

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 1.7e-14
                               BAT  15 dvlvalaaeldc.rveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtlleltvsgpsla 90 
                                       ++l ++ ++l + ++ele++vp  +   + +f+++gadp+ +++++ d+   e+v+ +++ +d+tl+e+++ gp++ 
  gi|336252316|ref|YP_004595423.1|  14 FPLGRVLEDLPAvEIELERIVPLREA-IIPLFWISGADPAVIETTLRDHAETESVEQLTAAEDRTLFEVRW-GPDIN 88 
                                       55555555554416********9885.99******************************************.89876 PP

                               BAT  91 s...tlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLv 139
                                           +l +  + + +a+ + +++++++++++ +d+ ++  al+e+   v+L+
  gi|336252316|ref|YP_004595423.1|  89 GviqALIDTRAKILEATGTADTWDFRLRFSSHEDLSAFNMALTESDVPVTLR 140
                                       6666************************************999987666665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.63
                               BAT 115 evPpgadvRsvvealeerypdveLvarr 142
                                       evP+++ + ++++++e + ++ + + rr
  gi|336252316|ref|YP_004595423.1| 172 EVPRRTTLTELADTVEVSDSALSQRLRR 199
                                       7888888888888877666555555554 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   2.7e-07   0.00054       3      48 ..     152     204 ..     152     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.7e-07
                                       HHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   3 asLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       + L++r+r+ l   +        +  Tl E++++  +S ++ +q+++rA + L
  gi|336252316|ref|YP_004595423.1| 152 DALSPRQRDALLTAYrqgyfevPRRTTLTELADTVEVSDSALSQRLRRATNAL 204
                                       68****************99987888***********************8876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.7   3.5e+03       3      18 ..      70      85 ..      67      88 .. 0.81
   2 !   16.9   0.6   2.2e-06    0.0044       2      47 ..     153     202 ..     152     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.7
                                      --HHHHHHHHHHHCTT CS
                            MarR_2  3 ltpaqarvLaaLgrrp 18
                                      lt a+ r L++++ +p
  gi|336252316|ref|YP_004595423.1| 70 LTAAEDRTLFEVRWGP 85
                                      7888889999998877 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.2e-06
                                       T--HHHHHHHHHHHCTTTS.....EEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2   2 gltpaqarvLaaLgrrpgr.....dltvgelarrlglsksavsrilkrLva 47 
                                       +l+p q+++L+  +r + +     + t +ela++  +s sa+s++l+r+  
  gi|336252316|ref|YP_004595423.1| 153 ALSPRQRDALLTAYRQG-YfevprRTTLTELADTVEVSDSALSQRLRRATN 202
                                       58999999999999997.67888788**********************975 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 ?   13.3   0.7   2.7e-05     0.054      17      40 ..     176     199 ..     174     200 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                     HTH_AsnC-type  17 RisyaeLAervGlSestvlrRvrr 40 
                                       R++ +eLA+ v +S s+  +R+rr
  gi|336252316|ref|YP_004595423.1| 176 RTTLTELADTVEVSDSALSQRLRR 199
                                       899********************9 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 ?   13.3   0.2   2.3e-05     0.047      17      42 ..     176     201 ..     174     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.3e-05
                            HTH_24  17 risqreLAerlglSpstvnrrlkrLe 42 
                                       r++ +eLA+ + +S s++++rl+r +
  gi|336252316|ref|YP_004595423.1| 176 RTTLTELADTVEVSDSALSQRLRRAT 201
                                       799********************976 PP

>> Arg_decarbox_C  Arginine decarboxylase C-terminal helical extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.12   2.4e+02      11      38 ..      50      79 ..      50      81 .. 0.90
   2 ?    6.3   0.0    0.0072        14      27      44 ..     152     169 ..     137     169 .. 0.87
   3 ?    1.5   0.0      0.23   4.6e+02      11      33 ..     189     214 ..     184     217 .] 0.66

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.12
                    Arg_decarbox_C 11 dpeeLlerlrrqveaa..grLtpeerqall 38
                                      dp  + ++lr+ +e+    +Lt++e ++l+
  gi|336252316|ref|YP_004595423.1| 50 DPAVIETTLRDHAETEsvEQLTAAEDRTLF 79
                                      7899999*******999********99886 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0072
                    Arg_decarbox_C  27 grLtpeerqalleeleag 44 
                                       ++L+p++r all+++++g
  gi|336252316|ref|YP_004595423.1| 152 DALSPRQRDALLTAYRQG 169
                                       68*************987 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.23
                    Arg_decarbox_C  11 dpeeLlerlrrqveaa...grLtpee 33 
                                       + + L +rlrr ++a      Lt+ee
  gi|336252316|ref|YP_004595423.1| 189 SDSALSQRLRRATNALvedTMLTDEE 214
                                       55677777777777665555777776 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 ?    6.5   0.0    0.0034       6.8      10      27 ..     153     170 ..     152     172 .. 0.91
   2 ?    3.9   0.1     0.021        42      31      50 ..     181     200 ..     176     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0034
                                       TS-HHHHHHHHHHHTS-- CS
                      Sigma70_r4_2  10 eLperqreifllrylegl 27 
                                       +L++rqr ++l  y +g+
  gi|336252316|ref|YP_004595423.1| 153 ALSPRQRDALLTAYRQGY 170
                                       7**********9999986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.021
                                       HHHHHHT--HHHHHHHHHHH CS
                      Sigma70_r4_2  31 EIAellgisegtVksrlsRA 50 
                                       E A   ++s+++  +rl+RA
  gi|336252316|ref|YP_004595423.1| 181 ELADTVEVSDSALSQRLRRA 200
                                       889999*************9 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016      0.32      16      61 ..     161     204 ..     159     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                           UPF0122  16 sLLTekqanylelyyadDlSlsEiAeefnvsrqavydnikrtekll 61 
                                       +LLT   + y+e+       l+E+A++ +vs +a+++ ++r+++ l
  gi|336252316|ref|YP_004595423.1| 161 ALLTAYRQGYFEVP--RRTTLTELADTVEVSDSALSQRLRRATNAL 204
                                       57777777777754..456899******************987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1763.35
//
Query:       gi|336252317|ref|YP_004595424.1|  [L=300]
Description: Pre-mRNA processing ribonucleoprotein, binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-40  139.2   0.0    2.3e-40  138.5   0.0    1.3  1  Nop       snoRNA binding domain, fibrillarin
  ------ inclusion threshold ------
      0.023   15.0   0.1       0.39   11.0   0.0    2.2  2  HutP      HutP


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 !  138.5   0.0   2.5e-44   2.3e-40      88     226 ..     137     276 ..     122     279 .. 0.93

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 2.5e-44
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HHHHCCCHH CS
                               Nop  88 ikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaekalfralk 164
                                       + +l++rv  l++  + l e++e++  ++APNl+aL G+ +aarLis aGgL++Lak P+ tiq+lGae alf +l+
  gi|336252317|ref|YP_004595424.1| 137 LVSLAERVAGLADEADALREFVEQQTPTVAPNLAALAGPVLAARLISLAGGLEELAKKPSGTIQVLGAEDALFAHLR 213
                                       67899************************************************************************ PP

                                       T-.--SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHH.HTT----SHHHHHHHHHHH CS
                               Nop 165 kk.ntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiD.afsekdgslGkklreeiek 226
                                       ++  +pk+G+iy ++ v+  t p++++ +aR++a K+a+aaR+D  ++e++ +l+ +l e ie+
  gi|336252317|ref|YP_004595424.1| 214 GHaPSPKHGIIYIHDAVR-GTHPENRGSAARAVAGKLAIAARVDhYSGERKPELDAELEERIET 276
                                       7768*************9.66***********************54445558999998888875 PP

>> HutP  HutP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.3e-05      0.39      28      90 ..      38     100 ..      24     111 .. 0.83
   2 ?    1.5   0.0     0.037   3.3e+02      75     103 ..     226     257 ..     217     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.3e-05
                                       TEEEEEEEEEESS....HHHHHHHHHHHHHHTTSS-SSSHHHHHHHHHHHHHHHHHHTTSHHSG CS
                              HutP  28 gikvaavevggeaeel.skkivesavvaAkregvikeehreehavahAvleAlsqvtrkavgln 90 
                                       ++ + av++g+ ++e      +++a++aA r  v ++e  +++ ++hAv+ A+ +  r+a++l+
  gi|336252317|ref|YP_004595424.1|  38 DWPTLAVRTGAAESEEaYYDRLKEATTAATRDAVAEREGADDRQLVHAVR-AMDDCERTANELA 100
                                       788889999987755437788899************************96.8888888888776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.037
                                       HHHHHHHHHTTSHHSG...EEEEEEEEEG--E CS
                              HutP  75 vleAlsqvtrkavgln...vglkigivregeh 103
                                       +++A+ +  +++ g +   v++k++i+ + +h
  gi|336252317|ref|YP_004595424.1| 226 IHDAVRGTHPENRGSAaraVAGKLAIAARVDH 257
                                       6889999988888877788********98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); 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 0.20s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2486.68
//
Query:       gi|336252318|ref|YP_004595425.1|  [L=213]
Description: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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  180.7   0.0    2.6e-53  180.5   0.0    1.0  1  Fibrillarin  Fibrillarin
  ------ inclusion threshold ------
       0.86    9.4   3.5        8.5    6.2   1.8    3.2  3  RTP1_C2      Required for nuclear transport of RNA pol II C-t


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 !  180.5   0.0   2.8e-57   2.6e-53      27     223 ..      22     211 ..       8     213 .] 0.91

  Alignments for each domain:
  == domain 1  score: 180.5 bits;  conditional E-value: 2.8e-57
                                       STT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S-.-S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEE CS
                       Fibrillarin  27 vpgekvYgEklikveeeEyRvWnpfrsKlaaailkglke.lpikkgskvLYlGaasGttvsHvsDivgeegvvyave 102
                                       ++ge vYgE     +e E+R Wnp rsKl+a++   +++ l    ++ vLYlGaasGttvsHv+D  g     yave
  gi|336252318|ref|YP_004595425.1|  22 TRGEPVYGEP----TEGEWRAWNPDRSKLGAMLELSMDTgLEGGDDETVLYLGAASGTTVSHVADFAG---PTYAVE 91 
                                       4577888875....467*****************99986245567889*****************987...78**** PP

                                       SSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS-.-EEEEEEESSSTTHHHHHHHHHHHHEEEEEEEEEEEEHH CS
                       Fibrillarin 103 fsprvlrelievakkRknivPileDArkPekYralve.kvDvifaDvaqpdqarilaknaklflkeggyllisikar 178
                                       f+ r +r+l+e + +R+ ++P+l+DArkPe+Y+++ve  vD i +Dva   qar++ +n   fl ++g ll+++kar
  gi|336252318|ref|YP_004595425.1|  92 FAARPVRDLLEAVASRPRLFPLLKDARKPETYAHVVEsDVDAIVQDVATRGQARVALENR-RFLADDGRLLLAVKAR 167
                                       ************************************988****************99996.59************** PP

                                       HHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEE CS
                       Fibrillarin 179 sidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgk 223
                                       s dvt+ep++vf++ +++l+e g+++le+ +le y+ dh+ vv++
  gi|336252318|ref|YP_004595425.1| 168 SEDVTREPAAVFEDVRTELEE-GYEILESERLEAYHADHLGVVAR 211
                                       *****************9975.7*******************986 PP

>> RTP1_C2  Required for nuclear transport of RNA pol II C-terminus 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.86   7.7e+03       5      12 ..      97     104 ..      95     106 .. 0.52
   2 ?    6.2   1.8   0.00095       8.5      18      30 ..     137     149 ..     124     150 .. 0.85
   3 ?   -1.1   0.0      0.17   1.6e+03      18      26 ..     169     177 ..     168     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.86
                           RTP1_C2   5 lyrtLkyV 12 
                                       +  +L+ V
  gi|336252318|ref|YP_004595425.1|  97 VRDLLEAV 104
                                       44455555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00095
                           RTP1_C2  18 DdlVReHArdvLE 30 
                                       D  +R++Ar++LE
  gi|336252318|ref|YP_004595425.1| 137 DVATRGQARVALE 149
                                       6678********9 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.17
                           RTP1_C2  18 DdlVReHAr 26 
                                        d++Re A+
  gi|336252318|ref|YP_004595425.1| 169 EDVTREPAA 177
                                       58****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1643.00
//
Query:       gi|336252319|ref|YP_004595426.1|  [L=188]
Description: hypothetical protein Halxa_0910 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0031   17.3   0.5     0.0055   16.5   0.5    1.4  1  Trp_oprn_chp    Tryptophan-associated transmembrane protein (
  ------ inclusion threshold ------
      0.016   15.4   0.1      0.029   14.5   0.1    1.4  1  PAS_7           PAS fold
       0.57    9.4   3.3        1.7    7.9   1.8    2.0  2  Attachment_P66  Borrelia burgdorferi attachment protein P66


Domain annotation for each model (and alignments):
>> 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 !   16.5   0.5   9.2e-07    0.0055      62     122 ..       4      72 ..       3     103 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.2e-07
                      Trp_oprn_chp  62 vrglgrrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaavelta........wpvla 122
                                       +r +g +vv++l++l+ga++++aa  + t ++   + ++a+ +++++++++ ++t         + ++a
  gi|336252319|ref|YP_004595426.1|   4 ARTIGVTVVAALVLLSGATLGFAATDAGTIQENETENETADNETADNETETETATVtfenqtsnGTAVA 72 
                                       578999*******************99988776666666554444444444442223344443333333 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   4.8e-06     0.029      68     104 ..      51      87 ..      22      89 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.8e-06
                             PAS_7  68 aaaragkphsfererpdgrvievrgnplpdgGfVtty 104
                                       +  ++ +  +fe ++++g+ + v++++lp+gGf +++
  gi|336252319|ref|YP_004595426.1|  51 ETETETATVTFENQTSNGTAVAVNNTTLPEGGFAVIH 87 
                                       2234567789***********************8776 PP

>> Attachment_P66  Borrelia burgdorferi attachment protein P66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.8   0.00028       1.7     143     184 ..      33      74 ..      21      80 .. 0.87
   2 ?    0.8   0.0     0.041   2.4e+02      33      68 ..     100     135 ..      91     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00028
                    Attachment_P66 143 lreksksndiisaltentstkttttnlefeeatklggalyld 184
                                       ++e+ ++n++    t + +t+t+t++++fe+ t  g+a+ ++
  gi|336252319|ref|YP_004595426.1|  33 IQENETENETADNETADNETETETATVTFENQTSNGTAVAVN 74 
                                       5678889999999999999*****************998765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.041
                    Attachment_P66  33 krelnlafsvgtgiglawnkdegekeswaikgsdsy 68 
                                        ++l+ ++  g+ +g +   d+ge+e  +++ ++s 
  gi|336252319|ref|YP_004595426.1| 100 VTNLSAEYEPGAVLGNSTFLDSGEHENVSVELNESL 135
                                       45667789999999*9999*******9999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1246  (0.0694963); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1532.25
//
Query:       gi|336252320|ref|YP_004595427.1|  [L=164]
Description: hypothetical protein Halxa_0912 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.059   13.5   1.0      0.059   13.5   1.0    2.4  2  DUF5422   Family of unknown function (DUF5422)


Domain annotation for each model (and alignments):
>> DUF5422  Family of unknown function (DUF5422)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.025   4.5e+02      94     113 ..      19      38 ..       8      45 .. 0.75
   2 ?   13.5   1.0   3.3e-06     0.059      42      66 ..      96     120 ..      72     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.025
                           DUF5422  94 fslaltivgivscitwapgf 113
                                       f   l + g+v+ + wap +
  gi|336252320|ref|YP_004595427.1|  19 FGALLLVPGLVATVLWAPFL 38 
                                       444566789********965 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.3e-06
                           DUF5422  42 agfllgilklitfpvlcaaglfvfp 66 
                                         f lg+l ++ fpvlca gl  f 
  gi|336252320|ref|YP_004595427.1|  96 LCFQLGVLYVVGFPVLCAVGLPRFG 120
                                       3799****************97775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1331.82
//
Query:       gi|336252321|ref|YP_004595428.1|  [L=362]
Description: carboxylate-amine ligase ybdK [Halopiger xanaduensis SH-6]
Scores for 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-78  262.9   0.3    4.1e-78  262.7   0.3    1.0  1  GCS2           Glutamate-cysteine ligase family 2(GCS2)
  ------ inclusion threshold ------
      0.081   12.6   0.7         12    5.5   0.0    2.6  2  Amidoligase_2  Putative amidoligase enzyme
       0.12   11.7   0.0       0.19   11.0   0.0    1.2  1  GCS            Glutamate-cysteine ligase


Domain annotation for each model (and alignments):
>> GCS2  Glutamate-cysteine ligase family 2(GCS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.7   0.3   6.8e-82   4.1e-78       1     291 []      15     297 ..      15     297 .. 0.97

  Alignments for each domain:
  == domain 1  score: 262.7 bits;  conditional E-value: 6.8e-82
                                       EEEEEEEEEEETTTTEE-S-HHHHHCCCTTT-S.SSEEEE-SSTTEEEEE--SBSSHHHHHHHHHHHHHHHHHHHHH CS
                              GCS2   1 lgvEeeflvvdlatgdlrgwseiledeaiiglseggsvvkelpegqvElstapleslaeaaeeisadleelrsvade 77 
                                       lg+Eee +vvd++++ ++  +++l++e    +  ++++++el++ ++E++t+ +e+ + a +++ + +++l ++a+e
  gi|336252321|ref|YP_004595428.1|  15 LGIEEECFVVDERGRPTS-GTDELVYEHDPPEILADRLDHELFKFVIETQTPLIENPDDARDALLEIRQALVEHAQE 90 
                                       69****************.79******************************************************** PP

                                       TT-EEE--SB-SS---------------THHHHHGG..G.G-S--B-EEEEEEE-SSHHHHH.HHHHHHHTTHHHHH CS
                              GCS2  78 lGlellglGthPfalrsedevtpkaryrrmleymdrvGvlgrqmmvaglhvqvnidssseedVevlrlvrallPvll 154
                                       +G+e++++G+hP a+++e e+++k+ryr++l+++++  + ++++++ag+hv+v++d++ +++V++ + +r+++P++l
  gi|336252321|ref|YP_004595428.1|  91 HGYEIAAAGLHPLAKWRELEHAEKPRYRSQLDRIQY--P-QHRNTTAGVHVHVGVDDA-DKAVWIANELRWYVPIML 163
                                       ************************************..7.*****************5.5556************** PP

                                       HHH--B-EETTEE-S-SB-GGGCCTTSTT-CS----SSHHH.HHHHHHHHTTSTT-SSGG.G--BSEEEETTTT.EE CS
                              GCS2 155 AlsAnSPfleGrdtgyaStRariftqtpqagelplafedgaaferyaryaldvpvidvrrfrlwldirpsslpgttl 231
                                       AlsAnSP+++G dtg++S+Ra+if+ +p+ +++p+ fed aaf r+ r++l+++ i++r+ +lw+d+rp++ +g t+
  gi|336252321|ref|YP_004595428.1| 164 ALSANSPYWNGFDTGLQSARAKIFEGLPN-TGMPTYFEDFAAFDRFERRMLETGSINDRG-ELWYDVRPHTAHG-TV 237
                                       *****************************.******************************.9************.** PP

                                       EEEEEE--...SSHHHHHHHHHHHHHHHHHHHHH------GGGGTT.HHHHHHHHHHHGG CS
                              GCS2 232 elrihdttlfPevrlrallearlldaqpadrldalpaavlvallddeaeenawdavrsgl 291
                                       elr  d++++P v+ + +++a++l ++ a+++ +  a       + +++e +w+a+r+g+
  gi|336252321|ref|YP_004595428.1| 238 ELRTPDGQANPDVVMAFVEYAHALVEALAEEYEDGAAGYGHDHRRELLDEHKWRAIRYGH 297
                                       ******************************9999888777777777************85 PP

>> Amidoligase_2  Putative amidoligase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1    0.0029        18     107     128 ..     128     148 ..     102     167 .. 0.73
   2 ?    5.5   0.0     0.002        12     224     252 ..     233     261 ..     203     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0029
                     Amidoligase_2 107 vgtnascglhvHldaevpdlea 128
                                       ++ n ++g+hvH++ ++ d  a
  gi|336252321|ref|YP_004595428.1| 128 QHRNTTAGVHVHVGVDDADK-A 148
                                       565777*******9888773.2 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.002
                     Amidoligase_2 224 erpTvEfRlpngtldaeeikawirlclal 252
                                       +++TvE R p+g+ + + ++a ++ + al
  gi|336252321|ref|YP_004595428.1| 233 AHGTVELRTPDGQANPDVVMAFVEYAHAL 261
                                       467**************999999998887 PP

>> GCS  Glutamate-cysteine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.2e-05      0.19      21      54 ..     142     175 ..     133     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.2e-05
                               GCS  21 aknieearllYdqlaplaPillalsaaspiykGl 54 
                                       + + ++a ++ ++l    Pi+lalsa sp ++G+
  gi|336252321|ref|YP_004595428.1| 142 VDDADKAVWIANELRWYVPIMLALSANSPYWNGF 175
                                       5678889999999******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); 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:                         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: 00:00:00.43
# Mc/sec: 2528.30
//
Query:       gi|336252322|ref|YP_004595429.1|  [L=430]
Description: hypothetical protein Halxa_0914 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.16   11.9   0.1        0.6   10.1   0.0    1.9  2  p6             Histone-like Protein p6
        2.1    8.6   4.6         11    6.3   1.2    2.7  2  DNA_ligase_IV  DNA ligase IV


Domain annotation for each model (and alignments):
>> p6  Histone-like Protein p6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   6.7e-05       0.6      38      63 ..     160     185 ..     151     192 .. 0.88
   2 ?   -2.8   0.1       0.7   6.3e+03      40      49 ..     309     318 ..     306     322 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.7e-05
                                p6  38 gnltmeqaqwrmkrkykgepvqvvsv 63 
                                       gn  ++qa  r+kr+y  ep + v v
  gi|336252322|ref|YP_004595429.1| 160 GNYGLDQALMRLKRQYPEEPTDYVFV 185
                                       899*****************987765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.7
                                p6  40 ltmeqaqwrm 49 
                                       l meqa+ r 
  gi|336252322|ref|YP_004595429.1| 309 LRMEQARVRY 318
                                       789**99886 PP

>> DNA_ligase_IV  DNA ligase IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.02   1.8e+02      12      16 ..     126     130 ..     125     137 .. 0.91
   2 ?    6.3   1.2    0.0012        11       2      16 ..     241     255 ..     240     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.02
                     DNA_ligase_IV  12 YGDSY 16 
                                       YGDSY
  gi|336252322|ref|YP_004595429.1| 126 YGDSY 130
                                       ***** PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0012
                     DNA_ligase_IV   2 kehFakEYDeYGDSY 16 
                                       k+ F++EYD ++D  
  gi|336252322|ref|YP_004595429.1| 241 KADFLREYDFHYDHW 255
                                       678**********65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3127.18
//
Query:       gi|336252323|ref|YP_004595430.1|  [L=546]
Description: amine oxidase [Halopiger xanaduensis SH-6]
Scores for 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-23   82.7   1.6    5.7e-23   81.9   1.6    1.4  1  Amino_oxidase   Flavin containing amine oxidoreductase
    1.5e-14   53.9   0.8    3.2e-14   52.9   0.3    1.9  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      3e-10   39.8   3.8    6.3e-08   32.1   2.2    2.2  2  FAD_binding_2   FAD binding domain
    5.3e-10   39.4   6.9    5.3e-10   39.4   6.9    2.8  2  DAO             FAD dependent oxidoreductase
    3.7e-09   36.2   0.3    1.4e-06   27.7   0.3    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    9.3e-07   27.9   0.4    1.8e-05   23.6   0.7    2.1  2  HI0933_like     HI0933-like protein
    1.6e-06   27.6   0.8    2.8e-06   26.8   0.8    1.4  1  FAD_binding_3   FAD binding domain
    2.1e-06   27.3   0.4    3.5e-06   26.6   0.4    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    2.7e-06   27.8   0.2    3.9e-05   24.1   0.8    2.5  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    3.4e-06   26.2   0.0       0.22   10.2   0.0    3.2  3  MCRA            MCRA family
      3e-05   23.4   0.6    4.6e-05   22.8   0.6    1.2  1  Thi4            Thi4 family
     0.0025   16.9   0.6     0.0046   16.1   0.6    1.4  1  Lycopene_cycl   Lycopene cyclase protein
     0.0056   15.8   2.1     0.0066   15.6   1.2    1.5  2  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.018   15.2   0.9       0.38   11.0   0.0    3.1  3  TetR_C_16       Tetracyclin repressor-like, C-terminal domain
      0.022   14.1   1.2      0.033   13.5   1.2    1.2  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.029   13.6   0.5      0.047   12.9   0.5    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.038   12.8   0.5      0.061   12.2   0.5    1.3  1  Trp_halogenase  Tryptophan halogenase
       0.13   12.2   2.6       0.44   10.5   0.7    2.5  3  NAD_binding_9   FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   1.6   5.7e-26   5.7e-23       1     451 [.      11     490 ..      11     491 .. 0.74

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 5.7e-26
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET.TTHHHHHHHHHTTCCCCEEEESCC..G CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg.agnpllellkelgledslslpdpg..a 74 
                                       + GL+aA++L+++G+dVtvlEa+dr+GG++r++     li+ G++ ++g +g  ++  + ++ +++  ++pd +  +
  gi|336252323|ref|YP_004595430.1|  11 IGGLTAAHELAARGVDVTVLEANDRFGGKARSI-----LIDDGPTPLHGeHGFRFFPAFYRHVVDTMARIPDGTgtV 82 
                                       68****************************996.....899999999999999999999999999999999999544 PP

                                       CEEEEETTEECCTTEECHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH...............HHHCCCCHHHH CS
                     Amino_oxidase  75 pkrvlskggrefpgdlspvpaewealleqgalsaellsleeklrlgleall...............qktldeldlds 136
                                       +++++++      ++l    ++ ++ +++g+ + +l+ + e lr +++  l                 + +e+++++
  gi|336252323|ref|YP_004595430.1|  83 ADNLVET-----EATLIASAEGADRIADTGRPD-SLRGWLEALRPAFADDLppsdvrfllerllyfLTACEERRENE 153
                                       4444443.....333333344455555544444.4445555555555555566666666666668888888999999 PP

                                       HHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTT...TTCBHHHHTCCCCH.HHHHTSCCCEE.... CS
                     Amino_oxidase 137 kslaesleelgrrepgdvevwdrliepelfaklefasglfagdp...selsaklalpllwe.legfggslllp.... 205
                                       +++  ++e+  + ++++ e  drl +          ++l+a  p   s+ + ++ + +l++   + ++++ ++    
  gi|336252323|ref|YP_004595430.1| 154 FDDVSWWEFIDAENRSP-EFRDRLAY--------ATQALVALRPqvgSARTIGAIYLQLLFgQLDPSRPTERIlnap 221
                                       99999999999999999.********........8*********655444444444443330333444444443333 PP

                                       ..TTHTHHHHHHHHHTTTTEEEETSEEEEEEEEETTC...EEEEETTSTEEEESEEEE-S-HHHHHSSEEES.CCSH CS
                     Amino_oxidase 206 ..rgGlsqlpealaeelrgldirlntrVkeikregdg...vtvtledgevveaDaVvvTvplgvlkailfsP.plpd 276
                                         +  ++  +++l++   g+d r n++V+e++ ++ g    +  l dge+v+a  +v++vp+  +   +f+  +l +
  gi|336252323|ref|YP_004595430.1| 222 tsEAWIDPWVRHLES--VGVDCRSNAPVRELAVDRRGrriAGAVLADGETVTAAEYVLAVPVEIAT--EFVTpELAR 294
                                       322226666666666..****************7777667888999********************..555548855 PP

                                       ..HHHHHHHHSEEEEEEEEEEEESSGGSGCSTSECE..CECCCEEETTTEEEEECC......ECCCSTTTEEE..EE CS
                     Amino_oxidase 277 ..ekaeairnlgfgsvnkvilefdrkfwednalgqg..vlvseltttlgeafissd......fpsrappgkgl..vl 341
                                         +k   i++l+++  n + +   + + + +++  +   + +  +t+   + ++ +       +++++ +  +  vl
  gi|336252323|ref|YP_004595430.1| 295 aaPKLGRIERLDTAWMNGIQFYLSENVALTRGH--QvyADAPWALTSISQRQFWREseydlaARGSEDVD--VegVL 367
                                       589************************777776..13467888888888888888877664433444444..35444 PP

                                       EEEEC.HHHHHHHTTS.....-HHHHHHHHHHHHHHHHTGTSSTCSE..EEEEECCTETTT.SSSEEE.BTTH.... CS
                     Amino_oxidase 342 lvyvg.gdaanelesl.....sdeelvqavlrdLrklfgeevpepka..tlvtrWhtdpla.rgsysyvsvgp.... 405
                                       +v  +  d    ++++     ++ee++ +++ +L+  ++   pe++     v++W  dp   +++  + +  p    
  gi|336252323|ref|YP_004595430.1| 368 SVIASdWDTPGTVHGKparecTREEVATEIWAQLKAHLN--GPEERLrdEMVVDWFLDPALeETADGLENRSPllin 442
                                       444442222223333345666**************9999..3333333467999*****99777777777777**** PP

                                       ..HHHHHHHHHCHHCSTTEEE.SGGGCTTTTTS.HHHHHHHHHHHHHHH CS
                     Amino_oxidase 406 ..ghedydplakpegdprlffAGehtsreypgt.vegAilSGlraAari 451
                                         g+++ +p+a p  + +l +A +++ ++   + +e A ++G+raAa+ 
  gi|336252323|ref|YP_004595430.1| 443 tvGSLRNRPSADP-AVANLTLASDYVRTNSDLAsMESADEAGRRAAAAA 490
                                       *************.****************9999************986 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 !   52.9   0.3   3.3e-17   3.2e-14       1      66 [.       6      73 ..       6      75 .. 0.89
   2 ?   -3.0   0.0       8.8   8.8e+03      10      19 ..     486     495 ..     460     507 .. 0.63

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 3.3e-17
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE.TT...CEECTS---EEETTHHHHCHHHHC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev.pg...vrvdygahifhgsgyypnvrrllr 66
                                      I+G+G++Gl+aA++La +g+dv++le++dr+GG+a+s+ + +g      ++g + f  +  y++v + ++
  gi|336252323|ref|YP_004595430.1|  6 IIGGGIGGLTAAHELAARGVDVTVLEANDRFGGKARSILIdDGptpLHGEHGFRFFPAF--YRHVVDTMA 73
                                      9*************************************884458888889******996..888877665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.8
                                       HHHHHHHCCT CS
                     NAD_binding_8  10 vaAylLakag 19 
                                       +aA++L + g
  gi|336252323|ref|YP_004595430.1| 486 AAAAALERLG 495
                                       4555555543 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   2.2   6.4e-11   6.3e-08       1      38 [.       3      40 ..       3      42 .. 0.96
   2 !    7.1   0.0    0.0024       2.4     135     188 ..     218     270 ..     172     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 6.4e-11
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38
                                      Dv++iG+G++GL+AA+e+a +G +v+v+e  ++fgg +
  gi|336252323|ref|YP_004595430.1|  3 DVVIIGGGIGGLTAAHELAARGVDVTVLEANDRFGGKA 40
                                      9*********************************9965 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0024
                                       ....HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT..EEEEEEEEETTTTCEE CS
                     FAD_binding_2 135 etlvtghallarlvesarkagvdfqerteadeLivedg..rvtGavvenpesgrev 188
                                        +  t  a + + v+++++ gvd + +++++eL v+ +  r+ Gav++   +g++v
  gi|336252323|ref|YP_004595430.1| 218 LNAPTSEAWIDPWVRHLESVGVDCRSNAPVRELAVDRRgrRIAGAVLA---DGETV 270
                                       4456889999999**********************75567*******9...44443 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   6.9   5.3e-13   5.3e-10       1     199 [.       3     278 ..       3     301 .. 0.65
   2 ?   -1.6   1.9       1.5   1.5e+03     135     135 ..     433     433 ..     318     544 .. 0.46

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 5.3e-13
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeel 75 
                                       dvviiGGGi Gl++A+eLa+rg  Vt+le++d++g    g++  +l     ++ ++    +   ++++++ ++ ++ 
  gi|336252323|ref|YP_004595430.1|   3 DVVIIGGGIGGLTAAHELAARGvdVTVLEANDRFG----GKARSILIDDGPTPLHG----E---HGFRFFPAFYRH- 67 
                                       9**********************************....77777775533212222....2...222222222221. PP

                                       SST.TSEEEEEEEEEESS........................................................... CS
                               DAO  76 gid.idyrrtGllslaad........................................................... 92 
                                        +d +   + G+  +a++                                                           
  gi|336252323|ref|YP_004595430.1|  68 VVDtMARIPDGTGTVADNlveteatliasaegadriadtgrpdslrgwlealrpafaddlppsdvrfllerllyflt 144
                                       22212233345555543344444445555556677777777777777777777777777777777777777777777 PP

                                       ......HHHHHHHHHHHHHH....HHTTTTEEEEEH.HHHHHHSTT..STTTSEEEE.ETTEEEEEHHHHHHH.... CS
                               DAO  93 ......eeelealdkllall....leagldaellda.eevrelepa..lpgllgalf.ypdtgqvdpakltaa.... 151
                                             e+e++++  +++      ++   + +l  a + + +l p+  ++++ ga++     gq+dp + t      
  gi|336252323|ref|YP_004595430.1| 145 aceerrENEFDDV-SWWEFIdaenRSPEFRDRLAYAtQALVALRPQvgSARTIGAIYlQLLFGQLDPSRPTERilna 220
                                       7777766777777.777776654433344446543435577999986555999**9946667***********6666 PP

                                       .........HHHHHHHTT-EEEESECEEEE..EEEETCEEEEEEECTEEE.EEEEEEEE- CS
                               DAO 152 .........laraaealGveilegtevtgl..eeedgkvwgverttpgen.daadavVna 199
                                                  r +e+ Gv+++ +++v++l  ++++ +++g  + ++ge+ +a    V+a
  gi|336252323|ref|YP_004595430.1| 221 ptseawidpWVRHLESVGVDCRSNAPVRELavDRRGRRIAGA-VLADGETvTA-AEYVLA 278
                                       77777777767777777************9333333555555.4455666233.335655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                                       E CS
                               DAO 135 l 135
                                       l
  gi|336252323|ref|YP_004595430.1| 433 L 433
                                       1 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 !   27.7   0.3   1.4e-09   1.4e-06       2      34 ..       3      35 ..       2      52 .. 0.88
   2 !    6.2   0.0    0.0052       5.2     176     245 ..     216     289 ..     213     308 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.4e-09
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegt 34
                                      dvv+iGgG++Gl+aa++la+ g++vt++e+++ 
  gi|336252323|ref|YP_004595430.1|  3 DVVIIGGGIGGLTAAHELAARGVDVTVLEANDR 35
                                      9***************************75544 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0052
                                       SSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE..EEE.EEETTSCEEEESEEEE-S-EEES-HHCS CS
                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 176 rll.raldkelsaaleealekeGvevklgtsvkeidgnge..kle.vvledgeeidadlvvvavGvrpstelle 245
                                       r+l  ++ +++ +   ++le  Gv+++ ++ v e+  + +  ++   vl dge++ a   v+av v++ te+++
  gi|336252323|ref|YP_004595430.1| 216 RILnAPTSEAWIDPWVRHLESVGVDCRSNAPVRELAVDRRgrRIAgAVLADGETVTAAEYVLAVPVEIATEFVT 289
                                       555555667777777899***************8888887667779******************9999999875 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.7   1.8e-08   1.8e-05       2      39 ..       3      40 ..       2      43 .. 0.95
   2 ?    1.7   0.0     0.082        82     108     161 ..     223     278 ..     215     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.8e-08
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKi 39
                                      dv++iGgG  Gl aA ++a+rg +V++le+++++g K 
  gi|336252323|ref|YP_004595430.1|  3 DVVIIGGGIGGLTAAHELAARGVDVTVLEANDRFGGKA 40
                                      8**********************************995 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.082
                                       CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE...TTEEEEESEEEE- CS
                       HI0933_like 108 aedivdallkelkeagvklrletevksvekeedgkfrvkt..kseeeleadklvlA 161
                                       +e  +d ++++l++ gv++r +  v++++ ++ g+    +   ++e+++a++ vlA
  gi|336252323|ref|YP_004595430.1| 223 SEAWIDPWVRHLESVGVDCRSNAPVRELAVDRRGRRIAGAvlADGETVTAAEYVLA 278
                                       6777999********************98887764333222579999999999999 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.8   2.8e-09   2.8e-06       2      42 ..       2      42 ..       1      48 [. 0.88

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.8e-09
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS- CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpra 42
                                      tdV+I+G+G  Gl++a++L+ +Gv+v+++e  ++   + r+
  gi|336252323|ref|YP_004595430.1|  2 TDVVIIGGGIGGLTAAHELAARGVDVTVLEANDRFGGKARS 42
                                      89****************************99887666666 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.4   3.5e-09   3.5e-06       1      42 [.       3      44 ..       3      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.5e-09
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsgl 42
                                      Dvv++GGg++G++AA   a +G  v ++e +++ GG + s l
  gi|336252323|ref|YP_004595430.1|  3 DVVIIGGGIGGLTAAHELAARGVDVTVLEANDRFGGKARSIL 44
                                      9***********************************987766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.8   3.9e-08   3.9e-05       2      35 ..       4      37 ..       3      46 .. 0.92
   2 ?   -2.7   0.0       9.1   9.1e+03      47      71 ..     231     255 ..     224     259 .. 0.83
   3 ?   -1.2   0.0       3.2   3.2e+03      53      69 ..     311     327 ..     305     330 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.9e-08
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      vv++GgG  gl +A +la+ g +Vtv+e++d++ 
  gi|336252323|ref|YP_004595430.1|  4 VVIIGGGIGGLTAAHELAARGVDVTVLEANDRFG 37
                                      8*******************************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.1
                                       HHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox  47 qeklekngievllntkveeiegsed 71 
                                        ++le  g++ + n+ v e+  + +
  gi|336252323|ref|YP_004595430.1| 231 VRHLESVGVDCRSNAPVRELAVDRR 255
                                       67899999*9999999999887765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.2
                                       TTEEEECSEEEEEEEEE CS
                         Pyr_redox  53 ngievllntkveeiegs 69 
                                       ngi+++l+++v+  +g+
  gi|336252323|ref|YP_004595430.1| 311 NGIQFYLSENVALTRGH 327
                                       8********99876665 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0017       1.7       3      47 ..       3      43 ..       1      92 [. 0.82
   2 !    4.9   0.0    0.0091       9.1     206     237 ..     224     255 ..     217     278 .. 0.82
   3 !   10.2   0.0   0.00022      0.22     384     430 ..     366     412 ..     316     486 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0017
                                      EEEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS---------- CS
                              MCRA  3 kaylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldga 47
                                      ++ ++G+Gi++L+aA  L      +g ++++le+++  gg+  ++
  gi|336252323|ref|YP_004595430.1|  3 DVVIIGGGIGGLTAAHEL----AARGVDVTVLEANDRFGGKARSI 43
                                      678************755....67899*********999987765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0091
                                       HHCCHHHHHHHHHTT-EEE-SEEEEEEEEEEE CS
                              MCRA 206 eslilPlvkyLkeqgVdfqfntkVtdiefeee 237
                                       e+ i P v++L++ gVd + n+ V+++ ++++
  gi|336252323|ref|YP_004595430.1| 224 EAWIDPWVRHLESVGVDCRSNAPVRELAVDRR 255
                                       77899***********************9954 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00022
                                       EEEEEES-SSSB-SSS-SBGGG--HHHHHHHHHHHHT--HHHHHHHC CS
                              MCRA 384 vlwgYglfpekeGdyvkKpmlectGeEileEllyhLgvpeekieell 430
                                       vl + +   +++G    Kp +ect eE+ +E+  +L+ + +  ee l
  gi|336252323|ref|YP_004595430.1| 366 VLSVIASDWDTPGTVHGKPARECTREEVATEIWAQLKAHLNGPEERL 412
                                       6777888899*************************998765555544 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.6   4.6e-08   4.6e-05      18      56 ..       2      39 ..       1      42 [. 0.94

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.6e-08
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                      +Dvvi+G+G  GLtaa+ la + ++ v++le++  +GG 
  gi|336252323|ref|YP_004595430.1|  2 TDVVIIGGGIGGLTAAHELAAR-GVDVTVLEANDRFGGK 39
                                      7*********************.**********999995 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.6   4.6e-06    0.0046       1      35 [.       3      35 ..       3      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasps 35
                                      Dvv+iG+G  gl  A++l  a+ g+ v+++ea + 
  gi|336252323|ref|YP_004595430.1|  3 DVVIIGGGIGGLTAAHEL--AARGVDVTVLEANDR 35
                                      9*****************..99********99875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.2   6.7e-06    0.0066       1      31 [.       3      32 ..       3      43 .. 0.87
   2 ?   -3.1   0.0       3.1     3e+03     123     147 ..     252     278 ..     245     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.7e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                                      dv++iGgG  G+ AA ++a +G++v+ + + 
  gi|336252323|ref|YP_004595430.1|  3 DVVIIGGGIGGLTAAHELAARGVDVTVL-EA 32
                                      79***********************988.33 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.1
                                       ECT..TEEEEEEETTS-EEEECEEEE- CS
                              GIDA 123 vee..kkvkgvvtedgetikakavvia 147
                                       v+   ++++g v++dget++a   v+a
  gi|336252323|ref|YP_004595430.1| 252 VDRrgRRIAGAVLADGETVTAAEYVLA 278
                                       433458999************999998 PP

>> TetR_C_16  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.63   6.3e+02       1      32 [.     253     285 ..     253     298 .. 0.73
   2 ?   11.0   0.0   0.00038      0.38      32      70 ..     381     419 ..     377     422 .. 0.89
   3 ?   -1.5   0.1         3     3e+03      58      72 ..     479     493 ..     460     505 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.63
                                       TTHHHHHHHHHHHHHH.HHT-HHHHHHHHH--- CS
                         TetR_C_16   1 eelGerlvravlevwe.pearepllallrsals 32 
                                       ++ G+r++ avl++ e   a+e  la+ + +++
  gi|336252323|ref|YP_004595430.1| 253 DRRGRRIAGAVLADGEtVTAAEYVLAVPVEIAT 285
                                       789***********9966666666666666654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00038
                                       ------HHHHHHHHHHHHHHCTTTS-STTHHHHHHHHHH CS
                         TetR_C_16  32 sseeaaellrefleeqvlaplaarlggpdaelRaalvas 70 
                                       + + a+e +re +++++ a+l+a+l gp+ +lR ++v+ 
  gi|336252323|ref|YP_004595430.1| 381 HGKPARECTREEVATEIWAQLKAHLNGPEERLRDEMVVD 419
                                       567799***************************999975 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3
                                       STTHHHHHHHHHHHH CS
                         TetR_C_16  58 gpdaelRaalvasql 72 
                                       +++a +Raa +a   
  gi|336252323|ref|YP_004595430.1| 479 ADEAGRRAAAAALER 493
                                       455555555555443 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 ?   13.5   1.2   3.3e-05     0.033      30      61 ..       3      34 ..       1      44 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                       v++iGgG+ Gl A++  ++ g +Vtvl+ + 
  gi|336252323|ref|YP_004595430.1|  3 DVVIIGGGIGGLTAAHELAARGVDVTVLEAND 34
                                      69**************************9986 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 ?   12.9   0.5   4.7e-05     0.047       1      30 [.       5      33 ..       2      41 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      +IiG+G  Gl+aa+el   g+ d+++lE +
  gi|336252323|ref|YP_004595430.1|  5 VIIGGGIGGLTAAHELAARGV-DVTVLEAN 33
                                      688888888888888888888.68888865 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   6.1e-05     0.061       1      34 [.       3      33 ..       3      37 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.1e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                      ++vi+GGG+ G +aA  la  +   ++vt++e++
  gi|336252323|ref|YP_004595430.1|  3 DVVIIGGGIGGLTAAHELAARG---VDVTVLEAN 33
                                      69*****************999...9*****987 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 ?   10.5   0.7   0.00044      0.44       1      39 [.       5      38 ..       5      43 .. 0.84
   2 ?   -3.2   0.0       7.3   7.3e+03      62      77 ..     105     120 ..      85     137 .. 0.73
   3 ?   -0.1   0.0      0.79   7.9e+02     122     153 ..     245     279 ..     224     280 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00044
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gag 39
                                      +i+G+G+ Gl+++ +L+ar      +++t+ + +   g g
  gi|336252323|ref|YP_004595430.1|  5 VIIGGGIGGLTAAHELAAR-----GVDVTVLEANDRfG-G 38
                                      7******************.....59*****9965525.4 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.3
                     NAD_binding_9  62 ftddpptfaeWlrerg 77 
                                        t +p++++ Wl++ +
  gi|336252323|ref|YP_004595430.1| 105 DTGRPDSLRGWLEALR 120
                                       5667799999998866 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.79
                     NAD_binding_9 122 aevvdleeradgq...avlladgaslaadaVvLAl 153
                                       a v +l+ +++g+     +ladg++++a + vLA+
  gi|336252323|ref|YP_004595430.1| 245 APVRELAVDRRGRriaGAVLADGETVTAAEYVLAV 279
                                       45555555444431235779*******99999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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: 0.67u 0.22s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 3860.64
//
Query:       gi|336252324|ref|YP_004595431.1|  [L=140]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-35  121.0   0.8      6e-35  120.8   0.8    1.0  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 !  120.8   0.8   3.3e-39     6e-35       4     141 .]       3     140 .]       1     140 [] 0.96

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 3.3e-39
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHHHCT CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaaeag 78 
                                       r+lV++D+s+ +++Ale+A++l   +++e ++l+v d++a +  ++a+++a++e+le+ + e+  +   a+++a+++
  gi|336252324|ref|YP_004595431.1|   3 RVLVPFDDSDPAREALEYAFDLF--PNGEFVALTVADTSAVPFIPNAADDAPDEQLEDLLGEATDQLaaAEDLAAER 77 
                                       9********************85..6689****************************999999888899******** PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       gv+ e++ + g+pa+ei+e+a+ +d+d +V+Gsrgrsg+ r+llGSv+e v+rh+++pV+vVr
  gi|336252324|ref|YP_004595431.1|  78 GVSIETHARIGSPAQEIVEFADTNDVDHVVMGSRGRSGVTRILLGSVAEVVVRHSSVPVTVVR 140
                                       **************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1061.22
//
Query:       gi|336252325|ref|YP_004595432.1|  [L=259]
Description: hypothetical protein Halxa_0917 [Halopiger xanaduensis SH-6]
Scores for 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-29  101.8  43.2    5.4e-29  101.5  43.2    1.1  1  TauE      Sulfite exporter TauE/SafE


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 !  101.5  43.2     3e-33   5.4e-29       2     235 ..      15     256 ..      11     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 3e-33
                              TauE   2 llagllaGfvagllGiGggliavPlLll.llppavavatsllavvatslsgalahrrrgnvd....wrlllllllgs 73 
                                       + ++++ G+    +G Gg ++++ l  l +l+  ++++t++++ v+t l+g++a++++g ++      l+++l+ +s
  gi|336252325|ref|YP_004595432.1|  15 ASIAFFSGIGITTIGPGGIFVTIALYSLtGLASGEVAGTAHATFVFTGLVGSAAYLHSGEMRtgdgRALAVVLSGSS 91 
                                       55778888888899988888888877775589999********************997754333334567778888* PP

                              TauE  74 liGallGallllllpsellkllfgvlllllallmllrkkr......srakgrerrptaillvligglvGllsGllGi 144
                                       ++Gal+Ga++ + +p +++ ll+g + + ++  +l+r++r          +  +r++ + l+ +g+++G+ sGllGi
  gi|336252325|ref|YP_004595432.1|  92 VVGALVGAYVNAFVPRSVFGLLLGGVAATVGGVILYRERRgfspvyDL--EPLQRRGQLTLAGLGFALGVCSGLLGI 166
                                       **********************************99888766654322..45667777777788888********** PP

                              TauE 145 GgGfllvpllllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlsertl 221
                                       Gg +l vp+l+l  g+p+  ava++ + +++i++++++gy+l+g+v++pl+++++ + llG+++G ++a+++++++l
  gi|336252325|ref|YP_004595432.1| 167 GGPVLAVPALVL-VGIPMLLAVAVAQVQSIFIAAFATTGYVLQGSVNVPLAVVVGTPLLLGVVVGWKVAHVVDPEKL 242
                                       **********96.7*************************************************************** PP

                              TauE 222 rrlfallllvlgvk 235
                                       +  ++++ll++g +
  gi|336252325|ref|YP_004595432.1| 243 KVSLGVVLLAVGPY 256
                                       ***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1853.48
//
Query:       gi|336252326|ref|YP_004595433.1|  [L=377]
Description: hypothetical protein Halxa_0918 [Halopiger xanaduensis SH-6]
Scores for 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-35  121.1  28.6    6.4e-35  120.8  28.6    1.0  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.8  28.6   3.6e-39   6.4e-35       9     320 ..      23     329 ..      16     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 3.6e-39
                   AI-2E_transport   9 llllalypfiselllplliAlvlayllnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvplliaqltqlvks 85 
                                       + +l++++++ ++l  +l+++vlay+l pv ++L +r v+ ++a+ +v++  l+++ l++++++++++ q+ ++ +s
  gi|336252326|ref|YP_004595433.1|  23 VSALLALFVLVPYLQFVLFGVVLAYILFPVQRRL-ERYVRPTIAAGAVVVGTLLAVLLPLVYVLTIAVRQSLDVARS 98 
                                       34444455555699999*****************.666666666666666667777777777777999999999999 PP

                   AI-2E_transport  86 lpayidslqnilnelpslleele.n.liqalkqslskilsnilssilnsllsllasllglilslvlvllllffllld 160
                                       l +        + e++ lle +     ++al  + ++ ++  ++++++s+ +++++l+gl++ l ++l++lf ll+d
  gi|336252326|ref|YP_004595433.1|  99 LRRG----DLNVAEIEALLEANGvAvDLAALYEANQDRIATAVQEVTMSVMGFVGNLPGLFIGLTVTLFILFALLRD 171
                                       9933....33333333333333322346788888899999999********************************** PP

                   AI-2E_transport 161 geklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvglanliPyi 237
                                       ge+l+  +  +lp +  e ++ +   l++ +++ + g+v va++++v++++gl+++gvp   +l++ ++++ l+P++
  gi|336252326|ref|YP_004595433.1| 172 GERLVAWVQWVLPVD-DEVLADLRGGLDELMWASVVGNVAVAAVQAVMLGVGLAVAGVPAVVFLTVATFVLTLLPLV 247
                                       *****9887777776.9999999999*************************************************** PP

                   AI-2E_transport 238 GavivlipiaiialltggikevlivlivvllvqliegnilePklmgkrlglhplvillsllaggklfGlvGlilavp 314
                                       Ga+ v++p+a +++ +g   ++  +++v+ l++++ + +l+P l+g++   + +++++ +++g+  fG vGl+++++
  gi|336252326|ref|YP_004595433.1| 248 GAFGVWLPVAGYLVAVGR-PTAGAAVVVYGLLVTFSDTYLRPALIGQTEAFNAATVVVGIFGGLVAFGAVGLFIGPV 323
                                       ******************.666666667777778888**************************************** PP

                   AI-2E_transport 315 ltavik 320
                                       +++  k
  gi|336252326|ref|YP_004595433.1| 324 VLGGSK 329
                                       987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); 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:                         8  (0.000446204); expected 0.2 (1e-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 0.23s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 2906.20
//
Query:       gi|336252327|ref|YP_004595434.1|  [L=412]
Description: NRAMP family Mn2+ and Fe2+ transporter-like protein [Halopiger xanaduensis SH-6]
Scores for 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-34  118.7  25.9    2.7e-34  118.7  25.9    1.5  1  Nramp     Natural resistance-associated macrophage protein


Domain annotation for each model (and alignments):
>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.7  25.9   1.5e-38   2.7e-34       5     341 ..      42     368 ..      40     375 .. 0.89

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 1.5e-38
                             Nramp   5 lqaGaqfGykLlwvlllstllaillqelsarLGlvTgkglaelirerlpkkvsillwilaelaiiatdlaeviGaAi 81 
                                       ++aG  fG+ Llwvl l+  +++++ e+sarL+   ++ l + i + ++ ++++ +++ +  ++ + ++a+ + a++
  gi|336252327|ref|YP_004595434.1|  42 TEAGMVFGFGLLWVLPLALGVGLAMHEMSARLAA-KNEPLMDYIADVIGDRAARPFAMGISFIMQFWSVANYALAGA 117
                                       589*****************************96.6899************************************** PP

                             Nramp  82 alnllfgipllvgvlitavlvllllflekggyrklEaliialvlvialsFiaelflvkpdwgevlkglvvPslpg.k 157
                                       al +l+ ++ l++++i+a+   + l+ e + y+++E +i+alvl+i  s+++ ++ ++p++g+v++g+v P + +  
  gi|336252327|ref|YP_004595434.1| 118 ALVYLTPLSNLYVGIIIAAGLGIALV-ELRVYSRVEGVIAALVLAIFGSYLVIVANLEPPMGAVASGFV-PGIVNeF 192
                                       ******88877777777777777777.7999************************************99.***9999 PP

                             Nramp 158 eslllavgilGatvmphnlflhsslvqerkitidrsekeealkyeriDtiialivaflinlailivaAavlysggkd 234
                                       e++++++++lG+tv   n+f+++s+ qe+ +++        ++++r D +++l+++ l +++++++aA ++ +g   
  gi|336252327|ref|YP_004595434.1| 193 EYITMIIALLGTTVYYPNFFIQTSMNQEKDWDV--------VSRYRRDHTVGLAAVVLLSATVIVAAAIAVPDGDL- 260
                                       ******************************776........889*******************9999999996665. PP

                             Nramp 235 vesledaaeaLepllGskaasvlFaigLlaaGlsStitgtlagqyvmegflglrislwlrrlitralafvpalivil 311
                                         +l+  ae L+ ++G ++   +F++++ aa++sS++    a+ +++ + +g+  +    + + r + f +al v+l
  gi|336252327|ref|YP_004595434.1| 261 --TLTAPAEPLTDMIG-PWVLGVFMLAVGAASFSSATGTLFAAGFMVPQSYGITTRFGDMH-FRRTVHFLIALSVAL 333
                                       ..9*************.7******************************9999998764433.556666666666666 PP

                             Nramp 312 ligaele....lvkllvlsqvllsl.llPfalipl 341
                                       +i         +v+l +++ +++++ +lP++++ l
  gi|336252327|ref|YP_004595434.1| 334 AIPILAYtgftPVSLALMMPAVNGVvGLPITALAL 368
                                       65555545566999999999888752699998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.37
# Mc/sec: 3363.59
//
Query:       gi|336252328|ref|YP_004595435.1|  [L=646]
Description: DNA gyrase subunit B [Halopiger xanaduensis SH-6]
Scores for 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-62  208.6   1.5    8.8e-62  207.6   1.5    1.5  1  DNA_gyraseB    DNA gyrase B
    2.9e-29  101.0   0.0    5.9e-29  100.0   0.0    1.5  1  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
    8.8e-24   84.2   0.1    2.8e-23   82.6   0.0    1.9  2  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    4.6e-18   65.3   0.0    1.3e-17   63.9   0.0    1.8  1  Toprim         Toprim domain
     0.0017   18.2   0.0     0.0035   17.2   0.0    1.5  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


Domain annotation for each model (and alignments):
>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.6   1.5   2.5e-65   8.8e-62       1     173 [.     233     402 ..     233     403 .. 0.99

  Alignments for each domain:
  == domain 1  score: 207.6 bits;  conditional E-value: 2.5e-65
                       DNA_gyraseB   1 GlkdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktln 77 
                                       G+++fve+ln+ +++++++v+++e+e+  ++ i+veva+q t++ + +i+ F+Nni+t+eGGtH++gfk+alt+t+n
  gi|336252328|ref|YP_004595435.1| 233 GIREFVEYLNETRSAMHDDVIYFEDEE--QN-IQVEVAMQATEELQGSIHAFANNINTREGGTHLTGFKTALTRTVN 306
                                       9**************************..99.***********9999****************************** PP

                       DNA_gyraseB  78 eyakkkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakki 154
                                       +ya+++++l + +++++gediregltav+svk+p+pqFeGQTK+kLgnsev++ive+++ e l  ++een+++a++i
  gi|336252328|ref|YP_004595435.1| 307 DYANENSMLSDLDNNLKGEDIREGLTAVISVKHPDPQFEGQTKTKLGNSEVRGIVESAMHEGLGTYFEENPDTAEAI 383
                                       ***************************************************************************** PP

                       DNA_gyraseB 155 lekaveaakareaarkare 173
                                       ++kaveaakar+aa+ka+e
  gi|336252328|ref|YP_004595435.1| 384 INKAVEAAKARMAAQKAEE 402
                                       ****************987 PP

>> DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   0.0   1.6e-32   5.9e-29       5      63 .]     577     635 ..     573     635 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 1.6e-32
                     DNA_gyraseB_C   5 eiqRfKGLGEmnpeqLweTTmdpetRrLlqvtiedaeeadelfstLmGkkvepRrefie 63 
                                       ++qRfKGLGEmnp+qLw+TTmdp++R L q+t+eda++ad++fs+LmG+ vepR++fi+
  gi|336252328|ref|YP_004595435.1| 577 QVQRFKGLGEMNPQQLWDTTMDPSNRILKQITVEDAAAADKMFSVLMGDAVEPRKQFIK 635
                                       8********************************************************96 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 !   82.6   0.0   7.7e-27   2.8e-23       1     110 [.      32     177 ..      32     179 .. 0.91
   2 ?   -2.3   0.0       1.8   6.4e+03      86     102 ..     272     292 ..     241     314 .. 0.55

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 7.7e-27
                                       EHHHHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT..............GTCSTT CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkf..atkageieveikaseddlvisveDnGiGipkedlk..............klfekf 61 
                                       +d+++L++++ ++vdN++++  a+++++i+v+i+  e d ++sv D+G+Gip++ ++              + ++kf
  gi|336252328|ref|YP_004595435.1|  32 TDSRGLHHLVYEVVDNSIDEalAGYCDDITVSIH--E-DGSVSVADDGRGIPVDTHDeydrpaleviltvlHAGGKF 105
                                       699*****************7777**********..7.*******************************877777** PP

                                       CHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEE........................EEETTTEEEEEEEEES CS
                         HATPase_c  62 sqddstkrggggtGlGlsivkklvelmgGeiwv........................esepgrGttftftlpl 110
                                       ++ +s++++gg +G+G+s+v++l+e+++ e+++                        e +++ Gt+++f+++ 
  gi|336252328|ref|YP_004595435.1| 106 DN-KSYQVSGGLHGVGVSVVNALSERLEAEVKRdggvfrhafeqgepvgdmervrdmEPDEETGTEVRFWPDT 177
                                       **.**********************99999999999999999999998888888866555588******9985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.8
                                       HHTTTEEEE....EEETTTEE CS
                         HATPase_c  86 elmgGeiwv....esepgrGt 102
                                       e ++G+i+     +++ ++Gt
  gi|336252328|ref|YP_004595435.1| 272 EELQGSIHAfannINTREGGT 292
                                       223333333222211112222 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   3.6e-21   1.3e-17       1      99 [.     431     539 ..     431     543 .. 0.91

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 3.6e-21
                                       EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH.....HHHHHHHHSEEEEE CS
                            Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildlet.efkpvye..eiedkkkvlka.....lkelakradeiila 69 
                                       el+i+Eg+s+ +++++a++++fqav++ +G++l++e+ ++++v+e  +i++++++++a     ++ +  r++++i+a
  gi|336252328|ref|YP_004595435.1| 431 ELFIAEGDSAGGSAKQARNPEFQAVLPIRGKVLNVEKhRLDRVLEndQIRNIITAIGAgvgdeFDLEDVRYKKVIMA 507
                                       69***********************************989999989999999999999******************* PP

                                       CSSSHHHHHHHHHHHHHHT....HHHTTTEEEEE CS
                            Toprim  70 tDpDreGeaiawellevlk....ellenkigrve 99 
                                       tD+D++G +i+++ll++++    +lle   g+v+
  gi|336252328|ref|YP_004595435.1| 508 TDADVDGAHIRTLLLTFFYrhmrPLLEG--GYVY 539
                                       ******************9666655555..6665 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 !   17.2   0.0   9.9e-07    0.0035       7      52 ..      41      86 ..      36     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9.9e-07
                       HATPase_c_3  7 laelvdNsld.Adaen...vkievnknrgktgeivieDdGkGmseeelkn 52
                                      + e+vdNs+d A a +   ++++++++    g++++ DdG G++ ++ ++
  gi|336252328|ref|YP_004595435.1| 41 VYEVVDNSIDeALAGYcddITVSIHED----GSVSVADDGRGIPVDTHDE 86
                                      88********95554433488888886....7***********9876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); 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: 0.60u 0.22s 00:00:00.82 Elapsed: 00:00:00.37
# Mc/sec: 5223.59
//
Query:       gi|336252329|ref|YP_004595436.1|  [L=827]
Description: DNA gyrase subunit A [Halopiger xanaduensis SH-6]
Scores for 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-156  522.2   0.0   1.2e-156  521.9   0.0    1.1  1  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
    5.5e-77  253.1  14.9    5.4e-14   51.4   0.2    6.4  6  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
     0.0022   16.1   0.2     0.0097   14.0   0.0    2.0  2  IKI3           IKI3 family
  ------ inclusion threshold ------
      0.063   13.0   3.8       0.11   12.2   3.8    1.3  1  DUF745         Protein of unknown function (DUF745)


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 !  521.9   0.0  2.8e-160  1.2e-156       1     425 [.      40     478 ..      40     479 .. 0.98

  Alignments for each domain:
  == domain 1  score: 521.9 bits;  conditional E-value: 2.8e-160
                     DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGn 76 
                                       Ra+P v DGlKPv+RriLyam+++  ++ ++++K++ +vGe++g+YhPHGd+++yd++vr+aqdf++++pl+d+qGn
  gi|336252329|ref|YP_004595436.1|  40 RALPRVEDGLKPVHRRILYAMHEMgVSSGSSHRKSSSIVGETMGDYHPHGDSAIYDTLVRMAQDFSMRYPLVDGQGN 116
                                       9**************************************************************************** PP

                     DNA_topoisoIV  77 fGsildgdkdAaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipp 153
                                       fGs+ dgd++Aa+RY+e+r+s+i++ell++i+k+tvd++ nyD++ +EP+vlp+++PnlLvnG++GIavGm+t+ipp
  gi|336252329|ref|YP_004595436.1| 117 FGSM-DGDPAAAQRYTEARMSPISEELLEDIEKDTVDFSANYDDRLQEPDVLPAAFPNLLVNGSSGIAVGMSTNIPP 192
                                       ****.************************************************************************ PP

                     DNA_topoisoIV 154 hnlkeiidaliallkgeea...ellelvlgPdfptgggiigkeeikeayetgrGkikvrakveie....e.ktivit 222
                                       hnl+e+ida+i+l+++++a   +l+e+v+gPdfptg+ i+g++ i +ay+tgrG+++vra++e+e    + ++iv+t
  gi|336252329|ref|YP_004595436.1| 193 HNLGEVIDATIELIDNPDAtveDLMEHVKGPDFPTGANIVGRDAIYSAYKTGRGRLRVRAEFEVEewknNrERIVVT 269
                                       ******************99********************************************99*99569***** PP

                     DNA_topoisoIV 223 ElPigvntskliekieelvkkkkik.isdirdesdr.gvrivielkrgaseekvleklykktkLessisvnnlvlfd 297
                                       ElP++ n+++l+e+i+e v++++i+ isd+rdesdr gvr+vielkrga++e+v++kl++  +Le+++ v nl+l+d
  gi|336252329|ref|YP_004595436.1| 270 ELPFQSNKARLVERIAEDVNEGEIEgISDLRDESDRdGVRVVIELKRGANSEVVKNKLLE-NHLEKTFGVINLALVD 345
                                       ***********************************99*******************9998.58************** PP

                     DNA_topoisoIV 298 kkpkylslkeilkeflevrlevyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee..l 372
                                       ++p++lslke l+e++++r+ev++rr+ey+le++e+r++ileg lka++++++v+e+ir+s+++++ak++L++   +
  gi|336252329|ref|YP_004595436.1| 346 GQPQVLSLKETLEEYVAHRREVVRRRSEYDLEEAEDRAHILEGRLKAVENAEDVVELIRDSETRSDAKENLQDAygF 422
                                       ***************************************************************************** PP

                     DNA_topoisoIV 373 seeqaeyllemrlrrLtkeeveklekeieelekeikelekllak...lkklikeel 425
                                       s++qa+++++m+l +Lt++e+ ++e+e+ee+++ei++l+++l++   l ++ik+el
  gi|336252329|ref|YP_004595436.1| 423 SQDQADHIVRMQLGSLTSMEAAEIEDEYEEVQAEIERLTAILESeqkLLEVIKDEL 478
                                       ******************************************99877788888877 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 !   42.1   0.1   9.7e-15   4.3e-11       4      47 ..     513     556 ..     510     557 .. 0.94
   2 !   45.2   0.0     1e-15   4.7e-12       1      45 [.     560     607 ..     560     610 .. 0.96
   3 !   38.3   0.0   1.5e-13   6.5e-10       5      47 ..     620     660 ..     616     661 .. 0.95
   4 !   51.4   0.2   1.2e-17   5.4e-14       2      47 ..     665     710 ..     664     711 .. 0.95
   5 !   39.0   0.3   9.2e-14   4.1e-10       3      47 ..     718     763 ..     715     764 .. 0.92
   6 !   42.8   0.2   5.7e-15   2.6e-11       1      48 []     767     814 ..     767     814 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 9.7e-15
                                       EEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   4 lliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                       +++T+  yvkr+p++++ +qgRg+kG++g + kegd++ +v+ +
  gi|336252329|ref|YP_004595436.1| 513 VVMTEDDYVKRMPIEDFDPQGRGGKGIIGADVKEGDRVATVFRA 556
                                       799**************************************986 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 1e-15
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS...ETTTTSSEEEEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgi...klkegdklvsvl 45 
                                       d+ll++T++G+v+ ++ +e+pe+gR+a+G+ ++   +l++g+ +++++
  gi|336252329|ref|YP_004595436.1| 560 DYLLCFTNQGKVYQLKTYEIPEMGRTARGKSAVnilDLDDGEDITAIV 607
                                       8*******************************************9987 PP

  == domain 3  score: 38.3 bits;  conditional E-value: 1.5e-13
                                       EEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   5 liTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                       ++T+nGyvkr++ +e+ +++  ++G+++ +l+egd+lv+v+v+
  gi|336252329|ref|YP_004595436.1| 620 MVTRNGYVKRTDGEEFDNIR--STGIIASDLEEGDELVDVEVT 660
                                       89******************..77****************998 PP

  == domain 4  score: 51.4 bits;  conditional E-value: 1.2e-17
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                       +l+++T+ G+ +rf+++e++++gR+a+Gv gikl ++d + +++ +
  gi|336252329|ref|YP_004595436.1| 665 DLVIATEGGMTIRFDEDEVRAMGRNARGVNGIKLQDDDAVAGLVAT 710
                                       89***************************************99865 PP

  == domain 5  score: 39.0 bits;  conditional E-value: 9.2e-14
                                       EEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTT.SSEEEEEEE CS
                     DNA_gyraseA_C   3 llliTsnGyvkrfplselpeqgRgakGvkgiklkeg.dklvsvlvv 47 
                                       ll++T+nGy+kr++lse+++q+R +kG + ik+ ++ + +++v  v
  gi|336252329|ref|YP_004595436.1| 718 LLTVTRNGYGKRTRLSEYSRQSRYGKGLIDIKTGDRnGPVTAVKAV 763
                                       8********************************9998888888776 PP

  == domain 6  score: 42.8 bits;  conditional E-value: 5.7e-15
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                       d l+l+++ G+++r++++e++  gR+++Gv+++  + +d + sv vv+
  gi|336252329|ref|YP_004595436.1| 767 DQLVLMSEDGQIVRTRVDEVSTVGRNTMGVIVMEVEGDDAVASVDVVP 814
                                       789******************************************996 PP

>> IKI3  IKI3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.12   5.5e+02      47     102 ..     572     630 ..     542     651 .. 0.62
   2 !   14.0   0.0   2.2e-06    0.0097      19     131 ..     700     804 ..     686     811 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.12
                                       XXXXXXXXXXXX......XXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              IKI3  47 aaievqrfekds......evevlasleaeeleekkdkivsveyladkeelvlalasGdillv 102
                                       ++++  +  + +      +   +++l+     e+ ++iv+++ lad+e + +++++G +  +
  gi|336252329|ref|YP_004595436.1| 572 YQLKTYEIPEMGrtargkSAVNILDLDD---GEDITAIVDTDALADDECVTMVTRNGYVKRT 630
                                       4444444444443333322234444443...478899999999***9999999999987655 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX.XXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXX CS
                              IKI3  19 esdlkvlasvfdtesdsilivlssteseaaievqrfekdsev.evlasleaeeleekkdkivsveyladkeelvlal 94 
                                       ++d+    ++ d+++d++l++++ + +    ++++++ +s+  + l+++++    +++  +++v+ + d+++lvl++
  gi|336252329|ref|YP_004595436.1| 700 DDDAVAGLVATDEADDKALLTVTRNGYGKRTRLSEYSRQSRYgKGLIDIKTG---DRNGPVTAVKAVDDDDQLVLMS 773
                                       445556667889999999*********9************9999*****977...78889***************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              IKI3  95 asGdillvtvdsdaeekeveivGsiesGieaaawspd 131
                                       + G+i+ +        +ev+ vG+   G+ +++   d
  gi|336252329|ref|YP_004595436.1| 774 EDGQIVRT------RVDEVSTVGRNTMGVIVMEVEGD 804
                                       ******99......44666777777777766665555 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.8   2.4e-05      0.11      62     164 ..     384     487 ..     380     492 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                            DUF745  62 qlveqleqelreaeavvqeekksl..qsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelae 136
                                        ++e   + +++ae+vv+ + +s   + +++n++ a   +++   ++ +++     ++ +++++e+  +++q+e++ 
  gi|336252329|ref|YP_004595436.1| 384 HILEGRLKAVENAEDVVELIRDSEtrSDAKENLQDAYGFSQDQADHIVRMQL-GSLTSMEAAEIEDEYEEVQAEIER 459
                                       5788888999*******987766511567899999*9999999999999975.4667778899************** PP

                            DUF745 137 ktqlleaAkkRveeLkkqlkearkdlek 164
                                        t++le+ +k +e +k +l+e+++++ +
  gi|336252329|ref|YP_004595436.1| 460 LTAILESEQKLLEVIKDELREVKEEYGD 487
                                       *************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (827 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1179  (0.0657594); expected 358.6 (0.02)
Passed bias filter:                      729  (0.0406604); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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: 0.81u 0.30s 00:00:01.11 Elapsed: 00:00:00.44
# Mc/sec: 5632.44
//
Query:       gi|336252330|ref|YP_004595437.1|  [L=177]
Description: Winged helix-turn-helix transcription repressor, HrcA DNA-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-37  124.8   0.1    1.1e-36  124.3   0.1    1.2  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
    1.1e-08   35.3   0.0    1.9e-08   34.6   0.0    1.3  1  Rrf2            Transcriptional regulator
    1.4e-06   28.2   0.0    2.2e-06   27.5   0.0    1.3  1  HTH_11          HTH domain
  ------ inclusion threshold ------
      0.026   14.4   0.0      0.047   13.6   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.033   14.2   0.0      0.065   13.3   0.0    1.5  1  HTH_20          Helix-turn-helix domain
      0.065   13.3   0.0       0.12   12.4   0.0    1.4  1  Put_DNA-bind_N  Putative DNA-binding protein N-terminus
      0.074   12.6   0.3       0.16   11.5   0.3    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> 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 !  124.3   0.1   4.3e-40   1.1e-36       1      78 [.       5      82 ..       5      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.3 bits;  conditional E-value: 4.3e-40
                      HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealkiqtl 78
                                      eLt++qk+il+aL++l+++++ a+Kge+iAe+++rn+Gt+RNq+qsLkal+LvegvpGPkGGYkPt++ayeal+iq++
  gi|336252330|ref|YP_004595437.1|  5 ELTPSQKKILRALTNLHKESEDAIKGEDIAEQVDRNPGTIRNQMQSLKALQLVEGVPGPKGGYKPTAAAYEALEIQQM 82
                                      69*************************************************************************997 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   7.3e-12   1.9e-08      11      66 ..      14      68 ..       5      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 7.3e-12
                                      HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEE CS
                              Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyr 66
                                      l+al+ L ke+e+  ++ e+iae+++ +p  ++  ++ L+   lv+ v G++GGy+
  gi|336252330|ref|YP_004595437.1| 14 LRALTNLHKESEDA-IKGEDIAEQVDRNPGTIRNQMQSLKALQLVEGVPGPKGGYK 68
                                      89**********98.****************************************6 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   8.6e-10   2.2e-06       6      55 .]      17      68 ..      10      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 8.6e-10
                            HTH_11  6 lelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GYr 55
                                      l+ L ++ ++ i ge++Ae+ ++   t+r+ +++L++l   +e++pg+  GY+
  gi|336252330|ref|YP_004595437.1| 17 LTNLHKESEDaIKGEDIAEQVDRNPGTIRNQMQSLKALQ-LVEGVPGPkgGYK 68
                                      44466666777***************************9.*********9996 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   1.8e-05     0.047      19      65 ..      24      70 ..       1      79 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE- CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYrav 65
                                      +++  + ++iae++++   ++ + ++sL+   lVe ++g +  Y+++
  gi|336252330|ref|YP_004595437.1| 24 SEDAIKGEDIAEQVDRNPGTIRNQMQSLKALQLVEGVPGPKGGYKPT 70
                                      45566789******************************997777765 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   2.5e-05     0.065      10      58 ..       8      61 ..       6      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
                                      HHHHHHHHHH.....STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 10 PvRrrilraL.....araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      P++ +ilraL      ++++   +++ae++d  + t++++++ L    Lve+v 
  gi|336252330|ref|YP_004595437.1|  8 PSQKKILRALtnlhkESEDAIKGEDIAEQVDRNPGTIRNQMQSLKALQLVEGVP 61
                                      9999*****************************************9*****986 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.6e-05      0.12      14      45 ..      14      45 ..      12      46 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.6e-05
                                      HHHHHHHHHTT--EE-HHHHHHHCTS-HHHHH CS
                    Put_DNA-bind_N 14 lryLeelkeegveriSSteLaealgvtaaqvR 45
                                      lr+L++l++e ++ i  +++ae+++ ++ ++R
  gi|336252330|ref|YP_004595437.1| 14 LRALTNLHKESEDAIKGEDIAEQVDRNPGTIR 45
                                      89**************************9999 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 ?   11.5   0.3   6.4e-05      0.16       3      47 ..       8      57 ..       6      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.4e-05
                            HTH_24  3 etdrkILelLqk.....nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                        ++kIL++L       +  i   ++Ae+++  p+t++ +++ L+   l+
  gi|336252330|ref|YP_004595437.1|  8 PSQKKILRALTNlhkesEDAIKGEDIAEQVDRNPGTIRNQMQSLKALQLV 57
                                      67899999999999998999999********************9876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1327.39
//
Query:       gi|336252331|ref|YP_004595438.1|  [L=226]
Description: DtxR family iron (metal) dependent repressor [Halopiger xanaduensis SH-6]
Scores for complete 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-28   98.5   0.7    3.3e-28   97.6   0.7    1.5  1  Fe_dep_repr_C    Iron dependent repressor, metal binding and 
    2.7e-20   72.3   0.4      6e-20   71.2   0.4    1.6  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    6.9e-13   48.7   0.7    2.1e-12   47.1   0.1    2.0  2  FeoA             FeoA domain
    4.6e-09   36.1   0.0    9.5e-09   35.1   0.0    1.5  1  MarR             MarR family
    1.5e-08   34.4   0.0    5.1e-08   32.7   0.0    1.9  1  MarR_2           MarR family
    5.6e-07   29.0   0.2    1.2e-06   27.9   0.0    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding
    9.3e-06   25.5   0.1      2e-05   24.5   0.1    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    3.8e-05   23.7   0.2    8.5e-05   22.6   0.1    1.5  1  DUF2250          Uncharacterized protein conserved in archaea
      4e-05   23.4   0.0    9.2e-05   22.3   0.0    1.6  1  TrmB             Sugar-specific transcriptional regulator Trm
      4e-05   23.9   0.1    9.6e-05   22.7   0.1    1.7  1  Rrf2             Transcriptional regulator
    7.3e-05   22.3   0.0    0.00019   21.0   0.0    1.7  1  GntR             Bacterial regulatory proteins, gntR family
    9.3e-05   22.8   0.2    0.00024   21.6   0.2    1.7  1  HTH_27           Winged helix DNA-binding domain
    0.00013   21.7   0.0     0.0006   19.6   0.0    2.2  1  HTH_IclR         IclR helix-turn-helix domain
    0.00014   21.9   0.0      0.002   18.1   0.0    2.7  2  HTH_20           Helix-turn-helix domain
    0.00016   21.5   0.0    0.00047   20.0   0.0    1.8  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0018   17.9   0.0     0.0032   17.1   0.0    1.3  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
     0.0026   17.7   0.1     0.0048   16.8   0.1    1.4  1  HTH_11           HTH domain
     0.0028   18.0   0.1      0.006   16.9   0.1    1.6  1  Penicillinase_R  Penicillinase repressor
     0.0036   17.2   0.2     0.0097   15.8   0.2    1.8  1  HTH_12           Ribonuclease R winged-helix domain
     0.0049   16.8   0.0      0.015   15.2   0.0    1.8  1  HTH_1            Bacterial regulatory helix-turn-helix protei
     0.0084   15.9   0.1      0.019   14.8   0.1    1.7  1  HxlR             HxlR-like helix-turn-helix
     0.0088   15.8   0.0      0.059   13.2   0.0    2.4  3  HTH_23           Homeodomain-like domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.018   15.0   0.0    1.3  1  HTH_45           Winged helix-turn-helix
      0.014   15.5   0.0       0.03   14.4   0.0    1.5  1  FeoC             FeoC like transcriptional regulator
      0.025   14.3   0.0      0.039   13.7   0.0    1.2  1  DUF4423          Domain of unknown function (DUF4423)
      0.025   13.6   0.0      0.042   12.9   0.0    1.3  1  Topoisom_bac     DNA topoisomerase
      0.029   14.4   0.0      0.081   13.0   0.0    1.8  1  Put_DNA-bind_N   Putative DNA-binding protein N-terminus
      0.074   12.9   0.1       0.18   11.6   0.0    1.8  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.077   12.8   0.0       0.42   10.4   0.0    2.1  2  LexA_DNA_bind    LexA DNA binding domain
      0.082   13.0   0.0       0.18   11.9   0.0    1.5  1  HTH_13           HTH DNA binding domain
       0.11   11.9   0.2         40    3.7   0.0    3.5  4  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
       0.17   11.7   0.0       0.34   10.7   0.0    1.5  1  HTH_10           HTH DNA binding domain


Domain annotation for each model (and alignments):
>> 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 !   97.6   0.7   5.9e-31   3.3e-28       1      69 [.      65     133 ..      65     134 .. 0.99

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 5.9e-31
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B-- CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpip 69 
                                       T++G+ +A+++vr+hrlle +L+++l++dw+e+h+eA rlEh++se+++ r+ + lg pe++Phg+pip
  gi|336252331|ref|YP_004595438.1|  65 TDEGETVALEVVRHHRLLEAYLTEHLDYDWSEVHDEADRLEHHISENFEARVADALGEPEVDPHGSPIP 133
                                       9*******************************************************************9 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 !   71.2   0.4   1.1e-22     6e-20       1      60 []       2      62 ..       2      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 1.1e-22
                                      X--HHHHHHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  1 dLvestEdYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      +L++++EdYL++IY+l+  + + +kt+++a +L+v  ++V+ ml kLe+ G+v+ eky+g+
  gi|336252331|ref|YP_004595438.1|  2 MLSDVMEDYLKVIYQLQRsTDDRIKTSEIAAELDVTSPTVTSMLDKLEDRGLVDREKYRGV 62
                                      89****************99***************************************97 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       4.1   2.3e+03       7      30 ..      66      88 ..      62      89 .. 0.76
   2 !   47.1   0.1   3.7e-15   2.1e-12       2      73 ..     147     219 ..     146     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.1
                                      -TT-EEEEEEE-TT.SSHHHHHHH CS
                              FeoA  7 keGergeiarisdedpellrrLre 30
                                      +eGe++  + ++++ + l+++L e
  gi|336252331|ref|YP_004595438.1| 66 DEGETVALEVVRHH-RLLEAYLTE 88
                                      67888888888887.788888887 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 3.7e-15
                                       EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEE..TTEEEEE-HHHHTTEEEE CS
                              FeoA   2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrv..gdtrvaLgreeAqaIlVe 73 
                                       + s+  eGe++++++++d+dpe+l +L+++G+ pG ++e+v+ apf g+++ r   +d+ v+L+  +A+++ V 
  gi|336252331|ref|YP_004595438.1| 147 TVSEFAEGETVVVEEVADRDPEVLSYLADHGVEPGVELEIVEVAPF-GMVTARSsaHDEPVSLPETVARHVRVS 219
                                       568999****************************************.5666666444999***********995 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   1.7e-11   9.5e-09      16      51 ..      23      58 ..      11      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.7e-11
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      + ++ se+a  l v+++tvt +ld+Le++Gl++R+k
  gi|336252331|ref|YP_004595438.1| 23 DRIKTSEIAAELDVTSPTVTSMLDKLEDRGLVDREK 58
                                      458999****************************87 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   9.2e-11   5.1e-08      10      55 ..      13      58 ..      10      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 9.2e-11
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      v++ L r+ + ++  +e+a++l+++ ++v+ +l++L+++GLv r++
  gi|336252331|ref|YP_004595438.1| 13 VIYQLQRSTDDRIKTSEIAAELDVTSPTVTSMLDKLEDRGLVDREK 58
                                      77888888888999****************************9985 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 !   27.9   0.0   2.2e-09   1.2e-06       7      47 ..      12      54 ..      11      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.2e-09
                            HTH_24  7 kILelLqk..nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      k++  Lq+  + ri  +e+A +l+++++tv+  l++Le+ Gl+
  gi|336252331|ref|YP_004595438.1| 12 KVIYQLQRstDDRIKTSEIAAELDVTSPTVTSMLDKLEDRGLV 54
                                      7788899999*******************************98 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 !   24.5   0.1   3.5e-08     2e-05      21      62 ..      24      67 ..      11      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.5e-08
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET.EE.EEES-H CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrg.rr.irildl 62
                                      ++   e+A+ l +t  tv+ +l +L+++gl++r+ +r ++++d 
  gi|336252331|ref|YP_004595438.1| 24 RIKTSEIAAELDVTSPTVTSMLDKLEDRGLVDREkYRgVTLTDE 67
                                      67889***************************643556*99996 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 !   22.6   0.1   1.5e-07   8.5e-05       8      78 ..       8      80 ..       3      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.5e-07
                           DUF2250  8 elalkvlkhlkkanvdYaks..iakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhHt 78
                                      e++lkv++ l++   d  k+  ia el++    v+++l+kLe+ GL++r + + +  t+     + ev +hH 
  gi|336252331|ref|YP_004595438.1|  8 EDYLKVIYQLQRSTDDRIKTseIAAELDVTSPTVTSMLDKLEDRGLVDREKYRGVTLTDEGETVALEVVRHHR 80
                                      6789************9886448999999999****************************************5 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.6e-07   9.2e-05      24      57 ..      26      59 ..      21      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.6e-07
                                      HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      +++eia el+v  ++v ++L +Led+GlV+rek 
  gi|336252331|ref|YP_004595438.1| 26 KTSEIAAELDVTSPTVTSMLDKLEDRGLVDREKY 59
                                      789****************************985 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.7e-07   9.6e-05       1      78 [.       1      75 [.       1      79 [. 0.89

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.7e-07
                                      X---HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHCCCSBHHH CS
                              Rrf2  1 MklsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppeeItlld 78
                                      M ls  +e  l++++ L++  +++ ++++eia++ ++  + +  +l kL+  glv  ++ +  G++L+ + e++ l  
  gi|336252331|ref|YP_004595438.1|  1 MMLSDVMEDYLKVIYQLQRSTDDR-IKTSEIAAELDVTSPTVTSMLDKLEDRGLVDREKYR--GVTLTDEGETVALEV 75
                                      6789999999************99.******************************988766..889998888887754 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.4e-07   0.00019      20      62 ..      21      62 ..       8      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.4e-07
                                      TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR 20 pGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGt 62
                                        d++ + +e+aae++V+ +tv   L++Le +glv r++ rG+
  gi|336252331|ref|YP_004595438.1| 21 TDDRI-KTSEIAAELDVTSPTVTSMLDKLEDRGLVDREKYRGV 62
                                      66888.999******************************9997 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 !   21.6   0.2   4.2e-07   0.00024      14      68 .]      20      68 ..      10      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.2e-07
                            HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                       +++r k ++++  l+v++ ++ ++l+kL+ +GLv r++      ++ v+lTd+G
  gi|336252331|ref|YP_004595438.1| 20 STDDRIKTSEIAAELDVTSPTVTSMLDKLEDRGLVDREK------YRGVTLTDEG 68
                                      56777788***************************5554......4689999998 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 !   19.6   0.0   1.1e-06    0.0006      12      51 ..      17      57 ..      11      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                                      -CTTBSS.-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 12 laeapqe.ltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      l + + +  + se+A++++++ +tv  +L  L+ +G+v ++
  gi|336252331|ref|YP_004595438.1| 17 LQRSTDDrIKTSEIAAELDVTSPTVTSMLDKLEDRGLVDRE 57
                                      55555553799***************************875 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.7e-06     0.002      27      58 ..      27      58 ..       8      60 .. 0.91
   2 ?   -0.0   0.0       1.7   9.4e+02      21      33 ..     142     154 ..     114     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.7e-06
                                      HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 27 aselaerldlskntlsyHLrvLeeagLvevvr 58
                                       se+a++ld++  t+   L++Le+ gLv++++
  gi|336252331|ref|YP_004595438.1| 27 TSEIAAELDVTSPTVTSMLDKLEDRGLVDREK 58
                                      69**************************9986 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.7
                                       TCTTB-HHHHHHH CS
                            HTH_20  21 raegltaselaer 33 
                                       r+eg t+se+ae 
  gi|336252331|ref|YP_004595438.1| 142 RPEGKTVSEFAEG 154
                                       6778888888875 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 !   20.0   0.0   8.5e-07   0.00047       5      46 ..      11      55 ..       9      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.5e-07
                                      HHHHHHHTT...SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLae...gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      lk++++L++      + +e+a+el+++ +tv   L kL++ GLV+
  gi|336252331|ref|YP_004595438.1| 11 LKVIYQLQRstdDRIKTSEIAAELDVTSPTVTSMLDKLEDRGLVD 55
                                      67888888888566899***************************6 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 !   17.1   0.0   5.7e-06    0.0032       1      54 [.       2      55 ..       2      58 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.7e-06
                      HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLve 54
                                      +L++v ++ l+ + +l+r  +  +K+ eiA+ l+  + tv  +l  L   gLv+
  gi|336252331|ref|YP_004595438.1|  2 MLSDVMEDYLKVIYQLQRSTDDRIKTSEIAAELDVTSPTVTSMLDKLEDRGLVD 55
                                      6999*******************************************9999997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   8.5e-06    0.0048       4      47 ..      12      55 ..      11      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.5e-06
                            HTH_11  4 qilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIe 47
                                      +++ +L +++++ i  +e+A eL+v+  tv   +++Le+ g  ++
  gi|336252331|ref|YP_004595438.1| 12 KVIYQLQRSTDDrIKTSEIAAELDVTSPTVTSMLDKLEDRG-LVD 55
                                      6778888888888*************************999.555 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.1e-05     0.006       9      56 ..      11      59 ..       3      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHS-EEHHHHHHT.--GGG---HHHHHHHHHHHHHTTS-EEEEE CS
                   Penicillinase_R  9 meilwekgeatvkevvee.leeekelaysTVktllrrLvkKgllsreke 56
                                      +++++++++ t + + +  +++e +++  TV+++l +L+++gl++rek 
  gi|336252331|ref|YP_004595438.1| 11 LKVIYQLQRSTDDRIKTSeIAAELDVTSPTVTSMLDKLEDRGLVDREKY 59
                                      78999999999999976559**************************996 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 !   15.8   0.2   1.7e-05    0.0097      33      64 ..      39      70 ..      13      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                            HTH_12 33 ravRyrLrkleergltrrvgyagreltEkGle 64
                                       +v   L kle+rgl+ r  y g +lt+ G++
  gi|336252331|ref|YP_004595438.1| 39 PTVTSMLDKLEDRGLVDREKYRGVTLTDEGET 70
                                      55666799**********************86 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 !   15.2   0.0   2.7e-05     0.015      20      60 .]      31      69 ..      27      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-05
                                      HHHHTS-HHHHHHHHHHHHHHHTS-SEEESS.SEEEE-HHHH CS
                             HTH_1 20 AeeLglsqpavsrqikrLEeelgvpLfeRtg.rglrLTeaGe 60
                                      A eL ++ p+v+ ++ +LE++    L++R + rg++LT++Ge
  gi|336252331|ref|YP_004595438.1| 31 AAELDVTSPTVTSMLDKLEDR---GLVDREKyRGVTLTDEGE 69
                                      899****************86...7****77458*******7 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   3.4e-05     0.019      16      76 ..      22      75 ..      10      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-05
                                      TS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHH CS
                              HxlR 16 kgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvl 76
                                      + + ++se++++l +++  + ++ L +Le  gl++re y  v       lt++G++++  +
  gi|336252331|ref|YP_004595438.1| 22 DDRIKTSEIAAEL-DVTSPTVTSMLDKLEDRGLVDREKYRGVT------LTDEGETVALEV 75
                                      3455789******.9************************9774......577777766555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00011     0.059      14      46 ..      17      53 ..      11      57 .. 0.76
   2 ?   -1.8   0.0       5.3     3e+03       4      20 ..      55      71 ..      53      72 .. 0.84
   3 ?   -2.2   0.0         7   3.9e+03      21      33 ..     210     222 ..     206     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                            HTH_23 14 lae....GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      l++    ++ ++eIA+eL+v+  Tv   l + +  Gl
  gi|336252331|ref|YP_004595438.1| 17 LQRstddRIKTSEIAAELDVTSPTVTSMLDKLEDRGL 53
                                      4533445999***************999988755665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.3
                            HTH_23  4 ereRlrillllaeGlsv 20
                                       re++r + l +eG +v
  gi|336252331|ref|YP_004595438.1| 55 DREKYRGVTLTDEGETV 71
                                      58999999999999987 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7
                            HTH_23  21 reIAreLgvsrrT 33 
                                       +++Ar+  vs  T
  gi|336252331|ref|YP_004595438.1| 210 ETVARHVRVSSPT 222
                                       6799999999776 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.3e-05     0.018       6      73 ..      12      79 ..       8      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-05
                            HTH_45  6 eIiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli.kkskekYvlTekGlelleklkele 73
                                      ++i+++ +++ +++ k ++i  + + +  ++ ++Ld+L ++gl+ +++    +lT++G+ +  ++ + +
  gi|336252331|ref|YP_004595438.1| 12 KVIYQLQRST-DDRIKTSEIAAELDVTSPTVTSMLDKLEDRGLVdREKYRGVTLTDEGETVALEVVRHH 79
                                      5666666666.7778889999999********************555778899*****99876666555 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.3e-05      0.03      13      48 ..      23      58 ..      13      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.3e-05
                              FeoC 13 grvslkeLsrhfkaspealeamLeqwvrkGrvekva 48
                                       r+  +e++ ++++++ ++ +mL+ ++ +G v +++
  gi|336252331|ref|YP_004595438.1| 23 DRIKTSEIAAELDVTSPTVTSMLDKLEDRGLVDREK 58
                                      69999**************************99876 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.9e-05     0.039      21      88 ..       9      74 ..       6      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.9e-05
                           DUF4423 21 WyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttsse 88
                                       y  vi++l +  d + +++e+a  l   ++   v + l+ L++ gl+++++   +  t++  t+  e
  gi|336252331|ref|YP_004595438.1|  9 DYLKVIYQLQRSTDDRIKTSEIAAELD--VTSPTVTSMLDKLEDRGLVDREKYRGVTLTDEGETVALE 74
                                      578899***9999**************..**********************99888877777666555 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.5e-05     0.042     343     403 ..      38      99 ..      37     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                      Topoisom_bac 343 paTraeiieklvergYverkk.kslvptelGkalvellekfkdlvspelTaeleekLdeIae 403
                                         T  ++++kl +rg v+r+k + +  t+ G++++  + + ++l +  lT +l  + +e+ +
  gi|336252331|ref|YP_004595438.1|  38 SPTVTSMLDKLEDRGLVDREKyRGVTLTDEGETVALEVVRHHRLLEAYLTEHLDYDWSEVHD 99 
                                       56999****************9************99997779*********99988888766 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014     0.081      13      44 ..      10      41 ..       7      42 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHHTT--EE-HHHHHHHCTS-HHHH CS
                    Put_DNA-bind_N 13 YlryLeelkeegveriSSteLaealgvtaaqv 44
                                      Yl+++ +l+++  +ri  +e+a++l+vt+ +v
  gi|336252331|ref|YP_004595438.1| 10 YLKVIYQLQRSTDDRIKTSEIAAELDVTSPTV 41
                                      ****************************9877 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 ?   11.6   0.0   0.00033      0.18      15      42 .]      22      49 ..      11      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                     HTH_AsnC-type 15 daRisyaeLAervGlSestvlrRvrrLe 42
                                      d Ri  +e+A+++ ++ +tv   +++Le
  gi|336252331|ref|YP_004595438.1| 22 DDRIKTSEIAAELDVTSPTVTSMLDKLE 49
                                      58******************98888876 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 ?   10.4   0.0   0.00075      0.42      29      60 ..      28      58 ..      24      61 .. 0.90
   2 ?   -1.3   0.0       3.3   1.9e+03      31      44 ..     212     225 ..     206     226 .] 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00075
                                      HHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GG CS
                     LexA_DNA_bind 29 reiaralglkSpsaveehLkaLerKGyierdp 60
                                       eia +l ++Sp +v + L +Le +G+++r+ 
  gi|336252331|ref|YP_004595438.1| 28 SEIAAELDVTSP-TVTSMLDKLEDRGLVDREK 58
                                      59********88.79**************975 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.3
                                       HHHHHTS-.HHHHH CS
                     LexA_DNA_bind  31 iaralglkSpsave 44 
                                       +ar+++++Sp  ve
  gi|336252331|ref|YP_004595438.1| 212 VARHVRVSSPTKVE 225
                                       79999****99987 PP

>> HTH_13  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   0.00032      0.18      19      50 ..      30      61 ..      25      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00032
                            HTH_13 19 vakeLkvtpraalklvkelglRElTGRgrfrA 50
                                      +a+eL+vt   ++++++ l+ R l  R+++r+
  gi|336252331|ref|YP_004595438.1| 30 IAAELDVTSPTVTSMLDKLEDRGLVDREKYRG 61
                                      899***************************95 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 ?    3.7   0.0     0.072        40      31      49 ..      28      46 ..      27      48 .. 0.90
   2 ?   -2.7   0.0       7.2     4e+03      35      50 ..      88     103 ..      87     104 .. 0.76
   3 ?    0.2   0.0      0.93   5.2e+02      10      26 ..     106     122 ..     105     123 .. 0.86
   4 ?    2.8   0.1      0.13        75      32      43 ..     211     222 ..     210     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.072
                      HTH_Tnp_ISL3 31 kavArqlgvSwtTVwrild 49
                                      +++A++l+v+  TV  +ld
  gi|336252331|ref|YP_004595438.1| 28 SEIAAELDVTSPTVTSMLD 46
                                      68*************9998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.2
                      HTH_Tnp_ISL3  35 rqlgvSwtTVwrildr 50 
                                       ++l+ +w+ V++  dr
  gi|336252331|ref|YP_004595438.1|  88 EHLDYDWSEVHDEADR 103
                                       5777789999987776 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.93
                      HTH_Tnp_ISL3  10 sriTlrleayilellle 26 
                                       ++i++ +ea ++ +l e
  gi|336252331|ref|YP_004595438.1| 106 HHISENFEARVADALGE 122
                                       6899*******998875 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.13
                      HTH_Tnp_ISL3  32 avArqlgvSwtT 43 
                                       +vAr+++vS  T
  gi|336252331|ref|YP_004595438.1| 211 TVARHVRVSSPT 222
                                       7********776 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00061      0.34      23      48 ..      24      49 ..      20      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00061
                            HTH_10 23 rvtlkeLAkelGIskstlsehLrkae 48
                                      r++++e+A el+++ +t++  L k e
  gi|336252331|ref|YP_004595438.1| 24 RIKTSEIAAELDVTSPTVTSMLDKLE 49
                                      899*****************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1651.29
//
Query:       gi|336252332|ref|YP_004595439.1|  [L=319]
Description: arginase [Halopiger xanaduensis SH-6]
Scores for 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-77  258.2   2.2    1.1e-76  258.0   2.2    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 !  258.0   2.2   6.3e-81   1.1e-76       2     277 ..       6     313 ..       5     315 .. 0.92

  Alignments for each domain:
  == domain 1  score: 258.0 bits;  conditional E-value: 6.3e-81
                                       EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTESCCSEEEEEEEEE--................. CS
                          Arginase   2 dvallGvPfdaagsgrpGarfGPraireasarleealeynlelgvleelkivdlgdvavt................. 61 
                                       +v ++G+P+d  g++r+G+++GP+air a   l+     +le+    ++  vd gd++++                 
  gi|336252332|ref|YP_004595439.1|   6 TVRIIGAPMDY-GANRRGVDMGPSAIRYA--GLAD----ELER---ASVAPVDDGDLSMPraeeidpdaddatgles 72 
                                       688********.*****************..3442....2322...3578889999999999999999********* PP

                                       ..............SSCHHHHHHHHHHHHHHHHHTTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----S CS
                          Arginase  62 ..............pvdneevleqieeavaeilkagklpivlGGDHsialgilralaekygkplgvihfDAHaDlrt 124
                                                     p + e+v+ +++++vae l++g++p+vlGGDHs+a+g+l++ a+   +++g i+fDAHaDl+t
  gi|336252332|ref|YP_004595439.1|  73 tggesagvenakflP-EIESVNARLADRVAETLADGEFPLVLGGDHSVAIGSLHGSARD--ADVGAIWFDAHADLNT 146
                                       ******999999755.78889*************************************7..57************** PP

                                       SCTTTBSSSTTSHHHH...........HHHHTSECGCEEEEEEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHH CS
                          Arginase 125 petegsgnshGtpfrr...........aaeegllkpkklvqiGirsvdneeyelakelgirvitmreidelglkavv 190
                                       pet++sgn hG+p+             +a++  l++++++++G+rs+d+ e+el++e++++++tm +id++g++avv
  gi|336252332|ref|YP_004595439.1| 147 PETSPSGNVHGMPLGAalgrgvfgdmdWAHSPRLREESVAYVGLRSIDERERELVRESEMTAFTMSDIDQRGMTAVV 223
                                       ***************99**********99999********************************************* PP

                                       HHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHHC....HSEEEEEEEE-B-GGGSSTT CS
                          Arginase 191 eeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlrellallrelae....klnlvgaDvvEvnPaldtea 263
                                       e +l++ ++++d +++S+D+D++Dp+ aPG+Gtp++gG+t+re++a+l+++++     + l+++DvvEvnP ld+ a
  gi|336252332|ref|YP_004595439.1| 224 EDALAVATDGTDGIHVSLDLDMIDPKAAPGVGTPVRGGVTYREAHAALEAVSRrhdrDGILRSMDVVEVNPILDE-A 299
                                       *******99*****************************************95545557889**************.5 PP

                                       THHHHHHHHHHHHH CS
                          Arginase 264 eqtarlaarlvrel 277
                                       ++ta+laa+l +++
  gi|336252332|ref|YP_004595439.1| 300 NETAALAAELTASA 313
                                       6*********9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2467.96
//
Query:       gi|336252333|ref|YP_004595440.1|  [L=389]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Halopiger xanaduensis SH-6]
Scores for complete 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-41  142.6   0.1    1.8e-41  142.3   0.1    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    8.6e-10   39.0   0.7    3.1e-08   34.1   0.0    2.6  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00021   21.3   1.1       0.73    9.8   0.0    3.1  3  NAD_binding_9  FAD-NAD(P)-binding
  ------ inclusion threshold ------
       0.25   11.8   4.0        1.1    9.6   0.1    3.2  3  Spore_SspJ     Small spore protein J (Spore_SspJ)


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 !  142.3   0.1     4e-45   1.8e-41       2     294 .]       4     304 ..       3     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: 142.3 bits;  conditional E-value: 4e-45
                                       SEEEE--SHHHHHHHHHHHH...HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH....HHHHCHHHHCCCCH CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq...agakvtlvelegtclnggcllskallgvaedaeias....evvkklnqgielll 71 
                                       +vvv+G+G AG  a ++l+     +a+ t + ++   +++   l +++++v +d++++s      v+++    +++ 
  gi|336252333|ref|YP_004595440.1|   4 NVVVLGAGYAGAGAVTKLQSeldGNARLTWI-ADVDYHLV---L-HEAHRVIRDPDVRSditfP-VTEIADPSTRFI 74 
                                       79******************88779******.66655555...4.5667777777777777764.455555555555 PP

                                       CCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                       Pyr_redox_2  72 geevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp...... 142
                                       + evv++d +++ v+l      d e ++yd++++A Gs++   gipG+++n  +l ++ld+a ++++  ++      
  gi|336252333|ref|YP_004595440.1|  75 RDEVVGLDVDEQVVEL-----ADSEAVEYDYVLVALGSQTAYYGIPGLEDNSLTL-KSLDDALEIHETVQEasqeat 145
                                       66*********99999.....56789**********************9999999.***********9999****** PP

                                       ....SEEEEES-SHHHHHHHHHHHHHT-......EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEE CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 ....krivvvGgGyiGvElAaalaklgk......evtlveardrllraldkelsaaleealekeGvevklgtsvkei 209
                                           ++iv+ G+G+ G+ +A+++a++ +      +++lvea++++ ++ d+e+++al++ le+ Gv++++   ++e+
  gi|336252333|ref|YP_004595440.1| 146 rgdpAQIVIGGAGLSGIQTAGEIAEFRDehrapiDIHLVEALEEIFPGNDPEIQQALRDLLEDAGVRIHTDDPITEA 222
                                       ***********************9998888999899***************************************** PP

                                       EETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC....TECC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx RF
                       Pyr_redox_2 210 dgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva....ggkg 282
                                       ++++     + ++g+ +++d  v+  G++ +++l  +++ le  e++++   ++ +t+++ ++aiGD a    g++ 
  gi|336252333|ref|YP_004595440.1| 223 TEEQ----IEFDEGDPLEYDVFVWTGGITGRDAL--DDAELEK-EHNRVNAEPNFQTSDERVFAIGDSAivdqGDQP 292
                                       *877....69*********************988..9*****9.********************************* PP

                                       SS--HHHHHHHH CS
                                       xxxxxxxxxxxx RF
                       Pyr_redox_2 283 gpelaqaAvqqG 294
                                        p +aqaA+q++
  gi|336252333|ref|YP_004595440.1| 293 APPTAQAAWQAA 304
                                       *********987 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.048   2.1e+02       1      12 [.       4      15 ..       4      29 .. 0.81
   2 !   34.1   0.0   6.9e-12   3.1e-08       2      69 ..     152     225 ..     151     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.048
                                      EEEEECSSHHHH CS
                         Pyr_redox  1 kvvvvGgGyigl 12
                                      +vvv+G+Gy g 
  gi|336252333|ref|YP_004595440.1|  4 NVVVLGAGYAGA 15
                                      59*******996 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 6.9e-12
                                       EEEECSSHHHHHHHHHHHHTT......SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelg......kkVtvversdkllrllDeeaskilqeklekngievllntkveeiegs 69 
                                       +v+ G+G++g+  Ag++ae++       ++++ve+ +++ ++ D+e++++l++ le+ g++++++  ++e +++
  gi|336252333|ref|YP_004595440.1| 152 IVIGGAGLSGIQTAGEIAEFRdehrapIDIHLVEALEEIFPGNDPEIQQALRDLLEDAGVRIHTDDPITEATEE 225
                                       8999*************99997766667************************************9999988765 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 ?   -0.3   0.0      0.22   9.7e+02       1      20 [.       6      25 ..       6      42 .. 0.80
   2 !    8.5   0.1   0.00042       1.9     116     155 ..      70     107 ..      63     108 .. 0.87
   3 !    9.8   0.0   0.00016      0.73       2      40 ..     154     194 ..     152     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.22
                     NAD_binding_9  1 aivGaGprGlavlerLlara 20
                                      ++ GaG +G+ ++++L ++ 
  gi|336252333|ref|YP_004595440.1|  6 VVLGAGYAGAGAVTKLQSEL 25
                                      578***********998887 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00042
                     NAD_binding_9 116 tvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       + +++r+evv l+ +  +q v lad + +++d+V +AlG 
  gi|336252333|ref|YP_004595440.1|  70 STRFIRDEVVGLDVD--EQVVELADSEAVEYDYVLVALGS 107
                                       56899*******976..557999****************6 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00016
                     NAD_binding_9   2 ivGaGprGlavlerLlara.kkkspleitlfdp.sepgagr 40 
                                       i GaG +G+ ++ ++++ + ++++p++i+l++  +e+ +g 
  gi|336252333|ref|YP_004595440.1| 154 IGGAGLSGIQTAGEIAEFRdEHRAPIDIHLVEAlEEIFPGN 194
                                       4499*************99899999*******977776665 PP

>> Spore_SspJ  Small spore protein J (Spore_SspJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.096   4.3e+02      15      36 ..     129     151 ..     119     154 .. 0.75
   2 ?    9.6   0.1   0.00025       1.1      16      39 ..     199     223 ..     196     226 .. 0.85
   3 ?   -1.2   0.1       0.6   2.7e+03      13      20 ..     258     265 ..     253     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.096
                        Spore_SspJ  15 dknavdgaLEdAgka.LkgDPLQ 36 
                                       d   ++    +A+++  +gDP Q
  gi|336252333|ref|YP_004595440.1| 129 DALEIHETVQEASQEaTRGDPAQ 151
                                       55567778889998526899988 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00025
                        Spore_SspJ  16 knavdgaLEdAgkaL.kgDPLQEAV 39 
                                       ++a++ +LEdAg  +  +DP+ EA 
  gi|336252333|ref|YP_004595440.1| 199 QQALRDLLEDAGVRIhTDDPITEAT 223
                                       67899*******9883599****96 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.6
                        Spore_SspJ  13 EKdknavd 20 
                                       EK++n v+
  gi|336252333|ref|YP_004595440.1| 258 EKEHNRVN 265
                                       9****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3069.21
//
Query:       gi|336252334|ref|YP_004595441.1|  [L=207]
Description: O-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-08   31.8   4.7    4.3e-07   29.6   0.4    2.7  3  Hexapep_2  Hexapeptide repeat of succinyl-transferase
    2.5e-07   30.2   0.3    2.5e-07   30.2   0.3    2.9  4  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 !    3.2   0.2    0.0083        74      16      24 ..      75      83 ..      74      84 .. 0.91
   2 ?   -2.2   0.0       0.4   3.6e+03      18      27 ..      99     108 ..      99     111 .. 0.69
   3 !   29.6   0.4   4.9e-11   4.3e-07       2      34 .]     128     162 ..     127     162 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0083
                                      ESEEE-TT- CS
                         Hexapep_2 16 iGvslGdnc 24
                                      iGv++Gd++
  gi|336252334|ref|YP_004595441.1| 75 IGVTVGDDV 83
                                      8******97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.4
                                       EEE-TT-EE- CS
                         Hexapep_2  18 vslGdncvvg 27 
                                       ++l+d ++vg
  gi|336252334|ref|YP_004595441.1|  99 ITLEDHAIVG 108
                                       5677777775 PP

  == domain 3  score: 29.6 bits;  conditional E-value: 4.9e-11
                                       EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvgaGvvita 34 
                                       v +G++ +iGa a++  Gv++G ++ v+a++ +t+
  gi|336252334|ref|YP_004595441.1| 128 VVVGERAMIGAGAIVlpGVEIGAEARVAANSLVTR 162
                                       89************99***************9995 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.04   3.6e+02      19      26 ..      76      83 ..      76      84 .. 0.86
   2 ?   -1.8   0.0      0.33   2.9e+03      22      33 ..     101     112 ..      99     114 .. 0.65
   3 !   30.2   0.3   2.8e-11   2.5e-07       2      36 .]     128     162 ..     127     162 .. 0.95
   4 ?   -3.0   0.0      0.81   7.3e+03      28      36 .]     164     172 ..     164     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.04
                                      TEEE-TTE CS
                           Hexapep 19 nVkIGdnv 26
                                      +V++Gd+v
  gi|336252334|ref|YP_004595441.1| 76 GVTVGDDV 83
                                      79999998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.33
                                       E-TTEEEETTEE CS
                           Hexapep  22 IGdnvkIgagvv 33 
                                       + d++++g  ++
  gi|336252334|ref|YP_004595441.1| 101 LEDHAIVGYDAT 112
                                       567777777665 PP

  == domain 3  score: 30.2 bits;  conditional E-value: 2.8e-11
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       +v+G+ ++Ig++a+++++V+IG  ++++a++ +++
  gi|336252334|ref|YP_004595441.1| 128 VVVGERAMIGAGAIVLPGVEIGAEARVAANSLVTR 162
                                       79*****************************9985 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 0.81
                                       EETTEEEES CS
                           Hexapep  28 Igagvvigg 36 
                                       +++g++++g
  gi|336252334|ref|YP_004595441.1| 164 VEPGTTVAG 172
                                       578888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1685.09
//
Query:       gi|336252335|ref|YP_004595442.1|  [L=278]
Description: hypothetical protein Halxa_0927 [Halopiger xanaduensis SH-6]
Scores for 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-36  124.5   0.0    6.1e-36  124.3   0.0    1.0  1  Nmad3     Nucleotide modification associated domain 3
  ------ inclusion threshold ------
       0.17   11.8   0.3       0.33   10.9   0.3    1.4  1  TraW_N    Sex factor F TraW protein N terminal


Domain annotation for each model (and alignments):
>> Nmad3  Nucleotide modification associated domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.3   0.0   6.8e-40   6.1e-36       2     222 ..       3     234 ..       2     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 124.3 bits;  conditional E-value: 6.8e-40
                             Nmad3   2 iilsrkGfDssaggvpsPilpdGsfvslPIPek.a.desritYadlkld..geelgdlvadltegk........... 63 
                                       ++l  +G+Ds++ g  +P+++dG+f+++PIPek + + ++ t ++++l+  +++ ++++adlt +            
  gi|336252335|ref|YP_004595442.1|   3 VVLAGIGADSTNLGALGPLYDDGRFEYIPIPEKtReTSESETLGSWALRasDDPEHRVAADLTTRIepqpvrggvet 79 
                                       89******************************98447778899*999998655559999999982244556666666 PP

                             Nmad3  64 ....lkaestvHlDPdlaeetlewrptyGqhgaaqghlrn.qgveeGDlflFfglfrrvekenerlrfvkgaewghy 135
                                             ++++ H DP++++ t      yG+ ++  g++ + +++e+GD++ F++++rr            g+++++y
  gi|336252335|ref|YP_004595442.1|  80 vtgeTLESWPFHRDPNFEALT------YGE-HRTSGYVTRlRALEPGDVVGFYAGLRRP----------GGERAHRY 139
                                       666578888********9987......***.77788888889*****************..........89999*** PP

                             Nmad3 136 lfGylqvdevlkveedevpeaewar....hphnahkkrandntlyvase.......kegsglfdrlealpLskpeag 201
                                       l+Gy++vd v  v + e+p  e ++    hp+nah+kra d + y+a++       +e  glfdr   ++Ls++  +
  gi|336252335|ref|YP_004595442.1| 140 LIGYFTVDHVD-VITPETPPPECEAifegHPENAHTKRARDGRPYLAEKtivlvdgREPGGLFDR-YPIRLSEYVVK 214
                                       **********9.55555555544444559*****************9999******9*******7.9******9977 PP

                             Nmad3 202 kesnwklpsffkkelvtelsy 222
                                       + ++ + + ++++++++++++
  gi|336252335|ref|YP_004595442.1| 215 PGNE-RPQYYLREAVESAWNV 234
                                       7554.4444555555555555 PP

>> TraW_N  Sex factor F TraW protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   3.7e-05      0.33       9      28 ..       4      23 ..       2      23 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.7e-05
                            TraW_N  9 lllapaAyAkdLGviGpvfP 28
                                      +l++ +A+ ++LG +Gp+++
  gi|336252335|ref|YP_004595442.1|  4 VLAGIGADSTNLGALGPLYD 23
                                      67788**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       168  (0.00937029); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 2267.63
//
Query:       gi|336252336|ref|YP_004595443.1|  [L=86]
Description: hypothetical protein Halxa_0928 [Halopiger xanaduensis SH-6]
Scores for 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  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 656.49
//
Query:       gi|336252337|ref|YP_004595444.1|  [L=60]
Description: hypothetical protein Halxa_0929 [Halopiger xanaduensis SH-6]
Scores for 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  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 461.54
//
Query:       gi|336252338|ref|YP_004595445.1|  [L=303]
Description: rRNA pseudouridine synthase [Halopiger xanaduensis SH-6]
Scores for 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-21   76.0   0.3    9.4e-13   48.8   0.0    3.2  2  TruB_N    TruB family pseudouridylate synthase (N terminal do
    2.3e-18   66.1   0.0    4.5e-18   65.2   0.0    1.5  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    1.5e-09   37.7   0.2    2.9e-09   36.8   0.2    1.4  1  PUA       PUA domain
    1.1e-08   35.1   0.1    2.1e-08   34.1   0.1    1.5  1  DKCLD     DKCLD (NUC011) domain
     0.0042   17.1   0.1      0.012   15.7   0.0    1.8  2  DUF3701   Phage integrase protein


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 !   48.8   0.0   2.6e-16   9.4e-13       6      50 ..      56     100 ..      52     107 .. 0.92
   2 !   20.9   0.1   9.9e-08   0.00036      76     149 .]     107     165 ..     101     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 2.6e-16
                                       -S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEE CS
                            TruB_N   6 akkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirl 50 
                                       ++++ h+GtLDp++tG+L++++g+aT+l++++le +KeY+a+++ 
  gi|336252338|ref|YP_004595445.1|  56 IDQAAHAGTLDPKVTGCLPIMLGDATRLAQVFLEGSKEYVAVLEC 100
                                       57899************************************9876 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 9.9e-08
                                       HHHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEE..EEEEEEEESTTTTH CS
                            TruB_N  76 kleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveep..evelevecskGtYi 149
                                       + e+v+++f+G i+q pp  SAv                  r+ r  +iy+le+le +e   ++ l+++c++GtY+
  gi|336252338|ref|YP_004595445.1| 107 DAESVVAEFEGPIYQKPPRKSAVA-----------------RRLRVREIYDLEVLERNEAdrQLLLRIRCESGTYV 165
                                       678999****************99.................899*************988789************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 !   65.2   0.0   1.3e-21   4.5e-18       1      63 [.     166     231 ..     166     232 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 1.3e-21
                                       HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT--H...HHHHEEEGGGGG CS
                          TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllykedee...LdrlllPlesal 63 
                                       R+Lc+D+G+aLg+g+h+ +LRRt+++pfd+ d+ +  ++ da++++ ed++   L +++ P e++l
  gi|336252338|ref|YP_004595445.1| 166 RKLCHDLGLALGTGGHMGHLRRTATTPFDDRDLYSAYEFLDALAFWLEDDDpepLSEIVDPAERIL 231
                                       9***********************************************555579*********998 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.2     8e-13   2.9e-09       1      51 [.     235     285 ..     235     290 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 8e-13
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGl 51 
                                       +rvv+ ++A++ +++ga ++ pGv+ev+ d+ egd Va+++++g +v++G 
  gi|336252338|ref|YP_004595445.1| 235 PRVVIPESAAREVANGAPVYEPGVLEVDSDVGEGDLVACYTPNGAAVCLGE 285
                                       79***********************************************97 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.1     6e-12   2.1e-08      30      57 ..       8      35 ..       6      36 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 6e-12
                                      GGG--HHHHHHTEEEEEEE-SSS-HHHH CS
                             DKCLD 30 PlkRpieeyikyGvinLDKPsnPsSHEV 57
                                      P +R+  e++ +Gv+nLDKP +PsSH+V
  gi|336252338|ref|YP_004595445.1|  8 PEERSPAELLTFGVVNLDKPPGPSSHQV 35
                                      999************************9 PP

>> DUF3701  Phage integrase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.4e-06     0.012       7      36 ..      26      56 ..      21      66 .. 0.82
   2 ?   -3.0   0.0       2.3   8.2e+03      23      37 ..     128     142 ..     126     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.4e-06
                           DUF3701  7 aeaPalsdavarWlsprvarrLaaagvk.tL 36
                                      +++   s++v+ Wl+++va+ La++g++ t+
  gi|336252338|ref|YP_004595445.1| 26 KPPGPSSHQVSGWLRDAVADTLAERGIDaTI 56
                                      5555679********************8555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.3
                           DUF3701  23 rvarrLaaagvktLa 37 
                                       +varrL+ +++  L 
  gi|336252338|ref|YP_004595445.1| 128 AVARRLRVREIYDLE 142
                                       799999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); 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:                         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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2382.80
//
Query:       gi|336252339|ref|YP_004595446.1|  [L=192]
Description: cytidylate kinase [Halopiger xanaduensis SH-6]
Scores for 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   76.5   0.3    3.4e-19   69.7   0.3    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
    1.4e-16   61.3   0.1    1.7e-16   60.9   0.1    1.1  1  AAA_18           AAA domain
    4.3e-13   49.8   0.0    7.4e-13   49.1   0.0    1.5  1  AAA_17           AAA domain
    1.1e-09   38.3   0.5    0.00027   20.8   0.0    2.1  2  Cytidylate_kin   Cytidylate kinase
    2.3e-07   31.0   0.0      5e-07   29.9   0.0    1.5  1  ADK              Adenylate kinase
    1.3e-06   28.7   0.2    1.2e-05   25.5   0.2    2.0  1  AAA_33           AAA domain
    0.00051   20.3   0.1     0.0015   18.8   0.1    1.8  1  AAA_28           AAA domain
     0.0022   18.4   0.9     0.0035   17.8   0.9    1.4  1  AAA_16           AAA ATPase domain
     0.0034   17.6   0.0     0.0056   17.0   0.0    1.4  1  AAA_22           AAA domain
     0.0074   16.7   0.0      0.011   16.1   0.0    1.4  1  AAA              ATPase family associated with various cellul
     0.0096   16.1   0.5      0.077   13.1   0.5    2.1  1  SKI              Shikimate kinase
  ------ inclusion threshold ------
      0.024   14.1   0.0      0.032   13.7   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
      0.024   14.3   0.1          5    6.8   0.0    2.4  3  Thymidylate_kin  Thymidylate kinase
      0.027   13.7   0.0       0.07   12.4   0.0    1.7  2  Zeta_toxin       Zeta toxin
      0.054   13.2   0.3       0.71    9.6   0.1    2.2  2  AAA_30           AAA domain
      0.059   13.8   0.0      0.093   13.1   0.0    1.3  1  RNA_helicase     RNA helicase
      0.063   13.3   0.0        0.1   12.6   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
      0.083   12.7   0.0       0.21   11.4   0.0    1.7  2  dNK              Deoxynucleoside kinase
       0.16   12.5   0.0       0.21   12.1   0.0    1.4  1  ABC_tran         ABC transporter
       0.18   11.7   0.0       0.27   11.2   0.0    1.3  1  Rad17            Rad17 P-loop domain


Domain annotation for each model (and alignments):
>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.3   3.8e-22   3.4e-19       3     178 ..       4     156 ..       2     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 3.8e-22
                   Cytidylate_kin2   3 TIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldekld 78 
                                       T+s+  Gsg++t +e LA+ + l+ ++  +i++e+a+e g ++ e+ ++ e                         +
  gi|336252339|ref|YP_004595446.1|   4 TVSGPPGSGKSTTAELLADAFDLDHVSGgDIFRELADERGYTPLEFNKLAE------------------------EN 56 
                                       999************************99*****************77777........................14 PP

                   Cytidylate_kin2  79 delfeaqervirela.aeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrra 154
                                       d++ +   r +re+a +e++ V+  R a  + +++   +r++l+ap ++r +r+aereg ++e a+e+ k+++  +a
  gi|336252339|ref|YP_004595446.1|  57 DQIDRDLDRRLREIArEEDDLVLESRLAGWLAAEQA-DFRFWLDAPVHVRGERIAEREGKDPERAAEETKAREASEA 132
                                       6666777888999998899**********7777755.9*************************************** PP

                   Cytidylate_kin2 155 kyykkytgqdwgdaenYdlvlnts 178
                                       ++y++y+g d+ d + Ydl +nt+
  gi|336252339|ref|YP_004595446.1| 133 QRYEEYYGIDIRDLTIYDLSVNTA 156
                                       **********************97 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.1   1.9e-19   1.7e-16       3     122 ..       5     128 ..       3     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.9e-19
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleeg 74 
                                       ++G+pG+GK+t a+ L++   +     g++ r++a e+g+   ++++  +e++++d+d      + l+e+++   e+
  gi|336252339|ref|YP_004595446.1|   5 VSGPPGSGKSTTAELLADAFDLdhvsgGDIFRELADERGYTPLEFNKLAEENDQIDRDL----DRRLREIAR---EE 74 
                                       89****************97779889999999999999999999999666666666666....555555543...57 PP

                            AAA_18  75 knlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakik.......e 122
                                       ++lv++++la ++ +++ d   ++L+a+ +++ eR+++R+ ++++++       e
  gi|336252339|ref|YP_004595446.1|  75 DDLVLESRLAGWLAAEQADFR-FWLDAPVHVRGERIAEREGKDPERAaeetkarE 128
                                       89*****************99.******************999998876554444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   8.3e-16   7.4e-13       2      79 ..       7      82 ..       6     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 8.3e-16
                                      E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH.HSSEEEEEE- CS
                            AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeea.kkkgvlvdgh 79
                                      G+PGsGK+t +e l++ +++ h+s Gd++re a ++g   +  e++kl +e + ++++ + ++++e a ++++++++  
  gi|336252339|ref|YP_004595446.1|  7 GPPGSGKSTTAELLADAFDLDHVSGGDIFRELADERGY--TPLEFNKLAEEND-QIDRDLDRRLREIArEEDDLVLESR 82
                                      9************************************9..4556666653333.3566666666665523455665554 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     3e-07   0.00027       2      37 ..       4      39 ..       3      48 .. 0.95
   2 !   15.8   0.3   9.8e-06    0.0088      97     172 ..      58     129 ..      47     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3e-07
                                      EEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
                    Cytidylate_kin  2 aiDGPagsGKssvaralaeklglkyldtgalYRala 37
                                      ++ GP gsGKs+ a +la+ ++l  ++ g ++R la
  gi|336252339|ref|YP_004595446.1|  4 TVSGPPGSGKSTTAELLADAFDLDHVSGGDIFRELA 39
                                      789******************************987 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.8e-06
                                       HHHHHHHHHHHTT-B.SSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHHHH CS
                    Cytidylate_kin  97 avRailvkklrelvk.karvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeikeRDk 172
                                       ++ + l ++lre+++ ++++v+e R  g     +a+++ +ldA v++R +R ++  + k    + e+  +e k+R +
  gi|336252339|ref|YP_004595446.1|  58 QIDRDLDRRLREIAReEDDLVLESRLAGWLAAEQADFRFWLDAPVHVRGERIAER-EGK----DPERAAEETKAREA 129
                                       67778999****998899******************************9987665.333....24444455555555 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   5.6e-10     5e-07       1      38 [.       5      42 ..       5      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 5.6e-10
                                      EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksg 38
                                      + G+Pg+GK t ae l++ + l h+s Gd++R+   + 
  gi|336252339|ref|YP_004595446.1|  5 VSGPPGSGKSTTAELLADAFDLDHVSGGDIFRELADER 42
                                      57******************************977665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.2   1.3e-08   1.2e-05       2     136 ..       3     130 ..       2     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.3e-08
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqskt...dytrvldrlyqilnelarkalsagrnvil 75 
                                       + + G+pGsGKst ae l+ + +  ++s  +++r l+ +   ++    ++++ +d++ + l +++r+ ++++ +++l
  gi|336252339|ref|YP_004595446.1|   3 LTVSGPPGSGKSTTAELLADAFDLDHVSGGDIFRELADERGYTPLefnKLAEENDQIDRDLDRRLREIAREEDDLVL 79 
                                       6678*********************************9777777622244445566999999999999999999998 PP

                            AAA_33  76 datnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrsevpeealdrq 136
                                              ++ a +l++  +++++    +++++  +  eR+a+R+ +  +r+  +++a ++ 
  gi|336252339|ref|YP_004595446.1|  80 E------SRLAGWLAAE-QADFR---FWLDAPVHVRGERIAEREGKDPERAAEETKAREAS 130
                                       5......4556666544.35555...77778888888888888777655555555555544 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.7e-06    0.0015       4      68 ..       5      71 ..       2     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
                            AAA_28  4 itGgestGKTtlleaLaar.gypvv..pEaareileekl..akgedalpwvedllafaervleeqleeea 68
                                      ++G++++GK+t++e La+  +  +v   +++re+ +e++    ++++l+++    ++ +  l+ +l+e a
  gi|336252339|ref|YP_004595446.1|  5 VSGPPGSGKSTTAELLADAfDLDHVsgGDIFRELADERGytPLEFNKLAEE--NDQIDRD-LDRRLREIA 71
                                      79***************8876666666999999999988554444555554..3333333.333333333 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   0.9   3.9e-06    0.0035      27     116 ..       3     117 ..       1     139 [. 0.51

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.9e-06
                            AAA_16  27 vllsGesGvGKsslvrellralekd..............ggiflrgkcdqlesaipysalaqalareellrqlldea 89 
                                       + +sG++G+GKs+ ++ l++a+  d              +g+            +p+     a +++++ r+l++++
  gi|336252339|ref|YP_004595446.1|   3 LTVSGPPGSGKSTTAELLADAFDLDhvsggdifreladeRGY------------TPLEFNKLAEENDQIDRDLDRRL 67 
                                       679*****************9999944443333333332122............22211111222223333333333 PP

                            AAA_16  90 esaeleawrekleeala.......................avpelagaea 116
                                       ++ ++e+++  le++la                        ++e +g+++
  gi|336252339|ref|YP_004595446.1|  68 REIAREEDDLVLESRLAgwlaaeqadfrfwldapvhvrgeRIAEREGKDP 117
                                       33333333333333333444444444446666666666664444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.2e-06    0.0056       7      30 ..       2      25 ..       1      79 [. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.2e-06
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqld 30
                                      +l+v G++G+GK+t+++ l++ +d
  gi|336252339|ref|YP_004595446.1|  2 LLTVSGPPGSGKSTTAELLADAFD 25
                                      5899****************9986 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 !   16.1   0.0   1.3e-05     0.011       3      35 ..       5      35 ..       3      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                                      EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelgvefleisgsell 35
                                      ++GppG GK+++a+ +a  +  ++  +sg +++
  gi|336252339|ref|YP_004595446.1|  5 VSGPPGSGKSTTAELLADAF--DLDHVSGGDIF 35
                                      79***************995..44455555555 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.5   8.6e-05     0.077       1     132 [.       9     139 ..       9     157 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.6e-05
                                       TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHT...S-HHHH..HHHHHHHHHHHHHHHHHHHHCCCS.SEEEEE-TT CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtg...ksiaei..feeegeegFrelEsevlkelleee.glViatGGG 71 
                                       +G+GKst+++llA++ +l+ +   +++ + +     +  e+  ++ee  + +r+l+++ l+e+++ee +lV+     
  gi|336252339|ref|YP_004595446.1|   9 PGSGKSTTAELLADAFDLDHVSGGDIFRELADergYTPLEFnkLAEENDQIDRDLDRR-LREIAREEdDLVLES--- 81 
                                       69*****************997766665544411033333311445666667777776.566666654777777... PP

                                       GGGSHHHHHHHHHHSEEEEEE--HHHHHHHHHHTTS.SGGGCSCHHHHHHHHHHHHHHHHHC CS
                               SKI  72 avlseenrellkekgiviyLdvsleellerlkadke.RPllqekskeeelleelaereplye 132
                                          + + + + ++    ++Ld+++++  er+++++   P   ++++ ++++ ++a+r + y 
  gi|336252339|ref|YP_004595446.1|  82 ---RLAGWLAAEQADFRFWLDAPVHVRGERIAEREGkDPERAAEET-KAREASEAQRYEEYY 139
                                       ...5555555557778899999999999999888883333333333.222333335555554 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.5e-05     0.032       3      26 ..       2      25 ..       1      65 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-05
                                      EEEEE--TTSSHHHHHHHHHHHHH CS
                             KTI12  3 LvvltGlPssGKstrakeLakale 26
                                      L++++G P sGKst a+ La+a+ 
  gi|336252339|ref|YP_004595446.1|  2 LLTVSGPPGSGKSTTAELLADAFD 25
                                      999*****************9986 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0056         5       3      21 ..       7      25 ..       5      30 .. 0.86
   2 ?   -2.3   0.0       3.4     3e+03     136     164 ..      48      72 ..      33      81 .. 0.49
   3 ?    5.1   0.0     0.018        16     118     154 ..      92     128 ..      76     152 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0056
                                      ESTTSSHHHHHHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlk 21
                                      G  G+GK+t aell+++++
  gi|336252339|ref|YP_004595446.1|  7 GPPGSGKSTTAELLADAFD 25
                                      778************9885 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                                       CTTSSTTTSHHHHHHHHHHHHHHHHHHHH CS
                   Thymidylate_kin 136 akrdeldeeeeeqldflrkvrerylelak 164
                                       ++++      ee+ ++ r + +r+ e+a+
  gi|336252339|ref|YP_004595446.1|  48 EFNKL----AEENDQIDRDLDRRLREIAR 72 
                                       44444....33444444444444444444 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.018
                                       -SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHH CS
                   Thymidylate_kin 118 PdltflldvdpevalkRlakrdeldeeeeeqldflrk 154
                                        d+ f ld +++v+ +R+a+r+ +d e + ++++ r+
  gi|336252339|ref|YP_004595446.1|  92 ADFRFWLDAPVHVRGERIAEREGKDPERAAEETKARE 128
                                       5889*****************9955333333333332 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.8e-05      0.07      19      41 ..       3      25 ..       1      60 [. 0.85
   2 ?   -1.5   0.0       1.4   1.3e+03     133     147 ..     117     131 ..      90     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.8e-05
                        Zeta_toxin 19 illgGqpGAGKselaellkdele 41
                                      + ++G pG+GKs++aell+d+++
  gi|336252339|ref|YP_004595446.1|  3 LTVSGPPGSGKSTTAELLADAFD 25
                                      5689***************9985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                        Zeta_toxin 133 kelSrlgvldRyeee 147
                                       +e +++++++R+  e
  gi|336252339|ref|YP_004595446.1| 117 PERAAEETKAREASE 131
                                       333444444444333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0008      0.71      21      42 ..       3      24 ..       1      28 [. 0.85
   2 ?    2.7   0.0     0.099        88     124     173 ..      22      71 ..      18      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0008
                            AAA_30 21 avltGpAGtGKttalkalreaw 42
                                       ++ Gp+G+GK+t+ + l++a+
  gi|336252339|ref|YP_004595446.1|  3 LTVSGPPGSGKSTTAELLADAF 24
                                      5789**********99988775 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.099
                            AAA_30 124 DerQlasVeaGgvlrdlveaagigtaeLtevvRqkeseeraaalalregd 173
                                       D   l+ V+ G+++r+l++++g +  e +++   +++  r++ ++lre  
  gi|336252339|ref|YP_004595446.1|  22 DAFDLDHVSGGDIFRELADERGYTPLEFNKLAEENDQIDRDLDRRLREIA 71 
                                       6666889999*******999999999999999998898898888888654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.093       2      23 ..       4      25 ..       3      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                      RNA_helicase  2 wlyGpsgeGKStlakeLakall 23
                                       ++Gp+g GKSt+a+ La+a+ 
  gi|336252339|ref|YP_004595446.1|  4 TVSGPPGSGKSTTAELLADAFD 25
                                      589*************999875 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   0.00012       0.1       5      23 ..       6      24 ..       3      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                      E--SSSSHHHHHHHGGGGB CS
                             AAA_5  5 vGppGtgKselaerlaaal 23
                                       GppG+gKs+ ae la a+
  gi|336252339|ref|YP_004595446.1|  6 SGPPGSGKSTTAELLADAF 24
                                      6***************997 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00024      0.21       1      27 [.       3      29 ..       3      48 .. 0.90
   2 ?   -1.9   0.0       2.7   2.5e+03     122     146 ..      91     115 ..      75     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                                      EEEEESTTSSHHHHHHHHHCCSTCEEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvf 27
                                      ++v+G+ g+GKst ++lL+++++  ++
  gi|336252339|ref|YP_004595446.1|  3 LTVSGPPGSGKSTTAELLADAFDLDHV 29
                                      589******************998776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.7
                                       H-SEEEEEE--HHHHHHHHHHCTTC CS
                               dNK 122 kpdlliYLkasletclerikkRgre 146
                                       + d+  +L+a++ +  eri +R+ +
  gi|336252339|ref|YP_004595446.1|  91 QADFRFWLDAPVHVRGERIAEREGK 115
                                       4677778888888888888888654 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   0.00023      0.21      15      42 ..       4      34 ..       1     138 [. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                                      EEEESTTSSHHHHHHHHTTSS--...SEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                          ABC_tran 15 aivGenGaGKStLlkllagllkp...teGei 42
                                       + G+ G+GKSt ++lla   +      G+i
  gi|336252339|ref|YP_004595446.1|  4 TVSGPPGSGKSTTAELLADAFDLdhvSGGDI 34
                                      678**************98776533345555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0003      0.27      47      68 ..       2      23 ..       1      42 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                             Rad17 47 iLLisGPsGCgkstvvkvLske 68
                                      +L +sGP+G gkst+ + L+  
  gi|336252339|ref|YP_004595446.1|  2 LLTVSGPPGSGKSTTAELLADA 23
                                      6889************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 1345.61
//
Query:       gi|336252340|ref|YP_004595447.1|  [L=315]
Description: hypothetical protein Halxa_0932 [Halopiger xanaduensis SH-6]
Scores for 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-41  139.7   3.8    1.1e-40  139.2   3.8    1.2  1  EMC3_TMCO1       Integral membrane protein EMC3/TMCO1-like
    7.8e-05   22.4   0.3       0.19   11.4   1.4    2.5  2  DUF2937          Protein of unknown function (DUF2937)
     0.0033   17.5   0.3     0.0055   16.8   0.3    1.4  1  Pinin_SDK_memA   pinin/SDK/memA/ protein conserved region
  ------ inclusion threshold ------
      0.019   14.4   0.3      0.036   13.5   0.3    1.3  1  DUF4746          Domain of unknown function (DUF4746)
      0.022   14.0   0.4      0.044   13.1   0.4    1.4  1  HemX             HemX, putative uroporphyrinogen-III C-methyl
      0.049   12.8   1.1      0.077   12.2   1.1    1.2  1  Tho2             Transcription factor/nuclear export subunit 
      0.074   12.5   7.9       0.11   11.9   7.9    1.2  1  Golgin_A5        Golgin subfamily A member 5
      0.081   12.8   8.9        5.9    6.8   8.9    2.3  1  60KD_IMP         60Kd inner membrane protein
       0.13   12.5   1.7        1.2    9.4   0.2    3.0  4  T3SS_needle_F    Type III secretion needle MxiH, YscF, SsaG, 
        0.2   11.0   1.0       0.36   10.1   1.0    1.4  1  DUF4407          Domain of unknown function (DUF4407)
       0.22    9.4   8.8        0.4    8.5   8.8    1.4  1  DUF4175          Domain of unknown function (DUF4175)
       0.54   10.6   8.9       0.97    9.8   7.1    2.4  1  DUF4199          Protein of unknown function (DUF4199)
       0.58    9.6   5.3       0.42   10.1   2.7    1.8  2  MIF4G_like_2     MIF4G like
       0.86   10.0   5.0       0.37   11.2   1.3    2.1  2  CCDC-167         Coiled-coil domain-containing protein 167
       0.94    8.8   4.0       0.78    9.1   2.2    1.6  2  Helo_like_N      Fungal N-terminal domain of STAND proteins
          1    9.3  10.6       0.22   11.4   6.8    1.8  2  Remorin_C        Remorin, C-terminal region
        1.6    8.2   3.7        2.9    7.4   3.7    1.3  1  Stevor           Subtelomeric Variable Open Reading frame
        3.4    8.0  16.4       0.46   10.8   3.4    2.9  3  ABC_tran_CTD     ABC transporter C-terminal domain
        4.6    7.7  13.4        3.7    8.0   7.6    2.9  3  Latarcin         Latarcin precursor
        6.6    7.2   6.3        2.4    8.5   3.1    1.8  2  Ntox1            Putative RNase-like toxin, toxin_1


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 !  139.2   3.8   1.2e-43   1.1e-40       1     169 [.     130     309 ..     130     310 .. 0.95

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 1.2e-43
                        EMC3_TMCO1   1 dlvldplirdwvllPivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqk.............. 63 
                                       dlvl pl      lP++ vi+ v++ltgl+s+llq +l++ + m k+qkr+k++q++++ +q               
  gi|336252340|ref|YP_004595447.1| 130 DLVLAPLDA---ALPFYAVIMSVALLTGLYSTLLQANLMNPEVMAKYQKRMKAMQEKMQDVQDrkqeaeergasdae 203
                                       577777777...9**************************************************************** PP

                        EMC3_TMCO1  64 .ngdklklkklekrqeelmedqsemmmdqmkpmivtmipqiliffwlnsffs.gfvv...aklpfpltgrfksllqr 135
                                        ++ ++ l++++++q+e m d+ +m+++q++pm+++m+++i++f+w+++++  g+v    +++++p++g+++ +   
  gi|336252340|ref|YP_004595447.1| 204 iERLENELESVREEQMEAMSDNLGMFKEQFRPMVWIMLLTIPLFLWMYWKILdGHVSeaeMTMIMPIAGEVS-FN-- 277
                                       999999*******************************************99864444666************.99.. PP

                        EMC3_TMCO1 136 glesldvrfvssiswYflcsfglsqiirklLgea 169
                                         esl +++ s+i+wYflcs+g++q++rk L+++
  gi|336252340|ref|YP_004595447.1| 278 --ESLLGPMWSWIVWYFLCSMGFTQLLRKSLNID 309
                                       ..9****************************987 PP

>> DUF2937  Protein of unknown function (DUF2937)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   1.4   0.00021      0.19      20      84 ..     166     224 ..     146     236 .. 0.75
   2 !    7.5   0.0    0.0034         3      15      40 ..     239     264 ..     227     267 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                           DUF2937  20 vPefadqYqqrLeghldelkrqlagfqatAkrffkgdlealiahyrqsedpvvradaesiqalve 84 
                                        Pe + +Yq+r++++ +e  + +++ +++A++ +    +a i+++++  + v +++ e+++   +
  gi|336252340|ref|YP_004595447.1| 166 NPEVMAKYQKRMKAM-QEKMQDVQDRKQEAEERGA--SDAEIERLENELESVREEQMEAMS---D 224
                                       5************96.6778899********9998..788899999998876665555554...4 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0034
                           DUF2937  15 ligvQvPefadqYqqrLeghldelkr 40 
                                       ++ + +P f+  Y + L+gh+ e++ 
  gi|336252340|ref|YP_004595447.1| 239 IMLLTIPLFLWMYWKILDGHVSEAEM 264
                                       67899******************985 PP

>> Pinin_SDK_memA  pinin/SDK/memA/ protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   6.1e-06    0.0055      37     101 ..     168     225 ..     151     259 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.1e-06
                    Pinin_SDK_memA  37 eiekrleekakeekeeleerkrekreeleeerraeqkelraleeklelkelmetwhenkkalanf 101
                                       e+  + ++++k  +e++  +  + r++  eer a ++e+++le +le +     ++e+++a++  
  gi|336252340|ref|YP_004595447.1| 168 EVMAKYQKRMKAMQEKM--QDVQDRKQEAEERGASDAEIERLENELESV-----REEQMEAMSDN 225
                                       67778888888888888..444567788899999999999999999554.....44444444433 PP

>> DUF4746  Domain of unknown function (DUF4746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3     4e-05     0.036      83     153 ..     169     239 ..     151     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                           DUF4746  83 tlekqekekektkakeaeltade.paeeeeaeeeeeeeaveeeeeeeeeeeeeeedkeltktktvkiPpiwv 153
                                       ++ k +k+ + +++ ++++ +d  +++ee   +++e e +e+e e+  ee+ e+ + +l  +k+ ++P +w+
  gi|336252340|ref|YP_004595447.1| 169 VMAKYQKRMKAMQE-KMQDVQDRkQEAEERGASDAEIERLENELESVREEQMEAMSDNLGMFKEQFRPMVWI 239
                                       44444455555543.34445555477888888888999*********************************6 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 ?   13.1   0.4   4.9e-05     0.044       9     107 ..     142     238 ..     138     241 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-05
                              HemX   9 llallvalavgaglyylgqqqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleq. 84 
                                       + a+++ +a+  gly    q + ++   +a+ q++++a++++++ v+  k++    +e+  + + ++e+le+ele+ 
  gi|336252340|ref|YP_004595447.1| 142 FYAVIMSVALLTGLYSTLLQANLMNPEVMAKYQKRMKAMQEKMQDVQDRKQE----AEERGASDAEIERLENELESv 214
                                       668899999998888877777655555559**********999994333333....334455566666666666551 PP

                              HemX  85 lqkqleelqqqlskvsga.erkdW 107
                                        ++q+e+++++l   + + ++  W
  gi|336252340|ref|YP_004595447.1| 215 REEQMEAMSDNLGMFKEQfRPMVW 238
                                       456677777777766666555555 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.1   8.6e-05     0.077      24      79 ..     170     224 ..     150     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.6e-05
                              Tho2  24 keqYekeieklkseieelakdrsderaaakkkkkekkrlkeliekLeeEkkeqieh 79 
                                        ++Y+k ++ ++++++++ +dr++e ++   +++e++rl++  e+++eE+ e ++ 
  gi|336252340|ref|YP_004595447.1| 170 MAKYQKRMKAMQEKMQDV-QDRKQEAEERGASDAEIERLENELESVREEQMEAMSD 224
                                       479***************.6666667778888999999999999999999887654 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   7.9   0.00013      0.11      79     141 ..     168     229 ..     156     234 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                         Golgin_A5  79 dleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleeelvrskatlqsri 141
                                       ++ a++q+ ++ ++e++q+++++ + e +++ + +ae+erl++el++++ee++++ +++ +  
  gi|336252340|ref|YP_004595447.1| 168 EVMAKYQKRMKAMQEKMQDVQDRKQ-EAEERGASDAEIERLENELESVREEQMEAMSDNLGMF 229
                                       6778999***************987.8889999*******************99877766555 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   8.9    0.0065       5.9      25      92 ..     172     265 ..     142     313 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0065
                          60KD_IMP  25 kssakmqelqPelkeiqekyk...............kdk.qklqqemmklYk......kegvnplaGclplLiqlpi 79 
                                       k +++m+++q +++++q++ +               +++ + + +e+m+  +      ke++ p+  ++ +L+++p+
  gi|336252340|ref|YP_004595447.1| 172 KYQKRMKAMQEKMQDVQDRKQeaeergasdaeierlENElESVREEQMEAMSdnlgmfKEQFRPM--VWIMLLTIPL 246
                                       44566666666666666666667777778888888733335566666665552222225677777..8899999999 PP

                          60KD_IMP  80 fialyrvlrsla......s 92 
                                       f+ +y+ +   +      +
  gi|336252340|ref|YP_004595447.1| 247 FLWMYWKILDGHvseaemT 265
                                       9999988877334444430 PP

>> T3SS_needle_F  Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.9   3.5e+03      40      54 ..      95     109 ..      76     111 .. 0.82
   2 ?    9.4   0.2    0.0013       1.2      26      44 ..     160     178 ..     156     181 .. 0.88
   3 ?   -0.9   0.1       2.2     2e+03       8      18 ..     180     190 ..     177     204 .. 0.45
   4 ?    0.1   0.0       1.1   9.7e+02      11      41 ..     203     233 ..     197     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.9
                                       HHHHHCHHHHHCHHH CS
                     T3SS_needle_F  40 QfklqqYsvfinaqS 54 
                                       Q+k +q+  + ++ S
  gi|336252340|ref|YP_004595447.1|  95 QSKWSQWDKMAGVAS 109
                                       999999998887766 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                                       HHHSTTXHHHHHHHHHHHH CS
                     T3SS_needle_F  26 lkadpsdPaaLakvQfklq 44 
                                       l+a++ +P+ +ak+Q ++ 
  gi|336252340|ref|YP_004595447.1| 160 LQANLMNPEVMAKYQKRMK 178
                                       6789************996 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.2
                                       HHCCTHHHHHH CS
                     T3SS_needle_F   8 lsqkvskaeke 18 
                                       +++k+++++ +
  gi|336252340|ref|YP_004595447.1| 180 MQEKMQDVQDR 190
                                       33333333333 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.1
                                       CTHHHHHHHHHHHHHHHHSTTXHHHHHHHHH CS
                     T3SS_needle_F  11 kvskaekelqdalealkadpsdPaaLakvQf 41 
                                       +++++e+el++  e + +++sd   + k Qf
  gi|336252340|ref|YP_004595447.1| 203 EIERLENELESVREEQMEAMSDNLGMFKEQF 233
                                       5677888888888877777788877777777 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.0    0.0004      0.36     192     243 ..     170     228 ..     144     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0004
                           DUF4407 192 ldaaqaelaelkakld.......atarlaalraelaeleaerakeraasqaaaaaddGl 243
                                       ++++q++++++++k++       +++++ a +ae+++le+e+++ r+++ +a +++ G+
  gi|336252340|ref|YP_004595447.1| 170 MAKYQKRMKAMQEKMQdvqdrkqEAEERGASDAEIERLENELESVREEQMEAMSDNLGM 228
                                       45555555555555555555555899999999999999999999999999988888776 PP

>> DUF4175  Domain of unknown function (DUF4175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   8.8   0.00044       0.4     475     521 ..     179     225 ..     174     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00044
                           DUF4175 475 dAekrLraAqerLkeALergasdeEikklmqeLreAlddylqaLaeq 521
                                       + ++++++ q+r +eA ergasd+Ei++l +eL +  ++ ++a++++
  gi|336252340|ref|YP_004595447.1| 179 AMQEKMQDVQDRKQEAEERGASDAEIERLENELESVREEQMEAMSDN 225
                                       56799******************************999999999876 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   7.1    0.0011      0.97      73     158 ..     146     242 ..     135     304 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                           DUF4199  73 gflislvagllsavfqyiyfnfidpdfienyiaeilekleeakeesae...eenaemseeei...ke........al 135
                                        + ++l++gl s+   ++  n+++p+ +++y + ++++ e++++ ++    +e+ ++s++ei   ++        ++
  gi|336252340|ref|YP_004595447.1| 146 IMSVALLTGLYST---LLQANLMNPEVMAKYQKRMKAMQEKMQDVQDRkqeAEERGASDAEIerlENelesvreeQM 219
                                       3333333333333...4444566899887777666555555444433320355556666677444113444444466 PP

                           DUF4199 136 esls...piivalqsflgnliiGlil 158
                                       e++s       +++  +  +++  +l
  gi|336252340|ref|YP_004595447.1| 220 EAMSdnlG---MFKEQFRPMVWIMLL 242
                                       65554330...333333333333333 PP

>> MIF4G_like_2  MIF4G like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.91   8.2e+02      12      36 ..       3      27 ..       1      40 [. 0.78
   2 ?   10.1   2.7   0.00046      0.42     158     214 ..     171     223 ..     160     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.91
                      MIF4G_like_2 12 aeaqelldlirkkapaeevlellde 36
                                       +a+++ dl+r+ a+ e+ le + e
  gi|336252340|ref|YP_004595447.1|  3 RTAEKINDLVREDASMEDALEAIRE 27
                                      5789999999999999998887765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00046
                      MIF4G_like_2 158 skvnkrvkkvrqeleelkkkeeeekakeeedkeeeeeleraeekleaaqkeqkelfl 214
                                        k +kr+k++++++++++++++e+    ee ++++ e+er+e++le++++eq e ++
  gi|336252340|ref|YP_004595447.1| 171 AKYQKRMKAMQEKMQDVQDRKQEA----EERGASDAEIERLENELESVREEQMEAMS 223
                                       567777777777777777775554....45588899999999999999999988765 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 ?   -0.5   0.1       1.9   1.7e+03       5      26 ..       7      28 ..       4      36 .. 0.64
   2 ?   11.2   1.3   0.00041      0.37      12      68 ..     169     221 ..     166     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.9
                          CCDC-167  5 eIdkleeklascrerLeaverr 26
                                      +I++l  + as+++ Lea+  r
  gi|336252340|ref|YP_004595447.1|  7 KINDLVREDASMEDALEAIRER 28
                                      5666666666777777776555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00041
                          CCDC-167  12 klascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeLksLrkeNrks 68 
                                        +a++++r++a+  ++++++    +R++  eE+++   ++e+ e+eL+s r+e    
  gi|336252340|ref|YP_004595447.1| 169 VMAKYQKRMKAMQEKMQDVQ----DRKQEAEERGASDAEIERLENELESVREEQMEA 221
                                       57889999999999999886....455556699999999999999999999997655 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.3   2.1e+03      36      62 ..       6      31 ..       3      43 .. 0.69
   2 ?    9.1   2.2   0.00087      0.78     157     202 ..     168     215 ..     151     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.3
                       Helo_like_N 36 ktvreLkeeleaLeevLesLeevavae 62
                                      +++++L++e +++e+ Le+++e +++e
  gi|336252340|ref|YP_004595447.1|  6 EKINDLVREDASMEDALEAIRE-RADE 31
                                      5677777777777777777777.4333 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00087
                       Helo_like_N 157 dttsdLeehLedideklealt..ekseeaseedeaelqrlkeEreste 202
                                       +  ++ +++++ ++ek+++++  ++++e++ +++ae++rl++E es++
  gi|336252340|ref|YP_004595447.1| 168 EVMAKYQKRMKAMQEKMQDVQdrKQEAEERGASDAEIERLENELESVR 215
                                       56678899************9444445556678999*******98865 PP

>> Remorin_C  Remorin, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       5.3   4.8e+03      46      74 ..      17      30 ..       4      33 .. 0.54
   2 ?   11.4   6.8   0.00024      0.22      15      68 ..     170     228 ..     165     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.3
                         Remorin_C 46 kleeklEkkrakaleklknklariekkAe 74
                                       +e  lE+ r++               A+
  gi|336252340|ref|YP_004595447.1| 17 SMEDALEAIRER---------------AD 30
                                      334444444444...............43 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00024
                         Remorin_C  15 kakikkrykreeakIaaWenekka.....kaeaelrkleeklEkkrakaleklknklar 68 
                                       +ak++kr+k +++k+++ +++k++     +  ae+++le++lE  r++++e ++++l +
  gi|336252340|ref|YP_004595447.1| 170 MAKYQKRMKAMQEKMQDVQDRKQEaeergASDAEIERLENELESVREEQMEAMSDNLGM 228
                                       89**************99998888677767889********************998866 PP

>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   3.7    0.0032       2.9      43     101 ..     165     224 ..     162     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0032
                            Stevor  43 lNeeaikkYqqthdpy.kqLkevveKngtkstggndaepmStiEkeLletYeevfgdesd 101
                                       +N e + kYq+  +++ +++++v +++++    g +  ++ ++E+eL    ee ++  sd
  gi|336252340|ref|YP_004595447.1| 165 MNPEVMAKYQKRMKAMqEKMQDVQDRKQEAEERGASDAEIERLENELESVREEQMEAMSD 224
                                       9*********987765278******99999999999999********9998887765554 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 ?   -1.3   0.4       3.1   2.7e+03      41      62 ..       6      27 ..       2      31 .. 0.65
   2 ?   10.8   3.4   0.00051      0.46      27      63 ..     160     197 ..     158     197 .. 0.95
   3 ?    5.8   0.5     0.018        16      15      30 ..     202     217 ..     199     230 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.1
                      ABC_tran_CTD 41 eklaelsaeleeleaeLeelye 62
                                      ek+++l +e +  e++Le+  e
  gi|336252340|ref|YP_004595447.1|  6 EKINDLVREDASMEDALEAIRE 27
                                      6667777777777777766544 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00051
                      ABC_tran_CTD  27 leaeladpelysdp.eklaelsaeleeleaeLeelyer 63 
                                       l+a l +pe+++++ +++++ +++++++++  +e++er
  gi|336252340|ref|YP_004595447.1| 160 LQANLMNPEVMAKYqKRMKAMQEKMQDVQDRKQEAEER 197
                                       899********999888*******************98 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.018
                      ABC_tran_CTD  15 aeIeaLEeeiaeleae 30 
                                       aeIe+LE+e++++ +e
  gi|336252340|ref|YP_004595447.1| 202 AEIERLENELESVREE 217
                                       6788888888877663 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.56     5e+02      27      53 ..       5      31 ..       2      36 .. 0.83
   2 ?    8.0   7.6    0.0042       3.7      33      64 ..     170     201 ..     161     222 .. 0.77
   3 ?    0.1   0.4       1.2   1.1e+03      39      73 ..     206     236 ..     201     239 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.56
                          Latarcin 27 memvnnlRkvqgRLeemvenlrkvedl 53
                                       e +n+l +    +e+++e++r++ d 
  gi|336252340|ref|YP_004595447.1|  5 AEKINDLVREDASMEDALEAIRERADE 31
                                      5789999999999*******9988775 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0042
                          Latarcin  33 lRkvqgRLeemvenlrkvedledtEEARgafk 64 
                                       + k q+R++ m e+++ v+d+++  E Rga++
  gi|336252340|ref|YP_004595447.1| 170 MAKYQKRMKAMQEKMQDVQDRKQEAEERGASD 201
                                       5689*****************9999*9*9654 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.2
                          Latarcin  39 RLeemvenlrkvedledtEEARg.afkklkdkfkkm 73 
                                       RLe+ +e +r     e+  EA +   +++k++f+ m
  gi|336252340|ref|YP_004595447.1| 206 RLENELESVR-----EEQMEAMSdNLGMFKEQFRPM 236
                                       4443333333.....455566666777888888766 PP

>> Ntox1  Putative RNase-like toxin, toxin_1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       4.2   3.8e+03      71      88 ..      14      31 ..       3      37 .. 0.68
   2 ?    8.5   3.1    0.0027       2.4      34      89 ..     167     221 ..     165     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.2
                             Ntox1 71 eaakLiqaletarlnggk 88
                                      e a++  ale++r  + +
  gi|336252340|ref|YP_004595447.1| 14 EDASMEDALEAIRERADE 31
                                      667778888888876654 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0027
                             Ntox1  34 PvlrveYkkelaaddelkeeneevealRkldaklaad..eaakLiqaletarlnggka 89 
                                       P +  +Y+k+++a   ++e++++v+  ++ + ++ a   e  +L ++le++r +  +a
  gi|336252340|ref|YP_004595447.1| 167 PEVMAKYQKRMKA---MQEKMQDVQDRKQEAEERGASdaEIERLENELESVREEQMEA 221
                                       6777889999975...889**************9998344579********9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2262  (0.126164); expected 358.6 (0.02)
Passed bias filter:                     1313  (0.0732333); expected 358.6 (0.02)
Passed Vit filter:                       197  (0.0109878); 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):              20  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.45
# Mc/sec: 2105.95
//
Query:       gi|336252341|ref|YP_004595448.1|  [L=815]
Description: flagellin domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-18   66.5   1.1    1.1e-17   64.8   1.1    1.9  1  VWA         von Willebrand factor type A domain
    5.3e-11   43.1   0.1    1.2e-10   42.0   0.1    1.6  1  VWA_2       von Willebrand factor type A domain
    0.00022   21.2   0.0    0.00084   19.3   0.0    2.0  1  VWA_3       von Willebrand factor type A domain
     0.0024   18.7   2.6     0.0044   17.9   1.3    2.2  2  Pilin_N     Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
      0.014   14.8   0.2       0.57    9.5   0.0    2.2  2  VWA_CoxE    VWA domain containing CoxE-like protein
      0.026   14.8   7.3       0.81   10.0   0.1    3.7  3  Bactofilin  Polymer-forming cytoskeletal


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   1.1   3.7e-21   1.1e-17       1     174 [.     578     773 ..     578     774 .. 0.89

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 3.7e-21
                                       EEEEEEE-STTSCHHHHH.HHHHHHHHHHHHHTB.......TTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHH CS
                               VWA   1 DivfvlDgSgsmgeenfe.kvkefikklveklev.......gpegtrvglvqfssevktefslndysskeellsaln 69 
                                       D++fvlD Sgsm++++   ++ ++ k++++ +++       g ++++ g+  f+ + ++  +l++  + ++++s+++
  gi|336252341|ref|YP_004595448.1| 578 DVTFVLDRSGSMRDNDPSeQRVDATKNFIGLMQGedssvleGDQSDQAGVYEFNQNGYERHHLSS--DLSSVNSSVE 652
                                       9***********65555558888888888888844556789************************..559******* PP

                                       TGSGGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS.S......................HTHHH CS
                               VWA  70 nlkysgggttntgkalkyaleklfkssagaRenakkviilltdGksnd.g......................dpkea 123
                                       +   ++ggt  + ++++ al+++ + +++    a++++ill+dG+++  +                      + +++
  gi|336252341|ref|YP_004595448.1| 653 T--SASGGTG-IYSGIEIALDEYERNRSS---SAEQHMILLSDGQNDPaTewvctdggwlgcdnwefydynqQTLDQ 723
                                       *..4888888.******************...9**********9995434899999999999999999999999999 PP

                                       HHHHHGCTEEEEEEEESSSHHHHHHHHHSSSSCHHCEEEESSHHHHHHHHH CS
                               VWA 124 aneakeqgikvfavGvgnadekelLnkiasepgeghvftvtdfeeleelfe 174
                                       a++a + +++++++G +++ + ++L +ia+e++ g ++ ++d +elee+fe
  gi|336252341|ref|YP_004595448.1| 724 AERAADMNVTIHTIGLSDDADSDMLGDIANETD-GDYYPAEDDDELEEIFE 773
                                       99999****************************.**************996 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 !   42.0   0.1     4e-14   1.2e-10       1     107 []     579     691 ..     579     691 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 4e-14
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallksl.......pgdrvglvtfsdgpevlipltkdkakilnalrnle 70 
                                       + fvlD SgSmr++d +++r +a k+++  + ++        + d+ g+  f+ + +   +l++d +++++ ++   
  gi|336252341|ref|YP_004595448.1| 579 VTFVLDRSGSMRDNDPSEQRVDATKNFIGLMQGEDssvlegdQSDQAGVYEFNQNGYERHHLSSDLSSVNSSVETSA 655
                                       67**************************88888444567765788**************************999988 PP

                             VWA_2  71 akgggtnlaaaLqlarkalkkrr.kgekrvivlitDge 107
                                         +ggt + ++++ a ++ +++r +++++ ++l++Dg+
  gi|336252341|ref|YP_004595448.1| 656 --SGGTGIYSGIEIALDEYERNRsSSAEQHMILLSDGQ 691
                                       ..6*****************9999************96 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 !   19.3   0.0   2.8e-07   0.00084       3     154 ..     579     760 ..     577     761 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.8e-07
                             VWA_3   3 vvivvDvsssmsaen..klvkdaLsvalrqLptndkiavllfgtkprplfpg......sravsaaelqealqkikel 71 
                                       v +v+D s sm+++   +  +da ++++ +L +++  +vl  + +++    +       r   +++l+ ++ ++++ 
  gi|336252341|ref|YP_004595448.1| 579 VTFVLDRSGSMRDNDpsEQRVDATKNFI-GLMQGEDSSVLEGDQSDQAGVYEfnqngyERHHLSSDLSSVNSSVET- 653
                                       6667777777777666666666667766.55555656666666554443333233344455567889999999999. PP

                             VWA_3  72 elslgasnlegaLkealrqp...akpgevrsvilltDgssaqge.....................ervsdlisrar. 123
                                       ++ +g++   + ++ al+     ++    ++ ill+Dg+ ++ +                     +++ d+ +ra+ 
  gi|336252341|ref|YP_004595448.1| 654 SA-SGGTGIYSGIEIALDEYernRSSSAEQHMILLSDGQNDPATewvctdggwlgcdnwefydynQQTLDQAERAAd 729
                                       67.9**********9997544557778889*********9886679****************999999999998776 PP

                             VWA_3 124 ekirfhalglgsslsaamlqaLAeasgGtye 154
                                        ++++h++gl ++++ +ml  +A ++ G y+
  gi|336252341|ref|YP_004595448.1| 730 MNVTIHTIGLSDDADSDMLGDIANETDGDYY 760
                                       99**************************996 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 !   17.9   1.3   1.5e-06    0.0044       1      75 [.      16      99 ..      16     109 .. 0.55
   2 ?   -3.2   0.0       5.7   1.7e+04      49      65 ..     158     174 ..     147     180 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasi......evk....idssastgkna....vslehkgG 64
                                      ++VSp +G++L+  +++I a++i a v+++  +  e++++a+       +v+    + ++++         v+le  +G
  gi|336252341|ref|YP_004595448.1| 16 RGVSPQVGIVLLFGMVIIGASLIFA-VGSIaLGSVETQAMAEQgeqmmlQVDngieTATGDN----VssgsVYLED-DG 88
                                      69******************99865.445422333333333333222224443322333333....1345588875.45 PP

                           Pilin_N 65 dsidtkdlkiv 75
                                      +   t+d +i+
  gi|336252341|ref|YP_004595448.1| 89 EYELTNDSQIT 99
                                      55555444444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.7
                           Pilin_N  49 sastgknavslehkgGd 65 
                                       ++++g +++ +++ gG+
  gi|336252341|ref|YP_004595448.1| 158 NGTEGRVELDITNLGGE 174
                                       33334444999****98 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.019        57      53      72 ..     572     591 ..     544     594 .. 0.77
   2 ?    9.5   0.0   0.00019      0.57     113     162 ..     641     692 ..     636     699 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.019
                          VWA_CoxE  53 rerkprelvllvDvSgSmaa 72 
                                        +r+p ++ +++D SgSm +
  gi|336252341|ref|YP_004595448.1| 572 ERRSPLDVTFVLDRSGSMRD 591
                                       457899************86 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00019
                          VWA_CoxE 113 aeaLarvsaaved.lgGgTrigaalaeflelvtrpa.LsrravvvlvsDgle 162
                                        + L +v+++ve   +GgT i+++++ +l+  +r+   s + +++l+sDg +
  gi|336252341|ref|YP_004595448.1| 641 SSDLSSVNSSVETsASGGTGIYSGIEIALDEYERNRsSSAEQHMILLSDGQN 692
                                       57899999999999**************999998760345679******954 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00027      0.81       9      78 ..     258     327 ..     251     344 .. 0.84
   2 ?    3.2   0.4     0.037   1.1e+02      20      57 ..     448     488 ..     429     494 .. 0.63
   3 ?    3.5   0.1      0.03        91      15      54 ..     499     541 ..     491     554 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
                        Bactofilin   9 ikGelevegdlridGkveGdieakgklvvgeggkvegnikaeevvvaGtvkGnveaee.kvelkktakveG 78 
                                       i+Ge  + +++ id ++ G ++a+++l++ e+ +v+ + + +   v+G+v+ ++ + + ++el+++a+++G
  gi|336252341|ref|YP_004595448.1| 258 IEGENPFASHVGIDPTIYGGLYADDDLTIDESVTVD-RYNGTVGWVSGNVTEDLLVANgELELASDANITG 327
                                       78999999*********************9988776.467777889****998887777**********99 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.037
                        Bactofilin  20 ridGkveGdieakgklvvgeggk....vegnikaeevvvaGt 57 
                                       +i+  v+G++e +  + v  +g+    v+g+i+ + v+v+G 
  gi|336252341|ref|YP_004595448.1| 448 DIHVAVDGNVELD-GVDVTGDGRaylyVSGDIDTDGVTVDGD 488
                                       3444566666665.5666666644444777777777777775 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.03
                        Bactofilin  15 vegdlridGkveGdi..eakgklvvgeggkvegnikaee.vvv 54 
                                       +++d+ +   ++G +   ++++l+v++++ v g+i a+e +++
  gi|336252341|ref|YP_004595448.1| 499 SDADVTVRNVFQGVMytPESNSLTVAKDTAVYGSIVAGEgIDI 541
                                       5678889999999996644779***********9998542665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (815 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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):               6  [number of targets reported over threshold]
# CPU time: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 5345.76
//
Query:       gi|336252342|ref|YP_004595449.1|  [L=506]
Description: hypothetical protein Halxa_0934 [Halopiger xanaduensis SH-6]
Scores for 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   2.8         26    5.2   0.0    3.4  3  Bactofilin  Polymer-forming cytoskeletal


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2    0.0029        52      45      94 ..     216     265 ..     212     269 .. 0.84
   2 ?   -0.1   0.0     0.067   1.2e+03      22      36 ..     339     354 ..     318     360 .. 0.51
   3 ?    5.2   0.0    0.0014        26      31      73 ..     435     476 ..     411     478 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0029
                        Bactofilin  45 gnikaeevvvaGtvkGnveaeekvelkktakveGdikaksleieegavfe 94 
                                       g  ++++v+v+   +G+v+ae   +  ++a  +G i+a  le++ ga+++
  gi|336252342|ref|YP_004595449.1| 216 GATTVRDVEVHDDRTGTVTAEFGYQEVSDAFKTGAIYATDLEVQGGAEID 265
                                       45667888999999999999998888889999999999999999999986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.067
                        Bactofilin  22 dGkveGdiea.kgklv 36 
                                          v+Gdi+a +++++
  gi|336252342|ref|YP_004595449.1| 339 TLVVDGDINAnDETIT 354
                                       3334444422233444 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0014
                        Bactofilin  31 akgklvvgeggkvegnikaeevvvaGtvkGnveaeekvelkkt 73 
                                       +++++ ++++ ++ g+i a++v+++G  kG+++ e   +l+++
  gi|336252342|ref|YP_004595449.1| 435 CDKQVCIHSNPNFFGSIIASSVEIQGG-KGSIDFEYDTQLQDE 476
                                       678999999999*************98.899998888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3615.35
//
Query:       gi|336252343|ref|YP_004595450.1|  [L=211]
Description: adenylate kinase [Halopiger xanaduensis SH-6]
Scores for 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-46  156.5   0.0    6.5e-46  156.2   0.0    1.1  1  ADK              Adenylate kinase
      4e-24   85.6   0.7    9.8e-24   84.3   0.1    1.8  2  AAA_17           AAA domain
    4.7e-08   33.6   0.1    1.3e-07   32.2   0.0    1.7  2  AAA_18           AAA domain
    1.7e-05   25.0   0.1    0.00098   19.3   0.0    2.5  3  AAA_33           AAA domain
     0.0062   16.3   0.0       0.01   15.6   0.0    1.3  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
  ------ inclusion threshold ------
      0.012   15.3   3.3         12    5.5   0.3    3.1  3  Thymidylate_kin  Thymidylate kinase
      0.023   14.7   0.3       0.11   12.5   0.3    2.1  1  ADK_lid          Adenylate kinase, active site lid
      0.076   12.3   0.1       0.19   11.0   0.1    1.8  1  Zeta_toxin       Zeta toxin
       0.11   12.4   0.0       0.21   11.5   0.0    1.5  1  Ploopntkinase3   P-loop Nucleotide Kinase3
       0.16   11.8   1.2        6.3    6.6   0.0    2.8  3  dNK              Deoxynucleoside kinase


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 !  156.2   0.0   3.6e-49   6.5e-46       1     150 [.       8     185 ..       8     186 .. 0.93

  Alignments for each domain:
  == domain 1  score: 156.2 bits;  conditional E-value: 3.6e-49
                                       EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT.-HHHHHHH...HHHHTTSS--HHHHHHHHHHHHHCHGT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksg.telGkeak...evmdkgelvpdevvvklvkeelekedk 73 
                                       ++GaPgaGKGtq++k+++++g+ h++tGd lR++ + + +++ +e     e+md+gelvpdevv+++v+e+l++   
  gi|336252343|ref|YP_004595450.1|   8 IMGAPGAGKGTQCAKITEEFGIDHITTGDALRSNKEMDiSDMDTEYDtpgEYMDQGELVPDEVVNAIVDEALSQA-- 82 
                                       79******************************9986542556555542238**********************87.. PP

                                       TTEEEEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT............................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                               ADK  74 kkgfllDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltg............................ 122
                                        +gf+lDG+PR++eqae+le       ++ldlvl+ldv ee lv+Rltg                            
  gi|336252343|ref|YP_004595450.1|  83 -DGFVLDGYPRNMEQAEELEG-----MTDLDLVLYLDVGEEELVHRLTGrrldpetdeiyhveynppedpevedrlv 153
                                       .9******************9.....789************************************************ PP

                                       ....GSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK 123 ....DneetvkkRletykkqtkplidyykkkg 150
                                           D+eetvk+Rl++y+++t+p+i++y+++g
  gi|336252343|ref|YP_004595450.1| 154 qredDTEETVKERLRVYQENTEPVIEHYEEEG 185
                                       *****************************986 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.1   5.5e-27   9.8e-24       1     123 [.       9     127 ..       9     138 .. 0.78
   2 ?   -0.7   0.1      0.98   1.8e+03     126     136 .]     154     164 ..     145     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 5.5e-27
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT......TSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHS CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrg......glakardemrklpleekkelqkeaaekiaeeakk 71 
                                       +G PG+GKgtqc+k+ e++g+ h+++Gd lr++ + +      + ++  ++m++++l++++ + +++ e++ +    
  gi|336252343|ref|YP_004595450.1|   9 MGAPGAGKGTQCAKITEEFGIDHITTGDALRSNKEMDisdmdtEYDTPGEYMDQGELVPDEVVNAIVDEALSQ---A 82 
                                       59*****************************773333222222234445666666666666666666666665...6 PP

                                       SEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHT CS
                            AAA_17  72 kgvlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdr 123
                                       +g+++dg+pr+ eqa++l+g++     +l  d++++l++ +ee++ r+  +r
  gi|336252343|ref|YP_004595450.1|  83 DGFVLDGYPRNMEQAEELEGMT-----DL--DLVLYLDVGEEELVHRLTGRR 127
                                       89****************9998.....45..9***************99886 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.98
                                       T-TS-SHHHHH CS
                            AAA_17 126 grdddneesik 136
                                       +r+dd+ee++k
  gi|336252343|ref|YP_004595450.1| 154 QREDDTEETVK 164
                                       45555555543 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   7.1e-11   1.3e-07       2     116 ..       7     129 ..       6     168 .. 0.79
   2 ?   -0.7   0.1       1.1   1.9e+03      45      51 ..     162     168 ..     133     205 .. 0.50

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 7.1e-11
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe....aldeskrldedkldklldaleenss 69 
                                       +++G+pG+GK t +  + ++ g+     g+ lr++   + +  + + +      d+ + + ++++++++d+   +  
  gi|336252343|ref|YP_004595450.1|   7 VIMGAPGAGKGTQCAKITEEFGIdhittGDALRSNKEMDISDMDTEYDtpgeYMDQGELVPDEVVNAIVDEALSQ-- 81 
                                       699****************9999*999966666655544444444444336655555555555555555555554.. PP

                            AAA_18  70 aleegknlvidghlaeleseaakdikk.....vvLtaspeelleRlekRgye 116
                                           ++  v+dg + ++e+++  ++ +      +L++ +eel  Rl  R+  
  gi|336252343|ref|YP_004595450.1|  82 ----ADGFVLDGYPRNMEQAEELEGMTdldlvLYLDVGEEELVHRLTGRRLD 129
                                       ....589*****************999*********************9844 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                            AAA_18  45 aldeskr 51 
                                        ++e +r
  gi|336252343|ref|YP_004595450.1| 162 TVKERLR 168
                                       2222222 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.5e-07   0.00098       3     122 ..       7     130 ..       6     139 .. 0.74
   2 ?    2.9   0.3     0.065   1.2e+02     108     138 ..     145     172 ..     134     183 .. 0.65
   3 ?   -2.3   0.0       2.5   4.6e+03     126     141 ..     193     208 ..     176     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.5e-07
                            AAA_33   3 llvGlpGsGKstlaerllkklgavllssdtlrr.rlfg......tdqqsktdytrvldr.lyqilnelarkalsagr 71 
                                       ++ G+pG+GK t   ++ ++ g  ++++ +++r + +       t+ +++ +y +  +    + +n+++++als++ 
  gi|336252343|ref|YP_004595450.1|   7 VIMGAPGAGKGTQCAKITEEFGIDHITTGDALRsNKEMdisdmdTEYDTPGEYMDQGELvPDEVVNAIVDEALSQAD 83 
                                       678*******************9999886666624444776655555555566666655245689999********* PP

                            AAA_33  72 nvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaang 122
                                       +++ld    ++ e+a+ l+   +    ++++++++ ee+l +Rl  R  + 
  gi|336252343|ref|YP_004595450.1|  84 GFVLDGY-PRNMEQAEELEGMTD---LDLVLYLDVGEEELVHRLTGRRLDP 130
                                       *****64.444444444445544...559*****************98765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.065
                            AAA_33 108 eetlkeRlakRaangddrsevpeealdrqka 138
                                       + + ++Rl +R+++++   e  +e l  +++
  gi|336252343|ref|YP_004595450.1| 145 DPEVEDRLVQREDDTE---ETVKERLRVYQE 172
                                       4478999999999754...344444444444 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.5
                            AAA_33 126 sevpeealdrqkarfe 141
                                        + p e++++ ka++e
  gi|336252343|ref|YP_004595450.1| 193 EQSPDEVWEDVKATIE 208
                                       3568899999998876 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.7e-06      0.01       4      52 ..       6      64 ..       3      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.7e-06
                         PduV-EutP  4 illiGkvgsGKttLtqalkg..........eelkYkktqaiefsdeviDtPGeylenrk 52
                                      ++++G+ g+GK t + ++++          ++l+ +k   i  +d+  DtPGey+++ +
  gi|336252343|ref|YP_004595450.1|  6 LVIMGAPGAGKGTQCAKITEefgidhittgDALRSNKEMDISDMDTEYDTPGEYMDQGE 64
                                      789***************9999999999989999999999999999*********9865 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.019        33       3      20 ..      10      27 ..       8      34 .. 0.85
   2 ?    5.1   0.0    0.0091        16     119     140 ..     107     128 ..      84     139 .. 0.84
   3 ?    5.5   0.3    0.0067        12     129     184 ..     147     202 ..     144     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.019
                                      ESTTSSHHHHHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerl 20
                                      G  GaGK tq++++ e +
  gi|336252343|ref|YP_004595450.1| 10 GAPGAGKGTQCAKITEEF 27
                                      677**********99876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0091
                                       SEEEEEESSHHHHHTSCCTTSS CS
                   Thymidylate_kin 119 dltflldvdpevalkRlakrde 140
                                       dl+++ldv +e+ + Rl+ r+ 
  gi|336252343|ref|YP_004595450.1| 107 DLVLYLDVGEEELVHRLTGRRL 128
                                       99******************98 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0067
                                       HHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHHHHHH CS
                   Thymidylate_kin 129 evalkRlakrdeldeeeeeqldflrkvrerylelakederiliidasksieevhee 184
                                       ev+ + ++++d  +e+++e+l+++++ +e   e ++e++ +  +d ++s +ev e+
  gi|336252343|ref|YP_004595450.1| 147 EVEDRLVQREDDTEETVKERLRVYQENTEPVIEHYEEEGVLERVDGEQSPDEVWED 202
                                       555444556666899*********************999999*******9999765 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 ?   12.5   0.3   6.1e-05      0.11       1      36 []     126     157 ..     126     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.1e-05
                                       EEE-TTT--EEETTTB--SSTTB-TTT--.-B--GG CS
                           ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLvqRsD 36 
                                       Rr  p   ++Yhv++npP  + + D     LvqR+D
  gi|336252343|ref|YP_004595450.1| 126 RRLDPETDEIYHVEYNPPEDPEVED----RLVQRED 157
                                       788888899***99****9877744....5777776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00011      0.19      15      41 ..       3      28 ..       1     105 [. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                        Zeta_toxin 15 rPklillgGqpGAGKselaellkdele 41
                                      +P l+++ G+pGAGK++  +++++e++
  gi|336252343|ref|YP_004595450.1|  3 QPQLVIM-GAPGAGKGTQCAKITEEFG 28
                                      7999998.68************99985 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.21       6      36 ..       6      36 ..       1      60 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                    Ploopntkinase3  6 iylvGqPGaGkstlmaeltkgfdrskveqee 36
                                      + ++G+PGaGk t  a++t+ f   ++++ +
  gi|336252343|ref|YP_004595450.1|  6 LVIMGAPGAGKGTQCAKITEEFGIDHITTGD 36
                                      5689*****************9998887554 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.11   1.9e+02       1      29 [.       6      34 ..       6      62 .. 0.71
   2 ?    6.6   0.0    0.0035       6.3     119     148 ..     102     131 ..      83     141 .. 0.76
   3 ?    0.3   0.5       0.3   5.4e+02     135     176 ..     147     187 ..     137     209 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
                                      EEEEESTTSSHHHHHHHHHCCSTCEEEE- CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvfeE 29
                                      +v+ G  gaGK t    +++++g+ +++ 
  gi|336252343|ref|YP_004595450.1|  6 LVIMGAPGAGKGTQCAKITEEFGIDHITT 34
                                      6899999******9999999999888775 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0035
                                       HCCH-SEEEEEE--HHHHHHHHHHCTTCCC CS
                               dNK 119 elakpdlliYLkasletclerikkRgreee 148
                                        +  +dl+ YL++  e++++r+  R    e
  gi|336252343|ref|YP_004595450.1| 102 GMTDLDLVLYLDVGEEELVHRLTGRRLDPE 131
                                       34459*****************98876555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.3
                                       HHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS-EE CS
                               dNK 135 tclerikkRgreeekkieldYlekLhekyeewlkklnevpvl 176
                                       +++ r+ +R++  e++++++ l+  +e+ e+ +++++e  vl
  gi|336252343|ref|YP_004595450.1| 147 EVEDRLVQREDDTEETVKER-LRVYQENTEPVIEHYEEEGVL 187
                                       67889999999999888765.677777777777777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1514.35
//
Query:       gi|336252344|ref|YP_004595451.1|  [L=163]
Description: hypothetical protein Halxa_0936 [Halopiger xanaduensis SH-6]
Scores for 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  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1285.04
//
Query:       gi|336252345|ref|YP_004595452.1|  [L=363]
Description: cytochrome c oxidase subunit II [Halopiger xanaduensis SH-6]
Scores for 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-16   58.0   0.0    1.8e-15   56.9   0.0    1.5  2  COX2          Cytochrome C oxidase subunit II, periplasmic do
      0.008   16.4   0.0       0.02   15.2   0.0    1.7  1  DUF5048       Domain of unknown function (DUF5048)
  ------ inclusion threshold ------
      0.017   15.1   0.3       0.32   11.0   0.1    2.3  2  FixH          FixH
      0.023   14.8   0.0       0.29   11.3   0.0    2.4  2  Cupredoxin_1  Cupredoxin-like domain
       0.15   12.0   0.2       0.46   10.5   0.0    1.9  2  UL2           UL2 protein


Domain annotation for each model (and alignments):
>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       3.2   1.1e+04       8      22 ..      35      49 ..      30      53 .. 0.74
   2 !   56.9   0.0   4.9e-19   1.8e-15      36     114 ..     123     201 ..      87     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.2
                              COX2  8 hqwywsyeytdfedl 22
                                      +  y +y+y d  ++
  gi|336252345|ref|YP_004595452.1| 35 YILYNAYKYRDTGEV 49
                                      567889999998776 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 4.9e-19
                              COX2  36 egelrllevdnrvvlpvetkirllvtaedvlhsfavpslgvkvdavpGrlnqvsllidreGvfyGqcselcGvnhss 112
                                       +  +      + +v+p ++ + +  t+ dv h+f +p l vk+da+pG  +q+++ +d +G +  +c elcG +hs 
  gi|336252345|ref|YP_004595452.1| 123 DNGVETSGYGEGLVVPADQAVWIETTSRDVWHTFGIPDLRVKADAIPGEYDQTWFKADEPGNHTAKCFELCGPQHSD 199
                                       5555555566789***************************************************************9 PP

                              COX2 113 mp 114
                                       m 
  gi|336252345|ref|YP_004595452.1| 200 ML 201
                                       95 PP

>> DUF5048  Domain of unknown function (DUF5048)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.5e-06      0.02      15     101 ..     191     280 ..     183     281 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.5e-06
                           DUF5048  15 vlsGgeydnitsdekalerakyelWknarltdsitlel.lliPWldvnekikyaak...ksniavdwiikslelnla 87 
                                        l+G ++ ++ sd ++le++ ye W n +lt +itle     P  ++   +    +   +++    +     + ++ 
  gi|336252345|ref|YP_004595452.1| 191 ELCGPQHSDMLSDVTVLEQSAYEEWMNEQLTATITLEDgNESPVTEGF-EVTLEHQnnsDYDQDLSHTFTPDSEEFD 266
                                       567899999***************************984555554443.3433333213333344455555677888 PP

                           DUF5048  88 eGtmtvtlsrfyPl 101
                                       +Gt+tvtl r  P+
  gi|336252345|ref|YP_004595452.1| 267 NGTITVTLERGGPY 280
                                       88888888776665 PP

>> FixH  FixH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.06   2.2e+02       9      39 ..      19      50 ..      14      53 .. 0.75
   2 ?   11.0   0.1     9e-05      0.32      74     147 ..     221     295 ..     208     298 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.06
                              FixH  9 llflialfavvvvvnltmlylAvstkd.glvv 39
                                      l+fl +  +v +vv+++ ly+A++  d g v 
  gi|336252345|ref|YP_004595452.1| 19 LVFLGLGTLVGIVVVSYILYNAYKYRDtGEVG 50
                                      5666677788899**********999844444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9e-05
                              FixH  74 eltitlrdaagkp.veaaaltlslshptdagkDkklkLt....eaangvYrapleallkGrWyvqlaaeeggeawrl 145
                                       + titl d + +p  e+ ++tl   + +d ++D ++++t    e +ng+ +++le    G +++++  ++ ++++  
  gi|336252345|ref|YP_004595452.1| 221 TATITLEDGNESPvTEGFEVTLEHQNNSDYDQDLSHTFTpdseEFDNGTITVTLE--RGGPYDLTI--SPTDGQFEE 293
                                       6789998877777667777777777777777777788984444445556666555..6********..888888776 PP

                              FixH 146 qg 147
                                       ++
  gi|336252345|ref|YP_004595452.1| 294 VE 295
                                       65 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.2e-05      0.29      36      92 ..     134     189 ..      82     199 .. 0.85
   2 ?    1.0   0.0      0.13   4.5e+02      22      80 ..     221     284 ..     201     299 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.2e-05
                      Cupredoxin_1  36 kievkagekvklkiknkdktp.eefesedlgeekvlapgktttitiaplkpGeYeftc 92 
                                        + v+a++ v ++   ++  + ++f ++dl+++ +  pg+  + ++++++pG ++  c
  gi|336252345|ref|YP_004595452.1| 134 GLVVPADQAVWIET--TSRDVwHTFGIPDLRVKADAIPGEYDQTWFKADEPGNHTAKC 189
                                       57899999665555..555556******************************998777 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                      Cupredoxin_1  22 tveitvkdggfePskievkagekvklkiknkdkt.........peefesedlgeekvlapgktttiti 80 
                                       t +it++dg  +P    v +g +v+l+ +n+++          p + e+++  +  +l+ g  + +ti
  gi|336252345|ref|YP_004595452.1| 221 TATITLEDGNESP----VTEGFEVTLEHQNNSDYdqdlshtftPDSEEFDNGTITVTLERGGPYDLTI 284
                                       5666666665554....556666666666666654444333333333444455555555555555555 PP

>> UL2  UL2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       3.3   1.2e+04      37      48 ..      16      27 ..      13      31 .. 0.75
   2 ?   10.5   0.0   0.00013      0.46      11      50 ..      49      92 ..      48      99 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.3
                               UL2 37 siflimlviwta 48
                                       ifl+ l + t 
  gi|336252345|ref|YP_004595452.1| 16 GIFLVFLGLGTL 27
                                      699999877665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00013
                               UL2 11 vedddayPsfGslPashaqyGfrl.....lrsiflimlviwtavw 50
                                      v dd+  Ps G lP+   + G +l     l +i +i lv+wt   
  gi|336252345|ref|YP_004595452.1| 49 VGDDEDLPSVGELPTGG-KGGKKLflsfgLSAIIVISLVVWTYGM 92
                                      67999*********864.44555522333677999******9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 3010.59
//
Query:       gi|336252346|ref|YP_004595453.1|  [L=827]
Description: cytochrome c oxidase subunit I [Halopiger xanaduensis SH-6]
Scores for 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-124  415.7  77.8     2e-124  415.7  77.8    3.0  3  COX1      Cytochrome C and Quinol oxidase polypeptide I
    6.4e-20   72.1  20.4    6.4e-20   72.1  20.4    3.1  3  COX3      Cytochrome c oxidase subunit III


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.7  77.8  2.3e-128    2e-124       2     432 .]      22     466 ..      21     466 .. 0.98
   2 ?   -4.7  15.3       0.9     8e+03      76     211 ..     636     765 ..     571     770 .. 0.58
   3 ?   -3.9  10.5      0.53   4.7e+03       6      90 ..     728     819 ..     723     827 .] 0.70

  Alignments for each domain:
  == domain 1  score: 415.7 bits;  conditional E-value: 2.3e-128
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCTCT......-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS CS
                              COX1   2 igllylilalvlllvggllgllirlqlafp......dletynqlrtlHgnlmiflfatpfilgfgnylvplllgard 72 
                                       +g++y++++l++ll+gg+++ll+r++l++p      d  ++nq++t Hg lm+f+f+ pf++gf+ny+vpl++ga+d
  gi|336252346|ref|YP_004595453.1|  22 VGMMYIATSLFFLLFGGVMALLFRTHLWAPggigllDGMQFNQAVTTHGFLMVFWFLSPFATGFANYFVPLQIGAKD 98 
                                       89**************************9988877777*************************************** PP

                                       -S-HHHHHHHHHHHHHHHHHHHHHHH..CSS-STTTTTTTC.............SHHHHHHHHHHHHHHHHHHHHHH CS
                              COX1  73 lafprlnalsfwlvvlgvvllllsll..gaattgwteYapls............evdlwllglllvvvssllgainf 135
                                       lafprlna+s+w++++++vll +s++  +a++ gwt Yapl+            ++++ +l+l+l+ +s+++g +nf
  gi|336252346|ref|YP_004595453.1|  99 LAFPRLNAMSYWFYLFSGVLLSMSYFlgQAFAGGWTLYAPLNvptyttameaatGGNATILALVLFTISITMGTVNF 175
                                       *************************99888************************9999******************* PP

                                       HHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT.-SSSC..E-HHHHHHHHHHHHTHH CS
                              COX1 136 ivtilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrslg.kffsp..gdplldqhlfWffgHpe 209
                                       +vti++ ra+g+ ++++p+f+w++l t++++l+a+++l +allll +dr++  ++f +  g+ ll++hlfWffgHpe
  gi|336252346|ref|YP_004595453.1| 176 LVTIHRSRAEGLGLWNMPMFTWSWLLTVWMMLFAFAALLAALLLLAVDRTFLtQYFATneGSSLLWAHLFWFFGHPE 252
                                       ****************************************************9**96667***************** PP

                                       HHHHHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTHHHHHHCC CS
                              COX1 210 VyililpalgivyyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslliavPsglkv 286
                                       Vyi+++palgi+ +++ +f+gr+l++ k++++a++l+++ sflvw+HH+f + ++  +k+l++++++ i +P+ l v
  gi|336252346|ref|YP_004595453.1| 253 VYIVFFPALGIMFEVFQTFTGRRLVGRKWVIIAMVLVAVQSFLVWMHHMFLSTINLEIKTLMMATTIGISLPFDLMV 329
                                       ***************************************************************************** PP

                                       CHHHHCCTTS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHH CS
                              COX1 287 fnwlatlwrgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyll 363
                                       f++++t+++g++rf+tp+lf++g++vlfi+gG+tGv+l+++ ++y + +tywvvaHfH+v++ +v+ +l++++yy++
  gi|336252346|ref|YP_004595453.1| 330 FSLIYTMVKGRVRFTTPFLFAMGALVLFILGGITGVFLGAVVLDYEFRGTYWVVAHFHYVMVSGVT-ALVGGLYYWW 405
                                       **************************************************************9988.999******* PP

                                       HHHHSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHHHHHH CS
                              COX1 364 pkltgrmlserlaklhfwllfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrtiggvl 432
                                       pk+tg+m+se l+kl f ++fiG++l+++p+++++    prr+++y       + +q +++++t+g+++
  gi|336252346|ref|YP_004595453.1| 406 PKITGKMYSEALGKLNFAVYFIGFNLLYFPLFLAW--ETPRRVFEY------PEGYQLYHQVATVGAFI 466
                                       *********************************99..99******9......4699**********996 PP

  == domain 2  score: -4.7 bits;  conditional E-value: 0.9
                                       HHHHHHHHH....................HHHHHHHHHHHHHHCSS-STTTTTTTC.SHHHHHHHHHHHHHHHHH.H CS
                              COX1  76 prlnalsfw....................lvvlgvvllllsllgaattgwteYaplsevdlwllglllvvvssll.g 131
                                       p ++ +  w                    +v++g++++++ +  + ++gw ++       +   gl+ + v  +  +
  gi|336252346|ref|YP_004595453.1| 636 PTMAIAERWpfggvdnmkmgvwvflasdvVVFGGAIGAFIFM--RLHMGWGNWH---LDSITTAGLVNTYVLLTSsF 707
                                       444444444444444444444444456634444444444333..5899998888...66666777777766666434 PP

                                       HHHHHHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT-SSSCE-HHHHHHHHHHHHTH CS
                              COX1 132 ainfivtilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrslgkffspgdplldqhlfWffgHp 208
                                        ++++ ++++rr +  t +    +  +++at++l+l+++ v a++                g+   d h++W+ +  
  gi|336252346|ref|YP_004595453.1| 708 TVILALAYAERRDK--TKM----L-GSMVATVLLALVFMGVKAYEY---------------GAKFADGHYWWYSIEY 762
                                       44444445555544..222....2.334444444444333333332...............4555666666665555 PP

                                       HHH CS
                              COX1 209 eVy 211
                                        +y
  gi|336252346|ref|YP_004595453.1| 763 SIY 765
                                       555 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHHHHHHHHHHHHHCTCT.......-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS-S- CS
                              COX1   6 ylilalvlllvggllgllirlqlafp.......dletynqlrtlHgnlmiflfatpfilgfgnylvplllgardlaf 75 
                                       +++++l++l+++g+ +    +++a         +   y ++  lH+  +i++++++++++  ++ v ++l+ +  ++
  gi|336252346|ref|YP_004595453.1| 728 MVATVLLALVFMGVKAYEYGAKFADGhywwysiEYSIYFVTTGLHALHVILGVIIALFMIYRILSVDAYLEDHRPVE 804
                                       56667777777777777777777521222344567999999999999999999999999999999999998887777 PP

                                       HHHHHHHHH.HHHHHH CS
                              COX1  76 prlnalsfw.lvvlgv 90 
                                        +  +++f+ + v  +
  gi|336252346|ref|YP_004595453.1| 805 HFGLYWHFVdI-VWVF 819
                                       77887888742.3333 PP

>> COX3  Cytochrome c oxidase subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.8      0.67     6e+03     204     250 ..     160     208 ..     109     213 .. 0.57
   2 ?   -4.3   4.8       1.4   1.3e+04     132     168 ..     286     325 ..     237     409 .. 0.59
   3 !   72.1  20.4   7.1e-24   6.4e-20      75     255 ..     651     826 ..     644     827 .] 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHHHHHH.HHTT--BSSB-HHH.HHHHHHHHHHHHHHHHHH CS
                              COX3 204 hviigtillavallr.llkyhltknhhlGf.eaailywhfvdvvwlfly 250
                                        +++ ti +++ + + l++ h ++   lG+ ++ ++ w ++  vw++l+
  gi|336252346|ref|YP_004595453.1| 160 ALVLFTISITMGTVNfLVTIHRSRAEGLGLwNMPMFTWSWLLTVWMMLF 208
                                       3333333333333331234455555555532455556666666666665 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHHHHTT...BHHHHHHHHHHHHHHHH CS
                              COX3 132 iillssGvtvtyahhslieg...nrkkalkgllltillav 168
                                       ++l++    + + hh +++    + k+ + ++++ i l +
  gi|336252346|ref|YP_004595453.1| 286 MVLVAVQSFLVWMHHMFLSTinlEIKTLMMATTIGISLPF 325
                                       5666666667777776655310022333333333333322 PP

  == domain 3  score: 72.1 bits;  conditional E-value: 7.1e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--GGGTSSSS-TT-----TTSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                              COX3  75 GlklGlilfiisevllflalfwaffhsalsPtvelGatwpPvGikavnPlevPllntiillssGvtvtyahhslieg 151
                                        +k+G+ +f+ s+v++f +   af        + l + w    ++++      l+nt +ll+s  tv  a     ++
  gi|336252346|ref|YP_004595453.1| 651 NMKMGVWVFLASDVVVFGGAIGAFIF------MRLHMGWGNWHLDSITT--AGLVNTYVLLTSSFTVILALAYAERR 719
                                       689********************985......56677899998998865..569****************9999999 PP

                                       BHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-TTSHHH......HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                              COX3 152 nrkkalkgllltillavlftllqaveyleasftisdgvy......GsvfylatGlhglhviigtillavallrllky 222
                                       ++ k+l +++ t+lla++f++++a+ey  a f+  dg y       s+++++tGlh lhvi+g i+ ++ ++r+l+ 
  gi|336252346|ref|YP_004595453.1| 720 DKTKMLGSMVATVLLALVFMGVKAYEYG-AKFA--DGHYwwysieYSIYFVTTGLHALHVILGVIIALFMIYRILSV 793
                                       ***************************6.5564..4444222222699***************************** PP

                                       --BSSB-HHHHHHHHHHHHHHHHHHHHHHHTTT CS
                              COX3 223 hltknhhlGfeaailywhfvdvvwlflyvsvyw 255
                                           + h   e   lywhfvd+vw+fl+  +y 
  gi|336252346|ref|YP_004595453.1| 794 DAYLEDHRPVEHFGLYWHFVDIVWVFLFPLFYL 826
                                       ****************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (827 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); 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: 0.77u 0.29s 00:00:01.06 Elapsed: 00:00:00.44
# Mc/sec: 5610.06
//
Query:       gi|336252347|ref|YP_004595454.1|  [L=567]
Description: Subtilisin [Halopiger xanaduensis SH-6]
Scores for 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-47  160.7   2.8      1e-46  159.6   2.8    1.6  1  Peptidase_S8  Subtilase family
  ------ inclusion threshold ------
       0.23   11.4   0.0       0.38   10.7   0.0    1.2  1  Blo-t-5       Mite allergen Blo t 5
        1.5    8.9   4.7        1.2    9.2   0.1    2.7  2  TPPK_C        Thiamine pyrophosphokinase C terminal


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.6   2.8   1.7e-50     1e-46       1     298 []     205     482 ..     205     482 .. 0.86

  Alignments for each domain:
  == domain 1  score: 159.6 bits;  conditional E-value: 1.7e-50
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanap 77 
                                       g+gv vavlDtG++pshpdl+  td   +++ + +  +a+f++a    t+ +  +++ +    HGthv G++a++ +
  gi|336252347|ref|YP_004595454.1| 205 GEGVRVAVLDTGIEPSHPDLELYTDD--PSDPTYPGGWAEFDDAGQRVTDSRPHDTG-V----HGTHVSGTVAGS-A 273
                                       79*******************77776..56667888899999999999999999998.3....************.* PP

                                       SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  78 eegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsiealainravnkk 154
                                        +g++ gvap+a++l   v+++ +g+    +++++++e+a+ +++dvinmslg    ++++ + ie   i++a+  +
  gi|336252347|ref|YP_004595454.1| 274 ATGTAIGVAPEAELLHGLVMNETNGTF---AQILAGMEWALAEDADVINMSLG---TTGTYPQFIE--PIRNAN-LS 341
                                       ***************999999988887...99*********************...6666666777..999***.79 PP

                                       T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT-..-B-TT.................-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx..........xxxxxxxxx RF
                      Peptidase_S8 155 gvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfS..srGpssd..........gklkpdiva 219
                                       g +vv + GN+g         ++ g+p++  + ++vga+  +g +a fS  +r + +d              pd+va
  gi|336252347|ref|YP_004595454.1| 342 GAIVVGAIGNEG--------PETSGSPGNVYETLSVGAVAADGTVAAFSggERLNRTDweatpsdwpdAYTVPDVVA 410
                                       ************........5677****************666666666222333333333333333566789**** PP

                                       E-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE.......SSSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                      Peptidase_S8 220 pGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdl.gkadniesfaq 295
                                       pG++i+st++  +        y  m GTSmA+P++ag a ll+s  p+ tp++++++l  t q   g+++++++ ++
  gi|336252347|ref|YP_004595454.1| 411 PGVDIASTMPDGG--------YARMPGTSMAAPHVAGTAGLLRSIEPEATPADLSSVLTETTQRPaGDQKSAVETRY 479
                                       *************........************************************9888766569********** PP

                                       STT CS
                                       xxx RF
                      Peptidase_S8 296 GaG 298
                                       G G
  gi|336252347|ref|YP_004595454.1| 480 GTG 482
                                       *98 PP

>> Blo-t-5  Mite allergen Blo t 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.4e-05      0.38      59      95 ..     109     145 ..      97     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.4e-05
                                       HHHHHHHHHHHHHHHHHHHHTTSS---HHHHHHHHHH CS
                           Blo-t-5  59 reltialnfiegakgflerelkRtDLnllekfnfeaa 95 
                                       r +t+a++f  +    le +l+R DL+ +e+f   +a
  gi|336252347|ref|YP_004595454.1| 109 RGITVAEEFWVTNAVLLEVNLERVDLETFERFEAVEA 145
                                       789****************************975444 PP

>> TPPK_C  Thiamine pyrophosphokinase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.1       0.2   1.2e+03      22      38 ..      11      27 ..       8      38 .. 0.76
   2 ?    9.2   0.1    0.0002       1.2      14      39 ..     538     563 ..     535     566 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.2
                            TPPK_C 22 AaLvAvavallvspagq 38
                                      +++v+++v ll+ +ag 
  gi|336252347|ref|YP_004595454.1| 11 SGIVPIVVCLLLLSAGP 27
                                      67899999998888775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0002
                            TPPK_C  14 gallllvlAaLvAvavallvspagqs 39 
                                       g+l+ + lA++++++v+ ++s++g++
  gi|336252347|ref|YP_004595454.1| 538 GQLATVGLAVVLGLCVVTALSGSGRE 563
                                       789999******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 4366.97
//
Query:       gi|336252348|ref|YP_004595455.1|  [L=87]
Description: hypothetical protein Halxa_0940 [Halopiger xanaduensis SH-6]
Scores for 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-07   30.6  11.0      4e-07   30.4  11.0    1.1  1  COX4_pro  Prokaryotic Cytochrome C oxidase subunit IV
  ------ inclusion threshold ------
       0.26   11.5   0.4       0.26   11.5   0.4    1.5  2  DUF4793   Domain of unknown function (DUF4793)


Domain annotation for each model (and alignments):
>> COX4_pro  Prokaryotic Cytochrome C oxidase subunit IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4  11.0   4.4e-11     4e-07       2      71 ..       9      79 ..       8      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 4.4e-11
                          COX4_pro  2 ivfvlllilTaiefalviiklg.kllaiiiilvlalvKavlillyFMHLkeekkglrllaliflvflilll 71
                                      +++v+l++l +  f++ +++   + +a++  + l ++K +li+ y+ HL ee++++++++ + ++++ ll+
  gi|336252348|ref|YP_004595455.1|  9 LIYVALVALATGKFVFFHFDFFtYGMAMAGTMGLIVAKSLLIAGYYQHLVEEPRAITYMMGTAVFMVFLLT 79
                                      689**************9998898888888888*********************99999999998888876 PP

>> DUF4793  Domain of unknown function (DUF4793)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.2       1.3   1.2e+04      94     102 ..       7      15 ..       4      19 .. 0.54
   2 ?   11.5   0.4   2.9e-05      0.26      85     107 ..      57      79 ..      43      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                           DUF4793  94 Yivfvilvl 102
                                       Y +++++++
  gi|336252348|ref|YP_004595455.1|   7 YTLIYVALV 15 
                                       555555544 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.9e-05
                           DUF4793  85 lscepRvivYivfvilvlllill 107
                                       l  epR+i+Y+++++++++++l+
  gi|336252348|ref|YP_004595455.1|  57 LVEEPRAITYMMGTAVFMVFLLT 79 
                                       5669****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 720.35
//
Query:       gi|336252349|ref|YP_004595456.1|  [L=466]
Description: AAA ATPase [Halopiger xanaduensis SH-6]
Scores for 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-12   45.6   0.0      1e-11   45.0   0.0    1.4  1  AAA_14           AAA domain
    1.5e-06   28.4   0.0      3e-06   27.4   0.0    1.5  1  DUF4143          Domain of unknown function (DUF4143)
     0.0013   19.0   0.0     0.0034   17.7   0.0    1.5  1  AAA_19           AAA domain
     0.0026   17.4   0.0      0.022   14.3   0.0    2.3  2  AAA_25           AAA domain
     0.0041   15.8   0.0     0.0065   15.1   0.0    1.2  1  DUF853           Bacterial protein of unknown function (DUF85
     0.0045   16.9   0.0     0.0085   16.0   0.0    1.4  1  NACHT            NACHT domain
     0.0067   16.4   0.1      0.015   15.3   0.1    1.5  1  HTH_Mga          M protein trans-acting positive regulator (M
     0.0093   15.9   0.0      0.026   14.5   0.0    1.7  1  HTH_11           HTH domain
  ------ inclusion threshold ------
      0.013   15.2   0.0       0.03   14.0   0.0    1.5  1  AAA_30           AAA domain
      0.015   15.7   0.1      0.059   13.7   0.1    2.1  1  AAA_16           AAA ATPase domain
       0.04   13.4   0.0      0.068   12.7   0.0    1.3  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
      0.048   13.4   0.0       0.08   12.7   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.062   13.6   0.0       0.86    9.9   0.0    2.2  2  AAA_22           AAA domain
      0.071   12.3   0.0       0.12   11.5   0.0    1.3  1  NB-ARC           NB-ARC domain
      0.077   13.0   0.0       0.81    9.7   0.0    2.1  2  ResIII           Type III restriction enzyme, res subunit
        0.1   13.0   0.0       0.76   10.2   0.0    2.2  2  RNA_helicase     RNA helicase
       0.11   11.8   0.0        0.2   10.9   0.0    1.4  1  Zeta_toxin       Zeta toxin
       0.11   13.0   0.0       0.21   12.0   0.0    1.5  1  AAA              ATPase family associated with various cellul
       0.15   11.1   0.0       0.25   10.4   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
       0.15   11.9   0.0       0.36   10.7   0.0    1.6  1  RuvB_C           RuvB C-terminal winged helix domain
       0.19   11.0   0.0       0.35   10.2   0.0    1.3  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.23   10.7   0.0       0.37   10.0   0.0    1.4  1  DUF2075          Uncharacterized conserved protein (DUF2075)


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 !   45.0   0.0   1.3e-14     1e-11       2     113 ..      46     166 ..      45     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1.3e-14
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell....vkkesilyinldderd......kkladpe...kllelileklkeekk 65 
                                       ++ + i Ga  +GKTt l+q++++l+    +++++++y+ + d+r+         +  +   ++ +++ ++  e+++
  gi|336252349|ref|YP_004595456.1|  46 NRFVNIAGAAGSGKTTTLHQIADDLIseddIPPRNVMYLPVGDPRFqignevI--Q--DavdEFATYYWQRDAEPGT 118
                                       78899*******************99********************5443221..2..13347889999985556** PP

                            AAA_14  66 tylflDEiqevpewekalkslvdegknldvivtGSnskllskeiatsl 113
                                        y+f+D ++ + +w++ +++++de+++l + vt       s ++ ++l
  gi|336252349|ref|YP_004595456.1| 119 GYVFIDDAHALGSWSDQVRDCLDEYDDLTIAVTLPTVARASTDAIEEL 166
                                       *************************99999999666666666655555 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   3.7e-09     3e-06       3     117 ..     264     412 ..     234     412 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3.7e-09
                                       xxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143   3 Dirklagvrdpeelrk.................................glverlppwsespnskkrlrkspKlyfv 46 
                                       D++++++ +d ++l+                                   ++e  +  ++s + k++ ++s +ly+ 
  gi|336252349|ref|YP_004595456.1| 264 DVPRYQQFDDRSDLHAlcavaamypghtlglknlselldcdrrtlqryiDILEDFFILTPSYQYKHERKRSVRLYLR 340
                                       555555555555555566666666666666666666666777777766633444444444567799*********** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  47 DtGLlvallgldkeelledsenkGallEnlVaqeLlky...sekegaklyyyrdkngaEvDfvielkggkivpi 117
                                       D+ Ll all+ld + ll ++  + +l+ ++++ +L +    ++  +  + ++++     vDfv+e+++g+ +pi
  gi|336252349|ref|YP_004595456.1| 341 DPVLLGALLDLDFDGLLPTQ-VEDNLISTVIFDHLKRLgfrYQDTNSPVGFWESG-DVDVDFVLETGEGTPIPI 412
                                       ***************88876.99*************99**97777********95.7********998888887 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.2e-06    0.0034       9      48 ..      45      84 ..      40      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.2e-06
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillv 48
                                      +++ + + + +G+GKT++l++i   l+++ +++p++++ +
  gi|336252349|ref|YP_004595456.1| 45 NNRFVNIAGAAGSGKTTTLHQIADDLISEDDIPPRNVMYL 84
                                      6788999**************************9998865 PP

>> AAA_25  AAA 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     0.022      12      85 ..      24      92 ..      15     147 .. 0.80
   2 ?   -0.1   0.0      0.71   5.8e+02     122     157 ..     345     380 ..     304     389 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                            AAA_25 12 vadlaapppprrwlvk.gllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsede 85
                                      vad   p ++ ++ +k + ++ + ++ +aGa g+GKtt + ++a ++ + +         +++V+y+   d++ +
  gi|336252349|ref|YP_004595456.1| 24 VADRYEPKRRSDYNYKlRRVRNNRFVNIAGAAGSGKTTTLHQIADDLISEDDI------PPRNVMYLPVGDPRFQ 92
                                      555555666666666666778899***********************988855......4679999888777755 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.71
                            AAA_25 122 ggtlltadvdaleaaieevegvrlvviDplsralgg 157
                                        g+ll+ d+d l  +  e + +  v++D l+r+   
  gi|336252349|ref|YP_004595456.1| 345 LGALLDLDFDGLLPTQVEDNLISTVIFDHLKRLGFR 380
                                       355688889998877666567*********997655 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.9e-06    0.0065      11      45 ..      36      70 ..      27      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.9e-06
                            DUF853 11 qelalalklanrhGliaGatGtGktvtLqvlaesl 45
                                       + +l+    nr   iaGa+G Gkt tL+++a+ l
  gi|336252349|ref|YP_004595456.1| 36 YNYKLRRVRNNRFVNIAGAAGSGKTTTLHQIADDL 70
                                      5566777789**********************987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     1e-05    0.0085       2      28 ..      48      74 ..      47      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegk 28
                                       v + G+aGsGKTt l+++a+++ +++
  gi|336252349|ref|YP_004595456.1| 48 FVNIAGAAGSGKTTTLHQIADDLISED 74
                                      57799****************987765 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 !   15.3   0.1   1.9e-05     0.015      21      49 ..     292     320 ..     290     324 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                           HTH_Mga  21 ltldelakeLglseltlqsdiseLnelFp 49 
                                       l+l+ l++ L++ ++tlq +i+ L ++F+
  gi|336252349|ref|YP_004595456.1| 292 LGLKNLSELLDCDRRTLQRYIDILEDFFI 320
                                       789************************95 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.2e-05     0.026      19      42 ..     295     318 ..     288     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
                            HTH_11  19 eeLAeeLnvSrrtvrrdIkaLeel 42 
                                       + L+e L++ rrt +r+I++Le+ 
  gi|336252349|ref|YP_004595456.1| 295 KNLSELLDCDRRTLQRYIDILEDF 318
                                       789******************986 PP

>> AAA_30  AAA 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      0.03      17      40 ..      45      68 ..      40      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalre 40
                                      ++r++ + G+AG+GKtt+l ++++
  gi|336252349|ref|YP_004595456.1| 45 NNRFVNIAGAAGSGKTTTLHQIAD 68
                                      457999*************99964 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   7.3e-05     0.059      16      52 ..      40      80 ..      37     235 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.3e-05
                            AAA_16 16 lervrsgrpelvllsGesGvGKsslvrellralekd......g 52
                                      l+rvr +  + v + G++G+GK++ + ++++ l  +      +
  gi|336252349|ref|YP_004595456.1| 40 LRRVRNN--RFVNIAGAAGSGKTTTLHQIADDLISEddipprN 80
                                      5677777..68999***************98766554444432 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 ?   12.7   0.0   8.4e-05     0.068      17      49 ..      50      82 ..      40      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.4e-05
                                      EEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEE CS
                     UvrD-helicase 17 lveAsAGsGKTfvlaerilrlikeeeiepdril 49
                                       ++ +AGsGKT++l +    li e  i p++++
  gi|336252349|ref|YP_004595456.1| 50 NIAGAAGSGKTTTLHQIADDLISEDDIPPRNVM 82
                                      58899*******************999999876 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 ?   12.7   0.0   9.8e-05      0.08       3      35 ..      51      83 ..      49     130 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.8e-05
                   Viral_helicase1  3 vhGvpGcGKStlirkllrtsliltvnrptaell 35
                                      ++G++G+GK+t + +++++  +   ++p+++++
  gi|336252349|ref|YP_004595456.1| 51 IAGAAGSGKTTTLHQIADDLISEDDIPPRNVMY 83
                                      79***************9942223455555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0011      0.86       4      29 ..      45      70 ..      41      88 .. 0.82
   2 ?    0.9   0.0      0.64   5.2e+02      92     114 ..     118     141 ..      95     163 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      + +++ + G +G+GKTt+l ++++ l
  gi|336252349|ref|YP_004595456.1| 45 NNRFVNIAGAAGSGKTTTLHQIADDL 70
                                      67888899***********9998876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.64
                            AAA_22  92 ielliiDEaqhlrs.eealeeLrs 114
                                       ++ + iD+a+ l s  ++++++ +
  gi|336252349|ref|YP_004595456.1| 118 TGYVFIDDAHALGSwSDQVRDCLD 141
                                       57899******9425444444433 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.12      17      43 ..      45      69 ..      36      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                      TSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqilnk 43
                                      +    +v + G +G+GKtt ++qi  +
  gi|336252349|ref|YP_004595456.1| 45 NNR--FVNIAGAAGSGKTTTLHQIADD 69
                                      444..9******************987 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 ?    9.7   0.0   0.00099      0.81      23      52 ..      44      74 ..      23      86 .. 0.79
   2 ?    0.8   0.0      0.53   4.3e+02     134     155 ..     116     141 ..      91     152 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00099
                                      TTSEEE.EEESTTSTHHHHHHHHHHHH-S.. CS
                            ResIII 23 rdkrgl.ikmaTGtGKTlvaaklierllkkg 52
                                      r++r++ i+ a G+GKT ++ ++++ l ++ 
  gi|336252349|ref|YP_004595456.1| 44 RNNRFVnIAGAAGSGKTTTLHQIADDLISED 74
                                      5556666****************99998765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.53
                                       S...EEEEETGGGTTS..TTTHHHHH CS
                            ResIII 134 d...viiiDEaHrlgak.kswreile 155
                                       +   +++iD aH lg+  +++r +l+
  gi|336252349|ref|YP_004595456.1| 116 PgtgYVFIDDAHALGSWsDQVRDCLD 141
                                       244499******99985235555544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00093      0.76       3      36 ..      51      84 ..      49      94 .. 0.83
   2 ?   -0.5   0.0         2   1.6e+03      51      81 ..     258     288 ..     250     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00093
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvys 36
                                      + G++g GK+t+ +++a++l ++ + + ++ +y 
  gi|336252349|ref|YP_004595456.1| 51 IAGAAGSGKTTTLHQIADDLISEDDIPPRNVMYL 84
                                      78******************98887777666664 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2
                      RNA_helicase  51 evvvidDfgqvkdeenpsdlaelirlvsstp 81 
                                       e +v+ D+++ ++  + sdl+ l+ ++ ++p
  gi|336252349|ref|YP_004595456.1| 258 ELTVYRDVPRYQQFDDRSDLHALCAVAAMYP 288
                                       67899*****99776788***9999998887 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   0.00024       0.2      18      43 ..      48      73 ..      33      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerq 43
                                       + ++G+ G+GK+++++ ++d+l ++
  gi|336252349|ref|YP_004595456.1| 48 FVNIAGAAGSGKTTTLHQIADDLISE 73
                                      6779****************998655 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 ?   12.0   0.0   0.00026      0.21       3      74 ..      51     133 ..      49     152 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                                       EESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCS..SSSTTHHHHHHHHHHHHHHHTS..TSEEEEEET CS
                               AAA   3 lyGppGtGKTllakavakel.........gvefleisgsell..skyvgesekkirelfkeakeka..kpsilfiDE 66 
                                       + G  G GKT++ +++a +l         +v +l +  +++   +++++++ ++++ +  +  + a  ++  +fiD+
  gi|336252349|ref|YP_004595456.1|  51 IAGAAGSGKTTTLHQIADDLiseddipprNVMYLPVGDPRFQigNEVIQDAVDEFATYYWQ--RDAepGTGYVFIDD 125
                                       67999**************977665553334455555554443344555555555555443..222345699***** PP

                                       GGGHHHHH CS
                               AAA  67 idalaksr 74 
                                       ++al++ +
  gi|336252349|ref|YP_004595456.1| 126 AHALGSWS 133
                                       ***98755 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 ?   10.4   0.0   0.00031      0.25     117     152 ..      35      69 ..      23      77 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                             T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyallke 152
                                       +++  lr+  r++  + ++G+ gsGKtt+l  +   
  gi|336252349|ref|YP_004595456.1|  35 DYNYKLRRV-RNNRFVNIAGAAGSGKTTTLHQIADD 69 
                                       556666665.8888899*************877655 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 ?   10.7   0.0   0.00045      0.36       6      44 ..     274     312 ..     273     322 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTT CS
                            RuvB_C   6 eldikyLkllkekfkggpvglktlaailgeeketiedvi 44 
                                       + d + L +++  + g+++glk+l+++l+ ++ t++  i
  gi|336252349|ref|YP_004595456.1| 274 RSDLHALCAVAAMYPGHTLGLKNLSELLDCDRRTLQRYI 312
                                       679999999*************************98765 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00042      0.35      41      58 ..      48      65 ..       6      73 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                                      SEEEE--TTSSHHHHHHH CS
                      FtsK_SpoIIIE 41 hllvaGatgsGKStalnt 58
                                       + +aGa gsGK+t+l+ 
  gi|336252349|ref|YP_004595456.1| 48 FVNIAGAAGSGKTTTLHQ 65
                                      4669************97 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00046      0.37       4      45 ..      49      92 ..      46     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
                           DUF2075  4 vlVtGvaGtGKtvvllnllael..eddeeertavylsvNhplvl 45
                                      v + G+aG+GKt  l +++ +l  edd   r++ yl v  p  +
  gi|336252349|ref|YP_004595456.1| 49 VNIAGAAGSGKTTTLHQIADDLisEDDIPPRNVMYLPVGDPRFQ 92
                                      5699******************7666666667777766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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):              22  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3275.31
//
Query:       gi|336252350|ref|YP_004595457.1|  [L=404]
Description: metallophosphoesterase [Halopiger xanaduensis SH-6]
Scores for 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-14   52.6   0.6    1.4e-13   51.9   0.6    1.4  1  Metallophos     Calcineurin-like phosphoesterase
    6.2e-08   33.0   5.7    6.5e-08   32.9   2.1    2.4  2  Metallophos_2   Calcineurin-like phosphoesterase superfamily 
  ------ inclusion threshold ------
      0.027   14.6   0.2        0.3   11.3   0.0    2.2  2  HGTP_anticodon  Anticodon binding domain


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 !   51.9   0.6   2.3e-17   1.4e-13       2     168 ..       8     176 ..       7     206 .. 0.59

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 2.3e-17
                                       EEEEEESBTB........TTCCTHHHHHHHHHHHH......HHHTTESEEEEESTSSSSS.....HHHHHHHHHHHH CS
                       Metallophos   2 rilvigDlHl........algggqlddllkllddl......lreekpdlvllaGDlvdrg.....dlekellellaa 59 
                                       ril+++D+H+        ++++  +d+++++l+ +      +++e +d+vl++GDl+d+      d+   +   l++
  gi|336252350|ref|YP_004595457.1|   8 RILHVSDTHIgyeqyrnpSRREDFFDAFEQALEIArgehpdHDNEPVDAVLHTGDLFDDQltsfdDVYA-CHAALRE 83 
                                       8**********999999999999999999999888555444444888************9996633333.4444566 PP

                                       HHHHTSEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE....EEEEEEESECEEETHHHH CS
                       Metallophos  60 lvkypipvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgs....lkvlllhGgspellvsld 132
                                       l + +ip+y++ GNHe       +  ++  +f       a + +++ l+          ++ + l+G    ++v+ +
  gi|336252350|ref|YP_004595457.1|  84 LREAGIPFYVIVGNHE-I----RRNTDFVDEF-------ALTSDAIRLSR----AptsiNDEVALYGI---DSVKKS 141
                                       6666************.2....2221211111.......11112222222....01122344444444...245666 PP

                                       HHHHHHHSCHHHHCC.......HHHHHHHHHHTTCSEEEEEES CS
                       Metallophos 133 klgslnleleapepg.......dewlkdlekrekadwvivlgH 168
                                       ++++ +l le++++g       +++++         ++  +gH
  gi|336252350|ref|YP_004595457.1| 142 DWEGADLTLEPSDDGqfrlvamHQLFSP--------PIDEIGH 176
                                       7777777777777666665444444444........4444443 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 !   32.9   2.1   1.1e-11   6.5e-08       2     162 ..       8     239 ..       8     242 .. 0.64
   2 ?    0.2   0.1      0.13   7.7e+02      46      89 ..     318     357 ..     302     397 .. 0.60

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.1e-11
                     Metallophos_2   2 klaiiSDlH.............snldaleav.......lealkevgvdaiihaGDl...eeeep....evleellel 51 
                                       +++++SD+H             + +da e++         +++++ vda++h+GDl   + +++     ++++l+el
  gi|336252350|ref|YP_004595457.1|   8 RILHVSDTHigyeqyrnpsrreDFFDAFEQAleiargeHPDHDNEPVDAVLHTGDLfddQLTSFddvyACHAALREL 84 
                                       699************999999844555555533334444445566699*******7544334444444244444444 PP

                     Metallophos_2  52 a....pvlaVrGNnD...............eevveedvlreaaelgtdl..............peeaelel.....a 90 
                                       +    p++++ GN++               +   + +++r+++ +++++               ++ +  l     +
  gi|336252350|ref|YP_004595457.1|  85 ReagiPFYVIVGNHEirrntdfvdefaltsD---AIRLSRAPTSINDEValygidsvkksdweGADLT--LepsddG 156
                                       4666***********6666655544433321...2233333333333335566666665543223334..3335333 PP

                     Metallophos_2  91 gekvlliHgdpl............gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe 155
                                       ++++  +H+  l            +   +l+++l++   ++d +++G  H++  ++++gv v +PGs ++   + p+
  gi|336252350|ref|YP_004595457.1| 157 QFRLVAMHQ--LfsppideighddSNILDLEPVLDRFGTDVDAIALGDCHERMGDTCRGVPVWYPGSTERTTRDTPQ 231
                                       333444444..357999**99887777788888888888899**************************998555444 PP

                     Metallophos_2 156 .tyaildt 162
                                        ++ +l++
  gi|336252350|ref|YP_004595457.1| 232 pSVDLLTI 239
                                       47666665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.13
                     Metallophos_2  46 eellelapvlaVrGNnDeevveedvlreaaelgtdlp.eeaelel 89 
                                       +++ + + v+a+ G+ De++     ++++ +++ +l+ + +ele+
  gi|336252350|ref|YP_004595457.1| 318 ADVSDERVVEAITGDLDEID-----GESEIDVDAELQsAVDELEI 357
                                       55555567899999999222.....33333333333223333333 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.1e-05       0.3      44      68 ..      80     104 ..      71     122 .. 0.84
   2 ?    0.5   0.1      0.11   6.7e+02      13      46 ..     356     389 ..     347     395 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.1e-05
                                       HHHHHHHTT-SEEEEE-HHHHHHTE CS
                    HGTP_anticodon  44 kireadllgipfavvvGekelekgt 68 
                                       ++re +++gipf v+vG+ e++++t
  gi|336252350|ref|YP_004595457.1|  80 ALRELREAGIPFYVIVGNHEIRRNT 104
                                       78999****************8877 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHH CS
                    HGTP_anticodon  13 eleeyakklaeeLraagirvelddsnesigkkir 46 
                                       e+ ++a++l + Lr+a+ +     + ++ +++++
  gi|336252350|ref|YP_004595457.1| 356 EISDEARELEDILRNADPDLANTRRRGNAKERFQ 389
                                       68899**********9944333335566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2822.65
//
Query:       gi|336252351|ref|YP_004595458.1|  [L=1058]
Description: SMC domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-17   62.3  18.2    8.6e-17   62.3  18.2    8.1  1  AAA_23          AAA domain
    1.4e-10   41.5   2.6    1.4e-10   41.5   2.6    4.2  1  AAA_15          AAA ATPase domain
      2e-09   36.8 128.5     0.0013   17.7  13.4    6.9  7  Spc7            Spc7 kinetochore protein
    1.1e-07   31.6   0.2    1.1e-07   31.6   0.2    6.6  9  AAA_27          AAA domain
    2.3e-07   30.6 111.5     0.0039   16.8  22.6    7.0  7  MscS_porin      Mechanosensitive ion channel porin domain
    4.1e-07   29.6   0.0    8.1e-07   28.7   0.0    1.5  1  AAA_29          P-loop containing region of AAA domain
    4.7e-07   30.0   0.0    1.5e-06   28.3   0.0    1.9  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
    7.5e-07   29.3 142.2     0.0003   20.9   8.7   10.4  9  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
      4e-05   23.8  91.9       0.13   12.5   1.8    9.1 10  FliJ            Flagellar FliJ protein
    0.00018   20.7  87.5      0.041   13.0   9.2    7.0  6  Atg14           Vacuolar sorting 38 and autophagy-related sub
    0.00028   19.7  99.7     0.0091   14.7  10.8    6.3  6  AAA_13          AAA domain
    0.00034   20.7  11.0    0.00034   20.7  11.0    8.2  7  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
    0.00035   20.2  62.8       0.02   14.4   2.8    5.4  2  Exonuc_VII_L    Exonuclease VII, large subunit
    0.00071   19.5   9.1    0.00071   19.5   9.1   13.6 12  Prefoldin_2     Prefoldin subunit
     0.0017   18.0 123.0       0.15   11.7   9.0    7.7  6  Filament        Intermediate filament protein
     0.0029   17.8   2.3     0.0029   17.8   2.3    8.4  7  Fib_alpha       Fibrinogen alpha/beta chain family
     0.0033   17.3   1.9      0.018   14.8   0.0    3.2  2  MukB            MukB N-terminal
      0.004   15.4 100.7      0.072   11.3  13.2    6.4  5  EzrA            Septation ring formation regulator, EzrA
      0.004   17.0   1.8      0.004   17.0   1.8    3.9  3  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
     0.0082   16.1   0.3      0.058   13.3   0.0    2.7  1  RsgA_GTPase     RsgA GTPase
  ------ inclusion threshold ------
      0.021   15.2   0.4       0.47   10.9   0.0    2.8  2  RNA_helicase    RNA helicase
      0.021   14.3   0.3      0.021   14.3   0.3    6.9  8  Allexi_40kDa    Allexivirus 40kDa protein
      0.025   14.9   0.0      0.025   14.9   0.0    4.6  2  V-SNARE_C       Snare region anchored in the vesicle membrane
      0.037   13.4 114.1      0.079   12.3  17.5    6.1  6  DUF4407         Domain of unknown function (DUF4407)
       0.16   11.8  96.2      0.027   14.3  11.3    7.8  8  DUF724          Protein of unknown function (DUF724)
       0.26   11.6   0.0       0.26   11.6   0.0    4.8  2  AAA_22          AAA domain
        0.4   11.1   0.0        0.4   11.1   0.0    4.5  3  AAA             ATPase family associated with various cellula
       0.47   10.6   0.0       0.47   10.6   0.0    5.4  7  AAA_33          AAA domain
       0.61    9.4 110.1      0.072   12.4   4.0    8.4  8  DUF3450         Protein of unknown function (DUF3450)
       0.61    8.3   5.8       0.17   10.1   0.6    2.7  3  Fusion_gly      Fusion glycoprotein F0
       0.74    9.9  39.9      0.087   12.9   4.0    8.6  8  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
        1.3    9.5 112.8       0.67   10.4  16.6    7.2  8  Fez1            Fez1
        1.7    8.7  74.3      0.014   15.4   5.1    8.6  9  Laminin_II      Laminin Domain II
        2.9    7.2 103.6      0.067   12.5   8.5    7.4  7  GAS             Growth-arrest specific micro-tubule binding
        4.1    7.4  74.7        0.7    9.9   7.2    9.7  9  DUF1664         Protein of unknown function (DUF1664)
        4.9    7.7  38.4     0.0078   16.7  11.3    6.6  1  ABC_tran        ABC transporter
        7.4    6.3  86.4        1.4    8.6   2.8    8.5  6  DUF4201         Domain of unknown function (DUF4201)


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 !   62.3  18.2   1.8e-19   8.6e-17       1     200 []       5     289 ..       5     310 .. 0.71

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 1.8e-19
                            AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdve.iesegkvkayve 76 
                                       +L+++ f+s+++ ++ F++gltl++GpNGaGK+Ti +A+   Ly     l++  + ++  +d + + ++gk++a  +
  gi|336252351|ref|YP_004595458.1|   5 RLSLSDFQSYDNLDVTFDDGLTLLHGPNGAGKSTITRALYTTLYP----LNG--KYKIGAHDLAdLIQDGKDSATST 75 
                                       799*****************************************7....444..344555555545566899999** PP

                            AAA_23  77 ltfenkdgrytrsiererelskkkgkttkka.......klelleideleqfisellgskkiilnlilflgqer.... 142
                                       l f+  d+ry  +i+ +++++ +   + + +       ++ +++ +e e+++s+l+g + + + ++ + +q +    
  gi|336252351|ref|YP_004595458.1|  76 LVFSVGDERY--RITVDISRKGDGRASANAEmtnleseETYSTKSSEIEEKVSQLFGMDAEAFANSTYAQQTEltrl 150
                                       *****99996..555555554443322211122221113334444999*************9999999999997777 PP

                            AAA_23 143 ............................feefelkdkke...................................... 153
                                                                   +         e                                      
  gi|336252351|ref|YP_004595458.1| 151 ieatpgeredildnllgltapdayeediN---------Emqktveswqqdkrsklqtvqedieeleaddpkatvqsk 218
                                       77666666666666666666666554441.........033334455555555555777777778888888888888 PP

                            AAA_23 154 .......................rleelekeleeledekkllekl.eqekekekeleeleeeleeilkele 200
                                                              rl+++e ++ee  ++++ l +l  ++ e ++++++l++e+ e++ e++
  gi|336252351|ref|YP_004595458.1| 219 aeeiddlearigdlsdgledgreRLRAIESDIEEYRERESDLSDLtDERDEAKDTIDDLQSEIDELEAEIQ 289
                                       88888888888888888888888777777777777777777777754556666667777777766666664 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   2.6   2.8e-13   1.4e-10       1     288 [.       1     383 [.       1     495 [. 0.55

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.8e-13
                            AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn....................... 54 
                                       Mk +++++  F s+++ ++ +++ lt+l G+N++GKS+i++al+  l      n                       
  gi|336252351|ref|YP_004595458.1|   1 MKFERLSLSDFQSYDNLDVTFDDGLTLLHGPNGAGKSTITRALYTTLYPL---Ngkykigahdladliqdgkdsats 74 
                                       99999**************************************8776654...4445678999*9999999999999 PP

                            AAA_15  55 ............................kkvikiekedleifeniseskdikIdvef.................... 83 
                                                                        ++ e+ e++  +s +++ k+   f                    
  gi|336252351|ref|YP_004595458.1|  75 tlvfsvgderyritvdisrkgdgrasanA--EMTNLESEETYSTKSSEIEEKVSQLFgmdaeafanstyaqqteltr 149
                                       99999999999999999999999888542..4444444444445677777777777788888887777655555555 PP

                            AAA_15  84 ......................aekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisv 138
                                                             +                               ++   ++++k  ++  +d++ ++
  gi|336252351|ref|YP_004595458.1| 150 lieatpgeredildnllgltapD------------------------------AYEEDINEMQKTVESWQQDKRSKL 196
                                       55555554444444444433330..............................333333333333333333333333 PP

                            AAA_15 139 ekkkskkelpkekeeklekekeelkid..kedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsek 213
                                       +  ++  e  +  + k++ +++  +id     + +l++ le   +        ++s i++++  +++ +  +++ ++
  gi|336252351|ref|YP_004595458.1| 197 QTVQEDIEELEADDPKATVQSKAEEIDdlEARIGDLSDGLEDGRERLR----AIESDIEEYRERESDLSDLTDERDE 269
                                       333333332222222222222222222222222222222222222222....2222222222222222222222222 PP

                            AAA_15 214 kssllgklkekileealqekl............................eeelteklkeiqeklkeidkklaeelk. 261
                                        +++++ l+++i e  + e                              e+e +e+ +e+++k++e++++++++ + 
  gi|336252351|ref|YP_004595458.1| 270 AKDTIDDLQSEIDELEA-E-IqecdeaiakqreriesrddevvdfdltnEDEAKEAVEEFETKYDEASSEVEQRRAe 344
                                       22222222222222111.1.112222233333355666666666666666666666666666666666666666555 PP

                            AAA_15 262 .kilkkkidkikkfnykgkkneeieik...........d 288
                                        ++ ++ ++ ++++   + ++ e+  +            
  gi|336252351|ref|YP_004595458.1| 345 vDSAEDTVERLEDELQSQREELEDAQNrlhareadveaA 383
                                       544444444444222222222221111233333333332 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6  16.5    0.0002     0.096     142     261 ..     179     299 ..     172     301 .. 0.64
   2 !   10.5  19.9    0.0004      0.19     152     259 ..     268     375 ..     260     378 .. 0.92
   3 !   11.6  10.6   0.00019      0.09     155     253 ..     377     479 ..     372     485 .. 0.90
   4 ?   -3.1   0.1       5.6   2.7e+03     198     218 ..     533     553 ..     518     557 .. 0.49
   5 !   13.5  15.9     5e-05     0.024     154     266 ..     577     690 ..     570     691 .. 0.88
   6 !   17.7  13.4   2.7e-06    0.0013     194     265 ..     685     758 ..     674     771 .. 0.79
   7 ?    1.9  25.3      0.17        82     159     283 ..     764     884 ..     754     907 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                              Spc7 142 egleenlegleedk.elLekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelaelkaeie 216
                                       +++++++e+ ++dk ++L+  +e ++el    +  ka++++++e++ + ++ +   d ++ Le  re+l++++++ie
  gi|336252351|ref|YP_004595458.1| 179 NEMQKTVESWQQDKrSKLQTVQEDIEELE--ADDPKATVQSKAEEIDDLEARIG--DlSDGLEDGRERLRAIESDIE 251
                                       34455555555554134555555555543..23334444444444444333333..347899999999999999888 PP

                              Spc7 217 e...kkkelaelqeqleeleekieelkeqkseleeeiaeaervleeck 261
                                       e   ++ +l++l+++++e +++i++l+++++ele+ei+e ++ + +++
  gi|336252351|ref|YP_004595458.1| 252 EyreRESDLSDLTDERDEAKDTIDDLQSEIDELEAEIQECDEAIAKQR 299
                                       621155678999999999999999999999999999999988888877 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0004
                              Spc7 152 eedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeq 228
                                       +e k+++++ ++e+del  e++e  +++ ++ e+++++ +e+ + d ++  e++e+++e +++++e + e+++++++
  gi|336252351|ref|YP_004595458.1| 268 DEAKDTIDDLQSEIDELEAEIQECDEAIAKQRERIESRDDEVVDFDLTNEDEAKEAVEEFETKYDEASSEVEQRRAE 344
                                       5677889999999**************************************************************** PP

                              Spc7 229 leeleekieelkeqkseleeeiaeaervlee 259
                                       +++ e+++e l+++ ++ +ee++ a++ l++
  gi|336252351|ref|YP_004595458.1| 345 VDSAEDTVERLEDELQSQREELEDAQNRLHA 375
                                       ************************9988765 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00019
                              Spc7 155 kelLekqeeeldellpeleeekaeleeeleklqe....aaeelesidkeeLeelreelaelkaeieekkkelaelqe 227
                                       ++ +e+ ee l e++++le++++ lee+l++  e     ++++e+  ++++  +ree ++ +ae+e+k+++ a+l +
  gi|336252351|ref|YP_004595458.1| 377 EADVEAAEETLGEAKDSLEQRREILEEQLQDYLEtpldDVDDHEAAVRDRMDDIREEKSDREAEYESKRDRRARLGD 453
                                       67889999999999999999999999999887766888899999999****************************** PP

                              Spc7 228 qleeleekieelkeqkseleeeiaea 253
                                       +++++e++++e++e++++++e ++ a
  gi|336252351|ref|YP_004595458.1| 454 EIDTIESELSEVRERRDDIRESLETA 479
                                       *******************9999876 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 5.6
                              Spc7 198 keeLeelreelaelkaeieek 218
                                        eeL+ +re++ e+ a ie +
  gi|336252351|ref|YP_004595458.1| 533 AEELADARETVGEATAHIEDL 553
                                       445555555555555444433 PP

  == domain 5  score: 13.5 bits;  conditional E-value: 5e-05
                              Spc7 154 dkelLekqeeeldellpeleeekaeleeeleklqeaaeel.esidkeeLeelreelaelkaeieekkkelaelqeql 229
                                       + ++Le+++ee++++ ++     ++  e+l++ qe a+ l e+   + L+ +  e+++l+aeie+k++  +elq+++
  gi|336252351|ref|YP_004595458.1| 577 QIQRLESEREEAETAADAAIDTLDAADERLNHVQEVADALfEAASFKALADVAIEIDDLEAEIEQKQQTRSELQDEM 653
                                       55789999999999999999999999*********877751556699****************************** PP

                              Spc7 230 eeleekieelkeqkseleeeiaeaervleeckgwses 266
                                       e+lee+i+ l+e ++e e+++   e+v +++  ++e 
  gi|336252351|ref|YP_004595458.1| 654 ESLEEEISRLEEAIAEGETALDTIEDVEDAETAVDEA 690
                                       ********************99999998887777665 PP

  == domain 6  score: 17.7 bits;  conditional E-value: 2.7e-06
                              Spc7 194 esid..keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwse 265
                                       +++d  + eLe +r+ela++k+ei e+++e+++ +++l++ +e+++++++  +e+ee++ e e+ + + ++ ++
  gi|336252351|ref|YP_004595458.1| 685 TAVDeaERELEDARDELADIKEEIGELEAEIEDIESDLDDAREDVKDAEADLQEAEEQLDEVESARSAAREARD 758
                                       333333789***************************************************99999988887643 PP

  == domain 7  score: 1.9 bits;  conditional E-value: 0.17
                              Spc7 159 ekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleek 235
                                       +  e+  + +  +l+ +++++ ++ e+lq+ ++e+e+++++   +  ++l+e+++e e   + ++++++qle+ +e+
  gi|336252351|ref|YP_004595458.1| 764 ATLESDQKGYRSRLDDKEEQVASKREELQQIEDEIEEVESDLEDTSPDDLKEQQNETE---TLIEQVESQLEDAQER 837
                                       4555555666777777777788888888887777777776655555677777777777...7777777777777777 PP

                              Spc7 236 ieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltg 283
                                        +e+++ ks++ee++++ ++ + e+k + e++v+  ++ ++++e +t+
  gi|336252351|ref|YP_004595458.1| 838 RDEARDAKSKAEERLNRLRDKR-ERKASLEEQVNWAQTLLNDFETITK 884
                                       7777777777777777555444.4566666667766666666666654 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.2   2.3e-10   1.1e-07       1      56 [.       1      53 [.       1     217 [. 0.88
   2 ?   -1.6   0.1       3.5   1.7e+03     159     196 ..     271     308 ..     239     326 .. 0.67
   3 ?   -1.8   1.6       3.9   1.9e+03     157     180 ..     358     381 ..     320     405 .. 0.54
   4 ?   -0.8   0.2         2   9.5e+02     138     203 ..     526     591 ..     516     595 .. 0.76
   5 ?    6.2   1.4     0.014       6.9     138     198 ..     606     668 ..     597     676 .. 0.62
   6 ?    0.8   0.9      0.62     3e+02     146     201 ..     692     747 ..     682     757 .. 0.74
   7 ?   -1.8   0.3       4.1     2e+03     157     201 ..     758     802 ..     748     817 .. 0.68
   8 ?   -2.4   0.3       5.9   2.9e+03     160     200 ..     800     841 ..     790     851 .. 0.61
   9 ?   -2.2   0.3       5.2   2.5e+03     162     192 ..     824     854 ..     810     871 .. 0.47

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.3e-10
                            AAA_27  1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGiper 56
                                      M++erL+L+ + ++++  ++f+   ++l+l++GpN AGKst+ rA+   l+ ++ +
  gi|336252351|ref|YP_004595458.1|  1 MKFERLSLSDFQSYDNLDVTFD---DGLTLLHGPNGAGKSTITRALYTTLYPLNGK 53
                                      9********************8...8************************987655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.5
                            AAA_27 159 revleaLeaeadelfkprkskkrainealeeleeakke 196
                                       ++++++L++e del ++ ++ ++ai++++e++e+ + e
  gi|336252351|ref|YP_004595458.1| 271 KDTIDDLQSEIDELEAEIQECDEAIAKQRERIESRDDE 308
                                       34455555555555555555555555555555555555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.9
                            AAA_27 157 slrevleaLeaeadelfkprkskk 180
                                       +l++ +e+Le+ +++l+++++  +
  gi|336252351|ref|YP_004595458.1| 358 ELQSQREELEDAQNRLHAREADVE 381
                                       233333334444444433333333 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2
                            AAA_27 138 leaegelgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelreaqvr 203
                                       l+ + + ++ L +a+  + + ++ +e+L++ a   +   +    a  +  ++++++++e +ea++ 
  gi|336252351|ref|YP_004595458.1| 526 LNDHRDAAEELADARETVGEATAHIEDLQSLAAGKWPLDGGDVGATHDYDTQIQRLESEREEAETA 591
                                       667778889999999999999999999999999988877777667777777777777776666655 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.014
                            AAA_27 138 leaegelgqlLfeasa..GlaslrevleaLeaeadelfkprkskkrainealeeleeakkelr 198
                                       l+   e++ +Lfea++  +la+++  +++Leae ++  ++r++ + ++   +ee++++++++ 
  gi|336252351|ref|YP_004595458.1| 606 LNHVQEVADALFEAASfkALADVAIEIDDLEAEIEQKQQTRSELQDEMESLEEEISRLEEAIA 668
                                       677889********9733455555555666666666555555555555555555555555444 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 0.62
                            AAA_27 146 qlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelreaq 201
                                       + L +a+  la+++e + +Leae +++ ++   +++ +++a+++l+ea+++l e +
  gi|336252351|ref|YP_004595458.1| 692 RELEDARDELADIKEEIGELEAEIEDIESDLDDAREDVKDAEADLQEAEEQLDEVE 747
                                       55566777778888888888888888888888888888888888888888877655 PP

  == domain 7  score: -1.8 bits;  conditional E-value: 4.1
                            AAA_27 157 slrevleaLeaeadelfkprkskkrainealeeleeakkelreaq 201
                                       + ++ +++Le++++ + ++   k+++++ ++eel++ + e++e +
  gi|336252351|ref|YP_004595458.1| 758 DAHAEIATLESDQKGYRSRLDDKEEQVASKREELQQIEDEIEEVE 802
                                       455556666666666555555566777777778887777777654 PP

  == domain 8  score: -2.4 bits;  conditional E-value: 5.9
                            AAA_27 160 evleaLeaea.delfkprkskkrainealeeleeakkelrea 200
                                       ev  +Le+   d+l ++++++++ i + +++le+a+++  ea
  gi|336252351|ref|YP_004595458.1| 800 EVESDLEDTSpDDLKEQQNETETLIEQVESQLEDAQERRDEA 841
                                       555555544414444445555566777777777777766554 PP

  == domain 9  score: -2.2 bits;  conditional E-value: 5.2
                            AAA_27 162 leaLeaeadelfkprkskkrainealeelee 192
                                       +e++e++ ++  ++r +++ a  +a+e+l++
  gi|336252351|ref|YP_004595458.1| 824 IEQVESQLEDAQERRDEARDAKSKAEERLNR 854
                                       3333333333333333333333333333333 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   4.3   3.2e-05     0.016      24     114 ..     163     256 ..     152     262 .. 0.85
   2 !   11.2  23.6   0.00039      0.19      27     172 ..     262     413 ..     258     440 .. 0.78
   3 ?    3.5   2.1     0.091        44      84     141 ..     424     481 ..     397     501 .. 0.74
   4 ?   -0.5   0.1       1.5   7.2e+02      69     119 ..     504     554 ..     485     558 .. 0.72
   5 ?    3.1  18.0      0.12        58      30     153 ..     576     694 ..     570     702 .. 0.81
   6 !   16.8  22.6   8.1e-06    0.0039      30     162 ..     637     767 ..     634     777 .. 0.91
   7 !    6.7  23.7    0.0099       4.8      67     173 ..     778     882 ..     758     900 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.2e-05
                        MscS_porin  24 qalnlLdkidkskkkaeelqkaiddaPk....elrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqe 96 
                                       + l  L++ d+++++++e qk++++ ++    +l+++q+++e+l ++++ +   + ++  +++Le r+ + s+ l++
  gi|336252351|ref|YP_004595458.1| 163 DNLLGLTAPDAYEEDINEMQKTVESWQQdkrsKLQTVQEDIEEL-EADDPKATVQSKAEEIDDLEARIGDLSDGLED 238
                                       5566788899*************9887644448***********.666666667778889***************** PP

                        MscS_porin  97 lqeqlaqlnsqlvelqtr 114
                                        +e+l  ++s++ e++ r
  gi|336252351|ref|YP_004595458.1| 239 GRERLRAIESDIEEYRER 256
                                       *************99887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00039
                        MscS_porin  27 nlLdkidkskkkaeelqkaiddaPkelrelqqeleal..qkkkeeaskeilaklsleeLeqrllqtssqlqelqeql 101
                                       +l d++d+ k+ +++lq  id+  +e++e  + +++   + ++ ++   +++ +  +e    +++ + +  e++++ 
  gi|336252351|ref|YP_004595458.1| 262 DLTDERDEAKDTIDDLQSEIDELEAEIQECDEAIAKQreRIESRDDEVVDFDLTNEDEAKEAVEEFETKYDEASSEV 338
                                       577999****************************9998888888889999999999999999999999999999999 PP

                        MscS_porin 102 aqlnsqlvelqtrperaqqqltearqrlqeirnrL....nstaaagealsqaqrtalqaelaaleaqieeleqel 172
                                        q  +++ ++++  er+  +l + r++l++ +nrL    ++ +aa+e l +a+  + q ++ + e+  ++le+ l
  gi|336252351|ref|YP_004595458.1| 339 EQRRAEVDSAEDTVERLEDELQSQREELEDAQNRLhareADVEAAEETLGEAKDSLEQRREILEEQLQDYLETPL 413
                                       999999999999999999999999999999999995433333333446666666655555555555556666665 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.091
                        MscS_porin  84 eqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaa 141
                                         r+++  ++ ++ +++  +  ++ + l + ++++ ++l+e r+r ++ir  L+   +
  gi|336252351|ref|YP_004595458.1| 424 RDRMDDIREEKSDREAEYESKRDRRARLGDEIDTIESELSEVRERRDDIRESLETAVD 481
                                       566667777777777777888888888999999999*************999955533 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.5
                        MscS_porin  69 easkeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaq 119
                                       + s+e++++  + +L  +l++++++  ++ e+la++ + + e+   +e +q
  gi|336252351|ref|YP_004595458.1| 504 DVSAEDIDTAFTGDLPDELDAALNDHRDAAEELADARETVGEATAHIEDLQ 554
                                       566777777777788888888888888888888888877777777666666 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.12
                        MscS_porin  30 dkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlns 106
                                       ++i++ +++ ee ++a d a  +l+++ ++l+   ++ ++a  e  +   l++   ++++ +++ ++ q+++++l++
  gi|336252351|ref|YP_004595458.1| 576 TQIQRLESEREEAETAADAAIDTLDAADERLNHV-QEVADALFEAASFKALADVAIEIDDLEAEIEQKQQTRSELQD 651
                                       5788888888888888899999999999999999.777777777777778888899********************* PP

                        MscS_porin 107 qlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrta 153
                                       +  +l+  ++r+ ++++e  ++l++i++      +a++a+ +a+r +
  gi|336252351|ref|YP_004595458.1| 652 EMESLEEEISRLEEAIAEGETALDTIEDVE----DAETAVDEAEREL 694
                                       **************************9933....3344555555544 PP

  == domain 6  score: 16.8 bits;  conditional E-value: 8.1e-06
                        MscS_porin  30 dkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlns 106
                                       ++i++ ++   elq+ +++  +e+  l++ +++ + + ++    ++a++  +e e++l+++ ++l++ +e++ +l++
  gi|336252351|ref|YP_004595458.1| 637 AEIEQKQQTRSELQDEMESLEEEISRLEEAIAEGETALDTIEDVEDAETAVDEAERELEDARDELADIKEEIGELEA 713
                                       68999999999***********************999999999********************************** PP

                        MscS_porin 107 qlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaale 162
                                       ++  +++ ++ a++   +a   lqe + +L++ + a +a ++a+ +   ae a le
  gi|336252351|ref|YP_004595458.1| 714 EIEDIESDLDDAREDVKDAEADLQEAEEQLDEVESARSAAREARDA--HAEIATLE 767
                                       ******************************9997777788888877..56666665 PP

  == domain 7  score: 6.7 bits;  conditional E-value: 0.0099
                        MscS_porin  67 keeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaag 143
                                       ++++ +   ++  l+++e ++++++s+l++++ +  +l++q +e++t +e++ +ql +a++r +e r++ ++ +++ 
  gi|336252351|ref|YP_004595458.1| 778 DDKEEQVASKREELQQIEDEIEEVESDLEDTSPD--DLKEQQNETETLIEQVESQLEDAQERRDEARDAKSKAEERL 852
                                       4444555566678999999999999999998765..88888999999999999999999999999999555554555 PP

                        MscS_porin 144 ealsqaqrtalqaelaaleaqieeleqell 173
                                       ++l++ +  +   e++  +aq+ +++ e  
  gi|336252351|ref|YP_004595458.1| 853 NRLRDKRERKASLEEQVNWAQTLLNDFETI 882
                                       599999999999999999999999888765 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 !   28.7   0.0   1.7e-09   8.1e-07       2      50 ..       4      51 ..       3      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.7e-09
                            AAA_29  2 krlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +rl+l + +++d+ ++++d +g tll Gp+G+GKST+  A+ + L+p +
  gi|336252351|ref|YP_004595458.1|  4 ERLSLSDFQSYDNLDVTFD-DGLTLLHGPNGAGKSTITRALYTTLYPLN 51
                                      68999999**********9.789***********************976 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 !   28.3   0.0   3.2e-09   1.5e-06      24      87 ..     935     998 ..     910    1001 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.2e-09
                           SbcCD_C  24 kelsrssgtlSGGekqflaylalaaalaalyssaeg.repalrlvfLDEAFsklDeesiatllel 87 
                                       +e+ r+ ++ SGGe+ +l+++al a++  ++ +++g r+++l +++LDE  + lD++ i++l ++
  gi|336252351|ref|YP_004595458.1| 935 SETARDPNKASGGEG-VLVTIALRAGVYRVLADQAGgRDDSLPPFILDEPTNHLDPTHIDRLEDA 998
                                       3489999********.*****************9978********************99988665 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.3     0.027        13      27     115 ..     174     260 ..     169     265 .. 0.79
   2 !   15.0   6.0   3.9e-05     0.019       7     104 ..     212     305 ..     207     311 .. 0.82
   3 !   17.1  20.1   9.2e-06    0.0045       2     111 ..     266     376 ..     265     376 .. 0.93
   4 !   20.9   8.7   6.1e-07    0.0003      58     126 ..     358     427 ..     357     430 .. 0.87
   5 !    7.9   1.4    0.0065       3.1      18      85 ..     414     481 ..     405     496 .. 0.75
   6 ?    4.1   0.4     0.096        47      49      80 ..     526     557 ..     520     560 .. 0.88
   7 ?    7.1  19.8     0.011       5.5       8     115 ..     576     690 ..     570     693 .. 0.69
   8 !   12.8   9.9   0.00019     0.094      43     103 ..     688     745 ..     680     756 .. 0.73
   9 ?   -2.0  29.7       7.3   3.5e+03       8     118 ..     761     868 ..     754     882 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.027
                        TPR_MLP1_2  27 lqedlekqaeiakeaqqkYerelvkhaedvkelqa..lreelnelkaeiaelkaeaesakaeleeseesweeqkeel 101
                                       ++ed++++++ ++  qq+  + l+   ed++el+a   ++ +++  +ei +l+a+  +++  le  +e +     ++
  gi|336252351|ref|YP_004595458.1| 174 YEEDINEMQKTVESWQQDKRSKLQTVQEDIEELEAddPKATVQSKAEEIDDLEARIGDLSDGLEDGRERL----RAI 246
                                       6899999999999999999999999999999998633799999999999999999999999998887655....455 PP

                        TPR_MLP1_2 102 ekelselekriedl 115
                                       e++++e ++r  dl
  gi|336252351|ref|YP_004595458.1| 247 ESDIEEYRERESDL 260
                                       66666666665555 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.9e-05
                        TPR_MLP1_2   7 eeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesa 83 
                                       +++++s+ ee++++ea++  l + le  +e++++ + + e+      e   +l++l +e +e+k++i +l++e +++
  gi|336252351|ref|YP_004595458.1| 212 KATVQSKAEEIDDLEARIGDLSDGLEDGRERLRAIESDIEEY----RERESDLSDLTDERDEAKDTIDDLQSEIDEL 284
                                       67889999***************************9977754....4444456666677777889999999999999 PP

                        TPR_MLP1_2  84 kaeleeseesweeqkeeleke 104
                                       +ae++e+ e++++q+e++e++
  gi|336252351|ref|YP_004595458.1| 285 EAEIQECDEAIAKQRERIESR 305
                                       999999999999999999876 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 9.2e-06
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkY.erelvkhaedvkelqalreelnelkaeiaelk 77 
                                       e ++++++i++l++e++e+ea++q+  e + kq+e+ +   +      l++  e+ ++++++ ++++e+ +e+++ +
  gi|336252351|ref|YP_004595458.1| 266 ERDEAKDTIDDLQSEIDELEAEIQECDEAIAKQRERIESRDDEVvDFDLTNEDEAKEAVEEFETKYDEASSEVEQRR 342
                                       678999******************************999887652679***************************** PP

                        TPR_MLP1_2  78 aeaesakaeleeseesweeqkeelekelselekr 111
                                       ae++sa+ ++e+ e ++++q+eele+  + l +r
  gi|336252351|ref|YP_004595458.1| 343 AEVDSAEDTVERLEDELQSQREELEDAQNRLHAR 376
                                       *************************998887765 PP

  == domain 4  score: 20.9 bits;  conditional E-value: 6.1e-07
                        TPR_MLP1_2  58 elqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelse.lekriedlneqNklLhdQl 126
                                       elq+ reel++++++++  +a++e+a+++l e++ s+e+++e le++l++ le+ ++d++++ +   d++
  gi|336252351|ref|YP_004595458.1| 358 ELQSQREELEDAQNRLHAREADVEAAEETLGEAKDSLEQRREILEEQLQDyLETPLDDVDDHEAAVRDRM 427
                                       79**********************************************9846777888877666655555 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0065
                        TPR_MLP1_2  18 eeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesaka 85 
                                       ++ +++++++++ +   +e+ ++ +  Ye+     a   +e+ ++ +el+e+++++ ++++++e+a  
  gi|336252351|ref|YP_004595458.1| 414 DDVDDHEAAVRDRMDDIREEKSDREAEYESKRDRRARLGDEIDTIESELSEVRERRDDIRESLETAVD 481
                                       44444555555555555566667788899999999999999999999999999999999999999865 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.096
                        TPR_MLP1_2  49 lvkhaedvkelqalreelnelkaeiaelkaea 80 
                                       l+ h ++++el+++re + e++a i++l++ a
  gi|336252351|ref|YP_004595458.1| 526 LNDHRDAAEELADARETVGEATAHIEDLQSLA 557
                                       78899********************9999865 PP

  == domain 7  score: 7.1 bits;  conditional E-value: 0.011
                        TPR_MLP1_2   8 eeikslkeekeeaeaklqklqedlekqaeiakeaqqkY.....erelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       ++i++l++e eeae+++ ++ + l +  e++++ q+       +      a+ + e+ +l +e+++ +++++el++e
  gi|336252351|ref|YP_004595458.1| 576 TQIQRLESEREEAETAADAAIDTLDAADERLNHVQEVAdalfeAASFKALADVAIEIDDLEAEIEQKQQTRSELQDE 652
                                       55666666666666666666666666666666666632000004445556777788889999999999999999999 PP

                        TPR_MLP1_2  80 aesakaeleeseesweeqkeele..kelselekriedl 115
                                        es+++e+++ ee+++e +++l+  ++++++e+ +++ 
  gi|336252351|ref|YP_004595458.1| 653 MESLEEEISRLEEAIAEGETALDtiEDVEDAETAVDEA 690
                                       99999999999999999999997445788888877776 PP

  == domain 8  score: 12.8 bits;  conditional E-value: 0.00019
                        TPR_MLP1_2  43 qkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelek 103
                                       +  erel   +++ +el++++ee+ el+aei+++++++++a+++++ +e+ ++e +e+l++
  gi|336252351|ref|YP_004595458.1| 688 DEAEREL---EDARDELADIKEEIGELEAEIEDIESDLDDAREDVKDAEADLQEAEEQLDE 745
                                       5555555...456778888888888888888888888888888888888888888888864 PP

  == domain 9  score: -2.0 bits;  conditional E-value: 7.3
                        TPR_MLP1_2   8 eeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesak 84 
                                       +ei++l+++++ ++++l   +e++ +++e++++ ++  e e v+   + ++  +l+e+ ne+++ i+++++++e+a+
  gi|336252351|ref|YP_004595458.1| 761 AEIATLESDQKGYRSRLDDKEEQVASKREELQQIED--EIEEVESDLEDTSPDDLKEQQNETETLIEQVESQLEDAQ 835
                                       555566666666666665555555555555555555..222233333333445777777777777777777777777 PP

                        TPR_MLP1_2  85 aeleeseesweeqkeelekelselekriedlneq 118
                                       +  +e++ + ++ +e+l + l++ ++r   l+eq
  gi|336252351|ref|YP_004595458.1| 836 ERRDEARDAKSKAEERLNR-LRDKRERKASLEEQ 868
                                       7777777776666666653.44444444444444 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   2.1      0.46   2.2e+02      13      80 ..     188     255 ..     172     256 .. 0.80
   2 !   12.5   1.8   0.00027      0.13      11      72 ..     250     306 ..     223     331 .. 0.72
   3 ?    5.5  17.5     0.038        18       1      84 [.     332     410 ..     332     448 .. 0.85
   4 ?    3.5   0.4      0.17        81      25      83 ..     424     477 ..     419     485 .. 0.85
   5 !   10.0   0.2    0.0016      0.77       1      86 [.     523     610 ..     523     616 .. 0.92
   6 !    8.6   5.4    0.0043       2.1       6      90 ..     624     702 ..     619     705 .. 0.87
   7 !    9.1   0.5    0.0031       1.5       1      35 [.     688     722 ..     681     727 .. 0.86
   8 !    8.2   5.0    0.0056       2.7      47     104 ..     701     758 ..     698     771 .. 0.82
   9 !    9.7  10.1    0.0019      0.94       1      80 [.     723     803 ..     716     809 .. 0.65
  10 ?    6.9  17.3     0.014       6.8       6     103 ..     776     866 ..     771     878 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.46
                              FliJ  13 elqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekare 80 
                                        +q++++kl+ +++ ++e++    +++   +a+e+  ++a i+ l + ++  ++ l   e ++e++re
  gi|336252351|ref|YP_004595458.1| 188 WQQDKRSKLQTVQEDIEELEADDPKATVQSKAEEIDDLEARIGDLSDGLEDGRERLRAIESDIEEYRE 255
                                       46778899999999999997777777668899999999999999999999999999999999999887 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00027
                              FliJ  11 qrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqae 72 
                                         e+++ e+ l  l+++r+e +  + + +     +e+  ++a i+  deaia+q++ ++   
  gi|336252351|ref|YP_004595458.1| 250 IEEYRERESDLSDLTDERDEAKDTIDDLQ-----SEIDELEAEIQECDEAIAKQRERIESRD 306
                                       45566677777777777777777777777.....7777777777777777777777776554 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.038
                              FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvek 77 
                                       dea  e+++ ++e+++ae  +e+le+++q+ +++l++++     ++l++++a  +a +e++ ++k +l+q ++ +e+
  gi|336252351|ref|YP_004595458.1| 332 DEASSEVEQRRAEVDSAEDTVERLEDELQSQREELEDAQ-----NRLHAREADVEAAEETLGEAKDSLEQRREILEE 403
                                       79999**********************************.....********************************* PP

                              FliJ  78 areewqe 84 
                                       + ++++e
  gi|336252351|ref|YP_004595458.1| 404 QLQDYLE 410
                                       ***9997 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.17
                              FliJ  25 eqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewq 83 
                                       ++ +++ ++++s++      ae+   +  +++l ++i+ +++el+  +++++  re + 
  gi|336252351|ref|YP_004595458.1| 424 RDRMDDIREEKSDRE-----AEYESKRDRRARLGDEIDTIESELSEVRERRDDIRESLE 477
                                       567788888888888.....999999999999999999999999999999999999876 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.0016
                              FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkqlsgea.q.glsaaelrnyqafisaldeaiaqqkqelaqaekqv 75 
                                       d+a +    a  el++a+e + e + +++++q+ ++g+    g ++ + + y  +i++l+++ ++++ + + a   +
  gi|336252351|ref|YP_004595458.1| 523 DAALNDHRDAAEELADARETVGEATAHIEDLQSLAAGKWpLdGGDVGATHDYDTQIQRLESEREEAETAADAAIDTL 599
                                       56777888899999************************9999*********************************** PP

                              FliJ  76 ekareewqear 86 
                                       ++a e++ + +
  gi|336252351|ref|YP_004595458.1| 600 DAADERLNHVQ 610
                                       **999998765 PP

  == domain 6  score: 8.6 bits;  conditional E-value: 0.0043
                              FliJ   6 eLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareew 82 
                                       +La +  e+++ e+++e+ +q+r+e+q ++++       +e+  +++ i+  ++a++ + +++++ae +v++a++e+
  gi|336252351|ref|YP_004595458.1| 624 ALADVAIEIDDLEAEIEQKQQTRSELQDEMESLE-----EEISRLEEAIAEGETALDTI-EDVEDAETAVDEAEREL 694
                                       6777778899999999999999999999999999.....99999999999999999987.57999999999999999 PP

                              FliJ  83 qearqerk 90 
                                         ar e+ 
  gi|336252351|ref|YP_004595458.1| 695 EDARDELA 702
                                       99998875 PP

  == domain 7  score: 9.1 bits;  conditional E-value: 0.0031
                              FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkql 35 
                                       dea+reL+ a+ el++ +e++ ele ++++ ++ l
  gi|336252351|ref|YP_004595458.1| 688 DEAERELEDARDELADIKEEIGELEAEIEDIESDL 722
                                       78999999999999999999999999999987765 PP

  == domain 8  score: 8.2 bits;  conditional E-value: 0.0056
                              FliJ  47 lrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkklekLkerekkeeq 104
                                       l  +++ i+ l+ +i+ ++++l++a+++v+ a++++qea+ ++  +e  +  +++++ 
  gi|336252351|ref|YP_004595458.1| 701 LADIKEEIGELEAEIEDIESDLDDAREDVKDAEADLQEAEEQLDEVESARSAAREARD 758
                                       56677889999*****************************999999988876665554 PP

  == domain 9  score: 9.7 bits;  conditional E-value: 0.0019
                              FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaq.glsaaelrnyqafisaldeaiaqqkqelaqaekqve 76 
                                       d+a++ ++ a++ lq+aee+l+e+e+ r+  ++   ++a+ +   ++++ y++ ++  +e++a+ ++el+q e ++e
  gi|336252351|ref|YP_004595458.1| 723 DDAREDVKDAEADLQEAEEQLDEVESARSAAREARDAHAEiATLESDQKGYRSRLDDKEEQVASKREELQQIEDEIE 799
                                       55666667777777777777777777777776666666644666666666666666666666666666666666666 PP

                              FliJ  77 kare 80 
                                       + ++
  gi|336252351|ref|YP_004595458.1| 800 EVES 803
                                       6555 PP

  == domain 10  score: 6.9 bits;  conditional E-value: 0.014
                              FliJ   6 eLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareew 82 
                                       +L   + ++++++e+l+++e++++e ++ l++++    + +l+  q+     ++ i+q +++l++a++++++ar++ 
  gi|336252351|ref|YP_004595458.1| 776 RLDDKEEQVASKREELQQIEDEIEEVESDLEDTS----PDDLKEQQN---ETETLIEQVESQLEDAQERRDEARDAK 845
                                       67778899999***************99999999....777777665...566679999999*************99 PP

                              FliJ  83 qearqerkklekLkerekkee 103
                                        +a+ +++ l+  +er++  e
  gi|336252351|ref|YP_004595458.1| 846 SKAEERLNRLRDKRERKASLE 866
                                       999999999888888776544 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 !    7.8  12.5    0.0032       1.6      34     124 ..     218     308 ..     158     313 .. 0.70
   2 !   13.0   9.2   8.4e-05     0.041      52     140 ..     321     409 ..     310     411 .. 0.75
   3 ?    3.7   5.6     0.055        27      32     110 ..     392     468 ..     385     484 .. 0.67
   4 !    7.2   4.3    0.0049       2.4      27     100 ..     574     670 ..     572     676 .. 0.79
   5 !    7.0  14.1    0.0054       2.6      25     129 ..     640     757 ..     638     772 .. 0.61
   6 !    8.9  16.2    0.0015       0.7      21     150 ..     774     918 ..     766     939 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0032
                             Atg14  34 lksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdk 110
                                         +e + l+ +i ++  g e++ ++ ++i+++ +  +e  s+ +dl ++  e kd+++ l++ei+e  +++++++++
  gi|336252351|ref|YP_004595458.1| 218 KAEEIDDLEARIGDLSDGLEDGRERLRAIESDIEEYRERESDLSDLTDERDEAKDTIDDLQSEIDELEAEIQECDEA 294
                                       33333344444444444444666777777777777777777777777779999999999999999999999999999 PP

                             Atg14 111 lkkRrsdleslqne 124
                                       ++k r+++es  +e
  gi|336252351|ref|YP_004595458.1| 295 IAKQRERIESRDDE 308
                                       99999998886655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.4e-05
                             Atg14  52 keeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleer 128
                                       ke++e+ e+k +  +  +e+ ++++ + ++ +++l+d l+++++e+e+++++l ++ +++    ++l  ++++le+r
  gi|336252351|ref|YP_004595458.1| 321 KEAVEEFETKYDEASSEVEQRRAEVDSAEDTVERLEDELQSQREELEDAQNRLHAREADVEAAEETLGEAKDSLEQR 397
                                       33444455666777777778888888888888888888888888888888888888888888888888888888888 PP

                             Atg14 129 rkkqiaklqdai 140
                                       r+ + ++lqd++
  gi|336252351|ref|YP_004595458.1| 398 REILEEQLQDYL 409
                                       888888888875 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.055
                             Atg14  32 aklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakls 108
                                        +l  ++e l+++++++le++   ++ +d +   ++++++++ +++d +++ +  +d++ +l +ei+    +l++ +
  gi|336252351|ref|YP_004595458.1| 392 DSLEQRREILEEQLQDYLETPL--DDVDDHEAAVRDRMDDIREEKSDREAEYESKRDRRARLGDEIDTIESELSEVR 466
                                       5678888889999999999988..77777777777777777777777777777777777777777765555544444 PP

                             Atg14 109 dk 110
                                       + 
  gi|336252351|ref|YP_004595458.1| 467 ER 468
                                       33 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0049
                             Atg14  27 lrerlaklksekeslkkkiekalegke.......................eaeqledkiknkkakleelksliadlr 80 
                                       + +++++l se+e+ ++  ++a+ + +                       +  + + +i+ + a +e++++++++l+
  gi|336252351|ref|YP_004595458.1| 574 YDTQIQRLESEREEAETAADAAIDTLDaaderlnhvqevadalfeaasfkALADVAIEIDDLEAEIEQKQQTRSELQ 650
                                       56788999999999999999999999999999998888888888888777677777788888888888888888888 PP

                             Atg14  81 erlqelkdklsqlkkeieek 100
                                       ++++ l++ +s+l ++i+e 
  gi|336252351|ref|YP_004595458.1| 651 DEMESLEEEISRLEEAIAEG 670
                                       88888888888888888775 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.0054
                             Atg14  25 yelrerlaklksekeslkkkiekalegke.................eaeqledkiknkkakleelksliadlrerlq 84 
                                       +++++    l+ e esl+++i++++e                    +++++e++++  ++ l ++k +i +l+++++
  gi|336252351|ref|YP_004595458.1| 640 EQKQQTRSELQDEMESLEEEISRLEEAIAegetaldtiedvedaetAVDEAERELEDARDELADIKEEIGELEAEIE 716
                                       66666666677777777776666655555444555555544444447777777777777777777777777777777 PP

                             Atg14  85 elkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerr 129
                                        ++ +l+  ++ ++++ + l++  ++l     + es+++  +e+r
  gi|336252351|ref|YP_004595458.1| 717 DIESDLDDAREDVKDAEADLQEAEEQLD----EVESARSAAREAR 757
                                       7777777777777777777777777773....4444444444444 PP

  == domain 6  score: 8.9 bits;  conditional E-value: 0.0015
                             Atg14  21 perlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97 
                                       ++rl ++ e++a+ ++e ++++ +ie+ ++  e     ++  + +k++ +e+ +li++ +++l+  ++++++ +++ 
  gi|336252351|ref|YP_004595458.1| 774 RSRLDDKEEQVASKREELQQIEDEIEEVESDLE-----DTSPDDLKEQQNETETLIEQVESQLEDAQERRDEARDAK 845
                                       45999*********************9999888.....334444444444444444444444444444444444444 PP

                             Atg14  98 eekkkklaklsdklk......................kRrsdleslqneleerrkkqiaklqdaikrieqklssl 150
                                        ++ ++l +l+dk                        +  ++ + +q++++er  + +++++++i+r  +++s+ 
  gi|336252351|ref|YP_004595458.1| 846 SKAEERLNRLRDKRErkasleeqvnwaqtllndfetiT--KTYSEVQTRMRERVLDRLKRHTNDIFRDLYQNSTY 918
                                       44444444444443333333345557776666666442..23335666666666666666666666665555555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.022        11      20      37 ..      27      44 ..      21      63 .. 0.90
   2 !   14.7  10.8   1.9e-05    0.0091     274     444 ..     134     307 ..     112     314 .. 0.52
   3 ?    1.0  20.6      0.27   1.3e+02     290     468 ..     297     477 ..     294     501 .. 0.72
   4 !    8.0  33.6     0.002      0.96     280     469 ..     573     800 ..     511     814 .. 0.74
   5 ?    1.5  24.5      0.19        92     318     453 ..     724     859 ..     719     880 .. 0.89
   6 ?    2.5  10.3     0.092        45      89     192 ..     815     920 ..     812     945 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.022
                            AAA_13 20 liYGwNGaGKTtLSrllr 37
                                      l+ G NGaGK+t+ r+l 
  gi|336252351|ref|YP_004595458.1| 27 LLHGPNGAGKSTITRALY 44
                                      689***********9985 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.9e-05
                            AAA_13 274 eahFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKr.k 349
                                       ea+ ++++ ++q +L +lie   ++++ +l++l  +++ +  ++  +e ++++++  +  +++L+++q+ +e+   +
  gi|336252351|ref|YP_004595458.1| 134 EAFANSTY-AQQTELTRLIEATPGEREDILDNLLGLTAPDAYEEDINEMQKTVESWQQDKRSKLQTVQEDIEELEaD 209
                                       34444444.55889999999999999999999966666554444456667777777777777777777777764313 PP

                            AAA_13 350 epfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklel.....hlveeleseldeykkkykkl 421
                                       +p +  +++s +++i+ ++  + ++ +  ++  e+   +e++ ee ++         ++  e+++ +d +++++++l
  gi|336252351|ref|YP_004595458.1| 210 DPKA--TVQSKAEEIDDLEARIGDLSDGLEDGRERLRAIESDIEEYRERESDlsdltDERDEAKDTIDDLQSEIDEL 284
                                       3333..33444444444444444444444444444444444433333321110000012344444444444444444 PP

                            AAA_13 422 ekaieklekelkeeeaelkklee 444
                                       e++i++ +++++++ ++++ +++
  gi|336252351|ref|YP_004595458.1| 285 EAEIQECDEAIAKQRERIESRDD 307
                                       44444444444444444444444 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.27
                            AAA_13 290 kliekveskksellek.lkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksve.lesvkaki 364
                                       k  e++es+ +e+++  l++  +++++ ++fe +++e+++e e+ +++ +++++ +e+  +e+ ++ e le++++++
  gi|336252351|ref|YP_004595458.1| 297 KQRERIESRDDEVVDFdLTNEDEAKEAVEEFETKYDEASSEVEQRRAEVDSAEDTVERLEDELQSQREeLEDAQNRL 373
                                       55667777777776655777788888888899999999999999999999999999999999988665589999999 PP

                            AAA_13 365 esikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeyk....kkykklekaieklekelkeeea 437
                                        + + +v++++e+     e  ++le+++e ++++l+ +l   l +++d  +    + ++++ ++ ++ e+e + + +
  gi|336252351|ref|YP_004595458.1| 374 HAREADVEAAEETLG---EAKDSLEQRREILEEQLQDYLETPL-DDVDDHEaavrDRMDDIREEKSDREAEYESKRD 446
                                       999999999998876...6788999999999999988665433.455544411225555555555555555555556 PP

                            AAA_13 438 elkkleeeikeLekqlrdekpaaeeinkeLk 468
                                       + + l +ei  +e +l+++++  ++i + L+
  gi|336252351|ref|YP_004595458.1| 447 RRARLGDEIDTIESELSEVRERRDDIRESLE 477
                                       6666666677777777777777776666665 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.002
                            AAA_13 280 efeekqerLekliekveskkselleklkavsdeasensafeed..keelkaeaealeeqLkglqraleaKrkepfk. 353
                                       +++ +++rLe+  e+ e++ + +++ l+a+ ++ +  ++ +++   +   +++  ++ +++ l+ ++e+K +  ++ 
  gi|336252351|ref|YP_004595458.1| 573 DYDTQIQRLESEREEAETAADAAIDTLDAADERLNHVQEVADAlfEAASFKALADVAIEIDDLEAEIEQKQQTRSEl 649
                                       68889999999999999999999999988888644444444442222222345667788999999999998877775 PP

                            AAA_13 354 svelesvkakie..................................sikklvaeineliakhNekvanleeekeeak 396
                                       + e+es++++i+                                   + +++a+i+e i +  + ++++e++  +a+
  gi|336252351|ref|YP_004595458.1| 650 QDEMESLEEEISrleeaiaegetaldtiedvedaetavdeaereleDARDELADIKEEIGELEAEIEDIESDLDDAR 726
                                       66688888888766677777777777777777777777777777777788888888888888888888888888888 PP

                            AAA_13 397 kklelhl..veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLka 469
                                       ++++  +  ++e+e++lde ++  +++++++ ++ +e++  e+++k ++ +  ++e+q+ ++++  ++i++e+++
  gi|336252351|ref|YP_004595458.1| 727 EDVKDAEadLQEAEEQLDEVES-ARSAAREARDAHAEIATLESDQKGYRSRLDDKEEQVASKREELQQIEDEIEE 800
                                       8887777334777777776663.3344556666666666666666666666666666666666666666666554 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.19
                            AAA_13 318 afeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekee 394
                                        ++ed+++++a +++ eeqL+++++a +a r+   +++e+  ++++ +   + +++ +e++a+  e  +++e+e ee
  gi|336252351|ref|YP_004595458.1| 724 DAREDVKDAEADLQEAEEQLDEVESARSAAREARDAHAEIATLESDQKGYRSRLDDKEEQVASKREELQQIEDEIEE 800
                                       46789*************************9999999**************************************** PP

                            AAA_13 395 akkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekql 453
                                       ++++le     +l+++ +e ++ ++++e ++e+++++ +e+ +++ k+ee+ + L+ + 
  gi|336252351|ref|YP_004595458.1| 801 VESDLEDTSPDDLKEQQNETETLIEQVESQLEDAQERRDEARDAKSKAEERLNRLRDKR 859
                                       ***************99999999*************99999999999999988777554 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.092
                            AAA_13  89 eesiekqekieklkkeikkleekleaaeaqlqkaek......ekkklekeledea.wkkivkkknsalsealkglky 158
                                       e+++e+++ ie+ ++++++++e+ ++a   ++kae+      +k++ +++le+++ w+   +   +++++  k +++
  gi|336252351|ref|YP_004595458.1| 815 EQQNETETLIEQVESQLEDAQERRDEARDAKSKAEErlnrlrDKRERKASLEEQVnWA---QTLLNDFETITKTYSE 888
                                       899********************99999999999995555544444444444333033...3334555555555555 PP

                            AAA_13 159 .eekfkerllkelkkknrkaaellsdeelkaklet 192
                                        +++  er+l++lk++   ++ + +d  +++  e+
  gi|336252351|ref|YP_004595458.1| 889 vQTRMRERVLDRLKRH---TNDIFRDLYQNSTYEA 920
                                       5777778888887775...4444455555555555 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 ?    3.2   4.8      0.17        81      67     112 ..     188     238 ..     172     252 .. 0.56
   2 ?    4.0  13.7     0.093        45      18     114 ..     221     319 ..     216     335 .. 0.67
   3 ?    1.9  22.4      0.44   2.1e+02      47     139 ..     317     409 ..     293     410 .. 0.88
   4 ?    1.8  18.8      0.46   2.2e+02       3      77 ..     329     407 ..     327     440 .. 0.78
   5 ?    3.5   2.3      0.14        69      50      90 ..     437     477 ..     414     482 .. 0.54
   6 ?    6.2  13.4      0.02       9.6      25     119 ..     577     669 ..     572     678 .. 0.86
   7 !   20.7  11.0     7e-07   0.00034      32     107 ..     679     754 ..     674     756 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.17
                    CENP-F_leu_zip  67 elreleldLvalrsekeeLe.....kelqkkqervseLeslnsslenllee 112
                                         ++ +++L++++++ eeLe       +q k e++++Le++  +l+  le+
  gi|336252351|ref|YP_004595458.1| 188 WQQDKRSKLQTVQEDIEELEaddpkATVQSKAEEIDDLEARIGDLSDGLED 238
                                       233444556666666666651111135788888888888888888777765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.093
                    CENP-F_leu_zip  18 kadsLkdkvenLerelemseenqekvileaEtskaevet...lkeeieelaeelreleldLvalrsekeeLekelqk 91 
                                       + d L+ ++  L   le+  e + +++ + E+ ++  +    l +e +e + +  +l++++++l  e +e ++ + k
  gi|336252351|ref|YP_004595458.1| 221 EIDDLEARIGDLSDGLEDGRERLRAIESDIEEYRERESDlsdLTDERDEAKDTIDDLQSEIDELEAEIQECDEAIAK 297
                                       55778888888888888888888888888888776543322277777888888888888888888888888888888 PP

                    CENP-F_leu_zip  92 kqervseLeslnsslenlleekE 114
                                       ++er+++ +   +++  +  e E
  gi|336252351|ref|YP_004595458.1| 298 QRERIESRDDEVVDFDLTN-EDE 319
                                       8888887777777765332.222 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.44
                    CENP-F_leu_zip  47 aEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekvqmkee 123
                                        +++k++ve+++++ +e ++e ++ ++++++     e Le elq ++e+ ++ +++    e  +e +E+   + k++
  gi|336252351|ref|YP_004595458.1| 317 EDEAKEAVEEFETKYDEASSEVEQRRAEVDSAEDTVERLEDELQSQREELEDAQNRLHAREADVEAAEETLGEAKDS 393
                                       56789999999999999999999999999999999999999999999999999999999999999999999999999 PP

                    CENP-F_leu_zip 124 skaaveeLqtqlkeln 139
                                        +++ e L+ ql++  
  gi|336252351|ref|YP_004595458.1| 394 LEQRREILEEQLQDYL 409
                                       9999999999999865 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.46
                    CENP-F_leu_zip   3 kkklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevet....lkeeieelaeelreleldL 75 
                                        k  ++ ++  + + + ds +d ve+Le el+ + e++e++        a ve+    l e ++ l+++++ le +L
  gi|336252351|ref|YP_004595458.1| 329 TKYDEASSEVEQRRAEVDSAEDTVERLEDELQSQREELEDAQNRLHAREADVEAaeetLGEAKDSLEQRREILEEQL 405
                                       56667778888899999**********************99877766666665522337888888999999999888 PP

                    CENP-F_leu_zip  76 va 77 
                                       ++
  gi|336252351|ref|YP_004595458.1| 406 QD 407
                                       76 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.14
                    CENP-F_leu_zip  50 skaevetlkeeieelaeelreleldLvalrsekeeLekelq 90 
                                         ae e+ ++   +l  e   +e++L+++r+ ++++ ++l+
  gi|336252351|ref|YP_004595458.1| 437 REAEYESKRDRRARLGDEIDTIESELSEVRERRDDIRESLE 477
                                       33344444444445555555555555555555555555554 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.02
                    CENP-F_leu_zip  25 kvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLes 101
                                       ++++Le+e e++e   +++i   + + + ++ ++e  + l e  +     L+++  e ++Le e+++kq++ seL+ 
  gi|336252351|ref|YP_004595458.1| 577 QIQRLESEREEAETAADAAIDTLDAADERLNHVQEVADALFEAAS--FKALADVAIEIDDLEAEIEQKQQTRSELQD 651
                                       789999999999999999999999999999999999999887654..357999999********************* PP

                    CENP-F_leu_zip 102 lnsslenlleekEqekvq 119
                                         +sle+ ++++E+  ++
  gi|336252351|ref|YP_004595458.1| 652 EMESLEEEISRLEEAIAE 669
                                       ***********9998665 PP

  == domain 7  score: 20.7 bits;  conditional E-value: 7e-07
                    CENP-F_leu_zip  32 elemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnssle 107
                                       ++e++e   +++++e E+++ e+  +keei el++e +++e+dL++ r++ ++ e +lq+  e+ +e es++s  +
  gi|336252351|ref|YP_004595458.1| 679 DVEDAETAVDEAERELEDARDELADIKEEIGELEAEIEDIESDLDDAREDVKDAEADLQEAEEQLDEVESARSAAR 754
                                       6789999999************************************************************998765 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 !   14.4   2.8   4.2e-05      0.02     152     258 ..     177     290 ..     112     310 .. 0.71
   2 ?    2.7  15.3      0.15        75     169     274 ..     775     891 ..     767     921 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.2e-05
                      Exonuc_VII_L 152 lerrlekaikrlleekkqrleklasrl.....kspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k 222
                                         ++++k +++  ++k+++l+++++++      +p++ +++k++++d+le+r+   l+  l+  rerl+ +++ + +
  gi|336252351|ref|YP_004595458.1| 177 DINEMQKTVESWQQDKRSKLQTVQEDIeeleaDDPKATVQSKAEEIDDLEARIGD-LSDGLEDGRERLRAIESDIeE 252
                                       33467777777778899999999888877774599*******************9.9999*********99977733 PP

                      Exonuc_VII_L 223 ekleekkerlkklkerle....lleekkerleeleeklea 258
                                         ++e++++l++l+++ +    ++++ +++++ele++++ 
  gi|336252351|ref|YP_004595458.1| 253 --YRERESDLSDLTDERDeakdTIDDLQSEIDELEAEIQE 290
                                       ..33333334333222222333455555555555555554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.15
                      Exonuc_VII_L 169 qrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlkekleekkerl.......kklker 238
                                       +rl+  +++++s++e l++ +++++e+e++le +    lk++++++e+l e+++++le+++er        +k +er
  gi|336252351|ref|YP_004595458.1| 775 SRLDDKEEQVASKREELQQIEDEIEEVESDLEDTSPDDLKEQQNETETLIEQVESQLEDAQERRdeardakSKAEER 851
                                       34444444455555555555555555555555555555777777666666666444444444443333333444555 PP

                      Exonuc_VII_L 239 lelleekkerleeleekle....alsplkvLkrGyaivrk 274
                                       l++l++k+er ++lee+++    +l+  +++++ y+ v++
  gi|336252351|ref|YP_004595458.1| 852 LNRLRDKRERKASLEEQVNwaqtLLNDFETITKTYSEVQT 891
                                       5566777666666666654111134555666666666555 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       7.1   3.5e+03      77     103 ..     104     129 ..      99     131 .. 0.57
   2 ?   -1.3   5.2       4.4   2.1e+03      58      96 ..     216     254 ..     176     260 .. 0.61
   3 ?    6.4   2.5     0.018       8.6      59      99 ..     262     302 ..     257     306 .. 0.70
   4 ?    3.0   5.2      0.19        93      57      97 ..     328     371 ..     317     376 .. 0.58
   5 ?   -0.2  12.2       1.9   9.4e+02      28     103 ..     342     409 ..     337     420 .. 0.73
   6 ?    4.0   0.2     0.096        47      62      93 ..     446     477 ..     434     482 .. 0.61
   7 ?   -1.8   0.1       6.1     3e+03      23      44 ..     521     542 ..     520     546 .. 0.84
   8 !   19.5   9.1   1.5e-06   0.00071      15     100 ..     572     661 ..     570     664 .. 0.90
   9 !    7.6  17.2    0.0075       3.6       7     101 ..     646     738 ..     642     742 .. 0.78
  10 ?    2.2  14.2      0.34   1.7e+02       5      95 ..     713     805 ..     709     809 .. 0.84
  11 ?    2.7   6.3      0.25   1.2e+02      58      97 ..     803     843 ..     801     849 .. 0.82
  12 ?    0.0   0.2       1.7   8.2e+02      70     101 ..     861     895 ..     854     900 .. 0.48

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 7.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                       Prefoldin_2  77 eiktlekqleklekeleelkeelqkkl 103
                                       e+++le+++++  ++ +e++e++ +++
  gi|336252351|ref|YP_004595458.1| 104 EMTNLESEETY-STKSSEIEEKVSQLF 129
                                       55666655544.455566666666665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.4
                                       E-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  58 qdkeevkeeLeerketlekeiktlekqleklekeleelk 96 
                                       q+k+e +++Le+r+ +l+  ++   ++l+ +e ++ee +
  gi|336252351|ref|YP_004595458.1| 216 QSKAEEIDDLEARIGDLSDGLEDGRERLRAIESDIEEYR 254
                                       455666666666666666666666666666666666665 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.018
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  59 dkeevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                                       d+++ ++e ++++++l+ ei++le ++++  + +++++e +
  gi|336252351|ref|YP_004595458.1| 262 DLTDERDEAKDTIDDLQSEIDELEAEIQECDEAIAKQRERI 302
                                       56666667777777777777777777777777777777766 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.19
                                       EE-HHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  57 kqdkeevkeeLeerketl...ekeiktlekqleklekeleelke 97 
                                       +++ +e+ +e+e+r +++   e  +++le++l++ ++ele+ ++
  gi|336252351|ref|YP_004595458.1| 328 ETKYDEASSEVEQRRAEVdsaEDTVERLEDELQSQREELEDAQN 371
                                       55666666777766655411144455555555555555555554 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                       Prefoldin_2  28 lkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkkl 103
                                         e++++++++e l+++ + ++        +++e+++++L +r++++e+  +tl + +++le++ e l+e+lq  l
  gi|336252351|ref|YP_004595458.1| 342 RAEVDSAEDTVERLEDELQSQR--------EELEDAQNRLHAREADVEAAEETLGEAKDSLEQRREILEEQLQDYL 409
                                       5555555555555555544443........4788899999999999999999999999999999999988888765 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.096
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  62 evkeeLeerketlekeiktlekqleklekele 93 
                                       + +++L ++++t+e e++++ ++ +++++ le
  gi|336252351|ref|YP_004595458.1| 446 DRRARLGDEIDTIESELSEVRERRDDIRESLE 477
                                       44555666666666666666666666665554 PP

  == domain 7  score: -1.8 bits;  conditional E-value: 6.1
                                       HHHHHHHHHHHHHHHHHHS-TT CS
                       Prefoldin_2  23 qletqlkelelvleelellded 44 
                                       +l++ l+++ ++ eel ++ e+
  gi|336252351|ref|YP_004595458.1| 521 ELDAALNDHRDAAEELADARET 542
                                       6788999999999999988775 PP

  == domain 8  score: 19.5 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHHHHHHHHHH....HHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  15 qqlaqqikqletqlkelelv....leelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktlekqlek 87 
                                       +++++qi+ le + +e+e++    +++l+ +de  +  + v d+l++    ++++++  ++++le+ei++ ++  ++
  gi|336252351|ref|YP_004595458.1| 572 HDYDTQIQRLESEREEAETAadaaIDTLDAADERLNHVQEVADALFEAASFKALADVAIEIDDLEAEIEQKQQTRSE 648
                                       6789999999999999987522227899999999******************************************* PP

                                       HHHHHHHHHHHHH CS
                       Prefoldin_2  88 lekeleelkeelq 100
                                       l+ e+e l+ee+ 
  gi|336252351|ref|YP_004595458.1| 649 LQDEMESLEEEIS 661
                                       **********986 PP

  == domain 9  score: 7.6 bits;  conditional E-value: 0.0075
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHH...HHHHHHHH CS
                       Prefoldin_2   7 fqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerke...tlekeikt 80 
                                        ++lq++++ l+++i  le+ + e e++l+++e++++ ++          ++++e++++eL + ke   +le+ei+ 
  gi|336252351|ref|YP_004595458.1| 646 RSELQDEMESLEEEISRLEEAIAEGETALDTIEDVEDAETAVDEA-----ERELEDARDELADIKEeigELEAEIED 717
                                       579***********************************7666664.....666677766665555411156888888 PP

                                       HHHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  81 lekqleklekeleelkeelqk 101
                                       +e+ l++ ++++++ ++ lq+
  gi|336252351|ref|YP_004595458.1| 718 IESDLDDAREDVKDAEADLQE 738
                                       888888888888888888886 PP

  == domain 10  score: 2.2 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETT..EEEEE-HHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   5 nkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGd..vlvkqdkeevkeeLeerketlekeik 79 
                                       ++ ++++++l++  +++k++e++l+e+e+ l+e+e++ + ++  +      + ++ d++  +++L++++e++  + +
  gi|336252351|ref|YP_004595458.1| 713 AEIEDIESDLDDAREDVKDAEADLQEAEEQLDEVESARSAAREARDAHAeiATLESDQKGYRSRLDDKEEQVASKRE 789
                                       677899999*******************************88888877633557899999*******9999999988 PP

                                       HHHHHHHHHHHHHHHH CS
                       Prefoldin_2  80 tlekqleklekeleel 95 
                                       +l++ ++++e+  ++l
  gi|336252351|ref|YP_004595458.1| 790 ELQQIEDEIEEVESDL 805
                                       8888888888755554 PP

  == domain 11  score: 2.7 bits;  conditional E-value: 0.25
                                       E-HHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  58 qdkeevk.eeLeerketlekeiktlekqleklekeleelke 97 
                                        d+e++  ++L+e++++ e+ i+++e+qle+ +++ +e ++
  gi|336252351|ref|YP_004595458.1| 803 SDLEDTSpDDLKEQQNETETLIEQVESQLEDAQERRDEARD 843
                                       5565555158***********************99999886 PP

  == domain 12  score: 0.0 bits;  conditional E-value: 1.7
                                       HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  70 rketlekeik...tlekqleklekeleelkeelqk 101
                                       rk++le++++   tl +  e++ k+++e+++  ++
  gi|336252351|ref|YP_004595458.1| 861 RKASLEEQVNwaqTLLNDFETITKTYSEVQTRMRE 895
                                       44444444432224444444555555555554444 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   7.4      0.26   1.2e+02     182     275 ..     103     207 ..      99     210 .. 0.77
   2 !    8.8  40.7    0.0022       1.1      24     260 ..     175     408 ..     172     411 .. 0.51
   3 ?    2.7  12.4      0.16        79      61     256 ..     411     609 ..     407     622 .. 0.84
   4 ?    3.3   6.9       0.1        50     218     262 ..     625     665 ..     607     684 .. 0.69
   5 !   11.7   9.0    0.0003      0.15     198     269 ..     681     748 ..     677     763 .. 0.51
   6 !    8.4  20.8     0.003       1.4     172     282 ..     754     863 ..     750     877 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.26
                                       XXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXX-HHHHHHHHHHHHHHHHH....HHHHHHHH..HHHHHHHH CS
                          Filament 182 aeknreeaeewykskleelqeaaek.....nsealrsakeeitelrrqiqsleie....leslkkqk..asleaqla 247
                                       ae  + e+ee+y++k +e++e++++      ++ ++s+  + tel r i++   e    l++l +    +++e+ ++
  gi|336252351|ref|YP_004595458.1| 103 AEMTNLESEETYSTKSSEIEEKVSQlfgmdAEAFANSTYAQQTELTRLIEATPGErediLDNLLGLTapDAYEEDIN 179
                                       56667799************999874433234557788889999999999876652233677765442279****** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 248 eleerleaeleklqeklseleeelaeir 275
                                       e+++++e+  ++ ++kl+ ++e+++e+ 
  gi|336252351|ref|YP_004595458.1| 180 EMQKTVESWQQDKRSKLQTVQEDIEELE 207
                                       **********************999875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0022
                                       XXXXXXXXXXXXXXXXXXXXXXX.XXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXX CS
                          Filament  24 EqenkeLeakieeleekksaevsklke.lyekeleelrkqldeltkerarlqleldnlreeledlrkky...ekeln 96 
                                       E++ +e++  +e +++ k+++ + ++e + e e ++ ++++++ ++e + l++ +++l + led r+++   e++++
  gi|336252351|ref|YP_004595458.1| 175 EEDINEMQKTVESWQQDKRSKLQTVQEdIEELEADDPKATVQSKAEEIDDLEARIGDLSDGLEDGRERLraiESDIE 251
                                       44444555555555555433333332202223444444444444444444444444444444444444311133344 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXX CS
                          Filament  97 kreevEaelkalrkdldeatlarvdLekkvesLkeelaflkkvheeEvkelqkqvs..eqvlvevdaarkldLteil 171
                                       + +e E++l +l  + dea  +  dL++++++L+ e++      +e +++ +++++  ++ +v+ d +++ + +e++
  gi|336252351|ref|YP_004595458.1| 252 EYRERESDLSDLTDERDEAKDTIDDLQSEIDELEAEIQ----ECDEAIAKQRERIEsrDDEVVDFDLTNEDEAKEAV 324
                                       44444444444444444444444444444444444443....44566666666666556666677766666677777 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 172 keiraqyeelaeknreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlae 248
                                       +e  ++y+e  +    e+e+  ++ ++ +++++e+ +++l+s +ee+++++ ++ ++e+++e+ +++    +++l+ 
  gi|336252351|ref|YP_004595458.1| 325 EEFETKYDEASS----EVEQR-RAEVDSAEDTVERLEDELQSQREELEDAQNRLHAREADVEAAEETLGEAKDSLEQ 396
                                       666666666544....33332.4556677777777777777777777777777777777777777666666666666 PP

                                       HHHHHHHHHHHH CS
                          Filament 249 leerleaelekl 260
                                         e le++l+++
  gi|336252351|ref|YP_004595458.1| 397 RREILEEQLQDY 408
                                       666666666655 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.16
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  61 kqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkdldeatlarvdLekkvesLkeelaflk 137
                                         ld++   +a ++  +d++ree  d  + ye++  +r  + +e+ ++  +l e   +r d+ + +e+  ++ ++  
  gi|336252351|ref|YP_004595458.1| 411 TPLDDVDDHEAAVRDRMDDIREEKSDREAEYESKRDRRARLGDEIDTIESELSEVRERRDDIRESLETAVDDPEVA- 486
                                       5688999999999999**********************************************98888888876654. PP

                                       XXXXXXXXXXXXXXX....XXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 138 kvheeEvkelqkqvs....eqvlvevdaarkld....Lteilkeiraqyeelaeknreeaeewykskleelqeaaek 206
                                         +e+ v+  ++ +s    +    ++d+a + d    L+++l++ r+  eela+  ++  e++  + +e+lq+ a+ 
  gi|336252351|ref|YP_004595458.1| 487 --FEAAVDRANEAASalgfDVSAEDIDTAFTGDlpdeLDAALNDHRDAAEELADARETVGEAT--AHIEDLQSLAAG 559
                                       ..55555555544443334444556888888888889****************9988888875..899****99999 PP

                                       XXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 207 nsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleae 256
                                       +           +++  qiq+le+e e+ + ++++  ++l  ++erl++ 
  gi|336252351|ref|YP_004595458.1| 560 KWPLDGGDVGATHDYDTQIQRLESEREEAETAADAAIDTLDAADERLNHV 609
                                       9988888889999**************************99999998764 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 218 itelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqe 262
                                       ++++  +i+ le+e+e+ +++++ l+++++ lee++++     +e
  gi|336252351|ref|YP_004595458.1| 625 LADVAIEIDDLEAEIEQKQQTRSELQDEMESLEEEISRL----EE 665
                                       667777888888888888888888888887777655443....22 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.0003
                                       XXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 198 eelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklselee 269
                                       e++++a+++ + +l+ a+ e+++++ +i +le+e+e++++  +  ++ ++++e+ l+++ e+l    +e+e+
  gi|336252351|ref|YP_004595458.1| 681 EDAETAVDEAERELEDARDELADIKEEIGELEAEIEDIESDLDDAREDVKDAEADLQEAEEQL----DEVES 748
                                       555566666666666666666666666666666666666665555555555555444333332....22222 PP

  == domain 6  score: 8.4 bits;  conditional E-value: 0.003
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHH CS
                          Filament 172 keiraqyeelaeknreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsle.ieleslkkqkasleaqla 247
                                       +e r+ + e+a  + +  ++ y+s+l++ +e+++++ e+l++ + ei+e+   ++  +  +l++++++ ++l +q++
  gi|336252351|ref|YP_004595458.1| 754 REARDAHAEIATLESD--QKGYRSRLDDKEEQVASKREELQQIEDEIEEVESDLEDTSpDDLKEQQNETETLIEQVE 828
                                       5666667666665444..478*********************************9887257***************9 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 248 eleerleaeleklqeklseleeelaeireemarql 282
                                          e  ++ +++++++ s+ ee l+++r++ +r+ 
  gi|336252351|ref|YP_004595458.1| 829 SQLEDAQERRDEARDAKSKAEERLNRLRDKRERKA 863
                                       999999999*******************9988864 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 ?    3.2   8.4      0.19        93      31     128 ..     197     298 ..     168     304 .. 0.48
   2 ?    4.5   8.3     0.076        37      29     130 ..     266     364 ..     260     382 .. 0.58
   3 ?    3.1   5.6      0.21     1e+02      35     104 ..     343     413 ..     322     441 .. 0.69
   4 ?    1.9   1.2      0.48   2.3e+02      30     115 ..     391     473 ..     377     482 .. 0.50
   5 !   17.8   2.3   6.1e-06    0.0029      31     127 ..     572     669 ..     569     673 .. 0.93
   6 ?    5.9   6.8     0.028        14      32     124 ..     710     804 ..     698     809 .. 0.63
   7 ?    1.5   8.2      0.62     3e+02      25      98 ..     812     887 ..     810     914 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.19
                                       CCCCHHHCCCCCC.....CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHH CS
                         Fib_alpha  31 kdvkkdleklene.....leeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqes 102
                                       ++v++d+e+le +     +++ +++  + e  + +++d l++  +  +  ++ i++++++   + ++l ++ d+   
  gi|336252351|ref|YP_004595458.1| 197 QTVQEDIEELEADdpkatVQSKAEEIDDLEARIGDLSDGLEDGRERLRAIESDIEEYRERES-DLSDLTDERDEAKD 272
                                       33344444443211111133333333333444444444444444444434555555555433.55555555555555 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 103 nirvLqnvlesneqkiqkLeqdidqk 128
                                       +i  Lq+ ++++e +iq+  ++i+++
  gi|336252351|ref|YP_004595458.1| 273 TIDDLQSEIDELEAEIQECDEAIAKQ 298
                                       56666666666666665555555555 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.076
                                       CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH........HHHHHHHHHHHHHHCCCHHHHHH CS
                         Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkd........ndnvikksskeleeeilrlketi 97 
                                        + + k+++++l++e++e++ + +e +e + + ++ ++++  +  d         ++++           ++++ + 
  gi|336252351|ref|YP_004595458.1| 266 ERDEAKDTIDDLQSEIDELEAEIQECDEAIAKQRERIESRDDEVVDfdltnedeAKEAV-----------EEFETKY 331
                                       55667788888888888888888888888888888887777777652222222223333...........3444444 PP

                                       HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  98 daqesnirvLqnvlesneqkiqkLeqdidqker 130
                                       d+  s++++ +  ++s e  +++Le + +++++
  gi|336252351|ref|YP_004595458.1| 332 DEASSEVEQRRAEVDSAEDTVERLEDELQSQRE 364
                                       444444444444444444444444444444433 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.21
                                       HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHH CS
                         Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.sni 104
                                        ++++ e+++e+++++ ++ +e  ++ ++ l+++++  +  ++++ + +++le++ + l+e++++   + +
  gi|336252351|ref|YP_004595458.1| 343 AEVDSAEDTVERLEDELQSQREELEDAQNRLHAREADVEAAEETLGEAKDSLEQRREILEEQLQDYLeTPL 413
                                       45666677777777777777777777777777777777777888888888888888877777766654444 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.48
                                       CCCCCHHHCCCCCCCCCCCCH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisns.tkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnir 105
                                       + +++++ e le++l+++ ++   +++++  +++d + +  ++k+d +    +++++ + + +rl ++id+ es++ 
  gi|336252351|ref|YP_004595458.1| 391 KDSLEQRREILEEQLQDYLETpLDDVDDHEAAVRDRMDDIREEKSDRE---AEYESKRD-RRARLGDEIDTIESELS 463
                                       444444444455555443322134444444455555444444444322...23333333.45566666666666666 PP

                                       HHHHHHHHHH CS
                         Fib_alpha 106 vLqnvlesne 115
                                       + ++  ++ +
  gi|336252351|ref|YP_004595458.1| 464 EVRERRDDIR 473
                                       6665555555 PP

  == domain 5  score: 17.8 bits;  conditional E-value: 6.1e-06
                                       CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilrlketidaqesnirv 106
                                       +d+++++++le+e ee++     a ++  + ++ l++ q+ ++   + +  k   ++  ei +l+++i ++ ++  +
  gi|336252351|ref|YP_004595458.1| 572 HDYDTQIQRLESEREEAETAADAAIDTLDAADERLNHVQEVADALfEAASFKALADVAIEIDDLEAEIEQKQQTRSE 648
                                       7899*************************************998788888888889999****************** PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 107 LqnvlesneqkiqkLeqdidq 127
                                       Lq+ +es+e++i++Le++i++
  gi|336252351|ref|YP_004595458.1| 649 LQDEMESLEEEISRLEEAIAE 669
                                       ******************986 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.028
                                       CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                         Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn..dnvikksskeleeeilrlketidaqesnirv 106
                                       +++ ++e++e++l+++++  k+ae   +e +++l e ++  +     +  +    +le+++  ++ ++d++e+++  
  gi|336252351|ref|YP_004595458.1| 710 ELEAEIEDIESDLDDAREDVKDAEADLQEAEEQLDEVESARSAAreARDAHAEIATLESDQKGYRSRLDDKEEQVAS 786
                                       44556666666666666666666666666666666555544443223333333446788888888888888888888 PP

                                       HHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 107 LqnvlesneqkiqkLeqd 124
                                        ++ l++ e +i++ e+d
  gi|336252351|ref|YP_004595458.1| 787 KREELQQIEDEIEEVESD 804
                                       888888888888888776 PP

  == domain 7  score: 1.5 bits;  conditional E-value: 0.62
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHHHHHHH CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrlketid 98 
                                        l+++++++++ +e++e++le+++++  ea++  ++ ++ l++   + + +   ++ ++  ++ l+ + +++ +t +
  gi|336252351|ref|YP_004595458.1| 812 DLKEQQNETETLIEQVESQLEDAQERRDEARDAKSKAEERLNRLRDKRERKaslEEQVNWAQTLLN-DFETITKTYS 887
                                       588999999999999999999999999888888877777766544443332223555554444444.5555555444 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.8e-05     0.018       7      52 ..       4      49 ..       1      58 [. 0.80
   2 ?   -1.6   0.9       3.9   1.9e+03     118     157 ..     806     849 ..     776     892 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.8e-05
                                      EEEEEEEETTEEEEEE-HHHHHHHHHS--SHHHHHHHHHHHHHHS- CS
                              MukB  7 ksltlinWnGffartfdldelvttlsGgnGaGksttmaafvtaliP 52
                                      + l l +++ +      +d+ +t l G nGaGkst+  a++t+l P
  gi|336252351|ref|YP_004595458.1|  4 ERLSLSDFQSYDNLDVTFDDGLTLLHGPNGAGKSTITRALYTTLYP 49
                                      555566666666666678999***********************98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.9
                                       EEEEEES--TT--HHHHHEE--S....SS--EE--HHHHHHHHH CS
                              MukB 118 kpfalqgleedvkltdvllekld....dkkarvrelnelkekle 157
                                       +  +  +l+e+++ t+ l+e+++    d ++r  e  + k+k+e
  gi|336252351|ref|YP_004595458.1| 806 EDTSPDDLKEQQNETETLIEQVEsqleDAQERRDEARDAKSKAE 849
                                       44555677777777777777655111133444444444444433 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7  12.9     0.007       3.4      57     183 ..     180     301 ..     160     306 .. 0.68
   2 !    8.2  21.4    0.0013      0.62      76     219 ..     259     403 ..     257     418 .. 0.69
   3 ?    3.5   2.1     0.034        16     351     408 ..     425     482 ..     404     497 .. 0.59
   4 !   11.3  13.2   0.00015     0.072     351     430 ..     623     701 ..     567     705 .. 0.74
   5 !    6.4  30.3    0.0044       2.1     193     382 ..     698     894 ..     696     917 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.007
                                       TTHHHHHHHHHHHHHHHHHHTHHHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTT CS
                              EzrA  57 eseekfeewkkkwdeiktkklpeieellfeaeelldkykfkkakkklaeleeeldeveekikkileelkelteseek 133
                                       e+++++e+    w++ k +kl+ ++e ++e+e++  k  +++  +++++le+++ ++   +++ +e l+ + +  e+
  gi|336252351|ref|YP_004595458.1| 180 EMQKTVES----WQQDKRSKLQTVQEDIEELEADDPKATVQSKAEEIDDLEARIGDLSDGLEDGRERLRAIESDIEE 252
                                       44444444....44447777888888888888888888888888888888888888888888888888888888777 PP

                                       THHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH---------- CS
                              EzrA 134 nreeieklkekYrelrkkllanrfsygealeelekqleniekefsefeel 183
                                        re+  +l +  +e r++ +++ +++++ ++ele +++++++ +++  e 
  gi|336252351|ref|YP_004595458.1| 253 YRERESDLSDLTDE-RDEAKDTIDDLQSEIDELEAEIQECDEAIAKQRER 301
                                       77777776665444.56666666666666666666666666666655554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0013
                                       HTHHHHHT-GGGT--S-S..HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHH.HTTTTTHHHHHHHHHHHHHHH CS
                              EzrA  76 klpeieellfeaeelldk..ykfkkakkklaeleeeldeveekikkileelkelt.eseeknreeieklkekYrelr 149
                                       +l +++++  ea++ +d    ++ +++++++e +e +++ +e+i++  +e+ ++  ++e + +e++e+ ++kY+e +
  gi|336252351|ref|YP_004595458.1| 259 DLSDLTDERDEAKDTIDDlqSEIDELEAEIQECDEAIAKQRERIESRDDEVVDFDlTNEDEAKEAVEEFETKYDEAS 335
                                       67778888888888888511468899999999999999999999999999999962567788999************ PP

                                       HT--TTTTHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                              EzrA 150 kkllanrfsygealeelekqleniekefsefeeltengdyveakeilkkleeeideleevieeiPellee 219
                                        +++++r++  +a++++e   ++++++ +e+e++ +     ea+  ++++ee + e ++ +e+  e+lee
  gi|336252351|ref|YP_004595458.1| 336 SEVEQRRAEVDSAEDTVERLEDELQSQREELEDAQNRLHAREAD--VEAAEETLGEAKDSLEQRREILEE 403
                                       *******9999888877766666666666666555433333332..455555555555555555555432 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 351 kelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkd 408
                                       +++++++++  + e + e+k     +l +e++++e++l+e+ e+ ++i+esl++  +d
  gi|336252351|ref|YP_004595458.1| 425 DRMDDIREEKSDREAEYESKRDRRARLGDEIDTIESELSEVRERRDDIRESLETAVDD 482
                                       3444555555555555555555555566666666666666666666666666655555 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 351 kelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeik 427
                                       k l ++  ++++le ++e+k+++ Selq+e+e+lee+++++ee   e +++l+++++ E +A+  +de ++el++++
  gi|336252351|ref|YP_004595458.1| 623 KALADVAIEIDDLEAEIEQKQQTRSELQDEMESLEEEISRLEEAIAEGETALDTIEDVE-DAETAVDEAERELEDAR 698
                                       4788889999********************************************98776.7999******9999998 PP

                                       HHS CS
                              EzrA 428 rki 430
                                        ++
  gi|336252351|ref|YP_004595458.1| 699 DEL 701
                                       776 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.0044
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSHHHHHHHHHHHHHSTTS--....SGGGSSSSSHHHHHHHHHHHHH CS
                              EzrA 193 keilkkleeeideleevieeiPelleelkkelpkqleelkegykemkeegY....aleelniekeieelekkieeil 265
                                       ++ l +++eei ele+ ie+i + l+++++++++  ++l+e  +++ e +     a e  +   ei +le + + + 
  gi|336252351|ref|YP_004595458.1| 698 RDELADIKEEIGELEAEIEDIESDLDDAREDVKDAEADLQEAEEQLDEVESarsaAREARDAHAEIATLESDQKGYR 774
                                       55566666666666666666666666666666666555555555554433200002333456666666666666666 PP

                                       HHHTT-..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSST CS
                              EzrA 266 erlkel..eledveeelktieeeidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlkqsYeLse 340
                                       +rl++   ++ + +eel++ie+ei+++ +dle    + ++ +++++e+++ +e++e+q+++ +e  d+ ++    +e
  gi|336252351|ref|YP_004595458.1| 775 SRLDDKeeQVASKREELQQIEDEIEEVESDLE--DTSPDDLKEQQNETETLIEQVESQLEDAQERRDEARDAKSKAE 849
                                       66644311445555666666666666666664..3566666666666666666666666666666666666665566 PP

                                       TTSTTHHHHHHHHHHHHHHH...HHHHHHHS-SS---STTGGGTH CS
                              EzrA 341 eeleklrelekelkelekdy...eeleekleekkvaYSelqeele 382
                                       e l++lr+  ++  +le+++   ++l +++e+ + +YSe+q +++
  gi|336252351|ref|YP_004595458.1| 850 ERLNRLRDKRERKASLEEQVnwaQTLLNDFETITKTYSEVQTRMR 894
                                       655555554444444443331114555566666666666666654 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 !   17.0   1.8   8.4e-06     0.004       1     240 [.      25     235 ..      25     314 .. 0.82
   2 ?   -1.5   0.4       3.5   1.7e+03     156     210 ..     425     473 ..     346     505 .. 0.64
   3 !    8.5   5.0    0.0032       1.5      67     278 ..     768     995 ..     761    1013 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.4e-06
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsll.dlydpeipfefeieeflsqgvryrygl 76 
                                       l++l GpNg+GKS++ +al+            t+  + +g++++ ++ l dl+++ ++++ ++  f   + ryr  +
  gi|336252351|ref|YP_004595458.1|  25 LTLLHGPNGAGKSTITRALY------------TTLYPLNGKYKIGAHDLaDLIQDGKDSATSTLVFSVGDERYRITV 89 
                                       68999**************6............445566666665555432778888888888887888888888888 PP

                            AAA_21  77 rlersqv..eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsra 151
                                       ++ r++   +    +  +l++  +++ k+s++ee+v+  ++ ++ + + + ++++ ++   ++   g++ + +++ +
  gi|336252351|ref|YP_004595458.1|  90 DISRKGDgrASANAEMTNLESEETYSTKSSEIEEKVSQLFGMDAEAFANSTYAQQTELTRLIEATPGEREDILDNLL 166
                                       88888888777777777777777999999999999999999999999999999888888888888888888888777 PP

                            AAA_21 152 wsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengd 228
                                         ++++       +    n  ++++  +   ++ +  + + +  e+e++d ++ +++ a+++++l            
  gi|336252351|ref|YP_004595458.1| 167 GLTAPDA------YEEDINEMQKTVESWQQDKRSKLQTVQEDIEELEADDPKATVQSKAEEIDDLEA---------- 227
                                       7777777......888888888888888888888888888888888888888888888888877544.......... PP

                            AAA_21 229 gqelparelSdG 240
                                            + +lSdG
  gi|336252351|ref|YP_004595458.1| 228 ----RIGDLSDG 235
                                       ....55555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.5
                            AAA_21 156 llldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeelia 210
                                       + +      +  + + +++++ + ++++++ rl ++++++e+els  +e+ ++i 
  gi|336252351|ref|YP_004595458.1| 425 DRM------DDIREEKSDREAEYESKRDRRARLGDEIDTIESELSEVRERRDDIR 473
                                       222......5555666666666667777777777777777777777766666554 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0032
                            AAA_21  67 sqgvryryglrlersqv..........eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvs 133
                                       s+ + yr +l+ +++qv          e+ + +ve++le++  +d +    e ++  e  ++      +++ e   +
  gi|336252351|ref|YP_004595458.1| 768 SDQKGYRSRLDDKEEQVaskreelqqiEDEIEEVESDLEDTSPDDLKEQQNETETLIEQVESQLEDAQERRDEARDA 844
                                       66677888888888888777777777788889999999999999999999999999999999999999999999999 PP

                            AAA_21 134 epndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeelia 210
                                       ++ ++++  +l d ++r++sl++  ++    + +l+++   + ++++++++++++v  +++++ ++ + +   ++++
  gi|336252351|ref|YP_004595458.1| 845 KSKAEERLNRLRDKRERKASLEEQVNWA---QTLLNDFETITKTYSEVQTRMRERVLDRLKRHTNDIFRDLY-QNST 917
                                       9999999999999999999888877776...999999999999************99999999999888655.5555 PP

                            AAA_21 211 svderlrergvvflengdgqelparelSdGtkrllalltallralkkg.............sllliDEpEngLHPkl 274
                                        ++++++e++   l+ g+   ++++++S G   l   +t+ lra   +             + +++DEp n+L+P  
  gi|336252351|ref|YP_004595458.1| 918 YEAVDIDENYDLRLVSGSETARDPNKASGGEGVL---VTIALRAGVYRvladqaggrddslPPFILDEPTNHLDPTH 991
                                       5566666669999999***********6666666...44444444444444558899******************76 PP

                            AAA_21 275 lrrl 278
                                       + rl
  gi|336252351|ref|YP_004595458.1| 992 IDRL 995
                                       6666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00012     0.058      83     148 ..       7      79 ..       1      87 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                                       -TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT.......-----S--------------SEEEEE CS
                       RsgA_GTPase  83 saktkegleelkellkdktsvlvGqSGvGKStLinallpe.......lelktgevseklgrGkhTTtavelle 148
                                       s ++ +++++l   ++d +++l G+ G+GKSt+  al  +        ++  +++ +  + Gk   t++ +++
  gi|336252351|ref|YP_004595458.1|   7 SLSDFQSYDNLDVTFDDGLTLLHGPNGAGKSTITRALYTTlyplngkYKIGAHDLADLIQDGKDSATSTLVFS 79 
                                       5566688999999*********************999876444444345555556666666666666666665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00097      0.47       2      92 ..      27     124 ..      26     129 .. 0.60
   2 ?    1.0   0.1       1.1   5.4e+02      32      78 ..     887     933 ..     870     942 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00097
                      RNA_helicase   2 wlyGpsgeGKStlakeLakall...kkl........klkkkdsvys...rnpeddfwdgYtgqevvvidDfgqvkde 64 
                                       +l+Gp+g GKSt+++ L ++l    +k+        +      ++     +++++ + +  ++ + +  D++++ d+
  gi|336252351|ref|YP_004595458.1|  27 LLHGPNGAGKSTITRALYTTLYplnGKYkigahdlaD------LIQdgkDSATSTLVFSVGDERYRITVDISRKGDG 97 
                                       689**************99998444222333322221......2221112234444555556677777777777666 PP

                      RNA_helicase  65 enpsdlaelirlvsstpyplnmasleek 92 
                                          s  ae+ +l s  +y ++  ++eek
  gi|336252351|ref|YP_004595458.1|  98 -RASANAEMTNLESEETYSTKSSEIEEK 124
                                       .555667777777777777777777776 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.1
                      RNA_helicase  32 dsvysrnpeddfwdgYtgqevvvidDfgqvkdee.npsdlaelirlvs 78 
                                       ++v    +++ ++d  ++++  ++ D++q+++ e  + d++  +rlvs
  gi|336252351|ref|YP_004595458.1| 887 SEV-QTRMRERVLDRLKRHTNDIFRDLYQNSTYEaVDIDENYDLRLVS 933
                                       222.257789999*****************977644447777777766 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.0      0.48   2.3e+02      82     142 ..     191     251 ..     157     279 .. 0.56
   2 ?    2.2   0.5      0.22   1.1e+02      82     147 ..     238     301 ..     222     335 .. 0.66
   3 ?   -0.3   1.1       1.3   6.3e+02      80     136 ..     338     375 ..     314     409 .. 0.42
   4 ?   14.3   0.3   4.3e-05     0.021      77     162 ..     410     497 ..     395     504 .. 0.85
   5 ?    1.8   1.2      0.29   1.4e+02      96     136 ..     631     669 ..     587     696 .. 0.62
   6 ?    2.9   0.7      0.13        65      78     143 ..     692     752 ..     669     774 .. 0.53
   7 ?    0.2   6.3      0.88   4.3e+02      78     147 ..     782     851 ..     773     869 .. 0.74
   8 ?    0.7   3.7      0.61     3e+02      60     138 ..     819     897 ..     813     924 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.48
                      Allexi_40kDa  82 elrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelssset 142
                                       + r++l+t+++++++l+++  k + + + ++  +l  ++  +   le+  ++l+ + s  +
  gi|336252351|ref|YP_004595458.1| 191 DKRSKLQTVQEDIEELEADDPKATVQSKAEEIDDLEARIGDLSDGLEDGRERLRAIESDIE 251
                                       3345555555555555555555555555555555555555555555555555555544444 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.22
                      Allexi_40kDa  82 elrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelsssetseseg 147
                                       + r++lr++++++++ ++ e+ l++ +++ ++ k  ++++ ++ +++el a+++e  ++ +++ e+
  gi|336252351|ref|YP_004595458.1| 238 DGRERLRAIESDIEEYRERESDLSDLTDERDEAK--DTIDDLQSEIDELEAEIQECDEAIAKQRER 301
                                       5566667777777776666666666555555554..667777777777777776665555554444 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.3
                      Allexi_40kDa  80 Lselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhaklde 136
                                       + + r+++   ++++++l++  ++++++ e+a+                   ++l+ 
  gi|336252351|ref|YP_004595458.1| 338 VEQRRAEVDSAEDTVERLEDELQSQREELEDAQ-------------------NRLHA 375
                                       233333333333333333333333333333322...................22221 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 4.3e-05
                      Allexi_40kDa  77 ttlLselrdalrtltklldklksvekklelsaetasdsk..llkklesietsleelhakldelsssetsesegPsss 151
                                       +t+L ++ d+  ++++ +d++++ ++  e++ e++ d++  l +++++ie +l e+ ++ d++ +s + + + P+++
  gi|336252351|ref|YP_004595458.1| 410 ETPLDDVDDHEAAVRDRMDDIREEKSDREAEYESKRDRRarLGDEIDTIESELSEVRERRDDIRESLETAVDDPEVA 486
                                       68999*******************99999988887776511669*******************************99 PP

                      Allexi_40kDa 152 ptkassaeaaa 162
                                        + a  + ++a
  gi|336252351|ref|YP_004595458.1| 487 FEAAVDRANEA 497
                                       88776655555 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.29
                      Allexi_40kDa  96 klksvekklelsaetasdskllkklesietsleelhaklde 136
                                       ++ ++e   e+++++++ s+l++++es+e+++ +l + + e
  gi|336252351|ref|YP_004595458.1| 631 EIDDLE--AEIEQKQQTRSELQDEMESLEEEISRLEEAIAE 669
                                       333333..344455556666678888888888777776644 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.13
                      Allexi_40kDa  78 tlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelsssets 143
                                        +L + rd+l  +++++ +l++  + +e + ++a      ++++  e +l+e  ++lde+ s+ + 
  gi|336252351|ref|YP_004595458.1| 692 RELEDARDELADIKEEIGELEAEIEDIESDLDDAR-----EDVKDAEADLQEAEEQLDEVESARSA 752
                                       34444444444444444444444444443333222.....34455556666666666666555444 PP

  == domain 7  score: 0.2 bits;  conditional E-value: 0.88
                      Allexi_40kDa  78 tlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelsssetseseg 147
                                        +++  r++l+++++++++++s+ + ++ +  +++++++ + +e +e +le+ +++ de   ++++++e+
  gi|336252351|ref|YP_004595458.1| 782 EQVASKREELQQIEDEIEEVESDLEDTSPDDLKEQQNETETLIEQVESQLEDAQERRDEARDAKSKAEER 851
                                       5566778888888888888888888888777777777777888999999999988888877776666554 PP

  == domain 8  score: 0.7 bits;  conditional E-value: 0.61
                      Allexi_40kDa  60 dvdsiinklnpvsllsqttlLselrdalrtltklldklksv.ekklelsaetasdskllkklesietsleelhakld 135
                                       +++ +i+++++  l   +    e rda  + ++ l++l+++ e+k +l+++ +  + ll+++e+i ++  e++++++
  gi|336252351|ref|YP_004595458.1| 819 ETETLIEQVESQ-LEDAQERRDEARDAKSKAEERLNRLRDKrERKASLEEQVNWAQTLLNDFETITKTYSEVQTRMR 894
                                       677888888777.566667778999*999*******9987615667788888889999**************99998 PP

                      Allexi_40kDa 136 els 138
                                       e +
  gi|336252351|ref|YP_004595458.1| 895 ERV 897
                                       744 PP

>> V-SNARE_C  Snare region anchored in the vesicle membrane C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   5.2e-05     0.025      30      59 ..     358     387 ..     350     391 .. 0.90
   2 ?   -1.3   0.0       5.6   2.7e+03      36      55 ..     727     746 ..     693     749 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.2e-05
                         V-SNARE_C  30 dLhsQretLkrarsklhnvanrlgksnsiL 59 
                                       +L+sQre L++a+++lh   +++  +  +L
  gi|336252351|ref|YP_004595458.1| 358 ELQSQREELEDAQNRLHAREADVEAAEETL 387
                                       79***************9999999988888 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.6
                         V-SNARE_C  36 etLkrarsklhnvanrlgks 55 
                                       e  k+a + l+++ ++l+ +
  gi|336252351|ref|YP_004595458.1| 727 EDVKDAEADLQEAEEQLDEV 746
                                       44444444444444444443 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  16.3    0.0016      0.78     114     239 ..     176     308 ..      90     312 .. 0.84
   2 ?    9.8  24.7   0.00093      0.45     130     238 ..     267     385 ..     240     403 .. 0.68
   3 ?    6.6  23.9    0.0092       4.4     111     250 ..     308     458 ..     306     501 .. 0.72
   4 ?    3.3   6.8     0.089        43     130     235 ..     508     619 ..     469     625 .. 0.73
   5 ?   12.3  17.5   0.00016     0.079     128     240 ..     632     743 ..     610     748 .. 0.79
   6 ?    1.1  24.5      0.44   2.1e+02     122     232 ..     745     862 ..     737     884 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                           DUF4407 114 eeqqeeakelkeqlaaaltaelaeleaqia............alqaeidaaearldalraeaqkeldgtk..gtgtt 176
                                       e  +e++k++ e+++++ +++l++ +++i+            +  +eid +ear+ +l + +           ++  
  gi|336252351|ref|YP_004595458.1| 176 EDINEMQKTV-ESWQQDKRSKLQTVQEDIEeleaddpkatvqSKAEEIDDLEARIGDLSDGL-------EdgRERLR 244
                                       4556666666.888888888888888888877777444444445555555555555555555.......34466677 PP

                           DUF4407 177 gvaGkgpaakekkaqldaaqaelaelkakld.atarlaalraelaeleaerakeraasqaaaaa 239
                                       +++ + ++++e++++l +++ e +e+k+++d  ++++++l+ae++e ++++ak+r++ +++ ++
  gi|336252351|ref|YP_004595458.1| 245 AIESDIEEYRERESDLSDLTDERDEAKDTIDdLQSEIDELEAEIQECDEAIAKQRERIESRDDE 308
                                       89999************************9999999*********9999999999998876665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00093
                           DUF4407 130 a.........ltaelaeleaqiaalqaeidaaearldalraeaq.keldgtkgtgttgvaGkgpaakekkaqldaaq 196
                                                 l++e++elea+i++ +++i+++++r++   +e+    l+++  +  ++v+  ++ ++e+ ++ ++++
  gi|336252351|ref|YP_004595458.1| 267 RdeakdtiddLQSEIDELEAEIQECDEAIAKQRERIESRDDEVVdFDLTNE-DEAKEAVEEFETKYDEASSEVEQRR 342
                                       122233333467777777777777777777777777666555440344444.44457799999************** PP

                           DUF4407 197 aelaelkakld.atarlaalraelaeleaerakeraasqaaaa 238
                                       ae+++++++++  +++l+++r+el+++++++++++a+ +aa++
  gi|336252351|ref|YP_004595458.1| 343 AEVDSAEDTVErLEDELQSQREELEDAQNRLHAREADVEAAEE 385
                                       ********99998888999999999999888888888888765 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0092
                           DUF4407 111 elaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..gtgttgvaGkgpaa 185
                                       e+ +++  +++e+ke ++ +++++++e+ +++++ +ae+d+ae+++++l++e+q++ +     +++  +++ + +aa
  gi|336252351|ref|YP_004595458.1| 308 EVVDFDLTNEDEAKEAVE-EFETKYDEASSEVEQRRAEVDSAEDTVERLEDELQSQREELEdaQNRLHAREADVEAA 383
                                       566666677777777766.7**********************************99986545555555555554444 PP

                           DUF4407 186 ke.kkaqldaaqaelaelkakld.........atarlaalraelaeleaerakeraasqaaaaaddGllarleal 250
                                       +e   ++ d ++++ + l+++l+          ++  aa r++++++++e+++++a+ +++++  + l+++++ +
  gi|336252351|ref|YP_004595458.1| 384 EEtLGEAKDSLEQRREILEEQLQdyletplddVDDHEAAVRDRMDDIREEKSDREAEYESKRDRRARLGDEIDTI 458
                                       443333344444455555555559999999996666666777777777777777777777777777777666653 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.089
                           DUF4407 130 a.........ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqa 197
                                       +         l +el+++ ++ +++ +e++ a++++ +++a+ ++  + + g+  + + G+  a++  ++q+++++ 
  gi|336252351|ref|YP_004595458.1| 508 EdidtaftgdLPDELDAALNDHRDAAEELADARETVGEATAHIEDLQSLAAGKW-PLDGGDVGATHDYDTQIQRLES 583
                                       134444555588888888888889999999999988888888877666655433.5567888888888999999999 PP

                           DUF4407 198 elaelkakldatarlaalraelaeleaerakeraasqa 235
                                       e +e+++   a+a++++l+a  ++l+  ++ + a ++a
  gi|336252351|ref|YP_004595458.1| 584 EREEAETA--ADAAIDTLDAADERLNHVQEVADALFEA 619
                                       99999999..9999999999999998888777777666 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 0.00016
                           DUF4407 128 aaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelka 204
                                        ++l+ae+++ ++ +++lq e++++e+++++l+++ ++  +    ++++ v+  ++a +e++++l++a+ ela++k+
  gi|336252351|ref|YP_004595458.1| 632 IDDLEAEIEQKQQTRSELQDEMESLEEEISRLEEAIAEGETA--LDTIEDVEDAETAVDEAERELEDARDELADIKE 706
                                       3349999999999999***************99999866554..677888999999999999999999999999999 PP

                           DUF4407 205 kld.atarlaalraelaeleaerakeraasqaaaaad 240
                                       ++   +a++++ ++ l++++++ ++++a+ q+a+++ 
  gi|336252351|ref|YP_004595458.1| 707 EIGeLEAEIEDIESDLDDAREDVKDAEADLQEAEEQL 743
                                       9878888888888888888888888888888877665 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.44
                           DUF4407 122 elkeqlaaa.....ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.......gtgttgvaGkgpaak 186
                                       e+++   aa     + ae+a+le++++  ++ +d +e++++ +r+e+q+  d                 + + ++ +
  gi|336252351|ref|YP_004595458.1| 745 EVESARSAAreardAHAEIATLESDQKGYRSRLDDKEEQVASKREELQQIEDE-IeevesdlE---DTSPDDLKEQQ 817
                                       22222111133455788888888888888888888888888888888754443.234543321...22223333322 PP

                           DUF4407 187 e.kkaqldaaqaelaelkakldatarlaalraelaeleaerakeraa 232
                                       +  ++ +++ + +l++++++  ++++++a+ +  ++l++ r+k++++
  gi|336252351|ref|YP_004595458.1| 818 NeTETLIEQVESQLEDAQER--RDEARDAKSKAEERLNRLRDKRERK 862
                                       22444455555555555555..5555555555555555555544433 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       4.9   2.4e+03     115     142 ..     102     128 ..      86     191 .. 0.60
   2 ?   11.2   9.0    0.0005      0.24      54     167 ..     199     316 ..     194     325 .. 0.78
   3 ?    6.6  10.7     0.013       6.3     105     182 ..     318     395 ..     314     398 .. 0.94
   4 ?    8.4   2.4    0.0036       1.7     100     156 ..     423     479 ..     421     516 .. 0.82
   5 ?    0.6   0.1      0.88   4.2e+02     134     170 ..     573     606 ..     480     623 .. 0.58
   6 ?   14.3  11.3   5.6e-05     0.027      99     184 ..     648     732 ..     609     735 .. 0.89
   7 ?   11.1  12.7   0.00054      0.26      95     183 ..     699     786 ..     687     790 .. 0.87
   8 ?    7.4  10.3    0.0074       3.6     103     184 ..     728     808 ..     726     811 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.9
                            DUF724 115 ekkieeeesekrkleeeidelekkilel 142
                                       + ++++ ese++ ++++ +e+e+k+++l
  gi|336252351|ref|YP_004595458.1| 102 NAEMTNLESEET-YSTKSSEIEEKVSQL 128
                                       444444444333.444445555555544 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0005
                            DUF724  54 llekvkklsiddsrseleslkeslaeLekhGFdVka.lqsrlnkLlslkdeqtklleerkkle...kkieeeesekr 126
                                       + e +++l++dd++++ +s+ e++ +Le+   d    l++  ++L ++ ++ ++++e++++l     +  e+++   
  gi|336252351|ref|YP_004595458.1| 199 VQEDIEELEADDPKATVQSKAEEIDDLEARIGDLSDgLEDGRERLRAIESDIEEYRERESDLSdltDERDEAKDTID 275
                                       6699*************************988887524444577888887777777776665500055666666667 PP

                            DUF724 127 kleeeidelekkilelerqlallkekkeaadkeiarlksea 167
                                        l++eidele +i+e  +  a  +e+ e+ d e+++    +
  gi|336252351|ref|YP_004595458.1| 276 DLQSEIDELEAEIQECDEAIAKQRERIESRDDEVVDFDLTN 316
                                       78999****************999**9*9999998876554 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.013
                            DUF724 105 tklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeF 181
                                       ++++e+ +++e k  e++se ++  +e+d  e ++ +le +l++ +e+ e+a++++ + ++++e++ee+l +++++ 
  gi|336252351|ref|YP_004595458.1| 318 DEAKEAVEEFETKYDEASSEVEQRRAEVDSAEDTVERLEDELQSQREELEDAQNRLHAREADVEAAEETLGEAKDSL 394
                                       57789999***************************************************************999987 PP

                            DUF724 182 e 182
                                       e
  gi|336252351|ref|YP_004595458.1| 395 E 395
                                       6 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0036
                            DUF724 100 lkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaa 156
                                       ++d+ + ++ee+++ e + e +++++++l +eid +e++ +e++++++ ++e  e+a
  gi|336252351|ref|YP_004595458.1| 423 VRDRMDDIREEKSDREAEYESKRDRRARLGDEIDTIESELSEVRERRDDIRESLETA 479
                                       789999****************************************99999655543 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.88
                            DUF724 134 elekkilelerqlallkekkeaadkeiarlkseaekl 170
                                       + + +i++le +++   e + aad+ i +l +  e+l
  gi|336252351|ref|YP_004595458.1| 573 DYDTQIQRLESERE---EAETAADAAIDTLDAADERL 606
                                       34444444444443...44555555555555555555 PP

  == domain 6  score: 14.3 bits;  conditional E-value: 5.6e-05
                            DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeele 175
                                       +l+de ++l+ee+++le+ i+e e++   + e++++ e ++ e er+l+ ++ +  + ++ei +l++e e++e +l+
  gi|336252351|ref|YP_004595458.1| 648 ELQDEMESLEEEISRLEEAIAEGETALDTI-EDVEDAETAVDEAERELEDARDELADIKEEIGELEAEIEDIESDLD 723
                                       6899*********************99965.6779****************************************** PP

                            DUF724 176 dveqeFeav 184
                                       d+++++++ 
  gi|336252351|ref|YP_004595458.1| 724 DAREDVKDA 732
                                       **9998875 PP

  == domain 7  score: 11.1 bits;  conditional E-value: 0.00054
                            DUF724  95 nkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekle 171
                                       ++L  +k+e  +l+ e++++e+++ +++++ + +e++++e e++  e+e  + +++e + +a +eia+l+s+++ ++
  gi|336252351|ref|YP_004595458.1| 699 DELADIKEEIGELEAEIEDIESDLDDAREDVKDAEADLQEAEEQLDEVESARSAAREAR-DAHAEIATLESDQKGYR 774
                                       57888999999999999999999999999999999999999999999999999888766.7789************* PP

                            DUF724 172 eeledveqeFea 183
                                        +l+d e+++ +
  gi|336252351|ref|YP_004595458.1| 775 SRLDDKEEQVAS 786
                                       *******99865 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.0074
                            DUF724 103 eqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveq 179
                                       + + ++  ++++e+++ e es+++ +  e ++   +i++le  ++  +++ +++++++a+ + e +++e+e+e+ve+
  gi|336252351|ref|YP_004595458.1| 728 DVKDAEADLQEAEEQLDEVESARS-AAREARDAHAEIATLESDQKGYRSRLDDKEEQVASKREELQQIEDEIEEVES 803
                                       556778889999999999999877.6777789999****************************************** PP

                            DUF724 180 eFeav 184
                                       + e++
  gi|336252351|ref|YP_004595458.1| 804 DLEDT 808
                                       99887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00053      0.26       4      29 ..      22      47 ..      19      68 .. 0.90
   2 ?    1.0   5.3         1   4.9e+02      31     100 ..     298     369 ..     284     442 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00053
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      ++g+++++G+ G+GK+t  r l  +l
  gi|336252351|ref|YP_004595458.1| 22 DDGLTLLHGPNGAGKSTITRALYTTL 47
                                      5799***************9987765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1
                            AAA_22  31 eeakaeeerpevvfvtlpsstsskdllrellralglelka......erlsseellealeqalraravielliiDEa 100
                                       +++ +e +++evv ++l+++ + k+  +e+  ++++  ++      e +s e+ +e+le+ l++++      +++a
  gi|336252351|ref|YP_004595458.1| 298 QRERIESRDDEVVDFDLTNEDEAKEAVEEFETKYDEASSEveqrraEVDSAEDTVERLEDELQSQRE----ELEDA 369
                                       33444449***************************98888***998777777777999999999987....44444 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   0.0   0.00082       0.4       2      23 ..      27      48 ..      26     126 .. 0.80
   2 ?   -1.7   0.5       7.4   3.6e+03      65     100 ..     453     495 ..     415     536 .. 0.67
   3 ?    0.2   1.2       1.9   9.4e+02      46      96 ..     613     663 ..     589     678 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00082
                                      EEESSTTSSHHHHHHHHHHHHT CS
                               AAA  2 llyGppGtGKTllakavakelg 23
                                      ll+Gp G GK+++ +a+ ++l 
  gi|336252351|ref|YP_004595458.1| 27 LLHGPNGAGKSTITRALYTTLY 48
                                      8****************99973 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7.4
                                       ETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS........S CS
                               AAA  65 DEidalaksrsgseseeeervvnqLlteldgvkkk........e 100
                                       DEid + ++  ++ +e ++++ + L t++d+ +          +
  gi|336252351|ref|YP_004595458.1| 453 DEIDTIESEL-SEVRERRDDIRESLETAVDDPEVAfeaavdraN 495
                                       7888885555.566667777777777777777765555544440 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHT CS
                               AAA  46 irelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgv 96 
                                         +lf++a+ ka + + + iD+++a ++++ +++++e ++ ++ L +e++++
  gi|336252351|ref|YP_004595458.1| 613 ADALFEAASFKAlADVAIEIDDLEAEIEQK-QQTRSELQDEMESLEEEISRL 663
                                       4456666666666679999****9999988.455555555566665555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00098      0.47       1      21 [.      25      45 ..      25     112 .. 0.89
   2 ?   -1.9   0.7       7.1   3.4e+03      95     134 ..     318     356 ..     291     367 .. 0.66
   3 ?   -1.3   0.2       4.6   2.2e+03     109     141 ..     367     395 ..     360     399 .. 0.76
   4 ?    0.0   0.2       1.8   8.6e+02      87     133 ..     612     660 ..     576     669 .. 0.65
   5 ?   -0.5   0.3       2.6   1.3e+03      25     121 ..     627     729 ..     617     749 .. 0.47
   6 ?   -0.5   0.4       2.6   1.3e+03      94     140 ..     756     798 ..     739     801 .. 0.70
   7 ?   -1.1   0.8       3.8   1.9e+03     117     141 ..     837     860 ..     809     907 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00098
                            AAA_33  1 lvllvGlpGsGKstlaerllk 21
                                      l+ll+G++G+GKst  + l+ 
  gi|336252351|ref|YP_004595458.1| 25 LTLLHGPNGAGKSTITRALYT 45
                                      679************999875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.1
                            AAA_33  95 lgvpvrivvvetdeetlkeRlakRaangddrsevpeeald 134
                                        ++++++  +et  +++ + +++R a+ d++ e + e l+
  gi|336252351|ref|YP_004595458.1| 318 DEAKEAVEEFETKYDEASSEVEQRRAEVDSA-EDTVERLE 356
                                       4556677778888888888888888876543.33334433 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.6
                            AAA_33 109 etlkeRlakRaangddrsevpeealdrqkarfe 141
                                       e ++ Rl++R+a+    +e+ ee+l + k+++e
  gi|336252351|ref|YP_004595458.1| 367 EDAQNRLHAREAD----VEAAEETLGEAKDSLE 395
                                       5567777777775....7888888888887765 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 1.8
                            AAA_33  87 rflklarrlgvp...vrivvvetdeetlkeRlakRaangddrsevpeeal 133
                                         ++l++ ++++   + ++ ++  e++++++ + R++ +d+ +e  ee +
  gi|336252351|ref|YP_004595458.1| 612 VADALFEAASFKalaDVAIEIDDLEAEIEQKQQTRSELQDE-MESLEEEI 660
                                       44555555555522245555555689999999999997653.44444444 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 2.6
                            AAA_33  25 avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvil.......datnlsrrer...arflkl 91 
                                        v ++ d+l   ++ ++q++ + +++  ++l + +  ++++a ++g +++          t ++++er   ++ ++l
  gi|336252351|ref|YP_004595458.1| 627 DVAIEIDDLEAEIEQKQQTRSE-LQDEMESLEEEI-SRLEEAIAEGETALDtiedvedAETAVDEAEReleDARDEL 701
                                       5555555555555554444433.333333333333.34444555554443333444444456666666333333333 PP

                            AAA_33  92 arrlgvpvrivvvetdeetlkeRla.kRaan 121
                                       a   + +++i  +e+  e +++ l  +R++ 
  gi|336252351|ref|YP_004595458.1| 702 A---DIKEEIGELEAEIEDIESDLDdAREDV 729
                                       3...455666666666666665553245555 PP

  == domain 6  score: -0.5 bits;  conditional E-value: 2.6
                            AAA_33  94 rlgvpvrivvvetdeetlkeRlakRaangddrsevpeealdrqkarf 140
                                         ++  +i ++e+d++ +++Rl  ++++    +  ++e l++  + +
  gi|336252351|ref|YP_004595458.1| 756 ARDAHAEIATLESDQKGYRSRLDDKEEQ----VASKREELQQIEDEI 798
                                       3466778999999999999999999997....445667776666655 PP

  == domain 7  score: -1.1 bits;  conditional E-value: 3.8
                            AAA_33 117 kRaangddrsevpeealdrqkarfe 141
                                       +R +++d +    ee l+r ++++e
  gi|336252351|ref|YP_004595458.1| 837 RRDEARD-AKSKAEERLNRLRDKRE 860
                                       2222222.22233333444333333 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.7    0.0025       1.2       7      99 ..     167     261 ..     164     263 .. 0.86
   2 ?   12.4   4.0   0.00015     0.072      39      94 ..     260     315 ..     254     319 .. 0.89
   3 ?    3.6  12.1     0.074        36      15      90 ..     332     407 ..     320     414 .. 0.80
   4 ?    8.7   1.6     0.002      0.95      41     107 ..     415     481 ..     408     490 .. 0.59
   5 ?    6.9   8.4    0.0068       3.3      15      97 ..     589     669 ..     581     679 .. 0.78
   6 ?    8.1   9.3     0.003       1.5      20      96 ..     675     751 ..     666     755 .. 0.80
   7 ?    6.1   4.9     0.012       5.8      43      92 ..     753     802 ..     748     810 .. 0.83
   8 ?   -1.6  13.7       2.7   1.3e+03      18     112 ..     810     904 ..     804     909 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0025
                           DUF3450   7 lllasgalaatldqalkeaekava.aaaqsqkkidkldd.ekqellaeyralkeeleslevyneqlerlvasqeqei 81 
                                        l+a+ a+++++++++k+ e++++ ++++ q+ ++++++ e+++ +a +++  ee+++le+    l++ +++ ++++
  gi|336252351|ref|YP_004595458.1| 167 GLTAPDAYEEDINEMQKTVESWQQdKRSKLQTVQEDIEElEADDPKATVQSKAEEIDDLEARIGDLSDGLEDGRERL 243
                                       566777889************98725678899888887548899999****************************** PP

                           DUF3450  82 asleeqieeieeierelv 99 
                                         +e +iee +e e++l+
  gi|336252351|ref|YP_004595458.1| 244 RAIESDIEEYRERESDLS 261
                                       ********9998888775 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00015
                           DUF3450  39 idklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieei 94 
                                        ++l+de++e ++ + +l++e+++le++ ++ ++ +a+q+++i+s + +  +++ +
  gi|336252351|ref|YP_004595458.1| 260 LSDLTDERDEAKDTIDDLQSEIDELEAEIQECDEAIAKQRERIESRDDEVVDFDLT 315
                                       6799****************************************998887766655 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.074
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       +++ +++++  ++  +a+  +++  d+l+ +++el++  ++l+++ ++ e+ +e l +  +s+eq+++ leeq+++
  gi|336252351|ref|YP_004595458.1| 332 DEASSEVEQRRAEVDSAEDTVERLEDELQSQREELEDAQNRLHAREADVEAAEETLGEAKDSLEQRREILEEQLQD 407
                                       4556677777788888888888888888899999999999999999999999999999999999999999998876 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.002
                           DUF3450  41 klddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmid 107
                                       ++dd  + + +++ +++ee+++ e++ e  ++  a +  ei+ +e +++e++e ++++   le+ +d
  gi|336252351|ref|YP_004595458.1| 415 DVDDHEAAVRDRMDDIREEKSDREAEYESKRDRRARLGDEIDTIESELSEVRERRDDIRESLETAVD 481
                                       4555555555555555555555555555555555555555555555555555555555555555555 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0068
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                       ++++d+a+++  +a +    +q+  d+l + ++   + + ++  e+++le++ eq ++  ++++ e++slee+i+++
  gi|336252351|ref|YP_004595458.1| 589 ETAADAAIDTLDAADERLNHVQEVADALFEAAS--FKALADVAIEIDDLEAEIEQKQQTRSELQDEMESLEEEISRL 663
                                       567788888888889999999999999988776..566788888888888888888888888888888888888888 PP

                           DUF3450  92 eeiere 97 
                                       ee  +e
  gi|336252351|ref|YP_004595458.1| 664 EEAIAE 669
                                       876555 PP

  == domain 6  score: 8.1 bits;  conditional E-value: 0.003
                           DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeier 96 
                                       ++++  e a +a  +++++ ++  de +++++e+ +l++e+e++e   +  ++ v+++e+++++ eeq++e+e  ++
  gi|336252351|ref|YP_004595458.1| 675 DTIEDVEDAETAVDEAERELEDARDELADIKEEIGELEAEIEDIESDLDDAREDVKDAEADLQEAEEQLDEVESARS 751
                                       3334445555556667777788888888999*****************************************98775 PP

  == domain 7  score: 6.1 bits;  conditional E-value: 0.012
                           DUF3450  43 ddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       ++e+++  ae+ +l++ ++  +   +  e++vas ++e++++e +iee+e
  gi|336252351|ref|YP_004595458.1| 753 AREARDAHAEIATLESDQKGYRSRLDDKEEQVASKREELQQIEDEIEEVE 802
                                       57888889999999999999999999999999999999999999999887 PP

  == domain 8  score: -1.6 bits;  conditional E-value: 2.7
                           DUF3450  18 ldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieei 94 
                                       +d+++++++++ +  +q++++ ++ ++ ++e  +   +++e+l++l+ ++ + ++++++q +  + l ++ e i+++
  gi|336252351|ref|YP_004595458.1| 810 PDDLKEQQNETETLIEQVESQLEDAQERRDEARDAKSKAEERLNRLRDKR-ERKASLEEQVNWAQTLLNDFETITKT 885
                                       55666666666666666666666666666666666666666666665443.34455566666666666666666666 PP

                           DUF3450  95 erelvpll.ekmidrLeqf 112
                                        +e++  + e+++drL+++
  gi|336252351|ref|YP_004595458.1| 886 YSEVQTRMrERVLDRLKRH 904
                                       6666666633456666654 PP

>> Fusion_gly  Fusion glycoprotein F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       3.1   1.5e+03     437     459 ..     379     401 ..     329     404 .. 0.62
   2 ?   -1.9   0.0       1.6   7.6e+02     117     142 ..     655     680 ..     649     692 .. 0.81
   3 ?   10.1   0.6   0.00035      0.17     419     466 ..     702     750 ..     675     755 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHHHHHHHCCCC CS
                        Fusion_gly 437 elskvnesleqskdlleesnkiL 459
                                       ++++++e l ++kd le+ ++iL
  gi|336252351|ref|YP_004595458.1| 379 DVEAAEETLGEAKDSLEQRREIL 401
                                       33445555555555555555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHTHHSSEEEECHC CS
                        Fusion_gly 117 knaeeiaklkeslektnkAveklqng 142
                                        ++eei +l e++++ + A  ++++ 
  gi|336252351|ref|YP_004595458.1| 655 SLEEEISRLEEAIAEGETALDTIEDV 680
                                       6799999******9999999998875 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00035
                                       CGS----.B---SHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTCCCHHH CS
                        Fusion_gly 419 lsiklgp.pisveevdisaelskvnesleqskdlleesnkiLdsvnkkl 466
                                         ik +  +++ e  di+++l+ + e+++++ + l+e++++Ld+v+   
  gi|336252351|ref|YP_004595458.1| 702 ADIKEEIgELEAEIEDIESDLDDAREDVKDAEADLQEAEEQLDEVESAR 750
                                       555555456777888******************************8765 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.24   1.1e+02      35      99 ..     146     208 ..     136     211 .. 0.74
   2 ?    5.2   0.1     0.042        20      28      95 ..     225     289 ..     212     305 .. 0.62
   3 ?    1.4   1.4      0.62     3e+02      65      80 ..     359     374 ..     314     433 .. 0.54
   4 ?    0.6   0.0       1.1   5.2e+02      36      80 ..     451     495 ..     445     516 .. 0.67
   5 ?    5.9   2.6     0.025        12      64     110 ..     624     676 ..     576     704 .. 0.56
   6 ?   12.9   4.0   0.00018     0.087      24     118 ..     638     732 ..     626     749 .. 0.83
   7 ?    3.0   5.9       0.2        97      24      64 ..     703     748 ..     696     842 .. 0.65
   8 ?    2.8   0.2      0.23   1.1e+02      23      79 ..     853     908 ..     848     917 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.24
                      Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLls 99 
                                       +l++l++a  ++ +++ ++l  l a   ++ ++ ++++++++ + q++ r++L++++ ++ +L +
  gi|336252351|ref|YP_004595458.1| 146 ELTRLIEATPGEREDILDNLLGLTA--PDAYEEDINEMQKTVESWQQDKRSKLQTVQEDIEELEA 208
                                       4555555555555666665555544..45778889999999999999999999999999999875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.042
                      Baculo_PEP_C  28 qnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsilt 95 
                                       +++ i ++l+  l++  ++L a+++d+++   e +++l++l+++ ++a  ++  +l++e++ l++++ 
  gi|336252351|ref|YP_004595458.1| 225 LEARI-GDLSDGLEDGRERLRAIESDIEE-YRERESDLSDLTDERDEAKDTID-DLQSEIDELEAEIQ 289
                                       45566.77777777777788888888887.56666666666665555555543.34444444444443 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.62
                      Baculo_PEP_C  65 ldtlltnLtdalnalq 80 
                                       l+++ ++L+da n+l 
  gi|336252351|ref|YP_004595458.1| 359 LQSQREELEDAQNRLH 374
                                       2222222222222221 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.1
                      Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq 80 
                                       l   +d+ie++L+++ e+  +  ++l+t++d+   + ++a+ + +
  gi|336252351|ref|YP_004595458.1| 451 LGDEIDTIESELSEVRERRDDIRESLETAVDDPEVAFEAAVDRAN 495
                                       566677777777777777666666666666666655555555544 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.025
                      Baculo_PEP_C  64 rldtlltnLtdalnalq......dtlrneLtnlnsiltnLlssvtNinstLnn 110
                                       +l++++ +++d  ++++       +l+ e+++l+ +++ L   ++  +++L  
  gi|336252351|ref|YP_004595458.1| 624 ALADVAIEIDDLEAEIEqkqqtrSELQDEMESLEEEISRLEEAIAEGETALDT 676
                                       44444444444444444333444445555556666666665555555555543 PP

  == domain 6  score: 12.9 bits;  conditional E-value: 0.00018
                      Baculo_PEP_C  24 airlqnvqilaqlatlldaietqLnalsedlksllaeldt..rldtlltnLtdalnalqdtlrneLtnlnsiltnLl 98 
                                        i  q+ q+ ++l+  ++++e++++ l+e++ +  ++ldt  +++++ t++++a  +l+ + r eL  ++ ++ +L 
  gi|336252351|ref|YP_004595458.1| 638 EI-EQKQQTRSELQDEMESLEEEISRLEEAIAEGETALDTieDVEDAETAVDEAERELE-DARDELADIKEEIGELE 712
                                       56.78999999********************999999999999***************8.679************** PP

                      Baculo_PEP_C  99 ssvtNinstLnnllqalnnl 118
                                       +++  i+s L    ++++  
  gi|336252351|ref|YP_004595458.1| 713 AEIEDIESDLDDAREDVKDA 732
                                       ******99998766666655 PP

  == domain 7  score: 3.0 bits;  conditional E-value: 0.2
                      Baculo_PEP_C  24 airlqnvqilaqlatlldaietqLnalsedlksllaeldt.........r 64 
                                       +i   + +i ++l++ +++ie+ L++  ed+k++ a+l++          
  gi|336252351|ref|YP_004595458.1| 703 DI---KEEI-GELEAEIEDIESDLDDAREDVKDAEADLQEaeeqldeveS 748
                                       44...4455.7788888888888888888888877777665554443440 PP

  == domain 8  score: 2.8 bits;  conditional E-value: 0.23
                      Baculo_PEP_C  23 nairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldt.lltnLtdalnal 79 
                                       n +r +     a l+++++  +t Ln++++ +++  +e++tr+ + +l++L++  n +
  gi|336252351|ref|YP_004595458.1| 853 NRLRDKRERK-ASLEEQVNWAQTLLNDFET-ITKTYSEVQTRMRErVLDRLKRHTNDI 908
                                       5555555544.899*************887.99999****988652567777777765 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   5.6       3.3   1.6e+03      54     137 ..     107     229 ..      92     245 .. 0.37
   2 ?    6.4  12.8     0.023        11      42     156 ..     191     300 ..     175     313 .. 0.61
   3 ?   10.4  16.6    0.0014      0.67      22     147 ..     211     362 ..     208     363 .. 0.68
   4 ?    7.9  23.6     0.008       3.9      38     157 ..     336     475 ..     315     478 .. 0.80
   5 ?    1.2   9.2       0.9   4.4e+02      55     141 ..     421     554 ..     401     614 .. 0.48
   6 ?    0.9  12.7       1.1   5.3e+02      63     114 ..     627     677 ..     569     698 .. 0.64
   7 ?    7.7  18.0    0.0093       4.5      16     141 ..     642     767 ..     642     769 .. 0.82
   8 ?    6.6  25.3      0.02       9.6      27     127 ..     757     879 ..     750     919 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.3
                              Fez1  54 ikeleesleektlelevcenelqrk....................................kseaellrekveklee 94 
                                       + e ee++++k+ e+e+  ++l  +                                     +  +  +e ++++++
  gi|336252351|ref|YP_004595458.1| 107 NLESEETYSTKSSEIEEKVSQLFGMdaeafanstyaqqteltrlieatpgeredildnllgLTAPDAYEEDINEMQK 183
                                       45555555555555443333333332222222222222222222333333333333333332222333333333333 PP

                              Fez1  95 elkelreelselsleeeeaa..lesdeakaq.rqeaeeleelkrev 137
                                        +++ +++ +++ ++ +e +  le+d+ ka  +++aee+++l++++
  gi|336252351|ref|YP_004595458.1| 184 TVESWQQDKRSKLQTVQEDIeeLEADDPKATvQSKAEEIDDLEARI 229
                                       3333333222211111111112223333322112234444444444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.023
                              Fez1  42 elrakleekeeeikel.....eesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeea 113
                                       + r+kl++ +e i+el     ++++++k++e++ +e+++   ++  e  re+++++e++++e re+ s+ls  ++e 
  gi|336252351|ref|YP_004595458.1| 191 DKRSKLQTVQEDIEELeaddpKATVQSKAEEIDDLEARIGDLSDGLEDGRERLRAIESDIEEYRERESDLSDLTDE- 266
                                       4444555444444444111115678888889999999999999999999999999999999999977775543333. PP

                              Fez1 114 alesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqas 156
                                           de      +++++++l++e+++l+ae++e  ++  +q++
  gi|336252351|ref|YP_004595458.1| 267 ---RDE------AKDTIDDLQSEIDELEAEIQECDEAIAKQRE 300
                                       ...233......2344555555555555555554444444333 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0014
                              Fez1  22 sqaevtqklseivalkaqlrelrakleekeeeikele...esleektlelevcenelqrkkseaellrekvekleee 95 
                                        +a v +k++ei  l a++ +l+  le+  e+++ +e   e+++e++ +l  + +e +++k++ + l+ ++++le+e
  gi|336252351|ref|YP_004595458.1| 211 PKATVQSKAEEIDDLEARIGDLSDGLEDGRERLRAIEsdiEEYRERESDLSDLTDERDEAKDTIDDLQSEIDELEAE 287
                                       56778899999999999999999999988888777773335678899999999999999999999999999999999 PP

                              Fez1  96 lkelreelselsleeeeaa.........................lesdeakaqrqe........aeeleelkrever 139
                                       ++e  e+++++ ++ e+ +                         +  d       e        + e+++ + +ver
  gi|336252351|ref|YP_004595458.1| 288 IQECDEAIAKQRERIES-RddevvdfdltnedeakeaveefetkY--D-------EasseveqrRAEVDSAEDTVER 354
                                       99999988885544333.247788988855555555544444321..2.......0222222224567777777777 PP

                              Fez1 140 lraeLkee 147
                                       l+ eL+ +
  gi|336252351|ref|YP_004595458.1| 355 LEDELQSQ 362
                                       77777665 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.008
                              Fez1  38 aqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa 114
                                       +++ + ra++++ e+++++le++l+++ +ele  +n+l+ +++++e  +e+++++++ l++ re l+e+ ++  e +
  gi|336252351|ref|YP_004595458.1| 336 SEVEQRRAEVDSAEDTVERLEDELQSQREELEDAQNRLHAREADVEAAEETLGEAKDSLEQRREILEEQLQDYLE-T 411
                                       678889999********************************9999999999999999999999988885544444.3 PP

                              Fez1 115 .....................lesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqass 157
                                                            ++sd+  + ++++++ ++l  e++ +++eL+e r+++++ ++s
  gi|336252351|ref|YP_004595458.1| 412 plddvddheaavrdrmddireEKSDREAEYESKRDRRARLGDEIDTIESELSEVRERRDDIRES 475
                                       589999999999988877665444444444455788999999*************999987665 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.9
                              Fez1  55 keleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa................. 114
                                         +++++++  +e    e+e + k+++   l ++++++e+el+e+re+  +  ++ e+a+                 
  gi|336252351|ref|YP_004595458.1| 421 AAVRDRMDDIREEKSDREAEYESKRDRRARLGDEIDTIESELSEVRERRDDIRESLETAVddpevafeaavdranea 497
                                       33444444444444444444444444444444444444444444444333332222222233333334333333333 PP

                              Fez1 115 ..............................lesdeakaqrqeaeeleelkreverlr 141
                                                                      + d+a++  +++e+++e ++++e l+
  gi|336252351|ref|YP_004595458.1| 498 asalgfdvsaedidtaftgdlpdeldaalnDHRDAAEELADARETVGEATAHIEDLQ 554
                                       344455555555666666666655555544222222222333444444444444444 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 1.1
                              Fez1  63 ektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa 114
                                       + + e++ +e+e+++k+++ + l++++e+leee+++l e+++e ++   +++
  gi|336252351|ref|YP_004595458.1| 627 DVAIEIDDLEAEIEQKQQTRSELQDEMESLEEEISRLEEAIAEGETA-LDTI 677
                                       33455888888888888888888888888888888888887774332.2222 PP

  == domain 7  score: 7.7 bits;  conditional E-value: 0.0093
                              Fez1  16 KqQLk.dsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvek 91 
                                       KqQ + + q e+ +  +ei  l   + e +++l++ e+ ++++e++++e ++ele   +el+  k+e   l+ ++e 
  gi|336252351|ref|YP_004595458.1| 642 KQQTRsELQDEMESLEEEISRLEEAIAEGETALDTIED-VEDAETAVDEAERELEDARDELADIKEEIGELEAEIED 717
                                       67776578888888888999999999999999988875.67888899999999999999999999999999999999 PP

                              Fez1  92 leeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlr 141
                                       +e++l + re++++++++ +ea+++ de++  r++a+e+++ ++e++ l+
  gi|336252351|ref|YP_004595458.1| 718 IESDLDDAREDVKDAEADLQEAEEQLDEVESARSAAREARDAHAEIATLE 767
                                       99999999999999888888888888888888888888888888777765 PP

  == domain 8  score: 6.6 bits;  conditional E-value: 0.02
                              Fez1  27 tqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrk........kseaellrekvekleee 95 
                                            ei +l ++ +  r++l++kee++ + +e+l++ ++e+e++e++l+ +        ++e+e+l e+ve+  e+
  gi|336252351|ref|YP_004595458.1| 757 RDAHAEIATLESDQKGYRSRLDDKEEQVASKREELQQIEDEIEEVESDLEDTspddlkeqQNETETLIEQVESQLED 833
                                       5556799999999****************************999999999884444444444444444444444444 PP

                              Fez1  96 lkelreelselsleeeeaalesdeakaqrqe..............a 127
                                        +e r+e++++++++ee  ++ +++++++++               
  gi|336252351|ref|YP_004595458.1| 834 AQERRDEARDAKSKAEERLNRLRDKRERKASleeqvnwaqtllndF 879
                                       4444444444333333332222222222222333333333333330 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.2    0.0054       2.6       6      81 ..     176     249 ..     172     266 .. 0.64
   2 ?    8.2   1.1    0.0048       2.3       2      79 ..     212     292 ..     211     309 .. 0.82
   3 ?    2.0   3.4      0.39   1.9e+02       6      68 ..     268     331 ..     252     344 .. 0.73
   4 ?    5.1   8.5     0.043        21       7      84 ..     319     396 ..     315     435 .. 0.54
   5 ?    1.0   1.1       0.8   3.9e+02      22      85 ..     409     472 ..     383     506 .. 0.68
   6 ?   -0.0   5.5       1.7   8.2e+02      32      96 ..     624     664 ..     570     670 .. 0.43
   7 ?    3.2   3.5      0.17        81      19      65 ..     632     678 ..     618     692 .. 0.58
   8 ?   15.4   5.1     3e-05     0.014      12      84 ..     680     752 ..     670     769 .. 0.66
   9 ?    5.9   8.4     0.025        12       9      89 ..     788     866 ..     774     888 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0054
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       +++ne  k v++  ++   +l+ ++e+++e++++    ++ v+++ + i+d +  + +L   +++  ++l+ ++  
  gi|336252351|ref|YP_004595458.1| 176 EDINEMQKTVESWQQDKRSKLQTVQEDIEELEAD--DPKATVQSKAEEIDDLEARIGDLSDGLEDGRERLRAIESD 249
                                       4556666666666666666666666666666655..5566677777777777777777777777777777766643 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0048
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXX--TTTTTGGGH CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetne...kvkdankairdArrsvkkLeklapqLldkl 75 
                                       k+++++  e +   ++ + +ls  le  +e l  i++++ee  e   +++d++   ++A++ + +L+ ++++L++ +
  gi|336252351|ref|YP_004595458.1| 212 KATVQSKAEEIDDLEARIGDLSDGLEDGRERLRAIESDIEEYREresDLSDLTDERDEAKDTIDDLQSEIDELEAEI 288
                                       6778888888888899999999999999999999999998876522267788899999***************9998 PP

                                       HHHH CS
                        Laminin_II  76 kelk 79 
                                       +e +
  gi|336252351|ref|YP_004595458.1| 289 QECD 292
                                       8755 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.39
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXX--TT CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdan.kairdArrsvkkLekla 68 
                                       +ea++t+   ++ + +l++++++  e + + ++ +e  +++v d+  +  ++A+++v + e + 
  gi|336252351|ref|YP_004595458.1| 268 DEAKDTIDDLQSEIDELEAEIQECDEAIAKQRERIESRDDEVVDFDlTNEDEAKEAVEEFETKY 331
                                       5777777777888888888888888888877777777777777654255666777777777665 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.043
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83 
                                       ea+e ++e + +  + s ++e+ ++++ +++++ve+ ++++++  + ++dA++     e  ++  ++ l e k   e
  gi|336252351|ref|YP_004595458.1| 319 EAKEAVEEFETKYDEASSEVEQRRAEVDSAEDTVERLEDELQSQREELEDAQNRLHAREADVEAAEETLGEAKDSLE 395
                                       55555555555666666666666666666666666666666666666666655555544444444444443333333 PP

                                       H CS
                        Laminin_II  84 a 84 
                                       +
  gi|336252351|ref|YP_004595458.1| 396 Q 396
                                       3 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.8
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH. CS
                        Laminin_II  22 lsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeas 85 
                                       l++ l+ + +    +++ ++ + e+ +d     ++ r+    L  +++ +++ l+e++++++  
  gi|336252351|ref|YP_004595458.1| 409 LETPLDDVDDHEAAVRDRMDDIREEKSDREAEYESKRDRRARLGDEIDTIESELSEVRERRDDI 472
                                       5556666666667777788888888888888888888888889999999999999998888763 PP

  == domain 6  score: -0.0 bits;  conditional E-value: 1.7
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHH CS
                        Laminin_II  32 klseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseik 96 
                                        l  ++ +++  ++++++++++  + ++++                          l ++is++ 
  gi|336252351|ref|YP_004595458.1| 624 ALADVAIEIDDLEAEIEQKQQTRSELQDEMES------------------------LEEEISRLE 664
                                       22222222233333333333333333333333........................333333333 PP

  == domain 7  score: 3.2 bits;  conditional E-value: 0.17
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX- CS
                        Laminin_II  19 laplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLe 65 
                                       + +l++++e+ ++  se+++++e  +e+++ + +ai++ +++  ++e
  gi|336252351|ref|YP_004595458.1| 632 IDDLEAEIEQKQQTRSELQDEMESLEEEISRLEEAIAEGETALDTIE 678
                                       55566666666666666666666666666666666655555544444 PP

  == domain 8  score: 15.4 bits;  conditional E-value: 3e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                       ++  +  + + + +le  +++l  i++++ e +++++d    ++dAr+ vk+ e  +++ +++l e++  ++a
  gi|336252351|ref|YP_004595458.1| 680 VEDAETAVDEAERELEDARDELADIKEEIGELEAEIEDIESDLDDAREDVKDAEADLQEAEEQLDEVESARSA 752
                                       3333334445556677777777777777777777777777777777777777777777777777777766665 PP

  == domain 9  score: 5.9 bits;  conditional E-value: 0.025
                                       XXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   9 netakevleqlaplsqnlentk.....eklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                        e ++++++ +++++ +le t+     e+ +e ++ +e+++ +++da++  ++Ar++ +k e+ +++L dk +    
  gi|336252351|ref|YP_004595458.1| 788 REELQQIEDEIEEVESDLEDTSpddlkEQQNETETLIEQVESQLEDAQERRDEARDAKSKAEERLNRLRDKRE---- 860
                                       4555555555555555555544111104444555555556677777777777777777777777777777733.... PP

                                       HHHH...HH CS
                        Laminin_II  81 leeasssls 89 
                                           ++sl 
  gi|336252351|ref|YP_004595458.1| 861 ---RKASLE 866
                                       ...333333 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 ?   11.8  10.6   0.00024      0.12       6     131 ..     174     304 ..     172     312 .. 0.85
   2 ?   -1.8  21.0       3.4   1.7e+03      37     165 ..     319     441 ..     313     470 .. 0.61
   3 ?   -2.2   0.0       4.5   2.2e+03      72     105 ..     521     554 ..     520     557 .. 0.68
   4 ?   12.5   8.5   0.00014     0.067      45     127 ..     621     703 ..     617     708 .. 0.94
   5 ?   10.4  12.4   0.00063       0.3      31     131 ..     704     807 ..     702     811 .. 0.83
   6 ?    4.1  20.4     0.054        26      33     131 ..     761     861 ..     757     865 .. 0.93
   7 ?   -0.1  13.3         1   4.8e+02      30     113 ..     812     895 ..     809     923 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                               GAS   6 HekafneiknYYnditrnNLelIkslKeeieelkkke.....ernekelseisqenkrlkepLkkaeeeveeLrkql 77 
                                       +e+ +ne+++  +  +++  ++ ++  e+ieel++ +     +++  e+++++++  +l++ L+  +e +   + ++
  gi|336252351|ref|YP_004595458.1| 174 YEEDINEMQKTVESWQQDKRSKLQTVQEDIEELEADDpkatvQSKAEEIDDLEARIGDLSDGLEDGRERLRAIESDI 250
                                       7788888888888888888899999999999997765333337788999**************************** PP

                               GAS  78 knyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfea 131
                                       ++y++  ++l  l  +  e+++ + dl+ e + le ++++  +++ + +++ e+
  gi|336252351|ref|YP_004595458.1| 251 EEYRERESDLSDLTDERDEAKDTIDDLQSEIDELEAEIQECDEAIAKQRERIES 304
                                       *************************************99998877666666554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.4
                               GAS  37 elkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleq 113
                                       e k+  e+ e + +e+s+e ++ + ++  ae  ve+L+ +l+ +++   +l+ +++rl+  e    d++   e l +
  gi|336252351|ref|YP_004595458.1| 319 EAKEAVEEFETKYDEASSEVEQRRAEVDSAEDTVERLEDELQSQRE---ELEDAQNRLHAREA---DVEAAEETLGE 389
                                       5566667777777788888888888888888888888877766554...44444444444443...34444555666 PP

                               GAS 114 rfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaql 165
                                         +++e+ r+ l+++ ++ +++   +++ ++  +  +++ ++ee   +ea+ 
  gi|336252351|ref|YP_004595458.1| 390 AKDSLEQRREILEEQLQDYLETPLDDVDDHEAAVRDRMDDIREEKSDREAEY 441
                                       6666666666666666666666666666666666666666666666666655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.5
                               GAS  72 eLrkqlknyekdkqslknlkarlkelekelkdlk 105
                                       eL ++l++++   ++l+ +++ + e++ +++dl+
  gi|336252351|ref|YP_004595458.1| 521 ELDAALNDHRDAAEELADARETVGEATAHIEDLQ 554
                                       6667777777777777777777777777777765 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00014
                               GAS  45 nekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekveke 121
                                         k l++++ e  +l+ ++++ ++ + eL+ +++  e++ ++l+++ a+ +++ + ++d++     + +   ++e++
  gi|336252351|ref|YP_004595458.1| 621 SFKALADVAIEIDDLEAEIEQKQQTRSELQDEMESLEEEISRLEEAIAEGETALDTIEDVEDAETAVDEAERELEDA 697
                                       56899************************************************************************ PP

                               GAS 122 rdelyk 127
                                       rdel +
  gi|336252351|ref|YP_004595458.1| 698 RDELAD 703
                                       ***987 PP

  == domain 5  score: 10.4 bits;  conditional E-value: 0.00063
                               GAS  31 lKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrk...qlknyekdkqslknlkarlkelekelkdl 104
                                        Keei el+++ e  e +l+++ ++ k+ +  L++aee+++e +    ++++ +   ++++ l++  k   + l d 
  gi|336252351|ref|YP_004595458.1| 704 IKEEIGELEAEIEDIESDLDDAREDVKDAEADLQEAEEQLDEVESarsAAREARDAHAEIATLESDQKGYRSRLDDK 780
                                       69999999999999999999999999999999999999877776522266666667777888889999999999999 PP

                               GAS 105 kwehevleqrfekvekerdelykkfea 131
                                       +++  +++++++++e+e++e+++  e+
  gi|336252351|ref|YP_004595458.1| 781 EEQVASKREELQQIEDEIEEVESDLED 807
                                       999999999999999999999988876 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.054
                               GAS  33 eeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekd..kqslknlkarlkelekelkdlkwe 107
                                        ei++l+  ++  + +l++ +++  + +e+L++ e e+ee + +l++ + d  k++ +++++ ++++e++l+d ++ 
  gi|336252351|ref|YP_004595458.1| 761 AEIATLESDQKGYRSRLDDKEEQVASKREELQQIEDEIEEVESDLEDTSPDdlKEQQNETETLIEQVESQLEDAQER 837
                                       699********************************************9877447788889999************** PP

                               GAS 108 hevleqrfekvekerdelykkfea 131
                                        +  ++  +k+e+  ++l++k e+
  gi|336252351|ref|YP_004595458.1| 838 RDEARDAKSKAEERLNRLRDKRER 861
                                       *******************99887 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 1
                               GAS  30 slKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                        lKe+ +e ++  e+ e +l++++++  + ++   kaee +++Lr + ++  +  ++ + +++ l++ e   k+ ++
  gi|336252351|ref|YP_004595458.1| 812 DLKEQQNETETLIEQVESQLEDAQERRDEARDAKSKAEERLNRLRDKRERKASLEEQVNWAQTLLNDFETITKTYSE 888
                                       46777777777777777777777777777777777777777777766666655555555555555555555554433 PP

                               GAS 107 ehevleq 113
                                        +  +++
  gi|336252351|ref|YP_004595458.1| 889 VQTRMRE 895
                                       3322222 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.6       1.8   8.6e+02      75      99 ..     182     206 ..     169     222 .. 0.47
   2 ?    9.7   1.1    0.0017      0.84      62     122 ..     223     286 ..     209     289 .. 0.88
   3 ?    9.9   7.2    0.0014       0.7      38     119 ..     276     361 ..     273     370 .. 0.87
   4 ?    5.1   2.1     0.046        22      47     121 ..     384     459 ..     361     461 .. 0.67
   5 ?    3.6   0.1      0.13        63      55      96 ..     442     483 ..     436     507 .. 0.75
   6 ?   -1.6   0.0       5.4   2.6e+03      66     107 ..     576     617 ..     570     626 .. 0.68
   7 ?    2.7  14.3      0.26   1.3e+02      35     122 ..     645     720 ..     608     770 .. 0.66
   8 ?    1.6   7.7      0.53   2.6e+02      56     117 ..     765     827 ..     738     835 .. 0.70
   9 ?    2.3   3.9      0.33   1.6e+02      42     110 ..     823     893 ..     816     903 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.8
                           DUF1664  75 ldeqkeiskeikeevtevredlsei 99 
                                       ++ ++  +++ ++++++v+ed++e+
  gi|336252351|ref|YP_004595458.1| 182 QKTVESWQQDKRSKLQTVQEDIEEL 206
                                       1111122222223333333333332 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0017
                           DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevre...dlseigedvesvkeavegleskleriee 122
                                       ++L++ri  + + l++  e  ++i+++++e re   dls++ ++ ++ k+++ +l+s+++++e+
  gi|336252351|ref|YP_004595458.1| 223 DDLEARIGDLSDGLEDGRERLRAIESDIEEYREresDLSDLTDERDEAKDTIDDLQSEIDELEA 286
                                       6899************************99875333899999*******************996 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0014
                           DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdk....kldeqkeiskeikeevtevredlseigedvesvkeav 110
                                        l++ ++++  ++++  e++a+++++++sr d+v +    + de ke+ +e + + +e+++++++ + +v+s +++v
  gi|336252351|ref|YP_004595458.1| 276 DLQSEIDELEAEIQECDEAIAKQRERIESRDDEVVDfdltNEDEAKEAVEEFETKYDEASSEVEQRRAEVDSAEDTV 352
                                       5788899999********************9987533333668999999999************************* PP

                           DUF1664 111 egleskler 119
                                       e le +l++
  gi|336252351|ref|YP_004595458.1| 353 ERLEDELQS 361
                                       ****99875 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.046
                           DUF1664  47 skqleqvseslaatkrhLssridr.vdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                        + l + ++sl++ ++ L+++++  +++ ld++ +  +++++ ++++re+ s+ + + es ++    l+ ++++ie
  gi|336252351|ref|YP_004595458.1| 384 EETLGEAKDSLEQRREILEEQLQDyLETPLDDVDDHEAAVRDRMDDIREEKSDREAEYESKRDRRARLGDEIDTIE 459
                                       3455556666666666666666432566677777777788888888888888878888877777777777777777 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.13
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredl 96 
                                       es ++ + +L ++id+++++l e+ e   +i+e ++++ +d 
  gi|336252351|ref|YP_004595458.1| 442 ESKRDRRARLGDEIDTIESELSEVRERRDDIRESLETAVDDP 483
                                       55677889999****************999999998876664 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 5.4
                           DUF1664  66 sridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                        +i+r++++ +e + ++ +  + ++++ e l++++e  +++ 
  gi|336252351|ref|YP_004595458.1| 576 TQIQRLESEREEAETAADAAIDTLDAADERLNHVQEVADALF 617
                                       567777777777777777777777777777777766665555 PP

  == domain 7  score: 2.7 bits;  conditional E-value: 0.26
                           DUF1664  35 TkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       T+  l+d +es+ +++ ++ e++a+    L           d  +++ ++ +  v+e++++l++ ++++  +ke + 
  gi|336252351|ref|YP_004595458.1| 645 TRSELQDEMESLEEEISRLEEAIAEGETAL-----------DTIEDV-EDAETAVDEAERELEDARDELADIKEEIG 709
                                       344444444444444444444444433333...........332222.22344455555555555555555555555 PP

                           DUF1664 112 gleskleriee 122
                                       +le+++e+ie+
  gi|336252351|ref|YP_004595458.1| 710 ELEAEIEDIES 720
                                       55555555553 PP

  == domain 8  score: 1.6 bits;  conditional E-value: 0.53
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseig.edvesvkeavegleskl 117
                                       +l++ ++   sr+d  ++++ +  e  ++i++e++ev++dl++++ +d+++ ++  e+l +++
  gi|336252351|ref|YP_004595458.1| 765 TLESDQKGYRSRLDDKEEQVASKREELQQIEDEIEEVESDLEDTSpDDLKEQQNETETLIEQV 827
                                       567777778888888888888888888899999999998888764234444444444443333 PP

  == domain 9  score: 2.3 bits;  conditional E-value: 0.33
                           DUF1664  42 avesvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                        +e+v +qle+ +   ++ +++k + ++r++r+ +k +  + + ++++   +++ +d ++i +  ++v++ +
  gi|336252351|ref|YP_004595458.1| 823 LIEQVESQLEDAQerrDEARDAKSKAEERLNRLRDKRERKASLEEQVNWA-QTLLNDFETITKTYSEVQTRM 893
                                       57899999999985556788999999999999999999888888887654.556667777777777776654 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.7  11.3   1.6e-05    0.0078       2      59 ..      15      72 ..      14     476 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.6e-05
                                      EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran  2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrk 59
                                      +n+++++  g ++ + G+nGaGKSt+ ++l+  l p +G+ ++  +dl +  q   + ++
  gi|336252351|ref|YP_004595458.1| 15 DNLDVTFDDG-LTLLHGPNGAGKSTITRALYTTLYPLNGKYKIGAHDLADliQ-DGKDSA 72
                                      6677777666.5679**************************999999888752.222222 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   9.5    0.0034       1.7      53     176 ..     173     296 ..     171     297 .. 0.89
   2 ?    3.4   8.6      0.12        58      55     129 ..     299     374 ..     295     403 .. 0.68
   3 ?    8.1   1.6    0.0041         2      81     136 ..     422     477 ..     418     486 .. 0.88
   4 ?    8.6   2.8    0.0029       1.4      88     176 ..     580     668 ..     567     669 .. 0.78
   5 ?    2.9  13.1      0.17        82      42     174 ..     678     804 ..     676     807 .. 0.62
   6 ?    0.3  10.8         1   5.1e+02      81     157 ..     812     889 ..     809     908 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0034
                           DUF4201  53 alnkkIeernkeLkrlkkkttktvhalthlkeklhml..eselselkkelkekeerlaklrkelykvklerdklrkq 127
                                       a+++ I+e +k ++  ++   ++++++++  e l +   +++++ + +e++++e+r+ +l + l+  +++   ++ +
  gi|336252351|ref|YP_004595458.1| 173 AYEEDINEMQKTVESWQQDKRSKLQTVQEDIEELEADdpKATVQSKAEEIDDLEARIGDLSDGLEDGRERLRAIESD 249
                                       688999999999999999999999999999998886622577889999***************************** PP

                           DUF4201 128 neklkqqggllrvPaLlkDYdktkekveekrksvkkLrrkvkilemrlk 176
                                        e+ +++  +l   +L+ + d+ k+ ++++++++++L+ ++++  ++++
  gi|336252351|ref|YP_004595458.1| 250 IEEYRERESDL--SDLTDERDEAKDTIDDLQSEIDELEAEIQECDEAIA 296
                                       *******9995..59**************************99988876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.12
                           DUF4201  55 nkkIeernkeLkrlkkkttktvha.lthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqne 129
                                       +++Ie+r++e++   ++  ++ ++ +++   k ++ +se+++++ e ++ e++ ++l++el++ ++e + ++++ +
  gi|336252351|ref|YP_004595458.1| 299 RERIESRDDEVVDFDLTNEDEAKEaVEEFETKYDEASSEVEQRRAEVDSAEDTVERLEDELQSQREELEDAQNRLH 374
                                       5778888888888888887777641556667777888888888888888888888888887766666555555443 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0041
                           DUF4201  81 hlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqgg 136
                                        ++++++ +++e s+++ e+++k +r+a+l +e+   + e + +r+++++++++++
  gi|336252351|ref|YP_004595458.1| 422 AVRDRMDDIREEKSDREAEYESKRDRRARLGDEIDTIESELSEVRERRDDIRESLE 477
                                       67888999999999999999999999999999999999999999999999999876 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0029
                           DUF4201  88 mleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkL 164
                                        lese +e+++  +   ++l++ +++l++v++  d l +  +        ++  +L  + +++++   e++++ ++L
  gi|336252351|ref|YP_004595458.1| 580 RLESEREEAETAADAAIDTLDAADERLNHVQEVADALFEAASFKALADVAIEIDDLEAEIEQKQQTRSELQDEMESL 656
                                       56666677777777777778888888888888888888777777777777888999999999999999999999999 PP

                           DUF4201 165 rrkvkilemrlk 176
                                       ++++ +le++++
  gi|336252351|ref|YP_004595458.1| 657 EEEISRLEEAIA 668
                                       999999999886 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.17
                           DUF4201  42 idFeqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvk 118
                                       +d e +++ + + + ++e+  +eL  +k+ ++    +++++   l+  ++ +++++ +l+e ee+l++++   + ++
  gi|336252351|ref|YP_004595458.1| 678 EDVEDAETAVDEAERELEDARDELADIKEEIGELEAEIEDIESDLDDAREDVKDAEADLQEAEEQLDEVESARSAAR 754
                                       55666666666666666666666666666666666666666666666666666666666666666666666666665 PP

                           DUF4201 119 lerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrrkvkilemr 174
                                       + rd ++++ + l+++   +r     +  d+++e+v++kr+++++++ +++++e+ 
  gi|336252351|ref|YP_004595458.1| 755 EARD-AHAEIATLESDQKGYR-S---R-LDDKEEQVASKREELQQIEDEIEEVESD 804
                                       5554.3445555555444433.2...2.5778888888888888888888888766 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 1
                           DUF4201  81 hlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllr.vPaLlkDYdktkekvee 156
                                       +lke  ++ e+  ++ +++l++ +er+++ r+  +k++++ ++lr+++e+  +  ++++ +  Ll+D++   + + e
  gi|336252351|ref|YP_004595458.1| 812 DLKEQQNETETLIEQVESQLEDAQERRDEARDAKSKAEERLNRLRDKRERKASLEEQVNwAQTLLNDFETITKTYSE 888
                                       5899999999999999***************************9999887666666665356677887765555554 PP

                           DUF4201 157 k 157
                                        
  gi|336252351|ref|YP_004595458.1| 889 V 889
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1058 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3338  (0.186179); expected 358.6 (0.02)
Passed bias filter:                     1005  (0.0560544); expected 358.6 (0.02)
Passed Vit filter:                       388  (0.0216409); expected 17.9 (0.001)
Passed Fwd filter:                       270  (0.0150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 6.09u 0.45s 00:00:06.54 Elapsed: 00:00:01.15
# Mc/sec: 2772.32
//
Query:       gi|336252352|ref|YP_004595459.1|  [L=453]
Description: NurA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 3611.32
//
Query:       gi|336252353|ref|YP_004595460.1|  [L=619]
Description: hypothetical protein Halxa_0945 [Halopiger xanaduensis SH-6]
Scores for 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-07   29.6   0.0    1.7e-06   28.3   0.0    1.6  2  DUF87         Helicase HerA, central domain
    0.00013   20.7   0.4     0.0027   16.4   0.0    2.1  2  DUF853        Bacterial protein of unknown function (DUF853)
    0.00037   19.5   0.0     0.0073   15.3   0.0    2.2  2  AAA_10        AAA-like domain
  ------ inclusion threshold ------
      0.021   14.2   0.0       0.29   10.5   0.0    2.1  2  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.038   14.3   0.0        1.7    8.9   0.0    2.3  2  AAA_22        AAA domain
      0.062   12.9   0.0       0.11   12.1   0.0    1.3  1  Zot           Zonular occludens toxin (Zot)


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   5.5e-10   1.7e-06      22     224 ..     236     481 ..     233     484 .. 0.78
   2 ?   -3.7   0.0       3.5   1.1e+04     115     181 ..     519     538 ..     488     562 .. 0.52

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.5e-10
                             DUF87  22 vtrHlAilgsTGsGKSntvavLleelle..............kkgatililDpHGEYgkal................ 68 
                                       +  H+++ gsT +GK+++++ L ++l+               ++++ ++++Dp  EY+ +                 
  gi|336252353|ref|YP_004595460.1| 236 IYTHTLVTGSTDAGKTHFTKNLYRQLATdqtyqiavgddgteDRRLGMVVVDPEAEYSGLGddpsaddlpdderqrl 312
                                       568*************************************999999********************99999999555 PP

                             DUF87  69 ............ekllsekvkvitpspsa......................kdkelkinpwsldpeelldllee..d 109
                                                                   a                      + +e+ i++ +++ +   +l++   +
  gi|336252353|ref|YP_004595460.1| 313 egqgievggintG---------------AcgshdlrtfapvvegkptpdidNIREFGIPFELVQSNP--ELIMPysS 372
                                       5555555555551...............355555555555556667778888899****99886553..33333355 PP

                             DUF87 110 dkpaaavqrsvleealdqakakeekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsfsnss 186
                                       + p +a++ + l++++++ +++++++ + + e  e  l e +        +  + +++ +++l d ++  + f +s 
  gi|336252353|ref|YP_004595460.1| 373 GGPTEAALPDCLNSYFNETTDPTYEGFMEYLEVNEATLREEH--------NIGENMWGAINRLVDRDYFSSVF-DSG 440
                                       6999999**********9999999999999998886665555........66677777777777777777777.666 PP

                             DUF87 187 tdliallleklekegkitiidlsg...vdelaqqlvvsvil 224
                                       t  ++++ ++l ++g++t++++s     d+ ++++vv ++l
  gi|336252353|ref|YP_004595460.1| 441 THQLTEISNELFQPGRVTVVPVSHlgdPDDPEMRVVVMALL 481
                                       77788888999*********998844457778888777776 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.5
                             DUF87 115 avqrsvleealdqakakeekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggs 181
                                       ++qr+++ e +                                               +++ ++g++
  gi|336252353|ref|YP_004595460.1| 519 TRQREAIVESF-----------------------------------------------RRIAKRGRK 538
                                       22333333333...............................................333332222 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.016        49      22      46 ..     238     262 ..     230     271 .. 0.86
   2 !   16.4   0.0   9.1e-07    0.0027     259     317 ..     503     565 ..     478     576 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.016
                            DUF853  22 rhGliaGatGtGktvtLqvlaesls 46 
                                        h l++G+t +Gkt   + l  +l+
  gi|336252353|ref|YP_004595460.1| 238 THTLVTGSTDAGKTHFTKNLYRQLA 262
                                       69************99999988876 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 9.1e-07
                            DUF853 259 lvfffdeahLLfndapkallekveqvvrLi....rskGvGvyfvtqnPldlPdtvLaqLGnrv 317
                                       lv+ +deah ++ d++    e +    r i    r    G+ +vtq+P+d+ d++ +qL +++
  gi|336252353|ref|YP_004595460.1| 503 LVLGLDEAHEFLGDTSTRQREAIVESFRRIakrgRKYDLGLSLVTQEPADVDDQIRSQLRTKI 565
                                       8999********999976666555555555111166669********************9887 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.035     1e+02      22      60 ..     238     291 ..     229     295 .. 0.75
   2 !   15.3   0.0   2.4e-06    0.0073     150     292 ..     410     559 ..     382     576 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.035
                            AAA_10  22 sasliiGdlGnGKSvlakllvlyisllg...............gkaliiDpkke 60 
                                        ++l++G++ +GK  ++k l  +++  +                 ++++Dp +e
  gi|336252353|ref|YP_004595460.1| 238 THTLVTGSTDAGKTHFTKNLYRQLATDQtyqiavgddgtedrrLGMVVVDPEAE 291
                                       589***************999888766666666666666665544566666655 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.4e-06
                            AAA_10 150 rkedekvareiarhlesvvkkslaklvfsdgs.....veeaislekkvtvlevedLdLPdkderlerlteekllsva 221
                                        +e++++++++   ++ +v+ +    vf+ g+     +++++    +vtv+ v  L  Pd+        e+++  +a
  gi|336252353|ref|YP_004595460.1| 410 LREEHNIGENMWGAINRLVDRDYFSSVFDSGThqlteISNELFQPGRVTVVPVSHLGDPDD-------PEMRVVVMA 479
                                       4778889999999999999999999999988611111334444446899999999999988.......334555555 PP

                            AAA_10 222 vlfviaafarefass...dkkefk...vvifDEawif...tssaeGkkllkelvRi...GRsynaavylvtqsadDv 286
                                       +l   + +a++  s    d +  +   v  +DEa  f   ts+ + ++++++ +Ri   GR+y   + lvtq++ Dv
  gi|336252353|ref|YP_004595460.1| 480 LL---SYIAQNKLSDddpDPHVAEtplVLGLDEAHEFlgdTSTRQREAIVESFRRIakrGRKYDLGLSLVTQEPADV 553
                                       55...44454444431113333332226779*****95656899999****999966669***************** PP

                            AAA_10 287 lkeelk 292
                                       +++  +
  gi|336252353|ref|YP_004595460.1| 554 DDQIRS 559
                                       987533 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.6e-05      0.29      27      66 ..     216     264 ..     204     268 .. 0.80
   2 ?    1.3   0.0     0.062   1.9e+02     192     242 ..     501     551 ..     483     552 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.6e-05
                                       TS-EEEEEGGGS-..........SEEEE--TTSSHHHHHHHHHHHHHTT CS
                      FtsK_SpoIIIE  27 sgnplvldlkkma.........shllvaGatgsGKStalntLilSlatt 66 
                                       sgnpl + l+  +          h+lv G+t  GK+ + ++L   lat 
  gi|336252353|ref|YP_004595460.1| 216 SGNPLAFHLPDGTgsastpaiyTHTLVTGSTDAGKTHFTKNLYRQLATD 264
                                       67777777777666777778889****************9998888875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.062
                                       -EEEEEEC-HHHHHHHHHHH....HHHHHHHHHHHCGGGTEEEEEEES--- CS
                      FtsK_SpoIIIE 192 pslvvivderieLrlaapkdssvlvedaivRlarkgraaglHlllatqrls 242
                                        +lv ++de  e   + +  ++ ++ + ++R+a++gr+  l l l tq+++
  gi|336252353|ref|YP_004595460.1| 501 TPLVLGLDEAHEFLGDTSTRQREAIVESFRRIAKRGRKYDLGLSLVTQEPA 551
                                       56777777777777777777899999***********98888888898887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00057       1.7       7      32 ..     239     264 ..     237     295 .. 0.76
   2 ?    2.7   0.0     0.047   1.4e+02      92     130 ..     502     548 ..     478     553 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00057
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldee 32 
                                       +++vtG + +GKT+  ++l +ql  +
  gi|336252353|ref|YP_004595460.1| 239 HTLVTGSTDAGKTHFTKNLYRQLATD 264
                                       899*******************9543 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.047
                            AAA_22  92 ielliiDEaqhlr...s....eealeeLrsllnl.srkgvqliLvGt 130
                                       + +l +DEa+ +    s    e+++e +r++++  +++++ l Lv +
  gi|336252353|ref|YP_004595460.1| 502 PLVLGLDEAHEFLgdtStrqrEAIVESFRRIAKRgRKYDLGLSLVTQ 548
                                       56899******555872456788888888888877788888888866 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.7e-05      0.11      84     142 ..     505     565 ..     487     607 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                               Zot  84 lviDEcqeifpvrakegrkdpevinafteh....RhlgwDivlltqdiskihkevralaekav 142
                                       l +DE++e+    ++   +++++++ f +     R++   + l+tq+++ +++++r     + 
  gi|336252353|ref|YP_004595460.1| 505 LGLDEAHEFLGDTSTR--QREAIVESFRRIakrgRKYDLGLSLVTQEPADVDDQIRSQLRTKI 565
                                       558*****99998886..456666666543222288888899*************97655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4352.75
//
Query:       gi|336252354|ref|YP_004595461.1|  [L=679]
Description: tyrosyl-DNA phosphodiesterase [Halopiger xanaduensis SH-6]
Scores for 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-07   29.2   0.0    1.7e-06   28.0   0.0    1.6  1  PLDc_2           PLD-like domain
     0.0023   17.3   0.0     0.0037   16.6   0.0    1.3  1  RE_NgoFVII       NgoFVII restriction endonuclease
     0.0074   16.7   0.0       0.06   13.7   0.0    2.5  2  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.015   14.2   0.0      0.025   13.5   0.0    1.4  1  Tyr-DNA_phospho  Tyrosyl-DNA phosphodiesterase
      0.041   14.3   1.1        3.9    7.9   0.0    3.2  3  AAA              ATPase family associated with various cellul
      0.045   14.0   0.0       0.22   11.8   0.0    2.2  2  AAA_22           AAA domain


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 !   28.0   0.0   5.5e-10   1.7e-06      21     131 ..      53     170 ..      39     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 5.5e-10
                            PLDc_2  21 sdreildallkaakrgvkvrilldskkd...dagavdeaslkelkellleagvevrvfetllgslHaKlylid.... 90 
                                        ++e+ld++ +a + + + +++++++++   ++   +e+ +++l++l +e  +++ +   +++ +H+Klyl +    
  gi|336252354|ref|YP_004595461.1|  53 ESPEMLDRVFDAIDVD-EMEVVVGDHTKdyrESLRGKEQLAARLERLQREDRLQIVLPALRNNEVHSKLYLLEhedg 128
                                       5777777777777777.88999999888777555557788889999988888887775424689********85555 PP

                            PLDc_2  91 gktvivGSsNltkrgldlnlElnvviedk.elakeleeeFer 131
                                        +t ivGS Nl+k+++++ +  nv++  + + ++++++ F++
  gi|336252354|ref|YP_004595461.1| 129 TRTNIVGSPNLSKKAWESVYQKNVIVVFRtDGNQRIDSVFDE 170
                                       55**************77665555554443569999999987 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.2e-06    0.0037      71     167 ..     103     201 ..      60     275 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-06
                                       EEEEXSSS....XBXXXEEEEEET.TEEEEEEESXXSXXTTS.XXXSBXEEEEEE.HHHHHHHHHHHHHHHHH.HXE CS
                        RE_NgoFVII  71 evkvsysv....kvHsKlYiwkkdgkplsAliGSANlssngl.rtrqrEtlvdldtedafkeldeyiqsllsksisk 142
                                        ++++       +vHsKlY+   ++ +   ++GS Nls  +  +  q+ ++v +   d  + +d+ +++  ++   +
  gi|336252354|ref|YP_004595461.1| 103 RLQIVLPAlrnnEVHSKLYLLEHEDGTRTNIVGSPNLSKKAWeSVYQKNVIVVFR-TDGNQRIDSVFDEWYAE--MR 176
                                       4444443345789*************************99886778888888877.55555588888877777..44 PP

                                       EGGGSXXSSXXXXXX-GGGSTT-EE CS
                        RE_NgoFVII 143 niaeveeniikeknsllsevegvek 167
                                       +  +v  + ++e+ ++l + +++e+
  gi|336252354|ref|YP_004595461.1| 177 DYGDVFMEDLTERVEELPNEQQEEE 201
                                       4444444334444444444444443 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   0.1      0.81   2.4e+03      82     119 ..     190     227 ..     162     284 .. 0.60
   2 !   13.7   0.0     2e-05      0.06      25      55 ..     406     434 ..     390     475 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.81
                            AAA_16  82 lrqlldeaesaeleawrekleealaavpelagaeasrl 119
                                       +++l +e+++ e+ aw +  +++ ++ +e++ a+  rl
  gi|336252354|ref|YP_004595461.1| 190 VEELPNEQQEEEVHAWIAGRTTSDSEEAEVEQALTDRL 227
                                       44444444444444444433333333333333322222 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggif 55 
                                       ++++++Ge+G+GK +l+r ++ +l  d g++
  gi|336252354|ref|YP_004595461.1| 406 PSLYIYGEPGSGKGTLARYAF-HLLSD-GHV 434
                                       799******************.56666.455 PP

>> Tyr-DNA_phospho  Tyrosyl-DNA phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.4e-06     0.025      54     137 ..      66     155 ..      40     220 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.4e-06
                                       T-...-EEEEEE...............ETTSEE-......TEEEEEE---.TT--B---EEEEEETTSEEEEEEESS CS
                   Tyr-DNA_phospho  54 dvrrkvkvvivhgakkeedeererle.ekakryp......nvelieakmpepfgthHsKmmilfyeddslrvvihta 123
                                       dv    ++ +v g ++++ +e  r + + a+r++      +++++ + + +  +  HsK+ +l +ed++   ++ + 
  gi|336252354|ref|YP_004595461.1|  66 DV---DEMEVVVGDHTKDYRESLRGKeQLAARLErlqredRLQIVLPALRN--NEVHSKLYLLEHEDGTRTNIVGSP 137
                                       44...5666666655555544444333444444455566678888888885..799***********99999999** PP

                                       -BSHHHHHSSB-E....E CS
                   Tyr-DNA_phospho 124 NlieaDwgnmtqg....v 137
                                       Nl ++ w+ + q     v
  gi|336252354|ref|YP_004595461.1| 138 NLSKKAWESVYQKnvivV 155
                                       *******99888654444 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 ?    3.0   0.1     0.044   1.3e+02      60     116 ..      63     117 ..      18     168 .. 0.73
   2 ?   -0.6   0.2      0.56   1.7e+03      66     101 ..     201     235 ..     184     240 .. 0.84
   3 ?    7.9   0.0    0.0013       3.9       1      22 [.     408     429 ..     408     463 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.044
                                       EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGST CS
                               AAA  60 silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkld 116
                                         + +DE++ ++++  +++ +e+ r  +qL + l++++++ +++ +++ + r +++ 
  gi|336252354|ref|YP_004595461.1|  63 DAIDVDEMEVVVGDH-TKDYRESLRGKEQLAARLERLQRE-DRLQIVLPALRNNEVH 117
                                       456689****99999.8888999999***********997.4465555555555544 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.56
                                       TGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSS CS
                               AAA  66 EidalaksrsgseseeeervvnqLlteldgvkkkes 101
                                       E++a +  r +++++ee +v ++L   l++ + +++
  gi|336252354|ref|YP_004595461.1| 201 EVHAWIAGR-TTSDSEEAEVEQALTDRLEEANVRKA 235
                                       889988888.78888999999999999999887644 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0013
                                       EEEESSTTSSHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel 22 
                                       +++yG pG GK +la+   + l
  gi|336252354|ref|YP_004595461.1| 408 LYIYGEPGSGKGTLARYAFHLL 429
                                       589************9877765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.1   6.4e+03      47      91 ..     193     236 ..     186     247 .. 0.68
   2 ?   11.8   0.0   7.5e-05      0.22       7      30 ..     407     430 ..     406     480 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.1
                            AAA_22  47 lpsstsskdllrellralglelkaerlsseellealeqalrarav 91 
                                       lp++   +++  +++  ++++ ++    +++l ++le+a  ++a+
  gi|336252354|ref|YP_004595461.1| 193 LPNEQQEEEVHAWIAGRTTSDSEE-AEVEQALTDRLEEANVRKAT 236
                                       566666777777888888876666.55555666666666555554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.5e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqld 30 
                                       +l+++Ge+G+GK tl+r  ++ l 
  gi|336252354|ref|YP_004595461.1| 407 SLYIYGEPGSGKGTLARYAFHLLS 430
                                       689**************9999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (679 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      732  (0.0408277); 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: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.42
# Mc/sec: 4887.85
//
Query:       gi|336252355|ref|YP_004595462.1|  [L=757]
Description: stem cell self-renewal protein Piwi [Halopiger xanaduensis SH-6]
Scores for complete 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   57.2   0.0    2.7e-15   56.4   0.0    1.3  1  Piwi      Piwi domain


Domain annotation for each model (and alignments):
>> Piwi  Piwi domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0   1.5e-19   2.7e-15      18     299 ..     475     742 ..     465     745 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 1.5e-19
                                       HHHHHHTCCCCEEEEEHHHHCTCCH.....HHHHHHHHHHHHHHHTT-BS-EEESSSTTSSE....EEEEEEEEEEC CS
                              Piwi  18 kkyletdlgiisqcillktilkrql.....kkqtltnvllkinvKlGgknvliveikleldvsptliiGidishgta 89 
                                       +k+ +  +gi+sq++   ti++        +++   n l  i++K Gg++ +i + ++  d+    ++G+d++++++
  gi|336252355|ref|YP_004595462.1| 475 LKRSLMRRGIPSQMMMKPTIDELLAinasaGNFSFINALSAIVAKAGGTPWVIGDLPGPTDA----FMGLDVTRDEN 547
                                       46667778*********999988448889999*****************8889999999999....********999 PP

                                       CCSCCCEEEEEEEEEETSSEEEEEEEEESSCCCCHHHH.HHHHHHHHHHHHHHTTTT-TTSEEEEEESS....S..S CS
                              Piwi  90 gtvdnpsvaavvasldkensrylaevstqassqellek.lkeiikellrefkksskkkkperiivyRdGvseGqfkq 165
                                       ++      +a + ++ ++++ ++ae++t +s+++  ++ ++++i++l+ +f  s+++ + +++++ RdG       +
  gi|336252355|ref|YP_004595462.1| 548 NQ----HAGASASVVLNNGAVFAAESTTLQSGEKFQADhINQFIRDLVHDFASSHEE-NIRHVTILRDG-------K 612
                                       99....344444444389*******************99*****************9.***********.......9 PP

                                       -HHHHHHHHHHHHHHHHHCTTTEEEEEEEECSCS--EEESESTCCCEETTTCE.EE....TTEEEEEEEECCEEECC CS
                              Piwi 166 vlnsEvkelkealkklkeqyqpkltvivvqkrhhtrfFasdkaeksqnippGt.vv....dkkitlpeekdfylcsh 237
                                       + +  v++++e l  ++     ++ ++ ++k  + r+ ++++ e  +   +G  +v    +++i++p   +     +
  gi|336252355|ref|YP_004595462.1| 613 IHE-QVDTIREGLSGMD----IEFDMVGIRKTGQPRVTTHEDDE-FKIADKGLgFVdtdrEESILHPWGVPET--TQ 681
                                       998.9*****8887777....6799************9987777.4445578734578888899999888766..78 PP

                                       CCEEEEEEEEEEEEEEES..S-CCHHHHHHHHHCTGGTTTT.SS-SS-HHHHHHHHHHHHHHT CS
                              Piwi 238 aglqgtvkPtkytvlvdeaklsadelqsltyklchmyqrst.rsvsiPapvyyAhklAkrvrn 299
                                          qgt +   + ++ d+       + +++y l+ m+  s  rs++ P p++yA+ +A  vr+
  gi|336252355|ref|YP_004595462.1| 682 DNQQGTPR--TIGIVKDSGPTDLHTITEQVYWLTEMHFGSPaRSTREPVPIKYADAAADYVRK 742
                                       99999988..788999*988888889999********988779***************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (757 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.29s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 5286.31
//
Query:       gi|336252356|ref|YP_004595463.1|  [L=195]
Description: hypothetical protein Halxa_0948 [Halopiger xanaduensis SH-6]
Scores for 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  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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 0.21s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1446.39
//
Query:       gi|336252357|ref|YP_004595464.1|  [L=345]
Description: integrase protein [Halopiger xanaduensis SH-6]
Scores for 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    6.1e-29  101.0   0.1    1.3  1  Phage_integrase  Phage integrase family
     0.0083   16.4   0.0      0.023   15.0   0.0    1.8  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
       0.03   14.3   0.2       0.25   11.3   0.0    2.2  2  Ribosomal_L2     Ribosomal Proteins L2, RNA binding 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 !  101.0   0.1     1e-32   6.1e-29       6     171 ..     151     333 ..     147     334 .. 0.92

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 1e-32
                                       HHHHHHHHCCGC.HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECT.HHHHHHH CS
                   Phage_integrase   6 deverllaalee.slkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravpls.eealell 80 
                                       +eve+l +     s ++r+ +l++ll+ tG+R sE+++ +++d+d ++g+i++  + +K+   r v  + + + +ll
  gi|336252357|ref|YP_004595464.1| 151 EEVEELWQDDALpSPALRNEILIRLLWYTGMRSSEIVRVKIGDIDRDEGRIRI--YAKKTDDYRDVWYPvNRMEPLL 225
                                       77888887666667899************************************..88899999999999899999** PP

                                       HHHHHHH....CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-S............SC--TTHHHHHHHHHH CS
                   Phage_integrase  81 kellska....leeaeksellfaskrgkplsrqtvrkafkraveeagie............kpltpHtlRhsfataL 141
                                        e+l+++    +  a++s +l++ ++++++ ++ v++++k a+++agi+             ++t+HtlRhsfat+ 
  gi|336252357|ref|YP_004595464.1| 226 NEWLGYRrsalSPYADESPYLLLTHQAEQMRASHVSRIVKDAARNAGINevlyvdaagkkrWKVTGHTLRHSFATHH 302
                                       *******999888899999***************************************988899************9 PP

                                       HHH.CTSHHHHHHHHT-SSCCHHHHHHCCCH CS
                   Phage_integrase 142 lea.gvdlrvvqkllGHssisttqiYthvak 171
                                       ++  + +++ +q+++GH  i+tt+ Y+  +k
  gi|336252357|ref|YP_004595464.1| 303 ANVlETPIHILQDVMGHDKIETTRKYISEDK 333
                                       995489********************98765 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 !   15.0   0.0   3.8e-06     0.023      30      84 .]      57     111 ..      45     111 .. 0.96
   2 ?   -3.8   0.0       2.8   1.7e+04      40      57 ..     251     268 ..     249     271 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.8e-06
                                       HHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHHHHHTT CS
                   Phage_int_SAM_1  30 lkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqflvreg 84 
                                        ++l+e+ + +le+++++d+ ++l++   e  s+ +l  +l ++r ++++ +r+g
  gi|336252357|ref|YP_004595464.1|  57 ARWLEEHYGINLEEANRSDLDDYLEYISGEFESTETLGGKLDSVRHLYDWMYRKG 111
                                       68***************************99********************9986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.8
                                       -TTT--HHHHHHHHHS-- CS
                   Phage_int_SAM_1  40 sleqlttedvraflaele 57 
                                       ++eq ++++v+++++  +
  gi|336252357|ref|YP_004595464.1| 251 QAEQMRASHVSRIVKDAA 268
                                       678888888888877655 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 ?    0.1   0.0      0.14   8.2e+02      27      46 ..     181     200 ..     171     209 .. 0.64
   2 ?   11.3   0.0   4.3e-05      0.25      31      62 ..     254     287 ..     239     296 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.14
                                       S---SS--EEEEEEE--TT- CS
                      Ribosomal_L2  27 krnkekvkgkVveieyDpgR 46 
                                        r+ e v+ k+ +i +D gR
  gi|336252357|ref|YP_004595464.1| 181 MRSSEIVRVKIGDIDRDEGR 200
                                       44455555556666655555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.3e-05
                                       SS--EEEEEEE--TT-SS-EEEEEETT..TEEEE CS
                      Ribosomal_L2  31 ekvkgkVveieyDpgRsApiAlvkyed..gekry 62 
                                       +  +  V +i +D +R+A i  v y d  g+kr+
  gi|336252357|ref|YP_004595464.1| 254 QMRASHVSRIVKDAARNAGINEVLYVDaaGKKRW 287
                                       334588*********************9999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); 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:                         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 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2650.85
//
Query:       gi|336252358|ref|YP_004595465.1|  [L=151]
Description: hypothetical protein Halxa_0950 [Halopiger xanaduensis SH-6]
Scores for 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:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1143.09
//
Query:       gi|336252359|ref|YP_004595466.1|  [L=81]
Description: hypothetical protein Halxa_0951 [Halopiger xanaduensis SH-6]
Scores for 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  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 659.15
//
Query:       gi|336252360|ref|YP_004595467.1|  [L=106]
Description: hypothetical protein Halxa_0952 [Halopiger xanaduensis SH-6]
Scores for 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:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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: 0.34u 0.20s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 922.70
//
Query:       gi|336252361|ref|YP_004595468.1|  [L=92]
Description: hypothetical protein Halxa_0953 [Halopiger xanaduensis SH-6]
Scores for 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  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.34u 0.20s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 817.36
//
Query:       gi|336252362|ref|YP_004595469.1|  [L=109]
Description: hypothetical protein Halxa_0954 [Halopiger xanaduensis SH-6]
Scores for 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  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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: 0.34u 0.20s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 957.02
//
Query:       gi|336252363|ref|YP_004595470.1|  [L=98]
Description: hypothetical protein Halxa_0955 [Halopiger xanaduensis SH-6]
Scores for 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:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 868.90
//
Query:       gi|336252364|ref|YP_004595471.1|  [L=129]
Description: hypothetical protein Halxa_0956 [Halopiger xanaduensis SH-6]
Scores for 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  (129 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:                        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: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1141.70
//
Query:       gi|336252365|ref|YP_004595472.1|  [L=90]
Description: hypothetical protein Halxa_0957 [Halopiger xanaduensis SH-6]
Scores for 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  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 696.47
//
Query:       gi|336252366|ref|YP_004595473.1|  [L=150]
Description: hypothetical protein Halxa_0958 [Halopiger xanaduensis SH-6]
Scores for 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  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1187.07
//
Query:       gi|336252367|ref|YP_004595474.1|  [L=293]
Description: hypothetical protein Halxa_0959 [Halopiger xanaduensis SH-6]
Scores for 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-43  147.6   0.0      6e-43  147.3   0.0    1.0  1  DUF4238   Protein of unknown function (DUF4238)
  ------ inclusion threshold ------
       0.13   12.2   0.1       0.25   11.3   0.1    1.5  1  CARD_2    Caspase recruitment domain


Domain annotation for each model (and alignments):
>> DUF4238  Protein of unknown function (DUF4238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.3   0.0   6.6e-47     6e-43       2     272 ..       8     267 ..       7     268 .. 0.89

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 6.6e-47
                           DUF4238   2 hHyvPrfyLknFakd.knklvnvydletkkieersvkricgekdmYtiknedsgedpnhiEktlaklEskaakiirk 77 
                                       +HyvPr +L++F+ d ++++v++yd+++k+ +++ v ++++e+ +Y+ k+e       ++E++l +lE+++ + ++k
  gi|336252367|ref|YP_004595474.1|   8 QHYVPRLHLRRFSTDpDENSVYCYDKQNKRSFPTGVDSTAAEDFFYDGKTE----LVPEMENFLENLEGRVGTPYEK 80 
                                       9************88889*****************************5555....9********************* PP

                           DUF4238  78 ilkegkstrtltreerkqlrkflfllkyRtprfreeydtedkeelesymrekkkfekpld..elldelkvildtkvd 152
                                       i++ ++s  +lt+ e+ +++ fl ++++Rt+  r        + +       + +e+ +    + +e+k++ld+  d
  gi|336252367|ref|YP_004595474.1|  81 IVD-NQSISCLTEAEKVTIALFLGVQMVRTRGSR-----SSMRGMV------EGIEESIGreNMPEEFKTELDEMKD 145
                                       ***.**************************9999.....2222222......2222222222556677777777777 PP

                           DUF4238 153 le..etllqeafeddaewfikhleelywalleassdedFitsDnPvflrndestgeeglsaysey..hillPlspkl 225
                                        e  ++l++++++d+  +f++ ++ l+w+l+ +++d +++tsD+P + +n+ + g +g+ + ++   +i++Pl+p +
  gi|336252367|ref|YP_004595474.1| 146 EEslRELQNNLIKDASSDFANIIAALDWHLFLNETDLPYYTSDFPAVRHNELDFGPYGNLGLRNRgvQIYFPLTPWM 222
                                       77777799999999999************************************************************ PP

                           DUF4238 226 lLvlrsnsleeekedakeiekisreyvkkiNaillqnAkkfiiardk 272
                                       lL++  +s++    +     + +re v    ++++q++++f++++ +
  gi|336252367|ref|YP_004595474.1| 223 LLLIVEPSVYPDLPEV--SNTTDRENVVFQRDLQVQRSNRFVYSCRD 267
                                       ***********98874..7899**********************987 PP

>> CARD_2  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   2.8e-05      0.25      32      91 ..      89     154 ..      79     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.8e-05
                                       TS-HHHHHHHH.....HHHHHHHHHHHHHHHHHHHCT...STTHHHHHHHHHHHTT-HHHHHHHHH CS
                            CARD_2  32 cLteedkeeIr.....aeeenkGniaaaeeLldrllrs.ekegWfkafldaLrktghselaeeleg 91 
                                       cLte +k +I      +  +++G ++ ++ +++ + +s  +e+ +++f + L++++ +e ++el++
  gi|336252367|ref|YP_004595474.1|  89 CLTEAEKVTIAlflgvQMVRTRGSRSSMRGMVEGIEESiGRENMPEEFKTELDEMKDEESLRELQN 154
                                       888888888864443356699****************************************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 2485.09
//
Query:       gi|336252368|ref|YP_004595475.1|  [L=107]
Description: hypothetical protein Halxa_0960 [Halopiger xanaduensis SH-6]
Scores for 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:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); 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: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 945.37
//
Query:       gi|336252369|ref|YP_004595476.1|  [L=242]
Description: Resolvase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   89.1   0.2    4.4e-25   88.5   0.2    1.3  1  Resolvase        Resolvase, N terminal domain
    9.1e-05   22.1   0.1    0.00024   20.8   0.1    1.7  1  HTH_23           Homeodomain-like domain
  ------ inclusion threshold ------
       0.05   13.6   0.0        0.1   12.6   0.0    1.5  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


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 !   88.5   0.2   7.3e-29   4.4e-25       3     145 ..       7     156 ..       5     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 7.3e-29
                                       EEEEES-----THHHHHHHHHHHH-S--...SE.......EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCC CS
                         Resolvase   3 gYaRvSteeqddslerQkealrayaken.glkivk....efeDkgvSGakleRpglkrllaalregkgdvlvvekld 74 
                                       +YaRvSt eqd  +++Qke+l + a ++ +  i+     + eD+ ++G++++R+g++++++++ eg+ + ++v +++
  gi|336252369|ref|YP_004595476.1|   7 IYARVSTPEQD--IAQQKEKLWNHAIDElE--IEPsnidVLEDE-ATGSNTDRDGYQEMMRRVCEGETERVIVRSIT 78 
                                       8**********..********999988752..433334346666.********************999********* PP

                                       CC-S...S-HHHHHHH.HHTT-EEEESS....SS----HHHH....HHHHHHHHHHHHHHHHHCT-TTHHHHHHHHH CS
                         Resolvase  75 RLaRsvrdlltlleel.rekgvslvsldeg..idtstpmgrl....llqilaalaeferelirertkeglaaakakG 144
                                       RL+R++rdl + ++e+  ++g+ lv++++g  i+++t++ +l    +l  l+  + +e e+i++rt +gl+aa ++G
  gi|336252369|ref|YP_004595476.1|  79 RLGRNMRDLNDAVHEIvVDNGCGLVVVNDGlhIEPDTEELNLeqkaILYGLSFASDIEHEMIKQRTIDGLRAAEEAG 155
                                       ****************9***********98885555554333444499999999*********************** PP

                                       H CS
                         Resolvase 145 k 145
                                       k
  gi|336252369|ref|YP_004595476.1| 156 K 156
                                       8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1     4e-08   0.00024       9      40 ..     184     216 ..     177     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4e-08
                            HTH_23   9 rillllae.GlsvreIAreLgvsrrTvyrwlkr 40 
                                       +++ +  e G+s r+I r+ gv+rrTv r++ r
  gi|336252369|ref|YP_004595476.1| 184 QAIVAKEElGWSDRRIQRQIGVPRRTVPRVVDR 216
                                       677788889******************888776 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.7e-05       0.1      17      56 ..      12      52 ..       6      81 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                                      SSTSTTHHHH.HHHHHHHHHHHT--GGGEEEEE-SS-SSHH CS
                   Ketoacyl-synt_C 17 sltapngeaq.araiekalaeagvdpedvdyveahgtgtpl 56
                                      s ++++ ++q +++ ++a++e++++p+++d++e  +tg++ 
  gi|336252369|ref|YP_004595476.1| 12 STPEQDIAQQkEKLWNHAIDELEIEPSNIDVLEDEATGSNT 52
                                      5666666666467899**********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.34
# Mc/sec: 2126.11
//
Query:       gi|336252370|ref|YP_004595477.1|  [L=76]
Description: hypothetical protein Halxa_0962 [Halopiger xanaduensis SH-6]
Scores for 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      0.033   14.4   0.0    1.4  1  DUF3006   Protein of unknown function (DUF3006)


Domain annotation for each model (and alignments):
>> DUF3006  Protein of unknown function (DUF3006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.9e-06     0.033      18      41 ..      34      56 ..      22      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-06
                           DUF3006 18 getidiprsdLpegakeGdvLeie 41
                                      g+t+ i++++Lp+ +keGdv++ +
  gi|336252370|ref|YP_004595477.1| 34 GDTVLIDADELPP-VKEGDVFREQ 56
                                      78899********.******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 662.01
//
Query:       gi|336252371|ref|YP_004595478.1|  [L=103]
Description: hypothetical protein Halxa_0963 [Halopiger xanaduensis SH-6]
Scores for 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  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 794.05
//
Query:       gi|336252372|ref|YP_004595479.1|  [L=65]
Description: hypothetical protein Halxa_0964 [Halopiger xanaduensis SH-6]
Scores for 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:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 513.58
//
Query:       gi|336252373|ref|YP_004595480.1|  [L=53]
Description: hypothetical protein Halxa_0965 [Halopiger xanaduensis SH-6]
Scores for 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  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 435.74
//
Query:       gi|336252374|ref|YP_004595481.1|  [L=469]
Description: ParB domain-containing protein nuclease [Halopiger xanaduensis SH-6]
Scores for 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   39.7   0.1    9.6e-10   38.6   0.1    1.6  1  ParBc            ParB-like nuclease domain
    8.9e-05   22.3   0.5    0.00024   20.9   0.0    2.0  2  N6_N4_Mtase      DNA methylase
     0.0033   15.7  21.3     0.0046   15.3  21.3    1.1  1  Nop14            Nop14-like family
     0.0063   17.1   0.2        1.8    9.3   0.1    2.9  2  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.052   14.3   0.1         12    6.7   0.0    3.7  4  Methyltransf_25  Methyltransferase domain
      0.055   13.1   0.1        3.2    7.4   0.0    2.4  2  UPF0020          Putative RNA methylase family UPF0020


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 !   38.6   0.1   3.2e-13   9.6e-10       3      89 ..      12     106 ..      10     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 3.2e-13
                             ParBc   3 vplseirpnplq..prkdspekieelvasIkkkGllqPiivrktr.....qgryeiiaGerRlrAakrlglkevpvi 72 
                                       +++++++p pl+  ++ d  +  e+l  sI++ G+ +Pi++++ +     +++  ii+G+rR +Aak  gl++vpv+
  gi|336252374|ref|YP_004595481.1|  12 LDPDSLEPHPLNddVYGDRTDPDEALLSSIEEIGVVEPIVADPQPeagevADQPTIISGHRRTEAAKKVGLEQVPVR 88 
                                       5667777444331144447788899*********************999999************************* PP

                             ParBc  73 vleid.deeamalslien 89 
                                          ++ d e+++  l +n
  gi|336252374|ref|YP_004595481.1|  89 FVRLEtDLERQERLLVHN 106
                                       *99998888887766665 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2      0.71   2.1e+03     192     210 ..     163     182 ..     151     184 .. 0.81
   2 !   20.9   0.0   8.1e-08   0.00024       2     111 ..     335     468 ..     334     469 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.71
                                       T-EEEETT.-TTTHHHHHHH CS
                       N6_N4_Mtase 192 gdivlDpF.aGSGtTavaak 210
                                        d v+D   +GSG T ++ak
  gi|336252374|ref|YP_004595481.1| 163 RDKVADTVgFGSGRTYDMAK 182
                                       7889999989*****99987 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 8.1e-08
                                       EEEEE--SSSSSCS.....................GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHH CS
                       N6_N4_Mtase   2 dlivtdpPYntgkdy................endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseik 62 
                                       d++v dpPY  g  +                     ++    +++ le      +e+rrvL ddg ++  ++d+   
  gi|336252374|ref|YP_004595481.1| 335 DCVVLDPPYAEGFYEtpdkpsdndywikdryVGTTGEQSATYHDAVLEMYAAAGEEARRVLRDDGLLIAKMQDEVSR 411
                                       89**********9989999999888888654333334444448999999999*********************9999 PP

                                       T.......HHHHHHHHHTT-EEEEEEEEEEES.....SSTTTSTCCS-B--EEEEEEEESS CS
                       N6_N4_Mtase  63 k.......elkaladeifggffllnvivwkkp.....nsmpesnkdrltsthEyilvfskn 111
                                       +       e+  +++e   +f  ++  v  +p     + m+e++  r+++ h y+lv+ k+
  gi|336252374|ref|YP_004595481.1| 412 NeqrlthiEVTNIYEEM--DFHAKDLFVVVRPdtptiGRMYEQR--RARKNHSYFLVYEKQ 468
                                       99999776555555555..5999999999999999888999988..8************97 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3  21.3   1.5e-06    0.0046     278     412 ..     118     250 ..     106     284 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-06
                             Nop14 278 eekerLeklEeeRlkRMrgeedeeeeeekkkkkkkeasaDdldddfvleeeeeeeefglgkglka............ 342
                                        e+e+Le+ E+eR +  +g+  +  e++++ ++++     + dddf   +++ ++++g+g+g ++            
  gi|336252374|ref|YP_004595481.1| 118 REAEELERIERERARQRQGTRTDIVENSSRGDEEM----SSPDDDFGKTRDKVADTVGFGSGRTYdmaktvwdaaqd 190
                                       689****************9444444444444433....456789999999999999****9965555666655422 PP

                             Nop14 343 ..taeeeeeededdfeedddlveseseeeeeeeeedeeeeedeeeeeeeeededdlsdleseeeeeedelee 412
                                         t      + e d+ + ++++  +  ++  +  + e e++de+  +        +sd+e+++++++de  e
  gi|336252374|ref|YP_004595481.1| 191 gdT----VAQHEVDKLDREEQSVYGAYQKVRDRVQTETESDDEDGTS--------SSDEEEQDSSSDDEEPE 250
                                       220....2222222222222222222222211111111111111111........11111112222222111 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1   0.00061       1.8      50      67 ..     322     339 ..     285     341 .. 0.66
   2 ?    4.7   0.0     0.016        47      78      95 ..     385     402 ..     373     403 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00061
                                       EECCCTSS-TT-EEEEEE CS
                   Methyltransf_11  50 adaeklpfednsfDlvvs 67 
                                        d+++lp+ d+sfD+vv+
  gi|336252374|ref|YP_004595481.1| 322 VDCRDLPYDDASFDCVVL 339
                                       5899************86 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                       ++a +e++RvL+ +Gll+
  gi|336252374|ref|YP_004595481.1| 385 AAAGEEARRVLRDDGLLI 402
                                       66779***********98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.7     5e+03       5      42 ..     171     217 ..     169     238 .. 0.54
   2 ?    2.0   0.0      0.12   3.5e+02       1      32 [.     284     313 ..     284     317 .. 0.87
   3 ?    6.7   0.0    0.0039        12      54      70 ..     323     339 ..     318     351 .. 0.92
   4 ?   -0.5   0.0      0.72   2.2e+03      82      97 .]     384     399 ..     373     399 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                                       T-TTSHHHHHHHCTS.....T....SSEEEEEESSHHHHHHHHHHHH CS
                   Methyltransf_25   5 GcGtGrltlalakrl.....g....kakvtgvDiseemleaarerae 42 
                                       G G+Gr+  ++ + +     g    +++v  +D  e+ +  a ++++
  gi|336252374|ref|YP_004595481.1| 171 GFGSGRTYDMAKTVWdaaqdGdtvaQHEVDKLDREEQSVYGAYQKVR 217
                                       66666544333322122222122335677777777777766666664 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.12
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHH CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDisee 32 
                                       + d+  G+G + +++     k+++t++Di+++
  gi|336252374|ref|YP_004595481.1| 284 IADVTYGEGVFWRQVPSG--KYELTATDIDPS 313
                                       67999*******999855..6*******9985 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0039
                                       BCCGBSSSTTTEEEEEE CS
                   Methyltransf_25  54 daedlpfedgsfDlvvs 70 
                                       d++dlp++d+sfD+vv+
  gi|336252374|ref|YP_004595481.1| 323 DCRDLPYDDASFDCVVL 339
                                       89*************96 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.72
                                       HHHHHHHHHHHEEEEE CS
                   Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                       +++a +e++rvL+++G
  gi|336252374|ref|YP_004595481.1| 384 YAAAGEEARRVLRDDG 399
                                       4567799******998 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0011       3.2     110     134 ..     322     346 ..     275     354 .. 0.84
   2 ?    3.2   0.0     0.021        63     136     168 ..     375     407 ..     371     435 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0011
                                       --GGG--STTS---EEEE------- CS
                           UPF0020 110 adaakLrlkegevdvivtnpPYGer 134
                                        d ++L+ +++++d +v +pPY e 
  gi|336252374|ref|YP_004595481.1| 322 VDCRDLPYDDASFDCVVLDPPYAEG 346
                                       68999**9999***********875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.021
                                       --HHHHHHHHHHHHHHHHHH-TT..-EEEEEES CS
                           UPF0020 136 gskkalekLYseflrelkrvlrgggrlvlltse 168
                                       + + a+ ++Y + ++e+ rvlr +g l++ +++
  gi|336252374|ref|YP_004595481.1| 375 TYHDAVLEMYAAAGEEARRVLRDDGLLIAKMQD 407
                                       5678999****************9887765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 3375.55
//
Query:       gi|336252375|ref|YP_004595482.1|  [L=280]
Description: hypothetical protein Halxa_0967 [Halopiger xanaduensis SH-6]
Scores for 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-05   23.7   0.0    6.3e-05   22.9   0.0    1.4  1  DUF1819   Putative inner membrane protein (DUF1819)
  ------ inclusion threshold ------
       0.15   11.5   0.1       0.26   10.7   0.1    1.4  1  DUF3645   Protein of unknown function (DUF3645)


Domain annotation for each model (and alignments):
>> DUF1819  Putative inner membrane protein (DUF1819)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     7e-09   6.3e-05       4     162 ..      25     192 ..      22     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7e-09
                                       -SGGGG----HHHHHHHHHHHHH---HHHHHHHHHTS-TT--------HHHHHHHHHHHTTS......-HHHHHHHH CS
                           DUF1819   4 sasltkgsfllaEsrkvaelllegkseaeirekaleeNifqkrtesrakriasevirRlklL......deellella 74 
                                       s+ lt+ ++l++   ++a+l+ ++ +++ ++e+ +ee   + +t+ + k i++++ +R k+         +l +++ 
  gi|336252375|ref|YP_004595482.1|  25 SMALTRCGLLVERAETLARLYAQHRDWTVVEEQWVEERFDERSTRGSSKGIYRALSSRFKTAgselpsIVQLPTVFD 101
                                       7899*********************************************************7444454445556666 PP

                                       HS-HH.HHHHHHHHHHHHH-HHHHHHHHHTHHHHTTSSS...-B--HHHHHHHHHHHHHH-TTS----HHHHHHHHH CS
                           DUF1819  75 egsie.eakqlllyaimkadrLlfdFmtevireklrlgd...eeltdedidiFfkrkaeqsekvaswsdstikKLkq 147
                                       +++++ +  q+l+++++++d+L+  +++  ++ +l+ +     ++++  ++  +++    +     + +st ++  +
  gi|336252375|ref|YP_004595482.1| 102 QCETKrDKAQVLYFYLVEDDPLV-KYIVHRYANRLQESGvdgLDFEQDTVERLLNEFHYDDGSEFDYAESTTRRWGE 177
                                       66655155566666777777776.58888888888875412256788888888888888888888888888888888 PP

                                       HHHHHHHHTTSBS-T CS
                           DUF1819 148 vllriLaeaglLesk 162
                                        l ++++e ++L+ +
  gi|336252375|ref|YP_004595482.1| 178 GLRSVMREIDVLDTQ 192
                                       888888888888833 PP

>> DUF3645  Protein of unknown function (DUF3645)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   2.9e-05      0.26      13      33 .]       9      29 ..       8      29 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.9e-05
                           DUF3645 13 AKDvPserSEFsHpDvvIvLT 33
                                      ++  Ps  S FsH +v + LT
  gi|336252375|ref|YP_004595482.1|  9 GTSLPSLDSTFSHEEVSMALT 29
                                      6678****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2154.60
//
Query:       gi|336252376|ref|YP_004595483.1|  [L=1227]
Description: hypothetical protein Halxa_0968 [Halopiger xanaduensis SH-6]
Scores for 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   13.9   0.0       0.21   12.1   0.0    1.9  1  ABC_tran  ABC transporter
        1.2    9.9   3.2        9.4    7.0   0.4    3.1  3  HWE_HK    HWE histidine kinase


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 ?   12.1   0.0   2.3e-05      0.21       7      65 ..      61     128 ..      57     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEE...EETTCEGGG..B-HHHCCHCEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx...xxxxxxxxx..xxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkp....teGei...lldgkdlke..qeleslrkeigvlp 65 
                                       +++ g  + + G  G+GKS Ll++l gll+     + +++   l dg++l++  ++++s + e +v+p
  gi|336252376|ref|YP_004595483.1|  61 DMRSGANYWLYGYYGSGKSHLLSVLRGLLDSewlrEREDVweqLTDGRELDTleTTWSSIHDEYEVIP 128
                                       6789999*********************9875565455553433344444444444444444444444 PP

>> HWE_HK  HWE histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0         2   1.8e+04      22      39 ..      39      56 ..      37      61 .. 0.80
   2 ?    7.0   0.4     0.001       9.4      28      77 ..     917     966 ..     913     970 .. 0.90
   3 ?    1.6   0.1      0.05   4.5e+02      17      54 ..     983    1020 ..     980    1039 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2
                                      SSXS-HHHHHHHHHHHHH CS
                            HWE_HK 22 rsaesleefaeklsgRLq 39
                                      + +e++e+f+ ++ +RL 
  gi|336252376|ref|YP_004595483.1| 39 HVTEESEDFMSDFFSRLL 56
                                      557899999999999995 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHHHHHHHHHHCTTS-EEHHHHHHHHHHHHHHHSTTSE CS
                            HWE_HK  28 eefaeklsgRLqALsaahdllsreewagaeLaelleeelapyedeaseri 77 
                                       ++++++l+gRL +L +   l+++++ ++  +++lle+ ++  e+++++ i
  gi|336252376|ref|YP_004595483.1| 917 QSANDTLAGRLGSLVEDVRLVAESDIQTRAVRNLLESFVEELEAKQQSAI 966
                                       78899************************************998776655 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.05
                                        HHHHSSSXS-HHHHHHHHHHHHHHHHHHHHHHHHCTTS CS
                            HWE_HK   17 arqtlrsaesleefaeklsgRLqALsaahdllsreewa 54  
                                        ++ t++ ++  ++++e  s RL AL + ++ l+ ++ +
  gi|336252376|ref|YP_004595483.1|  983 VEATNNAQDWYDDAEEVWSLRLPALTRIDSQLTLAQQS 1020
                                        778999999999*****************999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.86u 0.29s 00:00:01.14 Elapsed: 00:00:00.46
# Mc/sec: 7976.42
//
Query:       gi|336252377|ref|YP_004595484.1|  [L=193]
Description: hypothetical protein Halxa_0969 [Halopiger xanaduensis SH-6]
Scores for 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-14   53.6   0.0    2.8e-14   53.2   0.0    1.1  1  DUF1788      Domain of unknown function (DUF1788)
     0.0018   18.5   0.0     0.0028   17.9   0.0    1.3  1  EIIA-man     PTS system fructose IIA component
  ------ inclusion threshold ------
       0.11   12.5   0.4       0.32   10.9   0.3    1.8  2  Tautomerase  Tautomerase enzyme


Domain annotation for each model (and alignments):
>> DUF1788  Domain of unknown function (DUF1788)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   4.7e-18   2.8e-14      14     124 .]      74     183 ..      65     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 4.7e-18
                           DUF1788  14 eekkllekllemeekkgkeellealkkvlkseeelikkikekieek..eadvvfltgvGkvyPllRshtlLnnlqsv 88 
                                        e +++e +++  e+ + + ++e++++ l +  el++ + eki++   +++vv+lt  G++yP+ R+++lL++l+++
  gi|336252377|ref|YP_004595484.1|  74 VETDVFELAVDLGENSQPATITETMQDRLAE--ELVAVMVEKIDAPaqQRHVVLLTHLGSLYPFTRASELLDELDRR 148
                                       5677888899999999999999999999999..444444444444324568************************** PP

                           DUF1788  89 vkkvpvvlfyPGeydgqslslfnelkddnyYrafkl 124
                                         +  + + +PG   g +ls+f+e +++nyY a ++
  gi|336252377|ref|YP_004595484.1| 149 NVQSTIGIPFPGDIVGGKLSFFGE-ESRNYYPAHQI 183
                                       ***********************7.78899998775 PP

>> EIIA-man  PTS system fructose IIA component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   4.8e-07    0.0028      23      87 ..      86     150 ..      76     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.8e-07
                                       SSS-SCEEEEEC-TTS-CCCHHHHHHHHHCTS--TTEEEEEESSCCCHHHHHHHHCCTTSTTEEE CS
                          EIIA-man  23 gedqekviavggtpdesigtlaekikeaieevdsedevlvLvDlggatpfneaaleleekeelev 87 
                                       ge++++ ++   ++d  +++l + ++e+i++  ++ +v++L+ lg+  pf+ a+ +l e ++ +v
  gi|336252377|ref|YP_004595484.1|  86 GENSQPATITETMQDRLAEELVAVMVEKIDAPAQQRHVVLLTHLGSLYPFTRASELLDELDRRNV 150
                                       45467889999999***************88889**********************999988655 PP

>> Tautomerase  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.7     1e+04      17      25 ..      39      47 ..      36      48 .. 0.82
   2 ?   10.9   0.3   5.4e-05      0.32      17      42 ..     100     125 ..      91     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.7
                                      HHHHHHHHH CS
                       Tautomerase 17 aeLaervTe 25
                                      +++aer+Te
  gi|336252377|ref|YP_004595484.1| 39 RRVAERLTE 47
                                      678999997 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 5.4e-05
                                       HHHHHHHHHHHHHHHTS-GGG-EEEE CS
                       Tautomerase  17 aeLaervTealvealgaprsaivVvi 42 
                                       ++Lae++ +++ve ++ap +  +Vv+
  gi|336252377|ref|YP_004595484.1| 100 DRLAEELVAVMVEKIDAPAQQRHVVL 125
                                       68**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1434.90
//
Query:       gi|336252378|ref|YP_004595485.1|  [L=1280]
Description: hypothetical protein Halxa_0970 [Halopiger xanaduensis SH-6]
Scores for 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   17.7   0.1        7.3    6.9   0.0    4.1  3  AAA_22     AAA domain
  ------ inclusion threshold ------
       0.04   13.7   0.3        1.6    8.5   0.0    2.9  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
      0.087   12.6   0.0        2.2    8.1   0.0    3.2  2  SKA2       Spindle and kinetochore-associated protein 2
        0.2   12.0   0.8        2.7    8.3   0.1    3.1  3  DUF948     Bacterial protein of unknown function (DUF948)


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 !    6.9   0.0    0.0016       7.3       4      33 ..      61      90 ..      59     150 .. 0.82
   2 ?   -1.0   0.0      0.43   1.9e+03      53     111 ..     217     291 ..     186     309 .. 0.66
   3 !    5.0   0.3     0.006        27      38     127 ..    1186    1275 ..    1128    1277 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0016
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeea 33
                                      + ++l++ +  G+GKT+ll+ +   +d e+
  gi|336252378|ref|YP_004595485.1| 61 EPRFLYISATFGSGKTHLLKLIGFAADTES 90
                                      5789***************98876666555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.43
                            AAA_22  53 skdllrellralglelkaerlsseellealeqalrarav.....ielliiDEaqhlr....s........eealee 111
                                       ++++ + +  a+++   + + + +el++++e a ++ ++       l+ +DE+  ++    +        +eal+e
  gi|336252378|ref|YP_004595485.1| 217 REEVKQSIDDAIEEVDPD-EFDPDELVDRIEAAQESLSTpetetELLIGLDEVALFIgdgrHryrefqetMEALTE 291
                                       444445555555554444.667777777777777777777779666666999998776654145455344444444 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.006
                            AAA_22   38 erpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalrarav....ielliiDEaqhlr..se 106 
                                         ++e+++ ++ ++ + ++ l+el+++l++e  +     ++l + + +a++ ++     ++  +i+Ea+ l    +
  gi|336252378|ref|YP_004595485.1| 1186 DDVEQLLDEAENPFEVDERLEELASELQSEYPD-----HDLTQEVVDAVEGTSPpseeRVGELIEEAEQLLdgVD 1255
                                        566666667777788888999999999977666.....888888888888888888879999*******543449 PP

                            AAA_22  107 ealeeLrsllnlsrkgvqliL 127 
                                        e+l+ +r+ ++ +  + +++L
  gi|336252378|ref|YP_004595485.1| 1256 EQLRRIRETMD-ELEDGSVVL 1275
                                        99999999988.555555555 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 ?    8.5   0.0   0.00035       1.6       9      34 ..      72      97 ..      72     117 .. 0.73
   2 ?    1.8   0.1     0.039   1.7e+02      84     146 ..     514     576 ..     486     604 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00035
                            AAA_21  9 gsGKSnLLdaldllarl...drdvegltd 34
                                      gsGK++LL+++ ++a++   +    +l+ 
  gi|336252378|ref|YP_004595485.1| 72 GSGKTHLLKLIGFAADTeseF---ADLGE 97
                                      9**************984442...33333 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.039
                            AAA_21  84 eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltd 146
                                        e++ sv+++ es l++  ++++   ++n+++++++ +vs++++  l++++  ++q ++++++
  gi|336252378|ref|YP_004595485.1| 514 DESFESVRDDVESALTDLLEDRKILTETNDRGDEEYLLVSEEQEDILTRAKTRAQQIPSHRLS 576
                                       467899999******************************************999999988876 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.22     1e+03      21      56 ..     220     254 ..     198     262 .. 0.81
   2 ?    8.1   0.0   0.00049       2.2       3      91 ..    1184    1270 ..    1183    1278 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.22
                              SKA2  21 vqhrLekefqqsypdnaeNpvkLlerlkkvkeelqa 56 
                                       v++  ++ +++  pd+  +p +L+ r+++ +e l++
  gi|336252378|ref|YP_004595485.1| 220 VKQSIDDAIEEVDPDEF-DPDELVDRIEAAQESLST 254
                                       55666777777778885.***********9998876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00049
                              SKA2    3 avdklealFqkaesdLdyvqhrLe...kefqqsypdnaeNpvkLler.lkkvkeelqaLkeqceellaekkelid 73  
                                        +vd++e+l+++ae+  ++ ++rLe   +e+q +ypd+      L ++ + +v    +  +e++ el +e ++l d
  gi|336252378|ref|YP_004595485.1| 1184 SVDDVEQLLDEAENPFEV-DERLEelaSELQSEYPDHD-----LTQEvVDAVEGTSPPSEERVGELIEEAEQLLD 1252
                                        699999999999999885.5554422279999999996.....55542678999999999999999999999999 PP

                              SKA2   74 kirttlvanrellqqLqa 91  
                                         +  +l + re++ +L+ 
  gi|336252378|ref|YP_004595485.1| 1253 GVDEQLRRIRETMDELED 1270
                                        999999999999999875 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 ?   -1.0   0.0      0.49   2.2e+03       9      45 ..     479     527 ..     479     545 .. 0.51
   2 ?   -1.6   0.0      0.74   3.3e+03      44      74 ..    1168    1199 ..    1152    1214 .. 0.66
   3 ?    8.3   0.1    0.0006       2.7      32      79 ..    1223    1270 ..    1219    1275 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.49
                            DUF948   9 AFvvLviflivvllkl............kktldeaaatieelekqvdpi 45 
                                       AF+v v+   ++l+++            + +++++ ++ e+++++v++ 
  gi|336252378|ref|YP_004595485.1| 479 AFSVRVAKALYLLNQVrsevpstpanlaRLMVKSTDESFESVRDDVESA 527
                                       6667777777777777333333333333333444444444444444444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.74
                            DUF948   44 pilkevedllakvne.lledvneklekvdplt 74  
                                        p++++v ++l+ ++   ++dv++ l++ ++ +
  gi|336252378|ref|YP_004595485.1| 1168 PVTTDVSEMLSRSQPpSVDDVEQLLDEAENPF 1199
                                        66777777777766556677776666655544 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0006
                            DUF948   32 aatieelekqvdpilkevedllakvnelledvneklekvdplteavad 79  
                                        ++ ++ +e    p  + v +l++++++ll++v e+l ++ + +++++d
  gi|336252378|ref|YP_004595485.1| 1223 QEVVDAVEGTSPPSEERVGELIEEAEQLLDGVDEQLRRIRETMDELED 1270
                                        555666666666667778888888888888888899999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); 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):               4  [number of targets reported over threshold]
# CPU time: 0.94u 0.31s 00:00:01.25 Elapsed: 00:00:00.48
# Mc/sec: 8057.71
//
Query:       gi|336252379|ref|YP_004595486.1|  [L=391]
Description: hypothetical protein Halxa_0971 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.02   15.1   0.0      0.042   14.1   0.0    1.5  1  PaaB      Phenylacetic acid degradation B


Domain annotation for each model (and alignments):
>> PaaB  Phenylacetic acid degradation B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.3e-06     0.042      29      79 ..     261     312 ..     246     317 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-06
                              PaaB  29 emALlvArdvfvRRe.eavslwvvkseailastpeekeslfapakektYrhq 79 
                                       emAL++ r+vf+  + e ++ wvv++++++ ++ ++++s fa+a+   Y ++
  gi|336252379|ref|YP_004595486.1| 261 EMALETRRKVFLEGDfERLQQWVVETTDLTLADFKDSGSTFAKAEREGYPEP 312
                                       8**********98765899**************************9999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3045.71
//
Query:       gi|336252380|ref|YP_004595487.1|  [L=306]
Description: transcriptional regulator TrmB [Halopiger xanaduensis SH-6]
Scores for 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-16   58.4   0.6    7.1e-07   29.0   0.0    2.5  2  TrmB             Sugar-specific transcriptional regulator Trm
    9.2e-16   57.5   0.7    1.5e-08   34.4   0.3    2.5  2  MarR_2           MarR family
    3.4e-13   49.3   0.1    2.5e-05   24.1   0.0    2.4  2  MarR             MarR family
    4.7e-11   42.3   2.9    3.4e-06   26.8   0.1    2.9  3  HTH_IclR         IclR helix-turn-helix domain
    5.9e-10   38.9   0.3    5.4e-05   23.0   0.0    2.5  2  HTH_5            Bacterial regulatory protein, arsR family
    6.3e-10   38.5   0.1    0.00089   18.8   0.0    2.5  2  HTH_24           Winged helix-turn-helix DNA-binding
    6.4e-10   39.1   1.1    0.00061   19.9   0.3    2.6  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    6.9e-09   35.9   0.4    0.00077   19.8   0.0    2.4  2  Rrf2             Transcriptional regulator
    1.2e-08   34.7   0.1    6.4e-05   22.8   0.0    2.7  2  HTH_11           HTH domain
    4.7e-08   33.0   1.8     0.0024   17.9   0.0    2.5  2  HTH_20           Helix-turn-helix domain
    2.7e-07   30.5   0.8    0.00041   20.3   0.0    3.0  3  HTH_Crp_2        Crp-like helix-turn-helix domain
    4.6e-07   30.2   0.7     0.0054   17.2   0.2    2.5  2  HTH_27           Winged helix DNA-binding domain
    6.9e-06   26.0   0.2     0.0082   16.1   0.1    2.7  2  HTH_29           Winged helix-turn helix
    8.5e-06   25.3   0.3      0.032   13.9   0.0    3.1  3  GntR             Bacterial regulatory proteins, gntR family
    0.00026   21.0   0.2       0.14   12.3   0.0    3.0  2  HTH_28           Helix-turn-helix domain
    0.00052   20.4   0.0       0.28   11.5   0.0    2.5  2  Penicillinase_R  Penicillinase repressor
    0.00098   18.9   0.2        1.9    8.4   0.0    2.7  2  HTH_23           Homeodomain-like domain
     0.0021   17.8   0.1        2.3    7.9   0.1    2.3  2  DUF4423          Domain of unknown function (DUF4423)
     0.0042   17.0   0.0       0.03   14.3   0.0    2.2  2  HTH_45           Winged helix-turn-helix
     0.0052   16.7   0.9       0.25   11.3   0.2    2.5  2  HTH_1            Bacterial regulatory helix-turn-helix protei
      0.008   16.0   2.3      0.073   12.9   0.1    2.7  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0083   16.2   0.1          3    8.0   0.1    2.6  2  DUF2250          Uncharacterized protein conserved in archaea
  ------ inclusion threshold ------
      0.016   15.4   0.1        7.7    6.8   0.0    2.5  2  PaaX             PaaX-like protein
      0.021   14.6   0.0        3.5    7.5   0.0    3.0  3  HTH_10           HTH DNA binding domain
      0.022   14.5   0.0      0.092   12.5   0.0    2.1  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.029   14.4   0.4       0.19   11.8   0.1    2.3  2  FeoC             FeoC like transcriptional regulator
      0.048   13.8   0.2        5.3    7.3   0.0    3.1  2  HTH_17           Helix-turn-helix domain
      0.055   13.2   0.0        1.8    8.4   0.0    2.8  3  HTH_38           Helix-turn-helix domain
      0.061   13.2   0.0       0.99    9.3   0.0    2.1  2  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
      0.064   13.3   0.0        0.4   10.8   0.0    2.2  2  HTH_7            Helix-turn-helix domain of resolvase
      0.065   13.1   0.1         17    5.4   0.0    3.0  3  YdaS_antitoxin   Putative antitoxin of bacterial toxin-antito
      0.094   12.8   0.0       0.35   10.9   0.0    2.0  1  z-alpha          Adenosine deaminase z-alpha domain
       0.11   12.1   0.0        6.9    6.3   0.0    2.3  2  HTH_CodY         CodY helix-turn-helix domain
       0.11   13.1   0.0       0.55   10.8   0.0    2.1  2  Phage_rep_O      Bacteriophage replication protein O
       0.13   12.0   0.0        1.7    8.5   0.0    2.4  2  LexA_DNA_bind    LexA DNA binding domain
       0.15   12.1   0.0        0.8    9.8   0.0    2.2  1  SpoIIID          Stage III sporulation protein D
       0.18   11.7   0.1          2    8.3   0.0    2.2  2  DUF903           Bacterial protein of unknown function (DUF90


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 !   26.9   0.2   6.6e-09   3.2e-06       7      59 ..       3      53 ..       3      62 .. 0.89
   2 !   29.0   0.0   1.5e-09   7.1e-07      20      60 ..      96     136 ..      90     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 6.6e-09
                                      HHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB  7 seyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                      se E ++  aL  +g++t++ +aeel+++rs v e + ++e+kGlV+++++ +
  gi|336252380|ref|YP_004595487.1|  3 SEAELRALEAL--QGESTVSGLAEELDRSRSYVSELVDRMESKGLVHTSREGK 53
                                      57788888887..6*********************************998764 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 1.5e-09
                                       HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB  20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60 
                                       + pata+++ae+++v rs+v ++L+ Le++G++++++g+++
  gi|336252380|ref|YP_004595487.1|  96 QSPATATQLAEQVDVHRSTVHRSLSPLENRGMIYKSDGKYT 136
                                       679**********************************9987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.3   3.1e-11   1.5e-08       6      56 ..       5      51 ..       3      63 .. 0.89
   2 !   20.7   0.0   5.7e-07   0.00028       6      56 ..      87     133 ..      84     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3.1e-11
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      a++r+L aL  +     tv+ la++l+ s+s+vs +++r++++GLv +++ 
  gi|336252380|ref|YP_004595487.1|  5 AELRALEALQGES----TVSGLAEELDRSRSYVSELVDRMESKGLVHTSRE 51
                                      6788888888885....*****************************99865 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 5.7e-07
                                       HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2   6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                       a +r+L++L  +p    t+++la+  ++ +s+v+r l  L+ +G++ +++g
  gi|336252380|ref|YP_004595487.1|  87 ATLRILYYL-QSP---ATATQLAEQVDVHRSTVHRSLSPLENRGMIYKSDG 133
                                       667888888.566...6*****************************99876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   5.2e-08   2.5e-05      15      50 ..      14      49 ..       4      53 .. 0.90
   2 !   22.8   0.0   1.4e-07   6.6e-05       8      50 ..      88     131 ..      86     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.2e-08
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      qg+ +vs La+ l  s+s+v++++dr+e kGl++ s
  gi|336252380|ref|YP_004595487.1| 14 QGESTVSGLAEELDRSRSYVSELVDRMESKGLVHTS 49
                                      577899**************************9865 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR   8 iLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                       +Lrily+ ++ ++ ++La+++ v++stv r l  Le +G+i++s
  gi|336252380|ref|YP_004595487.1|  88 TLRILYYLQSpATATQLAEQVDVHRSTVHRSLSPLENRGMIYKS 131
                                       799****99879999**************************998 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 !   14.6   0.4   4.3e-05     0.021       9      50 ..       7      48 ..       7      50 .. 0.96
   2 !   26.8   0.1   6.9e-09   3.4e-06      17      50 ..      97     130 ..      87     132 .. 0.86
   3 ?   -2.2   0.0       7.5   3.7e+03       4      18 ..     270     284 ..     269     304 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.3e-05
                                      HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      L+al++ ++e t+s lA++++ ++S v+ l+  ++  G+v +
  gi|336252380|ref|YP_004595487.1|  7 LRALEALQGESTVSGLAEELDRSRSYVSELVDRMESKGLVHT 48
                                      899************************************975 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 6.9e-09
                                       SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                        + t ++lA++ ++++StvhR L+ L+++G++ +
  gi|336252380|ref|YP_004595487.1|  97 SPATATQLAEQVDVHRSTVHRSLSPLENRGMIYK 130
                                       56789*************************9976 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.5
                                       HHHHHHCT-CTTBSS CS
                          HTH_IclR   4 RalaiLdalaeapqe 18 
                                       R   +L++l ++++ 
  gi|336252380|ref|YP_004595487.1| 270 RVSNLLEYLDTEGES 284
                                       667788888877765 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 !   13.6   0.1   9.4e-05     0.046      11      46 ..      10      47 ..       7      48 .. 0.86
   2 !   23.0   0.0   1.1e-07   5.4e-05       5      47 .]      89     130 ..      87     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.4e-05
                                      HTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 11 Lae..gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      L+   ge +v+ laeel+ s+s vS+   +++  GLV+
  gi|336252380|ref|YP_004595487.1| 10 LEAlqGESTVSGLAEELDRSRSYVSELVDRMESKGLVH 47
                                      544559********************999999999996 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5   5 lkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                       l+IL++L+ +++++++lae++++ +stv + L+ L++ G+++k
  gi|336252380|ref|YP_004595487.1|  89 LRILYYLQ-SPATATQLAEQVDVHRSTVHRSLSPLENRGMIYK 130
                                       79999995.8*****************************9986 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 !   17.1   0.0   6.1e-06    0.0029       9      47 ..       7      46 ..       5      47 .. 0.90
   2 !   18.8   0.0   1.8e-06   0.00089       6      47 ..      89     128 ..      87     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.1e-06
                            HTH_24  9 LelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      L++L++ ++  + + LAe+l+ S+s v++ ++r+e++Gl+
  gi|336252380|ref|YP_004595487.1|  7 LRALEAlQGESTVSGLAEELDRSRSYVSELVDRMESKGLV 46
                                      566666678899999***********************98 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.8e-06
                            HTH_24   6 rkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       ++IL +Lq     + ++LAe++++ +stv+r l  Le+ G I
  gi|336252380|ref|YP_004595487.1|  89 LRILYYLQS--PATATQLAEQVDVHRSTVHRSLSPLENRGMI 128
                                       677777777..99***************************99 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 !   19.9   0.3   1.3e-06   0.00061      19      56 ..      13      50 ..       1      53 [. 0.83
   2 !   17.3   0.0   8.3e-06     0.004      10      51 ..      89     127 ..      88     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.3e-06
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                       ++  +++ lae+L+ s s Vse + ++e++G+v+++ 
  gi|336252380|ref|YP_004595487.1| 13 LQGESTVSGLAEELDRSRSYVSELVDRMESKGLVHTSR 50
                                      556667899**************************975 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 8.3e-06
                                       HHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress  10 LetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGy 51 
                                       L+ +Y l+   ++++ ++lae  +v+ s+V  +l+ Le+ G 
  gi|336252380|ref|YP_004595487.1|  89 LRILYYLQ---SPATATQLAEQVDVHRSTVHRSLSPLENRGM 127
                                       56677777...899************************9996 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1    0.0001     0.051      21      59 ..      14      50 ..       5      58 .. 0.82
   2 !   19.8   0.0   1.6e-06   0.00077      23      75 ..      96     145 ..      87     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.0001
                                      STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      +  +  +++ +ae+ + s+sy++ ++ +++ +glv++ r
  gi|336252380|ref|YP_004595487.1| 14 Q--GESTVSGLAEELDRSRSYVSELVDRMESKGLVHTSR 50
                                      3..346999**************************8654 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.6e-06
                                       CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHCCCSB CS
                              Rrf2  23 eepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppeeIt 75 
                                       ++p++++++ae++++++s + + l+ L++ g++    Gk   y+L+ + ee +
  gi|336252380|ref|YP_004595487.1|  96 QSPATATQLAEQVDVHRSTVHRSLSPLENRGMIYKSDGK---YTLNDEFEELS 145
                                       4578999********************************...99999988865 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1    0.0024       1.2       9      43 ..      10      44 ..       4      53 .. 0.78
   2 !   22.8   0.0   1.3e-07   6.4e-05       6      44 ..      89     127 ..      87     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0024
                            HTH_11  9 LleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      L + +g  + + LAeeL++Sr+ v   ++++e++g
  gi|336252380|ref|YP_004595487.1| 10 LEALQGESTVSGLAEELDRSRSYVSELVDRMESKG 44
                                      444555567888**********9999999998888 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.3e-07
                            HTH_11   6 lelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44 
                                       l++L+  ++p ++ +LAe+ +v r+tv+r +  Le  g+
  gi|336252380|ref|YP_004595487.1|  89 LRILYYLQSPATATQLAEQVDVHRSTVHRSLSPLENRGM 127
                                       5677777999************************99983 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.7   0.00013     0.061      19      61 .]      10      53 ..       5      53 .. 0.90
   2 !   17.9   0.0     5e-06    0.0024      13      54 ..      89     128 ..      86     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                                      H.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 19 L.araegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                      L a  ++ t+s lae+ld s++ +s  ++ +e+ gLv++ reg+
  gi|336252380|ref|YP_004595487.1| 10 LeALQGESTVSGLAEELDRSRSYVSELVDRMESKGLVHTSREGK 53
                                      45558999**********************************96 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 5e-06
                                       HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20  13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54 
                                       +ril +L    ++ta++lae++d++++t+++ L  Le  g +
  gi|336252380|ref|YP_004595487.1|  89 LRILYYL--QSPATATQLAEQVDVHRSTVHRSLSPLENRGMI 128
                                       6889999..9**************************998876 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 ?    6.9   0.1     0.012         6      27      53 ..      22      50 ..       8      64 .. 0.84
   2 !   20.3   0.0   8.4e-07   0.00041      19      61 ..      96     139 ..      83     141 .. 0.85
   3 ?   -1.3   0.0       4.5   2.2e+03      36      52 ..     145     161 ..     144     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                                      HHHHTTSSHHHHHHHHHHHHHTTSEE..E CS
                         HTH_Crp_2 27 lAsmlGltretvsrilseLkreglis..r 53
                                      lA+ l  +r+ vs +  +++ +gl+   r
  gi|336252380|ref|YP_004595487.1| 22 LAEELDRSRSYVSELVDRMESKGLVHtsR 50
                                      8999999******************9532 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 8.4e-07
                                       EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE..TEEEEES- CS
                         HTH_Crp_2  19 elpltqeelAsmlGltretvsrilseLkreglisr..grririld 61 
                                       + p t ++lA+ + ++r+tv r ls L+++g+i +  g+  +++d
  gi|336252380|ref|YP_004595487.1|  96 QSPATATQLAEQVDVHRSTVHRSLSPLENRGMIYKsdGK-YTLND 139
                                       568999***************************952244.88887 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.5
                                       HHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2  36 etvsrilseLkreglis 52 
                                       +tv r++++L+ +  ++
  gi|336252380|ref|YP_004595487.1| 145 STVAREFAHLRHRHRVE 161
                                       59999999999987766 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 !   17.2   0.2   1.1e-05    0.0054       9      61 ..       7      56 ..       4      62 .. 0.83
   2 !   10.8   0.0    0.0011      0.52       8      58 ..      88     134 ..      87     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-05
                            HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekr 61
                                      L+ ++  +++++ + l++ l+++ s +s+ +++++ kGLv++++   ++++k+
  gi|336252380|ref|YP_004595487.1|  7 LRALEALQGESTVSGLAEELDRSRSYVSELVDRMESKGLVHTSR---EGKQKQ 56
                                      55666677899999**************************7774...456655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0011
                            HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58 
                                       +L+ ++  + ++++++l++ ++v  s+++ sl+ L+++G +    ++ d++
  gi|336252380|ref|YP_004595487.1|  88 TLRILYYLQSPATATQLAEQVDVHRSTVHRSLSPLENRGMI----YKSDGK 134
                                       6888888889999**************************99....444555 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.7e-05    0.0082       8      50 ..      12      52 ..       8      64 .. 0.86
   2 ?    6.9   0.0     0.013       6.1      14      31 ..     100     117 ..      91     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-05
                            HTH_29  8 laeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrs 50
                                      + +G+stvs +A+ l+ sr++v   ++r+e +G   l + +r++
  gi|336252380|ref|YP_004595487.1| 12 ALQGESTVSGLAEELDRSRSYVSELVDRMESKG---LVHtSREG 52
                                      57899****************************...78767663 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.013
                            HTH_29  14 tvsqiAkllglsrrtvyr 31 
                                       t  q+A++++++r+tv r
  gi|336252380|ref|YP_004595487.1| 100 TATQLAEQVDVHRSTVHR 117
                                       778*************99 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.3    0.0067       3.2      27      56 ..      19      48 ..       5      52 .. 0.90
   2 !   13.9   0.0   6.5e-05     0.032      29      57 ..     103     131 ..     100     136 .. 0.88
   3 ?   -1.3   0.0       3.5   1.7e+03      28      36 ..     296     304 ..     287     305 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0067
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR 27 ereLaaefgVsrttvReALrrLeaeglver 56
                                      ++ La+e++ sr+ v e  +r e++glv+ 
  gi|336252380|ref|YP_004595487.1| 19 VSGLAEELDRSRSYVSELVDRMESKGLVHT 48
                                      677*************************87 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.5e-05
                                       HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR  29 eLaaefgVsrttvReALrrLeaeglverr 57 
                                       +La++ +V r+tv ++L+ Le +g++   
  gi|336252380|ref|YP_004595487.1| 103 QLAEQVDVHRSTVHRSLSPLENRGMIYKS 131
                                       8***********************98655 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.5
                                       HHHHHHHTS CS
                              GntR  28 reLaaefgV 36 
                                       reLa+ +gV
  gi|336252380|ref|YP_004595487.1| 296 RELADDYGV 304
                                       89*****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 !   12.3   0.0   0.00028      0.14       7      45 ..      10      46 ..       7      54 .. 0.86
   2 ?    5.6   0.0     0.037        18       8      31 ..      93     117 ..      89     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00028
                            HTH_28  7 kllaaGh.svreaArelgisrrtvyrWikryeegGiagLv 45
                                      +++++G+ +v+ +A+el  sr+ v+ ++ r e+ G+   v
  gi|336252380|ref|YP_004595487.1| 10 LEALQGEsTVSGLAEELDRSRSYVSELVDRMESKGL---V 46
                                      57889999*************************775...4 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.037
                            HTH_28   8 llaaG.hsvreaArelgisrrtvyr 31 
                                       ++++   +++++A+++ ++r+tv r
  gi|336252380|ref|YP_004595487.1|  93 YYLQSpATATQLAEQVDVHRSTVHR 117
                                       4554314999************955 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00058      0.28      21      60 ..      16      55 ..       3      84 .. 0.77
   2 ?    6.2   0.0     0.027        13      25      53 ..     102     130 ..      89     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00058
                                      HHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEE CS
                   Penicillinase_R 21 kevveeleeekelaysTVktllrrLvkKgllsrekegraf 60
                                      ++ v+ l+ee + ++s V  l+ r++ Kgl+ + +eg++ 
  gi|336252380|ref|YP_004595487.1| 16 ESTVSGLAEELDRSRSYVSELVDRMESKGLVHTSREGKQK 55
                                      445667777777789*********************9975 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.027
                                       HT--GGG---HHHHHHHHHHHHHTTS-EE CS
                   Penicillinase_R  25 eeleeekelaysTVktllrrLvkKgllsr 53 
                                       ++l+e+ ++++sTV+  l+ L+++g++ +
  gi|336252380|ref|YP_004595487.1| 102 TQLAEQVDVHRSTVHRSLSPLENRGMIYK 130
                                       6789999999***************9865 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0     0.004       1.9      18      46 ..      17      45 ..       6      48 .. 0.80
   2 !    7.8   0.1    0.0061       2.9      18      36 ..      99     117 ..      89     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.004
                            HTH_23 18 lsvreIAreLgvsrrTvyrwlkryreeGl 46
                                       +v+  A+eL++sr+ v+  + r + +Gl
  gi|336252380|ref|YP_004595487.1| 17 STVSGLAEELDRSRSYVSELVDRMESKGL 45
                                      577888*****************766887 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0061
                            HTH_23  18 lsvreIAreLgvsrrTvyr 36 
                                       ++ ++ A++ +v+r+Tv r
  gi|336252380|ref|YP_004595487.1|  99 ATATQLAEQVDVHRSTVHR 117
                                       578899***********98 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0047       2.3      27      97 ..       8      75 ..       5      77 .. 0.85
   2 !    7.7   0.0    0.0053       2.6      35      85 ..      98     144 ..      87     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0047
                           DUF4423 27 rellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevkseavrsy 97
                                      r+l +l+ + ++++ la+ l    s + v++ ++++++ gl++ +++gk +q ++s +   e    +v++y
  gi|336252380|ref|YP_004595487.1|  8 RALEALQGE-STVSGLAEELD--RSRSYVSELVDRMESKGLVHTSREGKQKQINRSDARAIELFDSFVQQY 75
                                      554455555.99*********..*****************************9998887777777777776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0053
                           DUF4423  35 fkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqteksltt 85 
                                         a+  +la+++   +  + v+++l+ L++ g++ k+  gky  ++++ + 
  gi|336252380|ref|YP_004595487.1|  98 P-ATATQLAEQVD--VHRSTVHRSLSPLENRGMIYKSD-GKYTLNDEFEEL 144
                                       4.78899******..*********************99.7**999987664 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.7   1.3e+03      23      52 ..      20      49 ..       8      56 .. 0.63
   2 !   14.3   0.0   6.1e-05      0.03      10      73 ..      90     152 ..      87     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.7
                            HTH_45 23 TkimykanLsykllnkYLdmLvekglikks 52
                                      + +  + + s + +++ +d + +kgl+++s
  gi|336252380|ref|YP_004595487.1| 20 SGLAEELDRSRSYVSELVDRMESKGLVHTS 49
                                      555555555556667777888889999554 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.1e-05
                            HTH_45  10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkele 73 
                                        IL ++ ++ a+ T++  +++   +++++ L+ L ++g+i ks++kY+l ++ +el    +e+ 
  gi|336252380|ref|YP_004595487.1|  90 RILYYL-QSPATATQLAEQVDVHRSTVHRSLSPLENRGMIYKSDGKYTLNDEFEELSTVAREFA 152
                                       689999.99****************************************998888777776665 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 !   11.3   0.2   0.00051      0.25       3      39 ..       6      42 ..       5      43 .. 0.95
   2 ?    3.2   0.0      0.18        89      19      40 ..     104     125 ..      89     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00051
                                      HHHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_1  3 qlrlfvavaeegsftrAAeeLglsqpavsrqikrLEe 39
                                       lr+++a+  e ++++ AeeL  s + vs  + r+E+
  gi|336252380|ref|YP_004595487.1|  6 ELRALEALQGESTVSGLAEELDRSRSYVSELVDRMES 42
                                      599********************************96 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.18
                                       HHHHHTS-HHHHHHHHHHHHHH CS
                             HTH_1  19 AAeeLglsqpavsrqikrLEee 40 
                                        Ae++ +  ++v r+++ LE++
  gi|336252380|ref|YP_004595487.1| 104 LAEQVDVHRSTVHRSLSPLENR 125
                                       59******************85 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 ?    2.0   0.3      0.39   1.9e+02       9      42 .]      10      41 ..       7      41 .. 0.82
   2 !   12.9   0.1   0.00015     0.073       7      38 ..      90     119 ..      89     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.39
                     HTH_AsnC-type  9 LeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LeaLq  +  +++ LAe++  S+s v + v+r+e
  gi|336252380|ref|YP_004595487.1| 10 LEALQ--GESTVSGLAEELDRSRSYVSELVDRME 41
                                      45555..7888999**********9999999997 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00015
                     HTH_AsnC-type   7 kILeaLqedaRisyaeLAervGlSestvlrRv 38 
                                       +IL  Lq  + ++ ++LAe+v + +stv+r +
  gi|336252380|ref|YP_004595487.1|  90 RILYYLQ--SPATATQLAEQVDVHRSTVHRSL 119
                                       6777777..7899****************965 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 !    8.0   0.1    0.0062         3      28      66 ..      22      63 ..       8      66 .. 0.82
   2 ?    5.5   0.0     0.039        19      11      58 ..      89     134 ..      85     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0062
                           DUF2250 28 iakeleipleevrellkkLeelGLlerve...gktikrteak 66
                                      +a+el+ ++++v+el++++e+ GL+       +k i+r++a+
  gi|336252380|ref|YP_004595487.1| 22 LAEELDRSRSYVSELVDRMESKGLVHTSRegkQKQINRSDAR 63
                                      57889999*****************86642226677777766 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.039
                           DUF2250  11 lkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegk 58 
                                       l++l++l+   +  a ++a++++++++ v++ l  Le+ G++ + +gk
  gi|336252380|ref|YP_004595487.1|  89 LRILYYLQS--PATATQLAEQVDVHRSTVHRSLSPLENRGMIYKSDGK 134
                                       677777765..5568999************************998876 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1      0.03        15      29      61 ..      22      54 ..      17      61 .. 0.88
   2 ?    6.8   0.0     0.016       7.7      28      68 ..     103     139 ..      99     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.03
                              PaaX 29 llaelGiseslvRaalsRlakaGwlvrekegrr 61
                                      l +el+ s s v   + R++ +G++  ++eg++
  gi|336252380|ref|YP_004595487.1| 22 LAEELDRSRSYVSELVDRMESKGLVHTSREGKQ 54
                                      678899999999999****************74 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                              PaaX  28 rllaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsd 68 
                                       +l +++++  s+v  +ls l+++G + +++      Y L d
  gi|336252380|ref|YP_004595487.1| 103 QLAEQVDVHRSTVHRSLSPLENRGMIYKSDGK----YTLND 139
                                       6889**********************999877....77776 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.19        90      25      50 ..      18      43 ..      16      45 .. 0.91
   2 ?    7.5   0.0    0.0073       3.5      24      48 ..      99     123 ..      95     126 .. 0.88
   3 ?   -1.0   0.0       3.3   1.6e+03      21      36 ..     290     305 ..     289     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.19
                            HTH_10 25 tlkeLAkelGIskstlsehLrkaesk 50
                                      t++ LA+el+ s+s +se + + esk
  gi|336252380|ref|YP_004595487.1| 18 TVSGLAEELDRSRSYVSELVDRMESK 43
                                      6778******************9998 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0073
                            HTH_10  24 vtlkeLAkelGIskstlsehLrkae 48 
                                       +t+ +LA++ ++ +st++  L+  e
  gi|336252380|ref|YP_004595487.1|  99 ATATQLAEQVDVHRSTVHRSLSPLE 123
                                       6899**************9998655 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3.3
                            HTH_10  21 PRrvtlkeLAkelGIs 36 
                                       PR  + +eLA++ G++
  gi|336252380|ref|YP_004595487.1| 290 PRWEEFRELADDYGVA 305
                                       6777889******996 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 ?   12.5   0.0   0.00019     0.092      16      56 ..     100     140 ..      90     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                          HTH_DeoR  16 sveelvellgvSeaTiRRDLneLeeqglltRthGGavsiss 56 
                                       + ++l+e+ +v   T+ R L+ Le+ g++ +  G ++++++
  gi|336252380|ref|YP_004595487.1| 100 TATQLAEQVDVHRSTVHRSLSPLENRGMIYKSDGKYTLNDE 140
                                       4579***************************9999999875 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0004      0.19       4      50 ..       6      52 ..       5      60 .. 0.91
   2 ?   -1.2   0.0       4.7   2.3e+03      14      47 ..      98     131 ..      91     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0004
                              FeoC  4 elkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50
                                      el+++ + +g+  ++ L+ +++ s + +  +++ ++ kG v    ++
  gi|336252380|ref|YP_004595487.1|  6 ELRALEALQGESTVSGLAEELDRSRSYVSELVDRMESKGLVHTSREG 52
                                      78999999*********************************988775 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.7
                              FeoC  14 rvslkeLsrhfkaspealeamLeqwvrkGrvekv 47 
                                        +   +L+ + ++  +++   L  ++ +G + k 
  gi|336252380|ref|YP_004595487.1|  98 PATATQLAEQVDVHRSTVHRSLSPLENRGMIYKS 131
                                       6777899999999999999999999988887765 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.011       5.3       3      42 ..      18      61 ..      18      61 .. 0.76
   2 ?    2.8   0.0      0.28   1.4e+02       3      20 ..     100     117 ..     100     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                            HTH_17  3 tveEaAelLgvsrstvyrlir...rgelpaa.kiGrrwriprsd 42
                                      tv+ +Ae L+ srs v +l++   ++ l ++ + G++  i rsd
  gi|336252380|ref|YP_004595487.1| 18 TVSGLAEELDRSRSYVSELVDrmeSKGLVHTsREGKQKQINRSD 61
                                      566689**************855566663446788888888876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.28
                            HTH_17   3 tveEaAelLgvsrstvyr 20 
                                       t  ++Ae  +v+rstv+r
  gi|336252380|ref|YP_004595487.1| 100 TATQLAEQVDVHRSTVHR 117
                                       67899***********97 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       0.6   2.9e+02      23      38 ..      19      34 ..      10      39 .. 0.79
   2 ?    8.4   0.0    0.0038       1.8      12      40 ..      90     118 ..      89     120 .. 0.85
   3 ?   -2.5   0.0       9.5   4.6e+03      35      40 ..     145     150 ..     145     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.6
                            HTH_38 23 lreIArrLgrspsTIs 38
                                      ++  A +L+rs+s +s
  gi|336252380|ref|YP_004595487.1| 19 VSGLAEELDRSRSYVS 34
                                      55689*******9665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0038
                            HTH_38  12 eIerllaeGlslreIArrLgrspsTIsRE 40 
                                       +I + l+   +  + A ++++++sT++R 
  gi|336252380|ref|YP_004595487.1|  90 RILYYLQSPATATQLAEQVDVHRSTVHRS 118
                                       5777777778999**************95 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 9.5
                            HTH_38  35 sTIsRE 40 
                                       sT++RE
  gi|336252380|ref|YP_004595487.1| 145 STVARE 150
                                       8****9 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.59   2.8e+02      53      96 ..      16      59 ..      12      71 .. 0.82
   2 ?    9.3   0.0     0.002      0.99      51     105 ..      96     150 ..      90     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.59
                   Phage_rep_org_N 53 pytaemlalifnreletvrlaLkvlkdlelieisedkvikiknw 96
                                      ++t   la +++r  + v   ++ +++++l+  s ++  k  n 
  gi|336252380|ref|YP_004595487.1| 16 ESTVSGLAEELDRSRSYVSELVDRMESKGLVHTSREGKQKQINR 59
                                      678888999**********************9988877666555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.002
                   Phage_rep_org_N  51 nipytaemlalifnreletvrlaLkvlkdlelieisedkvikikn.wekhqniesk 105
                                       + p ta +la  ++ + +tv+  L+ l++ ++i +s d+ +++++ +e++ ++  +
  gi|336252380|ref|YP_004595487.1|  96 QSPATATQLAEQVDVHRSTVHRSLSPLENRGMIYKS-DGKYTLNDeFEELSTVARE 150
                                       67899*****************************99.7778776547777666554 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 ?   -1.1   0.0       4.4   2.1e+03      20      36 ..      14      31 ..       7      33 .. 0.86
   2 ?   10.8   0.0   0.00082       0.4      18      42 ..      95     119 ..      88     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.4
                                      TT.--STTTSSSS---SS CS
                             HTH_7 20 eG.isiskIAkevnisRs 36
                                      +G +++s +A+e++ sRs
  gi|336252380|ref|YP_004595487.1| 14 QGeSTVSGLAEELDRSRS 31
                                      57699999****999997 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00082
                                       TTTT--STTTSSSS---SSSS--SS CS
                             HTH_7  18 leeGisiskIAkevnisRsTvYRyl 42 
                                       l+++ +++++A++v++ RsTv R l
  gi|336252380|ref|YP_004595487.1|  95 LQSPATATQLAEQVDVHRSTVHRSL 119
                                       5677899**************9965 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 ?    4.1   0.0     0.088        43      11      30 ..      19      38 ..      10      50 .. 0.83
   2 ?    5.4   0.0     0.035        17      11      27 ..     101     117 ..      96     122 .. 0.89
   3 ?   -1.8   0.0       5.8   2.8e+03      36      56 ..     240     258 ..     230     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.088
                    YdaS_antitoxin 11 qkaLAealgvsqqaVsqWlk 30
                                       + LAe+l+ s++ Vs +++
  gi|336252380|ref|YP_004595487.1| 19 VSGLAEELDRSRSYVSELVD 38
                                      577**************996 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.035
                    YdaS_antitoxin  11 qkaLAealgvsqqaVsq 27 
                                       +++LAe+++v++++V++
  gi|336252380|ref|YP_004595487.1| 101 ATQLAEQVDVHRSTVHR 117
                                       789************86 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 5.8
                    YdaS_antitoxin  36 paervpeIekatnGeVtreeL 56 
                                       +  +++ +   t   + r eL
  gi|336252380|ref|YP_004595487.1| 240 SQSYCLLLISETA--IERNEL 258
                                       5679999999999..999998 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00073      0.35      20      57 ..      97     134 ..      89     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00073
                                       CECCHHHHHHHHCC-HHHHHHHHHHHHHTTSEEEESSS CS
                           z-alpha  20 kaatalalergLstpkreiNrvLydlerkgkvyredgt 57 
                                       ++ata +l+ ++   +  + r L  le +g++y++dg+
  gi|336252380|ref|YP_004595487.1|  97 SPATATQLAEQVDVHRSTVHRSLSPLENRGMIYKSDGK 134
                                       79************9*********************96 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 ?    3.2   0.0      0.13        64       3      35 ..      15      47 ..      13      54 .. 0.88
   2 ?    6.3   0.0     0.014       6.9       6      34 ..     100     128 ..      97     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.13
                          HTH_CodY  3 GrLtaskiaDriGitrsvivnaLrkLesaGiie 35
                                      G  t s +a+++   rs +   + ++es G++ 
  gi|336252380|ref|YP_004595487.1| 15 GESTVSGLAEELDRSRSYVSELVDRMESKGLVH 47
                                      7779999***********************986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                          HTH_CodY   6 taskiaDriGitrsvivnaLrkLesaGii 34 
                                       ta ++a+++ + rs +  +L  Le  G+i
  gi|336252380|ref|YP_004595487.1| 100 TATQLAEQVDVHRSTVHRSLSPLENRGMI 128
                                       899************************98 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 ?   -1.6   0.0       8.6   4.2e+03      55      89 ..      22      58 ..      18      60 .. 0.73
   2 ?   10.8   0.0    0.0011      0.55      51      93 ..     100     142 ..      95     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 8.6
                       Phage_rep_O 55 lveltgisrtkvskalkeLirekviikeg..rkvgvn 89
                                      l+e  + sr+ vs+ ++ + +++ + + +  ++  +n
  gi|336252380|ref|YP_004595487.1| 22 LAEELDRSRSYVSELVDRMESKGLVHTSRegKQKQIN 58
                                      5566677899999999999999988765555776666 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0011
                       Phage_rep_O  51 snsqlveltgisrtkvskalkeLirekviikegrkvgvnknis 93 
                                       + +ql+e ++++r+ v++ l  L ++++i k   k+  n + +
  gi|336252380|ref|YP_004595487.1| 100 TATQLAEQVDVHRSTVHRSLSPLENRGMIYKSDGKYTLNDEFE 142
                                       789*****************************99999998765 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 ?    0.3   0.0       1.3   6.2e+02      38      58 ..      28      48 ..      18      53 .. 0.79
   2 ?    8.5   0.0    0.0035       1.7      24      62 ..      97     134 ..      92     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.3
                                      -.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind 38 kSpsaveehLkaLerKGyier 58
                                      +S s v e   ++e KG++  
  gi|336252380|ref|YP_004595487.1| 28 RSRSYVSELVDRMESKGLVHT 48
                                      5778888999999****9975 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0035
                                       S---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG- CS
                     LexA_DNA_bind  24 ypPsireiaralglkSpsaveehLkaLerKGyierdpgk 62 
                                        p +  ++a+++ ++  s+v+  L  Le++G+i   +gk
  gi|336252380|ref|YP_004595487.1|  97 SPATATQLAEQVDVH-RSTVHRSLSPLENRGMIYKSDGK 134
                                       57788999*****99.99***************999887 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0016       0.8      14      40 ..      93     119 ..      86     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                           SpoIIID  14 yiveskatvRkaakvfgvskstvhkDv 40 
                                       y ++s at  + a++ +v +stvh+ +
  gi|336252380|ref|YP_004595487.1|  93 YYLQSPATATQLAEQVDVHRSTVHRSL 119
                                       567899******************976 PP

>> DUF903  Bacterial protein of unknown function (DUF903)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0042         2      32      47 ..      50      65 ..      42      66 .. 0.86
   2 ?    0.6   0.0       1.1   5.4e+02      24      36 ..     272     284 ..     259     286 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0042
                                      TTS-EEEEEGGGEEEE CS
                            DUF903 32 eeGkevqInkddVkqi 47
                                       eGk++qIn++d + i
  gi|336252380|ref|YP_004595487.1| 50 REGKQKQINRSDARAI 65
                                      69*********98877 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                                       TSCEEEEBTTS-E CS
                            DUF903  24 tGmyeYeDeeGke 36 
                                       ++++eY D eG+ 
  gi|336252380|ref|YP_004595487.1| 272 SNLLEYLDTEGES 284
                                       899********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2462.01
//
Query:       gi|336252381|ref|YP_004595488.1|  [L=270]
Description: hypothetical protein Halxa_0973 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0025   17.5   0.8     0.0079   15.8   0.1    2.0  2  NTP_transf_5   Uncharacterised nucleotidyltransferase
     0.0051   17.0   0.1      0.078   13.2   0.0    2.5  3  Glyoxalase     Glyoxalase/Bleomycin resistance protein/Dioxyg
  ------ inclusion threshold ------
       0.13   12.5   0.3       0.89    9.8   0.1    2.2  2  Rio2_N         Rio2, N-terminal
       0.43   10.4   6.1        0.4   10.5   2.3    2.6  3  Phi-29_GP16_7  Bacteriophage phi-29 early protein GP16.7


Domain annotation for each model (and alignments):
>> NTP_transf_5  Uncharacterised nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.8e-06    0.0079      95     144 ..      45     100 ..      42     171 .. 0.74
   2 ?    0.1   0.1      0.11   5.1e+02     112     122 ..     188     198 ..     108     263 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-06
                      NTP_transf_5  95 gDiDllvk.redldraeelLeelGyelesd.gsek.....hevyyrekkgveielhw 144
                                       +DiDl+v   +dl+  +++L+++Gy   ++ g+e+     +++++   +g++i++  
  gi|336252381|ref|YP_004595488.1|  45 KDIDLIVTdGDDLRVLQAVLLDNGYNVVKEpGEEYddlgaQRILEN-DDGCRIDIFN 100
                                       8******96777*************877764444444443444444.8888888764 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.11
                      NTP_transf_5 112 lLeelGyeles 122
                                        L+el  +++ 
  gi|336252381|ref|YP_004595488.1| 188 ALLELEEQHNI 198
                                       33222222222 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   1.7e-05     0.078      73     126 ..      43      96 ..      15      98 .. 0.83
   2 ?   -2.0   0.0      0.87   3.9e+03      21      58 ..      97     134 ..      96     135 .. 0.81
   3 ?    1.1   0.1     0.097   4.4e+02      82      99 ..     238     255 ..     140     262 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                                       TSEEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEE CS
                        Glyoxalase  73 tvhhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGill 126
                                       t   + +i++d +d+   +  l ++g++vv+epg +y + +  ++ +  dG ++
  gi|336252381|ref|YP_004595488.1|  43 TTKDIDLIVTDGDDLRVLQAVLLDNGYNVVKEPGEEYDDLGAQRILENDDGCRI 96 
                                       6778999**********************************9998888899877 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.87
                                       HHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEE CS
                        Glyoxalase  21 kvLGfklvkktdnteeteglriaffhaggghielvlne 58 
                                       ++++ ++++k +  e++     a+++ag+ +++lv+ e
  gi|336252381|ref|YP_004595488.1|  97 DIFNQQVIDKLVLSEGMRRRSEAYLDAGRLSVALVSSE 134
                                       57888888888877777889999999999999998765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.097
                                       EEHCHHHHHHHHHHHTTG CS
                        Glyoxalase  82 ldvedvgkaldrlkeagv 99 
                                       l+ edv++a+++l e++v
  gi|336252381|ref|YP_004595488.1| 238 LSPEDVDEAIEHLVEKDV 255
                                       567899999999988875 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.28   1.2e+03       7      15 ..      55      63 ..      51      72 .. 0.87
   2 ?    9.8   0.1    0.0002      0.89      10      55 ..     212     257 ..     204     263 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.28
                            Rio2_N  7 edfrvLtav 15
                                      +d+rvL+av
  gi|336252381|ref|YP_004595488.1| 55 DDLRVLQAV 63
                                      79*****98 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0002
                            Rio2_N  10 rvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklis 55 
                                       rv + +E+     e ++++++e    l+ e+v++++++l++++ ++
  gi|336252381|ref|YP_004595488.1| 212 RVYREIEVLQAFNESISRSELEAAVDLSPEDVDEAIEHLVEKDVVE 257
                                       89999*************************************9987 PP

>> Phi-29_GP16_7  Bacteriophage phi-29 early protein GP16.7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.12   5.3e+02      77     122 ..     151     196 ..     130     200 .. 0.68
   2 ?    1.8   0.6     0.043   1.9e+02      70     104 ..     184     218 ..     146     220 .. 0.64
   3 ?   10.5   2.3   8.9e-05       0.4      32      91 ..     202     263 ..     193     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.12
                                       HHHHHTT----HHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHHHS CS
                     Phi-29_GP16_7  77 dlyeqsniripsdiiedlvnqrlqseqevlnyietqrtywklenqk 122
                                       d++   +  +  d+ied ++q+++   + l    ++ +   le+q+
  gi|336252381|ref|YP_004595488.1| 151 DMFSLVQTELDFDVIEDELEQQIDLLGQELFVTHANEALLELEEQH 196
                                       5555555666778888888887765544455555555555555554 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.043
                                       HHHHHHHHHHHHTT----HHHHHHHHTT--SSHHH CS
                     Phi-29_GP16_7  70 acevavldlyeqsniripsdiiedlvnqrlqseqe 104
                                        ++ a+l+l eq ni  p       + +r+  e e
  gi|336252381|ref|YP_004595488.1| 184 HANEALLELEEQHNISTPLAERVSEITERVYREIE 218
                                       44557788888888877754444445555555555 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 8.9e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSSXSSS-HHHH..HHHHHHHHTT----HHHH CS
                     Phi-29_GP16_7  32 ledyledlnkrvvqrtqilselnevisnrsidktvnlsacev..avldlyeqsniripsdii 91 
                                       l + + ++  rv +  ++l  +ne is   ++ +v+ls  +v  a+  l e+  + i  d+i
  gi|336252381|ref|YP_004595488.1| 202 LAERVSEITERVYREIEVLQAFNESISRSELEAAVDLSPEDVdeAIEHLVEKDVVEIDDDVI 263
                                       5566788999****************************8776558999**********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2029.89
//
Query:       gi|336252382|ref|YP_004595489.1|  [L=282]
Description: hypothetical protein Halxa_0974 [Halopiger xanaduensis SH-6]
Scores for 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   14.3   0.0      0.045   13.6   0.0    1.3  1  YkuI_C    EAL-domain associated signalling protein domain


Domain annotation for each model (and alignments):
>> YkuI_C  EAL-domain associated signalling protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.5e-06     0.045      29      72 ..     171     215 ..     160     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-06
                            YkuI_C  29 lyelseklkkrlkellkklkkaedydelllklakeldeva.frvy 72 
                                        y+ se++ + +++ l++  k+++ dell+++ +e+d+v+ fr y
  gi|336252382|ref|YP_004595489.1| 171 RYDDSERIATSITANLERASKTTSLDELLTQVEEEVDDVTvFRRY 215
                                       5899**********************************8648877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1901.89
//
Query:       gi|336252383|ref|YP_004595490.1|  [L=227]
Description: hypothetical protein Halxa_0975 [Halopiger xanaduensis SH-6]
Scores for complete 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   0.4     0.0031   17.3   0.0    2.3  2  HNH_repeat  Homing endonuclease repeat
  ------ inclusion threshold ------
      0.024   14.6   0.4       0.21   11.5   0.2    2.4  2  DUF3018     Protein  of unknown function (DUF3018)
       0.17   12.0   1.1         19    5.4   0.1    2.3  2  Sigma70_r3  Sigma-70 region 3


Domain annotation for each model (and alignments):
>> HNH_repeat  Homing endonuclease repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.3e-07    0.0031       1      23 []       7      29 ..       7      29 .. 0.95
   2 !    6.0   0.1    0.0018        11       2      20 ..      68      86 ..      67      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.3e-07
                        HNH_repeat  1 EELIElvQkqAaELGRtPkkkEF 23
                                      E ++++++ +A+ELG tP+ +E+
  gi|336252383|ref|YP_004595490.1|  7 EDMLDALHRLAEELGETPTTTEM 29
                                      78899*****************9 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0018
                        HNH_repeat  2 ELIElvQkqAaELGRtPkk 20
                                       L++ ++++A EL  tP+k
  gi|336252383|ref|YP_004595490.1| 68 DLLNEIRQLARELNQTPTK 86
                                      799**********888887 PP

>> DUF3018  Protein  of unknown function (DUF3018)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   3.5e-05      0.21       9      52 ..      49      90 ..      47      94 .. 0.85
   2 ?   -0.3   0.0      0.17     1e+03       9      20 ..     109     120 ..     102     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.5e-05
                           DUF3018  9 ekLraaGLRPvqiW.VPDtrrpefaeeirrqsalvaqdpeeaell 52
                                      e+Lr+aG+ P q+W VP   + +  +eir+ ++ ++q p++++++
  gi|336252383|ref|YP_004595490.1| 49 EALREAGFEPNQVWkVP---TDDLLNEIRQLARELNQTPTKEQMD 90
                                      78************444...6788999999999999998888776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.17
                           DUF3018   9 ekLraaGLRPvq 20 
                                       e+ r+aGL P q
  gi|336252383|ref|YP_004595490.1| 109 EAVRQAGLEPNQ 120
                                       789*****9977 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.004        24       9      26 ..      12      29 ..       6      35 .. 0.88
   2 ?    5.4   0.1    0.0032        19       7      24 ..      70      87 ..      66      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.004
                                      HHHHHHHHHSSXXXHHHH CS
                        Sigma70_r3  9 aqreLeqelgrePtpeEi 26
                                      a ++L +elg +Pt++E 
  gi|336252383|ref|YP_004595490.1| 12 ALHRLAEELGETPTTTEM 29
                                      6689************96 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0032
                                      HHHHHHHHHHHSSXXXHH CS
                        Sigma70_r3  7 kraqreLeqelgrePtpe 24
                                       + +r+L +el+ +Pt e
  gi|336252383|ref|YP_004595490.1| 70 LNEIRQLARELNQTPTKE 87
                                      566899999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1710.67
//
Query:       gi|336252384|ref|YP_004595491.1|  [L=347]
Description: hypothetical protein Halxa_0976 [Halopiger xanaduensis SH-6]
Scores for 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-05   23.0   0.0    7.5e-05   22.2   0.0    1.3  1  NucS      Endonuclease NucS


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.2e-09   7.5e-05     106     158 ..      24      79 ..       9      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.2e-09
                              NucS 106 seaelaeliiehpd.LieeGfkpvareyava.iG.ivdiLgkdeegklvivelkrr 158
                                        e +l e ii+ p+ +++e f+++ re  v  iG  +d+L+ d++ ++v++elkr 
  gi|336252384|ref|YP_004595491.1|  24 REDDLREWIINSPEsILGEDFRLIGREVSVKqIGdGIDLLAIDRDANVVAIELKRG 79 
                                       5899******9996478**********9986356359*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2568.53
//
Query:       gi|336252385|ref|YP_004595492.1|  [L=336]
Description: hypothetical protein Halxa_0977 [Halopiger xanaduensis SH-6]
Scores for 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-19   70.1   0.3    3.4e-19   69.5   0.3    1.3  1  DUF4868   Domain of unknown function (DUF4868)
  ------ inclusion threshold ------
      0.076   13.0   0.7       0.62   10.1   0.1    2.4  2  Pox_A31   Poxvirus A31 protein


Domain annotation for each model (and alignments):
>> DUF4868  Domain of unknown function (DUF4868)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.3   3.8e-23   3.4e-19       6     188 .]     140     323 ..     135     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 3.8e-23
                           DUF4868   6 gllikiergnkklflykkiypitrlkkskklillifqdnefkkvdkdllrIdknfDlliideeilivnkkslerifg 82 
                                       ++ i+  ++++  +++ ++   +++ +++  ++++   ++ +kvd++l+ I  ++D + +d+ ++i++ +++e+if+
  gi|336252385|ref|YP_004595492.1| 140 AIRIRDADNDQMAIAFLNYSRRQIMGRTSR-ARMLVGSEKHRKVDDSLISIPDRVDSIYYDGMMYIFDQSRFEKIFD 215
                                       555666677888888888888888888887.7999999999************************************ PP

                           DUF4868  83 fkevikeeaqkviseieelgl.ienveklkeyveindlkklrklakikkkgvllykqedl..ieklkkvpklklnik 156
                                       + + ++  a+ vi+ iee+++ + ++e +ke v   + + lr + k+ + gv  y++ dl     + +++  +++++
  gi|336252385|ref|YP_004595492.1| 216 YLAEYERCADDVIDRIEETDIpFHDFEMFKEAVY-GNNRVLRLMYKVHERGV--YEDMDLddAAYIRDNFDTDVKFE 289
                                       ********************989********666.999**************..55555511344555565555555 PP

                           DUF4868 157 fea..ngkIvltekkqvedliklLnDdylkSelT 188
                                        +   +  I++++k++v+  ++ +nDd l S+lT
  gi|336252385|ref|YP_004595492.1| 290 ENGdgEMSIKMDDKRDVWAVLRFFNDDHLDSPLT 323
                                       44433447************************98 PP

>> Pox_A31  Poxvirus A31 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.09   8.1e+02      30      45 ..      95     110 ..      72     114 .. 0.80
   2 ?   10.1   0.1   6.9e-05      0.62      15      61 ..     182     228 ..     170     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.09
                           Pox_A31  30 kyknikfifykPkekt 45 
                                         ++ +f+ y P e++
  gi|336252385|ref|YP_004595492.1|  95 RDRDQTFVQYEPTENI 110
                                       56899*******9875 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 6.9e-05
                           Pox_A31  15 fanlnlalpkkkkkvkyknikfifykPkektvekylaaaeiyhsdli 61 
                                         +  +++p +   + y ++++if + + +++  yla+ e + +d+i
  gi|336252385|ref|YP_004595492.1| 182 VDDSLISIPDRVDSIYYDGMMYIFDQSRFEKIFDYLAEYERCADDVI 228
                                       5566789***********************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2618.20
//
Query:       gi|336252386|ref|YP_004595493.1|  [L=189]
Description: hypothetical protein Halxa_0978 [Halopiger xanaduensis SH-6]
Scores for 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  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1352.19
//
Query:       gi|336252387|ref|YP_004595494.1|  [L=1441]
Description: hypothetical protein Halxa_0979 [Halopiger xanaduensis SH-6]
Scores for 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   39.3   0.0      3e-05   23.4   0.0    3.1  3  N6_Mtase         N-6 DNA Methylase
      0.003   17.4   0.1      0.009   15.8   0.1    1.8  1  Methyltransf_31  Methyltransferase domain
     0.0072   16.0   0.0       0.22   11.2   0.0    2.4  2  UPF0020          Putative RNA methylase family UPF0020


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 ?   -1.0   0.0      0.14   8.3e+02      25      38 ..     227     240 ..     190     244 .. 0.53
   2 !   23.4   0.0   5.1e-09     3e-05      48     105 ..     309     378 ..     303     401 .. 0.87
   3 !   11.8   0.0   1.8e-05      0.11      98     202 ..     477     586 ..     459     666 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.14
                          N6_Mtase  25 gGeffTPrevskli 38 
                                       + +f+TP+ v++++
  gi|336252387|ref|YP_004595494.1| 227 ANQFYTPHWVVRML 240
                                       34899999998876 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 5.1e-09
                          N6_Mtase  48 esvyDpacGsggllvqaekvlkee............dgktkelsiyGqeknettyrLakmNlllhgieyk 105
                                         v+DpacGsg +l+ a +vl++               ++ + ++yG++++  + +La  Nl+l+g   +
  gi|336252387|ref|YP_004595494.1| 309 IRVIDPACGSGHFLLYAFDVLERIyraetdldhaeiPREILRNNLYGVDLDMRACQLAAFNLYLKGRTRA 378
                                       459*****************987799999999988878889999********************997766 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 1.8e-05
                          N6_Mtase  98 llhgieykkvkirlgdtlekpkfe........kdkkfdvvvaNppfnqkewkektlekderfreavapksnadlafl 166
                                       +lh    +  + r +d++  +  +          +  dv + Npp+++k+ +  ++ +d   +e    +s+  + f 
  gi|336252387|ref|YP_004595494.1| 477 ILHSLRDAVDQHREEDSFLAQDLRsfvrlldvLAQDYDVALMNPPYGSKN-RMPDVVQDY-VEEHYRYSSEFYINFF 551
                                       7888888888888889877666656999999888999************3.345555554.56667777777778** PP

                          N6_Mtase 167 lhiieslkpkGraavvlangvLfrggkegkIrkalv 202
                                         +  + k++Gr++++++   +++ ++ ++ r++++
  gi|336252387|ref|YP_004595494.1| 552 EVCDRVSKEDGRIGMLVPRSFMYK-NRYQDFRSDFI 586
                                       **********************97.56677777766 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.5e-06     0.009       4      81 ..     308     397 ..     306     435 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-06
                   Methyltransf_31   4 glrvlDlGCGtGeltfelae.........elgpkae.........vvGiDiseeaielArenaqklgldnveFeqgd 62 
                                       ++rv+D++CG+G++++ +++         +  ++ae         ++G+D + +a +lA  n+  +g +++e e ++
  gi|336252387|ref|YP_004595494.1| 308 DIRVIDPACGSGHFLLYAFDvleriyraeTDLDHAEipreilrnnLYGVDLDMRACQLAAFNLYLKGRTRAEAEGAS 384
                                       789*****************9977776552333344777788888***************************99999 PP

                   Methyltransf_31  63 ieeleklledekfDlilsn 81 
                                        +++++        +++++
  gi|336252387|ref|YP_004595494.1| 385 GFDMPEV------GIVCAD 397
                                       9999963......344444 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   3.7e-05      0.22      30      96 ..     309     370 ..     305     387 .. 0.80
   2 ?    1.9   0.0     0.026   1.6e+02     118     135 ..     509     526 ..     492     584 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.7e-05
                                       S-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHH.HH--EEEEES-HHHHHHHHHHH CS
                           UPF0020  30 epllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeear.aelklygsDldrrvvqgareNa 96 
                                        + +DP CGsG +l+ a  + ++i+       +   +++ae   +  + +lyg+Dld r+ q a  N+
  gi|336252387|ref|YP_004595494.1| 309 IRVIDPACGSGHFLLYAFDVLERIYR------AETDLDHAEIPREiLRNNLYGVDLDMRACQLAAFNL 370
                                       5789*************999999993......333455555555545666************999887 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.026
                                       TTS---EEEE-------- CS
                           UPF0020 118 kegevdvivtnpPYGerl 135
                                         +++dv + npPYG + 
  gi|336252387|ref|YP_004595494.1| 509 LAQDYDVALMNPPYGSKN 526
                                       45579999*******753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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):               3  [number of targets reported over threshold]
# CPU time: 0.98u 0.32s 00:00:01.30 Elapsed: 00:00:00.49
# Mc/sec: 8835.21
//
Query:       gi|336252388|ref|YP_004595495.1|  [L=449]
Description: hypothetical protein Halxa_0980 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.34   11.7   1.8       0.54   11.1   0.7    1.8  2  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.53   9.4e+03      21      31 ..      93     103 ..      91     109 .. 0.86
   2 ?   11.1   0.7     3e-05      0.54       3      59 ..     361     425 ..     360     437 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.53
                                       XXXXXXXXXXX CS
                     PSK_trans_fac  21 tgeskteAvrr 31 
                                       t+es  eAvrr
  gi|336252388|ref|YP_004595495.1|  93 TKESSSEAVRR 103
                                       89999999997 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3e-05
                                       XXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXX......XX--HHHHHHHHHHHH CS
                     PSK_trans_fac   3 LnIkdpeverlareLarltge..skteAvrrAleerlerlrre......raepllerllallrra 59 
                                       Ln+  +e+e+ ++++ + tge  s +e +++A+e+  ++l+++      +++++ + ++a+l r+
  gi|336252388|ref|YP_004595495.1| 361 LNVSAEEAEDVVQSVLSDTGEttSRIEGIEEAVEKLESELDSRshdyelDESKRDDLIDAILSRE 425
                                       8999*****************7778999******9999998877778877777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3360.91
//
Query:       gi|336252389|ref|YP_004595496.1|  [L=405]
Description: adenosinetriphosphatase [Halopiger xanaduensis SH-6]
Scores for 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-42  143.1   0.0    1.4e-41  142.0   0.0    1.6  1  AAA              ATPase family associated with various cellul
    9.4e-07   28.5   0.1    2.6e-06   27.1   0.1    1.8  1  AAA_lid_3        AAA+ lid domain
      1e-05   25.4   0.0    1.9e-05   24.4   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.2e-05   25.5   0.0    2.4e-05   24.5   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
    5.7e-05   23.6   0.2     0.0012   19.3   0.2    2.4  1  AAA_16           AAA ATPase domain
      0.002   18.7   0.0       0.01   16.4   0.0    2.2  2  AAA_18           AAA domain
     0.0031   17.5   0.2      0.065   13.2   0.0    3.0  3  AAA_5            AAA domain (dynein-related subfamily)
      0.005   17.2   0.0      0.011   16.1   0.0    1.6  1  RNA_helicase     RNA helicase
     0.0068   15.6   0.0      0.011   14.9   0.0    1.3  1  TIP49            TIP49 P-loop domain
  ------ inclusion threshold ------
       0.01   16.1   0.1       0.48   10.7   0.0    2.5  2  AAA_22           AAA domain
       0.01   16.0   0.0      0.021   15.0   0.0    1.6  1  AAA_33           AAA domain
      0.033   13.9   0.0      0.068   12.9   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.053   13.4   0.0       0.13   12.2   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
      0.056   13.2   0.0       0.11   12.2   0.0    1.4  1  AAA_30           AAA domain
      0.058   13.1   0.0       0.13   12.0   0.0    1.6  1  AAA_24           AAA domain
      0.071   13.0   0.0        5.1    6.9   0.0    2.2  2  ATPase_2         ATPase domain predominantly from Archaea
        0.1   12.4   0.0       0.16   11.7   0.0    1.3  1  AAA_11           AAA domain
       0.11   12.2   0.0         11    5.6   0.0    2.4  2  Thymidylate_kin  Thymidylate kinase


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 !  142.0   0.0   1.4e-44   1.4e-41       2     132 .]     190     321 ..     189     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 142.0 bits;  conditional E-value: 1.4e-44
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTC CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgs 77 
                                       l+yGppGtGKT +a+ + ++++++f++i g+e++sk vg++e+ ire+f++a+e++ psi+f+DEid++a +r  ++
  gi|336252389|ref|YP_004595496.1| 190 LFYGPPGTGKTHFARILSESISAQFYRIRGPEIVSKGVGDTERLIREIFDDAREES-PSIIFFDEIDSIAVDRgGEG 265
                                       8******************************************************9.****************7777 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                       ++++++r+v+qLl++ldg++  +++v+vi+atn+++++d+allr gRfd ++++++
  gi|336252389|ref|YP_004595496.1| 266 TRDFSQRIVAQLLAVLDGFDGAQENVFVIAATNQINEIDDALLRpGRFDWQVHFPR 321
                                       9************************************************9999875 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   2.6e-09   2.6e-06       3      43 ..     348     388 ..     346     390 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.6e-09
                         AAA_lid_3   3 dlkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                                       +++++ +rTeG++GA l al +eA+ l++  g++ei  +d+
  gi|336252389|ref|YP_004595496.1| 348 NIDQVMSRTEGWTGAKLRALLNEAGVLCVAAGRDEIRHSDL 388
                                       899999******************************99998 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 !   24.4   0.0   1.9e-08   1.9e-05      12      95 ..     161     256 ..     149     261 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.9e-08
                            RuvB_N  12 qekvkeklkifieaakk....reealdhvllyGpPGlGkttlakiiakelgvklkitsgPvleka..gdlaalltnl 82 
                                       qe+ +e++++f++ + +     +e+    l+yGpPG Gkt +a+i+++ + +++    gP +  +  gd   l+ ++
  gi|336252389|ref|YP_004595496.1| 161 QEQFRERVELFLTESDAlstvGTEPRMGALFYGPPGTGKTHFARILSESISAQFYRIRGPEIVSKgvGDTERLIREI 237
                                       67777777777765443111135666778*******************************98665225777776665 PP

                            RuvB_N  83 ......eekdvlfideihr 95 
                                             e+  ++f dei  
  gi|336252389|ref|YP_004595496.1| 238 fddareESPSIIFFDEIDS 256
                                       3322223346888888875 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   2.4e-08   2.4e-05       6     105 ..     189     283 ..     184     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.4e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                        l+ gp g+Gkt  a+ l+e +++    ++ r+   e+      + + + +   ++    a e+   i+++DEid i
  gi|336252389|ref|YP_004595496.1| 189 ALFYGPPGTGKTHFARILSESISA----QFYRIRGPEIVS----KGVGDTERLIREIFDDAREESpsIIFFDEIDSI 257
                                       689*******************96....9**********9....66666665555555555555556********** PP

                                       ---..---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk..essgadvSregVqrdLLqileg 105
                                       +    ++ ++d S+  V   LL +l+g
  gi|336252389|ref|YP_004595496.1| 258 AVDrgGEGTRDFSQRIVA-QLLAVLDG 283
                                       *9999999*****98665.57888886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   1.2e-06    0.0012      24     127 ..     185     281 ..     173     294 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-06
                            AAA_16  24 p.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawre 99 
                                       p    l++G++G+GK+  +r l ++++++ ++ +rg    +           + ++e+l+r++ d+a++ +++    
  gi|336252389|ref|YP_004595496.1| 185 PrMGALFYGPPGTGKTHFARILSESISAQ-FYRIRGPEIVS---------KGVGDTERLIREIFDDAREESPSIIFF 251
                                       347899*********************99.66677766666.........223334478888888855555444444 PP

                            AAA_16 100 kleeala..avpelagaeasrllellkrll 127
                                          +++a   ++e +++ ++r+ ++l + l
  gi|336252389|ref|YP_004595496.1| 252 DEIDSIAvdRGGEGTRDFSQRIVAQLLAVL 281
                                       333433323333333333355555555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     1e-05      0.01       3      66 ..     191     279 ..     190     328 .. 0.68
   2 ?   -1.1   0.0       2.6   2.6e+03      25      69 ..     337     361 ..     321     393 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-05
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe....aldeskrlde 54 
                                         G+pG+GKt +a+ Ls++                         +++ d a+e+ +++ +++e    a+d+  +  +
  gi|336252389|ref|YP_004595496.1| 191 FYGPPGTGKTHFARILSESISAqfyrirgpeivskgvgdterlIREIFDDAREESPSIIFFDEidsiAVDRGGEGTR 267
                                       57****************96225677888866666666666666666666666666666666666665555555555 PP

                            AAA_18  55 dkldklldalee 66 
                                       d+ ++++ +l +
  gi|336252389|ref|YP_004595496.1| 268 DFSQRIVAQLLA 279
                                       555555555554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.6
                            AAA_18  25 gvnlrdvakenglllevdpealdeskrldedkldklldaleenss 69 
                                       g+                    + s+ + e++ d++++  e++  
  gi|336252389|ref|YP_004595496.1| 337 GY--------------------NLSDTITEENIDQVMSRTEGWTG 361
                                       33....................55556666666666666666655 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   6.6e-05     0.065       3      30 ..     190     217 ..     188     261 .. 0.77
   2 ?   -1.4   0.0       2.1   2.1e+03      70     120 ..     280     297 ..     266     313 .. 0.62
   3 ?   -2.3   0.0         4   3.9e+03      58      70 ..     363     375 ..     328     403 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.6e-05
                                       EEE--SSSSHHHHHHHGGGGBS--EEEE CS
                             AAA_5   3 lLvGppGtgKselaerlaaalnreveyv 30 
                                       l  GppGtgK+ +a+ l++ + +++  +
  gi|336252389|ref|YP_004595496.1| 190 LFYGPPGTGKTHFARILSESISAQFYRI 217
                                       789****************997776655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                                       EEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEE CS
                             AAA_5  70 vlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviata 120
                                       vlD+++ a+ +v+                                 via++
  gi|336252389|ref|YP_004595496.1| 280 VLDGFDGAQENVF---------------------------------VIAAT 297
                                       4555554444444.................................44444 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4
                                       -------G-SEEE CS
                             AAA_5  58 plvraaregeilv 70 
                                       +l    +e+ +l+
  gi|336252389|ref|YP_004595496.1| 363 KLRALLNEAGVLC 375
                                       3333333333333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.1e-05     0.011       2      39 ..     190     227 ..     189     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnp 39 
                                       ++yGp+g+GK+++a+ L+++++ ++  ++ ++++s+++
  gi|336252389|ref|YP_004595496.1| 190 LFYGPPGTGKTHFARILSESISAQFYRIRGPEIVSKGV 227
                                       69********************9998888888877665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.1e-05     0.011      53     102 ..     189     236 ..     158     241 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  53 vLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqa 102
                                        L+ Gp+gtGkt  a  +s++++    f  + g e+ s  v  te l+++
  gi|336252389|ref|YP_004595496.1| 189 ALFYGPPGTGKTHFARILSESIS--AQFYRIRGPEIVSKGVGDTERLIRE 236
                                       6899******************9..68******************99875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00048      0.48       9      30 ..     190     211 ..     184     224 .. 0.81
   2 ?    2.5   0.0      0.16   1.6e+02      74     105 ..     229     262 ..     220     303 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00048
                            AAA_22   9 vvtGesGtGKTtllrrlleqld 30 
                                       + +G++GtGKT+ +r l e+  
  gi|336252389|ref|YP_004595496.1| 190 LFYGPPGTGKTHFARILSESIS 211
                                       679************9988764 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.16
                            AAA_22  74 sseellealeqalraravielliiDEaqhlr...s 105
                                       ++e+l++ + + +r+ +  +++  DE++ +     
  gi|336252389|ref|YP_004595496.1| 229 DTERLIREIFDDAREESP-SIIFFDEIDSIAvdrG 262
                                       789999999999999999.*********9865541 PP

>> AAA_33  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     0.021       3      39 ..     190     228 ..     189     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                            AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdtlrrrlfg 39 
                                       l+ G+pG+GK+++a+ l +     +++++ +++ ++ +g
  gi|336252389|ref|YP_004595496.1| 190 LFYGPPGTGKTHFARILSESISaqFYRIRGPEIVSKGVG 228
                                       689************998877778899999885544433 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 ?   12.9   0.0   6.8e-05     0.068      49      71 ..     188     210 ..     164     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-05
                         IstB_IS21  49 nivllGpsGvGKshlaialgvea 71 
                                       + ++ Gp+G+GK+h+a  l+ + 
  gi|336252389|ref|YP_004595496.1| 188 GALFYGPPGTGKTHFARILSESI 210
                                       56899***********9887665 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 ?   12.2   0.0   0.00013      0.13       3      31 ..     190     218 ..     188     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                             AAA_3   3 llegvPGlaktllvkalakaldlefkriq 31 
                                       l+ g PG++kt +++ l+++++++f ri+
  gi|336252389|ref|YP_004595496.1| 190 LFYGPPGTGKTHFARILSESISAQFYRIR 218
                                       67789**********************96 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   0.00011      0.11       8      50 ..     176     218 ..     173     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                            AAA_30   8 aavealltsgdrvavltGpAGtGKttalkalreaweaaggrvi 50 
                                       +a+ ++ t++++ a+  Gp+GtGKt+  + l e + a+ +r+ 
  gi|336252389|ref|YP_004595496.1| 176 DALSTVGTEPRMGALFYGPPGTGKTHFARILSESISAQFYRIR 218
                                       6777888899999999****************99999988776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.13       6      22 ..     190     206 ..     187     258 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                            AAA_24   6 liyGpsgiGKTtlakel 22 
                                       l yGp+g+GKT++a+ l
  gi|336252389|ref|YP_004595496.1| 190 LFYGPPGTGKTHFARIL 206
                                       67************977 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 ?    5.0   0.0      0.02        20      14      39 ..     180     205 ..     175     217 .. 0.76
   2 ?    6.9   0.0    0.0051       5.1      78     225 ..     206     358 ..     202     362 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.02
                          ATPase_2  14 ilerepneiyfiYGpegsGKtaLlke 39 
                                        + +ep++  + YGp g GKt + + 
  gi|336252389|ref|YP_004595496.1| 180 TVGTEPRMGALFYGPPGTGKTHFARI 205
                                       566788888999*********98764 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0051
                          ATPase_2  78 lekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlgln........gaellvkeLl 146
                                       l++ ++ ++ + ++ ei+++   + ++ i +++++ +++    ii++De+  +    ++         ++  v++Ll
  gi|336252389|ref|YP_004595496.1| 206 LSESISAQFYRIRGPEIVSKGVGDTERLIREIFDDAREESP-SIIFFDEIDSIA---VDrggegtrdFSQRIVAQLL 278
                                       66677777777888888888888999999999999888844.799*****9998...344556666667789***** PP

                          ATPase_2 147 nliesltkekhlcvviclsSeglfiervyneselegrhky.ilvddldketalnflkegfkeleel....skedfee 218
                                        +++     ++ ++vi+++ +   i+++++   + gr ++ ++      e+ +++++ + +e ++l    ++e++++
  gi|336252389|ref|YP_004595496.1| 279 AVLDGFDGAQENVFVIAATNQ---INEIDDALLRPGRFDWqVHFPRPSDEHRREIFNTL-REGYNLsdtiTEENIDQ 351
                                       *****************9986...44455777777888887666666677777777775.66666656666777777 PP

                          ATPase_2 219 iyryvGG 225
                                       + + + G
  gi|336252389|ref|YP_004595496.1| 352 VMSRTEG 358
                                       7766665 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.16      19      40 ..     188     209 ..     170     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                            AAA_11  19 itliqGPPGtgKTktivellsq 40 
                                        +l+ GPPGtgKT++   l ++
  gi|336252389|ref|YP_004595496.1| 188 GALFYGPPGTGKTHFARILSES 209
                                       47999********987655554 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.011        11       3      28 ..     193     217 ..     191     243 .. 0.79
   2 ?    4.6   0.0     0.023        22     105     183 ..     232     305 ..     223     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.011
                                       ESTTSSHHHHHHHHHHHHHHTTE.EE CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvv 28 
                                       G  G+GKt +a++l e ++++ ++ +
  gi|336252389|ref|YP_004595496.1| 193 GPPGTGKTHFARILSESISAQFYR-I 217
                                       6779*****************997.4 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.023
                                       HHHHHHGGGTTS.E-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHH.TTSTEEEEETTS-HH CS
                   Thymidylate_kin 105 dlvlslnedvll.kPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelak.ederiliidasksie 179
                                       +l++++ +d+   +P ++f+ ++d ++a+ R +++        +++++  ++ +  l+ ++ ++e++++i a+++i+
  gi|336252389|ref|YP_004595496.1| 232 RLIREIFDDAREeSPSIIFFDEID-SIAVDRGGEGTR-----DFSQRIVAQLLA-VLDGFDgAQENVFVIAATNQIN 301
                                       667777777766899999999977.799999999999.....444444555555.4666666789***********9 PP

                                       HHHH CS
                   Thymidylate_kin 180 evhe 183
                                       e+ +
  gi|336252389|ref|YP_004595496.1| 302 EIDD 305
                                       9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 3138.70
//
Query:       gi|336252390|ref|YP_004595497.1|  [L=730]
Description: PglZ domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-09   38.3   0.0    2.8e-09   37.3   0.0    1.5  1  PglZ      PglZ domain


Domain annotation for each model (and alignments):
>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   1.6e-13   2.8e-09       3     170 ..     473     638 ..     471     643 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.6e-13
                              PglZ   3 vfvIisDalryeaweelkqlLnk......edrfeael..savlgvlPslTklgraallpgkkllykeksaldvlvde 71 
                                       v++ ++Dalr++ ++ l++ L+        d+ e+++     lg lPs T++g+aal pg+      ++++  lvd+
  gi|336252390|ref|YP_004595497.1| 473 VALFVIDALRLDLARRLADELRDyvatlpADAPEFAIdeDVWLGTLPSETEFGKAALTPGEI-----QMFDVSLVDG 544
                                       8999********988777666651111222333444576789******************98.....478899**** PP

                              PglZ  72 esseglenrekilekklglavkaddllelkkderrellkdkevvyivhnkvDalgdkasteqksfeaveeslkelke 148
                                       e +   +nr    ++ ++l       ++ ++d++    + ++v y + n +D++g+k+++  +  +  ++ +  l+e
  gi|336252390|ref|YP_004595497.1| 545 ELQPLRNNRRVTTNRRESLLGGDGWTVTREEDDG---WQSTRVAY-FKNDIDDIGEKELSDLE--AMLARRVDSLAE 615
                                       *****99999998866655544444444444444...45677766.6899******7777655..44578999**** PP

                              PglZ 149 lvksllee.ngykvlltaDHGfi 170
                                        +   le+ +  + ++ +DHGf+
  gi|336252390|ref|YP_004595497.1| 616 FIGTKLEQgEWDQAYVLTDHGFV 638
                                       ********8889**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.24s 00:00:00.80 Elapsed: 00:00:00.37
# Mc/sec: 5914.11
//
Query:       gi|336252391|ref|YP_004595498.1|  [L=425]
Description: hypothetical protein Halxa_0983 [Halopiger xanaduensis SH-6]
Scores for 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  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.54u 0.21s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3175.23
//
Query:       gi|336252392|ref|YP_004595499.1|  [L=972]
Description: helicase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-23   80.8   0.0    2.1e-22   79.6   0.0    1.7  1  Helicase_C    Helicase conserved C-terminal domain
    2.9e-18   65.7   0.0    2.6e-16   59.3   0.0    2.4  2  SNF2_N        SNF2 family N-terminal domain
    7.2e-12   45.6   0.0    2.1e-11   44.1   0.0    1.9  1  ResIII        Type III restriction enzyme, res subunit
    1.5e-05   24.8   0.0      4e-05   23.5   0.0    1.7  1  DEAD          DEAD/DEAH box helicase
    0.00024   20.3   0.1    0.00024   20.3   0.1    2.7  2  RapA_C        RNA polymerase recycling family C-terminal
    0.00088   19.0   0.0      0.098   12.3   0.0    2.4  2  Helicase_C_4  C-terminal domain on Strawberry notch homologue
     0.0034   16.3   0.6      0.017   14.1   0.6    1.9  1  AAA_34        P-loop containing NTP hydrolase pore-1
  ------ inclusion threshold ------
      0.076   12.2   3.2      0.078   12.2   0.0    2.6  4  DUF2075       Uncharacterized conserved protein (DUF2075)
       0.33   11.3   1.9        9.1    6.6   1.6    2.9  2  KxDL          Uncharacterized conserved protein
        7.2    6.1  11.0       0.35   10.4   2.4    2.8  3  Exonuc_VII_L  Exonuclease VII, large subunit
        8.5    5.4   7.4         23    3.9   7.4    1.7  1  Atg14         Vacuolar sorting 38 and autophagy-related subun


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 !   79.6   0.0   1.3e-25   2.1e-22       5     111 .]     475     583 ..     470     583 .. 0.88

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 1.3e-25
                                       HHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSS CS
                        Helicase_C   5 allellkleeeggkilifvntidrlek.vklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvaerG 79 
                                        + +ll +e+ ++k l+f++++d+l+  +++++ +  + +++v+hg+  ++er +i ++fn+g+ ++L atd+a++G
  gi|336252392|ref|YP_004595499.1| 475 FISQLL-EEQPDEKLLLFTEYRDTLDYlLEYVQDEPwADEILVIHGDVDKEERARIEDEFNHGQPRLLFATDAASEG 550
                                       345556.99****************8777777444489*************************************** PP

                                       STST.TESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  80 idip.kvnlVinfdlprnvtsyiqriGRtgRag 111
                                       id++ +++ + n++lp+n+ ++ qriGR++R+g
  gi|336252392|ref|YP_004595499.1| 551 IDLQhSCHIMANYELPWNPNRLEQRIGRIHRYG 583
                                       ***96688888********************86 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.2     2e+03       1      12 [.     114     125 ..     114     131 .. 0.78
   2 !   59.3   0.0   1.6e-19   2.6e-16      59     327 ..     131     374 ..     119     395 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                                       HHHHHHHHH... CS
                                       xxxxxxxxxxxx RF
                            SNF2_N   1 yQkeavkwmlkR 12 
                                       yQ +av+w +++
  gi|336252392|ref|YP_004595499.1| 114 YQLDAVNWVMQK 125
                                       9*******8543 PP

  == domain 2  score: 59.3 bits;  conditional E-value: 1.6e-19
                                       EE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE--SSHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  59 iLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlvyggqkkm 135
                                       ++ D+ GLGKT+++  +++++ a           +++a+ +L vvPa l ++W ++++r+   + l+v      + +
  gi|336252392|ref|YP_004595499.1| 131 LIGDDVGLGKTIEAGLILKELAA-----------RNRADRVLFVVPAHLQKKWIRDMDRFFDVD-LTVADRAWVEGE 195
                                       789**********9555552222...........2345669*******************9987.666554444445 PP

                                       ----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--T...TSHHHHHHHH--..-S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx..xxx RF
                            SNF2_N 136 kkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlkns...tskaaeavskLs..tsn 207
                                       + +  + a+ + +d++ ++t+   l+++      r +l +  w+ vv+DE+h+  +     sk+a++v +    ++ 
  gi|336252392|ref|YP_004595499.1| 196 RRRLGEEANIWNQDQQQLVTSMAFLRQDE----FRPALRDAFWDVVVVDEAHKAAKRgdsPSKTANMVDTVTgnSDS 268
                                       6666788899999*************888....899*****************999877679*******97655788 PP

                                       EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHHHHHHHHHHHHHTT-STTEE---GGGT.....--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxx RF
                            SNF2_N 208 rwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpieaqaekgrsrLlqllqrlmlrrakkdv.....ekn 279
                                        ++l++TP   + e + +L++++ +    e++  ++                  + + r+m+rr k+d+     e+ 
  gi|336252392|ref|YP_004595499.1| 269 LLLLSATPHDGKGEAFRSLVEYIDPFLVAENRELSQ------------------ETVDRVMIRRGKTDIydedgERV 327
                                       99********************99888875544433..................46799***********9987888 PP

                                       ---EEEEEEEEE--HHHHHHHH....................HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 280 lPpkteeiiflklskverksYnrllevlrkkalakllkrseaalksss 327
                                       +P+++++ + +++++ er++Y  + ++  k++ + + k +e a+ ++ 
  gi|336252392|ref|YP_004595499.1| 328 FPDREVNSVSVSMTHDERQFYR-AVTDYVKNVYNRSEKLNEPAVGFAM 374
                                       *********************9.8888888888888888877766655 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 !   44.1   0.0   1.3e-14   2.1e-11       3     170 ..     110     277 ..     108     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.3e-14
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       +l +yQ +a++ +++kl    ++r+li    G GKT+ a  + ++l+  ++ +++lf+vp  +l +++++++ +f++
  gi|336252392|ref|YP_004595499.1| 110 RLEPYQLDAVNWVMQKL----RQRALIGDDVGLGKTIEAGLILKELAARNRADRVLFVVPA-HLQKKWIRDMDRFFD 181
                                       689***********999....59*************************************6.7*************9 PP

                                       G....GEEEESSS-B--...........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.....T CS
                            ResIII  80 eaykeigkkvsgdkkka....kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak....k 148
                                        + + +   + + ++++     ++ +++ + lvt+   l +d+      +  l++ + dv+++DEaH++++     +
  gi|336252392|ref|YP_004595499.1| 182 VDLTVADRAWVEGERRRlgeeANIWNQDQQQLVTSMAFLRQDE-----FRPALRDAFWDVVVVDEAHKAAKRgdspS 253
                                       9988855555544444446555778899999999999999999.....88888888889************876653 PP

                                       TTHHHHHT-..--SEEEEEESS-S CS
                            ResIII 149 swreilekf..keavllglTATpe 170
                                       +  + ++ +  ++  ll l+ATp 
  gi|336252392|ref|YP_004595499.1| 254 KTANMVDTVtgNSDSLLLLSATPH 277
                                       44444333323446788899**96 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.4e-08     4e-05       2     170 ..     113     277 ..     112     282 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.4e-08
                                       HHHHHHHHHHHTT..CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                       xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgg..gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                       ++Q  a+++++++  +  l+  ++G GKT  + + + +  +   ++++ ++l+v+P   L ++ ++++ +f++ +dl
  gi|336252392|ref|YP_004595499.1| 113 PYQLDAVNWVMQKlrQRALIGDDVGLGKTIEAGLILKELAA---RNRADRVLFVVPA-HLQKKWIRDMDRFFD-VDL 184
                                       6788888888866557999999*********9998776663...68888*******7.5**************.565 PP

                                       EEE..EEETTSSHHHHHHHH..HTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxx..xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  77 rvl..liiggvaardqlskl..dngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnql 149
                                       +v   ++++g+++r   ++   +++ + +v+    l +   +  l+     ++V+DEa++  +   +d  ++ +n +
  gi|336252392|ref|YP_004595499.1| 185 TVAdrAWVEGERRRLGEEANiwNQDQQQLVTSMAFLRQDEFRPALRDAFWDVVVVDEAHKAAKR--GDSPSKTANMV 259
                                       5553366776655432222211333666666665555533345545555599***********8..44444444555 PP

                                       HHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 150 pqitcdgklqrqvivlSATlp 170
                                       ++ t   + +  +++lSAT++
  gi|336252392|ref|YP_004595499.1| 260 DTVTG--N-SDSLLLLSATPH 277
                                       43344..4.234********9 PP

>> RapA_C  RNA polymerase recycling family C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.5e-07   0.00024      83     200 ..     673     791 ..     637     806 .. 0.79
   2 ?   -1.6   5.3      0.66   1.1e+03     237     322 ..     854     942 ..     849     961 .. 0.56

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.5e-07
                                       HHHHHTT-SHHHHHHHHHHHCCC-....-TTHHHHCHHHHHHHTEEEE--SSSSEEEEE-STT--TT-S--S--EE- CS
                            RapA_C  83 LLElnScrpekaeelveaiaeedn....dteleeflerlfdaigveqedkseksivlrpsehmlveafpglpedGlt 155
                                       L + + ++ e+ +++ e + e+++    + +++ef er+++a+g e e+++ + +  +  + +   + pg ++    
  gi|336252392|ref|YP_004595499.1| 673 LVDTSTFDAESRRQIQEVVDESEDvygsEGDIREFFERAVEAFGGEFEKRGTNLYQAELPDGI---NSPGQDATFGP 746
                                       5566666666666666666665542222678999******************99999999988...57898888889 PP

                                       S-HHHHTTS-S---STTSTHHHHHHHHHTT--SSSSB--S-S-SS CS
                            RapA_C 156 vTfdRetAlareDvqFltwehPlvrgaldlilsselGnaavallk 200
                                        TfdR+ A+ +eD+ +l  +    + ++  +l++e G+  + ll 
  gi|336252392|ref|YP_004595499.1| 747 FTFDRDFAMDHEDITYLAPDTDVLQRLMARVLEDERGEVGLKLLP 791
                                       9************************************99988876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.66
                                       --B-SSSS-B--S-STTTSTT-------STTSSTTSSS-SHHHHTT...TTTTTTSSSHHHHHH..HHHHHHHHHHH CS
                            RapA_C 237 rllldekgkdlsekvsfeslnkqlkkvkkklarklvkakrkeiekl...lkkaeklaeeqaeel..ieeakaraeqe 308
                                       r++ld++ + l    + + ++ +++++k++l +k  +  + e+e+l    ++ ++ +e+  ee   +++a ++++ +
  gi|336252392|ref|YP_004595499.1| 854 RTVLDAQSD-LRTA-ADRYVSVRVNEIKNHLQEKRHEETARELENLeeyAQAERERIESFIEEYerKADAGSDMDIA 928
                                       666666554.3322.22455556677777777777766666655541103444444555444441144556678888 PP

                                       HHHHTHHHHTHHHH CS
                            RapA_C 309 lsaEleRLeaLkav 322
                                       +    eRLe+L+  
  gi|336252392|ref|YP_004595499.1| 929 IRGQQERLEQLEDR 942
                                       88888888888765 PP

>> Helicase_C_4  C-terminal domain on Strawberry notch homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.021        34     215     262 ..     460     507 ..     365     515 .. 0.66
   2 !   12.3   0.0     6e-05     0.098      54     116 ..     530     585 ..     520     597 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.021
                      Helicase_C_4 215 leaealekdlskvskfLnRllglevelQnalfkyftetleaeiekakk 262
                                       +e   ++++++kv++f+  ll  + ++  +lf+ + +tl+  +e  + 
  gi|336252392|ref|YP_004595499.1| 460 AEDLPVDSKAQKVRRFISQLLEEQPDEKLLLFTEYRDTLDYLLEYVQD 507
                                       34445678899****************************998887665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6e-05
                      Helicase_C_4  54 keaFmdgeKliaiiSeAastGiSlhadrraenqrrRvhitlelpwsadkaiqqlGrthRsnqa 116
                                       +++F +g+ +++  ++Aas Gi l+ + +       ++   elpw+ ++  q +Gr hR  q 
  gi|336252392|ref|YP_004595499.1| 530 EDEFNHGQPRLLFATDAASEGIDLQHSCH-------IMANYELPWNPNRLEQRIGRIHRYGQE 585
                                       5789********************97654.......67779******************8885 PP

>> AAA_34  P-loop containing NTP hydrolase pore-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.6     1e-05     0.017      56     190 ..     123     251 ..      88     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                            AAA_34  56 pdgkRaGfllGDgaGvGkgrqiagiilenllqgrkkavwvsvsedLkeDaerDlkdigaseievvalnklkegkkik 132
                                        ++ R+  l+GD+ G+Gk+ + + i+ e  +++r   v + v ++L++   rD++     +++v   + ++ + +  
  gi|336252392|ref|YP_004595499.1| 123 MQKLRQRALIGDDVGLGKTIEAGLILKELAARNRADRVLFVVPAHLQKKWIRDMDRFFDVDLTVADRAWVEGE-RR- 197
                                       34558888***********99888888888899999*****************98876655666555444333.33. PP

                            AAA_34 133 eseelkeGvlFvtYstliseskkkkksrleqlveWlgedfdGvivfDEchkaknlaks 190
                                        +   +  +    +++l+++       r +++   l + f  v+v DE+hka++   s
  gi|336252392|ref|YP_004595499.1| 198 -RLGEEANIWNQDQQQLVTSMAF---LRQDEFRPALRDAFWDVVVVDEAHKAAKRGDS 251
                                       .2333444555556666655444...57777777788888888888888888776543 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   4.8e-05     0.078      86     123 ..     231     266 ..     185     273 .. 0.71
   2 ?   -3.8   0.0       3.4   5.6e+03     149     210 ..     326     387 ..     320     397 .. 0.64
   3 ?   -3.8   0.0       3.5   5.6e+03      60      91 ..     465     488 ..     444     510 .. 0.63
   4 ?   -2.3   0.2       1.3   2.1e+03      48      77 ..     887     918 ..     858     937 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.8e-05
                           DUF2075  86 epkedvvivDEAhrlltksdqaekqseenqlkelmkra 123
                                       +   dvv+vDEAh++ +++d+  k  + n+++++  ++
  gi|336252392|ref|YP_004595499.1| 231 DAFWDVVVVDEAHKAAKRGDSPSK--TANMVDTVTGNS 266
                                       44469************9999554..578887776664 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.4
                           DUF2075 149 klakkleveleekvhLksqfRvaaseaviewvdalldgkkekakplss..qenfdirvfddlee 210
                                       +++++ ev+ ++  ++++  R++  +av+++v+++ +++++ ++p +      ++ r+++++ +
  gi|336252392|ref|YP_004595499.1| 326 RVFPDREVNSVSV-SMTHDERQF-YRAVTDYVKNVYNRSEKLNEPAVGfaMALMQKRLVSSVGA 387
                                       5666666666555.777777774.4678889999988888887777645555555555555555 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 3.5
                           DUF2075  60 kkeafeklssfinnlsefkkaeekkeepkedv 91 
                                        +++++k++ fi +l         +e+p+e++
  gi|336252392|ref|YP_004595499.1| 465 VDSKAQKVRRFISQLL--------EEQPDEKL 488
                                       4555666666666655........44444444 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.3
                           DUF2075  48 realakke..ekkkkkeafeklssfinnlsef 77 
                                        e+ a++    ++  +++ e+ +sfi++++++
  gi|336252392|ref|YP_004595499.1| 887 HEETARELenLEEYAQAERERIESFIEEYERK 918
                                       22222222455666677777888888888744 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.26   4.3e+02      26      49 ..     648     671 ..     625     681 .. 0.78
   2 ?    6.6   1.6    0.0056       9.1      24      80 ..     886     945 ..     871     947 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.26
                              KxDL  26 nkknreLlelnalsqerlaklrar 49 
                                        ++++eL+e++++ q+ l++  +r
  gi|336252392|ref|YP_004595499.1| 648 SATKEELEEMIEERQRTLEEWYER 671
                                       6899**************998776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0056
                              KxDL  24 rlnkknreLlelnalsq...erlaklrarfkqgtkllkevkkdLesifkkirslkaklak 80 
                                       r +++ reL++l +++q   er +++ +++++++ + +++   ++  ++++++l+++++k
  gi|336252392|ref|YP_004595499.1| 886 RHEETARELENLEEYAQaerERIESFIEEYERKADAGSDMDIAIRGQQERLEQLEDRIEK 945
                                       66889999999999998333588889999*************************999987 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 ?   -0.2   0.3      0.37   6.1e+02     204     204 ..     427     427 ..     235     508 .. 0.52
   2 ?   -1.3   0.0      0.79   1.3e+03     137     181 ..     606     676 ..     570     712 .. 0.58
   3 ?   10.4   2.4   0.00021      0.35     152     234 ..     859     952 ..     835     967 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.37
                      Exonuc_VII_L 204 k 204
                                       k
  gi|336252392|ref|YP_004595499.1| 427 K 427
                                       1 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.79
                      Exonuc_VII_L 137 lvvpdkaeleeqleeler.........................rlekaikrlleekkqrlekl.asrlksp 181
                                       ++  + +e+++ql ++++                          +++++++++ee+++ le++ +++l + 
  gi|336252392|ref|YP_004595499.1| 606 MLQTKVEEIRSQLGNTADvlgilddidvdslimesiendeppsATKEELEEMIEERQRTLEEWyERSLVDT 676
                                       44444444444444444433333333333333333333333335555556666666666666523333232 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00021
                      Exonuc_VII_L 152 lerrlekaikrll.........eekkqrleklasrlkspeellerkrqrldeleerleralkkq......lkkkrer 213
                                       +++ l++a++r++         + +++r e++a++l++ ee  +++r+r++++ e+ er+ +        ++ ++er
  gi|336252392|ref|YP_004595499.1| 859 AQSDLRTAADRYVsvrvneiknHLQEKRHEETARELENLEEYAQAERERIESFIEEYERKADAGsdmdiaIRGQQER 935
                                       33333333333332222222222233455566666666666777777776666666666322224444447777777 PP

                      Exonuc_VII_L 214 leelkerlkekleekkerlkk 234
                                       le+l++r++    +++e+l++
  gi|336252392|ref|YP_004595499.1| 936 LEQLEDRIE----KRREELRR 952
                                       777775552....22222222 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 ?    3.9   7.4     0.014        23      45     119 ..     878     951 ..     863     966 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.014
                             Atg14  45 iekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdle 119
                                       i+  l++k+  e+++++++n+ ++++  + +i++  e+ ++  d  s  + +i+ ++++l++l d + kRr++l+
  gi|336252392|ref|YP_004595499.1| 878 IKNHLQEKR-HEETARELENLEEYAQAERERIESFIEEYERKADAGSDMDIAIRGQQERLEQLEDRIEKRREELR 951
                                       444444444.45555566666666666666666666665555555555555555555555555555555555433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (972 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1492  (0.0832171); expected 358.6 (0.02)
Passed bias filter:                      736  (0.0410508); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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):              11  [number of targets reported over threshold]
# CPU time: 0.93u 0.30s 00:00:01.23 Elapsed: 00:00:00.46
# Mc/sec: 6384.86
//
Query:       gi|336252393|ref|YP_004595500.1|  [L=42]
Description: hypothetical protein Halxa_0985 [Halopiger xanaduensis SH-6]
Scores for 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:                       112  (0.00624686); expected 358.6 (0.02)
Passed bias filter:                       94  (0.0052429); 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: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 344.71
//
Query:       gi|336252394|ref|YP_004595501.1|  [L=337]
Description: metallophosphoesterase [Halopiger xanaduensis SH-6]
Scores for complete 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-13   51.7   0.7    7.5e-13   49.4   0.1    2.2  3  Metallophos    Calcineurin-like phosphoesterase
    7.8e-08   32.7   2.0    1.7e-07   31.6   2.1    1.6  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 ?    0.1   0.0      0.11   9.7e+02      71      89 ..      22      40 ..       5      78 .. 0.60
   2 !   49.4   0.1   8.4e-17   7.5e-13       3      79 ..      95     181 ..      93     249 .. 0.80
   3 ?   -3.3   0.0       1.2     1e+04       4      21 ..     271     284 ..     269     296 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.11
                                      C-TTS...CHHHHHHHHHHHHH CS
                       Metallophos 71 lGNHe...gfeeellnkygylg 89
                                      +GNHe       +   +  +l 
  gi|336252394|ref|YP_004595501.1| 22 HGNHEvpvE---DADGRVSDLR 40
                                      789994430...3333333333 PP

  == domain 2  score: 49.4 bits;  conditional E-value: 8.4e-17
                                       EEEEESBTB......TTCCTHHHHHHHHHHHH...HHHTTESEEEEESTSSSSS....HHHHHHHHHHHHHHHHTSE CS
                       Metallophos   3 ilvigDlHl......algggqlddllkllddl...lreekpdlvllaGDlvdrg....dlekellellaalvkypip 66 
                                       +l+++D+Hl      +++ g+ ++l+++ld +    + +++d+++++GD++d+      +++ ++e ++ l + +ip
  gi|336252394|ref|YP_004595501.1|  95 LLHVSDTHLgrpltdKEHMGNANQLERFLDAVnlaVK-SRVDAIIHTGDIFDDDvdeaTVQT-VEEHVELLADAGIP 169
                                       79***************************99977445.5***************77655555.6666666666699* PP

                                       EEEEC-TTSCHHH CS
                       Metallophos  67 vylllGNHegfee 79 
                                       +y ++GNH  ++ 
  gi|336252394|ref|YP_004595501.1| 170 IYYVRGNHG-CDR 181
                                       ********8.444 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.2
                                       EEEESBTBTTCCTHHHHH CS
                       Metallophos   4 lvigDlHlalgggqlddl 21 
                                       l +gDlH        +++
  gi|336252394|ref|YP_004595501.1| 271 LALGDLH----KHKRAYI 284
                                       5789999....4444444 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 !   31.6   2.1   1.9e-11   1.7e-07       3      81 ..      95     196 ..      93     289 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.9e-11
                     Metallophos_2   3 laiiSDlH...........snldaleav...lealkevgvdaiihaGDl.....eeeepevleellela.....pvl 55 
                                       l+++SD+H           +n ++le++   ++ + + +vdaiih+GD+      e++ +++ee  el+     p++
  gi|336252394|ref|YP_004595501.1|  95 LLHVSDTHlgrpltdkehmGNANQLERFldaVNLAVKSRVDAIIHTGDIfdddvDEATVQTVEEHVELLadagiPIY 171
                                       79*****************55555555522266677889*********877433333334666666666999***** PP

                     Metallophos_2  56 aVrGNnD.eevveedvlreaaelgtdl 81 
                                       +VrGN+  +    +++l++++e g+ +
  gi|336252394|ref|YP_004595501.1| 172 YVRGNHGcD--RGDAFLQSQTEAGRMI 196
                                       *****9831..3344445554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2434.91
//
Query:       gi|336252395|ref|YP_004595502.1|  [L=212]
Description: hypothetical protein Halxa_0987 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      0.008   16.4   0.1      0.014   15.6   0.1    1.4  1  RIG-I_C-RD  C-terminal domain of RIG-I
  ------ inclusion threshold ------
      0.086   13.1   1.7       0.54   10.5   0.0    2.4  2  ESSS        ESSS subunit of NADH:ubiquinone oxidoreductase (c


Domain annotation for each model (and alignments):
>> 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 !   15.6   0.1   1.6e-06     0.014      18      85 ..     135     199 ..     130     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-06
                        RIG-I_C-RD  18 irvienshhvvvnpefkelvkvkekkkkekkfedfekkgkikCkkCkkdwGimmkykgvelpvLkiks 85 
                                       i++i++    vv++++++l +       +    + + + k+ C +C+++ Gi+  ++  e+p+++ +s
  gi|336252395|ref|YP_004595502.1| 135 IEKIQQRLQKVVEKSVRRLTEHD---VIQIGSPEATVSVKVTCGDCGRTYGITTLFRRRECPCVANES 199
                                       55555555555555555555444...33333345566789***********************98766 PP

>> ESSS  ESSS subunit of NADH:ubiquinone oxidoreductase (complex I)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.7     0.056     5e+02      85      99 ..      20      35 ..      13      42 .. 0.74
   2 ?   10.5   0.0   6.1e-05      0.54      68     100 ..      66      95 ..      45     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.056
                              ESSS 85 EA.erllkrREaeglp 99
                                      EA erll+rRE e+  
  gi|336252395|ref|YP_004595502.1| 20 EAdERLLRRRENEDAS 35
                                      55379999**988654 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 6.1e-05
                              ESSS  68 vfvaYlpdtsiqeWArrEAerllkrREaeglpi 100
                                        ++  l d  +++ ArrEA+r+l   E +g+++
  gi|336252395|ref|YP_004595502.1|  66 NYYRLLTDDTVMTTARREARRKL---EEAGIDV 95 
                                       57778899999************...9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1726  (0.0962686); expected 358.6 (0.02)
Passed bias filter:                      999  (0.0557198); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 1641.84
//
Query:       gi|336252396|ref|YP_004595503.1|  [L=275]
Description: hypothetical protein Halxa_0988 [Halopiger xanaduensis SH-6]
Scores for 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  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2034.26
//
Query:       gi|336252397|ref|YP_004595504.1|  [L=72]
Description: hypothetical protein Halxa_0989 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0029   17.9   0.8     0.0041   17.5   0.8    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
      0.029   14.3   0.2      0.032   14.2   0.2    1.0  1  DinB             DinB family
       0.08   12.8   1.6       0.16   11.8   0.1    2.0  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
       0.15   12.1   4.9       0.22   11.6   3.2    1.8  2  Zn_Tnp_IS91      Transposase zinc-binding domain
        6.2    7.0   6.8        2.7    8.2   2.5    2.3  2  Zn-ribbon_8      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 !   17.5   0.8   1.1e-06    0.0041       5      43 ..       7      46 ..       4      61 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga......stpwfki 43
                                      +C+ Cg ++++  + + +       +C +Cg+      s+ ++ +
  gi|336252397|ref|YP_004595504.1|  7 DCDACGTEQEWTVERNLR-----HNSCSECGMrhmislSEREAFE 46
                                      7***********998888.....57*******6444443222222 PP

>> DinB  DinB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   8.9e-06     0.032      35      93 ..      10      69 ..       2      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.9e-06
                                      --SSTTS--HHHHHHHHHHHHHHHHHHHHH...SSSGGGT---------HHHHHHHHHHH CS
                              DinB 35 aengegfqsvkqtlnHvldveelwlsrleg.eegapavddqterkeleeldalrealder 93
                                      a  +e+ ++v++ l H   +e + ++ +++ e +a +++++++++++e  d+lr++ +e+
  gi|336252397|ref|YP_004595504.1| 10 ACGTEQEWTVERNLRHNSCSECGMRHMISLsEREAFEHKQKSQSEQQEMFDKLRKWDEEE 69
                                      5568999***********************888999999999999999999999999887 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.24   8.6e+02      15      20 ..       7      12 ..       2      14 .. 0.70
   2 ?   11.8   0.1   4.4e-05      0.16      11      26 ..      23      38 ..      19      49 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.24
                         zf-C2H2_3 15 qCkeCg 20
                                       C  Cg
  gi|336252397|ref|YP_004595504.1|  7 DCDACG 12
                                      399**9 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4.4e-05
                         zf-C2H2_3 11 fgasqCkeCgMvYnpg 26
                                       ++  C+eCgM  + +
  gi|336252397|ref|YP_004595504.1| 23 LRHNSCSECGMRHMIS 38
                                      55667******87776 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 ?   11.6   3.2     6e-05      0.22      39      74 ..       5      42 ..       1      49 [. 0.75
   2 ?    1.7   0.0     0.075   2.7e+02       7      36 ..      43      71 ..      37      72 .] 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6e-05
                       Zn_Tnp_IS91 39 ryeCeeCg..hekivyfsCksrhCpsCqkkateewlek 74
                                      +  C+ Cg  +e +v    ++++C++C+ +++    e+
  gi|336252397|ref|YP_004595504.1|  5 TDDCDACGteQEWTVERNLRHNSCSECGMRHMISLSER 42
                                      678****8334467777788888*****9998777765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.075
                       Zn_Tnp_IS91  7 eeflekkkklrpsqrkavekilrCrtaalG 36
                                      e+f++k +k +++q++ ++k+++  +++ G
  gi|336252397|ref|YP_004595504.1| 43 EAFEHK-QKSQSEQQEMFDKLRKWDEEEVG 71
                                      556666.67788888888888877766666 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.5   0.00074       2.7       8      34 ..       8      33 ..       7      37 .. 0.71
   2 ?    0.2   0.1      0.23   8.1e+02      13      13 ..      57      57 ..      41      70 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00074
                       Zn-ribbon_8  8 CeeCghefevlqsis.dapltaCPeCgs 34
                                      C++Cg+e e  ++ + +     C eCg 
  gi|336252397|ref|YP_004595504.1|  8 CDACGTEQEWTVERNlR--HNSCSECGM 33
                                      *******9944433322..556****95 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.23
                       Zn-ribbon_8 13 h 13
                                      +
  gi|336252397|ref|YP_004595504.1| 57 E 57
                                      3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1586  (0.08846); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 523.11
//
Query:       gi|336252398|ref|YP_004595505.1|  [L=53]
Description: hypothetical protein Halxa_0990 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0071   16.3   0.9     0.0078   16.2   0.9    1.1  1  Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibito


Domain annotation for each model (and alignments):
>> 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 !   16.2   0.9   4.3e-07    0.0078       9      50 ..       4      48 ..       1      50 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.3e-07
                                      CEEE-TTTTTTSEETTE.........E-TTTTTSSEEE-HHHHHH CS
                         Anti-TRAP  9 LEtkCdaCngsGkiepe..eprasl.eCPkCsGkglipTaqGqkL 50
                                        t+Cd  ++ G+i  +  +p + l +CP+C+ +  +  ++G+ L
  gi|336252398|ref|YP_004595505.1|  4 VKTECDRRDRGGEITYTgvDPDGELrNCPDCGCEVAVDPEAGEAL 48
                                      5789**********9998999999879****99988888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 409.53
//
Query:       gi|336252399|ref|YP_004595506.1|  [L=54]
Description: hypothetical protein Halxa_0991 [Halopiger xanaduensis SH-6]
Scores for 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:                       616  (0.0343577); 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:                         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 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 433.29
//
Query:       gi|336252400|ref|YP_004595507.1|  [L=322]
Description: hypothetical protein Halxa_0992 [Halopiger xanaduensis SH-6]
Scores for 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   16.4   0.2       0.14   11.8   0.0    2.7  3  ScdA_N          Domain of Unknown function (DUF542)
  ------ inclusion threshold ------
      0.038   14.3   0.1       0.32   11.3   0.1    2.2  2  TcdB_N          TcdB toxin N-terminal helical domain
      0.075   13.0   0.9      0.075   13.0   0.9    2.3  2  DUF2205         Short coiled-coil protein
        0.1   13.0   0.0        1.3    9.4   0.0    2.3  2  Rrf2            Transcriptional regulator
       0.38   11.1   0.0       0.38   11.1   0.0    3.5  3  HTH_Tnp_1       Transposase
       0.45   11.0   6.1       0.11   13.0   1.5    2.1  2  Arm-DNA-bind_5  Arm DNA-binding domain
        1.3    9.5   6.8          7    7.2   0.8    2.6  2  DUF4140         N-terminal domain of unknown function (DUF414


Domain annotation for each model (and alignments):
>> ScdA_N  Domain of Unknown function (DUF542)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   5.5e-05      0.14      30      54 ..     168     192 ..     167     194 .. 0.92
   2 ?    1.6   0.0     0.086   2.2e+02      35      54 ..     238     257 ..     235     259 .. 0.87
   3 ?   -3.8   0.0         4     1e+04      36      53 ..     284     301 ..     282     302 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.5e-05
                            ScdA_N  30 GkvsLaeAckekgidleevlaeLea 54 
                                       G +sL eA+ ++g+d+e v+++L  
  gi|336252400|ref|YP_004595507.1| 168 GYESLPEAADRRGVDAEDVARALSR 192
                                       899******************9976 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.086
                            ScdA_N  35 aeAckekgidleevlaeLea 54 
                                       +e ++  g+d+e v++ +ea
  gi|336252400|ref|YP_004595507.1| 238 EEIARANGVDVEVVEEFIEA 257
                                       578999*********99987 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 4
                            ScdA_N  36 eAckekgidleevlaeLe 53 
                                       +++ + gidl   + eLe
  gi|336252400|ref|YP_004595507.1| 284 DVADDLGIDLGDRVTELE 301
                                       566677888776666665 PP

>> TcdB_N  TcdB toxin N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00013      0.32      18      44 ..      97     123 ..      90     126 .. 0.82
   2 ?   -0.0   0.0      0.43   1.1e+03      11      40 ..     252     281 ..     248     284 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                       TTS-HHHHHHHHHHHHHHHHHHHHHST CS
                            TcdB_N  18 seeqskkkyellkklkkeidnYnnlyk 44 
                                        e+   + +e+l+++++eid+++  + 
  gi|336252400|ref|YP_004595507.1|  97 AEKPAAELREELNRINDEIDEWREEHD 123
                                       567777899**************8865 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.43
                                       HHHHHTTTTS-HHHHHHHHHHHHHHHHHHH CS
                            TcdB_N  11 eeklnklseeqskkkyellkklkkeidnYn 40 
                                       ee++  +se+ +    + + ++ + +++Y 
  gi|336252400|ref|YP_004595507.1| 252 EEFIEAMSEQEQAIIDDRIEEIEDDTRRYS 281
                                       678889999999999999*9*999999997 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.9   2.9e-05     0.075      10      47 ..      85     123 ..      82     124 .. 0.89
   2 ?   -1.3   0.1      0.86   2.2e+03      10      28 ..     255     273 ..     247     284 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
                           DUF2205  10 veklerearerLqq.qakeLqssLqaLaervdeVkeehd 47 
                                        +kl  ++rerL +  a eL + L+ + + +de +eehd
  gi|336252400|ref|YP_004595507.1|  85 EQKLRLQKRERLAEkPAAELREELNRINDEIDEWREEHD 123
                                       57888899****87369*********************8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.86
                           DUF2205  10 veklerearerLqqqakeL 28 
                                       +e++++++++ ++ +++e+
  gi|336252400|ref|YP_004595507.1| 255 IEAMSEQEQAIIDDRIEEI 273
                                       5555555555555555544 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00052       1.3      26      52 ..      44      70 ..      37      80 .. 0.87
   2 ?    0.6   0.0      0.28   7.3e+02      27      52 ..     236     261 ..     228     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00052
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHT CS
                              Rrf2 26 vsseeiaerqnispsylekilakLrka 52
                                       +++ ia++ +++p++++ +la+L+k+
  gi|336252400|ref|YP_004595507.1| 44 RNVDWIADEADVNPEFARSMLAELAKS 70
                                      57899*******************997 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                                       -HHHHHHHHTS-HHHHHHHHHHHHHT CS
                              Rrf2  27 sseeiaerqnispsylekilakLrka 52 
                                       s eeia+  ++  +++e  ++ ++++
  gi|336252400|ref|YP_004595507.1| 236 SGEEIARANGVDVEVVEEFIEAMSEQ 261
                                       5689*************999988875 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.38       6      38 ..      26      58 ..      22      62 .. 0.94
   2 ?   -1.4   0.5       1.2     3e+03      48      69 ..      93     117 ..      84     123 .. 0.49
   3 ?    0.8   0.1      0.25   6.3e+02      24      52 ..     235     263 ..     230     283 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                         HTH_Tnp_1  6 rwsdefKariVreslepgksvsevArrhgvspn 38
                                       ws+e+++++V  +l + ++v  +A + +v+p+
  gi|336252400|ref|YP_004595507.1| 26 DWSREERVEAVDDTLHEPRNVDWIADEADVNPE 58
                                      7******************************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                         HTH_Tnp_1  48 regeeaspae...feltaleeenre 69 
                                       re +++ pa     el  + +e+ e
  gi|336252400|ref|YP_004595507.1|  93 RERLAEKPAAelrEELNRINDEIDE 117
                                       3444444444233455555555554 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.25
                         HTH_Tnp_1  24 ksvsevArrhgvspnqLykWrrqyregee 52 
                                       +s  e+Ar  gv+ +     + + +e+e 
  gi|336252400|ref|YP_004595507.1| 235 RSGEEIARANGVDVEVVEEFIEAMSEQEQ 263
                                       56789999999998877777776644444 PP

>> Arm-DNA-bind_5  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.5   4.2e-05      0.11      40      79 ..      83     122 ..      81     130 .. 0.92
   2 ?   -0.9   0.2      0.92   2.3e+03      62      82 ..     260     282 ..     254     286 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.2e-05
                    Arm-DNA-bind_5  40 wdkkkgkvkerepntlelnskirqerekledivrklrqke 79 
                                       wd++k ++++re+ +++ ++++r+e  +++d+++++r + 
  gi|336252400|ref|YP_004595507.1|  83 WDEQKLRLQKRERLAEKPAAELREELNRINDEIDEWREEH 122
                                       ************************************9875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.92
                    Arm-DNA-bind_5  62 rqerekledivrklrqkek..ta 82 
                                       +qe+++++d + +++++ +  + 
  gi|336252400|ref|YP_004595507.1| 260 EQEQAIIDDRIEEIEDDTRryST 282
                                       67888888888888887765554 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 ?    4.8   0.7     0.015        39      57      89 ..      91     123 ..      68     126 .. 0.70
   2 ?    7.2   0.8    0.0027         7      35      88 ..     228     284 ..     226     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                           DUF4140  57 vpnreaeeeelkalraeleeledelaaledela 89 
                                       + +++ +e+  ++lr+el++++de+++ ++e +
  gi|336252400|ref|YP_004595507.1|  91 QKRERLAEKPAAELREELNRINDEIDEWREEHD 123
                                       334444444477888888888888877777655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0027
                           DUF4140  35 dedSlrVegaga...atildvqvervpnreaeeeelkalraeleeledelaaledel 88 
                                       d+++l V++ ++   a   dv+v +++ +   e+e + +++++ee+ed+ ++++ e 
  gi|336252400|ref|YP_004595507.1| 228 DDSTLNVRSGEEiarANGVDVEVVEEFIEAMSEQEQAIIDDRIEEIEDDTRRYSTED 284
                                       788899985443412444555666677777777799**************9998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1155  (0.0644208); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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 0.21s 00:00:00.72 Elapsed: 00:00:00.36
# Mc/sec: 2685.58
//
Query:       gi|336252401|ref|YP_004595508.1|  [L=244]
Description: hypothetical protein Halxa_0993 [Halopiger xanaduensis SH-6]
Scores for 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-06   25.0  12.3    1.1e-05   24.6  12.3    1.1  1  CALCOCO1         Calcium binding and coiled-coil domain (CALC
    6.6e-05   23.2  10.5      9e-05   22.8  10.5    1.2  1  ATG16            Autophagy protein 16 (ATG16)
    0.00037   20.6   9.6    0.00037   20.6   9.6    1.7  1  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
    0.00049   18.8   1.1    0.00059   18.6   1.1    1.1  1  FapA             Flagellar Assembly Protein A
    0.00089   18.8   5.8      0.079   12.4   1.1    2.1  2  DUF4618          Domain of unknown function (DUF4618)
     0.0011   19.5   4.1     0.0013   19.2   4.1    1.2  1  Fez1             Fez1
     0.0017   17.4   7.1     0.0024   16.9   7.1    1.1  1  IFT57            Intra-flagellar transport protein 57
     0.0031   17.9   5.6      0.073   13.5   1.1    2.3  2  Snapin_Pallidin  Snapin/Pallidin
     0.0033   17.6   1.3     0.0078   16.4   1.3    1.7  1  HALZ             Homeobox associated leucine zipper
     0.0056   16.9   1.2       0.54   10.5   0.1    2.3  2  DUF948           Bacterial protein of unknown function (DUF94
     0.0066   16.9   0.4      0.012   16.1   0.4    1.4  1  T3SSipB          Type III cell invasion protein SipB
     0.0086   16.1   5.6     0.0086   16.1   5.6    2.4  2  bZIP_1           bZIP transcription factor
     0.0087   15.0   3.9       0.01   14.8   3.9    1.1  1  DUF812           Protein of unknown function (DUF812)
  ------ inclusion threshold ------
      0.011   16.1  11.4      0.017   15.5  11.4    1.4  1  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
      0.012   15.5   6.9      0.016   15.1   6.9    1.2  1  Sigma70_ner      Sigma-70, non-essential region
      0.018   15.4  11.0        0.4   11.1   2.7    2.4  2  FlaC_arch        Flagella accessory protein C (FlaC)
      0.019   14.2  12.3      0.027   13.7  12.3    1.2  1  HAP1_N           HAP1 N-terminal conserved region
      0.021   14.8   0.8      0.033   14.2   0.8    1.2  1  DUF1043          Protein of unknown function (DUF1043)
      0.022   14.8   4.7      0.069   13.2   4.7    1.7  1  DUF1664          Protein of unknown function (DUF1664)
      0.025   13.7   6.8      0.032   13.4   6.8    1.2  1  Tmemb_cc2        Predicted transmembrane and coiled-coil 2 pr
      0.028   13.3   3.2      0.038   12.8   3.2    1.1  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
      0.037   14.1  14.5      0.069   13.2  14.5    1.4  1  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.041   12.8  12.6      0.059   12.2  12.6    1.1  1  Spc7             Spc7 kinetochore protein
      0.048   11.8  10.3      0.061   11.5  10.3    1.0  1  HOOK             HOOK protein
       0.05   13.8  15.3        0.1   12.8  15.3    1.5  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
      0.063   12.4   5.1        0.2   10.8   3.0    2.0  2  RmuC             RmuC family
      0.064   13.9  10.5       0.13   12.9   8.6    2.1  2  YabA             Initiation control protein YabA
      0.072   13.2   5.1       0.12   12.5   5.1    1.3  1  DUF4337          Domain of unknown function (DUF4337)
      0.075   11.0   4.7       0.42    8.5   4.4    1.7  2  Prominin         Prominin
      0.083   13.2   8.3       0.22   11.8   3.0    2.1  2  DUF5082          Domain of unknown function (DUF5082)
      0.098   12.8   0.8       0.23   11.6   0.8    1.7  1  MbeD_MobD        MbeD/MobD like
       0.11   11.4   0.3       0.12   11.3   0.3    1.0  1  LMBR1            LMBR1-like membrane protein
       0.12   11.7   4.1       0.17   11.2   4.1    1.2  1  DUF4407          Domain of unknown function (DUF4407)
       0.14    9.9   5.8       0.18    9.6   5.8    1.0  1  Nup88            Nuclear pore component
       0.15   11.3   5.2       0.23   10.7   5.2    1.2  1  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.16   12.7   1.1        2.7    8.7   0.2    2.3  2  Sas10_Utp3       Sas10/Utp3/C1D family
       0.17   11.3  10.4       0.24   10.8  10.4    1.1  1  Golgin_A5        Golgin subfamily A member 5
       0.17   12.3   4.0        3.5    8.1   0.6    2.4  2  LPP              Lipoprotein leucine-zipper
       0.18   12.3   9.0      0.058   13.8   5.3    2.0  2  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
        0.2   12.0   2.7        3.9    7.8   0.3    2.4  2  DUF3734          Patatin phospholipase
       0.23   10.5   4.0       0.36    9.9   4.0    1.3  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.31   11.8   6.0       0.69   10.6   5.9    1.6  1  DUF2203          Uncharacterized conserved protein (DUF2203)
       0.33   10.8   7.1       0.54   10.1   7.1    1.3  1  DUF724           Protein of unknown function (DUF724)
       0.33   10.5   7.6       0.69    9.5   7.6    1.5  1  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
       0.34   10.7   3.5       0.44   10.3   3.5    1.1  1  AAA_11           AAA domain
       0.36    8.7   3.1       0.44    8.4   3.1    1.0  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.43   10.5  16.4      0.049   13.6   8.5    2.0  2  Ax_dynein_light  Axonemal dynein light chain
       0.44    9.4   9.7       0.59    9.0   9.7    1.1  1  Kre28            Spindle pole body component
       0.45   10.7   6.2        1.7    8.8   6.3    1.8  1  Fib_alpha        Fibrinogen alpha/beta chain family
       0.47   10.3  12.1       0.16   11.8   4.6    2.4  2  DivIC            Septum formation initiator
       0.47    9.7   8.5       0.86    8.9   8.5    1.4  1  DUF3450          Protein of unknown function (DUF3450)
       0.63    8.2   6.3       0.83    7.8   2.2    1.9  2  COG6             Conserved oligomeric complex COG6
       0.64    9.6   7.4       0.67    9.5   2.7    2.1  2  Fzo_mitofusin    fzo-like conserved region
       0.66   10.0   7.4        1.1    9.3   7.4    1.4  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.73   10.6   7.0       0.39   11.5   2.1    2.6  2  Occludin_ELL     Occludin homology domain
       0.78    8.3   7.3       0.98    8.0   7.3    1.1  1  AAA_13           AAA domain
       0.84   10.3   7.0        9.3    6.9   6.7    2.2  1  BST2             Bone marrow stromal antigen 2
       0.87   10.3   7.0        4.5    8.0   5.2    2.5  2  KfrA_N           Plasmid replication region DNA-binding N-ter
       0.93    9.6   8.8        1.4    9.0   8.8    1.2  1  ADIP             Afadin- and alpha -actinin-Binding
          1    8.9   7.7        1.5    8.4   7.7    1.1  1  GCIP             Grap2 and cyclin-D-interacting
        1.2    9.7   6.7         66    4.1   6.7    2.6  1  YtxH             YtxH-like protein
        1.3    9.2   6.1          2    8.6   6.1    1.3  1  CREPT            Cell-cycle alteration and expression-elevate
        1.3    9.0   4.2        3.4    7.6   3.7    1.8  2  DUF4446          Protein of unknown function (DUF4446)
        1.6    8.3  10.9        2.2    7.8  10.9    1.1  1  TMCO5            TMCO5 family
        1.7    8.5   6.1        3.6    7.5   6.1    1.5  1  Cauli_AT         Aphid transmission protein
        1.8    7.8   4.1        2.4    7.3   4.1    1.2  1  TMPIT            TMPIT-like protein
        1.8    8.6   7.2        3.2    7.8   7.2    1.3  1  Laminin_II       Laminin Domain II
          2    8.4   5.9       0.82    9.7   2.8    1.8  2  FlxA             FlxA-like protein
        2.3    8.4  10.0        8.6    6.5   0.9    2.3  2  IFP_35_N         Interferon-induced 35 kDa protein (IFP 35) N
        2.4    8.5  13.1          9    6.6  13.1    1.8  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        2.9    8.4   8.9        3.2    8.3   2.5    2.5  3  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
        3.2    7.6  10.9        3.5    7.5   1.4    2.1  2  CCDC24           Coiled-coil domain-containing protein 24 fam
        3.5    7.9  10.8         11    6.4  10.8    1.7  1  OmpH             Outer membrane protein (OmpH-like)
        4.1    7.9  18.2        3.4    8.2  10.5    2.4  2  ZapB             Cell division protein ZapB
        4.1    7.8   9.4        2.9    8.2   3.0    2.2  2  BLOC1_2          Biogenesis of lysosome-related organelles co
        4.6    7.7   8.1        6.8    7.1   6.4    2.2  1  Syntaxin_2       Syntaxin-like protein
        4.7    7.3   8.5         23    5.1   8.3    2.0  1  COG2             COG (conserved oligomeric Golgi) complex com
        5.6    7.1   9.3        2.2    8.4   3.6    2.6  2  Swi5             Swi5


Domain annotation for each model (and alignments):
>> 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 !   24.6  12.3   4.6e-08   1.1e-05      31     112 ..     103     184 ..      88     189 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.6e-08
                          CALCOCO1  31 lLqnrLeeclreraeLlqaqeaanrqrekekeeykrdreeldrerkelesrveelkeelkesrekveeleekqkele 107
                                       l +  L+e + +++eL    ea++ + e e+ + k++  ++ +++kele++ +el+ee+ke+ +kv+  ee+ k+++
  gi|336252401|ref|YP_004595508.1| 103 LVRDLLDEIRDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKKTK 179
                                       556789****************************************************************9999998 PP

                          CALCOCO1 108 rlsee 112
                                       ++ ee
  gi|336252401|ref|YP_004595508.1| 180 KIAEE 184
                                       87765 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8  10.5   3.9e-07     9e-05      82     179 ..      82     180 ..      54     184 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.9e-07
                             ATG16  82 klaqlreelaelyksrgelaqrllelneelqkleeklkedeerla.eleaeraaletklkdreeelrekeklvqdlq 157
                                       + ++lree+ ++ ++ ++    +++l +e+++ +++lke  e+++ e+e+er +l+ +  + +++++e+e+ +++l+
  gi|336252401|ref|YP_004595508.1|  82 AHYALREEVLDATREMNDEMGLVRDLLDEIRDNQSELKESIEAVEdEAEDERGNLKSEFGQWRNRVKELEEENKELR 158
                                       5679************************************999963799**************************** PP

                             ATG16 158 DElsaLqlqlnqaEeklrklek 179
                                       +E+  L  ++n +Ee+++k++k
  gi|336252401|ref|YP_004595508.1| 159 EEVKELSDKVNANEERSKKTKK 180
                                       *******************997 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   9.6   1.6e-06   0.00037      59     117 ..     108     166 ..      86     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.6e-06
                        TPR_MLP1_2  59 lqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlne 117
                                       l ++r+  +elk+ i+ +++eae+ + +l+ +  +w ++ +ele+e +el++ +++l++
  gi|336252401|ref|YP_004595508.1| 108 LDEIRDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSD 166
                                       78999999************************************************986 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.1   2.6e-06   0.00059     333     419 ..      95     178 ..      52     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.6e-06
                              FapA 333 pelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeele 409
                                        e+++++  ++++l e+++++ +lk++i+ ++++++++    + k+++ + ++  ++l+ee +el+ee kel+++++
  gi|336252401|ref|YP_004595508.1|  95 REMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDE--RGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVN 169
                                       56666667788999999999999999999999954433..5788888888888888888888888888888888888 PP

                              FapA 410 sk.keeakikv 419
                                          +   + k+
  gi|336252401|ref|YP_004595508.1| 170 ANeE--RSKKT 178
                                       7731..22222 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.3    0.0028      0.64     172     227 ..      77     133 ..      65     136 .. 0.83
   2 !   12.4   1.1   0.00034     0.079     190     224 ..     135     169 ..     132     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0028
                           DUF4618 172 ktlkatqeaLlqktle.nqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeepr 227
                                       ++ +  + aL +++l+ +++++ e+  +r+  +e++ + +eLk+++e+ + +ae+ r
  gi|336252401|ref|YP_004595508.1|  77 QWSDLAHYALREEVLDaTREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDER 133
                                       555556677777777625789*******************************99987 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00034
                           DUF4618 190 vlkkeiekfrefieeleeeipeLkaeveqLqaqae 224
                                       +lk+e  ++r+ ++eleee +eL++ev++L+ +++
  gi|336252401|ref|YP_004595508.1| 135 NLKSEFGQWRNRVKELEEENKELREEVKELSDKVN 169
                                       688999************************98876 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   4.1   5.7e-06    0.0013      40     122 ..      94     180 ..      83     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.7e-06
                              Fez1  40 lrelrakleekeeeikeleesleektlelevcenelqrk....kseaellrekvekleeelkelreelselsleeee 112
                                       +re++ ++    + ++e++++ +e ++++e +e+e + +    kse    r++v++leee kelree++els + + 
  gi|336252401|ref|YP_004595508.1|  94 TREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDErgnlKSEFGQWRNRVKELEEENKELREEVKELSDKVNA 170
                                       578888888888888888999999999999999998887788899999999***************99998866555 PP

                              Fez1 113 aalesdeaka 122
                                       ++++s+++k+
  gi|336252401|ref|YP_004595508.1| 171 NEERSKKTKK 180
                                       4444443333 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   7.1   1.1e-05    0.0024     230     323 ..      91     184 ..      83     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-05
                             IFT57 230 kkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltre 306
                                        +  +++++++  ++  l+++ ++ s+  e ie+ E   + +  +l +e+ + +++++e++e+ k+l e+v+el+++
  gi|336252401|ref|YP_004595508.1|  91 LDATREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDK 167
                                       5667899********************************************************************** PP

                             IFT57 307 laeiseelekvkqemee 323
                                        +  +e+ +k+k+  ee
  gi|336252401|ref|YP_004595508.1| 168 VNANEERSKKTKKIAEE 184
                                       ***99999999987776 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.049        11      20      41 ..     106     127 ..      96     133 .. 0.84
   2 !   13.5   1.1   0.00032     0.073      11      51 ..     136     176 ..     129     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.049
                   Snapin_Pallidin  20 eklkelrqsQeeLleqldrlne 41 
                                       + l e+r++Q+eL+e+++   +
  gi|336252401|ref|YP_004595508.1| 106 DLLDEIRDNQSELKESIEAVED 127
                                       5689*************98665 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00032
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe 51 
                                       l+++  + ++++kel+++ +eL+e++++l++k++ +ee  +
  gi|336252401|ref|YP_004595508.1| 136 LKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSK 176
                                       677888999************************99888877 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.3   3.4e-05    0.0078       9      42 ..     135     168 ..     130     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.4e-05
                              HALZ   9 vLKasYdaLksdydsLkkenekLkaelqeLkekl 42 
                                        LK+ + + + ++  L++en++L+ e++eL++k+
  gi|336252401|ref|YP_004595508.1| 135 NLKSEFGQWRNRVKELEEENKELREEVKELSDKV 168
                                       6999999999*********************996 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 ?    5.1   0.1      0.12        27      38      79 ..      86     127 ..      76     131 .. 0.84
   2 !   10.5   0.1    0.0024      0.54      24      70 ..     136     181 ..     134     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.12
                            DUF948  38 lekqvdpilkevedllakvnelledvneklekvdplteavad 79 
                                       l+++v   ++e++d +  v++ll+++++   ++++ +eav+d
  gi|336252401|ref|YP_004595508.1|  86 LREEVLDATREMNDEMGLVRDLLDEIRDNQSELKESIEAVED 127
                                       567788888999999999999999999999999999999887 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0024
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekv 70 
                                       lk+ + + +++++ele++ +++ +ev++l +kvn+  e+ ++k++k+
  gi|336252401|ref|YP_004595508.1| 136 LKSEFGQWRNRVKELEEENKELREEVKELSDKVNA-NEERSKKTKKI 181
                                       778889999*************************9.44444444444 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 !   16.1   0.4   5.2e-05     0.012      35     127 ..      92     181 ..      78     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.2e-05
                                       HHTTTTT----STHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHH CS
                           T3SSipB  35 kaqqeaasklSdelqtalseakgatddleaaieka.dqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQa 110
                                        a++e++ ++   ++++l+e ++ + +l+++ie++ d+a+ +  +++    +  +r+keL   e e ++l+++++ +
  gi|336252401|ref|YP_004595508.1|  92 DATREMNDEMG-LVRDLLDEIRDNQSELKESIEAVeDEAEDERGNLKSEFGQWRNRVKEL---EEENKELREEVKEL 164
                                       56777777775.46899**************99864789999******************...999*********** PP

                                       H..HHHHHHHHHHHHHH CS
                           T3SSipB 111 gaaadalqadealqKkl 127
                                        ++ +a +   + +Kk+
  gi|336252401|ref|YP_004595508.1| 165 SDKVNANEERSKKTKKI 181
                                       *9999998888666664 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2       3.3   7.7e+02      42      50 ..     115     123 ..      94     142 .. 0.59
   2 !   16.1   5.6   3.8e-05    0.0086      30      57 ..     142     169 ..     129     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 3.3
                                       HHHHHHHHH CS
                            bZIP_1  42 NksLksele 50 
                                        ++Lk+ +e
  gi|336252401|ref|YP_004595508.1| 115 QSELKESIE 123
                                       233444444 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  30 eLerrvkaLekeNksLkseleelkkeve 57 
                                       +  +rvk+Le+eNk+L++e++el+++v+
  gi|336252401|ref|YP_004595508.1| 142 QWRNRVKELEEENKELREEVKELSDKVN 169
                                       6679********************9986 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   3.9   4.5e-05      0.01     312     379 ..     100     180 ..      14     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.5e-05
                            DUF812 312 e.............elakkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeene 375
                                       e             ++++ +e+ e ++ + e+e  +l++++ +++++++eleee k+l++++k++++++++++e  +
  gi|336252401|ref|YP_004595508.1| 100 EmglvrdlldeirdNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSK 176
                                       14444444443333233556777888888888888888888888888888888888888888888888888777777 PP

                            DUF812 376 elek 379
                                       +++k
  gi|336252401|ref|YP_004595508.1| 177 KTKK 180
                                       7665 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 ?   15.5  11.4   7.4e-05     0.017      11      79 ..     109     179 ..      88     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.4e-05
                       Uso1_p115_C  11 aslkdeneklkaelqslskalesleqk..eakkaaesqakeleaenkklekeleklraelkeekekekekq 79 
                                        +++d +++lk ++++ ++++e+++    +++ + +++ kele+enk+l++e+++l+ ++++ +e+ k+++
  gi|336252401|ref|YP_004595508.1| 109 DEIRDNQSELKESIEAVEDEAEDERGNlkSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKKTK 179
                                       5678888899999999999999999889999999**************************99999988664 PP

>> Sigma70_ner  Sigma-70, non-essential region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   6.9   6.8e-05     0.016       6      92 ..      88     180 ..      87     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.8e-05
                       Sigma70_ner   6 aellelydrveageirLrdiidGflDeeeeeeeeeeeedeeeeeee..eddd......eeeseseaadeeelkeeal 74 
                                       +e+l+   +++++   +rd++d + D+++e +e+ e+ ++e+e+e      +       +  ++++++++el+ee++
  gi|336252401|ref|YP_004595508.1|  88 EEVLDATREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERgnL--KsefgqwRNRVKELEEENKELREEVK 162
                                       589999999*************999955444444444444444443441..13457887788899999999999999 PP

                       Sigma70_ner  75 ekfeelreqyeklrkalk 92 
                                       e  +++ ++ e+ +k+ k
  gi|336252401|ref|YP_004595508.1| 163 ELSDKVNANEERSKKTKK 180
                                       999999888887777433 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   1.9     0.012       2.7       4      36 ..      96     128 ..      94     132 .. 0.88
   2 ?   11.1   2.7    0.0017       0.4       4      37 ..     135     168 ..     128     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.012
                         FlaC_arch   4 elEnklsklsteletvkkeneelsksveelken 36 
                                       e+  +++ +   l+ ++++++el++s+e ++++
  gi|336252401|ref|YP_004595508.1|  96 EMNDEMGLVRDLLDEIRDNQSELKESIEAVEDE 128
                                       7888888899999****************9986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0017
                         FlaC_arch   4 elEnklsklsteletvkkeneelsksveelkenV 37 
                                       +l +++++   +++ +++en+el+++v+el ++V
  gi|336252401|ref|YP_004595508.1| 135 NLKSEFGQWRNRVKELEEENKELREEVKELSDKV 168
                                       5777888888899999999999999999999998 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7  12.3   0.00012     0.027     111     200 ..      89     175 ..      68     184 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00012
                            HAP1_N 111 sareeiaqlrhelslkddLLqlysdseeeseeeseeseelreeesleslqklvqldlLqeklreLeeeNekLreeas 187
                                       ++ + + +++ e+ l  dLL  + d++ e +e+ e     ++e + e  +   ++   +++++eLeeeN++Lree +
  gi|336252401|ref|YP_004595508.1|  89 EVLDATREMNDEMGLVRDLLDEIRDNQSELKESIEAV---EDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVK 162
                                       3344444555555555555554444433333333333...33333333344445566789***************** PP

                            HAP1_N 188 qLktetdtlEekE 200
                                       +L+++ ++ Ee+ 
  gi|336252401|ref|YP_004595508.1| 163 ELSDKVNANEERS 175
                                       **88888888765 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.8   0.00014     0.033      23      95 ..     112     182 ..     102     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00014
                           DUF1043  23 lkkqkklekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlaksseeLlpeleeqelfqqkkle 95 
                                         +q++l++ +e+ ++e e+ + +l++ f q ++ +++l+e+ ++L + +++ s++   +++e++ +++kk++
  gi|336252401|ref|YP_004595508.1| 112 RDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKV--NANEERSKKTKKIA 182
                                       5789***************************************************99..55555555555554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   4.7    0.0003     0.069      36     119 ..      87     170 ..      77     184 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0003
                           DUF1664  36 krslsdavesvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkea 109
                                       +    da  ++  ++  v    +++++ + +L++ i+ v+++ ++      ++k+e  + r+ ++e++e+ ++++e 
  gi|336252401|ref|YP_004595508.1|  87 REEVLDATREMNDEMGLVRdllDEIRDNQSELKESIEAVEDEAEDE---RGNLKSEFGQWRNRVKELEEENKELREE 160
                                       5555566666666665554333566666666777777766555443...3344444444444444444444444444 PP

                           DUF1664 110 vegleskler 119
                                       v++l  k++ 
  gi|336252401|ref|YP_004595508.1| 161 VKELSDKVNA 170
                                       4444444433 PP

>> Tmemb_cc2  Predicted transmembrane and coiled-coil 2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   6.8   0.00014     0.032     211     297 ..      92     174 ..      54     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00014
                         Tmemb_cc2 211 saesesqeklekileelqeikeeqerleeelerlkeqlkkelkllkqaLqeeryryerLEeqlndlteLhqnEienL 287
                                        a++e + ++  + + l ei+++q++l+e++e+++++ + e   lk+ + + r r+++LEe   +l     +E+++L
  gi|336252401|ref|YP_004595508.1|  92 DATREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELR----EEVKEL 164
                                       45666777788888999*******************************************9876664....466666 PP

                         Tmemb_cc2 288 Kqelasmeek 297
                                        ++++  ee+
  gi|336252401|ref|YP_004595508.1| 165 SDKVNANEER 174
                                       6666666665 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.2   0.00017     0.038     173     253 ..     101     181 ..      90     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                        Fmp27_WPPW 173 kelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesseeeesk 249
                                       + l+++ l+e++++ ++l+e++e +e++ e e+ +lk+e+ + ++ +kel+e+ + l++ +++l+ + +++ee ++k
  gi|336252401|ref|YP_004595508.1| 101 MGLVRDLLDEIRDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKK 177
                                       567888899**********************999******************************9999977666555 PP

                        Fmp27_WPPW 250 skel 253
                                       +k+ 
  gi|336252401|ref|YP_004595508.1| 178 TKKI 181
                                       4444 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 ?   13.2  14.5    0.0003     0.069      49     126 ..      96     177 ..      84     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0003
                    CENP-F_leu_zip  49 tskaevetlkeeieelaeelreleldLvalr....sekeeLekelqkkqervseLeslnsslenlleekEqekvqmk 121
                                       +   e+  +++ ++e++ + +el+  ++a+      e+ +L+ e  ++++rv+eLe+ n +l++ ++e+ ++    +
  gi|336252401|ref|YP_004595508.1|  96 EMNDEMGLVRDLLDEIRDNQSELKESIEAVEdeaeDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANE 172
                                       455677778888999999******999999977778899****************************9977655555 PP

                    CENP-F_leu_zip 122 eeska 126
                                       e+sk+
  gi|336252401|ref|YP_004595508.1| 173 ERSKK 177
                                       55554 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  12.6   0.00026     0.059     158     241 ..      97     180 ..      85     187 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                              Spc7 158 LekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleelee 234
                                       +++++ ++ +ll+e++ +++el+e +e  +++ae+     k e  + r++++el++e +e+++e++el +++++ ee
  gi|336252401|ref|YP_004595508.1|  97 MNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEE 173
                                       45555556666666666666666666666665555444446666666666666666666666666666666665555 PP

                              Spc7 235 kieelke 241
                                       + +++k+
  gi|336252401|ref|YP_004595508.1| 174 RSKKTKK 180
                                       5555543 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  10.3   0.00026     0.061     485     576 ..      85     177 ..      64     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                              HOOK 485 elledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaed.ssllkkkleehleklkevqeelqkkkeql 560
                                       +l e+    + e+++e  l ++ + e++ +  el+++ ++ + +aed   +lk+++ +  +++ke++ee+++ +e +
  gi|336252401|ref|YP_004595508.1|  85 ALREEVLDATREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDeRGNLKSEFGQWRNRVKELEEENKELREEV 161
                                       456777778888999999999999999999999999999999999987899************************** PP

                              HOOK 561 eelepklssnkqkiee 576
                                        el+ k+++n ++ ++
  gi|336252401|ref|YP_004595508.1| 162 KELSDKVNANEERSKK 177
                                       *******999877655 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  15.3   0.00046       0.1      39     131 ..      88     180 ..      86     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00046
                     Jnk-SapK_ap_N  39 eslasrneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkakna 115
                                       e+++   +e + e+ ++r+ l++++ ++++ ke  ++ e+e e    ++++e  + +++v++leeen+el   +k++
  gi|336252401|ref|YP_004595508.1|  88 EEVLDATREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKEL 164
                                       56677788999999999999999999999999999999999999999999999999999999999999999999999 PP

                     Jnk-SapK_ap_N 116 adqlsrleekeaelkk 131
                                       +d++++ ee++++ kk
  gi|336252401|ref|YP_004595508.1| 165 SDKVNANEERSKKTKK 180
                                       9*******99999876 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2    0.0037      0.86     215     269 ..      74     128 ..      72     138 .. 0.87
   2 ?   10.8   3.0   0.00085       0.2       7      58 ..     115     166 ..     104     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0037
                              RmuC 215 vamlwrqeaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkk 269
                                       v+  w ++a     ee++++ +e+ d+++ + + l++++++ +++++s++ + ++
  gi|336252401|ref|YP_004595508.1|  74 VSDQWSDLAHYALREEVLDATREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDE 128
                                       67789999999999**********************************9986555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00085
                              RmuC   7 lkplkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLtk 58 
                                        ++lke++e++e++ e+e  + ++e+++ ++ +kel+e n++l++e ++L++
  gi|336252401|ref|YP_004595508.1| 115 QSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSD 166
                                       4567777777777777777777778888899999999999999999988876 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.6      0.74   1.7e+02       5      47 ..      89     131 ..      86     139 .. 0.55
   2 ?   12.9   8.6   0.00058      0.13      12      66 ..     128     182 ..     113     187 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.74
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLelenek 47 
                                       e++d+ +e++++++ + + l+e++++ +el e  +++e e e 
  gi|336252401|ref|YP_004595508.1|  89 EVLDATREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAED 131
                                       5555566666666666666666666666655555555555444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00058
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXX CS
                              YabA  12 eleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkel 66 
                                       e e++ ++l++e+++ +++++el een+eL+ e ++l ++++ +e+++k++kk  
  gi|336252401|ref|YP_004595508.1| 128 EAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKKTKKIA 182
                                       33455668999999***************************76666666655544 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   5.1    0.0005      0.12      48     117 ..     111     186 ..     105     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0005
                           DUF4337  48 ikehlaeleleqlelllkak.aeelaaavdkkiakykkkiarykkekkeikkkAkeleaerdeaneasdk....... 116
                                       i+ +  el +e++e+ +  + ae+ + + +++  ++++++++ ++e ke++++ kel +++++++e+s+k       
  gi|336252401|ref|YP_004595508.1| 111 IRDNQSEL-KESIEAVE--DeAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKKtkkiaee 184
                                       56666666.44444433..248999999***************************************9986666666 PP

                           DUF4337 117 .f 117
                                        +
  gi|336252401|ref|YP_004595508.1| 185 aW 186
                                       64 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2    0.0079       1.8     237     280 ..      90     133 ..      79     142 .. 0.60
   2 ?    8.5   4.4    0.0018      0.42     642     706 ..     109     173 ..      95     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0079
                          Prominin 237 aLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvk 280
                                       +L++ +++ +++  ++++L +++++++eL++s +  +d  ++ +
  gi|336252401|ref|YP_004595508.1|  90 VLDATREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDER 133
                                       55555666666666666666666666666666665555555555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0018
                          Prominin 642 ngkknlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensdlqesikkllaaveraen 706
                                        + ++ +++lk++ + +++  ++   +l+s+  + +++vk+l+een++l+e++k+l ++v++ e+
  gi|336252401|ref|YP_004595508.1| 109 DEIRDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEE 173
                                       344677899999999999999999999*********************************99886 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3      0.13        29      44      98 ..      75     130 ..      67     131 .. 0.89
   2 ?   11.8   3.0   0.00096      0.22       3      74 ..     131     210 ..     129     221 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.13
                           DUF5082  44 kqkkkklekplnssesWkGk.eennydgirsnlessyqtyvdkldelidaieeEIe 98 
                                       +++ ++l+++++ +e +  + e n++ g +++l ++++  +++l+e i a+e+E e
  gi|336252401|ref|YP_004595508.1|  75 SDQWSDLAHYALREEVLDATrEMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAE 130
                                       6677899999999999999989999***************************9965 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00096
                           DUF5082   3 tkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnsse.....sWkGkeennydgirs. 73 
                                        ++ +l+++ ++ r++++ lee  ++L+e  ++lsd+ ++ ++  kk +k++ +       sW  + +n  +g+r  
  gi|336252401|ref|YP_004595508.1| 131 DERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKKTKKIAEEAWawsvgSWIDNVRNPDNGQRLp 207
                                       68999***********************7777777665555555555554444444444578888888877777765 PP

                           DUF5082  74 ..n 74 
                                         +
  gi|336252401|ref|YP_004595508.1| 208 wmD 210
                                       555 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8     0.001      0.23       5      61 ..     115     171 ..     111     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.001
                         MbeD_MobD   5 ekqLLsAlEqLQqdYeqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesL 61 
                                       + +L   +E    + e  + + +s f ++++ ++  + en  L+e v++Ls  V+  
  gi|336252401|ref|YP_004595508.1| 115 QSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNAN 171
                                       56677777888888888888899*******99999999999*************975 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00052      0.12     199     303 ..      78     187 ..      41     215 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00052
                             LMBR1 199 deelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklks........... 264
                                        ++l ++      l++e  +a+re++d +  v+ l ++i++++   + l+e ++ v  e++++  +           
  gi|336252401|ref|YP_004595508.1|  78 WSDLAHYA-----LREEVLDATREMNDEMGLVRDLLDEIRDNQ---SELKESIEAVEDEAEDERGNlksefgqwrnr 146
                                       45555554.....455555588888888888888888888888...4555555555555555544455577777777 PP

                             LMBR1 265 ..nenkteeslaklekqlikalqkrertekqwkrllekale 303
                                         + ++  ++l ++ k+l  +++ +e+++k+ k++ e+a++
  gi|336252401|ref|YP_004595508.1| 147 vkELEEENKELREEVKELSDKVNANEERSKKTKKIAEEAWA 187
                                       76666677788888888888888888888888888888865 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.1   0.00072      0.17     133     220 ..      95     182 ..      65     188 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00072
                           DUF4407 133 aelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakldat 209
                                        e++++   +++l  ei+  +++l++  +++++e++ ++g+  +       + ke +++++++++e++el++k++a+
  gi|336252401|ref|YP_004595508.1|  95 REMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNAN 171
                                       44445555555555555555555555555555555555555544444444556666666666666666666666666 PP

                           DUF4407 210 arlaalraela 220
                                       ++++++ +++a
  gi|336252401|ref|YP_004595508.1| 172 EERSKKTKKIA 182
                                       66655555554 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.8   0.00079      0.18     591     669 ..     104     182 ..      84     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00079
                             Nup88 591 lAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelekikeklkslknalkqvkkkldkqrkqiakske 667
                                       + + ++ei+d+Q +l + +++v  +++++  +l +   + ++ +++++e+ k+l +++k++  k++  +++ +k+k+
  gi|336252401|ref|YP_004595508.1| 104 VRDLLDEIRDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKKTKK 180
                                       556789***************************99999*******************************99999988 PP

                             Nup88 668 ee 669
                                       ++
  gi|336252401|ref|YP_004595508.1| 181 IA 182
                                       74 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 ?   10.7   5.2   0.00099      0.23      38     111 ..     109     183 ..      93     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00099
                              HemX  38 aelqqqlaaleqqlaqveaeke.qkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsgaerkdWlLae 111
                                       +e++++ ++l+++ ++ve e+e +  +l++++ q  +++++le+e+++l ++++el++++++ + +++k+ ++ae
  gi|336252401|ref|YP_004595508.1| 109 DEIRDNQSELKESIEAVEDEAEdERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKKTKKIAE 183
                                       5556666666666666666555156689999*******************************9999999999998 PP

>> Sas10_Utp3  Sas10/Utp3/C1D family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1         1   2.4e+02       1      27 [.     108     135 ..     108     146 .. 0.76
   2 ?    8.7   0.2     0.012       2.7       2      28 ..     148     177 ..     147     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 1
                        Sas10_Utp3   1 leslsksldelqeslepllskakaee.k 27 
                                       l+++ ++ +el+es+e + ++a++e  +
  gi|336252401|ref|YP_004595508.1| 108 LDEIRDNQSELKESIEAVEDEAEDERgN 135
                                       6788899999999999999977766642 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.012
                        Sas10_Utp3   2 eslsksldelqeslepllskakaee...kk 28 
                                       ++l+++ +el+e +++l++k++a+e   kk
  gi|336252401|ref|YP_004595508.1| 148 KELEEENKELREEVKELSDKVNANEersKK 177
                                       899*****************8887765432 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  10.4     0.001      0.24      45     137 ..      90     182 ..      78     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.001
                         Golgin_A5  45 lsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlke 121
                                       + ++  e+++e  l+r+ l + + + ++l+  ++ +e++++ e  +l+ +  + +++++e +++++e+++e+++l++
  gi|336252401|ref|YP_004595508.1|  90 VLDATREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSD 166
                                       45566788899999999999999999999999999999999999999999999999999999999999999999999 PP

                         Golgin_A5 122 elryleeelvrskatl 137
                                       +++++ee  +++k+  
  gi|336252401|ref|YP_004595508.1| 167 KVNANEERSKKTKKIA 182
                                       9999999988888755 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2      0.13        30      16      38 ..     108     130 ..      94     137 .. 0.80
   2 ?    8.1   0.6     0.015       3.5       2      37 ..     147     182 ..     145     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.13
                               LPP  16 vdqlssdvnsakaaaqaakeEAa 38 
                                        d++ ++++++k+ ++a+ +EA+
  gi|336252401|ref|YP_004595508.1| 108 LDEIRDNQSELKESIEAVEDEAE 130
                                       68889999999999999999995 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.015
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaakeEA 37 
                                       ++eL ++ ++L ++v++ls++vn+ ++ ++++k+ A
  gi|336252401|ref|YP_004595508.1| 147 VKELEEENKELREEVKELSDKVNANEERSKKTKKIA 182
                                       677777778888888888888888887777776544 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       9.4   2.2e+03      40      64 ..     108     132 ..     103     135 .. 0.70
   2 ?   13.8   5.3   0.00025     0.058      28      67 ..     136     174 ..     129     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 9.4
                       Fungal_TACC  40 ldklelenkslkqeieqLkkqleae 64 
                                       ld+++ ++++lk+ ie ++++ e e
  gi|336252401|ref|YP_004595508.1| 108 LDEIRDNQSELKESIEAVEDEAEDE 132
                                       6777777778888888777766655 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00025
                       Fungal_TACC  28 lkkgyeakyqkkldklelenkslkqeieqLkkqleaerkE 67 
                                       lk ++  ++++++++le+enk+l++e+++L+++++a+++ 
  gi|336252401|ref|YP_004595508.1| 136 LKSEF-GQWRNRVKELEEENKELREEVKELSDKVNANEER 174
                                       88999.89**************************976543 PP

>> DUF3734  Patatin phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.28        65      10      52 ..      90     133 ..      83     137 .. 0.86
   2 ?    7.8   0.3     0.017       3.9      13      48 ..     150     185 ..     142     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.28
                           DUF3734  10 ntdalkriqrlrrairelleklpeelre.dpevkeleelgcekr 52 
                                       ++da +++++   ++r+ll+++ +++ e +++++++e+ ++++r
  gi|336252401|ref|YP_004595508.1|  90 VLDATREMNDEMGLVRDLLDEIRDNQSElKESIEAVEDEAEDER 133
                                       67888999999999*********999999999999999888776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.017
                           DUF3734  13 alkriqrlrrairelleklpeelredpevkeleelg 48 
                                        +++ ++lr+ ++el++k+ ++++++++ k+++e +
  gi|336252401|ref|YP_004595508.1| 150 LEEENKELREEVKELSDKVNANEERSKKTKKIAEEA 185
                                       4678899************99999999988887755 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 ?    9.9   4.0    0.0016      0.36      61     132 ..     100     175 ..      67     188 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0016
                             Atg14  61 kiknkkakleelksliadlrerlqelkdkls....qlkkeieekkkklaklsdklkkRrsdleslqneleerrkkq 132
                                       +    ++ l+e++  +++l+e ++ ++d  +    +lk+e  + ++++++l +++k+ r++ + l+++++++++++
  gi|336252401|ref|YP_004595508.1| 100 EMGLVRDLLDEIRDNQSELKESIEAVEDEAEdergNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERS 175
                                       4444455555555555555555544443332111155666666666666666666666666666666666555543 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   5.9     0.003      0.69       7      73 ..      96     172 ..      93     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.003
                           DUF2203   7 eAnalLpllkelleelralrkeleeleeeleeakaeaekse..........aaeleaeleeleaeieelveeieelG 73 
                                       e n+ + l+++ll+e+r+ ++el+e  e++e++ ++++ +            +ele+e +el++e++el +++++  
  gi|336252401|ref|YP_004595508.1|  96 EMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERGNLksefgqwrnrVKELEEENKELREEVKELSDKVNANE 172
                                       67888999*****************9998888777654333678888888878888888888888888888887765 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   7.1    0.0024      0.54      99     169 ..     110     177 ..      99     188 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0024
                            DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaek 169
                                       +++d+q++l+e ++++e + e+   e+ +l++e+ +  ++++ele++++ l+e+ ++ + ++ + +   +k
  gi|336252401|ref|YP_004595508.1| 110 EIRDNQSELKESIEAVEDEAED---ERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKK 177
                                       5888888888888888877665...5558899*******************94444444443333333333 PP

>> HAUS6_N  HAUS augmin-like complex subunit 6 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   7.6     0.003      0.69     137     213 ..     110     183 ..      79     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.003
                           HAUS6_N 137 aaskkaqdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelkaekeaakkekkeas 213
                                        + +++++l+++++a++ +++    +++++     ++++++++le++ +elr+e +el+++++a++e++kk+kk a+
  gi|336252401|ref|YP_004595508.1| 110 EIRDNQSELKESIEAVEDEAEDERGNLKSE---FGQWRNRVKELEEENKELREEVKELSDKVNANEERSKKTKKIAE 183
                                       345566677777777777777777777777...8****************************988776666665443 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.5    0.0019      0.44     115     186 ..      97     180 ..      53     188 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0019
                            AAA_11 115 krlekeekaqlakeiskeleklakelrafeeeeek............eklkkskekskskleqerrklkkerkelsk 179
                                        + e+    +l +ei++++ +l+++++a e+e+e+            +++ k+ e+++++l++e ++l+++++ +++
  gi|336252401|ref|YP_004595508.1|  97 MNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDergnlksefgqwRNRVKELEEENKELREEVKELSDKVNANEE 173
                                       33333335567777888888888888877777776667776566555555555555555555555555555555555 PP

                            AAA_11 180 eleeaee 186
                                       +++++++
  gi|336252401|ref|YP_004595508.1| 174 RSKKTKK 180
                                       5554444 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 ?    8.4   3.1    0.0019      0.44      34     116 ..      96     178 ..      84     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0019
                        V_ATPase_I  34 emerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavle 110
                                       em+ ++ ++++ +++ ++++ + +e+ e  e++ e+e  +l++e+ +  +++kel+e++++l++e++el ++ +  e
  gi|336252401|ref|YP_004595508.1|  96 EMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANE 172
                                       55555556666666655556565666778888888888888888888888888888888888888888887766665 PP

                        V_ATPase_I 111 kakefl 116
                                       + ++  
  gi|336252401|ref|YP_004595508.1| 173 ERSKKT 178
                                       555444 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 ?    1.8   1.2      0.86     2e+02     121     161 ..      94     134 ..      79     142 .. 0.54
   2 ?   13.6   8.5   0.00021     0.049     123     166 ..     142     185 ..     133     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.86
                   Ax_dynein_light 121 kselekkikeLeeekeelekqvaelkaklealekrekerrq 161
                                       + e+++++  +++  +e++++ +elk+ +ea+e +++++r 
  gi|336252401|ref|YP_004595508.1|  94 TREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERG 134
                                       44555554444444455555555666666666666655554 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00021
                   Ax_dynein_light 123 elekkikeLeeekeelekqvaelkaklealekrekerrqeeekk 166
                                       + ++++keLeee++el+++v+el  k++a e+r+k+ +++ e+ 
  gi|336252401|ref|YP_004595508.1| 142 QWRNRVKELEEENKELREEVKELSDKVNANEERSKKTKKIAEEA 185
                                       56789*********************************999876 PP

>> Kre28  Spindle pole body component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   9.7    0.0026      0.59     165     257 ..      86     183 ..      73     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0026
                             Kre28 165 inelyLettneide....CwelLnEleelrdrrnkvekqtseekdteddlveetYeeWks.lqkslqekeelkeeld 236
                                       ++e+ L++t e+++      +lL+E+++ +++ ++  + + +e++ e + +   + +W++ +++  +e++el+ee +
  gi|336252401|ref|YP_004595508.1|  86 LREEVLDATREMNDemglVRDLLDEIRDNQSELKESIEAVEDEAEDERGNLKSEFGQWRNrVKELEEENKELREEVK 162
                                       67788888877765122245677777777765555556666777779999********8724444445566777777 PP

                             Kre28 237 rLkkekkeleevkkksknkee 257
                                       +L ++++  ee +kk+k+ +e
  gi|336252401|ref|YP_004595508.1| 163 ELSDKVNANEERSKKTKKIAE 183
                                       777777777766666655444 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 ?    8.8   6.3    0.0073       1.7      26     107 ..      90     178 ..      85     185 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0073
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHCCCHHHH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.......dnvikksskeleeeilrlke 95 
                                       +l+  +++++++  +++ l+ei+++++e +e +++++d  +++  + k +        + +++ +kel+ee+ +l +
  gi|336252401|ref|YP_004595508.1|  90 VLDATREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERGNLKSEfgqwrnrVKELEEENKELREEVKELSD 166
                                       56667888888888888888999888888888888888877665555543233411233444556678888888888 PP

                                       HHHCCHHHHHHH CS
                         Fib_alpha  96 tidaqesnirvL 107
                                       +++a+e++ ++ 
  gi|336252401|ref|YP_004595508.1| 167 KVNANEERSKKT 178
                                       888887765555 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.8      0.37        86      19      54 ..      94     128 ..      81     134 .. 0.75
   2 ?   11.8   4.6    0.0007      0.16      22      62 ..     136     176 ..     132     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                             DivIC  19 ykqlkqeiaalqaelaklkaeneeLeaevkdLksde 54 
                                        ++++ e+    + l+++++ + eL++ ++  + de
  gi|336252401|ref|YP_004595508.1|  94 TREMNDEMGLVRDLLDEIRDNQSELKESIEAVE-DE 128
                                       566777777777788888888888888888873.44 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0007
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXX CS
                             DivIC  22 lkqeiaalqaelaklkaeneeLeaevkdLksdedyieerAR 62 
                                       lk+e  +  + +++l +en+eL +evk+L++  ++ eer +
  gi|336252401|ref|YP_004595508.1| 136 LKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSK 176
                                       67788888899999999999999999999777777776665 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   8.5    0.0038      0.86      30      97 ..     117     184 ..      93     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0038
                           DUF3450  30 aaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeiere 97 
                                       + ++++++  d+ +de+ +l++e+ + ++++++le +n++l++ v+++  +++  ee+ ++ ++i++e
  gi|336252401|ref|YP_004595508.1| 117 ELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKKTKKIAEE 184
                                       3345556666788889999*****************************************99999876 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.2    0.0036      0.83      24      92 ..      86     158 ..      83     162 .. 0.83
   2 ?    7.1   1.7    0.0059       1.4      24      78 ..     125     179 ..     123     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0036
                              COG6  24 iekellkineefleefqpvaeqLkriesdveklnelcdemkkklssa....keetsdlleeaeeLkeekkkle 92 
                                       + +e+l++++e+ +e++ v++ L++i+++ ++l+e+++ ++++ +      k+e ++  + ++eL+ee+k+l+
  gi|336252401|ref|YP_004595508.1|  86 LREEVLDATREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDErgnlKSEFGQWRNRVKELEEENKELR 158
                                       6789************************************999987622224566888888888888888876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0059
                              COG6  24 iekellkineefleefqpvaeqLkriesdveklnelcdemkkklssakeetsdll 78 
                                       +e e+ ++ ++  +ef++ ++++k++e++ ++l e ++e+++k+++++e++++  
  gi|336252401|ref|YP_004595508.1| 125 VEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKKTK 179
                                       677777888888899*****************************99999887654 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.65   1.5e+02     106     139 ..      86     119 ..      73     131 .. 0.59
   2 ?    9.5   2.7    0.0029      0.67      98     145 ..     135     185 ..     132     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.65
                     Fzo_mitofusin 106 lcqqvdetekeleeeikelekeiekleevqkkak 139
                                       l+++v  +++e+++e+  ++  ++++ + q+++k
  gi|336252401|ref|YP_004595508.1|  86 LREEVLDATREMNDEMGLVRDLLDEIRDNQSELK 119
                                       5555555666666665555555555555554443 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0029
                     Fzo_mitofusin  98 elsstfarlcqqvde...tekeleeeikelekeiekleevqkkakllrnka 145
                                       +l+s f +++++v+e    +kel+ee+kel+ ++++ ee +kk k++ ++a
  gi|336252401|ref|YP_004595508.1| 135 NLKSEFGQWRNRVKEleeENKELREEVKELSDKVNANEERSKKTKKIAEEA 185
                                       5788899999888651115679**********************9998877 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 ?    9.3   7.4    0.0048       1.1      80     135 ..     114     170 ..      70     187 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0048
                           UPF0242  80 ldeglktkeealeel.qeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfee 135
                                       ++ +lk+  ea+e+  ++e  +Lk e+ +  + +++l+een++L+e+ ++ +  +++
  gi|336252401|ref|YP_004595508.1| 114 NQSELKESIEAVEDEaEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNA 170
                                       223344444455543134455677777777777777777777777776665553332 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3      0.24        55      19      87 ..      79     152 ..      67     153 .. 0.66
   2 ?   11.5   2.1    0.0017      0.39       7      61 ..     130     184 ..     125     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.24
                      Occludin_ELL  19 keYkeYkelhael...eevskkfseLerelkelkegskeykkieeeilqeykklkk..dpeyqekkkrceyLke 87 
                                       ++ ++Y   ++ l   +e+++++  +++ l+e +++++e k+ +e + +e ++ +   ++e+ + ++r+++L+e
  gi|336252401|ref|YP_004595508.1|  79 SDLAHYALREEVLdatREMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERGnlKSEFGQWRNRVKELEE 152
                                       55555543333331114455555556678888888888999999998888887765578899999999999876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0017
                      Occludin_ELL   7 aeqrerYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieee 61 
                                       +++r + k eF +  ++ kel++e +e++++++eL++++++ +e+sk++kki+ee
  gi|336252401|ref|YP_004595508.1| 130 EDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKKTKKIAEE 184
                                       567888899999999999*********************************9987 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   7.3    0.0043      0.98     384     462 ..     107     184 ..      75     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0043
                            AAA_13 384 kvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaa 460
                                         +++ ++++e+k+++e+ +  e+e+e  ++k+++ +  + +++le+e ke  +e+k+l +++++ e++ ++ k++a
  gi|336252401|ref|YP_004595508.1| 107 LLDEIRDNQSELKESIEA-VEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKKTKKIA 182
                                       456778888888888888.4556778878888888888888888888888888888888888888888888888888 PP

                            AAA_13 461 ee 462
                                       ee
  gi|336252401|ref|YP_004595508.1| 183 EE 184
                                       76 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.7      0.04       9.3      53      90 ..     135     169 ..      89     172 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                              BST2  53 sLekekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90 
                                        L+   ++  +++++v+el++e+k+L +++++ + +v+
  gi|336252401|ref|YP_004595508.1| 135 NLK---SEFGQWRNRVKELEEENKELREEVKELSDKVN 169
                                       444...444458999****************9998875 PP

>> KfrA_N  Plasmid replication region DNA-binding N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       2.3   5.2e+02       9      45 ..       9      43 ..       5      57 .. 0.83
   2 ?    8.0   5.2      0.02       4.5      59     113 ..     107     166 ..      74     173 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 2.3
                            KfrA_N  9 adallaeGerpTveavrerlGgGspntisrvlkewea 45
                                        al+++G r++   + e + gG p  i++ ++ew a
  gi|336252401|ref|YP_004595508.1|  9 LTALFKRG-RCSTTELKEMT-GGKPRLIKHRIDEWLA 43
                                      56788888.77888888888.9*************77 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.02
                            KfrA_N  59 lPealaeal..laalwqaaleeaee...elaaaraelqaaraaleaeraeaearveelea 113
                                       l +++ +    l++  +a  +eae+    l+++  +++ + ++le+e +e++++v+el +
  gi|336252401|ref|YP_004595508.1| 107 LLDEIRDNQseLKESIEAVEDEAEDergNLKSEFGQWRNRVKELEEENKELREEVKELSD 166
                                       334444444566777777777777777778888888888888888888888888888765 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   8.8    0.0062       1.4      33     115 ..      96     179 ..      82     185 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0062
                              ADIP  33 niaaiinviysLlqardrdl.eqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktle 108
                                       +++  + ++ +Ll   + ++ e +es ++   + e e  +l+s++ +  +++++le e++ + ++ ++l  k+ + e
  gi|336252401|ref|YP_004595508.1|  96 EMNDEMGLVRDLLDEIRDNQsELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANE 172
                                       56666778889998877776145566666666667777788888888888888888888888888888888887777 PP

                              ADIP 109 qklknek 115
                                       +  k++k
  gi|336252401|ref|YP_004595508.1| 173 ERSKKTK 179
                                       7777665 PP

>> GCIP  Grap2 and cyclin-D-interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   7.7    0.0064       1.5     122     197 ..      95     169 ..      90     188 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0064
                                       HHHHHHHHHHHHHHHHHHHHHHH....S-------------.........-----TTS--HHHHHHHHHHHHHHHHH CS
                              GCIP 122 raieevlglvkDaleEmkelleeedeeedededdldddede.........ergnqdrklseeekevikavlkllkat 189
                                       r++   +glv D l+E+ + ++e    ++++e ++d+ ede         +  n+ ++l+ee ke+ ++v++     
  gi|336252401|ref|YP_004595508.1|  95 REMNDEMGLVRDLLDEIRDNQSE---LKESIEAVEDEAEDErgnlksefgQWRNRVKELEEENKELREEVKE----- 163
                                       78899999**********99999...5566666666666665534444443344444555555555555444..... PP

                                       HHHHHHHH CS
                              GCIP 190 vallkkls 197
                                         l +k++
  gi|336252401|ref|YP_004595508.1| 164 --LSDKVN 169
                                       ..444443 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   6.7      0.29        66      42      71 ..     130     169 ..      79     186 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.29
                              YtxH  42 kelleeakeka.................kekaedlkekvkekadelk 71 
                                       ++                          +e+ ++l+e+vke +d++ 
  gi|336252401|ref|YP_004595508.1| 130 EDE-------RgnlksefgqwrnrvkelEEENKELREEVKELSDKVN 169
                                       222.......2333333355555545556666666666666666654 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.1    0.0085         2      46     115 ..     104     174 ..      84     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0085
                             CREPT  46 aekllkqveealellaeYnkrLeaele.eRkklakmledfleaqkellakaeekleelkeklekvksvrke 115
                                        + ll+++++ ++ l+e  +  e+e e eR +l++   ++ + +kel ++++e  ee+ke  +kv+++++ 
  gi|336252401|ref|YP_004595508.1| 104 VRDLLDEIRDNQSELKESIEAVEDEAEdERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEER 174
                                       467999*******************973699**********************************998765 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1       2.1   4.9e+02      51      75 ..     105     129 ..      84     133 .. 0.67
   2 ?    7.6   3.7     0.015       3.4      26      78 ..     117     171 ..     112     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 2.1
                           DUF4446  51 leeveelkeeseelekeieeleekl 75 
                                        + ++e++++++el+++ie++e++ 
  gi|336252401|ref|YP_004595508.1| 105 RDLLDEIRDNQSELKESIEAVEDEA 129
                                       4556777777777777777777665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.015
                           DUF4446  26 klkkkykklmkgk..dgksleellkekleeveelkeeseelekeieeleeklkks 78 
                                       +lk++++++  ++  ++ +l++ + +  ++v+el+ee++el++e++el++k++++
  gi|336252401|ref|YP_004595508.1| 117 ELKESIEAVEDEAedERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNAN 171
                                       5666666666643237889*******************************99876 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  10.9    0.0098       2.2      33     106 ..     104     180 ..      86     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0098
                             TMCO5  33 iqslereitkldsllereedeeenfsenekedalkeLele.......taklekkneiLlkevveLqkkisrkeskqd 102
                                       +++l++ei      ++ e +e  + +e e ed+  +L+ e          le++n+ L +ev eL  k++ +e++++
  gi|336252401|ref|YP_004595508.1| 104 VRDLLDEIRD----NQSELKESIEAVEDEAEDERGNLKSEfgqwrnrVKELEEENKELREEVKELSDKVNANEERSK 176
                                       3444444444....4445566777889999999999*********99999********************9997655 PP

                             TMCO5 103 dlek 106
                                       +++k
  gi|336252401|ref|YP_004595508.1| 177 KTKK 180
                                       5555 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   6.1     0.016       3.6      65     149 ..      98     183 ..      89     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.016
                          Cauli_AT  65 lsylGLekDesealsksksPfgsvfkklkkifkegged.kekktklletLkeaqnrikkleeetkklaekivtekll 140
                                       +  +GL +D  +++  ++s +++  + ++   ++  ++ k++  +  + +ke ++  k+l ee+k+l++k+++++  
  gi|336252401|ref|YP_004595508.1|  98 NDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERGNlKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEER 174
                                       55578888888888888887776666666554444333144555566778888889999999999999999999888 PP

                          Cauli_AT 141 keevkdlde 149
                                        ++ k++ e
  gi|336252401|ref|YP_004595508.1| 175 SKKTKKIAE 183
                                       888888766 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.1     0.011       2.4       5      73 ..     116     183 ..      87     190 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelke 73 
                                       +el+++++++e++a   + +  +l++   ++++++k+ +++ kel++++k+l+ +v+  ee+++++++++e
  gi|336252401|ref|YP_004595508.1| 116 SELKESIEAVEDEA---EDERGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNanEERSKKTKKIAE 183
                                       23333333333333...333344444445555555555555555555555555543332444444444444 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   7.2     0.014       3.2       6      93 ..      95     179 ..      88     185 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       +e n+ +  v + l ++  n +++ke+++ +++++e       +++    + r+ vk+Le++  +L + +kel  + 
  gi|336252401|ref|YP_004595508.1|  95 REMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAEDERG---NLKSEFGQWRNRVKELEEENKELREEVKELSDKV 168
                                       6778888888888999999999999999999888555444...4444555566777777777777777777777766 PP

                                       HH...HHHHHH CS
                        Laminin_II  83 eassslsdnis 93 
                                       +a++  s++ +
  gi|336252401|ref|YP_004595508.1| 169 NANEERSKKTK 179
                                       66555555544 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       8.1   1.9e+03      50      61 ..     114     125 ..      90     143 .. 0.61
   2 ?    9.7   2.8    0.0036      0.82      16      55 ..     144     182 ..     136     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 8.1
                              FlxA  50 qqqliqaQIqql 61 
                                        q ++++ I+++
  gi|336252401|ref|YP_004595508.1| 114 NQSELKESIEAV 125
                                       222222222222 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0036
                              FlxA  16 asqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliq 55 
                                        +++++L+++ k+l +++kels++    +ee++k+ + i 
  gi|336252401|ref|YP_004595508.1| 144 RNRVKELEEENKELREEVKELSDK-VNANEERSKKTKKIA 182
                                       6789*******************9.777888999988886 PP

>> IFP_35_N  Interferon-induced 35 kDa protein (IFP 35) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.9     0.037       8.6       1      23 [.     107     129 ..     107     139 .. 0.88
   2 ?    6.3   2.6     0.045        10       2      21 ..     147     166 ..     146     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.037
                          IFP_35_N   1 liaeitkeniqLkeeiqkLeaEL 23 
                                       l++ei +++++Lke i  +e E 
  gi|336252401|ref|YP_004595508.1| 107 LLDEIRDNQSELKESIEAVEDEA 129
                                       799**************999885 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.045
                          IFP_35_N   2 iaeitkeniqLkeeiqkLea 21 
                                       ++e+++en++L ee++ L  
  gi|336252401|ref|YP_004595508.1| 147 VKELEEENKELREEVKELSD 166
                                       789*************6644 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 ?    6.6  13.1     0.039         9      32     100 ..      95     164 ..      85     187 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.039
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  32 leldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaelekl 100
                                        e+++++  ++  l+e++ ++ el ++I+   ++  +++  l+ e  +  +++k+le+e kel++e+++l
  gi|336252401|ref|YP_004595508.1|  95 REMNDEMGLVRDLLDEIRDNQSELKESIEAVEDEAeDERGNLKSEFGQWRNRVKELEEENKELREEVKEL 164
                                       4444444444444444444444444444444444433444444444444444444444444444444433 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 ?    1.8   0.5       1.5   3.5e+02       7      24 ..     112     129 ..      84     137 .. 0.74
   2 ?    6.5   6.4      0.05        12       7      66 ..     116     170 ..     108     174 .. 0.83
   3 ?    8.3   2.5     0.014       3.2      16      49 ..     146     179 ..     142     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 1.5
                       Cep57_MT_bd   7 qspkeaLaevlkeLedEf 24 
                                        + + +L+e +++ edE 
  gi|336252401|ref|YP_004595508.1| 112 RDNQSELKESIEAVEDEA 129
                                       445666666666666665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.05
                       Cep57_MT_bd   7 qspkeaLaevlkeLedEfehlklelqelaaqynaldpslgkrkRkdLaeeleelvkrlEa 66 
                                       ++ ke+ + v  e edE + lk e+ + + + ++l+     ++ k+L ee++el ++++a
  gi|336252401|ref|YP_004595508.1| 116 SELKESIEAVEDEAEDERGNLKSEFGQWRNRVKELE-----EENKELREEVKELSDKVNA 170
                                       5567777788888999999****************9.....8889999999999888765 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.014
                       Cep57_MT_bd  16 vlkeLedEfehlklelqelaaqynaldpslgkrk 49 
                                        +keLe+E ++l+ e +el+++ na + ++ k k
  gi|336252401|ref|YP_004595508.1| 146 RVKELEEENKELREEVKELSDKVNANEERSKKTK 179
                                       69***********************995555444 PP

>> CCDC24  Coiled-coil domain-containing protein 24 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.4     0.015       3.5       6      43 ..      84     121 ..      80     138 .. 0.87
   2 ?    5.1   2.5     0.082        19     166     195 ..     150     179 ..     138     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.015
                            CCDC24   6 raLGeslvdesleLraEvdaLleilqdvreesdqlaes 43 
                                        aL e+++d + e+  E++  +++l ++r+++++l+es
  gi|336252401|ref|YP_004595508.1|  84 YALREEVLDATREMNDEMGLVRDLLDEIRDNQSELKES 121
                                       6899*************************777777654 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.082
                            CCDC24 166 LeeEceaLerdieyLqecleeeadlqkrvs 195
                                       LeeE + L+++++ L   ++ ++++ k+++
  gi|336252401|ref|YP_004595508.1| 150 LEEENKELREEVKELSDKVNANEERSKKTK 179
                                       899999999999999999999999888887 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  10.8     0.048        11      34     103 ..     110     179 ..      88     187 .. 0.40

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.048
                                       HHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHH CS
                              OmpH  34 eleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkqqellkpil..dkinkaik 103
                                       e+++ + el++ +e+ +++a+++ + + + e+ + ++++++ ++++++el+++ +el +++   ++  k +k
  gi|336252401|ref|YP_004595508.1| 110 EIRDNQSELKESIEAVEDEAEDE-RGNLKSEFGQWRNRVKE-LEEENKELREEVKELSDKVNanEERSKKTK 179
                                       44444444444444444444442.33333332222222222.222223333333222222111122222222 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.9     0.044        10      25      65 ..     106     150 ..      90     150 .. 0.77
   2 ?    8.2  10.5     0.015       3.4      24      56 ..     144     175 ..     135     190 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.044
                              ZapB  25 meieeLkeeneelkeenrele....eeneqlkeereawqerlkkL 65 
                                         ++e +  ++elke ++++e     e  +lk e  +w++r+k L
  gi|336252401|ref|YP_004595508.1| 106 DLLDEIRDNQSELKESIEAVEdeaeDERGNLKSEFGQWRNRVKEL 150
                                       556788888899999999999555556666779999*****9986 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.015
                              ZapB  24 qmeieeLkeeneelkeenreleeeneqlkeere 56 
                                       +++++eL+een+el ee +el+ ++++  eer+
  gi|336252401|ref|YP_004595508.1| 144 RNRVKELEEENKELREEVKELSDKVNAN-EERS 175
                                       4555555555555555555555333332.2222 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 ?    3.2   0.5      0.49   1.1e+02      49      85 ..      90     126 ..      63     130 .. 0.72
   2 ?    8.2   3.0     0.013       2.9      13      58 ..     138     183 ..     133     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.49
                           BLOC1_2  49 kleklnekyeelqpylqqidqiekqvteLeeavseLD 85 
                                        l++++e+++e+    + +d+i ++ +eL+e +++++
  gi|336252401|ref|YP_004595508.1|  90 VLDATREMNDEMGLVRDLLDEIRDNQSELKESIEAVE 126
                                       4666777777888888888888888888888877665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.013
                           BLOC1_2  13 aeleatvedyklLeklNeaasekykklkdvaaslekkleklnekye 58 
                                       +e+   ++ +k Le+ N++  e++k+l+d+++  e+ ++k+++  e
  gi|336252401|ref|YP_004595508.1| 138 SEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKKTKKIAE 183
                                       5556667889999999999999999999999999999999988666 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   6.4      0.03       6.8       4      73 ..     107     184 ..      86     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.03
                        Syntaxin_2   4 nlqkinsnvstleklvkqLgtk.kd........teelreklhelieeinelikktnellkklsqldnsssdsqqklq 71 
                                        l +i  n s+l++ ++ +++   d          + r++++el ee +el ++++el  k++++++ s++ ++k++
  gi|336252401|ref|YP_004595508.1| 107 LLDEIRDNQSELKESIEAVEDEaEDergnlkseFGQWRNRVKELEEENKELREEVKELSDKVNANEERSKK-TKKIA 182
                                       577788888888888888888742244445545778889*************************9999865.88887 PP

                        Syntaxin_2  72 ke 73 
                                       +e
  gi|336252401|ref|YP_004595508.1| 183 EE 184
                                       66 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 ?    5.1   8.3       0.1        23      28     100 ..     104     176 ..      95     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.1
                              COG2  28 LeslrrdLeaylkllekellelvnedyad.FvslSghLvglqeeleevesplaaarkkvesvreklsereeeve 100
                                       +++l +++++ +++l++++ e v+++ +d   +l ++    +++++e+e + +++r++v+++ +k++++ee+ +
  gi|336252401|ref|YP_004595508.1| 104 VRDLLDEIRDNQSELKESI-EAVEDEAEDeRGNLKSEFGQWRNRVKELEEENKELREEVKELSDKVNANEERSK 176
                                       6789999999999999997.789999999999999999999999****************99999999988654 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       1.7   3.8e+02       8      27 ..     111     130 ..      89     140 .. 0.64
   2 ?    8.4   3.6    0.0094       2.2       3      41 ..     145     179 ..     143     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHHHHHH CS
                              Swi5   8 leeqleelekelaelkeelk 27 
                                       ++++ +el+++++++++e +
  gi|336252401|ref|YP_004595508.1| 111 IRDNQSELKESIEAVEDEAE 130
                                       44444555555555555444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0094
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHH CS
                              Swi5   3 aeikeleeqleelekelaelkeelkekkdpeetvkrhIk 41 
                                       +++kelee+ +el++e++el+++ +++++ +    ++ k
  gi|336252401|ref|YP_004595508.1| 145 NRVKELEEENKELREEVKELSDKVNANEERS----KKTK 179
                                       6899*******************99665322....2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2369  (0.132132); expected 358.6 (0.02)
Passed bias filter:                     1256  (0.0700541); expected 358.6 (0.02)
Passed Vit filter:                       302  (0.0168442); expected 17.9 (0.001)
Passed Fwd filter:                        88  (0.00490825); 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: 0.82u 0.30s 00:00:01.11 Elapsed: 00:00:00.41
# Mc/sec: 1789.97
//
Query:       gi|336252402|ref|YP_004595509.1|  [L=856]
Description: hypothetical protein Halxa_0994 [Halopiger xanaduensis SH-6]
Scores for 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   50.2   0.0    1.4e-12   48.1   0.0    1.9  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
       0.17   12.0   0.1       0.95    9.5   0.0    2.3  2  Sel_put   Selenoprotein, putative


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 !   48.1   0.0   1.5e-16   1.4e-12       2     227 ..     481     733 ..     480     749 .. 0.66
   2 ?   -1.0   0.0      0.15   1.4e+03      87     137 ..     759     828 ..     722     837 .. 0.48

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.5e-16
                          PDDEXK_1   2 lSvsrletfleCplrfflryllglreeeeleapdlGtlvHaaleefye..wkkldkedleelleeaveelwpell.l 75 
                                       +S+s+l+tf +Cp+ +++ ++   ++   +++   G+l+H+ +e fy    + ++++d++el++ +++e+ p  + +
  gi|336252402|ref|YP_004595509.1| 481 VSQSSLNTFINCPRDYYFDRIVDNPDRDYFQK---GNLFHDYAE-FYVnhPDVVEGADRSELVDLMLAEMRPYVPdV 553
                                       7*****************99888877777777...********7.66657444444466666655555554443303 PP

                          PDDEXK_1  76 eeeilessarlrylaeklkevleklverlaeeleakrg..frpvalelefg..............gekvrLkGriDr 136
                                       e e le++++ + ++ ++  ++ ++ +r+  + e+++g  f   ++e +++              g     kG++D+
  gi|336252402|ref|YP_004595509.1| 554 ELEPLETEFEIGLDTIEQFVAADPPTDREYSHYERQEGdnFFADHFEKSIDspiterwfenpnlgG-----KGKVDL 625
                                       333377777766666666666666677666655555557999999**8777889999998665544.....9***** PP

                          PDDEXK_1 137 vddkegelriiDyKtgsappkske.....laelkegl.....QlllYllalaegeelkeegepagalylrleepkvk 203
                                       +  +e    ++DyK+g ++  sk       +e+         Q llYl+  +++   ++  e+++ +++++ e  + 
  gi|336252402|ref|YP_004595509.1| 626 IHAPET---LLDYKSGGRKSASKVvsrsdIEEI---SdepdfQALLYLAHHRQE--HPD--ERLEFVFFHFLE--LV 690
                                       **9999...******995544444554433344...155599999999888887..333..388888888833..22 PP

                          PDDEXK_1 204 ...................deevvkkm......alteeeleallqelee 227
                                                          +             a ++e ++al++ + e
  gi|336252402|ref|YP_004595509.1| 691 ddvvagepdledalvrvtyH------PmpfrtyAGNREAFDALCDGVAE 733
                                       34556555554444333333......04444447777777777776655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.15
                          PDDEXK_1  87 rylaeklkevleklverlaeeleakrg...frpvale..lefg..................gekvrLkGriDrv 137
                                       +   +  + ++++++ r++e+ +a+ g   + + + e  l                          L+++iDr+
  gi|336252402|ref|YP_004595509.1| 759 PETDDTDELLATDFAARFTEYAKAEVGdyvYVEDGTEsaL--KklvrirgrnyfegevdafE--DFLNAQIDRI 828
                                       3333333444444444555555555553222222222111..12222322222222221110..1356666666 PP

>> Sel_put  Selenoprotein, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       1.6   1.5e+04      24      35 ..     239     250 ..     238     252 .. 0.84
   2 ?    9.5   0.0   0.00011      0.95      17      36 ..     656     677 ..     648     679 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.6
                           Sel_put  24 rYvehmrrhHpd 35 
                                       +Y++  r+ H d
  gi|336252402|ref|YP_004595509.1| 239 TYLRLLRTAHSD 250
                                       899999999988 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00011
                           Sel_put  17 vGepdYer..YvehmrrhHpdk 36 
                                         epd+++  Y++h+r++Hpd+
  gi|336252402|ref|YP_004595509.1| 656 SDEPDFQAllYLAHHRQEHPDE 677
                                       5566666555***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (856 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.41
# Mc/sec: 6262.37
//
Query:       gi|336252403|ref|YP_004595510.1|  [L=959]
Description: UvrD/REP helicase [Halopiger xanaduensis SH-6]
Scores for 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-52  176.7   0.1    2.3e-51  175.2   0.1    1.7  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
    5.6e-30  104.9   0.0    1.2e-18   67.6   0.0    2.2  2  UvrD_C           UvrD-like helicase C-terminal domain
    1.1e-27   97.1   0.0    9.2e-27   94.2   0.0    2.3  1  AAA_19           AAA domain
    3.8e-10   40.1   0.8    4.3e-09   36.7   0.5    2.3  2  PDDEXK_1         PD-(D/E)XK nuclease superfamily
    4.5e-09   36.0   0.1    0.00085   19.1   0.0    2.9  2  UvrD_C_2         UvrD-like helicase C-terminal domain
    1.1e-05   25.2   0.0    7.7e-05   22.5   0.0    2.1  2  AAA_30           AAA domain
    0.00052   19.9   0.0        0.3   10.9   0.0    2.2  2  AAA_11           AAA domain
     0.0008   19.2   0.2        4.1    7.1   0.1    3.5  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0039   16.8   0.1       0.24   11.0   0.0    3.0  2  AAA_12           AAA domain
      0.005   16.2   0.0     0.0092   15.3   0.0    1.4  1  DUF2800          Protein of unknown function (DUF2800)
     0.0058   16.1   0.1        3.2    7.2   0.0    2.6  2  PhoH             PhoH-like protein


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 !  175.2   0.1   1.4e-54   2.3e-51       2     314 ..       7     362 ..       6     363 .. 0.77

  Alignments for each domain:
  == domain 1  score: 175.2 bits;  conditional E-value: 1.4e-54
                                       SHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT CS
                     UvrD-helicase   2 npeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessd 78 
                                       n+ q+e i  ++g  +v A+AG+GKTf+++ r+++l++++ +ep++il++TFTn Aa E+keR+ + +  +      
  gi|336252403|ref|YP_004595510.1|   7 NERQQELIDATSGIHVVDAGAGTGKTFTITRRYANLLEQGDVEPEDILLITFTNNAAGEMKERVVANCDYS------ 77 
                                       6889**************************************************************99876...... PP

                                       -HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTT....SHTTTEEECHHHHHHCCHHHHHHHHHSC...HSHTTTT CS
                     UvrD-helicase  79 derlrlalqnlseanisTlHsfcqkilkkeanrig....ldpnfrildeedeedlkqqellkellek...saddsln 148
                                               + l++a i T+H++c+ +l ++ +++     +d +++ +++  e+ ++ +  + + l++   +    + 
  gi|336252403|ref|YP_004595510.1|  78 -------MSALRDAPINTFHGYCHDLLIRHGFDAPtrlgIDDRITSSTQLLENEVIEEDRFRKFLDQfieA----HP 143
                                       .......478********************99877677777777777777777666666666666643222....33 PP

                                       HHHHHHHHHHHHHHCCCCCH......................................................... CS
                     UvrD-helicase 149 ldkkkleklikelsksrnik......................................................... 168
                                          + ++ l    s    ik                                                         
  gi|336252403|ref|YP_004595510.1| 144 DYHDYFRTLNDATSILDLIKelaakgvfptdegwfrdgesfldgdyeefktlfdeanepnegangatqsdlrdglsg 220
                                       33333333333333333333566779999999999777777777777777766666655555555544333333322 PP

                                       HHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS................................TSCSHHHHHH CS
                     UvrD-helicase 169 keelslskskaeelrelvskakekqlspkelkkaf................................ekasdlqkki 213
                                       +                                                                  e  +dl+ ++
  gi|336252403|ref|YP_004595510.1| 221 F---------------------------------ErnrcyepdapnegelrdgypqiddawasrafeEDRDDLKAFV 264
                                       2.................................0233333333333445555555556777777789999****** PP

                                       HHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE CS
                     UvrD-helicase 214 aeflkeyqeqkkeenalDfsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllasgheelfmvG 290
                                        +++ ey     ++n l fs ll+++ ++l e+++l+e +  +++++l+DE+QDT++iQ+++  lla +  +l++vG
  gi|336252403|ref|YP_004595510.1| 265 HDVYLEYIAFALQRNYLNFSFLLMFTFAMLCEDHSLRESV--QFDHVLVDEFQDTSEIQFKLALLLAGTD-NLCVVG 338
                                       ************************************9987..69*****************988888776.9***** PP

                                       -GGG--GGGGTB-THHHHHHHHHS CS
                     UvrD-helicase 291 DpkQsIYgFRgAdielflkkkkdf 314
                                       D kQsIY+F+ A ++++ +++++ 
  gi|336252403|ref|YP_004595510.1| 339 DWKQSIYSFQYASVDNIRRFEERL 362
                                       ******************999875 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 !   35.1   0.0   5.8e-12   9.5e-09       1     139 [.     386     543 ..     386     556 .. 0.83
   2 !   67.6   0.0   7.5e-22   1.2e-18     244     346 ..     597     738 ..     591     741 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 5.8e-12
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxx..xxx.......xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C   1 ivLekNyRStksLlkaankfl.enilnr.rale..kek.......ktvekge.kivvleaeteeeEaekiaatikal 65 
                                       i+L +NyRSt+s+l+ +++ l   ++++ +++   + +       +t    e     +ea t ++E e i   i+++
  gi|336252403|ref|YP_004595510.1| 386 ISLVENYRSTQSILDFSEHSLtLPATGSeEVDPeiQ-DditslaaTT----EhDHSNIEAFTCDDEQEAILTRIQEI 457
                                       789*****************9323333323333533.2698754322....22455678888899999999999999 PP

                                       x............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  66 l............ekneklediavLvRsnkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkllankqdki 130
                                       +             +++ ++d+avL+R+    ++++      gip+   ++ ++F +e+   +la l++l  +++k 
  gi|336252403|ref|YP_004595510.1| 458 VgnreyaveddgeLRAPTYDDVAVLTRTRDFGRELQACAADYGIPVAYEGGVELFGTEQSILLLAWLRILEHEDSKR 534
                                       99999*****999899*******************************999*************************99 PP

                                       xxxxxxxxx RF
                            UvrD_C 131 alkrilkrl 139
                                        +  +l++ 
  gi|336252403|ref|YP_004595510.1| 535 GWAVVLEEA 543
                                       999998875 PP

  == domain 2  score: 67.6 bits;  conditional E-value: 7.5e-22
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                            UvrD_C 244 LysllkelekkeeeeeveeklneileiatLseseleeskkk...ekipiiTiHqAKGlEFdvVflagleegtfP... 314
                                       L+sll+ + +   + +++ ++ ++le + L ++  +e++++   +++++ TiH+AKGlE ++V++a++++ +fP   
  gi|336252403|ref|YP_004595510.1| 597 LVSLLQGTFD--STHHNRGDIVRFLERS-LDADATHEVEDNpggDSVTVQTIHAAKGLEHPIVIMANMNQHRFPpsg 670
                                       5666666666..77889999******99.***********99*********************************** PP

                                       .................................xxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 315 .................................syrskk.......ekrleEEkRlfYVaiTRAkkrLfisy 346
                                                                                      ++ +EE+Rl+YVaiTRA + + +s+
  gi|336252403|ref|YP_004595510.1| 671 ggadriryeervglrqskrytdahgrphlydnwR----YrllskclGREYDEERRLLYVAITRAESHVLFSA 738
                                       ************9999888888888887776552....034557787789**************99988775 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.2   0.0   5.6e-30   9.2e-27       1     146 []      10     348 ..      10     348 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 5.6e-30
                            AAA_19   1 qreavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae......... 68 
                                       q+e + ++++++ +v aG+GtGKT +++ + a l+e+g+v+pe+ill++ft+ Aa e++er+ +++ +         
  gi|336252403|ref|YP_004595510.1|  10 QQELI-DATSGIHVVDAGAGTGKTFTITRRYANLLEQGDVEPEDILLITFTNNAAGEMKERV-VANCDysmsalrda 84 
                                       66777.889999************************************************99.44444889999999 PP

                            AAA_19  69 .atTiHrlal................................................................... 77 
                                        ++T+H+                                                                      
  gi|336252403|ref|YP_004595510.1|  85 pINTFHGYCHdllirhgfdaptrlgiddritsstqllenevieedrfrkfldqfieahpdyhdyfrtlndatsildl 161
                                       9*****9988******************************************************************* PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|336252403|ref|YP_004595510.1| 162 ikelaakgvfptdegwfrdgesfldgdyeefktlfdeanepnegangatqsdlrdglsgfernrcyepdapnegelr 238
                                       ***************************************************************************** PP

                            AAA_19  78 ..........................................ldfddlltealelle.eaeeekklqeeellivDEf 111
                                                                                 l+f  ll+ ++++l  +++ ++ + + ++++vDEf
  gi|336252403|ref|YP_004595510.1| 239 dgypqiddawasrafeedrddlkafvhdvyleyiafalqrnyLNFSFLLMFTFAMLCeDHSLRESV-QFDHVLVDEF 314
                                       ***********************************9999999888888888888887444455555.556******* PP

                            AAA_19 112 qdvdelqyrLlkallgekkklllvGDpdQliyvfr 146
                                       qd++e q++L   l+g+++ l++vGD +Q+iy+f+
  gi|336252403|ref|YP_004595510.1| 315 QDTSEIQFKLALLLAGTDN-LCVVGDWKQSIYSFQ 348
                                       ***********99997777.*************95 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 ?    0.7   0.0      0.24     4e+02      34      56 ..     806     828 ..     796     843 .. 0.68
   2 !   36.7   0.5   2.6e-12   4.3e-09     118     203 ..     850     930 ..     832     955 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.24
                          PDDEXK_1  34 pdlGtlvHaaleefyewkkldke 56 
                                       +++Gt vH+ +e++   ++++++
  gi|336252403|ref|YP_004595510.1| 806 MEFGTRVHDFAERYAIGEAVEPT 828
                                       589*********99884444444 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 2.6e-12
                          PDDEXK_1 118 ale...lefggekvrLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepag 191
                                       +     ++++g++v++ G++D++  ++++++i+DyKt +    +++  e +++ Ql +Y  +++++  +++++ ++ 
  gi|336252403|ref|YP_004595510.1| 850 ENVylpVSVDGQQVTISGIVDLLHVTDDWVEIVDYKTDR---GRHA--EAEYRKQLSVYYHVVRQE--YPDRR-VST 918
                                       222222455589************99***********99...7777..889999************..76554.788 PP

                          PDDEXK_1 192 alylrleepkvk 203
                                        +y+  + ++v+
  gi|336252403|ref|YP_004595510.1| 919 SIYYTADGERVE 930
                                       888877555555 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 !   13.6   0.0   2.7e-05     0.043       2      24 ..     640     662 ..     639     669 .. 0.84
   2 !   19.1   0.0   5.2e-07   0.00085      31      49 ..     716     734 ..     709     736 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                          UvrD_C_2   2 ayaltihkaQGsefpaVivfdpd 24 
                                       +++ tih a+G+e p+Vi+++++
  gi|336252403|ref|YP_004595510.1| 640 VTVQTIHAAKGLEHPIVIMANMN 662
                                       6788***************7765 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 5.2e-07
                          UvrD_C_2  31 gelrrrlLYtavTRArekl 49 
                                       +++ rrlLY+a+TRA  ++
  gi|336252403|ref|YP_004595510.1| 716 YDEERRLLYVAITRAESHV 734
                                       4568***********9987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   4.7e-08   7.7e-05       3      73 ..       7      77 ..       5     120 .. 0.80
   2 ?   -0.4   0.0      0.49   8.1e+02      90     127 ..     307     342 ..     286     344 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.7e-08
                            AAA_30  3 naeQaaavealltsgdrvavltGpAGtGKttalkal.reaweaag...grviglAptgkaAkvLaeelgieasti 73
                                      n+ Q+++++  +tsg  ++v+ ++AGtGKt++++   ++++e+     +++++++ t++aA +++e + ++++  
  gi|336252403|ref|YP_004595510.1|  7 NERQQELID--ATSG--IHVVDAGAGTGKTFTITRRyANLLEQGDvepEDILLITFTNNAAGEMKERVVANCDYS 77
                                      667888886..4566..99***********9997653788877658899****************9877666554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.49
                            AAA_30  90 tllivDEagmvdtkqlaallkaaekagakvilvGDerQ 127
                                       + ++vDE   ++  q++  l  a +    + +vGD +Q
  gi|336252403|ref|YP_004595510.1| 307 DHVLVDEFQDTSEIQFKLALLLAGT--DNLCVVGDWKQ 342
                                       7799999999988888877766655..78999****99 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00018       0.3      17      86 ..      18      76 ..       5     217 .. 0.83
   2 !    6.9   0.0    0.0029       4.7     206     253 ..     295     342 ..     237     342 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                            AAA_11 17 seitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrglldsegeky 86
                                      s+i ++    GtgKT+ti+  +++l      e+   +++ iL+ + +N+A  e+ er++         +y
  gi|336252403|ref|YP_004595510.1| 18 SGIHVVDAGAGTGKTFTITRRYANL-----LEQGDVEPEDILLITFTNNAAGEMKERVVA------NCDY 76
                                      4467888889***************.....4568999********************998......3333 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0029
                            AAA_11 206 agsklleklakkfdvviIDEAaqavEpstliPl.rlgakkvvLvGDpkQ 253
                                       +  ++l++   +fd v++DE     E++   +l + g+ ++  vGD kQ
  gi|336252403|ref|YP_004595510.1| 295 CEDHSLRESV-QFDHVLVDEFQDTSEIQFKLALlLAGTDNLCVVGDWKQ 342
                                       5678888886.******************9999456679********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 ?    4.2   0.0     0.019        31       2      22 ..      22      42 ..      21      85 .. 0.74
   2 !    7.1   0.1    0.0025       4.1      59     113 ..     301     351 ..     289     427 .. 0.80
   3 ?    3.6   0.0     0.028        46     211     232 ..     715     736 ..     699     738 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.019
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrts 22
                                      vv++ +G GK+  i + + + 
  gi|336252403|ref|YP_004595510.1| 22 VVDAGAGTGKTFTITRRYANL 42
                                      8*************9988764 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0025
                   Viral_helicase1  59 ks.tkgkililDEylllhaGyilllaalskaklvilfGDplQipfhsrnasfllah 113
                                       ++  +++ +++DE++     +++l++ l++ ++++++GD +Q+ ++      ++a+
  gi|336252403|ref|YP_004595510.1| 301 REsVQFDHVLVDEFQDTSEIQFKLALLLAGTDNLCVVGDWKQSIYSF-----QYAS 351
                                       3336799*******99997666669999**************98884.....4444 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.028
                   Viral_helicase1 211 lisesrenllvAlTRhrkslvi 232
                                       ++ e+r  l+vA+TR+ + +++
  gi|336252403|ref|YP_004595510.1| 715 EYDEERRLLYVAITRAESHVLF 736
                                       4567899*********998776 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.078   1.3e+02      18      36 ..     386     404 ..     331     487 .. 0.62
   2 !   11.0   0.0   0.00015      0.24     124     193 ..     616     735 ..     612     739 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.078
                            AAA_12  18 vlLdtqYRmhpeIsrfpsk 36 
                                       + L ++YR+ ++I++f+++
  gi|336252403|ref|YP_004595510.1| 386 ISLVENYRSTQSILDFSEH 404
                                       3455566666666666554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00015
                            AAA_12 124 vellkkklkekeeekseke.....ievntvdgfQGrekdviilslVRsn...ekk...................... 170
                                       v++l++ l+++++++ e +     ++v+t+ +  G e  ++i+    ++   + +                      
  gi|336252403|ref|YP_004595510.1| 616 VRFLERSLDADATHEVEDNpggdsVTVQTIHAAKGLEHPIVIMANMNQHrfpP-Sgggadriryeervglrqskryt 691
                                       567777888777777666688888*******************9998865541.1456667778888899999999* PP

                            AAA_12 171 ...................eig..flkderrlNValTRAkskli 193
                                                           +g    +++r l Va+TRA s+++
  gi|336252403|ref|YP_004595510.1| 692 dahgrphlydnwryrllskCLGreYDEERRLLYVAITRAESHVL 735
                                       ****************99835542667777789******99875 PP

>> DUF2800  Protein of unknown function (DUF2800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.6e-06    0.0092     112     151 ..     860     903 ..     835     912 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.6e-06
                           DUF2800 112 e....gfGtaDvviiaddvLeviDlKyGkgvkVsaekNpQlalY 151
                                              G  D++ ++dd++e++D+K  +g +++ae  +Ql +Y
  gi|336252403|ref|YP_004595510.1| 860 GqqvtISGIVDLLHVTDDWVEIVDYKTDRGRHAEAEYRKQLSVY 903
                                       224447899*********************************99 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0     0.002       3.2       7      50 ..       8      49 ..       5     165 .. 0.72
   2 !    6.1   0.0    0.0041       6.7     122     159 ..     308     344 ..     302     383 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.002
                                      HHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-S CS
                              PhoH  7 keQkeylealkkndivfaiGpaGtGKtylavalavealkkkkvk 50
                                      ++Q+e+++a   + i ++ + aGtGKt+  +   +++l++++v+
  gi|336252403|ref|YP_004595510.1|  8 ERQQELIDAT--SGIHVVDAGAGTGKTFTITRRYANLLEQGDVE 49
                                      5666666664..456677788*******9999999999999886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0041
                                       EEEE-SGGG--HHHHHHHHTTB-TT-EEEEEE------ CS
                              PhoH 122 fvilDEAQnttkeqmkmfltRlGenskvvvtGdvtqid 159
                                        v++DE Q+t++ q k  l   G +  + v+Gd++q  
  gi|336252403|ref|YP_004595510.1| 308 HVLVDEFQDTSEIQFKLALLLAGTDN-LCVVGDWKQSI 344
                                       599*****************999986.5667***9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (959 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 0.77u 0.28s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 6151.65
//
Query:       gi|336252404|ref|YP_004595511.1|  [L=239]
Description: hypothetical protein Halxa_0996 [Halopiger xanaduensis SH-6]
Scores for 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   19.0   0.8      0.001   18.4   0.8    1.2  1  HopW1-1          Type III T3SS secreted effector HopW1-1/HopP
    0.00082   19.6   9.0    0.00082   19.6   9.0    2.6  3  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
     0.0011   18.4   4.7     0.0011   18.4   4.7    1.8  1  GAS              Growth-arrest specific micro-tubule binding
      0.003   17.5   3.1        1.2    9.0   0.0    2.9  2  NOG1_N           NOG1 N-terminal helical domain
     0.0061   14.9   0.6     0.0079   14.5   0.6    1.1  1  SEN1_N           SEN1 N terminal
     0.0076   15.7  13.1      0.011   15.2  13.1    1.3  1  Golgin_A5        Golgin subfamily A member 5
  ------ inclusion threshold ------
      0.013   15.8   5.7      0.013   15.8   5.7    2.6  2  Tup_N            Tup N-terminal
       0.04   13.8   6.5      0.083   12.8   6.5    1.6  1  DASH_Spc19       Spc19
      0.053   12.4   4.3      0.077   11.8   4.3    1.2  1  Nup188_C         Nuclear pore protein NUP188 C-terminal domai
      0.061   12.2  14.2      0.096   11.5  14.2    1.4  1  Spc7             Spc7 kinetochore protein
       0.12   11.9   4.5       0.21   11.0   4.5    1.5  1  FIN1             Filaments in between nuclei protein-1
       0.14   12.0   6.9      0.081   12.7   3.6    2.2  2  Synaptobrevin    Synaptobrevin
       0.14   10.6   1.3       0.17   10.4   1.3    1.1  1  Herpes_UL25      Herpesvirus UL25 family
        0.3   11.2   4.7       0.88    9.7   0.4    3.0  3  AcylCoA_dehyd_C  Acyl-CoA dehydrogenase C terminal
       0.36    9.7   5.1       0.44    9.4   5.1    1.2  1  LMBR1            LMBR1-like membrane protein
       0.52   10.0  11.9      0.082   12.6   7.9    1.6  1  GrpE             GrpE
       0.62   10.3   8.1       0.33   11.1   5.4    1.9  2  DUF4047          Domain of unknown function (DUF4047)
       0.63   10.2  11.5        0.3   11.2   3.6    2.9  3  Uds1             Up-regulated During Septation
       0.64    9.0   8.1       0.88    8.6   8.1    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.71   10.3   5.1        1.4    9.3   3.8    2.2  1  Syntaxin_2       Syntaxin-like protein
       0.77    8.9   4.4        1.1    8.4   4.4    1.2  1  TMPIT            TMPIT-like protein
       0.89    9.6  11.9       0.27   11.3   7.0    2.6  2  COG2             COG (conserved oligomeric Golgi) complex com
          1    9.5   6.2         12    6.1   0.2    3.2  3  TrmO_C           TrmO C-terminal domain
        1.1    9.4   6.4        0.8    9.7   3.2    2.3  3  DUF1664          Protein of unknown function (DUF1664)
        1.1   10.1   6.7        2.1    9.1   3.3    2.9  3  Occludin_ELL     Occludin homology domain
        1.3    9.7  14.8       0.34   11.6   8.7    2.5  2  Ead_Ea22         Ead/Ea22-like protein
        1.8    8.2   8.2        3.5    7.3   5.1    2.6  3  DUF932           Domain of unknown function (DUF932)
        2.3    8.7  22.9      0.092   13.3  16.0    2.0  2  APG6_N           Apg6 coiled-coil region
        2.6    7.8   4.5          4    7.2   3.6    1.8  1  Iron_permease    Low affinity iron permease
        2.7    8.2   6.4        2.7    8.2   4.9    1.8  1  Fib_alpha        Fibrinogen alpha/beta chain family
        3.1    7.9  10.8        1.4    9.0   7.0    2.2  3  Nup54            Nucleoporin complex subunit 54
        3.7    6.8   6.8        5.5    6.3   6.6    1.3  1  DUF4407          Domain of unknown function (DUF4407)
        4.3    7.8  16.5        7.1    7.1   0.3    4.0  4  ZapA             Cell division protein ZapA
          5    7.7   5.0         33    5.1   2.5    3.3  2  YtxH             YtxH-like protein
        6.6    7.0  10.3         14    6.0   7.4    2.9  2  DUF3782          Protein of unknown function (DUF3782)
        8.4    6.3  10.6         44    3.9  10.6    2.3  1  DivIC            Septum formation initiator
        8.6    4.8   8.7         15    4.1   8.7    1.4  1  FapA             Flagellar Assembly Protein A


Domain annotation for each model (and alignments):
>> HopW1-1  Type III T3SS secreted effector HopW1-1/HopPmaA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.8   2.1e-06     0.001     206     303 ..      53     154 ..      46     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.1e-06
                           HopW1-1 206 seslqsqsdevvsllrshadtlkeleklPealaaltenCpdvstrddlrelaeeaGellq.qlresdllprseeiss 281
                                       +++l+++ +evv  +    + l ele+    l+a+ e+ + +s++    ++ e+a e+++ +l++s+  +r ++is 
  gi|336252404|ref|YP_004595511.1|  53 KKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAEDYNVTSAESYEESVREAANEIIRdELKVSERWERVQQISE 129
                                       67899999*************************************************99637*************** PP

                           HopW1-1 282 eageasvrs.revve..Pkltlsqa 303
                                       + +e+++   r+  e  P++t +q 
  gi|336252404|ref|YP_004595511.1| 130 KWQETPIDVlRDIYEqdPRITSKQV 154
                                       ******9862344446699999985 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 !   19.6   9.0   1.7e-06   0.00082      25      83 ..      36      94 ..      31     110 .. 0.92
   2 ?   -0.7   0.2       3.4   1.6e+03      44      67 ..     105     129 ..      95     145 .. 0.47
   3 ?   -1.4   0.1       5.4   2.6e+03      63      81 ..     211     229 ..     170     235 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.7e-06
                       TMF_TATA_bd 25 EgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetl 83
                                      ++E +  ++ele + ++++++r+ei ++++e+ee+++  +elee e+el+++ e y+ +
  gi|336252404|ref|YP_004595511.1| 36 DVEFTDPRDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAEDYNVT 94
                                      7899999*********************************************9999754 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.4
                       TMF_TATA_bd  44 eareeivk.lmkeneelkelkkele 67 
                                       ea++ei++  +k +e+ ++ ++ +e
  gi|336252404|ref|YP_004595511.1| 105 EAANEIIRdELKVSERWERVQQISE 129
                                       3333333212233333333333222 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 5.4
                       TMF_TATA_bd  63 kkeleelekeleelqerye 81 
                                       ++++++ e+ l+e  er +
  gi|336252404|ref|YP_004595511.1| 211 EEHSADCESLLREAAERMD 229
                                       2333333333444444333 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 !   18.4   4.7   2.2e-06    0.0011      47     100 ..      44      97 ..      32     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.2e-06
                               GAS  47 kelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkeleke 100
                                        el++i q++k+l+++++++ +evee+r++l + e+  ++l+++ + ++++  e
  gi|336252404|ref|YP_004595511.1|  44 DELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAEDYNVTSAE 97 
                                       578899999999999999999999999999999999999999999888887665 PP

>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   1.2    0.0069       3.4      75     117 ..      58     100 ..       6     145 .. 0.83
   2 !    9.0   0.0    0.0026       1.2     104     139 ..     201     235 ..     196     239 .] 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0069
                            NOG1_N  75 relldvlvdkdelkksLaqvkwarklirkigkeyvnklkkadd 117
                                        e+ +v+++++e++ +L++++  ++  + i+++y    +++ +
  gi|336252404|ref|YP_004595511.1|  58 DEIEEVVAEVEEMRNRLSELEERESELQAIAEDYNVTSAESYE 100
                                       577899**************************99766655554 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0026
                            NOG1_N 104 igkeyvnklkkaddkkeakelrreafgrvasvlkkv 139
                                       i+ eyv++++++++   ++ l rea +r+ ++++++
  gi|336252404|ref|YP_004595511.1| 201 IEDEYVSRVAEEHSA-DCESLLREAAERMDETFEEI 235
                                       899*******99995.5***************9987 PP

>> SEN1_N  SEN1 N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.6   1.6e-05    0.0079     486     595 ..      35     138 ..       7     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                            SEN1_N 486 agleklkpkskekkkeldaakaafNkalkaireliarllerlsd.fsspselkellsdpeaaqalisllfspddely 561
                                       + +e ++++++e  ++++++k++  ++++++++ ++++ +rls+  +++sel+++ +d ++ +a      s +++++
  gi|336252404|ref|YP_004595511.1|  35 RDVE-FTDPRDE-LEDIRQQKKQLRDEIEEVVAEVEEMRNRLSElEERESELQAIAEDYNVTSA-----ESYEESVR 104
                                       4444.4444344.569****************************5567899*****99998876.....69****** PP

                            SEN1_N 562 qaalnllkqafdvdsRldalralleknltatlra 595
                                       +aa +++++   v+ R + ++++ ek  ++ ++ 
  gi|336252404|ref|YP_004595511.1| 105 EAANEIIRDELKVSERWERVQQISEKWQETPIDV 138
                                       *************************998887765 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2  13.1   2.2e-05     0.011      46     149 ..      43     150 ..       9     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-05
                         Golgin_A5  46 saeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlq..eleeqleeerka.keev..eaele 117
                                        +el++++q++++lr+e++++  ++e++r+ l +le+++ +e + + e  +  ++e+  e+ r+a +e +  e +++
  gi|336252404|ref|YP_004595511.1|  43 RDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERE-SELQAIAEDYNvtSAESYEESVREAaNEIIrdELKVS 118
                                       689*********************************998.6666666654310333322222222022231133445 PP

                         Golgin_A5 118 rlkeelryleeelvrskatlqsrikdrekeie 149
                                       +  e ++ + e  +++  ++   i +++  i 
  gi|336252404|ref|YP_004595511.1| 119 ERWERVQQISEKWQETPIDVLRDIYEQDPRIT 150
                                       56667777777777776666666666666664 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   5.7   2.6e-05     0.013       6      58 ..      31      84 ..      27      94 .. 0.89
   2 ?    0.5   0.5       1.6   7.7e+02      14      41 ..      85     110 ..      81     140 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-05
                             Tup_N  6 Ldavkq.EfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrki 58
                                      Ld ++  Ef     e++ +++qk+ +   i++ ++E++ +r+ l eLee+ +++
  gi|336252404|ref|YP_004595511.1| 31 LDEIRDvEFTDPRDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESEL 84
                                      7888855*****************************************987765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.6
                             Tup_N  14 dalsqeasslkaqkdeyelkiqsqiqEl 41 
                                       +a++++++++    + ye ++++ ++E+
  gi|336252404|ref|YP_004595511.1|  85 QAIAEDYNVTS--AESYEESVREAANEI 110
                                       44555555444..456777777777666 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   6.5   0.00017     0.083      49     111 ..      48     109 ..      45     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                                       THHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT- CS
                        DASH_Spc19  49 dleaakaslaeeiePqieellekaekeleklerreetLkaklelqegrlsnaesskkeeeese 111
                                       d+++ k++l++eie  ++e +e++++ l++le+re++L+a +e  ++   ++ +++ +e+++e
  gi|336252404|ref|YP_004595511.1|  48 DIRQQKKQLRDEIEEVVAE-VEEMRNRLSELEERESELQAIAEDYNVTSAESYEESVREAANE 109
                                       99************98886.7899*****************9999888877444433333333 PP

>> Nup188_C  Nuclear pore protein NUP188 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   4.3   0.00016     0.077     287     358 ..      28     102 ..      25     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                                       HHHHHHHHT...T-.SS--------HHHHHHHHHHHHT-HHHHHHHB---SHHHHHHHHS---.SS-S-SSHHHHH CS
                          Nup188_C 287 trilealre...vn.ardipevewdaasvkedvefwlssrklLrerlvplgerelelarkkaedesskaenrLeek 358
                                       +++l+++r+   ++   ++++++ +++++++++e+ + + + +r+rl  l+ere el+   ++  + ++ +  ee 
  gi|336252404|ref|YP_004595511.1|  28 QLVLDEIRDvefTDpRDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAED-YNVTSAESYEES 102
                                       5789999995542247899*************************************9987776.344444444554 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  14.2    0.0002     0.096     190     281 ..      34     127 ..       3     153 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                              Spc7 190 aeelesid.keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiae..aervleeckgw 263
                                        +++e  d ++eLe +r++ ++l  eiee  +e++e++++l elee+ +el++  ++++   ae  +e+v+e+  ++
  gi|336252404|ref|YP_004595511.1|  34 IRDVEFTDpRDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAEDYNVTSAEsyEESVREAANEI 110
                                       44444444466666666666666666666666666666666666666666655555544443331145555555555 PP

                              Spc7 264 sesevsrlkeevkaleel 281
                                        ++e++ + e+ ++++++
  gi|336252404|ref|YP_004595511.1| 111 IRDELK-VSERWERVQQI 127
                                       555542.22222222222 PP

>> FIN1  Filaments in between nuclei protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.5   0.00044      0.21     196     243 .]      34      80 ..       4      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00044
                              FIN1 196 kksvkfelpeddeeeeikkelkdikklleellerqdelesrlskleeq 243
                                        ++v f  p+d e e+i+++ k++++ +ee+++  +e+ +rls+lee+
  gi|336252404|ref|YP_004595511.1|  34 IRDVEFTDPRD-ELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEER 80 
                                       5899******9.58********************************96 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.6   0.00017     0.081       3      56 ..      44      97 ..      42     103 .. 0.94
   2 ?   -0.1   0.1       1.7   8.3e+02      10      39 ..     101     130 ..      96     134 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                                      XHHHHHHHHHHCCCCHHCCHHHHCHCCCCCHHHHCCCCHHHHHHHHHHHHHHHH CS
                     Synaptobrevin  3 dklakikaevdevkdimkeNidkvlergekldeLvdktenLqssaqqFkkqark 56
                                      d+l+ i+++ ++ +d ++e + +v e +++l+eL+++ ++Lq+ a++++ ++ +
  gi|336252404|ref|YP_004595511.1| 44 DELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAEDYNVTSAE 97
                                      7899********************************************998865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.7
                                       HHHHCCCCHHCCHHHHCHCCCCCHHHHCCC CS
                     Synaptobrevin  10 aevdevkdimkeNidkvlergekldeLvdk 39 
                                       + v e  + ++++  kv er e++ ++++k
  gi|336252404|ref|YP_004595511.1| 101 ESVREAANEIIRDELKVSERWERVQQISEK 130
                                       556666666677777888999998888876 PP

>> Herpes_UL25  Herpesvirus UL25 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.3   0.00035      0.17      55     103 ..      43      92 ..      24     153 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00035
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.X CS
                       Herpes_UL25  55 raeLdnlaqkavalaeeierrlkevEellekiaeleaaaaaeeaaaar.p 103
                                       r eL++++q++ +l  eie+ ++evEe+ +++ ele+  ++ +a a+   
  gi|336252404|ref|YP_004595511.1|  43 RDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAEDyN 92 
                                       57999*************************99999444433333333221 PP

>> AcylCoA_dehyd_C  Acyl-CoA dehydrogenase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4    0.0018      0.88       6      47 ..      31      72 ..      28      81 .. 0.90
   2 ?   -1.2   0.0       4.4   2.1e+03       4      37 ..      98     133 ..      95     141 .. 0.60
   3 ?    1.6   0.0       0.6   2.9e+02      11      42 ..     208     239 .]     197     239 .] 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0018
                                      HHHHHTGGGS---GGGHHHHHHHHHHHHHHHHHHHHHHTT-- CS
                   AcylCoA_dehyd_C  6 laqikeyeaeevseeleelkarlkemtekyeeavakVkeakd 47
                                      l+ i+++e ++ ++ele+++++ k++ ++ ee+va+V+e ++
  gi|336252404|ref|YP_004595511.1| 31 LDEIRDVEFTDPRDELEDIRQQKKQLRDEIEEVVAEVEEMRN 72
                                      57899999999**************************98876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.4
                                       HHHHHHHTGGGS---GGGHHHH..HHHHHHHHHHHH CS
                   AcylCoA_dehyd_C   4 tylaqikeyeaeevseeleelk..arlkemtekyee 37 
                                       +y + ++e ++e +++el+  +  +r++++ ek++e
  gi|336252404|ref|YP_004595511.1|  98 SYEESVREAANEIIRDELKVSErwERVQQISEKWQE 133
                                       566666666666666666543322566666666655 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.6
                                       TGGGS---GGGHHHHHHHHHHHHHHHHHHHHH CS
                   AcylCoA_dehyd_C  11 eyeaeevseeleelkarlkemtekyeeavakV 42 
                                       ++++e+ +++ + l++  ++m e++ee+v +V
  gi|336252404|ref|YP_004595511.1| 208 RVAEEHSADCESLLREAAERMDETFEEIVYRV 239
                                       45555556666677888899999999998776 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.1    0.0009      0.44     208     311 ..      45     146 ..      32     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0009
                             LMBR1 208 eaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklksnenkteeslaklekqlikal 284
                                       e++ ++++k++  +e+e+++ ev+++r+++se +++++ l+ i +  + + ae  +++  ++++++++ e ++ +++
  gi|336252404|ref|YP_004595511.1|  45 ELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAEDYNVTSAESYEESVREAANEIIRDELKVSERW 121
                                       5677888899999*******************9999999******99999999999999999*************** PP

                             LMBR1 285 qkrertekqwkrllekalelediiknk 311
                                       ++ ++++++w++    +  l di ++ 
  gi|336252404|ref|YP_004595511.1| 122 ERVQQISEKWQETPIDV--LRDIYEQD 146
                                       **********9876666..66666655 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   7.9   0.00017     0.082       4      86 ..      50     133 ..      44     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                                       ...CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              GrpE   4 eeeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralk 80 
                                       ++++++++de+ee  +e+ee+++++ el+e+  +l+a +e ++   ++  ee  ++a  ++++d L+v +  er+ +
  gi|336252404|ref|YP_004595511.1|  50 RQQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAEDYNVTSAESYEESVREAANEIIRDELKVSERWERVQQ 126
                                       678999*******************************************************************9988 PP

                                       C...HHH CS
                              GrpE  81 sak.ene 86 
                                        ++ ++e
  gi|336252404|ref|YP_004595511.1| 127 ISEkWQE 133
                                       7665444 PP

>> DUF4047  Domain of unknown function (DUF4047)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   5.4   0.00069      0.33      38     111 ..      25     101 ..      14     113 .. 0.83
   2 ?   -0.6   0.2       2.9   1.4e+03      46      71 ..     107     133 ..      88     142 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00069
                           DUF4047  38 qhkelilheyeemksklkvdsveeieqalsvwkqgrekikaerealqkvyteieep...ynqvqeelkvnksesskq 111
                                         ++l+l+e ++++     d +e+i+q+ ++ +++ e ++ae e +++   e+ee     + + e+  v+  es ++
  gi|336252404|ref|YP_004595511.1|  25 FLHQLVLDEIRDVEFTDPRDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEEReseLQAIAEDYNVTSAESYEE 101
                                       4568999999999999999******************************9999886111566789999999999765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.9
                           DUF4047  46 eyeemksklkvds.veeieqalsvwkq 71 
                                         e ++ +lkv+   e ++q  + w++
  gi|336252404|ref|YP_004595511.1| 107 ANEIIRDELKVSErWERVQQISEKWQE 133
                                       334456666665315666666677776 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.6   0.00063       0.3      48     116 ..      17      85 ..       5      88 .. 0.76
   2 ?   -0.2   0.2       2.2   1.1e+03      47      91 ..     100     110 ..      88     140 .. 0.50
   3 ?    2.7   0.0      0.27   1.3e+02      51     105 ..     174     228 ..     167     236 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00063
                              Uds1  48 tklrdaarsLsrlyssskksakssaarsnskssreslakaeeelaeserkvdelaselekleeraaevr 116
                                         + d    L++l  ++ ++ +   +r++ +++r+++++  +e++e  + v+e+ + l +leer+ e++
  gi|336252404|ref|YP_004595511.1|  17 DEYDDQQDFLHQLVLDEIRDVEFTDPRDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQ 85 
                                       5555555566666666666655556666777889999999*************************9998 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.2
                              Uds1  47 etklrdaarsLsrlyssskksakssaarsnskssreslakaeeel 91 
                                       e ++r+aa++                                  +
  gi|336252404|ref|YP_004595511.1| 100 EESVREAANE----------------------------------I 110
                                       2223333322..................................2 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.27
                              Uds1  51 rdaarsLsrlyssskksakssaarsnskssreslakaeeelaeserkvdelasel 105
                                       r+  ++L rly++++k++++++ +    +++  ++ aee+ a++e+   e+a+ +
  gi|336252404|ref|YP_004595511.1| 174 REEGVRLVRLYCEENKDEERYNGSGVYIEDEYVSRVAEEHSADCESLLREAAERM 228
                                       5556789999999999988555545555555555555555555555555444443 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 ?    8.6   8.1    0.0018      0.88      42     146 ..       6     109 ..       3     154 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
                             Atg14  42 kkkiekalegkeeaeqledkiknkkakleelks.liadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsd 117
                                       +kk++++le+ +  e ++++   ++  l+e++  +  d r++l+ ++++ +ql++eiee  ++++++++ l++  ++
  gi|336252404|ref|YP_004595511.1|   6 RKKLNRMLEESD--EYDDQQDFLHQLVLDEIRDvEFTDPRDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEER 80 
                                       567777777777..444444445555666666414466777777777777777777777777777777777744444 PP

                             Atg14 118 leslqneleerrkkqiaklqdaikrieqk 146
                                        + lq   e +  ++ +++ +++++ ++ 
  gi|336252404|ref|YP_004595511.1|  81 ESELQAIAEDYNVTSAESYEESVREAANE 109
                                       44455555555555555555555433332 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.8    0.0029       1.4      25      70 ..      42      87 ..      30     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0029
                        Syntaxin_2 25 kkd.teelreklhelieeinelikktnellkklsqldnsssdsqqkl 70
                                      ++d  e++r++ ++l++ei e++ +++e  ++ls+l++ +s   q +
  gi|336252404|ref|YP_004595511.1| 42 PRDeLEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESE-LQAI 87
                                      5655789999*************************9999975.3333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.4    0.0023       1.1       8      83 ..      43     118 ..      36     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0023
                             TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk 83 
                                       ++e++++++++k+++ ++ee+ +  +++++++++ ++r +el++  ++++ ++ e++ee v+e ++e+ + +  ++
  gi|336252404|ref|YP_004595511.1|  43 RDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAEDYNVTSAESYEESVREAANEIIRDELKVS 118
                                       6788888888999999999999999999999999999999999999999988888888888888888776665544 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 ?   11.3   7.0   0.00055      0.27      66     119 ..      41      96 ..      36     128 .. 0.82
   2 ?   -1.7   0.0       5.8   2.8e+03      17      47 ..     204     236 ..     200     239 .] 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00055
                              COG2  66 glqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr..ellkll 119
                                       + ++ele ++++ +++r+++e+v+++++e+++++++  e  +el++    + + + 
  gi|336252404|ref|YP_004595511.1|  41 DPRDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAedYNVTSA 96 
                                       5689******************************9987777777765544444444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.8
                              COG2  17 qFvse..lrhgvpLeslrrdLeaylkllekell 47 
                                       ++vs   ++h  + esl r+ ++ + ++ +e++
  gi|336252404|ref|YP_004595511.1| 204 EYVSRvaEEHSADCESLLREAAERMDETFEEIV 236
                                       666665455666677777776666666666665 PP

>> TrmO_C  TrmO C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.038        18       4      34 ..      36      65 ..      33      66 .. 0.85
   2 ?   -2.0   0.1       8.3     4e+03       9      30 ..      68      89 ..      67      91 .. 0.78
   3 ?    6.1   0.2     0.025        12       8      43 ..     118     153 ..     112     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.038
                            TrmO_C  4 eVeFseeaeaqlqqlqksapdlkqlIeevLa 34
                                      +VeF++  +++l+ + +++++l+  Ieev+a
  gi|336252404|ref|YP_004595511.1| 36 DVEFTDP-RDELEDIRQQKKQLRDEIEEVVA 65
                                      6888887.556799999************86 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.3
                            TrmO_C  9 eeaeaqlqqlqksapdlkqlIe 30
                                      ee++++l++l++++++l+++ e
  gi|336252404|ref|YP_004595511.1| 68 EEMRNRLSELEERESELQAIAE 89
                                      5778889999999999988765 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.025
                            TrmO_C   8 seeaeaqlqql.qksapdlkqlIeevLaqDPRPaYkk 43 
                                       se+ e+  qq+ +k+++    +++++ +qDPR   k+
  gi|336252404|ref|YP_004595511.1| 118 SERWERV-QQIsEKWQETPIDVLRDIYEQDPRITSKQ 153
                                       5556665.55548889999*************55555 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.8    0.0018      0.87      86     122 ..      43      79 ..       4      81 .. 0.86
   2 ?    9.7   3.2    0.0017       0.8      55     122 ..      47      79 ..      36     116 .. 0.63
   3 ?   -0.6   0.1       2.6   1.3e+03      56      85 ..     102     131 ..      88     146 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0018
                           DUF1664  86 keevtevredlseigedvesvkeavegleskleriee 122
                                       ++e++++r++ +++++++e+v + ve++ ++l+++ee
  gi|336252404|ref|YP_004595511.1|  43 RDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEE 79 
                                       6788899999999999999999999999999999887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0017
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       e+++++k++L ++i++v ++++e+                                    ++l+++ee
  gi|336252404|ref|YP_004595511.1|  47 EDIRQQKKQLRDEIEEVVAEVEEM-----------------------------------RNRLSELEE 79 
                                       345555555555555555555555...................................555555443 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.6
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskei 85 
                                       s++++ +++ ++  +v ++ + +++is++ 
  gi|336252404|ref|YP_004595511.1| 102 SVREAANEIIRDELKVSERWERVQQISEKW 131
                                       333333333333333333333333333333 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.4      0.41     2e+02      39      96 ..       7      60 ..       3      63 .. 0.57
   2 ?    9.1   3.3    0.0044       2.1      25      61 ..      54      90 ..      43     132 .. 0.86
   3 ?   -0.4   0.1         4   1.9e+03      30      46 ..     116     132 ..      91     153 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.41
                      Occludin_ELL 39 seLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKkli 96
                                      ++L+r+l+e++e +++ + +++ +l+e +++    e+ + + ++e+++++ + ++  i
  gi|336252404|ref|YP_004595511.1|  7 KKLNRMLEESDEYDDQQDFLHQLVLDEIRDV----EFTDPRDELEDIRQQKKQLRDEI 60
                                      4555555555555555555555555555554....66666666666666666666555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0044
                      Occludin_ELL 25 kelhaeleevskkfseLerelkelkegskeykkieee 61
                                      k+l +e+eev ++++e++++l+el+e+++e + i+e+
  gi|336252404|ref|YP_004595511.1| 54 KQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAED 90
                                      78999************************99999987 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 4
                      Occludin_ELL  30 eleevskkfseLerelk 46 
                                       +++e ++++++++++++
  gi|336252404|ref|YP_004595511.1| 116 KVSERWERVQQISEKWQ 132
                                       33333444444444433 PP

>> Ead_Ea22  Ead/Ea22-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   8.7    0.0007      0.34      42     135 ..      19     110 ..       4     129 .. 0.65
   2 ?    1.3   0.1         1   4.9e+02       8      21 ..     221     234 ..     214     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0007
                          Ead_Ea22  42 nddefklgrtvakehdaefiaaanpatvlaLLDelekkqqrikeleee.....aenedialtvgklrv...eleaae 110
                                       +dd++++++       +++++ + +       Dele   q++k+l++e     ae e+++ + ++l++   el+a  
  gi|336252404|ref|YP_004595511.1|  19 YDDQQDFLH-------QLVLDEIRDVEFTDPRDELEDIRQQKKQLRDEieevvAEVEEMRNRLSELEEresELQA-- 86 
                                       333333444.......44444444444444458888744444444444255577777777777777774444444.. PP

                          Ead_Ea22 111 krlekenveqadaaeveitalrqri 135
                                        ++e+ nv  a+++e+++++++++i
  gi|336252404|ref|YP_004595511.1|  87 -IAEDYNVTSAESYEESVREAANEI 110
                                       .44788**************99965 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1
                          Ead_Ea22   8 LREvaekatqgeer 21 
                                       LRE+ae++ ++ e 
  gi|336252404|ref|YP_004595511.1| 221 LREAAERMDETFEE 234
                                       9******9988765 PP

>> DUF932  Domain of unknown function (DUF932)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.1      0.21     1e+02     115     140 ..      46      71 ..       4      84 .. 0.47
   2 ?    7.3   5.1    0.0073       3.5     117     217 ..      48     177 ..      39     184 .. 0.50
   3 ?    0.8   0.0      0.73   3.5e+02      98     132 ..     204     235 ..     195     239 .] 0.73

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.21
                            DUF932 115 vieakkaLglvveefeefeeeaeala 140
                                       +++++++ ++ ++e+ee+ +e+e+++
  gi|336252404|ref|YP_004595511.1|  46 LEDIRQQKKQLRDEIEEVVAEVEEMR 71 
                                       33333333333333333333333333 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0073
                            DUF932 117 eakkaLglvveefeefeeea....ealaavklteaeaeafaeavlpepkeaaeerkk...........ralaalalr 178
                                       +++++ ++ ++e+ee+ +e+    ++l++++  e e +a+ae+   ++ e+     +           r   ++++r
  gi|336252404|ref|YP_004595511.1|  48 DIRQQKKQLRDEIEEVVAEVeemrNRLSELEERESELQAIAEDYNVTSAESY----EesvreaaneiiRDELKVSER 120
                                       4444444444444444444400004444555555555555554433333333....334457889999666666666 PP

                            DUF932 179 fe.....at.............edrgadlesvkgTaWgllnavteyldhgrrtrsve 217
                                       +e     ++              ++++++ s +   +g   +  e+ ++++ tr++ 
  gi|336252404|ref|YP_004595511.1| 121 WErvqqiSEkwqetpidvlrdiYEQDPRITSKQVKPYGRKSVPEEWQTRVGDTREEG 177
                                       663322200222345555555544445554555556777777777777777777665 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.73
                            DUF932  98 gatgevkvrHtgnvdakvieakkaLglvveefeef 132
                                       + ++ v   H+++ ++ ++ea++   ++ e+fee+
  gi|336252404|ref|YP_004595511.1| 204 EYVSRVAEEHSADCESLLREAAE---RMDETFEEI 235
                                       555678889**************...555555555 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  16.0   0.00019     0.092      17      99 ..       8      89 ..       3     110 .. 0.79
   2 ?   -1.8   0.2       8.6   4.2e+03      49      54 ..     217     222 ..     183     235 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00019
                            APG6_N 17 qleqaekerdaY...eeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeele 92
                                      +l+++ +e d+Y   ++fl++l  ++      d e  + ++ele++++++++l  e++e+ +e ee+++ l++lee ++
  gi|336252404|ref|YP_004595511.1|  8 KLNRMLEESDEYddqQDFLHQLVLDEIR----DVEFTDPRDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERES 82
                                      4444444444442226788888877544....55999****************************************** PP

                            APG6_N 93 aleeeee 99
                                      +l++  e
  gi|336252404|ref|YP_004595511.1| 83 ELQAIAE 89
                                      *997655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 8.6
                            APG6_N  49 leelee 54 
                                       +e+l +
  gi|336252404|ref|YP_004595511.1| 217 CESLLR 222
                                       222222 PP

>> Iron_permease  Low affinity iron permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   3.6    0.0082         4      67     120 ..      52     104 ..      46     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0082
                     Iron_permease  67 dskaiqlkLdeLirasksaknrlidleelteeeleelakeyerlaeaakeeeev 120
                                        +k+++ +++e+++  ++ +nrl +lee  e+el+++a+ y+ +++++ ee+  
  gi|336252404|ref|YP_004595511.1|  52 QKKQLRDEIEEVVAEVEEMRNRLSELEE-RESELQAIAEDYNVTSAESYEESVR 104
                                       457788899******************9.689*********9887776665544 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 ?    8.2   4.9    0.0056       2.7      28     108 ..      51     128 ..      43     151 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0056
                                       CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHH CS
                         Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesni 104
                                       +++k++++++e++  e+ee++n+ +e ee  +e++ + ++ + ++++    +++s +e  +ei+r + ++++  +++
  gi|336252404|ref|YP_004595511.1|  51 QQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAEDYNVTSAE---SYEESVREAANEIIRDELKVSERWERV 124
                                       56666666666666666666666666666666666665555555543...222222222224444444443333333 PP

                                       HHHH CS
                         Fib_alpha 105 rvLq 108
                                       +++ 
  gi|336252404|ref|YP_004595511.1| 125 QQIS 128
                                       3332 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   7.0    0.0029       1.4      64     133 ..      36     107 ..       3     112 .. 0.69
   2 ?    0.4   0.1       1.3   6.3e+02      45      86 ..      93     133 ..      87     148 .. 0.70
   3 ?   -1.6   0.0       5.6   2.7e+03     110     124 ..     211     225 ..     179     238 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHHHHHHHHHS-H..HH.HHHH CS
                             Nup54  64 qkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelrarletleaqlndp..aqlkgrv 133
                                       + + ++   +le++++++++l   + ++++ +e +r+r + l++ E el+a  e+ +    +   ++++   
  gi|336252404|ref|YP_004595511.1|  36 DVEFTDPRDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIAEDYNVTSAESyeESVREAA 107
                                       4446677789***************************************99998666555542224444444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Nup54  45 vaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelsh 86 
                                       v+ ++++ +++++ ++e+  + +l++s+r e++++   + ++
  gi|336252404|ref|YP_004595511.1|  93 VTSAESYEESVREAANEII-RDELKVSERWERVQQISEKWQE 133
                                       5566666777777777777.7788888888888776555555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5.6
                                       HHHHHHHHHHHHHHS CS
                             Nup54 110 eelrarletleaqln 124
                                       ee +a +e+l ++  
  gi|336252404|ref|YP_004595511.1| 211 EEHSADCESLLREAA 225
                                       333333333333333 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.6     0.011       5.5     106     172 ..       2      90 ..       1     153 [. 0.66

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                           DUF4407 106 keIdaelaeeqqeeakelkeqlaaa...............ltaelaeleaqiaalqaeidaaearldalraeaqkel 167
                                       +eI++++  +  ee +e+++q +                  ++el+++++q ++l+ ei++  a++++ r+ + +  
  gi|336252404|ref|YP_004595511.1|   2 PEIQRKKLNRMLEESDEYDDQQDFLhqlvldeirdveftdPRDELEDIRQQKKQLRDEIEEVVAEVEEMRNRLSELE 78 
                                       68888888888888888877755448889999999999998888888888888999999999999888888888554 PP

                           DUF4407 168 dgtk.......g 172
                                       + ++        
  gi|336252404|ref|YP_004595511.1|  79 ERESelqaiaeD 90 
                                       443333322220 PP

>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.4      0.02       9.8      58      84 ..      44      77 ..       7      81 .. 0.80
   2 ?    7.1   0.3     0.015       7.1       9      30 ..      90     111 ..      83     128 .. 0.89
   3 ?   -1.1   0.1       5.3   2.6e+03      11      31 ..     182     203 ..     179     211 .. 0.75
   4 ?    2.5   0.3       0.4     2e+02      19      36 ..     218     235 ..     204     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.02
                              ZapA 58 dellklkkraeeleaele.......elaerleel 84
                                      del++ ++++++l++e+e       e+++rl+el
  gi|336252404|ref|YP_004595511.1| 44 DELEDIRQQKKQLRDEIEevvaeveEMRNRLSEL 77
                                      7999999999999999995555544555555555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.015
                              ZapA   9 eytlaceegeeeylreaaklvd 30 
                                       +y++++ e+ ee +reaa+++ 
  gi|336252404|ref|YP_004595511.1|  90 DYNVTSAESYEESVREAANEII 111
                                       7******************996 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 5.3
                              ZapA  11 tlaceeg.eeeylreaaklvde 31 
                                       +l cee  +ee++     ++++
  gi|336252404|ref|YP_004595511.1| 182 RLYCEENkDEERYNGSGVYIED 203
                                       7889977359998888877766 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.4
                              ZapA  19 eeylreaaklvdekikei 36 
                                       e  lreaa++ de ++ei
  gi|336252404|ref|YP_004595511.1| 218 ESLLREAAERMDETFEEI 235
                                       899*********999887 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.5     0.067        33      34      70 ..      53     110 ..       5     178 .. 0.80
   2 ?    0.5   0.0       1.9   9.3e+02      30      59 ..     206     235 ..     203     239 .] 0.63

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.067
                              YtxH  34 addlkekakelleeakeka.....................kekaedlkekvkekadel 70 
                                        ++l++ ++e++ e++e                       + +ae + e+v+e a+e+
  gi|336252404|ref|YP_004595511.1|  53 KKQLRDEIEEVVAEVEEMRnrlseleereselqaiaedynVTSAESYEESVREAANEI 110
                                       4444444444443333333444444455566667777777777777777777777765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.9
                              YtxH  30 lkekaddlkekakelleeakekakekaedl 59 
                                       +++ a++ + + ++ll ea+e++ e++e++
  gi|336252404|ref|YP_004595511.1| 206 VSRVAEEHSADCESLLREAAERMDETFEEI 235
                                       555666666677777777777666666665 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   7.4     0.028        14       6      61 ..      56     118 ..      44     131 .. 0.69
   2 ?   -1.7   0.0       6.6   3.2e+03      15      32 ..     215     233 ..     203     238 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.028
                           DUF3782   6 leee....eeetkedleelekeieklertigaLGaRWGlvs....EeafReglkeiLeealgvk 61 
                                       l++e     +e++e++++l++ +e+ e+ ++a++  + ++s    Ee++Re+  ei++++l+v+
  gi|336252404|ref|YP_004595511.1|  56 LRDEieevVAEVEEMRNRLSE-LEERESELQAIAEDYNVTSaesyEESVREAANEIIRDELKVS 118
                                       444422223444444444444.66678899*******9987666799*************8872 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.6
                           DUF3782  15 edleelek.eieklertig 32 
                                        d e l + + e++++t++
  gi|336252404|ref|YP_004595511.1| 215 ADCESLLReAAERMDETFE 233
                                       3333332213344444443 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  10.6     0.091        44      20      61 ..      47      88 ..      39     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.091
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXX CS
                             DivIC 20 kqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerA 61
                                       +++q+ ++l +e++++ ae ee+  ++++L+  e+ ++++A
  gi|336252404|ref|YP_004595511.1| 47 EDIRQQKKQLRDEIEEVVAEVEEMRNRLSELEERESELQAIA 88
                                      567788888888888888888888888888877777777776 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   8.7      0.03        15     331     364 ..      52      85 ..       3     145 .. 0.49

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.03
                              FapA 331 depelkeklkeleeeleeleeeleklkkkikklp 364
                                       ++++l+++++e+  e+ee++++l +l+++ ++l+
  gi|336252404|ref|YP_004595511.1|  52 QKKQLRDEIEEVVAEVEEMRNRLSELEERESELQ 85 
                                       2233333333333333333333333333322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2536  (0.141447); expected 358.6 (0.02)
Passed bias filter:                     1000  (0.0557756); expected 358.6 (0.02)
Passed Vit filter:                       188  (0.0104858); expected 17.9 (0.001)
Passed Fwd filter:                        48  (0.00267723); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.77u 0.30s 00:00:01.07 Elapsed: 00:00:00.47
# Mc/sec: 1523.91
//
Query:       gi|336252405|ref|YP_004595512.1|  [L=479]
Description: hypothetical protein Halxa_0997 [Halopiger xanaduensis SH-6]
Scores for 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  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3318.56
//
Query:       gi|336252406|ref|YP_004595513.1|  [L=78]
Description: hypothetical protein Halxa_0998 [Halopiger xanaduensis SH-6]
Scores for 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:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 575.11
//
Query:       gi|336252407|ref|YP_004595514.1|  [L=342]
Description: hypothetical protein Halxa_0999 [Halopiger xanaduensis SH-6]
Scores for 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   13.0   0.4         19    5.6   0.0    2.3  2  zinc_ribbon_9    zinc-ribbon
       0.14   11.9   0.0       0.43   10.3   0.0    1.8  2  T2SS-T3SS_pil_N  Pilus formation protein N terminal region
          2    8.8   3.8         37    4.7   3.9    2.3  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind


Domain annotation for each model (and alignments):
>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0038        23      19      29 ..      11      21 ..       1      23 [. 0.65
   2 ?    5.6   0.0    0.0032        19      19      29 ..      36      48 ..      26      51 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0038
                     zinc_ribbon_9 19 dsdvlCPhCgg 29
                                      + + +CP+C+ 
  gi|336252407|ref|YP_004595514.1| 11 NTNLTCPQCEE 21
                                      34458****75 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0032
                     zinc_ribbon_9 19 dsdv..lCPhCgg 29
                                      d+d+  +CP+C+ 
  gi|336252407|ref|YP_004595514.1| 36 DPDAylICPYCEA 48
                                      4453348****86 PP

>> T2SS-T3SS_pil_N  Pilus formation protein N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   7.3e-05      0.43      16      47 ..     128     159 ..     123     161 .. 0.91
   2 ?   -3.3   0.0       1.3   7.9e+03       7      33 ..     168     194 ..     166     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.3e-05
                   T2SS-T3SS_pil_N  16 rlpepvervavgnpkiadvtvlsprevlltGk 47 
                                       rl+   +r a g+ +i++ +++ p+e+++t++
  gi|336252407|ref|YP_004595514.1| 128 RLDDSYTRAALGDSAIVALHPIGPDELVVTAN 159
                                       5677889***********************85 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.3
                   T2SS-T3SS_pil_N   7 levgksrllrlpepvervavgnpkiad 33 
                                       +e+g    +  +++++r    np+ +d
  gi|336252407|ref|YP_004595514.1| 168 VEMGDELEVVYDAKLSRTNATNPAWVD 194
                                       778888888888888888888887666 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   3.9    0.0062        37       2      39 ..      13      48 ..      12      51 .. 0.82
   2 ?    4.5   0.6    0.0072        43       4      17 ..      42      56 ..      39      62 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0062
                           zf-Di19  2 sftCPyCgkeltvkeLveHvedeHrveskevvCPvCae 39
                                      ++tCP C++ +++  L+   e+   +   + +CP C++
  gi|336252407|ref|YP_004595514.1| 13 NLTCPQCEERIDTLHLQPAGEN--IDPDAYLICPYCEA 48
                                      579******9999999987766..77888999999975 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0072
                           zf-Di19  4 tCPyCgk.eltvkeL 17
                                       CPyC+   + ++ L
  gi|336252407|ref|YP_004595514.1| 42 ICPYCEAwFFPENGL 56
                                      6****9855666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); 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:                         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: 00:00:00.42
# Mc/sec: 2450.66
//
Query:       gi|336252408|ref|YP_004595515.1|  [L=555]
Description: hypothetical protein Halxa_1000 [Halopiger xanaduensis SH-6]
Scores for 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   12.7   0.0        0.3   11.0   0.0    1.9  2  DUF4268   Domain of unknown function (DUF4268)


Domain annotation for each model (and alignments):
>> DUF4268  Domain of unknown function (DUF4268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.33   5.9e+03      65      85 ..     297     317 ..     285     320 .. 0.79
   2 ?   11.0   0.0   1.7e-05       0.3      72     130 ..     489     544 ..     481     547 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.33
                           DUF4268  65 nkeifekLkeqkeeieeelge 85 
                                       + ++ +++ke++e +++elg+
  gi|336252408|ref|YP_004595515.1| 297 QSRVLDAIKEERERLKQELGS 317
                                       677889999999999999985 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 1.7e-05
                           DUF4268  72 Lkeqkeeieeelge..eleW.erleekkasrisriyvlkedvdikdkedwpeiiswliekme 130
                                       + e++ +ie+elg    +eW + ++e+ +++i++       vd+ d+e w e+ s li+++ 
  gi|336252408|ref|YP_004595515.1| 489 FSEYRGDIEAELGIdsVFEWgDVSPERAGKEINAL------VDVGDRERWTELASSLIDTVR 544
                                       678999******874468899999********554......46889***********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 4187.25
//
Query:       gi|336252409|ref|YP_004595516.1|  [L=391]
Description: integrase protein [Halopiger xanaduensis SH-6]
Scores for 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-16   58.8   0.0    1.7e-15   57.2   0.0    1.7  2  Phage_integrase  Phage integrase family
    0.00025   21.0   8.4    0.00055   19.9   8.4    1.6  1  DZR              Double zinc ribbon
     0.0042   15.8   0.0     0.0089   14.7   0.0    1.4  1  UPF0236          Uncharacterised protein family (UPF0236)
  ------ inclusion threshold ------
      0.056   13.8   0.0       0.16   12.3   0.0    1.8  1  PqqD             Coenzyme PQQ synthesis protein D (PqqD)
      0.094   12.5   0.2        0.2   11.4   0.1    1.6  1  USP8_interact    USP8 interacting
       0.49   10.5   1.3       0.81    9.8   1.3    1.2  1  DUF2614          Zinc-ribbon containing domain
        1.2    9.0   9.6       0.65    9.9   7.2    1.8  2  C1_1             Phorbol esters/diacylglycerol binding domain
        2.5    7.6   5.8         20    4.7   2.8    2.4  2  zf-ribbon_3      zinc-ribbon domain
        9.2    6.2  10.7        6.1    6.8   5.6    2.2  2  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)


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 ?   -1.8   0.0       1.2   2.3e+03      69     119 ..      57     105 ..      27     114 .. 0.50
   2 !   57.2   0.0   8.6e-19   1.7e-15       8     171 ..     147     305 ..     143     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                                       EEECTHHHHHHHHHHHHHHCHCCTTTSBSSBET..TSSB--HHHHHHHHHHHH CS
                   Phage_integrase  69 avplseealellkellskaleeaeksellfask..rgkplsrqtvrkafkrav 119
                                       +v + e+a +l+  l +++    e +e++   +   ++p +++++r a+k+ +
  gi|336252409|ref|YP_004595516.1|  57 NVRMAEHAGSLVDALEDEE----EVKEIVRWIHrtYDNPETNRDYRVALKQFG 105
                                       4444444444443333333....333333222212344555555555555555 PP

  == domain 2  score: 57.2 bits;  conditional E-value: 8.6e-19
                                       HHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGG.EECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHH CS
                   Phage_integrase   8 verllaaleeslkirdklllellyetGlRisEllsLrvkd.ldlengvilvheregKgskeravplseealellkel 83 
                                       v  l++ +++    rd++l++++++ G R +El+sL+++d  d e+g+      +gK++ +r v l    ++ l+++
  gi|336252409|ref|YP_004595516.1| 147 VLPLIEETRN---PRDAALVAVAWDAGPRSGELRSLTLGDvTDYEHGYQVT--VRGKMG-QRSVGLVP-SVPFLQRW 216
                                       5555555555...89*************************88899998777..788887.57777764.5899**** PP

                                       HHHH.CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SS CS
                   Phage_integrase  84 lska.leeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHss 159
                                       l+ +  ++ ++  +  +++++ p+  +++r+a+k a+e+a+++kp+t+  +R+s a++L+ +g+++  +++  G++ 
  gi|336252409|ref|YP_004595516.1| 217 LEAHpGDALDDPLWSKLKEPTAPT-YNALRTAIKDAAERANVDKPVTFTNFRKSSASHLASRGMNQAHIEDHHGWTR 292
                                       ****77777778888888877775.689************************************************* PP

                                       CCHH.HHHHCCCH CS
                   Phage_integrase 160 istt.qiYthvak 171
                                        s + ++Y+ v++
  gi|336252409|ref|YP_004595516.1| 293 GSDVaSRYVSVFA 305
                                       ****9***99875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   8.4   2.8e-07   0.00055       1      44 [.     334     380 ..     334     386 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.8e-07
                               DZR   1 CpqCgeelppdarfCseCgtklkavaa...edrCpsCgekvdpearf 44 
                                       Cp+C++++p +++ C +C+++l ++a+    ++C+ Cge +   ++ 
  gi|336252409|ref|YP_004595516.1| 334 CPRCHQKTPREKQNCIHCRQHLTKEATieqRQTCDWCGETIRGYSEH 380
                                       **********************98888*99********998766665 PP

>> UPF0236  Uncharacterised protein family (UPF0236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.5e-06    0.0089     322     372 ..      65     115 ..      58     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.5e-06
                           UPF0236 322 eeavkiakdekkkekikelvrriesmpesirdYrerlserGveveglrglg 372
                                       +++v +++de++ ++i + + r   +pe+ rdYr+ l++ G  ++++ g +
  gi|336252409|ref|YP_004595516.1|  65 GSLVDALEDEEEVKEIVRWIHRTYDNPETNRDYRVALKQFGRRATEVNGDS 115
                                       78999************************************9999998865 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.1e-05      0.16      13      61 ..      58     104 ..      37     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.1e-05
                                       EE--CHHHHHHHH-SSSS-HHHHHHHHHHHCT--HHHHHHHHHHHHHHH CS
                              PqqD  13 isLnetgafiWklldgersveeivaalaeeydvdeeeaeadvlafldqL 61 
                                       +++ e++  + ++l++e  v eiv  + + yd +e   ++d +  l+q 
  gi|336252409|ref|YP_004595516.1|  58 VRMAEHAGSLVDALEDEEEVKEIVRWIHRTYDNPE--TNRDYRVALKQF 104
                                       3899**********99999*************998..888888777775 PP

>> USP8_interact  USP8 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0001       0.2      15      68 ..      33      85 ..      11      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                     USP8_interact 15 elkkevaeqkqqlseqkrelellkeyiralrstnpvlraladqlerdevlrWve 68
                                      ++++e++   +q+ + +r+l+ll++ +r+  ++ + + al+d+ e +e++rW++
  gi|336252409|ref|YP_004595516.1| 33 KFSDELMLIPSQVGD-HRHLKLLRHNVRMAEHAGSLVDALEDEEEVKEIVRWIH 85
                                      444444444445444.578*********************************87 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.3   0.00041      0.81      65     102 ..     329     364 ..     323     368 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00041
                           DUF2614  65 avqvvcpeceketkvlGrvdlcmhcdepltldksleGk 102
                                       +  v+cp c+++t      + c+hc++ lt + ++e +
  gi|336252409|ref|YP_004595516.1| 329 TAPVECPRCHQKTPR--EKQNCIHCRQHLTKEATIEQR 364
                                       5689******99864..5679*********99999876 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 ?   -2.7   0.0       2.8   5.5e+03       2      12 ..      82      92 ..      82      93 .. 0.83
   2 ?    9.9   7.2   0.00032      0.65       7      37 ..     341     373 ..     332     375 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.8
                                      -EEEE--SS-- CS
                              C1_1  2 hwvhrnfkqpt 12
                                      +w hr++++p 
  gi|336252409|ref|YP_004595516.1| 82 RWIHRTYDNPE 92
                                      5*****99885 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00032
                                       --SS--B-TTT-SB-.-S.SSS-EEEETTT--E CS
                              C1_1   7 nfkqptfCkhCgefl.wg.kekqglkCswCkll 37 
                                       + ++++ C hC+++l ++    q  +C+wC+++
  gi|336252409|ref|YP_004595516.1| 341 TPREKQNCIHCRQHLtKEaTIEQRQTCDWCGET 373
                                       458999*********8667999********986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   2.8      0.01        20       3      22 ..     332     351 ..     331     355 .. 0.92
   2 ?    3.4   0.1     0.027        54      17      24 ..     365     372 ..     362     374 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.01
                       zf-ribbon_3   3 vrCPnCGaplssddnvCpyC 22 
                                       v+CP+C ++   + ++C +C
  gi|336252409|ref|YP_004595516.1| 332 VECPRCHQKTPREKQNCIHC 351
                                       69******9999******99 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.027
                       zf-ribbon_3  17 nvCpyCGt 24 
                                       ++C +CG+
  gi|336252409|ref|YP_004595516.1| 365 QTCDWCGE 372
                                       78****96 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   5.6    0.0031       6.1      26      48 ..     334     356 ..     331     357 .. 0.91
   2 ?    1.8   0.2      0.11   2.2e+02      25      41 ..     366     385 ..     361     386 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0031
                                       -HHHHHHHHHTT-B-TTT--B-- CS
                        zf-C3HC4_3  26 CeeCaekllkrkkkCpiCrrpie 48 
                                       C +C +k  ++k++C  Cr++ +
  gi|336252409|ref|YP_004595516.1| 334 CPRCHQKTPREKQNCIHCRQHLT 356
                                       99******************876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.11
                                       E-HHHHHHHHH...TT-B-T CS
                        zf-C3HC4_3  25 lCeeCaekllk...rkkkCp 41 
                                       +C +C e+++    + + Cp
  gi|336252409|ref|YP_004595516.1| 366 TCDWCGETIRGyseHLPACP 385
                                       79999998865554555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      722  (0.04027); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2941.23
//
Query:       gi|336252410|ref|YP_004595517.1|  [L=313]
Description: hypothetical protein Halxa_1002 [Halopiger xanaduensis SH-6]
Scores for complete 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   25.2   0.0    8.1e-05   22.9   0.0    2.0  2  AAA_22           AAA domain
     0.0012   18.1   0.1       0.07   12.4   0.2    2.6  3  KAP_NTPase       KAP family P-loop domain
  ------ inclusion threshold ------
      0.011   16.1   1.7      0.011   16.1   1.7    2.0  2  AAA_16           AAA ATPase domain
        0.1   12.7   0.2        2.9    8.0   0.0    2.3  2  PTPlike_phytase  Inositol hexakisphosphate


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 !   22.9   0.0   1.8e-08   8.1e-05       4     135 ..      61     205 ..      46     207 .. 0.81
   2 ?   -0.5   0.0       0.3   1.3e+03      37      69 ..     252     290 ..     236     312 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.8e-08
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.erpevv..fvtlpsstsskdllrellralglelka....... 70 
                                       +ag++ ++ e G+GK++    + + l         +++e++  ++   +s + + ++++ll al +  ++       
  gi|336252410|ref|YP_004595517.1|  61 RAGHVSIIDERGAGKSHFRDLVYNALSD-----GpRSDEFYiaRIREVESLTTRRVYTRLLDALAE-YDDldipdey 131
                                       789999999****************953.....35566666355555555599999*******996.33369***** PP

                            AAA_22  71 ..erlsseellealeqalraravielliiDEaqhlr...s..eealeeLrsllnl..srkgvqliLvGtpelrk 135
                                         ++++ ++l+e ++++l+a+++  ++ +D  +      +   ++l  L s  +l  sr  + l+L+Gtp +++
  gi|336252410|ref|YP_004595517.1| 132 phATDDVRQLVEDVAEQLEAQDKACVVQVDQLEDAArnaRtfRQLLAALQSVGDLgdSRPVFVLFLFGTPLAAE 205
                                       ***********************99999******6544325666666666666669999999********5554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.3
                            AAA_22  37 e.....erpevv.fvtlpsstsskdllrellralglelk 69 
                                               ++ + +v   s+++++++++e  +a+  ++ 
  gi|336252410|ref|YP_004595517.1| 252 GypsdpFAASAIeRVVERSDGTPRSVRQECYHAFRAGAR 290
                                       244434334444688888888999999888888776554 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 ?    2.2   0.0     0.019        87      30      78 ..      72     120 ..      65     124 .. 0.88
   2 !   12.4   0.2   1.6e-05      0.07     152     211 ..     133     197 ..     114     201 .. 0.84
   3 ?   -0.8   0.0      0.16     7e+02     292     314 ..     257     279 ..     200     282 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.019
                        KAP_NTPase  30 GsGKssllnkledelkefakpvrflfaefnawsfkggddavaellaaLa 78 
                                       G+GKs++  ++ ++l++   +++f +a++    + ++  +  +ll+aLa
  gi|336252410|ref|YP_004595517.1|  72 GAGKSHFRDLVYNALSDGPRSDEFYIARIREVESLTTRRVYTRLLDALA 120
                                       99****************9999*****9999888887777777777776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.6e-05
                        KAP_NTPase 152 klqteveelladmektLdalqkrlVvviDdLDrc..eteevlqlleavkllfsl...kpvvfila 211
                                         +++v +l +d ++ L+a++k+ Vv +D L+       + +qll a++ +++l   +pv +++ 
  gi|336252410|ref|YP_004595517.1| 133 HATDDVRQLVEDVAEQLEAQDKACVVQVDQLEDAarNARTFRQLLAALQSVGDLgdsRPVFVLFL 197
                                       56788999***********************97722456899*********99999888888876 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.16
                        KAP_NTPase 292 aldlskilltedfsdvnpRemkr 314
                                       ++  s i ++ ++sd +pR++++
  gi|336252410|ref|YP_004595517.1| 257 PFAASAIERVVERSDGTPRSVRQ 279
                                       55667788888899999999985 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   1.7   2.5e-06     0.011      18     168 ..      56     193 ..      45     195 .. 0.73
   2 ?   -1.9   0.0      0.85   3.8e+03      56      81 ..     242     266 ..     207     300 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.5e-06
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd....ggiflrgkcdqlesaipysalaqalareellrqlldeae 90 
                                       +   +r + v ++ e+G GKs   + +++al++     +++ +r + +++            l+++++++ lld+  
  gi|336252410|ref|YP_004595517.1|  56 SHLINRAGHVSIIDERGAGKSHFRDLVYNALSDGprsdEFYIARIREVES------------LTTRRVYTRLLDA-- 118
                                       444555688999999*************9888877776677777777777............7777899999988.. PP

                            AAA_16  91 saeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwade...aslqllaaLlrlles 164
                                         ++e+++  +++++         +  ++++l+ + +++l+ +++  v+ +D+l++a     + +qllaaL + ++ 
  gi|336252410|ref|YP_004595517.1| 119 --LAEYDDLDIPDEYP-------HATDDVRQLVEDVAEQLEAQDKACVVQVDQLEDAARnarTFRQLLAALQSVGDL 186
                                       ..88888888888888.......44489999999999888888999*********8888333455555555554444 PP

                            AAA_16 165 ...kpll 168
                                          +p++
  gi|336252410|ref|YP_004595517.1| 187 gdsRPVF 193
                                       4423555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.85
                            AAA_16  56 lrgkcdqlesaipysa.laqalareel 81 
                                       ++++ +++e++ p ++  a+a+ + ++
  gi|336252410|ref|YP_004595517.1| 242 AWARDEEYEEGYPSDPfAASAI-E-RV 266
                                       3344444444444444333333.2.23 PP

>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00064       2.9      85     115 ..      10      40 ..       1      43 [. 0.83
   2 ?    2.5   0.0     0.031   1.4e+02      55     135 ..      59     157 ..      40     162 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00064
                                       ...EE-HHHHHHHTT-EEEEEEE-TTS---H CS
                   PTPlike_phytase  85 tpeevyerelaeelslrYaRipitdekapee 115
                                        + e  +r  ae+++++ aRip+t+e+ p++
  gi|336252410|ref|YP_004595517.1|  10 DETESAQRAYAEQFGIESARIPFTAETLPDA 40 
                                       5667888999*****************9986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.031
                                       EEEHHHHHTT-CCG-EE.................E-S-.............EE-HHHHHHHTT-EEEEEEE-TTS-- CS
                   PTPlike_phytase  55 kksegrvlvhdeteegk.................dvktlqevweeve.tpeevyerelaeelslrYaRipitdekap 113
                                        + +g v++ de   gk                 d+  +  ++e  + t+++vy r+l+     +Y  + i+de+  
  gi|336252410|ref|YP_004595517.1|  59 INRAGHVSIIDERGAGKshfrdlvynalsdgprsDEFYIARIREVESlTTRRVYTRLLDALA--EYDDLDIPDEYPH 133
                                       44555555555555555555555555555555665555555544444799999999998875..6778999999999 PP

                                       -HHHHHHHHHHHHTS..-TT-EEE CS
                   PTPlike_phytase 114 eeedfdalvsilkea..pektalv 135
                                          d+ +lv+ ++e   ++++a+v
  gi|336252410|ref|YP_004595517.1| 134 ATDDVRQLVEDVAEQleAQDKACV 157
                                       999999999877776333355555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2355.10
//
Query:       gi|336252411|ref|YP_004595518.1|  [L=102]
Description: hypothetical protein Halxa_1003 [Halopiger xanaduensis SH-6]
Scores for 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   18.9   0.3      0.012   16.3   0.1    2.0  2  ThiS       ThiS family
     0.0095   15.9   0.3      0.011   15.7   0.3    1.1  1  DUF3600    Domain of unknown function (DUF3600)
  ------ inclusion threshold ------
      0.036   14.9   0.2      0.052   14.4   0.2    1.4  1  DUF3235    Protein of unknown function (DUF3235)
      0.066   13.0   0.1      0.084   12.7   0.1    1.1  1  PPP1R35_C  Protein phosphatase 1 regulatory subunit 35 C-term


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 !   16.3   0.1   2.6e-06     0.012      24      70 ..      29      68 ..       6      68 .. 0.77
   2 ?    0.9   0.0      0.16   7.1e+02      22      39 ..      72      89 ..      69     101 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.6e-06
                                      HHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEE CS
                              ThiS 24 vaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevai 70
                                      ++   +aL++       e+ + +avN+e+  +    +el+d De+++
  gi|336252411|ref|YP_004595518.1| 29 LDRYYDALDAGP----KEKTIGIAVNEEMHAF---YQELQDADEIEV 68
                                      555566666666....67**************...**********97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.16
                                      SBHHHHHHHHHHHTCHHG CS
                              ThiS 22 stvaelleaLgerypela 39
                                      +++++ +e+L+ r+++ +
  gi|336252411|ref|YP_004595518.1| 72 QSIRDHIEKLAHRHEQVF 89
                                      578899999999997766 PP

>> DUF3600  Domain of unknown function (DUF3600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   2.4e-06     0.011      87     155 ..      27      97 ..      12     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-06
                           DUF3600  87 yelqPyfdklndqpsskev..ltaeeydqyieallteetvrvklgvssaikveevPeelkeefikaeavle 155
                                       ++l  y+d l+  p  k +    +ee +++ + l   + + v + +s   ++e++ +  ++ f++a + le
  gi|336252411|ref|YP_004595518.1|  27 FDLDRYYDALDAGPKEKTIgiAVNEEMHAFYQELQDADEIEVDVSQSIRDHIEKLAHRHEQVFERAMRKLE 97 
                                       78999*******999997622678*****************************************988775 PP

>> DUF3235  Protein of unknown function (DUF3235)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   1.2e-05     0.052      20      72 ..       6      60 ..       2      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHHHHHHHT--HHHHHHHHHHHHHHH..HHHTTT----HHHHHHHHCT CS
                           DUF3235 20 vaaaaataqkavadlaatsdelavDavydalkd..alakaGiavpaqvtdfYkAn 72
                                        +a ++a+  + d + +++e  +D  ydal +  + +  Giav +++++fY+  
  gi|336252411|ref|YP_004595518.1|  6 FNDAMDEAEGDADDGSDAESEFDLDRYYDALDAgpKEKTIGIAVNEEMHAFYQEL 60
                                      5678889999999******************983345668************965 PP

>> PPP1R35_C  Protein phosphatase 1 regulatory subunit 35 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.9e-05     0.084       8      54 ..      55     101 ..      51     102 .] 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                         PPP1R35_C   8 alkkeleslqeaefdaaraveekleksettkksieekaaegvNvprd 54 
                                       a+ +el+   e e+d  +++++++ek  +  +++ e+a +++ ++r+
  gi|336252411|ref|YP_004595518.1|  55 AFYQELQDADEIEVDVSQSIRDHIEKLAHRHEQVFERAMRKLEIERE 101
                                       67899*************************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1361  (0.0759105); expected 358.6 (0.02)
Passed bias filter:                      756  (0.0421663); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 769.83
//
Query:       gi|336252412|ref|YP_004595519.1|  [L=302]
Description: metallophosphoesterase [Halopiger xanaduensis SH-6]
Scores for 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-12   45.7   0.1    1.3e-11   45.0   0.1    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    9.5e-07   29.5   3.6    1.4e-05   25.7   3.6    2.1  1  Metallophos    Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.084   12.2   0.0       0.12   11.7   0.0    1.2  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 !   45.0   0.1   2.1e-15   1.3e-11       2     129 ..       5     151 ..       5     174 .. 0.74

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.1e-15
                     Metallophos_2   2 klaiiSDlHsnldaleavlealkevgvdaiihaGD......leeeep...........e.vleellelapvlaVrGN 60 
                                       +l+++ D H+  + le+v+e+ ++++ d+i+h+GD                       e   ++l e+ ++++++GN
  gi|336252412|ref|YP_004595519.1|   5 RLLVMGDNHGDTESLETVVEETEGAEFDYIVHTGDitdahrR----GvgtaadqlrelEpLFADLAERGELVYIYGN 77 
                                       5899*******************************4444440....04444433332233666666666******** PP

                     Metallophos_2  61 nDeev..veedvlreaaelgtdlpeeaelelagek............vlliHgdplgvkdalaellkeaeegsdvvv 123
                                        D+e    ++   r +   gt+lp+   +++ag++            vl++Hg+       l e +++   + + ++
  gi|336252412|ref|YP_004595519.1|  78 RDSERggDKHVTERYELSPGTRLPKGGAVKVAGQRftadpddvgdddVLVTHGQ-------LPEPFYS--FDGRAYF 145
                                       **555677777888888889999888888875555555555666666******8.......3444444..23347** PP

                     Metallophos_2 124 cGHtHv 129
                                       cGHtH+
  gi|336252412|ref|YP_004595519.1| 146 CGHTHR 151
                                       *****8 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   3.6   2.3e-09   1.4e-05       2     127 ..       5     135 ..       4     152 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.3e-09
                                       EEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.........HHHHHHHHHHHHHHHHTSEEEE CS
                       Metallophos   2 rilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrg.........dlekellellaalvkypipvyl 69 
                                       r+lv+gD H     g+ ++l+++++++    + d+++++GD++d           +l + l+ l+a l + +  ++ 
  gi|336252412|ref|YP_004595519.1|   5 RLLVMGDNH-----GDTESLETVVEETEGA-EFDYIVHTGDITDAHrrgvgtaadQLRE-LEPLFADLAE-RGELVY 73 
                                       789******.....*************888.9*************99988776542222.3444444444.5778** PP

                                       EC-TTS...CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEE CS
                       Metallophos  70 llGNHe...gfeeellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvlllhGgspel 127
                                       + GN +   g ++ + ++y+ +  +  p+   ++v +    a+  +   ++vl+ hG  pe 
  gi|336252412|ref|YP_004595519.1|  74 IYGNRDserGGDKHVTERYELSPGTRLPKGGAVKVAGQRFTADPDDVGdDDVLVTHGQLPEP 135
                                       ******87755556666666666665555555555555555553333355888888875554 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.9e-05      0.12       6      57 ..       4      55 ..       1      73 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
                                      -EEEEEE--TT-GGGHHHHHHHHHHH--SEEEEES-----HHHHHHHHHHHH CS
                     Metallophos_3  6 rkvlaisdlkgevellerlveviedkdpDllvlvGdlvkaeakadeyesaqe 57
                                      +++l + d +g++e le +ve  e  + D +v +Gd+  a+ ++   +  q+
  gi|336252412|ref|YP_004595519.1|  4 QRLLVMGDNHGDTESLETVVEETEGAEFDYIVHTGDITDAHRRGVGTAADQL 55
                                      68899999*****************************888777655554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); 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:                         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 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2124.77
//
Query:       gi|336252413|ref|YP_004595520.1|  [L=114]
Description: hypothetical protein Halxa_1005 [Halopiger xanaduensis SH-6]
Scores for 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:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 893.02
//
Query:       gi|336252414|ref|YP_004595521.1|  [L=87]
Description: hypothetical protein Halxa_1006 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.043   13.2   0.1      0.045   13.1   0.1    1.0  1  DUF3458_C  Domain of unknown function (DUF3458_C) ARM repeats


Domain annotation for each model (and alignments):
>> DUF3458_C  Domain of unknown function (DUF3458_C) ARM repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.5e-06     0.045      66     139 ..       7      77 ..       3      87 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-06
                                       S---H.HHHCTT-SSB-HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHC--SHHHHHHHHHHHHHHHHHHHHH CS
                         DUF3458_C  66 tlPse.aelaeqlkevdpdaihaarealrkalaealedellalyealaaegayspdaaaagrRaLknlaLsylaa 139
                                       +lP+e ++l+e+   +d d+  ++ e++ +a ae+l++e ++ y++   +g+y+  +    +R+L   + ++ + 
  gi|336252414|ref|YP_004595521.1|   7 ELPQEfRDLIEEQ-IADHDQFDTVDEFVARATAEKLQQEAKEEYRK---QGTYTDGPITEEERQLHRRLVDLGVI 77 
                                       6676534555554.47****************************97...46677777777788888887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 664.08
//
Query:       gi|336252415|ref|YP_004595522.1|  [L=114]
Description: hypothetical protein Halxa_1007 [Halopiger xanaduensis SH-6]
Scores for 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:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 911.51
//
Query:       gi|336252416|ref|YP_004595523.1|  [L=110]
Description: hypothetical protein Halxa_1008 [Halopiger xanaduensis SH-6]
Scores for 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   15.5   0.0       0.02   15.2   0.0    1.2  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit
      0.021   14.8   0.1      0.032   14.2   0.1    1.2  1  PUA         PUA domain
      0.041   13.9   0.0      0.072   13.2   0.0    1.4  1  TGS         TGS domain
       0.12   12.3   0.1       0.16   11.9   0.1    1.2  1  DUF4180     Domain of unknown function (DUF4180)


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 ?   15.2   0.0   4.6e-06      0.02      22      76 ..      15      69 ..       4      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.6e-06
                                      ECSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCSSSSEEEEESCS CS
                        ATP-synt_F 22 evtdeeeieealkelleredigiilitekiaeeirelideykeealPaileIPsk 76
                                      e+ +++ei + ++el e +++ ++  t++++++++ ++d++++ +  +i+e+P k
  gi|336252416|ref|YP_004595523.1| 15 EARTTSEIVDLMQELEEGDSVRVVSETQDVLARVDANVDAWRDWEDDLIIEVPLK 69
                                      477899***********************************************87 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   7.1e-06     0.032      24      56 ..      22      54 ..      19      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.1e-06
                                      EEEEETT--TTSEEEEEETTSCEEEEEEESS-H CS
                               PUA 24 vvevegdfeegdvVaivdedgelvavGlanyss 56
                                      +v+   ++eegd V++v+e + ++a++ an+++
  gi|336252416|ref|YP_004595523.1| 22 IVDLMQELEEGDSVRVVSETQDVLARVDANVDA 54
                                      7788899***********************997 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.6e-05     0.072      36      59 ..      15      38 ..       3      39 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                                      EEEECSEEEETTSBB-SSEEEEEE CS
                               TGS 36 yAlVnGqrvgldhvLedgdvveIv 59
                                       A+   ++v+l ++Le+gd v++v
  gi|336252416|ref|YP_004595523.1| 15 EARTTSEIVDLMQELEEGDSVRVV 38
                                      5777779***************98 PP

>> DUF4180  Domain of unknown function (DUF4180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.5e-05      0.16      71     111 ..       7      47 ..       3      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
                           DUF4180  71 aivGDisaylaaskaLrdfvyEsnkgkqiffvadeeeaear 111
                                       +++ D s+++++ +++ d+++E  +g+++++v++++++ ar
  gi|336252416|ref|YP_004595523.1|   7 VFIADTSNEARTTSEIVDLMQELEEGDSVRVVSETQDVLAR 47 
                                       6788*******************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 916.24
//
Query:       gi|336252417|ref|YP_004595524.1|  [L=487]
Description: preprotein translocase subunit SecY [Halopiger xanaduensis SH-6]
Scores for 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-69  233.3  20.3    4.4e-69  233.1  20.3    1.1  1  SecY             SecY translocase
    4.4e-12   45.6   2.1    1.7e-11   43.7   2.1    2.2  1  Plug_translocon  Plug domain of Sec61p


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 !  233.1  20.3   4.9e-73   4.4e-69       1     306 []      73     465 ..      73     465 .. 0.84

  Alignments for each domain:
  == domain 1  score: 233.1 bits;  conditional E-value: 4.9e-73
                                       BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC........... CS
                              SecY   1 sifaLGImPyitasIilqLl.tvvipkleelkkegeegrkkinqitryltvvlalvqalgialslg........... 65 
                                       si+++GI+P++tasI+lqLl ++   +l  l+ ++++++ ++++++++l+vv+ ++++l ++++ g           
  gi|336252417|ref|YP_004595524.1|  73 SILQVGIGPIVTASIVLQLLgGA---NLLGLDTNDPRDQVLYQGLQKVLVVVMVALTGLPMVFASGflpaqqslsig 146
                                       89******************887...777788779*************************99886799********* PP

                                       .......HH.HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHCCHSS.........-HHHH...... CS
                              SecY  66 .......lalllivlqltagtvllmwLgEqitekGiGnGisllifagivarlpkals.........gliel...... 120
                                               + ll++lq++ag+vll++++E+++++G+G+Gi l+i+ag+++rl++ ++         +   +      
  gi|336252417|ref|YP_004595524.1| 147 glqfgqtQVQLLMFLQIFAGGVLLLYMDEVVSKWGVGSGIGLFIIAGVSQRLVAGFIqpaqggffyN---Wymiltg 220
                                       ******9668*******************************************99996777643330...3555555 PP

                                       .......SS...........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBSTT....S.S-EEEEETTCCCSCHH CS
                              SecY 121 .......ale.........gilallllllvtllvillvvyveeaerripvqyakrgrkggqssylPlklnyagviPi 181
                                              + +         +   +++ ll+tll++ +vvy e+++++ip+++a+    +g+++++P+kl+ya+v+P+
  gi|336252417|ref|YP_004595524.1| 221 qmevgsvV-StdglstllmTDGGMIIPLLTTLLIFGIVVYAESVRVEIPLSHARV---KGARGRFPVKLIYASVLPM 293
                                       55545441.144444444422389*****************************54...59***************** PP

                                       HHHHHHHHHHHCCCCS.........................................TCCCS......THHHHHHHH CS
                              SecY 182 Ifassllalpstiaqfl........................................lalls......psvlyvvly 212
                                       I++++l+a  +++ q+l                                            +      + ++++ + 
  gi|336252417|ref|YP_004595524.1| 294 ILVRALQANIQMLGQILnsqwagmpsalgqytegeavggffyylapiyrpqdwmwwtG---AvtqeawQVLIRISVD 367
                                       ********65555555555555555555555577777777777666666655543332...1444454666789999 PP

                                       HHHHHH....HHHHHHTCT.THHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                              SecY 213 vlliif....Fayfyteit.fnpkevaenlkksggfipgir.pgketakyLekvlsritliGalflaliavlpdllg 283
                                       ++++i+    Fa+f++e+t + p+ +a+++++sg++ipg+r +   ++k++e++++++t+iG+++++l+av +++lg
  gi|336252417|ref|YP_004595524.1| 368 LTFMIVggaiFAVFWVETTdMGPEATAQQIQNSGMQIPGFRqNVGVIEKVMERYIPQVTVIGGALVGLLAVWANMLG 444
                                       99999999*********************************999********************************* PP

                                       TS.TT.TTHHHHHHHHHHHHHHH CS
                              SecY 284 asligafggtslLivVgvaletv 306
                                       +  ig+++gt+lL++V+++++++
  gi|336252417|ref|YP_004595524.1| 445 T--IGSVTGTGLLLAVSITYKLY 465
                                       *..999*************9975 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   2.1   1.9e-15   1.7e-11       1      35 []      38      72 ..      38      72 .. 0.98

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.9e-15
                                      HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                   Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                      +lY++l++i L G++s++ +D+f+++Rai+A+++G
  gi|336252417|ref|YP_004595524.1| 38 VLYFFLTNISLLGMQSGGANDLFGQFRAILAGSQG 72
                                      79********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 3918.34
//
Query:       gi|336252418|ref|YP_004595525.1|  [L=170]
Description: 50S ribosomal protein L15 [Halopiger xanaduensis SH-6]
Scores for 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   61.9   0.3    9.5e-17   61.9   0.3    1.5  2  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


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 ?   -4.3   1.2         1   1.8e+04      10      20 ..       9      19 ..       6      23 .. 0.55
   2 !   61.9   0.3   5.3e-21   9.5e-17       2     127 ..      26     142 ..      25     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 1
                                      TTTTTTT-S-- CS
                    Ribosomal_L27A 10 kGqkkrsgvkk 20
                                      +G++++sg+++
  gi|336252418|ref|YP_004595525.1|  9 RGSRTHSGGSH 19
                                      56666666433 PP

  == domain 2  score: 61.9 bits;  conditional E-value: 5.3e-21
                                       GGGTSSTTTTTTTTT-S--......S--.........---.GGG..---EEEEHHHHHHTTTTGTTS.--...---- CS
                    Ribosomal_L27A   2 GktgGrGhkGqkkrsgvkkkpgfeGGqmplyrrlpkrGfk.nskfkkeykvvnlkdLdelideerle.la...deae 73 
                                       G++gGrG++G+ k++  + +p+   G++         Gfk  +  ++e +++++++Lde +     e +a   d+ +
  gi|336252418|ref|YP_004595525.1|  26 GHRGGRGRAGRSKHEFHNYEPK---GKH---------GFKrPQDIREEVAEIDVQKLDEDAILYAAEgVAeetDDGY 90 
                                       9*************97554443...899.........***755578999*********86555554444466799** PP

                                       EEEGGGTTTTSSS....SEEEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A  74 eidleelaeaglikkkdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                        id+++++e g   + d vKvlg+g+++++l+v+a++fS +A+ek   aGG ++
  gi|336252418|ref|YP_004595525.1|  91 AIDARDVVEDGH--EVDTVKVLGSGQVRNALEVTADAFSDAAEEKLADAGGDAV 142
                                       *******66653..47899********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1402.09
//
Query:       gi|336252419|ref|YP_004595526.1|  [L=155]
Description: 50S ribosomal protein L30P [Halopiger xanaduensis SH-6]
Scores for complete 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-10   41.1   0.0    2.1e-10   40.3   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 !   40.3   0.0   1.2e-14   2.1e-10       3      51 .]       4      52 ..       3      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.2e-14
                                      EEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHHHCCCGE CS
                     Ribosomal_L30  3 VtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLkkVkhlV 51
                                      V+++r+ +++ + v++tL++L  + +n+   ++ t ++ Gm++kV+++V
  gi|336252419|ref|YP_004595526.1|  4 VVQVRGEVNRQQTVQDTLEMLNIHSVNHCALVPETDTYTGMVNKVNDYV 52
                                      9**************************55555555*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1286.10
//
Query:       gi|336252420|ref|YP_004595527.1|  [L=223]
Description: 30S ribosomal protein S5 [Halopiger xanaduensis SH-6]
Scores for complete 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-23   82.4   0.5    4.6e-23   81.0   0.1    1.9  2  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
    3.5e-22   77.6   0.2    6.3e-22   76.8   0.0    1.5  2  Ribosomal_S5_C  Ribosomal protein S5, C-terminal 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 !   81.0   0.1   5.1e-27   4.6e-23       1      65 []      52     116 ..      52     116 .. 0.98
   2 ?   -1.6   0.0      0.31   2.8e+03      47      60 ..     189     202 ..     184     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 5.1e-27
                                       XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                      Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                       l+++vl+i++vq++t++Grr +f+++v+vG+++G+vG+++g  ++v  Ai+kAi  Ak+n+++vp
  gi|336252420|ref|YP_004595527.1|  52 LDDEVLDINMVQRMTDSGRRVKFRCVVAVGNRDGYVGYAEGRDDQVGSAIQKAIGIAKLNMIEVP 116
                                       689************************************************************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHT CS
                      Ribosomal_S5  47 atAirkAiekAkkn 60 
                                       a+A  +A e+A ++
  gi|336252420|ref|YP_004595527.1| 189 AKATFNALENASQS 202
                                       67888888888765 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 ?   -3.6   0.0      0.87   7.8e+03       7      19 ..     108     120 ..     105     120 .. 0.78
   2 !   76.8   0.0   7.1e-26   6.3e-22       1      65 [.     137     202 ..     137     208 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.87
                                       EEEEEEE--TT-- CS
                    Ribosomal_S5_C   7 vkvllkpaprGtG 19 
                                       +k+ ++  prG G
  gi|336252420|ref|YP_004595527.1| 108 AKLNMIEVPRGSG 120
                                       6778899999987 PP

  == domain 2  score: 76.8 bits;  conditional E-value: 7.1e-26
                                       EEEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT CS
                    Ribosomal_S5_C   1 tgkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrsp 65 
                                       tgk g+v+v ++pap+G G+ a+++v+avl laGi++ ++ks+g +r+++n++kAtf+AL++ ++ 
  gi|336252420|ref|YP_004595527.1| 137 TGKAGSVEVEVIPAPEGLGLAASDTVHAVLDLAGIENAWTKSHGnTRTTVNLAKATFNALENASQS 202
                                       69***********************************************************97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1928.55
//
Query:       gi|336252421|ref|YP_004595528.1|  [L=182]
Description: 50S ribosomal protein L18P/L5E [Halopiger xanaduensis SH-6]
Scores for 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-31  108.1   0.0    1.4e-19   70.7   0.0    2.2  2  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 
    1.4e-09   38.3   0.0    2.2e-09   37.7   0.0    1.2  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


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 !   70.7   0.0   1.6e-23   1.4e-19       2      98 ..       6      95 ..       5     100 .. 0.95
   2 !   35.7   0.0   8.8e-13   7.9e-09     130     163 .]     100     133 ..      95     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 1.6e-23
                     Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvglt 80
                                      r++v +rrrre +tdY++r rl+        + k Rlv r +nk++++q+++   +gd++la+a+s++l++yg ++   
  gi|336252421|ref|YP_004595528.1|  6 RYKVPMRRRREVRTDYHQRLRLLK-------SGKPRLVARKSNKHTTAQLITPGPQGDETLASAHSSDLEEYGWEAPTS 77
                                      9*********************85.......5678******************************************** PP

                     Ribosomal_L5e 81 nyaaaYatglllarrllk 98
                                      n +aaY+tgll ++r+++
  gi|336252421|ref|YP_004595528.1| 78 NISAAYLTGLLAGQRAVE 95
                                      *************99875 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 8.8e-13
                     Ribosomal_L5e 130 kaiLdvGLartttgakvfgalkgavdgglsiphs 163
                                       +a+Ld+GL+++t g+kvf++ +ga+d+gl+iph+
  gi|336252421|ref|YP_004595528.1| 100 EAVLDIGLNTATPGNKVFAVQEGAIDAGLEIPHN 133
                                       699******************************7 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 !   37.7   0.0   2.4e-13   2.2e-09       7     115 ..      12     129 ..       7     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.4e-13
                                       HCHHHHHH..TTT--.TTSSS-EEEEEE-SS-EEEEEE-T..TT--EEEEECS-SCCCT..S-SSSCHHHHHHHHHH CS
                    Ribosomal_L18p   7 rkrRhkRi..rkkls.gtaerprlvvfrsnrhiyaQvidd..vkgktlasastlekelk..lkstknkeaakkvgel 76 
                                       r+rR+ R   +++l+  ++ +prlv  +sn+h  aQ+i    + ++tlasa + + e       t+n++aa   g l
  gi|336252421|ref|YP_004595528.1|  12 RRRREVRTdyHQRLRlLKSGKPRLVARKSNKHTTAQLITPgpQGDETLASAHSSDLEEYgwEAPTSNISAAYLTGLL 88 
                                       6666666522345555667799****************85327889***99888877666688999*********** PP

                                       HHHHHCHHCHTC-EE--TTSS..S-CHHHHHHHHHHCTSSB CS
                    Ribosomal_L18p  77 iAerakekgiekvvfDrggyk..YhGrvaalAdaaReaGlk 115
                                         +ra+e+g+e++v D g ++     +v a+ ++a +aGl+
  gi|336252421|ref|YP_004595528.1|  89 AGQRAVEAGVEEAVLDIGLNTatPGNKVFAVQEGAIDAGLE 129
                                       ****************9865411456899999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.33
# Mc/sec: 1628.28
//
Query:       gi|336252422|ref|YP_004595529.1|  [L=149]
Description: 50S ribosomal protein L19e [Halopiger xanaduensis SH-6]
Scores for 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-57  192.8   6.3    3.2e-57  192.6   6.3    1.0  1  Ribosomal_L19e  Ribosomal protein L19e
     0.0013   18.4   1.1     0.0013   18.4   1.1    2.1  2  SHOCT           Short C-terminal domain
  ------ inclusion threshold ------
       0.03   14.5   0.9        2.4    8.4   0.3    2.4  2  AbiEi_4         Transcriptional regulator, AbiEi antitoxin
      0.042   13.4   0.4      0.047   13.2   0.4    1.1  1  Lant_dehydr_C   Lantibiotic biosynthesis dehydratase C-term
        2.9    6.1   5.5        3.1    6.0   5.5    1.0  1  CDC45           CDC45-like protein


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 !  192.6   6.3     9e-61   3.2e-57       1     142 [.       3     144 ..       3     146 .. 0.99

  Alignments for each domain:
  == domain 1  score: 192.6 bits;  conditional E-value: 9e-61
                                       -THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGG CS
                    Ribosomal_L19e   1 dlklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsG 77 
                                       dl++qkrlaa+vl+vG+nr+wldp+++ +iaeAitr++ir+l+++g I+++++kgnsr+rarer++k+++g+++g+G
  gi|336252422|ref|YP_004595529.1|   3 DLSAQKRLAADVLDVGENRIWLDPDAQGDIAEAITRDEIRELVEEGRIQAEDAKGNSRGRARERNAKRSYGHQKGPG 79 
                                       5899************************************************************************* PP

                                       G--S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT- CS
                    Ribosomal_L19e  78 krkGtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiek 142
                                       kr+G+k+aR++eke+W ++iRa+Rr+L+elr+k++++ ++YrelY+ka Ggef++++ L +yi++
  gi|336252422|ref|YP_004595529.1|  80 KRRGKKGARQNEKEEWESKIRAQRRKLRELRDKGELTPTQYRELYKKAGGGEFRSVRYLLNYIDD 144
                                       ***************************************************************87 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.4   5.2e+03      15      19 ..      36      40 ..      34      45 .. 0.73
   2 !   18.4   1.1   3.7e-07    0.0013       2      23 ..     102     123 ..     101     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.4
                             SHOCT 15 IteEE 19
                                      It++E
  gi|336252422|ref|YP_004595529.1| 36 ITRDE 40
                                      77776 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.7e-07
                             SHOCT   2 aLekLkeLyarGeIteEEFeak 23 
                                       + +kL+eL+++Ge+t   +++ 
  gi|336252422|ref|YP_004595529.1| 102 QRRKLRELRDKGELTPTQYREL 123
                                       679*************999886 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.013        48      24      38 ..      36      50 ..      20      51 .. 0.81
   2 ?    8.4   0.3   0.00067       2.4      27      46 ..     104     124 ..      97     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.013
                           AbiEi_4 24 ispsalrrLvrkGwL 38
                                      i++  +r+Lv++G++
  gi|336252422|ref|YP_004595529.1| 36 ITRDEIRELVEEGRI 50
                                      55555********98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00067
                           AbiEi_4  27 salrrLvrkGwLvrlr.rGvY 46 
                                       + lr+L++kG+L+    r +Y
  gi|336252422|ref|YP_004595529.1| 104 RKLRELRDKGELTPTQyRELY 124
                                       45**********998777666 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 ?   13.2   0.4   1.3e-05     0.047     160     273 ..       8     129 ..       3     142 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHSSSS-HHHHH..HHHHHHHHHHHHTSTTHHH.HHHHHHHHHHHTHHHHHHH..HHHHHHHHH-SSS CS
                     Lant_dehydr_C 160 lglalqlvdvllstfgldleekvdlleryaeaflaefsdtkkalrealdrkyraqrealear..lravlaaaaepes 234
                                        +la++++dv    + ld +++ d++e  ++    e ++ +++ r +++++  + r + ++r   r++ ++   +++
  gi|336252422|ref|YP_004595529.1|   8 KRLAADVLDVGENRIWLDPDAQGDIAEAITR---DEIRELVEEGRIQAEDAKGNSRGRARERnaKRSYGHQKGPGKR 81 
                                       5667777777777777777777777777777...5555555556666666555444444443104455566666666 PP

                                       -SS.....HHHHHHHHHHHHHHHHHHHHHHTTS-----.........T CS
                     Lant_dehydr_C 235 egesadlppflaewaerlrelrrrlealeasgeltlds.........l 273
                                        g+++ +++  +ew ++ r+ rr+l++l ++gelt  +          
  gi|336252422|ref|YP_004595529.1|  82 RGKKGARQNEKEEWESKIRAQRRKLRELRDKGELTPTQyrelykkagG 129
                                       77777777999************************9666666655554 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.5   0.00088       3.1     125     219 ..      43     120 ..       6     134 .. 0.46

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00088
                             CDC45 125 aleeeeesdeedeeeeeeddddeeeeeeeeedeedeeedeeeskkkrksksdeeee........sddddersrkrrr 193
                                       +l ee                          + + e+++++++++ r+++++++          + ++  r++++++
  gi|336252422|ref|YP_004595529.1|  43 ELVEEG-------------------------RIQAEDAKGNSRGRARERNAKRSYGhqkgpgkrRGKKGARQNEKEE 94 
                                       222222.........................2222333333333333322222111111222223333344444444 PP

                             CDC45 194 sepsakklrrqlkkerrkyeavleky 219
                                       +e++ +++rr+l+++r+k e + ++y
  gi|336252422|ref|YP_004595529.1|  95 WESKIRAQRRKLRELRDKGELTPTQY 120
                                       44444455555555555555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1059  (0.0590663); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1158.17
//
Query:       gi|336252423|ref|YP_004595530.1|  [L=239]
Description: 50S ribosomal protein L32e [Halopiger xanaduensis SH-6]
Scores for 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-32  110.8   0.2    8.2e-32  109.9   0.2    1.5  1  Ribosomal_L32e   Ribosomal protein L32
    4.5e-13   49.6   4.4    5.5e-13   49.3   0.9    2.8  2  HHH_5            Helix-hairpin-helix domain
    1.1e-06   28.3   0.0      7e-06   25.8   0.0    2.2  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    1.4e-06   27.8   1.8      0.061   13.2   0.0    3.2  3  HHH              Helix-hairpin-helix motif
    1.2e-05   25.2   0.6    2.9e-05   24.1   0.6    1.6  1  HHH_2            Helix-hairpin-helix motif
    0.00034   20.8   0.0     0.0019   18.4   0.0    2.2  2  Cdd1             Pathogenicity locus
  ------ inclusion threshold ------
      0.044   14.1   2.2          1    9.7   0.2    2.9  3  HHH_8            Helix-hairpin-helix domain
      0.054   13.8   0.1        5.7    7.3   0.1    2.7  2  HHH_3            Helix-hairpin-helix motif
       0.13   13.3   2.3       0.96   10.5   0.4    2.8  3  LytR_C           LytR cell envelope-related transcriptional a


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 !  109.9   0.2   4.1e-35   8.2e-32       1     108 []     122     227 ..     122     227 .. 0.99

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 4.1e-35
                                       ------TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE CS
                    Ribosomal_L32e   1 tkkFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenk 77 
                                       +++F+r++++ +++  eswr+prG  +++r+ +kg+ + +++G+++p+++rg +psGf++v+V+nv++Le ++  ++
  gi|336252423|ref|YP_004595530.1| 122 KPQFKRQDYHMKKRTPESWRRPRGQLSKQRKGIKGKGPKVQAGFRTPEAVRGKHPSGFEEVYVENVDDLEGVDGDRE 198
                                       689************************************************************************** PP

                                       ..EEEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                    Ribosomal_L32e  78 syaaeiahsVsskkrkeiverAaelgikVtN 108
                                         a++ia+sV+++kr+ i+e A+  +i+V+N
  gi|336252423|ref|YP_004595530.1| 199 --AVRIASSVGARKRERIEEVAEDEDIRVLN 227
                                       ..****************************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 !   49.3   0.9   2.8e-16   5.5e-13       3      54 ..      10      61 ..       8      64 .. 0.95
   2 ?    0.0   0.1      0.67   1.3e+03      22      31 ..     164     173 ..     152     218 .. 0.62

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2.8e-16
                                      HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHH CS
                             HHH_5  3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriile 54
                                      eL ++sG+G++ A al +aG+es+ed+++ad+++La++ GiG+ +A ri+  
  gi|336252423|ref|YP_004595530.1| 10 ELEDISGVGASKADALREAGFESIEDVKEADQDDLAEAEGIGNALAARIKAD 61
                                      899**********************************************865 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.67
                                       T--SHHHHHH CS
                             HHH_5  22 Giesvedlaa 31 
                                       G++++e++  
  gi|336252423|ref|YP_004595530.1| 164 GFRTPEAVRG 173
                                       5555555443 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 !   25.8   0.0   3.5e-09     7e-06       1      42 [.       9      51 ..       9      54 .. 0.89
   2 ?   -0.9   0.0      0.77   1.5e+03      19      30 ..     162     173 ..     161     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.5e-09
                   DNA_pol_lambd_f  1 qlFtkvyGVGpktAkkwyakGirtledlra.krakLtreqqiG 42
                                      q++  + GVG+++A  + ++G+ ++ed+++ ++++L ++  iG
  gi|336252423|ref|YP_004595530.1|  9 QELEDISGVGASKADALREAGFESIEDVKEaDQDDLAEAEGIG 51
                                      68999*************************8778888776666 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.77
                   DNA_pol_lambd_f  19 akGirtledlra 30 
                                       ++G+rt e +r 
  gi|336252423|ref|YP_004595530.1| 162 QAGFRTPEAVRG 173
                                       78****999986 PP

>> HHH  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   3.1e-05     0.061      11      29 ..       9      27 ..       4      28 .. 0.89
   2 !   12.4   0.2   5.7e-05      0.11       1      28 [.      32      59 ..      32      60 .. 0.93
   3 ?   -0.8   0.0      0.88   1.7e+03       2      18 ..     179     195 ..     178     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                                      HHHHTSTT-SHHHHHHHHH CS
                               HHH 11 eeLlalPGVGpktAeaIls 29
                                       eL++++GVG ++A+a ++
  gi|336252423|ref|YP_004595530.1|  9 QELEDISGVGASKADALRE 27
                                      69**************876 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.7e-05
                                      SHHHHHTSSHHHHHTSTT-SHHHHHHHH CS
                               HHH  1 sleglipasreeLlalPGVGpktAeaIl 28
                                      s+e +++a+ ++L++ +G+G + A +I 
  gi|336252423|ref|YP_004595530.1| 32 SIEDVKEADQDDLAEAEGIGNALAARIK 59
                                      6899********************9996 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.88
                                       HHHHHTSSHHHHHTSTT CS
                               HHH   2 leglipasreeLlalPG 18 
                                       +e +   ++++L+ + G
  gi|336252423|ref|YP_004595530.1| 179 FEEVYVENVDDLEGVDG 195
                                       56667778999999987 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.6   1.4e-08   2.9e-05       8      52 ..      14      59 ..      11      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.4e-08
                             HHH_2  8 IrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsiv 52
                                      I  VG++ A +L ++ F+s++  k+a+ ++L+e ++iG+  A+ i+
  gi|336252423|ref|YP_004595530.1| 14 ISGVGASKADALREAgFESIEDVKEADQDDLAEAEGIGNALAARIK 59
                                      778*********9866**************************9996 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   9.4e-07    0.0019       3      43 ..       6      46 ..       4      62 .. 0.92
   2 ?   -0.8   0.0      0.92   1.8e+03      24      40 ..     162     178 ..     158     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.4e-07
                              Cdd1  3 kalkelqdiPniGkalaedlvelGirsveelkgedpeelye 43
                                      ++ +el+di ++G + a+ l+e G++s+e++k+ d ++l e
  gi|336252423|ref|YP_004595530.1|  6 DEPQELEDISGVGASKADALREAGFESIEDVKEADQDDLAE 46
                                      56799*****************************9999876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.92
                              Cdd1  24 elGirsveelkgedpee 40 
                                       + G+r++e ++g++p  
  gi|336252423|ref|YP_004595530.1| 162 QAGFRTPEAVRGKHPSG 178
                                       56899999999999964 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.023        47      46      65 ..       9      27 ..       2      29 .. 0.83
   2 ?    9.7   0.2   0.00053         1      33      64 ..      23      59 ..      22      60 .. 0.75
   3 ?   -3.3   0.0       6.1   1.2e+04      55      66 ..     206     217 ..     197     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.023
                                      TTHCTTSTT--HHHHHHHHH CS
                             HHH_8 46 eeeltklpgiGkkiaakiee 65
                                      + el+++ g+G++ a+ ++e
  gi|336252423|ref|YP_004595530.1|  9 Q-ELEDISGVGASKADALRE 27
                                      3.59*********9999988 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00053
                                      CCCCC-SS.-HHHHTT....HCTTSTT--HHHHHHHH CS
                             HHH_8 33 raiealpe.eitslee....eltklpgiGkkiaakie 64
                                      +a+++ ++  i++++e    +l +  giG+++aa+i+
  gi|336252423|ref|YP_004595530.1| 23 DALREAGFeSIEDVKEadqdDLAEAEGIGNALAARIK 59
                                      666777766777773334589**************96 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 6.1
                                       --HHHHHHHHHH CS
                             HHH_8  55 iGkkiaakieei 66 
                                       +G++ +++iee 
  gi|336252423|ref|YP_004595530.1| 206 VGARKRERIEEV 217
                                       777778888886 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.026        51      14      45 ..       9      35 ..       7      39 .. 0.72
   2 ?    7.3   0.1    0.0029       5.7       8      30 ..      36      58 ..      35      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.026
                             HHH_3 14 eeLqklpGlgpklAknIvayReknGpfksree 45
                                      +eL+ ++G+g+++A+++ ++      f+s+e+
  gi|336252423|ref|YP_004595530.1|  9 QELEDISGVGASKADALREAG-----FESIED 35
                                      689999999999999875543.....555555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0029
                             HHH_3  8 iNtAsaeeLqklpGlgpklAknI 30
                                      +  A+ ++L+  +G+g +lA +I
  gi|336252423|ref|YP_004595530.1| 36 VKEADQDDLAEAEGIGNALAARI 58
                                      567999****************9 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00048      0.96      12      66 ..      14      66 ..      12      87 .. 0.64
   2 ?    0.0   0.0      0.89   1.8e+03      17      33 ..      88     104 ..      80     119 .. 0.79
   3 ?    0.1   0.0      0.85   1.7e+03      43      69 ..     180     213 ..     152     228 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00048
                            LytR_C 12 vsGlAarvadaLeerGf.tvgevgnagnadee.....ttivyreaaaaaakalaaalglge 66
                                      +sG+ a+ adaL+e+Gf  + +   + +ad++       i      +a a +++a++g  e
  gi|336252423|ref|YP_004595530.1| 14 ISGVGASKADALREAGFeSIED---VKEADQDdlaeaEGIG-----NALAARIKADVGDLE 66
                                      89***************66666...4444333222321111.....135556666666555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.89
                            LytR_C  17 arvadaLeerGftvgev 33 
                                       ++v ++L++rG t  ++
  gi|336252423|ref|YP_004595530.1|  88 EDVETELRARGLTEKTP 104
                                       57899999999977664 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.85
                            LytR_C  43 ttivy.......reaaa...aaakalaaalglgelqe 69 
                                        +++        +       ++a ++a+++g  +++ 
  gi|336252423|ref|YP_004595530.1| 180 EEVYVenvddleG---VdgdREAVRIASSVGARKRER 213
                                       4444433333221...023247778888887555333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1899.10
//
Query:       gi|336252424|ref|YP_004595531.1|  [L=177]
Description: 50S ribosomal protein L6P [Halopiger xanaduensis SH-6]
Scores for complete 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  102.4   1.0    2.8e-14   53.5   0.1    2.1  2  Ribosomal_L6  Ribosomal protein L6
  ------ inclusion threshold ------
       0.51   10.5   4.2          2    8.6   0.2    3.1  4  HSP20         Hsp20/alpha crystallin family


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 !   53.5   0.1   3.2e-18   2.8e-14       1      76 []       7      79 ..       7      79 .. 0.98
   2 !   48.1   0.1   1.6e-16   1.4e-12       1      76 []      91     165 ..      91     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 3.2e-18
                                      CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                      Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                      iP++v+v+i++   v+v Gp g++tr++++  +v v+v++++v+ ++ s++ k+++  +gt+ s+i n  +GVteg
  gi|336252424|ref|YP_004595531.1|  7 IPDNVTVEIDH-LDVTVDGPEGSVTRRLWYP-DVSVDVDDDSVVIESESEDAKTNA-TVGTFESHITNAFHGVTEG 79
                                      8*********8.*******************.9999999*****************.*****************98 PP

  == domain 2  score: 48.1 bits;  conditional E-value: 1.6e-16
                                       CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHH CS
                      Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGV 73 
                                       +P+ vrv+++++ ++++lG+k +++ +i+ +++v+v+      ++ v+sg dke+v    A+i++ +++  ++ +++
  gi|336252424|ref|YP_004595531.1|  91 FPMQVRVEGDDVVIENFLGEKAPRRTTIHGDTEVTVD-----DEQLVLSGPDKEDVgqtaADIEQLTRVSGKDTRVF 162
                                       8**********************************99.....788999***************************** PP

                                       HTC CS
                      Ribosomal_L6  74 teg 76 
                                       ++g
  gi|336252424|ref|YP_004595531.1| 163 QDG 165
                                       *98 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.18   1.6e+03      20      37 ..       8      25 ..       3      35 .. 0.78
   2 ?    8.6   0.2   0.00023         2      22      48 ..      37      63 ..      29      74 .. 0.80
   3 ?   -2.1   0.0      0.48   4.3e+03      23      34 ..      93     104 ..      79     111 .. 0.67
   4 ?    1.7   0.1     0.032   2.9e+02      22      42 ..     121     140 ..     115     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.18
                                      CCCEEEEEETTEEEEEEE CS
                             HSP20 20 keelkvkvednrvlvkge 37
                                      +++++v+++   v+v g 
  gi|336252424|ref|YP_004595531.1|  8 PDNVTVEIDHLDVTVDGP 25
                                      678888888888888875 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00023
                                      CEEEEEETTEEEEEEE--..---TT-- CS
                             HSP20 22 elkvkvednrvlvkgeheeeeedekgl 48
                                      ++ v+v+d++v++++e e+ + + ++ 
  gi|336252424|ref|YP_004595531.1| 37 DVSVDVDDDSVVIESESEDAKTNATVG 63
                                      89****************666665554 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.48
                                       EEEEEETTEEEE CS
                             HSP20  23 lkvkvednrvlv 34 
                                       ++v ve++ v++
  gi|336252424|ref|YP_004595531.1|  93 MQVRVEGDDVVI 104
                                       456666666666 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.032
                                       CEEEEEETTEEEEEEE--..- CS
                             HSP20  22 elkvkvednrvlvkgeheeee 42 
                                       + +v+v+d++++ +g  + e+
  gi|336252424|ref|YP_004595531.1| 121 DTEVTVDDEQLVLSGPDK-ED 140
                                       7799*********99888.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1350.05
//
Query:       gi|336252425|ref|YP_004595532.1|  [L=130]
Description: 30S ribosomal protein S8 [Halopiger xanaduensis SH-6]
Scores for 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-24   84.1   0.0    9.4e-24   83.8   0.0    1.1  1  Ribosomal_S8  Ribosomal protein S8


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 !   83.8   0.0   5.2e-28   9.4e-24       1     127 []       5     130 .]       5     130 .] 0.89

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 5.2e-28
                                       -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCCEEEEE-BSSS-SBSSSEEEE- CS
                      Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkkikielkynkkkksvikklkrv 75 
                                       Dp++++l+ i Nae++++ + ev pas+ + ++l+v+ ++Gyi++fe++ + k  ++++elk   ++++ +k   r+
  gi|336252425|ref|YP_004595532.1|   5 DPLSNALSGIDNAESVGHLTHEVtPASNEIGSVLEVFYDRGYIDGFEYVdDGKAGQFEVELKGAINECGPVK--PRY 79 
                                       9***********************************************977777788888887776677766..355 PP

                                       SBTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                      Ribosomal_S8  76 skpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                       s ++ + + k ++     + +G ++v+Ts+G+m++ eAr++++GG+v+ayv+
  gi|336252425|ref|YP_004595532.1|  80 SAGADE-FEKWEKRFLPARDFGALVVTTSSGIMSHYEAREQGIGGQVIAYVY 130
                                       555554.8888888888999*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1037.07
//
Query:       gi|336252426|ref|YP_004595533.1|  [L=68]
Description: 30S ribosomal protein S14 [Halopiger xanaduensis SH-6]
Scores for complete 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   43.7   2.2      2e-11   43.5   2.2    1.1  1  Ribosomal_S14  Ribosomal protein S14p/S29e
     0.0067   16.3   0.4     0.0085   16.0   0.4    1.2  1  DUF4428        Domain of unknown function (DUF4428)


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 !   43.5   2.2   2.2e-15     2e-11      11      54 .]      26      68 .]      17      68 .] 0.90

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.2e-15
                                      .CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE-- CS
                     Ribosomal_S14 11 ptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKaS 54
                                       t +   C+ +Gr +G++ k+ +  +R+cfRe A++   +G+kK++
  gi|336252426|ref|YP_004595533.1| 26 RTGQEEACQRCGRKQGLVGKYDInlCRQCFREIARD---MGFKKYR 68
                                      4778899**************9999***********...*****96 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.4   9.5e-07    0.0085       2      31 ..      33      60 ..      32      68 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.5e-07
                           DUF4428  2 CaiCgkKigllkrlkleDgyvCkdClkKl.s 31
                                      C  Cg K gl +     D ++C  C+ ++  
  gi|336252426|ref|YP_004595533.1| 33 CQRCGRKQGLVG---KYDINLCRQCFREIaR 60
                                      677*********...************9952 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 520.88
//
Query:       gi|336252427|ref|YP_004595534.1|  [L=180]
Description: 50S ribosomal protein L5 [Halopiger xanaduensis SH-6]
Scores for 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-21   75.2   0.0    1.1e-20   73.6   0.0    1.9  2  Ribosomal_L5_C  ribosomal L5P family C-terminus
    1.7e-16   60.2   0.1    2.7e-16   59.6   0.1    1.3  1  Ribosomal_L5    Ribosomal protein L5
  ------ inclusion threshold ------
      0.094   12.9   0.5       0.21   11.8   0.5    1.6  1  Hva1_TUDOR      Hypervirulence associated proteins TUDOR doma


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 !   73.6   0.0   1.8e-24   1.1e-20       1      82 [.      68     147 ..      68     165 .. 0.82
   2 ?   -1.5   0.0      0.49   2.9e+03       4      24 ..     153     173 ..     150     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 1.8e-24
                    Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivtta 77 
                                       piG+kvtLrge+++efl+++l ++           +s+fd++Gn+sfGi+e+++fp  eyd++ gifG+d+t+ + +
  gi|336252427|ref|YP_004595534.1|  68 PIGAKVTLRGEDAHEFLETALPLADL--S------ASQFDDTGNFSFGIEEHTDFPSQEYDPNVGIFGLDVTVNLVR 136
                                       8*****************99887754..3......77**************************************99 PP

                    Ribosomal_L5_C  78 k...tde...e 82 
                                       +   +++    
  gi|336252427|ref|YP_004595534.1| 137 PgyrVSKrdkA 147
                                       97773333441 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.49
                    Ribosomal_L5_C   4 vkvtLrgekmyefldkllevv 24 
                                        k  L+ e+++ fl++ ++v 
  gi|336252427|ref|YP_004595534.1| 153 SKHRLNPEDAVAFLESTFDVT 173
                                       566788999999999988775 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.1   4.5e-20   2.7e-16       2      57 .]      12      64 ..      11      64 .. 0.98

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 4.5e-20
                                      CTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                      Ribosomal_L5  2 vMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                       M++Pr+eK+v++mgvG+ g++   l ka+++++e+t Q+ v+t+akk+ ++F+iR
  gi|336252427|ref|YP_004595534.1| 12 EMREPRVEKVVVHMGVGQGGRE---LGKAEDIIEEVTEQESVRTQAKKTEPDFGIR 64
                                      6*********************...******************************9 PP

>> Hva1_TUDOR  Hypervirulence associated proteins TUDOR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   3.5e-05      0.21      10      45 ..      30      65 ..      27      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.5e-05
                        Hva1_TUDOR 10 gGestGkVeevltedteakgvtvnaskddPryeien 45
                                      gG+  Gk e++++e te++ v+ +a+k +P + i++
  gi|336252427|ref|YP_004595534.1| 30 GGRELGKAEDIIEEVTEQESVRTQAKKTEPDFGIRQ 65
                                      89999*************************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); 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:                         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 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1375.13
//
Query:       gi|336252428|ref|YP_004595535.1|  [L=233]
Description: 30S ribosomal protein S4e [Halopiger xanaduensis SH-6]
Scores for complete 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-22   79.0   0.0    3.6e-22   78.0   0.0    1.5  1  Ribosomal_S4e  Ribosomal family S4e
    5.5e-11   42.4   0.2    7.9e-11   41.9   0.2    1.3  1  RS4NT          RS4NT (NUC023) domain
    2.6e-05   23.9   0.0    4.5e-05   23.1   0.0    1.4  1  S4             S4 domain
  ------ inclusion threshold ------
      0.027   14.3   0.0      0.079   12.8   0.0    1.8  2  S4_2           S4 domain
      0.055   13.4   0.5       0.16   11.9   0.5    1.9  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 !   78.0   0.0     1e-25   3.6e-22       2      74 ..      91     164 ..      90     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 1e-25
                                       TEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEES.STT-STTEEEEEETTTTE CS
                     Ribosomal_S4e   2 genyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtiryp.dpdikvnDtvkidleenk 74 
                                       +e+yr+++d+ gr+al++I++e a+ +L Ki +k+ v++g +ql++hdG++++++   +++ nD+++id ++++
  gi|336252428|ref|YP_004595535.1|  91 EEYYRVFPDEGGRLALTEIDAEAAESRLGKIDNKQQVPGGDTQLTLHDGTNVLVEdGAEYSSNDSIVIDNDDKS 164
                                       79*****************************************************7567**********99886 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.2   2.2e-14   7.9e-11       4      35 ..       2      33 ..       1      35 [. 0.95

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 2.2e-14
                                      ---EETTTS-TTS---SSSSSEE----SSSS- CS
                             RS4NT  4 kkHLKrlaAPkhWpldkkegvfavkPspGPHk 35
                                       kH Krl+ Pk+Wp+++k+ +f+vk  +GPH 
  gi|336252428|ref|YP_004595535.1|  2 TKHQKRLSVPKTWPVERKTDTFTVKAGAGPHG 33
                                      69*****************************6 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.3e-08   4.5e-05       2      48 .]      38      85 ..      37      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.3e-08
                                      EHHHHH.HHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                                S4  2 RLdkvl.arlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                      +L ++l   lg++ s +eAr + ++  +lVNG++++d   +++  D+i
  gi|336252428|ref|YP_004595535.1| 38 PLVVLLrDVLGYVDSTKEARYALSEDAILVNGQPINDEQRPIGIFDII 85
                                      678888866*****************************9999988876 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.2e-05     0.079      16      59 ..      46      89 ..      34      96 .. 0.82
   2 ?   -3.1   0.0         2   7.3e+03      28      39 ..     134     146 ..     128     150 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                              S4_2 16 laglvesGgeaKafiaegeVkvNGevetrRgkKlraGdvVeidg 59
                                      ++g+v+s  ea++ ++e +++vNG+  +   + +   d++ ++g
  gi|336252428|ref|YP_004595535.1| 46 VLGYVDSTKEARYALSEDAILVNGQPINDEQRPIGIFDIIAFPG 89
                                      568999*******************9998888888888888743 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                              S4_2  28 afiaeg.eVkvNG 39 
                                         + +g +V+v +
  gi|336252428|ref|YP_004595535.1| 134 LTLHDGtNVLVED 146
                                       5555554455544 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.5   4.6e-05      0.16       2      32 .]     174     208 ..     173     208 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                                       TSEEEESSSTTTTCEEEEEEEETTT....TEEEEE CS
                               KOW   2 GdhVkVvsGphkGktGkVvkvdqhk....vrVfvd 32 
                                       G  V  ++G h Gk+G+V+ +d  +    ++V+vd
  gi|336252428|ref|YP_004595535.1| 174 GALVTAIRGNHGGKIGEVETIDVTPgsgsNTVTVD 208
                                       899**************************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1764.67
//
Query:       gi|336252429|ref|YP_004595536.1|  [L=123]
Description: 50S ribosomal protein L24 [Halopiger xanaduensis SH-6]
Scores for 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   82.3   0.0    3.2e-23   82.0   0.0    1.1  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    2.8e-06   27.1   1.9    5.8e-06   26.1   1.9    1.6  1  KOW            KOW motif


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 !   82.0   0.0   3.6e-27   3.2e-23       1      80 [.       2     114 ..       2     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 3.6e-27
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xx RF
                     Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................gv 45 
                                       s+++ kqr +   ap+h+r+k ++a Ls++Lre+y++r+ +++                                 v
  gi|336252429|ref|YP_004595536.1|   2 SKQPHKQRTQTERAPLHKRQKQLHATLSDDLREEYDTRRTRVNagdtvevmrgdhageegevlkailedgvihveDV 78 
                                       89*************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                     Ribosomal_L26  46 trekangttvpvgihpSkvvItklkl.DkdrkkiLe 80 
                                       t+e a+g++vp++++pS+v It+l+l D++r++ Le
  gi|336252429|ref|YP_004595536.1|  79 TVETADGEEVPRPLDPSNVRITELDLeDERREARLE 114
                                       **************************9999999997 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   1.9   6.5e-10   5.8e-06       2      32 .]      46      76 ..      45      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.5e-10
                                      TSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW  2 GdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                      Gd+V+V++G h+G++G+V+k + +   ++v+
  gi|336252429|ref|YP_004595536.1| 46 GDTVEVMRGDHAGEEGEVLKAILEDGVIHVE 76
                                      9**********************99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 911.58
//
Query:       gi|336252430|ref|YP_004595537.1|  [L=132]
Description: 50S ribosomal protein L14P [Halopiger xanaduensis SH-6]
Scores for 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-37  126.6   0.4    6.4e-37  126.4   0.4    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 !  126.4   0.4   3.5e-41   6.4e-37       3     122 .]      13     132 .]      12     132 .] 0.95

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 3.5e-41
                                       CSS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS- CS
                     Ribosomal_L14   3 qlktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGs 75 
                                       ++++ +++aDN+ga+e+++i+v g++    ++++a +Gd+++vsv k++p   +++++v++av+vr++k++rr+dG+
  gi|336252430|ref|YP_004595537.1|  13 KKGSLVTCADNTGARELKVISVAGYHgtknRQPKAGLGDKVTVSVTKGTP---EMRRQVLEAVIVRQRKSIRRPDGT 86 
                                       568999*****************8876665679*****************...89********************** PP

                                       EEEESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
                     Ribosomal_L14  76 virfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApevl 122
                                        ++f+dnaaV++++++ep+Gt+i+gp+are++e+ f  i+s+A++++
  gi|336252430|ref|YP_004595537.1|  87 RLKFEDNAAVIIDENEEPRGTEIKGPIAREVAER-FGAIASTATMIV 132
                                       *********************************9.********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 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:                        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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 934.07
//
Query:       gi|336252431|ref|YP_004595538.1|  [L=144]
Description: 30S ribosomal protein S17P [Halopiger xanaduensis SH-6]
Scores for 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-25   88.6   1.9    2.8e-25   88.2   1.9    1.1  1  Ribosomal_S17    Ribosomal protein S17
    0.00011   22.5   0.0    0.00019   21.7   0.0    1.4  1  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 !   88.2   1.9   3.1e-29   2.8e-25       1      68 []      39     108 ..      39     108 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 3.1e-29
                                       EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS..--TT-EEEEEEECECSSSEEEEEEE CS
                     Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns..vkvGDiVrieecrPlSktkrfvvve 68 
                                       G+Vvs+ m+kTvvV++e+ v  pky++y+krr+++ ah +     + vGD+V+i+e+rPlSktk++vvve
  gi|336252431|ref|YP_004595538.1|  39 GTVVSTDMEKTVVVEREYDVAVPKYNRYMKRRSRIPAHVPGVLepLSVGDTVKIAETRPLSKTKSHVVVE 108
                                       99**************************************99999***********************96 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 !   21.7   0.0   2.1e-08   0.00019      36      69 .]       3      37 ..       1      37 [. 0.88

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-08
                                      --TT----GGGGS.-----TTSSSSSS----S-EE CS
                   Ribosomal_S17_N 36 vglgfktPkeAie.gtYiDkKCPFtGnvsirGriL 69
                                      +gl  +tP e ++ ++Y   KCPF G+ s+rG++L
  gi|336252431|ref|YP_004595538.1|  3 IGLDVETPPEPENpEEYDYEKCPFYGELSVRGQVL 37
                                      899999*9998873678889*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1142.20
//
Query:       gi|336252432|ref|YP_004595539.1|  [L=153]
Description: ribonuclease P protein component 1 [Halopiger xanaduensis SH-6]
Scores for 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-28   96.1   0.0      1e-27   95.9   0.0    1.0  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 !   95.9   0.0   5.6e-32     1e-27       1      83 [.       6     143 ..       6     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 5.6e-32
                                       HHHCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEE...ECTTEEEEEESTTCEEEEEE............. CS
                           UPF0086   1 ekLlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkiv...tkksrvktvpKegsvFefev............. 61 
                                       e+L +++l+G++v+Vv+s+++s+vgi+G+Vv Et++tl+i+     +srv tvpK+gs+Fef++             
  gi|336252432|ref|YP_004595539.1|   6 ETLPRHELNGLPVRVVESTDDSRVGIAGRVVIETTKTLSIEirnDGESRVITVPKSGSTFEFAItddaadsakgsgt 82 
                                       589*************************************944324577**************************** PP

                                       ........................................TTEEEEEECCCCSSXHHHHHC CS
                           UPF0086  62 .......................................kdvlevevdGsqlryrpadRae 83 
                                                                              +++++v+vdGs+l++rpa+R+e
  gi|336252432|ref|YP_004595539.1|  83 askladtqpsaagngeedraagdtdshrgdpegdrraagEGAAYVTVDGSRLLSRPARRTE 143
                                       ***************************************999*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1142.83
//
Query:       gi|336252433|ref|YP_004595540.1|  [L=73]
Description: 50S ribosomal protein L29 [Halopiger xanaduensis SH-6]
Scores for 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-19   68.1   0.3    6.1e-19   67.7   0.3    1.1  1  Ribosomal_L29  Ribosomal L29 protein
  ------ inclusion threshold ------
      0.028   14.5   0.2       0.32   11.1   0.1    2.0  2  Med9           RNA polymerase II transcription mediator compl
      0.069   12.2   0.0      0.079   12.0   0.0    1.0  1  FUSC-like      FUSC-like inner membrane protein yccS


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 !   67.7   0.3     1e-22   6.1e-19       2      56 ..       8      63 ..       7      63 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 1e-22
                                      HHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHH CS
                     Ribosomal_L29  2 elrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlre 56
                                      e+r+++ +e +e+l+el++eL+n +   a+g ++enp+ri ++R++IARikTv+re
  gi|336252433|ref|YP_004595540.1|  8 EIRDMTPAERQEELEELETELLNSKSVLAAGgAPENPGRIGELRRTIARIKTVQRE 63
                                      9****************************999***********************8 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   5.3e-05      0.32      49      74 ..      11      36 ..       2      38 .. 0.88
   2 ?    1.9   0.0     0.041   2.4e+02      27      47 ..      46      66 ..      39      73 .] 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.3e-05
                              Med9 49 drsveeqeaeieeleeqlakKrelLk 74
                                      d +++e+++e+eele +l + +++L+
  gi|336252433|ref|YP_004595540.1| 11 DMTPAERQEELEELETELLNSKSVLA 36
                                      789***************99999986 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.041
                              Med9 27 ktgelrhkLkkarelirelpg 47
                                       +gelr  + +++++ re  +
  gi|336252433|ref|YP_004595540.1| 46 RIGELRRTIARIKTVQREEGD 66
                                      578888888888887776555 PP

>> FUSC-like  FUSC-like inner membrane protein yccS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.3e-05     0.079     228     282 ..       8      62 ..       6      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                         FUSC-like 228 aillnkpyqhserleraleeleqslellakqnnekekellaalrallrnLrtier 282
                                        i++ +p +++e+le+++ el +s + la+  +++++  + +lr+++++++t++r
  gi|336252433|ref|YP_004595540.1|   8 EIRDMTPAERQEELEELETELLNSKSVLAAGGAPENPGRIGELRRTIARIKTVQR 62 
                                       589999**********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 566.12
//
Query:       gi|336252434|ref|YP_004595541.1|  [L=320]
Description: 30S ribosomal protein S3 [Halopiger xanaduensis SH-6]
Scores for 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-22   78.7   0.7    1.4e-21   76.8   0.6    2.1  3  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
      6e-17   61.2   0.1    1.4e-16   60.0   0.1    1.7  1  KH_2            KH domain
  ------ inclusion threshold ------
      0.034   14.0   1.3      0.092   12.6   0.2    2.4  3  KH_1            KH domain
      0.054   13.6   0.0       0.66   10.1   0.0    2.6  2  KH_5            NusA-like KH domain


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 ?   -2.9   0.0       2.3     1e+04      60      81 ..      14      35 ..      10      36 .. 0.81
   2 !   76.8   0.6     3e-25   1.4e-21       1      83 []      99     182 ..      99     182 .. 0.98
   3 ?   -2.9   0.0       2.4   1.1e+04      54      75 ..     257     278 ..     250     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                                      HHH-EEEEEEEEETTEEEEEEE CS
                    Ribosomal_S3_C 60 radidyavaeaktkyGiiGvkV 81
                                      r++id+ ++e   + G  G +V
  gi|336252434|ref|YP_004595541.1| 14 RSQIDEFFQEELGRAGYGGMEV 35
                                      7789999999888888888877 PP

  == domain 2  score: 76.8 bits;  conditional E-value: 3e-25
                                       HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTE CS
                    Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyG 75 
                                       +a++le+++ fR+a +++i r+m+aga G++i++sG+++ + ++r ek+++G++++  +++++ +d++ a+a +k G
  gi|336252434|ref|YP_004595541.1|  99 LANALERGWYFRKAGHTTIDRIMEAGALGAEIVLSGKVT-GARSRVEKFNRGYIKHngEPAEEIVDEGQATAVMKLG 174
                                       689************************************.89*********************************** PP

                                       EEEEEEEE CS
                    Ribosomal_S3_C  76 iiGvkVwI 83 
                                       +iGv+V+I
  gi|336252434|ref|YP_004595541.1| 175 TIGVTVKI 182
                                       ******98 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.4
                                       ---TCHHHH-EEEEEEEEETTE CS
                    Ribosomal_S3_C  54 vplhtlradidyavaeaktkyG 75 
                                       v+ + ++ad d+ ++e+    G
  gi|336252434|ref|YP_004595541.1| 257 VIEEEVDADADEEFEEVDVPEG 278
                                       6667888999999999887666 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.1   3.2e-20   1.4e-16       2      77 ..      17      89 ..      16      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 3.2e-20
                                      HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETTTG CS
                              KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkkpe 77
                                      i+e++++e+  ag++++e+ +t+ ++ iv+++++pg+vIGkgG+ni+k++++l++++ +le+ +V   + +V +p+
  gi|336252434|ref|YP_004595541.1| 17 IDEFFQEELGRAGYGGMEVAKTPMGTQIVLKAEKPGMVIGKGGENIRKVTTALEEKF-NLEDPQVD--VQEVDEPD 89
                                      899******************************************************.5******9..78888886 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   2.1e-05     0.092       4      25 ..      44      65 ..      41      68 .. 0.81
   2 ?   -2.8   0.0       1.4   6.1e+03      21      33 ..     116     130 ..     113     140 .. 0.65
   3 ?   -3.4   0.0         2   9.1e+03      30      38 ..     177     185 ..     175     196 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                                      EEEGGGHHHHHHTGGGHHHHHH CS
                              KH_1  4 ilvPsslvgriIGkgGsnIkeI 25
                                      i +++++ g +IGkgG+nI++ 
  gi|336252434|ref|YP_004595541.1| 44 IVLKAEKPGMVIGKGGENIRKV 65
                                      5666677799**********86 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.4
                                       HHHHHHHH.H.T-EE CS
                              KH_1  21 nIkeIree.t.gakI 33 
                                       +I +I+e    ga I
  gi|336252434|ref|YP_004595541.1| 116 TIDRIMEAgAlGAEI 130
                                       788888832445555 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2
                                       T-EEEEESS CS
                              KH_1  30 gakIkvpks 38 
                                       g+ +k++++
  gi|336252434|ref|YP_004595541.1| 177 GVTVKIIPP 185
                                       888888843 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.29   1.3e+03      50      66 ..       3      19 ..       2      20 .. 0.87
   2 ?   10.1   0.0   0.00015      0.66      19      41 ..      51      72 ..      42      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.29
                              KH_5 50 DlaefianalsPaevls 66
                                      D ++fi+n l+++++++
  gi|336252434|ref|YP_004595541.1|  3 DEQQFIENGLQRSQIDE 19
                                      7799********99975 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00015
                              KH_5 19 vGaivgkkGsrikavsseLkgek 41
                                       G ++gk+G++i++v   L +ek
  gi|336252434|ref|YP_004595541.1| 51 PGMVIGKGGENIRKVTTAL-EEK 72
                                      6999***************.776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1434  (0.0799822); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); 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):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.41
# Mc/sec: 2370.27
//
Query:       gi|336252435|ref|YP_004595542.1|  [L=163]
Description: 50S ribosomal protein L22 [Halopiger xanaduensis SH-6]
Scores for 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-20   71.7   0.0      6e-20   71.4   0.0    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 !   71.4   0.0   3.4e-24     6e-20       2     102 ..      18     148 ..      17     149 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 3.4e-24
                                       EEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST............................THHHHHHHHH CS
                     Ribosomal_L22   2 kgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk............................aakfvlklLk 48 
                                       + ++ ++s+k+ +evar ++g++v +A +yL++  ++k+                            ++ ++l+lL+
  gi|336252435|ref|YP_004595542.1|  18 MLRERHMSHKHSKEVARELKGRTVGDAQDYLQDviDQKQsvpfkshnagaghrsdlegwdagkypekVSGEFLDLLE 94 
                                       678889****************************988889************************************* PP

                                       HHHHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEE CS
                     Ribosomal_L22  49 naeanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvl 102
                                       n+ ana+++g d +s+ I+++ ++k  +  +r++rA+Gr++ ++ + + +e+v+
  gi|336252435|ref|YP_004595542.1|  95 NVAANADHQGFDGESMEIVHVAAHKVGESVGRKPRAMGRASSWNTPQVDVEIVV 148
                                       ****************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1239.81
//
Query:       gi|336252436|ref|YP_004595543.1|  [L=141]
Description: 30S ribosomal protein S19 [Halopiger xanaduensis SH-6]
Scores for 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-32  109.8   0.0      6e-32  109.4   0.0    1.2  1  Ribosomal_S19    Ribosomal protein S19
  ------ inclusion threshold ------
      0.012   15.9   1.6      0.017   15.4   1.6    1.3  1  Siah-Interact_N  Siah interacting protein, N terminal
      0.083   11.9   0.1      0.091   11.8   0.1    1.1  1  Citrate_synt     Citrate synthase, C-terminal domain


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 !  109.4   0.0     1e-35     6e-32       1      81 []      42     124 ..      42     124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 1e-35
                                       .HHHSS.TTCCCHHHHHHH.HHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-S CS
                     Ribosomal_S19   1 rslkkg.pfvqesllkkvr.kakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspT 75 
                                       rs+k+g + ++++ll+++r k ++e+++ +i+th+Rd+ IlPe+vglt++VynG++f +v+i++emvGh+LgEF++T
  gi|336252436|ref|YP_004595543.1|  42 RSIKRGlSVEKQKLLEEARdKGEEETANAPIRTHLRDMPILPEFVGLTFEVYNGQSFERVRIEPEMVGHYLGEFQLT 118
                                       89****9999********95666888*************************************************** PP

                                       S----S CS
                     Ribosomal_S19  76 rkpvkh 81 
                                       r+ v+h
  gi|336252436|ref|YP_004595543.1| 119 RTSVEH 124
                                       ****99 PP

>> Siah-Interact_N  Siah interacting protein, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.6   2.9e-06     0.017       2      49 ..      20      68 ..      19      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-06
                   Siah-Interact_N  2 aleelq.kDlEElkkLlekAtRkrVkdlLsaeirKleteilklkekqka 49
                                      +l+elq + lEE+ +Ll   +R  +k  Ls+e++Kl  e     e+++a
  gi|336252436|ref|YP_004595543.1| 20 TLDELQdMELEEVAELLPARQRRSIKRGLSVEKQKLLEEARDKGEEETA 68
                                      688998569***************************9999555554444 PP

>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.5e-05     0.091      17      64 ..       8      48 ..       2      88 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
                                      TTTTE.EEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHH CS
                      Citrate_synt 17 gekge.lrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeel 64
                                      g++ge  +YRG++++eL     ++eeva lL     P   + +++k+ l
  gi|336252436|ref|YP_004595543.1|  8 GREGEeFTYRGHTLDELQ--DMELEEVAELL-----PA-RQRRSIKRGL 48
                                      5556679*********87..799********.....63.4444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); 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:                         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: 1119.94
//
Query:       gi|336252437|ref|YP_004595544.1|  [L=240]
Description: 50S ribosomal protein L2 [Halopiger xanaduensis SH-6]
Scores for complete 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-45  154.1   2.7      3e-45  153.5   2.7    1.3  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    1.2e-18   66.9   0.0    4.9e-18   64.8   0.0    2.1  2  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


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 !  153.5   2.7   3.3e-49     3e-45       1     120 [.      90     220 ..      90     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 153.5 bits;  conditional E-value: 3.3e-49
                                       SSSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCT CS
                    Ribosomal_L2_C   1 kvGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehk 77 
                                       k+Gn+lpl++ipeG+ v+n+e ++g+ggk+ar++G  a +++++++ ++++lpSgev++++ +crAtiGvv++g+++
  gi|336252437|ref|YP_004595544.1|  90 KPGNTLPLAEIPEGVPVCNVEANQGDGGKFARASGVNADLITHDRNAAVIQLPSGEVKRLDPQCRATIGVVAGGGRT 166
                                       68*************************************************************************** PP

                                       T----STTHHHHT.....TBS----SSSS-TTTSSS--SS....SS..--SSSS CS
                    Ribosomal_L2_C  78 ekklgkAgrkrwl.....grrpkvrGvamnpvdHphGGGe....Gk..tksrka 120
                                       ek+++kAg+k+++     +++p+vrGvamn+vdHp+GGG     Gk  ++sr+a
  gi|336252437|ref|YP_004595544.1| 167 EKPMVKAGNKHHKmkargTKWPRVRGVAMNAVDHPFGGGGrqhpGKpkSVSRDA 220
                                       *****************99*******************9866776643444655 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 !   64.8   0.0   5.5e-22   4.9e-18       1      75 [.      11      81 ..      11      83 .. 0.94
   2 ?   -1.7   0.0      0.32   2.9e+03      42      59 ..     149     166 ..     131     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 5.5e-22
                                      TB-TT.--BSSTT--------EE-B--S---SS..--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE CS
                      Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkrnkek..vkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtv 75
                                      Gr++s +r+++++++         +d+k ++++  v+g+Vv+ie+Dp+RsAp+A v++edg++r+i+ peg++vG+++
  gi|336252437|ref|YP_004595544.1| 11 GRGTStFRAPSHRYKA-------KLDHKNEEDDdvVRGTVVDIEHDPARSAPVAAVEFEDGDQRLILVPEGISVGEEI 81
                                      9***************.......899988666678****************************************998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.32
                                       --TT-SS-EEEEEETTTE CS
                      Ribosomal_L2  42 yDpgRsApiAlvkyedge 59 
                                        Dp   A i+ v+ +  +
  gi|336252437|ref|YP_004595544.1| 149 LDPQCRATIGVVAGGGRT 166
                                       588888999998877644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.19s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1853.18
//
Query:       gi|336252438|ref|YP_004595545.1|  [L=84]
Description: 50S ribosomal protein L23 [Halopiger xanaduensis SH-6]
Scores for complete 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   60.6   2.0    4.8e-16   58.9   2.0    1.7  1  Ribosomal_L23  Ribosomal protein L23
  ------ inclusion threshold ------
      0.063   13.3   0.1      0.075   13.0   0.1    1.2  1  CE2_N          Carbohydrate esterase 2 N-terminal
       0.12   12.3   0.9       0.21   11.5   0.9    1.5  1  SSrecog        Structure-specific recognition protein (SSRP1)


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 !   58.9   2.0   8.1e-20   4.8e-16       2      60 ..       4      64 ..       3      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 8.1e-20
                                      SEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE.--EBES CS
                     Ribosomal_L23  2 vilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnv.kgkkkr 60
                                      +i  P++tEk+++ ++  nk+ F V++da+K+ei++ ve+ F+V V++Vnt++  kgkkk 
  gi|336252438|ref|YP_004595545.1|  4 IIEHPLVTEKAMNDMDFeNKLQFVVNPDATKPEIRDVVEERFDVSVDNVNTQVTmKGKKKA 64
                                      7889***********9769********************************8761555552 PP

>> CE2_N  Carbohydrate esterase 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.3e-05     0.075      38      78 ..      37      77 ..      14      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                                      ..SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEEEEEEEE CS
                             CE2_N 38 kedkgknrlaviiDgkrvkdlkldgeektytlaeglepgeh 78
                                       +d+ ++r++v++D+  +++ ++ +++ t++l e++ ++e+
  gi|336252438|ref|YP_004595545.1| 37 IRDVVEERFDVSVDNVNTQVTMKGKKKATVRLSEDDDAQEV 77
                                      5668899**********999999888888***999999986 PP

>> SSrecog  Structure-specific recognition protein (SSRP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.9   3.5e-05      0.21      20      54 ..      41      76 ..      15      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.5e-05
                           SSrecog 20 nkpafeiplsevs.ncnlagknEvaleFhqdddaae 54
                                       ++ f++++ +v+ +++++gk+  ++ +++ddda+e
  gi|336252438|ref|YP_004595545.1| 41 VEERFDVSVDNVNtQVTMKGKKKATVRLSEDDDAQE 76
                                      5678********74789**************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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 0.19s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 691.70
//
Query:       gi|336252439|ref|YP_004595546.1|  [L=250]
Description: 50S ribosomal protein L4P [Halopiger xanaduensis SH-6]
Scores for 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-46  156.7   0.1    6.2e-46  156.5   0.1    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 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 !  156.5   0.1   3.4e-50   6.2e-46       1     191 [.      16     249 ..      16     250 .] 0.93

  Alignments for each domain:
  == domain 1  score: 156.5 bits;  conditional E-value: 3.4e-50
                                       EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.....STTSTT-- CS
                      Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.....spiargGg 71 
                                       veL p+vF++++r+dli rav+a +anr+q ++++  a+ ++ +  +++++  G+G+A+v++       +p++++G+
  gi|336252439|ref|YP_004595546.1|  16 VEL-PAVFETNYRPDLIARAVRAAQANRKQDYGADEfAGLRTPA--ESFGS--GRGMAHVPRQDgrgrrVPQTVKGR 87 
                                       789.****************************************..6****..*********9999999******** PP

                                       -SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES.---..-S...........S--HHHHHHHHHHTT-. CS
                      Ribosomal_L4  72 vahgpkperdystklnkKvrrlAlrsaLsakakqglllvvd.nle.ple...........esktkelvellkklgl. 134
                                       +ah+pk+e+d+++++n K+++lA+rsa++a+++++l+  ++ +++ ++e             ktke+v++l++ gl 
  gi|336252439|ref|YP_004595546.1|  88 KAHPPKAEKDWTESINTKEKKLAVRSAIAATTDDELVAERGhEFDdDAEipvvvddefedLVKTKEVVSFLEAAGLa 164
                                       *****************************************8555455555778888889999**********8888 PP

                                       .........................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEE CS
                      Ribosomal_L4 135 .........................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvit 182
                                                                ++ks+L+v+s+ +++  +aarnl+g++v+++ ++n++dl+++++    +v+t
  gi|336252439|ref|YP_004595546.1| 165 ddieradegrsirsgrgktrgrkykTPKSILFVTSS-ESGPSRAARNLAGADVTTAAEVNAEDLAPGAQpgrlTVWT 240
                                       8888888888888899999999998999******96.99************************************** PP

                                       HHHHHHHHH CS
                      Ribosomal_L4 183 ksaveklee 191
                                       +sa+e++++
  gi|336252439|ref|YP_004595546.1| 241 ESALEEVAD 249
                                       *****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 2177.44
//
Query:       gi|336252440|ref|YP_004595547.1|  [L=339]
Description: 50S ribosomal protein L3 [Halopiger xanaduensis SH-6]
Scores for 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-108  362.1   0.1   1.4e-107  359.9   0.1    1.8  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 !  359.9   0.1    8e-112  1.4e-107       1     369 []       1     339 []       1     339 [] 0.94

  Alignments for each domain:
  == domain 1  score: 359.9 bits;  conditional E-value: 8e-112
                                       XX.S.SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEE CS
                      Ribosomal_L3   1 mshrkfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavt 77 
                                       m++   +apr+gslGf prkRa++e+++++s+P d+ +   +l++f+GyKaGmth+V ++d+ +s+++++e +++vt
  gi|336252440|ref|YP_004595547.1|   1 MPQS--NAPRKGSLGFGPRKRASSEVPRFNSWPDDEGQ--PTLQGFAGYKAGMTHVVMVDDQSNSPTEGMEQTVPVT 73 
                                       7766..9**************************99998..789********************************** PP

                                       EEEC--EEEEEEEEEEEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHH CS
                      Ribosomal_L3  78 vvetppmvivgvvgyvetprGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadleeik 154
                                       +vetppm++v++++y++t++G++++++vw+++   e++r l                  y+ +  ++ +   lee +
  gi|336252440|ref|YP_004595547.1|  74 IVETPPMRAVALRAYEDTAYGKQPVTEVWTDEFVSELDRVL------------DLPGDDYDPDAAEDELRGLLEEGR 138
                                       ****************************************9............223455655556666665555433 PP

                                       HSCSCEEEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTC..EEECCCCS-TTSEEEEEEEE---EE CS
                      Ribosomal_L3 155 keasvvrviahtvirktkslaqKkahllEiqvngGtiaekldfarealek..tvavaavFrqgeliDvigvtkGkGf 229
                                            vrvi+htv  +++s+ +Kk++++E++v+gG + e++dfa e le+   + +++vFr+ge++D+ gvtkGkG+
  gi|336252440|ref|YP_004595547.1| 139 --VDDVRVITHTVPTEIPSVPKKKPDVMETRVGGGAVEERVDFALELLEDggEHVMNDVFRAGEYVDASGVTKGKGT 213
                                       ..356**********************************************99************************ PP

                                       E-HHHHCT----STTTSSS..SSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.S CS
                      Ribosomal_L3 230 eGvvkRWgvkklprkthrg..lRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdlt 304
                                       +G+vkRWgv+k+++k++r+  +R+++++g+w+p+rV+stv+++Gq+Gyh+Rtelnk++ +ig+              
  gi|336252440|ref|YP_004595547.1| 214 QGPVKRWGVQKRKGKHARQgwRRRIGNLGPWNPSRVRSTVPQQGQTGYHQRTELNKRLVDIGD-------------- 276
                                       *******************9*******************************************.............. PP

                                       S..SS.TTTCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TTCTSS CS
                      Ribosomal_L3 305 ekeitPmGGfvhyGevkndfilvkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidtaskfg 369
                                       + + t +GGf++yGev+++  l+kGs pGp++rlv++r+++++  +++ ++ev  ++++tas++g
  gi|336252440|ref|YP_004595547.1| 277 GADATVDGGFINYGEVDGPHALIKGSLPGPEQRLVRFRPAIRPGDQPRLDPEV--RYVSTASNQG 339
                                       4556889**********************************************..********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2380.19
//
Query:       gi|336252441|ref|YP_004595548.1|  [L=292]
Description: hypothetical protein Halxa_1033 [Halopiger xanaduensis SH-6]
Scores for 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-71  239.1   0.0    7.7e-71  238.9   0.0    1.0  1  Methyltrn_RNA_3  Putative RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_3  Putative RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.9   0.0   4.3e-75   7.7e-71       1     286 []       2     288 ..       2     288 .. 0.92

  Alignments for each domain:
  == domain 1  score: 238.9 bits;  conditional E-value: 4.3e-75
                   Methyltrn_RNA_3   1 tvsiaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelF 77 
                                       tvs+++Pss++++a++++++t+++g++ARaa+iF+ d++vv++d+++e+ +   +  f++++L+Y++tPpYLr+e +
  gi|336252441|ref|YP_004595548.1|   2 TVSVLVPSSLTREAEDKREATRKLGYVARAATIFRADRLVVYPDRDGETGRF--DGGFVSTVLRYAATPPYLRNEAW 76 
                                       89***********************************************998..9********************** PP

                   Methyltrn_RNA_3  78 plhkelkyaglLppldaphhl..rsseegeyreGvvvekskekkskkklVniGlkkevklel..kqevpegtRVtVk 150
                                       ++++el+yag+Lppl+a      +s+++g++r+G+v+e+ +e+++   +Vn+Gl+++++l++  ++ev+eg+RVtV+
  gi|336252441|ref|YP_004595548.1|  77 GMRDELEYAGVLPPLRAVSQTgsESNDSGSLRQGIVTEVGPEGRV---RVNCGLQHPISLNTppDMEVDEGERVTVR 150
                                       *****************9999966666****************99...9**************************** PP

                   Methyltrn_RNA_3 151 lsseesveakvVspsepreeaglywGYsVrlakslsavftespfeggydlsigtserge.kveeklaelekkkefkh 226
                                       +ss+++v+ak+V+++ p        G sV+++ +lsa+++++    ++ ++i++s++ge  +  +l++l+ +++++ 
  gi|336252441|ref|YP_004595548.1| 151 ISSRRPVRAKLVDEPLP--------GLSVEQT-DLSAALSRE----DAGVRIAASRHGErLTVGRLETLAGRIDRDG 214
                                       *****************........*******.*******98....99***********889999****9999**** PP

                   Methyltrn_RNA_3 227 llivfGg.vrgleaal.............eadeelkle.gekaeelFdlwlntvpnqgsrtirtEEavliaLalL 286
                                       l+++fG+ +rgl+a+l             +ad+  ++e  +++   Fdlwlntvp+qgs+ +rtEEa++++La L
  gi|336252441|ref|YP_004595548.1| 215 LTVAFGApERGLPAILgieasdvaaayggDADDG-NVEpTADPGPGFDLWLNTVPDQGSEVVRTEEALFATLAPL 288
                                       ****************555555555554433322.23345555555**************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2270.08
//
Query:       gi|336252442|ref|YP_004595549.1|  [L=150]
Description: hypothetical protein Halxa_1034 [Halopiger xanaduensis SH-6]
Scores for 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-30  103.7   0.4    6.4e-30  103.5   0.4    1.1  1  DUF4112          Domain of unknown function (DUF4112)
  ------ inclusion threshold ------
      0.021   14.5   0.4       0.03   14.1   0.4    1.3  1  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l


Domain annotation for each model (and alignments):
>> DUF4112  Domain of unknown function (DUF4112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.5   0.4   7.2e-34   6.4e-30       2     103 ..      29     129 ..      28     131 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 7.2e-34
                           DUF4112   2 lkkvrklayllDkalripgcglrfGldpiigliPvvGdvisallslylvleakkaeglpkslllrmlvnialDllig 78 
                                       l++++ +a++lD+ +r+pg+++rfGldpi+g++P++Gd++  ++sly+v ea ++ g++ s+l rml+nia+D++ g
  gi|336252442|ref|YP_004595549.1|  29 LDRMHVVARVLDEGMRVPGTNFRFGLDPIVGILPGAGDTAVGVVSLYIVAEA-ARLGVSLSTLGRMLANIAVDVIGG 104
                                       689999**********************************************.9999******************** PP

                           DUF4112  79 lvPvvGdlfdvlfkantrNaallek 103
                                        vPv+G lfd+++k+n+ N+ l  +
  gi|336252442|ref|YP_004595549.1| 105 SVPVLGVLFDAFWKSNKWNVVLALE 129
                                       *******************988655 PP

>> Phage_holin_2_4  Bacteriophage holin family, superfamily II-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   3.3e-06      0.03      15      56 ..      79     120 ..      67     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-06
                   Phage_holin_2_4  15 katggGavvsfaGflasselialvGlavAliGlLvnWyYkre 56 
                                        a+  G + s +G ++++ ++ ++G  v ++G+L   ++k +
  gi|336252442|ref|YP_004595549.1|  79 EAARLGVSLSTLGRMLANIAVDVIGGSVPVLGVLFDAFWKSN 120
                                       567789999*************************99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1124.91
//
Query:       gi|336252443|ref|YP_004595550.1|  [L=122]
Description: hypothetical protein Halxa_1035 [Halopiger xanaduensis SH-6]
Scores for 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   80.3   0.4    1.2e-22   79.9   0.4    1.2  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.4   6.8e-27   1.2e-22       3      75 .]      33     106 ..      31     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 6.8e-27
                            HalOD1   3 espstaVveavaavegvdptelep.LydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75 
                                        +++t++v+a+a+++++d+ + e  Lyd++DpdALd+Lf+++adg++r+ g+v+Ft+ ++eV V+++g++ V+p
  gi|336252443|ref|YP_004595550.1|  33 ATITTTIVHALASIAETDVSQGEFsLYDSVDPDALDRLFSKKADGTERTGGHVAFTALEHEVYVYANGDVIVYP 106
                                       689*******************999***********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 969.68
//
Query:       gi|336252444|ref|YP_004595551.1|  [L=111]
Description: hypothetical protein Halxa_1036 [Halopiger xanaduensis SH-6]
Scores for 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-24   84.2   0.6    5.2e-24   84.0   0.6    1.0  1  Thiamine_BP  Thiamine-binding protein
  ------ inclusion threshold ------
      0.017   15.4   1.6      0.028   14.7   0.8    1.8  2  HalOD1       Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> Thiamine_BP  Thiamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.6   5.8e-28   5.2e-24       3      92 .]       7      92 ..       5      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 5.8e-28
                                      EEEEECSSSSSGHHHHHHHHHHHHHTTSSEEEEETTEEEEEEE.HHHHHHHHHHHHHHHHCTTSSEEEEEEEEEEESSS CS
                       Thiamine_BP  3 isviPlgtegesvskyVakvvevlkesglkyeltpmgTtiege.ldevmevvkkahealfeaGakRvstvikiddrrdk 80
                                      +sv+P+   ++s+s  Vak+v++l++ +++ye++pmgT+ie+e  de++++ ++ahea+   +a+Rvstv+kidd+r +
  gi|336252444|ref|YP_004595551.1|  7 LSVAPVI--EGSMSGEVAKAVDALEDYDVEYETNPMGTVIEAEsTDELFAAAQAAHEAV---DADRVSTVLKIDDKRTR 80
                                      7999*96..7*************************************************...789************** PP

                                      ---HHHHHHHHH CS
                       Thiamine_BP 81 eqtleeKvksve 92
                                      +++++eKv++ve
  gi|336252444|ref|YP_004595551.1| 81 DESAAEKVDAVE 92
                                      *********996 PP

>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.8   3.1e-06     0.028       4      48 ..      16      61 ..      14      75 .. 0.84
   2 ?    0.2   0.1       0.1   9.4e+02      28      48 ..      60      80 ..      60      91 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-06
                            HalOD1  4 spstaVveavaavegvdpt.elepLydaiDpdALdaLfasradgea 48
                                      s+s +V++av a+e+ d++ e +p+  +i  +  d+Lfa +++ ++
  gi|336252444|ref|YP_004595551.1| 16 SMSGEVAKAVDALEDYDVEyETNPMGTVIEAESTDELFAAAQAAHE 61
                                      67899************97467******************666554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                            HalOD1 28 ydaiDpdALdaLfasradgea 48
                                      ++a+D d   ++++ ++++++
  gi|336252444|ref|YP_004595551.1| 60 HEAVDADRVSTVLKIDDKRTR 80
                                      689999999999887444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 840.85
//
Query:       gi|336252445|ref|YP_004595552.1|  [L=69]
Description: Heavy metal transport/detoxification protein [Halopiger xanaduensis SH-6]
Scores for 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-13   49.8   0.4    3.7e-13   49.7   0.4    1.0  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 !   49.7   0.4   2.1e-17   3.7e-13       1      62 []       5      66 ..       5      66 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 2.1e-17
                               HMA  1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                      t+ v gm C+gC+ +v+ +L++l+gV++++ + + ++v Ve+d++ ++  +i + i +agy+
  gi|336252445|ref|YP_004595552.1|  5 TLEVRGMSCDGCEETVTGALEALEGVSAATASREDDEVRVEHDEARVDEATIANVIADAGYE 66
                                      6789******************************************88899**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 556.75
//
Query:       gi|336252446|ref|YP_004595553.1|  [L=310]
Description: methenyltetrahydromethanopterin cyclohydrolase [Halopiger xanaduensis SH-6]
Scores for 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-116  386.4   0.0   1.1e-115  386.3   0.0    1.0  1  MCH       Cyclohydrolase (MCH)


Domain annotation for each model (and alignments):
>> MCH  Cyclohydrolase (MCH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.3   0.0    6e-120  1.1e-115       1     311 []       3     308 ..       3     308 .. 1.00

  Alignments for each domain:
  == domain 1  score: 386.3 bits;  conditional E-value: 6e-120
                                       -HHHHHHHHHHHHHHTHHHHT-EEEE-TTS-EEEESSSSS---HHHHHHHHHHHTTT-EEEEEEEEEETTEEEEEEE CS
                               MCH   1 SvnelalelveellekaeelrieveelengatviDaGveaeGgleAGlllaeiclggLaevslelsevkgaklpave 77 
                                       S+n++a+elv+e+l++aeel+i  ++len+atv+D+Gve +Gg+eAGlll+ei+++gLa+ s el+e++g+++ +ve
  gi|336252446|ref|YP_004595553.1|   3 SLNRMAIELVDEALDYAEELNIGGYDLENEATVLDFGVEFDGGIEAGLLLTEIQTAGLATPSHELGEIDGVPVHTVE 79 
                                       89*************************************************************************** PP

                                       EEESSHHHHHTTTTS--EEEEETTEEEEEESTTHHHHTSHHHHHHHT-----S-EEEEEESSS---HHHHHHHHHHH CS
                               MCH  78 vstdhPvlacLasqkAgWelsaekffalgsGPaRalaakeelfeelgyedeadaavlvlesdklPdeevvekvaeec 154
                                       +std+P+l++L+sqkAgWel++e+f++lgsGPaRal+a+ee f+++gy+d++d ++l++e+d+lP+e+++e+vae +
  gi|336252446|ref|YP_004595553.1|  80 LSTDQPALSLLCSQKAGWELTTEDFEGLGSGPARALVAQEEEFRRVGYTDAFDLTALAVETDELPPESAAEQVAELA 156
                                       ***************************************************************************** PP

                                       TS-GGGEEEEEE-SSSHHHHHHHHTTHHHHHHHHHHHTT--GGGEEEEEEEEE-----SSHHHHHHHHHHHHHHH-E CS
                               MCH 155 gvepenvtllvaptaSlaGsvqvaaRvvevalhkleelgfdlekivsavgtaPiapvakdelkamgrtndailYggr 231
                                       +vep++v+ll++ptaSl+Gs++ aaR++e+a+++l+elg+++ +ivsa+g+aP+apva+de +a++rtndai+Ygg+
  gi|336252446|ref|YP_004595553.1| 157 EVEPSSVFLLAYPTASLVGSITNAARAAELATFRLTELGYEPLDIVSATGRAPVAPVAGDERTAIARTNDAIAYGGT 233
                                       ***************************************************************************** PP

                                       EEEEES...TTHHHHHHHSSGGGSTTTTS-HHHHHHHTTTTGGGS-GGGSS-SEEEEEETTT--EEEEE---HHHHH CS
                               MCH 232 vhltveaedeeaedlakklpssaskdygkpFaeifkeaeydfykidkalFspAevtvndletgktfkaGelneella 308
                                       +hltv+    e +d++++++s+a++d+g+pF e+f++ +++f +++++lF+pA+vt+ d+  g t+++Ge++e+lla
  gi|336252446|ref|YP_004595553.1| 234 AHLTVR----EDSDVFDSVASTAAEDHGRPFGEVFDDLDWEFEEVPSDLFAPAKVTI-DVLGGPTYVHGETDEDLLA 305
                                       ******....999********************************************.******************* PP

                                       HHT CS
                               MCH 309 esf 311
                                       esf
  gi|336252446|ref|YP_004595553.1| 306 ESF 308
                                       **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 2689.35
//
Query:       gi|336252447|ref|YP_004595554.1|  [L=215]
Description: HAD-superfamily hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-21   75.3   0.0    1.3e-20   74.2   0.0    1.6  2  HAD_2           Haloacid dehalogenase-like hydrolase
    3.2e-15   57.0   0.3    1.7e-13   51.3   0.1    2.1  2  Hydrolase       haloacid dehalogenase-like hydrolase
    1.9e-10   40.7   0.0    4.2e-10   39.6   0.0    1.6  1  Hydrolase_like  HAD-hyrolase-like
    0.00014   22.3   0.3    0.00029   21.3   0.3    1.6  1  HAD             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 ?   -2.2   0.0      0.83   3.7e+03       1      10 [.      14      23 ..      14      27 .. 0.82
   2 !   74.2   0.0   2.9e-24   1.3e-20      76     178 .]      81     183 ..      50     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.83
                             HAD_2  1 iiFDlDgTll 10
                                      i F lDgTl 
  gi|336252447|ref|YP_004595554.1| 14 ICFELDGTLC 23
                                      5699****97 PP

  == domain 2  score: 74.2 bits;  conditional E-value: 2.9e-24
                             HAD_2  76 kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkk 152
                                        +v  ++g++ +Le+L +++y+lg+vT++  e ++ kle+ g+e+y +++v++   +  KP+pe++  ale+l+ ++
  gi|336252447|ref|YP_004595554.1|  81 WTVDSVPGAEAVLETL-AEEYRLGVVTNGAPELQRAKLEAAGLEDYVETVVCGGYETPAKPAPEPFDVALEELDSSP 156
                                       578899**********.99********************************************************** PP

                             HAD_2 153 eeviyvGDsp.tDieaakkagikviav 178
                                       e+++ vG s  +D+ +a++agi+ +++
  gi|336252447|ref|YP_004595554.1| 157 ERAVHVGNSLsSDVAGARAAGIQPVWI 183
                                       **********9***********98885 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.0    0.0095        43       1      23 [.      11      34 ..      11      68 .. 0.77
   2 !   51.3   0.1   3.9e-17   1.7e-13     119     210 .]      85     177 ..      42     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0095
                                      SSEEEEESBTTTBCHH.HHHHHHH CS
                                      xxxxxxxxxxxxxxxx.xxxxxxx RF
                         Hydrolase  1 iktvvfDkdGTLttge.psvedvi 23
                                      ++t++f +dGTL+t   ps  d+ 
  gi|336252447|ref|YP_004595554.1| 11 VETICFELDGTLCTRIrPSADDLE 34
                                      579**********76557777765 PP

  == domain 2  score: 51.3 bits;  conditional E-value: 3.9e-17
                                       BHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 119 vkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeeva 194
                                         p+a+ ++++L +  ++++++t++ pe +++ ++ +G +dy++ v+++  et akp pe +  a++eL  +pe+ +
  gi|336252447|ref|YP_004595554.1|  85 SVPGAEAVLETLAEE-YRLGVVTNGAPELQRAKLEAAGlEDYVETVVCGGYETPAKPAPEPFDVALEELDSSPERAV 160
                                       479*********976.99*********************************************************** PP

                                       EEESSHH.HHHHHHHTT CS
                                       xxxxxxx.xxxxxxxxx RF
                         Hydrolase 195 mVGDgvn.DaaalaaAg 210
                                       +VG ++  D+a+++aAg
  gi|336252447|ref|YP_004595554.1| 161 HVGNSLSsDVAGARAAG 177
                                       ****************8 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   9.3e-14   4.2e-10       4      75 .]     139     209 ..     137     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 9.3e-14
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEE.SSSSS-TTTHHHHHHHHT---SEEES- CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLV.ltGvtrpedleepehkptyvaddlaea 75 
                                       KP+pe +d ale+l+s pe+ + +G +l +D+agA++aG++ v + +tG + ++d  ++  +p+y +++l e+
  gi|336252447|ref|YP_004595554.1| 139 KPAPEPFDVALEELDSSPERAVHVGNSLSSDVAGARAAGIQPVWIpRTGTEIASD--QFDPTPEYTLESLGEL 209
                                       *******************************************994568888877..46779****9999885 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.3   6.5e-08   0.00029      50     184 ..      43     170 ..      14     174 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 6.5e-08
                               HAD  50 draglaelleallaglseelaaelerfv...aevirpk..l.ldpgalellaahraaGdrvvvvSgglrplveplla 120
                                       +r+++ae   +   +l+++l+ e++r+v    ++ir +  +   pga ++l+  +a+ +r+ vv++g  +l +++l+
  gi|336252447|ref|YP_004595554.1|  43 RRRDAAEPTIEPKPRLKPALETEADRLVadeTDAIRDRwtVdSVPGAEAVLE-TLAEEYRLGVVTNGAPELQRAKLE 118
                                       344444444444444555555555555543333333333313338*******.88********************** PP

                               HAD 121 elgadevlatelevddrltgelglegkpvrgegkvaalrewlaaegegidleevvayGDsp.sDl 184
                                       + g ++ + t      ++ g+   +++p + +  +  ++     e+ + ++e+ v +G+s  sD+
  gi|336252447|ref|YP_004595554.1| 119 AAGLEDYVET------VVCGG---YETPAKPAPEPFDVAL----EELDSSPERAVHVGNSLsSDV 170
                                       ***8888888......88888...7777777666766666....667777777777787764555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       176  (0.0098165); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1622.62
//
Query:       gi|336252448|ref|YP_004595555.1|  [L=533]
Description: protein synthesis factor GTP-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-35  121.9   0.0    3.4e-35  121.4   0.0    1.1  1  GTP_EFTU         Elongation factor Tu GTP binding domain
    1.2e-11   44.9   0.4    3.6e-11   43.3   0.4    1.9  1  GTP_EFTU_D2      Elongation factor Tu domain 2
    6.4e-07   29.7   0.0    5.4e-06   26.7   0.0    2.4  1  GTP_EFTU_D3      Elongation factor Tu C-terminal domain
  ------ inclusion threshold ------
      0.012   15.6   0.1       0.38   10.6   0.0    2.3  2  RsgA_GTPase      RsgA GTPase
      0.029   14.5   0.0       0.11   12.5   0.0    2.0  1  MMR_HSR1         50S ribosome-binding GTPase
      0.052   13.4   0.0      0.087   12.7   0.0    1.3  1  Polysacc_deac_1  Polysaccharide deacetylase
      0.055   13.2   0.3        0.5   10.1   0.0    2.0  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.14   12.3   0.2       0.26   11.4   0.2    1.3  1  DUF2120          Uncharacterized protein conserved in archaea


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 !  121.4   0.0   1.5e-38   3.4e-35       2     189 ..     124     340 ..     123     344 .. 0.87

  Alignments for each domain:
  == domain 1  score: 121.4 bits;  conditional E-value: 1.5e-38
                                       CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.............. CS
                          GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.............. 64 
                                       +++ +g++ghvDhGK+TL+++L++ + ++ + +++a    +lD +++E erg++ + + + +               
  gi|336252448|ref|YP_004595555.1| 124 EHVVVGTAGHVDHGKSTLVGSLVTGKPDDGDGATRA----YLDVQPHEVERGLSADLSYAVYGfdedgpvrvrnpnr 196
                                       6899*******************9888877755544....6******************99999************* PP

                                       .......TTCSSEEEEEEEESSSGGGHHHHHHH..HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESC CS
                          GTP_EFTU  65 .......ketkkylinliDtPGHvdFskevirg..lrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKm 132
                                               e++++l++++Dt GH+ + +++irg   ++lD+ +lvv+a++G++  t+e+l ++l+ ++p+iv+i+K 
  gi|336252448|ref|YP_004595555.1| 197 kadraavVEEADRLVSFVDTVGHEPWLRTTIRGlvGQKLDYGLLVVAADDGPTRTTREHLGVLLATDLPTIVAITKT 273
                                       ***987559************************7779**************************************** PP

                                       GST.HHHHHHHHHHHHHHHHHH............HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHH CS
                          GTP_EFTU 133 Drl.kaelkeiveevkqklsrk............eeklekygekgekevpvvfgSalkgegvktllealv 189
                                       D + +++++e+ +ev++ l+++            ++++e++ e   + vp+v +Sa++ +g++tl e ++
  gi|336252448|ref|YP_004595555.1| 274 DAVsEERVEEVEREVERLLREVdksplrvarhgvDAAVEEINE---RVVPIVETSAITMDGLETLDELFD 340
                                       ***8888889999999888555777777776544444433333...689*************97655544 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 !   43.3   0.4   1.6e-14   3.6e-11       1      73 [.     366     436 ..     366     437 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.6e-14
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       G va g+v+sG+++ Gde+ i+++++ ++++ ++++s+e++  ++d a ag  +G+ ++++  +  i++G++l
  gi|336252448|ref|YP_004595555.1| 366 GAVASGTVMSGEVEAGDELLIGPMPD-GRFEEVEVRSIEMHYHRVDKAQAGRIVGIALKGIQESA-IERGMVL 436
                                       89*******************99886.6669*****************************99999.******9 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 !   26.7   0.0   2.4e-09   5.4e-06       3     111 ..     444     529 ..     442     530 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.4e-09
                                       EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEEC.C CS
                       GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnviveveli.k 78 
                                       +p+++feA+v++l++  +t i +gY+pv ++ t  +++   ++       +e+        + pGd+ +++v+ + +
  gi|336252448|ref|YP_004595555.1| 444 EPVREFEAEVMVLNH--PTRIGDGYEPVVHLETIGEAA---AF----Y--PEDG------RLLPGDTGEATVRFKfR 503
                                       6899***********..*****************9988...45....1..2222......36899999999987647 PP

                                       EEEE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  79 pialekgseypqlGrFaiReggrTvaaGvvtei 111
                                       p  +e+g+      +F  Reg++  ++G+vt++
  gi|336252448|ref|YP_004595555.1| 504 PYLVEEGQ------KFVFREGRS-KGVGTVTDV 529
                                       89999999......999998654.588888876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.053   1.2e+02      96     121 ..     122     147 ..      80     164 .. 0.66
   2 ?   10.6   0.0   0.00017      0.38      17      77 ..     236     293 ..     227     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.053
                                       HCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallp 121
                                         ++ ++  +G+   GKStL+ +l+ 
  gi|336252448|ref|YP_004595555.1| 122 DDEHVVVGTAGHVDHGKSTLVGSLVT 147
                                       333344444555557******99976 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00017
                                       -EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTS CS
                       RsgA_GTPase  17 dqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgy 77 
                                       d  l+vv+++  +  +++    L ++ +++++ +++++K+D ++ee+ +ee++ e+e+l  
  gi|336252448|ref|YP_004595555.1| 236 DYGLLVVAAD--DGPTRTTREHLGVLLATDLPTIVAITKTDAVSEER-VEEVEREVERLLR 293
                                       6667888887..5556677788999999******************9.7777777666533 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.1e-05      0.11       2     114 .]     128     272 ..     127     304 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-05
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE............................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke............................... 47 
                                       v+ +G+   GKStL+ +l+    +  d  g+Tr     + +  + e                               
  gi|336252448|ref|YP_004595555.1| 128 VGTAGHVDHGKSTLVGSLVTG--KPDDGDGATRAYLDVQPH--EVErglsadlsyavygfdedgpvrvrnpnrkadr 200
                                       7789**************974..556666777655444433..1111233455666666666777777778888888 PP

                                       ..........EEEEECGGCSSHHHHHHHHHHHHHH..HHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEE CS
                          MMR_HSR1  48 ..........ielvDtpGliegaseekglgkafla..leeadlillvvdaseeklkpldeeleelleeakkplilvl 112
                                                 + +vDt+G  e     + l+ +++    ++ d  llvv a  ++ ++  +e   +l  ++ p+i+++
  gi|336252448|ref|YP_004595555.1| 201 aavveeadrlVSFVDTVG-HE----PW-LRTTIRGlvGQKLDYGLLVVAAD-DGPTRTTREHLGVLLATDLPTIVAI 270
                                       8888888888********.44....66.55555542144578888888766.4455555666666666667777766 PP

                                       ES CS
                          MMR_HSR1 113 nk 114
                                       +k
  gi|336252448|ref|YP_004595555.1| 271 TK 272
                                       65 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.9e-05     0.087       8      67 ..     239     308 ..     232     326 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.9e-05
                                       EEEEEEEESSCSCHHHHHHHHHHCT--EEEEE-HHH.HCH-.........HHHHHHHHHTTEEEEE--SS CS
                   Polysacc_deac_1   8 svalTfDdgprdntteilpvLkkykvkatffviggl.vedy.........pdevremaasGveignHtin 67 
                                        +++ +Ddgp+ +t+e l vL + +++  + ++ +  v ++         + ++re+ +s+  ++ H+++
  gi|336252448|ref|YP_004595555.1| 239 LLVVAADDGPTRTTREHLGVLLATDLPTIVAITKTDaVSEErveeverevERLLREVDKSPLRVARHGVD 308
                                       578899**********************999999963444488888999999999999999999999986 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   0.1      0.13     3e+02       1      18 [.     127     147 ..     127     162 .. 0.76
   2 ?   10.1   0.0   0.00022       0.5     150     222 ..     257     326 ..     251     343 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.13
                        ATP_bind_1   1 vvGpaG...sGKttfvgalse 18 
                                       vvG+aG    GK+t+vg+l+ 
  gi|336252448|ref|YP_004595555.1| 127 VVGTAGhvdHGKSTLVGSLVT 147
                                       5666663336*******9975 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00022
                        ATP_bind_1 150 samlrlelPhvvvlnkfDllkeklekeleffedvealslllekeeekykklaeaiaelleefal.vlrflplss 222
                                        ++l ++lP++v+++k+D ++e++    e+  +ve+l +  +  ++  +     + +++ee ++ v  ++  s+
  gi|336252448|ref|YP_004595555.1| 257 GVLLATDLPTIVAITKTDAVSEER--VEEVEREVERLLREVD--KSPLRVARHGVDAAVEEINErVVPIVETSA 326
                                       578999*************99442..3333334444444333..334444455555555554431223334444 PP

>> DUF2120  Uncharacterized protein conserved in archaea (DUF2120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00011      0.26      30     100 ..     273     342 ..     265     349 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                           DUF2120  30 gvsrkkeeleeleskleellekldaeevdleseeakkliekldesireveeieeevdafglerlkeslEal 100
                                         + ++e++ee+e+++e+ll ++d+  + ++ + +++ +e+++e + + +e+  ++ + gle l e ++ l
  gi|336252448|ref|YP_004595555.1| 273 TDAVSEERVEEVEREVERLLREVDKSPLRVARHGVDAAVEEINERVVPIVETS-AITMDGLETLDELFDRL 342
                                       555567789***************************************99988.88888999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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 0.26s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 3903.68
//
Query:       gi|336252449|ref|YP_004595556.1|  [L=70]
Description: hypothetical protein Halxa_1041 [Halopiger xanaduensis SH-6]
Scores for 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   15.0   1.7      0.016   15.0   1.7    1.9  2  zf-HIT          HIT zinc finger
      0.023   14.9  12.0      0.026   14.7   5.9    2.1  2  zf-B_box        B-box zinc finger
       0.49   10.5  12.5        2.9    8.0   1.2    2.1  2  DZR             Double zinc ribbon
       0.65   10.2   7.1       0.92    9.7   7.1    1.2  1  Prok-RING_2     Prokaryotic RING finger family 2
       0.88    9.3   7.6        2.1    8.1   0.1    2.6  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.89    7.3   4.1       0.89    7.3   4.1    1.0  1  PolC_DP2        DNA polymerase II large subunit DP2


Domain annotation for each model (and alignments):
>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.7   5.4e-06     0.016       3      24 ..       5      27 ..       3      29 .. 0.94
   2 ?   -0.4   0.1      0.37   1.1e+03       4      11 ..      37      44 ..      34      46 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.4e-06
                                      -B-TTT-S.B-SEE-TTT--EES CS
                            zf-HIT  3 klCgvCgf.pakYkCpkCntryC 24
                                      +lC++C    a+ +C +C+t  C
  gi|336252449|ref|YP_004595556.1|  5 GLCQICESrQAQERCDNCGTLAC 27
                                      79*****************9888 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.37
                                      B-TTT-SB CS
                            zf-HIT  4 lCgvCgfp 11
                                      lC+ C   
  gi|336252449|ref|YP_004595556.1| 37 LCADCASQ 44
                                      78888765 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   5.9   8.8e-06     0.026       4      28 ..       5      29 ..       2      33 .. 0.94
   2 ?    4.1   0.4     0.017        51      22      31 ..      34      43 ..      31      46 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.8e-06
                          zf-B_box  4 tkCpeHknkpatlfCedCqqplCee 28
                                        C+++++++a+  C +C+++ Ce+
  gi|336252449|ref|YP_004595556.1|  5 GLCQICESRQAQERCDNCGTLACEQ 29
                                      57*********************96 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.017
                          zf-B_box 22 qqplCeeCst 31
                                      ++ lC++C +
  gi|336252449|ref|YP_004595556.1| 34 DTNLCADCAS 43
                                      5789999943 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  12.4     0.021        62      14      48 ..       6      41 ..       2      42 .. 0.70
   2 ?    8.0   1.2   0.00099       2.9       4      23 ..      27      46 ..      25      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.021
                               DZR 14 fCseCgtklkavaaedrCpsCgek.v....dpearfCpeC 48
                                       C+ C ++      ++rC++Cg+  +    +++++ C  C
  gi|336252449|ref|YP_004595556.1|  6 LCQICESRQA----QERCDNCGTLaCeqhyEQDTNLCADC 41
                                      6999999998....79999999863311114566678777 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00099
                               DZR  4 CgeelppdarfCseCgtklk 23
                                      C++  ++d + C +C ++ +
  gi|336252449|ref|YP_004595556.1| 27 CEQHYEQDTNLCADCASQAR 46
                                      88888888899999988765 PP

>> Prok-RING_2  Prokaryotic RING finger family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   7.1   0.00031      0.92      12      49 ..       6      43 ..       2      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00031
                       Prok-RING_2 12 lcatahplaglrqcvlcGrWacdacWkdeyytckscaG 49
                                      lc+  ++     +c  cG  ac+  ++ +  +c  ca 
  gi|336252449|ref|YP_004595556.1|  6 LCQICESRQAQERCDNCGTLACEQHYEQDTNLCADCAS 43
                                      5666666667789***********************95 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 ?    2.2   3.8     0.049   1.5e+02      18      24 ..      17      23 ..       6      24 .. 0.80
   2 ?    8.1   0.1    0.0007       2.1       3      18 ..      38      53 ..      37      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.049
                                      ---SSS- CS
                    DNA_RNApol_7kD 18 iRCkeCG 24
                                       RC +CG
  gi|336252449|ref|YP_004595556.1| 17 ERCDNCG 23
                                      59****9 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0007
                                      -SSS--B----SSS-- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgdpi 18
                                      C++C+++ +  +gdp+
  gi|336252449|ref|YP_004595556.1| 38 CADCASQARPGSGDPV 53
                                      *********9999998 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 ?    7.3   4.1    0.0003      0.89     620     675 ..       6      67 ..       2      70 .] 0.66

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0003
                          PolC_DP2 620 kCkkCgketlearCeeCgekt......eeklvCkkceeeveeekcekcekeakavkkkkidl 675
                                        C+ C+++  + rC++Cg+        + ++ C +c ++++  + + +++ ++  ++ ++d+
  gi|336252449|ref|YP_004595556.1|   6 LCQICESRQAQERCDNCGTLAceqhyeQDTNLCADCASQARPGSGDPVTNPNQDPDHDDVDV 67 
                                       6999***********99975411111123456888888877666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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):               6  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 555.33
//
Query:       gi|336252450|ref|YP_004595557.1|  [L=266]
Description: Orotidine 5'-phosphate decarboxylase [Halopiger xanaduensis SH-6]
Scores for 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-33  114.1   0.0    8.1e-33  113.9   0.0    1.1  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil
  ------ inclusion threshold ------
       0.14   11.9   0.0       0.31   10.8   0.0    1.5  1  DUF2859    Protein of unknown function (DUF2859)


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 !  113.9   0.0     9e-37   8.1e-33      14     219 ..      42     243 ..      16     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 9e-37
                                       HHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHHSTCHHHHTTESE CS
                         OMPdecase  14 elleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqatagsarikewadi 89 
                                       ++ + + ++++ +++v+K++ +++e+ +  +++++++a+a+ +++++++D+K+aDIGnt +++a+       e +d+
  gi|336252450|ref|YP_004595557.1|  42 AFNRRIIDATHeHAAVFKPNAAFYEDPDGWRALEETVAYAHGKNVPVLLDAKRADIGNTTRQYAK-----LLETVDA 113
                                       455455555555*************99966**********************************8.....99***** PP

                                       EEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH.H....SHHHHHHHHHHHHHHHTTESEEECCCHT CS
                         OMPdecase  90 vtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe.k....gytqacveaarehkaedfvmGfvaqetl 161
                                       +tv++++G +s+++++  a    + g+++l+++s++g+++ q+ +    +  ++ v a+++  +e+  +G+v+++t 
  gi|336252450|ref|YP_004595557.1| 114 ITVNPYMGRDSLQPFLADA----ESGVFVLCRTSNPGGADIQDlEletgEPVYERVAALADLWNENDNVGLVVGATQ 186
                                       ****************999....458*****************9445789999999999999999************ PP

                                       H....HHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSS.SHH CS
                         OMPdecase 162 n....ateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkag.dpv 219
                                       +    +++e+ +d+++l+pgig+ qggd+++  ++   +l++  g  +++ +RgI+ ag ++ 
  gi|336252450|ref|YP_004595557.1| 187 PeeleELREQVPDLPFLVPGIGA-QGGDAEAAVEY---GLAD--GVGLVNSSRGIIFAGeNDG 243
                                       *8665444449***********9.****9999977...4433..667**********994444 PP

>> DUF2859  Protein of unknown function (DUF2859)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.5e-05      0.31      95     123 ..     174     202 ..     165     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.5e-05
                           DUF2859  95 elqAvGlvvnvesaaalqelrelaeglel 123
                                       e   vGlvv +++ ++l+elre++++l+ 
  gi|336252450|ref|YP_004595557.1| 174 ENDNVGLVVGATQPEELEELREQVPDLPF 202
                                       56789*********************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1930.93
//
Query:       gi|336252451|ref|YP_004595558.1|  [L=139]
Description: hypothetical protein Halxa_1044 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0002   20.6   0.9    0.00035   19.9   0.9    1.4  1  zf-ribbon_3     zinc-ribbon domain
    0.00084   19.3   2.1     0.0015   18.5   2.1    1.4  1  DZR             Double zinc ribbon
      0.001   19.0   1.6     0.0015   18.5   1.6    1.2  1  zinc-ribbons_6  zinc-ribbons
     0.0025   17.9   2.5     0.0041   17.3   2.5    1.3  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
  ------ inclusion threshold ------
      0.012   15.5   0.3      0.022   14.6   0.3    1.4  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
      0.034   13.7   0.7      0.075   12.6   0.7    1.5  1  RecR            RecR protein
      0.039   14.0   0.6      0.049   13.6   0.6    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.05   13.8   1.4      0.074   13.2   1.4    1.2  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.17   12.1   4.2       0.55   10.4   4.2    1.8  1  Zn-ribbon_8     Zinc ribbon domain
       0.24   11.4   1.9        3.9    7.5   0.1    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        0.3   10.8   3.4        4.3    7.1   0.2    2.4  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.93    9.5   4.4         16    5.5   0.2    2.4  2  Nudix_N_2       Nudix N-terminal
       0.97    9.4   6.4         10    6.1   0.0    2.8  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
        1.3    9.2   5.3         15    5.8   0.2    2.3  2  UPF0547         Uncharacterised protein family UPF0547
        1.6    8.5   5.1        7.6    6.4   4.6    2.1  3  zinc_ribbon_2   zinc-ribbon domain


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 !   19.9   0.9   2.9e-07   0.00035       4      24 ..      75      96 ..      72      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.9e-07
                       zf-ribbon_3  4 rCPnCGap.lssddnvCpyCGt 24
                                      +C++CG++ ++++ ++Cp C t
  gi|336252451|ref|YP_004595558.1| 75 HCSACGTVyIADEKQFCPTCET 96
                                      9******66***********87 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   2.1   1.3e-06    0.0015       1      32 [.      76     108 ..      68     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                               DZR   1 CpqCgee.lppdarfCseCgtklkavaaedrCp 32 
                                       C+ Cg+  + ++++fC++C t++++v +  +C 
  gi|336252451|ref|YP_004595558.1|  76 CSACGTVyIADEKQFCPTCETEVEQVRSTLACR 108
                                       999999878999999999999999888888886 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.6   1.3e-06    0.0015      14      44 ..      71     103 ..      56     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                                       SSEEE-TTT--..EEEEEEE-SSS-S---EEEE CS
                    zinc-ribbons_6  14 geqyhCeaCqe..dlkkealCpeCeqelevlka 44 
                                       g+ +hC+aC +    +++++Cp+Ce e+e ++ 
  gi|336252451|ref|YP_004595558.1|  71 GNLFHCSACGTvyIADEKQFCPTCETEVEQVRS 103
                                       4679******96666899**********99875 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 !   17.3   2.5   3.4e-06    0.0041       9      31 ..      74      96 ..      72     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.4e-06
                      NOB1_Zn_bind  9 lrChaCfkvtkdmtkkFCpkCGn 31
                                        C aC +v+   +k+FCp+C  
  gi|336252451|ref|YP_004595558.1| 74 FHCSACGTVYIADEKQFCPTCET 96
                                      57*******************75 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 ?   14.6   0.3   1.9e-05     0.022      24      50 .]      74     101 ..      66     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                                       EE-HHHHHHHHH.TT-B-TTT--B--EE CS
                        zf-C3HC4_3  24 vlCeeCaekllk.rkkkCpiCrrpiekv 50 
                                       + C++C + + + +k+ Cp C +++e+v
  gi|336252451|ref|YP_004595558.1|  74 FHCSACGTVYIAdEKQFCPTCETEVEQV 101
                                       57******99998************986 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.7   6.3e-05     0.075      14      35 ..      71      95 ..      67      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                                      HH-EE-TTT--E...ESSSS-CCCC CS
                              RecR 14 ekvrhCsrCgnl...teedlCaICs 35
                                       ++ hCs Cg++   +e+  C+ C 
  gi|336252451|ref|YP_004595558.1| 71 GNLFHCSACGTVyiaDEKQFCPTCE 95
                                      5788********99777789****7 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 ?   13.6   0.6   4.1e-05     0.049      69      99 ..      72     101 ..      36     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                                       -EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                              HypA  69 vkvrCreCgkefeleekalrCpkCgsadvei 99 
                                         ++C+ Cg+ +  +ek++ Cp+C+++  ++
  gi|336252451|ref|YP_004595558.1|  72 NLFHCSACGTVYIADEKQF-CPTCETEVEQV 101
                                       5689*****9999876655.****9975554 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 ?   13.2   1.4   6.2e-05     0.074      17      40 .]      75      95 ..      74      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.2e-05
                     Auto_anti-p27 17 tCpvCgvPLmrdrkggkvyCvaCd 40
                                      +C+ Cg++   d  +++ +C++C+
  gi|336252451|ref|YP_004595558.1| 75 HCSACGTVYIAD--EKQ-FCPTCE 95
                                      9**********6..456.*****5 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.2   0.00046      0.55       6      39 ..      74     101 ..      73     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00046
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdaplta.CPeCgsevrrv 39 
                                       ++C +Cg+++      +d  +++ CP+C  ev++v
  gi|336252451|ref|YP_004595558.1|  74 FHCSACGTVYI-----AD--EKQfCPTCETEVEQV 101
                                       89*****6665.....33..7788****9999875 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 ?    7.5   0.1    0.0033       3.9      41      59 ..      68      86 ..      53      88 .. 0.82
   2 ?    3.5   0.3     0.058        70      30      51 ..      90     109 ..      89     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0033
                    OrfB_Zn_ribbon 41 alsgrtfkCpnCgfeadrD 59
                                      +  g++f+C++Cg+++ +D
  gi|336252451|ref|YP_004595558.1| 68 DAPGNLFHCSACGTVYIAD 86
                                      568899********99888 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.058
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpn 51 
                                        C+ C  ++++   + t+ C++
  gi|336252451|ref|YP_004595558.1|  90 FCPTCETEVEQ--VRSTLACRQ 109
                                       5*********9..999999975 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 ?    4.3   0.3     0.026        31      23      29 ..      75      81 ..      74      83 .. 0.62
   2 ?    7.1   0.2    0.0036       4.3       4      22 ..      89     107 ..      86     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.026
                     zf-NADH-PPase 23 vCpaCgl 29
                                      +C+aCg+
  gi|336252451|ref|YP_004595558.1| 75 HCSACGT 81
                                      5666665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0036
                     zf-NADH-PPase   4 rFCgrCGaptepaeggwar 22 
                                       +FC++C +++e+++   a+
  gi|336252451|ref|YP_004595558.1|  89 QFCPTCETEVEQVRSTLAC 107
                                       9*****8888888877765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.8     0.019        23       2      30 ..      75      81 ..      74      83 .. 0.55
   2 ?    5.5   0.2     0.013        16       2      12 ..      90     100 ..      89     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.019
                                      B-TTT--B-EEE--TT-SS-EEEETTTTE CS
                         Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCgt 30
                                      +                      C+aCgt
  gi|336252451|ref|YP_004595558.1| 75 H----------------------CSACGT 81
                                      4......................555555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.013
                                       B-TTT--B-EE CS
                         Nudix_N_2   2 FCsqCGtpvel 12 
                                       FC+ C t+ve+
  gi|336252451|ref|YP_004595558.1|  90 FCPTCETEVEQ 100
                                       9****999986 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 ?    6.1   0.0    0.0087        10      14      34 ..      66      86 ..      64      88 .. 0.76
   2 ?    2.6   3.6      0.11   1.3e+02       2       8 ..      89      95 ..      89     110 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0087
                                      EECSCCCEEEESSSS-EEESS CS
                    RNA_POL_M_15KD 14 kedkegknfeCrqCgYeepad 34
                                      ++d  g+ f C+ Cg ++ ad
  gi|336252451|ref|YP_004595558.1| 66 RVDAPGNLFHCSACGTVYIAD 86
                                      66777866*******998555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                                      EBESTTT CS
                    RNA_POL_M_15KD  2 kFCpkCg 8 
                                      +FCp+C 
  gi|336252451|ref|YP_004595558.1| 89 QFCPTCE 95
                                      7*****5 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.012        15      17      25 ..      76      84 ..      70      85 .. 0.85
   2 ?    5.3   1.0     0.018        21       3      10 ..      91      98 ..      89      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                           UPF0547 17 CphCGyvFq 25
                                      C+ CG+v++
  gi|336252451|ref|YP_004595558.1| 76 CSACGTVYI 84
                                      ******987 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.018
                           UPF0547  3 CPeCeakv 10
                                      CP Ce++v
  gi|336252451|ref|YP_004595558.1| 91 CPTCETEV 98
                                      99999998 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   0.4     0.018        22      13      21 ..      72      81 ..      69      83 .. 0.77
   2 ?    6.4   4.6    0.0064       7.6       2      19 ..      76      94 ..      75      98 .. 0.92
   3 ?    3.9   0.7     0.039        46       1      10 [.      90      99 ..      90     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.018
                     zinc_ribbon_2 13 akF.CpyCGt 21
                                      + F C+ CGt
  gi|336252451|ref|YP_004595558.1| 72 NLFhCSACGT 81
                                      5677999998 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0064
                     zinc_ribbon_2  2 CpnCGael.qdnakFCpyC 19
                                      C+ CG+    d+ +FCp C
  gi|336252451|ref|YP_004595558.1| 76 CSACGTVYiADEKQFCPTC 94
                                      9*******779******99 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.039
                     zinc_ribbon_2  1 fCpnCGaelq 10
                                      fCp C +e++
  gi|336252451|ref|YP_004595558.1| 90 FCPTCETEVE 99
                                      8999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1075.91
//
Query:       gi|336252452|ref|YP_004595559.1|  [L=86]
Description: hypothetical protein Halxa_1045 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0026   17.8   0.9     0.0029   17.6   0.9    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0043   16.9   1.4       0.92    9.4   0.3    2.4  2  TFIIS_C          Transcription factor S-II (TFIIS)
  ------ inclusion threshold ------
      0.016   16.0   1.6      0.024   15.4   1.6    1.3  1  zinc_ribbon_15   zinc-ribbon family
      0.059   13.1   5.3        0.1   12.3   5.3    1.5  1  Rubredoxin_2     Rubredoxin metal binding domain
      0.096   12.3   0.9        2.7    7.7   0.2    2.2  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.11   12.0   5.1        2.6    7.6   0.7    2.4  2  zf-ribbon_3      zinc-ribbon domain
       0.12   12.5   0.6       0.12   12.5   0.6    2.3  2  UPF0547          Uncharacterised protein family UPF0547
       0.54   10.4  10.7       0.76    9.9   9.3    2.0  1  Zn-ribbon_8      Zinc ribbon domain
       0.91   10.5   5.9        2.4    9.2   0.9    2.2  2  zf-C2H2_4        C2H2-type zinc finger
        8.9    6.1  11.7       0.78    9.5   0.7    2.4  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI


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 !   17.6   0.9   1.6e-06    0.0029      67      98 ..      25      54 ..      11      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                                      E--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 67 vpvkvrCreCgkefeleekalrCpkCgsadve 98
                                        v ++Cr+Cg++f++  +  rCp Cg++++ 
  gi|336252452|ref|YP_004595559.1| 25 GTVIYECRHCGTDFDEPCD--RCPVCGATEIA 54
                                      567899*********7756..9*****99875 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 !    9.4   0.3   0.00052      0.92      25      38 ..      25      38 ..      10      39 .. 0.80
   2 !    6.6   0.0    0.0039         7       2      15 ..      44      57 ..      43      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00052
                           TFIIS_C 25 mtvfykCtkCghrW 38
                                       tv+y+C  Cg  +
  gi|336252452|ref|YP_004595559.1| 25 GTVIYECRHCGTDF 38
                                      499********987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0039
                           TFIIS_C  2 kCpkCgsreayffq 15
                                      +Cp Cg +e+  ++
  gi|336252452|ref|YP_004595559.1| 44 RCPVCGATEIATYE 57
                                      6*******998765 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.6   1.3e-05     0.024      54      86 .]      17      49 ..       9      49 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                    zinc_ribbon_15 54 gkeiekkessekkeCknCgkeveeefkyCpkCg 86
                                      g+e+e+++ +  +eC++Cg+  +e ++ Cp Cg
  gi|336252452|ref|YP_004595559.1| 17 GDETEATAGTVIYECRHCGTDFDEPCDRCPVCG 49
                                      4555666666699*******************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 ?   12.3   5.3   5.8e-05       0.1       1      22 [.      29      50 ..      29      52 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.8e-05
                      Rubredoxin_2  1 YvCsqCGfesakwfGrCpsCgs 22
                                      Y+C++CG ++     rCp Cg+
  gi|336252452|ref|YP_004595559.1| 29 YECRHCGTDFDEPCDRCPVCGA 50
                                      9*******************96 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0015       2.7       5      13 ..      27      35 ..      23      37 .. 0.84
   2 ?    3.4   0.0     0.033        59       8      14 ..      44      50 ..      43      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
                                      -EEE-TTT- CS
                   Desulfoferrod_N  5 evYkCevCG 13
                                       +Y C +CG
  gi|336252452|ref|YP_004595559.1| 27 VIYECRHCG 35
                                      58******* PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.033
                                      E-TTT-- CS
                   Desulfoferrod_N  8 kCevCGn 14
                                      +C vCG 
  gi|336252452|ref|YP_004595559.1| 44 RCPVCGA 50
                                      8*****5 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3    0.0036       6.4      19      25 ..      31      37 ..      31      38 .. 0.89
   2 ?    7.6   0.7    0.0015       2.6       4      10 ..      44      50 ..      42      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0036
                       zf-ribbon_3 19 CpyCGtk 25
                                      C +CGt+
  gi|336252452|ref|YP_004595559.1| 31 CRHCGTD 37
                                      *****98 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0015
                       zf-ribbon_3  4 rCPnCGa 10
                                      rCP CGa
  gi|336252452|ref|YP_004595559.1| 44 RCPVCGA 50
                                      8*****8 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   6.5e-05      0.12      16      26 .]      30      40 ..      29      40 .. 0.90
   2 ?    2.3   2.0       0.1   1.8e+02      15      21 ..      43      49 ..      42      51 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.5e-05
                           UPF0547 16 fCphCGyvFqa 26
                                      +C+hCG++F++
  gi|336252452|ref|YP_004595559.1| 30 ECRHCGTDFDE 40
                                      7********85 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.1
                           UPF0547 15 qfCphCG 21
                                       +Cp CG
  gi|336252452|ref|YP_004595559.1| 43 DRCPVCG 49
                                      5688887 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   9.3   0.00042      0.76       6      35 ..      29      52 ..      28      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00042
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs.e 35
                                      Y+C+ Cg++f++           CP Cg+ e
  gi|336252452|ref|YP_004595559.1| 29 YECRHCGTDFDEP-------CDRCPVCGAtE 52
                                      9**********43.......345*****954 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 ?    9.2   0.9    0.0013       2.4       1      13 [.      29      41 ..      29      43 .. 0.85
   2 ?    4.0   0.3     0.066   1.2e+02       2       9 ..      44      51 ..      43      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                         zf-C2H2_4  1 fkCpiCgksFssk 13
                                      ++C++Cg+ F  +
  gi|336252452|ref|YP_004595559.1| 29 YECRHCGTDFDEP 41
                                      89********766 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.066
                         zf-C2H2_4  2 kCpiCgks 9 
                                      +Cp+Cg++
  gi|336252452|ref|YP_004595559.1| 44 RCPVCGAT 51
                                      6****975 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 ?    0.8   4.5      0.23   4.1e+02      24      29 ..      31      36 ..      31      36 .. 0.96
   2 ?    9.5   0.7   0.00044      0.78       6      13 ..      44      54 ..      39      62 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.23
                           zf-RRN7 24 CrrCht 29
                                      Cr+C+t
  gi|336252452|ref|YP_004595559.1| 31 CRHCGT 36
                                      *****8 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00044
                           zf-RRN7  6 pCgvCgc...r 13
                                      +C+vCg+    
  gi|336252452|ref|YP_004595559.1| 44 RCPVCGAteiA 54
                                      8******6653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 714.34
//
Query:       gi|336252453|ref|YP_004595560.1|  [L=263]
Description: AsnC family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-14   52.1   0.9    9.7e-14   51.0   0.9    1.6  1  TrkA_C          TrkA-C domain
      4e-10   39.4   1.4    7.3e-10   38.5   0.2    2.0  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    4.4e-10   38.9   0.1    4.2e-09   35.8   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
    2.8e-05   24.1   0.0    6.4e-05   22.9   0.0    1.6  1  HTH_20          Helix-turn-helix domain
      3e-05   23.9   0.0    7.3e-05   22.6   0.0    1.6  1  HTH_11          HTH domain
    0.00028   20.7   0.1    0.00098   19.0   0.1    1.9  2  MarR_2          MarR family
    0.00048   19.8   0.0     0.0011   18.7   0.0    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
     0.0019   18.0   0.0     0.0033   17.2   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0055   16.8   0.1      0.011   15.8   0.1    1.5  1  HTH_28          Helix-turn-helix domain
     0.0072   16.2   0.0      0.017   15.0   0.0    1.6  1  MarR            MarR family
  ------ inclusion threshold ------
       0.02   14.3   0.0      0.026   13.9   0.0    1.1  1  PTase_Orf2      Aromatic prenyltransferase Orf2
      0.022   14.9   0.0      0.042   14.1   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.026   14.9   0.0      0.055   13.8   0.0    1.5  1  Rrf2            Transcriptional regulator
      0.062   12.9   0.1       0.13   11.8   0.1    1.4  1  HTH_CodY        CodY helix-turn-helix domain
      0.099   12.5   0.0       0.19   11.6   0.0    1.4  1  HTH_23          Homeodomain-like domain
       0.19   11.5   1.2       0.25   11.2   0.1    1.7  2  HTH_30          PucR C-terminal helix-turn-helix domain


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 !   51.0   0.9   8.6e-17   9.7e-14       1      60 [.     179     241 ..     179     244 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 8.6e-17
                                       CEEEEEE--GGGTTSBHHHHT....HHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkeln....lrargvlvvairRggeliipsgdtvLeeGDvllvvgsps 60 
                                       +vevtv++++p++G+tl e++    l +   lv+ai R++++i p gdt++++ Dv++v+++ +
  gi|336252453|ref|YP_004595560.1| 179 VVEVTVAEDAPIAGRTLEEADddgiLDD-HTLVIAIERDDDVITPHGDTEIRPYDVVTVFSPTD 241
                                       79*****************888888887.*******************************9877 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 !   38.5   0.2   6.5e-13   7.3e-10       1      42 []      11      53 ..      11      53 .. 0.95
   2 ?   -1.7   0.1       2.4   2.6e+03      23      30 ..      90      97 ..      87     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 6.5e-13
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisya.eLAervGlSestvlrRvrrLe 42
                                      LDeiDr+I+ aL+ daR + a ++Ae+v +S++t+++R+++Le
  gi|336252453|ref|YP_004595560.1| 11 LDEIDRRIVYALMGDARNTAApAIAEEVSVSPATIRNRIAKLE 53
                                      8***************987765********************8 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
                     HTH_AsnC-type 23 LAervGlS 30
                                      LA+rvG  
  gi|336252453|ref|YP_004595560.1| 90 LARRVGTV 97
                                      89***975 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 !   35.8   0.0   3.7e-12   4.2e-09       1      48 []      11      59 ..      11      59 .. 0.98
   2 ?    0.5   0.0       0.4   4.5e+02      23      37 ..      90     104 ..      89     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 3.7e-12
                            HTH_24  1 ldetdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      lde+dr+I  +L+ ++r +    +Ae++ +Sp+t++ r+ +Lee G+I+
  gi|336252453|ref|YP_004595560.1| 11 LDEIDRRIVYALMGDARnTAAPAIAEEVSVSPATIRNRIAKLEEHGVIE 59
                                      7****************99999**************************7 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.4
                            HTH_24  23 LAerlglSpstvnrr 37 
                                       LA+r+g  p+ vn r
  gi|336252453|ref|YP_004595560.1|  90 LARRVGTVPGVVNVR 104
                                       8***********987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.7e-08   6.4e-05      13      56 ..      16      60 ..      11      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.7e-08
                                      HHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 13 rrilraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      rri  aL  +a+   a+++ae++++s++t+++++++Lee+g +e+
  gi|336252453|ref|YP_004595560.1| 16 RRIVYALmGDARNTAAPAIAEEVSVSPATIRNRIAKLEEHGVIEG 60
                                      5555556467778889***************************96 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   6.5e-08   7.3e-05      13      44 ..      26      57 ..      16      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.5e-08
                            HTH_11 13 rgpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                        +  +  +Aee +vS +t+r++I++Lee gv
  gi|336252453|ref|YP_004595560.1| 26 ARNTAAPAIAEEVSVSPATIRNRIAKLEEHGV 57
                                      55566789*********************994 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   8.7e-07   0.00098       8      52 ..      16      59 ..      11      73 .. 0.85
   2 ?   -1.8   0.0       2.7   3.1e+03       3      33 ..      67      96 ..      65     102 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.7e-07
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +r+ +aL    + + ++ ++a++  +s++++ +++++L+++G +e
  gi|336252453|ref|YP_004595560.1| 16 RRIVYALMGDAR-NTAAPAIAEEVSVSPATIRNRIAKLEEHGVIE 59
                                      566677766664.479***************************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.7
                                      --HHHHHHHHHHHCTTTSEE.EHHHHHHHHTS CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdl.tvgelarrlgl 33
                                      +++a+  +++   ++ +  +  v  larr g 
  gi|336252453|ref|YP_004595560.1| 67 FERADGSLMNLFLCHAP--FdEVEGLARRVGT 96
                                      56666666777777777..4488888888876 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 !   18.7   0.0   9.4e-07    0.0011      20      49 ..      34      63 ..      26      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 9.4e-07
                          HTH_DeoR 20 lvellgvSeaTiRRDLneLeeqglltRthG 49
                                      ++e+  vS+aTiR+ +++Lee g+++  h 
  gi|336252453|ref|YP_004595560.1| 34 IAEEVSVSPATIRNRIAKLEEHGVIEGYHA 63
                                      899*********************987775 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 !   17.2   0.0     3e-06    0.0033       5      46 ..      16      59 ..      12      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3e-06
                                      HHHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLae..gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++I+++L+   +++ +  +aee+ +s++t++   +kL+e G++e
  gi|336252453|ref|YP_004595560.1| 16 RRIVYALMGdaRNTAAPAIAEEVSVSPATIRNRIAKLEEHGVIE 59
                                      69*******9999****************************986 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   9.9e-06     0.011      13      44 ..      29      61 ..      16      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.9e-06
                            HTH_28 13 hsvreaArelgisrrtvyrWikryeegG.iagL 44
                                       +++++A+e+ +s+ t++  i ++ee+G i+g 
  gi|336252453|ref|YP_004595560.1| 29 TAAPAIAEEVSVSPATIRNRIAKLEEHGvIEGY 61
                                      47889***********************66876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.6e-05     0.017      21      52 ..      29      63 ..      22      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                                      H...HHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR 21 s...eLakklgvskstvtrvldrLekkGlieRsks 52
                                      +    +a+ ++vs++t+ + + +Le++G ie ++ 
  gi|336252453|ref|YP_004595560.1| 29 TaapAIAEEVSVSPATIRNRIAKLEEHGVIEGYHA 63
                                      445589************************97665 PP

>> PTase_Orf2  Aromatic prenyltransferase Orf2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.3e-05     0.026     129     229 ..      38     136 ..      17     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-05
                        PTase_Orf2 129 lenvPeslrqhekkfleagldkvrvvavDyrsrt...vNlYfrakapleleevatlirlvGseppseeklalmreaf 202
                                       +   P+++r++  k+ e+g+ +  +++vD+       +Nl++  +ap++  ev  l r vG+ p   ++ +lm + +
  gi|336252453|ref|YP_004595560.1|  38 VSVSPATIRNRIAKLEEHGVIEGYHATVDFERADgslMNLFL-CHAPFD--EVEGLARRVGTVPGVVNVRELMGGRM 111
                                       4446**************************875412277765.567765..78999********9999999999999 PP

                        PTase_Orf2 203 tvav.TidldsgdieRvsfyalklpend 229
                                       ++ v  + +d+ d++R++    +l++ +
  gi|336252453|ref|YP_004595560.1| 112 NLHVlAVGTDTSDLRRIGR---ELEKMN 136
                                       987537899*******987...444444 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 ?   14.1   0.0   3.7e-05     0.042      13      52 ..      19      58 ..      17      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.7e-05
                                      HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                      +Y l ++        +ae+  vsp+++   + kLe+ G +
  gi|336252453|ref|YP_004595560.1| 19 VYALMGDARNTAAPAIAEEVSVSPATIRNRIAKLEEHGVI 58
                                      677777666667778*********************9976 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.9e-05     0.055      22      56 ..      25      59 ..      16      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-05
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      + +  ++ +iae++++sp  ++  +akL+++g+++
  gi|336252453|ref|YP_004595560.1| 25 DARNTAAPAIAEEVSVSPATIRNRIAKLEEHGVIE 59
                                      445578999************************98 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   0.1   0.00012      0.13       7      35 ..      31      59 ..      26      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                          HTH_CodY  7 askiaDriGitrsvivnaLrkLesaGiie 35
                                      a  ia+++ +  + i n + kLe  G+ie
  gi|336252453|ref|YP_004595560.1| 31 APAIAEEVSVSPATIRNRIAKLEEHGVIE 59
                                      679*************************9 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00017      0.19      21      46 ..      32      58 ..      26      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                            HTH_23 21 reIAreLgvsrrTvyrwlkryreeG.l 46
                                      ++IA+e  vs+ T+++ + + +e+G +
  gi|336252453|ref|YP_004595560.1| 32 PAIAEEVSVSPATIRNRIAKLEEHGvI 58
                                      58*************999999999955 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 ?   -3.6   0.2       8.9   9.9e+03      31      37 ..       9      15 ..       8      18 .. 0.78
   2 ?   11.2   0.1   0.00023      0.25      16      38 ..      32      54 ..      26      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.9
                                      HHHHHHH CS
                            HTH_30 31 yRLrrie 37
                                      yRL+ i 
  gi|336252453|ref|YP_004595560.1|  9 YRLDEID 15
                                      9999885 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00023
                                      HHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_30 16 satAkaLhvHrnTlryRLrriee 38
                                       a A++  v++ T+r+R+ ++ee
  gi|336252453|ref|YP_004595560.1| 32 PAIAEEVSVSPATIRNRIAKLEE 54
                                      689*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2242.35
//
Query:       gi|336252454|ref|YP_004595561.1|  [L=505]
Description: cation transporter [Halopiger xanaduensis SH-6]
Scores for 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-60  204.3  14.6    2.4e-32  112.1   1.6    2.0  2  TrkH            Cation transport protein
  ------ inclusion threshold ------
       0.03   14.1   0.0       0.03   14.1   0.0    3.5  3  Form-deh_trans  Formate dehydrogenase N, transmembrane
       0.11   12.8   0.2       0.32   11.3   0.0    1.9  2  DUF575          Protein of unknown function (DUF575)


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 !  112.1   1.6     4e-36   2.4e-32       5     241 ..      42     274 ..      40     300 .. 0.90
   2 !   97.6   5.5   9.5e-32   5.7e-28     316     489 ..     319     497 ..     313     504 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 4e-36
                              TrkH   5 ifkggiitialgavllfldkeskyplalkddfqivkaaeialsvdgtlklll.......esaslafldalfeavsgl 74 
                                       +++++++t++lga+l +l +  + +l  +++f  v  +++++   g+++ +l       +sa +   +a fe++sgl
  gi|336252454|ref|YP_004595561.1|  42 FAAAVVVTVVLGAALELLSD--DRELGQREGFLMVAFTWLSVGLVGAIPFYLaglaagpDSAFYSLVNAAFESMSGL 116
                                       56788999999999999955..558************************99999996666666666*********** PP

                              TrkH  75 tttglsvivveesl..prsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkelrslseliki 149
                                       tttg++ +   + +  +r++l +r++lq++Gglg++ +a   l  l  g+a+l ++e q + +  k ++++++++++
  gi|336252454|ref|YP_004595561.1| 117 TTTGATIMNGWDFAnqSRAILLWRQILQWLGGLGILIVAIGLLSNLMVGGAQLMETETQTKNV-TKLTPQIESTARL 192
                                       ********97665555************************9997777***********76665.6789********* PP

                              TrkH 150 lvvyyvgleilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivillvaiif 226
                                       ++ +yvgl++la++++   + +  +  e +       l++a+ h++++++++Gfs  ++S+a f+   ++++++++f
  gi|336252454|ref|YP_004595561.1| 193 IWGLYVGLTVLAAATF--YALQLLGLAENM------HLFNAVAHALTSVSTAGFSPEAESIAAFEP--IVQWAITPF 259
                                       ****************..888888899999......****************************97..9******** PP

                              TrkH 227 iilGnigFpillrvi 241
                                       ++lG+++F++l+ v 
  gi|336252454|ref|YP_004595561.1| 260 MLLGATNFVLLYYVV 274
                                       ***********9876 PP

  == domain 2  score: 97.6 bits;  conditional E-value: 9.5e-32
                              TrkH 316 vlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkavsk 391
                                       +++++F +vs+ t+ G++++ ++ + +  k +l l m+ gg++gSt+ +I++++ +++++ + +++ +  +p+av++
  gi|336252454|ref|YP_004595561.1| 319 IRHGVFNVVSMVTTtGYASANFDLWTAGAKHVLFLCMFLGGMAGSTTCSIKTLRWLVIVKGLYRNFFTSIHPEAVRP 395
                                       789**********99************************************************************** PP

                              TrkH 392 ksidgkhlerqllvdlws.lflvlliilileglklsdvq..epdfsffdiLfevvSaygtvGLSlG.aknaslsaql 464
                                       ++++   ++++ + d+++ ++l ++i+++l++l + d +  ++  + f++L++ +S + ++G+ +G a  +   a +
  gi|336252454|ref|YP_004595561.1| 396 VRLGDGVVDEETITDIFAyVMLAIVIFFLLTVLIVVDAArsGTTVTEFEALGAAASIFLNIGPAFGmAGPMDNYAGF 472
                                       *****************8566777777888888888876224678889******************779******** PP

                              TrkH 465 ttisklvlialmirGrlrglpvlld 489
                                       +    +v++++m++Gr +++pvl++
  gi|336252454|ref|YP_004595561.1| 473 PATTRAVMVIMMWIGRIEIIPVLVL 497
                                       **********************997 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 ?   -1.7   2.0      0.43   2.6e+03      14      29 ..      41      56 ..      39      59 .. 0.88
   2 ?   14.1   0.0     5e-06      0.03       3      39 ..     134     170 ..     133     174 .. 0.86
   3 ?   -3.5   0.5       1.6   9.7e+03      15      26 ..     291     302 ..     290     304 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.43
                                      HHHHHHHHHHHHHHHH CS
                    Form-deh_trans 14 plgalgmaatalagff 29
                                      p++a++++ ++l++++
  gi|336252454|ref|YP_004595561.1| 41 PFAAAVVVTVVLGAAL 56
                                      8999999999999986 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5e-06
                                       HHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHH--B-S CS
                    Form-deh_trans   3 plVelWKGvlKplgalgmaatalagffHYitvGPnev 39 
                                        ++ lW+ +l +lg lg+ ++a++ +   ++ G++  
  gi|336252454|ref|YP_004595561.1| 134 RAILLWRQILQWLGGLGILIVAIGLLSNLMVGGAQLM 170
                                       5788*********************999999888655 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHH CS
                    Form-deh_trans  15 lgalgmaatala 26 
                                       lg+++ +++++a
  gi|336252454|ref|YP_004595561.1| 291 LGLVVGISAIVA 302
                                       666666666665 PP

>> DUF575  Protein of unknown function (DUF575)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.5   1.5e+04      20      38 ..     153     171 ..     149     183 .. 0.65
   2 ?   11.3   0.0   5.3e-05      0.32       3      56 ..     277     328 ..     275     339 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.5
                            DUF575  20 ikaiPivGhivvGveWlvs 38 
                                       i ai ++ +++vG   l+ 
  gi|336252454|ref|YP_004595561.1| 153 IVAIGLLSNLMVGGAQLME 171
                                       6788888888888666654 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.3e-05
                            DUF575   3 dfsrplcsritnfalGvikaiPivGhivvGveWlvsrilertvkkpeftsdvas 56 
                                       df rpl s    f lG++ +i  +   ++G++  +   le t++++ f   v+s
  gi|336252454|ref|YP_004595561.1| 277 DFERPLESEELRFYLGLVVGISAIVAFIIGIDPEMDFGLEATIRHGVFN--VVS 328
                                       9********************************************9995..444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 4029.75
//
Query:       gi|336252455|ref|YP_004595562.1|  [L=452]
Description: TrkA-N domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-49  167.0   8.0    2.7e-24   85.6   1.2    2.7  2  TrkA_N           TrkA-N domain
      3e-27   94.3  13.1      1e-14   54.1   0.1    3.6  3  TrkA_C           TrkA-C domain
    2.5e-12   47.0   0.1    1.7e-05   24.9   0.1    2.6  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    6.6e-11   42.6   6.4    5.8e-06   26.7   1.1    2.9  3  NAD_binding_7    Putative NAD(P)-binding
    1.7e-07   31.6   3.6    0.00042   20.6   0.9    2.6  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    2.8e-07   31.0   1.2      0.013   16.1   0.0    3.6  4  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    2.9e-07   30.0   0.4    9.3e-07   28.4   0.4    1.8  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    7.8e-06   25.3   3.6      0.012   15.0   0.0    2.4  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    2.1e-05   24.0   0.0      0.049   12.9   0.0    2.5  2  FAD_binding_3    FAD binding domain
    5.5e-05   23.1   0.1       0.14   12.0   0.1    2.5  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    9.5e-05   22.1   0.1     0.0017   18.0   0.0    2.6  2  ApbA             Ketopantoate reductase PanE/ApbA
    0.00018   21.4   0.0      0.027   14.4   0.0    2.5  2  Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion
    0.00082   19.6   0.0          1    9.5   0.0    2.9  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00088   18.6   1.2       0.83    8.8   0.0    3.1  3  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
     0.0011   19.5   4.3       0.15   12.6   0.0    3.7  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
     0.0017   17.8   0.5      0.047   13.1   0.0    2.4  2  adh_short        short chain dehydrogenase
     0.0021   17.6   2.0       0.17   11.4   0.3    2.8  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0029   18.4   0.4        1.2   10.0   0.1    2.7  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0051   16.8   2.4      0.029   14.3   0.1    3.1  3  ADH_zinc_N       Zinc-binding dehydrogenase
     0.0068   16.8   0.5        2.3    8.7   0.1    2.8  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0092   15.6   1.1      0.041   13.5   0.1    2.3  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
  ------ inclusion threshold ------
      0.017   14.5   0.0        2.8    7.3   0.0    2.5  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.058   13.4   0.0       0.64   10.0   0.0    2.3  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
       0.12   12.7   0.9        1.6    9.0   0.1    2.6  2  Toprim           Toprim domain
       0.18   12.1   0.3         97    3.4   0.0    3.3  3  LTD              Lamin Tail Domain
       0.24   11.0   5.4       0.19   11.3   0.7    2.7  3  DAO              FAD dependent oxidoreductase
       0.74    9.1   7.8        2.6    7.4   0.5    3.6  4  ThiF             ThiF family
          1    8.8   5.5       0.18   11.3   0.1    2.4  3  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
        5.2    6.9   9.7        1.7    8.5   1.3    3.7  3  Rossmann-like    Rossmann-like 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 !   85.6   1.2   4.4e-27   2.7e-24       1     103 [.      11     112 ..      11     128 .. 0.92
   2 !   84.6   0.9   9.4e-27   5.8e-24       1     116 []     237     353 ..     237     353 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 4.4e-27
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddean 76 
                                       ++i+G+G+vGr++a +L +++ dvv++d+d ++veel+    + ++ gd+t+ e+L+ea++e+ad+via+t++de+n
  gi|336252455|ref|YP_004595562.1|  11 VVIVGAGEVGRAIAANLDDSH-DVVIVDRDGDVVEELTYSLdVLALEGDGTELETLREADVERADLVIACTDSDESN 86 
                                       79*****************99.7***************999899********************************* PP

                                       HHHHHHHHHHTSSSEEEEEESSGGGHH CS
                            TrkA_N  77 ilavllakelnpkkkiiaraqdpehae 103
                                       ++++ + k+  + + +iar++++   e
  gi|336252455|ref|YP_004595562.1|  87 VVVCGATKTVSD-AFTIARVRRRTLLE 112
                                       ********8666.89*****9987765 PP

  == domain 2  score: 84.6 bits;  conditional E-value: 9.4e-27
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT..SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg..levvvgdatdeevLeeagiekadaviaatgdde 74 
                                       ++i+G++++G + a+e+++ g+ +  +i++d++r++e++e    + v+  datd ++L++ ++++ad+viaa++ de
  gi|336252455|ref|YP_004595562.1| 237 VVIVGASEIGFQAAREFEDhGY-RPRLIERDHDRAREVAEALpdTLVMESDATDADFLAREHVDEADVVIAALDGDE 312
                                       79*****************777.599****************6556999**************************** PP

                                       HHHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  75 anilavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                       +n+l++llak l  + +++a +++ e+ael++++g+dv+i+p
  gi|336252455|ref|YP_004595562.1| 313 KNLLVSLLAKRLGVD-RTVAVIENLEYAELFETVGVDVAINP 353
                                       **********98886.8***********************98 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.1   1.6e-17     1e-14       1      66 [.     159     223 ..     159     225 .. 0.97
   2 ?   -2.4   0.1       6.9   4.3e+03      22      51 ..     253     286 ..     249     286 .. 0.73
   3 !   47.3   1.3   2.1e-15   1.3e-12       1      67 [.     383     450 ..     383     452 .] 0.92

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 1.6e-17
                                       CEEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelr 66 
                                       ++e++++a+sp+v++t+ e++  + + + +ai R++++i+++gd vL++GD+++v+gs +++++++
  gi|336252455|ref|YP_004595562.1| 159 MAEFEIDADSPIVDTTVEEADCYD-SLTFAAIFRDDDMIVARGDAVLRAGDRVVVIGSADSVSDFA 223
                                       68**********************.*************************************9996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.9
                                       HHHHS-EEEEEE-T....-EEES--TT-B--TT- CS
                            TrkA_C  22 lrargvlvvairRg....geliipsgdtvLeeGD 51 
                                       ++++g +   i R+     e+  + +dt  +e D
  gi|336252455|ref|YP_004595562.1| 253 FEDHGYRPRLIERDhdraREVAEALPDTLVMESD 286
                                       6666888888877766778888888888877766 PP

  == domain 3  score: 47.3 bits;  conditional E-value: 2.1e-15
                                       CEEEEEE--GGGTTSBHHHHT..HHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkeln..lrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       ++e++v+++s l+G t+ ++   l++ +v + ai R gel+ p+g tv+e+GD+++v+++ + l+e+ e
  gi|336252455|ref|YP_004595562.1| 383 VIEFEVAPDSVLAGETIVDATthLPD-RVVIGAISRAGELVTPRGGTVIEPGDHVVVFVDAAVLDEVVE 450
                                       689****************6566888.**********************************99999866 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   2.8e-08   1.7e-05      12      88 ..       8      85 ..       3     101 .. 0.81
   2 !   19.4   0.0   1.4e-06   0.00085      11      86 ..     233     311 ..     221     327 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.8e-08
                                      T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E..T-EEEEGCGHHHH.HHT-SEEEE-SSSSS CS
                      Shikimate_DH 12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkge..eiealkleelkel.laeadvvisatasee 87
                                      + +v+++GaGe+++ +a +L     ++vv++ R+ + ++el  +l+    e   ++le l+e+ +++ad+vi++t s e
  gi|336252455|ref|YP_004595562.1|  8 TVRVVIVGAGEVGRAIAANLD--DSHDVVIVDRDGDVVEELTYSLDVLalEGDGTELETLREAdVERADLVIACTDSDE 84
                                      579*****************8..5578**************999854411445678888876559**********9976 PP

                                      - CS
                      Shikimate_DH 88 p 88
                                       
  gi|336252455|ref|YP_004595562.1| 85 S 85
                                      4 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.4e-06
                                       TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCG...H.HHHHHT-SEEEE-S CS
                      Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealklee...l.kellaeadvvisat 83 
                                       +  +v+++Ga e++ ++a+ + ++g++    + R+++ra+e+ae l ++ +   + ++   l +e+++eadvvi+a 
  gi|336252455|ref|YP_004595562.1| 233 DADEVVIVGASEIGFQAAREFEDHGYR-PRLIERDHDRAREVAEALPDTLVMESDATDadfLaREHVDEADVVIAAL 308
                                       4578***********************.67789*************88766555555522233689********997 PP

                                       SSS CS
                      Shikimate_DH  84 ase 86 
                                          
  gi|336252455|ref|YP_004595562.1| 309 DGD 311
                                       655 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 !   26.7   1.1   9.4e-09   5.8e-06       9      83 ..      10      94 ..       7     105 .. 0.73
   2 ?   -1.6   0.0       6.1   3.8e+03      25      40 ..     202     217 ..     198     236 .. 0.61
   3 !   17.5   0.2   6.8e-06    0.0042       8      87 ..     235     326 ..     229     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 9.4e-09
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele......elvklaeee..l....ekdlegadlviaatddreln 75
                                      +v++vG+Gev+   + +l ++  +v++v+ +  + +e      + + l+ +   l    e+d+e+adlvia+td +e n
  gi|336252455|ref|YP_004595562.1| 10 RVVIVGAGEVGRAIAANLDDS-HDVVIVDRDG-DVVEeltyslDVLALEGDGteLetlrEADVERADLVIACTDSDESN 86
                                      89*********9988888777.99***99995.23332334443333432222213346899****************9 PP

                     NAD_binding_7 76 eriaeaak 83
                                        ++ a k
  gi|336252455|ref|YP_004595562.1| 87 VVVCGATK 94
                                      99887766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.1
                     NAD_binding_7  25 klleagakvtvvapev 40 
                                        +l+ag +v+v+  + 
  gi|336252455|ref|YP_004595562.1| 202 AVLRAGDRVVVIGSAD 217
                                       5678888888886553 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 6.8e-06
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapevkeele..........elvklaeeel..ekdlegadlviaatddr 72 
                                        +v++vG+ e++ + +r + + g +  ++  +  ++ e             ++++ ++  ++++++ad+viaa d +
  gi|336252455|ref|YP_004595562.1| 235 DEVVIVGASEIGFQAAREFEDHGYRPRLIERDHDRAREvaealpdtlvMESDATDADFlaREHVDEADVVIAALDGD 311
                                       589****************************96333334444443222112234444455778************** PP

                     NAD_binding_7  73 elneriaeaakarri 87 
                                       e n  +  +ak+ ++
  gi|336252455|ref|YP_004595562.1| 312 EKNLLVSLLAKRLGV 326
                                       999998888886654 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 !   20.6   0.9   6.8e-07   0.00042       1      79 [.      11      82 ..      11      96 .. 0.87
   2 !   10.9   0.1   0.00067      0.42       1      77 [.     237     308 ..     237     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.8e-07
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE-SS CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnlsp 78
                                      v+i+GaG vG+a+a  l +++dv    +++dr+ + +e+l     + ++ a + d  + e  L ++ ++ +dlv+ ++ 
  gi|336252455|ref|YP_004595562.1| 11 VVIVGAGEVGRAIAANLDDSHDV----VIVDRDGDVVEELT---YSLDVLALEGDGTELET-LREAdVERADLVIACTD 81
                                      89*******************86....*********99998...78999999999999999.66666999999998875 PP

                                      G CS
                   Sacchrp_dh_NADP 79 p 79
                                      +
  gi|336252455|ref|YP_004595562.1| 82 S 82
                                      5 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00067
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       v+i+Ga  +G  +a++ ++h+ +  +  +++r++++++++a++   ++   ++ da + + +  +++ e+d+v+ ++
  gi|336252455|ref|YP_004595562.1| 237 VVIVGASEIGFQAAREFEDHG-Y--RPRLIERDHDRAREVAEA--LPDTLVMESDATDADFLAREHVDEADVVIAAL 308
                                       79*****************98.6..99*********9999985..57777788888888886788899999999775 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 !   16.1   0.0     2e-05     0.013       1      55 [.      10      59 ..      10      90 .. 0.74
   2 !   11.5   0.0   0.00054      0.33       2      70 ..     237     309 ..     236     333 .. 0.80
   3 ?   -2.0   0.0       9.1   5.6e+03      39      60 ..     338     359 ..     314     365 .. 0.71
   4 ?   -1.7   0.1       7.4   4.6e+03      56      80 ..     427     451 ..     391     452 .] 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-05
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdn 55
                                      ++ i+GaG++g+a+a +l  +    h++v++ +r+ + +eel  +l v + ++d 
  gi|336252455|ref|YP_004595562.1| 10 RVVIVGAGEVGRAIAANLDDS----HDVVIV-DRDGDVVEELTYSLDVLALEGDG 59
                                      57899***********88877....9***88.**********9999955554432 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00054
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE-S CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvlav 69 
                                       + i+Ga ++g+  a+ +  +g   +  +++ +r+ ++a+e ae+l                 + e ++eadvv+ a+
  gi|336252455|ref|YP_004595562.1| 237 VVIVGASEIGFQAAREFEDHG---YRPRLI-ERDHDRAREVAEALPdtlvmesdaT-DADFLAREHVDEADVVIAAL 308
                                       6799*****************...888877.9*************99888775532.22224678899999999987 PP

                                       - CS
                     F420_oxidored  70 k 70 
                                        
  gi|336252455|ref|YP_004595562.1| 309 D 309
                                       5 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 9.1
                                       HHHHHHHHC-EEECECHHHHHH CS
                     F420_oxidored  39 aeelaeelgvkvtavdneeaae 60 
                                        +el e++gv+v   + ee+ae
  gi|336252455|ref|YP_004595562.1| 338 YAELFETVGVDVAINPREETAE 359
                                       4567788888888777777776 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 7.4
                                       HHHHHH-SEEEE-S-HHHHHHHHHH CS
                     F420_oxidored  56 eeaaeeadvvvlavkpedveevlse 80 
                                        +++e  d vv+ v  ++++ev+++
  gi|336252455|ref|YP_004595562.1| 427 GTVIEPGDHVVVFVDAAVLDEVVEA 451
                                       4567778888888888888888876 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 !   28.4   0.4   1.5e-09   9.3e-07       2     232 ..      10     321 ..       9     358 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.5e-09
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias..................... 57 
                                       +vv++G+G  G a a +l   +++v++v+++g  + +   +s  +l+ ++d+ +++                     
  gi|336252455|ref|YP_004595562.1|  10 RVVIVGAGEVGRAIAANLDD-SHDVVIVDRDG-DVVEELTYSLDVLALEGDGTELEtlreadveradlviactdsde 84 
                                       79*****************9.9******6555.45666888888888888877777899****************** PP

                                       ..............................................................HHHHCHHHHCCCCHC CS
                                       ..............................................................xxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ..............................................................evvkklnqgielllg 72 
                                                                                                     + v+ +  g+ ++++
  gi|336252455|ref|YP_004595562.1|  85 snvvvcgatktvsdaftiarvrrrtlletwegsqgafgvdfmvctdlltaqtifrisglpssQDVDTFVGGLVRMAE 161
                                       ***********************************************************999778999999887777 PP

                                       CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCTTC.....TTBEECCSECHHHHHHCCSS-T.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx....xxxxxxxxxxxxxxxxxxxxxxx.. RF
                       Pyr_redox_2  73 eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gipGv....aenvgklvrtldsaealklkllp.. 142
                                          ++id ++  +++++ +    e   yd+l  A  ++  d+    G+    a + + ++ + ds+  + ++ +p  
  gi|336252455|ref|YP_004595562.1| 162 ---FEIDADS-PIVDTTVE----EADCYDSLTFAAIFRDDDMiVARGDavlrAGDRVVVIGSADSVSDFAQDVVPva 230
                                       ...*******.55554433....455666776666666666643335555553333344467888888888888899 PP

                                       ....SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEE CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 ....krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngek 215
                                           + +v+vG++ iG   A ++ + g++  l+e+     r++ ++l ++l  +  + + ++  ++ v e+d     
  gi|336252455|ref|YP_004595562.1| 231 sddaDEVVIVGASEIGFQAAREFEDHGYRPRLIERDHDRAREVAEALPDTLVMESDATDADFLAREHVDEAD---VV 304
                                       99999************************9999998888899999999999888888888888888887776...33 PP

                                       EEEEETTSCEEEESEEE CS
                                       xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 216 levvledgeeidadlvv 232
                                       +   ++d++ + ++l+ 
  gi|336252455|ref|YP_004595562.1| 305 IAALDGDEKNLLVSLLA 321
                                       34777777776666665 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 !   10.1   1.2   0.00059      0.37      28      98 ..       8      79 ..       3      89 .. 0.81
   2 !   15.0   0.0   1.9e-05     0.012      30      99 ..     236     308 ..     226     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00059
                                      --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCHHHHHHHH.HHHH-SEEEE- CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlksqeellae.avkeadvvigt 98
                                        +v+++G+G +G  Aia+      +V+++D + ++ e+l   l    +e    + e+l+e  v++ad+vi +
  gi|336252455|ref|YP_004595562.1|  8 TVRVVIVGAGEVG-RAIAANLDDSHDVVIVDRDGDVVEELTYsLDVLALEGDGTELETLREaDVERADLVIAC 79
                                      569**********.58888888899***************987766667777777666655269999999975 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.9e-05
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE..HCHHHHHHHHHHHH-SEEEE-- CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev..lksqeellaeavkeadvvigtv 99 
                                       +v+++G+   G qA++     g + ++++ +++r++++ + l  + v     +    l +e+v eadvvi + 
  gi|336252455|ref|YP_004595562.1| 236 EVVIVGASEIGFQAAREFEDHGYRPRLIERDHDRAREVAEaLPDTLVMEsdATDADFLAREHVDEADVVIAAL 308
                                       79************************************99777775555333444456789*********984 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0018       1.1       2      36 ..       9      42 ..       8      73 .. 0.89
   2 !   12.9   0.0   7.9e-05     0.049       3      38 ..     236     271 ..     234     280 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0018
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                      + V+IVGaG +G   a  L     +vv+v++  + 
  gi|336252455|ref|YP_004595562.1|  9 VRVVIVGAGEVGRAIAANLDDS-HDVVIVDRDGDV 42
                                      78***********999999999.9******98765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.9e-05
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCC CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvv 38 
                                       +V+IVGa+  G+ +a++   +G r +l+e+  ++++
  gi|336252455|ref|YP_004595562.1| 236 EVVIVGASEIGFQAAREFEDHGYRPRLIERDHDRAR 271
                                       79****************************998776 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 !   12.0   0.1   0.00023      0.14       2      42 ..      11      50 ..      10      87 .. 0.83
   2 !    8.6   0.0    0.0025       1.5       2      49 ..     237     284 ..     236     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekaleki 42
                                      v ++GaG +G+ iaa +    ++Vv+vd++ + +e+ + ++
  gi|336252455|ref|YP_004595562.1| 11 VVIVGAGEVGRAIAANL-DDSHDVVIVDRDGDVVEELTYSL 50
                                      89************986.6789********99999876655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0025
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCC CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiekslekl 49 
                                       v ++Ga  +G + a  f  +g++ +l++++++++++++e++ ++l   
  gi|336252455|ref|YP_004595562.1| 237 VVIVGASEIGFQAAREFEDHGYRPRLIERDHDRAREVAEALPDTLVME 284
                                       89***********************************99998876554 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.7e-06    0.0017       1      76 [.      11      80 ..      11     108 .. 0.68
   2 ?    1.1   0.0      0.45   2.8e+02       1      38 [.     237     275 ..     237     335 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.7e-06
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH..HHHHCEEEEETT.CEEEEEECEEECCHSCCCCS-ESEEEE- CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea..lkknGlrltseg.geeilrppealsaeekselepidlvivt 75
                                      ++i+GaG +G+ +aa+L    +dv++++r+   +e+   + + l l+++g + e+lr+          + e +dlvi +
  gi|336252455|ref|YP_004595562.1| 11 VVIVGAGEVGRAIAANL-DDSHDVVIVDRDGdVVEEltYSLDVLALEGDGtELETLREA---------DVERADLVIAC 79
                                      68***************.569**********8888744444555555555222222222.........44444555444 PP

                                      S CS
                              ApbA 76 v 76
                                      +
  gi|336252455|ref|YP_004595562.1| 80 T 80
                                      4 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.45
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHH CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkk 38 
                                       ++i+Ga  iG   a +   +g+ + li r+  r+ ++ +
  gi|336252455|ref|YP_004595562.1| 237 VVIVGASEIGFQAAREFEDHGYRPRLIERDHdRAREVAE 275
                                       579999999999999999999999999999977776655 PP

>> Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.07        43      74      93 ..     200     219 ..     187     229 .. 0.82
   2 !   14.4   0.0   4.4e-05     0.027      31      88 ..     385     440 ..     373     449 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.07
                   Castor_Poll_mid  74 ddevlqegdkllviaedddt 93 
                                        d vl++gd+++vi++ d+ 
  gi|336252455|ref|YP_004595562.1| 200 GDAVLRAGDRVVVIGSADSV 219
                                       5899**********998765 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.4e-05
                   Castor_Poll_mid  31 efylkelpelegkkyedvllafqeavviGikvassgkiylnPeddevlqegdkllvia 88 
                                       ef +   + l+g + +d+++++++ vviG  +++ g++ + P+  +v++ gd+++v  
  gi|336252455|ref|YP_004595562.1| 385 EFEVAPDSVLAGETIVDATTHLPDRVVIGA-ISRAGEL-VTPRGGTVIEPGDHVVVFV 440
                                       455666678********************9.6777887.68*************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 !    9.5   0.0    0.0017         1       2      64 ..      11      81 ..      10     102 .. 0.74
   2 !    7.1   0.0    0.0095       5.8       3      66 ..     238     311 ..     236     345 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0017
                                      EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........EEE-SSHHHH.HHHCSEEEE-SS CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........akaaesieel.vasldvvitmvk 64
                                      + ++G G+ G+ +a nl    ++v++++r+ + veel  +          + +e+++e+ v+++d+vi +  
  gi|336252455|ref|YP_004595562.1| 11 VVIVGAGEVGRAIAANLD-DSHDVVIVDRDGDVVEELTYSLdvlalegdGTELETLREAdVERADLVIACTD 81
                                      5689************96.5799*************987756666666655555555433666677777654 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0095
                                       EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..........EEE-SSHHHHHHHCSEEEE-SSSH CS
                     NAD_binding_2   3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..........akaaesieelvasldvvitmvkag 66 
                                        ++G  ++G + a++++++gy+  +++r++++++e++++            +a   ++e v+++dvvi  +  +
  gi|336252455|ref|YP_004595562.1| 238 VIVGASEIGFQAAREFEDHGYRPRLIERDHDRAREVAEALpdtlvmesdaTDADFLAREHVDEADVVIAALDGD 311
                                       689********************************999977788866663222233346677778888887543 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 ?    4.7   0.0     0.025        15       1      34 [.      12      44 ..      11      50 .. 0.83
   2 ?    2.0   0.2      0.17     1e+02     163     184 ..     206     227 ..     199     232 .. 0.87
   3 !    8.8   0.0    0.0013      0.83     164     202 ..     234     272 ..     226     281 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.025
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nign 34
                                      +I+GaG  G a+a +l ++   d++i++++  +++
  gi|336252455|ref|YP_004595562.1| 12 VIVGAGEVGRAIAANLDDSH--DVVIVDRDgDVVE 44
                                      79******999999998887..599*999766666 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.17
                       Pyr_redox_3 163 agqkvvViGgknSavDaAlelv 184
                                       ag++vvViG  +S  D A ++v
  gi|336252455|ref|YP_004595562.1| 206 AGDRVVVIGSADSVSDFAQDVV 227
                                       5899************998765 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0013
                       Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseieke 202
                                        ++vv++G+++ ++ aA e+ ++g + +++ r++ + +e
  gi|336252455|ref|YP_004595562.1| 234 ADEVVIVGASEIGFQAAREFEDHGYRPRLIERDHDRARE 272
                                       579****************************99977665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.3      0.03        19       1      31 [.      10      39 ..      10      48 .. 0.83
   2 !   12.6   0.0   0.00024      0.15       2      31 ..     237     266 ..     236     287 .. 0.89
   3 ?   -1.2   0.0       5.2   3.2e+03      11      31 ..     335     355 ..     333     376 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.03
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvvers 31
                                      +vv+vG+G +g   A++l +   +V +v+r 
  gi|336252455|ref|YP_004595562.1| 10 RVVIVGAGEVGRAIAANLDDSH-DVVIVDRD 39
                                      79**************998866.77777776 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00024
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvvers 31 
                                       vv+vG++ ig  +A ++ ++g +  ++er 
  gi|336252455|ref|YP_004595562.1| 237 VVIVGASEIGFQAAREFEDHGYRPRLIERD 266
                                       9***************************96 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.2
                                       HHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  11 glElAgalaelgkkVtvvers 31 
                                       +lE+A+ +   g +V +  r+
  gi|336252455|ref|YP_004595562.1| 335 NLEYAELFETVGVDVAINPRE 355
                                       689999999999999876655 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.14        86       3      56 ..      11      57 ..       9      74 .. 0.75
   2 !   13.1   0.0   7.7e-05     0.047       3      64 ..     237     293 ..     235     310 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.14
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE- CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqv 56
                                      v+++Ga+  +Graia +l  +  +vv+vdr  + +ee+  +l      +la+++
  gi|336252455|ref|YP_004595562.1| 11 VVIVGAG-EVGRAIAANLDDS-HDVVIVDRDGDVVEELTYSLD-----VLALEG 57
                                      7888887.59*******9887.889999**9998877766655.....455555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.7e-05
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHH CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreev 64 
                                       v+++Gas  IG + a+e+   G++  +++r  ++++eva+ l ++    l+++ D td++ +
  gi|336252455|ref|YP_004595562.1| 237 VVIVGAS-EIGFQAAREFEDHGYRPRLIERDHDRAREVAEALPDT----LVMESDATDADFL 293
                                       7899998.6**********************************85....6666666666543 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 !   11.4   0.3   0.00027      0.17       2      40 ..      10      47 ..       9      93 .. 0.89
   2 ?    5.0   0.1     0.025        16     144     177 ..     381     416 ..     344     423 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHC CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdkln 40
                                      +++++G+G vG   aa l    h+v++vD d   v++l 
  gi|336252455|ref|YP_004595562.1| 10 RVVIVGAGEVGRAIAANLDD-SHDVVIVDRDGDVVEELT 47
                                      899************99965.7**********9999985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.025
                                       TTCEEEEE------TTSHHHHHHS..-S-EEEEESS CS
                    UDPG_MGDP_dh_N 144 gvdfdvvsnPEflregsavkdlln..pdrvviGvee 177
                                       ++ ++  + P  ++ g+++ d  +  pdrvviG+ +
  gi|336252455|ref|YP_004595562.1| 381 AEVIEFEVAPDSVLAGETIVDATThlPDRVVIGAIS 416
                                       344556667**********99765449******865 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 !   10.0   0.1     0.002       1.2       1      73 [.       9      83 ..       9     100 .. 0.76
   2 ?    5.9   0.0     0.034        21       3      73 ..     237     311 ..     236     333 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.002
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS....HHHHHTCT..TESEEEE-S-GG CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd....leelladp..eidavivatpng 73
                                      +rv+i+GaG +g+  +++l +s   ++vv ++d+d    e++  s++v a +     le l + +  ++d+vi +t ++
  gi|336252455|ref|YP_004595562.1|  9 VRVVIVGAGEVGRAIAANLDDS---HDVV-IVDRDGDVVEELTYSLDVLALEGdgteLETLREADveRADLVIACTDSD 83
                                      59************99777766...5555.9999999999997777777555455556666666565899998888775 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.034
                                       EEEETTSHHHHHHHHHHHHTTTTEEEE.EEECSSHHHHHHHHHHTTHE.EESSHHHHHTCT..TESEEEE-S-GG CS
                      GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrleevv.alldpdaeraeavaesfgve.aysdleelladp..eidavivatpng 73 
                                       v+i+Ga  ig + +r + ++  + +++    d+  e aea+ +++++e   +d + l+++   e+d+vi a   +
  gi|336252455|ref|YP_004595562.1| 237 VVIVGASEIGFQAAREFEDHGYRPRLIeRDHDRAREVAEALPDTLVMEsDATDADFLAREHvdEADVVIAALDGD 311
                                       89*******999999999996666443034555555555557888888555555555554455566655554444 PP

>> 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       1.9   1.2e+03      83     116 ..      85     117 ..      62     125 .. 0.66
   2 ?   -0.7   0.0       2.1   1.3e+03      76      92 ..     201     217 ..     196     255 .. 0.71
   3 !   14.3   0.1   4.7e-05     0.029       8      55 ..     319     366 ..     315     384 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.9
                                       EEEEECSC.TSSEEEEEHHHHH.HTT-EEEEE-SSC CS
                        ADH_zinc_N  83 GrlvvvGg.gkgeeefdlrnll.lkeksilGsllgs 116
                                         +vv+G+  +     d++ ++  +++++l ++ gs
  gi|336252455|ref|YP_004595562.1|  85 SNVVVCGAtKTV---SDAFTIArVRRRTLLETWEGS 117
                                       467888863333...344444445777777777776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.1
                                       HHCEEEEEEEEECSCTS CS
                        ADH_zinc_N  76 lkllkpgGrlvvvGggk 92 
                                        ++l+ g r+vv+G   
  gi|336252455|ref|YP_004595562.1| 201 DAVLRAGDRVVVIGSAD 217
                                       56899999999999732 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 4.7e-05
                                       HHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTT CS
                        ADH_zinc_N   8 qlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltg 55 
                                        lAk lG+ +++av  + e +el +  G+d++in++e +  e+i ++t+
  gi|336252455|ref|YP_004595562.1| 319 LLAKRLGVdRTVAVIENLEYAELFETVGVDVAINPRE-ETAEEIVRFTR 366
                                       68*********************************77.89999988885 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 !    8.7   0.1    0.0037       2.3       1      83 [.      10      89 ..      10      97 .. 0.78
   2 ?    5.5   0.0     0.035        21      12      87 ..     246     321 ..     236     335 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0037
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG....GGTTTECEBEEEGGGGGCTT-SEEEE-SC CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk....aleegkdlkvedvdeeelkevdivflalp 75
                                      +v ivG  G vG++++  L+++ +v +v      r +G  ++e+         eg   ++e+  e++++++d+v+ +++
  gi|336252455|ref|YP_004595562.1| 10 RVVIVG-AGEVGRAIAANLDDSHDVVIVD-----R-DGDVVEELTYsldvLALEGDGTELETLREADVERADLVIACTD 81
                                      699999.79**********9966665554.....3.5666666666565545667778888899*************** PP

                                      HHHHHHHH CS
                    Semialdhyde_dh 76 agvskela 83
                                      ++ s+ ++
  gi|336252455|ref|YP_004595562.1| 82 SDESNVVV 89
                                      *9998665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.035
                                       HHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG....GGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHH CS
                    Semialdhyde_dh  12 GqellrlLeehpevelvvllsssrsaGkklaeavk....aleegkdlkvedvdeeelkevdivflalpagvskelap 84 
                                       G + +r  e+h +    +l+ ++++  +++aea +    + ++ +d  +     e ++e+d+v+ al+++  + l+ 
  gi|336252455|ref|YP_004595562.1| 246 GFQAAREFEDHGY--RPRLIERDHDRAREVAEALPdtlvMESDATDADF--LAREHVDEADVVIAALDGDEKNLLVS 318
                                       5555555555553..3455566666777788888874434444444444..559999************99888877 PP

                                       HHH CS
                    Semialdhyde_dh  85 kla 87 
                                        la
  gi|336252455|ref|YP_004595562.1| 319 LLA 321
                                       765 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 !   13.5   0.1   6.6e-05     0.041       6      68 ..      10      80 ..       7      98 .. 0.73
   2 ?   -0.7   0.0       1.4   8.9e+02       7      48 ..     237     278 ..     233     317 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-05
                                      -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-........HHHHHHHHTT-EEEEHHHH.HHT-SEEEE-S CS
                              IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregs........ksvkkAkeegfevltvaea.vkkadvvmili 68
                                      +++++G G  G+a a nl ds  dvv+  r+g+          v   + +g e  t++ea v++ad+v+  +
  gi|336252455|ref|YP_004595562.1| 10 RVVIVGAGEVGRAIAANLDDSH-DVVIVDRDGDvveeltysLDVLALEGDGTELETLREAdVERADLVIACT 80
                                      799***************9996.6777667666455554322334457788999998888678888887654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                                       EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT CS
                              IlvN   7 iaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeeg 48 
                                       ++++G    G   a+++ d g    +  r++++  + A++  
  gi|336252455|ref|YP_004595562.1| 237 VVIVGASEIGFQAAREFEDHGYRPRLIERDHDRAREVAEALP 278
                                       566666666666666666666655555555554444443322 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 ?    7.3   0.0    0.0045       2.8      38      67 ..      10      38 ..       3      82 .. 0.80
   2 ?    4.6   0.0     0.029        18      37      89 ..     235     282 ..     220     302 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0045
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydr 67
                                      +v i+G+G++G+a+a  l     +v+++dr
  gi|336252455|ref|YP_004595562.1| 10 RVVIVGAGEVGRAIAANLDDSH-DVVIVDR 38
                                      799************9987543.4555555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.029
                                       SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHH CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleell 89 
                                        +v i+G+ +IG ++a+ ++  g +   ++r +++ +e++e        ++l+
  gi|336252455|ref|YP_004595562.1| 235 DEVVIVGASEIGFQAAREFEDHGYRPRLIERDHDRAREVAEA-----LPDTLV 282
                                       5799****************9999888888886655533332.....233333 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 ?   10.0   0.0     0.001      0.64       2      39 ..      11      47 ..      10      89 .. 0.91
   2 ?    0.7   0.0      0.74   4.6e+02       2      42 ..     237     277 ..     236     308 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHH CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieein 39
                                      + ++GaG  G a+A+ l +  h+v++  r+ +++ee+ 
  gi|336252455|ref|YP_004595562.1| 11 VVIVGAGEVGRAIAANLDDS-HDVVIVDRDGDVVEELT 47
                                      889**************886.59999999999999875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.74
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHS CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineeh 42 
                                       + ++Ga   G   A+ ++++g + rl+ r+++ ++e+ e+ 
  gi|336252455|ref|YP_004595562.1| 237 VVIVGASEIGFQAAREFEDHGYRPRLIERDHDRAREVAEAL 277
                                       77888888888888888888888888888887777776654 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0027       1.6      11      74 ..      20      84 ..      10      85 .. 0.75
   2 ?    1.3   0.1      0.62   3.8e+02      56      74 ..     294     312 ..     247     324 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0027
                                      HHHHHHTHT.STEEEEEEESSSSEEEHSTTEEEEE....ECTTTHHHHHHHHHHH.HHHSEEEEECSSSH CS
                            Toprim 11 aktiakalg.sgfqavtaslGhildletefkpvye....eiedkkkvlkalkela.kradeiilatDpDr 74
                                       ++ia  l+ s +++++   G +++  t     y      +e++ + l++l+e   +rad +i +tD D+
  gi|336252455|ref|YP_004595562.1| 20 GRAIAANLDdSHDVVIVDRDGDVVEELT-----YSldvlALEGDGTELETLREADvERADLVIACTDSDE 84
                                      5556655554566677777788888888.....55556688899999999******************96 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.62
                                       HHHHHHHHSEEEEECSSSH CS
                            Toprim  56 lkelakradeiilatDpDr 74 
                                        +e   +ad +i a+D+D+
  gi|336252455|ref|YP_004595562.1| 294 AREHVDEADVVIAALDGDE 312
                                       3444499**********97 PP

>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.71   4.4e+02      84     110 ..      23      48 ..       4      50 .. 0.64
   2 ?    3.2   0.0      0.18   1.1e+02      57      98 ..     202     240 ..     175     251 .. 0.74
   3 ?    3.4   0.0      0.16        97      51      70 ..     422     441 ..     393     447 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.71
                               LTD  84 ssavwnnggdavaLydasgevvdsvgy 110
                                       ++a+++ ++  v+++d +g vv +++y
  gi|336252455|ref|YP_004595562.1|  23 IAANLD-DSHDVVIVDRDGDVVEELTY 48 
                                       444444.4556666699*******999 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.18
                               LTD  57 gtlaageyvvvwsgsgttsasngskas.ssavwnnggdavaLy 98 
                                        +l ag+ vvv  ++++   s+   a+ + +v+++++d+v+++
  gi|336252455|ref|YP_004595562.1| 202 AVLRAGDRVVVIGSADSV--SDF--AQdVVPVASDDADEVVIV 240
                                       589*********997544..222..223778888899998876 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.16
                               LTD  51 tfpngtgtlaageyvvvwsg 70 
                                       + p g +++++g++vvv+ +
  gi|336252455|ref|YP_004595562.1| 422 VTPRGGTVIEPGDHVVVFVD 441
                                       3333336**********865 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7   0.00031      0.19       1      29 [.      10      39 ..      10      45 .. 0.87
   2 ?   -1.7   0.0       2.6   1.6e+03     255     287 ..     203     236 ..     169     238 .. 0.59
   3 ?    0.4   0.1      0.62   3.8e+02       2      31 ..     237     268 ..     236     443 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                      EEEEECTSHHHHHHHHHHHHTT.EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg.Vtllekg 29
                                      +vvi+G+G +G ++A  L   + V++++++
  gi|336252455|ref|YP_004595562.1| 10 RVVIVGAGEVGRAIAANLDDSHdVVIVDRD 39
                                      59****************65557******8 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
                                       EEEETTSEEEE.EESSE.EETTCSSTSCSHHHHHH CS
                               DAO 255 vtprkdgrvlv.Ggtad.eesgdddpevdeedide 287
                                       v+ r+++rv+v G+ ++  +++ d+++v ++d+de
  gi|336252455|ref|YP_004595562.1| 203 VL-RAGDRVVViGSADSvSDFAQDVVPVASDDADE 236
                                       33.34566666366554655555556777777665 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.62
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdi 31 
                                       vvi+G+  iG  +A+e   +g    l+e++++
  gi|336252455|ref|YP_004595562.1| 237 VVIVGASEIGFQAAREFEDHGyrPRLIERDHD 268
                                       56666666666666666555555555555543 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.5    0.0041       2.6      18      37 ..       8      27 ..       4      40 .. 0.89
   2 ?    3.2   0.1     0.078        48      81     126 ..      43      89 ..      40     100 .. 0.82
   3 ?   -0.9   0.0       1.3   8.2e+02      20      38 ..     236     254 ..     224     270 .. 0.84
   4 ?   -0.5   0.1         1   6.2e+02      97     127 ..     287     318 ..     267     337 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0041
                                      TSEEEEE--SHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                              ThiF 18 dskvllvGaGglGsellknL 37
                                      +++v++vGaG +G  ++ nL
  gi|336252455|ref|YP_004595562.1|  8 TVRVVIVGAGEVGRAIAANL 27
                                      589**************998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.078
                                       HHHT-TTSEEEEEES-CCG.CCS-HHHHTT-SEEEEESSSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  81 lqeinpdveveavteritd.etvleellesvDlVvdalDniearrlv 126
                                       ++e+  +++v a++++ t+ et+ e  +e++DlV+ ++D+ e+ + v
  gi|336252455|ref|YP_004595562.1|  43 VEELTYSLDVLALEGDGTElETLREADVERADLVIACTDSDESNVVV 89 
                                       5666677888888888888888888889***********98877665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.3
                                       EEEEE--SHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              ThiF  20 kvllvGaGglGsellknLa 38 
                                       +v++vGa  +G  +++++ 
  gi|336252455|ref|YP_004595562.1| 236 EVVIVGASEIGFQAAREFE 254
                                       699********99999875 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1
                                       CCGCC.S-HHHHTT-SEEEEESSSHHHHHHHH CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  97 itdet.vleellesvDlVvdalDniearrlvn 127
                                        td   +++e + ++D+V+ alD  e  +lv 
  gi|336252455|ref|YP_004595562.1| 287 ATDADfLAREHVDEADVVIAALDGDEKNLLVS 318
                                       344333477889999********877777765 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 ?   -1.5   0.2       2.4   1.5e+03       6      57 ..      19      66 ..      16      73 .. 0.80
   2 ?   11.3   0.1    0.0003      0.18       4      57 ..     243     294 ..     240     323 .. 0.86
   3 ?   -2.1   0.1       3.8   2.3e+03      10      42 ..     338     369 ..     336     388 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.4
                                      HHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHH CS
                      adh_short_C2  6 IGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqve 57
                                      +GraiA  l +   +vv++d++ +    veel+ +l+  +le D t+ e+++
  gi|336252455|ref|YP_004595562.1| 19 VGRAIAANLDDS-HDVVIVDRDGDV---VEELTYSLDVLALEGDGTELETLR 66
                                      588888888765.799999999998...999999888888888887777665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0003
                                       TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.EEE--TTSHHHHH CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae.vlecDVtdeeqve 57 
                                       s IG+++A+++ ++G++  l  ++ ++   ++e+ae+l+ + v+e D+td + ++
  gi|336252455|ref|YP_004595562.1| 243 SEIGFQAAREFEDHGYRPRLIERDHDR---AREVAEALPDTlVMESDATDADFLA 294
                                       67******************9999998...9999999999967*******99865 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.8
                                       HHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTT CS
                      adh_short_C2  10 iAkalaeeGaevvltdlneeakkrveelaeelg 42 
                                        A+++   G +v++  ++e a+ ++ ++++++ 
  gi|336252455|ref|YP_004595562.1| 338 YAELFETVGVDVAINPREETAE-EIVRFTRAGR 369
                                       6899999999999998888874.4444444444 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.3    0.0027       1.7      11      48 ..       9      45 ..       3     106 .. 0.62
   2 ?    1.1   0.1      0.54   3.3e+02      12      63 ..     236     286 ..     225     333 .. 0.76
   3 ?   -0.5   0.1       1.7     1e+03       8      41 ..     407     442 ..     399     446 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0027
                     Rossmann-like 11 lsvGiisaGrvGtalgaaleraghvvvgisaisaasre 48
                                      + v i++aG+vG a++a l+ + h vv +    ++ +e
  gi|336252455|ref|YP_004595562.1|  9 VRVVIVGAGEVGRAIAANLDDS-HDVVIVDRDGDVVEE 45
                                      6799***************986.555555555555444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.54
                     Rossmann-like  12 svGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvleve 63 
                                       +v i++a ++G   +  +e  g+    i    + +re ae+ lPd+ v+e +
  gi|336252455|ref|YP_004595562.1| 236 EVVIVGASEIGFQAAREFEDHGYRPRLIERDHDRAREVAEA-LPDTLVMESD 286
                                       57899999999999999999999999999988889998875.8999888763 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.7
                     Rossmann-like   8 sarlsvGiis.aGr.vGtalgaaleraghvvvgisa 41 
                                       + r+ +G is aG+ v +  g+ +e  +hvvv + a
  gi|336252455|ref|YP_004595562.1| 407 PDRVVIGAISrAGElVTPRGGTVIEPGDHVVVFVDA 442
                                       678888988767873556667889999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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):              29  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 3269.32
//
Query:       gi|336252456|ref|YP_004595563.1|  [L=514]
Description: cation transporter [Halopiger xanaduensis SH-6]
Scores for 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-68  229.4   7.9    2.6e-66  224.1   7.9    2.0  1  TrkH      Cation transport protein


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 !  224.1   7.9   1.5e-70   2.6e-66      20     490 ..      58     507 ..      44     513 .. 0.85

  Alignments for each domain:
  == domain 1  score: 224.1 bits;  conditional E-value: 1.5e-70
                              TrkH  20 lfldkeskyplalkddfqivkaaeialsvdgtlklll..esaslafldalfeavsgltttglsvi..vveeslprsg 92 
                                        +++ e++  + ++++f++v  +++   v g+++ +l  ++      +alfe++sg+tttg++v+  +++e+ +r++
  gi|336252456|ref|YP_004595563.1|  58 ALRRLEPEPDPGAREAFMVVALTWLFAAVFGAVPFVLagNGTVAHPVNALFESMSGFTTTGATVMgdISFETHSRAM 134
                                       444556667788999*******************988655555556*******************33356777**** PP

                              TrkH  93 ltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkelrslselikilvvyyvgleilafvllvvli 169
                                       l++r+ +q++Gg+g++vla+++l  +  g+a+l ++e +++ ++ k ++ ++e++++l++ yvg+++l++ ll   +
  gi|336252456|ref|YP_004595563.1| 135 LMWRQLTQWVGGMGIIVLAVAILSQMAVGGAQLMEAETPGPGVS-KLTPHIAETARVLWIAYVGFTVLYITLL--YA 208
                                       ***********************9999**************998.579**********************999..66 PP

                              TrkH 170 ytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivillvaiifiilGnigFpillrviiaikk 246
                                           +y   +        ++a+ h+++++ ++Gfs  + S++ f    v+++++++f+++ +++F+++  v +    
  gi|336252456|ref|YP_004595563.1| 209 AHLAGYAPSM------DAYNAVAHGLTTLPTGGFSPEARSIEAFSP--VVQWLVVPFMFIAGVNFVLWWHVVSGDPR 277
                                       6677799999......999*************************87..********************999876544 PP

                              TrkH 247 kilrdlkqikeslsflldlprrcftLllasgfvwllllelavlnvtdnilfillde..gslvvksipkgsrvlkalF 321
                                                      l+d ++r       +g+v +l++        + +lf  + e  + ++ ++++   +++ a+F
  gi|336252456|ref|YP_004595563.1| 278 T-------------MLRDNEFRLY-----LGAVTVLSIV------GTAMLFYSTLEgpDGQIGGNLE--RSARYATF 328
                                       4.............4679999999.....3444444443......2234555555522344445555..89999*** PP

                              TrkH 322 qsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkavskksidgk 397
                                       q +s+    G++ +d++++   +k+ll+++m+igg+ gSt ggI+ ++ +++ +++++ei +  +p+av+++++ g+
  gi|336252456|ref|YP_004595563.1| 329 QIASLVNStGYANIDFAQWNGPTKGLLLFAMFIGGSTGSTGGGIKVLRWLVILKTFRREIFTTIHPEAVRPVRMNGR 405
                                       ****97666******************************************************************** PP

                              TrkH 398 hlerqllvdlws.......lflvlliilileglklsdvqepdfsffdiLfevvSaygtvGLSlG.a.knaslsaqlt 465
                                        l++++++ ++s       lf+v +++l +   ++   ++pdf+++di +++++++g++G++lG     +    +++
  gi|336252456|ref|YP_004595563.1| 406 ILDEDAVRGIYSfsllflvLFFVGIALLAVDAARVGLYADPDFEVIDIVGASIATLGNIGPGLGtVtGPMGGYNDFP 482
                                       ***********9666444444444445556677889999*************************65566778899** PP

                              TrkH 466 tisklvlialmirGrlrglpvlldr 490
                                        +sk ++i+ m++Grl+++pvl++ 
  gi|336252456|ref|YP_004595563.1| 483 LSSKGLMIVYMWIGRLEIFPVLVLL 507
                                       *********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3708.95
//
Query:       gi|336252457|ref|YP_004595564.1|  [L=145]
Description: Glyoxalase/bleomycin resistance protein/dioxygenase [Halopiger xanaduensis SH-6]
Scores for 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-13   49.4   0.1    6.2e-13   49.1   0.1    1.1  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    2.7e-10   40.5   0.1    3.3e-10   40.2   0.1    1.1  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    6.2e-07   29.4   0.0    2.2e-05   24.4   0.0    2.1  1  Glyoxalase_2  Glyoxalase-like domain
    0.00053   20.1   0.2     0.0012   19.0   0.2    1.6  1  Glyoxalase_3  Glyoxalase-like domain
     0.0021   18.8   0.5     0.0046   17.7   0.5    1.6  1  Glyoxalase_6  Glyoxalase-like domain


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 !   49.1   0.1   1.7e-16   6.2e-13       3     128 .]      11     140 ..       9     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.7e-16
                                       EEEEEEESHHHHHHHHHHHHHTSEEEEEEEE.........EESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCB CS
                        Glyoxalase   3 dhvallvgdleksldFYtkvLGfklvkktdn.........teeteglriaffhaggghielvlneapsgaakhvkki 70 
                                       +hv + v dle+ l+FY++vLGf++ +++              +  +++  + a+g ++e+v +e+   a +     
  gi|336252457|ref|YP_004595564.1|  11 HHVGITVEDLEAVLPFYRDVLGFDVADRFQVdgeafstavGVDDAAANFVHLEADGIRVEIVEYEPQARASPDA--- 84 
                                       9*****************************66666665543334666666666666666666666666666655... PP

                                       SC.TSEEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  71 ee.tvhhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                        + +  +  ++ ++v d++ ++  l +  v+   ep+++ +g+++ f  rDp  +l+e+
  gi|336252457|ref|YP_004595564.1|  85 -GlNQPGAKHLGFTVADLESFYADLPDD-VETLSEPQTTATGNSILF-LRDPEDNLVEV 140
                                       .477999999*******99999999875.5***************88.*********96 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.1   9.3e-14   3.3e-10       1      94 [.      11     115 ..      11     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 9.3e-14
                                       EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EET.........TTTEEEEEEEETTEEEEEEEESSTT.-THHH..T CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepq.........evdlafallgsgsvqieLieplegp.eflae..h 65 
                                       +++gi VeDlea + ++ ++lG+++ +r++++ +         ++   f++l    +++e +e  +++  + ++  +
  gi|336252457|ref|YP_004595564.1|  11 HHVGITVEDLEAVLPFYRDVLGFDVADRFQVDGEafstavgvdDAAANFVHLEADGIRVEIVEYEPQArASPDAglN 87 
                                       8*****************************9987344444333456677666665599999987776646667789* PP

                                       S-EEEEEEEEES-HHHHHHHHCTTTEEEE CS
                      Glyoxalase_4  66 geglhhlaywvddldaavarleeqGfevv 94 
                                       ++g  hl++ v dl+   a+l +  +e +
  gi|336252457|ref|YP_004595564.1|  88 QPGAKHLGFTVADLESFYADLPDD-VETL 115
                                       *****************9999885.5544 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   6.1e-09   2.2e-05       6     115 ..      15     142 ..      11     145 .] 0.72

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6.1e-09
                                       -EES-HHHHHHHHHHTT---EEEE-SSE.EEETTS-EE...............EEHHHHHH.......-------S- CS
                      Glyoxalase_2   6 lvvkdieeskkFYedvlelkikldfGen.vsfetgfal...............kedlkeli.......nldesiaeq 59 
                                       ++v+d+e    FY+dvl   +   f      f+t + +               +    e++        +++   +q
  gi|336252457|ref|YP_004595564.1|  15 ITVEDLEAVLPFYRDVLGFDVADRFQVDgEAFSTAVGVddaaanfvhleadgiR---VEIVeyepqarASPDAGLNQ 88 
                                       689999999999999999999988843313577777664444444444322221...22233333222233344456 PP

                                       -SS-EEEEEES-HHHHHHHH..GGGS-EEEEEEE-TTS-EEEEEE-TT--EEEEEE CS
                      Glyoxalase_2  60 snnfeLyFevedvdaflqklkeaeniellhelkekpWgqrvirfyDpDkhiiEige 115
                                           +L+F v+d+++f  +l   +++e l e++  + g  ++ + Dp+ +++E+ e
  gi|336252457|ref|YP_004595564.1|  89 PGAKHLGFTVADLESFYADL--PDDVETLSEPQTTATGNSILFLRDPEDNLVEVLE 142
                                       67789***************..788****************************976 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   3.4e-07    0.0012       2      99 ..      11     112 ..      11     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.4e-07
                      Glyoxalase_3   2 DHvvlavpdleeaaarfarrlGftvtpggehpgl.........gtaNalvmf.gdg.YlEllavdpeapaperprlf 67 
                                       +Hv++ v+dle+    +++ lGf v+++ +  g           +a   v++ +dg  +E+++++p+a+a + +   
  gi|336252457|ref|YP_004595564.1|  11 HHVGITVEDLEAVLPFYRDVLGFDVADRFQVDGEafstavgvdDAAANFVHLeADGiRVEIVEYEPQARASPDA--- 84 
                                       7*************************777777666666666665555666666789999*****9999984222... PP

                      Glyoxalase_3  68 gldrlakgeglhtlalrtddidataarlraaG 99 
                                           l+ ++g+++l ++++d++  +a+l +  
  gi|336252457|ref|YP_004595564.1|  85 ---GLN-QPGAKHLGFTVADLESFYADLPDDV 112
                                       ...455.5*****************9998754 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.5   1.3e-06    0.0046       4     106 ..      15     140 ..      12     141 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                      Glyoxalase_6   4 ldaadpaalaaFwaaalgweveree............aaledpegvgpaaedaatllfqrvpe.............. 54 
                                       + ++d +a+  F++++lg++v+++             +  + ++ +   ++d+ +       +              
  gi|336252457|ref|YP_004595564.1|  15 ITVEDLEAVLPFYRDVLGFDVADRFqvdgeafstavgV-DDAAANFVHLEADGIR-------Veiveyepqaraspd 83 
                                       567899*****************998777777665421.1111222222333333.......144444557888899 PP

                      Glyoxalase_6  55 ...paknrvHldlavedldaevarlvalGArvlreprdgthgr..vlaDPeGneFcv 106
                                           +    Hl ++v+dl+   a l +   +  +++   t+     l+DPe n   v
  gi|336252457|ref|YP_004595564.1|  84 aglNQPGAKHLGFTVADLESFYADLPDDVETLSEPQTTATGNSilFLRDPEDNLVEV 140
                                       888555569*********988888888777777777666655599999999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1074.65
//
Query:       gi|336252458|ref|YP_004595565.1|  [L=122]
Description: methylglyoxal synthase [Halopiger xanaduensis SH-6]
Scores for 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-14   51.7   0.0    8.8e-14   51.5   0.0    1.1  1  MGS       MGS-like domain


Domain annotation for each model (and alignments):
>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   4.9e-18   8.8e-14       2      95 .]      16     108 ..      15     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 4.9e-18
                                       HHHHHHHHHHTT..CEEEEEHHHHHHHH.HTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHH CS
                               MGS   2 lvelakklkelg..fellATgGTakllk.eagipvtevvektgegerlggrveildaikngeidlvintlypfkatv 75 
                                       l+e+a++++e +  +el+ATg+T+k l  ++ ++    +e+ ++g +lgg++ i++++++++ d v+++ +p++a++
  gi|336252458|ref|YP_004595565.1|  16 LIEFAQNHEEQLreYELIATGTTGKRLMeATDLE----IERKESG-PLGGDMMIGAEVAEEKLDGVVFLRDPLRAQP 87 
                                       89********9999*************9556889....8888889.******************************* PP

                                       H.CHHHHHHHHHHHTTSHEES CS
                               MGS  76 a.kdgykirraaenidIplpt 95 
                                       + +d  ++ r++++ d  l+t
  gi|336252458|ref|YP_004595565.1|  88 HePDISALLRICDVRDTALAT 108
                                       *999999*****999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 919.09
//
Query:       gi|336252459|ref|YP_004595566.1|  [L=162]
Description: TrkA-C domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-18   64.0   0.3    2.8e-17   62.3   0.0    1.9  2  TrkA_C           TrkA-C domain
     0.0031   17.5   0.0        0.1   12.6   0.0    2.2  2  Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion
  ------ inclusion threshold ------
        0.1   12.2   0.1        1.2    8.7   0.0    2.3  2  ArsA_HSP20       HSP20-like domain found in ArsA


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 ?   -1.0   0.0      0.27   1.6e+03      34      34 ..      35      35 ..      16      58 .. 0.44
   2 !   62.3   0.0   4.7e-21   2.8e-17       2      70 .]      89     159 ..      88     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.27
                                      - CS
                            TrkA_C 34 R 34
                                      R
  gi|336252459|ref|YP_004595566.1| 35 R 35
                                      3 PP

  == domain 2  score: 62.3 bits;  conditional E-value: 4.7e-21
                                       EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrellg 70 
                                        ++ v+  + ++G+tl e+ +r+r gv v+ai+Rg + +  p+++tvLe GD+l+vvg++++ ae++ llg
  gi|336252459|ref|YP_004595566.1|  89 EWFNVTDTAEIAGQTLEEAAIRERtGVSVIAIQRGdDLISPPTPETVLEVGDTLVVVGEREECAEFETLLG 159
                                       578999*****************************555556666**********************99876 PP

>> Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.016        97      28      56 ..      33      61 ..      23      81 .. 0.81
   2 !   12.6   0.0   1.7e-05       0.1      32      94 ..      91     152 ..      75     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.016
                   Castor_Poll_mid 28 eknefylkelpelegkkyedvllafqeav 56
                                       k e+ylke p  +g k ++v  ++   v
  gi|336252459|ref|YP_004595566.1| 33 GKREVYLKENPDADGDKLFEVSDRLARKV 61
                                      5889************9999988876655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.7e-05
                   Castor_Poll_mid  32 fylkelpelegkkyedvllafqeav.viGikvassgkiylnPeddevlqegdkllviaedddtk 94 
                                       f++++  e++g++ e++ ++    v vi i   +   ++  P+ ++vl+ gd l+v++e ++  
  gi|336252459|ref|YP_004595566.1|  91 FNVTDTAEIAGQTLEEAAIRERTGVsVIAI--QRGDDLISPPTPETVLEVGDTLVVVGEREECA 152
                                       999999*********999887766525666..554578888999**************988765 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 ?    8.7   0.0    0.0002       1.2       9      40 ..       7      39 ..       3      39 .. 0.91
   2 ?    0.5   0.0     0.075   4.5e+02      20      33 ..     135     148 ..     133     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0002
                        ArsA_HSP20  9 dLPfvdke.eidlsrsgdeLtIkignfrRqitL 40
                                      dLP+v k+ e++l++++   +++ +  +R++ L
  gi|336252459|ref|YP_004595566.1|  7 DLPGVGKKfEVELENDERLVIVTHNTGKREVYL 39
                                      8****7776********************9987 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.075
                        ArsA_HSP20  20 lsrsgdeLtIkign 33 
                                       + ++gd+L++  ++
  gi|336252459|ref|YP_004595566.1| 135 VLEVGDTLVVVGER 148
                                       5678******8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); 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:                         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 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1263.49
//
Query:       gi|336252460|ref|YP_004595567.1|  [L=427]
Description: sodium/hydrogen exchanger [Halopiger xanaduensis SH-6]
Scores for 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-48  162.9  41.9    1.1e-47  162.6  41.9    1.0  1  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 !  162.6  41.9   6.2e-52   1.1e-47       3     374 ..      14     398 ..      12     403 .. 0.91

  Alignments for each domain:
  == domain 1  score: 162.6 bits;  conditional E-value: 6.2e-52
                                       HHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.......................HHHCHCCHHHHCHHCCH CS
                    Na_H_Exchanger   3 llillallvgllarrlklpeivgliiaGlllGpsglglieps..................eedlevlselglilllF 61 
                                       +l+++++++g+la+r+++++i+++i++G+llG ++lg ++ +                  ++ + v  e+g++lllF
  gi|336252460|ref|YP_004595567.1|  14 VLFVAVAVAGYLANRINQSVIPFYILVGMLLGEHVLGTVDFPallgmdlvphgsdlalveTDFIYVGHEIGIVLLLF 90 
                                       556668888889*************************55544777777888889*****99**************** PP

                                       HHHCTCGCCTGCCTHHHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTC CS
                    Na_H_Exchanger  62 laGleldlrelrknlksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvpe 138
                                        +Gle++l +l++ +  i + +++ ++i++ + Gl+l++   l   +l a+l ++i+ +++ +++++ l ++g + +
  gi|336252460|ref|YP_004595567.1|  91 FLGLEFNLGRLLASKERIGKAGTVDLAINFGV-GLVLGYA--LFGAFLPAFLTAGIVYISSSAIITKSLLDLGWIAN 164
                                       ********************************.*****74..3358999999999999999999999999******* PP

                                       CCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHH CS
                    Na_H_Exchanger 139 rlgtlllgesvlnDavavvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrftdddrele 215
                                       +    +lg++v++D++  v+l+v+ al+ ++   +++l+++++++ ++++++ll+ l + w+ r +     d+ e+ 
  gi|336252460|ref|YP_004595567.1| 165 DESDAMLGTLVFEDLFIAVYLSVATALVLGSGDVGAALGQIGIAVGFILALLLLVYLGTEWFQRGLDT---DSHEFV 238
                                       ****************************9888899999999999999999999999999988777766...89**** PP

                                       HHHHHHHHHHHHHHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHH CS
                    Na_H_Exchanger 216 vllvlllallaallaellgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsv 292
                                       vl +l + ll+a++a +lgvs +++af++G+++s +++ ++l+  le++r ++f+ +fF+ +Gl +d++++   l v
  gi|336252460|ref|YP_004595567.1| 239 VLRALGVTLLIAGAALSLGVSEAVAAFFVGMAFSSTDHVHDLENLLEPLR-DAFAAIFFFWIGLVTDPSLF---LGV 311
                                       **************************************************.9***************9999...*** PP

                                       HHHHHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHH......XHHHHTTSSTTTCS CS
                    Na_H_Exchanger 293 lilvllilvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpal......gllarelyallivv 363
                                         l++++++a + +++++++l  r++ ls r ++ +g+g+++rg+++l++a+l+ +       +  a++ ya+++++
  gi|336252460|ref|YP_004595567.1| 312 AGLIAVAVIATTPTKLVSGYLGGRIYDLSERRSVRVGLGMSTRGEFSLIIASLALQGagtglaEGVAADIYAFAVGY 388
                                       ********************************************************999988855666888888888 PP

                                       TSXHHHHHHHH CS
                    Na_H_Exchanger 364 vlftvlvqGls 374
                                       vl++ ++ G+s
  gi|336252460|ref|YP_004595567.1| 389 VLVMSVL-GTS 398
                                       8888773.443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.37
# Mc/sec: 3435.51
//
Query:       gi|336252461|ref|YP_004595568.1|  [L=219]
Description: HAD-superfamily hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-25   89.7   0.0    2.9e-25   89.4   0.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    6.6e-16   59.2   1.6    2.2e-15   57.5   1.6    1.7  1  Hydrolase       haloacid dehalogenase-like hydrolase
    7.8e-11   41.9   0.3    1.6e-10   40.9   0.3    1.6  1  Hydrolase_like  HAD-hyrolase-like
    1.1e-07   32.5   2.2    1.5e-07   32.0   2.2    1.1  1  HAD             haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.057   13.3   0.0      0.074   12.9   0.0    1.4  1  Acid_PPase      Acid Phosphatase
      0.071   13.2   0.0       0.17   12.0   0.0    1.6  1  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 !   89.4   0.0   9.6e-29   2.9e-25       1     175 [.       5     183 ..       5     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 9.6e-29
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglsl.....rellrklgeseeeeekieellrkynee 72 
                                       ++FDlD Tl+  +    ++++ +++  g ++ls+e++ ++ g +l     + ++  l  + e + + + +   y+e 
  gi|336252461|ref|YP_004595568.1|   5 VVFDLDYTLAVPTRDRETILQDAVDAVGAPSLSREDYLEVHGRHLtresrEPIFADLLADRESDADPAAVATAYRET 81 
                                       79**********************************99998876511111457777777777777************ PP

                             HAD_2  73 kkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklk 149
                                         +  ++p++gv+ +L +L + +y++g+ T++  +a+++kle lg+e+ Fd  +++ + e  KPdp+ +e++  +l+
  gi|336252461|ref|YP_004595568.1|  82 IAD-ALEPLPGVEAMLADL-RTEYRVGLLTNGPVRAQRDKLETLGWEDAFDAALVTGELEAGKPDPRAFEAIAAELD 156
                                       ***.***************.99******************************************************* PP

                             HAD_2 150 lkkeeviyvGDsp.tDieaakkagikv 175
                                       +++++++yvGD    D+ +a +ag++ 
  gi|336252461|ref|YP_004595568.1| 157 VDPADAVYVGDDVdADVTGATNAGMTP 183
                                       *************9***********75 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   1.6   7.4e-19   2.2e-15       3     210 .]       4     180 ..       2     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 7.4e-19
                                       EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewlta 79 
                                       +vvfD+d TL   ++  e++++ a                    v a  a s + +++ ++ gr    + ++  +++
  gi|336252461|ref|YP_004595568.1|   4 AVVFDLDYTLAVPTRDRETILQDA--------------------VDAVGAPSLSREDYLEVHGRHLTRESREPIFAD 60 
                                       899999999999998999999999....................889999999999999999997555555556666 PP

                                       HHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  80 ldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG 156
                                       l           + +s++  +a+         tiad l++ p+++ ++a L+   ++v+llt++  + ++  ++ lG
  gi|336252461|ref|YP_004595568.1|  61 L---------LADRESDADPAAVA---TAYRETIADALEPLPGVEAMLADLRTE-YRVGLLTNGPVRAQRDKLETLG 124
                                       6.........45555555555555...455578888888*************65.99******************** PP

                                       .GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 157 .ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                        +d+fda + + + + +kp+p++++a++ eL ++p++ + VGD v  D+ ++ +Ag
  gi|336252461|ref|YP_004595568.1| 125 wEDAFDAALVTGELEAGKPDPRAFEAIAAELDVDPADAVYVGDDVDaDVTGATNAG 180
                                       *****88888888889***********************************99997 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.3   5.2e-14   1.6e-10       2      49 ..     140     187 ..     139     211 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 5.2e-14
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEES CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVl 49 
                                       +gKP p ++++++++l++dp++ +++GD++++D+ gA naG++ v Vl
  gi|336252461|ref|YP_004595568.1| 140 AGKPDPRAFEAIAAELDVDPADAVYVGDDVDADVTGATNAGMTPVQVL 187
                                       59*****************************************99886 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   2.2   4.9e-11   1.5e-07       1     180 [.       5     168 ..       5     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 4.9e-11
                               HAD   1 alfDfDgTL.ldg.dslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaele 74 
                                       ++fD+D TL +++ d  + l +  +  +a  +  + re +l+ +   + +l r++++  ++ lla+ + +++ a ++
  gi|336252461|ref|YP_004595568.1|   5 VVFDLDYTLaVPTrDRETILQD-AV--DAVGAPSLSREDYLEVH---GRHLTRESREPIFADLLADREsDADPAAVA 75 
                                       79*******7777444445555.33..33444567777788888...7778888999999999999999******** PP

                               HAD  75 rfvaevirpkl.ldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvr 150
                                        +++e i+ +l   pg+ ++la  ++  +rv ++++g+ +  + +l+ lg              +++   + g + +
  gi|336252461|ref|YP_004595568.1|  76 TAYRETIADALePLPGVEAMLA-DLRTEYRVGLLTNGPVRAQRDKLETLG----WED------AFDAA-LVTGELEA 140
                                       ***9999999553379999999.66888**********************....555......44444.55555777 PP

                               HAD 151 gegkvaalrewlaaegegidleevvayGDs 180
                                       g+ +++a ++   a++ + d+++ v++GD 
  gi|336252461|ref|YP_004595568.1| 141 GKPDPRAFEA--IAAELDVDPADAVYVGDD 168
                                       8888899999..99999************5 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.5e-05     0.074       2      22 ..       1      21 [.       1     102 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                                      --SEEEE-STTTSSSS-TTTS CS
                        Acid_PPase  2 lpklivFDLDyTLWpfevdtl 22
                                      +p+++vFDLDyTL  +  d  
  gi|336252461|ref|YP_004595568.1|  1 MPQAVVFDLDYTLAVPTRDRE 21
                                      69***********87776655 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.8e-05      0.17      12      51 ..      85     123 ..      81     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.8e-05
                                       TTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHH CS
                       Hydrolase_6  12 gdkaipgaaealnalraagkpvvllTNnsskseeeyakkl 51 
                                         +++pg++ +l  lr + ++v llTN+  + +++ ++ l
  gi|336252461|ref|YP_004595568.1|  85 ALEPLPGVEAMLADLRTE-YRVGLLTNGPVRAQRDKLETL 123
                                       5689***********987.9************99888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); 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:                         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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 1875.88
//
Query:       gi|336252462|ref|YP_004595569.1|  [L=265]
Description: alpha/beta hydrolase fold protein [Halopiger xanaduensis SH-6]
Scores for complete 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-25   91.2  15.3    1.6e-25   91.0  15.3    1.0  1  Abhydrolase_6   Alpha/beta hydrolase family
    3.1e-18   66.4   0.0    6.3e-14   52.2   0.1    2.1  2  Abhydrolase_1   alpha/beta hydrolase fold
    3.7e-10   39.5   0.0    6.4e-10   38.7   0.0    1.3  1  Hydrolase_4     Serine aminopeptidase, S33
    0.00044   20.4   0.0    0.00064   19.9   0.0    1.2  1  Thioesterase    Thioesterase domain
  ------ inclusion threshold ------
      0.012   15.2   0.0       0.26   10.8   0.0    2.1  2  DLH             Dienelactone hydrolase family
       0.13   12.0   0.0        9.7    5.8   0.0    2.1  2  PGAP1           PGAP1-like protein
       0.16   11.6   0.0       0.34   10.6   0.0    1.5  1  TFA2_Winged_2   TFA2 Winged helix domain 2
        1.3    9.3   6.6        4.1    7.7   0.0    3.6  4  Se-cys_synth_N  Selenocysteine synthase N terminal


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0  15.3   7.2e-29   1.6e-25       1     219 [.      14     251 ..      14     252 .. 0.62

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 7.2e-29
                                       EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT....TTSEEEEEETCH CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldledladlaalldelaa..gggpvvlvGHSlG 75 
                                       ++l+HG+g+s + Wl + L  l+a++ +v+a+DlpGhG ++p+p +   +++l ++++++ +  + + v +vG+S+G
  gi|336252462|ref|YP_004595569.1|  14 LVLVHGLGGSWRTWL-PVLDDLAAER-EVIAVDLPGHGATPPSPGET-SIETLTDAVTSFLEanDLRGVDIVGNSMG 87 
                                       79******9999996.4667777777.77*********554444333.337776666666556789*********** PP

                                       HHHHHHHHHCC..EE.EEES-..----TTT.........S----TTHHHHHHTT-C.......CCCHCCH...S-HS CS
                     Abhydrolase_6  76 Galalaaaplalvvg.vlldppptalpagl.........laaalelllallallrl.......lawlsre...plpr 132
                                       G l+l++a+  +v + v+ldp   ++ ++          la+ ++l++ l ++l++        ++l  +   ++p 
  gi|336252462|ref|YP_004595569.1|  88 GRLVLELARRGVVGAtVALDP---GGFWTGweryffyatLAPSIRLVRLLQPVLTPltesaagRTLLL-AqlsARPW 160
                                       ******7777775559*****...33333333333444322222222222222221111111211111.12323444 PP

                                       CCCCHHHCCCCHCHCCCGHHHHCCHHC....HTTCCHHTT-TTGCEEE.CTT-C..HHHHCHHCCCH.STTEEETCE CS
                     Abhydrolase_6 133 lfladedadaawrarlarlaallaglg....llpaaawadlpvpllvl.ggeDp..lvprllerlla.qagarlpvv 201
                                       ++ ad++  ++  +++a+ + ++  l         +  ad+p p+ v+ +g+ +  ++pr + r+ a  ++arl + 
  gi|336252462|ref|YP_004595569.1| 161 ELPADVA--REELRTFADSPVFDELLRrlafGPGQPGTADAPGPV-VIgWGRKDlvTLPRQATRATArFPDARL-HW 233
                                       6666666..444444444443333222222122266999999999.665766665999999999999*******.** PP

                                       ...SSS-HHHHSHHHHHH CS
                     Abhydrolase_6 202 lpgaGHlphleepdevae 219
                                       ++g+GH+ph ++p+e+++
  gi|336252462|ref|YP_004595569.1| 234 FEGSGHYPHWDAPAETVR 251
                                       **********99999987 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.1   2.8e-17   6.3e-14       2      93 ..      13      97 ..      12     121 .. 0.93
   2 !   12.5   0.0   3.8e-05     0.085     211     257 .]     198     246 ..     137     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2.8e-17
                                      EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEE CS
                     Abhydrolase_1  2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGh 80
                                      +lv++hGl+gs+  w    + ++La  + +vi++Dl+G+g ++p+p +     ++ ++ d +  +l+a +++ + +vG 
  gi|336252462|ref|YP_004595569.1| 13 PLVLVHGLGGSWRTWLP--VLDDLAA-EREVIAVDLPGHGATPPSPGE----TSIETLTDAVTSFLEANDLRGVDIVGN 84
                                      8****************..******9.*******************65....67888********************** PP

                                      THHHHHHHHHHHH CS
                     Abhydrolase_1 81 SmGGmialayaae 93
                                      SmGG+++l++a +
  gi|336252462|ref|YP_004595569.1| 85 SMGGRLVLELARR 97
                                      **********976 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.8e-05
                                       HS..EEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHSH CS
                     Abhydrolase_1 211 la..ptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlaflegp 257
                                        a  p+++ +g++D ++ p++  + ++ +p++rl+ ++++gH+ +++ p
  gi|336252462|ref|YP_004595569.1| 198 DApgPVVIGWGRKDLVTLPRQATRATARFPDARLHWFEGSGHYPHWDAP 246
                                       2255***************8888888899*****************975 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   2.9e-13   6.4e-10       7     235 ..      14     242 ..      11     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.9e-13
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGh 83 
                                       +vlvHGl+ + +    + ++Laa + +v+a+D  GhG +++  g  +s+++++d + +f+e     +  + + ++G 
  gi|336252462|ref|YP_004595569.1|  14 LVLVHGLGGSWRTWLPVLDDLAA-EREVIAVDLPGHGATPPSPG-ETSIETLTDAVTSFLE----ANDLRGVDIVGN 84 
                                       79*******************97.58**************9999.6777777777777764....444556789*** PP

                       Hydrolase_4  84 SmGGliallyllrypdkvaglilsaPalkikakl.......kappllklllkllgkllpklqvsnnlkadslsrdpe 153
                                       SmGG ++l+++ r     + +   + +   ++++       +  +l++ll+ +l +l  +    + l+ ++ls  p+
  gi|336252462|ref|YP_004595569.1|  85 SMGGRLVLELARRGVVGATVALDPGGFWTGWERYffyatlaPSIRLVRLLQPVLTPLTESAAG-RTLLLAQLSARPW 160
                                       ***********9888744444444444444444489887643566777788888888877777.999********** PP

                       Hydrolase_4 154 vvaayeadplvhgkitvrlllelldamkrleeraakit..lPllllhGeaDkvvdpeasrelyerlgskdktlklyp 228
                                       ++ a  a + ++      ++ ell+ +++   +   ++   P+ +  G +D v+ p+++ ++ +r +  d +l++++
  gi|336252462|ref|YP_004595569.1| 161 ELPADVAREELRTFADSPVFDELLRRLAFGPGQPGTADapGPVVIGWGRKDLVTLPRQATRATARFP--DARLHWFE 235
                                       ***999999999999999**********99887777773367***********************99..9******* PP

                       Hydrolase_4 229 glyHell 235
                                       g  H  +
  gi|336252462|ref|YP_004595569.1| 236 GSGHYPH 242
                                       ****877 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.9e-07   0.00064       2      86 ..      13      97 ..      12      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.9e-07
                                      EEEEE--TTCCSGGGHHHHHHCTTCEEEEEEECSTTST..SHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHH CS
                      Thioesterase  2 pLflfppagGsasvfrslasklsdpvvevlavqlpgre..rdepplesieelaaeyaealrqiqpegPyalfGhSlGgl 78
                                      pL+l+++ gGs +        l ++  ev+av lpg++   ++p  +sie+l + ++  l++   +  ++++G S+Gg 
  gi|336252462|ref|YP_004595569.1| 13 PLVLVHGLGGSWRTWLPVLDDLAAE-REVIAVDLPGHGatPPSPGETSIETLTDAVTSFLEANDLR-GVDIVGNSMGGR 89
                                      89**********************7.************988899999*******************.68********** PP

                                      HHHHHHHH CS
                      Thioesterase 79 lAfevArq 86
                                      l  e+Ar+
  gi|336252462|ref|YP_004595569.1| 90 LVLELARR 97
                                      ******97 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.26      84     127 ..      65     105 ..      53     117 .. 0.81
   2 ?    2.1   0.0     0.052   1.2e+02     142     187 ..     198     239 ..     192     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                               DLH  84 aavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaava 127
                                       +av    + +  +   v +vG  mGG+l+l+la+++  v a+va
  gi|336252462|ref|YP_004595569.1|  65 DAVTSFLEAN--DLRGVDIVGNSMGGRLVLELARRG-VVGATVA 105
                                       5555555555..567899******************.8999997 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.052
                               DLH 142 kikapilalfgeeDefipadevekleealkaanvdlelkvYpgagH 187
                                       ++ +p+++  g +D +    ++ + +    a+ +d++l++++g gH
  gi|336252462|ref|YP_004595569.1| 198 DAPGPVVIGWGRKDLVTLPRQATRAT----ARFPDARLHWFEGSGH 239
                                       56678888888888766555544444....5569***********9 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0043       9.7       3      20 ..      10      27 ..       8      45 .. 0.82
   2 ?    4.1   0.0     0.014        32      87     104 ..      73      90 ..      57     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0043
                             PGAP1  3 sGipVlFvpGnagsykqv 20
                                      +G+p ++v+G++gs + +
  gi|336252462|ref|YP_004595569.1| 10 TGEPLVLVHGLGGSWRTW 27
                                      89************9988 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.014
                             PGAP1  87 ekeptsviliGHSmGGiv 104
                                        ++ + v ++G SmGG +
  gi|336252462|ref|YP_004595569.1|  73 ANDLRGVDIVGNSMGGRL 90 
                                       567788**********65 PP

>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015      0.34       7      47 ..       3      43 ..       3      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                     TFA2_Winged_2  7 lalLkkrpkaeGikvkdLkdswpdveealeeLeaegeilvl 47
                                      l+++++ +++  + v  L  sw    + l++L+ae+e++ +
  gi|336252462|ref|YP_004595569.1|  3 LNHIRRGTGEPLVLVHGLGGSWRTWLPVLDDLAAEREVIAV 43
                                      7899999999999*************************976 PP

>> Se-cys_synth_N  Selenocysteine synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       0.4     9e+02      28      37 ..      63      72 ..      61      73 .. 0.86
   2 ?   -3.6   0.1       6.3   1.4e+04      23      33 ..      86      96 ..      85      97 .. 0.73
   3 ?    2.2   0.4     0.098   2.2e+02      10      37 ..     151     176 ..     148     177 .. 0.91
   4 ?    7.7   0.0    0.0018       4.1       8      33 ..     181     225 ..     180     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.4
                    Se-cys_synth_N 28 vrdavrafLd 37
                                      ++dav  fL+
  gi|336252462|ref|YP_004595569.1| 63 LTDAVTSFLE 72
                                      89******98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.3
                    Se-cys_synth_N 23 lpRalvrdavr 33
                                      ++  lv+++ r
  gi|336252462|ref|YP_004595569.1| 86 MGGRLVLELAR 96
                                      66678888887 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.098
                    Se-cys_synth_N  10 LLtalearallaalpRalvrdavrafLd 37 
                                       LL++l+ar+   +lp ++ r+ +r f d
  gi|336252462|ref|YP_004595569.1| 151 LLAQLSARPW--ELPADVAREELRTFAD 176
                                       8999999999..9***********9977 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0018
                    Se-cys_synth_N   8 DaLLtal...................earallaalpRalvrdavr 33 
                                       D+LL+ l                   ++r++l  lpR++ r+  r
  gi|336252462|ref|YP_004595569.1| 181 DELLRRLafgpgqpgtadapgpvvigWGRKDLVTLPRQATRATAR 225
                                       89999999999999999999999999***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2011.62
//
Query:       gi|336252463|ref|YP_004595570.1|  [L=143]
Description: hypothetical protein Halxa_1056 [Halopiger xanaduensis SH-6]
Scores for 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  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1193.52
//
Query:       gi|336252464|ref|YP_004595571.1|  [L=158]
Description: hypothetical protein Halxa_1057 [Halopiger xanaduensis SH-6]
Scores for complete 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-51  173.5   0.1    2.2e-51  173.3   0.1    1.0  1  DUF2240   Uncharacterized protein conserved in archaea (DUF22
  ------ inclusion threshold ------
      0.011   16.4   3.4      0.017   15.8   3.3    1.5  1  ABATE     Putative stress-induced transcription regulator


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 !  173.3   0.1   2.5e-55   2.2e-51       1     141 [.       2     139 ..       2     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 173.3 bits;  conditional E-value: 2.5e-55
                           DUF2240   1 elkiavaapfkkkrkdklsesdfvfalsldrkwlspdqakklldraeeegLlekkdgdlvpnfdvaeveiPlgFkpd 77 
                                       +l++a aapf ++++++l+e +fv+alsldr+w+spdqak+l+d+a+ egLle++++dlv+ fd++ev++P+ F pd
  gi|336252464|ref|YP_004595571.1|   2 SLRVAAAAPFIQNGTTRLEEGEFVVALSLDRDWFSPDQAKRLIDIATREGLLERDGDDLVAGFDPSEVTVPEEFVPD 78 
                                       68999************************************************************************ PP

                           DUF2240  78 eellkekstferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegvdvddli 141
                                       e++l+e+s+fer+lda++a  g ek+e+v+ in+lq +l+  v++eaaa+v+a++eg+dvdd++
  gi|336252464|ref|YP_004595571.1|  79 EDILQERSAFERVLDALVA-DGAEKHEAVGAINALQGDLG--VTIEAAAVVYARREGLDVDDIA 139
                                       *******************.99******************..********************87 PP

>> ABATE  Putative stress-induced transcription regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   3.3   1.9e-06     0.017      49     123 ..      64     146 ..      14     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-06
                                       ................HHHHHHHHHHHHHHTHHHH.........HHHHHHHHHS----EEEE-TTS-E......... CS
                             ABATE  49 a.............elararaLRealrallaaaaagdpppaaalaalnallaaappaprLvrhddgpvdrardwhll 112
                                                     + ++ ++ R+a+ ++l+a +a+ + + +a+ a+nal            ++d +v+ ++++ ++
  gi|336252464|ref|YP_004595571.1|  64 FdpsevtvpeefvpD-EDILQERSAFERVLDALVADGAEKHEAVGAINAL------------QGDLGVTIEAAAVVY 127
                                       344444445556777.899999************999*************............233333222222222 PP

                                       .........EEESTT--HH CS
                             ABATE 113 a........llatlAadaa 123
                                       a        + a++A+da+
  gi|336252464|ref|YP_004595571.1| 128 ArregldvdDIAPIARDAI 146
                                       234444456899*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1181.03
//
Query:       gi|336252465|ref|YP_004595572.1|  [L=235]
Description: hypothetical protein Halxa_1058 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00016   21.5   0.0    0.00026   20.8   0.0    1.3  1  RVT_3     Reverse transcriptase-like
  ------ inclusion threshold ------
       0.02   15.1   0.0      0.027   14.7   0.0    1.2  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 !   20.8   0.0   2.8e-08   0.00026       2      77 ..      36     110 ..      35     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.8e-08
                             RVT_3   2 fdgafkkksgaggagvvirdsnGevllagaeklqgkasveeAElqALlrGLqlalklgirr..lvvegDsktvvqll 76 
                                       +dg  + +++ gg+g+vi + +G +++ +a+  ++  ++ +AE++AL  GL + +++  r   + v +D++ +++++
  gi|336252465|ref|YP_004595572.1|  36 TDG--SFRESGGGLGAVIETRDGTRVARIATA-DTPPDNNVAEYRALHLGLDVLAARAPRDarVGVLVDHDALASNV 109
                                       689..5588999******************77.9999**************99887776644477777888777777 PP

                             RVT_3  77 n 77 
                                       n
  gi|336252465|ref|YP_004595572.1| 110 N 110
                                       6 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     3e-06     0.027       4      59 ..      32      87 ..      29     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-06
                                      EEEEEEEEEECTTTCEEEEEEE.CTT..E.EEEEEECCCCHHHHHHHHHHHHHHHTT. CS
                           RNase_H  4 vvvYtDGsclgnpgeggagavl.ykegar.nisapleeaqtnnraELsAvieaLkalk 59
                                        v tDGs +  ++ gg gav+  ++g+r  + a+   + +nn aE +A++  L  l 
  gi|336252465|ref|YP_004595572.1| 32 FYVATDGSFR--ESGGGLGAVIeTRDGTRvARIATADTPPDNNVAEYRALHLGLDVLA 87
                                      5688****55..788899998867777664444444479***********99988543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1743.32
//
Query:       gi|336252466|ref|YP_004595573.1|  [L=518]
Description: ABC transporter periplasmic protein [Halopiger xanaduensis SH-6]
Scores for 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-68  230.7   1.2    3.3e-68  230.4   1.2    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
        0.2   12.1   4.0        2.9    8.4   0.2    3.3  3  ORF_12_N   ORF 12 gene product N-terminal


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.4   1.2   3.6e-72   3.3e-68       1     374 [.      84     442 ..      84     445 .. 0.92

  Alignments for each domain:
  == domain 1  score: 230.4 bits;  conditional E-value: 3.6e-72
                                       SEEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTE CS
                         SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddyt 77 
                                       e++p++ e+ w+  +D  t +++ R++v F+ G+++tA+Dv+++++r++d + +  + +    +  ++++ea+dd+t
  gi|336252466|ref|YP_004595573.1|  84 ELEPRIVEE-WT-HPDDSTMELTVRDDVVFHEGQEMTASDVAYTINRAVDEEVGIASEQADR-YPGVVGAEAPDDTT 157
                                       689******.45.899999********************************99998877775.89************ PP

                                       EEEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTTSCSSSSE CS
                         SBP_bac_5  78 vrftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgggkpkldr 154
                                       v ++ ++  +   + +a v+  +  +++   ++++ +  +++ gtGPY+++e++p+++i+++ ++dYw g+ p ld 
  gi|336252466|ref|YP_004595573.1| 158 VLIEHESVPSIVEFNVATVATVVS-QEW--MEEREQPVTDELNGTGPYQVDEYTPDEEITFTTFDDYW-GETPDLDP 230
                                       ****66665555555555555555.444..5666688899999*************************.******** PP

                                       EEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS CS
                         SBP_bac_5 155 iefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyAi 231
                                       ++f+  +++++r+ +l++Ge d v+++ppsd++ ++ea++++v ++ ++++  +l++ ++ +pfd +++RqA++yA+
  gi|336252466|ref|YP_004595573.1| 231 VRFRGASEASTRVSELETGESDLVVNVPPSDVANIDEAEDVEV-RTVTSLRNIFLVMPNDDEPFDSQEFRQAMNYAV 306
                                       *******************************************.********************************* PP

                                       -HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETTSH CS
                         SBP_bac_5 232 DreeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltlllasgsp 308
                                       D ++i+++vl g + p+ +++p+++ g++++ +p+  ++d+e+A++l ++ Gy ++           +tl+ + g  
  gi|336252466|ref|YP_004595573.1| 307 DVDAIIENVLDGFGSPTSQPIPEGIFGYNDDLDPY--PHDLEQAEQLVEDSGYSGVE----------ITLESPEGRY 371
                                       *********************************98..66*****************7..........********** PP

                                       HHH.HHHHHHHHHHHHTT.EEEEEEEECHH...HHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTC CS
                         SBP_bac_5 309 aek.aiaeliqqqlkkiG.ikvevktvdwa...atylervkdgdfdmillgwgadypdpdnflnpflsssg 374
                                       +++ ++ae  +qq +++  +  +++ +d++   + +l++  ++ +d++l gwg  + d+d+ l p++ s++
  gi|336252466|ref|YP_004595573.1| 372 LNDtEVAETAAQQIDQLEnVSCDFQITDFEtitESSLDADPSTSPDFFLIGWGNPTYDADYGLAPWFVSGQ 442
                                       **99************766********999999888899***************************98876 PP

>> ORF_12_N  ORF 12 gene product N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2   0.00032       2.9      25      80 ..     173     224 ..     162     229 .. 0.76
   2 ?   -2.4   0.0      0.76   6.8e+03      14      33 ..     284     303 ..     283     312 .. 0.80
   3 ?    3.1   0.1     0.014   1.3e+02      24      61 ..     448     488 ..     435     493 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00032
                          ORF_12_N  25 aeevaerfsaeflaevpaeelaevlaqlraagPftvtsyegvesaavvtlesstge 80 
                                       ++ va+ +s+e ++e    + + v+++l ++gP+ v +y+++e+   +t+++  ge
  gi|336252466|ref|YP_004595573.1| 173 VATVATVVSQEWMEE----REQPVTDELNGTGPYQVDEYTPDEEITFTTFDDYWGE 224
                                       555666666666666....6678899***************999888877776665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.76
                          ORF_12_N  14 ldalnsdapiaaeevaerfs 33 
                                       l + n+d+p + +e+++ ++
  gi|336252466|ref|YP_004595573.1| 284 LVMPNDDEPFDSQEFRQAMN 303
                                       56889999999999988765 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.014
                          ORF_12_N  24 aaeevaerfsaeflaevpaee...laevlaqlraagPftvt 61 
                                       + ee++e++ +++ ++ p e+   l+e  a+l+ a+P+++ 
  gi|336252466|ref|YP_004595573.1| 448 EDEEIEEKILESQQTSDPDEReqlLQEINADLHEAAPWVFL 488
                                       55677777766666654433233466667799******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.25s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3908.31
//
Query:       gi|336252467|ref|YP_004595574.1|  [L=329]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-40  136.8  12.0    1.2e-39  136.0  12.0    1.4  1  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
          2    8.7   4.4        8.4    6.8   0.2    3.0  3  Sigma_reg_N   Sigma factor regulator N-terminal


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 !  136.0  12.0   1.3e-43   1.2e-39       1     184 [.     115     327 ..     115     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 136.0 bits;  conditional E-value: 1.3e-43
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..............................vils 47 
                                       +i+lG+++a++r+ + d+  + ++ v+ s+P f+l+i+l+l++                               +++
  gi|336252467|ref|YP_004595574.1| 115 AIPLGVISATRRHDPADYGATLFSLVGISTPNFWLGIMLILLLpvqlgvfpvsqrpvgfgtavyslvttgyfnDLIT 191
                                       69**************************************999******************************9*** PP

                      BPD_transp_1  48 ilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllgg 124
                                       ++ h  lp+i+l+++++a ++rl+r++++++l k +v a +a+G++   i +k+vl+n+++piit l+l++g l+gg
  gi|336252467|ref|YP_004595574.1| 192 WFRHVTLPAITLGTYFTALITRLTRSGMIDELGKPYVTATEAKGLPGVLIRFKHVLRNTMIPIITVLGLQLGTLIGG 268
                                       ***************************************************************************** PP

                      BPD_transp_1 125 avlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       av++e ++ wpGlg++l++a+ + d + i+ g+++++++ ++++n+v+d+l++ l+prv+
  gi|336252467|ref|YP_004595574.1| 269 AVITESVFDWPGLGRRLIDALYAGDWPVIQ-GVLIFIGVGFVVINVVVDALYATLNPRVT 327
                                       ******************************.***************************97 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 ?    2.4   0.0     0.021   1.9e+02      19      59 ..     104     146 ..      99     150 .. 0.74
   2 ?    6.8   0.2   0.00093       8.4       8      35 ..     242     269 ..     241     275 .. 0.85
   3 ?   -3.4   0.4       1.4   1.2e+04      24      34 ..     302     312 ..     297     323 .. 0.45

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.021
                       Sigma_reg_N  19 slivlllifvil..vvtllylaekegnklrevlelaveitsPN 59 
                                       +++++++ + i   +  +++ + + + ++  +l ++v i++PN
  gi|336252467|ref|YP_004595574.1| 104 AIAATIVAIGIAipLGVISATRRHDPADYGATLFSLVGISTPN 146
                                       4555555444443677777779999999**************9 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00093
                       Sigma_reg_N   8 krksilrivlislivlllifvilvvtll 35 
                                       ++k+ lr+++i +i++l + + ++++++
  gi|336252467|ref|YP_004595574.1| 242 RFKHVLRNTMIPIITVLGLQLGTLIGGA 269
                                       89****************9999976655 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.4
                       Sigma_reg_N  24 llifvilvvtl 34 
                                       ++i v +vv++
  gi|336252467|ref|YP_004595574.1| 302 IFIGVGFVVIN 312
                                       22222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); 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:                         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 0.18s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2731.22
//
Query:       gi|336252468|ref|YP_004595575.1|  [L=336]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for complete 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-33  116.6   9.1    1.1e-33  116.6   9.1    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
     0.0022   17.9   0.0     0.0022   17.9   0.0    3.1  4  OppC_N        N-terminal TM domain of oligopeptide transport 


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 ?    0.1   0.0     0.066   5.9e+02     157     177 ..      22      42 ..       8      45 .. 0.57
   2 !  116.6   9.1   1.2e-37   1.1e-33       1     183 [.     127     330 ..     127     332 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.066
                      BPD_transp_1 157 gvlalviavlllnlvadilqr 177
                                       + l ++++++l+ ++a il++
  gi|336252468|ref|YP_004595575.1|  22 LGLSIAVVIILVATFAPILAT 42 
                                       344555555555555555544 PP

  == domain 2  score: 116.6 bits;  conditional E-value: 1.2e-37
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf...............vilsilghlilpv...iil 59 
                                       g+++G++a+ ++++++d+ ++++ +++l++Ps+vlai l+ vf                +++   +++lp+   +++
  gi|336252468|ref|YP_004595575.1| 127 GVPFGLVAG-YFSGRIDDSMMRIADIMLAFPSLVLAIALIGVFgrsvqyipdpivlsgLVDGMPEYAVLPGtvtLVV 202
                                       89*******.***********************************************99999999999996567888 PP

                      BPD_transp_1  60 lllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG 136
                                       +l+ +++++r+ r +al+++++++v+aar lGas ++i+ k+vlPn+l+pii ++ l++++++   + l++lg ++ 
  gi|336252468|ref|YP_004595575.1| 203 ALVNWVWFARVARGEALSIRNEEYVKAARSLGASNRTILLKHVLPNSLTPIIVLATLQVAAIILLESSLSYLGFSGT 279
                                       99***********************************************************************5544 PP

                      BPD_transp_1 137 lgtllleailgydyseis....nggvlalviavlllnlvadilqrlldprv 183
                                         ++  e+++g+dy  ++     ++ +a+v+av+ +nl+ d+l + ldp +
  gi|336252468|ref|YP_004595575.1| 280 TLSWGYEISQGQDYLRTAwwvsTIPGIAIVLAVISINLLGDWLRDSLDPNI 330
                                       555666666666666555888***************************987 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.5e-07    0.0022      12      42 ..      16      48 ..      11      60 .. 0.79
   2 ?   -1.1   0.4      0.21   1.9e+03      23      35 ..     159     174 ..     153     185 .. 0.71
   3 ?   -5.8   2.6         2   1.8e+04      21      32 ..     254     265 ..     253     267 .. 0.66
   4 ?   -1.5   0.0       0.3   2.6e+03      20      36 ..     306     322 ..     305     328 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-07
                            OppC_N 12 rNklAvvglvilllllliaifaPliaPydp..q 42
                                      r  +A +gl i ++++l+a faP +a ++p  +
  gi|336252468|ref|YP_004595575.1| 16 RSLMAKLGLSIAVVIILVATFAPILATHNPntT 48
                                      666899********************9998652 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.21
                            OppC_N  23 lllllliaifa...Pl 35 
                                       +l+++li +f+    +
  gi|336252468|ref|YP_004595575.1| 159 VLAIALIGVFGrsvQY 174
                                       5678888888733344 PP

  == domain 3  score: -5.8 bits;  conditional E-value: 2
                            OppC_N  21 villlllliaif 32 
                                       ++l++l ++ai+
  gi|336252468|ref|YP_004595575.1| 254 IVLATLQVAAII 265
                                       567777777765 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.3
                            OppC_N  20 lvilllllliaifaPli 36 
                                        +i+l+++ i ++++++
  gi|336252468|ref|YP_004595575.1| 306 IAIVLAVISINLLGDWL 322
                                       44555555555667776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2715.57
//
Query:       gi|336252469|ref|YP_004595576.1|  [L=431]
Description: oligopeptide/dipeptide ABC transporter ATPase [Halopiger xanaduensis SH-6]
Scores for 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   84.6   0.0    1.6e-23   83.8   0.0    1.4  1  ABC_tran   ABC transporter
    2.8e-17   63.0   0.0      6e-17   61.9   0.0    1.6  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    1.7e-07   31.4   0.2    0.00016   21.6   0.0    2.1  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    0.00087   19.6   0.3       0.12   12.7   0.3    2.3  1  AAA_22     AAA domain
     0.0056   16.7   0.0      0.026   14.5   0.0    1.9  2  AAA_5      AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.019   15.0   0.0      0.062   13.4   0.0    1.7  2  DUF87      Helicase HerA, central domain
      0.021   15.2   0.4      0.061   13.7   0.4    1.9  1  AAA_16     AAA ATPase domain
      0.077   12.8   0.0       0.15   11.8   0.0    1.4  1  AAA_29     P-loop containing region of AAA domain
      0.091   12.2   0.0        6.3    6.2   0.0    2.2  2  SMC_N      RecF/RecN/SMC N terminal domain
       0.13   12.2   0.2       0.48   10.3   0.0    2.0  2  NACHT      NACHT domain
       0.13   11.5   0.0       0.23   10.7   0.0    1.4  2  DUF2075    Uncharacterized conserved protein (DUF2075)
       0.14   11.7   0.0        7.3    6.1   0.0    2.3  2  AAA_25     AAA domain
       0.24   10.9   0.0        0.4   10.2   0.0    1.2  1  AAA_7      P-loop containing dynein motor region


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 !   83.8   0.0   1.1e-26   1.6e-23       2     136 ..      26     234 ..      25     235 .. 0.91

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 1.1e-26
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx....................... RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke....................... 51 
                                       ++++l +++ge+ +ivGe+G+GKS  ++ ++ l +       G+i+++++dl +                       
  gi|336252469|ref|YP_004595576.1|  26 DDLDLRIERGEVFGIVGESGSGKSVTARSIMDLIDSpgeiVDGTIEFNDADLADrvredhpeavdgnfvdlqaiper 102
                                       799******************************99766667777777777777777777777788888888888887 PP

                                       B-HHHCCHCEEEE-SS..--S-TTSBHHHH..............................................H CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxx..............................................x RF
                          ABC_tran  52 qeleslrkeigvlpqe..pqlfpeltvren..............................................e 80 
                                       ++++    ++++++q+  ++++p ltv+e+                                              e
  gi|336252469|ref|YP_004595576.1| 103 IRRSLRGTSFSMIFQDpeSSFNPSLTVGEQlaeavevqrrasanprstrsrtesseyslgnfvlstvlpsqkyvteE 179
                                       888888899*******98999****************************************************9999 PP

                                       HHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  81 sdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       s+e++ ++l+ +g+++ + +++++ p+++SgG+ qr ++a+al+ +p++l++DEpt
  gi|336252469|ref|YP_004595576.1| 180 SRERAVELLELVGIPD-PVERADEYPHEYSGGMLQRAMIAQALAGEPDVLIADEPT 234
                                       99999********999.888899********************************9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0   4.3e-20     6e-17       1      65 []     286     352 ..     286     352 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 4.3e-20
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeG..CpFapRCpfaleeC 65 
                                       vErg+ +++fd+  HPYT++Ll s+p+l+    +le i+g++psl +++ G  C Fa+RCp a+e C
  gi|336252469|ref|YP_004595576.1| 286 VERGTLEDVFDDHVHPYTEGLLGSIPDLEDAGGRLEPIPGNVPSLLDHEMGdrCHFADRCPKAMEDC 352
                                       8***************************999999*********9999999888*************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 !    8.1   0.0    0.0015         2       2     103 ..      38     159 ..      37     167 .. 0.90
   2 !   21.6   0.0   1.2e-07   0.00016     232     302 ..     202     270 ..     171     271 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0015
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarl................drdvegltdelsggggirkipslldlydpeipfefei 62 
                                        +++G  gsGKS   + +  l +                 ++ v+ +++e+ +g+  + ++   + +     + f+ 
  gi|336252469|ref|YP_004595576.1|  38 FGIVGESGSGKSVTARSIMDLIDSpgeivdgtiefndadlADRVREDHPEAVDGNFVDLQAIPERIRRSLRGTSFSM 114
                                       689*********9999998888889999************************************************* PP

                            AAA_21  63 eeflsqgvryryglrlersqv.....eeklssvetllesgllldkr 103
                                       + f++ ++ ++ +l+++++       +++ s++++  +s++ + + 
  gi|336252469|ref|YP_004595576.1| 115 I-FQDPESSFNPSLTVGEQLAeavevQRRASANPRSTRSRTESSEY 159
                                       *.****************9998888888888888888887776665 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.2e-07
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                         ++e S G+++  a+++  l+  +  ++l+ DEp + L+  +++ +l+ll+el++ +g  ++l TH+  ++
  gi|336252469|ref|YP_004595576.1| 202 EYPHEYSGGMLQR-AMIAQALAGEP--DVLIADEPTTALDVTIQAQVLDLLDELQEeTGMTILLITHNLGVI 270
                                       457888*******.99999998776..9***********************8888889**********9887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.3   8.4e-05      0.12      10      30 ..      40      60 ..      32     272 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.4e-05
                            AAA_22 10 vtGesGtGKTtllrrlleqld 30
                                      ++GesG+GK++++r +++  d
  gi|336252469|ref|YP_004595576.1| 40 IVGESGSGKSVTARSIMDLID 60
                                      89************9998775 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 !   14.5   0.0   1.9e-05     0.026       4      60 ..      40      94 ..      38     102 .. 0.91
   2 ?   -1.3   0.0       1.5     2e+03      57      91 ..     210     251 ..     202     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                                      EE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........---- CS
                             AAA_5  4 LvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplv 60
                                      +vG++G+gKs  a+++  ++ ++ e+v +t   + +dl  r++  +++ + vd+ +v
  gi|336252469|ref|YP_004595576.1| 40 IVGESGSGKSVTARSIMDLIDSPGEIVDGTIEFNDADLADRVR--EDHPEAVDGNFV 94
                                      69**************************************999..777777777766 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                                       --------......G-SEEEEESGGG--.HHHHHHHHHHHHS CS
                             AAA_5  57 splvraar......egeilvlDEverae.sevlnsLlsllee 91 
                                       + l ra+       e+++l+ DE ++a    +++ +l ll+e
  gi|336252469|ref|YP_004595576.1| 210 GMLQRAMIaqalagEPDVLIADEPTTALdVTIQAQVLDLLDE 251
                                       556666666677789999999999999856667778888886 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.5e-05     0.062      26      45 ..      38      57 ..      27      66 .. 0.90
   2 ?   -1.7   0.0       1.8   2.5e+03     117     146 ..     173     200 ..     124     262 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                             DUF87 26 lAilgsTGsGKSntvavLle 45
                                      ++i+g++GsGKS t++++++
  gi|336252469|ref|YP_004595576.1| 38 FGIVGESGSGKSVTARSIMD 57
                                      89***************987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.8
                             DUF87 117 qrsvleealdqakakeekeklssdepvekl 146
                                       q+ v ee  ++a+  e+ e + + +pve+ 
  gi|336252469|ref|YP_004595576.1| 173 QKYVTEESRERAV--ELLELVGIPDPVERA 200
                                       4444444444444..444444444444433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   4.4e-05     0.061      22      52 ..      33      85 ..      19     263 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekd......................g 52
                                       r+e+  ++GesG+GKs  +r++++ +                         +
  gi|336252469|ref|YP_004595576.1| 33 ERGEVFGIVGESGSGKSVTARSIMDLIDSPgeivdgtiefndadladrvredH 85
                                      44577889****************87777644444433333333333333332 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 ?   11.8   0.0   0.00011      0.15      15      37 ..      28      50 ..      23      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                            AAA_29 15 htieidlkgatlltGpsGsGKST 37
                                       +++i++ +++ ++G+sGsGKS 
  gi|336252469|ref|YP_004595576.1| 28 LDLRIERGEVFGIVGESGSGKSV 50
                                      567888666999**********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 ?    4.1   0.0      0.02        27      27      44 ..      38      55 ..      26      59 .. 0.81
   2 ?    6.2   0.0    0.0046       6.3     162     213 ..     228     281 ..     113     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.02
                                      EEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnlldAi 44
                                        ivG+ GSGKs    +i
  gi|336252469|ref|YP_004595576.1| 38 FGIVGESGSGKSVTARSI 55
                                      579*********776666 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0046
                                       EEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 162 yllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvgvtk 213
                                        + De   aLD +  ++v +ll+e +++  + ++ i+++ ++++++   vgv+ 
  gi|336252469|ref|YP_004595576.1| 228 LIADEPTTALDVTIQAQVLDLLDELQEEtgMTILLITHNLGVIARMCDRVGVMY 281
                                       5679*******************9888855788999**9999999988888876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00035      0.48       5      26 ..      40      61 ..      36      67 .. 0.88
   2 ?   -1.2   0.2       1.3   1.7e+03      75      75 ..     219     219 ..     147     268 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                                      EEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  5 lqGeaGsGKTtLlqklalawae 26
                                      + Ge+GsGK++ ++++++++ +
  gi|336252469|ref|YP_004595576.1| 40 IVGESGSGKSVTARSIMDLIDS 61
                                      89***************99865 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                                       H CS
                             NACHT  75 v 75 
                                        
  gi|336252469|ref|YP_004595576.1| 219 Q 219
                                       0 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00017      0.23       3      77 ..      37     129 ..      35     146 .. 0.83
   2 ?   -3.7   0.0       3.9   5.3e+03      79     102 ..     215     238 ..     197     266 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                           DUF2075   3 vvlVtGvaGtGKtvvllnllael..................eddeeertavylsvNhplvlvlrealakkeekkkkk 61 
                                       v+ + G++G+GK+v + +++  +                   d  +e +   + +N   ++++ e+++++ ++++++
  gi|336252469|ref|YP_004595576.1|  37 VFGIVGESGSGKSVTARSIMDLIdspgeivdgtiefndadlADRVREDHPEAVDGNFVDLQAIPERIRRSLRGTSFS 113
                                       77799***************999888887777777766666666699999*************************** PP

                           DUF2075  62 eafeklssfinnlsef 77 
                                         f++++s  n+  + 
  gi|336252469|ref|YP_004595576.1| 114 MIFQDPESSFNPSLTV 129
                                       ******9998877655 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.9
                           DUF2075  79 kaeekkeepkedvvivDEAhrllt 102
                                         ++++   + dv+i DE   +l+
  gi|336252469|ref|YP_004595576.1| 215 AMIAQALAGEPDVLIADEPTTALD 238
                                       455666677778888888777776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.044        61      30      50 ..      32      52 ..      25      57 .. 0.86
   2 ?    6.1   0.0    0.0053       7.3     166     188 ..     243     265 ..     214     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.044
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      + +ge+  ++G +g+GK++ a
  gi|336252469|ref|YP_004595576.1| 32 IERGEVFGIVGESGSGKSVTA 52
                                      7899999***********987 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0053
                            AAA_25 166 galvealeriarrtgaavllvhH 188
                                       +++++ l++++++tg ++ll+ H
  gi|336252469|ref|YP_004595576.1| 243 AQVLDLLDELQEETGMTILLITH 265
                                       799999****************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 ?   10.2   0.0   0.00029       0.4      29      71 ..      31      74 ..      26      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00029
                             AAA_7 29 llknkkpvllvGptGtGKtviikdllkkld.kekylsltinfsa 71
                                       ++++  + +vG++G+GK+v+++++++ +d + +++  ti+f+ 
  gi|336252469|ref|YP_004595576.1| 31 RIERGEVFGIVGESGSGKSVTARSIMDLIDsPGEIVDGTIEFND 74
                                      5666777789**************99988856677777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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 0.25s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3354.10
//
Query:       gi|336252470|ref|YP_004595577.1|  [L=471]
Description: oligopeptide/dipeptide ABC transporter ATPase [Halopiger xanaduensis SH-6]
Scores for 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-33  113.6   0.0    1.5e-32  113.0   0.0    1.3  1  ABC_tran       ABC transporter
    1.5e-17   63.8   0.1    3.6e-17   62.6   0.1    1.7  1  oligo_HPY      Oligopeptide/dipeptide transporter, C-terminal
    8.6e-07   29.0   0.5    0.00026   20.9   0.5    2.4  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    0.00044   20.5   0.7     0.0036   17.6   0.7    2.2  1  AAA_22         AAA domain
    0.00098   18.6   0.1     0.0031   17.0   0.1    1.7  1  SMC_N          RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.096   12.7   0.1        2.7    8.0   0.0    2.4  2  AAA_5          AAA domain (dynein-related subfamily)
        0.1   13.2   0.2       0.56   10.8   0.0    2.4  3  AAA_18         AAA domain
       0.12   12.0   0.6        6.4    6.3   0.1    2.5  2  AAA_25         AAA domain
       0.16   11.3   0.0       0.26   10.6   0.0    1.3  1  AIG1           AIG1 family
       0.17   10.7   0.0       0.24   10.3   0.0    1.1  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
        0.2   12.0   8.1      0.035   14.5   1.1    2.7  3  AAA_16         AAA ATPase 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 !  113.0   0.0     9e-36   1.5e-32       2     137 .]      64     215 ..      63     215 .. 0.94

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 9e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       + vs++++ege++++vGe+G+GKSt  ++l++l +pt G+++++g+++ +   + l+++r   +v++q+  ++l+p+
  gi|336252470|ref|YP_004595577.1|  64 DGVSFDIYEGETLGLVGESGCGKSTTGETLLRLQEPTDGRVEFEGQNVYDlagEALTEFRTDAQVVFQDpfSSLDPR 140
                                       78**************************************************9****************9999**** PP

                                       SBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +t+++            ++de+ e++++ l+ ++l  + +++ p+++SgGq+qr+ +aral+ +p++l+lDEpt+
  gi|336252470|ref|YP_004595577.1| 141 MTIGDIvqqpldihdvgTEDERRERVRDLLERVGLSVDQLDRYPHEFSGGQRQRIGIARALALEPDFLVLDEPTS 215
                                       *****9***********77777777777777777777999999******************************96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.1   2.2e-20   3.6e-17       1      61 [.     266     328 ..     266     331 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 2.2e-20
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd..klekikgeapslerldeGCpFapRCpfa 61 
                                       vE+gp+++lf+ p+HPYTkaLl+svpr     +    e++ g++ps+++ ++GC+F++RCp +
  gi|336252470|ref|YP_004595577.1| 266 VEIGPVADLFEVPKHPYTKALLESVPRASTDERerDRETLTGDVPSPRDPPSGCRFRTRCPAV 328
                                       8**************************9988888889***********************976 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 !    5.5   0.0    0.0081        13       3      25 ..      77      99 ..      76     141 .. 0.77
   2 !   20.9   0.5   1.6e-07   0.00026     231     302 ..     181     250 ..     151     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0081
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl 25
                                      +l+G  g+GKS+  ++l  l+  
  gi|336252470|ref|YP_004595577.1| 77 GLVGESGCGKSTTGETLLRLQEP 99
                                      69***************999753 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1.6e-07
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                       ++ ++e+S G+++ ++++ al+  +   ++l++DEp + L+ ++++ +l ll++l++  +   +l +H+ +++
  gi|336252470|ref|YP_004595577.1| 181 DRYPHEFSGGQRQRIGIARALALEP---DFLVLDEPTSALDVSVQAQVLNLLDDLQDeFDLTYLLISHDLSVI 250
                                       5678999*******99999999888...9***********************9999999**********9887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.7   2.2e-06    0.0036      10     128 ..      78     243 ..      72     249 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.2e-06
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee......................erpevvfvtlpsst....sskdllrel 60 
                                       ++GesG+GK+t+ ++ll+  +     ++                       +++vvf ++ ss     +  d+ ++ 
  gi|336252470|ref|YP_004595577.1|  78 LVGESGCGKSTTGETLLRLQEP----TDgrvefegqnvydlagealtefrTDAQVVFQDPFSSLdprmTIGDIVQQP 150
                                       79****************9742....334566877777777777777776556666444444332222555555555 PP

                            AAA_22  61 lralglelka.erlsseellealeqalrarav......................ielliiDEaqh.lr...seeale 110
                                       l + ++++++ +r + ++lle++   +++ ++                      + +l++DE    l+   ++++l+
  gi|336252470|ref|YP_004595577.1| 151 LDIHDVGTEDeRRERVRDLLERVGLSVDQLDRyphefsggqrqrigiaralalePDFLVLDEPTSaLDvsvQAQVLN 227
                                       55555544446444444555555444444444777888888888888888899999******999898955599*** PP

                            AAA_22 111 eLrsllnlsrkgvqliLv 128
                                        L +l++  +++++ +L+
  gi|336252470|ref|YP_004595577.1| 228 LLDDLQD--EFDLTYLLI 243
                                       **99999..999998887 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 !   17.0   0.1   1.9e-06    0.0031      29     205 ..      78     253 ..      67     265 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.9e-06
                                       EEESTTSSHHHHHHHHHHHCTT...TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  29 ivGpNGSGKsnlldAilFvLGer..sakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrv 103
                                       +vG+ G+GKs   + +l  L e      ++  +++ dl  + +  ++ + a+  ++f+++ ++    +++++i   v
  gi|336252470|ref|YP_004595577.1|  78 LVGESGCGKSTTGETLL-RLQEPtdGRVEFEGQNVYDLAGE-ALTEFRTDAQ--VVFQDPFSS---LDPRMTIGDIV 147
                                       67777777777777773.33322112224445555555544.4444444444..445555444...56777777766 PP

                                       ETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 104 krkgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                       ++  +  + +  ++ +++ v++lle++g+s +       ++SgG+++ + +a  +A++      + +lDe  +aLD 
  gi|336252470|ref|YP_004595577.1| 148 QQPLD-IHDVGTEDERRERVRDLLERVGLSVDqldryphEFSGGQRQRIGIARALALEP----DFLVLDEPTSALDV 219
                                       66666.677888899999************99888888899*************99864....599*********** PP

                                       HHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                             SMC_N 174 knvkkvaellkekskn..aQfivislreemleka 205
                                       +  ++v +ll+  +++    ++ is++  +++++
  gi|336252470|ref|YP_004595577.1| 220 SVQAQVLNLLDDLQDEfdLTYLLISHDLSVIRHV 253
                                       ***********98887335678888887777665 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 ?    8.0   0.0    0.0016       2.7       4      22 ..      78      96 ..      75     113 .. 0.88
   2 ?    2.0   0.0      0.12   1.9e+02      61      91 ..     200     231 ..     161     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                                      EE--SSSSHHHHHHHGGGG CS
                             AAA_5  4 LvGppGtgKselaerlaaa 22
                                      LvG++G+gKs+  e l+++
  gi|336252470|ref|YP_004595577.1| 78 LVGESGCGKSTTGETLLRL 96
                                      9***********9999887 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.12
                                       ----G-SEEEEESGGG--.HHHHHHHHHHHHS CS
                             AAA_5  61 raaregeilvlDEverae.sevlnsLlsllee 91 
                                         a e++ lvlDE + a   +v++ +l+ll++
  gi|336252470|ref|YP_004595577.1| 200 ALALEPDFLVLDEPTSALdVSVQAQVLNLLDD 231
                                       3344999********99989**********97 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.9   9.5e+03      25      40 ..      35      50 ..      25      57 .. 0.77
   2 ?   10.8   0.0   0.00034      0.56       3      44 ..      78     127 ..      76     145 .. 0.82
   3 ?   -2.1   0.0       3.3   5.4e+03      75      84 ..     399     408 ..     381     440 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.9
                            AAA_18 25 gvnlrdvakengllle 40
                                      ++nl+++++en++ll+
  gi|336252470|ref|YP_004595577.1| 35 VRNLQKYFWENDSLLD 50
                                      6788999999988765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00034
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf........gvnlrdvakenglllevdpe 44 
                                       l G +G+GK+t ++ L ++ +         g+n+ d+a e  +++  d++
  gi|336252470|ref|YP_004595577.1|  78 LVGESGCGKSTTGETLLRLQEPtdgrvefeGQNVYDLAGEALTEFRTDAQ 127
                                       7899************77753346678889*******9999888887776 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.3
                            AAA_18  75 knlvidghla 84 
                                       ++ +++  la
  gi|336252470|ref|YP_004595577.1| 399 HDEIVEEALA 408
                                       2223333333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.032        53      32      48 ..      72      88 ..      62      95 .. 0.88
   2 ?    6.3   0.1    0.0039       6.4     132     188 ..     196     245 ..     144     246 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.032
                            AAA_25 32 agelallaGapgtGKtt 48
                                      +ge+  l+G +g+GK+t
  gi|336252470|ref|YP_004595577.1| 72 EGETLGLVGESGCGKST 88
                                      788899**********9 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0039
                            AAA_25 132 aleaaieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                        +++a+   e ++++v+D  ++al+ + +     +++++ l++++++++ + ll+ H
  gi|336252470|ref|YP_004595577.1| 196 GIARALAL-E-PDFLVLDEPTSALDVSVQ-----AQVLNLLDDLQDEFDLTYLLISH 245
                                       45555555.5.999999999999999988.....99********************9 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.26       3      22 ..      76      95 ..      74     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                                      EEEESSTTSSHHHHHHHHHT CS
                              AIG1  3 ivlvGktgnGkSaTgNsilg 22
                                      + lvG +g+GkS+Tg ++l+
  gi|336252470|ref|YP_004595577.1| 76 LGLVGESGCGKSTTGETLLR 95
                                      669**************997 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 ?   10.3   0.0   0.00015      0.24       5      72 ..      64     135 ..      60     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                     TrwB_AAD_bind   5 agvplpkeretqhilivGttGsGKtqalekllrairarg.....draivlDltGafvsrfydegkdillnPlD 72 
                                       +gv++    e + + +vG  G GK+++ e llr  +        +   v+Dl G+ + +f  + + +  +P+ 
  gi|336252470|ref|YP_004595577.1|  64 DGVSFDIY-EGETLGLVGESGCGKSTTGETLLRLQEPTDgrvefEGQNVYDLAGEALTEFRTDAQVVFQDPFS 135
                                       56666543.5667889****************9877666555556778****************988889985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.1   2.1e-05     0.035      25     163 ..      74     233 ..      67     262 .. 0.50
   2 ?   -2.1   0.0       2.7   4.4e+03      86     107 ..     291     316 ..     279     392 .. 0.64
   3 ?    0.3   0.6       0.5   8.2e+02      80     107 ..     401     433 ..     342     453 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggif.lrgkcdql..esa.........ipy.salaqalareellrqllde 88 
                                       e + l+GesG+GKs+  ++llr  e ++g + ++g+++    ++a         + + +++ ++   +  + ++ ++
  gi|336252470|ref|YP_004595577.1|  74 ETLGLVGESGCGKSTTGETLLRLQEPTDGRVeFEGQNVYDlaGEAltefrtdaqVVFqDPFSSLD-PRMTIGDIVQQ 149
                                       66779****************75555556666666666663322232222222211222233333.22444444444 PP

                            AAA_16  89 ........aesaeleawrekleealaavpelagaea.....srllellkrllallsrderplvlvlDdlqwadeasl 152
                                               +e+  +e+ r+ le++  +v++l++  +     +r +  ++r+lal      p  lvlD+   a + s 
  gi|336252470|ref|YP_004595577.1| 150 pldihdvgTEDERRERVRDLLERVGLSVDQLDRYPHefsggQRQRIGIARALALE-----PDFLVLDEPTSALDVSV 221
                                       5555444433444555555555544455555554444444433333333333221.....22444444444444444 PP

                            AAA_16 153 ql.laaLlrlle 163
                                       q+   +Ll++l+
  gi|336252470|ref|YP_004595577.1| 222 QAqVLNLLDDLQ 233
                                       333333333333 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.7
                            AAA_16  86 ldeaesaeleawrekleeala.....a 107
                                        ++ +++e+e++re+l++ +      +
  gi|336252470|ref|YP_004595577.1| 291 PRA-STDERERDRETLTGDVPsprdpP 316
                                       444.33367777777766666332220 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.5
                            AAA_16  80 ellrqlldeaesaeleawrekleeala.....a 107
                                       e++++ l+e+++++++a++e+l+++++     a
  gi|336252470|ref|YP_004595577.1| 401 EIVEEALAELATSDWDAAAERLRAEYEsvcerA 433
                                       444455555777777777777777777555552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 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:                        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: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 3615.46
//
Query:       gi|336252471|ref|YP_004595578.1|  [L=120]
Description: hypothetical protein Halxa_1064 [Halopiger xanaduensis SH-6]
Scores for 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   16.0   0.0      0.005   16.0   0.0    1.1  1  Nup96          Nuclear protein 96
  ------ inclusion threshold ------
      0.076   12.9   0.1       0.42   10.5   0.0    2.0  2  HTH_5          Bacterial regulatory protein, arsR family
       0.14   12.5   0.0       0.17   12.2   0.0    1.3  1  Peptidase_S76  Serine peptidase of plant viral polyprotein, P


Domain annotation for each model (and alignments):
>> Nup96  Nuclear protein 96
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.4e-07     0.005       9      71 ..       5      66 ..       2     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.4e-07
                             Nup96  9 ghqveeAcelAldagdlrLAtllsqaggddevrkdlqeQleeWreekvdseieeell.kiyelL 71
                                      + ++e+Ac+l+++++   L  ll+    +++  +dl +Q+ +W+ e+  + ie+e + ++y  L
  gi|336252471|ref|YP_004595578.1|  5 ATRMEAACSLLAESKRRYLLYLLA--EDGEKNIEDLITQITAWEHEQPIETIEKEARqRVYVTL 66
                                      6799*******************9..566677799*****************998762566555 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 ?   10.5   0.0     7e-05      0.42       2      22 ..      18      39 ..      17      43 .. 0.90
   2 ?   -0.1   0.0      0.14   8.6e+02      32      47 .]      67      82 ..      64      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7e-05
                                      HHHHHHHHHHTT.SSEEHHHHH CS
                             HTH_5  2 ptRlkILklLae.gelcvcela 22
                                      ++R+ +L+lLae ge+ + +l 
  gi|336252471|ref|YP_004595578.1| 18 SKRRYLLYLLAEdGEKNIEDLI 39
                                      69****************9996 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.14
                                      HHHHHHHHHHTTSEEE CS
                             HTH_5 32 vShHLkkLreaGLVek 47
                                      v  HL +L + ++Ve+
  gi|336252471|ref|YP_004595578.1| 67 VHNHLPRLADYDIVEY 82
                                      678*****99999986 PP

>> Peptidase_S76  Serine peptidase of plant viral polyprotein, P1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.9e-05      0.17      34      74 ..      34      71 ..       8      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                     Peptidase_S76 34 tvsDlakelteicveegiPiiiidkeKrkaiprVklkHvlr 74
                                      +++Dl++++t    e+ +Pi+ i+ke r+++  V l H   
  gi|336252471|ref|YP_004595578.1| 34 NIEDLITQITA--WEHEQPIETIEKEARQRV-YVTLVHNHL 71
                                      48888888875..69999*************.888888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 993.40
//
Query:       gi|336252472|ref|YP_004595579.1|  [L=316]
Description: hypothetical protein Halxa_1065 [Halopiger xanaduensis SH-6]
Scores for 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-37  127.2  25.1    1.4e-20   73.9   9.2    2.1  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
        8.5    6.4   8.8       0.84    9.7   0.4    2.6  3  TMEM234   Putative transmembrane family 234


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 !   59.4   7.9   4.5e-20     4e-16       6     135 ..       9     147 ..       7     149 .. 0.91
   2 !   73.9   9.2   1.5e-24   1.4e-20       5     135 ..     164     297 ..     161     299 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 4.5e-20
                              EamA   6 lallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl......aklslkd...wllllllgll 73 
                                       l+l+ + +w+++fv++ ++l+ ++p+ ++++r+ +ag+l+l +a++  g         ++++ +   w+  ++ ++l
  gi|336252472|ref|YP_004595579.1|   9 LFLVLSALWGTAFVAISAGLEHLPPVLFAALRYDVAGLLMLGYAAYAVGGAdgadgeTWYPR-GrdeWATAAVGAAL 84 
                                       45677788********************************9998888887767777444444.3488********** PP

                              EamA  74 gtvlafllffyalkktsasnaslitslePvftlilsvlll.gekltlkqllgivlillGvlli 135
                                        +++++ ++f ++++t+a+ as+++sl+Pv+t+ ++ ll     l+   ++g++++l+Gv++i
  gi|336252472|ref|YP_004595579.1|  85 LIAAYHAFLFVGQQHTTAAAASIVVSLSPVLTTGFARLLMpSDALSPAGMAGVCIGLVGVAVI 147
                                       ****************************************999******************98 PP

  == domain 2  score: 73.9 bits;  conditional E-value: 1.5e-24
                              EamA   5 llallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl...aklslkdwllllllgllgtvla 78 
                                       ll++laa ++a++ vl++++ ++++  t+ ++++l +++ll  ++l  ++++    + +++++ +l++l++ +++++
  gi|336252472|ref|YP_004595579.1| 164 LLVFLAAASFALGSVLTRRIDASLPIETMEAWSMLGGALLLHGVSLALGEPFepaTWTDPQALGALAYLAVGASAIG 240
                                       89***************************************9999999999988777778889999*********** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       fll+f +l++++a ++ ++++++P+f+++ ++l+l e +  ++l+g++li++G ll+
  gi|336252472|ref|YP_004595579.1| 241 FLLYFDLLERLGAVEINMVSYVAPIFAAVVGWLYLDEVVDAMTLFGFGLIVVGFLLV 297
                                       ******************************************************997 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2       1.2   1.1e+04       1      10 [.      10      19 ..      10      21 .. 0.82
   2 ?    1.8   0.2     0.026   2.3e+02      69     115 ..     100     147 ..      83     148 .. 0.76
   3 ?    9.7   0.4   9.3e-05      0.84      57     115 ..     240     297 ..     229     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.2
                           TMEM234  1 lllvgilWGi 10
                                      +l+ ++lWG 
  gi|336252472|ref|YP_004595579.1| 10 FLVLSALWGT 19
                                      588999**96 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.026
                           TMEM234  69 dlslavpiaNslafvfTvlte.lllgekvlkkktvlgmllvvvgialc 115
                                         + a  i+ sl+ v+T+  + ll+  + l+   ++g+++ +vg+a++
  gi|336252472|ref|YP_004595579.1| 100 TTAAAASIVVSLSPVLTTGFArLLMPSDALSPAGMAGVCIGLVGVAVI 147
                                       3445566777899888876664788899999999***99999999986 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 9.3e-05
                           TMEM234  57 gSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                       g +l+f ll++   ++   ++  +a +f +++++l  ++v+ + t+ g +l+vvg  l+
  gi|336252472|ref|YP_004595579.1| 240 GFLLYFDLLERLG-AVEINMVSYVAPIFAAVVGWLYLDEVVDAMTLFGFGLIVVGFLLV 297
                                       6677777777765.5667777889999****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); 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: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2312.34
//
Query:       gi|336252473|ref|YP_004595580.1|  [L=113]
Description: hypothetical protein Halxa_1066 [Halopiger xanaduensis SH-6]
Scores for 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:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 916.07
//
Query:       gi|336252474|ref|YP_004595581.1|  [L=743]
Description: AAA family ATPase [Halopiger xanaduensis SH-6]
Scores for 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-100  332.3   0.0    2.1e-49  167.3   0.0    2.4  2  AAA              ATPase family associated with various cellul
    1.2e-30  105.5   0.0    6.7e-30  103.1   0.1    2.3  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    6.5e-30  102.7   2.3    1.4e-14   53.6   1.0    2.6  2  AAA_lid_3        AAA+ lid domain
    1.4e-15   56.8   0.2      8e-15   54.4   0.2    2.2  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    3.2e-15   56.2   0.0      8e-07   28.9   0.0    2.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    8.1e-14   52.4   1.1    1.3e-05   25.7   0.2    4.3  3  AAA_16           AAA ATPase domain
      1e-12   48.5   0.0    1.8e-05   24.9   0.0    2.8  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.3e-12   47.9   1.9     0.0001   22.3   0.1    4.2  2  AAA_5            AAA domain (dynein-related subfamily)
    4.3e-11   43.2   0.5     0.0011   19.2   0.1    4.1  4  AAA_22           AAA domain
      1e-10   41.9   0.0    6.8e-05   23.1   0.0    2.7  2  AAA_33           AAA domain
    1.2e-10   41.2   0.0    0.00041   19.7   0.0    3.2  3  TIP49            TIP49 P-loop domain
    8.4e-08   32.2   0.0      0.017   14.9   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    1.2e-07   31.9   0.0      0.005   16.9   0.0    2.4  2  AAA_14           AAA domain
    5.7e-07   30.1   0.0      0.067   13.7   0.0    3.0  2  AAA_18           AAA domain
    6.8e-07   29.6   0.0      0.057   13.8   0.0    2.5  2  RNA_helicase     RNA helicase
    1.2e-06   28.0   0.1      0.055   12.8   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.4e-06   28.0   1.6        2.1    7.9   0.0    4.4  4  AAA_25           AAA domain
    4.9e-06   26.2   0.0       0.12   11.8   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
      7e-06   25.8   0.0        0.2   11.3   0.0    3.1  2  Sigma54_activat  Sigma-54 interaction domain
    7.2e-06   25.9   0.0      0.085   12.7   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
      9e-06   26.0   0.0      0.038   14.2   0.0    2.6  2  AAA_28           AAA domain
    2.1e-05   24.0   0.9        0.5    9.7   0.0    3.5  3  ATPase           KaiC
    2.4e-05   24.3   0.0       0.18   11.8   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    3.7e-05   23.6   0.0       0.14   11.9   0.0    2.5  2  AAA_24           AAA domain
    4.4e-05   22.8   0.0       0.24   10.5   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
      5e-05   23.2   0.6      0.015   15.2   0.0    2.9  2  Vps4_C           Vps4 C terminal oligomerisation domain
    6.2e-05   22.5   0.8       0.44   10.0   0.0    3.1  3  PhoH             PhoH-like protein
    6.7e-05   23.4   0.0       0.46   11.0   0.0    2.6  2  ABC_tran         ABC transporter
    7.2e-05   22.6   0.5       0.51   10.0   0.0    3.0  2  AAA_30           AAA domain
    7.3e-05   22.7   0.0       0.31   10.8   0.0    2.4  2  AAA_11           AAA domain
    0.00013   21.3   0.0       0.12   11.5   0.0    2.4  2  NB-ARC           NB-ARC domain
    0.00025   21.1   0.0       0.88    9.4   0.0    3.5  3  ATPase_2         ATPase domain predominantly from Archaea
     0.0003   20.2   0.0       0.34   10.1   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00038   20.9   0.0          1    9.8   0.0    3.5  2  AAA_17           AAA domain
    0.00044   19.4   0.2       0.51    9.4   0.1    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00046   20.1   0.2       0.57   10.1   0.0    3.1  2  NACHT            NACHT domain
    0.00053   19.3   0.3       0.89    8.8   0.0    2.6  2  Zeta_toxin       Zeta toxin
     0.0017   18.5   0.0        2.9    8.0   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0018   17.8   0.9       0.54    9.6   0.0    2.8  3  IPT              Isopentenyl transferase
     0.0021   18.0   0.3        3.9    7.3   0.0    3.2  2  NTPase_1         NTPase
     0.0028   18.0   0.8        4.2    7.7   0.0    2.9  2  AAA_19           AAA domain
     0.0056   16.5   0.0        4.1    7.2   0.0    2.7  2  Bac_DnaA         Bacterial dnaA  protein
     0.0074   16.0   0.1        4.4    7.0   0.0    2.4  2  Cytidylate_kin   Cytidylate kinase
  ------ inclusion threshold ------
      0.015   15.0   0.0        1.2    8.8   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.021   14.8   0.0        8.8    6.3   0.0    2.5  2  ResIII           Type III restriction enzyme, res subunit
      0.023   13.9   0.1        4.6    6.4   0.0    2.8  3  KAP_NTPase       KAP family P-loop domain
      0.033   14.3   0.0        7.8    6.6   0.0    2.5  2  SKI              Shikimate kinase
      0.034   14.4   0.0        4.1    7.6   0.0    2.4  2  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.042   13.5   0.0        4.3    6.9   0.0    2.6  2  Zot              Zonular occludens toxin (Zot)
      0.047   13.5   0.0        3.8    7.3   0.0    2.4  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.054   13.4   0.0         11    5.9   0.0    2.7  2  Rad17            Rad17 P-loop domain
      0.056   13.6   0.0        4.6    7.4   0.0    2.4  2  Torsin           Torsin
       0.07   12.0   0.0        1.9    7.3   0.0    2.2  2  AFG1_ATPase      AFG1-like ATPase
      0.092   12.9   0.0        8.8    6.4   0.0    2.4  2  Cytidylate_kin2  Cytidylate kinase-like family
       0.25   11.0   0.5         68    3.1   0.0    3.4  3  Guanylate_kin    Guanylate kinase


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 !  167.3   0.0   6.4e-52   2.1e-49       1     131 [.     226     355 ..     226     356 .. 0.98
   2 !  162.7   0.0   1.7e-50   5.5e-48       1     130 [.     499     629 ..     499     631 .. 0.96

  Alignments for each domain:
  == domain 1  score: 167.3 bits;  conditional E-value: 6.4e-52
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+GppGtGKTllakava+e++++f++i g+e++sky gese+++re+f++a e++ psi+fiDE+d++a++r++ 
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETSASFFSIAGPEIISKYYGESEQQLREIFEDATEES-PSIIFIDELDSIAPKREDV 301
                                       79******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLlt++dg++++ ++vivi+atnr+d++dpal+r gRfdr+iei+
  gi|336252474|ref|YP_004595581.1| 302 TGEVERRVVAQLLTMMDGLESR-GQVIVIAATNRVDSVDPALRRpGRFDREIEIG 355
                                       *********************7.56***************************996 PP

  == domain 2  score: 162.7 bits;  conditional E-value: 1.7e-50
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..T CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..s 75 
                                       vllyGppGtGKTl+akava+e++++f+++ g++llsk+vgesek ir++f++a++ + p+++f+DE+dala+ r   
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANETNANFISVRGPQLLSKWVGESEKAIRQTFRKARQVS-PTVIFFDELDALAPGRggG 574
                                       79******************************************************9.****************987 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkiei 130
                                       ++ s+++ervvnqLlteldg+++  ++v+vigatnrpd++dpallr gRfdr + i
  gi|336252474|ref|YP_004595581.1| 575 ETGSNVSERVVNQLLTELDGLEDM-EDVMVIGATNRPDMIDPALLRsGRFDRLVMI 629
                                       7899*******************7.55************************98876 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 !  103.1   0.1   2.1e-32   6.7e-30       1      84 [.       5      88 ..       5      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 2.1e-32
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVt 79
                                      +L Va+a+++d+grgi+r+dp+++ +l+l+pgd++eieg  +T+a+vw+a+++d++++++r+dg+tR+na+v+iG++Vt
  gi|336252474|ref|YP_004595581.1|  5 QLEVAKAYPNDSGRGIARLDPDTLLHLKLSPGDIIEIEGADTTAAKVWRADRQDWNTDTVRIDGFTRQNADVGIGERVT 83
                                      699*****99*****************************999************************************* PP

                                      EEEE- CS
                           CDC48_N 80 Vrkae 84
                                      +rkae
  gi|336252474|ref|YP_004595581.1| 84 IRKAE 88
                                      ***97 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0   2.9e-15   9.6e-13       1      41 [.     378     418 ..     378     423 .. 0.92
   2 !   53.6   1.0   4.4e-17   1.4e-14       1      44 [.     653     698 ..     653     699 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 2.9e-15
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitme 41 
                                       dv+l +LA +T+G++GAD+++l +eAa+ Alrr ++ei+ +
  gi|336252474|ref|YP_004595581.1| 378 DVNLGHLADETHGFVGADIESLTKEAAMKALRRYLPEIDLD 418
                                       9*********************************9997754 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 4.4e-17
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgike..itmedfe 44 
                                       dv+l e+Ae T+Gy+G Dl+++ reAa++Alr+++++  ++m++f+
  gi|336252474|ref|YP_004595581.1| 653 DVSLREIAEITDGYVGSDLESIAREAAIEALREDEEAdvVEMRHFR 698
                                       9***********************************657******7 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 ?   -1.3   0.0       5.9   1.9e+03      18      28 ..      32      42 ..       2      51 .. 0.78
   2 !   54.4   0.2   2.4e-17     8e-15       2      63 ..     107     177 ..     106     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 5.9
                                      EE-TTEEEEEC CS
                           CDC48_2 18 pvtkGdlvvfe 28
                                       +++Gd++ +e
  gi|336252474|ref|YP_004595581.1| 32 KLSPGDIIEIE 42
                                      47888888776 PP

  == domain 2  score: 54.4 bits;  conditional E-value: 2.4e-17
                                       .SCCCCH.HHHCCCTTEEE-TTEEEEECCT.........CCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                           CDC48_2   2 idgdema.ylkrqFlgrpvtkGdlvvfefk.........gqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                       + +d +a ++krq+l+rpv+  d+v+++ +         gq+i+l +v+teP g+v ite+T +el+++p +
  gi|336252474|ref|YP_004595581.1| 107 FGSD-AAgMVKRQILKRPVVGRDIVPVMSStnhpfmrspGQAIPLIAVETEPEGVVLITEDTDVELREEPIS 177
                                       6778.666*****************998877778889********************************976 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 !   28.9   0.0   2.4e-09     8e-07      32     103 ..     222     301 ..     200     343 .. 0.85
   2 !   24.0   0.0   8.4e-08   2.7e-05      35      70 ..     498     533 ..     467     569 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.4e-09
                            RuvB_N  32 aldhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsrav 100
                                       +   vll+GpPG Gkt lak +a+e  +++ + +gP +      e +++l  ++ + +e+   ++fide+  ++++ 
  gi|336252474|ref|YP_004595581.1| 222 PPQGVLLHGPPGTGKTLLAKAVANETSASFFSIAGPEIiskyygESEQQLREIFEDATEEspSIIFIDELDSIAPKR 298
                                       55679*******************************875444444567899999887655237*******9999988 PP

                            RuvB_N 101 eev 103
                                       e+v
  gi|336252474|ref|YP_004595581.1| 299 EDV 301
                                       876 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 8.4e-08
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvle 70 
                                        vllyGpPG Gkt +ak +a+e ++++ +  gP l 
  gi|336252474|ref|YP_004595581.1| 498 GVLLYGPPGTGKTLMAKAVANETNANFISVRGPQLL 533
                                       69******************************9874 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.2   3.9e-08   1.3e-05      24     140 ..     223     328 ..     193     337 .. 0.71
   2 !   16.8   0.0   2.2e-05    0.0071      25      62 ..     497     531 ..     488     540 .. 0.81
   3 ?    4.4   0.0      0.14        45     122     148 ..     543     568 ..     540     604 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3.9e-08
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysa.laqalareellrqlldeaesaeleawr 98 
                                       p+ vll+G++G+GK+ l+++++++ +++  +f ++g    +     y+    q+l r e++++  +e   +    + 
  gi|336252474|ref|YP_004595581.1| 223 PQGVLLHGPPGTGKTLLAKAVANETSAS--FFsIAGPEIIS----KYYGeSEQQL-R-EIFEDATEE---SPSIIFI 288
                                       489*******************988877..33355555555....4544366666.5.677766666...4455555 PP

                            AAA_16  99 ekleealaavpelagaeasrllellkrllallsrderplvlv 140
                                       ++l++ +    +++g+ ++r+ ++l  +++ l+++++ ++ v
  gi|336252474|ref|YP_004595581.1| 289 DELDSIAPKREDVTGEVERRVVAQLLTMMDGLESRGQ-VI-V 328
                                       6566666677777777779********9999988777.33.3 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.2e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdq 62 
                                         vll+G++G+GK+ ++++++++ +++   f++ +  q
  gi|336252474|ref|YP_004595581.1| 497 AGVLLYGPPGTGKTLMAKAVANETNAN---FISVRGPQ 531
                                       689******************977766...66655555 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.14
                            AAA_16 122 llkrllallsrderplvlvlDdlqwad 148
                                       ++++ ++++++  +p+v+++D+l+ + 
  gi|336252474|ref|YP_004595581.1| 543 AIRQTFRKARQ-VSPTVIFFDELDALA 568
                                       56777889999.889*********665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   5.5e-08   1.8e-05       6     105 ..     226     319 ..     222     332 .. 0.87
   2 !   20.3   0.0   1.4e-06   0.00046       4     103 ..     497     592 ..     494     597 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 5.5e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a+  ++    ++  +   e++     + + +++++ ++    a e+   i+++DE+d i
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETSA----SFFSIAGPEIIS----KYYGESEQQLREIFEDATEESpsIIFIDELDSI 294
                                       6889*****************996....999999999999....99999999999999999888889********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk e  + +v r  V+  LL +++g
  gi|336252474|ref|YP_004595581.1| 295 APKrEDVTGEVERR-VVAQLLTMMDG 319
                                       **877777777665.77778899987 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.4e-06
                                       --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGG CS
                             AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEid 78 
                                       + +ll gp g+Gkt++aka+a+  ++    ++i +   +ll     + + ++++  ++   +a +    ++++DE+d
  gi|336252474|ref|YP_004595581.1| 497 AGVLLYGPPGTGKTLMAKAVANETNA----NFISVRGPQLLS----KWVGESEKAIRQTFRKARQVSptVIFFDELD 565
                                       567999******************96....999999999999....44444444444555555555467******** PP

                                       G----...---------HHHHHHHHHHH CS
                             AAA_2  79 Kihpk...essgadvSregVqrdLLqil 103
                                         +p    +++g++vS+  V++ LL  l
  gi|336252474|ref|YP_004595581.1| 566 ALAPGrggGETGSNVSER-VVNQLLTEL 592
                                       ****99977788888866.555555544 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 !   22.3   0.1   3.1e-07    0.0001       1     136 [.     225     344 ..     225     346 .. 0.70
   2 !   21.1   0.0   7.2e-07   0.00024       1     135 [.     498     618 ..     498     620 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.1e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ la+ +a  + ++++ +++++ ++      ++    g+ + +  ++ + a+  +++i+++DE++
  gi|336252474|ref|YP_004595581.1| 225 GVLLHGPPGTGKTLLAKAVANETSASFFSIAGPEIIS------KYY---GESEQQLREIFEDATeeSPSIIFIDELD 292
                                       59******************************98444......444...3444444555555555799********* PP

                                       G--...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  76 rae...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                        +     +v++++ +    + l +++g e  +        ++ via++n++d    +++palr+
  gi|336252474|ref|YP_004595581.1| 293 SIApkrEDVTGEVERRVVAQLLTMMDGLESRG--------QVIVIAATNRVD----SVDPALRR 344
                                       88722234555554444444444333333332........299999999999....88888886 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 7.2e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEver 76 
                                       +vlL GppGtgK+ +a+ +a  +n+++  v +++      l+ ++   ++ ++   + + +a + ++ ++++DE++ 
  gi|336252474|ref|YP_004595581.1| 498 GVLLYGPPGTGKTLMAKAVANETNANFISVRGPQ------LLSKWV--GESEKAIRQTFRKARQvSPTVIFFDELDA 566
                                       59**************************999998......777777..44444555555544448999999999998 PP

                                       --.HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  77 ae.sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                       +      ++  s  +er +   ++ ++ +  +d  +e+++vi+++n++d     ++pal+
  gi|336252474|ref|YP_004595581.1| 567 LApGRGGGETGSNVSERVVN--QLLTELDGLED--MEDVMVIGATNRPD----MIDPALL 618
                                       77566677777777777766..33333333332..45588888888888....6666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   3.5e-06    0.0011       8      60 ..     226     278 ..     221     281 .. 0.79
   2 ?    5.3   0.0     0.069        23      71     118 ..     264     319 ..     249     337 .. 0.71
   3 !   14.8   0.0   7.8e-05     0.025       9      45 ..     500     527 ..     496     537 .. 0.82
   4 ?    1.1   0.0       1.4   4.4e+02      81     105 ..     543     573 ..     538     604 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.5e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrel 60 
                                       ++++G++GtGKT+l++ ++++   +++   ++pe++ +++  s+  +++++++ 
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETS-ASFFSIAGPEIIsKYYGESEQQLREIFEDA 278
                                       689*****************984.344444788888888888888888888775 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.069
                            AAA_22  71 erlsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnl 118
                                       ++ s+++l+e +e+a ++     ++ iDE + +   +         +++ +L ++++ 
  gi|336252474|ref|YP_004595581.1| 264 YGESEQQLREIFEDATEESPS--IIFIDELDSIApkRedvtgeveRRVVAQLLTMMDG 319
                                       467899999999999999988..*********98762345555666666666666665 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 7.8e-05
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfv 45 
                                       +++G++GtGKT+ ++ ++++          ++ +++v
  gi|336252474|ref|YP_004595581.1| 500 LLYGPPGTGKTLMAKAVANET---------NANFISV 527
                                       79*****************98.........5555555 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 1.4
                            AAA_22  81 aleqalrarav..ielliiDEaqhlr....s 105
                                       a++q +r+++   + ++  DE + l      
  gi|336252474|ref|YP_004595581.1| 543 AIRQTFRKARQvsPTVIFFDELDALApgrgG 573
                                       566666666667889*********9765441 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.1e-07   6.8e-05       2      80 ..     226     334 ..     226     360 .. 0.78
   2 !   16.2   0.0   2.8e-05    0.0091       2      48 ..     499     547 ..     499     657 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.1e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       vll+G+pG+GK+ la+ +++++   ++ ++ ++++++++g+ +q+++                              
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETSasFFSIAGPEIISKYYGESEQQLReifedateespsiifideldsiapkredVT 302
                                       799****************999999999************8888887778888888888888888888887665433 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatnl 80 
                                        +v+ r+ ++l  + +   s+g+ +++ atn+
  gi|336252474|ref|YP_004595581.1| 303 GEVERRVVAQLLTMMDGLESRGQVIVIAATNR 334
                                       34666677777777777677777777777775 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.8e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdy 48 
                                       vll G+pG+GK+  a+ +++++   ++ ++ ++l+++ +g+ ++ +++ 
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANETNanFISVRGPQLLSKWVGESEKAIRQT 547
                                       7899***************999988999999999999998766665543 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.4   1.1e+03     165     196 ..      27      58 ..      23      69 .. 0.81
   2 !   17.3   0.0   6.6e-06    0.0022      51      97 ..     224     268 ..     216     291 .. 0.87
   3 !   19.7   0.0   1.3e-06   0.00041      52     108 ..     498     553 ..     496     556 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.4
                                       HHHHHT--TT-EEEEETTT--EEE-SSS-SS- CS
                             TIP49 165 ellkekvkegDviviekesGkvkklGrseara 196
                                       +ll+ k++ gD+i ie +  +  k+ r++ + 
  gi|336252474|ref|YP_004595581.1|  27 TLLHLKLSPGDIIEIEGADTTAAKVWRADRQD 58 
                                       67788999********9999999998887665 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 6.6e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       ++vLl Gp+gtGkt la a+++e +    f +++g e+ s     +e
  gi|336252474|ref|YP_004595581.1| 224 QGVLLHGPPGTGKTLLAKAVANETS--ASFFSIAGPEIISKYYGESE 268
                                       689********************87..789********998766665 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 1.3e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrksig 108
                                       +vLl Gp+gtGkt +a a+++e +    f+++ g ++ s  v  +e ++ q++rk+ +
  gi|336252474|ref|YP_004595581.1| 498 GVLLYGPPGTGKTLMAKAVANETN--ANFISVRGPQLLSKWVGESEkAIRQTFRKARQ 553
                                       69*******************987..78**************99985799*****965 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 !   14.9   0.0   5.2e-05     0.017      45      71 ..     221     247 ..     211     256 .. 0.85
   2 !   14.6   0.0   6.1e-05      0.02      48      78 ..     497     527 ..     492     568 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.2e-05
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgvea 71 
                                       e  ++++l Gp+G+GK+ la a++ e+
  gi|336252474|ref|YP_004595581.1| 221 EPPQGVLLHGPPGTGKTLLAKAVANET 247
                                       566899****************99876 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.1e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsv 78 
                                       ++++l Gp+G+GK+ +a a++ e+ ++ +sv
  gi|336252474|ref|YP_004595581.1| 497 AGVLLYGPPGTGKTLMAKAVANETNANFISV 527
                                       6899****************99887766665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.5e-05     0.005       5      76 ..     226     294 ..     223     350 .. 0.76
   2 !   12.6   0.0   0.00033      0.11       5      76 ..     499     567 ..     497     628 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.5e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT l+k +++e      s++ i+  +   k + ++e+ l++i+e ++ee  +++f+DE   +
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETS---ASFFSIAGPEIISKYYGESEQQLREIFEDATEESPSIIFIDELDSI 294
                                       7899***************8888...89999988887777777777667777777667799*******9888 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00033
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT ++k +++e      +++ +   +   k   ++ek ++  ++k+++   t++f+DE   +
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANETN---ANFISVRGPQLLSKWVGESEKAIRQTFRKARQVSPTVIFFDELDAL 567
                                       6799*************998777...777777766666666666554554444444445789******8776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0    0.0002     0.067       1      25 [.     226     268 ..     226     360 .. 0.68
   2 !   13.3   0.0   0.00028     0.092       1      25 [.     499     526 ..     499     603 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.0002
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................g 25 
                                       +ll G+pG+GKt lak++++++ ++                  
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETsASffsiagpeiiskyygesE 268
                                       7899**************9998433565565544444444441 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00028
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf..g 25 
                                       +ll G+pG+GKt +ak++++++ ++  +
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANETnANfiS 526
                                       799***************9997322451 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   0.00018     0.057       1      27 [.     226     258 ..     226     333 .. 0.72
   2 !   13.4   0.0   0.00023     0.075       1      26 [.     499     524 ..     499     567 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00018
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl......k 27 
                                       ++l+Gp+g+GK++lak +a++ + ++      +
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETSASFfsiagpE 258
                                       689**************9998887763333221 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00023
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       ++lyGp+g+GK+++ak +a++   ++
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANETNANF 524
                                       689**************999887655 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   0.1   0.00023     0.074      25      43 ..     226     244 ..     222     249 .. 0.90
   2 !   12.8   0.0   0.00017     0.055      25      43 ..     499     517 ..     496     554 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll GppG+GKt+lak+++
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVA 244
                                       79*************9875 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00017
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt++ak+++
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVA 517
                                       79*************9875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.011       3.4      36      54 ..     226     244 ..     222     257 .. 0.87
   2 ?    6.1   0.0     0.023       7.6     128     175 ..     269     316 ..     261     332 .. 0.83
   3 !    7.9   0.0    0.0065       2.1      36      53 ..     499     516 ..     491     522 .. 0.87
   4 ?    2.3   0.0      0.33   1.1e+02     128     172 ..     542     588 ..     525     606 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll G+pgtGKt la  +a
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVA 244
                                       689***********97666 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.023
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeri 175
                                       ++++++ ++++e e +  + iD l+++ +  e+   +v +++v++l  +
  gi|336252474|ref|YP_004595581.1| 269 QQLREIFEDATE-ESPSIIFIDELDSIAPKREDVTGEVeRRVVAQLLTM 316
                                       678899999999.99***************9999999878888887655 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0065
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll+G+pgtGKt +a  +
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAV 516
                                       69***********98655 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.33
                            AAA_25 128 advdaleaaieevegvrlvviDplsralgg...densnsdvgalveal 172
                                        ++++  +++++v  + ++ +D l+++ +g   +e+ ++  +++v++l
  gi|336252474|ref|YP_004595581.1| 542 KAIRQTFRKARQVS-PTVIFFDELDALAPGrggGETGSNVSERVVNQL 588
                                       57888899999975.***********9999885444443335555554 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 !   11.7   0.0   0.00043      0.14      31      62 ..     221     252 ..     211     295 .. 0.79
   2 !   11.8   0.0   0.00038      0.12      35      62 ..     498     524 ..     491     535 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00043
                             AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkeky 62 
                                       +  + vll Gp GtGKt+++k + ++ + + +
  gi|336252474|ref|YP_004595581.1| 221 EPPQGVLLHGPPGTGKTLLAKAVANETSASFF 252
                                       556789****************9999885554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00038
                             AAA_7  35 pvllvGptGtGKtviikdllkkldkeky 62 
                                        vll+Gp GtGKt+++k + ++ +  ++
  gi|336252474|ref|YP_004595581.1| 498 GVLLYGPPGTGKTLMAKAVANETN-ANF 524
                                       59****************999988.444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0     0.001      0.33      22      46 ..     223     247 ..     204     259 .. 0.84
   2 !   11.3   0.0   0.00062       0.2      22      51 ..     496     522 ..     486     535 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.001
                                       SS-EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheas 46 
                                       +  vl++G  GtGK+lla+a+ +++
  gi|336252474|ref|YP_004595581.1| 223 PQGVLLHGPPGTGKTLLAKAVANET 247
                                       4679****************98765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00062
                                       SS-EEEECSTTSSHHHHHHHHHHHSTTTTS CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkek 51 
                                       ++ vl+ G  GtGK+l+a+a+ ++++   +
  gi|336252474|ref|YP_004595581.1| 496 PAGVLLYGPPGTGKTLMAKAVANETN---A 522
                                       578*****************987654...4 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 !   10.9   0.0   0.00092       0.3       2      30 ..     226     254 ..     225     337 .. 0.91
   2 !   12.7   0.0   0.00026     0.085       2      43 ..     499     538 ..     498     628 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00092
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll+g PG++ktll+ka+a+  +++f  i
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETSASFFSI 254
                                       89******************999998665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00026
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilG 43 
                                       vll g PG++ktl++ka+a+  +++f  ++  p ll   + G
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANETNANFISVR-GPQLLSKWV-G 538
                                       7999*********************98886.466665443.3 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   0.00012     0.038       2      49 ..     226     274 ..     225     306 .. 0.74
   2 !    9.1   0.0    0.0044       1.4       2      24 ..     499     522 ..     498     562 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00012
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv 49 
                                       + + G+++tGKT l++a a++   + +  a+ ei+++ + + e++l++ 
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANEtSASFFSIAGPEIISKYYGESEQQLREI 274
                                       6799***************765455555555555555555555555554 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0044
                            AAA_28   2 ivitGgestGKTtlleaLaar.gy 24 
                                       + + G+++tGKT +++a a++ + 
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANEtNA 522
                                       6799***************65443 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0015       0.5      13      37 ..     217     241 ..     212     250 .. 0.84
   2 ?    1.0   0.0      0.66   2.2e+02     121     155 ..     284     321 ..     256     336 .. 0.65
   3 !    9.3   0.0     0.002      0.66      21      37 ..     498     514 ..     486     527 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                            ATPase  13 kgGipegrvvlitGepGtGKtifal 37 
                                       k Gi   + vl+ G pGtGKt++a+
  gi|336252474|ref|YP_004595581.1| 217 KLGIEPPQGVLLHGPPGTGKTLLAK 241
                                       568888899**************97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.66
                            ATPase 121 krvviDsitgl...ayeekeavaReilrqlvrvlkklg 155
                                       + + iD ++++    ++ + +v R+ + ql++++ +l+
  gi|336252474|ref|YP_004595581.1| 284 SIIFIDELDSIapkREDVTGEVERRVVAQLLTMMDGLE 321
                                       55666655555321555666789999999999997764 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.002
                            ATPase  21 vvlitGepGtGKtifal 37 
                                        vl++G pGtGKt++a+
  gi|336252474|ref|YP_004595581.1| 498 GVLLYGPPGTGKTLMAK 514
                                       589************97 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00054      0.18      19      51 ..     223     257 ..     198     274 .. 0.74
   2 !    9.9   0.0    0.0021       0.7      21      51 ..     498     530 ..     468     534 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00054
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        + +lL+G+ G+GKT l++++a++   +  ++  P
  gi|336252474|ref|YP_004595581.1| 223 PQGVLLHGPPGTGKTLLAKAVANETSASffSIAGP 257
                                       4459******************9987766666666 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0021
                                       EEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        +lL+G+ G+GKT +++++a++ + +  +v+ P
  gi|336252474|ref|YP_004595581.1| 498 GVLLYGPPGTGKTLMAKAVANETNANfiSVRGP 530
                                       399******************998876666655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0031         1       5      22 ..     226     243 ..     223     301 .. 0.73
   2 !   11.9   0.0   0.00042      0.14       5      22 ..     499     516 ..     496     564 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0031
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l+ Gp+g+GKT lak  
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAV 243
                                       799************988 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00042
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l+yGp+g+GKT +ak  
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAV 516
                                       89*************987 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   0.00073      0.24      52     116 ..     222     291 ..     212     338 .. 0.63
   2 !    9.8   0.0    0.0013      0.41      51      81 ..     494     524 ..     443     564 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00073
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..ev.ek...edlkelpklvellrerperfilfvDDL 116
                                       p + vLL G  GtGK  l ka+ ne++++   +   e+ +k   e+ ++l +++e   +++   i+f+D L
  gi|336252474|ref|YP_004595581.1| 222 PPQGVLLHGPPGTGKTLLAKAVANETSASFFSIAgpEIiSKyygESEQQLREIFEDA-TEESPSIIFIDEL 291
                                       56789*********************9998655433441331113344444444443.3345678898887 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0013
                            DUF815  51 lpannvLLwGarGtGKSslvkallneyaeeg 81 
                                        p   vLL+G  GtGK  + ka+ ne++++ 
  gi|336252474|ref|YP_004595581.1| 494 DPPAGVLLYGPPGTGKTLMAKAVANETNANF 524
                                       45678********************998876 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 ?    5.1   0.1     0.071        23      17      45 ..     420     448 ..     414     457 .. 0.86
   2 !   15.2   0.0   4.7e-05     0.015      29      55 ..     692     718 ..     676     723 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.071
                            Vps4_C  17 mdipsdkllePpvtlkDflkalkkarptV 45 
                                       +dip++ +    v+++Df  al+++ p+ 
  gi|336252474|ref|YP_004595581.1| 420 EDIPPSLIDRMIVKREDFRGALNEVEPSA 448
                                       68999989999***************995 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.7e-05
                            Vps4_C  29 vtlkDflkalkkarptVskeDLekhee 55 
                                       v++++f +a++++rpt++++ L+ +e+
  gi|336252474|ref|YP_004595581.1| 692 VEMRHFRQAMENVRPTITEDILDYYER 718
                                       89******************9999987 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0013      0.44      22      42 ..     226     246 ..     212     253 .. 0.86
   2 !    8.9   0.1     0.003      0.96      22      42 ..     499     519 ..     496     527 .. 0.86
   3 ?   -0.6   0.0       2.3   7.5e+02     163     205 .]     674     717 ..     662     717 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0013
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v   Gp GtGKt+la a+a e
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANE 246
                                       6789***********999865 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.003
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v   Gp GtGKt++a a+a e
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANE 519
                                       5678***********999865 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.3
                                       -----THHHHHHTTT-TTEEEEE--G.GG----HHHHHHHHHH- CS
                              PhoH 163 gkksGlaealevlknvegieivelkk.kdvvRhplvkkivkaye 205
                                         +++  eal+  ++ + +e+ ++++  + vR ++++ i++ ye
  gi|336252474|ref|YP_004595581.1| 674 IAREAAIEALREDEEADVVEMRHFRQaMENVRPTITEDILDYYE 717
                                       44555555555555556666666654157899999998888875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0    0.0014      0.46       6      37 ..     218     249 ..     216     332 .. 0.79
   2 !    9.7   0.0    0.0036       1.2      12      92 ..     497     592 ..     490     608 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0014
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkp 37 
                                       l +++ + v + G+ G+GK+ L+k++a++++ 
  gi|336252474|ref|YP_004595581.1| 218 LGIEPPQGVLLHGPPGTGKTLLAKAVANETSA 249
                                       678888999******************99876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0036
                                       SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH........ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx........ RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren........ 79 
                                         v + G+ G+GK+ ++k++a++++  +  i ++g +l ++   +++k i+  + +  q+ p++   ++        
  gi|336252474|ref|YP_004595581.1| 497 AGVLLYGPPGTGKTLMAKAVANETN--ANFISVRGPQLLSKWVGESEKAIRQTFRKaRQVSPTVIFFDEldalapgr 571
                                       56889******************97..57888899999888888888888887777667777776555566666666 PP

                                       ........HHHTCHHHHHHHS CS
                                       ........xxxxxxxxxxxxx RF
                          ABC_tran  80 ........esdeeiekalskl 92 
                                                s++ ++++l++l
  gi|336252474|ref|YP_004595581.1| 572 gggetgsnVSERVVNQLLTEL 592
                                       666666654444455655555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0016      0.51      21      42 ..     226     247 ..     213     257 .. 0.81
   2 !    9.3   0.0    0.0026      0.83      22      44 ..     500     522 ..     493     530 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0016
                            AAA_30  21 avltGpAGtGKttalkalreaw 42 
                                       ++l+Gp+GtGKt + ka+++  
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANET 247
                                       789*************998755 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0026
                            AAA_30  22 vltGpAGtGKttalkalreawea 44 
                                       +l Gp+GtGKt + ka+++  +a
  gi|336252474|ref|YP_004595581.1| 500 LLYGPPGTGKTLMAKAVANETNA 522
                                       789*************9876655 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   0.00094      0.31      20      40 ..     226     246 ..     212     280 .. 0.80
   2 !    9.3   0.0    0.0027      0.87      20      42 ..     499     521 ..     476     556 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00094
                            AAA_11  20 tliqGPPGtgKTktivellsq 40 
                                       +l++GPPGtgKT    ++ ++
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANE 246
                                       79**********766655555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0027
                            AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                       +l+ GPPGtgKT +  ++ ++ +
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANETN 521
                                       6899********88888877775 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00038      0.12      10      44 ..     216     247 ..     210     279 .. 0.80
   2 !    7.1   0.0    0.0084       2.7      23      44 ..     499     520 ..     490     547 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00038
                                       HHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  10 ekLlekdelqslvvalvGmgGvGKttlakqilnks 44 
                                       +kL   + +q   v l+G +G GKt lak + n+ 
  gi|336252474|ref|YP_004595581.1| 216 KKLG-IEPPQ--GVLLHGPPGTGKTLLAKAVANET 247
                                       5555.44455..689****************9994 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0084
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       v l+G +G GKt +ak + n+ 
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANET 520
                                       679*************999983 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 !    9.4   0.0    0.0027      0.88      15      83 ..     218     290 ..     212     331 .. 0.58
   2 ?    6.1   0.0     0.028         9      23      44 ..     499     520 ..     491     528 .. 0.81
   3 ?   -0.9   0.0       3.9   1.3e+03     113     155 ..     544     598 ..     523     608 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0027
                          ATPase_2  15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal......... 82 
                                       l  ep + +++ Gp g GKt L k ++++ +      ++ ia  e+ ++++ e+   e++ +++ + +         
  gi|336252474|ref|YP_004595581.1| 218 LGIEPPQGVLLHGPPGTGKTLLAKAVANETS----ASFFSIAGPEIISKYYGES---EQQLREIFEDAteespsiif 287
                                       556777788999********99999999984....4678888888888888888...33333333333233322222 PP

                          ATPase_2  83 ..g 83 
                                          
  gi|336252474|ref|YP_004595581.1| 288 idE 290
                                       220 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.028
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienl 44 
                                       +++YGp g GKt + k ++++ 
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANET 520
                                       689*********9888888775 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.9
                          ATPase_2 113 ikkkgkk......iiiiiDelqkli......dlglngaellvkeLlnliesltke 155
                                       i+++ +k       +i++Del  l       + g+n +e +v++Ll+ ++ l   
  gi|336252474|ref|YP_004595581.1| 544 IRQTFRKarqvspTVIFFDELDALApgrgggETGSNVSERVVNQLLTELDGLEDM 598
                                       333333333366689999**98874222222455556666666666666655555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0     0.001      0.34       4      33 ..     226     249 ..     223     305 .. 0.70
   2 !    8.0   0.0    0.0046       1.5       4      35 ..     499     523 ..     496     563 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.001
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeert 33 
                                       vl +G +GtGKt+++ ++++e       + 
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANET------SA 249
                                       6889*************99998......33 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0046
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertav 35 
                                       vl  G +GtGKt+++ ++++e        +a+
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANET-------NAN 523
                                       6789************999998.......333 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.029       9.3       2      26 ..     230     254 ..     229     301 .. 0.78
   2 !    9.8   0.0    0.0031         1       1      49 [.     502     551 ..     502     563 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.029
                                       E-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsa 26 
                                       G+PG GK+ +++ ++ +   +++s 
  gi|336252474|ref|YP_004595581.1| 230 GPPGTGKTLLAKAVANETSASFFSI 254
                                       9**************9999888874 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0031
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTS CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrkl 49 
                                       +G+PG GK+ +++ ++ + +  ++s  G  l +    ++ +  r+ +rk+
  gi|336252474|ref|YP_004595581.1| 502 YGPPGTGKTLMAKAVANETNANFISVrGPQLLSKWVGESEKAIRQTFRKA 551
                                       7*****************99888886555555444444434455555555 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 !    7.8   0.0    0.0048       1.6     117     137 ..     226     246 ..     219     250 .. 0.89
   2 !    9.4   0.1    0.0016      0.51     117     137 ..     499     519 ..     497     525 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0048
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v+++Gp+ tGkt la+a a+ 
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANE 246
                                       899**************9985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0016
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v++yGp+ tGkt +a+a a+ 
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANE 519
                                       799**************9985 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0017      0.57       3      23 ..     226     246 ..     224     251 .. 0.89
   2 ?    6.4   0.0     0.024       7.9       3      23 ..     499     519 ..     498     524 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0017
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l+G++G GKT L++ +a +
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANE 246
                                       79**************99976 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G GKT +++ +a +
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANE 519
                                       789*************99876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0056       1.8      14      40 ..     221     247 ..     213     256 .. 0.87
   2 !    8.8   0.0    0.0027      0.89      16      50 ..     496     528 ..     489     533 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0056
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdel 40 
                                       e P  +ll G pG GK+ la+++++e+
  gi|336252474|ref|YP_004595581.1| 221 EPPQGVLLHGPPGTGKTLLAKAVANET 247
                                       56899******************9997 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0027
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       P+ +ll G pG GK+ +a+++++e+  + n++ + 
  gi|336252474|ref|YP_004595581.1| 496 PAGVLLYGPPGTGKTLMAKAVANET--NANFISVR 528
                                       8889********************9..88888775 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 ?    7.8   0.0     0.011       3.4      24      47 ..     226     249 ..     220     299 .. 0.68
   2 !    8.0   0.0    0.0088       2.9      23      47 ..     498     522 ..     493     569 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.011
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       v+l G++G+gk+l A++ +++ + 
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETSA 249
                                       9****************9988765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0088
                                       -EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgp 47 
                                        v+l G++G+gk+l+A++ +++   
  gi|336252474|ref|YP_004595581.1| 498 GVLLYGPPGTGKTLMAKAVANETNA 522
                                       69****************9987654 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       5.7   1.9e+03     133     156 ..     195     218 ..     194     219 .. 0.84
   2 ?    5.5   0.0      0.03       9.9       5      30 ..     227     252 ..     224     255 .. 0.90
   3 !    9.6   0.0    0.0017      0.54       5      36 ..     500     531 ..     497     554 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.7
                               IPT 133 akakkRvrqmlrpeeegaslldEl 156
                                       +  ++Rvr+m++   +++ +++ l
  gi|336252474|ref|YP_004595581.1| 195 QSEIQRVREMVELPMKHPQIFKKL 218
                                       56799*******999999988765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.03
                               IPT   5 lifGatttGKtaeaiklaketgapvi 30 
                                       l++G+ +tGKt  a ++a+et+a+  
  gi|336252474|ref|YP_004595581.1| 227 LLHGPPGTGKTLLAKAVANETSASFF 252
                                       899*******************9865 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0017
                               IPT   5 lifGatttGKtaeaiklaketgapvivlDRvq 36 
                                       l++G+ +tGKt +a ++a+et a  i++   q
  gi|336252474|ref|YP_004595581.1| 500 LLYGPPGTGKTLMAKAVANETNANFISVRGPQ 531
                                       89*********************999876555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.012       3.9       2      32 ..     226     256 ..     225     262 .. 0.88
   2 ?    6.9   0.0     0.017       5.5       2      32 ..     499     529 ..     498     544 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.012
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt l k v+++ + s ++++G
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETSASFFSIAG 256
                                       6789***************999888777776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.017
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt + k v+++ + + ++v+G
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANETNANFISVRG 529
                                       6788****************99888888887 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2      0.02       6.5      12      31 ..     225     244 ..     220     251 .. 0.81
   2 ?    7.7   0.0     0.013       4.2      13      33 ..     499     519 ..     494     552 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.02
                            AAA_19  12 vllvtaGpGtGKTrvlkhiv 31 
                                        +l+ ++pGtGKT + k++ 
  gi|336252474|ref|YP_004595581.1| 225 GVLLHGPPGTGKTLLAKAVA 244
                                       5899*********9877765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.013
                            AAA_19  13 llvtaGpGtGKTrvlkhival 33 
                                       +l+ ++pGtGKT + k++ ++
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANE 519
                                       7899********998877665 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.025         8      37      61 ..     226     250 ..     219     270 .. 0.91
   2 ?    7.2   0.0     0.012       4.1      37      66 ..     499     528 ..     495     557 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.025
                                       EEEE-SSSSSHHHHHHHHHHHHHHH CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlen 61 
                                       ++++g+ G Gkt L ka++ne+ ++
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETSAS 250
                                       79******************98765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelr 66 
                                       +++yg+ G Gkt + ka++ne+ +n+ + r
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANETNANFISVR 528
                                       79*******************999886655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.014       4.4       3      28 ..     228     253 ..     226     256 .. 0.90
   2 ?    6.7   0.0     0.017       5.4       4      28 ..     502     526 ..     499     528 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.014
                                       EE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                       + GP g+GK  +a+a+a++ ++++++
  gi|336252474|ref|YP_004595581.1| 228 LHGPPGTGKTLLAKAVANETSASFFS 253
                                       68******************999986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.017
                                       E-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyld 28 
                                        GP g+GK  +a+a+a++ ++++++
  gi|336252474|ref|YP_004595581.1| 502 YGPPGTGKTLMAKAVANETNANFIS 526
                                       6********************9986 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 ?    4.1   0.0       0.1        33       2      22 ..     227     247 ..     226     291 .. 0.71
   2 ?    8.8   0.0    0.0037       1.2       5      77 ..     503     570 ..     499     571 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.1
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts 22 
                                       + hG pG GK+ l + ++++ 
  gi|336252474|ref|YP_004595581.1| 227 LLHGPPGTGKTLLAKAVANET 247
                                       68*************999994 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0037
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEylllhaG 77 
                                       G pG GK+ + + ++++   ++ ++r    ll++++ ++++    t++++ +         ++++DE  +l +G
  gi|336252474|ref|YP_004595581.1| 503 GPPGTGKTLMAKAVANETnANFISVRG-PQLLSKWVGESEKAIRQTFRKARQVS-----PTVIFFDELDALAPG 570
                                       78***************9977777777.99******888888888888665533.....35999**98777665 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 ?    6.3   0.0     0.027       8.8      21      50 ..     220     249 ..     195     299 .. 0.81
   2 ?    5.8   0.0     0.038        12      24      51 ..     496     523 ..     442     565 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.027
                                       ..TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                            ResIII  21 skrdkrglikmaTGtGKTlvaaklierllk 50 
                                       ++  + +l++ + GtGKTl+a +++ + + 
  gi|336252474|ref|YP_004595581.1| 220 IEPPQGVLLHGPPGTGKTLLAKAVANETSA 249
                                       46778899************9888777665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.038
                                       TSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                            ResIII  24 dkrglikmaTGtGKTlvaaklierllkk 51 
                                          +l+  + GtGKTl+a +++ +   +
  gi|336252474|ref|YP_004595581.1| 496 PAGVLLYGPPGTGKTLMAKAVANETNAN 523
                                       4567888999******998888777664 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 ?   -2.0   0.0       4.8   1.6e+03      19      44 ..     222     247 ..     213     255 .. 0.83
   2 ?    6.4   0.0     0.014       4.6     170     198 ..     277     307 ..     262     331 .. 0.78
   3 ?    3.5   0.0      0.11        36      19      47 ..     495     523 ..     483     569 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.8
                        KAP_NTPase  19 tpivvgLygkWGsGKssllnkledel 44 
                                       +p  v L g+ G+GK+ l + + +e 
  gi|336252474|ref|YP_004595581.1| 222 PPQGVLLHGPPGTGKTLLAKAVANET 247
                                       56668999999*****9999887775 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                        KAP_NTPase 170 a..lqkrlVvviDdLDrceteevlqlleavk 198
                                       +  ++++ +++iD+LD++ +++   + e+ +
  gi|336252474|ref|YP_004595581.1| 277 DatEESPSIIFIDELDSIAPKREDVTGEVER 307
                                       24456999************99888877755 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.11
                        KAP_NTPase  19 tpivvgLygkWGsGKssllnkledelkef 47 
                                       +p  v Lyg+ G+GK+ + + + +e + +
  gi|336252474|ref|YP_004595581.1| 495 PPAGVLLYGPPGTGKTLMAKAVANETNAN 523
                                       667799**************999999877 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.024       7.8       1      45 [.     232     281 ..     232     282 .. 0.77
   2 ?    5.2   0.0     0.063        21       1      22 [.     505     526 ..     505     551 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.024
                                       TTSSHHHHHHHHHHHHTSEEEEH..HHHHHHHHT...S-HHHHHHHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl..Deliekrtg...ksiaeifeeegee 45 
                                       +G+GK+ ++k++A++ + +f+ +   e+i+k  g   ++ +eife+ +ee
  gi|336252474|ref|YP_004595581.1| 232 PGTGKTLLAKAVANETSASFFSIagPEIISKYYGeseQQLREIFEDATEE 281
                                       69******************987445788887774345577788877775 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.063
                                       TTSSHHHHHHHHHHHHTSEEEE CS
                               SKI   1 mGaGKstvGkllAkklglefiD 22 
                                       +G+GK+ ++k++A++ + +fi 
  gi|336252474|ref|YP_004595581.1| 505 PGTGKTLMAKAVANETNANFIS 526
                                       69******************95 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 ?    7.6   0.0     0.013       4.1       2      31 ..     226     255 ..     225     284 .. 0.85
   2 ?    4.3   0.0      0.13        43       2      30 ..     499     527 ..     498     529 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.013
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAlltiD 31 
                                       +++hG+P +GKt  a ++a +  a++++i 
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETSASFFSIA 255
                                       689******************999999985 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.13
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       +++ G+P +GKt  a ++a + +a ++++
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANETNANFISV 527
                                       5789*****************99999987 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.013       4.3       4      64 ..     227     292 ..     226     312 .. 0.80
   2 ?    3.7   0.0      0.13        43       4      61 ..     500     562 ..     497     568 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.013
                               Zot   4 lvtGapGsgKts..gavkkdllp..alkegRkiitnidGlrlerieqvlgekvs.tarliridnpe 64 
                                       l +G+pG+gKt+  +av ++     ++ +g +ii +  G   ++++ +++++ + ++ +i+id+ +
  gi|336252474|ref|YP_004595581.1| 227 LLHGPPGTGKTLlaKAVANETSAsfFSIAGPEIISKYYGESEQQLREIFEDATEeSPSIIFIDELD 292
                                       789********722467776655545558**********99******99999999999**999544 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.13
                               Zot   4 lvtGapGsgKtsg..avkkdllp..alkegRkiitnidGlrlerieqvlgekvs.tarlirid 61 
                                       l +G+pG+gKt+   av ++ +    ++ g ++  +  G   ++i+q ++++ + ++ +i+ d
  gi|336252474|ref|YP_004595581.1| 500 LLYGPPGTGKTLMakAVANETNAnfISVRGPQLLSKWVGESEKAIRQTFRKARQvSPTVIFFD 562
                                       789********8622577666553223357777777777777777777777777766677665 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.012       3.8       4      34 ..     226     256 ..     224     329 .. 0.87
   2 ?    3.8   0.0      0.14        47       4      33 ..     499     528 ..     497     552 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.012
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgv 34 
                                       +lL+G + +GK+ la+a+ + + ++++ ++ 
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETSASFFSIAG 256
                                       89************************99875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.14
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                       +lL G + +GK+ +a+a+ + +++ ++ + 
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANETNANFISVR 528
                                       89******************9999998875 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.12        40      46      73 ..     224     251 ..     215     282 .. 0.83
   2 ?    5.9   0.0     0.034        11      48     112 ..     499     564 ..     490     569 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.12
                             Rad17  46 riLLisGPsGCgkstvvkvLskelgikl 73 
                                       + +L+ GP+G gk+   k ++ e + ++
  gi|336252474|ref|YP_004595581.1| 224 QGVLLHGPPGTGKTLLAKAVANETSASF 251
                                       55799**********9999999987766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.034
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqiesfkel 112
                                       +L+ GP+G gk+ + k ++ e   +++    p +l +     ++ ++  + k  +  + +  f el
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANETNANFISVRGPQLLSKWVGeSEKAIRQTFRKARQVSPTVIFFDEL 564
                                       5899******************99999998888875543326666777777777777777777776 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.014       4.6      56      77 ..     226     247 ..     214     253 .. 0.88
   2 ?    3.4   0.0      0.23        75      57      77 ..     500     520 ..     492     528 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.014
                                       EEEEE-TTSSHHHHHHHHHHHH CS
                            Torsin  56 lsfhGwtGtGknfvaeiiaenl 77 
                                       + +hG +GtGk  +a+ +a+++
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANET 247
                                       569***************9986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.23
                                       EEEE-TTSSHHHHHHHHHHHH CS
                            Torsin  57 sfhGwtGtGknfvaeiiaenl 77 
                                        ++G +GtGk  +a+ +a+++
  gi|336252474|ref|YP_004595581.1| 500 LLYGPPGTGKTLMAKAVANET 520
                                       5799*************9986 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0059       1.9      52      79 ..     214     240 ..     190     247 .. 0.80
   2 ?    2.2   0.0      0.21        69      59      78 ..     493     512 ..     470     520 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0059
                       AFG1_ATPase  52 fgrkrksvepvrglYlwGgvGrGKtylm 79 
                                       +++k    ep++g+ l+G+ G GKt l 
  gi|336252474|ref|YP_004595581.1| 214 IFKK-LGIEPPQGVLLHGPPGTGKTLLA 240
                                       4444.3678****************985 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.21
                       AFG1_ATPase  59 vepvrglYlwGgvGrGKtyl 78 
                                       v p+ g+ l+G+ G GKt +
  gi|336252474|ref|YP_004595581.1| 493 VDPPAGVLLYGPPGTGKTLM 512
                                       6799*************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 ?    6.4   0.0     0.027       8.8       8      53 ..     232     281 ..     228     328 .. 0.75
   2 ?    3.9   0.0      0.17        54       8      56 ..     505     554 ..     501     591 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.027
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevde...r 53 
                                        G+g++ +++a+A++    f++ + +e ++k  g se+++ e +++   +
  gi|336252474|ref|YP_004595581.1| 232 PGTGKTLLAKAVANETSASFFSIAGPEIISKYYGESEQQLrEIFEDateE 281
                                       69*********************************999995444443222 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.17
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevdersrl 56 
                                        G+g++ +++a+A++ + +f++ + ++ ++k  g se+ + +++ +++ +
  gi|336252474|ref|YP_004595581.1| 505 PGTGKTLMAKAVANETNANFISVRGPQLLSKWVGESEKAIrQTFRKARQV 554
                                       59*******************************99999997777664444 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.25        82       5      31 ..     226     252 ..     223     259 .. 0.86
   2 ?    0.7   0.0       1.1   3.6e+02      76      94 ..     261     279 ..     254     298 .. 0.84
   3 ?    3.1   0.0      0.21        68       5      30 ..     499     524 ..     496     530 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.25
                                       EEEESTTTSSHHHHHHHHHHHSTTTEE CS
                     Guanylate_kin   5 vvlvgpsgaGksslkkaLlselpekfg 31 
                                       v l gp g+Gk  l ka+ +e + +f 
  gi|336252474|ref|YP_004595581.1| 226 VLLHGPPGTGKTLLAKAVANETSASFF 252
                                       7899**************999998883 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.1
                                       TEEEEEEHHHHHHHHHTTS CS
                     Guanylate_kin  76 gnlygtsveaieevlekgk 94 
                                       +++yg+s ++ +e++e + 
  gi|336252474|ref|YP_004595581.1| 261 SKYYGESEQQLREIFEDAT 279
                                       789************9875 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.21
                                       EEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   5 vvlvgpsgaGksslkkaLlselpekf 30 
                                       v l gp g+Gk  + ka+ +e + +f
  gi|336252474|ref|YP_004595581.1| 499 VLLYGPPGTGKTLMAKAVANETNANF 524
                                       6899**************99998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (743 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        55  (0.00306766); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              55  [number of targets reported over threshold]
# CPU time: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.46
# Mc/sec: 4827.78
//
Query:       gi|336252475|ref|YP_004595582.1|  [L=459]
Description: hypothetical protein Halxa_1068 [Halopiger xanaduensis SH-6]
Scores for 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-135  450.1   5.9     9e-135  449.5   5.9    1.3  1  DUF111         Protein of unknown function DUF111
     0.0067   15.9   0.1      0.032   13.6   0.1    2.1  2  Transcrip_reg  Transcriptional regulator
  ------ inclusion threshold ------
        0.1   11.8   6.3       0.14   11.4   6.3    1.1  1  Zip            ZIP Zinc transporter
        4.7    6.5  19.1        8.2    5.8  19.1    1.3  1  SelP_N         Selenoprotein P, N terminal region


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 !  449.5   5.9    2e-138    9e-135       1     372 [.      10     443 ..      10     444 .. 0.96

  Alignments for each domain:
  == domain 1  score: 449.5 bits;  conditional E-value: 2e-138
                            DUF111   1 lyldcssGisGDmllgALldlgadkeeleealeklgleeveleiekvkksgisatkvdve................. 60 
                                       l +d ++G+sGDmll+AL+d+gad+++le+  ++l++   e++i ++ k+gi++t+vdv                  
  gi|336252475|ref|YP_004595582.1|  10 LAFDGRMGASGDMLLAALVDAGADPDALEAVEATLEI---EYRIAETVKCGIASTTVDVVltgesgdssghehehde 83 
                                       679***********************99888888987...999********************************** PP

                            DUF111  61 .....................................eeehehehrslaeieeiieaaslsekvkekalaiferlae 100
                                                                            ++e + +hrs++e++ei+++++l+++v+++alaif+rl e
  gi|336252475|ref|YP_004595582.1|  84 hshqhdghdhsrhehdhghddhnhadghssdgdhdhvHAEGHGPHRSYREVREIVADMALPAAVEDDALAIFKRLGE 160
                                       999999999999999988888888888888888887777777788******************************** PP

                            DUF111 101 AeakvhgvpleevhfhEvGavDaivdivgaalaldeLgvekvvasplalGsGtvrcahGilPvPaPAvlellkelkl 177
                                       Aea+vhg +le++hfhEvGa Dai+d+vgaa+++++L+++++v++pl++G+Gtv ++hG++PvP+PAv+e+++e+++
  gi|336252475|ref|YP_004595582.1| 161 AEASVHGETLEDIHFHEVGADDAIADVVGAAALVHDLEPDRIVTTPLSTGGGTVGMSHGEYPVPTPAVVEIAREADW 237
                                       ***************************************************************************** PP

                            DUF111 178 kl..gevegElvTPTGaAilaalaeefgslpamkvekiGyGaGkrdleeipnvlRvlleeeeeelekeevvvletni 252
                                       +l  g+v++El+TPTGaAila++ae +++lp++++e++GyGaG  dl+ +pnvlR+l+++ + +l k++++vletn+
  gi|336252475|ref|YP_004595582.1| 238 SLrgGPVDRELLTPTGAAILAHFAEGVDELPSLELEASGYGAGGYDLDPHPNVLRALVGRGDGSLVKDDIAVLETNL 314
                                       99999************************************************************************ PP

                            DUF111 253 DDlspevlgyvlerLleaGAlDvfltpilmKKgRpavllsvlckeedaeeleellfretttlGvRese.verlvler 328
                                       DD++pevlg ++e+L +aGA+Dv++ p++mKK+Rp++l++v+ck+ed+++++++l++et+tlGvR    ++r++++r
  gi|336252475|ref|YP_004595582.1| 315 DDATPEVLGGLQETLSDAGARDVSILPATMKKSRPGHLVKVICKPEDRQRVARALAEETGTLGVRDAGaTHRWIARR 391
                                       ******************************************************************998******** PP

                            DUF111 329 eietvetelg....evrvKva....eevvkvkpEyedvkkiAeetglplkev 372
                                       e+etve+el+    ev+vK+a    +ev++v++Eyed+k++A+et+l+++ev
  gi|336252475|ref|YP_004595582.1| 392 EFETVELELEgetyEVTVKIAsdadGEVYDVSAEYEDAKAVARETELSIREV 443
                                       ********9999*********987555************************9 PP

>> Transcrip_reg  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.27   1.2e+03     105     164 ..     128     183 ..     119     208 .. 0.68
   2 !   13.6   0.1   7.2e-06     0.032     152     212 ..     325     395 ..     309     432 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHTT-EEE-TTSSGGGEEEEEEEEEECCHCT-HHHHHHHHHHHHTESEE CS
                     Transcrip_reg 105 nrtaaevrsifsknggnlgesgsvsflFerkgvivveekeeevdedelleaaieaGaeDv 164
                                        r   evr+i+       + +     +F+r g  + + +  +++ +++  +  e+Ga+D 
  gi|336252475|ref|YP_004595582.1| 128 HRSYREVREIVADMALPAAVEDDALAIFKRLGEAEASVH--GETLEDI--HFHEVGADDA 183
                                       688899999999999988888899999999999988444..3333333..2234444443 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.2e-06
                                       HHHHHHHHTESEEEEE......TTTC....EEEEEEGGGHHHHHHHHHHT.TT---SE..EEEEEEESS-EE- CS
                     Transcrip_reg 152 lleaaieaGaeDveed......eeee...vievitepedlaavkkaLeea.ggleves..aeleyipkeevel 212
                                       l e + +aGa Dv         +       ++vi++ped ++v++aL e+ g l v++  a +++i++ e e 
  gi|336252475|ref|YP_004595582.1| 325 LQETLSDAGARDVSILpatmkkS--RpghLVKVICKPEDRQRVARALAEEtGTLGVRDagATHRWIARREFET 395
                                       568889********878876541..155699****************66657666766447788888754443 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   6.3   3.1e-05      0.14     107     165 ..      73     131 ..      56     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                               Zip 107 kektpkkasssssesaakksvsndkveeseekedhvaeadtdadskeelrngkqekses 165
                                       +   ++++++++s++++++ +s ++++  +++++h+ ++ +d d+++ +++g++++ + 
  gi|336252475|ref|YP_004595582.1|  73 DSSGHEHEHDEHSHQHDGHDHSRHEHDHGHDDHNHADGHSSDGDHDHVHAEGHGPHRSY 131
                                       45667889999999999999999999999999999999999999999999999988765 PP

>> SelP_N  Selenoprotein P, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  19.1    0.0018       8.2     177     230 ..      74     126 ..      38     133 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0018
                            SelP_N 177 eaeektehehahshkqghkhhekhghhHkekeelsesqqeepeeeekpaksglh 230
                                       ++ +++eh+ +hsh++ ++ h++h+h+H+++++ + + +++++++++ + +g+ 
  gi|336252475|ref|YP_004595582.1|  74 SSGHEHEHD-EHSHQHDGHDHSRHEHDHGHDDHNHADGHSSDGDHDHVHAEGHG 126
                                       221222222.23344445555666777777666666666665555554445553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3152.32
//
Query:       gi|336252476|ref|YP_004595583.1|  [L=256]
Description: hypothetical protein Halxa_1069 [Halopiger xanaduensis SH-6]
Scores for 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  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); 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:                        10  (0.000557756); 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 0.27s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 1902.64
//
Query:       gi|336252477|ref|YP_004595584.1|  [L=214]
Description: hypothetical protein Halxa_1071 [Halopiger xanaduensis SH-6]
Scores for 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  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1713.47
//
Query:       gi|336252478|ref|YP_004595585.1|  [L=493]
Description: hypothetical protein Halxa_1072 [Halopiger xanaduensis SH-6]
Scores for 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:                      1969  (0.109822); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3609.40
//
Query:       gi|336252479|ref|YP_004595586.1|  [L=115]
Description: hypothetical protein Halxa_1073 [Halopiger xanaduensis SH-6]
Scores for 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:                      1125  (0.0627475); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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: 00:00:00.39
# Mc/sec: 885.21
//
Query:       gi|336252480|ref|YP_004595587.1|  [L=206]
Description: hypothetical protein Halxa_1074 [Halopiger xanaduensis SH-6]
Scores for 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  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); 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:                         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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1440.57
//
Query:       gi|336252481|ref|YP_004595588.1|  [L=252]
Description: hypothetical protein Halxa_1075 [Halopiger xanaduensis SH-6]
Scores for 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   14.2   0.2       0.06   13.0   0.2    1.7  1  DUF460    Protein of unknown function (DUF460)
      0.064   12.9   0.0       0.11   12.2   0.0    1.3  1  Big_3_3   Bacterial Ig-like domain (group 3)


Domain annotation for each model (and alignments):
>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   6.7e-06      0.06      28      48 ..      79      99 ..      57     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.7e-06
                            DUF460 28 rkkklivGiDPGittgiavld 48
                                      ++ ++i+G+DPG + giavl 
  gi|336252481|ref|YP_004595588.1| 79 DDGRTIIGVDPGRKPGIAVLA 99
                                      56789**************85 PP

>> Big_3_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.2e-05      0.11      42      77 ..     124     159 ..     108     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.2e-05
                           Big_3_3  42 dntpPtvsisegkkisdgavvkglenlritladald 77 
                                       + + P+v+i +g++ +   +v++le++r++l+d++ 
  gi|336252481|ref|YP_004595588.1| 124 EAADPVVRIGDGSRLQSAKLVNDLEDVRVELVDETG 159
                                       7789*****************************864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1834.17
//
Query:       gi|336252482|ref|YP_004595589.1|  [L=255]
Description: DNA repair and recombination protein radB [Halopiger xanaduensis SH-6]
Scores for 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   94.6   0.1    2.6e-26   92.4   0.1    1.8  1  Rad51            Rad51
    2.9e-12   46.6   0.6    4.7e-12   45.9   0.6    1.2  1  AAA_25           AAA domain
    5.9e-11   42.3   0.5    2.6e-09   36.9   0.1    2.1  2  RecA             recA bacterial DNA recombination protein
    1.8e-09   37.3   0.0    6.3e-09   35.5   0.0    1.8  1  ATPase           KaiC
    7.1e-08   32.3   0.0    1.1e-07   31.6   0.0    1.3  1  Zot              Zonular occludens toxin (Zot)
    1.1e-06   28.5   0.0    5.6e-06   26.2   0.0    2.1  1  AAA_24           AAA domain
    2.6e-06   27.0   0.0    3.5e-06   26.5   0.0    1.1  1  DnaB_C           DnaB-like helicase C terminal domain
  ------ inclusion threshold ------
       0.05   13.3   0.1       0.15   11.8   0.0    1.7  2  IstB_IS21        IstB-like ATP binding protein
      0.075   13.2   0.0       0.14   12.3   0.0    1.4  1  Isochorismatase  Isochorismatase family
       0.14   12.5   0.2       0.36   11.2   0.2    1.7  1  DUF1805          Domain of unknown function (DUF1805)
       0.16   11.9   0.0       0.21   11.5   0.0    1.2  1  ATPase_2         ATPase domain predominantly from Archaea


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 !   92.4   0.1   1.6e-29   2.6e-26      19     252 ..       6     246 ..       3     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 1.6e-29
                                       E--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHH... CS
                             Rad51  19 lttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveia... 92 
                                       + tG+  +DelLgGG+e g++t ++G   +Gkt l+ + +v + +      ++g avyidteg    +r  ++    
  gi|336252482|ref|YP_004595589.1|   6 IPTGCGPVDELLGGGFERGTVTQVYGPPAAGKTNLALSAAVETAV------ADGTAVYIDTEGV-SVDRFEQLLsar 75 
                                       78********************************99998887665......599********85.344444443345 PP

                                       ...................HHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH--- CS
                             Rad51  93 ...................erykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfs 150
                                                             ++d e+v +++ ++ a   e+q+e ++ a + +a ++  l++vDs+t  yR + +
  gi|336252482|ref|YP_004595589.1|  76 vegesatarsdgsdsgagdTDTNVDVETVASRIVIEDALDFEEQAEAVRDAEE-FA-ERADLIVVDSATGFYRLERT 150
                                       78888999******999976679***********************9988655.54.6889**************** PP

                                       ----THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTE CS
                             Rad51 151 grgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgee 227
                                       g g+  +  + +++ +++L  la ++++avv+tnqv +++d        d ++P gG+ l h + + l l + +g +
  gi|336252482|ref|YP_004595589.1| 151 GAGDEGEALRTVARQVTHLLSLARKYDLAVVLTNQVFSDPDS-------DRTRPLGGNTLEHWTGVVLRLERFRGGN 220
                                       *****************************************9.......9*************************** PP

                                       EEEEEES-SSS-S-E.EEEEEETTEE CS
                             Rad51 228 RivkvvdsPnlpele.avfaigeeGi 252
                                       R + + +  + p  e ++f i+++G+
  gi|336252482|ref|YP_004595589.1| 221 RRATLEKHRSKPAGEsVQFRITDRGL 246
                                       *9999999999887636799999997 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.6   2.9e-15   4.7e-12      21     188 ..      12     185 ..       4     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 2.9e-15
                            AAA_25  21 prrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                       p++ l++g   +g+++ ++G+p++GKt lal+ a+++a             g+ +y+++E+       R+++++ a+
  gi|336252482|ref|YP_004595589.1|  12 PVDELLGGGFERGTVTQVYGPPAAGKTNLALSAAVETAVA----------DGTAVYIDTEGVS---VDRFEQLLSAR 75 
                                       56778887779***************************64..........479********97...66677666666 PP

                            AAA_25  98 ..................rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralg 156
                                                         + d +++v ++a+   + +++   +    +++ +a+++a e +e+++l+v+D+ + +++
  gi|336252482|ref|YP_004595589.1|  76 vegesatarsdgsdsgagDTDTNVDVETVAS---RIVIE---DALDFEEQAEAVRDAEEFAERADLIVVDSATGFYR 146
                                       6667889999999997765566666666544...33333...2333556655555444444559************* PP

                            AAA_25 157 gdensnsd.......vgalvealeriarrtgaavllvhH 188
                                        + + + d       v++ v++l ++ar+++ av+l+ +
  gi|336252482|ref|YP_004595589.1| 147 LERTGAGDegealrtVARQVTHLLSLARKYDLAVVLTNQ 185
                                       *99999888888887799*****************9876 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.1   1.6e-12   2.6e-09      32      91 ..       4      62 ..       1      78 [. 0.92
   2 ?    3.9   0.0      0.02        32     114     191 ..     115     188 ..      94     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.6e-12
                                      -EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS- CS
                              RecA 32 etissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaeh 91
                                      e+i++G   +d  lG GG+ +G ++++yGp ++Gkt lal+a +e+  ++g+a++id+e 
  gi|336252482|ref|YP_004595589.1|  4 EAIPTGCGPVDELLG-GGFERGTVTQVYGPPAAGKTNLALSAAVETAVADGTAVYIDTEG 62
                                      799************.*****************************************995 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.02
                                       SSHHHHHHHHHHHHTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT--EEEEEEE-- CS
                              RecA 114 dtGeqaleiadalvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksntvvifinqir 190
                                       d  eqa  + da   +   dlivvds + +  + e  G  gd   g   r +++ +  l +  +k + +v++ nq+ 
  gi|336252482|ref|YP_004595589.1| 115 DFEEQAEAVRDAEEFAERADLIVVDSATGFY-RLERTGA-GD--EGEALRTVARQVTHLLSLARKYDLAVVLTNQVF 187
                                       6678888888888888889*******87764.5555543.33..355567777888888888888888888888875 PP

                                       - CS
                              RecA 191 e 191
                                        
  gi|336252482|ref|YP_004595589.1| 188 S 188
                                       4 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   3.9e-12   6.3e-09       1     224 [.       6     246 ..       6     251 .. 0.69

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.9e-12
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       ++tg    De+l gG+ +g+v+ ++G p +GKt +al  +++ a+  +   v++ +e  ++d  e+  s  ++ e  
  gi|336252482|ref|YP_004595589.1|   6 IPTGCGPVDELLGGGFERGTVTQVYGPPAAGKTNLALSAAVETAVA-DGTAVYIDTEGVSVDRFEQLLSARVEGESA 81 
                                       6899999***************************************.9999***99999955555555444444333 PP

                            ATPase  78 eeegklaiidasesaeesaee.............kdkedleelieelaeaikeika.krvviDsitgl.ayeeke.. 137
                                        ++      d s s+++++               +d  d ee +e +++a +  +    +v+Ds tg+   e  +  
  gi|336252482|ref|YP_004595589.1|  82 TAR-----SDGSDSGAGDTDTnvdvetvasriviEDALDFEEQAEAVRDAEEFAERaDLIVVDSATGFyRLER-Tga 152
                                       333.....3333333332222233334444555589999999999999998877654899*******943332.212 PP

                            ATPase 138 ....avaReilrqlvrvl...kklgvTailvsekss.....seeaaggygveefivdgvivLdlkeieeelvRtlei 202
                                           + +R+  rq+++ l   +k+++  +l++++ s       +  gg+ +e+   +g +vL+l++ ++  +R    
  gi|336252482|ref|YP_004595589.1| 153 gdegEALRTVARQVTHLLslaRKYDLAVVLTNQVFSdpdsdRTRPLGGNTLEH--WTG-VVLRLERFRGGNRR-ATL 225
                                       22224567665655555444499**********98889888888999******..445.45666666654333.345 PP

                            ATPase 203 vkmRgtkhskkehpfeIteegi 224
                                        k R+++     + f It++g 
  gi|336252482|ref|YP_004595589.1| 226 EKHRSKPAGE-SVQFRITDRGL 246
                                       6888877654.45788888775 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0     7e-11   1.1e-07       5     128 ..      29     188 ..      25     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 7e-11
                               Zot   5 vtGapGsgKtsgavkkdllpalkegRkiitnidGlrlerieqvlgekvs....tar..................... 56 
                                       v+G+p +gKt  a++  +  a+ +g  ++ + +G  ++r+eq+l   v+    tar                     
  gi|336252482|ref|YP_004595589.1|  29 VYGPPAAGKTNLALSAAVETAVADGTAVYIDTEGVSVDRFEQLLSARVEgesaTARsdgsdsgagdtdtnvdvetva 105
                                       79*********************************************998866666******************999 PP

                               Zot  57 ..liridnpegaetlkefakwatid.kgallviDEcqeifpvrakegrkd.........pevinaftehRhlgwDiv 121
                                         ++  d  +++e+ +++++    + +  l+v+D +  ++  +++ g+ d          +v + +  +R++   +v
  gi|336252482|ref|YP_004595589.1| 106 srIVIEDALDFEEQAEAVRDAEEFAeRADLIVVDSATGFYRLERT-GAGDegealrtvaRQVTHLLSLARKYDLAVV 181
                                       97443358999999999999999886888***************9.677789999999777779999********** PP

                               Zot 122 lltqdis 128
                                       l+ q +s
  gi|336252482|ref|YP_004595589.1| 182 LTNQVFS 188
                                       **99987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   3.4e-09   5.6e-06       4      91 ..      26     158 ..      23     236 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.4e-09
                            AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtek.Glksldadkfpdie......................... 47 
                                         ++yGp+ +GKT la+++         ++++idte+ ++++ +     ++e                         
  gi|336252482|ref|YP_004595589.1|  26 VTQVYGPPAAGKTNLALSAavetavaDGTAVYIDTEGvSVDRFEQLLSARVEgesatarsdgsdsgagdtdtnvdve 102
                                       678****************99999999999******96666666666666669999999999888888888888777 PP

                            AAA_24  48 ............swedfldevvel......aaeladyktlviDtideleelclaevirqnek 91 
                                                    +e+              ++  ++ + +v+D+++ +++l +  + +  e+
  gi|336252482|ref|YP_004595589.1| 103 tvasriviedalDFEEQ------AeavrdaEEFAERADLIVVDSATGFYRLERTGAGDEGEA 158
                                       77766655544444444......1555665999999************99766655555554 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 !   26.5   0.0   2.2e-09   3.5e-06       2     179 ..       6     187 ..       5     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.2e-09
                                       BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHH CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C   2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidsk 77 
                                       ++tg   +D+l++ G+++g+++ + + p+ Gkt lal+ a ++av +  + +++  e  + + +++lls++ e +s 
  gi|336252482|ref|YP_004595589.1|   6 IPTGCGPVDELLGgGFERGTVTQVYGPPAAGKTNLALSAAVETAVADG-TAVYIDTEGVSVDRFEQLLSARVEGESA 81 
                                       678888899987527*************************99998666.5566788888899999999998888888 PP

                                       HHHHTTSXHHHH.HHHHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHH.TTEEEEEEEEGGGTBTS.CS....S CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xx....x RF
                            DnaB_C  78 klrtgklkeedw.eklteaieelseaklfiddtpaltvseirskarrlkke.kglgliviDyLqlmegs.ee....k 147
                                       ++r+   ++    ++ +  +e+++ ++++i+d   l  +e  + +r  ++  ++ +liv+D         ++    +
  gi|336252482|ref|YP_004595589.1|  82 TARSDGSDSGAGdTDTNVDVETVA-SRIVIEDA--LDFEEQAEAVRDAEEFaERADLIVVDSATGFYRLeRTgagdE 155
                                       887754333222022233345444.58999995..6778888888887665899*******8765443212232323 PP

                                       SCCCHHHHHHHHHHHHHHHHCTSXEEEEEEXS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 148 enreqevseisrsLkalakelnvpvialsqLs 179
                                        +  + v++   +L +la+  ++ v+   q+ 
  gi|336252482|ref|YP_004595589.1| 156 GEALRTVARQVTHLLSLARKYDLAVVLTNQVF 187
                                       34455666666678899********9999975 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 ?   11.8   0.0     9e-05      0.15      50      99 ..      27      80 ..      13      88 .. 0.67
   2 ?   -1.9   0.0       1.5   2.4e+03      94     117 ..     118     141 ..     107     153 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9e-05
                         IstB_IS21 50 ivllGpsGvGKshlaialgve.avraglsvlfvrve....dLveelkrarrdgkl 99
                                        + Gp+ +GK+ la + +ve av++g++v+   +e    d +e+l  ar +g+ 
  gi|336252482|ref|YP_004595589.1| 27 TQVYGPPAAGKTNLALSAAVEtAVADGTAVYI-DTEgvsvDRFEQLLSARVEGES 80
                                      5689************9998725667776654.4331112556666666666655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                         IstB_IS21  94 rrdgklaralkrllkvdllilDdl 117
                                       ++ + +  a +   ++dl+++D  
  gi|336252482|ref|YP_004595589.1| 118 EQAEAVRDAEEFAERADLIVVDSA 141
                                       444555555555667889999863 PP

>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.6e-05      0.14       3      53 ..     135     191 ..     134     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.6e-05
                   Isochorismatase   3 lvviDmqndfv....eegvkeseeisavveninkllkaarkagipviftrdvhe..l 53 
                                       l+v+D   +f+     ++++e e+ + v +++ +ll  ark ++ v+ t++v++   
  gi|336252482|ref|YP_004595589.1| 135 LIVVDSATGFYrlerTGAGDEGEALRTVARQVTHLLSLARKYDLAVVLTNQVFSdpD 191
                                       89************999************************************9321 PP

>> DUF1805  Domain of unknown function (DUF1805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00022      0.36      22      53 ..      59      91 ..      44      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                      ....-S--SHHHHHHSB-SEE-HHHHHTT--TT CS
                           DUF1805 22 vag.sGVrtledllaapvesvteaAeelGikeG 53
                                       ++ ++V  +e+ll+a ve  + +A++ G   G
  gi|336252482|ref|YP_004595589.1| 59 DTEgVSVDRFEQLLSARVEGESATARSDGSDSG 91
                                      33459********************99887766 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   0.00013      0.21      19      71 ..      23      77 ..      19     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                          ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...e 71
                                      + ++  +YGp   GKt L   ++ +    d   +y i+ +++s +++++ +    e
  gi|336252482|ref|YP_004595589.1| 23 RGTVTQVYGPPAAGKTNLALSAAVETAVADGTAVY-IDTEGVSVDRFEQLLSarvE 77
                                      567888*************9999999776666665.56788888888777665432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 1896.74
//
Query:       gi|336252483|ref|YP_004595590.1|  [L=230]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-31  109.8   1.4    1.7e-31  109.2   1.4    1.2  1  BAT           GAF and HTH_10 associated domain
    1.8e-21   75.7   0.0    2.6e-21   75.2   0.0    1.2  1  HTH_10        HTH DNA binding domain
     0.0006   19.4   0.2     0.0081   15.8   0.2    2.2  1  Sigma70_r4_2  Sigma-70, region 4
  ------ inclusion threshold ------
      0.048   13.8   0.0      0.088   13.0   0.0    1.4  1  HTH_Tnp_1_2   Helix-turn-helix of insertion element transposa


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.2   1.4   3.7e-35   1.7e-31       1     144 [.       9     152 ..       9     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 3.7e-35
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       D+vve+e++++d++ +lva++a++++ v+l +l prsdg ++ f +v+ga pe++ ++ e+++++ + rvvs ++d+
  gi|336252483|ref|YP_004595590.1|   9 DTVVEVEFTVTDPRYPLVAMSAATGGDVTLIQLLPRSDGAYTIFHRVSGAPPERFLAVIEEYEGI-EGRVVSGGEDA 84 
                                       9****************************************************************.89999998885 PP

                               BAT  78 .tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrer 144
                                        + ++++++g+++   l++ G+ + +++  dg+ar+v+e+P+   + +v++ ++++yp+ve varr+ 
  gi|336252483|ref|YP_004595590.1|  85 iIEVRIETAGEFFTIGLTDTGAIPTELSSHDGTARIVAEIPSIYSASEVIDEFQAAYPEVEIVARRQK 152
                                       4566666889********************************************************97 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   5.7e-25   2.6e-21       1      52 [.     172     223 ..     172     224 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 5.7e-25
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT +q e+l lAy +G++d+PR++t +eLA e+++s++t++ehLr+ae+kl+
  gi|336252483|ref|YP_004595590.1| 172 LTSRQHEALLLAYVNGFYDWPRKTTGEELAAEMDVSATTFHEHLRSAERKLL 223
                                       9*************************************************98 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 !   15.8   0.2   1.8e-06    0.0081       2      54 .]     163     222 ..     162     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHTTS-HHHHHHHHHHHTS--.......-HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2   2 qalrealaeLperqreifllrylegl.......sykEIAellgisegtVksrlsRArkkL 54 
                                       +  ++ l +L+ rq e++ll y++g+       + +E A+++++s +t   +l+ A +kL
  gi|336252483|ref|YP_004595590.1| 163 ELYETVLGMLTSRQHEALLLAYVNGFydwprktTGEELAAEMDVSATTFHEHLRSAERKL 222
                                       5678899******************77777777999999999******999999999987 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 ?   13.0   0.0     2e-05     0.088       7      48 ..     171     216 ..     162     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                       HS-HHHHHHHHHHHHHHH....--S-HHHHHHHHTS-HHHHHHHHH CS
                       HTH_Tnp_1_2   7 eLtakQkkaaellvendy....ekltldeiaeevgvsrsTlykWkk 48 
                                        Lt++Q  a  l   n +     k+t +e+a+e+ vs +T+++ ++
  gi|336252483|ref|YP_004595590.1| 171 MLTSRQHEALLLAYVNGFydwpRKTTGEELAAEMDVSATTFHEHLR 216
                                       499******99997777779999999****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1843.28
//
Query:       gi|336252484|ref|YP_004595591.1|  [L=385]
Description: signal transduction protein with CBS domains [Halopiger xanaduensis SH-6]
Scores for 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-36  122.2  11.9    6.9e-12   45.6   1.4    4.5  4  CBS              CBS domain
     0.0031   18.3   0.2       0.01   16.6   0.1    1.9  1  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma
  ------ inclusion threshold ------
      0.017   15.8   0.1        8.8    7.0   0.0    3.1  3  GAF              GAF domain
      0.038   13.8   0.4       0.85    9.5   0.2    2.6  2  DUF3126          Protein of unknown function (DUF3126)


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 !   16.5   0.1   1.9e-06    0.0085       2      53 ..       4      54 ..       3      58 .. 0.89
   2 !   19.2   0.0   2.7e-07    0.0012       8      55 ..      74     120 ..      63     122 .. 0.84
   3 !   45.6   0.2   1.6e-15   7.3e-12       1      55 [.     129     183 ..     129     185 .. 0.96
   4 !   45.6   1.4   1.5e-15   6.9e-12       1      55 [.     207     263 ..     207     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-06
                                      HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                      +di t +++ v+  t ++++  ++++ +  ++ +V +dg++ G++++r +l+
  gi|336252484|ref|YP_004595591.1|  4 ADIATQEYIEVDVGTRMGKVRSMFEDGNPKGI-IVTNDGEYEGVISEREVLQ 54
                                      68999999****************888888**.6657************997 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.7e-07
                                       SCEEEETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHHHHH CS
                               CBS   8 dvvtvppdttleealelmrekgvsrl.PVVdedgklvGivtlrDllral 55 
                                       + + v+ +++++e ++ ++e++   + PV   +g+l G++t+  +l+a+
  gi|336252484|ref|YP_004595591.1|  74 PAPKVDREEDVRETARVLIESNA-KVaPVF-QNGELWGVITDDAILEAV 120
                                       4569*************999996.555***.7**************997 PP

  == domain 3  score: 45.6 bits;  conditional E-value: 1.6e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+di t d+vt+ +d+ ++ a++ +re+g+srlPV++e+g l G+vt +D+++++
  gi|336252484|ref|YP_004595591.1| 129 VEDIYTADPVTIEEDDGIGRAINYLRENGISRLPVLNENGYLTGVVTTHDIADFV 183
                                       899**********************9999***********999********9986 PP

  == domain 4  score: 45.6 bits;  conditional E-value: 1.5e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEE.EEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklv.GivtlrDllral 55 
                                       V dim+++v t++ d+t ++a+e m ek++ +l V+ ++d+++v G++t++D+lral
  gi|336252484|ref|YP_004595591.1| 207 VYDIMNSPVETINLDATAKDAVEVMLEKDYAGLIVTpEDDDRVViGVITKTDVLRAL 263
                                       679******************************666855556555**********98 PP

>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.3e-06      0.01      18      82 ..     293     366 ..     276     368 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.3e-06
                                       HHHHHCCGGGG.....-EEEEEEE.EE........EEEEEEEEECTTEEEEEEEEESSHHHHHHHHHHHHHHHHHHC CS
                   Ribosomal_S30AE  18 vekklekleky....fieadVtls.kk........kkvevtirlakgkviraeeesedlyaaidlavdklerqlrky 81 
                                       +e+  +   ky    + +a+V+++ +k         ++++++r+ +++ + ++ e    ++a++ a++kler +   
  gi|336252484|ref|YP_004595591.1| 293 IEEVAD---KYqdmqVHHAHVRFKeHKeklrgtplVHCQIRLRT-NKDQVAGTGEGYGAESAFRVALEKLERNVLEM 365
                                       333333...55333348999999994456788877789999965.56677777888****************99776 PP

                                       H CS
                   Ribosomal_S30AE  82 k 82 
                                       k
  gi|336252484|ref|YP_004595591.1| 366 K 366
                                       6 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.002       8.8      92     106 ..      98     112 ..      67     115 .. 0.87
   2 ?    4.4   0.0     0.013        56      54     111 ..     130     180 ..     113     194 .. 0.74
   3 ?    0.0   0.0      0.28   1.2e+03      44      81 ..     286     318 ..     219     329 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.002
                                       EEEEEETTEEEEEEE CS
                               GAF  92 vvPlvndgelwGllv 106
                                       v+P++++gelwG+++
  gi|336252484|ref|YP_004595591.1|  98 VAPVFQNGELWGVIT 112
                                       89***********85 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.013
                                       HHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEE.TTEEEEEEEEEESS CS
                               GAF  54 qvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvn.dgelwGllvlhnps 111
                                       + + t +p++i+   +d+   +    ++l++ gi     +P++n +g l G+++ h+  
  gi|336252484|ref|YP_004595591.1| 130 EDIYTADPVTIE---EDDGIGR--AINYLRENGI---SRLPVLNeNGYLTGVVTTHDIA 180
                                       444556777777...6666666..5679999999...599***99999*******9844 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.28
                                       EEETTSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHH CS
                               GAF  44 fmkngrgicgqvlatgqplvipdstpdprfaqynrrdl 81 
                                       +  +++g + +v+ + q++++++  ++ rf +  +++ 
  gi|336252484|ref|YP_004595591.1| 286 REGVVEG-IEEVADKYQDMQVHH--AHVRFKE--HKEK 318
                                       1111333.447777777777776..7777777..5544 PP

>> DUF3126  Protein of unknown function (DUF3126)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.067     3e+02      28      45 ..      97     114 ..      89     115 .. 0.85
   2 ?    9.5   0.2   0.00019      0.85      21      49 ..     219     247 ..     212     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.067
                           DUF3126  28 dsaEvylgdefiGvifkD 45 
                                       + a v+ ++e  Gvi++D
  gi|336252484|ref|YP_004595591.1|  97 KVAPVFQNGELWGVITDD 114
                                       56889***********99 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00019
                           DUF3126  21 karpkkddsaEvylgdefiGvifkDeedg 49 
                                       +    ++d +Ev+l+ ++ G+i   e+d+
  gi|336252484|ref|YP_004595591.1| 219 NLDATAKDAVEVMLEKDYAGLIVTPEDDD 247
                                       44556899***************998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2838.79
//
Query:       gi|336252485|ref|YP_004595592.1|  [L=101]
Description: lycopene cyclase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 822.07
//
Query:       gi|336252486|ref|YP_004595593.1|  [L=262]
Description: SCP-like extracellular [Halopiger xanaduensis SH-6]
Scores for 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-12   47.2   0.1    5.7e-12   46.6   0.1    1.3  1  CAP       Cysteine-rich secretory protein family


Domain annotation for each model (and alignments):
>> CAP  Cysteine-rich secretory protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.1   3.2e-16   5.7e-12       3     101 ..     120     231 ..     118     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 3.2e-16
                                       HHHHHHHHTT----EE-HHHHHHHHHHHHHHHHH.T---S-GGG--HHHHHHTT-T..................... CS
                               CAP   3 ahNeyRaaaglppLkwdatLekaAqdhardcaashsdsssspeggdllkyaenagk..................... 58 
                                        +Ne Ra++gl pL+wd t +++ ++h++d+a ++++ ++ p+g+ + ++ ++ ++                     
  gi|336252486|ref|YP_004595593.1| 120 EVNERRAEHGLEPLAWDGTVASVGRAHSADMARRDYFAHTNPDGQGPHDRFTEVDDycraygenialtwvdrpverp 196
                                       79*****************************************************9999999999999999999999 PP

                                       .....EEEEEES--CCCHHHHHHTSHH.............HHHHHT-S CS
                               CAP  59 .....eniaaaseaaedavdsWysepgtynkgketegsighftnllwp 101
                                            ++ ++a++ a+  v++W+++ +             h++ +l +
  gi|336252486|ref|YP_004595593.1| 197 ggnevVEYQTAERLATGLVNQWMNSTA-------------HREAILEE 231
                                       99887788888999*************.............99999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2017.14
//
Query:       gi|336252487|ref|YP_004595594.1|  [L=260]
Description: ribonuclease BN [Halopiger xanaduensis SH-6]
Scores for 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-45  155.2  26.2    2.7e-45  155.0  26.2    1.0  1  Virul_fac_BrkB  Virulence factor BrkB


Domain annotation for each model (and alignments):
>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.0  26.2   1.5e-49   2.7e-45       2     255 ..      16     254 ..      15     257 .. 0.92

  Alignments for each domain:
  == domain 1  score: 155.0 bits;  conditional E-value: 1.5e-49
                    Virul_fac_BrkB   2 eddlsllAaalayytllSlfPlllvllavlgllglddelqeqlldllaevlpegaaevvedilqrllnqaslgllgl 78 
                                       ++d++ lAa++ayy++ Sl+P++l++l v +l+g +++++e l+ ++ ++lpe++ ++v d l++ + +a +++++l
  gi|336252487|ref|YP_004595594.1|  16 DRDITFLAAGFAYYAFVSLIPMVLLALVVGSLVG-GENAAERLILVAGDFLPEAGETLVVDALSAESGRAEATVVAL 91 
                                       67999**************************966.789***************777999999988888889****** PP

                    Virul_fac_BrkB  79 avllwsasggvsalrralnkiygveesrsflrkrllsllllllllvllllslvlsvflqslllasapllglglelse 155
                                       +v  w a++++++l  a++ +y+     s+l ++ + l+++l++  +l+l++++ ++l +++ a+    +       
  gi|336252487|ref|YP_004595594.1|  92 VVATWGALKVFRGLSLAFDMVYDEVADDSLLDQIRDGLTVILAGTGALALMVAIGAVLSVAADAV----P------- 157
                                       ************************66579*****************************9954422....2....... PP

                    Virul_fac_BrkB 156 llllqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwllvkilfslylsnfasynaiYGslgalii 232
                                         ++ +l+w+++ll lvl+f+ +Y+vlp+v v + +++pGa++aa++w++++i+f++y +n+++y ++YG++ga+++
  gi|336252487|ref|YP_004595594.1| 158 --FAGTLSWVTLLLGLVLVFLPIYYVLPPVPVAVGEVWPGAVFAAVGWTILQIGFQIYAANAGQY-QAYGAVGAVLL 231
                                       ..47889998889999*********************************************8888.55********* PP

                    Virul_fac_BrkB 233 lllWlylsalilLlGaelnaelq 255
                                       ++ Wly+ ++ilL+Ga+ln++ +
  gi|336252487|ref|YP_004595594.1| 232 FVTWLYFAGIILLVGAVLNVVRA 254
                                       *******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1968.60
//
Query:       gi|336252488|ref|YP_004595595.1|  [L=273]
Description: hypothetical protein Halxa_1082 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        1.4    9.7  10.6          2    9.2  10.6    1.3  1  PRCC      Mitotic checkpoint regulator, MAD2B-interacting


Domain annotation for each model (and alignments):
>> PRCC  Mitotic checkpoint regulator, MAD2B-interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  10.6   0.00011         2      13     152 ..      71     217 ..      53     240 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00011
                              PRCC  13 ssaaaksaptisyeplvssapeaeeseeedppetepepasqpeaenadleakkaaksseamvpepteqdp.vkensk 88 
                                       ss a++ a+ ++ + + ++  +++ ++++++ ++++ pa q+e+e+a ++++  +++     +e t++   ++e + 
  gi|336252488|ref|YP_004595595.1|  71 SSDASSDASGTTVTTTTVESDSDPLESVAAEFDEDDVPAPQTETETAVPDSA--SEA-----DETTAETGaGDEAAV 140
                                       2222222222222222222222222222222222222222222222222222..222.....222333335666666 PP

                              PRCC  89 nypgyyllpsgsqqpqedasdlnlddealrqLlGrrgg.............nrkreeikeakiieinedeelkaneq 152
                                       + ++++++ s  ++ q+++ +++ dde  ++L +r ++              ++re+  e++ ++ ++d+   ++++
  gi|336252488|ref|YP_004595595.1| 141 TAESTTTDDSSTTPIQDAEPASAEDDEDAEDLAARIERgdvtgadvraaeaGEGRESTPEIDDVDLSMDDLETGAAE 217
                                       66777777776555666888889999999999999888888999999999989999999999999999987655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 1919.66
//
Query:       gi|336252489|ref|YP_004595596.1|  [L=302]
Description: auxin efflux carrier [Halopiger xanaduensis SH-6]
Scores for 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   82.2  23.0    3.6e-14   52.0  12.2    2.0  2  Mem_trans  Membrane transport protein
  ------ inclusion threshold ------
       0.55   10.1   2.5       0.74    9.7   0.1    2.2  2  DUF412     Protein of unknown function, DUF412


Domain annotation for each model (and alignments):
>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   3.0   2.2e-13     2e-09       2     141 ..       3     141 ..       2     155 .. 0.81
   2 !   52.0  12.2     4e-18   3.6e-14     241     386 ..     158     297 ..     153     298 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2.2e-13
                         Mem_trans   2 vleavvplyvimllgYgsvkwvkiftpdqcsginrfVvlfavPllifhfisqnnpyemllrfiladvlvklivlill 78 
                                       v+  ++ l+v+ llg g   + ++++   +  +n +  ++a+P+lif +  + +  e ll+ +l   l ++ +++  
  gi|336252489|ref|YP_004595596.1|   3 VVSRLLALLVLLLLGTGLRTT-GVLNTTRTATLNAVAYYVALPALIFVSTYDRDIGE-LLSPALFGGLLFVLFATAG 77 
                                       6778999********999999.*****************************977766.8888888888888899999 PP

                         Mem_trans  79 llgallskifkgslewtitlfslstlpNtlvlgipllkalyge...ygvslmvqvvvlqciiiytl 141
                                       +++ +     + s   ++++++ s  +N++ lg+pl+ a + +      s+++ vv+l +  + ++
  gi|336252489|ref|YP_004595596.1|  78 IAWLVHRN--RSSTPRRSVAIVQSYHSNLGYLGLPLVAATFNDdvtAIASVVLGVVTLTQLPLTII 141
                                       99999999..9********************************55322222223334444444444 PP

  == domain 2  score: 52.0 bits;  conditional E-value: 4e-18
                         Mem_trans 241 rklirnPntyssllglilslvsfkwnvimpkiiqksisilgdaglpmalfslGlfLalqpkkiacgnsvatfalavR 317
                                       r l  nP + +++ gl ++ v++ ++    + +++ +++lg  +lp+al+ +G++L  +  +i++g+  +   +a++
  gi|336252489|ref|YP_004595596.1| 158 RGLATNPVLAALIGGLAIGSVGVSIP----APVASGLDVLGMLSLPLALLCVGASLQVDLPSIDLGATGS--VIALK 228
                                       77899*******************99....***************************************9..8**** PP

                         Mem_trans 318 lilgPlvmlvavlavgLrgslllvaivqaAlPqgivlfviAkeynvherelstllifgmlialpitlvy 386
                                        + +P++ ++++ a+ + +++l++ +v   +P+++  fv+A+e + +++ +s  +++++l+++ ++ v+
  gi|336252489|ref|YP_004595596.1| 229 IVCMPVIAWFVFSALAVDATTLTATVVMLGTPSAVSTFVFATELGGDKEFASLNVFLTTLVSIATLFVL 297
                                       ***************************************************************999886 PP

>> DUF412  Protein of unknown function, DUF412
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   8.3e-05      0.74      33     105 ..      32     104 ..      25     138 .. 0.86
   2 ?   -0.2   0.5     0.097   8.7e+02      36      67 ..     227     265 ..     193     272 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 8.3e-05
                            DUF412  33 atrfaikvmpalavltlvlqlylagsealpqailtalfllsLPlQGlywlGkraktpLppslaswykeikekl 105
                                       at  a+ +  al +l++v+++    +e l+ a++ +l+++     G+ wl +r +++ p +++ + ++ ++ l
  gi|336252489|ref|YP_004595596.1|  32 ATLNAVAYYVALPALIFVSTYDRDIGELLSPALFGGLLFVLFATAGIAWLVHRNRSSTPRRSVAIVQSYHSNL 104
                                       556667777777777888888888888********************************99999999888776 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.097
                            DUF412  36 faikvmpalavltlvlqlylagse........alpqailt 67 
                                       + i +mp++a + +   l++ +++          p+a+ t
  gi|336252489|ref|YP_004595596.1| 227 LKIVCMPVIAWFVFSA-LAVDATTltatvvmlGTPSAVST 265
                                       4555677777665433.33333222334444444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2179.47
//
Query:       gi|336252490|ref|YP_004595597.1|  [L=342]
Description: Anthranilate phosphoribosyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-98  328.1   2.9    4.9e-98  327.7   2.9    1.1  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    1.1e-16   60.4   7.0    2.1e-16   59.5   4.4    2.3  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
     0.0094   15.6   0.0      0.025   14.3   0.0    1.7  1  DUF2717          Protein of unknown function (DUF2717)


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 !  327.7   2.9  8.2e-102   4.9e-98       2     252 ..      71     321 ..      70     322 .. 0.99

  Alignments for each domain:
  == domain 1  score: 327.7 bits;  conditional E-value: 8.2e-102
                                       TTBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEE CS
                   Glycos_transf_3   2 kdlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgf 78 
                                       ++lvD++gTGGd+  t+N+St++aiv+A+aGv+vakhgn svss+sGsaDvLe++gvn+  +p  ve+++e++g+gf
  gi|336252490|ref|YP_004595597.1|  71 EPLVDTCGTGGDDYDTINVSTTSAIVAAGAGVPVAKHGNYSVSSSSGSADVLEEVGVNVGAEPPAVEEAIEDDGIGF 147
                                       579************************************************************************** PP

                                       EEHHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHH CS
                   Glycos_transf_3  79 lfapeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldev 155
                                       ++ap +h+amk v+++r+elg+rT+fn+LGPL+npa +++q++gvy+++l++ la +l+++ veralvvhg+G+de+
  gi|336252490|ref|YP_004595597.1| 148 MLAPVFHPAMKAVIGPRKELGMRTIFNVLGPLTNPAGADAQVVGVYDPDLVPVLADALSRMDVERALVVHGAGTDEI 224
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTS CS
                   Glycos_transf_3 156 sllakttvaelkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagk 232
                                       +++++t vae++ + ++ey+lep+d+gl++++ e+++gg+p+ena+ ++++ eg+ + ak+d++l+nagaa+++ag+
  gi|336252490|ref|YP_004595597.1| 225 AIHGETRVAEVDGEAVEEYALEPADLGLSEHDIEDIAGGSPEENADDMRGIVEGDVTGAKQDVILANAGAAIYVAGE 301
                                       ***************************************************************************** PP

                                       SSSHHHHHHHHHHHHHTSHH CS
                   Glycos_transf_3 233 adslkegvakaeevidsGkA 252
                                       adsl++g++ a+e+i+sG A
  gi|336252490|ref|YP_004595597.1| 302 ADSLEAGANAALEAIESGDA 321
                                       ******************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 !   59.5   4.4   3.5e-20   2.1e-16       1      63 []       2      63 ..       2      63 .. 0.97
   2 ?    0.8   0.0     0.073   4.4e+02      14      33 ..     264     283 ..     263     312 .. 0.83

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 3.5e-20
                                      HHHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N  1 kdiikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63
                                      k++++++ +ge+Lt+e++r+a +++++ ++t+aqi+A+L+Alr+kGet++Eia++a+ mre++
  gi|336252490|ref|YP_004595597.1|  2 KEYVERVTEGEDLTQEDARAASTAVFE-DATEAQIGALLAALRAKGETEAEIAGFAQGMREAA 63
                                      689************************.89******************************975 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.073
                                       -HHHHHHHHHHHHTTSS-HH CS
                   Glycos_trans_3N  14 taeeirfaihgilkgevtda 33 
                                       ++ee ++ ++gi++g+vt a
  gi|336252490|ref|YP_004595597.1| 264 SPEENADDMRGIVEGDVTGA 283
                                       57888888999999999865 PP

>> DUF2717  Protein of unknown function (DUF2717)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.2e-06     0.025      40      68 ..      38      66 ..      23      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-06
                           DUF2717 40 lidalrkaGysesyiaGfldGlnlasevl 68
                                      l+ alr++G  e+ iaGf +G++ a++++
  gi|336252490|ref|YP_004595597.1| 38 LLAALRAKGETEAEIAGFAQGMREAARTI 66
                                      5689*********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2555.11
//
Query:       gi|336252491|ref|YP_004595598.1|  [L=224]
Description: phosphoribosylanthranilate isomerase [Halopiger xanaduensis SH-6]
Scores for 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-41  142.9   0.0    1.2e-41  142.7   0.0    1.0  1  PRAI      N-(5'phosphoribosyl)anthranilate (PRA) isomerase
  ------ inclusion threshold ------
      0.059   12.4   0.0       0.23   10.5   0.0    1.9  1  FMN_dh    FMN-dependent dehydrogenase
       0.07   12.5   0.1       0.21   10.9   0.0    1.9  2  TMP-TENI  Thiamine monophosphate synthase


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 !  142.7   0.0   1.9e-45   1.2e-41       1     193 [.       6     207 ..       6     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: 142.7 bits;  conditional E-value: 1.9e-45
                                       TCE----SHHHHHHHHHHTSSEEEEE--..TTBTTB--HHHHHHHCCCS--E..EEEEESSS-HHHHHHHHHHCTEC CS
                              PRAI   1 akicgltrasdvkaavkagadelglifa..esskrevseeqaqellekvpak..lVGVfvNqpieevlriaqelgld 73 
                                       +k+cglt+ +d+ +av+agad++g+i +  + ++revs e a+ l+++vp+   +V V++  + +  +++++ +g d
  gi|336252491|ref|YP_004595598.1|   6 VKVCGLTNEADLETAVDAGADAVGVICDvpVDTPREVSVERARDLVSSVPPFatTVLVTMASDPDRAVELVERVGPD 82 
                                       699**********************97622568*****************4446*********************** PP

                                       EEEE-CGG.-HHHHHHHHHHS-TTSEEEEEEE-SSS--S-SSTT-.SEEEEE....SSS-SSSXXXXGGGGTTSXX. CS
                              PRAI  74 vvQLHGdedeqeyeellktelpvikalkvaesvdevkearradhv.dllllD....sgaGGtGelldwsliskllks 145
                                       ++QLHGd  ++++ e l+++  v   l  ++  dev +a+r+d   d ll+D    sg GGtGe+ dw++ +   ++
  gi|336252491|ref|YP_004595598.1|  83 AIQLHGDA-DRDVLERLRSDTGVDVLLAIDS--DEVAAAERYDRLvDGLLVDtvdeSGGGGTGETHDWDRTKAAAAD 156
                                       ********.8888888888888888888888..889******9988***************************9999 PP

                                       ..TTEEEESSXXTTTHHHHHT.TXXSEEEEXGGGEEE.TEEXHHHHHHHHH CS
                              PRAI 146 ..lkviLAGGLtpeNvaeaiklegvlgvDvssGVEtn.GvkDlekirkfvq 193
                                          ++iLAGGLtpeNvaea+++ ++++vDv+sGVE++ GvkD e +r+fv+
  gi|336252491|ref|YP_004595598.1| 157 leSPLILAGGLTPENVAEAVRTVEPFAVDVASGVEAEgGVKDPEAVRSFVD 207
                                       99***********************************************97 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   3.8e-05      0.23     127     234 ..      15     176 ..       8     179 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHHCTESEEEEESSTSS---BHHHHHCT-....-BSTT-T.G.TTGGGSTSGSCCTTH.............. CS
                            FMN_dh 127 ellkraeaagykalvltvDtpvlgkRerdlrngf....slppklklrnllqelakpewaaeal.............. 185
                                       + l+ a +ag++a+ + +D+pv+  Re  ++       s+pp   ++ l+ ++ +p+ a e +              
  gi|336252491|ref|YP_004595598.1|  15 ADLETAVDAGADAVGVICDVPVDTPREVSVERARdlvsSVPPF-ATTVLVTMASDPDRAVELVervgpdaiqlhgda 90 
                                       56889999************99999986655533112144443.445677777777777777656667777777777 PP

                                       ..........................................THHHHHHCCCHB-TC--HHHHHHHHHHHSSEEEEE CS
                            FMN_dh 186 ........................................kkasaaaefvgkqldpsltwddikwlreqtklplvvK 222
                                                                               +++    e  g    ++ +wd  k   + ++ pl++ 
  gi|336252491|ref|YP_004595598.1|  91 drdvlerlrsdtgvdvllaidsdevaaaerydrlvdgllvDTVD---ESGGGGTGETHDWDRTKAAAADLESPLILA 164
                                       77777777777777777766665554444444444332221111...222222233447777777777777777777 PP

                                       EE-SHHHHHHHH CS
                            FMN_dh 223 Gvltaedakrav 234
                                       G lt+e++ +av
  gi|336252491|ref|YP_004595598.1| 165 GGLTPENVAEAV 176
                                       777777776666 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.16   9.9e+02     159     177 ..      12      30 ..       5      34 .. 0.61
   2 ?   10.9   0.0   3.6e-05      0.21     135     170 ..     143     178 ..      70     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.16
                          TMP-TENI 159 itlenvaevleagadgvav 177
                                        ++++++++++agad v v
  gi|336252491|ref|YP_004595598.1|  12 TNEADLETAVDAGADAVGV 30 
                                       4555666666666666655 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 3.6e-05
                          TMP-TENI 135 eplgleglkelaealeiPvvaiGGitlenvaevlea 170
                                       e+ ++++ k++a+ le P++  GG+t+envae++++
  gi|336252491|ref|YP_004595598.1| 143 ETHDWDRTKAAAADLESPLILAGGLTPENVAEAVRT 178
                                       5678999************************98864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); 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:                         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 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1724.71
//
Query:       gi|336252492|ref|YP_004595599.1|  [L=556]
Description: anthranilate synthase component I [Halopiger xanaduensis SH-6]
Scores for 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-91  305.0   0.0    8.8e-90  300.7   0.0    2.1  2  Chorismate_bind  chorismate binding enzyme
    4.2e-18   65.9   0.1    1.9e-15   57.3   0.0    3.5  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 ?    2.1   0.0     0.013   1.2e+02      34      89 ..      43     126 ..      23     152 .. 0.74
   2 !  300.7   0.0   9.8e-94   8.8e-90       2     258 .]     270     527 ..     269     527 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.013
                                       ESS-B-HHHHHHHHHC......TBSSSEEEEEEETT.......................EEEEEEESSEEEEEETTS CS
                   Chorismate_bind  34 leaavdplalyralra......rnpapysflleled.......................sellgaSPElllkveggr 81 
                                       le + +pla+y+al+       r +++y+flle  +                       ++ +g  PE +++ve g 
  gi|336252492|ref|YP_004595599.1|  43 LEVETTPLAAYAALTGrsagsdRDRSSYAFLLESAEktassdpdgafrpssaeadrharFSYVGYDPEAVVTVESG- 118
                                       34556677777777654555547788899999555556677777888888888888888889***********966. PP

                                       EEEEECEE CS
                   Chorismate_bind  82 rietepia 89 
                                       ++ +e +a
  gi|336252492|ref|YP_004595599.1| 119 EASVETLA 126
                                       88888877 PP

  == domain 2  score: 300.7 bits;  conditional E-value: 9.8e-94
                                       HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEE CS
                   Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkve 78 
                                       ++dY+e+v+k+ke++ +gd+y+ v+sr+ ++    +vdpl +y+a+r  np+py++lle++d +++gaSPE+l++v+
  gi|336252492|ref|YP_004595599.1| 270 KADYEESVRKAKEHVLDGDIYQGVISRKRELC--GDVDPLGFYEAMRDVNPSPYMYLLEHDDLTVVGASPETLISVR 344
                                       679*****************************..9****************************************** PP

                                       TTSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEE CS
                   Chorismate_bind  79 ggrrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhl 155
                                       g+ ++ ++piaGT  rg++p ed++l+ e+l+deKeraEh m+vdl+rnd+++v+++gsv+v+e+++v +ys+v+h+
  gi|336252492|ref|YP_004595599.1| 345 GR-EVMSNPIAGTCDRGSSPVEDRRLAGEMLADEKERAEHTMLVDLARNDVRRVSEAGSVRVDEFMNVLKYSHVQHI 420
                                       65.************************************************************************** PP

                                       EEEEEEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEET. CS
                   Chorismate_bind 156 vstiegelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkd. 231
                                        st++g+l+ d +++d+ +a fP+g+++GaPk rameiid+lE+++Rg+Y+G vgy + +g+a++a+vIRta v+d 
  gi|336252492|ref|YP_004595599.1| 421 ESTVTGRLAADADAFDATRASFPAGTLSGAPKIRAMEIIDDLEAQPRGLYGGGVGYYSWTGDADFAIVIRTATVEDd 497
                                       **************************************************************************666 PP

                                       ...TEEEEEEEEEEETT--HHHHHHHHHHH CS
                   Chorismate_bind 232 ...kelrlgaGaGIvadSdpeaEyeEtlaK 258
                                          ++++++aGaG+vadSdp++EyeEt++K
  gi|336252492|ref|YP_004595599.1| 498 gerDRITVQAGAGLVADSDPKSEYEETEKK 527
                                       89999***********************98 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 !   57.3   0.0   2.1e-19   1.9e-15      17     140 ..      70     217 ..      46     219 .. 0.73
   2 ?    1.5   0.0     0.034   3.1e+02      85      99 ..     463     478 ..     403     503 .. 0.81

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 2.1e-19
                     Anth_synt_I_N  17 hkflLeSaenegge................grySfigldpflelkskngeveveg.......pegeeleeeepldal 70 
                                       ++flLeSae+  ++                +r+S++g+dp +++++++ge++ve+       +  + + +++ +dal
  gi|336252492|ref|YP_004595599.1|  70 YAFLLESAEKTASSdpdgafrpssaeadrhARFSYVGYDPEAVVTVESGEASVETlaedaslTGVDTAPDGDTVDAL 146
                                       555555555444334444444444455557*************************98887655555555566***** PP

                     Anth_synt_I_N  71 rellerfrsaedseptelpfvgGlvGylgYDlvreieklp..ksakddlnlpdarlilydtlivfDhkerrl 140
                                       r+ + +++ a+ +e++   + gGlvG+l+YD+v  +  ++    + ++  +pda+++l+ ++i+fD   +++
  gi|336252492|ref|YP_004595599.1| 147 RAAMPDVELANFPEHDRQHLEGGLVGFLAYDAVYDL-WIEevGLERPESRFPDAQFVLTTKTIAFDERDGTV 217
                                       ********77666688888*************8776.3442234556666****************988776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.034
                     Anth_synt_I_N  85 ptelp.fvgGlvGylg 99 
                                       +++++ ++gG vGy++
  gi|336252492|ref|YP_004595599.1| 463 EAQPRgLYGGGVGYYS 478
                                       5556669*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 4038.70
//
Query:       gi|336252493|ref|YP_004595600.1|  [L=213]
Description: glutamine amidotransferase of anthranilate synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-45  155.0   0.0    2.1e-45  154.8   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
      7e-07   29.2   0.1    3.3e-06   27.0   0.1    1.8  1  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 !  154.8   0.0   2.4e-49   2.1e-45       2     189 ..      25     212 ..      24     213 .] 0.96

  Alignments for each domain:
  == domain 1  score: 154.8 bits;  conditional E-value: 2.4e-49
                                       EEESSTSTHHHHHHHHHHTT.-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT....TTTHHHHHHHHCTSTS- CS
                            GATase   2 liDnydsvtenlvhalvelg.vkvevvpidasaeeilellknpdgilvsgGpgspg....vegkieaikearenkiP 73 
                                       ++Dnyds+t+nlv+++ +l   ++ v++++as e i+    +pd+i++s+Gpg+p+    v+ ++++++e+   ++P
  gi|336252493|ref|YP_004595600.1|  25 FVDNYDSFTYNLVEYVSQLPdTETAVLKNTASLEDIR--SVEPDAIIISPGPGHPKndrdVGVTMDVLREVSP-EVP 98 
                                       69*****************879*********999996..689*******************************.*** PP

                                       EEEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEET CS
                            GATase  74 iLGICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtaksed 150
                                        LG+CLG+ ++++e+g+++ ++  ++ hg+ + +++d+++++ gl++ +++ ++H++ +++   +p+++evta+ ++
  gi|336252493|ref|YP_004595600.1|  99 TLGVCLGLEAAVYEYGGTIGRAP-EPIHGKASSVDHDGSGVFDGLEQGFRAGRYHSLIATE---VPDCFEVTATADH 171
                                       ***********************.9************************************...********99987 PP

                                       TE..EEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHHH CS
                            GATase 151 de..elmeiiekknpfvgvQFHPEststpegpellfnflik 189
                                        +   +m+++++++p+ +vQFHPEs++t  g+ +++nfl +
  gi|336252493|ref|YP_004595600.1| 172 ADetLVMGVRHREYPIEAVQFHPESVLTAVGHDVIENFLAE 212
                                       766689*******************************9865 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   3.7e-10   3.3e-06      84     216 .]      75     195 ..      62     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3.7e-10
                     Peptidase_C26  84 eeadpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgslla 160
                                       ++ +++Rd    + + ++++ +vP lg+C+Gl+     +GGt+ ++ e       h       ++ +v+ + ++++ 
  gi|336252493|ref|YP_004595600.1|  75 GHPKNDRDVGVTMDVLREVSPEVPTLGVCLGLEAAVYEYGGTIGRAPEP----I-H------GKASSVDHDGSGVFD 140
                                       567788998777777888999*********************9887763....2.2......345678999999999 PP

                     Peptidase_C26 161 ellgseeievnslHhqaikelaeelrveAvae..DgviEaieseeakafvlgvQwHPE 216
                                        l +   ++   +H+   +e+ + ++v+A+a+  D++   + ++++++++ +vQ+HPE
  gi|336252493|ref|YP_004595600.1| 141 GLEQ--GFRAGRYHSLIATEVPDCFEVTATADhaDETL-VMGVRHREYPIEAVQFHPE 195
                                       8866..9***********************98766654.4555555699********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1605.55
//
Query:       gi|336252494|ref|YP_004595601.1|  [L=60]
Description: hypothetical protein Halxa_1088 [Halopiger xanaduensis SH-6]
Scores for 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   11.4   1.6       0.27   10.8   1.6    1.3  1  HTH_CodY     CodY helix-turn-helix domain
        6.1    6.8   9.2        1.9    8.4   5.8    2.0  2  VPDSG-CTERM  VPDSG-CTERM motif


Domain annotation for each model (and alignments):
>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.6     3e-05      0.27       6      34 ..      29      57 ..      23      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3e-05
                          HTH_CodY  6 taskiaDriGitrsvivnaLrkLesaGii 34
                                      +a k+a r+Gi  +v+  aL    s G+i
  gi|336252494|ref|YP_004595601.1| 29 IAIKLAVRVGIVAAVVLAALYATGSLGVI 57
                                      57899**********************99 PP

>> VPDSG-CTERM  VPDSG-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.8   0.00022       1.9       6      22 ..       7      23 ..       6      23 .. 0.93
   2 ?   -2.3   0.1      0.48   4.3e+03       9      18 ..      43      47 ..      41      49 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00022
                       VPDSG-CTERM  6 GSTlaLLglgLlgLlgl 22
                                      GST++L++ +L++++++
  gi|336252494|ref|YP_004595601.1|  7 GSTVLLALAALAAFAVA 23
                                      **************986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.48
                       VPDSG-CTERM  9 laLLglgLlg 18
                                      ++L     ++
  gi|336252494|ref|YP_004595601.1| 43 VVL-----AA 47
                                      344.....33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1150  (0.0641419); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 447.65
//
Query:       gi|336252495|ref|YP_004595602.1|  [L=1041]
Description: ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent [Halopiger xanaduensis SH-6]
Scores for 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-155  518.1   0.0   2.8e-155  517.8   0.0    1.1  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    5.2e-25   87.3   0.1      2e-24   85.4   0.0    2.1  2  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
    0.00087   19.3   0.1      0.042   13.8   0.0    3.1  3  DUF2461          Conserved hypothetical protein (DUF2461)


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 !  517.8   0.0  4.8e-159  2.8e-155       1     524 []     175     772 ..     175     772 .. 0.94

  Alignments for each domain:
  == domain 1  score: 517.8 bits;  conditional E-value: 4.8e-159
                                       EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRr 77 
                                       s+Cfv s+ed++++I++t+keaa+++++ggG+G+ +++lR+ g+ v++t+g asGp++fm+++d+++++++qgG+Rr
  gi|336252495|ref|YP_004595602.1| 175 SACFVDSPEDDIDDIHQTAKEAAQVFQSGGGMGYAFWRLRPYGDAVGSTGGIASGPITFMRTYDQMCETIAQGGARR 251
                                       79*************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXX...........................................XXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................................xxxxxxxx RF
                   Ribonuc_red_lgC  78 GAamvylevwHpDiekfidaKekntgee.........................................enrlsnln 113
                                       GA+m++++v+HpD+++fi+aK+k+++                                           e +lsn+n
  gi|336252495|ref|YP_004595602.1| 252 GAQMGVMRVSHPDVIQFIHAKNKDVSLAetlrlndpddfthnsfqealeeareliddegrvpkhlrnavEGHLSNFN 328
                                       *********************998773358999999999************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX............................XXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 114 isvgvpdlFmeavkedkdwtLfsPrtvvkleklygeefeeeyeeleekakik...kkevkakeLfeeiaesawetge 187
                                       isvg++d+Fmea+++d+++t+++Prt +   ++  ee +e y+     ++++   + +++a+eL+++i+e a+e+ge
  gi|336252495|ref|YP_004595602.1| 329 ISVGITDDFMEALQNDEEFTFTNPRTGE--PHIATEETKELYDMFGLGEHVEvgeELSIPAEELWDDIVEGAHENGE 403
                                       *************************733..3566677777777654443333222449******************* PP

                                       XXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXX..................... CS
                                       xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                   Ribonuc_red_lgC 188 PgvlfkDtiNrrnvlekak..ggkIratNlCgEiplleyesvavCnLasinLakfv..................... 241
                                       Pgv++ +++N+++ ++ +k   ++I atN+CgE+pl eye+   CnL++inL+++                      
  gi|336252495|ref|YP_004595602.1| 404 PGVIYLERVNKQHSFDIEKhpDHRILATNPCGEQPLEEYEA---CNLGHINLSTLAdleapdwrvwydehgdeydsi 477
                                       ***************99987889******************...********************************* PP

                                       ..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 242 ..kkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladalaklgipydseealk 316
                                         + d+  ++++d++e+++ i++ +r+L+nv++++++p+++ie++ +++R+iGlG+mgla+++++lg++y+se +++
  gi|336252495|ref|YP_004595602.1| 478 eaAVDAFLEEAVDFEEFDRRIEMGTRFLENVVTMSDFPVEKIEQKVREMRKIGLGIMGLAQLYIQLGMEYGSEASNE 554
                                       *9889999********************************************************************* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 317 farkitelltyyaykaSvelAkergpfplfekskyskgilpvdefeeke...kedweeLreeikkyGlrnamvtala 390
                                       +ar+++ ++++ a  +S+elA+erg+f +++ksky++ + + ++fe+++   + dwe+         +rn++vt++a
  gi|336252495|ref|YP_004595602.1| 555 VARQLMTHINHSAKWTSHELAEERGSFDEWDKSKYANPTEYREWFEKQTgldADDWED------GFPIRNHNVTTIA 625
                                       **************************************99999997655444555555......6789********* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........XXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxx RF
                   Ribonuc_red_lgC 391 PTgsiSliagtssgiePifalvykksvtv.....geflevnpvfeeeLkklglwseellkkiles........vqgl 454
                                       PTg++S++ +t+ g+ePi++ +y+k+v++     ++++e++++f++ L++++++ e+++++ +e+        v+gl
  gi|336252495|ref|YP_004595602.1| 626 PTGTTSMVGNTTGGCEPIYNVAYYKNVSDdvqgdEMLVEFDDYFLRVLEDNDIDVEAVKEEAQEQmatnqfngVEGL 702
                                       ***************************99888655699***********************95556678999***** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 455 eeipeeikrvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                        ++p++i ++f+t+ d++++dh  +q a+q+ +d++iSkt+n pn+ t ed k+++ + +++G KgvtyY
  gi|336252495|ref|YP_004595602.1| 703 STVPDAIGELFVTTGDLSAKDHAGVQVACQQGVDSAISKTVNAPNDSTLEDAKDVFEYIYEHGGKGVTYY 772
                                       *********************************************************************9 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0   3.4e-28     2e-24       2      83 .]      27     172 ..      26     172 .. 0.98
   2 ?   -3.3   0.0       1.6   9.4e+03      27      40 ..     236     249 ..     233     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 3.4e-28
                   Ribonuc_red_lgN   2 kltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealyd............................... 47 
                                       +++++++++l++rYl+kd++ge++E  +++f+Rv +++a+aea ++                               
  gi|336252495|ref|YP_004595602.1|  27 LTDNAYHNILPARYLRKDADGELIEEQEDLFERVGKNIALAEAVFEarkrdaeitvtpdqlkpdhprrdelaeevfg 103
                                       5789999************************************88899***************************** PP

                   Ribonuc_red_lgN  48 .................................kleedkdlaeefydlmssqkflpasPtlmnaGtelg 83 
                                                                         +++++d+a+ef+ +m +++f+p+sPtlmnaG+el+
  gi|336252495|ref|YP_004595602.1| 104 agttaededettlsiyninkfaydtvvpelpdeIRDHVEDVADEFQGMMENLDFMPNSPTLMNAGDELQ 172
                                       ******************************************************************986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.6
                   Ribonuc_red_lgN  27 spqqmfmRvAlala 40 
                                       +++qm++ +A++ a
  gi|336252495|ref|YP_004595602.1| 236 TYDQMCETIAQGGA 249
                                       77888888887655 PP

>> DUF2461  Conserved hypothetical protein (DUF2461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       0.1     6e+02     125     185 ..      50     112 ..      47     123 .. 0.75
   2 ?   -0.3   0.0      0.14   8.4e+02     119     155 ..     135     173 ..     125     190 .. 0.76
   3 !   13.8   0.0     7e-06     0.042       6      51 ..     455     499 ..     452     509 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.1
                           DUF2461 125 idenpeelraileekaflklf.kelkeea.lkrapkgfdkdhpdiellklksftvskkledee 185
                                       i+e+ + ++++ ++ a+++   ++ k++a  +++p + ++dhp+ + l    f ++++ ede+
  gi|336252495|ref|YP_004595602.1|  50 IEEQEDLFERVGKNIALAEAVfEARKRDAeITVTPDQLKPDHPRRDELAEEVFGAGTTAEDED 112
                                       5666666666666655555443444556669999**************999999999998876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.14
                           DUF2461 119 aklReaidenpeelraileekaflklfke..lkeealkr 155
                                       +++R+++++ ++e++ ++e+ +f     +    +++l++
  gi|336252495|ref|YP_004595602.1| 135 DEIRDHVEDVADEFQGMMENLDFMPNSPTlmNAGDELQQ 173
                                       579***************999998876432335566655 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 7e-06
                           DUF2461   6 LkdLaknNdReWfkahkaeYerakkpfealveelteelaevdpeip 51 
                                       L+dL++ + R W+++h +eY+++++ ++a++ee   +++e+d +i+
  gi|336252495|ref|YP_004595602.1| 455 LADLEAPDWRVWYDEHGDEYDSIEAAVDAFLEEA-VDFEEFDRRIE 499
                                       899******************************8.66888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1041 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); 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: 0.83u 0.30s 00:00:01.12 Elapsed: 00:00:00.46
# Mc/sec: 6832.89
//
Query:       gi|336252496|ref|YP_004595603.1|  [L=48]
Description: hypothetical protein Halxa_1090 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.083   13.0   4.0       0.83    9.8   4.0    2.1  1  zf-ACC     Acetyl-coA carboxylase zinc finger domain
       0.14   12.3   8.1       0.16   12.1   8.1    1.1  1  zf-Mss51   Zinc-finger of mitochondrial splicing suppressor 5
       0.19   11.7   6.2       0.29   11.1   6.2    1.5  1  Ogr_Delta  Ogr/Delta-like zinc finger


Domain annotation for each model (and alignments):
>> 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 ?    9.8   4.0   0.00014      0.83       4      24 ..      18      35 ..      17      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00014
                            zf-ACC  4 CpsCgemlykkeLernlyVCP 24
                                      Cp+C++ +yk+     +yVCP
  gi|336252496|ref|YP_004595603.1| 18 CPHCEQPMYKRHC---KYVCP 35
                                      **********976...78887 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 ?   12.1   8.1   2.7e-05      0.16       2      33 ..      18      48 .]      17      48 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.7e-05
                          zf-Mss51  2 CPvpkhkqtapkhvdfeCpdCGiptycseehw 33
                                      CP+++ +   ++h ++ Cp+ G+ + c    w
  gi|336252496|ref|YP_004595603.1| 18 CPHCE-QPMYKRHCKYVCPQHGVIYDCADTFW 48
                                      ****5.6669***************9998777 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 ?   11.1   6.2   4.9e-05      0.29       1      17 [.      17      33 ..      17      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.9e-05
                         Ogr_Delta  1 rCPhCgapaaartsrnl 17
                                      +CPhC++p++ r+  + 
  gi|336252496|ref|YP_004595603.1| 17 PCPHCEQPMYKRHCKYV 33
                                      5***********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 362.28
//
Query:       gi|336252497|ref|YP_004595604.1|  [L=237]
Description: circadian clock protein KaiC [Halopiger xanaduensis SH-6]
Scores for 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-45  154.5   0.0      3e-45  154.4   0.0    1.0  1  ATPase           KaiC
    9.7e-08   31.1   0.1     0.0011   17.7   0.0    2.7  3  GvpD             GvpD gas vesicle protein
    1.7e-06   27.5   0.0      3e-06   26.8   0.0    1.3  1  DnaB_C           DnaB-like helicase C terminal domain
     0.0002   21.0   0.0     0.0007   19.2   0.0    1.9  1  AAA_25           AAA domain
    0.00045   20.2   0.0     0.0021   18.1   0.0    2.1  2  AAA_14           AAA domain
    0.00053   19.8   0.0     0.0021   17.8   0.0    1.8  2  AAA_24           AAA domain
    0.00095   19.6   0.2     0.0073   16.7   0.2    2.1  1  AAA              ATPase family associated with various cellul
     0.0051   17.1   0.0     0.0071   16.6   0.0    1.5  1  AAA_22           AAA domain
     0.0057   16.9   0.0       0.17   12.1   0.0    2.1  2  AAA_28           AAA domain
     0.0071   16.2   0.0      0.015   15.1   0.0    1.6  1  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0091   16.2   0.0      0.018   15.2   0.0    1.7  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.012   14.9   0.1      0.022   14.0   0.1    1.4  1  Rad51            Rad51
      0.015   15.9   0.0      0.028   15.0   0.0    1.5  1  AAA_18           AAA domain
      0.016   14.7   0.1       0.45    9.9   0.0    2.6  3  RecA             recA bacterial DNA recombination protein
      0.019   15.3   0.0      0.032   14.6   0.0    1.4  1  AAA_16           AAA ATPase domain
      0.019   14.9   0.0      0.026   14.4   0.0    1.2  1  ATPase_2         ATPase domain predominantly from Archaea
      0.031   13.3   0.0      0.049   12.7   0.0    1.2  1  T2SSE            Type II/IV secretion system protein
      0.033   13.3   0.1       0.62    9.1   0.0    2.0  2  PAXNEB           PAXNEB protein
      0.044   13.4   0.0       0.14   11.7   0.0    1.8  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.046   13.5   0.0      0.078   12.7   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
      0.056   12.6   0.0      0.084   12.1   0.0    1.2  1  NB-ARC           NB-ARC domain
      0.058   12.6   0.0      0.071   12.3   0.0    1.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.066   13.1   0.3       0.19   11.6   0.1    1.8  2  NTPase_1         NTPase
      0.067   13.6   0.1       0.14   12.6   0.0    1.6  1  RNA_helicase     RNA helicase
      0.083   12.6   0.0       0.12   12.1   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.12   12.3   0.0       0.18   11.7   0.0    1.3  1  NACHT            NACHT domain
       0.12   12.1   0.0       0.23   11.1   0.0    1.4  1  AAA_30           AAA domain
       0.13   12.7   0.2       0.24   11.8   0.2    1.4  1  AAA_17           AAA domain
       0.15   11.8   0.0        0.2   11.4   0.0    1.2  1  AAA_11           AAA domain
       0.16   11.8   0.0       0.38   10.6   0.0    1.4  1  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.4   0.0   5.1e-48     3e-45       2     230 ..       4     233 ..       3     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: 154.4 bits;  conditional E-value: 5.1e-48
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                       +tg++g+De+++gG+ ++r + ++G pG+GKt+f+ qFl kg+ + ge  ++v++ e++++l  +++++   ++k  
  gi|336252497|ref|YP_004595604.1|   4 STGVPGFDELVDGGLLRDRLYIVSGPPGSGKTTFCSQFLTKGVFE-GETALYVSMHESEQELVSDMTNFEFGFDKAV 79 
                                       7*****************************************999.******************************* PP

                            ATPase  79 eegklaiidasesaeesaee........kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrql 147
                                       ++gk+ ++d++es++++  +        ++  ++e+l+++l + i+++++ rvviDs   l ++  ++++ e l ++
  gi|336252497|ref|YP_004595604.1|  80 SSGKMKFMDVFESETKRFFSsssgrgsgEGPGSVENLSNKLVSFIESKGIDRVVIDSTMLL-EYYFSDEVGE-LVTF 154
                                       *************998766678999*999********************************.6666666665.5678 PP

                            ATPase 148 vrvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegi 224
                                       ++ lk  + T +l+se+++  +   g+ +++    gvi +++ ++++ ++R ++i+kmRgt+++ ++ p+e te+g 
  gi|336252497|ref|YP_004595604.1| 155 LTKLKRADATVLLISEMTDPTSYSDGHYLSH----GVIFMHNYLESGGMTRGVQIIKMRGTEIDCDIRPIEFTERGL 227
                                       8899************988777777766666....****************************************** PP

                            ATPase 225 kvleek 230
                                       +v +++
  gi|336252497|ref|YP_004595604.1| 228 RVDPDE 233
                                       *99876 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.8e-06    0.0011      14      71 ..      25      89 ..      20      96 .. 0.73
   2 ?    1.1   0.0       0.2   1.2e+02     128     168 ..     109     147 ..     106     160 .. 0.79
   3 !    9.3   0.0   0.00065      0.39     144     204 ..     159     223 ..     130     229 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.8e-06
                              GvpD 14 likGaPGtGktlftlrgldv.lrresdvlyvstr.vddetvseay.....fsgeaeldktalldl 71
                                      ++ G PG+Gkt+f  ++l+  + + +  lyvs   +++e vs++      f+   +  k +++d+
  gi|336252497|ref|YP_004595604.1| 25 IVSGPPGSGKTTFCSQFLTKgVFEGETALYVSMHeSEQELVSDMTnfefgFDKAVSSGKMKFMDV 89
                                      799***************96366777889**975389999*999766633333333336666665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.2
                              GvpD 128 sPediktvkndlvvlaresgvrlvlvletaansrle.yivdG 168
                                        P +++ + n+lv + + +g+  v++  t     le y+ d 
  gi|336252497|ref|YP_004595604.1| 109 GPGSVENLSNKLVSFIESKGIDRVVIDSTML---LEyYFSDE 147
                                       588999****************999987754...44145555 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00065
                              GvpD 144 resgvrlvlvletaan...srleyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqP..ft 204
                                       + +++ ++l++e   +   s   y+  Gv+ ++   +  g + r +++ k+rG  i+  ++P  ft
  gi|336252497|ref|YP_004595604.1| 159 KRADATVLLISEMTDPtsySDGHYLSHGVIFMHNYLES-GGMTRGVQIIKMRGTEIDCDIRPieFT 223
                                       34556667777776651115568*********766664.666689************999994444 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 !   26.8   0.0     5e-09     3e-06       2     142 ..       3     141 ..       3     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5e-09
                                       BXSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHH CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C   2 lstgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidsk 77 
                                       lstg   +D+l+ +Gl +  l+i+ + p+ Gkt+++ ++ ++ + +   + +++s+  s+++lv+ +   e + d k
  gi|336252497|ref|YP_004595604.1|   3 LSTGVPGFDELVdGGLLRDRLYIVSGPPGSGKTTFCSQFLTKGVFE-GETALYVSMHESEQELVSDMTNFEFGFD-K 77 
                                       57888889998835799***********************998875.558999**************99998886.5 PP

                                       HHHHTTSXHHHHHHHHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHHTTEEEEEEEEGGGTB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  78 klrtgklkeedweklteaieelseaklfiddtpaltvseirskarrlkkekglgliviDyLqlme 142
                                       ++ +gk+k  d+ + +++ + +s+++     +   +v+++ +k+  + ++kg++ +viD   l+e
  gi|336252497|ref|YP_004595604.1|  78 AVSSGKMKFMDVFESETK-RFFSSSSGRGSGEGPGSVENLSNKLVSFIESKGIDRVVIDSTMLLE 141
                                       677788875444333222.2333334444445555788888888888777888888888777777 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06    0.0007      23      79 ..      11      57 ..       3     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                            AAA_25 23 rwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsa 79
                                      + lv+g l ++ l ++ G+pg+GKtt++++   + + +G+           + lyvs 
  gi|336252497|ref|YP_004595604.1| 11 DELVDGGLLRDRLYIVSGPPGSGKTTFCSQFLTKGVfEGE-----------TALYVSM 57
                                      5689988889*******************99877665665...........3444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.5e-06    0.0021       3      52 ..      22      71 ..      20      98 .. 0.77
   2 ?   -1.2   0.0       3.3     2e+03      66      85 ..     141     160 ..     112     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.5e-06
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekl 52
                                      ++++++G+  +GKTt++ q++ +   + e  ly+++ + +++  +d +++
  gi|336252497|ref|YP_004595604.1| 22 RLYIVSGPPGSGKTTFCSQFLTKGVFEGETALYVSMHESEQELVSDMTNF 71
                                      7899*****************99999**********99888655554333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.3
                            AAA_14  66 tylflDEiqevpewekalks 85 
                                       +y f DE+ e+ ++ + lk+
  gi|336252497|ref|YP_004595604.1| 141 EYYFSDEVGELVTFLTKLKR 160
                                       46788888888888888776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.4e-06    0.0021       6      76 ..      25     139 ..      21     151 .. 0.61
   2 ?   -0.5   0.0       1.4   8.4e+02     110     133 ..     150     173 ..     143     182 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.4e-06
                            AAA_24   6 liyGpsgiGKTtlakel.......gpkplfi..............dtekGlks.ldadkfpdie............. 47 
                                       ++ Gp+g+GKTt+++++       g+++l++              ++e G+++ +   k++ +              
  gi|336252497|ref|YP_004595604.1|  25 IVSGPPGSGKTTFCSQFltkgvfeGETALYVsmheseqelvsdmtNFEFGFDKaVSSGKMKFMDvfesetkrffsss 101
                                       678**************999999888888887777777777777755555532022222221112244455555555 PP

                            AAA_24  48 ..........swedfldevvelaaeladyktlviDtide 76 
                                                 s+e++ +++v++  e ++++ +viD+   
  gi|336252497|ref|YP_004595604.1| 102 sgrgsgegpgSVENLSNKLVSF-IESKGIDRVVIDSTML 139
                                       5555555555555555555554.5666788888888655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.4
                            AAA_24 110 efrrllkklqelrknvifiahekt 133
                                       e++ +l+kl+ ++ +v +i++++ 
  gi|336252497|ref|YP_004595604.1| 150 ELVTFLTKLKRADATVLLISEMTD 173
                                       44556677777777**99998876 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 !   16.7   0.2   1.2e-05    0.0073       2      92 ..      25     123 ..      24     181 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-05
                                       EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHHHH CS
                               AAA   2 llyGppGtGKTllakavakel...gvefleisgsellskyvgesekkirelfkeakeka..kpsilfiDEidalaks 73 
                                       +++GppG GKT+++++  ++    g + l +s++e  +++v+  + +++  f++a ++   k   +f  E  ++++s
  gi|336252497|ref|YP_004595604.1|  25 IVSGPPGSGKTTFCSQFLTKGvfeGETALYVSMHESEQELVS-DMTNFEFGFDKAVSSGkmKFMDVFESETKRFFSS 100
                                       789*************99994333455566666665544333.3445555555554443222222333344444444 PP

                                       H....TTCCCHHHHHHHHHHHHH CS
                               AAA  74 r....sgseseeeervvnqLlte 92 
                                       +    sg+  ++ e++ n+L+++
  gi|336252497|ref|YP_004595604.1| 101 SsgrgSGEGPGSVENLSNKLVSF 123
                                       44444444444444444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.2e-05    0.0071       5      29 ..      21      45 ..      19     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                      +++ +v G++G+GKTt + ++l + 
  gi|336252497|ref|YP_004595604.1| 21 DRLYIVSGPPGSGKTTFCSQFLTKG 45
                                      57899**************999875 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   0.00028      0.17       3      57 ..      25      88 ..      23     102 .. 0.66
   2 ?    2.9   0.0       0.2   1.2e+02      78     119 ..     129     172 ..     128     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00028
                            AAA_28  3 vitGgestGKTtlleaLaar........gypvvpEaareileeklakgedalpwv.edllafae 57
                                      +++G++++GKTt ++++  +         y+ ++E+  e++++ + ++++  ++v   +++f +
  gi|336252497|ref|YP_004595604.1| 25 IVSGPPGSGKTTFCSQFLTKgvfegetaLYVSMHESEQELVSDMTNFEFGFDKAVsSGKMKFMD 88
                                      79************99886545553222333448888888888885555433444455666655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.2
                            AAA_28  78 cDrglldtlaYarayggeaeaelea.aarekrydl.vfllppap 119
                                       +Dr ++d+++ +++y+ +   el+    + kr d+ v+l  ++ 
  gi|336252497|ref|YP_004595604.1| 129 IDRVVIDSTMLLEYYFSDEVGELVTfLTKLKRADAtVLLISEMT 172
                                       699************99955566665888999999777777655 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 !   15.1   0.0   2.5e-05     0.015       1      17 [.      26      42 ..      26      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                        ATP_bind_1  1 vvGpaGsGKttfvgals 17
                                      v Gp+GsGKttf++++ 
  gi|336252497|ref|YP_004595604.1| 26 VSGPPGSGKTTFCSQFL 42
                                      78************986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     3e-05     0.018       2      22 ..      24      44 ..      23     173 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkk 22
                                       ++ G+pGsGK+t+  + l k
  gi|336252497|ref|YP_004595604.1| 24 YIVSGPPGSGKTTFCSQFLTK 44
                                      6899**********9998754 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.6e-05     0.022      17      57 ..       1      41 [.       1      51 [. 0.94

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-05
                                      -EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                             Rad51 17 lqlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57
                                      ++l+tG   +Del++GG+    +  + G  +sGkt +c ++
  gi|336252497|ref|YP_004595604.1|  1 MRLSTGVPGFDELVDGGLLRDRLYIVSGPPGSGKTTFCSQF 41
                                      579***********************************985 PP

>> AAA_18  AAA 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     0.028       2      18 ..      25      41 ..      25      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.6e-05
                            AAA_18  2 lltGtpGvGKttlakeL 18
                                      +++G+pG+GKtt++   
  gi|336252497|ref|YP_004595604.1| 25 IVSGPPGSGKTTFCSQF 41
                                      699***********876 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00075      0.45      34      88 ..       3      56 ..       1      69 [. 0.85
   2 ?    1.3   0.0      0.32   1.9e+02     125     141 ..     122     138 ..     109     148 .. 0.83
   3 ?   -0.9   0.0       1.6   9.3e+02      32      62 ..     181     212 ..     165     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00075
                                      E--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                              RecA 34 issGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafid 88
                                      +s+G  ++d  +  GGl + r+  + Gp  sGktt++ + +++   +g +a ++ 
  gi|336252497|ref|YP_004595604.1|  3 LSTGVPGFDELVD-GGLLRDRLYIVSGPPGSGKTTFCSQFLTKGVFEGETALYVS 56
                                      5777777777665.9***********************99999999999988876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.32
                                       HHHTTT--SEEEEE-TT CS
                              RecA 125 alvrsgaidlivvdsva 141
                                       ++++s +id +v+ds  
  gi|336252497|ref|YP_004595604.1| 122 SFIESKGIDRVVIDSTM 138
                                       5799**********975 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.6
                                       -EE--S-HHHHHHTSSSSEETT.SEEEEEEST CS
                              RecA  32 etissGslaldialGiGGlpkG.riieiyGpe 62 
                                       + +s G + + + l  GG+ +G +ii++ G+e
  gi|336252497|ref|YP_004595604.1| 181 HYLSHGVIFMHNYLESGGMTRGvQIIKMRGTE 212
                                       56889999999999*******96688888877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.3e-05     0.032      25      46 ..      22      43 ..      10      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.3e-05
                            AAA_16 25 elvllsGesGvGKsslvrellr 46
                                      +l ++sG++G+GK++   ++l+
  gi|336252497|ref|YP_004595604.1| 22 RLYIVSGPPGSGKTTFCSQFLT 43
                                      7899*************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 ?   14.4   0.0   4.3e-05     0.026      20      71 ..      21      79 ..      18     168 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-05
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesi..skldefie......e 71
                                      ++ y + Gp gsGKt++  +++++    ++  +y++  ++e++  s +++f e       
  gi|336252497|ref|YP_004595604.1| 21 DRLYIVSGPPGSGKTTFCSQFLTKGVFEGETALYVSMHESEQElvSDMTNF-EfgfdkaV 79
                                      568999*******************99999999987655444311445555.24543321 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 ?   12.7   0.0   8.2e-05     0.049     127     151 ..      19      43 ..       7      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.2e-05
                             T2SSE 127 rerglilvsGgTgsGKttllyallk 151
                                        +  l +vsG+ gsGKtt+    l+
  gi|336252497|ref|YP_004595604.1|  19 LRDRLYIVSGPPGSGKTTFCSQFLT 43 
                                       5567789***********9987765 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0     0.001      0.62      19      83 ..       3      66 ..       1      70 [. 0.84
   2 ?    2.3   0.0      0.12        73     191     243 ..     116     160 ..      72     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.001
                            PAXNEB 19 tStGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlr 83
                                       StG+p +D+l+ GGL    + ++      + +++ +  Fl  Gv ++ + l++s++++++e+++
  gi|336252497|ref|YP_004595604.1|  3 LSTGVPGFDELVDGGLLRDRLYIVSG-PPGSGKTTFCSQFLTKGVFEGETALYVSMHESEQELVS 66
                                      6***************8888777774.355556667889*****************999999876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.12
                            PAXNEB 191 iqqllkkesfsaptkknvlRivipsLlspllydyppeeskpedllkFLhsLra 243
                                       ++++l +  f ++  k + R+vi s +    y     +++  +l++FL++L+ 
  gi|336252497|ref|YP_004595604.1| 116 LSNKLVS--FIES--KGIDRVVIDSTMLLEYYF----SDEVGELVTFLTKLKR 160
                                       3333333..3333..4589****9987766644....8999999****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 ?   11.7   0.0   0.00024      0.14       3      22 ..      24      43 ..      22      64 .. 0.87
   2 ?   -1.2   0.0       2.2   1.3e+03      68      94 ..     115     140 ..     107     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                                      EEEEESTTCCHHHHHHHHHC CS
                              cobW  3 tvltGflGsGKTtLlnhlle 22
                                      ++++G++GsGKTt+ ++ l+
  gi|336252497|ref|YP_004595604.1| 24 YIVSGPPGSGKTTFCSQFLT 43
                                      799**********9988874 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.2
                                       -HHHHHHHHHHHHTT-SEEEEEECTTT CS
                              cobW  68 dllkelealeereerldviliEttGla 94 
                                       +l+++l ++ e +  +d+++i +t l+
  gi|336252497|ref|YP_004595604.1| 115 NLSNKLVSFIESK-GIDRVVIDSTMLL 140
                                       5666666666766.6888888887555 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 ?   12.7   0.0   0.00013     0.078      50      90 ..      24      64 ..      12      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                         IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveel 90
                                       ++ Gp+G GK+ +   + +++v +g   l+v++++  +el
  gi|336252497|ref|YP_004595604.1| 24 YIVSGPPGSGKTTFCSQFLTKGVFEGETALYVSMHESEQEL 64
                                      5789******************************9877776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014     0.084      24      73 ..      25      69 ..      11      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                                      EEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXH CS
                            NB-ARC 24 alvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletil 73
                                       ++G +G+GKtt  +q l k     g F++   + vs + +++e++ ++ 
  gi|336252497|ref|YP_004595604.1| 25 IVSGPPGSGKTTFCSQFLTK-----GVFEGETALYVSMHESEQELVSDMT 69
                                      589***************99.....9999999999999999999988875 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012     0.071       2      46 ..      22      64 ..      21      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                           DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlv 46
                                      ++++V+G +G+GKt   +++l++     e++ta y+s  +++++ 
  gi|336252497|ref|YP_004595604.1| 22 RLYIVSGPPGSGKTTFCSQFLTKG--VFEGETALYVSMHESEQEL 64
                                      689******************998..8888888888877777665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00032      0.19       3      20 ..      25      42 ..      23      51 .. 0.87
   2 ?   -1.5   0.0       3.6   2.1e+03     102     117 ..     146     161 ..     112     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                                      EEE--TTSSHHHHHHHHH CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvl 20
                                      +++GppG+GKtT++++ l
  gi|336252497|ref|YP_004595604.1| 25 IVSGPPGSGKTTFCSQFL 42
                                      79************9865 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.6
                                       ---STTGGG-HHHHHH CS
                          NTPase_1 102 DEiGkmElkskkfkea 117
                                       DE+G++  +  k+k+a
  gi|336252497|ref|YP_004595604.1| 146 DEVGELVTFLTKLKRA 161
                                       7888887777777766 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   0.00023      0.14       2      36 ..      25      55 ..      24      75 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvys 36
                                      +++Gp+g GK+t++ ++ ++      ++ +  +y+
  gi|336252497|ref|YP_004595604.1| 25 IVSGPPGSGKTTFCSQFLTKGV----FEGETALYV 55
                                      689************9544332....344444444 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 ?   12.1   0.0    0.0002      0.12       2      32 ..      25      62 ..      24      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrts.......liltvnrpta 32
                                      +v+G pG+GK+t + ++l +        l ++++ +  
  gi|336252497|ref|YP_004595604.1| 25 IVSGPPGSGKTTFCSQFLTKGvfegetaLYVSMHESEQ 62
                                      79****************98665555555555555544 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    0.0003      0.18       1      22 [.      22      43 ..      22      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                                      SCEEEEC-TTTCHHHHHHHHHH CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklal 22
                                      rl i+ G++GsGKTt+  ++ +
  gi|336252497|ref|YP_004595604.1| 22 RLYIVSGPPGSGKTTFCSQFLT 43
                                      6789************988765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00039      0.23      18      36 ..      21      39 ..      15      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                            AAA_30 18 drvavltGpAGtGKttalk 36
                                      dr+ ++ Gp+G+GKtt  +
  gi|336252497|ref|YP_004595604.1| 21 DRLYIVSGPPGSGKTTFCS 39
                                      6799************876 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00041      0.24       2      15 ..      28      41 ..      27      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00041
                                      E-TTSSHHHHHHHH CS
                            AAA_17  2 GgPGsGKgtqcekl 15
                                      G+PGsGK+t c++ 
  gi|336252497|ref|YP_004595604.1| 28 GPPGSGKTTFCSQF 41
                                      9**********986 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00034       0.2      17      40 ..      21      44 ..      12      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                            AAA_11 17 seitliqGPPGtgKTktivellsq 40
                                      + + +++GPPG+gKT++  ++l +
  gi|336252497|ref|YP_004595604.1| 21 DRLYIVSGPPGSGKTTFCSQFLTK 44
                                      45689***********99888765 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00063      0.38      18      68 ..      39      89 ..      35     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00063
                              MEDS 18 vpfikaglargekvlyvasastldelrealrkagldvdaalesgqleilda 68
                                      ++f+++g+ +ge  lyv   ++++el + + + +   d+a+ sg+++++d 
  gi|336252497|ref|YP_004595604.1| 39 SQFLTKGVFEGETALYVSMHESEQELVSDMTNFEFGFDKAVSSGKMKFMDV 89
                                      68*************99999**************************99986 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:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 1657.39
//
Query:       gi|336252498|ref|YP_004595605.1|  [L=207]
Description: hypothetical protein Halxa_1092 [Halopiger xanaduensis SH-6]
Scores for 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   12.1   0.1       0.21   11.4   0.1    1.3  1  GspL_C    GspL periplasmic domain


Domain annotation for each model (and alignments):
>> GspL_C  GspL periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   1.2e-05      0.21      77     150 ..      33     106 ..      25     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.2e-05
                                       -HHHHHHHHHHHHHHHTSTT-EEEEEEEETTTTCEEE.EEEESSCHHHHHHHHHHHCTEEEEEEEEEEETTEEEE CS
                            GspL_C  77 gdallkllaalqtaleqvpelelqsldYdgkrgelrl.qleakdfaafeqlrakaatkfqveqgqlasegdkvsg 150
                                       g++ ++ l ++++a++ + + +  +l Y ++r+++r  + e++   +++ql ++ ++ + +  +++ s+g++   
  gi|336252498|ref|YP_004595605.1|  33 GKDHPGELERISDATATNYDRSFAELAYQKGRQHVRQlEGEGSPREIWQQLVTEKNE-LDLWADPAGSGGSSDDT 106
                                       66778899***************************955*************999999.55555566655555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1609.09
//
Query:       gi|336252499|ref|YP_004595606.1|  [L=257]
Description: hypothetical protein Halxa_1093 [Halopiger xanaduensis SH-6]
Scores for 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-14   51.9   0.7    9.9e-14   51.9   0.7    1.9  2  SNARE_assoc  SNARE associated Golgi protein


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 ?   -1.7   0.3      0.21   3.8e+03      87      92 ..      26      31 ..       6      60 .. 0.53
   2 !   51.9   0.7   5.5e-18   9.9e-14       2     119 ..      68     204 ..      67     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.21
                       SNARE_assoc 87 yvaGlt 92
                                      ++aG++
  gi|336252499|ref|YP_004595606.1| 26 VTAGVL 31
                                      222222 PP

  == domain 2  score: 51.9 bits;  conditional E-value: 5.5e-18
                       SNARE_assoc   2 PsevllvaaGvlfglllgtlvtslgallGaslayllgrylgr...............kalrrkllsekrvka....l 59 
                                       P++ l+v++G+ +g+ lg++++++g+l+  + ++l++r l                 + ++ +   e+++++    +
  gi|336252499|ref|YP_004595606.1|  68 PTTPLSVVVGYGYGVALGVPIALAGILVTVLPVFLAVRLLSGsdngtteaaantdadREAVGAGTLERALRRtdaaV 144
                                       9999************************************9998888888777555533333333333333334444 PP

                       SNARE_assoc  60 erlverygfla.....llllrllpivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                       +r+ e     a     ++ +rl pi P+d+++++a++++v++ +F+++t+iG +pw++  +++G+
  gi|336252499|ref|YP_004595606.1| 145 DRYYET----AgptrgVIASRLAPI-PSDAATCAAATSDVRLHQFLVGTAIGELPWTVAAVVVGA 204
                                       444444....244445********6.8**********************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1972.92
//
Query:       gi|336252500|ref|YP_004595607.1|  [L=155]
Description: hypothetical protein Halxa_1094 [Halopiger xanaduensis SH-6]
Scores for 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  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1197.90
//
Query:       gi|336252501|ref|YP_004595608.1|  [L=428]
Description: hypothetical protein Halxa_1095 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.092   12.8   0.0       0.18   11.9   0.0    1.4  1  bPH_1     Bacterial PH domain
       0.12   13.0   4.1       0.43   11.2   4.1    2.0  1  SlyX      SlyX


Domain annotation for each model (and alignments):
>> bPH_1  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.18      25     111 ..     106     187 ..     102     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                                       GCGCT--EEEEEE-TSEEEEEESSEEEEEE---SSS--EEEEEEETTTEEEEEEEEESTTSSEEEEEEEETTTCCEE CS
                             bPH_1  25 llidgEkilfafklirDevvFTnkrlilvdkqgvtgkKkeyksipyssIsevsiEtagtfDldaeLkiwisgeeepi 101
                                       + ++gE++ +++++++ +++ T++rl+   + g ++   +y+ ++y+ +++ s+E    +    ++ + ++g+ + i
  gi|336252501|ref|YP_004595608.1| 106 ITEPGETVAKTYRFSELTLIVTSERLVK--HIGSAVWDEDYEEYHYEDVTNLSFEDGS-VA--TQIVLEVDGRPQRI 177
                                       6789*********************976..556677789**************99643.33..46666666666656 PP

                                       EEECGCCCHH CS
                             bPH_1 102 kvefkkkedi 111
                                       k   ++  d+
  gi|336252501|ref|YP_004595608.1| 178 KAPNEEANDL 187
                                       6555555555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.1   4.8e-05      0.43      11      42 ..     395     426 ..     391     428 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX  11 klafqedtieeLndvvaeqqqqidrlqrqlrl 42 
                                       +l  +e ++e+ +dv+ +qq++i++l ++lr+
  gi|336252501|ref|YP_004595608.1| 395 RLEALEAAVERQSDVIEQQQRTIEQLIEELRQ 426
                                       66678889999999999999999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1261  (0.070333); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 3126.95
//
Query:       gi|336252502|ref|YP_004595609.1|  [L=100]
Description: hypothetical protein Halxa_1096 [Halopiger xanaduensis SH-6]
Scores for 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-22   77.6   1.9    8.8e-22   77.2   1.9    1.2  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   1.9   4.9e-26   8.8e-22       3      74 ..       5      80 ..       3      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 4.9e-26
                            HalOD1  3 espstaVveavaavegvdptel.epLydaiDpdALdaLfasradge...aradgsvsFtyegyeVtVrsdgeieVe 74
                                      e+ps++Vvea+aa+egvdp +l +pLyd+ DpdALd+L +s ++g+   ++a ++v+Fty+ y+V V+   e+ V+
  gi|336252502|ref|YP_004595609.1|  5 EQPSVRVVEAIAAAEGVDPAALePPLYDVLDPDALDTLTDSLCRGAdqfDDAAARVEFTYRTYRVEVEIGDEVDVT 80
                                      89********************666****************888884445666********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 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:                        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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 769.67
//
Query:       gi|336252503|ref|YP_004595610.1|  [L=354]
Description: DNA methylase N-4/N-6 domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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  119.9   0.0    1.7e-34  119.6   0.0    1.1  1  N6_N4_Mtase      DNA methylase
  ------ inclusion threshold ------
      0.078   12.7   0.0        5.4    6.6   0.0    2.3  2  UPF0020          Putative RNA methylase family UPF0020
       0.13   12.9   0.3         11    6.7   0.2    3.1  2  Methyltransf_11  Methyltransferase domain


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 !  119.6   0.0   2.8e-38   1.7e-34       1     227 [.      23     268 ..      23     272 .. 0.89

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 2.8e-38
                                       EEEEEE--SSSSSCS.................GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT.. CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy............endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk.. 63 
                                       + l+vt+pPY + + +               e  ++   +e+++  l +v++e+ rvL d+g++++n++d + +   
  gi|336252503|ref|YP_004595610.1|  23 IELVVTSPPYPMIEMWddlfadldpavaDALEAGDGRRAFEAMHAQLDRVWDELERVLVDGGIACVNVGDATRSVdg 99 
                                       689**********************99877888888889*********************************988** PP

                                       ........HHHHHHHHHTT-EEEEEEEEEEES.........SSTTTSTCCS-B--EEEEEEEESSTT-..---GGGS CS
                       N6_N4_Mtase  64 ........elkaladeifggffllnvivwkkp.........nsmpesnkdrltsthEyilvfsknkkyllkfnldai 123
                                                +++ a e+ g f  l ++ w+kp         ++m  +n+ ++t +hEyilvf+k+++          
  gi|336252503|ref|YP_004595610.1| 100 sfrvypnhARVLEAFESRG-FDPLPDVLWRKPansaakfmgSGMIPPNA-YVTLEHEYILVFRKGGES--------- 165
                                       ******9999999999999.*************9999999779999998.******************......... PP

                                       SBSS-HHHHHHHHHHCHHHCC-B--BSEEE-SCCCTTSTTS-CHH.----SS---HHHHHHHHHHHS-TT-EEEETT CS
                       N6_N4_Mtase 124 kvpyeekdklekrgaytskkkgkkiediWdlseiqsnekkskgdt.kkkHpaqkPvallerlIklstkkgdivlDpF 199
                                         ++e  + ++++ ay+ ++++++++d+W  ++   ++ +s+ d+ +++  a  P++++ rlI +++  gd+vlDpF
  gi|336252503|ref|YP_004595610.1| 166 -REFEPGADRRYEAAYFWEERNRWFSDVWTEVRGELQALESPDDDlRER-SAAYPLEIPYRLICMYSAYGDTVLDPF 240
                                       .44444444445555899***********65555555566665556777.9************************** PP

                                       -TTTHHHHHHHHTT-EEEEEESSHHHHH CS
                       N6_N4_Mtase 200 aGSGtTavaakelgrkfiGieieeeyve 227
                                        G+GtT  aa+  gr++iG+e e  ++e
  gi|336252503|ref|YP_004595610.1| 241 WGTGTTTLAALCAGRDSIGYELEAAFLE 268
                                       **********************988776 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0    0.0066        39     108     131 ..       8      32 ..       1      53 [. 0.88
   2 ?    6.6   0.0   0.00091       5.4      29      54 ..     233     258 ..     227     340 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0066
                                       EE--GGG--.STTS---EEEE---- CS
                           UPF0020 108 sqadaakLr.lkegevdvivtnpPY 131
                                        + da++L   ++++++++vt pPY
  gi|336252503|ref|YP_004595610.1|   8 FVGDARDLSaVDDESIELVVTSPPY 32 
                                       56799999987778*********** PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00091
                                       TS-EEETT-TTSHHHHHHHHHHTT-- CS
                           UPF0020  29 gepllDPmCGsGtilIEaallgania 54 
                                       g++ lDP+ G+Gt  + a   g++ +
  gi|336252503|ref|YP_004595610.1| 233 GDTVLDPFWGTGTTTLAALCAGRDSI 258
                                       899**********9987766666666 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0019        11      75      95 ..      59      87 ..       2      88 .. 0.62
   2 ?    1.4   0.0     0.087   5.2e+02       6      63 ..     242     314 ..     237     324 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0019
                                      C........CHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11 75 e........dpekalkeiaRvLkpgGllv 95
                                               +++++++e+ RvL  gG+ +
  gi|336252503|ref|YP_004595610.1| 59 RrafeamhaQLDRVWDELERVLVDGGIAC 87
                                      0444444458999************9976 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.087
                                       TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-...............EEEETTEECCCTSS-TT-EE CS
                   Methyltransf_11   6 GtGrlaealakrgarvvgvDlskemlklakekaseegl...............kvefvvadaeklpfednsfD 63 
                                       GtG  + a   +g++ +g +l +++l++ +++  + +                 v+ ++ad +++ +  + +D
  gi|336252503|ref|YP_004595610.1| 242 GTGTTTLAALCAGRDSIGYELEAAFLERFENQLADVPAlsrsvgrtrlerhreFVSQRRADGSTFDYDAEHYD 314
                                       5566666555567888888888888888776666655544433333333322233336666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); 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:                         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: 2458.84
//
Query:       gi|336252504|ref|YP_004595611.1|  [L=189]
Description: hypothetical protein Halxa_1098 [Halopiger xanaduensis SH-6]
Scores for 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   16.2   0.2     0.0048   15.6   0.2    1.1  1  Peptidase_S46  Peptidase S46
  ------ inclusion threshold ------
        7.6    6.8  11.3        2.1    8.6   1.8    2.5  2  PEP-CTERM      PEP-CTERM motif


Domain annotation for each model (and alignments):
>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   5.4e-07    0.0048      85     131 ..      62     109 ..      60     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.4e-07
                                       -EE-SSGGGSBE-.TT--EEEEEEEEE-HHHHTTTTTTSS-CHHHHHH CS
                     Peptidase_S46  85 GFlAksreeElpa.pglrvtvleritdVTkrvkaalkaeeeeeeraka 131
                                       GFlA +++ El+  p   ++  e i+dVT+r +++++++e+e+e++++
  gi|336252504|ref|YP_004595611.1|  62 GFLAGRQSTELEEsPLEDIEEPEIIEDVTERAESQMASDETETEMESE 109
                                       9***********99***********************99999998765 PP

>> PEP-CTERM  PEP-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   2.3     0.015   1.4e+02       9      22 ..      53      67 ..      49      68 .. 0.69
   2 ?    8.6   1.8   0.00023       2.1       9      23 .]     122     138 ..     119     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.015
                         PEP-CTERM  9 lLlGlG.llGlalrR 22
                                      + +GlG +lG+++ R
  gi|336252504|ref|YP_004595611.1| 53 AVFGLGaALGFLAGR 67
                                      689**9677754445 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00023
                         PEP-CTERM   9 lLlGlG.llG.lalrRr 23 
                                       lLl+lG ++G ++lrRr
  gi|336252504|ref|YP_004595611.1| 122 LLLALGvVAGaVFLRRR 138
                                       7999*945559999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1290.53
//
Query:       gi|336252505|ref|YP_004595612.1|  [L=230]
Description: hypothetical protein Halxa_1099 [Halopiger xanaduensis SH-6]
Scores for 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  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1669.08
//
Query:       gi|336252506|ref|YP_004595613.1|  [L=196]
Description: NADPH-dependent FMN reductase [Halopiger xanaduensis SH-6]
Scores for 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-35  120.9   0.0    4.6e-35  120.7   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    1.1e-10   41.5   0.0    1.6e-10   41.0   0.0    1.2  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 !  120.7   0.0   5.1e-39   4.6e-35       2     153 ..       6     147 ..       5     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 5.1e-39
                                       EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEE CS
                           FMN_red   2 kilvisGSlrkgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadalii 78 
                                        i++++GSlr+ s tr ++e+a+ea++e ga++elidl++++lp   +d d +   ++  d++ l e++++ada+++
  gi|336252506|ref|YP_004595613.1|   6 HIAAVCGSLRDASATRLALERALEAAAEGGATTELIDLREYDLP--TFDPDRDR--EDAGDAELLAERLREADAIVL 78 
                                       699*************************9***************..99988854..699999*************** PP

                                       EEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEEEETSH CS
                           FMN_red  79 vtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraavavgka 153
                                       +tP Y+gsys++lK+alD+ +     +e+r+K v+l+av+gg +    a e+lr+v++ l+a+v+p+ +va++k 
  gi|336252506|ref|YP_004595613.1|  79 GTPMYHGSYSSPLKAALDYSG----FDEFRDKTVGLLAVSGG-AFPVTALEHLRSVCRALNAWVLPH-EVAIPKS 147
                                       ********************8....9**************99.77889*******************.9999886 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   1.8e-14   1.6e-10       5     102 ..       9      97 ..       6     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.8e-14
                                       EEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTTC.HHHHHHHHHHHHCSSE CS
                      Flavodoxin_2   5 iinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeekp.adveseqiekllaada 80 
                                        + ++ r   s ++ ++++++ea+++ g ++ + +dL +  lp +++       + +++   d+e  + e+l++ada
  gi|336252506|ref|YP_004595613.1|   9 AVCGSLRD-ASATRLALERALEAAAEGG-ATTELIDLREYDLPTFDP-------DRDREDaGDAELLA-ERLREADA 75 
                                       56677777.5999***************.9****************9.......44443337777777.******** PP

                                       EEEEEE-BTTB--HHHHHHHHH CS
                      Flavodoxin_2  81 ivlqfPlwwfgvPailKgwiDr 102
                                       ivl++P++  ++++ lK+ +D+
  gi|336252506|ref|YP_004595613.1|  76 IVLGTPMYHGSYSSPLKAALDY 97 
                                       *****************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1528.60
//
Query:       gi|336252507|ref|YP_004595614.1|  [L=363]
Description: daunorubicin resistance ABC transporter ATPase subunit [Halopiger xanaduensis SH-6]
Scores for 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-30  103.9   0.0    1.4e-29  103.4   0.0    1.2  1  ABC_tran         ABC transporter
    1.2e-14   54.9   0.0    8.6e-10   38.9   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    9.1e-08   32.7   0.0    1.7e-07   31.9   0.0    1.5  1  DUF4162          Domain of unknown function (DUF4162)
     0.0033   17.1   0.0     0.0072   16.1   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
     0.0096   15.7   0.0        2.2    7.9   0.0    2.1  2  AAA_15           AAA ATPase domain
  ------ inclusion threshold ------
      0.012   15.0   0.0        1.5    8.2   0.0    2.3  2  SMC_N            RecF/RecN/SMC N terminal domain
      0.023   14.6   0.0      0.032   14.1   0.0    1.1  1  Rad17            Rad17 P-loop domain
      0.029   14.9   0.8      0.053   14.0   0.7    1.3  1  AAA_23           AAA domain
      0.029   14.8   0.0       0.15   12.5   0.0    2.1  1  AAA              ATPase family associated with various cellul
      0.031   14.7   0.1      0.073   13.5   0.1    1.7  1  AAA_16           AAA ATPase domain
       0.04   13.6   0.0      0.072   12.8   0.0    1.5  1  AAA_30           AAA domain
      0.079   12.8   0.1       0.14   12.0   0.1    1.3  1  Erythro_esteras  Erythromycin esterase
       0.08   12.6   0.0       0.12   12.0   0.0    1.2  1  SRP54            SRP54-type protein, GTPase domain
        0.2   11.0   0.0       0.31   10.4   0.0    1.3  1  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 !  103.4   0.0   1.1e-32   1.4e-29       2     136 ..      51     193 ..      50     194 .. 0.93

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 1.1e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + v+l++ +ge  +++G+nGaGK+t +k++a ll+pt Ge++++g d+++    + r++ig++ qe++++pelt++e
  gi|336252507|ref|YP_004595614.1|  51 RGVDLTVPQGEFFGFLGPNGAGKTTTIKVFATLLSPTDGEVRVNGFDVQS-APGKIRESIGYMAQETSVDPELTAEE 126
                                       5799**********************************************.77889********************* PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e+ ++++++l+ ++l +++d+++     ++SgG+k+r+  a al+ +p+l++lDEpt
  gi|336252507|ref|YP_004595614.1| 127 NlrfaceaygvprgERADRVAELLDLVELADVADKRA----DEFSGGMKKRLDAATALVHRPPLVFLDEPT 193
                                       ***********77777777777777777777777777....*****************************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 !   14.1   0.0   2.4e-05     0.031       1      25 [.      62      86 ..      62     126 .. 0.76
   2 !   38.9   0.0   6.7e-13   8.6e-10     234     297 ..     163     223 ..     132     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                      + ++ GpNg+GK++ ++ +  l + 
  gi|336252507|ref|YP_004595614.1| 62 FFGFLGPNGAGKTTTIKVFATLLSP 86
                                      56799**************988663 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 6.7e-13
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       a+e+S G+k+ l  +tal  ++   +l+++DEp +gL+Pk+  rl++ +++ +++g+ ++ltT+
  gi|336252507|ref|YP_004595614.1| 163 ADEFSGGMKKRLDAATALVHRP---PLVFLDEPTTGLDPKARNRLWDYFRDINDRGTTIFLTTQ 223
                                       6789****************99...************************999999********7 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.3e-10   1.7e-07       1      80 [.     247     339 ..     247     340 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.3e-10
                                       E-HHHHHTTS-SSEEEEE........-------...---EEE..E-TTS-EEEEE--.-----------.----EEE CS
                           DUF4162   1 GtleeiKrsygknrieve........adaeellee.pgveev..eeeggelelkled.eeaanellkal.tsgveir 64 
                                       G++  +Kr+ g++ + +e        + a+e+++e +g+e+   + ++++++++ e   +   +ll al ++g++++
  gi|336252507|ref|YP_004595614.1| 247 GSPAALKRRVGGEVLDLEldggrparDRAAEIAREfDGFEDAtvSVTDEGVSVTAEAaRQRGTDLLVALrDAGLTVT 323
                                       89999*************98877664224443333366777655555677999999889**********77****** PP

                                       EEEEE---HHHHHHHH CS
                           DUF4162  65 sFeeeePsLndIFiek 80 
                                        F+++ P+L+d+F+  
  gi|336252507|ref|YP_004595614.1| 324 GFNVRSPTLDDVFLAI 339
                                       *************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 !   16.1   0.0   5.6e-06    0.0072      19      55 ..      57      94 ..      47      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.6e-06
                            AAA_29 19 idlkg.atlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      +  +g ++ + Gp+G+GK+T +  +++lL p+  +vr N
  gi|336252507|ref|YP_004595614.1| 57 VP-QGeFFGFLGPNGAGKTTTIKVFATLLSPTDgEVRVN 94
                                      54.44478899********************98788777 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0017       2.2      28      50 ..      65      87 ..      54     129 .. 0.85
   2 !    5.7   0.0    0.0078       9.9     326     363 ..     186     222 ..     179     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                            AAA_15 28 liGkNnsGKSsilealdlFlnnk 50
                                      + G+N++GK++ ++++  +l+ +
  gi|336252507|ref|YP_004595614.1| 65 FLGPNGAGKTTTIKVFATLLSPT 87
                                      88**************9999866 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0078
                            AAA_15 326 illiEEPEahLHpqaqkvlikllkelandnktQviitT 363
                                       +++++EP + L p+a + l+++++++ + +   +++tT
  gi|336252507|ref|YP_004595614.1| 186 LVFLDEPTTGLDPKARNRLWDYFRDINDRGT-TIFLTT 222
                                       799**********************999886.899998 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 ?    4.4   0.0     0.016        21      26      44 ..      62      80 ..      52      97 .. 0.76
   2 ?    8.2   0.0    0.0011       1.5     136     208 ..     165     231 ..     126     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.016
                                      EEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                      f   +GpNG+GK+  +   
  gi|336252507|ref|YP_004595614.1| 62 FFGFLGPNGAGKTTTIKVF 80
                                      66678********887655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0011
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadkl 208
                                       ++SgG k+     L  A+  v++ pl++lDe    LD k ++++ ++++  +++   i   l+++ le+ad+l
  gi|336252507|ref|YP_004595614.1| 165 EFSGGMKK----RLDAATALVHRPPLVFLDEPTTGLDPKARNRLWDYFRDINDRGTTIF--LTTQYLEEADQL 231
                                       66777666....334466678999************************98886654443..445566666655 PP

>> Rad17  Rad17 P-loop 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     0.032      51     114 ..      66     130 ..      59     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-05
                             Rad17  51 sGPsGCgkstvvkvLskelgiklre.wlnpvslkepdnqksdfkgltekesrflsqiesfkeleL 114
                                        GP G gk+t++kv +  l++   e  +n+  +++++ +  +  g + +e +  + + + ++l  
  gi|336252507|ref|YP_004595614.1|  66 LGPNGAGKTTTIKVFATLLSPTDGEvRVNGFDVQSAPGKIRESIGYMAQETSVDPELTAEENLRF 130
                                       59*****************998766369***********99999999999888777766555544 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.7   4.1e-05     0.053      21      43 ..      62      84 ..      51     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-05
                            AAA_23 21 ltlItGpNGaGKTTildAiklaL 43
                                      ++ + GpNGaGKTT +  +   L
  gi|336252507|ref|YP_004595614.1| 62 FFGFLGPNGAGKTTTIKVFATLL 84
                                      7889**********998877766 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   0.00012      0.15       3      35 ..      65      99 ..      63     240 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                      EESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelgve..fleisgsell 35
                                      + Gp G GKT+++k  a+ l+ +   ++++g ++ 
  gi|336252507|ref|YP_004595614.1| 65 FLGPNGAGKTTTIKVFATLLSPTdgEVRVNGFDVQ 99
                                      68***************999744113444444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.7e-05     0.073      29     143 ..      65     191 ..      53     229 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-05
                            AAA_16  29 lsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysa.laqalareellrqlldeaesaeleawreklee 103
                                       + G+ G GK++ ++ +++ l+ ++g + ++g  +q+   +p    + + +   ++++q+ + + +  +e+  ++ +e
  gi|336252507|ref|YP_004595614.1|  65 FLGPNGAGKTTTIKVFATLLSPTDGEVrVNGFDVQS---AP--GkIRESI---GYMAQETSVDPELTAEENLRFACE 133
                                       68***************9999997666455544444...22..1233444...344444444444444555555555 PP

                            AAA_16 104 ala.................avpelagaeasrllellkrll.allsrderplvlvlDd 143
                                       a++                 + +++a++ a  +   +k+ l a ++  +rp +++lD+
  gi|336252507|ref|YP_004595614.1| 134 AYGvprgeradrvaelldlvELADVADKRADEFSGGMKKRLdAATALVHRPPLVFLDE 191
                                       5556666666666666666667777777778888888888866666666678888885 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.6e-05     0.072      23      71 ..      65     114 ..      53     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                            AAA_30  23 ltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Laeelgieas 71 
                                         Gp G+GKtt++k+ + ++    g+v +     + A   ++e++g  a+
  gi|336252507|ref|YP_004595614.1|  65 FLGPNGAGKTTTIKVFATLLSPTDGEVRVNGFDVQSAPGkIRESIGYMAQ 114
                                       679*****************999888888777766665447777776444 PP

>> Erythro_esteras  Erythromycin esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00011      0.14      65     111 ..      88     136 ..      84     183 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                       SS--EEEEEE-S---HHHHHHHHHHHHC...HCCCCHHHHHHHCCHGGCS CS
                   Erythro_esteras  65 kervrfyGlDlqslresldavldyLakv...dpelagaareryaclapla 111
                                       + +vr+ G+D+qs   ++++ + y+a+    dpel ++ + r+ac  +++
  gi|336252507|ref|YP_004595614.1|  88 DGEVRVNGFDVQSAPGKIRESIGYMAQEtsvDPELTAEENLRFACE-AYG 136
                                       445***********************998889**********9997.443 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.4e-05      0.12       6      38 ..      65      97 ..      61     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.4e-05
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      ++G++GaGKTtt+   a ll+    +v +   D
  gi|336252507|ref|YP_004595614.1| 65 FLGPNGAGKTTTIKVFATLLSPTDGEVRVNGFD 97
                                      79************9999998877777666666 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00024      0.31      26      66 ..      64     104 ..      44     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                      Mg_chelatase  26 llvGppGsGKtmlakrlpsllpplseeealevakiasvagk 66 
                                        ++Gp G+GKt  +k +++ll+p + e  ++   ++s  gk
  gi|336252507|ref|YP_004595614.1|  64 GFLGPNGAGKTTTIKVFATLLSPTDGEVRVNGFDVQSAPGK 104
                                       589*********************99999999999888774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 2758.70
//
Query:       gi|336252508|ref|YP_004595615.1|  [L=312]
Description: ABC-2 type transporter [Halopiger xanaduensis SH-6]
Scores for 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  10.8    3.3e-33  114.9  10.8    1.1  1  ABC2_membrane    ABC-2 type transporter
    8.5e-17   61.3   8.9    8.5e-17   61.3   8.9    1.5  2  ABC2_membrane_3  ABC-2 family transporter protein
     0.0045   16.3  16.8      0.013   14.8  16.8    1.6  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.12   10.6   2.5       0.17   10.1   2.5    1.3  1  Fusion_gly       Fusion glycoprotein F0


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 !  114.9  10.8   7.3e-37   3.3e-33       3     210 .]      45     261 ..      43     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 7.3e-37
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr............pgllffsvlflafsa 67 
                                       +++ +kr  l+++r+p+ + +++l+qp++++++f+ vfgn+    d++nr            p + +  +l    + 
  gi|336252508|ref|YP_004595615.1|  45 VWVNFKRWNLKAVRNPFVL-VVSLVQPIIFLVLFTEVFGNVA--GDAVNRgipgigyetylvPAIAIQVALAA--AV 116
                                       78999***********999.99*****************864..45556677778889997444444444444..59 PP

                     ABC2_membrane  68 ltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls...rf.flfllllllt 140
                                       ++++++v ++e+g++e+ lvsp+  + a++++k+++e+ ++++q++i+l + ++l g ++    ++ + ++++ +l+
  gi|336252508|ref|YP_004595615.1| 117 TSGIGLVNDIENGMFEKVLVSPM-NRTAVFVGKTAAEVFRIAVQVAIILGLGVLL-GAEIAtglAGaLGIVAVGVLF 191
                                       ***********************.******************************9.999998775579999****** PP

                     ABC2_membrane 141 alaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnlf 210
                                       +l +++++ ++++l++++e  ++ a+l+ +pll+ls +f p++++p+w++ +a++nP+ty+v+a rs ++
  gi|336252508|ref|YP_004595615.1| 192 SLWFIAFSNALAILTRDQESTIIGANLLQFPLLFLSSAFLPLETLPGWIRTFARFNPVTYGVDAARSLML 261
                                       ******************************************************************9985 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 ?   -1.7   0.1      0.27   1.2e+03     214     230 ..      63      82 ..      61      98 .. 0.64
   2 !   61.3   8.9   1.9e-20   8.5e-17     158     324 ..      97     267 ..      94     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.27
                   ABC2_membrane_3 214 flvyllqlllilll...afg 230
                                       ++v+l+q +++l+l   +fg
  gi|336252508|ref|YP_004595615.1|  63 LVVSLVQPIIFLVLfteVFG 82 
                                       56777777777665466665 PP

  == domain 2  score: 61.3 bits;  conditional E-value: 1.9e-20
                   ABC2_membrane_3 158 nvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afglg 232
                                       +++ +lv++i+i +++  a+    ++v++ e+++ e  lvs++++++ +++k  + ++  ++q+++il+l  ++g +
  gi|336252508|ref|YP_004595615.1|  97 GYETYLVPAIAIQVALAAAVTSGIGLVNDIENGMFEKVLVSPMNRTAVFVGKTAAEVFRIAVQVAIILGLgvLLGAE 173
                                       68899***9999999999999999********************************************977799987 PP

                   ABC2_membrane_3 233 ipfg..nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPff 307
                                       i  g  + + ++ + +lf+l +ia++ +l  l++++e+++i + ++ ++l++++ ++ ple+lp++++++++++P +
  gi|336252508|ref|YP_004595615.1| 174 IATGlaGALGIVAVGVLFSLWFIAFSNALAILTRDQESTIIGANLLQFPLLFLSSAFLPLETLPGWIRTFARFNPVT 250
                                       877777888899***************************************************************** PP

                   ABC2_membrane_3 308 apglgllrlitgdplwe 324
                                       +  ++  +l+  +  ++
  gi|336252508|ref|YP_004595615.1| 251 YGVDAARSLMLDQDVMT 267
                                       ******99995554444 PP

>> 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 !   14.8  16.8   2.8e-06     0.013      80     213 ..     105     231 ..      53     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-06
                   ABC2_membrane_2  80 imavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivl 156
                                       ++a+ +++ aa+++   ++ + e+g  +  L +P+ R ++ +gK  + +     iav + ++  l+l++ l+ +i++
  gi|336252508|ref|YP_004595615.1| 105 AIAIQVALAAAVTSGIGLVNDIENGMFEKVLVSPMNRTAVFVGKTAAEVFR---IAVQVAII--LGLGVLLGAEIAT 176
                                       566677777888887789999****************************99...77766666..889999999999* PP

                   ABC2_membrane_2 157 aledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivl 213
                                        l+  l +v++ vl+ l   f+a++ +l++++r++++ +  a  l + l++l++ +l
  gi|336252508|ref|YP_004595615.1| 177 GLAGALGIVAVGVLFSL--WFIAFSNALAILTRDQESTIIGANLLQFPLLFLSSAFL 231
                                       *9999999999998888..78************777776666666666666666554 PP

>> Fusion_gly  Fusion glycoprotein F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.5   3.7e-05      0.17      93     119 ..     103     129 ..     100     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.7e-05
                                       EEHHHH-EEEHHHHHHHHHHHHHHHHH CS
                        Fusion_gly  93 lgaiAlgvAtaAqitAgiAlakalkna 119
                                       + aiA+ vA aA++t+gi l++ ++n 
  gi|336252508|ref|YP_004595615.1| 103 VPAIAIQVALAAAVTSGIGLVNDIENG 129
                                       5689******************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2283.31
//
Query:       gi|336252509|ref|YP_004595616.1|  [L=311]
Description: HhH-GPD family protein [Halopiger xanaduensis SH-6]
Scores for 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-17   61.7   0.0    1.2e-16   61.0   0.0    1.3  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
    1.7e-09   37.0   0.0    3.7e-09   36.0   0.0    1.6  1  HHH       Helix-hairpin-helix motif


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 !   61.0   0.0   1.4e-20   1.2e-16       1     107 [.      47     181 ..      47     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 1.4e-20
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTT.HHHHHHHHHHHHHHHH.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.......... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGf.yrrKakyikelArilv.......... 66 
                                       vs+++sqqt+  r+ +++e++ er+  pt  dla+ad ++++  ++ + + y+++aky++e+Ar++           
  gi|336252509|ref|YP_004595616.1|  47 VSEVMSQQTQLDRVVAAWEEFLERW--PTTADLAAADRADVVGFWTDHSLgYNNRAKYLHEAARQVEseyggdfpet 121
                                       799*********************8..9*****************99555367************************ PP

                                       .......................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                       .......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 .......................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                              +  +   vvD++v+r+l r + + ++  ++  e++++el++
  gi|336252509|ref|YP_004595616.1| 122 pdelqelmgvgpytanavasfafN--NGDAVVDTNVKRVLYRAFDVPDD--DEAFEEAAQELMP 181
                                       *********************663..44599***************886..8999999988876 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   4.1e-13   3.7e-09       1      30 []     113     142 ..     113     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 4.1e-13
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                                       +++g++p +++eL++l GVGp+tA+a++s+
  gi|336252509|ref|YP_004595616.1| 113 EYGGDFPETPDELQELMGVGPYTANAVASF 142
                                       599************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2162.53
//
Query:       gi|336252510|ref|YP_004595617.1|  [L=285]
Description: triphosphoribosyl-dephospho-CoA protein [Halopiger xanaduensis SH-6]
Scores for 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  227.2   4.6    3.3e-67  227.1   4.6    1.0  1  CitG      ATP:dephospho-CoA triphosphoribosyl transferase


Domain annotation for each model (and alignments):
>> CitG  ATP:dephospho-CoA triphosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.1   4.6   1.9e-71   3.3e-67       1     281 []       7     277 ..       7     277 .. 0.90

  Alignments for each domain:
  == domain 1  score: 227.1 bits;  conditional E-value: 1.9e-71
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHH CS
                              CitG   1 aelavlAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekaml 77 
                                       a+ a+lAlllEv+ tpKPG+Vdrr++    D++f++Fla+++ +++ +e aa             +++G ++e+a+ 
  gi|336252510|ref|YP_004595617.1|   7 AQHARLALLLEVAGTPKPGNVDRRRDL--ADLRFDHFLAGTVGAQRGLEMAA-----------DGAGVGPAFERAVE 70 
                                       6899***********************..***********************...........5679********** PP

                                       HH..------HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--HHHHHHH.HHHHHH--......--- CS
                              CitG  78 aa..tggvNThkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltvedavaf.rairlakv......eel 145
                                        +  +gg+NT++Ga++ll++l  aa           l   +  +++v++++tv+da+af ra+++++v      e +
  gi|336252510|ref|YP_004595617.1|  71 GMsaQGGGNTQFGALLLLVPLTRAARDD--------L--SQPVVEAVVEDTTVADAAAFyRAFEHVDVfvadppE-D 136
                                       **************************66........3..34459*************************999862.2 PP

                                       ............HHHHHH.TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHH CS
                              CitG 146 ............kdelvekksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallal 210
                                                     +l  +++ltl++v++ s   d +++e+++gF+++f +a  +l+ea   ++   d++++++l l
  gi|336252510|ref|YP_004595617.1| 137 mapldvrrgadaVPALE-ERGLTLLDVMAGSVPGDDVAREWVTGFERSFGAAE-RLAEA---EGPPLDRAAAVFLSL 208
                                       46667777655444444.59******************************555.66664...57888999******* PP

                                       HHHS--HHHHHHHHHHHHHHHHHHHH..........H-SHHHHHHHHHHHHHHT---HHHHHHHHHHHHHH CS
                              CitG 211 laelpDtnilrrgGaegaeevqeeArallaaggvaaeaglealeeldrelvernisPGgsADllaatlfla 281
                                       lae pDt+++ ++G+++a+evqe+A +l+++   a e+++ea+e++ ++lv+r+i+PG++AD++aa+lf+a
  gi|336252510|ref|YP_004595617.1| 209 LAERPDTLVADKHGEDVAREVQERAVELHER--RAVETDREAVEAFADDLVDRGINPGTTADITAAGLFIA 277
                                       *******************************..3444479*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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 0.22s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2101.92
//
Query:       gi|336252511|ref|YP_004595618.1|  [L=216]
Description: hypothetical protein Halxa_1105 [Halopiger xanaduensis SH-6]
Scores for 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-40  138.3   0.0    2.7e-40  138.0   0.0    1.1  1  DUF447    Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.0   0.0   1.5e-44   2.7e-40       1     173 [.      26     207 ..      26     210 .. 0.93

  Alignments for each domain:
  == domain 1  score: 138.0 bits;  conditional E-value: 1.5e-44
                                       EEEEEEEE-TT.-EEEEEEEEEE...SSSE...........EEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHH CS
                            DUF447   1 yEvivtTksek.rpnaaPiGviv...kgdk...........vvlrlfkgsrTleNllengelvinvtdDpllfakaa 62 
                                       +E++vtT++++ r+naa++Gv +   +  +           v++ ++ ++rT  N+ ++ge +++++dDp++f++aa
  gi|336252511|ref|YP_004595618.1|  26 TETVVTTLGPNgRWNAAALGVFAgdsD--SsgdcsdntdsrVTATTWGRTRTRGNFHREGEGYVQFVDDPVVFVDAA 100
                                       6**********************7650..245556666778************************************ PP

                                       HS---GGGEEEETTTCTT.EETT-SEEEEEEEEEE....CTCECCEEEEEEEEEEEEETTB---B-HHHHHHHHHHH CS
                            DUF447  63 lgdleesdfdsetkpakiavlksaeawveveveev....egdsealelelepvkeeileervkpfnRgdaaviEaaV 135
                                       l+ le++d           +l+sa awv+v ve +    e+ +e+ ++el+p+ + ++++ v+++nRg++av+Ea+V
  gi|336252511|ref|YP_004595618.1| 101 LSILERDDP----------ILESAAAWVRVAVEPIergtENGTEWEKWELQPLAATVERTTVPTINRGFGAVVEATV 167
                                       **7777755..........9*************99999999999********************************* PP

                                       HHHCCCC..SHHHHHHHHHHHHHHHHHHH--HHHHHHHHH CS
                            DUF447 136 latRldi..edkeklleeieylssvikktggerekealel 173
                                       +a+Rld+   d+e+l+++++y+ sv+++ gg+re+eale+
  gi|336252511|ref|YP_004595618.1| 168 AASRLDVpgYDEETLRDRLAYYDSVVERAGGPREREALER 207
                                       *************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1675.35
//
Query:       gi|336252512|ref|YP_004595619.1|  [L=332]
Description: hypothetical protein Halxa_1106 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.39   10.6   8.1        1.3    8.9   8.1    1.9  1  DUF5337          Family of unknown function (DUF5337)
       0.84    9.7  26.1        0.1   12.7  10.8    2.4  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        5.1    7.5  17.6       0.34   11.3   0.9    3.1  3  DUF2628          Protein of unknown function (DUF2628)
         10    5.8   9.1       0.35   10.5   2.2    2.0  2  DUF4131          Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF5337  Family of unknown function (DUF5337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   8.1   0.00028       1.3      19      65 ..      34      82 ..      28      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00028
                           DUF5337 19 viavtmllwlgaqwigeqlglsnRyalLfdLaAlAal..iwalvvtyql 65
                                      +i  + ++wlga ++ +  g s  +++L+ L+AlA +  +w l++ y l
  gi|336252512|ref|YP_004595619.1| 34 IIYLSLVAWLGARFLWGDGGTSLLIVALVMLIALASFayVWRLIQRYAL 82
                                      578899*****************************88335677777766 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 ?   12.7  10.8   2.2e-05       0.1      37      89 ..      20      75 ..      11      88 .. 0.76
   2 ?    2.5   7.4     0.032   1.5e+02      30      83 ..     206     264 ..     202     279 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
                   Phage_holin_3_6 37 agllgaagvlallalllllvalalala.a...lwlaalivaavllvlagvlalvglk 89
                                      ++ +g+++v+al+++++l++ ++l+   +      + liva+v+l++ + +a+v ++
  gi|336252512|ref|YP_004595619.1| 20 LLQFGIGVVFALFGIIYLSLVAWLGARfLwgdGGTSLLIVALVMLIALASFAYV-WR 75
                                      6789******************98887657877777788877777666655554.43 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.032
                   Phage_holin_3_6  30 akragsgagllgaagvlallalllllvalalala.a....lwlaalivaavllvlagvl 83 
                                       +k ++   +l++++++++ + ll+ll+ + +al+ +     +++  +v+++++v+   l
  gi|336252512|ref|YP_004595619.1| 206 WKMVLGSTLLIVGGMYVLSFVLLTLLAPVSVALDfLptslEMISWSLVGGMVAVVHTGL 264
                                       55666677889999999999999999999888865566666666666777777665544 PP

>> DUF2628  Protein of unknown function (DUF2628)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   7.1     0.061   2.8e+02      41      92 ..      11      76 ..       9      79 .. 0.67
   2 ?   -2.6   0.0       1.7   7.5e+03      54      77 ..     130     162 ..     120     177 .. 0.47
   3 ?   11.3   0.9   7.6e-05      0.34       7      78 ..     187     259 ..     181     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.061
                           DUF2628 41 lwlkalvllviavavsvvlavl..........gfsdavrll.........lalliaillgle..anslyylkl 92
                                       ++k+l ++++++ ++vv a++                  +          +lli +l++l   a+ +y ++l
  gi|336252512|ref|YP_004595619.1| 11 VYRKTLPYVLLQFGIGVVFALFgiiylslvawL-------GarflwgdggTSLLIVALVMLIalASFAYVWRL 76
                                      69****************999966655544430.......144445566655555555555533666888875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                           DUF2628  54 avsvvlavl.........gfsdavrlllallia 77 
                                       ++++vl  +          ++  ++  l+ li+
  gi|336252512|ref|YP_004595619.1| 130 VIDAVLKQFnkavarieeMIPVPIPQQLQTLIS 162
                                       344443333443343333333333333444444 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 7.6e-05
                           DUF2628   7 kelerfafvedgkirlsfnvwAfffgfiwLlyrklwlkalvllviavavsvvlavl..gfsdavrlllalliai 78 
                                       ++++r++  +dg + l ++ w +++g   L++ ++++  +vll +   vsv+l +l  ++++  + l++ ++a+
  gi|336252512|ref|YP_004595619.1| 187 RNENRWQSARDG-LVLYAKTWKMVLGSTLLIVGGMYVLSFVLLTLLAPVSVALDFLptSLEMISWSLVGGMVAV 259
                                       45689999****.9999***********************************9998775555555555555555 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.2   7.7e-05      0.35      11      90 ..      31     111 ..      15     127 .. 0.56
   2 ?   -1.3   0.5      0.33   1.5e+03      37      49 ..     211     223 ..     178     295 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.7e-05
                           DUF4131  11 alllllllllllllrr...rprrrvllllllllllallgfalrapqpnandlsqllesgqeviveGvvaslpeltgs 84 
                                       +++++ l l ++l  r       + ll+++l++l+al+ fa+  +  ++  l+ +     +++v ++++++ e+ ++
  gi|336252512|ref|YP_004595619.1|  31 LFGIIYLSLVAWLGARflwGDGGTSLLIVALVMLIALASFAYVWRLIQRYALYMVK--TGHIAVIAHIVEEDEVPEN 105
                                       22222222222222225554444445555555554444444444444444344444..7888899999999999988 PP

                           DUF4131  85 gtrfvl 90 
                                       + ++ +
  gi|336252512|ref|YP_004595619.1| 106 QIKYGV 111
                                       887765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.33
                           DUF4131  37 llllllallgfal 49 
                                       +  ll+++++++l
  gi|336252512|ref|YP_004595619.1| 211 GSTLLIVGGMYVL 223
                                       3333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); 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):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2331.02
//
Query:       gi|336252513|ref|YP_004595620.1|  [L=63]
Description: 30S ribosomal protein S17e [Halopiger xanaduensis SH-6]
Scores for complete 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   47.3   0.1    2.1e-12   47.0   0.1    1.0  1  Ribosomal_S17e  Ribosomal S17
  ------ inclusion threshold ------
      0.067   13.8   0.0      0.067   13.8   0.0    1.0  1  HNF-1_N         Hepatocyte nuclear factor 1 (HNF-1), N termin
      0.079   13.4   0.0      0.099   13.0   0.0    1.1  1  DUF4019         Protein of unknown function (DUF4019)


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 !   47.0   0.1   3.5e-16   2.1e-12       8      56 ..       7      55 ..       2      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 3.5e-16
                                      HHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHH CS
                    Ribosomal_S17e  8 tvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvth 56
                                       vKk+ + ++e+y   +t+dF++nk  +e+ + ++sk +rn+iaGyvt+
  gi|336252513|ref|YP_004595620.1|  7 YVKKTGNLLLERYPDAFTTDFEQNKDSVEKLTNVESKGVRNRIAGYVTR 55
                                      69*********************************************96 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 ?   13.8   0.0   1.1e-05     0.067     120     157 ..      24      61 ..       9      63 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                           HNF-1_N 120 ieeaaeqrakveellredswrvkeeikaflqqhrIsQr 157
                                       + ++++++ +ve+l + +s+ v++ i +++++++ sQ+
  gi|336252513|ref|YP_004595620.1|  24 TTDFEQNKDSVEKLTNVESKGVRNRIAGYVTRKKGSQA 61 
                                       6789********************************98 PP

>> DUF4019  Protein of unknown function (DUF4019)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.7e-05     0.099      74     104 .]      22      52 ..      18      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                           DUF4019  74 qfetefenkkqavEtvtlrkeedgkWrvvgY 104
                                        f+t+fe++k++vE++t ++ ++ + r++gY
  gi|336252513|ref|YP_004595620.1|  22 AFTTDFEQNKDSVEKLTNVESKGVRNRIAGY 52 
                                       59****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 479.77
//
Query:       gi|336252514|ref|YP_004595621.1|  [L=85]
Description: hypothetical protein Halxa_1108 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.22   11.5   6.2       0.31   11.0   6.2    1.2  1  DctQ             Tripartite ATP-independent periplasmic trans
        3.1    7.8   7.6        8.2    6.5   2.6    2.1  2  OppC_N           N-terminal TM domain of oligopeptide transpo


Domain annotation for each model (and alignments):
>> DctQ  Tripartite ATP-independent periplasmic transporters, DctQ component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   6.2   3.4e-05      0.31      67     124 ..      23      77 ..      19      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.4e-05
                              DctQ  67 liadllallfaavliwagwlevaaalfeettpvlglplwwvylvlpigaallalvala 124
                                       +++ ll++l++++++w+g+      + +   + l++ +++  l+++ +++++al+a+ 
  gi|336252514|ref|YP_004595621.1|  23 AVVSLLCFLLGIFMAWTGY---QGGTLPVAGTELNIVTGMAGLMITAFFGVIALFAAI 77 
                                       578999*************...455555666677799999999999999999998875 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2    0.0045        40      15      30 ..      22      37 ..      21      47 .. 0.87
   2 ?    6.5   2.6   0.00091       8.2      16      36 ..      58      78 ..      56      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0045
                            OppC_N 15 lAvvglvillllllia 30
                                      +Avv+l  +ll +++a
  gi|336252514|ref|YP_004595621.1| 22 AAVVSLLCFLLGIFMA 37
                                      69*******9988887 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00091
                            OppC_N 16 AvvglvilllllliaifaPli 36
                                       ++gl i +++ +ia+fa   
  gi|336252514|ref|YP_004595621.1| 58 GMAGLMITAFFGVIALFAAIY 78
                                      69***************8654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 635.93
//
Query:       gi|336252515|ref|YP_004595622.1|  [L=344]
Description: aspartate-semialdehyde dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-35  121.7   0.0    3.6e-35  121.0   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    6.5e-29  101.3   0.0      1e-28  100.7   0.0    1.3  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    8.9e-05   22.6   0.0    0.00016   21.8   0.0    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    9.7e-05   23.1   0.0    0.00018   22.2   0.0    1.4  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
     0.0019   17.8   0.0     0.0039   16.8   0.0    1.5  1  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
  ------ inclusion threshold ------
      0.027   15.3   0.0      0.054   14.3   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


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 !  121.0   0.0   1.2e-38   3.6e-35       1     119 [.       4     129 ..       4     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.0 bits;  conditional E-value: 1.2e-38
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG......GGTTTECEBEEEGGGGGC.TT-SEE CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk......aleegkdlkvedvdeeel.kevdiv 70 
                                       +v+++GatG+vGq+l++lL+ hp++e+++l++s++saGk++++a+k      ++e++++++v+++d++++ ++vd++
  gi|336252515|ref|YP_004595622.1|   4 RVGVLGATGAVGQRLIQLLDPHPDFEIAALTASESSAGKTYRQAAKwrvdspIPEDVAEMTVRETDPDDVpNDVDLI 80 
                                       79*************************************************************************** PP

                                       EE-SCHHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGG CS
                    Semialdhyde_dh  71 flalpagvskelapklaeagvkviDlssdfRlkddavyvlpevnreaik 119
                                       f++lp++v +e++p + eag +v ++ss+ R++dd+++v+pevn+e+++
  gi|336252515|ref|YP_004595622.1|  81 FSSLPSSVGAEVEPPFCEAGYVVSSNSSNGRMDDDIPLVIPEVNAEHLD 129
                                       **********************************************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 !  100.7   0.0   3.4e-32     1e-28       2     183 ..     160     324 ..     159     325 .. 0.86

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 3.4e-32
                                       HHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHH CS
                   Semialdhyde_dhC   2 kPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreel 78 
                                       ++L++  ++le+v+v+t+qavSGaG+                     gv +++i +N+ip+i++eedk e+e+r+ l
  gi|336252515|ref|YP_004595622.1| 160 AALAE--YGLEKVHVSTLQAVSGAGY--------------------DGVTSMEIIDNAIPFIGSEEDKLETESRKLL 214
                                       56666..57*****************....................7****************************** PP

                                       HHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCS........TTEEEEESSHCHHSS CS
                   Semialdhyde_dhC  79 kavaetkkileftekvsatcvrVPvlrGhseavtiklklkdveveeveellaaa........pevkvvvneeedrPt 147
                                       +  +  +  ++   +vsa+c+r+P ++Gh+e v+++++ +d ++++v e++++         p++ ++v e +drP+
  gi|336252515|ref|YP_004595622.1| 215 GDFDGAELSHNSM-QVSASCNRIPTIDGHLENVWVETE-EDLTADAVAEAMREYpsldlrssPDPLIHVFEVPDRPQ 289
                                       *****88777776.5**********************7.5555555555555555559******************* PP

                                       HHHHTTC..SSSEEEEEEEEETTCTTEEEEEEEEETTT CS
                   Semialdhyde_dhC 148 paavagg..tnsvsVGRirkdemgdeglklvvvgDNll 183
                                       p++++    ++++  G +++ + +   l++ ++++N++
  gi|336252515|ref|YP_004595622.1| 290 PRMDRTLgdGMAIAAGGLQESP-FG--LQYNCLAHNTI 324
                                       *****77668888888888888.44..78999999997 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   5.4e-08   0.00016       1      63 [.       3      62 ..       3      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5.4e-08
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHH CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddlee 63
                                      ++v+v+Ga+G +G++++++++ ++d+e++a   +++s   gk   ++++  +++ ++ +d++e
  gi|336252515|ref|YP_004595622.1|  3 VRVGVLGATGAVGQRLIQLLDPHPDFEIAALTASESS--AGKTYRQAAKW-RVDSPIPEDVAE 62
                                      69****************************9999874..44444443333.566666665555 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 !   22.2   0.0   6.2e-08   0.00018       1      49 [.       5      53 ..       5      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.2e-08
                                      EEEESTTSHHHHHHHHHHHHCTTTEEEEEEEE.SSTHHHHHHHHHHHT-S CS
                   DXP_reductoisom  1 vviLGsTGSIGtqtLdvieenpdkfevvalaa.gsnvellaeqakefkpk 49
                                      v +LG+TG +G+  ++++  +p  fe++al+a +s+  + ++qa++++++
  gi|336252515|ref|YP_004595622.1|  5 VGVLGATGAVGQRLIQLLDPHP-DFEIAALTAsESSAGKTYRQAAKWRVD 53
                                      579*******************.7********889999*******99876 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 !   16.8   0.0   1.3e-06    0.0039      72     111 ..     229     268 ..     222     280 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                                       EEEEEEEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH CS
                           Gp_dh_C  72 ldglAvrVPtpnvsvvdlvvelekevtveevnaalkeaae 111
                                       ++++  r+Pt+++++ ++ ve+e++ t++ v +a++e + 
  gi|336252515|ref|YP_004595622.1| 229 VSASCNRIPTIDGHLENVWVETEEDLTADAVAEAMREYPS 268
                                       566778******************************9875 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 ?   14.3   0.0   1.8e-05     0.054       1      86 [.       3     100 ..       3     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                                       EEEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH..HHHTTHE..EESS...........HHHHHTCT CS
                      GFO_IDH_MocA   1 lrvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeav..aesfgve..aysd...........leelladp 61 
                                       +rv++ Ga G +g++ + +l +++++ e++al  +++++ ++   a++++v+     +            +++++  
  gi|336252515|ref|YP_004595622.1|   3 VRVGVLGAtGAVGQRLI-QLLDPHPDFEIAALTASESSAGKTYrqAAKWRVDspIP-EdvaemtvretdPDDVPN-- 75 
                                       59******8888*****.999999******************95555555557522.244446644443444444.. PP

                                       TESEEEE-S-GGGHHHHHHHHHHTT CS
                      GFO_IDH_MocA  62 eidavivatpngtheelakaaleag 86 
                                       ++d+++   p++ ++e++  + eag
  gi|336252515|ref|YP_004595622.1|  76 DVDLIFSSLPSSVGAEVEPPFCEAG 100
                                       7899999999888888887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); 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:                         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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2522.91
//
Query:       gi|336252516|ref|YP_004595623.1|  [L=149]
Description: hypothetical protein Halxa_1110 [Halopiger xanaduensis SH-6]
Scores for 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-06   25.7   0.5    8.6e-05   22.5   0.5    2.3  1  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.061   13.2   0.0       0.13   12.2   0.0    1.6  1  HTH_5     Bacterial regulatory protein, arsR 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 !   22.5   0.5   9.6e-09   8.6e-05       4      36 ..      37      70 ..      34     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.6e-09
                                      HHHHS-HHHHHHHHHH.STCTTB-HHHHHHHHTS CS
                            HTH_20  4 aeALahPvRrrilraL.araegltaselaerldl 36
                                      + ALa+P Rr++lr+L   + ++ ++ela+ l +
  gi|336252516|ref|YP_004595623.1| 37 FGALADPHRRAVLRYLaDNESPVAVAELADHLTI 70
                                      78**************999999*******99953 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 ?   12.2   0.0   1.4e-05      0.13       1      27 [.      42      70 ..      42      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
                                      SHHHHHHHHHHTT..SSEEHHHHHHHHTS CS
                             HTH_5  1 dptRlkILklLae..gelcvcelaeelgl 27
                                      dp R+ +L++La+  ++  v ela++l +
  gi|336252516|ref|YP_004595623.1| 42 DPHRRAVLRYLADneSPVAVAELADHLTI 70
                                      89***********9999*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1210.99
//
Query:       gi|336252517|ref|YP_004595624.1|  [L=145]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-10   42.0   0.4    1.4e-10   41.8   0.4    1.0  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 !   41.8   0.4   8.1e-15   1.4e-10       4     140 ..       8     138 ..       7     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 8.1e-15
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       +I+V+v + ++ +     Al+   ++ +++++++vi+    ++ +++ e+ ee ++e  e++++      +ae    
  gi|336252517|ref|YP_004595624.1|   8 TIVVPVGDPDDGE-RTAAALAPYLEPTSTVVVVNVIEKAGGAPDKASTEQREEYAEEIFERTRD-----PLAESPAS 78 
                                       79****5555555.55566666777789999999999887777777666666666666666665.....46799999 PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       +++ ++ + d+ + i  +a +++ad +V   r  +++ +ll G v+++++++a+ pV++ 
  gi|336252517|ref|YP_004595624.1|  79 VETAILYGTDVVDRIFAEATDRNADAVVFVPREGNRFVELLTGGVARRLVKEASMPVVAL 138
                                       9999************************999999***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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 0.21s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 1266.83
//
Query:       gi|336252518|ref|YP_004595625.1|  [L=335]
Description: phosphoglycerate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for complete 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-53  180.8   0.0    2.2e-53  180.3   0.0    1.2  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    7.3e-12   45.1   0.0    8.6e-12   44.9   0.0    1.1  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
     0.0073   15.9   0.0      0.096   12.3   0.0    2.1  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
     0.0084   15.5   0.0      0.013   14.8   0.0    1.3  1  ThiF           ThiF family
  ------ inclusion threshold ------
      0.013   15.9   0.0       0.03   14.8   0.0    1.6  1  NAD_binding_7  Putative NAD(P)-binding
       0.02   15.4   0.0      0.043   14.4   0.0    1.6  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
      0.021   15.2   0.1       0.26   11.7   0.0    2.6  3  DUF4440        Domain of unknown function (DUF4440)
      0.052   13.8   0.8       0.96    9.7   0.1    2.8  3  TrkA_N         TrkA-N 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 !  180.3   0.0   9.7e-57   2.2e-53       2     178 .]     123     297 ..     122     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 180.3 bits;  conditional E-value: 9.7e-57
                                       HHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHH CS
                      2-Hacid_dh_C   2 alllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeee 77 
                                       +++l+++rr++ a++++r++ew   ++++ +el+g+tv i+GlG+IG++va+rl++fg++ i++  +++k   +++ 
  gi|336252518|ref|YP_004595625.1| 123 GAILHFTRRFHVAERRQRRREW---RHYQAHELQGSTVTIVGLGAIGRSVAERLEPFGVDTIGVRYTPEKGGpTDDV 196
                                       789*******************...9***************************************999987789999 PP

                                       HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES-- CS
                      2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvf 154
                                        g+e + ++++la++D+++l++plt+ tr+l+++e++  + ++a+l+N+aRG++vd++aL+eaL+ ++i+ga lDv+
  gi|336252518|ref|YP_004595625.1| 197 IGFEGDAFHDALARTDYLVLACPLTETTRGLVDREAFVTIDPEAVLVNVARGPVVDTDALVEALRGNQIRGASLDVT 273
                                       9**************************************************************************** PP

                                       SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 155 eeeplpedspllelpnviltPHia 178
                                       ++eplped+pl+++ nv +tPH a
  gi|336252518|ref|YP_004595625.1| 274 DPEPLPEDHPLWNFGNVQITPHNA 297
                                       **********************87 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 !   44.9   0.0   3.9e-15   8.6e-12      28     127 ..      50     322 ..      18     332 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 3.9e-15
                                       SSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                        2-Hacid_dh  28 llteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGilVtnvpgystesvAElt.. 102
                                        + +e  e++++a+ +     t +++++lea+++L+v a+a +G+ ++ +d ++erG++Vtn+ g++   + E++  
  gi|336252518|ref|YP_004595625.1|  50 RTPAEEREAIRGAEYVTG--MT-LEEDLLEAAENLEVFACAYAGTGHLPMDRLEERGVTVTNASGVHGPNIGEHVlg 123
                                       445555667777776544..44.88**************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|336252518|ref|YP_004595625.1| 124 ailhftrrfhvaerrqrrrewrhyqahelqgstvtivglgaigrsvaerlepfgvdtigvrytpekggptddvigfe 200
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|336252518|ref|YP_004595625.1| 201 gdafhdalartdylvlacpltettrglvdreafvtidpeavlvnvargpvvdtdalvealrgnqirgasldvtdpep 277
                                       ***************************************************************************** PP

                                       ....................T-BHHHHHHHHHHHHHHHHHHHTTC CS
                                       ....................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ....................aaTeeaqeniaeeaaenlvaflkge 127
                                                           + T   + ++a+++aen ++f + +
  gi|336252518|ref|YP_004595625.1| 278 lpedhplwnfgnvqitphnaGHTPRYYDRLADIVAENARRFGEAG 322
                                       ***************************************997664 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 ?    1.3   0.0       0.1   2.2e+02      93     130 ..      64     101 ..      54     121 .. 0.79
   2 !   12.3   0.0   4.3e-05     0.096       2      69 ..     152     219 ..     151     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.1
                                       ESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHT CS
                              IlvN  93 fahGfnihfglikppkdvdvvlvAPkgpGhlvreeyee 130
                                       +  G+ +  +l+++ ++++v+ +A  g Ghl ++  ee
  gi|336252518|ref|YP_004595625.1|  64 YVTGMTLEEDLLEAAENLEVFACAYAGTGHLPMDRLEE 101
                                       66789999999*******************97766543 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.3e-05
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S- CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliP 69 
                                       l+g +++++G G+ G++ a+ l   g+d +   ++ +k   +    gfe    ++a +++d +++  P
  gi|336252518|ref|YP_004595625.1| 152 LQGSTVTIVGLGAIGRSVAERLEPFGVDTIGVRYTPEKGGPTDDVIGFEGDAFHDALARTDYLVLACP 219
                                       7999***********************97544445555667777789999999999999999888877 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.9e-06     0.013      12      47 ..     148     183 ..     135     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.9e-06
                                       HHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  12 gqekLrdskvllvGaGglGsellknLalsGvgkltl 47 
                                        +++L+ s+v +vG+G++G  +++ L   Gv  + +
  gi|336252518|ref|YP_004595625.1| 148 QAHELQGSTVTIVGLGAIGRSVAERLEPFGVDTIGV 183
                                       57889*************************999876 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 ?   14.8   0.0   1.3e-05      0.03       2      92 ..     149     246 ..     148     252 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                     NAD_binding_7   2 fldlkgkkvlvvGgGevAarkvrklleagakvtv..vapevkeeleelvklaeeelekdlegad.lviaatddreln 75 
                                       +++l+g +v +vG G ++ + +++l ++g + +   ++pe    +++ + ++ + +++ l+++d lv+a+ + +e  
  gi|336252518|ref|YP_004595625.1| 149 AHELQGSTVTIVGLGAIGRSVAERLEPFGVDTIGvrYTPEKGGPTDDVIGFEGDAFHDALARTDyLVLAC-PLTETT 224
                                       699**************************77554156888888999******************555555.455544 PP

                     NAD_binding_7  76 eriae.aa....karrilvnva 92 
                                       + +++ +a      + +lvnva
  gi|336252518|ref|YP_004595625.1| 225 RGLVDrEAfvtiDPEAVLVNVA 246
                                       4443323322224477777776 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 ?   14.4   0.0   1.9e-05     0.043       2      76 ..     157     225 ..     156     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedvee 76 
                                       + i+G G +g+++a++l   g    + + + + +pek   + + +g   ++ +  +a++++d +vla++ + ++ 
  gi|336252518|ref|YP_004595625.1| 157 VTIVGLGAIGRSVAERLEPFG---VDTI-GVRYTPEKGGPTDDVIG--FEGDAFHDALARTDYLVLACPLTETTR 225
                                       789******************...5655.5699********99988..6676799**************987765 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.3   7.4e+03      48      48 ..     141     141 ..     119     167 .. 0.52
   2 ?   11.7   0.0   0.00012      0.26      25      64 ..     237     277 ..     234     307 .. 0.80
   3 ?   -0.1   0.0      0.53   1.2e+03      17      42 ..     304     329 ..     296     333 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.3
                                       H CS
                           DUF4440  48 e 48 
                                       +
  gi|336252518|ref|YP_004595625.1| 141 R 141
                                       1 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00012
                                       EEEEEEE-TT.S-EEEHHHHHHHHHCCHCEEEEEEEEEEEE CS
                           DUF4440  25 apdavlvgps.gtvldkeellealeagfaagrslelteeev 64 
                                       +p+avlv+   g+v d+++l+eal+ + ++g sl++t++e 
  gi|336252518|ref|YP_004595625.1| 237 DPEAVLVNVArGPVVDTDALVEALRGNQIRGASLDVTDPEP 277
                                       79999995554***********************9999765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.53
                                       HHHHHHCEEEEEEEE-TTS-EEEHHH CS
                           DUF4440  17 aealaallapdavlvgpsgtvldkee 42 
                                       +++la+++a++a+ +g  g+  d e+
  gi|336252518|ref|YP_004595625.1| 304 YDRLADIVAENARRFGEAGSDADLEN 329
                                       689***********999998777665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.19   4.3e+02      36      62 ..      56      83 ..      34     114 .. 0.78
   2 ?    9.7   0.1   0.00043      0.96       2      29 ..     158     185 ..     157     198 .. 0.81
   3 ?   -1.5   0.0       1.3   2.9e+03      26      54 ..     250     277 ..     239     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.19
                                      HHHHTTSEEEES-TTSHHHHHHT.TGGG CS
                            TrkA_N 36 elreeglevvvgdatdeevLeea.giek 62
                                      + + +g+e+v g   +e++Le+a ++e 
  gi|336252518|ref|YP_004595625.1| 56 REAIRGAEYVTGMTLEEDLLEAAeNLEV 83
                                      4456789999999999999999944444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00043
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEES CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidk 29 
                                        i+GlG +Grs+ae+L+  g  d +++  
  gi|336252518|ref|YP_004595625.1| 158 TIVGLGAIGRSVAERLEPfGV-DTIGVRY 185
                                       79**************97554.4666655 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.3
                                       EEESSHHHHHHHHHTTSEEEES-TTSHHH CS
                            TrkA_N  26 vidkdeerveelreeglevvvgdatdeev 54 
                                       v+d+d + ve lr + ++    d+td+e 
  gi|336252518|ref|YP_004595625.1| 250 VVDTD-ALVEALRGNQIRGASLDVTDPEP 277
                                       67776.68999999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2816.26
//
Query:       gi|336252519|ref|YP_004595626.1|  [L=463]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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   42.4   2.7    1.7e-05   24.6   0.0    2.4  2  DAO             FAD dependent oxidoreductase
    8.9e-11   41.6   0.0    6.3e-06   25.6   0.2    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.9e-08   33.3   0.1    0.00097   18.5   0.1    2.1  2  FAD_binding_3   FAD binding domain
    2.2e-06   27.8   0.3      0.023   14.7   0.0    2.5  3  NAD_binding_9   FAD-NAD(P)-binding
    6.6e-06   25.1   0.5    0.00071   18.4   1.3    2.1  2  HI0933_like     HI0933-like protein
    6.9e-06   25.7   0.0    1.2e-05   24.9   0.0    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
    8.5e-05   21.8   0.4    0.00018   20.7   0.4    1.6  2  FAD_binding_2   FAD binding domain
    0.00012   22.2   0.2    0.00035   20.7   0.2    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0003   19.8   0.2      0.039   12.8   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
    0.00034   19.8   3.4    0.00051   19.2   0.1    2.3  3  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.024   13.7   0.2        0.1   11.6   0.2    1.8  2  Lycopene_cycl   Lycopene cyclase protein
      0.041   13.1   0.0      0.074   12.3   0.0    1.4  1  Thi4            Thi4 family
      0.046   13.0   0.1      0.069   12.4   0.1    1.2  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.065   13.8   0.1        1.3    9.6   0.3    2.3  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.091   12.0   0.0       0.17   11.2   0.0    1.3  1  Amino_oxidase   Flavin containing amine oxidoreductase
        0.2   10.8   0.3       0.54    9.5   0.4    1.6  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.9   2.9e-06    0.0033       1      31 [.       5      36 ..       5      66 .. 0.89
   2 !   24.6   0.0   1.5e-08   1.7e-05     121     238 ..      89     205 ..      65     291 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.9e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdi 31
                                      dv+i+GGG +G+s+A  +a++g  ++l+e+g  
  gi|336252519|ref|YP_004595626.1|  5 DVAIVGGGPAGASAAERAAAHGaeTVLFEQG-V 36
                                      8****************************98.4 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.5e-08
                                       HHHHSTTSTTTSEEEEETTEEEE.EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEE.......TCEEEEEEECT.E CS
                               DAO 121 vrelepalpgllgalfypdtgqv.dpakltaalaraaealGveilegtevtgleeed.......gkvwgverttp.g 188
                                       + e++     +     yp+ g   + a++  +l+++ae++G++++ gt vt+le  d       g  +++  t + g
  gi|336252519|ref|YP_004595626.1|  89 AVEIST----TGMDATYPEFGYTfHRARMDDWLYERAEDAGADLRVGTSVTDLET-DlrasspkGPTHTL--TLSnG 158
                                       444442....33446899987766*****************************65.33445654555555..33337 PP

                                       EEEEEEEEEE--GGGHH.HHHTTCTTTSEEEEEEEEEEEEEECCTHSTGSG CS
                               DAO 189 endaadavVnaaGawsd.llgllkeldlpispvrgqvlvlkplseklvspa 238
                                        + +a++vV+a G++ +  l     ld+ + p r+ +  l+p++   + ++
  gi|336252519|ref|YP_004595626.1| 159 DQLEAQYVVLADGPQRRiTL---DALDQFTAPGRSVSDYLSPPEA-NHIAY 205
                                       6635699********77444...4445556777777777756443.22333 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 !   25.6   0.2   5.6e-09   6.3e-06       2      31 ..       5      34 ..       4      46 .. 0.88
   2 !   13.7   0.0   2.4e-05     0.027     165     242 ..      96     177 ..      80     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 5.6e-09
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEET CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvel 31
                                      dv+++GgGpAG +aa+++a++ga+++l+e+
  gi|336252519|ref|YP_004595626.1|  5 DVAIVGGGPAGASAAERAAAHGAETVLFEQ 34
                                      8***************************63 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.4e-05
                                       T-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.......EEEEEETTSCEEEESEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 165 gkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.......klevvledgeeidadlvvva 234
                                       g ++t+ e + ++   +  ++ ++l e+ e+ G ++++gtsv++++ + +        ++++l++g++++a++vv+a
  gi|336252519|ref|YP_004595626.1|  96 GMDATYPEFGYTF---HRARMDDWLYERAEDAGADLRVGTSVTDLETDLRasspkgpTHTLTLSNGDQLEAQYVVLA 169
                                       5555544444444...679999*********************99998888899988888***************** PP

                                       S-EEES-H CS
                                       xxxxxxxx RF
                       Pyr_redox_2 235 vGvrpste 242
                                        G + + +
  gi|336252519|ref|YP_004595626.1| 170 DGPQRRIT 177
                                       *9876665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   8.6e-07   0.00097       2      32 ..       4      34 ..       3      41 .. 0.93
   2 !   12.9   0.0   4.3e-05     0.049      91     165 ..      98     173 ..      67     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.6e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                      +dV+IVG+GpaG+++a   + +G ++vl e+
  gi|336252519|ref|YP_004595626.1|  4 VDVAIVGGGPAGASAAERAAAHGAETVLFEQ 34
                                      89***********************999886 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.3e-05
                                       HCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEE..ECCTTEEEEEEEEEEEE--GTT CS
                     FAD_binding_3  91 elesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevr..dketgeeetvrakYlvGaDGgr 165
                                       +  + pe  +++   +++  L+e+ae +g+++r +t v+ le d    +++      +  +  +++a+Y+v aDG +
  gi|336252519|ref|YP_004595626.1|  98 D-ATYPEFGYTFHRARMDDWLYERAEDAGADLRVGTSVTDLETDLRASSPKGPthTLTLSNGDQLEAQYVVLADGPQ 173
                                       4.56666677778889999*************************99988876533333455568***********86 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 !   10.4   0.3   0.00044      0.49       1      20 [.       7      26 ..       7      37 .. 0.87
   2 !   14.7   0.0   2.1e-05     0.023      92     155 ..     109     172 ..     103     173 .. 0.95
   3 ?   -3.2   0.0       6.7   7.5e+03       7      36 ..     279     311 ..     279     318 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
                     NAD_binding_9  1 aivGaGprGlavlerLlara 20
                                      aivG+Gp+G++++er +a+ 
  gi|336252519|ref|YP_004595626.1|  7 AIVGGGPAGASAAERAAAHG 26
                                      8**************99985 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.1e-05
                     NAD_binding_9  92 pRalyGrYlrdlfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                        Ra + ++l +++e++ a+l+ g++v+ ++++  + ++++ + +++l++g++l+a++VvLA G 
  gi|336252519|ref|YP_004595626.1| 109 HRARMDDWLYERAEDAGADLRVGTSVTDLETDLRASSPKGPTHTLTLSNGDQLEAQYVVLADGP 172
                                       6999999******************************************************885 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6.7
                     NAD_binding_9   7 prGlavlerLlara...kkkspleitlfdpsep 36 
                                       p+G   ++rLl+r+   + + + +i ++++++ 
  gi|336252519|ref|YP_004595626.1| 279 PSGSEYIRRLLEREygdEYDIEEDIPIVEDRGK 311
                                       678888899999987655556677888877654 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.3   6.3e-07   0.00071       2      32 ..       5      35 ..       4      37 .. 0.95
   2 ?    3.6   0.0     0.019        21     113     163 ..     115     171 ..     106     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.3e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                      dv+++GgG+AG  aA++aa++g++++l+e++
  gi|336252519|ref|YP_004595626.1|  5 DVAIVGGGPAGASAAERAAAHGAETVLFEQG 35
                                      89**************************986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHT-EEE-S--EEEE......ECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 113 dallkelkeagvklrletevksv......ekeedgkfrvktkseeeleadklvlAtG 163
                                       d l +++++ag +lr+ t+v+++      ++ ++ +++++++++++lea+++vlA G
  gi|336252519|ref|YP_004595626.1| 115 DWLYERAEDAGADLRVGTSVTDLetdlraSSPKGPTHTLTLSNGDQLEAQYVVLADG 171
                                       5688999**************996555543445556888889*************88 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0     1e-08   1.2e-05       1      30 [.       5      34 ..       5     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1e-08
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      Dv +vGGgpaG  AA  Aa +Ga+++L e+
  gi|336252519|ref|YP_004595626.1|  5 DVAIVGGGPAGASAAERAAAHGAETVLFEQ 34
                                      9**************************996 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.4   1.6e-07   0.00018       1      33 [.       5      37 ..       5      56 .. 0.95
   2 ?   -2.9   0.0       2.4   2.6e+03     146     170 ..     116     140 ..      93     181 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.6e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      Dv ++G+G AG +AA +aa +G+++++ e++ +
  gi|336252519|ref|YP_004595626.1|  5 DVAIVGGGPAGASAAERAAAHGAETVLFEQGVP 37
                                      9****************************9866 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.4
                                       HHHHHHHTCTEEEEESEEEEEEEEC CS
                     FAD_binding_2 146 rlvesarkagvdfqerteadeLive 170
                                        l+e+a++ag d++  t++++L ++
  gi|336252519|ref|YP_004595626.1| 116 WLYERAEDAGADLRVGTSVTDLETD 140
                                       5788888888888888888888664 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 !   20.7   0.2   3.1e-07   0.00035       1      28 [.       8      35 ..       8      37 .. 0.97

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.1e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      IvG+G +G++aA ++a +g++ +l+e++
  gi|336252519|ref|YP_004595626.1|  8 IVGGGPAGASAAERAAAHGAETVLFEQG 35
                                      9*************************86 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4      0.01        12       1      22 [.       5      26 ..       5      34 .. 0.80
   2 !   12.8   0.0   3.4e-05     0.039     144     220 ..     101     183 ..      53     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.01
                                      EEEEE--SHHHHHHHHHHHHHT CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakal 22
                                      ++ ivGGG+aG  aA   a ++
  gi|336252519|ref|YP_004595626.1|  5 DVAIVGGGPAGASAAERAAAHG 26
                                      699*********9998766655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.4e-05
                                       -S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEE.....EEE-T.TS-EEEEEETTS-EEE-SEEEE-SGGG-III CS
                    Trp_halogenase 144 alsyAyhldaalyakfLrrvaearGvtrvegkvve.....vqlde.dgrveslrledgreveadlfiDcsGfrglli 214
                                         +++y + +a+++++L + ae++G + + g++v+      +    +g  + l+l++g ++ea+ ++ + G ++++ 
  gi|336252519|ref|YP_004595626.1| 101 YPEFGYTFHRARMDDWLYERAEDAGADLRVGTSVTdletdLRASSpKGPTHTLTLSNGDQLEAQYVVLADGPQRRIT 177
                                       45799**********************999887642221133344689*************************9999 PP

                                       IIIT-- CS
                    Trp_halogenase 215 eqaLkt 220
                                         aL++
  gi|336252519|ref|YP_004595626.1| 178 LDALDQ 183
                                       998875 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   0.1   4.6e-07   0.00051       1      30 [.       5      34 ..       5      51 .. 0.89
   2 ?    1.0   0.0      0.16   1.8e+02     126     155 ..     148     175 ..     130     201 .. 0.75
   3 ?   -4.3   0.8       6.2     7e+03     369     386 ..     351     368 ..     333     372 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.6e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLith 30
                                      dv ++GgG AG  AA  aa  Ga+++L+ +
  gi|336252519|ref|YP_004595626.1|  5 DVAIVGGGPAGASAAERAAAHGAETVLFEQ 34
                                      799************************944 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.16
                                       TEEEEEEETTS-EEEECEEEE--TT-BT-E CS
                              GIDA 126 kkvkgvvtedgetikakavviatGtflkgk 155
                                       + ++ +++++g +++a+ vv+a G+  + +
  gi|336252519|ref|YP_004595626.1| 148 GPTHTLTLSNGDQLEAQYVVLADGP--QRR 175
                                       556778999****************..333 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 6.2
                                       SHHHHHHHHHHHHHHHHH CS
                              GIDA 369 GYeEaaaqGllAGinaar 386
                                       GY  a+ +G +AG+ a  
  gi|336252519|ref|YP_004595626.1| 351 GYHVAVRTGKIAGRLAGT 368
                                       899999999999998865 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   0.2   9.2e-05       0.1       1      31 [.       5      33 ..       5      40 .. 0.84
   2 ?   -0.8   0.0      0.54     6e+02     119     148 ..     150     178 ..      96     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.2e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                      Dv+++G+GpAg s A+r   a+ g + vl e
  gi|336252519|ref|YP_004595626.1|  5 DVAIVGGGPAGASAAERA--AAHGAETVLFE 33
                                      9****************9..77777766665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.54
                     Lycopene_cycl 119 eslvvleggrkirarlvvdarglaslkkar 148
                                         + +l++g +++a+ vv a g ++++  +
  gi|336252519|ref|YP_004595626.1| 150 THTLTLSNGDQLEAQYVVLADG-PQRRITL 178
                                       4578899999999999999999.7766444 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.6e-05     0.074      18      51 ..       4      36 ..       1      41 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.6e-05
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersv 51
                                       Dv+ivG+G++G +aa   a + + +++++e+ v
  gi|336252519|ref|YP_004595626.1|  4 VDVAIVGGGPAGASAAERAAAH-GAETVLFEQGV 36
                                      7****************99999.99999999866 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 ?   12.4   0.1   6.1e-05     0.069      29      60 ..       4      35 ..       1      46 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.1e-05
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                        v ++GgG aG +A++ a++ ga++++++  
  gi|336252519|ref|YP_004595626.1|  4 VDVAIVGGGPAGASAAERAAAHGAETVLFEQG 35
                                      679***********************999865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3    0.0012       1.3       2      30 ..       6      34 ..       5      37 .. 0.93
   2 ?    1.3   0.0      0.46   5.1e+02      42      69 ..     113     140 ..      82     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                      v++vGgG  g  +A+ +a++g+++ ++e 
  gi|336252519|ref|YP_004595626.1|  6 VAIVGGGPAGASAAERAAAHGAETVLFEQ 34
                                      89*********************999885 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                         Pyr_redox  42 askilqeklekngievllntkveeiegs 69 
                                       + ++l e+ e+ g +++ +t+v+ +e++
  gi|336252519|ref|YP_004595626.1| 113 MDDWLYERAEDAGADLRVGTSVTDLETD 140
                                       7789999****************99987 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.17     219     259 ..     122     169 ..     110     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                       TTTTEEEETSEEEEEEEE.....ETTC..EEEEETTSTEEEESEEEE- CS
                     Amino_oxidase 219 elrgldirlntrVkeikr.....egdg..vtvtledgevveaDaVvvT 259
                                       e  g d+r++t V+++++     ++ g   t+tl++g+++ea +Vv++
  gi|336252519|ref|YP_004595626.1| 122 EDAGADLRVGTSVTDLETdlrasSPKGptHTLTLSNGDQLEAQYVVLA 169
                                       5799****************997555577*****************98 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 ?    9.5   0.4   0.00048      0.54       2      30 ..       8      35 ..       7      39 .. 0.86
   2 ?   -3.0   0.0       3.1   3.5e+03     119     133 ..     157     171 ..     147     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00048
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg 30
                                      I+G+GPaG +aa  +  +g e  +  E+g
  gi|336252519|ref|YP_004595626.1|  8 IVGGGPAGASAAERAAAHGAE-TVLFEQG 35
                                      9******************96.5677766 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
                       Pyr_redox_3 119 sketyeAkkviiAtG 133
                                       + +++eA++v++A G
  gi|336252519|ref|YP_004595626.1| 157 NGDQLEAQYVVLADG 171
                                       446999*****9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3167.84
//
Query:       gi|336252520|ref|YP_004595627.1|  [L=36]
Description: hypothetical protein Halxa_1114 [Halopiger xanaduensis SH-6]
Scores for 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:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); 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 0.21s 00:00:00.53 Elapsed: 00:00:00.37
# Mc/sec: 295.34
//
Query:       gi|336252521|ref|YP_004595628.1|  [L=125]
Description: hypothetical protein Halxa_1115 [Halopiger xanaduensis SH-6]
Scores for complete 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   47.3   0.7    2.5e-12   46.7   0.3    1.5  2  HTH_20    Helix-turn-helix domain
    0.00033   20.4   0.1    0.00062   19.5   0.1    1.5  1  HTH_IclR  IclR helix-turn-helix domain
     0.0017   18.2   0.2     0.0041   17.0   0.1    1.6  2  MarR_2    MarR family
     0.0029   17.8   0.0     0.0042   17.3   0.0    1.3  1  pXO2-72   Uncharacterized protein pXO2-72
     0.0036   17.1   0.0      0.007   16.2   0.0    1.5  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0062   16.4   0.6     0.0086   15.9   0.1    1.6  2  HTH_5     Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.033   14.2   0.0    1.5  1  HTH_7     Helix-turn-helix domain of resolvase
      0.022   14.7   0.1      0.045   13.7   0.1    1.5  1  HTH_11    HTH domain
      0.066   13.4   0.0        0.1   12.7   0.0    1.5  1  FUR       Ferric uptake regulator 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 !   46.7   0.3   1.2e-15   2.5e-12       2      59 ..      16      71 ..      15      73 .. 0.95
   2 ?   -2.7   0.0       3.3   6.5e+03      35      48 ..     104     117 ..      96     117 .. 0.62

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.2e-15
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      +i  AL++P  r+i r L  +e++tasel +r++++++tl++ L+ L e  L+e  +e
  gi|336252521|ref|YP_004595628.1| 16 EICAALDDPDCREIIRNL--EEPMTASELTDRCEIPQSTLYRKLELLTESTLLEESTE 71
                                      7899**************..**********************************9887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.3
                                       TS-HHHHHHHHHHH CS
                            HTH_20  35 dlskntlsyHLrvL 48 
                                       d +  t++ +L++L
  gi|336252521|ref|YP_004595628.1| 104 DRPARTADERLAEL 117
                                       56666777777665 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   0.1   3.1e-07   0.00062      11      49 ..      29      67 ..      28      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.1e-07
                                      T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +++   +++t sel +r+ +p St +R L  L+e  ++e
  gi|336252521|ref|YP_004595628.1| 29 IIRNLEEPMTASELTDRCEIPQSTLYRKLELLTESTLLE 67
                                      5677889*************************9988887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.7   7.4e+03      23      31 ..      13      21 ..       9      22 .. 0.78
   2 !   17.0   0.1   2.1e-06    0.0041      16      56 ..      31      71 ..      27      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.7
                                      EHHHHHHHH CS
                            MarR_2 23 tvgelarrl 31
                                      ++ e++++l
  gi|336252521|ref|YP_004595628.1| 13 SAEEICAAL 21
                                      788999987 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.1e-06
                                      CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 16 rrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      r+ ++++t++el++r+ +++s++ r l+ L +  L+e+++ 
  gi|336252521|ref|YP_004595628.1| 31 RNLEEPMTASELTDRCEIPQSTLYRKLELLTESTLLEESTE 71
                                      4444459*****************************99974 PP

>> pXO2-72  Uncharacterized protein pXO2-72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.1e-06    0.0042       4      40 ..      32      68 ..      29      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-06
                           pXO2-72  4 tLdeimttreaCdrWeitleaLrmkLkrlkdselldk 40
                                       L+e mt+ e  dr ei + +L  kL+ l +s ll++
  gi|336252521|ref|YP_004595628.1| 32 NLEEPMTASELTDRCEIPQSTLYRKLELLTESTLLEE 68
                                      5899*****************************9985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.5e-06     0.007      20      55 ..      34      69 ..      30      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.5e-06
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      ++p+ta+e+  + ++p+s+ Y+ L+ L +  l e +
  gi|336252521|ref|YP_004595628.1| 34 EEPMTASELTDRCEIPQSTLYRKLELLTESTLLEES 69
                                      689**********************99887776665 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 ?   -3.5   0.1       5.2     1e+04      19      25 ..      15      21 ..      13      22 .. 0.76
   2 !   15.9   0.1   4.3e-06    0.0086      13      44 ..      34      65 ..      23      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.2
                                      HHHHHHH CS
                             HTH_5 19 celaeel 25
                                       e++++l
  gi|336252521|ref|YP_004595628.1| 15 EEICAAL 21
                                      5899998 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.3e-06
                                      TSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                             HTH_5 13 egelcvcelaeelglsqstvShHLkkLreaGL 44
                                      e++++++el++  +++qst+ + L  L e+ L
  gi|336252521|ref|YP_004595628.1| 34 EEPMTASELTDRCEIPQSTLYRKLELLTESTL 65
                                      57**********************99988655 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 ?   14.2   0.0   1.7e-05     0.033      10      43 ..      25      58 ..      20      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                                      HHGGGGSSTTTT--STTTSSSS---SSSS--SS- CS
                             HTH_7 10 dinrvvkLleeGisiskIAkevnisRsTvYRyla 43
                                      d  ++++ lee++++s++ ++  i  sT+YR+l+
  gi|336252521|ref|YP_004595628.1| 25 DCREIIRNLEEPMTASELTDRCEIPQSTLYRKLE 58
                                      56688899************************95 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.3e-05     0.045       7      42 ..      28      63 ..      26      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                            HTH_11  7 elLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      e++++ ++p++++eL ++ ++  +t +r ++ L+e+
  gi|336252521|ref|YP_004595628.1| 28 EIIRNLEEPMTASELTDRCEIPQSTLYRKLELLTES 63
                                      57888899*************************875 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.3e-05       0.1      35      62 ..      43      70 ..      10      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.3e-05
                                      HTTTT--HHHHHHHHHHHHHTTSEEEEE CS
                               FUR 35 eedpeislaTVYrtLklleeaglvkele 62
                                       ++ ei  +T+Yr L+ll+e+ l++e +
  gi|336252521|ref|YP_004595628.1| 43 TDRCEIPQSTLYRKLELLTESTLLEEST 70
                                      45678999***************98754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1020.82
//
Query:       gi|336252522|ref|YP_004595629.1|  [L=96]
Description: hypothetical protein Halxa_1116 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.066   12.7   0.6       0.13   11.7   0.6    1.4  1  Rax2      Cortical protein marker for cell polarity
        8.8    6.4   9.7       0.96    9.4   4.3    1.9  2  DUF485    Protein of unknown function, DUF485


Domain annotation for each model (and alignments):
>> Rax2  Cortical protein marker for cell polarity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   1.4e-05      0.13     167     196 ..       8      37 ..       5      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.4e-05
                              Rax2 167 lIgLAlALgtvallgllgiilayirkkreg 196
                                        I+ AlA+  +++l++ gii ++++k  + 
  gi|336252522|ref|YP_004595629.1|   8 EIAVALAVVKTIILVVGGIITYFAFKAYRR 37 
                                       5999*******************9997654 PP

>> DUF485  Protein of unknown function, DUF485
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.4     0.064   5.7e+02      54      69 ..       8      23 ..       1      34 [. 0.46
   2 ?    9.4   4.3   0.00011      0.96       5      64 ..      31      91 ..      28      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.064
                            DUF485 54 glllgllqivltfllt 69
                                       ++++l+++ + +l++
  gi|336252522|ref|YP_004595629.1|  8 EIAVALAVVKTIILVV 23
                                      4444444443333333 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00011
                            DUF485  5 kFqeLvrkrrrfafpltaiflvvYfgfvllvafapdllatkvgegni..tvglllgllqivl 64
                                      +F++ +r+r+r    l++ f +v +gfvl+ +f+  ll  +++ g++  ++ +l+g+l+i+ 
  gi|336252522|ref|YP_004595629.1| 31 AFKAYRRTRQRALGYLAVGFGLVTLGFVLAGMFD-LLLDVELVLGVLleSLLVLAGFLVIAY 91
                                      59999*************************9999.999999998855234555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 778.77
//
Query:       gi|336252523|ref|YP_004595630.1|  [L=390]
Description: multicopper oxidase type 2 [Halopiger xanaduensis SH-6]
Scores for 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  100.3   6.9    6.4e-16   58.3   0.1    2.9  2  Cu-oxidase_2  Multicopper oxidase
    6.2e-23   81.1   2.1    7.9e-17   61.4   0.3    2.4  2  Cu-oxidase_3  Multicopper oxidase
    3.9e-11   43.3   0.0    9.6e-11   42.0   0.0    1.7  2  Cu-oxidase    Multicopper oxidase
  ------ inclusion threshold ------
      0.016   15.3   0.0        1.1    9.5   0.0    2.7  2  Cupredoxin_1  Cupredoxin-like domain


Domain annotation for each model (and alignments):
>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   3.4   2.3e-14     1e-10      27     136 ..     117     213 ..     104     214 .. 0.87
   2 !   58.3   0.1   1.4e-19   6.4e-16      26     125 ..     263     356 ..     242     369 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.3e-14
                                       CTTTSSEEEEEETTEEEEEEEEE-SSS.-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEE CS
                      Cu-oxidase_2  27 efsentnvitlpkgevveiviqnntkl.pHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwva 102
                                       e s   +++++++ge+ e+ ++n++   pH++H HG+     g++  +           + ++    ++v+pg+  +
  gi|336252523|ref|YP_004595630.1| 117 EPSVPGPIYRMQEGETFELSFENTEHDrPHTVHVHGV-----GKSWRD-----------DGAPISTRIDVQPGESHT 177
                                       556678899***************************9.....555555...........66678889********** PP

                                       EEEES.S-EEEEEEESSH..HHHHTT-EEEEEEECH CS
                      Cu-oxidase_2 103 irfkadnpGvwllHCHil..wHldqGmalqfvvrpd 136
                                       ++ + d pG  ++HCH++   Hld+Gm++ + v+p+
  gi|336252523|ref|YP_004595630.1| 178 YELEGDVPGTHFYHCHVQthNHLDMGMYGILRVDPE 213
                                       ******************9999*******9999875 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 1.4e-19
                                       CCTT.TSSEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEE CS
                      Cu-oxidase_2  26 eefs.entnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwv 101
                                       ++f+ e  +++++  g++v++ + n +  +H fH HGh+f v+++++++        +   +  + d+v + p ++v
  gi|336252523|ref|YP_004595630.1| 263 ATFNpELGSPLVVGAGDTVRVHVVNAGYEQHAFHTHGHRFTVVEKDGSP--------IPEAARYQEDVVGIAPAERV 331
                                       3444356789999******************************999999........455566689*********** PP

                                       EEEEES..S-EEEEEEESSHHHHHT CS
                      Cu-oxidase_2 102 airfkad.npGvwllHCHilwHldq 125
                                       +++f+ad  pG + +HCH   H+++
  gi|336252523|ref|YP_004595630.1| 332 TLEFEADsEPGIYPVHCHKVDHVTT 356
                                       ******98***********999876 PP

>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.3   1.8e-20   7.9e-17      23     117 ..     119     213 ..     111     214 .. 0.94
   2 !   18.9   0.1   2.6e-07    0.0012      25     107 ..     269     358 ..     251     373 .. 0.76

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 1.8e-20
                                       SSBS-EEEEETT-EEEEEEEE-S.SS-B-EEEET--S-GG.....GSCSGGG-B-TT-EEEEEEE--S-SEEEEEEE CS
                      Cu-oxidase_3  23 qfpgptievregdtvvvnvtNkl.dentsihwhGlqqrktswmDGvpgvtqcpiqpgesftyrftvkqqagtlwYhs 98 
                                       ++pgp  +++eg+t +++++N   d++ ++h+hG+  ++    DG+p  t   +qpges ty+++ +   gt++Yh 
  gi|336252523|ref|YP_004595630.1| 119 SVPGPIYRMQEGETFELSFENTEhDRPHTVHVHGVGKSWR--DDGAPISTRIDVQPGESHTYELEGDV-PGTHFYHC 192
                                       69*******************99899***********999..**************************.******** PP

                                       --TT.HHH.TT-EEEEEEE-H CS
                      Cu-oxidase_3  99 hlsl.qqa.aGlaGaiiiedk 117
                                       h+++ ++  +G++G++ ++++
  gi|336252523|ref|YP_004595630.1| 193 HVQThNHLdMGMYGILRVDPE 213
                                       ****64448********9985 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.6e-07
                                       BS-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSCSGGG.......-B-TT-EEEEEEE--S-SEEE CS
                      Cu-oxidase_3  25 pgptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpgvtqc.......piqpgesftyrftvkqqagtl 94 
                                       +g  + v  gdtv+v+v+N+  e+ + h hG +      +DG p             i+p e++t +f+++ + g +
  gi|336252523|ref|YP_004595630.1| 269 LGSPLVVGAGDTVRVHVVNAGYEQHAFHTHGHRFTVV-EKDGSPIPEAAryqedvvGIAPAERVTLEFEADSEPGIY 344
                                       57778999***********************998877.89**8863322112222269999*********9999999 PP

                                       EEEE--TTHHH.TT CS
                      Cu-oxidase_3  95 wYhshlslqqa.aG 107
                                         h h   + + +G
  gi|336252523|ref|YP_004595630.1| 345 PVHCHKVDHVTtDG 358
                                       99999776433344 PP

>> Cu-oxidase  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.72   3.2e+03      64      89 ..     127     152 ..      69     203 .. 0.67
   2 !   42.0   0.0   2.1e-14   9.6e-11       2     143 ..     221     357 ..     220     373 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.72
                                       EEEETTEEEEEEEESSS-BEEEEETS CS
                        Cu-oxidase  64 vepgktyrlriinvsaddslnfsIeG 89 
                                       ++ g+t  l + n+  d  +++ ++G
  gi|336252523|ref|YP_004595630.1| 127 MQEGETFELSFENTEHDRPHTVHVHG 152
                                       44555555554444444444444443 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 2.1e-14
                                       EEEEEEEEETCBCTTSCBC.HSSCHCHHHHHTT--SEEEETTBSS.......CTTTTSGGGEEEEETTEEEEEEEES CS
                        Cu-oxidase   2 eyvitlsDwyhkdakelekellasgkapadtppvpdavlingkggfnatladkdgaslatltvepgktyrlriinvs 78 
                                       ey++tl +w  + ++     ++ +++++ +    p+ +++ng++ ++ t     +     l v +g+t+r++++n++
  gi|336252523|ref|YP_004595630.1| 221 EYFLTLREWDSRLHER----EAGGDADYDAGDRSPNLYTVNGRSAPA-TF---NPELGSPLVVGAGDTVRVHVVNAG 289
                                       5788888884433333....3344444444567799******77765.33...3457788999************99 PP

                                       SS-BEEEEETSB-EEEEEETCETTS...EEEESCEEE-TTEEEEEEEEE-SSSEEEEEEEE.GSSSCHH CS
                        Cu-oxidase  79 addslnfsIeGHkltVvevDgvyve...pvevdsldIavGqrysvlvtanqapgnYwivas.grsnlie 143
                                        ++ + f  +GH++tVve Dg+++     ++ d + Ia+++r++  ++a+ +pg Y ++++ + +++ +
  gi|336252523|ref|YP_004595630.1| 290 YEQ-HAFHTHGHRFTVVEKDGSPIPeaaRYQEDVVGIAPAERVTLEFEADSEPGIYPVHCHkVDHVTTD 357
                                       865.67778**************998889999*****************999********774444333 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00024       1.1      40      96 ..     128     196 ..     123     202 .. 0.88
   2 ?    2.6   0.0     0.032   1.4e+02      42      92 ..     278     348 ..     263     358 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00024
                      Cupredoxin_1  40 kagekvklkiknkdkt.peefesed...........lgeekvlapgktttitiaplkpGeYeftcdmhm 96 
                                       ++ge ++l ++n+    p+++ ++            ++++ +++pg+++t +++ + pG++ ++c  + 
  gi|336252523|ref|YP_004595630.1| 128 QEGETFELSFENTEHDrPHTVHVHGvgkswrddgapISTRIDVQPGESHTYELEGDVPGTHFYHCHVQT 196
                                       789999*****998763699999999999999999999999************************9875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.032
                      Cupredoxin_1  42 gekvklkiknkdktpeefesed...................lgeekvlapgktttitiapl.kpGeYeftc 92 
                                       g  v+++++n + + + f  +                     +    +ap +  t++++++ +pG Y+ +c
  gi|336252523|ref|YP_004595630.1| 278 GDTVRVHVVNAGYEQHAFHTHGhrftvvekdgspipeaaryQEDVVGIAPAERVTLEFEADsEPGIYPVHC 348
                                       44444444444444333332221111111222222222221122244677777777776542577777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); 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 0.21s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3137.82
//
Query:       gi|336252524|ref|YP_004595631.1|  [L=496]
Description: dihydrolipoamide dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-66  222.8   3.9    5.4e-66  222.8   3.9    1.9  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    8.1e-37  125.8   0.8    1.5e-36  125.0   0.1    1.9  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    3.3e-24   85.3   1.5    2.7e-20   72.7   0.0    3.4  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      3e-11   43.0   1.4    4.5e-08   32.6   0.7    2.4  2  GIDA            Glucose inhibited division protein A
    2.3e-08   33.7   0.1     0.0041   16.4   0.1    3.1  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.4e-08   33.5   7.2    4.5e-06   26.0   0.4    3.2  3  FAD_binding_2   FAD binding domain
    3.5e-08   33.5   0.5      0.003   17.7   0.2    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    9.6e-08   31.1   3.1    1.3e-05   24.1   0.1    2.6  3  HI0933_like     HI0933-like protein
      6e-07   29.0   2.9     0.0096   15.2   0.6    3.2  3  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    3.9e-06   26.5   0.4    3.9e-06   26.5   0.4    1.9  2  FAD_oxidored    FAD dependent oxidoreductase
    1.5e-05   24.4   2.3      0.036   13.3   0.2    2.3  2  FAD_binding_3   FAD binding domain
    2.1e-05   24.2   0.6    0.00098   18.7   0.0    2.4  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    0.00016   21.6   0.2     0.0011   18.9   0.0    2.2  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    0.00022   20.6   2.8      0.048   12.9   0.3    3.0  3  Thi4            Thi4 family
    0.00031   20.4  14.9      0.027   14.1   1.1    3.6  4  DAO             FAD dependent oxidoreductase
    0.00083   19.8   0.2        1.2    9.7   0.0    2.7  2  NAD_binding_7   Putative NAD(P)-binding
    0.00089   18.4   3.2       0.13   11.3   0.6    2.4  2  Lycopene_cycl   Lycopene cyclase protein
     0.0015   18.7   0.2       0.44   10.8   0.0    2.8  2  TrkA_N          TrkA-N domain
     0.0066   15.4   1.5      0.029   13.2   0.1    2.1  2  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
      0.028   13.8   0.2       0.87    8.9   0.0    2.8  3  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.037   14.5   5.4       0.26   11.8   1.5    3.3  2  XdhC_C          XdhC Rossmann 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 !  222.8   3.9   6.3e-69   5.4e-66       2     294 .]      11     355 ..      10     355 .. 0.94
   2 ?   -0.8   0.1      0.85   7.3e+02     147     192 ..     435     486 ..     408     493 .. 0.68

  Alignments for each domain:
  == domain 1  score: 222.8 bits;  conditional E-value: 6.3e-69
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias.................. 57 
                                       dv+viG+GpAG+ aa++++q   +vtlve    +gtcln gc++skal  + + a++a+                  
  gi|336252524|ref|YP_004595631.1|  11 DVLVIGAGPAGYVAAIRAGQLDQDVTLVEkdaYGGTCLNYGCIPSKALITATDIAHEARhaeemgihadpaidlagm 87 
                                       8***************************9999**************9999999999999999*************** PP

                                       .....HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC.......TCEEEEEESEEEE---EEE-BCTCTTC.TT CS
                                       .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .....evvkklnqgielllgeevvkidpgkkkvklekkke.......gdeekiaydklvlAtGssprdlgipGvaen 122
                                            +vv++l+ g+e+l ++++v++ +g ++++ e++++       +  e++++++ v+AtGs+p  +  p   e 
  gi|336252524|ref|YP_004595631.1|  88 vgwkdDVVDQLTGGVEKLCKANGVNLLEGTATFTGENTVRvshsgegQGSETLEFEHAVVATGSRPIEI--PNF-E- 160
                                       **************************************99******97779**************9876..766.3. PP

                                       BEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 123 vgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGve 199
                                       +g+    l+s +al l+ +p+++vvvG+GyiG+ElA+++aklg +vt++e +d +l+++d++l++ ++++ e+ G+e
  gi|336252524|ref|YP_004595631.1| 161 YGDE-PVLNSRQALALESVPDSLVVVGAGYIGMELASVFAKLGTDVTVIEMLDSILPGYDDDLKRPVKQRAEDLGIE 236
                                       3334.789********************************************************************* PP

                                       EEESCEEEEEEETTE..EEEEEETTSCE........................EEESEEEE-S-EEES-HHCS.HCCT CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxx........................xxxxxxxxxxxxxxxxxxxx.xxxx RF
                       Pyr_redox_2 200 vklgtsvkeidgnge..klevvledgee........................idadlvvvavGvrpstelle.eklg 249
                                       + +g ++ e +++++   ++vv e  ++                        +da+ v+vavG++p +++l+  ++g
  gi|336252524|ref|YP_004595631.1| 237 FEFGYTASEWTERDDgdGIRVVAEPADRaaadggaaagetdadtdaeaepleLDAEKVLVAVGREPVSDTLDlAEAG 313
                                       ***********999999666666666666677777889999999999****************************** PP

                                       -EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 250 lelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                       +e+d+rg+i +d++ rtnv++i+a+GDva   g p+la++ +++G
  gi|336252524|ref|YP_004595631.1| 314 VETDDRGFIDTDSQARTNVEHIFAVGDVA---GEPMLAHKGSAEG 355
                                       *****************************...*******999887 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.85
                                       EES-SHHHHHHHHHHHHHT-....EEEEEESSSSSS..TTS-HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                       Pyr_redox_2 147 vvGgGyiGvElAaalaklgk....evtlveardrll..raldkelsaaleea 192
                                         G++ +G E +    +lg      +tl + ++++   ++l +++ +a+e+a
  gi|336252524|ref|YP_004595631.1| 435 LLGASIVGPEASELVGELGLavelGATLEDVASTVHahPTLSESVMEAAENA 486
                                       6799999999999988887744333566666666665555555555555544 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 !  125.0   0.1   1.8e-39   1.5e-36       1     109 [.     374     482 ..     374     483 .. 0.99

  Alignments for each domain:
  == domain 1  score: 125.0 bits;  conditional E-value: 1.8e-39
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       +p+vvftdpe+a+vG+te +A++ag + ++g fpf+a+gral+ +e++gfvK+va+ ++g +lGa+ivGp+a+el+ 
  gi|336252524|ref|YP_004595631.1| 374 MPAVVFTDPEIATVGMTESDAEEAGFDPVTGVFPFRASGRALTTGESDGFVKVVAESDDGYLLGASIVGPEASELVG 450
                                       69*************************************************************************** PP

                                       HHHHHHHTTSBHHHHHTSBSSSSSTGGGGHCH CS
                     Pyr_redox_dim  78 elavaikagltvedladtihihPtlsealkea 109
                                       el +a++ g+t ed+a+t+h+hPtlse++ ea
  gi|336252524|ref|YP_004595631.1| 451 ELGLAVELGATLEDVASTVHAHPTLSESVMEA 482
                                       ****************************9998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0018       1.6       2      30 ..      12      40 ..      11      43 .. 0.94
   2 !   72.7   0.0   3.1e-23   2.7e-20       1      76 [.     181     255 ..     181     264 .. 0.93
   3 ?   -0.8   0.1       2.7   2.3e+03       5      26 ..     449     470 ..     446     491 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                      v+v+G+G  g  +A  + +l ++Vt+ve 
  gi|336252524|ref|YP_004595631.1| 12 VLVIGAGPAGYVAAIRAGQLDQDVTLVEK 40
                                      89*************************96 PP

  == domain 2  score: 72.7 bits;  conditional E-value: 3.1e-23
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesv 76 
                                       ++vvvG+Gyig+ElA+++a+lg +Vtv+e+ d +l+++D+++ + ++++ e++gie+ ++ ++ e+++ +dg  ++
  gi|336252524|ref|YP_004595631.1| 181 SLVVVGAGYIGMELASVFAKLGTDVTVIEMLDSILPGYDDDLKRPVKQRAEDLGIEFEFGYTASEWTERDDG-DGI 255
                                       58*****************************************************************99998.334 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.7
                                       ECSSHHHHHHHHHHHHTTSEEE CS
                         Pyr_redox   5 vGgGyiglElAgalaelgkkVt 26 
                                       vG   +++El+++l + ++ V+
  gi|336252524|ref|YP_004595631.1| 449 VGELGLAVELGATLEDVASTVH 470
                                       5666789999999999998886 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.7   5.2e-11   4.5e-08       1      67 [.      11      78 ..      11     157 .. 0.90
   2 !    8.8   0.0   0.00089      0.76       2      30 ..     182     209 ..     181     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 5.2e-11
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHH CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggiakgllvrEidalggliikaa 67
                                      dv ViG+G AG+ AA+ a +l  +v+L+      +t+++ +C ps   i +  + +E ++ + +++  a
  gi|336252524|ref|YP_004595631.1| 11 DVLVIGAGPAGYVAAIRAGQLDQDVTLVekDAYGGTCLNYGCIPSKALITATDIAHEARHAE-EMGIHA 78
                                      79**************************7777789**********************99954.444444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00089
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLith 30 
                                       ++V+G+G  G+e A   a+lG +v+ i +
  gi|336252524|ref|YP_004595631.1| 182 LVVVGAGYIGMELASVFAKLGTDVTVI-E 209
                                       69**********************998.3 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 !   16.4   0.1   4.9e-06    0.0041       1      39 [.      13      50 ..      13      79 .. 0.92
   2 !   10.9   0.0   0.00023      0.19     121     197 ..     138     212 ..     130     251 .. 0.73
   3 ?    2.7   0.0     0.072        62     258     305 .]     291     339 ..     274     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.9e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyry 39
                                      ++iGaGPaG  aai + +++  d++ +Ek++ g +  +y
  gi|336252524|ref|YP_004595631.1| 13 LVIGAGPAGYVAAIRAGQLDQ-DVTLVEKDAYGGTCLNY 50
                                      69******************9.8**********999998 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00023
                       Pyr_redox_3 121 etyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgs 197
                                       et+e ++ ++AtG     + +n++  +  ++ +s    + +   + +vV+G++  +++ A  +++ g +Vtv+   +
  gi|336252524|ref|YP_004595631.1| 138 ETLEFEHAVVATGS-RPIEIPNFEYGD-EPVLNSRQALALESVPDSLVVVGAGYIGMELASVFAKLGTDVTVIEMLD 212
                                       56677778888887.444667777777.5666666555556677788888888888888888888888888886655 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.072
                       Pyr_redox_3 258 kddvvlatGykpdlsflkk..slfeldedgrpvlteeteetnvpglflaG 305
                                        ++v++a+G +p  + l+   +++e+d+ g++  + ++  tnv+ +f +G
  gi|336252524|ref|YP_004595631.1| 291 AEKVLVAVGREPVSDTLDLaeAGVETDDRGFIDTD-SQARTNVEHIFAVG 339
                                       46778889999988886654488888777777755.5678*******998 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.4   5.3e-09   4.5e-06       1      35 [.      11      44 ..      11      51 .. 0.92
   2 ?    5.2   0.2     0.011         9       2      30 ..     182     210 ..     181     214 .. 0.92
   3 ?    4.9   0.1     0.013        11     374     405 ..     312     345 ..     271     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.3e-09
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                      Dv+ViG+G AG++AA++a +  ++v++vek  + g
  gi|336252524|ref|YP_004595631.1| 11 DVLVIGAGPAGYVAAIRAGQLDQDVTLVEKDAY-G 44
                                      9*****************************988.3 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvek 30 
                                       ++V+G+G  G+  A   a+ G +v+v+e 
  gi|336252524|ref|YP_004595631.1| 182 LVVVGAGYIGMELASVFAKLGTDVTVIEM 210
                                       69************************995 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.013
                                       -EEEBETTSBE..STTEEESSBTEEE-STCEESS CS
                     FAD_binding_2 374 gGvetdengrv..ldadgqpipGLYAaGevaagg 405
                                       +Gvetd++g    ++++ ++++  +A+G va+  
  gi|336252524|ref|YP_004595631.1| 312 AGVETDDRGFIdtDSQARTNVEHIFAVGDVAGEP 345
                                       6888888887766888888************755 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 !   17.7   0.2   3.6e-06     0.003       1      35 [.      14      47 ..      14      66 .. 0.88
   2 !   13.6   0.0   7.1e-05     0.061       1      31 [.     184     214 ..     184     240 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.6e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      ++GaG +G vaA ++ + + dv+l+ek    GG +
  gi|336252524|ref|YP_004595631.1| 14 VIGAGPAGYVAAIRAGQLDQDVTLVEKD-AYGGTC 47
                                      8**************************6.555655 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.1e-05
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       +vGaG  G+ +A+  ak g dv+++e+ d++
  gi|336252524|ref|YP_004595631.1| 184 VVGAGYIGMELASVFAKLGTDVTVIEMLDSI 214
                                       8*************************98875 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   1.6e-08   1.3e-05       2      33 ..      11      42 ..      10      49 .. 0.92
   2 ?   -2.6   0.0       1.9   1.6e+03     118     164 ..     105     151 ..      96     154 .. 0.70
   3 !    7.1   0.1    0.0022       1.9       3      34 ..     182     213 ..     180     216 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.6e-08
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      dv+viG+G+AG  aAi+a++ +++V+l+ek  
  gi|336252524|ref|YP_004595631.1| 11 DVLVIGAGPAGYVAAIRAGQLDQDVTLVEKDA 42
                                      89***************************975 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                                       HHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 118 elkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                        +k++gv+l   t+  + e++   +++ + +++e+le ++ v+AtG+
  gi|336252524|ref|YP_004595631.1| 105 LCKANGVNLLEGTATFTGENTVRVSHSGEGQGSETLEFEHAVVATGS 151
                                       56667777766666666655555555555578999999999999997 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0022
                                       EEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakk 34 
                                       ++v+G+G  G+  A   ak g +V+++e  ++
  gi|336252524|ref|YP_004595631.1| 182 LVVVGAGYIGMELASVFAKLGTDVTVIEMLDS 213
                                       79*************************97665 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 !   15.2   0.6   1.1e-05    0.0096      20      60 ..       3      41 ..       1      72 [. 0.89
   2 !   10.3   0.0   0.00036      0.31      30      60 ..     181     211 ..     170     232 .. 0.86
   3 ?    1.6   0.0      0.17   1.5e+02     127     153 ..     454     479 ..     450     491 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                                      TCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C 20 aGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                      +G v+  +   vlviG+G aG  A+  a +l+++Vt+++++
  gi|336252524|ref|YP_004595631.1|  3 VGDVT--TGTDVLVIGAGPAGYVAAIRAGQLDQDVTLVEKD 41
                                      56666..6789*************************99986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00036
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvr 60 
                                         +v+G+G  G++ +++ ++lg +Vtv+++ 
  gi|336252524|ref|YP_004595631.1| 181 SLVVVGAGYIGMELASVFAKLGTDVTVIEML 211
                                       679************************9975 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.17
                                       TTGGGT-SBTT--TBBTTSEEEEETTE CS
                       AlaDh_PNT_C 127 vAidqGGnvetsrltthgepvveekgv 153
                                       +A++ G ++e+++ t h++p+++ + v
  gi|336252524|ref|YP_004595631.1| 454 LAVELGATLEDVASTVHAHPTLS-ESV 479
                                       89*******************98.555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.4   4.6e-09   3.9e-06       1      36 [.      11      45 ..      11      67 .. 0.91
   2 ?   -1.0   0.2         1   8.8e+02       2      30 ..     182     210 ..     181     214 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.6e-09
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGG 36
                                      Dv+V+G+gpaG++AAi A + ++ v Lve++ + GG
  gi|336252524|ref|YP_004595631.1| 11 DVLVIGAGPAGYVAAIRAGQLDQDVTLVEKDAY-GG 45
                                      9****************************9765.44 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLvee 30 
                                       +vVvG+g  G+  A   a+ G  v ++e 
  gi|336252524|ref|YP_004595631.1| 182 LVVVGAGYIGMELASVFAKLGTDVTVIEM 210
                                       69***********************9995 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2   4.3e-05     0.036       2      33 ..      10      41 ..       9      44 .. 0.87
   2 !   10.6   0.2   0.00027      0.23       5      33 ..     183     211 ..     180     216 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-05
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      tdVl++GaGpaG ++a    +   +v+lvek 
  gi|336252524|ref|YP_004595631.1| 10 TDVLVIGAGPAGYVAAIRAGQLDQDVTLVEKD 41
                                      89**************9888887788888886 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00027
                                       EEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                       ++VGaG  G+ la++ ++ G +v+++e  
  gi|336252524|ref|YP_004595631.1| 183 VVVGAGYIGMELASVFAKLGTDVTVIEML 211
                                       69************************976 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 ?    3.5   0.2     0.054        46       3      33 ..      12      42 ..      10      57 .. 0.87
   2 !   18.7   0.0   1.1e-06   0.00098       3      31 ..     182     210 ..     180     239 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.054
                                      EEEE--STTHHHHHHHHHHCTSEEEEE-S-H CS
                    UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvDide 33
                                      + viG+G  G v a+   ++  +v++v +d+
  gi|336252524|ref|YP_004595631.1| 12 VLVIGAGPAGYVAAIRAGQLDQDVTLVEKDA 42
                                      78*************************9987 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.1e-06
                                       EEEE--STTHHHHHHHHHHCTSEEEEE-S CS
                    UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDi 31 
                                       ++v+G+GY+G+  a v+a++g +v+++ +
  gi|336252524|ref|YP_004595631.1| 182 LVVVGAGYIGMELASVFAKLGTDVTVIEM 210
                                       579**********************9976 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 ?   -0.2   0.1      0.96   8.2e+02       2      31 ..      12      41 ..      11      44 .. 0.89
   2 !   18.9   0.0   1.3e-06    0.0011       3      50 ..     183     230 ..     181     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.96
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdis 31
                                      v viGaG  G   a  + + + +V+lv+ +
  gi|336252524|ref|YP_004595631.1| 12 VLVIGAGPAGYVAAIRAGQLDQDVTLVEKD 41
                                      78*********9999999999999999875 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.3e-06
                                       EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCT CS
                           3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklv 50 
                                        v+GaG +G ++a+vfa+ g +V+++++ +++l    + +++ +++ +
  gi|336252524|ref|YP_004595631.1| 183 VVVGAGYIGMELASVFAKLGTDVTVIEMLDSILPGYDDDLKRPVKQRA 230
                                       79*************************988888777777776666655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.3   5.6e-05     0.048      18      67 ..      10      57 ..       5     119 .. 0.71
   2 !    5.9   0.1    0.0078       6.7      19      49 ..     181     210 ..     169     218 .. 0.84
   3 ?   -0.1   0.0      0.54   4.6e+02      61     112 ..     433     484 ..     430     492 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEE CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsai 67
                                      +Dv+++GaG++G  aa   ++  d  v+++e+  ++GG     G + s+ 
  gi|336252524|ref|YP_004595631.1| 10 TDVLVIGAGPAGYVAAIRAGQL-DQDVTLVEKD-AYGGTCLNYGCIPSKA 57
                                      8***************999998.99*****987.6666655555544443 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0078
                                       EEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4  19 DvvivGaGssGLtaayylakkpdlkvailer 49 
                                        +v+vGaG  G+  a ++ak  +  v+++e 
  gi|336252524|ref|YP_004595631.1| 181 SLVVVGAGYIGMELASVFAKL-GTDVTVIEM 210
                                       589*****************9.888999885 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.54
                                       STTBSEEEEETTTHHHHHHTT---EEESSEEEESEHHHHHHHHHHHHHTSTT CS
                              Thi4  61 GqlfsaivvrkpakelLdelgikyedegdyvvvkdaalftstllskvlqlan 112
                                       G l  a +v  +a+el+ elg++ e   +   v+ ++ +  tl   v++ a+
  gi|336252524|ref|YP_004595631.1| 433 GYLLGASIVGPEASELVGELGLAVELGATLEDVASTVHAHPTLSESVMEAAE 484
                                       66777889999************99999999999999999999999988665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.1   3.1e-05     0.027       1      36 [.      11      46 ..      11      74 .. 0.85
   2 !    5.9   0.2    0.0094         8     146     202 ..      96     151 ..      65     177 .. 0.72
   3 !    9.2   0.4   0.00094       0.8       2      28 ..     182     210 ..     181     215 .. 0.93
   4 ?   -2.3   0.1       2.9   2.5e+03     155     186 ..     229     260 ..     226     323 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                      dv++iG+G +G  +A  + +    Vtl+ek+   g g+
  gi|336252524|ref|YP_004595631.1| 11 DVLVIGAGPAGYVAAIRAGQLDqdVTLVEKD-AYG-GT 46
                                      8*****************776569******9.655.44 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0094
                                       HHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE..EECTEEE.EEEEEEEE--GG CS
                               DAO 146 akltaalaraaealGveilegtevtgleeedgkvwgve..rttpgen.daadavVnaaGa 202
                                        +lt ++ + ++a+Gv++legt     e+     ++v    + +g++  ++++ V+a+G 
  gi|336252524|ref|YP_004595631.1|  96 DQLTGGVEKLCKANGVNLLEGTATFTGEN----TVRVShsGEGQGSEtLEFEHAVVATGS 151
                                       578899999************66555544....34443443333444236789*****94 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00094
                                       EEEECTSHHHHHHHHHHHHTT..EEEEES CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllek 28 
                                       +v++G+G+iG+  A   a+ g  Vt++e+
  gi|336252524|ref|YP_004595631.1| 182 LVVVGAGYIGMELASVFAKLGtdVTVIEM 210
                                       69*****************999*****97 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 2.9
                                       HHHHTT-EEEESECEEEE.EEEETCEEEEEEEC CS
                               DAO 155 aaealGveilegtevtgl.eeedgkvwgvertt 186
                                       +ae+lG+e+ +g ++ +  e++dg++ +v +++
  gi|336252524|ref|YP_004595631.1| 229 RAEDLGIEFEFGYTASEWtERDDGDGIRV-VAE 260
                                       56666777777666666424444444444.222 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 !    7.5   0.1    0.0062       5.3       6      40 ..       8      42 ..       6     111 .. 0.77
   2 !    9.7   0.0    0.0014       1.2       9      37 ..     181     209 ..     173     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0062
                     NAD_binding_7  6 kgkkvlvvGgGevAarkvrklleagakvtvvapev 40
                                      +g  vlv+G+G+ ++  + +  + + +vt+v ++ 
  gi|336252524|ref|YP_004595631.1|  8 TGTDVLVIGAGPAGYVAAIRAGQLDQDVTLVEKDA 42
                                      6789*******9999999999999999****9996 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvva 37 
                                       + +vvG+G ++++ ++ +++ g +vtv+ 
  gi|336252524|ref|YP_004595631.1| 181 SLVVVGAGYIGMELASVFAKLGTDVTVIE 209
                                       679************************85 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.6   0.00015      0.13       1      35 [.      11      43 ..      11     161 .. 0.64
   2 !    7.2   0.1    0.0026       2.2       2      36 ..     182     214 ..     181     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasps 35
                                      Dv+viGaGpAg   A r    + +  v+l+e  + 
  gi|336252524|ref|YP_004595631.1| 11 DVLVIGAGPAGYVAAIRA--GQLDQDVTLVEKDAY 43
                                      9*****************..99********87654 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0026
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       +vv+GaG  g+ lA     ak g  v++ie  +s+
  gi|336252524|ref|YP_004595631.1| 182 LVVVGAGYIGMELASVF--AKLGTDVTVIEMLDSI 214
                                       79*************99..**********987776 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.033        28       1      30 [.      12      41 ..      12      43 .. 0.91
   2 !   10.8   0.0   0.00051      0.44       2      29 ..     183     210 ..     182     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.033
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESS CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkd 30
                                      +++iG+G  G+  a +  + ++ dv++++kd
  gi|336252524|ref|YP_004595631.1| 12 VLVIGAGPAGYVAAIRAGQlDQ-DVTLVEKD 41
                                      68***************99777.7*****99 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00051
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEES CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidk 29 
                                       +++G+G +G++la  + + g  dv+vi+ 
  gi|336252524|ref|YP_004595631.1| 183 VVVGAGYIGMELASVFAKlGT-DVTVIEM 210
                                       8*****************666.8****96 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   3.4e-05     0.029       1      38 [.      11      45 ..      11      62 .. 0.82
   2 ?    0.9   0.2      0.18   1.6e+02       2      33 ..     182     210 ..     181     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS-- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigt 38
                                      +++++G+G+aG++aA+  ++      +vtlve+++ g 
  gi|336252524|ref|YP_004595631.1| 11 DVLVIGAGPAGYVAAIRAGQLD---QDVTLVEKDAYGG 45
                                      699************9766655...68******98775 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
                                       EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlves 33 
                                       +v+vG+G  G   A+++ak +   ++vt++e 
  gi|336252524|ref|YP_004595631.1| 182 LVVVGAGYIGMELASVFAKLG---TDVTVIEM 210
                                       79*****************99...88999985 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 ?    0.8   0.1      0.32   2.8e+02      34      66 ..       7      39 ..       2      63 .. 0.87
   2 ?    8.9   0.0     0.001      0.87      38      66 ..     181     209 ..     165     219 .. 0.88
   3 ?   -0.8   0.0      0.99   8.5e+02     119     141 ..     291     313 ..     287     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.32
                                      GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEES CS
                      2-Hacid_dh_C 34 lsgktvGiiGlGrIGqavakrlkafgmkviayd 66
                                       +g  v +iG+G  G  +a r+ +++ +v+ ++
  gi|336252524|ref|YP_004595631.1|  7 TTGTDVLVIGAGPAGYVAAIRAGQLDQDVTLVE 39
                                      578899****************99999998776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.001
                                       EEEEES-SHHHHHHHHHHHHTT-EEEEES CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviayd 66 
                                        + ++G+G IG ++a +++++g +v++++
  gi|336252524|ref|YP_004595631.1| 181 SLVVVGAGYIGMELASVFAKLGTDVTVIE 209
                                       688*********************99875 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.99
                                       TTEEEEESS-GGGB-HHHHHHHH CS
                      2-Hacid_dh_C 119 kgailiNtaRGglvdeeaLleaL 141
                                        + +l+ ++R ++ d+ +L+ea 
  gi|336252524|ref|YP_004595631.1| 291 AEKVLVAVGREPVSDTLDLAEAG 313
                                       5679***************9985 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.23     2e+02       1      32 [.      12      43 ..      12     105 .. 0.79
   2 ?   11.8   1.5   0.00031      0.26       1      29 [.     182     210 ..     182     400 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.23
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GG CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpree 32
                                      ++++Gag+ +   a  a +l+ +vt+v++++ 
  gi|336252524|ref|YP_004595631.1| 12 VLVIGAGPAGYVAAIRAGQLDQDVTLVEKDAY 43
                                      589************************99874 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00031
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdp 29 
                                       lv++Gag ++ +la++ a+lg +vtv++ 
  gi|336252524|ref|YP_004595631.1| 182 LVVVGAGYIGMELASVFAKLGTDVTVIEM 210
                                       79************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3572.22
//
Query:       gi|336252525|ref|YP_004595632.1|  [L=548]
Description: dihydrolipoyllysine-residue acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-89  298.4   0.0    4.1e-89  298.0   0.0    1.2  1  2-oxoacid_dh     2-oxoacid dehydrogenases acyltransferase (ca
    4.6e-24   84.0   2.0    9.2e-24   83.1   2.0    1.5  1  Biotin_lipoyl    Biotin-requiring enzyme
    1.6e-22   79.6   0.8    5.7e-16   58.6   0.1    3.1  3  E3_binding       e3 binding domain
    5.4e-07   29.3   0.9      0.003   17.3   0.4    2.7  2  Biotin_lipoyl_2  Biotin-lipoyl like
    2.1e-05   24.4   0.8    5.4e-05   23.1   0.8    1.8  1  GCV_H            Glycine cleavage H-protein
      0.002   18.1   0.5     0.0043   17.0   0.5    1.6  1  RnfC_N           RnfC Barrel sandwich hybrid domain
      0.008   16.9   2.7       0.15   12.8   0.3    2.6  2  HlyD_3           HlyD family secretion protein
  ------ inclusion threshold ------
      0.027   13.7   0.0       0.07   12.3   0.0    1.7  1  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
       0.05   13.4   0.3        6.2    6.6   0.0    2.5  2  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot


Domain annotation for each model (and alignments):
>> 2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.0   0.0   2.1e-92   4.1e-89       3     233 .]     314     547 ..     312     547 .. 0.96

  Alignments for each domain:
  == domain 1  score: 298.0 bits;  conditional E-value: 2.1e-92
                                       XXXXXXXXXXXXXXXXXXXXXX.XXXEEEEEEEEE-HHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHH-GG CS
                      2-oxoacid_dh   3 eeervplsgirkaiakrlteskqeiphftlsdevdvtallelrkelkekeakeekakltlldflikavalAlkefPe 79 
                                       +e+r+p++g+rk+ia+++ esk ++ph+t++devdvt+l+e r+elk +++++  ++lt+++f++kav++Al+e+Pe
  gi|336252525|ref|YP_004595632.1| 314 RERREPFRGVRKRIAEAMVESKYSAPHVTHHDEVDVTELVEAREELKPRAEERG-IRLTYMPFIMKAVVAALQEYPE 389
                                       6899********************************************997544.7********************* PP

                                       GG-EE.EESEEEE--SS--EEEE--------EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE-- CS
                      2-oxoacid_dh  80 lnasvdeeekeivvkkhvniGvAvatprGLlvPviknadkkslleiakelkelaekaregklkpedleggtftisNl 156
                                       +na +dee++eiv+++++niGvA+at+ GL+vPv+++ad+k+ll++++e++el++kare++++p +l+g+tfti+N+
  gi|336252525|ref|YP_004595632.1| 390 MNAVIDEENDEIVYRDYYNIGVATATDVGLMVPVLEDADEKGLLQLSSEMNELVQKARERSISPGELRGSTFTITNV 466
                                       ***************************************************************************** PP

                                       -------------TT-SEEEEE---.B--TT..STT-..HT---EEEEEEEEETTT--HHHHHHHHHHHHHTT-HHX CS
                      2-oxoacid_dh 157 GmlGvtsftPiinppqvaIlgvgrikerpvv..kege..lvvrkvmtlslsaDHRvidGaeaarFlntlkkllenpe 229
                                       G++G++++tPiin+p++ Il++g+ik+rp v  ++g+  +++r+v+tlsls+DHR+idGa aarF+nt+ ++lenp+
  gi|336252525|ref|YP_004595632.1| 467 GAIGGEYATPIINYPEAGILAIGEIKRRPRVveRDGQesIEPRSVLTLSLSFDHRLIDGAIAARFTNTVMEYLENPQ 543
                                       *****************************6634555599************************************** PP

                                       XXXX CS
                      2-oxoacid_dh 230 elll 233
                                       +lll
  gi|336252525|ref|YP_004595632.1| 544 LLLL 547
                                       9985 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   2.0   4.6e-27   9.2e-24       2      71 ..       4      74 ..       3      76 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 4.6e-27
                                      EEEESSSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEE CS
                     Biotin_lipoyl  2 eiksPmiGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdlla 71
                                      e+k+P++Ge v+eg  v++lv++Gd+V+++q++aeve++K+ +e++ap++G+v e++v+ G+ v+vg++++
  gi|336252525|ref|YP_004595632.1|  4 EFKLPDVGEGVAEGeLVSWLVEEGDEVSEDQSVAEVETDKALVEVPAPVNGTVRELHVEAGEVVDVGTVII 74
                                      79*******************************************************************98 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.1   2.9e-19   5.7e-16       1      36 []     132     167 ..     132     167 .. 0.98
   2 !   18.2   0.0   1.2e-06    0.0024       2      22 ..     239     259 ..     238     266 .. 0.91
   3 ?   -2.8   0.0       4.3   8.5e+03      11      24 ..     446     459 ..     446     459 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2.9e-19
                                       SBE-HHHHHHHHHCT--TTTS---CTTTBE-HHHHC CS
                        E3_binding   1 vlAsPaaRklAkelGidLsdvkGtGpgGRItkeDVl 36 
                                       ++A P++R++A+e GidL+++ G+GpgGRIt++DV+
  gi|336252525|ref|YP_004595632.1| 132 IFAPPRVRRMAREEGIDLAQLEGSGPGGRITAADVE 167
                                       79*********************************7 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.2e-06
                                       BE-HHHHHHHHHCT--TTTS- CS
                        E3_binding   2 lAsPaaRklAkelGidLsdvk 22 
                                       lA Pa R++A+e+G+d+++v+
  gi|336252525|ref|YP_004595632.1| 239 LAAPATRRIAQEQGVDIDAVP 259
                                       699****************97 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.3
                                       HHHCT--TTTS--- CS
                        E3_binding  11 AkelGidLsdvkGt 24 
                                       A+e  i++ ++ G+
  gi|336252525|ref|YP_004595632.1| 446 ARERSISPGELRGS 459
                                       89****99999997 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00027      0.54      10      37 ..      16      43 ..       9      48 .. 0.86
   2 !   17.3   0.4   1.5e-06     0.003       3      35 ..      46      78 ..      38      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                   Biotin_lipoyl_2 10 sGrVaqlnVkdGqrVkaGdvLaelDsra 37
                                       G +++++V++G++V + +  ae ++++
  gi|336252525|ref|YP_004595632.1| 16 EGELVSWLVEEGDEVSEDQSVAEVETDK 43
                                      5999**************9888887765 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.5e-06
                   Biotin_lipoyl_2  3 vsIaapvsGrVaqlnVkdGqrVkaGdvLaelDs 35
                                      v++ apv+G+V +l+V+ G +V  G v++  D 
  gi|336252525|ref|YP_004595632.1| 46 VEVPAPVNGTVRELHVEAGEVVDVGTVIISFDV 78
                                      7899*************************9996 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.8   2.7e-08   5.4e-05      38      74 ..      23      59 ..       7      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.7e-08
                                      ---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                             GCV_H 38 lpevgtkvkkgeslaavEsvKaasevyapvsGevvev 74
                                      l e+g++v++++s+a vE+ Ka  ev+apv+G+v e 
  gi|336252525|ref|YP_004595632.1| 23 LVEEGDEVSEDQSVAEVETDKALVEVPAPVNGTVREL 59
                                      6799******************************986 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 !   17.0   0.5   2.1e-06    0.0043      39      99 ..      17      77 ..      14      79 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.1e-06
                            RnfC_N 39 GapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlvahgsgveavvienD 99
                                      G+  + lv++gd+V + q +ae e+    ++v a+v GtV +++  +  +  +v +v+i+ D
  gi|336252525|ref|YP_004595632.1| 17 GELVSWLVEEGDEVSEDQSVAEVETdKALVEVPAPVNGTVRELHVEAG-EVVDVGTVIISFD 77
                                      5666789***************98777799**********98764332.3333556666655 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2      0.04        81       8      40 ..      17      48 ..      14      49 .. 0.88
   2 !   12.8   0.3   7.4e-05      0.15       2      29 ..      48      75 ..      47      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.04
                            HlyD_3  8 Gvvvelnveegevvqagdelleiippdtllvea 40
                                      G++v++ veeg+ v++ + ++e+  +d++lve+
  gi|336252525|ref|YP_004595632.1| 17 GELVSWLVEEGDEVSEDQSVAEVE-TDKALVEV 48
                                      89999******************9.77777776 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.4e-05
                            HlyD_3  2 lrApvdGvvvelnveegevvqagdelle 29
                                      + Apv G+v el+ve+gevv  g+++ +
  gi|336252525|ref|YP_004595632.1| 48 VPAPVNGTVRELHVEAGEVVDVGTVIIS 75
                                      569*********************9875 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.5e-05      0.07     100     137 ..      37      74 ..      19      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 100 ektgkvqktvtvkapisGvVteknvreGqyvqpgdtlf 137
                                       ++ ++ +  v+v ap++G+V e++v  G++v+ g++++
  gi|336252525|ref|YP_004595632.1|  37 AEVETDKALVEVPAPVNGTVRELHVEAGEVVDVGTVII 74 
                                       44555567799*********************999886 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.017        33      80     107 ..      16      43 ..      12      48 .. 0.89
   2 ?    6.6   0.0    0.0031       6.2      80     106 ..      53      79 ..      48      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.017
                                       TTTTEEES----SEE-SEEEEEEE-HHH CS
                        PTS_EIIA_1  80 kgegFellvkegdkVkagdklvevdlea 107
                                       +ge  + lv+egd+V++ + ++ev+ ++
  gi|336252525|ref|YP_004595632.1|  16 EGELVSWLVEEGDEVSEDQSVAEVETDK 43 
                                       68888999***************98875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0031
                                       TTTTEEES----SEE-SEEEEEEE-HH CS
                        PTS_EIIA_1  80 kgegFellvkegdkVkagdklvevdle 106
                                       +g++ el+v++g+ V  g+ ++++d+e
  gi|336252525|ref|YP_004595632.1|  53 NGTVRELHVEAGEVVDVGTVIISFDVE 79 
                                       788889*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 4045.78
//
Query:       gi|336252526|ref|YP_004595633.1|  [L=341]
Description: Pyruvate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for complete 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  178.3   0.0    1.4e-52  177.9   0.0    1.1  1  Transket_pyr     Transketolase, pyrimidine binding domain
      2e-35  121.4   0.0    3.5e-35  120.6   0.0    1.4  1  Transketolase_C  Transketolase, C-terminal domain


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 !  177.9   0.0   1.6e-56   1.4e-52       3     176 ..      21     195 ..      19     196 .. 0.97

  Alignments for each domain:
  == domain 1  score: 177.9 bits;  conditional E-value: 1.6e-56
                                       EEHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEE CS
                      Transket_pyr   3 iawrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviv 77 
                                       ++  +a+++ la+++++d++vv++g+Dv+  gg+f +++gl +++ge+rvid++++E++++g+a+G+a+ g l++++
  gi|336252526|ref|YP_004595633.1|  21 LTLVQAVRDGLATEMERDEDVVVMGEDVGknGGVFRATEGLYDEFGENRVIDTPLAESGIVGTAIGMAAYG-LRPVA 96 
                                       5677999****************************************************************.9**** PP

                                       EEEEHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHH CS
                      Transket_pyr  78 eaqFgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkh 152
                                       e+qF+ F+ +A  qi+ ++a  + +++g++++++v+r+p+g g ++peh+s ++ea++ + pglkv+ Ps+pa++k+
  gi|336252526|ref|YP_004595633.1|  97 EMQFMGFIYPAfdQIVSHAARLRTRSRGRYTCPLVVRAPYGGGIRAPEHHSESTEAMFVHQPGLKVAIPSTPADAKG 173
                                       ***************************************************************************** PP

                                       HHHHHHHSSS.SEEEEEE-SSEEC CS
                      Transket_pyr 153 llrrairredrkPvvlrlpksllr 176
                                       ll  air  +++Pv++++pk  +r
  gi|336252526|ref|YP_004595633.1| 174 LLTSAIR--SPDPVIFLEPKLIYR 195
                                       *******..678********9997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.0     4e-39   3.5e-35       1     124 []     211     331 ..     211     331 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 4e-39
                                       TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                   Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                       g+a ++reg+d+ + ++G+m +  leAae+L+ e i++eVvdlr+++plD+eti +s +ktgr  vv+ea k+gG+g
  gi|336252526|ref|YP_004595633.1| 211 GEAAVRREGSDISVYTWGAMTRPTLEAAENLAGE-IDVEVVDLRSLSPLDEETIVDSFEKTGRAAVVHEAPKTGGLG 286
                                       7999***************************988.****************************************** PP

                                       HHHHHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
                   Transketolase_C  78 sevaaalaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                       +e++a+l+eea+ + +apv+r++g+d+  p++  +le+++++ a++i
  gi|336252526|ref|YP_004595633.1| 287 AEIIATLQEEALLYQEAPVERITGFDT--PFPLYALEDYYLPEAARI 331
                                       ***************************..888889********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2687.93
//
Query:       gi|336252527|ref|YP_004595634.1|  [L=369]
Description: pyruvate dehydrogenase E1 component subunit alpha [Halopiger xanaduensis SH-6]
Scores for 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-88  295.2   0.0    4.7e-88  295.0   0.0    1.0  1  E1_dh           Dehydrogenase E1 component
    2.2e-07   30.4   0.0    3.2e-07   29.8   0.0    1.2  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
    0.00043   20.1   0.3     0.0015   18.3   0.1    2.0  2  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.032   13.9   0.0    1.6  1  HTH_41          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.0   0.0   1.1e-91   4.7e-88       2     299 ..      40     332 ..      39     333 .. 0.96

  Alignments for each domain:
  == domain 1  score: 295.0 bits;  conditional E-value: 1.1e-91
                                       HHHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-TT CS
                             E1_dh   2 klvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkvk 78 
                                       + ++l+r +d+++++++r++r+g+y +  gqe ++vg+a+al+++D+++++YRe+ v l+rglsle  l++++g++ 
  gi|336252527|ref|YP_004595634.1|  40 EQMRLARHFDERAVSLQRQGRMGTYPPLSGQEGAQVGSAHALDQDDWVFPSYREHAVGLVRGLSLERTLLYWMGHE- 115
                                       67999***********************************************************************. PP

                                       TSSGTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EE CS
                             E1_dh  79 gkggsrhelmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvi 155
                                             + ++y ++ ++++    ++++q p++ G+a a+k ++++++ i+++GDgA+++Gd++e+ln+a +++ p++
  gi|336252527|ref|YP_004595634.1| 116 ------Q-GNYIPEDVNMFSVAVPIATQIPHATGAAWASKLKDEEKTFICYFGDGATSEGDFHEGLNFAGVFDTPTV 185
                                       ......5.9999***************************************************************** PP

                                       EEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHT....TT--EEEEEEE--SS CS
                             E1_dh 156 fvveNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaerare....gkgpllielvtYRyg 228
                                       f+++NN+++is+++e+++as +la++a ++g  g++Vdg+Dplavy++++ A+e ++     + +p+lie+v YR+g
  gi|336252527|ref|YP_004595634.1| 186 FFCNNNQWAISVPRERQTASATLAQKATAYGFEGVQVDGMDPLAVYKVTRDAVEKTKDpgegELRPTLIEAVQYRFG 262
                                       *******************************************************9864332457************ PP

                                       -SSTTSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS----G CS
                             E1_dh 229 gHsesDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskkelep 299
                                        H++ Ddps yr  +eve ++ k dpi rl+++L ++g++++e +++i++++r++v +a++ aes + ++p
  gi|336252527|ref|YP_004595634.1| 263 AHTTADDPSVYREDDEVERWKRK-DPIPRLETFLRNNGLLDDERVDAIDERIREAVADAIETAESVERPDP 332
                                       ************88888887766.****************************************9988877 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 !   29.8   0.0   7.2e-11   3.2e-07     114     178 ..     134     198 ..     125     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 7.2e-11
                    DXP_synthase_N 114 stsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsiskn 178
                                       +t i  a+G a a++lk+e+k+ ++  GDga + G  +e+ln +g  ++  +   N+N+++is +
  gi|336252527|ref|YP_004595634.1| 134 ATQIPHATGAAWASKLKDEEKTFICYFGDGATSEGDFHEGLNFAGVFDTPTVFFCNNNQWAISVP 198
                                       68999*******************************************************99863 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 !   18.3   0.1   3.4e-07    0.0015      26     130 ..     129     244 ..     107     262 .. 0.57
   2 ?   -3.7   0.0         2   8.9e+03     137     145 ..     315     323 ..     303     338 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.4e-07
                                       TTS-TTTHHHHHHHHHHH....STTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-SBCCC.HHHH..HHH CS
                      TPP_enzyme_C  26 glgtmGyglpaAiGakla....kpdrevvaivGDGgflmi.lqelatavrrnlpitvvvlnNegygm.tggq..qep 94 
                                       + + +  ++p A+Ga+ a    +++++ +++ GDG++    ++e  +++      tv+  nN+ ++  + ++  + +
  gi|336252527|ref|YP_004595634.1| 129 VAVPIATQIPHATGAAWAsklkDEEKTFICYFGDGATSEGdFHEGLNFAGVFDTPTVFFCNNNQWAIsVPRErqTAS 205
                                       677788899******99544435589***********9999877777666655555555555555440444332222 PP

                                       HTCCTTTTSBB....BS----HHHHHHHTTSEEEEESSH CS
                      TPP_enzyme_C  95 fggkrksgpagk...dlkpvdfaklaealGakgarveka 130
                                       ++   k++ +g    + + +d+ ++ +     + + +++
  gi|336252527|ref|YP_004595634.1| 206 ATLAQKATAYGFegvQVDGMDPLAVYKVTRDAVEKTKDP 244
                                       222222222322333444444444444443334444444 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2
                                       HHHHHHHCS CS
                      TPP_enzyme_C 137 ealkealek 145
                                       ea+++a+e+
  gi|336252527|ref|YP_004595634.1| 315 EAVADAIET 323
                                       333333322 PP

>> HTH_41  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   7.2e-06     0.032      32      47 ..      49      64 ..      41      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.2e-06
                            HTH_41 32 ddkaislerrGrlGtf 47
                                      d++a+sl+r+Gr+Gt+
  gi|336252527|ref|YP_004595634.1| 49 DERAVSLQRQGRMGTY 64
                                      799************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2793.93
//
Query:       gi|336252528|ref|YP_004595635.1|  [L=91]
Description: hypothetical protein Halxa_1122 [Halopiger xanaduensis SH-6]
Scores for 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   21.6   0.0     0.0002   21.4   0.0    1.1  1  Band_7    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 !   21.4   0.0   1.1e-08    0.0002       2      51 ..      25      75 ..      24      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.1e-08
                            Band_7  2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsv.sl 51
                                      +++ege   +  fG++++vlepGl  + Pf+++++ ++ +++t+d  + ++
  gi|336252528|ref|YP_004595635.1| 25 TVREGELKALLVFGEMEAVLEPGLNVVPPFVSKTYPIDPQTMTIDAADdRI 75
                                      566776655666*******************************99888544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 705.08
//
Query:       gi|336252529|ref|YP_004595636.1|  [L=315]
Description: Lipoyl synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-13   51.5   0.3    4.2e-13   50.0   0.2    1.8  2  Radical_SAM  Radical SAM superfamily
    2.3e-10   40.8   0.0      5e-10   39.8   0.0    1.5  1  LIAS_N       N-terminal domain of lipoyl synthase of Radical_
  ------ inclusion threshold ------
      0.013   15.5   0.1        3.9    7.5   0.0    3.0  3  B12-binding  B12 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 !   50.0   0.2     7e-17   4.2e-13       5     165 ..      69     226 ..      65     228 .. 0.85
   2 ?   -1.5   0.0      0.49     3e+03      61      90 ..     257     283 ..     232     308 .. 0.61

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 7e-17
                                       SEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC....CCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx RF
                       Radical_SAM   5 rgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla....vpg 77 
                                         C+++C+fC++      +g  + l+++e ++ ++++ ae g ++v+l++ + ++ pd     +++  ++    +pg
  gi|336252529|ref|YP_004595636.1|  69 DRCSRACNFCDVE-----TGGMEPLDPDEPENVAEAV-AEIGLDYVVLTSVDRDDLPDQGAGHFAETIREikarHPG 139
                                       68***********.....5888888888888888888.7888**************888777777777775566688 PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSET.EEEEEEEB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikr.vvdrivgl 152
                                       i + v ++ +  +e  ++++ ++++d++++++e++     + +++ r+ ++e+ l +le   +   +  +++ i+++
  gi|336252529|ref|YP_004595636.1| 140 ILVEVLIPDFQGEEQLVRKIIDAEPDVIAHNVETVERL--QYPVRdRRAGYEQSLSVLEQVDRE-SDIyTKTSIMLG 213
                                       8888888888887************************5..66666699***********99766.3445******** PP

                                       TTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 153 pGendeeleelle 165
                                       +Ge d+e+  +l 
  gi|336252529|ref|YP_004595636.1| 214 HGEYDHEVYRTLA 226
                                       *******998876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.49
                                       TTHHHHHHHHHHTCCCTEEEEEEECSSCHG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  61 pdfvellerlaklavpgiritvetngtlpd 90 
                                       pd++e ++r a++   ++ + + ++g++++
  gi|336252529|ref|YP_004595636.1| 257 PDKYETWRRVAEE---ELGFLYCASGPMVR 283
                                       5555555555554...44444444444432 PP

>> LIAS_N  N-terminal domain of lipoyl synthase of Radical_SAM family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   8.3e-14     5e-10      72     108 .]       5      41 ..       2      41 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 8.3e-14
                            LIAS_N  72 rLPswlktkiPlGknynkikndlreLnLhtvCeeaRC 108
                                       r P+wlk + P G++++ i+++lr+ nLhtvCeea C
  gi|336252529|ref|YP_004595636.1|   5 RKPDWLKMRPPSGREFTDIRETLRDRNLHTVCEEANC 41 
                                       78**********************************9 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00065       3.9      39      84 ..      92     142 ..      75     144 .. 0.87
   2 ?    4.9   0.1    0.0042        25      36      58 ..     148     170 ..     141     240 .. 0.85
   3 ?   -0.4   0.0      0.19   1.1e+03      70     115 ..     261     302 ..     212     306 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00065
                       B12-binding  39 enedivaairaekpdvvglSal.....ltsqleavkelvellkrirprvkv 84 
                                       e+e++++a+++   d v+l+++     + +   +++e+++++k+++p++ v
  gi|336252529|ref|YP_004595636.1|  92 EPENVAEAVAEIGLDYVVLTSVdrddlPDQGAGHFAETIREIKARHPGILV 142
                                       349999*************9999999999999***************9987 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0042
                       B12-binding  36 anvenedivaairaekpdvvglS 58 
                                         +  e++v++i++ +pdv++  
  gi|336252529|ref|YP_004595636.1| 148 DFQGEEQLVRKIIDAEPDVIAHN 170
                                       333459**************975 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.19
                       B12-binding  70 elvellkrirprvkvvvGGahpsldpeetleaklgiddvvvgeged 115
                                       e+ ++++++  ++   + G+ ++  ++    + l  +d+v+ eg++
  gi|336252529|ref|YP_004595636.1| 261 ETWRRVAEEELGFLYCASGPMVRSSYKA--GE-LF-VDAVLREGKS 302
                                       4455555556666666777777777777..32.44.6667777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); 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:                         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: 00:00:00.38
# Mc/sec: 2491.62
//
Query:       gi|336252530|ref|YP_004595637.1|  [L=466]
Description: MATE efflux family protein [Halopiger xanaduensis SH-6]
Scores for complete 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-47  161.2  25.5    6.9e-27   94.1  10.0    2.4  2  MatE             MatE
    1.2e-08   35.2   3.2    1.2e-08   35.2   3.2    4.5  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 !   94.1  10.0   7.7e-31   6.9e-27       1     160 [.      24     183 ..      24     184 .. 0.99
   2 !   72.8   7.5   2.8e-24   2.5e-20      16     159 ..     264     411 ..     255     413 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 7.7e-31
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P++++nl+++l + idtl++gr + +a+Aav+i ++++ ll ++++g+++++++lv+q++Ga    + ++a++ g++
  gi|336252530|ref|YP_004595637.1|  24 PLFVQNLVQVLQQVIDTLWLGRHSLEAVAAVGINFPLTGLLAAVAIGVGVGTQVLVSQRVGADELAAGRRAAFNGTV 100
                                       99*************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       l+l++++ + l++++ +++ + lf++ + v+e+a+ yl +++l+  +la +++l + + g g+t+++ly++++++ +
  gi|336252530|ref|YP_004595637.1| 101 LGLVVGAGTGLATWAVARDVVALFGAGAVVTEYAAAYLAVYALVFAVLAASEALEAGFIGWGDTRAALYVNAVAVAV 177
                                       ***************************************************************************** PP

                              MatE 155 niplny 160
                                       n+++++
  gi|336252530|ref|YP_004595637.1| 178 NVVVDP 183
                                       ***987 PP

  == domain 2  score: 72.8 bits;  conditional E-value: 2.8e-24
                              MatE  16 dtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvl 91 
                                       +++lv  + +++ lAa +i+ +++ + fv+++gl  a+++++gq+lGa+ ++ra++++ +g+ ++ +  +++ ++ +
  gi|336252530|ref|YP_004595637.1| 264 MIWLVVLVgDAVGLAAFTIGARVSTVAFVPAMGLQQAAQSMIGQSLGAELPERARRTTWIGVAIASAGLCLVGAIQW 340
                                       677888888999*****************************************************99999999999* PP

                              MatE  92 lfseqilslftqdee..vlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipln 159
                                       l +e++  lf   ++   le+a++ylril++g+ a++ + +l++ ++ga +t+++l+++l+ + l+++p++
  gi|336252530|ref|YP_004595637.1| 341 LVPEPLSVLFVPGATaaELEVAAEYLRILAYGYWAIGATYLLQAGFNGARRTRTSLVATLLQYwLVRLPIA 411
                                       **********77666669*************************************************9987 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 ?   -1.6   4.7      0.29   2.6e+03      43     104 ..      54     112 ..      17     136 .. 0.52
   2 !   35.2   3.2   1.3e-12   1.2e-08       1      78 [.     137     220 ..     137     233 .. 0.91
   3 ?    1.0   1.5     0.044     4e+02      76     116 ..     300     346 ..     259     358 .. 0.52
   4 !    7.1   4.9   0.00057       5.2       1      81 [.     365     448 ..     365     456 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.29
                   Polysacc_synt_C  43 lilnllliplfgivGaaiatvlallvvavlnlyalrrllgikl.ellrrllkpllaalvmgiv 104
                                       +++n++l+ l+    aa+a+ ++  +  ++  +    +l       ++ ++  l+++++ g++
  gi|336252530|ref|YP_004595637.1|  54 VGINFPLTGLL----AAVAIGVGVGTQVLVSQRVGADELAAGRrAAFNGTVLGLVVGAGTGLA 112
                                       44444444222....222232322222222222222222222232344444444444444444 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 1.3e-12
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvav 71 
                                       +La++al++ +l+ s  l + ++g g +++al++++++++v++++  +li      p++g+ Gaa+at +++ +++v
  gi|336252530|ref|YP_004595637.1| 137 YLAVYALVFAVLAASEALEAGFIGWGDTRAALYVNAVAVAVNVVVDPFLIfgwwiaPELGVAGAAAATGVGYGCGLV 213
                                       699***********************************************988888888*****************9 PP

                   Polysacc_synt_C  72 lnlyalr 78 
                                       + + ++ 
  gi|336252530|ref|YP_004595637.1| 214 VGIAMAL 220
                                       9866554 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.044
                   Polysacc_synt_C  76 alrrllgikl......ellrrll.kpllaalvmgivvylllllllgll 116
                                       a++  +g +l        +r+++  +++a++++ +v   +++l+++ l
  gi|336252530|ref|YP_004595637.1| 300 AAQSMIGQSLgaelpeRARRTTWiGVAIASAGLCLVGA-IQWLVPEPL 346
                                       44444444445555754355555466666666666633.555554433 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.00057
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalviga.lvklilnllliplfgi..vGaaiatvlallvvavlnl 74 
                                       +L+ila++   ++ + +l++ ++g  r+++ l+a+++   lv l +       +g+  +G+ +a +l+ +v+a+ + 
  gi|336252530|ref|YP_004595637.1| 365 YLRILAYGYWAIGATYLLQAGFNGARRTRTSLVATLLQYwLVRLPIAAAAGLVLGTdvTGVFWAVTLSNVVAAIGLG 441
                                       699*******************************999752688888888777777555*****************99 PP

                   Polysacc_synt_C  75 yalrrll 81 
                                       ++ r ++
  gi|336252530|ref|YP_004595637.1| 442 WYYRYET 448
                                       9877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3219.99
//
Query:       gi|336252531|ref|YP_004595638.1|  [L=236]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-28   97.4   0.0      9e-28   96.8   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    7.1e-25   87.6   0.0    1.1e-24   86.9   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    1.1e-23   83.7   0.0    1.5e-23   83.3   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    8.1e-22   77.8   0.0    1.1e-21   77.4   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    7.2e-19   68.0   0.0    1.1e-18   67.5   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    4.7e-16   59.4   0.0    7.1e-16   58.8   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.3e-05   24.0   0.0    1.5e-05   23.8   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
    1.7e-05   24.4   0.0    3.7e-05   23.4   0.0    1.5  1  MTS              Methyltransferase small domain
    4.9e-05   22.9   0.0    6.4e-05   22.5   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      6e-05   22.9   0.0    9.9e-05   22.2   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      9e-05   21.5   0.0     0.0001   21.3   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
    0.00029   20.3   0.0    0.00041   19.8   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    0.00037   20.5   0.0    0.00049   20.1   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.001   18.5   0.0     0.0019   17.5   0.0    1.4  1  GidB             rRNA small subunit methyltransferase G
     0.0013   18.4   0.0     0.0017   18.0   0.0    1.2  1  NodS             Nodulation protein S (NodS)
     0.0016   18.2   0.0     0.0022   17.7   0.0    1.3  1  TPMT             Thiopurine S-methyltransferase (TPMT)
     0.0027   17.3   0.0     0.0045   16.6   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
     0.0055   16.4   0.0       0.01   15.5   0.0    1.5  1  UPF0020          Putative RNA methylase family UPF0020
     0.0095   15.2   0.0      0.014   14.7   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
  ------ inclusion threshold ------
      0.024   14.6   0.0      0.038   13.9   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
      0.027   14.2   0.0      0.039   13.7   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
      0.033   13.3   0.0      0.064   12.3   0.0    1.5  1  DREV             DREV methyltransferase
      0.048   13.0   0.0      0.062   12.6   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
       0.14   12.5   0.0       0.24   11.7   0.0    1.4  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
       0.14   12.5   0.0       0.29   11.5   0.0    1.6  1  Mur_ligase       Mur ligase family, catalytic domain
       0.17   11.5   0.0       0.21   11.2   0.0    1.1  1  Methyltransf_15  RNA cap guanine-N2 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 !   96.8   0.0   1.3e-30     9e-28       1      96 []      66     164 ..      66     164 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 1.3e-30
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-...EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl...kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       LdvGcGtG ++  la+ g++v+gvD+++eml++a++ka+ ++    ++ f ++dae lp++d+ fD+v++++ + ++
  gi|336252531|ref|YP_004595638.1|  66 LDVGCGTGVVSLLLAELGHDVTGVDFAPEMLERARTKARAADRpdrSIAFCRGDAEALPLPDGAFDVVTARHLIWTL 142
                                       8*********************************9999998888999****************************** PP

                                       CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                       ++p+ al+e+ RvL+pgG+lv+
  gi|336252531|ref|YP_004595638.1| 143 PNPQTALAEWQRVLEPGGRLVL 164
                                       *******************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.0   1.6e-27   1.1e-24       1      97 []      65     160 ..      65     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 1.6e-27
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCGBSSSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaedlpfedgsfDlvvssgal 74 
                                       vLd+GcGtG ++l la+ +  ++vtgvD+++emle+ar++a++++    ++ f +gdae+lp++dg fD+v++++ +
  gi|336252531|ref|YP_004595638.1|  65 VLDVGCGTGVVSLLLAELG--HDVTGVDFAPEMLERARTKARAADRpdrSIAFCRGDAEALPLPDGAFDVVTARHLI 139
                                       9***************995..*******************999444489************************7554 PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                         l+  + ++al+e+ rvL+pgG
  gi|336252531|ref|YP_004595638.1| 140 WTLP--NPQTALAEWQRVLEPGG 160
                                       4455..56699***********9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   0.0   2.2e-26   1.5e-23       4     118 ..      62     173 ..      60     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 2.2e-26
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre..naqklgldnveFeqgdieeleklledekfDli 78 
                                       + rvlD+GCGtG  ++ la elg   +v+G+D+ +e++e+Ar+  +a++     + F++gd+e+l+  l d  fD++
  gi|336252531|ref|YP_004595638.1|  62 DRRVLDVGCGTGVVSLLLA-ELGH--DVTGVDFAPEMLERARTkaRAADRPDRSIAFCRGDAEALP--LPDGAFDVV 133
                                       679****************.7765..799**************6555666666*************..9******** PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedprllael 118
                                       +++ ++ +l++p+ +l e +rvl+pgg+l++ +  +  + 
  gi|336252531|ref|YP_004595638.1| 134 TARHLIWTLPNPQTALAEWQRVLEPGGRLVLLEGYWDHDE 173
                                       ******************************9998844443 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0   1.6e-24   1.1e-21      20     164 ..      59     209 ..      36     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 1.6e-24
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaae..........pqgkfdlI 86 
                                         ++ rvLd+GcGtG ++ +l+e g++vtgvD  pe+ e+a+++  a + + +++  a+          p+g fd++
  gi|336252531|ref|YP_004595638.1|  59 GSQDRRVLDVGCGTGVVSLLLAELGHDVTGVDFAPEMLERARTKARAADRPDRSI--AFcrgdaealplPDGAFDVV 133
                                       45677************************************96666666666333..223344445667999***** PP

                   Methyltransf_23  87 vlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpag..rhisffsarslkelleeaGle 161
                                       ++r+++ ++p+p  +l+  ++ l+pgG+l+l+e   ++ +d+ ++  +y++ ++   +     a++l+e le+aGl+
  gi|336252531|ref|YP_004595638.1| 134 TARHLIWTLPNPQTALAEWQRVLEPGGRLVLLEG--YWDHDEPWD--EYEAVHEdlPLYDGRPADALREELERAGLR 206
                                       *********************************8..445555555..55554431244577789************9 PP

                   Methyltransf_23 162 vve 164
                                       ++e
  gi|336252531|ref|YP_004595638.1| 207 DIE 209
                                       987 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.0   1.6e-21   1.1e-18      33     153 ..      47     166 ..      42     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 1.6e-21
                                       HHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS..TEEEEE--T CS
                   Ubie_methyltran  33 rlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki..nieflqana 107
                                       r W +   +  ++ + ++vlDv +Gtg +++ l++      +v+++D+ ++mL+ ++ k++       +i f  ++a
  gi|336252531|ref|YP_004595638.1|  47 REWTDTGDDAGSGSQDRRVLDVGCGTGVVSLLLAELG---HDVTGVDFAPEMLERARTKARAADRPdrSIAFCRGDA 120
                                       77888888999999999***********999887754...5799***********99888766554449******** PP

                                       TT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran 108 eeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                       e+Lp  d++fDvvt  + +  +++ ++aL e  rvl pGGrlv le
  gi|336252531|ref|YP_004595638.1| 121 EALPLPDGAFDVVTARHLIWTLPNPQTALAEWQRVLEPGGRLVLLE 166
                                       ********************************************99 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0     1e-18   7.1e-16       1      99 []      66     162 ..      66     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1e-18
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsai..edakeklakrennnnnnvelealdlldldggssfDlvvasnv 75 
                                       L++GcGtG ++  l+e   + ++tgvD+ p+++  +++k++ a+r +++ ++++ +a+ l   dg  +fD+v+a ++
  gi|336252531|ref|YP_004595638.1|  66 LDVGCGTGVVSLLLAEL--GHDVTGVDFAPEMLerARTKARAADRPDRSIAFCRGDAEALPLPDG--AFDVVTARHL 138
                                       8****************..**************77777788899999999******999987777..9********* PP

                   Methyltransf_12  76 lhhlkdirevldnirklLkpgGrl 99 
                                       +  l++++ +l++  ++L pgGrl
  gi|336252531|ref|YP_004595638.1| 139 IWTLPNPQTALAEWQRVLEPGGRL 162
                                       **********************97 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 !   23.8   0.0   2.2e-08   1.5e-05     113     217 ..      57     164 ..      21     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.2e-08
                   Methyltransf_29 113 aaggkvrtvlDvGCg..vasfgayllsrdvltlslapkDeheaqvqf.aLeRgvpailavlg.tkrlpyPsrsfdli 185
                                        +g++ r vlDvGCg  v s+  + l +dv+ + +ap+   +a+ +  a +R  ++i    g ++ lp P  +fd++
  gi|336252531|ref|YP_004595638.1|  57 GSGSQDRRVLDVGCGtgVVSLLLAELGHDVTGVDFAPEMLERARTKArAADRPDRSIAFCRGdAEALPLPDGAFDVV 133
                                       567889********73356666666899*********99888887643888988888777762578*********98 PP

                   Methyltransf_29 186 hCsrCridwteedgilllevdRvlRpgGyfvl 217
                                         +r +i    +  + l e +Rvl pgG +vl
  gi|336252531|ref|YP_004595638.1| 134 T-ARHLIWTLPNPQTALAEWQRVLEPGGRLVL 164
                                       5.8999987889999*************9886 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   5.3e-08   3.7e-05      31     100 ..      61     132 ..      56     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.3e-08
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC...EEEEE-STTT.TSTTS-EEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle...vevvasdvle.eveekkfdl 100
                                       ++++vlD+GcG+Gv+++ la+   +  vt vd   + le a++ ++a +     + +   d+ +  ++++ fd+
  gi|336252531|ref|YP_004595638.1|  61 QDRRVLDVGCGTGVVSLLLAELGHD--VTGVDFAPEMLERARTKARAADRPdrsIAFCRGDAEAlPLPDGAFDV 132
                                       5689*****************9988..99***999999999999887665445566666665442344556665 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   9.3e-08   6.4e-05     161     233 ..      61     136 ..      55     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.3e-08
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk....eekadvivaN 233
                                       ++++vlDvG+G+G+ ++  a Lg+ +v++vD  +  ++ a+  a+  +  ++   +  +++ +    ++ +dv+ a 
  gi|336252531|ref|YP_004595638.1|  61 QDRRVLDVGCGTGVVSLLLAELGH-DVTGVDFAPEMLERARTKARAADRPDRSIAFCRGDAEAlplpDGAFDVVTAR 136
                                       6789*******************7.69************99999888777754344544444333456778888775 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 !   22.2   0.0   1.4e-07   9.9e-05      74     171 ..      62     164 ..      59     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.4e-07
                                       T-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC..SEEEEES-GGGTTGGG-SEEEEEE CS
                              PCMT  74 garvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle..nvivvvgDGrkGyeekaPYdaihv 148
                                         rvL+vG+G+G  + +la+l ++++   +++  +e+ e+a+ + ++ d+   ++++  gD +    +   +d++  
  gi|336252531|ref|YP_004595638.1|  62 DRRVLDVGCGTGVVSLLLAELGHDVT---GVDFAPEMLERARTKARAADRPdrSIAFCRGDAEALPLPDGAFDVVTA 135
                                       579**************999866665...*****************9998777999999999887777778887755 PP

                                       SSBBSS--H......HHHHTEEEEEEEEE CS
                              PCMT 149 gaaapeiPe......alidQLkeGGrlvv 171
                                             +P+      ++ + L++GGrlv+
  gi|336252531|ref|YP_004595638.1| 136 RHLIWTLPNpqtalaEWQRVLEPGGRLVL 164
                                       44444443311111156677888888885 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 !   21.3   0.0   1.5e-07    0.0001     112     218 ..      58     165 ..      24     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.5e-07
                                       .--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---.GGGS-T.---EEEE CS
                    Methyltransf_9 112 sdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplg.ieqlpe.leafdtv 186
                                       s  ++r++ldvGcg+G     +++e  + v G+d +   l   ++  +  +   r++ +  g  e lp    afd+v
  gi|336252531|ref|YP_004595638.1|  58 SGSQDRRVLDVGCGTGVVSL-LLAELGHDVTGVDFAPEMLERARTKARAADRPDRSIAFCRGdAEALPLpDGAFDVV 133
                                       55689***********8765.788899999****999998877766666655555555554448999996789**** PP

                                       EEES-GGG-S-HHHHHHHHHCTEEEEEEEEEE CS
                    Methyltransf_9 187 fsmGvlyhrrsPldhllqlkdqlvkgGelvle 218
                                        +  +++    P   l + +  l  gG lvl 
  gi|336252531|ref|YP_004595638.1| 134 TARHLIWTLPNPQTALAEWQRVLEPGGRLVLL 165
                                       *****************************985 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     6e-07   0.00041      33      61 ..      64      92 ..      54     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6e-07
                                      EEEEES-TTSHHHHHHHHTT-EEEEEES- CS
                              TehB 33 kvldlgcgqgrnslylsllgydvtawdkn 61
                                      +vld+gcg g  sl l+ lg+dvt +d  
  gi|336252531|ref|YP_004595638.1| 64 RVLDVGCGTGVVSLLLAELGHDVTGVDFA 92
                                      79***********************9965 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   7.1e-07   0.00049      21      75 ..      57     107 ..      38     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.1e-07
                   Methyltransf_32  21 akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75 
                                        + s++ +v+DvG+G g  s  la     +++ v+g+d   e+ e+a++ a++  
  gi|336252531|ref|YP_004595638.1|  57 GSGSQDRRVLDVGCGTGVVSLLLAE----LGHDVTGVDFAPEMLERARTKARAAD 107
                                       55678899****************9....7******************9998876 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.8e-06    0.0019      48     157 ..      62     175 ..      55     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.8e-06
                                       CC-.EEEETSTTTTTHHHHHHH-TTSE.EEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC.TTTTT-EEEEEEC CS
                              GidB  48 krdkviDvGsGaGlPGipLaiarpelk.ltLleslekkiaFLeevkeelklenveivearaee.kqeeekydvvtsR 122
                                       +r +v+DvG G G+ ++ La +  ++  +        +++  + +  + + + +++++ +ae+   +   +dvvt+R
  gi|336252531|ref|YP_004595638.1|  62 DR-RVLDVGCGTGVVSLLLAELGHDVTgVDFAPEMLERARTKARAADRPDRS-IAFCRGDAEAlPLPDGAFDVVTAR 136
                                       23.6****************99999998777777777777777899999988.**********99999********* PP

                                       -S....SSHHHHHHHHCCCEEEEEEEEEEESS--HHHHH CS
                              GidB 123 Al....aslnelteillkllkegglilalKGksaedele 157
                                        l     + ++  +  +++l++gg++++l G +++de  
  gi|336252531|ref|YP_004595638.1| 137 HLiwtlPNPQTALAEWQRVLEPGGRLVLLEGYWDHDEPW 175
                                       8732223444444444667****************9965 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.4e-06    0.0017      46     143 ..      64     163 ..      38     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.4e-06
                              NodS  46 dalevGcaaGalterlapyckrltvvdvveeaiararervk..essh..iswivsdvqqfst.dekfdlivvaevly 117
                                        +l+vGc +G ++  la + + +t vd  +e ++rar++ +  + ++  i++   d + + + d  fd++    +++
  gi|336252531|ref|YP_004595638.1|  64 RVLDVGCGTGVVSLLLAELGHDVTGVDFAPEMLERARTKARaaDRPDrsIAFCRGDAEALPLpDGAFDVVTARHLIW 140
                                       69*******************************99887655114443337778888888864256788766555554 PP

                              NodS 118 yiedvaelraavrnlvsllapdgqlv 143
                                        +    + ++a+ +  ++l p+g+lv
  gi|336252531|ref|YP_004595638.1| 141 TLP---NPQTALAEWQRVLEPGGRLV 163
                                       443...44566666666677766666 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.2e-06    0.0022      36      82 ..      60     106 ..      44     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.2e-06
                                       S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTS CS
                              TPMT  36 kaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanle 82 
                                        +  rvl  +CG ++    lAe g++v Gv++++  +e++ ++a   
  gi|336252531|ref|YP_004595638.1|  60 SQDRRVLDVGCGTGVVSLLLAELGHDVTGVDFAPEMLERARTKARAA 106
                                       566799999*****************************987776653 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.6e-06    0.0045      14     101 ..      62     155 ..      59     171 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.6e-06
                              MetW  14 gsrvldlGcGdGellellkeekqvdgrGleldeegvaecv.........akGlsviqgdldkdlenfedksfdyvvl 81 
                                         rvld+GcG G +  ll+e  + d  G++   e + ++           + ++  +gd++      +d +fd+v  
  gi|336252531|ref|YP_004595638.1|  62 DRRVLDVGCGTGVVSLLLAE-LGHDVTGVDFAPEMLERARtkaraadrpDRSIAFCRGDAEA--LPLPDGAFDVVTA 135
                                       569*********98777765.55555555544444443330000001114667777777764..4679********9 PP

                              MetW  82 sqtlqatrnpkevldellri 101
                                          + ++ np++ l e  r+
  gi|336252531|ref|YP_004595638.1| 136 RHLIWTLPNPQTALAEWQRV 155
                                       99999******999999988 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.5e-05      0.01      79     125 ..      86     133 ..      60     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                                       EEEEES-HHHHHHHHHHHHHTT.-GGGEEEEE--GGG--STTS---EE CS
                           UPF0020  79 lygsDldrrvvqgareNaekag.vgdliefsqadaakLrlkegevdvi 125
                                       + g+D+ ++++++ar++a++a   + +i+f   da +L+l++g +dv+
  gi|336252531|ref|YP_004595638.1|  86 VTGVDFAPEMLERARTKARAADrPDRSIAFCRGDAEALPLPDGAFDVV 133
                                       89******************9725668******************998 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     2e-05     0.014      64     172 ..      63     172 ..      60     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                                       SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS----..-TTEEEEES-TTTS-----..SEEEEESS CS
                    Methyltransf_2  64 kslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehlsage..eervefvgGdffkdslPea..Daillkrv 136
                                       ++++DvG GtG++    +++   ++++ f  pe  e+A+++  a+   +++++f  Gd    +lP++  D++   ++
  gi|336252531|ref|YP_004595638.1|  63 RRVLDVGCGTGVVSLLLAELGHDVTGVDF-APEMLERARTKARAADrpDRSIAFCRGDAEALPLPDGafDVVTARHL 138
                                       5789*********9999999888888888.49*******998555412678*********99999551233333333 PP

                                       GGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TT CS
                    Methyltransf_2 137 lhDwsdekcvklLkrvkkalpagGkvivveavlgad 172
                                          w+  + ++ L++ ++ l +gG++++ e   ++d
  gi|336252531|ref|YP_004595638.1| 139 --IWTLPNPQTALAEWQRVLEPGGRLVLLEGYWDHD 172
                                       ..499999999******************9876554 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.6e-05     0.038      14      65 ..      61     110 ..      57     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-05
                   Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagled 65 
                                       +++rv+D+G+  g++++ l++ g  + v+ +D +++ le+a+++++ a+  d
  gi|336252531|ref|YP_004595638.1|  61 QDRRVLDVGCGTGVVSLLLAELG--HDVTGVDFAPEMLERARTKARAADRPD 110
                                       5679*************999766..57****************999876644 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.7e-05     0.039      40      77 ..      55      90 ..      41     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-05
                   Methyltransf_16 40 lganelsklsvlELGsGtGlvGlavaellpeakviltD 77
                                      +  + +++++vl++G GtG+v l +ael  + +v+  D
  gi|336252531|ref|YP_004595638.1| 55 DAGSGSQDRRVLDVGCGTGVVSLLLAEL--GHDVTGVD 90
                                      45677899*******************9..66666555 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.3e-05     0.064      87     135 ..      54     102 ..      33     166 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.3e-05
                              DREV  87 espasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkk 135
                                        +  s+ +d+++ld+G G G ++  +a+  ++v   + + +m +r + k
  gi|336252531|ref|YP_004595638.1|  54 DDAGSGSQDRRVLDVGCGTGVVSLLLAELGHDVTGVDFAPEMLERARTK 102
                                       4567899********************9999987777777776665544 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.9e-05     0.062      64     113 ..      63     111 ..      58     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.9e-05
                                       -EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS- CS
                              CMAS  64 mtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerk 113
                                        ++Ld+GcG G +    +e  + +v g+ +  e  ++a+ +  ++d  ++
  gi|336252531|ref|YP_004595638.1|  63 RRVLDVGCGTGVVSLLLAEL-GHDVTGVDFAPEMLERARTKARAADRPDR 111
                                       689********999988887.******************99999997765 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00035      0.24      57      88 ..      60      91 ..      39      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00035
                      AdoMet_MTase 57 eketsfvdvgcgngllvyvlaaegykgygidl 88
                                       ++    dvgcg g++  +la  g+   g+d 
  gi|336252531|ref|YP_004595638.1| 60 SQDRRVLDVGCGTGVVSLLLAELGHDVTGVDF 91
                                      4566789**************99***999996 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00042      0.29      15      46 ..      75     107 ..      69     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00042
                                       HHHHHHHTTSEEEEEESSHC.HHHTT-EEEES- CS
                        Mur_ligase  15 galflalkGykvdGsdfies.lialGaaavvgh 46 
                                       ++l+la  G+ v+G df+++ l+ +  +a  ++
  gi|336252531|ref|YP_004595638.1|  75 VSLLLAELGHDVTGVDFAPEmLERARTKARAAD 107
                                       6799****************6555545555555 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 ?   11.2   0.0    0.0003      0.21       2      60 ..      63     122 ..      62     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgv.sdkitlvlgdvfe 60 
                                       r +lD+ +G+G  +  +a+ ++ v +++  +e l+ a   a++ +  +  i ++ gd + 
  gi|336252531|ref|YP_004595638.1|  63 RRVLDVGCGTGVVSLLLAELGHDVTGVDFAPEMLERARTKARAADRpDRSIAFCRGDAEA 122
                                       579***************************************999855669999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1639.96
//
Query:       gi|336252532|ref|YP_004595639.1|  [L=177]
Description: hypothetical protein Halxa_1126 [Halopiger xanaduensis SH-6]
Scores for complete 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   60.6   0.0    2.5e-16   59.6   0.0    1.4  1  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 !   59.6   0.0   1.4e-20   2.5e-16       1      75 [.      81     153 ..      81     157 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 1.4e-20
                             bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaee 75 
                                       + +t+y+it+++++ + Gi++r+ +++ ++rIq+ +leq  l+r+lg+g++ i+tag+++  +el + + p++e+
  gi|336252532|ref|YP_004595639.1|  81 WTTTRYVITSEELYKKCGIVSRDVTQFRIDRIQNTTLEQDMLGRLLGYGDLTIYTAGSGD--PELTFERTPRPER 153
                                       89999******************************************************7..9999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.19s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1450.32
//
Query:       gi|336252533|ref|YP_004595640.1|  [L=784]
Description: DEAD/DEAH box helicase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-25   87.9   0.0    2.2e-24   86.2   0.0    1.9  3  DEAD        DEAD/DEAH box helicase
      1e-14   54.3   0.0    1.4e-14   53.9   0.0    1.2  1  Sec63       Sec63 Brl domain
    1.7e-11   44.4   0.0    2.8e-11   43.7   0.0    1.3  1  ResIII      Type III restriction enzyme, res subunit
    5.3e-09   36.4   0.0    2.2e-08   34.4   0.0    2.1  1  Helicase_C  Helicase conserved C-terminal domain
    6.7e-05   23.4   2.1     0.0001   22.9   0.7    2.1  2  HHH_5       Helix-hairpin-helix domain
  ------ inclusion threshold ------
       0.12   11.2   0.0       0.17   10.6   0.0    1.1  1  UTP25       Utp25, U3 small nucleolar RNA-associated SSU proc


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 !   86.2   0.0   7.5e-28   2.2e-24       2     174 ..      21     183 ..      20     185 .. 0.85
   2 ?   -3.1   0.0       1.8   5.5e+03      87     128 ..     260     300 ..     234     323 .. 0.76
   3 ?   -3.6   0.0       2.6   7.9e+03      94     112 ..     416     436 ..     398     447 .. 0.66

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 7.5e-28
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       ++Q+ea+p++l ++++v+++a+T+sGKT+ + +++++++      +g  al+++P+r+L+++  +++ +f + +d++
  gi|336252533|ref|YP_004595640.1|  21 RMQREALPALLeREENVVASAPTASGKTALAELAICKAL-----ADGGTALFIAPLRALTNEKEDDWDRFEN-LDYS 91 
                                       68*********5556*********************999.....56889******************99999.7888 PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH....HCTSSH.CTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddll....stgkln.lsqvrflVlDEadrlldqgfsdfinrilnql 149
                                       v +++g+ +   + ++  +++di+v+tp++ld+ +    s ++ + + +v + V+DE++ l  + ++  ++  +++l
  gi|336252533|ref|YP_004595640.1|  92 VYVVTGERDL--NPRRA-RRADILVMTPEKLDSATrkhdS-RRYDfVTDVDVCVIDEVHLLDADRRGSVLEVTISRL 164
                                       8877775444..44444.67*************8866533.333379****************************** PP

                                       HHHCTTSTTTSEEEEEESSBSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 150 pqitcdgklqrqvivlSATlpkdvk 174
                                        +  cd +    v++lSAT+p +v+
  gi|336252533|ref|YP_004595640.1| 165 -RRLCDPR----VVALSATMP-NVD 183
                                       .5678756....********9.665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.8
                                       HHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  87 ardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlD 128
                                       a++ ++++ ++ d+ +g  g  d ++++++l+ +++r  VlD
  gi|336252533|ref|YP_004595640.1| 260 AEKARDEI-AERDVPMGARGDYDFHTESKELENDKLRNSVLD 300
                                       34444455.567888888888888998899999999988888 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.6
                                       HHTT..CSEEEEEHHHHHHHH CS
                                       xxxx..xxxxxxxxxxxxxxx RF
                              DEAD  94 ldng..vdivvgtpgrlddll 112
                                       l+ +  ++i +gt   ldd++
  gi|336252533|ref|YP_004595640.1| 416 LETHlnAEIAMGTITDLDDVM 436
                                       332234999999999999987 PP

>> Sec63  Sec63 Brl domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   4.8e-18   1.4e-14       2     156 ..     488     711 ..     487     773 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 4.8e-18
                                       CHHHHHHHHHT--HHHHHHHHHHS-.....TT--HHHHHHHHHTSGGGGGS---TTHHHHHHHHHHTSSS--SSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             Sec63   2 telGriaShYyisyetiklfneslk.....pnttlkdlLeilssasEFeeipvReeEkkelkkLlekvpikvkedie 73 
                                       t  G +aS+Yy++ et + f e +       + ++ d+Le++++a EFe+++ R++E++ ++++l     +  +d+e
  gi|336252533|ref|YP_004595640.1| 488 TSRGVLASKYYLRLETAAKFAELCDrveegHDLETGDVLEAVATAGEFESVSARQDERDAIDAVLVG--QE-YGDLE 561
                                       6789*****************9887444434557889***************************933..23.38*** PP

                                       SHHHHHHHHHHHHHTT---SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHTS-TT..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                             Sec63  74 speaKvniLlqayisrlklegsdlvsDlkyilqnairilralveillskgwlslalslleLskmveqrlwds..... 145
                                         + Kv  +l +  s ++ +  +l+sD++ i +na+r+++al  +l +   +++a+ + +    +e+++  +     
  gi|336252533|ref|YP_004595640.1| 562 AGQRKVLAILRSAASGTT-P-AELASDAWVIRRNATRLVSALGAFLDRFVGPHAANLARRAEARIENGVSADavglt 636
                                       *************99998.4.69*************************************99999999997779999 PP

                                       ...................................................S--EEE.EEEE............C CS
                                       ...................................................xxxxxx.xxxx............x RF
                             Sec63 146 ...................................................lPklei.eaev............q 156
                                                                                          lP++ei + +             +
  gi|336252533|ref|YP_004595640.1| 637 aidgvgpgrasklakeglstpgdiadagidglidaglsegvaervyegaqsLPSIEIdWGDFpetvatgenevrE 711
                                       999999999999999999999999999999999999999999999999999999999555556644444444442 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 !   43.7   0.0   9.5e-15   2.8e-11       3     170 ..      18     180 ..      16     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 9.5e-15
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       e++ +Q ea+ +ll     +r+++++  ++T +GKT +a ++++++l+   +   +lf++p ++l++  ++++ +f 
  gi|336252533|ref|YP_004595640.1|  18 EFNRMQREALPALL-----EREENVVASAPTASGKTALAeLAICKALADG-G--TALFIAPLRALTNEKEDDWDRFE 86 
                                       57889999999998.....899*****************99999999885.4..79********************* PP

                                       GG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T....... CS
                            ResIII  79 seaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk....... 148
                                       + +y     +v+g+++ +  +++  ++ilv+t ++ld++ ++    +     +  dv +iDE+H l a+        
  gi|336252533|ref|YP_004595640.1|  87 NLDY--SVYVVTGERDLN-PRRARRADILVMTPEKLDSATRK-HDSRRYDFVTDVDVCVIDEVHLLDADRrgsvlev 159
                                       9999..677888888877.789999***************33.4444445556667************734433333 PP

                                       TTHHHHHT---SEEEEEESS-S CS
                            ResIII 149 swreilekfkeavllglTATpe 170
                                       ++ + l+ + +  +++l+AT++
  gi|336252533|ref|YP_004595640.1| 160 TISR-LRRLCDPRVVALSATMP 180
                                       3333.44445599999999975 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 !   34.4   0.0   7.5e-12   2.2e-08      12     111 .]     239     379 ..     224     379 .. 0.62

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 7.5e-12
                                       HTTTTSEEEEEESSHH...HH...................HHHHHH........HHHT......TSTEEEESTTSTH CS
                        Helicase_C  12 leeeggkilifvntid...rl...................ekvkll........lekk......gikvavlhgelpq 52 
                                       + +e+g++l+fv +++   r+                   +             le+          va +h+ l++
  gi|336252533|ref|YP_004595640.1| 239 HLREDGQALVFVASRQdtvRAaekardeiaerdvpmgargD----YdfhteskeLENDklrnsvLDGVAFHHAGLSK 311
                                       45666777777777775331133333333333333333330....03333222211112333344567788999*** PP

                                       HHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS..........SSHHHHHHHHTTSSSTT CS
                        Helicase_C  53 nereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp..........rnvtsyiqriGRtgRag 111
                                       n+r+ i e f++g++ +L +t+ ++ G+++p   +Vi  d +           ++ ++ q+ GR+gR g
  gi|336252533|ref|YP_004595640.1| 312 NDRDLIEEWFKQGHVELLFSTSTLAWGVNLPARCVVI-RDTKlhdplegevdMSPLDVLQMLGRAGRPG 379
                                       *******************************655555.55554566666665667************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 ?   -3.9   0.0         6   1.8e+04      16      31 ..     572     585 ..     565     588 .. 0.64
   2 !   22.9   0.7   3.4e-08    0.0001       4      56 ..     635     686 ..     634     687 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 6
                                       HHHHTTT--SHHHHHH CS
                             HHH_5  16 lallsaGiesvedlaa 31 
                                       ++ +s+  +++++la+
  gi|336252533|ref|YP_004595640.1| 572 RSAASG--TTPAELAS 585
                                       334444..78999987 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 3.4e-08
                                       HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                       L+ ++G+Gp +A +l++ G +++ d+a+a ++ L ++ G+++  Aer+ + ++
  gi|336252533|ref|YP_004595640.1| 635 LTAIDGVGPGRASKLAKEGLSTPGDIADAGIDGLIDA-GLSEGVAERVYEGAQ 686
                                       899**********************************.**********99876 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 ?   10.6   0.0   5.7e-05      0.17     161     207 ..     108     152 ..     104     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.7e-05
                             UTP25 161 ssdiiiaSPlglrliieeedkkkrdtdfLsSiEvlivdqadvlemQn 207
                                       ++di++  P +l  +  ++d   r +df+  ++v+++d++++l +  
  gi|336252533|ref|YP_004595640.1| 108 RADILVMTPEKLDSATRKHD--SRRYDFVTDVDVCVIDEVHLLDADR 152
                                       68************999777..899****************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (784 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:                        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):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.43
# Mc/sec: 5497.86
//
Query:       gi|336252534|ref|YP_004595641.1|  [L=216]
Description: HAD-superfamily hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-30  104.7   0.0    6.8e-30  104.5   0.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.8e-17   64.4   0.3    8.5e-17   62.1   0.3    1.9  1  Hydrolase       haloacid dehalogenase-like hydrolase
    7.7e-10   39.5   0.5    8.9e-10   39.3   0.5    1.1  1  HAD             haloacid dehalogenase-like hydrolase
    1.7e-09   37.6   0.2    7.6e-09   35.5   0.1    2.1  2  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
       0.17   12.0   0.0       0.37   10.9   0.0    1.5  1  Ufm1            Ubiquitin fold modifier 1 protein


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 !  104.5   0.0   1.9e-33   6.8e-30       1     177 [.       4     183 ..       4     184 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 1.9e-33
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkk.. 75 
                                       ++FD+Dg+l+++e+++ ++ +  +    +    + +++++ g+++re++++l+ ++ +  +++e+ ++++e   +  
  gi|336252534|ref|YP_004595641.1|   4 VLFDMDGVLVNSEDYWTEFQADDILPAAV-PDANVDVAEVTGMNYRETYDYLEAEYGTAISRAEFEDRFEETAREiy 79 
                                       79*****************9988877766.44566899******************999977777777777766666 PP

                             HAD_2  76 .kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekk.KPdpeviekaleklkl 150
                                        ++v+ +dg+++lL eL e+g++ ++v+s+ ++ ++  le++++e+ Fd++v++ed+    KP+p+v+e a  + ++
  gi|336252534|ref|YP_004595641.1|  80 rEHVEALDGLHDLLAELGERGVERALVSSSPHDWIDIVLERFDLEDSFDHVVSAEDIDAAgKPEPDVFEYAASEVGV 156
                                       6********************************************************9988**************** PP

                             HAD_2 151 kkeeviyvGDsptDieaakkagikvia 177
                                        +ee+++v+Ds +++ea+ +ag  v+a
  gi|336252534|ref|YP_004595641.1| 157 PAEECVVVEDSENGVEAGSRAGAVVVA 183
                                       **********************98876 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.3   2.4e-20   8.5e-17       1     210 []       1     178 [.       1     178 [. 0.82

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 2.4e-20
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewl 77 
                                       + +v+fD+dG+L+++e   +++ +                     l aa  +   ++++++         +   ++l
  gi|336252534|ref|YP_004595641.1|   1 MQAVLFDMDGVLVNSEDYWTEFQADD------------------ILPAAVPDANVDVAEVTG-----MNYRETYDYL 54 
                                       679*************6666655555..................345555555666666666.....7778888888 PP

                                       HHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  78 taldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq 154
                                       +a+     +g ai+ a+ ++r +     r+     +  +    +++ +++a+L ++g+e +l++++ +   + ++++
  gi|336252534|ref|YP_004595641.1|  55 EAE-----YGTAISRAEFEDRFEETA--REIYREHV--E--ALDGLHDLLAELGERGVERALVSSSPHDWIDIVLER 120
                                       888.....888888888887776666..44444444..4..88********************************** PP

                                       TT.GGGE.SEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 155 lG.ddyf.daviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       ++ +d f ++v a di++ +kp+p+ +++a+ e +++ ee+++V+D+ n+++a+ +Ag
  gi|336252534|ref|YP_004595641.1| 121 FDlEDSFdHVVSAEDIDAAGKPEPDVFEYAASEVGVPAEECVVVEDSENGVEAGSRAG 178
                                       *******77777777777************************************9998 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.5   2.5e-13   8.9e-10       1     150 [.       4     147 ..       4     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 2.5e-13
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerf 76 
                                       +lfD+Dg L++++  +++++f +    p     + + +  ++++  + + r+ ++ l++++  + s +e+++++e+ 
  gi|336252534|ref|YP_004595641.1|   4 VLFDMDGVLVNSE--DYWTEFQADDILPA----AVPDANVDVAEVTGMNYRETYDYLEAEYGTAISrAEFEDRFEET 74 
                                       79**********3..47777555554444....44444444444445555566666777777888888888888888 PP

                               HAD  77 vaevirpk..lldpgalellaahraaGdrvvvvSgglrplvepllaelg....adevlatelevddrltgelglegk 147
                                        +e++r+   +l  g+ +lla+  ++G++ ++vS+++  ++ ++l++++    +d+v++ e     ++++  g +++
  gi|336252534|ref|YP_004595641.1|  75 AREIYREHveAL-DGLHDLLAELGERGVERALVSSSPHDWIDIVLERFDledsFDHVVSAE-----DIDAA-GKPEP 144
                                       888888774323.7*******999*************************777777777764.....55555.22333 PP

                               HAD 148 pvr 150
                                       +v+
  gi|336252534|ref|YP_004595641.1| 145 DVF 147
                                       333 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         1   3.7e+03      42      59 ..       7      24 ..       3      40 .. 0.59
   2 !   35.5   0.1   2.1e-12   7.6e-09       2      71 ..     139     203 ..     138     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                                      T-EEEEESSSSS-TTTHH CS
                    Hydrolase_like 42 GwksvLVltGvtrpedle 59
                                       +++vLV +  +  e ++
  gi|336252534|ref|YP_004595641.1|  7 DMDGVLVNSEDYWTEFQA 24
                                      577788887776664433 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 2.1e-12
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SE CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvadd 71 
                                       +gKPep ++++a+ ++g++ ee++++ D+ +  ++++ +aG+  v+++  ++++ dl+     ++ ++d+
  gi|336252534|ref|YP_004595641.1| 139 AGKPEPDVFEYAASEVGVPAEECVVVEDS-ENGVEAGSRAGAVVVAYRIDAHGDLDLS----PADEIVDS 203
                                       69***************************.******************9999998877....45777776 PP

>> Ufm1  Ubiquitin fold modifier 1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0001      0.37      29      68 ..     145     184 ..     136     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                              Ufm1  29 avlkfaaeeFkvpaatsaiitndGvginpqqtagnvflky 68 
                                        v  +aa e  vpa++++++ +   g+     ag v + y
  gi|336252534|ref|YP_004595641.1| 145 DVFEYAASEVGVPAEECVVVEDSENGVEAGSRAGAVVVAY 184
                                       6899*************************99999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); 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:                         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 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1688.06
//
Query:       gi|336252535|ref|YP_004595642.1|  [L=230]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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   38.9   0.1    1.6e-09   38.3   0.1    1.3  1  Methyltransf_11  Methyltransferase domain
    1.5e-09   38.4   0.1    2.7e-09   37.6   0.1    1.4  1  Methyltransf_25  Methyltransferase domain
    2.4e-08   34.0   0.0    3.4e-08   33.5   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.5e-05   24.7   0.0    2.9e-05   23.7   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
     0.0001   23.0   0.1    0.00025   21.7   0.1    1.7  1  Methyltransf_12  Methyltransferase domain
    0.00016   20.8   0.0     0.0002   20.4   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
    0.00025   20.9   0.1    0.00033   20.5   0.1    1.2  1  Methyltransf_31  Methyltransferase domain
     0.0033   16.9   0.0      0.084   12.3   0.0    2.1  2  TehB             Tellurite resistance protein TehB
  ------ inclusion threshold ------
      0.039   14.5   1.2       0.16   12.5   0.1    2.0  2  DUF123           Domain of unknown function DUF123
        7.2    4.5   7.2        9.2    4.2   7.2    1.0  1  AF-4             AF-4 proto-oncoprotein


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 !   38.3   0.1   8.9e-13   1.6e-09       1      87 [.      51     141 ..      51     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 8.9e-13
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-....EEEETTEECCCTSS-TT-EEEEEEES-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl....kvefvvadaeklpfednsfDlvvssevlh 72 
                                       L++Gc +Gr++ +l+ +g +++ g+++++ + ++ ++++++        ++ ++  +e   fed++fD+v+s e+l+
  gi|336252535|ref|YP_004595642.1|  51 LELGCSSGRHLSHLHANGfENLAGLEMNAHAFDVMEDAYPDLADdgtfYLDAIEDAVE--DFEDDQFDAVYSVETLQ 125
                                       89*************9999****************99999998855443444444444..5**************** PP

                                       C-.CCHHHHHHHHHHH CS
                   Methyltransf_11  73 hv.edpekalkeiaRv 87 
                                       h+ +d + +++e+ R+
  gi|336252535|ref|YP_004595642.1| 126 HLhPDAAWVFDELSRI 141
                                       **999*******9997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.1   1.5e-12   2.7e-09       1      92 [.      50     141 ..      50     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.5e-12
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGB..SSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedl..pfedgsfDlvvssgalh 75 
                                       vL+lGc +Gr++ +l+++ g +++ g+++++ + + ++  + +   + +f+   +ed   +fed++fD+v+s+ +l+
  gi|336252535|ref|YP_004595642.1|  50 VLELGCSSGRHLSHLHAN-GFENLAGLEMNAHAFDVMEDAYPDLADDGTFYLDAIEDAveDFEDDQFDAVYSVETLQ 125
                                       9***************99.69********************776559999999999953359**********999** PP

                                       GSSHHHHHHHHHHHHHH CS
                   Methyltransf_25  76 hlsdedlekalkeiarv 92 
                                       hl+ +d++ +++e++r+
  gi|336252535|ref|YP_004595642.1| 126 HLH-PDAAWVFDELSRI 141
                                       *99.6778899999886 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   1.9e-11   3.4e-08       6     101 ..      31     134 ..      22     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.9e-11
                   Methyltransf_23   6 eeelsdklerllpklraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae..kakkaqkdqfdeqeaae. 78 
                                        e++++ ler l+ + +++ vL++Gc +G+ l++l +ngf +++g +++ +a +  e   ++ a +  f+ + +++ 
  gi|336252535|ref|YP_004595642.1|  31 SERIRRRLERHLD-RGRDATVLELGCSSGRHLSHLHANGFeNLAGLEMNAHAFDVMEdaYPDLADDGTFYLDAIEDa 106
                                       4778888888887.999***********************9999****98766655555333344444433322224 PP

                   Methyltransf_23  79 ....pqgkfdlIvlrevlehvp.dppel 101
                                           ++++fd +++ e+l h++ d + +
  gi|336252535|ref|YP_004595642.1| 107 vedfEDDQFDAVYSVETLQHLHpDAAWV 134
                                       4444788**************9445444 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.6e-08   2.9e-05      15     113 ..      48     153 ..      41     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.6e-08
                              MetW  15 srvldlGcGdGellellkeekqvdgrGleldeeg..vaec....vakGlsviqgdldkdlenfedksfdyvvlsqtl 85 
                                       ++vl+lGc  G  l+ l+ +   +  Gle+++++  v+e     +a   +   + +++ +e fed++fd v    tl
  gi|336252535|ref|YP_004595642.1|  48 ATVLELGCSSGRHLSHLHANGFENLAGLEMNAHAfdVMEDaypdLADDGTFYLDAIEDAVEDFEDDQFDAVYSVETL 124
                                       68***************876656668999887762244431111233334566789999****************** PP

                              MetW  86 qatr.npkevldellrigrraivsfPnfG 113
                                       q ++ +++ v+del ri+ + +++  n G
  gi|336252535|ref|YP_004595642.1| 125 QHLHpDAAWVFDELSRIAGELLITAENEG 153
                                       ***944678***********999988766 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   1.4e-07   0.00025       1      91 [.      51     140 ..      51     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.4e-07
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       Le+Gc +G+ l++l ++  + ++ g++ +++a++  +    +  ++ +  ++  ++ + ++++ ++fD+v++ ++l+
  gi|336252535|ref|YP_004595642.1|  51 LELGCSSGRHLSHLHAN-GFENLAGLEMNAHAFDVMEDAYPDLADDGTFYLDAIEDAV-EDFEDDQFDAVYSVETLQ 125
                                       8*************999.666666*********7777777777766655555554444.445557************ PP

                   Methyltransf_12  78 hl.kdirevldnirk 91 
                                       hl +d + v+d++ +
  gi|336252535|ref|YP_004595642.1| 126 HLhPDAAWVFDELSR 140
                                       **9998888887765 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 !   20.4   0.0   1.1e-07    0.0002     100     196 ..      31     128 ..      22     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHH.HHHHCCTTTTSSEE..EE--- CS
                    Methyltransf_9 100 sdwkWdrvlphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqf.eavrkllgedqrah..llplg 173
                                       s++   r+++hl   ++ t+l++Gc++G hl  + ++g +   G++ +   +  + +a   l  +d   +   +  +
  gi|336252535|ref|YP_004595642.1|  31 SERIRRRLERHLDRGRDATVLELGCSSGRHLSHLHANGFENLAGLEMNAHAFDVMeDAYPDLA-DDGTFYldAIEDA 106
                                       6666789***************************************88765555505666665.4444330135556 PP

                                       GGGS-T---EEEEEEES-GGG-S CS
                    Methyltransf_9 174 ieqlpeleafdtvfsmGvlyhrr 196
                                       +e+++  + fd+v+s+  l h +
  gi|336252535|ref|YP_004595642.1| 107 VEDFE-DDQFDAVYSVETLQHLH 128
                                       66665.478*******9999965 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   1.8e-07   0.00033       4      99 ..      47     140 ..      44     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.8e-07
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       + +vl+lGC +G+ +  l+ + +   ++ G++++++a  +++        d  +F    ie++ +++ed++fD + s
  gi|336252535|ref|YP_004595642.1|  47 DATVLELGCSSGRHLSHLHANGF--ENLAGLEMNAHAFDVMEDA-YPDLADDGTFYLDAIEDAVEDFEDDQFDAVYS 120
                                       679****************5433..4699************995.55556679*********5545*********** PP

                   Methyltransf_31  81 nevl.naladpdkileeier 99 
                                        e+l ++ +d + ++ e++r
  gi|336252535|ref|YP_004595642.1| 121 VETLqHLHPDAAWVFDELSR 140
                                       ****7666777766666555 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   4.7e-05     0.084      32      93 ..      48     116 ..      41     133 .. 0.69
   2 ?    2.5   0.0     0.046        82     150     184 ..     187     221 ..     171     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.7e-05
                                       -EEEEES-TTSHHHHHHHHTT-E.EEEEES-HHHHHHHHHHHHHTT......-TTEEEEE--GGG---- CS
                              TehB  32 gkvldlgcgqgrnslylsllgyd.vtawdknensiafleeikeken......lknistalydineakld 93 
                                       + vl+lgc +gr   +l ++g++ +  ++ n+++   +e+     +      l++i+ a+ d ++ ++d
  gi|336252535|ref|YP_004595642.1|  48 ATVLELGCSSGRHLSHLHANGFEnLAGLEMNAHAFDVMEDAYPDLAddgtfyLDAIEDAVEDFEDDQFD 116
                                       579*******************62567899999999888764322101112245555555555554444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.046
                                       -B-TTHHHHHTTTSEEEEEE--EEEEEEE-TTS-E CS
                              TehB 150 tfkegelkeyykdwellkynedvgelhktdengnr 184
                                        + ++e+  yy+dw+ +  +    el  t+ + + 
  gi|336252535|ref|YP_004595642.1| 187 NYVNDEFPLYYRDWNGIFTDRGCTELDATEGRRDT 221
                                       677889999******99999999999888765555 PP

>> DUF123  Domain of unknown function DUF123
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   8.9e-05      0.16       2      32 ..      16      46 ..      15      51 .. 0.89
   2 ?    0.9   0.2      0.37   6.6e+02      77      93 ..      49      65 ..      45      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.9e-05
                            DUF123  2 elkkgvylYvGsalgsgglasRvkrHaslsk 32
                                      e+++ +y+Y G    s+++++R++rH+++ +
  gi|336252535|ref|YP_004595642.1| 16 EFSPEYYAYYGPDETSERIRRRLERHLDRGR 46
                                      68999*********************87755 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.37
                            DUF123 77 pvagfGasDckcesHLl 93
                                      +v ++G+s  ++ sHL+
  gi|336252535|ref|YP_004595642.1| 49 TVLELGCSSGRHLSHLH 65
                                      5679***********96 PP

>> AF-4  AF-4 proto-oncoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   7.2    0.0051       9.2     483     513 ..     158     189 ..     148     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0051
                              AF-4 483 eSDSesEssssdseanepp.rtatpepeppat 513
                                       +SDSe +ss sds+an++p r+a+++p+ +  
  gi|336252535|ref|YP_004595642.1| 158 DSDSEPDSSGSDSSANRTPdRAASSDPDVNYV 189
                                       6999999*********9996778888997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1720.65
//
Query:       gi|336252536|ref|YP_004595643.1|  [L=64]
Description: cold-shock DNA-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   70.1   0.2    1.2e-19   69.9   0.2    1.0  1  CSD              'Cold-shock' DNA-binding domain
  ------ inclusion threshold ------
      0.037   13.7   2.4       0.05   13.3   2.4    1.3  1  OB_RNB           Ribonuclease B OB domain
      0.089   12.7   0.7      0.092   12.6   0.7    1.1  1  Peptidase_M10_C  Peptidase M10 serralysin C terminal


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.2   1.9e-23   1.2e-19       2      65 ..       3      63 ..       2      64 .] 0.97

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.9e-23
                                      EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                               CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                      +GtV  fn+  g+GFI++ed d+dvF+H+ ++ g++   L+eg e+eF++++  kgp+A+nV++
  gi|336252536|ref|YP_004595643.1|  3 NGTVDFFNDTGGYGFIETEDSDDDVFFHMEDVGGED---LTEGTEIEFDIEQAPKGPRATNVVR 63
                                      7*******************************9999...***********************86 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.4   8.3e-06      0.05       8      28 ..      13      33 ..       4      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.3e-06
                                      SS-EEEEECT.TEEEEE-HHH CS
                            OB_RNB  8 kGFGFlipdegkeDifippeq 28
                                       G+GF+++++ ++D+f + e+
  gi|336252536|ref|YP_004595643.1| 13 GGYGFIETEDSDDDVFFHMED 33
                                      59**************87766 PP

>> Peptidase_M10_C  Peptidase M10 serralysin C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.7   1.5e-05     0.092       9      44 ..       4      39 ..       1      50 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                                      --EEETT--S--GGGBE-STT----EEE---SS--E CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_M10_C  9 dtvyGfnsntgrdfysaedasdklifsvWdaGGndt 44
                                       tv  fn + g  f+ +ed++d + f + d GG+d 
  gi|336252536|ref|YP_004595643.1|  4 GTVDFFNDTGGYGFIETEDSDDDVFFHMEDVGGEDL 39
                                      58888*****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 518.65
//
Query:       gi|336252537|ref|YP_004595644.1|  [L=198]
Description: ThiJ/PfpI domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-28   99.2   0.5    2.6e-28   98.9   0.5    1.1  1  DJ-1_PfpI  DJ-1/PfpI family
    0.00037   20.1   0.0      0.016   14.8   0.0    2.1  2  GATase_3   CobB/CobQ-like glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.5     3e-32   2.6e-28       5     164 ..       8     173 ..       4     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 3e-32
                                       EEEETTBEHHHHHHHHHHHHH.....TTEEEEEEESS.TSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--B..... CS
                         DJ-1_PfpI   5 vlladgvedvElivpvdvlkr.....agikvdvvsvd.keevkgsrGlkvtvdaslddvkaaeyDalvlpGG..... 70 
                                       ++l+dg++++++i p++vl++     a+++v++v+++ ++ v+ s+ l+v +d +l+     + D+l++pGG     
  gi|336252537|ref|YP_004595644.1|   8 IVLFDGFDELDAIGPYEVLENaahagASLDVQLVTLEeTDLVTASHELRVEPDGTLG-----RPDLLIVPGGgwtta 79 
                                       899*****************878888999999***997778899999*******999.....8*********44433 PP

                                       HHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEE CS
                         DJ-1_PfpI  71 ragperlrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlv 147
                                       + g   ++e+ ++ + v e + +g +va++C+g+++La+ag+l+gr +T++    ++le++ a++vd+rvv dg+++
  gi|336252537|ref|YP_004595644.1|  80 NGGVRAVVEDGVLPDAVDERYAEGATVASVCTGAMILAEAGLLEGRPATTHQVAAEDLEASAANVVDERVVDDGDVL 156
                                       34556788888999*************************************************************** PP

                                       EESSGGGHHHHHHHHHH CS
                         DJ-1_PfpI 148 Tsrgpgaaiefalelle 164
                                       T+ g+++ i++al l+e
  gi|336252537|ref|YP_004595644.1| 157 TAGGVTSGIDLALWLVE 173
                                       ************99987 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 !   14.8   0.0   1.7e-06     0.016      30      90 ..      57     118 ..      36     134 .. 0.84
   2 !    3.6   0.0    0.0049        44      29      75 ..     141     187 ..     127     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-06
                          GATase_3  30 vplkdeslgedadlvilpGgkdtiqd...lallresgldeaikeaaeaggpvlgiCGGlqmLGe 90 
                                       v+ +d +lg+ +dl+i+pGg  t+++    a+ ++  l +a+ e +++g++v  +C G ++L e
  gi|336252537|ref|YP_004595644.1|  57 VE-PDGTLGR-PDLLIVPGGGWTTANggvRAVVEDGVLPDAVDERYAEGATVASVCTGAMILAE 118
                                       44.6788877.********99998863335677778999***********************87 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0049
                          GATase_3  29 fvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeag 75 
                                        +++ de++ +d d++  +G  + i+ + +l e+++ e+i++a++++
  gi|336252537|ref|YP_004595644.1| 141 AANVVDERVVDDGDVLTAGGVTSGIDLALWLVEREFGEDIAAAVTEE 187
                                       455566777789*****************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.35
# Mc/sec: 1690.88
//
Query:       gi|336252538|ref|YP_004595645.1|  [L=176]
Description: hypothetical protein Halxa_1132 [Halopiger xanaduensis SH-6]
Scores for 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   0.3      0.046   13.9   0.3    1.7  1  DUF2749   Protein of unknown function (DUF2749)
        0.6    9.4  18.0       0.79    9.0  18.0    1.2  1  BUD22     BUD22
        7.4    6.8   7.4       0.28   11.4   1.4    1.7  2  DUF4148   Domain of unknown function (DUF4148)


Domain annotation for each model (and alignments):
>> DUF2749  Protein of unknown function (DUF2749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   7.7e-06     0.046       1      40 [.       1      39 [.       1      50 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.7e-06
                           DUF2749  1 msprilIvlviavaagagtilwlvvqpragtsgsgeaqRe 40
                                      m++ +lI+ +iav +++++  +  v  +a++s ++ea  +
  gi|336252538|ref|YP_004595645.1|  1 MNRTTLIAAAIAVLVATTGLAAA-VPGNAPASPADEADAN 39
                                      99**********98777776666.8999****99998755 PP

>> BUD22  BUD22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  18.0   0.00013      0.79     150     254 ..      33     170 ..       4     176 .] 0.38

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00013
                             BUD22 150 kkkkkkkkkkkkeeeeeeesdkeeesedsedeekeeseddeeeeeededdedaee...................... 204
                                       ++++++++++++e+ +       +es+++ +  +++ +++ +++++ ++     +                      
  gi|336252538|ref|YP_004595645.1|  33 ADEADANATNTHENGN------GNESNGAAN-ANAAGSANANADDDRAG-----Ngqgpavdlpdrvpdhvsaihdr 97 
                                       2222222222222222......222222222.11222222222222222.....12233455666777778777777 PP

                             BUD22 205 ........................deedeeaeerelaqydgllasddeded..eyneetdeesseesdssdssesa 254
                                                               d+e+++++ +++ + d+   + ded d   + +et++e +++s ++ ++esa
  gi|336252538|ref|YP_004595645.1|  98 issflsgdlenplgdeisdvtpgdDDESSDDDGDDTDADDA---DADEDGDddADANETESEVDDDSTDDADDESA 170
                                       77777777777776666666655322222222222222222...11222220011112222222222222222222 PP

>> DUF4148  Domain of unknown function (DUF4148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.4   4.6e-05      0.28       1      29 [.       1      43 [.       1      46 [. 0.79
   2 ?   -2.7   0.5       1.2   7.2e+03      38      48 ..      56      66 ..      55      74 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.6e-05
                           DUF4148  1 Mkstliaaalaaavaaaaala..............ahskspkT 29
                                      M++t+++aa++a ++a+++la              a+++++ T
  gi|336252538|ref|YP_004595645.1|  1 MNRTTLIAAAIAVLVATTGLAaavpgnapaspadeADANATNT 43
                                      9*99999999998888888888999988888877766666666 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                           DUF4148 38 aqaeaaGylps 48
                                      a+a aaG  ++
  gi|336252538|ref|YP_004595645.1| 56 ANANAAGSANA 66
                                      56777774432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 1313.42
//
Query:       gi|336252539|ref|YP_004595646.1|  [L=421]
Description: hypothetical protein Halxa_1133 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0068   16.3   0.0       0.01   15.7   0.0    1.2  1  DUF4897   Domain of unknown function (DUF4897)
  ------ inclusion threshold ------
       0.02   15.4   0.0      0.046   14.2   0.0    1.5  1  HTH_27    Winged helix DNA-binding domain
      0.098   12.4   0.0       0.19   11.5   0.0    1.4  1  HTH_39    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DUF4897  Domain of unknown function (DUF4897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.7e-06      0.01      39     147 ..     116     229 ..      97     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-06
                           DUF4897  39 eqYqkaseetfekylsqlseevgreikvvslessatereg..ileveEka.vlkglvkvengvvetslgdi..klnl 110
                                       ++Y+++  +  +  +   s+ +gre+    + +  ++r+      v+ +a + +g+v+ve++   +  gd    l l
  gi|336252539|ref|YP_004595646.1| 116 DNYTRSFADRMRTTVATASDATGREMRADGFAVETERRSFarEYGVVRYAfRWHGFVAVEDDGTVLRAGDAieGLFL 192
                                       678888888899999999999*****9999988887754312344555552789******99999999986324777 PP

                           DUF4897 111 agdselvvslPkdaklisvePtPtkivenellWkges 147
                                        + + l +  P   +l s++P P ++ e ++lW+g +
  gi|336252539|ref|YP_004595646.1| 193 DDGTRLLLEWPAGYELESATPDPDERRERAVLWRGGQ 229
                                       88899****************************9854 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 ?   14.2   0.0   7.8e-06     0.046       5      49 ..     346     390 ..     343     399 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.8e-06
                            HTH_27   5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49 
                                       + +vL+l+r r++r+k+ ++++ l  +d+ +s++++ L e + +e
  gi|336252539|ref|YP_004595646.1| 346 EEQVLRLVRDRGGRMKQQAVVEELGWTDAKTSKVVSGLREDDALE 390
                                       5689**********************************9988775 PP

>> HTH_39  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   3.2e-05      0.19      35      59 ..     139     163 ..     125     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.2e-05
                            HTH_39  35 keLrekGyeIktervteaterGrth 59 
                                       +e+r++G++++ter+ +a+e G+ +
  gi|336252539|ref|YP_004595646.1| 139 REMRADGFAVETERRSFAREYGVVR 163
                                       79*******************9855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 3345.66
//
Query:       gi|336252540|ref|YP_004595647.1|  [L=244]
Description: hypothetical protein Halxa_1134 [Halopiger xanaduensis SH-6]
Scores for 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-07   30.7   2.0    3.8e-07   30.0   1.6    1.6  1  CdvA           CdvA-like coiled-coil domain
      0.006   15.3   1.3     0.0075   15.0   1.3    1.0  1  AAA_13         AAA domain
  ------ inclusion threshold ------
      0.028   13.3   0.4      0.034   13.0   0.4    1.0  1  Fmp27_WPPW     RNA pol II promoter Fmp27 protein domain
      0.032   14.1   0.7      0.042   13.7   0.7    1.1  1  DUF724         Protein of unknown function (DUF724)
      0.037   13.3   1.7      0.059   12.7   1.7    1.2  1  DUF3450        Protein of unknown function (DUF3450)
      0.063   13.4   0.6       0.69   10.1   0.1    2.5  2  DUF2802        Protein of unknown function (DUF2802)
       0.16   12.2   5.8       0.69   10.2   5.1    2.1  2  ABC_tran_CTD   ABC transporter C-terminal domain
       0.58   10.8   3.4        5.5    7.7   2.5    2.7  2  SlyX           SlyX
        1.1    7.7   7.2        1.3    7.4   7.2    1.1  1  FUSC           Fusaric acid resistance protein family


Domain annotation for each model (and alignments):
>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   1.6   1.9e-10   3.8e-07      27     108 ..      77     157 ..      73     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.9e-10
                              CdvA  27 leealkklkekakelkeklkkrlkeledqikslekalanlkisyasGEidEeaYksaieairellesaleekeeikk 103
                                       +  +l++ ++++++ +  +++r+++ e  +++le+ la+l  s ++GE+++  Y++a  ++  +++s+++e+e +++
  gi|336252540|ref|YP_004595647.1|  77 YAAELATAENNESK-AAIIDERIATTETRLATLERRLATLNESREAGELNDGRYRAAVAKTVAEIRSLERELETVES 152
                                       55566666666555.4689********************************************************99 PP

                              CdvA 104 llekl 108
                                       + + +
  gi|336252540|ref|YP_004595647.1| 153 AAADV 157
                                       87766 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.3   3.7e-06    0.0075     371     480 ..      65     175 ..      49     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.7e-06
                            AAA_13 371 vaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeik 447
                                       +aein ++++     +  ++e +e k ++   +++  e  l ++++ ++ l+++ e  e +     a+++k  +ei+
  gi|336252540|ref|YP_004595647.1|  65 QAEINGSVSERAYAAELATAENNESKAAIIDERIATTETRLATLERRLATLNESREAGELNDGRYRAAVAKTVAEIR 141
                                       567777888777777888999******************************************************** PP

                            AAA_13 448 eLekqlrdekpaaeeinkeLkaf.GlgeleLkfe 480
                                        Le++l++++ aa+++ + + a  G  ++ ++  
  gi|336252540|ref|YP_004595647.1| 142 SLERELETVESAAADVPDRVLAEqGVDRDAIRTL 175
                                       **********999998765544449988887765 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   1.7e-05     0.034     168     243 ..      86     164 ..      73     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                        Fmp27_WPPW 168 pervqkelleeRleeleeqiekleekleelelkseke...deelkeeieelekeikelkeklefletlledlkesee 241
                                        ++ ++ +++eR+++ e+++++le++l +l++++e     d ++++ + ++  ei++l+++le++e++  d+  +  
  gi|336252540|ref|YP_004595647.1|  86 NNESKAAIIDERIATTETRLATLERRLATLNESREAGelnDGRYRAAVAKTVAEIRSLERELETVESAAADVPDRVL 162
                                       45778899*********************99999998899999************************9999877665 PP

                        Fmp27_WPPW 242 ss 243
                                       ++
  gi|336252540|ref|YP_004595647.1| 163 AE 164
                                       44 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   2.1e-05     0.042     118     187 ..      84     153 ..      68     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                            DUF724 118 ieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFeavasa 187
                                        e++es+ + ++e i+ +e + ++ler+la+l e +ea + +  r ++ ++k   e+++ e+e e+v sa
  gi|336252540|ref|YP_004595647.1|  84 AENNESKAAIIDERIATTETRLATLERRLATLNESREAGELNDGRYRAAVAKTVAEIRSLERELETVESA 153
                                       456677777899******************************************************9987 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.7   2.9e-05     0.059      22      96 ..      81     155 ..      66     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                           DUF3450  22 lkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeier 96 
                                       l++ae+  ++aa + ++i   +   ++l++++ +l+e  e+ e+   ++++ va+  +ei sle+++e +e  ++
  gi|336252540|ref|YP_004595647.1|  81 LATAENNESKAAIIDERIATTETRLATLERRLATLNESREAGELNDGRYRAAVAKTVAEIRSLERELETVESAAA 155
                                       566777777888899999***************************************************998765 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00034      0.69       3      37 ..      95     133 ..      94     137 .. 0.88
   2 ?    0.8   0.1      0.28   5.5e+02      38      49 ..     161     172 ..     132     177 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00034
                           DUF2802   3 gqrlaelekrlkqleerleel....eqqdpqsklYsqAi 37 
                                       ++r+a+ e+rl  le+rl+ l    e+ + ++++Y+ A+
  gi|336252540|ref|YP_004595647.1|  95 DERIATTETRLATLERRLATLnesrEAGELNDGRYRAAV 133
                                       8999**************999888888889999999886 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.28
                           DUF2802  38 klvrqGasveel 49 
                                        l++qG++++ +
  gi|336252540|ref|YP_004595647.1| 161 VLAEQGVDRDAI 172
                                       366666666665 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 ?   10.2   5.1   0.00034      0.69      10      61 ..      98     151 ..      73     153 .. 0.85
   2 ?    4.9   0.3     0.015        30      15      33 ..     138     156 ..     119     183 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00034
                      ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpely.sdp.eklaelsaeleeleaeLeely 61 
                                       +++ e +++ LE ++a+l++  ++ el   ++ +++a++ ae+  le eLe+ +
  gi|336252540|ref|YP_004595647.1|  98 IATTETRLATLERRLATLNESREAGELNdGRYrAAVAKTVAEIRSLERELETVE 151
                                       56788999999999999999888888876667888***************9976 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.015
                      ABC_tran_CTD  15 aeIeaLEeeiaeleaelad 33 
                                       aeI +LE e++++e + ad
  gi|336252540|ref|YP_004595647.1| 138 AEIRSLERELETVESAAAD 156
                                       4555555555555555554 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.5    0.0028       5.5       2      25 ..      95     118 ..      94     171 .. 0.71
   2 ?   -0.8   0.1       1.3   2.5e+03      37      37 ..     169     169 ..     140     195 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   2 eerleeLEiklafqedtieeLndv 25 
                                       +er+   E++la +e+ + +Ln+ 
  gi|336252540|ref|YP_004595647.1|  95 DERIATTETRLATLERRLATLNES 118
                                       789999999999999999999975 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                                       H CS
                              SlyX  37 q 37 
                                       +
  gi|336252540|ref|YP_004595647.1| 169 R 169
                                       1 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   7.2   0.00066       1.3     186     301 ..      70     188 ..       9     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00066
                              FUSC 186 reaararlaadilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpelaallae 262
                                        + + ++ aa++++ e+  s aa  ++ri+ +  +l+ l +r+++l  +  + + +  r ra+ a++v+e++ l +e
  gi|336252540|ref|YP_004595647.1|  70 GSVSERAYAAELATAENNESKAAIIDERIATTETRLATLERRLATLNESREAGELNDGRYRAAVAKTVAEIRSLERE 146
                                       245788999*************************************999999999999**********998888888 PP

                              FUSC 263 laal..eaaaaaealeaalaalrarlralrrale.adadtaa 301
                                       l+++  +aa+ +++  a+    r+++r lr++++ +d +  a
  gi|336252540|ref|YP_004595647.1| 147 LETVesAAADVPDRVLAEQGVDRDAIRTLRERASeLDGPETA 188
                                       888877777788888888888888888888888852222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1780.75
//
Query:       gi|336252541|ref|YP_004595648.1|  [L=101]
Description: MazG nucleotide pyrophosphohydrolase [Halopiger xanaduensis SH-6]
Scores for complete 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   31.4   0.3    2.3e-07   30.9   0.3    1.2  1  MazG         MazG nucleotide pyrophosphohydrolase domain
     0.0037   17.5   0.1     0.0045   17.2   0.1    1.3  1  MazG-like    MazG-like family
  ------ inclusion threshold ------
       0.07   13.8   0.7       0.11   13.1   0.6    1.4  1  Hemerythrin  Hemerythrin HHE cation binding domain


Domain annotation for each model (and alignments):
>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.3   3.9e-11   2.3e-07       8      69 ..      25      90 ..      19      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3.9e-11
                                      HHHHHHHHHHHHHHHT.....T-HH..HHH.HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH CS
                              MazG  8 aylleEvgEvaeaIkk.....edrd..ele.eELGDvLlqvlflaniaeeeggidledvaetileKlerR 69
                                      + l+ EvgE+a   ++      d d  e+e +E+GD L+ +l la +    ++id  +++e++leK+e+R
  gi|336252541|ref|YP_004595648.1| 25 LDLASEVGELAKDANEstaygSDPDglEIEsDEIGDALFALLALADS----LEIDAGEAIEEALEKYEER 90
                                      6799*********9998888766664444358**************8....******************9 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   7.6e-07    0.0045      35      72 ..      55      93 ..      26     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.6e-07
                         MazG-like 35 ldeLAdviiylylLAdrlGidfee.ideklkkklkkypv 72
                                       de+ d++  l+ LAd l+id  e i+e l+k ++++  
  gi|336252541|ref|YP_004595648.1| 55 SDEIGDALFALLALADSLEIDAGEaIEEALEKYEERLAE 93
                                      59******************************9997665 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   1.8e-05      0.11      71     117 ..      46      92 ..      33      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHCHTCGGSTCHHHHHHHHHHHHHHH CS
                       Hemerythrin  71 avldvlereHdeirelleelrellkgleepsaaafaelleeladllr 117
                                       +++d+le e dei++ l +l +l+++le  +++a +e+le++++ l+
  gi|336252541|ref|YP_004595648.1|  46 SDPDGLEIESDEIGDALFALLALADSLEIDAGEAIEEALEKYEERLA 92 
                                       6799************************999999999*****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 856.58
//
Query:       gi|336252542|ref|YP_004595649.1|  [L=398]
Description: metal dependent phosphohydrolase [Halopiger xanaduensis SH-6]
Scores for complete 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   41.6   3.8    3.4e-10   40.2   3.8    1.8  1  HD        HD domain
     0.0043   17.1   0.1      0.016   15.3   0.1    2.0  1  Clp_N     Clp amino terminal domain, pathogenicity island com


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 !   40.2   3.8   3.7e-14   3.4e-10       1      67 [.      52     117 ..      52     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 3.7e-14
                                       HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeil 67 
                                       r+eHsl+V++la r  ++l+  ++  ++l++aaL HD+G+gpfg++ e + e   +   H+++ + +l
  gi|336252542|ref|YP_004595649.1|  52 RFEHSLGVYHLASRAVDRLEVdDALADRLRAAALVHDVGHGPFGHQTEAAIER--HTDRHHDEIEWLL 117
                                       79*****************977777899*****************99988443..3334666555444 PP

>> Clp_N  Clp amino terminal domain, pathogenicity island component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.8e-06     0.016      22      48 ..     116     142 ..     116     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-06
                                       HHHSCTSHHHHHHHHTTSSHHHHHHHH CS
                             Clp_N  22 LleeddGlaarlLkkaGvdldalrkai 48 
                                       Ll+++dG++ r+L+++G+d++a+ + +
  gi|336252542|ref|YP_004595649.1| 116 LLSDPDGDLGRVLAEQGLDPAAVAATV 142
                                       89********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3000.37
//
Query:       gi|336252543|ref|YP_004595650.1|  [L=173]
Description: hypothetical protein Halxa_1137 [Halopiger xanaduensis SH-6]
Scores for 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-20   72.6   0.0    4.5e-20   72.3   0.0    1.1  1  AAA_33      AAA domain
    4.4e-06   26.1   0.1    7.1e-06   25.4   0.1    1.4  1  Zeta_toxin  Zeta toxin
    0.00077   19.0   0.0    0.00086   18.8   0.0    1.1  1  KTI12       Chromatin associated protein KTI12
     0.0026   18.2   0.1     0.0077   16.7   0.1    1.7  1  AAA_17      AAA domain
     0.0079   15.5   0.9       0.64    9.3   0.9    2.4  1  6PF2K       6-phosphofructo-2-kinase
  ------ inclusion threshold ------
       0.01   16.1   0.0      0.026   14.8   0.0    1.8  1  AAA_22      AAA domain
      0.035   14.7   0.1       0.34   11.5   0.1    2.5  2  AAA_18      AAA domain
      0.051   13.6   0.1      0.072   13.1   0.1    1.2  1  DUF3275     Protein of unknown function (DUF3275)
      0.072   12.9   0.0      0.091   12.6   0.0    1.2  1  CPT         Chloramphenicol phosphotransferase-like protein


Domain annotation for each model (and alignments):
>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.0   2.2e-23   4.5e-20       1     143 []       6     143 ..       6     143 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 2.2e-23
                            AAA_33   1 lvllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvilda 77 
                                       l++ +GlpG+GKs  +   + +l+a++ +sd++r++lf+    ++++ ++ ++ +y+ l e+a   l+ag nv+lda
  gi|336252543|ref|YP_004595650.1|   6 LIVYCGLPGVGKSAASAYTASNLPAERYRSDEVRKQLFP----DPEYTAEETQATYDELLERAWPDLEAGSNVVLDA 78 
                                       7999**********************************6....4678888999************************ PP

                            AAA_33  78 tnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrsevpeealdrqkarferp 143
                                       t+ ++r r r   la + g++     v++d ++ + R++ R  + d+ s++++++    k++fe++
  gi|336252543|ref|YP_004595650.1|  79 TFKTKRLRNRAATLADDVGAEAIFTRVTCDADVVETRIENRTST-DSVSDADLRVYRLVKESFEPL 143
                                       *******************************************5.8899**************986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   3.5e-09   7.1e-06      15     169 ..       3     139 ..       1     165 [. 0.82

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.5e-09
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRe.lhPeyeeilkadpkkaseltqkdaselvekllqe 90 
                                       rP+li+  G pG GKs+++++++ +l     + r   D++R+ l+P+        p+ ++e tq+   el e++   
  gi|336252543|ref|YP_004595650.1|   3 RPTLIVYCGLPGVGKSAASAYTASNL----PAERYRSDEVRKqLFPD--------PEYTAEETQATYDELLERAWPD 67 
                                       8************************9....45566899998625776........667999************9987 PP

                        Zeta_toxin  91 aiengyniivegtlrspdvvkklaealkkaGYevevvvvavkkelSrlgvldRyeee.vaegRlvpkeehdeafegl 166
                                        +e+g n++++ t+++    +++a+ + + G e     v+++  +  +++++R +++ v        +   ++++ +
  gi|336252543|ref|YP_004595650.1|  68 -LEAGSNVVLDATFKTKRLRNRAATLADDVGAEAIFTRVTCDADVVETRIENRTSTDsVS-------DADLRVYRLV 136
                                       .59*****************************************************9422.......2333333444 PP

                        Zeta_toxin 167 res 169
                                       +es
  gi|336252543|ref|YP_004595650.1| 137 KES 139
                                       444 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.3e-07   0.00086       3     125 ..       6     140 ..       4     173 .] 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.3e-07
                                       EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHHHHHHHTT.SEEEE-S- CS
                             KTI12   3 LvvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslrsavkrdLskekvVIvDsl 79 
                                       L+v +GlP +GKs +++  a+ l +e ++   ++++ +     +y+  ++ +a+ ++l + +  dL+    V++D++
  gi|336252543|ref|YP_004595650.1|   6 LIVYCGLPGVGKSAASAYTASNLPAERYRSDEVRKQLFP--DPEYTA-EETQATYDELLERAWPDLEAGSNVVLDAT 79 
                                       9***************************99999999887..555655.455677899999999************** PP

                                       --SHHHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHHHHTT-S.................S CS
                             KTI12  80 nyikgfRYeLyciakaakttlcvvyvvapldvlvkwneereekee...............y 125
                                         +k  R     +a  +  + +   v++++dv+ ++ e+r+  ++               +
  gi|336252543|ref|YP_004595650.1|  80 FKTKRLRNRAATLADDVGAEAIFTRVTCDADVVETRIENRTSTDSvsdadlrvyrlvkesF 140
                                       *****************************99999999999887765555555555555550 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   3.9e-06    0.0077       2     130 ..      11     126 ..      10     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.9e-06
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdg 78 
                                       G+PG+GK+ +++  + ++  + +  +d +r+        ++ ++ +++ +   +el+++a  ++   ++ ++v++d 
  gi|336252543|ref|YP_004595650.1|  11 GLPGVGKSAASAYTASNLPAERYR-SDEVRKQL-----FPDPEYTAEETQATYDELLERAWPDL---EAGSNVVLDA 78 
                                       9********************999.99999774.....45556665555555555555555555...46899***** PP

                                       -SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS- CS
                            AAA_17  79 hprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrddd 130
                                        + +k+ +   ++l ++v +e+   +++ + +d++ ++e r++ rt+ ++  
  gi|336252543|ref|YP_004595650.1|  79 TFKTKRLRNRAATLADDVGAEA---IFTRVTCDAD-VVETRIENRTSTDSVS 126
                                       **99999999999999999998...9999999998.6666666677665443 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.9   0.00032      0.64      95     149 ..      69     122 ..       1     147 [. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00032
                                       S--SEEEEES---SHHHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHHHHHHTTT CS
                             6PF2K  95 eegqvaifDAtNttrerRklilefveennlkvlflesicsdeeiikeNikevkls 149
                                       e g+  + DAt  t+  R+   + + + + +++f  ++c d +++++ i++ +++
  gi|336252543|ref|YP_004595650.1|  69 EAGSNVVLDATFKTKRLRNRAATLADDVGAEAIFTRVTC-DADVVETRIENRTST 122
                                       677778999999999999999999999999999999999.678888888876654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.3e-05     0.026       6      81 ..       5      88 ..       2     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv....fvtlpsst.sskdllrellralglelka...erlsse 76
                                      +++v +G +G+GK+   +  +++l++e +  +e ++++    ++t+ +   + ++ll++   +l+ + +    ++ +++
  gi|336252543|ref|YP_004595650.1|  5 TLIVYCGLPGVGKSAASAYTASNLPAERYRSDEVRKQLfpdpEYTAEETQaTYDELLERAWPDLEAGSNVvldATFKTK 83
                                      67999********************999998866666645444444444444555554444444433333666455555 PP

                            AAA_22 77 ellea 81
                                      +l+++
  gi|336252543|ref|YP_004595650.1| 84 RLRNR 88
                                      55544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00017      0.34       1     115 [.       7     121 ..       7     131 .. 0.54
   2 ?    1.6   0.1      0.19   3.9e+02      99     117 ..     105     123 ..      82     169 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknl 77 
                                       I+ +G pGvGK+  + + ++ l   +  +d +++    +          +   e+ ++   ++le++  +le g+n+
  gi|336252543|ref|YP_004595650.1|   7 IVYCGLPGVGKSAASAYTASNLPAERYRSDEVRKQLFPD---------PEYTAEETQATYDELLERAWPDLEAGSNV 74 
                                       5669***********999887633333333333322222.........22222333333333444333356667777 PP

                            AAA_18  78 vidghlaele.seaakdikk........vvLtaspeelleRlekRgy 115
                                       v+d      +   +a  +            +t++ ++   R+e+R  
  gi|336252543|ref|YP_004595650.1|  75 VLDATFKTKRlRNRAATLADdvgaeaifTRVTCDADVVETRIENRTS 121
                                       77765544441222222222566677666677777777777777765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.19
                            AAA_18  99 LtaspeelleRlekRgyee 117
                                       +t++ ++   R+e+R  ++
  gi|336252543|ref|YP_004595650.1| 105 VTCDADVVETRIENRTSTD 123
                                       5666666666666665443 PP

>> DUF3275  Protein of unknown function (DUF3275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.6e-05     0.072     145     192 ..      43      93 ..      15     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.6e-05
                           DUF3275 145 apapvaaegktededaaLFGelWp...leesvkLDatvdrrvlRaqiarlk 192
                                        p p+ ++++t+++ ++L    Wp   ++ +v LDat   ++lR++ a l 
  gi|336252543|ref|YP_004595650.1|  43 FPDPEYTAEETQATYDELLERAWPdleAGSNVVLDATFKTKRLRNRAATLA 93 
                                       6889999999**************9777889***************99985 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.6e-05     0.091      62     131 ..      50     120 ..      19     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                                       -HHHHHHHHHHHHHHHHHHHTT-EEEEEE--TTTHHHHHHHHHHHT..TS-EEEEEEE--HHHHHHHHHHHT CS
                               CPT  62 gpeldlllaalyeavaamaraGnnvivDdvilekewlvdllrrlls..gldvllVGvrcplevlerRelerg 131
                                         e++++++ l e     ++aG nv++D  + +k+ l +++  l    g + ++  v c+ +v+e R  +r+
  gi|336252543|ref|YP_004595650.1|  50 AEETQATYDELLERAWPDLEAGSNVVLDATFKTKR-LRNRAATLADdvGAEAIFTRVTCDADVVETRIENRT 120
                                       55666666777776677789********9999999.67777566651156899**************88875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); 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:                         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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1321.15
//
Query:       gi|336252544|ref|YP_004595651.1|  [L=353]
Description: phosphonate ABC transporter periplasmic phosphonate-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-49  167.9   0.1    3.4e-49  167.7   0.1    1.1  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
  ------ inclusion threshold ------
      0.033   14.3   1.8      0.054   13.5   1.8    1.2  1  PTN13_u3        Unstructured linker region on PTN13 protein b
       0.12   12.7   0.0        1.1    9.6   0.0    2.4  2  DUF4177         Domain of unknown function (DUF4177)


Domain annotation for each model (and alignments):
>> 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 !  167.7   0.1   5.6e-53   3.4e-49       1     243 []      71     335 ..      71     335 .. 0.93

  Alignments for each domain:
  == domain 1  score: 167.7 bits;  conditional E-value: 5.6e-53
                                       EEE--SS-HHHHHHHHHHHHHHHHHHH........SSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS- CS
                    Phosphonate-bd   1 igvlPsespaelkeayqpladyLseel........GvevelvvatdyaavvealragqvDiaflgplayvqardqag 69 
                                       +g+ Ps  +++l+ +y+pl d++++ +        G  ++ +++++y+a++++l +g++D+a +gp+a+   +  ++
  gi|336252544|ref|YP_004595651.1|  71 FGISPSVPQEDLEVQYSPLEDHVESYVtenydtadGLSIQSTIGSNYSAIIQSLGQGTMDFAETGPFAAGLGVMTDN 147
                                       799**********************9999999999999*************************************** PP

                                       EEEEEEEEETT--SEEEEEEEEETTSS--SHHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHH......... CS
                    Phosphonate-bd  70 veplatrvrsdGsasyrsviivradsdiqsledLkgktiafvspsStsGylvpaalLvkeagldpedd......... 137
                                       +e +++r + +G  +y+s+i+v++dsdi++l+dL gk++af ++ StsG l+p++ L+ e gld++++         
  gi|336252544|ref|YP_004595651.1| 148 AEIILQRYG-YGGWTYKSIIAVPTDSDITELSDLSGKSVAFSDQLSTSGALYPLYALSTEGGLDIGNLpdgngsqae 223
                                       ********9.********************************************************54444445555 PP

                                       SSEEEE--HHHHHHHHHTTSSSEEEEEHHHHHHHHHH-HHHHTTE.EEEEEEEEEE--EEEEETTS-HHHHHHHHHH CS
                    Phosphonate-bd 138 fsevfsgshdaavlavlsgdadaaavsadaledlvaegpedkdel.rviassppipndpvvvrkelseelkekiqda 213
                                       f++ f+g+h +++  + +g++daaa+  ++++     +p++ +e+ + +++ + +p++p+vv++el ee+k++iq+a
  gi|336252544|ref|YP_004595651.1| 224 FDARFAGGHVGSYTLLEQGQVDAAAMGGFVRDTSTGPAPDEFEEVaTTLHEDEGLPRAPIVVSPELGEEEKNAIQQA 300
                                       *******************************9998777777766536689999************************ PP

                                       HHH---S.....HHHHHHHHHTTEEEEEE--GGGG CS
                    Phosphonate-bd 214 llslaet.....eegkkllealgiegfvpaddsdy 243
                                       +l+ + +     +++    ++l+++ + +a+++dy
  gi|336252544|ref|YP_004595651.1| 301 FLEGPDSiyhgaDGEEGTDDDLWFSDVREASQEDY 335
                                       ***9988999978888888888************9 PP

>> PTN13_u3  Unstructured linker region on PTN13 protein between PDZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.8   9.1e-06     0.054     138     176 ..      24      62 ..      20      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.1e-06
                          PTN13_u3 138 leysDrGDSDmDEetYssSQekqkkkkessssnimekln 176
                                       ++  D GDSD D+ t s SQ    ++ +s++++ +++l 
  gi|336252544|ref|YP_004595651.1|  24 SDGGDGGDSDGDNTTTSESQATTESNGNSTTTEESNQLA 62 
                                       56789********************99999888887775 PP

>> DUF4177  Domain of unknown function (DUF4177)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00018       1.1      21      45 ..     146     169 ..     131     178 .. 0.76
   2 ?   -0.6   0.0      0.29   1.7e+03      12      31 ..     321     340 ..     316     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00018
                           DUF4177  21 eeleeyqeilnelAkeGWrlvsii..p 45 
                                       ++ e    il++++  GW ++sii  p
  gi|336252544|ref|YP_004595651.1| 146 DNAEI---ILQRYGYGGWTYKSIIavP 169
                                       55566...***************9644 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.29
                           DUF4177  12 glgngkieeeeleeyqeiln 31 
                                        l+ +++ e+++e+yq +++
  gi|336252544|ref|YP_004595651.1| 321 DLWFSDVREASQEDYQSVID 340
                                       55667888999*****9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2881.57
//
Query:       gi|336252545|ref|YP_004595652.1|  [L=267]
Description: phosphonate ABC transporter ATPase [Halopiger xanaduensis SH-6]
Scores for 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-33  113.7   0.1    1.2e-32  113.2   0.1    1.2  1  ABC_tran     ABC transporter
    1.3e-06   28.5   0.0      0.018   14.9   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.2e-05   25.8   0.1    1.7e-05   25.2   0.1    1.2  1  AAA_16       AAA ATPase domain
    5.8e-05   22.6   0.1     0.0029   17.1   0.1    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    9.6e-05   22.3   0.0    0.00025   21.0   0.0    1.6  2  RsgA_GTPase  RsgA GTPase
    0.00071   19.3   1.2     0.0016   18.2   1.2    1.6  1  AAA_30       AAA domain
    0.00097   18.8   0.0     0.0019   17.9   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0052   16.8   0.1       0.02   15.0   0.1    2.0  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0062   16.1   0.0      0.015   14.9   0.0    1.6  1  AAA_25       AAA domain
  ------ inclusion threshold ------
      0.026   14.5   0.3       0.14   12.2   0.0    2.0  2  AAA_5        AAA domain (dynein-related subfamily)
      0.028   14.2   0.0       0.18   11.5   0.0    2.0  2  IstB_IS21    IstB-like ATP binding protein
       0.04   14.5   0.0      0.067   13.7   0.0    1.7  1  AAA_18       AAA domain
      0.066   13.5   0.2       0.16   12.3   0.2    1.9  1  AAA_22       AAA domain
      0.069   13.3   0.1      0.096   12.8   0.1    1.5  1  AAA_33       AAA domain
       0.07   12.7   0.1       0.16   11.5   0.0    1.6  2  AAA_27       AAA domain
      0.086   13.3   0.0       0.15   12.5   0.0    1.5  1  AAA_23       AAA domain
      0.096   12.9   0.5        1.5    9.1   0.5    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.15   10.7   0.0        6.3    5.3   0.0    2.0  2  AAA_13       AAA domain
       0.24   11.1   0.0         14    5.3   0.0    2.1  2  AAA_15       AAA ATPase 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 !  113.2   0.1   1.3e-35   1.2e-32       1     137 []      20     168 ..      20     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 1.3e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++vs+++ ege v ++G++GaGKSt+l++l gl++pteG++++ +++++       r+ +g+++qe+ l + +t+ 
  gi|336252545|ref|YP_004595652.1|  20 LDDVSFTIPEGEFVILLGPSGAGKSTMLRVLNGLTEPTEGTVRVGDQEVQG-----NRSDVGMVFQEHYLIESKTAF 91 
                                       79****************************************888877777.....9******************99 PP

                                       HH..................HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xx..................xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..................esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                        n                  +s+++   + +al+++gl + + +++    +s+SgGqkqrv +aral+++p+l+l+D
  gi|336252545|ref|YP_004595652.1|  92 GNaltgalsrnsllrsmlgmHSEADklnALEALDTVGLLDEAGQRA----ESMSGGQKQRVGIARALVQEPQLVLAD 164
                                       999***************9944444233677777777777666666....*************************** PP

                                       STTT CS
                                       xxxx RF
                          ABC_tran 134 Epta 137
                                       Ep a
  gi|336252545|ref|YP_004595652.1| 165 EPVA 168
                                       **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 !   11.7   0.0   0.00018      0.17       1      23 [.      32      54 ..      32      92 .. 0.77
   2 !   14.9   0.0   1.9e-05     0.018     234     290 ..     137     198 ..     107     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      + +l Gp g+GKS+ L+ l +l 
  gi|336252545|ref|YP_004595652.1| 32 FVILLGPSGAGKSTMLRVLNGLT 54
                                      679****************9994 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.9e-05
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr........nga 290
                                       a ++S G+k+  +++ al + +    l+l DEp ++L+Pk+ r +++ lk++++         + 
  gi|336252545|ref|YP_004595652.1| 137 AESMSGGQKQRVGIARALVQEP---QLVLADEPVASLDPKAARDVMRYLKKAATeenlttitSLH 198
                                       6688999999988888888888...99**********************6665545555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   1.8e-08   1.7e-05      22     126 ..      28     185 ..      17     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.8e-08
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekd.................ggiflrgkcdqlesaipysa.laqalaree 80 
                                       +++e v+l G+sG GKs+++r l   l++                  ++  + ++    es++++   l+ al+r++
  gi|336252545|ref|YP_004595652.1|  28 PEGEFVILLGPSGAGKSTMLRVLN-GLTEPtegtvrvgdqevqgnrsDVGMVFQEHYLIESKTAFGNaLTGALSRNS 103
                                       34599***************9998.5666667666666666666665333333333333456999777********* PP

                            AAA_16  81 llrqlldeaesaeleawrekleeala....................................avpelagaeasrlle 121
                                       llr +l ++++a+   + e+l+++                                      +v++l++++a+++ +
  gi|336252545|ref|YP_004595652.1| 104 LLRSMLGMHSEADKLNALEALDTVGLldeagqraesmsggqkqrvgiaralvqepqlvladePVASLDPKAARDVMR 180
                                       ********777666666666666555777777777777777777777777777777777777777777777666666 PP

                            AAA_16 122 llkrl 126
                                        lk++
  gi|336252545|ref|YP_004595652.1| 181 YLKKA 185
                                       65555 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 !   17.1   0.1   3.1e-06    0.0029     118     201 ..     121     201 ..      21     218 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.1e-06
                                       E-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEE.E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                             SMC_N 118 vtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQf.i 193
                                        +  +   ll +ag   e++SgG+k+ v +a       v+   l+l De  a LD k  + v ++lk++ ++  +  
  gi|336252545|ref|YP_004595652.1| 121 LEALDTVGLLDEAGQRAESMSGGQKQRVGIARA----LVQEPQLVLADEPVASLDPKAARDVMRYLKKAATEENLtT 193
                                       233466678888888888********9988754....466777999*********************8776654404 PP

                                       EE-SSHHH CS
                                       xxxxxxxx RF
                             SMC_N 194 vislreem 201
                                       ++sl++  
  gi|336252545|ref|YP_004595652.1| 194 ITSLHQVN 201
                                       44554443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.7e-07   0.00025      85     130 ..      15      61 ..       5      73 .. 0.76
   2 ?   -2.6   0.0       4.7   4.4e+03      13      39 ..     185     211 ..     173     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.7e-07
                                       TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       +++ +l++++  + + ++++l+G+SG+GKSt++ +l++ +e   g v
  gi|336252545|ref|YP_004595652.1|  15 EDTVALDDVSFTIPEgEFVILLGPSGAGKSTMLRVLNGLTEPTEGTV 61 
                                       55566778888887779*******************98655544444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.7
                                       EES--EEEEEEESTTTT--HHHHHHHH CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfL 39 
                                       +a  ++l  ++sl++ ++  ++ drfL
  gi|336252545|ref|YP_004595652.1| 185 AATEENLTTITSLHQVNIAREFGDRFL 211
                                       555566777778888888777777777 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.2   1.7e-06    0.0016      19     114 ..      31     184 ..      23     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g............................grviglAptgkaAkv..Lae 64 
                                        +++l Gp G+GK+t+l++l+ + e   g                            ++ +g A tg+ +++  L+ 
  gi|336252545|ref|YP_004595652.1|  31 EFVILLGPSGAGKSTMLRVLNGLTEPTeGtvrvgdqevqgnrsdvgmvfqehyliesKTAFGNALTGALSRNslLRS 107
                                       5899*********************9956888888888888888888888888888888888888888888776777 PP

                            AAA_30  65 elgi..eastiakllkrlk........................grarlepgtllivDE.agmvdtkqlaallkaaek 114
                                        lg+  ea+ ++ l    +                        +ra +++ +l++ DE ++ +d k ++++++ ++k
  gi|336252545|ref|YP_004595652.1| 108 MLGMhsEADKLNALEALDTvglldeagqraesmsggqkqrvgiARALVQEPQLVLADEpVASLDPKAARDVMRYLKK 184
                                       77765566666665544447777777778888888777777775566666688888884455666666666666665 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   0.0     2e-06    0.0019      13      39 ..      21      47 ..      17      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      d+ +++i + ++++l GpsG+GKST+l
  gi|336252545|ref|YP_004595652.1| 21 DDVSFTIPEGEFVILLGPSGAGKSTML 47
                                      556778875559*************98 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.1e-05      0.02       2      64 ..      33     137 ..      32     198 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                                       EEEEESTTSSHHHHHHHHHT.....S.TEEESSSTTSSSSEEEEEEEETTEE......................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg.....e.kaivsdkpgtTrdinegrvklkgke......................... 47 
                                       v+++G + +GKSt+++ l g     e +++v+d+         g v  +  +                         
  gi|336252545|ref|YP_004595652.1|  33 VILLGPSGAGKSTMLRVLNGlteptEgTVRVGDQEVQGNRSDVGMVFQE--Hyliesktafgnaltgalsrnsllrs 107
                                       899************9997755454247788888777777777766422..13455556677777777777778888 PP

                                       .............EEEEECGGCSS..HHHHHH CS
                          MMR_HSR1  48 .............ielvDtpGlie..gaseek 64 
                                                    +e +Dt+Gl++  g  ++ 
  gi|336252545|ref|YP_004595652.1| 108 mlgmhseadklnaLEALDTVGLLDeaG--QRA 137
                                       888888888888899999999875231..221 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.6e-05     0.015      30      50 ..      27      47 ..      23      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +p+ge+++l G++g+GK+t++
  gi|336252545|ref|YP_004595652.1| 27 IPEGEFVILLGPSGAGKSTML 47
                                      8******************97 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   0.00015      0.14       2      24 ..      33      56 ..      32      73 .. 0.82
   2 ?   -0.2   0.0      0.94   8.9e+02      32      75 ..     182     225 ..     174     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                      EEEE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal.n 24
                                      v+L+Gp+G gKs++ + l  ++  
  gi|336252545|ref|YP_004595652.1| 33 VILLGPSGAGKSTMLRVLNGLTeP 56
                                      89**************99988864 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.94
                                       --TT--HHHHH--B--.........--------G-SEEEEESGG CS
                             AAA_5  32 ltrdtteedlkgrreikngttslvdsplvraaregeilvlDEve 75 
                                       l++  tee+l+  +++ + + +++ +     +r ge++++++ +
  gi|336252545|ref|YP_004595652.1| 182 LKKAATEENLTTITSLHQVNIAREFGDRFLGIRDGEVIFDGDAD 225
                                       67788999999999998555555555444458999999998876 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 ?   11.5   0.0    0.0002      0.18      22      63 ..       4      46 ..       1      52 [. 0.84
   2 ?    0.1   0.0       0.6   5.6e+02     105     150 ..     153     199 ..     137     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                         IstB_IS21 22 idfraarsldkrkvkeLatlsf.iekkenivllGpsGvGKshl 63
                                      i+f++ +++  + + +L   sf i + e ++llGpsG+GKs +
  gi|336252545|ref|YP_004595652.1|  4 IEFENVTKIYGEDTVALDDVSFtIPEGEFVILLGPSGAGKSTM 46
                                      78888888888889999999995678899***********965 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.6
                         IstB_IS21 105 rllkvdllilDdlgllpldqaeaellfeviekr.yerrsiiitsnlp 150
                                       +l++   l+l d  +  ld ++a+++++ ++k+  e + + its  +
  gi|336252545|ref|YP_004595652.1| 153 ALVQEPQLVLADEPVASLDPKAARDVMRYLKKAaTEENLTTITSLHQ 199
                                       45555445666667889999999999998887515666677777544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.1e-05     0.067       1      25 [.      33      72 ..      33     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf...............g 25
                                      ++l G++G+GK+t+ + L+ +++                 
  gi|336252545|ref|YP_004595652.1| 33 VILLGPSGAGKSTMLRVLNGLTEPtegtvrvgdqevqgnR 72
                                      79***************95543223444444444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00016      0.16       6      27 ..      31      52 ..      28     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                            AAA_22  6 gilvvtGesGtGKTtllrrlle 27
                                       ++++ G+sG+GK+t lr l  
  gi|336252545|ref|YP_004595652.1| 31 EFVILLGPSGAGKSTMLRVLNG 52
                                      5899***********9997655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1    0.0001     0.096       2      32 ..      33      67 ..      32     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                            AAA_33  2 vllvGlpGsGKstlaerl..lkklg..avllssdt 32
                                      v+l G++G+GKst ++ l  l + +  +v++   +
  gi|336252545|ref|YP_004595652.1| 33 VILLGPSGAGKSTMLRVLngLTEPTegTVRVGDQE 67
                                      7999**********998755333334666666555 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   0.00017      0.16      19      48 ..      23      52 ..      12      54 .. 0.82
   2 ?   -3.1   0.1       5.1   4.8e+03     141     172 ..      88     118 ..      83     140 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisd 48
                                      ++f   e ++ +++Gp  AGKst+lr ++ 
  gi|336252545|ref|YP_004595652.1| 23 VSFTIPEGEFVILLGPSGAGKSTMLRVLNG 52
                                      455566899****************98765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.1
                            AAA_27 141 egelgqlLfeasaGlaslrevleaLeaeadel 172
                                       +   g++L  a +  +sl + +  +++ead+l
  gi|336252545|ref|YP_004595652.1|  88 KTAFGNALTGALSR-NSLLRSMLGMHSEADKL 118
                                       55555555555554.33333344455555554 PP

>> AAA_23  AAA domain
   #    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      17      39 ..      25      50 ..       3      84 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                            AAA_23 17 F...skgltlItGpNGaGKTTildAi 39
                                      F   +  ++++ Gp GaGK+T l+ +
  gi|336252545|ref|YP_004595652.1| 25 FtipEGEFVILLGPSGAGKSTMLRVL 50
                                      35566778999***********9876 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 ?    9.1   0.5    0.0016       1.5      62      89 ..     156     183 ..     129     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                       + ++lv+ DE  ++lD++ ++ ++++l+
  gi|336252545|ref|YP_004595652.1| 156 QEPQLVLADEPVASLDPKAARDVMRYLK 183
                                       4589*********************997 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.025        24      22      70 ..      36      83 ..      30      98 .. 0.78
   2 ?    5.3   0.0    0.0067       6.3     525     559 ..     156     189 ..     146     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.025
                            AAA_13 22 YGwNGaGKTtLSrllrslelgetepkfangsieitngeeldirVfNrdF 70
                                       G  GaGK+t+ r+l+ l+ + te     g  e++ +++   +Vf + +
  gi|336252545|ref|YP_004595652.1| 36 LGPSGAGKSTMLRVLNGLT-EPTEGTVRVGDQEVQGNRSDVGMVFQEHY 83
                                      5889*************95.45566666666688777777778887766 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0067
                            AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkk 559
                                       ++ + v  D Pv SLD ++   v+ ++k+ +  ++
  gi|336252545|ref|YP_004595652.1| 156 QEPQLVLADEPVASLDPKAARDVMRYLKKAA-TEE 189
                                       6788999*********************998.233 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.015        14      19      46 ..      27      53 ..      19      88 .. 0.83
   2 ?    4.1   0.0     0.033        31     323     357 ..     157     191 ..     112     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.015
                            AAA_15 19 idlseeltvliGkNnsGKSsilealdlF 46
                                      i+  e + +l G+ ++GKS+ l++l+ +
  gi|336252545|ref|YP_004595652.1| 27 IPEGE-FVILLGPSGAGKSTMLRVLNGL 53
                                      44445.99***************99865 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.033
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnkt 357
                                       ++ ++l +EP a+L p+a + ++++lk++a +++ 
  gi|336252545|ref|YP_004595652.1| 157 EPQLVLADEPVASLDPKAARDVMRYLKKAATEENL 191
                                       5689999***********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 1923.99
//
Query:       gi|336252546|ref|YP_004595653.1|  [L=330]
Description: phosphonate ABC transporter inner membrane subunit [Halopiger xanaduensis SH-6]
Scores for 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   17.3   0.5      0.003   16.6   0.5    1.4  1  MMPL       MMPL family


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 !   16.6   0.5   1.6e-07     0.003     153     246 ..     221     318 ..     198     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-07
                              MMPL 153 lvvilviLlivyrSlvaallplltvvvsllaalglv.......lilalllglelstfvlgllvvlliavGtDYallL 222
                                         v + +L  v rS++a++l +l + + ++++lg+v       +i +  + ++ +++++gl +v+++  G+    l+
  gi|336252546|ref|YP_004595653.1| 221 QTVSFGMLSQVSRSFIAWTLYILEINTRIAISLGVVgagglglMIRNSQDLFAFQQTAAGLIMVFIVVLGIE---LI 294
                                       4567889999************9887766666665422222226777788899999***************9...99 PP

                              MMPL 223 vsRyreelaagedreeaviravas 246
                                        sR+r +l+ ge+  +++ +av++
  gi|336252546|ref|YP_004595653.1| 295 SSRIRARLRPGEHDSKGLVEAVRD 318
                                       *********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2417.27
//
Query:       gi|336252547|ref|YP_004595654.1|  [L=262]
Description: DNA topoisomerase type IA zn finger domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-06   26.2   0.0    6.2e-06   25.7   0.0    1.2  1  NucS            Endonuclease NucS
    0.00026   20.7   4.5      0.035   13.9   0.4    2.6  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
  ------ inclusion threshold ------
       0.15   12.2  15.2       0.18   12.0   1.6    3.8  3  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.82    9.6   3.3        1.2    9.2   0.3    2.6  3  zinc_ribbon_4   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.4e-09   6.2e-06       3      88 ..       5      86 ..       3      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.4e-09
                              NucS  3 avlvvlarCkvsyeGraksrLeegerlivikpdGaflvhkdrkvePvnWqppkssltaevedgslilksirrkpeeeLk 81
                                      a++v+   C+v  eG  + +   g+   v+kpd ++lvh    ++Pv W +   s+  + +dg+  +    +k  + L+
  gi|336252547|ref|YP_004595654.1|  5 AIRVLAGDCTVITEGTEREEY-RGRMTTVVKPDNTVLVHDSDGYQPVAWLTRADSVSSDRSDGFTLV---AKKDAQTLR 79
                                      6899999********998876.689999***********************9999998999998764...567777888 PP

                              NucS 82 veieeve 88
                                      +  +e +
  gi|336252547|ref|YP_004595654.1| 80 IAAHEQD 86
                                      8888765 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 !    7.8   0.3   0.00064       2.9       2      16 ..     101     115 ..     100     118 .. 0.86
   2 !   13.9   0.4   7.7e-06     0.035       5      32 ..     183     209 ..     178     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00064
                                       EE-SSS--EEEEEE- CS
                    zf-C4_Topoisom   2 ekCPkCggdLvlkrg 16 
                                       ++CP C g Lv+ rg
  gi|336252547|ref|YP_004595654.1| 101 GTCPDCSGALVRSRG 115
                                       79********98776 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.7e-06
                                       SSS--EEEEEE-SSSEEEEESST.T--- CS
                    zf-C4_Topoisom   5 PkCggdLvlkrgkkGkFvGCsnYPeCkf 32 
                                       P C gdL + r + G   GC +YP+C++
  gi|336252547|ref|YP_004595654.1| 183 PGCDGDLRILR-RGGLIAGCEHYPDCDT 209
                                       33778876643.567999********85 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 ?   12.0   1.6   4.1e-05      0.18      17      40 .]     102     122 ..     101     122 .. 0.90
   2 ?    4.4   0.4    0.0092        41      16      27 ..     138     148 ..     137     158 .. 0.83
   3 ?    3.5   1.0     0.018        82      17      36 ..     221     237 ..     218     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
                     Auto_anti-p27  17 tCpvCgvPLmrdrkggkvyCvaCd 40 
                                       tCp+C+  L+r+r+   v C+ C+
  gi|336252547|ref|YP_004595654.1| 102 TCPDCSGALVRSRG---VHCIDCG 122
                                       7**********985...69****6 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0092
                     Auto_anti-p27  16 etCpvCgvPLmr 27 
                                        +C+ Cg P mr
  gi|336252547|ref|YP_004595654.1| 138 HNCD-CGLPRMR 148
                                       5795.******9 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.018
                     Auto_anti-p27  17 tCpvCgvPLmrdrkggkvyC 36 
                                        C  Cg P ++++ g++  C
  gi|336252547|ref|YP_004595654.1| 221 ECA-CGLPTFETQSGTR--C 237
                                       585.*******975444..4 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.19   8.6e+02       4       9 ..     102     107 ..     100     109 .. 0.83
   2 ?    9.2   0.3   0.00026       1.2       3      25 ..     116     139 ..     115     143 .. 0.82
   3 ?   -3.4   0.0       2.1   9.6e+03       6      14 ..     205     213 ..     205     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.19
                     zinc_ribbon_4   4 tCpsCk 9  
                                       tCp C+
  gi|336252547|ref|YP_004595654.1| 102 TCPDCS 107
                                       799996 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00026
                     zinc_ribbon_4   3 itCpsCkakyeiddek.lpakgvk 25 
                                       ++C  C+a+y ++++  ++ +g +
  gi|336252547|ref|YP_004595654.1| 116 VHCIDCGARYGVPSDAtIRNDGHN 139
                                       79***********99878877765 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.1
                     zinc_ribbon_4   6 psCkakyei 14 
                                       p C + ++ 
  gi|336252547|ref|YP_004595654.1| 205 PDCDTGFAM 213
                                       779998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2009.20
//
Query:       gi|336252548|ref|YP_004595655.1|  [L=354]
Description: tRNA-splicing endonuclease [Halopiger xanaduensis SH-6]
Scores for 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-32  108.9   0.4      2e-26   91.9   0.1    3.7  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    8.1e-24   83.1   0.2    7.6e-11   41.5   0.0    2.7  3  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
     0.0055   16.9   0.1        3.1    8.0   0.1    2.5  2  tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-t
  ------ inclusion threshold ------
       0.13   12.5   1.5        0.3   11.3   0.1    2.4  3  TPR_9            Tetratricopeptide repeat


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 !   10.9   0.0   8.3e-05      0.37       3      61 ..      83     151 ..      81     164 .. 0.75
   2 !   91.9   0.1   4.5e-30     2e-26       1      85 []     259     346 ..     259     346 .. 0.99

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.3e-05
                                       HHHHHHHHHHHTT-EEEECGGG........TSSEEEE..TSCTTTSSCSEEEEEEETTSEEEHHHHHHH CS
                     tRNA_int_endo   3 lkyavyrdLrekGyvvrsGlkF........GadFrvY..qrrpslehseylVvvvsedeeldwpdlsaa 61 
                                        ++ vy+dLr++G+++ +             adF+v+  +++p+ ++  y ++++ e++ ++  +l++ 
  gi|336252548|ref|YP_004595655.1|  83 VRFLVYADLRSRGFYLSPADESwvedpptgEADFAVFprGKGPGDGEIAYALRIIGERTDVSAAELAEG 151
                                       6899**********9987754222222222788999988888888888888888888888888777665 PP

  == domain 2  score: 91.9 bits;  conditional E-value: 4.5e-30
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE...TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY...qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklil 74 
                                       f++++avy+dLre+++v+++G+kFGadFr Y   ++  +l+hse+lV+v + d  ++++dl+ +vrlah+v+K++++
  gi|336252548|ref|YP_004595655.1| 259 FERRLAVYTDLRERDVVPKTGYKFGADFRTYaavDSVAELDHSELLVRVHPADYVFEPRDLALDVRLAHGVRKTMVF 335
                                       899*******************************9****************************************** PP

                                       EEETTTSCEEE CS
                     tRNA_int_endo  75 aivdaegdvty 85 
                                       a+vd++gdv++
  gi|336252548|ref|YP_004595655.1| 336 ALVDDDGDVDW 346
                                       *********98 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 !   41.5   0.0   1.7e-14   7.6e-11       9      57 ..      13      61 ..       6      73 .. 0.83
   2 ?   -2.5   0.0      0.94   4.2e+03      49      63 ..     150     164 ..     148     166 .. 0.78
   3 !   38.8   0.0   1.2e-13   5.4e-10       2      55 ..     187     243 ..     186     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.7e-14
                                      EEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEE.TT CS
                   tRNA_int_endo_N  9 rvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevv.kg 57
                                       v v   +a++r +++++YG p   + + Ls+vEA++Ll++G+le v ++
  gi|336252548|ref|YP_004595655.1| 13 LVYVGG-DARQRYHDSRGYGYPISSNEIALSPVEAAHLLYRGDLEAVvDD 61
                                      678887.999***********************************98643 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.94
                                       TTSEEEETTSEEE-H CS
                   tRNA_int_endo_N  49 kGklevvkggeplsf 63 
                                        G+l vv++++++++
  gi|336252548|ref|YP_004595655.1| 150 EGVLAVVDEESEITY 164
                                       699999988888875 PP

  == domain 3  score: 38.8 bits;  conditional E-value: 1.2e-13
                                       EEEEETTEEEESSHHHHHHHHHTTT-SEE.....CCTSSEEEEHHHHHHHHHTTSEEEE CS
                   tRNA_int_endo_N   2 egeLsgdrvlvedeeaakrlyekgfYGkp.....lidepLqLslvEAlYLlekGklevv 55 
                                       e++L+ drv+v+  +   +lye+ fYG+p      +  +Lq sl+EA+YL+e+G +++ 
  gi|336252548|ref|YP_004595655.1| 187 EADLLADRVVVW--DPPLELYERLFYGQPlegreYDRPTLQCSLLEAAYLAERGAIDLD 243
                                       68999*******..6999***********9999888889*****************975 PP

>> tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0023        10      25      69 ..      12      56 ..       2      59 .. 0.71
   2 !    8.0   0.1   0.00069       3.1      54      70 ..     226     242 ..     213     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0023
                   tRNA_int_end_N2 25 rvvvvespkarGkhfktmGvsra.rrgrlwLlpeEaLYLvErGsld 69
                                        v+v  + ar  +  + G+    +++ + L p Ea +L+ rG l+
  gi|336252548|ref|YP_004595655.1| 12 GLVYVGGD-ARQRYHDSRGYGYPiSSNEIALSPVEAAHLLYRGDLE 56
                                      55555533.5666666666544558999***************997 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00069
                   tRNA_int_end_N2  54 LlpeEaLYLvErGsldi 70 
                                           Ea YL+ErG +d+
  gi|336252548|ref|YP_004595655.1| 226 CSLLEAAYLAERGAIDL 242
                                       5567**********997 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   6.6e-05       0.3      23      62 ..      40      79 ..      34      81 .. 0.91
   2 ?   -3.9   0.1       3.6   1.6e+04      19      27 ..     193     201 ..     192     207 .. 0.66
   3 ?   -2.6   0.0       1.4   6.4e+03      15      26 ..     298     309 ..     285     312 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.6e-05
                             TPR_9 23 llaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62
                                      +l P ++  ++ RG l+a +++ ++A+ d++ ++a +p +
  gi|336252548|ref|YP_004595655.1| 40 ALSPVEAAHLLYRGDLEAVVDDANGARLDFQSFVAREPGD 79
                                      678889999999*************************977 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.6
                             TPR_9  19 erllllaPd 27 
                                       +r+++++P 
  gi|336252548|ref|YP_004595655.1| 193 DRVVVWDPP 201
                                       788888773 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.4
                             TPR_9  15 lavverllllaP 26 
                                       l  +e+l+ ++P
  gi|336252548|ref|YP_004595655.1| 298 LDHSELLVRVHP 309
                                       344455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); 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:                         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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2855.90
//
Query:       gi|336252549|ref|YP_004595656.1|  [L=428]
Description: Tubulin/FtsZ GTPase [Halopiger xanaduensis SH-6]
Scores for 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-13   49.0   0.0    1.7e-09   38.1   0.0    2.3  2  Tubulin    Tubulin/FtsZ family, GTPase domain
     0.0035   16.6   0.2        2.4    7.3   0.0    2.2  2  Tubulin_2  Tubulin like


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 !   38.1   0.0   1.9e-13   1.7e-09       4     160 ..       5     140 ..       2     148 .. 0.84
   2 !    8.6   0.0   0.00022         2     156     193 ..     183     219 ..     178     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.9e-13
                                       EEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE--C CS
                           Tubulin   4 vigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllgk 80 
                                       vigvG++G++i++++   + +e                    ++++ + a+dtd   l  + a      ++++    
  gi|336252549|ref|YP_004595656.1|   5 VIGVGGAGCRIADAIRA-ADDE----------------ATAPSFVADAFAFDTDVDGLTDLGAI-----SETHRHRY 59 
                                       8*************999.3333................334789*****************999.....33444444 PP

                                       CCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE...SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEE CS
                           Tubulin  81 egagnngaggypevgkeaaeeileeirkevekcds..lqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvv 155
                                        ++   g  g+ + g e+ ee+ +e+ +++++ +   +++f+++ +lgG TG G +p ++  l+  y + +v+   +
  gi|336252549|ref|YP_004595656.1|  60 GETIDRGLDGNLHRGLEVGEECVDELSRQLDQGQPslADAFLVVVGLGGATGGGTAPHLVANLQTLY-DEPVYVLAT 135
                                       45789999**********************9665333899**************************9.778999999 PP

                                       E--GG CS
                           Tubulin 156 lPsef 160
                                       lP + 
  gi|336252549|ref|YP_004595656.1| 136 LPAKS 140
                                       99854 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00022
                                       E--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHH CS
                           Tubulin 156 lPsefsevvvepynailalkelieesdavividNdaLl 193
                                       +P  + +  ++++na+++l++l   + a+i++dN+ +l
  gi|336252549|ref|YP_004595656.1| 183 IPEAE-TRPLAEKNAVETLERLDGLATATICFDNELWL 219
                                       56544.678899**********************9775 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0   0.00027       2.4       2      49 ..       5      49 ..       5      67 .. 0.74
   2 !    7.0   0.0   0.00031       2.8     156     189 ..      98     131 ..      75     152 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00027
                         Tubulin_2  2 viGLGGtGgkvlaelrrrlreelgslelpdkvq.FlyiDtdeneknrlk 49
                                      viG+GG G+++ +++r    e+      p  v+   ++Dtd++ +++l+
  gi|336252549|ref|YP_004595656.1|  5 VIGVGGAGCRIADAIRAADDEAT----APSFVAdAFAFDTDVDGLTDLG 49
                                      7**************98766655....6777777778888888777664 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00031
                         Tubulin_2 156 lnvfVvgSLaGGTGSGiflDvayllrkilkeekq 189
                                         + Vv++L G TG G++  ++ +l+ +++e   
  gi|336252549|ref|YP_004595656.1|  98 DAFLVVVGLGGATGGGTAPHLVANLQTLYDEPVY 131
                                       4588***********************9988653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3219.08
//
Query:       gi|336252550|ref|YP_004595657.1|  [L=877]
Description: hypothetical protein Halxa_1145 [Halopiger xanaduensis SH-6]
Scores for 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   22.1   4.1    0.00014   22.1   4.1    2.9  3  DUF4129          Domain of unknown function (DUF4129)
    0.00046   20.6   7.6       0.25   11.7   0.3    3.4  3  DUF4198          Domain of unknown function (DUF4198)
     0.0029   17.6   7.9       0.47   10.5   0.6    3.6  3  CarbopepD_reg_2  CarboxypepD_reg-like domain


Domain annotation for each model (and alignments):
>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       1.4   8.2e+03      21      30 ..     657     668 ..     639     687 .. 0.52
   2 ?   -0.4   0.8      0.24   1.4e+03       3      13 ..     699     709 ..     697     748 .. 0.80
   3 !   22.1   4.1   2.3e-08   0.00014       2      69 .]     782     850 ..     781     850 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                           DUF4129  21 TprEyarrv..r 30 
                                       +p+ +++r+  +
  gi|336252550|ref|YP_004595657.1| 657 SPTSLLERLgdA 668
                                       344455555332 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.24
                           DUF4129   3 rallraLaerg 13 
                                       ra++raL+++g
  gi|336252550|ref|YP_004595657.1| 699 RAVVRALERAG 709
                                       89999999996 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 2.3e-08
                           DUF4129   2 yrallraLaergldrr.pgeTprEyarrvriapspaaalaalaelfeearYGgrpasaeeyrrlvealr 69 
                                       +r+l++   + ++++r ++ Tp+E+ r + + + p+ ++++++++f++  YG  ++s++ ++r+++a+r
  gi|336252550|ref|YP_004595657.1| 782 LRELWAEFVQLVRPPRlRTKTPGEVGRYAVEKGFPEPPVRTVVDAFRDGEYGETAPSEDRLERVRAAVR 850
                                       68999999999777777************7778899******************************987 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.5   0.00023       1.4     149     200 ..     353     394 ..     331     403 .. 0.75
   2 !   11.7   0.3   4.2e-05      0.25     157     201 ..     471     521 ..     459     528 .. 0.76
   3 ?    1.9   0.0     0.041   2.4e+02     163     210 ..     555     608 ..     547     611 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00023
                           DUF4198 149 ageelevqvlldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlp 200
                                        g ++ v+v+ dG P++ga+v        + d++     +tdadG vt  +p
  gi|336252550|ref|YP_004595657.1| 353 PGSTVAVTVTGDGDPVEGATVY-------FNDEQVG---TTDADGTVTGEVP 394
                                       4667777777777777777777.......4555555...9*****9986665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.2e-05
                           DUF4198 157 vlldGkPlagaeveveyggt......ryrdapdeikvktdadGvvtftlpk 201
                                       +++dG P ag+ v+v+   +      + ++  +e++ +td+dG + +++p+
  gi|336252550|ref|YP_004595657.1| 471 LTIDGGPIAGTNVTVVATVNgnpipqGTVTVDNEAYGTTDDDGAAVIPVPE 521
                                       5788999998888877776644555555555555555**********9986 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.041
                           DUF4198 163 Plag..aeveveyggtryrdapdeikv......ktdadGvvtftlpkaGlwlleae 210
                                       Pl+g  ++  +eyg+++  +a+    v      +t+adG +t+ lp a +  ++ae
  gi|336252550|ref|YP_004595657.1| 555 PLPGrsVDARLEYGNESVANATIL--VdgaaaaTTGADGAATVGLPLADRATITAE 608
                                       566522334466766633333322..1224456**********9998766555555 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.6   7.8e-05      0.47       5      35 ..     359     388 ..     358     418 .. 0.81
   2 !    7.0   0.2   0.00093       5.6       4      39 ..     484     518 ..     483     549 .. 0.80
   3 ?    2.2   0.1      0.03   1.8e+02      10      57 ..     568     614 ..     565     623 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.8e-05
                   CarbopepD_reg_2   5 VvdketkeplpgatVyvkgtkkgtvTdenGn 35 
                                       V+ +++++p++gatVy+++ ++gt Td++G+
  gi|336252550|ref|YP_004595657.1| 359 VTVTGDGDPVEGATVYFNDEQVGT-TDADGT 388
                                       67788899***********99997.899997 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00093
                   CarbopepD_reg_2   4 tVvdketkeplpgatVyvkgtkkgtvTdenGnFelk 39 
                                       tVv + +++p+p+ tV+v +   gt Td++G   + 
  gi|336252550|ref|YP_004595657.1| 484 TVVATVNGNPIPQGTVTVDNEAYGT-TDDDGAAVIP 518
                                       6889999***********9999987.8999976665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.03
                   CarbopepD_reg_2  10 tkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGykt 57 
                                       ++e+++ at++v g    ++T ++G  ++  + a++ t++++y G + 
  gi|336252550|ref|YP_004595657.1| 568 GNESVANATILVDGAA-AATTGADGAATVGLPLADRATITAEYEGARA 614
                                       5799********8875.5679999998888777788888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (877 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.85u 0.30s 00:00:01.14 Elapsed: 00:00:00.47
# Mc/sec: 5632.90
//
Query:       gi|336252551|ref|YP_004595658.1|  [L=262]
Description: hypothetical protein Halxa_1146 [Halopiger xanaduensis SH-6]
Scores for 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  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2056.37
//
Query:       gi|336252552|ref|YP_004595659.1|  [L=470]
Description: hypothetical protein Halxa_1147 [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.0   0.0    4.2e-15   55.8   0.0    1.7  1  DUF58        Protein of unknown function DUF58
    1.1e-07   32.0   0.0    3.6e-07   30.4   0.0    1.9  1  DUF11        Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.017   15.3   0.4      0.048   13.9   0.1    2.0  2  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0     7e-19   4.2e-15       1      85 [.     197     283 ..     197     284 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 7e-19
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstg..dekletavsaaaslar 75 
                                       g +f+++R+Y++gDpl+rIdW+ +ARtgel +  + +++a++v++v+d ++ +  +  +   +++  a++a +   +
  gi|336252552|ref|YP_004595659.1| 197 GYEFHSTRDYRRGDPLSRIDWRRYARTGELGTVLYREQEATNVVVVVDGRAVSGVAPGRgrPDGITLAAYAGVVTGN 273
                                       579*************************************************8876655779999999999999999 PP

                             DUF58  76 qlldegdrvg 85 
                                        ll++g++vg
  gi|336252552|ref|YP_004595659.1| 274 ALLEAGHNVG 283
                                       9999999998 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   6.1e-11   3.6e-07       4      80 ..      66     134 ..      63     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 6.1e-11
                             DUF11   4 tvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtr 80 
                                         +++++ pG+ v++ ltv+N + +++++v++ D +P++l  + + a+        ++++L age+  l+++++++r
  gi|336252552|ref|YP_004595659.1|  66 DCTPRTPLPGERVEVALTVRNESDRTLPDVRIVDGVPENLDVIGGDAR--------GATTLRAGEEIELEYAIQPRR 134
                                       56788999****************************************........5569**********9999887 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   8.1e-06     0.048       3      69 ..      74     140 ..      73     156 .. 0.92
   2 ?   -3.4   0.0         2   1.2e+04      51      66 ..     233     248 ..     217     254 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.1e-06
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGd 69 
                                       pGe+v++ ltv n+ ++++ +v++   +Pe+  v   + + a++l++Ge+ e + +++p  g+  +d
  gi|336252552|ref|YP_004595659.1|  74 PGERVEVALTVRNESDRTLPDVRIVDGVPENLDVIGGDARGATTLRAGEEIELEYAIQPRRGTYVFD 140
                                       8*********************************************************988887666 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2
                       NPCBM_assoc  51 etveatvkVtppagaa 66 
                                       e+  ++v V +  +a+
  gi|336252552|ref|YP_004595659.1| 233 EQEATNVVVVVDGRAV 248
                                       5555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 3673.98
//
Query:       gi|336252553|ref|YP_004595660.1|  [L=566]
Description: hypothetical protein Halxa_1148 [Halopiger xanaduensis SH-6]
Scores for 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  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); 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):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.25s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 3844.46
//
Query:       gi|336252554|ref|YP_004595661.1|  [L=326]
Description: ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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-64  215.4   0.2      3e-64  214.7   0.2    1.3  1  AAA_3            ATPase family associated with various cellul
    2.4e-19   68.9   2.7      6e-19   67.7   2.7    1.7  1  AAA_lid_2        AAA lid domain
    2.6e-16   59.9   0.0    5.9e-16   58.7   0.0    1.6  2  AAA_5            AAA domain (dynein-related subfamily)
    8.5e-07   29.5   0.0    2.1e-06   28.2   0.0    1.7  1  AAA              ATPase family associated with various cellul
    2.5e-06   27.3   0.0    1.5e-05   24.8   0.0    2.0  1  Sigma54_activat  Sigma-54 interaction domain
     0.0014   18.4   0.0      0.019   14.7   0.0    2.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.019   14.1   0.0      0.025   13.7   0.0    1.3  1  MCM              MCM P-loop domain
       0.02   14.3   0.1        2.2    7.6   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.04   14.0   0.0      0.073   13.2   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)


Domain annotation for each model (and alignments):
>> 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 !  214.7   0.2   1.5e-67     3e-64       1     131 []      49     179 ..      49     179 .. 0.99

  Alignments for each domain:
  == domain 1  score: 214.7 bits;  conditional E-value: 1.5e-67
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       hvlle+vPG++ktl++ ++a+al+lef+riqftpdllPsdi+G++vf+e++ efef++Gpvfan++ladeinrappk
  gi|336252554|ref|YP_004595661.1|  49 HVLLEDVPGTGKTLTALTVAQALGLEFSRIQFTPDLLPSDITGSHVFNEATGEFEFTEGPVFANVVLADEINRAPPK 125
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                       tq+alleam+e qvtv+g+t++lp+pflv+atqnP+eqeGt++lpeaq drf++
  gi|336252554|ref|YP_004595661.1| 126 TQAALLEAMDEGQVTVDGTTRDLPDPFLVIATQNPVEQEGTFELPEAQRDRFMV 179
                                       ****************************************************95 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   2.7     3e-22     6e-19       1      72 [.     242     314 ..     242     315 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 3e-22
                         AAA_lid_2   1 latrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeivee 72 
                                       +atra+ ++e+g+s+r + +  ++aArA+Aa+egr+yV+p+Dvk++a +V++HRl+   +++ eg++  ++v++
  gi|336252554|ref|YP_004595661.1| 242 RATRADDRVEIGISPR-GIQRYYEAARARAAIEGREYVAPDDVKRIAVPVMQHRLVltTDAQIEGVDGATVVRD 314
                                       58**************.****************************************99*****9999999987 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 !   58.7   0.0     3e-19   5.9e-16       1     138 []      49     177 ..      49     177 .. 0.96
   2 ?   -2.9   0.0       3.1   6.2e+03      62      79 ..     270     289 ..     237     314 .. 0.58

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 3e-19
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       +vlL   pGtgK+  a  +a+al+ e+  +q+t d+ ++d++g+  ++   g+ +++++p+      + +++ DE++
  gi|336252554|ref|YP_004595661.1|  49 HVLLEDVPGTGKTLTALTVAQALGLEFSRIQFTPDLLPSDITGSHVFNeaTGEFEFTEGPVF-----ANVVLADEIN 120
                                       6888889*****************************************999***********.....9********* PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra+++++++Ll  ++e ++   +g+++   ++      f viat np++  +  el +a r+Rf
  gi|336252554|ref|YP_004595661.1| 121 RAPPKTQAALLEAMDEGQVT-VDGTTRDLPDP------FLVIATQNPVEqEGTFELPEAQRDRF 177
                                       *******************9.88999998988......***********9999**********9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.1
                                       ---G-S.EEEEESGGG--.H CS
                             AAA_5  62 aarege.ilvlDEverae.s 79 
                                       aa eg+  +  D+v+r+  +
  gi|336252554|ref|YP_004595661.1| 270 AAIEGReYVAPDDVKRIAvP 289
                                       33333303333555555533 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 !   28.2   0.0   1.1e-09   2.1e-06       2     130 ..      51     183 ..      50     185 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.1e-09
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHHHHHHHHHHHHHHHTS.......TSEEEEEETGGG CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisg.sell.skyvgesekkirelfkeakeka.......kpsilfiDEida 69 
                                       ll   pGtGKTl+a  va+ lg ef +i+  ++ll s++ g       ++f+ea  +           +++ DEi +
  gi|336252554|ref|YP_004595661.1|  51 LLEDVPGTGKTLTALTVAQALGLEFSRIQFtPDLLpSDITGS------HVFNEATGEFeftegpvFANVVLADEINR 121
                                       67778*******************999996267774443322......23333211112222344348********* PP

                                       HHHHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEET CS
                               AAA  70 laksrsgseseeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrkiei 130
                                         ++            +++Ll+++d+ +           ++++vi++ n        +l++a + +Rf +k  i
  gi|336252554|ref|YP_004595661.1| 122 APPKT-----------QAALLEAMDEGQVTvdgttrdlPDPFLVIATQNPveqegTFELPEAQR-DRFMVKSSI 183
                                       *9999...........************9999*****977799999999865555556777777.888777655 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   7.3e-09   1.5e-05      11     146 ..      36     162 ..      31     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 7.3e-09
                                       HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEH CS
                   Sigma54_activat  11 lleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkG 87 
                                        le++ ++a  + +vl++   GtGK+l a ++ +a   +  + +++    +p+++  s++F  + G F  +e    G
  gi|336252554|ref|YP_004595661.1|  36 FLETVLTAALARGHVLLEDVPGTGKTLTALTVAQALGLE-FSRIQFTPDLLPSDITGSHVFNEATGEFEFTE----G 107
                                       6678888999999****************9998877643.33466666678888888888888888886554....4 PP

                                       HHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-HH CS
                   Sigma54_activat  88 lfekadgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedle 146
                                        +      +++ Dei++ p+++Q+ Ll++++eg+v+  G+++  +  + +i at++ +e
  gi|336252554|ref|YP_004595661.1| 108 PVF---ANVVLADEINRAPPKTQAALLEAMDEGQVTVDGTTRDLPDPFLVI-ATQNPVE 162
                                       433...347888************************999999998666655.5555555 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 !   14.7   0.0   9.4e-06     0.019      18     112 ..      36     138 ..      21     146 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.4e-06
                            RuvB_N  18 klkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlekagdlaa..llt......nlee. 84 
                                        l+ +++aa +r     hvll   PG Gkt  a  +a+ lg ++ +i  +P l  ++d+++  +++      +++e 
  gi|336252554|ref|YP_004595661.1|  36 FLETVLTAALAR----GHVLLEDVPGTGKTLTALTVAQALGLEFsRIQFTPDLL-PSDITGshVFNeatgefEFTEg 107
                                       466666666666....5************************9873445555553.3333321112110110012221 PP

                            RuvB_N  85 ...kdvlfideihrlsraveevlysamedfr 112
                                           +v++ dei r  ++++  l  am++ +
  gi|336252554|ref|YP_004595661.1| 108 pvfANVVLADEINRAPPKTQAALLEAMDEGQ 138
                                       1113566677777777777777777776655 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05     0.025      95     175 ..      87     162 ..      38     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                                       SHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE CS
                               MCM  95 agLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAa 171
                                       +++t + v +e+tgef +  G +      v++ De+++   +++ al+Eam++ ++++   G +  L+    v+a  
  gi|336252554|ref|YP_004595661.1|  87 SDITGSHVFNEATGEFEFTEGPVFA---NVVLADEINRAPPKTQAALLEAMDEGQVTVD--GTTRDLPDPFLVIATQ 158
                                       5667777777777777777777654...399*************************997..6679999999999999 PP

                                       --SS CS
                               MCM 172 npka 175
                                       np++
  gi|336252554|ref|YP_004595661.1| 159 NPVE 162
                                       9984 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0011       2.2      14      44 ..      39      69 ..      28      76 .. 0.74
   2 ?    4.4   0.0     0.011        21     109     160 ..     113     162 ..     106     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
                      Mg_chelatase 14 aleiaaaGgHnlllvGppGsGKtmlakrlps 44
                                      ++  aa  + ++ll   pG+GKt+ a  +++
  gi|336252554|ref|YP_004595661.1| 39 TVLTAALARGHVLLEDVPGTGKTLTALTVAQ 69
                                      44456666667999**********9977765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.011
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcp 160
                                       v++ DE+     k+  +L e +++g+vt+  ++++   p  f ++a+ Np  
  gi|336252554|ref|YP_004595661.1| 113 VVLADEINRAPPKTQAALLEAMDEGQVTVDGTTRD--LPDPFLVIATQNPVE 162
                                       6788*************************987765..588899******975 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.7e-05     0.073       6     111 ..      50     142 ..      46     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-05
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------..THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeev..ehlvsrligappgyvgaeegGivllDEidKi 80 
                                       +ll +  g+Gkt++a ++a+ l +    ++ r+  +  l   ++  +h+ ++ +g+ ++  g     +vl DEi ++
  gi|336252554|ref|YP_004595661.1|  50 VLLEDVPGTGKTLTALTVAQALGL----EFSRIQFTPDLLPSDItgSHVFNEATGEFEFTEGPVFANVVLADEINRA 122
                                       677788899999999999999998....899998888777333212455555555555555555555********** PP

                                       ------------HHHHHHHHHHHH--EE--- CS
                             AAA_2  81 hpkessgadvSregVqrdLLqileggtltdk 111
                                        p             q +LL  +++g++t  
  gi|336252554|ref|YP_004595661.1| 123 PP-----------KTQAALLEAMDEGQVTVD 142
                                       **...........99*************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2441.52
//
Query:       gi|336252555|ref|YP_004595662.1|  [L=531]
Description: tryptophanyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-44  151.0   0.0    2.1e-26   92.9   0.0    2.1  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)


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 !   92.9   0.0   1.2e-30   2.1e-26       2     175 ..      91     255 ..      90     267 .. 0.91
   2 !   56.0   0.0   2.1e-19   3.8e-15     167     293 .]     376     505 ..     374     505 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 1.2e-30
                                       HHS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b   2 kerplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlak 78 
                                       + +p +v+sG++PTg++H+G+ +++  +++ q++g ++++liaDl+A   + +  +++++ ++++++  +   +la 
  gi|336252555|ref|YP_004595662.1|  91 NDEPAAVLSGFMPTGDPHIGHKLVFDEIIWHQQQGADAYALIADLEANAARGM--SWEEIDEHARDYLLS---LLAL 162
                                       568999**************8888899999999********************..9**************...**** PP

                                       TCHTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSS.S.C--BHHHHHHHHHHHHHHHHTCHSE CS
                      tRNA-synt_1b  79 gldpekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrlee.g.egislgeftYplLqaaDilllkadl 153
                                       g+dpe+ +++ qs+  e ++la  l   +++ + ++++ f+  ++++++ +    ++++++Yp+L +      k+++
  gi|336252555|ref|YP_004595662.1| 163 GFDPEEGTLYRQSTNRELQDLAFELGADANFSEFQSIYGFDG-ETDVSHmQsVVTQMADILYPQLEE-----PKPTV 233
                                       ******************************************.66666643335699********75.....79*** PP

                                       EEEEGGGHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 154 vpgGsDQkqnielgrdlarrfn 175
                                        p+G DQ+ +++l+rdla+r++
  gi|336252555|ref|YP_004595662.1| 234 IPVGPDQDPHVRLARDLAERMR 255
                                       *******************985 PP

  == domain 2  score: 56.0 bits;  conditional E-value: 2.1e-19
                                       HHHHHHHHHHH...STTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHH CS
                      tRNA-synt_1b 167 grdlarrfnkk...evfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllk 238
                                       +++lar+++ +     f++p++++++++tgl+G+ KmS+S + s I L+d++e+ ++k++ a+t  +e  e ++ + 
  gi|336252555|ref|YP_004595662.1| 376 AEELAREIEVEnggYGFQPPSSIYHRFMTGLTGG-KMSSSIPASHISLLDDPEDGYDKVKAATTGGREtaEEQREKG 451
                                       5778888877778899******************.*******************************99999****** PP

                                       HHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 239 lktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnelle 293
                                       ++   ++ ++e + +++  ++ + a+ ++ e+v ++  +gd+k+++a+ ++e+le
  gi|336252555|ref|YP_004595662.1| 452 GRADECP-VYELYAYLLAGDDDEFAKRVYDECVGGERLCGDCKEQAAQLMKEFLE 505
                                       *******.********99999899***************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      784  (0.043728); 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: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 3563.15
//
Query:       gi|336252556|ref|YP_004595663.1|  [L=477]
Description: hypothetical protein Halxa_1151 [Halopiger xanaduensis SH-6]
Scores for 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   13.5   0.2       0.33   11.5   0.2    2.1  2  Phage_connect_1  Phage gp6-like head-tail connector protein
        1.6    9.1   7.3       0.62   10.4   0.6    3.0  3  LPP20            LPP20 lipoprotein


Domain annotation for each model (and alignments):
>> Phage_connect_1  Phage gp6-like head-tail connector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.94   8.4e+03      29      52 ..      70      93 ..      65     126 .. 0.71
   2 ?   11.5   0.2   3.7e-05      0.33      15      47 ..     243     280 ..     237     294 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.94
                   Phage_connect_1 29 Aeeyikdylgrkleadedgielpe 52
                                      A +y+++ l+r+l+a+ ++i+ ++
  gi|336252556|ref|YP_004595663.1| 70 AARYARESLERELTAVFEAIDWSF 93
                                      778888888888854444544444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.7e-05
                   Phage_connect_1  15 ddddDalLesliqaAeeyikdylgrkl.....eadedg 47 
                                        +++D+ +esli+ Ae+ ++++ +r++       d+d+
  gi|336252556|ref|YP_004595663.1| 243 SESEDDGIESLIEEAESGVESASERSNvteaaPSDADA 280
                                       579************************88766333333 PP

>> LPP20  LPP20 lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.12   1.1e+03      20      34 ..      34      48 ..      32      58 .. 0.85
   2 ?    0.1   0.5      0.12     1e+03      28      69 ..     246     292 ..     229     308 .. 0.63
   3 ?   10.4   0.6   6.9e-05      0.62      16      74 ..     327     395 ..     312     406 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.12
                             LPP20 20 eaeslraAkqnAlrd 34
                                      ++esl+aA ++Al+d
  gi|336252556|ref|YP_004595663.1| 34 SDESLEAALADALSD 48
                                      57899********98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.12
                             LPP20  28 kqnAlrdiaeqiqvqvksssstqets.....aavqnsettnesvsqv 69 
                                       + +++ +++e+    v s s+++        +a   set+++++++ 
  gi|336252556|ref|YP_004595663.1| 246 EDDGIESLIEEAESGVESASERSNVTeaapsDADAASETQQQETDTA 292
                                       56666677776655555555543333477775555555555555443 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 6.9e-05
                             LPP20  16 lgvGeaeslraAkqnAlrdiaeqiqvqvksssstqets..........aavqnsettnesvsqvvesvl 74 
                                       ++ ++ + ++ A+++A+++ +e++++ v++  s++e +          +++++ + +n+s+ + ve + 
  gi|336252556|ref|YP_004595663.1| 327 TAEASERGSDDARADAANSESESVSTSVSAAKSESEPEsdddgfgtlsGTTTTTRVSNDSFGSDVEWET 395
                                       5555566669******************99888877666666655555555555555555555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 3347.66
//
Query:       gi|336252557|ref|YP_004595664.1|  [L=508]
Description: MarR family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-80  269.6   0.0    2.9e-80  269.3   0.0    1.1  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    8.3e-05   22.6   2.4    8.3e-05   22.6   2.4    4.1  4  DprA_WH          DprA winged helix domain
     0.0008   18.9   0.0     0.0031   17.1   0.0    1.9  2  HTH_24           Winged helix-turn-helix DNA-binding
     0.0033   16.9   0.1       0.15   11.5   0.0    2.5  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
     0.0054   15.9   0.2       0.61    9.1   0.1    2.5  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
      0.008   16.1   0.3      0.027   14.3   0.1    2.0  2  MarR_2           MarR family
     0.0082   16.0   0.0       0.02   14.8   0.0    1.7  1  MarR             MarR family
  ------ inclusion threshold ------
      0.025   14.4   0.0       0.07   13.0   0.0    1.8  1  HTH_IclR         IclR helix-turn-helix domain
      0.027   14.7   3.4        1.7    8.9   0.3    2.4  2  LPD22            Large polyvalent protein associated domain 2
      0.033   14.1   0.1       0.97    9.4   0.0    2.8  3  TrmB             Sugar-specific transcriptional regulator Trm
       0.13   12.6   0.0       0.32   11.4   0.0    1.6  1  Rrf2             Transcriptional regulator


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 !  269.3   0.0   1.8e-83   2.9e-80       2     244 ..     226     503 ..     225     504 .. 0.98

  Alignments for each domain:
  == domain 1  score: 269.3 bits;  conditional E-value: 1.8e-83
                                       .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-.. CS
                      tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka.. 76 
                                       ++v++++++ e g++h+l++++e++k++++ +gf+e+egp+v+++f++ d+L++pqdhpaR+++d F l++p+++  
  gi|336252557|ref|YP_004595664.1| 226 YNVEADAEQFEGGNVHILRQTAERVKDVLVGMGFQEMEGPHVDADFWINDCLFMPQDHPARTHWDRFALEEPTHIdd 302
                                       89*******************************************************************999999** PP

                                       ...............................ECESEEE-SSTHHHHHHHH.....TTS-SSEEEEEEEEEEBSST-S CS
                      tRNA-synt_2d  77 ...............................veekllLRthttavqirtl.....ekkkppikiisigrvfRrdavD 117
                                                                      +++ l LR htt+++ r+l      + +pp++++s+++v+R+d++D
  gi|336252557|ref|YP_004595664.1| 303 lpedlvdrverahkegvgedgegyhspwdedFARALALRGHTTSLSTRYLsgeqiGEIEPPARFFSVEKVYRNDTLD 379
                                       *******************************999****************998777889****************** PP

                                       SSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEE CS
                      tRNA-synt_2d 118 athlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGm 194
                                        thl eF+q+eg+v+ e++s++dl+g++ee++ ++ g e +++f+p+y+p+tePs+e++ ++ + +++ +E++++G+
  gi|336252557|ref|YP_004595664.1| 380 PTHLLEFFQIEGWVMAEDLSVRDLMGTFEEFYAQF-GIE-DIQFKPHYNPYTEPSFELFGTH-PTTGELVEIGNSGI 453
                                       ***********************************.***.**********************.9************* PP

                                       E-HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT...HHHHGG CS
                      tRNA-synt_2d 195 vrpevleavgideevsgfafGlGveRlamlkygieDiRelven..dlrflrq 244
                                       +r+e+le++g+  e +++a+Gl++eRl ml+yg+eDiR+++ +  dl++lr+
  gi|336252557|ref|YP_004595664.1| 454 FREEMLEPLGV--ECDVMAWGLALERLLMLMYGFEDIRDIHGTlcDLELLRN 503
                                       ***********..****************************99888888875 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   2.4   5.1e-08   8.3e-05      11      56 ..       4      50 ..       2      51 .. 0.91
   2 ?    2.4   0.1       0.1   1.7e+02      22      47 ..      88     113 ..      69     114 .. 0.79
   3 ?   -1.5   0.9       1.8   2.9e+03       4      30 ..     132     158 ..     129     162 .. 0.73
   4 ?    0.2   0.2      0.52   8.4e+02      24      32 ..     296     304 ..     293     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.1e-08
                           DprA_WH 11 ddlerrvLaaLgp.ePvhvDqLvrrtglpaaevsaaLleLELaGlve 56
                                       + + +vL+a ++ e+++vD+L+++t lp+++v  a  eLE +Glv+
  gi|336252557|ref|YP_004595664.1|  4 PESQVAVLEAASAdEATSVDALAEATDLPPETVTGAVFELEDEGLVA 50
                                      677889***999857**************************999996 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.1
                           DprA_WH  22 gpePvhvDqLvrrtglpaaevsaaLl 47 
                                         +Pv++ q++ ++gl+  +v  aL+
  gi|336252557|ref|YP_004595664.1|  88 DTDPVQMGQVIGASGLEGPQVDIALS 113
                                       678****************9988886 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.8
                           DprA_WH   4 ppaepplddlerrvLaaLgpePvhvDq 30 
                                       + a p++d+++ ++ ++ g   ++ D+
  gi|336252557|ref|YP_004595664.1| 132 SDADPDADAEANALATLKGTGETPRDA 158
                                       567777888888888887888777776 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.52
                           DprA_WH  24 ePvhvDqLv 32 
                                       eP+h+D+L 
  gi|336252557|ref|YP_004595664.1| 296 EPTHIDDLP 304
                                       8******95 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 !   17.1   0.0   1.9e-06    0.0031       5      47 ..       7      49 ..       3      50 .. 0.93
   2 ?   -1.6   0.0       1.3   2.1e+03      27      35 ..     175     183 ..     174     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.9e-06
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      + ++Le+  ++  +s   LAe+++l+p tv+  + +Le+eGl+
  gi|336252557|ref|YP_004595664.1|  7 QVAVLEAASADEATSVDALAEATDLPPETVTGAVFELEDEGLV 49
                                      5678999999*******************************98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                            HTH_24  27 lglSpstvn 35 
                                       +g+S +tv+
  gi|336252557|ref|YP_004595664.1| 175 VGISETTVR 183
                                       8******97 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 ?    2.7   0.0     0.046        75      16      37 ..     241     262 ..     232     263 .. 0.82
   2 !   11.5   0.0   8.9e-05      0.15      97     209 ..     364     470 ..     357     475 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.046
                   tRNA_synthFbeta  16 nkeqklrrklrdllagaGlnEv 37 
                                       +  +++ ++++d+l+g+G++E+
  gi|336252557|ref|YP_004595664.1| 241 HILRQTAERVKDVLVGMGFQEM 262
                                       55678899************96 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.9e-05
                   tRNA_synthFbeta  97 vrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepaehpal 172
                                        r+F + kv+++d  + +   e  ++ + ++ ++            ++ dl g+ e++ +++gie+++f+p  +p+ 
  gi|336252557|ref|YP_004595664.1| 364 ARFFSVEKVYRNDtLDPTHLLEFFQIEGWVMAED-----------LSVRDLMGTFEEFYAQFGIEDIQFKPHYNPYT 429
                                       7899999999999766677777778877777777...........9*************************999999 PP

                   tRNA_synthFbeta 173 hpgrsAeikvdgk......evGvlGelhpevleafdlkqrvyv 209
                                       +p      +          e+G  G +  e+le ++++  v++
  gi|336252557|ref|YP_004595664.1| 430 EPSFELFGTH--PttgelvEIGNSGIFREEMLEPLGVECDVMA 470
                                       9954333322..1234455888888888888888877777665 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 !    9.1   0.1   0.00037      0.61      93     122 ..     365     393 ..     331     416 .. 0.82
   2 ?    4.3   0.0     0.011        18     287     307 ..     471     491 ..     457     493 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00037
                                       EEEEEEEEE--S--BTTB-S-CEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqieaem 122
                                       r f++ +++R+  ++ ++ l EF qie  +
  gi|336252557|ref|YP_004595664.1| 365 RFFSVEKVYRNDTLDPTHLL-EFFQIEGWV 393
                                       89*************99999.*****9644 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.011
                                       EEEEHHHHHHHHCT-SSGGGC CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 287 lglGldRlvmlllgsesIrdv 307
                                       +gl l+Rl+ml+ g e+Ird+
  gi|336252557|ref|YP_004595664.1| 471 WGLALERLLMLMYGFEDIRDI 491
                                       7999***************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.7e-05     0.027       6      52 ..       6      50 ..       2      64 .. 0.85
   2 ?   -3.7   0.0       7.3   1.2e+04      42      51 ..     166     175 ..     164     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +q  vL a  + +    +v +la++++l++ +v+ ++ +L++ GLv 
  gi|336252557|ref|YP_004595664.1|  6 SQVAVLEAASADEA--TSVDALAEATDLPPETVTGAVFELEDEGLVA 50
                                      67788888888887..8*****************************4 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.3
                                       HHHHHHTTSE CS
                            MarR_2  42 lkrLvaaGLv 51 
                                       l+ L ++GLv
  gi|336252557|ref|YP_004595664.1| 166 LEQLDRRGLV 175
                                       6778888888 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   1.3e-05      0.02       2      48 ..       4      50 ..       3      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                                      -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                       ++q+ +L+  +  ++ sv  La++  + + tvt ++ +Le++Gl+ 
  gi|336252557|ref|YP_004595664.1|  4 PESQVAVLEAASADEATSVDALAEATDLPPETVTGAVFELEDEGLVA 50
                                      5789999**************************************96 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 ?   13.0   0.0   4.3e-05      0.07      13      51 ..      14      52 ..       8      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                                      CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 13 aeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      a+a+++ ++  lA++t+lp+ tv + +  L+ +G+v  d
  gi|336252557|ref|YP_004595664.1| 14 ASADEATSVDALAEATDLPPETVTGAVFELEDEGLVAVD 52
                                      6788888*****************************876 PP

>> LPD22  Large polyvalent protein associated domain 22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2    0.0078        13       7      37 ..       8      38 ..       3      65 .. 0.86
   2 ?    8.9   0.3     0.001       1.7       8      46 ..     129     170 ..     125     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0078
                             LPD22  7 lelaqnenPDeaAralrlaeelGlppdvver 37
                                      +++ ++++ Dea ++ +lae++ lpp+ v+ 
  gi|336252557|ref|YP_004595664.1|  8 VAVLEAASADEATSVDALAEATDLPPETVTG 38
                                      45558899*******************9975 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.001
                             LPD22   8 elaqnenPDeaAralrlaeelG...lppdvvernleaferaa 46 
                                       ++ ++++PD+ A+a++la   G    p+d+v+ + + +e+ +
  gi|336252557|ref|YP_004595664.1| 129 TADSDADPDADAEANALATLKGtgeTPRDAVDVDADTLEQLD 170
                                       556899************99998899*****99999999987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00059      0.97      21      56 ..      18      53 ..       3      69 .. 0.88
   2 ?   -2.3   0.0       2.6   4.3e+03      21      51 ..      90     120 ..      74     126 .. 0.64
   3 ?    1.0   0.0      0.24   3.9e+02      41      58 ..     164     181 ..     163     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00059
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      +  ++d +ae++++p  +v  ++ +Led GlV + +
  gi|336252557|ref|YP_004595664.1| 18 EATSVDALAEATDLPPETVTGAVFELEDEGLVAVDE 53
                                      667899**************************9876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.6
                                       CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTS CS
                              TrmB  21 gpatadeiaeelgvprskvYevLrsLedkGl 51 
                                       +p ++ ++  ++g++ ++v  +L++  +kG+
  gi|336252557|ref|YP_004595664.1|  90 DPVQMGQVIGASGLEGPQVDIALSNYARKGY 120
                                       4555667777788888888888888777775 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.24
                                       HHHHHHHHCTSEEEESST CS
                              TrmB  41 evLrsLedkGlVerekgr 58 
                                       ++L++L ++GlV +++ +
  gi|336252557|ref|YP_004595664.1| 164 DTLEQLDRRGLVGISETT 181
                                       689*********988765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.32      15      57 ..       9      51 ..       6      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                      HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      ++L++ + +e  s++++ae ++++p+ +   + +L+ +glv +
  gi|336252557|ref|YP_004595664.1|  9 AVLEAASADEATSVDALAEATDLPPETVTGAVFELEDEGLVAV 51
                                      56778888888*****************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); 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:                        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 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3692.67
//
Query:       gi|336252558|ref|YP_004595665.1|  [L=570]
Description: Phenylalanyl-tRNA synthetase subunit beta [Halopiger xanaduensis SH-6]
Scores for 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-42  144.1   0.0    5.5e-42  143.6   0.0    1.2  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    1.4e-16   60.6   1.1    6.8e-16   58.3   0.7    2.4  2  B5               tRNA synthetase B5 domain
    3.4e-13   49.7   0.0    5.5e-13   49.0   0.0    1.3  1  B3_4             B3/4 domain
    2.1e-06   27.8   2.2     0.0011   19.1   0.1    3.6  3  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain
    3.4e-06   26.7   0.0    5.4e-06   26.1   0.0    1.3  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)


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 !  143.6   0.0   1.5e-45   5.5e-42       2     214 .]     361     566 ..     360     566 .. 0.95

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 1.5e-45
                   tRNA_synthFbeta   2 pstlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldkll......eddderkavelanPlsedqs 72 
                                       +++ P + t++g ++++ +l+r +r+ l+g+G+ + +++ +++e+ + + l      +     +  +++ P sed++
  gi|336252558|ref|YP_004595665.1| 361 EPRYPDVGTVGG-RHERSRLERSVREQLVGLGFEDLLNFHMINEAANYERLdvepgtDVYGAGEPATIKEPYSEDFT 436
                                       577899999999.99*******************************999987866543446677************* PP

                   tRNA_synthFbeta  73 vlRtsLlpglLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkg 148
                                       +lRt ++p+lL vl+rN +r  +   l Eig +   d se+++++e+r++++vl+ ++           ++++d+k+
  gi|336252558|ref|YP_004595665.1| 437 MLRTWVTPSLLMVLERNTHRAYP-QDLAEIGFTAEVDdSENTGVAEHRRVGAVLASHE-----------AGYEDAKA 501
                                       ***********************.*************9********************...........******** PP

                   tRNA_synthFbeta 149 ivealleslgiekvefepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEldl 214
                                        ++al++++ + ++e  p++hp++  gr+A++++dg evGv+Ge+hp+vl ++dl+ +v++fE+dl
  gi|336252558|ref|YP_004595665.1| 502 RLQALCRRFDV-DLETPPTDHPTFISGRTASVVIDGDEVGVIGEVHPKVLVEHDLEVPVAGFEFDL 566
                                       ***********.****************************************************97 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.63   2.3e+03       6      54 ..       9      89 ..       4      93 .. 0.50
   2 !   58.3   0.7   1.9e-19   6.8e-16       2      67 .]     288     357 ..     287     357 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.63
                                      HHHHHHHTS---H.HHHHHHHHHTT-E................................EESSTTCEEEE--TT-.TT- CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxx...............................xxxxxxxxxxxxxxxxx.xxx RF
                                B5  6 ekinkllGidlse.eeiikiLkrlgce...............................riekdkdlllVtvPswR.sDl 51
                                      ++++ l+G + +  ee ++ L  lg+e                               r  + +d   V+vPs+   D 
  gi|336252558|ref|YP_004595665.1|  9 DELRDLTGREEKGdEELKDDLFGLGLEfegrteggafelefapdrldrlsvegvarslR-YQYGDARGVHVPSTNdADW 86
                                      55555666533322566666666666655555555555555555555555556665541.3344445556666543444 PP

                                      -SH CS
                                      xxx RF
                                B5 52 ere 54
                                      + e
  gi|336252558|ref|YP_004595665.1| 87 TIE 89
                                      444 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 1.9e-19
                                       EEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTT....CEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   2 slrvekinkllGidlseeeiikiLkrlgceriekdkd....lllVtvPswRsDlereeDliEEvaRlyGY 67 
                                       ++++++i+ +lGidl+++e+i++ +r g+e++++++d    +++VtvP++R+D++++ D+i++  R+yG+
  gi|336252558|ref|YP_004595665.1| 288 TVAHDRIETILGIDLDPDEVIDLAERSGLEAEKDEDDdgdlVYEVTVPPYRVDVLHPLDIIDDLGRAYGF 357
                                       6899**************************754444489999***************************7 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   1.5e-16   5.5e-13       2     134 ..      98     249 ..      97     254 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.5e-16
                                       SSEEEEEEEES--.-----HHHHHHHHHTT-----HHHHHHHHHHHHHT-.....-EEEEEGGGTB........TEE CS
                              B3_4   2 cpryaarvlrgvkktapspewlqrrLrragirpinnvVDitNyvmlelgq.....PlhafDldkiq........gdi 65 
                                       +p+++++v+r+v+ + +                +++++ ++++++  +g+     +++++Dl  ++        ++i
  gi|336252558|ref|YP_004595665.1|  98 RPYVTGAVIRDVDLDDEA---------------LESLIQLQEKLHATMGRkrakgAIGIHDLTMLKgspategnPTI 159
                                       789999999999998888...............9*******************************9999999966** PP

                                       E.EEE--TTEEEEBTTS-EEEE-T.....................TSEEEETEEEEEEETTTEEBTTTB--TT--EE CS
                              B3_4  66 v.vrlakegeklvtldgkerelde.....................edlviadsekpvslagvmggeeskvsedTknv 120
                                       + v l +++ ++v+ld ++re+++                     +++ i+d+ +  s ++v++g +++vs d+++ 
  gi|336252558|ref|YP_004595665.1| 160 EyVGLEPDEDTFVPLD-SDREMSPaevleehgtgqtyadlvseyeRYPAIYDDLGLFSFPPVINGRRTEVSTDSRDL 235
                                       ****************.779998889**************************99988******************** PP

                                       EEEEEE--HHHHHH CS
                              B3_4 121 fleaaafdpvsirk 134
                                       f+e+++ d+ +i k
  gi|336252558|ref|YP_004595665.1| 236 FVEMTGTDQWTIDK 249
                                       *******9988876 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 !   19.1   0.1   3.1e-07    0.0011       1      78 [.       1      67 [.       1      72 [. 0.90
   2 ?   -4.2   0.0         5   1.8e+04      31      42 ..      86      97 ..      85     104 .. 0.78
   3 !    6.3   0.2    0.0032        12       6      68 ..     289     342 ..     285     351 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.1e-07
                         PhetRS_B1  1 MPtisvkkeaLfkalgke.lteeeledllfefGlElDeiveeeekkkadkkseeviykidipAnryDLLcleglaralk 78
                                      MPt+ ++ ++L +++g+e   +eel+d lf +GlE+   +e  +            + ++ +  r D L++eg+ar l+
  gi|336252558|ref|YP_004595665.1|  1 MPTVDIDPDELRDLTGREeKGDEELKDDLFGLGLEFEGRTEGGA------------FELEFAPDRLDRLSVEGVARSLR 67
                                      ****************774889**************99887776............99999999999999999999987 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 5
                         PhetRS_B1 31 fGlElDeiveee 42
                                      + +E+De v +e
  gi|336252558|ref|YP_004595665.1| 86 WTIEVDESVPDE 97
                                      569999998776 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0032
                         PhetRS_B1   6 vkkeaLfkalgkelteeeledllfefGlElDeiveeeekkkadkkseeviykidipAnryDLL 68 
                                       v ++++ + lg +l+ +e+ dl  + GlE    ++++          + +y + +p  r D+L
  gi|336252558|ref|YP_004595665.1| 289 VAHDRIETILGIDLDPDEVIDLAERSGLEAEKDEDDDG---------DLVYEVTVPPYRVDVL 342
                                       77888889999999999999999999999888877777.........8899999999999987 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 !   26.1   0.0   1.5e-09   5.4e-06      13     216 ..     370     566 ..     363     570 .] 0.90

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.5e-09
                                       HSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHH CS
                      tRNA-synt_2d  13 agklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthtta 89 
                                        g++h  +++ + ++e ++ lgfe + + ++ +e  n + L+v+  + +  + +   +k+p +  e+ ++LRt  t+
  gi|336252558|ref|YP_004595665.1| 370 VGGRHERSRLERSVREQLVGLGFEDLLNFHMINEAANYERLDVEPGTDVYGAGEPATIKEPYS--EDFTMLRTWVTP 444
                                       58899***********************9999**************************99999..88********** PP

                                       HHHHHH...TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEE CS
                      tRNA-synt_2d  90 vqirtl...ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrp 163
                                         + +l   +++  p+ +  ig +   d+ + t  ae   v  +++ ++   +d k+ l++l++++   +v++   p
  gi|336252558|ref|YP_004595665.1| 445 SLLMVLernTHRAYPQDLAEIGFTAEVDDSENTGVAEHRRVGAVLASHEAGYEDAKARLQALCRRF---DVDLETPP 518
                                       ******77556669********9999999*************************************...56699999 PP

                                       CEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEE CS
                      tRNA-synt_2d 164 syfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsgfafGl 216
                                       +  p    +  ++v++     +  E++  G v+p+vl + +++  v gf f l
  gi|336252558|ref|YP_004595665.1| 519 TDHPTFISGRTASVVI-----DGDEVGVIGEVHPKVLVEHDLEVPVAGFEFDL 566
                                       9999888888888888.....3349999*************976777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); 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:                         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 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 4055.97
//
Query:       gi|336252559|ref|YP_004595666.1|  [L=65]
Description: hypothetical protein Halxa_1154 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0012   18.9   0.0     0.0012   18.8   0.0    1.1  1  SymE_toxin      Toxin SymE, type I toxin-antitoxin system
  ------ inclusion threshold ------
      0.013   15.4   0.4       0.02   14.8   0.4    1.3  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> SymE_toxin  Toxin SymE, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.4e-07    0.0012      22      53 ..      23      54 ..       6      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-07
                        SymE_toxin 22 eltLkGeWLeqaGFatGqpltisVmegrlvit 53
                                       l+L  + L  aG ++G ++ ++V++g+++i+
  gi|336252559|ref|YP_004595666.1| 23 HLNLHEDELAVAGMDIGDEVFVRVRDGKIIIQ 54
                                      56666677889********************7 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 ?   14.8   0.4   2.3e-06      0.02      20      42 ..      35      57 ..      28      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-06
                                      CEECTCEEEEEECTTCCCCCCCH CS
                    MazE_antitoxin 20 gireGdevelevdgdkiilrplk 42
                                      g + Gdev ++v ++kii+ +  
  gi|336252559|ref|YP_004595666.1| 35 GMDIGDEVFVRVRDGKIIIQKAD 57
                                      8899***********99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 522.61
//
Query:       gi|336252560|ref|YP_004595667.1|  [L=102]
Description: Non-histone chromosomal MC1 family protein [Halopiger xanaduensis SH-6]
Scores for 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-48  161.4   0.3    5.6e-48  161.2   0.3    1.0  1  MC1       Non-histone chromosomal protein MC1


Domain annotation for each model (and alignments):
>> MC1  Non-histone chromosomal protein MC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.2   0.3   3.1e-52   5.6e-48       2      96 .]       7     101 ..       5     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 161.2 bits;  conditional E-value: 3.1e-52
                               MC1   2 krnfalrdedGeeisvfsGkqPrqaaLkaarrletadseeeakeeeirLrekGtkkvhiyegkaeeeeaPddkpdWl 78 
                                       krnfalrd+dGee+svfsG++PrqaaLkaarrle+ +se++a++ e++LrekGt+kvhiyeg+a+e++aPddkpdW+
  gi|336252560|ref|YP_004595667.1|   7 KRNFALRDSDGEETSVFSGNTPRQAALKAARRLEPGSSEADADRVELKLREKGTDKVHIYEGWAWEQTAPDDKPDWM 83 
                                       9**************************************************************************** PP

                               MC1  79 edkitkanvskqgiekle 96 
                                       +d+it+anvskqgie+le
  gi|336252560|ref|YP_004595667.1|  84 PDEITEANVSKQGIEHLE 101
                                       ****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 803.97
//
Query:       gi|336252561|ref|YP_004595668.1|  [L=44]
Description: hypothetical protein Halxa_1156 [Halopiger xanaduensis SH-6]
Scores for 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  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       186  (0.0103743); expected 358.6 (0.02)
Passed bias filter:                      141  (0.00786435); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); 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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 343.61
//
Query:       gi|336252562|ref|YP_004595669.1|  [L=441]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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-32  110.5  41.0    8.3e-32  110.5  41.0    1.4  2  MFS_1       Major Facilitator Superfamily


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 !  110.5  41.0   4.6e-36   8.3e-32       8     353 .]      21     379 ..      11     379 .. 0.83
   2 ?   -2.9   0.2      0.13   2.4e+03     235     257 ..     389     409 ..     380     421 .. 0.51

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 4.6e-36
                             MFS_1   8 salarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfass 84 
                                        +  ++ ++p+    +a+++g+s++++g++ ++  ++  ++ +++G+l+d++G+  +   ++++ + ++++ +f ++
  gi|336252562|ref|YP_004595669.1|  21 GFVIWFSFAPFTG-EIADEFGLSVAQLGIVSSAAVIAVPLGRIVIGPLTDKWGAPVTAGGTMVVVGTFAIISAF-AQ 95 
                                       3333444555555.89****************************************999999999999666669.55 PP

                             MFS_1  85 lw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgg..lla.sslg......Wr 151
                                        + ++ ++r++++l+ g+ f +g+  +++wf +ee g a g++++  ++Ga lg+ +    l+   ++g      Wr
  gi|336252562|ref|YP_004595669.1|  96 TYeVFTASRIIASLA-GITFVIGIQHVSEWFEEEELGTAEGIFAGIGNAGAGLGAYFTLprLFGeGYVGplfdanWR 171
                                       566***********9.8*************************************8887766777556668888**** PP

                             MFS_1 152 avfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg.ll 227
                                       a+f+  +++++++++l   +++ ++ +++rk+++++    +  +l++ w ++ ++     +l ++++++fg+ + + 
  gi|336252562|ref|YP_004595669.1| 172 AAFFYTGALAVVVGIL--YFVFGDAAKSERKREATK----ASVSLKQ-WCYIATRYGAV-VLSVAYVMTFGLELaMN 240
                                       ***************9..999999*******99999....99*****.99999999442.444444444444447** PP

                             MFS_1 228 tllplylqevlglsglllaglllallalvgailallagrlsdrlgr..............rrrlllallllllaalg 290
                                        +l +y +e +g s  ++a+++ a +++++  l++++g++sd + r              +  ++ +l+++++a +g
  gi|336252562|ref|YP_004595669.1| 241 GWLGTYYREAFGQSDIVIAATFAATFSIAAGLLRPIGGYVSDLVARketdilpwfegryrEQWTFATLVFVMCAMFG 317
                                       **************6699999999999999999**********5555555566677777355555555555555556 PP

                             MFS_1 291 lallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                       +  +++t +  +++++ +l+G+g +f+ ++++a++  ++p + +g+++g+++ +gs gg++ p
  gi|336252562|ref|YP_004595669.1| 318 MTAAGLTGNIYAAVVAGFLVGMGCAFAEGAIFAQVPAMFP-DSSGSVAGVVGGIGSSGGSIYP 379
                                       6666666777777779999********************8.******************9976 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.13
                             MFS_1 235 qevlglsglllaglllallalvg 257
                                       + +lg++  + a+++++++al +
  gi|336252562|ref|YP_004595669.1| 389 NLHLGYA--VVAATMIPIIALSA 409
                                       4455555..44444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 3155.72
//
Query:       gi|336252563|ref|YP_004595670.1|  [L=250]
Description: rhodopsin [Halopiger xanaduensis SH-6]
Scores for complete 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-25   89.9  23.9    2.1e-25   89.6  23.9    1.0  1  Bac_rhodopsin  Bacteriorhodopsin-like protein
  ------ inclusion threshold ------
       0.46   10.4   2.2        1.1    9.1   0.1    2.1  2  GRA6           Granule antigen protein (GRA6)
       0.99    9.7   6.3       0.82   10.0   0.9    2.6  2  Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
        1.8    8.5   9.7        0.5   10.3   2.4    3.0  2  PetG           Cytochrome B6-F complex subunit 5


Domain annotation for each model (and alignments):
>> Bac_rhodopsin  Bacteriorhodopsin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6  23.9   4.7e-29   2.1e-25       2     221 ..       6     218 ..       5     220 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 4.7e-29
                                       HHHHHHHHHHHHHHHHHHHHTTTSSTCCHHHHHHHHHHHHHHHHHHHHHHHTTTTEEEEEETTEEEEEETHHHHHHH CS
                     Bac_rhodopsin   2 tvfsvfallalvatllfvvtsrrvkdgekrkllvipllitaiaavaYltmalglGltgveaefehrqvfyarYidWl 78 
                                       t   v++l+++vatl f++++rr+ +  +r+ ++++ +  +++a+aY+ m +   ++g        ++ +ar+++++
  gi|336252563|ref|YP_004595670.1|   6 TAIGVSTLVFVVATLAFLAWTRRLPAACRRYGYAATAA-VGVMAIAYVGMTAIEFVIG-------GNTDLARFLGYT 74 
                                       67789****************************99999.8**********88776677.......5779******** PP

                                       HHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTSTH CS
                     Bac_rhodopsin  79 lttPllvlvlaelagadrrtllvlvladvvmivgglvgaliestyrwvyftisvaallvvlylllgelaraakslss 155
                                        ++  +v+v +++ag+drr+ l+l++ ++  ++++lvg + +++   ++ +  +a l++ +yll+g+++raa+s+s 
  gi|336252563|ref|YP_004595670.1|  75 AMWIPIVYVTSAIAGVDRRAALLLLAIVLGRVWITLVGYFLDGIAGQIASLLPFALLIAGIYLLYGPFTRAAASRSG 151
                                       ***878*********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTSS.CHHHHHHHHHHHHHHHHHHHHHHHHCCHTTCHH CS
                     Bac_rhodopsin 156 errslfntLrnlvvvlwilYpvawllgeeGngi.qpdveavvygilDlvtkvgfglillaaatslgs 221
                                       er  lf +L+ l+v++wi+  +  l+ + G g+ + +v  +  ++++ +  +gf+ ++l++ ++l+ 
  gi|336252563|ref|YP_004595670.1| 152 ERSLLFTKLKHLIVLGWIGLVINGLIAADGLGLvDDFVALLTLVYVEAILLLGFAGLVLRNVDALEA 218
                                       *************************************************************999876 PP

>> GRA6  Granule antigen protein (GRA6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.5      0.11   4.9e+02     155     184 ..       8      34 ..       5      50 .. 0.78
   2 ?    9.1   0.1   0.00026       1.1      17      68 ..     192     248 ..     187     250 .] 0.73

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.11
                              GRA6 155 iGavvlaasvalltafflrrsgrrapgePr 184
                                       iG   l  +va l af+    +rr p++ r
  gi|336252563|ref|YP_004595670.1|   8 IGVSTLVFVVATL-AFLA--WTRRLPAACR 34 
                                       89999999****9.7666..5789888877 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00026
                              GRA6  17 ltvvtv.avtlvvfvGvlvsslGgaavaaesegvkaaps....etgssggqqeavGt 68 
                                       lt+v v a+ l+ f G+++  + + ++aae++g+++++     e +s ++  e v t
  gi|336252563|ref|YP_004595670.1| 192 LTLVYVeAILLLGFAGLVLRNVDALEAAAEGGGLRSSRTdadlEDSSRAETAENVET 248
                                       5655443899999**********************9887222234566666666655 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.9   0.00018      0.82      30      81 ..       6      56 ..       2      82 .. 0.81
   2 ?    2.3   0.4     0.044     2e+02      30      84 ..     117     171 ..      68     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00018
                                      HHHHHHHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHHHH CS
                     Cytochrom_B_C 30 kllGvvamgaaivilfllpwldrskvksiryrkplakvllallvvsfvvLgy 81
                                        +Gv ++++ +++l++l w  r +    ry    a++++ +++++ v ++ 
  gi|336252563|ref|YP_004595670.1|  6 TAIGVSTLVFVVATLAFLAWTRRLPAACRRYG-YAATAAVGVMAIAYVGMTA 56
                                      6789************************9999.6666666666666665554 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHT CS
                     Cytochrom_B_C  30 kllGvvamgaaivilfllpwldrskvksiryrkplakvllallvvsfvvLgylGv 84 
                                        ++G +a +  +++l++  +l   + + ++  +   + ll++ + +++vLg++G 
  gi|336252563|ref|YP_004595670.1| 117 GIAGQIASLLPFALLIAGIYLLYGPFTRAAASRSGERSLLFTKLKHLIVLGWIGL 171
                                       5567777777777777777777777776666667888888888888999999886 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 ?   10.3   2.4   0.00011       0.5       5      23 ..      97     115 ..      96     117 .. 0.92
   2 ?    0.8   0.8     0.099   4.4e+02       9      22 ..     164     177 ..     162     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                              PetG   5 LLlGiVLGLvpVTlaGLFv 23 
                                       LLl iVLG v +Tl+G F 
  gi|336252563|ref|YP_004595670.1|  97 LLLAIVLGRVWITLVGYFL 115
                                       8999************996 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.099
                              PetG   9 iVLGLvpVTlaGLF 22 
                                       iVLG +   + GL 
  gi|336252563|ref|YP_004595670.1| 164 IVLGWIGLVINGLI 177
                                       9*****99999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); 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:                         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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1710.63
//
Query:       gi|336252564|ref|YP_004595671.1|  [L=545]
Description: methyl-accepting chemotaxis sensory transducer [Halopiger xanaduensis SH-6]
Scores for complete 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-37  129.4  25.6    1.2e-37  129.4  25.6    5.0  5  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
      3e-16   59.5  13.4    3.4e-09   36.9   0.2    5.7  4  HAMP            HAMP domain
    3.9e-06   26.9  35.9     0.0073   16.3   1.1    5.5  5  DUF1664         Protein of unknown function (DUF1664)
    0.00016   21.0  48.9      0.039   13.2   0.8    5.0  5  DUF3450         Protein of unknown function (DUF3450)
     0.0023   17.3  21.4       0.26   10.6   0.3    3.4  3  GAS             Growth-arrest specific micro-tubule binding
     0.0037   17.5  47.0      0.083   13.2   3.0    7.4  8  DUF948          Bacterial protein of unknown function (DUF948
     0.0055   16.9  35.6      0.034   14.4   0.8    5.0  4  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding
     0.0056   16.9  28.4        0.4   11.0   1.9    6.2  5  BLOC1_2         Biogenesis of lysosome-related organelles com
     0.0061   16.6  45.7       0.38   10.8   1.5    5.2  6  Laminin_II      Laminin Domain II
     0.0092   15.7  11.6        1.3    8.7   0.1    5.0  5  RPW8            Arabidopsis broad-spectrum mildew resistance 
     0.0093   14.9  45.0        0.6    8.9   9.3    3.5  3  Spc7            Spc7 kinetochore protein
  ------ inclusion threshold ------
       0.01   16.1   3.2       0.01   16.1   3.2    4.6  4  I_LWEQ          I/LWEQ domain
      0.011   15.9   3.5      0.011   15.9   3.5    4.2  4  ATG16           Autophagy protein 16 (ATG16)
      0.013   14.6  27.9        1.6    7.8   0.6    5.7  7  RmuC            RmuC family
      0.017   14.9   9.5      0.028   14.1   3.4    3.2  3  DUF4201         Domain of unknown function (DUF4201)
      0.024   14.8  22.6       0.54   10.4   2.1    4.7  5  Fib_alpha       Fibrinogen alpha/beta chain family
      0.053   13.7  30.7      0.046   13.9  10.5    3.2  3  CENP-Q          CENP-Q, a CENPA-CAD centromere complex subuni
       0.12   13.1  36.5        1.4    9.7   0.8    5.3  6  DUF2203         Uncharacterized conserved protein (DUF2203)
       0.12   12.2  25.5          2    8.3   2.3    5.6  6  Sec34           Sec34-like family
       0.14   11.8   3.1        4.1    7.0   0.2    2.6  2  Rota_NSP4       Rotavirus non structural protein
       0.16   11.6   0.1       0.16   11.6   0.1    3.4  4  DCB             Dimerisation and cyclophilin-binding domain o
       0.18   11.5  11.6        2.3    7.9   0.3    4.5  6  Hormone_1       Somatotropin hormone family
       0.22    9.7  32.4       0.16   10.1   1.2    2.8  2  EzrA            Septation ring formation regulator, EzrA
       0.27   10.7  43.3       0.41   10.2  11.5    3.4  3  MscS_porin      Mechanosensitive ion channel porin domain
       0.34   11.3  19.0       0.55   10.6   0.4    5.2  5  Syntaxin_2      Syntaxin-like protein
       0.41   10.9  28.1       0.19   12.0   2.5    4.2  4  DUF5082         Domain of unknown function (DUF5082)
       0.73    9.9  46.7      0.021   14.9   8.7    4.4  4  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
        1.1    9.0  17.9        2.1    8.2   0.2    6.5  7  DASH_Duo1       DASH complex subunit Duo1
        1.1    7.8  37.5         54    2.2  23.4    2.9  2  AAA_13          AAA domain
        1.2    9.8  26.7       0.56   10.8   0.1    5.0  4  BST2            Bone marrow stromal antigen 2
        1.5    6.9  23.7       0.17   10.0   2.7    4.1  4  COG6            Conserved oligomeric complex COG6
        1.7    8.4  56.5      0.044   13.6  21.3    3.6  3  ERM             Ezrin/radixin/moesin family
        1.7    9.0  36.6       0.55   10.6   1.1    3.2  3  Fez1            Fez1
        1.8    7.4  16.1         92    1.7  16.1    2.8  1  LMBR1           LMBR1-like membrane protein
          2    7.5  17.8        1.1    8.3   2.8    3.6  3  Atg14           Vacuolar sorting 38 and autophagy-related sub
        2.3    7.5  30.8       0.28   10.5   1.7    3.6  3  CorA            CorA-like Mg2+ transporter protein
        2.7    7.9   6.7         23    4.8   0.3    3.5  4  Vip3A_N         Vegetative insecticide protein 3A N terminal
        2.8    8.3  18.3        1.5    9.2  13.9    2.7  2  SLX9            Ribosome biogenesis protein SLX9
        2.8    8.1  37.4        2.6    8.2  15.9    4.0  3  Jnk-SapK_ap_N   JNK_SAPK-associated protein-1
        3.5    7.9  32.5        9.8    6.5   2.8    5.5  6  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
        3.7    7.7  34.8        1.2    9.2   9.9    4.0  4  Mod_r           Modifier of rudimentary (Mod(r)) protein
        4.1    7.8  30.5      0.047   14.0   7.8    4.5  4  TBCA            Tubulin binding cofactor A
        4.2    4.8  48.4       0.36    8.3  26.3    2.0  2  DUF3584         Protein of unknown function (DUF3584)
        4.5    7.8  30.2        5.8    7.5   1.1    4.8  4  Spectrin        Spectrin repeat
        5.2    7.5  37.9        2.7    8.4   1.4    5.0  5  CENP-H          Centromere protein H (CENP-H)
        6.3    6.7  18.0        9.5    6.1   0.1    4.8  4  Sec8_exocyst    Sec8 exocyst complex component specific domai
        6.4    5.3  11.7        3.2    6.3   0.7    3.3  3  Tweety          Tweety
        6.6    7.3  54.4        1.5    9.4  19.1    4.7  4  APG6_N          Apg6 coiled-coil region
        6.9    7.5   9.5         27    5.5   1.7    4.6  3  Occludin_ELL    Occludin homology domain
        7.4    5.7  22.7        5.7    6.1   0.4    4.0  4  TMPIT           TMPIT-like protein
        7.6    7.2  21.7         30    5.3   4.3    5.2  4  YabA            Initiation control protein YabA
        8.6    6.4  31.7        1.3    9.1  10.7    4.1  4  ADIP            Afadin- and alpha -actinin-Binding
        9.7    6.7  40.1        8.4    6.9   0.1    7.3  6  NPV_P10         Nucleopolyhedrovirus P10 protein


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   4.0       1.3   4.3e+02      86     136 ..     135     185 ..     101     214 .. 0.61
   2 !    8.6   4.7    0.0045       1.5      93     156 ..     202     269 ..     190     276 .. 0.70
   3 !    8.1  10.5    0.0064       2.1      89     171 ..     226     305 ..     219     306 .. 0.75
   4 !  129.4  25.6   3.4e-40   1.2e-37       4     171 ..     313     480 ..     303     481 .. 0.88
   5 ?    5.3   3.9     0.046        16     132     166 ..     472     510 ..     470     515 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.3
                                       HHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHH CS
                         MCPsignal  86 qaakeiealiieiqkeindsvesleetrqrveegselveetgealkeivea 136
                                       ++a++ ++  +e   + +d  e l+etr ++e   e     +e ++e+ +a
  gi|336252564|ref|YP_004595671.1| 135 ERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAERFSEVMDA 185
                                       333333333333335555555555555555555555444444445554444 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0045
                                       HHH..............HHHHHHHHHHHHHHHHHCCHHH....HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  93 aliieiqkeindsvesleetrqrveegselveetgealk....eiveavaevadlvqeiaaaseeqsa 156
                                       ++i++i    n+ ++ ++et   v  +++ vee   +l+    ei +a  evad+vqeia  ++eq+ 
  gi|336252564|ref|YP_004595671.1| 202 EAIAAIATSFNEMLDRMSETMVDVRGSANAVEEISVELEdssaEIRTASREVADSVQEIADGAAEQTD 269
                                       56777888888888888888888887777777765555311226777777888888888888877765 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0064
                                       HHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  89 keiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqav 165
                                       +  +++++ei  e +ds + +  + ++v+ +++++++ +   +e ++  +  a++v++++aa+ee +++  e+++  
  gi|336252564|ref|YP_004595671.1| 226 RGSANAVEEISVELEDSSAEIRTASREVADSVQEIADGA---AEQTDDLDAAAAEVSDLSAATEEVASTTGEIADQS 299
                                       555678888999999999999888888877766665544...45567777888888999999999999999999998 PP

                                       HHHHHH CS
                         MCPsignal 166 eevakv 171
                                       e v+++
  gi|336252564|ref|YP_004595671.1| 300 ESVTEL 305
                                       888876 PP

  == domain 4  score: 129.4 bits;  conditional E-value: 3.4e-40
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHH CS
                         MCPsignal   4 aeeaseeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkL 80 
                                       a ea e+ +e  ++ + vv++ +e+++++++i++ii+ id+iadQTNlLA+NA+iEAA AG  G GFaVVAdE+++L
  gi|336252564|ref|YP_004595671.1| 313 AAEAAENIDELVENTETVVETADELTRETEQIEEIIALIDDIADQTNLLAVNASIEAATAGADGSGFAVVADEIKAL 389
                                       2222222222233334466777777777************************************************* PP

                                       HHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  81 Aersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsas 157
                                       Ae++++a  +ie  ++ i   ++++++ + e+++++ +++++v++ ++ l++i+ +v++v+ ++q+ia+++++q+ s
  gi|336252564|ref|YP_004595671.1| 390 AEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQADS 466
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHH CS
                         MCPsignal 158 ieevnqaveevakv 171
                                       ++e +  v+ va+v
  gi|336252564|ref|YP_004595671.1| 467 AQELSAIVDDVAAV 480
                                       ******99999887 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.046
                                       HHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 132 eiveavaev....adlvqeiaaaseeqsasieevnqave 166
                                        iv+ va v    a+  q++aaasee sa+i++v+++ +
  gi|336252564|ref|YP_004595671.1| 472 AIVDDVAAVsnetATKAQQVAAASEETSATIDSVSTTAT 510
                                       455555555000045678999999999999999998765 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.2     1e-11   3.4e-09       3      53 .]      75     125 ..      73     125 .. 0.92
   2 !   22.0   0.4   4.5e-07   0.00015      11      52 ..     177     219 ..     170     220 .. 0.87
   3 ?    4.0   0.1       0.2        66      11      39 ..     251     280 ..     250     306 .. 0.82
   4 ?    1.2   0.3       1.4   4.8e+02      23      45 ..     402     426 ..     383     441 .. 0.69

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1e-11
                                       HHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHHH CS
                              HAMP   3 arrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLre 53 
                                        ++++  LrrL   ++ri++G++d++l++++ DEiGeL  ++ +M+d+L++
  gi|336252564|ref|YP_004595671.1|  75 GGNVSLALRRLGNGTERIGDGEFDVDLETDRVDEIGELYGSVARMRDSLED 125
                                       5667778*****************************************985 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 4.5e-07
                                       HHHHHHHHHHTTTBTSSTCCTTSSSH.HHHHHHHHHHHHHHHH CS
                              HAMP  11 rrLaraarriaaGdldtrlpvsgrDE.iGeLarafNaMldrLr 52 
                                       +r ++++++ a+Gdl++rl++  +DE i+++a +fN+Mldr  
  gi|336252564|ref|YP_004595671.1| 177 ERFSEVMDACADGDLTQRLEPQVDDEaIAAIATSFNEMLDRMS 219
                                       567788888889**************9*************975 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHTTT......BTSSTCCTTSSSHHHH CS
                              HAMP  11 rrLaraarriaaG......dldtrlpvsgrDEiGe 39 
                                       r++a+++++ia+G      dld+        E+ +
  gi|336252564|ref|YP_004595671.1| 251 REVADSVQEIADGaaeqtdDLDAA-----AAEVSD 280
                                       789999*******99999888875.....344444 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 1.4
                                       T......BTSSTCCTTSSSHHHHHHHHHH CS
                              HAMP  23 G......dldtrlpvsgrDEiGeLarafN 45 
                                       G      d +++    + +EiGe+  ++ 
  gi|336252564|ref|YP_004595671.1| 402 GtlesirDRTET----TANEIGEVESNIT 426
                                       334444466665....8899999876665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   3.1     0.029       9.7      51     111 ..     110     170 ..     101     181 .. 0.70
   2 !   16.3   1.1   2.2e-05    0.0073      34     107 ..     223     296 ..     215     302 .. 0.90
   3 ?    6.9   3.4     0.018         6      49     120 ..     280     351 ..     271     369 .. 0.71
   4 !   15.4   0.9   4.1e-05     0.014      53     121 ..     382     450 ..     362     453 .. 0.93
   5 ?    6.1   1.6     0.032        11      49     115 ..     448     514 ..     446     524 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.029
                           DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                        +++ s+a+ ++ L++ ++ ++++++  +++++e +e  ++++++ ++++e   ++++  e
  gi|336252564|ref|YP_004595671.1| 110 GELYGSVARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNE 170
                                       5667777777777888888888877777777777777777777777777776666665544 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.2e-05
                           DUF1664  34 vTkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                       v  r+ ++ave++s +le+ s++++++ r+ ++ ++++ +   eq++   + ++ev++++  ++e+ +   ++ 
  gi|336252564|ref|YP_004595671.1| 223 VDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEIADGAAEQTDDLDAAAAEVSDLSAATEEVASTTGEIA 296
                                       5568889*****************************************************99999988877765 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.018
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       +l    e++a+t  +++++ ++v +  +e  e+++e +e+++e+ e+++++ e  +++ +  e++e+ ++ i
  gi|336252564|ref|YP_004595671.1| 280 DLSAATEEVASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTETVVETADELTRETEQIEEIIALI 351
                                       466666777777777777777777777777777777777777777777777777777777777777666655 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 4.1e-05
                           DUF1664  53 vseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       v ++++a  ++ ++ +d ++ +l++  + ++ +++e+ ev+++++++ + v+ +++  e++++++e+++
  gi|336252564|ref|YP_004595671.1| 382 VADEIKALAEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQVD 450
                                       77889999999999**************************************************99986 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.032
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       q++   +++a+t ++ ++  +++ + +d+++++s+e++ + ++v    +e++  ++sv+++ ++l+ 
  gi|336252564|ref|YP_004595671.1| 448 QVDGSIQQIASTADDQADSAQELSAIVDDVAAVSNETATKAQQVAAASEETSATIDSVSTTATDLGD 514
                                       6777888899999999999999999999999999999999999999999999999999998888865 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4  13.3   0.00021     0.071      13     108 ..     122     221 ..     112     225 .. 0.80
   2 ?    1.2   1.4      0.54   1.8e+02      20      70 ..     238     288 ..     225     292 .. 0.72
   3 !   10.2   4.7     0.001      0.34       8      73 ..     289     354 ..     281     370 .. 0.88
   4 !   13.2   0.8   0.00012     0.039      12      96 ..     377     461 ..     360     466 .. 0.90
   5 ?    5.2   1.4     0.034        11      14      64 ..     477     527 ..     466     532 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00021
                           DUF3450  13 alaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeq..eiasleeq 87 
                                       +l++tl++++ e+e+a++a+++++++ d+l+de+++l++   ++++++e+l ++ e+ ++++++       ++le q
  gi|336252564|ref|YP_004595671.1| 122 SLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAERFSEVMDACADgdLTQRLEPQ 198
                                       45899**************************************************9999999876531124445444 PP

                           DUF3450  88 i..eeieeierelvpllekmidr 108
                                          e i +i+++   +l++m ++
  gi|336252564|ref|YP_004595671.1| 199 VddEAIAAIATSFNEMLDRMSET 221
                                       41156888888888888888766 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.54
                           DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneql 70 
                                       ++++ ++++ +a++++   +++++d ++e  +++ a+ +e+++l++  e++
  gi|336252564|ref|YP_004595671.1| 238 ELEDSSAEIRTASREVADSVQEIADGAAEQTDDLDAAAAEVSDLSAATEEV 288
                                       556667777777888888888888888888888888888888887776665 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.001
                           DUF3450   8 llasgalaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerl 73 
                                       + ++g +a++ +++ + +e+  +aaa++ ++id+l ++++++++   +l++e+e++e   +  +++
  gi|336252564|ref|YP_004595671.1| 289 ASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTETVVETADELTRETEQIEEIIALIDDI 354
                                       5567778************************************************99876665555 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.00012
                           DUF3450  12 galaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqi 88 
                                       +++a  +d++++ ae++++a  +++   +++ d +++ ++e+ ++++ + s++   + le+ +++   e+++++ +i
  gi|336252564|ref|YP_004595671.1| 377 SGFAVVADEIKALAEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSI 453
                                       334888999******************************************************************** PP

                           DUF3450  89 eeieeier 96 
                                       ++i  +++
  gi|336252564|ref|YP_004595671.1| 454 QQIASTAD 461
                                       ***99876 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.034
                           DUF3450  14 laatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeelesle 64 
                                       +aa  +++  +a++  aa++++++ id+++  +++l ++ r+lk+ l++ +
  gi|336252564|ref|YP_004595671.1| 477 VAAVSNETATKAQQVAAASEETSATIDSVSTTATDLGDDARDLKRLLDAFT 527
                                       46777888899999999**************************99888766 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 !    8.3   5.8    0.0038       1.3      96     191 ..     122     216 ..     111     225 .. 0.65
   2 !    7.5   2.1    0.0069       2.3      30     132 ..     238     344 ..     232     363 .. 0.84
   3 !   10.6   0.3   0.00076      0.26      99     195 ..     384     483 ..     378     487 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0038
                               GAS  96 elekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEk.keaqleevlaa 171
                                       +le+ l dl+ e+e  +q   ++e+  d+l+++ e+ +qe++ +++ +n  L    ++ +e +++ ++  l++ l +
  gi|336252564|ref|YP_004595671.1| 122 SLEDTLADLETEQERAQQAQREAEERADQLEDEREQ-LQETRAEIERQNERLVAEAERFSEVMDAcADGDLTQRL-E 196
                                       566667777777777777777777666666666655.66777777777777766667666666663446666666.5 PP

                               GAS 172 anldpaalsavsekleevle 191
                                        ++d++a++a++ +++e+l+
  gi|336252564|ref|YP_004595671.1| 197 PQVDDEAIAAIATSFNEMLD 216
                                       66666666666666666665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0069
                               GAS  30 slKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                       +l +  +e+++  ++    ++ei+    + ++ L +a +ev  L ++ ++  +   +++ + + ++el++e ++   
  gi|336252564|ref|YP_004595671.1| 238 ELEDSSAEIRTASREVADSVQEIADGAAEQTDDLDAAAAEVSDLSAATEEVASTTGEIADQSESVTELTEEGREAAA 314
                                       5777889999999999999********************************************99999999988776 PP

                               GAS 107 eh....evleqrfekvekerdelykkfeaa 132
                                       e+    + l +  e+v +  del+++ e+ 
  gi|336252564|ref|YP_004595671.1| 315 EAaeniDELVENTETVVETADELTRETEQI 344
                                       652222567788888999999999888774 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00076
                               GAS  99 kelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknll...LekklkalqeelEkkeaqleevlaaa 172
                                       +e+k+l +e     + +e   +++ + +++  + i ev  ++   +++   Le +l+++  e+E+ +  ++++ ++a
  gi|336252564|ref|YP_004595671.1| 384 DEIKALAEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIvddLESRLETIAGEVEQVDGSIQQIASTA 460
                                       5666666666666666665555555555666666888888888777765558************************* PP

                               GAS 173 nldpaalsavsekleevlesKnq 195
                                       + ++++++++s+ +++v +  n+
  gi|336252564|ref|YP_004595671.1| 461 DDQADSAQELSAIVDDVAAVSNE 483
                                       ****************9887776 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 ?    0.7   5.1       1.9   6.4e+02      40      84 ..     202     246 ..      51     251 .. 0.82
   2 !   13.2   3.0   0.00024     0.083      17      88 ..     218     289 ..     203     290 .. 0.76
   3 !   10.5   1.7    0.0017      0.57      33      88 ..     252     306 ..     245     311 .. 0.61
   4 ?    3.6   6.5      0.23        79      30      80 ..     308     354 ..     285     375 .. 0.56
   5 ?    6.1   0.4      0.04        14      45      87 ..     382     425 ..     363     427 .. 0.72
   6 !    8.3   3.1    0.0079       2.7      25      85 ..     394     454 ..     377     461 .. 0.55
   7 !   10.4   2.8    0.0018       0.6      24      82 ..     421     479 ..     417     484 .. 0.80
   8 !    9.7   4.4    0.0029      0.97      22      88 ..     454     520 ..     451     521 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.9
                            DUF948  40 kqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                       + + +i +  +++l+ + e++ dv++  ++v+++  +++d ++ +
  gi|336252564|ref|YP_004595671.1| 202 EAIAAIATSFNEMLDRMSETMVDVRGSANAVEEISVELEDSSAEI 246
                                       455667777777777777777777777777777777777766666 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00024
                            DUF948  17 livvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       +  +++ ++  ++++++   ele+   +i + ++++ + v+e++++  e+++++d+  ++v dl+++ +e+ 
  gi|336252564|ref|YP_004595671.1| 218 MSETMVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEIADGAAEQTDDLDAAAAEVSDLSAATEEVA 289
                                       445666666677777777777778888888888889999999999*********************998875 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0017
                            DUF948  33 atieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       +  +++++ +d+  ++++dl a + e ++d++  +e+v + t ++ad +esv el+
  gi|336252564|ref|YP_004595671.1| 252 EVADSVQEIADGAAEQTDDLDAAAAE-VSDLSAATEEVASTTGEIADQSESVTELT 306
                                       33344444445555555555555555.55577777777777777777777777776 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.23
                            DUF948  30 eaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadl 80 
                                       e +++ +e  +++d++++++e++++++ e    +++++e+++++++ + d+
  gi|336252564|ref|YP_004595671.1| 308 EGREAAAEAAENIDELVENTETVVETADE----LTRETEQIEEIIALIDDI 354
                                       33333344445555555555555555555....333444444444444444 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.04
                            DUF948  45 ilkevedllakvnelledvneklekvdplte.avadlgesvsel 87 
                                       + +e+++l +++ + ++d+++ le++   te  ++++ge  s++
  gi|336252564|ref|YP_004595671.1| 382 VADEIKALAEETMDAVDDIEGTLESIRDRTEtTANEIGEVESNI 425
                                       56788888888888888888888888665551455666665555 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0079
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                        + +d ++ t+e+++++++ + +e+ ++ +++  ++  v +   +++++  +v+++  s++
  gi|336252564|ref|YP_004595671.1| 394 MDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQ 454
                                       4456666667777777777776666655555555444444444444444444444444444 PP

  == domain 7  score: 10.4 bits;  conditional E-value: 0.0018
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlge 82 
                                       +++ ++++a+ +++le++++ i  eve++   ++++++   ++ ++ ++l + v d+++
  gi|336252564|ref|YP_004595671.1| 421 VESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQADSAQELSAIVDDVAA 479
                                       567788999********************999999888777777777777666666654 PP

  == domain 8  score: 9.7 bits;  conditional E-value: 0.0029
                            DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                        ++++t+d  a++ +el   vd +   ++++ +k++++++  +e ++++d++ + + dlg+  ++l+
  gi|336252564|ref|YP_004595671.1| 454 QQIASTADDQADSAQELSAIVDDVAAVSNETATKAQQVAAASEETSATIDSVSTTATDLGDDARDLK 520
                                       6788999999***************************************************999885 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 ?    7.1   6.9     0.018       5.9      30      83 ..     122     175 ..     109     188 .. 0.73
   2 ?    5.1  10.3     0.075        26      15      81 ..     240     310 ..     219     361 .. 0.66
   3 ?    0.6   0.0       1.9   6.3e+02      60      91 ..     391     422 ..     382     426 .. 0.77
   4 !   14.4   0.8    0.0001     0.034       5     108 ..     423     523 ..     419     526 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.018
                       TMF_TATA_bd  30 slkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetl 83 
                                       sl+++l+ le+e+++a++   +  ++ ++l+++ ++l+e+++e+e  +er+ + 
  gi|336252564|ref|YP_004595671.1| 122 SLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAE 175
                                       567777777888888888888888888888888888888888887777776654 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.075
                       TMF_TATA_bd  15 erlsseirrlEgElaslkeelerleaer....deareeivklmkeneelkelkkeleelekeleelqerye 81 
                                       e  s+eir    E+a + +e++  +ae+    d+a++e+ +l++ +ee++++ +e+++++++++el+e+  
  gi|336252564|ref|YP_004595671.1| 240 EDSSAEIRTASREVADSVQEIADGAAEQtddlDAAAAEVSDLSAATEEVASTTGEIADQSESVTELTEEGR 310
                                       45567777777777777776665443332222677778888888888888888888888877777665432 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.9
                       TMF_TATA_bd  60 kelkkeleelekeleelqeryetlLellGeks 91 
                                       +e+ + ++++e  le++++r et+   +Ge +
  gi|336252564|ref|YP_004595671.1| 391 EETMDAVDDIEGTLESIRDRTETTANEIGEVE 422
                                       45566788888899999999999988888875 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 0.0001
                       TMF_TATA_bd   5 ssagpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqerye 81 
                                       s+ ++++++v+ l+s++    gE++++  +++++++  d+ ++   +l++ ++++++ ++e ++  +++++ +e+ +
  gi|336252564|ref|YP_004595671.1| 423 SNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQADSAQELSAIVDDVAAVSNETATKAQQVAAASEETS 499
                                       56678899****************************************************99999999998888777 PP

                       TMF_TATA_bd  82 tlLellGeksEeveELraDvaDlKemy 108
                                       ++   +   s    +L +D  DlK ++
  gi|336252564|ref|YP_004595671.1| 500 AT---IDSVSTTATDLGDDARDLKRLL 523
                                       76...6778889999999999999876 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 ?    6.1   0.9     0.041        14      12      56 ..     124     168 ..     104     184 .. 0.52
   2 ?    4.5   1.1      0.13        44      40      77 ..     268     305 ..     211     308 .. 0.66
   3 !   11.0   1.9    0.0012       0.4      31      78 ..     315     362 ..     310     367 .. 0.91
   4 ?    7.2   1.8     0.018         6      25      81 ..     404     460 ..     382     489 .. 0.58
   5 ?    1.2   0.1       1.4   4.6e+02      43      79 ..     478     514 ..     463     526 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.041
                           BLOC1_2  12 eaeleatvedyklLeklNeaasekykklkdvaaslekkleklnek 56 
                                       e +l+   ++ +  ++  ++a+e+ ++l+d+ ++l+++  +++++
  gi|336252564|ref|YP_004595671.1| 124 EDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQ 168
                                       333333333333333333344444444444444444443333333 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.13
                           BLOC1_2  40 kdvaaslekkleklnekyeelqpylqqidqiekqvteL 77 
                                       +d ++ +++++++l++  ee+++   +i +  ++vteL
  gi|336252564|ref|YP_004595671.1| 268 TDDLDAAAAEVSDLSAATEEVASTTGEIADQSESVTEL 305
                                       34444555566666666666666666666666666666 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0012
                           BLOC1_2  31 aasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78 
                                       +a+e++++l ++++ + +++++l ++ e++++ +  id+i +q++ L 
  gi|336252564|ref|YP_004595671.1| 315 EAAENIDELVENTETVVETADELTRETEQIEEIIALIDDIADQTNLLA 362
                                       68999**************************************98776 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.018
                           BLOC1_2  25 LeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81 
                                       Le +  ++++  +++ +v +++++++  ++ ++  l+    +++q++ +++++ +++
  gi|336252564|ref|YP_004595671.1| 404 LESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTA 460
                                       444444444444444444444444444444444455555555555555555555444 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 1.4
                           BLOC1_2  43 aaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                       aa  ++++ k ++  ++ ++    id + ++ t+L +
  gi|336252564|ref|YP_004595671.1| 478 AAVSNETATKAQQVAAASEETSATIDSVSTTATDLGD 514
                                       3333333444444444555555555555555555544 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   3.2     0.077        26      14      62 ..     118     166 ..     103     186 .. 0.49
   2 ?    5.2   0.6      0.06        20      12      62 ..     204     254 ..     198     260 .. 0.73
   3 !    9.1   4.6    0.0038       1.3       6      83 ..     223     300 ..     211     315 .. 0.75
   4 !    9.1   9.2    0.0037       1.2       1     112 [.     250     364 ..     250     374 .. 0.76
   5 !   10.8   1.5    0.0011      0.38       5      71 ..     383     449 ..     380     461 .. 0.64
   6 !    9.3   4.1    0.0032       1.1       4      69 ..     459     524 ..     456     528 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.077
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  14 evleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvk 62 
                                          + l++  ++le ++e +++++r++ee  ++++d  +++++ r ++ 
  gi|336252564|ref|YP_004595671.1| 118 RMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIE 166
                                       3333344444444444444444444444444444444444444443333 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvk 62 
                                       ++++    +++  ++++t  ++ + ++ vee+  +++d++  ir A+r+v 
  gi|336252564|ref|YP_004595671.1| 204 IAAIATSFNEMLDRMSETMVDVRGSANAVEEISVELEDSSAEIRTASREVA 254
                                       555666677777777777777888888888888888888888888888775 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0038
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                        ++  +a++v+e+  +l+    +++    e+++sv+e+ + + + +  ++ A  +v++L    +++ +   e+  ++
  gi|336252564|ref|YP_004595671.1| 223 VDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEIADGAAEQTDDLDAAAAEVSDLSAATEEVASTTGEIADQS 299
                                       45666777777777777777778888888888889999999999999999999999999888877776655555555 PP

                                       H CS
                        Laminin_II  83 e 83 
                                       e
  gi|336252564|ref|YP_004595671.1| 300 E 300
                                       4 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0037
                                       XXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGG CS
                        Laminin_II   1 skelaaeanetakevleqlapls...qnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldk 74 
                                       s+e+a++++e+a    eq+ +l+   ++++ +++  +e++++  e+ ++ ++ ++ +++ r++  +  +++++L++ 
  gi|336252564|ref|YP_004595671.1| 250 SREVADSVQEIADGAAEQTDDLDaaaAEVSDLSAATEEVASTTGEIADQSESVTELTEEGREAAAEAAENIDELVEN 326
                                       577888888888777777777752226899999999******99********************************* PP

                                       HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHT---E CS
                        Laminin_II  75 lkelkqleeassslsdniseikelIaqARkaAnkikvs 112
                                        +++ +  ++     ++i+ei +lI    ++ n  +v 
  gi|336252564|ref|YP_004595671.1| 327 TETVVETADELTRETEQIEEIIALIDDIADQTNLLAVN 364
                                       99999999994444455555555555555555555555 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.0011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       a+e++  a+e+ + + +++  le +++  ++ ++++ e++ ++ +  ++++d ++   ++  +++q+
  gi|336252564|ref|YP_004595671.1| 383 ADEIKALAEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQV 449
                                       6666777777777777777777777777777777777777777777777777666666666555554 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.0032
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklap 69 
                                       +a++  ++a+e  +++ ++++  ++t  k++++++  eet + +++ +++  d ++  ++L++l++
  gi|336252564|ref|YP_004595671.1| 459 TADDQADSAQELSAIVDDVAAVSNETATKAQQVAAASEETSATIDSVSTTATDLGDDARDLKRLLD 524
                                       6888889999999*************************************************9987 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.84   2.8e+02      35      75 ..     121     161 ..     114     186 .. 0.76
   2 !    8.7   0.1    0.0038       1.3      27      67 ..     208     248 ..     202     260 .. 0.85
   3 ?    3.6   0.2      0.15        51      28      86 ..     279     338 ..     271     368 .. 0.74
   4 ?    5.8   0.1      0.03        10      20      56 ..     418     454 ..     411     476 .. 0.80
   5 ?   -1.7   0.0       6.4   2.2e+03      16      58 ..     470     512 ..     466     527 .. 0.49

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.84
                              RPW8  35 krLestleritPvvkeieklnkeldrpreeieeLkklLeka 75 
                                       ++Le+tl ++++  ++ ++ + e +++ +++e+ +++L++ 
  gi|336252564|ref|YP_004595671.1| 121 DSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQET 161
                                       57888888888888888888888877777777777777654 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0038
                              RPW8  27 sldfksilkrLestleritPvvkeieklnkeldrpreeiee 67 
                                       +++f+ +l+r+ +t+ +++ + + +e+++ el+   +ei  
  gi|336252564|ref|YP_004595671.1| 208 ATSFNEMLDRMSETMVDVRGSANAVEEISVELEDSSAEIRT 248
                                       578999**************************766667765 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.15
                              RPW8  28 ldfksilkrLestleritPvvkeieklnkel.drpreeieeLkklLekaekLVekcsklk 86 
                                       +d +   ++ +st  +i+   + + +l++e  +   e  e++ +l e+ e  Ve   +l 
  gi|336252564|ref|YP_004595671.1| 279 SDLSAATEEVASTTGEIADQSESVTELTEEGrEAAAEAAENIDELVENTETVVETADELT 338
                                       555666677777777777778888888877777777778888888888888877766654 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.03
                              RPW8  20 ileakkksldfksilkrLestleritPvvkeieklnk 56 
                                       i e++ + ++++ i+++Les le+i+  v++++   +
  gi|336252564|ref|YP_004595671.1| 418 IGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQ 454
                                       6788899999********************9985444 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 6.4
                              RPW8  16 llkaileakkksldfksilkrLestleritPvvkeieklnkel 58 
                                       l  ++ +++  s +++ + ++ ++  e+ +  ++ + +  ++l
  gi|336252564|ref|YP_004595671.1| 470 LSAIVDDVAAVSNETATKAQQVAAASEETSATIDSVSTTATDL 512
                                       4444444444455555555555555554444444444444444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  12.8     0.012       4.1     167     230 ..     118     180 ..     101     205 .. 0.57
   2 !    6.8  12.8    0.0082       2.8     140     280 ..     207     346 ..     201     371 .. 0.61
   3 !    8.9   9.3    0.0018       0.6     151     289 ..     337     491 ..     327     505 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                              Spc7 167 ellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqle 230
                                       ++ ++le   a+le e e+ q+a++e ++   ++Le  re+l+e  aeie+++++l    e+  
  gi|336252564|ref|YP_004595671.1| 118 RMRDSLEDTLADLETEQERAQQAQRE-AEERADQLEDEREQLQETRAEIERQNERLVAEAERFS 180
                                       34444444455555555555554444.2234455555555555555555555444444444444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0082
                              Spc7 140 LkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelka 213
                                       + ++ +e l+ + e    +  + + ++e+  ele   ae++   ++  + ++e+++    + ++L ++  e+++l+a
  gi|336252564|ref|YP_004595671.1| 207 IATSFNEMLDRMSETMVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEIADgaaEQTDDLDAAAAEVSDLSA 283
                                       66677788888888888888888888888888888888888887777777777766554667888888888777777 PP

                              Spc7 214 eieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkalee 280
                                         e    e+a+ + ++++++e+++el+e+ +e+ +e ae  + l e+ +   +  ++l+ e +++ee
  gi|336252564|ref|YP_004595671.1| 284 ATE----EVASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTETVVETADELTRETEQIEE 346
                                       777....444444444444444444444444444444444333333333333333333333333333 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0018
                              Spc7 151 leedkelLekqeeeldellpeleeekaeleeeleklqe...............aaeelesid..keeLeelreelae 210
                                       l+++ e++e+  +++d++ ++++    + + e+++  +               a+e ++++d  +  Le++r++ ++
  gi|336252564|ref|YP_004595671.1| 337 LTRETEQIEEIIALIDDIADQTNLLAVNASIEAATAGAdgsgfavvadeikalAEETMDAVDdiEGTLESIRDRTET 413
                                       5555555555555555555555444444444444444444444444444444444667777767889********** PP

                              Spc7 211 lkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkiv 287
                                         +ei e + ++++  + +++le+++e+++ + +++   i++  ++ +  +  s++e+s++ + v a+ ++t  k  
  gi|336252564|ref|YP_004595671.1| 414 TANEIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTAD-DQADSAQELSAIVDDVAAVSNETATKAQ 489
                                       *****************************************9999887.6778999***********9999988766 PP

                              Spc7 288 sl 289
                                       ++
  gi|336252564|ref|YP_004595671.1| 490 QV 491
                                       55 PP

>> I_LWEQ  I/LWEQ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   5.9       3.5   1.2e+03      96     132 ..     138     173 ..     103     182 .. 0.48
   2 ?    3.5   7.5      0.23        79      35     103 ..     239     310 ..     202     326 .. 0.58
   3 ?   16.1   3.2     3e-05      0.01      19     120 ..     324     422 ..     316     449 .. 0.79
   4 ?   -1.2   8.1       6.2   2.1e+03      47     115 ..     447     508 ..     413     515 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.5
                            I_LWEQ  96 kekqeeeeseeeeld..isklslvqakrqemeaqvkilk 132
                                       +++q+e    ee+ d   ++ +  q +r+e+e q + l 
  gi|336252564|ref|YP_004595671.1| 138 QQAQRE---AEERADqlEDEREQLQETRAEIERQNERLV 173
                                       111111...223333222344445555555555554443 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.23
                            I_LWEQ  35 gkakeeeLivaakevaastaqLvvasrvKadknskslk...rLeaaskaVkkatkelvkavkeakekqeeee 103
                                        ++++ e+ +a++eva s+  +   +  ++d+ + + +   +L+aa ++V+++t e+  + ++++e +ee +
  gi|336252564|ref|YP_004595671.1| 239 LEDSSAEIRTASREVADSVQEIADGAAEQTDDLDAAAAevsDLSAATEEVASTTGEIADQSESVTELTEEGR 310
                                       235666666677777777666664333333333322222446677777777777777777777666666654 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 3e-05
                            I_LWEQ  19 aaaanlLveaadavvqgkakeeeLivaakevaastaqLvvasrvKadknskslkrLeaaskaVkkatkelvkavkea 95 
                                       ++ +++ ve+ad++++++++ ee+i+  + +a +t  L v + + a + +   +    ++ ++k  ++e + av ++
  gi|336252564|ref|YP_004595671.1| 324 VENTETVVETADELTRETEQIEEIIALIDDIADQTNLLAVNASIEAATAGADGSGFAVVADEIKALAEETMDAVDDI 400
                                       678999******************************************************99999999999999999 PP

                            I_LWEQ  96 kekqeeeeseeeeldisklslvqak 120
                                       + + e+ +   ++++ ++ ++ +  
  gi|336252564|ref|YP_004595671.1| 401 EGTLESIR---DRTETTANEIGEVE 422
                                       99888753...33443333333333 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 6.2
                            I_LWEQ  47 kevaastaqLvvasrvKadknskslkrLeaaskaVkkatkelvkavkeakekqeeeeseeeeldiskls 115
                                       ++v  s+ q+  a    ad++ +s ++L+a   +V+   +e   +++++++++ee    + ++d  +++
  gi|336252564|ref|YP_004595671.1| 447 EQVDGSIQQI--A--STADDQADSAQELSAIVDDVAAVSNETATKAQQVAAASEET---SATIDSVSTT 508
                                       3444444443..2..24566667778888888889888888888888888888885...4556644444 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8  16.1      0.36   1.2e+02      78     132 ..     122     176 ..     110     196 .. 0.57
   2 ?    6.0  12.3     0.036        12      17     161 ..     204     338 ..     190     344 .. 0.76
   3 ?   15.9   3.5   3.4e-05     0.011      12     156 ..     339     477 ..     338     500 .. 0.84
   4 ?    6.6   3.9     0.025       8.3      32     114 ..     433     501 ..     408     526 .. 0.55

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.36
                             ATG16  78 sleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaer 132
                                       sle++la l +e++ +++++ e ++r  +l++e ++l+e+  e e++ ++l ae 
  gi|336252564|ref|YP_004595671.1| 122 SLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEA 176
                                       4555555555555555555555555544444444444444444444444444444 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.036
                             ATG16  17 faeliqaynrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelael 93 
                                        a++   +n++ldr+s+     +   +a ++ +          e e+s++ +  + s +++++ q++a   +e+++ 
  gi|336252564|ref|YP_004595671.1| 204 IAAIATSFNEMLDRMSETMVDVRGSANAVEEISV---------ELEDSSA-EIRTASREVADSVQEIADGAAEQTDD 270
                                       5566667777777777776665555333333222.........1111111.23345667888899999999999999 PP

                             ATG16  94 yksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDEls 161
                                       + + +   + l +++ee++    ++  ++e++ el++e ++   + +++ +el e +++v +  DEl+
  gi|336252564|ref|YP_004595671.1| 271 LDAAAAEVSDLSAATEEVASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTETVVETADELT 338
                                       99999999999999999999999999999999999999999999999999999999999999999986 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 3.4e-05
                             ATG16  12 rqekafaeliqaynrLldrtsaleaenaklekaaasaks.sksskksakekeasasqsnskqsakiqsleqklaqlr 87 
                                       r+++  +e+i+   +++d+t++l+   a++e+a+a a     +  +++ + +a+++       + + + e +l ++r
  gi|336252564|ref|YP_004595671.1| 339 RETEQIEEIIALIDDIADQTNLLAVN-ASIEAATAGADGsGFAVVADEIKALAEETM------DAVDDIEGTLESIR 408
                                       5678899***************9765.666555554444444545555566665555......99************ PP

                             ATG16  88 eelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdl 156
                                       +  +++  + ge ++ ++++ + +++le++l++ + +++++  +++++    +d+++  +e+ + v+d+
  gi|336252564|ref|YP_004595671.1| 409 DRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQADSAQELSAIVDDV 477
                                       ***************************************************************999976 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.025
                             ATG16  32 saleaenaklekaaasakssksskksakekeasasq..snskqsakiqsleqklaqlreelaelyksrgelaqrlle 106
                                       + le++ +++   a ++++            +   +  + ++++++ ++++q+l+++ +++a++  + ++ aq++ +
  gi|336252564|ref|YP_004595671.1| 433 DDLESRLETI---AGEVEQ-----------VDG--SiqQIASTADDQADSAQELSAIVDDVAAVSNETATKAQQVAA 493
                                       2222222222...222222...........111..122444455566788899999999999999999999999998 PP

                             ATG16 107 lneelqkl 114
                                       ++ee ++ 
  gi|336252564|ref|YP_004595671.1| 494 ASEETSAT 501
                                       88887665 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.7    0.0092       3.1       8      59 ..     131     182 ..     112     187 .. 0.64
   2 ?    0.8   0.1      0.62   2.1e+02       5      53 ..     213     257 ..     202     273 .. 0.39
   3 ?    7.8   0.6    0.0047       1.6     222     287 ..     244     308 ..     229     312 .. 0.85
   4 ?    7.7   1.5    0.0052       1.7     225     282 ..     282     345 ..     271     354 .. 0.73
   5 ?    5.2   0.1      0.03        10     227     283 ..     382     434 ..     354     448 .. 0.67
   6 ?    5.0   0.2     0.033        11     224     283 ..     421     482 ..     419     489 .. 0.78
   7 ?    6.2   0.4     0.015       4.9      14      61 ..     477     524 ..     467     531 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0092
                              RmuC   8 kplkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLtka 59 
                                       ++ +e+ ++ +++ ee  ++ ++e+e+l+e   e++++ne+l  eae+ +++
  gi|336252564|ref|YP_004595671.1| 131 ETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAERFSEV 182
                                       3334455555555555557777777777777777777777777777766665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.62
                              RmuC   5 ellkplkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgdea 53 
                                       e+l+++ e++ +++ +     ++++e   +l+ +  e+++ ++++ d+ 
  gi|336252564|ref|YP_004595671.1| 213 EMLDRMSETMVDVRGSA----NAVEEISVELEDSSAEIRTASREVADSV 257
                                       33333333333333222....2222222223333333333333333222 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0047
                              RmuC 222 eaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaeklkelgvk 287
                                       ++++  ++e+a+ ++e+ d  ++ ++dl+++  ++++++ + ++ v +++g+i  + e++ el ++
  gi|336252564|ref|YP_004595671.1| 244 AEIRTASREVADSVQEIADGAAEQTDDLDAAAAEVSDLSAATEE-VASTTGEIADQSESVTELTEE 308
                                       46677788999999999999999999999999999999999999.88888********99999876 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0052
                              RmuC 225 eknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle......gnilrkaeklk 282
                                       +  +ee+a++ ge+ d+ e+++e  e+ +++  +a +++d++v+++e      ++++r+ e+++
  gi|336252564|ref|YP_004595671.1| 282 SAATEEVASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTEtvvetaDELTRETEQIE 345
                                       5667888888888888888888888888888888888888877766544444455555555554 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.03
                              RmuC 227 naeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaeklke 283
                                        a+ei  l++e +d +  ++ +le+++++ e++ +++ ++ ++ +    ++a  +++
  gi|336252564|ref|YP_004595671.1| 382 VADEIKALAEETMDAVDDIEGTLESIRDRTETTANEIGEVESNIT----STATIVDD 434
                                       578888888888888888888888888888888888777444443....33333333 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.033
                              RmuC 224 qeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle..gnilrkaeklke 283
                                       +e n +  a+ + +l +++e+++ ++e++  +++++ ++ d+ +++ +  + i+  +  + +
  gi|336252564|ref|YP_004595671.1| 421 VESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQADSAQelSAIVDDVAAVSN 482
                                       56778888889999999999999999999999999999999977777667777776666654 PP

  == domain 7  score: 6.2 bits;  conditional E-value: 0.015
                              RmuC  14 lekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLtkaLk 61 
                                       +++++++  ++ +++a + e+ ++ + ++++++++lgd+a++L++ L 
  gi|336252564|ref|YP_004595671.1| 477 VAAVSNETATKAQQVAAASEETSATIDSVSTTATDLGDDARDLKRLLD 524
                                       4555566566668999999999***********************996 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.4   8.4e-05     0.028      85     135 ..     126     176 ..     106     181 .. 0.75
   2 ?    2.0   0.2      0.44   1.5e+02      72     139 ..     295     362 ..     280     365 .. 0.71
   3 ?   -1.1   0.0       4.1   1.4e+03      67     103 ..     420     456 ..     397     516 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.4e-05
                           DUF4201  85 klhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqg 135
                                        l  le+e++++++  +e eer ++l++e +++++ r+ +++qne+l ++ 
  gi|336252564|ref|YP_004595671.1| 126 TLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEA 176
                                       455677888888888888888888888888888888888888888887765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.44
                           DUF4201  72 ttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllr 139
                                       +++++  +t+l e   + ++e +e  +el e +e+  +  +el++  ++ + + +  +++ +q+ ll 
  gi|336252564|ref|YP_004595671.1| 295 IADQSESVTELTEEGREAAAEAAENIDELVENTETVVETADELTRETEQIEEIIALIDDIADQTNLLA 362
                                       55555666677777777777777777777777777777777777777777777777777777777766 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.1
                           DUF4201  67 rlkkkttktvhalthlkeklhmleselselkkelkek 103
                                       +  +++t+t  ++ +l  +l +++ e+++   +++++
  gi|336252564|ref|YP_004595671.1| 420 EVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQI 456
                                       3334444444444444444444444444444444443 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 ?    6.9   0.8      0.02       6.8      27      91 ..     117     170 ..     110     187 .. 0.55
   2 ?    4.2   0.1      0.13        45      30      83 ..     208     261 ..     201     280 .. 0.70
   3 ?    5.1   1.6     0.069        23      36     113 ..     277     353 ..     259     370 .. 0.55
   4 ?   10.4   2.1    0.0016      0.54      23     114 ..     383     477 ..     381     497 .. 0.82
   5 ?    6.0   0.8     0.036        12      36      84 ..     431     479 ..     421     523 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.02
                                       CCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC CS
                         Fib_alpha  27 lkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeil 91 
                                        +++ +++++l++le e e++++ ++eaee   +++d  ++ q++             e+e++ +
  gi|336252564|ref|YP_004595671.1| 117 ARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETR-----------AEIERQNE 170
                                       3444555556666666666666666666666666665555544444...........44443333 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.13
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikkss 83 
                                        +++++ l+++ +++ +++ s + +ee+++e++ds +e  + +++    +++++
  gi|336252564|ref|YP_004595671.1| 208 ATSFNEMLDRMSETMVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEIA 261
                                       567778888888888888888888888888888887777777666555555554 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.069
                                       HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHH CS
                         Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvle 112
                                       ++++l    ee++++t e+ + ++++++ ++e  + +++  + i ++ ++ e  +++  ++++++ ++i+++  +++
  gi|336252564|ref|YP_004595671.1| 277 EVSDLSAATEEVASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTE-TVVETADELTRETEQIEEIIALID 352
                                       4555555555555555555555555555555555555544555555555555.444444444455555555444444 PP

                                       H CS
                         Fib_alpha 113 s 113
                                       +
  gi|336252564|ref|YP_004595671.1| 353 D 353
                                       4 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0016
                                       HHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...CCCHHHHH CS
                         Fib_alpha  23 qdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskelee...eilrlket 96 
                                       +d ++   +++ + ++++e +le+i+++t+++ + + e+++ ++++ +  +d ++ ++ ++ e+e+    i+++  t
  gi|336252564|ref|YP_004595671.1| 383 ADEIKALAEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQvdgSIQQIAST 459
                                       677778888999999************************99999999999998776666665544322288999999 PP

                                       HHCCHHHHHHHHHHHHHH CS
                         Fib_alpha  97 idaqesnirvLqnvlesn 114
                                        d+q  + ++L  ++++ 
  gi|336252564|ref|YP_004595671.1| 460 ADDQADSAQELSAIVDDV 477
                                       999999999999998875 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.036
                                       HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikkssk 84 
                                        +++le++le+i+ + ++++  +++i ++  ++  s+++ + ++ +++ 
  gi|336252564|ref|YP_004595671.1| 431 IVDDLESRLETIAGEVEQVDGSIQQIASTADDQADSAQELSAIVDDVAA 479
                                       4555555555555555555555555555554444444443333333322 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 ?   13.9  10.5   0.00014     0.046      41     163 ..     120     235 ..     107     240 .. 0.77
   2 ?    5.3   6.6     0.059        20      18     161 ..     272     457 ..     249     461 .. 0.58
   3 ?    6.4   0.9     0.028       9.4      28     104 ..     412     489 ..     410     525 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00014
                            CENP-Q  41 LspelhslelLeaeiekeeralerdyeaLreLeknakaearerke.klkkehvllqesdseelslleassdevlgea 116
                                        + ++++l++Le e e++++a  + +e   +Le + + ++++r e + ++ + l+ e+     +++++  d   + a
  gi|336252564|ref|YP_004595671.1| 120 RDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEiE-RQNERLVAEA-----ERFSEVMD---ACA 187
                                       56788999999*******99999999999***999999999999955.4445566533.....23333333...223 PP

                            CENP-Q 117 sgtvfsdlepeldee.llpllqqLgshLesmrgnlaqlegllpalers 163
                                       +g  ++ lep+ d+e +++++++ ++ L+ m++++ +++g   a+e++
  gi|336252564|ref|YP_004595671.1| 188 DGDLTQRLEPQVDDEaIAAIATSFNEMLDRMSETMVDVRGSANAVEEI 235
                                       5678888998876662677777******************99999986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.059
                            CENP-Q  18 dggkekeldfeklldekaaleaqLspelhslelLeaeiekeera.lerdyeaLreLeknakaearerkeklkkehvl 93 
                                       d + +++ d+ ++++e a+   + + + +s+ +L +e +++ ++  e+  e  ++ e+ ++++ +  +e+++ e+ +
  gi|336252564|ref|YP_004595671.1| 272 DAAAAEVSDLSAATEEVASTTGEIADQSESVTELTEEGREAAAEaAENIDELVENTETVVETADELTRETEQIEEII 348
                                       56667788888899999999999999999999998886655444044444444444444444444455533333333 PP

                            CENP-Q  94 lqesdseelslleassdevlgea................................................sgtvfs 122
                                       + ++d +++++l a +      a                                                + ++  
  gi|336252564|ref|YP_004595671.1| 349 ALIDDIADQTNLLAVN------AsieaatagadgsgfavvadeikalaeetmdavddiegtlesirdrtetTANEIG 419
                                       3323222222222222......0222234566777777776677777777777777766766777666544222222 PP

                            CENP-Q 123 dlepeldeellpllqqLgshLesmrgnlaqlegllpale 161
                                       + e ++   +++++  L+s Le++ g ++q++g  ++++
  gi|336252564|ref|YP_004595671.1| 420 EVE-SNITSTATIVDDLESRLETIAGEVEQVDGSIQQIA 457
                                       222.23445666666888888888888888887777776 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.028
                            CENP-Q  28 eklldekaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknakaearerke.klkkehvllqesdseels 103
                                       e++ +e+ ++e++ + +   +++Le+ +e    + e+   ++++   +a ++a + +e  +    v + +++++++ 
  gi|336252564|ref|YP_004595671.1| 412 ETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQADSAQElSAIVDDVAAVSNETATKA 488
                                       56667777777888888888888888888888888888888888888888888886664433333444333333332 PP

                            CENP-Q 104 l 104
                                       +
  gi|336252564|ref|YP_004595671.1| 489 Q 489
                                       2 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.9     0.073        25      10      80 ..     125     169 ..      97     187 .. 0.48
   2 ?    9.0   0.6    0.0066       2.2       9      80 ..     212     282 ..     207     284 .. 0.90
   3 ?    6.6   3.8     0.037        13       5      80 ..     271     345 ..     269     359 .. 0.74
   4 ?    0.8   3.5       2.3   7.7e+02      47      70 ..     362     401 ..     313     441 .. 0.47
   5 ?    4.2   0.3       0.2        68      17      74 ..     388     451 ..     380     458 .. 0.45
   6 ?    9.7   0.8    0.0041       1.4       8      93 ..     449     533 ..     445     536 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.073
                           DUF2203  10 alLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdle 80 
                                       ++L  l+   e+++++++e+ee++++le+++++                          ++e+ +e+   +
  gi|336252564|ref|YP_004595671.1| 125 DTLADLETEQERAQQAQREAEERADQLEDEREQ--------------------------LQETRAEIERQN 169
                                       334444444444444444444444444444444..........................333333333333 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0066
                           DUF2203   9 nalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdle 80 
                                       n++L +++e++ ++r  ++ +ee++ ele+++ae ++ + +e + +++e+++ + e ++ +++  +ev dl+
  gi|336252564|ref|YP_004595671.1| 212 NEMLDRMSETMVDVRGSANAVEEISVELEDSSAEIRT-ASREVADSVQEIADGAAEQTDDLDAAAAEVSDLS 282
                                       789999***************************9865.58999999***************99999999885 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.037
                           DUF2203   5 leeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdle 80 
                                       l+ A a +  l+  +ee+++++ e+++ +e+++e ++e ++ +aae++++++el ++ e +ve+ +el  e  ++e
  gi|336252564|ref|YP_004595671.1| 271 LDAAAAEVSDLSAATEEVASTTGEIADQSESVTELTEEGRE-AAAEAAENIDELVENTETVVETADELTRETEQIE 345
                                       67899999999999999999999999999999999988754.4677777777777777777766666655544444 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 2.3
                           DUF2203  47 e................aaeleaeleeleaeieelveeie 70 
                                       +                +a  + e+++l++e  ++v+ ie
  gi|336252564|ref|YP_004595671.1| 362 AvnasieaatagadgsgFAVVADEIKALAEETMDAVDDIE 401
                                       0222222222233333344444444444444444444444 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.2
                           DUF2203  17 elleelralrkeleeleeeleeakaeaekse.......aaeleaeleeleaeieelveeieelGv 74 
                                        l ee +++ +++e + e++++ ++++++ e        ++ ++ ++ le+++e +  e+e++  
  gi|336252564|ref|YP_004595671.1| 388 ALAEETMDAVDDIEGTLESIRDRTETTAN-EigevesnITSTATIVDDLESRLETIAGEVEQVDG 451
                                       44455555555555555544444444332.22333333334444444444444444444444444 PP

  == domain 6  score: 9.7 bits;  conditional E-value: 0.0041
                           DUF2203   8 AnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleaglv 84 
                                           ++++ ++ ++ ++ ++el  +++++++ ++e++ ++a++ +a+ ee +a i+++ ++ ++lG + +dl+ +l 
  gi|336252564|ref|YP_004595671.1| 449 VDGSIQQIASTADDQADSAQELSAIVDDVAAVSNETA-TKAQQVAAASEETSATIDSVSTTATDLGDDARDLKRLLD 524
                                       5556778888888888999999999999999998865.4599999999************************98888 PP

                           DUF2203  85 DFpakldge 93 
                                        F  +  g+
  gi|336252564|ref|YP_004595671.1| 525 AFTLEEGGR 533
                                       887766665 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.3    0.0084       2.8      15      66 ..     116     167 ..     102     187 .. 0.78
   2 ?    1.8   0.1      0.61   2.1e+02      16      64 ..     212     260 ..     201     265 .. 0.59
   3 ?    6.0   0.2      0.03        10      16      63 ..     268     315 ..     251     321 .. 0.73
   4 ?    8.3   2.3    0.0059         2       9      72 ..     289     352 ..     281     368 .. 0.82
   5 ?    5.1   0.5     0.055        19       9      53 ..     422     466 ..     382     480 .. 0.50
   6 ?    3.0   0.6      0.26        87      18      63 ..     462     504 ..     445     529 .. 0.44

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0084
                             Sec34  15 lleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                       + +  d+++++L++le++ ++ ++  ++ +e+++ql +e+++l+e+  eie 
  gi|336252564|ref|YP_004595671.1| 116 VARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIER 167
                                       5555577788888888888888888888889999999999999998888875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.61
                             Sec34  16 leqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeei 64 
                                        e +d++ e++ +++ + ++v+e + +l++++ ++ +  +++ + ++ei
  gi|336252564|ref|YP_004595671.1| 212 NEMLDRMSETMVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEI 260
                                       3344455555555566666666666666666666666666666666665 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.03
                             Sec34  16 leqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaee 63 
                                        +++d+a  ++++l+   ++v++ t ++ +++e+++e +++ +e a e
  gi|336252564|ref|YP_004595671.1| 268 TDDLDAAAAEVSDLSAATEEVASTTGEIADQSESVTELTEEGREAAAE 315
                                       567788888888999999999999999999988888877776666655 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0059
                             Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFe 72 
                                        +++ e+ +q +++ e+ ee +e   + +e+  +l e++e+++e  ++l++ +e+iee +   +
  gi|336252564|ref|YP_004595671.1| 289 ASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTETVVETADELTRETEQIEEIIALID 352
                                       5677889999999999999999999999999999999999999999999999999999876655 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.055
                             Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqllee 53 
                                       e+++++  + +d++++ Le++  ++++v+ + +++ +++++  ++
  gi|336252564|ref|YP_004595671.1| 422 ESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQADS 466
                                       223333333344444444444444444444444444444444444 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.26
                             Sec34  18 qtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaee 63 
                                       +  +  ++L+ + +++ +vs++t    ++++q+ +  ++ + + ++
  gi|336252564|ref|YP_004595671.1| 462 DQADSAQELSAIVDDVAAVSNETA---TKAQQVAAASEETSATIDS 504
                                       333333333333333333333333...3333333333333333332 PP

>> Rota_NSP4  Rotavirus non structural protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2     0.012       4.1      86     121 ..     155     191 ..     148     211 .. 0.82
   2 ?    4.4   0.3     0.079        27      94     138 ..     315     358 ..     304     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.012
                         Rota_NSP4  86 keqi.ttkdeiekqmdrvvkemrrqlemidklttrei 121
                                       +eq+  t+ eie+q +r+v e  r  e++d  +  ++
  gi|336252564|ref|YP_004595671.1| 155 REQLqETRAEIERQNERLVAEAERFSEVMDACADGDL 191
                                       67762599********************998765554 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.079
                         Rota_NSP4  94 eiekqmdrvvkemrrqlemidklttreieqvellkriydkltvqt 138
                                       e   ++d +v +    +e  d l tre eq+e +  + d ++ qt
  gi|336252564|ref|YP_004595671.1| 315 EAAENIDELVENTETVVETADEL-TRETEQIEEIIALIDDIADQT 358
                                       666789999*99*********99.59******9999999988887 PP

>> DCB  Dimerisation and cyclophilin-binding domain of Mon2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.5         1   3.5e+02       5      57 ..     118     169 ..     115     194 .. 0.63
   2 ?   -1.2   0.4         4   1.4e+03      25      56 ..     243     274 ..     228     349 .. 0.59
   3 ?   -2.4   0.0       9.4   3.2e+03      13      60 ..     385     431 ..     379     456 .. 0.58
   4 ?   11.6   0.1   0.00048      0.16       6      49 ..     469     512 ..     464     528 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1
                               DCB   5 kllealqsdlkalsseskrkhskvkeasekgilkLktikssseeeeqslaeas 57 
                                       +++++l+  l  l +e +r ++  +ea e+   +L+  +++ +e++ ++ ++ 
  gi|336252564|ref|YP_004595671.1| 118 RMRDSLEDTLADLETEQERAQQAQREA-EERADQLEDEREQLQETRAEIERQN 169
                                       678889999999999988776666654.4555666666666544444444443 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4
                               DCB  25 hskvkeasekgilkLktikssseeeeqslaea 56 
                                       +++++ as ++   +++i++   e++ +l +a
  gi|336252564|ref|YP_004595671.1| 243 SAEIRTASREVADSVQEIADGAAEQTDDLDAA 274
                                       55555555555555555555443333333332 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 9.4
                               DCB  13 dlkalsseskrkhskvkeasekgilkLktikssseeeeqslaeaseei 60 
                                       ++kal++e+     +++ + e++  + +t +++  e+e+++ ++   i
  gi|336252564|ref|YP_004595671.1| 385 EIKALAEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITST-ATI 431
                                       55566666665555555555555555555555554445555444.444 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00048
                               DCB   6 llealqsdlkalsseskrkhskvkeasekgilkLktikssseee 49 
                                        l+a++ d  a+s+e+  k ++v++ase+ + ++ +++++ ++ 
  gi|336252564|ref|YP_004595671.1| 469 ELSAIVDDVAAVSNETATKAQQVAAASEETSATIDSVSTTATDL 512
                                       5778999******************************9998443 PP

>> Hormone_1  Somatotropin hormone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3    0.0068       2.3      89     152 ..     107     173 ..      99     189 .. 0.82
   2 ?    0.9   0.1      0.92   3.1e+02      99     149 ..     212     262 ..     177     291 .. 0.72
   3 ?   -1.3   0.0       4.4   1.5e+03     109     144 ..     271     306 ..     266     323 .. 0.85
   4 ?    1.1   0.4      0.83   2.8e+02     110     145 ..     314     349 ..     281     360 .. 0.73
   5 ?   -1.5   0.0       5.3   1.8e+03     123     157 ..     383     417 ..     380     429 .. 0.76
   6 ?    5.6   0.1     0.036        12      95     161 ..     425     491 ..     406     509 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0068
                                       ---HHHHHHHHHHHHTTTTGGGGGG....GGGSSS------TTTGGGHHHHHHHH...HHHHHHHH- CS
                         Hormone_1  89 tsneeLlklslllleswkePLkhlvtelssmkevsetilskakeieeklkeLleg...ierilskve 152
                                        ++ eL  +++ + +s +  L +l te +  +++  +  ++a ++e++ ++L+e    ier+ +++ 
  gi|336252564|ref|YP_004595671.1| 107 DEIGELYGSVARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETraeIERQNERLV 173
                                       567799999*******************************************986222555555544 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.92
                                       HHHHHTTTTGGGGGG....GGGSSS------TTTGGGHHHHHHHHHHHHHH CS
                         Hormone_1  99 lllleswkePLkhlvtelssmkevsetilskakeieeklkeLlegierils 149
                                         +l+ + e + +++   ++++e s ++  +  ei   ++e+ + +++i+ 
  gi|336252564|ref|YP_004595671.1| 212 NEMLDRMSETMVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEIAD 262
                                       456666666666666677777777777777777777777777777777765 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.4
                                       GGGGG....GGGSSS------TTTGGGHHHHHHHHH CS
                         Hormone_1 109 LkhlvtelssmkevsetilskakeieeklkeLlegi 144
                                       L+  ++e+s++ +++e++ s   ei ++++ + e  
  gi|336252564|ref|YP_004595671.1| 271 LDAAAAEVSDLSAATEEVASTTGEIADQSESVTELT 306
                                       677889999999999999999999999999988765 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.83
                                       GGGG....GGGSSS------TTTGGGHHHHHHHHHH CS
                         Hormone_1 110 khlvtelssmkevsetilskakeieeklkeLlegie 145
                                        + ++++ ++ e++et+ + a e+ +++++++e i 
  gi|336252564|ref|YP_004595671.1| 314 AEAAENIDELVENTETVVETADELTRETEQIEEIIA 349
                                       455666777888888888888888888888888775 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 5.3
                                       S------TTTGGGHHHHHHHHHHHHHHHH------ CS
                         Hormone_1 123 setilskakeieeklkeLlegierilskvevpver 157
                                        ++i + a+e ++   +++  +e+i  ++e+++++
  gi|336252564|ref|YP_004595671.1| 383 ADEIKALAEETMDAVDDIEGTLESIRDRTETTANE 417
                                       57788889999999999999999999999876554 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.036
                                       HHHHHHHHHTTTTGGGGGG....GGGSSS------TTTGGGHHHHHHHHHHHHHHHH---------- CS
                         Hormone_1  95 lklslllleswkePLkhlvtelssmkevsetilskakeieeklkeLlegierilskvevpverkeke 161
                                       + +++ +++  ++ L+ ++ e++++ ++ ++i s a +  ++ +eL + +  ++   ++++++ ++ 
  gi|336252564|ref|YP_004595671.1| 425 ITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQADSAQELSAIVDDVAAVSNETATKAQQV 491
                                       56778888999999*********************************99999888777655554443 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9  23.4      0.07        24     110     336 ..     109     348 ..     100     366 .. 0.80
   2 ?   10.1   1.2   0.00046      0.16     338     420 ..     389     471 ..     384     487 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.07
                                       HHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH------------. CS
                              EzrA 110 ldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleniekefsefeelte. 185
                                       + e+  +++++++ l++ +   e ++e+ ++++ + +e  ++l+++r++++e+ +e+e q e +  e + f+e+++ 
  gi|336252564|ref|YP_004595671.1| 109 IGELYGSVARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAERFSEVMDa 185
                                       5566678889999999999999999999******************************9988887777777666652 PP

                                       ..----HH..........HHHHHHHHHHHHHHHHHHHHHHH...HHHTTTTTTSHHHHHHHHHHHHHSTTS--SGGG CS
                              EzrA 186 ..ngdyve..........akeilkkleeeideleevieeiP...elleelkkelpkqleelkegykemkeegYalee 247
                                         +gd ++           + i  + +e++d+++e + ++    + +ee++ el +  +e+++  +e  ++  ++ +
  gi|336252564|ref|YP_004595671.1| 186 caDGDLTQrlepqvddeaIAAIATSFNEMLDRMSETMVDVRgsaNAVEEISVELEDSSAEIRTASREVADSVQEIAD 262
                                       22677654222222222267788889999999999999998333467888889999999999999999888888877 PP

                                       SSSSSHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHT CS
                              EzrA 248 lniekeieelekkieeilerlkeleledveeelktieeeidsLyddlekEveAkkeveknlkelkeklehlekqnke 324
                                           ++ ++l+++ +e+ ++ +    e+v++   +i+++ +s+ ++ e+  eA  e  +n++el e+ e + +  +e
  gi|336252564|ref|YP_004595671.1| 263 -GAAEQTDDLDAAAAEVSDLSA--ATEEVASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTETVVETADE 336
                                       .455666777777777666644..568999999******************************************** PP

                                       TGGG-TTTS-GG CS
                              EzrA 325 lkeeldrlkqsY 336
                                       l++e++++++  
  gi|336252564|ref|YP_004595671.1| 337 LTRETEQIEEII 348
                                       *******98765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00046
                                       SSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 338 LseeeleklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAre 414
                                       L+ee ++ ++++e  l++++++ e+  +++ e +   ++ +  +++le++le+i  ++e+++ s++++ +   +  +
  gi|336252564|ref|YP_004595671.1| 389 LAEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQAD 465
                                       8899999999999999*******999999999999999999999999999999999999999999988766555555 PP

                                       HHHHHH CS
                              EzrA 415 qldeik 420
                                       +++e++
  gi|336252564|ref|YP_004595671.1| 466 SAQELS 471
                                       555554 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  11.5    0.0012      0.41      84     139 ..     120     175 ..     114     185 .. 0.76
   2 ?    4.3   9.1     0.074        25      26     143 ..     251     365 ..     214     374 .. 0.88
   3 ?    8.2   6.7    0.0048       1.6      33     147 ..     384     499 ..     381     512 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                        MscS_porin  84 eqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnst 139
                                          l++t+++l+++qe+ +q++ ++ e  +++e  ++ql e r +++  + rL + 
  gi|336252564|ref|YP_004595671.1| 120 RDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAE 175
                                       56788888888888888888888888888888888888888888888888887433 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.074
                        MscS_porin  26 lnlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqla 102
                                        ++ d  ++ ++ a+e  + +d a +e+ +l++ +e+    ++++ +  +++ s +eL  +  ++ ++ +e+  +l 
  gi|336252564|ref|YP_004595671.1| 251 REVADSVQEIADGAAEQTDDLDAAAAEVSDLSAATEEV---ASTTGEIADQSESVTELTEEGREAAAEAAENIDELV 324
                                       56667778888889999999999999999999999999...77777777888999********************** PP

                        MscS_porin 103 qlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaag 143
                                       +  + +ve+ + ++r  +q+ e    +++i ++ n +a + 
  gi|336252564|ref|YP_004595671.1| 325 ENTETVVETADELTRETEQIEEIIALIDDIADQTNLLAVNA 365
                                       ******************************98887775554 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0048
                        MscS_porin  33 dkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilakls.leeLeqrllqtssqlqelqeqlaqlnsql 108
                                       d+ k+ aee  +a+dd   +l++++ ++e+ +++  e   +i ++ +  ++Le+rl++   +++++   ++q+ s +
  gi|336252564|ref|YP_004595671.1| 384 DEIKALAEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATiVDDLESRLETIAGEVEQVDGSIQQIASTA 460
                                       56666777777889999999999999999996666666666655555158899999999999999999999999999 PP

                        MscS_porin 109 velqtrperaqqqltearqrlqeirnrLnstaaageals 147
                                         + ++ +++ +   +     +e  ++ ++ aaa+e+ s
  gi|336252564|ref|YP_004595671.1| 461 DDQADSAQELSAIVDDVAAVSNETATKAQQVAAASEETS 499
                                       999999999999999988888888888877777666544 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.7       2.9   9.7e+02      10      61 ..     111     163 ..     103     185 .. 0.55
   2 ?    4.5   0.0      0.13        46      18      62 ..     222     266 ..     204     287 .. 0.82
   3 ?    4.8   0.4      0.11        37      28      64 ..     306     342 ..     275     368 .. 0.65
   4 ?    0.2   0.1       2.9     1e+03      45      54 ..     396     405 ..     341     434 .. 0.51
   5 ?   10.6   0.4    0.0016      0.55       2      65 ..     436     500 ..     435     524 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.9
                        Syntaxin_2  10 snvstleklvkqLgtk.kdteelreklhelieeinelikktnellkklsqldn 61 
                                       ++  +  +++++L++   d e  +e++++ + e+ e + + ++  ++l++   
  gi|336252564|ref|YP_004595671.1| 111 ELYGSVARMRDSLEDTlADLETEQERAQQAQREAEERADQLEDEREQLQETRA 163
                                       55555556666665553455555566666666666666665555555555443 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.13
                        Syntaxin_2  18 lvkqLgtkkdteelreklhelieeinelikktnellkklsqldns 62 
                                       +v+  g+++  ee+  +l+++  ei++ ++++ +++++++  +  
  gi|336252564|ref|YP_004595671.1| 222 MVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEIADGAAE 266
                                       45556888999**************************99876555 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.11
                        Syntaxin_2  28 teelreklhelieeinelikktnellkklsqldnsss 64 
                                       tee re + e  e+i el+++t+  ++  ++l++ ++
  gi|336252564|ref|YP_004595671.1| 306 TEEGREAAAEAAENIDELVENTETVVETADELTRETE 342
                                       5555555555556666666666555555555555443 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 2.9
                        Syntaxin_2  45 likktnellk 54 
                                        + +++  l+
  gi|336252564|ref|YP_004595671.1| 396 AVDDIEGTLE 405
                                       3333333222 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.0016
                        Syntaxin_2   2 ssnlqkinsnvstleklvkqLgtk.kdteelreklhelieeinelikktnellkklsqldnsssd 65 
                                       +s l +i++ v + +  ++q+ +   d+ +  ++l  +++++  ++++t  + +++++ ++ +s 
  gi|336252564|ref|YP_004595671.1| 436 ESRLETIAGEVEQVDGSIQQIASTaDDQADSAQELSAIVDDVAAVSNETATKAQQVAAASEETSA 500
                                       78999***************8777268999**************************999988765 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.5   0.00056      0.19       1      52 [.     130     181 ..     130     235 .. 0.76
   2 ?    5.7   5.5     0.051        17       3     104 ..     244     348 ..     242     363 .. 0.80
   3 ?    6.5   0.5     0.029       9.9      76     122 ..     390     436 ..     381     443 .. 0.81
   4 ?    0.2   0.3       2.5   8.5e+02      28     104 ..     438     516 ..     437     526 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00056
                           DUF5082   1 lktkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklek 52 
                                       l t+ +++q+++ e+++++++le+  e L+e++ +++ ++e+l ++ +  ++
  gi|336252564|ref|YP_004595671.1| 130 LETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAERFSE 181
                                       57899*************************************9887766544 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.051
                           DUF5082   3 tkisklqaqiaelrseia.aleekIerLkeaktklsdekeslkqkkkklekplnsse...sWkGkeennydgirsnl 75 
                                       ++i+++ +++a+  +eia +  e+   L +a  ++sd ++++++  +   +++ +se   +++ + ++   ++++n+
  gi|336252564|ref|YP_004595671.1| 244 AEIRTASREVADSVQEIAdGAAEQTDDLDAAAAEVSDLSAATEEVASTTGEIADQSEsvtELTEEGREAAAEAAENI 320
                                       68999999999999998636899999***999999998888888877777777666655588888888888888899 PP

                           DUF5082  76 essyqtyvdkldelidaieeEIerLenqi 104
                                       ++ +++ ++ ++++ d++ +E+e++e+ i
  gi|336252564|ref|YP_004595671.1| 321 DELVENTETVVETA-DELTRETEQIEEII 348
                                       99999988877764.89999999998755 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.029
                           DUF5082  76 essyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                        +++   vd+++ +  +i + +e+ +n+i e ++++ ++ + +++l+
  gi|336252564|ref|YP_004595671.1| 390 AEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIVDDLE 436
                                       55566678889999999999999999999999999999988888885 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 2.5
                           DUF5082  28 rLkeaktklsdekeslkqkkkklekplnssesWkGk..eennydgirsnlessyqtyvdkldelidaieeEIerLen 102
                                       rL++   ++++++ s++q  +   +++ s +++       + ++++ +   +++ +  +++ ++id++++  ++L  
  gi|336252564|ref|YP_004595671.1| 438 RLETIAGEVEQVDGSIQQIASTADDQADSAQELSAIvdDVAAVSNETATKAQQVAAASEETSATIDSVSTTATDLGD 514
                                       66777777777777777777777777777776666632223455555566666667777777777777666666655 PP

                           DUF5082 103 qi 104
                                       + 
  gi|336252564|ref|YP_004595671.1| 515 DA 516
                                       55 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   8.7   6.3e-05     0.021      54     123 ..     104     173 ..      97     179 .. 0.84
   2 ?    1.9  14.8      0.66   2.2e+02      10     116 ..     236     338 ..     224     362 .. 0.66
   3 ?    1.9   0.1      0.65   2.2e+02      72     114 ..     385     427 ..     379     442 .. 0.52
   4 ?    5.2   4.7     0.063        21       2     110 ..     417     521 ..     416     527 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.3e-05
                        TPR_MLP1_2  54 edvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlneqNklLh 123
                                       + v+e+ +l   ++++++ +++  a++e+ ++  ++++ + ee+ ++le+e ++l++ + +++ qN+ L 
  gi|336252564|ref|YP_004595671.1| 104 DRVDEIGELYGSVARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLV 173
                                       5566777777778888889999999999999999999999999999999999999999999999999886 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.66
                        TPR_MLP1_2  10 ikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakae 86 
                                         +l+++++e +++ +++ + +++ a+ a+e  +     l   a++v +l+a+ ee+++++ eia+  +++ ++++e
  gi|336252564|ref|YP_004595671.1| 236 SVELEDSSAEIRTASREVADSVQEIADGAAEQTD----DLDAAAAEVSDLSAATEEVASTTGEIADQSESVTELTEE 308
                                       4455555556666666666666666666666555....677777777777777777777777777777777777777 PP

                        TPR_MLP1_2  87 leeseesweeqkeelekelselekriedln 116
                                         e+ ++ +e  +el ++ + + +  ++l+
  gi|336252564|ref|YP_004595671.1| 309 GREAAAEAAENIDELVENTETVVETADELT 338
                                       777777777777777777777666666665 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.65
                        TPR_MLP1_2  72 eiaelkaeaesakaeleeseesweeqkeelekelselekried 114
                                       ei+ l +e  +a  ++e   es+  + e+  +e+ e+e+ i+ 
  gi|336252564|ref|YP_004595671.1| 385 EIKALAEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITS 427
                                       4555555555555555555555555555555555555555443 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.063
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       e+ ++e++i+s  +  +++e++l+++  ++e+   + ++           +a+ ++el+a+ ++++ + +e a+  +
  gi|336252564|ref|YP_004595671.1| 417 EIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIAS----TADDQADSAQELSAIVDDVAAVSNETATKAQ 489
                                       677888888888888888888888888888888777776666....6666778888888888888777777777777 PP

                        TPR_MLP1_2  79 eaesakaeleeseesweeqkeelekelselek 110
                                       ++ +a++e ++   s +++ + l ++ ++l++
  gi|336252564|ref|YP_004595671.1| 490 QVAAASEETSATIDSVSTTATDLGDDARDLKR 521
                                       77777777777777777777777776666665 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       3.3   1.1e+03      14      41 ..     114     141 ..     105     144 .. 0.76
   2 ?    2.5   0.1      0.37   1.3e+02       1      33 [.     150     182 ..     150     189 .. 0.79
   3 ?    0.1   0.1       2.1     7e+02      11      35 ..     210     234 ..     204     254 .. 0.80
   4 ?    2.0   0.5      0.54   1.8e+02      25      61 ..     312     348 ..     297     349 .. 0.78
   5 ?    2.5   0.2      0.36   1.2e+02       2      21 ..     337     356 ..     336     369 .. 0.89
   6 ?    8.2   0.2    0.0062       2.1       5      45 ..     393     433 ..     388     437 .. 0.92
   7 ?    1.3   0.0      0.89     3e+02       9      31 ..     439     461 ..     432     489 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.3
                         DASH_Duo1  14 evienviesLkkaksniervketvestn 41 
                                         +  +++sL+++  ++e+ +e+ ++++
  gi|336252564|ref|YP_004595671.1| 114 GSVARMRDSLEDTLADLETEQERAQQAQ 141
                                       5677788888888888888888877765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.37
                         DASH_Duo1   1 aLekEleqLrkinevienviesLkkaksnierv 33 
                                       +Le E eqL++ ++ ie  +e L +  +  ++v
  gi|336252564|ref|YP_004595671.1| 150 QLEDEREQLQETRAEIERQNERLVAEAERFSEV 182
                                       6999*************9999987666555555 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2.1
                         DASH_Duo1  11 kinevienviesLkkaksniervke 35 
                                       ++ne+++ + e++ ++++  + v+e
  gi|336252564|ref|YP_004595671.1| 210 SFNEMLDRMSETMVDVRGSANAVEE 234
                                       6788888888888888777777665 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.54
                         DASH_Duo1  25 kaksniervketvestntLLdkWirIlsqtehtqrll 61 
                                       +a +  e++ e ve+t+t +++  ++   te++ +++
  gi|336252564|ref|YP_004595671.1| 312 AAAEAAENIDELVENTETVVETADELTRETEQIEEII 348
                                       3448889999999999999999888888888888877 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.36
                         DASH_Duo1   2 LekEleqLrkinevienvie 21 
                                       L +E eq+++i++ i+++ +
  gi|336252564|ref|YP_004595671.1| 337 LTRETEQIEEIIALIDDIAD 356
                                       99*************99865 PP

  == domain 6  score: 8.2 bits;  conditional E-value: 0.0062
                         DASH_Duo1   5 EleqLrkinevienviesLkkaksniervketvestntLLd 45 
                                        ++ +++i  ++e++++  +++ ++i +v+++++st t++d
  gi|336252564|ref|YP_004595671.1| 393 TMDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIVD 433
                                       47899*********************************998 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.89
                         DASH_Duo1   9 LrkinevienviesLkkaksnie 31 
                                       L++i   +e+v++s++++ s  +
  gi|336252564|ref|YP_004595671.1| 439 LETIAGEVEQVDGSIQQIASTAD 461
                                       45555555555555555555444 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2  23.4      0.16        54     284     466 ..     105     298 ..      97     354 .. 0.56
   2 ?    1.3  14.6       0.3     1e+02     283     455 ..     325     500 ..     310     514 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.16
                            AAA_13 284 kqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksve.les 359
                                        ++++ +l  +v++++++l + l+++ +e+++ ++++++ ee  +++e  +eqL++ + ++e+  +++++++e  ++
  gi|336252564|ref|YP_004595671.1| 105 RVDEIGELYGSVARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAErFSE 181
                                       46667777777888888888888777777666666667777777777777777888888888888888886663233 PP

                            AAA_13 360 vkakie...............sikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkyk 419
                                       v +                  +       i ++ +++Ne+ +++ e   +++ +  + +    ele+   e  ++ +
  gi|336252564|ref|YP_004595671.1| 182 VMDACAdgdltqrlepqvddeA-------IAAIATSFNEMLDRMSETMVDVRGSANAVEeiSVELEDSSAEIRTASR 251
                                       3333323556665544444441.......333344444444444444333332222211002223333334445555 PP

                            AAA_13 420 klekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinke 466
                                       ++++++++  + ++e++++l ++++e+++L + ++++  +  ei+++
  gi|336252564|ref|YP_004595671.1| 252 EVADSVQEIADGAAEQTDDLDAAAAEVSDLSAATEEVASTTGEIADQ 298
                                       55555555555556666666666666666666665555555555443 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.3
                            AAA_13 283 ekqerLekliekveskkselleklkavsdeasensafeedkeelka........eaealeeqLkglqraleaKrkep 351
                                       e++e+  ++++++ ++++++ e + a++d+   + +    ++ ++a         + ++++++k+l ++  + ++++
  gi|336252564|ref|YP_004595671.1| 325 ENTETVVETADELTRETEQIEEII-ALIDDIADQTNLLAVNASIEAatagadgsGFAVVADEIKALAEETMDAVDDI 400
                                       234555555555544444332222.2222211112222222222220001111122333333333333333333333 PP

                            AAA_13 352 fksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaiekl 428
                                           +les+ +++e   +++ e++ +i++   +v++le++ e+++ ++e+  v    +++    ++ ++ +++++  
  gi|336252564|ref|YP_004595671.1| 401 EG--TLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQ--VDGSIQQIASTADDQADSAQELSAI 473
                                       33..4788888888888888888888888888888888888888888888..3333566666667777777777777 PP

                            AAA_13 429 ekelkeeeaelkkleeeikeLekqlrd 455
                                        +++++ ++e++++++++++  ++++ 
  gi|336252564|ref|YP_004595671.1| 474 VDDVAAVSNETATKAQQVAAASEETSA 500
                                       777777777777777777776666654 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.9    0.0029      0.97      50      91 .]     126     167 ..     108     169 .. 0.84
   2 ?   10.8   0.1    0.0016      0.56      24      90 ..     213     279 ..     208     280 .. 0.93
   3 ?   -0.1   1.8       4.1   1.4e+03      39      88 ..     294     343 ..     279     371 .. 0.52
   4 ?    1.3   0.5       1.5   5.2e+02      30      85 ..     415     470 ..     391     490 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC CS
                              BST2  50 LkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaever 91 
                                         a+Le e+ ++q++q++++e  +++++  ++Lq+++ae+er
  gi|336252564|ref|YP_004595671.1| 126 TLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIER 167
                                       457889999999999999999999999999999999999886 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                              BST2  24 rqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90 
                                       + L +  e++ +    a++ ++++v+L++s  + ++ s++    vqe+ +  +++++ L+ a aev 
  gi|336252564|ref|YP_004595671.1| 213 EMLDRMSETMVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEIADGAAEQTDDLDAAAAEVS 279
                                       568899999999999************************************************9985 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  39 qaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeae 88 
                                       ++a  ++ v +L++   +  a++ ++  ++ e  + + + +++L    ++
  gi|336252564|ref|YP_004595671.1| 294 EIADQSESVTELTEEGREAAAEAAENIDELVENTETVVETADELTRETEQ 343
                                       55555555555555555444444444333333333333333333333333 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  30 qeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqda 85 
                                        +++ e e ++++   +v +L++ Le    + ++    +q++     +++++ q+ 
  gi|336252564|ref|YP_004595671.1| 415 ANEIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQADSAQEL 470
                                       45566667777777777777777777666555555555555555555555444444 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.7   0.00052      0.17      38     105 ..     112     179 ..     100     181 .. 0.90
   2 ?    2.6   0.3     0.093        31      38     102 ..     242     306 ..     230     308 .. 0.84
   3 ?    2.4   5.6      0.11        37     408     551 ..     314     469 ..     310     490 .. 0.74
   4 ?    1.9   0.5      0.15        51      40     105 ..     464     526 ..     452     531 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00052
                              COG6  38 efqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqkllkaflkkF 105
                                        ++ va+  +++e+++++l++  ++ +++ ++a+e+ ++l +e e+L+e+++++e +++ l a  ++F
  gi|336252564|ref|YP_004595671.1| 112 LYGSVARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAERF 179
                                       5778889999************************************************9998877777 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.093
                              COG6  38 efqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqkllkafl 102
                                       ++ +++++ +++ ++v+++++   e ++ l++a +e sdl   +ee  ++  ++  + + +++++
  gi|336252564|ref|YP_004595671.1| 242 SSAEIRTASREVADSVQEIADGAAEQTDDLDAAAAEVSDLSAATEEVASTTGEIADQSESVTELT 306
                                       56778888889999999999999999999999999999999999999999999999888888765 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.11
                              COG6 408 sealskllelletyesslaseaser...ekdfeevlsalldpllqacersakkle.kkdk........aifliNcld 472
                                        ea +++ el+e+ e+ +++ a+e     +++ee+++ l+d + ++++ +a + + + +         a+++  +  
  gi|336252564|ref|YP_004595671.1| 314 AEAAENIDELVENTETVVET-ADELtreTEQIEEIIA-LIDDIADQTNLLAVNASiEAATagadgsgfAVVADEIKA 388
                                       67889999999999998888.4443455788888888.9****9999999966664333368999999999999999 PP

                              COG6 473 liqstLspysfaskkveelqaqieelvdtLveeqaselleksgLsdllnllnmiqpee.....destyeplsenplm 544
                                       l+++t+  ++ ++  +e+++++ e++ +++ e + +   + + ++dl + l++i  e      +    +++++ ++ 
  gi|336252564|ref|YP_004595671.1| 389 LAEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVeqvdgSI---QQIASTADD 462
                                       99999999999999999999999999999999999999999999999999999986546543322...333333333 PP

                              COG6 545 epeslke 551
                                       +++s +e
  gi|336252564|ref|YP_004595671.1| 463 QADSAQE 469
                                       3333333 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.15
                              COG6  40 qpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqkllkaflkkF 105
                                          a++L++i +dv++ ++   + ++++ +a+eets  ++++++  +++       + lk++l+ F
  gi|336252564|ref|YP_004595671.1| 464 ADSAQELSAIVDDVAAVSNETATKAQQVAAASEETSATIDSVSTTATDL---GDDARDLKRLLDAF 526
                                       5557788899999999999999999999999999888888776655443...33333344444444 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6  21.3   0.00013     0.044       4      68 ..     117     181 ..     115     188 .. 0.95
   2 ?    0.0  16.1       1.8   6.2e+02      23     198 ..     217     341 ..     190     370 .. 0.45
   3 ?    5.8   3.3      0.03        10      32     138 ..     394     500 ..     382     529 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00013
                               ERM   4 erekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlke 68 
                                        r ++ le+ L  l+ e e+aq+a re+ee+a++L+ ++++++e + + e++++++ +e +r+ e
  gi|336252564|ref|YP_004595671.1| 117 ARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAERFSE 181
                                       58899********************************************************9976 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.8
                               ERM  23 kaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeese 99 
                                       ++ e + +    a+  +e + ++e  + +     +e+    q+++  a+++    ++ ++++ + ++ ++++++   
  gi|336252564|ref|YP_004595671.1| 217 RMSETMVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEIADGAAEQTDDLDAAAAEVSDLSAATEEVASTTG 293
                                       33333333333333333333333334444444444444444444444444444444444444433333333333333 PP

                               ERM 100 rkeeeaerLkeeleeareaeeeakekllealstpskseseenveeseteeeeenseeesaeletdeveklsleieee 176
                                       + + + e   e  ee rea  ea+e++ e+++++                                           
  gi|336252564|ref|YP_004595671.1| 294 EIADQSESVTELTEEGREAAAEAAENIDELVENT------------------------------------------- 327
                                       3333333333333333333333333333333333........................................... PP

                               ERM 177 RvtylekskrlqeqLkeLksel 198
                                               + + e  +eL++e 
  gi|336252564|ref|YP_004595671.1| 328 --------ETVVETADELTRET 341
                                       ........22222222222222 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.03
                               ERM  32 eetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerL 108
                                        + ++  +  ++  +   e  +++  e+e  i+  +    + e+  e ++ ++++++  ++++++  + ++  a++L
  gi|336252564|ref|YP_004595671.1| 394 MDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQADSAQEL 470
                                       34455555556666666666666666677777777777777778888888888888888888888888888888888 PP

                               ERM 109 keeleeareaeeeakekllealstpskses 138
                                        + +  + +  +e+++k ++++++++++++
  gi|336252564|ref|YP_004595671.1| 471 SAIVDDVAAVSNETATKAQQVAAASEETSA 500
                                       888888888888888887777777754422 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  11.4      0.04        13      31     103 ..     114     186 ..     103     203 .. 0.79
   2 ?    2.8   9.4       0.4   1.4e+02      29     152 ..     217     345 ..     202     359 .. 0.42
   3 ?   10.6   1.1    0.0016      0.55      37     126 ..     387     492 ..     382     534 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.04
                              Fez1  31 seivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreel 103
                                       + +  ++ +l ++ a+le+++e++++++ ++ee++++le   ++lq++++e e  +e++ +  e ++e+ ++ 
  gi|336252564|ref|YP_004595671.1| 114 GSVARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAERFSEVMDAC 186
                                       5667789999999999999999999999999999999999999999999999988887776666666665555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.4
                              Fez1  29 klse.ivalkaqlrelrakleekeeeikeleesleektlelevcenelqrk...kseaellrekvekleeelkelre 101
                                       ++se +v ++++   +++   e e++  e++++++e +++++++ +  +++    + a      ++++ ee++++  
  gi|336252564|ref|YP_004595671.1| 217 RMSEtMVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEIADGAAEQtddLDAAAAEVSDLSAATEEVASTTG 293
                                       44443455555544444333333333333333333333333333333333311122222222333344444444444 PP

                              Fez1 102 elselsleeeeaalesdeakaqrqe.aeeleelkreverlraeLkeerqkke 152
                                       e++++s++ +e ++e +ea a+ +e  +el e +++v +   eL+ e ++ e
  gi|336252564|ref|YP_004595671.1| 294 EIADQSESVTELTEEGREAAAEAAEnIDELVENTETVVETADELTRETEQIE 345
                                       4444444444444444443333332222222333333333334444444444 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0016
                              Fez1  37 kaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeea 113
                                       ka   e+  ++++ e +++++++++e+ ++e+ ++e+++  + + ++ l+ ++e++  e++++  ++++ +++++++
  gi|336252564|ref|YP_004595671.1| 387 KALAEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQ 463
                                       66667777778888888888888888888888888888888888888888878877777777777666665554444 PP

                              Fez1 114 a................lesdeakaqrqe 126
                                       a                ++ +++kaq+ +
  gi|336252564|ref|YP_004595671.1| 464 AdsaqelsaivddvaavSNETATKAQQVA 492
                                       44455555555555544222222332222 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7  16.1      0.27        92     136     253 ..      24     290 ..       6     529 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.27
                             LMBR1 136 ivlglliyvliil.........qklsllsiksllpilislantwGlvllilllGyGlvelPrslwr........... 192
                                       +v+g++++ ++++         ++ +   i  l ++++  +  +Gl+ ++l + + l +                  
  gi|336252564|ref|YP_004595671.1|  24 CVIGVTLLFAVVFgqhvvsgsaEETEARAIAGLSGLVVVFVMNLGLLGIVLGGNVSL-A------Lrrlgngterig 93 
                                       333333333333333333333322222222234444444444444333332222222.2......133444777788 PP

                             LMBR1 193 ..................................eiksdldeelkklyfeaaklntekeeaereledllkevkklrk 235
                                                                          + ++ +e+ ++++ ea++  +++e+  ++l+++  e++++++
  gi|336252564|ref|YP_004595671.1|  94 dgefdvdletdrvdeigelygsvarmrdsledtlADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNE 170
                                       88888877777777777777777766666666664455556677788888888888888888999999999999999 PP

                             LMBR1 236 sisesdp.lrkyleeilk........................................................... 252
                                       ++  +++ ++++++ + +                                                           
  gi|336252564|ref|YP_004595671.1| 171 RLVAEAErFSEVMDACADgdltqrlepqvddeaiaaiatsfnemldrmsetmvdvrgsanaveeisveledssaeir 247
                                       99999987889999999999999999988888888777666666666665666666666555555555555555555 PP

                             LMBR1 253 ..........................................k 253
                                                                                 +
  gi|336252564|ref|YP_004595671.1| 248 tasrevadsvqeiadgaaeqtddldaaaaevsdlsaateevaS 290
                                       4444333333333333333333333333332222222222221 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 ?    8.3   2.8    0.0032       1.1      60     111 ..     121     172 ..     100     196 .. 0.60
   2 ?    2.9   2.3      0.14        46      38     121 ..     246     330 ..     219     359 .. 0.59
   3 ?    3.5   0.2     0.092        31      32     112 ..     433     499 ..     379     524 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0032
                             Atg14  60 dkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdkl 111
                                       d ++ + a+le+ + + ++ +++ +e  d+l+  +++++e++++++++++ l
  gi|336252564|ref|YP_004595671.1| 121 DSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERL 172
                                       4444444455555555555555555555555555555555555555555544 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.14
                             Atg14  38 keslkkkiekalegke.eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkk 113
                                         +  +++ + +++    a +++d+++  +a +++l + +++  + + e+ d+ ++ ++ +ee ++  a+  +++ +
  gi|336252564|ref|YP_004595671.1| 246 IRTASREVADSVQEIAdGAAEQTDDLDAAAAEVSDLSAATEEVASTTGEIADQSESVTELTEEGREAAAEAAENIDE 322
                                       33333333333333222334677778888888888888888888888888888888888888888777777776664 PP

                             Atg14 114 Rrsdlesl 121
                                         +  e +
  gi|336252564|ref|YP_004595671.1| 323 LVENTETV 330
                                       33333333 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.092
                             Atg14  32 aklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakls 108
                                        +l s+ e++ +++e              +++ + +++ ++  ++ad+ ++l+ + d++     e++ k +++a+ s
  gi|336252564|ref|YP_004595671.1| 433 DDLESRLETIAGEVE--------------QVDGSIQQIASTADDQADSAQELSAIVDDVAAVSNETATKAQQVAAAS 495
                                       233333333333333..............333333344444444444444444444444444444444444444444 PP

                             Atg14 109 dklk 112
                                       ++++
  gi|336252564|ref|YP_004595671.1| 496 EETS 499
                                       4443 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   7.2      0.52   1.8e+02     146     216 ..     102     180 ..      77     194 .. 0.56
   2 ?    7.3   5.7    0.0074       2.5      99     223 ..     240     349 ..     220     366 .. 0.53
   3 ?   10.5   1.7   0.00082      0.28     118     227 ..     381     489 ..     374     508 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.52
                              CorA 146 kkeilrelaqlrrrlvklrralapnrevlk.........rllakaddkllddedkeylrdlldelerllemlealre 213
                                       + + ++e+ +l  +++++r++l ++ + l+         ++ a +++++l+de+ e+l++ + e+er  e l a +e
  gi|336252564|ref|YP_004595671.1| 102 ETDRVDEIGELYGSVARMRDSLEDTLADLEteqeraqqaQREAEERADQLEDER-EQLQETRAEIERQNERLVAEAE 177
                                       556677777777777777777777777774333222222222233333333333.4444444444444444444444 PP

                              CorA 214 rle 216
                                       r +
  gi|336252564|ref|YP_004595671.1| 178 RFS 180
                                       444 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0074
                              CorA  99 kdeggkpkspgellyrlldeivdrlfellekleeeldeledel.edstkkeilrelaqlrrrlvkl....rralapn 170
                                       +d + + +++++ ++  ++ei+d  +e++++l++   e++d    +++ ++  +e+a+  +++++l    r+a+a+ 
  gi|336252564|ref|YP_004595671.1| 240 EDSSAEIRTASREVADSVQEIADGAAEQTDDLDAAAAEVSDLSaATEEVASTTGEIADQSESVTELteegREAAAEA 316
                                       44445555555555555555555555555555555555555555555555555555555555555555555555555 PP

                              CorA 171 revlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtys 223
                                        e ++                    +l +++e ++e+++ l + +e++ ++++
  gi|336252564|ref|YP_004595671.1| 317 AENID--------------------ELVENTETVVETADELTRETEQIEEIIA 349
                                       55555....................5555555555555555555555544432 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00082
                              CorA 118 eivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedke 192
                                        ++d++ +l e+  + +d++e +l   +++++  ++e+ +++ +++   +++ +++  l + +a ++ +++d    +
  gi|336252564|ref|YP_004595671.1| 381 VVADEIKALAEETMDAVDDIEGTLesIRDRTETTANEIGEVESNITSTATIVDDLESRL-ETIA-GEVEQVDGSI-Q 454
                                       57888999999999999999999988888899999999999999999999999999999.7777.6777777775.7 PP

                              CorA 193 ylrdlldelerllemlealrerleslqdtysslls 227
                                       ++    d+ + ++++l+a+ + +  ++++ ++  +
  gi|336252564|ref|YP_004595671.1| 455 QIASTADDQADSAQELSAIVDDVAAVSNETATKAQ 489
                                       78888888888888899998888888888877655 PP

>> Vip3A_N  Vegetative insecticide protein 3A N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       2.4   8.2e+02      48     100 ..     110     162 ..      93     188 .. 0.79
   2 ?   -0.5   0.4         3     1e+03      48      95 ..     279     326 ..     247     364 .. 0.55
   3 ?    3.6   0.9      0.16        55      39     112 ..     343     420 ..     314     436 .. 0.71
   4 ?    4.8   0.3     0.069        23      45     102 ..     437     494 ..     420     509 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.4
                           Vip3A_N  48 ndisgkldgvngslndliaqgnlntelskeilkianeqnqvlndvnnkldain 100
                                        ++ g +  +  sl+d +a+ + + e +++  + a+e+   l+d  ++l+   
  gi|336252564|ref|YP_004595671.1| 110 GELYGSVARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETR 162
                                       45566677778899999999999999999999999999999999998887655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3
                           Vip3A_N  48 ndisgkldgvngslndliaqgnlntelskeilkianeqnqvlndvnnk 95 
                                        d+s   + v  + +++  q +  tel+ e  + a e  + ++++ ++
  gi|336252564|ref|YP_004595671.1| 279 SDLSAATEEVASTTGEIADQSESVTELTEEGREAAAEAAENIDELVEN 326
                                       455555555555555555566666666666555555554444433222 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.16
                           Vip3A_N  39 eilknqqllndisgk..ldgvngslndli..aqgnlntelskeilkianeqnqvlndvnnkldaintmlrvylpkit 111
                                       +i     l++di+++  l  vn s++     a+g   + ++ ei  +a+e    ++d++  l++i    ++    i 
  gi|336252564|ref|YP_004595671.1| 343 QIEEIIALIDDIADQtnLLAVNASIEAATagADGSGFAVVADEIKALAEETMDAVDDIEGTLESIRDRTETTANEIG 419
                                       444555678888875226689999987662257888889999*******************9999887776666655 PP

                           Vip3A_N 112 s 112
                                        
  gi|336252564|ref|YP_004595671.1| 420 E 420
                                       5 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.069
                           Vip3A_N  45 qllndisgkldgvngslndliaqgnlntelskeilkianeqnqvlndvnnkldaintm 102
                                         l+ i+g ++ v+gs++++ +  + +++ ++e+  i ++   v n+  +k + + + 
  gi|336252564|ref|YP_004595671.1| 437 SRLETIAGEVEQVDGSIQQIASTADDQADSAQELSAIVDDVAAVSNETATKAQQVAAA 494
                                       45899*****************************************999998877665 PP

>> SLX9  Ribosome biogenesis protein SLX9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  13.9    0.0044       1.5      48     115 ..     120     198 ..     113     370 .. 0.85
   2 ?   -0.1   0.1       3.4   1.2e+03      46      94 ..     430     490 ..     390     507 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0044
                              SLX9  48 lesLadaLpdleeeege.kkekkekeqaqqgkvkkaekslkskpgalkrkkklekkEmerfkkvLa........... 112
                                        +sL+d L dle+e+++ +++++e+e++ ++ + ++e+ ++++ + ++++++l  +E erf++v+            
  gi|336252564|ref|YP_004595671.1| 120 RDSLEDTLADLETEQERaQQAQREAEERADQLEDEREQLQETRAEIERQNERL-VAEAERFSEVMDacadgdltqrl 195
                                       489********987777666666666666666666555667777777777777.***********866666666666 PP

                              SLX9 113 hps 115
                                       +p+
  gi|336252564|ref|YP_004595671.1| 196 EPQ 198
                                       444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.4
                              SLX9  46 tdlesLadaLpdle...............eeegekkekkekeqaqqgkvkkaek.slkskpgalk 94 
                                       t +++L++ L+ ++               +    ++++ +++q+ ++ v      s+++ ++a++
  gi|336252564|ref|YP_004595671.1| 430 TIVDDLESRLETIAgeveqvdgsiqqiasT----ADDQADSAQELSAIVDDVAAvSNETATKAQQ 490
                                       455666666666665555444444332210....2222222222222222211224444444444 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  15.9    0.0078       2.6      56     150 ..     120     214 ..     114     226 .. 0.67
   2 ?    0.4   8.5         2   6.8e+02      60     152 ..     233     332 ..     210     359 .. 0.56
   3 ?    7.6   0.3     0.012         4      47     136 ..     385     473 ..     378     521 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0078
                     Jnk-SapK_ap_N  56 reeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkke 132
                                       r+ le+   ++e e+e  ++a++e ee  dq+e+er++lqe  ++ e +n++l + a+ +++ + ++ + +  ++ e
  gi|336252564|ref|YP_004595671.1| 120 RDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAERFSEVMDACADGDLTQRLE 196
                                       555555555556666666677777777788888899999999999**9*9999988888888877777766666555 PP

                     Jnk-SapK_ap_N 133 ysklheretellkklkel 150
                                        +   e    +  +  e+
  gi|336252564|ref|YP_004595671.1| 197 PQVDDEAIAAIATSFNEM 214
                                       555555444444444444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2
                     Jnk-SapK_ap_N  60 eqLeteyerekelrkrae....eeleeiedqweeerkelqek...veqleeenrelelkaknaadqlsrleekeael 129
                                       e++  e+e+  ++ + a     + ++ei d   e++ +l+++   v++l   ++e+   + ++adq +++ e  +e 
  gi|336252564|ref|YP_004595671.1| 233 EEISVELEDSSAEIRTASrevaDSVQEIADGAAEQTDDLDAAaaeVSDLSAATEEVASTTGEIADQSESVTELTEEG 309
                                       44444444444443333322336777777777777777776511134444445555544445555555555555555 PP

                     Jnk-SapK_ap_N 130 kkeysklheretellkklkelve 152
                                       ++  +++ e+  el+++   +ve
  gi|336252564|ref|YP_004595671.1| 310 REAAAEAAENIDELVENTETVVE 332
                                       55555555555555555555544 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.012
                     Jnk-SapK_ap_N  47 eeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrle 123
                                       e +a +ee  ++++++e  +e  +   + + +e+ e+e ++ + +  +++  ++le+   e+e +++ + +q+++  
  gi|336252564|ref|YP_004595671.1| 385 EIKALAEETMDAVDDIEGTLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVE-QVDGSIQQIASTA 460
                                       556667778888888888888888888888888888888888888888888888888888888.8888888888888 PP

                     Jnk-SapK_ap_N 124 ekeaelkkeyskl 136
                                       + +a++ +e s+ 
  gi|336252564|ref|YP_004595671.1| 461 DDQADSAQELSAI 473
                                       8888887777765 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 ?    6.5   2.8     0.029       9.8      58     100 ..     126     168 ..     103     188 .. 0.58
   2 ?    5.6   2.2     0.054        18      37     103 ..     224     291 ..     201     308 .. 0.58
   3 ?    2.9   7.0      0.36   1.2e+02      23      99 ..     263     343 ..     246     360 .. 0.55
   4 ?    2.7   3.6      0.42   1.4e+02      14     105 ..     320     419 ..     315     429 .. 0.69
   5 ?    4.6   0.3      0.11        38      39     102 ..     398     458 ..     376     462 .. 0.76
   6 ?    4.5   0.3      0.12        41      39      93 ..     468     522 ..     458     528 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.029
                                       HCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  58 eIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                       + + +  ++e a++   e++e  ++l++  ++l+e +ae+e  
  gi|336252564|ref|YP_004595671.1| 126 TLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQ 168
                                       4444444555555555555555555555555555555555443 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.054
                                       HHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                      Seryl_tRNA_N  37 krrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaelekllla 103
                                         r   +++ee+  e    s+eI  a+++  +  +e+ + ++e  ++l+a+ ae+++l+a+ e+++++
  gi|336252564|ref|YP_004595671.1| 224 DVRGSANAVEEISVELEDSSAEIRTASREVaDSVQEIADGAAEQTDDLDAAAAEVSDLSAATEEVAST 291
                                       44555555555555555555555555555544444444445555555555555555555555555443 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.36
                                       CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  23 edkadvdelleldekrrelqveleelqaerNel...skeIgkakkkk.edaeeliaevkelkeelkaleaelkelea 95 
                                       +++++ d+l ++ ++   l +++ee+ +   e+   s+++ ++ +++ e a+e  + ++el e+++++ ++ +el+ 
  gi|336252564|ref|YP_004595671.1| 263 GAAEQTDDLDAAAAEVSDLSAATEEVASTTGEIadqSESVTELTEEGrEAAAEAAENIDELVENTETVVETADELTR 339
                                       45556666666666666666666666655544422255666666666644444444444444444444444444444 PP

                                       HHHH CS
                      Seryl_tRNA_N  96 elek 99 
                                       e e+
  gi|336252564|ref|YP_004595671.1| 340 ETEQ 343
                                       4333 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.42
                                       HHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHCCCCCCTT......S-TCCCCCCCHHHHHH CS
                      Seryl_tRNA_N  14 vkeklkkRgedkadvdelleldekrrelqveleelqaerN..elskeIgkakkkk......edaeeliaevkelkee 82 
                                       ++e +++ +  +++ del    e+ +e+++ ++++  + N  +++++I+ a +          a+e++a ++e  + 
  gi|336252564|ref|YP_004595671.1| 320 IDELVENTETVVETADELTRETEQIEEIIALIDDIADQTNllAVNASIEAATAGAdgsgfaVVADEIKALAEETMDA 396
                                       33333444456778888888888888888888888888874445666766665435566777778888888888888 PP

                                       HHHHHHHHHHHHHHHHHHHCTS- CS
                      Seryl_tRNA_N  83 lkaleaelkeleaeleklllaiP 105
                                       ++++e +l+ ++++ e+ + +i+
  gi|336252564|ref|YP_004595671.1| 397 VDDIEGTLESIRDRTETTANEIG 419
                                       88888888888887777776665 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Seryl_tRNA_N  39 relqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklll 102
                                         ++ +le+++ +  + ++eIg+   +   +++    v++l  +l+++  e+++++  ++++++
  gi|336252564|ref|YP_004595671.1| 398 DDIEGTLESIRDRTETTANEIGEVESN---ITSTATIVDDLESRLETIAGEVEQVDGSIQQIAS 458
                                       456667888888999999999998864...6777777899999999999999999999988875 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  39 relqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkel 93 
                                       +el + ++++ a +Ne + + ++  ++ e++++ i++v++  ++l +   +lk l
  gi|336252564|ref|YP_004595671.1| 468 QELSAIVDDVAAVSNETATKAQQVAAASEETSATIDSVSTTATDLGDDARDLKRL 522
                                       5666667777777888888888888887888877777777777777766666665 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 ?    9.2   9.9    0.0035       1.2      29     105 ..     121     200 ..     101     226 .. 0.78
   2 ?   -0.2   0.2       2.8   9.5e+02      34     118 ..     238     257 ..     198     288 .. 0.40
   3 ?    7.7   2.7      0.01       3.5      19     108 ..     286     375 ..     256     383 .. 0.83
   4 ?    3.3   4.4      0.25        83      19     112 ..     387     500 ..     382     528 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0035
                             Mod_r  29 kqlkeekeellaeneslaeknlslep...eleelrselqekleelkelekefeekeqeldellqkfspdallarLqt 102
                                       ++l++ + +l++e+e+  +++ + e+   +le++r++lqe++ e+++ ++++ +  ++ +e+++ + +  l +rL+ 
  gi|336252564|ref|YP_004595671.1| 121 DSLEDTLADLETEQERAQQAQREAEEradQLEDEREQLQETRAEIERQNERLVAEAERFSEVMDACADGDLTQRLEP 197
                                       45666666666666655555555544566**********************************************98 PP

                             Mod_r 103 ava 105
                                       +v+
  gi|336252564|ref|YP_004595671.1| 198 QVD 200
                                       876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.8
                             Mod_r  34 ekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspdallarLqtavaeaeee 110
                                       e+e+  ae++                                                                   
  gi|336252564|ref|YP_004595671.1| 238 ELEDSSAEIR-----------------------------------------------------------------TA 249
                                       2222222222.................................................................22 PP

                             Mod_r 111 Sealaeef 118
                                       S+++a+++
  gi|336252564|ref|YP_004595671.1| 250 SREVADSV 257
                                       22222111 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.01
                             Mod_r  19 ealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspda 95 
                                       e++++t+ e+ ++ e+ +el +e ++ a +  ++ +el e+ + + e+ +el++  ++ ee  +  d++ +++++ a
  gi|336252564|ref|YP_004595671.1| 286 EEVASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTETVVETADELTRETEQIEEIIALIDDIADQTNLLA 362
                                       45555668899999999999999999999999999999999999999999999999999999999999999999999 PP

                             Mod_r  96 llarLqtavaeae 108
                                       + a  ++a+a a+
  gi|336252564|ref|YP_004595671.1| 363 VNASIEAATAGAD 375
                                       9988888887665 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.25
                             Mod_r  19 ealvktl.pevkqlkeekeellaenesla....................eknlsl.epeleelrselqekleelkel 73 
                                       +al++++ + v++++  +e++++ +e +a                    e+ l+    e+e++  ++q+  ++++  
  gi|336252564|ref|YP_004595671.1| 387 KALAEETmDAVDDIEGTLESIRDRTETTAneigevesnitstativddlESRLETiAGEVEQVDGSIQQIASTADDQ 463
                                       55555444667777777777777777777666666555555555554446666665557777777777777777777 PP

                             Mod_r  74 ekefeekeqeldellqkfspdallarLqtavaeaeeeSe 112
                                        ++ +e+ +  d++    ++ a++a  q+ +a++ee S 
  gi|336252564|ref|YP_004595671.1| 464 ADSAQELSAIVDDVAAVSNETATKA--QQVAAASEETSA 500
                                       7777777777777766666666555..344444444444 PP

>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   7.8   0.00014     0.047      19      80 ..     127     188 ..     113     198 .. 0.77
   2 ?    5.1   3.0     0.087        29      13      76 ..     286     349 ..     278     360 .. 0.76
   3 ?    1.5   0.1       1.1   3.7e+02      28      74 ..     403     449 ..     391     469 .. 0.77
   4 ?   -0.8   0.1       5.9     2e+03      40      58 ..     485     503 ..     453     530 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00014
                              TBCA  19 ekEleeqearleklkadgdedeydlkkqeevleetkamipdlkkrlekavekLeelleeeee 80 
                                         +le++++r ++ + + +e   +l+ ++e l+et+a i+  ++rl ++ e+++e++++  +
  gi|336252564|ref|YP_004595671.1| 127 LADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAERFSEVMDACAD 188
                                       44566677777777776655689**********************************99844 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.087
                              TBCA  13 KEeasYekEleeqearleklkadgded.eydlkkqeevleetkamipdlkkrlekavekLeelle 76 
                                        E as   E+++q + + +l ++g e      ++  e++e t+++++++++ l+ + e+ ee+++
  gi|336252564|ref|YP_004595671.1| 286 EEVASTTGEIADQSESVTELTEEGREAaAEAAENIDELVENTETVVETADE-LTRETEQIEEIIA 349
                                       68899999**************99776455566668888888888877654.6777777777665 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 1.1
                              TBCA  28 rleklkadgdedeydlkkqeevleetkamipdlkkrlekavekLeel 74 
                                       +le++++  ++   ++ + e  +  t +++ dl++rle+   + e++
  gi|336252564|ref|YP_004595671.1| 403 TLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQV 449
                                       55666665544477777888888999999999****99998888765 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 5.9
                              TBCA  40 eydlkkqeevleetkamip 58 
                                         + ++   + eet a i 
  gi|336252564|ref|YP_004595671.1| 485 ATKAQQVAAASEETSATID 503
                                       2333333455566665554 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2  15.7      0.15        50     464     536 ..     124     198 ..     103     201 .. 0.83
   2 ?    8.3  26.3    0.0011      0.36     245     532 ..     213     501 ..     192     510 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.15
                           DUF3584 464 eEeleqieeadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaerrleqlrqale..eleeqlsPq 536
                                       e++l ++e ++e+ ++aq+e+e++ ++ e++ +++++ r++ + ++e+l  +++r +++ +a++  +l + l Pq
  gi|336252564|ref|YP_004595671.1| 124 EDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAERFSEVMDACAdgDLTQRLEPQ 198
                                       678889999999999999999999999999999999999999999999999999999999988622577777776 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0011
                           DUF3584 245 peieklqeefeqleslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeaidelnqelsaakakl 321
                                       + ++++ e + ++ +  + +  +++el++   ++++   ev+ + +e+   +++++d+l  a++e+ ++lsaa +++
  gi|336252564|ref|YP_004595671.1| 213 EMLDRMSETMVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEIADGAAEQTDDLDAAAAEV-SDLSAATEEV 288
                                       3345666777788999999999*************************************9988887.69******** PP

                           DUF3584 322 aakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkikeeleeelek 398
                                       a    e+    e+  +  +++ e +++ +++++++ ++ e + e  d lt + ++++e        +++ +  +++ 
  gi|336252564|ref|YP_004595671.1| 289 ASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTETVVETADELTRETEQIEEIIALIDDIADQTNLLAVNA 365
                                       ********************************************************976654444444444444433 PP

                           DUF3584 399 lkerleaireekdrlkaaieealeal...esqlrkqleaqkeelneeekelesrlselklrlds.atateEeleqie 471
                                           ++a+  +     a+  ++ +al       ++  e   e+++++ +  +++++e +  ++s at+ +++  ++e
  gi|336252564|ref|YP_004595671.1| 366 SI--EAATAGADGSGFAVVADEIKALaeeTMDAVDDIEGTLESIRDRTETTANEIGEVESNITStATIVDDLESRLE 440
                                       33..444444445554555555555510044556778899999**************999987636899999***** PP

                           DUF3584 472 eadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaerrleqlrqaleeleeq 532
                                           ++e+ + ++++      + ++  ++l +  d      ++ + +++q+++a ee    
  gi|336252564|ref|YP_004595671.1| 441 TIAGEVEQVDGSIQQIASTADDQADSAQELSAIVDDVAAVSNETATKAQQVAAASEETSAT 501
                                       ***************9999999999999999999999999999999999999999887655 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   7.0     0.029       9.8      28      97 ..     108     177 ..     102     181 .. 0.88
   2 ?    6.2   1.7     0.042        14      26     101 ..     236     311 ..     204     315 .. 0.83
   3 ?    3.3   4.1      0.35   1.2e+02      42      97 ..     287     335 ..     264     366 .. 0.48
   4 ?    7.5   1.1     0.017       5.8      12     103 ..     399     491 ..     383     493 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.029
                                       SCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  28 dlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaa 97 
                                       ++g+ + +v ++ + +++  a+l+++qer ++ +  ae+ +d  +++ e+++e+ +e++++ e L + a+
  gi|336252564|ref|YP_004595671.1| 108 EIGELYGSVARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAE 177
                                       567778888899999999****************9999999999999************99998877665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.042
                                       CSSCSSSHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  26 sedlgkdleevqallkkhkaleaelaa.qqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaerkq 101
                                       s +l+ + +e+++  ++  +  +e+a+ + e+ ++l++ a ++ d    a+ee+ +++ e+ ++ e++ el++e ++
  gi|336252564|ref|YP_004595671.1| 236 SVELEDSSAEIRTASREVADSVQEIADgAAEQTDDLDAAAAEVSDL-SAATEEVASTTGEIADQSESVTELTEEGRE 311
                                       4455666777777777888889999999999999999999999766.7999********************999775 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  42 khkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaa 97 
                                       +      e+a+q e v++l+e +++        ++e  e ++el e+ e + e+a+
  gi|336252564|ref|YP_004595671.1| 287 EVASTTGEIADQSESVTELTEEGREA-------AAEAAENIDELVENTETVVETAD 335
                                       22222334444444444444333333.......33333333333333333333332 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHH..CCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHH CS
                          Spectrin  12 eleeWieekeell..ssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleeln 86 
                                       ++e  +e ++     + +++g+  +++ +  +  ++le  l++  ++v++++   +++++   +++++  + l+++ 
  gi|336252564|ref|YP_004595671.1| 399 DIEGTLESIRDRTetTANEIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIAST-ADDQADSAQELSAIV 474
                                       555555554333322567777777777788889999****************999999555.588888888899999 PP

                                       HHHHHHHHHHHHHHHHH CS
                          Spectrin  87 erWeeLkelaaerkqkL 103
                                       +  ++++  +a++ q++
  gi|336252564|ref|YP_004595671.1| 475 DDVAAVSNETATKAQQV 491
                                       99999988888888775 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 ?    7.9   6.3     0.012       3.9       7      75 ..     108     172 ..     103     188 .. 0.68
   2 ?    8.4   1.4     0.008       2.7       9      73 ..     216     283 ..     209     290 .. 0.66
   3 ?    2.9   4.8      0.42   1.4e+02      12      71 ..     285     344 ..     272     363 .. 0.44
   4 ?   -0.4   0.1       4.4   1.5e+03      27      53 ..     395     421 ..     382     448 .. 0.43
   5 ?    6.2   2.0     0.041        14       5      61 ..     446     502 ..     442     526 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.012
                            CENP-H   7 qrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeelekleael 75 
                                       ++ el  +++++  +l++++++l++ ++ + +++r+ +e a +l+ ++++ ++++    +e+e+  + l
  gi|336252564|ref|YP_004595671.1| 108 EIGELYGSVARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETR----AEIERQNERL 172
                                       5567777888999999999999999999999999999999999955555544444....3333333322 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.008
                            CENP-H   9 delssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeeleklea 73 
                                       d++s+++ +   + ++++e   e+e ++ ++++++re a +++e a  ++++    + +++e++ l a
  gi|336252564|ref|YP_004595671.1| 216 DRMSETMVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEIADGAAEQTddlDAAAAEVSDLSA 283
                                       66666777777777777777777777777777777777777777777776666455445555555544 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.42
                            CENP-H  12 ssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeelekl 71 
                                        +e++ ++ e+++  e++te+++e +++ ++ +e + el e ++   ++ ++l++e e++
  gi|336252564|ref|YP_004595671.1| 285 TEEVASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTETVVETADELTRETEQI 344
                                       333333333444444444444444444444444444444333333222222222222222 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 4.4
                            CENP-H  27 eeltevekenlrlkrknrelaaellel 53 
                                       ++++++e    +++ ++++ a+e+ e 
  gi|336252564|ref|YP_004595671.1| 395 DAVDDIEGTLESIRDRTETTANEIGEV 421
                                       333333333333333333333333222 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.041
                            CENP-H   5 ieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek 61 
                                       +eq d  +++++ ++ + ++  +el+ +  +  +++++++++a++++  ++e++++ 
  gi|336252564|ref|YP_004595671.1| 446 VEQVDGSIQQIASTADDQADSAQELSAIVDDVAAVSNETATKAQQVAAASEETSATI 502
                                       789999999*************************************66666555444 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.5     0.043        15      76     121 ..     125     170 ..     111     184 .. 0.85
   2 ?    6.1   0.1     0.028       9.5      58     112 ..     202     256 ..     189     263 .. 0.83
   3 ?    2.0   0.8      0.52   1.7e+02      81     139 ..     295     354 ..     285     369 .. 0.60
   4 ?    2.2   0.4      0.44   1.5e+02      76     135 ..     420     480 ..     383     487 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.043
                      Sec8_exocyst  76 kilssiqesqekvselKesleeakkklstkkkeLkelnarsakyke 121
                                        +l  ++  qe+ ++ +++ ee   +l++++++L+e+ a+  +++e
  gi|336252564|ref|YP_004595671.1| 125 DTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNE 170
                                       5677788889999999999999999999999999999988877665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.028
                      Sec8_exocyst  58 evvnehhqaFnssiasYskilssiqesqekvselKesleeakkklstkkkeLkel 112
                                       e++ +   +Fn+     s+++  +  s++ v+e+  +le++ +++ t + e  + 
  gi|336252564|ref|YP_004595671.1| 202 EAIAAIATSFNEMLDRMSETMVDVRGSANAVEEISVELEDSSAEIRTASREVADS 256
                                       566667789************************************9999887765 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.52
                      Sec8_exocyst  81 iqesqekvselKesleeakkklstkkkeLkelnarsa.kykevieiLdaieelkkvpdki 139
                                       i++  e+v+el e+ +ea ++  ++ +eL e  ++ + + +e+ +  ++iee+ ++ d i
  gi|336252564|ref|YP_004595671.1| 295 IADQSESVTELTEEGREAAAEAAENIDELVENTETVVeTADELTRETEQIEEIIALIDDI 354
                                       555556666666666666666666666665554444313445555566666666665554 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.44
                      Sec8_exocyst  76 kilssiqesqekvselKesleeakkklstkkkeLkelnarsakykevieiLdai.eelkkv 135
                                       ++ s+i++ ++ v +l  +le    ++++ + ++++++ +   + +  + L+ai +++++v
  gi|336252564|ref|YP_004595671.1| 420 EVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQADSAQELSAIvDDVAAV 480
                                       5667788888888888888888888888888888888888877777777777753455555 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.61   2.1e+02     116     156 ..     116     156 ..       7     195 .. 0.50
   2 ?    2.5   2.4      0.13        45     114     168 ..     255     309 ..     226     367 .. 0.50
   3 ?    6.3   0.7    0.0094       3.2      93     177 ..     392     476 ..     376     484 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.61
                            Tweety 116 eesleekleeeLtkleeifakrtdlletlrlvqeqveevvq 156
                                        ++++ +le++L+ le+  ++ ++ ++  +    q+e   +
  gi|336252564|ref|YP_004595671.1| 116 VARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDERE 156
                                       33444444444444443332222222222222222222222 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                            Tweety 114 eteesleekleeeLtkleeifakrtdlletlrlvqeqveevvqqlselpflkkkd 168
                                       ++ +++    +e+   l+   a+  dl ++++ v +++ e+++q ++++ l +++
  gi|336252564|ref|YP_004595671.1| 255 DSVQEIADGAAEQTDDLDAAAAEVSDLSAATEEVASTTGEIADQSESVTELTEEG 309
                                       5555555555555555555555555555555555555555555544444333321 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0094
                            Tweety  93 qltyslrkanhtlagikklvseteesleekleeeLtkleeifakrtdlletlrlvqeqveevvqqlselp.flkkkd 168
                                       + + ++++++ tl +i++++++t++++  ++e+++t+  +i++  ++ let+    eqv+  +qq+++ +    ++ 
  gi|336252564|ref|YP_004595671.1| 392 ETMDAVDDIEGTLESIRDRTETTANEIG-EVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTAdDQADSA 467
                                       56789999******************97.589999********9999999999988888888888887773333334 PP

                            Tweety 169 vsltelaeq 177
                                        +l++++++
  gi|336252564|ref|YP_004595671.1| 468 QELSAIVDD 476
                                       455555555 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  19.1    0.0044       1.5      45     101 ..     123     179 ..     100     188 .. 0.69
   2 ?    3.1   5.1      0.37   1.3e+02      10      96 ..     214     304 ..     193     311 .. 0.63
   3 ?    0.2  12.0       3.1     1e+03      15      93 ..     268     346 ..     264     364 .. 0.62
   4 ?    7.9   3.3     0.012       4.2      13     105 ..     385     505 ..     380     530 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0044
                            APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerf 101
                                        ++ l++le e e+ +++++e++e  ++le+ere+l++ +a++e++ e+l +e erf
  gi|336252564|ref|YP_004595671.1| 123 LEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEAERF 179
                                       234666777777777777777777777777777777777777777777777777766 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.37
                            APG6_N  10 LleeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleee....leklekeeeelleeLkelekereelea 82 
                                       +l+++ + + +++   +a ee   +l++++ e ++   e++++ +e     ++  ++ +++ +e  +l ++ ee+++
  gi|336252564|ref|YP_004595671.1| 214 MLDRMSETMVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEiadgAAEQTDDLDAAAAEVSDLSAATEEVAS 290
                                       67777788888888888888888888877766665333333333331111333555555666666666666666666 PP

                            APG6_N  83 elaaleeelealee 96 
                                          +++ ++e + e
  gi|336252564|ref|YP_004595671.1| 291 TTGEIADQSESVTE 304
                                       65555555555544 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 3.1
                            APG6_N  15 dkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeel 91 
                                       +  l++a +e  ++++  +++ +++ e  +q e++ el ee ++  +e +e + eL e  ++  e ++el   +e+ 
  gi|336252564|ref|YP_004595671.1| 268 TDDLDAAAAEVSDLSAATEEVASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTETVVETADELTRETEQI 344
                                       56788888888888888888888877776666666666666555555555555554444444444444444444444 PP

                            APG6_N  92 ea 93 
                                       e+
  gi|336252564|ref|YP_004595671.1| 345 EE 346
                                       43 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.012
                            APG6_N  13 eldkqleqaekerdaYeeflkklkkekkeeek............................qdeeleeleeeleklek 61 
                                       e++   e++ +  d+ e  l+ ++++++++ +                            + e+++ + ++++ + +
  gi|336252564|ref|YP_004595671.1| 385 EIKALAEETMDAVDDIEGTLESIRDRTETTANeigevesnitstativddlesrletiagEVEQVDGSIQQIASTAD 461
                                       55556666666667777777777766555443344444444444444444444444433344444444444555555 PP

                            APG6_N  62 eeeelleeLkelekereeleaelaaleeelealeeeeerfwrey 105
                                       ++++  +eL ++ +  +++ +e a+ +++ +a  ee  + + + 
  gi|336252564|ref|YP_004595671.1| 462 DQADSAQELSAIVDDVAAVSNETATKAQQVAAASEETSATIDSV 505
                                       55555555555555555555555555555555555555555555 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.7     0.081        27      24      79 ..     113     169 ..     110     183 .. 0.70
   2 ?    1.4   0.2       1.6   5.5e+02      34      34 ..     274     274 ..     201     358 .. 0.64
   3 ?    1.4   0.0       1.6   5.5e+02      29      65 ..     423     459 ..     407     490 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.081
                      Occludin_ELL  24 YkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekk 79 
                                       Y ++ ++ +++++++++Le+e +++++ ++e +++++++ +e ++l++  +e  ++ 
  gi|336252564|ref|YP_004595671.1| 113 YGSVARMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQEtRAEIERQN 169
                                       555666667778888888888888888888888888888887777766334444444 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.6
                      Occludin_ELL  34 v 34 
                                       +
  gi|336252564|ref|YP_004595671.1| 274 A 274
                                       2 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.6
                      Occludin_ELL  29 aeleevskkfseLerelkelkegskeykkieeeilqe 65 
                                       +++++++  + +Le++l++ + + ++++  +++i ++
  gi|336252564|ref|YP_004595671.1| 423 SNITSTATIVDDLESRLETIAGEVEQVDGSIQQIAST 459
                                       5566666666666666666666666666666665543 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   5.1      0.15        51       7      59 ..     130     185 ..     105     232 .. 0.50
   2 ?    5.6   2.4     0.024         8       3      59 ..     277     333 ..     232     367 .. 0.49
   3 ?    5.5   0.2     0.025       8.3      24      85 ..     396     456 ..     374     488 .. 0.42
   4 ?    6.1   0.4     0.017       5.7       8      88 ..     429     508 ..     416     525 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.15
                             TMPIT   7 lekefkeleetakeykq...kleelsklqskcskeikkqkkrlkelksslkklkks 59 
                                       le+e+++ +++++e ++   +le+  ++ ++++ ei++q++rl +  ++++++  +
  gi|336252564|ref|YP_004595671.1| 130 LETEQERAQQAQREAEEradQLEDEREQLQETRAEIERQNERLVAEAERFSEVMDA 185
                                       33333333333333333000333333333333344444444444444443333333 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.024
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkks 59 
                                       e+++l+  ++e+ +t  e+  ++e++++l ++ ++++++  +++ el ++ +++ ++
  gi|336252564|ref|YP_004595671.1| 277 EVSDLSAATEEVASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTETVVET 333
                                       233333333333333333333333333333333333333333333333333333333 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.025
                             TMPIT  24 kleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkev 85 
                                        +++++   ++++ ++++  +++ e++s+++++ + v ++ e+++e+++ e+++ + +++++
  gi|336252564|ref|YP_004595671.1| 396 AVDDIEGTLESIRDRTETTANEIGEVESNITSTATIV-DDLESRLETIAGEVEQVDGSIQQI 456
                                       2222222222222222222222222222222222222.222223333333333333333333 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.017
                             TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlke 84 
                                       ++ +++le++ +++  ++e++  ++++++++++ q   ++el++ ++++ +  ++e++++++++++  +e+++++++
  gi|336252564|ref|YP_004595671.1| 429 ATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQADSAQELSAIVDDVAAV-SNETATKAQQVAAASEETSATIDS 504
                                       5556778888899999999999999999999999999999999999998765.678899999999999998888887 PP

                             TMPIT  85 vesl 88 
                                       v+ +
  gi|336252564|ref|YP_004595671.1| 505 VSTT 508
                                       7765 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   4.3     0.088        30      11      51 ..     142     182 ..     106     205 .. 0.59
   2 ?    2.4   0.2      0.71   2.4e+02      12      61 ..     210     259 ..     199     309 .. 0.54
   3 ?    4.9   1.5      0.12        42      14      52 ..     310     348 ..     296     372 .. 0.76
   4 ?    3.4   0.2      0.35   1.2e+02      21      52 ..     429     460 ..     390     522 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.088
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  11 eeleeqleelleeleelkeelaelleenaeLeleneklrer 51 
                                       +e ee+ ++l +e e+l+e+ ae+  +n++L +e e++ e 
  gi|336252564|ref|YP_004595671.1| 142 REAEERADQLEDEREQLQETRAEIERQNERLVAEAERFSEV 182
                                       33445555555555555555555555555555555555554 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.71
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXX CS
                              YabA  12 eleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkeke 61 
                                       +++e l++++e++ +++ + +++ e   eLe    ++r+  +e  ++ +e
  gi|336252564|ref|YP_004595671.1| 210 SFNEMLDRMSETMVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQE 259
                                       55555555555555555555555555555555555555554222222222 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  14 eeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                        e  +e  e+++el e++++++e  +eL+ e e++ e +
  gi|336252564|ref|YP_004595671.1| 310 REAAAEAAENIDELVENTETVVETADELTRETEQIEEII 348
                                       5667788999************************99987 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  21 leeleelkeelaelleenaeLeleneklrerl 52 
                                        + +++l+++l+++  e +++    +++ ++ 
  gi|336252564|ref|YP_004595671.1| 429 ATIVDDLESRLETIAGEVEQVDGSIQQIASTA 460
                                       33333333333333333333333333333222 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  10.7    0.0038       1.3      53     111 ..     118     176 ..     116     184 .. 0.91
   2 ?    2.0   0.6      0.59     2e+02      32     108 ..     202     279 ..     188     298 .. 0.79
   3 ?    0.7   1.5       1.5   4.9e+02      66     128 ..     285     347 ..     276     352 .. 0.79
   4 ?    8.1   0.5     0.008       2.7      54     137 ..     403     485 ..     395     519 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0038
                              ADIP  53 eqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqkl 111
                                       ++r sl++t+ +le+e er q++ +  +++  qle e +++q++ +++e+++++l + +
  gi|336252564|ref|YP_004595671.1| 118 RMRDSLEDTLADLETEQERAQQAQREAEERADQLEDEREQLQETRAEIERQNERLVAEA 176
                                       7899***********************************************99987655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.59
                              ADIP  32 eniaaiinviysLlqardrdleqreslnetirkleaeierlqskierlktqleqlerela.lvqakerqlekklktl 107
                                       e iaai    +++l + ++ +     ++  +++++ e+e  +++i+  +++++++ +e+a  + +++ +l ++ ++ 
  gi|336252564|ref|YP_004595671.1| 202 EAIAAIATSFNEMLDRMSETMVDVRGSANAVEEISVELEDSSAEIRTASREVADSVQEIAdGAAEQTDDLDAAAAEV 278
                                       556677777788888888888888888899999999**********************9988888888887766655 PP

                              ADIP 108 e 108
                                       +
  gi|336252564|ref|YP_004595671.1| 279 S 279
                                       4 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.5
                              ADIP  66 eaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqi 128
                                       + e ++ + +i   ++++++l+ e   + a+ +++  +l + ++++ ++++el+r   ++++i
  gi|336252564|ref|YP_004595671.1| 285 TEEVASTTGEIADQSESVTELTEEGREAAAEAAENIDELVENTETVVETADELTRETEQIEEI 347
                                       556667777888888888888888888888888888888889999999999999988777765 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.008
                              ADIP  54 qreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqikt 130
                                       + es  ++ ++  +ei   +s+i +  t + +le++l++   +  q   ++++  +++  +++++q l  +++++++
  gi|336252564|ref|YP_004595671.1| 403 TLESIRDRTETTANEIGEVESNITSTATIVDDLESRLETIAGEVEQVDGSIQQIASTADDQADSAQELSAIVDDVAA 479
                                       6789999999999******************************************************9999999975 PP

                              ADIP 131 qyahelk 137
                                        +++e+ 
  gi|336252564|ref|YP_004595671.1| 480 -VSNETA 485
                                       .444444 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.4       1.1   3.7e+02      27      60 ..     134     167 ..     100     201 .. 0.68
   2 ?    6.9   0.1     0.025       8.4      17      61 ..     212     260 ..     202     266 .. 0.77
   3 ?    4.1   1.0      0.19        63      16      55 ..     267     306 ..     255     311 .. 0.76
   4 ?    5.6   3.2     0.063        21      25      63 ..     318     356 ..     310     364 .. 0.89
   5 ?    4.1   5.7      0.19        64      13      64 ..     432     480 ..     380     486 .. 0.74
   6 ?    2.9   0.8      0.45   1.5e+02       6      55 ..     470     513 ..     466     529 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1.1
                           NPV_P10  27 vddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                        ++ q+  ++ +e  ++L++  +qL+e  +++e 
  gi|336252564|ref|YP_004595671.1| 134 QERAQQAQREAEERADQLEDEREQLQETRAEIER 167
                                       4444444555555555555555555555554443 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.025
                           NPV_P10  17 ddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet....kvenI 61 
                                       ++ +d +++ + dv+   + v+e++ +L++ sa++ + +     +v++I
  gi|336252564|ref|YP_004595671.1| 212 NEMLDRMSETMVDVRGSANAVEEISVELEDSSAEIRTASRevadSVQEI 260
                                       566788889999*********************9998777222244444 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.19
                           NPV_P10  16 vddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaele 55 
                                         d +da  ++v d+++  ++v   + ++ +qs++++el 
  gi|336252564|ref|YP_004595671.1| 267 QTDDLDAAAAEVSDLSAATEEVASTTGEIADQSESVTELT 306
                                       4566777888888888888888888888888888888886 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.063
                           NPV_P10  25 qqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       +++d++ en ++v e  ++L + ++q++e+ + +++I d
  gi|336252564|ref|YP_004595671.1| 318 ENIDELVENTETVVETADELTRETEQIEEIIALIDDIAD 356
                                       578999********************9999999999987 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.19
                           NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                       + +++++++ +  +v++v+  +++   + +  d+q+++ +el++ v+++  +
  gi|336252564|ref|YP_004595671.1| 432 VDDLESRLETIAGEVEQVDGSIQQ---IASTADDQADSAQELSAIVDDVAAV 480
                                       445555666666666666665544...6677777777777777788777766 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.45
                           NPV_P10   6 LlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaele 55 
                                       L  I +d++av++      qqv+  +e+          +d+ s++ ++l 
  gi|336252564|ref|YP_004595671.1| 470 LSAIVDDVAAVSNETATKAQQVAAASEETSA------TIDSVSTTATDLG 513
                                       5567777777777776666666555444333......3444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2615  (0.145853); expected 358.6 (0.02)
Passed bias filter:                      913  (0.0509231); expected 358.6 (0.02)
Passed Vit filter:                       213  (0.0118802); 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):              53  [number of targets reported over threshold]
# CPU time: 2.26u 0.42s 00:00:02.68 Elapsed: 00:00:00.62
# Mc/sec: 2658.44
//
Query:       gi|336252565|ref|YP_004595672.1|  [L=596]
Description: GAF sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for 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-16   59.7   0.0    6.4e-16   58.9   0.0    1.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.8e-13   49.7   3.4    3.8e-13   49.3   2.0    2.0  2  HisKA        His Kinase A (phospho-acceptor) domain
    1.2e-06   28.9   1.6    2.9e-05   24.4   0.0    3.1  3  GAF_2        GAF domain
    1.3e-06   28.7   0.0    0.00041   20.7   0.0    2.7  2  GAF_3        GAF domain
    2.5e-06   28.1   0.0    1.4e-05   25.7   0.0    2.2  1  GAF          GAF domain
  ------ inclusion threshold ------
      0.063   13.1   0.0       0.11   12.3   0.0    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
       0.17   11.4   0.4       0.39   10.3   0.0    1.8  2  HisKA_4TM    Archaeal 4TM region of histidine kinase


Domain annotation for each model (and alignments):
>> 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 !   58.9   0.0   2.5e-19   6.4e-16       2     106 ..     471     565 ..     470     571 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 2.5e-19
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlG 77 
                                       d+ rL+q++ nlv Nav+++  +  i ve +    d  +  eD+G G+p++ ++++fe  +s         ggtGlG
  gi|336252565|ref|YP_004595672.1| 471 DPGRLQQALENLVRNAVEHNDAGVGILVEGT----DDGFALEDDGAGVPPDRRERVFEeGYSG-------AGGTGLG 536
                                       899***************9444445566655....789999*****************77777.......9****** PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEE CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftf 106
                                       lsiv+ +v+ +g +++v++ +++G +f +
  gi|336252565|ref|YP_004595672.1| 537 LSIVETVVSAHGWDVSVTDGKQGGARFEI 565
                                       ******9999****************987 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   2.0   1.5e-16   3.8e-13       2      66 ..     373     432 ..     372     433 .. 0.94
   2 ?   -3.0   0.0       3.1   7.8e+03      33      48 ..     471     486 ..     459     487 .. 0.75

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 1.5e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l+rf++ ++H+Lr+PL++i+g+a+++ +    teel + le i   a+r++++++dlL l+r +a
  gi|336252565|ref|YP_004595672.1| 373 LERFASVISHDLRNPLNVISGTADLIAE----TEELHR-LEHIAAAADRMESMIDDLLLLARDGA 432
                                       78************************88....588888.***********************986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
                                       -HSSCHHHHHHHHHHH CS
                             HisKA  33 lteelkeyletiesea 48 
                                        + +l+++le ++++a
  gi|336252565|ref|YP_004595672.1| 471 DPGRLQQALENLVRNA 486
                                       4578899999888875 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.6     4e+03       3      21 ..     153     172 ..     151     220 .. 0.72
   2 !   24.4   0.0   1.1e-08   2.9e-05      82     138 .]     302     358 ..     292     358 .. 0.89
   3 ?    2.1   0.0     0.088   2.3e+02       4      45 ..     475     518 ..     473     544 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHS.S.. CS
                             GAF_2   3 dleelldlvldelvel.gaa 21 
                                       +++++  +vl+ ++ l gaa
  gi|336252565|ref|YP_004595672.1| 153 SISDVSGTVLEIARSLmGAA 172
                                       67777777777777755643 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1.1e-08
                                       HHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  82 glpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       +  ++++gl + lavP++ + ++ Gvl+++ ++++++ ++  ++L++l+e+i+  ie
  gi|336252565|ref|YP_004595672.1| 302 HPYLERRGLEALLAVPIVIDWELRGVLVVGQDHRRPWPDRLCRQLRTLGELIGHTIE 358
                                       344889999999*****************9999999*****************9997 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.088
                                       HHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEE..EEEES-TT CS
                             GAF_2   4 leelldlvldelvel.gaalgyillvdddgglrla..awgeaeee 45 
                                       l++ l+++++ +ve  +a +g++++  ddg + l+   +g ++++
  gi|336252565|ref|YP_004595672.1| 475 LQQALENLVRNAVEHnDAGVGILVEGTDDG-FALEddGAGVPPDR 518
                                       789999********9458899988866544.44445433333333 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.011        28      17      47 ..     191     221 ..     183     280 .. 0.67
   2 !   20.7   0.0   1.6e-07   0.00041      80     129 .]     310     359 ..     297     359 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                             GAF_3  17 lgaevgalllldedgnklqvaagwdgkpals 47 
                                       l+a+++ ++ +de+  +l ++++wd++ +  
  gi|336252565|ref|YP_004595672.1| 191 LNADRCLVFDYDEEAARLEPTHAWDAARSGA 221
                                       799*********************6654443 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.6e-07
                             GAF_3  80 draalavPLvagr.qviGvlalastkprafdaedlelleslArqiataier 129
                                       ++a+lavP+v+ + +++Gvl++++++ r++ ++  + l++l+ +i+  ier
  gi|336252565|ref|YP_004595672.1| 310 LEALLAVPIVI-DwELRGVLVVGQDHRRPWPDRLCRQLRTLGELIGHTIER 359
                                       6789*******.66***********************************98 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   5.7e-09   1.4e-05      13     131 ..     187     355 ..     175     357 .. 0.62

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.7e-09
                                       HHHHHTESEEEEEE..................................EEETTEEECEEEEECCEEEETTSHHHH.. CS
                               GAF  13 lrellgadrvalyl..................................pdydGlhydipqasrwlfmkngrgicg.. 53 
                                       ++  l+adr++++                                   pd dG +  +++ ++ +++ +++ + g  
  gi|336252565|ref|YP_004595672.1| 187 IGARLNADRCLVFDydeeaarlepthawdaarsgadspesaptasasvPDVDG-T--LSADASDVEPMEPSAFPGfe 260
                                       677899******88666666666555555444444444444444444433333.1..11111112222222222244 PP

                                       HHHHHSSSEEESTGG.......TSTTHHTT...............HHHHHHHHTTESEEEEEEEEETTEEEEEEEEE CS
                               GAF  54 qvlatgqplvipdst.......pdprfaqy...............nrrdllenmgirsslvvPlvndgelwGllvlh 108
                                         l++ ++  ip +t       p      +                 + +le+ g  ++l+vP+v d el G+lv+ 
  gi|336252565|ref|YP_004595672.1| 261 DSLREYDAHAIPPTTdrpeidvP------DgfigdlgpneggeagDTHPYLERRGLEALLAVPIVIDWELRGVLVVG 331
                                       66666666666654423222211......12333356666677776789999************************* PP

                                       E.SSSCSHHHHHHHHHHHHHHHHH CS
                               GAF 109 n.psppftreelellqvladqvav 131
                                       + +++p+ +  ++ l++l+++++ 
  gi|336252565|ref|YP_004595672.1| 332 QdHRRPWPDRLCRQLRTLGELIGH 355
                                       *74447***********9999875 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 ?   12.3   0.0   4.3e-05      0.11       4      54 ..     476     523 ..     474     572 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                       HATPase_c_3   4 ekAlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknal 54 
                                       ++Al  lv+N+++ +   v i v+  +   + +  eDdG+G++++  ++++
  gi|336252565|ref|YP_004595672.1| 476 QQALENLVRNAVEHNDAGVGILVEGTD---DGFALEDDGAGVPPDRRERVF 523
                                       68999*******************976...7************99777666 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00015      0.39     133     163 ..     369     399 ..     348     400 .. 0.72
   2 ?   -3.5   0.1       2.6   6.6e+03       6      31 ..     534     559 ..     533     562 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                         HisKA_4TM 133 isdalafvndlirhdlrndlvvirgyaeaie 163
                                         + l    ++i hdlrn l+vi g a+ i+
  gi|336252565|ref|YP_004595672.1| 369 KNEHLERFASVISHDLRNPLNVISGTADLIA 399
                                       444555556789***************9986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.6
                         HisKA_4TM   6 vfGlvlaaaaivhhgaeaaaidsvrG 31 
                                       ++Gl ++ + +  hg +++  d+ +G
  gi|336252565|ref|YP_004595672.1| 534 GLGLSIVETVVSAHGWDVSVTDGKQG 559
                                       67999999999999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); 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 0.28s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 4274.19
//
Query:       gi|336252566|ref|YP_004595673.1|  [L=272]
Description: Prephenate dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-46  159.0   0.0    1.3e-46  158.7   0.0    1.1  1  PDT       Prephenate dehydratase
    5.3e-06   26.1   0.0    1.7e-05   24.5   0.0    1.9  1  ACT       ACT domain


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 !  158.7   0.0   1.4e-50   1.3e-46       3     180 ..       5     174 ..       3     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: 158.7 bits;  conditional E-value: 1.4e-50
                                       EES-TTSHHHHHHCCCS.....EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEEEEE CS
                               PDT   3 ylGpegtyshqAalkvfkaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkivgEvv 79 
                                        lGpegtysh+A+ +v+  +d  +   +s++++++av+ ge + +v+PiENs+eGsV+e+lD L++  d+ +v+E+v
  gi|336252566|ref|YP_004595673.1|   5 TLGPEGTYSHRATTAVA--DDDAIDFRQSVTSIVDAVAGGEYERGVIPIENSIEGSVTESLDALAE-YDVAVVREIV 78 
                                       69************999..666677789**************************************.99******** PP

                                       EE---EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHHHH. CS
                               PDT  80 lpiehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaael. 155
                                        pi+h+Lla+      e  +v Sh+qal+Qcr +Le+++p+++ +av+sta+ ++   a++d ++a i++   ae  
  gi|336252566|ref|YP_004595673.1|  79 TPIRHALLAQGP----EFDTVASHSQALAQCRAYLEREYPDATLEAVASTAQGVEF--AREDPSVAGIGHPANAENg 149
                                       *******98764....59**************************************..99*********98888762 PP

                                       TT-EEEECS-SS-S--EEEEEEEEE CS
                               PDT 156 yglkvleeniedkknntTRFlvlak 180
                                        +l+vl+e+i+d++ n TRF+ +a 
  gi|336252566|ref|YP_004595673.1| 150 TNLEVLAEDIQDRDSNATRFFAIAP 174
                                       6********************9985 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.9e-09   1.7e-05      11      63 ..     196     248 ..     188     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.9e-09
                                       TTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHH CS
                               ACT  11 PGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealk 63 
                                       PGlL +++  +a+r+iN +++e+r+s+ +++++vf ++++       ++eal+
  gi|336252566|ref|YP_004595673.1| 196 PGLLLELLEPFAQRDINMARVESRPSGQRLGDYVFHIDIEAGLYERRTKEALE 248
                                       9****************************999999988877444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2148.01
//
Query:       gi|336252567|ref|YP_004595674.1|  [L=141]
Description: CBS domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   84.8   3.4    1.5e-11   44.6   0.4    2.1  2  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 !   44.6   0.4   8.4e-16   1.5e-11       8      53 ..      10      54 ..       3      57 .. 0.88
   2 !   41.3   0.2   8.9e-15   1.6e-10       1      54 [.      67     120 ..      67     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 8.4e-16
                                      SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  8 dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                      dvvt++pdt+l+ +++++ e++v+++ +V e++++vGivt+rD++ 
  gi|336252567|ref|YP_004595674.1| 10 DVVTASPDTDLGTIAQRLSENNVGSVVIV-ENDEPVGIVTDRDIAL 54
                                      89****************9999****668.8999**********85 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 8.9e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       ++d+mt  + t+p d++  e+ e ++e++ +r+PVVde+gkl Givtl Dl+  
  gi|336252567|ref|YP_004595674.1|  67 AEDVMTGSLTTIPADADPIEISEAIKEENARRFPVVDENGKLTGIVTLDDLVAT 120
                                       579**********************999999********************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1062.75
//
Query:       gi|336252568|ref|YP_004595675.1|  [L=151]
Description: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen [Halopiger xanaduensis SH-6]
Scores for 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-29  101.5   0.0    3.5e-29  101.3   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
      5e-18   65.2   0.0    5.6e-18   65.1   0.0    1.0  1  Redoxin     Redoxin
    8.1e-06   25.9   0.0    1.4e-05   25.2   0.0    1.3  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme
     0.0083   15.7   0.0       0.01   15.4   0.0    1.1  1  DUF899      Bacterial protein of unknown function (DUF899)


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 !  101.3   0.0   7.7e-33   3.5e-29       1     123 [.       5     123 ..       5     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 7.7e-33
                                       TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfi 77 
                                       +gd ap++ ++n+dg++v+l+ +   p+vl+fyp+d++p+C  e+ +++++ye ++++gv+v+gvs+d ++sh++f+
  gi|336252568|ref|YP_004595675.1|   5 IGDDAPSVAAQNQDGDDVRLE-FDE-PTVLYFYPRDDTPGCSIEANQFQREYETYRDAGVDVYGVSTDGVDSHRSFC 79 
                                       89*****************85.555.9************************************************** PP

                                       HH-H.SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  78 ekeslnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                       e+e+l+f+ll+D++g+va a++v     g+a r+tf++  +gk+++
  gi|336252568|ref|YP_004595675.1|  80 EAEGLEFDLLADPDGAVAAAFDVDVRG-GAAARTTFFLA-DGKVQA 123
                                       ***********************9876.*********98.588886 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0   1.2e-21   5.6e-18       3     142 ..       6     137 ..       4     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 1.2e-21
                                       TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHH CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkef 79 
                                       gd aP++  ++  +dg +v l+   + ++v++f+p+ ++P Cs e+++++  +e +++ gvdv +v++d  +  ++f
  gi|336252568|ref|YP_004595675.1|   6 GDDAPSVAAQN--QDGDDVRLEF--DEPTVLYFYPRDDTPGCSIEANQFQREYETYRDAGVDVYGVSTDGVDSHRSF 78 
                                       899***99766..********87..7788******************888888999********************* PP

                                       HHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT.STTS CS
                           Redoxin  80 wgkeglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet.eesn 142
                                       +++egl f +l+D+++a+++a++++++       ++ r++ + +dgkv +++  ++p +  ++ 
  gi|336252568|ref|YP_004595675.1|  79 CEAEGLEFDLLADPDGAVAAAFDVDVRGG-----AAARTTFFLADGKVQAVYESVDPDGhAREV 137
                                       ***********************996654.....999****************99995554444 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 !   25.2   0.0   3.2e-09   1.4e-05       2      53 ..      50     102 ..      49     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.2e-09
                        AhpC-TSA_2   2 Lsrdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalgl 53 
                                       ++r+ +++++agv++++++ + + s ++F++ +g  f+l++Dp++++ +a+ +
  gi|336252568|ref|YP_004595675.1|  50 FQREYETYRDAGVDVYGVSTDGVdSHRSFCEAEGLEFDLLADPDGAVAAAFDV 102
                                       68999******************77********************99988866 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.3e-06      0.01      85     177 ..      40     127 ..      32     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-06
                            DUF899  85 CpgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsleeeqaseelpgl 161
                                        pgCs+ a++++++ +  + ++v +  vs   +++  ++ +  G ++++ ++ +  + + f v ++       + + 
  gi|336252568|ref|YP_004595675.1|  40 TPGCSIEANQFQREYETYRDAGVDVYGVSTDGVDSHRSFCEAEGLEFDLLADPDGAVAAAFDVDVRG-----GAAAR 111
                                       58************************************************************97775.....47777 PP

                            DUF899 162 svflrddgrvfhtYst 177
                                       ++f+  dg+v   Y +
  gi|336252568|ref|YP_004595675.1| 112 TTFFLADGKVQAVYES 127
                                       8899999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); 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:                         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 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1186.29
//
Query:       gi|336252569|ref|YP_004595676.1|  [L=139]
Description: heat shock protein Hsp20 [Halopiger xanaduensis SH-6]
Scores for 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   66.4   0.0    2.6e-18   66.0   0.0    1.1  1  HSP20       Hsp20/alpha crystallin family
    2.7e-13   49.3   0.0    4.4e-13   48.6   0.0    1.4  1  ArsA_HSP20  HSP20-like domain found in ArsA
     0.0031   17.6   0.8     0.0043   17.1   0.8    1.3  1  GvpH        GvpH
  ------ inclusion threshold ------
       0.16   13.0   0.0       0.21   12.6   0.0    1.2  1  CS          CS domain
       0.19   12.2   0.0       0.36   11.3   0.0    1.4  1  PIH1_CS     PIH1 CS-like 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 !   66.0   0.0   7.3e-22   2.6e-18       2     101 ..      39     138 ..      38     139 .] 0.91

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 7.3e-22
                                       --SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--....---TT----SS---EEEEEE--STTB-TTT-EEEE CS
                             HSP20   2 ikeeeeefevkldvpglkkeelkvkvednrvlvkgehe..eeeedekglikerssrkFsrkftLPenvdadkvkasl 76 
                                       + ++ +e+ v++d+pg +++++++++ ++++  ++++e   e  ++++l++er+++  +r+++LPe v++d v+a +
  gi|336252569|ref|YP_004595676.1|  39 VADTGDEYVVTADLPGYDTDDIDLTLSEGTLRLEANREdeREYAEGEYLRRERTRKTANRRIRLPEPVEEDGVSAGY 115
                                       67899*********************************766777999****************************** PP

                                       ETTEEEEEEEBSS--..-------- CS
                             HSP20  77 kdGvLtvtvpkkepekkkkerkiqi 101
                                       +dGvLtv +pk    +  ++++i+i
  gi|336252569|ref|YP_004595676.1| 116 EDGVLTVRLPKIGGGN--ESKEIDI 138
                                       ***********99995..5666665 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 !   48.6   0.0   1.2e-16   4.4e-13       1      63 []      43     124 ..      43     124 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.2e-16
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig....................nfrRqitLPsvlarkevtsAkfedg 57 
                                       +deyv+++dLP+ d+++idl+ s+ +L ++++                      +R+i LP+ + ++ v sA++edg
  gi|336252569|ref|YP_004595676.1|  43 GDEYVVTADLPGYDTDDIDLTLSEGTLRLEANredereyaegeylrrertrkTANRRIRLPEPVEEDGV-SAGYEDG 118
                                       69************************************************99999************99.******* PP

                        ArsA_HSP20  58 vLeIrF 63 
                                       vL++r+
  gi|336252569|ref|YP_004595676.1| 119 VLTVRL 124
                                       ****96 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.8   1.2e-06    0.0043      96     130 ..      39      71 ..       8      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                              GvpH  96 asddsdelvvvadlpGvtdedvdvaletdeqaltl 130
                                        +d +de vv adlpG   +d+d +l   e++l l
  gi|336252569|ref|YP_004595676.1|  39 VADTGDEYVVTADLPGYDTDDIDLTLS--EGTLRL 71 
                                       5799********************998..555555 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     6e-05      0.21       7      76 .]      41     126 ..      35     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6e-05
                                       EETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECE................BSS-BETTTEEEEE CS
                                CS   7 QtldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliege................LfgpIdpeesswti 65 
                                        t de vvt  ++++  +++d++++++e +l+++  ++ e+++ ege                L +p++ +  s   
  gi|336252569|ref|YP_004595676.1|  41 DTGDEYVVTADLPGY--DTDDIDLTLSEGTLRLEAnREdEREYAEGEylrrertrktanrrirLPEPVEEDGVSAGY 115
                                       6788899*******9..******************988899999****99999999999999999999999888877 PP

                                       ETTEEEEEEEB CS
                                CS  66 eskkveitLkK 76 
                                       e+  + + L K
  gi|336252569|ref|YP_004595676.1| 116 EDGVLTVRLPK 126
                                       77777776655 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0001      0.36      31      96 ..      44     124 ..      38     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                           PIH1_CS  31 kelaieielPllksikevklrvgerrlel...................eskkakyfLslkLpYpvdedkveAkFvkk 88 
                                       +e++++ +lP++  + +++l ++e +l l                      ++    +++Lp pv+ed v+A ++  
  gi|336252569|ref|YP_004595676.1|  44 DEYVVTADLPGY-DTDDIDLTLSEGTLRLeanredereyaegeylrreR-TRKTANRRIRLPEPVEEDGVSAGYED- 117
                                       699*********.7899*********************99999998743.3346666899************9964. PP

                           PIH1_CS  89 tklLkvkl 96 
                                          L+v+l
  gi|336252569|ref|YP_004595676.1| 118 -GVLTVRL 124
                                       .4566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1139.20
//
Query:       gi|336252570|ref|YP_004595677.1|  [L=265]
Description: hypothetical protein Halxa_1165 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.26   11.1   0.1       0.26   11.1   0.1    2.4  2  LapA_dom  Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   1.4e-05      0.26      27      61 ..       5      39 ..       1      42 [. 0.89
   2 ?   -2.3   4.0      0.22   3.9e+03      25      36 ..     251     262 ..     248     265 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.4e-05
                          LapA_dom 27 fgiGallgwllslwsylrlrrelrrlkkkikklek 61
                                      f++ + +g+ l+ w+ l   relr  +  i++le 
  gi|336252570|ref|YP_004595677.1|  5 FVLAVAAGFMLFGWMALSSARELRDRQATIDELES 39
                                      7888899999999********************96 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.22
                          LapA_dom  25 vafgiGallgwl 36 
                                       v fg+G+l+++l
  gi|336252570|ref|YP_004595677.1| 251 VLFGLGVLVAIL 262
                                       789*****9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2006.22
//
Query:       gi|336252571|ref|YP_004595678.1|  [L=898]
Description: leucyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for complete 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-72  244.9   3.5    3.5e-26   91.6   0.6    4.9  4  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    9.5e-55  185.0   0.0      2e-54  183.9   0.0    1.5  2  tRNA-synt_1_2   Leucyl-tRNA synthetase, Domain 2
    7.5e-40  136.9   1.4    1.9e-22   79.6   0.0    4.6  5  tRNA-synt_1g    tRNA synthetases class I (M)
    4.8e-18   65.6   0.0    8.6e-18   64.7   0.0    1.4  1  Anticodon_1     Anticodon-binding domain of tRNA
    5.1e-09   35.9   0.1    1.9e-06   27.5   0.0    2.4  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
    1.1e-05   24.6   0.0     0.0015   17.6   0.0    2.7  2  tRNA-synt_1f    tRNA synthetases class I (K)
     0.0012   18.8   4.2       0.38   10.8   0.3    2.6  2  DZR             Double zinc ribbon
     0.0089   15.4   5.9          2    8.0   0.1    4.0  4  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
       0.11   12.6   7.9        3.4    7.9   4.8    3.3  2  Zn-ribbon_8     Zinc ribbon domain
       0.17   11.8   0.2       0.44   10.5   0.1    1.7  1  Phage-MuB_C     Mu B transposition protein, C terminal
       0.18   11.1   0.1       0.53    9.6   0.0    1.8  2  tRNA-synt_1b    tRNA synthetases class I (W and Y)
        0.5   10.4   7.1       0.91    9.6   0.0    3.6  4  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
          5    6.7  11.5        4.7    6.8   0.4    3.6  3  TF_Zn_Ribbon    TFIIB zinc-binding


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 !   91.6   0.6   2.5e-29   3.5e-26       2     179 ..      15     172 ..      14     176 .. 0.92
   2 !   22.1   0.1   2.8e-08   3.8e-05     361     413 ..     174     226 ..     168     230 .. 0.91
   3 !   36.6   0.0   1.1e-12   1.6e-09     204     349 ..     262     421 ..     255     429 .. 0.74
   4 !   91.0   0.0   3.8e-29   5.3e-26     416     601 ..     429     626 ..     424     627 .. 0.78

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 2.5e-29
                       tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaiea 78 
                                       ++e W+e+dv+++    + + ++++l    Py  G+lH+Gh+ + t+ d   r++rm+G +vl+ +GwD  Gl+ e 
  gi|336252571|ref|YP_004595678.1|  15 WQEAWDEADVYRTP--DDVDDPTYVLGMY-PYPSGKLHMGHVRNYTITDAYARFRRMQGDHVLHPMGWDAFGLPAEN 88 
                                       7899********99..7777999999875.7*******************************************997 PP

                       tRNA-synt_1  79 kvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgl 155
                                       + +++                   + r+w    ++++r+q++ +G  +D+dre  T  +e+    ++ f r++++gl
  gi|336252571|ref|YP_004595678.1|  89 AAKER-----------------DTNPRDWTFDCIDTMRDQMESMGFGYDWDREIATCVPEYYRWNQWLFERFHEEGL 148
                                       64333.................245699************************************************* PP

                       tRNA-synt_1 156 iyrgkklvnwstklktalselEve 179
                                       + r+   vnw+++++t+l++  ve
  gi|336252571|ref|YP_004595678.1| 149 VERRDAEVNWCPHCETVLADEQVE 172
                                       *******************98886 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 2.8e-08
                       tRNA-synt_1 361 svpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswl 413
                                       +  +c+r ++p++ r  eqWf +++e ad++l+a+++ +  p+s +++  +w+
  gi|336252571|ref|YP_004595678.1| 174 EAELCWRCDTPVETRELEQWFLKITEYADELLEAIDDLEGWPNSVRQMQRNWI 226
                                       5678********************************************99998 PP

  == domain 3  score: 36.6 bits;  conditional E-value: 1.1e-12
                       tRNA-synt_1 204 iaTTtPeTllgdtavavnpeldyvitkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiad 280
                                       + TT+  T+ g t  a++p+  + i++e l   +  ++ ++++e   +   de     +g+++++p+++ +ip+ + 
  gi|336252571|ref|YP_004595678.1| 262 AFTTRIDTIHGATFFALAPD--HPISEE-LAEENEDVRRFIEEEA--DPDGDEPNGVETGLTATNPVTGDEIPVFVA 333
                                       67888888888888888888..333333.2222223333333332..333444444447999*************** PP

                       tRNA-synt_1 281 dyvdkeaGtGvVkiaPahdedDyevgkkynlevinildedgtlteea...................aefeglkvfda 338
                                       d+v ++ GtG+    P+hde D++ ++k++l+++ ++  + +  ee                    ++++gl+ + a
  gi|336252571|ref|YP_004595678.1| 334 DFVLSDVGTGALMAVPGHDERDHAFAEKHDLDIVPVIAPEPEDGEEPqapdvedaaytedgvlinsGDYSGLDSETA 410
                                       *******************************7766666555444444456778888888889***9*********** PP

                       tRNA-synt_1 339 rkkvveelkek 349
                                       r+ ++e+++  
  gi|336252571|ref|YP_004595678.1| 411 RERLTEDIDSA 421
                                       ***99998765 PP

  == domain 4  score: 91.0 bits;  conditional E-value: 3.8e-29
                       tRNA-synt_1 416 iqdWciSRqrwWGhriplfvsketeevvvreelkelv.agreeeeaekkalekeakdkl..kkekgelekdedvlDv 489
                                        +dW iSRqr+WG++ip+   ++ + v+v ee   ++  +  +++++  ++++e k++   +++  + ++++d++D+
  gi|336252571|ref|YP_004595678.1| 429 LRDWGISRQRYWGTPIPVVHCDDCGPVTVPEEDLPVElPEFINTTGNPLDAAEEWKETTcpECG-ADATRETDTMDT 504
                                       68***********************999987544433034445555666666677766654444.45789******* PP

                       tRNA-synt_1 490 WFsSgswpfstl.....gypeedteelkkffpadmlleGlDiirgWvarlillslaltgse......Pfkevlvhgl 555
                                         +S+  +   +     + p+  +e  ++  p d ++ G+      +  + +++  l ++e      Pf+++l +g+
  gi|336252571|ref|YP_004595678.1| 505 FVDSSWYFLRYVspgleDAPFD-RERANDWMPVDQYVGGIEHAVMHLLYSRFFTKVLADHEglehrePFENLLAQGM 580
                                       ****877665551111144444.7888889***********99988887777777777666677777*********9 PP

                       tRNA-synt_1 556 vrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                       v   eG KmSKs+gNv++p+ ++++ygad  Rl+++  ++  rd ++
  gi|336252571|ref|YP_004595678.1| 581 VQ-LEGEKMSKSKGNVVSPQRIVEEYGADTARLFMMqAAQPERDFDW 626
                                       86.68*******************************88888999877 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 !  183.9   0.0   1.4e-57     2e-54       1     183 [.     223     417 ..     223     419 .. 0.92
   2 ?   -4.0   0.0       6.4   8.8e+03     154     177 ..     665     688 ..     653     693 .. 0.63

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 1.4e-57
                     tRNA-synt_1_2   1 rnWIGrseGleiefkveesee...............klevfttrpdtlfGvtfvalapehplveklaekkkelaafi 62 
                                       rnWIGr+ G e++f+v+e  +                ++ fttr dt++G+tf+alap+hp+ e+lae+++++++fi
  gi|336252571|ref|YP_004595678.1| 223 RNWIGRQYGSEVDFEVSEAPRassgrgegnepreygPVTAFTTRIDTIHGATFFALAPDHPISEELAEENEDVRRFI 299
                                       8****************9954478899999999999***************************************** PP

                     tRNA-synt_1_2  63 eevkkksesereletkekeGvftglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqv 139
                                       ee ++ +  e        +Gv+tgl+a++P+tg++ip++va++vl++ gtga+mavP+hd+rD++Fa+k++l+i +v
  gi|336252571|ref|YP_004595678.1| 300 EEEADPDGDEP-------NGVETGLTATNPVTGDEIPVFVADFVLSDVGTGALMAVPGHDERDHAFAEKHDLDIVPV 369
                                       99887777765.......9********************************************************** PP

                     tRNA-synt_1_2 140 ikpedee.kkle...eseeayteegilvnsgefdglkskeakekiakk 183
                                       i+pe e+ ++ +   ++++ayte+g+l+nsg+++gl+s++a+e++++ 
  gi|336252571|ref|YP_004595678.1| 370 IAPEPEDgEEPQapdVEDAAYTEDGVLINSGDYSGLDSETARERLTED 417
                                       **87766544442226999***********************998875 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 6.4
                     tRNA-synt_1_2 154 eayteegilvnsgefdglkskeak 177
                                       e   e +i + ++e+d+l++++a 
  gi|336252571|ref|YP_004595678.1| 665 ENEIEATIAIATDEYDDLTFNKAL 688
                                       334456677777777777776665 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 !   79.6   0.0   1.4e-25   1.9e-22       6     141 ..      40     177 ..      35     180 .. 0.92
   2 !    9.1   0.0   0.00034      0.47     169     219 ..     178     227 ..     174     232 .. 0.90
   3 !    4.9   0.0    0.0067       9.3     214     238 ..     421     445 ..     405     453 .. 0.78
   4 ?   -2.5   0.1       1.2   1.7e+03     136     150 ..     485     499 ..     480     504 .. 0.78
   5 !   39.0   0.0     3e-13   4.1e-10     303     372 ..     559     632 ..     544     642 .. 0.83

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 1.4e-25
                                       --B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT CS
                      tRNA-synt_1g   6 alpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkkln 82 
                                         pY++gklH+Gh++++ ++D++aR++r++g++vl+  g D++G p e +A++++++p++ + +  +++++++++++
  gi|336252571|ref|YP_004595678.1|  40 MYPYPSGKLHMGHVRNYTITDAYARFRRMQGDHVLHPMGWDAFGLPAENAAKERDTNPRDWTFDCIDTMRDQMESMG 116
                                       679**********************************************************************9966 PP

                                       ---..SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE.... CS
                      tRNA-synt_1g  83 isf..dkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPk 141
                                         +  d  + t   e ++  q +f++++e+gl+++++ e+ +cp++e+ l+d++veg+   
  gi|336252571|ref|YP_004595678.1| 117 FGYdwDREIATCVPEYYRWNQWLFERFHEEGLVERRDAEVNWCPHCETVLADEQVEGEAEL 177
                                       655116788999*********************************************8655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00034
                                       ........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHH CS
                      tRNA-synt_1g 169 saisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlk 219
                                       +  +++  e++e e++f+k+ +++++l e i  + + ++++v+++ ++w+ 
  gi|336252571|ref|YP_004595678.1| 178 CWRCDTPVETRELEQWFLKITEYADELLEAI-DDLEGWPNSVRQMQRNWIG 227
                                       77899999***********************.77779************96 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0067
                                       H.HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 214 vkewlkegLkdlaisrdldwGipvP 238
                                       ++e  + +L+d+ isr+  wG p+P
  gi|336252571|ref|YP_004595678.1| 421 AEEAKQYQLRDWGISRQRYWGTPIP 445
                                       55566778****************9 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.2
                                       EE........-TTS- CS
                      tRNA-synt_1g 136 egtCPkckseeargd 150
                                       e tCP+c+++  r++
  gi|336252571|ref|YP_004595678.1| 485 ETTCPECGADATRET 499
                                       689*****9987765 PP

  == domain 5  score: 39.0 bits;  conditional E-value: 3e-13
                                       HHHH....TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHH CS
                      tRNA-synt_1g 303 illg....aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfv 372
                                       +l +    ++ +  +++ a++++++eg+K+SkS+g+vv ++ ++e++ ad+ R +++++a+ ++D+d+s+e + 
  gi|336252571|ref|YP_004595678.1| 559 VLADheglEHREPFENLLAQGMVQLEGEKMSKSKGNVVSPQRIVEEYGADTARLFMMQAAQPERDFDWSEEGVR 632
                                       5544444344455689****************************************************988654 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 !   64.7   0.0   6.2e-21   8.6e-18       2     146 ..     662     783 ..     661     792 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 6.2e-21
                       Anticodon_1   2 rwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrlla 78 
                                       r++ +e++ +++ +t+ y+++ fnka+++ +++ + +l + y e ++p+             e++   l++++rll+
  gi|336252571|ref|YP_004595678.1| 662 RYVENEIEATIAIATDEYDDLTFNKALRETQDL-VRTL-RQYAEYAEPHA------------ETYERGLSAVVRLLS 724
                                       8999****************************5.8889.9********98............99************* PP

                       Anticodon_1  79 PfmPfitEelwqreeeelgkkesimlaewpekaeelekeleeeevellkeivkairk.lrselkikpss 146
                                       P++P++tEel+    ++lg++e+++ a+wp +a   + ++    ve ++++v+  r+ +r +++++  +
  gi|336252571|ref|YP_004595678.1| 725 PVAPHLTEELY----DRLGHDEFVVDAAWP-TA---TVDR--DRVEKRRRLVENTREdVRDIIEVAGIE 783
                                       ***********....***************.55...3332..234444445555544466666655544 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 !    5.8   0.1    0.0055       7.6      21      47 ..      46      72 ..      32      77 .. 0.78
   2 !   27.5   0.0   1.4e-09   1.9e-06     227     298 ..     561     633 ..     541     636 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0055
                                      S--BHHHHHHHHHHHHHHHHHHHTT-E CS
                      tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYd 47
                                       + h+Gh+R++ ++D  +r+ +++g +
  gi|336252571|ref|YP_004595678.1| 46 GKLHMGHVRNYTITDAYARFRRMQGDH 72
                                      578**************9998877755 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 1.4e-09
                                       HHHHHHSSS--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS.-TTS-EEE-HHHHHH CS
                      tRNA-synt_1e 227 aqseaafdkqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsa.hyrsqldfkeellee 298
                                       a +e +  ++  +  l +g++++egekmsks +n+++ + +++++ + + Rl++++a + ++ +d++ee +++
  gi|336252571|ref|YP_004595678.1| 561 ADHEGLEHREPFENLLAQGMVQLEGEKMSKSKGNVVSPQRIVEEYGADTARLFMMQAaQPERDFDWSEEGVRS 633
                                       55666666777788899***********************************998752678889999987765 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 ?    3.8   0.0     0.016        22      33      69 ..      44      80 ..      20      83 .. 0.84
   2 !   17.6   0.0   1.1e-06    0.0015     273     320 ..     580     627 ..     570     664 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                      tRNA-synt_1f 33 pSGliHiGnlrevltadlvaralrkrgeevrlilisD 69
                                      pSG++H+G +r+   +d+ ar  r +g++v + + +D
  gi|336252571|ref|YP_004595678.1| 44 PSGKLHMGHVRNYTITDAYARFRRMQGDHVLHPMGWD 80
                                      9****************99998888888776666555 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.1e-06
                      tRNA-synt_1f 273 lillkggekmssSkGnvltledwlevaepevlrflilr.rkPkkakkld 320
                                       +++l+g+ kms+SkGnv++++ ++e +  ++ r+++++ ++P++ ++ +
  gi|336252571|ref|YP_004595678.1| 580 MVQLEGE-KMSKSKGNVVSPQRIVEEYGADTARLFMMQaAQPERDFDWS 627
                                       5667666.****************9999999998887724677666654 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.3   0.00027      0.38       9      40 ..     153     187 ..     149     190 .. 0.80
   2 !    8.7   0.3    0.0013       1.7      15      41 ..     449     498 ..     441     502 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                               DZR   9 ppdarfCseCgtklkavaa...edrCpsCgekvdp 40 
                                       +++ + C++C t l  ++    ++ C++C+++v+ 
  gi|336252571|ref|YP_004595678.1| 153 DAEVNWCPHCETVLADEQVegeAELCWRCDTPVET 187
                                       556678*******98655589999*****999876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0013
                               DZR  15 CseCgtklkavaa.......................edrCpsCgekvdpe 41 
                                       C++Cg    ++++                       e++Cp+Cg++++ e
  gi|336252571|ref|YP_004595678.1| 449 CDDCGPVTVPEEDlpvelpefinttgnpldaaeewkETTCPECGADATRE 498
                                       788886654444477777778888888888888899********998766 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0082        11      15      26 .]     155     166 ..     153     166 .. 0.82
   2 ?    1.2   0.0       0.2   2.7e+02       5      15 ..     178     188 ..     176     189 .. 0.87
   3 ?    0.1   0.2      0.44     6e+02       3      23 ..     447     453 ..     445     459 .. 0.69
   4 !    8.0   0.1    0.0014         2       2      16 ..     485     500 ..     484     502 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0082
                       zf-ribbon_3  15 ddnvCpyCGtkl 26 
                                       ++n Cp+C t+l
  gi|336252571|ref|YP_004595678.1| 155 EVNWCPHCETVL 166
                                       6788****9987 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.2
                       zf-ribbon_3   5 CPnCGaplssd 15 
                                       C++C++p++++
  gi|336252571|ref|YP_004595678.1| 178 CWRCDTPVETR 188
                                       ******98875 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.44
                       zf-ribbon_3   3 vrCPnCGaplssddnvCpyCG 23 
                                       v              +C  CG
  gi|336252571|ref|YP_004595678.1| 447 V--------------HCDDCG 453
                                       3..............566665 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0014
                       zf-ribbon_3   2 tvrCPnCGa.plssdd 16 
                                       +++CP+CGa   ++ d
  gi|336252571|ref|YP_004595678.1| 485 ETTCPECGAdATRETD 500
                                       6789999986666666 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     0.054        74      23      34 ..     152     164 ..     141     171 .. 0.69
   2 ?    7.9   4.8    0.0025       3.4      17      38 ..     476     497 ..     443     498 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.054
                       Zn-ribbon_8  23 daplta.CPeCgs 34 
                                       +++++  CP+C  
  gi|336252571|ref|YP_004595678.1| 152 RDAEVNwCPHCET 164
                                       3456677****76 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0025
                       Zn-ribbon_8  17 vlqsisdapltaCPeCgsevrr 38 
                                       +l ++ + ++t+CPeCg++++r
  gi|336252571|ref|YP_004595678.1| 476 PLDAAEEWKETTCPECGADATR 497
                                       555555777999******8887 PP

>> Phage-MuB_C  Mu B transposition protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00032      0.44       2      45 ..     758     801 ..     757     806 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00032
                                       ----TT--SS-SGGGTTHHHHSSSSSSSHHHHHHHTTSSS-S-H CS
                       Phage-MuB_C   2 RigkrvsikktkkeDvkaiaaAwgltdeelmkllqeiaekpGaL 45 
                                       R+ kr ++ + + eDv+ i++  g++d+++++++++   k+ aL
  gi|336252571|ref|YP_004595678.1| 758 RVEKRRRLVENTREDVRDIIEVAGIEDPQAIDVVVAPDWKYDAL 801
                                       8999*****************************98866666666 PP

>> 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 ?   -2.2   0.1       1.5     2e+03      14      23 ..      44      53 ..      33      55 .. 0.80
   2 ?    9.6   0.0   0.00038      0.53     184     208 ..     573     595 ..     549     672 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                                      TSSS-BGGGH CS
                      tRNA-synt_1b 14 PTgklHlGyl 23
                                      P+gklH G++
  gi|336252571|ref|YP_004595678.1| 44 PSGKLHMGHV 53
                                      8*******96 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00038
                                       EEEEET-BBSTTSSSBTTCETTCGC CS
                      tRNA-synt_1b 184 egltvplltgldGekKmSKSagnsa 208
                                       e l+ + +++l+Ge KmSKS+gn +
  gi|336252571|ref|YP_004595678.1| 573 ENLLAQGMVQLEGE-KMSKSKGN-V 595
                                       5678889*******.********.3 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 ?    1.7   1.6      0.19   2.7e+02       2      20 ..     159     181 ..     159     184 .. 0.82
   2 ?   -1.2   0.1       1.6   2.2e+03       5      12 ..     181     189 ..     177     192 .. 0.80
   3 ?    9.6   0.0   0.00066      0.91       1      14 [.     487     500 ..     487     510 .. 0.87
   4 ?   -3.2   0.1       6.5     9e+03      10      17 ..     822     829 ..     822     830 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.19
                    DNA_ligase_ZBD   2 CPvCGsavvRee..geai..yRC 20 
                                       CP C + +  e+  gea   +RC
  gi|336252571|ref|YP_004595678.1| 159 CPHCETVLADEQveGEAElcWRC 181
                                       ********977766777766888 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                    DNA_ligase_ZBD   5 CGsavv.Re 12 
                                       C+++v+ Re
  gi|336252571|ref|YP_004595678.1| 181 CDTPVEtRE 189
                                       9****9887 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00066
                    DNA_ligase_ZBD   1 hCPvCGsavvReeg 14 
                                       +CP+CG+ + Re +
  gi|336252571|ref|YP_004595678.1| 487 TCPECGADATRETD 500
                                       7*********9976 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 6.5
                    DNA_ligase_ZBD  10 vReegeai 17 
                                       +Re+g+a+
  gi|336252571|ref|YP_004595678.1| 822 IREQGDAA 829
                                       59****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 ?    2.8   1.0     0.059        81      21      35 ..     158     172 ..     144     183 .. 0.79
   2 ?    2.5   0.2     0.077   1.1e+02      22      41 ..     449     470 ..     447     472 .. 0.78
   3 ?    6.8   0.4    0.0034       4.7       2      17 ..     487     503 ..     486     506 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.059
                                       EESSSSBEEEECCCC CS
                      TF_Zn_Ribbon  21 vCtdCGlVlednsid 35 
                                        C+ C++Vl d++++
  gi|336252571|ref|YP_004595678.1| 158 WCPHCETVLADEQVE 172
                                       7********999875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.077
                                       ESSSSBEE..EECCCCCCCHHH CS
                      TF_Zn_Ribbon  22 CtdCGlVl..ednsidegpewr 41 
                                       C dCG+V   e++  +e pe++
  gi|336252571|ref|YP_004595678.1| 449 CDDCGPVTvpEEDLPVELPEFI 470
                                       *****98755788888888775 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0034
                                       EETTTTCEE.CHEETST CS
                      TF_Zn_Ribbon   2 kCPnCgstn.lveDper 17 
                                       +CP+Cg +   ++D++ 
  gi|336252571|ref|YP_004595678.1| 487 TCPECGADAtRETDTMD 503
                                       7*****97757888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (898 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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):              13  [number of targets reported over threshold]
# CPU time: 0.77u 0.25s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 5547.29
//
Query:       gi|336252572|ref|YP_004595679.1|  [L=395]
Description: sodium/calcium exchanger membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-20   71.7  49.1      8e-18   64.8  14.5    2.4  3  Na_Ca_ex  Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.5      0.42   7.6e+03       8      17 ..       9      18 ..       4      27 .. 0.39
   2 !   18.9  20.0   6.2e-08    0.0011       6     150 ..      59     194 ..      55     195 .. 0.76
   3 !   64.8  14.5   4.5e-22     8e-18       1     150 [.     243     385 ..     243     386 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.42
                                      HHHHHHHHHH CS
                          Na_Ca_ex  8 lslllisvla 17
                                      + l+++++++
  gi|336252572|ref|YP_004595679.1|  9 VVLVVLVAAS 18
                                      2222222222 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 6.2e-08
                                       HHHHHHHHHHHHHHHHHHHHHHHH.HTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHT CS
                          Na_Ca_ex   6 filslllisvladflvssaeeiak.slgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlll 81 
                                       +++ +++ +++++++ + ++++++  lg+  s+++l ++ +g  + ++i++++   +g    a+g++lG  ++++++
  gi|336252572|ref|YP_004595679.1|  59 ILVLIAGAILMTACVEKLIDYLTRaALGLQVSLFALAIVFTGFEFDDTILALVLSGGGLEGAALGTALGTGLAIVGV 135
                                       555555555555555555555554359************************************************** PP

                                       HHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  82 viGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                       +++l+a++++++vd   l  d  +l+ +a ll l+ ++l       g+lt++ g++ll++++l+  +++
  gi|336252572|ref|YP_004595679.1| 136 TLALAAIVKPFPVD---LPTDYVVLFALAPLL-LVPFVLA------GTLTFVHGVLLLAAFVLIFGYLI 194
                                       ********775555...455663333333333.3344445......***************99876665 PP

  == domain 3  score: 64.8 bits;  conditional E-value: 4.5e-22
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHH CS
                          Na_Ca_ex   1 llfvlfilslllisvladflvssaeeia.kslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsni 76 
                                       +l+++f++  l+++v+a++l ++ +e+a + +g+ ++v+G t+l+l  ++ +++++i  +++g +++++gnv+Gs++
  gi|336252572|ref|YP_004595679.1| 243 WLWLGFAVLALVGVVFASMLLEAGSEVAvDGFGVEETVFGATVLTLILTFEDIMLTIEPVRRGVPEIGVGNVIGSVL 319
                                       5899************************779********************************************** PP

                                       HHHHTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  77 fnlllviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                       f +++ +G+i+l++ l++ ++ l+++l++ ++v++l+  +++l       +gr++++ g++l +lY++y +++l
  gi|336252572|ref|YP_004595679.1| 320 FSVTGNVGVIMLLSELTISGSVLTFHLPAVIVVTALA--AYFL---H---EGRVKRWHGFLLGGLYVAYWIVAL 385
                                       *************999999999999997755544444..2333...2...3******************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2722.87
//
Query:       gi|336252573|ref|YP_004595680.1|  [L=87]
Description: glutaredoxin [Halopiger xanaduensis SH-6]
Scores for 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-12   46.7   0.0    4.8e-12   46.1   0.0    1.3  1  GST_N_3       Glutathione S-transferase, N-terminal domain
    7.2e-05   23.0   0.0    0.00012   22.3   0.0    1.4  1  GST_N_2       Glutathione S-transferase, N-terminal domain
    0.00039   20.6   0.0    0.00076   19.6   0.0    1.4  1  Glutaredoxin  Glutaredoxin


Domain annotation for each model (and alignments):
>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   8.1e-16   4.8e-12       1      71 [.       4      86 ..       4      87 .] 0.86

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 8.1e-16
                                      EES-TTSHHHHHHHHHHHHHT--EEEE---.........TTTT.HHHHHHH-TT--SSEEETT..S-EEESHHHHHHHH CS
                           GST_N_3  1 LygfpaSpyarrvrlaLnekglpvevvevt.........pgeh.deellaknplgkvPvLedd..gealtdSlaIidyL 67
                                      Ly ++++p++  vr++L+ +g+++ +++             e   +++ a+ +   +P+L+d+  ge l++S++I+++L
  gi|336252573|ref|YP_004595680.1|  4 LYQAEGCPHSETVRETLTDLGVSYVIHNPRrpgheggdvLNEQvLDAMTAIGGEDMIPFLVDTdrGETLYESEDIVEFL 82
                                      9*************************99877777766653333588999999********8544899************ PP

                                      HHHH CS
                           GST_N_3 68 eely 71
                                      ee y
  gi|336252573|ref|YP_004595680.1| 83 EEHY 86
                                      **98 PP

>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0     2e-08   0.00012       2      69 ..      10      84 ..       9      85 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2e-08
                                      -HHHHHHHHHHHHCT--EEEEEEH...-TTSHHHHH........HHHCTTTSSSEEE-C.TTEEEESHHHHHHHHHH CS
                           GST_N_2  2 CPwahRvlialalkglediisvvvlepkgfekseef........prlnprgtVPvLwdk.dgqvineSseIlrylet 69
                                      CP +  v+ +l  +g+ ++i+    ++ g+e ++ +         ++ +  ++P L+d+  g  ++eS +I+++le+
  gi|336252573|ref|YP_004595680.1| 10 CPHSETVRETLTDLGVSYVIHNP--RRPGHEGGDVLneqvldamTAIGGEDMIPFLVDTdRGETLYESEDIVEFLEE 84
                                      99999999999999999999774..33333333222333333335555666*******75777************98 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.3e-07   0.00076       2      30 ..       3      31 ..       2      31 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-07
                                      EEEESTSSHHHHHHHHHHHHTTGGEEEEE CS
                      Glutaredoxin  2 vlftkptCpyCkkakrlLkelgvkfeeid 30
                                      +l++  +Cp++  ++++L++lgv++ +++
  gi|336252573|ref|YP_004595680.1|  3 ELYQAEGCPHSETVRETLTDLGVSYVIHN 31
                                      7999*********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 643.26
//
Query:       gi|336252574|ref|YP_004595681.1|  [L=728]
Description: hypothetical protein Halxa_1169 [Halopiger xanaduensis SH-6]
Scores for 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-16   59.3   0.0    6.2e-12   45.6   0.2    2.5  2  CCG         Cysteine-rich domain
    7.9e-10   38.1  12.4    1.9e-05   24.3   1.3    2.6  2  Fer4        4Fe-4S binding domain
      1e-09   38.3  10.2    5.8e-08   32.7  10.6    2.9  3  Fer4_10     4Fe-4S dicluster domain
    4.5e-09   36.6   5.6    4.5e-09   36.6   5.6    1.9  1  Fer4_8      4Fe-4S dicluster domain
    1.6e-08   34.6   8.7    1.9e-08   34.4   6.5    2.1  2  Fer4_9      4Fe-4S dicluster domain
    6.5e-08   33.0   9.0    6.5e-08   33.0   9.0    2.0  1  Fer4_7      4Fe-4S dicluster domain
      1e-07   31.6  11.6    0.00019   21.3   1.7    2.7  2  Fer4_2      4Fe-4S binding domain
    5.4e-05   23.2  10.9      0.012   15.7   0.4    2.9  3  Fer4_21     4Fe-4S dicluster domain
    0.00025   21.0  23.2    0.00039   20.4   4.3    2.9  3  Fer4_6      4Fe-4S binding domain
    0.00028   21.7  13.3     0.0007   20.5  11.5    2.4  2  Fer4_16     4Fe-4S double cluster binding domain
    0.00041   20.8  13.7    0.00045   20.7  10.9    2.5  2  Fer4_17     4Fe-4S dicluster domain
     0.0005   20.9   4.3      0.049   14.5   0.2    2.9  2  Fer4_22     4Fe-4S dicluster domain
    0.00078   19.8  18.1      0.004   17.5   0.8    2.9  2  Fer4_4      4Fe-4S binding domain
  ------ inclusion threshold ------
      0.052   13.4   0.0      0.092   12.6   0.0    1.3  1  Acid_PPase  Acid Phosphatase
       0.17   12.1  11.2       0.73   10.0   1.2    2.8  3  Fer4_18     4Fe-4S dicluster domain
       0.41   11.0   3.1        1.7    9.1   0.8    2.4  2  CopD        Copper resistance protein D
       0.47   11.2  10.3       0.52   11.1   0.4    3.2  2  Fer4_15     4Fe-4S single cluster domain
        0.5   10.9  17.5       0.45   11.1   1.5    3.2  3  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
        2.8    9.1  25.5       0.69   11.0   5.3    2.9  2  Fer4_3      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 !   11.3   0.0   0.00033      0.31       9      84 ..     461     537 ..     452     538 .. 0.91
   2 !   45.6   0.2   6.6e-15   6.2e-12       1      83 [.     598     688 ..     598     690 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                               CCG   9 llraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgCllql 84 
                                        ++ +++ v ++l+ +le++ v + +l ++e+  G+  +r g+e l  +la ++vet+e+ + d+iv ++p+ ++++
  gi|336252574|ref|YP_004595681.1| 461 SYDERNKRVARSLATILEEADVSFGILfDDEKYDGNDVRRIGEEFLYVELAGHHVETWEDCEFDKIVCTDPHSYNTF 537
                                       577889***************************************************************99977766 PP

  == domain 2  score: 45.6 bits;  conditional E-value: 6.6e-15
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaee.....t 68 
                                       v+y+d+Chl+r++  y+++r+++ +  + +++e++++ +++ CCG ggg  +++  +  +  ++++++a e     +
  gi|336252574|ref|YP_004595681.1| 598 VTYHDPCHLGRYNdeYEAPRELI-EATGCELAEMPRNrADSFCCGGGGGGLWMDFeEDPKPSEERLREALEdtaagA 673
                                       89************777777755.555***********************999775333555555554444333226 PP

                               CCG  69 gadaivtacpgCllq 83 
                                        +++ v+acp C ++
  gi|336252574|ref|YP_004595681.1| 674 AVEKFVVACPMCMTM 688
                                       7***********987 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   1.3     2e-08   1.9e-05       4      22 ..     308     326 ..     306     327 .. 0.93
   2 !   18.0   4.1     2e-06    0.0019       6      21 ..     371     386 ..     369     387 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2e-08
                                       ETTTSSS-THHHHHSTTTE CS
                              Fer4   4 deekCigCGaCvevCPvgA 22 
                                       d++ C++CG+C +vCP  A
  gi|336252574|ref|YP_004595681.1| 308 DQDACTKCGRCSSVCPAKA 326
                                       99**************987 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2e-06
                                       TTSSS-THHHHHSTTT CS
                              Fer4   6 ekCigCGaCvevCPvg 21 
                                       e C++C+aC+++CPv+
  gi|336252574|ref|YP_004595681.1| 371 ESCMACMACMDACPVE 386
                                       89************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 !   32.7  10.6   6.1e-11   5.8e-08       4      56 .]     307     384 ..     304     384 .. 0.84
   2 !   18.5   1.5   1.7e-06    0.0016       6      24 ..     370     397 ..     362     432 .. 0.73
   3 ?   -0.6   0.0       1.6   1.5e+03      18      23 ..     681     686 ..     666     707 .. 0.67

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 6.1e-11
                           Fer4_10   4 idddtCirCgkCvkaCPadl.........................tsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       +d+d C++Cg+C ++CPa++                         + +  ++    +  + + +e+C++c aC++aC
  gi|336252574|ref|YP_004595681.1| 307 LDQDACTKCGRCSSVCPAKAsdrpldprnvildlkryreereagaEPQPIIADGGTSVIDTETMESCMACMACMDAC 383
                                       799****************9********************99885444444444444445559************** PP

                           Fer4_10  56 P 56 
                                       P
  gi|336252574|ref|YP_004595681.1| 384 P 384
                                       9 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.7e-06
                           Fer4_10   6 ddtCirCgkCvkaCPadl.........t 24 
                                        ++C+ C +C++aCP+ +         +
  gi|336252574|ref|YP_004595681.1| 370 MESCMACMACMDACPVEIehlqsftrlQ 397
                                       578************9877776665552 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.6
                           Fer4_10  18 aCPadl 23 
                                       aCP+++
  gi|336252574|ref|YP_004595681.1| 681 ACPMCM 686
                                       566644 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   5.6   4.7e-12   4.5e-09       2      65 .]     309     387 ..     308     387 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.7e-12
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaae...dvqeeqvlee.................eealwsCttcgaCt 58 
                                        ++C++Cg+C s Cp+     +++ld+r+   +   + +e++   +                  e+++sC++c+aC 
  gi|336252574|ref|YP_004595681.1| 309 QDACTKCGRCSSVCPAKA--SDRPLDPRNVILDlkrYREERE---AgaepqpiiadggtsvidTETMESCMACMACM 380
                                       579***********9322..2455666666555433222222...13456777777888888899************ PP

                            Fer4_8  59 evCpvgi 65 
                                       ++Cpv+i
  gi|336252574|ref|YP_004595681.1| 381 DACPVEI 387
                                       ****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 !   34.4   6.5     2e-11   1.9e-08       1      49 [.     311     386 ..     311     388 .. 0.96
   2 ?   -0.7   0.0       1.8   1.7e+03      10      24 ..     680     694 ..     659     701 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2e-11
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase...........................eaCigCgaCveaCpkg 49 
                                       +Ct+Cg+C ++Cpa++  +   +r + l+ +++                           e+C+ C+aC++aCp +
  gi|336252574|ref|YP_004595681.1| 311 ACTKCGRCSSVCPAKASDRPLDPRNVILDLKRYreereagaepqpiiadggtsvidtetmESCMACMACMDACPVE 386
                                       6************************9999998899***************************************87 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.8
                            Fer4_9  10 eaCpagvvvedaaer 24 
                                        aCp+++++++++++
  gi|336252574|ref|YP_004595681.1| 680 VACPMCMTMYEDGRK 694
                                       467777766666655 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   9.0   6.9e-11   6.5e-08       1      51 [.     311     386 ..     311     387 .. 0.64

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 6.9e-11
                            Fer4_7   1 rCigCgaCvaaCpvkaield............eeenek................gtekv.eidpekClgCgaCvavC 48 
                                       +C++Cg+C ++Cp+ka + +            +    +                gt  + +  +e+C+ C aC+++C
  gi|336252574|ref|YP_004595681.1| 311 ACTKCGRCSSVCPAKASDRPldprnvildlkrY----ReereagaepqpiiadgGTSVIdTETMESCMACMACMDAC 383
                                       5************99999664444444433221....1223344444444444433444455699************ PP

                            Fer4_7  49 Ptg 51 
                                       P++
  gi|336252574|ref|YP_004595681.1| 384 PVE 386
                                       *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 !   21.3   1.7   2.1e-07   0.00019       5      22 .]     307     324 ..     303     324 .. 0.91
   2 !   14.7   2.6   2.5e-05     0.024       8      21 ..     371     384 ..     364     385 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.1e-07
                            Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                        d d+C+ Cg C s+CPa
  gi|336252574|ref|YP_004595681.1| 307 LDQDACTKCGRCSSVCPA 324
                                       799**************8 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.5e-05
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                       ++C++C aC +aCP
  gi|336252574|ref|YP_004595681.1| 371 ESCMACMACMDACP 384
                                       59************ PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.4   1.3e-05     0.012      37      53 ..     308     324 ..     291     328 .. 0.77
   2 !   12.9   1.5   9.4e-05     0.089      37      54 ..     369     386 ..     352     389 .. 0.77
   3 ?   -2.1   0.1       4.7   4.4e+03      41      49 ..     679     687 ..     667     689 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                           Fer4_21  37 vedeCvGCnlCssvCPv 53 
                                        +d C+ C  CssvCP 
  gi|336252574|ref|YP_004595681.1| 308 DQDACTKCGRCSSVCPA 324
                                       47899999999999995 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.4e-05
                           Fer4_21  37 vedeCvGCnlCssvCPve 54 
                                       + ++C++C  C++ CPve
  gi|336252574|ref|YP_004595681.1| 369 TMESCMACMACMDACPVE 386
                                       4699************94 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.7
                           Fer4_21  41 CvGCnlCss 49 
                                        v+C +C++
  gi|336252574|ref|YP_004595681.1| 679 VVACPMCMT 687
                                       455555553 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   4.3   4.1e-07   0.00039       5      23 ..     308     326 ..     308     327 .. 0.95
   2 !   11.6   4.5   0.00025      0.24       7      21 ..     371     385 ..     369     388 .. 0.89
   3 ?   -2.4   0.4       6.2   5.9e+03       8      12 ..     681     685 ..     679     687 .. 0.54

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.1e-07
                            Fer4_6   5 dpdkCigCgdCvrvCPega 23 
                                       d+d+C+ Cg+C +vCP++a
  gi|336252574|ref|YP_004595681.1| 308 DQDACTKCGRCSSVCPAKA 326
                                       89**************987 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00025
                            Fer4_6   7 dkCigCgdCvrvCPe 21 
                                       ++C  C++C+++CP 
  gi|336252574|ref|YP_004595681.1| 371 ESCMACMACMDACPV 385
                                       79************7 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.2
                            Fer4_6   8 kCigC 12 
                                       +C  C
  gi|336252574|ref|YP_004595681.1| 681 ACPMC 685
                                       35555 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 !   20.5  11.5   7.4e-07    0.0007       2      66 ..     312     385 ..     311     386 .. 0.61
   2 !   10.0   2.6    0.0014       1.3       2      16 ..     373     387 ..     372     420 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.4e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy..........ntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       C++Cg+C +vCP++a + + +++  + + + y          + +  ++ +  + +++  e ++ C +C+d+CP+
  gi|336252574|ref|YP_004595681.1| 312 CTKCGRCSSVCPAKASDRPLDPRNVILDLKRYreereagaepQPIIADGGTSVIDTET-MESCMACMACMDACPV 385
                                       ***************9998444443333333322344444442222222222223333.4789***********7 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0014
                           Fer4_16   2 CgtCgkCaevCPtna 16 
                                       C  C +C+++CP++ 
  gi|336252574|ref|YP_004595681.1| 373 CMACMACMDACPVEI 387
                                       999*********976 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   2.7    0.0003      0.28      44      59 ..     310     325 ..     288     327 .. 0.80
   2 !   20.7  10.9   4.8e-07   0.00045       1      60 [.     311     387 ..     311     388 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                       + C++Cg+C+++CP++
  gi|336252574|ref|YP_004595681.1| 310 DACTKCGRCSSVCPAK 325
                                       78************75 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 4.8e-07
                           Fer4_17   1 rCiqCgyClpeCpsyea.ydnepkkllraakl................glleeaekeekaslCieCgeCerkCPqgl 60 
                                       +C++Cg C  +Cp  +  ++ +p++++ ++k                    + +++ e++++C+ C  C  +CP ++
  gi|336252574|ref|YP_004595681.1| 311 ACTKCGRCSSVCPAKASdRPLDPRNVILDLKRyreereagaepqpiiaDGGTSVIDTETMESCMACMACMDACPVEI 387
                                       6************866544455554444433323222224344444532334456669****************876 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   5.2e-05     0.049      72      95 ..     302     325 ..     290     326 .. 0.87
   2 ?    6.9   0.1     0.012        11      77      96 .]     368     387 ..     352     431 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.2e-05
                           Fer4_22  72 efkekfgesgCvGCgRCieacpvk 95 
                                       ++ke  ++ +C+ CgRC+++cp+k
  gi|336252574|ref|YP_004595681.1| 302 TWKELLDQDACTKCGRCSSVCPAK 325
                                       56777899*************986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
                           Fer4_22  77 fgesgCvGCgRCieacpvki 96 
                                         +++C+ C  C++acpv+i
  gi|336252574|ref|YP_004595681.1| 368 ETMESCMACMACMDACPVEI 387
                                       55667777777777777765 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   4.2   0.00028      0.26       1      16 [.     309     324 ..     309     329 .. 0.92
   2 !   17.5   0.8   4.3e-06     0.004       2      16 ..     371     385 ..     370     397 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       q+ C+ Cg+C ++CP 
  gi|336252574|ref|YP_004595681.1| 309 QDACTKCGRCSSVCPA 324
                                       799************6 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.3e-06
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e+C  C++C++aCP+
  gi|336252574|ref|YP_004595681.1| 371 ESCMACMACMDACPV 385
                                       89************6 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.7e-05     0.092      73     161 ..     432     520 ..     387     521 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.7e-05
                                       HHHHHHHHHHTT-G..........GGESEEEESSS.-H..HHHHHHHHHHH---GGGEEEEES-HHHHHHHHTTT-E CS
                        Acid_PPase  73 pdlarelLklleindakekekklldvfddveiykg.sk..tkhfeklkkktgieyedmlfFDdesrnievesrlgvt 146
                                        d+a++l   ++i+da+e+e+  l +++d   y+  +k  ++ + ++ ++ ++++   ++FDde+ + ++++r+g +
  gi|336252574|ref|YP_004595681.1| 432 ADWADDL--EFDITDAREEEVDYLWYVGDYPSYDErNKrvARSLATILEEADVSFG--ILFDDEKYDGNDVRRIGEE 504
                                       5666665..68888999999999999999777775133114566677778888776..99***************** PP

                                       EEE-SS.S--HHHHHH CS
                        Acid_PPase 147 fvlvpd.Gltreefek 161
                                       f++v+  G   e++e+
  gi|336252574|ref|YP_004595681.1| 505 FLYVELaGHHVETWED 520
                                       ****866999999875 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.4    0.0054       5.1      57      74 ..     308     325 ..     257     330 .. 0.80
   2 ?   10.0   1.2   0.00077      0.73      50      76 ..     362     388 ..     330     397 .. 0.66
   3 ?   -2.2   0.0         5   4.7e+03      62     104 ..     673     717 ..     653     720 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0054
                           Fer4_18  57 gagdcidcescvkvcPtg 74 
                                       ++  c++c+ c +vcP +
  gi|336252574|ref|YP_004595681.1| 308 DQDACTKCGRCSSVCPAK 325
                                       5678************86 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00077
                           Fer4_18  50 keerkekgagdcidcescvkvcPtgid 76 
                                       +    ++++  c++c +c++ cP++i+
  gi|336252574|ref|YP_004595681.1| 362 TSVIDTETMESCMACMACMDACPVEIE 388
                                       444566777889999999999998886 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5
                           Fer4_18  62 idcescvkvcPtgidi.rkGlqleci.scllcidacdkvmeklgk 104
                                        + e+ v  cP+ + +  +G +        + +d  + ++e++gk
  gi|336252574|ref|YP_004595681.1| 673 AAVEKFVVACPMCMTMyEDGRKTGDFeDQIEIVDVAELIVEAIGK 717
                                       455666777777665412344433221344555666666666555 PP

>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.45   4.3e+02      34      69 ..      16      47 ..       7      74 .. 0.64
   2 ?    9.1   0.8    0.0018       1.7      12      89 ..     100     176 ..      85     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.45
                              CopD 34 gllttayGrlllaKlalllvllalaalnrfrlvprl 69
                                      g+++t y+ +  + +a  +++++++++ rf+    +
  gi|336252574|ref|YP_004595681.1| 16 GISATEYA-VFYLLTAITIAVFLYGVYRRFAR---Y 47
                                      56677777.44444555666666777777643...3 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0018
                              CopD  12 laavavvlvtGvvnallrvg..lagllttayGrlllaKlalllvllalaalnrfrlvprleaatgaggqalrhrlrr 86 
                                       ++a+ +++v G v   +  g  ++g +  ay+ ++ a+ +l++v l++a + r++++ +    +g+++++ + +l  
  gi|336252574|ref|YP_004595681.1| 100 FIATSILAVDGYVYKPIFQGhfWEGDFYLAYQFVVDAMGLLFVVGLGMAIYRRYWVRNER--LWGRHTSSED-DLFI 173
                                       56777788888888777778877999999*************************998654..3888888777.6655 PP

                              CopD  87 saa 89 
                                       +  
  gi|336252574|ref|YP_004595681.1| 174 WTL 176
                                       555 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 ?   11.1   0.4   0.00055      0.52       3      20 ..     307     324 ..     306     347 .. 0.91
   2 ?    2.4   4.1      0.29   2.7e+02       6      46 ..     371     408 ..     364     448 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00055
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       +D+daC+ cg+C  ++p 
  gi|336252574|ref|YP_004595681.1| 307 LDQDACTKCGRCSSVCPA 324
                                       7**************985 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.29
                           Fer4_15   6 daCigcglCvaeapevfeldedglasvl.lddgeiaegevpd 46 
                                       + C+ c +C++++p  +e++  +l+s++ l+++ +++g+v++
  gi|336252574|ref|YP_004595681.1| 371 ESCMACMACMDACP--VEIE--HLQSFTrLQRQMTDQGDVDS 408
                                       68***********9..4444..44444334555555555554 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 ?   11.1   1.5   0.00048      0.45       2      18 ..     308     324 ..     307     339 .. 0.95
   2 ?    8.9   2.5    0.0022       2.1       4      17 ..     371     384 ..     368     392 .. 0.94
   3 ?   -0.9   0.4       2.7   2.5e+03      20      53 ..     651     684 ..     650     685 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00048
                           Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                       D+d C+ cg C +++P 
  gi|336252574|ref|YP_004595681.1| 308 DQDACTKCGRCSSVCPA 324
                                       99**************5 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0022
                           Fer4_13   4 dtCiacgaCvelaP 17 
                                       ++C+ac+aC +++P
  gi|336252574|ref|YP_004595681.1| 371 ESCMACMACMDACP 384
                                       79***********9 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.7
                           Fer4_13  20 FeeddeggasvvaeqptseeekadaeeAadaCPv 53 
                                       Feed++ +  +  e  ++++  a +e+ + aCP+
  gi|336252574|ref|YP_004595681.1| 651 FEEDPKPSEERLREALEDTAAGAAVEKFVVACPM 684
                                       8889998888888888889999999999999995 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   5.3   0.00074      0.69       1      15 []     312     326 ..     312     326 .. 0.95
   2 ?    9.2   5.9    0.0028       2.7       1      13 [.     373     385 ..     373     387 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00074
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       Ct Cg+C  vCP +A
  gi|336252574|ref|YP_004595681.1| 312 CTKCGRCSSVCPAKA 326
                                       ************887 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0028
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+ C+aC+++CPv
  gi|336252574|ref|YP_004595681.1| 373 CMACMACMDACPV 385
                                       988*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (728 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.66u 0.24s 00:00:00.90 Elapsed: 00:00:00.40
# Mc/sec: 5400.00
//
Query:       gi|336252575|ref|YP_004595682.1|  [L=196]
Description: hypothetical protein Halxa_1170 [Halopiger xanaduensis SH-6]
Scores for 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   14.4   1.2      0.028   14.4   1.2    2.3  2  DUF1451    Zinc-ribbon containing domain
       0.03   14.7   0.3        0.1   12.9   0.1    2.0  2  HTH_Tnp_1  Transposase
      0.073   12.9   0.1          4    7.4   0.0    2.5  2  HTH_23     Homeodomain-like domain
       0.29   11.1   1.1        1.2    9.1   0.1    2.1  2  ApoO       Apolipoprotein O
       0.42   10.4   6.1      0.057   13.2   2.1    1.5  2  UPF0193    Uncharacterised protein family (UPF0193)
        2.7    8.2   7.5        2.4    8.4   5.8    1.8  1  zf-C4H2    Zinc finger-containing protein


Domain annotation for each model (and alignments):
>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.2   9.5e-06     0.028       3      51 ..      33      81 ..      31     117 .. 0.85
   2 ?    0.0   1.0      0.26   7.8e+02       5      46 ..     152     193 ..     120     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.5e-06
                           DUF1451  3 leeaeekseeeleelvekakeklseaeeltkeelelvaeylkrDleeaa 51
                                      le++e+++ee+le+++++++e+ + + +lt++el +va++  +D ++aa
  gi|336252575|ref|YP_004595682.1| 33 LERDEQTDEERLENVITQMRERYEFETDLTNDELGEVAKAFYDDESDAA 81
                                      788999*********************************9999987776 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.26
                           DUF1451   5 eaeekseeeleelvekakeklseaeeltkeelelvaeylkrD 46 
                                       +a+++ ++e++ ++ +a+  ++ + ++ ++ le  +e ++ D
  gi|336252575|ref|YP_004595682.1| 152 TANDRYRDEFDSILADAELSEQMTTDVREDGLEDATEGMETD 193
                                       456666777778888888888888888888777777777766 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.8   8.5e+03      23      38 ..      76      91 ..      69      95 .. 0.60
   2 ?   12.9   0.1   3.4e-05       0.1      29      63 ..     126     160 ..     120     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.8
                         HTH_Tnp_1 23 gksvsevArrhgvspn 38
                                      + s + +A + gv+++
  gi|336252575|ref|YP_004595682.1| 76 DESDAAIADEVGVDAE 91
                                      4555667777777766 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.4e-05
                         HTH_Tnp_1  29 vArrhgvspnqLykWrrqyregeeaspaefeltal 63 
                                       +A++++vs++q ++ rr ++++  ++ a+++++++
  gi|336252575|ref|YP_004595682.1| 126 LAEEYDVSEAQIRRYRRVAEAEDQSRTANDRYRDE 160
                                       89*****************9888888888777665 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.041   1.2e+02      10      29 ..      69      88 ..      66      90 .. 0.84
   2 ?    7.4   0.0    0.0013         4      23      39 ..     126     142 ..     123     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.041
                            HTH_23 10 illllaeGlsvreIAreLgv 29
                                      +++++ +  s ++IA+e gv
  gi|336252575|ref|YP_004595682.1| 69 VAKAFYDDESDAAIADEVGV 88
                                      667777789**********8 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0013
                            HTH_23  23 IAreLgvsrrTvyrwlk 39 
                                        A+e++vs+ +++r+++
  gi|336252575|ref|YP_004595682.1| 126 LAEEYDVSEAQIRRYRR 142
                                       69*************97 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00039       1.2       9      50 ..      34      78 ..       4      82 .. 0.86
   2 ?    0.5   0.1      0.18   5.4e+02      12      39 ..     129     158 ..     113     180 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00039
                              ApoO  9 s...eeptdrLeegvrslRkslepytsavqdelnkvkskvetaeq 50
                                      +   +++++rLe+ ++++R+  e +t+ ++del +v +++++ e+
  gi|336252575|ref|YP_004595682.1| 34 ErdeQTDEERLENVITQMRERYEFETDLTNDELGEVAKAFYDDES 78
                                      044478999****************************99998775 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.18
                              ApoO  12 ptdrLeegvrslRksl..epytsavqdeln 39 
                                       + d  e+++r+ R+ +  e+++ +++d+++
  gi|336252575|ref|YP_004595682.1| 129 EYDVSEAQIRRYRRVAeaEDQSRTANDRYR 158
                                       455566677777764411344555555543 PP

>> UPF0193  Uncharacterised protein family (UPF0193)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.1   1.9e-05     0.057     123     184 ..       4      69 ..       1      86 [. 0.77
   2 ?   -2.3   0.1       1.1   3.3e+03     140     163 ..     135     159 ..     124     175 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                           UPF0193 123 eKrrLqnimAtgkdlkekk.pkkknvkkeeee.evkevDrfeelvkeIeeRkeFLeeMea..LGqg 184
                                       + + L +i+   +d +e+  ++++n + + e  e+++++r+e+++ +++eR eF +++++  LG++
  gi|336252575|ref|YP_004595682.1|   4 KTEELRDIFTDVTDGEETVtESQENTRGSLERdEQTDEERLENVITQMRERYEFETDLTNdeLGEV 69 
                                       55789999999999999887556666655555599*******************999864337765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                           UPF0193 140 kk.pkkknvkkeeeeevkevDrfee 163
                                       ++ ++ + v++ e ++ + +Dr+ +
  gi|336252575|ref|YP_004595682.1| 135 AQiRRYRRVAEAEDQSRTANDRYRD 159
                                       4434444444444445555555544 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.8   0.00079       2.4      51     115 ..       5      65 ..       1     153 [. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00079
                           zf-C4H2  51 veeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrselglekledleeee 115
                                        eeLr I +D+ + E+++ e++e+++ sle+ +++ e  ++l + + ++r+    e   dl+++e
  gi|336252575|ref|YP_004595682.1|   5 TEELRDIFTDVTDGEETVTESQENTRGSLERDEQTDE--ERLENVITQMRERYEFE--TDLTNDE 65 
                                       79***************************99888766..58999999999987777..4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1398  (0.0779742); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1408.50
//
Query:       gi|336252576|ref|YP_004595683.1|  [L=250]
Description: hypothetical protein Halxa_1171 [Halopiger xanaduensis SH-6]
Scores for 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-05   23.2   2.8      0.049   13.5   0.3    2.3  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
     0.0015   18.7   0.0      0.005   17.0   0.0    1.8  2  Cas_Cas4  Domain of unknown function DUF83
  ------ inclusion threshold ------
       0.27   10.7   0.1        2.2    7.7   0.2    2.0  2  Exo5      Exonuclease V - a 5' deoxyribonuclease


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 !   13.5   0.3   8.1e-06     0.049       4     100 ..       8     117 ..       5     130 .. 0.64
   2 !    9.9   0.1    0.0001      0.62     206     254 ..     189     236 ..     138     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.1e-06
                          PDDEXK_1   4 vsrletfleCplrfflryllgl..re.eeeleap.dlGtlvHaaleefye.............wkkldkedleelle 63 
                                       +s l+t + Cp+++++r+ +    r+ ++e+ea  dl t + ++le+                ++++  +++e+l+ 
  gi|336252576|ref|YP_004595683.1|   8 FSDLRTAAYCPRKYYYRRTADDgeRQpPPEVEAVrDLATRYDELLEAPPTalddepiavsaaqYRETLAAARERLS- 83 
                                       689*****************9987335899999559*********9666655555544433322222222333333. PP

                          PDDEXK_1  64 eaveelwpellleeeilessarlrylaeklkevlekl 100
                                       +a +   + + + e+ le+s   +  ++++++++e++
  gi|336252576|ref|YP_004595683.1|  84 AAET---DLEHEGEDDLETSDGSGGERDHWRRLCEPA 117
                                       1111...111223333777777777777777777765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0001
                          PDDEXK_1 206 evvkkmalteeeleallqeleelaeeilagefparpskkCeyCpyksvC 254
                                       +vv+++alt    +++++ l+++ +e+ ++  + ++  kCe C++++ C
  gi|336252576|ref|YP_004595683.1| 189 GVVRSIALTTRRKARYRRVLRTV-REMDGPPARTTNRSKCEGCEFADEC 236
                                       55666677777777777777775.999999999999999*******999 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 ?   -1.3   0.0      0.35   2.1e+03       5      17 ..      11      23 ..       8      29 .. 0.79
   2 !   17.0   0.0   8.4e-07     0.005      93     160 ..     170     236 ..     158     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.35
                          Cas_Cas4  5 iqyyliCkrklwl 17
                                      ++  ++C+rk ++
  gi|336252576|ref|YP_004595683.1| 11 LRTAAYCPRKYYY 23
                                      56678*****997 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 8.4e-07
                          Cas_Cas4  93 Le.kkgveikeGvleypkekkreevelteelreelekaikeieeiissekppkvkkkkiCkkCayaelC 160
                                       L  ++   ++++ leyp     +++ lt +++ + +++++ ++e+     p +++++++C+ C++a+ C
  gi|336252576|ref|YP_004595683.1| 170 LAwEHETAVDRAWLEYPAYGVVRSIALTTRRKARYRRVLRTVREMD--GPPARTTNRSKCEGCEFADEC 236
                                       555677778889*****************************99974..4689999999**********9 PP

>> Exo5  Exonuclease V - a 5' deoxyribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.05     3e+02      12      36 ..       4      28 ..       1      40 [. 0.77
   2 ?    7.7   0.2   0.00036       2.2     350     366 ..     221     237 ..     208     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.05
                              Exo5 12 kklsVtdLvspaWCElqyeYtLtkl 36
                                      +++  +dL + a+C  +y+Y  t  
  gi|336252576|ref|YP_004595683.1|  4 SRVPFSDLRTAAYCPRKYYYRRTAD 28
                                      566679**************87765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00036
                              Exo5 350 ieeafkCrsCeFaeeCe 366
                                        ++  kC+ CeFa+eC 
  gi|336252576|ref|YP_004595683.1| 221 TTNRSKCEGCEFADECG 237
                                       345589**********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1900.79
//
Query:       gi|336252577|ref|YP_004595684.1|  [L=403]
Description: Homoserine O-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-27   96.5   0.0    2.6e-27   96.1   0.0    1.1  1  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
       0.01   15.1   0.0      0.018   14.3   0.0    1.3  1  Hydrolase_4    Serine aminopeptidase, S33
      0.088   12.3   0.2        5.5    6.4   0.1    2.5  3  Peptidase_S9   Prolyl oligopeptidase 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 !   96.1   0.0   4.3e-31   2.6e-27       1     257 []      37     358 ..      37     358 .. 0.89

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 4.3e-31
                                       SEEEEE-STTTCGGG................GTTGHHHHHHHHT..TSEEEEEEETTSTTSSSTTTGB......... CS
                     Abhydrolase_1   1 pvlvilhGlpgssdv................waerglapaLakd..gfdvillDlrGvgySspapacin........ 51 
                                       ++++i+h+l+gs++v                w++  ++p+ a d  +++v++ + +G++y++++pa+ n        
  gi|336252577|ref|YP_004595684.1|  37 NAVLICHALTGSAHVarrpdsggetagqaraWWGDVVGPGKAIDttEYFVVCANAPGSCYGTTGPASENpetgepyg 113
                                       68************9***************************99***********************99******** PP

                                       CHHSHHHHHHHHH...HHHHHCTTSSEE.EEEETHHHHHHHHHHHHHGGGEEEEEEESE....CSSCCHHHHHHHHH CS
                     Abhydrolase_1  52 ddygtasvaddld...rildalgddklt.lvGhSmGGmialayaaeyperVkalvllga....idpaaslieaqrqq 120
                                       +d++ ++v d+ +   ++ld lg+++++ ++G+S GGm +l ++ +yp+   +   +++     + + +l+  +r++
  gi|336252577|ref|YP_004595684.1| 114 TDFPPVTVGDWTRaqrQLLDELGVGRVHaVIGGSVGGMNVLDWLRRYPDDLERAGVVASaarlDPQCLALDTVARRA 190
                                       *************88777*****************************8887655444444698899*********** PP

                                       HHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHH..............HCHHHCCHHHHHHHCHHHHH CS
                     Abhydrolase_1 121 aksfpdffdgyaadcarnpagplladelaaleqrhrlvdalkf..............pdkskrfpssgsdnasslat 183
                                       + s+p+++ g ++ + ++ +g+  a++l+++ + ++ + a kf              pd +      ++  +s+l++
  gi|336252577|ref|YP_004595684.1| 191 ITSDPNWNGGHYYGGPEPEDGLARARQLGHIMYLSKTSMARKFgrrsagretvreepPDPA-AGFFPYREVESYLDY 266
                                       ***********************************99998888999999999998854444.444446788888888 PP

                                       HHHHHHHHHHHCCHHHHHHHHHC.............THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS.....EEE CS
                     Abhydrolase_1 184 galksieqwpttdsaklllrlre.............lknvlaptlvisgtsDplvppkaledlaqllpk.....krl 242
                                       +a k++++++++ + +  +  +              l +     l++s t D+ ++ +++e la++ ++     + +
  gi|336252577|ref|YP_004595684.1| 267 QAEKFVDRFDANSYLYMTRAMDDfdlsagyesdadaLAAFEGELLLLSFTGDWHFTVEQSETLADAAREadvdvAHH 343
                                       888888888888888888887779999999887666555555************************6666788888* PP

                                       EEEETCSSSHHHHSH CS
                     Abhydrolase_1 243 vvisdagHlaflegp 257
                                       v++sd gH+afl++p
  gi|336252577|ref|YP_004595684.1| 344 VIESDHGHDAFLVEP 358
                                       ************986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.9e-06     0.018      77     116 ..     140     179 ..     121     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.9e-06
                       Hydrolase_4  77 plfllGhSmGGliallyllrypdkvaglilsaPalkikak 116
                                        + ++G S+GG+ +l +l rypd+++++ ++a+a +++++
  gi|336252577|ref|YP_004595684.1| 140 VHAVIGGSVGGMNVLDWLRRYPDDLERAGVVASAARLDPQ 179
                                       5789*******************99955444444455444 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.1   6.7e+03     179     206 ..      43      70 ..      36      74 .. 0.75
   2 ?    3.2   0.0    0.0086        51      67      87 ..     142     162 ..     118     212 .. 0.80
   3 ?    6.4   0.1   0.00092       5.5     132     186 ..     298     351 ..     271     361 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.1
                                       EEETTS-SSTTSSHHHHHHHHHHHHHHH CS
                      Peptidase_S9 179 lifpdegHgvgkprakveelarllaFlk 206
                                       +  +++ H++++p++  e   +  a++ 
  gi|336252577|ref|YP_004595684.1|  43 HALTGSAHVARRPDSGGETAGQARAWWG 70 
                                       5678899999999988887777777765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0086
                                       EEEEETHHHHHHHHHHHH-GG CS
                      Peptidase_S9  67 aitGgSyGGyltgaalnqrpd 87 
                                       a+ GgS GG++++  l + pd
  gi|336252577|ref|YP_004595684.1| 142 AVIGGSVGGMNVLDWLRRYPD 162
                                       789********9988776665 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.00092
                                       HHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-S.EEEEEETTS-S CS
                      Peptidase_S9 132 spyspldnvkaypplLlihGlaDdrvppaealklvaaLqkkgkn.vlllifpdegH 186
                                       s ++ l++   + +lLl+  + D   +++++++l++a ++++++ +  +i+ d gH
  gi|336252577|ref|YP_004595684.1| 298 SDADALAA--FEGELLLLSFTGDWHFTVEQSETLADAAREADVDvAHHVIESDHGH 351
                                       44555555..78999999999***********************999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); 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:                         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 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3185.96
//
Query:       gi|336252578|ref|YP_004595685.1|  [L=445]
Description: O-acetylhomoserine/O-acetylserine sulfhydrylase [Halopiger xanaduensis SH-6]
Scores for 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-137  456.9   0.0   4.2e-137  456.7   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    4.5e-08   32.8   0.8    6.6e-08   32.2   0.4    1.4  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    4.7e-08   32.6   0.0      8e-08   31.8   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
    7.6e-05   21.8   0.0    0.00013   21.1   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
    0.00031   20.1   0.0    0.00055   19.3   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.061   13.3   0.3       0.31   11.0   0.0    2.2  2  Sugarporin_N     Maltoporin periplasmic N-terminal extension


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 !  456.7   0.0  1.4e-140  4.2e-137       2     382 .]      21     434 ..      20     434 .. 0.99

  Alignments for each domain:
  == domain 1  score: 456.7 bits;  conditional E-value: 1.4e-140
                                       HHHHHTTTTCHTTTTBSS--B---SBBBESSHHHH...CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESS CS
                   Cys_Met_Meta_PP   2 Tllvhagqekdeqtgavavpiyltstykfkdvdea...fageekgyeYsRsgnptrsvleeriaaLeggeaalavss 75 
                                       T  vhagq++d++tga+a+piy+t++y+f+d+d+a    a e++gy+YsR+ npt+++leer+aaLegg+ a+a++s
  gi|336252578|ref|YP_004595685.1|  21 TRSVHAGQHPDPETGAMAPPIYQTTSYVFDDADTAaarYALEDDGYIYSRISNPTVNTLEERLAALEGGTGAVATAS 97 
                                       889****************************9999899999************************************ PP

                                       HHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT- CS
                   Cys_Met_Meta_PP  76 GmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllk 152
                                       GmaA+++a l l++aGd++v+s+d Yggt ++++k++++  ie++fv t + +e e ai+e t  v++Et++np l 
  gi|336252578|ref|YP_004595685.1|  98 GMAALDSATLVLAEAGDNVVCSTDTYGGTTAYFSKTASRRDIEARFVPTLEYDEYEDAIDEDTAFVHVETIGNPSLV 174
                                       ***************************************************************************** PP

                                       ---HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHH.. CS
                   Cys_Met_Meta_PP 153 vvDiekiaklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflq.. 227
                                       ++D+e++a++a+++gv++vvDntfa+p+l+rpl++gaD+v +S+TK+l G +++v+Gv+v+ g+++++++ +     
  gi|336252578|ref|YP_004595685.1| 175 TPDFERVAEIAHDNGVPLVVDNTFATPALCRPLEHGADVVWESTTKWLHGSGTTVGGVLVDGGSFDWGEHGYDEVag 251
                                       *********************************************************************87755479 PP

                                       ............................HHHT-B--HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEEE CS
                   Cys_Met_Meta_PP 228 ............................nalGavlspfdawlllrGlkTLslRlerhqenAlkvAefLekhpkvekv 276
                                                                   ++lG+  spfdaw++l+Gl+ + lR+erh enA  vA +L+ h+ v +v
  gi|336252578|ref|YP_004595685.1| 252 pnhayhdvdfsrdfpeapfaetvrfralRSLGNQQSPFDAWQTLQGLESMPLRVERHCENAAVVADYLQDHEDVAWV 328
                                       ***************************************************************************** PP

                                       E-TTSTTSTTHHHHHHHSSSG-SEEEEEESSHHHHHHHHHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCHHHHHH CS
                   Cys_Met_Meta_PP 277 yYpglpshpqhelakkqlkgaggvlsFelkseeekakkfvdnlklfslaeslGgveslielpasmthasipkeerea 353
                                        Ypgl+shp h+ a ++l ++gg+++F l+++ e+ k+f++n++++++++++G++++l+++pas+th ++++eere+
  gi|336252578|ref|YP_004595685.1| 329 TYPGLESHPTHDNATRYLDDFGGMVAFGLEGGYEAGKAFCENVEVAQFLANIGDAKTLVIHPASTTHGQLTPEEREE 405
                                       ***************************************************************************** PP

                                       TTS-TTEEEEE--SS-HHHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 354 agvtddliRlsvGiEdvdDliaDlkqale 382
                                       agvt+dliR+svGiEd +D++ Dl+qa+e
  gi|336252578|ref|YP_004595685.1| 406 AGVTEDLIRMSVGIEDPKDILTDLEQAIE 434
                                       ***************************85 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 !   32.2   0.4   2.2e-11   6.6e-08      12     151 ..      59     202 ..      49     211 .. 0.82
   2 ?   -3.8   0.0         2   6.1e+03     234     270 ..     298     334 ..     284     345 .. 0.66

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2.2e-11
                                       HHHTSS-SSS....SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT CS
                   DegT_DnrJ_EryC1  12 evlksgwlts....gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelg 84 
                                        +l+ + ++     +p+v+ +E+++aa  g   a+a++sG aAl  a  +l    gd V+  + t+ +t +  +++ 
  gi|336252578|ref|YP_004595685.1|  59 YALEDDGYIYsrisNPTVNTLEERLAALEGGTGAVATASGMAALDSATLVLAEA-GDNVVCSTDTYGGTTAYFSKTA 134
                                       555544333225669******************************999998776.9*************99888776 PP

                                       -EEEEE-B-TTTS.SB-GGGCGGG--TTEEEEEEB-GGGB--....-HHHHHHHHHHCT-EEEEE-TT-TT- CS
                   DegT_DnrJ_EryC1  85 akpvfvDvdpdty.nidpaaieaaitertkaIlpVhlyGqva....dmdalkaiaakhglkvieDaAhAlGa 151
                                        +    D+++  + +++ ++ e ai e t+  + V++ G+++    d++++ +ia++ g++++ D   A  a
  gi|336252578|ref|YP_004595685.1| 135 SR---RDIEARFVpTLEYDEYEDAIDEDTAF-VHVETIGNPSlvtpDFERVAEIAHDNGVPLVVDNTFATPA 202
                                       65...58886654368999*********965.689****9977778*******************8777665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2
                                       HCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTS CS
                   DegT_DnrJ_EryC1 234 LerldelvarRreiaelykeeLaelegtaelttpket 270
                                       Le +   v+r  e+a++  + L++ e +a +t p  +
  gi|336252578|ref|YP_004595685.1| 298 LESMPLRVERHCENAAVVADYLQDHEDVAWVTYPGLE 334
                                       5566666777777777777777777766655555544 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 !   31.8   0.0   2.7e-11     8e-08      41     194 ..      72     202 ..      43     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.7e-11
                                       -BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-TH....HHHHHHHT CS
                     Aminotran_1_2  41 gpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyas....yknilrls 113
                                       ++++   +lee+la + g          +av + sG  al++a   l++  +gd+++ ++ ty+     +++ +  +
  gi|336252578|ref|YP_004595685.1|  72 SNPT-VNTLEERLAALEG--------GTGAVATASGMAALDSATLVLAE--AGDNVVCSTDTYGGttayFSKTASRR 137
                                       4444.78999******99........666***********999999997..************76222266777889 PP

                                       TSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETT CS
                     Aminotran_1_2 114 ggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaY 190
                                       ++e + +p       +l  +++e+a++e       t ++ ve++ NP+ + ++ e + ++   a+ +++ l+vD ++
  gi|336252578|ref|YP_004595685.1| 138 DIEARFVP-------TLEYDEYEDAIDE------DTAFVHVETIGNPSLVTPDFERVAEI---AHDNGVPLVVDNTF 198
                                       99******.......*************......899*************9999999999...*************9 PP

                                       TTCB CS
                     Aminotran_1_2 191 agfv 194
                                       a+ +
  gi|336252578|ref|YP_004595685.1| 199 ATPA 202
                                       9755 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.3e-08   0.00013      80     210 ..     104     229 ..      75     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.3e-08
                                       HCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB CS
                       Aminotran_5  80 slars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGti 155
                                       s+     ++gd++v ++  + +++    + a r+ ++ +++p      l+ de+e++++e+t+ v++  + n + + 
  gi|336252578|ref|YP_004595685.1| 104 SATLVlAEAGDNVVCSTDTYGGTTAYFSKTASRRDIEARFVPT-----LEYDEYEDAIDEDTAFVHVETIGNPSLVT 175
                                       2222357899999999999999998899999999999999988.....9999************************* PP

                                       --HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EE CS
                       Aminotran_5 156 qpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGv 210
                                        ++e+++++a+++g+ ++vD + a +     + + g+D++  s+ K l  +G++v
  gi|336252578|ref|YP_004595685.1| 176 PDFERVAEIAHDNGVPLVVDNTFATPALCRPL-EHGADVVWESTTKWLHGSGTTV 229
                                       ********************999988876665.5699999999999666667665 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.9e-07   0.00055      30     169 ..      72     197 ..      49     323 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.9e-07
                                       --HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT CS
                   Beta_elim_lyase  30 edktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea 106
                                        ++tvn+Le+++a+l g  +a+ +++G aA   +  +l++ g++v+++ +  ++  +t   +  a+   rd++ +  
  gi|336252578|ref|YP_004595685.1|  72 SNPTVNTLEERLAALEGGTGAVATASGMAALDSATLVLAEAGDNVVCSTD--TYGGTTAYFSKTAS--RRDIEARFV 144
                                       478*******************************************9865..34444444444444..467777766 PP

                                       TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 107 GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                        +++ ++ e+ai+e  +    ++++ +++  n      +     ++va+ia+++g+pl++D +
  gi|336252578|ref|YP_004595685.1| 145 PTLEYDEYEDAIDE--D----TAFVHVETIGNP----SLVTPDFERVAEIAHDNGVPLVVDNT 197
                                       8999**********..4....789999987774....45555689**************9965 PP

>> Sugarporin_N  Maltoporin periplasmic N-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0001      0.31      20      36 ..      71      87 ..      66      88 .. 0.85
   2 ?   -1.7   0.2      0.96   2.9e+03      32      44 ..     426     438 ..     426     441 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                      Sugarporin_N 20 vaaaasltiEaRLaaLE 36
                                      +++ + +t+E+RLaaLE
  gi|336252578|ref|YP_004595685.1| 71 ISNPTVNTLEERLAALE 87
                                      4788899*********9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.96
                      Sugarporin_N  32 LaaLEkrLqeAeq 44 
                                       L +LE++ ++A q
  gi|336252578|ref|YP_004595685.1| 426 LTDLEQAIEAATQ 438
                                       6789**9999977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); 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:                         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: 00:00:00.41
# Mc/sec: 3244.21
//
Query:       gi|336252579|ref|YP_004595686.1|  [L=84]
Description: hypothetical protein Halxa_1174 [Halopiger xanaduensis SH-6]
Scores for 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:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 620.46
//
Query:       gi|336252580|ref|YP_004595687.1|  [L=197]
Description: Imidazoleglycerol-phosphate dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-60  203.2   1.2    3.2e-60  202.6   1.2    1.3  1  IGPD      Imidazoleglycerol-phosphate dehydratase
  ------ inclusion threshold ------
      0.095   12.5   0.7        2.3    8.0   0.1    2.4  2  ClpS      ATP-dependent Clp protease adaptor protein ClpS


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 !  202.6   1.2   3.6e-64   3.2e-60       1     144 []      33     175 ..      33     175 .. 0.99

  Alignments for each domain:
  == domain 1  score: 202.6 bits;  conditional E-value: 3.6e-64
                                       ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEE CS
                              IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaeval 77 
                                       Tgigf+dhmL+++akhg fdl+v+++gdle+ddHhtvedv+ialGqa++ealgd++gi R+++  +p+Dea+a +++
  gi|336252580|ref|YP_004595687.1|  33 TGIGFFDHMLESVAKHGLFDLEVDCDGDLEIDDHHTVEDVAIALGQAVDEALGDRSGIVRYADRRVPLDEAVAGAVV 109
                                       9**************************************************************************** PP

                                       E--SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                              IGPD  78 dlsgrpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                       d+sgrp + +++e+++++ig ++ ++ ++f esla++ag+tlh++v+ genahh vealfKa+ar+L
  gi|336252580|ref|YP_004595687.1| 110 DVSGRPRFYFDGEFSQDSIGGFTSDMARHFAESLAMNAGLTLHLEVT-GENAHHEVEALFKALARTL 175
                                       **********************************************9.*****************87 PP

>> ClpS  ATP-dependent Clp protease adaptor protein ClpS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1   0.00026       2.3      28      54 ..       8      34 ..       5      47 .. 0.85
   2 ?    2.3   0.1     0.017   1.5e+02      13      29 ..      64      80 ..      62      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00026
                                      HSSS-HHHHHHHHHHHHHHSEEEEEEE CS
                              ClpS 28 vfgkskeeAteimlevhreGravvgvg 54
                                      v + + e+A+e+++ ++ +G a+v +g
  gi|336252580|ref|YP_004595687.1|  8 VTRETAETAIECTIAIDGDGTAAVDTG 34
                                      667899******************876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.017
                                      -S-S-HHHHHHHHHHHS CS
                              ClpS 13 DdvttmefVvevLqkvf 29
                                      Dd++t+e V   L +++
  gi|336252580|ref|YP_004595687.1| 64 DDHHTVEDVAIALGQAV 80
                                      9********99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1594.84
//
Query:       gi|336252581|ref|YP_004595688.1|  [L=263]
Description: hypothetical protein Halxa_1176 [Halopiger xanaduensis SH-6]
Scores for 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   14.9   0.0      0.053   13.9   0.0    1.6  1  Lar_restr_allev  Restriction alleviation protein Lar
        2.4    8.0   8.8        3.1    7.6   8.8    1.2  1  SPX              SPX 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 ?   13.9   0.0   5.9e-06     0.053       3      36 ..       4      43 ..       2      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-06
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigq.......cvyCadCga 36
                                      L  C+fC  +av  ++  +++  ++       +v C dC++
  gi|336252581|ref|YP_004595688.1|  4 LRNCDFCDAEAVGAFEVVPPE-LEPteaeqrrVVLCGDCEV 43
                                      889************977775.44469999*********99 PP

>> SPX  SPX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   8.8   0.00034       3.1      62     156 ..      89     201 ..      42     257 .. 0.36

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00034
                               SPX  62 e..............rtepstsaaadesgnsaadasssepkdeae.......................slprrspls 101
                                                      + + ++s+a+++++ + a+          +                       s  +++p +
  gi|336252581|ref|YP_004595688.1|  89 DettqkrrrttspnaTVSDGDSSATADGTPADAP----------TsdsepksepgitfetdeadiadsSAGQSDPDA 155
                                       0112221111111111111111111111111111..........122111122223333332222222111111111 PP

                               SPX 102 rssrssssygglvssppsansssssddssesnpadssssssssesesssssspsl 156
                                        +++ ++s++  +s+++ a++s+s+          +++ss++se++++++ s+s+
  gi|336252581|ref|YP_004595688.1| 156 AIESGDESADTTESTETTARPSESEV---------DPDSSDASETGGATDASESR 201
                                       11111111111111111111111111.........12222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1876.74
//
Query:       gi|336252582|ref|YP_004595689.1|  [L=167]
Description: amino acid-binding ACT domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   20.2   0.6     0.0011   18.7   0.1    2.1  2  ACT       ACT domain
    0.00057   19.6   0.1     0.0017   18.1   0.0    1.8  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 ?   -3.2   0.0      0.83   7.5e+03      17      28 ..      18      29 ..      17      30 .. 0.79
   2 !   18.7   0.1   1.2e-07    0.0011      12      66 ..     107     159 ..      97     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.83
                                      HHHHHHHTTSEE CS
                               ACT 17 vfgaladrgiNi 28
                                      v ++l +rg+++
  gi|336252582|ref|YP_004595689.1| 18 VIRLLLERGFSV 29
                                      668889999998 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.2e-07
                                       THHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  12 GlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                       G+ a ++g+lad+gi+i+   +   e  + ++  + +v+d+e + +v+ ++++le
  gi|336252582|ref|YP_004595689.1| 107 GIVAGITGTLADNGISIRQTISEDPE--FTDEPKLYLVTDQELPGDVITEIRDLE 159
                                       99**************9977777775..589999999999999999999999986 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       0.4   3.6e+03      11      26 ..      35      50 ..      34      51 .. 0.79
   2 !   18.1   0.0   1.9e-07    0.0017      20      44 ..     105     129 ..      92     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.4
                                      E-S-.---SS--HHHH CS
                             ACT_7 11 vvgsglpfdvtGivak 26
                                      vv++g+ + +tGi+ +
  gi|336252582|ref|YP_004595689.1| 35 VVSGGIEIPNTGIARE 50
                                      7888898899999876 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.9e-07
                                       S--HHHHHHHHHHTTT---EEEE-S CS
                             ACT_7  20 vtGivaklaspLaeagIsifqiSty 44 
                                       + Giva++++ La++gIsi q+ ++
  gi|336252582|ref|YP_004595689.1| 105 QEGIVAGITGTLADNGISIRQTISE 129
                                       569****************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1312.74
//
Query:       gi|336252583|ref|YP_004595690.1|  [L=125]
Description: hypothetical protein Halxa_1178 [Halopiger xanaduensis SH-6]
Scores for 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  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 998.47
//
Query:       gi|336252584|ref|YP_004595691.1|  [L=202]
Description: hypothetical protein Halxa_1179 [Halopiger xanaduensis SH-6]
Scores for 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-30  104.6   0.0      4e-30  104.3   0.0    1.1  1  UPF0029   Uncharacterized protein family UPF0029
    9.2e-13   47.9   1.2    1.1e-12   47.6   0.1    1.8  2  DUF1949   Domain of unknown function (DUF1949)
     0.0021   18.1   0.0     0.0038   17.2   0.0    1.4  1  EFG_C     Elongation factor G C-terminus


Domain annotation for each model (and alignments):
>> UPF0029  Uncharacterized protein family UPF0029
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.0   6.6e-34     4e-30       2     104 ..      20     127 ..      19     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 6.6e-34
                                       TEEEEEEEEE-SSHHHHHHHHHHH--..TTSSEEEEEE....EE....TT.....EE-TTSST..SHHHHHHHHHHT CS
                           UPF0029   2 kSrFiavlaaveseeevkaileelkkenkkathniyAyrlrqkvekvned.....sdddgEpa..AGkkllelLeke 71 
                                        S+Fi+++ +v+s + ++a++ee+++e+ +athn+ Ayr+r   +    +     s+ddgEp+  AGk+ l++L ++
  gi|336252584|ref|YP_004595691.1|  20 GSEFIGHARPVDSVDAAEAFVEEVRAEYDDATHNVPAYRVRADADG---EllrgySSDDGEPSgsAGKPALNVLAQR 93 
                                       69************************************99888854...234567********************** PP

                                       TB-SEEEEEEEE--SS--HHHHH.HHHHHHHHHH CS
                           UPF0029  72 klenvlvvvtRwfGGikLGpgrl.raiseaarea 104
                                       +len++vvvtR+fGG++LG g+l ra+s+a+++a
  gi|336252584|ref|YP_004595691.1|  94 DLENCAVVVTRYFGGTELGVGGLvRAYSRAVKDA 127
                                       *******************************998 PP

>> DUF1949  Domain of unknown function (DUF1949)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.81   4.9e+03      23      25 ..      43      45 ..      33      52 .. 0.48
   2 !   47.6   0.1   1.9e-16   1.1e-12       1      56 []     144     198 ..     144     198 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.81
                           DUF1949 23 vdt 25
                                      v +
  gi|336252584|ref|YP_004595691.1| 43 VRA 45
                                      333 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 1.9e-16
                           DUF1949   1 ltvdYadlgkverlLeqfgativdteYtddVtltlavpeeeveafkaaLtdltsGr 56 
                                       ++v+Y+d g+v+ +Le+ g++  d++Y++dVt+  +vp ee++a++++L+ +tsGr
  gi|336252584|ref|YP_004595691.1| 144 IAVEYDDSGTVRGILESEGYEF-DADYAADVTFDARVPLEEADALRDRLRSATSGR 198
                                       689***************9999.********************************8 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 !   17.2   0.0   6.4e-07    0.0038       5      69 ..     138     199 ..     135     202 .] 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.4e-07
                                       EEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS- CS
                             EFG_C   5 PivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGeg 69 
                                       P ++v i v+ + +g+v + l+s      +++ d  + v+  a++Pl e   ++++Lrs+T+G+ 
  gi|336252584|ref|YP_004595691.1| 138 PHERVSIAVEYDDSGTVRGILESEG---YEFDADYAADVTFDARVPLEEADALRDRLRSATSGRV 199
                                       6667777777777777776665544...3344445679*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1680.52
//
Query:       gi|336252585|ref|YP_004595692.1|  [L=288]
Description: hypothetical protein Halxa_1180 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0085   16.2   0.2     0.0085   16.2   0.2    2.2  3  bPH_6          Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_6  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1      0.47   8.3e+03      59      65 ..      85      91 ..      79     114 .. 0.60
   2 ?   -3.3   0.0      0.57     1e+04      41      55 ..     142     156 ..     135     158 .. 0.66
   3 !   16.2   0.2   4.7e-07    0.0085       2      36 ..     216     250 ..     215     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.47
                             bPH_6 59 dpelvad 65
                                      +++++a 
  gi|336252585|ref|YP_004595692.1| 85 RRRRAAV 91
                                      3333333 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.57
                             bPH_6  41 ldlrdgelvplpavq 55 
                                       + ++ ge++++ ++q
  gi|336252585|ref|YP_004595692.1| 142 AATTPGEPIATYRWQ 156
                                       444557888888887 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 4.7e-07
                             bPH_6   2 prvrvdpdGvevrnlfrtrrlpWsaiagvrfpegr 36 
                                       p+ r+ + G+  r+++   ++pW+++ +vr++eg 
  gi|336252585|ref|YP_004595692.1| 216 PEIRIYENGLVKRRPYTAAFVPWDDVDRVRLREGE 250
                                       889999**************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2477.46
//
Query:       gi|336252586|ref|YP_004595693.1|  [L=909]
Description: TRAP transporter, 4TM/12TM fusion protein [Halopiger xanaduensis SH-6]
Scores for 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-78  262.9  51.4    2.8e-54  184.5  26.6    2.6  2  DctM      Tripartite ATP-independent periplasmic transporter,


Domain annotation for each model (and alignments):
>> DctM  Tripartite ATP-independent periplasmic transporter, DctM component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.5  26.6   1.6e-58   2.8e-54       1     283 [.     226     530 ..     226     576 .. 0.78
   2 !   83.5  16.9   7.2e-28   1.3e-23     265     410 ..     620     775 ..     608     777 .. 0.96

  Alignments for each domain:
  == domain 1  score: 184.5 bits;  conditional E-value: 1.6e-58
                              DctM   1 lvsllvllalgvpvaislalasl..lllallgelllgv...........pleqilaqrvve........glssfall 56 
                                       l++llvl+a+++++++ l+  ++  +++a  g +++ +           ++ +i+ +  ++        ++++++  
  gi|336252586|ref|YP_004595693.1| 226 LGLLLVLEATRRTLGPLLMGLVAffIVYARWGHFVPRDsiigslaiqneTWGNIVYNLWYTveagvmstPVTVSVR- 301
                                       5799***********9987766646666666777666688998888888666666666666777533223333333. PP

                              DctM  57 aipfFvlaGivlersGlakrlidlaaalvGrvrGGlakvsvvgsalfgaiSGsavAnvaavGsitipamkrsGykre 133
                                        i +F+l+G++le+sG++k +idla+al+G+ +GG+ak+svv+s ++g++SGs++An++++G++tip+mkrsGy +e
  gi|336252586|ref|YP_004595693.1| 302 FIYIFILFGAFLEMSGAGKWFIDLAYALTGTRQGGPAKASVVSSGFMGMLSGSSIANTVTTGAFTIPLMKRSGYSPE 378
                                       3455************************************************************************* PP

                              DctM 134 faaaviaasstlgqiiPPslglivfama.vlgvsigdlfaaaiipglllavglllavaiaakkenlrsktkaelkrl 209
                                       f++av++++s +gq++PP++g+++f+++ +lgv+++d+++aa++p++  ++g+ ++v+++a + ++ + +++el+ +
  gi|336252586|ref|YP_004595693.1| 379 FSGAVESSASSGGQMLPPVMGAAAFLIVeYLGVPYADVIIAATLPAIAFFFGMWIMVHFEAVRGGIGGLPRDELPAV 455
                                       ***************************************************************************** PP

                              DctM 210 gqalkeaipalllpliiligillgiftpteagavavvyalviallv.....yrrlt.leevaaa.llstakttaavl 279
                                       g  ++e++ +l+ + ++l+++++   +   ag + +v+  ++ ++v     + r+  l+++ a+ l++ta ++    
  gi|336252586|ref|YP_004595693.1| 456 GSRFREGWFYLVPIALLLYYLVVARLSIGRAGWYTIVAIVALIAVVaayneRNRVPlLGTIGAIyLAQTAAYA---- 528
                                       ********65555555555555555666688888888887777777554332222202222222445554444.... PP

                              DctM 280 fila 283
                                         +a
  gi|336252586|ref|YP_004595693.1| 529 --VA 530
                                       ..33 PP

  == domain 2  score: 83.5 bits;  conditional E-value: 7.2e-28
                              DctM 265 aaallstakttaavlfilaaagifaglltltgvplklselllslsggk.llfLilvnllvlvlGmfldttaaiiilv 340
                                       ++++ s+a+t+++v++++aaag++ g+++++g++ +l++l+ ++sgg+ ll+L l+ + +++ Gm+++tta++iil 
  gi|336252586|ref|YP_004595693.1| 620 LKSMDSGARTATTVVVAVAAAGVVPGVISVSGLGPNLAALIDAVSGGSmLLLLSLTGVASIIFGMGMPTTAMYIILI 696
                                       6778899****************************************9888999*********************** PP

                              DctM 341 pilaPaaaklgidpihfgvvivlnlsiglitPPvGlalfvassia.........kvsveeivkalvPflvvlvvalv 408
                                       ++l   + ++gi  +++++++++++ ++++tPPv++a+f+++++a         +++   + k lvPf++v+++ ++
  gi|336252586|ref|YP_004595693.1| 697 AMLETPLVEAGIVALAAHLFVLYFGLMADVTPPVAVAAFAGAGVAkadelktasTAFLLSLNKILVPFAFVFSPGIL 773
                                       ***999*********************************************9988999***************9998 PP

                              DctM 409 li 410
                                       l+
  gi|336252586|ref|YP_004595693.1| 774 LL 775
                                       86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (909 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.68u 0.25s 00:00:00.93 Elapsed: 00:00:00.41
# Mc/sec: 6627.53
//
Query:       gi|336252587|ref|YP_004595694.1|  [L=183]
Description: hypothetical protein Halxa_1182 [Halopiger xanaduensis SH-6]
Scores for 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   82.3   0.0    3.6e-23   81.7   0.0    1.3  1  DUF1850   Domain of unknown function (DUF1850)
  ------ inclusion threshold ------
       0.16   11.8   0.7       0.23   11.2   0.7    1.2  1  VirB8     VirB8 protein


Domain annotation for each model (and alignments):
>> DUF1850  Domain of unknown function (DUF1850)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.0     4e-27   3.6e-23       1      86 []      56     139 ..      56     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 4e-27
                           DUF1850   1 ftlswtHSVektpveEdyrvegggLvleetrfksfGaGlpspaeagervedgwfvlrinrpleelrlrvggiadhrl 77 
                                       +tl++tHSVektpve+ y v+g +L ++++ f s+GaGlp+++  +e+ edg fv+ +n ++ el++++g++a h+l
  gi|336252587|ref|YP_004595694.1|  56 VTLAYTHSVEKTPVEDIYVVDGTELRMDRMVFYSHGAGLPTNEPIEET-EDG-FVVYPNASYAELNVVPGSVAGHEL 130
                                       69*****************************************99996.555.55779******************* PP

                           DUF1850  78 cvdgreypL 86 
                                       +v++++y+L
  gi|336252587|ref|YP_004595694.1| 131 VVGDERYDL 139
                                       *******98 PP

>> VirB8  VirB8 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.7   2.6e-05      0.23      18      70 ..       6      53 ..       2      67 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.6e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX.XXXXXXXXXXXX CS
                             VirB8 18 rnwrlvafvslliavlavgavvlllplktvePyvvevdkttGeveavapaaek 70
                                      r+  +v +++l++  ++++av++ +  kt    +v  d++tGe    ap+++ 
  gi|336252587|ref|YP_004595694.1|  6 RHVVVV-LLVLAVLGASAIAVATATDEKT----LVVADADTGERLLEAPVDDG 53
                                      444344.6667776777778888888888....8899******9999999544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1399.52
//
Query:       gi|336252588|ref|YP_004595695.1|  [L=356]
Description: TRAP transporter solute receptor, TAXI family [Halopiger xanaduensis SH-6]
Scores for 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-71  240.7   1.2    2.6e-71  240.4   1.2    1.0  1  NMT1_3          NMT1-like family
    3.8e-09   36.8   1.6    5.9e-08   32.9   0.1    2.2  2  NMT1            NMT1/THI5 like
    1.4e-08   34.6   2.8    2.6e-08   33.8   2.8    1.5  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
  ------ inclusion threshold ------
      0.018   14.9   0.3      0.038   13.8   0.3    1.6  1  TAT_signal      TAT (twin-arginine translocation) pathway sig


Domain annotation for each model (and alignments):
>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.4   1.2   5.7e-75   2.6e-71       3     285 ..      79     355 ..      78     356 .] 0.97

  Alignments for each domain:
  == domain 1  score: 240.4 bits;  conditional E-value: 5.7e-75
                            NMT1_3   3 TastgGtyYpvGvaiatliseklakdqkvkasaqssaGsveNiqllkkgeadlailqsdvayeAyeGeg..efegkk 77 
                                       +++tgGtyYp+ +   +++se++++d     ++qs+++sveN+ +l  +e ++a++q+d+ay Ay+G+g  efeg +
  gi|336252588|ref|YP_004595695.1|  79 AGGTGGTYYPLSGDFKSIVSENTPHD----LQVQSTGASVENVGALGREETEFALIQNDIAYFAYNGTGleEFEG-N 150
                                       69********************9877....589**********************************98778**9.7 PP

                            NMT1_3  78 plknlraitmlyaevfqlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealglsekdlklleelgygesad 154
                                        l+n+r +++ly+e++++++++dsgi+s++dl+g +v+ G+ gsGt+++a++ile++gl + d++  ++ +++++ad
  gi|336252588|ref|YP_004595695.1| 151 ALENIRGVATLYPETIHVITQADSGIESLEDLEGASVNTGDLGSGTQVNALQILESAGLGDGDFDE-QNSDFATAAD 226
                                       9***************************************************************97.788******* PP

                            NMT1_3 155 alkdgqldgaalvaGvPvsavtqlaasedikliplddeqldkllkeypvftkyvipagtypq.dedikTiavpnflv 230
                                       +++dg +d+a++v+G Pv+++ +la+++di l++++++ ++++ ++ ++f++ ++pagty++ ded++T++v+++++
  gi|336252588|ref|YP_004595695.1| 227 QIRDGDVDAAFVVGGWPVGSIEELATTSDIALVEVSGDVRESIMSDAEWFAEDTVPAGTYDGiDEDVETVSVQAMIA 303
                                       *************************************************************99************** PP

                            NMT1_3 231 vradldeelvYeitkaifenldelnsihkaakeislekalaglpvplHpGAerYY 285
                                       +++ +dee v e+t aif+n+d++ +   +a  is ++a +g+p+ lHpGA  Y+
  gi|336252588|ref|YP_004595695.1| 304 THEAVDEEIVEEVTTAIFDNTDQITQ---KADFISADSAQDGMPIDLHPGADAYF 355
                                       *********************98766...55669********************9 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.1   1.3e-11   5.9e-08      62     160 ..     154     251 ..     104     271 .. 0.87
   2 ?    3.1   0.3     0.018        79     100     145 ..     290     335 ..     284     348 .. 0.63

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.3e-11
                                       -EEEEEEEE-S--EEEEEECCC--SSGGGGTTSEEEE-S.-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHH CS
                              NMT1  62 pvvsvaallqeplsglivlkdsgikspkDLkGkrigyvg.spfekallkallakdggdpsdvtlvnvggtslakall 137
                                        ++ va+l+  ++ ++i+++dsgi+s++DL+G  + +   ++ ++ +  ++l+++g+   d+  +n ++  +a+++ 
  gi|336252588|ref|YP_004595695.1| 154 NIRGVATLY-PETIHVITQADSGIESLEDLEGASVNTGDlGSGTQVNALQILESAGLGDGDFDEQNSDFATAADQIR 229
                                       688899999.66889*********************99967779999****************************** PP

                                       CTSSSEEECEETTTHHHHHHHTT CS
                              NMT1 138 tgkvDaaiggyenwegveleseg 160
                                       +g vDaa+ ++ +w + ++e+ +
  gi|336252588|ref|YP_004595695.1| 230 DGDVDAAF-VVGGWPVGSIEELA 251
                                       *******9.99999888777655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.018
                                       S-TTHHHHHHHHHHHTT-.-GGG-EEEE-.TT-HHHHHHCTSSSEEE CS
                              NMT1 100 gspfekallkallakdgg.dpsdvtlvnvggtslakalltgkvDaai 145
                                         ++e   ++a++a++ + d++ v+ v++  ++ + + +t+k+D++ 
  gi|336252588|ref|YP_004595695.1| 290 DEDVETVSVQAMIATHEAvDEEIVEEVTTAIFDNT-DQITQKADFIS 335
                                       44566667777777666557777777777666654.55555577765 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 !   33.8   2.8   5.8e-12   2.6e-08      89     216 ..     168     322 ..      91     341 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 5.8e-12
                                       EEEETTSS--SHHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEEE... CS
                    Phosphonate-bd  89 iivradsdiqsledLkgktiafvspsStsGylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdadaaa... 162
                                       +i++ads+i+sledL+g+++  ++    sG++v a ++++ agl  + df+e+  ++  +a++++ +gd+daa+   
  gi|336252588|ref|YP_004595695.1| 168 VITQADSGIESLEDLEGASVNTGDLG--SGTQVNALQILESAGLGDG-DFDEQ-NSDFATAADQIRDGDVDAAFvvg 240
                                       79**********************87..69***************66.56664.567999**************888 PP

                                       ....................EEHHHHHHHHHH-HHHHTTEEEEE.........EEEEEE--EEEEETTS-HHHHHHH CS
                    Phosphonate-bd 163 ....................vsadaledlvaegpedkdelrvia.........ssppipndpvvvrkelseelkeki 210
                                                           vs d++e+  ++++   ++++            ++  + +++++ +++++ee++e++
  gi|336252588|ref|YP_004595695.1| 241 gwpvgsieelattsdialveVSGDVRESIMSDAEWFAEDTVPAGtydgidedvETVSV-QAMIATHEAVDEEIVEEV 316
                                       8888887777766666655555555555554332222333322133333344366666.778899999999999999 PP

                                       HHHHHH CS
                    Phosphonate-bd 211 qdalls 216
                                       ++a+++
  gi|336252588|ref|YP_004595695.1| 317 TTAIFD 322
                                       999887 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   8.6e-06     0.038       1      23 [.       4      25 ..       4      28 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.6e-06
                        TAT_signal  1 klSRRdFLKgsAAaaAAaalggc 23
                                      +++RR F+ +s+ a+ A+++g c
  gi|336252588|ref|YP_004595695.1|  4 DINRRRFIAASGIAGLAGLAG-C 25
                                      59*************777555.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2703.38
//
Query:       gi|336252589|ref|YP_004595696.1|  [L=704]
Description: peptidase S9 prolyl oligopeptidase active site domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-57  192.5   0.2      9e-57  192.0   0.2    1.2  1  Peptidase_S9   Prolyl oligopeptidase family
    3.5e-18   65.0   7.3    3.4e-08   33.2   0.1    5.2  5  PD40           WD40-like Beta Propeller Repeat
    9.3e-08   32.0   0.1    1.7e-06   27.9   0.2    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    3.8e-07   29.9   0.0    6.7e-07   29.1   0.0    1.3  1  DLH            Dienelactone hydrolase family
      4e-07   29.0   0.4     0.0045   15.7   0.0    2.2  2  AXE1           Acetyl xylan esterase (AXE1)
    1.8e-05   24.2   0.9      0.032   13.5   0.3    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
      0.002   16.9   0.0       0.41    9.4   0.0    3.5  4  DPPIV_N        Dipeptidyl peptidase IV (DPP IV) N-terminal re
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.36   11.0   0.0    1.8  2  Abhydrolase_4  TAP-like protein
       0.26   10.0   0.0       0.39    9.5   0.0    1.1  1  Peptidase_S28  Serine carboxypeptidase S28
       0.27   11.1   0.0        6.6    6.6   0.0    2.1  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.0   0.2     5e-60     9e-57       4     210 ..     464     672 ..     461     674 .. 0.97

  Alignments for each domain:
  == domain 1  score: 192.0 bits;  conditional E-value: 5e-60
                                       -.HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHH CS
                      Peptidase_S9   4 s.selqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltg 79 
                                       + +e+q+la+rGyvv+++n+rGs+gyGe+ + a++r++g+++++D++a+++a+ +++yvd +++++tGgS+GG++t+
  gi|336252589|ref|YP_004595696.1| 464 MwHEFQTLAARGYVVFWCNPRGSTGYGEDHATAIERDWGEVTLTDVLAGVDAVREREYVDDDEIFVTGGSFGGFMTA 540
                                       4489************************************************************************* PP

                                       HHHHH-GGG-SEEEEESE---CCCHHCSTTSTHH.HCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-S CS
                      Peptidase_S9  80 aalnqrpdlFkaavaevpvvdvlrydsdtdllte.eymewgnpeeneegykelspyspldnvkaypplLlihGlaDd 155
                                       +a++ ++d+F aav++++v+d++ ++ +td++   e ++ ++p+e++e  +e+sp++++    +++p+Ll+h++ D+
  gi|336252589|ref|YP_004595696.1| 541 WAVG-NTDRFTAAVSQRGVYDLTGFYGSTDAFHLlEGDFDTTPWEEPEFLWEQSPVAHVPD--VDTPTLLMHSDRDY 614
                                       ****.**************************99999*************************..************** PP

                                       SS-THHHHHHHHHHH--S-SEEEEEETTS-S...STTSSHHHHHHHHHHHHHHHHHCT CS
                      Peptidase_S9 156 rvppaealklvaaLqkkgknvlllifpdegH...gvgkprakveelarllaFlkealg 210
                                       r+p ++a+ ++  L+k+g++++l+ +p egH   ++g+p + v++++r++++++ + +
  gi|336252589|ref|YP_004595696.1| 615 RTPANTAELFYLGLKKHGVDTRLVRYPREGHelsRSGEPAHVVDRIERIARWFDGYSD 672
                                       *******************************999999999999**********99876 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.5e-06    0.0045      10      30 ..      14      34 ..       9      40 .. 0.88
   2 !   33.2   0.1   1.9e-11   3.4e-08       3      38 .]      56      92 ..      54      92 .. 0.91
   3 !   10.5   0.0   0.00026      0.46      16      26 ..     115     125 ..     114     133 .. 0.91
   4 ?    4.5   0.0     0.019        35       2      28 ..     202     227 ..     201     239 .. 0.81
   5 ?   -2.9   0.1       4.2   7.6e+03      14      26 ..     317     329 ..     316     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.5e-06
                                      .EEEEEE-TTSSEEEEEEECT CS
                              PD40 10 negaPsfSPDGkrlaFsSdRg 30
                                      + ++P++SPDG r aF+++ +
  gi|336252589|ref|YP_004595696.1| 14 HAEEPRLSPDGDRVAFVRRTP 34
                                      789**************9865 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 1.9e-11
                                      E--SSSS.EEEEEE-TTSSEEEEEEECT.TCEE.EEE CS
                              PD40  3 rltntpgnegaPsfSPDGkrlaFsSdRgsGkpd.Iyv 38
                                      + t  +g +  P++ PDG+rlaF+S+Rg+G+ + ++v
  gi|336252589|ref|YP_004595696.1| 56 QFTARDGVDSQPRWHPDGSRLAFVSTRGEGDRQqLWV 92
                                      67888999**********************9999997 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00026
                                       E-TTSSEEEEE CS
                              PD40  16 fSPDGkrlaFs 26 
                                       +SPDG+rl F+
  gi|336252589|ref|YP_004595696.1| 115 WSPDGSRLCFT 125
                                       **********9 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.019
                                       EE--SSSS.EEEEEE-TTSSEEEEEEE CS
                              PD40   2 krltntpgnegaPsfSPDGkrlaFsSd 28 
                                       +rlt ++ +++aP++  D  + +++S 
  gi|336252589|ref|YP_004595696.1| 202 TRLTDGDRDYIAPTWGDDE-TVYYASK 227
                                       79*************8876.7777665 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 4.2
                                       EEE-TTSSEEEEE CS
                              PD40  14 PsfSPDGkrlaFs 26 
                                       +++ P G  l+F+
  gi|336252589|ref|YP_004595696.1| 317 FTWAPEGDDLYFT 329
                                       7999999999998 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.2   9.4e-10   1.7e-06       1      98 [.     445     549 ..     445     560 .. 0.79
   2 ?    1.5   0.0      0.11   1.9e+02     206     251 ..     593     646 ..     562     648 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 9.4e-10
                                       SEEEEE-STTT.....CGGGGTTGHHHHHHHHTTSEEEEEEETTS.TTSSSTTTGB....CHHSHHHHHHHHHHH.. CS
                     Abhydrolase_1   1 pvlvilhGlpg.....ssdvwaerglapaLakdgfdvillDlrGv.gySspapacin...ddygtasvaddldri.. 66 
                                       p+lv +hG+p       + +w+e   +++La +g+ v+  ++rG+ gy++ + + i     + ++ +v + +d++  
  gi|336252589|ref|YP_004595696.1| 445 PLLVEIHGGPHahwttAGTMWHE---FQTLAARGYVVFWCNPRGStGYGEDHATAIErdwGEVTLTDVLAGVDAVre 518
                                       67899******776655555888...99****************769**********55555555555555667788 PP

                                       HHHCTTSSEEEEEETHHHHHHHHHHHHHGGGE CS
                     Abhydrolase_1  67 ldalgddkltlvGhSmGGmialayaaeyperV 98 
                                       ++  +dd++ + G+S+GG++ +++     +r 
  gi|336252589|ref|YP_004595696.1| 519 REYVDDDEIFVTGGSFGGFMTAWAVGN-TDRF 549
                                       ******************988776654.5555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
                                       C....THHHHSEEEEEEETTCSSSCH.HHHHHHHHCHTS...EEEEEEETCSSS CS
                     Abhydrolase_1 206 e....lknvlaptlvisgtsDplvpp.kaledlaqllpk...krlvvisdagHl 251
                                       +    + +v  ptl+++++ D  +p   a  ++ +l ++    rlv+++ +gH 
  gi|336252589|ref|YP_004595696.1| 593 SpvahVPDVDTPTLLMHSDRDYRTPAnTAELFYLGLKKHgvdTRLVRYPREGHE 646
                                       26666778999***************8888888888777899999999999996 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   3.7e-10   6.7e-07      35     192 ..     470     650 ..     461     671 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.7e-10
                               DLH  35 rlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavaylksvpevstkkvgvvGfCmGGal 111
                                        la  GYv++  +         ++ ++ a+a++  + +v     l d+ a v++++++++v+++++ v+G  +GG +
  gi|336252589|ref|YP_004595696.1| 470 TLAARGYVVFWCNPRGST----GYGEDHATAIERDWGEV----TLTDVLAGVDAVREREYVDDDEIFVTGGSFGGFM 538
                                       677888888877643333....45555556664444444....4555559999999999999*************99 PP

                               DLH 112 alllaaevpevdaavafYG...............................lspekeleeaakikapilalfgeeDef 157
                                       +     + +++ aav+  G                               l  ++++++++++ +p l ++ ++D  
  gi|336252589|ref|YP_004595696.1| 539 TAWAVGNTDRFTAAVSQRGvydltgfygstdafhllegdfdttpweepefLWEQSPVAHVPDVDTPTLLMHSDRDYR 615
                                       8877777789999998666666666666********************99999************************ PP

                               DLH 158 ipadevekleealkaanvdlelkvYpgagHaFand 192
                                        pa+++e +   lk+++vd +l+ Yp  gH   + 
  gi|336252589|ref|YP_004595696.1| 616 TPANTAELFYLGLKKHGVDTRLVRYPREGHELSRS 650
                                       ******************************65554 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.5e-06    0.0045      58     130 ..     413     496 ..     399     505 .. 0.80
   2 !   11.4   0.1   5.2e-05     0.093     156     201 ..     507     552 ..     501     558 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-06
                                       EEEEEEGGGEEEEEEEEEES.SS......SSEEEEEEEE-.....TT--GGGHHHHHHHHHTT-EEEEEE-TTTS.. CS
                              AXE1  58 dltfegvrgarikaklvlPkeke......eklPavvefhG.....YegsrgeihdllnyaaaGyavvvmdvRGqgge 123
                                       ++ fe+  g++i+++++ P e +      e+ P++ve hG     +++    +h+  + aa Gy+v+  + RG  g+
  gi|336252589|ref|YP_004595696.1| 413 EVWFESEDGTEIQGWVLTPPEFDadaspgETYPLLVEIHGgphahWTTAGTMWHEFQTLAARGYVVFWCNPRGSTGY 489
                                       689**************996532222333789*******95544445556789999********************* PP

                                       SSB-SSC CS
                              AXE1 124 sedkvgs 130
                                        ed+ + 
  gi|336252589|ref|YP_004595696.1| 490 GEDHATA 496
                                       9996554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.2e-05
                                       HHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEE CS
                              AXE1 156 lDavrlveivaslpevDeeRvavlGasqGGalalavaalekrikav 201
                                       +D+   v++v++ + vD++ ++v+G+s GG ++  + +  +r  a+
  gi|336252589|ref|YP_004595696.1| 507 TDVLAGVDAVREREYVDDDEIFVTGGSFGGFMTAWAVGNTDRFTAA 552
                                       799999************************9986555555555544 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.3   1.8e-05     0.032      17     104 ..     461     552 ..     446     555 .. 0.74
   2 !    8.8   0.0   0.00048      0.86     185     234 ..     596     647 ..     591     652 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                       Hydrolase_4  17 sgryaelaeaLaaqGfavyalDhrGhGrse..gkrghvpsf.ddyvdDlaafvekvkeehpel..plfllGhSmGGl 88 
                                       +g + + ++ Laa+G+ v+  + rG    +   +++  +++ +  ++D+ a v++v+e++     ++f+ G S GG+
  gi|336252589|ref|YP_004595696.1| 461 AGTMWHEFQTLAARGYVVFWCNPRGSTGYGedHATAIERDWgEVTLTDVLAGVDAVREREYVDddEIFVTGGSFGGF 537
                                       666778899***************96443323334444555155689**********77765568************ PP

                       Hydrolase_4  89 iallyllrypdkvagl 104
                                       +++ ++ +  + ++++
  gi|336252589|ref|YP_004595696.1| 538 MTAWAVGNTDR-FTAA 552
                                       98876655544.5555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00048
                       Hydrolase_4 185 eraakitlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyHel 234
                                       ++++++++P+ll+h+++D  ++ + ++ +y  l++   d +l  yp   Hel
  gi|336252589|ref|YP_004595696.1| 596 AHVPDVDTPTLLMHSDRDYRTPANTAELFYLGLKKHgvDTRLVRYPREGHEL 647
                                       5678899***********************999998899***********98 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.036        64      45      62 ..      15      32 ..       6      34 .. 0.85
   2 !    9.4   0.0   0.00023      0.41       3      80 ..      23     105 ..      21     113 .. 0.78
   3 ?    1.3   0.0     0.065   1.2e+02     106     119 ..     113     126 ..     106     128 .. 0.85
   4 ?   -2.5   0.0      0.94   1.7e+03      42      60 ..     311     329 ..     277     335 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.036
                                      BSEEEEESSTTEEEEEET CS
                           DPPIV_N 45 lqlakwSPagdklafvrn 62
                                      ++ +++SP+gd++afvr 
  gi|336252589|ref|YP_004595696.1| 15 AEEPRLSPDGDRVAFVRR 32
                                      56789***********85 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00023
                                       TSSEEEEEECEEEESSSEETTEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEEEET......TEEEEESTTTS CS
                           DPPIV_N   3 dgkflllatnaeknwRhsytaeyyiydletneveelspgeeklqlakwSPagdklafvrn......nnLyvrelatg 73 
                                       dg+++ +   ++ +  +syta+ +++++  +e ++ +  ++  + ++w P+g +lafv        + L+v  +  g
  gi|336252589|ref|YP_004595696.1|  23 DGDRVAF-VRRTPDDDDSYTATAFVVPVGGDEPTQFTARDGVDSQPRWHPDGSRLAFVSTrgegdrQQLWVVPTDGG 98 
                                       5555555.55555566899****************99999*****************97522222267888888888 PP

                                       EEEECES CS
                           DPPIV_N  74 keiqlTs 80 
                                       ++++lTs
  gi|336252589|ref|YP_004595696.1|  99 EARRLTS 105
                                       8888886 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.065
                                       EEE-TTSSEEEEEE CS
                           DPPIV_N 106 vwWspdgsrlaylr 119
                                       + Wspdgsrl +++
  gi|336252589|ref|YP_004595696.1| 113 LEWSPDGSRLCFTQ 126
                                       67999999999976 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 0.94
                                       TT.BSEEEEESSTTEEEEE CS
                           DPPIV_N  42 eeklqlakwSPagdklafv 60 
                                        + +  ++w+P+gd+l+f+
  gi|336252589|ref|YP_004595696.1| 311 IGHRCSFTWAPEGDDLYFT 329
                                       5666677888888888886 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.3   5.9e+03      30      76 ..     438     489 ..     428     498 .. 0.66
   2 ?   11.0   0.0    0.0002      0.36      29      81 ..     598     653 ..     585     661 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.3
                     Abhydrolase_4  30 takgaapvLllqnerDpaTPyegakklakalgg.a...vlvtvege.GHgal 76 
                                         +g++ +Ll++  + p     +a ++ ++++  a    +v + +  G +++
  gi|336252589|ref|YP_004595696.1| 438 ASPGETYPLLVEIHGGPHAHWTTAGTMWHEFQTlAargYVVFWCNPrGSTGY 489
                                       4567788899999999999888999999888876334444444444455555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0002
                     Abhydrolase_4  29 stakgaapvLllqnerDpaTPyegakklakalgg.a...vlvtvegeGHgalaagnt 81 
                                       +++ +++p+Ll+ + rD  TP ++a+ +   l++ +   +lv +  eGH+ +++g++
  gi|336252589|ref|YP_004595696.1| 598 VPD-VDTPTLLMHSDRDYRTPANTAELFYLGLKKhGvdtRLVRYPREGHELSRSGEP 653
                                       222.469*************************99756779**********9987665 PP

>> Peptidase_S28  Serine carboxypeptidase S28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00022      0.39      92     130 ..     505     542 ..     491     552 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00022
                     Peptidase_S28  92 aLaDlasfikalkqkfklsssskwitfGgSYsgsLaawa 130
                                        L D+ + + a+++  ++ ++ ++ + GgS++g + awa
  gi|336252589|ref|YP_004595696.1| 505 TLTDVLAGVDAVRE-REYVDDDEIFVTGGSFGGFMTAWA 542
                                       699*********95.556677778899***********7 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0037       6.6     108     164 ..     595     648 ..     509     660 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0037
                                       B--GGG--SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S--- CS
                            BAAT_C 108 lipvekakgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGHlie 164
                                       +  v + ++p ll+ +  D  +p+++ ae     Lkk+g +  ++l+ Yp  GH + 
  gi|336252589|ref|YP_004595696.1| 595 VAHVPDVDTPTLLMHSDRDYRTPANT-AELFYLGLKKHGVD--TRLVRYPREGHELS 648
                                       34455678888999999999888765.66888889998888..88999999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (704 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:                        23  (0.00128284); 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: 0.64u 0.25s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 4935.41
//
Query:       gi|336252590|ref|YP_004595697.1|  [L=66]
Description: hypothetical protein Halxa_1185 [Halopiger xanaduensis SH-6]
Scores for 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-15   54.6   0.4    8.5e-15   54.6   0.4    1.0  1  DUF2892   Protein of unknown function (DUF2892)


Domain annotation for each model (and alignments):
>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.4   4.7e-19   8.5e-15       1      63 [.       1      63 [.       1      66 [] 0.96

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 4.7e-19
                           DUF2892  1 MkkNvgtldRilrivvGlvllllallglsggwgwllglvGavllltgltgfCplyallgintc 63
                                      M+kNvg++dR +r v++++ll++++ +     g l+ ++G   l+t+l+  Cp+ al+gi+tc
  gi|336252590|ref|YP_004595697.1|  1 MDKNVGGTDRTMRTVLAAALLVVGYRNRDRTLGALAFVAGSDVLATALIQRCPVNALFGIDTC 63
                                      99**************************7777******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 547.60
//
Query:       gi|336252591|ref|YP_004595698.1|  [L=315]
Description: Mannonate dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-77  259.2   0.3      1e-59  202.2   0.1    2.0  2  UxuA          D-mannonate dehydratase (UxuA)
    2.8e-21   76.0   0.2    3.6e-21   75.6   0.2    1.2  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> UxuA  D-mannonate dehydratase (UxuA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   4.3e-19   3.8e-15      25     136 ..      22     133 ..      10     140 .. 0.85
   2 !  202.2   0.1   1.1e-63     1e-59     173     345 ..     141     314 ..     134     315 .] 0.96

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 4.3e-19
                                       T--EEEE--TTS-T.TS---HHHHHHHHHHHHHTT-EEEEEE-----HHHHHT-TTHHHHHHHHHHHHHHHHHTT-- CS
                              UxuA  25 Gvkgvvsalhdipa.gevWekeeilklkeeiekagltlevvesvpvhediklgteerdryienykqtirnlakiGvk 100
                                       G++  v  +  + + +  We++ ++++++   ++g++l+vve+ p++++  lg+  rd++ie +k  i n++++G++
  gi|336252591|ref|YP_004595698.1|  22 GIDTAVVRF--WGVdEAWWEYDTLMQTRNRFADHGFSLDVVEDRPPMNATVLGEAGRDEEIETVKTLIENMGRLGID 96 
                                       554444333..33414568999******************************************************* PP

                                       EEEE---S.S--S--SEEEEE-TTS-EEEEE-HHHHH CS
                              UxuA 101 vvCYnfmp.vldWtrtdleykledgskalrfdkkeie 136
                                       + C+ +    ++ +rt  ++++  gs+ + +d++ ++
  gi|336252591|ref|YP_004595698.1|  97 TYCWVWTEnPVGVIRTSDSRPGRGGSQRIGYDNEWMD 133
                                       ******852589********************98766 PP

  == domain 2  score: 202.2 bits;  conditional E-value: 1.1e-63
                                       TT--HHHHHHHHHHHHHHHHHHHHHHT-EEEE---SSSS-.BTTB--SSSSHHHHHHHHHH--STTEEEEEEHHHHT CS
                              UxuA 173 kkideeklrenlayFlkeiiPvaeevgvklaihPDDPPlp.ifGlpRivstkedlqrlldlvdspangitlCtGslg 248
                                       ++i e++l+ nl+yFl+e++Pvaee+gv la+hPDDPP++ ++G+pRiv++ +d++r+ldl+dsp +g+t+C+G+++
  gi|336252591|ref|YP_004595698.1| 141 SDITEAELWANLEYFLDEVVPVAEEYGVNLALHPDDPPRSpVRGVPRIVKSVDDYRRILDLHDSPRHGVTFCQGNFA 217
                                       5899**********************************988************************************ PP

                                       TSTT--HHHHHHHHGGGEEEEE--EEEE-SSTT-EEEE-TTSSSS-HHHHHHHHHHHHHHH-EE-----B-GGGG.. CS
                              UxuA 249 aradndlvemikefadriyFahlRnikreedeksFveaahleGsvdlaevvkalleeeyrrylRpDhgrlllddk.. 323
                                       a++  d +e i+ef+dri+F+h+R+++      sFve+ h eG +d+ + + a+  +++++++RpDh + ++++   
  gi|336252591|ref|YP_004595698.1| 218 AME-TDTIEAIREFGDRIHFVHFRDVEGD--GDSFVETWHDEGPTDMRAAIDAYRAVGFDGPIRPDHVPRMVGEDdr 291
                                       *99.788899****************998..568*************************************999877 PP

                                       .--STT--HHHHHHHHHHHHHHH CS
                              UxuA 324 .klrPGYslidRllgiaylrGll 345
                                        ++  GY+ ++Rl +i+y++Gll
  gi|336252591|ref|YP_004595698.1| 292 eDAMSGYTDMGRLFAIGYIKGLL 314
                                       7899*****************97 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 !   75.6   0.2     4e-25   3.6e-21       3     194 ..      17     248 ..      15     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 4e-25
                                       HHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHH CS
                      AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraiela 79 
                                        a+++G+d+  +++++ + +++   ++l + r++++++g+ + +++  +  ++ +   +ea r+e ++ +k  ie +
  gi|336252591|ref|YP_004595698.1|  17 MAKQLGIDTAVVRFWGVDEAWWE-YDTLMQTRNRFADHGFSLDVVEDRPPMNATVL--GEAGRDEEIETVKTLIENM 90 
                                       6999************9999995.89999**********99777766666666443..44447777*********** PP

                                       HHHTBSEEEEEBCC..................................GBCTTTSGHHHHHHHHHHHHHHHHHHHHH CS
                      AP_endonuc_2  80 aaLGapllvlhpGt..................................agagpkgseeeawerlaeslneladyaek 122
                                        +LG+++                                          +  ++ +e+e w++l   l+e++++ae+
  gi|336252591|ref|YP_004595698.1|  91 GRLGIDTYCWV--WtenpvgvirtsdsrpgrggsqrigydnewmdrapEHPASDITEAELWANLEYFLDEVVPVAEE 165
                                       ******96555..22468889999******************9999776677777777******************* PP

                                       HTSEEEEE--TTTTSSSTC........HHHHHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EE CS
                      AP_endonuc_2 123 egvklalEtlagsgvelgd........eelarlldavdspnvgvclDtgHlliaeedvddalraladrikhvHikDa 191
                                       +gv lal++ +++ +  ++        ++++r+ld  dsp+ gv++  g++ ++e+d ++a+r+++dri++vH+ D+
  gi|336252591|ref|YP_004595698.1| 166 YGVNLALHPDDPPRSPVRGvprivksvDDYRRILDLHDSPRHGVTFCQGNFAAMETDTIEAIREFGDRIHFVHFRDV 242
                                       **************87777********************************************************** PP

                                       SS...T CS
                      AP_endonuc_2 192 kg...d 194
                                       +g    
  gi|336252591|ref|YP_004595698.1| 243 EGdgdS 248
                                       994440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2475.47
//
Query:       gi|336252592|ref|YP_004595699.1|  [L=139]
Description: Cupin 2 barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-11   42.5   0.1    6.3e-11   41.8   0.1    1.4  1  Cupin_2          Cupin domain
    0.00017   21.5   0.0     0.0002   21.3   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
     0.0032   16.8   0.0     0.0038   16.6   0.0    1.1  1  KduI             KduI/IolB family
     0.0043   16.9   0.0     0.0056   16.6   0.0    1.1  1  Cupin_7          ChrR Cupin-like domain
     0.0096   15.8   0.0      0.013   15.4   0.0    1.2  1  AraC_binding     AraC-like ligand binding domain
  ------ inclusion threshold ------
      0.045   13.4   0.0      0.064   12.9   0.0    1.1  1  DMSP_lyase       Dimethlysulfonioproprionate lyase
      0.061   12.9   0.0       0.11   12.1   0.0    1.3  1  Cupin_1          Cupin
       0.24   11.9   0.0       0.39   11.2   0.0    1.4  1  Ppnp             Pyrimidine/purine nucleoside phosphorylase


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 !   41.8   0.1   2.8e-14   6.3e-11       3      64 ..      51     115 ..      49     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 2.8e-14
                                       EEEETTEEEE..EECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS.- CS
                           Cupin_2   3 velppGesap..shrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgde.p 64 
                                       ++ +pGe+ p   h+H+ ++e f+Vl+G++ ++  ge + + +G ++  ++  pHr  N+ d+ +
  gi|336252592|ref|YP_004595699.1|  51 FRAEPGEQLPlaYHYHETQEEAFIVLSGTLQVETPGEAFSVPEGSVFTAEPESPHRAYNPDDAdD 115
                                       5678999999899**********************************************988753 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   8.9e-08    0.0002      62     133 ..      45     118 ..      38     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.9e-08
                   MannoseP_isomer  62 ryqvkritvkPgeklslqkhhhra..ehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkipleli 133
                                       +  + r   +Pge+l l  h+h +  e ++v++Gt +v++  e + + e        ++ hr  np   +  + 
  gi|336252592|ref|YP_004595699.1|  45 NVAINRFRAEPGEQLPLAYHYHETqeEAFIVLSGTLQVETPGEAFSVPEGSVFTAEPESPHRAYNPDDADDAVE 118
                                       556889999*************753389*******************998777777788999999987653333 PP

>> KduI  KduI/IolB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.7e-06    0.0038      24      95 ..      43     118 ..      24     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                                       CCCBECCCEEEECHHCHHCH...GCSEEEEEEEECCEEEECCTT.EEEEE-TTSSGGG...S..EEEEE-TT--EEE CS
                              KduI  24 weyvgfsvlkLaageslele...tedrEvcvvllaGkvtvevageefeelgeRksvFe...gkpdavYvpkgakvti 94 
                                        e v ++  + ++ge+l l+    e++E ++++l+G+++ve+ ge f+  ++  svF    ++p+ +Y p +a+  +
  gi|336252592|ref|YP_004595699.1|  43 LENVAINRFRAEPGEQLPLAyhyHETQEEAFIVLSGTLQVETPGEAFSVPEG--SVFTaepESPHRAYNPDDADDAV 117
                                       6778899999999**99999888899999*************9955555444..7**98788999999999988776 PP

                                       E CS
                              KduI  95 t 95 
                                       +
  gi|336252592|ref|YP_004595699.1| 118 E 118
                                       5 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.5e-06    0.0056      29      85 ..      51     114 ..      34     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.5e-06
                                       EEE-TTEE--..-EE-TT-EE.EEEEEEEEEETT..EEE..ETTEEEEE-TT-EE--EESS-EE CS
                           Cupin_7  29 vryapgsafs..ahkHpggee.ilVLeGvfsdee..gdy..paGsylrnppgsshapvseeGct 85 
                                        r++pg++++   h H+  ee ++VL+G+++ e+  + +  p+Gs + + p+s h+ + ++++ 
  gi|336252592|ref|YP_004595699.1|  51 FRAEPGEQLPlaYHYHETQEEaFIVLSGTLQVETpgEAFsvPEGSVFTAEPESPHRAYNPDDAD 114
                                       4678888876226889888773569******9975456788****************9998876 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 !   15.4   0.0   5.7e-06     0.013      20      66 ..      65     112 ..      50     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.7e-06
                                       TT-.SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TT CS
                      AraC_binding  20 vhd.eyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdse 66 
                                        h+ + +  +v++Gt +++  g+ + +++G++f   p+ pH+ +  ++
  gi|336252592|ref|YP_004595699.1|  65 YHEtQEEAFIVLSGTLQVETPGEAFSVPEGSVFTAEPESPHRAYNPDD 112
                                       55544555689******************************9877665 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.9e-05     0.064     111     153 ..      64     106 ..      58     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                        DMSP_lyase 111 Hhhaa.eelYlvlsggaefrqgeaewlsrgiGevifnepgikha 153
                                       H h+  ee+++vlsg   +   +++ +s+  G+v+ +ep+++h+
  gi|336252592|ref|YP_004595699.1|  64 HYHETqEEAFIVLSGTLQVETPGEA-FSVPEGSVFTAEPESPHR 106
                                       878777*********9777665555.78889***********97 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.8e-05      0.11      35     113 ..      48     122 ..      40     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.8e-05
                                       EEEEEE.TTEEEEE..EEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEES.SSSEE CS
                           Cupin_1  35 aarvdlepgglllP..hyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsg.depav 108
                                       + r++ epg +l++  hyh   +e ++vl G++ v+  +pg     +   + eG vf   +  +h +yn +  ++av
  gi|336252592|ref|YP_004595699.1|  48 INRFRAEPGEQLPLayHYHETQEEAFIVLSGTLQVE--TPG-----EAFSVPEGSVFTAEPESPHRAYNPDdADDAV 117
                                       55566666666665337788999***********54..455.....3578999****99999999999998456777 PP

                                       EEEEE CS
                           Cupin_1 109 aivvf 113
                                       +++++
  gi|336252592|ref|YP_004595699.1| 118 EVIAI 122
                                       77765 PP

>> Ppnp  Pyrimidine/purine nucleoside phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017      0.39      31      73 ..      60     100 ..      39     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                                       SECEEEEESS-EEEEEEESEEEEEETT-SS-EEEETT-EEEE- CS
                              Ppnp  31 pgeyeFgtsakEvmevvsGelevklpgeeewktykagesFevp 73 
                                       p  y+++ +++E   v+sG+l+v+ pge    ++ +g+ F+ +
  gi|336252592|ref|YP_004595699.1|  60 PLAYHYHETQEEAFIVLSGTLQVETPGEA--FSVPEGSVFTAE 100
                                       667***********************987..556666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1078.32
//
Query:       gi|336252593|ref|YP_004595700.1|  [L=225]
Description: uracil phosphoribosyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-48  162.7   0.0    9.1e-48  162.4   0.0    1.0  1  UPRTase       Uracil phosphoribosyltransferase
      7e-10   38.6   0.1    9.5e-10   38.2   0.1    1.1  1  Pribosyltran  Phosphoribosyl transferase domain


Domain annotation for each model (and alignments):
>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.4   0.0     1e-51   9.1e-48       3     207 .]      13     224 ..      11     224 .. 0.96

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 1e-51
                           UPRTase   3 shpllkakltilRdastsrkdfrelvdriarllaeealsallpveevtvttplgkeysgelldeekialVpilRaGe 79 
                                        h l+k  l+ +Rd +t++ +fr+ + +++r+ ++e++   +++e v+++tpl+++  +++   ++++++ +lRa  
  gi|336252593|ref|YP_004595700.1|  13 THALAKDTLSRIRDVETEQVSFRKGLVKLGRICGYEIIDGRMETEYVEIETPLEQTMGERVRGLDDVVIINVLRAAT 89 
                                       79999**********************************99*********************99************* PP

                           UPRTase  80 gmeealrellpearvghlglqreeet.......lepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergv 149
                                       +++e+l++++p+ar g +   r+ee           +  y kLP+  +++tv++ Dp++aTG+++++++++++++ v
  gi|336252593|ref|YP_004595700.1|  90 PFVEGLLKAFPRARQGVISASRDEEAgrdedgsFPISVDYVKLPEITEDDTVIIADPMLATGSTMCTVLDHVTSNAV 166
                                       ************************99666666533347899************************************ PP

                           UPRTase 150 geekIlvlsvlaseegvkrlaeefpkvkvvtaavDeeldekgyivpGlGDfGDRlFgT 207
                                       + e+ +vls ++++eg+ r+ eefp+ ++ t+++D+ ld++g+ivpGlGD+GDR F T
  gi|336252593|ref|YP_004595700.1| 167 EPENLIVLSAVSAPEGLLRVDEEFPEADLLTVSIDDYLDDDGFIVPGLGDAGDRAFRT 224
                                       ********************************************************98 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.1   1.1e-13   9.5e-10      29     137 ..      77     190 ..      58     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.1e-13
                                       GGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE............EE----TTSEEEEE-SEESSSH CS
                      Pribosyltran  29 kpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes....rlledpagkkVliVDDildtGg 101
                                         +v++ ++r + pf+  l +++      v + +++++ + +   ++  +s    +l+e++++ +V+i D +l+tG+
  gi|336252593|ref|YP_004595700.1|  77 DDVVIINVLRAATPFVEGLLKAFPRARQGVISASRDEEAGRDEDGSF-PISvdyvKLPEITEDDTVIIADPMLATGS 152
                                       5689*******************888887777777777777765433.33357779********************* PP

                                       HHHHHHHHH..HCC-BSEEEEEEEEE-HHHHHHHHHH- CS
                      Pribosyltran 102 TllaalelL..kekgpeevriavlvdkpateeevdkna 137
                                       T++ +l+++   +++pe +++   v  p++ ++vd ++
  gi|336252593|ref|YP_004595700.1| 153 TMCTVLDHVtsNAVEPENLIVLSAVSAPEGLLRVDEEF 190
                                       *******9833467777999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1696.31
//
Query:       gi|336252594|ref|YP_004595701.1|  [L=251]
Description: hypothetical protein Halxa_1189 [Halopiger xanaduensis SH-6]
Scores for 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  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1787.35
//
Query:       gi|336252595|ref|YP_004595702.1|  [L=257]
Description: hypothetical protein Halxa_1190 [Halopiger xanaduensis SH-6]
Scores for 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   14.4   0.3      0.083   13.0   0.3    1.6  1  Tape_meas_lam_C  Lambda phage tail tape-measure protein (Tape
        3.7    5.7  10.0        5.6    5.1  10.0    1.2  1  CDC45            CDC45-like protein


Domain annotation for each model (and alignments):
>> Tape_meas_lam_C  Lambda phage tail tape-measure protein (Tape_meas_lam_C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   9.3e-06     0.083       7      47 ..     126     166 ..     123     168 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.3e-06
                   Tape_meas_lam_C   7 vkrglaeYaesasnvagqvaeaatsafdsmedalaefvttG 47 
                                       ++ ++ ++ es+  va  +++a  +a++  ed + ++v+t 
  gi|336252595|ref|YP_004595702.1| 126 AEAAVDNWKESIDYVARAADSASRKALRRVEDTVYQNVMTQ 166
                                       78899**********************************95 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  10.0   0.00062       5.6     108     224 ..      52     175 ..      28     184 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.00062
                             CDC45 108 DDgdieeeleeereayealeeeeesdeedeeeeeeddddeeeeeeeeedeedeeedeeeskkkrksksdeeeesddd 184
                                       DD d ee+l++  e++e+ + + +++ e + +e+  d+ + ee + e++++  +ed +++++k +++ ++ ee+d +
  gi|336252595|ref|YP_004595702.1|  52 DDRD-EEQLADAFEEWEEWRPKAHETLEVDVSEKTADQASVEEGKGEKAGKGPDEDIKTAGEKLSESYEQLEEDDAE 127
                                       5666.899999999999999999998666677777888888888888888888888888777777554444444444 PP

                             CDC45 185 dersrkrrrse........psakklrrqlkkerrkyeavlekyysqgt 224
                                       +   + ++  +        +s+k+lrr + +  ++  ++l+ yy + +
  gi|336252595|ref|YP_004595702.1| 128 AAVDNWKESIDyvaraadsASRKALRRVEDTVYQNVMTQLAPYYFDNE 175
                                       444444444443333222245555555566666666667777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1119  (0.0624129); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2012.57
//
Query:       gi|336252596|ref|YP_004595703.1|  [L=363]
Description: polar amino acid ABC transporter inner membrane subunit [Halopiger xanaduensis SH-6]
Scores for 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   63.3   7.7    2.3e-17   63.3   7.7    2.2  2  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 ?   -3.3   4.8      0.35   6.2e+03      46      76 ..      96     127 ..      28     135 .. 0.65
   2 !   63.3   7.7   1.3e-21   2.3e-17       2     184 ..     131     323 ..     126     324 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.35
                      BPD_transp_1  46 lsilghlilpv.iillllsaapyvrlirraal 76 
                                        s +  ++l++ i+ +l s a+y++l++ aa+
  gi|336252596|ref|YP_004595703.1|  96 ASLFDGTALAIdIAPALASGAWYTILLTVAAI 127
                                       23333333332244444444444444444443 PP

  == domain 2  score: 63.3 bits;  conditional E-value: 1.3e-21
                      BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf..............vilsilghlilpviillll 62 
                                       + +++ +a  + ++++l++l + ++++++++P ++ +++l++ +               +  +  ++++ +i+ +++
  gi|336252596|ref|YP_004595703.1| 131 FCIAVPVAvlRVYGGPLRWLALAYTELIRGTPLLAQLFVLYYGLplavwlneidvigrGF--VPEYAFWIAILGFTI 205
                                       344555559999****************************9999**********964322..356888889****** PP

                      BPD_transp_1  63 saapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgt 139
                                          +y    +r+al+s+++++  aara G+s+ + +r+vvlP++l+++i+   + +++l++ ++l+ f++    +  
  gi|336252596|ref|YP_004595703.1| 206 NGSAYQAEYIRGALESVDEGQLTAARAIGLSKLEGIRYVVLPQTLRYAIPAWTNELVYLIKYSSLAGFIT----VPE 278
                                       **********************************************************************....766 PP

                      BPD_transp_1 140 llleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       l  +a+ +   ++ +  +++ l+i++l ++l+a  +++ +++rv 
  gi|336252596|ref|YP_004595703.1| 279 LYYRASRIASSTFEYTPIYVLLAIVYLGIVLSATNVMDRVERRVA 323
                                       66666666666666668**************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2973.23
//
Query:       gi|336252597|ref|YP_004595704.1|  [L=284]
Description: phosphonate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-33  113.9   0.0      1e-32  113.5   0.0    1.2  1  ABC_tran      ABC transporter
    2.4e-12   47.3   0.0    4.7e-05   23.4   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    7.9e-07   28.7   0.0    2.9e-06   26.9   0.0    1.7  1  SMC_N         RecF/RecN/SMC N terminal domain
    6.1e-05   22.7   0.0    0.00013   21.6   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
    0.00058   19.7   0.0       0.01   15.6   0.0    2.0  2  AAA_15        AAA ATPase domain
    0.00079   19.9   0.1     0.0015   18.9   0.1    1.5  1  AAA_16        AAA ATPase domain
    0.00088   19.8   0.0     0.0011   19.5   0.0    1.3  1  AAA_23        AAA domain
     0.0021   18.0   0.0     0.0043   17.0   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
     0.0027   18.0   0.0     0.0043   17.3   0.0    1.6  1  AAA_22        AAA domain
     0.0059   15.5   0.0        1.6    7.4   0.0    2.3  2  ABC_ATPase    Predicted ATPase of the ABC class
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.019   14.7   0.0    1.5  1  AAA_30        AAA domain
      0.013   15.1   0.2      0.048   13.2   0.2    2.0  1  AAA_25        AAA domain
      0.016   14.6   0.0       0.26   10.6   0.0    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.024   14.8   0.1      0.042   14.0   0.1    1.6  1  AAA_33        AAA domain
      0.052   12.3   0.1       0.34    9.6   0.0    1.9  2  Adeno_IVa2    Adenovirus IVa2 protein
      0.079   12.7   0.0       0.55    9.9   0.0    2.0  2  AAA_24        AAA domain
       0.12   12.4   0.0        0.4   10.7   0.0    1.8  2  AAA_5         AAA domain (dynein-related subfamily)


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 !  113.5   0.0   9.5e-36     1e-32       3     137 .]      61     207 ..      59     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 9.5e-36
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqepqlfpeltvr 77 
                                        ++l++ +g + ++vG++G+GKStLl++l  l+  ++G++ l +++++   ++ ++ r++ig+++q+ +lf +lt+r
  gi|336252597|ref|YP_004595704.1|  61 GIDLEIDRGDVEVLVGPSGSGKSTLLRCLNLLTPVDSGHVYLGDTEVTApeTDPNEIRQQIGMVFQDINLFAHLTAR 137
                                       6899********************************************9999999********************** PP

                                       HH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       en              e+++++++ l+++gl + +d    s p++LSgGqkqrv +aral+ +p+++l+DEpt+
  gi|336252597|ref|YP_004595704.1| 138 ENvtlglrkvkgipkdEARQRADAELERVGLADQAD----SYPAQLSGGQKQRVGIARALAMDPEVMLFDEPTS 207
                                       *************77666677777777777777544....556*****************************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 !   21.9   0.0   1.2e-07   0.00013       3      26 ..      73      97 ..      72     127 .. 0.78
   2 !   23.4   0.0   4.4e-08   4.7e-05     234     297 ..     176     236 ..     129     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl.d 26
                                      vl+Gp gsGKS+LL++l ll  +  
  gi|336252597|ref|YP_004595704.1| 73 VLVGPSGSGKSTLLRCLNLLTPVdS 97
                                      8******************965543 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 4.4e-08
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       +++lS G+k+  +++ al+ ++    + l+DEp + L+P+l  ++le+++el + g   +++TH
  gi|336252597|ref|YP_004595704.1| 176 PAQLSGGQKQRVGIARALAMDP---EVMLFDEPTSALDPELSNEVLEVMDELVEAGMTMVVVTH 236
                                       6789999999999999999999...9***********************999998999999999 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 !   26.9   0.0   2.7e-09   2.9e-06      11     204 ..      51     243 ..      44     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.7e-09
                                       TTEECEEEEEETT....S.SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEE CS
                                       xxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  11 ksyagktvilpfs....k.sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveit 82 
                                       ksy +++v l ++    +  + ++vGp GSGKs ll  +  +   +s  ++   +++  +++ ++ ++  + ++ ++
  gi|336252597|ref|YP_004595704.1|  51 KSYGDEEVLLGIDleidRgDVEVLVGPSGSGKSTLLRCLNLLTPVDSG-HVYLGDTE--VTAPETDPNEIRQQIGMV 124
                                       66666665443331111314789****************655555554.77766665..455689999999****** PP

                                       EEETTEE.SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS- CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  83 fdnedkk.lkiekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkp 158
                                       f++ +     + +e+v++  r++++   + + ++ +++ + v  l  +a+ ++ +LSgG+k+ v +a  +A+    p
  gi|336252597|ref|YP_004595704.1| 125 FQDINLFaHLTARENVTLGLRKVKGIPKDEARQRADAELERV-GLADQADSYPAQLSGGQKQRVGIARALAMD---P 197
                                       *99998834456677999999998888777767777766665.6889999999**************999874...5 PP

                                       -SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N 159 aplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlek 204
                                       + ++l+De  +aLD +  ++v e+++e  +  + ++v++++ ++ + 
  gi|336252597|ref|YP_004595704.1| 198 E-VMLFDEPTSALDPELSNEVLEVMDELVEAgMTMVVVTHEMRFARG 243
                                       5.579**********************99887889999998877665 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 !   21.6   0.0   1.2e-07   0.00013      17      48 ..      64      94 ..      58      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                      +eid+ ++ +l+GpsGsGKSTll     lL+p
  gi|336252597|ref|YP_004595704.1| 64 LEIDRGDVEVLVGPSGSGKSTLL-RCLNLLTP 94
                                      688877799*************9.44556665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.6e-06      0.01      17      83 ..      64     125 ..      59     164 .. 0.75
   2 ?    2.1   0.0      0.12   1.2e+02     323     364 ..     196     236 ..     151     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.6e-06
                            AAA_15  17 veidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef 83 
                                        eid  + + vl+G+ +sGKS++l+ l+l+   +    +  +++ + ++   e + ++++ +I + f
  gi|336252597|ref|YP_004595704.1|  64 LEIDRGD-VEVLVGPSGSGKSTLLRCLNLLTPVD----SGHVYLGDTEVTAPETDPNEIRQQIGMVF 125
                                       4555555.99******************998877....55667777777777777777777777777 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       ++ + l++EP   L p++ +++ + + el++ +    ++ TH
  gi|336252597|ref|YP_004595704.1| 196 DPEVMLFDEPTSALDPELSNEVLEVMDELVEAGM-TMVVVTH 236
                                       457899**************************97.6777777 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.4e-06    0.0015      28     127 ..      73     225 ..      63     235 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.4e-06
                            AAA_16  28 llsGesGvGKsslvrellralekdg.giflrgkcdql..esa.....ipysalaqalareellrqllde........ 88 
                                       +l+G+sG+GKs+l+r+l   l+  + g++  g+++    e++         ++ q +    l++ l ++        
  gi|336252597|ref|YP_004595704.1|  73 VLVGPSGSGKSTLLRCLN-LLTPVDsGHVYLGDTEVTapETDpneirQQIGMVFQDI---NLFAHLTARenvtlglr 145
                                       699************999.45554336664444444422111222222222233333...33333333344444444 PP

                            AAA_16  89 .....aesaeleawrekleeala........................................avpelagaeasrll 120
                                            +     +++r++ +++l+                                        ++++l++++++ +l
  gi|336252597|ref|YP_004595704.1| 146 kvkgiP----KDEARQRADAELErvgladqadsypaqlsggqkqrvgiaralamdpevmlfdePTSALDPELSNEVL 218
                                       454442....2233333333333444567777777777777778888777888888888888877788888777777 PP

                            AAA_16 121 ellkrll 127
                                       e++ +l+
  gi|336252597|ref|YP_004595704.1| 219 EVMDELV 225
                                       7777776 PP

>> AAA_23  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    0.0011       9      42 ..      52      92 ..      44     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
                            AAA_23  9 sfrdqe....idF...skgltlItGpNGaGKTTildAikla 42
                                      s++d+e    id+      + +++Gp G+GK+T+l+++ l 
  gi|336252597|ref|YP_004595704.1| 52 SYGDEEvllgIDLeidRGDVEVLVGPSGSGKSTLLRCLNLL 92
                                      6666663444455775557889***************9875 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   4.1e-06    0.0043      99     120 ..      69      90 ..      49     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.1e-06
                                       TSEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinall 120
                                       +++ vlvG+SG GKStL+  l+
  gi|336252597|ref|YP_004595704.1|  69 GDVEVLVGPSGSGKSTLLRCLN 90 
                                       4899*************98775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.1e-06    0.0043       9      61 ..      73     122 ..      66     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.1e-06
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevv....fvtlpsstsskdllrell 61 
                                       v++G+sG+GK+tllr l    + +      + +v+    +vt+p+   + ++++++ 
  gi|336252597|ref|YP_004595704.1|  73 VLVGPSGSGKSTLLRCLNLLTPVD------SGHVYlgdtEVTAPETD-PNEIRQQIG 122
                                       89***************9998875......33333454344444433.666666654 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 !    7.4   0.0    0.0015       1.6     242     265 ..      66      90 ..      60      92 .. 0.90
   2 !    5.6   0.0    0.0056       5.9     322     353 ..     178     209 ..     169     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0015
                                       E-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAle 265
                                       i +G v ++vG+   GKsTLL+ l+
  gi|336252597|ref|YP_004595704.1|  66 IDRGdVEVLVGPSGSGKSTLLRCLN 90 
                                       78899*****************986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0056
                                       S--HHHHHHHHHHHHHHTT-SEEEEEGGGS-H CS
                        ABC_ATPase 322 dASGStsqAanimealeagakllLiDEDtsAt 353
                                       + SG   q + i++al ++ +++L+DE tsA 
  gi|336252597|ref|YP_004595704.1| 178 QLSGGQKQRVGIARALAMDPEVMLFDEPTSAL 209
                                       669999************************95 PP

>> AAA_30  AAA 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     0.019      19      76 ..      70     131 ..      64     235 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g....grviglAptgkaAkvLaeelgieastiakl 76 
                                        v vl+Gp G+GK+t+l+ l+ +   + g    g+  + Ap+    +++++++g+  + i+ +
  gi|336252597|ref|YP_004595704.1|  70 DVEVLVGPSGSGKSTLLRCLNLLTPVDsGhvylGDTEVTAPETDP-NEIRQQIGMVFQDINLF 131
                                       499***************998877766445555555566665543.45555666555555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   4.5e-05     0.048      30      55 ..      66      91 ..      62     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.5e-05
                            AAA_25 30 lpagelallaGapgtGKttlaldlal 55
                                      + +g++ +l+G++g+GK+tl+  l l
  gi|336252597|ref|YP_004595704.1| 66 IDRGDVEVLVGPSGSGKSTLLRCLNL 91
                                      67999***************855433 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   0.00025      0.26      26      50 ..      73      97 ..      48     120 .. 0.81
   2 ?    2.1   0.0       0.1   1.1e+02      86     138 ..     174     233 ..     128     257 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                      Mg_chelatase 26 llvGppGsGKtmlakrlpsllppls 50
                                      +lvGp+GsGK+ l ++l+ l p  s
  gi|336252597|ref|YP_004595704.1| 73 VLVGPSGSGKSTLLRCLNLLTPVDS 97
                                      689**************98877655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.1
                      Mg_chelatase  86 skaalvGggskpkpG.eislahn.GvLfLDEl.....pefkrkvlevLRePledgevtis 138
                                       s  a + gg+k + G + +la    v+++DE      pe++++vlev+ e +e+g  ++ 
  gi|336252597|ref|YP_004595704.1| 174 SYPAQLSGGQKQRVGiARALAMDpEVMLFDEPtsaldPELSNEVLEVMDELVEAGMTMVV 233
                                       555555566666665233455432588888843334479999999999999998876554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.9e-05     0.042       3      19 ..      73      89 ..      71     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.9e-05
                            AAA_33  3 llvGlpGsGKstlaerl 19
                                      +lvG++GsGKstl++ l
  gi|336252597|ref|YP_004595704.1| 73 VLVGPSGSGKSTLLRCL 89
                                      79***********9965 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   0.00033      0.34      90     116 ..      72      95 ..      63     121 .. 0.82
   2 ?    0.3   0.0      0.23   2.4e+02     234     257 ..     227     250 ..     220     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00033
                        Adeno_IVa2  90 GviyGPtGsGksqllrnlissklisPi 116
                                        v+ GP GsGks llr l   +l+ P+
  gi|336252597|ref|YP_004595704.1|  72 EVLVGPSGSGKSTLLRCL---NLLTPV 95 
                                       6899************87...555555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.23
                        Adeno_IVa2 234 tgfsvlvvlhnlnPrsdiagniad 257
                                       +g +++vv h++   ++ a ni+ 
  gi|336252597|ref|YP_004595704.1| 227 AGMTMVVVTHEMRFARGGATNITF 250
                                       5889*************9999975 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   0.00052      0.55       6      28 ..      73      92 ..      70     159 .. 0.75
   2 ?    0.3   0.0      0.47     5e+02     107     132 ..     213     238 ..     211     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00052
                            AAA_24  6 liyGpsgiGKTtlakelgpkplf 28
                                      +++Gpsg+GK+tl++ l    l+
  gi|336252597|ref|YP_004595704.1| 73 VLVGPSGSGKSTLLRCL---NLL 92
                                      799***********998...333 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.47
                            AAA_24 107 laeefrrllkklqelrknvifiahek 132
                                       l +e+ ++++ l e++ + +++ he 
  gi|336252597|ref|YP_004595704.1| 213 LSNEVLEVMDELVEAGMTMVVVTHEM 238
                                       67899999999999999888888875 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   0.00037       0.4       3      23 ..      73      93 ..      72     127 .. 0.80
   2 ?   -1.6   0.0       2.3   2.4e+03      65      91 ..     196     223 ..     175     253 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00037
                                      EEE--SSSSHHHHHHHGGGGB CS
                             AAA_5  3 lLvGppGtgKselaerlaaal 23
                                      +LvGp+G+gKs+l + l  ++
  gi|336252597|ref|YP_004595704.1| 73 VLVGPSGSGKSTLLRCLNLLT 93
                                      69***********99887766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.3
                                       G-SEEEEESGGG--.HHHHHHHHHHHHS CS
                             AAA_5  65 egeilvlDEverae.sevlnsLlsllee 91 
                                        +e++++DE + a  +e  n++l +++e
  gi|336252597|ref|YP_004595704.1| 196 DPEVMLFDEPTSALdPELSNEVLEVMDE 223
                                       6677777777776667777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2155.68
//
Query:       gi|336252598|ref|YP_004595705.1|  [L=299]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-16   59.7  10.1    3.1e-16   59.7  10.1    1.5  1  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
          1    9.2   6.4        4.4    7.2   3.3    2.6  2  DUF1232       Protein of unknown function (DUF1232)


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 !   59.7  10.1   3.4e-20   3.1e-16       5     181 ..      85     290 ..      81     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 3.4e-20
                      BPD_transp_1   5 Gilaa.......lnrnkkldkllrpliivllslPsfvlaillvlvf.........................vilsil 49 
                                       G+la+       ++  +  + ++r +  +l+++P++v+++l ++v+                            +++
  gi|336252598|ref|YP_004595705.1|  85 GFLAGfpagaieVYGDGYSRSFVRKFGVLLRGTPILVIMLLTYFVLpidivlvalertlgaidfvlgptpfTAPTDV 161
                                       44444444488899999999*****************99997777799999999****************999999* PP

                      BPD_transp_1  50 ghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggav 126
                                         +++++ ++l + +a+y   i+r+al+s++++++eaar  G+sr + +r+v++P+al+  ++g+ + f+++l++++
  gi|336252598|ref|YP_004595705.1| 162 PEAFFAATLALGFRSAAYQSQIFRGALQSIDEGQMEAARSIGMSRLEAIRHVIVPQALRRSVPGFQNEFTIVLKDTS 238
                                       ***************************************************************************** PP

                      BPD_transp_1 127 lleflgswpGlgtllleailgydyseis.nggvlalviavlllnlvadilqrlldp 181
                                       ++  +g    lg ll +++  +  + ++   ++l++ +++++l++ ++   ++++ 
  gi|336252598|ref|YP_004595705.1| 239 IAFAIG----LGELLKRSQDLFTQQTTAvLEVILFISLVYFVLTFTTNRTLDFVSN 290
                                       ******....**99887765544443334477777777777777777766666655 PP

>> DUF1232  Protein of unknown function (DUF1232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   3.3    0.0005       4.4       4      19 ..     120     135 ..     119     136 .. 0.88
   2 ?    2.2   0.1     0.018   1.6e+02       3      16 ..     266     279 ..     266     296 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0005
                           DUF1232   4 liagalaYlisPiDlI 19 
                                       l++  l Y+++PiD++
  gi|336252598|ref|YP_004595705.1| 120 LVIMLLTYFVLPIDIV 135
                                       788899********96 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.018
                           DUF1232   3 lliagalaYlisPi 16 
                                       ++++  l+Y+++ +
  gi|336252598|ref|YP_004595705.1| 266 VILFISLVYFVLTF 279
                                       588999****9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2282.08
//
Query:       gi|336252599|ref|YP_004595706.1|  [L=306]
Description: ABC transporter periplasmic protein family 3 [Halopiger xanaduensis SH-6]
Scores for 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-54  183.3   0.6      5e-54  183.1   0.6    1.0  1  SBP_bac_3        Bacterial extracellular solute-binding prote
    5.6e-08   33.0   0.0    4.2e-07   30.2   0.0    2.2  1  Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine
  ------ inclusion threshold ------
      0.023   14.5   0.0       0.05   13.5   0.0    1.6  1  TAT_signal       TAT (twin-arginine translocation) pathway si
      0.027   14.4   0.1       0.87    9.5   0.0    2.2  2  NMT1             NMT1/THI5 like


Domain annotation for each model (and alignments):
>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.1   0.6   1.1e-57     5e-54       1     224 [.      77     299 ..      77     300 .. 0.95

  Alignments for each domain:
  == domain 1  score: 183.1 bits;  conditional E-value: 1.1e-57
                                       EEEEE-S-BTTTBEE-TTS-EESHHHHHHHHHHHHCT-E.EEEEE-SGGGHHHHHHTTSSSEEESSEB--HHHHTTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3   1 lrvgvdadypPfsykdengeltGfdvdlakaiakrlgvk.vefvpvswdelipalksgkvDiaiaaititpeReekv 76 
                                       ++ g+ ++++Pf++   +gel+Gfd+dl++a+ +++ ++  e++++++d+lipal++g++D+++aa+tit+eR++ +
  gi|336252599|ref|YP_004595706.1|  77 IIAGTAPGFEPFEMTR-DGELVGFDIDLLEAVVDETEYElAEWNEYEFDSLIPALENGNIDVIAAAMTITEERQQSI 152
                                       5789************.***************************99******************************* PP

                                       EEESESEEEEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHC.....TSEEEEESSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  77 dFsqpyfsagqvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkk.....gaeivefdtleealqaL 148
                                       +F++py+sa+q++lv+++ + +++ ++   dL++++vg+q g+t e+ ++e+l +     + + +++d++  a+q+L
  gi|336252599|ref|YP_004595706.1| 153 AFTEPYYSANQSVLVQSGGDFAPEALE---DLEDREVGAQSGTTGETVVQEQLIDeglisDDQYTSYDNYVYAVQEL 226
                                       ****************96566667776...******************999887789998778899*********** PP

                                       HTTSSSEEEEEHHHHHHHHHHCCGCCEEEEECGGCECEEEEEEETTTHHHHHHHHHHHHHHHHTTHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 149 kngrvdavvadspvlaylvkknpdkkvvlveeplsseeyaiavrkgdseLrkainkalaelkadgtlakisekWfg 224
                                       + g  da+v d+pv a +++ ++ + ++      ++eey+++v+++ s+L++a+ +++a+++++g++++i + Wf+
  gi|336252599|ref|YP_004595706.1| 227 ERGLLDAIVIDEPVGATFADSRDVEVAFT---FETGEEYGFGVQQDASDLQTALSDGIAAVRESGQYDEITQTWFD 299
                                       *********************99999999...99*****************************************7 PP

>> Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine-binding site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   9.3e-11   4.2e-07      53     112 ..     109     168 ..      85     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 9.3e-11
                                       TT-----BETTTTEB-HHHHHHHTTS-SEE-SS-B--HHHHTTSEEESESEEE-EEEEEE CS
                   Lig_chan-Glu_bd  53 edgkyGskkekkkewnGmigellekkadlavapltitaeReevvdFtkpfmelgisilik 112
                                       ++++y   + ++ e + +i  l ++++d++ a++tit+eR++ + Ft+p+++   s+l++
  gi|336252599|ref|YP_004595706.1| 109 DETEYELAEWNEYEFDSLIPALENGNIDVIAAAMTITEERQQSIAFTEPYYSANQSVLVQ 168
                                       33444444555668999************************************9999986 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.1e-05      0.05       2      24 ..       8      31 ..       7      32 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                        TAT_signal  2 lSRRdFLKgsAAaa.AAaalggca 24
                                      ++RR+ LK ++ a+   ++l+gc+
  gi|336252599|ref|YP_004595706.1|  8 FDRRTYLKLTGTAGvTVTGLAGCL 31
                                      89******9999995555599995 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.019        86     125     150 ..     119     144 ..     102     155 .. 0.79
   2 ?    9.5   0.0   0.00019      0.87      86     147 ..     176     236 ..     153     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.019
                                       EE-.TT-HHHHHHCTSSSEEECEETT CS
                              NMT1 125 vnvggtslakalltgkvDaaiggyen 150
                                        +++++sl++al +g++D++ ++++ 
  gi|336252599|ref|YP_004595706.1| 119 NEYEFDSLIPALENGNIDVIAAAMTI 144
                                       46788999***********9976654 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00019
                                       SSGGGGTTSEEEE-S-TTHHHHHHHHHHHTT-.-GGG-EEEE-.TT-HHHHHHCTSSSEEECE CS
                              NMT1  86 kspkDLkGkrigyvgspfekallkallakdgg.dpsdvtlvnvggtslakalltgkvDaaigg 147
                                       + ++DL+ + +g + +  +++++++ l  +g+ + +++t  ++ +  ++++l +g  Da++ +
  gi|336252599|ref|YP_004595706.1| 176 EALEDLEDREVGAQSGTTGETVVQEQLIDEGLiSDDQYTSYDN-YVYAVQELERGLLDAIV-I 236
                                       5789***********99999999998888887799*******9.777779********998.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2459.71
//
Query:       gi|336252600|ref|YP_004595707.1|  [L=397]
Description: phosphate transporter [Halopiger xanaduensis SH-6]
Scores for 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  150.9  34.7    4.5e-44  150.9  34.7    1.6  2  PHO4      Phosphate transporter family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1     0.047   8.4e+02      67      90 ..       8      31 ..       5      32 .. 0.77
   2 !  150.9  34.7   2.5e-48   4.5e-44       7     337 .]      31     385 ..      24     385 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.047
                              PHO4 67 laallgaavwlllatvlglPvStt 90
                                         l++a++ l++a+ +g  +S +
  gi|336252600|ref|YP_004595707.1|  8 ATFLVAAVASLFMAWAIGAGSSGS 31
                                      557888999999999999888865 PP

  == domain 2  score: 150.9 bits;  conditional E-value: 2.5e-48
                              PHO4   7 anafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselm.lgmlaallgaavwlllatv 82 
                                       +  fa++vg++a+++++A +l++++ f+Gavl+Ga+V+e+++ +++     +  +l   ++++al  aa+++++ ++
  gi|336252600|ref|YP_004595707.1|  31 STPFAPAVGANAISVMKAGFLVGLLGFVGAVLQGANVSEAVGAELI-----QGVTLSpPAATIALTIAAALVAIGVF 102
                                       678*******************************************.....3334445699999999********** PP

                              PHO4  83 lglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklknalralpv 159
                                       +g+P+ t+++++Ga+iG++la+  g +  w k ++i++ w+l+P++gg +a+ ++ ++++  +     +  +  l  
  gi|336252600|ref|YP_004595707.1| 103 TGYPIATAFTVTGAVIGVGLAM--GGGPAWAKYTEIAALWILTPFVGGGLAYGIARVLRAELID---ESYLIMGLAA 174
                                       *********************6..45889*******************************9552...3334445555 PP

                              PHO4 160 lvlvtiailalsilfkge....................................sk.kddeeteklfkflqvvsaal 199
                                       +v v++a + ++il  g+                                       + +   e+  + +++v ++l
  gi|336252600|ref|YP_004595707.1| 175 FVGVLVANIEFAILNPGQaggdsiagavstmlpgsaligsvamtiviaalwagvLAlDLRGGLERGERHFLLVLGGL 251
                                       5666666666666666542222222222222222222222222222222222222233344444445666******* PP

                              PHO4 200 vsfahGanDvanaiGpllaalisiykask.evplw.vlllgglaialGlllgGkrviktvGekitkkltpsrGfaae 274
                                       v+f+ G+++v  a+Gpl+ +        +   pl  +l+ gg++++lG ++g++r+ik+++++++ +l p r++ a+
  gi|336252600|ref|YP_004595707.1| 252 VAFSAGGSQVGLAVGPLIPLS------GDvGLPLPaLLVGGGFGLLLGSWTGAPRMIKAISQDYS-SLGPRRSI-AA 320
                                       *****************6654......3445677549999*************************.6*******.56 PP

                              PHO4 275 laaaltvl.lasklglPvStThvlvgavvGvGlak.kresavnwklvrnivlaWvlTlpvsalls 337
                                       l+ +++++  a  +g+PvS+++++v+a++G G a  +   +v+ + ++ +vlaW+ +l  s+++s
  gi|336252600|ref|YP_004595707.1| 321 LIPSFMIAqSAVLFGIPVSFNEIIVSAIIGSGYAAaGAGGGVSARKMAYTVLAWIGSLAGSIAIS 385
                                       6666666669**********************999644569*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.35
# Mc/sec: 3354.91
//
Query:       gi|336252601|ref|YP_004595708.1|  [L=246]
Description: hypothetical protein Halxa_1196 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0081   15.8   1.0     0.0081   15.8   1.0    1.6  2  DUF1449   Protein of unknown function (DUF1449)
  ------ inclusion threshold ------
        7.1    6.5   8.5        7.8    6.4   3.3    2.1  2  DUF2975   Protein of unknown function (DUF2975)


Domain annotation for each model (and alignments):
>> DUF1449  Protein of unknown function (DUF1449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.0     9e-07    0.0081      42     108 ..       6      82 ..       1     105 [. 0.75
   2 ?   -2.2   0.0       0.3   2.6e+03      84     106 ..      99     121 ..      92     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9e-07
                           DUF1449  42 dadvepdvdad...........galsklLgWLrvgrvPvLilLvlfLtlFglvGlv.lqslvasllgallpallaaa 106
                                       dad+ +d   d           +   +lL  L+vg   ++i +++f  l+ l+G +  qs+v++l+ a+l ++la a
  gi|336252601|ref|YP_004595708.1|   6 DADAPADP--DdllqwrrdattSRSIRLLWSLGVGTFFAVITIIVFWRLYDLTGQIgGQSVVVALFAAILVTILALA 80 
                                       33322222..133555555554577888888***********************88469*************99987 PP

                           DUF1449 107 ia 108
                                       ++
  gi|336252601|ref|YP_004595708.1|  81 AS 82 
                                       65 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.3
                           DUF1449  84 Glvlqslvasllgallpallaaa 106
                                       G +lq ++ + lga+  + +++ 
  gi|336252601|ref|YP_004595708.1|  99 GTALQRAADAALGAIAMGAIIVT 121
                                       77888888888888777766654 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.3   0.00087       7.8      61     114 ..      30      78 ..      23      84 .. 0.69
   2 ?    3.0   0.2      0.01        89      49     106 ..     100     155 ..      95     167 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00087
                           DUF2975  61 riglaliaaalllaagivalallaelelapgvvllllgvafaslvigllvlvla 114
                                       r+ ++l + ++ ++++i++++ l +     ++  +++  ++++l++++lv++la
  gi|336252601|ref|YP_004595708.1|  30 RLLWSLGVGTFFAVITIIVFWRLYD-----LTGQIGGQSVVVALFAAILVTILA 78 
                                       4668888889999999999999999.....223445555555555555555554 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.01
                           DUF2975  49 evFspanvrrLrriglaliaaalllaagivalallae.lelapgvvllllgvafaslvi 106
                                       ++ ++a+   L +i++ +i+++l+ ++ +v  + l   l   p    ++l + ++ l++
  gi|336252601|ref|YP_004595708.1| 100 TALQRAADAALGAIAMGAIIVTLMGIGRYVSQNNLLGdLGAGP---FTGLAALTIPLAL 155
                                       6677777788888999999888888888887766666333333...2222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2107.33
//
Query:       gi|336252602|ref|YP_004595709.1|  [L=479]
Description: hypothetical protein Halxa_1197 [Halopiger xanaduensis SH-6]
Scores for 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-49  167.2   0.7    4.7e-49  166.5   0.7    1.4  1  DUF21      Cyclin M transmembrane N-terminal domain
    6.9e-21   74.1   3.3    6.9e-21   74.1   3.3    2.0  2  CorC_HlyC  Transporter associated domain
    1.3e-13   51.1   3.1    1.7e-06   28.4   0.2    3.1  2  CBS        CBS domain
  ------ inclusion threshold ------
      0.056   12.9   0.1      0.056   12.9   0.1    1.8  2  WSS_VP     White spot syndrome virus structural envelope prot
        7.7    6.9   6.8        3.9    7.9   2.9    2.1  2  DUF4233    Protein of unknown function (DUF4233)


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 !  166.5   0.7   1.3e-52   4.7e-49       2     176 .]      35     215 ..      33     215 .. 0.98

  Alignments for each domain:
  == domain 1  score: 166.5 bits;  conditional E-value: 1.3e-52
                             DUF21   2 iivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvel 78 
                                        iv+l++ls+ffs++E+A+++l ++r+e ++e+g  +a+ ++ l ++p+rlL+t+l+gn+lvni++s++atal++ +
  gi|336252602|ref|YP_004595709.1|  35 TIVILIALSGFFSSSEIAMFNLPKHRIEGMVEEGVDRAELVETLKSDPHRLLVTILVGNNLVNIAMSSIATALLGLY 111
                                       679999*********************************************************************** PP

                             DUF21  79 laegalavviatvivtllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlil......ese 149
                                       ++ g + v+++t+ vt ++l+fgE +Pks+a+++ e+++l +++pl+v  ++lyPl+++++ l++ +       ++ 
  gi|336252602|ref|YP_004595709.1| 112 FESGLTPVLLSTFGVTAIVLLFGESVPKSYAVENTESWSLSVSRPLKVTEYVLYPLIIVFDYLTRQVNrligssGAI 188
                                       *9999999***************************************************999999999999***99* PP

                             DUF21 150 sepavseeelkklveeseeegvieeee 176
                                       ++p+v+++e+++++e++e+egv+ee+e
  gi|336252602|ref|YP_004595709.1| 189 ESPYVTRDEIQEMIESGEREGVLEEDE 215
                                       *************************98 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       3.8   1.4e+04      32      51 ..     342     361 ..     333     362 .. 0.65
   2 !   74.1   3.3   1.9e-24   6.9e-21       2      80 ..     367     444 ..     366     445 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.8
                                       -SBHHHHHHHHH-S---TT- CS
                         CorC_HlyC  32 yeTlgGlllellgriPkege 51 
                                         T+ +++ e +g+i + ge
  gi|336252602|ref|YP_004595709.1| 342 LVTMEDMVEEIIGEILEGGE 361
                                       45666677777777777666 PP

  == domain 2  score: 74.1 bits;  conditional E-value: 1.9e-24
                                       EECTTEEEEETT-BHHHHHHHHTSTTHH.CT-SBHHHHHHHHH-S---TT-EEEEEETTEEEEEEEEETTCEEEEEE CS
                         CorC_HlyC   2 eldegsylvdGslpldeleeelglelpe.edyeTlgGlllellgriPkegesvevdleglrftVlemdgrrIkkvrv 77 
                                       e+de++ lv G++++++++e+l+++lpe e++eT++G+++++ gr+ +ege++++d  g+r+tV+++++ rI   r+
  gi|336252602|ref|YP_004595709.1| 367 EIDERTVLVRGEVNIEDVNEALEIDLPEgEEFETIAGFIFNRAGRLVEEGEEITYD--GVRITVEDVENTRIMMARL 441
                                       79**************************889********************77777..******************9 PP

                                       EE- CS
                         CorC_HlyC  78 ekl 80 
                                       +kl
  gi|336252602|ref|YP_004595709.1| 442 TKL 444
                                       986 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.2   4.7e-10   1.7e-06       1      54 [.     230     286 ..     230     289 .. 0.87
   2 !   22.0   0.2   4.6e-08   0.00017      10      55 ..     307     352 ..     297     354 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 4.7e-10
                                       HHHHSBS..SCEEEETTSBHHHHHHH.HHHHTSSEEEEE.ETTTBEEEEEEHHHHHHH CS
                               CBS   1 Vgdimtr..dvvtvppdttleealel.mrekgvsrlPVV.dedgklvGivtlrDllra 54 
                                       V+++mt+  d+  vp d+++ ea+e+ + ++g+ r+PV   + +++ G+v+ rDl+r 
  gi|336252602|ref|YP_004595709.1| 230 VKEVMTPrlDMTAVPKDASIDEAIETcI-QSGHARIPVYeGSLDNVMGVVHIRDLVRD 286
                                       899****77779**************88.99999*****533337**********985 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 4.6e-08
                                       EEEETTSBHHHHHHHHHHHTSS.EEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  10 vtvppdttleealelmrekgvs.rlPVVdedgklvGivtlrDllral 55 
                                       + vp++ ++ e+l +mre++ + ++ V+de g   G+vt++D ++ +
  gi|336252602|ref|YP_004595709.1| 307 LHVPESKNVDELLTEMRENRMHmAI-VIDEFGTTEGLVTMEDMVEEI 352
                                       6899************999975355.88**************99887 PP

>> WSS_VP  White spot syndrome virus structural envelope protein VP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.9       0.8   2.9e+03       8      26 ..      22      40 ..      19      45 .. 0.81
   2 ?   12.9   0.1   1.6e-05     0.056      26     124 ..     222     321 ..     218     348 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.8
                            WSS_VP  8 svvaailailalivvvivi 26
                                      +++  ++ il li +vi i
  gi|336252602|ref|YP_004595709.1| 22 EIDRSMVTILGLITIVILI 40
                                      5677889999999999987 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.6e-05
                            WSS_VP  26 ivvfnievtkkvvankdeklrvPveaev...kvlsirGrsnyfklversldtdtlGkvkvknGksDkelke.kkaDl 98 
                                       i++fn+++ k+v +   ++ +vP +a +   +   i+ + +   + e+sld   +G v++++   D +  e +++Dl
  gi|336252602|ref|YP_004595709.1| 222 IFRFNNTIVKEVMTPRLDMTAVPKDASIdeaIETCIQSGHARIPVYEGSLDN-VMGVVHIRDLVRDLNYGEtNDGDL 297
                                       99*********************99866111556666666677789*****9.9********999999866257888 PP

                            WSS_VP  99 vitsvegdrtlevtkgeekeleltlk 124
                                        ++ +    tl+v  +++ + el   
  gi|336252602|ref|YP_004595709.1| 298 ELADLIQ-PTLHVPESKNVD-ELLTE 321
                                       8888755.477777666666.44444 PP

>> DUF4233  Protein of unknown function (DUF4233)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.9    0.0011       3.9       4      53 ..       1      48 [.       1      56 [. 0.84
   2 ?    0.3   0.1      0.24   8.6e+02      39      78 ..      92     130 ..      72     167 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0011
                           DUF4233  4 magtLvlEaivvlLallvaiglrdtepatvlsvggvlavallllagllrr 53
                                      ma   +lEa+  ++ ++v  gl + ++++v ++g++++v+l++l+g+ + 
  gi|336252602|ref|YP_004595709.1|  1 MALSVLLEAVLAAFEAPVV-GL-EIDRSMVTILGLITIVILIALSGFFSS 48
                                      566778************9.99.566899999999*********998876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.24
                           DUF4233  39 vlavallllagllrrpwglalglvlQvlliaagfvvpamf 78 
                                       +  ++ ++++ + +   gl ++++l  +l+ + f v+a++
  gi|336252602|ref|YP_004595709.1|  92 GNNLVNIAMSSIATALLGLYFESGLTPVLL-STFGVTAIV 130
                                       555555555555555555555555555555.444443332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); 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: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3545.18
//
Query:       gi|336252603|ref|YP_004595710.1|  [L=97]
Description: glutaredoxin [Halopiger xanaduensis SH-6]
Scores for complete 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   51.2   0.0    1.4e-13   51.0   0.0    1.1  1  GST_N_3       Glutathione S-transferase, N-terminal domain
    3.8e-12   46.2   0.1    5.6e-12   45.7   0.1    1.2  1  Glutaredoxin  Glutaredoxin
    2.6e-11   43.7   0.0    3.1e-11   43.4   0.0    1.1  1  GST_N_2       Glutathione S-transferase, N-terminal domain
    1.5e-05   25.3   0.0    1.9e-05   24.9   0.0    1.2  1  GST_N         Glutathione S-transferase, N-terminal domain
  ------ inclusion threshold ------
      0.028   14.8   0.1      0.038   14.4   0.1    1.5  1  DUF836        Glutaredoxin-like domain (DUF836)
      0.077   12.8   0.1       0.12   12.1   0.1    1.5  1  TraF          F plasmid transfer operon protein
       0.14   11.9   0.0       0.19   11.4   0.0    1.3  1  Redoxin       Redoxin


Domain annotation for each model (and alignments):
>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   5.5e-17   1.4e-13       2      74 ..      21      96 ..      20      97 .] 0.90

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 5.5e-17
                                      ES-TTSHHHHHHHHHHHHHT--EEEE---TTTT.HHHHHHH-TT--SSEEETTS-..EEESHHHHHHHHHHHH-GG CS
                           GST_N_3  2 ygfpaSpyarrvrlaLnekglpvevvevtpgeh.deellaknplgkvPvLeddge..altdSlaIidyLeelypgp 74
                                      y   ++py+ rv+ +Lne +l+++ + v+p ++ ++ ++++ + ++vPv +d ++   + +S+ I++yLe++y+g+
  gi|336252603|ref|YP_004595710.1| 21 YRLQGCPYCERVARLLNEFDLEYQSRFVEPMHSkRNVVKRVAGVRTVPVVVDENTgiTMAESANIVEYLESTYGGE 96
                                      77899***********************99998577778888*********985545****************986 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.1   2.2e-15   5.6e-12       1      54 [.      18      71 ..      18      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 2.2e-15
                                      EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEE CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvf 54
                                      ++ +  ++CpyC ++ rlL+e+ ++++ + v+ +++ r  +k+++gvrtvP+v+
  gi|336252603|ref|YP_004595710.1| 18 ITFYRLQGCPYCERVARLLNEFDLEYQSRFVEPMHSKRNVVKRVAGVRTVPVVV 71
                                      678999**********************************************97 PP

>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   1.2e-14   3.1e-11       2      69 ..      26      91 ..      25      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.2e-14
                                      -HHHHHHHHHHHHCT--EEEEEEH...-TTSHHHHHHHHCTTTSSSEEE-C.TTEEEESHHHHHHHHHH CS
                           GST_N_2  2 CPwahRvlialalkglediisvvvlepkgfekseefprlnprgtVPvLwdk.dgqvineSseIlrylet 69
                                      CP++ Rv  +l++  le++  +v   +  ++k   ++r+ +  tVPv +d+ +g   +eS+ I++yle+
  gi|336252603|ref|YP_004595710.1| 26 CPYCERVARLLNEFDLEYQSRFV---EPMHSKRNVVKRVAGVRTVPVVVDEnTGITMAESANIVEYLES 91
                                      ***********************...3445666789**************84444888*********97 PP

>> GST_N  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   7.6e-09   1.9e-05       2      75 ..      17      90 ..      16      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 7.6e-09
                                      EEEEESSSTSHTHHHHHHHHHHTT-EEEEEEECSTTTCGGCHHHHHHCTTS-SSEEEET..TEEEESHHHHHHHHH CS
                             GST_N  2 vltlysirgsprahrirlllaakgveyevvpldfeageekspellklnplgkvPaLedn..gkkltESraIleYia 75
                                      ++t y   g+p+ +r+  ll + ++ey+  ++++  +  k+   +++     vP+++d+  g + +ES  I+eY++
  gi|336252603|ref|YP_004595710.1| 17 PITFYRLQGCPYCERVARLLNEFDLEYQSRFVEPMHS--KRNVVKRVAGVRTVPVVVDEntGITMAESANIVEYLE 90
                                      7899*****************************8333..33555556666************************97 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.5e-05     0.038       2      28 ..      18      44 ..      17      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                      EEEEE-TT-HHHHHHHHHHHHHCCCTT CS
                            DUF836  2 ltLyskpgChlCeqakekLkelkleeg 28
                                      +t+y  +gC+ Ce++  +L e+ le +
  gi|336252603|ref|YP_004595710.1| 18 ITFYRLQGCPYCERVARLLNEFDLEYQ 44
                                      899*****************9877765 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   4.9e-05      0.12     135     159 ..      19      44 ..      18      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.9e-05
                              TraF 135 fFyr.gkcpyceaqapilqafadkyg 159
                                        Fyr ++cpyce  a  l++f  +y+
  gi|336252603|ref|YP_004595710.1|  19 TFYRlQGCPYCERVARLLNEFDLEYQ 44 
                                       6999999**************99996 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.5e-05      0.19      22     102 ..       7      82 ..       2      93 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.5e-05
                                       EHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHHTT-TSEEEE-TTSHHH CS
                           Redoxin  22 slsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgkeglkfpvlsDgsaaft 98 
                                       s+++ +g    ++f++   cP+C + ++ l++++ ++ ++ v+    + ++++ vk+++g     +pv++D++  +t
  gi|336252603|ref|YP_004595710.1|   7 STDASTGDDPPITFYRLQGCPYCERVARLLNEFDLEYQSRFVEP---MHSKRNVVKRVAGVRT--VPVVVDENTGIT 78 
                                       4555677788899*************988888887777774444...7777777888877776..777788777777 PP

                                       HHTT CS
                           Redoxin  99 kalG 102
                                        a  
  gi|336252603|ref|YP_004595710.1|  79 MAES 82 
                                       6655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 706.81
//
Query:       gi|336252604|ref|YP_004595711.1|  [L=171]
Description: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen [Halopiger xanaduensis SH-6]
Scores for complete 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-13   50.8   0.0    1.8e-13   50.5   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    3.5e-07   30.0   0.0    5.6e-07   29.4   0.0    1.4  1  Redoxin     Redoxin
    0.00035   20.7   0.0    0.00048   20.2   0.0    1.2  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme
  ------ inclusion threshold ------
      0.075   13.1   0.0        0.1   12.6   0.0    1.2  1  DUF4082     Domain of unknown function (DUF4082)


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 !   50.5   0.0     4e-17   1.8e-13       2     122 ..      18     147 ..      17     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 4e-17
                                       TSB----EEE...STTCEEEECHHH.TT.SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHH CS
                          AhpC-TSA   2 gdkapdfelk...nadgetvslsdy.kg.kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspesh 73 
                                       g++apdf+ +   ++  e+ sls++ ++ + ++++f+p+  ++ ++  + ++ ++  + ++ g  v+gv++ +p+ +
  gi|336252604|ref|YP_004595711.1|  18 GEEAPDFTRPlvnDEYWENRSLSKLaADaERTIVVFTPMTGSFLAKYVWDEIDERGWN-DADGTRVVGVTASTPYGV 93 
                                       89********9988889********74469************************9965.558*************** PP

                                       HHHHHH-H.SSEEEE-TTSHHHHHTT-EETT.....TTECSCEEEEE-TTSBEE CS
                          AhpC-TSA  74 kkfiekeslnfpllsDeegkvakaygvlkee.....kglalratfvidkegkir 122
                                       k+f e++++   l++D+  +va++ygv ++       + + +a f +d+e +++
  gi|336252604|ref|YP_004595711.1|  94 KRFLEENGYDAALFADPGADVARSYGVEHDLdgmegITEPRPAIFAVDEELTVE 147
                                       ****************************999**9999999*********99886 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.3e-10   5.6e-07       3     128 ..      18     145 ..      16     164 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.3e-10
                                       TSBB---ECCEET.TCEEEEEHHH.HTTSE.EEEEEESTTT-HHHHHTHH..HHHTHHHHHHCSTTTEEEEEESSSH CS
                           Redoxin   3 gdkaPdftlplaa.tdgnsvslse.fkgkk.vvvnfvpgafcPtCsaehp..yleklaellkekgvdvvavvadnda 74 
                                       g++aPdft pl++ +  ++ sls+  ++   ++v+f p   ++   a+ +  ++++      + g  vv+v+a++  
  gi|336252604|ref|YP_004595711.1|  18 GEEAPDFTRPLVNdEYWENRSLSKlAADAErTIVVFTPM--TGSFLAKYVwdEIDERGWN-DADGTRVVGVTASTPY 91 
                                       889999995554414456667777644433156666666..5555555555799999888.99999**999999988 PP

                                       HHHHHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEE CS
                           Redoxin  75 fvkefwgkeglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvv 128
                                        vk+f++++g +  +++D++a++++++G++ + d  eg+  pr a++  d  ++
  gi|336252604|ref|YP_004595711.1|  92 GVKRFLEENGYDAALFADPGADVARSYGVEHDLDGMEGITEPRPAIFAVDEELT 145
                                       8*****************************999999997777666655555444 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 !   20.2   0.0   1.1e-07   0.00048      10      55 ..      76     122 ..      68     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-07
                        AhpC-TSA_2  10 daagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalglkr 55 
                                       da g+++v+++  +p ++k+F +++g ++ l++Dp a++ ++ g++ 
  gi|336252604|ref|YP_004595711.1|  76 DADGTRVVGVTASTPyGVKRFLEENGYDAALFADPGADVARSYGVEH 122
                                       789************99*********************999999875 PP

>> DUF4082  Domain of unknown function (DUF4082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.3e-05       0.1      44      99 ..      48     104 ..      39     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                           DUF4082  44 htgslWsa.tgtlLasatftnetasGwqtvtlsspvavtagttYvvsyhapsgryaa 99 
                                       +t+ ++++ tg+ La+    +  + Gw ++  +  v vta t Y v  + ++++y a
  gi|336252604|ref|YP_004595711.1|  48 RTIVVFTPmTGSFLAKYVWDEIDERGWNDADGTRVVGVTASTPYGVKRFLEENGYDA 104
                                       5667777779******999999************************99999777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1278.87
//
Query:       gi|336252605|ref|YP_004595712.1|  [L=218]
Description: Sua5/YciO/YrdC/YwlC family protein [Halopiger xanaduensis SH-6]
Scores for 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-48  162.8   0.0    6.3e-48  162.6   0.0    1.0  1  Sua5_yciO_yrdC  Telomere recombination


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 !  162.6   0.0   3.5e-52   6.3e-48       1     179 []      30     203 ..      30     203 .. 0.94

  Alignments for each domain:
  == domain 1  score: 162.6 bits;  conditional E-value: 3.5e-52
                                       HHHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSS CS
                    Sua5_yciO_yrdC   1 ealrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGp 77 
                                       ea+r+Gg+v++ptetvYgLa+da +++av+r++e+Kgr+++kp+++ v+ +e++ +    e +e+  + +e+f+PGp
  gi|336252605|ref|YP_004595712.1|  30 EAIREGGLVVYPTETVYGLAADALDADAVKRVFEVKGRDRSKPVSLAVPTFETAIEAGYIEATERERAFAEEFLPGP 106
                                       689***************************************************99888889999999********* PP

                                       CEEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS CS
                    Sua5_yciO_yrdC  78 itlllkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildg 154
                                       +t+l +r +e +p+++++g ++vG+r+Pd++ a +Ll a+++p+++TSan+sgeps+ + ee+ +++++++ ++ldg
  gi|336252605|ref|YP_004595712.1| 107 VTVLCER-REVVPDVLTAGGEQVGIRVPDCEPAMALLAAAERPITSTSANVSGEPSARTVEEIGQQVRDEA-VVLDG 181
                                       ******7.555*********************************************************997.9**** PP

                                       ---SSS---EEEETTSSTSSECEXX CS
                    Sua5_yciO_yrdC 155 geiavgvdstVvdltegkpkilRrG 179
                                       ge+ +g++stVvdl+    +i RrG
  gi|336252605|ref|YP_004595712.1| 182 GET-QGTESTVVDLST--GTIHRRG 203
                                       *66.56********96..6777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1704.76
//
Query:       gi|336252606|ref|YP_004595713.1|  [L=114]
Description: hypothetical protein Halxa_1201 [Halopiger xanaduensis SH-6]
Scores for 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:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 941.40
//
Query:       gi|336252607|ref|YP_004595714.1|  [L=516]
Description: S-adenosylhomocysteine deaminase [Halopiger xanaduensis SH-6]
Scores for 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-39  134.6   0.0    2.3e-38  132.4   0.0    1.8  1  Amidohydro_1  Amidohydrolase family
    4.1e-17   62.8   4.0    7.5e-12   45.5   0.3    2.3  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 !  132.4   0.0   2.5e-42   2.3e-38       1     344 []     107     464 ..     107     464 .. 0.88

  Alignments for each domain:
  == domain 1  score: 132.4 bits;  conditional E-value: 2.5e-42
                                       EEEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.. CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattst.. 61 
                                       iv PG+++aH+H  q  +rg+     +++ l            pe+a+ +   g+ + l++G tt++d    +    
  gi|336252607|ref|YP_004595714.1| 107 IVAPGFVNAHLHTWQAGVRGIagdwSFMEYLetmlgeisshYEPEDAYLGNLFGALEQLNAGATTILDWFHIANSpe 183
                                       699*********99998888898884444446677*********************************554444448 PP

                                       HHHHHHHHHHTSSSEEEEEEESSEGGS.......GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSH CS
                      Amidohydro_1  62 giealleaaeelplglrilggkvsldr.......gsaetskasreklkagaaetikgkadgvvk.valapheapafs 130
                                       ++++ ++ +e++  g+r++++ +++         +s+et ++ +++l+++     +++a++++   a++ +++   +
  gi|336252607|ref|YP_004595714.1| 184 HTDRAIDGLEDA--GVRAVFAHGPPGDdsatwweESTETHPDDIRRLHRE-----RFPANDGLLtLAMGIRGPDYST 253
                                       ***********8..***********99***********************.....5666666666************ PP

                                       HHHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHH CS
                      Amidohydro_1 131 deelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellk 207
                                       de ++  +++a++ ++p ++H++++     +++++                lgll++  l  +h   lt  e+el+ 
  gi|336252607|ref|YP_004595714.1| 254 DEVVARDIELARELGIPASMHIGSLGPGGVETLEE----------------LGLLGD-DLNYVHANRLTEREFELIG 313
                                       **********************6633333234444................445555.67778999999999***** PP

                                       HHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTT........TT CS
                      Amidohydro_1 208 erlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllye........de 276
                                           + +v+  p  ++  + g++alr+ ld+G++ +lg+D   s+ s+++++++r+al +qr+l ++        ++
  gi|336252607|ref|YP_004595714.1| 314 DS--GGSVSITPEVEMQMGMGMPALRQTLDAGAIPSLGVD-IVSNVSGDMFTQTRFALQTQRALDNQptveageqVS 387
                                       **..6666666*****************************.************************999999988888 PP

                                       HCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC.........CTCGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 277 egglslkealrmaTingAkalglddkvGsievGkdADlvvvdl.........dilaafvglkkdgnvkkvivkGklv 344
                                       +  l++ +al++aTi gA+algl+d+vGs+++Gk+AD v++++         d+ +++v+++   nv++v v+G+lv
  gi|336252607|ref|YP_004595714.1| 388 DLSLTARQALEFATIEGARALGLEDQVGSLTPGKRADVVLFETddlnttpahDPVETIVFQSGIENVDTVLVDGDLV 464
                                       999****************************************97766444444********************987 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   9.8e-08   0.00088       2      26 ..     100     124 ..      99     145 .. 0.83
   2 !   45.5   0.3   8.3e-16   7.5e-12     208     472 ..     207     464 ..     129     465 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.8e-08
                      Amidohydro_3   2 viDakGrlvlPGFvDsHtHlagggv 26 
                                       +iDa  ++v+PGFv +H+H+  +gv
  gi|336252607|ref|YP_004595714.1| 100 TIDAGDAIVAPGFVNAHLHTWQAGV 124
                                       8******************877774 PP

  == domain 2  score: 45.5 bits;  conditional E-value: 8.3e-16
                      Amidohydro_3 208 ikelldaaerlglplspgseeltigavklfadgvlgsrtalltepyftgwpdfedealaelvaaadergldvaihai 284
                                         + + ++e+ +++++ + ++l  + + ++++      t+++   + +g    +de++a+ +++a+e g+++ +h+ 
  gi|336252607|ref|YP_004595714.1| 207 GDDSATWWEESTETHPDDIRRLHRERFPANDG----LLTLAMG--I-RGPDYSTDEVVARDIELARELGIPASMHIG 276
                                       55555566666666663334444444444433....1222222..2.244444667799999999999999999975 PP

                      Amidohydro_3 285 gdaavd.dvldafeaaaekngnqdrr.rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstp 359
                                         +    ++l+++       g+ +      ha  +te++ e + + ++  ++ p ++            +++ g ++
  gi|336252607|ref|YP_004595714.1| 277 SLGPGGvETLEEL-------GLLGDDlNYVHANRLTEREFELIGDSGGSVSITPEVEM-----------QMGMGMPA 335
                                       4444442344444.......55555445668888899999999999999999977777...........888999** PP

                      Amidohydro_3 360 vkellnagvkvalgsDapvgpfdpwprigaavmrktrrgg..........evlrpdeelsleealalyTrgpAkalg 426
                                       ++  l+ag   +lg D  v+ +    + ++ + ++t r            +    d  l+ ++al   T ++A+alg
  gi|336252607|ref|YP_004595714.1| 336 LRQTLDAGAIPSLGVD-IVSNVSGDMFTQTRFALQTQRALdnqptveageQ--VSDLSLTARQALEFATIEGARALG 409
                                       ****************.6666666666677777777666678898877433..34556999**************** PP

                      Amidohydro_3 427 ledrkGtLevGadADlvvldadpldvdppelaear.........vrltvvdGrvv 472
                                       led  G+L +G++AD+v++++d l  +p+++  ++         v  ++vdG  v
  gi|336252607|ref|YP_004595714.1| 410 LEDQVGSLTPGKRADVVLFETDDLNTTPAHDPVETivfqsgienVDTVLVDGDLV 464
                                       *********************************9999999999999999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3860.96
//
Query:       gi|336252608|ref|YP_004595715.1|  [L=253]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-14   51.1   0.1    1.4e-13   50.5   0.1    1.3  1  HTH_10        HTH DNA binding domain
    6.3e-06   25.8   0.4      8e-05   22.2   0.4    2.2  1  Sigma70_r4_2  Sigma-70, region 4
      0.007   16.1   0.1      0.015   15.0   0.1    1.5  1  HTH_psq       helix-turn-helix, Psq domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.024   14.4   0.0    1.6  1  HTH_30        PucR C-terminal helix-turn-helix domain
      0.052   13.1   0.0      0.097   12.2   0.0    1.4  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.061   13.5   0.0       0.11   12.7   0.0    1.3  1  HTH_Tnp_1_2   Helix-turn-helix of insertion element transposa


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 !   50.5   0.1   4.5e-17   1.4e-13       4      51 ..     183     230 ..     180     232 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 4.5e-17
                            HTH_10   4 kqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskl 51 
                                       kq+e+l lA+e+GY+++PRr++++e+A++ ++  stl+++L +ae  l
  gi|336252608|ref|YP_004595715.1| 183 KQREALELAVEYGYYETPRRMSIQEIAEAEDVPTSTLQYRLTRAEAWL 230
                                       8*******************************************9766 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 !   22.2   0.4   2.7e-08     8e-05       9      53 ..     178     229 ..     178     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.7e-08
                                       TTS-HHHHHHHHHHHTS-.......--HHHHHHHHT--HHHHHHHHHHHHHH CS
                      Sigma70_r4_2   9 aeLperqreifllryleg.......lsykEIAellgisegtVksrlsRArkk 53 
                                       aeLp +qre+++l  + g       +s++EIAe  +++ +t ++rl RA + 
  gi|336252608|ref|YP_004595715.1| 178 AELPYKQREALELAVEYGyyetprrMSIQEIAEAEDVPTSTLQYRLTRAEAW 229
                                       69***************966666667***********************876 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 !   15.0   0.1     5e-06     0.015       2      40 ..     185     226 ..     184     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5e-06
                           HTH_psq   2 pealaaAleavv..nGk.mSirkAArkYgiPrsTLwrrkrgk 40 
                                       +eal++A+e+    +   mSi++ A   ++P+sTL++r+ + 
  gi|336252608|ref|YP_004595715.1| 185 REALELAVEYGYyeTPRrMSIQEIAEAEDVPTSTLQYRLTRA 226
                                       799999999866674444******************998776 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 ?   14.4   0.0   8.1e-06     0.024      13      39 ..     203     229 ..     201     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.1e-06
                                       T-HHHHHHHHTS-HHHHHHHHHHHHHH CS
                            HTH_30  13 gnisatAkaLhvHrnTlryRLrrieel 39 
                                       ++i++ A+a  v   Tl+yRL r+e  
  gi|336252608|ref|YP_004595715.1| 203 MSIQEIAEAEDVPTSTLQYRLTRAEAW 229
                                       699*********************975 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   3.3e-05     0.097      17      42 ..     201     227 ..     197     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.3e-05
                            HTH_24  17 r.isqreLAerlglSpstvnrrlkrLe 42 
                                       r +s++e+Ae+ +++ st+ +rl r e
  gi|336252608|ref|YP_004595715.1| 201 RrMSIQEIAEAEDVPTSTLQYRLTRAE 227
                                       55*********************9876 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 ?   12.7   0.0   3.5e-05      0.11       7      50 ..     179     227 ..     174     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                                       HS-HHHHHHHHHHHHHHH....--S-HHHHHHHHTS-HHHH.HHHHH-H CS
                       HTH_Tnp_1_2   7 eLtakQkkaaellvendy....ekltldeiaeevgvsrsTl.ykWkkkk 50 
                                       eL  kQ+ a el ve  y     +++++eiae   v  sTl y+  + +
  gi|336252608|ref|YP_004595715.1| 179 ELPYKQREALELAVEYGYyetpRRMSIQEIAEAEDVPTSTLqYRLTRAE 227
                                       6889**************99999*****************955554555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1818.13
//
Query:       gi|336252609|ref|YP_004595716.1|  [L=215]
Description: phosphoserine phosphatase SerB [Halopiger xanaduensis SH-6]
Scores for 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   86.9   1.3    2.6e-24   86.7   1.3    1.1  1  HAD              haloacid dehalogenase-like hydrolase
    6.8e-15   55.9  11.6    7.4e-13   49.3   5.7    2.1  2  Hydrolase        haloacid dehalogenase-like hydrolase
    7.7e-11   42.2   1.3    6.7e-09   35.9   0.1    2.9  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
    6.7e-07   29.6   0.2    7.1e-05   23.0   0.0    2.4  2  HAD_2            Haloacid dehalogenase-like hydrolase
     0.0029   17.2   0.0     0.0051   16.3   0.0    1.4  1  UMPH-1           Pyrimidine 5'-nucleotidase (UMPH-1)
  ------ inclusion threshold ------
      0.065   12.6   0.0       0.83    9.0   0.0    2.0  2  Put_Phosphatase  Putative Phosphatase
       0.14   11.7   0.0       0.17   11.4   0.0    1.2  1  HXXSHH           Protein of unknown function (DUF1552)
        0.2   11.2   0.0       0.42   10.1   0.0    1.5  1  S6PP             Sucrose-6F-phosphate phosphohydrolase


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 !   86.7   1.3   1.2e-27   2.6e-24       1     188 []       4     175 ..       4     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 1.2e-27
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerf 76 
                                       + fDfDgTL d+++  ll +   r+g  ++ +++ e+   a+++e+++    +  +  +all+gl+ ee +a +++ 
  gi|336252609|ref|YP_004595716.1|   4 VAFDFDGTLSDSEMTVLLGQ---RCGVAEDMAEITER---AMNDEIGYA---ESLRERAALLEGLAaEEAEAAFDEV 71 
                                       67******************...77775555555555...555558887...778889999*****99999999999 PP

                               HAD  77 vaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelg..adevlatelevdd...rltgelglegkp 148
                                       v        l++ga +l+a+  +aG+++++++gg+++ v + l++ g  +d++++++l  ++    ltg   +eg++
  gi|336252609|ref|YP_004595716.1|  72 V--------LREGAADLIAELNEAGVTTAILTGGFERGVAAALEREGvsVDHIVSNRLPMNAdgtELTGA--VEGPL 138
                                       9........77*********************************************77777778******..***** PP

                               HAD 149 vrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                       + g  k +al++   a   g dl+++va+GD+ +Dlp+l+
  gi|336252609|ref|YP_004595716.1| 139 IEG-TKDDALED--LADDVGVDLDDTVAVGDGANDLPMLK 175
                                       ***.9*******..88888999999*************97 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.3   0.00028      0.64       1      19 [.       1      19 [.       1      24 [. 0.90
   2 !   49.3   5.7   3.3e-16   7.4e-13      85     210 .]      38     178 ..      25     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
                                      SSEEEEESBTTTBCHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  1 iktvvfDkdGTLttgepsv 19
                                      +++v+fD+dGTL ++e+ v
  gi|336252609|ref|YP_004595716.1|  1 MTVVAFDFDGTLSDSEMTV 19
                                      679*************977 PP

  == domain 2  score: 49.3 bits;  conditional E-value: 3.3e-16
                                       HHHHHHHHHHHHCHHHHHHTTHHHHHHHHH.HTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                         Hydrolase  85 dlgaaigsaqsqgrtvallqaralavftia.dplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.... 156
                                        ++++ig a+s  + +all++ a ++ ++a d+  ++++aa+++a+L++ag+ +++ltg++++ + +a+++ G    
  gi|336252609|ref|YP_004595716.1|  38 AMNDEIGYAESLRERAALLEGLAAEEAEAAfDEVVLREGAADLIAELNEAGVTTAILTGGFERGVAAALEREGvsvd 114
                                       3689999999999999999554443333337****************************************999985 PP

                                       ...GGGESEEEEHHCES...........STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       ...xxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 157 ...ddyfdaviasdiet...........vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                               + +    ++           + + + ++++ +++  +++  ++++VGDg+nD+++l+ Ag
  gi|336252609|ref|YP_004595716.1| 115 hivS----NRLPMNADGteltgavegplIEGTKDDALEDLADDVGVDLDDTVAVGDGANDLPMLKVAG 178
                                       5543....3333333323444684445555559999999999999********************998 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.035        79       1      14 [.       4      17 ..       4      23 .. 0.85
   2 ?    0.7   0.0      0.16   3.6e+02      18      55 ..      75     112 ..      69     120 .. 0.76
   3 !   35.9   0.1     3e-12   6.7e-09     187     228 ..     142     183 ..     139     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.035
                                      EEEEIIIIIS-TTS CS
                       Hydrolase_3  1 ialDlDGTLlnsdk 14
                                      +a+D DGTL +s+ 
  gi|336252609|ref|YP_004595716.1|  4 VAFDFDGTLSDSEM 17
                                      79*******98875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                       Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                       e +++ i++l e+g++ +i TG   r+v   le  g++
  gi|336252609|ref|YP_004595716.1|  75 EGAADLIAELNEAGVTTAILTGGFERGVAAALEREGVS 112
                                       667899***************97777777766666655 PP

  == domain 3  score: 35.9 bits;  conditional E-value: 3e-12
                                       SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEE CS
                       Hydrolase_3 187 sKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAm 228
                                       +K  al++la   +++l++++a+GDg ND++ML++agl++  
  gi|336252609|ref|YP_004595716.1| 142 TKDDALEDLADDVGVDLDDTVAVGDGANDLPMLKVAGLAIGF 183
                                       7999*********************************99865 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.2e-08   7.1e-05       2     117 ..       5     110 ..       4     120 .. 0.79
   2 ?    4.2   0.1     0.019        42     139     173 ..     145     179 ..     137     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.2e-08
                             HAD_2   2 iFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkev 78 
                                        FD+DgTl d+e +++   +  ++e  + e++e  ++  ig         l e+     ++e l  +  e   + ev
  gi|336252609|ref|YP_004595716.1|   5 AFDFDGTLSDSEMTVLLGQRCGVAED-MAEITERAMNDEIGYAE-----SLRERAA---LLEGLAAEEAEAAFD-EV 71 
                                       6**********998887766666555.66777777777777655.....4444333...899998888888888.9* PP

                             HAD_2  79 kpydgvkelLeeLkeagyklgivTsksreaveekleqlg 117
                                        + +g+ +l+ eL+eag++ +i T + ++ v   le+ g
  gi|336252609|ref|YP_004595716.1|  72 VLREGAADLIAELNEAGVTTAILTGGFERGVAAALEREG 110
                                       *************************98888877777655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.019
                             HAD_2 139 eviekaleklklkkeeviyvGDsptDieaakkagi 173
                                       + +e + +  +++ ++++ vGD  +D+   k ag+
  gi|336252609|ref|YP_004595716.1| 145 DALEDLADDVGVDLDDTVAVGDGANDLPMLKVAGL 179
                                       56677788899***************988888876 PP

>> UMPH-1  Pyrimidine 5'-nucleotidase (UMPH-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.3e-06    0.0051      88     157 ..      70     139 ..      53     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.3e-06
                            UMPH-1  88 kialrdgveelfekleklnvPvlifsaGlgdvleevlrqanvvysnvkvvsnfldfdedGv.lk.gfkdkli 157
                                       ++ lr+g+ +l+++l++  v + i   G    +   l +++v+    ++vsn+l  + dG+ l+ +++++li
  gi|336252609|ref|YP_004595716.1|  70 EVVLREGAADLIAELNEAGVTTAILTGGFERGVAAALEREGVSVD--HIVSNRLPMNADGTeLTgAVEGPLI 139
                                       678**************************************9887..89********999633314566666 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00037      0.83       1      91 [.       2      90 ..       2     131 .. 0.68
   2 ?    1.7   0.1     0.065   1.5e+02     166     182 ..     155     171 ..     142     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00037
                   Put_Phosphatase  1 ilvvfDFDktiidedsdnwvvdelpatelfeelretlrkg..lwnelmdrvlkelheqgvseadikkvlrsiplspglv 77
                                      ++v+fDFD t+ d++    + +  +  e ++e+ e   ++   + e + +  + l+  g   ++ ++++ ++ l  g  
  gi|336252609|ref|YP_004595716.1|  2 TVVAFDFDGTLSDSEMTVLLGQRCGVAEDMAEITERAMNDeiGYAESLRERAALLE--GLAAEEAEAAFDEVVLREGAA 78
                                      59************999999999999999999987654331257777766666664..445555566666666666666 PP

                   Put_Phosphatase 78 elikslakkkleld 91
                                      +li +l  ++ ++ 
  gi|336252609|ref|YP_004595716.1| 79 DLIAEL--NEAGVT 90
                                      666666..444555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.065
                   Put_Phosphatase 166 gveyerliYvGDganDl 182
                                       gv  +  + vGDganDl
  gi|336252609|ref|YP_004595716.1| 155 GVDLDDTVAVGDGANDL 171
                                       667788899*******8 PP

>> HXXSHH  Protein of unknown function (DUF1552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.7e-05      0.17      39     109 ..      50     136 ..      23     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.7e-05
                            HXXSHH  39 kdkllvlsGldhkvaqe................gdgHesgagalltganvaktegadiasgiSiDqviAerlgeqtr 99 
                                       +++  +l+Gl  ++a++                + + ++ ++a+ltg  +++++ a  ++g+S+D+++ +rl  ++ 
  gi|336252609|ref|YP_004595716.1|  50 RERAALLEGLAAEEAEAafdevvlregaadliaELNEAGVTTAILTGGFERGVAAALEREGVSVDHIVSNRLPMNAD 126
                                       5555556666555555556666666666666654455667899******999999988999***********99988 PP

                            HXXSHH 100 fpsLelgves 109
                                        + L+ +ve+
  gi|336252609|ref|YP_004595716.1| 127 GTELTGAVEG 136
                                       8888888876 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00019      0.42     164     199 ..     141     176 ..     138     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00019
                                       -SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTS CS
                              S6PP 164 askgeAlryLakkleleleqilvcGdsgnDeellig 199
                                       + k++Al+ La+  +++l+ ++ +Gd  nD  +l+ 
  gi|336252609|ref|YP_004595716.1| 141 GTKDDALEDLADDVGVDLDDTVAVGDGANDLPMLKV 176
                                       6899****************************9953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1553.72
//
Query:       gi|336252610|ref|YP_004595717.1|  [L=543]
Description: PAS/PAC sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for 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   79.5   1.7    2.1e-10   40.8   0.1    2.9  4  PAS_4        PAS fold
    6.9e-21   74.5   0.0    3.2e-10   40.2   0.0    2.7  3  PAS_9        PAS domain
    5.1e-17   62.4   0.0    9.7e-17   61.5   0.0    1.5  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
      2e-16   60.0   0.0    1.9e-11   43.9   0.0    2.8  2  PAS          PAS fold
    6.6e-14   51.5   0.0      3e-07   30.3   0.0    3.6  3  PAS_8        PAS domain
    1.2e-07   31.7   0.2    1.2e-07   31.7   0.2    2.0  2  HATPase_c_2  Histidine kinase-like ATPase domain
      1e-05   25.7   0.0    0.00013   22.2   0.0    2.4  2  PAS_3        PAS fold
     0.0035   17.3   0.3      0.011   15.8   0.1    2.0  2  HisKA        His Kinase A (phospho-acceptor) domain
     0.0061   16.5   0.0      0.011   15.6   0.0    1.4  1  HATPase_c_5  GHKL domain
  ------ inclusion threshold ------
      0.023   14.5   0.0      0.041   13.7   0.0    1.3  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
      0.044   13.3   0.1      0.075   12.6   0.1    1.3  1  HisKA_4TM    Archaeal 4TM region of histidine kinase
      0.068   13.3   0.0        1.5    9.0   0.0    2.6  2  PAS_7        PAS fold
       0.13   11.9   0.0       0.22   11.1   0.0    1.3  1  PAS_12       UPF0242 C-terminal PAS-like domain


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   2.2e-12   3.1e-09       2     110 .]      45     156 ..      44     156 .. 0.93
   2 !   40.8   0.1   1.5e-13   2.1e-10       2     110 .]     166     277 ..     165     277 .. 0.86
   3 ?   -2.0   0.0         3   4.2e+03      51      74 ..     343     366 ..     326     404 .. 0.60
   4 ?   -2.7   0.1       4.9   6.8e+03      53      53 ..     389     389 ..     344     436 .. 0.59

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.2e-12
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.... 74 
                                        +++++l+ +d+++r+l+aN+a++e++g++p+el+G++   l pe++++++++ l++ l+++e +++++   l    
  gi|336252610|ref|YP_004595717.1|  45 ANTSEGLLTIDEHSRILFANPAIEEILGYEPAELVGESKMVLIPERLRPAHAAGLEKYLRTGEKHIDWDGIELpalh 121
                                       578999************************************************************99987778899 PP

                             PAS_4  75 .pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        +g e++++++l+     +G+ + + +++rDi++r++
  gi|336252610|ref|YP_004595717.1| 122 kDGHEVPVLVSLREH-SYKGQ-RIFTGLFRDISDRKE 156
                                       9***********998.57999.6778999***99985 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 1.5e-13
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlae....llpeedaarleralrrvlegeepiefleelll 74 
                                       +++ +++  l pdg+ l +N++a e +g+++++++Gk+l+e     ++ee ++  ++ ++r+ +ge + ++l +   
  gi|336252610|ref|YP_004595717.1| 166 NNTYQLTGLLEPDGTLLEVNRTALEFAGVERDDVVGKPLWEapcfAANEEGRTVSRTGVDRASDGEFFRDELRVQGA 242
                                       677788999*******************************8777455555777777889999999888888887777 PP

                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                         ++ +++++++P++ + G+++ ++v +rD+T+++r
  gi|336252610|ref|YP_004595717.1| 243 -NRTAVIDFSIRPIDRDGGKPQLLVVEGRDVTALKR 277
                                       .*************777777************9886 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3
                             PAS_4  51 rleralrrvlegeepiefleelll 74 
                                       ++++  ++++e++e++++l   +l
  gi|336252610|ref|YP_004595717.1| 343 EIAATATELIETNETAKELAGATL 366
                                       444444444444444444443333 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 4.9
                             PAS_4  53 e 53 
                                       +
  gi|336252610|ref|YP_004595717.1| 389 R 389
                                       1 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   2.3e-13   3.2e-10       2     104 .]      49     153 ..      48     153 .. 0.92
   2 !   31.4   0.0   1.2e-10   1.7e-07       8     104 .]     176     274 ..     171     274 .. 0.86
   3 ?   -2.7   0.0       5.2   7.1e+03      12      27 ..     350     365 ..     344     406 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.3e-13
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrk..kerevevvlirknge 74 
                                       +g l ++++ ril+aN+a +++lGy p+e++g s   l+     p ++  l+++l++g+k       e+   +k+g 
  gi|336252610|ref|YP_004595717.1|  49 EGLLTIDEHSRILFANPAIEEILGYEPAELVGESKMVLIpeRLRPAHAAGLEKYLRTGEKhiDWDGIELPALHKDGH 125
                                       6788888***************************9999999889*****************999999********** PP

                             PAS_9  75 tfwvlltaspvkdddgelvgiivilrDite 104
                                       +++vl++++    ++++++   +++rDi++
  gi|336252610|ref|YP_004595717.1| 126 EVPVLVSLREHSYKGQRIFT--GLFRDISD 153
                                       ********888777777777..9*****96 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 1.2e-10
                             PAS_9   8 npdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrk.kerevevvlirkngetfwvllt 81 
                                        pdg++l +N++al++ G  +++v+gk++++    + ++e++   r  +++ ++ +++++e+  +  n++ +  +++
  gi|336252610|ref|YP_004595717.1| 176 EPDGTLLEVNRTALEFAGVERDDVVGKPLWEAPcfAANEEGRTVSRTGVDRASDgEFFRDELRVQGANRTAVI-DFS 251
                                       59**************************9998866555555555555555555589***********998887.*** PP

                             PAS_9  82 aspvkdddgelvgiivilrDite 104
                                       ++p+  d+g+ ++++v  rD+t+
  gi|336252610|ref|YP_004595717.1| 252 IRPIDRDGGKPQLLVVEGRDVTA 274
                                       ****999**************95 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5.2
                             PAS_9  12 rilyaNeaalrllGys 27 
                                       +++  Ne+a++l G +
  gi|336252610|ref|YP_004595717.1| 350 ELIETNETAKELAGAT 365
                                       4678888888887744 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 !   61.5   0.0   7.1e-20   9.7e-17       4     110 ..     414     520 ..     411     522 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 7.1e-20
                                       HHHHHHHHHHHHHHHHHHS..TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS..TTCHHCSTCHTSTSSSH CS
                         HATPase_c   4 krLrqiisnlvdNavkfat..kageieveikaseddlvisveDnGiGipkedlkklfe..kfsqddstkrggggtGl 76 
                                       +rLr ++ +++dNav++ t    ++iev + a+e d+ i+v+D+G+Gip+ ++  +f   + +q         g+Gl
  gi|336252610|ref|YP_004595717.1| 414 SRLRTVLEEVIDNAVRH-TdeRRPKIEVDVVATETDVAIRVTDDGPGIPEPERTGIFNdePITQ------LDHGNGL 483
                                       79***************.62455566666666789*******************9**8889999......348**** PP

                                       HHHHHHHHHHHTTTEEEEEEET...TTEEEEEEEEES CS
                         HATPase_c  77 GlsivkklvelmgGeiwvesep...grGttftftlpl 110
                                       Gl +v  + e +gG++++es+    g+G+++t+++p 
  gi|336252610|ref|YP_004595717.1| 484 GLWLVGLVLEEYGGDLEYESTAdgtGGGSCVTVRVPR 520
                                       *******7778*******999989999******9996 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   1.4e-14   1.9e-11       2     113 .]      39     151 ..      38     151 .. 0.95
   2 !   13.4   0.0   4.2e-05     0.058       8      47 ..     166     205 ..     159     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.4e-14
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r+++ ++ ++ + +De  ril++N+a+ee+lG+++ e++g+s + li+e  +  +a+ le++l++ge+  +++  
  gi|336252610|ref|YP_004595717.1|  39 FFRQLVANTSEGLLTIDEHSRILFANPAIEEILGYEPAELVGESKMVLIPERLRPAHAAGLEKYLRTGEKHIDWDGI 115
                                       6899*********************************************987666********************98 PP

                                       EEC...TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fkl...rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +     +dg +++++v  +    +g++   f g +rdi
  gi|336252610|ref|YP_004595717.1| 116 ELPalhKDGHEVPVLVSLREHSYKGQR--IFTGLFRDI 151
                                       8889*********************99..699999998 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.2e-05
                                       HHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGG CS
                               PAS   8 eslpdpifvvDedgrilyvNaaaeellGlsreevlgksll 47 
                                       +++   + ++  dg  l+vN++a e+ G +r++v+gk+l 
  gi|336252610|ref|YP_004595717.1| 166 NNTYQLTGLLEPDGTLLEVNRTALEFAGVERDDVVGKPLW 205
                                       5555555566789************************985 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   2.2e-10     3e-07       2      52 ..      39      90 ..      38     106 .. 0.81
   2 !   16.0   0.0   6.6e-06    0.0092      16      57 ..     174     215 ..     159     225 .. 0.73
   3 ?    0.2   0.0      0.59   8.1e+02      23      45 ..     351     375 ..     334     402 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.2e-10
                             PAS_8  2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvl 52
                                      ++r+l+ + ++g++ +d+  ri+++N+a +e+lGy+ a+l ge   +l+p+ 
  gi|336252610|ref|YP_004595717.1| 39 FFRQLVANTSEGLLTIDEHSRILFANPAIEEILGYEpAELVGESKMVLIPER 90
                                      79***************5559***************9998888776555444 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 6.6e-06
                             PAS_8  16 vvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrplle 57 
                                       ++  +g+ +++vN++ale+ G++ +d+ g++l +  p +  ++e
  gi|336252610|ref|YP_004595717.1| 174 LLEpDGT-LLEVNRTALEFAGVErDDVVGKPL-WEAPCFAANEE 215
                                       4564555.***********************9.77777766665 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.59
                             PAS_8  23 ivdvNqaalellGys..adlkgell 45 
                                       +++ N++a el G +   +  +e++
  gi|336252610|ref|YP_004595717.1| 351 LIETNETAKELAGATlgGERPREPV 375
                                       7889********9664444444444 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       2.4   3.3e+03      70      91 ..       9      30 ..       7      39 .. 0.65
   2 !   31.7   0.2   8.8e-11   1.2e-07      30     122 ..     413     515 ..     380     518 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.4
                       HATPase_c_2 70 evaDsGpgfdpetlpdpteeep 91
                                      +v+D+G++  +e+ + + +  p
  gi|336252610|ref|YP_004595717.1|  9 RVTDDGAPPSAEPPAADRLAPP 30
                                      699***9977776555544444 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 8.8e-11
                       HATPase_c_2  30 d.eirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslkegGrGlal 104
                                       d ++r ++eE++ Nav+h  +++p  ++ev +  +e+ + ++v+D+Gpg  +pe     + e  ++ +  +G+Gl l
  gi|336252610|ref|YP_004595717.1| 413 DsRLRTVLEEVIDNAVRHTDERRP--KIEVDVVATETDVAIRVTDDGPGiPEPERTGIFNDEPITQLDHGNGLGLWL 487
                                       358999***************999..788888899999***********888875444444445899999******9 PP

                       HATPase_c_2 105 ikglvDev....ey......dgegnvvt 122
                                       +  + +e+    ey      +g+g +vt
  gi|336252610|ref|YP_004595717.1| 488 VGLVLEEYggdlEYestadgTGGGSCVT 515
                                       9877777666556666555444455555 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   9.4e-08   0.00013       2      72 ..      61     133 ..      60     145 .. 0.83
   2 ?    0.6   0.0      0.51   7.1e+02       3      75 ..     183     255 ..     181     267 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.4e-08
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkge.pyege...yRirrkdGeyrwveara 72 
                                       +++++++eeilGy+p+el g     ++++ pe  r+   + l+++l++ge +++++      ++kdG+ + v  + 
  gi|336252610|ref|YP_004595717.1|  61 LFANPAIEEILGYEPAELVGE---SKMVLIPERlRPAHAAGLEKYLRTGEkHIDWDgieLPALHKDGHEVPVLVSL 133
                                       79*******************...7888888887999*********999986665544499999999999887665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.51
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeD...rervrealqealkkgepyegeyRirrkdGeyrwveararvi 75 
                                        v+++  e  G++++++ gk   w   +       r   r+ ++  +++ge +  e R++ ++ +   ++ ++r+i
  gi|336252610|ref|YP_004595717.1| 183 EVNRTALEFAGVERDDVVGK-PLWEAPCFAANeegRTVSRTGVD-RASDGEFFRDELRVQGANRTA-VIDFSIRPI 255
                                       57788888888888888888.33333333322222333344444.446888888888888888766.566666777 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   7.7e-06     0.011       9      31 ..     289     331 ..     282     362 .. 0.72
   2 ?   -3.5   0.0       7.9   1.1e+04      34      48 ..     413     427 ..     401     431 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.7e-06
                                       HHHHHHHHHHHHHHHHHHHHC...................... CS
                             HisKA   9 vaHELrtPLsailgnaeaLkre....................g 31 
                                       + H Lr+ L+ai g+ae+L +e                    +
  gi|336252610|ref|YP_004595717.1| 289 LRHNLRNDLNAIHGFAELLLEElecefesggaggaadtaslpA 331
                                       68*****************887666666666665555544443 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.9
                                       HSSCHHHHHHHHHHH CS
                             HisKA  34 teelkeyletiesea 48 
                                       + +l+  le ++++a
  gi|336252610|ref|YP_004595717.1| 413 DSRLRTVLEEVIDNA 427
                                       456666666666665 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   8.1e-06     0.011       6      89 ..     416     503 ..     411     507 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.1e-06
                       HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg....ekkkle...sskskkeehGiGlksir 75 
                                       l ++l  ++dNA+   ++   ++++I++ v  ++ ++ i+++    g    e   ++     ++ ++ +G+Gl  + 
  gi|336252610|ref|YP_004595717.1| 416 LRTVLEEVIDNAVRHTDE---RRPKIEVDVVATETDVAIRVTDDGPGipepERTGIFndePITQLDHGNGLGLWLVG 489
                                       678899999999866555...579*******************98776655333333232346778899******** PP

                       HATPase_c_5  76 eivkkykgnlsiea 89 
                                        ++++y+g+l++e 
  gi|336252610|ref|YP_004595717.1| 490 LVLEEYGGDLEYES 503
                                       **********9986 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 ?   13.7   0.0     3e-05     0.041       4      48 ..     417     463 ..     414     470 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
                       HATPase_c_3   4 ekAlaelvdNsld.Adaen..vkievnknrgktgeivieDdGkGmsee 48 
                                       +++l e++dN++   d ++  +++ v   +  +  i+++DdG G++e 
  gi|336252610|ref|YP_004595717.1| 417 RTVLEEVIDNAVRhTDERRpkIEVDVVATE-TDVAIRVTDDGPGIPEP 463
                                       67899******9744444433666666654.5799**********985 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.5e-05     0.075     126     161 ..     271     306 ..     265     309 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.5e-05
                         HisKA_4TM 126 dasrakrisdalafvndlirhdlrndlvvirgyaea 161
                                       d +  kr    l  +  l+rh+lrndl+ i+g+ae 
  gi|336252610|ref|YP_004595717.1| 271 DVTALKRRERHLQVLHRLLRHNLRNDLNAIHGFAEL 306
                                       5566677777889999******************96 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0011       1.5       2      33 ..      45      76 ..      44      92 .. 0.86
   2 ?    1.0   0.0      0.34   4.6e+02      59      98 ..     153     192 ..     141     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                             PAS_7  2 enmsqGisvfDadlrLvawNrrylelldlpee 33
                                       n s+G++ +D+  r+++ N  + e+l++ + 
  gi|336252610|ref|YP_004595717.1| 45 ANTSEGLLTIDEHSRILFANPAIEEILGYEPA 76
                                      6899************************9543 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.34
                             PAS_7  59 veaeverrlaaaragkphsfererpdgrvievrgnplpdg 98 
                                        ++e +rr++a+ +++ + +   +pdg+ +ev++++l+  
  gi|336252610|ref|YP_004595717.1| 153 DRKERRRRFEAVFNNTYQLTGLLEPDGTLLEVNRTALEFA 192
                                       4556677888888888888888999******999998755 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.22      65      93 ..      56      84 ..      40      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                            PAS_12 65 kenkllfaNaqirallGwssdkflqdfse 93
                                         ++lfaN  i+++lG+++ +++ + + 
  gi|336252610|ref|YP_004595717.1| 56 EHSRILFANPAIEEILGYEPAELVGESKM 84
                                      5679****************999877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3802.05
//
Query:       gi|336252611|ref|YP_004595718.1|  [L=528]
Description: D-3-phosphoglycerate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for complete 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-60  203.6   0.0      3e-60  202.6   0.0    1.5  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    2.9e-37  127.3   0.4      5e-37  126.6   0.4    1.4  1  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    1.1e-05   25.0   0.0    7.4e-05   22.4   0.0    2.2  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    2.3e-05   24.1   0.6    6.4e-05   22.6   0.0    2.2  2  ACT             ACT domain
    0.00016   22.0   0.0    0.00072   19.9   0.0    2.1  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0014   19.1   0.0     0.0037   17.7   0.0    1.8  1  NAD_binding_7   Putative NAD(P)-binding
     0.0031   17.7   2.2      0.018   15.2   0.0    3.0  4  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.017   15.4   0.0      0.096   13.0   0.0    2.4  1  TrkA_N          TrkA-N domain
      0.018   15.1   0.1       0.11   12.6   0.0    2.1  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
      0.027   14.2   0.1      0.098   12.4   0.0    1.9  2  ELFV_dehydrog   Glutamate/Leucine/Phenylalanine/Valine dehydr
      0.027   14.8   1.3      0.078   13.3   0.2    2.4  2  PDZ             PDZ 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 !  202.6   0.0   1.8e-63     3e-60       1     178 []     105     279 ..     105     279 .. 0.97

  Alignments for each domain:
  == domain 1  score: 202.6 bits;  conditional E-value: 1.8e-63
                                       HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77 
                                       +a+++a++r +++a+ ++++gew +++++lg el+gkt+G++GlGr+Gq+vak+l ++gm+++ayd++ ++e+ +++
  gi|336252611|ref|YP_004595718.1| 105 VAMAFATARSIPQAHIRLKDGEW-AKSDYLGAELNGKTLGVVGLGRVGQEVAKKLDSLGMDIVAYDPYISEER-AQR 179
                                       6899*******************.9*******************************************99777.999 PP

                                       HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES-- CS
                      2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvf 154
                                        g+elv+lee l+++D++++h+pltpet++li++eel+++ +g +liN+aRGg+vde+aL++ +++g++agaalDvf
  gi|336252611|ref|YP_004595718.1| 180 IGAELVDLEESLKQADFLTVHTPLTPETEGLISEEELDMLGDG-YLINCARGGVVDEDALAAKVEDGTLAGAALDVF 255
                                       *************************************999865.8******************************** PP

                                       SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 155 eeeplpedspllelpnviltPHia 178
                                       +eeplp+dsplle++++i+tPH++
  gi|336252611|ref|YP_004595718.1| 256 AEEPLPDDSPLLEHDEIIVTPHLG 279
                                       **********************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 !  126.6   0.4   3.1e-40     5e-37       1     134 []       3     311 ..       3     311 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 3.1e-40
                                       EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDl 77 
                                       vl+++p+++++l+ l+++g+eve+  el  e+lle+++da++livrs t+vt+ev+ea+ +L +++rag+GvDn+D+
  gi|336252611|ref|YP_004595718.1|   3 VLVTDPIDDAGLDALRDAGHEVETGYELEGEDLLEAVSDAHGLIVRSGTEVTEEVFEAAGELVIVGRAGIGVDNIDI 79 
                                       79***************999********************************************************* PP

                                       HHHHHTT-EEEE-TTTTHHHHHHHH.................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                        2-Hacid_dh  78 daakerGilVtnvpgystesvAElt.................................................... 102
                                       daa+ +G++V+n+p+ + +++AE+t                                                    
  gi|336252611|ref|YP_004595718.1|  80 DAATDHGVIVANAPEGNVRAAAEHTvamafatarsipqahirlkdgewaksdylgaelngktlgvvglgrvgqevak 156
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|336252611|ref|YP_004595718.1| 157 kldslgmdivaydpyiseeraqrigaelvdleeslkqadfltvhtpltpetegliseeeldmlgdgylincarggvv 233
                                       ***************************************************************************** PP

                                       ..............................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                       ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ..............................................aaTeeaqeniaeeaaenlvaflkgespanav 133
                                                                                     a+Te aqen+a+ +ae++ a+l ge++ana+
  gi|336252611|ref|YP_004595718.1| 234 dedalaakvedgtlagaaldvfaeeplpddspllehdeiivtphlgASTEAAQENVATSTAEQVNAALIGEPVANAL 310
                                       ***************************************************************************98 PP

                                       S CS
                                       x RF
                        2-Hacid_dh 134 n 134
                                       n
  gi|336252611|ref|YP_004595718.1| 311 N 311
                                       7 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 ?   -0.8   0.0      0.62     1e+03      22      57 ..      16      53 ..      12      61 .. 0.69
   2 !   22.4   0.0   4.6e-08   7.4e-05       2     100 ..     137     234 ..     136     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.62
                                      HHHHTT--EEEEE-TT-HHHHHHHH..TT-EEEEHHHH CS
                              IlvN 22 nlrdsgldvvvglregsksvkkAke..egfevltvaea 57
                                       lrd+g +v  g + +++ + +A +  +g+ v + +e+
  gi|336252611|ref|YP_004595718.1| 16 ALRDAGHEVETGYELEGEDLLEAVSdaHGLIVRSGTEV 53
                                      69999999999999888766666541145555555555 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 4.6e-08
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHH.HHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelq.kevy 77 
                                       l+gk++ v+G G  G+  a++l   g+d+v    +   s ++A++ g e ++++e  k+ad++++ +P + + + ++
  gi|336252611|ref|YP_004595718.1| 137 LNGKTLGVVGLGRVGQEVAKKLDSLGMDIVA-Y-DPYISEERAQRIGAELVDLEESLKQADFLTVHTPLTPEtEGLI 211
                                       789*************************864.4.444589*************************999765414566 PP

                                       HHHTGGG--TT-EEEESSSHHHH CS
                              IlvN  78 eeeiepnlkegkalafahGfnih 100
                                       +ee  + l +g  + +a G  + 
  gi|336252611|ref|YP_004595718.1| 212 SEEELDMLGDGYLINCARGGVVD 234
                                       77777888888888888886665 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       6.2     1e+04      23      51 ..     391     416 ..     391     425 .. 0.52
   2 !   22.6   0.0   3.9e-08   6.4e-05       2      64 ..     452     512 ..     451     515 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.2
                                       HTTSEEEEEEEEEESTTECEEEEEEEEEE CS
                               ACT  23 drgiNidsieqrssedkvagivfvvivvd 51 
                                       drg+ ++   +r  ed     + + ++++
  gi|336252611|ref|YP_004595718.1| 391 DRGVDVTESKTRQAED---FQSLISVTAG 416
                                       5777777777777776...3333333333 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 3.9e-08
                                       EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT   2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64 
                                       ++ ++  D+PG+++ ++++++++g+Ni+ +  ++     +g++ +v  vd e+++e++++l++
  gi|336252611|ref|YP_004595718.1| 452 MVVTRNTDEPGVIGLIGSVMGKHGVNIAGMFNAREAH--GGEALTVYNVDSEVPDEAKAELNE 512
                                       5677889*********************887666666..6*********************97 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 ?   -3.1   0.0       6.7   1.1e+04      58      72 ..      33      47 ..      19      55 .. 0.81
   2 !   19.9   0.0   4.4e-07   0.00072      21      75 ..     153     202 ..     151     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.7
                                      S-CHHHHTT-SEEEE CS
                    UDPG_MGDP_dh_C 58 dsleealkgadaivi 72
                                      ++l ea+++a+ +++
  gi|336252611|ref|YP_004595718.1| 33 EDLLEAVSDAHGLIV 47
                                      578999999999987 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 4.4e-07
                                       HHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S- CS
                    UDPG_MGDP_dh_C  21 diieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaivilte 75 
                                       +++++L + g+++++yDP+++ee++++     g+e+v +lee lk+ad + ++t+
  gi|336252611|ref|YP_004595718.1| 153 EVAKKLDSLGMDIVAYDPYISEERAQR----IGAELV-DLEESLKQADFLTVHTP 202
                                       6899*********************99....578888.7***********99986 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 !   17.7   0.0   2.3e-06    0.0037       4      70 ..     136     202 ..     133     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.3e-06
                     NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatd 70 
                                       +l+gk+  vvG G+v+++ ++kl + g +++ ++p ++ee  +++ ++  +le++l++ad++ + t+
  gi|336252611|ref|YP_004595718.1| 136 ELNGKTLGVVGLGRVGQEVAKKLDSLGMDIVAYDPYISEERAQRIGAELVDLEESLKQADFLTVHTP 202
                                       6899********************************9999999999999999*****9998877765 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 ?   -2.2   0.0       2.5   4.1e+03      63      94 ..      47      79 ..      19     114 .. 0.59
   2 !   15.2   0.0   1.1e-05     0.018       2      61 ..     142     199 ..     141     245 .. 0.72
   3 ?   -3.6   0.0         7   1.1e+04      43      82 ..     394     434 ..     380     441 .. 0.56
   4 ?    0.3   0.1      0.43     7e+02       2      40 ..     464     508 ..     462     519 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.5
                                      SSSHHHHHHHHHS.HCCC--TT-EEEE-S---H CS
                     NAD_binding_2 63 vkagkavdevieg.llealkkgdilidgstssp 94
                                      v++g++v e +++   e +  g+  i + ++++
  gi|336252611|ref|YP_004595718.1| 47 VRSGTEVTEEVFEaAGELVIVGRAGIGVDNIDI 79
                                      445544444444422233333333333333333 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.1e-05
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-..SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavyn..rtkekveelvaegakaaesieelvasldvvit 61 
                                       +g++GlG  G++ a++l + g+++++y+   ++e+++++ ae +    ++ee ++++d+  +
  gi|336252611|ref|YP_004595718.1| 142 LGVVGLGRVGQEVAKKLDSLGMDIVAYDpyISEERAQRIGAELV----DLEESLKQADFLTV 199
                                       79**************************5445555555554444....44445555555555 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 7
                                       EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS..HCCC--T CS
                     NAD_binding_2  43 akaaesieelvasldvvitmvkagkavdevieg..llealkk 82 
                                       ++++es    +++ +  ++ v+ag++ d+v+ +  l+e +++
  gi|336252611|ref|YP_004595718.1| 394 VDVTESKTRQAEDFQS-LISVTAGNDDDSVTVEgtLFEGVDP 434
                                       4444454444544433.3456666666666555566666655 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.43
                                       EEEE-..-SHHHHHHHHHH....HHTT-EEEEE-SSHHHHHHHHH CS
                     NAD_binding_2   2 igfiG..lGvMGsnmalnl....lkagykvavynrtkekveelva 40 
                                       ig+iG  +G+ G n+a  +    ++ g  ++vyn+++e  +e+ a
  gi|336252611|ref|YP_004595718.1| 464 IGLIGsvMGKHGVNIAGMFnareAHGGEALTVYNVDSEVPDEAKA 508
                                       677775566777778776655556778999999999988887765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.9e-05     0.096       3      36 ..     144     179 ..     142     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.9e-05
                                       EES-SHHHHHHHHHHHHTTEEEEEEES..SHHHHHH CS
                            TrkA_N   3 iiGlGrvGrslaeeLseggkdvvvidk..deervee 36 
                                       ++GlGrvG+++a++L + g+d+v+ d   +eer+++
  gi|336252611|ref|YP_004595718.1| 144 VVGLGRVGQEVAKKLDSLGMDIVAYDPyiSEERAQR 179
                                       8****************5547988775224455555 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 ?   -0.7   0.0      0.83   1.4e+03      72     124 ..      35      85 ..      12     104 .. 0.77
   2 ?   12.6   0.0   6.6e-05      0.11      21      86 ..     137     201 ..     121     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.83
                                       HHHCTTT-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTT CS
                     AdoHcyase_NAD  72 leevvkkadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaalean 124
                                       l e+v++a+ ++  +G++  +t e +++  + +iv+  G    +id++a + +
  gi|336252611|ref|YP_004595718.1|  35 LLEAVSDAHGLIVRSGTE--VTEEVFEAAGELVIVGRAGIGVDNIDIDAATDH 85 
                                       556777777777777765..789999999999999999988888888876655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.6e-05
                                       -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-H.HHHHHHHCTT-EE--HHHCTTT-SEEEE-S CS
                     AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdP.icalqaameGfevvtleevvkkadivvttt 86 
                                       l Gk+  v+G G vG+  a+ l +lG  ++    dP i+  +a   G e+v lee +k+ad++   t
  gi|336252611|ref|YP_004595718.1| 137 LNGKTLGVVGLGRVGQEVAKKLDSLGMDIV--AYDPyISEERAQRIGAELVDLEESLKQADFLTVHT 201
                                       78************************8765..57885777899999***************987655 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   0.0     6e-05     0.098      28     135 ..     135     242 ..     127     252 .. 0.67
   2 ?   -2.8   0.0       2.5   4.1e+03      63      95 ..     465     499 ..     452     520 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6e-05
                                       S-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-H.HHHHHHHHCSSSSTTHSHH..STSTSE CS
                     ELFV_dehydrog  28 dslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldi.eellelkeerksvkeykks..sekkae 101
                                        +l+gk++ + G G vg+ +a++l +lg+ +va    + +i ++    i +el++l+e+ k+ + ++ +   + ++e
  gi|336252611|ref|YP_004595718.1| 135 AELNGKTLGVVGLGRVGQEVAKKLDSLGMDIVAY---DPYISEERAQRIgAELVDLEESLKQADFLTVHtpLTPETE 208
                                       3599***************************995...4566666655442566666666555333332222223344 PP

                                       .EESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTH CS
                     ELFV_dehydrog 102 .yieneeellelkvdilvPcAtqneideenakali 135
                                         i++e el  l   +l+ cA+  ++de+ ++a++
  gi|336252611|ref|YP_004595718.1| 209 gLISEE-ELDMLGDGYLINCARGGVVDEDALAAKV 242
                                       355553.6666666677777777777777776666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.5
                                       ESSEEEEETTEE-HHHHHHHHHCSSS..STTHSHH CS
                     ELFV_dehydrog  63 DssGviydpeGldieellelkeerks..vkeykks 95 
                                          G ++ ++G++i+ + + +e++++  ++ y+ +
  gi|336252611|ref|YP_004595718.1| 465 GLIGSVMGKHGVNIAGMFNAREAHGGeaLTVYNVD 499
                                       55688999999999999999888887676666543 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       5.3   8.6e+03      20      36 ..      78      95 ..      67     102 .. 0.57
   2 ?   13.3   0.2   4.8e-05     0.078      10      54 ..     472     520 ..     466     528 .] 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.3
                                      TTSS.SSSSEEEEEECTT CS
                               PDZ 20 sdqr.gdkgifvsevlpg 36
                                      + +  +d+g++v++  +g
  gi|336252611|ref|YP_004595718.1| 78 DIDAaTDHGVIVANAPEG 95
                                      222247889998876555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.8e-05
                                       SESSEEEEEETTSS...SSSSEEEEEECTTSHHHHHT.SSTTEEEEEET CS
                               PDZ  10 gglGfslkggsdqr...gdkgifvsevlpggaaeadg.lkvGDkIlsvN 54 
                                       g+ G++++g+ ++r   g + + v +v    ++ea+  l+++D+I++v+
  gi|336252611|ref|YP_004595718.1| 472 GKHGVNIAGMFNAReahGGEALTVYNVDSEVPDEAKAeLNEDDRIIGVD 520
                                       5679999999999988889999**************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); 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:                        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 0.24s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3932.65
//
Query:       gi|336252612|ref|YP_004595719.1|  [L=312]
Description: hypothetical protein Halxa_1207 [Halopiger xanaduensis SH-6]
Scores for 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  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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: 0.45u 0.18s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2557.97
//
Query:       gi|336252613|ref|YP_004595720.1|  [L=340]
Description: G-D-S-L family lipolytic protein [Halopiger xanaduensis SH-6]
Scores for complete 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   97.2   0.0    1.5e-27   96.8   0.0    1.1  1  Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family
    4.6e-15   56.5   0.2    7.1e-15   55.9   0.2    1.3  1  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
  ------ inclusion threshold ------
      0.033   13.9   0.0      0.061   13.0   0.0    1.3  1  His_Phos_1     Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> 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 !   96.8   0.0   2.6e-31   1.5e-27       2     174 ..     158     332 ..     157     336 .. 0.93

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 2.6e-31
                     Lipase_GDSL_3   2 kpivvYGsSitqGasasRpglaytailsrklgrevvnLgfsGnalleaeladvlaevda.svfvldllpN.....as 72 
                                       ++ + YG+Sit+Ga++s p l y+  ++r ++++v+n g sG+a  e+++ad+la+ d  +v+ l l +N     ++
  gi|336252613|ref|YP_004595720.1| 158 RRYLAYGTSITEGAASSAPHLNYVSHVARGIDADVLNFGCSGSAYCEPAMADYLASRDDwDVATLALSVNmanrgFT 234
                                       78889****************************************************999**********999999* PP

                     Lipase_GDSL_3  73 aeeirerleyfvktlrkahPktpillvedlsttkglvdeklekeveaknkaleelvkklkkekekklylisskellg 149
                                       +e++rer++yfv+++++ahP++pi  v    +  + ++   +++  ++++al+e+v+      +  l l++++el++
  gi|336252613|ref|YP_004595720.1| 235 VEQFRERADYFVNRIAAAHPEKPIACVTLFPYFADVIEGGDAQRAADFRAALREVVADS---SHDTLSLVEGAELME 308
                                       ****************************99999999999999999***********998...7889********877 PP

                     Lipase_GDSL_3 150 kdeeatvdgiHpsdlGllryadale 174
                                        ++  + d  Hp d G+ ++ + l 
  gi|336252613|ref|YP_004595720.1| 309 LTGL-AADLLHPGDTGMEAIGEGLA 332
                                       7776.57**********99877665 PP

>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.2   1.2e-18   7.1e-15       1     179 []     162     326 ..     162     326 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 1.2e-18
                                       EEESHHHHTCTTBCCHCHHCCCCCCCHHHTT-EEEEE.EEHCCH-H..HHHHHHHHCTGGG-TSEEEEE--CCCCCT CS
                     Lipase_GDSL_2   1 alGDSiTaGygadgggrsypaylarllaarlgldvvnnlgvsGattallrllerlrdllrlkpdlvtiliGtNDlgr 77 
                                       a+G SiT+G    ++  +  +y  + +a+  ++dv n +g+sG    +++++++l   +r ++d+ t+ + +N ++r
  gi|336252613|ref|YP_004595720.1| 162 AYGTSITEGA---ASSAPHLNY-VSHVARGIDADVLN-FGCSGSAYCEPAMADYLA--SRDDWDVATLALSVNMANR 231
                                       6899*****9...89999****.**************.******999999999998..899**************** PP

                                       T--HHHHHHH..HHHHHHHHCCC...GEEECEEEEE-TTT-TTSTCCHHHHHHHHHHHHHHHHHHCT-EEE-HHHHH CS
                     Lipase_GDSL_2  78 gvpaaaaaandnleelidalraaapgarilvlgplpptpeaaadarelnaviaaynealrevaaeegvpfvDlhdal 154
                                       g ++++++++   + +++++ aa+p+ +i +++ +p +    +  +   +++a++++alrev a+      D+ +++
  gi|336252613|ref|YP_004595720.1| 232 GFTVEQFRER--ADYFVNRIAAAHPEKPIACVTLFPYFADVIEGGDA--QRAADFRAALREVVADSSH---DTLSLV 301
                                       **********..9*****************88888888888888776..9***************766...555557 PP

                                       HHCCCCCGGBBTTS.SSB-HHHHHH CS
                     Lipase_GDSL_2 155 adsgerladlladdglHPnaaGyrl 179
                                       ++ +    ++la d lHP + G+++
  gi|336252613|ref|YP_004595720.1| 302 EGAELMELTGLAADLLHPGDTGMEA 326
                                       777766666666666*******975 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 ?   13.0   0.0     1e-05     0.061     112     146 ..     228     262 ..     205     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                                       GG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE CS
                        His_Phos_1 112 rppggEsledvaaRvaaaleelaarhegetvlvVs 146
                                        +++g ++e++++R++ +++++aa+h+++ +++V+
  gi|336252613|ref|YP_004595720.1| 228 MANRGFTVEQFRERADYFVNRIAAAHPEKPIACVT 262
                                       445599**************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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: 2574.85
//
Query:       gi|336252614|ref|YP_004595721.1|  [L=126]
Description: phosphoribosyl-AMP cyclohydrolase [Halopiger xanaduensis SH-6]
Scores for 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-35  119.9   0.1    4.5e-35  119.3   0.1    1.3  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase


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 !  119.3   0.1   2.5e-39   4.5e-35       1      74 []      29     102 ..      29     102 .. 0.99

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 2.5e-39
                                       EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
                            PRA-CH   1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74 
                                       mlay++ eale+t etg+a+yySrsr++lW KG+tSg+vq+v+eir+DcD+D++l+ v+q+g aCHtg++sCFy
  gi|336252614|ref|YP_004595721.1|  29 MLAYVSPEALERTRETGRAHYYSRSRDELWEKGATSGHVQDVEEIRVDCDADTILYLVDQEGGACHTGHRSCFY 102
                                       9************************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.40u 0.19s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1042.52
//
Query:       gi|336252615|ref|YP_004595722.1|  [L=395]
Description: hypothetical protein Halxa_1210 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0081   15.8   1.0      0.013   15.2   0.2    1.7  2  EcoR124_C       Type I restriction and modification enzyme - 
  ------ inclusion threshold ------
      0.028   13.3  13.1       0.03   13.2   2.0    3.5  4  Spc7            Spc7 kinetochore protein
       0.12   11.9   0.2       0.12   11.9   0.2    2.8  3  Mu-like_Pro     Mu-like prophage I protein
        1.3    8.1   4.2        1.2    8.3   0.1    2.3  2  DLP_helical     Dynamin-like helical domain
        6.1    7.4   7.9        2.4    8.6   0.3    3.0  3  DUF3106         Protein of unknown function (DUF3106)
        6.7    6.6   8.1        9.5    6.1   0.3    3.3  4  DASH_Spc19      Spc19


Domain annotation for each model (and alignments):
>> EcoR124_C  Type I restriction and modification enzyme - subunit R C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       0.9   2.7e+03     122     122 ..      90      90 ..      36     131 .. 0.59
   2 !   15.2   0.2   4.2e-06     0.013     130     229 ..     155     260 ..     136     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.9
                                       X CS
                         EcoR124_C 122 i 122
                                       +
  gi|336252615|ref|YP_004595722.1|  90 F 90 
                                       1 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.2e-06
                                       XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.... CS
                         EcoR124_C 130 eeddkeereeiekalrs.saelrskkdlieefindlkkkleddkedieeefeefknkekekeleelieeegld.... 201
                                        +d  ++r+ei++++ s +  l+     +++ ++ l++ +e  +e ++e+f ++++++  +e+ +l e+ +l     
  gi|336252615|ref|YP_004595722.1| 155 RKDAAKRRREIDDEIASkERLLELGDADLDAPVERLREPIETYNEAVREAFAQYRQEASVREVFALLERSRLYpfvg 231
                                       356677778999999997777777778888888888776668889******************************** PP

                                       ....XXXXXXXXXXXXXXXX...XXXXXXXXX CS
                         EcoR124_C 202 ....eealkkfikeilkrgkfdalgteilkll 229
                                           +e+l+++++++ + +++    +e+l+++
  gi|336252615|ref|YP_004595722.1| 232 ydqpPEDLREYVDTSADGEYA---IPELLEYA 260
                                       ***999********9999997...44444444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1    0.0092        28     196     234 ..      24      62 ..      18      71 .. 0.81
   2 ?   13.2   2.0     1e-05      0.03     171     280 ..      89     199 ..      77     218 .. 0.82
   3 ?   -2.6   0.0      0.67     2e+03      60      75 ..     267     282 ..     233     296 .. 0.51
   4 ?    2.5   0.6     0.018        54     153     195 ..     343     387 ..     327     393 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0092
                              Spc7 196 idkeeLeelreelaelkaeieekkkelaelqeqleelee 234
                                          eeLe++re+++++++ ie + +++ e  ++  ++++
  gi|336252615|ref|YP_004595722.1|  24 TPLEELEAARERFDRVQQRIEDRGADTVETAADAYRSAT 62 
                                       5679*****************999998887776665555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1e-05
                              Spc7 171 eleeekaeleeeleklqeaaeelesidkeeLeelr.eelaelkaeieekkkelaelqeqleeleekieelkeqksel 246
                                       ++ +  ++l + le+  ++++ l++idk +L e   e+ +++ +  +++ + l+e+++ +e+l+++ ++++++++e+
  gi|336252615|ref|YP_004595722.1|  89 QFATLVENLPDDLERRDAFEDALDAIDKRRLSESDfERARDALEPAAAFADLLDEREAAREDLAAARKDAAKRRREI 165
                                       4455556777788888889999999******98763566677777889999************************** PP

                              Spc7 247 eeeiaeaervleeckgwsesevsrlkeevkalee 280
                                        +eia++er+le      +  v+rl+e  ++  e
  gi|336252615|ref|YP_004595722.1| 166 DDEIASKERLLELGDADLDAPVERLREPIETYNE 199
                                       ************9988888888888887777665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.67
                              Spc7  60 LeLYqhscreLkkyis 75 
                                       Le Y      Lk++++
  gi|336252615|ref|YP_004595722.1| 267 LEHYVADADRLKRRVA 282
                                       3333333344444444 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.018
                              Spc7 153 edkelLekqeeeldellpeleeeka..eleeeleklqeaaeeles 195
                                        d+e+L+   + + +l pe +e+ a  ++ +ele l+e+++ le+
  gi|336252615|ref|YP_004595722.1| 343 IDYERLQTAAQAVAQLTPEQRERLAdgRVAAELEALREEKRALEA 387
                                       588899999999999999999999877899999999998888775 PP

>> Mu-like_Pro  Mu-like prophage I protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2     4e-05      0.12     214     290 ..      22      98 ..      17     121 .. 0.84
   2 ?   -0.2   0.5      0.19   5.7e+02     159     222 ..     142     198 ..      96     247 .. 0.45
   3 ?    1.3   0.1     0.067     2e+02     116     149 ..     336     373 ..     311     393 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4e-05
                       Mu-like_Pro 214 kyvpveaaqalqaelaalkakiaekeaealiekAlkeGkltpalkdwaralakkdlaalkaflekapkiaalsalqt 290
                                         +p+e+++a+++++  ++++i+++ a+++ ++A + +  t+ l+d+  +   ++ + +ka++e   + a l ++  
  gi|336252615|ref|YP_004595722.1|  22 DATPLEELEAARERFDRVQQRIEDRGADTVETAADAYRSATKLLEDYVDRATGTGRENFKAYVELEGQFATLVENLP 98 
                                       56899**********************999999999999999**********************9999998877544 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.19
                       Mu-like_Pro 159 gleedateeqilaalkalkeekaavaealglkagaktaeasaevaaLsaka.......vDlakyvp.....veaaq 222
                                       + +e a e+ + a  +                a+++  e+++e+a+    +        Dl   v+     +e+++
  gi|336252615|ref|YP_004595722.1| 142 DEREAAREDLAAARKD----------------AAKRRREIDDEIASK---ErllelgdADLDAPVErlrepIETYN 198
                                       2222221111111111................111111111111111...12223323333333333333355544 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.067
                       Mu-like_Pro 116 ALTntPaldgmeelaalaaateqeeekekeeek.....e 149
                                       AL n+P +   e+l+  a+a +q ++++ e+        
  gi|336252615|ref|YP_004595722.1| 336 ALLNDPDI-DYERLQTAAQAVAQLTPEQRERLAdgrvaA 373
                                       55555555.444444444444444444432222222220 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0004       1.2      88     148 ..      27      87 ..      20      89 .. 0.93
   2 ?    0.3   0.5      0.11   3.3e+02     100     124 ..     147     171 ..     121     212 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0004
                       DLP_helical  88 kevekleesakriekelaelkkeieearielreelkayfsdLilqvkglsletieeFlere 148
                                       +e+e ++e++ r +++++    +  e++++++++ +++ +d ++++ g+ +e++++++e e
  gi|336252615|ref|YP_004595722.1|  27 EELEAARERFDRVQQRIEDRGADTVETAADAYRSATKLLEDYVDRATGTGRENFKAYVELE 87 
                                       57899999************************************************99865 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.11
                       DLP_helical 100 iekelaelkkeieearielreelka 124
                                        +++la ++k+  + r+e+ +e+++
  gi|336252615|ref|YP_004595722.1| 147 AREDLAAARKDAAKRRREIDDEIAS 171
                                       3444444444444444444444433 PP

>> DUF3106  Protein of unknown function (DUF3106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.3   6.8e+03      64      75 ..      30      41 ..      25      62 .. 0.58
   2 ?    1.9   0.6       0.1   3.1e+02      61      88 ..     142     169 ..     115     177 .. 0.76
   3 ?    8.6   0.3   0.00082       2.4      47      81 ..     347     383 ..     332     390 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.3
                           DUF3106 64 eqarenyqklkq 75
                                      e+are++++++q
  gi|336252615|ref|YP_004595722.1| 30 EAARERFDRVQQ 41
                                      556666666653 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.1
                           DUF3106  61 eqreqarenyqklkqLppeereelrekw 88 
                                       ++re+are ++++++ ++++r+e+ ++ 
  gi|336252615|ref|YP_004595722.1| 142 DEREAAREDLAAARKDAAKRRREIDDEI 169
                                       5799999999999999999998887765 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00082
                           DUF3106  47 rlqermeewakLspeqreqaren..yqklkqLppeer 81 
                                       rlq   ++ a+L+peqre++ +    ++l++L  e+r
  gi|336252615|ref|YP_004595722.1| 347 RLQTAAQAVAQLTPEQRERLADGrvAAELEALREEKR 383
                                       4444445555555555554443211223334444444 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       3.9   1.2e+04      51      57 ..      30      36 ..      21      55 .. 0.52
   2 ?   -0.2   0.4      0.28   8.3e+02      68     144 ..      93     169 ..      82     196 .. 0.48
   3 ?    3.4   0.0     0.022        65      12      42 ..     257     287 ..     252     288 .. 0.89
   4 ?    6.1   0.3    0.0032       9.5     126     155 ..     361     390 ..     327     391 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.9
                                      HHHHHHH CS
                        DASH_Spc19 51 eaakasl 57
                                      eaa++ +
  gi|336252615|ref|YP_004595722.1| 30 EAARERF 36
                                      2222222 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXXXXXXXXXXXXXX CS
                        DASH_Spc19  68 llekaekeleklerreetLka..klelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskkkltkeelerlkk 142
                                       l+e + + le+ +  e++L a  k++l e+  ++a++  + +++ ++  +e+e ++++ ++++k   ++++ +++ +
  gi|336252615|ref|YP_004595722.1|  93 LVENLPDDLERRDAFEDALDAidKRRLSESDFERARDALEPAAAFADLLDEREAAREDLAAARK--DAAKRRREIDD 167
                                       5555555555555555555432245555555555444444443333333322222222211111..22222233333 PP

                                       XX CS
                        DASH_Spc19 143 Lk 144
                                         
  gi|336252615|ref|YP_004595722.1| 168 EI 169
                                       33 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.022
                                       HHHHHHHHHHHHHHHTTHHHHHHHHHHH--- CS
                        DASH_Spc19  12 vslLqssietLdsgvsdfprlkkvLkttrvF 42 
                                       ++  + s ++L++ v+d  rlk+   t+r F
  gi|336252615|ref|YP_004595722.1| 257 LEYADYSRSKLEHYVADADRLKRRVATQRTF 287
                                       56778899**************9999**999 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0032
                                       ..XXXX.XXXXXXXXXXXXXXXXXXXXXXXX CS
                        DASH_Spc19 126 ekskkk.ltkeelerlkkLkqkKerLkytle 155
                                       e+++ + ++++ +++l++L+++K++L+ +le
  gi|336252615|ref|YP_004595722.1| 361 EQRE-RlADGRVAAELEALREEKRALEAALE 390
                                       1222.24788899**************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1079  (0.0601818); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); 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):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.40
# Mc/sec: 2978.13
//
Query:       gi|336252616|ref|YP_004595723.1|  [L=133]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-33  114.6   0.6    5.6e-33  114.4   0.6    1.0  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 !  114.4   0.6   3.1e-37   5.6e-33       1     141 []       1     133 []       1     133 [] 0.96

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 3.1e-37
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       m ++ lV++D+se+++ Ale+Al    ++++e++++hvid+ + g+++ ++  a e e +  +a +      a+a++
  gi|336252616|ref|YP_004595723.1|   1 MTRHLLVPMDDSETARGALEHALSI--HPDDEITVIHVIDDLEAGYAGGPAGGADEVEPDFFAAVQ------AMADE 69 
                                       789*********************7..66779**************************99999987......5789* PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        g +v+++v+eg  a++ile+a++ed+d iV+Gs grsg+sr+llGSv+e v r++ +pV++V+
  gi|336252616|ref|YP_004595723.1|  70 YGRSVDTTVVEGTSADAILEYARDEDVDQIVMGSEGRSGVSRMLLGSVAETVTRKSRIPVTIVP 133
                                       ***************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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: 0.39u 0.19s 00:00:00.58 Elapsed: 00:00:00.34
# Mc/sec: 1154.92
//
Query:       gi|336252617|ref|YP_004595724.1|  [L=169]
Description: hypothetical protein Halxa_1212 [Halopiger xanaduensis SH-6]
Scores for 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-18   67.7   8.2    1.7e-18   67.0   8.2    1.3  1  HPP       HPP family


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 !   67.0   8.2   9.3e-23   1.7e-18       1     109 [.      30     150 ..      30     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 9.3e-23
                               HPP   1 liaslGAsavllfavpesplaqPrnvvgGhlisalvGvaiaklfgl................sllwlaaalavalai 61 
                                       l++slG sa++l    +s++a+Pr+v+gGh i+a++G+++++l+g                 + l +++ la+ l++
  gi|336252617|ref|YP_004595724.1|  30 LFPSLGPSAFVLALFQDSEAASPRRVIGGHAIGAAAGLLAYHLLGGgvsmttatdpgsiaglR-LAASGVLATTLTA 105
                                       79*******************************************9***********999843.33699******** PP

                               HPP  62 almlltrtlhPPagAtaliavlgkeikelgwafllvpvllgslllvlv 109
                                         ml+t+t hPPa+At+li+ lg  ++ l+ a+++    + ++l++++
  gi|336252617|ref|YP_004595724.1| 106 GGMLATDTRHPPACATTLIVSLGLLSRPLEGALIVC---TVVVLVIAH 150
                                       ***********************9866666555544...333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1283.09
//
Query:       gi|336252618|ref|YP_004595725.1|  [L=454]
Description: phosphoglucosamine mutase [Halopiger xanaduensis SH-6]
Scores for 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-34  116.6   0.0    1.1e-33  115.9   0.0    1.4  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    6.8e-30  103.7   2.7    4.8e-29  101.0   0.3    2.6  2  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.3e-15   57.3   0.1    4.3e-15   55.7   0.1    1.9  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
    1.7e-15   57.2   0.0    3.5e-15   56.2   0.0    1.6  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
  ------ inclusion threshold ------
       0.24   11.9   5.0        2.1    8.8   0.1    2.9  3  Usp          Universal stress protein family


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 !  115.9   0.0     3e-37   1.1e-33       3     135 ..       3     129 ..       1     132 [. 0.94

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 3e-37
                                       GBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-H CS
                         PGM_PMM_I   3 kfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllpt 79 
                                        fg sG Rg+++ +eltp++v+++++a++++  a     +v ++rDtR+++r+la+a+a+gla++G +v +lg++pt
  gi|336252618|ref|YP_004595725.1|   3 VFGSSGTRGVAN-EELTPAFVLRVAKAAGTAWGA----DRVGIARDTRYTGRMLADAAASGLASTGTDVDRLGVVPT 74 
                                       7***********.77******************9....6************************************** PP

                                       HHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT- CS
                         PGM_PMM_I  80 PavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekee 135
                                       P ++ ++++ ++   ++itaSHnpp+yng+K++ ++G+++s ++ e+Ie+ + +e+
  gi|336252618|ref|YP_004595725.1|  75 PGAQSYAEREGV-PIVVITASHNPPQYNGVKLVGPDGIELSVSDLETIEETLLTES 129
                                       ******999555.55**********************************9988776 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 ?    2.2   0.1      0.08   2.9e+02      81      99 ..      54      72 ..      35      76 .. 0.75
   2 !  101.0   0.3   1.3e-32   4.8e-29       2     103 .]     150     250 ..     149     250 .. 0.99

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.08
                                      GG-SEEEEE-TTS-BEEEE CS
                        PGM_PMM_II 81 egadlglafDgDaDRlgvv 99
                                        a+  +++  D+DRlgvv
  gi|336252618|ref|YP_004595725.1| 54 AAASGLASTGTDVDRLGVV 72
                                      45555667888*******9 PP

  == domain 2  score: 101.0 bits;  conditional E-value: 1.3e-32
                                       HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHG CS
                        PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielv 78 
                                       +Y+++l++++d+++i+ ++l+v++dp+hGag+ + +e ++elg++vv++n +pd++fp++ p+p + ++l++l++lv
  gi|336252618|ref|YP_004595725.1| 150 DYVDELLAAADRDRIADADLTVALDPGHGAGALTSPEFFRELGCRVVTVNGQPDGHFPGRDPEPVP-DNLEDLGRLV 225
                                       7*****************************************************************.********** PP

                                       GGGG-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  79 kkegadlglafDgDaDRlgvvderG 103
                                       ++++ad+g+a+DgDaDR +++de+G
  gi|336252618|ref|YP_004595725.1| 226 RATDADVGIAHDGDADRAIFFDEHG 250
                                       **********************987 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 !   55.7   0.1   1.2e-18   4.3e-15      14      73 ..     385     447 ..     369     448 .. 0.80

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.2e-18
                                       EECCCCCTTH....HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHHHH CS
                        PGM_PMM_IV  14 aalaallkva....sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevaell 73 
                                       +a a ++ +a    ++ +g + +++d+++l  RpSGTepl+r+y+Ea++d+++ +la+e++e l
  gi|336252618|ref|YP_004595725.1| 385 DAAANHAHAAdaelNTRDGYRLDYGDAWVL-ARPSGTEPLVRIYAEARDDDRATDLADEMYETL 447
                                       3333333333668999**************.****************************99865 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 !   56.2   0.0   9.8e-19   3.5e-15       2     107 ..     255     359 ..     254     365 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 9.8e-19
                                       HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTT.....ECEEEETTCE CS
                       PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeeg.....avlGgEeSgh 73 
                                       gd++la la + le+   ++ + v+ v  s+ l +v+ + g+ l  t++G+ +++ +++e +     + ++gE +g+
  gi|336252618|ref|YP_004595725.1| 255 GDATLAALAAAELED---GD-TTVSAVNVSQRLVDVVTEVGADLELTPIGSTNIITRIRELEdkgkrVPIAGEGNGG 327
                                       788888888777663...45.59*************************************9666778********** PP

                                       EEETTTBSS--HHHHHHHHHHHHHHHTS-HHHHH CS
                       PGM_PMM_III  74 iifldeattkDGilaallvleilaetgkslsell 107
                                       i+f+ +  t+DG+ +a+++le++ae+  ++se++
  gi|336252618|ref|YP_004595725.1| 328 IFFPGFRLTRDGAFTAARFLELVAER--PVSEIV 359
                                       ************************95..899987 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00059       2.1      23     102 ..      78     162 ..      76     180 .. 0.92
   2 ?    4.3   0.1     0.015        53      70     106 ..     254     294 ..     194     294 .. 0.79
   3 ?   -2.1   0.3       1.4     5e+03      14      33 ..     379     398 ..     374     405 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00059
                                       HHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.....HHHHHHCTTCEEEEEEEESSHHHH CS
                               Usp  23 lelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.....akaaaeaggvkvevvveegdpaee 94 
                                          a++ g +++++++++ ++++    +  + + e +++ +++ e++      a a +++ g ++ev+ +  d  +e
  gi|336252618|ref|YP_004595725.1|  78 QSYAEREGVPIVVITASHNPPQYNGVKLVGPDGIELSVSDLETIEETLltesfAVAPWDETGRVREVDGVTRDYVDE 154
                                       567999****************************************99***************************** PP

                                       HHHHHHHT CS
                               Usp  95 ilevaeee 102
                                       +l +a++ 
  gi|336252618|ref|YP_004595725.1| 155 LLAAADRD 162
                                       **999764 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.015
                                       H....HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSE CS
                               Usp  70 a....akaaaeaggvkvevvveegdpaeeilevaeeedadl 106
                                       +    ++a+a+a+ ++ +++v   ++++ +++v+ e +adl
  gi|336252618|ref|YP_004595725.1| 254 EgdatLAALAAAELEDGDTTVSAVNVSQRLVDVVTEVGADL 294
                                       022346788999***************************98 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHCTSEE CS
                               Usp  14 eskkAlewAlelakargael 33 
                                       e ++ l+ A++ a+a +ael
  gi|336252618|ref|YP_004595725.1| 379 ERDAMLDAAANHAHAADAEL 398
                                       45578888888999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3482.07
//
Query:       gi|336252619|ref|YP_004595726.1|  [L=298]
Description: hypothetical protein Halxa_1214 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.02   14.7   0.8      0.086   12.6   0.8    2.0  1  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.8   4.8e-06     0.086      69     163 ..     168     257 ..      27     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.8e-06
                                       GGGG-EEEEEEEEEEEESTT-TT---SHHHHHHSS--EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHTEEEEES CS
                        SBP_bac_11  69 qaesavplassplviavpkgnpkkikgwadLlkpglklavadPttspsGlaalalleaagaqellkalekkvvklge 145
                                       +   + + a+     a+ +g +k   gw +L++  ++ + adP+t+p+ l   +++ aag   +++al +   +++e
  gi|336252619|ref|YP_004595726.1| 168 D--VRDVSATGVPLAATAEGLYKLGNGWMELAGGPFTAVAADPRTEPGRLTRATAVSAAG---SVHALVDDEWTERE 239
                                       4..5666677777788899999999*************************9999******...99999887666777 PP

                                       SHHHHHHHHHTTT-SEEE CS
                        SBP_bac_11 146 ssrqlltaveageadagi 163
                                       +++  + av+ gea +++
  gi|336252619|ref|YP_004595726.1| 240 GPDESIVAVGYGEAVYAV 257
                                       777777777777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2163.91
//
Query:       gi|336252620|ref|YP_004595727.1|  [L=200]
Description: hypothetical protein Halxa_1215 [Halopiger xanaduensis SH-6]
Scores for 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  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1571.88
//
Query:       gi|336252621|ref|YP_004595728.1|  [L=287]
Description: ribose-phosphate pyrophosphokinase [Halopiger xanaduensis SH-6]
Scores for complete 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   0.0    1.2e-17   63.9   0.0    2.1  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    1.1e-11   44.5   0.9    6.5e-11   42.0   0.2    2.2  2  Pribosyltran    Phosphoribosyl transferase domain
    5.1e-08   33.2   0.5    9.7e-08   32.3   0.5    1.4  1  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    5.5e-05   22.7   0.0     0.0001   21.8   0.0    1.4  1  UPRTase         Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
       0.16   10.5   0.0       0.21   10.1   0.0    1.1  1  Terminase_1     Phage Terminase


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 !   63.9   0.0   3.4e-21   1.2e-17       2     113 ..       1     115 [.       1     117 [. 0.93
   2 ?    0.9   0.0      0.11   4.1e+02      12      57 ..     171     218 ..     166     258 .. 0.78

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 3.4e-21
                    Pribosyltran_N   2 kifagssskeLaekiakrlgvelgkakvsrfadgEikveiee....svrgkdvfiiqslskpvndnlmelllmidal 74 
                                       +i++gs+s++La++++++l+ +l+ ++  rf+dgE    +      +   +  +i+ s++++  d+ +ell + da+
  gi|336252621|ref|YP_004595728.1|   1 MIVSGSASQALAAALSSELEEPLAAVEYDRFPDGELLAAVPGladaDSSPDRAVIVASTVSS--DAHVELLQLQDAA 75 
                                       59***********************************9998866555667788999999998..999********** PP

                    Pribosyltran_N  75 rrasakritaViPylgysrqdrk.ksrepisaklvaklLe 113
                                       r+a a +++ V+Py+gy+rqd++ +  +p+sa+ va+ ++
  gi|336252621|ref|YP_004595728.1|  76 REAGAGEVVTVLPYMGYGRQDEAfEAGHPVSARAVARAIS 115
                                       ***********************999**********9876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.11
                    Pribosyltran_N  12 Laekiakrlgvelgk.akvsrfadgEikveiee.svrgkdvfiiqsls 57 
                                       Lae + + +g   ++  + +r +  E++++ ++ +v g+dv++  ++ 
  gi|336252621|ref|YP_004595728.1| 171 LAETVRDAYGEGETDyFEKTRHSGTEVEITPSDvDVSGRDVVVADDII 218
                                       677777777655554256777888888888877799999999987765 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.081   2.9e+02      43      76 ..      11      44 ..       6     106 .. 0.74
   2 !   42.0   0.2   1.8e-14   6.5e-11      12     134 ..     142     258 ..     134     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.081
                                      HHHHHHHHSTT-EE-EEEEEE-TTT--EE..... CS
                      Pribosyltran 43 fakiladeLevplayvrkvkyrpdgseeaargss 76
                                      +a +l++eLe pla v+  ++ ++    a++g+ 
  gi|336252621|ref|YP_004595728.1| 11 LAAALSSELEEPLAAVEYDRFPDGELLAAVPGLA 44
                                      7889999999999988877776666666666654 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 1.8e-14
                                       EEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-TTT--EE........EE----TT CS
                      Pribosyltran  12 ldavarlaaeileeyngkpdvvvgiargGvpfakiladeL.evplayvrkvkyrpdgseeaargssdesrlledpag 87 
                                       +da+ rla+ + e+   + +v++ ++ g++ +a  + d+  e++ +y +k+++++   e ++           d+ g
  gi|336252621|ref|YP_004595728.1| 142 VDAAGRLAEPLPED--LEDPVFLSPDAGAIDLAETVRDAYgEGETDYFEKTRHSGTEVEITP--------SDVDVSG 208
                                       66788888888888..999*********************9999*****9999887777776........4569*** PP

                                       SEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEE...E-HHHHHHHH CS
                      Pribosyltran  88 kkVliVDDildtGgTllaalelLkekgpeevriavlv...dkpateeevd 134
                                       + V++ DDi++tG+T+ +a+  L+++g+ +v + +++   ++ a ++ ++
  gi|336252621|ref|YP_004595728.1| 209 RDVVVADDIIATGSTMSEAVGVLEDRGVGRVFVTCVHpllARDAYAKLSR 258
                                       *****************************988888876666666665555 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.5   2.7e-11   9.7e-08      80     147 ..     205     272 ..     197     282 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 2.7e-11
                                       --TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS-- CS
                    Pribosyl_synth  80 dvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntiph 147
                                       dv+Gr  ++ dd+i   +++ +a  vl++rG  +++v + h ll+ da ++l  + ++ +  t+ti +
  gi|336252621|ref|YP_004595728.1| 205 DVSGRDVVVADDIIATGSTMSEAVGVLEDRGVGRVFVTCVHPLLARDAYAKLSRAGVEAIYGTDTIER 272
                                       9****************************************************************976 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.9e-08    0.0001     116     170 ..     201     257 ..     186     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.9e-08
                           UPRTase 116 Pkki..aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrla 170
                                       P+++  + r v++ D +iaTG+++ +a+ +L +rgvg   ++++  l ++ + ++l+
  gi|336252621|ref|YP_004595728.1| 201 PSDVdvSGRDVVVADDIIATGSTMSEAVGVLEDRGVGRVFVTCVHPLLARDAYAKLS 257
                                       5555558899**************************988888887777777666665 PP

>> Terminase_1  Phage Terminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   5.8e-05      0.21     270     341 ..     204     279 ..     179     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.8e-05
                       Terminase_1 270 rdlsGrdvyiGvDlSrkdDvtavvvafped...gkvylka.ysflpesakekikkldkekieyeeaiergedeasd 341
                                        d+sGrdv +  D+   + +++  v++ ed   g+v++   +++l + a  k+++++ e i    +ierg   +s 
  gi|336252621|ref|YP_004595728.1| 204 VDVSGRDVVVADDIIATGSTMSEAVGVLEDrgvGRVFVTCvHPLLARDAYAKLSRAGVEAIYGTDTIERGASAVSV 279
                                       589************************999554599*985499****************999999***99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); 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 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2293.23
//
Query:       gi|336252622|ref|YP_004595729.1|  [L=187]
Description: Heme NO binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   83.4   0.0    1.9e-23   83.2   0.0    1.0  1  HNOB             Haem-NO-binding
  ------ inclusion threshold ------
       0.16   12.3   0.2         16    5.9   0.1    2.3  2  Thyroglob_assoc  Thyroglobulin_1 repeat associated disordered


Domain annotation for each model (and alignments):
>> HNOB  Haem-NO-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.0   2.2e-27   1.9e-23       1     162 [.       2     159 ..       2     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 2.2e-27
                                       BHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTTSS--TTSBTTHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                              HNOB   1 yGivleslqelveekygeevwdeileeagleekvftthetYddslllklveaaskvlglsadelleafGeyfvkffs 77 
                                       +Giv+++l+ +v+++ +ee+w++++++a+le + +  + +Ydd+++ +++e++ ++  ++++++ + fG+ +   + 
  gi|336252622|ref|YP_004595729.1|   2 HGIVHKTLETYVVDRTDEETWERVVDRADLEPRLYLQVSHYDDREIDAVLETLTELAPQDRRTIERGFGRTLAPELL 78 
                                       59*************************************************************************** PP

                                       HHHTHHHHTHTTCSHHHHHHHHHH.HHHHHHHHHSTTSS--EEEEEEEETTEEEEEEEESS.SSTHHHHHHHHHHHH CS
                              HNOB  78 ekgydkllrvlgrnlfeFLknldn.lHvevlklsypkakpPsfrceeeddnglvlhYrSkR.kgladyvlGllkgva 152
                                        +++++++r + r++ e+L+nl++ +  e+ +   +ka +P ++ +  d n+++++Y ++R + ++ +++G+l+g+ 
  gi|336252622|ref|YP_004595729.1|  79 -STFNAHIR-TDRDVLELLANLEQtVR-EIDTA-TEKASLPDISSRP-DGNEVTVTYDTHReTTYCGLAHGVLEGLL 150
                                       .********.899***********566.99998.9*********998.*************889************9 PP

                                       .HHTTEEEEE CS
                              HNOB 153 kklfnekvei 162
                                          f+ + ++
  gi|336252622|ref|YP_004595729.1| 151 -TAFDADGTV 159
                                       .999877655 PP

>> Thyroglob_assoc  Thyroglobulin_1 repeat associated disordered domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0018        16       5      32 ..     109     136 ..     107     140 .. 0.93
   2 ?    4.2   0.0    0.0063        56       2      21 ..     157     176 ..     156     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0018
                   Thyroglob_assoc   5 teKppqregsGKdDgskptptmetqPqv 32 
                                       teK++ ++ s++ Dg++ t t +t++++
  gi|336252622|ref|YP_004595729.1| 109 TEKASLPDISSRPDGNEVTVTYDTHRET 136
                                       89**********************9976 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0063
                   Thyroglob_assoc   2 GSvteKppqregsGKdDgsk 21 
                                       G vte++ +re  G dD ++
  gi|336252622|ref|YP_004595729.1| 157 GTVTEQACGREDEGEDDVDA 176
                                       99*************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 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:                        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: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 1587.44
//
Query:       gi|336252623|ref|YP_004595730.1|  [L=736]
Description: hypothetical protein Halxa_1218 [Halopiger xanaduensis SH-6]
Scores for 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-08   32.6   2.0    1.9e-06   28.0   0.2    3.2  3  CARDB          CARDB
  ------ inclusion threshold ------
       0.06   13.3   3.0       0.67   10.0   0.3    3.4  2  ALF            Short repeats of unknown function
       0.28   10.8   4.7        2.2    7.8   1.0    2.6  2  Chorion_3      Chorion family 3


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 ?   -1.4   0.1      0.48   2.9e+03      31      61 ..     129     159 ..     126     176 .. 0.62
   2 !   28.0   0.2   3.2e-10   1.9e-06      14      82 ..     530     595 ..     522     616 .. 0.79
   3 ?    2.2   0.0     0.036   2.2e+02       8      70 ..     615     674 ..     609     691 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.48
                                       SSS-EEEEEEEEEETTEEEEEEEESEE-CTE CS
                             CARDB  31 GtaasgatkvalyldgelvgtvtvpsLaage 61 
                                       G+ ++++ +v+l ++++ vg +  ++ ++++
  gi|336252623|ref|YP_004595730.1| 129 GKTDEPTLRVTLPANRTAVGRTATAATDSSD 159
                                       6666777777777777777554443333333 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 3.2e-10
                                       EEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEE CS
                             CARDB  14 eafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltv 82 
                                       ++ +ge+++i +t++N+G+ + g+  ++l +dg++v+    + Laag++tt ++twt++ + g+++l++
  gi|336252623|ref|YP_004595730.1| 530 AVPAGESVRIPATIANTGDRN-GTADATLQVDGDVVD-YREQRLAAGSTTTANLTWTPT-KLGTYDLRI 595
                                       566899************987.778999*******87.5559****************9.776666653 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.036
                                       EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE CS
                             CARDB   8 ntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwt 70 
                                        tl p++a +g+ +t t+tv+ +G++  gat +++  ++   ++v+v ++aag+++tv+    
  gi|336252623|ref|YP_004595730.1| 615 LTLDPETAAPGDPITATATVEATGDGP-GATLLEFRTSEGA-TEVPV-AVAAGDTVTVDRELR 674
                                       4569999****************9985.6666777766666.55666.567777777765555 PP

>> ALF  Short repeats of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2     0.035   2.1e+02      18      40 ..     355     379 ..     345     381 .. 0.79
   2 ?   10.0   0.3   0.00011      0.67       7      20 ..     447     460 ..     441     461 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.035
                               ALF  18 AAqaALdaG..tpaalraFLetGqy 40 
                                       AA  AL+ G  + a++r++L++G +
  gi|336252623|ref|YP_004595730.1| 355 AATVALERGlvDFADVREYLAAGER 379
                                       67777755555889*******9966 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00011
                               ALF   7 llatgGpaVraAAq 20 
                                       l ++gGp+VraAA+
  gi|336252623|ref|YP_004595730.1| 447 LEDAGGPEVRAAAE 460
                                       33489********8 PP

>> Chorion_3  Chorion family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.0   0.00038       2.2      24      89 ..      26      87 ..       2     106 .. 0.58
   2 ?    3.5   0.1     0.008        48       9      68 ..     284     348 ..     278     363 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00038
                         Chorion_3 24 gggGGkGsgdlgagasagleelvnaaaGGaassgGaiegadaeivaspeeagrlssvqaqlqalna 89
                                      g+  G+Gs+  +a a++    +  a++G a ss+ +  +a +   a+ + ++ l +   q +a +a
  gi|336252623|ref|YP_004595730.1| 26 GA--GGGSSGSSAVAES--GSIETASIGSASSSASTASAASSASGATLHRTTTLRQLPDQPGAFEA 87
                                      23..3333333333333..23556778888777766665555555666666666665555555555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.008
                         Chorion_3   9 alaaaplasasYGsagggGGkGsgdlgaga......sagleelvnaaaGGaassgGaiegadaeiv 68 
                                       +++aap  +a++G++g + G   + ++a+a      sa l+e+v++  G a ss G++  +d  ++
  gi|336252623|ref|YP_004595730.1| 284 FFVAAP-TEADWGPEGVQYGRADAWVAADAelsdpgSAWLHEYVHVRQGYARSSVGTTSETDWLVE 348
                                       556655.57888999988888877776665333334789****************99887765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (736 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 5279.46
//
Query:       gi|336252624|ref|YP_004595731.1|  [L=1068]
Description: Isoleucyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-177  592.1   1.1   1.4e-177  591.6   1.1    1.1  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
      8e-29  100.6   0.2    1.7e-28   99.5   0.2    1.6  1  Anticodon_1    Anticodon-binding domain of tRNA
      2e-25   89.4   0.3    1.3e-09   37.3   0.0    3.7  3  tRNA-synt_1g   tRNA synthetases class I (M)
    2.3e-05   24.0   0.0    6.4e-05   22.6   0.0    1.7  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
     0.0071   15.7   0.0       0.84    8.9   0.0    2.6  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 !  591.6   1.1  3.9e-181  1.4e-177       2     602 .]      20     645 ..      19     645 .. 0.96

  Alignments for each domain:
  == domain 1  score: 591.6 bits;  conditional E-value: 3.9e-181
                       tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaiea 78 
                                       ++e W+e d++++++e++ + ++f +vdgPPy  Gs H+G  ++ktlkd+  r+ rm+G++v+ +pG+D++Gl+ie+
  gi|336252624|ref|YP_004595731.1|  20 VFEYWDEVDAYEQTVEHRSDGESFFFVDGPPYTSGSAHMGTTWNKTLKDVYLRFFRMQGYDVTDRPGYDMHGLPIET 96 
                                       6899************************************************************************* PP

                       tRNA-synt_1  79 kvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgl 155
                                        ve++lg ++kk+ +++g+e+f+++++++++e+ e  +++++++Gv++D+d++y+T+ +e++ea ++ f + a++gl
  gi|336252624|ref|YP_004595731.1|  97 RVEERLGFENKKDIEEFGEENFIQECKDYAEEQLEGLQSDFQDFGVWMDWDDPYKTVRPEYMEAAWWGFSKAAERGL 173
                                       ***************************************************************************** PP

                       tRNA-synt_1 156 iyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv..... 227
                                       + +g++ +  +++++ta+++ Evey+d++d++i+v+f+l+d e  k+vi+TTtP+T++++t vav+ e dyv     
  gi|336252624|ref|YP_004595731.1| 174 VEKGHRSISQCPRCETAIANNEVEYEDVEDPSIYVKFDLEDREG-KIVIWTTTPWTIPANTFVAVDEEGDYVgvrae 249
                                       ********************************************.*****************************999 PP

                       tRNA-synt_1 228 ..itkeklilaeallkslvkke..sekkiledergkeLegkevelpl.........vnrkipiiaddyvdke.aGtG 290
                                          ++e l +ae + ++++k+   ++++++e+ +g+eL+g  +e+p+         ++ ++ + a dyvd+   GtG
  gi|336252624|ref|YP_004595731.1| 250 tdGEEELLYVAEPKFEEVLKAGryDDYEVVEELTGEELIGWSYEHPMaervpdypdHEGACEVYAADYVDTHgDGTG 326
                                       76667788899*********9885666*****************************9************98637*** PP

                       tRNA-synt_1 291 vVkiaPahdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcer 367
                                       +V+ aP+h+e+D+e g++ + ++ +++  dg++teea+++eg+ v da++ +v++l++ g ll +++i+hs+++c+r
  gi|336252624|ref|YP_004595731.1| 327 LVHSAPGHGEEDFERGRELGFPIFCPVGGDGVYTEEAGNYEGQFVRDANEDIVADLEADGSLLAEQTITHSYGHCWR 403
                                       ***************************************************************************** PP

                       tRNA-synt_1 368 skkpiiyrateqWfvrvkeladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvske...te 440
                                        ++ ii  +t+qWf+ +++++d++l+++e+ q+ p++ +++r+ +++e+++dW++SRqr+WG ++p++  ++    e
  gi|336252624|ref|YP_004595731.1| 404 CDTGIIQIVTDQWFITITDIKDELLENIEDSQWHPDWaRDNRFRDFVEEAPDWNVSRQRYWGIPLPVWTPEDrddDE 480
                                       *************************************999****************************965411156 PP

                       tRNA-synt_1 441 evvvreelkelvagreee.eaekkalekeakdkl..kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkf 514
                                       +++v+ + +el++   ++ + e+ +l+k+++d+l   ++  ++++++dv+DvW +S+    +tl+ype   + +++ 
  gi|336252624|ref|YP_004595731.1| 481 DMIVVGDREELAERVDQNvDPEEVDLHKDTVDELtiTEDGTTYTRVPDVFDVWLDSSVASWGTLNYPED-DSRFDEL 556
                                       78888899888886655514577899*******987777889**************************9.889**** PP

                       tRNA-synt_1 515 fpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli 591
                                       +pad++le  D++rgW+ + + ++ a +g+ P++evl+hg  +  +Gr mSKs+   idp + i+++g d++R +l+
  gi|336252624|ref|YP_004595731.1| 557 WPADFILEAHDQTRGWFWSQLGMGSAAIGDIPYEEVLMHGHALMPDGRAMSKSKDILIDPHEAIDRHGRDVMRTFLL 633
                                       *************************************************************************9999 PP

                       tRNA-synt_1 592 .lsdvgrdinls 602
                                        ++++g+d++++
  gi|336252624|ref|YP_004595731.1| 634 sNNPQGEDMRFD 645
                                       8999****9986 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 !   99.5   0.2   4.6e-32   1.7e-28       1     149 [.     693     842 ..     693     845 .. 0.92

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 4.6e-32
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       d w+l++l+++ +e+te++e+ r +k ++al ef+++d++++y+++v++r++ e+++ ++a a+++++ vl++ + l
  gi|336252624|ref|YP_004595731.1| 693 DEWVLARLQSTKAEMTEHFEDRRQDKTVDALIEFVVEDVSRFYVQAVRERMWEEEDSASKAaAYATIYRVLRETVAL 769
                                       89**************************************************9998777787*************** PP

                       Anticodon_1  77 laPfmPfitEelwqreeeel.gkk..esimlaewpekaeel.ekeleeeevellkeivkairklrselkikpsse.l 148
                                       laP +Pfi+Ee++    ++l g++  +++++++wp+ +e++ +++l ee+v++l++i +a  ++r++ + k +++ +
  gi|336252624|ref|YP_004595731.1| 770 LAPYAPFISEEIY----GTLtGDDgyDTVHMEDWPAVEEYWqDEQL-EEDVAFLRAIEEAGANARQQAGRKLRWPvP 841
                                       *************....777466699*********98888887777.9*********************99999944 PP

                       Anticodon_1 149 k 149
                                       +
  gi|336252624|ref|YP_004595731.1| 842 R 842
                                       4 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 !   32.7   0.0   8.9e-12   3.2e-08       8     136 ..      50     197 ..      45     200 .. 0.74
   2 !   14.7   0.0   2.7e-06    0.0098     168     239 ..     400     474 ..     374     485 .. 0.81
   3 !   37.3   0.0   3.7e-13   1.3e-09     219     376 ..     508     654 ..     489     662 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 8.9e-12
                                       B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH..........TTS-HHHHHHHHHHHH CS
                      tRNA-synt_1g   8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek..........egvtpeelvekvheei 74 
                                       pY++g+ H+G   +    D++ R+ r++g++v+   g D+hG pie++ e+          e+   e+++++ ++  
  gi|336252624|ref|YP_004595731.1|  50 PYTSGSAHMGTTWNKTLKDVYLRFFRMQGYDVTDRPGYDMHGLPIETRVEErlgfenkkdiEEFGEENFIQECKDYA 126
                                       8************99999*****************************988632222111112233445566666555 PP

                                       HHHHHHTT---SEEE.........ETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
                      tRNA-synt_1g  75 kelfkklnisfdkyg.........rttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                                       +e+++ l+  f ++g         +t   e  e++   f+k  e+gl+++++ +   cp++e+ +++ +ve
  gi|336252624|ref|YP_004595731.1| 127 EEQLEGLQSDFQDFGvwmdwddpyKTVRPEYMEAAWWGFSKAAERGLVEKGHRSISQCPRCETAIANNEVE 197
                                       55555555555555322222222288888888888889999999999999999999999999999988876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.7e-06
                                       .........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET....T CS
                      tRNA-synt_1g 168 ksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP....g 239
                                       ++  +++  +   t+++f  + +++++l e ie ++ +      +  +++++e   d+++sr+  wGip+P    +
  gi|336252624|ref|YP_004595731.1| 400 HCWRCDTGIIQIVTDQWFITITDIKDELLENIEDSQWHPDWARDNRFRDFVEE-APDWNVSRQRYWGIPLPvwtpE 474
                                       566677777666799*****************888877778888999999999.9***************966551 PP

  == domain 3  score: 37.3 bits;  conditional E-value: 3.7e-13
                                       HT----EE-ESS-SSS-EETTECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHH CS
                      tRNA-synt_1g 219 kegLkdlaisrdldwGipvPgaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikF 295
                                       k+ + +l+i+ d     +vP     v+ VWld  +    ++++      ++++++e W          fi     + 
  gi|336252624|ref|YP_004595731.1| 508 KDTVDELTITEDGTTYTRVP----DVFDVWLDSSVASWGTLNYPE----DDSRFDELWP-------ADFILEAHDQT 569
                                       55666777777777777777....589999999998888887765....7789*****4.......46777777777 PP

                                       HHTHHHHHHHH...TT----S-EEEE--EEE.--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-H CS
                      tRNA-synt_1g 296 HtifwPaillg...aelklpkkvvaheyltv.egkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfsw 368
                                          fw  + +g    +    ++v  h++  + +g+ +SkS+ ++++++ea++r   d++R +l++++p+ +D+ f w
  gi|336252624|ref|YP_004595731.1| 570 RGWFWSQLGMGsaaIGDIPYEEVLMHGHALMpDGRAMSKSKDILIDPHEAIDRHGRDVMRTFLLSNNPQGEDMRFDW 646
                                       899**9999996542333557889999865538999***************************************** PP

                                       HHHHHHHH CS
                      tRNA-synt_1g 369 edfvervN 376
                                       + ++   N
  gi|336252624|ref|YP_004595731.1| 647 DGMQTMEN 654
                                       *9998777 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 !   22.6   0.0   1.8e-08   6.4e-05      11     136 ..     207     349 ..     203     369 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.8e-08
                     tRNA-synt_1_2  11 eiefkveeseeklevfttrpdtlfGvtfvalapehplveklaekk..kel....aafieevkkksesereletkeke 81 
                                        ++f++e++e k+ ++tt p t+   tfva+  e + v   ae++  +el    +   eev k  + +     +e +
  gi|336252624|ref|YP_004595731.1| 207 YVKFDLEDREGKIVIWTTTPWTIPANTFVAVDEEGDYVGVRAETDgeEELlyvaEPKFEEVLKAGRYDDYEVVEELT 283
                                       799*********************************99877444310333111123345666666777777778899 PP

                     tRNA-synt_1_2  82 Gv.ftglkaihPitgek.........ipiwvanyvl.meygtgavmavPahdqrDfeFakkynlpi 136
                                       G    g    hP+ ++           +++ a+yv   + gtg v + P+h ++Dfe  ++ + pi
  gi|336252624|ref|YP_004595731.1| 284 GEeLIGWSYEHPMAERVpdypdhegaCEVYAADYVDtHGDGTGLVHSAPGHGEEDFERGRELGFPI 349
                                       987899*******9988899999999*********626789***************9887777776 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 !    3.8   0.0    0.0085        30      21      49 ..      54      82 ..      35      83 .. 0.89
   2 !    8.9   0.0   0.00023      0.84     229     283 ..     581     635 ..     576     650 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0085
                                      S--BHHHHHHHHHHHHHHHHHHHTT-EEE CS
                      tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvq 49
                                        +h+G + +    D+  r+++++gYdv+
  gi|336252624|ref|YP_004595731.1| 54 GSAHMGTTWNKTLKDVYLRFFRMQGYDVT 82
                                      578************************96 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00023
                                       HHHHSSS--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS CS
                      tRNA-synt_1e 229 seaafdkqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsa 283
                                       s a  d ++ +  +h   l+ +g+ msks + +i  ++++ ++   ++R +lls+
  gi|336252624|ref|YP_004595731.1| 581 SAAIGDIPYEEVLMHGHALMPDGRAMSKSKDILIDPHEAIDRHGRDVMRTFLLSN 635
                                       566777999999***************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1068 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); 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: 0.84u 0.25s 00:00:01.08 Elapsed: 00:00:00.47
# Mc/sec: 6804.54
//
Query:       gi|336252625|ref|YP_004595732.1|  [L=80]
Description: hypothetical protein Halxa_1220 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.66   10.1   5.4       0.97    9.5   5.4    1.2  1  DUF2892   Protein of unknown function (DUF2892)


Domain annotation for each model (and alignments):
>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   5.4   5.4e-05      0.97      14      50 ..      19      65 ..      13      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 5.4e-05
                           DUF2892 14 ivvGlvllllallglsggw..........gwllglvGavllltgltg 50
                                      ++++++l ++++++  +++          +++l+++Gav++ +g+ g
  gi|336252625|ref|YP_004595732.1| 19 AIAASALTIGGIAAEYASTqhlgagdqtvALWLAAIGAVMIYAGVYG 65
                                      4666666666666666666799999999*999************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 606.95
//
Query:       gi|336252626|ref|YP_004595733.1|  [L=253]
Description: Uracil-DNA glycosylase superfamily [Halopiger xanaduensis SH-6]
Scores for 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-27   95.4   0.0      4e-27   95.1   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 !   95.1   0.0   2.3e-31     4e-27       1     144 [.      70     233 ..      70     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 2.3e-31
                                       HHC-CTT-SEEEEESSTCHHH.........HHHSSSS.-.STT--HHHHHHHCCCCCCCHHGCTEEEEESSS..... CS
                               UDG   1 pgegppdakvvivGeaPgaee.........datglpFsg.ragnllrkllneaglkrdleseqgvyitnvvkcrp.. 65 
                                       +g+gp da v++vGeaPg+ +         + tg+ ++  ++g+++r++l+++g ++        y+tn+vkc+p  
  gi|336252626|ref|YP_004595733.1|  70 WGTGPLDASVIVVGEAPGPGNpdadrwkggNWTGKGYTSrHSGRRIRRMLAQVGYDE------TAYYTNAVKCFPad 140
                                       689*****************999**************999***************99......99*********966 PP

                                       ....S.ECGCTTCCCCTCCHHHHHHHHHHHHSSEEEEESHHHHHH.....HHHHSCESCCCSCT.......SEEEEE CS
                               UDG  66 ...pg.nrdtptsaeikacaplleeeiellkprlivllGktaakall...geklgklrgklleak......irvlpl 129
                                          p+ nr +pt++e ++c+p l  e+e + p++++++Gk+a k++l   g++l+++ + +le+       ++++p 
  gi|336252626|ref|YP_004595733.1| 141 pedPSsNR-EPTPEERANCRPHLLTELETIDPTVVLATGKHATKTVLaaeGKELDGFIDCVLEPVrcealdVWLVPI 216
                                       55534499.************************************9999999************5567889****** PP

                                       S-SSTTTTT..TTTSHH CS
                               UDG 130 phPsplnrn..ffksnp 144
                                       +hPs++ ++    +++p
  gi|336252626|ref|YP_004595733.1| 217 LHPSYQDVWigRLGYEP 233
                                       *****999966444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1955.41
//
Query:       gi|336252627|ref|YP_004595734.1|  [L=139]
Description: histidine triad (HIT) protein [Halopiger xanaduensis SH-6]
Scores for 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-28   98.4   0.0    3.7e-28   98.1   0.0    1.1  1  HIT       HIT domain
    5.9e-16   59.0   0.0    7.3e-16   58.7   0.0    1.1  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
  ------ inclusion threshold ------
      0.033   14.0   0.0      0.048   13.5   0.0    1.2  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.0   6.1e-32   3.7e-28       1      97 [.      10     106 ..      10     107 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 6.1e-32
                                       TGCC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEE CS
                               HIT   1 ekeipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinn 77 
                                       e+eip++vvyed+ +lafld +p apgh+Lvipk+++++l+d++e+  ++l  ++ +++ a+++ + +++++v+ nn
  gi|336252627|ref|YP_004595734.1|  10 EGEIPARVVYEDETTLAFLDANPLAPGHTLVIPKDEYERLNDVPEDVATDLYDTIHRMVPAVEEAVDADATTVAFNN 86 
                                       579************************************************************************** PP

                                       SGGGT-SSSS-EEEEEEC-T CS
                               HIT  78 gahagqsvahlHiHviprre 97 
                                       g++agq+v+h+H H++pr+e
  gi|336252627|ref|YP_004595734.1|  87 GEAAGQEVPHVHCHIVPRFE 106
                                       *****************986 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.0   1.2e-19   7.3e-16       2     106 ..       3     107 ..       2     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 1.2e-19
                                       -HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG-....-TTTTTHHHHHHHHHHHHHHHTT CS
                            DcpS_C   2 wvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdL....tkehlpllkemrekakkvieeky 74 
                                       ++f ++++g++p+rvvyede+++++ D++p a+ h lvipk++ + l+d+     ++ ++ + +m+  ++++++   
  gi|336252627|ref|YP_004595734.1|   3 TIFSQIVEGEIPARVVYEDETTLAFLDANPLAPGHTLVIPKDEYERLNDVpedvATDLYDTIHRMVPAVEEAVDADA 79 
                                       6899*********************************************777769999***************9988 PP

                                       -T-EEEEE--SCCCT--S-S--EEEEE..... CS
                            DcpS_C  75 nevdaeelrvgvhyqPsvyhlHlHvisldfes 106
                                              ++ g  + + v h+H+H++  +fe+
  gi|336252627|ref|YP_004595734.1|  80 ---TTVAFNNGEAAGQEVPHVHCHIVP-RFEG 107
                                       ...56889*****************96.6655 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     8e-06     0.048      39     108 ..      28     103 ..      16     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8e-06
                                       ---S-SSTT-EEEEESS--SSTTSS-H....HHHHHHHHHHHHHHHHHHHTT--EEEEEE-...SSS-----EEEEE CS
                          CwfJ_C_1  39 lpkgpLssgHvliipieHisallslde....evldeirkfrkalvkmykkqdkdavvfEis...sersvHlaiqvip 108
                                       l  +pL+ gH l+ip +  + l  ++e    ++ d i++   a+ +  ++ d  +v f +     ++ +H++++++p
  gi|336252627|ref|YP_004595734.1|  28 LDANPLAPGHTLVIPKDEYERLNDVPEdvatDLYDTIHRMVPAVEEAVDA-DATTVAFNNGeaaGQEVPHVHCHIVP 103
                                       4459******************9999944445566677777777766655.45566665443449999*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1128.64
//
Query:       gi|336252628|ref|YP_004595735.1|  [L=78]
Description: hypothetical protein Halxa_1223 [Halopiger xanaduensis SH-6]
Scores for 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:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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 0.20s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 645.90
//
Query:       gi|336252629|ref|YP_004595736.1|  [L=338]
Description: peptidase A24B, FlaK domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   40.3   1.4    5.8e-08   33.2   0.1    2.9  4  Arc_PepC_II    Archaeal Peptidase A24 C-terminus Type II
    7.2e-07   29.6  10.0    7.2e-07   29.6  10.0    1.8  2  Peptidase_A24  Type IV leader peptidase family


Domain annotation for each model (and alignments):
>> 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 ?   -2.7   0.0         1   8.9e+03      60      70 ..      34      44 ..      31      47 .. 0.76
   2 ?   -4.2   0.2         2   1.8e+04      64      77 ..     140     153 ..     138     155 .. 0.73
   3 !    5.1   0.0    0.0036        32       5      29 ..     166     190 ..     163     201 .. 0.91
   4 !   33.2   0.1   6.4e-12   5.8e-08      64      92 .]     304     332 ..     280     332 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1
                       Arc_PepC_II 60 kglieetvWvt 70
                                       + +++tvW+ 
  gi|336252629|ref|YP_004595736.1| 34 TRRVSSTVWIP 44
                                      5679999**95 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 2
                       Arc_PepC_II  64 eetvWvtygvPfli 77 
                                        + v v+ ++P+++
  gi|336252629|ref|YP_004595736.1| 140 TNAVVVAVAIPVVL 153
                                       45688999999876 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0036
                       Arc_PepC_II   5 ymligyrvkvkellkkflflleefe 29 
                                       +m++g++v  ++l ++++ lle  e
  gi|336252629|ref|YP_004595736.1| 166 VMVLGWPVATESLSERHGQLLETPE 190
                                       699******************9866 PP

  == domain 4  score: 33.2 bits;  conditional E-value: 6.4e-12
                       Arc_PepC_II  64 eetvWvtygvPflipitaGfiialvlGDl 92 
                                       eetvW+++g Pfl+p+++G++ia+ +GDl
  gi|336252629|ref|YP_004595736.1| 304 EETVWISPGTPFLVPVFVGLVIAVTYGDL 332
                                       358*************************6 PP

>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6  10.0     8e-11   7.2e-07       2      92 ..      19     135 ..      18     155 .. 0.72
   2 ?   -3.6   0.0       1.7   1.5e+04      96     100 ..     320     324 ..     292     332 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 8e-11
                     Peptidase_A24   2 vlltillvlsviDldtrtlpdeltlpllllgvlfa......qllllglpnlaqavlgalvgalvllli..slvdeqa 70 
                                       v+l + + ++v D++tr+++  +++pl+llg  +         + +  +  a++++ a++ +++++ i  +++  ++
  gi|336252629|ref|YP_004595736.1|  19 VALPVFAWVAVRDIKTRRVSSTVWIPLALLGAALLvweaqlARAAGPHAWTAEFLVPAAISLGFVVPIayLFWWFGG 95 
                                       778888999**********************99999***6633344555566777777777766666544577888* PP

                     Peptidase_A24  71 mGgGDvklaavlgaflgwerl..................l 92 
                                       +Gg+D+k ++vl+++++ +                     
  gi|336252629|ref|YP_004595736.1|  96 FGGADAKALLVLALLFPTFPEyavgswtlplttsplgalS 135
                                       ****************954433455555566666644441 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.7
                     Peptidase_A24  96 lvail 100
                                       +v  +
  gi|336252629|ref|YP_004595736.1| 320 FVGLV 324
                                       22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2752.99
//
Query:       gi|336252630|ref|YP_004595737.1|  [L=292]
Description: methyl-accepting chemotaxis sensory transducer [Halopiger xanaduensis SH-6]
Scores for 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  155.9  45.9    1.1e-43  149.1  27.9    3.2  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
    1.1e-06   28.8  32.3     0.0048   17.1   4.3    4.2  4  DUF948           Bacterial protein of unknown function (DUF94
    9.7e-05   22.4  25.7       0.09   12.8   0.7    4.1  4  DUF1664          Protein of unknown function (DUF1664)
    0.00021   21.3  37.0      0.029   14.4   5.2    4.1  4  Laminin_II       Laminin Domain II
     0.0036   17.8  24.7        2.3    8.8   1.0    4.0  3  Syntaxin-6_N     Syntaxin 6, N-terminal
     0.0089   16.2  13.7       0.23   11.6   1.4    2.8  3  CREPT            Cell-cycle alteration and expression-elevate
       0.01   16.0   2.4       0.01   16.0   2.4    4.4  4  COG2             COG (conserved oligomeric Golgi) complex com
  ------ inclusion threshold ------
      0.019   14.1  15.6       0.24   10.5   1.5    3.9  4  RmuC             RmuC family
      0.032   14.7  11.9      0.047   14.2   0.4    3.7  4  PIN_6            PIN domain of ribonuclease
      0.041   14.4   1.0      0.041   14.4   1.0    3.8  4  Spectrin         Spectrin repeat
      0.064   13.6  25.5        2.2    8.6   0.5    4.8  4  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.077   13.2  17.7       0.14   12.3   2.1    3.1  2  Fib_alpha        Fibrinogen alpha/beta chain family
       0.15   11.9   6.8       0.51   10.2   0.1    4.0  3  DASH_Dam1        DASH complex subunit Dam1
       0.15   12.5  20.1       0.11   13.1   3.0    3.3  4  FlgN             FlgN protein
       0.34    9.2  20.9        1.1    7.5  14.3    2.2  2  MAD              Mitotic checkpoint protein
       0.34   10.8   8.6          3    7.7   3.2    2.7  3  STAT_alpha       STAT protein, all-alpha domain
       0.44   10.5   5.2       0.19   11.7   0.5    2.5  3  HisK_N           Histidine kinase N terminal
       0.58    9.8  26.6      0.054   13.2   4.9    3.6  3  LXG              LXG domain of WXG superfamily
       0.63   10.1  16.6       0.36   10.9   0.6    3.4  3  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.75    9.0  17.0        1.5    8.1   4.1    2.2  2  CorA             CorA-like Mg2+ transporter protein
       0.84    9.3  29.4       0.25   11.0   3.6    3.4  3  Laminin_I        Laminin Domain I
       0.93    9.1  34.3       0.11   12.2   2.1    3.9  4  YkyA             Putative cell-wall binding lipoprotein
       0.96    9.9  14.1        5.7    7.4   1.5    4.0  6  Snapin_Pallidin  Snapin/Pallidin
          1   10.1  23.0          3    8.6   2.8    3.6  4  DUF2203          Uncharacterized conserved protein (DUF2203)
        1.1    8.0  28.5       0.34    9.7   7.2    2.6  3  Spc7             Spc7 kinetochore protein
        1.2    8.3  29.4        3.1    6.9   3.0    2.9  3  ISG65-75         Invariant surface glycoprotein
        1.2    8.9  16.3          3    7.6   8.1    2.6  2  SKA1             Spindle and kinetochore-associated protein 1
        1.5    9.0  27.1        2.7    8.2   0.9    4.2  4  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        1.6    9.0  19.0          5    7.3   6.7    3.9  3  SesA             N-terminal domain on NACHT_NTPase and P-loop
          2    8.3  17.0         15    5.4   4.2    4.0  4  Sec34            Sec34-like family
        2.2    7.8  15.4        2.5    7.7   0.4    3.9  4  Fzo_mitofusin    fzo-like conserved region
        2.6    7.9  21.9          4    7.3   8.3    3.0  2  CheZ             Chemotaxis phosphatase, CheZ
        2.8    7.7  18.0       0.55   10.0   0.7    3.9  3  SKA2             Spindle and kinetochore-associated protein 2
        3.3    7.9  14.1       0.34   11.1   0.5    3.4  3  COG5             Golgi transport complex subunit 5
        3.4    6.7  11.7        6.9    5.7   2.1    3.1  3  Atg14            Vacuolar sorting 38 and autophagy-related su
        3.5    6.2  15.1          3    6.4   3.2    2.9  2  Dor1             Dor1-like family
        3.9    5.3  14.4        3.2    5.6   4.7    2.2  2  Prominin         Prominin
          4    7.9  29.1        1.3    9.5   9.7    2.6  3  T3SSipB          Type III cell invasion protein SipB
        4.8    5.6   9.8         31    2.9   9.8    2.0  1  FUSC             Fusaric acid resistance protein family
        5.1    7.1   8.3        4.7    7.2   2.0    3.2  3  DUF489           Protein of unknown function (DUF489)
        5.2    7.2  11.3         14    5.9   1.4    4.2  3  Med9             RNA polymerase II transcription mediator com
        6.4    5.8  29.6        6.8    5.7  14.6    3.0  3  APG17            Autophagy protein Apg17
        6.5    5.9  16.6        2.4    7.3   1.1    3.1  4  TMPIT            TMPIT-like protein
        7.6    7.0  27.1        5.4    7.5   2.3    3.8  4  CENP-H           Centromere protein H (CENP-H)
        7.9    4.3  18.8        1.8    6.4  12.0    2.0  2  V_ATPase_I       V-type ATPase 116kDa subunit family
        7.9    6.1   9.5          1    9.1   1.1    2.9  4  Peptidase_M9_N   Peptidase family M9 N-terminal


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   5.8     8e-05     0.031     107     157 ..      30      80 ..       9      96 .. 0.65
   2 !  149.1  27.9   2.8e-46   1.1e-43       6     169 ..      83     260 ..      78     263 .. 0.88
   3 ?    2.5   0.9      0.28   1.1e+02     134     163 ..     260     289 ..     256     292 .] 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8e-05
                                       ...HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 107 esleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsas 157
                                       ++ + +    ee sel++e  e+++ei+++v+ ++++v+eiaa+s++  + 
  gi|336252630|ref|YP_004595737.1|  30 NISKMVSGSSEEISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEV 80 
                                       333334444555667778888888888888888888888888887765333 PP

  == domain 2  score: 149.1 bits;  conditional E-value: 2.8e-46
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCH CS
                         MCPsignal   6 easeeAeeggkevanvvkqmeeieks..............skeisdiieVideiadQTNlLALNAaiEAARAGeqGr 68 
                                       +a++ A++g  + ++++++m+++++                +ei  i++Vi+eiadQTN+LALNA+iEAARAGe+G+
  gi|336252630|ref|YP_004595737.1|  83 SAEDLADDGCDVAEDAIDAMDNVDDAnadvaeavsrlqerIDEIDTIVDVINEIADQTNMLALNASIEAARAGESGD 159
                                       5555566665556666666666665555666666666666************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH CS
                         MCPsignal  69 GFaVVAdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvq 145
                                        FaVVA+EV++LAe+s + a+eie l+++i+ e++++ve +++++++ve+g e v+et + l+ei +av+e ++  +
  gi|336252630|ref|YP_004595737.1| 160 RFAVVANEVKSLAEESRENAEEIEGLVADIKDETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAE 236
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 146 eiaaaseeqsasieevnqaveeva 169
                                       e+a+a++eq++s eev++ v+  a
  gi|336252630|ref|YP_004595737.1| 237 EVATATDEQASSTEEVATMVDSTA 260
                                       ******************998765 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 134 veavaevadlvqeiaaaseeqsasieevnq 163
                                       +e+++ va+ ++ +aaa eeq + ie   +
  gi|336252630|ref|YP_004595737.1| 260 AENAQTVAKKISRVAAANEEQQEKIEALGE 289
                                       567778888888888888888888776655 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 !   15.3   1.0   4.6e-05     0.018      21      81 ..      28      88 ..      21      91 .. 0.84
   2 ?    7.5   1.8     0.012       4.7      40      85 ..      96     141 ..      92     144 .. 0.82
   3 !   17.1   4.3   1.2e-05    0.0048      18      88 ..     162     232 ..     161     233 .. 0.93
   4 ?    5.3   3.6     0.062        24      35      73 ..     238     276 ..     231     292 .] 0.56

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.6e-05
                            DUF948 21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlg 81
                                      ll+++k+++  ++ i el ++  ++++e++d +++  +++e++   +++v+++ ++++dl+
  gi|336252630|ref|YP_004595737.1| 28 LLNISKMVSGSSEEISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLA 88
                                      7888999999999999999999999999999999999999999999999999988888876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.012
                            DUF948  40 kqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                       +++   +++v+d+ a v e ++ ++e+++++d++++ +++++++ +
  gi|336252630|ref|YP_004595737.1|  96 EDAIDAMDNVDDANADVAEAVSRLQERIDEIDTIVDVINEIADQTN 141
                                       5666778999999999999999999999999999999999988766 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 1.2e-05
                            DUF948  18 ivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       +vv +++k++++e ++  ee+e  v  i +e++++++++ +  e+v+  +e+v++ ++ ++++ ++v e +
  gi|336252630|ref|YP_004595737.1| 162 AVVANEVKSLAEESRENAEEIEGLVADIKDETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEAT 232
                                       578899999******************************************************99998765 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.062
                            DUF948  35 ieelekqvdpilkevedllakvnelledvneklekvdpl 73 
                                       +++ +++  + ++ev+++++ + e ++ v +k+ +v + 
  gi|336252630|ref|YP_004595737.1| 238 VATATDEQASSTEEVATMVDSTAENAQTVAKKISRVAAA 276
                                       444455555556666666666666666666666655443 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.7   0.00023      0.09      56     111 ..      27      82 ..      10      89 .. 0.79
   2 !    9.6   0.8    0.0023       0.9      48      87 ..     103     142 ..      94     173 .. 0.79
   3 !    7.8   2.5    0.0083       3.2      46     111 ..     164     229 ..     158     232 .. 0.63
   4 !    7.6   7.4    0.0093       3.6      39     121 ..     200     288 ..     198     291 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00023
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       +l +  +  s   +++ +  deq+e+ +ei++ev++++  ++ei   +++vke+ +
  gi|336252630|ref|YP_004595737.1|  27 ELLNISKMVSGSSEEISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSS 82 
                                       555555666666678888899*************************9999998755 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0023
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeike 87 
                                        ++++  +++a++  +L++rid++d+ +d  +ei+ +++ 
  gi|336252630|ref|YP_004595737.1| 103 DNVDDANADVAEAVSRLQERIDEIDTIVDVINEIADQTNM 142
                                       3567788899999999999999999999999999998875 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0083
                           DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       v+++++++ e+ ++  ++++  ++ + ++ de+ e +++ +eev++  e+++e+ + +e++++av+
  gi|336252630|ref|YP_004595737.1| 164 VANEVKSLAEESRENAEEIEGLVADIKDETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVT 229
                                       666666666666666666666666666666666666666666666666666666666666666664 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0093
                           DUF1664  39 lsdavesvskqleqvs......eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkea 109
                                       +s+a e+v + +e+v       e++ ++  + ++  ++v +  deq+  ++e++  v++  e+ +++ ++++ v +a
  gi|336252630|ref|YP_004595737.1| 200 ISNANEEVETGIEHVNetvdilEEIDDAVTEATQGAEEVATATDEQASSTEEVATMVDSTAENAQTVAKKISRVAAA 276
                                       678888999999988866666688999999*********************************************** PP

                           DUF1664 110 veglesklerie 121
                                        e+ ++k+e + 
  gi|336252630|ref|YP_004595737.1| 277 NEEQQEKIEALG 288
                                       ***999999886 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   2.9    0.0046       1.8       6      72 ..      19      88 ..      14      90 .. 0.52
   2 !   12.6   1.9   0.00027       0.1       4      58 ..      94     148 ..      92     153 .. 0.93
   3 !   14.4   5.2   7.5e-05     0.029       1      70 [.     168     237 ..     168     240 .. 0.91
   4 ?    5.7   7.4     0.036        14       4      74 ..     220     290 ..     217     292 .] 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0046
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXX--TTTTTG CS
                        Laminin_II  6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvk...dankairdArrsvkkLeklapqLl 72
                                      +e+ ++++e l++ + +s   e+++e + e  ++++e+ ++v+   +  + i+  +++vk++   a++L 
  gi|336252630|ref|YP_004595737.1| 19 DEVGDSVTELLNISKMVSGSSEEISELADEQSETMHEIADEVStlsATVEEIAASSNQVKEVSSSAEDLA 88
                                      5555555555555555555555555555555555555555555322334445555666666666666665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00027
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdAr 58 
                                       +a++a + + +v +  a++++ +++++e + ei++ v+ +ne +++ n+    A+
  gi|336252630|ref|YP_004595737.1|  94 VAEDAIDAMDNVDDANADVAEAVSRLQERIDEIDTIVDVINEIADQTNMLALNAS 148
                                       6899********************************************9888775 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 7.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTT CS
                        Laminin_II   1 skelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapq 70 
                                       +k+la+e  e a+e++  +a+++ ++++t e++s++n++ve   e+v++   ++++  ++v + ++ a++
  gi|336252630|ref|YP_004595737.1| 168 VKSLAEESRENAEEIEGLVADIKDETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAEE 237
                                       5999********************************************9999999999888888877765 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.036
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGG CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldk 74 
                                       +++e+++ ++e  +  +++++ +++  ++ +e+++ v+ t e+++   k i  +  +  + +++++ L ++
  gi|336252630|ref|YP_004595737.1| 220 ILEEIDDAVTEATQGAEEVATATDEQASSTEEVATMVDSTAENAQTVAKKISRVAAANEEQQEKIEALGER 290
                                       5799*****************************************99999888877777777777766655 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 !    8.1   2.2    0.0097       3.8      13      70 ..      24      73 ..      15      89 .. 0.48
   2 !    8.8   1.0    0.0059       2.3       8      71 ..      68     137 ..      68     150 .. 0.81
   3 !    8.8  10.2    0.0062       2.4       1      70 [.     159     229 ..     159     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0097
                      Syntaxin-6_N 13 slnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvrivekn 70
                                      s+ ++ ++ +  +         +see++e+ +e  +++++i  +++ L  tv+ + ++
  gi|336252630|ref|YP_004595737.1| 24 SVTELLNISKMVSG--------SSEEISELADEQSETMHEIADEVSTLSATVEEIAAS 73
                                      44444444444433........456666666666666666666666666666433222 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0059
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwerlledtsss......tseeldetrteLrkalrsiewdledLeetvriveknp 71 
                                       ee+  s n+++++ ++ e+l +d+ +         +++d+++ ++ +a++ +++ +++++  v+++++  
  gi|336252630|ref|YP_004595737.1|  68 EEIAASSNQVKEVSSSAEDLADDGCDVaedaidAMDNVDDANADVAEAVSRLQERIDEIDTIVDVINEIA 137
                                       57777788888888888888777776346777789****************************9997644 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0062
                      Syntaxin-6_N   1 DPFfevkeeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvrivek.....n 70 
                                       D F +v++eV++ +++ ++  ++ e l  d     ++e det +++ +a +++e+ +e  +etv+i+e+      
  gi|336252630|ref|YP_004595737.1| 159 DRFAVVANEVKSLAEESRENAEEIEGLVAD----IKDETDETVEQISNANEEVETGIEHVNETVDILEEiddavT 229
                                       6799********************998887....5899**************************99988444430 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.5     0.051        20      32     120 ..      26     116 ..      13     119 .. 0.81
   2 !   11.6   1.4   0.00059      0.23       6     118 ..      52     170 ..      47     175 .. 0.86
   3 !    9.4   4.2    0.0028       1.1      35     123 ..     195     287 ..     180     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.051
                             CREPT  32 sdvsllekik..dkeeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkekl 106
                                       +++  ++k+   ++ee  +l+++ +e ++ +a+ ++ L+a +ee    ++++++  ++  +l+++    +e+  + +
  gi|336252630|ref|YP_004595737.1|  26 TELLNISKMVsgSSEEISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADDGCDVAEDAIDAM 102
                                       55555666633578889999999999999999999999999999999999999999999999999999999888888 PP

                             CREPT 107 ekvksvrkelkshi 120
                                       ++v+ +++++ + +
  gi|336252630|ref|YP_004595737.1| 103 DNVDDANADVAEAV 116
                                       88888888887665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00059
                             CREPT   6 aLkeLensassdaavReriaklPpevsdvs.llekikd.....keeaekllkqveealellaeYnkrLeaeleeRkk 76 
                                       +++e+ +++s+  a+ e+ia+  ++v++vs  +e + d      e+a   +++v++a + +ae ++rL++ ++e  +
  gi|336252630|ref|YP_004595737.1|  52 TMHEIADEVSTLSATVEEIAASSNQVKEVSsSAEDLADdgcdvAEDAIDAMDNVDDANADVAEAVSRLQERIDEIDT 128
                                       567888889999999999999999999986257788762333347888999************************** PP

                             CREPT  77 lakmledfleaqkellakaeekleelkeklekvksvrkelks 118
                                       +   ++++  + ++l+ +a  ++++  e  ++   v +e+ks
  gi|336252630|ref|YP_004595737.1| 129 IVDVINEIADQTNMLALNASIEAARAGESGDRFAVVANEVKS 170
                                       *************************99999999999999998 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0028
                             CREPT  35 sllekik.dkeeaekllkqveealellaeYnkrLeaeleeRkklakmledf...leaqkellakaeekleelkekle 107
                                       + +e+i+  +ee e+ +++v+e + +l+e     ++ ++  +++a+  ++    +e + + ++ ++e+++ + +k++
  gi|336252630|ref|YP_004595737.1| 195 ETVEQISnANEEVETGIEHVNETVDILEEIDDAVTEATQGAEEVATATDEQassTEEVATMVDSTAENAQTVAKKIS 271
                                       5678887467889999**********************99999998877651115556667889999999******* PP

                             CREPT 108 kvksvrkelkshiqsL 123
                                       +v ++++e +++i+ L
  gi|336252630|ref|YP_004595737.1| 272 RVAAANEEQQEKIEAL 287
                                       **********999987 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 !   16.0   2.4   2.6e-05      0.01      43     113 ..      14      84 ..      11     108 .. 0.89
   2 ?    3.8   0.3      0.15        57      77     111 ..     104     138 ..      79     153 .. 0.53
   3 ?    4.7   2.1     0.075        29      69     105 ..     177     213 ..     158     231 .. 0.65
   4 ?    2.6   3.5      0.35   1.4e+02      69     113 ..     236     280 ..     218     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.6e-05
                              COG2  43 ekellelvnedyadFvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                       e+ l++ v + + + +++S+   g  ee++e+  + ++++ ++ + ++ ls++ ee+ +  ++ ke+ +  
  gi|336252630|ref|YP_004595737.1|  14 ERTLADEVGDSVTELLNISKMVSGSSEEISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSA 84 
                                       57899999999***********************************************9999999887765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.15
                              COG2  77 plaaarkkvesvreklsereeeveskleeakelee 111
                                       ++  a  +v ++++ l+er+ e++  ++  +e+++
  gi|336252630|ref|YP_004595737.1| 104 NVDDANADVAEAVSRLQERIDEIDTIVDVINEIAD 138
                                       23444444555555555555555555544444444 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.075
                              COG2  69 eeleevesplaaarkkvesvreklsereeevesklee 105
                                       e+ ee+e  +a ++++ ++++e++s++ eeve  +e 
  gi|336252630|ref|YP_004595737.1| 177 ENAEEIEGLVADIKDETDETVEQISNANEEVETGIEH 213
                                       4555666666666666666666666666666665554 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.35
                              COG2  69 eeleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                       ee+ + + + a+ +++v  ++++ +e+ ++v +k++  ++++e++
  gi|336252630|ref|YP_004595737.1| 236 EEVATATDEQASSTEEVATMVDSTAENAQTVAKKISRVAAANEEQ 280
                                       455666667778888888888888888999988888877776665 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.28   1.1e+02     248     287 ..      27      66 ..      14      73 .. 0.47
   2 ?    8.0   0.1    0.0035       1.4     223     274 ..      72     123 ..      69     142 .. 0.87
   3 ?   10.5   1.5   0.00062      0.24     222     284 ..     173     238 ..     163     245 .. 0.83
   4 ?    1.5   1.8      0.34   1.3e+02     230     259 ..     251     280 ..     229     292 .] 0.35

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.28
                              RmuC 248 dleklgkklekaqksydkavkklegnilrkaeklkelgvk 287
                                       +l ++ k ++ +++++ +++++ ++++ + a+++ +l+++
  gi|336252630|ref|YP_004595737.1|  27 ELLNISKMVSGSSEEISELADEQSETMHEIADEVSTLSAT 66 
                                       4444444444444444444444444444444444444333 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0035
                              RmuC 223 aqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegni 274
                                       a +++++e+ + +++l d+ + ++ed  ++ +++++a+ ++ +av++l+++i
  gi|336252630|ref|YP_004595737.1|  72 ASSNQVKEVSSSAEDLADDGCDVAEDAIDAMDNVDDANADVAEAVSRLQERI 123
                                       567899******************************************9555 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00062
                              RmuC 222 eaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle...gnilrkaeklkel 284
                                       e+ ++naeei  l+++++d+  + +e+++++++++e+  ++++++v+ le   + +++  +  +e+
  gi|336252630|ref|YP_004595737.1| 173 EESRENAEEIEGLVADIKDETDETVEQISNANEEVETGIEHVNETVDILEeidDAVTEATQGAEEV 238
                                       67789***************************************9999998865555555555555 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.34
                              RmuC 230 eiaellgelydkfekfgedleklgkkleka 259
                                       e+a+ + +  ++ ++++++++++  + e+ 
  gi|336252630|ref|YP_004595737.1| 251 EVATMVDSTAENAQTVAKKISRVAAANEEQ 280
                                       222222222222222222222222222222 PP

>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1      0.15        57      28      66 ..      40      84 ..      21      92 .. 0.53
   2 ?   14.2   0.4   0.00012     0.047       3      46 ..     106     149 ..     105     168 .. 0.87
   3 ?    0.6   0.9       2.1   8.3e+02      13      35 ..     204     226 ..     158     247 .. 0.60
   4 ?    1.5   1.0       1.1   4.4e+02      13      44 ..     204     235 ..     195     275 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.15
                             PIN_6 28 eVvaEirdkkare......rlellplelevrePspesvkkvtefa 66
                                      e ++E+ d+++++      ++++l  ++e   +s+++vk v++ a
  gi|336252630|ref|YP_004595737.1| 40 EEISELADEQSETmheiadEVSTLSATVEEIAASSNQVKEVSSSA 84
                                      556666666666533333333333345555555555555555555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00012
                             PIN_6   3 lDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellp 46 
                                        Da+a +++ +s+lq+  +++ t+ +V++Ei d+++   l+  +
  gi|336252630|ref|YP_004595737.1| 106 DDANADVAEAVSRLQERIDEIDTIVDVINEIADQTNMLALNASI 149
                                       599999999*************************9988887755 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 2.1
                             PIN_6  13 lsslqnlaeklyttpeVvaEird 35 
                                        +++++  e++  t ++++Ei d
  gi|336252630|ref|YP_004595737.1| 204 NEEVETGIEHVNETVDILEEIDD 226
                                       33344444455555555555555 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 1.1
                             PIN_6  13 lsslqnlaeklyttpeVvaEirdkkarerlel 44 
                                        +++++  e++  t ++++Ei d+ +++    
  gi|336252630|ref|YP_004595737.1| 204 NEEVETGIEHVNETVDILEEIDDAVTEATQGA 235
                                       56667777888899999999999877663222 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.0   0.00011     0.041      26     103 ..      46     123 ..      38     125 .. 0.87
   2 ?    0.5   0.0       2.1   8.3e+02      43      66 ..     116     139 ..     109     154 .. 0.75
   3 ?    2.4   4.1      0.54   2.1e+02      31      75 ..     192     235 ..     139     258 .. 0.62
   4 ?    2.0   2.7      0.73   2.9e+02      20      66 ..     235     282 ..     226     292 .] 0.44

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00011
                                       CSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  26 sedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaerkqk 102
                                        ++ +++++e+ + + ++ a  +e+aa  ++vk++   ae+l+d g++ +e+  + +++++++ +++ e++ + +++
  gi|336252630|ref|YP_004595737.1|  46 ADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADDGCDVAEDAIDAMDNVDDANADVAEAVSRLQER 122
                                       3556789999************************************9999999999999999999999998887776 PP

                                       H CS
                          Spectrin 103 L 103
                                       +
  gi|336252630|ref|YP_004595737.1| 123 I 123
                                       5 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  43 hkaleaelaaqqervkalnelaek 66 
                                         +l++ +++ ++ v+ +ne+a++
  gi|336252630|ref|YP_004595737.1| 116 VSRLQERIDEIDTIVDVINEIADQ 139
                                       556777777888888888877765 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.54
                                       SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTH CS
                          Spectrin  31 kdleevqallkkhkaleaelaaqqervkalnelaeklldeghsas 75 
                                       ++ e+v++  ++ +++e  ++   e v+ l+e+ ++++++  + +
  gi|336252630|ref|YP_004595737.1| 192 ETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEA-TQGA 235
                                       2334455555566666666666666666666666666444.3444 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.73
                                       HHHHHCCSSC.SSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  20 keellssedl.gkdleevqallkkhkaleaelaaqqervkalnelaek 66 
                                       +ee ++ +d  +++ eev ++++   +  +++a +  rv a ne +++
  gi|336252630|ref|YP_004595737.1| 235 AEEVATATDEqASSTEEVATMVDSTAENAQTVAKKISRVAAANEEQQE 282
                                       555554443335555555555554444444444444444444422222 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 ?    8.4   0.8    0.0067       2.6      41      86 ..      33      79 ..      15      90 .. 0.49
   2 ?    8.6   0.5    0.0056       2.2      33      79 ..      99     145 ..      93     149 .. 0.80
   3 ?    5.4   4.6     0.058        23      38      91 ..     192     245 ..     156     250 .. 0.71
   4 ?    3.6   1.0      0.21        81      10      72 ..     258     289 ..     243     292 .] 0.40

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0067
                           BLOC1_2 41 dvaaslekklekln.ekyeelqpylqqidqiekqvteLeeavseLDe 86
                                      +++++ ++++++l  e++e++++  +++  + ++v+e+ +  +++ e
  gi|336252630|ref|YP_004595737.1| 33 KMVSGSSEEISELAdEQSETMHEIADEVSTLSATVEEIAASSNQVKE 79
                                      44444444444443122234444444444444444444444444433 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0056
                           BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                       +   ++++d+ a++++ +++l+e+ +e++  ++ i++i +q++ L  
  gi|336252630|ref|YP_004595737.1|  99 IDAMDNVDDANADVAEAVSRLQERIDEIDTIVDVINEIADQTNMLAL 145
                                       55567778888899999999999999999999999999999988865 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.058
                           BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                       + ++ ++++++  e+++   e++++ ++ +++i++ vte ++ ++e+ + + e+
  gi|336252630|ref|YP_004595737.1| 192 ETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAEEVATATDEQ 245
                                       445666677777777777777888888888888888888888777777776665 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.21
                           BLOC1_2  10 yleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiek 72 
                                          ++ + ++++++ + + Ne+++ek+++l                                +
  gi|336252630|ref|YP_004595737.1| 258 STAENAQTVAKKISRVAAANEEQQEKIEALG-------------------------------E 289
                                       2222233333333333344444444444433...............................3 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 ?   12.3   2.1   0.00036      0.14      22     114 ..      45     140 ..      42     154 .. 0.79
   2 ?    4.8   7.7     0.077        30      30     121 ..     190     287 ..     164     292 .] 0.45

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00036
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHHHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrlke 95 
                                       l+d  +++ +++ +++++l  ++eei+ s+++++e++++ +d   +    ++d       + + + ++ e ++rl+e
  gi|336252630|ref|YP_004595737.1|  45 LADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADDGCDVAEDAidaMDNVDDANADVAEAVSRLQE 121
                                       566667889999*******************************9999999998654455677778888889999999 PP

                                       HHHCCHHHHHHHHHHHHHH CS
                         Fib_alpha  96 tidaqesnirvLqnvlesn 114
                                       +id+  + + v+ ++ ++ 
  gi|336252630|ref|YP_004595737.1| 122 RIDEIDTIVDVINEIADQT 140
                                       9988777777777766543 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.077
                                       CCCCCHHHCCCCCCCCCCCC...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......CCCHHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisn...stkeaeelvkeikdslrekqkskkdndnvikksskelee......eilrlketi 97 
                                       + ++++++e++ n  ee++      +e+ ++ +ei+d ++e+ + +++  +++ + +++ ee        ++  +t+
  gi|336252630|ref|YP_004595737.1| 190 KDETDETVEQISNANEEVETgieHVNETVDILEEIDDAVTEATQGAEEVATATDEQASSTEEvatmvdSTAENAQTV 266
                                       55555555555444444433000333333334455555555555555433333333333331000000222222222 PP

                                       HCCHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  98 daqesnirvLqnvlesneqkiqkL 121
                                           ++i       e++++ki+ L
  gi|336252630|ref|YP_004595737.1| 267 A---KKISRVAAANEEQQEKIEAL 287
                                       2...33333334444444444444 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0013      0.51       3      33 ..      51      81 ..      49      84 .. 0.88
   2 ?    2.6   0.2       0.3   1.2e+02       9      31 ..     113     135 ..     100     149 .. 0.62
   3 ?   -0.5   0.1       2.9   1.1e+03      11      30 ..     203     222 ..     194     232 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0013
                         DASH_Dam1  3 pafaeLaDsletLdknledLqqihesLsdfN 33
                                      ++++e+aD+++tL++ +e++   ++++++++
  gi|336252630|ref|YP_004595737.1| 51 ETMHEIADEVSTLSATVEEIAASSNQVKEVS 81
                                      689*****************99999988766 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.3
                         DASH_Dam1   9 aDsletLdknledLqqihesLsd 31 
                                       a++++ L++++++++ i + +++
  gi|336252630|ref|YP_004595737.1| 113 AEAVSRLQERIDEIDTIVDVINE 135
                                       45555555555555554444433 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.9
                         DASH_Dam1  11 sletLdknledLqqihesLs 30 
                                       + e++++ +e+ +++ + L+
  gi|336252630|ref|YP_004595737.1| 203 ANEEVETGIEHVNETVDILE 222
                                       44444444444444433333 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.0   0.00027      0.11      19     131 ..      32     155 ..      16     161 .. 0.70
   2 ?    5.6   2.9     0.053        21      46     126 ..     118     198 ..     101     209 .. 0.65
   3 ?    3.5   7.3      0.23        91      56     132 ..     142     225 ..     123     265 .. 0.55
   4 ?    2.0   8.8      0.71   2.8e+02      34     111 ..     198     278 ..     168     291 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00027
                                       HHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--.........SCHHHHHHHHCT..T CS
                              FlgN  19 eeLlelleeEteaLkagdieaLeelleekqellekleqleqkrakllaelgls.........aeeatlsellak..e 84 
                                       +++ +   eE   L +++ e ++e+++e  +l +++e+++    ++ +  +             e+ ++++  +  +
  gi|336252630|ref|YP_004595737.1|  32 SKMVSGSSEEISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAedladdgcdVAEDAIDAMD-NvdD 107
                                       566667789999999999999999999988777766666655444444333335458766653344444443.2588 PP

                                       CCHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHCCHHHHHHHHHCCHX CS
                              FlgN  85 edeelkelwqelkelleelkelne.lNgrlieqslefnqrllnllqga 131
                                       +++ ++e++++l+e+++e+  + + +N+ + ++++  ++ ++++ +++
  gi|336252630|ref|YP_004595737.1| 108 ANADVAEAVSRLQERIDEIDTIVDvINEIADQTNMLALNASIEAARAG 155
                                       999999999999999999999766145555567888888888877766 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.053
                                       HHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                              FlgN  46 ekqellekleqleqkrakllaelglsaeeatlsellakeedeelkelwqelkelleelkelnelNgrlieqslefnq 122
                                       + qe +++++++ + + ++ ++ +  a +a+++++ a e+ ++ + + +e+k+l+ee +e +e  + l+ +  + ++
  gi|336252630|ref|YP_004595737.1| 118 RLQERIDEIDTIVDVINEIADQTNMLALNASIEAARAGESGDRFAVVANEVKSLAEESRENAEEIEGLVADIKDETD 194
                                       44445555555555555555555555666666666666888888888888888888888888888888777666666 PP

                                       HHHH CS
                              FlgN 123 rlln 126
                                       ++++
  gi|336252630|ref|YP_004595737.1| 195 ETVE 198
                                       6555 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHTT--.....SCHHHHHHHHCT..TCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH CS
                              FlgN  56 qleqkrakllaelgls.....aeeatlsellak..eedeelkelwqelkelleelkelnelNgrlieqslefnqrll 125
                                        l+ + +   a++g+s         +++ l+++  e +ee++ l++++k+ ++e  e+ +  ++ +e+ +e++++++
  gi|336252630|ref|YP_004595737.1| 142 MLALNASIEAARAGESgdrfaVVANEVKSLAEEsrENAEEIEGLVADIKDETDETVEQISNANEEVETGIEHVNETV 218
                                       44444444444444444445422334444444445555566666655555555555555555555555555555555 PP

                                       HHCCHXX CS
                              FlgN 126 nllqgaa 132
                                       ++l + +
  gi|336252630|ref|YP_004595737.1| 219 DILEEID 225
                                       5555444 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.71
                                       TT...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCTTCCHHHHHHHHH....HHHHHHHH CS
                              FlgN  34 ag...dieaLeelleekqellekleqleqkrakllaelglsaeeatlsellakeedeelkelwqe....lkelleel 103
                                       ++     e+ e+ +e+ +e+++ le+++++  ++++ ++++  +at +++    + ee+++++++     +++++++
  gi|336252630|ref|YP_004595737.1| 198 EQisnANEEVETGIEHVNETVDILEEIDDAVTEATQGAEEV-ATATDEQAS---STEEVATMVDStaenAQTVAKKI 270
                                       44333568888889999999999999999999999999999.445555553...33333333333222244444455 PP

                                       HHHHHHHH CS
                              FlgN 104 kelnelNg 111
                                        +++ +N+
  gi|336252630|ref|YP_004595737.1| 271 SRVAAANE 278
                                       55555554 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.0    0.0084       3.3     134     204 ..      39     121 ..       9     144 .. 0.63
   2 ?    7.5  14.3    0.0028       1.1      35     183 ..     108     265 ..      95     292 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0084
                               MAD 134 leelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqs...........qeddslivknsksel.ar 198
                                        ee+ e  d++ +++ e+ + +++l +  +e a++ +++ke +   +              d    v ++++ + + 
  gi|336252630|ref|YP_004595737.1|  39 SEEISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDladdgcdvaedAIDAMDNVDDANADVaEA 115
                                       46777788888999999999999999999999999999999888877744444444332222223333333333333 PP

                               MAD 199 ipelek 204
                                       +++l++
  gi|336252630|ref|YP_004595737.1| 116 VSRLQE 121
                                       344444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0028
                               MAD  35 kasalkrqleeesdrnqelqkrikllekre.eekeealreqiElarlkkk......nlealnkkekekesklaeare 104
                                       + ++ ++ + + ++r  e+++ + ++++   +++  al++ iE ar+ +         ++++++++e  ++ +e++ 
  gi|336252630|ref|YP_004595737.1| 108 ANADVAEAVSRLQERIDEIDTIVDVINEIAdQTNMLALNASIEAARAGESgdrfavVANEVKSLAEESRENAEEIEG 184
                                       44566777777788888888888888888767777899999999997553111111457888999999999999*** PP

                               MAD 105 visalknelaelkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqs 181
                                       +   +k+e+ e  +qi +++ e+++  + ++e    l++ +  ++e++q  ++  ++++e a + + + ++    ++
  gi|336252630|ref|YP_004595737.1| 185 LVADIKDETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAEEVATATDEQASSTEEVATMVDSTAE 261
                                       ***************************************************99999999999999888887665554 PP

                               MAD 182 ..qe 183
                                         q+
  gi|336252630|ref|YP_004595737.1| 262 naQT 265
                                       2222 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3     0.044        17       3      83 ..      41     133 ..      24     147 .. 0.47
   2 ?    2.3   0.0      0.36   1.4e+02       8      85 ..     102     181 ..      95     192 .. 0.46
   3 ?    7.7   3.2    0.0077         3       3      93 ..     181     284 ..     179     287 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.044
                        STAT_alpha   3 eieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkleqeraesekkelkkqkellqqmlna............ 67 
                                       ei++  +e +++++e+  ++++L  + ee +   +++++ +++  + ++  +  +++ +++m n             
  gi|336252630|ref|YP_004595737.1|  41 EISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADDGCDVAEDAIDAMDNVddanadvaeavs 117
                                       44444444555555555555555555566666666655554444444444444444444444332221111111222 PP

                        STAT_alpha  68 LdqkRkelvdklkell 83 
                                         q+R + +d++ +++
  gi|336252630|ref|YP_004595737.1| 118 RLQERIDEIDTIVDVI 133
                                       2233444444444444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.36
                        STAT_alpha   8 leelrskvqeteqdirkLedeqeeFdfqyqelqkleqeraesekkelkkqkellqqmlna...LdqkRkelvdklke 81 
                                       ++++ + + ++ + +++L++  +e d  +  ++++ ++++++   + + + +   ++  +   + ++ k+l+++ +e
  gi|336252630|ref|YP_004595737.1| 102 MDNVDDANADVAEAVSRLQERIDEIDTIVDVINEI-ADQTNMLALNASIEAARAGESGDRfavVANEVKSLAEESRE 177
                                       55666666677777777777776666555555555.22222222112222222222111122244444444444444 PP

                        STAT_alpha  82 llnl 85 
                                         ++
  gi|336252630|ref|YP_004595737.1| 178 NAEE 181
                                       4444 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0077
                        STAT_alpha   3 eieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkl.............eqeraesekkelkkqkellqqmln 66 
                                       eie  ++++++++ et+++i++ ++e e+   +++e   +              +e++ +++ e++   e+++ m+ 
  gi|336252630|ref|YP_004595737.1| 181 EIEGLVADIKDETDETVEQISNANEEVETGIEHVNETVDIleeiddavteatqGAEEVATATDEQASSTEEVATMVD 257
                                       66677777777777777777776666644444444433334444555555566577777788889999999999*** PP

                        STAT_alpha  67 aLdqkRkelvdklkellnlleslqekl 93 
                                       +  +  + +++k++++    e++qek+
  gi|336252630|ref|YP_004595737.1| 258 STAENAQTVAKKISRVAAANEEQQEKI 284
                                       ****************99999999986 PP

>> HisK_N  Histidine kinase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   0.00048      0.19      33     122 ..      54     143 ..      31     148 .. 0.88
   2 ?   -1.1   0.0       4.4   1.7e+03      95     117 ..     197     219 ..     168     232 .. 0.64
   3 ?   -1.7   0.0       6.8   2.7e+03      37      62 ..     261     287 ..     243     291 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00048
                                       HHHHHHHHHHHHHHHHHHTTSS-GGGGHHHHHHHHHHHHHHT--THHHHHHHHHHHHHHHHHHHCC---HHHHHHHH CS
                            HisK_N  33 eevkeNgealfelviellkeeiseedlkelaekiakeRveanvnigdfvyNvnvgrsivlkallklnvsldelqlli 109
                                       +e+    ++l  +v e+  ++ + +++ + ae +a +  ++  +  d + Nv  +   v +a+++l+  +de+ +++
  gi|336252630|ref|YP_004595737.1|  54 HEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADDGCDVAEDAIDAMDNVDDANADVAEAVSRLQERIDEIDTIV 130
                                       56666677777888888889999999**************999999******************************* PP

                                       HHHHHHHHHHHHH CS
                            HisK_N 110 dkinefFDkflyy 122
                                       d ine+ D+  + 
  gi|336252630|ref|YP_004595737.1| 131 DVINEIADQTNML 143
                                       ******9986655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.4
                                       HHCC---HHHHHHHHHHHHHHHH CS
                            HisK_N  95 llklnvsldelqllidkinefFD 117
                                       + ++    +e+++ i+++ne  D
  gi|336252630|ref|YP_004595737.1| 197 VEQISNANEEVETGIEHVNETVD 219
                                       33333444556666666666665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 6.8
                                       HHHHHHHHHHHHHHT.TSS-GGGGHHH CS
                            HisK_N  37 eNgealfelviellk.eeiseedlkel 62 
                                       eN +++ + + ++   +e+++e+++ l
  gi|336252630|ref|YP_004595737.1| 261 ENAQTVAKKISRVAAaNEEQQEKIEAL 287
                                       444444444444332033333335555 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   5.8     0.084        33      98     190 ..      43     134 ..      24     143 .. 0.60
   2 ?   13.2   4.9   0.00014     0.054     104     176 ..     164     236 ..     126     238 .. 0.87
   3 ?    3.2   2.9      0.16        62     110     164 ..     233     287 ..     229     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.084
                               LXG  98 dfLeqelenglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksalan 174
                                       + L +e++  + +   ++++l   +++i as +++ ++++   +   d+ + a++ ++  +++++d++++  +a++ 
  gi|336252630|ref|YP_004595737.1|  43 SELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADDGCDVAEDAID-AMDNVDDANADVAEAVSR 118
                                       2355556666666666666666666666666666655555555555555555555544.666666666666677777 PP

                               LXG 175 lesdlkalktyvseLe 190
                                       l++ ++++ t+v+ ++
  gi|336252630|ref|YP_004595737.1| 119 LQERIDEIDTIVDVIN 134
                                       7777777666666555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00014
                               LXG 104 lenglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksalanle 176
                                       ++n++k + e+ +e ++ei+  +a+++d  + +  ++s+ +++++  +++v+et++ le++d   ++a++ +e
  gi|336252630|ref|YP_004595737.1| 164 VANEVKSLAEESRENAEEIEGLVADIKDETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAE 236
                                       7899999********************************************************9999988776 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.16
                               LXG 110 kakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledf 164
                                       +  e++++ +de  + +++v ++v+ +  + ++v ++++++    +e+ ek+e++
  gi|336252630|ref|YP_004595737.1| 233 QGAEEVATATDEQASSTEEVATMVDSTAENAQTVAKKISRVAAANEEQQEKIEAL 287
                                       5567788888888888999999999999999999999999888888888888765 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 ?   10.9   0.6   0.00093      0.36      16     100 ..      61     149 ..      36     155 .. 0.66
   2 ?    3.8   5.2      0.15        57      28      95 ..     168     246 ..     157     269 .. 0.47
   3 ?    1.6   2.0      0.68   2.7e+02      23      60 ..     250     288 ..     232     292 .] 0.57

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00093
                             Mod_r  16 eklealvk....tlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldell 88 
                                       + l+a v+    ++++vk++ ++ e+l +   ++ae+ ++  + +++  ++++e+ + l+e  +e +      +e+ 
  gi|336252630|ref|YP_004595737.1|  61 STLSATVEeiaaSSNQVKEVSSSAEDLADDGCDVAEDAIDAMDNVDDANADVAEAVSRLQERIDEIDTIVDVINEIA 137
                                       33333333333377888888888888888888888888888887777777777777777777777777777777777 PP

                             Mod_r  89 qkfspdallarL 100
                                       ++++  al a  
  gi|336252630|ref|YP_004595737.1| 138 DQTNMLALNASI 149
                                       666666665554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.15
                             Mod_r  28 vkqlkeekeellaenesla...........eknlsl.epeleelrselqekleelkelekefeekeqeldellqkfs 92 
                                       vk+l ee  e  +e+e l            e ++s+ ++e+e   ++++e+ + l+e+ +++ e +q  +e+   ++
  gi|336252630|ref|YP_004595737.1| 168 VKSLAEESRENAEEIEGLVadikdetdetvE-QISNaNEEVETGIEHVNETVDILEEIDDAVTEATQGAEEVATATD 243
                                       3333333333333333333222222222213.233325566666666666666666666666665555555554444 PP

                             Mod_r  93 pda 95 
                                       ++a
  gi|336252630|ref|YP_004595737.1| 244 EQA 246
                                       443 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.68
                             Mod_r  23 ktl.pevkqlkeekeellaeneslaeknlslepeleelr 60 
                                       +++   v++  e+ + + +++ ++a +n ++++++e l 
  gi|336252630|ref|YP_004595737.1| 250 EEVaTMVDSTAENAQTVAKKISRVAAANEEQQEKIEALG 288
                                       333233555566666666666666666666666666554 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.1    0.0038       1.5     134     222 ..      39     130 ..      14     149 .. 0.79
   2 ?    6.1   6.0     0.015         6      96     216 ..     166     285 ..     137     291 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0038
                              CorA 134 ldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrlla.kaddkllddedkeylrdlldelerllem 207
                                        +e+++    +++t +ei++e+++l  ++ ++  + ++ +ev ++  +  +d+  + +++ + ++++ d  + ++e 
  gi|336252630|ref|YP_004595737.1|  39 SEEISELAdeQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDlADDGCDVAEDAIDAMDNVDDANADVAEA 115
                                       3444444455599999***************************7777788888899999999999999999999999 PP

                              CorA 208 lealrerleslqdty 222
                                       ++ l+er++ +  + 
  gi|336252630|ref|YP_004595737.1| 116 VSRLQERIDEIDTIV 130
                                       999999999987664 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.015
                              CorA  96 krlkdeggkpkspgellyrlldeivdrlfellekleeeldeledel.edstkkeilrelaqlrrrlvkl.rralapn 170
                                       +++k+  ++ +  +e ++ l+  i d+ +e++e+++   +e+e+ + + +++ +il+e+ +  +++++  +++++++
  gi|336252630|ref|YP_004595737.1| 166 NEVKSLAEESRENAEEIEGLVADIKDETDETVEQISNANEEVETGIeHVNETVDILEEIDDAVTEATQGaEEVATAT 242
                                       33343344555555555555555556666666666666666666664444444444444444444333312222222 PP

                              CorA 171 revlkrllakaddkllddedkeylrdlldelerllemlealrerle 216
                                        e      ++++  ++ d  +e+ +++  +++r++   e ++e++e
  gi|336252630|ref|YP_004595737.1| 243 DEQA---SSTEEVATMVDSTAENAQTVAKKISRVAAANEEQQEKIE 285
                                       2222...112345555555556666666666666666666666665 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.6   0.00064      0.25      14     112 ..      50     147 ..      28     157 .. 0.72
   2 ?    4.5   3.2     0.061        24      43     101 ..     162     221 ..     153     229 .. 0.77
   3 ?    5.2   7.6     0.039        15      48     110 ..     227     289 ..     220     292 .] 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00064
                         Laminin_I  14 pykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaek 90 
                                       ++ + + ++d  + L+  +++++a + +++      e+La +    ++ a  + ++  + na++ +++++ +e  ++
  gi|336252630|ref|YP_004595737.1|  50 SETMHE-IADEVSTLSATVEEIAASSNQVKEVSSSAEDLADDGCDVAEDAIDAMDNVDDANADVAEAVSRLQERIDE 125
                                       333443.5555566666677777777777777677777777777777888888888888888888888999999999 PP

                         Laminin_I  91 ikkladnikeilekvatlnene 112
                                       i  ++d i+ei  ++  l  n+
  gi|336252630|ref|YP_004595737.1| 126 IDTIVDVINEIADQTNMLALNA 147
                                       9999999999999988776655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.061
                         Laminin_I  43 eilekelesLaqeteeLqkkatqvlakaq.kvnaesertlnnakeLaekikkladnikei 101
                                        +  +e++sLa+e +e +++ +   a+ + ++ + +e+++n  +e ++ i+ +++++ ++
  gi|336252630|ref|YP_004595737.1| 162 AVVANEVKSLAEESRENAEEIEGLVADIKdETDETVEQISNANEEVETGIEHVNETVDIL 221
                                       556689999999999999999998887541577778888888888888888888888776 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.039
                         Laminin_I  48 elesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlne 110
                                       ++++  q +ee ++   +   ++++v   ++ t +na++ a+ki ++a+  +e  ek+++l+e
  gi|336252630|ref|YP_004595737.1| 227 AVTEATQGAEEVATATDEQASSTEEVATMVDSTAENAQTVAKKISRVAAANEEQQEKIEALGE 289
                                       67777888999999999999999************************************9998 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   2.5    0.0096       3.8      41     111 ..      34     103 ..      17     108 .. 0.58
   2 ?   12.2   2.1   0.00027      0.11       5      85 ..      62     141 ..      58     157 .. 0.91
   3 ?    3.9   9.7     0.097        38       4     118 ..      96     212 ..      95     218 .. 0.76
   4 ?    4.6   8.3     0.061        24      41     108 ..     220     289 ..     213     292 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0096
                              YkyA  41 iielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieeiedeelkkeaeelieame 111
                                       +++ + +e +++ ++ +e    + +  + l+   e i ++ +++++++++ e++ d+   + ae+ i+am+
  gi|336252630|ref|YP_004595737.1|  34 MVSGSSEEISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADD-GCDVAEDAIDAMD 103
                                       444444454444444444444444444455555666667777777777777777554.4555666666665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00027
                              YkyA   5 kiyealeeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeak 81 
                                       +++ ++ee++++ ++++e  ++ ++l  +  ++ e+ i+  md+ d+ ++ ++ea++ ++eR +++++  ++i+e  
  gi|336252630|ref|YP_004595737.1|  62 TLSATVEEIAASSNQVKEVSSSAEDLADDGCDVAEDAID-AMDNVDDANADVAEAVSRLQERIDEIDTIVDVINEIA 137
                                       667899********************************8.99******************************99988 PP

                              YkyA  82 eefe 85 
                                       ++ +
  gi|336252630|ref|YP_004595737.1| 138 DQTN 141
                                       8766 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.097
                              YkyA   4 ekiyealeeavelEkefeeqqekLtelekkeqelyeeiielgmde.fdkikklsdeale.nveeReellekekesi. 77 
                                       e++ +a++++ ++  +++e+ + L+e   +   + + i+e   +  + ++++ ++ a +    +R   +++e +s+ 
  gi|336252630|ref|YP_004595737.1|  96 EDAIDAMDNVDDANADVAEAVSRLQERIDEIDTIVDVINEIADQTnMLALNASIEAARAgESGDRFAVVANEVKSLa 172
                                       67788999999999999999999999999999999988887555536666666666654245578888888888874 PP

                              YkyA  78 eeakeefekikeeieeiedeelkkeaeelieameeryeayd 118
                                       ee++e+ e+i+  + +i+de   + +e+  +a ee ++ ++
  gi|336252630|ref|YP_004595737.1| 173 EESRENAEEIEGLVADIKDE-TDETVEQISNANEEVETGIE 212
                                       7899*************988.77888888877777665555 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.061
                              YkyA  41 iielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieei..edeelkkeaeelie 108
                                       i+e   d   + ++ ++e+ + ++e+ +  e+  ++++++ e+ +++ ++i+ +   +ee+++++e+l e
  gi|336252630|ref|YP_004595737.1| 220 ILEEIDDAVTEATQGAEEVATATDEQASSTEEVATMVDSTAENAQTVAKKISRVaaANEEQQEKIEALGE 289
                                       55544455889999***************************************98778889999998865 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.077        30      36      83 ..      35      81 ..      20      89 .. 0.59
   2 ?    5.5   0.5      0.06        23      13      83 ..      68     137 ..      61     148 .. 0.55
   3 ?    4.1   0.2      0.16        63      15      54 ..     102     142 ..      87     174 .. 0.75
   4 ?   -1.3   0.1       7.9   3.1e+03      56      56 ..     191     191 ..     163     211 .. 0.45
   5 ?    3.8   0.1      0.19        76      16      60 ..     191     233 ..     179     244 .. 0.81
   6 ?    7.4   1.5     0.015       5.7      13      86 ..     219     291 ..     212     292 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.077
                   Snapin_Pallidin 36 ldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklk 83
                                      ++  +e++ el+++q+ e++ ++   +  L++   ++ + +++++++ 
  gi|336252630|ref|YP_004595737.1| 35 VSGSSEEISELADEQS-ETMHEIADEVSTLSATVEEIAASSNQVKEVS 81
                                      4445555555555555.5566665555555555555555555555554 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.06
                   Snapin_Pallidin  13 pkldeldeklkelrqsQeeLleq.ldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklk 83 
                                        ++ +  +++ke+  s e+L+++ +d   ++++ + ++++  + +d+ e + +L++   ++ ++ ++++++ 
  gi|336252630|ref|YP_004595737.1|  68 EEIAASSNQVKEVSSSAEDLADDgCDVAEDAIDAMDNVDD--ANADVAEAVSRLQERIDEIDTIVDVINEIA 137
                                       5566777778888888888876536666666666666666..444444444444443333333333333333 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.16
                   Snapin_Pallidin  15 ldeldeklkelrqsQeeLleqldrlnekLkeleeaqe.aev 54 
                                       +d++d+  +++ +  + L+e++d+  + ++ ++e+++ +++
  gi|336252630|ref|YP_004595737.1| 102 MDNVDDANADVAEAVSRLQERIDEIDTIVDVINEIADqTNM 142
                                       56666666777777777777777777777777777774333 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 7.9
                   Snapin_Pallidin  56 p 56 
                                        
  gi|336252630|ref|YP_004595737.1| 191 D 191
                                       2 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.19
                   Snapin_Pallidin  16 deldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlke 60 
                                       de+de+++++ +  ee+   ++  ne ++ lee+++  +++++ +
  gi|336252630|ref|YP_004595737.1| 191 DETDETVEQISNANEEVETGIEHVNETVDILEEIDD--AVTEATQ 233
                                       78999999****************999999999998..6666555 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.015
                   Snapin_Pallidin  13 pkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRa 86 
                                         l+e+d+ + e +q  ee++   d+++++ +e++ + + ++ +++++ akK++++    ++ +e+++ l +R+
  gi|336252630|ref|YP_004595737.1| 219 DILEEIDDAVTEATQGAEEVATATDEQASSTEEVATMVD-STAENAQTVAKKISRVAAANEEQQEKIEALGERV 291
                                       56899***************************9999999.8999999999999999988888888888887776 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.5     0.051        20      14      80 ..      20      81 ..      10      95 .. 0.63
   2 ?    6.9   1.4     0.026        10       5      70 ..      53     127 ..      46     137 .. 0.53
   3 ?    8.6   2.8    0.0077         3      12      85 ..     116     198 ..     103     208 .. 0.63
   4 ?    5.1   5.5     0.095        37       7      74 ..     216     289 ..     210     292 .] 0.63

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.051
                           DUF2203 14 llkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdle 80
                                      ++ + ++el +  k +   +ee++e  +e     ++e  +e++   + ++++veei +   +vk+++
  gi|336252630|ref|YP_004595737.1| 20 EVGDSVTELLNISKMVSGSSEEISELADE-----QSETMHEIADEVSTLSATVEEIAASSNQVKEVS 81
                                      56666666666666666666666666666.....455556666666666677777777777776664 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.026
                           DUF2203   5 leeAnalLpllkelleelralrkeleeleeeleeakaeaekse.............aaeleaeleeleaeieelvee 68 
                                       ++e  + + +l+ ++ee++a  ++++e++++ e+  ++    +                ++a+++e+ ++++e ++e
  gi|336252630|ref|YP_004595737.1|  53 MHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADD----GcdvaedaidamdnVDDANADVAEAVSRLQERIDE 125
                                       44445555566666666666666666555544444444....04444676666666444455555555555555555 PP

                           DUF2203  69 ie 70 
                                       i+
  gi|336252630|ref|YP_004595737.1| 126 ID 127
                                       54 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0077
                           DUF2203  12 Lpllkelleelralrkeleelee.........eleeakaeaekse.......aaeleaeleeleaeieelveeieel 72 
                                       + +l+e+++e+ +  + ++e+++         ++e+a               +a  ++e+++l++e +e  eeie l
  gi|336252630|ref|YP_004595737.1| 116 VSRLQERIDEIDTIVDVINEIADqtnmlalnaSIEAA-------RagesgdrFAVVANEVKSLAEESRENAEEIEGL 185
                                       4455555555554444444444422222111133333.......134455669999********************* PP

                           DUF2203  73 GvevkdleaglvD 85 
                                        +++kd     v+
  gi|336252630|ref|YP_004595737.1| 186 VADIKDETDETVE 198
                                       *****97666655 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.095
                           DUF2203   7 eAnalLpllkelleelralrkeleeleeeleeakaeaekse.........aaeleaeleeleaeieelveeieelGv 74 
                                       e  ++L ++++ ++e+ + ++e++++ +e +++++e    +         a++ ++++++++a  ee  e+ie+lG 
  gi|336252630|ref|YP_004595737.1| 216 ETVDILEEIDDAVTEATQGAEEVATATDEQASSTEEV---AtmvdstaenAQTVAKKISRVAAANEEQQEKIEALGE 289
                                       4455666666666666666666666555444443333...1334566666888888888999999999999999885 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   8.0     0.012       4.6     143     281 ..      20     129 ..      14     177 .. 0.52
   2 ?    9.7   7.2   0.00088      0.34     155     271 ..     102     221 ..      85     223 .. 0.80
   3 ?    8.0  11.3    0.0029       1.1     136     241 ..     185     289 ..     182     292 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                              Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkaeiee 217
                                       ++ + +++l + +++++ + ee++el +e +e   e+ +e+ +l + +ee++++    +e+ +  e+la+   +++e
  gi|336252630|ref|YP_004595737.1|  20 EVGDSVTELLNISKMVSGSSEEISELADEQSETMHEIADEVSTLSATVEEIAASSnqVKEVSSSAEDLADDGCDVAE 96 
                                       55555555555566666666666666666666666666666666666666555322234455555555555444443 PP

                              Spc7 218 kkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleel 281
                                             +  +++++ ++++                            ++ vsrl+e+ ++++ +
  gi|336252630|ref|YP_004595737.1|  97 DA---IDAMDNVDDANADV----------------------------AEAVSRLQERIDEIDTI 129
                                       22...12222222222222............................22222222222222222 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00088
                              Spc7 155 kelLekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelre..elaelkaeieekkkelaelqeq 228
                                        +++++ ++ + e++ +l+e+ +e+   ++ ++e a++ + +  ++++e++r   + ++  +  +e k   +e +e+
  gi|336252630|ref|YP_004595737.1| 102 MDNVDDANADVAEAVSRLQERIDEIDTIVDVINEIADQTNMLAlNASIEAARAgeSGDRFAVVANEVKSLAEESREN 178
                                       56788889999999999999999999999999999999999888999999996213444455556677888999999 PP

                              Spc7 229 leeleekieelkeqkseleeeiaeaervleeckgwsesevsrl 271
                                        ee+e  ++++k++ +e+ e+i++a++ +e   ++ ++ v+ l
  gi|336252630|ref|YP_004595737.1| 179 AEEIEGLVADIKDETDETVEQISNANEEVETGIEHVNETVDIL 221
                                       9999999******************999998777766666655 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0029
                              Spc7 136 llegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles..idkeeLeelreelae 210
                                       l+ ++k++ +e++e++ + +e++e   e ++e ++ lee  ++++e  +  +e a+  ++  +  ee++++ ++ ae
  gi|336252630|ref|YP_004595737.1| 185 LVADIKDETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAEEVATATDEqaSSTEEVATMVDSTAE 261
                                       78899999999999999999999999999999999999999988888888877544433322668888888888888 PP

                              Spc7 211 lkaeieekkkelaelqeqleeleekieelke 241
                                       + ++++   k+++++ +  ee++ekie+l e
  gi|336252630|ref|YP_004595737.1| 262 NAQTVA---KKISRVAAANEEQQEKIEALGE 289
                                       888888...6666666666666666666655 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.0    0.0081       3.1      55     141 ..      17      99 ..       3     110 .. 0.56
   2 ?    6.2   2.7     0.013       5.2      56     140 ..     109     196 ..     100     197 .. 0.81
   3 ?    5.6  15.2      0.02       7.8      40     134 ..     182     275 ..     165     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0081
                          ISG65-75  55 llketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekaekask 131
                                       l +e+ d ++ + n  + v+  +e++ +l +e+    + t+ ++ +  +++ ++ ++++++++++k++ + ae++++
  gi|336252630|ref|YP_004595737.1|  17 LADEVGDSVTELLNISKMVSGSSEEISELADEQ----SETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLAD 89 
                                       445555666666666666666666666666663....2222222223345555555566666666666666666666 PP

                          ISG65-75 132 kakeaakkAl 141
                                       +  + a++A+
  gi|336252630|ref|YP_004595737.1|  90 DGCDVAEDAI 99 
                                       6666666654 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.013
                          ISG65-75  56 lketkdklayienakekvdyyvekleslleeake...kgtltesdaeklkkaceeAkaknkkarekakkalekaeka 129
                                        +++ ++++ +++ ++++d  v+ ++++ ++ +    +++++++ a +    ++ + +++k+  e++ + +e++e +
  gi|336252630|ref|YP_004595737.1| 109 NADVAEAVSRLQERIDEIDTIVDVINEIADQTNMlalNASIEAARAGESGDRFAVVANEVKSLAEESRENAEEIEGL 185
                                       4566777778888888888888888888777665666899999999999999************************* PP

                          ISG65-75 130 skkakeaakkA 140
                                       + + k+ + ++
  gi|336252630|ref|YP_004595737.1| 186 VADIKDETDET 196
                                       **999999887 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.02
                          ISG65-75  40 lkkladkvreetadyllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkar 116
                                       +++l+  + ++++d+ ++++ ++ + +e+ +e v+++v+ le++ +   e ++  e+ a+  ++++  ++++++  +
  gi|336252630|ref|YP_004595737.1| 182 IEGLVADI-KDETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAEEVATATDEQASSTEEVATMVD 257
                                       67788888.78888889999999999999999999999888888888777777777777777777777777777777 PP

                          ISG65-75 117 ekakkalekaekaskkak 134
                                       ++a++a ++a+k s+ a+
  gi|336252630|ref|YP_004595737.1| 258 STAENAQTVAKKISRVAA 275
                                       777777777766666554 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.7     0.025       9.9      18      84 ..      46     112 ..      28     135 .. 0.74
   2 ?    7.6   8.1    0.0077         3      30     118 ..     177     266 ..     162     286 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.025
                                       ......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXX CS
                              SKA1  18 pallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkk 84 
                                        + ++e++ +i +evs+l  +++++ +  ++ +e+ ++++++ +  ++  e +    +n+ +   + 
  gi|336252630|ref|YP_004595737.1|  46 ADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADDGCDVAEDAIDAMDNVDDANADV 112
                                       4445678889999999999999999999999999999999888888888888666666666655554 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0077
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  30 aevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaassaeeskssspeeeeetes 106
                                       ++ +++e l++++k+e +e  e+i+++++e+e  +++ +++  ++e++ + + + t+  +++ ++++++ +++e+ +
  gi|336252630|ref|YP_004595737.1| 177 ENAEEIEGLVADIKDETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAEEVATATDEQASSTEEVA 253
                                       667899*****************************9999999999******99999999988888887777665544 PP

                                       XXX..XXXXXXXXX CS
                              SKA1 107 kke..keeeaekak 118
                                       +      +e++++ 
  gi|336252630|ref|YP_004595737.1| 254 TMVdsT-AENAQTV 266
                                       433431.2222221 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 ?    8.2   0.9     0.007       2.7      55      99 ..      31      76 ..      10      79 .. 0.74
   2 ?    8.2   2.4    0.0073       2.9      29     100 ..      51     126 ..      48     137 .. 0.72
   3 ?    7.8   5.1    0.0097       3.8      27     100 ..     164     238 ..     145     243 .. 0.85
   4 ?    1.7   4.3      0.79   3.1e+02      58     104 ..     237     287 ..     217     291 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.007
                                      HHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N 55 lskeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaelek 99
                                      +sk ++  +++  e a+e  + + e+ +e+++l+a+++e+ a  ++
  gi|336252630|ref|YP_004595737.1| 31 ISKMVSGSSEEIsELADEQSETMHEIADEVSTLSATVEEIAASSNQ 76
                                      5555555555446788888888888888888888888888877665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0073
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  29 delleldekrrelqveleelqaerNel...skeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaelekl 100
                                       +++ e+ ++  +l +++ee+ a +N++   s + + + +++ + ae+ i+ ++++ +  +++ ++++ l+++++++
  gi|336252630|ref|YP_004595737.1|  51 ETMHEIADEVSTLSATVEEIAASSNQVkevSSSAEDLADDGcDVAEDAIDAMDNVDDANADVAEAVSRLQERIDEI 126
                                       6677888999999999999999998751116666666666697777777777777777777777777777777664 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0097
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  27 dvdelleldekrrelqveleelqaerN.elskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                          e+ +l e+ re   e+e l a  + e  ++++++++++e+ e  i+ v+e  + l++++++++e+++  e++
  gi|336252630|ref|YP_004595737.1| 164 VANEVKSLAEESRENAEEIEGLVADIKdETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAEEV 238
                                       567899999999********999997625667899999999********************99999998876665 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.79
                                       HCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                      Seryl_tRNA_N  58 eIgkakkkk....edaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                       e++ a +++    e+ + ++++++e+ + ++++  +++++++e+++++ a+
  gi|336252630|ref|YP_004595737.1| 237 EVATATDEQasstEEVATMVDSTAENAQTVAKKISRVAAANEEQQEKIEAL 287
                                       444444444444455555555555555555555555555555555555554 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.36   1.4e+02      21      58 ..      46      83 ..      21      90 .. 0.71
   2 ?    4.8   1.5     0.078        30      45      84 ..      95     142 ..      86     195 .. 0.53
   3 ?    7.3   6.7     0.013         5      19     111 ..     190     287 ..     179     291 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.36
                              SesA 21 ikglpeaFrevgkrLplvqetLedaksqlesskldedt 58
                                      + +  e+ +e+++++ ++++t e++  + ++ k+ +++
  gi|336252630|ref|YP_004595737.1| 46 ADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSS 83
                                      45567788888888888888888887777776666554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.078
                              SesA  45 aksqlesskldedtesaikpvlesckekatkleeifekv........a 84 
                                       a++++++ ++ +d+++ + +++ + +e+++++++i + +        +
  gi|336252630|ref|YP_004595737.1|  95 AEDAIDAMDNVDDANADVAEAVSRLQERIDEIDTIVDVIneiadqtnM 142
                                       556666666666666666777777777777766666666433222230 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.013
                              SesA  19 kd.....ikglpeaFrevgkrLplvqetLedaksqlesskldedtesaikpvlesckekatkleeifekvapapad. 89 
                                       kd     ++++ +a +ev+  ++ v et +  ++  ++ ++ ++    +++v+++ +e+a + ee+ + v  ++++ 
  gi|336252630|ref|YP_004595737.1| 190 KDetdetVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQ---GAEEVATATDEQASSTEEVATMVDSTAENa 263
                                       55544557788888888888888888887777664444444443...367888999999999999888885555554 PP

                              SesA  90 srl..eryrkavrslgkgskVEtL 111
                                       +++  +  r a+++  +++k+E+L
  gi|336252630|ref|YP_004595737.1| 264 QTVakKISRVAAANEEQQEKIEAL 287
                                       444425555556678999999998 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.9     0.042        16      26      61 ..      46      81 ..      25     107 .. 0.54
   2 ?    2.1   0.1      0.42   1.6e+02       3      30 ..     117     144 ..     115     151 .. 0.84
   3 ?    5.4   4.2      0.04        15       2      67 ..     197     262 ..     166     271 .. 0.85
   4 ?    3.5   0.9      0.16        61      16      63 ..     246     286 ..     226     292 .] 0.42

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.042
                             Sec34 26 Leeleekfksvsektsslheaceqlleeqkrleela 61
                                       +e +e +++++++ s+l+++ e++ ++ ++++e++
  gi|336252630|ref|YP_004595737.1| 46 ADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVS 81
                                      333333334444444444444444433333333332 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.42
                             Sec34   3 dqLeskeeecdelleqtdealeqLeele 30 
                                       ++L+++ +e+d++++ ++e+ +q + l 
  gi|336252630|ref|YP_004595737.1| 117 SRLQERIDEIDTIVDVINEIADQTNMLA 144
                                       6799999999999999999999988765 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.04
                             Sec34   2 ldqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieek 67 
                                       ++q+++ +ee+++ +e+++e+ + Lee+ + +++ ++  +++ +a+++  ++++++ +++++  e+
  gi|336252630|ref|YP_004595737.1| 197 VEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAEEVATATDEQASSTEEVATMVDSTAEN 262
                                       578888888888889999999999999999999999999999999988888888888887776655 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.16
                             Sec34  16 leqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaee 63 
                                        ++t+e+ + +++  e+ ++v++k s++ +a        ++ +e  e+
  gi|336252630|ref|YP_004595737.1| 246 ASSTEEVATMVDSTAENAQTVAKKISRVAAAN-------EEQQEKIEA 286
                                       23333333333333333333333333333333.......333333333 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.4    0.0063       2.5     103     150 ..      42      89 ..      27     100 .. 0.86
   2 ?    5.9   0.2     0.022       8.5     108     149 ..     103     144 ..      94     152 .. 0.84
   3 ?    2.8   0.6       0.2        79     103     136 ..     193     226 ..     171     244 .. 0.62
   4 ?    0.2   1.4       1.3   4.9e+02      95     148 ..     220     273 ..     203     287 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0063
                     Fzo_mitofusin 103 farlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslles 150
                                       +++l  +  et +e+ +e+++l++++e++++ +++ k +   a+ l+ 
  gi|336252630|ref|YP_004595737.1|  42 ISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLAD 89 
                                       56788888899999************************9999998876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.022
                     Fzo_mitofusin 108 qqvdetekeleeeikelekeiekleevqkkakllrnkaslle 149
                                        +vd +++++ e +++l+++i++++++    + + +++++l+
  gi|336252630|ref|YP_004595737.1| 103 DNVDDANADVAEAVSRLQERIDEIDTIVDVINEIADQTNMLA 144
                                       579999999999999999999999999998888888887775 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.2
                     Fzo_mitofusin 103 farlcqqvdetekeleeeikelekeiekleevqk 136
                                        ++  +q+ ++++e+e+ i++++++++ lee+  
  gi|336252630|ref|YP_004595737.1| 193 TDETVEQISNANEEVETGIEHVNETVDILEEIDD 226
                                       3344455566666666666666666666666655 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.3
                     Fzo_mitofusin  95 vqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkasll 148
                                       + +e++ ++ + +q  +e+ +  +e+ ++ e+  ++++++ ++a+++ +k s++
  gi|336252630|ref|YP_004595737.1| 220 ILEEIDDAVTEATQGAEEVATATDEQASSTEEVATMVDSTAENAQTVAKKISRV 273
                                       445555566666666666666666666666666666666666666666665555 PP

>> CheZ  Chemotaxis phosphatase, CheZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   8.3      0.01         4       5     107 ..      40     142 ..      36     211 .. 0.88
   2 ?    2.3   7.2      0.36   1.4e+02      22      90 ..     215     279 ..     195     292 .] 0.58

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.01
                                       XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CheZ   5 eeiGkltReLhdalrelgldekllekaaeeipdardrLeyvielTeqAAertldavekalpladklkeeakeleeew 81 
                                       eei +l+ e  ++++e+  + ++l+ + eei  ++++ + v +  e+ A+   d+ e+a   +d++++  ++++e+ 
  gi|336252630|ref|YP_004595737.1|  40 EEISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADDGCDVAEDAIDAMDNVDDANADVAEAV 116
                                       68899999999*******9999******************************************************* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CheZ  82 erllerelekeefrelvkeveaflke 107
                                       +rl+er  e +++ ++++e+ + ++ 
  gi|336252630|ref|YP_004595737.1| 117 SRLQERIDEIDTIVDVINEIADQTNM 142
                                       ****9998888877777766665554 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.36
                                       XXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CheZ  22 gldekllekaaeeipdardrLeyvielTeqAAertldavekalpladklkeeakeleeewerllerele 90 
                                       +   ++le+  +++++a++  e v++ T++ A+     +e+ + ++d+ +e+a++++++++r+++++ e
  gi|336252630|ref|YP_004595737.1| 215 NETVDILEEIDDAVTEATQGAEEVATATDEQASS----TEEVATMVDSTAENAQTVAKKISRVAAANEE 279
                                       4334466777777777777777777777766654....3555666666666666666666665554433 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.7    0.0014      0.55      45     103 ..      26      86 ..      24      93 .. 0.84
   2 ?    3.1   0.8       0.2        78      46      88 ..     160     202 ..      96     218 .. 0.72
   3 ?    2.3   4.0      0.37   1.4e+02      34     109 ..     212     287 ..     203     288 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                              SKA2  45 erlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasa.elppls.eeeq 103
                                       ++l ++ + ++  +e++ el+ e+ e++ +i   +++   +++++ as+ +++  s ++e+
  gi|336252630|ref|YP_004595737.1|  26 TELLNISKMVSGSSEEISELADEQSETMHEIADEVSTLSATVEEIAASSnQVKEVSsSAED 86 
                                       56778888888999*********************************99877766645555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.2
                              SKA2  46 rlkkvkeelqaLkeqceellaekkelidkirttlvanrellqq 88 
                                       r++ v +e+++L e+ +e ++e + l+  i+    ++ e + +
  gi|336252630|ref|YP_004595737.1| 160 RFAVVANEVKSLAEESRENAEEIEGLVADIKDETDETVEQISN 202
                                       5556677777777777777777777766666666666555554 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.37
                              SKA2  34 pdnaeNpvkLlerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasa.elpplseeeqeaaenl 109
                                       ++  ++ v +le++ +  +e ++  e++     e+  +++++ t + ++ e  q   +++  + +++ee qe+ e+l
  gi|336252630|ref|YP_004595737.1| 212 EHV-NETVDILEEIDDAVTEATQGAEEVATATDEQASSTEEVATMVDSTAENAQTVAKKIsRVAAANEEQQEKIEAL 287
                                       444.4778888888888888888888888889999999******************999987777778888877765 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.5      0.86   3.3e+02      67      92 ..      45      71 ..      15      90 .. 0.54
   2 ?   11.1   0.5   0.00086      0.34      14      50 ..      95     131 ..      90     154 .. 0.85
   3 ?    2.9   1.2       0.3   1.2e+02      39     112 ..     201     273 ..     183     289 .. 0.43

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.86
                                      XXXXXX.XXXXXXXXXXXXXXXXXXXX CS
                              COG5 67 skslss.vlselksslesLsasyerlk 92
                                       + ++s +++e+  +++ Lsa +e + 
  gi|336252630|ref|YP_004595737.1| 45 LADEQSeTMHEIADEVSTLSATVEEIA 71
                                      333333344444444444444444332 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00086
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              COG5  14 anallkatnnnddteldlstplkrlnydiqeldkrlr 50 
                                       a++++ a  n dd+++d++ +++rl++ i+e+d+ ++
  gi|336252630|ref|YP_004595737.1|  95 AEDAIDAMDNVDDANADVAEAVSRLQERIDEIDTIVD 131
                                       789999999************************8665 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.3
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHH CS
                              COG5  39 nydiqeldkrlrqlitsnhleLlehlskskslss.vlselksslesLsasyerlkskvlepyeeaeklqsalkrl 112
                                       + + +e+++ ++   +++  ++le++++  ++     +e+ +  ++  +s e + + v    e+a+++ ++++r+
  gi|336252630|ref|YP_004595737.1| 201 SNANEEVETGIEH--VNETVDILEEIDDAVTEATqGAEEVATATDEQASSTEEVATMVDSTAENAQTVAKKISRV 273
                                       3333333333322..223333333333332222223334444444444444444444444444444444444443 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 ?    2.7   0.1      0.14        56      77     113 ..      36      79 ..      12     155 .. 0.49
   2 ?    3.7   0.3     0.069        27      59      98 ..     169     208 ..     145     217 .. 0.69
   3 ?    5.7   2.1     0.018       6.9      50     109 ..     230     289 ..     211     292 .] 0.77

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.14
                             Atg14  77 adlrerlqelkdklsqlkkeieekkkklaklsdklk.......k 113
                                       + ++e+++el d +s+   ei++   +l++  ++++       +
  gi|336252630|ref|YP_004595737.1|  36 SGSSEEISELADEQSETMHEIADEVSTLSATVEEIAassnqvkE 79 
                                       44444444444444444444444433333333333322222220 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.069
                             Atg14  59 edkiknkkakleelksliadlrerlqelkdklsqlkkeie 98 
                                       ++ ++ +++++ee+  l+ad+++++ e  +++s+ ++e+e
  gi|336252630|ref|YP_004595737.1| 169 KSLAEESRENAEEIEGLVADIKDETDETVEQISNANEEVE 208
                                       4444556667777777777777777777777777776665 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.018
                             Atg14  50 egkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsd 109
                                       e ++ ae+ +++ + ++ + ee  + + ++ e+ q++ +k+s+  +++ee+++k+++l +
  gi|336252630|ref|YP_004595737.1| 230 EATQGAEEVATATDEQASSTEEVATMVDSTAENAQTVAKKISRVAAANEEQQEKIEALGE 289
                                       334456688888999999999999999999999999999999999999999999998755 PP

>> Dor1  Dor1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.2    0.0077         3      71     157 ..      55     141 ..      23     149 .. 0.49
   2 ?    3.5   4.2      0.06        23      15     104 ..     167     256 ..     159     289 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0077
                              Dor1  71 kLteectrfskkaeeisekrkenkllldkheqllellelPqlmdrcirng.yy.dealeLeayvsrLkqristnpvi 145
                                       ++  e+   s+  eei  + +++k ++   e+l ++     + + +i +  +  d   + +++vsrL++ri +++ i
  gi|336252630|ref|YP_004595737.1|  55 EIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADD--GCDVAEDAIDAMdNVdDANADVAEAVSRLQERIDEIDTI 129
                                       222233333333333333344444444444444433..223333555544443044568999999999999997777 PP

                              Dor1 146 qsiaaeveetvq 157
                                        ++++e+   + 
  gi|336252630|ref|YP_004595737.1| 130 VDVINEIADQTN 141
                                       777766655443 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.06
                              Dor1  15 epelLaeeaeeilaqiqdLarknyktlidaaealeairqelediraqledLvlklpkLteectrfskkaeeisekrk 91 
                                       e ++Laee++e  ++i  L  ++     ++ e++++  +e+e   +++++ v+ l++++ ++t+  + aee+ +  +
  gi|336252630|ref|YP_004595737.1| 167 EVKSLAEESRENAEEIEGLVADIKDETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAEEVATATD 243
                                       66799999**************9999999999999999****999**************************999977 PP

                              Dor1  92 enkllldkheqll 104
                                       e  +  +++++++
  gi|336252630|ref|YP_004595737.1| 244 EQASSTEEVATMV 256
                                       7666666655555 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   7.3      0.03        12     240     411 ..      41     207 ..      14     209 .. 0.52
   2 ?    5.6   4.7    0.0081       3.2     168     276 ..     165     270 ..     161     285 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.03
                          Prominin 240 elerllenlkeakeqLeqvnklekeLrksgsqL...rdglrgvkrdlnqalsnlCqs.eeCskilssleiekldtsk 312
                                       e+ +l++   e +e ++++ +  + L  + +++   ++ +++v  + ++++ + C   e+  +++++++      ++
  gi|336252630|ref|YP_004595737.1|  41 EISELAD---EQSETMHEIADEVSTLSATVEEIaasSNQVKEVSSSAEDLADDGCDVaEDAIDAMDNVDD----ANA 110
                                       3333333...333334444444444444444430004445555556666666677733666666666655....344 PP

                          Prominin 313 cl.dqlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkipreald 388
                                       ++ ++++ ++e ++++++++ + +++i+  + +++ +++  ++   a+   d +  +a++ + + +++++   e ++
  gi|336252630|ref|YP_004595737.1| 111 DVaEAVSRLQERIDEIDTIV-DVINEIA--DQTNMLALNASIEAARAGESGDRFAVVANEVKSLAEESREN-AEEIE 183
                                       44455566666666666663.2233333..33445566666666666666666666666666666666666.66666 PP

                          Prominin 389 avisdle.nterssktfddvveky 411
                                        ++ d++ +t +++++ ++  e++
  gi|336252630|ref|YP_004595737.1| 184 GLVADIKdETDETVEQISNANEEV 207
                                       666666666666666655555544 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0081
                          Prominin 168 degleesketvkrgledlrtflkdvpqhidhvlvqnyeelekhvsddLddagkhlgldladtlesnvlpaLaelerl 244
                                        +++++  e+ +++ e++ +++ d+ ++ d+ ++q  ++++++v++ ++++++ +  d+ ++++++v++a +  e++
  gi|336252630|ref|YP_004595737.1| 165 ANEVKSLAEESRENAEEIEGLVADIKDETDETVEQ-ISNANEEVETGIEHVNETV--DILEEIDDAVTEATQGAEEV 238
                                       56788888999999999999999999999999999.9999999999999999875..78888888888888888888 PP

                          Prominin 245 lenlkeakeqLeqvnklekeLrksgsqLrdgl 276
                                       ++++ e   + e+v  +  +  + +++  + +
  gi|336252630|ref|YP_004595737.1| 239 ATATDEQASSTEEVATMVDSTAENAQTVAKKI 270
                                       88888888888888877777766666665555 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 ?    2.2   0.7      0.59   2.3e+02      44      93 ..      38      87 ..      23      91 .. 0.50
   2 ?    9.5   9.7    0.0033       1.3      34     148 ..      63     183 ..      50     192 .. 0.67
   3 ?    4.6  10.6      0.11        41      46     147 ..     191     284 ..     184     290 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.59
                                      --STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB 44 lSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93
                                       S+e+ ++ +e ++   ++ + +  +     ++ a  ++v+e+  + ++L
  gi|336252630|ref|YP_004595737.1| 38 SSEEISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDL 87
                                      34455555555555555555555444444444444444444444444444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0033
                                       HHHTTTTT----STHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------C.HHH CS
                           T3SSipB  34 skaqqeaasklSdelqtalseakgatdd....leaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekak.lea 105
                                         a++e+  + S++++++ s a++++dd    +e+ai+++d+++ a  ++ ++v+  q+r++e++       + +++
  gi|336252630|ref|YP_004595737.1|  63 LSATVEEIAASSNQVKEVSSSAEDLADDgcdvAEDAIDAMDNVDDANADVAEAVSRLQERIDEIDTIVDVINEiADQ 139
                                       56788888889999999999999998874444788999999999888888899999999999995533333330233 PP

                                       HHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTXX CS
                           T3SSipB 106 aeqQagaa.adalqadealqKkldaasklsekakakekevDdis 148
                                        +  a +a  +a+ a e  ++   +a+ ++  a ++++++ +i 
  gi|336252630|ref|YP_004595737.1| 140 TNMLALNAsIEAARAGESGDRFAVVANEVKSLAEESRENAEEIE 183
                                       33333333567777777777776666666666666666655554 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.11
                                       STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH...HHHHHHHH CS
                           T3SSipB  46 delqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaa.adalqade 121
                                       de  + +++ ++a +++e  ie++++     ++ + +v+ea +  +e+         + a  +Qa      a+ +d 
  gi|336252630|ref|YP_004595737.1| 191 DETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAEEV---------ATATDEQASSTeEVATMVDS 258
                                       445556667777777777777777777777777777777777777777.........55555666655455777888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTX CS
                           T3SSipB 122 alqKkldaasklsekakakekevDdi 147
                                       +++ +  +a+k+s  a a e++  +i
  gi|336252630|ref|YP_004595737.1| 259 TAENAQTVAKKISRVAAANEEQQEKI 284
                                       88888888888888887777776655 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   9.8     0.081        31     183     330 ..      46     191 ..       9     290 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.081
                              FUSC 183 aeareaararlaadilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpelaal 259
                                       a++++++++++a+++ +l+a ++  a+ s+++ + +  +  l  +  ++   +    ++  + +a  a+av  l++ 
  gi|336252630|ref|YP_004595737.1|  46 ADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADDGCDVAEDAIDAMDNVDDANADVAEAVSRLQER 122
                                       33446788999999999999999999999999999999999999999999999999999999999999998889999 PP

                              FUSC 260 laelaaleaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslraleaaiaa 330
                                       ++e++++ +   + a+++++ al a ++a+r+ ++   d+ a+++ ++++l +e ++  ++++ l a+i++
  gi|336252630|ref|YP_004595737.1| 123 IDEIDTIVDVINEIADQTNMLALNASIEAARAGES--GDRFAVVANEVKSLAEESRENAEEIEGLVADIKD 191
                                       99999985555567778888888888888888888..5555666666666666666666666666655555 PP

>> DUF489  Protein of unknown function (DUF489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       1.2   4.5e+02      81     118 ..      25      62 ..       9      84 .. 0.62
   2 ?    0.9   0.5         1     4e+02      95     115 ..     113     133 ..      38     166 .. 0.63
   3 ?    7.2   2.0     0.012       4.7      13      71 ..     165     223 ..     160     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHSTTHHHHHHHHHHTTHHHHTTS-TT CS
                            DUF489  81 alsllalerkLsknkealaklgerieqierqlehfdll 118
                                       + +ll++++ +s ++e +++l++++++  ++ +    +
  gi|336252630|ref|YP_004595737.1|  25 VTELLNISKMVSGSSEEISELADEQSETMHEIADEVST 62 
                                       56677777777777777777777666655555433222 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1
                                       TTHHHHHHHHHHTTHHHHTTS CS
                            DUF489  95 kealaklgerieqierqlehf 115
                                        ea+++l+eri++i++ ++  
  gi|336252630|ref|YP_004595737.1| 113 AEAVSRLQERIDEIDTIVDVI 133
                                       345555666666665555543 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHS---HHHHHHHHHHHH--S-SSHHHHTTSGGGGHHHHHHHHHHHHT--S CS
                            DUF489  13 aklvqqlArtGqadeealetllkslletdpestedvygglanlklGletlleqlekekk 71 
                                       a+ v++lA++ + ++e++e l+  + + ++e++e++ + ++++++G+e ++e+++  ++
  gi|336252630|ref|YP_004595737.1| 165 ANEVKSLAEESRENAEEIEGLVADIKDETDETVEQISNANEEVETGIEHVNETVDILEE 223
                                       789**********************************************9998876655 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.4   5.3e+02      14      38 ..     106     126 ..      96     141 .. 0.61
   2 ?    4.1   0.4      0.13        50      24      67 ..     161     208 ..     126     216 .. 0.74
   3 ?    5.9   1.4     0.036        14      36      66 ..     261     291 ..     212     292 .] 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.4
                              Med9  14 ekdpnlsskdletktgelrhkLkka 38 
                                       ++++     d+  +++ l+ +++++
  gi|336252630|ref|YP_004595737.1| 106 DDAN----ADVAEAVSRLQERIDEI 126
                                       3444....67777777777777765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.13
                              Med9  24 letktgelrhkLkkarelirelpg....idrsveeqeaeieeleeqla 67 
                                       +   ++e++   ++ re  +e++g    i   ++e  ++i + +e+++
  gi|336252630|ref|YP_004595737.1| 161 FAVVANEVKSLAEESRENAEEIEGlvadIKDETDETVEQISNANEEVE 208
                                       555667777777889999999999988888888888899988888876 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.036
                              Med9  36 kkarelirelpgidrsveeqeaeieeleeql 66 
                                       ++a ++ ++++ +    eeq+++ie+l e++
  gi|336252630|ref|YP_004595737.1| 261 ENAQTVAKKISRVAAANEEQQEKIEALGERV 291
                                       688999999999**************98886 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   5.5      0.09        35     231     321 ..      33     127 ..       8     135 .. 0.55
   2 ?    4.8   0.3     0.033        13      11      59 ..     100     146 ..      92     171 .. 0.67
   3 ?    5.7  14.6     0.017       6.8     223     320 ..     190     287 ..     163     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.09
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH........HHHHHHHHHHHHHHHH CS
                             APG17 231 eVlekDaaeledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgk....klpeylaifkaeeefl 303
                                       + ++  ++e+++  +e  e+++e+ ++ ++ls++ eei ++++++k++ +  e++ +      ++ +  + + ++  
  gi|336252630|ref|YP_004595737.1|  33 KMVSGSSEEISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADdgcdVAEDAIDAMDNVDDAN 109
                                       44555556666666666666666666666666666666666666666666666663312212222233233333333 PP

                                       HH...HHHHHHHHHHHHH CS
                             APG17 304 erweeekekieekleele 321
                                       +  +e  ++++e+++e++
  gi|336252630|ref|YP_004595737.1| 110 ADVAEAVSRLQERIDEID 127
                                       333445555555555555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHII CS
                             APG17  11 seaqtlcqrAnelltsarqeleeavkllakteflrdglkqQlkllekir 59 
                                         a+  + +An  +++a ++l+e+ + ++++  +++ +++Q ++l+ ++
  gi|336252630|ref|YP_004595737.1| 100 D-AMDNVDDANADVAEAVSRLQERIDEIDTIVDVINEIADQTNMLA-LN 146
                                       4.66677777777777777777777777777777777777777764.34 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.017
                                       CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHH CS
                             APG17 223 eeereelleVlekDaaeledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkae 299
                                       ++e +e +e +++ ++e+e  +++++e+++++e++ +++ e ++ +e++ +a+ ++ +  eev + ++++ ++ ++ 
  gi|336252630|ref|YP_004595737.1| 190 KDETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAEEVATATDEQASSTEEVATMVDSTAENAQTV 266
                                       46778889999999999999999999999999999999999999999999999999999999999999999988888 PP

                                       HHHHHH...HHHHHHHHHHHH CS
                             APG17 300 eeflerweeekekieekleel 320
                                       ++ ++r ++ +e+ +ek+e l
  gi|336252630|ref|YP_004595737.1| 267 AKKISRVAAANEEQQEKIEAL 287
                                       888888777777777777665 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.1    0.0062       2.4      10      61 ..      41      92 ..      18     146 .. 0.45
   2 ?    2.7   0.9      0.15        60      35      77 ..     164     206 ..      96     220 .. 0.55
   3 ?    4.9   2.4     0.034        13      12      87 ..     166     240 ..     156     253 .. 0.60
   4 ?    3.9   3.3     0.069        27       5      74 ..     222     290 ..     212     292 .] 0.63

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0062
                             TMPIT 10 efkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk 61
                                      e+ el ++++e ++++++  +  s++++ei+  ++++ke++ss ++l  +  
  gi|336252630|ref|YP_004595737.1| 41 EISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSSAEDLADDGC 92
                                      3333333333333333333333333334444444444444444444433322 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.15
                             TMPIT  35 cskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelke 77 
                                       +++e+k+  ++ +e  ++++ l +++k+e++e+ve++++  +e
  gi|336252630|ref|YP_004595737.1| 164 VANEVKSLAEESRENAEEIEGLVADIKDETDETVEQISNANEE 206
                                       3333344444444444444444444444444444444444444 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.034
                             TMPIT  12 keleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeves 87 
                                       +e+++ a+e +++ ee++ l  +++ e+++  +++++ ++++++  ++v +e+ +++ee+++ + e+++  +ev+ 
  gi|336252630|ref|YP_004595737.1| 166 NEVKSLAEESRENAEEIEGLVADIKDETDETVEQISNANEEVETGIEHV-NETVDILEEIDDAVTEATQGAEEVAT 240
                                       3444445555666666666666666666666666666666666655554.46666777777777666666665554 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.069
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkee 74 
                                       ee+ + + e  + a+e+ + ++e +++ +++++ +++  ++++ + ++++++ ++ +ee++e++e l e+
  gi|336252630|ref|YP_004595737.1| 222 EEIDDAVTEATQGAEEVATATDEQASSTEEVATMVDSTAENAQTVAKKISRVAAA-NEEQQEKIEALGER 290
                                       4455555555555566666666666666666666666666666666666666655.47888888877665 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 ?    4.1   3.2      0.15        58       8      88 ..      46      80 ..      12     137 .. 0.50
   2 ?    0.4   0.1       2.1   8.3e+02       5      42 ..     102     139 ..      96     158 .. 0.59
   3 ?    7.5   2.3     0.014       5.4       5      78 ..     137     210 ..     133     218 .. 0.81
   4 ?    6.2   6.5     0.035        14       4      73 ..     220     289 ..     217     292 .] 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.15
                            CENP-H  8 rdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeelekleaelkksrqrwrvvk 86
                                       de s+++ +++ e+++l + ++e+ +++ ++k                                              
  gi|336252630|ref|YP_004595737.1| 46 ADEQSETMHEIADEVSTLSATVEEIAASSNQVK---------------------------------------------- 78
                                      233333333333333333333333333333332.............................................. PP

                            CENP-H 87 nv 88
                                      +v
  gi|336252630|ref|YP_004595737.1| 79 EV 80
                                      22 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2.1
                            CENP-H   5 ieqrdelssellklsqelrelqeeltevekenlrlkrk 42 
                                       +++ d+++ ++++  + l+e  +e++++   + ++  +
  gi|336252630|ref|YP_004595737.1| 102 MDNVDDANADVAEAVSRLQERIDEIDTIVDVINEIADQ 139
                                       44555555556666666666655555555555555444 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.014
                            CENP-H   5 ieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeelekleaelkks 78 
                                        +q+++l++++   ++   e  ++ + v  e ++l +++re a+e++ l  + + e +++ e+++++ +e+++ 
  gi|336252630|ref|YP_004595737.1| 137 ADQTNMLALNASIEAARAGESGDRFAVVANEVKSLAEESRENAEEIEGLVADIKDETDETVEQISNANEEVETG 210
                                       5666677777777777777778888999999***************9999999999989999999999999875 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.035
                            CENP-H   4 lieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeeleklea 73 
                                       ++e++d++++e+ + ++e++++++e ++ ++e   +   ++e a++++++ +  ++ +e+++e++e+l +
  gi|336252630|ref|YP_004595737.1| 220 ILEEIDDAVTEATQGAEEVATATDEQASSTEEVATMVDSTAENAQTVAKKISRVAAANEEQQEKIEALGE 289
                                       6889999999999999999999999999999999999999999999976666666666678888887765 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 ?    1.9   0.8       0.1        40      57     101 ..      39      83 ..      15     114 .. 0.62
   2 ?    6.4  12.0    0.0046       1.8      30     162 ..     121     274 ..      99     287 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.1
                        V_ATPase_I  57 eeaeesleapeekeldeleeelekleeelkelnenleklkkelne 101
                                       +e+ ++l+++++++++e+ +e+++l + ++e+ ++++++k+  ++
  gi|336252630|ref|YP_004595737.1|  39 SEEISELADEQSETMHEIADEVSTLSATVEEIAASSNQVKEVSSS 83 
                                       333445555555566666666666666666666555555554433 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0046
                        V_ATPase_I  30 rrcdemerklrfleeeieklekavikeeea.....................eesleapeekeldeleeele.kleee 84 
                                        r+de++  +++++e  ++++    +++ +                      +++++++++e++ l ++++ +++e 
  gi|336252630|ref|YP_004595737.1| 121 ERIDEIDTIVDVINEIADQTNMLALNAS-IeaaragesgdrfavvanevksLAEESRENAEEIEGLVADIKdETDET 196
                                       4677777777777766666444333333.347789999999999999988777777788888888888887256677 PP

                        V_ATPase_I  85 lkelnenleklkkelnelvelkavlekakefleeeeeeeeeeeseeeeeekeeeeeeeseeeeeeelleeeeelsfv 161
                                       ++++++ +e++++  +++ e+  +le++++ ++e+++ +ee  + ++e+++++ee +++ ++++e++++ ++++s v
  gi|336252630|ref|YP_004595737.1| 197 VEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQGAEEVATATDEQASSTEEVATMVDSTAENAQTVAKKISRV 273
                                       8899999999999***************9999887544444443333333333333333333333333333334444 PP

                        V_ATPase_I 162 a 162
                                       a
  gi|336252630|ref|YP_004595737.1| 274 A 274
                                       4 PP

>> Peptidase_M9_N  Peptidase family M9 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.7      0.69   2.7e+02      86     154 ..      57     125 ..      52     153 .. 0.67
   2 ?   -1.6   0.0       4.8   1.9e+03      36      69 ..     151     183 ..     127     190 .. 0.58
   3 ?   -0.9   0.0       2.9   1.1e+03     115     160 ..     188     233 ..     184     239 .. 0.79
   4 ?    9.1   1.1    0.0026         1     106     143 ..     231     268 ..     212     285 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.69
                    Peptidase_M9_N  86 akevgdyssalsqavaqaldaflanpnakdvtdeqgevlaelliliDsakqnaetlsvvkrlLnqynse 154
                                       a+ev+++s ++++  a++ +    ++ a d  d+  +v ++++  +D+++ ++  ++++ + L++  +e
  gi|336252630|ref|YP_004595737.1|  57 ADEVSTLSATVEEIAASSNQVKEVSSSAEDLADDGCDVAEDAIDAMDNVDDANADVAEAVSRLQERIDE 125
                                       677888887777766666666667777777888888899999999999987666555555555544444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.8
                    Peptidase_M9_N  36 sakavfseanmqavanalkqeaaaYtgenskgie 69 
                                       +a+a  s ++ + van++k+ a++   en+++ie
  gi|336252630|ref|YP_004595737.1| 151 AARAGESGDRFAVVANEVKSLAEE-SRENAEEIE 183
                                       444445555666666666666665.334445555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.9
                    Peptidase_M9_N 115 dvtdeqgevlaelliliDsakqnaetlsvvkrlLnqynsevaanva 160
                                       d +de +e+++++      ++   e ++++ ++L++ +++v++ ++
  gi|336252630|ref|YP_004595737.1| 188 DIKDETDETVEQISNANEEVETGIEHVNETVDILEEIDDAVTEATQ 233
                                       6778888888888888888888888899999999998888887765 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0026
                    Peptidase_M9_N 106 aflanpnakdvtdeqgevlaelliliDsakqnaetlsv 143
                                       a    +++ + tdeq ++ +e+ +++Ds+ +na+t+++
  gi|336252630|ref|YP_004595737.1| 231 ATQGAEEVATATDEQASSTEEVATMVDSTAENAQTVAK 268
                                       44556778899***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2642  (0.147359); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); expected 358.6 (0.02)
Passed Vit filter:                       144  (0.00803168); expected 17.9 (0.001)
Passed Fwd filter:                        93  (0.00518713); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              46  [number of targets reported over threshold]
# CPU time: 1.52u 0.35s 00:00:01.87 Elapsed: 00:00:00.53
# Mc/sec: 1648.49
//
Query:       gi|336252631|ref|YP_004595738.1|  [L=133]
Description: hypothetical protein Halxa_1226 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.079   14.0   0.9       0.13   13.3   0.9    1.5  1  SpoIIAA-like  SpoIIAA-like


Domain annotation for each model (and alignments):
>> SpoIIAA-like  SpoIIAA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.9   7.5e-06      0.13       2      95 ..      23     130 ..      11     131 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.5e-06
                                       EEEEEEEEE-HHHHHH.HHHHHHHHCCSSSEEEEEEE........HHHHHHHCC......CGGECEEEEE-SSCCCC CS
                      SpoIIAA-like   2 iaveisgkitaedykevliellekalahgkirllvdl........ediklglah......lsrfrrvAvvtdkkwik 64 
                                       ++++++   + e++k+ +++lle    ++  ++  d+        ed+ + +++        ++r  A+v ++++i 
  gi|336252631|ref|YP_004595738.1|  23 VTFTWDEFASGERFKDGANALLEYVQSNDVAKVIHDTsgiqahddEDLAWLQSEwypkmvDAGLRYSAIVHQESVIS 99 
                                       56677777788888886666664332355556666666666666777765552245555778889999999998866 PP

                                       CC..CCHHCCH.-CCEEEEE..SSHHHHHHHH CS
                      SpoIIAA-like  65 al.vallasalflslevkvFkleeeeeAlaWL 95 
                                       ++  + +   +  ++++k + ++++eeA++W+
  gi|336252631|ref|YP_004595738.1| 100 QMdTEDFVEDV-KDMPYKLMHTADLEEAREWM 130
                                       66122333333.2579***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1076.44
//
Query:       gi|336252632|ref|YP_004595739.1|  [L=129]
Description: ferredoxin [Halopiger xanaduensis SH-6]
Scores for 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-15   55.3   0.4    6.3e-15   54.9   0.4    1.2  1  Fer2      2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.074   13.1   0.2       0.14   12.3   0.2    1.6  1  Fer2_4    2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.4   7.1e-19   6.3e-15       9      74 ..      40     104 ..      33     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 7.1e-19
                                       EEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE.CTTSSSSTHHHHHTTEEEEGGG CS
                              Fer2   9 evevadgettlldaaeenggidipysCggggCgtClvevlegev.qsdetelegeeldegklrlaCq 74 
                                       +++va+ge+ +l+aae + g+d p+sC++g+C+ C++ v++ge+  ++++ l++ee +e+ +rl+C 
  gi|336252632|ref|YP_004595739.1|  40 TLDVAEGEY-ILEAAEAQ-GYDWPFSCRAGACANCAAIVVDGEIdMDMQQILSDEEVEEKNVRLTCI 104
                                       789******.******88.*************************7767******************6 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 ?   12.3   0.2   1.5e-05      0.14      13      50 ..      41      68 ..      34     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                            Fer2_4 13 vtvpeGdtvasAllangvdvprsckygrprgelcagge 50
                                      + v eG+ +++A+ a+g d+p sc            g+
  gi|336252632|ref|YP_004595739.1| 41 LDVAEGEYILEAAEAQGYDWPFSCRA----------GA 68
                                      6899*******************998..........33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 00:00:00.38
# Mc/sec: 1008.98
//
Query:       gi|336252633|ref|YP_004595740.1|  [L=393]
Description: phosphate transporter [Halopiger xanaduensis SH-6]
Scores for 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-39  133.7  33.9    8.8e-39  133.5  32.4    1.8  2  PHO4      Phosphate transporter family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.5  32.4   4.9e-43   8.8e-39       2     309 ..      21     309 ..      20     332 .. 0.81
   2 ?   -1.8   0.0     0.069   1.2e+03     114     140 ..     362     388 ..     327     391 .. 0.80

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 4.9e-43
                              PHO4   2 GanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdve.lfdpselmlgmlaallgaavwl 77 
                                       G   ++ af+++vg++++t   A+ l++if f+Ga+++G +V++t+++++v+++ +f     m   +a+l+  +  l
  gi|336252633|ref|YP_004595740.1|  21 GGSTTGPAFGPAVGANVITKLMAAGLMSIFFFVGAWTIGPNVVDTLGNELVHTTdIF----TMRSNVAVLFFIGGAL 93 
                                       6677889********************************************543233....357999********** PP

                              PHO4  78 llatvlglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvk....ekl 150
                                       ++ ++ g+P+St+++ vGa+++ +la+     ++w+ l++iv+ w+++P++g+ +a ++   +   i  +    e+ 
  gi|336252633|ref|YP_004595740.1|  94 FVGNYAGVPASTSMTAVGAIAALGLAT---GELNWSVLGEIVVWWIVAPIIGFWVAGVVGRYFYPRIN-EwvaiEAN 166
                                       **************************5...569**********************9988765544422.12233333 PP

                              PHO4 151 knalralpvlvlvtiailalsilfkgeskkddeeteklfkflqvvsaalvsfahGanDvanaiGpllaalisiykas 227
                                       + +++++ v      + ++  + f+    ++ ++ e + +f++v  ++l++f+ G +++anai+p++ +        
  gi|336252633|ref|YP_004595740.1| 167 RDGRQMITVD----RSGAVPRLQFQ----ENATRREITGAFVVVAIGCLMGFSSGTSNIANAIAPIYGTGA------ 229
                                       3333333322....22222222222....334455555699*************************55331...... PP

                              PHO4 228 kevplwvlllgglaialGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgavvGv 304
                                             ++l+gg+a+a+G +++++r   t+G++it +l  + +++++++++++v+++s +g+P S+  +++++++G 
  gi|336252633|ref|YP_004595740.1| 230 -LEMGTLILIGGAAVAIGCFTIARRTLDTLGNDIT-NLPLTAAIVVAVISSTIVIVLSSIGVPASFVVIATMSIIGL 304
                                       .1245799***************************.6**************************************** PP

                              PHO4 305 Glakk 309
                                       G+ + 
  gi|336252633|ref|YP_004595740.1| 305 GWGRA 309
                                       **992 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.069
                              PHO4 114 klvkivlswvlsPllggiiaallfllv 140
                                       + ++++l+  + P+++ + a+l+f +v
  gi|336252633|ref|YP_004595740.1| 362 TTARVILMQNVVPIISTVGAYLTFRFV 388
                                       567888888999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3105.52
//
Query:       gi|336252634|ref|YP_004595741.1|  [L=141]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-24   84.7   2.7    9.3e-24   84.5   2.7    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 !   84.5   2.7   5.2e-28   9.3e-24       1     141 []       1     141 []       1     141 [] 0.91

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 5.2e-28
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH....HHH CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada....aka 73 
                                       m  ++lV++Dgse s++Ale+Ale    ++ael++lhv+  +++ ++ +   + +++ ++++++ ++       + a
  gi|336252634|ref|YP_004595741.1|   1 MVSHVLVPMDGSEMSERALEYALEVY--PDAELTVLHVVGGPSPMWAEATGLALADDFEAKAREHADVIFdrarEIA 75 
                                       6789********************75..5589***************999999999999999997777779988889 PP

                                       HHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  74 aaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       a ++ +v+ ++++e g+p ++i+  a++  ++ +V+G++g +  +r+++G+v+e+v+r++p+pV+vVr
  gi|336252634|ref|YP_004595741.1|  76 ADADSDVTLDTEIELGHPVRAIINRADD--YETVVIGTHGGTVADRVFVGNVAERVVRRSPVPVVVVR 141
                                       9999999999999999999999987776..89********888888*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1009.40
//
Query:       gi|336252635|ref|YP_004595742.1|  [L=479]
Description: amino acid permease-associated protein [Halopiger xanaduensis SH-6]
Scores for 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-44  151.3  36.3    4.3e-44  151.0  36.3    1.0  1  AA_permease_2   Amino acid permease
    1.9e-35  122.4  33.3    2.5e-35  122.0  33.3    1.2  1  AA_permease     Amino acid permease
     0.0022   16.9   6.7      0.011   14.6   6.7    2.0  1  Spore_permease  Spore germination protein
  ------ inclusion threshold ------
      0.029   14.5   1.8      0.029   14.5   1.8    2.9  3  AA_permease_C   C-terminus of AA_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 !  151.0  36.3   9.7e-48   4.3e-44       2     402 ..      48     446 ..      47     470 .. 0.86

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 9.7e-48
                     AA_permease_2   2 sllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkv 76 
                                       +l + +a+ ig++ig+gifv +  +a+ +gpa++ ++ i+++i  l v+l   El++a+p+sgG y + +++ g ++
  gi|336252635|ref|YP_004595742.1|  48 GLAGGLAIGIGTMIGAGIFVFPglAAGRAGPAAAGSFAIGAVIA-LLVALPASELATAMPKSGGGYYFISRGLGTLA 123
                                       66777899************99977778***************9.89****************************** PP

                     AA_permease_2  77 aflsawfnwfayvpvlasilsvaasyllnalgp..dlqgntwltyliaiaililvalinirgikesakiqnilgilk 151
                                       + +++ ++w++ v+++a++l+ ++ y +  l++   ++gn w + l a ++ ++++++n+ g+   ak+qn ++ l 
  gi|336252635|ref|YP_004595742.1| 124 GTVVGLSLWLGLVFATAFYLVGFGYYAVDTLAEvgVVVGNGWVVPL-ALVFGAGFTVLNVTGTENAAKLQNGIVALL 199
                                       ******************************9988888899998888.99***********************99999 PP

                     AA_permease_2 152 illpliiliilglitvdgggfsslstetdtffpn.gwpg....vllgllivlwsfdGfesaanvseevkk..kdvpk 221
                                       +  +l++++  g+  +d+ gf      +++ +p+ + p+    vl + + v+ s+ Gf  +a v+ e++   +++p+
  gi|336252635|ref|YP_004595742.1| 200 L-SILAFFL--GFGGLDALGFV-----GESATPErFAPFgavpVLTTAALVFTSYLGFAQIATVAGEMRDpgRNLPL 268
                                       9.6766666..99999888887.....44444554444433238999999*****************888779**** PP

                     AA_permease_2 222 aifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrv 298
                                       a++ ++++v+vly+ + ++++ + + + +a l+++   +  + + + g+ +a+++v+++ l+ + ++n+ ++++sr 
  gi|336252635|ref|YP_004595742.1| 269 AMVGSVVVVGVLYVATIFVATSAFGSERLADLGETA--MVEVGRHYLGPLGAVAIVFGGLLATVSSANASILSTSRA 343
                                       ******************************999864..7777788888***************************** PP

                     AA_permease_2 299 lealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrk 374
                                       ++a++rd  lPr+ +++n ++g+p +a+ l     l+l   ++   +  +++l++v+s++++++y+l+ ++++ +r+
  gi|336252635|ref|YP_004595742.1| 344 VYAVSRDALLPRWASRINlRYGTPHVALGLAGGPILAL---TA---TGRVTILAEVASFLHLVMYGLICVALVAIRR 414
                                       **********************************5332...33...468**************************** PP

                     AA_permease_2 375 krphlkr.....pgkilvaiigalfllfllval 402
                                       ++p +       pg ++v+  +  ++ f l+ +
  gi|336252635|ref|YP_004595742.1| 415 DEPTWYDpdfrvPG-YPVVPAAGAVASFGLIGF 446
                                       ***98442344454.444444433333333333 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.0  33.3   5.5e-39   2.5e-35       3     392 ..      53     414 ..      51     467 .. 0.83

  Alignments for each domain:
  == domain 1  score: 122.0 bits;  conditional E-value: 5.5e-39
                       AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviG 79 
                                       l i +g +iG+g+fv  g +++ aGp++a  +++++ v+ +lv+l  +e+at++pksgg y+++sr lg  +G v+G
  gi|336252635|ref|YP_004595742.1|  53 LAIGIGTMIGAGIFVFPGLAAGRAGPAAA-GSFAIGAVIALLVALPASELATAMPKSGGGYYFISRGLGTLAGTVVG 128
                                       6799**********************655.9********************************************** PP

                       AA_permease  80 lnylfswitvlaleltaasiliqfwelvtdlpkawvt..........gavflvvlliinlvgvkvygeaefilalik 146
                                       l++++  +++ a+ l++ +++        d + + ++          ++vf + ++++n+ g +  ++ +  +  ++
  gi|336252635|ref|YP_004595742.1| 129 LSLWLGLVFATAFYLVGFGYY------AVDTLAEVGVvvgngwvvplALVFGAGFTVLNVTGTENAAKLQNGIVALL 199
                                       **6665555555555555554......444443333345555577***************************99999 PP

                       AA_permease 147 iiaiiafiivg...iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvai 220
                                       + +++ f+ +g   + + +g+  +++                + p            ++  ++ v+ ++ G+  +a+
  gi|336252635|ref|YP_004595742.1| 200 LSILAFFLGFGgldALGFVGESATPE---------------RFAPF-------GAVPVLTTAALVFTSYLGFAQIAT 254
                                       99999999888777777777777777...............34444.......26699******************* PP

                       AA_permease 221 iagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinavil 297
                                       +agE++dP +++P a+   v+ ++++Yv  ++++++ ++   l  l ++a     +v ++++   ++ a+ i+++ l
  gi|336252635|ref|YP_004595742.1| 255 VAGEMRDPGRNLPLAMVGSVVVVGVLYVATIFVATSAFGSERLADLGETA-----MVEVGRHYLGPLGAVAIVFGGL 326
                                       ******************************************99999776.....778888888888899999999* PP

                       AA_permease 298 taalssansslysasRvlyslakdglaPkvlkkvs.krgvPlraillsmiisllalllaslnlaapivfnfllaisa 373
                                       +a++ssan+s+ s+sR++y+ ++d l+P+++++++ ++g P++a+ l     l++              ++l  ++ 
  gi|336252635|ref|YP_004595742.1| 327 LATVSSANASILSTSRAVYAVSRDALLPRWASRINlRYGTPHVALGLAGGPILALTATGR--------VTILAEVAS 395
                                       *********************************99899******9876655554442222........445666666 PP

                       AA_permease 374 liglivwlliilsylrfRk 392
                                       +  l++++li+++++ +R+
  gi|336252635|ref|YP_004595742.1| 396 FLHLVMYGLICVALVAIRR 414
                                       7777777777777766666 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   6.7   2.5e-06     0.011      12     239 ..      57     297 ..      52     301 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-06
                    Spore_permease  12 vsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpekt.liellkkilgkwLGsllsilfil 87 
                                       + +++G+gi ++p+ +a +a+p +  s  ++++i+l+++l +++l   +p++   + +++ +lg++ G + ++ + l
  gi|336252635|ref|YP_004595742.1|  57 IGTMIGAGIFVFPGLAAGRAGPAAAGSFAIGAVIALLVALPASELATAMPKSGgGYYFISRGLGTLAGTVVGLSLWL 133
                                       679**********************************************9875267888999999988888777777 PP

                    Spore_permease  88 yFlllaafelRefseliqvflledtpl........wiiilllllvilYlv..vkGieslar...eflfiivilliil 151
                                         ++  af l  f+     ++++++          w++ l l++ + ++v  v G e+ a+   +++ +++ +l+++
  gi|336252635|ref|YP_004595742.1| 134 GLVFATAFYLVGFGY----YAVDTLAEvgvvvgngWVVPLALVFGAGFTVlnVTGTENAAKlqnGIVALLLSILAFF 206
                                       777777777777653....3333333300000111444444444333333113455555554442222222222222 PP

                    Spore_permease 152 ll.....illfslklaeiknlrPvlgngikpvlkslkttslsflgveillllvpflkdkkkvkkaallg.vlistll 222
                                       l       l f+ ++a ++   P    g +pvl  +  +  s+lg+  +  +   ++d+ + +  a++g v+++++l
  gi|336252635|ref|YP_004595742.1| 207 LGfggldALGFVGESATPERFAP---FGAVPVLTTAALVFTSYLGFAQIATVAGEMRDPGRNLPLAMVGsVVVVGVL 280
                                       22111113455555555666555...489*******************************999999997367889** PP

                    Spore_permease 223 yllttlivilvlsveql 239
                                       y+ t++++ ++++ e l
  gi|336252635|ref|YP_004595742.1| 281 YVATIFVATSAFGSERL 297
                                       ************98865 PP

>> AA_permease_C  C-terminus of AA_permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       1.1     5e+03      32      45 ..      55      68 ..      52      72 .. 0.74
   2 ?   -3.3   1.0       2.2     1e+04      30      43 ..     136     149 ..     124     151 .. 0.64
   3 ?   14.5   1.8   6.4e-06     0.029       1      47 [.     424     470 ..     424     473 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                     AA_permease_C 32 fgvwmliglliYfl 45
                                      +g+ ++ig  i+++
  gi|336252635|ref|YP_004595742.1| 55 IGIGTMIGAGIFVF 68
                                      56788888888876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.2
                     AA_permease_C  30 irfgvwmliglliY 43 
                                       + +++  l+g+ +Y
  gi|336252635|ref|YP_004595742.1| 136 VFATAFYLVGFGYY 149
                                       44555667777777 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 6.4e-06
                     AA_permease_C   1 FkvPlvPflPalsIlvNiyLmlqLdsltwirfgvwmliglliYflYg 47 
                                       F+vP +P++Pa++ ++ + L+  ++ ++ +  +++m++    Y++Y 
  gi|336252635|ref|YP_004595742.1| 424 FRVPGYPVVPAAGAVASFGLIGFMQPTSQLIGVAVMVATAGWYVYYA 470
                                       9***********************99998888888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); 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:                         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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3556.71
//
Query:       gi|336252636|ref|YP_004595743.1|  [L=251]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-06   28.5   5.3    7.5e-05   23.3   2.8    2.9  2  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 ?    0.1   0.0      0.06   1.1e+03       5      53 ..       4      51 ..       1      99 [. 0.56
   2 !   23.3   2.8   4.2e-09   7.5e-05       3     141 .]     108     230 ..     106     230 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.06
                                      EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHH CS
                               Usp  5 IlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadee 53
                                      IlV++    e + +    ++l++  + ++   hv+++++++  +     
  gi|336252636|ref|YP_004595743.1|  4 ILVPL-AVLEGESVSPGLVRLLEPADVTVLGYHVLPEQTPPDQARVQYG 51
                                      55555.5555555555556666666777777777776666554443333 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 4.2e-09
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                       +r lV++ g  +++++l + ++l  +r+  ++l  + d++a+g    ++  a+e  +    ++           +  
  gi|336252636|ref|YP_004595743.1| 108 DRLLVPLTGDVAADRVLAFVADLIDDREIGVTLFLATDAEADGRLLLEE--AAETLSSRGIDT-----------EST 171
                                       6889999999999999999999999986665555555555554443333..333333333322...........245 PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        +v    ++g   +++ e  ++   d +VvG r   +l+ ll+G+ +e++++++  pVlvVr
  gi|336252636|ref|YP_004595743.1| 172 LVVSEGALGGRTFDALRE--DAAAHDAVVVGERA-PSLQSLLFGDEAERLAAESVGPVLVVR 230
                                       566666666666666555..4455899*******.**************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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: 0.45u 0.17s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2097.26
//
Query:       gi|336252637|ref|YP_004595744.1|  [L=258]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-06   26.6   5.0    2.2e-05   25.0   4.3    2.0  2  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 ?   -0.4   0.0     0.085   1.5e+03      56     107 ..      56     108 ..      35     112 .. 0.46
   2 !   25.0   4.3   1.2e-09   2.2e-05       5     141 .]     120     241 ..     117     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.085
                                       HHHHHHHHHHHHHHHHHHH.HHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEE CS
                               Usp  56 eeeleleeaeleadaakaa.aeaggvkvevvveegdpaeeilevaeeedadli 107
                                         e+ +++a++e+++ + a ++ag +++   v  +d   +  +va + ++d +
  gi|336252637|ref|YP_004595744.1|  56 AREQFQRRAARELEERCSAfEAAGCPVTSRLVFTHDRFKTFERVAVDAGCDAV 108
                                       22222222222222223330334444444444444445555666666666655 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.2e-09
                                       EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCE CS
                               Usp   5 IlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvk 81 
                                       +lVa+    + ++ ++  +  +++++ + +llhv+ ++++ +++++  ++   +le+++             + + +
  gi|336252637|ref|YP_004595744.1| 120 MLVAIRSDINVEHKARLVATVLEDTDIDATLLHVVGDERDRERGEELLATMATALEDAGL------------DPDRV 184
                                       677776555556667777778888999999999999999999999999999999999997............45789 PP

                                       EEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  82 vevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        + vv++ +p e+il +ae+   d +V G ++  +++r+++ + +e++++++  pVlvVr
  gi|336252637|ref|YP_004595744.1| 185 SRSVVVDDSPTEAILAAAED--HDVLVAGESR-PSIRRYVFRDRAERLAKRTADPVLVVR 241
                                       99999999999999988887..899*******.**************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 2226.43
//
Query:       gi|336252638|ref|YP_004595745.1|  [L=392]
Description: phosphate transporter [Halopiger xanaduensis SH-6]
Scores for 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  137.1  27.4    1.5e-39  136.0  27.4    1.5  1  PHO4      Phosphate transporter family
  ------ inclusion threshold ------
       0.13   12.0   0.5        1.1    9.0   0.1    2.7  2  SpoVS     Stage V sporulation protein S (SpoVS)


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.0  27.4   1.6e-43   1.5e-39       2     312 ..      21     309 ..      20     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 136.0 bits;  conditional E-value: 1.6e-43
                              PHO4   2 GanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselm.lgmlaallgaavwl 77 
                                       G   ++ af+++vg+ a++ + A +l+++f f+Ga+++G +V++ +++++v     d+++++  + + +l+  +v l
  gi|336252638|ref|YP_004595745.1|  21 GGATTGPAFGPAVGADAISKTAAGLLMTVFFFVGAWTIGRRVVDKLGRELV----TDTAIFTlEASVGVLFFIGVAL 93 
                                       55667889******************************************9....3555565359999********* PP

                              PHO4  78 llatvlglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklknal 154
                                       ++ +++g+P+St+++ vG+++G +laa     ++w  +++i++ w++sP++g+ ++ ++   + ++   ++++  ++
  gi|336252638|ref|YP_004595745.1|  94 FIGNFFGVPASTSMTAVGSIAGLGLAA---GELDWAVMGEIAIWWIVSPFIGFWVSLIIGRYFYAAL--NRRIVIER 165
                                       **************************6...469**************************99888882..33444444 PP

                              PHO4 155 ralpvlvlvtiailalsilfkgesk......kddeeteklf.kflqvvsaalvsfahGanDvanaiGpllaalisiy 224
                                          p++++                       +++++ ++l   ++++  +++++++ G +++ana++pl +   ++ 
  gi|336252638|ref|YP_004595745.1| 166 SEGPLFTIDRSR------------AvpipvpSETTNRRELGgVAMVIAIGCVMAYSSGTSNIANAVAPL-VGSGEL- 228
                                       455544222111............11222233334444444389999**********************.544222. PP

                              PHO4 225 kaskevplwvlllgglaialGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgav 301
                                                 +++g++a+++G+l++++r  +t+G+++t+ l  + +++ +++++++v+++s++g+P S+  ++++++
  gi|336252638|ref|YP_004595745.1| 229 -----EMNPAIVIGCFAVGIGTLTIARRTLETMGSELTE-LPLTAAIVTATVSSTLVIFLSAIGIPASFVIIATMCI 299
                                       .....222489***************************5.************************************* PP

                              PHO4 302 vGvGlakkres 312
                                       +G G+ +  ++
  gi|336252638|ref|YP_004595745.1| 300 IGLGWGR-ATR 309
                                       *****99.344 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 ?   -0.5   0.0      0.12   1.1e+03      32      46 ..      32      46 ..      29      74 .. 0.85
   2 ?    9.0   0.1   0.00013       1.1       8      78 ..     209     279 ..     205     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.12
                                      E-SHHHHHHHHHHHH CS
                             SpoVS 32 aiGagAvnqavkAia 46
                                      a+Ga+A++++  ++ 
  gi|336252638|ref|YP_004595745.1| 32 AVGADAISKTAAGLL 46
                                      899999998877665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00013
                                       T--HHHHHHHHHHHHHHTSEEEEEE-SHHHHHHHHHHHHHHHHHHGGGTEEEEEEEEEEEEEETTEEEEEE CS
                             SpoVS   8 ksnpnkvagAiagvlrekgkvevqaiGagAvnqavkAiaiargflapegidlvvvPaFveveidgeerTai 78 
                                       +s ++++a+A+a ++ + +  +  ai +g     +  ++iar+ l++ g++l+  P  + + +   + T +
  gi|336252638|ref|YP_004595745.1| 209 SSGTSNIANAVAPLVGSGELEMNPAIVIGCFAVGIGTLTIARRTLETMGSELTELPLTAAIVTATVSSTLV 279
                                       5778899999999887766555569999999999*******************999988888777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.35
# Mc/sec: 3343.92
//
Query:       gi|336252639|ref|YP_004595746.1|  [L=130]
Description: hypothetical protein Halxa_1234 [Halopiger xanaduensis SH-6]
Scores for 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   15.1   1.3      0.037   14.6   1.3    1.2  1  ATP-cone         ATP cone domain
      0.032   13.7   0.2      0.044   13.3   0.2    1.2  1  DUF2884          Protein of unknown function (DUF2884)
      0.037   14.3   0.2      0.049   13.9   0.2    1.1  1  DUF5082          Domain of unknown function (DUF5082)
       0.12   11.6   0.2       0.14   11.4   0.2    1.0  1  CobD_Cbib        CobD/Cbib protein
       0.17   12.1   1.1       0.37   11.0   0.3    1.8  2  CSN4_RPN5_eIF3a  CSN4/RPN5/eIF3a helix turn helix domain
        1.3    8.6   4.9        1.7    8.2   4.9    1.1  1  GCIP             Grap2 and cyclin-D-interacting


Domain annotation for each model (and alignments):
>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.3   1.2e-05     0.037      12      68 ..      54     114 ..      51     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                       E--HHHHHHHHHHHHHH.-HHHHHHHHHHHHHHH...HHHHIIT-BHHHHHHHHHHHHHHS CS
                          ATP-cone  12 pfdvekIkraiekAceg.seeeideiaeeveaev...rkrlrdgisteeIqdlvektlieh 68 
                                        fd+e  +r +e+ +e+ +e+ i e+++ v++++    +r+++ +  +eI dl+e+t +e 
  gi|336252639|ref|YP_004595746.1|  54 RFDPEWMTREVEATVEEaVEQSIGEQVDAVQDQIetvDERIDRRPREDEIEDLLEETVAED 114
                                       69999999999999999877777777777765554438889999*************9944 PP

>> DUF2884  Protein of unknown function (DUF2884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   1.5e-05     0.044     134     167 ..      60      93 ..      47     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                           DUF2884 134 fdkefeqeieelveesiGsilsalgsemlesegd 167
                                       +++e+e+ +ee+ve+siG+ ++a+ +++ + ++ 
  gi|336252639|ref|YP_004595746.1|  60 MTREVEATVEEAVEQSIGEQVDAVQDQIETVDER 93 
                                       4789**********************99887766 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   1.6e-05     0.049      57     102 ..      56     108 ..      47     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                           DUF5082  57 sesWkGk.eennydgirs.nlessyqtyvdkldelidaie.....eEIerLen 102
                                       + +W  +  e++++++++ ++ +++++++d+++++  +i+     +EIe+L +
  gi|336252639|ref|YP_004595746.1|  56 DPEWMTReVEATVEEAVEqSIGEQVDAVQDQIETVDERIDrrpreDEIEDLLE 108
                                       4578877799999999999********************73332257777655 PP

>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   4.6e-05      0.14      43     143 ..      13     118 ..       3     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.6e-05
                         CobD_Cbib  43 laGvllalllvllallvallllllalaallglvlealllkltlalrsLleevrk.vakalk....gdleaaReavsm 114
                                       ++Gvl+ + +vl+++  + + ++l l  l+ ++l+++  ++ +  + + +ev++ v++a++    ++++a + +++ 
  gi|336252639|ref|YP_004595746.1|  13 AYGVLIFVSVVLIVIEGTRVGVALGLGVLVSYALHVIWKMARFDPEWMTREVEAtVEEAVEqsigEQVDAVQDQIET 89 
                                       4788887777777766444444433333334567777777777777777777775666664122246999******* PP

                         CobD_Cbib 115 iVgRdtseldeeeiarAavEsvaENlsDg 143
                                       + +R  ++  e+ei     E+vaE+++D 
  gi|336252639|ref|YP_004595746.1|  90 VDERIDRRPREDEIEDLLEETVAEDATDD 118
                                       **************************996 PP

>> CSN4_RPN5_eIF3a  CSN4/RPN5/eIF3a helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   0.00012      0.37      20      38 ..      48      66 ..      45      69 .. 0.89
   2 ?   -1.4   0.0      0.92   2.8e+03      11      27 ..      74      90 ..      73      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                   CSN4_RPN5_eIF3a 20 liEKIasaePeWmakalee 38
                                      +i K+a  +PeWm + +e+
  gi|336252639|ref|YP_004595746.1| 48 VIWKMARFDPEWMTREVEA 66
                                      68899************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.92
                   CSN4_RPN5_eIF3a 11 QSLCyQVNeliEKIasa 27
                                      QS+  QV  + + I ++
  gi|336252639|ref|YP_004595746.1| 74 QSIGEQVDAVQDQIETV 90
                                      77777898888888877 PP

>> GCIP  Grap2 and cyclin-D-interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.9   0.00056       1.7     111     162 ..      63     113 ..      58     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00056
                                       TS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....S------------- CS
                              GCIP 111 klpkdNktAilraieevlglvkDaleEmkelleeedeeedededdldddede 162
                                       ++  +  +A+ + i e+++ v+D +e ++e  +  +  ede+ed l++   e
  gi|336252639|ref|YP_004595746.1|  63 EVEATVEEAVEQSIGEQVDAVQDQIETVDERIDR-RPREDEIEDLLEETVAE 113
                                       57778899**************************.56667777776665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1540  (0.0858944); expected 358.6 (0.02)
Passed bias filter:                      971  (0.0541581); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.33
# Mc/sec: 1162.60
//
Query:       gi|336252640|ref|YP_004595747.1|  [L=616]
Description: Citrate transporter [Halopiger xanaduensis SH-6]
Scores for 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  197.6  14.6    4.1e-58  196.9  14.6    1.3  1  CitMHS         Citrate transporter
    6.7e-24   84.8  37.4    2.7e-16   59.7  18.6    3.1  3  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    1.6e-18   66.2   6.6    5.7e-11   42.1   0.9    2.4  2  TrkA_C         TrkA-C domain


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 !  196.9  14.6   6.9e-62   4.1e-58       1     299 [.      32     560 ..      32     561 .. 0.84

  Alignments for each domain:
  == domain 1  score: 196.9 bits;  conditional E-value: 6.9e-62
                                       xxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   1 lvllileklrldvvallvlvll.......vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlagg 70 
                                       lvl+++e+l++dv+a+l++v+l        +++e+ +sg+a+++++++l++ i+++++++tGl++ l+++++ +ag 
  gi|336252640|ref|YP_004595747.1|  32 LVLFLTERLPIDVTAILLIVILvvlepwtGIDPETGISGFANEATITVLAMLILSGGISRTGLVQELGRRMAAFAGD 108
                                       69*******************9*999999999999****************************************** PP

                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  71 krd.llvllvlltallsafvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaarpg 145
                                       +    l+++v++t  +s+f++n++vv++++p+v ++a+r ++++p+ llipl++a++igg+lt+iGt+         
  gi|336252640|ref|YP_004595747.1| 109 SIHrQLFATVAATSPVSGFLNNTPVVALLVPVVTDVANR-GNTSPSkLLIPLSYASQIGGMLTLIGTS--------- 175
                                       **************************************9.9999999*********************......... PP

                                       xxxxxxxx........................xxxxxxxx..xxxxxxxxxxxxxxxxxxxx............... RF
                            CitMHS 146 lslpnlll........................lalllvgl..lplvllfmfgvalalpvnap............... 181
                                          +n+l+                        l++l++++  l+l++++     + lp  +p               
  gi|336252640|ref|YP_004595747.1| 176 ---TNILAsdisgrlgseypelhrfsmfeftqLGALVTLVggLYLIFAG----HYLLPERVPpradyleeydvgnyv 245
                                       ...9999999999999999999999999999955555555226666666....555555555777799999999999 PP

                                       ......................................................xxxxxxxxxxxxxxxxxxx.... RF
                            CitMHS 182 ......................................................kvkkqkaiieaiarsllpv.... 200
                                                                                                               v    
  gi|336252640|ref|YP_004595747.1| 246 advavvpgsplvgesigdataalgpeidvvqvvrdadrsiaprqetrlhegdvlV-----------------Vrtnr 305
                                       9999999999988888888888888888776666666555555555444444441.................15555 PP

                                       ............................................................................. RF
                            CitMHS 201 ............................................................................. 200
                                                                                                                    
  gi|336252640|ref|YP_004595747.1| 306 daitaledaegiepvgqprldgdlsaeegiitelvvsldsrligerldpeafreefdaavlglrhrgeliaerivgt 382
                                       55555666666677788888888888888888888888888888888888888888888888888888888888888 PP

                                       ....................................................................xxxxxxx.. RF
                            CitMHS 201 ....................................................................atillla.. 207
                                                                                                           a        
  gi|336252640|ref|YP_004595747.1| 383 rlgvgdtllvqaapetlerlsrrddvivarepsqpdyradkapvavaimigvvavaaleiypilisalA-----Gvv 454
                                       999998888888888888999999999999999999999999999988877777666666666666663.....044 PP

                                       .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.x..xxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 208 .............ykkveWsvlllfaGvfllvgaleqtGilealadll.ga.g..gplvalalvlgliallsafisn 267
                                                    y++veW++++l+aGv++l+ ale++G + +la ++ ++ +  + +++l+l++ l+all+++isn
  gi|336252640|ref|YP_004595747.1| 455 amvvtgvldanelYDAVEWDIIFLLAGVIPLGIALEESGGAALLAFAVvETaSvlPTIAVLWLFYMLTALLTNVISN 531
                                       4447789********************************9999996663446345777777999************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 268 vavaalmapialgmapalgllspsplalalav 299
                                       +a ++l++p+a+++a+++g   ++p+a++lav
  gi|336252640|ref|YP_004595747.1| 532 NASVVLLIPVAAAAAAGIG---ANPFAFVLAV 560
                                       *************999999...********98 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   4.8   6.2e-10   3.7e-06      20     130 ..      10     120 ..       1     125 [. 0.86
   2 !    8.8   0.3   0.00012      0.72     378     459 ..     127     218 ..     123     224 .. 0.73
   3 !   59.7  18.6   4.5e-20   2.7e-16     296     466 ..     448     614 ..     424     616 .] 0.95

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.2e-10
                     Na_sulph_symp  20 lPapd.gleskawrllaifiaaivglileplplavialialsllavligvlaakalsevlsgfssdttlLvfaalli 95 
                                        Pa +  l++ a ++++++++a v + +e lp  v+a++ + +l+vl  ++     ++ +sgf +++t+ v+a l++
  gi|336252640|ref|YP_004595747.1|  10 EPAAQpALTTDALVVFGVVLVALVLFLTERLPIDVTAILLIVILVVLEPWTG-IDPETGISGFANEATITVLAMLIL 85 
                                       5554325889999**********************************99999.8889******************** PP

                     Na_sulph_symp  96 aaavektgLgkRiAlvlvkivGkrtliLgyalvla 130
                                       + ++  tgL + +  ++  + G +  +  +a+v+a
  gi|336252640|ref|YP_004595747.1|  86 SGGISRTGLVQELGRRMAAFAGDSIHRQLFATVAA 120
                                       ********988888888888888887777777765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00012
                     Na_sulph_symp 378 faSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpiv......fgagy.....lkvkdy 443
                                       f  +t  +a l+p++  va+      p  + ++l  a+ ++g+l+ ++t+ n ++      +g++y     +++ ++
  gi|336252640|ref|YP_004595747.1| 127 FLNNTPVVALLVPVVTDVANRG-NTSPSKLLIPLSYASQIGGMLTLIGTSTNILAsdisgrLGSEYpelhrFSMFEF 202
                                       6678999*************99.7779999*********************99863333335555522222444556 PP

                     Na_sulph_symp 444 wrlGfilsiigllill 459
                                        +lG++++++g l l+
  gi|336252640|ref|YP_004595747.1| 203 TQLGALVTLVGGLYLI 218
                                       6677777776655555 PP

  == domain 3  score: 59.7 bits;  conditional E-value: 4.5e-20
                     Na_sulph_symp 296 vaivvlvillllrvldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfv 372
                                        a+ ++v ++++ vld +  + +   W++++ll+g+i l   le+sg    l+ +++ + s + p++a++ ++ ++ 
  gi|336252640|ref|YP_004595747.1| 448 SALAGVVAMVVTGVLDAN-ELYDAVEWDIIFLLAGVIPLGIALEESGGAALLAFAVVETAS-VLPTIAVLWLFYMLT 522
                                       5788999999******99.788899********************************9999.99************* PP

                     Na_sulph_symp 373 lvhylfaSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGfi 449
                                       ++ +   S+ A ++ l+p+ +a+a +i ga+p  ++l++++a s a fl p++   n  v+g g     dy+r+G++
  gi|336252640|ref|YP_004595747.1| 523 ALLTNVISNNASVVLLIPVAAAAAAGI-GANPFAFVLAVTFAASTA-FLGPIGYQTNLFVYGPGGYRFTDYARIGAP 597
                                       ***************************.******************.****************************** PP

                     Na_sulph_symp 450 lsiigllillllgalww 466
                                       l++i  ++ +l +a +w
  gi|336252640|ref|YP_004595747.1| 598 LQLILSVVTVLGIAFFW 614
                                       ******99999999999 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.9   9.6e-15   5.7e-11       1      66 [.     245     312 ..     245     315 .. 0.91
   2 !   26.9   0.6   5.2e-10   3.1e-06       2      67 ..     337     404 ..     336     406 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 9.6e-15
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelr 66 
                                       ++ v+v +gsplvG +++++       + vv ++R+ ++ i p+ +t+L+eGDvl+v ++++++ +l+
  gi|336252640|ref|YP_004595747.1| 245 VADVAVVPGSPLVGESIGDATAALGpEIDVVQVVRDaDRSIAPRQETRLHEGDVLVVRTNRDAITALE 312
                                       57899**************6655559*************************************98876 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 5.2e-10
                                       EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T-EEES--T.T-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRggeliipsg.dtvLeeGDvllvvgspsdlaelre 67 
                                       +e++v+ +s+l+G +l+   +r++ ++ v+++r++geli  +   t+L  GD+llv + p++l++l +
  gi|336252640|ref|YP_004595747.1| 337 TELVVSLDSRLIGERLDPEAFREEfDAAVLGLRHRGELIAERIvGTRLGVGDTLLVQAAPETLERLSR 404
                                       799*****************************999899999999********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); 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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4335.91
//
Query:       gi|336252641|ref|YP_004595748.1|  [L=249]
Description: 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino) imidazole-4-carboxamide isomerase [Halopiger xanaduensis SH-6]
Scores for 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-78  264.0   4.0    1.1e-78  263.8   4.0    1.0  1  His_biosynth     Histidine biosynthesis protein
    9.9e-13   47.8   0.1    5.1e-06   25.8   0.0    2.1  2  Dus              Dihydrouridine synthase (Dus)
      5e-12   45.6   0.6    4.2e-08   32.8   0.1    2.1  2  DHO_dh           Dihydroorotate dehydrogenase
    1.3e-10   41.0   6.1    5.9e-05   22.5   0.3    2.1  2  ThiG             Thiazole biosynthesis protein ThiG
    5.7e-08   31.9   1.3    0.00099   18.0   0.2    2.2  2  Trp_syntA        Tryptophan synthase alpha chain
      2e-07   30.7  13.5    1.5e-05   24.6   4.8    2.1  2  NMO              Nitronate monooxygenase
    5.7e-06   25.6   2.0     0.0016   17.5   0.3    2.2  2  IMPDH            IMP dehydrogenase / GMP reductase domain
    5.7e-06   25.7   1.0     0.0013   18.0   0.0    3.3  4  IGPS             Indole-3-glycerol phosphate synthase
    1.2e-05   24.9   5.1     0.0088   15.5   0.3    2.3  2  PcrB             PcrB family
    3.2e-05   23.2   3.2     0.0077   15.4   0.5    2.6  3  NanE             Putative N-acetylmannosamine-6-phosphate epi
    3.5e-05   23.3   1.2      0.002   17.5   0.1    2.2  2  G3P_antiterm     Glycerol-3-phosphate responsive antiterminat
      9e-05   21.9   3.6     0.0033   16.8   0.7    2.2  2  TMP-TENI         Thiamine monophosphate synthase
     0.0028   17.7   4.3        0.6   10.2   0.1    2.6  2  B12-binding      B12 binding domain
     0.0058   15.7  10.8      0.042   12.9   2.1    2.1  2  FMN_dh           FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.096   12.5   0.0         16    5.4   0.0    2.9  3  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
       0.13   12.5   0.0       0.25   11.6   0.0    1.4  1  TBP-binding      TATA box-binding protein binding
       0.17   11.3   1.4       0.43    9.9   0.1    2.2  2  Ribul_P_3_epim   Ribulose-phosphate 3 epimerase family
        5.1    7.5   8.3         14    6.1   2.4    2.8  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain


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 !  263.8   4.0   1.1e-81   1.1e-78       1     229 []      10     235 ..      10     235 .. 0.98

  Alignments for each domain:
  == domain 1  score: 263.8 bits;  conditional E-value: 1.1e-81
                                       EEEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEE CS
                      His_biosynth   1 riipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvq 77 
                                       ++ipa+D++dG+vV+lv+G+r +e+  +gdpve+a+r+ ++ga+ lh+vDld+a+eg++an d++e ++e+v++p q
  gi|336252641|ref|YP_004595748.1|  10 EVIPAVDVQDGEVVQLVQGERGTEK-TYGDPVEAARRWIDAGAESLHLVDLDGAFEGQRANADAIEGVLEAVDVPTQ 85 
                                       59*******************6655.569************************************************ PP

                                       EESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHH CS
                      His_biosynth  78 vGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelak 154
                                       +GGGIr+ ed++ lle+g+d+vi+gtaav+npe+++e++e++++ ++vv++Da++g +v+++gw+e  g+++ve a+
  gi|336252641|ref|YP_004595748.1|  86 LGGGIRTAEDAAGLLERGVDRVILGTAAVENPEIVREISEEYPD-SVVVSLDAKDG-EVVVEGWTEGAGVSPVEAAE 160
                                       ********************************************.***********.******************** PP

                                       HHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS- CS
                      His_biosynth 155 kleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegelt 229
                                       ++e+lga++il+t++d +G l+G+  e ++el ea++ipviasGGv++led+++l++ g++av+vgsalyeg++t
  gi|336252641|ref|YP_004595748.1| 161 RYEDLGAAAILFTNVDVEGQLEGVATEPVRELVEATDIPVIASGGVATLEDVRALAEGGAAAVVVGSALYEGNFT 235
                                       ************************************************************************986 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   5.1e-09   5.1e-06     165     226 ..      62     124 ..      29     139 .. 0.82
   2 !   20.3   0.0   2.4e-07   0.00024     173     229 ..     187     243 ..     154     249 .] 0.80

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.1e-09
                                       TT-C.G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.H CS
                               Dus 165 nyeg.tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.s 226
                                        +eg +a+ +aI+ v +av +p    G+I++aeda   le+ G+d v+ g +a +nP +++e s
  gi|336252641|ref|YP_004595748.1|  62 AFEGqRANADAIEGVLEAVDVPTQLGGGIRTAEDAAGLLER-GVDRVILGTAAVENPEIVREiS 124
                                       456669**********************************9.*****************98644 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 2.4e-07
                                       HHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHH CS
                               Dus 173 eaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.stav 229
                                       e ++e+ +a  ipvia G++ ++ed++a  e  Ga +v++g + ++  + ++e ++av
  gi|336252641|ref|YP_004595748.1| 187 EPVRELVEATDIPVIASGGVATLEDVRALAEG-GAAAVVVGSALYEGNFTLEEaQAAV 243
                                       6689999999****************876555.**********999887777744444 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00014      0.14     250     291 ..      87     127 ..      69     131 .. 0.89
   2 !   32.8   0.1   4.2e-11   4.2e-08     226     286 ..     181     238 ..     178     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                       ESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHH CS
                            DHO_dh 250 vGGiesgeDalekieaGAslvqvytalvfegpkiakkikkel 291
                                        GGi ++eDa   +e G   v ++ta   e+p i+++i +e 
  gi|336252641|ref|YP_004595748.1|  87 GGGIRTAEDAAGLLERGVDRVILGTAA-VENPEIVREISEEY 127
                                       59************************9.89********9986 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 4.2e-11
                                       GHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHH CS
                            DHO_dh 226 lkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakk 286
                                       l  +a++ +rel + ++  ip+I++GG+ + eD+   +e GA++v v++al +eg +  ++
  gi|336252641|ref|YP_004595748.1| 181 LEGVATEPVRELVEATD--IPVIASGGVATLEDVRALAEGGAAAVVVGSAL-YEGNFTLEE 238
                                       6679*************..********************************.999987765 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.3   5.9e-08   5.9e-05     133     213 ..      38     119 ..      32     125 .. 0.85
   2 !   21.2   1.2   1.4e-07   0.00014     136     217 ..     158     239 ..     127     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.9e-08
                                       -HH.HHHHHHHTT-SEBEEBSSSTTS----S.-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHH CS
                              ThiG 133 Dlv.larrleevGcaavmPlaapiGsglGll.nkealkiiieeakvPvivDAGigspsdaaqamelGadavllntav 207
                                       D+v +arr  ++G++++  l    G+ +G + n+ a++ ++e ++vP  +  Gi++++daa  +e G+d v+l ta 
  gi|336252641|ref|YP_004595748.1|  38 DPVeAARRWIDAGAESL-HLVDLDGAFEGQRaNADAIEGVLEAVDVPTQLGGGIRTAEDAAGLLERGVDRVILGTAA 113
                                       55526799999999987.477788998997527889***************************************98 PP

                                       HTSSSH CS
                              ThiG 208 aeakdp 213
                                        e  ++
  gi|336252641|ref|YP_004595748.1| 114 VENPEI 119
                                       776665 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSS CS
                              ThiG 136 larrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakd 212
                                       +a+r e++G+aa++     +   l  +++e ++ ++e +++Pvi   G+ + +d+ +  e Ga av++ +a+ e + 
  gi|336252641|ref|YP_004595748.1| 158 AAERYEDLGAAAILFTNVDVEGQLEGVATEPVRELVEATDIPVIASGGVATLEDVRALAEGGAAAVVVGSALYEGNF 234
                                       799***********999998666655667889***************************************987765 PP

                                       HHHHH CS
                              ThiG 213 pvamA 217
                                         + A
  gi|336252641|ref|YP_004595748.1| 235 TLEEA 239
                                       55555 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   3.9e-05     0.039     188     233 ..      71     117 ..      63     140 .. 0.85
   2 !   18.0   0.2   9.9e-07   0.00099     188     230 ..     187     230 ..     176     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.9e-05
                                       HHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHH CS
                         Trp_syntA 188 elverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkki 233
                                       +++e + ++ +vP+ +G Gi+t+e+++ +  ++ d vi G a v++ 
  gi|336252641|ref|YP_004595748.1|  71 DAIEGVLEAVDVPTQLGGGIRTAEDAAGLLeRGVDRVILGTAAVENP 117
                                       57888889999*****************9999**********99864 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 9.9e-07
                                       HHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHH CS
                         Trp_syntA 188 elverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalv 230
                                       e v++l ++t+ Pv    G++t e+v+++a  +a++v+vGSal 
  gi|336252641|ref|YP_004595748.1| 187 EPVRELVEATDIPVIASGGVATLEDVRALAeGGAAAVVVGSALY 230
                                       679999************************899*********85 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   1.6   0.00014      0.14     183     224 ..      71     112 ..      40     119 .. 0.88
   2 !   24.6   4.8   1.5e-08   1.5e-05     146     225 ..     156     229 ..     113     233 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                               NMO 183 aLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                         ++ vl+avd+P    GGi ++++ a  L +G   v +gt+
  gi|336252641|ref|YP_004595748.1|  71 DAIEGVLEAVDVPTQLGGGIRTAEDAAGLLERGVDRVILGTA 112
                                       567889***********************************8 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.5e-08
                               NMO 146 vkearkvearGaDalivqGpe.aGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqi 221
                                       v++a   e +Ga a+  +  + +G  +G   v     ++ v + ++a diPviA GG+ + ++v a    GA++v +
  gi|336252641|ref|YP_004595748.1| 156 VEAAERYEDLGAAAILFTNVDvEGQLEG---V----ATEPVRELVEATDIPVIASGGVATLEDVRALAEGGAAAVVV 225
                                       5555555555555555554441222333...2....2345677899******************************* PP

                               NMO 222 gtrf 225
                                       g+++
  gi|336252641|ref|YP_004595748.1| 226 GSAL 229
                                       *997 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0015       1.5     110     173 ..      44     110 ..      29     123 .. 0.69
   2 !   17.5   0.3   1.6e-06    0.0016     194     239 ..     184     229 ..     146     240 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
                                       HHHHHTT-SEEE...EE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE- CS
                                       xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 110 kalveagvdvlv...vdsahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvG 173
                                       ++ ++ag++ l    +d a   ++   +a++ + ++v+  + ++G + tae a+ L+e g+d v  G
  gi|336252641|ref|YP_004595748.1|  44 RRWIDAGAESLHlvdLDGAFEGQRANADAIEGVLEAVDVPTQLGGGIRTAEDAAGLLERGVDRVILG 110
                                       5555555554431114555555556667777777777545567999999999999999999988776 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHT.T-SEEEESCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                             IMPDH 194 tAvaevaeaakkagvpviaDGGikysgdivkAlaa.GadavmlGsll 239
                                        A   v e ++ +++pvia GG+ + +d+ +Ala  Ga av++Gs l
  gi|336252641|ref|YP_004595748.1| 184 VATEPVRELVEATDIPVIASGGVATLEDV-RALAEgGAAAVVVGSAL 229
                                       34445666677777777777777777775.56664256777777765 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.8     8e+02      69     110 ..      38      82 ..      31      88 .. 0.71
   2 ?    3.3   0.0      0.04        40     217     251 ..      89     123 ..      85     125 .. 0.89
   3 ?   -0.2   0.0      0.45   4.5e+02      68      85 ..     153     170 ..     150     182 .. 0.85
   4 !   18.0   0.0   1.3e-06    0.0013     202     244 ..     189     232 ..     180     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.8
                                       -HHHHHHHHTTT.-SEEEEE--CCCC---C...CHHHHHHHH-SS CS
                              IGPS  69 dpaeiAkkyeeagAsaiSVLteekyFqGsl...edLrevrqavsl 110
                                       dp+e A+ + +agA+ +        F+G+    + ++ v +av++
  gi|336252641|ref|YP_004595748.1|  38 DPVEAARRWIDAGAESLHLVDLDGAFEGQRanaDAIEGVLEAVDV 82 
                                       789999999999999998877778898875111344445555555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.04
                                       SS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHH CS
                              IGPS 217 GiktredveklkeegvnafLvGeslmrqedvekai 251
                                       Gi+t+ed+  l e gv+ ++ G++ +++++  ++i
  gi|336252641|ref|YP_004595748.1|  89 GIRTAEDAAGLLERGVDRVILGTAAVENPEIVREI 123
                                       9***********************99998876665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.45
                                       --HHHHHHHHTTT.-SEE CS
                              IGPS  68 fdpaeiAkkyeeagAsai 85 
                                       + p+e A+ ye+ gA+ai
  gi|336252641|ref|YP_004595748.1| 153 VSPVEAAERYEDLGAAAI 170
                                       568999999999999998 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 1.3e-06
                                       HCHCC-.TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC- CS
                              IGPS 202 Laklvp.kdvllvaeSGiktredveklkeegvnafLvGeslmrq 244
                                       +++lv+ +d+ ++a  G++t edv++l+e g+ a+ vG++l + 
  gi|336252641|ref|YP_004595748.1| 189 VRELVEaTDIPVIASGGVATLEDVRALAEGGAAAVVVGSALYEG 232
                                       45555535699*****************************9765 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   8.8e-06    0.0088     185     223 ..      86     124 ..      56     127 .. 0.81
   2 !   11.3   0.5   0.00017      0.17     171     215 ..     189     233 ..     169     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.8e-06
                                       EESS--SHHHHHHHHCC.SSEEEE-CHHHHHHHCHHHHHH CS
                              PcrB 185 vGGGirsaEkAkevvea.ADvivvGnvveekderkidail 223
                                        GGGir aE+A+  +e   D ++ G++  e++ + +++i 
  gi|336252641|ref|YP_004595748.1|  86 LGGGIRTAEDAAGLLERgVDRVILGTAAVENP-EIVREIS 124
                                       7****************9*********99999.5566665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00017
                                       HHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH CS
                              PcrB 171 vialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd 215
                                       v +l+   +++ +i  GG+   E+ +  +e  A ++vvG +++e +
  gi|336252641|ref|YP_004595748.1| 189 VRELVE-ATDIPVIASGGVATLEDVRALAEGgAAAVVVGSALYEGN 233
                                       444443.5678999****************99***********976 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 !    7.6   0.1     0.002         2     145     185 ..      82     122 ..      64     131 .. 0.83
   2 ?   -1.0   0.0      0.83   8.3e+02     138     170 ..     133     170 ..     120     178 .. 0.58
   3 !   15.4   0.5   7.7e-06    0.0077     137     176 ..     189     229 ..     153     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.002
                                       --EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHH CS
                              NanE 145 lkviaeGrintPekakkaieiGvdavvvGsaitrleeiakk 185
                                       + +   G i t e a+  +e Gvd v++G+a     ei++ 
  gi|336252641|ref|YP_004595748.1|  82 VPTQLGGGIRTAEDAAGLLERGVDRVILGTAAVENPEIVRE 122
                                       555667999*********************99888888765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.83
                                       HHHHHTT--EEEES---....SHHHHHH.HHTT--SEE CS
                              NanE 138 kalseaglkviaeGrin....tPekakk.aieiGvdav 170
                                        +l +++ +v++eG  +    +P +a++   ++G++a+
  gi|336252641|ref|YP_004595748.1| 133 VSLDAKDGEVVVEGWTEgagvSPVEAAErYEDLGAAAI 170
                                       44555555666665544222278766551556888877 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 7.7e-06
                                       HHHHHHT.T--EEEES---SHHHHHHHHTT--SEEEE-HHH CS
                              NanE 137 vkalsea.glkviaeGrintPekakkaieiGvdavvvGsai 176
                                       v++l+ea ++ via G + t e  +   e G++avvvGsa+
  gi|336252641|ref|YP_004595748.1| 189 VRELVEAtDIPVIASGGVATLEDVRALAEGGAAAVVVGSAL 229
                                       67777763799*****************************8 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 ?    4.5   0.1     0.021        21     130     167 ..      72     109 ..      68     114 .. 0.87
   2 !   17.5   0.1     2e-06     0.002     125     168 ..     183     226 ..     169     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.021
                                       HHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                      G3P_antiterm 130 vikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                        i+ + +++++p   GG i+t ed   +l+ G++ v  
  gi|336252641|ref|YP_004595748.1|  72 AIEGVLEAVDVPTQLGGGIRTAEDAAGLLERGVDRVIL 109
                                       678889999************************99865 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2e-06
                                       GGGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                      G3P_antiterm 125 glvpkvikeikkelkipiiaGGLietkedveealkaGaiavsts 168
                                       g++ + ++e+ ++++ip+ia+G + t edv+++ + Ga av ++
  gi|336252641|ref|YP_004595748.1| 183 GVATEPVRELVEATDIPVIASGGVATLEDVRALAEGGAAAVVVG 226
                                       677788999*******************************9875 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.1    0.0072       7.2     138     177 ..      69     109 ..      63     113 .. 0.83
   2 !   16.8   0.7   3.3e-06    0.0033     107     181 .]     157     229 ..     141     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0072
                          TMP-TENI 138 gleglkelaealeiPvvaiGGit.lenvaevleagadgvav 177
                                       + + ++ + ea+ +P+   GGi+ +e++a +le g+d+v +
  gi|336252641|ref|YP_004595748.1|  69 NADAIEGVLEAVDVPTQLGGGIRtAEDAAGLLERGVDRVIL 109
                                       6677888999************62679999*******9976 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.3e-06
                          TMP-TENI 107 eeaeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGi.tlenvaevleagadgvavvsai 181
                                       e ae+ e+lga  i +  +   d   + e +  e ++el+ea+ iPv+a GG+ tle+v +++e ga+ v v sa+
  gi|336252641|ref|YP_004595748.1| 157 EAAERYEDLGAAAILFTNV---DVEGQLEGVATEPVRELVEATDIPVIASGGVaTLEDVRALAEGGAAAVVVGSAL 229
                                       5566666666666666665...55555577888999****************9578****************9985 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1    0.0006       0.6      21      59 ..      97     135 ..      89     142 .. 0.82
   2 !    7.7   1.3    0.0034       3.4      38     112 ..     153     227 ..     141     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0006
                       B12-binding  21 aaalrdagfeVqll.ganvenedivaairaekpdvvglSa 59 
                                       a+ l++ g++ ++l  a ven++iv++i +e pd v++S+
  gi|336252641|ref|YP_004595748.1|  97 AGLLER-GVDRVILgTAAVENPEIVREISEEYPDSVVVSL 135
                                       455666.77555552678899*****************97 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0034
                       B12-binding  38 venedivaairaekpdvvglSal.ltsqleav.kelvellkrirprvkvvvGGahpsldpeetleaklgiddvvvge 112
                                       v++ + +++ +++ + +++++ + +  qle+v +e v++l ++  +++v++ G +++l   + l++  g++ vvvg 
  gi|336252641|ref|YP_004595748.1| 153 VSPVEAAERYEDLGAAAILFTNVdVEGQLEGVaTEPVRELVEA-TDIPVIASGGVATLEDVRALAE-GGAAAVVVGS 227
                                       6667778888888888888888777888888767778887676.689******9*9****999988.999****997 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   1.7    0.0014       1.4     228     302 ..      41     112 ..      39     116 .. 0.85
   2 !   12.9   2.1   4.2e-05     0.042     223     310 ..     152     236 ..     151     243 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0014
                                       HHHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
                            FMN_dh 228 edakraveaGvdgivvSNHGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRp 302
                                       e a+r ++aG++ + + +  G  ++g  a  d++  + eav+  ++  + gGir+ +D++  l  G d v+lG +
  gi|336252641|ref|YP_004595748.1|  41 EAARRWIDAGAESLHLVDLDG-AFEGQRANADAIEGVLEAVD--VPTQLGGGIRTAEDAAGLLERGVDRVILGTA 112
                                       667788888888888888777.78999999999999999997..999999*********9999999999999976 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.2e-05
                                       EE-SHHHHHHHHHTTESEEEE--GGGT.SSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEE CS
                            FMN_dh 223 GvltaedakraveaGvdgivvSNHGGR.qldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavl 298
                                       Gv  +e a+r  ++G+ +i+  N     ql+g+  + +   e+vea +  i+v+++gG+ + +Dv      GA av+
  gi|336252641|ref|YP_004595748.1| 152 GVSPVEAAERYEDLGAAAILFTNVDVEgQLEGV--ATEPVRELVEATD--IPVIASGGVATLEDVRALAEGGAAAVV 224
                                       677778888888888888888886543155554..3355667777775..**************96555578999** PP

                                       ESHHHHHHHHHH CS
                            FMN_dh 299 lGRpflyglaag 310
                                       +G ++  g+ + 
  gi|336252641|ref|YP_004595748.1| 225 VGSALYEGNFTL 236
                                       *99887776655 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 ?    5.4   0.0     0.016        16      12      26 ..      41      55 ..      37      61 .. 0.89
   2 ?   -2.9   0.0       6.1   6.1e+03      21      28 ..      89      96 ..      88      98 .. 0.81
   3 ?    3.8   0.0     0.052        52      21      31 ..     205     218 ..     201     240 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.016
                   DNA_pol_lambd_f 12 ktAkkwyakGirtle 26
                                      ++A++w+++G  +l 
  gi|336252641|ref|YP_004595748.1| 41 EAARRWIDAGAESLH 55
                                      57**********995 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.1
                   DNA_pol_lambd_f 21 Girtledl 28
                                      Girt ed+
  gi|336252641|ref|YP_004595748.1| 89 GIRTAEDA 96
                                      89998886 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.052
                   DNA_pol_lambd_f  21 Girtledlra...k 31 
                                       G+ tled+ra   +
  gi|336252641|ref|YP_004595748.1| 205 GVATLEDVRAlaeG 218
                                       999******95541 PP

>> TBP-binding  TATA box-binding protein binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00025      0.25       9      29 ..     163     183 ..     156     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                       TBP-binding   9 sgldLtGfLFGNIdesGqLed 29 
                                       ++l  + +LF N+d +GqLe+
  gi|336252641|ref|YP_004595748.1| 163 EDLGAAAILFTNVDVEGQLEG 183
                                       6777899************95 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 ?   -0.2   0.1      0.57   5.7e+02     165     196 ..      80     112 ..      62     114 .. 0.78
   2 ?    9.9   0.1   0.00043      0.43     156     198 .]     189     230 ..     161     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.57
                                       ---EEEEESS--T.TTCHHHHHHT--EEEESHH CS
                    Ribul_P_3_epim 165 ldlkievDGGvkl.dnieqiaeagadvlVagsa 196
                                       +d+  +  GG+++ + ++ + e g+d ++ g+a
  gi|336252641|ref|YP_004595748.1|  80 VDVPTQLGGGIRTaEDAAGLLERGVDRVILGTA 112
                                       45666778999752678899999**99999987 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00043
                                       HHHHHHHHT---EEEEESS-.-TTTCHHHHHHT--EEEESHHHH CS
                    Ribul_P_3_epim 156 vrklidekeldlkievDGGv.kldnieqiaeagadvlVagsavf 198
                                       vr+l+++  +d+ + + GGv +l+ ++++ae ga ++V+gsa++
  gi|336252641|ref|YP_004595748.1| 189 VRELVEA--TDIPVIASGGVaTLEDVRALAEGGAAAVVVGSALY 230
                                       6666665..8999999***945799*****************97 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 ?    4.2   0.1     0.054        53       2      28 ..      87     113 ..      86     145 .. 0.72
   2 ?    6.1   2.4     0.014        14       2      64 ..     150     216 ..     149     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.054
                   Glyco_trans_4_4   2 GigryvaelaraLaarGheVtvltpap 28 
                                       G+g+++ae a++L +rG++ ++l +a+
  gi|336252641|ref|YP_004595748.1|  87 GGGIRTAEDAAGLLERGVDRVILGTAA 113
                                       899***************766554333 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.014
                   Glyco_trans_4_4   2 GigryvaelaraLaarGheVtvltpapapg.....apeleedgvrvhrlpvprrpspladlaalralr 64 
                                       G+g+   e a++++++G+   ++t  + +g     a e +++ v+ + +pv +++ ++a+l+ +ral+
  gi|336252641|ref|YP_004595748.1| 150 GAGVSPVEAAERYEDLGAAAILFTNVDVEGqlegvATEPVRELVEATDIPVIASG-GVATLEDVRALA 216
                                       7788888999999999999999995555552222244577889999999999886.677777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 1778.62
//
Query:       gi|336252642|ref|YP_004595749.1|  [L=410]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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  119.1  56.5    1.9e-21   76.4  26.3    2.0  2  MFS_1     Major Facilitator Superfamily


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 !   47.5  23.6   6.3e-17   1.1e-12       3     194 ..      13     214 ..      11     226 .. 0.76
   2 !   76.4  26.3   1.1e-25   1.9e-21       6     167 ..     225     387 ..     221     407 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 6.3e-17
                             MFS_1   3 laaflsalarsilgpalplalaedlgispse..........igllltlyalgaavaslplGrlsdrfGrrr.vlllg 68 
                                        ++f + ++  +l+p +  +l e+lg+++s+            + l++ ++++++++ ++G  sd  Grr  ++++g
  gi|336252642|ref|YP_004595749.1|  13 AVVFAVLFSQLLLYPGVA-TLVETLGADASTsafaatpldaSMWFLVAEFAAYVAFVGVWGMASDVTGRRTpFIVAG 88 
                                       567788888888888888.89999885555544444444435557777999********************999999 PP

                             MFS_1  69 lllfalg.lllllfa....sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpll 140
                                        l+ a+g ++l++++    +++  +l+lr++qG+++ ++f++ ++++ d+  +  +gr +g ++++++lGa++g+++
  gi|336252642|ref|YP_004595749.1|  89 SLAGAVGyAALAAVPaigsIPFEGVLLLRLFQGAMTIGAFSLTMTMLMDLDGG--HGRNMGAAGIAIGLGAAIGAPV 163
                                       999999954444432454444446*************************9988..********************** PP

                             MFS_1 141 ggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpa 194
                                       gg l+  +   a+ +++a+++++++ +  + l e+++++++ + + +++g+ ++
  gi|336252642|ref|YP_004595749.1| 164 GGQLT-EVDPIAPLVVAAGLLVVVGAV--VSLIEDRTPSQKRTARALLEGVRRR 214
                                       *****.667778888888888888775..5665666666555555553333333 PP

  == domain 2  score: 76.4 bits;  conditional E-value: 1.1e-25
                             MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                       f+  +++++++++ +l+ ++ +g+++ + glll+++++ +a++++p+G+lsdr+Gr   +++g +++++g+l+l+ a
  gi|336252642|ref|YP_004595749.1| 225 FVDRMTAGFFALVGTLYFQDVFGVDAGTTGLLLACFFAPFALLQYPMGALSDRIGRTIPIVVGSICYGVGILALSAA 301
                                       566666777777777799****************************************************5555544 PP

                             MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                       +++ + +v+ v  G+ ++++ p+ +al++d++ + erg+a++ ++++ slG++ g+l+gg +as++g+ ++f+++++
  gi|336252642|ref|YP_004595749.1| 302 PTVATAAVGMVGIGVLGALVSPTTMALVTDLADEGERGLAMAGFNLAGSLGFLGGYLIGGTVASNYGYGLSFLVVGG 378
                                       77779************************************************************************ PP

                             MFS_1 160 vsllafv.l 167
                                       + +  +v  
  gi|336252642|ref|YP_004595749.1| 379 LEIAIAVvT 387
                                       *99998842 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.24s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3032.55
//
Query:       gi|336252643|ref|YP_004595750.1|  [L=167]
Description: blue (type 1) copper domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   31.9   0.0    2.3e-07   31.2   0.0    1.4  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
     0.0086   15.9   7.5      0.012   15.4   7.5    1.2  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
  ------ inclusion threshold ------
      0.011   16.3   0.8      0.011   16.3   0.8    1.7  2  Secretin_N_2  Secretin N-terminal domain


Domain annotation for each model (and alignments):
>> 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 !   31.2   0.0   3.8e-11   2.3e-07      26      99 .]      98     167 .]      79     167 .] 0.76

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 3.8e-11
                                       EEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEE.EEEEETTTTTTTSEEEEEEE CS
                       Copper-bind  26 kvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagt.YkffCsPHaaagMkgkvtve 99 
                                       ++ + + ++  HN++l +d+ +  +  +  + ++e     +G+++ ++f+++ +  +++C+PH a+ M+g+++ve
  gi|336252643|ref|YP_004595750.1|  98 TIGWPQGDGGTHNIELRNDSGDVVEGYETETTNEE----EPGDSQMIEFEATSEiVEYVCQPHEAQ-MVGEIQVE 167
                                       34455558999*******99654444444444434....59*********77777*********99.*****996 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   7.5     2e-06     0.012       2      25 ..       7      30 ..       6      31 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      +SRR  LK ++Aaa  a+++gc++
  gi|336252643|ref|YP_004595750.1|  7 VSRRKALKVTGAAATTALVAGCGG 30
                                      7*********************98 PP

>> Secretin_N_2  Secretin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   0.8   1.8e-06     0.011      29      73 ..      31      76 ..      12      79 .. 0.59
   2 ?   -1.7   0.1      0.75   4.5e+03      57      65 ..     122     130 ..     103     148 .. 0.50

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-06
                      Secretin_N_2 29 sgsssssssssssssgsssssssssnss..sgtkietesesdfwgeL 73
                                       g++++++++++  s++s+++++ss ++   gt+ie + ++  w+ +
  gi|336252643|ref|YP_004595750.1| 31 GGNGNGNGNGNG-DSNDSGNGGGSSGTEiePGTTIELDAQTTEWTGI 76
                                      333333333333.2444444444444448899****99999999987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.75
                      Secretin_N_2  57 sgtkietes 65 
                                       +g ++et++
  gi|336252643|ref|YP_004595750.1| 122 EGYETETTN 130
                                       333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); 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:                         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 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1251.59
//
Query:       gi|336252644|ref|YP_004595751.1|  [L=373]
Description: Alanine--glyoxylate transaminase [Halopiger xanaduensis SH-6]
Scores for 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-29  100.6   0.0    1.1e-28  100.3   0.0    1.1  1  Aminotran_5    Aminotransferase class-V
  ------ inclusion threshold ------
       0.02   13.3   0.1       0.14   10.6   0.0    2.0  2  Glyco_hydro_1  Glycosyl hydrolase family 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 !  100.3   0.0   1.2e-32   1.1e-28       3     289 ..      19     289 ..      18     337 .. 0.89

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 1.2e-32
                                       EBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHH CS
                       Aminotran_5   3 ldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlval 79 
                                       l  +++t++ ++V++++++           + +h+  ++t+ ++++ e+ +e++++++ e ii t ++te ++  +l
  gi|336252644|ref|YP_004595751.1|  19 LYIPGPTEVREDVIEEMSQP----------MFGHRMDRMTDLYTTVVEDTKEFLGTDN-EVIILTGSGTEFMESSIL 84 
                                       56788899999999998888..........899************************7.****************** PP

                                       HCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-...-TTEEEEEEESBETTTT CS
                       Aminotran_5  80 slarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekll...nektklvaithvsnvtG 153
                                       +l      ++ ++vt+ +  +++   +++a+r g +v+ ++ ++++ ++++ ++++l   + ++++v+  +++++tG
  gi|336252644|ref|YP_004595751.1|  85 NL-----VDEDVLVTTCGSFSER--QANVAERLGKNVDTLEYEWGQAVKPEGVREKLeesDTDYDAVTCVMNESSTG 154
                                       **.....5688************..9999****************************6555788999999******* PP

                                       EB--HHHHHHHHHHT.T-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS......S CS
                       Aminotran_5 154 tiqpveeigklakkk.galvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekl....epl 224
                                       + +p+eeig+++ ++ + +++vDa++a+g   +d+++ ++D+++ s +K +  P+G+ v +v++e+ e+        
  gi|336252644|ref|YP_004595751.1| 155 VRNPIEEIGDVVAEYpDTYFIVDAVSALGGDYVDIDEHNIDVIFTSVQKaFAMPPGLAVCVVSDEAYERElqkdSAS 231
                                       **************88*********************************9999***********9987654443445 PP

                                       S.STTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH CS
                       Aminotran_5 225 llggemveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeylle 289
                                        +gg    + sl+++  +++ +   + Tp ++ + + ++ ++++ e g  a +++++e+aey++e
  gi|336252644|ref|YP_004595751.1| 232 WYGGF---QRSLDYYDRKGQTH---S-TPAIPVMLAYRKQMKHMLEEGHGARDERHREMAEYTRE 289
                                       56666...45555555334433...3.*****************999999999999999999976 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 ?   10.6   0.0   1.5e-05      0.14     313     444 ..     101     233 ..      41     240 .. 0.69
   2 ?    0.6   0.0     0.016   1.4e+02     232     301 ..     277     344 ..     249     361 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 1.5e-05
                                       --SSGGGGG-..SBSS-B-SSSS-B-HHHHHHHHHHHHHTS----EEEEE----EE-BSSS.HHH--HHHHHHHHHH CS
                     Glyco_hydro_1 313 teekkleeev..dpslpktdigwiiepeglrkllellkkeYqklpiyiteNGlgakdeiee.gkveDdkRidYlkeh 386
                                       +++++++e+   ++++ + ++g +++peg+r+ le  +++Y+ + +++ e   g+++ iee g+v  ++  +Y   +
  gi|336252644|ref|YP_004595751.1| 101 ERQANVAERLgkNVDTLEYEWGQAVKPEGVREKLEESDTDYDAVTCVMNESSTGVRNPIEEiGDVVAEYPDTY---F 174
                                       44555555552244555566666788*******************************9977655544433333...3 PP

                                       HHHHHHHH.HTT--EEEEEEE-SB----GGGTTSEE--SEEEETTTTTEE.EE-HHHHHH CS
                     Glyco_hydro_1 387 lnevkkai.edgvdlkgYvawsllDnfewaegyskrfGlvyvdrnetleR.tpkkSakwy 444
                                       ++ + +a+  d vd+    +  ++  ++ a ++     ++ v  +e  eR  +k+Sa wy
  gi|336252644|ref|YP_004595751.1| 175 IVDAVSALgGDYVDIDEHNIDVIFTSVQKAFAMPPGLAVCVVS-DEAYEReLQKDSASWY 233
                                       5555555556777777766666666555555555444445555.5555552356677777 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.016
                                       HHHH.HHHHHHHHHHTHHHHHHHHHSS--HHHHHHHGGG..S----HHHHHHHTT--SEEEEEEEEEEEEE CS
                     Glyco_hydro_1 232 eedk.eaaeraleflngwfldpvvkGdYpeemkellrergalpeiteedkellkgkadflglnyYtsrlvk 301
                                        e++ e ae ++e++ + f+    +G Y ++++++++++ +  ++ +e  + +++++df+  n Y s+l +
  gi|336252644|ref|YP_004595751.1| 277 DERHrEMAEYTREWAREHFAMFPEEG-YESQTVSCIENT-QGINV-AETIDAVSEEYDFVFSNGYGSQLGE 344
                                       34444666777777777776555555.888889999888.33333.5678899999999999999888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2842.21
//
Query:       gi|336252645|ref|YP_004595752.1|  [L=450]
Description: Subtilisin [Halopiger xanaduensis SH-6]
Scores for complete 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-49  168.7   2.6    2.6e-49  168.1   2.6    1.2  1  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.1   2.6   1.4e-53   2.6e-49       1     286 [.     143     387 ..     143     406 .. 0.91

  Alignments for each domain:
  == domain 1  score: 168.1 bits;  conditional E-value: 1.4e-53
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanap 77 
                                       g gv +++lDtG++++h+ l+v                   +++ + ++ + +++d +g    HGthvAGia+a  +
  gi|336252645|ref|YP_004595752.1| 143 GTGVDIGILDTGIQTDHCSLEVA-----------------GGRNFTASGPPGDYEDRHG----HGTHVAGIAGAL-D 197
                                       78999****************33.................3555667788899999999....************.9 PP

                                       SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  78 eegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsiealainravnkk 154
                                       ++ +++g ap+a  ++vkvld++g      +eli++i++++ ++v++i+mslg++t+ ++  +     ai  a  ++
  gi|336252645|ref|YP_004595752.1| 198 NDLGVVGTAPNANCYAVKVLDDEGRGRY--SELIAGIDWCMSNDVELISMSLGGETESETLAE-----AIASAH-EE 266
                                       9999********************9886..9**********************7666666665.....888998.89 PP

                                       T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CCCCCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 155 gvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgnivstwsrq 231
                                       g l+ ++aGN+g+ g+++ + +++ +p+t + v++v+a+++++++a++Ss G+++      d++apG+nivs++  +
  gi|336252645|ref|YP_004595752.1| 267 GHLLLSAAGNEGNPGDGTCDAETMTYPATHEDVLAVAATDEDDSLASYSSVGSAV------DLLAPGTNIVSSVVDN 337
                                       *****************************************************98......6*************** PP

                                       CHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT...--HHHHHHHHHCCS-EE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 232 snnsaglssyqsmsGTSmAsPnaagaaAlllsalpk...ltpetvraallntAqdlgk 286
                                       +        y   sGTSmA+P+++g+aAl+++  ++     +e vr+al  +A+++ +
  gi|336252645|ref|YP_004595752.1| 338 E--------YAEASGTSMACPFVTGVAALVWETVDEdgpGPNEAVRQALTESAEPVFE 387
                                       *........***********************999889999************98833 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); 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:                         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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3493.36
//
Query:       gi|336252646|ref|YP_004595753.1|  [L=96]
Description: translation initiation factor 1A [Halopiger xanaduensis SH-6]
Scores for 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-25   86.8   0.2    7.6e-25   86.5   0.2    1.1  1  eIF-1a         Translation initiation factor 1A / IF-1
     0.0099   16.0   0.0      0.018   15.2   0.0    1.4  1  ChapFlgA_N     FlgA N-terminal domain
  ------ inclusion threshold ------
      0.076   12.7   0.0      0.098   12.4   0.0    1.1  1  Sclerostin     Sclerostin (SOST)
       0.13   12.0   0.0       0.24   11.2   0.0    1.4  1  zinc_ribbon_5  zinc-ribbon domain


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 !   86.5   0.2   1.7e-28   7.6e-25       1      64 []      18      80 ..      18      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 1.7e-28
                                      EEEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                            eIF-1a  1 gevigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                      +ev ++V+ +lg n+++V+++d g+e++a+ipgk+ ++iwi+++d+VlVe+++ +++k++I++r
  gi|336252646|ref|YP_004595753.1| 18 DEVFATVTDMLGANRVKVRCAD-GQERTARIPGKMQKRIWIREDDVVLVEPWDWQDEKADITWR 80
                                      589*****************96.***************************************98 PP

>> ChapFlgA_N  FlgA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.9e-06     0.018      33      74 ..      14      50 ..       7      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.9e-06
                        ChapFlgA_N 33 lpacdeaLevelpsgsrplGrtsvkvrcngpeppwtvyvpvr 74
                                      +p+ d   ev+ ++ +++lG ++vkvrc+ ++   t ++p++
  gi|336252646|ref|YP_004595753.1| 14 MPEDD---EVF-ATVTDMLGANRVKVRCADGQE-RTARIPGK 50
                                      55555...888.999***************998.68877765 PP

>> Sclerostin  Sclerostin (SOST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.2e-05     0.098     117     147 ..      17      47 ..       6      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                                       S------EEEEEEEEEEEEB-TTSSSEEEEE CS
                        Sclerostin 117 ssqefrcvndktrtqriqlqcedGatrtykv 147
                                       + + f  v+d   ++r++++c dG  rt ++
  gi|336252646|ref|YP_004595753.1|  17 DDEVFATVTDMLGANRVKVRCADGQERTARI 47 
                                       4556899*********************987 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.3e-05      0.24      11      29 ..      20      38 ..      13      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.3e-05
                     zinc_ribbon_5 11 kFklvdsklKksgkkVrCa 29
                                       F  v++ l  + +kVrCa
  gi|336252646|ref|YP_004595753.1| 20 VFATVTDMLGANRVKVRCA 38
                                      68889*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); 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:                         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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 764.35
//
Query:       gi|336252647|ref|YP_004595754.1|  [L=59]
Description: hypothetical protein Halxa_1242 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        2.2    7.8  10.2        2.4    7.6  10.2    1.0  1  MS_channel  Mechanosensitive ion channel


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 ?    7.6  10.2   0.00013       2.4       7      53 ..      10      56 ..       7      59 .] 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHH CS
                        MS_channel  7 liivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGi 53
                                      ++ vv++l  + l+ +   ++ a+++++ ++lgl++k+l+s+++ ++
  gi|336252647|ref|YP_004595754.1| 10 IVGVVVLLGGIGLIAYANPIIAAGMALVLVGLGLVVKSLVSGMLQSF 56
                                      57789999999999999**************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 494.22
//
Query:       gi|336252648|ref|YP_004595755.1|  [L=84]
Description: hypothetical protein Halxa_1243 [Halopiger xanaduensis SH-6]
Scores for 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:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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: 0.35u 0.18s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 746.47
//
Query:       gi|336252649|ref|YP_004595756.1|  [L=657]
Description: hypothetical protein Halxa_1244 [Halopiger xanaduensis SH-6]
Scores for 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-51  172.5   0.4    1.6e-50  170.5   0.1    2.2  2  DUF460           Protein of unknown function (DUF460)
    0.00036   20.8   2.1    0.00036   20.8   2.1    4.3  3  acVLRF1          Actinobacteria/chloroflexi VLRF1 release fac
      0.001   17.4  11.1     0.0014   16.9  11.1    1.1  1  FPP              Filament-like plant protein, long coiled-coi
     0.0018   16.7  20.4     0.0032   15.9  20.4    1.3  1  MAD              Mitotic checkpoint protein
     0.0032   17.1   5.2     0.0062   16.1   5.2    1.5  1  Exonuc_VII_L     Exonuclease VII, large subunit
     0.0037   17.5   6.4       0.53   10.6   1.5    2.5  2  DUF5082          Domain of unknown function (DUF5082)
     0.0049   16.4  19.6     0.0089   15.5  19.6    1.3  1  HMMR_N           Hyaluronan mediated motility receptor N-term
     0.0051   15.8  11.0       0.01   14.8  11.0    1.5  1  DUF812           Protein of unknown function (DUF812)
     0.0053   16.2  12.3      0.012   14.9  12.3    1.6  1  DUF4407          Domain of unknown function (DUF4407)
  ------ inclusion threshold ------
       0.02   15.3   2.4       0.02   15.3   2.4    2.1  2  DUF4094          Domain of unknown function (DUF4094)
      0.064   12.6   8.4        0.1   12.0   8.4    1.2  1  FAM76            FAM76 protein
      0.085   13.1   0.1        9.9    6.4   0.0    3.2  3  BtrH_N           Butirosin biosynthesis protein H, N-terminal
      0.085   12.8   7.7        0.4   10.6   2.9    2.5  2  Prefoldin        Prefoldin subunit
       0.17   10.0  23.1       0.42    8.7  22.9    1.6  2  HOOK             HOOK protein
       0.17   11.2   6.0        0.3   10.4   6.0    1.3  1  YPEB             YpeB sporulation
       0.21   10.2   7.0       0.35    9.5   7.0    1.3  1  AAA_13           AAA domain
       0.22   11.6  11.0       0.38   10.8   7.1    2.4  2  DUF1664          Protein of unknown function (DUF1664)
        0.3   10.1  14.9        0.5    9.4  14.9    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.36   10.5  16.5      0.092   12.4  12.7    1.9  1  DUF2968          Protein of unknown function (DUF2968)
       0.38   11.2  11.8        1.3    9.5   2.1    2.6  2  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
        0.4   10.5  12.4       0.92    9.3  12.4    1.7  1  DUF724           Protein of unknown function (DUF724)
       0.49   10.7   2.1        1.6    9.0   0.9    2.4  2  DUF948           Bacterial protein of unknown function (DUF94
       0.51   10.8   3.7        1.5    9.3   1.4    2.7  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.53    8.7   4.4       0.82    8.1   4.4    1.2  1  Herpes_UL6       Herpesvirus UL6 like
       0.72   10.3  12.3        1.8    9.0   2.8    3.0  2  FlaC_arch        Flagella accessory protein C (FlaC)
        1.1    7.8   7.7        2.1    6.9   7.7    1.4  1  FapA             Flagellar Assembly Protein A
        1.2    9.2  26.9        1.6    8.7   4.4    3.0  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
        1.2    8.9   4.4        7.6    6.3   1.1    2.7  3  Lectin_N         Hepatic lectin, N-terminal domain
        1.2    9.4   9.9        1.2    9.5   3.8    2.7  2  BLOC1_2          Biogenesis of lysosome-related organelles co
        1.3    9.4  16.9       0.18   12.1   7.0    2.7  2  DUF641           Plant protein of unknown function (DUF641)
        1.3    9.0  28.1       0.24   11.4  12.1    3.3  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        1.5    9.1  10.0        1.2    9.3   1.8    2.7  2  FlaG             FlaG protein
        1.7    7.5  22.2        6.2    5.6  22.1    1.9  1  Spc7             Spc7 kinetochore protein
        1.9    6.3   8.5        2.8    5.7   8.5    1.2  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        2.5    8.2  19.4        5.2    7.1  19.4    1.5  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
        2.8    8.1  19.3        1.4    9.1   1.0    2.6  2  bZIP_1           bZIP transcription factor
        3.3    7.8  18.0         14    5.8   7.8    2.5  2  BRE1             BRE1 E3 ubiquitin ligase
        4.8    7.0   9.7         10    5.9   9.7    1.5  1  HeLo             Prion-inhibition and propagation
        4.9    7.2   6.4         13    5.8   5.6    1.9  2  FlxA             FlxA-like protein
        5.3    7.7  13.2        2.5    8.8   5.5    3.0  3  SlyX             SlyX
        5.3    6.9  18.5         14    5.5  18.5    1.8  1  DASH_Spc19       Spc19
          6    7.2  17.1        2.4    8.4   5.1    3.2  2  XhlA             Haemolysin XhlA
        6.1    6.7  18.0       0.76    9.6   4.2    3.1  2  TRAF_BIRC3_bd    TNF receptor-associated factor BIRC3 binding
        6.5    6.0   8.8         19    4.5   8.7    1.7  1  CorA             CorA-like Mg2+ transporter protein
        6.5    6.8   9.2        9.1    6.3   4.3    2.5  2  Laminin_II       Laminin Domain II
        7.7    6.7   8.0        4.1    7.6   3.4    2.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
        9.1    6.5  29.3       0.39   11.0   6.3    2.9  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        9.2    6.4  31.9         23    5.1  27.5    3.1  2  Tropomyosin_1    Tropomyosin like


Domain annotation for each model (and alignments):
>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.5   3.2e+03      69      84 ..      50      65 ..      30      67 .. 0.72
   2 !  170.5   0.1   4.2e-53   1.6e-50       3     141 .]     219     350 ..     217     350 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.5
                            DUF460 69 eliselGkpvivAtDv 84
                                      + + +  +p+ivAtD 
  gi|336252649|ref|YP_004595756.1| 50 RRLIDDEEPAIVATDN 65
                                      4555556899****95 PP

  == domain 2  score: 170.5 bits;  conditional E-value: 4.2e-53
                            DUF460   3 kskdvkvevesvekdkiefeplkkkrkkklivGiDPGittgiavldldgevlalkssreldreevieliselGkpvi 79 
                                       +s dv+ve+e++++d ief+pl +kr++++ivGiDPG+tt++a++ l+gevl++ ssr+ d++evie+i+e G+p++
  gi|336252649|ref|YP_004595756.1| 219 RSGDVRVEIERERRDGIEFRPL-AKRRDHVIVGIDPGTTTAVAIVGLEGEVLDVWSSRTSDTAEVIEWIVERGRPIV 294
                                       789*******************.9***************************************************** PP

                            DUF460  80 vAtDvspppetvkklarslkavlyvPeedlsveeKeelaeklsekekvkykddHeRDalaAA 141
                                       vA+Dv+p+petv+k++rs++a+ ++Pe+dl v+eK++ +++      + y++dH+RDa+aAA
  gi|336252649|ref|YP_004595756.1| 295 VAADVTPMPETVEKFRRSFDAAGWAPETDLPVDEKQHRTRE------HPYENDHQRDAMAAA 350
                                       *****************************************......779***********9 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   2.1   9.7e-07   0.00036      35      97 ..     150     214 ..     123     247 .. 0.74
   2 ?   -1.1   2.9         6   2.2e+03      65     104 ..     363     407 ..     338     434 .. 0.57
   3 ?    5.4   0.5     0.057        21      81     129 ..     582     636 ..     557     637 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 9.7e-07
                           acVLRF1  35 grtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae..vvlgGdrslvaevledarlap 97 
                                        +t  GGwS  R+ Rr+ +++++ +++v+ ++++   +++ +   + gG  +++ +v++++   p
  gi|336252649|ref|YP_004595756.1| 150 RSTGSGGWSEDRYTRRIHGSVKRRAREVESELEEANLAYETDtrEAYGGYANAIFTVEAKPSEIP 214
                                       46999***************************998765555556777888888777777766554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 6
                           acVLRF1  65 aaarllaeesae.....vvlgGdrslvaevledarlaplatlare 104
                                       ++ar l +++++      v++G++s+ a +++ +++++ +t  +e
  gi|336252649|ref|YP_004595756.1| 363 RIARKLPPGVDRgevtaRVVAGEESVEAVLADLEDDDESETDETE 407
                                       333333333333555667889998876666666555544433333 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.057
                           acVLRF1  81 Gdrslvaevledar..lap...latlareell.dvpdprravLedavrraravrv 129
                                       G  ++++e+l d++   +p   +a + ++el+ + +d+++av++d+++rar+ r+
  gi|336252649|ref|YP_004595756.1| 582 GLSEIADEILFDEEipVGPaddVAMQEVDELAvAREDDVEAVIDDWHERARDRRL 636
                                       55555555555533222223336667777888789999*************9886 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9  11.1   3.7e-06    0.0014     682     786 ..     398     505 ..     328     525 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.7e-06
                               FPP 682 sneskkeenkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslkesksl...aetqlkc 755
                                        +es+++e++++  el+e + + ++l+ ++++ ++++++l  +l+++   +++l+seLe++++ +++    + ++  
  gi|336252649|ref|YP_004595756.1| 398 DDESETDETEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKERKevrKDREVTR 474
                                       23344555555555555555555555555555555555555555555555555555555554433321113334444 PP

                               FPP 756 mkesyesletrateleaelnelkqkieaLev 786
                                            e le    e+++e++el++k+e++++
  gi|336252649|ref|YP_004595756.1| 475 YRRKAERLEYERDEAREEVEELEKKVERMKA 505
                                       4445555555555555555555555555544 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9  20.4   8.7e-06    0.0032     367     475 ..     398     504 ..     387     517 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.7e-06
                               MAD 367 kelteseaspklleRieeaedlvqkvqahneeveaqlevaeeevggykqqastlerelqalrqqesladassskeev 443
                                       ++ +e++  +++ + + e e+ +++++ + e ++ +++ +e  +    ++++ le el+a r++e ++ +   + ev
  gi|336252649|ref|YP_004595756.1| 398 DDESETDETEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKERKEVR--KDREV 472
                                       444444444466777888899999999999999999999999999999***************9998888..679** PP

                               MAD 444 dslkkkleeLelerqrLreqkeelElelerre 475
                                       +  ++k e Le er++ re+ eelE ++er +
  gi|336252649|ref|YP_004595756.1| 473 TRYRRKAERLEYERDEAREEVEELEKKVERMK 504
                                       ****************************9864 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 !   16.1   5.2   1.7e-05    0.0062     155     243 ..     411     508 ..     341     542 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-05
                      Exonuc_VII_L 155 rlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq............lkkkrerleelke 219
                                       r  ++ ++++++ k+++e+l+s++ + e++le+k +r+d+le++le+a +k+            +       ++ +e
  gi|336252649|ref|YP_004595756.1| 411 RELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKErkevrkdrevtrY-------RRKAE 480
                                       22222234556666666666666677777777777777777777777544443432222221111.......11112 PP

                      Exonuc_VII_L 220 rlkekleekkerlkklkerle....lle 243
                                       rl+ + +e++e++++l++++e    l +
  gi|336252649|ref|YP_004595756.1| 481 RLEYERDEAREEVEELEKKVErmkaLWK 508
                                       2212222222222222222222222233 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.5    0.0014      0.53      68     107 ..     415     458 ..     388     461 .. 0.79
   2 !    8.9   0.2    0.0047       1.8       4      32 ..     478     506 ..     475     525 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0014
                           DUF5082  68 ydgirs.nlessyqtyvdkldelidaieeE...IerLenqisea 107
                                       ++++r  +l+ ++++ ++++d+l+d++e++   I +Le++++ a
  gi|336252649|ref|YP_004595756.1| 415 EEEKRIkDLKRQVERLQSHVDTLEDRLEQKddrIDDLESELEAA 458
                                       45555579999999999999999999998755577788877665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0047
                           DUF5082   4 kisklqaqiaelrseiaaleekIerLkea 32 
                                       k ++l+++ +e+r+e++ le+k+er k+ 
  gi|336252649|ref|YP_004595756.1| 478 KAERLEYERDEAREEVEELEKKVERMKAL 506
                                       66899********************9975 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5  19.6   2.4e-05    0.0089     205     318 ..     392     504 ..     384     518 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-05
                            HMMR_N 205 vaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskq 281
                                       +a L++     e e  e+  + ++l+e+ ++++ +++q+e+ +  ++ le+ l++k+d i +L s+Le+   +  k+
  gi|336252649|ref|YP_004595756.1| 392 LADLEDD---DESETDETEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKERKE 465
                                       4556655...477777888888**********************************************988855555 PP

                            HMMR_N 282 vkdlnekcklle..kekeelvreeeekeqtlsaEleelk 318
                                       v++  e  +     + +e +  e++e  ++l++ +e +k
  gi|336252649|ref|YP_004595756.1| 466 VRKDREVTRYRRkaERLEYERDEAREEVEELEKKVERMK 504
                                       554433222211112233233344444444444444444 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8  11.0   2.7e-05      0.01     316     428 ..     397     509 ..     310     529 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                            DUF812 316 kkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellp 392
                                        + e+e + ++++ +el+e +++i++l++++e+l++ +++le++++q ++ ++ +++e e    + +++ +    + 
  gi|336252649|ref|YP_004595756.1| 397 DDDESETDETEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKERKEVRKDREVT 473
                                       44566666666777777777777777777777777777777777777777777777766666666666666666666 PP

                            DUF812 393 daeeniekLqalveasaqrlvelakqWekhRvplie 428
                                             e+L+ + +++++++ el+k+ e+ ++ +  
  gi|336252649|ref|YP_004595756.1| 474 RYRRKAERLEYERDEAREEVEELEKKVERMKALWKL 509
                                       677777777777777777777777777766665554 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9  12.3   3.3e-05     0.012     118     243 ..     396     524 ..     385     528 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-05
                           DUF4407 118 eeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqlda 194
                                       e+ +e ++  +++   el+e+e++i++l+++++ +++++d+l++ ++++ d      +   + + +aa++k+++  +
  gi|336252649|ref|YP_004595756.1| 396 EDDDESETDETEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDR-----IDDLESELEAARRKERKEVR 467
                                       3344444455556777777777777777777777777777777777755443.....33345555555555555555 PP

                           DUF4407 195 aqaelaelkakld........atarlaalraelaeleaerakeraasqaaaaaddGl 243
                                       +++e++ +++k +        a++++++l+++ ++++a  + +++++ + +a++ Gl
  gi|336252649|ref|YP_004595756.1| 468 KDREVTRYRRKAErleyerdeAREEVEELEKKVERMKALWKLDHSNFSDVSAKKEGL 524
                                       555555555554455555557888888888888888888888888888888888877 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   2.4   5.2e-05      0.02      37      87 ..     400     460 ..     377     461 .. 0.75
   2 ?   -1.5   0.1         9   3.4e+03      56      76 ..     480     501 ..     463     511 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.2e-05
                           DUF4094  37 elklvsedcds...kdaesrskdilgevskthkaiqtL.......dktissLemeLaaara 87 
                                       e+++ ++++++    ++e+r kd+ ++v++ ++ + tL       d +i+ Le eL+aar 
  gi|336252649|ref|YP_004595756.1| 400 ESETDETEHQPrelTEEEKRIKDLKRQVERLQSHVDTLedrleqkDDRIDDLESELEAARR 460
                                       44443444444545556666889999*********************************96 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 9
                           DUF4094  56 dilg.evskthkaiqtLdktis 76 
                                       + l+ e ++++++++ L+k++ 
  gi|336252649|ref|YP_004595756.1| 480 ERLEyERDEAREEVEELEKKVE 501
                                       4455566667777777777765 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   8.4   0.00027       0.1     196     298 ..     395     499 ..     322     503 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                             FAM76 196 laeekesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelek 272
                                       l +  es+++++++   + +++   +++Lk ++++l+ ++++ +  l +kd  i +l +el+  +++ r+ +++ ++
  gi|336252649|ref|YP_004595756.1| 395 LEDDDESETDETEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKERKEVRKDRE 471
                                       33344444455556666777788899999999999999999999999999999999999999999999888887665 PP

                             FAM76 273 ..eakekieklekkirellkevaelskk 298
                                          +++k e+le +  e + ev el+kk
  gi|336252649|ref|YP_004595756.1| 472 vtRYRRKAERLEYERDEAREEVEELEKK 499
                                       2267899999999999999999999987 PP

>> BtrH_N  Butirosin biosynthesis protein H, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.026       9.9      64     100 ..      31      67 ..       5      82 .. 0.80
   2 ?   -0.4   0.0       3.4   1.3e+03      54      81 ..      99     125 ..      76     135 .. 0.72
   3 ?    2.1   0.0      0.58   2.2e+02      76     102 ..     280     303 ..     258     313 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.026
                            BtrH_N  64 glkvevketkdpeeawkalkeeLdaGrpvivqvdvyy 100
                                        ++++ +e+++    +++l++ +d+ +p+iv++d+ y
  gi|336252649|ref|YP_004595756.1|  31 LVRYDGEEVRRDVVSHRKLRRLIDDEEPAIVATDNMY 67 
                                       5667777888888899******************876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.4
                            BtrH_N  54 dlekrlakrlglkvevketkdpeeawka 81 
                                       +   r+akr+g+ +  +  k++e+a  +
  gi|336252649|ref|YP_004595756.1|  99 EPLSRVAKRHGIPYGKQPMKEAEAAA-R 125
                                       78899*********976666666554.4 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.58
                            BtrH_N  76 eeawkalkeeLdaGrpvivqvdvyyLp 102
                                       +e  +     +++Grp +v++dv  +p
  gi|336252649|ref|YP_004595756.1| 280 AEVIE---WIVERGRPIVVAADVTPMP 303
                                       33333...33599*********98776 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.9    0.0011       0.4      79     116 ..     420     457 ..     415     461 .. 0.92
   2 ?    4.0   0.2      0.12        45       2      39 ..     476     513 ..     469     534 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  79 iellkkkleelekqlekleeeleklkdqittleanlaq 116
                                       i+ lk+++e l++ +++le+ le++ d+i+ le +l++
  gi|336252649|ref|YP_004595756.1| 420 IKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEA 457
                                       789******************************99986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT- CS
                         Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkkedegk 39 
                                       ++++e+l+ e+++ +e+ eelek  e+ k l k d + 
  gi|336252649|ref|YP_004595756.1| 476 RRKAERLEYERDEAREEVEELEKKVERMKALWKLDHSN 513
                                       44555555555555555555555555555555555555 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  12.3    0.0018      0.67     507     583 ..     380     457 ..     374     470 .. 0.81
   2 ?    8.7  22.9    0.0011      0.42     339     459 ..     407     534 ..     395     537 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0018
                              HOOK 507 rileLeaqveelqkalqeq.gskaedssllkkkleehleklkevqeelqkkkeqleelepklssnkqkieeleeaLk 582
                                       r+   e+ ve +  +l+++ +s+++++ +  ++l+e  +++k+++ ++++ + +++ le +l+++  +i++le  L+
  gi|336252649|ref|YP_004595756.1| 380 RVVAGEESVEAVLADLEDDdESETDETEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELE 456
                                       5556677888888887765156667788999******************************************9997 PP

                              HOOK 583 k 583
                                       +
  gi|336252649|ref|YP_004595756.1| 457 A 457
                                       4 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0011
                              HOOK 339 lqktveleeelkkanalrsqlelykkqvqelhkklseeskkadklefelkkleekl.ealqkeke.........rll 405
                                        ++ +el ee k+ + l+ q+e ++ +v  l+++l+++  + d le el + + k  + + k++e         rl 
  gi|336252649|ref|YP_004595756.1| 407 EHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKErKEVRKDREvtryrrkaeRLE 483
                                       5778999**************************************99987655443123333333333333333*** PP

                              HOOK 406 aerdaLketneELkcaqlqqkelsqadalaskssssgenlaaellpaevrekli 459
                                        erd  +e +eEL+      k l + d+++    s ++  ++ l+p++v ek+ 
  gi|336252649|ref|YP_004595756.1| 484 YERDEAREEVEELEKKVERMKALWKLDHSNF---SDVSAKKEGLVPVKVVEKFT 534
                                       **************96666666766664444...44466677799**9999986 PP

>> YPEB  YpeB sporulation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   6.0    0.0008       0.3     106     198 ..     407     497 ..     396     532 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0008
                              YPEB 106 dldgepLteeeyktLeeLyeqakelekeLrkvqekvaegglrwgelekalaseqekadntiidgnfktvekevekyp 182
                                       + + ++Lteee k +++L++q ++l+    ++++++++++ r+ +le +l+++++k+++++ ++  ++v +   k  
  gi|336252649|ref|YP_004595756.1| 407 EHQPRELTEEE-KRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKERKEVRKD--REVTRYRRKAE 480
                                       44556788766.79************************************99888888776666..67777777777 PP

                              YPEB 183 eliydGpf.sdhlekkt 198
                                        l+y+  +  +++e+ +
  gi|336252649|ref|YP_004595756.1| 481 RLEYERDEaREEVEELE 497
                                       77775555433333333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   7.0   0.00094      0.35     356     442 ..     419     503 ..     374     536 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00094
                            AAA_13 356 elesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekel 432
                                        ++++k ++e++++ v+++++  ++   ++++le+e e+a+ k ++ + +  + e+++y +k ++le +  ++ +e+
  gi|336252649|ref|YP_004595756.1| 419 RIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKERKEVRK--DREVTRYRRKAERLEYERDEAREEV 493
                                       34555555555555555555555555555555555555555555554444..4455555555555555555555444 PP

                            AAA_13 433 keeeaelkkl 442
                                       +e e++++ +
  gi|336252649|ref|YP_004595756.1| 494 EELEKKVERM 503
                                       4444444443 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.5     0.023       8.6      64     116 ..     402     454 ..     375     461 .. 0.55
   2 ?   10.8   7.1     0.001      0.38      45     121 ..     422     504 ..     418     506 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.023
                           DUF1664  64 Lssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                        +++ ++  ++l e ++ +k++k++v++++++++++++ +e+ ++ + +les+
  gi|336252649|ref|YP_004595756.1| 402 ETDETEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESE 454
                                       34444444455555555555555555555555555555555555555555555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.001
                           DUF1664  45 svskqleqvseslaatkrhLss...ridrvdkkldeqkeis.kei..keevtevredlseigedvesvkeavegles 115
                                       ++ +q+e++++++ +  ++L++   rid ++++l++  +   ke+  ++evt+ r++ ++++ + ++ +e ve+le+
  gi|336252649|ref|YP_004595756.1| 422 DLKRQVERLQSHVDTLEDRLEQkddRIDDLESELEAARRKErKEVrkDREVTRYRRKAERLEYERDEAREEVEELEK 498
                                       56677888887777777777653337999999999876543144411579*************************** PP

                           DUF1664 116 klerie 121
                                       k+er++
  gi|336252649|ref|YP_004595756.1| 499 KVERMK 504
                                       ***996 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 ?    9.4  14.9    0.0013       0.5      19     115 ..     408     504 ..     393     525 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                             Atg14  19 ngperlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkk 95 
                                       ++p+ l+e+ +r+++lk + e l+++++ ++ + e+++++ d+++++ ++++++  +  ++ +++ + + k ++l  
  gi|336252649|ref|YP_004595756.1| 408 HQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKERKEVRKDREVTRYRRKAERLEY 484
                                       56788888888888888888888888887777777777777777777777777777777777777777777777777 PP

                             Atg14  96 eieekkkklaklsdklkkRr 115
                                       e +e+++++++l +k+ +++
  gi|336252649|ref|YP_004595756.1| 485 ERDEAREEVEELEKKVERMK 504
                                       77777777777777774333 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4  12.7   0.00025     0.092      85     175 ..     411     504 ..     390     507 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00025
                           DUF2968  85 adfarqtaelaeveirrikleaqkaqlerqiaasearaerLqadlavarqQe.qavaerQkqa..rkeaaaLeaqre 158
                                       +++++  +++ +   +  +l++  ++le  ++++++r+  L+++l+ ar  e ++v +  + +  r++a+ Le +r+
  gi|336252649|ref|YP_004595756.1| 411 RELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKErKEVRKDREVTryRRKAERLEYERD 487
                                       4555555666666666678999999********************998766516787776655227899******** PP

                           DUF2968 159 aaqaqlralqrqirqLq 175
                                       +a++++++l++++++++
  gi|336252649|ref|YP_004595756.1| 488 EAREEVEELEKKVERMK 504
                                       *************9876 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   3.9     0.086        32      22      70 ..     417     465 ..     413     471 .. 0.86
   2 ?    9.5   2.1    0.0035       1.3      34      63 ..     473     502 ..     464     506 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.086
                       Fungal_TACC  22 EqKVkllkkgyeakyqkkldklelenkslkqeieqLkkqleaer.kEKqe 70 
                                       E+++k lk++  ++ q+++d le   ++  + i+ L+++lea+r kE++e
  gi|336252649|ref|YP_004595756.1| 417 EKRIKDLKRQV-ERLQSHVDTLEDRLEQKDDRIDDLESELEAARrKERKE 465
                                       88899999999.799*************************9875156665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0035
                       Fungal_TACC  34 akyqkkldklelenkslkqeieqLkkqlea 63 
                                       ++y+ k ++le e+++ ++e+e+L+k++e 
  gi|336252649|ref|YP_004595756.1| 473 TRYRRKAERLEYERDEAREEVEELEKKVER 502
                                       68*************************986 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  12.4    0.0025      0.92     105     184 ..     414     496 ..     395     515 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0025
                            DUF724 105 tklleerkklekkieeeesekrkleeeidelekkilelerqlallk...ekkeaadkeiarlkseaekleeeledve 178
                                       t+ ++++k+l++++e  +s+   le+ +++++ +i +le +l++++   +k+ ++d+e+ r + +ae+le e ++++
  gi|336252649|ref|YP_004595756.1| 414 TEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARrkeRKEVRKDREVTRYRRKAERLEYERDEAR 490
                                       66788899************************************99998888899********************** PP

                            DUF724 179 qeFeav 184
                                       +e+e++
  gi|336252649|ref|YP_004595756.1| 491 EEVEEL 496
                                       999987 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 ?    9.0   0.9    0.0044       1.6      29      73 ..     404     451 ..     390     460 .. 0.83
   2 ?   -0.9   0.0       5.3     2e+03      29      45 ..     487     503 ..     470     521 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0044
                            DUF948  29 deaaatieele...kqvdpilkevedllakvnelledvneklekvdpl 73 
                                       de++++ +el+   k+++ + ++ve+l ++v +l + +++k +++d l
  gi|336252649|ref|YP_004595756.1| 404 DETEHQPRELTeeeKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDL 451
                                       5666666666655599*****************************987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 5.3
                            DUF948  29 deaaatieelekqvdpi 45 
                                       dea++ +eelek+v+ +
  gi|336252649|ref|YP_004595756.1| 487 DEAREEVEELEKKVERM 503
                                       56666666666666544 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.4    0.0041       1.5      12      52 ..     419     456 ..     413     463 .. 0.73
   2 ?   -0.6   0.0       4.9   1.8e+03      10      23 ..     490     503 ..     471     521 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0041
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLa 52 
                                        ik+++ +V+ lq++vd +++ l++     +++d++  +L+
  gi|336252649|ref|YP_004595756.1| 419 RIKDLKRQVERLQSHVDTLEDRLEQK---DDRIDDLESELE 456
                                       58888899999999998888887773...466666666655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 4.9
                           NPV_P10  10 radikavddkVdal 23 
                                       r++++++++kV+ +
  gi|336252649|ref|YP_004595756.1| 490 REEVEELEKKVERM 503
                                       33344444444333 PP

>> Herpes_UL6  Herpesvirus UL6 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.4    0.0022      0.82     323     432 ..     377     482 ..     375     517 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0022
                        Herpes_UL6 323 vsnslvdknklldasqpGfgkggasaqssekteqglkksv.snsvikcleeqineqfdtiekLkkenelllkklkel 398
                                       v+ ++v   ++++a  + + + ++s  ++++te++ ++   +++ ik l+ q++++  ++++L++  e+   ++ +l
  gi|336252649|ref|YP_004595756.1| 377 VTARVVAGEESVEAVLADLEDDDES--ETDETEHQPRELTeEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDL 451
                                       5566666666666666666666653..333333333333313456899***************************** PP

                        Herpes_UL6 399 ekeLerlreeakk.eakarevdlltsstdaslenl 432
                                       e+eLe++r+++ k  +k rev+ +  +     e+l
  gi|336252649|ref|YP_004595756.1| 452 ESELEAARRKERKeVRKDREVTRYRRKA----ERL 482
                                       *******888887334444444333332....222 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 ?    9.0   2.8    0.0048       1.8       1      36 [.     419     454 ..     417     468 .. 0.93
   2 ?    7.2   0.2     0.018       6.6      10      34 ..     480     504 ..     469     508 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0048
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelken 36 
                                       ri++l  ++++l++ ++t+++ +e+  + +++l+ +
  gi|336252649|ref|YP_004595756.1| 419 RIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESE 454
                                       89******************************9976 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.018
                         FlaC_arch  10 sklsteletvkkeneelsksveelk 34 
                                       ++l+ e + +++e eel+k+ve++k
  gi|336252649|ref|YP_004595756.1| 480 ERLEYERDEAREEVEELEKKVERMK 504
                                       4555555555666666666666554 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   7.7    0.0055       2.1     334     412 ..     429     508 ..     387     544 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0055
                              FapA 334 elkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeles 410
                                        l++ ++ le++le+  +++++l+++++  +    +++ e +k  ++ +++++ e+l+ e  e +ee +el++++e+
  gi|336252649|ref|YP_004595756.1| 429 RLQSHVDTLEDRLEQKDDRIDDLESELEAARR---KERKEVRKDREVTRYRRKAERLEYERDEAREEVEELEKKVER 502
                                       22333344444444444444444444444443...333445566666666666677777777777777777777777 PP

                              FapA 411 k....k 412
                                       +    k
  gi|336252649|ref|YP_004595756.1| 503 MkalwK 508
                                       744440 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 ?   -1.7   0.0       7.2   2.7e+03      24      49 ..     172     190 ..     161     199 .. 0.56
   2 ?    5.9  13.0     0.033        12      43     105 ..     395     457 ..     383     468 .. 0.64
   3 ?    8.7   4.4    0.0043       1.6      31      85 ..     470     524 ..     467     526 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.2
                    CENP-F_leu_zip  24 dkvenLerelemseenqekvileaEt 49 
                                        ++        ++e+++e++ l  Et
  gi|336252649|ref|YP_004595756.1| 172 RRA-------REVESELEEANLAYET 190
                                       333.......3444455555555554 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.033
                    CENP-F_leu_zip  43 vileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnss 105
                                       ++ + E++  e e    e+ e +++ ++l+ +++ l+s  ++Le  l++k +r+++Les  + 
  gi|336252649|ref|YP_004595756.1| 395 LEDDDESETDETEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEA 457
                                       334445555555555555555566678888888888888888888888888888888876544 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0043
                    CENP-F_leu_zip  31 relemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeL 85 
                                       re+    ++ e+++ e +++++eve+l++++e++++  +  ++++++++  ke L
  gi|336252649|ref|YP_004595756.1| 470 REVTRYRRKAERLEYERDEAREEVEELEKKVERMKALWKLDHSNFSDVSAKKEGL 524
                                       888899999*************************987777777888888888765 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       7.6   2.8e+03      65     106 ..     136     191 ..     133     194 .. 0.69
   2 ?    6.3   1.1      0.02       7.6      72     110 ..     417     455 ..     411     468 .. 0.86
   3 ?    2.4   0.0      0.33   1.2e+02      76     110 ..     480     514 ..     472     517 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 7.6
                          Lectin_N  65 snfssstlaeiqalss..............qggslsekvtsleaklekkqqdlkad 106
                                       s f+ +t++++   +s                gs++++ + +e++le+ + + ++d
  gi|336252649|ref|YP_004595756.1| 136 SAFTDTTEVKVARGRStgsggwsedrytrrIHGSVKRRAREVESELEEANLAYETD 191
                                       56777777777776666666666666666546788888888888888887777776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.02
                          Lectin_N  72 laeiqalssqggslsekvtsleaklekkqqdlkadhsel 110
                                       +  i++l+ q ++l+ +v +le +le+k+  ++   sel
  gi|336252649|ref|YP_004595756.1| 417 EKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESEL 455
                                       6789**************************999999988 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.33
                          Lectin_N  76 qalssqggslsekvtsleaklekkqqdlkadhsel 110
                                       + l+ + +++ e+v+ le k+e+ ++  k dhs++
  gi|336252649|ref|YP_004595756.1| 480 ERLEYERDEAREEVEELEKKVERMKALWKLDHSNF 514
                                       56778889999**********************86 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   3.8    0.0031       1.2      42      94 ..     402     454 ..     397     456 .. 0.77
   2 ?    2.5   0.4      0.49   1.8e+02      52      79 ..     481     505 ..     457     511 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0031
                           BLOC1_2  42 vaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                       +++++e +  +l e+++ ++ +++q+++++ +v++Le+  ++ D  + +LE+ 
  gi|336252649|ref|YP_004595756.1| 402 ETDETEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESE 454
                                       56667777778888888888888888888888888888888888888888876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.49
                           BLOC1_2  52 klnekyeelqpylqqidqiekqvteLee 79 
                                       +l+    e ++  ++++++ek+v+++++
  gi|336252649|ref|YP_004595756.1| 481 RLEY---ERDEAREEVEELEKKVERMKA 505
                                       3333...555666666666777666654 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 ?   12.1   7.0   0.00048      0.18      70     124 ..     410     464 ..     395     468 .. 0.84
   2 ?    1.0   3.6       1.3     5e+02      85     120 ..     470     505 ..     463     512 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00048
                            DUF641  70 eaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkk 124
                                       + e +e e++i+++++ ++ ++ +v+ le  l++kd  i+ L+++Le+a+++++k
  gi|336252649|ref|YP_004595756.1| 410 PRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKERK 464
                                       3566778899999************************************999887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.3
                            DUF641  85 sllktyeitvkkleaelkakdseieeLkekLeeaek 120
                                       + +  y   +++le e ++ ++e+eeL++k+e++++
  gi|336252649|ref|YP_004595756.1| 470 REVTRYRRKAERLEYERDEAREEVEELEKKVERMKA 505
                                       345668888899999999999999999999888765 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.9    0.0013      0.47      41      73 ..     412     444 ..     410     444 .. 0.94
   2 ?   11.4  12.1   0.00065      0.24       7      69 ..     441     506 ..     440     509 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0013
                        TMF_DNA_bd  41 knkelekeikelkkkleklekeleeleerlkea 73 
                                       ++ e ek ik+lk+++e+l++ +++le+rl+++
  gi|336252649|ref|YP_004595756.1| 412 ELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQK 444
                                       67899*************************986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00065
                        TMF_DNA_bd   7 lkeKDeqIaqLmeEGekLskkelkl...nntikkLrkknkelekeikelkkkleklekeleeleer 69 
                                       l++KD++I+ L +E+e+ + ke+k+      + + r k++ le+e +e  +++e+lek++e+++++
  gi|336252649|ref|YP_004595756.1| 441 LEQKDDRIDDLESELEAARRKERKEvrkDREVTRYRRKAERLEYERDEAREEVEELEKKVERMKAL 506
                                       799**************99877654222889*******************************9976 PP

>> FlaG  FlaG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.4       0.2        74      17      50 ..     401     439 ..     387     448 .. 0.53
   2 ?    9.3   1.8    0.0032       1.2      14      79 ..     476     541 ..     458     547 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.2
                                       -----SS-------HHH.....HHHHHHHHHHHHTTSS- CS
                              FlaG  17 eekaekaeeekevseee.....leeaveklnkklsslnt 50 
                                       +e++e++ + +e++eee     l++ ve+l++ +++l+ 
  gi|336252649|ref|YP_004595756.1| 401 SETDETEHQPRELTEEEkrikdLKRQVERLQSHVDTLED 439
                                       222233333333333321222366677777776666655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0032
                                       HHS-----SS-------HHHHHHHHHHHHHHHTTSS--EEEEEEEETTEEEEEEEETTT-SEEEEE CS
                              FlaG  14 kseeekaekaeeekevseeeleeaveklnkklsslnteleFsvdedtkrvvVkviDketgevIrqi 79 
                                       + ++e+ e +++e+ ++ eele+ ve+++   +  +++++    ++ + v Vkv++k t+  Ir+ 
  gi|336252649|ref|YP_004595756.1| 476 RRKAERLEYERDEAREEVEELEKKVERMKALWKLDHSNFSDVSAKKEGLVPVKVVEKFTKGAIREA 541
                                       4455666677777777777899999999999999888888888888888***************96 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  22.1     0.017       6.2     178     281 ..     387     485 ..     375     520 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.017
                              Spc7 178 eleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeae 254
                                       ++e+ l++l++      +++ +e e   +el+e ++ i+ +k+++++lq+ +++le+++e+ ++++++le+e++ a 
  gi|336252649|ref|YP_004595756.1| 387 SVEAVLADLEDDD----ESETDETEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELE-AA 458
                                       4444444444422....244555555566666666666666666666666666666666666666666666666.44 PP

                              Spc7 255 rvleeckgwsesevsrlkeevkaleel 281
                                       r +e+++  ++ ev r++ + ++le +
  gi|336252649|ref|YP_004595756.1| 459 RRKERKEVRKDREVTRYRRKAERLEYE 485
                                       556666666666666666666666643 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 ?    5.7   8.5    0.0076       2.8      18     103 ..     406     504 ..     375     544 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0076
                        V_ATPase_I  18 vnafqrkfvkevrrcdemerklrfleeeieklekavikeeea.............eesleapeekeldeleeelekl 81 
                                       +++  r+ ++e +r+ +++r+++ l+++++ le+   ++++              +e++e ++++e+ ++ ++ e+l
  gi|336252649|ref|YP_004595756.1| 406 TEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRiddleseleaarrKERKEVRKDREVTRYRRKAERL 482
                                       33334566666666666666666666666665555555555455555555555554445555555555555555555 PP

                        V_ATPase_I  82 eeelkelnenleklkkelnelv 103
                                       e e  e +e+ e+l+k++++++
  gi|336252649|ref|YP_004595756.1| 483 EYERDEAREEVEELEKKVERMK 504
                                       5555555555555555544433 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 ?    7.1  19.4     0.014       5.2      80     175 ..     406     506 ..     383     510 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.014
                           UPF0242  80 ld...eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae.dfeelkleleeq.Laekqell 151
                                       ++    +l+++e+ +++l+ + e+L+ ++d  e  le+   +   L+++lea+ + + +e++++ e +  ++k e+l
  gi|336252649|ref|YP_004595756.1| 406 TEhqpRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRkERKEVRKDREVTrYRRKAERL 482
                                       22333567788899999999999999999999999999999999999999998877899999999864267777888 PP

                           UPF0242 152 qeyqetieeqrsvlekrqdqieqL 175
                                       +  + +  e  ++lek+ ++ + L
  gi|336252649|ref|YP_004595756.1| 483 EYERDEAREEVEELEKKVERMKAL 506
                                       888889999999999999887766 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.0    0.0037       1.4      25      63 ..     417     455 ..     416     456 .. 0.91
   2 ?    3.1  11.7      0.27        99      21      61 ..     463     505 ..     456     508 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  25 qaeieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                       +++i+ L+r+v+ L++   +L ++le+  + ++ L+s++
  gi|336252649|ref|YP_004595756.1| 417 EKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESEL 455
                                       57999**************************99999986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.27
                                       HH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  21 Rq..RKqaeieeLerrvkaLekeNksLkseleelkkevekLks 61 
                                       R+  RK  e+ +  r+++ Le e  + ++e+eel+k+ve +k 
  gi|336252649|ref|YP_004595756.1| 463 RKevRKDREVTRYRRKAERLEYERDEAREEVEELEKKVERMKA 505
                                       444499***********************************96 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   7.5     0.044        17      38      91 ..     411     465 ..     386     468 .. 0.86
   2 ?    5.8   7.8     0.037        14       7      59 ..     454     505 ..     453     515 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.044
                              BRE1  38 aekakadqkyfaamrskdalenelkkLnkllsKsselieqLke.lekefvrklke 91 
                                        e +++++ +++++r+ + l+  + +L   l+++ + i++L+  le++ +++ ke
  gi|336252649|ref|YP_004595756.1| 411 RELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESeLEAARRKERKE 465
                                       589999***********************************98788777766665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.037
                              BRE1   7 klekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalen 59 
                                       +le+a+++ +++++k   e+t+   k  rle e ++a+++  +++++ + +++
  gi|336252649|ref|YP_004595756.1| 454 ELEAARRKERKEVRKD-REVTRYRRKAERLEYERDEAREEVEELEKKVERMKA 505
                                       6899*********988.99*****************************99986 PP

>> HeLo  Prion-inhibition and propagation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   9.7     0.027        10      61     179 ..     399     510 ..     378     532 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.027
                                       -SHH.......HHHHHHHHHHHHHHHHHHHHHHHHHHHH--CGG.......G-B--GGGS-HHHHHHH.HHHHHHHH CS
                              HeLo  61 sdkrlddestrralvleileqiealleefeklqeryglklekqdasssslalssereksfraefellkrlmrkaakk 137
                                       ++ + d+++++ ++++e  ++i++l  + e+lq++    +++ +        +++r +++++e+e+ +r +rk ++k
  gi|336252649|ref|YP_004595756.1| 399 DESETDETEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLE-------QKDDRIDDLESELEAARRKERKEVRK 468
                                       44456677777778888888888888888888888777777655.......56788899999999999888899988 PP

                                       HS----S-----EEE-SHHHHHHHHHHHHHHHHHHHHTTT-H CS
                              HeLo 138 rqkrtslpkrlrWaivdkkkfeelvkdlkelvdsLeeLlpas 179
                                         + t+ ++++    +++++ +e v++l++ v+++++L +  
  gi|336252649|ref|YP_004595756.1| 469 DREVTRYRRKAERLEYERDEAREEVEELEKKVERMKALWKLD 510
                                       889*********************************998743 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   5.6     0.035        13      32      73 ..     391     435 ..     385     468 .. 0.67
   2 ?    4.8   3.1     0.072        27      24      84 ..     418     474 ..     416     502 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.035
                              FlxA  32 qLkelsesdeltkeekkkqqqli...qaQIqqlqaQIaqlqqqqa 73 
                                        L +l ++de  ++e + q  ++   ++ I++l+ Q+++lq+  +
  gi|336252649|ref|YP_004595756.1| 391 VLADLEDDDESETDETEHQPRELteeEKRIKDLKRQVERLQSHVD 435
                                       588999998888888887777774445679999999999998643 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.072
                              FlxA  24 kQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqqaekaqekqqsek 84 
                                       k ik+l+ q++ l++    t e++ +q++     I++l+++++   ++++++ ++ ++ ++
  gi|336252649|ref|YP_004595756.1| 418 KRIKDLKRQVERLQSH-VDTLEDRLEQKD---DRIDDLESELEAARRKERKEVRKDREVTR 474
                                       5566666666666666.555555555554...47777777777777777777666666555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.3      0.01       3.8      20      57 ..     407     444 ..     389     450 .. 0.80
   2 ?    8.8   5.5    0.0066       2.5      13      60 ..     414     461 ..     411     467 .. 0.77
   3 ?    1.2   3.3       1.6   5.9e+02       3      54 ..     446     500 ..     444     506 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXX CS
                              SlyX  20 eeLndvvaeqqqqidrlqrqlrllaerlkeleessgas 57 
                                       e   ++++e +++i+ l+rq+++l+ ++ +le++ +++
  gi|336252649|ref|YP_004595756.1| 407 EHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQK 444
                                       66667899999999999999999999999999987754 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0066
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXX CS
                              SlyX  13 afqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseae 60 
                                       +  e+ i++L ++v + q  +d l+ +l++  +r+ +le++ +a++++
  gi|336252649|ref|YP_004595756.1| 414 TEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRK 461
                                       556788888888888888888888888888888888888888776653 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                              SlyX   3 erleeLEiklafq...edtieeLndvvaeqqqqidrlqrqlrllaerlkeleess 54 
                                       +r+++LE++l      e+   + +++v++ +++ +rl+ + ++ +e+++ele++ 
  gi|336252649|ref|YP_004595756.1| 446 DRIDDLESELEAArrkERKEVRKDREVTRYRRKAERLEYERDEAREEVEELEKKV 500
                                       5666666665443111333334477899999999999999999999999998765 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  18.5     0.038        14      72     149 ..     416     502 ..     393     510 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.038
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXXX..........XXXXXXX CS
                        DASH_Spc19  72 aekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskkk..........ltkeele 138
                                        ek ++ l+r+ e L++ ++ +e rl++++++ ++ e++ e+++++e++e  +++++ ++             e  e
  gi|336252649|ref|YP_004595756.1| 416 EEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKERKEV-RKDREVTRyrrkaerleyERDEARE 491
                                       367777777777777777777777777765555555554444443333222.2222222223222233422222224 PP

                                       XXXXXXXXXXX CS
                        DASH_Spc19 139 rlkkLkqkKer 149
                                       ++++L +k er
  gi|336252649|ref|YP_004595756.1| 492 EVEELEKKVER 502
                                       44444444444 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.1    0.0064       2.4       6      50 ..     413     457 ..     411     460 .. 0.80
   2 ?    5.2   1.4     0.065        24      11      46 ..     470     505 ..     465     508 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0064
                              XhlA   6 lerietkldnleervdkleekaaeaeekiknleedlkklesnqkW 50 
                                       l++ e+++++l+ +v++l+ + ++ e ++++  +++++les +  
  gi|336252649|ref|YP_004595756.1| 413 LTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEA 457
                                       777788999999999999999999999999999999999887655 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.065
                              XhlA  11 tkldnleervdkleekaaeaeekiknleedlkkles 46 
                                       +++  +  + ++le   +ea+e++++le++++++++
  gi|336252649|ref|YP_004595756.1| 470 REVTRYRRKAERLEYERDEAREEVEELEKKVERMKA 505
                                       566777778889999999999999999999999886 PP

>> TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   5.9      0.74   2.8e+02      23      60 ..     423     460 ..     411     465 .. 0.83
   2 ?    9.6   4.2     0.002      0.76      24      59 ..     469     504 ..     468     507 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.74
                     TRAF_BIRC3_bd  23 LnrEverssttieaverqrrldqekieaLekKvrqLer 60 
                                       L+r ver ++ ++ +e   ++  + i+ Le  +++ +r
  gi|336252649|ref|YP_004595756.1| 423 LKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARR 460
                                       78999999999999999999999999999887776665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.002
                     TRAF_BIRC3_bd  24 nrEverssttieaverqrrldqekieaLekKvrqLe 59 
                                       +rEv r   ++e +e  r +++e +e LekKv+ ++
  gi|336252649|ref|YP_004595756.1| 469 DREVTRYRRKAERLEYERDEAREEVEELEKKVERMK 504
                                       59******************************9875 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   8.7     0.051        19     116     163 ..     430     482 ..     404     518 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.051
                              CorA 116 ldeivdrlfellekleeeldeledel...edstkkeil..relaqlrrrlvkl 163
                                       l++ vd+l++ le+ ++++d+le+el   +++++ke +  re++++rr++ +l
  gi|336252649|ref|YP_004595756.1| 430 LQSHVDTLEDRLEQKDDRIDDLESELeaaRRKERKEVRkdREVTRYRRKAERL 482
                                       7999**********************998555555554226788888888877 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.3     0.024       9.1      15      81 ..     388     454 ..     376     468 .. 0.52
   2 ?    2.0   0.8      0.53     2e+02      37      71 ..     469     503 ..     447     520 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.024
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II  15 vleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       v+++la+l+ + e + ++ ++  r++ e ++ +kd++++++  ++ v +Le  ++q  d++  l+  
  gi|336252649|ref|YP_004595756.1| 388 VEAVLADLEDDDESETDETEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESE 454
                                       4444444444444455555555555444455555555555555555555555555544444444443 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.53
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II  37 nrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       +r+v +   k++ +    ++Ar++v +Lek+++++
  gi|336252649|ref|YP_004595756.1| 469 DREVTRYRRKAERLEYERDEAREEVEELEKKVERM 503
                                       44555556677777778888999999999988875 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 ?    7.6   3.4     0.011       4.1      65     129 ..     395     459 ..     381     465 .. 0.74
   2 ?    5.0   5.9     0.067        25      31     106 ..     421     502 ..     417     518 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  65 lrekqkskkdn.dnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqke 129
                                       l+++ +s++d+ ++  +++++e e++i +lk+++ +  s++  L + le+++ +i +Le++ ++ +
  gi|336252649|ref|YP_004595756.1| 395 LEDDDESETDEtEHQPRELTEE-EKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAAR 459
                                       4444455554436666666666.559999*****9999********************99877655 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.067
                                       CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHH...HHHHHHCCCHHHHHHHCCH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvikks...skeleeeilrlketidaqe 101
                                       kd+k+++e+l++++++++++ ++ ++ + ++++ l+++ ++++++   d+ ++++   +++le e  + +e++ + e
  gi|336252649|ref|YP_004595756.1| 421 KDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKERKEvrkDREVTRYrrkAERLEYERDEAREEVEELE 497
                                       55666666666666666666666666666666666555555544323333333330003444444444444444444 PP

                                       HHHHH CS
                         Fib_alpha 102 snirv 106
                                       ++++ 
  gi|336252649|ref|YP_004595756.1| 498 KKVER 502
                                       44444 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 ?    4.6  10.7     0.094        35      52     102 ..     406     456 ..     386     467 .. 0.85
   2 ?   11.0   6.3     0.001      0.39      23      62 ..     467     506 ..     462     515 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.094
                       TMF_TATA_bd  52 lmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELraDva 102
                                         ++  el+e++k++++l++++e lq++ +tl   l +k++++++L+ +++
  gi|336252649|ref|YP_004595756.1| 406 TEHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELE 456
                                       5556678999************************************99886 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.001
                       TMF_TATA_bd  23 rlEgElaslkeelerleaerdeareeivklmkeneelkel 62 
                                       r++ E++ ++++ erle erdearee+ +l k++e++k+l
  gi|336252649|ref|YP_004595756.1| 467 RKDREVTRYRRKAERLEYERDEAREEVEELEKKVERMKAL 506
                                       7899********************************9975 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1         1   3.9e+02      77      93 ..     169     185 ..     154     194 .. 0.79
   2 ?    5.1  27.5     0.061        23      10     104 ..     407     501 ..     392     506 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1
                     Tropomyosin_1  77 altrkiqlLEeeleesd 93 
                                       +++r+ + +E elee++
  gi|336252649|ref|YP_004595756.1| 169 SVKRRAREVESELEEAN 185
                                       78999999999999986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.061
                     Tropomyosin_1  10 eeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrkiqlLE 86 
                                       e+      e e+++K+l  + ++  +++  L+ +++q ++ ++ le++l+ a++k  ++ +k+ +   + rk + LE
  gi|336252649|ref|YP_004595756.1| 407 EHQPRELTEEEKRIKDLKRQVERLQSHVDTLEDRLEQKDDRIDDLESELEAARRKERKEVRKDREVTRYRRKAERLE 483
                                       44444556778889999999999999999999999999999999999999999999999999999999999999999 PP

                     Tropomyosin_1  87 eeleesdkkLkettekLr 104
                                        e +e+ ++++e  +k +
  gi|336252649|ref|YP_004595756.1| 484 YERDEAREEVEELEKKVE 501
                                       999999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2209  (0.123208); expected 358.6 (0.02)
Passed bias filter:                      933  (0.0520386); expected 358.6 (0.02)
Passed Vit filter:                       235  (0.0131073); expected 17.9 (0.001)
Passed Fwd filter:                        85  (0.00474092); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              48  [number of targets reported over threshold]
# CPU time: 1.12u 0.30s 00:00:01.42 Elapsed: 00:00:00.44
# Mc/sec: 4471.76
//
Query:       gi|336252650|ref|YP_004595757.1|  [L=66]
Description: hypothetical protein Halxa_1245 [Halopiger xanaduensis SH-6]
Scores for 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   12.0   0.0       0.18   11.6   0.0    1.2  1  DUF5113   Domain of unknown function (DUF5113)


Domain annotation for each model (and alignments):
>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.9e-06      0.18     122     154 ..       8      40 ..       1      45 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.9e-06
                           DUF5113 122 ksLesycrqlersaknknvllilvvlllvvllv 154
                                        +Le+++++le+  + ++v+l+l + +l vl+v
  gi|336252650|ref|YP_004595757.1|   8 DELEARIERLESRVRSLTVGLVLSIGGLGVLTV 40 
                                       48***********************99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 510.56
//
Query:       gi|336252651|ref|YP_004595758.1|  [L=324]
Description: aryl-alcohol dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-73  246.2   0.0    4.4e-73  246.0   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
      0.016   15.1   0.1      0.039   13.8   0.1    1.7  1  RHH_5         CopG-like RHH_1 or ribbon-helix-helix domain, R


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 !  246.0   0.0   4.9e-77   4.4e-73       1     291 [.      15     313 ..      15     316 .. 0.94

  Alignments for each domain:
  == domain 1  score: 246.0 bits;  conditional E-value: 4.9e-77
                                       .EEEE-SSS-ST...TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE...-- CS
                      Aldo_ket_red   1 elglGtwqlgsk..eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv...dl 72 
                                       +++lG +++g++  +  ++ee+ el++ra++ GinffDtA+vY  g+see+lG +l++   +r+ +++a+Kv   + 
  gi|336252651|ref|YP_004595758.1|  15 KICLGCMSFGTDrnWMLDPEESRELIERAIDLGINFFDTANVYSAGESEEILGDVLAD--YDRDRMVVASKVrfsGA 89 
                                       69***********99*******************************************..**************999 PP

                                       SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH CS
                      Aldo_ket_red  73 rdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka 149
                                        d+ +  gls++ i+++le sl rLg d++Dl+++Hr+d+++p ie +l+al++ v+  k+r++G S+  + q  +a
  gi|336252651|ref|YP_004595758.1|  90 TDHRNATGLSRKTIEQELEHSLDRLGMDTLDLYQIHRWDYDTP-IETTLRALDDAVRRDKVRHVGASSMWAHQFLEA 165
                                       9******************************************.***********************8887776667 PP

                                       ....HHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------... CS
                      Aldo_ket_red 150 ....kkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd... 219
                                           ++++  ++ + q+ y+l  ++ee++++++c++++v++i++spl+ G+l +  ++ + + ++e++ +       
  gi|336252651|ref|YP_004595758.1| 166 rrvsEREGLAPFETMQNLYHLAYREEEREMYPVCEQYDVGTIPWSPLAAGYLARPHEEFQTTTRGEHEAKE--Agvp 240
                                       7999999**********************************************777766666655555432..2579 PP

                                       .TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS
                      Aldo_ket_red 220 .ertsknldaaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaelde 291
                                        +++++  + +e+++ela e+gv++aq+al++ +++++v+ +i+g+s++e+le+ ++ale++ls+++v++l+e
  gi|336252651|ref|YP_004595758.1| 241 yHEFPGSEEINERVQELADEKGVTMAQIALAWHFQNDNVTAPIVGTSSVEHLEEAVEALEIDLSDSDVDYLEE 313
                                       9********************************************************************9987 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.4e-06     0.039      10      31 ..     248     269 ..     247     271 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-06
                             RHH_5  10 eelleeLeewAdeegRsvSnla 31 
                                       ee++e+++e+Ade g+++++ a
  gi|336252651|ref|YP_004595758.1| 248 EEINERVQELADEKGVTMAQIA 269
                                       8******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); 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 0.22s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2602.22
//
Query:       gi|336252652|ref|YP_004595759.1|  [L=311]
Description: ribonuclease Z [Halopiger xanaduensis SH-6]
Scores for 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-20   71.6   2.9    2.6e-17   63.0   2.9    2.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    9.7e-13   48.6   6.1    1.9e-11   44.3   1.1    2.2  2  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.022   14.4   0.0      0.042   13.5   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 !   63.0   2.9   4.3e-21   2.6e-17       3     201 .]      33     269 ..      32     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 4.3e-21
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE..EEEEEEHHHHHHCCTTC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkk..lplyapkgvlavleanf 74 
                                       +L+Dag ++  q++r         +  ++  +++th H DH+ g++ l +   + +++  l ++ p+g++++l++  
  gi|336252652|ref|YP_004595759.1|  33 LLFDAGEGTQRQMMRFG-------TGFSVSHLFVTHLHGDHVLGIPGLLQtmdFNDREepLAIHTPLGTRRKLKSLV 102
                                       699*****888877776.......44599*********************98855555679999************* PP

                                       GHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C.................................TC CS
                     Lactamase_B_2  75 vylaleeepavnvheldwgesfelgdggleitatparhksgr.................................rl 118
                                        +l  +++++v+++e+  g+    +d + ei+++   h++                                   ++
  gi|336252652|ref|YP_004595759.1| 103 NALDNDPAFPVRINEVGDGDVAYRAD-EYEIRVFGTDHDTRSvgyalveddrkgrfdreraeelgvpvgpkfsqlHE 178
                                       99999999********9888776676.68***********999****999999966666666666666555555444 PP

                                       CE-TTTSEEEEEE........CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSHHH CS
                     Lactamase_B_2 119 drnagdtlGlrie........gggkrvyyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeeave 186
                                       ++  ++  G ++e        ++g++++y+gDt  + + + e  + +dll++d+t+ ed+  ++ +  H+t  +a+e
  gi|336252652|ref|YP_004595759.1| 179 GTPVELEDGTVVEpeqvvgdpRPGRTIVYTGDTRPTAATL-EVADEPDLLIHDATFAEDRADRAaKTAHATATQAAE 254
                                       44444667777777777777888888********998775.59999*************986669************ PP

                                       HCTTSSSSEEEEESB CS
                     Lactamase_B_2 187 aaadlgakrlvliHi 201
                                       +a+++gakrl l+Hi
  gi|336252652|ref|YP_004595759.1| 255 IANRAGAKRLALMHI 269
                                       **************8 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   1.1   3.2e-15   1.9e-11       7     144 ..      22     150 ..      16     171 .. 0.86
   2 !    7.0   0.5    0.0009       5.4      98     162 ..     178     242 ..     149     276 .. 0.70

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3.2e-15
                                       EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                       Lactamase_B   7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                       + +++  +g+ +L+D+G +t+++++      +   +  v+++++THlH DH+ g +gl ++ d++ ++++++ + ++
  gi|336252652|ref|YP_004595759.1|  22 SGIFVSREGEGLLFDAGEGTQRQMM------RFGTGFSVSHLFVTHLHGDHVLGIPGLLQTMDFNDREEPLAIHTPL 92 
                                       5578899******************......79******************************************** PP

                                       CHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCC CS
                       Lactamase_B  84 meeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggk 144
                                       +  ++  +      +   ++  p++  e++dg+++ r + y +  +g+ h+  +v+y    
  gi|336252652|ref|YP_004595759.1|  93 GTRRKLKSLVN---ALDNDPAFPVRINEVGDGDVAYRADEYEIRVFGTDHDTRSVGYALVE 150
                                       ****7776666...46888889999999999999999999999999999998888887655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0009
                                       TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B  98 lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl 162
                                         ++++  ++++ e++++ +++r++  ++++  + ++ + +e  ++  l+  Da++a+++++   
  gi|336252652|ref|YP_004595759.1| 178 EGTPVELEDGTVVEPEQVVGDPRPGRTIVYTGDTRPTAATLEVADEPDLLIHDATFAEDRADRAA 242
                                       45677777777778888888888888888888888888888888888888888888777666555 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     7e-06     0.042       7      59 ..      16      65 ..      12      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7e-06
                     Lactamase_B_4  7 tsDtsgPlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkvsws 59
                                      t + + + ++++ + +  lf + gEgtQR ++  ++ +s +++ F+t+ +  +
  gi|336252652|ref|YP_004595759.1| 16 TTERNPSGIFVSREGEGLLF-DAGEGTQRQMMRFGTGFS-VSHLFVTHLH-GD 65
                                      5555556778888888889*.************999996.8899999988.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); 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:                         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 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2387.60
//
Query:       gi|336252653|ref|YP_004595760.1|  [L=406]
Description: hypothetical protein Halxa_1248 [Halopiger xanaduensis SH-6]
Scores for 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   12.3   0.2        0.6   10.3   0.0    2.1  2  Transglut_C  Transglutaminase family, C-terminal ig like doma
       0.18   12.5   9.8        3.1    8.5   2.7    3.5  3  fn3_5        Fn3-like domain


Domain annotation for each model (and alignments):
>> Transglut_C  Transglutaminase family, C-terminal ig like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   6.7e-05       0.6       4      44 ..     168     209 ..     167     233 .. 0.80
   2 ?   -1.5   0.0      0.31   2.7e+03      20      37 ..     261     277 ..     249     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.7e-05
                                       EEEESSCEBTTSEEEEEEEEEE-SSS-B.EEEEEEEEEEEEE CS
                       Transglut_C   4 kievlesavlgqdltvsvllkNplseel.kdvklnlcaqtve 44 
                                       +i+v++sa  +  ++v+++++Np++ ++ ++v+++l + +ve
  gi|336252653|ref|YP_004595760.1| 168 SIDVPSSATTNGTIDVNATISNPTEFTTqQNVEVRLDGAVVE 209
                                       599*********************977525777777766665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.31
                                       EEEEEE-SSS-BEEEEEE CS
                       Transglut_C  20 svllkNplseelkdvkln 37 
                                        +++ N++++e  +v+ n
  gi|336252653|ref|YP_004595760.1| 261 AITVANTSENE-STVTFN 277
                                       58899999999.898876 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.7   0.00034       3.1      12      86 ..     112     193 ..     104     207 .. 0.75
   2 ?    4.0   1.9     0.009        81      62      87 ..     209     233 ..     186     297 .. 0.61
   3 ?    2.2   0.3     0.032   2.8e+02      13     106 ..     261     294 ..     248     324 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00034
                             fn3_5  12 ftltlkNtsnkaltykvsandvlTdladkeegklilkaaspeike...aaltfetskvtvpAnssk....tvtvtld 81 
                                        t t++  ++ ++ty++++++   d+ + e+g ++ + a  + +e    +++f+ +++ vp  +++    +v++t++
  gi|336252653|ref|YP_004595760.1| 112 LTATVHQDTDGDETYTYAESEGEEDRPYLEDGFPVSDTATVTTAEeqgLTNSFAVESIDVPSSATTngtiDVNATIS 188
                                       577899999***********9999999999999999988887777788999*********96444311004444444 PP

                             fn3_5  82 lpsda 86 
                                        p+++
  gi|336252653|ref|YP_004595760.1| 189 NPTEF 193
                                       44444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.009
                             fn3_5  62 etskvtvpAnssktvtvtldlpsdak 87 
                                       e + + ++A++s++vt+++d+ s+a+
  gi|336252653|ref|YP_004595760.1| 209 ERQLLELEAEESRDVTFQVDA-SEAA 233
                                       556667777777777777777.4333 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.032
                             fn3_5  13 tltlkNtsnkaltykvsandvlTdladkeegklilkaaspeikeaaltfetskvtvpAnssktvtvtldlpsdakkk 89 
                                        +t+ Nts+++ t +++  +                                                         
  gi|336252653|ref|YP_004595760.1| 261 AITVANTSENESTVTFNVAT--------------------------------------------------------- 280
                                       35555555555554444441......................................................... PP

                             fn3_5  90 ngyfveGfvtlkdsedk 106
                                           + Gfv ++d  d 
  gi|336252653|ref|YP_004595760.1| 281 ---PADGFVAVEDRADG 294
                                       ...12344444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2948.35
//
Query:       gi|336252654|ref|YP_004595761.1|  [L=334]
Description: Replication factor C [Halopiger xanaduensis SH-6]
Scores for 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   52.4   0.1    3.1e-13   50.3   0.0    2.0  2  AAA              ATPase family associated with various cellul
    2.9e-12   46.7   0.0    5.3e-12   45.8   0.0    1.4  1  DNA_pol3_delta2  DNA polymerase III, delta subunit
      4e-11   43.2   0.3    9.6e-11   42.0   0.1    1.7  1  Rep_fac_C        Replication factor C C-terminal domain
    9.5e-08   32.4   0.0    2.6e-07   31.0   0.0    1.7  1  AAA_22           AAA domain
    2.8e-06   27.8   0.3    5.5e-05   23.6   0.0    2.7  2  AAA_16           AAA ATPase domain
    1.5e-05   25.5   0.0    4.8e-05   23.9   0.0    1.8  1  AAA_18           AAA domain
    1.6e-05   24.6   0.0    0.00054   19.7   0.0    2.6  3  Sigma54_activat  Sigma-54 interaction domain
     0.0001   21.8   0.0    0.00017   21.0   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00015   21.8   2.0     0.0014   18.6   0.4    2.8  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00022   21.2   0.0    0.00064   19.7   0.0    1.9  1  NACHT            NACHT domain
    0.00044   20.6   0.1      0.003   17.9   0.0    2.1  2  AAA_19           AAA domain
    0.00045   20.1   0.0     0.0012   18.7   0.0    1.6  1  AAA_11           AAA domain
     0.0006   19.2   0.0     0.0033   16.7   0.0    2.0  2  Zeta_toxin       Zeta toxin
     0.0007   19.6   0.0     0.0019   18.2   0.0    1.7  1  AAA_14           AAA domain
     0.0008   19.2   0.0     0.0013   18.4   0.0    1.3  1  AAA_24           AAA domain
     0.0019   18.3   0.0      0.012   15.8   0.0    1.9  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0026   16.8   0.0     0.0062   15.6   0.0    1.6  1  T2SSE            Type II/IV secretion system protein
     0.0079   15.9   0.2       0.25   11.0   0.0    2.4  2  His_Phos_1       Histidine phosphatase superfamily (branch 1)
      0.008   16.1   0.0      0.013   15.4   0.0    1.3  1  Rad17            Rad17 P-loop domain
     0.0094   15.7   0.0      0.026   14.3   0.0    1.7  1  IstB_IS21        IstB-like ATP binding protein
     0.0098   16.0   0.0      0.022   14.9   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
  ------ inclusion threshold ------
      0.015   15.2   0.2      0.086   12.7   0.0    2.2  2  Bac_DnaA         Bacterial dnaA  protein
      0.015   15.4   0.0       0.03   14.5   0.0    1.6  1  AAA_33           AAA domain
      0.024   14.4   0.2      0.091   12.5   0.0    2.0  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.046   12.9   0.0      0.073   12.3   0.0    1.2  1  TIP49            TIP49 P-loop domain
      0.054   13.2   0.0       0.11   12.2   0.0    1.6  1  AAA_30           AAA domain
      0.061   13.0   0.0        6.9    6.3   0.0    2.6  2  Lipoprotein_16   Uncharacterized lipoprotein
      0.072   12.7   0.0        3.1    7.3   0.0    2.3  2  AAA_25           AAA domain
      0.075   13.2   0.3      0.075   13.2   0.3    2.9  3  Metal_resist     Heavy-metal resistance
      0.091   12.5   0.2        6.3    6.5   0.0    2.3  2  DEAD             DEAD/DEAH box helicase
       0.11   12.5   0.0       0.23   11.5   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.16   11.4   0.0       0.54    9.7   0.0    1.8  2  AAA_7            P-loop containing dynein motor region


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 !   50.3   0.0   5.5e-16   3.1e-13       1     124 [.      36     170 ..      36     178 .. 0.87
   2 ?   -1.0   0.1       4.1   2.3e+03      65      90 ..     247     272 ..     238     312 .. 0.70

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 5.5e-16
                                       EEEESSTTSSHHHHHHHHHHHHT....HEEEEEETTTCSSS..............STTHHHHHHHHHHHHH.HHTS. CS
                               AAA   1 vllyGppGtGKTllakavakelg....vefleisgsellsk..............yvgesekkirelfkea.keka. 57 
                                       +ll GppG GKT++a+a+a+e++     +++ei++++++                +vg s+++ r++++++ ke+a 
  gi|336252654|ref|YP_004595761.1|  36 LLLQGPPGSGKTAAARALAREAHvdpdNDLIEINVADFFGRtkteikndprfaqfLVGRSSMSKRDMINRVlKESAs 112
                                       699*******************7333366**********6679**************************96255558 PP

                                       ......TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTS CS
                               AAA  58 ......kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRf 124
                                             + + +++D+++ +            e+ +++L + +++  +   ++ +i+at +p kl p+++ +R+
  gi|336252654|ref|YP_004595761.1| 113 yssvsgEYKTILLDNAEDVR-----------EDFQQALRRIMEQHHR---TTQFIVATRQPTKLIPPIR-SRC 170
                                       99999666999999999993...........457***********99...478****************.887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.1
                                       ETGGGHHHHHTTCCCHHHHHHHHHHH CS
                               AAA  65 DEidalaksrsgseseeeervvnqLl 90 
                                       DEi+++  + + +e ++++++++ Ll
  gi|336252654|ref|YP_004595761.1| 247 DEIESMLDDAEAGEFTDARSTLDDLL 272
                                       78888877776666666666666665 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 !   45.8   0.0   9.5e-15   5.3e-12      22     160 ..      36     176 ..      26     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 9.5e-15
                   DNA_pol3_delta2  22 yLfeGdegigkkelalnlakallceeknetkpcgecksckkieqgkhpDviviet.eekersikldqir.elieels 96 
                                       +L++G+ g+gk ++a +la++   + +n+  + +  +   + +++   D  +++   ++++  k d i+  l+e++s
  gi|336252654|ref|YP_004595761.1|  36 LLLQGPPGSGKTAAARALAREAHVDPDNDLIEINVADFFGRTKTEIKNDPRFAQFlVGRSSMSKRDMINrVLKESAS 112
                                       699************************99988889999999999999999999763444344555888746789999 PP

                   DNA_pol3_delta2  97 rkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfs 160
                                        +++ +++k i++++ae +++  + al +++E  ++ + fi+ t++++kl+++irSRc  ++++
  gi|336252654|ref|YP_004595761.1| 113 YSSVSGEYKTILLDNAEDVREDFQQALRRIMEQHHRTTQFIVATRQPTKLIPPIRSRCFPVSVR 176
                                       **********************************************************999876 PP

>> 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 !   42.0   0.1   1.7e-13   9.6e-11       3      87 ..     246     328 ..     245     329 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.7e-13
                                       HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-HH CS
                         Rep_fac_C   3 pteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGaseh 79 
                                       ++eie++l+ +++g+f++a+++l++llv++G+ +e++l  + r+  +   ++ +  ++i  l+++ie+ l eG+s++
  gi|336252654|ref|YP_004595761.1| 246 DDEIESMLDDAEAGEFTDARSTLDDLLVDEGLDGEEVLDAILRIGRKR--YQGEKLARIHRLAADIEFELHEGTSDR 320
                                       579********99*******************************8874..889999999999*************** PP

                                       HHHHHHHH CS
                         Rep_fac_C  80 lqlsalla 87 
                                       ++ s lla
  gi|336252654|ref|YP_004595761.1| 321 IHVSHLLA 328
                                       ******98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   4.6e-10   2.6e-07       8     127 ..      36     154 ..      31     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 4.6e-10
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdl..lrellralglelkaerlsseelle 80 
                                       l++ G++G+GKT  +r l+++++ +     ++ ++++++++     + +++    +++++l  + +    s++++++
  gi|336252654|ref|YP_004595761.1|  36 LLLQGPPGSGKTAAARALAREAHVD-----PDNDLIEINVADFFgrTKTEIknDPRFAQFLVGRSS---MSKRDMIN 104
                                       6889*****************9876.....599*********999999999744555555555555...5******* PP

                            AAA_22  81 aleqalrarav....ielliiDEaqhlrseealeeLrsllnlsrkgvqliL 127
                                       ++ + + +++      + +++D+a+ + +e+  + Lr++++ ++  +q+i+
  gi|336252654|ref|YP_004595761.1| 105 RVLKESASYSSvsgeYKTILLDNAEDV-REDFQQALRRIMEQHHRTTQFIV 154
                                       ***************************.99999999999997666677765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   9.9e-08   5.5e-05      10     160 ..      20     144 ..      16     155 .. 0.47
   2 ?    0.2   0.0       1.6   8.7e+02      64     106 ..     232     273 ..     203     317 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 9.9e-08
                            AAA_16  10 eqLlsalervrsgrpelvllsGesGvGKsslvrellralekd..............ggiflrgkcdqlesaipysal 72 
                                       + ++++ler+ + +p ++ll G++G+GK++ +r+l+r++  d              g                    
  gi|336252654|ref|YP_004595761.1|  20 DDVREYLERAVD-EPINLLLQGPPGSGKTAAARALAREAHVDpdndlieinvadffG-------------------- 75 
                                       677899998885.5789*******************977766444444333222210.................... PP

                            AAA_16  73 aqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwade 149
                                              +  ++++++      ++++++l ++ +       +++  ++++lk+ ++++s  ++   ++lD++++++e
  gi|336252654|ref|YP_004595761.1|  76 -------RTKTEIKND------PRFAQFLVGRSS------MSKRDMINRVLKESASYSSVSGEYKTILLDNAEDVRE 133
                                       .......111222222......222222222222......1111223333333333333333333333333333333 PP

                            AAA_16 150 aslqllaaLlr 160
                                       + +q+l+ +++
  gi|336252654|ref|YP_004595761.1| 134 DFQQALRRIME 144
                                       33333333333 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.6
                            AAA_16  64 esaipysalaqalareellrqlldeaesaeleawrekleeala 106
                                       +++++y +l ++   ++ ++ +ld+ae+ e+ ++r +l++ l 
  gi|336252654|ref|YP_004595761.1| 232 TMNAAYETLGEVG-LDDEIESMLDDAEAGEFTDARSTLDDLLV 273
                                       5556666666655.34677888888888888888888888777 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   8.5e-08   4.8e-05       2      67 ..      37     146 ..      36     163 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 8.5e-08
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf........................................gvnlrdvakengll 38 
                                       ll G+pG+GKt  a++L+++ ++                                         + ++ v+ke+ ++
  gi|336252654|ref|YP_004595761.1|  37 LLQGPPGSGKTAAARALAREAHVdpdndlieinvadffgrtkteikndprfaqflvgrssmskRDMINRVLKESASY 113
                                       588**************999777999999955555555555555555555555555555555555555555555555 PP

                            AAA_18  39 levdpe....aldeskrldedkldklldaleen 67 
                                        +v  e     ld+ + ++ed++++l +++e++
  gi|336252654|ref|YP_004595761.1| 114 SSVSGEyktiLLDNAEDVREDFQQALRRIMEQH 146
                                       555555555555555555555555555555555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   9.7e-07   0.00054      10      61 ..      21      73 ..      15      79 .. 0.87
   2 ?    1.4   0.0       0.4   2.2e+02      96     121 ..     122     147 ..     116     153 .. 0.89
   3 ?   -1.9   0.0       4.3   2.4e+03      66      86 ..     249     269 ..     246     295 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.7e-07
                                      HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTT.TTS-EEEEETTTS CS
                   Sigma54_activat 10 elleqikkvaktdlsvlitGesGtGKellaraiheaskr.kekpfvavncaai 61
                                      +++e ++++++ ++++l++G  G+GK+  ara+ ++ +   ++ ++++n+a++
  gi|336252654|ref|YP_004595761.1| 21 DVREYLERAVDEPINLLLQGPPGSGKTAAARALAREAHVdPDNDLIEINVADF 73
                                      6788999**************************98665516899*****9985 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.4
                                       EEEEETGGGS-HHHHHHHHHHHHHSE CS
                   Sigma54_activat  96 tlfLDeigelplelQekLlrvlqege 121
                                       t++LD+ +++  ++Q+ L r++++++
  gi|336252654|ref|YP_004595761.1| 122 TILLDNAEDVREDFQQALRRIMEQHH 147
                                       899******************99865 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.3
                                       HHHHHHEBSSSSSTTTSS-BE CS
                   Sigma54_activat  66 leseLFGhekGaFtGAekekk 86 
                                       +es L   e+G Ft+A+++  
  gi|336252654|ref|YP_004595761.1| 249 IESMLDDAEAGEFTDARSTLD 269
                                       567777789999999998755 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     3e-07   0.00017       9     134 ..      20     147 ..      15     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3e-07
                      Mg_chelatase   9 eeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag.kkeeekllkrrpfraphhs 84 
                                       ++ ++ le a+    nlll GppGsGKt  a++l+       +++ +e++      + k+e ++  + + f   + s
  gi|336252654|ref|YP_004595761.1|  20 DDVREYLERAVDEPINLLLQGPPGSGKTAAARALAREAHVDPDNDLIEINVADFFGRtKTEIKNDPRFAQFLVGRSS 96 
                                       566777777888888*******************99877777788888877665554344455666777899999** PP

                      Mg_chelatase  85 askaalvGg..gskpkpGeislahnGvLfLDElpefkrkvlevLRePledge 134
                                       +sk  ++     +++    +s   + + +LD + + +++  ++LR+ +e+++
  gi|336252654|ref|YP_004595761.1|  97 MSKRDMINRvlKESASYSSVSGEYKTI-LLDNAEDVREDFQQALRRIMEQHH 147
                                       *******98334466667777766665.59****************999875 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   0.4   2.6e-06    0.0014       1      95 [.      35     149 ..      35     167 .. 0.80
   2 ?    0.3   0.1       1.1   6.3e+02      49      77 ..     221     252 ..     179     257 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.6e-06
                                       EEEEE--SSSSHHHHHHHGGGGB....S--EEEEE--TT-..-HHHHH--B--.................------- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal....nreveyvqltrdt..teedlkgrreik........ngttslvdsplvraa 63 
                                       ++lL+GppG+gK+  a+ la+       + + +++  ++   t++++k   +++        ++++ + + +l+++a
  gi|336252654|ref|YP_004595761.1|  35 NLLLQGPPGSGKTAAARALAREAhvdpDNDLIEINVADFFgrTKTEIKNDPRFAqflvgrssMSKRDMINRVLKESA 111
                                       69******************988889755666666665543366777777776688877777777778888888887 PP

                                       -......G-SEEEEESGGG--HHHHHHHHHHHHSSEEE CS
                             AAA_5  64 r......egeilvlDEveraesevlnsLlslleerrll 95 
                                              e ++++lD  e ++ + +++L +++e+ ++ 
  gi|336252654|ref|YP_004595761.1| 112 SyssvsgEYKTILLDNAEDVREDFQQALRRIMEQHHRT 149
                                       79999999999999999999999999999999998876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.1
                                       ........--------...G-SEEEEESGGG- CS
                             AAA_5  49 ngttslvdsplvraar...egeilvlDEvera 77 
                                        +tt+  +++l+ +a     ge+ ++DE+e +
  gi|336252654|ref|YP_004595761.1| 221 AQTTVEDEGELTMNAAyetLGEVGLDDEIESM 252
                                       55666666777766667888999999999865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.1e-06   0.00064       3     132 ..      36     162 ..      35     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-06
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCS CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvsevwavllel 79 
                                       ++lqG++GsGKT+ ++ la+++  + ++      v  ++ r+ ++++n +++a++l+     ++++  +    ++  
  gi|336252654|ref|YP_004595761.1|  36 LLLQGPPGSGKTAAARALAREAHVDPDNDLIEINVADFFGRTKTEIKNDPRFAQFLVGRSSMSKRDMIN----RVLK 108
                                       689******************9999888875455556667777777777999**999876665555444....3333 PP

                                       CCCEE.........EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCH CS
                             NACHT  80 perlL.........lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpral 132
                                       +             ++lD ++++++d++q         L++++++ + ++  +++t +p++l
  gi|336252654|ref|YP_004595761.1| 109 ESASYssvsgeyktILLDNAEDVREDFQQ--------ALRRIMEQHHRTTQFIVATRQPTKL 162
                                       333334779999999**************........9999999988888888888888877 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   5.3e-06     0.003      12     130 ..      35     147 ..      26     156 .. 0.80
   2 ?   -0.2   0.1       2.1   1.2e+03      74     121 ..     239     286 ..     181     294 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.3e-06
                            AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddllteal 88 
                                       +ll+ ++pG+GKT   ++  +++    + ++ ei ++ f gr   e+++      + a+ + + + +   d +    
  gi|336252654|ref|YP_004595761.1|  35 NLLLQGPPGSGKTAAARALAREAHVDPDNDLIEINVADFFGRTKTEIKNDP----RFAQFLVGRSSMSKRDMI---N 104
                                       57899*****************99999999******************988....335555444345455555...5 PP

                            AAA_19  89 elleeaeeekklqeee.llivDEfqdvdelqyrLlkallgekk 130
                                        +l+e+++ + +  e+ +++ D + dv e  ++ l++++++++
  gi|336252654|ref|YP_004595761.1| 105 RVLKESASYSSVSGEYkTILLDNAEDVREDFQQALRRIMEQHH 147
                                       77888888899988889***********999999999986665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.1
                            AAA_19  74 rlalldfddlltealelle...eaeeekklqeeellivDEfqdvdelqyrL 121
                                        l+++++dd+++ +l   e    ++ +++l   + l+vDE  d +e+  ++
  gi|336252654|ref|YP_004595761.1| 239 TLGEVGLDDEIESMLDDAEageFTDARSTL---DDLLVDEGLDGEEVLDAI 286
                                       344467777775544443333222333333...478999977766655555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.1e-06    0.0012       6      96 ..      22     128 ..      18     163 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.1e-06
                            AAA_11   6 qreaiksalseseitliqGPPGtgKTktivellsqll..................srrkseeeksakpriLvCapSN 64 
                                        re +++a+ e+   l+qGPPG+gKT +  +l ++++                  +  k e ++++     + + S 
  gi|336252654|ref|YP_004595761.1|  22 VREYLERAVDEPINLLLQGPPGSGKTAAARALAREAHvdpdndlieinvadffgrT--KTEIKNDPRFAQFLVGRSS 96 
                                       56778999999999*********************997766555555444444320..2222233333333334444 PP

                            AAA_11  65 aAvDellerllrglldsegekykpkivRvgne 96 
                                        +  +++ r+l++  + +  + + k++ + n+
  gi|336252654|ref|YP_004595761.1|  97 MSKRDMINRVLKESASYSSVSGEYKTILLDNA 128
                                       44444445555544444444444555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     6e-06    0.0033      12      50 ..      29      69 ..      19      77 .. 0.80
   2 ?   -0.3   0.0         1   5.6e+02     152     187 ..     121     157 ..      89     165 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6e-06
                        Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdele..rqgnvvrld 50
                                      + ++P+ +ll G pG+GK+++a++l++e +  ++++ ++++
  gi|336252654|ref|YP_004595761.1| 29 AVDEPINLLLQGPPGSGKTAAARALAREAHvdPDNDLIEIN 69
                                      3389**********************998766777777776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1
                        Zeta_toxin 152 Rlvpkeehdeafeglresvealeeek.qldrvkikdr 187
                                         +  ++ +++ e ++++++++ e++ ++ + ++++r
  gi|336252654|ref|YP_004595761.1| 121 KTILLDNAEDVREDFQQALRRIMEQHhRTTQFIVATR 157
                                       5555555566666666666665555434444445544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.4e-06    0.0019       5      97 ..      36     154 ..      33     166 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.4e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikell.vkkesilyinldderd..................kkladpe......klleli 56 
                                       l+++G+  +GKT  ++ l++e    ++++ ++in+ d                     +     +       +++++
  gi|336252654|ref|YP_004595761.1|  36 LLLQGPPGSGKTAAARALAREAHvDPDNDLIEINVADFFGrtkteikndprfaqflvgR-----SsmskrdMINRVL 107
                                       6899*****************9977788999***9994333334444444444444431.....0433342344444 PP

                            AAA_14  57 leklke.....ekktylflDEiqev.pewekalkslvdeg.knldviv 97 
                                       +e++ +      + + ++lD +  v +++++al+++++++ +  ++iv
  gi|336252654|ref|YP_004595761.1| 108 KESA-SyssvsGEYKTILLDNAEDVrEDFQQALRRIMEQHhRTTQFIV 154
                                       4442.14578756667********9456**********8856677776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.4e-06    0.0013       3      87 ..      34     141 ..      32     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.4e-06
                            AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie....................swedfldevvel 59 
                                       +++l+ Gp+g+GKT  a+ l  + + +d ++ l ++++++f   +                    s           
  gi|336252654|ref|YP_004595761.1|  34 INLLLQGPPGSGKTAAARAL-AREAHVDPDNDLIEINVADFFGRTkteikndprfaqflvgrssmS----------K 99 
                                       68999***************.999999999988888888774333455555555556666665552..........0 PP

                            AAA_24  60 ..............aaeladyktlviDtideleelclaevir 87 
                                                     +    +ykt+ +D+++++ e   + ++r
  gi|336252654|ref|YP_004595761.1| 100 rdminrvlkesasySSVSGEYKTILLDNAEDVREDFQQALRR 141
                                       4444444555666699999***********998877766654 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 !   15.8   0.0   2.1e-05     0.012      10      47 ..      22      59 ..      17      81 .. 0.86
   2 ?   -0.1   0.0       1.6   9.2e+02      69     107 ..     119     156 ..      82     162 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.1e-05
                                      HHHHHHHHHT-SS-EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2 10 lkerLeqaaqsklpvfltGekGsgkelvArlLhknsgp 47
                                       +e Le a+ +  +++l G++Gsgk+  Ar+L+ ++  
  gi|336252654|ref|YP_004595761.1| 22 VREYLERAVDEPINLLLQGPPGSGKTAAARALAREAHV 59
                                      6789****************************987665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.6
                                       TTSEEEEEE-TT--HHHHHHHHHHHHHHTTTT-EEEEEE CS
                   Sigma54_activ_2  69 kggtLylkdiadlskaeqkeLlellakaeksslrlVsts 107
                                       +  t++l + +d  ++ q+ L  ++++  +   +++ ++
  gi|336252654|ref|YP_004595761.1| 119 EYKTILLDNAEDVREDFQQALRRIMEQH-HRTTQFIVAT 156
                                       5568899999999999999998888777.7777777776 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 !   15.6   0.0   1.1e-05    0.0062     115     155 ..      19      59 ..       9      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                             T2SSE 115 kekiaevlrkavrerglilvsGgTgsGKttllyallkeink 155
                                       +++++e l++av e  ++l+ G+ gsGKt  + al  e + 
  gi|336252654|ref|YP_004595761.1|  19 QDDVREYLERAVDEPINLLLQGPPGSGKTAAARALAREAHV 59 
                                       67899*************************99999887665 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 !   11.0   0.0   0.00045      0.25      58     103 ..      46      89 ..      44     108 .. 0.81
   2 ?    2.6   0.1      0.17        95      92     146 ..     101     155 ..      93     163 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00045
                                       HHHHHHHHCTT--EEE-GGGS----GGGTT-B.HHHHHH..HSHHH CS
                        His_Phos_1  58 qTaeliaealglpveldegLrEidfGdweglttaeiaeeypeelea 103
                                       +Ta++ a a++  v  d +L Ei++ d+ g+t++ei+++   ++++
  gi|336252654|ref|YP_004595761.1|  46 KTAAARALAREAHVDPDNDLIEINVADFFGRTKTEIKND--PRFAQ 89 
                                       58888888999***********************99987..44444 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.17
                                       HHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE CS
                        His_Phos_1  92 eiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVs 146
                                       ++ ++  +e + +++ + +++     + edv++  ++al++++++h+  t  +V+
  gi|336252654|ref|YP_004595761.1| 101 DMINRVLKESASYSSVSGEYKTILLDNAEDVREDFQQALRRIMEQHHRTTQFIVA 155
                                       55555555556666666666666677899******************99977776 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.4e-05     0.013      39     157 ..      25     144 ..      10     159 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.4e-05
                             Rad17  39 vLesrkkr..iLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn...qksdfkgltekesrf......ls 104
                                       +Le++  +   LL+ GP+G gk+ + + L++e  ++  + l  +++  +d+    k+++k +    + f      +s
  gi|336252654|ref|YP_004595761.1|  25 YLERAVDEpiNLLLQGPPGSGKTAAARALAREAHVDPDNDLIEINV--ADFfgrTKTEIKNDPRFAQ-FlvgrssMS 98 
                                       4555544453599*******************98887777766663..3332234444444433322.323332344 PP

                             Rad17 105 qiesfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrdsdalrevir 157
                                       + +  + ++  +a y         + ++ k il+++  ++ +   +alr ++ 
  gi|336252654|ref|YP_004595761.1|  99 KRDMINRVLKESASY-------SSVSGEYKTILLDNAEDVREDFQQALRRIME 144
                                       444444443333333.......4556888888887655443333344444444 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 !   14.3   0.0   4.6e-05     0.026      44      72 ..      30      58 ..      16      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-05
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialgveav 72
                                      +++  n++l Gp+G GK+  a al++ea 
  gi|336252654|ref|YP_004595761.1| 30 VDEPINLLLQGPPGSGKTAAARALAREAH 58
                                      566679*******************9984 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.8e-05     0.022       3     105 ..      33     145 ..      31     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.8e-05
                                       ---EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS......... CS
                             AAA_2   3 iisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG......... 70 
                                        i++ll gp g+Gkt +a+ala+  +v+ ++ li ++  ++      ++ ++++   +++ vg+             
  gi|336252654|ref|YP_004595761.1|  33 PINLLLQGPPGSGKTAAARALAREAHVDPDNDLIEINVADFFG--RTKTEIKNDPRFAQFLVGRSSMSkrdminrvl 107
                                       5899***********************9999999999999988..78888888888888888888888888888888 PP

                                       ..............EEEEETGGG-------------HHHHHHHHHHHH- CS
                             AAA_2  71 ..............ivllDEidKihpkessgadvSregVqrdLLqileg 105
                                                      +llD+ + + +           + q++L +i+e+
  gi|336252654|ref|YP_004595761.1| 108 kesasyssvsgeykTILLDNAEDVRE-----------DFQQALRRIMEQ 145
                                       88888888888889999999999888...........888888888886 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.7   9.6e+02      37      75 ..      36      74 ..      24     103 .. 0.72
   2 ?   12.7   0.0   0.00015     0.086     112     208 ..     128     221 ..     119     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.7
                                      EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHH CS
                          Bac_DnaA 37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeF 75
                                      l++ g+ G Gkt   +a++ e+  +  +  +    a+ F
  gi|336252654|ref|YP_004595761.1| 36 LLLQGPPGSGKTAAARALAREAHVDPDNDLIEINVADFF 74
                                      788999999999999999998876655555544444444 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00015
                                       -HHHHHHHHHHHHHHHTTT-EE..EEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT--- CS
                          Bac_DnaA 112 kektqeelfhtfnalleegkqv..vlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaeklev 186
                                        e+++e++ + +  ++e++++   ++ + r+P++l      +rsr    + v +  p ++  +a+l++ +eae+++ 
  gi|336252654|ref|YP_004595761.1| 128 AEDVREDFQQALRRIMEQHHRTtqFIVATRQPTKLI---PPIRSR---CFPVSVRSPTTDETVAVLERILEAEDVDY 198
                                       566666666666666666554322456667776553...456666...36789999********************* PP

                                       -TTHHHHHHHH--S-HHH.HHHH CS
                          Bac_DnaA 187 peevlefiaervtdnvRe.lega 208
                                         + lef+a++ + n+R+ + ga
  gi|336252654|ref|YP_004595761.1| 199 DADGLEFVANYADGNLRQaILGA 221
                                       ****************9734555 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   5.3e-05      0.03       3      32 ..      37      63 ..      36     182 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.3e-05
                            AAA_33  3 llvGlpGsGKstlaerllkklgavllssdt 32
                                      ll G+pGsGK+  a+ l+++    +++ d+
  gi|336252654|ref|YP_004595761.1| 37 LLQGPPGSGKTAAARALAREA---HVDPDN 63
                                      688***************985...444444 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 ?   12.5   0.0   0.00016     0.091      35      59 ..      35      59 ..      23      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                            RuvB_N 35 hvllyGpPGlGkttlakiiakelgv 59
                                       +ll+GpPG Gkt+ a+ +a+e +v
  gi|336252654|ref|YP_004595761.1| 35 NLLLQGPPGSGKTAAARALAREAHV 59
                                      479******************9876 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013     0.073      53      89 ..      36      74 ..      32      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                      XXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXX CS
                             TIP49 53 vLlaGpsgtGktalaiaiskelg..edvpfvalsgsevy 89
                                      +Ll+Gp+g+Gkta a a+++e     d   + ++ ++++
  gi|336252654|ref|YP_004595761.1| 36 LLLQGPPGSGKTAAARALAREAHvdPDNDLIEINVADFF 74
                                      89*****************99653266667777766666 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   0.00019      0.11      21      42 ..      36      58 ..      22     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                            AAA_30 21 avltGpAGtGKttalkal.reaw 42
                                       +l+Gp+G+GKt a +al rea+
  gi|336252654|ref|YP_004595761.1| 36 LLLQGPPGSGKTAAARALaREAH 58
                                      689**************955555 PP

>> Lipoprotein_16  Uncharacterized lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.07        39     121     158 ..      54      91 ..      33      92 .. 0.86
   2 ?    6.3   0.0     0.012       6.9      30      62 ..     114     145 ..     101     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.07
                    Lipoprotein_16 121 eregalsasnakiekalnkllsevlkeilnDpelqqfl 158
                                        re  + ++n+ ie ++ + + +  +ei nDp ++qfl
  gi|336252654|ref|YP_004595761.1|  54 AREAHVDPDNDLIEINVADFFGRTKTEIKNDPRFAQFL 91 
                                       4667889*****************************98 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                    Lipoprotein_16  30 akinegdgelallsasedvrlllqqalrqqlss 62 
                                       +++++ + +++ll  +edvr  +qqalr+ +++
  gi|336252654|ref|YP_004595761.1| 114 SSVSG-EYKTILLDNAEDVREDFQQALRRIMEQ 145
                                       44455.6778899***************98876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0055       3.1      22      55 ..      22      55 ..       7      59 .. 0.78
   2 ?    3.0   0.0      0.12        66      75     107 ..     124     155 ..     110     216 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0055
                            AAA_25 22 rrwlvkgllpagelallaGapgtGKttlaldlal 55
                                      +r ++++ + +    ll G+pg+GKt++a  la 
  gi|336252654|ref|YP_004595761.1| 22 VREYLERAVDEPINLLLQGPPGSGKTAAARALAR 55
                                      55566666666667899***********999886 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.12
                            AAA_25  75 lyvsaEdsedelrrRlravgealrddarllvld 107
                                       l+ +aEd ++++++ lr+++e++ +  + +++ 
  gi|336252654|ref|YP_004595761.1| 124 LLDNAEDVREDFQQALRRIMEQHHR-TTQFIVA 155
                                       5668999999999999999988732.2222222 PP

>> Metal_resist  Heavy-metal resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       3.9   2.2e+03      79     101 ..      36      58 ..      21      66 .. 0.69
   2 ?    0.8   0.1      0.96   5.4e+02      57      76 ..     130     149 ..     117     157 .. 0.54
   3 ?   13.2   0.3   0.00013     0.075      65     108 ..     257     300 ..     254     309 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.9
                                       HHCCSSSSHHHHHHHHHHHHHHH CS
                      Metal_resist  79 llaaepfDaaaieaalaeiraaq 101
                                       ll + p+ + + +aa+a +r+a+
  gi|336252654|ref|YP_004595761.1|  36 LLLQGPPGSGKTAAARALAREAH 58 
                                       56666666666666666666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.96
                                       HHHHHHHHHHHHHHHHHHHH CS
                      Metal_resist  57 dharelralrrelraarrel 76 
                                       d +++++ + r++++++ + 
  gi|336252654|ref|YP_004595761.1| 130 DVREDFQQALRRIMEQHHRT 149
                                       44444444444444444443 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHHHCCSSSSHHHHHHHHHHHHHHHHHHHHHH CS
                      Metal_resist  65 lrrelraarrelaallaaepfDaaaieaalaeiraaqaalraqi 108
                                       ++ e ++ar  l++ll+ e +D++ + +a+ +i + +++ +++ 
  gi|336252654|ref|YP_004595761.1| 257 EAGEFTDARSTLDDLLVDEGLDGEEVLDAILRIGRKRYQGEKLA 300
                                       678999*******************************9998765 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.011       6.3      16      32 ..      35      51 ..      23      62 .. 0.82
   2 ?    3.5   0.1     0.092        52     120     154 ..     118     151 ..      75     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                                      EEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                              DEAD 16 dvlvaaeTGsGKTlafl 32
                                      ++l++++ GsGKT+a+ 
  gi|336252654|ref|YP_004595761.1| 35 NLLLQGPPGSGKTAAAR 51
                                      7899**********985 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.092
                                       TTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 120 sqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                        + +++ lD a  + ++ f++ ++ri++q +++t+
  gi|336252654|ref|YP_004595761.1| 118 GEYKTILLDNAEDVRED-FQQALRRIMEQHHRTTQ 151
                                       4558899*******998.***********965554 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0004      0.23      21      46 ..      32      60 ..       8      66 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                                      E...EEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE 21 v...ilLeGdLGaGKTtlvrglakalgve 46
                                          +lL+G+ G+GKT+ +r+la++ +v+
  gi|336252654|ref|YP_004595761.1| 32 EpinLLLQGPPGSGKTAAARALAREAHVD 60
                                      03349*******************98775 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 ?    9.7   0.0   0.00096      0.54      26      58 ..      26      58 ..      21      80 .. 0.82
   2 ?   -1.5   0.0       2.7   1.5e+03      38      60 ..      91     113 ..      85     158 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00096
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikdllkkld 58
                                      le  +++  ++ll Gp G+GKt+ ++ l ++ +
  gi|336252654|ref|YP_004595761.1| 26 LERAVDEPINLLLQGPPGSGKTAAARALAREAH 58
                                      6777888899**************999877654 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                             AAA_7  38 lvGptGtGKtviikdllkkldke 60 
                                       lvG +  +K  +i+++lk+  + 
  gi|336252654|ref|YP_004595761.1|  91 LVGRSSMSKRDMINRVLKESASY 113
                                       67777777777777766655432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1032  (0.0575604); expected 358.6 (0.02)
Passed bias filter:                      897  (0.0500307); 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: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.41
# Mc/sec: 2459.81
//
Query:       gi|336252655|ref|YP_004595762.1|  [L=145]
Description: thioesterase superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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-18   65.6   0.0    6.1e-18   64.9   0.0    1.3  1  4HBT      Thioesterase superfamily
  ------ inclusion threshold ------
       0.15   12.6   0.0       0.18   12.3   0.0    1.2  1  4HBT_2    Thioesterase-like 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 !   64.9   0.0   6.8e-22   6.1e-18       2      77 ..      24      98 ..      23     100 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 6.8e-22
                                      SSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                              4HBT  2 GvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77
                                      +++hgG+++++lDe++++ +++ +g+ ++v++   ++df rp+r+gd+ +vea v   grts+ v  + ++e++r 
  gi|336252655|ref|YP_004595762.1| 24 NTLHGGNLMKWLDEVGAMSAMRFAGE-TCVTAQVNELDFERPIRIGDTALVEAYVYDEGRTSVHVALRAWREEPRS 98
                                      79***********************9.*********************************************9875 PP

>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     2e-05      0.18      26     117 ..      32     125 ..       6     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                            4HBT_2  26 vkflertglksrsiarrgiglilssa.hvryrrplkfpdrltvefrvididaktliiehrfls..nadgkk..aarv 97 
                                       +k+l + g    +++  g  +++++  ++++ rp++ +d   ve  v d+ +++++++ r  +  +++g +  + + 
  gi|336252655|ref|YP_004595762.1|  32 MKWLDEVGAM-SAMRFAGETCVTAQVnELDFERPIRIGDTALVEAYVYDEGRTSVHVALRAWReePRSGETekTTES 107
                                       5666555553.33333344445555459************99********************976666666669999 PP

                            4HBT_2  98 eerivvmdygkrskkapvPp 117
                                         + v +d +++  ++pvP+
  gi|336252655|ref|YP_004595762.1| 108 SFTFVAIDADGT--PVPVPD 125
                                       999999999887..888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1112.61
//
Query:       gi|336252656|ref|YP_004595763.1|  [L=263]
Description: transcriptional regulator TrmB [Halopiger xanaduensis SH-6]
Scores for 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-17   60.7   0.0    2.8e-16   59.2   0.0    1.9  2  TrmB            Sugar-specific transcriptional regulator TrmB
    5.9e-09   35.4   0.0    8.4e-09   34.9   0.0    1.3  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
     0.0089   16.0   0.1        4.3    7.4   0.0    3.2  3  HRDC            HRDC domain
     0.0098   16.3   0.4       0.79   10.1   0.1    2.3  2  Radical_SAM     Radical SAM superfamily
  ------ inclusion threshold ------
      0.013   16.0   1.2       0.26   11.8   0.1    3.2  4  HTH_27          Winged helix DNA-binding domain
      0.019   14.8   0.1      0.053   13.4   0.1    1.8  1  MarR_2          MarR family
      0.042   13.7   0.2        2.8    7.8   0.0    2.7  2  HTH_IclR        IclR helix-turn-helix domain


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 !   59.2   0.0   1.1e-19   2.8e-16       1      66 [.      17      82 ..      17      84 .. 0.97
   2 ?   -3.0   0.0       2.7     7e+03      16      31 ..     219     234 ..     212     235 .. 0.71

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.1e-19
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE-- CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravd 66
                                      Lq+lGLs+yEa++ + Ll+lg  t+++i +  gvpr++vYe+ ++L + G++++++ +p+++  ++
  gi|336252656|ref|YP_004595763.1| 17 LQELGLSQYEAQTLINLLRLGTGTTQDITRVNGVPRTRVYEATERLHELGFIDIQHTTPRKFTIIS 82
                                      89***********************************************************99876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.7
                                       HHHHHCCCHHCHHCCC CS
                              TrmB  16 aLlklgpatadeiaee 31 
                                         l++g+  a+ei e 
  gi|336252656|ref|YP_004595763.1| 219 SALANGSGGATEIEET 234
                                       4468899999999885 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   3.3e-12   8.4e-09       2      97 ..     120     221 ..     119     254 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 3.3e-12
                                       EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHH.HHHHHHHHHHHTT-EEEEEESS.......----GGGSSSSE CS
                    Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLe.elreeliaaaergvtVllliyp.......dedleeldleev 70 
                                       vw+v++re+v +r++e+I++A+++++ ++  elL  e  e+l++a +rgv+++l  ++        e+ +  +l e+
  gi|336252656|ref|YP_004595763.1| 120 VWTVTGREAVASRVDEFIADADEQIVYMTVDELLTdEHLEQLQDADDRGVEIYLAGISddvqdqiHETVPSAELFET 196
                                       9*******************************9973689****************9997666444333334444444 PP

                                       EEEEE-S---S.EEEEETTTEEEEE-S CS
                    Regulator_TrmB  71 atevrvrrsgapllvivDrkrgvvapr 97 
                                         e r        l+i+D++ ++v+  
  gi|336252656|ref|YP_004595763.1| 197 LWEWRDTPA--GSLLITDEETALVSAL 221
                                       444444444..5699999999999754 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.41     1e+03      30      59 ..      28      57 ..      27      65 .. 0.74
   2 ?    4.2   0.0     0.017        44      23      60 ..      77     118 ..      75     120 .. 0.79
   3 !    7.4   0.0    0.0017       4.3       2      14 ..     191     203 ..     190     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.41
                                      HHHHHHHHH---SHHHHHTSTTT-HHHHHH CS
                              HRDC 30 ktLleiAeklPttleeLlqiegvgkrklek 59
                                      +tL+++ +    t+++ ++++gv + ++ +
  gi|336252656|ref|YP_004595763.1| 28 QTLINLLRLGTGTTQDITRVNGVPRTRVYE 57
                                      578888888888999999999988776655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.017
                                       HHHHS-HHHHHHHHHH.---SHHHHHTS...TTT-HHHHHHH CS
                              HRDC  23 pyvvfpdktLleiAek.lPttleeLlqi...egvgkrkleky 60 
                                        +++ +++t++ + +  +  t  eL+++    g  + + e++
  gi|336252656|ref|YP_004595763.1|  77 KFTIISEETIIRMLNTqRENTITELAECfeaIGPAQPQREQF 118
                                       58999*********999999******9985555555555555 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHH CS
                              HRDC   2 lallkaLrewRee 14 
                                       ++l++ L+ewR+ 
  gi|336252656|ref|YP_004595763.1| 191 AELFETLWEWRDT 203
                                       689********97 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.016        41      92     145 ..      12      70 ..       2     104 .. 0.69
   2 !   10.1   0.1   0.00031      0.79      66     129 ..     132     192 ..      99     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.016
                                       HHHHHHHHTT....-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETE CS
                                       xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  92 eklerllelg....vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrv 145
                                       e l+rl elg      +  ++l  +   +++++++  g  + +v+ea+e+l+e+g+ ++
  gi|336252656|ref|YP_004595763.1|  12 EALDRLQELGlsqyEAQTLINLLRLGTGTTQDITRvNGVPRTRVYEATERLHELGFIDI 70 
                                       5566666666444422222333333333556666667789999************9873 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00031
                                       HHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  66 llerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfee 129
                                        +++ ++   ++  i++ t   l+++e+le l ++    v++ l  ++d+ v++ ++ +    e
  gi|336252656|ref|YP_004595763.1| 132 RVDEFIAD--ADEQIVYMTVDELLTDEHLEQLQDADDRGVEIYLAGISDD-VQDQIHETVPSAE 192
                                       44455555..688889999999999*************************.9999874444444 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 ?   -0.8   0.0      0.89   2.3e+03      36      47 ..      11      22 ..       4      24 .. 0.83
   2 ?   11.8   0.1    0.0001      0.26       2      52 ..      23      72 ..      22      84 .. 0.84
   3 ?   -1.6   0.0       1.5   3.9e+03       8      25 ..      86     102 ..      82     104 .. 0.63
   4 ?    0.7   0.0      0.29   7.4e+02      16      58 ..     125     168 ..     115     173 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.89
                            HTH_27 36 syslkkLtekGL 47
                                      +++l++L e GL
  gi|336252656|ref|YP_004595763.1| 11 AEALDRLQELGL 22
                                      499******998 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0001
                            HTH_27  2 trqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertg 52
                                      ++ +a++L ++  r+++ +  d+ ++  v  + + ++ ++L+e G++  ++
  gi|336252656|ref|YP_004595763.1| 23 SQYEAQTLINLL-RLGTGTTQDITRVNGVPRTRVYEATERLHELGFIDIQH 72
                                      566899988888.8*********************************4333 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.5
                            HTH_27   8 vLhlirhrrrrkkladlc 25 
                                       +++ ++ ++r++++++l+
  gi|336252656|ref|YP_004595763.1|  86 IIRMLN-TQRENTITELA 102
                                       455555.77777777775 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.29
                            HTH_27  16 rrrkkladlcgrlnvedshis.yslkkLtekGLvertgdeadrr 58 
                                       +r++ ++++ ++    d +i+   +++L   + +e+ +d+ dr+
  gi|336252656|ref|YP_004595763.1| 125 GREAVASRVDEFIADADEQIVyMTVDELLTDEHLEQLQDADDRG 168
                                       56666666666666667788867899999999999999975555 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.1e-05     0.053       1      53 [.      20      70 ..      14      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                                      TT--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  1 lgltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      lgl+  +a+ L +L r + +  t ++++r  g+++ +v  + +rL + G++  
  gi|336252656|ref|YP_004595763.1| 20 LGLSQYEAQTLINLLRLGTG--TTQDITRVNGVPRTRVYEATERLHELGFIDI 70
                                      58888899*****9999984..****************************975 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 ?    7.8   0.0    0.0011       2.8      20      48 ..      40      68 ..      28      70 .. 0.85
   2 ?    2.8   0.0      0.04     1e+02       8      26 ..      86     103 ..      85     105 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                                      BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyv 48
                                      t +++ r  g+p++ v+  +  L+elG++
  gi|336252656|ref|YP_004595763.1| 40 TTQDITRVNGVPRTRVYEATERLHELGFI 68
                                      578999999******************97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.04
                                       HHCT-CTTBSS-BHHHHHH CS
                          HTH_IclR   8 iLdalaeapqeltlselAr 26 
                                       i+++l+++++  t++elA+
  gi|336252656|ref|YP_004595763.1|  86 IIRMLNTQREN-TITELAE 103
                                       899*******9.*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2008.87
//
Query:       gi|336252657|ref|YP_004595764.1|  [L=412]
Description: RNA methylase [Halopiger xanaduensis SH-6]
Scores for 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-21   74.6   0.1    6.3e-20   71.7   0.1    2.2  1  UPF0020          Putative RNA methylase family UPF0020
    6.1e-06   26.9   0.0    1.5e-05   25.6   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    1.8e-05   24.8   0.0      8e-05   22.8   0.0    1.9  1  THUMP            THUMP domain
    0.00016   22.2   0.0    0.00043   20.9   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    0.00087   18.8   0.0       0.45    9.9   0.0    2.2  2  AviRa            RRNA methyltransferase AviRa
  ------ inclusion threshold ------
      0.033   14.0   0.0        0.4   10.5   0.0    2.3  2  Methyltransf_23  Methyltransferase domain
       0.16   11.5   0.0       0.24   10.9   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.24   10.6   0.0       0.38   10.0   0.0    1.2  1  N6_Mtase         N-6 DNA Methylase


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 !   71.7   0.1   2.8e-23   6.3e-20       4     195 ..     233     406 ..     230     408 .. 0.78

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 2.8e-23
                                       S-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EE CS
                           UPF0020   4 RefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelkly 80 
                                       ++f++p+++ + LA+a  ++ag++ g+++lDPmCG+G+ l+Ea+l+ga+++                          
  gi|336252657|ref|YP_004595764.1| 233 KPFFQPGSMDPLLARAVANVAGARTGRTILDPMCGTGGGLVEAGLVGADVI-------------------------- 283
                                       7899***********************************************.......................... PP

                                       EEES-HHHHHHHHHHHHH.........TT-G.GGEEEEE--GGG--STTS---EEEE---------.-HHHHHHHHH CS
                           UPF0020  81 gsDldrrvvqgareNaek.........agvg.dliefsqadaakLrlkegevdvivtnpPYGerlg.skkalekLYs 146
                                       g D +r++ +gareN+ +         +gv+ +++++   da+ L+l+++ vd +v + PYG+  + ++++le+L  
  gi|336252657|ref|YP_004595764.1| 284 GTDAQRKMAEGARENLAHflesddpspTGVErGSWHVGRGDATRLPLADDAVDGVVFDAPYGRQSKiDTHRLEDLVA 360
                                       ***************9873333333334554369************9999************976624556688888 PP

                                       HHHHHHHHH-TT..-EEEEEESSHHHHHCC---..ESEEEEEEETTEEEEE CS
                           UPF0020 147 eflrelkrvlrgggrlvlltsenkalekaleer..alrkvkeknvklglll 195
                                       + l e+ rv    +r+v+++   ++  + ++e+  +l++  e++v+ +l++
  gi|336252657|ref|YP_004595764.1| 361 SALAEARRVG---SRAVVVAD--RSWRSEAREAgwELAASFERRVHRSLTR 406
                                       8888877744...45665554..4445555555236666667778777765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   6.5e-09   1.5e-05       1      70 [.     261     340 ..     261     372 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.5e-09
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH.........TTT...TEEEEESBCCGBSSSTTTE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee.........egl...nvefvqgdaedlpfedgsf 65 
                                       +Ld  cGtG  + ++    g a+v+g+D + +m e are++++          g+   ++++ +gda++lp++d+ +
  gi|336252657|ref|YP_004595764.1| 261 ILDPMCGTGGGLVEAGLV-G-ADVIGTDAQRKMAEGARENLAHflesddpspTGVergSWHVGRGDATRLPLADDAV 335
                                       89**********999855.6.********************99998866544333866777778999********** PP

                                       EEEEE CS
                   Methyltransf_25  66 Dlvvs 70 
                                       D vv 
  gi|336252657|ref|YP_004595764.1| 336 DGVVF 340
                                       ***98 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   3.6e-08     8e-05      18     136 ..      47     183 ..      35     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.6e-08
                                       EEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEE.....................EEEEESSHHHHHHHHHH CS
                             THUMP  18 eagkgrivvelkgekpeedeellkealekargiqrvipv.....................cevceadledileaake 73 
                                       +++ ++ ++el+ge+   d+ +++ea + a+g+ r+ p+                      e ++++  d++ +a++
  gi|336252657|ref|YP_004595764.1|  47 RRRPNVYLLELGGED---DAFAAYEAESAATGVRRIAPGlavargiapervrglaythraSELIGRTDADVE-SARA 119
                                       555566667777775...777777777777777777777777777777777777777775444444444444.3444 PP

                                       HHHHHHHHCT-..EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETT CS
                             THUMP  74 ivkkkfeeeke..tFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikd 136
                                       + +   ++ +   t aVr++ ++    ++  + +re+G  +v+++  +Vdle Pd ++rv + + 
  gi|336252657|ref|YP_004595764.1| 120 LLEAASIDRDRdaTVAVRSTDVHGSTGVSTERAERELGQVLVDRGF-SVDLEAPDHLLRVAFSEG 183
                                       4444444444445******9999998********************.*************98776 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.9e-07   0.00043       1      87 [.     262     369 ..     262     372 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.9e-07
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-............EEEETTEECCCTSS-TT-EEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl............kvefvvadaeklpfednsfDlv 65 
                                       Ld  cGtG  + +    ga+v+g+D   +m + a+e+     +            +  + ++da++lp++d+ +D v
  gi|336252657|ref|YP_004595764.1| 262 LDPMCGTGGGLVEAGLVGADVIGTDAQRKMAEGARENLAHFLEsddpsptgvergSWHVGRGDATRLPLADDAVDGV 338
                                       677799999999999999**************99999887665778888888888667799**************** PP

                                       EEES........-CCC-.CCHHHHHHHHHHH CS
                   Methyltransf_11  66 vsse........vlhhv.edpekalkeiaRv 87 
                                       v             h + + +++al+e++Rv
  gi|336252657|ref|YP_004595764.1| 339 VFDApygrqskiDTHRLeDLVASALAEARRV 369
                                       9876555555432333345566666666665 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0002      0.45      40     100 ..     246     300 ..     241     306 .. 0.82
   2 !    6.6   0.0    0.0021       4.7     148     201 ..     317     370 ..     310     389 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0002
                             AviRa  40 qralellekkeegapltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLs 100
                                       +ra++ +  +++ ++ t+ Dp CG++  l   gl+ +    +v+++D ++++ e a++NL+
  gi|336252657|ref|YP_004595764.1| 246 ARAVANV--AGARTGRTILDPMCGTGGGLVEAGLVGA----DVIGTDAQRKMAEGARENLA 300
                                       5666655..5555689********9999999999875....689***************97 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0021
                             AviRa 148 eievfkaditekeeeaekevdivitDlPYGelvswqge.seepvkqlleslaavl 201
                                       +++v + d t + + a  +vd v+ D PYG +++ +++  e+ v++ l++ ++v 
  gi|336252657|ref|YP_004595764.1| 317 SWHVGRGDAT-RLPLADDAVDGVVFDAPYGRQSKIDTHrLEDLVASALAEARRVG 370
                                       5667777877.44555667***************999944666777776666544 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.2   4.5e+02       7      40 ..      35      68 ..      26      89 .. 0.82
   2 ?   10.5   0.0   0.00018       0.4      12      62 ..     244     304 ..     236     357 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.2
                   Methyltransf_23  7 eelsdklerllpklraggrvLdiGcGtGillevl 40
                                      +++   ++ l+p++r++  +L++G  +  ++ + 
  gi|336252657|ref|YP_004595764.1| 35 RFAESGRLILAPRRRPNVYLLELGGEDDAFAAYE 68
                                      555666777899999999*******999998865 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00018
                   Methyltransf_23  12 klerllpk...lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.......k 62 
                                       +l+r++++    r+g  +Ld  cGtG  l ++   g++v+g D+ +++ e a+       +
  gi|336252657|ref|YP_004595764.1| 244 LLARAVANvagARTGRTILDPMCGTGGGLVEAGLVGADVIGTDAQRKMAEGARenlahflE 304
                                       4445554444499*************************************99744444440 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 ?   10.9   0.0   0.00011      0.24       2      42 ..     259     299 ..     258     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNa 42 
                                       r+ilD+++G+GG  ++  lv+  vi+ + +++  + a +N 
  gi|336252657|ref|YP_004595764.1| 259 RTILDPMCGTGGGLVEAGLVGADVIGTDAQRKMAEGARENL 299
                                       689***************************99988888886 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00017      0.38      28      64 ..     235     275 ..     224     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                          N6_Mtase  28 ffTPrevsklivell....epksgesvyDpacGsggllvqa 64 
                                       ff P ++  l+++ +      ++g++++Dp cG+gg lv+a
  gi|336252657|ref|YP_004595764.1| 235 FFQPGSMDPLLARAVanvaGARTGRTILDPMCGTGGGLVEA 275
                                       6666666655555554444889999************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); 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:                         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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3157.32
//
Query:       gi|336252658|ref|YP_004595765.1|  [L=186]
Description: TATA-box binding family protein [Halopiger xanaduensis SH-6]
Scores for 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-58  193.1   0.0    5.1e-28   96.9   0.0    2.0  2  TBP              Transcription factor TFIID (or TATA-binding 
    1.2e-05   25.5   0.0       0.01   16.1   0.0    2.2  2  T4bSS_IcmS       Type IVb secretion, IcmS, effector-recruitme
    0.00025   21.1   0.0       0.69   10.1   0.0    2.2  2  DUF3378          Domain of unknown function (DUF3378)
  ------ inclusion threshold ------
       0.11   13.2   0.0         12    6.8   0.0    2.2  2  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma


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 !   96.9   0.0   1.1e-31   5.1e-28       2      84 ..       8      88 ..       7      89 .. 0.97
   2 !   94.6   0.0   5.7e-31   2.6e-27       2      84 ..      99     181 ..      98     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 1.1e-31
                                      EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHH CS
                               TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiap 80
                                      ++i+Nvvas+ +g+eldL+ +a+++  ++a Y+pe+fpglvyr ++pk +aliF+sGk+v+tGaks+++++e ++ +++
  gi|336252658|ref|YP_004595765.1|  8 INIENVVASTGIGQELDLQSVAMDL--EGADYDPEQFPGLVYRTQNPKSAALIFRSGKIVCTGAKSTDDVHESLRIVFD 84
                                      79********************998..**************************************************** PP

                                      HHHH CS
                               TBP 81 ilkk 84
                                      +l++
  gi|336252658|ref|YP_004595765.1| 85 KLRE 88
                                      *997 PP

  == domain 2  score: 94.6 bits;  conditional E-value: 5.7e-31
                                       EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakki 78 
                                       + +qN+v sa+lg +l+L+++a  +  +n+eYepe+fpglvyrl++p+v+al+F sGk+vitG k++e+++ a++ki
  gi|336252658|ref|YP_004595765.1|  99 IVVQNIVTSADLGRNLNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPEVVALLFGSGKLVITGGKKPEDAEHAVDKI 175
                                       679*******************99779************************************************** PP

                                       HHHHHH CS
                               TBP  79 apilkk 84 
                                       +  l++
  gi|336252658|ref|YP_004595765.1| 176 VSRLED 181
                                       *99976 PP

>> T4bSS_IcmS  Type IVb secretion, IcmS, effector-recruitment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.3e-06      0.01      12      75 ..      17      84 ..       5      91 .. 0.75
   2 !    7.6   0.0    0.0011       4.8      14      59 ..     110     157 ..      99     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.3e-06
                        T4bSS_IcmS 12 eeadddfdddasaisaeeveedtglleqliraadqlaSlaLffglkatvekaeval....lGvkvvFD 75
                                        ++++ d++  a+  e  + d ++ ++l+ ++++ +S+aL f+ ++ v     ++      +++vFD
  gi|336252658|ref|YP_004595765.1| 17 TGIGQELDLQSVAMDLEGADYDPEQFPGLVYRTQNPKSAALIFRSGKIVCTGAKSTddvhESLRIVFD 84
                                      44788888899999999999************************998775544444111134566666 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0011
                        T4bSS_IcmS  14 adddfdddasai..saeeveedtglleqliraadqlaSlaLffglkat 59 
                                       ++ + +++a ai    e++e + ++ ++l+ + d+ + +aL fg ++ 
  gi|336252658|ref|YP_004595765.1| 110 LGRNLNLNAIAIglGLENIEYEPEQFPGLVYRLDDPEVVALLFGSGKL 157
                                       55666666665522579***************************9875 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00036       1.6      24      56 ..      39      71 ..      25      77 .. 0.87
   2 !   10.1   0.0   0.00015      0.69      24      61 ..     132     169 ..     127     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00036
                           DUF3378 24 skkppyavfaakkndttItaYtSgKVlFQGkna 56
                                       ++ p+ v++ ++++    +++SgK++  G++ 
  gi|336252658|ref|YP_004595765.1| 39 PEQFPGLVYRTQNPKSAALIFRSGKIVCTGAKS 71
                                      5689***********************999875 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00015
                           DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeaeAs 61 
                                        ++ p+ v++ ++++++  ++ SgK+++ G +  ++A+
  gi|336252658|ref|YP_004595765.1| 132 PEQFPGLVYRLDDPEVVALLFGSGKLVITGGKKPEDAE 169
                                       5789**************************98877775 PP

>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0027        12      48      75 ..      59      87 ..      43      95 .. 0.79
   2 ?    4.3   0.0     0.016        70      50      75 ..     155     180 ..     139     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0027
                                      ECTTEE.EEEEEEESSHHHHHHHHHHHHH CS
                   Ribosomal_S30AE 48 lakgkv.iraeeesedlyaaidlavdkle 75
                                      +++gk+  ++ ++++d++++++ ++dkl+
  gi|336252658|ref|YP_004595765.1| 59 FRSGKIvCTGAKSTDDVHESLRIVFDKLR 87
                                      45555524456778*************97 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.016
                                       TTEEEEEEEEESSHHHHHHHHHHHHH CS
                   Ribosomal_S30AE  50 kgkviraeeesedlyaaidlavdkle 75 
                                       ++ vi++ ++ ed + a+d+ v +le
  gi|336252658|ref|YP_004595765.1| 155 GKLVITGGKKPEDAEHAVDKIVSRLE 180
                                       34447776778*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1466.45
//
Query:       gi|336252659|ref|YP_004595766.1|  [L=334]
Description: membrane associated potassium channel [Halopiger xanaduensis SH-6]
Scores for 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-05   23.4   8.7    4.3e-05   23.4   8.7    1.8  2  Ion_trans_2      Ion channel
  ------ inclusion threshold ------
      0.053   13.2   0.1       0.11   12.2   0.1    1.4  1  Cation_ATPase_C  Cation transporting ATPase, C-terminus


Domain annotation for each model (and alignments):
>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.4       1.2   1.1e+04      59      72 ..       6      19 ..       4      23 .. 0.59
   2 !   23.4   8.7   4.8e-09   4.3e-05      10      77 ..      81     154 ..      63     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.2
                                      HHHHHHHHHHHHHH CS
                       Ion_trans_2 59 illGlalfalflav 72
                                      +l Gl+l+++++ +
  gi|336252659|ref|YP_004595766.1|  6 LLAGLVLLVATTVD 19
                                      56666666665544 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 4.8e-09
                                       HHHHHHT.............T---HHHHHHHHHHHHTTS----SSTT.-----HHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2  10 gaviysl.........eegwekwsfldalYfsfvtltTiGYGdivpe.tdagrlftivyillGlalfalflavlgkv 76 
                                         v+            + + +  ++   +Y++  t++T G Gd++p+ + +  + + +++ +G+a+++l +++++ v
  gi|336252659|ref|YP_004595766.1|  81 TLVF--AsspialvstR-TGAPADWPGRFYYVAYTMFTDGNGDYTPTrDVW-EIASSFTTATGMAYVTLGISYIIAV 153
                                       2233..23366666553.34467************************5555.*****************99999876 PP

                                       H CS
                       Ion_trans_2  77 l 77 
                                       +
  gi|336252659|ref|YP_004595766.1| 154 I 154
                                       5 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.2e-05      0.11      56     116 ..      59     163 ..      53     169 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.2e-05
                   Cation_ATPase_C  56 iqgllqalvtllvffltll.............................lfgisekenkls................. 86 
                                       i g l++++tl++++  l+                             +                            
  gi|336252659|ref|YP_004595766.1|  59 IAGPLILVLTLVMWIGLLWlgwtlvfasspialvstrtgapadwpgrfY----------Yvaytmftdgngdytptr 125
                                       6799999999999977776666666666666555555555555555550..........045555555555555666 PP

                   Cation_ATPase_C  87 ........snyaqtmaFitlvlsqifnalnlrsrresl 116
                                               +  a  ma++tl +s i+ ++ + s+++s+
  gi|336252659|ref|YP_004595766.1| 126 dvweiassFTTATGMAYVTLGISYIIAVIGAVSEKRSF 163
                                       77778888999**********************88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 2753.75
//
Query:       gi|336252660|ref|YP_004595767.1|  [L=71]
Description: hypothetical protein Halxa_1255 [Halopiger xanaduensis SH-6]
Scores for 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-06   27.0   0.0    4.3e-06   26.6   0.0    1.2  1  MarR            MarR family
    6.3e-06   26.0   0.0    7.3e-06   25.8   0.0    1.2  1  MarR_2          MarR family
    6.8e-05   23.0   0.0    0.00011   22.3   0.0    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0049   16.6   0.5      0.011   15.6   0.0    1.7  2  HTH_IclR        IclR helix-turn-helix domain
     0.0062   16.5   0.0     0.0075   16.2   0.0    1.2  1  HTH_11          HTH domain
  ------ inclusion threshold ------
      0.064   12.8   0.0      0.091   12.3   0.0    1.2  1  HTH_24          Winged helix-turn-helix DNA-binding


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 !   26.6   0.0   1.4e-09   4.3e-06       4      49 ..       5      50 ..       2      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.4e-09
                                      HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      ++ v+L+ l+e+gp +v+ La  l +++ t+t   d L  +G+++R
  gi|336252660|ref|YP_004595767.1|  5 PERVLLTVLDERGPTRVTALATELDTHPITITQYCDDLQSDGYVYR 50
                                      67799****************************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.4e-09   7.3e-06       7      56 ..       6      53 ..       2      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.4e-09
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      ++ +L +L  r++   +v++la +l+  + ++++ +++L++ G+v r+++
  gi|336252660|ref|YP_004595767.1|  6 ERVLLTVLDERGP--TRVTALATELDTHPITITQYCDDLQSDGYVYRVSA 53
                                      5556667777777..8*****************************99965 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 !   22.3   0.0   3.8e-08   0.00011      11      52 ..       7      48 ..       6      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.8e-08
                                      HHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 11 etIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                      ++++t+ +e+++ +++ la +L+ +p ++++    L++dGyv
  gi|336252660|ref|YP_004595767.1|  7 RVLLTVLDERGPTRVTALATELDTHPITITQYCDDLQSDGYV 48
                                      57889999*********************************9 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 !   15.6   0.0   3.6e-06     0.011       9      50 ..       9      50 ..       6      52 .. 0.85
   2 ?   -1.1   0.1      0.57   1.7e+03      12      26 ..      58      71 .]      57      71 .] 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.6e-06
                                      HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      L  +  ++++ +++ lA +++ ++ t   ++  L+  Gyv +
  gi|336252660|ref|YP_004595767.1|  9 LLTVLDERGPTRVTALATELDTHPITITQYCDDLQSDGYVYR 50
                                      44555566667*****************************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.57
                                      -CTTBSS-BHHHHHH CS
                          HTH_IclR 12 laeapqeltlselAr 26
                                      ++ea++e +l+ lA+
  gi|336252660|ref|YP_004595767.1| 58 ISEAGRE-RLASLAE 71
                                      7788887.8888875 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.5e-06    0.0075       5      44 ..       9      53 ..       4      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg......v 44
                                      +l+ L ++rgp     LA eL+    t+ +++++L++ g      +
  gi|336252660|ref|YP_004595767.1|  9 LLTVL-DERGPTRVTALATELDTHPITITQYCDDLQSDGyvyrvsA 53
                                      55566.9********************************8844444 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 ?   12.3   0.0     3e-05     0.091       8      47 ..       9      48 ..       6      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                            HTH_24  8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +L +L + + +  + LA +l+  p t++++ + L+++G++
  gi|336252660|ref|YP_004595767.1|  9 LLTVLDERGPTRVTALATELDTHPITITQYCDDLQSDGYV 48
                                      5788999999999**************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 543.04
//
Query:       gi|336252661|ref|YP_004595768.1|  [L=141]
Description: hypothetical protein Halxa_1256 [Halopiger xanaduensis SH-6]
Scores for 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  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1140.19
//
Query:       gi|336252662|ref|YP_004595769.1|  [L=286]
Description: ATP phosphoribosyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-49  167.2   0.2    3.9e-49  166.7   0.2    1.2  1  HisG            ATP phosphoribosyltransferase
    2.2e-25   88.6   0.1    5.2e-25   87.4   0.1    1.7  1  HisG_C          HisG, C-terminal domain
    0.00027   21.0   0.0     0.0024   17.9   0.0    2.2  2  NMT1            NMT1/THI5 like
  ------ inclusion threshold ------
      0.016   14.8   0.1      0.058   13.0   0.0    2.0  2  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
      0.033   13.5   0.2      0.054   12.9   0.2    1.3  1  LysR_substrate  LysR substrate binding 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 !  166.7   0.2   1.1e-52   3.9e-49       1     158 [.      49     201 ..      49     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: 166.7 bits;  conditional E-value: 1.1e-52
                                       -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESEEEEEEEEETTSS--SGCGG.TT-.EEEEES-HHH CS
                              HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgkcklvvavpeesevkslkdlvedkgkriaTsypnl 77 
                                       raadip+yV++ga+dlGitG D+v+E++  ++v elldL+fg+c+lv+a+pe+ +++s++dl   +g ++aT++pn+
  gi|336252662|ref|YP_004595769.1|  49 RAADIPEYVADGAADLGITGYDQVREAR-VDNVSELLDLEFGRCRLVLAAPEDGDIESVADL---EGGTVATEFPNI 121
                                       89************************85.559***************************998...5669******** PP

                                       HHHHHHHTT-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHHSHHHHHHH CS
                              HisG  78 akkyfeekglkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslkkkekieel 154
                                       ++++f++ g++ +i+++sG++E++p++++aDaIvD+++tG+TL+ n+L ++e++l ss +L+ +++ l+ + k++e+
  gi|336252662|ref|YP_004595769.1| 122 TADFFADTGVEPDIVEVSGATELTPHVEMADAIVDITSTGTTLKMNRLAVVEEVLASSVRLFGREDVLE-EPKVDEV 197
                                       **************************************************************8888887.5577776 PP

                                       HHHH CS
                              HisG 155 lerl 158
                                        + l
  gi|336252662|ref|YP_004595769.1| 198 RTAL 201
                                       6555 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.1   1.5e-28   5.2e-25       1      73 []     207     283 ..     207     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 1.5e-28
                                       TTTEEEEEEEEEGGGHHHHHHH---SSS-EEEE-.....SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEEEE-S- CS
                            HisG_C   1 ArkyvllmynvpkesleevlkilPGlrsPTvspla....degwvaVsavveekevaevideLkaaGAsdIlvlpiek 73 
                                       A+++++lm+nvp+++le v +++PG+ +PTv+++a    d+g vaV+avv+e++v+e+i e+k+aGAsd+lv +ie+
  gi|336252662|ref|YP_004595769.1| 207 AEGKRYLMMNVPEDRLETVRDVIPGMGGPTVMDIAdengDDGKVAVHAVVDERDVFETITEVKKAGASDVLVNEIER 283
                                       899*******************************98888899*********************************96 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   6.6e-07    0.0024      30     145 ..      49     155 ..      40     171 .. 0.68
   2 ?   -2.8   0.0       1.4   5.1e+03      85     103 ..     201     219 ..     195     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.6e-07
                                       STTHHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--.EEEEEECCC--SSGGGGTTSEEEE-S-TTHH CS
                              NMT1  30 dpsdatelvasgkadfgvsyqesllaarakglpvvsvaallqepl.sglivlkdsgikspkDLkGkrigyvgspfek 105
                                         +d +e+va g+ad+g++  +++  ar  +  v  +  l        l++ +d++i+s++DL+G ++++       
  gi|336252662|ref|YP_004595769.1|  49 RAADIPEYVADGAADLGITGYDQVREARVDN--VSELLDLEFGRCrLVLAAPEDGDIESVADLEGGTVATEF----P 119
                                       34899******************99776654..55555554444404555666666*********9998766....4 PP

                                       HHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEE CS
                              NMT1 106 allkallakdggdpsdvtlvnvggtslakalltgkvDaai 145
                                        +  ++ a  g++p+ v++   g t+l++++ +  +Da++
  gi|336252662|ref|YP_004595769.1| 120 NITADFFADTGVEPDIVEV--SGATELTPHV-EM-ADAIV 155
                                       4556788889999999988..5567766433.22.34444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.4
                                       -SSGGGGTTSEEEE-S-TT CS
                              NMT1  85 ikspkDLkGkrigyvgspf 103
                                       ++s+k  +Gkr+ +++ p+
  gi|336252662|ref|YP_004595769.1| 201 LSSVKQAEGKRYLMMNVPE 219
                                       6789999999998887665 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 ?   13.0   0.0   1.6e-05     0.058      43     116 ..      54     122 ..      17     133 .. 0.85
   2 ?   -1.1   0.0      0.32   1.2e+03     202     232 ..     189     219 ..     158     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                                       HHHHHTTS-SEEE--HHHHHHHHHHS-EEEEEEEEETT--SEEEEEEEEETTSS--SHHHHGG-EEEE--TT-T CS
                    Phosphonate-bd  43 vealragqvDiaflgplayvqardqagveplatrvrsdGsasyrsviivradsdiqsledLkgktiafvspsSt 116
                                        e ++ g +D++ +g  ++ +ar  +  e+l  + +     + r v+++++d di+s++dL+g t+a + p+ t
  gi|336252662|ref|YP_004595769.1|  54 PEYVADGAADLGITGYDQVREARVDNVSELLDLEFG-----RCRLVLAAPEDGDIESVADLEGGTVATEFPNIT 122
                                       566788889999999888888887777788877777.....99************************9888766 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.32
                                       S-HHHHHHHHHHHHH---SHHHHHHHHHTTE CS
                    Phosphonate-bd 202 lseelkekiqdallslaeteegkkllealgi 232
                                       l+e  ++++++al s++++e+ + l+  +  
  gi|336252662|ref|YP_004595769.1| 189 LEEPKVDEVRTALSSVKQAEGKRYLMMNVPE 219
                                       6677788899999999987777766665555 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.5e-05     0.054      34     134 ..      40     136 ..      32     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                                       TEEEEEEEESHHHHHHHHHTTSSSEEEEESSS.......CCTTEEEEEEEEEEEEEEEETTSGGGGSSSE.CGGGGC CS
                    LysR_substrate  34 evelelvegdseelldllaegelDlairagpp.......edsglearpLaeeplvlvaspdhpLargepv.sledLa 102
                                       + ++++  +  +++ + +a+g +Dl+i++ ++       + s+l   ++++ +lvl+a++d        + s +dL+
  gi|336252662|ref|YP_004595769.1|  40 DPDVSVLFARAADIPEYVADGAADLGITGYDQvrearvdNVSELLDLEFGRCRLVLAAPEDG------DIeSVADLE 110
                                       556778888888************************************************94......344777777 PP

                                       TSEEEEESTTSTHHHHHHHHHHCTTEECEEEE CS
                    LysR_substrate 103 deplilleegsglrdlledalreaglkprval 134
                                       + +  +      +     d+++++g++p++ +
  gi|336252662|ref|YP_004595769.1| 111 GGTVAT-----EFPNITADFFADTGVEPDI-V 136
                                       777766.....5666666666677777766.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2164.55
//
Query:       gi|336252663|ref|YP_004595770.1|  [L=64]
Description: hypothetical protein Halxa_1258 [Halopiger xanaduensis SH-6]
Scores for 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   0.1       0.26   10.8   0.0    1.6  2  DUF1281   Protein of unknown function (DUF1281)


Domain annotation for each model (and alignments):
>> DUF1281  Protein of unknown function (DUF1281)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   1.4e-05      0.26       8      37 ..       3      32 ..       1      45 [. 0.81
   2 ?    0.1   0.0     0.028   5.1e+02       6      22 ..      35      51 ..      31      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.4e-05
                           DUF1281  8 vlqslkLflAGcaGiLkPvktlsyapypaL 37
                                      v++++ Lfl G aG L P ++l +  +  L
  gi|336252663|ref|YP_004595770.1|  3 VIAGVLLFLVGTAGFLWPERALRFWFLGLL 32
                                      788999***************999765444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.028
                           DUF1281  6 rAvlqslkLflAGcaGi 22
                                       A+ ++ kLf+ G++G+
  gi|336252663|ref|YP_004595770.1| 35 DALSDAGKLFFRGLGGV 51
                                      57788899*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 485.20
//
Query:       gi|336252664|ref|YP_004595771.1|  [L=771]
Description: heavy metal translocating P-type ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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-48  164.4   5.1    3.9e-48  163.4   1.3    2.5  2  E1-E2_ATPase   E1-E2 ATPase
    1.4e-43  149.7   6.1    2.7e-43  148.7   6.1    1.5  1  Hydrolase      haloacid dehalogenase-like hydrolase
    0.00011   22.1   0.0     0.0015   18.3   0.0    2.1  2  Hydrolase_3    haloacid dehalogenase-like hydrolase
     0.0022   18.4   1.2     0.0051   17.2   0.3    2.1  2  HAD            haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.24   11.4   0.0    1.5  1  DUF1198        Protein of unknown function (DUF1198)
       0.14   12.1   0.8       0.24   11.3   0.8    1.3  1  DUF2796        Protein of unknown function (DUF2796)
       0.23   11.4   0.1         36    4.2   0.0    3.0  3  DUF1980        Domain of unknown function (DUF1980)


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 !  163.4   1.3   1.5e-51   3.9e-48       2     181 .]     221     403 ..     220     403 .. 0.97
   2 ?    1.7   0.1     0.061   1.6e+02      96     157 ..     697     758 ..     675     765 .. 0.84

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 1.5e-51
                                       SS--EEEEE...-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-E CS
                      E1-E2_ATPase   2 llpptakvi...rdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtv 75 
                                       l+p+ta +i   + g++ee+++++l+ GD+vl+++g +vpaDg++ +g+++v+es++TGEs+pv+ke gd+v++Gt+
  gi|336252664|ref|YP_004595771.1| 221 LMPDTAERIanpETGETEEVAVDDLEEGDLVLVRPGANVPADGVVESGESNVNESMVTGESKPVSKESGDEVIGGTT 297
                                       788999999777789************************************************************** PP

                                       EEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHH CS
                      E1-E2_ATPase  76 vvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallral 152
                                       + +g+++++V atge+t l+ i+rlveea+++++++q  +d+ +++l+ ++l +a+++++++ +  ++    + r++
  gi|336252664|ref|YP_004595771.1| 298 NRDGSLRVRVSATGEETALAGIVRLVEEAQQSRSRTQVLADRAAGWLFYAALGAAAVTAVAWSIAIGFGLPVVERVV 374
                                       ****************************************************************999999******* PP

                                       HHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 153 allvaaiPcaLplavplalalgarrlakk 181
                                       ++lv+a+P aL+lavpl++a+ ++ +a++
  gi|336252664|ref|YP_004595771.1| 375 TVLVIACPHALGLAVPLVVAINTSMAARN 403
                                       *********************99999885 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.061
                                       TTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHH CS
                      E1-E2_ATPase  96 kiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallva 157
                                        +arlv+ ++++  ++q+++   +++ v++  l+a +++ i ++l   +   l++a +++va
  gi|336252664|ref|YP_004595771.1| 697 DVARLVRLSRKSYRKMQENIAWAAGYNVFALPLAAGILAPIGIVLSPAVGAVLMSASTVIVA 758
                                       6899999999999****************************999998886666666666665 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.7   6.1     1e-46   2.7e-43       2     210 .]     420     670 ..     419     670 .. 0.92

  Alignments for each domain:
  == domain 1  score: 148.7 bits;  conditional E-value: 1e-46
                                       SEEEEESBTTTBCHHHHHHHHHHHH......CHHHHHHHHHHHHCHHHHHHHHHHHHH...HHHHHHHHHETTTE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx.. RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa......alalaaaletgsehpigkalvaaakar...sgaltgfatfigrg.. 67 
                                       +t+vfDk+GTLt+ge+ v+dv           lalaaa e  seh i++a+ ++a++r    ++++gf++++grg  
  gi|336252664|ref|YP_004595771.1| 420 DTIVFDKTGTLTEGEQGVVDVATADewtddnVLALAAAVERDSEHMIAQAIREEAQDRdlsVPDVHGFEALEGRGvr 496
                                       89*************999998888878888899999999999****************6655555**********99 PP

                                       .......................................HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH CS
                                       .......................................xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 .......................................ayaigkpewltal..dippdlgaaigsaqsqgrtvall 103
                                                                              a+a+g p +l++l  +   dl+   ++a s+g+ v+++
  gi|336252664|ref|YP_004595771.1| 497 atiepeavpaaasdgvgsdstdssassnrragsaerdghAVAVGGPNLLRHLevEPGADLERFADEAGSRGEGVVYV 573
                                       99999999999999999999999999999999999999999999999999998888889999999999999999999 PP

                                       ..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHH CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                         Hydrolase 104 ..qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdiet.vakpspe 177
                                         + r+++ +++ad   +++   ea+ +L+++ +ev++ltgd+   a+++a++lG           i+t +a+++pe
  gi|336252664|ref|YP_004595771.1| 574 lrDERVVGAVALADV--IREASYEAIDALHEMSVEVAMLTGDDADVAHSVADELG-----------IDTvFAEVLPE 637
                                       888899999999998..888888********************************...........8888******* PP

                                       HHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 178 gkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       +k  +ireLq++++ vamVGDgvnDa+al +A+
  gi|336252664|ref|YP_004595771.1| 638 DKDVKIRELQEQGHLVAMVGDGVNDAPALTRAD 670
                                       *****************************9997 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.092   2.4e+02      16      57 ..     589     630 ..     586     634 .. 0.90
   2 !   18.3   0.0     6e-07    0.0015     206     248 ..     653     695 ..     643     702 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.092
                                       --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSE CS
                       Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgldlp 57 
                                       i e + eai  l+e  ++v+  TG     +++v++elg+d+ 
  gi|336252664|ref|YP_004595771.1| 589 IREASYEAIDALHEMSVEVAMLTGDDADVAHSVADELGIDTV 630
                                       7788999*******************************9965 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 6e-07
                                       EEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGG CS
                       Hydrolase_3 206 viafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnne 248
                                       v+ +GDg ND + L++a++g A+g++++ + + Ad v   n+ 
  gi|336252664|ref|YP_004595771.1| 653 VAMVGDGVNDAPALTRADVGLAIGSGTDVAVESADVVLVENDP 695
                                       7899*********************************999886 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   3.7e+03       2      31 ..     423     455 ..     422     504 .. 0.47
   2 !   17.2   0.3     2e-06    0.0051      83     187 ..     586     666 ..     531     667 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                               HAD   2 lfDfDgTLldgdsle...lllrfllrrgaprlw 31 
                                       +fD  gTL+ g+ +    + ++ ++  + + l+
  gi|336252664|ref|YP_004595771.1| 423 VFDKTGTLTEGEQGVvdvATADEWTDDNVLALA 455
                                       666667777775554344222222222222222 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 2e-06
                               HAD  83 pklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalr 159
                                         ++++  +e+++a ++  ++v++++g    +++ +++elg    ++t       +++e+ +e+k+v+     ++l+
  gi|336252664|ref|YP_004595771.1| 586 ADVIREASYEAIDALHEMSVEVAMLTGDDADVAHSVADELG----IDT-------VFAEVLPEDKDVKI----RELQ 647
                                       2246677788888888*************************....888.......66777778888888....9999 PP

                               HAD 160 ewlaaegegidleevvayGDspsDlpll 187
                                       e         + + v  +GD+++D p+l
  gi|336252664|ref|YP_004595771.1| 648 E---------QGHLVAMVGDGVNDAPAL 666
                                       9.........44447788********98 PP

>> DUF1198  Protein of unknown function (DUF1198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.4e-05      0.24       6      47 ..     190     231 ..     186     260 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.4e-05
                                       XXXXXXXXXXXXXXXXHHHHHHHHHHHHHHT--THHHHHHHH CS
                           DUF1198   6 latlvvvfivGfrvltsdtrraikrlserLkiepvyveslld 47 
                                       l+tl+v+f++G+++     rra+ +l e+ ++ p + e + +
  gi|336252664|ref|YP_004595771.1| 190 LVTLIVIFLLGHWIEMRSVRRASGALDELAELMPDTAERIAN 231
                                       89*************************999999877776665 PP

>> DUF2796  Protein of unknown function (DUF2796)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.8   9.5e-05      0.24      69     124 ..      38      97 ..       3     117 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.5e-05
                           DUF2796  69 kleeaevessleeeeedeeeeed......ehdheheeeskkkdhdheeaeHsdieaeyefeC 124
                                       ++ +   + s+ +e+ d  +e++      +h++ he+++ ++  + ++++H+d+  +  f C
  gi|336252664|ref|YP_004595771.1|  38 RVCNCYRDASEPNEHGD-RDERHggsgggDHESGHERDH-DDGTHVDHSDHEDMFKRRFFVC 97 
                                       33333333333322222.222224567666666666666.4444448999999988777777 PP

>> DUF1980  Domain of unknown function (DUF1980)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.062   1.6e+02      61      83 ..      81     105 ..      67     111 .. 0.78
   2 ?    4.2   0.0     0.014        36      68     109 ..     369     411 ..     348     460 .. 0.78
   3 ?    0.5   0.0      0.19   4.9e+02      65      91 ..     712     738 ..     698     748 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.062
                           DUF1980  61 hdHe..eksfikkllsylilviPll 83 
                                        dH+  e  f ++++++l l++P+l
  gi|336252664|ref|YP_004595771.1|  81 VDHSdhEDMFKRRFFVCLALALPVL 105
                                       34555588999************98 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.014
                           DUF1980  68 fikkllsylilviPlllglllptk.vldssiakakGfnfslak 109
                                        +++++ +l+++ P  lgl +p + ++++s+a+  G+ +    
  gi|336252664|ref|YP_004595771.1| 369 VVERVVTVLVIACPHALGLAVPLVvAINTSMAARNGMLVRDRI 411
                                       57899***************997516899***999*9776554 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.19
                           DUF1980  65 eksfikkllsylilviPlllglllptk 91 
                                        ++ i+ ++ y ++++Pl +g+l p  
  gi|336252664|ref|YP_004595771.1| 712 MQENIAWAAGYNVFALPLAAGILAPIG 738
                                       4556777899*************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (771 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); 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: 0.70u 0.26s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 5140.70
//
Query:       gi|336252665|ref|YP_004595772.1|  [L=236]
Description: circadian clock protein KaiC [Halopiger xanaduensis SH-6]
Scores for 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-45  155.0   0.0    2.2e-45  154.8   0.0    1.0  1  ATPase           KaiC
    3.9e-08   32.4   0.1    9.9e-07   27.7   0.1    2.9  1  GvpD             GvpD gas vesicle protein
    8.6e-07   28.5   0.0    1.3e-06   28.0   0.0    1.2  1  DnaB_C           DnaB-like helicase C terminal domain
    5.1e-06   26.2   0.0    1.1e-05   25.1   0.0    1.5  1  AAA_25           AAA domain
    0.00044   20.4   0.0     0.0011   19.1   0.0    1.6  1  AAA_33           AAA domain
     0.0017   18.6   0.0     0.0039   17.5   0.0    1.7  1  AAA_22           AAA domain
     0.0018   18.7   0.3      0.016   15.7   0.3    2.1  1  AAA              ATPase family associated with various cellul
     0.0024   17.9   0.0      0.012   15.7   0.0    2.0  2  AAA_14           AAA domain
     0.0028   17.4   0.0     0.0065   16.2   0.0    1.6  2  AAA_24           AAA domain
     0.0041   17.0   0.0     0.0069   16.2   0.0    1.4  1  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 
     0.0043   17.5   0.0     0.0073   16.7   0.0    1.6  1  AAA_16           AAA ATPase domain
     0.0087   15.4   0.1       0.02   14.2   0.0    1.6  2  Rad51            Rad51
  ------ inclusion threshold ------
       0.01   15.6   0.4      0.027   14.3   0.1    1.9  3  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.011   15.7   0.0      0.016   15.2   0.0    1.2  1  ATPase_2         ATPase domain predominantly from Archaea
      0.015   15.9   0.1      0.022   15.3   0.1    1.6  1  AAA_18           AAA domain
      0.039   13.9   0.0      0.065   13.2   0.0    1.4  1  NACHT            NACHT domain
      0.041   13.6   0.0      0.087   12.5   0.0    1.7  1  AAA_30           AAA domain
      0.043   12.9   0.0      0.069   12.2   0.0    1.2  1  T2SSE            Type II/IV secretion system protein
      0.049   13.1   0.2       0.63    9.5   0.0    2.3  2  RecA             recA bacterial DNA recombination protein
      0.051   13.2   0.1       0.13   11.8   0.0    1.7  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.053   13.3   0.0      0.078   12.7   0.0    1.2  1  DUF835           Protein of unknown function (DUF835)
      0.056   13.7   0.0       0.41   10.9   0.0    2.0  2  AAA_28           AAA domain
      0.091   13.2   0.2       0.19   12.2   0.2    1.5  1  AAA_17           AAA domain
      0.098   12.4   0.0       0.23   11.2   0.0    1.6  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.11   12.4   0.0       0.21   11.5   0.0    1.5  1  NTPase_1         NTPase
       0.12   12.1   0.0       0.16   11.7   0.0    1.2  1  AAA_11           AAA domain
       0.13   12.7   0.0       0.21   12.0   0.0    1.5  1  RNA_helicase     RNA helicase
       0.17   11.1   0.0        0.3   10.2   0.0    1.3  1  NB-ARC           NB-ARC domain
       0.17   11.6   0.0       0.33   10.7   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
       0.18   11.1   0.0       0.68    9.2   0.0    1.8  2  Zeta_toxin       Zeta toxin


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.8   0.0   3.7e-48   2.2e-45       2     230 ..       4     232 ..       3     233 .. 0.92

  Alignments for each domain:
  == domain 1  score: 154.8 bits;  conditional E-value: 3.7e-48
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                       +tg++g+De+++gG+ ++r + ++G pG+GKt+f++qFl kga + ge g++v++ e++++l  +++s+   +++  
  gi|336252665|ref|YP_004595772.1|   4 STGVPGFDELVDGGLLRDRLYIVSGPPGSGKTTFCAQFLTKGAFN-GETGLYVSMHESEQELVADMSSFQFGFDQAV 79 
                                       7*******************************************9.******************************* PP

                            ATPase  79 eegklaiidasesaeesaee.......kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlv 148
                                       + g++ ++d+++s++++  +       ++ +++e+l+++l ++i++ +++rvviDs   l+y+ +++v  ++l +++
  gi|336252665|ref|YP_004595772.1|  80 NAGQMKFMDVFASETKRFFSsssrggsDGPDNVENLTNKLVSYIESNGVERVVIDSTMLLEYYFSDEV--DQLITFL 154
                                       ************99987665788999999*****************************9944444443..5666777 PP

                            ATPase 149 rvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegik 225
                                       + lk  + T + vse+++  +   g+ +++    gv+ +++ ++++ ++R l+ +kmRgt+++ ++h +e t++g +
  gi|336252665|ref|YP_004595772.1| 155 SKLKRADATVLVVSEMTDPTSYSDGHYLAH----GVLFMHNYLESGGMTRGLQLIKMRGTEIDCDIHHLEFTDRGLR 227
                                       7889999********888777777766666....******************************************* PP

                            ATPase 226 vleek 230
                                       v++++
  gi|336252665|ref|YP_004595772.1| 228 VHPDQ 232
                                       *9986 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   1.7e-09   9.9e-07      14     201 ..      25     217 ..      20     228 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.7e-09
                              GvpD  14 likGaPGtGktlftlrgldvlrres.dvlyvstr.vddetvseay.....fsgeaeldktalldllkdp...leldl 80 
                                       ++ G PG+Gkt+f  ++l+    ++   lyvs   +++e v ++      f++  +  + +++d++      +    
  gi|336252665|ref|YP_004595772.1|  25 IVSGPPGSGKTTFCAQFLTKGAFNGeTGLYVSMHeSEQELVADMSsfqfgFDQAVNAGQMKFMDVFASEtkrFFSSS 101
                                       799***************98765551569999753899******988866555555558888877654411122222 PP

                              GvpD  81 d...vdvPiekldl.esllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlv 153
                                            d P +  +l + l+++++  ++  ++++  +ds  l+  y++ + d   ++ t   +l    r + + +++v
  gi|336252665|ref|YP_004595772.1| 102 SrggSDGPDNVENLtNKLVSYIE--SNGVERVV--IDSTMLLEYYFSDEVD---QLITFLSKLK---RAD-ATVLVV 167
                                       21114566544444245777777..66666655..5994444444444333...3444444444...544.444455 PP

                              GvpD 154 letaan...srleyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlq 201
                                       +e   +   s   y++ Gv+ ++   +  g + r l+l k+rG  i+  ++
  gi|336252665|ref|YP_004595772.1| 168 SEMTDPtsySDGHYLAHGVLFMHNYLE-SGGMTRGLQLIKMRGTEIDCDIH 217
                                       5555441116678********976666.4666799**********997665 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 !   28.0   0.0   2.1e-09   1.3e-06       2     143 ..       3     141 ..       3     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.1e-09
                                       BXSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHH CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C   2 lstgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidsk 77 
                                       lstg   +D+l+ +Gl +  l+i+ + p+ Gkt+++ ++ ++ a + + + +++s+  s+++lv+ + s + + d +
  gi|336252665|ref|YP_004595772.1|   3 LSTGVPGFDELVdGGLLRDRLYIVSGPPGSGKTTFCAQFLTKGAFNGE-TGLYVSMHESEQELVADMSSFQFGFD-Q 77 
                                       57888889998835799*************************998666.66889***************999986.5 PP

                                       HHHHTTSXHHHHHHHHHHHHH.HHHSEEEEEEXSSXCHHHHHHHHHHHHHHTTEEEEEEEEGGGTBT CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  78 klrtgklkeedweklteaiee.lseaklfiddtpaltvseirskarrlkkekglgliviDyLqlmeg 143
                                       +++ g++k  d+  +++++++ +s+++    d p+ +v+++ +k+  + +++g++ +viD   l+e 
  gi|336252665|ref|YP_004595772.1|  78 AVNAGQMKFMDV--FASETKRfFSSSSRGGSDGPD-NVENLTNKLVSYIESNGVERVVIDSTMLLEY 141
                                       688899986443..333333303444444455554.7888888888888888888888888888774 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.8e-08   1.1e-05      23     186 ..      11     167 ..       3     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.8e-08
                            AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal. 97 
                                       + lv+g l ++ l ++ G+pg+GKtt++ +   + a  G+           + lyvs  +se+el   ++     + 
  gi|336252665|ref|YP_004595772.1|  11 DELVDGGLLRDRLYIVSGPPGSGKTTFCAQFLTKGAfNGE-----------TGLYVSMHESEQELVADMSSFQFGFd 76 
                                       5689988889********************9999996665...........67**************9999775444 PP

                            AAA_25  98 ..rddarllvldlagveslpLfakd.rggtl....ltadvdaleaaieevegvrlvviDplsralggdensnsdvga 167
                                            ++  ++d+  +e  + f++  rgg+     ++  +++l   ie+ +gv+ vviD+    +  +   +++v++
  gi|336252665|ref|YP_004595772.1|  77 qaVNAGQMKFMDVFASETKRFFSSSsRGGSDgpdnVENLTNKLVSYIES-NGVERVVIDST---MLLEYYFSDEVDQ 149
                                       4445666677776555445555554133333444678888888888899.89*******74...4445555566788 PP

                            AAA_25 168 lvealeriarrtgaavllv 186
                                       l++ l ++ +r +a+vl+v
  gi|336252665|ref|YP_004595772.1| 150 LITFLSKL-KRADATVLVV 167
                                       88888888.6788888877 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.9e-06    0.0011       2     101 ..      24     166 ..      23     177 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.9e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdt.................................lrrrlfgt 40 
                                        ++ G+pGsGK+t+  + l k +     +  +s  +                                 + +r f +
  gi|336252665|ref|YP_004595772.1|  24 YIVSGPPGSGKTTFCAQFLTKGAfngetGLYVSMHEseqelvadmssfqfgfdqavnagqmkfmdvfasETKRFFSS 100
                                       6899**************98877888884445555555899999999999999998888877777776666666655 PP

                            AAA_33  41 dqqsktdytrvldrlyqilnelarkalsagrn.vildat......nlsr.rerarflklarrlgvpvri 101
                                         +     ++  d++ + +n+l+    s g   v++d+t      + ++ ++   fl+ ++r+++ v++
  gi|336252665|ref|YP_004595772.1| 101 SSRGG---SDGPDNVENLTNKLVSYIESNGVErVVIDSTmlleyyFSDEvDQLITFLSKLKRADATVLV 166
                                       44444...4577788888899999999999888999999555543333334444444444444444444 PP

>> AAA_22  AAA 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    0.0039       5      29 ..      21      45 ..      19     172 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.5e-06
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                      +++ +v G++G+GKTt ++++l + 
  gi|336252665|ref|YP_004595772.1| 21 DRLYIVSGPPGSGKTTFCAQFLTKG 45
                                      57899**************999874 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 !   15.7   0.3   2.6e-05     0.016       2      74 ..      25     101 ..      24     178 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-05
                                       EEESSTTSSHHHHHHHHHHH..H.THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHHHH CS
                               AAA   2 llyGppGtGKTllakavake..l.gvefleisgsellskyvgesekkirelfkeakeka..kpsilfiDEidalaks 73 
                                       +++GppG GKT+++ +  ++  + g + l +s++e  +++v + +++++  f++a +    k   +f  E  ++++s
  gi|336252665|ref|YP_004595772.1|  25 IVSGPPGSGKTTFCAQFLTKgaFnGETGLYVSMHESEQELVAD-MSSFQFGFDQAVNAGqmKFMDVFASETKRFFSS 100
                                       789***********99999844122333445555544443333.333444444432222233344555555555555 PP

                                       H CS
                               AAA  74 r 74 
                                       +
  gi|336252665|ref|YP_004595772.1| 101 S 101
                                       5 PP

>> AAA_14  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       3      49 ..      22      68 ..      20      99 .. 0.80
   2 ?   -0.2   0.0       1.6   9.8e+02      66      85 ..     140     159 ..     106     164 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-05
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49
                                      ++++++G+  +GKTt++ q++ +   + e  ly+++ + +++  ad 
  gi|336252665|ref|YP_004595772.1| 22 RLYIVSGPPGSGKTTFCAQFLTKGAFNGETGLYVSMHESEQELVADM 68
                                      7899*****************9988999*******999877555544 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
                            AAA_14  66 tylflDEiqevpewekalks 85 
                                       +y f DE+ ++ ++ + lk+
  gi|336252665|ref|YP_004595772.1| 140 EYYFSDEVDQLITFLSKLKR 159
                                       57888999988888888876 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   1.1e-05    0.0065       6      84 ..      25     146 ..      21     152 .. 0.60
   2 ?   -1.8   0.0       3.6   2.1e+03     111     132 ..     147     171 ..     141     178 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                            AAA_24   6 liyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel................ 59 
                                       ++ Gp+g+GKTt+++++       g++ l++ + ++ ++l ad      s++   d++v                  
  gi|336252665|ref|YP_004595772.1|  25 IVSGPPGSGKTTFCAQFltkgafnGETGLYVSMHESEQELVADMS----SFQFGFDQAVNAgqmkfmdvfasetkrf 97 
                                       678**************5555555555555544443333333322....2222222222224444444444446777 PP

                            AAA_24  60 ........................aaeladyktlviDtideleelclae 84 
                                                               + e ++ + +viD+   le + ++e
  gi|336252665|ref|YP_004595772.1|  98 fssssrggsdgpdnvenltnklvsYIESNGVERVVIDSTMLLEYYFSDE 146
                                       7777777777777777777777777777777888888766666655555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.6
                            AAA_24 111 frrllkklqelrk...nvifiahek 132
                                       + +l++ l++l+    +v ++++++
  gi|336252665|ref|YP_004595772.1| 147 VDQLITFLSKLKRadaTVLVVSEMT 171
                                       4444444444444444888888775 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-05    0.0069      18     130 ..      39     159 ..      35     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                              MEDS  18 vpfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeety.......lrgggfdpermleal 87 
                                       ++f+++g  +ge  lyv   ++++el + +++     d+a+++gq++++d             + gg+d    +e+l
  gi|336252665|ref|YP_004595772.1|  39 AQFLTKGAFNGETGLYVSMHESEQELVADMSSFQFGFDQAVNAGQMKFMDVFASEtkrffssSSRGGSDGPDNVENL 115
                                       79**************999****************************998644444477788777777777888999 PP

                              MEDS  88 rralakal.adgyaglrvigemtwalrsp..aereelleyEallne 130
                                        ++l  ++  +g +  rv+++ t +l+    +e+++l+++ ++l +
  gi|336252665|ref|YP_004595772.1| 116 TNKLVSYIeSNGVE--RVVIDSTMLLEYYfsDEVDQLITFLSKLKR 159
                                       99999999445554..446666654443211477777777666665 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   1.2e-05    0.0073      25      62 ..      22      61 ..      10     171 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-05
                            AAA_16 25 elvllsGesGvGKsslvrellr..alekdggiflrgkcdq 62
                                      +l ++sG++G+GK++   ++l+  a++++ g++++ +  +
  gi|336252665|ref|YP_004595772.1| 22 RLYIVSGPPGSGKTTFCAQFLTkgAFNGETGLYVSMHESE 61
                                      7899***************998555555544444444444 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   3.3e-05      0.02      17      57 ..       1      41 [.       1      52 [. 0.93
   2 ?   -2.3   0.0       3.6   2.2e+03     129     142 ..     124     137 ..     103     171 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.3e-05
                                      -EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                             Rad51 17 lqlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57
                                      ++l+tG   +Del++GG+    +  + G  +sGkt +c ++
  gi|336252665|ref|YP_004595772.1|  1 MRLSTGVPGFDELVDGGLLRDRLYIVSGPPGSGKTTFCAQF 41
                                      579***********************************986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                                       HHS-EEEEEEETTT CS
                             Rad51 129 aedkfallivDsvt 142
                                        ++ +  +++Ds +
  gi|336252665|ref|YP_004595772.1| 124 ESNGVERVVIDSTM 137
                                       44444444444443 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 ?   14.3   0.1   4.5e-05     0.027       1      17 [.      26      42 ..      26      64 .. 0.85
   2 ?   -2.7   0.0       6.6   3.9e+03     195     218 ..     110     132 ..      77     151 .. 0.64
   3 ?   -1.3   0.0       2.5   1.5e+03     111     120 ..     147     156 ..     108     191 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.5e-05
                        ATP_bind_1  1 vvGpaGsGKttfvgals 17
                                      v Gp+GsGKttf+ ++ 
  gi|336252665|ref|YP_004595772.1| 26 VSGPPGSGKTTFCAQFL 42
                                      78***********9876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.6
                        ATP_bind_1 195 ekykklaeaiaelleefalvlrfl 218
                                       + +++l++++++++e  +   r++
  gi|336252665|ref|YP_004595772.1| 110 DNVENLTNKLVSYIESNGVE-RVV 132
                                       44555566666666555544.444 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.5
                        ATP_bind_1 111 lakiveeLes 120
                                         +++  L++
  gi|336252665|ref|YP_004595772.1| 147 VDQLITFLSK 156
                                       2333333333 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 ?   15.2   0.0   2.6e-05     0.016      20     141 ..      21     150 ..      18     172 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-05
                          ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie........eeeekkklekalgiavpk 88 
                                       ++ y + Gp gsGKt++  +++++    ++  +y++  ++e++  +d +           +  + k+ +++++++++
  gi|336252665|ref|YP_004595772.1|  21 DRLYIVSGPPGSGKTTFCAQFLTKGAFNGETGLYVSMHESEQELVADMS-SfqfgfdqaVNAGQMKFMDVFASETKR 96 
                                       568999*********************9*99999987776665544443.234666555333344455555666666 PP

                          ATPase_2  89 aeleeilk..eksklvfkaielllekikkkgkkiiiiiDelqklidlglngaell 141
                                       +         +   +v++  ++l   i+ +g + ++ iD    l ++ +++  +l
  gi|336252665|ref|YP_004595772.1|  97 FFSSSSRGgsDGPDNVENLTNKLVSYIESNGVERVV-IDSTMLLEYYFSDEVDQL 150
                                       555444437667777888888888888888887554.455555554444444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   3.7e-05     0.022       2      25 ..      25      52 ..      25     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.7e-05
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf....g 25
                                      +++G+pG+GKtt++     +++f    g
  gi|336252665|ref|YP_004595772.1| 25 IVSGPPGSGKTTFCAQFLTKGAFngetG 52
                                      699**********976655544555554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00011     0.065       1      23 [.      22      44 ..      22      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                      SCEEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklala 23
                                      rl i+ G++GsGKTt+ +++ ++
  gi|336252665|ref|YP_004595772.1| 22 RLYIVSGPPGSGKTTFCAQFLTK 44
                                      6789************9999876 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   0.00015     0.087      18      38 ..      21      41 ..      18     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                            AAA_30 18 drvavltGpAGtGKttalkal 38
                                      dr+ ++ Gp+G+GKtt  ++ 
  gi|336252665|ref|YP_004595772.1| 21 DRLYIVSGPPGSGKTTFCAQF 41
                                      6799************98775 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 ?   12.2   0.0   0.00012     0.069     127     150 ..      19      42 ..       7      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                             T2SSE 127 rerglilvsGgTgsGKttllyall 150
                                        +  l +vsG+ gsGKtt+    l
  gi|336252665|ref|YP_004595772.1|  19 LRDRLYIVSGPPGSGKTTFCAQFL 42 
                                       5567789***********987666 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0     0.001      0.63      34      87 ..       3      55 ..       1      82 [. 0.84
   2 ?    1.3   0.0      0.32   1.9e+02     113     141 ..     109     137 ..     106     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.001
                                      E--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEE CS
                              RecA 34 issGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafi 87
                                      +s+G  ++d  +  GGl + r+  + Gp  sGktt++ + +++   +g +  ++
  gi|336252665|ref|YP_004595772.1|  3 LSTGVPGFDELVD-GGLLRDRLYIVSGPPGSGKTTFCAQFLTKGAFNGETGLYV 55
                                      5777777777665.9**********************99999888777776666 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.32
                                       -SSHHHHHHHHHHHHTTT--SEEEEE-TT CS
                              RecA 113 pdtGeqaleiadalvrsgaidlivvdsva 141
                                       pd+ e+  + + + ++s++++ +v+ds  
  gi|336252665|ref|YP_004595772.1| 109 PDNVENLTNKLVSYIESNGVERVVIDSTM 137
                                       888888888888899***********976 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 ?   11.8   0.0   0.00022      0.13       3      23 ..      24      44 ..      22      64 .. 0.86
   2 ?   -1.6   0.0         3   1.8e+03      72     119 ..     118     167 ..     110     179 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                      EEEEESTTCCHHHHHHHHHCT CS
                              cobW  3 tvltGflGsGKTtLlnhllen 23
                                      ++++G++GsGKTt+  + l++
  gi|336252665|ref|YP_004595772.1| 24 YIVSGPPGSGKTTFCAQFLTK 44
                                      799**********99988854 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3
                                       HHHHHHHHHTT-SEEEEEECTTTTHHHH..HTT.SHHHHHCCCECEEEEEE CS
                              cobW  72 elealeereerldviliEttGlaePapv..aft.eeelksdltldavvavv 119
                                       +l ++ e +  +++++i +t l+e  ++  + +  + l++  ++da+v vv
  gi|336252665|ref|YP_004595772.1| 118 KLVSYIESN-GVERVVIDSTMLLEYYFSdeVDQlITFLSKLKRADATVLVV 167
                                       555555555.56777777666665555532222223333344555555555 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013     0.078      47     105 ..      98     158 ..      81     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                            DUF835  47 ltkveeentvsPtnlekltetivkflkeaekgvvliDgleyLv..lengFesvlkflltlk 105
                                       ++++++ ++  P+n+e+lt+++v+++++++ + v+iD+  +L    + + ++ + fl++lk
  gi|336252665|ref|YP_004595772.1|  98 FSSSSRGGSDGPDNVENLTNKLVSYIESNGVERVVIDSTMLLEyyFSDEVDQLITFLSKLK 158
                                       45556667778**************************855554225577888899998888 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00068      0.41       3      39 ..      25      69 ..      23      96 .. 0.68
   2 ?    0.5   0.0         1   6.1e+02      80     119 ..     130     171 ..     127     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00068
                            AAA_28  3 vitGgestGKTtlleaLa.......argypvv.pEaareileekl 39
                                      +++G++++GKTt ++++        ++g  v  +E+  e++ + +
  gi|336252665|ref|YP_004595772.1| 25 IVSGPPGSGKTTFCAQFLtkgafngETGLYVSmHESEQELVADMS 69
                                      79***********99887344333333533334777777766655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1
                            AAA_28  80 rglldtlaYarayggeaeaelea.aarekrydl.vfllppap 119
                                       r ++d+++ +++y+ +   +l     + kr d+ v+++ ++ 
  gi|336252665|ref|YP_004595772.1| 130 RVVIDSTMLLEYYFSDEVDQLITfLSKLKRADAtVLVVSEMT 171
                                       778899999999999944455554788999999666666654 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00031      0.19       2      16 ..      28      42 ..      27      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00031
                                      E-TTSSHHHHHHHHH CS
                            AAA_17  2 GgPGsGKgtqceklv 16
                                      G+PGsGK+t c++  
  gi|336252665|ref|YP_004595772.1| 28 GPPGSGKTTFCAQFL 42
                                      9**********9865 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 ?   11.2   0.0   0.00038      0.23       2      22 ..      25      45 ..      24      96 .. 0.81
   2 ?   -1.9   0.0       3.7   2.2e+03     132     179 ..     118     160 ..     108     172 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrts 22
                                      +v+G pG+GK+t + ++l + 
  gi|336252665|ref|YP_004595772.1| 25 IVSGPPGSGKTTFCAQFLTKG 45
                                      79**************99885 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.7
                   Viral_helicase1 132 sdvaeilsakvgteveversgelkvetepkgqekvlvyltftqalkea 179
                                       ++v +i+s    ++v++++++ l  e+ ++++  v +++tf  +lk+a
  gi|336252665|ref|YP_004595772.1| 118 KLVSYIESNG-VERVVIDSTMLL--EYYFSDE--VDQLITFLSKLKRA 160
                                       4455555555.555555555555..5555555..77777777777764 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00035      0.21       3      20 ..      25      42 ..      23      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00035
                                      EEE--TTSSHHHHHHHHH CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvl 20
                                      +++GppG+GKtT++ + l
  gi|336252665|ref|YP_004595772.1| 25 IVSGPPGSGKTTFCAQFL 42
                                      79***********98766 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00027      0.16      17      40 ..      21      44 ..      12      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                            AAA_11 17 seitliqGPPGtgKTktivellsq 40
                                      + + +++GPPG+gKT++ +++l +
  gi|336252665|ref|YP_004595772.1| 21 DRLYIVSGPPGSGKTTFCAQFLTK 44
                                      45689***********99998875 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   0.00035      0.21       2      21 ..      25      44 ..      24      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00035
                      RNA_helicase  2 wlyGpsgeGKStlakeLaka 21
                                      +++Gp+g GK+t++ ++ ++
  gi|336252665|ref|YP_004595772.1| 25 IVSGPPGSGKTTFCAQFLTK 44
                                      689************96554 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0005       0.3      24      72 ..      25      68 ..      11      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                                      EEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXX CS
                            NB-ARC 24 alvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeileti 72
                                       ++G +G+GKtt  +q l k     g F++   + vs + +++e++ ++
  gi|336252665|ref|YP_004595772.1| 25 IVSGPPGSGKTTFCAQFLTK-----GAFNGETGLYVSMHESEQELVADM 68
                                      589**************999.....888888888888888888887665 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 ?   10.7   0.0   0.00054      0.33      50      91 ..      24      65 ..      12      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00054
                         IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveelk 91
                                       ++ Gp+G GK+ + + + ++++ +g   l+v++++  +el 
  gi|336252665|ref|YP_004595772.1| 24 YIVSGPPGSGKTTFCAQFLTKGAFNGETGLYVSMHESEQELV 65
                                      5789*****************************998777775 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0011      0.68      17      40 ..      22      45 ..      18      59 .. 0.82
   2 ?   -1.2   0.0       1.7     1e+03      80     104 ..     112     137 ..     109     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                        Zeta_toxin 17 klillgGqpGAGKselaellkdel 40
                                       l++++G pG+GK++  + + ++ 
  gi|336252665|ref|YP_004595772.1| 22 RLYIVSGPPGSGKTTFCAQFLTKG 45
                                      589************998887765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                        Zeta_toxin  80 aselvekllqeaiengyn.iivegtl 104
                                       +  l++kl+ ++ +ng++ +++++t+
  gi|336252665|ref|YP_004595772.1| 112 VENLTNKLVSYIESNGVErVVIDSTM 137
                                       66789999999999999658999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 1645.38
//
Query:       gi|336252666|ref|YP_004595773.1|  [L=147]
Description: hypothetical protein Halxa_1261 [Halopiger xanaduensis SH-6]
Scores for 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  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1169.43
//
Query:       gi|336252667|ref|YP_004595774.1|  [L=116]
Description: hypothetical protein Halxa_1262 [Halopiger xanaduensis SH-6]
Scores for 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   11.9   0.8       0.18   11.5   0.8    1.1  1  DUF716    Family of unknown function (DUF716)
        1.2    8.1   3.2        1.5    7.7   3.2    1.1  1  PalH      PalH/RIM21


Domain annotation for each model (and alignments):
>> DUF716  Family of unknown function (DUF716)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8     2e-05      0.18      33      79 ..      11      63 ..       2      64 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2e-05
                            DUF716 33 vhlLLvlvvalsllsalleallpksfll......elvrsvllilqGtWflqmG 79
                                          L+ +v+ls+l+ ++ +l+++  ++       +++ vl ++ G+W +++G
  gi|336252667|ref|YP_004595774.1| 11 SIAYLLHAVTLSMLVLFIFILVRTDRPAsvplavFFASVVLAMVVGLWRWKTG 63
                                      555666777777777777666554443323334345566777899*****998 PP

>> PalH  PalH/RIM21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.2   0.00017       1.5      72     117 ..      13      54 ..       6      57 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00017
                              PalH  72 lfslsaicVitwmLvlllfllprknhkrplllklavllvaivltia 117
                                       ++ l a  V+  mLvl++f+l r    rp  + lav ++++vl ++
  gi|336252667|ref|YP_004595774.1|  13 AYLLHA--VTLSMLVLFIFILVR--TDRPASVPLAVFFASVVLAMV 54 
                                       555555..555566666666666..3489************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 884.21
//
Query:       gi|336252668|ref|YP_004595775.1|  [L=363]
Description: hypothetical protein Halxa_1263 [Halopiger xanaduensis SH-6]
Scores for 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-26   92.7  17.7    2.2e-26   92.7  17.7    1.9  2  SpoIIM    Stage II sporulation protein M


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.9     0.048   8.7e+02      49      81 ..     104     147 ..      99     161 .. 0.62
   2 !   92.7  17.7   1.2e-30   2.2e-26       3     155 ..     174     342 ..     171     343 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.048
                            SpoIIM  49 lllfllGllllgiptilvllin...........GfvlGavaalv 81 
                                        llf+l ++++g ++++v               G+v Gav+a  
  gi|336252668|ref|YP_004595775.1| 104 TLLFALAVAAFGTAVVTVATTGdpapaagagalGVVFGAVGAAA 147
                                       56777777666666666554446777666666677777776555 PP

  == domain 2  score: 92.7 bits;  conditional E-value: 1.2e-30
                            SpoIIM   3 llflvgillgallaa..........snfaeqisseskensalslflaifanNlrvalllfllGllllgiptilvlli 69 
                                        lf++g++ g++l            + f+e++s+ + e+ +++l++++f+ N + a+l+ ++G l+lg++t++v+++
  gi|336252668|ref|YP_004595775.1| 174 GLFAIGTVGGIALLLagydllemvaELFEEMLSEVEDETGGIELTATFFILNNSRAFLMAIAGALTLGLLTAFVMVF 250
                                       6999****999999988888776643333555566666666777777777666667999999999************ PP

                            SpoIIM  70 nGfvlGavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal...rsrrkalkeakrellklllllvp. 142
                                       nG+++G ++a + +  gl ++l++++Phgi+elpa++ia+++g+r+ +++      ++++   k +l++ + l+++ 
  gi|336252668|ref|YP_004595775.1| 251 NGIIIGNMGASIGQSVGLDYILVGLAPHGIFELPALFIAAGVGFRIVYRFgerLVGSRDAFFTKPYLARTAALIAFg 327
                                       ********999999966*****************************9999776334455566999999999999999 PP

                            SpoIIM 143 ..llliAaliEafvt 155
                                         ll++Aa++Ea+vt
  gi|336252668|ref|YP_004595775.1| 328 wlLLVLAAFVEAYVT 342
                                       99************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); 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:                         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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2658.93
//
Query:       gi|336252669|ref|YP_004595776.1|  [L=434]
Description: 5-methylthioadenosine/S-adenosylhomocysteine deaminase [Halopiger xanaduensis SH-6]
Scores for complete 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-64  218.9   3.6    1.4e-64  218.6   3.6    1.0  1  Amidohydro_1  Amidohydrolase family
    1.2e-24   87.7  17.1    1.8e-18   67.3  13.4    2.9  2  Amidohydro_3  Amidohydrolase family
    0.00019   20.9   0.0    0.00039   19.8   0.0    1.5  1  A_deaminase   Adenosine/AMP deaminase
     0.0028   17.6   0.0     0.0059   16.6   0.0    1.6  1  CYTH          CYTH domain


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 !  218.6   3.6   3.1e-68   1.4e-64       1     343 [.      53     400 ..      53     401 .. 0.93

  Alignments for each domain:
  == domain 1  score: 218.6 bits;  conditional E-value: 3.1e-68
                                       EEEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgi 63 
                                       +v+PG+++ H H+ +sllrg     +l+ wl          ++ e+++ ++e g+ +++ksGtt +adm++     +
  gi|336252669|ref|YP_004595776.1|  53 LVTPGFVNGHCHVAMSLLRGYaddkPLDAWLqediwpaegeLTAEDVRTGAELGLLEMIKSGTTAFADMYF----DV 125
                                       59*********************************************************************....9* PP

                                       HHHHHHHHTSSSEEEEEEESSEGGS.GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHH CS
                      Amidohydro_1  64 ealleaaeelplglrilggkvsldr.gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealk 139
                                       + ++ a+ee+  glr+ +g ++++  +++e  +a +e+ ++  a+   g adg++++a++ph+ ++++ e+l+e + 
  gi|336252669|ref|YP_004595776.1| 126 PEIAAAVEEA--GLRARLGHGIVTVaKDDEGARADAETSLEV-AREYDGAADGRISTAFMPHSLTTVGTEYLEEFVP 199
                                       *********8..****99999998896667777777777666.5666889*************************** PP

                                       HHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEE CS
                      Amidohydro_1 140 eakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagva 216
                                       +a+++++p++ Ha et+ ev+ ++++ g    +  +l +a + g+l++    +ahgvh++ +e+ ll+e+  +++v 
  gi|336252669|ref|YP_004595776.1| 200 KARDAGVPIHYHANETEDEVAPIVEEEG---VR--PLAYAAERGMLEP-EDFVAHGVHVDESEIQLLAEA--GTSVI 268
                                       ********************99999999...66..9******9*****.999******************..***** PP

                                       HHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHH CS
                      Amidohydro_1 217 hcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTing 293
                                       hcp+sn++l+sg++++ ++ d+Gv vglgtDgaas+n l++l+e r+a++l ++ ++  +++ ++++ + +m+T + 
  gi|336252669|ref|YP_004595776.1| 269 HCPASNMKLASGMAPVQRLRDAGVTVGLGTDGAASNNDLSMLDEARDAAMLGKLAAA--DAAAVPAEAVAEMMTAGS 343
                                       *************************************************77774444..47779************* PP

                                       HHHTT-TTTSSSS-TTSB--EEEECC...CT......CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 294 AkalglddkvGsievGkdADlvvvdl...di......laafvglkkdgnvkkvivkGkl 343
                                       A+a+gl  + G++e+G +ADl+v+dl   ++       +++++ + +  v++++++G++
  gi|336252669|ref|YP_004595776.1| 344 ADAIGL--ESGRLEEGAPADLAVIDLekaHLtprhdlVSHLAYAAAAADVRHTVCDGRV 400
                                       ******..9*****************87722557788********************97 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1     1e-07   0.00046       1      24 [.      45      68 ..      45      82 .. 0.80
   2 !   67.3  13.4   4.1e-22   1.8e-18     194     472 ..     129     401 ..      75     402 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-07
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagg 24
                                      e+ Da+G lv+PGFv  H H+a  
  gi|336252669|ref|YP_004595776.1| 45 ETLDAEGSLVTPGFVNGHCHVAMS 68
                                      689*****************5543 PP

  == domain 2  score: 67.3 bits;  conditional E-value: 4.1e-22
                      Amidohydro_3 194 feltaeeklplrvi..ikelldaaerlglplspgseeltigavklfadgvlgsrtalltepyftgwpdfedealael 268
                                       +++ +e++l  r+   i  ++++ e  ++     +    ++  + +ad  +++ ta + +    + +++  e l+e 
  gi|336252669|ref|YP_004595776.1| 129 AAAVEEAGLRARLGhgIVTVAKDDEGARADAE--TSLEVAREYDGAAD--GRISTAFMPH----SLTTVGTEYLEEF 197
                                       33333333444444332223333333222222..22223333444555..4777777777....566777777**** PP

                      Amidohydro_3 269 vaaadergldvaihaigdaavd......dvldafeaaaekngnqdrr.rlehaegvtesqiervaalqvaagvqpvf 338
                                       v +a+++g++++ ha+++++        ++++ +++aae+  ++  +  ++h+  v+es+i+ +a+ +     +p++
  gi|336252669|ref|YP_004595776.1| 198 VPKARDAGVPIHYHANETEDEVapiveeEGVRPLAYAAERGMLEP-EdFVAHGVHVDESEIQLLAEAGTSVIHCPAS 273
                                       ***************998887733333444444444444444444.2599999999**************9999999 PP

                      Amidohydro_3 339 nfedelldsrlgperargstpvkellnagvkvalgsD..apvgpfdpwprigaavmrktrrggevlrpdeelsleea 413
                                       n            + a+g +pv++l++agv+v lg+D  a  + +  + + ++a m+ + + +    +   ++ e++
  gi|336252669|ref|YP_004595776.1| 274 NM-----------KLASGMAPVQRLRDAGVTVGLGTDgaASNNDLSMLDEARDAAMLGKLAAA----DAAAVPAEAV 335
                                       99...........889999*******************999******************8775....999******* PP

                      Amidohydro_3 414 lalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear.........vrltvvdGrvv 472
                                       + ++T+g+A a+gle   G+Le+Ga+ADl+v+d + ++++p ++             vr+tv+dGrv+
  gi|336252669|ref|YP_004595776.1| 336 AEMMTAGSADAIGLES--GRLEEGAPADLAVIDLEKAHLTPRHDLVSHlayaaaaadVRHTVCDGRVL 401
                                       ****************..***************9999999987666669*****************96 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   8.8e-08   0.00039     218     312 ..     246     335 ..     239     341 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.8e-08
                                       ECE-GGGGGSHHHHHHHHHCT-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCC.T-SHHHHHHHH CS
                       A_deaminase 218 igHGvrlrkdpvLqyllalaqiplevcPlSNvalgafleyaenPlkeflerglnvslntDDPlqf.gttLieeYaia 293
                                       ++HGv++ +++   +lla+a + +  cP+SN++l    +    P++++ ++g+ v l+tD  +   ++++ +e   a
  gi|336252669|ref|YP_004595776.1| 246 VAHGVHVDESE--IQLLAEAGTSVIHCPASNMKL----ASGMAPVQRLRDAGVTVGLGTDGAASNnDLSMLDEARDA 316
                                       68****99887..58999****************....78899*****************87754155688888888 PP

                                       HHHHT--HHHHHHHHHHHH CS
                       A_deaminase 294 aqvfklseedlaelarNsv 312
                                       a   kl ++d a +   +v
  gi|336252669|ref|YP_004595776.1| 317 AMLGKLAAADAAAVPAEAV 335
                                       8888888888877766666 PP

>> CYTH  CYTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.3e-06    0.0059      25      88 ..     108     168 ..      93     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-06
                                       CTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEEEETTTEEEEEEEEECSSST.EEEEEEEECCCE CS
                              CYTH  25 lrakeettveqrdtYydtpdrdlartdeaLRiRraegdgeeltlKgpgvdge.reevegevsreE 88 
                                       l++ + +t +++d+Y+d p+ + a   + LR R   g+g + t+ + + ++    e++ ev+  E
  gi|336252669|ref|YP_004595776.1| 108 LEMIKSGTTAFADMYFDVPEIAAAVEEAGLRAR--LGHGIV-TVAKDDEGARaDAETSLEVA-RE 168
                                       666788999************************..577766.66666544435666666666.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3292.89
//
Query:       gi|336252670|ref|YP_004595777.1|  [L=267]
Description: hypothetical protein Halxa_1265 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00078   19.7  14.3     0.0013   19.0  14.3    1.4  1  Invasin_D3       Invasin, domain 3
     0.0029   17.4   0.6     0.0085   15.9   0.6    1.8  1  DUF824           Salmonella repeat of unknown function (DUF82
      0.006   16.8   6.6      0.016   15.5   6.6    1.7  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.019   15.1   0.9      0.033   14.3   0.9    1.3  1  MG4              Macroglobulin domain MG4
        0.2   12.3   2.4       0.34   11.6   1.6    1.8  1  YtkA             YtkA-like
       0.69   10.4   3.6       0.63   10.5   1.9    1.7  2  DUF4179          Domain of unknown function (DUF4179)


Domain annotation for each model (and alignments):
>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0  14.3   4.2e-07    0.0013       9      92 ..      40     128 ..      28     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.2e-07
                        Invasin_D3   9 aspasivAdGkststltvtlkDangnpvsgltvtfsttsag......tlsavtdngdGtytatLta.ttagtatitp 78 
                                       ++pa  vA   + +t+tvt  +a+++pv+ +tv ++   +g       +++ t+ +dGt t      +++  + it+
  gi|336252670|ref|YP_004595777.1|  40 VEPAINVAQ-DADATVTVTDANADNEPVADATVDVTLA-DGedasyaDTGTYTTGEDGTVTLDAPTgNESVDVAITA 114
                                       556665665.455669****************999977.55555677778999*****999887544889999**** PP

                        Invasin_D3  79 tvnGvaiaatatvt 92 
                                       tvnG+++++tat++
  gi|336252670|ref|YP_004595777.1| 115 TVNGTTAETTATLE 128
                                       ****9999999987 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 !   15.9   0.6   2.8e-06    0.0085      18      42 ..      53      79 ..      50      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.8e-06
                            DUF824 18 titvkD..asGnPvpnapftltRgdgk 42
                                      t+tv+D  a+++Pv++a++ +t++dg+
  gi|336252670|ref|YP_004595777.1| 53 TVTVTDanADNEPVADATVDVTLADGE 79
                                      677776115788*************97 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   6.6   5.4e-06     0.016       4      71 ..      54     129 ..      51     138 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.4e-06
                   CarboxypepD_reg   4 GrVtda..sgapiagatVtvtnadtg.....tvastttdadGafrlrglpp.gtysvtvsapGyatatreevtlta 71 
                                        +Vtda  +++p+a atV vt ad++      + + tt++dG+ +l++ +   + +v ++a+   t++ ++ tl++
  gi|336252670|ref|YP_004595777.1|  54 VTVTDAnaDNEPVADATVDVTLADGEdasyaDTGTYTTGEDGTVTLDAPTGnESVDVAITATVNGTTAETTATLEP 129
                                       589**76689**********98776544444488999*********955556666666677777766666677765 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.9   1.1e-05     0.033      18      86 ..      54     123 ..      51     130 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                               MG4  18 ikVlvkdpdgspaknvpVkiealk...seteekeslttdedGtakfsintpedaksltitvktkdpslpeen 86 
                                       ++V   ++d++p++  +V +++ +    +  +  ++tt edGt+ +   t +++  ++it+    ++ ++e+
  gi|336252670|ref|YP_004595777.1|  54 VTVTDANADNEPVADATVDVTLADgedASYADTGTYTTGEDGTVTLDAPTGNESVDVAITA--TVNGTTAET 123
                                       455556899*************556444456677888******987766666555555555..444555555 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.6   0.00011      0.34      17      48 ..      47      79 ..      31      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                              YtkA 17 pkagentivvt.vtqggkpVedadvkvefwmpa 48
                                      +++ ++t++vt  +++++pV da+v+v+  + +
  gi|336252670|ref|YP_004595777.1| 47 AQDADATVTVTdANADNEPVADATVDVTLADGE 79
                                      36677788888888*************998765 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.9   0.00021      0.63       6      79 ..       7      64 ..       2      67 .. 0.75
   2 ?   -2.2   0.0         2   5.9e+03      60      68 ..     112     120 ..      96     152 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00021
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.--SS-HHHHT--SS-HHHHSEEEEEEEEETTEEEEEEEEEE-SS CS
                           DUF4179  6 ikkvaaaaaalvllllssrllspalAsalnpvigslfeklsdskgeqeyvkpvnksaednGitvtvnevvaDgn 79
                                      +  + a+a +l +l++++++++ a ++a                  ++ v+p    a+d + tvtv+++ aD+ 
  gi|336252670|ref|YP_004595777.1|  7 LAVMLATALLLSVLFAGGGIATVAASNAS----------------ANDSVEPAINVAQDADATVTVTDANADNE 64
                                      44455555555566666666666666666................9*************************985 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                                       EEEEETTEE CS
                           DUF4179  60 ksaednGit 68 
                                       ++a+ nG t
  gi|336252670|ref|YP_004595777.1| 112 ITATVNGTT 120
                                       333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1838.80
//
Query:       gi|336252671|ref|YP_004595778.1|  [L=433]
Description: adenosylhomocysteinase [Halopiger xanaduensis SH-6]
Scores for complete 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-51  175.8   0.0    6.1e-27   94.5   0.4    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    7.5e-48  162.6   1.1    1.7e-47  161.5   0.4    1.8  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    6.4e-10   38.7   0.1    1.2e-09   37.8   0.1    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    4.9e-06   26.2   0.1    1.3e-05   24.9   0.1    1.7  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
  ------ inclusion threshold ------
      0.015   15.5   0.1      0.035   14.3   0.1    1.6  1  TrkA_N         TrkA-N domain
      0.019   15.0   0.0      0.038   14.1   0.0    1.5  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase


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 !   94.5   0.4     2e-30   6.1e-27       6     138 ..      19     148 ..      15     150 .. 0.93
   2 !   81.0   0.0   2.8e-26   8.4e-23     171     287 ..     148     428 ..     144     433 .] 0.98

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 2e-30
                                       -GGGH.HHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--H CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase   6 disla.efGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqd 81 
                                       d++ a e Gr++++ a + mp l ++ree+ +++p++g ria ++h+ ++ta+L+etL + Gaev  + Cn  st d
  gi|336252671|ref|YP_004595778.1|  19 DLESArEEGRRKMDWAAQHMPILESVREEFVDDQPFEGERIAMAMHVEAKTAMLVETLAEGGAEVAVTGCNPLSTHD 95 
                                       66554278********************************************************************* PP

                                       HHHHHHCCT.TEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHH CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  82 eaaaaiaea.gvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhk 138
                                       +++aa+ ++ +++ +a +g   eey   ie ++++     ep + +DdG Dl + +h+
  gi|336252671|ref|YP_004595778.1|  96 DVSAALDTHeNITSYAKRGVDDEEYYAAIEAVIAH-----EPTITVDDGMDLVAAIHE 148
                                       ******9777***********************55.....79**************98 PP

  == domain 2  score: 81.0 bits;  conditional E-value: 2.8e-26
                                       THHCCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                         AdoHcyase 171 kkytellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD........................... 220
                                       + y+el++ i G  eetttGvhrL  + ++g L+ p + vnd+  k  fD                           
  gi|336252671|ref|YP_004595778.1| 148 EDYPELIDGIVGGCEETTTGVHRLRAMDDDGALEYPVFAVNDTPMKRLFDnvhgtgesslasiamttnlswagknvv 224
                                       789************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|336252671|ref|YP_004595778.1| 225 vagygycgkgvakkaagqnanvivteveprraleahmegydvmpmdeaaevgdvfltttgnrdviveehfeqmkdgv 301
                                       ***************************************************************************** PP

                                       ............................................................S-HHHHHHHHHHHHHHH CS
                                       ............................................................xxxxxxxxxxxxxxxxx RF
                         AdoHcyase 221 ............................................................hpsfvmsasftnqvlaq 237
                                                                                                   hp  vm++sf  q++  
  gi|336252671|ref|YP_004595778.1| 302 llanaghfdieidldalddlavdryeardgveayemddgrrlnviaegrlvnlaapvslgHPVEVMDQSFGVQAVCV 378
                                       ***************************************************************************** PP

                                       HHHHHTTSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 238 ielfkkekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyigv 287
                                        e+ ++ ++y  +v+ +p +lD ++a+++le+ g++ ++lt++q +y++ 
  gi|336252671|ref|YP_004595778.1| 379 REMLENGEEYGPGVHDVPDELDKEIAEIKLEAEGVEHDSLTDTQRDYMDS 428
                                       ***********************************************985 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 ?   -1.2   0.0      0.63   1.9e+03      40      59 ..      74      93 ..      68     108 .. 0.75
   2 !  161.5   0.4   5.6e-51   1.7e-47       1     159 [.     198     356 ..     198     359 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.63
                                      HHHHHCT-EEEEE-S-HHHH CS
                     AdoHcyase_NAD 40 aslkglGarvivtevdPica 59
                                      ++l + Ga v vt  +P+++
  gi|336252671|ref|YP_004595778.1| 74 ETLAEGGAEVAVTGCNPLST 93
                                      56778899999999999875 PP

  == domain 2  score: 161.5 bits;  conditional E-value: 5.6e-51
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTT CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvk 77 
                                       n++g+ es + +i  +t++  aGk++vvaGyG  GkG a+   g+ a vivtev+P  al a meG++v+ ++e+++
  gi|336252671|ref|YP_004595778.1| 198 NVHGTGESSLASIAMTTNLSWAGKNVVVAGYGYCGKGVAKKAAGQNANVIVTEVEPRRALEAHMEGYDVMPMDEAAE 274
                                       7889999********************************************************************** PP

                                       T-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSB CS
                     AdoHcyase_NAD  78 kadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrl 154
                                        +d+++tttGn+d+i  eh+++mkd ++++n Ghfd eid++al   a+++ e +  v+ ++++dg+++ ++aeGrl
  gi|336252671|ref|YP_004595778.1| 275 VGDVFLTTTGNRDVIVEEHFEQMKDGVLLANAGHFDIEIDLDALDDLAVDRYEARDGVEAYEMDDGRRLNVIAEGRL 351
                                       ***************************************************************************** PP

                                       CHHHT CS
                     AdoHcyase_NAD 155 lnlgc 159
                                       +nl++
  gi|336252671|ref|YP_004595778.1| 352 VNLAA 356
                                       ***85 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 !   37.8   0.1   4.1e-13   1.2e-09      33     128 ..     217     308 ..     198     325 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 4.1e-13
                                       -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSB CS
                      2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhli 109
                                       + +gk v + G+G  G+ vak++++ +++vi++++ +++  e++ +g++++ ++e+ +  D+       t  +r++i
  gi|336252671|ref|YP_004595778.1| 217 SWAGKNVVVAGYGYCGKGVAKKAAGQNANVIVTEVEPRRALEAHMEGYDVMPMDEAAEVGDVFLT----TTGNRDVI 289
                                       6789**********************************99999999***************9875....5679**** PP

                                       SHHHHHCSTTTEEEEESS- CS
                      2-Hacid_dh_C 110 naeelakmkkgailiNtaR 128
                                        +e++++mk+g++l N++ 
  gi|336252671|ref|YP_004595778.1| 290 VEEHFEQMKDGVLLANAGH 308
                                       ****************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 !   24.9   0.1   4.3e-09   1.3e-05       4     101 ..     220     313 ..     217     322 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.3e-09
                                       TS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHH CS
                              IlvN   4 gkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeee 80 
                                       gk+++v GyG  G+  a++   +  +v+v+  e +  + +A+ eg++v+ ++ea++  dv ++ +    +++v+ ee
  gi|336252671|ref|YP_004595778.1| 220 GKNVVVAGYGYCGKGVAKKAAGQNANVIVTEVEPR-RALEAHMEGYDVMPMDEAAEVGDVFLTTT---GNRDVIVEE 292
                                       89***************************999988.6778*******************976655...456666677 PP

                                       TGGG--TT-EEEESSSHHHHT CS
                              IlvN  81 iepnlkegkalafahGfnihf 101
                                         +++k+g  la a  f+i  
  gi|336252671|ref|YP_004595778.1| 293 HFEQMKDGVLLANAGHFDIEI 313
                                       77899*****99999999975 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.2e-05     0.035       1      48 [.     223     270 ..     223     275 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES- CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgd 48 
                                       ++++G+G  G+ +a++   ++ +v+v + +++r+ e+  eg++v+  d
  gi|336252671|ref|YP_004595778.1| 223 VVVAGYGYCGKGVAKKAAGQNANVIVTEVEPRRALEAHMEGYDVMPMD 270
                                       79*****************7667******************9998666 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05     0.038       9      99 ..     217     298 ..     207     340 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSS CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatas 85 
                                       s+++k+v++ G G  ++ vak+ + ++++ v+v+  + +ra  l  +++g+   +++++e   + +  dv ++ t+ 
  gi|336252671|ref|YP_004595778.1| 217 SWAGKNVVVAGYGYCGKGVAKKAAGQNAN-VIVTEVEPRRA--LEAHMEGY--DVMPMDE---AAEVGDVFLTTTGN 285
                                       7899********************99999.88888777776..55566555..5566655...55889**9999999 PP

                                       SS-SB-HHHHHCCH CS
                      Shikimate_DH  86 eepilekeeveeal 99 
                                       +++i+e+ ++e+++
  gi|336252671|ref|YP_004595778.1| 286 RDVIVEE-HFEQMK 298
                                       9998875.555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3338.89
//
Query:       gi|336252672|ref|YP_004595779.1|  [L=241]
Description: hypothetical protein Halxa_1267 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.082   13.4   0.0       0.72   10.3   0.0    2.1  2  MG2       MG2 domain


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.047   8.4e+02       4      54 ..      53     111 ..      50     123 .. 0.60
   2 ?   10.3   0.0     4e-05      0.72      30      80 ..     139     190 ..     125     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.047
                                       EEES-SEE-TT-EEEEEEEEES......TTCSB---..EEEEEEEE-TTSSEEEEEEEE CS
                               MG2   4 vytDRglYrPgetVslkallrd......etlqglak..lplkltirdpdgkevkelpla 54 
                                       v++ R+ + Pge+++l +++         +l+ + +  +   ++++dp+  ++++ + a
  gi|336252672|ref|YP_004595779.1|  53 VFLKRPRLSPGERIELGIFVSGlervdeTELSVFYDgeRDELIDLEDPGTVRQSSNETA 111
                                       56678888899999998888665343333333333355555566666666666665555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 4e-05
                                       B---EEEEEEEE-TTSSEEEEEEEEE-CTTE..EEEEEE--TT--SEEEEEEE CS
                               MG2  30 glaklplkltirdpdgkevkelplatdetgg..aesefalpeaaklGeysvel 80 
                                       ++  +p++l+  dp++   +++pl+ ++ gg  +  e+++ +aa++G+ys+ +
  gi|336252672|ref|YP_004595779.1| 139 PFV-HPTTLDRGDPGEYALERKPLEGTDGGGpsYILEINTRAAAPTGSYSLPI 190
                                       333.5999999*************99999987788999999*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1968.57
//
Query:       gi|336252673|ref|YP_004595780.1|  [L=314]
Description: PAS sensor protein [Halopiger xanaduensis SH-6]
Scores for 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-11   42.6   0.3    1.9e-10   40.9   0.3    1.8  1  PAS_4         PAS fold
    4.4e-09   36.5   0.0    7.9e-09   35.7   0.0    1.4  1  PAS_9         PAS domain
     0.0042   17.4   0.0     0.0069   16.7   0.0    1.3  1  PAS_3         PAS fold
  ------ inclusion threshold ------
      0.074   13.2   0.0       0.18   11.9   0.0    1.7  2  Response_reg  Response regulator receiver domain
       0.11   12.7   0.0       0.23   11.7   0.0    1.5  1  OKR_DC_1_N    Orn/Lys/Arg decarboxylase, N-terminal domain
       0.14   12.1   0.0       0.27   11.2   0.0    1.5  1  PAS           PAS fold
        1.4    9.4   8.2       0.72   10.3   0.4    3.1  2  HEAT_2        HEAT repeats


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.3   7.6e-14   1.9e-10       4     101 ..     194     290 ..     192     293 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 7.6e-14
                             PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeepiefleelllpgeer 79 
                                       + da+av +pdgr ++aN+ +a+ fg+++e+l+G+++ ++++++ +a+  ++a+  +++g++   +++ ++++ge++
  gi|336252673|ref|YP_004595780.1| 194 SRDAIAVAGPDGRLEAANCWFAAQFGYDRETLRGRSWTDFFTADaVAHLEATAIPTAADGWRWTGTCTGRRRSGEPV 270
                                       679*****************************************9999999**********88888888888***** PP

                             PAS_4  80 hyelrllPlrdesGevigvlvi 101
                                       ++ +rl  l  e+G  ++v++ 
  gi|336252673|ref|YP_004595780.1| 271 PVHVRLAGL--EDGSLVFVVEA 290
                                       *********..56988888765 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   3.1e-12   7.9e-09       2      95 ..     196     287 ..     195     293 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 3.1e-12
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfw 77 
                                       d+i++  pdgr++ aN  ++  +Gy++e + g+s+td+f t++  ++ ++ a+ +  +   ++++ + +r++ge+++
  gi|336252673|ref|YP_004595780.1| 196 DAIAVAGPDGRLEAANCWFAAQFGYDRETLRGRSWTDFF-TADAVAHLEATAIPTAADgWRWTGTCTGRRRSGEPVP 271
                                       6899999********************************.999999999999999999999**************** PP

                             PAS_9  78 vlltaspvkdddgelvgi 95 
                                       v+++++ +   dg lv++
  gi|336252673|ref|YP_004595780.1| 272 VHVRLAGLE--DGSLVFV 287
                                       ********5..6667664 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.7e-06    0.0069      11      85 ..     217     287 ..     210     291 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.7e-06
                             PAS_3  11 ilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengkpvrv 85 
                                        +Gy++e l+g+  sw d+   +  ++++++    +++g +++g    rr++Ge + v+ r   +  e+g  v+v
  gi|336252673|ref|YP_004595780.1| 217 QFGYDRETLRGR--SWTDFFTADAVAHLEATAIPTAADGWRWTGTCTGRRRSGEPVPVHVRLAGL--EDGSLVFV 287
                                       59**********..**********9999999999999************************9998..77777766 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.2e-05      0.18      44      90 ..      74     123 ..      40     132 .. 0.74
   2 ?   -3.0   0.0       3.1     8e+03      48      63 ..     180     195 ..     179     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.2e-05
                                       ESEEEEESS...CSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHH CS
                      Response_reg  44 vdlillDin...mpgmdGlellkeireedpelpviiltahseeedaveal 90 
                                        d+++l      mp  d + +l+++r++ ++lpvi+++ +s++e ++ + 
  gi|336252673|ref|YP_004595780.1|  74 ADCLVLEHAasgMPAADAVAVLERVRDRYSSLPVIVVSDASTDEGTTTVT 123
                                       6777766532229999**********************777766555544 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
                                       EEESSCSSSEHHHHHH CS
                      Response_reg  48 llDinmpgmdGlellk 63 
                                       l D++m  + G++l +
  gi|336252673|ref|YP_004595780.1| 180 LSDLSMRLLAGIQLSR 195
                                       6799**99***99875 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     9e-05      0.23      23      76 ..      57     117 ..      41     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9e-05
                        OKR_DC_1_N  23 vtstdDlls.vieqnsriaavvlsvd......deaaelldeirernedlPvFllaetrtse 76 
                                       + st + ++ ++e  ++++++vl+ +       +a ++l+ +r+r   lPv ++++ +t+e
  gi|336252673|ref|YP_004595780.1|  57 AFSTAESTApLLERLADADCLVLEHAasgmpaADAVAVLERVRDRYSSLPVIVVSDASTDE 117
                                       5555554442788999********99******9999*******************988665 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.27       6      99 ..     190     282 ..     186     289 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC. CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl. 81 
                                        ++ ++d+i v   dgr   +N  ++ ++G++re + g+s  d++  +     +++le  +  +      ++  ++ 
  gi|336252673|ref|YP_004595780.1| 190 GIQLSRDAIAVAGPDGRLEAANCWFAAQFGYDRETLRGRSWTDFFTAD----AVAHLEATAIPTAADGWRWTGTCTg 262
                                       57889999999999******************************9887....4444444444444333333333334 PP

                                       ..TTSSEEEEEEEEEEEEET CS
                               PAS  82 ..rdgrpihlevraspvrda 99 
                                         r g+p++++vr + + d+
  gi|336252673|ref|YP_004595780.1| 263 rrRSGEPVPVHVRLAGLEDG 282
                                       77799999999988766665 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.4   0.00028      0.72      43      76 ..      11      47 ..       6      57 .. 0.82
   2 ?    0.3   2.3      0.38   9.7e+02       2      24 ..      65      86 ..      64     157 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
                            HEAT_2 43 edpavRraaaeaLgaigdpe...alpaLkellddddd 76
                                      +dp++Rraa++ L+a  +p+   a + L+++l+d+  
  gi|336252673|ref|YP_004595780.1| 11 PDPRTRRAAITVLVATHRPSlgrAPDRLEAALRDECG 47
                                      79************99876655588999999998755 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.38
                            HEAT_2  2 daLlqalendpdpevrraairaL 24
                                      ++Ll++l  d+d+ v  +a+  +
  gi|336252673|ref|YP_004595780.1| 65 APLLERL-ADADCLVLEHAASGM 86
                                      5788888.788888877777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 2715.01
//
Query:       gi|336252674|ref|YP_004595781.1|  [L=95]
Description: hypothetical protein Halxa_1269 [Halopiger xanaduensis SH-6]
Scores for 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   82.2   0.4    2.8e-23   82.0   0.4    1.1  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.4   1.5e-27   2.8e-23       2      74 ..      19      87 ..      18      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 1.5e-27
                            HalOD1  2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVe 74
                                       +sps ++v+a+a+++++dp el+pLyd++Dp+ALd++++     + +++++v+F y g+ V Vrsdg i ++
  gi|336252674|ref|YP_004595781.1| 19 HDSPSLRIVDALADATDTDPLELDPLYDVVDPEALDRFLEA----DPTGEATVAFGYGGHSVEVRSDGAIAID 87
                                      689**************************************....667889*******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 761.92
//
Query:       gi|336252675|ref|YP_004595782.1|  [L=1656]
Description: PAS/PAC sensor protein [Halopiger xanaduensis SH-6]
Scores for 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-66  219.7  10.0    3.1e-20   72.3   0.1    7.1  7  PAS_3         PAS fold
    1.1e-53  180.1  32.0    7.9e-18   64.7   0.1    7.1  6  PAS_4         PAS fold
    6.3e-52  174.2   1.1    3.5e-13   49.7   0.0    6.5  6  PAS_9         PAS domain
    1.4e-51  174.5  18.8    1.4e-51  174.5  18.8    3.9  2  BAT           GAF and HTH_10 associated domain
    1.6e-46  157.0   4.1    1.2e-19   70.3   0.0    6.0  6  PAS           PAS fold
    5.5e-23   80.5   5.7    5.7e-10   39.0   0.1    4.9  4  PAS_8         PAS domain
    9.2e-23   81.1  15.2    2.9e-15   56.8   0.6    5.8  5  GAF_2         GAF domain
    2.4e-16   59.3   0.0    5.9e-16   58.0   0.0    1.7  1  HTH_10        HTH DNA binding domain
    3.8e-09   37.0   0.0      0.001   19.4   0.0    4.8  4  GAF_3         GAF domain
      4e-08   34.0   0.0      0.082   13.5   0.0    4.6  4  GAF           GAF domain
    3.8e-06   27.1   8.9        1.6    8.9   0.1    7.8  6  PAS_7         PAS fold
    3.6e-05   24.3   0.0     0.0002   21.9   0.0    2.4  2  PAS_10        PAS domain
    7.5e-05   22.8   0.0      0.055   13.6   0.0    3.2  3  PAS_11        PAS domain
    0.00062   19.6   0.3        2.8    7.7   0.0    4.0  4  dCache_1      Cache domain
     0.0013   18.2   0.2     0.0053   16.2   0.2    2.1  1  Sigma70_r4    Sigma-70, region 4
  ------ inclusion threshold ------
      0.019   15.0   0.0      0.051   13.6   0.0    1.7  1  DUF2111       Uncharacterized protein conserved in archaea (D
      0.022   14.7   2.2      0.027   14.4   0.2    2.3  1  Sigma70_ECF   ECF sigma factor
      0.025   14.5   0.2      0.088   12.8   0.2    2.0  1  HTH_1         Bacterial regulatory helix-turn-helix protein, 
      0.068   12.8   0.7       0.31   10.7   0.0    2.7  1  Sigma70_r4_2  Sigma-70, region 4
       0.14   12.0   0.0       0.38   10.6   0.0    1.7  1  HTH_5         Bacterial regulatory protein, arsR family
        0.2   11.4   1.2       0.52   10.1   1.2    1.7  1  DUF4051       Protein of unknown function (DUF4051)
        2.8    7.9  12.6       0.12   12.3   5.3    2.4  2  Trypan_PARP   Procyclic acidic repetitive protein (PARP)


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       3.2   2.6e+03      33      58 ..     134     160 ..     131     162 .. 0.89
   2 !   14.0   0.0   5.6e-05     0.045       3      84 ..     342     420 ..     341     424 .. 0.89
   3 !   45.5   0.1   8.5e-15   6.9e-12       2      80 ..     467     543 ..     466     548 .. 0.91
   4 !   30.7   0.0   3.6e-10   2.9e-07       3      87 ..     601     681 ..     599     683 .. 0.92
   5 !   11.3   0.0    0.0004      0.33       2      70 ..     724     789 ..     723     801 .. 0.82
   6 !   72.3   0.1   3.8e-23   3.1e-20       2      88 ..     847     932 ..     846     933 .. 0.96
   7 !   45.6   0.0   7.9e-15   6.4e-12       4      84 ..     978    1056 ..     975    1061 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.2
                             PAS_3  33 eDrervrealqealkkgepyege.yRi 58 
                                       +D+  + e  +++l++ e+y +e yRi
  gi|336252675|ref|YP_004595782.1| 134 DDLTSAVERRERHLAESERYRTElYRI 160
                                       8999999999**********9988998 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.6e-05
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirden 79 
                                        ++++  +++Gys +el++   +   +   + r  ++e+++e++++ge   +e  + +kdGe +  e  a+vi d +
  gi|336252675|ref|YP_004595782.1| 342 RWNDALTDVTGYSHAELEAM--DEPLYFDADARTAIEESVAEVFETGE-TRVEAPLTTKDGERIPHEFVASVIEDPD 415
                                       59******************..5444555555****************.799************************* PP

                             PAS_3  80 gkpvr 84 
                                       g+ ++
  gi|336252675|ref|YP_004595782.1| 416 GNQIE 420
                                       99775 PP

  == domain 3  score: 45.5 bits;  conditional E-value: 8.5e-15
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       + + ++  +i G++p+     +e+ l++ hp Dr+r+rea+++al++ge+ye e R+r++  +  wv++ +++i+d 
  gi|336252675|ref|YP_004595782.1| 467 VQWTDETARIHGVDPD-TDPGIEDALEYYHPADRPRLREAIDRALERGESYELELRMRTATDDRQWVRTIGEPIYD- 541
                                       67999********997.55556****************************************************55. PP

                             PAS_3  79 ng 80 
                                       +g
  gi|336252675|ref|YP_004595782.1| 542 DG 543
                                       44 PP

  == domain 4  score: 30.7 bits;  conditional E-value: 3.6e-10
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirden 79 
                                        ++++ e+i+G+s++++l++       + p+Dr+  +  ++++l++ +    e ++rr dG+ + v+ +a +ird +
  gi|336252675|ref|YP_004595782.1| 601 LWNPAAERIFGWSESDVLDD----PLPIVPDDRDDHQPIFERVLEGETIAGLETKRRREDGSLIDVSVSAAPIRDAD 673
                                       6*******************....33578***************999988*************************** PP

                             PAS_3  80 gkpvrvig 87 
                                       g++v   g
  gi|336252675|ref|YP_004595782.1| 674 GEIVGTMG 681
                                       **998877 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.0004
                             PAS_3   2 iyvserveeilGyspeellgk.veswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwvea 70 
                                       + +++r+ + lGy + ellg+ v ++ +l   +D   + e ++     ge+ ++e R+rr+dG+++ +e 
  gi|336252675|ref|YP_004595782.1| 724 VEANRRFADELGYAEGELLGTkVWKYDELFDADDALGLLEGMA----VGERRKFEGRFRRRDGSTFPIEV 789
                                       7899*****************6666777777777777777775....4666789**********999886 PP

  == domain 6  score: 72.3 bits;  conditional E-value: 3.8e-23
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       i +s++ e+++G++p  ++g++e +  +vhp+D +rv++al++a++++e y +e+R+rr dG+++w+ ar+r + d 
  gi|336252675|ref|YP_004595782.1| 847 IDWSGTLERLVGLEPGAFEGTYEAFERRVHPDDVDRVEAALEAAVEERELYRTEFRMRREDGDWIWIGARGRLVTDA 923
                                       89************************************************************************9*9 PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g   r++g+
  gi|336252675|ref|YP_004595782.1| 924 DGG-RRMVGI 932
                                       999.668887 PP

  == domain 7  score: 45.6 bits;  conditional E-value: 7.9e-15
                             PAS_3    4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78  
                                        +s++ +++ ++s+ +++ ++e+ +++ hp+Dr+ vre+l++al++ ++ye e Rir+ +Ge  wv+a +++i  e
  gi|336252675|ref|YP_004595782.1|  978 WSDELYRLHDLSR-DVEPDLETTIECYHPDDRPLVREELERALETETEYELEARIRTDSGENKWVRAIGEPI-HE 1050
                                        8999999999986.6777788***************************************************.66 PP

                             PAS_3   79 ngkpvr 84  
                                         g  v 
  gi|336252675|ref|YP_004595782.1| 1051 GGDLVA 1056
                                        666655 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.6     2e-11   1.6e-08       1     110 []     324     432 ..     324     432 .. 0.97
   2 !   14.4   0.8   4.1e-05     0.034      40     109 ..     489     566 ..     467     567 .. 0.81
   3 !   64.7   0.1   9.7e-21   7.9e-18       2     110 .]     584     691 ..     583     691 .. 0.94
   4 !   42.8   0.1   6.3e-14   5.1e-11       1     109 [.     707     813 ..     707     814 .. 0.92
   5 !   27.3   1.1   3.9e-09   3.2e-06      18     109 ..     847     940 ..     830     941 .. 0.90
   6 !   15.5   0.3   1.9e-05     0.015      44     109 ..    1003    1068 ..     995    1069 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2e-11
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ld+l d+++v+d+d   +++N a  ++ g++ +el  +    ++ +++++++e+ +++v e++e+  ++  ++ +ge
  gi|336252675|ref|YP_004595782.1| 324 LDALDDVFYVVDEDRSLRRWNDALTDVTGYSHAELEAMDEPLYFDADARTAIEESVAEVFETGETRVEAPLTTKDGE 400
                                       799************************************999***********************999999999*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       + ++e+ ++ ++d++G  +  ++i+rDi++r+r
  gi|336252675|ref|YP_004595782.1| 401 RIPHEFVASVIEDPDGN-QIEVGIARDISDRKR 432
                                       *****************.88889********97 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.1e-05
                             PAS_4  40 la.ellpeedaarleralrrvlegeepiefleelllpgeerhyelrl........lPlrdesGevigvlvisrDiTe 107
                                       +a e++ + d++rl++a++r+le +e++e +  +++  ++r +  ++        +   d++ e++gv + +++iT+
  gi|336252675|ref|YP_004595782.1| 489 DAlEYYHPADRPRLREAIDRALERGESYELELRMRTATDDRQWVRTIgepiyddgTA-ADSETEIVGVRGSIQEITA 564
                                       555777778***************************888888888888777777444.4789999999999999999 PP

                             PAS_4 108 rr 109
                                       r+
  gi|336252675|ref|YP_004595782.1| 565 RK 566
                                       97 PP

  == domain 3  score: 64.7 bits;  conditional E-value: 9.7e-21
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                       +++p+al++ld+d +v+ +N+aa+++fg++  ++l+ +l  ++p+ d+++++++ +rvlege+ +  ++ +++ +g+
  gi|336252675|ref|YP_004595782.1| 584 EASPAALVALDRDENVTLWNPAAERIFGWSESDVLDDPLP-IVPD-DRDDHQPIFERVLEGETIAGLETKRRReDGS 658
                                       79**************************************.7777.***************877777777777**** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                          +++++ P+rd++Ge++g+++ + DiTer++
  gi|336252675|ref|YP_004595782.1| 659 LIDVSVSAAPIRDADGEIVGTMGALEDITERKE 691
                                       *******************************85 PP

  == domain 4  score: 42.8 bits;  conditional E-value: 6.3e-14
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       +d +pd++ v+d+dg+++ aN+++a+ +g++  ellG +++ +    da++    l+ ++ ge++ ++  +++++g+
  gi|336252675|ref|YP_004595782.1| 707 FDDSPDIINVVDADGTIVEANRRFADELGYAEGELLGTKVWKYDELFDADDALGLLEGMAVGERRKFEGRFRRRDGS 783
                                       799**************************************765555999*************99999999999*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       + ++e++l++l+ e+     +l+i+rDiTer+
  gi|336252675|ref|YP_004595782.1| 784 TFPIEVHLIRLDLEDE--NRFLAICRDITERK 813
                                       ***********55444..6***********97 PP

  == domain 5  score: 27.3 bits;  conditional E-value: 3.9e-09
                             PAS_4  18 lyaNaaaaelfgappeellGktla...ellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlrd 90 
                                       ++++ + ++l+g++p ++ G   a    ++p+ d +r+e+al++++e++e ++++  +++ +g++ ++  r + + d
  gi|336252675|ref|YP_004595782.1| 847 IDWSGTLERLVGLEPGAFEGTYEAferRVHPD-DVDRVEAALEAAVEERELYRTEFRMRReDGDWIWIGARGRLVTD 922
                                       667778889************99996558888.******************************************** PP

                             PAS_4  91 esGevigvlvisrDiTerr 109
                                       ++G+ +  ++i+ D+Ter+
  gi|336252675|ref|YP_004595782.1| 923 ADGG-RRMVGILNDVTERV 940
                                       ****.*************7 PP

  == domain 6  score: 15.5 bits;  conditional E-value: 1.9e-05
                             PAS_4   44 lpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGevigvlvisrDiTerr 109 
                                        + ++d++ +++ l+r+le+e+ +e +   ++ +ge +++     P++ e G+ +++ + ++DiT+++
  gi|336252675|ref|YP_004595782.1| 1003 YHPDDRPLVREELERALETETEYELEARIRTdSGENKWVRAIGEPIH-EGGDLVAYRGALQDITAQK 1068
                                        44559**********************99999**************5.7999************997 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   7.6e-10   6.2e-07       3     104 .]     330     429 ..     328     429 .. 0.84
   2 !    8.5   0.0    0.0028       2.3      43      89 ..     499     543 ..     473     564 .. 0.80
   3 !   41.7   0.0   1.3e-13   1.1e-10       5     104 .]     591     688 ..     587     688 .. 0.93
   4 !   49.7   0.0   4.3e-16   3.5e-13       3     104 .]     713     811 ..     711     811 .. 0.92
   5 !   20.2   0.0   6.4e-07   0.00052      14     104 .]     847     938 ..     836     938 .. 0.78
   6 !   16.7   0.0   7.8e-06    0.0064      42     104 .]    1007    1066 ..     977    1066 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 7.6e-10
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwv 78 
                                        + ++++d  + ++N+a+ +++Gys++e+   +    f  d++a+  +++ + +  +  e +ve  l++k+ge+++ 
  gi|336252675|ref|YP_004595782.1| 330 VFYVVDEDRSLRRWNDALTDVTGYSHAELEAMDEPLYF--DADARTAIEESVAEVFEtGETRVEAPLTTKDGERIPH 404
                                       566676888666*******************7776666..77777777777777777778***************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                       ++ as + d dg+ +  ++i rDi++
  gi|336252675|ref|YP_004595782.1| 405 EFVASVIEDPDGNQIE-VGIARDISD 429
                                       *******999777777.7******96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0028
                             PAS_9  43 dpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkddd 89 
                                        p+ +e +++ale+g+   +e e+ +++ ++ + wv+    p++dd+
  gi|336252675|ref|YP_004595782.1| 499 RPRLREAIDRALERGE--SYELELRMRTATDDRQWVRTIGEPIYDDG 543
                                       56678899********..*************************5554 PP

  == domain 3  score: 41.7 bits;  conditional E-value: 1.3e-13
                             PAS_9   5 lidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvllt 81 
                                       +  + d +++ +N+aa+r++G s+ +vl  ++  + ++ ++++  ++++le  +      e+  +r++g+ + v ++
  gi|336252675|ref|YP_004595782.1| 591 VALDRDENVTLWNPAAERIFGWSESDVLDDPLPIVPDDRDDHQPIFERVLEGET--IAGLETKRRREDGSLIDVSVS 665
                                       33568888*********************9999999999999999999999999..********************* PP

                             PAS_9  82 aspvkdddgelvgiivilrDite 104
                                       a+p++d+dge+vg  + l+Dite
  gi|336252675|ref|YP_004595782.1| 666 AAPIRDADGEIVGTMGALEDITE 688
                                       **********************8 PP

  == domain 4  score: 49.7 bits;  conditional E-value: 4.3e-16
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgks...itdlfvtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                        i +++ dg+i+ aN+ +++ lGy + e+lg++   +++lf  d++++  l + +  g+   r +e  ++r++g+tf
  gi|336252675|ref|YP_004595782.1| 713 IINVVDADGTIVEANRRFADELGYAEGELLGTKvwkYDELF--DADDALGLLEGMAVGE--RRKFEGRFRRRDGSTF 785
                                       555788***************************88888999..****************..**************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       +++++++++  +d++ ++  +i+rDite
  gi|336252675|ref|YP_004595782.1| 786 PIEVHLIRLDLEDENRFL--AICRDITE 811
                                       *********777766666..*******8 PP

  == domain 5  score: 20.2 bits;  conditional E-value: 6.4e-07
                             PAS_9  14 lyaNeaalrllGyspeevlgks..itdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvk 86 
                                       ++++ +++rl G  p ++ g++  ++  +  ++ ++ +  l+aa+e+ +   ++ e  ++r++g  +w+ ++ + v 
  gi|336252675|ref|YP_004595782.1| 847 IDWSGTLERLVGLEPGAFEGTYeaFERRVhpDDVDRVEAALEAAVEERE--LYRTEFRMRREDGDWIWIGARGRLVT 921
                                       78999999************87543333345555555555555555555..************************** PP

                             PAS_9  87 dddgelvgiivilrDite 104
                                       d+dg+ + +++il+D+te
  gi|336252675|ref|YP_004595782.1| 922 DADGGRR-MVGILNDVTE 938
                                       9977666.47*******8 PP

  == domain 6  score: 16.7 bits;  conditional E-value: 7.8e-06
                             PAS_9   42 tdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104 
                                        + p  +e+l++ale+ +  e+e e  +++++ge  wv++   p++ ++g lv++ + l+Dit+
  gi|336252675|ref|YP_004595782.1| 1007 DRPLVREELERALETET--EYELEARIRTDSGENKWVRAIGEPIH-EGGDLVAYRGALQDITA 1066
                                        55566788888999999..*************************7.6899***********95 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.3       3.1   2.5e+03      89     118 ..      62      91 ..      55      95 .. 0.77
   2 !  174.5  18.8   1.7e-54   1.4e-51       1     155 [.    1416    1583 ..    1416    1584 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.1
                               BAT  89 lastlaehGgtvrsaeaedgrarlvvevPp 118
                                       + +   e  ++v ++ ++d +++ v evP 
  gi|336252675|ref|YP_004595782.1|  62 VERLANEVEAYVDRLDITDRGTDPVTEVPV 91 
                                       444445789999999999999999999995 PP

  == domain 2  score: 174.5 bits;  conditional E-value: 1.7e-54
                               BAT    1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpee.............vrdaaedl 62  
                                        ++vveL+le++d+ddvl+++a+ +d+rv++egl ++s++e+l+ff+++ga++++             +rd++edl
  gi|336252675|ref|YP_004595782.1| 1416 ESVVELTLEFSDADDVLSRIAEGADARVAYEGLSTSSEEEALLFFEIEGAETDDaadtgdaedgasaARDVLEDL 1490
                                        68*************************************************999999****************** PP

                               BAT   63 davedvrvvseeddgtlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdve 137 
                                        +av+d+rv++++ddg+l+e+tv+g++las+l++hG+++rs++a+++r+ ++++vPpg+dvR++ve+l++ryp+v+
  gi|336252675|ref|YP_004595782.1| 1491 VAVTDYRVIAATDDGWLVEATVAGDVLASRLVRHGASPRSIAADGDRTVVTADVPPGTDVREFVEMLADRYPSVD 1565
                                        *************************************************************************** PP

                               BAT  138 Lvarrererpvrtrrefr 155 
                                        L++rr+++r+++trre++
  gi|336252675|ref|YP_004595782.1| 1566 LRSRRHVQRDTHTRRELV 1583
                                        ****************97 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.5e-06    0.0012       5     113 .]     322     427 ..     318     427 .. 0.78
   2 ?   -2.1   0.0       4.6   3.7e+03      46      84 ..     490     527 ..     467     544 .. 0.59
   3 !   70.3   0.0   1.5e-22   1.2e-19       1     113 []     577     686 ..     577     686 .. 0.90
   4 !   38.8   0.0   9.2e-13   7.5e-10       2     113 .]     702     809 ..     701     809 .. 0.89
   5 !   21.5   0.1   2.2e-07   0.00018       2     113 .]     825     936 ..     824     936 .. 0.76
   6 ?    3.5   0.0     0.082        66      46     113 .]     999    1064 ..     973    1064 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                                       HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC CS
                               PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl 81 
                                        +l++l+d   vvDed     +N+a ++ +G+s  e+       ++  +      ++    ++++e +++ge++++ 
  gi|336252675|ref|YP_004595782.1| 322 DLLDALDDVFYVVDEDRSLRRWNDALTDVTGYSHAELEAMDEPLYFDAD------ARTAIEESVAEVFETGETRVEA 392
                                       5899******************************999999999777655......3334444455555555555555 PP

                                       ....TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  82 ....rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                           +dg+ i+ e  as + d++g+    +g++rdi
  gi|336252675|ref|YP_004595782.1| 393 plttKDGERIPHEFVASVIEDPDGNQ-IEVGIARDI 427
                                       555689******************97.556666665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.6
                                       GGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTS CS
                               PAS  46 lldliheeddaelaelleqlleqgeesrageisfklrdg 84 
                                        l+++h+ d+  l+e++ ++le ge+ + + + ++    
  gi|336252675|ref|YP_004595782.1| 490 ALEYYHPADRPRLREAIDRALERGESYELELRMRTA-TD 527
                                       466777777667777777777777766654444444.44 PP

  == domain 3  score: 70.3 bits;  conditional E-value: 1.5e-22
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e+l ai+e++p++ +++D+d +++++N+aae+++G+s+++vl  +l   i+++d++ +++ + ++ ++ge   + e+
  gi|336252675|ref|YP_004595782.1| 577 ERLNAIIEASPAALVALDRDENVTLWNPAAERIFGWSESDVLDDPLP--IVPDDRD-DHQPIFERVLEGETIAGLET 650
                                       5789*******************************************..7777665.77777777777777777777 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++++ dg+ i + v a+p+rda+gei g +g l di
  gi|336252675|ref|YP_004595782.1| 651 KRRREDGSLIDVSVSAAPIRDADGEIVGTMGALEDI 686
                                       77777***************************9998 PP

  == domain 4  score: 38.8 bits;  conditional E-value: 9.2e-13
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBG..GGGBSTTHHHHHHHHHHHHHHHTT-ECCCC CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgksl..ldliheeddaelaelleqlleqgeesrage 76 
                                       +l+a+++++pd i vvD+dg i+++N+ +++ lG+++ e+lg ++  +d+++  d   +a  l++ +++ge+++ +e
  gi|336252675|ref|YP_004595782.1| 702 RLEALFDDSPDIINVVDADGTIVEANRRFADELGYAEGELLGTKVwkYDELFDAD---DALGLLEGMAVGERRK-FE 774
                                       799*****************************************97778888776...6777777777776655.56 PP

                                       EEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  77 isfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        +f++rdg+++++ev+   +  ++++   fl ++rdi
  gi|336252675|ref|YP_004595782.1| 775 GRFRRRDGSTFPIEVHLIRLDLEDEN--RFLAICRDI 809
                                       678888*******************9..9******98 PP

  == domain 5  score: 21.5 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTS.BGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgk.slldliheeddaelaelleqlleqgeesragei 77 
                                       +l+  le + ++ + ++ d++ + ++ + e+l Gl++    g    ++ ++++dd +++e+ ++++ + +e    e 
  gi|336252675|ref|YP_004595782.1| 825 RLELALEGTNTGLWEWNVDTDEIDWSGTLERLVGLEPGAFEGTyEAFERRVHPDDVDRVEAALEAAVEERELYRTEF 901
                                       68899********************************6666641567778888865444444444444444433455 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       + ++ dg  i++  r + v+da+g +   +g+l+d+
  gi|336252675|ref|YP_004595782.1| 902 RMRREDGDWIWIGARGRLVTDADGGR-RMVGILNDV 936
                                       55559*******************76.888888886 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.082
                                        GGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS   46 lldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113 
                                         ++ +h++d+  ++e+le++le+ +e +  e ++++  g+ ++++    p+ ++g+ +  + g l+di
  gi|336252675|ref|YP_004595782.1|  999 TIECYHPDDRPLVREELERALETETEYEL-EARIRTDSGENKWVRAIGEPIHEGGDLV-AYRGALQDI 1064
                                        45567777776888888888888888887.6666776****************99987.777777776 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   0.00017      0.14       6      44 ..     323     362 ..     314     384 .. 0.82
   2 !   39.0   0.1     7e-13   5.7e-10       1      60 [.     577     637 ..     577     644 .. 0.87
   3 !   28.0   0.1     2e-09   1.6e-06       1      55 [.     701     756 ..     701     769 .. 0.83
   4 ?   -1.0   0.0       2.4     2e+03       2      37 ..     825     860 ..     824     889 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                             PAS_8   6 lfesspdgiavvdlgdrivdvNqaalellGys.adlkgel 44 
                                       l+++++d   vvd+++ ++ +N+a  + +Gys a+l +++
  gi|336252675|ref|YP_004595782.1| 323 LLDALDDVFYVVDEDRSLRRWNDALTDVTGYShAELEAMD 362
                                       89***********7777***************99888765 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 7e-13
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrplle.dae 60 
                                       erl a++e+sp +++ +d++++++ +N+aa++++G+s  d+++++l +++p+ r+  +   e
  gi|336252675|ref|YP_004595782.1| 577 ERLNAIIEASPAALVALDRDENVTLWNPAAERIFGWSeSDVLDDPL-PIVPDDRDDHQpIFE 637
                                       79****************8888***************999999999.999999888874333 PP

  == domain 3  score: 28.0 bits;  conditional E-value: 2e-09
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                       +rl+alf+ spd i vvd++++iv++N+++++ lGy   +l+g +++++ + ++  
  gi|336252675|ref|YP_004595782.1| 701 ARLEALFDDSPDIINVVDADGTIVEANRRFADELGYAeGELLGTKVWKYDELFDAD 756
                                       69****************5555**************99999888887666666555 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 2.4
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys 37 
                                       rl+ ++e  + g++ ++ + d  +d+  + ++l G++
  gi|336252675|ref|YP_004595782.1| 825 RLELALEGTNTGLWEWNvDTD-EIDWSGTLERLVGLE 860
                                       899999********9666566.788888888888866 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.038        31       8     126 ..     172     293 ..     166     298 .. 0.67
   2 ?    1.0   0.0      0.59   4.8e+02      92     110 ..     663     682 ..     574     703 .. 0.76
   3 ?   -1.1   0.1       2.5   2.1e+03      14     106 ..     952    1056 ..     944    1084 .. 0.51
   4 !   23.6   0.7   6.2e-08   5.1e-05       2     137 ..    1088    1219 ..    1087    1220 .. 0.83
   5 !   56.8   0.6   3.5e-18   2.9e-15       2     137 ..    1263    1404 ..    1262    1405 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.038
                                       HHHHHHHHHH.SS..EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-.GGG-S-HH CS
                             GAF_2   8 ldlvldelve.lgaalgyillvdddgg.lrlaawgeaeeefgaaldrplgeglvgealrtgrpvilnd.leedpdkk 81 
                                        ++vl+  +e lg+++g++  +d++++ +++  ++   + + +a +++l+   + +a+     + + + ++e +   
  gi|336252675|ref|YP_004595782.1| 172 IRRVLELGCErLGVEAGFVSRIDPERErYTVQFAR-GSDLVQEAEESDLSTMYCRHAIDADGILEIYNaPAEGYEDE 247
                                       689999998889***********766635544333.33333333334454446999999865444555377766666 PP

                                       HHHHHHHTT--EEEEEE-TTS---EEEEES........--HHHHHHH CS
                             GAF_2  82 glpaghaglrsflavPlisegrvvGvlnlyankppa..fdeedlelL 126
                                       ++  ++ +++  l+  +  +g ++G l+++a +p++  f+  +++++
  gi|336252675|ref|YP_004595782.1| 248 PSY-AELDVGCYLGGRIEVDGDLYGTLCFVAREPRTepFTGPERTFV 293
                                       666.8888888899999445679999998666665566776666665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.59
                                       -EEEEEE-T.TS---EEEEE CS
                             GAF_2  92 sflavPlis.egrvvGvlnl 110
                                       s  a P+++ +g++vG ++ 
  gi|336252675|ref|YP_004595782.1| 663 SVSAAPIRDaDGEIVGTMGA 682
                                       45689************996 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.5
                                        HHHHS.S....EEEEEEE-TTS-........EEEE......EEEES-TTSTT-S-B--..-TTHHHHHHHHTS-E CS
                             GAF_2   14 elvel.g.aa.lgyillvdddgg........lrla......awgeaeeefgaaldrpl..geglvgealrtgrpv 69  
                                         l+++   a+  g+ l v d+++        +rl+       +  ++   + ++d+++  +e  +++al+t  + 
  gi|336252675|ref|YP_004595782.1|  952 LLERVqRmADiGGWELDVTDEPQvaiwsdelYRLHdlsrdvEPDLETTIECYHPDDRPlvREE-LERALETETEY 1025
                                        444443334445687777788882222222222223333333333333444444443333333.34555553222 PP

                                        EES-GGG-S-HHHHHHHHHTT--EEEEEE-TTS---E CS
                             GAF_2   70 ilndleedpdkkglpaghaglrsflavPlisegrvvG 106 
                                         l      +++++   g+ ++ + ++ P+ ++g +v+
  gi|336252675|ref|YP_004595782.1| 1026 EL------EARIRTDSGENKWVRAIGEPIHEGGDLVA 1056
                                        22......23333344666666667777777666665 PP

  == domain 4  score: 23.6 bits;  conditional E-value: 6.2e-08
                                        HHHHHHHHHHHHHHHH.S.S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B.--.-TTHHHHHHHHTS-EEES CS
                             GAF_2    2 adleelldlvldelve.l.gaalgyillvdddgglrlaawgeaeeefgaaldr.pl.geglvgealrtgrpviln 72  
                                        +++  +++l+ ++++e l ga++g++ll+ + ++++ +a++++ ee  + +++ ++ g++l++  + tg  ++++
  gi|336252675|ref|YP_004595782.1| 1088 TTEPAVAELAAETATElLeGASAGVYLLDAETNRFEPVASAGDFEERTGGAPSvAVgGDSLLWNTYVTGTQTVVD 1162
                                        6788999*********558899**999999999999888888877776666554667888999999999777754 PP

                                        -GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2   73 dleedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137 
                                                +g p+ + +  s+l vPl   g  +G+++l  + p a d+e ++l+e+l +++  a 
  gi|336252675|ref|YP_004595782.1| 1163 G---GSGASGTPLFGDDASSGLLVPL---G-EHGAFVL-LAPPAAIDDETRRLFETLVATVEAAF 1219
                                        4...567799**9*************...8.7888887.478888**************998886 PP

  == domain 5  score: 56.8 bits;  conditional E-value: 3.5e-18
                                        HHHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B--..-TTHHHHHHHHTS-EEES CS
                             GAF_2    2 adleelldlvldelvel.gaalgyillvdddgg.lrlaawgeaeeefgaaldrpl..geglvgealrtgrpviln 72  
                                         + +e+ ++v ++lve  ++a+++i+  d+++  l+ ++w+++ +e  +a++ +l  g  ++ + +rt  p++++
  gi|336252675|ref|YP_004595782.1| 1263 ESRDEIERTVPERLVEAdDIAFAWIGAADPGETtLEPRTWAGTSPEYLDAVSLDLssGTEPAVRTARTETPTVVE 1337
                                        6889************955********99554447788*********999977664455588899999******* PP

                                        -GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2   73 dleedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137 
                                        ++ +d    +++  a  +gl+s +avPl  e+  +Gvl++ya++p+af++ +++++ el+e ia ai
  gi|336252675|ref|YP_004595782.1| 1338 NVVDDLQEGAWRttALNEGLQSAVAVPLEFEEYGYGVLAVYADEPDAFTDLERTVFAELGEGIANAI 1404
                                        *77766666666669*************555579********************************9 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   7.3e-19   5.9e-16       1      52 [.    1590    1641 ..    1590    1642 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 7.3e-19
                            HTH_10    1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52  
                                        LT++qlevl++Ay +G+F++PR+ t +e+A+ l ++++t+  hLr a+++l+
  gi|336252675|ref|YP_004595782.1| 1590 LTERQLEVLRTAYFAGFFEWPRESTGEEVAELLEVTQPTVNRHLRLAQQRLL 1641
                                        9************************************************997 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.047        38       3     129 .]     169     306 ..     167     306 .. 0.65
   2 ?    2.7   0.0      0.19   1.5e+02      13     113 ..     579     696 ..     572     701 .. 0.65
   3 ?    3.8   0.0     0.084        68      15      88 ..    1103    1185 ..    1092    1211 .. 0.61
   4 !   19.4   0.0   1.2e-06     0.001      52     127 ..    1319    1404 ..    1268    1406 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.047
                             GAF_3   3 dellekllkllvkllgaevgalllldedgn..klqvaagwdgkpalsesldedsalarralssgevvse........ 69 
                                       de +  +l+l+++ lg+e+g++   d++++  ++q a+g+d  +  +e  d  +  +r a++ ++++ e        
  gi|336252675|ref|YP_004595782.1| 169 DEKIRRVLELGCERLGVEAGFVSRIDPEREryTVQFARGSDLVQEAEE-SDLSTMYCRHAIDADGIL-Eiynapaeg 243
                                       788888999999999999999999998888323444555544444433.234455555555555543.223334422 PP

                             GAF_3  70 ....psfaeedglpdraalavPLvagr.qviGvlal..astkprafdaedlelleslArqiataier 129
                                           ps+ae   l+ +++l   + + +  ++G+l++  + +++++f+  ++ +++  +r+++ +++r
  gi|336252675|ref|YP_004595782.1| 244 yedePSYAE---LDVGCYLGGRIEV-DgDLYGTLCFvaREPRTEPFTGPERTFVDLATRWVSHELDR 306
                                       211255444...8889999999999.559******9423445666****************999986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.19
                             GAF_3  13 lvkllgaevgalllldedgnklqvaagwdgkpalse.............sldedsalarralssgevvsepsf...a 73 
                                       l+ +  a+ +al+ ld+d+n   ++ + +    +se               d +++ + r+l+ ge +++++    +
  gi|336252675|ref|YP_004595782.1| 579 LNAIIEASPAALVALDRDENVTLWNPAAERIFGWSEsdvlddplpivpdDRDDHQPIFERVLE-GETIAGLETkrrR 654
                                       556666666666677777666666655544444555555555665555566678888888888.5566674432213 PP

                             GAF_3  74 eedglpdraalavPLvagr.qviGvlal.astkprafdaedl 113
                                       e  +l d ++ a+P+++ + + +G++++ +   +r+ ++++l
  gi|336252675|ref|YP_004595782.1| 655 EDGSLIDVSVSAAPIRDADgEIVGTMGAlEDITERKERERRL 696
                                       3445789999*******99*******9647778777776665 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.084
                             GAF_3   15 kllgaevgalllldedgnklqvaagw.dgkpalse......sld..edsalar.ralssgevvse.psfaeedgl 78  
                                        +ll   ++ ++lld++ n++ ++a+  d +    e      s+    ds+l+  ++ +++ vv +  ++ +++  
  gi|336252675|ref|YP_004595782.1| 1103 ELLEGASAGVYLLDAETNRFEPVASAgDFE----ErtggapSVAvgGDSLLWNtYVTGTQTVVDGgSGASGTPLF 1173
                                        45555677899************9985333....33333565544355555556777777665332222334444 PP

                             GAF_3   79 pdraa..lavPL 88  
                                         d a   l+vPL
  gi|336252675|ref|YP_004595782.1| 1174 GDDASsgLLVPL 1185
                                        433333466666 PP

  == domain 4  score: 19.4 bits;  conditional E-value: 1.2e-06
                             GAF_3   52 edsalarralssgev.vsepsfae.........edglpdraalavPLvagrqviGvlalastkprafdaedlell 116 
                                         ++  a r++ ++ + v+e+ +++         + +  +++a+avPL  ++  +Gvla++ ++p af++ ++  +
  gi|336252675|ref|YP_004595782.1| 1319 SGTEPAVRTARTETPtVVENVVDDlqegawrttALNEGLQSAVAVPLEFEEYGYGVLAVYADEPDAFTDLERTVF 1393
                                        4444455555555542333333332212222112235679*********99************************ PP

                             GAF_3  117 eslArqiatai 127 
                                         +l+  ia+ai
  gi|336252675|ref|YP_004595782.1| 1394 AELGEGIANAI 1404
                                        **********9 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00019      0.16       4     130 ..     170     301 ..     167     304 .. 0.73
   2 ?    1.2   0.0      0.67   5.5e+02      89     107 ..     663     682 ..     604     706 .. 0.81
   3 ?   -0.8   0.0       2.7   2.2e+03       6      75 ..    1094    1175 ..    1069    1219 .. 0.49
   4 !   13.5   0.0    0.0001     0.082      48     133 .]    1320    1404 ..    1273    1404 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECC.......EEEET...TSHHHHHHHHHSSSEEESTGG.. CS
                               GAF   4 elldtvveelrellgadrvalylpdydGlhydipqasrw.......lfmkn...grgicgqvlatgqplvipdst.. 68 
                                       e  ++v+e  +e lg++ + + + d +  +y + q +r            +    ++ c +++  + +l i ++   
  gi|336252675|ref|YP_004595782.1| 170 EKIRRVLELGCERLGVEAGFVSRIDPERERY-TVQFARGsdlvqeaE---EsdlSTMYCRHAIDADGILEIYNAPae 242
                                       55688999999**********9955555556.555555544454433...134588999999999999999953212 PP

                                       ...TSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS...CSHHHHHHHHHHHHHHHH CS
                               GAF  69 ...pdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp...pftreelellqvladqva 130
                                          ++p +a         +  +  +l+  + +dg+l+G+l+++ + p   pft  e+ ++    + v+
  gi|336252675|ref|YP_004595782.1| 243 gyeDEPSYA---------ELDVGCYLGGRIEVDGDLYGTLCFVAREPrtePFTGPERTFVDLATRWVS 301
                                       332444455.........59************************6666689**999999987777776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.67
                                       EEEEEEEEE.TTEEEEEEEE CS
                               GAF  89 sslvvPlvn.dgelwGllvl 107
                                       s+ ++P+++ dge++G++ +
  gi|336252675|ref|YP_004595782.1| 663 SVSAAPIRDaDGEIVGTMGA 682
                                       8999****88******9976 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.7
                                        HHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECC.......EEEETTSH..HHH......HHHHHSSSEEES CS
                               GAF    6 ldtvveelrellgadrvalylpdydGlhydipqasrw.......lfmkngrg..icg......qvlatgqplvip 65  
                                        ++ ++e++ ell+   + +yl d++ +++  p as+               +   +g       ++ tg   v++
  gi|336252675|ref|YP_004595782.1| 1094 AELAAETATELLEGASAGVYLLDAETNRF-EPVASAGdfeertgG-----APsvAVGgdsllwNTYVTGTQTVVD 1162
                                        33344445555555666666644444444.444444422222221.....1111111233333555555555555 PP

                                        T...GGTSTTHHT CS
                               GAF   66 d...stpdprfaq 75  
                                        +   ++ +p f +
  gi|336252675|ref|YP_004595782.1| 1163 GgsgASGTPLFGD 1175
                                        4333335555555 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 0.0001
                                        TSHHHHHHHHHSSSEEESTGGTSTTHHTT.HHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHH CS
                               GAF   48 grgicgqvlatgqplvipdstpdprfaqy.nrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreele 120 
                                        g+  + ++++t  p v++++ +d   +q  ++r ++ n g +s+++vPl  ++  +G+l+++   p  ft+ e+ 
  gi|336252675|ref|YP_004595782.1| 1320 GTEPAVRTARTETPTVVENVVDD---LQEgAWRTTALNEGLQSAVAVPLEFEEYGYGVLAVYADEPdAFTDLERT 1391
                                        3333447889999999**64333...333358899*****************99*********66667******* PP

                                        HHHHHHHHHHHHH CS
                               GAF  121 llqvladqvaval 133 
                                        ++ +l++ +a+a+
  gi|336252675|ref|YP_004595782.1| 1392 VFAELGEGIANAI 1404
                                        **99999999887 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1         5   4.1e+03      57      95 ..     127     165 ..     119     168 .. 0.77
   2 ?    2.5   0.0      0.19   1.5e+02       2      32 ..     325     355 ..     324     380 .. 0.87
   3 !    8.9   0.1     0.002       1.6       6     114 ..     588     693 ..     583     694 .. 0.61
   4 ?    4.8   0.0     0.036        29       8      40 ..     714     745 ..     708     817 .. 0.62
   5 ?    2.7   0.1      0.16   1.3e+02      58     114 ..     882     943 ..     864     944 .. 0.70
   6 ?    3.2   0.0      0.11        92      61     114 ..    1013    1071 ..     972    1072 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5
                             PAS_7  57 gdveaeverrlaaaragkphsfererpdgrvievrgnpl 95 
                                       ++ +a+v+  ++a++++++h  e er + +  ++++ p 
  gi|336252675|ref|YP_004595782.1| 127 ERLAAAVDDLTSAVERRERHLAESERYRTELYRITSDPS 165
                                       456778888888999999999999999999988888876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.19
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpe 32 
                                       + +++ + v+D+d  L+ wN+   ++ +++ 
  gi|336252675|ref|YP_004595782.1| 325 DALDDVFYVVDEDRSLRRWNDALTDVTGYSH 355
                                       55666789**************999988876 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.002
                             PAS_7   6 qGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsferer 82 
                                        +++ +D+d+++++wN    ++++++e+ v     l++ l +  +      +d +  +er+l + ++ +   ++r+r
  gi|336252675|ref|YP_004595782.1| 588 AALVALDRDENVTLWNPAAERIFGWSESDV-----LDDPLPIVPDDR----DDHQPIFERVL-EGETIAGLETKRRR 654
                                       678999*******************99988.....333333332211....12223344444.45555666667777 PP

                             PAS_7  83 pdgrvievrgnpl.......pdgGfVttytDiTerrrae 114
                                       +dg  i+v  ++        +  G++   +DiTer++ e
  gi|336252675|ref|YP_004595782.1| 655 EDGSLIDVSVSAApirdadgEIVGTMGALEDITERKERE 693
                                       777777665555433442223346666677777777766 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.036
                             PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgvp 40 
                                       i v+Dad+ +v  Nrr+ + l++ e+ +  g++
  gi|336252675|ref|YP_004595782.1| 714 INVVDADGTIVEANRRFADELGYAEGEL-LGTK 745
                                       679****************999998766.4444 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.16
                             PAS_7  58 dveaeverrlaaaragkphsfererpdgrviev..rgnpl..pdgG..fVttytDiTerrrae 114
                                       +vea++e+ ++  r+  ++ f  +r+dg +i +  rg+ +  +dgG  +V + +D+Ter++ e
  gi|336252675|ref|YP_004595782.1| 882 RVEAALEAAVE-ERELYRTEFRMRREDGDWIWIgaRGRLVtdADGGrrMVGILNDVTERVEYE 943
                                       56667777774.455666777888888888776224555566678866899*********987 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.11
                             PAS_7   61 aeverrlaaara.gkphsfererpdgrvievrgnplpdgGfVtty....tDiTerrrae 114 
                                        +e+er l+  ++ + + ++     ++++++  g+p+ +gG ++ y    +DiT++++ e
  gi|336252675|ref|YP_004595782.1| 1013 EELERALETETEyELEARIRTDSGENKWVRAIGEPIHEGGDLVAYrgalQDITAQKERE 1071
                                        444444433333255566666778899*************9998855557*****9987 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       8.7   7.1e+03      14      39 ..     333     358 ..     322     413 .. 0.54
   2 !   21.9   0.0   2.4e-07    0.0002       1     106 []     579     687 ..     579     687 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.7
                            PAS_10  14 flDdnlqirrFtpaakklfklipadv 39 
                                        +D++  +rr+++a + +  + +a++
  gi|336252675|ref|YP_004595782.1| 333 VVDEDRSLRRWNDALTDVTGYSHAEL 358
                                       57888888888887766666555544 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.4e-07
                            PAS_10   1 lnnlLnstpieltflDdnlqirrFtpaakklfklipadvGrpladihpkkavknveeviealrtgek.devevvvp. 75 
                                       ln ++++ p +l+ lD++ +++ ++paa+++f   ++dv ++   i+p+   ++ + ++e++ +ge+    e+++  
  gi|336252675|ref|YP_004595782.1| 579 LNAIIEASPAALVALDRDENVTLWNPAAERIFGWSESDVLDDPLPIVPD-DRDDHQPIFERVLEGETiAGLETKRRr 654
                                       799999*******************************985555556555.456678888888888887445555543 PP

                            PAS_10  76 kngkw..vlvrylpyrdedgeiaGvvetfvDit 106
                                       ++g +  v v   p+rd dgei G++  + Dit
  gi|336252675|ref|YP_004595782.1| 655 EDGSLidVSVSAAPIRDADGEIVGTMGALEDIT 687
                                       88998345566779**************99997 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.031        26      44      90 ..     494     539 ..     490     555 .. 0.88
   2 !   13.6   0.0   6.7e-05     0.055      44      93 ..     875     923 ..     869     930 .. 0.92
   3 ?   -1.7   0.0       3.9   3.2e+03      44      81 ..    1003    1041 ..    1000    1046 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.031
                            PAS_11  44 chpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklf 90 
                                        hp+d+ +l+++    + ++ge+ ++  R+r+++d+  +v+t ++  
  gi|336252675|ref|YP_004595782.1| 494 YHPADRPRLREAIDRAL-ERGESYELELRMRTATDDRQWVRTIGEPI 539
                                       69***************.******************99999977665 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.7e-05
                            PAS_11  44 chpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfknq 93 
                                       +hp+d+ +++ +l+  + +++e   + +R+r ++++++++ ++++l ++ 
  gi|336252675|ref|YP_004595782.1| 875 VHPDDVDRVEAALEAAV-EERELYRTEFRMRREDGDWIWIGARGRLVTDA 923
                                       7****************.99999999*******************99875 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.9
                            PAS_11   44 chpqdlstlkshlrevissngeatsslyRLrl..sqdkfv 81  
                                         hp+d+  +++ l+  + ++++  ++  R+r+  +++k+v
  gi|336252675|ref|YP_004595782.1| 1003 YHPDDRPLVREELERAL-ETETEYELEARIRTdsGENKWV 1041
                                        59***************.9999999999999944444444 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.9     4e+03      10      30 ..      57      77 ..      55      79 .. 0.87
   2 !    7.7   0.0    0.0034       2.8      79     148 ..     469     543 ..     417     555 .. 0.72
   3 !    7.3   0.0    0.0043       3.5      39     159 ..     556     685 ..     544     689 .. 0.58
   4 ?   -1.7   0.0       2.5   2.1e+03      58      95 ..     697     732 ..     682     751 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.9
                          dCache_1 10 qllglaeqlanniedvldsle 30
                                      +  +++e+lan++e+++d+l+
  gi|336252675|ref|YP_004595782.1| 57 SDRTTVERLANEVEAYVDRLD 77
                                      66789************9986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0034
                          dCache_1  79 lvdadGqviassdpssppnleg...tddpadrdwykealaggg..gkpvisdpyvdqt..ggkpvitiavpiyddsg 148
                                       + d+  ++  ++ p+++p+ e    ++ padr+ ++ea+++    g+++  ++ + ++    ++v ti +piydd g
  gi|336252675|ref|YP_004595782.1| 469 WTDETARIHGVD-PDTDPGIEDaleYYHPADRPRLREAIDRALerGESYELELRMRTAtdDRQWVRTIGEPIYDD-G 543
                                       555555555544.44444555568877777777766666666666699999998555555679**********96.6 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0043
                          dCache_1  39 npslqdlleepnraneasreslqallksilksn.......pdisgvylvdadGqviassdpssppnleg....tddp 104
                                         s+q+     +r  e   ++++++l+ i ++        +  ++v+l ++  + i+ +++s+            +p
  gi|336252675|ref|YP_004595782.1| 556 RGSIQEITARKER--ERELRETNERLNAIIEASpaalvalDRDENVTLWNPAAERIFGWSESDV----LddplPIVP 626
                                       5555555555555..5555666666777666662222222233455555555555554444433....134454444 PP

                          dCache_1 105 adrdw....ykealaggggkpvisdpy.vdqtggk..pvitiavpiyddsgkfiGvlaadld 159
                                        drd     + ++l+g+   +   ++  +  + g    v + a+pi+d++g+++G+++a  d
  gi|336252675|ref|YP_004595782.1| 627 DDRDDhqpiFERVLEGE--TIAGLETKrRRED-GSliDVSVSAAPIRDADGEIVGTMGALED 685
                                       44444455599999999..5655555543334.444699******************98755 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 2.5
                          dCache_1  58 eslqallksilksnpdisgvylvdadGqviassdpssp 95 
                                       e ++a+l+ +++  pdi +  +vdadG+++ ++++  +
  gi|336252675|ref|YP_004595782.1| 697 ETTTARLEALFDDSPDIIN--VVDADGTIVEANRRFAD 732
                                       5566777777777775555..55999999987766544 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   6.6e-06    0.0053       1      48 [.    1586    1640 ..    1586    1640 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.6e-06
                                        HHHHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4    1 aLasLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48  
                                        +L+ L+er+ evl+  +        ++ T eE++e l +++ +V ++++ A ++L
  gi|336252675|ref|YP_004595782.1| 1586 LLDPLTERQLEVLRTAYfagffewPRESTGEEVAELLEVTQPTVNRHLRLAQQRL 1640
                                        5899*****************9998999********************9998877 PP

>> DUF2111  Uncharacterized protein conserved in archaea (DUF2111)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.3e-05     0.051      29      79 ..     628     682 ..     625     687 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.3e-05
                           DUF2111  29 dedYtgpvLeevleegkv....ikkvpkeGaYkGvpvvvaPikekegkviaaiGv 79 
                                       d+d   p+ e+vle +++    +k++ + G+   v+v  aPi++ +g++++++G 
  gi|336252675|ref|YP_004595782.1| 628 DRDDHQPIFERVLEGETIagleTKRRREDGSLIDVSVSAAPIRDADGEIVGTMGA 682
                                       5566778999999988773333589999*************************96 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   3.3e-05     0.027     127     183 ..    1580    1644 ..    1554    1646 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                       Sigma70_ECF  127 dealerlls.ldpeqarlvelrkleGl.......sveEiAeklgvskrtverrlalaRawlerel 183 
                                         e +  ll+ l ++q++++  ++++G+       + eE+Ae l+v + tv+r+l+la ++l ++l
  gi|336252675|ref|YP_004595782.1| 1580 RELVASLLDpLTERQLEVLRTAYFAGFfewpresTGEEVAELLEVTQPTVNRHLRLAQQRLLSQL 1644
                                        57888999999***************96666665579********************98887665 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 ?   12.8   0.2   0.00011     0.088      18      51 ..    1617    1650 ..    1611    1653 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                        HHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSS CS
                             HTH_1   18 rAAeeLglsqpavsrqikrLEeelgvpLfeRtgr 51  
                                        + Ae L ++qp+v r+++   ++l  +Lfe  +r
  gi|336252675|ref|YP_004595782.1| 1617 EVAELLEVTQPTVNRHLRLAQQRLLSQLFETETR 1650
                                        579***************************9887 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 ?   10.7   0.0   0.00038      0.31      27      52 ..    1613    1638 ..    1580    1640 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                                        --HHHHHHHHT--HHHHHHHHHHHHH CS
                      Sigma70_r4_2   27 lsykEIAellgisegtVksrlsRArk 52  
                                        ++ +E+Aell+++  tV+++l+ A +
  gi|336252675|ref|YP_004595782.1| 1613 STGEEVAELLEVTQPTVNRHLRLAQQ 1638
                                        5789*****************99855 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   0.00047      0.38      20      37 ..    1617    1634 ..    1611    1642 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                                        HHHHHHTS-HHHHHHHHH CS
                             HTH_5   20 elaeelglsqstvShHLk 37  
                                        e ae l+++q+tv +HL+
  gi|336252675|ref|YP_004595782.1| 1617 EVAELLEVTQPTVNRHLR 1634
                                        789**************8 PP

>> DUF4051  Protein of unknown function (DUF4051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.2   0.00063      0.52      31      47 ..    1229    1245 ..    1221    1250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00063
                           DUF4051   31 qdRDAllEarnklyrra 47  
                                        ++RDA lEarn+++rr+
  gi|336252675|ref|YP_004595782.1| 1229 RERDAELEARNRRLRRQ 1245
                                        79**************7 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.3   0.00015      0.12      55      89 ..      81     115 ..      47     135 .. 0.53
   2 ?   -2.0   0.7       4.1   3.4e+03      61     102 ..     994    1026 ..     986    1038 .. 0.34

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                       Trypan_PARP  55 ngtdpepepepepepepepepepepetepeeepep 89 
                                        gtdp  e   +pe  pe epe e e+epe+ep  
  gi|336252675|ref|YP_004595782.1|  81 RGTDPVTEVPVGPELGPEAEPESESESEPESEPAA 115
                                       34444444444444333333333333333333321 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.1
                       Trypan_PARP   61 pepepepepepepepepepetepeeepepepepepepepepe 102 
                                        p+ e   e    p+  p    e e   e         e+e e
  gi|336252675|ref|YP_004595782.1|  994 PDLETTIE-CYHPDDRPLVREELERALE--------TETEYE 1026
                                        22222222.1122222222222222222........222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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):              22  [number of targets reported over threshold]
# CPU time: 1.05u 0.26s 00:00:01.31 Elapsed: 00:00:00.43
# Mc/sec: 11506.37
//
Query:       gi|336252676|ref|YP_004595783.1|  [L=275]
Description: abortive infection protein [Halopiger xanaduensis SH-6]
Scores for complete 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-16   60.2   4.5    1.8e-16   60.2   4.5    2.7  2  CPBP        CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
       0.29   11.4  13.6       0.56   10.4  13.4    1.6  1  EI24        Etoposide-induced protein 2.4 (EI24)
       0.46   10.4   0.1       0.46   10.4   0.1    2.2  2  PDR_CDR     CDR ABC transporter


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 ?   -0.5   2.7      0.28   1.6e+03      43      77 ..      21      84 ..       8     117 .. 0.54
   2 !   60.2   4.5   3.1e-20   1.8e-16       5      91 ..     142     239 ..     136     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.28
                                      HHHHHHHHCSGGG.....HHHH..........................HHHHHHHHHHHHHHHHTT CS
                              CPBP 43 issilFglaHlpn.....gpsv..........................llaalaGlvlgylylktg 77
                                      i   +Fg++ +pn     +  +                          + ++laG ++ +++ ++ 
  gi|336252676|ref|YP_004595783.1| 21 IGLTIFGVLVAPNvttlpA--FlldpalidgpaeasiagrtalltlnfVGMFLAGAIYLVVTDRGW 84
                                      5555666666666554330..133333344444444444444444444777777777766665554 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 3.1e-20
                                       HHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG..........HHH.HHHHHHHHHHHH CS
                              CPBP   5 llvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn..........gps.vllaalaGlvlg 70 
                                       l+++ +++++++ +EE+lfR +++++l   +s+t ai+i+s++F+l+H+            ++  +++++  +l++g
  gi|336252676|ref|YP_004595783.1| 142 LIMIGIVFFFNAPAEEFLFRNIVQKRLYDAFSQTQAIVIASVIFALIHFFSyavsstsllaTMVpIVTVFGGSLIFG 218
                                       6777789999********************999*****************98888777766444569999999**** PP

                                       HHHHHTT-HHHHHHHHHHHHH CS
                              CPBP  71 ylylktgsllaaillHallnl 91 
                                       yly k+ +ll++i++Ha +n 
  gi|336252676|ref|YP_004595783.1| 219 YLYAKSENLLVPIAAHATFNG 239
                                       *******************96 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  13.4   9.4e-05      0.56      18     128 ..      64     223 ..      14     233 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.4e-05
                                       HHHHHHHHHHHHHHHHHHHHH.....................-............TTHHHHHHHHHHHHH....... CS
                              EI24  18 llllplllnlllfllllvlll.....................w............vllasllvllllllp....... 54 
                                       l ++ ++l+++         +                     w            +       ++l   +       
  gi|336252676|ref|YP_004595783.1|  64 LNFVGMFLAGA---------IylvvtdrgwsyvdlhvpskrgWgyvgigiasmiaF-------YIL---Vnvvvtvl 121
                                       22222222222.........133457888566666666666658777755532221.......222...12224446 PP

                                       ...................HHHHHHHHHHHHHHHHHHHHHHHHH.HH....CCTTSHH....HHHHHHHHHHHHHHH CS
                              EI24  55 ...................lwlfplvalllaapfygllaekvekrhl....glvksla....eslkslllllllllv 104
                                                          ++++ +++++++ap  + l++ + +++l    +  ++ a    + ++ l+ ++ +++ 
  gi|336252676|ref|YP_004595783.1| 122 slpsaenevmrfiendqtmVLIMIGIVFFFNAPAEEFLFRNIVQKRLydafS--QTQAiviaSVIFALIHFFSYAVS 196
                                       77899*************999999***************9998877666442..22224465778888888888887 PP

                                       HHHH...HHTTHHH....HHHHHHHHH CS
                              EI24 105 llpl...liPvvglilsplllswltay 128
                                       ++ l   ++P+v ++   l++++l+a+
  gi|336252676|ref|YP_004595783.1| 197 STSLlatMVPIVTVFGGSLIFGYLYAK 223
                                       777766666999999888888888876 PP

>> PDR_CDR  CDR ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   7.8e-05      0.46      39      86 ..      89     136 ..      69     142 .. 0.83
   2 ?   -3.3   0.1       1.5   9.1e+03      52      60 ..     183     191 ..     173     201 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.8e-05
                           PDR_CDR  39 fgyssshlwrnfgiliaflifflalyllatelisaekskgevlvfkrg 86 
                                       ++  s+  w  +gi ia +i f +l  ++++++s  + + ev+ f  +
  gi|336252676|ref|YP_004595783.1|  89 LHVPSKRGWGYVGIGIASMIAFYILVNVVVTVLSLPSAENEVMRFIEN 136
                                       55566778999**************************99999988665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.5
                           PDR_CDR  52 iliafliff 60 
                                       +++a + ff
  gi|336252676|ref|YP_004595783.1| 183 VIFALIHFF 191
                                       233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2120.01
//
Query:       gi|336252677|ref|YP_004595784.1|  [L=172]
Description: Resolvase, Holliday junction-type [Halopiger xanaduensis SH-6]
Scores for 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-30  105.6   0.0    1.4e-30  105.1   0.0    1.2  1  Hjc       Archaeal holliday junction resolvase (hjc)
  ------ inclusion threshold ------
       0.15   12.2   0.0       0.31   11.1   0.0    1.5  1  NHL       NHL repeat


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 !  105.1   0.0   1.5e-34   1.4e-30       2      91 ..       9      99 ..       8     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 1.5e-34
                                      HHHHHHHHHHHTT-EEEEBSCSSSSSS.SS-SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHHTCEEEEEE CS
                               Hjc  2 yERelvkiLrergfavvRsagSggatk.plpDviAirgdvvlviEvKsskkeriylkkeqvekllefarkaggelllav 79
                                       ERelv+ L+e gfav+R+++Sg+at+ +lpDv+A+ g+ +++iE Kss++++iyl  e+ve l+ fa+++g+++ ++v
  gi|336252677|ref|YP_004595784.1|  9 RERELVNELDEAGFAVMRAPASGSATErELPDVLAGDGEQFYAIEAKSSSGDPIYLTGEEVEALIYFAQNFGAKPRIGV 87
                                      7************************999*************************************************** PP

                                      EETTTEEEEEEG CS
                               Hjc 80 klqgkewkllvv 91
                                      ++++++w+++++
  gi|336252677|ref|YP_004595784.1| 88 RFDREDWYFFHP 99
                                      **********97 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.5e-05      0.31      13      27 ..     100     114 ..     100     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.5e-05
                                       TEEEEEECCCTEEEE CS
                               NHL  13 GdiyVaDsenhrvqv 27 
                                       Gd+yV+D +n rv++
  gi|336252677|ref|YP_004595784.1| 100 GDLYVTDGGNYRVKK 114
                                       89***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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: 0.38u 0.19s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1517.79
//
Query:       gi|336252678|ref|YP_004595785.1|  [L=158]
Description: hypothetical protein Halxa_1273 [Halopiger xanaduensis SH-6]
Scores for 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  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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 0.19s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1392.41
//
Query:       gi|336252679|ref|YP_004595786.1|  [L=210]
Description: zinc finger SWIM domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00021   20.9   0.7    0.00034   20.2   0.0    1.7  2  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.9e-08   0.00034       1      37 [.      51      80 ..      36      82 .. 0.86
   2 ?   -3.3   0.1      0.42   7.6e+03      13      17 ..     112     116 ..     107     117 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.9e-08
                              SWIM  1 yrVtlddervrlnkatCsCpefqkngipCkHalAvll 37
                                      y+V+l+         +C+Cp+  + g  CkH+  v++
  gi|336252679|ref|YP_004595786.1| 51 YLVDLG-------AGRCTCPDHVFRGARCKHVRRVAI 80
                                      555666.......99*****************99986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.42
                              SWIM  13 nkatC 17 
                                       ++++C
  gi|336252679|ref|YP_004595786.1| 112 EPCYC 116
                                       57777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1509.33
//
Query:       gi|336252680|ref|YP_004595787.1|  [L=77]
Description: hypothetical protein Halxa_1275 [Halopiger xanaduensis SH-6]
Scores for 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   23.4   0.3    4.2e-05   23.2   0.3    1.0  1  DUF3341   Protein of unknown function (DUF3341)


Domain annotation for each model (and alignments):
>> DUF3341  Protein of unknown function (DUF3341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.3   2.4e-09   4.2e-05      33      95 ..       3      68 ..       1      70 [. 0.74

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.4e-09
                                      SS--TT-TTTSS--SS-STHHHHHHHHHHHHH.HHHHH...HIIIIISS---STT--SS-HHHHHHH CS
                           DUF3341 33 PfpvhgldealglkksrlpliallgGllGlal.alllq...vytsvvdyplnigGkPlfslpafipi 95
                                      P+ +++l  a++ +++rl+++++ g++lG++l ++ l    + + ++d+pl +gG P +  +  ++i
  gi|336252680|ref|YP_004595787.1|  3 PLALEQLI-AMNANETRLRYAIFHGAILGASLlGIGLLlpiLGIRTIDWPLLVGGPPAVGAIHACLI 68
                                      55555554.699999**************9742333322237888************9987766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 569.73
//
Query:       gi|336252681|ref|YP_004595788.1|  [L=202]
Description: hypothetical protein Halxa_1276 [Halopiger xanaduensis SH-6]
Scores for 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:                       342  (0.0190752); 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:                         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 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1547.84
//
Query:       gi|336252682|ref|YP_004595789.1|  [L=368]
Description: Pyrrolo-quinoline quinone repeat-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-41  142.7  13.8    3.3e-21   76.0   3.7    3.1  2  PQQ_2        PQQ-like domain
    1.7e-41  139.7  36.0    2.4e-08   34.2   0.1    8.2  8  PQQ_3        PQQ-like domain
    6.3e-22   76.4  14.1    5.3e-07   29.3   0.0    8.1  9  PQQ          PQQ enzyme repeat
  ------ inclusion threshold ------
      0.015   15.6   0.0       0.61   10.4   0.0    3.2  3  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   5.6   2.4e-23   1.1e-19      15     150 ..      28     154 ..      27     160 .. 0.89
   2 !   76.0   3.7   7.4e-25   3.3e-21       7     226 ..     140     359 ..     139     359 .. 0.86

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 2.4e-23
                             PQQ_2  15 elWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqlial 91 
                                       e W+vdla     g+  +vl+  t++++t++g+l ald++tG+ +W ++ ++ + +ap  +++rv ++++dg ++a+
  gi|336252682|ref|YP_004595789.1|  28 EAWSVDLA--APVGP--PVLDHETVYAGTERGTLFALDRETGRRRWAVETQAATDEAPVATRDRVAFATADGIVRAV 100
                                       78***994..44788..99********************************************************** PP

                             PQQ_2  92 daedGkrlWstqqrseepaelrssaspava..gdtvvvgessgklvaldpkdGkvlWerel 150
                                       d ++G+ +W+t+++++ep+        a++  gd+++vg+   + +al +++G+ +W +e 
  gi|336252682|ref|YP_004595789.1| 101 DRATGDPAWRTELQGTEPTA------LALSeaGDRLYVGH-TAGSTALAVDSGEAVWTHET 154
                                       **********9999976666......3333449*******.7777999999******9986 PP

  == domain 2  score: 76.0 bits;  conditional E-value: 7.4e-25
                             PQQ_2   7 aldaatGaelWrvdlar......plgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaeg 77 
                                       al+ ++G+ +W+ + ++      ++   +  a  +g +++vat g  +++l+a++G++ W+t ++gp+v+ p+va +
  gi|336252682|ref|YP_004595789.1| 140 ALAVDSGEAVWTHETETrvvgcpAIADDR--AW-AGPRVYVATAGEAVICLEAESGEENWTTPADGPAVAGPTVAAD 213
                                       667779*******8755344332255555..55.89***************************************** PP

                             PQQ_2  78 rvvvvasdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerel.aap 153
                                        v+v+++ g+l+a++a++G+  +s ++  +   +l+ss++   + +t +vg ++g l++ d + G++     l ++ 
  gi|336252682|ref|YP_004595789.1| 214 LVYVADESGTLLAMNADSGQPWFS-YEIDG---PLASSPTVLPDAETTFVGAADGYLHVTDTTFGRRKLRGWLfSK- 285
                                       ********************9999.66663...3444666666699*********************999999655. PP

                             PQQ_2 154 rgtselsrvgdisgrpvvaegtVyassgqgrllaldlatgrrl.wske.issinglpildgdllyvvsa..gelial 226
                                        +++ l+  g +s++pvv+++ ++++   g+l  ld+a g    w ++  ++i + p++  + lyv+++  g+l++l
  gi|336252682|ref|YP_004595789.1| 286 -KGVPLD--GPVSASPVVVGNVLCVADETGSLYGLDVADGCSHlWHRAlDGAISHAPAVGRERLYVGDDddGTLTCL 359
                                       .456676..9*********99*******************9777*99978999999************559*99986 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.1   5.4e-12   2.4e-08       2      40 .]      27      64 ..      27      64 .. 0.96
   2 !   16.5   0.5     2e-06     0.009       1      40 []      65     104 ..      65     104 .. 0.86
   3 !   11.2   0.2     9e-05       0.4       1      37 [.     105     144 ..     105     145 .. 0.79
   4 !   20.7   0.2   9.5e-08   0.00042       1      40 []     146     191 ..     146     191 .. 0.82
   5 !   29.7   0.5   1.4e-10   6.3e-07       1      40 []     192     231 ..     192     231 .. 0.96
   6 !    7.9   0.3   0.00097       4.4       6      37 ..     237     270 ..     236     272 .. 0.85
   7 !   22.9   0.2     2e-08   8.8e-05       7      40 .]     288     321 ..     281     321 .. 0.93
   8 !   19.4   0.2   2.4e-07    0.0011       4      36 ..     326     359 ..     325     361 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 5.4e-12
                             PQQ_3  2 evlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40
                                      e+ Wsv+l +pv ++p++d  +vy+gt+ Gtl+AlD et
  gi|336252682|ref|YP_004595789.1| 27 EEAWSVDLAAPV-GPPVLDHETVYAGTERGTLFALDRET 64
                                      689*********.9***********************98 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2e-06
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       G+++W+v++ +++  +p++  ++v ++t dG ++A+D +t
  gi|336252682|ref|YP_004595789.1|  65 GRRRWAVETQAATDEAPVATRDRVAFATADGIVRAVDRAT 104
                                       899*******99998887776677777889*******998 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 9e-05
                             PQQ_3   1 GevlWsvqlpgpvnsspavd..gglvyvgtg.dGtlyAlD 37 
                                       G++ W+++l g   +++a++  g+++yvg +   t  A+D
  gi|336252682|ref|YP_004595789.1| 105 GDPAWRTELQGTEPTALALSeaGDRLYVGHTaGSTALAVD 144
                                       899******99666788886559******99666666655 PP

  == domain 4  score: 20.7 bits;  conditional E-value: 9.5e-08
                             PQQ_3   1 GevlWsvqlpgpvnssp......avdgglvyvgtgdGtlyAlDaet 40 
                                       Ge +W++++  +v++ p      a +g +vyv+t    + +l+ae+
  gi|336252682|ref|YP_004595789.1| 146 GEAVWTHETETRVVGCPaiaddrAWAGPRVYVATAGEAVICLEAES 191
                                       7889***********9*444444444557***************96 PP

  == domain 5  score: 29.7 bits;  conditional E-value: 1.4e-10
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       Ge+ W+++ +gp++++p+v+ +lvyv+++ Gtl A +a++
  gi|336252682|ref|YP_004595789.1| 192 GEENWTTPADGPAVAGPTVAADLVYVADESGTLLAMNADS 231
                                       8999*******************************99975 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.00097
                             PQQ_3   6 svqlpgpvnsspav..dgglvyvgtgdGtlyAlD 37 
                                       s++++gp+ ssp+v  d  + +vg+ dG l+  D
  gi|336252682|ref|YP_004595789.1| 237 SYEIDGPLASSPTVlpDAETTFVGAADGYLHVTD 270
                                       6899********7756778**********98755 PP

  == domain 7  score: 22.9 bits;  conditional E-value: 2e-08
                             PQQ_3   7 vqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       v+l+gpv +sp+v+g+++ v+++ G+ly lD ++
  gi|336252682|ref|YP_004595789.1| 288 VPLDGPVSASPVVVGNVLCVADETGSLYGLDVAD 321
                                       4899***************************875 PP

  == domain 8  score: 19.4 bits;  conditional E-value: 2.4e-07
                             PQQ_3   4 lWsvqlpgpvnsspavdgglvyvgtg.dGtlyAl 36 
                                       lW + l+g++  +pav+  ++yvg++ dGtl++l
  gi|336252682|ref|YP_004595789.1| 326 LWHRALDGAISHAPAVGRERLYVGDDdDGTLTCL 359
                                       7********************************9 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         2   8.8e+03      21      32 ..      27      38 ..      27      41 .. 0.79
   2 !   29.3   0.0   1.2e-10   5.3e-07       2      37 ..      47      82 ..      47      83 .. 0.92
   3 !   16.5   0.0   1.3e-06    0.0056       3      30 ..      88     115 ..      86     117 .. 0.89
   4 !    6.0   0.0    0.0028        13       2      34 ..     129     160 ..     128     163 .. 0.85
   5 !   11.6   0.0   4.8e-05      0.21       2      36 ..     174     208 ..     173     210 .. 0.93
   6 !   10.6   0.0   9.9e-05      0.44       2      36 ..     214     248 ..     213     250 .. 0.87
   7 ?   -1.2   0.1      0.53   2.4e+03       4      16 ..     258     270 ..     257     276 .. 0.80
   8 ?    3.9   0.2     0.012        55       2      20 ..     303     322 ..     302     323 .. 0.83
   9 ?   -0.4   0.0      0.28   1.3e+03       3      14 ..     346     358 ..     345     359 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2
                                      CEEEEEESSSCG CS
                               PQQ 21 kvlWrfktggpv 32
                                      ++ W++++ +pv
  gi|336252682|ref|YP_004595789.1| 27 EEAWSVDLAAPV 38
                                      678999998876 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 1.2e-10
                                      EEEEEETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ  2 vvylgsadGylyAlDadTGkvlWrfktggpvlslpi 37
                                      +vy+g+  G+l+AlD++TG+ +W ++t+++ +  p+
  gi|336252682|ref|YP_004595789.1| 47 TVYAGTERGTLFALDRETGRRRWAVETQAATDEAPV 82
                                      69**************************99887765 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.3e-06
                                       EEEEETTSEEEEEETTTCCEEEEEESSS CS
                               PQQ   3 vylgsadGylyAlDadTGkvlWrfktgg 30 
                                       v  ++adG ++A+D++TG+  Wr++++g
  gi|336252682|ref|YP_004595789.1|  88 VAFATADGIVRAVDRATGDPAWRTELQG 115
                                       667899******************9987 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0028
                                       EEEEE.ETTSEEEEEETTTCCEEEEEESSSCGSS CS
                               PQQ   2 vvylg.sadGylyAlDadTGkvlWrfktggpvls 34 
                                       ++y+g +a+ + +A+D  +G+ +W+++t+  v++
  gi|336252682|ref|YP_004595789.1| 129 RLYVGhTAGSTALAVD--SGEAVWTHETETRVVG 160
                                       6788888888889999..**********999876 PP

  == domain 5  score: 11.6 bits;  conditional E-value: 4.8e-05
                                       EEEEEETTSEEEEEETTTCCEEEEEESSSCGSSES CS
                               PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggpvlslp 36 
                                       +vy+++a+  +  l a++G++ W+++++gp ++ p
  gi|336252682|ref|YP_004595789.1| 174 RVYVATAGEAVICLEAESGEENWTTPADGPAVAGP 208
                                       69****************************99877 PP

  == domain 6  score: 10.6 bits;  conditional E-value: 9.9e-05
                                       EEEEEETTSEEEEEETTTCCEEEEEESSSCGSSES CS
                               PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggpvlslp 36 
                                        vy+++  G+l+A +ad+G+   +++++gp  s+p
  gi|336252682|ref|YP_004595789.1| 214 LVYVADESGTLLAMNADSGQPWFSYEIDGPLASSP 248
                                       79*****************9988888888887776 PP

  == domain 7  score: -1.2 bits;  conditional E-value: 0.53
                                       EEEETTSEEEEEE CS
                               PQQ   4 ylgsadGylyAlD 16 
                                       ++g adGyl   D
  gi|336252682|ref|YP_004595789.1| 258 FVGAADGYLHVTD 270
                                       78899***98655 PP

  == domain 8  score: 3.9 bits;  conditional E-value: 0.012
                                       EEEEE.ETTSEEEEEETTTC CS
                               PQQ   2 vvylg.sadGylyAlDadTG 20 
                                       +v +  +  G ly lD+++G
  gi|336252682|ref|YP_004595789.1| 303 NVLCVaDETGSLYGLDVADG 322
                                       566666889*********99 PP

  == domain 9  score: -0.4 bits;  conditional E-value: 0.28
                                       EEEE.ETTSEEEE CS
                               PQQ   3 vylg.sadGylyA 14 
                                       +y+g ++dG+l  
  gi|336252682|ref|YP_004595789.1| 346 LYVGdDDDGTLTC 358
                                       79*******9976 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00014      0.61       6      79 ..      84     155 ..      82     167 .. 0.85
   2 ?   -3.5   0.0         3   1.4e+04      55      71 ..     217     233 ..     213     241 .. 0.57
   3 ?    0.9   0.0      0.12   5.5e+02      50      70 ..     302     322 ..     300     364 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                       ANAPC4_WD40   6 tmDLiAlatedgell.vfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvk 79 
                                       t+D +A+at+dg ++ v R  g   w +  + ++ e ++La ++ g  L v++  g+  l  + sg+ v + +++
  gi|336252682|ref|YP_004595789.1|  84 TRDRVAFATADGIVRaVDRATGDPAWRT--ELQGTEPTALALSEAGDRLYVGHTAGSTAL-AVDSGEAVWTHETE 155
                                       68999*********6378**********..89999*********************9876.46777776665554 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3
                       ANAPC4_WD40  55 vaysdgevrlldaesgk 71 
                                       va + g++  ++a sg+
  gi|336252682|ref|YP_004595789.1| 217 VADESGTLLAMNADSGQ 233
                                       55555555555555555 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.12
                       ANAPC4_WD40  50 gklLavaysdgevrlldaesg 70 
                                       g++L+va + g++  ld+ +g
  gi|336252682|ref|YP_004595789.1| 302 GNVLCVADETGSLYGLDVADG 322
                                       677777777777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2417.75
//
Query:       gi|336252683|ref|YP_004595790.1|  [L=343]
Description: DNA repair and recombination protein radA [Halopiger xanaduensis SH-6]
Scores for 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-75  251.2   0.1      8e-74  248.1   0.1    1.9  1  Rad51            Rad51
    2.4e-11   44.1   0.0    8.2e-11   42.3   0.0    2.0  2  HHH_5            Helix-hairpin-helix domain
    3.2e-08   33.4   0.0     0.0069   15.9   0.0    2.2  2  RecA             recA bacterial DNA recombination protein
    3.3e-07   29.8   1.9     0.0027   17.5   0.2    2.9  3  HHH              Helix-hairpin-helix motif
      1e-06   28.7   0.1      4e-06   26.8   0.0    2.1  1  HHH_2            Helix-hairpin-helix motif
      3e-06   26.9   0.1    6.3e-06   25.9   0.1    1.5  1  AAA_25           AAA domain
    3.4e-05   24.0   0.0     0.0001   22.4   0.0    1.8  1  Cdd1             Pathogenicity locus
    0.00029   20.3   0.3     0.0014   18.0   0.1    2.0  2  ATPase           KaiC
     0.0004   20.1   0.0     0.0024   17.7   0.0    2.3  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0055   16.9   0.0        2.6    8.4   0.0    2.9  3  HHH_3            Helix-hairpin-helix motif
     0.0071   16.6   0.0      0.019   15.2   0.0    1.7  1  DUF4332          Domain of unknown function (DUF4332)
  ------ inclusion threshold ------
      0.017   15.4   0.4      0.072   13.4   0.4    2.0  1  AAA_22           AAA domain
      0.031   14.6   0.0       0.15   12.4   0.0    2.2  2  IMS_HHH          IMS family HHH motif
      0.067   13.6   0.0       0.19   12.2   0.0    1.8  1  BAF              Barrier to autointegration factor
       0.11   12.3   0.6       0.34   10.7   0.4    1.9  2  DUF2520          Domain of unknown function (DUF2520)
       0.11   12.5   0.0       0.16   11.9   0.0    1.3  1  ATPase_2         ATPase domain predominantly from Archaea


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 !  248.1   0.1   7.1e-77     8e-74       2     252 ..      65     340 ..      64     342 .. 0.93

  Alignments for each domain:
  == domain 1  score: 248.1 bits;  conditional E-value: 7.1e-77
                                       S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEE CS
                             Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyid 78 
                                       gf +++ +le+r+++ +l+    ++D+lLgGGiet+site++Gef+sGk+q++h+++v vqlp+e+gG  g a++id
  gi|336252683|ref|YP_004595790.1|  65 GFETGSTVLERRNKIGKLSWHIDEVDDLLGGGIETQSITEVYGEFGSGKSQVTHQMAVNVQLPKEVGGLHGSAMFID 141
                                       8999************************************************************************* PP

                                       SSS---GGGGHHHH........................HHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS CS
                             Rad51  79 tegtfrperlveia........................erykldkeevlenvayaRaytiehqeellqqaaallaed 131
                                       +e tfrper+ ++                         e  +   +++le++ +a+a++++hq+ l ++a +l +e+
  gi|336252683|ref|YP_004595790.1| 142 SEDTFRPERIDDMVrglpddvieatledreiegsadneEALDELVDAILEKIHVAKAFNSNHQMLLAEKAQELASEH 218
                                       ************9999***********999988887544445556899****************9988777666554 PP

                                       -.....EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.---------- CS
                             Rad51 132 k.....fallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkk 203
                                       +     ++ll vDs+ta++R+++ grgela+Rqqkl+k+l+ L k+ + ++ av++tnqv +++d     f +dp++
  gi|336252683|ref|YP_004595790.1| 219 EdseypIRLLAVDSLTAHFRAEYVGRGELADRQQKLNKHLHDLDKVGNLYNTAVIVTNQVASNPDS----FFGDPTQ 291
                                       33333389*********************************************************9....99***** PP

                                       --HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EEEEEEETTEE CS
                             Rad51 204 PigGlvlahasttRlalrkgkgeeRivkvvdsPnlpeleavfaigeeGi 252
                                       PigG++l+h+st R++lrk kg++Riv++vd+Pnl++ eav+ +++ G+
  gi|336252683|ref|YP_004595790.1| 292 PIGGNILGHKSTFRIYLRKSKGDKRIVRLVDAPNLADGEAVMRVEDGGL 340
                                       ********************************************99997 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   7.3e-14   8.2e-11       3      57 .]       5      59 ..       3      59 .. 0.97
   2 ?   -2.8   0.0       9.4     1e+04      21      34 ..      84      97 ..      82     107 .. 0.61

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 7.3e-14
                                      HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                             HHH_5  3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                      +L +++G+Gp+tA +l +aG++s++ la a++ eL+   ++G+ tA  i+ +++d
  gi|336252683|ref|YP_004595790.1|  5 DLETLPGVGPATAEKLQDAGFDSFQSLAVASPSELSNTADVGESTAADIVNAARD 59
                                      899**************************************************98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.4
                                      TT--SHHHHHHS-H CS
                             HHH_5 21 aGiesvedlaaadv 34
                                        i+ v+dl+   +
  gi|336252683|ref|YP_004595790.1| 84 WHIDEVDDLLGGGI 97
                                      55788888876633 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   6.2e-06    0.0069      40      96 ..      88     149 ..      72     164 .. 0.78
   2 !   15.3   0.0     9e-06      0.01     116     223 ..     208     312 ..     162     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.2e-06
                                       HHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH..HT.T...--EEEEESS----HH CS
                              RecA  40 aldialGiGGlpkGriieiyGpessGkttlalhaiaeaq..kk.g...gvaafidaehaldpk 96 
                                        +d  lG GG+    i+e+yG   sGk+ ++ ++ +++q  k+ g   g a fid+e ++ p+
  gi|336252683|ref|YP_004595790.1|  88 EVDDLLG-GGIETQSITEVYGEFGSGKSQVTHQMAVNVQlpKEvGglhGSAMFIDSEDTFRPE 149
                                       5677788.9**********************999988884433232226799*****998876 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 9e-06
                                       HHHHHHHHHHHHTTT.--SEEEEE-TTT---STT-..----------HHHHHHHHHHHHHHHHHTTT--EEEEEEE- CS
                              RecA 116 Geqaleiadalvrsg.aidlivvdsvaalvpkaei..eGemgdskvglqarlmsqalrkltgaisksntvvifinqi 189
                                        e+a e+a    +s   i l+ vds++a   +ae    Ge++d +  l      + l  l  + +  nt+vi  nq+
  gi|336252683|ref|YP_004595790.1| 208 AEKAQELASEHEDSEyPIRLLAVDSLTAHF-RAEYvgRGELADRQQKL-----NKHLHDLDKVGNLYNTAVIVTNQV 278
                                       577777777776665368999999999976.44441357777776555.....566677777777889********* PP

                                       ----------------HHHHHHH-SEEEEEEEES CS
                              RecA 190 rekiGvmfgnpetttGGralkfyasvrldvrrie 223
                                              fg+p    GG+ l   ++ r+ +r+++
  gi|336252683|ref|YP_004595790.1| 279 ASNPDSFFGDPTQPIGGNILGHKSTFRIYLRKSK 312
                                       *******************************986 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   2.4e-06    0.0027      12      26 ..       5      19 ..       4      20 .. 0.92
   2 !   10.8   0.0   0.00032      0.35       1      28 [.      27      54 ..      27      56 .. 0.93
   3 ?   -2.8   0.1       6.4   7.2e+03       4      12 ..     161     169 ..     160     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-06
                                      HHHTSTT-SHHHHHH CS
                               HHH 12 eLlalPGVGpktAea 26
                                      +L++lPGVGp+tAe+
  gi|336252683|ref|YP_004595790.1|  5 DLETLPGVGPATAEK 19
                                      8************97 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00032
                                      SHHHHHTSSHHHHHTSTT-SHHHHHHHH CS
                               HHH  1 sleglipasreeLlalPGVGpktAeaIl 28
                                      s+++l  as+ eL     VG++tA  I 
  gi|336252683|ref|YP_004595790.1| 27 SFQSLAVASPSELSNTADVGESTAADIV 54
                                      7999*********************997 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.4
                                       HHHTSSHHH CS
                               HHH   4 glipasree 12 
                                        +i+a++e+
  gi|336252683|ref|YP_004595790.1| 161 DVIEATLED 169
                                       6899**997 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   3.6e-09     4e-06       9      54 ..      10      56 ..       8      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.6e-09
                             HHH_2  9 rhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsivef 54
                                      + VG +tA++L  + F+s++ L+ as  eL++  d+Ge +A++iv+ 
  gi|336252683|ref|YP_004595790.1| 10 PGVGPATAEKLQDAgFDSFQSLAVASPSELSNTADVGESTAADIVNA 56
                                      89*********9765*****************************986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   5.6e-09   6.3e-06      11     188 ..      78     277 ..      70     282 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5.6e-09
                            AAA_25  11 svadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelr 87 
                                       ++++l + + ++++l++g +  ++++ ++G  g+GK+ ++ ++a+ v + k++ g     +g  ++++ Ed+    +
  gi|336252683|ref|YP_004595790.1|  78 KIGKLSWHIDEVDDLLGGGIETQSITEVYGEFGSGKSQVTHQMAVNVQLPKEVGG----LHGSAMFIDSEDTF--RP 148
                                       6778889999**************************************9887766....79***********8..79 PP

                            AAA_25  88 rRlravgeal................rddarllvldlagv..eslpLfak.drggtl.ltadvdaleaaieeveg.v 143
                                       +R+  + + l                ++d ++++  l++   e+++++++  ++++  l+++ ++l+ + e+ e  +
  gi|336252683|ref|YP_004595790.1| 149 ERIDDMVRGLpddvieatledreiegSADNEEALDELVDAilEKIHVAKAfNSNHQMlLAEKAQELASEHEDSEYpI 225
                                       **********7777888888888876333333333333333677888766323333358999999998888865489 PP

                            AAA_25 144 rlvviDplsralgg.....densnsdv..galvealeriarrtgaavllvhH 188
                                       rl+ +D+l++ +++     +e ++++   ++ + +l+++   ++ av+++ +
  gi|336252683|ref|YP_004595790.1| 226 RLLAVDSLTAHFRAeyvgrGELADRQQklNKHLHDLDKVGNLYNTAVIVTNQ 277
                                       9999999999877755555555555533377777777777777777776655 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   9.2e-08    0.0001       7      44 ..       5      42 ..       3      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.2e-08
                              Cdd1  7 elqdiPniGkalaedlvelGirsveelkgedpeelyek 44
                                      +l+++P++G+a+ae+l++ G+ s++ l+  +p el + 
  gi|336252683|ref|YP_004595790.1|  5 DLETLPGVGPATAEKLQDAGFDSFQSLAVASPSELSNT 42
                                      79********************************9876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.2e-06    0.0014       5      42 ..      86     123 ..      82     133 .. 0.91
   2 ?   -0.3   0.0      0.51   5.7e+02     117     144 ..     222     247 ..     177     322 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                            ATPase   5 IeglDeilkgGipegrvvlitGepGtGKtifalqFlik 42 
                                       I + D++l gGi  ++++ ++Ge G+GK+ +  q +++
  gi|336252683|ref|YP_004595790.1|  86 IDEVDDLLGGGIETQSITEVYGEFGSGKSQVTHQMAVN 123
                                       8899*************************999998876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.51
                            ATPase 117 eikakrvviDsitglayeekeavaReil 144
                                       e+ ++ + +Ds+t++     e v R +l
  gi|336252683|ref|YP_004595790.1| 222 EYPIRLLAVDSLTAH--FRAEYVGRGEL 247
                                       555667777777766..22222222222 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 !   17.7   0.0   2.1e-06    0.0024       8      42 ..      11      46 ..       6      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                   DNA_pol_lambd_f  8 GVGpktAkkwyakGirtledlra.krakLtreqqiG 42
                                      GVGp+tA+k+ ++G+ +++ l    +++L++  ++G
  gi|336252683|ref|YP_004595790.1| 11 GVGPATAEKLQDAGFDSFQSLAVaSPSELSNTADVG 46
                                      9*******************9887668888877776 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0023       2.6      14      32 ..       4      22 ..       3      32 .. 0.88
   2 ?    5.5   0.0     0.019        21      11      33 ..      34      56 ..      30      70 .. 0.86
   3 ?   -2.9   0.0       7.7   8.6e+03      18      42 ..     154     178 ..     153     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0023
                             HHH_3 14 eeLqklpGlgpklAknIva 32
                                      ++L++lpG+gp++A+++++
  gi|336252683|ref|YP_004595790.1|  4 ADLETLPGVGPATAEKLQD 22
                                      589************9986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.019
                             HHH_3 11 AsaeeLqklpGlgpklAknIvay 33
                                      As +eL+  + +g+++A  Iv++
  gi|336252683|ref|YP_004595790.1| 34 ASPSELSNTADVGESTAADIVNA 56
                                      9*******************964 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 7.7
                             HHH_3  18 klpGlgpklAknIvayReknGpfks 42 
                                       ++ Gl + ++++ ++ Re  G   +
  gi|336252683|ref|YP_004595790.1| 154 MVRGLPDDVIEATLEDREIEGSADN 178
                                       5789999999999999988876555 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.7e-05     0.019      53      90 ..       4      41 ..       3      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-05
                           DUF4332 53 AdLarikgigeeyaeLLeaaGvdsvaeLaqrnpanLhq 90
                                      AdL   +g+g++ ae L  aG ds ++La  +p++L +
  gi|336252683|ref|YP_004595790.1|  4 ADLETLPGVGPATAEKLQDAGFDSFQSLAVASPSELSN 41
                                      89999*****************************9975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   6.4e-05     0.072       4      98 ..      99     231 ..      97     276 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.4e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.....................................erpevv 43 
                                       t++i+ v+Ge G+GK+ +  +++ + +  +   e                                      +++ +
  gi|336252683|ref|YP_004595790.1|  99 TQSITEVYGEFGSGKSQVTHQMAVNVQLPK---EvgglhgsamfidsedtfrperiddmvrglpddvieatLEDREI 172
                                       899*****************9999875444...45568888888876666555555555555333333333222222 PP

                            AAA_22  44 fvtlpsstsskdllrellralglelkaerlsseellealeqalrarav.....ielliiD 98 
                                       +  + +++ +++l  ++l+++++ +   + + + ll+  +q l + +      i+ll +D
  gi|336252683|ref|YP_004595790.1| 173 EGSADNEEALDELVDAILEKIHVAKAF-NSNHQMLLAEKAQELASEHEdseypIRLLAVD 231
                                       333333335555555555555555555.33333333444444444444355555555555 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.15      13      31 ..       6      24 ..       5      25 .. 0.88
   2 ?   -2.5   0.0       7.7   8.6e+03       9      18 ..      98     107 ..      88     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                           IMS_HHH 13 itkipGiGgklgekLeklG 31
                                      +  +pG+G+ ++ekL++ G
  gi|336252683|ref|YP_004595790.1|  6 LETLPGVGPATAEKLQDAG 24
                                      6779************988 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.7
                           IMS_HHH   9 wplpitkipG 18 
                                       +  +it+++G
  gi|336252683|ref|YP_004595790.1|  98 ETQSITEVYG 107
                                       5678999988 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00017      0.19      15      41 ..       1      27 [.       1      32 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                               BAF 15 mgdKevtalaGigevlgkkLeekGfdk 41
                                      m d + ++l+G+g+  ++kL+++Gfd 
  gi|336252683|ref|YP_004595790.1|  1 MPDADLETLPGVGPATAEKLQDAGFDS 27
                                      5677889******************96 PP

>> DUF2520  Domain of unknown function (DUF2520)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.36   4.1e+02      63      85 ..     171     194 ..     163     197 .. 0.69
   2 ?   10.7   0.4    0.0003      0.34      36      64 ..     192     220 ..     184     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.36
                                       T-S.-..HHHHHHHHHHHHHHHHH CS
                           DUF2520  63 gld.ekdaakallpLleatlenal 85 
                                       +++ ++d ++al +L++a le+++
  gi|336252683|ref|YP_004595790.1| 171 EIEgSADNEEALDELVDAILEKIH 194
                                       445456778888888888888876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0003
                                       HHHHHHHHHHCCHHHHHHHHHHHHHCTT- CS
                           DUF2520  36 lyHaAavlasNflvtlvalaaellreagl 64 
                                       + H+A ++ sN+ + l+++a+el +e++ 
  gi|336252683|ref|YP_004595790.1| 192 KIHVAKAFNSNHQMLLAEKAQELASEHED 220
                                       68*********************999854 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 ?   11.9   0.0   0.00014      0.16      18      82 ..      98     176 ..      84     233 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdk......yviyyialreesiskldefie........eeeekkklek 80 
                                       e+++i  +YG  gsGK+++  +++ n +  ++        +++++  + + +++d++++         + e++++e 
  gi|336252683|ref|YP_004595790.1|  98 ETQSITEVYGEFGSGKSQVTHQMAVNVQLPKEvgglhgSAMFIDSEDTFRPERIDDMVRglpddvieATLEDREIEG 174
                                       689999****************9999855544577777888888888888888888866666666652333333333 PP

                          ATPase_2  81 al 82 
                                        +
  gi|336252683|ref|YP_004595790.1| 175 SA 176
                                       32 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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 0.25s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 2558.88
//
Query:       gi|336252684|ref|YP_004595791.1|  [L=265]
Description: hypothetical protein Halxa_1279 [Halopiger xanaduensis SH-6]
Scores for 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  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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 0.21s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2100.03
//
Query:       gi|336252685|ref|YP_004595792.1|  [L=143]
Description: SUF system FeS assembly protein [Halopiger xanaduensis SH-6]
Scores for 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   89.0   0.1    3.3e-25   88.7   0.1    1.1  1  NifU_N    NifU-like N terminal domain
  ------ inclusion threshold ------
      0.039   13.8   0.0      0.055   13.3   0.0    1.2  1  SufE      Fe-S metabolism associated domain


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 !   88.7   0.1   3.7e-29   3.3e-25       1     119 [.       7     127 ..       7     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 3.7e-29
                                       CSCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEE....EETTTTEEEEEEEEEESSHHHHHHHHHH CS
                            NifU_N   1 aysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqik....vdeetdriedakFktfGCgsaiAsssll 73 
                                       +y++++ldhyknPrn G le+      +    +p+cGD++r+ +k    vd++   i+++ F + GC++++As+s+l
  gi|336252685|ref|YP_004595792.1|   7 MYRQQILDHYKNPRNYGELEDPTF---THVGENPMCGDEIRMDVKldgtVDDDDATIQQVAFSGDGCAISQASASML 80 
                                       59*******************994...666679*********99933334566779********************* PP

                                       HHHHTTSBHHHHCCCCHHHHHHHHTC.SCSSSCHCSCHHHHHHHHHH CS
                            NifU_N  74 telvkgktleealkitnkeiaeelgg.lpkeklhcsvlaedalkaav 119
                                        + ++g+t+ e l++ ++++ + lg  + + +++c+vlae++++ ++
  gi|336252685|ref|YP_004595792.1|  81 SKELQGMTVSELLEMDRDDVIDMLGVdISPMRVKCAVLAEKVAQDGA 127
                                       ************************8559**************99875 PP

>> SufE  Fe-S metabolism associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.1e-06     0.055      56     108 ..      63     112 ..      44     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.1e-06
                                       EEEEEEESSHHHHHHHHHHHHHCTTEECCCCTCC-TCHHHHHTTSHHHHCHHH CS
                              SufE  56 lkfeadsdarivkGllalllevlsgktpeeilavdledfleelglsehlspsR 108
                                       + f++d   +i+++ +++l + l+g t +e+l++d +d+++ lg++  +sp R
  gi|336252685|ref|YP_004595792.1|  63 VAFSGDG-CAISQASASMLSKELQGMTVSELLEMDRDDVIDMLGVD--ISPMR 112
                                       5555554.5699******************************9986..46666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1055.26
//
Query:       gi|336252686|ref|YP_004595793.1|  [L=185]
Description: Heme NO binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-36  125.1   0.0    2.9e-36  124.9   0.0    1.0  1  HNOB      Haem-NO-binding
    5.4e-09   35.9   0.1    9.1e-09   35.2   0.1    1.4  1  V4R       V4R domain
     0.0018   18.3   0.0     0.0027   17.7   0.0    1.3  1  MetOD1    Metanogen output domain 1


Domain annotation for each model (and alignments):
>> HNOB  Haem-NO-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.9   0.0   4.9e-40   2.9e-36       1     163 [.       2     161 ..       2     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 4.9e-40
                                       BHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTTSS--TTSBTTHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                              HNOB   1 yGivleslqelveekygeevwdeileeagleekvftthetYddslllklveaaskvlglsadelleafGeyfvkffs 77 
                                       +Givl+ l+++v+e+yg +vw ++ e ag++++ + +++ Y+d+++l+lv+aa +++gl++ +ll afG+++v ++ 
  gi|336252686|ref|YP_004595793.1|   2 HGIVLKGLKDFVTEEYGADVWTDLHEAAGFRTRLYVPVTEYPDEIVLELVDAATDLTGLEEPTLLAAFGRFLVPHLL 78 
                                       59*************************************************************************** PP

                                       HHHTHHHHTHTTC.SHHHHHHHHHH.HHHHHHHHHSTTSS--EEEEEEEETTEEEEEEEESSSSTHHHHHHHHHHHH CS
                              HNOB  78 ekgydkllrvlgr.nlfeFLknldn.lHvevlklsypkakpPsfrceeeddnglvlhYrSkRkgladyvlGllkgva 152
                                        ++y+ +++  ++ +  e+++n+++ +H+ +   +  + +pP++r ++ dd+++ l Y+S+R gl+ +++Gll+g+a
  gi|336252686|ref|YP_004595793.1|  79 -STYGVHVD--REwTGLELIANVETyIHEALRAKQSGEFTPPELRTRRVDDRRVALAYESDR-GLCALARGLLEGIA 151
                                       .********..778**************555555555*************************.************** PP

                                       .HHTTEEEEEE CS
                              HNOB 153 kklfnekveie 163
                                        ++++e ++ie
  gi|336252686|ref|YP_004595793.1| 152 -DYYDEPLHIE 161
                                       .*******998 PP

>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   1.5e-12   9.1e-09      11      61 ..     130     178 ..     122     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.5e-12
                                       S-TT---SS---HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEEEE CS
                               V4R  11 laglpgkeePvCyleaGllagalsellgkrveveEveCaaeGhdhCeFeve 61 
                                       + ++  +++ +C+l +Gll+g++   + +++++e+ +C++eG+d C+F+v+
  gi|336252686|ref|YP_004595793.1| 130 ALAY-ESDRGLCALARGLLEGIA-DYYDEPLHIEQRRCMHEGADCCVFVVT 178
                                       4555.77899*************.8************************96 PP

>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.5e-07    0.0027     112     152 ..     137     177 ..     132     180 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.5e-07
                            MetOD1 112 PifCllcraivsrsftwtglkgsveqkktlgngdekCvFei 152
                                         +C l r++++ +++  +  +++eq+ ++ +g+++CvF  
  gi|336252686|ref|YP_004595793.1| 137 RGLCALARGLLEGIADYYDEPLHIEQRRCMHEGADCCVFVV 177
                                       679************************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1533.99
//
Query:       gi|336252687|ref|YP_004595794.1|  [L=82]
Description: hypothetical protein Halxa_1282 [Halopiger xanaduensis SH-6]
Scores for 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:                      1175  (0.0655363); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 610.75
//
Query:       gi|336252688|ref|YP_004595795.1|  [L=223]
Description: metal dependent phosphohydrolase [Halopiger xanaduensis SH-6]
Scores for 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-13   49.2   3.5    1.1e-12   48.3   3.5    1.4  1  HD        HD domain
  ------ inclusion threshold ------
      0.074   13.0   0.0       0.15   11.9   0.0    1.5  1  DUF4202   Domain of unknown function (DUF4202)
       0.15   11.4   0.0       0.21   10.9   0.0    1.2  1  DUF2817   Protein of unknown function (DUF2817)


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 !   48.3   3.5   1.8e-16   1.1e-12       3     121 ..      23     128 ..      22     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.8e-16
                                       HHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH CS
                                HD   3 eHsleVaklarrlaedlge..eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld 77 
                                        H ++Va la+ l +++      d+ ++ la +lHDiG  ++          ++++ +H+++ga+ + e++ + g d
  gi|336252688|ref|YP_004595795.1|  23 HHVRRVAALAETLIDRHPDgdAVDERVVTLAIYLHDIGRERED---------RGEIDDHATWGAREAGEILTDVGAD 90 
                                       7*****************9**********************54.........477899**************99999 PP

                                       ...HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  78 ...ledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                          +e v + +r h+ s           +++ +lea+iv++aD+l+a
  gi|336252688|ref|YP_004595795.1|  91 pdaIERVRHCVRTHRYSNA---------AEPETLEAKIVSDADNLDA 128
                                       ******************8.........56***************98 PP

>> DUF4202  Domain of unknown function (DUF4202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.5e-05      0.15      84     129 ..      72     117 ..      69     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                           DUF4202  84 lkkrqAelaaelleeagydeeeiervaalvrkeelkrdeetqlLED 129
                                       +++  A+ a e+l+++g d + ierv++ vr ++ ++ +e ++LE 
  gi|336252688|ref|YP_004595795.1|  72 HATWGAREAGEILTDVGADPDAIERVRHCVRTHRYSNAAEPETLEA 117
                                       5677899****************************99888888875 PP

>> DUF2817  Protein of unknown function (DUF2817)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.5e-05      0.21     192     256 ..      48     112 ..      41     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.5e-05
                           DUF2817 192 snrtlreilkehlaaaervaviDlHTGlGprgkgeiivsseedkealerarkwwgkevtskaegs 256
                                          tl   l++ ++++e    iD H   G r +gei+ +  +d++a+er+r+  ++++ s+a++ 
  gi|336252688|ref|YP_004595795.1|  48 RVVTLAIYLHDIGREREDRGEIDDHATWGAREAGEILTDVGADPDAIERVRHCVRTHRYSNAAEP 112
                                       5567778889999999*************************************999988877663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1640.00
//
Query:       gi|336252689|ref|YP_004595796.1|  [L=136]
Description: hypothetical protein Halxa_1284 [Halopiger xanaduensis SH-6]
Scores for 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   0.1        9.4    6.4   0.1    2.4  2  HTH_20    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 ?    6.4   0.1   0.00052       9.4       1      31 [.      17      50 ..      17      53 .. 0.89
   2 ?    4.6   0.0    0.0018        33      42      58 ..      68      84 ..      67      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00052
                                      HHHHHHHS-HHHHHHHHHH...STCTTB-HHHHH CS
                            HTH_20  1 dqiaeALahPvRrrilraL...araegltasela 31
                                      d+++eAL+   Rr + ++L   ++++ ++++e a
  gi|336252689|ref|YP_004595796.1| 17 DRVFEALSAAPRRHLVDELmdvPDGGTVSLPEAA 50
                                      689****************999888888888876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0018
                                      HHHHHHHHHCTTEEEEC CS
                            HTH_20 42 syHLrvLeeagLvevvr 58
                                      ++HL  L++ag+ve +r
  gi|336252689|ref|YP_004595796.1| 68 HRHLPLLADAGFVEWQR 84
                                      68***********9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1025.28
//
Query:       gi|336252690|ref|YP_004595797.1|  [L=414]
Description: cysteine desulfurase [Halopiger xanaduensis SH-6]
Scores for 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-151  503.3   0.0   4.2e-151  503.1   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    3.4e-09   36.5   0.3    5.9e-09   35.7   0.3    1.5  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    5.8e-08   32.4   0.0    6.7e-08   32.1   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00018   20.6   0.1    0.00051   19.1   0.1    1.6  1  SelA             L-seryl-tRNA selenium transferase
     0.0042   15.7   0.0     0.0095   14.5   0.0    1.6  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 !  503.1   0.0  1.2e-154  4.2e-151       1     371 []      31     402 ..      31     402 .. 1.00

  Alignments for each domain:
  == domain 1  score: 503.1 bits;  conditional E-value: 1.2e-154
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlv 77 
                                       +yld+aAttq+p++V+da+++yy++ nanvhr++hhl++ea+ a+eea+++vae+ina+ +ee+ift++tte+ nlv
  gi|336252690|ref|YP_004595797.1|  31 VYLDNAATTQTPDRVVDAMSDYYRQTNANVHRGIHHLSQEASIAYEEAHDRVAEFINADGREEVIFTKNTTEGENLV 107
                                       7**************************************************************************** PP

                                       HHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTT CS
                       Aminotran_5  78 alslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtG 153
                                       a+s++ + l pgd+iv+te+ehha lv+wq++ +rtga+v++i++de+g+ld+d++++l++++t++v+  hvsn++G
  gi|336252690|ref|YP_004595797.1| 108 AYSWGLNeLGPGDRIVLTEMEHHASLVTWQQIGERTGADVEYIRVDETGRLDMDHARELITDDTAIVSAVHVSNTLG 184
                                       ******9********************************************************************** PP

                                       EB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTS CS
                       Aminotran_5 154 tiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggem 230
                                       t++pv e+++la+++gal ++D+aqav+ +p+dvk++++Df+afsghK+ gPtGiGvly++++lle++ep l+gg+m
  gi|336252690|ref|YP_004595797.1| 185 TVNPVSELTELAHEHGALSFIDGAQAVPNRPVDVKDIDADFYAFSGHKMAGPTGIGVLYGKRDLLEEMEPYLYGGGM 261
                                       ***************************************************************************** PP

                                       EEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CT CS
                       Aminotran_5 231 veevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaer 307
                                       +++v++e++t+ + p+kfe GTp++a+++gl++a+++le++g+e+i++he+e a+y++erl++ ++v++ygp++ + 
  gi|336252690|ref|YP_004595797.1| 262 IRKVTFEDSTWGDLPWKFEPGTPPIAEAVGLHEAVDWLEDVGMERIQAHEEEIAAYAYERLAAEDDVEIYGPEPGPD 338
                                       ***************************************************************************** PP

                                       CBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 308 rasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                       r ++vsfn++gvha+d+a++++++ +avr+G hc+qpl++ l+++++ RaS+y+ynt+eevd+l
  gi|336252690|ref|YP_004595797.1| 339 RGGLVSFNLEGVHAHDLASIMNDHTVAVRAGDHCTQPLHDKLGVPASTRASFYVYNTREEVDKL 402
                                       **************************************************************97 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 !   35.7   0.3   1.7e-12   5.9e-09      31     150 ..      84     212 ..      29     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.7e-12
                                       HHHHHHT-SEEEEESSHHHHHHHHHHHTTTT...TT-EEEEESSS-THHHHHHH....HTT-EEEEE-B-TTTSSB- CS
                   DegT_DnrJ_EryC1  31 afaaylgvkhaiavssGtaAlhlaLralgvg...pgdeVIvpsltFvatanavl....elgakpvfvDvdpdtynid 100
                                       +f +  g + +i + + t++  l+    g++   pgd ++ + +   a+  + +    ++ga++ ++ vd +t  +d
  gi|336252690|ref|YP_004595797.1|  84 EFINADGREEVIFTKNTTEGENLVAYSWGLNelgPGDRIVLTEMEHHASLVTWQqigeRTGADVEYIRVD-ETGRLD 159
                                       55556678999********988877775554444************9987555511125789999****9.9***** PP

                                       GGGCGGG--TTE...EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1 101 paaieaaitert...kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                        ++++++it  t   +a+ + +++G v+ +++l+++a++hg   + D A+A+ 
  gi|336252690|ref|YP_004595797.1| 160 MDHARELITDDTaivSAVHVSNTLGTVNPVSELTELAHEHGALSFIDGAQAVP 212
                                       ************444455555579***************************86 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   1.9e-11   6.7e-08      30     225 ..      71     254 ..      38     369 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.9e-11
                                       --HHHHHHHHHHHHHT...T-SEEEEES-HHHHHHHHH.....HHH--TTEEEEEETT.-HHHHSSTTHHHHCC--E CS
                   Beta_elim_lyase  30 edktvnrLedavaelf...gkeaalfvpqGtaAnsill.....killqrgeevivtep.ahihfdetgaiaelagvk 97 
                                        +  +++  d+vae +   g e ++f+ + t ++++       + l  +g+ +++te   h    + ++i e  g+ 
  gi|336252690|ref|YP_004595797.1|  71 ASIAYEEAHDRVAEFInadGREEVIFTKNTTEGENLVAyswglNEL-GPGDRIVLTEMeHHASLVTWQQIGERTGAD 146
                                       455677888888886522267899*********9998877764444.59999999988577788888********** PP

                                       EEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHH CS
                   Beta_elim_lyase  98 lrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfana 174
                                       +  ++ +e+G +d++  +++i+++    + ++++ + +T  t       ++ + e++++a+++g   ++DgA  + +
  gi|336252690|ref|YP_004595797.1| 147 VEYIRVDETGRLDMDHARELITDDT---AIVSAVHVSNTLGT-------VNPVSELTELAHEHGALSFIDGAQAVPN 213
                                       ***********************44...58888888888875.......5556778899*************88887 PP

                                       HHHHTS-CHHHHTTSSEEEEESSSTT--SS-.EEEEE-HH....HHHHHHHH CS
                   Beta_elim_lyase 175 akslgeivkemfsyvDsvtmslkKdllanvG.gvlafrddeledylaerveq 225
                                            ++vk++   +D   +s+ K    + G gvl +++d l     e +e 
  gi|336252690|ref|YP_004595797.1| 214 R---PVDVKDI--DADFYAFSGHKM-AGPTGiGVLYGKRDLL-----EEMEP 254
                                       7...8999998..689999***997.5579999999999933.....33333 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.4e-07   0.00051     113     234 ..     147     253 ..     137     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-07
                                       BEEEEESBSSB--HHHHHHT--TTEEEEEEE---SEEEEES-B---HHHHHHHHHHHT--EEEEEES-B-S-GGGGT CS
                              SelA 113 vkLvevGttnkthlkDyekainentalllkvhtsnyrieGftkevelaeLvelgkekglpvleDlGsGllvdlseyg 189
                                       v+   v  t +  +   ++ i+++ta++  vh sn    G ++ v  +eL+el++e+g  ++ D          +  
  gi|336252690|ref|YP_004595797.1| 147 VEYIRVDETGRLDMDHARELITDDTAIVSAVHVSNT--LGTVNPV--SELTELAHEHGALSFIDG---------AQA 210
                                       4456788889999999999***************95..6777655..79********99888773.........346 PP

                                       -----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHHH CS
                              SelA 190 lskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkkelieklk 234
                                       +++ P   + + +  d  +fsG k+ G    G++ Gk++l+e+++
  gi|336252690|ref|YP_004595797.1| 211 VPNRPVDVKDIDA--DFYAFSGHKMAGPTGIGVLYGKRDLLEEME 253
                                       7899988777776..***************************996 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 !   14.5   0.0   2.7e-06    0.0095      88     179 ..     116     212 ..     107     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.7e-06
                                       S-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHH CS
                   Cys_Met_Meta_PP  88 lkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.....sdleelekaikentklvylEtptnpllkvvDieki 159
                                       l  Gd+iv+++  +  +    +++ +++g +v+++ +      d+++ ++ i++ t +v    ++n l  v  + ++
  gi|336252690|ref|YP_004595797.1| 116 LGPGDRIVLTEMEHHASLVTWQQIGERTGADVEYIRVdetgrLDMDHARELITDDTAIVSAVHVSNTLGTVNPVSEL 192
                                       5679***********************999999987733444567888999************************** PP

                                       HHHHHHTT-EEEEEGTTTHT CS
                   Cys_Met_Meta_PP 160 aklakkagvlvvvDntfasp 179
                                       ++la+++g+l ++D + a p
  gi|336252690|ref|YP_004595797.1| 193 TELAHEHGALSFIDGAQAVP 212
                                       **************987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2928.20
//
Query:       gi|336252691|ref|YP_004595798.1|  [L=296]
Description: hypothetical protein Halxa_1286 [Halopiger xanaduensis SH-6]
Scores for 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   3.9      0.081   13.3   3.3    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
      0.037   14.1   0.4      0.072   13.2   0.4    1.5  1  Mut7-C           Mut7-C RNAse 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 ?    2.0   0.0     0.031   2.8e+02      47      61 ..     223     237 ..     213     238 .. 0.80
   2 !   13.3   3.3     9e-06     0.081       3      36 ..     253     289 ..     251     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.031
                   Lar_restr_allev  47 eaeaekeaieaWNrR 61 
                                        a+  ++ i+ WNrR
  gi|336252691|ref|YP_004595798.1| 223 GAQVLADQIPDWNRR 237
                                       5677788899****9 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 9e-06
                   Lar_restr_allev   3 LkpCPfCggravlersqrvvaeigq...cvyCadCga 36 
                                       L+ CP C+g+  l++++  +  ++q    ++C+dC+a
  gi|336252691|ref|YP_004595798.1| 253 LERCPRCNGPVSLGEETVESCCRSQqvyAITCDDCEA 289
                                       789*************888776666999********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   0.4     8e-06     0.072      33     130 ..     188     288 ..     168     291 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8e-06
                            Mut7-C  33 ellalaakekrillTrdreLlkraklkkgvl........ltsrdveeqlreviarlglklslkpelsrCvaCngele 101
                                       e +++ ++++r+ +  d +L+ r + + ++l        l  + +  + r + +r +l+  l+  l+rC +Cng+++
  gi|336252691|ref|YP_004595798.1| 188 EAVTIDRRDERVSVRVDERLVGRWESEPALLadlagaqvLADQIPDWNRRPLAHRSRLANGLRAFLERCPRCNGPVS 264
                                       55555666666666666666666666655333333332223333444445677888999999999**********98 PP

                            Mut7-C 102 evekeevkervpekvyeeadeftrCekCr 130
                                         e++     v+++ ++++  +++C++C+
  gi|336252691|ref|YP_004595798.1| 265 LGEET-----VESCCRSQQVYAITCDDCE 288
                                       65543.....6888888888899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2353.17
//
Query:       gi|336252692|ref|YP_004595799.1|  [L=327]
Description: ABC transporter-like protein [Halopiger xanaduensis SH-6]
Scores for 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-25   87.9   0.0    1.2e-24   87.4   0.0    1.2  1  ABC_tran     ABC transporter
      7e-12   45.8   0.1    3.1e-08   33.8   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0018   18.2   4.4     0.0031   17.4   3.4    1.9  1  BAT          GAF and HTH_10 associated domain
     0.0019   18.8   0.0      0.006   17.3   0.0    1.8  2  DUF4162      Domain of unknown function (DUF4162)
  ------ inclusion threshold ------
      0.025   15.1   0.1      0.037   14.5   0.1    1.2  1  AAA_23       AAA domain
      0.034   14.1   0.0      0.057   13.3   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
      0.038   13.7   0.0       0.09   12.5   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.038   14.2   0.0        0.1   12.9   0.0    1.7  1  AAA_22       AAA domain
       0.14   11.7   0.0       0.36   10.4   0.0    1.6  2  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 !   87.4   0.0   5.9e-28   1.2e-24       2     136 ..      20     158 ..      19     159 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 5.9e-28
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + ++l+++ege+ +++G+nGaGKSt +++l+  ++pt+G+ ++ g d +  e  + + +ig++p+   + p+l  r+
  gi|336252692|ref|YP_004595799.1|  20 DGLDLTVREGEVFGFLGPNGAGKSTTINMLLDFTRPTAGSATVLGYDAQA-EADRISPRIGIIPEGFDIYPRLDGRR 95 
                                       7899**********************************************.99999**********99999999888 PP

                                       H........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +        ++d++++++l+++gl+  + +++   + ++S G++qr+a+ +al+ +p+ll++DEp+
  gi|336252692|ref|YP_004595799.1|  96 HvefavetkDADDDPDDVLDRVGLEPAARDRA---AGEYSTGMRQRLAMGMALVGDPDLLIMDEPS 158
                                       89999999888888***********9888887...8*****************************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 !   10.0   0.2   0.00028      0.56       2      23 ..      32      53 ..      31      95 .. 0.70
   2 !   33.8   0.0   1.5e-11   3.1e-08     227     297 ..     121     188 ..      90     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00028
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                       ++ GpNg+GKS+ +  l  + 
  gi|336252692|ref|YP_004595799.1| 32 FGFLGPNGAGKSTTINMLLDFT 53
                                      5789*********998875554 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 1.5e-11
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       +  +++ a e S G+++ la+  al  ++   +ll+ DEp +gL+P+ +r+l +l+++++++g+ v++++H
  gi|336252692|ref|YP_004595799.1| 121 PAARDRAAGEYSTGMRQRLAMGMALVGDP---DLLIMDEPSSGLDPHGIRELQDLVRAEAERGTTVFFSSH 188
                                       56678899999***************999...9***********************999999********* PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   3.4   1.6e-06    0.0031      31     108 ..     215     290 ..     205     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                               BAT  31 eglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtlleltvsgpslastlaehGgtvrsaeaed 107
                                       +gl ++ +ge++v + ++g  +ee++ +a ++d+v+dv   +++ + t +  + ++ ++++ l++ G+t+r+++++d
  gi|336252692|ref|YP_004595799.1| 215 DGLRESIGGESTVGLALAG-PAEELAPVAKSIDGVTDVAASGRTLECTIVDPA-AKATVVTELVDAGATIRDVRIRD 289
                                       5666666788888888888.559****************99988886666666.69*******************98 PP

                               BAT 108 g 108
                                        
  gi|336252692|ref|YP_004595799.1| 290 V 290
                                       5 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.9   5.8e+03      40      57 ..      99     117 ..      81     120 .. 0.68
   2 !   17.3   0.0     3e-06     0.006       3      79 ..     214     298 ..     213     300 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.9
                                       EEEEE--.----------- CS
                           DUF4162  40 lelkled.eeaanellkal 57 
                                       + ++ +d ++++ ++l+++
  gi|336252692|ref|YP_004595799.1|  99 FAVETKDaDDDPDDVLDRV 117
                                       3344457788888888876 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3e-06
                                       HHHHHTTS-SSEEE.EE..-------......---EEEE-TTS-EEEEE-------------.----EEEEEEEE-- CS
                           DUF4162   3 leeiKrsygknrie.ve..adaeellee....pgveeveeeggelelkledeeaanellkal.tsgveirsFeeeeP 71 
                                       ++ +++s+g++  + +   + aeel+ +    +gv++v   g++le+++ d +a+ ++ ++l ++g++ir ++ +  
  gi|336252692|ref|YP_004595799.1| 214 IDGLRESIGGESTVgLAlaGPAEELAPVaksiDGVTDVAASGRTLECTIVDPAAKATVVTELvDAGATIRDVRIRDV 290
                                       5667777755554446675334444433333388999999999*******************88************* PP

                                       -HHHHHHH CS
                           DUF4162  72 sLndIFie 79 
                                       sL+  F  
  gi|336252692|ref|YP_004595799.1| 291 SLESLFAS 298
                                       ***99976 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.9e-05     0.037      20      39 ..      30      49 ..      13      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                            AAA_23 20 gltlItGpNGaGKTTildAi 39
                                       ++ + GpNGaGK+T ++ +
  gi|336252692|ref|YP_004595799.1| 30 EVFGFLGPNGAGKSTTINML 49
                                      6899***********99865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.9e-05     0.057      90     121 ..      19      51 ..       3      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       ++ l   +++ ++  ++G+ G+GKSt in+ll 
  gi|336252692|ref|YP_004595799.1|  19 VDGLDLTVREgEVFGFLGPNGAGKSTTINMLLD 51 
                                       555655666558999***************976 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 ?   12.5   0.0   4.5e-05      0.09      15      39 ..      22      46 ..      17      52 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                       ++++++ +++ + Gp+G+GKST +
  gi|336252692|ref|YP_004595799.1| 22 LDLTVREGEVFGFLGPNGAGKSTTI 46
                                      5566665558999**********87 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.2e-05       0.1      12     122 ..      36     180 ..      29     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                            AAA_22  12 GesGtGKTtllrrlleqldeeakaee.........................erpevv.......fvtlpsst.sskd 55 
                                       G+ G+GK+t++++ll+     a  ++                              +       +v+ +++t + +d
  gi|336252692|ref|YP_004595799.1|  36 GPNGAGKSTTINMLLDFTRPTAGSATvlgydaqaeadrisprigiipegfdI----YprldgrrHVEFAVETkDADD 108
                                       9***************986555555599999999999999888888844440....355555568888888877777 PP

                            AAA_22  56 llrellralglelkaerlsseell.ealeqalrarav....ielliiDEaqh.lrseealeeLrsllnl.srkg 122
                                          ++l  +gle  a r++    + + ++q l   ++    + lli DE    l  +  ++eL +l+   ++ g
  gi|336252692|ref|YP_004595799.1| 109 DPDDVLDRVGLEPAA-RDRAAGEYsTGMRQRLAMGMAlvgdPDLLIMDEPSSgL-DPHGIRELQDLVRAeAERG 180
                                       799999999999999.55544444377777777777788889999999988888.6666666666666543444 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00018      0.36      10      49 ..      12      52 ..       4      54 .. 0.80
   2 ?   -2.7   0.0       1.8   3.6e+03     135     163 ..     170     198 ..     160     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                            AAA_27 10 ryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                       yG +t    ld+   e ++   +GpN AGKst+++ + d+
  gi|336252692|ref|YP_004595799.1| 12 EYGDLTAVdGLDLTVREGEVFGFLGPNGAGKSTTINMLLDF 52
                                      578877643688888888888889**********9988775 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.8
                            AAA_27 135 ealleaegelgqlLfeasaGlaslrevle 163
                                       ++l++ae e g+++f +s  l+++++v +
  gi|336252692|ref|YP_004595799.1| 170 QDLVRAEAERGTTVFFSSHILEHVEAVCD 198
                                       67899999999999999888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2285.08
//
Query:       gi|336252693|ref|YP_004595800.1|  [L=293]
Description: ABC-2 type transporter [Halopiger xanaduensis SH-6]
Scores for complete 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-42  145.8  10.0    1.8e-41  142.3  10.0    1.9  1  ABC2_membrane_2  ABC-2 family transporter protein
    2.9e-10   40.4  11.3    3.7e-10   40.1   9.3    2.0  2  ABC2_membrane_4  ABC-2 family transporter protein
    1.7e-06   27.4   9.8    1.7e-06   27.4   9.8    1.4  1  ABC2_membrane_3  ABC-2 family transporter protein
      1e-05   25.1  11.2    1.7e-05   24.3  11.2    1.4  1  ABC2_membrane    ABC-2 type transporter
    0.00032   20.3   8.3      0.001   18.6   8.3    1.8  1  ABC2_membrane_5  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.092   12.5   0.4      0.092   12.5   0.4    1.7  2  DUF4564          Domain of unknown function (DUF4564)
        4.1    7.1   6.4         10    5.9   6.4    1.6  1  DUF3464          Photosynthesis affected mutant 68


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 !  142.3  10.0   6.9e-45   1.8e-41       2     288 .]       7     293 .]       6     293 .] 0.95

  Alignments for each domain:
  == domain 1  score: 142.3 bits;  conditional E-value: 6.9e-45
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                       ++a+kEf d+ rs+ +++l  ll+ i v++ y    ++ +   a++  + + +                        
  gi|336252693|ref|YP_004595800.1|   7 TVARKEFDDAGRSKLLWALIGLLVGI-VVIGYAAIWYTADDVTAAEMLSFLGF------------------------ 58 
                                       69************************.88888877777777777776666666........................ PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgiv 155
                                        ++ +++p+ a+++g+ a++gE+ +g++kllL +P  R ++++gK++g++a+   +a a++ ++l+al+++++l   
  gi|336252693|ref|YP_004595800.1|  59 -PLQTIVPIAALIAGYMAVVGERRSGSIKLLLGLPPNRTDVVFGKLLGRMAV---VAAAVVLAFLVALVLSAVLFGG 131
                                       .99*************************************************...********************** PP

                   ABC2_membrane_2 156 laledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp...qei 229
                                       +++ d+l ++++++l+++  +f++l++++S+ + ++ +++al++g++++l+ l+ +v +g  +l  g+ +p   +++
  gi|336252693|ref|YP_004595800.1| 132 VPIVDWLGFAAVTLLFGV--AFAGLAVGVSAAVATRGKSMALVVGIYMLLVALWELVTAGPYYLVYGEGPPveaETW 206
                                       **************9999..88**************************************888888888889999** PP

                   ABC2_membrane_2 230 ndflsllsptsayntllneilagsdlna.............................lgstatnllilllllavllv 277
                                        ++l+ ++p say+tl +e  +g+ +                                +++++ +++ll +l+v+++
  gi|336252693|ref|YP_004595800.1| 207 YLLLEQFNPMSAYTTLASETVEGT-VPPftfqyglesfeasqltpaeryagagdapfFLQDWFGVVVLLCWLVVPVA 282
                                       ***********************9.55589*********************************************** PP

                   ABC2_membrane_2 278 lgyvlFkrkDl 288
                                       +gy++F++ Dl
  gi|336252693|ref|YP_004595800.1| 283 IGYYRFQKTDL 293
                                       *********97 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 !   40.1   9.3   1.4e-13   3.7e-10      11     173 ..      18     177 ..      10     182 .. 0.72
   2 ?   -1.2   0.0      0.68   1.8e+03     137     157 ..     263     283 ..     255     292 .. 0.58

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.4e-13
                   ABC2_membrane_4  11 rskivwllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLlti 87 
                                       rsk++w+l+ +++ +++++ +++   +++++ +ae+ s+  f+  l +++p+   i + + +  E+ ++ +k Ll +
  gi|336252693|ref|YP_004595800.1|  18 RSKLLWALIGLLVGIVVIGYAAIW-YTADDVTAAEMLSFLGFP--LQTIVPIAALIAGYMAVVGERRSGSIKLLLGL 91 
                                       9*********99999998877754.466788889999885555..5567888888888888999************* PP

                   ABC2_membrane_4  88 PvsrtklllaKlivllllsv.llmlvtflitvlfallsgfvg.fsvklvlellkkclelgllvffavlpiialvllk 162
                                       P +rt ++++Kl+  + +++ +++l+++++ vl a+l+g+v+ +++ +++ +   + + ++++++ v+   a+++  
  gi|336252693|ref|YP_004595800.1|  92 PPNRTDVVFGKLLGRMAVVAaAVVLAFLVALVLSAVLFGGVPiVDWLGFAAVTLLFGVAFAGLAVGVS--AAVATRG 166
                                       ************97665555166666667777889999999857777665554444444444444444..3566666 PP

                   ABC2_membrane_4 163 ksyvlpliltl 173
                                       ks +l +++ +
  gi|336252693|ref|YP_004595800.1| 167 KSMALVVGIYM 177
                                       66666666555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.68
                   ABC2_membrane_4 137 llkkclelgllvffavlpiia 157
                                       +l+ ++ +++l++ +v+p+ +
  gi|336252693|ref|YP_004595800.1| 263 FLQDWFGVVVLLCWLVVPVAI 283
                                       555666666666666666422 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 !   27.4   9.8   6.7e-10   1.7e-06     165     320 ..      58     230 ..      42     286 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 6.7e-10
                   ABC2_membrane_3 165 g.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill..l.....afglgi 233
                                       + l  i++i   ++  + ++v E++s+ ++l+l  + +++  +++k+lg ++v +  ++l++l  l     +fg g+
  gi|336252693|ref|YP_004595800.1|  58 FpLQTIVPIAALIAGYM-AVVGERRSGSIKLLLGLPPNRTDVVFGKLLGRMAVVAAAVVLAFLvaLvlsavLFG-GV 132
                                       44555666666666555.79*******************************99999998888744333444555.9* PP

                   ABC2_membrane_3 234 pfgnlglllllfllfglayialgyllsslfknsetaqilifivil........llsgffgglfpledlp....salk 298
                                       p+ +++ +  + llfg a++ l+  +s+++ + ++ ++l++ + +        ++ g +++++  e +p    ++  
  gi|336252693|ref|YP_004595800.1| 133 PIVDWLGFAAVTLLFGVAFAGLAVGVSAAVATRGKSMALVVGIYMllvalwelVTAGPYYLVY-GEGPPveaeTWYL 208
                                       *****************************9999777776555555255556643333344443.3445544435555 PP

                   ABC2_membrane_3 299 wifsiiPffapglgllrlitgd 320
                                        +  ++P++a++ +    + g+
  gi|336252693|ref|YP_004595800.1| 209 LLEQFNPMSAYTTLASETVEGT 230
                                       5566667777666655555555 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3  11.2   6.8e-09   1.7e-05       3     173 ..       5     180 ..       3     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.8e-09
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgt..vfgnlg..nsedglnrpgllffsvlflafsaltsvapvf 75 
                                       i+++ ++ef  + r++   llw li  l+ ++v+g+  +++ ++  + ++ l+++g+   +++ +a +++  +a+v 
  gi|336252693|ref|YP_004595800.1|   5 IGTVARKEFDDAGRSK---LLWALIGLLVGIVVIGYaaIWYTADdvTAAEMLSFLGFPLQTIVPIAALIAGYMAVVG 78 
                                       6778888888888888...47888888888888776225665667445555599************9********** PP

                     ABC2_membrane  76 erergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv.....gldlsrfflflllllltalaassl 147
                                       er+ g+++ +l  p   + ++v++k+l+ ++v ++++++ +l++++l      g+++  ++ f +++ll+++a+ +l
  gi|336252693|ref|YP_004595800.1|  79 ERRSGSIKLLLGLPP-NRTDVVFGKLLGRMAVVAAAVVLAFLVALVLSavlfgGVPIVDWLGFAAVTLLFGVAFAGL 154
                                       ***************.**************************9999865566677775559999************* PP

                     ABC2_membrane 148 gllisalapsfedasqlaslvllpll 173
                                       ++ +sa + +    + l+  ++++l+
  gi|336252693|ref|YP_004595800.1| 155 AVGVSAAVATRGKSMALVVGIYMLLV 180
                                       ******99999999999999999886 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 !   18.6   8.3   4.1e-07     0.001      40     164 ..      61     182 ..      19     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.1e-07
                   ABC2_membrane_5  40 fsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitllllii.avlikgnvtise 115
                                        +i++++ +i  + +++  +++s++ k+ll LP +r ++V  K l+   ++++a+++ +l++++ + ++ g v i +
  gi|336252693|ref|YP_004595800.1|  61 QTIVPIAALIAGY-MAVVGERRSGSIKLLLGLPPNRTDVVFGKLLGRMAVVAAAVVLAFLVALVlSAVLFGGVPIVD 136
                                       3334444444433.45555***************************99999999999998887648899999*9999 PP

                   ABC2_membrane_5 116 vllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvai 164
                                       +l ++++ l+++++f  +   +       +g+  ++++++gi +llva+
  gi|336252693|ref|YP_004595800.1| 137 WLGFAAVTLLFGVAFAGLAVGVSAAVA-TRGK--SMALVVGIYMLLVAL 182
                                       999999999998888777766666666.3333..444444444445444 PP

>> DUF4564  Domain of unknown function (DUF4564)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   3.6e-05     0.092      24      53 ..      27      57 ..      23      70 .. 0.81
   2 ?   -2.8   1.0       1.8   4.5e+03      23      59 ..     147     182 ..     145     186 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
                           DUF4564 24 sllvgiasvGlaaayyssDsl.lwklvyvig 53
                                      +llvgi  +G+aa+ y++D++ ++ ++ ++g
  gi|336252693|ref|YP_004595800.1| 27 GLLVGIVVIGYAAIWYTADDVtAAEMLSFLG 57
                                      79*****************996556655555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.8
                           DUF4564  23 wsllvgiasvGlaaayyssDsllwklvyvigcllval 59 
                                       ++++++  +vG+ aa+ +  ++++ +v +  +llval
  gi|336252693|ref|YP_004595800.1| 147 FGVAFAGLAVGVSAAVATRGKSMALVVGI-YMLLVAL 182
                                       56667777888888888777776655443.3456665 PP

>> DUF3464  Photosynthesis affected mutant 68
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   6.4     0.004        10      53     116 ..      97     158 ..      94     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.004
                           DUF3464  53 evVskRmirRvalfsGiPlalGlatfvvfylivskelvdlptwvvllvslvlFglgvlGlsYGv 116
                                       +vV  +++ R+a+++ + ++l++++  v  +++    v +  w+ +++ ++lFg+++ Gl+ Gv
  gi|336252693|ref|YP_004595800.1|  97 DVVFGKLLGRMAVVA-AAVVLAFLVALVLSAVL-FGGVPIVDWLGFAAVTLLFGVAFAGLAVGV 158
                                       68999999***9655.44555655554444443.4568999********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 2051.42
//
Query:       gi|336252694|ref|YP_004595801.1|  [L=97]
Description: hypothetical protein Halxa_1289 [Halopiger xanaduensis SH-6]
Scores for complete 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-30  105.2   0.3    1.7e-30  105.1   0.3    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 !  105.1   0.3   9.7e-35   1.7e-30       2      92 .]       6      96 ..       5      96 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 9.7e-35
                                      EETTE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-EE CS
                            DUF424  2 rtddllklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVlv 80
                                      r+++++ lvavcd+++lg+tf+   ++l+v+e+fygg  ++e ++i++L++a+iaNivg +av+la+++G++d+ +Vl+
  gi|336252694|ref|YP_004595801.1|  6 RQTEEGLLVAVCDSDVLGETFETDAVSLTVNEEFYGGDEVEESAVIDSLARADIANIVGTRAVELAIEEGFIDEANVLE 84
                                      789999************************************************************************* PP

                                      ETTEEEEEEEE- CS
                            DUF424 81 idgvphaqigkl 92
                                      +++++haq+ ++
  gi|336252694|ref|YP_004595801.1| 85 VGETRHAQLLRM 96
                                      *********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 723.85
//
Query:       gi|336252695|ref|YP_004595802.1|  [L=295]
Description: hypothetical protein Halxa_1290 [Halopiger xanaduensis SH-6]
Scores for 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-21   73.1   7.2      5e-05   22.9   0.0    5.8  6  TPR_1            Tetratricopeptide repeat
    6.3e-17   60.3  15.6      0.004   17.2   0.0    5.8  6  TPR_2            Tetratricopeptide repeat
    5.9e-14   51.0   4.0      0.014   15.5   0.3    5.3  5  TPR_8            Tetratricopeptide repeat
      1e-13   51.7  13.3    1.2e-06   29.1   0.4    3.9  4  TPR_16           Tetratricopeptide repeat
    1.2e-12   48.0  19.9    2.3e-09   37.4   4.8    4.1  3  TPR_12           Tetratricopeptide repeat
    1.4e-09   37.3  11.1    0.00058   19.7   0.1    4.8  4  TPR_7            Tetratricopeptide repeat
      4e-09   36.2   0.1      0.011   16.1   0.0    4.3  4  TPR_17           Tetratricopeptide repeat
    7.7e-08   32.4  11.5     0.0079   16.3   0.2    4.4  4  TPR_9            Tetratricopeptide repeat
    5.4e-07   29.3  20.9      0.004   17.0   0.7    5.2  5  TPR_10           Tetratricopeptide repeat
    1.2e-06   28.8  20.8      0.002   18.8   0.9    5.2  5  TPR_14           Tetratricopeptide repeat
    2.6e-06   27.0   3.4       0.18   11.5   0.0    4.7  5  TPR_11           TPR repeat
    3.2e-05   24.3  10.1        0.5   10.9   0.0    4.5  5  TPR_19           Tetratricopeptide repeat
    7.1e-05   23.1  16.3      0.013   16.1   1.8    5.7  5  TPR_4            Tetratricopeptide repeat
     0.0003   19.8   0.2    0.00062   18.8   0.1    1.5  1  NARP1            NMDA receptor-regulated protein 1
    0.00065   19.9   1.8      0.067   13.4   0.1    2.7  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
     0.0074   16.3   5.8       0.37   10.9   0.7    3.4  2  ANAPC5           Anaphase-promoting complex subunit 5
  ------ inclusion threshold ------
       0.04   14.6   5.4         27    5.7   0.1    4.6  4  TPR_6            Tetratricopeptide repeat
      0.097   12.7   0.4        0.4   10.7   0.1    2.1  2  LisH             LisH
       0.12   12.1   1.3         14    5.5   0.0    2.7  2  SPOB_a           Sensor_kinase_SpoOB-type, alpha-helical doma
       0.14   12.6   0.3       0.41   11.1   0.3    1.8  1  Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; D
       0.21   11.9   4.5        1.3    9.4   0.6    2.6  2  TPR_20           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00092      0.78       8      26 ..      71      89 ..      64      97 .. 0.85
   2 !   22.9   0.0   5.9e-08     5e-05       2      31 ..     102     131 ..     102     134 .. 0.95
   3 !   16.6   0.0   5.9e-06    0.0051       2      33 ..     139     170 ..     138     171 .. 0.92
   4 !   12.8   0.0   9.2e-05     0.079       1      30 [.     172     201 ..     172     201 .. 0.96
   5 !   10.3   0.2   0.00056      0.48       4      22 ..     209     227 ..     206     232 .. 0.83
   6 ?   -1.2   0.0       2.5   2.1e+03      12      20 ..     266     274 ..     264     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00092
                                      HHHHHHTT-HHHHHHHHHH CS
                             TPR_1  8 GnayfklgkydeAleyyek 26
                                      G+ y++ ++y++A e++e+
  gi|336252695|ref|YP_004595802.1| 71 GLNYMQINRYEQATEAFER 89
                                      778**************98 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 5.9e-08
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                       +a+ n+G+a+ +l+++deA+ + ++AL+++
  gi|336252695|ref|YP_004595802.1| 102 EAWVNKGVAHAELEEWDEAIGAHREALRID 131
                                       69***************************9 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 5.9e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                        a  nl++a+ + g+  +Ale+ e+A+e+++ 
  gi|336252695|ref|YP_004595802.1| 139 TAETNLAYALWEFGETAQALEHAERAVEIDER 170
                                       5779**************************86 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 9.2e-05
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a+ ++n++  + + g  +eAl + + A++l
  gi|336252695|ref|YP_004595802.1| 172 AEGWFNRAFFLSERGLSEEALHCIDNAIRL 201
                                       799************************987 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00056
                                       HHHHHHHHHHTT-HHHHHH CS
                             TPR_1   4 lynlGnayfklgkydeAle 22 
                                       l  +++++ +lg+ydeA+e
  gi|336252695|ref|YP_004595802.1| 209 LEEKAHILEELGEYDEAEE 227
                                       55689************98 PP

  == domain 6  score: -1.2 bits;  conditional E-value: 2.5
                                       HHTT-HHHH CS
                             TPR_1  12 fklgkydeA 20 
                                       f++g++++A
  gi|336252695|ref|YP_004595802.1| 266 FQQGEPEDA 274
                                       89*****98 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.2   0.00024      0.21       4      26 ..      67      89 ..      64      97 .. 0.86
   2 !   17.2   0.0   4.7e-06     0.004       2      32 ..     102     132 ..     101     134 .. 0.94
   3 !   14.6   0.2   3.1e-05     0.027       6      32 ..     143     169 ..     138     171 .. 0.92
   4 !   12.3   0.0   0.00017      0.14       1      30 [.     172     201 ..     172     205 .. 0.95
   5 !   11.6   0.4   0.00028      0.24       2      27 ..     207     232 ..     206     238 .. 0.87
   6 ?   -1.0   0.0         3   2.6e+03      10      20 ..     264     274 ..     263     275 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                             TPR_2  4 lynlGlayyklgdyeeAleafek 26
                                      l   Gl y++ ++ye+A eafe+
  gi|336252695|ref|YP_004595802.1| 67 LLDVGLNYMQINRYEQATEAFER 89
                                      66779*****************8 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 4.7e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       ea+ n G a+++l +++eA+ a ++Al++d 
  gi|336252695|ref|YP_004595802.1| 102 EAWVNKGVAHAELEEWDEAIGAHREALRIDD 132
                                       89**************************985 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 3.1e-05
                             TPR_2   6 nlGlayyklgdyeeAleafekAleldP 32 
                                       nl++a+++ g+ ++Ale+ e+A+e+d+
  gi|336252695|ref|YP_004595802.1| 143 NLAYALWEFGETAQALEHAERAVEIDE 169
                                       8************************97 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00017
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       ae+++n++  + ++g  eeAl++ + A++l
  gi|336252695|ref|YP_004595802.1| 172 AEGWFNRAFFLSERGLSEEALHCIDNAIRL 201
                                       799*************************98 PP

  == domain 5  score: 11.6 bits;  conditional E-value: 0.00028
                             TPR_2   2 ealynlGlayyklgdyeeAleafekA 27 
                                       ++l + + ++++lg+y+eA+e  ++A
  gi|336252695|ref|YP_004595802.1| 207 QVLEEKAHILEELGEYDEAEEIADEA 232
                                       678899**************998888 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 3
                             TPR_2  10 ayyklgdyeeA 20 
                                       +++++g++e+A
  gi|336252695|ref|YP_004595802.1| 264 SAFQQGEPEDA 274
                                       689******98 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0037       3.1       8      26 ..      71      89 ..      67      89 .. 0.89
   2 ?    6.7   0.0     0.012       9.9       2      31 ..     102     131 ..     101     134 .. 0.92
   3 !   12.1   0.0   0.00021      0.18       6      32 ..     143     169 ..     142     171 .. 0.95
   4 ?    5.5   0.0     0.028        24       1      30 [.     172     201 ..     172     201 .. 0.93
   5 !   15.5   0.3   1.7e-05     0.014       1      31 [.     206     236 ..     206     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0037
                                      HHHHHHTT-HHHHHHHHHH CS
                             TPR_8  8 gsiylklgdyeeAkeyyek 26
                                      g+ y++ ++ye+A e++e+
  gi|336252695|ref|YP_004595802.1| 71 GLNYMQINRYEQATEAFER 89
                                      888**************96 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.012
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                       ea++n+g ++ +l++ +eA+ + ++al++d
  gi|336252695|ref|YP_004595802.1| 102 EAWVNKGVAHAELEEWDEAIGAHREALRID 131
                                       79******************9999999998 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00021
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldp 32 
                                       nl++++++ g+  +A e  e+a+e+d+
  gi|336252695|ref|YP_004595802.1| 143 NLAYALWEFGETAQALEHAERAVEIDE 169
                                       8************************97 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.028
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       ae ++n +  +++ g  eeA  ++  a++l
  gi|336252695|ref|YP_004595802.1| 172 AEGWFNRAFFLSERGLSEEALHCIDNAIRL 201
                                       689********************9999976 PP

  == domain 5  score: 15.5 bits;  conditional E-value: 1.7e-05
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a+++  +++i+++lg+y+eA+e   +a e++
  gi|336252695|ref|YP_004595802.1| 206 AQVLEEKAHILEELGEYDEAEEIADEANEMR 236
                                       5677889****************99998886 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.4   1.4e-09   1.2e-06       2      66 ..      69     133 ..      68     135 .. 0.93
   2 !   17.5   1.8   5.8e-06     0.005       2      54 ..     143     192 ..     142     192 .. 0.96
   3 !   15.6   0.2   2.3e-05      0.02      10      60 ..     185     232 ..     182     239 .. 0.92
   4 ?   -0.6   0.0       2.6   2.3e+03       6      16 ..     264     274 ..     263     274 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.4e-09
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       + ++ +++ ++y++A +a+e++   + ++ +  eA+ ++g+a++++ +++eA+ + r+alr + +
  gi|336252695|ref|YP_004595802.1|  69 DVGLNYMQINRYEQATEAFERTAHFAEDDRVEQEAWVNKGVAHAELEEWDEAIGAHREALRIDDS 133
                                       67899************************************************999999998765 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.8e-06
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                                       +la+a+++ g+ ++A++ +e+a++ d    + ae +++++  + ++g  +eA+
  gi|336252695|ref|YP_004595802.1| 143 NLAYALWEFGETAQALEHAERAVEID---ERFAEGWFNRAFFLSERGLSEEAL 192
                                       79************************...*******************99995 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 2.3e-05
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                       +g  ++A++  + a++++    ++a+ l +++ ++ ++g+++eA++  ++a
  gi|336252695|ref|YP_004595802.1| 185 RGLSEEALHCIDNAIRLG---MRNAQVLEEKAHILEELGEYDEAEEIADEA 232
                                       67789*************...************************888776 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.6
                            TPR_16   6 aalragdyddA 16 
                                       +a+++g+++dA
  gi|336252695|ref|YP_004595802.1| 264 SAFQQGEPEDA 274
                                       57788888877 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.053        45       9      70 ..      70      89 ..      63      96 .. 0.58
   2 !   37.4   4.8   2.7e-12   2.3e-09       5      76 ..     103     169 ..     100     170 .. 0.93
   3 !   13.4   1.0   8.4e-05     0.072       3      36 ..     206     239 ..     204     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.053
                            TPR_12  9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlellee 70
                                      +++ +++                                           +rye+A e++e+
  gi|336252695|ref|YP_004595802.1| 70 VGLNYMQI------------------------------------------NRYEQATEAFER 89
                                      44444455..........................................555555555555 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 2.7e-12
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a++n ++++++l+++deA+  +++al+i       +h  +at+  nL+ +++++g++++Ale+ e+a++i+e
  gi|336252695|ref|YP_004595802.1| 103 AWVNKGVAHAELEEWDEAIGAHREALRID---DSSEH--AATAETNLAYALWEFGETAQALEHAERAVEIDE 169
                                       899**************************...44678..9******************************98 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 8.4e-05
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrl 36 
                                       a++l + a++l +lg+ydeA+e+ ++a e+++r+
  gi|336252695|ref|YP_004595802.1| 206 AQVLEEKAHILEELGEYDEAEEIADEANEMRERA 239
                                       56777899999***********999998888776 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.023        20       9      32 ..      74      97 ..      71     100 .. 0.80
   2 !   19.7   0.1   6.8e-07   0.00058       1      34 [.     103     136 ..     103     138 .. 0.89
   3 !    7.9   0.3    0.0041       3.5       4      29 ..     143     168 ..     142     173 .. 0.84
   4 !    8.4   0.2    0.0027       2.3       6      21 ..     213     228 ..     208     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.023
                             TPR_7  9 ysrlGdyeeAielyeqsLaltkdp 32
                                      y + ++ye+A e +e+   +++d+
  gi|336252695|ref|YP_004595802.1| 74 YMQINRYEQATEAFERTAHFAEDD 97
                                      8899************55555554 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 6.8e-07
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       a++n ++++ +l +++eAi+ ++++L+++++ e+
  gi|336252695|ref|YP_004595802.1| 103 AWVNKGVAHAELEEWDEAIGAHREALRIDDSSEH 136
                                       6899********************9988887766 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0041
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLalt 29 
                                       nLa +  + G++++A+e+ e++ +++
  gi|336252695|ref|YP_004595802.1| 143 NLAYALWEFGETAQALEHAERAVEID 168
                                       9********************55554 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0027
                             TPR_7   6 arlysrlGdyeeAiel 21 
                                       a++ ++lG+y+eA+e+
  gi|336252695|ref|YP_004595802.1| 213 AHILEELGEYDEAEEI 228
                                       899**********996 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.15   1.3e+02      14      33 ..     102     121 ..     101     122 .. 0.93
   2 ?   -0.6   0.0       2.6   2.2e+03      17      33 ..     142     158 ..     126     159 .. 0.85
   3 !   16.1   0.0   1.3e-05     0.011       2      33 ..     161     192 ..     160     193 .. 0.94
   4 !   11.1   0.0   0.00049      0.42       3      34 .]     196     227 ..     194     227 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.15
                            TPR_17  14 daynnLAelllknGdlmtAr 33 
                                       +a+ n++++++++ ++++A+
  gi|336252695|ref|YP_004595802.1| 102 EAWVNKGVAHAELEEWDEAI 121
                                       69***************996 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.6
                            TPR_17  17 nnLAelllknGdlmtAr 33 
                                       +nLA++l + G++++A+
  gi|336252695|ref|YP_004595802.1| 142 TNLAYALWEFGETAQAL 158
                                       58999988888888886 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.3e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                        ++a+e+d   a+ ++n+A +l+++G +++A+
  gi|336252695|ref|YP_004595802.1| 161 AERAVEIDERFAEGWFNRAFFLSERGLSEEAL 192
                                       69************************999995 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00049
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtArq 34 
                                        +a++l   na ++ ++A +l+++G++++A++
  gi|336252695|ref|YP_004595802.1| 196 DNAIRLGMRNAQVLEEKAHILEELGEYDEAEE 227
                                       678888889*********************96 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   9.3e-06    0.0079      28      63 ..      63      98 ..      57     101 .. 0.92
   2 !    7.0   0.2    0.0075       6.4      31      70 ..     103     142 ..     100     145 .. 0.87
   3 !   11.6   0.2   0.00028      0.24      10      56 ..     153     199 ..     144     201 .. 0.89
   4 !    8.5   0.5    0.0026       2.3       8      48 ..     185     225 ..     182     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.3e-06
                             TPR_9 28 dpeerrdRGlllaqlGclsaAladLeaylalapdap 63
                                      d++e++d Gl ++q +++++A +++e+ ++ a+d++
  gi|336252695|ref|YP_004595802.1| 63 DAQELLDVGLNYMQINRYEQATEAFERTAHFAEDDR 98
                                      899************************999999875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0075
                             TPR_9  31 errdRGlllaqlGclsaAladLeaylalapdapdaeaira 70 
                                        +   G+++a+l+ + +A+ +   +l+++++ + a++++ 
  gi|336252695|ref|YP_004595802.1| 103 AWVNKGVAHAELEEWDEAIGAHREALRIDDSSEHAATAET 142
                                       7999**********************99998888887765 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00028
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl 56 
                                       + ++al+ +er + ++ + +e ++ R++ l ++G  ++Al + + ++
  gi|336252695|ref|YP_004595802.1| 153 ETAQALEHAERAVEIDERFAEGWFNRAFFLSERGLSEEALHCIDNAI 199
                                       6799************************************9988776 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0026
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaA 48 
                                       +  +e+al +++  + l  + ++ + + + +l++lG + +A
  gi|336252695|ref|YP_004595802.1| 185 RGLSEEALHCIDNAIRLGMRNAQVLEEKAHILEELGEYDEA 225
                                       567899********************************998 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.071        60       9      28 ..      71      90 ..      67      95 .. 0.86
   2 !    6.7   0.1    0.0078       6.7       7      31 ..     106     130 ..     105     130 .. 0.92
   3 !   17.0   0.7   4.7e-06     0.004       6      33 ..     142     169 ..     138     170 .. 0.92
   4 ?   -1.3   0.0       2.7   2.3e+03       8      29 ..     178     199 ..     177     201 .. 0.76
   5 !   12.7   2.1   0.00011     0.091       9      35 ..     213     239 ..     206     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.071
                            TPR_10  9 analrqrgrydeAealleea 28
                                      +  + q +ry++A + +e++
  gi|336252695|ref|YP_004595802.1| 71 GLNYMQINRYEQATEAFERT 90
                                      78899***********9997 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0078
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       N ++a+ ++ ++deA   ++eal+i
  gi|336252695|ref|YP_004595802.1| 106 NKGVAHAELEEWDEAIGAHREALRI 130
                                       5699*******************86 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 4.7e-06
                            TPR_10   6 nNLanalrqrgrydeAealleealairr 33 
                                       +NLa al++ g+ ++A++++e+a++i +
  gi|336252695|ref|YP_004595802.1| 142 TNLAYALWEFGETAQALEHAERAVEIDE 169
                                       7***********************9965 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 2.7
                            TPR_10   8 LanalrqrgrydeAealleeal 29 
                                        a  l++rg  +eA+   + a+
  gi|336252695|ref|YP_004595802.1| 178 RAFFLSERGLSEEALHCIDNAI 199
                                       5778999999999998766666 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 0.00011
                            TPR_10   9 analrqrgrydeAealleealairrrl 35 
                                       a++l ++g+ydeAe++++ea ++r+r+
  gi|336252695|ref|YP_004595802.1| 213 AHILEELGEYDEAEEIADEANEMRERA 239
                                       789999*****************9997 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.82     7e+02       5      34 ..      68      97 ..      64     108 .. 0.68
   2 !   10.4   0.5    0.0012         1       3      35 ..     103     135 ..     101     142 .. 0.83
   3 !   18.8   0.9   2.3e-06     0.002       7      43 ..     144     180 ..     140     181 .. 0.94
   4 ?    2.9   0.0       0.3   2.6e+02       8      42 ..     179     213 ..     178     215 .. 0.89
   5 !    9.4   0.4    0.0024         2       7      27 ..     212     232 ..     207     243 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.82
                            TPR_14  5 lalaeallalGdpdeAiallrralalaPdd 34
                                      l+ +  +++  ++++A ++++r    a dd
  gi|336252695|ref|YP_004595802.1| 68 LDVGLNYMQINRYEQATEAFERTAHFAEDD 97
                                      5556668888999*******9963333333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0012
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPdda 35 
                                       a+   + a+++l+++deAi + r+al+ + +++
  gi|336252695|ref|YP_004595802.1| 103 AWVNKGVAHAELEEWDEAIGAHREALRIDDSSE 135
                                       67777889*******************987765 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 2.3e-06
                            TPR_14   7 laeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       la al++ G++++A+++++ra++ +  +ae w+  a+
  gi|336252695|ref|YP_004595802.1| 144 LAYALWEFGETAQALEHAERAVEIDERFAEGWFNRAF 180
                                       89******************************98885 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.3
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                                       a +l ++G  +eA+ + + a++l+  +a+++ + a
  gi|336252695|ref|YP_004595802.1| 179 AFFLSERGLSEEALHCIDNAIRLGMRNAQVLEEKA 213
                                       6689999********************99998876 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.0024
                            TPR_14   7 laeallalGdpdeAiallrra 27 
                                        a++l++lG++deA++++++a
  gi|336252695|ref|YP_004595802.1| 212 KAHILEELGEYDEAEEIADEA 232
                                       5899*************9998 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.068        58       1      18 [.      71      88 ..      71      90 .. 0.82
   2 !    8.1   0.0    0.0024       2.1       3      27 ..     110     134 ..     108     152 .. 0.80
   3 !   11.5   0.0   0.00021      0.18       8      36 ..     152     180 ..     145     186 .. 0.88
   4 ?    0.1   0.0      0.77   6.6e+02      11      42 .]     189     220 ..     182     220 .. 0.82
   5 ?    0.5   0.1      0.57   4.9e+02       4      13 ..     216     225 ..     213     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.068
                            TPR_11  1 GdayyeqGkyeeAieaYk 18
                                      G  y++ ++ye+A ea++
  gi|336252695|ref|YP_004595802.1| 71 GLNYMQINRYEQATEAFE 88
                                      5669999*****988876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0024
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdn 27 
                                       a  e+ +++eAi a ++Al++d ++
  gi|336252695|ref|YP_004595802.1| 110 AHAELEEWDEAIGAHREALRIDDSS 134
                                       567899***************9765 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00021
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGl 36 
                                       G+  +A+e+ ++A+++d+ +ae ++n+++
  gi|336252695|ref|YP_004595802.1| 152 GETAQALEHAERAVEIDERFAEGWFNRAF 180
                                       8999**********************985 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.77
                            TPR_11  11 eeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       eeA+ +  +A++l   na ++ + ++++ ++G
  gi|336252695|ref|YP_004595802.1| 189 EEALHCIDNAIRLGMRNAQVLEEKAHILEELG 220
                                       899999999***99999999988888888777 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.57
                            TPR_11   4 yyeqGkyeeA 13 
                                       + e+G+y+eA
  gi|336252695|ref|YP_004595802.1| 216 LEELGEYDEA 225
                                       5589*****9 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.39   3.3e+02      35      52 ..      74      91 ..      63     101 .. 0.79
   2 ?    6.0   0.5      0.02        17       6      60 ..      79     136 ..      73     144 .. 0.74
   3 !   10.9   0.0   0.00058       0.5       2      50 ..     149     197 ..     148     210 .. 0.90
   4 !    9.2   0.6     0.002       1.7      31      55 ..     212     236 ..     196     244 .. 0.82
   5 ?    1.4   0.0      0.56   4.8e+02      35      61 ..     265     292 ..     248     294 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.39
                            TPR_19 35 llalgqldeAealLdalp 52
                                      +++ +++++A ++ ++  
  gi|336252695|ref|YP_004595802.1| 74 YMQINRYEQATEAFERTA 91
                                      788899999988887755 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                            TPR_19   6 dyaeAlalleqal...qedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                       +y++A +++e+     ++d   +ea+ +   a+ +l ++deA+ +  ++++ d  ++ 
  gi|336252695|ref|YP_004595802.1|  79 RYEQATEAFERTAhfaEDDRVEQEAWVNKGVAHAELEEWDEAIGAHREALRIDDSSEH 136
                                       7999999999954232444449999999999999******999887777777766555 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00058
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLda 50 
                                       ++ g  a+Al++ e+a + d   ae + + A  l + g  +eA  ++d 
  gi|336252695|ref|YP_004595802.1| 149 WEFGETAQALEHAERAVEIDERFAEGWFNRAFFLSERGLSEEALHCIDN 197
                                       567999*************************************988875 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.002
                            TPR_19  31 LAeallalgqldeAealLdalpeed 55 
                                        A +l +lg++deAe++ d++ e+ 
  gi|336252695|ref|YP_004595802.1| 212 KAHILEELGEYDEAEEIADEANEMR 236
                                       588999***********99987765 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.56
                            TPR_19  35 llalgqldeAealL.dalpeedpddary 61 
                                        +++g++++A  ++ d+  ++d+dd+++
  gi|336252695|ref|YP_004595802.1| 265 AFQQGEPEDADVTItDPGRASDRDDEDW 292
                                       6899999999877614445555555666 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.8   1.6e+03       3      20 ..     103     120 ..     101     121 .. 0.86
   2 !   16.1   1.8   1.5e-05     0.013       5      26 .]     142     163 ..     138     163 .. 0.91
   3 ?    1.7   0.0      0.65   5.5e+02       4      21 ..     175     192 ..     172     194 .. 0.88
   4 !    8.9   0.2    0.0031       2.7       8      26 .]     213     231 ..     206     231 .. 0.85
   5 ?    1.8   0.0      0.59   5.1e+02      10      20 ..     264     274 ..     263     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.8
                             TPR_4   3 allaLArallalGdldeA 20 
                                       a ++ + a+++l ++deA
  gi|336252695|ref|YP_004595802.1| 103 AWVNKGVAHAELEEWDEA 120
                                       7788999***99999998 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.5e-05
                             TPR_4   5 laLArallalGdldeAraller 26 
                                        +LA al++ G+ ++A++++er
  gi|336252695|ref|YP_004595802.1| 142 TNLAYALWEFGETAQALEHAER 163
                                       79******************98 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.65
                             TPR_4   4 llaLArallalGdldeAr 21 
                                         ++A  l ++G ++eA+
  gi|336252695|ref|YP_004595802.1| 175 WFNRAFFLSERGLSEEAL 192
                                       5799************97 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0031
                             TPR_4   8 ArallalGdldeAraller 26 
                                       A  l +lG++deA++++++
  gi|336252695|ref|YP_004595802.1| 213 AHILEELGEYDEAEEIADE 231
                                       888999*********9986 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.59
                             TPR_4  10 allalGdldeA 20 
                                        ++++G++++A
  gi|336252695|ref|YP_004595802.1| 264 SAFQQGEPEDA 274
                                       6899*****99 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   7.2e-07   0.00062     199     255 ..     179     235 ..     152     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.2e-07
                                       HHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 199 AqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                       A +  + g  e+Al++id+ai+      ++   Ka+il+  G+ ++A e+++ea ++
  gi|336252695|ref|YP_004595802.1| 179 AFFLSERGLSEEALHCIDNAIRLGMRNAQVLEEKAHILEELGEYDEAEEIADEANEM 235
                                       55666777889*******************************************998 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 ?    4.4   0.0     0.053        45      39      78 ..      83     123 ..      64     127 .. 0.67
   2 !   13.4   0.1   7.8e-05     0.067       7      79 ..     156     229 ..     150     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.053
                                       HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  39 ykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                        ++A+e +  + + +   +++++ ++ +  +L++++eAi a
  gi|336252695|ref|YP_004595802.1|  83 ATEAFERTAHFaEDDRVEQEAWVNKGVAHAELEEWDEAIGA 123
                                       33444444444333444558888888888899999999876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.8e-05
                                       HHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   7 nAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                        A+ +aer+++ + + +e  +  A  l ++g  ++A++ +++a +l  ++ +++  +A+ l +L++y+eA+ + 
  gi|336252695|ref|YP_004595802.1| 156 QALEHAERAVEIDERFAEGWFNRAFFLSERGLSEEALHCIDNAiRLGMRNAQVLEEKAHILEELGEYDEAEEIA 229
                                       678888888876666777777777778888889*************************************9875 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.7   0.00044      0.37       6      72 ..      72     132 ..      67     149 .. 0.75
   2 ?    5.4   0.5     0.022        19      38      74 ..     169     205 ..     131     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00044
                            ANAPC5   6 lnalrakdYqqaldsLhryFDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleeairlAr 72 
                                       ln ++ ++Y+qa+++  r   +     e+   +  q a +n  + ha++++++eA+ a +ea r+  
  gi|336252695|ref|YP_004595802.1|  72 LNYMQINRYEQATEAFERTAHF----AEDD--RVEQEAWVNKGVAHAELEEWDEAIGAHREALRIDD 132
                                       6777888888888875554444....4444..44569**************************9954 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.022
                            ANAPC5  38 ksyqyalLnlaslhadfghneeAvkaleeairlAren 74 
                                       +++    +n a + ++ g  eeA++ + +airl   n
  gi|336252695|ref|YP_004595802.1| 169 ERFAEGWFNRAFFLSERGLSEEALHCIDNAIRLGMRN 205
                                       5666667888888888899999999999999987655 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.13   1.1e+02       6      25 ..      70      89 ..      67      91 .. 0.85
   2 ?    2.6   0.0      0.31   2.7e+02       1      22 [.     102     123 ..     102     130 .. 0.86
   3 ?    5.7   0.1     0.032        27       5      28 ..     143     166 ..     140     168 .. 0.87
   4 ?    1.2   0.0      0.84   7.1e+02       9      23 ..     215     229 ..     207     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                                      HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  6 lalsyrklgdtdkAlealer 25
                                       +l y + +++++A ea+er
  gi|336252695|ref|YP_004595802.1| 70 VGLNYMQINRYEQATEAFER 89
                                      688899978*********98 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlea 22 
                                       +A  + + ++ +l ++d+A+ a
  gi|336252695|ref|YP_004595802.1| 102 EAWVNKGVAHAELEEWDEAIGA 123
                                       6888999*****88*****965 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                       +la+++ + g+t++Ale  er ++
  gi|336252695|ref|YP_004595802.1| 143 NLAYALWEFGETAQALEHAERAVE 166
                                       6899999966*******9999886 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.84
                                       HHHHHHHHHHHHHHH CS
                             TPR_6   9 syrklgdtdkAleal 23 
                                        +++lg++d+A e+ 
  gi|336252695|ref|YP_004595802.1| 215 ILEELGEYDEAEEIA 229
                                       677899*****9886 PP

>> LisH  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00047       0.4       8      25 ..      72      89 ..      72      89 .. 0.94
   2 ?   -1.1   0.1       2.4   2.1e+03      16      24 ..     151     159 ..     151     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00047
                                      HHHHHHCT-HHHHHHHHH CS
                              LisH  8 ydYLvkeGyeetAeaFek 25
                                      ++Y++ + ye++ eaFe+
  gi|336252695|ref|YP_004595802.1| 72 LNYMQINRYEQATEAFER 89
                                      69**************96 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.4
                                       -HHHHHHHH CS
                              LisH  16 yeetAeaFe 24 
                                       + etA+a+e
  gi|336252695|ref|YP_004595802.1| 151 FGETAQALE 159
                                       679****97 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.016        14      33      50 ..      74      91 ..      71      98 .. 0.84
   2 ?    4.4   0.4     0.035        30      35      55 ..     218     238 ..     214     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.016
                            SPOB_a 33 ylqLgkydkaeeyieevv 50
                                      y+q+++y++a+e  e+ +
  gi|336252695|ref|YP_004595802.1| 74 YMQINRYEQATEAFERTA 91
                                      9***********888765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.035
                            SPOB_a  35 qLgkydkaeeyieevvkelke 55 
                                       +Lg+yd+aee+ +e+ ++ ++
  gi|336252695|ref|YP_004595802.1| 218 ELGEYDEAEEIADEANEMRER 238
                                       89*********9998887665 PP

>> Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00048      0.41      23      72 ..     182     230 ..     179     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00048
                                       HHHTT--HHHHHHHHHHHHHHHSSSS-HHHHHHHHHHHTTTSCCHHHHHH CS
                   Acetyltransf_11  23 LkRrgfseeeikalkkayrllyrsglsleealeeleeeaeespevqelld 72 
                                       L  rg+see+++ + +a rl +r+   lee +  le e+ e +e++e+ d
  gi|336252695|ref|YP_004595802.1| 182 LSERGLSEEALHCIDNAIRLGMRNAQVLEEKAHILE-ELGEYDEAEEIAD 230
                                       788**********************9****998885.6666777777765 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.6    0.0015       1.3      13      45 ..      55      87 ..      49     126 .. 0.84
   2 ?    3.4   0.3      0.11        96      22      58 ..     138     174 ..     123     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                            TPR_20 13 aalaanpddldarldlAlallaagryeeAleqL 45
                                       ++a++  d +  ld+ l +++ +rye+A e++
  gi|336252695|ref|YP_004595802.1| 55 HNVASDEVDAQELLDVGLNYMQINRYEQATEAF 87
                                      56899999********************99876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.11
                            TPR_20  22 ldarldlAlallaagryeeAleqLleilkrdrkwedd 58 
                                         a+ +lA al + g+ ++Ale+  + ++ d  ++++
  gi|336252695|ref|YP_004595802.1| 138 ATAETNLAYALWEFGETAQALEHAERAVEIDERFAEG 174
                                       468889**********************999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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):              21  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1947.04
//
Query:       gi|336252696|ref|YP_004595803.1|  [L=185]
Description: 2'-5' RNA ligase [Halopiger xanaduensis SH-6]
Scores for 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-29  100.5   0.0    1.6e-15   57.0   0.0    2.1  2  LigT_PEase       LigT like Phosphoesterase
    2.3e-20   73.0   0.1    2.6e-20   72.9   0.1    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    1.7e-08   34.6   0.0    2.2e-08   34.3   0.0    1.2  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain
     0.0021   17.6   0.0     0.0026   17.3   0.0    1.1  1  HVSL             Uncharacterised conserved protein


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 !   57.0   0.0   3.7e-19   1.6e-15       1      87 []       7      92 ..       7      92 .. 0.89
   2 !   41.5   0.0   2.5e-14   1.1e-10       7      87 .]      98     176 ..      94     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 3.7e-19
                                      EE-CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHH..HHTSBEEEEEEEEEEEE CS
                        LigT_PEase  1 lgppeeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaei..asgaepfelkvdgvglf 77
                                      +++p+e+ae +a l+ae++    + gl ++ p++ HiTL+flg+v+e+++p+l+++la +  ++g+epfe ++ g+g+f
  gi|336252696|ref|YP_004595803.1|  7 VDLPDELAESVADLQAEFA---DAGGLNVTDPEQAHITLKFLGDVEERRLPDLKQELAAAveDAGVEPFEARFGGLGVF 82
                                      6789999999999999999...66688888************************999986335799************* PP

                                      EECCSCCEEE CS
                        LigT_PEase 78 psrlrprviy 87
                                      ps ++  v++
  gi|336252696|ref|YP_004595803.1| 83 PSLEYISVVW 92
                                      **99999998 PP

  == domain 2  score: 41.5 bits;  conditional E-value: 2.5e-14
                                       HHHHHHHHHHHHHHHHCCTTEEET.SGGGSEEEEEEEEEES.HHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC CS
                        LigT_PEase   7 iaeelarlaaeleralaklglkpv.rpfnpHiTLaflgevd.eekvpellealaeiasgaepfelkvdgvglfpsrl 81 
                                         eelarl++ +e++  ++g+ p+ ++f+pH+TLa+      +e v+el+++ +    +     ++vd+v l +s+l
  gi|336252696|ref|YP_004595803.1|  98 GGEELARLHEAVEDRTTAMGFEPEdHDFTPHVTLARMEHAAgKELVQELVQERDPTIGE-----MRVDEVRLTESTL 169
                                       5689*********************************988899******9999876433.....************* PP

                                       .SCCEEE CS
                        LigT_PEase  82 .rprviy 87 
                                          +++y
  gi|336252696|ref|YP_004595803.1| 170 tDDGPVY 176
                                       *****98 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 !   72.9   0.1   5.9e-24   2.6e-20       2     147 ..      10     166 ..       9     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 5.9e-24
                   2_5_RNA_ligase2   2 ppslaapiealrrslydka....yprwppHitLlypfvededl.adlaellsrlak..etepfevrldgfgvFeh.k 70 
                                       p++la+ +++l++++ d +    +   ++HitL+++++ +e   +dl+++l+++++    epfe+r++g+gvF++ +
  gi|336252696|ref|YP_004595803.1|  10 PDELAESVADLQAEFADAGglnvTDPEQAHITLKFLGDVEERRlPDLKQELAAAVEdaGVEPFEARFGGLGVFPSlE 86 
                                       8899999999997777777666555666********988887779*******99997789**************986 PP

                   2_5_RNA_ligase2  71 ks.vvylsv.sdsealqalraallealpeagdkedsgeftPHlTiaqsadstsaaellekl.aqalpple.fevdev 143
                                          vv+     + e+l +l++a+++   + g   ++++ftPH+T+a+ ++++  +el+++l ++  p++  ++vdev
  gi|336252696|ref|YP_004595803.1|  87 YIsVVWFGTeTGGEELARLHEAVEDRTTAMGFEPEDHDFTPHVTLARMEHAAG-KELVQELvQERDPTIGeMRVDEV 162
                                       66699988899***************9999999999*************7777.66666665777777656****** PP

                   2_5_RNA_ligase2 144 allr 147
                                        l +
  gi|336252696|ref|YP_004595803.1| 163 RLTE 166
                                       9876 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 !   34.3   0.0   4.9e-12   2.2e-08      38     207 .]      33     184 ..       3     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 4.9e-12
                                       --TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS--EEEEEEEEEE.....TTTEEEEEE--SHHHHHH CS
                         AKAP7_NLS  38 ikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkplslrlkGletfnddpakarVlYakveeesneekL 114
                                       ++pe+ H+Tl  l   ++ ++ + k+ L  +   ++da   +p++ r+ Gl++f  +     V++ + e+    e+L
  gi|336252696|ref|YP_004595803.1|  33 TDPEQAHITLKFLGDVEERRLPDLKQELAAA---VEDA-GVEPFEARFGGLGVF-PSLEYISVVWFGTETG--GEEL 102
                                       6789999999888776777777777666555...6666.359************.577779*******965..69** PP

                                       HHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHTT--S--GG.GGGGGTT-EEEEEE--EEEEEESSS CS
                         AKAP7_NLS 115 qeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkkqakskesfdareilkqfkdfefgeekineihLsqles 191
                                        +l++++ ++  + g++ e+   ++++H+Tl+  +++++k+  ++        l q +d   ge ++ e+ L + + 
  gi|336252696|ref|YP_004595803.1| 103 ARLHEAVEDRTTAMGFEPEDH--DFTPHVTLARMEHAAGKELVQE--------LVQERDPTIGEMRVDEVRLTESTL 169
                                       ************999987765..48****************9888........677899999999999999999999 PP

                                       ---TTS--EEEEEEE- CS
                         AKAP7_NLS 192 ddesdgyYkviasvkl 207
                                       +d+    Y++++s++l
  gi|336252696|ref|YP_004595803.1| 170 TDD-GPVYSTVESFPL 184
                                       999.999999999886 PP

>> HVSL  Uncharacterised conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.7e-07    0.0026      82     206 ..      31     153 ..       5     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.7e-07
                              HVSL  82 dlgaplplHiSLSrplvlrthqkdsfldslkkelkssakrrFevsfsglkwvsndektRsFlvlrvkspendeLkkl 158
                                       +++ p++ Hi+L     +++    ++ ++l ++++ +++++Fe +f gl ++++ e   +  v+  ++++ +eL +l
  gi|336252696|ref|YP_004595803.1|  31 NVTDPEQAHITLKFLGDVEERRLPDLKQELAAAVEDAGVEPFEARFGGLGVFPSLEYISV--VWFGTETGGEELARL 105
                                       56677788888887777788888899999******99******************98775..3434677789***** PP

                              HVSL 159 leavnkvleefglpplykdeaFHiSiawslgepseeekeellseleka 206
                                        eav++  + +g +p   d  +H+ +a + +   +e+ +el +e + +
  gi|336252696|ref|YP_004595803.1| 106 HEAVEDRTTAMGFEPEDHDFTPHVTLARMEHAAGKELVQELVQERDPT 153
                                       *****************************9998888888887776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1350.62
//
Query:       gi|336252697|ref|YP_004595804.1|  [L=76]
Description: membrane protein [Halopiger xanaduensis SH-6]
Scores for complete 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   31.2   5.1    1.5e-07   31.2   5.1    2.2  2  PLDc_N           Phospholipase_D-nuclease N-terminal
  ------ inclusion threshold ------
       0.57   10.1   5.7        1.2    9.1   5.6    1.5  1  Wzy_C_2          Virulence factor membrane-bound polymerase, 
        1.1    9.3  10.0        1.7    8.7  10.0    1.2  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        1.3    9.2   9.8       0.95    9.6   1.2    2.4  2  CcmD             Heme exporter protein D (CcmD)
        4.7    5.9   5.1        5.5    5.6   5.1    1.1  1  DUF2207          Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   2.2      0.25   8.8e+02      27      40 ..       5      18 ..       3      19 .. 0.77
   2 !   31.2   5.1   4.1e-11   1.5e-07       4      42 .]      26      67 ..      17      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.25
                            PLDc_N 27 lflPvlGailYllf 40
                                      ++   +Ga+++l+f
  gi|336252697|ref|YP_004595804.1|  5 IIAAGFGAFAFLIF 18
                                      445569******99 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 4.1e-11
                            PLDc_N  4 iialidiird...rnpss.klaWllvilflPvlGailYllfGr 42
                                      + ++++ + d   +++    ++W++v++f P+lG++lY l+Gr
  gi|336252697|ref|YP_004595804.1| 26 LGMVVWTYSDaqrNST-HpAFLWAVVVFFAPLLGLVLYVLLGR 67
                                      4556666666653333.36***********************9 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   5.6   0.00033       1.2      21      75 ..      14      69 ..      10      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00033
                           Wzy_C_2 21 wYspfllaaflvl.glldsksrsrrlrlrpklvlrvvalvlallglalllsilhdy 75
                                      +++ f +++++ l +++++ s ++r + +p+++  vv++ ++llgl+l++ + +d 
  gi|336252697|ref|YP_004595804.1| 14 AFLIFAVLMAVYLgMVVWTYSDAQRNSTHPAFLWAVVVFFAPLLGLVLYVLLGRDA 69
                                      45556666666665556668899999999********************9999985 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 ?    8.7  10.0   0.00047       1.7      37      88 ..       7      67 ..       3      73 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00047
                   Phage_holin_3_6 37 agllgaagvlallalllllvalalal.a.a.......lwlaalivaavllvlagvlalvgl 88
                                      a+ +ga ++l +  l+++ ++++++  + a       + l+a++v+ + l+  ++ +l+g+
  gi|336252697|ref|YP_004595804.1|  7 AAGFGAFAFLIFAVLMAVYLGMVVWTySdAqrnsthpAFLWAVVVFFAPLLGLVLYVLLGR 67
                                      3333333333333333333333333342234555678888888888777777777777776 PP

>> CcmD  Heme exporter protein D (CcmD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.9     0.013        47      10      30 ..      14      34 ..       8      39 .. 0.72
   2 ?    9.6   1.2   0.00027      0.95      10      31 ..      48      69 ..      41      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.013
                              CcmD 10 sYgitllvlagLilwslrdrr 30
                                      ++ i+++++a+ + ++++ + 
  gi|336252697|ref|YP_004595804.1| 14 AFLIFAVLMAVYLGMVVWTYS 34
                                      777888888877777777655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00027
                              CcmD 10 sYgitllvlagLilwslrdrrr 31
                                      ++ ++++ l+gL+l++l+ r +
  gi|336252697|ref|YP_004595804.1| 48 AVVVFFAPLLGLVLYVLLGRDA 69
                                      7899*************99976 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   5.1    0.0015       5.5     386     430 ..       8      65 ..       2      74 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0015
                           DUF2207 386 lglgliilgl.ilillallllvll...............lvfllilllillliaiivlllf 430
                                       +g+g++ +++ ++++++ l+   +                +++++++++ +l+++++++l+
  gi|336252697|ref|YP_004595804.1|   8 AGFGAFAFLIfAVLMAVYLG---MvvwtysdaqrnsthpAFLWAVVVFFAPLLGLVLYVLL 65 
                                       22222222220222223333...14459999999998886666666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1139  (0.0635284); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 567.41
//
Query:       gi|336252698|ref|YP_004595805.1|  [L=346]
Description: hypothetical protein Halxa_1293 [Halopiger xanaduensis SH-6]
Scores for 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  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2701.46
//
Query:       gi|336252699|ref|YP_004595806.1|  [L=50]
Description: 50S ribosomal protein L39e [Halopiger xanaduensis SH-6]
Scores for complete 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-20   72.9   7.1    1.3e-20   72.7   7.1    1.1  1  Ribosomal_L39  Ribosomal L39 protein


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 !   72.7   7.1   7.3e-25   1.3e-20       1      40 [.       8      47 ..       8      49 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 7.3e-25
                     Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtk 40
                                      kK+rLaK  +qN++vPaWv++ktd +v++npkrR+WRr++
  gi|336252699|ref|YP_004595806.1|  8 KKKRLAKLENQNSRVPAWVMMKTDMEVQRNPKRRNWRRSD 47
                                      7*************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 400.22
//
Query:       gi|336252700|ref|YP_004595807.1|  [L=92]
Description: 50S ribosomal protein L31e [Halopiger xanaduensis SH-6]
Scores for 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   0.1    3.8e-08   33.5   0.1    1.1  1  Ribosomal_L31e  Ribosomal protein L31e
  ------ inclusion threshold ------
       0.16   12.3   0.0         14    6.1   0.0    2.2  2  Rap1a           Rap1a immunity proteins


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 !   33.5   0.1   4.2e-12   3.8e-08      13      78 ..      16      83 ..       8      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 4.2e-12
                    Ribosomal_L31e 13 krihgvgfkkraprAlkeikkfamkemg.tpdv.ridtrLnkavwakgirnvpyrirvrlsrkrnedE 78
                                      + +++   ++ a  A++ +++  +k++   +d  r+d+++n++vw++g  n+p+++rvr +r +++ E
  gi|336252700|ref|YP_004595807.1| 16 RDVKKGANHEAADLAMRLVREHLAKHFAvDEDAiRLDPSINETVWENGRSNPPRKLRVRAARFEEDGE 83
                                      66788888899999*************9444558**************************99777665 PP

>> Rap1a  Rap1a immunity proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0    0.0061        54      40      64 ..      19      43 ..       3      44 .. 0.77
   2 ?    6.1   0.0    0.0015        14      30      53 ..      54      77 ..      49      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0061
                             Rap1a 40 kklpaerlkerAaslvveaLaeafP 64
                                      kk  + + +  A  lv e La++f+
  gi|336252700|ref|YP_004595807.1| 19 KKGANHEAADLAMRLVREHLAKHFA 43
                                      455556677789999*******996 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0015
                             Rap1a 30 elreivyeylkklpaerlkerAas 53
                                      +++e+v e  ++ p+++l  rAa 
  gi|336252700|ref|YP_004595807.1| 54 SINETVWENGRSNPPRKLRVRAAR 77
                                      79********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 760.73
//
Query:       gi|336252701|ref|YP_004595808.1|  [L=221]
Description: translation initiation factor 6 [Halopiger xanaduensis SH-6]
Scores for 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-75  250.6   0.3    9.4e-75  250.3   0.3    1.1  1  eIF-6     eIF-6 family


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 !  250.3   0.3   5.3e-79   9.4e-75       1     197 []       3     199 ..       3     199 .. 0.99

  Alignments for each domain:
  == domain 1  score: 250.3 bits;  conditional E-value: 5.3e-79
                                       .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHH CS
                             eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeele 77 
                                       rl+++gs ++Gvfar+t++++lv+++v++++v+ +++eL+v+++ett++gs++vG+l++gN+ngllv+s+v + e e
  gi|336252701|ref|YP_004595808.1|   3 RLAFAGSAYVGVFARATDSCVLVRQDVDDDVVADLSDELEVPAIETTVGGSSTVGALATGNENGLLVSSRVLEYERE 79 
                                       6899************************************************************************* PP

                                       HHHHHHH---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE CS
                             eIF-6  78 klkeslkleverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllv 154
                                       +l+e++++++++l+ +++A+GNv+laND++A+vhpdl++e+++ii+d+L+v+v+rg++ag++tvG+aav+tn+g+l+
  gi|336252701|ref|YP_004595808.1|  80 RLEEAVDVPIAELPGNVNAAGNVVLANDYGAYVHPDLTREAIQIIEDTLEVPVERGDLAGVRTVGTAAVATNTGVLC 156
                                       ***************************************************************************** PP

                                       -TT--HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                             eIF-6 155 hpkateeeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                       hpkat+eel++lee l+v++++gTvN+G +lvgsgl+aN+ g+
  gi|336252701|ref|YP_004595808.1| 157 HPKATDEELDFLEEALDVRADVGTVNYGAPLVGSGLIANEAGY 199
                                       ***************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1663.83
//
Query:       gi|336252702|ref|YP_004595809.1|  [L=112]
Description: hypothetical protein Halxa_1297 [Halopiger xanaduensis SH-6]
Scores for 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  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); 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:                         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 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 890.19
//
Query:       gi|336252703|ref|YP_004595810.1|  [L=103]
Description: hypothetical protein Halxa_1298 [Halopiger xanaduensis SH-6]
Scores for 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   19.2   0.1     0.0023   18.5   0.1    1.3  1  ASCH      ASCH domain


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   1.3e-07    0.0023      50     105 ..      47     102 ..      45     103 .] 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-07
                                       EEEEEEEEEHHHHHHHHHCHCC--.-HCHHHHHHHCC...HHHHHCCEEEEEEEEEEEEE CS
                              ASCH  50 vevtkvevkpfeevteehalkege.sleewrevheef...yeeeseeyedelvvveefel 105
                                       +evt v+ +++ ++t+e+a +eg+ +le  r+ +e+    +e+     +d +vv+ +fe+
  gi|336252703|ref|YP_004595810.1|  47 FEVTTVTERTLGDLTDEDARAEGMdDLETYRRMLERVhddFEWD----DDSEVVLHQFEK 102
                                       689**********************9999998888885556665....699999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 768.29
//
Query:       gi|336252704|ref|YP_004595811.1|  [L=63]
Description: ribosomal LX protein [Halopiger xanaduensis SH-6]
Scores for complete 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   38.3   0.0    1.3e-09   38.2   0.0    1.1  1  Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
  ------ inclusion threshold ------
      0.033   14.3   0.2      0.042   13.9   0.2    1.2  1  YhzD            YhzD-like protein


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 !   38.2   0.0   1.5e-13   1.3e-09      68     120 ..       3      55 ..       1      56 [. 0.96

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.5e-13
                                       ...........TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEE CS
                    Ribosomal_L18A  68 nygiwlrydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekv 120
                                        +++  r+++r+g  +f   +++ +e+ a e +Y+elgs+h++kr++I+ e v
  gi|336252704|ref|YP_004595811.1|   3 QFTVTGRFQTRDGFAEFETTIEAENENVAREHAYAELGSQHNLKRTQIELEDV 55 
                                       689999*******************************************9988 PP

>> YhzD  YhzD-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   4.7e-06     0.042       1      46 [.       1      48 [.       1      50 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-06
                              YhzD  1 MetYflTv.Fd.ksGeklLdetfeAadDeeAkekGekkLkekgleekt 46
                                      M+++++T  F+ ++G   +++t+eA++++ A+e++ + L  +   ++t
  gi|336252704|ref|YP_004595811.1|  1 MSQFTVTGrFQtRDGFAEFETTIEAENENVAREHAYAELGSQHNLKRT 48
                                      7777777656525788889********************988888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 518.98
//
Query:       gi|336252705|ref|YP_004595812.1|  [L=150]
Description: Prefoldin subunit alpha [Halopiger xanaduensis SH-6]
Scores for complete 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-26   92.5  10.4    1.7e-26   92.5  10.4    2.0  2  Prefoldin        Prefoldin subunit
    3.3e-07   30.6  28.1    0.00059   20.2   6.2    2.2  2  ZapB             Cell division protein ZapB
      7e-07   29.2  27.0    0.00046   20.1   7.1    2.6  2  Prefoldin_2      Prefoldin subunit
      3e-05   23.1  23.1     0.0014   17.5   7.5    2.1  2  Spc7             Spc7 kinetochore protein
    5.5e-05   23.4  16.4     0.0037   17.5   1.1    2.2  2  Spc24            Spc24 subunit of Ndc80
    6.9e-05   23.2  21.1     0.0043   17.5   5.7    2.5  2  NPV_P10          Nucleopolyhedrovirus P10 protein
    9.9e-05   22.9  30.2      0.019   15.5  10.9    2.1  2  APG6_N           Apg6 coiled-coil region
    0.00015   21.8  15.3      0.016   15.1   1.3    2.1  2  Ax_dynein_light  Axonemal dynein light chain
    0.00024   21.3   4.8    0.00024   21.3   4.8    3.3  2  TSC22            TSC-22/dip/bun family
    0.00032   20.1  18.7      0.023   14.0   6.0    2.1  2  GAS              Growth-arrest specific micro-tubule binding
    0.00035   21.2  16.0      0.024   15.2   1.9    2.2  2  YabA             Initiation control protein YabA
    0.00054   20.1  16.5     0.0065   16.6   5.7    2.1  2  DUF4337          Domain of unknown function (DUF4337)
    0.00068   19.1  16.4      0.054   12.9   2.8    2.1  2  DUF4618          Domain of unknown function (DUF4618)
    0.00079   19.1   1.0       0.72    9.6   0.0    2.2  2  DUF3287          Protein of unknown function (DUF3287)
     0.0008   19.4  14.9       0.04   14.0   3.1    2.3  2  DUF1664          Protein of unknown function (DUF1664)
    0.00088   19.3  21.6      0.067   13.2   6.2    2.2  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.001   18.5  24.5      0.017   14.4   8.4    2.1  2  DUF3450          Protein of unknown function (DUF3450)
     0.0011   19.5  32.9       0.27   11.9  15.2    3.1  3  SlyX             SlyX
     0.0018   18.6  22.5      0.012   15.9   5.8    2.5  2  DUF5082          Domain of unknown function (DUF5082)
     0.0018   17.6   9.0     0.0021   17.4   9.0    1.1  1  MIS13            Mis12-Mtw1 protein family
     0.0019   17.8  16.7      0.094   12.2   4.9    2.1  2  LRRFIP           LRRFIP family
     0.0019   17.8  15.0       0.12   11.9   3.0    2.2  2  DUF4795          Domain of unknown function (DUF4795)
     0.0024   18.1  21.4     0.0072   16.6   6.5    2.1  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
     0.0025   18.1  24.2      0.085   13.2   9.0    2.7  2  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0027   16.7  24.0      0.082   11.8   9.7    2.0  2  DUF812           Protein of unknown function (DUF812)
     0.0028   17.6  12.8      0.092   12.6   5.4    2.2  2  DASH_Spc19       Spc19
     0.0028   17.4  15.0      0.033   13.9   2.8    2.1  2  DUF4201          Domain of unknown function (DUF4201)
     0.0031   17.0  25.2     0.0067   15.9  10.6    2.1  2  DUF4349          Domain of unknown function (DUF4349)
     0.0032   17.5  12.5       0.11   12.5   3.3    2.2  2  Laminin_II       Laminin Domain II
     0.0032   17.6  22.8      0.022   14.9   6.8    2.2  2  Tropomyosin_1    Tropomyosin like
     0.0039   16.9  16.3       0.01   15.6   4.1    2.3  2  Synaptobrevin    Synaptobrevin
     0.0044   16.6  29.0      0.037   13.6  10.6    2.1  2  MscS_porin       Mechanosensitive ion channel porin domain
     0.0048   16.7  20.6     0.0059   16.4   3.7    2.3  2  SKA2             Spindle and kinetochore-associated protein 2
     0.0052   16.7  17.5      0.071   13.0   5.6    2.2  2  Sec34            Sec34-like family
     0.0053   17.1  18.2       0.66   10.4   5.9    3.7  3  FlaC_arch        Flagella accessory protein C (FlaC)
     0.0055   16.1  20.0      0.055   12.8  19.7    1.9  1  DUF4407          Domain of unknown function (DUF4407)
     0.0055   16.9  16.2      0.086   13.0   1.4    2.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
     0.0073   16.5  11.4      0.021   15.0  11.4    2.0  1  Uds1             Up-regulated During Septation
     0.0077   14.9  19.7      0.061   12.0   5.7    2.0  2  AAA_13           AAA domain
     0.0077   16.5  19.7       0.16   12.2   6.7    2.1  2  ATG16            Autophagy protein 16 (ATG16)
     0.0081   16.6   5.7     0.0081   16.6   5.7    2.1  2  GPS2_interact    G-protein pathway suppressor 2-interacting d
     0.0083   14.9  18.4       0.02   13.6   3.2    2.2  2  Tektin           Tektin family
     0.0084   15.9   9.9      0.082   12.7   1.1    3.2  2  DASH_Dam1        DASH complex subunit Dam1
     0.0093   15.6  19.3        0.2   11.2   6.1    2.1  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
  ------ inclusion threshold ------
      0.011   16.0   4.2      0.019   15.2   4.2    1.5  1  Nmad5            Nucleotide modification associated domain 5
      0.011   15.8   8.6       0.13   12.3   1.1    2.9  2  Vps51            Vps51/Vps67
      0.012   16.0  16.6       0.32   11.3   4.5    2.1  2  Muted            Organelle biogenesis, Muted-like protein
      0.012   15.0  15.2      0.076   12.4   3.9    2.1  2  Not3             Not1 N-terminal domain, CCR4-Not complex com
      0.013   15.5  27.2      0.086   12.9   9.3    2.2  2  DHR10            Designed helical repeat protein 10 domain
      0.019   14.6  15.7       0.36   10.4   3.6    2.1  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
       0.02   15.0   4.8       0.02   15.0   4.8    2.2  2  GCN5L1           GCN5-like protein 1 (GCN5L1)
      0.022   14.9  13.3      0.027   14.6   1.6    2.2  2  Cob_adeno_trans  Cobalamin adenosyltransferase
      0.023   14.4  15.1      0.037   13.7   3.0    2.1  2  Syntaxin         Syntaxin
      0.023   14.8  19.4       0.24   11.5   5.4    2.1  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
      0.024   14.4  30.5      0.027   14.2   9.5    3.2  3  DivIC            Septum formation initiator
      0.026   14.6   3.9      0.026   14.6   3.9    2.7  2  SAS4             Something about silencing, SAS, complex subu
      0.033   13.9  13.7       0.16   11.7   2.0    2.1  2  SHE3             SWI5-dependent HO expression protein 3
      0.035   14.2  24.0      0.032   14.3   7.8    2.1  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
      0.035   14.2  10.8      0.035   14.2  10.8    3.2  1  TolA_bind_tri    TolA binding protein trimerisation
      0.037   13.7  10.0       0.47   10.1   1.1    2.4  2  DUF4988          Domain of unknown function
      0.038   13.8  17.6      0.086   12.7   2.9    3.1  2  CdvA             CdvA-like coiled-coil domain
      0.039   13.6   6.9       0.92    9.2   0.7    2.4  2  RPW8             Arabidopsis broad-spectrum mildew resistance
      0.047   13.7  18.0       0.34   11.0   5.3    2.4  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.047   12.3  16.3       0.12   11.0   3.5    2.0  2  FapA             Flagellar Assembly Protein A
      0.047   12.6  19.1      0.061   12.3   6.5    2.1  2  IFT57            Intra-flagellar transport protein 57
      0.049   13.1   5.7        0.9    9.0   0.4    2.0  2  Allexi_40kDa     Allexivirus 40kDa protein
      0.049   14.0   3.0        2.4    8.6   0.5    2.4  2  MtrB             Tetrahydromethanopterin S-methyltransferase 
       0.05   13.8   2.7       0.05   13.8   2.7    2.8  2  XhlA             Haemolysin XhlA
      0.059   11.4   6.5      0.072   11.1   6.5    1.1  1  PRTP             Herpesvirus processing and transport protein
      0.066   11.1  15.5       0.13   10.2   3.5    2.0  2  V_ATPase_I       V-type ATPase 116kDa subunit family
      0.068   12.6  17.6       0.35   10.3   3.2    2.2  2  HBM              Helical bimodular sensor domain
      0.069   11.8  11.8       0.22   10.2   1.5    2.1  2  Dor1             Dor1-like family
      0.071   13.4  11.8       0.12   12.7   2.7    2.5  2  kleA_kleC        Uncharacterized KorC regulated protein A
      0.076   12.3  18.2       0.25   10.6   3.9    2.0  2  Dynamitin        Dynamitin
      0.098   13.5  12.5      0.074   13.9   4.3    2.1  2  Cytochrom_C_2    Cytochrome C'
        0.1   12.4  26.7      0.084   12.7   9.3    2.1  2  ERM              Ezrin/radixin/moesin family
       0.12   10.8  20.5      0.054   11.8   5.4    2.0  2  MAD              Mitotic checkpoint protein
       0.12   12.2  23.4        0.1   12.4   4.5    2.3  2  DUF4515          Domain of unknown function (DUF4515)
       0.12   11.8  24.8        0.1   12.1   9.6    2.0  2  Golgin_A5        Golgin subfamily A member 5
       0.12   12.4  15.2       0.84    9.7   2.9    2.1  2  MCU              Mitochondrial calcium uniporter
       0.13   11.0  17.6       0.32    9.7   5.2    2.1  2  FbpA             Fibronectin-binding protein A N-terminus (Fb
       0.15   11.9   9.4       0.86    9.4   1.7    2.2  2  DUF1465          Protein of unknown function (DUF1465)
       0.15   12.2  15.1       0.33   11.0   3.7    2.4  2  ORF6C            ORF6C domain
       0.15   12.8  15.2       0.84   10.4   1.9    2.5  2  Occludin_ELL     Occludin homology domain
       0.15   12.5  19.9        1.1    9.7   3.5    2.1  2  T3SSipB          Type III cell invasion protein SipB
       0.16   11.0  12.7       0.56    9.2   3.2    2.0  2  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.17   11.5   2.0       0.22   11.1   2.0    1.1  1  Cas_DxTHG        CRISPR-associated (Cas) DxTHG family
       0.17   11.9  18.9        0.5   10.4   7.6    2.2  2  Sipho_Gp157      Siphovirus Gp157
       0.17   11.6  21.8       0.47   10.1   6.5    2.3  2  YkyA             Putative cell-wall binding lipoprotein
       0.17   12.3  21.8        1.5    9.3   6.7    2.5  2  DUF4200          Domain of unknown function (DUF4200)
       0.17   12.0   6.2        5.8    7.0   1.7    2.5  2  TFR_dimer        Transferrin receptor-like dimerisation domai
       0.18   11.9  28.0        1.7    8.7   9.1    2.5  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.18   11.9  20.2       0.51   10.4   6.1    2.2  2  ADIP             Afadin- and alpha -actinin-Binding
       0.19   11.1  16.6       0.32   10.4   4.5    2.1  2  Cluap1           Clusterin-associated protein-1
       0.19   11.5  19.2       0.43   10.3   4.8    2.1  2  TACC_C           Transforming acidic coiled-coil-containing p
        0.2    9.8  15.4       0.34    9.1   4.2    2.0  2  COG6             Conserved oligomeric complex COG6
       0.21   10.9  17.0       0.48    9.7  17.0    1.5  1  DUF2353          Uncharacterized coiled-coil protein (DUF2353
       0.23   11.8  24.9       0.99    9.8   8.2    3.0  2  Csm1_N           Csm1 N-terminal domain
       0.23   11.7  29.2      0.075   13.3   8.2    2.3  2  FliJ             Flagellar FliJ protein
       0.24   11.3  10.9       0.18   11.7   3.2    2.2  2  Sec8_exocyst     Sec8 exocyst complex component specific doma
       0.25   11.3  15.9        0.2   11.6   4.9    2.3  2  AAA_lid_9        AAA lid domain
       0.25   10.4  17.3       0.13   11.4   5.2    2.0  2  Tmemb_cc2        Predicted transmembrane and coiled-coil 2 pr
       0.27   11.6  28.6       0.88    9.9  11.1    2.4  2  YlqD             YlqD protein
       0.27   11.4  17.4       0.54   10.5   3.9    2.6  2  JIP_LZII         JNK-interacting protein  leucine zipper II
       0.28   11.3  10.1          2    8.5   2.2    2.4  2  DUF2730          Protein of unknown function (DUF2730)
       0.28   11.7  23.3      0.063   13.8   4.5    2.1  2  AAA_23           AAA domain
       0.28   10.6   3.8       0.17   11.3   0.1    2.0  2  Med14            Mediator complex subunit MED14
       0.29   11.2  15.5      0.087   12.9   3.7    2.3  2  TLE_N            Groucho/TLE N-terminal Q-rich domain
        0.3   11.4  20.9       0.26   11.6   4.3    2.7  2  THOC7            Tho complex subunit 7
        0.3   11.3  19.0       0.37   11.1   3.9    2.5  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.31   11.3  15.3       0.64   10.3   3.2    2.5  2  DUF948           Bacterial protein of unknown function (DUF94
       0.31   11.1  21.5       0.52   10.4   6.3    2.2  2  DivIVA           DivIVA protein
       0.33   10.3  17.0       0.29   10.5   7.9    2.4  2  FliD_C           Flagellar hook-associated protein 2 C-termin
       0.34   11.1  24.8       0.45   10.7   7.1    2.3  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
       0.35   11.4  22.1       0.93   10.0   6.9    2.3  2  Spectrin         Spectrin repeat
        0.4    8.8  21.2       0.87    7.7   5.6    2.1  2  EzrA             Septation ring formation regulator, EzrA
       0.44   10.7  14.4        1.9    8.6   2.7    2.3  2  End3             Actin cytoskeleton-regulatory complex protei
       0.47    9.3   5.6       0.59    9.0   5.6    1.1  1  LMBR1            LMBR1-like membrane protein
       0.51    9.4  19.0        1.6    7.8   7.1    2.1  2  RmuC             RmuC family
       0.56   10.8   8.2    2.1e+02    2.5   8.2    2.5  1  Hemerythrin      Hemerythrin HHE cation binding domain
       0.56    8.3  26.9    1.2e+02    0.6  26.9    2.0  1  HOOK             HOOK protein
       0.57   10.0  27.4        2.8    7.8  12.4    2.7  3  Phage_GP20       Phage minor structural protein GP20
        0.6    9.2  11.5       0.86    8.6   2.5    2.1  2  FH2              Formin Homology 2 Domain
       0.66   10.7   6.2        6.3    7.5   0.7    2.1  2  Plk4_PB2         Polo-like Kinase 4 Polo Box 2
       0.66    9.2   9.4       0.56    9.4   2.2    2.0  2  ISG65-75         Invariant surface glycoprotein
       0.68    9.7  14.7        2.2    8.1   4.7    2.1  2  SKA1             Spindle and kinetochore-associated protein 1
        0.7    9.5  21.1        2.5    7.8   8.2    2.2  2  GrpE             GrpE
        0.7   10.1   9.7          6    7.1   0.4    2.3  2  Acyl-CoA_dh_C    Acetyl-CoA dehydrogenase C-terminal like
       0.74    9.8  44.6        0.6   10.1  14.7    2.8  2  FlxA             FlxA-like protein
       0.77    9.8  15.9        1.2    9.2   2.0    2.2  2  T2SSM            Type II secretion system (T2SS), protein M
       0.84    8.9  31.0        1.1    8.5  11.3    2.1  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.89    8.8  21.3       0.58    9.4   4.1    2.1  2  DUF4763          Domain of unknown function (DUF4763)
        0.9    7.4  14.0          1    7.2   3.2    1.8  2  Prominin         Prominin
       0.97    9.3  23.5       0.36   10.7   9.2    2.3  2  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
       0.97    9.4  14.0        2.9    7.8   2.1    2.2  2  DUF4446          Protein of unknown function (DUF4446)
          1    9.8  10.6        2.3    8.7   0.6    2.6  2  NBD94            Nucleotide-Binding Domain 94 of RH
        1.1    8.8  14.9        1.2    8.7   2.7    2.2  2  Fzo_mitofusin    fzo-like conserved region
        1.1    8.8  14.3        9.9    5.6  14.3    2.0  1  Vps5             Vps5 C terminal like
        1.1    9.7  21.8        0.5   10.8   7.1    2.4  2  CC2-LZ           Leucine zipper of domain CC2 of NEMO, NF-kap
        1.1    9.9  12.4       0.55   10.9   0.3    3.0  3  GTP-bdg_M        GTP-binding GTPase Middle Region
        1.2    9.2  19.9       0.36   10.9   5.3    2.2  2  COG2             COG (conserved oligomeric Golgi) complex com
        1.2    8.9   9.0        4.8    7.0   1.7    2.0  2  Spc29            Spindle Pole Component 29
        1.2    8.8  15.2        2.2    8.0   4.1    2.1  2  DUF932           Domain of unknown function (DUF932)
        1.3    8.9   9.5        1.7    8.5   1.8    2.2  2  Cauli_AT         Aphid transmission protein
        1.4    7.4   9.3        1.9    6.9   9.3    1.2  1  FUSC             Fusaric acid resistance protein family
        1.5    9.0  21.7       0.65   10.2   5.2    2.2  2  CENP-Q           CENP-Q, a CENPA-CAD centromere complex subun
        1.5    9.4  22.6        3.8    8.1   8.5    2.4  2  bZIP_Maf         bZIP Maf transcription factor
        1.6    9.0  30.8        7.3    6.9   9.6    4.3  4  Osmo_CC          Osmosensory transporter coiled coil
        1.6    8.9  11.2        1.4    9.1   0.5    2.1  2  SPT16            FACT complex subunit (SPT16/CDC68)
        1.7    8.5  12.1       0.95    9.3   2.6    2.1  2  Mt_ATP-synt_D    ATP synthase D chain, mitochondrial (ATP5H)
        1.8    8.7  18.4        1.3    9.1   0.4    3.4  3  bZIP_1           bZIP transcription factor
          2    8.9   8.0        8.4    6.9   2.1    2.3  2  L31              Mitochondrial ribosomal protein L31
        2.1    9.3  20.0        1.4    9.9   4.0    2.3  2  PRKG1_interact   cGMP-dependent protein kinase interacting do
        2.3    8.6  24.4        6.7    7.2   9.8    2.2  2  CENP-H           Centromere protein H (CENP-H)
        2.3    7.8  30.0        2.4    7.7  10.2    2.3  2  DUF2968          Protein of unknown function (DUF2968)
        2.4    8.8  13.6       0.34   11.5   1.8    2.6  2  Sas10_Utp3       Sas10/Utp3/C1D family
        2.5    7.5  24.7       0.46    9.9   9.3    2.1  2  DUF3552          Domain of unknown function (DUF3552)
        2.7    6.5   9.4       0.17   10.5   3.3    1.8  1  DUF3138          Protein of unknown function (DUF3138)
        2.7    7.8  11.3       0.52   10.1   0.6    2.2  2  USP8_interact    USP8 interacting
        2.7    6.8  12.5       0.65    8.9   1.7    2.1  2  Vps53_N          Vps53-like, N-terminal
        2.8    7.5  28.1        4.2    6.9   7.2    2.3  2  PspA_IM30        PspA/IM30 family
        2.8    7.1  11.9        1.2    8.3   2.1    2.0  2  Tho2             Transcription factor/nuclear export subunit 
        2.8    8.4  25.6         13    6.3   9.6    3.2  2  DUF4140          N-terminal domain of unknown function (DUF41
        2.9    7.8   8.2        8.4    6.3   0.5    2.8  2  MtrG             Tetrahydromethanopterin S-methyltransferase,
        2.9    8.2  13.5        5.2    7.4   3.9    2.3  2  DUF641           Plant protein of unknown function (DUF641)
        2.9    7.7  20.8        4.8    7.0   8.4    2.2  2  DUF724           Protein of unknown function (DUF724)
        2.9    7.6  15.2        4.8    6.9   4.3    2.1  2  zf-CpG_bind_C    CpG binding protein zinc finger C terminal d
          3    7.0  16.4        0.6    9.3   1.7    2.0  2  TMPIT            TMPIT-like protein
          3    7.1  18.0        9.4    5.5  17.7    1.8  1  CASP_C           CASP C terminal
        3.1    7.7  15.8        3.4    7.6   4.4    2.1  2  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
        3.3    8.1  26.0       0.12   12.7   4.8    3.8  4  HalX             HalX domain
        3.7    7.7  17.4        1.9    8.6   3.7    2.9  2  DUF1192          Protein of unknown function (DUF1192)
        3.7    6.3  19.0          3    6.6   3.9    2.0  2  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
        3.7    7.4  19.8        2.6    7.9   7.0    2.2  2  Nsp1_C           Nsp1-like C-terminal region
        3.8    6.6  15.9        3.5    6.7   4.8    2.1  2  DLP_helical      Dynamin-like helical domain
        3.9    8.1  16.2       0.94   10.1   2.0    2.7  2  Syntaxin-6_N     Syntaxin 6, N-terminal
        3.9    7.5  11.6        1.1    9.3   2.3    2.3  2  DUF1515          Protein of unknown function (DUF1515)
          4    7.6  22.0        1.8    8.7   4.8    2.3  2  Med9             RNA polymerase II transcription mediator com
        4.1    7.5  16.2       0.42   10.7   3.5    2.3  2  MRP-L28          Mitochondrial ribosomal protein L28
        4.2    7.4  14.1       0.44   10.5   3.1    2.4  2  Med10            Transcription factor subunit Med10 of Mediat
        4.2    7.9  20.9        6.4    7.3   6.9    2.4  2  UPF0449          Uncharacterised protein family UPF0449
        4.5    5.8   6.8        1.6    7.3   0.4    2.0  2  Tweety           Tweety
        4.5    7.3   9.1        4.7    7.3   1.4    2.3  2  FAD-SLDH         Membrane bound FAD containing D-sorbitol deh
        4.6    7.3  19.2        6.7    6.8   3.9    2.2  2  Nup54            Nucleoporin complex subunit 54
        4.9    5.4   8.0        3.6    5.9   0.4    2.0  2  Hemagglutinin    Haemagglutinin
          5    7.8  33.3        1.6    9.4  10.7    3.0  2  KfrA_N           Plasmid replication region DNA-binding N-ter
        5.2    7.8  13.1        2.2    8.9   1.4    2.6  2  DUF4665          Domain of unknown function (DUF4665)
        5.3    7.8  17.3        3.8    8.3   3.8    2.4  2  DUF2203          Uncharacterized conserved protein (DUF2203)
        5.4    7.2  12.9         11    6.2   1.0    2.5  2  PHM7_cyt         Cytosolic domain of 10TM putative phosphate 
        5.6    7.5  22.6        3.3    8.2   5.4    3.0  3  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
        5.8    7.4  26.4       0.54   10.7   5.6    2.9  2  LPP              Lipoprotein leucine-zipper
        6.6    7.0  24.2        6.6    7.1   4.0    3.3  3  WXG100           Proteins of 100 residues with WXG
        6.6    6.0  18.2      2e+02    1.1  18.2    2.2  1  CorA             CorA-like Mg2+ transporter protein
        6.8    7.2  27.3        6.1    7.4   6.8    2.2  2  DUF16            Protein of unknown function DUF16
        6.8    7.6  27.2        6.8    7.6   8.1    2.7  2  Rho_Binding      Rho Binding
        7.3    6.7  25.7        7.4    6.6   6.6    2.9  3  DUF2205          Short coiled-coil protein
        7.4    5.2  10.5       0.46    9.2   1.3    2.0  2  Vps52            Vps52 / Sac2 family
        7.6    6.2  13.6        2.8    7.6   5.6    2.1  2  CCDC106          Coiled-coil domain-containing protein 106
        7.7    6.7  24.7        1.2    9.3   6.9    2.4  2  BRE1             BRE1 E3 ubiquitin ligase
        7.8    6.7  24.2        2.6    8.2   6.4    3.1  3  Swi5             Swi5
        8.2    5.7  11.0        7.5    5.8   1.8    2.1  2  FAM76            FAM76 protein
        9.7    6.7  20.2        4.9    7.7   6.8    2.5  2  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
        9.8    6.4   7.4         19    5.5   2.2    2.1  2  Pro_CA           Carbonic anhydrase


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 !   12.7   3.6     0.001      0.09      90     120 .]       3      33 ..       2      33 .. 0.92
   2 !   92.5  10.4   1.9e-28   1.7e-26       1     120 []      16     132 ..      16     132 .. 0.99

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  90 ekqlekleeeleklkdqittleanlaqlyqk 120
                                       ++ql++l +el+++++qi+ l+an+++l+q+
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQE 33 
                                       68999********************999985 PP

  == domain 2  score: 92.5 bits;  conditional E-value: 1.9e-28
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHH CS
                         Prefoldin   1 lkeeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyvekslee 77 
                                       ++e++e+lqa++++l+++++e++++ e+l+tl++   g +v+vplg+g+y++a+++d d+++vdlGa+y++e++ ++
  gi|336252705|ref|YP_004595812.1|  16 IQEQIEALQANVEELQQEKTEIDEAVEALETLET---GSTVQVPLGGGAYLRATIEDIDEAIVDLGADYAAEFEQDD 89 
                                       689*******************************...**************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  78 Aiellkkkleelekqlekleeeleklkdqittleanlaqlyqk 120
                                       A++ l++k++++++ +++++ee+++l ++ ++le++++ql+q+
  gi|336252705|ref|YP_004595812.1|  90 AVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ 132
                                       *****************************************96 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   6.2   6.7e-06   0.00059       1      45 [.       1      45 [.       1      72 [. 0.85
   2 !   16.6  13.9     9e-05    0.0079       5      55 ..      90     140 ..      86     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.7e-06
                              ZapB  1 mslelLeqLEskiqkaidtitlLqmeieeLkeeneelkeenrele 45
                                      m  ++L+qL +  q+  ++i++Lq  +eeL++e+ e  e  ++le
  gi|336252705|ref|YP_004595812.1|  1 MGQQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45
                                      667999999999999999999999999999999999999888776 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9e-05
                              ZapB   5 lLeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeer 55 
                                         + LE+k ++  d+i++  +ei+eL+ e+e+l++++++l+++  q + ++
  gi|336252705|ref|YP_004595812.1|  90 AVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       5799*************************************8777766555 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   7.1   5.2e-06   0.00046       1      51 [.       7      57 ..       3      76 .. 0.86
   2 !   17.2   8.3   4.2e-05    0.0037      57     105 ..      84     132 ..      80     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.2e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEE CS
                       Prefoldin_2  1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklv 51
                                      q+l  ++q++q+q+++l++++++l+++++e++++ e+le+l+   +v+   
  gi|336252705|ref|YP_004595812.1|  7 QQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLETGSTVQVPL 57
                                      788999***********************************9998776544 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 4.2e-05
                                       EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS- CS
                       Prefoldin_2  57 kqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkklqq 105
                                       +++++++ + Le++k+t++ +i+++++++ +le e e+l+++ q+++qq
  gi|336252705|ref|YP_004595812.1|  84 EFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ 132
                                       67899*****************************************998 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   7.5   1.6e-05    0.0014     198     241 ..       3      46 ..       1      54 [. 0.90
   2 !   11.8   7.6   0.00091      0.08     146     246 ..      89     134 ..      62     146 .. 0.46

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.6e-05
                              Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelke 241
                                       +++L++l +el+e++++ie+++++++elq++++e++e++e+l++
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALET 46 
                                       78999********************************9999986 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00091
                              Spc7 146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkel 222
                                       + +++le+ k++++++ +e++e   ele+e ++le+++++lq++a                                
  gi|336252705|ref|YP_004595812.1|  89 DAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQA-------------------------------- 133
                                       333334444444444444444444444444444444444444422................................ PP

                              Spc7 223 aelqeqleeleekieelkeqksel 246
                                                              +
  gi|336252705|ref|YP_004595812.1| 134 -----------------------M 134
                                       .......................1 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.1   4.2e-05    0.0037       4      43 ..       4      43 ..       2      78 .. 0.63
   2 !   11.3   8.1    0.0035      0.31       2      44 ..      94     136 ..      93     150 .] 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.2e-05
                             Spc24  4 nekfriakelsdleselesleselaelkeeleeleeesee 43
                                      ++++++++el+++++++e+l+++ +el++e +e++e  e+
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEA 43
                                      4555566666666666666666666666666655554433 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0035
                             Spc24   2 ldnekfriakelsdleselesleselaelkeeleeleeeseek 44 
                                       l+n+k ++   ++++++e+ +lese ++l+++ ++l+++  ++
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQ 136
                                       7899999999999999999999999999999999999998872 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   5.7   4.8e-05    0.0043       3      56 ..       3      49 ..       1      76 [. 0.59
   2 !   11.4   7.5    0.0038      0.34      11      53 ..      89     131 ..      87     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.8e-05
                           NPV_P10  3 qniLlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56
                                      q  L +  ++ ++++++++alq++v+++q++  +       +d+  ++L++let
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTE-------IDEAVEALETLET 49
                                      5556666666666666666666666666666666.......5555555555555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0038
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLae 53 
                                       +++ a+++k d +++++d+v+e++ +++  +e+L++q++qL++
  gi|336252705|ref|YP_004595812.1|  89 DAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQ 131
                                       68999***********************************985 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5  11.3    0.0009      0.08      47      89 ..       4      46 ..       2      53 .. 0.79
   2 !   15.5  10.9   0.00021     0.019      44      98 ..      86     140 ..      61     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0009
                            APG6_N 47 eeleeleeeleklekeeeelleeLkelekereeleaelaalee 89
                                      ++l++l +el++++++ e+l+++ +el++e+ e++++++ale 
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALET 46
                                      4677888888888888888888888888888888888888875 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 0.00021
                            APG6_N  44 kqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeee 98 
                                       +qd+ +++le++ +++++  +e  ee++ele+e e+le++ ++l++++ + + ++
  gi|336252705|ref|YP_004595812.1|  86 EQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       2788888999999999999999999999999999999999999999888877665 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 !   15.1   1.3   0.00018     0.016     126     168 ..       4      46 ..       2      75 .. 0.76
   2 !   12.2   6.7    0.0014      0.13     118     163 ..      95     140 ..      79     148 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 0.00018
                   Ax_dynein_light 126 kkikeLeeekeelekqvaelkaklealekrekerrqeeekkhe 168
                                       +++++L +e +e+++q++ l+a++e+l+++++e  ++ e  ++
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALET 46 
                                       6778888888888888888888888888888887777776555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0014
                   Ax_dynein_light 118 eqgkselekkikeLeeekeelekqvaelkaklealekrekerrqee 163
                                       e++k+ ++++i e++ee +ele++ ++l++++++l++++ +++ ++
  gi|336252705|ref|YP_004595812.1|  95 ENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       5667777777777777777777777777777777777766655443 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   6.7       6.3   5.6e+02      18      38 ..      15      35 ..       4      53 .. 0.71
   2 !   21.3   4.8   2.8e-06   0.00024      11      55 ..     100     144 ..     100     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 6.3
                             TSC22 18 vLkekIkeLeernseleeENs 38
                                      + +e+I  L+++++el++E +
  gi|336252705|ref|YP_004595812.1| 15 EIQEQIEALQANVEELQQEKT 35
                                      556777777777777777754 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.8e-06
                             TSC22  11 AVrEeVevLkekIkeLeernseleeENslLkalaspeqleqlsak 55 
                                       +V + +++  e+I+eLe++ ++le++ ++L+++a ++q++q+ + 
  gi|336252705|ref|YP_004595812.1| 100 TVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMGQG 144
                                       58889999*********************************9775 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 !   14.0   6.0   0.00027     0.023      46      91 ..       3      48 ..       2      54 .. 0.74
   2 !   12.2   4.8   0.00099     0.087      88     124 ..      99     135 ..      63     146 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00027
                               GAS 46 ekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlk 91
                                      +++l+++sqe ++++e++++++++veeL+++  + ++  ++l+ l+
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLE 48
                                      5677888888888888888888888888888888777777777665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00099
                               GAS  88 knlkarlkelekelkdlkwehevleqrfekvekerde 124
                                       + +  r+ e+++e+ +l+ e+e+leq+ ++++++  +
  gi|336252705|ref|YP_004595812.1|  99 DTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQ 135
                                       3334455666666666666666666666666654322 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.9   0.00028     0.024       8      48 ..       4      44 ..       2      59 .. 0.77
   2 !   11.6   6.5    0.0038      0.34       8      62 ..      89     143 ..      83     150 .] 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 0.00028
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  8 dkleeleeqleelleeleelkeelaelleenaeLelenekl 48
                                      ++l++l+++l+e++e++e+l+++++el +e +e+    e l
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44
                                      57888888888888888888888888888888877655555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0038
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXX CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekek 62 
                                       d++++le++ +++ ++++e++ee+ael  e ++Le + ++l+++  +++ ++  +
  gi|336252705|ref|YP_004595812.1|  89 DAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMGQ 143
                                       5688888888899999999999999999999999999999988874444444333 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.0     0.011      0.94      65     105 ..       7      46 ..       1      54 [. 0.73
   2 !   16.6   5.7   7.4e-05    0.0065      68     113 ..      94     139 ..      70     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.011
                           DUF4337  65 kakaeelaaavdkkiakykkkiarykkekkeikkkAkelea 105
                                       ++ ++el+ +++++i+++++++++ ++ek+ei +  ++le 
  gi|336252705|ref|YP_004595812.1|   7 QQLSQELQ-EIQEQIEALQANVEELQQEKTEIDEAVEALET 46 
                                       22355566.46678999999999999999999999988886 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 7.4e-05
                           DUF4337  68 aeelaaavdkkiakykkkiarykkekkeikkkAkeleaerdeanea 113
                                        e++++ vd++i++++++ia+ ++e+++++++A++l++++ +++++
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       567788999******************************9998876 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   5.8   0.00093     0.082      62     108 ..       3      48 ..       1      56 [. 0.63
   2 !   12.9   2.8   0.00061     0.054     182     224 ..      92     134 ..      63     143 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00093
                           DUF4618  62 kkqleqakaeLqeweekeekklekLeqqleqlnakvqklqeelnvLs 108
                                       ++ql+q+ +eLqe++e++e   ++  ++l+q ++++ ++ e l++L+
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQAN-VEELQQEKTEIDEAVEALETLE 48 
                                       677788888888877776653333.3455555666666666666665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00061
                           DUF4618 182 lqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqae 224
                                        +   ++ ++   i+++ e+i ele e ++L+++ +qLq+qa 
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAM 134
                                       4444455566667777777777777777777777777777765 PP

>> DUF3287  Protein of unknown function (DUF3287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0081      0.72      63     123 ..       5      65 ..       3      70 .. 0.91
   2 ?    8.2   0.4     0.021       1.9      73     105 ..      93     125 ..      86     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0081
                           DUF3287  63 kHrrlcderqklgkkrqtleaRiarveRklreleseprdWeeleldevariPdsllvylkl 123
                                       + ++l++e q+++ +++ l+a + +++ +  e++      e le ++++++P     yl++
  gi|336252705|ref|YP_004595812.1|   5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLETGSTVQVPLGGGAYLRA 65 
                                       56899***********************************************887777776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.021
                           DUF3287  73 klgkkrqtleaRiarveRklreleseprdWeel 105
                                        l  k +t+  Ri +v+ ++ elese  + e+ 
  gi|336252705|ref|YP_004595812.1|  93 ALENKKDTVDDRIDEVNEEIAELESESEQLEQQ 125
                                       688999********************9998865 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   3.1   0.00045      0.04      73     114 ..       4      45 ..       2      50 .. 0.61
   2 !   11.2   4.2    0.0033      0.29      68     115 ..      91     136 ..      63     145 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00045
                           DUF1664  73 kkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       ++l++ ++  +ei+e++++++ +++e++++ ++++eave le
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45 
                                       455555555666666666666666666666666666666665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0033
                           DUF1664  68 idrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       +d +++k d + + + e++ee++e++++ ++++++ +++++    +++
  gi|336252705|ref|YP_004595812.1|  91 VDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ--AMQQ 136
                                       344444444444444444444444444444444444444442..2223 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 !   12.2   7.5    0.0015      0.13      58     103 ..       3      48 ..       2      55 .. 0.83
   2 !   13.2   6.2   0.00076     0.067      15      64 ..      94     141 ..      64     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0015
                    CENP-F_leu_zip  58 keeieelaeelreleldLvalrsekeeLekelqkkqervseLesln 103
                                       ++++++l++el+e++ +++al+ + eeL++e  +  e v+ Le+l+
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLE 48 
                                       5788899999999999999999999999999999999999999876 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00076
                    CENP-F_leu_zip  15 serkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieel 64 
                                        e k+d + d++++ + e+ ++e++ e+++ +a + ++  ++++++++++
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQ--QAMQQQMQQM 141
                                       46677777777777777777777777776666655443..4566666666 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   8.2    0.0032      0.28      50      95 ..       3      48 ..       1      56 [. 0.63
   2 !   14.4   8.4    0.0002     0.017      30      93 ..      82     143 ..      57     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0032
                           DUF3450 50 laeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeie 95
                                      ++++++l++el++++ + e l++ v++++qe ++++e  e +e +e
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLE 48
                                      4566666666666666666666666666666666666666666655 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 0.0002
                           DUF3450  30 aaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                       aa+ +    +d+l+++k+++ +++ +++ee+++le + eqle++ ++++q+   +++q++++ +
  gi|336252705|ref|YP_004595812.1|  82 AAEFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ--AMQQQMQQMGQ 143
                                       555566677888999999999999999999999999999998887777665..45666666555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   9.2    0.0057       0.5      17      56 ..       4      43 ..       2      52 .. 0.87
   2 ?    1.3   0.0       6.2   5.5e+02      13      29 ..      61      77 ..      60      83 .. 0.85
   3 !   11.9  15.2     0.003      0.27       3      59 ..      89     145 ..      87     150 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0057
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                              SlyX 17 dtieeLndvvaeqqqqidrlqrqlrllaerlkeleessga 56
                                      +++++L++++ e q+qi++lq+ +++l+++  e++e+ +a
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEA 43
                                      789*************************999888887665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 6.2
                                      HHHHHHHHHHHHHHHHH CS
                              SlyX 13 afqedtieeLndvvaeq 29
                                      a++  tie+ ++++++ 
  gi|336252705|ref|YP_004595812.1| 61 AYLRATIEDIDEAIVDL 77
                                      79999*******99875 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXX CS
                              SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgasea 59 
                                       + +++LE k    +d i+e n+++ae + + ++l++q ++l+++  + + +++++++
  gi|336252705|ref|YP_004595812.1|  89 DAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMGQGQ 145
                                       67899***************************************9555555443332 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   5.8   0.00013     0.012       9      54 ..       3      48 ..       2      55 .. 0.59
   2 ?    8.7   8.0     0.023         2      77     117 ..      92     132 ..      80     143 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 0.00013
                           DUF5082  9 qaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekpl 54
                                      q+q  +l++e++ ++e+Ie L++  ++l++ek +++++ ++le+ +
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLE 48
                                      5566666666666666666666666666666666666665555554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.023
                           DUF5082  77 ssyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsq 117
                                       ++ ++ +d +d+ id+++eEI +Le++ +++++  ++lq+q
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ 132
                                       55566677777777777778888887777777777777766 PP

>> MIS13  Mis12-Mtw1 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   9.0   2.4e-05    0.0021     171     278 ..       4     141 ..       1     150 [] 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHHHHHHHHHCCCH...HH.HHHHHHTT-----------S--........................... CS
                             MIS13 171 ekikalknEikeWaklladskdpdkeiqkekklvdseakidsdtqepdta........................... 220
                                       +++++l++E +e ++ ++ ++    e+q+ek+++d+ ++ +++++  +t                            
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLETGSTVqvplgggaylratiedideaivdlgad 80 
                                       78899999999999999889988899999999999999999999998888899************************ PP

                                       .......HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSTTTSSXXXXXX CS
                             MIS13 221 .......qrilsdnanveskletkvDeLqdsvhkLdsaskalnelstqklqklsrllakrskkek 278
                                              +  ++  +n ++++++++De+++++  L+s s+ l + ++q       +++++ +++ 
  gi|336252705|ref|YP_004595812.1|  81 yaaefeqDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQ----QQAMQQQMQQM 141
                                       ******9999***************************8877765554444....44444444333 PP

>> LRRFIP  LRRFIP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   4.0    0.0012      0.11     221     265 ..       2      46 ..       1      57 [. 0.80
   2 !   12.2   4.9    0.0011     0.094     208     263 ..      89     143 ..      63     150 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0012
                            LRRFIP 221 ldvrLkklaeekeeLleeveklkqqleeekskksssasseelege 265
                                       + ++L++l++e +e++e++e l++++ee +++k + ++  e+ ++
  gi|336252705|ref|YP_004595812.1|   2 GQQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALET 46 
                                       6789*************************9998887777654444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0011
                            LRRFIP 208 eaaellesagegtldvrLkklaeekeeLleeveklkqqleeekskksssasseele 263
                                       +a ++le+  + t d+r+ ++ ee  eL +e e+l+qq ++ ++++ +++ ++  +
  gi|336252705|ref|YP_004595812.1|  89 DAVDALENK-KDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMGQ 143
                                       456667776.889999****999999999999999999999888666655555333 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   4.2    0.0016      0.14      28      66 ..       4      42 ..       2      54 .. 0.62
   2 !   11.9   3.0    0.0014      0.12      11     153 ..      93     138 ..      60     148 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0016
                           DUF4795 28 ekvkelekrledkekklealkkqieelekvkadkeevee 66
                                      ++ ++l+++l++ ++++eal+  +eel+++k + +e  e
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVE 42
                                      455666777777777777777777777777655333332 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0014
                           DUF4795  11 klqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdqfD 87 
                                        l+++                                                                        
  gi|336252705|ref|YP_004595812.1|  93 ALENKK----------------------------------------------------------------------- 98 
                                       222222....................................................................... PP

                           DUF4795  88 eakkeLekmleellekleeqeealkkaldtLqeelkekld.....rlelepLkeqleerlkelq.kelqeam 153
                                                                       + ++ ++d       ele+ +eqle++ ++lq +++q++m
  gi|336252705|ref|YP_004595812.1|  99 --------------------------------DTVDDRIDevneeIAELESESEQLEQQAQQLQqQAMQQQM 138
                                       ................................3334444444333334444444444444444433333333 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   6.9     0.044       3.9      84     127 ..       6      49 ..       2      55 .. 0.77
   2 !   16.6   6.5   8.2e-05    0.0072      50     126 ..      65     140 ..      60     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.044
                     Jnk-SapK_ap_N  84 edqweeerkelqekveqleeenrelelkaknaadqlsrleekea 127
                                        +q+ +e +e+qe++e l+ +++el++   ++++ +++le  e+
  gi|336252705|ref|YP_004595812.1|   6 LQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLET 49 
                                       57888888888899999998888888888888888888887665 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 8.2e-05
                     Jnk-SapK_ap_N  50 aeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleeke 126
                                       a++e+  e++ +L  +y  e e+  + +  le++ d+++++  e++e++++le+e ++le++a+++++q+ + + ++
  gi|336252705|ref|YP_004595812.1|  65 ATIEDIDEAIVDLGADYAAEFEQDDAVD-ALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       6789999999999999999998877665.9******************************66666666665554443 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 !   13.2   9.0   0.00096     0.085      51      92 ..       4      45 ..       2      47 .. 0.93
   2 !   11.7   5.4    0.0028      0.25      22      64 ..      91     133 ..      77     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00096
                           BLOC1_2 51 eklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92
                                      ++l+++++elq+  +qi++++++v+eL++   e+De + +LE
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45
                                      68999999*******************************999 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0028
                           BLOC1_2  22 yklLeklNeaasekykklkdvaaslekkleklnekyeelqpyl 64 
                                       ++ Le+   ++  +++++++++a+le+++e+l+++ ++lq++ 
  gi|336252705|ref|YP_004595812.1|  91 VDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQA 133
                                       5667777778888888888888888888888888888887764 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   6.3    0.0013      0.11     329     374 ..       3      48 ..       1      58 [. 0.77
   2 !   11.8   9.7   0.00093     0.082     325     380 ..      84     139 ..      68     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0013
                            DUF812 329 eeeleelqeqieeleskieeleeeikklessikqveeeleeekeen 374
                                       +++l++l+++++e++++ie+l++++++l+++ ++++e++e++++  
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLE 48 
                                       5678888888888888888888888888888888888888777654 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00093
                            DUF812 325 kkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneeleke 380
                                       ++++++ +++l+++ ++++ +i+e++eei++les+ +q+e+++++++++  +++ +
  gi|336252705|ref|YP_004595812.1|  84 EFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       56788888888888888888888888888888888888888888888888877765 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.8     0.007      0.62      68      98 ..       5      35 ..       3      77 .. 0.63
   2 !   12.6   5.4     0.001     0.092      62     110 ..      98     146 ..      82     150 .] 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.007
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DASH_Spc19 68 llekaekeleklerreetLkaklelqegrls 98
                                      +l+++++el++ +++ e+L+a++e +++   
  gi|336252705|ref|YP_004595812.1|  5 QLQQLSQELQEIQEQIEALQANVEELQQEKT 35
                                      4555555555555555555555554443322 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.001
                                       TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT CS
                        DASH_Spc19  62 ePqieellekaekeleklerreetLkaklelqegrlsnaesskkeeees 110
                                       +  +++ ++++++e+++le++ e+L+++++++++   ++++++  + ++
  gi|336252705|ref|YP_004595812.1|  98 KDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMGQGQQ 146
                                       5678999999999************999998888888876666665555 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.8   0.00037     0.033      90     131 ..       3      44 ..       1      52 [. 0.86
   2 ?    9.3   4.5      0.01      0.89      95     137 ..      93     135 ..      85     143 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00037
                           DUF4201  90 eselselkkelkekeerlaklrkelykvklerdklrkqnekl 131
                                       +++l++l +el+e++e++++l+++++++++e++ +++  e l
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44 
                                       6899999***********************999998766655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.01
                           DUF4201  95 elkkelkekeerlaklrkelykvklerdklrkqneklkqqggl 137
                                       +l+++ ++ ++r++++ +e+ +++ e ++l++q ++l+qq  +
  gi|336252705|ref|YP_004595812.1|  93 ALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQ 135
                                       4555566677777777777777777777777777777777544 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.8     0.035       3.1     119     144 ..       7      32 ..       4      37 .. 0.90
   2 !   15.9  10.6   7.6e-05    0.0067      77     146 ..      63     133 ..      34     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.035
                           DUF4349 119 leiereLsevqaeieslegqlryLdn 144
                                        ++++eL+e+q++ie+l+++ ++L++
  gi|336252705|ref|YP_004595812.1|   7 QQLSQELQEIQEQIEALQANVEELQQ 32 
                                       5789*******************997 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 7.6e-05
                           DUF4349  77 rstsaeDVTeqyvDleaRlkaleasedrllallekaksvedll.eiereLsevqaeieslegqlryLdnqv 146
                                          + eD+ e +vDl a  +a  ++ d + al +k+++v+d + e+++e++e ++e e+le+q ++L++q 
  gi|336252705|ref|YP_004595812.1|  63 LRATIEDIDEAIVDLGADYAAEFEQDDAVDALENKKDTVDDRIdEVNEEIAELESESEQLEQQAQQLQQQA 133
                                       37788************************************8758***********************996 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   3.3    0.0012      0.11      17      59 ..       4      42 ..       2      55 .. 0.45
   2 !   10.5   1.8    0.0052      0.46      34      78 ..      92     134 ..      64     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0012
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II 17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArr 59
                                      +ql++lsq+l++++e+++ ++++vee +    + ++ i++A +
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQ----QEKTEIDEAVE 42
                                      4444444445555554444444433322....22233333333 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0052
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II  34 seinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                         ++++ + +++ +++ n+ i++ ++++ +Le++a+qL ++   +
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ--AM 134
                                       44555556666777777777777777777777777777766..33 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   7.9      0.02       1.8      35      76 ..       4      45 ..       2      52 .. 0.51
   2 !   14.9   6.8   0.00025     0.022      34      84 ..      88     140 ..      67     147 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.02
                     Tropomyosin_1 35 qeiksLtkknqqleeevekleeklkeakekaeesekkktnne 76
                                      q++++L++ +q+++e++e l+++++e ++++ e +++    e
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45
                                      455555555555555555555555555555544444433333 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 0.00025
                     Tropomyosin_1  34 eqeiksLtkknqqleeevekleeklkeakekaeesekkktnne..altrkiql 84 
                                       ++ +  L++k +++++ +++++e++ e ++++e+ e+++++    a+++++q+
  gi|336252705|ref|YP_004595812.1|  88 DDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQqqAMQQQMQQ 140
                                       55555555555555555555555555555555544444443333345555544 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.4      0.05       4.4       2      47 ..       3      51 ..       2      53 .. 0.81
   2 !   15.6   4.1   0.00012      0.01      25      60 ..     104     139 ..      85     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.05
                                      XXHHHHHHHHHHCCCCH...HCCHHHHCHCCCCCHHHHCCCCHHHHHHH CS
                     Synaptobrevin  2 ndklakikaevdevkdi...mkeNidkvlergekldeLvdktenLqssa 47
                                      +++l+++ +e++e+++    ++ N++++ + + ++de v+  e+L++ +
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQieaLQANVEELQQEKTEIDEAVEALETLETGS 51
                                      67888888888888875111679*****************999999877 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 0.00012
                                       HCHCCCCCHHHHCCCCHHHHHHHHHHHHHHHHHHHH CS
                     Synaptobrevin  25 kvlergekldeLvdktenLqssaqqFkkqarklkrk 60 
                                       ++ e +e++ eL++++e+L+++aqq ++qa +++ +
  gi|336252705|ref|YP_004595812.1| 104 RIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       455667888999999999999999999999887655 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6  10.6   0.00042     0.037      91     137 ..       3      48 ..       2      58 .. 0.58
   2 !    9.2  10.4     0.009       0.8      61     109 ..      92     141 ..      64     149 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00042
                        MscS_porin  91 ssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLn 137
                                       ++qlq+l+++l+++++q+ +lq   e++qq+ te  ++ +++++ L+
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALET-LE 48 
                                       45666666666666666666666666666666666666666655.43 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.009
                        MscS_porin  61 eal.qkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlv 109
                                       +al +kk++ +++ +  +  ++eLe++ +q ++q q+lq+q  q + q  
  gi|336252705|ref|YP_004595812.1|  92 DALeNKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQM 141
                                       22222223333333333333333333333333333333333333333333 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   3.7   6.7e-05    0.0059      41      76 ..       7      42 ..       2      54 .. 0.86
   2 ?    6.0   9.1      0.11        10      45      85 ..     103     143 ..      82     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.7e-05
                              SKA2 41 vkLlerlkkvkeelqaLkeqceellaekkelidkir 76
                                       +L ++l++++e+++aL++++eel++ek e+ ++++
  gi|336252705|ref|YP_004595812.1|  7 QQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVE 42
                                      5899*************************9876655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.11
                              SKA2  45 erlkkvkeelqaLkeqceellaekkelidkirttlvanrel 85 
                                        r+ +v+ee+++L+++ e+l ++ ++l +++ ++ ++++  
  gi|336252705|ref|YP_004595812.1| 103 DRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMGQ 143
                                       6999*****************99999999988887777765 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   5.6    0.0008     0.071      24      65 ..       4      45 ..       2      48 .. 0.90
   2 !    9.5   4.1    0.0098      0.87      11      54 ..      90     133 ..      82     144 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0008
                             Sec34 24 eqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65
                                      +qL++l+++ ++++e+ ++l+++ e+l +e+++++e +e++e
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45
                                      8999***************************99999998876 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0098
                             Sec34  11 ecdelleqtdealeqLeeleekfksvsektsslheaceqlleeq 54 
                                        +d+l ++ d++ + ++e++e+  + ++++++l+++++ql ++ 
  gi|336252705|ref|YP_004595812.1|  90 AVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQA 133
                                       45556666666666666666666666666666666666665443 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 !   10.4   5.9    0.0075      0.66       3      37 ..       7      41 ..       3      49 .. 0.58
   2 ?    0.8   0.0       7.6   6.7e+02      26      40 ..      63      77 ..      60      79 .. 0.84
   3 ?    7.8   5.6      0.05       4.4       3      40 ..      92     129 ..      90     142 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0075
                         FlaC_arch  3 delEnklsklsteletvkkeneelsksveelkenV 37
                                      ++l ++l++++ ++e ++++ eel+++ +e++e V
  gi|336252705|ref|YP_004595812.1|  7 QQLSQELQEIQEQIEALQANVEELQQEKTEIDEAV 41
                                      34555555555555555555555555555555555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 7.6
                         FlaC_arch 26 lsksveelkenVkdl 40
                                      l+ ++e+++e + dl
  gi|336252705|ref|YP_004595812.1| 63 LRATIEDIDEAIVDL 77
                                      678999999999876 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.05
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       d lEnk + ++ +++ v +e+ el+++ e+l+++ ++l
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQL 129
                                       55666666666666666666666666666655554433 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8  19.7   0.00062     0.055     128     236 ..       6     136 ..       2     145 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00062
                           DUF4407 128 aaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaake................. 187
                                        ++l++el+e+++qi+alqa++++++++ ++  +++++  + ++g++ +   G g++ ++                 
  gi|336252705|ref|YP_004595812.1|   6 LQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLETGSTVQVPLGGGAYLRAtiedideaivdlgadya 82 
                                       34577888888888888888888888776666666666666656888888999999999999999999999999888 PP

                           DUF4407 188 ...........kkaqldaaqaelaelkakld.atarlaalraelaeleaerakeraasqaa 236
                                                          +++ +++++++d  ++++a+l++e ++le+++++ +++  ++
  gi|336252705|ref|YP_004595812.1|  83 aefeqddavdaL-------ENKKDTVDDRIDeVNEEIAELESESEQLEQQAQQLQQQAMQQ 136
                                       666633333332.......333333333333444444444444444444444444444333 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 !   13.0   1.4   0.00097     0.086      26      73 ..       9      56 ..       4      87 .. 0.76
   2 ?    9.1   7.4     0.015       1.4      24      73 ..      92     141 ..      89     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00097
                                      CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskk 73
                                      l++  +++++++e l+ ++ee++++++e++e v+++++  +    + +
  gi|336252705|ref|YP_004595812.1|  9 LSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLETGSTVQVP 56
                                      677778999999999999999999999999999999887776666655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.015
                                       HCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  24 dlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskk 73 
                                       d+l++++ +v+++++++++e++e+++++++ e+  ++++++  ++q ++ 
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQM 141
                                       67888888889999999999999999999999888888888887777765 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0  11.4   0.00024     0.021      20     118 ..       3     132 ..       1     140 [. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 0.00024
                              Uds1  20 leeVeelkkelkaLeerlealrkkLa....letklrdaarsLsrlyssskksak....................... 69 
                                       ++++++l++el+ ++e++eal+++++     +t + +a ++L++l + s+ +                         
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEelqqEKTEIDEAVEALETLETGSTVQ-Vplgggaylratiedideaivdlg 78 
                                       5677778888888888888877775321112688999999999999555555.36********************98 PP

                              Uds1  70 .....ssaarsnskssreslakaeeelaeserkvdelaselekleeraaevrrr 118
                                            ++ +++     ++++++ ++ ++e ++ + el+se e+le++a++++++
  gi|336252705|ref|YP_004595812.1|  79 adyaaEFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ 132
                                       887754444444444445566667777777777777788888888888777776 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   6.1    0.0051      0.45     423     465 ..       4      46 ..       2      50 .. 0.89
   2 !   12.0   5.7   0.00069     0.061     392     456 ..      70     136 ..      63     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0051
                            AAA_13 423 kaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeink 465
                                       +++++l +el+e+++++++l+++++eL+++ +++ +a+e +++
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALET 46 
                                       7889999999999999999999999999999999999998875 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00069
                            AAA_13 392 keeakkklelhlveelese..ldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrde 456
                                         ea ++l +++++e+e++  +d++++k++ +++ i ++++e++e e+e ++le+++++L++q  ++
  gi|336252705|ref|YP_004595812.1|  70 IDEAIVDLGADYAAEFEQDdaVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQ 136
                                       5667777778888877654226777888888888888888888888888888888888888776665 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   6.7    0.0018      0.16     101     144 ..       3      46 ..       2      55 .. 0.76
   2 !   10.5   5.0     0.006      0.53     102     147 ..      89     134 ..      63     144 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0018
                             ATG16 101 aqrllelneelqkleeklkedeerlaeleaeraaletklkdree 144
                                       +q+l++l++elq+ +e++++ +++++el++e++++ ++++ +e 
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALET 46 
                                       68888888888888888888888888888888888887777665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.006
                             ATG16 102 qrllelneelqkleeklkedeerlaeleaeraaletklkdreeelr 147
                                       + + +l+++ ++ ++++ e +e++aele+e ++le++ ++++++  
  gi|336252705|ref|YP_004595812.1|  89 DAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAM 134
                                       4455555555555555555555555555555555555555555433 PP

>> GPS2_interact  G-protein pathway suppressor 2-interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   4.9      0.63        56      34      71 ..       4      41 ..       3      54 .. 0.83
   2 !   16.6   5.7   9.1e-05    0.0081      15      71 ..      84     140 ..      76     150 .] 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.63
                     GPS2_interact 34 qnidkvDREiakveqqiskLkkkqkeleeeaakpkeee 71
                                      q++++   E+  +++qi+ L+   +el++e+++  e+ 
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAV 41
                                      7888888999*******************998765554 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9.1e-05
                     GPS2_interact  15 eaeqeqelvpsrlsKdeLlqnidkvDREiakveqqiskLkkkqkeleeeaakpkeee 71 
                                       e eq++++ +    Kd     id v  Eia  e++ ++L ++ ++l+++a++ + ++
  gi|336252705|ref|YP_004595812.1|  84 EFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       56777777788889999999******************************9985443 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   7.4     0.021       1.8      53      91 ..       7      45 ..       3      49 .. 0.47
   2 !   13.6   3.2   0.00023      0.02      47      93 ..      86     132 ..      64     143 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.021
                            Tektin 53 ediefwkeeLekeleelkeeieaLeeekrrlekaleale 91
                                      +++++  +e+++++e+l++ +e+L++ek+++++a+eale
  gi|336252705|ref|YP_004595812.1|  7 QQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45
                                      444444444444444444444444444444444444443 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00023
                            Tektin  47 rLeeRiediefwkeeLekeleelkeeieaLeeekrrlekalealeep 93 
                                       + ++ ++ +e+ k+++++ ++e++eei +Le+e ++le++ ++l+++
  gi|336252705|ref|YP_004595812.1|  86 EQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ 132
                                       44555566666666666666666666666666666666666666554 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   1.1   0.00093     0.082       2      31 ..      10      39 ..       4      47 .. 0.87
   2 ?    6.8   1.8     0.066       5.8       4      31 ..     104     131 ..     101     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00093
                         DASH_Dam1  2 epafaeLaDsletLdknledLqqihesLsd 31
                                      +++++e+++++e+L++n+e+Lqq + ++++
  gi|336252705|ref|YP_004595812.1| 10 SQELQEIQEQIEALQANVEELQQEKTEIDE 39
                                      6789******************98888776 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.066
                         DASH_Dam1   4 afaeLaDsletLdknledLqqihesLsd 31 
                                       ++ e ++++++L++  e+L+q  ++L++
  gi|336252705|ref|YP_004595812.1| 104 RIDEVNEEIAELESESEQLEQQAQQLQQ 131
                                       5677778888888888888877777764 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   6.1    0.0023       0.2      63     106 ..       3      46 ..       1      56 [. 0.82
   2 !   10.7   5.2    0.0032      0.28      54     100 ..      92     139 ..      64     145 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0023
                      HAUS-augmin3  63 qedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqv 106
                                       q++ ++l+++l+e++e++eaL++ ++eLq+ek  + +  + L+ 
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALET 46 
                                       56788899999999999999999999999999988877777765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0032
                      HAUS-augmin3  54 ktiepsdlkq.edvellevileeeeesleaLeqelqeLqkekalklkr 100
                                       + +e+++++  +  ++++++++e+e+  e+Leq++q+Lq++   ++ +
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTVdDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       333322222236667777788888888888888888888776665544 PP

>> Nmad5  Nucleotide modification associated domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   4.2   0.00021     0.019      51     155 ..      11     132 ..       3     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 0.00021
                             Nmad5  51 aalreiikeieklqsklpkeglstnk.........pkstgsvidvnla.Garvelyfng........kkletvvlas 109
                                       ++l+ei ++ie+lq+++++  +++ +            tgs+++v l  Ga  ++ +++             +++++
  gi|336252705|ref|YP_004595812.1|  11 QELQEIQEQIEALQANVEELQQEKTEideavealeTLETGSTVQVPLGgGAYLRATIEDideaivdlGADYAAEFEQ 87 
                                       67888888888888888877776666555666666677777777777766655555555666776644455567777 PP

                             Nmad5 110 vdeiaketkslpkvvleadnplvkrfdelekaqeelrekrkaikat 155
                                        d ++  +++++ +v ++ +++ +++ ele + e+l++++++++++
  gi|336252705|ref|YP_004595812.1|  88 DDAVDALENKKD-TVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ 132
                                       777777777777.666777899999999999999999999988775 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.3     0.067         6      57      80 ..      10      33 ..       3      46 .. 0.55
   2 ?   12.3   1.1    0.0015      0.13      55      84 ..     107     136 ..      88     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.067
                             Vps51 57 sdtIrkmksemdkldqklselkqa 80
                                      s+++++++++++ l+++++el+q+
  gi|336252705|ref|YP_004595812.1| 10 SQELQEIQEQIEALQANVEELQQE 33
                                      445555555555555555555554 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0015
                             Vps51  55 sasdtIrkmksemdkldqklselkqaiski 84 
                                       +++++I++++se ++l+q+ ++l+q   + 
  gi|336252705|ref|YP_004595812.1| 107 EVNEEIAELESESEQLEQQAQQLQQQAMQQ 136
                                       589********************9976554 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.5    0.0037      0.32      59      93 ..       5      39 ..       1      52 [. 0.65
   2 ?   10.7   4.2    0.0056       0.5      63     107 ..      94     137 ..      65     148 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0037
                             Muted 59 clesmkenLselnkkleaalekverllqkeleeek 93
                                       l++++++L+e+++++ea++ +ve+l+q++ e ++
  gi|336252705|ref|YP_004595812.1|  5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDE 39
                                      45667777777777777777777777777555443 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0056
                             Muted  63 mkenLselnkkleaalekverllqkeleeekrkseqlqekeeerk 107
                                       ++++  ++ +++++++e++ +l+++ +e+ +++++qlq++ ++++
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESE-SEQLEQQAQQLQQQAMQQQ 137
                                       4444444445555555555555544.3333334444444332222 PP

>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.5     0.013       1.1     126     157 ..       7      38 ..       2      55 .. 0.68
   2 ?   12.4   3.9   0.00086     0.076     113     168 ..      86     141 ..      61     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.013
                              Not3 126 ewlkdaideLneqvekleaeieklsskkkkkk 157
                                       + l++ ++e++eq+e+l+a++e+l+++k++ +
  gi|336252705|ref|YP_004595812.1|   7 QQLSQELQEIQEQIEALQANVEELQQEKTEID 38 
                                       55788899999999999999999988654433 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00086
                              Not3 113 kldpkekekeearewlkdaideLneqvekleaeieklsskkkkkkkskekarveel 168
                                       ++d++ ++ e+ ++ ++d ide+ne++ +le+e e+l+++ ++ ++++ +++++++
  gi|336252705|ref|YP_004595812.1|  86 EQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQM 141
                                       44666666677777888888888888888888888888888777655554555544 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 ?    8.7   9.9     0.019       1.7       3      46 ..       5      48 ..       3      52 .. 0.45
   2 ?   12.9   9.3   0.00097     0.086      39      90 ..      85     136 ..      65     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.019
                             DHR10  3 slaeekeelaelErkarelqakidalqvvekdlrsciklleeie 46
                                      +l++  +el+e ++++ +lqa ++ lq+ ++++ +++++le++e
  gi|336252705|ref|YP_004595812.1|  5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLE 48
                                      44444444444444444444444444444444444444444444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00097
                             DHR10  39 iklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlena 90 
                                       +++ + + a  +k ++++++++e +++++e+e e+++le++ ++lq+q  + 
  gi|336252705|ref|YP_004595812.1|  85 FEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQ 136
                                       5555556666677788888888888888888888888888888888886544 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.4    0.0049      0.43      77     113 ..       7      43 ..       2      51 .. 0.78
   2 ?   10.4   3.6    0.0041      0.36      79     124 ..      94     137 ..      65     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0049
                     PI3K_P85_iSH2  77 eaqehEieklqenleqlksrlkelhsskekLeedlkq 113
                                       ++ ++E +++qe++e l++ ++el+++k +++e++++
  gi|336252705|ref|YP_004595812.1|   7 QQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEA 43 
                                       4457899999999999999999999999999888765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0041
                     PI3K_P85_iSH2  79 qehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleRe 124
                                        e+ ++++++ ++++++ + el+s++e+Le++ +q  ++ +  +++
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAM--QQQ 137
                                       36677788888888888888888888888887665544433..333 PP

>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   3.2      0.35        31      42      79 ..       6      43 ..       3      50 .. 0.52
   2 ?   15.0   4.8   0.00023      0.02      22      69 ..      92     139 ..      81     144 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.35
                            GCN5L1 42 vaeayanqkklekeakalqanvakfakqtdqWlalves 79
                                      ++++ ++ +++ +++ alqanv++++++ ++  ++ve+
  gi|336252705|ref|YP_004595812.1|  6 LQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEA 43
                                      44444455555555555555555555555554444444 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 0.00023
                            GCN5L1  22 eaiesaaaltealvdklnsgvaeayanqkklekeakalqanvakfakq 69 
                                       +a+e+ ++  +  +d++n+++ae+ ++ ++le++a++lq+++++ + q
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       444555555566678999999999999999999999999998876655 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.0       0.1       9.3      49      93 ..       5      46 ..       1      61 [. 0.76
   2 ?   14.6   1.6   0.00031     0.027      53     107 ..      63     131 ..      48     143 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.1
                                      TTHHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHH CS
                   Cob_adeno_trans 49 eeeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelek 93
                                      + ++l+++L+eiq+++  l+a++   e ++ek++i+e+ ve+le+
  gi|336252705|ref|YP_004595812.1|  5 QLQQLSQELQEIQEQIEALQANVE--ELQQEKTEIDEA-VEALET 46
                                      357888899999999999999985..556777778777.888876 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 0.00031
                                       HHHHHHHHHHHHHHHHHHHHT.............-BTCCG-S--..HHHHHHHHHHHHHHHHHS--EES CS
                   Cob_adeno_trans  53 lkeaLeeiqneLfdlgaelatp............ekkkekkkit..eeeveelekeideleaelpplks 107
                                       l++++e+i + ++dlga+ a++            +k++ + +i+  +ee++ele+e ++le++ ++l++
  gi|336252705|ref|YP_004595812.1|  63 LRATIEDIDEAIVDLGADYAAEfeqddavdalenKKDTVDDRIDevNEEIAELESESEQLEQQAQQLQQ 131
                                       6889****************8887777775444311122222221112245555555555555555444 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.0   0.00042     0.037       1      41 [.       6      46 ..       6      74 .. 0.88
   2 ?    6.5   4.8     0.065       5.7      45      80 ..      99     134 ..      61     146 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00042
                          Syntaxin  1 leeffkeveeikkeiekleeevkklkkqneesktstraksv 41
                                      l+++ +e +ei+++ie+l+ +v++l+++++e+ ++++a ++
  gi|336252705|ref|YP_004595812.1|  6 LQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALET 46
                                      578889**************************999988766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.065
                          Syntaxin  45 krmesdikeikkraesvkarLeaLdksnkenekksg 80 
                                       + ++  i+e++++  +++++ e+L++++++ ++++ 
  gi|336252705|ref|YP_004595812.1|  99 DTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAM 134
                                       444444444444444444444444444444443332 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 ?    9.5   6.0     0.011      0.98      53      88 ..       3      38 ..       1      51 [. 0.75
   2 ?   11.5   5.4    0.0027      0.24      54     102 ..      92     140 ..      62     146 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.011
                             Mod_r 53 epeleelrselqekleelkelekefeekeqeldell 88
                                      +++l++l++elqe  e++++l++++ee++qe  e+ 
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEID 38
                                      678888888888888888888888888888876654 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0027
                             Mod_r  54 peleelrselqekleelkelekefeekeqeldellqkfspdallarLqt 102
                                       + le++++ + ++++e++e  +e+e   ++l++  q+++++a+++++q+
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       3677777777777777666666666666666666666666666666665 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   9.5   0.00031     0.027      23      59 ..       3      39 ..       1      46 [. 0.73
   2 ?    1.3   0.1       3.3   2.9e+02      12      41 ..      60      89 ..      51     107 .. 0.53
   3 ?    5.8   9.6      0.13        12      19      47 ..     105     133 ..     101     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00031
                                      HHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                             DivIC 23 kqeiaalqaelaklkaeneeLeaevkdLksdedyiee 59
                                      +q++++l +el+++++++e+L+a+v++L++++  i+e
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDE 39
                                      5777777777777777777777777777777776665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 3.3
                                      XXXXXXHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC 12 gkkgllaykqlkqeiaalqaelaklkaene 41
                                      g++   ++ ++++ i++l a++a+  ++ +
  gi|336252705|ref|YP_004595812.1| 60 GAYLRATIEDIDEAIVDLGADYAAEFEQDD 89
                                      555556666666666666555555444444 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC  19 ykqlkqeiaalqaelaklkaeneeLeaev 47 
                                       + ++++eia+l+ e ++l ++ ++L+++ 
  gi|336252705|ref|YP_004595812.1| 105 IDEVNEEIAELESESEQLEQQAQQLQQQA 133
                                       56788888888888888888888888875 PP

>> SAS4  Something about silencing, SAS, complex subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   4.5         4   3.6e+02      24      56 ..      10      34 ..       1      55 [. 0.49
   2 ?   14.6   3.9    0.0003     0.026      24      63 ..     109     148 ..     105     150 .] 0.89

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 4
                              SAS4 24 niekeraesEadrlerllekLqgqdwlrvlgki 56
                                       +e ++++++ + l+  +e+Lq++         
  gi|336252705|ref|YP_004595812.1| 10 SQELQEIQEQIEALQANVEELQQE--------K 34
                                      333333333333333333333332........2 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 0.0003
                              SAS4  24 niekeraesEadrlerllekLqgqdwlrvlgkitkindpk 63 
                                       n+e+ + esE ++le++ ++Lq+q +++ ++++++ + p+
  gi|336252705|ref|YP_004595812.1| 109 NEEIAELESESEQLEQQAQQLQQQAMQQQMQQMGQGQQPD 148
                                       89******************************99766655 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.2     0.023         2      73     114 ..       4      45 ..       2      55 .. 0.77
   2 ?   11.7   2.0    0.0018      0.16      65     104 ..     102     141 ..      65     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH CS
                              SHE3  73 kelselkesveelklekkqlkkrlenssaseteleeelerlk 114
                                       ++l++l+++ +e++++ ++l+ ++e++++++te  e +e l+
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45 
                                       678888888888888888888888888888888888777776 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH CS
                              SHE3  65 errlkdlekelselkesveelklekkqlkkrlenssaset 104
                                       + r+ ++++e++el+++ e+l+++ +ql++++ +++ +++
  gi|336252705|ref|YP_004595812.1| 102 DDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQM 141
                                       2467777777777777777777777777777666555544 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 ?    6.1   8.2      0.12        11     119     153 ..       6      39 ..       2      54 .. 0.36
   2 ?   14.3   7.8   0.00037     0.032      86     137 ..      86     137 ..      61     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.12
                           UPF0242 119 nqqLqekleaiaedfeelkleleeqLaekqellqe 153
                                        qqL+++l++i+e++e+l+ ++e +L+++++ ++e
  gi|336252705|ref|YP_004595812.1|   6 LQQLSQELQEIQEQIEALQANVE-ELQQEKTEIDE 39 
                                       22222222222222222222222.12222222222 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00037
                           UPF0242  86 tkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelk 137
                                       ++++a+  l+++++   +++d+ +ee+++l+ e +qL++++++ +++  +++
  gi|336252705|ref|YP_004595812.1|  86 EQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQ 137
                                       467799999999999999********************99999888643332 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 ?   14.2  10.8    0.0004     0.035      24      57 ..       3      36 ..       2      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.0004
                     TolA_bind_tri 24 qqqlealqqelreLRGqiEelqyqleqleerQrd 57
                                      qqql++l+qel+e++ qiE lq ++e+l++   +
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTE 36
                                      9***************************997654 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.1    0.0053      0.47       1      33 [.      16      48 ..       3      67 .. 0.64
   2 ?    8.8   1.5     0.013       1.2       2      33 ..     102     133 ..     101     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0053
                           DUF4988  1 leddvndlkdrvaaleeqvkelndniealkkll 33
                                      +++++++l+  v+ l+++  e+++ +eal++l 
  gi|336252705|ref|YP_004595812.1| 16 IQEQIEALQANVEELQQEKTEIDEAVEALETLE 48
                                      345555566666666666666666666665554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.013
                           DUF4988   2 eddvndlkdrvaaleeqvkelndniealkkll 33 
                                       +d+++++++++a le++ ++l+++ ++l++ +
  gi|336252705|ref|YP_004595812.1| 102 DDRIDEVNEEIAELESESEQLEQQAQQLQQQA 133
                                       69**************************8765 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.9   0.00097     0.086      81     115 ..      17      51 ..       3      56 .. 0.89
   2 ?    5.5   6.6      0.16        14      31      73 ..      91     136 ..      80     143 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00097
                              CdvA  81 ksaieairellesaleekeeikklleklsklelee 115
                                       +++iea++ + e +++ek+ei++++e l++le+++
  gi|336252705|ref|YP_004595812.1|  17 QEQIEALQANVEELQQEKTEIDEAVEALETLETGS 51 
                                       789****************************9985 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.16
                              CdvA  31 lkklkekakelke...klkkrlkeledqikslekalanlkisyasG 73 
                                       +++l++k++++ +   +++++++ele++ ++le+   +l+ + ++ 
  gi|336252705|ref|YP_004595812.1|  91 VDALENKKDTVDDridEVNEEIAELESESEQLEQQAQQLQQQAMQQ 136
                                       4444444444433000334455555555555555544444444433 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.8     0.034         3      31      69 ..       7      45 ..       2      53 .. 0.64
   2 ?    9.2   0.7      0.01      0.92       4      71 ..      58     125 ..      55     141 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.034
                              RPW8 31 ksilkrLestleritPvvkeieklnkeldrpreeieeLk 69
                                      +  +++L++  e+i+ + +++e+l++e  + +e +e L+
  gi|336252705|ref|YP_004595812.1|  7 QQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45
                                      455666777777777777777777777766666666664 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.01
                              RPW8   4 vgGAalgaalgellkaileakkk.sldfks..ilkrLestleritPvvkeieklnkeldrpreeieeLkkl 71 
                                        gGA l a+++++ +ai++     +++f+    ++ Le+   +  +v ++i+++n+e+ + ++e e+L+++
  gi|336252705|ref|YP_004595812.1|  58 GGGAYLRATIEDIDEAIVDLGADyAAEFEQddAVDALEN---KKDTVDDRIDEVNEEIAELESESEQLEQQ 125
                                       59****************976541445532113333433...23333345555555554444455555443 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   5.3    0.0038      0.34      33      76 ..       6      48 ..       2      83 .. 0.65
   2 ?    8.9   2.4     0.017       1.5      32     100 ..      91     118 ..      53     131 .. 0.52
   3 ?    8.1   5.0      0.03       2.7      34      78 ..      92     135 ..      86     143 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0038
                      Baculo_PEP_C 33 laqlatlldaietqLnalsedlksllaeldtrldtlltnLtdal 76
                                      l ql++ l++i++q++al++++++ l++ +t++d+++++L++  
  gi|336252705|ref|YP_004595812.1|  6 LQQLSQELQEIQEQIEALQANVEE-LQQEKTEIDEAVEALETLE 48
                                      378888888888888888888888.4556778888888887643 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.017
                      Baculo_PEP_C  32 ilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlss 100
                                       +  +l++ +                                        dt++ +++ +n ++++L s+
  gi|336252705|ref|YP_004595812.1|  91 V-DALENKK----------------------------------------DTVDDRIDEVNEEIAELESE 118
                                       2.3444444........................................55555555555555555443 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.03
                      Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalna 78 
                                        +l++ +d+++ ++++++e++ + l++ +++l++++++L+++  +
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTVDDRIDEVNEEIAE-LESESEQLEQQAQQLQQQAMQ 135
                                       67899999999999999999998.444566777777777765443 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.5    0.0013      0.12     378     430 ..       4      54 ..       1      70 [. 0.59
   2 ?    7.5   5.0     0.015       1.3     331     376 ..      97     142 ..      71     148 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0013
                              FapA 378 eqlkklletkeklkeeleeleeelkelkeeleskkeeakikvnkeiypgvkik 430
                                       +ql++l +++++++e++e+l+++ +el++e  +   ++ +++ +++  g +++
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEI--DEAVEALETLETGSTVQ 54 
                                       4555555555555555555555555555555555..44555555555555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.015
                              FapA 331 depelkeklkeleeeleeleeeleklkkkikklpklkaekqlesek 376
                                       ++ +++++++e++ee+ ele+e e+l+++ ++l++ + ++q+++  
  gi|336252705|ref|YP_004595812.1|  97 KKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMG 142
                                       4456777888888888888888888888888888844455554444 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   6.5   0.00069     0.061     277     317 ..       4      44 ..       2      49 .. 0.93
   2 ?    6.5   4.7     0.038       3.4     282     328 ..      94     141 ..      70     147 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00069
                             IFT57 277 qeyreaqeelsevkekykqlsegvseltrelaeiseelekv 317
                                       q+++++++el+e++e+++ l+++v+el++e +ei+e +e++
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44 
                                       7899********************************99976 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.038
                             IFT57 282 aqeelsevkekykqlsegvseltrelaeiseelekvkqe.meergssm 328
                                       ++++ ++v +++++++e++ el+ e ++++++ ++++q+ m+++ ++m
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQaMQQQMQQM 141
                                       445566666667777777777777766666666666543255555555 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.8     0.037       3.3     114     147 ..       7      40 ..       1      57 [. 0.50
   2 ?    9.0   0.4      0.01       0.9      60     131 ..      69     142 ..      59     147 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.037
                      Allexi_40kDa 114 skllkklesietsleelhakldelsssetseseg 147
                                       ++l ++l+ i++++e+l+a+++el +++t+  e 
  gi|336252705|ref|YP_004595812.1|   7 QQLSQELQEIQEQIEALQANVEELQQEKTEIDEA 40 
                                       3444455555555555555555555554443333 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.01
                      Allexi_40kDa  60 dvdsiinklnpv..sllsqttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelh 131
                                       d+d+ i +l++   + + q   +  l ++  t+++ +d++++   +le + e+ +++  + + +++++++++++
  gi|336252705|ref|YP_004595812.1|  69 DIDEAIVDLGADyaAEFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMG 142
                                       55555555554300233466666666666666666666666666666666666666665556666666666654 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1       0.2        18      27      50 ..       9      32 ..       2      54 .. 0.82
   2 ?    8.6   0.5     0.027       2.4      21      51 ..      95     125 ..      68     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.2
                              MtrB 27 vllsldpvleeidkLekiaddlvn 50
                                      +  +l++++e+i+ L++ +++l +
  gi|336252705|ref|YP_004595812.1|  9 LSQELQEIQEQIEALQANVEELQQ 32
                                      567899************999976 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.027
                              MtrB  21 earedvvllsldpvleeidkLekiaddlvns 51 
                                       e+++d v   +d+v+eei++Le+ +++l+++
  gi|336252705|ref|YP_004595812.1|  95 ENKKDTVDDRIDEVNEEIAELESESEQLEQQ 125
                                       4578899999***************999875 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.0      0.19        16       3      37 ..      10      44 ..       3      49 .. 0.75
   2 ?   13.8   2.7   0.00057      0.05      18      46 ..      89     117 ..      85     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.19
                              XhlA  3 kerlerietkldnleervdkleekaaeaeekiknl 37
                                       ++l++i+++++ l+  v++l++ ++e +e ++ l
  gi|336252705|ref|YP_004595812.1| 10 SQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44
                                      46788888888888888888888888877776665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00057
                              XhlA  18 ervdkleekaaeaeekiknleedlkkles 46 
                                       + vd le+k+++++ +i++++e++++les
  gi|336252705|ref|YP_004595812.1|  89 DAVDALENKKDTVDDRIDEVNEEIAELES 117
                                       589************************98 PP

>> PRTP  Herpesvirus processing and transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   6.5   0.00081     0.072     312     449 ..       6     140 ..       1     149 [. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00081
                              PRTP 312 akkrgstvkkvaitlsaLfsreelleklrkaveralfgerlehffdlveeelaaierlfvGgvfsspddtiealkkd 388
                                        ++ ++++++++++++aL ++ e+l+++++++++a+  e+le +++ +  ++      ++      +d++i  l +d
  gi|336252705|ref|YP_004595812.1|   6 LQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAV--EALETLETGSTVQVPLGGGAYLRATIEDIDEAIVDLGAD 80 
                                       344556889999999999999999999999998754..4455555555555555666677778888999999999** PP

                              PRTP 389 cikaflkkplfkrllkkenelyarlkeiLeeirgrledgeaeaedesteealksagaseae 449
                                        +++f++     +l +k++ + +r+ e+ eei+ +le++ ++ e+++++ +++  +++ ++
  gi|336252705|ref|YP_004595812.1|  81 YAAEFEQDDAVDALENKKDTVDDRIDEVNEEIA-ELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       ******************************999.566666666665555554443333332 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 ?    7.2   4.3     0.011         1      68     112 ..       3      47 ..       1      55 [. 0.74
   2 ?   10.2   3.5    0.0015      0.13      43     117 ..      64     137 ..      60     150 .] 0.54

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                        V_ATPase_I  68 ekeldeleeelekleeelkelnenleklkkelnelvelkavleka 112
                                       +++l++l++el++++e+++ l++n e+l++e++e+ e+ + le+ 
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETL 47 
                                       567788888888888888888888888888888877777766654 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0015
                        V_ATPase_I  43 eeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefle 117
                                       +++ie+ ++a++     +   e ++++ +d le++ +++++++ e+ne+  +l++e ++l+++ + l++ +   +
  gi|336252705|ref|YP_004595812.1|  64 RATIEDIDEAIVDLGA-DYAAEFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQ 137
                                       5555555555444443.4555556666666666666666666666666666666666666666665544332222 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.2    0.0039      0.35     192     232 ..       4      44 ..       2      54 .. 0.48
   2 ?    8.2   6.6     0.016       1.5      97     148 ..      87     138 ..      61     144 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0039
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               HBM 192 aalqqlesalskYRaaleqfkaavaaieqarkemteqgdei 232
                                       ++lqql+++l++  +++e+++a v++ +q ++e+ e ++ +
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44 
                                       34444444444444444444444444444444444444433 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCS-S-HHHHHHHHHHHHHHHHHHHH CS
                               HBM  97 rnaaRqeldsaaeraleaideleaevlqtpeadserlaqlqaiaelkrqvql 148
                                       +++a  +l+++ ++++++ide+++e++++ +++++  +q+q++++  +q q+
  gi|336252705|ref|YP_004595812.1|  87 QDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQM 138
                                       4667789999999*************99777664444556666555544444 PP

>> Dor1  Dor1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.5    0.0025      0.22      47      86 ..       5      44 ..       2      54 .. 0.81
   2 ?    7.2   3.0      0.02       1.8      19      95 ..      63     140 ..      60     150 .] 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0025
                              Dor1 47 aleairqelediraqledLvlklpkLteectrfskkaeei 86
                                      +l++++qel++i++q+e L  ++++L++e t++ ++ e +
  gi|336252705|ref|YP_004595812.1|  5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44
                                      6778899999999999999999999999999988877655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.02
                              Dor1  19 LaeeaeeilaqiqdLarknyktlidaaealeairqelediraqledLvlklpkLteectrfskkaeeisek..rken 93 
                                       L++++e i++ i dL  + y +  ++ +a +a+ ++ + +++ ++++ +++ +L++e ++  ++a+++ ++  +++ 
  gi|336252705|ref|YP_004595812.1|  63 LRATIEDIDEAIVDLGAD-YAAEFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQamQQQM 138
                                       788888888888888754.7777788888888888888999999999999988888888888888888777553333 PP

                              Dor1  94 kl 95 
                                       + 
  gi|336252705|ref|YP_004595812.1| 139 QQ 140
                                       33 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.8      0.24        22      12      44 ..       6      38 ..       4      78 .. 0.65
   2 ?   12.7   2.7    0.0013      0.12      14      53 ..     100     139 ..      90     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.24
                         kleA_kleC 12 LpevatdlvarRdkiAaklaeAeeLvrqaeeLR 44
                                      L++ +++l+   ++i a++a+ eeL+++  e+ 
  gi|336252705|ref|YP_004595812.1|  6 LQQLSQELQEIQEQIEALQANVEELQQEKTEID 38
                                      566667777777777777777777776655543 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0013
                         kleA_kleC  14 evatdlvarRdkiAaklaeAeeLvrqaeeLRakvyeesaa 53 
                                        v++ +    ++iA++  e e+L++qa++L +++++++  
  gi|336252705|ref|YP_004595812.1| 100 TVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       356667777789**********************998765 PP

>> Dynamitin  Dynamitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.5     0.019       1.6      94     139 ..       3      48 ..       2      56 .. 0.79
   2 ?   10.6   3.9    0.0028      0.25      73     136 ..      81     139 ..      60     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.019
                         Dynamitin  94 eqklqRLqrEveeleeEvekakeaakeseeeeldpvelaeqleslq 139
                                       +q lq L  E++e++e++e+ +++ +e ++e+ +  e +e le+l+
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLE 48 
                                       5788999999999999999999998887777777777777777765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0028
                         Dynamitin  73 ykasssreyeladege.eketleqklqRLqrEveeleeEvekakeaakeseeeeldpvelaeqle 136
                                       y+a+  ++ + +d  e +k+t+ +++   + E++ele+E e+ +++a++ +++      + +q++
  gi|336252705|ref|YP_004595812.1|  81 YAAE-FEQDDAVDALEnKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQA-----MQQQMQ 139
                                       5555.444444444446999****************999999988887643222.....223332 PP

>> Cytochrom_C_2  Cytochrome C'
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.2      0.49        43      72     107 ..      12      42 ..       3      54 .. 0.50
   2 ?   13.9   4.3   0.00084     0.074      28     111 ..      60     143 ..      46     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.49
                                       THHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHH CS
                     Cytochrom_C_2  72 dkekfkakaaaleeaaaeLaaaakagdlaalkaafg 107
                                       + ++++++++al+++++eL++ +      ++ +a++
  gi|336252705|ref|YP_004595812.1|  12 ELQEIQEQIEALQANVEELQQEK-----TEIDEAVE 42 
                                       33344444444444444444433.....33444443 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00084
                                       ST--HHHHHHHHHHHHHHHCSGGGGC-TTGSSSSS--B-THHHHTHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHH CS
                     Cytochrom_C_2  28 apydaeavaaaaealaalakklpalFpegsdkgektkakpeiWedkekfkakaaaleeaaaeLaaaakagdlaalka 104
                                        +y ++++++  ea+ +l ++  a F+++ + ++  + k+ + ++ +++++++a+le++ ++L+++a++ +++a+++
  gi|336252705|ref|YP_004595812.1|  60 GAYLRATIEDIDEAIVDLGADYAAEFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQ 136
                                       4577888888889999999999999999999988889999999999******************************* PP

                                       HHHHHHH CS
                     Cytochrom_C_2 105 afgkvgk 111
                                       +++++g+
  gi|336252705|ref|YP_004595812.1| 137 QMQQMGQ 143
                                       ***9986 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   9.4      0.11       9.9      12      52 ..       4      44 ..       1      52 [. 0.40
   2 ?   12.7   9.3   0.00095     0.084      74     120 ..      95     141 ..      82     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.11
                               ERM 12 erLkqlqeeaekaqeaLreseetaelLaekarraeeeaelL 52
                                      ++L+ql +e ++ qe+ +  +  +e+L++++ +  e+ e L
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44
                                      33333333333333333333333333333333333333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00095
                               ERM  74 eeekeklerklreaeleaarleeeserkeeeaerLkeeleeareaee 120
                                       e++k+ + ++++e+++e+a+le+ese+ e++a++L++++++ ++++ 
  gi|336252705|ref|YP_004595812.1|  95 ENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQM 141
                                       6778899999999999***********99******999999998875 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   7.2     0.056         5     124     165 ..       3      44 ..       1      54 [. 0.70
   2 ?   11.8   5.4   0.00062     0.054     432     479 ..      96     141 ..      63     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.056
                               MAD 124 elelsekeseleelqerldllkkklseleqliqqlekkqkel 165
                                       +++l++ ++el+e+qe+ + l+++++el+q + + +++ + l
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44 
                                       567777777777777777777777777777776666555544 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00062
                               MAD 432 sladassskeevdslkkkleeLelerqrLreqkeelElelerreLqgd 479
                                       +++d    ++ +d++  ++ eLe e ++L++q ++l  + +++++q++
  gi|336252705|ref|YP_004595812.1|  96 NKKDT--VDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQM 141
                                       33333..45678888888888888888888888888888888888887 PP

>> DUF4515  Domain of unknown function (DUF4515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  11.0      0.12        11     166     206 .]       7      47 ..       3      47 .. 0.84
   2 ?   12.4   4.5    0.0012       0.1     154     201 ..      87     134 ..      64     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.12
                           DUF4515 166 qeLrkeLlqliketkkLekekskLeeqkqrlkeeqeyleaL 206
                                       q+L +eL++ ++++++L+++ ++L+++k+++ e +e le L
  gi|336252705|ref|YP_004595812.1|   7 QQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETL 47 
                                       89999999999999999999999999999999888877765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0012
                           DUF4515 154 lseftrsvkreNqeLrkeLlqliketkkLekekskLeeqkqrlkeeqe 201
                                        ++++ +++ + +    +  + ++e+ +Le+e+++Le+q q+l+++  
  gi|336252705|ref|YP_004595812.1|  87 QDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAM 134
                                       455666666666666777777788888888888888888888877643 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   7.2     0.076       6.7      54      99 ..       4      48 ..       1      56 [. 0.56
   2 ?   12.1   9.6    0.0011       0.1      41      98 ..      83     140 ..      65     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.076
                         Golgin_A5 54 qerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqele 99
                                      q+ ++l +elq+ ++qie l++++++l++++ +e++++ e l+ le
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEK-TEIDEAVEALETLE 48
                                      3444555666666666666666666665443.55555555555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0011
                         Golgin_A5  41 sstalsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqel 98 
                                       ++ ++ +++d+l++++d++ + + ++n++i +l +e ++le+q+q+ ++++++q+ + 
  gi|336252705|ref|YP_004595812.1|  83 AEFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       455678899*********************************9988776666555443 PP

>> MCU  Mitochondrial calcium uniporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.9    0.0095      0.84      51      93 ..       8      50 ..       3      65 .. 0.84
   2 ?    8.9   4.6     0.017       1.5      50      90 ..      99     139 ..      60     146 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0095
                                      TSSSSSHHHHHHHHHHHHH-SHHHHHHHHTCCCGGGCHHHHGG CS
                               MCU 51 eqlkkereleekleelreelepleekkeeidekAerrtrrllw 93
                                      + +++ +e++e++e+l++++e+l+++k+eide+ e+ ++ ++ 
  gi|336252705|ref|YP_004595812.1|  8 QLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLETG 50
                                      446778999***********************99988877665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.017
                                       STSSSSSHHHHHHHHHHHHH-SHHHHHHHHTCCCGGGCHHH CS
                               MCU  50 eeqlkkereleekleelreelepleekkeeidekAerrtrr 90 
                                       +    +  e++e+++el++e e+le++ ++++++A +++ +
  gi|336252705|ref|YP_004595812.1|  99 DTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       22234444555555555555555555555555555555444 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 ?    7.3   4.4      0.02       1.7     389     432 ..       6      47 ..       4      57 .. 0.84
   2 ?    9.7   5.2    0.0037      0.32     392     441 ..      94     143 ..      89     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.-HHHHHHH CS
                              FbpA 389 ykKlkraveaveeqieetkeeleylesveaaleqaesledleei 432
                                        + l +  ++++eqie+ ++++e l++ ++++++a   e+le +
  gi|336252705|ref|YP_004595812.1|   6 LQQLSQELQEIQEQIEALQANVEELQQEKTEIDEA--VEALETL 47 
                                       57889999*************************66..5555544 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.-HHHHHHHHHHHHHTTS CS
                              FbpA 392 lkraveaveeqieetkeeleylesveaaleqaesledleeikeELieegy 441
                                       l+++++ v  +i e++ee++ les  ++leq+++  + +++++ +++ g+
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMGQ 143
                                       7899**************************88788888888888877665 PP

>> DUF1465  Protein of unknown function (DUF1465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.1      0.05       4.4     106     142 ..       4      40 ..       2      50 .. 0.52
   2 ?    9.4   1.7    0.0097      0.86      91     136 ..      95     140 ..      75     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX.XXX CS
                           DUF1465 106 eelqeLierserLyervrrLdrelreeaeaaeaaenp 142
                                       ++lq+L ++ ++++e++  L++++ e ++++++ +++
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEA 40 
                                       4555666666666666666666655555554433333 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0097
                                       --..-----------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXX CS
                           DUF1465  91 aaaeasdaeavaeLpeelqeLierserLyervrrLdrelreeaeaa 136
                                       ++++++ ++ ++e+ ee++eL ++se+L ++ ++L+++  +++ ++
  gi|336252705|ref|YP_004595812.1|  95 ENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       3334777888999999999999999999999999998877776665 PP

>> ORF6C  ORF6C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   3.6     0.088       7.8       8      44 ..       5      41 ..       2      55 .. 0.64
   2 ?   11.0   3.7    0.0038      0.33      10      53 ..      99     142 ..      87     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.088
                             ORF6C  8 alkehdekieeidervkkLeenmpldesekeeiqkkv 44
                                      +l+++ ++++ei+e+++ L+ n    ++ek ei+++v
  gi|336252705|ref|YP_004595812.1|  5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAV 41
                                      4555566666666666666666555555566665555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0038
                             ORF6C  10 kehdekieeidervkkLeenmpldesekeeiqkkvkkkvvellg 53 
                                         +d +i+e++e++++Le +    e++++++q+++ ++ ++ +g
  gi|336252705|ref|YP_004595812.1|  99 DTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMG 142
                                       56799*************99999999999999999888877766 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.9    0.0095      0.84      24      61 ..       6      43 ..       3      53 .. 0.77
   2 ?    7.5   5.7     0.077       6.8      27      61 ..     101     137 ..      75     148 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0095
                      Occludin_ELL 24 YkelhaeleevskkfseLerelkelkegskeykkieee 61
                                       ++l +el+e++++++ L+++++el+++++e+++++e 
  gi|336252705|ref|YP_004595812.1|  6 LQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEA 43
                                      56788888888888888888888888888888877776 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.077
                      Occludin_ELL  27 lhaeleevskkfseLerelkelkegsk..eykkieee 61 
                                       + ++++ev+++++eLe+e ++l+++ +  + + ++++
  gi|336252705|ref|YP_004595812.1| 101 VDDRIDEVNEEIAELESESEQLEQQAQqlQQQAMQQQ 137
                                       3445666666666666666666666663333333333 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 ?    9.7   3.5     0.013       1.1      17      60 ..       3      45 ..       1      54 [. 0.48
   2 ?    8.9   8.6     0.022         2      65     118 ..      87     135 ..      62     145 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.013
                                      HHCHHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHH CS
                           T3SSipB 17 nkSLsqLenrlaawkamskaqqeaasklSdelqtalseakgatd 60
                                      ++ L+qL++ l+  + +++a q++ ++l +e +t ++ea +a +
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQE-KTEIDEAVEALE 45
                                      4445555555555555555555554444443.333344444333 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.022
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH..HHHHH CS
                           T3SSipB  65 aiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaaadalq 118
                                       + +++d ++ + d ++ ++de+ + + eL   e e  +le++ qQ++++  a+q
  gi|336252705|ref|YP_004595812.1|  87 QDDAVDALENKKDTVDDRIDEVNEEIAEL---ESESEQLEQQAQQLQQQ--AMQ 135
                                       34556777777777777888888888888...77777777777777743..333 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 ?    7.7   2.1     0.019       1.7      61      97 ..       5      41 ..       2      56 .. 0.47
   2 ?    9.2   3.2    0.0063      0.56      47      93 ..      92     136 ..      62     146 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.019
                             Atg14 61 kiknkkakleelksliadlrerlqelkdklsqlkkei 97
                                      +++++++ l+e++ +i+ l+++++el++  ++ ++++
  gi|336252705|ref|YP_004595812.1|  5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAV 41
                                      3344444444444444444444444444333333333 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0063
                             Atg14  47 kalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsql 93 
                                       +ale+k+  ++ +d+i+  ++ + el s++++l+++ q+l+++  q+
  gi|336252705|ref|YP_004595812.1|  92 DALENKK--DTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQ 136
                                       2333333..44455555555555555555555555555555444433 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 ?   11.1   2.0    0.0025      0.22     206     329 ..       6     126 ..       2     144 .. 0.35

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0025
                         Cas_DxTHG 206 lkklkeklkkeleefskalelirp.lellekaeklekeiveklkeeleei.esleeeesakplel............ 268
                                       l++l++    el+e+ + +e++++ +e l              ++e++ei e     e+++ le             
  gi|336252705|ref|YP_004595812.1|   6 LQQLSQ----ELQEIQEQIEALQAnVEEL--------------QQEKTEIdEAV---EALETLETgstvqvplggga 61 
                                       444455....6666666666666322222..............22222221111...11111122222333333355 PP

                         Cas_DxTHG 269 ..........................................lldeikkklekf......lkkqikwclekgliqqa 297
                                                                                  +de++++++++      l++q             
  gi|336252705|ref|YP_004595812.1|  62 ylratiedideaivdlgadyaaefeqddavdalenkkdtvddRIDEVNEEIAELeseseqLEQQ------------- 125
                                       5555222222222222222222222233333333344444444444444444443333332222............. PP

                         Cas_DxTHG 298 ltllreliislllegedilnkkkrreeieeel 329
                                                                       
  gi|336252705|ref|YP_004595812.1| 126 -------------------------------A 126
                                       ...............................1 PP

>> Sipho_Gp157  Siphovirus Gp157
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.5     0.042       3.7       2      36 ..      13      45 ..       5      55 .. 0.71
   2 ?   10.4   7.6    0.0057       0.5      14      74 ..      76     136 ..      62     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.042
                       Sipho_Gp157  2 LyelaeqykellelleeedvdeeeeeikdtLesle 36
                                      L e++eq+++l++++ee++ ++   ei ++ e+le
  gi|336252705|ref|YP_004595812.1| 13 LQEIQEQIEALQANVEELQQEK--TEIDEAVEALE 45
                                      6788888888888888887553..45666555554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0057
                       Sipho_Gp157  14 elleeedvdeeeeeikdtLesleeeieeKaeniakviknleaeaeaikeeekrLaerkksl 74 
                                       +l  + + + e++   d+Le+ +++++++++++   i +le+e+e++++++++L++ + + 
  gi|336252705|ref|YP_004595812.1|  76 DLGADYAAEFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQ 136
                                       3334445555566677788888899999999999999999999999999999999876544 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   7.3     0.037       3.2      24      63 ..       3      44 ..       2      51 .. 0.52
   2 ?   10.1   6.5    0.0054      0.47      57     110 ..      88     138 ..      63     145 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.037
                              YkyA 24 qekLtelekkeqelyeeiiel..gmdefdkikklsdealenv 63
                                      q++L++l ++ qe+ e+i +l  + +e+++ k+++dea+e +
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALqaNVEELQQEKTEIDEAVEAL 44
                                      667777777777777776544113333444444444444433 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0054
                              YkyA  57 dealenveeReellekekesieeakeefekikeeieeiedeelkkeaeelieam 110
                                       d+a++ +e++++ ++     i+e +ee+ ++++e e++e+++++ + ++++++m
  gi|336252705|ref|YP_004595812.1|  88 DDAVDALENKKDTVDD---RIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQM 138
                                       4444555555554444...45555555555555555555555555555555544 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   7.1     0.026       2.3      67     103 ..       5      41 ..       2      49 .. 0.48
   2 ?    9.3   6.7     0.016       1.5      57      94 ..      94     131 ..      81     144 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.026
                           DUF4200  67 kaeeerklkkekeaeikklkaeietlkseiekleekl 103
                                       + ++ +++ +e +++i+ l+a++e+l++e+++ +e++
  gi|336252705|ref|YP_004595812.1|   5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAV 41 
                                       3444444444444444444444444444444444444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.016
                           DUF4200  57 ndakraralkkaeeerklkkekeaeikklkaeietlks 94 
                                        ++k+     +++e ++++ e e+e ++l+++ ++l++
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQ 131
                                       33444444444444444444444444444444444443 PP

>> TFR_dimer  Transferrin receptor-like dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.066       5.9       3      29 ..      13      39 ..       5      57 .. 0.73
   2 ?    7.0   1.7     0.066       5.8       3      36 ..     105     136 ..      88     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.066
                         TFR_dimer  3 ldpLeeaikkfkkaaeefdkwadkwed 29
                                      l++++e+i++++ ++ee+++++ ++++
  gi|336252705|ref|YP_004595812.1| 13 LQEIQEQIEALQANVEELQQEKTEIDE 39
                                      678888888888888888888888775 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.066
                         TFR_dimer   3 ldpLeeaikkfkkaaeefdkwadkwedvggaess 36 
                                       +d+++e i+++++++e+++++a+++++  +a ++
  gi|336252705|ref|YP_004595812.1| 105 IDEVNEEIAELESESEQLEQQAQQLQQ--QAMQQ 136
                                       578899999999999999999999995..22222 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   9.1     0.019       1.7      57      93 ..       4      40 ..       3      52 .. 0.53
   2 ?    8.5  10.9     0.022       1.9       5      51 ..      93     139 ..      85     146 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.019
                        TPR_MLP1_2 57 kelqalreelnelkaeiaelkaeaesakaeleesees 93
                                      ++lq+l +el+e++++i+ l+a++e++++e  e  e+
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEA 40
                                      4566666666666666666666555555443333332 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.022
                        TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvk 51 
                                       +le+++++++++++e ++++++l+++ e+ +++a++ qq+  ++ ++
  gi|336252705|ref|YP_004595812.1|  93 ALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       66777777777777777777777777777777777777665555444 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   6.1     0.047       4.2      60     100 ..       4      44 ..       2      51 .. 0.71
   2 ?   10.4   6.1    0.0058      0.51      58      96 ..     101     139 ..      82     147 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.047
                              ADIP  60 etirkleaeierlqskierlktqleqlerelalvqakerql 100
                                       +++++l+ e++  q +ie l++++e+l++e +   ++   l
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44 
                                       67778888888888888888888888887776665555554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0058
                              ADIP  58 lnetirkleaeierlqskierlktqleqlerelalvqak 96 
                                       + ++i + + ei+ l+s+ e+l++q +ql++++ ++q +
  gi|336252705|ref|YP_004595812.1| 101 VDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       444555555555555555555555555555554444333 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.2     0.043       3.8     168     214 ..       7      42 ..       2      51 .. 0.51
   2 ?   10.4   4.5    0.0036      0.32     159     213 ..      83     137 ..      61     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.043
                            Cluap1 168 kalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqk 214
                                       ++l++++++++e++e +++++e+l+++++++++             +
  gi|336252705|ref|YP_004595812.1|   7 QQLSQELQEIQEQIEALQANVEELQQEKTEIDEA-----------VE 42 
                                       3445555555555555555555555555555544...........44 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0036
                            Cluap1 159 rqleleeiekalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraq 213
                                       +++e+++   al+++ ++v+++++++++++++les+ ++Le++ ++ +q+  ++q
  gi|336252705|ref|YP_004595812.1|  83 AEFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQ 137
                                       6788889999999******************************999887765544 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 ?   10.3   4.8    0.0049      0.43       8      50 ..       4      46 ..       2      52 .. 0.91
   2 ?    7.3   6.4     0.043       3.8     137     184 ..      98     139 ..      65     147 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0049
                            TACC_C  8 aalekvkeeveekeeeiqelkkkveelkkenqemkkivaefek 50
                                      ++l+++ +e +e +e+i+ l+++veel++e++e+ + v++ e+
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALET 46
                                      6889999***************************999998876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.043
                            TACC_C 137 kahaeekLekAneeiaqvrskakaetaalqasLrkeqlkvqSLeksle 184
                                       k++ ++++++ neeia+ +s+  +e++  qa+    ql+ q+++++++
  gi|336252705|ref|YP_004595812.1|  98 KDTVDDRIDEVNEEIAELESE--SEQLEQQAQ----QLQQQAMQQQMQ 139
                                       333344444444444444322..222222221....222222222222 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.5     0.018       1.6      44      85 ..       4      45 ..       2      54 .. 0.71
   2 ?    9.1   4.2    0.0038      0.34      43      93 ..      88     138 ..      63     141 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.018
                              COG6 44 eqLkriesdveklnelcdemkkklssakeetsdlleeaeeLk 85
                                      +qL+++++++++++e ++ ++ ++++ ++e +++ e +e+L+
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45
                                      677777777777777777777777777777777777777665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0038
                              COG6  43 aeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklel 93 
                                       +++++++e++ +  ++ +de+++++ + ++e+++l ++a++L+++  + ++
  gi|336252705|ref|YP_004595812.1|  88 DDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQM 138
                                       445555555555555555555555555555555555555555555555555 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  17.0    0.0055      0.48       9      97 ..       4     132 ..       2     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0055
                           DUF2353   9 eALliLskeLekcrqerdqyklmaeqLqerlsalkkqleeekakaadlkee.......................... 59 
                                       + L+ Ls+eL++++++ + +++ +e+Lq++  ++ +  e  ++ ++  + +                          
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLETGSTVQvplgggaylratiedideaivdlgad 80 
                                       56899*********************************99999999887779************************* PP

                           DUF2353  60 ..............kekekklsqlleesreenkalkleveeLrqklkeaqgD 97 
                                                     ++k+ ++ + + e+ ee  +l+ e e+L q+ + +q+ 
  gi|336252705|ref|YP_004595812.1|  81 yaaefeqddavdalENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ 132
                                       *************99999999999*********************9999874 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   8.2     0.011      0.99      33      69 ..       3      39 ..       1      40 [. 0.89
   2 ?    6.1   9.3      0.16        14      32      68 ..      94     130 ..      91     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.011
                            Csm1_N 33 sqkletkdqeiesLkeqlaeleekvkeleerrkkqeE 69
                                      +q+l++ +qe+++++eq+++l+++v+el++++++  E
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDE 39
                                      6999************************999987665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.16
                            Csm1_N  32 LsqkletkdqeiesLkeqlaeleekvkeleerrkkqe 68 
                                       L++k +t d++i ++ e++aele+++++le+++++ +
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQ 130
                                       6777888888888888888888888888888877654 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   8.2   0.00085     0.075      51      96 ..       3      48 ..       2      52 .. 0.78
   2 ?    4.3  12.8       0.5        44      51      88 ..     102     139 ..      72     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00085
                              FliJ 51 qafisaldeaiaqqkqelaqaekqvekareewqearqerkklekLk 96
                                      q+++++l +++++++++++ ++++ve+ ++e  e    +++le+L+
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLE 48
                                      6778888888888888888888888888888888888888888876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.5
                              FliJ  51 qafisaldeaiaqqkqelaqaekqvekareewqearqe 88 
                                          i+ ++e+ia++++e +q+e+q ++ +++ ++++ +
  gi|336252705|ref|YP_004595812.1| 102 DDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       55677788888888888888888888877777777654 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.2     0.002      0.18      85     131 ..       3      49 ..       1      56 [. 0.92
   2 ?    4.5   0.9      0.33        30      87     118 ..     100     131 ..      66     145 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.002
                      Sec8_exocyst  85 qekvselKesleeakkklstkkkeLkelnarsakykevieiLdaiee 131
                                       q+++++l ++l+e ++++++ +++ +el+++  + +e +e L+ +e 
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLET 49 
                                       8999***************************************9986 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.33
                      Sec8_exocyst  87 kvselKesleeakkklstkkkeLkelnarsak 118
                                       +v +  ++++e  ++l+ ++++L++ +++ ++
  gi|336252705|ref|YP_004595812.1| 100 TVDDRIDEVNEEIAELESESEQLEQQAQQLQQ 131
                                       33333334444444444444444443333222 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   3.2      0.17        15      63      88 ..      12      37 ..       2      49 .. 0.46
   2 ?   11.6   4.9    0.0023       0.2      47      98 ..      88     139 ..      65     145 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.17
                         AAA_lid_9 63 kkeskpeeleklekelaklekekeal 88
                                      + ++ +e++e+l++++++l++ek+++
  gi|336252705|ref|YP_004595812.1| 12 ELQEIQEQIEALQANVEELQQEKTEI 37
                                      22233334444444444444444443 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0023
                         AAA_lid_9  47 dkAIDllDeaaarvrlkkeskpeeleklekelaklekekealekeeekekae 98 
                                       d A+D l++   +v  + ++ +ee+++le+e ++le++ ++l+++  +++ +
  gi|336252705|ref|YP_004595812.1|  88 DDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       6666666666666666666666666666666666666666666666655555 PP

>> Tmemb_cc2  Predicted transmembrane and coiled-coil 2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   5.2    0.0014      0.13     217     261 ..       3      46 ..       1      51 [. 0.90
   2 ?    5.3   4.3       0.1         9     209     250 ..      94     135 ..      64     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0014
                         Tmemb_cc2 217 qeklekileelqeikeeqerleeelerlkeqlkkelkllkqaLqe 261
                                       q++l+++ +elqei+e+ e l++++e+l++  k+e++ + +aL++
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQ-EKTEIDEAVEALET 46 
                                       789*************************98.89999998888875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.1
                         Tmemb_cc2 209 sksaesesqeklekileelqeikeeqerleeelerlkeqlkk 250
                                        ++++ + + +++++ ee++e+++e e+le++ ++l++q  +
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQ 135
                                       455666677788888888888888888888888888866433 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   9.5     0.059       5.2      42      96 ..       5      54 ..       1      56 [. 0.59
   2 ?    9.9  11.1      0.01      0.88      22      60 ..     105     143 ..      83     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.059
                              YlqD 42 qakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvqkLelgsevk 96
                                      q+++l +e+++     i+e  e ++++ +e++++k ++++ +e +++Le gs v+
  gi|336252705|ref|YP_004595812.1|  5 QLQQLSQELQE-----IQEQIEALQANVEELQQEKTEIDEAVEALETLETGSTVQ 54
                                      33333333332.....333333334455677888888899999999999998875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.01
                              YlqD  22 qqqlqaqieqldkelqqLefqakrlikeikkqsaqqiee 60 
                                       +++++++i +l++e +qLe+qa++l +++ +q++qq+ +
  gi|336252705|ref|YP_004595812.1| 105 IDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMGQ 143
                                       467788888889999999999999888888888887655 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   5.7      0.12        10      33      64 ..      11      42 ..       3      50 .. 0.53
   2 ?   10.5   3.9    0.0061      0.54      23      64 ..      93     134 ..      89     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.12
                          JIP_LZII 33 arvdeLtsereiLreEleslqkakerlesrik 64
                                      +++ e++++ e+L+  +e+lq++k+++ + ++
  gi|336252705|ref|YP_004595812.1| 11 QELQEIQEQIEALQANVEELQQEKTEIDEAVE 42
                                      33445555555555555555555555555555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0061
                          JIP_LZII  23 aLnvvkddLIarvdeLtsereiLreEleslqkakerlesrik 64 
                                       aL+  kd    r+de ++e   L++E e+l+++ ++l+++  
  gi|336252705|ref|YP_004595812.1|  93 ALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAM 134
                                       566666666789************************999864 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.2     0.023         2      63      91 ..       4      32 ..       2      49 .. 0.54
   2 ?    7.5   1.1     0.047       4.2      50      93 ..      92     133 ..      68     143 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.023
                           DUF2730 63 kdlekLkllladlrgelkaleaevrqlsh 91
                                      ++l++L+ +l++++ +++al+a+v++l++
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQ 32
                                      45555555555555555555555555543 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.047
                           DUF2730  50 teletkvenLPtakdlekLkllladlrgelkaleaevrqlshqv 93 
                                       ++le k +++   + +++++ ++a+l+ e+++le++ +ql++q+
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTV--DDRIDEVNEEIAELESESEQLEQQAQQLQQQA 133
                                       4444444433..23355677777777777777777777777664 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  10.8      0.66        58     153     196 ..       4      48 ..       2      52 .. 0.73
   2 ?   13.8   4.5   0.00071     0.063     150     198 ..      86     135 ..      56     141 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.66
                            AAA_23 153 erleelekeleeledekkllekl.eqekekekeleeleeeleeil 196
                                       ++l++l++el+e++++++ l+++ e++++++ e++e  e+le+++
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANvEELQQEKTEIDEAVEALETLE 48 
                                       678888888888888888888876666667778877777777665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00071
                            AAA_23 150 dkkerleelekeleeledekkllekle.qekekekeleeleeeleeilke 198
                                       ++ +++++le+++++  d+++++++++ +++++ ++le+  ++l+++ ++
  gi|336252705|ref|YP_004595812.1|  86 EQDDAVDALENKKDTVDDRIDEVNEEIaELESESEQLEQQAQQLQQQAMQ 135
                                       34467888888888888888888888524445666666666666666444 PP

>> Med14  Mediator complex subunit MED14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0019      0.17      73     126 ..       6      59 ..       3     112 .. 0.85
   2 ?    0.2   1.0       4.7   4.2e+02      74      99 ..     113     140 ..      96     147 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHCCCCCHCCCCCHHHHHHCCHHHHHHHHCHHCHCTTCHCHCCCCCC CS
                             Med14  73 laflrqqneafedaadalkelkeslanaklpnpdlktAleVLstGrysrlpsli 126
                                       l++l+q+ + +++ ++al+++ e+l++ k+   +   Ale L tG+  ++p  +
  gi|336252705|ref|YP_004595812.1|   6 LQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLETGSTVQVPLGG 59 
                                       56889999999999********************************99999766 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 4.7
                                       HHHHHHHHCCCCCHCCC..CCHHHHHHC CS
                             Med14  74 aflrqqneafedaadal..kelkeslan 99 
                                       a l++++e++e+ a++l  +++++++++
  gi|336252705|ref|YP_004595812.1| 113 AELESESEQLEQQAQQLqqQAMQQQMQQ 140
                                       5566666666666666644445555554 PP

>> TLE_N  Groucho/TLE N-terminal Q-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.7   0.00099     0.087      24      56 ..       6      38 ..       2      42 .. 0.91
   2 ?    4.0   4.0      0.58        51      15      56 ..      96     137 ..      84     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00099
                             TLE_N 24 cdrikeefqflqaqyhsLklecekLasektemq 56
                                      ++++ +e+q +q+q++ L+ ++e L++ekte+ 
  gi|336252705|ref|YP_004595812.1|  6 LQQLSQELQEIQEQIEALQANVEELQQEKTEID 38
                                      678899*************************85 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.58
                             TLE_N  15 slkftvlescdrikeefqflqaqyhsLklecekLasektemq 56 
                                       + k tv + +d + ee+  l+++ ++L  + ++L+++ ++ q
  gi|336252705|ref|YP_004595812.1|  96 NKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQ 137
                                       56789999999999**99999999999999999998866544 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.3     0.003      0.26      67      97 ..       3      33 ..       1      53 [. 0.77
   2 ?    5.4   8.5      0.23        20      70     107 ..      91     128 ..      65     142 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.003
                             THOC7 67 erereryeaekeeieseieavreeieelkaq 97
                                      +++ +++ +e +ei+++iea++++ eel+++
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQE 33
                                      5778888888888888888888888888775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.23
                             THOC7  70 reryeaekeeieseieavreeieelkaqLeearatran 107
                                       ++ +e++k+++++ i +v eei+el+++ e+  ++ ++
  gi|336252705|ref|YP_004595812.1|  91 VDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQ 128
                                       45566777777777777777777776665555554443 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 ?   11.1   3.9    0.0041      0.37      37      78 ..       5      46 ..       2      52 .. 0.59
   2 ?    5.9   7.2      0.16        15      43     101 ..      96     130 ..      61     145 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0041
                                      HHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHH CS
                      Seryl_tRNA_N 37 krrelqveleelqaerNelskeIgkakkkkedaeeliaevke 78
                                      + ++l +el+e+q++  +l+++++++ ++k +++e ++  ++
  gi|336252705|ref|YP_004595812.1|  5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALET 46
                                      455666666666666666666666666666666666555555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  43 veleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                       ++                        ++ + ++++e++ee+++le e ++le++ ++l 
  gi|336252705|ref|YP_004595812.1|  96 NK------------------------KDTVDDRIDEVNEEIAELESESEQLEQQAQQLQ 130
                                       22........................333334444444444444444444444443332 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 ?   10.3   3.2    0.0073      0.64      33      81 ..       4      48 ..       2      54 .. 0.72
   2 ?    6.6   4.3      0.11       9.5      29      65 ..      99     135 ..      62     143 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0073
                            DUF948 33 atieelekqvdpilkevedllakvnelledvneklekvdplteavadlg 81
                                      +++++l +++++i +++e+l a+v+e    ++++  ++d+ +ea+++l 
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEE----LQQEKTEIDEAVEALETLE 48
                                      66777777777777777777777777....6777777777777777665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.11
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvne 65 
                                       d + ++i+e+++++ ++  e+e+l +++++l+++  +
  gi|336252705|ref|YP_004595812.1|  99 DTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQ 135
                                       4555666666666666666666666666665554332 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   7.2      0.09       7.9      32      69 ..       4      41 ..       3      49 .. 0.84
   2 ?   10.4   6.3    0.0059      0.52      20      59 ..      98     137 ..      95     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.09
                                      HHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXX CS
                            DivIVA 32 kdyeallkeneelkekvkeleeklkeykeleetLkktl 69
                                      +++++l +e +e++e++++l+ +++e ++ ++++ +++
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAV 41
                                      67889999999999999999999999999999988875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0059
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXX CS
                            DivIVA  20 edeVdeFLdqvakdyeallkeneelkekvkeleeklkeyk 59 
                                       +d Vd+ +d+v +++ +l +e+e+l+++ ++l+++ ++ +
  gi|336252705|ref|YP_004595812.1|  98 KDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQ 137
                                       789******************************9988765 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.7      0.17        15     187     221 ..      12      45 ..       2      49 .. 0.61
   2 ?   10.5   7.9    0.0032      0.29     190     238 ..      92     141 ..      66     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.17
                                       TT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHH CS
                            FliD_C 187 ssngtlqtasknltkqikdldkkiedldkrletle 221
                                          + +q++++ l+ ++++l+++ +++d+++e+le
  gi|336252705|ref|YP_004595812.1|  12 EL-QEIQEQIEALQANVEELQQEKTEIDEAVEALE 45 
                                       22.55666677777777777777777776666655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0032
                                       SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHH.HHHHHHHHHHHH CS
                            FliD_C 190 gtlqtasknltkqikdldkkiedldkrletleerlkk.qfaalekavskl 238
                                       ++l++++++++++i++++++i++l++++e+le++ ++ q +a+++ ++++
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQlQQQAMQQQMQQM 141
                                       578899*************************9998765788899999988 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 ?   10.7   7.1    0.0051      0.45      18      63 ..       3      48 ..       1      54 [. 0.60
   2 ?    6.2   9.6      0.13        12      37      76 ..      93     132 ..      83     146 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0051
                       TMF_TATA_bd 18 sseirrlEgElaslkeelerleaerdeareeivklmkeneelkelk 63
                                      ++++++l  El++++e++e l+a+ +e+++e  ++ + +e+l++l+
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLE 48
                                      4566666666666666666666666666666666666666655544 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.13
                       TMF_TATA_bd  37 rleaerdeareeivklmkeneelkelkkeleelekeleel 76 
                                        le+++d++ + i ++ +e  el++++++le++ ++l++ 
  gi|336252705|ref|YP_004595812.1|  93 ALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ 132
                                       4555555555555544444444444444444444433321 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   6.9      0.01      0.93      41      83 ..       4      42 ..       2      54 .. 0.59
   2 ?    7.4   7.3      0.07       6.2      35      84 ..      90     140 ..      61     146 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.01
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHH CS
                          Spectrin 41 kkhkaleaelaaqqervkalnelaeklldeghsaseeieerle 83
                                      +++++l +el++ qe+++al++  e+l++e+     ei e +e
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEK----TEIDEAVE 42
                                      5666666777777777777776666666653....33333333 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTTHTTHHHHHHHHHH CS
                          Spectrin  35 evqallkkhkaleaelaaqqervkalnelaekl.ldeghsaseeieerlee 84 
                                       +v al++k +++ + +++  e++ +l+  +e+l +++++ ++++ ++++++
  gi|336252705|ref|YP_004595812.1|  90 AVDALENKKDTVDDRIDEVNEEIAELESESEQLeQQAQQLQQQAMQQQMQQ 140
                                       333333333333333333333333333444444333333334444444433 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   7.7     0.013       1.2     100     142 ..       3      45 ..       2      49 .. 0.84
   2 ?    7.7   5.6    0.0099      0.87      79     144 ..      69     132 ..      62     143 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.013
                                       THHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHH CS
                              EzrA 100 kkklaeleeeldeveekikkileelkelteseeknreeieklk 142
                                       +++l++l +el+e++e+i+++++ ++el++ +++  e++e+l+
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45 
                                       5788899999999999999999999999999999999888886 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0099
                                       HHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHH CS
                              EzrA  79 eieellfeaeelldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkek 144
                                       +i+e + ++   +d+   ++   ++++le++ d+v+ +i++++ee++el +  e+ +++ ++l+++
  gi|336252705|ref|YP_004595812.1|  69 DIDEAIVDLG--ADYAAEFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ 132
                                       5555555443..333344455566777777777777777777777777777777777777777654 PP

>> End3  Actin cytoskeleton-regulatory complex protein END3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.0     0.033       2.9     165     194 ..       4      33 ..       1      47 [. 0.76
   2 ?    8.6   2.7     0.022       1.9      96     129 ..     102     135 ..      61     148 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.033
                              End3 165 knlksvkedietveeqVegLesylssrkee 194
                                       ++l+++++++++++eq+e L++ +++ ++e
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQE 33 
                                       678888888888888888888777766665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.022
                              End3  96 dweevrLkreLaeLeeklekveeeaekrkekere 129
                                       d   ++++ e+aeLe++ e++e++a++ +++  +
  gi|336252705|ref|YP_004595812.1| 102 DDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQ 135
                                       2224444555555555555555555433222222 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.6    0.0066      0.59     195     305 ..      13     136 ..       2     148 .. 0.39

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0066
                             LMBR1 195 ksdldeelkklyfeaaklntekeeaerele..dllkevkklrksisesdplrkyleeilk...kvPeeiaeklks.. 264
                                        ++++e++++l++++++l++ek+e  + +e  ++l+  ++++  +   + lr  +e+i +      +++a + ++  
  gi|336252705|ref|YP_004595812.1|  13 LQEIQEQIEALQANVEELQQEKTEIDEAVEalETLETGSTVQVPLGGGAYLRATIEDIDEaivDLGADYAAEFEQdd 89 
                                       33445555555555555555555444433322233333333333333333444444444444433333333333355 PP

                             LMBR1 265 ......nenkteeslaklekqlikalqkrertekqwkrllekalele 305
                                             n+++t +  +++ ++ i +l+ + ++ +q  + l++++  +
  gi|336252705|ref|YP_004595812.1|  90 avdaleNKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQ 136
                                       55545444444444444443333333333333333333333331111 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   4.0      0.02       1.8      19      56 ..       7      44 ..       2      57 .. 0.47
   2 ?    7.8   7.1     0.018       1.6      21      64 ..      94     139 ..      85     146 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.02
                              RmuC 19 ekveeeskeeaeeleslkeqlkelqelneqlgdeaenL 56
                                      +++++e +e +e+ e+l+++++elq+ ++++++  e+L
  gi|336252705|ref|YP_004595812.1|  7 QQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44
                                      33333334444444444444444444444444444444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.018
                              RmuC  21 veeeskeeaeeleslkeqlkelqelneqlgdeaenL.tkaLk.nsk 64 
                                       +e++++++ ++  +++e++ el++ +eql+++a++L ++a++ + +
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLqQQAMQqQMQ 139
                                       4445566666677777777777777777777777773344543333 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   8.2       2.4   2.1e+02      68      94 ..      86     112 ..       1     141 [. 0.48

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 2.4
                                       C.HHHHHHHHHHHHHHHHHHHHHHHHC CS
                       Hemerythrin  68 ggravldvlereHdeirelleelrell 94 
                                       + ++ +d+le+  d ++++++e++e +
  gi|336252705|ref|YP_004595812.1|  86 EQDDAVDALENKKDTVDDRIDEVNEEI 112
                                       233444444444444444444444444 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6  26.9       1.4   1.2e+02     180     277 ..       5     140 ..       2     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.4
                              HOOK 180 ekdelaQrcheldkqlsllqeEknaLlaenkklqerlsele.................................... 220
                                       + ++l+Q ++e+++q+ +lq   + L++e++++ e ++ le                                    
  gi|336252705|ref|YP_004595812.1|   5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALEtletgstvqvplgggaylratiedideaivdlgady 81 
                                       45688888888888999998888888888888888888888777777777777777777777777778888888888 PP

                              HOOK 221 ..ngeesgtiqltskkylelqkqleqlqeelfrlEtarddyrlkceelekevlelqqrn 277
                                         ++e++ +++  ++k   +  ++++++ee+  lE+  +++  ++++l+++ ++ q+++
  gi|336252705|ref|YP_004595812.1|  82 aaEFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       88888888888888888888888888888888888888888888888888888877765 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 ?    5.9   8.0      0.12        10      25      66 ..       4      42 ..       2      56 .. 0.53
   2 ?    4.1   0.4      0.42        37      49      86 ..      58      95 ..      34      96 .. 0.70
   3 ?    7.8  12.4     0.031       2.8      17      69 ..      88     137 ..      68     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.12
                        Phage_GP20 25 eerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknk 66
                                      ++ ++l ++l++ ++q+e L+++   +eeLq++ +e+ ++++
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQAN---VEELQQEKTEIDEAVE 42
                                      45556666666666666666555...3333333333333333 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.42
                        Phage_GP20 49 kdneeLqkqieelqaknkkakaeyeakiadlkldnaie 86
                                      ++ + L ++ie++ +++ +  a+y+a+ ++ +  +a+e
  gi|336252705|ref|YP_004595812.1| 58 GGGAYLRATIEDIDEAIVDLGADYAAEFEQDDAVDALE 95
                                      56778999999999999999999999999988888876 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.031
                        Phage_GP20  17 kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkak 69 
                                        +++d +e+ +dt+ +++++ ++++ +L+ +   +e+L++q ++lq+++ +++
  gi|336252705|ref|YP_004595812.1|  88 DDAVDALENKKDTVDDRIDEVNEEIAELESE---SEQLEQQAQQLQQQAMQQQ 137
                                       678999**********************877...9************998866 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.5    0.0098      0.86     277     317 ..       5      45 ..       1      55 [. 0.70
   2 ?    6.2   1.8     0.053       4.7     268     312 ..      95     137 ..      63     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0098
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHH CS
                               FH2 277 nleslekevkklekglkklekelessekkeepsdkflevlk 317
                                       +l++l++e++++++++++l+ ++e+ ++++++ d+ +e+l+
  gi|336252705|ref|YP_004595812.1|   5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45 
                                       66777777777777777777777777776666666666665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.053
                                       TTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-TH CS
                               FH2 268 knvkkaakvnleslekevkklekglkklekelessekkeepsdkf 312
                                       +n k++    ++++ +e+ +le++ ++le+++++ ++  + +++ 
  gi|336252705|ref|YP_004595812.1|  95 ENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQ--QAMQQQ 137
                                       5555555556777888888888888888888777777..222222 PP

>> Plk4_PB2  Polo-like Kinase 4 Polo Box 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.7     0.071       6.3      57      95 ..       9      47 ..       2      57 .. 0.74
   2 ?    6.2   0.5      0.19        17      34      83 ..      90     134 ..      74     146 .. 0.40

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.071
                          Plk4_PB2 57 seeeleslsselkkllehaeeclkqclklesalssleke 95
                                       ++el+++++++++l   +ee +++  ++++a+++le+ 
  gi|336252705|ref|YP_004595812.1|  9 LSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETL 47
                                      346788888999999999999999999999888888765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.19
                          Plk4_PB2  34 kvtkssgekvkiieksgksltleseeeleslsselkkllehaeeclkqcl 83 
                                        v   +++k ++ ++ +     e +ee+++l+se ++l ++a++ ++q++
  gi|336252705|ref|YP_004595812.1|  90 AVDALENKKDTVDDRID-----EVNEEIAELESESEQLEQQAQQLQQQAM 134
                                       44443333322211111.....1112233333333333333333333322 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.8      0.22        19      62     101 ..       5      44 ..       2      53 .. 0.58
   2 ?    9.4   2.2    0.0064      0.56      52     105 ..      79     133 ..      61     147 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.22
                          ISG65-75  62 klayienakekvdyyvekleslleeakekgtltesdaekl 101
                                       +l+++ +++++++++ e l++ +ee ++++t  ++++e l
  gi|336252705|ref|YP_004595812.1|   5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44 
                                       5555556666666666666666666655555555555544 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0064
                          ISG65-75  52 adyllk.etkdklayienakekvdyyvekleslleeakekgtltesdaeklkkac 105
                                       ady  + e +d+++ +en+k+ vd + +++++ ++e + +++  e++a++l++++
  gi|336252705|ref|YP_004595812.1|  79 ADYAAEfEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQA 133
                                       5554442455667777888888888888887777777777666666666665543 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.7     0.024       2.2      37      71 ..       4      38 ..       1      54 [. 0.55
   2 ?    7.6   2.3     0.035       3.1      35      76 ..      94     137 ..      64     149 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.024
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XX CS
                              SKA1 37 ellnklkkelqeeeeaikklkkeieaslkqqeklq 71
                                      ++l++l +elqe +e+i+ l++++e+ +++++++ 
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEID 38
                                      45555555555555555555555555554444433 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.035
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXX CS
                              SKA1  35 leellnklkkelqeeeeaikklkkeieaslkqqek..lqhlken 76 
                                       le++ + + ++++e +e i +l++e e+  +q ++   q ++++
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQlqQQAMQQQ 137
                                       33333333333333333333333333333222222101111111 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.0     0.028       2.5      12      45 ..       4      37 ..       2      50 .. 0.47
   2 ?    7.8   8.2     0.028       2.5      10      52 ..      94     136 ..      81     146 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.028
                                      HHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTH CS
                              GrpE 12 deeeeleeeleelekevkelkekllrllaefenl 45
                                      +++++l +el+e+++++++l+ ++++l++e  ++
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEI 37
                                      3344444444444444444444444444443333 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.028
                                       THHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHH CS
                              GrpE  10 eedeeeeleeeleelekevkelkekllrllaefenlrkrteke 52 
                                       +e+++++ + +++e ++e++el+++ ++l++++++l++++ ++
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQ 136
                                       3334444444444444444444444444444444444443333 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 ?    7.1   0.4     0.068         6       2      57 ..      13      65 ..      12      68 .. 0.86
   2 ?    6.9   3.5     0.075       6.7       8      49 ..     100     143 ..      67     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.068
                     Acyl-CoA_dh_C  2 laeieatvaraalkelaaaleaalealqeateallakaakgdpeealaaavpyLel 57
                                      l+ei++ ++  al++ +++l++  +++ ea+eal + +++g   ++ ++   yL++
  gi|336252705|ref|YP_004595812.1| 13 LQEIQEQIE--ALQANVEELQQEKTEIDEAVEALET-LETGSTVQVPLGGGAYLRA 65
                                      579999999..8999999****99999999999888.7777888888888888886 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.075
                     Acyl-CoA_dh_C   8 tvara..alkelaaaleaalealqeateallakaakgdpeeala 49 
                                       tv++   +++e++a+le   e+l++ +++l ++a++++ ++++ 
  gi|336252705|ref|YP_004595812.1| 100 TVDDRidEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMGQ 143
                                       44432446888999999999999999999999999887777765 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  14.7    0.0067       0.6      42      74 ..       4      36 ..       2      54 .. 0.82
   2 ?    4.7  21.9      0.34        30      24      92 ..      65     139 ..      60     150 .] 0.56

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0067
                              FlxA 42 ltkeekkkqqqliqaQIqqlqaQIaqlqqqqae 74
                                      +  ++ ++  q+iq+QI++lqa ++ lqq+++e
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTE 36
                                      456788899999999999999999999999987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.34
                              FlxA  24 kQiknlqkqLkelses..deltkeekk......kqqqliqaQIqqlqaQIaqlqqqqaekaqekqqsekeekskskq 92 
                                         i+++ + + +l+++       e+        ++++++   I+ ++ +Ia l+++ ++ +q++qq ++++++++ q
  gi|336252705|ref|YP_004595812.1|  65 ATIEDIDEAIVDLGADyaA--EFEQDDavdaleNKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       5566677777777777542..22222223444567777777777777777777776666666666666666555442 PP

>> T2SSM  Type II secretion system (T2SS), protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.0     0.013       1.2      41      71 ..       4      34 ..       2      68 .. 0.67
   2 ?    6.3   6.4      0.11       9.3      41      78 ..     103     140 ..      94     149 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.013
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             T2SSM 41 erieraqaelqklraqlawveeqaaevralr 71
                                      ++ +++ +elq+ ++q+++++++ +e+++ +
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEK 34
                                      5566677777777777777777777776655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXX CS
                             T2SSM  41 erieraqaelqklraqlawveeqaaevralr.aapasal 78 
                                       +ri++  +e+++l+++ +++e+qa+++++   + ++ ++
  gi|336252705|ref|YP_004595812.1| 103 DRIDEVNEEIAELESESEQLEQQAQQLQQQAmQ-QQMQQ 140
                                       556666666666666666666666666655522.22222 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 ?    8.5  11.3     0.012       1.1      26      72 ..       2      48 ..       1      55 [. 0.86
   2 ?    6.5  12.1     0.051       4.5      45      98 ..      82     135 ..      52     149 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.012
                              HemX 26 gqqqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqla 72
                                      gqqq q+l++e +e+q+q++al+++++++++ek++ +e  e+l++l+
  gi|336252705|ref|YP_004595812.1|  2 GQQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLE 48
                                      899999999999****************9999999999888888765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.051
                              HemX  45 aaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlsk 98 
                                       aa  +q ++v+a++++k+++ +r+++ +e++++le+e+eql++q ++lqqq  +
  gi|336252705|ref|YP_004595812.1|  82 AAEFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQ 135
                                       333333333677777777777777777777777777777777777666666433 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.1    0.0065      0.58      94     133 ..       5      44 ..       2      53 .. 0.48
   2 ?    5.3   9.3      0.12        10      84     126 ..      94     136 ..      83     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0065
                           DUF4763  94 lltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkel 133
                                       +l++ ++e++e+q +   L+  ++elqq +++ ++++++l
  gi|336252705|ref|YP_004595812.1|   5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44 
                                       2233344444444444444444444444444444444444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.12
                           DUF4763  84 ecvdedlelelltseqpeileLqrnnhkLrqqlaelqqhlkas 126
                                        + ++d+ ++++++++ ei eL  ++ +L qq ++lqq+  ++
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQ 136
                                       56677888899999*********************99975443 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   3.2     0.012         1     240     278 ..       5      43 ..       2      49 .. 0.78
   2 ?    5.2   3.7     0.049       4.3     212     288 ..      67     139 ..      61     148 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.012
                          Prominin 240 elerllenlkeakeqLeqvnklekeLrksgsqLrdglrg 278
                                       +l++l ++l+e++eq+e+++++ +eL+++++++ +++++
  gi|336252705|ref|YP_004595812.1|   5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEA 43 
                                       677888888888888888888888888888888877764 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.049
                          Prominin 212 sddLddagkhlgldladtlesnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrd.lnqal 287
                                       ++d+d+a   lg d a+++e+      +++++l ++  ++ + + +vn+   eL ++++qL++  ++ +++ ++q +
  gi|336252705|ref|YP_004595812.1|  67 IEDIDEAIVDLGADYAAEFEQD-----DAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQaMQQQM 138
                                       5667777777777777777777.....66666666666666666666666666666666666666655443134444 PP

                          Prominin 288 s 288
                                       +
  gi|336252705|ref|YP_004595812.1| 139 Q 139
                                       3 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 ?   10.7   9.2     0.004      0.36      30      64 ..       4      38 ..       2      40 .. 0.90
   2 ?    4.4   6.3      0.39        34      20      56 ..     107     141 ..      91     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.004
                            GIT_CC 30 akiqqLlkvNtslsdelrlLQskvqkLqaeNaqlr 64
                                       ++qqL +  ++++++++ LQ +v++Lq+e ++++
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEID 38
                                      58999999999*******************99876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.39
                            GIT_CC  20 elKkalaaseakiqqLlkvNtslsdelrlLQskvqkL 56 
                                       e+ +++a  e+  +qL +  ++l+++   +Q+++q++
  gi|336252705|ref|YP_004595812.1| 107 EVNEEIAELESESEQLEQQAQQLQQQ--AMQQQMQQM 141
                                       78889999999999999999999986..445444444 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.1     0.033       2.9      38      76 ..       4      42 ..       1      53 [. 0.65
   2 ?    7.2   4.4     0.053       4.7      38      82 ..      96     141 ..      83     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.033
                           DUF4446 38 kdgksleellkekleeveelkeeseelekeieeleeklk 76
                                      ++ ++l + l+e  e++e+l++++eel++e +e++e ++
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVE 42
                                      555666666666666666666666666666666666554 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.053
                           DUF4446  38 kdgksleellkekleeveelkeeseelekeieeleek.lkkslqkv 82 
                                       ++++++++ + e  ee+ el++ese+le++ ++l+++ +++++q++
  gi|336252705|ref|YP_004595812.1|  96 NKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQaMQQQMQQM 141
                                       4667889999999999999*****9999999999865267777776 PP

>> NBD94  Nucleotide-Binding Domain 94 of RH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.6     0.026       2.3       9      40 ..       8      39 ..       2      47 .. 0.82
   2 ?    6.9   1.4     0.093       8.2      11      40 ..      95     124 ..      86     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.026
                             NBD94  9 tkidkkkkiyeniekllnEleeiekektslee 40
                                      +  +++++i e+ie l   +ee+++ekt ++e
  gi|336252705|ref|YP_004595812.1|  8 QLSQELQEIQEQIEALQANVEELQQEKTEIDE 39
                                      555678999*******************9987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.093
                             NBD94  11 idkkkkiyeniekllnEleeiekektslee 40 
                                        +kk+++ ++i+++ +E++e+e e   le+
  gi|336252705|ref|YP_004595812.1|  95 ENKKDTVDDRIDEVNEEIAELESESEQLEQ 124
                                       578889999999999999999999877664 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.5     0.091       8.1      93     136 ..       7      49 ..       1      57 [. 0.52
   2 ?    8.7   2.7     0.013       1.2     108     139 ..      99     130 ..      82     144 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.091
                     Fzo_mitofusin  93 hqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqk 136
                                       +q+ qel++  +++++  + + +el++e +e+++ +e+le++++
  gi|336252705|ref|YP_004595812.1|   7 QQLSQELQEIQEQIEA-LQANVEELQQEKTEIDEAVEALETLET 49 
                                       3333344333333322.223334566666667777777776655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.013
                     Fzo_mitofusin 108 qqvdetekeleeeikelekeiekleevqkkak 139
                                        +vd   +e++eei+ele+e e+le+  ++++
  gi|336252705|ref|YP_004595812.1|  99 DTVDDRIDEVNEEIAELESESEQLEQQAQQLQ 130
                                       45555556666666666666666655444332 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  14.3      0.11       9.9      30     168 ..       3     141 ..       2     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.11
                              Vps5  30 kqeldslesqLkkLykaiellvsqrkelasataelakslesLaslelskslsralsqlaeveerikellerqaeqdv 106
                                       +q+l++l ++L+++++ ie+l+++ +el +   e+ +++e+L +le   ++   l   a + ++i+++ e   +   
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLETGSTVQVPLGGGAYLRATIEDIDEAIVDLGA 79 
                                       689*****************************************************************999987655 PP

                              Vps5 107 .ltLgetideylrligsvksvfeqRvk.lwqkwqsaeqelskkkeqleKlekaaksqqdklqql 168
                                        +  ++  d+ + +++  k+  ++R + + +++ + e+e ++  +q+++l+++a +q  ++qq+
  gi|336252705|ref|YP_004595812.1|  80 dYAAEFEQDDAVDALENKKDTVDDRIDeVNEEIAELESESEQLEQQAQQLQQQAMQQ--QMQQM 141
                                       15556668999**************86266789999999999999999999995555..77766 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 ?   10.8   7.1    0.0056       0.5      13      59 ..       3      49 ..       1      54 [. 0.91
   2 ?    4.7   6.7      0.42        37       9      48 ..      97     137 ..      81     145 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0056
                            CC2-LZ 13 keeieeLkaqlqaaeealaakqeeidelkeeikkkeeeletisvlka 59
                                      ++++++L+++lq+ +e+++a q +++el++e ++ +e +e ++ l +
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLET 49
                                      6799*********************************9999888865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.42
                            CC2-LZ   9 ekvk.keeieeLkaqlqaaeealaakqeeidelkeeikkke 48 
                                       +k    + i+e+++++ + e   ++ +++ ++l++++ +++
  gi|336252705|ref|YP_004595812.1|  97 KKDTvDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQ 137
                                       22233566666666666666666666666666666665554 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.7      0.27        24      46      73 ..       8      35 ..       2      40 .. 0.82
   2 ?   10.9   0.3    0.0063      0.55      46      77 ..      93     124 ..      51     127 .. 0.85
   3 ?    6.3   1.7      0.17        15      12      44 ..     111     145 ..     111     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.27
                                      XXHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         GTP-bdg_M 46 kleldrrlireriaklkkeLekvkkkre 73
                                      +l  + ++i+e+i+ l+ ++e+++++++
  gi|336252705|ref|YP_004595812.1|  8 QLSQELQEIQEQIEALQANVEELQQEKT 35
                                      6677788999999999999999998876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0063
                                       XXHHHHHHHHHHHHHHHHHHHHHHHHHH.... CS
                         GTP-bdg_M  46 kleldrrlireriaklkkeLekvkkkrelqrk 77 
                                        le ++ ++++ri+++++e+++++++ e++ +
  gi|336252705|ref|YP_004595812.1|  93 ALENKKDTVDDRIDEVNEEIAELESESEQLEQ 124
                                       6999*********************9998776 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHCXXXXXXXXX..X....XXXXXX CS
                         GTP-bdg_M  12 elAqlkyllprLeglgkelsrqgGgig..trGpGe 44 
                                       e+A+l+ +  +Le+++++l++q+ +++   +G+G+
  gi|336252705|ref|YP_004595812.1| 111 EIAELESESEQLEQQAQQLQQQAMQQQmqQMGQGQ 145
                                       79*****************9997765544677775 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 ?   10.9   5.3    0.0041      0.36      68     119 ..       3      47 ..       2      58 .. 0.52
   2 ?    4.1   6.8      0.53        47      69     114 ..      89     137 ..      63     143 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0041
                              COG2  68 qeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellkll 119
                                       q++l++++++l+++++++       ++ +++ve+  +e++e+ e+ e l+ l
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQI-------EALQANVEELQQEKTEIDEAVEALETL 47 
                                       445555555555555555.......555555555555555555544444444 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.53
                              COG2  69 eeleevesplaaarkkvesvreklser...eeeveskleeakeleekre 114
                                       ++++ +e +  ++ +++++v+e+++e    +e++e++ ++ ++ +++++
  gi|336252705|ref|YP_004595812.1|  89 DAVDALENKKDTVDDRIDEVNEEIAELeseSEQLEQQAQQLQQQAMQQQ 137
                                       4555555555555555555555555440004555555555554444443 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.0     0.067       5.9     125     167 ..       5      47 ..       2      56 .. 0.52
   2 ?    7.0   1.7     0.054       4.8     106     154 ..      85     133 ..      61     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.067
                             Spc29 125 klddqkleIkeLkreleqqrtvnseLqekvaeleeevkrlaal 167
                                       +l++   e++e++ ++e  ++  +eLq+  +e++e v+ l++l
  gi|336252705|ref|YP_004595812.1|   5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETL 47 
                                       3333344444555555555555555555555555555666555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.054
                             Spc29 106 esrldsiyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekv 154
                                         + d +    +k + ++  +d+ ++eI eL+ e eq +   ++Lq++ 
  gi|336252705|ref|YP_004595812.1|  85 FEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQA 133
                                       5556667777788899999999999999999999999999999998864 PP

>> DUF932  Domain of unknown function (DUF932)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.6     0.057         5     113     154 ..       4      45 ..       2     100 .. 0.82
   2 ?    8.0   4.1     0.025       2.2     109     150 ..      99     140 ..      96     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.057
                            DUF932 113 akvieakkaLglvveefeefeeeaealaavklteaeaeafae 154
                                       +++++ +++L+++ e++e++++++e+l++ k + +ea + +e
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45 
                                       7899999************************99999988888 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.025
                            DUF932 109 gnvdakvieakkaLglvveefeefeeeaealaavklteaeae 150
                                       ++vd++++e+++++ +  +e+e++e++a++l++  ++++ ++
  gi|336252705|ref|YP_004595812.1|  99 DTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       6899********************************998876 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.8      0.02       1.7     111     155 ..       4      48 ..       2      53 .. 0.82
   2 ?    5.1   1.1      0.22        20     109     144 ..      90     126 ..      64     143 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.02
                          Cauli_AT 111 etLkeaqnrikkleeetkklaekivtekllkeevkdlderlseir 155
                                       + L++ ++  ++++e+++ l+ +++  ++ k+e+ +  e l++++
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLE 48 
                                       568888889999999999999999999999999999888887765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.22
                          Cauli_AT 109 lletLkeaqn....rikkleeetkklaekivtekllkeev 144
                                        ++ L++ ++    ri++++ee+ +l+++ +    l+++ 
  gi|336252705|ref|YP_004595812.1|  90 AVDALENKKDtvddRIDEVNEEIAELESESEQ---LEQQA 126
                                       34445555444334555555555555544332...22222 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   9.3     0.022       1.9     181     316 ..       4     143 ..       1     147 [. 0.53

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.022
                              FUSC 181 egaeareaararlaadilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpela 257
                                       ++ ++ +++++++ ++i al+a ++ +  e+++i ++++al  l +  +  ++l  + +                l+
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLETGSTVQVPLGGGAY----------------LR 64 
                                       33444445555555555555555555555555555555555555555555555443322................33 PP

                              FUSC 258 allaelaal...................eaaaaaealeaalaalrarlralrrale.adadtaalllarlaellael 314
                                       a++++++++                   + ++ +++ +++++++ +++++l+++ e +++++++l +++++++++++
  gi|336252705|ref|YP_004595812.1|  65 ATIEDIDEAivdlgadyaaefeqddavdALENKKDTVDDRIDEVNEEIAELESESEqLEQQAQQLQQQAMQQQMQQM 141
                                       33333333344444444444544455554445677777788888888877777777666666777777777777777 PP

                              FUSC 315 aq 316
                                        q
  gi|336252705|ref|YP_004595812.1| 142 GQ 143
                                       66 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 ?    4.9   8.5      0.31        27      34      73 ..       6      45 ..       3      54 .. 0.57
   2 ?   10.2   5.2    0.0074      0.65      32      82 ..      89     139 ..      76     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.31
                            CENP-Q 34 kaaleaqLspelhslelLeaeiekeeralerdyeaLreLe 73
                                       ++l+++L+  ++++e L+a++e+++++  +  ea + Le
  gi|336252705|ref|YP_004595812.1|  6 LQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45
                                      4667777777777777777666655554444444443333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0074
                            CENP-Q  32 dekaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknakaeare 82 
                                       d+  ale++ ++  + +++  +ei ++e + e+ +++ ++L+++a  ++ +
  gi|336252705|ref|YP_004595812.1|  89 DAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       566799**************************************9998866 PP

>> bZIP_Maf  bZIP Maf transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   8.5     0.043       3.8      51      91 ..       4      44 ..       3      45 .. 0.92
   2 ?    7.1   6.1     0.091       8.1      53      84 ..     112     141 ..      86     148 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.043
                          bZIP_Maf 51 qqkeelekekeeleeelerlqqelsrlrqekdalkrkneql 91
                                      qq ++l +e +e +e+ e+lq+++++l+qek+++ ++ e+l
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44
                                      67788*****************************9998876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.091
                          bZIP_Maf  53 keelekekeeleeelerlqqelsrlrqekdal 84 
                                         ele+e e+le++ ++lqq+   ++   +++
  gi|336252705|ref|YP_004595812.1| 112 IAELESESEQLEQQAQQLQQQAMQQQM--QQM 141
                                       456777777777777777776544443..333 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   8.5       1.3   1.2e+02      12      38 ..       4      30 ..       2      39 .. 0.66
   2 ?    0.4   0.7       9.2   8.1e+02      22      32 ..      35      45 ..      26      49 .. 0.77
   3 ?    5.8   0.1      0.18        16      20      31 ..      66      77 ..      62      83 .. 0.89
   4 ?    6.9   9.6     0.083       7.3       9      41 ..      93     125 ..      86     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 1.3
                                      XXXTHHHHHHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC 12 ehYdnIEqkvedideeIaaLeekRqrL 38
                                      ++ ++  q++++i e+I+aL++  ++L
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEEL 30
                                      666777777888888888887744433 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 9.2
                                      HHHHHHHHHHH CS
                           Osmo_CC 22 edideeIaaLe 32
                                       +ide ++aLe
  gi|336252705|ref|YP_004595812.1| 35 TEIDEAVEALE 45
                                      57889888887 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.18
                                      HHHHHHHHHHHH CS
                           Osmo_CC 20 kvedideeIaaL 31
                                      ++edide I +L
  gi|336252705|ref|YP_004595812.1| 66 TIEDIDEAIVDL 77
                                      7********988 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.083
                                       XXXXXXTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC   9 lLqehYdnIEqkvedideeIaaLeekRqrLvdq 41 
                                        L+++ d +  ++++++eeIa+Le   ++L +q
  gi|336252705|ref|YP_004595812.1|  93 ALENKKDTVDDRIDEVNEEIAELESESEQLEQQ 125
                                       578888999***************955555443 PP

>> SPT16  FACT complex subunit (SPT16/CDC68)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.5     0.015       1.4      77     110 ..      10      43 ..       4      72 .. 0.81
   2 ?    4.3   4.5      0.47        42      77     118 ..     102     143 ..      84     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.015
                             SPT16  77 ekklqevfreikelkkkvkkreaekkekedlveq 110
                                       +++lqe+ ++i+ l+ +v++ ++ek e ++ ve 
  gi|336252705|ref|YP_004595812.1|  10 SQELQEIQEQIEALQANVEELQQEKTEIDEAVEA 43 
                                       5789*********************999887764 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.47
                             SPT16  77 ekklqevfreikelkkkvkkreaekkekedlveqekLilsks 118
                                       +++++ev +ei el+++ ++ e+++++ ++ + q+++++  +
  gi|336252705|ref|YP_004595812.1| 102 DDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMGQ 143
                                       45699999****************999999999999876654 PP

>> Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   2.1      0.27        24      91     123 ..       8      40 ..       2      49 .. 0.62
   2 ?    9.3   2.6     0.011      0.95      67     126 ..      80     138 ..      61     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.27
                                       HHHHHHHHCHHHHHHHHHHHHHHHHHHHHHT-X CS
                     Mt_ATP-synt_D  91 eekevkkeikefkeeskkrieelekeleklksl 123
                                       + ++  +ei+e +e+ ++++eel++e  +++++
  gi|336252705|ref|YP_004595812.1|   8 QLSQELQEIQEQIEALQANVEELQQEKTEIDEA 40 
                                       344445566666677777777777766666554 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.011
                                       HHHHHHHH--------TTTTHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHT-XXXX CS
                     Mt_ATP-synt_D  67 eFekkYealkipypedkyteevdaeekevkkeikefkeeskkrieelekeleklksllpf 126
                                       ++  ++e+ + +   ++++  vd   +ev++ei+e  +es++  ++++ +l++ +    +
  gi|336252705|ref|YP_004595812.1|  80 DYAAEFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQ-QLQQQAMQQQM 138
                                       677777777777777777888888888888888888888876655555.44444444444 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   5.8       0.4        35      25      43 ..      17      35 ..       2      49 .. 0.49
   2 ?    9.1   0.4     0.015       1.3      34      63 ..      90     119 ..      83     120 .. 0.92
   3 ?    8.9   2.7     0.018       1.6      26      49 ..     110     133 ..     102     141 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.4
                                      HHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 25 qaeieeLerrvkaLekeNk 43
                                      q++ie+L+  v++L++e +
  gi|336252705|ref|YP_004595812.1| 17 QEQIEALQANVEELQQEKT 35
                                      3344444444444444444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  34 rvkaLekeNksLkseleelkkevekLkskv 63 
                                        v+aLe++  +  ++++e ++e+++L+s++
  gi|336252705|ref|YP_004595812.1|  90 AVDALENKKDTVDDRIDEVNEEIAELESES 119
                                       699***********************9986 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  26 aeieeLerrvkaLekeNksLksel 49 
                                       +ei+eLe+++++Le++ ++L++++
  gi|336252705|ref|YP_004595812.1| 110 EEIAELESESEQLEQQAQQLQQQA 133
                                       566666666666666666665544 PP

>> L31  Mitochondrial ribosomal protein L31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3      0.28        25      17      56 ..       3      42 ..       1      53 [. 0.66
   2 ?    6.9   2.1     0.095       8.4      28      64 ..      99     134 ..      93     145 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.28
                               L31 17 ktqkarqrkRlkavDevieavkeslkkkgvslkalekaka 56
                                      ++q +++ + l+++ e iea+++ +++ +++ +++++a +
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVE 42
                                      5566666777777777777777777766666666665554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.095
                               L31  28 kavDevieavkeslkkkgvslkalekakaelpkesem 64 
                                        +vD+ i++v+e +++ + + ++le++ ++l++++ m
  gi|336252705|ref|YP_004595812.1|  99 DTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQA-M 134
                                       57888888888888888888888887766555432.2 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.0     0.015       1.4      11      48 ..       4      41 ..       2      54 .. 0.69
   2 ?    5.2   8.1      0.45        40      11      57 ..      96     141 ..      80     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.015
                    PRKG1_interact 11 eenerLkreLeelekelselkseleklkqqrqesvskr 48
                                      ++ ++L +eL+e++++++ l++++e+l+q+++e  ++ 
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAV 41
                                      56678899999999999999999999987655533332 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.45
                    PRKG1_interact  11 eenerLkreLeelekelselkseleklkqqrqesvskrssllelekr 57 
                                       +++++  ++++e+++e++el+se e+l+qq  +++++++   +++++
  gi|336252705|ref|YP_004595812.1|  96 NKKDTVDDRIDEVNEEIAELESESEQLEQQA-QQLQQQAMQQQMQQM 141
                                       5667778899999999999999999998664.445555555555444 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 ?    7.1   7.1     0.081       7.1      14      49 ..       5      40 ..       2      54 .. 0.48
   2 ?    7.2   9.8     0.076       6.7      15      64 ..      91     140 ..      63     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.081
                            CENP-H 14 ellklsqelrelqeeltevekenlrlkrknrelaae 49
                                      +l++lsqel+e+qe+++ ++++  +l++++ e+ + 
  gi|336252705|ref|YP_004595812.1|  5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEA 40
                                      344444444444444444444444444444443333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.076
                            CENP-H  15 llklsqelrelqeeltevekenlrlkrknrelaaellelakekesekekl 64 
                                       + +l+++  ++ ++++ev++e+ +l+ ++++l ++ ++l+++++++++++
  gi|336252705|ref|YP_004595812.1|  91 VDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       55667777777888888888888888888888888888888888887443 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  10.2     0.027       2.4     147     179 ..       3      35 ..       1      36 [. 0.93
   2 ?    6.0  11.8     0.096       8.5     104     178 ..      94     140 ..      61     147 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.027
                           DUF2968 147 rkeaaaLeaqreaaqaqlralqrqirqLqaqqe 179
                                       +++ ++L+++ +++q+q++alq ++++Lq++++
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKT 35 
                                       7999*************************9975 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.096
                           DUF2968 104 leaqkaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaqq 178
                                       le                              + +v +r +++ +e a Le++ e++++q ++lq+q  q q qq
  gi|336252705|ref|YP_004595812.1|  94 LEN----------------------------KKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       444............................44555555555555555555555555555555555555555444 PP

>> Sas10_Utp3  Sas10/Utp3/C1D family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.8    0.0039      0.34       2      29 ..       7      35 ..       6      56 .. 0.52
   2 ?    2.6   4.3       2.5   2.2e+02       9      27 ..     106     127 ..      62     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0039
                        Sas10_Utp3  2 eslsksldelqeslepllskakaee.kks 29
                                      ++ls++l+e+qe++e l++++++ + +k+
  gi|336252705|ref|YP_004595812.1|  7 QQLSQELQEIQEQIEALQANVEELQqEKT 35
                                      56666666666666666665444443222 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 2.5
                        Sas10_Utp3   9 delqeslepllskakaee...k 27 
                                       de++e +++l s++++ e   +
  gi|336252705|ref|YP_004595812.1| 106 DEVNEEIAELESESEQLEqqaQ 127
                                       5555555555543222222111 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   7.4       0.4        35     106     140 ..       4      38 ..       2      52 .. 0.65
   2 ?    9.9   9.3    0.0052      0.46      93     137 ..      93     137 ..      83     147 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.4
                           DUF3552 106 esleekekelkqkeqsleekeeeleelveeqrqeL 140
                                       ++l++  +el++ ++++e+ ++++eel++e+++  
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEID 38 
                                       56777777777777777777777777776665543 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0052
                           DUF3552  93 tLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqr 137
                                       +L++k+++++++ ++++e+  el++++++le++ ++l++   +q+
  gi|336252705|ref|YP_004595812.1|  93 ALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQ 137
                                       455555555555555555555555555555555555554433333 PP

>> DUF3138  Protein of unknown function (DUF3138)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.3    0.0019      0.17      23      95 ..      16     117 ..       4     130 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0019
                           DUF3138  23 tadrikalkaqltalqrqvkelraalaaak.............................aaaGgkissqkaaaaaaa 70 
                                         ++i+al+a++++lq++ +e+ +a++a +                                G++ ++      a +
  gi|336252705|ref|YP_004595812.1|  16 IQEQIEALQANVEELQQEKTEIDEAVEALEtletgstvqvplgggaylratiedideaiVDLGADYAAEFEQDDAVD 92 
                                       46899999999999999999999999998888899999988777755555555554444333333333333333334 PP

                           DUF3138  71 aaeaaaalteddvaqlkeqianael 95 
                                       a e+     +d + +++e+ia+ e 
  gi|336252705|ref|YP_004595812.1|  93 ALENKKDTVDDRIDEVNEEIAELES 117
                                       4444445555555555555555555 PP

>> USP8_interact  USP8 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.6    0.0059      0.52       4      47 ..       4      47 ..       2      77 .. 0.81
   2 ?    2.4   4.4       1.4   1.2e+02       6      39 ..     105     136 ..      87     147 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0059
                     USP8_interact  4 elvqkqqqkiaelkkevaeqkqqlseqkrelellkeyiralrst 47
                                      +++q+ +q+++e++++++  + +++e ++e + + e++ al + 
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETL 47
                                      56888889999999999999999999999988888888888765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 1.4
                     USP8_interact   6 vqkqqqkiaelkkevaeqkqqlseqkrelellke 39 
                                       +++ +++iael++e+++ +qq ++ +++   +++
  gi|336252705|ref|YP_004595812.1| 105 IDEVNEEIAELESESEQLEQQAQQLQQQ--AMQQ 136
                                       4445555555555555444444332222..1222 PP

>> Vps53_N  Vps53-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.7    0.0074      0.65      64     104 ..       4      44 ..       2      53 .. 0.70
   2 ?    3.6   3.5      0.31        27      60      91 ..      99     130 ..      61     145 .. 0.43

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0074
                           Vps53_N  64 kaieelfqkikeikdkaekseemvkeitrdIkqLDiAKknl 104
                                       + +++l+q+++ei+++ e  ++ v+e+ ++  ++D A   l
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44 
                                       56777777777777777777777777777777777665544 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.31
                           Vps53_N  60 eeaqkaieelfqkikeikdkaekseemvkeit 91 
                                       + +++ i e+ ++i e+ + +e+ e+  +++ 
  gi|336252705|ref|YP_004595812.1|  99 DTVDDRIDEVNEEIAELESESEQLEQQAQQLQ 130
                                       22223333333333333333333333333322 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   7.2     0.047       4.2     104     137 ..       3      36 ..       2      50 .. 0.74
   2 ?    6.6  12.5     0.057         5      98     149 ..      89     140 ..      80     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.047
                         PspA_IM30 104 etqlaqqrsaveqlrkqlealetkieelkakkel 137
                                       ++ql+q+ +  +++++q+eal +++eel+++k++
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTE 36 
                                       5677777777788888888888888888887775 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.057
                         PspA_IM30  98 kqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaakaqe 149
                                       + + ale + + + + ++++ +++++le   e+l+++ + l+ ++ ++++q+
  gi|336252705|ref|YP_004595812.1|  89 DAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       5678888899999999999999999999999999999999999988888886 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   2.5       0.2        18      32      82 ..       7      43 ..       2      52 .. 0.52
   2 ?    8.3   2.1     0.014       1.2      42      92 ..      87     139 ..      61     149 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.2
                              Tho2 32 eklkseieelakdrsderaaakkkkkekkrlkeliekLeeEkkeqiehvek 82
                                      ++l              +++ ++ +++++ l++++e+L++Ek+e  e+ve+
  gi|336252705|ref|YP_004595812.1|  7 QQL--------------SQELQEIQEQIEALQANVEELQQEKTEIDEAVEA 43
                                      333..............3444455555555555555555555555444443 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.014
                              Tho2  42 akdrsde.raaakkkkkekkrlkeliekLeeEkkeqiehvekvkkr.Lkeekk 92 
                                       + d  d+ +++++  ++++++++e i++Le+E ++ +++ ++ +++ ++++++
  gi|336252705|ref|YP_004595812.1|  87 QDDAVDAlENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQaMQQQMQ 139
                                       33334444566666666677777777777777666666555544331444443 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 ?    6.2   8.0      0.16        14      57      91 ..      11      44 ..       2      50 .. 0.53
   2 ?    6.3   9.6      0.15        13      65      91 ..      88     129 ..      49     141 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.16
                           DUF4140 57 vpnreaeeeelkalraeleeledelaaledelaaa 91
                                      ++ +e++e+ ++al+a +eel++e+++++++ +a+
  gi|336252705|ref|YP_004595812.1| 11 QELQEIQEQ-IEALQANVEELQQEKTEIDEAVEAL 44
                                      223333332.5566666666666666666655555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.15
                           DUF4140  65 e...............elkalraeleeledelaaledelaaa 91 
                                       +               +++++++e+ ele e ++le++++ +
  gi|336252705|ref|YP_004595812.1|  88 DdavdalenkkdtvddRIDEVNEEIAELESESEQLEQQAQQL 129
                                       233334443222233235555555555555555555555555 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.5     0.095       8.4      10      35 ..       4      29 ..       1      38 [. 0.80
   2 ?    5.1   1.2      0.24        21      14      35 ..      93     114 ..      84     127 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.095
                              MtrG 10 ddfnevkkrLdeieekvefvnsEiaq 35
                                      ++ +++ + L+ei+e++e  ++ + +
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEE 29
                                      67889999999999999998887654 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.24
                              MtrG  14 evkkrLdeieekvefvnsEiaq 35 
                                       +++++ d ++++++ vn Eia+
  gi|336252705|ref|YP_004595812.1|  93 ALENKKDTVDDRIDEVNEEIAE 114
                                       5566666677777777666654 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 ?    7.4   3.9     0.059       5.2      73     111 ..       6      44 ..       2      52 .. 0.73
   2 ?    6.4   2.1      0.12        11      70     103 ..      95     128 ..      63     146 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.059
                            DUF641  73 eseleaeiqeqrsllktyeitvkkleaelkakdseieeL 111
                                        ++l++e+qe ++ ++++++ v++l++e ++ d+ +e L
  gi|336252705|ref|YP_004595812.1|   6 LQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44 
                                       467788888888888888888888888877766666665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.12
                            DUF641  70 eaeeseleaeiqeqrsllktyeitvkkleaelka 103
                                       e+++ +++ +i+e  + ++ +e  +++le++ ++
  gi|336252705|ref|YP_004595812.1|  95 ENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQ 128
                                       2334444444444444444444444444444333 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.9      0.11       9.4     124     165 ..       5      46 ..       2      56 .. 0.58
   2 ?    7.0   8.4     0.054       4.8     121     164 ..      94     137 ..      79     149 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.11
                            DUF724 124 ekrkleeeidelekkilelerqlallkekkeaadkeiarlks 165
                                       + ++l++e++e++++i  l+ + + l+++k + d+ + +l++
  gi|336252705|ref|YP_004595812.1|   5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALET 46 
                                       445556666666666666666666666555555555555544 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.054
                            DUF724 121 eesekrkleeeidelekkilelerqlallkekkeaadkeiarlk 164
                                        e++k  +++ ide++++i+ele ++++l ++ ++ +++ ++ +
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQ 137
                                       34455555555555555555555555555533333333222222 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 ?    6.7   3.2     0.062       5.5      26      67 ..       8      49 ..       3      56 .. 0.81
   2 ?    6.9   4.3     0.054       4.8      29      74 ..      96     141 ..      78     150 .] 0.51

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.062
                     zf-CpG_bind_C 26 enkkklekirkeqeeakkklkelekklkkLeeliekakklsl 67
                                      +  ++l++i+++ e+++++++el++++++++e +e  ++l+ 
  gi|336252705|ref|YP_004595812.1|  8 QLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLET 49
                                      557889999999999999999999999999999988777654 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.054
                     zf-CpG_bind_C  29 kklekirkeqeeakkklkelekklkkLeeliekakklslkeeeeee 74 
                                       +k++++  +  e++++++ele+++++Le+  ++ ++++++++ ++ 
  gi|336252705|ref|YP_004595812.1|  96 NKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQM 141
                                       3444455555555555555555555555555555555544444332 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.7    0.0068       0.6      37      97 ..       4      63 ..       2      80 .. 0.50
   2 ?    3.6   7.2      0.37        33      13      66 ..      93     139 ..      78     148 .. 0.44

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0068
                             TMPIT 37 keikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesllpkknglyl 97
                                      +++++ +++l+e++++++ l+++v ee ++e +e++e ++  ++         p   g yl
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANV-EELQQEKTEIDEAVEALETLETGSTVQVPLGGGAYL 63
                                      344444444555555555554444.233334444444444444444444444455555555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.37
                             TMPIT  13 eleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeee 66 
                                       +       +++k +++   ++++ +ei++ + + ++l+++ ++l++++ +++ +
  gi|336252705|ref|YP_004595812.1|  93 A-------LENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       2.......3333333444444444444444444444444444444433222222 PP

>> CASP_C  CASP C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  17.7      0.11       9.4       4     129 ..       3     134 ..       2     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.11
                            CASP_C   4 qeelseleaeleeqkeLnekLEndllkvqseasnaskasdassagsevsrka.ese.gr......ksptssiisgae 72 
                                       q++l++l++el+e +e +e L ++++++q+e+++  +a +a ++ ++ s+ + +   g       +   ++i++  +
  gi|336252705|ref|YP_004595812.1|   3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLETGSTVQvPLGgGAylratiEDIDEAIVDLGA 79 
                                       799*****************************987766666555444444332332322332222222333333333 PP

                            CASP_C  73 esesaesss..essiLpivtsQRDRFrkrnaeLEeelrkqeetvsslraeiaslqkDNl 129
                                       +       +  ++  ++ + +  D   +r+ e++ee+++ e++ ++l +++++lq+  +
  gi|336252705|ref|YP_004595812.1|  80 DYA--A--EfeQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAM 134
                                       222..2..14488999***************************************9765 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 ?    6.2   3.5       0.1       9.2     111     149 ..       4      42 ..       2      54 .. 0.64
   2 ?    7.6   4.4     0.039       3.4      99     149 ..      84     134 ..      61     141 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.1
                       EMP24_GP25L 111 ekletleselkkleekldsikreqkylrereerlrdtne 149
                                       ++l++l +el++++e+++ ++ +++ l++ +++  +++e
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVE 42 
                                       556666666666666666666666666666666666555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.039
                       EMP24_GP25L  99 seasdykdsakkekletleselkkleekldsikreqkylrereerlrdtne 149
                                       ++++d++ +a ++k +t+ +++++++e + ++++e + l+++ ++l++++ 
  gi|336252705|ref|YP_004595812.1|  84 EFEQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAM 134
                                       334444555557777777777777777777777777777777777776654 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.8    0.0014      0.12      34      66 ..      10      39 ..       7      47 .. 0.82
   2 ?    1.4   0.5       4.7   4.1e+02      40      60 ..      63      83 ..      61      94 .. 0.65
   3 ?    3.4   4.7       1.1        99      29      60 ..      83     114 ..      81     122 .. 0.78
   4 ?    2.3   7.0       2.4   2.1e+02      15      54 ..      94     129 ..      91     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0014
                              HalX 34 seeYqeLearleelraqldetldelddaddfea 66
                                      s+e qe+++++e+l+a ++e+ +e     ++++
  gi|336252705|ref|YP_004595812.1| 10 SQELQEIQEQIEALQANVEELQQE---KTEIDE 39
                                      89*******************999...344443 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 4.7
                              HalX 40 Learleelraqldetldeldd 60
                                      L+a++e++ + + ++ +++ +
  gi|336252705|ref|YP_004595812.1| 63 LRATIEDIDEAIVDLGADYAA 83
                                      778888888888887777333 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 1.1
                              HalX  29 aeLadseeYqeLearleelraqldetldeldd 60 
                                       ae +++++ ++Le   +++ +++de+ +e+ +
  gi|336252705|ref|YP_004595812.1|  83 AEFEQDDAVDALENKKDTVDDRIDEVNEEIAE 114
                                       78899999999999999999999998888666 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 2.4
                              HalX  15 LasKravLeaekseaeLadseeYqeLearleelraqldet 54 
                                       L++K+++ +   +    + +ee +eLe++ e+l++q+ ++
  gi|336252705|ref|YP_004595812.1|  94 LENKKDTVDDRID----EVNEEIAELESESEQLEQQAQQL 129
                                       6666666666666....46899999999999999887765 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.7     0.021       1.9      14      45 ..       3      36 ..       1      47 [. 0.79
   2 ?    6.7   2.7     0.084       7.4      22      45 ..     105     128 ..      99     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.021
                           DUF1192 14 gqDLslLSve..ELeerIalLeaEIaRleaaiak 45
                                      +q L++LS e  E++e I++L+a ++ l+++ ++
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQElqEIQEQIEALQANVEELQQEKTE 36
                                      578999996444*************999998664 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.084
                           DUF1192  22 veELeerIalLeaEIaRleaaiak 45 
                                       ++E +e Ia+Le+E + le++ ++
  gi|336252705|ref|YP_004595812.1| 105 IDEVNEEIAELESESEQLEQQAQQ 128
                                       789999999999999999998775 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   3.9     0.034         3     175     239 ..       8      47 ..       1      89 [. 0.60
   2 ?    5.4   7.6     0.076       6.7     172     215 ..      97     141 ..      85     148 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.034
                        Fmp27_WPPW 175 lleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkes 239
                                        l++                           +e++e+ie+l+ +++el+++++ +++++e l++ 
  gi|336252705|ref|YP_004595812.1|   8 QLSQE-------------------------LQEIQEQIEALQANVEELQQEKTEIDEAVEALETL 47 
                                       11111.........................23344444444444444444444444444444444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.076
                        Fmp27_WPPW 172 qkelleeRleeleeqiekleekleelelkseke.deelkeeieel 215
                                       +k+ +++R++e++e+i++le++ e+le++ ++  +++++++++++
  gi|336252705|ref|YP_004595812.1|  97 KKDTVDDRIDEVNEEIAELESESEQLEQQAQQLqQQAMQQQMQQM 141
                                       344455555555555555555555555555554444444444443 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 ?    5.5   4.9      0.16        14      46      84 ..       7      45 ..       2      50 .. 0.73
   2 ?    7.9   7.0      0.03       2.6      66     114 ..      91     139 ..      65     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.16
                            Nsp1_C 46 neWDrvLvengekIskLysevleaeqeqnkidqeLeyie 84
                                      ++  + L e  e+I++L+ +v+e +qe+++id+  e +e
  gi|336252705|ref|YP_004595812.1|  7 QQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALE 45
                                      445566677778888888888888888888888777666 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.03
                            Nsp1_C  66 vleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellsklesqksd 114
                                       v + e+++  +d++++ ++++  eLes  +++E+++++l++++ +q+ +
  gi|336252705|ref|YP_004595812.1|  91 VDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQ 139
                                       5566889999999999999999999999999999999999777666654 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   3.3      0.07       6.2      72     103 ..       9      40 ..       2      50 .. 0.49
   2 ?    6.7   4.8      0.04       3.5      70     116 ..      92     138 ..      64     145 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.07
                       DLP_helical  72 lerqlpeaeerleelekevekleesakrieke 103
                                       l+++l+e++e++e+l+++ve+l+++  +i + 
  gi|336252705|ref|YP_004595812.1|   9 LSQELQEIQEQIEALQANVEELQQEKTEIDEA 40 
                                       34444444444444444444444444444443 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.04
                       DLP_helical  70 dvlerqlpeaeerleelekevekleesakriekelaelkkeieeari 116
                                       d le++  ++ +r++e+++e+++le++++++e++ ++l+++  + ++
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQM 138
                                       66666667777777777777777777777777777776666655554 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 ?   10.1   2.0     0.011      0.94      44      77 ..       7      38 ..       2      55 .. 0.44
   2 ?    2.8   6.5         2   1.8e+02      38      84 ..      86     132 ..      61     144 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.011
                      Syntaxin-6_N 44 teLrkalrsiewdledLeetvriveknpskfkid 77
                                      ++L ++l++i++++e L+  v+ ++++  k +id
  gi|336252705|ref|YP_004595812.1|  7 QQLSQELQEIQEQIEALQANVEELQQE--KTEID 38
                                      334444444444444444444333332..22222 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 2
                      Syntaxin-6_N  38 eldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrr 84 
                                       e d++ + L+++ ++++  +++ +e ++ +e++ ++ + ++++l+++
  gi|336252705|ref|YP_004595812.1|  86 EQDDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ 132
                                       45555555666666666666666666655555444444444443332 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.3     0.013       1.1       7      57 ..       3      53 ..       2      79 .. 0.79
   2 ?    3.7   2.2      0.67        59      37      67 ..     100     130 ..      59     145 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.013
                           DUF1515  7 lqqlgtllaevkelredlkrsedrsdasrakmyrkmdelvervtaleg.svv 57
                                      +qql++l +e++e++e++   +   +  + + +  +de ve +++le+ s+v
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQ-QEKTEIDEAVEALETLETgSTV 53
                                      5999************9987655444443.3456799******999951444 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.67
                           DUF1515  37 kmyrkmdelvervtalegsvvklkaditsvk 67 
                                        +  ++de+ e ++ le+   +l++   +++
  gi|336252705|ref|YP_004595812.1| 100 TVDDRIDEVNEEIAELESESEQLEQQAQQLQ 130
                                       3344555555555555555555444433333 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.8     0.021       1.8      19      63 ..       4      48 ..       2      52 .. 0.78
   2 ?    4.6   9.3      0.38        33      20      70 ..      90     140 ..      66     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.021
                              Med9 19 lsskdletktgelrhkLkkarelirelpgidrsveeqeaeieele 63
                                      ++ ++l+++++e++ +++   + ++el+     ++e  + +e+le
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLE 48
                                      678999999999999999999999999996666666666666665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.38
                              Med9  20 sskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKr 70 
                                        +  le+k + + ++++++ e i+el+  ++  e+q +++++   q ++++
  gi|336252705|ref|YP_004595812.1|  90 AVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       5667899999999**************************999887777765 PP

>> MRP-L28  Mitochondrial ribosomal protein L28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.5    0.0047      0.42      86     119 ..       4      37 ..       2      56 .. 0.85
   2 ?    2.5   4.9       1.7   1.5e+02      94     130 ..      97     133 ..      86     146 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0047
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTT CS
                           MRP-L28  86 yrqqekekdeqlirqqleaqeealeeLkkvseeL 119
                                       ++ q+  ++ q+i++q+ea++  +eeL+++ +e+
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEI 37 
                                       67888899**********************9987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHHHHHHHH-TTTCTTCS-XXTTS CS
                           MRP-L28  94 deqlirqqleaqeealeeLkkvseeLYeaAvkrdegl 130
                                       ++++++  +  ++e + eL+++se+L ++A + +++ 
  gi|336252705|ref|YP_004595812.1|  97 KKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQA 133
                                       4455555555566666666666666666655544443 PP

>> Med10  Transcription factor subunit Med10 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.1     0.005      0.44       1      59 [.       3      56 ..       3      59 .. 0.70
   2 ?    2.5   3.3       1.6   1.4e+02      29      51 ..     106     128 ..      61     148 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.005
                                      HHHHHHHHHHHHHHHHHHHS--TT.S-TTHHHHHHHHHHHHHHHHHHHHH..HH--EEE CS
                             Med10  1 eqqlkeviqsllelgvqvsdydenessqevlaqklktlvesLqelsktaskllqdikiP 59
                                      +qql+++ q+l e++ q+++ ++n ++ ++ ++++++ ve+L++   +++   +++++P
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALET---LET--GSTVQVP 56
                                      69********************9755555555555555555555...555..4556666 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 1.6
                                       THHHHHHHHHHHHHHHHHHHHH. CS
                             Med10  29 evlaqklktlvesLqelsktask 51 
                                       +++++++ +l+++ ++l+++a++
  gi|336252705|ref|YP_004595812.1| 106 DEVNEEIAELESESEQLEQQAQQ 128
                                       22333333333333333333332 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   5.6      0.13        12      72      98 ..       7      33 ..       3      43 .. 0.64
   2 ?    7.3   6.9     0.072       6.4      35      89 ..      82     139 ..      63     146 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.13
                           UPF0449 72 erLeeakeeLkqkceeLktageeLeee 98
                                      ++L+++ +e++++ e L+++ eeL++e
  gi|336252705|ref|YP_004595812.1|  7 QQLSQELQEIQEQIEALQANVEELQQE 33
                                      566666666667777777777777665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.072
                           UPF0449  35 lsdsveedkkass..seeedleaeveelYeqvrtylelnerLeeakeeLkqkc..eeLk 89 
                                        ++ +e+d++ ++  ++++  ++ ++e+ e++ ++ + +e+Le++ ++L+q+   ++++
  gi|336252705|ref|YP_004595812.1|  82 AAE-FEQDDAVDAleNKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAmqQQMQ 139
                                       333.4444444441123334444477777777777777777777777777763113344 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4     0.018       1.6     121     163 ..       7      49 ..       2      71 .. 0.59
   2 ?    1.9   1.2      0.77        68     119     151 ..     101     133 ..      80     147 .. 0.39

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.018
                            Tweety 121 ekleeeLtkleeifakrtdlletlrlvqeqveevvqqlselpf 163
                                       ++l++eL++++e++++ +  +e l++ +++++e+v++l+ l++
  gi|336252705|ref|YP_004595812.1|   7 QQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEALETLET 49 
                                       3455555555555555555555555555556666655555554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.77
                            Tweety 119 leekleeeLtkleeifakrtdlletlrlvqeqv 151
                                       ++ +++e  +++ e+ ++ ++l +  +++q+q+
  gi|336252705|ref|YP_004595812.1| 101 VDDRIDEVNEEIAELESESEQLEQQAQQLQQQA 133
                                       222222222222222222222222222222221 PP

>> FAD-SLDH  Membrane bound FAD containing D-sorbitol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.2      0.32        28      58      91 ..       2      35 ..       1      54 [. 0.65
   2 ?    7.3   1.4     0.053       4.7      63      93 ..     113     143 ..      81     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.32
                          FAD-SLDH 58 garlyaalvaedaefkaqlaaLaallekqkakdv 91
                                      g++ +++l++e +e+++q++aL+a +e+ + ++ 
  gi|336252705|ref|YP_004595812.1|  2 GQQQLQQLSQELQEIQEQIEALQANVEELQQEKT 35
                                      6677788888888888888888887755444433 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.053
                          FAD-SLDH  63 aalvaedaefkaqlaaLaallekqkakdvea 93 
                                       a l +e +++++q+++L++ + +q+++++ +
  gi|336252705|ref|YP_004595812.1| 113 AELESESEQLEQQAQQLQQQAMQQQMQQMGQ 143
                                       5688889999999999999999999988755 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.9     0.076       6.7      44      71 ..       5      38 ..       2      51 .. 0.44
   2 ?    6.3   7.4      0.11       9.9      41      90 ..      87     135 ..      85     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.076
                                      HHHHHHHHHHHHHHHHHHHH......HHHHHHHH CS
                             Nup54 44 evaqhrerlkeisdrleele......qkhqlets 71
                                      +++q+ + l+ei++++e+l+      q++++e+ 
  gi|336252705|ref|YP_004595812.1|  5 QLQQLSQELQEIQEQIEALQanveelQQEKTEID 38
                                      4444444444444444444411111113334433 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Nup54  41 QqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllr 90 
                                       Q+++v++++++ +++ dr++e++ ++ +e+ ++ e++ ++ ++l+++ ++
  gi|336252705|ref|YP_004595812.1|  87 QDDAVDALENKKDTVDDRIDEVN-EEIAELESESEQLEQQAQQLQQQAMQ 135
                                       78888888888888888888888.88888888888888888888888775 PP

>> Hemagglutinin  Haemagglutinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4     0.041       3.6     389     418 ..       4      33 ..       1      55 [. 0.80
   2 ?    3.4   2.1      0.22        20     359     419 ..      78     133 ..      72     142 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.041
                                       TEEEBXSSXXTTTTHHHHHHHHHHHHHHHH CS
                     Hemagglutinin 389 kqleavgkelnelekrieeldkkvddgfld 418
                                       +ql+++++el e++++ie l+ +v+++  +
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQE 33 
                                       799*******************99998765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.22
                                       EEEEEEXHHHHHHHHHHHHHHHHHHHHHTTTEEEBXSSXXTTTTHHHHHHHHHHHHHHHHH CS
                     Hemagglutinin 359 Gsavaadkkstqeainkitkkvnsliekenkqleavgkelnelekrieeldkkvddgfldv 419
                                       G+ +aa+ +   +a++ + +k +++ ++    ++ v +e+ ele + e+l+++ + +    
  gi|336252705|ref|YP_004595812.1|  78 GADYAAEFEQ-DDAVDALENKKDTVDDR----IDEVNEEIAELESESEQLEQQAQQLQQQA 133
                                       7788887764.57888888887777554....45566666666666666666655554444 PP

>> KfrA_N  Plasmid replication region DNA-binding N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  11.2      0.15        13      78     113 ..       4      39 ..       1      48 [. 0.71
   2 ?    9.4  10.7     0.018       1.6      74     114 ..      92     132 ..      58     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.15
                            KfrA_N  78 eaeeelaaaraelqaaraaleaeraeaearveelea 113
                                       ++ ++l ++ +e+q++++al+a ++e++++  e ++
  gi|336252705|ref|YP_004595812.1|   4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDE 39 
                                       566777777777777777777777777777666554 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.018
                            KfrA_N  74 aaleeaeeelaaaraelqaaraaleaeraeaearveeleae 114
                                        ale+ +++++ + +e+ +++a+le+e +++e+++++l+++
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ 132
                                       46777788888888899999999999999999999988887 PP

>> DUF4665  Domain of unknown function (DUF4665)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.4     0.025       2.2      44      81 ..       3      40 ..       1      54 [. 0.72
   2 ?    3.2   4.4       1.5   1.3e+02      44      85 ..     102     136 ..      90     148 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.025
                           DUF4665 44 kekvenldkalvdiqkdlkslskklkletkkkekvkkk 81
                                      +++ ++l+++l++iq+++++l  +++  +++k+++ + 
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEA 40
                                      56788899999999999999988777777777777543 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 1.5
                           DUF4665  44 kekvenldkalvdiqkdlkslskklkletkkkekvkkkkeke 85 
                                       ++++ ++++++++++ + ++l +       + ++++++  ++
  gi|336252705|ref|YP_004595812.1| 102 DDRIDEVNEEIAELESESEQLEQ-------QAQQLQQQAMQQ 136
                                       34555555555555555444444.......333333222222 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.8     0.043       3.8       5      39 ..      13      47 ..       2      83 .. 0.48
   2 ?    5.3   5.7      0.36        32      20      58 ..     103     141 ..      84     147 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.043
                           DUF2203  5 leeAnalLpllkelleelralrkeleeleeeleea 39
                                      l+e ++ +  l+  +eel++ ++e+ e++e+le+ 
  gi|336252705|ref|YP_004595812.1| 13 LQEIQEQIEALQANVEELQQEKTEIDEAVEALETL 47
                                      22333333333333333333333333333333333 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.36
                           DUF2203  20 eelralrkeleeleeeleeakaeaekseaaeleaeleel 58 
                                       +++ ++++e++ele+e e+ +++a++ ++++++++++++
  gi|336252705|ref|YP_004595812.1| 103 DRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQM 141
                                       234455555666666555555555555556666665554 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.0      0.13        11      96     119 ..       6      29 ..       2      54 .. 0.71
   2 ?    5.8   4.7      0.17        15      94     131 ..     103     140 ..      82     148 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.13
                          PHM7_cyt  96 idyyrekleeldeeieeerekvkk 119
                                       ++ ++++l+e++e+ie+++++v++
  gi|336252705|ref|YP_004595812.1|   6 LQQLSQELQEIQEQIEALQANVEE 29 
                                       567788888888888888887733 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.17
                          PHM7_cyt  94 daidyyrekleeldeeieeerekvkkkplgaaFvtfes 131
                                       d id  +e++ el+ e e++++++++ +++a+  ++++
  gi|336252705|ref|YP_004595812.1| 103 DRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       44666666666666666666665555555555444443 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 ?    8.2   5.4     0.038       3.3      21      66 ..       3      46 ..       2      49 .. 0.82
   2 ?    1.3   0.0       5.2   4.6e+02      56      71 ..      86     101 ..      63     103 .. 0.83
   3 ?    4.3   8.1      0.65        57      12      52 ..     100     140 ..      96     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.038
                       Cep57_MT_bd 21 edEfehlklelqelaaqynaldpslgkrkRkdLaeeleelvkrlEa 66
                                      + ++++l+ elqe ++q++al+  ++ ++ ++ + e++e v++lE 
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQ--ANVEELQQEKTEIDEAVEALET 46
                                      5689999999999999999999..7777777778888888888886 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 5.2
                       Cep57_MT_bd  56 eleelvkrlEaKadqI 71 
                                       e ++ v++lE K+d +
  gi|336252705|ref|YP_004595812.1|  86 EQDDAVDALENKKDTV 101
                                       677899******9976 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.65
                       Cep57_MT_bd  12 aLaevlkeLedEfehlklelqelaaqynaldpslgkrkRkd 52 
                                       +  + + e  +E+++l  e ++l++q ++l++ + +++ ++
  gi|336252705|ref|YP_004595812.1| 100 TVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQ 140
                                       56678899999999999999999999999997776666555 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   5.6    0.0061      0.54       1      32 [.       5      36 ..       4      45 .. 0.69
   2 ?    6.8   7.5       0.1         9       2      34 ..     105     137 ..     104     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0061
                               LPP  1 kldeLssqVsqLkskvdqlssdvnsakaaaqa 32
                                      +l++Ls+++++ ++++++l+++v++++++  +
  gi|336252705|ref|YP_004595812.1|  5 QLQQLSQELQEIQEQIEALQANVEELQQEKTE 36
                                      46778888888888888888877777665544 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.1
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaak 34 
                                       +de+++++ +L+s+ +ql++++++++++a++ +
  gi|336252705|ref|YP_004595812.1| 105 IDEVNEEIAELESESEQLEQQAQQLQQQAMQQQ 137
                                       899***********************9999865 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 ?    7.1   4.0     0.074       6.6      58      83 ..       4      29 ..       2      32 .. 0.62
   2 ?    3.5   0.2      0.94        83       2      25 ..      23      46 ..      22      50 .. 0.70
   3 ?    4.9  10.4      0.34        30       7      61 ..      92     146 ..      86     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.074
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100 58 qaaqklvdaLeeisealkqaanafed 83
                                      q++q+l ++L+ei+e++++  +++e+
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEE 29
                                      56666666666666666666666554 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.94
                                      HCSHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  2 ikvdpeelrqaaarfqkqaeeled 25
                                      ++++ eel+q  ++++++ e le+
  gi|336252705|ref|YP_004595812.1| 23 LQANVEELQQEKTEIDEAVEALET 46
                                      567777777777777777777765 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHH CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaq 61 
                                       ++l+ +  ++++  +e+ +e+++l++e ++l+++ +   ++a q++++++ q++q
  gi|336252705|ref|YP_004595812.1|  92 DALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMGQGQQ 146
                                       6677777888888888888888888888888887788888888888888877765 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1  18.2       2.2     2e+02     127     230 ..      13     141 ..       2     144 .. 0.42

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 2.2
                              CorA 127 lekleeeldeledel.edstkkeilrelaqlrrrlvkl.............rralapnrevlk........rlla.. 179
                                       l+++ e+++ l+ ++ e +++k +++e ++  ++l +              r  + +  e++         ++ +  
  gi|336252705|ref|YP_004595812.1|  13 LQEIQEQIEALQANVeELQQEKTEIDEAVEALETLETGstvqvplgggaylRATIEDIDEAIVdlgadyaaEFEQdd 89 
                                       44444444444444443333333333333322222222222334444444455555555555533332222222221 PP

                              CorA 180 .kaddkllddedkeylrdlldelerllemlealrerleslqdtyssllserl 230
                                         +  ++ +d+  ++++++ +e++ l+ ++e+l +++++lq++ ++++ +++
  gi|336252705|ref|YP_004595812.1|  90 aVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQM 141
                                       1111111111222236666666666777777777777777777777766666 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.8      0.07       6.1      48      87 ..       4      43 ..       1      56 [. 0.59
   2 ?    5.9  12.4       0.2        18      27      77 ..      96     146 ..      80     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.07
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHH CS
                             DUF16 48 eqinkleqkvekqgekikelkveqkaqgeelnkvdetlel 87
                                      +q+++l q+ ++ +e+i+ l+++++  ++e  ++de++e 
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEA 43
                                      5566666666666666666666666655555544444443 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.2
                                       HB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
                             DUF16  27 efkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgee 77 
                                       + kd  + r+ +++++++ l+ + ++leq+ ++++++ ++++ +q  qg++
  gi|336252705|ref|YP_004595812.1|  96 NKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQMQQMGQGQQ 146
                                       334556777777777777777777777777777777777777777777775 PP

>> Rho_Binding  Rho Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   8.1     0.077       6.8       3      39 ..       4      40 ..       3      50 .. 0.67
   2 ?    5.1  11.1      0.45        39       3      30 ..     110     137 ..      86     147 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.077
                       Rho_Binding  3 kdvenlakekeelnkklkkleeelekakeeeeeiekl 39
                                      +++++l++e +e++++++ l+ ++e++++e+ ei++ 
  gi|336252705|ref|YP_004595812.1|  4 QQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEA 40
                                      5677788888888888877777777777666666554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.45
                       Rho_Binding   3 kdvenlakekeelnkklkkleeelekak 30 
                                       +++++l++e e+l+++ ++l+++  +++
  gi|336252705|ref|YP_004595812.1| 110 EEIAELESESEQLEQQAQQLQQQAMQQQ 137
                                       4566777777777777777666666665 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   6.6     0.084       7.4      14      50 ..       2      38 ..       1      47 [. 0.75
   2 ?    5.2  10.2      0.23        20      24      63 ..      90     129 ..      68     138 .. 0.79
   3 ?    0.1   5.0       9.6   8.5e+02      19      30 ..     120     131 ..     118     144 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.084
                           DUF2205 14 erearerLqqqakeLqssLqaLaervdeVkeehdKLe 50
                                      ++++ ++L+q  +e+q+  +aL + v+e ++e+  ++
  gi|336252705|ref|YP_004595812.1|  2 GQQQLQQLSQELQEIQEQIEALQANVEELQQEKTEID 38
                                      6677788888888888888888888888888876655 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.23
                           DUF2205  24 qakeLqssLqaLaervdeVkeehdKLesenrfLqqYIgdL 63 
                                        +++L +  + + +r+deV ee   Lese++ L q   +L
  gi|336252705|ref|YP_004595812.1|  90 AVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQL 129
                                       57778888888999****************9999877776 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 9.6
                           DUF2205  19 erLqqqakeLqs 30 
                                       e+L+qqa++Lq+
  gi|336252705|ref|YP_004595812.1| 120 EQLEQQAQQLQQ 131
                                       567777777775 PP

>> Vps52  Vps52 / Sac2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.3    0.0052      0.46      41      82 ..       3      44 ..       2      47 .. 0.94
   2 ?    1.0   2.2       1.6   1.4e+02      13      63 ..      88     138 ..      78     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0052
                             Vps52 41 qsdlssissdikklqekSnelqlrLenrkaveaklsklvddl 82
                                      q++l+++s++++ +qe+  +lq + e  +  ++++ + v+ l
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVEAL 44
                                      789*********************************999865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.6
                             Vps52  13 seniaslhnqiaaidsvleqledlLeeFqsdlssissdikklqekSnelql 63 
                                        + +  l n+ + +d+ ++++ + + e +s+ +++ ++ ++lq++ ++ q+
  gi|336252705|ref|YP_004595812.1|  88 DDAVDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQAMQQQM 138
                                       456667788888888888888888888888888888888888888776665 PP

>> CCDC106  Coiled-coil domain-containing protein 106
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.6     0.032       2.8       4      32 ..       6      34 ..       3      48 .. 0.90
   2 ?    4.0   1.0       0.4        35      30     107 ..      96     134 ..      61     150 .] 0.42

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.032
                           CCDC106  4 ltklkkqLevkkEkiswlqkriedLeeeR 32
                                      l++l ++L+  +E+i++lq  +e+L++e+
  gi|336252705|ref|YP_004595812.1|  6 LQQLSQELQEIQEQIEALQANVEELQQEK 34
                                      789999*********************97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.4
                           CCDC106  30 eeRdFLRcqlekfissksleaeaekeskskksekkaeksesessssseesddsssdssessessegsstekkkkkkk 106
                                       + +d    +++++                                       ++  ++ +ses++ ++++++ +++ 
  gi|336252705|ref|YP_004595812.1|  96 NKKDTVDDRIDEV---------------------------------------NEEIAELESESEQLEQQAQQLQQQA 133
                                       3333333333332.......................................2222333333333322222222221 PP

                           CCDC106 107 k 107
                                        
  gi|336252705|ref|YP_004595812.1| 134 M 134
                                       1 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   6.9     0.013       1.2       2      37 ..       3      38 ..       2      47 .. 0.68
   2 ?    3.9   7.5      0.62        55       2      35 ..     109     140 ..     108     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.013
                              BRE1  2 qkELvklekafeelseqlskkvkeltileekklrle 37
                                      q+ L++l+++ +e +eq+++++++++ l+++k+ ++
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEID 38
                                      566777777777777777777777777777776654 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.62
                              BRE1   2 qkELvklekafeelseqlskkvkeltileekklr 35 
                                       + E+ +le + e+l++q+++++++  ++++++++
  gi|336252705|ref|YP_004595812.1| 109 NEEIAELESESEQLEQQAQQLQQQ--AMQQQMQQ 140
                                       689******************776..66666665 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.4     0.029       2.6       4      41 ..       5      42 ..       3      50 .. 0.55
   2 ?    1.6   0.1       3.3   2.9e+02      30      44 ..      89     109 ..      63     111 .. 0.57
   3 ?    5.0   7.0      0.29        26       2      29 ..     109     136 ..     101     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.029
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHH CS
                              Swi5  4 eikeleeqleelekelaelkeelkekkdpeetvkrhIk 41
                                      ++++l ++l+e+++++++l+++ +e ++ ++++++ ++
  gi|336252705|ref|YP_004595812.1|  5 QLQQLSQELQEIQEQIEALQANVEELQQEKTEIDEAVE 42
                                      55566666666666666666655555544444444443 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 3.3
                                       H.......HHHHHHHHHHHHH CS
                              Swi5  30 k......dpeetvkrhIklLh 44 
                                       +      ++++tv++ I+ ++
  gi|336252705|ref|YP_004595812.1|  89 DavdaleNKKDTVDDRIDEVN 109
                                       122233357788888887665 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Swi5   2 eaeikeleeqleelekelaelkeelkek 29 
                                       ++ei+ele++ e+le++ ++l+++  ++
  gi|336252705|ref|YP_004595812.1| 109 NEEIAELESESEQLEQQAQQLQQQAMQQ 136
                                       4677888888888888888887776654 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.0      0.12        11     264     296 ..       6      38 ..       1      42 [. 0.82
   2 ?    5.8   1.8     0.085       7.5     228     269 ..      91     132 ..      67     146 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.12
                             FAM76 264 reklkelekeakekieklekkirellkevaels 296
                                        ++l++  +e++e+ie+l+++++el++e++e+ 
  gi|336252705|ref|YP_004595812.1|   6 LQQLSQELQEIQEQIEALQANVEELQQEKTEID 38 
                                       467888889999999**********99999886 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.085
                             FAM76 228 iaslkkqleqkdqellekdkkitelkaellekekelreklke 269
                                       +  l+ + ++ d  + e + +i+el +e ++ e++ ++  ++
  gi|336252705|ref|YP_004595812.1|  91 VDALENKKDTVDDRIDEVNEEIAELESESEQLEQQAQQLQQQ 132
                                       444555555556666666666666666666666555443222 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   6.8     0.056       4.9      37      71 ..       3      37 ..       2      45 .. 0.91
   2 ?    4.5   5.5      0.54        48      36      60 ..     108     132 ..      68     141 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.056
                       Fungal_TACC 37 qkkldklelenkslkqeieqLkkqleaerkEKqeL 71
                                      q++l++l++e ++ +++ie L+ ++e  ++EK+e+
  gi|336252705|ref|YP_004595812.1|  3 QQQLQQLSQELQEIQEQIEALQANVEELQQEKTEI 37
                                      789*****************************986 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.54
                       Fungal_TACC  36 yqkkldklelenkslkqeieqLkkq 60 
                                        ++++ +le e ++l+q+ +qL++q
  gi|336252705|ref|YP_004595812.1| 108 VNEEIAELESESEQLEQQAQQLQQQ 132
                                       3455666666666666666666665 PP

>> Pro_CA  Carbonic anhydrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2      0.53        47      83     126 ..       8      46 ..       1      73 [. 0.48
   2 ?    5.5   2.2      0.21        19      80     127 ..      97     141 ..      78     146 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHHHHHHCHHHHHTTSSHHHHHHHHHHHHHHHHHHH CS
                            Pro_CA  83 aidkwlekirealekveeelesekekearerlleeenVaeqlen 126
                                       ++++ l++i+e +e+ +++ e+     ++e++ e  + +e le+
  gi|336252705|ref|YP_004595812.1|   8 QLSQELQEIQEQIEALQANVEE----LQQEKT-EIDEAVEALET 46 
                                       3333333333333333332222....222222.22223333333 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.21
                                       TSSHHHHHHHHHHHHHHHCHHHHHTTSSHHHHHHHHHHHHHHHHHHHH CS
                            Pro_CA  80 eagaidkwlekirealekveeelesekekearerlleeenVaeqlenL 127
                                       +++ +d+ +++++e +++ e+   ++++ e+++++l +++ ++q++++
  gi|336252705|ref|YP_004595812.1|  97 KKDTVDDRIDEVNEEIAELES---ESEQLEQQAQQLQQQAMQQQMQQM 141
                                       233444444444444444333...333456666666777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4381  (0.244353); expected 358.6 (0.02)
Passed bias filter:                     1492  (0.0832171); expected 358.6 (0.02)
Passed Vit filter:                       438  (0.0244297); expected 17.9 (0.001)
Passed Fwd filter:                       300  (0.0167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             203  [number of targets reported over threshold]
# CPU time: 1.45u 0.37s 00:00:01.81 Elapsed: 00:00:00.54
# Mc/sec: 837.33
//
Query:       gi|336252706|ref|YP_004595813.1|  [L=494]
Description: signal recognition particle-docking protein FtsY [Halopiger xanaduensis SH-6]
Scores for 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-68  228.2   0.2    9.3e-68  227.7   0.2    1.2  1  SRP54            SRP54-type protein, GTPase domain
    4.8e-13   49.1   0.7    4.8e-13   49.1   0.7    2.4  2  SRP54_N          SRP54-type protein, helical bundle domain
    2.4e-05   24.3   0.0    4.3e-05   23.5   0.0    1.3  1  APS_kinase       Adenylylsulphate kinase
     0.0005   19.8   0.7     0.0023   17.7   0.7    2.1  1  AAA_30           AAA domain
    0.00063   19.5   0.8      0.019   14.6   0.0    2.8  2  Thymidylate_kin  Thymidylate kinase
     0.0008   19.5   0.1     0.0016   18.5   0.1    1.6  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00092   18.5   1.4    0.00098   18.4   0.1    1.7  2  Zeta_toxin       Zeta toxin
     0.0024   17.8   0.3     0.0095   15.9   0.1    2.0  2  NTPase_1         NTPase
      0.003   16.9   0.0     0.0056   16.0   0.0    1.4  1  6PF2K            6-phosphofructo-2-kinase
      0.006   16.8   0.0      0.015   15.4   0.0    1.7  1  AAA_33           AAA domain
     0.0069   16.6   0.3     0.0069   16.6   0.3    3.4  3  AAA_28           AAA domain
     0.0077   17.2   0.2      0.051   14.5   0.2    2.4  1  LytR_C           LytR cell envelope-related transcriptional a
     0.0079   16.6   0.0     0.0079   16.6   0.0    2.8  1  AAA_16           AAA ATPase domain
     0.0083   15.7   0.2      0.017   14.7   0.2    1.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
       0.01   16.1   0.1       0.12   12.6   0.0    2.2  2  AAA_22           AAA domain
      0.011   16.2   0.1      0.011   16.2   0.1    2.8  2  AAA_17           AAA domain
       0.02   14.7   0.0      0.036   13.9   0.0    1.4  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.022   14.2   0.0      0.034   13.6   0.0    1.2  1  KTI12            Chromatin associated protein KTI12
      0.027   14.2   0.0      0.048   13.4   0.0    1.4  1  AAA_24           AAA domain
      0.031   13.3   0.0      0.064   12.2   0.0    1.4  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.05   13.1   0.0       0.08   12.4   0.0    1.2  1  PPK2             Polyphosphate kinase 2 (PPK2)
      0.054   13.8   0.1        0.1   12.9   0.1    1.5  1  AAA_19           AAA domain
      0.098   11.8   0.3       0.32   10.1   0.1    1.9  2  ArsA_ATPase      Anion-transporting ATPase
       0.11   12.3   0.1       0.38   10.5   0.0    1.9  2  AAA_29           P-loop containing region of AAA domain
        0.2   11.1   0.0       0.33   10.5   0.0    1.2  1  AAA_7            P-loop containing dynein motor region


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 !  227.7   0.2   1.3e-70   9.3e-68       1     195 [.     294     488 ..     294     489 .. 0.99

  Alignments for each domain:
  == domain 1  score: 227.7 bits;  conditional E-value: 1.3e-70
                                       SEEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHH CS
                             SRP54   1 pnvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeave 77 
                                       p vi++ G++G+GKTt++aK++++l+++g++++++  Dt+Ra+A eQ++++a+ l+ ++i+++++ dpaav+++ave
  gi|336252706|ref|YP_004595813.1| 294 PVVIVFTGVNGVGKTTSIAKMSRYLEERGYSTVMANGDTYRAGANEQIQEHADALDTKCISHEQGGDPAAVLYDAVE 370
                                       579************************************************************************** PP

                                       HHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSS CS
                             SRP54  78 kakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgda 154
                                        a++++idvvl DTaGrl++d+ lm++l+ki +vv+pd +l+v +a++gq+av+ a++F+ea++i+g++ltk D+d+
  gi|336252706|ref|YP_004595813.1| 371 YAEANDIDVVLGDTAGRLHTDEGLMDQLAKIDRVVDPDMTLFVDEAVAGQDAVNRAREFNEAAEIDGAVLTKADADS 447
                                       ***************************************************************************** PP

                                       STTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                             SRP54 155 kgGaalsiaaelklPikfigvGekiedleefdperlvsrll 195
                                       +gGaa+s+a+ +++Pi f+gvG+ ++ le+fdp+++v+rll
  gi|336252706|ref|YP_004595813.1| 448 NGGAAISVAHVTGKPILFLGVGQGYDHLERFDPDEMVDRLL 488
                                       ****************************************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 ?   -0.2   0.6       1.6   1.2e+03       9      32 ..       6      29 ..       2      43 .. 0.60
   2 !   49.1   0.7   6.7e-16   4.8e-13       5      74 ..     203     272 ..     199     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.6
                                      HHHHCCSSCGHHHHHHHHHHHHHH CS
                           SRP54_N  9 lkklsgkskideedleealkelee 32
                                        kl + +k  ee+ ee ++e+e+
  gi|336252706|ref|YP_004595813.1|  6 KEKLGSFRKDAEEAAEENVEEVED 29
                                      444444555555555554444664 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 6.7e-16
                                       HHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHH CS
                           SRP54_N   5 lnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkde 74 
                                        +s++k+   k +i eedle+ l ele aLl++DV + vv+++++n++++ +ge +   +++++ ++++++d+
  gi|336252706|ref|YP_004595813.1| 203 AKSLVKG---KFVIEEEDLEDPLHELELALLSSDVEMGVVDEILDNLRDELIGETRaftTSTGDVIEEALRDA 272
                                       4555555...99*****************************************777*9999**********97 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   5.9e-08   4.3e-05       1      49 [.     293     341 ..     293     351 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5.9e-08
                                       S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                        APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49 
                                       ++vv+ +tG+ g GK+t   +++++L+e+g+s+++ +Gd+ R g n+++
  gi|336252706|ref|YP_004595813.1| 293 KPVVIVFTGVNGVGKTTSIAKMSRYLEERGYSTVMANGDTYRAGANEQI 341
                                       5799**************9************************999876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.7   3.1e-06    0.0023      14      82 ..     290     400 ..     277     441 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.1e-06
                            AAA_30  14 ltsgdrvavltGpAGtGKttalkalreaweaaggrvigl.AptgkaAkvLaeelgieastiakllkrlk........ 81 
                                       ++++  v v tG+ G GKtt+++++ + +e++g++ +++   t +a    +e+++ +a+ ++    +++        
  gi|336252706|ref|YP_004595813.1| 290 IEDKPVVIVFTGVNGVGKTTSIAKMSRYLEERGYSTVMAnGDTYRAG--ANEQIQEHADALDTKCISHEqggdpaav 364
                                       3444567788**********************977665413333333..2333333333333333233233444444 PP

                            AAA_30  82 ...................................g 82 
                                                                          +
  gi|336252706|ref|YP_004595813.1| 365 lydaveyaeandidvvlgdtagrlhtdeglmdqlaK 400
                                       444443333333333333333444444444444441 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.7e-05     0.019       2      29 ..     300     328 ..     299     373 .. 0.87
   2 ?    2.4   0.0      0.15   1.1e+02     114     140 ..     404     431 ..     391     442 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                                       EESTTSSHHHHHHHHHHHHHHTTE..EEE CS
                   Thymidylate_kin   2 EGlDGaGKttqaellkerlkeegik.vvl 29 
                                        G++G+GKtt ++++ ++l+e+g++ v+ 
  gi|336252706|ref|YP_004595813.1| 300 TGVNGVGKTTSIAKMSRYLEERGYStVMA 328
                                       59**********************95544 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.15
                                       TTSE-SEEEEEE..SSHHHHHTSCCTTSS CS
                   Thymidylate_kin 114 vllkPdltflld..vdpevalkRlakrde 140
                                       v+  Pd+t+++d  v  + a++R+++ +e
  gi|336252706|ref|YP_004595813.1| 404 VV-DPDMTLFVDeaVAGQDAVNRAREFNE 431
                                       44.9*******977778888888887776 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 !   18.5   0.1   2.3e-06    0.0016       3      55 ..     298     406 ..     296     464 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.3e-06
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep......................... 54 
                                       +  +  GvGKTt  a++ r+l +rg+ +++   D+ +       g  ++i++                         
  gi|336252706|ref|YP_004595813.1| 298 VFTGVNGVGKTTSIAKMSRYLEERGYSTVMANGDTYRA------GANEQIQEhadaldtkcisheqggdpaavlyda 368
                                       556667************************99998743......333444444455566666666666666666666 PP

                                       .....................................C CS
                                       .....................................x RF
                              CbiA  55 .....................................d 55 
                                                                            d
  gi|336252706|ref|YP_004595813.1| 369 veyaeandidvvlgdtagrlhtdeglmdqlakidrvvD 406
                                       66666666666666666666655555555555555551 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       4.2     3e+03     160     182 ..      14      36 ..      11      47 .. 0.79
   2 !   18.4   0.1   1.4e-06   0.00098      13     120 ..     291     401 ..     283     441 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.2
                        Zeta_toxin 160 deafeglresvealeeekqldrv 182
                                       ++a e+++e+ve++e e +l++v
  gi|336252706|ref|YP_004595813.1|  14 KDAEEAAEENVEEVEDEEDLEDV 36 
                                       67788999999999999988776 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.4e-06
                        Zeta_toxin  13 qerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelh.Peyeeilka.dpkkaseltqkdaselvek 86 
                                       +++P++i+  G  G GK++ ++++ ++le r+ + v  ++D++R+    + +e+ +a d k  s     d   +   
  gi|336252706|ref|YP_004595813.1| 291 EDKPVVIVFTGVNGVGKTTSIAKMSRYLEeRGYSTVMANGDTYRAGAnEQIQEHADAlDTKCISHEQGGDPAAVLYD 367
                                       589*************************9888899*********854045666666657777777788888888999 PP

                        Zeta_toxin  87 llqeaiengyniivegtlrspdvvkklaealkka 120
                                       ++++a  n +++++  t    ++ + l+++l+k 
  gi|336252706|ref|YP_004595813.1| 368 AVEYAEANDIDVVLGDTAGRLHTDEGLMDQLAKI 401
                                       9999999999999988888888888788877765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.3   2.4e+03      70     104 ..     207     242 ..     191     242 .. 0.76
   2 !   15.9   0.1   1.3e-05    0.0095       2      29 ..     297     324 ..     296     330 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.3
                                       EETTEEE-HHHHHHHHHHHHHHHHHHH-..EEEE--- CS
                          NTPase_1  70 rvgkyvvdvesfeelalealrkalsead..viviDEi 104
                                         gk+v++ e++e+  l+ l+ al ++d  + v+DEi
  gi|336252706|ref|YP_004595813.1| 207 VKGKFVIEEEDLEDP-LHELELALLSSDveMGVVDEI 242
                                       468999999999986.788888885555448899998 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.3e-05
                                       EEEE--TTSSHHHHHHHHHHHH...GGG CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvk 29 
                                       ++ TG  GvGKtT + k+++ l+++g++
  gi|336252706|ref|YP_004595813.1| 297 IVFTGVNGVGKTTSIAKMSRYLEERGYS 324
                                       788**********************986 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.8e-06    0.0056      10      60 ..     291     342 ..     285     378 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.8e-06
                                       ..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS.- CS
                             6PF2K  10 knsklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaska.l 60 
                                       +++++viv+ G    gKt+   k++ryl+  g++t + n   yr  a+++ +
  gi|336252706|ref|YP_004595813.1| 291 EDKPVVIVFTGVNGVGKTTSIAKMSRYLEERGYSTVMANGDTYRAGANEQiQ 342
                                       6899***********************************9999998887742 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.2e-05     0.015       1     134 [.     296     441 ..     296     446 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
                            AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlrrrlfgtdqqskt......dytrvldrlyqilnelarka 66 
                                       ++++ G++G+GK+t + ++   l+++g  +v  + dt+r    ++ q++         + +   +  + l + ++ a
  gi|336252706|ref|YP_004595813.1| 296 VIVFTGVNGVGKTTSIAKMsryLEERGysTVMANGDTYRAGANEQIQEHADaldtkcISHEQGGDPAAVLYDAVEYA 372
                                       799************99874446677777777789998887776444433322222222222223455788888888 PP

                            AAA_33  67 lsagrnvildatnls.rrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrsevpeeald 134
                                        +  ++v+l  t  + + +   +++la+   v +  +++ +de+++ +    Ra++ ++++e + ++l 
  gi|336252706|ref|YP_004595813.1| 373 EANDIDVVLGDTAGRlHTDEGLMDQLAKIDRVVDPDMTLFVDEAVAGQDAVNRAREFNEAAEIDGAVLT 441
                                       899999999666555155556888888877777888899999999999999999998888899888876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   1.7       3.2   2.3e+03      29      69 ..      18      55 ..       5      87 .. 0.64
   2 ?    0.3   0.0         1   7.3e+02     135     163 .]     259     287 ..     230     287 .. 0.75
   3 !   16.6   0.3   9.7e-06    0.0069       2      48 ..     297     350 ..     296     442 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.2
                            AAA_28 29 Eaareileeklakgedalpwvedllafaervleeqleeeaa 69
                                      Eaa e +e + +++e +l++v d  a++++ +++ +ee+ a
  gi|336252706|ref|YP_004595813.1| 18 EAAEENVE-EVEDEE-DLEDV-DEAAVEAEAEAADAEEAGA 55
                                      33333332.222222.25554.5555555555554444444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1
                            AAA_28 135 eaiderlrealrelgipviivpsgdveeR 163
                                       + + ++++ealr++ ++vi v + d++eR
  gi|336252706|ref|YP_004595813.1| 259 TSTGDVIEEALRDAIYDVISVGQFDFNER 287
                                       4455788899999********99999998 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 9.7e-06
                            AAA_28   2 ivitGgestGKTtlleaLa....argypvv...pEaareileeklakgedalpw 48 
                                       iv+tG  + GKTt +++++    +rgy++v    +++r   +e+ +++ dal+ 
  gi|336252706|ref|YP_004595813.1| 297 IVFTGVNGVGKTTSIAKMSryleERGYSTVmanGDTYRAGANEQIQEHADALDT 350
                                       9**************8888554467***99555566666666666666666554 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   7.2e-05     0.051       8      83 ..     303     383 ..     302     384 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.2e-05
                            LytR_C   8 NgtgvsGlAarvadaLeerGf.tvgevgnagnadeettivyreaaaaaakalaaalglgelqedsvkdas....... 76 
                                       Ng g++   a+++++LeerG+ tv + g++  a          +a+++ ++ a+al  + +++++  d++       
  gi|336252706|ref|YP_004595813.1| 303 NGVGKTTSIAKMSRYLEERGYsTVMANGDTYRA----------GANEQIQEHADALDTKCISHEQGGDPAavlydav 369
                                       999******************555542233333..........3334455666666666666666666666666777 PP

                            LytR_C  77 .......vtvvlGk 83 
                                              ++vvlG+
  gi|336252706|ref|YP_004595813.1| 370 eyaeandIDVVLGD 383
                                       77777789999995 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0079      22      64 ..     292     334 ..     284     416 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdqle 64 
                                       + p +++++G  GvGK++ + +  r+le++g  ++ ++ d ++
  gi|336252706|ref|YP_004595813.1| 292 DKPVVIVFTGVNGVGKTTSIAKMSRYLEERGYSTVMANGDTYR 334
                                       5678899**********************97555666666662 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 !   14.7   0.2   2.3e-05     0.017       2     152 ..     296     445 ..     295     459 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkeleal 76 
                                       v+v+tG  G GKTt + ++    +++g+++    ++ +  + ++++ ++++     l + ci +    d  ++l + 
  gi|336252706|ref|YP_004595813.1| 296 VIVFTGVNGVGKTTSIAKMSryLEERGYSTVMANGDTYRAGANEQIQEHAD----ALDTKCISHEQGGDPAAVLYDA 368
                                       899****************97777788888888899998888888776664....6899999999887777766655 PP

                                       HHHH..TT-SEEEEEECTTTTHHHH.HTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-H CS
                              cobW  77 eere..erldviliEttGlaePapv.afteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKt 150
                                       +e    +++dv+l  t G ++  +  + +  ++ + +  d++++v +a +  ++  + ++++++  a  d  vl+K+
  gi|336252706|ref|YP_004595813.1| 369 VEYAeaNDIDVVLGDTAGRLHTDEGlMDQLAKIDRVVDPDMTLFVDEAVAG-QDAVNRAREFNEA-AEIDGAVLTKA 443
                                       55444569**********776666624446777777777777776666332.3444444444433.34466677777 PP

                                       HH CS
                              cobW 151 Dl 152
                                       D 
  gi|336252706|ref|YP_004595813.1| 444 DA 445
                                       75 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.64   4.6e+02      70     110 ..     205     252 ..     167     277 .. 0.75
   2 ?   12.6   0.0   0.00017      0.12       7      64 ..     296     348 ..     290     416 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.64
                            AAA_22  70 a........erlsseellealeqalraravielliiDEa.qhlrseeale 110
                                       +        e+ ++e+ l+ le al + +v e+ ++DE+ ++l ++e++ 
  gi|336252706|ref|YP_004595813.1| 205 SlvkgkfviEEEDLEDPLHELELALLSSDV-EMGVVDEIlDNL-RDELIG 252
                                       24444456688999999*************.*******74668.555554 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00017
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...sskdllrellral 64 
                                       ++v tG  G+GKTt+++++ + l+e+        ++ +v ++++t   +  +  +e + al
  gi|336252706|ref|YP_004595813.1| 296 VIVFTGVNGVGKTTSIAKMSRYLEER--------GYSTVMANGDTyraGANEQIQEHADAL 348
                                       6899****************999754........444444444443344444444444444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.2   0.1   1.5e-05     0.011       1     109 [.     300     414 ..     300     431 .. 0.72
   2 ?   -1.0   0.1       3.1   2.2e+03     111     124 ..     479     492 ..     476     494 .] 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-05
                                       EE-TTSSHHHHHHHHHHHH...TEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHH..HHHHHHH..HHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky...gfthlsa.Gdllreeakrgglakardemrklpleekkelq..keaaeki..aeea 69 
                                       +G+ G+GK+t ++k+ + +   g++ + a Gd  r+ a+++  +++ d++++  +++++  +  + + +++  ae++
  gi|336252706|ref|YP_004595813.1| 300 TGVNGVGKTTSIAKMSRYLeerGYSTVMAnGDTYRAGANEQ-IQEHADALDTKCISHEQGGDpaAVLYDAVeyAEAN 375
                                       69*************965544466654444******98766.46788888865555544333113334444113444 PP

                                       HSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE CS
                            AAA_17  70 kkkgvlvdghprikeqagfldglpkevleelkpdaiille 109
                                       + + vl d+  r+ +++g++d+l k + + ++pd+ ++++
  gi|336252706|ref|YP_004595813.1| 376 DIDVVLGDTAGRLHTDEGLMDQLAK-IDRVVDPDMTLFVD 414
                                       5577999999***999999988875.99999**9999987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.1
                                       -HHHHHHHHHHHTT CS
                            AAA_17 111 dpeeilerrlkdrt 124
                                       dp+e+++r+l+d+ 
  gi|336252706|ref|YP_004595813.1| 479 DPDEMVDRLLEDED 492
                                       899********974 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 ?   13.9   0.0     5e-05     0.036       2      34 ..     300     332 ..     299     381 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5e-05
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLDP 34 
                                       +G+ G+GKtt + ++s +le+rg+s  + N D+
  gi|336252706|ref|YP_004595813.1| 300 TGVNGVGKTTSIAKMSRYLEERGYSTVMANGDT 332
                                       799**********************99999775 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.7e-05     0.034       4      46 ..     297     339 ..     294     354 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.7e-05
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSS CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgiekds 46 
                                       +v+tG+  +GK+t  ++++++lee+++s v+ + ++++   ++
  gi|336252706|ref|YP_004595813.1| 297 IVFTGVNGVGKTTSIAKMSRYLEERGYSTVMANGDTYRAGANE 339
                                       89*******************************9999854443 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.6e-05     0.048       2      77 ..     294     388 ..     293     428 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.6e-05
                            AAA_24   2 klkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.....swedfldevvel....... 59 
                                       ++ i+ +G +g+GKTt+++++       g+++++ + +              +     ++++  d++++        
  gi|336252706|ref|YP_004595813.1| 294 PVVIVFTGVNGVGKTTSIAKMsryleerGYSTVMANGDT------------YRaganeQIQEHADALDTKcisheqg 358
                                       568999***************555555555555555444............22232223333333333335556667 PP

                            AAA_24  60 ............aaeladyktlviDtidel 77 
                                                   +ae +d++++  Dt++ l
  gi|336252706|ref|YP_004595813.1| 359 gdpaavlydaveYAEANDIDVVLGDTAGRL 388
                                       777777777777778888888888888877 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 ?   12.2   0.0   8.9e-05     0.064      30      59 ..     295     324 ..     287     333 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.9e-05
                                       EEEEEEE-TTSSHHHHHHHHHHHHHCTT-- CS
                              MeaB  30 qvvGltGvPGaGkstlvealglelrrrGkr 59 
                                        v+ +tGv G+Gk t + ++   l +rG+ 
  gi|336252706|ref|YP_004595813.1| 295 VVIVFTGVNGVGKTTSIAKMSRYLEERGYS 324
                                       57899***********************85 PP

>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.08      21      64 ..     284     327 ..     277     351 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                       HHHSGGGGG-EEEEEEEESTTS-HHHHHHHHHTTS-GGG-EEEE CS
                              PPK2  21 lqekvkaegkklvvifegrDaAGKgGaikrvtealnprvarvva 64 
                                       + e+++ e+k +v++f g ++ GK   i+++  +l+ r++  v 
  gi|336252706|ref|YP_004595813.1| 284 FNERIAIEDKPVVIVFTGVNGVGKTTSIAKMSRYLEERGYSTVM 327
                                       567889999*****************************998775 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00015       0.1       7     111 ..     291     416 ..     285     425 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                            AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgr..Aakelrerlaalgae............. 68 
                                       + k  v++ t+  G GKT+ + ++ ++l+e+g     ++++   t r  A ++++e  +al+ +             
  gi|336252706|ref|YP_004595813.1| 291 EDKPVVIVFTGVNGVGKTTSIAKMSRYLEERGY---STVMANGDTYRagANEQIQEHADALDTKcisheqggdpaav 364
                                       4455566778999*********99999999984...45666655555116788999998888877777777777666 PP

                            AAA_19  69 .................atTiHrlalldfddlltealelleeaeeekklqeee.llivDEf 111
                                                         +T  rl   ++d+      +l+++ ++ + + + + +l+vDE+
  gi|336252706|ref|YP_004595813.1| 365 lydaveyaeandidvvlGDTAGRL---HTDE------GLMDQLAKIDRVVDPDmTLFVDEA 416
                                       666555555333333333333333...2333......333333333444466669999986 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00045      0.32       3      35 ..     296     328 ..     295     337 .. 0.91
   2 ?   -1.6   0.0       1.7   1.2e+03     106     134 ..     358     386 ..     332     401 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00045
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                       ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvlli 35 
                                       vi+++G  GVGKtt+ a ++ +l e g+++++ 
  gi|336252706|ref|YP_004595813.1| 296 VIVFTGVNGVGKTTSIAKMSRYLEERGYSTVMA 328
                                       799************************999875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
                                       THHHHHHHHHHHHHHHCSSSSEEEEESBS CS
                       ArsA_ATPase 106 GideilsfeellkyvkeeeydvvvlDtaP 134
                                       G d ++ +   ++y ++++ dvv+ Dta 
  gi|336252706|ref|YP_004595813.1| 358 GGDPAAVLYDAVEYAEANDIDVVLGDTAG 386
                                       55677778888899999999999999995 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 ?   10.5   0.0   0.00053      0.38       7      39 ..     277     311 ..     273     316 .. 0.86
   2 ?   -2.4   0.1       5.6     4e+03      51      59 ..     426     434 ..     423     435 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00053
                            AAA_29   7 vNWgtfdg.htieidlkg.atlltGpsGsGKSTll 39 
                                       +  g fd  ++i i+ k  ++++tG +G+GK+T +
  gi|336252706|ref|YP_004595813.1| 277 ISVGQFDFnERIAIEDKPvVIVFTGVNGVGKTTSI 311
                                       556889999999999888999***********965 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.6
                            AAA_29  51 kvrfNkaan 59 
                                        ++fN+aa+
  gi|336252706|ref|YP_004595813.1| 426 AREFNEAAE 434
                                       478****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 ?   10.5   0.0   0.00045      0.33      36      68 ..     297     329 ..     284     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00045
                             AAA_7  36 vllvGptGtGKtviikdllkkldkekylsltin 68 
                                       ++++G  G+GKt+ i ++ + l+++ y++++ n
  gi|336252706|ref|YP_004595813.1| 297 IVFTGVNGVGKTTSIAKMSRYLEERGYSTVMAN 329
                                       5789*******************9999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1176  (0.0655921); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                        48  (0.00267723); 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: 0.98u 0.31s 00:00:01.29 Elapsed: 00:00:00.50
# Mc/sec: 2955.51
//
Query:       gi|336252707|ref|YP_004595814.1|  [L=566]
Description: Ferredoxin--nitrite reductase [Halopiger xanaduensis SH-6]
Scores for complete 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-51  173.9   0.0    1.6e-37  128.5   0.0    2.3  2  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    1.8e-27   95.0   0.1    1.8e-12   46.9   0.0    3.3  3  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
     0.0063   16.6   0.1       0.24   11.5   0.0    2.5  2  DGC           DGC domain
  ------ inclusion threshold ------
      0.013   15.7   3.7        2.5    8.4   0.9    2.9  2  zf-HC2        Putative zinc-finger
       0.17   12.2   1.6         15    5.9   0.0    3.1  3  Toxin_TOLIP   Snake toxin and toxin-like protein


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.5   0.0   4.5e-41   1.6e-37       2     155 ..     143     297 ..     142     301 .. 0.95
   2 !   43.1   0.0   8.2e-15   2.9e-11       6     150 ..     400     550 ..     396     556 .. 0.92

  Alignments for each domain:
  == domain 1  score: 128.5 bits;  conditional E-value: 4.5e-41
                                       SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdeke 78 
                                       g++ rnv +cp+agl+ ++++++++++ a+ d ++++ ++ +lPrKfKi ++gc ++c+++++nD+g+ + kk+   
  gi|336252707|ref|YP_004595814.1| 143 GDSARNVLGCPAAGLDDHECFNAQPVIDAVSDYFTENREYANLPRKFKITITGCAHDCAQSQINDVGMTPAKKEIDG 219
                                       7899*******************************************************************996444 PP

                                       E...EEEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHH CS
                                       x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  79 i...gfnilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekve 152
                                       +   gf + vGGgl+  +++++ +   +fvp+e+ +e+++a+ +++++ gdr+nr   R++ylve++G +kF e+++
  gi|336252707|ref|YP_004595814.1| 220 EyyyGFHVRVGGGLSDGPRMASDLD--VFVPPEDAVEFCRAVAQTFKELGDRNNRGVCRMRYLVEQMGADKFEEAIR 294
                                       4688****************99999..7**********************************************998 PP

                                       HCC CS
                                       xxx RF
                           NIR_SIR 153 eel 155
                                        + 
  gi|336252707|ref|YP_004595814.1| 295 DRC 297
                                       765 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 8.2e-15
                                       CCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                           NIR_SIR   6 rnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei... 79 
                                       r  ++c+g+++c  a+++t++ +k++ +el +++++++    +++ +sgc   c++ ++ Dig+ g + + + +   
  gi|336252707|ref|YP_004595814.1| 400 RGAVGCTGTEFCNYAIIETKKRTKRWARELDERIDTPDDLEVVRMHMSGCSASCAQPQIADIGFRGETVKLEDEnsp 476
                                       77899*********************************99*************************988776666789 PP

                                       .........EEEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHH CS
                                       .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  80 .........gfnilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekF 147
                                                g+ + +GG lg++++    +     vp+e v++++e++ + y+    ++ +  eR+ ++  r+  e++
  gi|336252707|ref|YP_004595814.1| 477 neegdnlveGMDFGIGGALGADNEFLDWIE--RAVPAEGVIPALEQLFDAYN----EDRNDGERFYEWARRVDNERL 547
                                       ********************9988777777..58******************....999*************99999 PP

                                       HHH CS
                                       xxx RF
                           NIR_SIR 148 rek 150
                                       r  
  gi|336252707|ref|YP_004595814.1| 548 RTL 550
                                       865 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   5.1e-16   1.8e-12       2      68 ..      52     133 ..      51     134 .. 0.94
   2 ?   -3.0   0.0       1.9   6.8e+03       5      19 ..     218     230 ..     215     238 .. 0.61
   3 !   44.2   0.0   3.6e-15   1.3e-11       1      65 [.     320     385 ..     320     387 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 5.1e-16
                      NIR_SIR_ferr   2 kqkdgkgyymvrlrvpnGritaeqlraladia................ekygsgeirlTtrQnlqlhgvpeedleei 62 
                                        qk+ + y+m+r +vp+G +t+eq++ + + a                e +g+  +++TtrQ +q h+v+ +d++e+
  gi|336252707|ref|YP_004595814.1|  52 SQKQDD-YFMIRTKVPGGYLTPEQAEVIGECAtdyatapeeyggeeqnELWGDAFLDITTRQDIQKHWVEVSDVPEM 127
                                       689955.55**************************************99**************************** PP

                      NIR_SIR_ferr  63 leeLae 68 
                                       +e+ +e
  gi|336252707|ref|YP_004595814.1| 128 WERYDE 133
                                       *98665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.9
                      NIR_SIR_ferr   5 dgkgyymvrlrvpnG 19 
                                       dg+  y+++++v  G
  gi|336252707|ref|YP_004595814.1| 218 DGE--YYYGFHVRVG 230
                                       777..4555555532 PP

  == domain 3  score: 44.2 bits;  conditional E-value: 3.6e-15
                      NIR_SIR_ferr   1 hkqkdgkgyymvrlrvpnGritaeqlraladiaekyg..sgeirlTtrQnlqlhgvpeedleeilee 65 
                                       h+qk+ +g+ +v+++v +Gr+  +++ + a+ a+kyg  +  irl t+Qn++++++pee+++++l+e
  gi|336252707|ref|YP_004595814.1| 320 HDQKQ-DGLKYVGFNVIAGRMGGDEFAEAARAAKKYGteDTSIRLATDQNFLITHIPEENVDDLLAE 385
                                       78999.8999***************************766************************997 PP

>> DGC  DGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   6.6e-05      0.24      53      78 ..     190     215 ..     169     220 .. 0.85
   2 ?    2.1   0.0     0.055     2e+02      57      74 ..     447     464 ..     440     485 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.6e-05
                               DGC  53 iiaidGCpleCakkilekagvkpdeh 78 
                                        i+i GC+ +Ca+  ++++g++p+++
  gi|336252707|ref|YP_004595814.1| 190 KITITGCAHDCAQSQINDVGMTPAKK 215
                                       599*******************9875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.055
                               DGC  57 dGCpleCakkilekagvk 74 
                                        GC+ +Ca+  +++ g++
  gi|336252707|ref|YP_004595814.1| 447 SGCSASCAQPQIADIGFR 464
                                       6********999998884 PP

>> zf-HC2  Putative zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.9    0.0007       2.5       4      23 ..      16      35 ..      15      35 .. 0.89
   2 ?    6.9   0.1    0.0021       7.4      17      33 ..     435     451 ..     428     451 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0007
                                      HHHHHHHHHCCT-SCCCHCC CS
                            zf-HC2  4 vrelLsaYlDGeLspeerar 23
                                      v e +++Y++G+Ls+ee ++
  gi|336252707|ref|YP_004595814.1| 16 VIEDVYDYAEGDLSDEEIEE 35
                                      78889************985 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0021
                                       SCCCHCCCHHHHCHTCH CS
                            zf-HC2  17 speerarveaHLaeCpd 33 
                                       +p++ + v+ H ++C++
  gi|336252707|ref|YP_004595814.1| 435 TPDDLEVVRMHMSGCSA 451
                                       799************85 PP

>> Toxin_TOLIP  Snake toxin and toxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0041        15      34      52 ..     188     206 ..     175     211 .. 0.78
   2 ?   -2.5   0.1       1.8   6.5e+03      58      67 .]     403     412 ..     399     412 .. 0.77
   3 ?    3.8   0.0     0.019        67      39      52 ..     446     459 ..     437     464 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0041
                       Toxin_TOLIP  34 hkelvekgCaatCpevkes 52 
                                       + ++ + gCa +C + +++
  gi|336252707|ref|YP_004595814.1| 188 KFKITITGCAHDCAQSQIN 206
                                       5567899*******99976 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                       Toxin_TOLIP  58 asCCetdlCN 67 
                                       ++C  t++CN
  gi|336252707|ref|YP_004595814.1| 403 VGCTGTEFCN 412
                                       4588899998 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.019
                       Toxin_TOLIP  39 ekgCaatCpevkes 52 
                                       + gC+a+C + ++ 
  gi|336252707|ref|YP_004595814.1| 446 MSGCSASCAQPQIA 459
                                       67*******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 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:                        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: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3950.78
//
Query:       gi|336252708|ref|YP_004595815.1|  [L=552]
Description: Coenzyme F420 hydrogenase [Halopiger xanaduensis SH-6]
Scores for 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  102.2   0.0    5.3e-29  101.0   0.0    1.5  1  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    6.5e-20   71.1   0.1    1.4e-19   70.0   0.1    1.5  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    1.3e-09   38.1   5.9    1.3e-09   38.1   5.9    2.0  2  Fer4_21      4Fe-4S dicluster domain
    3.2e-09   36.2  18.0    5.6e-07   29.1   4.2    3.2  3  Fer4         4Fe-4S binding domain
    3.6e-09   37.4   2.1     0.0057   17.6   0.1    3.7  3  Fer4_16      4Fe-4S double cluster binding domain
    2.1e-08   34.1   6.5    2.1e-08   34.1   6.5    2.5  2  Fer4_10      4Fe-4S dicluster domain
    3.3e-08   33.5   7.6    6.8e-08   32.5   4.9    2.6  2  Fer4_9       4Fe-4S dicluster domain
    6.3e-06   26.7  21.3    0.00029   21.4  10.9    3.3  4  Fer4_7       4Fe-4S dicluster domain
    7.8e-06   25.7   3.7    7.8e-06   25.7   3.7    3.2  3  Fer4_6       4Fe-4S binding domain
    4.8e-05   23.2   3.3    4.8e-05   23.2   3.3    3.3  3  Fer4_2       4Fe-4S binding domain
    9.6e-05   22.9   7.3      0.014   15.9   0.2    2.9  2  Fer4_17      4Fe-4S dicluster domain
     0.0015   18.9  21.3     0.0015   18.9   4.2    3.4  3  Fer4_4       4Fe-4S binding domain
     0.0057   16.8   2.0     0.0057   16.8   2.0    1.8  1  Fer4_18      4Fe-4S dicluster domain
     0.0067   16.9  13.7       0.11   13.1   4.3    3.1  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.048   14.6   4.7      0.048   14.6   4.7    3.1  3  Fer4_3       4Fe-4S binding domain
      0.092   13.2  14.6       0.55   10.7   3.9    3.2  4  Fer4_8       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   4.7e-32   5.3e-29       4     140 ..     348     489 ..     345     501 .. 0.90

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 4.7e-32
                       FrhB_FdhB_C   4 vavvGtPCqiaalrklqk........kklkekilltiglfCggnfspealrk..lleelgvdpedvkklefrgkgkf 70 
                                       +a+vGtPC+i+++r+lq+        ++  +++ +ti l+C++nf++ +l+   + e++g+dped+ k+++  +gk+
  gi|336252708|ref|YP_004595815.1| 348 LALVGTPCEIEGIRALQDfewdyqaqNQGIRAVDYTIALMCTKNFNYYSLMGemVQEQRGIDPEDIGKMDV-LHGKM 423
                                       89***************999999999889999*************999999889*****************.89*** PP

                       FrhB_FdhB_C  71 rvelkd...ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellek 140
                                       +++ +d     e ++++++++  ++C+ C d+t+ +AD++vG+v      g +++++s v++rte+g +++e 
  gi|336252708|ref|YP_004595815.1| 424 MIYGHDgemILEEDIENFHDAALKGCDECADFTGFCADVTVGSV------G-SSDEYSSVIIRTEQGMKAWEL 489
                                       **888875533445669999************************......8.*****************9984 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 !   70.0   0.1   1.2e-22   1.4e-19       4      72 ..     256     324 ..     254     329 .. 0.90

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 1.2e-22
                       FrhB_FdhB_N   4 ArstdkeirkkaqsGGivtallkylLeegiidgvivvaps.kdpwrpkpviattkeellaaaGskYtlsp 72 
                                       A++ d +   +aq+GG+vt +l+ lLeeg+idg++ +++s ++ w+++ ++attkeel++ aG++Y+++ 
  gi|336252708|ref|YP_004595815.1| 256 AKVDD-DWTDQAQDGGVVTGILATLLEEGEIDGALIATESeEEAWKAESFLATTKEELIENAGTVYNQTL 324
                                       55555.5889******************************99*************************765 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   5.9   1.1e-12   1.3e-09       1      52 [.     178     225 ..     178     230 .. 0.87
   2 ?   -2.2   0.1       4.3   4.8e+03      43      48 ..     448     453 ..     438     472 .. 0.71

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.1e-12
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                       A+ide +Ci+Cg C+ aC+    + i + ++  l+ + + C+GC lC + CP
  gi|336252708|ref|YP_004595815.1| 178 AVIDEGRCIQCGTCVAACP---SDSIGVGDD-DLPKLVKMCTGCSLCWDFCP 225
                                       89*****************...589987655.55778889************ PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.3
                           Fer4_21  43 GCnlCs 48 
                                       GC+ C+
  gi|336252708|ref|YP_004595815.1| 448 GCDECA 453
                                       555554 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   4.2     5e-10   5.6e-07       2      23 ..     179     200 ..     178     201 .. 0.93
   2 !   15.6   1.3   9.3e-06      0.01       7      21 ..     213     227 ..     211     230 .. 0.90
   3 ?   -0.7   0.2       1.3   1.4e+03      10      16 ..     448     454 ..     447     455 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 5e-10
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       vide +Ci CG+Cv +CP + I
  gi|336252708|ref|YP_004595815.1| 179 VIDEGRCIQCGTCVAACPSDSI 200
                                       8*****************9976 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 9.3e-06
                                       TSSS-THHHHHSTTT CS
                              Fer4   7 kCigCGaCvevCPvg 21 
                                       +C+gC +C + CP g
  gi|336252708|ref|YP_004595815.1| 213 MCTGCSLCWDFCPRG 227
                                       7************98 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.3
                                       S-THHHH CS
                              Fer4  10 gCGaCve 16 
                                       gC +C++
  gi|336252708|ref|YP_004595815.1| 448 GCDECAD 454
                                       9****97 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 !   17.6   0.1   5.1e-06    0.0057       1      18 [.     184     201 ..     151     207 .. 0.87
   2 !   13.6   0.1   8.7e-05     0.098       2      31 ..     214     241 ..     213     268 .. 0.73
   3 ?    3.4   0.0      0.13   1.5e+02      41      62 ..     434     454 ..     415     456 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.1e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                       rC++Cg C+ +CP++ i 
  gi|336252708|ref|YP_004595815.1| 184 RCIQCGTCVAACPSDSIG 201
                                       599999999999998886 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 8.7e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeieareci 31 
                                       C++C  C + CP + ++ +  +++++   +
  gi|336252708|ref|YP_004595815.1| 214 CTGCSLCWDFCPRGGLRYE--RQWKITGGE 241
                                       ****************999..666665544 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.13
                           Fer4_16  41 laedeekckkqeaitgCdiCqd 62 
                                       l+ed+e+ +   a++gCd C+d
  gi|336252708|ref|YP_004595815.1| 434 LEEDIENFH-DAALKGCDECAD 454
                                       556666666.7788******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 !   34.1   6.5   1.9e-11   2.1e-08       2      56 .]     178     225 ..     177     233 .. 0.96
   2 ?   -0.4   0.1       1.1   1.2e+03      36      49 ..     440     453 ..     425     462 .. 0.60

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.9e-11
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +vid+ +Ci+Cg+Cv+aCP+         +  +++   k v+ Ctgc  C + CP
  gi|336252708|ref|YP_004595815.1| 178 AVIDEGRCIQCGTCVAACPS-------DSIGVGDDDLPKLVKMCTGCSLCWDFCP 225
                                       689*****************.......999999999999***************9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                           Fer4_10  36 eavrkkvekCtgcg 49 
                                       +  + +++ C++c 
  gi|336252708|ref|YP_004595815.1| 440 NFHDAALKGCDECA 453
                                       44445566666663 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   4.9   6.1e-11   6.8e-08       1      49 [.     184     227 ..     168     229 .. 0.92
   2 ?    0.2   0.0      0.76   8.5e+02      33      42 ..     443     459 ..     413     462 .. 0.65

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 6.1e-11
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       +C++Cg+Cv+aCp++ +   +      +++     C+gC  C + Cp+g
  gi|336252708|ref|YP_004595815.1| 184 RCIQCGTCVAACPSDSIGVGDDDLPKLVKM-----CTGCSLCWDFCPRG 227
                                       6****************8888888877765.....************97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.76
                            Fer4_9  33 e...eaCigCga....C 42 
                                       +   + C +C +    C
  gi|336252708|ref|YP_004595815.1| 443 DaalKGCDECADftgfC 459
                                       04446688888733334 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   2.6   1.1e-06    0.0013      29      51 ..     176     198 ..     152     199 .. 0.74
   2 !   21.4  10.9   2.6e-07   0.00029       1      51 [.     184     227 ..     184     228 .. 0.89
   3 !   11.3   0.6   0.00035      0.39       2      21 ..     214     233 ..     213     250 .. 0.80
   4 ?   -1.5   0.1       3.7   4.1e+03       2       9 ..     449     453 ..     435     467 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                            Fer4_7  29 ekveidpekClgCgaCvavCPtg 51 
                                       ++++id+ +C++Cg Cva+CP++
  gi|336252708|ref|YP_004595815.1| 176 DEAVIDEGRCIQCGTCVAACPSD 198
                                       67789999999999999999986 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2.6e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       rCi+Cg CvaaCp++ i + +++       +     +C+gC  C + CP g
  gi|336252708|ref|YP_004595815.1| 184 RCIQCGTCVAACPSDSIGVGDDD-------LPKLVKMCTGCSLCWDFCPRG 227
                                       8******************8874.......445579*************86 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00035
                            Fer4_7   2 CigCgaCvaaCpvkaielde 21 
                                       C+gC  C + Cp + ++++ 
  gi|336252708|ref|YP_004595815.1| 214 CTGCSLCWDFCPRGGLRYER 233
                                       99*********999888764 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 3.7
                            Fer4_7   2 CigCgaCv 9  
                                       C +C   +
  gi|336252708|ref|YP_004595815.1| 449 CDEC---A 453
                                       3333...2 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   3.7     7e-09   7.8e-06       2      22 ..     178     198 ..     177     200 .. 0.90
   2 ?    3.5   1.5     0.072        81       8      20 ..     213     225 ..     212     229 .. 0.87
   3 ?   -1.2   0.4       2.2   2.5e+03      11      16 ..     448     453 ..     447     455 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 7e-09
                            Fer4_6   2 veidpdkCigCgdCvrvCPeg 22 
                                       ++id+ +Ci+Cg Cv++CP +
  gi|336252708|ref|YP_004595815.1| 178 AVIDEGRCIQCGTCVAACPSD 198
                                       79*****************76 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.072
                            Fer4_6   8 kCigCgdCvrvCP 20 
                                        C+gC  C + CP
  gi|336252708|ref|YP_004595815.1| 213 MCTGCSLCWDFCP 225
                                       5*******99999 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.2
                            Fer4_6  11 gCgdCv 16 
                                       gC++C+
  gi|336252708|ref|YP_004595815.1| 448 GCDECA 453
                                       899996 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   3.3   4.3e-08   4.8e-05       3      21 ..     178     196 ..     176     197 .. 0.92
   2 !    7.8   2.0    0.0034       3.8       9      21 ..     213     225 ..     208     226 .. 0.90
   3 ?   -2.0   0.6       4.4   4.9e+03      10      18 ..     449     461 ..     447     462 .. 0.64

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.3e-08
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       +v+d+ rCi+Cg+Cv aCP
  gi|336252708|ref|YP_004595815.1| 178 AVIDEGRCIQCGTCVAACP 196
                                       689**************** PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0034
                            Fer4_2   9 rCigCgaCvsaCP 21 
                                       +C+gC+ C + CP
  gi|336252708|ref|YP_004595815.1| 213 MCTGCSLCWDFCP 225
                                       8*******999*9 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.4
                            Fer4_2  10 CigC....gaCvs 18 
                                       C +C    g C +
  gi|336252708|ref|YP_004595815.1| 449 CDECadftGFCAD 461
                                       7777666667765 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   1.2e-05     0.014      44      59 ..     183     198 ..     151     200 .. 0.77
   2 !   10.4   0.1   0.00064      0.72       2      16 ..     214     228 ..     206     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                       ++Ci+Cg C+++CP++
  gi|336252708|ref|YP_004595815.1| 183 GRCIQCGTCVAACPSD 198
                                       5788888888888875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00064
                           Fer4_17   2 CiqCgyClpeCpsye 16 
                                       C++C+ C + Cp++ 
  gi|336252708|ref|YP_004595815.1| 214 CTGCSLCWDFCPRGG 228
                                       888888888888754 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   4.2   1.4e-06    0.0015       3      16 ..     184     197 ..     182     199 .. 0.92
   2 !    9.9   1.6     0.001       1.2       3      16 ..     213     226 ..     212     234 .. 0.90
   3 ?   -0.2   1.1       1.7   1.9e+03       6      13 ..     448     455 ..     447     460 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.4e-06
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       rCi+Cg CvaaCP+
  gi|336252708|ref|YP_004595815.1| 184 RCIQCGTCVAACPS 197
                                       9************7 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.001
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        C+gC  C ++CP 
  gi|336252708|ref|YP_004595815.1| 213 MCTGCSLCWDFCPR 226
                                       7************6 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.7
                            Fer4_4   6 gCgsCvaa 13 
                                       gC+ C ++
  gi|336252708|ref|YP_004595815.1| 448 GCDECADF 455
                                       8****987 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   2.0   5.1e-06    0.0057      50      95 ..     175     224 ..     151     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.1e-06
                           Fer4_18  50 keerkekgagdcidcescvkvcPtg.idirkG....lqleciscllcidac 95 
                                        +e +  ++g ci+c++cv+ cP + i + +     l   c  c+lc d c
  gi|336252708|ref|YP_004595815.1| 175 LDE-AVIDEGRCIQCGTCVAACPSDsIGVGDDdlpkLVKMCTGCSLCWDFC 224
                                       443.456789*************74355443222226668*********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 !   13.1   4.3   9.7e-05      0.11       1      18 [.     180     197 ..     180     198 .. 0.94
   2 !    7.7   1.9    0.0045         5       6      17 ..     214     225 ..     212     227 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.7e-05
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       +D+ +Ci cg+Cv+++P 
  gi|336252708|ref|YP_004595815.1| 180 IDEGRCIQCGTCVAACPS 197
                                       7999*************5 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0045
                           Fer4_13   6 CiacgaCvelaP 17 
                                       C++c +C++++P
  gi|336252708|ref|YP_004595815.1| 214 CTGCSLCWDFCP 225
                                       ************ PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   4.7   4.3e-05     0.048       1      14 [.     185     198 ..     185     199 .. 0.94
   2 ?    8.3   2.8    0.0045         5       1      14 [.     214     227 ..     214     228 .. 0.94
   3 ?   -2.1   0.7       9.5   1.1e+04       1       5 [.     449     453 ..     448     462 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.3e-05
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C++Cg+Cv +CP++
  gi|336252708|ref|YP_004595815.1| 185 CIQCGTCVAACPSD 198
                                       ************86 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0045
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       CtgC++C + CP g
  gi|336252708|ref|YP_004595815.1| 214 CTGCSLCWDFCPRG 227
                                       ************87 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 9.5
                            Fer4_3   1 CtgCg 5  
                                       C+ C 
  gi|336252708|ref|YP_004595815.1| 449 CDECA 453
                                       77774 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.9   0.00049      0.55       4      17 ..     184     197 ..     181     206 .. 0.86
   2 ?    7.3   1.1    0.0058       6.5      48      63 ..     211     226 ..     198     229 .. 0.76
   3 ?    7.8   0.8    0.0041       4.6       3      16 ..     212     225 ..     210     269 .. 0.69
   4 ?   -1.5   0.1       3.3   3.6e+03      44      55 ..     435     453 ..     387     461 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00049
                            Fer4_8   4 kCieCgaCqsaCpv 17 
                                       +Ci+Cg C +aCp+
  gi|336252708|ref|YP_004595815.1| 184 RCIQCGTCVAACPS 197
                                       79999999999995 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0058
                            Fer4_8  48 lwsCttcgaCtevCpv 63 
                                       ++ Ct+c  C + Cp 
  gi|336252708|ref|YP_004595815.1| 211 VKMCTGCSLCWDFCPR 226
                                       6677777777777776 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0041
                            Fer4_8   3 ekCieCgaCqsaCp 16 
                                       + C++C++C + Cp
  gi|336252708|ref|YP_004595815.1| 212 KMCTGCSLCWDFCP 225
                                       45777777777776 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 3.3
                            Fer4_8  44 e.......eealwsCttcg 55 
                                       e       + al+ C +c 
  gi|336252708|ref|YP_004595815.1| 435 EedienfhDAALKGCDECA 453
                                       0333444467788888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); 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:                        18  (0.00100396); 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 0.26s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 3452.06
//
Query:       gi|336252709|ref|YP_004595816.1|  [L=309]
Description: phosphoesterase PA-phosphatase-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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   63.9   2.2    1.2e-17   63.9   2.2    2.2  2  PAP2             PAP2 superfamily
    2.1e-08   34.1   6.4    2.1e-08   34.1   6.4    1.9  2  PAP2_3           PAP2 superfamily
  ------ inclusion threshold ------
       0.04   14.5   0.3       0.11   13.1   0.3    1.7  1  PAP2_C           PAP2 superfamily C-terminal
       0.26   10.8  27.3       0.69    9.4   5.8    2.5  2  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   2.2   2.8e-21   1.2e-17       6     132 ..      56     180 ..      53     184 .. 0.79
   2 ?   -1.1   0.2      0.32   1.5e+03      64      98 ..     189     223 ..     187     231 .. 0.45

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 2.8e-21
                              PAP2   6 llalalaall.tsvlKdlvgrpRPfflaeetkldtqvstletses.keakesfPSgHsafafalalllall..lrrk 78 
                                       l++l+la++    +lK+++  pRP+ + ++ ++ + v     ++  ++ +++fPSgH+ +++++++ la    ++++
  gi|336252709|ref|YP_004595816.1|  56 LVGLLLAGFGiLLALKYAFALPRPDRTLVQLETLPAVVRPLYEATgTADGYGFPSGHAFMTTVVYVSLAGRlsIGTA 132
                                       334444433313568********************987665555599999********8888888777765115666 PP

                              PAP2  79 rkkiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayrlvq 132
                                       r++      +l +++++++v+lsR++lgvH+l Dv aG++ G++l+++a +l +
  gi|336252709|ref|YP_004595816.1| 133 RQR------LLGAATVIAVVCLSRVALGVHYLVDVAAGAAGGLLLVLAAEWLLD 180
                                       666......7999999***********************999999998877765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.32
                              PAP2  64 afalalllalllrrkrkkig.lvllalillllavlv 98 
                                       a++++++la+  + +++ ++   +l+l + l  ++ 
  gi|336252709|ref|YP_004595816.1| 189 AAFALAVLASASAALIASDDpDAVLLLGASL-GAFG 223
                                       4444445555555555554423444444444.4444 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   6.4   4.7e-12   2.1e-08      41     188 ..      34     172 ..      13     174 .. 0.79
   2 ?   -2.0   0.0      0.54   2.4e+03      72      88 ..     255     271 ..     238     301 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 4.7e-12
                            PAP2_3  41 fqvtllvlvllf.lrrrerlreflttlllatllgllvyalfPaagPrlleeagfvdtvaaaslagalrdgasravll 116
                                       f+++l+  ++l+ + +re++  ++ +ll+ + + l++ ++f   +P      ++v++++  +++          +l+
  gi|336252709|ref|YP_004595816.1|  34 FLTLLVGGFYLYrTDDREEGAVLVGLLLAGFGILLALKYAFALPRP----DRTLVQLETLPAVV---------RPLY 97 
                                       5666777788889999999999999*********************....44455555555555.........5999 PP

                            PAP2_3 117 rgtienglaafPSlHvawallvalalw.....rlrrkrllrvlalllnvlmivatvatgnHYlvDviaGvalalvai 188
                                       ++t ++  + fPS H+ ++++v++ l+      ++r+r   + a+ + +++ ++ va+g HYlvDv+aG+a +l+ +
  gi|336252709|ref|YP_004595816.1|  98 EATGTADGYGFPSGHAFMTTVVYVSLAgrlsiGTARQR--LLGAATVIAVVCLSRVALGVHYLVDVAAGAAGGLLLV 172
                                       99999999*************99987532211234444..3334556778899*****************9888765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.54
                            PAP2_3  72 lgllvyalfPaagPrll 88 
                                       +gl++ a+ P ag+ ++
  gi|336252709|ref|YP_004595816.1| 255 IGLAIGAFAPLAGALVY 271
                                       67777777777777555 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   2.4e-05      0.11       8      64 ..     110     167 ..     108     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                            PAP2_C   8 SGHtvvltlavlfileyspkkla.ilkvillllallglfliiasrkHYtvDVllglyi 64 
                                       SGH++++t++++ +    +   a    + ++++ ++ +++ +a   HY vDV  g+  
  gi|336252709|ref|YP_004595816.1| 110 SGHAFMTTVVYVSLAGRLSIGTArQRLLGAATVIAVVCLSRVALGVHYLVDVAAGAAG 167
                                       9******9999887766655554245566788889999999***********999765 PP

>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.8   0.00015      0.69     108     186 ..      19      97 ..      12     148 .. 0.76
   2 ?    3.7  16.8    0.0081        36     116     247 ..     156     295 ..     127     309 .] 0.70

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00015
                   LPG_synthase_TM 108 kalasvvverlldllalvllgllallllggllaegaavllllalallllavlalllllllrrrlarlarvlkrlarl 184
                                       +a  + ++ +l d+ +l ll++ ++l+ +  ++ega++++ll++++++l++l  +++l ++ r +  +  l++++r 
  gi|336252709|ref|YP_004595816.1|  19 AAIVVALLTQLGDVWFLTLLVGGFYLYRTDDREEGAVLVGLLLAGFGILLALKYAFALPRPDRTLVQLETLPAVVRP 95 
                                       5666777899************************9998888888888888888888888888877777777777776 PP

                   LPG_synthase_TM 185 la 186
                                       l 
  gi|336252709|ref|YP_004595816.1|  96 LY 97 
                                       55 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0081
                   LPG_synthase_TM 116 erlldllalvllgllallllggllaegaa..vllllalallllavla...........lllllllrrrlarlarvlk 179
                                         l+d++a ++ gll++l+  +ll+  aa    +++ala+l+ a+ a           ll+++l  +  + l r+ +
  gi|336252709|ref|YP_004595816.1| 156 HYLVDVAAGAAGGLLLVLAAEWLLDRYAAdrGTAAFALAVLASASAAliasddpdavlLLGASLGAFGGWQLVRLGE 232
                                       44555555555555555444444444444666666666666666666777999999888888888888999999999 PP

                   LPG_synthase_TM 180 rlarllarfarklasakrklvlasprrlllafllslliwllealtlylllralgvdvslalll..lilla 247
                                       rl  + +  + +++         ++ ++ + +++ +++ l+ al+++ l+ +   ++s al +  +++la
  gi|336252709|ref|YP_004595816.1| 233 RLPERDRDRRSRSRTD-------RRPAIRIGLAIGAFAPLAGALVYFGLVSMPVPAASGALGFglAAVLA 295
                                       9988887777666653.......55677888999999999999999999988888888888874333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2271.50
//
Query:       gi|336252710|ref|YP_004595817.1|  [L=215]
Description: hypothetical protein Halxa_1305 [Halopiger xanaduensis SH-6]
Scores for 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   39.9   9.3    1.2e-08   35.1   9.2    2.2  1  Bactofilin   Polymer-forming cytoskeletal
    0.00031   20.8   1.7       0.65   10.1   0.0    2.8  2  Phage_spike  Phage spike trimer
  ------ inclusion threshold ------
       0.16   10.6   9.9       0.35    9.4   8.9    1.7  1  FapA         Flagellar Assembly Protein A
       0.54   10.1   4.7       0.53   10.1   0.9    2.7  3  Hexapep      Bacterial transferase hexapeptide (six repeats)
        6.3    6.8   9.3       0.88    9.5   4.0    2.3  2  TAT_signal   TAT (twin-arginine translocation) pathway signal


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   9.2   3.3e-12   1.2e-08      21      97 ..     130     211 ..      83     212 .. 0.66

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.3e-12
                        Bactofilin  21 i..dGkveGdieakgklvvgeggkvegnika.eevvva.Gt.vkGnveaeekvelkktakveGdikaksleieegav 92 
                                       +  d++++G++ea++++ + +g+ ++gn++a + v+++ G  ++Gn+ea+++v ++++a+++G+++ + +++  +a+
  gi|336252710|ref|YP_004595817.1| 130 LedDAELDGNLEAGDDVRLDPGAAIDGNVEAgGGVILSnGAeIDGNLEADGTVAVAGDAEIDGNVTGSAVTVAGDAE 206
                                       24456666777666677777777777777774333332365566777777777777777777777777777777777 PP

                        Bactofilin  93 feGkl 97 
                                       ++G++
  gi|336252710|ref|YP_004595817.1| 207 IDGEI 211
                                       66664 PP

>> Phage_spike  Phage spike trimer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00018      0.65      19      54 .]     133     169 ..     122     169 .. 0.90
   2 !    8.7   0.6   0.00049       1.7      21      52 ..     171     201 ..     170     215 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00018
                                       EEEEEEEEEEE.EEEESSEEEEES-EEEESS-EEETT CS
                       Phage_spike  19 evecTgnLtvg.tltvqgGGtikGdithsgGnlssnG 54 
                                       + e  gnL+ g  + +  G+ i G++++ gG + snG
  gi|336252710|ref|YP_004595817.1| 133 DAELDGNLEAGdDVRLDPGAAIDGNVEAGGGVILSNG 169
                                       567899***************************9998 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00049
                                       EEEEEEEEE.EEEESSEEEEES-EEEESS-EEE CS
                       Phage_spike  21 ecTgnLtvg.tltvqgGGtikGdithsgGnlss 52 
                                       e+ gnL+ + t++v g+++i G++  +g +++ 
  gi|336252710|ref|YP_004595817.1| 171 EIDGNLEADgTVAVAGDAEIDGNV--TGSAVTV 201
                                       568999999999999999999999..5555554 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   8.9   9.9e-05      0.35     144     245 ..     119     212 ..     108     215 .] 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 9.9e-05
                              FapA 144 dvplkagkgtevseedgnkliAaidGrpvvkkngisVdpvleikgdVdlstGnIkfkGsViikGnVeegmkVkasgd 220
                                       d ++ ag  ++++ +d     A+ dG + + +  ++ dp   i+g+V    G I  +G  +i Gn e++ +V   gd
  gi|336252710|ref|YP_004595817.1| 119 DDDVEAGYQVALE-DD-----AELDGNLEAGDD-VRLDPGAAIDGNVEAGGGVILSNGA-EIDGNLEADGTVAVAGD 187
                                       5566666666665.66.....788888888888.9999999**************9996.9**************** PP

                              FapA 221 itikGvvesatieAggnItikgGii 245
                                        +i G+v+++ ++  g+ +i g i 
  gi|336252710|ref|YP_004595817.1| 188 AEIDGNVTGSAVTVAGDAEIDGEIT 212
                                       *******************999875 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.35   1.2e+03      13      26 ..     109     122 ..     104     130 .. 0.74
   2 ?   10.1   0.9   0.00015      0.53       5      35 ..     143     173 ..     143     174 .. 0.95
   3 ?   -1.3   0.1      0.59   2.1e+03       8      22 ..     193     207 ..     183     208 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.35
                                       TEEEETTEEE-TTE CS
                           Hexapep  13 faviggnVkIGdnv 26 
                                        +v+ +++ + d+v
  gi|336252710|ref|YP_004595817.1| 109 SVVLESDASVDDDV 122
                                       56777777777776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00015
                                       ETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   5 GsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       G++v ++p+a i gnV+ G +v++ +g+ i 
  gi|336252710|ref|YP_004595817.1| 143 GDDVRLDPGAAIDGNVEAGGGVILSNGAEID 173
                                       99**************************996 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.59
                                       EEE-TTEEEETTEEE CS
                           Hexapep   8 vlIgpfaviggnVkI 22 
                                       ++ g+ ++++g+++I
  gi|336252710|ref|YP_004595817.1| 193 NVTGSAVTVAGDAEI 207
                                       444555566666655 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.0   0.00024      0.88       3      25 ..      10      30 ..       9      31 .. 0.89
   2 ?   -1.3   0.2      0.63   2.3e+03      14      22 ..     195     203 ..     194     204 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00024
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                      SRR +L   AA +AA++l+gc++
  gi|336252710|ref|YP_004595817.1| 10 SRRRLLW--AASGAAVGLAGCTG 30
                                      7888888..************97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.63
                        TAT_signal  14 aaAAaalgg 22 
                                       ++ A++++g
  gi|336252710|ref|YP_004595817.1| 195 TGSAVTVAG 203
                                       455555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); 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 0.21s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1671.62
//
Query:       gi|336252711|ref|YP_004595818.1|  [L=202]
Description: phosphinothricin acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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  118.4   0.0    3.6e-34  118.1   0.0    1.0  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    2.2e-14   53.7   0.1    3.4e-14   53.1   0.1    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.1e-10   40.1   0.0    4.4e-10   39.6   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.2e-09   37.1   0.1    4.8e-09   36.5   0.1    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.2e-09   37.2   0.0    5.7e-09   36.8   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
      0.003   17.5   0.0     0.0055   16.6   0.0    1.4  1  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   0.0   1.2e-37   3.6e-34       1     155 []       7     160 ..       7     160 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 1.2e-37
                    Acetyltransf_4   1 iraateeDakeilaiyaeyvvntaitfeyevssveefekflealdsekeyvflvae.sdrivGyaylgqfkkr.akd 75 
                                       ir at++Da++ ++iya   + ta+tfe+  +++ e++ ++e++  ++ey++lv e +++++Gyay+  ++ r a+d
  gi|336252711|ref|YP_004595818.1|   7 IRVATPDDAAAVRDIYAPFCESTAVTFEETPPTAAEVAERIEST--LEEYPWLVCEiDGEVAGYAYAHRLRERrAYD 81 
                                       89***************99************************8..******************************* PP

                    Acetyltransf_4  76 wkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiD 152
                                       w +els+y+a +d+++ g+gr+l+++l  vl +q+i+  +a +  pn + + fh+++GFe vg+f  +++   +w D
  gi|336252711|ref|YP_004595818.1|  82 WVVELSIYVA-EDARQSGVGRALYESLFAVLERQGIRDAYAVTTLPNPETVGFHEKMGFERVGDFPAVGYTEDEWRD 157
                                       *********9.79**************************************************************99 PP

                    Acetyltransf_4 153 miw 155
                                         w
  gi|336252711|ref|YP_004595818.1| 158 VAW 160
                                       888 PP

>> 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   1.1e-17   3.4e-14      23     117 .]      40     139 ..      16     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.1e-17
                                       H.....HHHHHHSTTCEEEEEEETTEEEEEEEEEEEET.TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTT CS
                    Acetyltransf_1  23 e.....feesfsleaegllvaeedgeliGfisllkipd.ekggvayieslaVspeyrgkGlGsaLlealeerareeg 93 
                                       +     + es  le+  +lv+e dge++G++ ++   +  +++ ++  s++V++++r +G+G+aL+e l   ++++g
  gi|336252711|ref|YP_004595818.1|  40 AaevaeRIES-TLEEYPWLVCEIDGEVAGYAYAHRLRErRAYDWVVELSIYVAEDARQSGVGRALYESLFAVLERQG 115
                                       2222223333.233335666***********99999998667888888***********************99999* PP

                                       ESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  94 ikkivlaveedndaairlYeklGF 117
                                       i+  ++ ++ +n  +++++ek+GF
  gi|336252711|ref|YP_004595818.1| 116 IRDAYAVTTLPNPETVGFHEKMGF 139
                                       *666999****************9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   1.5e-13   4.4e-10      18     111 ..      39     144 ..      21     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.5e-13
                   Acetyltransf_10  18 spealrerie..egealllvaeeggkivGvi...elrdgs....hisll.fVdpeyrgqGigkaLleaveeeaekdg 84 
                                       ++++++erie   +e+  lv+e +g+++G++   +lr+++     ++l  +V++++r+ G+g+aL e + + +e++g
  gi|336252711|ref|YP_004595818.1|  39 TAAEVAERIEstLEEYPWLVCEIDGEVAGYAyahRLRERRaydwVVELSiYVAEDARQSGVGRALYESLFAVLERQG 115
                                       346777777445799****************8888877667888666545*************************** PP

                   Acetyltransf_10  85 ikl..eltvnaspyavpfYeklGFkavge 111
                                       i+   ++t   +p+ v+f ek+GF++vg+
  gi|336252711|ref|YP_004595818.1| 116 IRDayAVTTLPNPETVGFHEKMGFERVGD 144
                                       **99999999999*************985 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.1   1.6e-12   4.8e-09       5      76 .]      56     141 ..      52     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.6e-12
                                       EEEEEETTEEEEEEEEEEES.....TCTEE.....EEE-GGGTTSSHHHHHHH..H..TT.SEEE.EE.EEEETHHH CS
                    Acetyltransf_7   5 vfVaeddgkivGfialslld.....aeitr.....laVdpeyrgkGiGraLle..a..ae.kgii.le.qlelnaek 64 
                                        +V+e dg++ G++++++l      +   +     ++V++++r  G+GraL e  +   e +gi+  + +++l +++
  gi|336252711|ref|YP_004595818.1|  56 WLVCEIDGEVAGYAYAHRLRerrayD---WvvelsIYVAEDARQSGVGRALYEslFavLErQGIRdAYaVTTLPNPE 129
                                       689*********99999887876441...145678*****************9643552258866423455665559 PP

                                       HHHHHHHTTEEE CS
                    Acetyltransf_7  65 aikfYeklGFee 76 
                                       +++f ek+GFe+
  gi|336252711|ref|YP_004595818.1| 130 TVGFHEKMGFER 141
                                       9*********95 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   1.9e-12   5.7e-09       3     138 .]       6     140 ..       4     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.9e-12
                    Acetyltransf_3   3 lLrplteeDlealfel...rsdpevmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdlee 76 
                                        +r +t++D++a+  +   + + + +++  +p+t +e  e++e+++      e+y w++++ d++v G++  ++l e
  gi|336252711|ref|YP_004595818.1|   6 RIRVATPDDAAAVRDIyapFCESTAVTFEETPPTAAEVAERIESTL------EEYPWLVCEIDGEVAGYAYAHRLRE 76 
                                       689999999888766523344566555888899**********655......669******99978****9888887 PP

                    Acetyltransf_3  77 edee...aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       ++     +el++++a+++++ G+++   ++l  ++ e++g++  +av+   N+  +  +ek+Gfe
  gi|336252711|ref|YP_004595818.1|  77 RRAYdwvVELSIYVAEDARQSGVGRALYESLFAVL-ERQGIRDAYAVTTLPNPETVGFHEKMGFE 140
                                       7666999*************************999.8889************************7 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.8e-06    0.0055      26      79 ..      87     141 ..      69     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-06
                                       EEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EE CS
                              FR47  26 alqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfek 79 
                                       +++v +++r+ G g+ l ++l + + ++g+ ++ +v+   N +   + ek+Gfe 
  gi|336252711|ref|YP_004595818.1|  87 SIYVAEDARQSGVGRALYESLFAVLERQGIrDAYAVTTLPNPETVGFHEKMGFER 141
                                       589************************9974799*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1413.95
//
Query:       gi|336252712|ref|YP_004595819.1|  [L=224]
Description: phospholipase/carboxylesterase [Halopiger xanaduensis SH-6]
Scores for complete 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-22   80.8   0.0    4.9e-22   78.8   0.0    1.7  1  Abhydrolase_2  Phospholipase/Carboxylesterase
      5e-10   39.3   0.0    6.9e-10   38.8   0.0    1.2  1  DLH            Dienelactone hydrolase family
    8.9e-08   31.7   0.8      0.094   12.0   0.0    3.1  3  Hydrolase_4    Serine aminopeptidase, S33
    1.3e-05   24.8   0.8      0.049   13.1   0.0    3.1  3  Peptidase_S9   Prolyl oligopeptidase family
    0.00048   19.8   0.0     0.0016   18.1   0.0    1.8  2  Abhydrolase_1  alpha/beta hydrolase fold
    0.00082   18.9   0.0    0.00098   18.7   0.0    1.2  1  Esterase_phd   Esterase PHB depolymerase
     0.0019   17.9   0.0     0.0033   17.1   0.0    1.3  1  FSH1           Serine hydrolase (FSH1)
     0.0021   18.0   0.2        1.6    8.5   0.0    2.4  2  Abhydrolase_3  alpha/beta hydrolase fold
     0.0028   17.2   0.0     0.0041   16.7   0.0    1.3  1  PE-PPE         PE-PPE domain
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.025   14.4   0.0    1.2  1  Palm_thioest   Palmitoyl protein thioesterase
       0.18   11.6   0.0       0.59   10.0   0.0    1.6  2  DUF829         Eukaryotic protein of unknown function (DUF829
       0.19   12.0   0.0        3.9    7.9   0.0    2.3  2  DUF3243        Protein of unknown function (DUF3243)
        0.2   11.6   0.0       0.26   11.2   0.0    1.3  1  Cutinase       Cutinase


Domain annotation for each model (and alignments):
>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   3.5e-25   4.9e-22      13     213 ..      28     218 ..      17     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 3.5e-25
                                       --EEEEEE--TT--SHHHHHHHH.TT--TTEEEEEE---EEE-GGGTT-EEE-SS-B--SSTTS-B-HHHHHHHHHH CS
                     Abhydrolase_2  13 aqavviflHGlGdsghawaeaakteaalpnikfifphgpelpvtlnggmrmpaWfdlvglspekkedeagikksaek 89 
                                       a+a+++++HG G+++ ++ ++ + e++ + +++  p++ +        +    W++   l+p + ++e g +  ++ 
  gi|336252712|ref|YP_004595819.1|  28 AEAAIVLVHGRGATARSIVQMGE-EIHREGVALLAPQAAR--------R---TWYPNSFLEPVE-KNEPGRSSGLQA 91 
                                       6899*******************.8888888888887754........4...799988888877.7888******** PP

                                       HHHHHHHHHHTT--GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTTTTS-GGG...GG-EEEEEE CS
                     Abhydrolase_2  90 leelidaelkkgipssriiigGFSqGaalalylaltlpkklggivafsgalplsqklessatavt...kklpilqiH 163
                                       +e+ i++  ++gip +ri++ GFSqGa l+ + +   p+++gg vafsg l+ ++  ++    v     ++p +++ 
  gi|336252712|ref|YP_004595819.1|  92 IEDAIGEANDAGIPTDRIMVLGFSQGACLSSEYVARNPQRYGGLVAFSGGLIGQAIDPDDYLDVEsdlENTPAFLGC 168
                                       ****************************************************999999998888766679******* PP

                                       ETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS--HHHHHHHHHHH CS
                     Abhydrolase_2 164 geeDpvvplalgkaakevlkkllkkvelksyeglaHsideeemqdikefl 213
                                        + Dp +p     +++ vl++l+ +v+ ++yeg++H   e+e++++ e +
  gi|336252712|ref|YP_004595819.1| 169 SDSDPHIPEERVHETADVLEELNADVTTRIYEGMGHGVNEDELAFVGEMV 218
                                       *******************************************9987765 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0     5e-13   6.9e-10      14     193 ..      30     210 ..      19     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 5e-13
                               DLH  14 pvvvviqeifGvn.dnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavayl 89 
                                        ++v ++  +G +   i ++ e + +eG + laP+  +r    pn+  e    + e+ ++   +  l+ +++a+  +
  gi|336252712|ref|YP_004595819.1|  30 AAIVLVHG-RGATaRSIVQMGEEIHREGVALLAPQAARRTW-YPNSFLE---PV-EKNEPG-RSSGLQAIEDAIGEA 99 
                                       45555554.55555888899999999999999999988888.4444433...33.555555.677899999*****9 PP

                               DLH  90 ksvpevstkkvgvvGfCmGGalalllaaev.pevdaavafYG......lspekeleeaaki.kapilalfgeeDefi 158
                                       +  +   t++++v Gf  G+ l+ ++ a++ ++  + vaf G        p+  l+   ++ ++p +    + D++i
  gi|336252712|ref|YP_004595819.1| 100 NDAG-IPTDRIMVLGFSQGACLSSEYVARNpQRYGGLVAFSGgligqaIDPDDYLDVESDLeNTPAFLGCSDSDPHI 175
                                       9999.999******************99997889999****9999988788888887777636899999******** PP

                               DLH 159 padevekleealkaanvdlelkvYpgagHaFands 193
                                       p + v++++  l++ n+d+   +Y+g gH+ ++d+
  gi|336252712|ref|YP_004595819.1| 176 PEERVHETADVLEELNADVTTRIYEGMGHGVNEDE 210
                                       *****************************987765 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1   0.00068      0.94       2      36 ..      27      61 ..      26      64 .. 0.92
   2 !   12.0   0.0   6.8e-05     0.094      74     111 ..     105     142 ..      89     151 .. 0.84
   3 !    8.3   0.0   0.00093       1.3     191     234 ..     161     206 ..     149     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00068
                       Hydrolase_4  2 epkavvvlvHGlaehsgryaelaeaLaaqGfavya 36
                                      +++a++vlvHG++ +++   +++e+  ++G+a +a
  gi|336252712|ref|YP_004595819.1| 27 DAEAAIVLVHGRGATARSIVQMGEEIHREGVALLA 61
                                      5789**************************99876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.8e-05
                       Hydrolase_4  74 pelplfllGhSmGGliallyllrypdkvaglilsaPal 111
                                       p+ ++++lG S G+ ++ +y++r+p+++ gl+ ++  l
  gi|336252712|ref|YP_004595819.1| 105 PTDRIMVLGFSQGACLSSEYVARNPQRYGGLVAFSGGL 142
                                       66799**************************9988665 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00093
                       Hydrolase_4 191 tlPllllhGeaDkvvdpeas...relyerlgskdktlklypglyHel 234
                                       ++P +l ++++D+ +++e     ++++e+l++ d+t ++y+g+ H +
  gi|336252712|ref|YP_004595819.1| 161 NTPAFLGCSDSDPHIPEERVhetADVLEELNA-DVTTRIYEGMGHGV 206
                                       499*************9999444555555554.************87 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.14     2e+02      23      60 ..       3      40 ..       1      54 [. 0.63
   2 !    7.3   0.0    0.0021       2.9      62      95 ..     105     138 ..      89     142 .. 0.88
   3 !   13.1   0.0   3.5e-05     0.049     141     191 ..     156     209 ..     145     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.14
                                      TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS CS
                      Peptidase_S9 23 rGsggyGeafhdagkrklgqnefdDfiaaaealakegy 60
                                      rG+g++Ge+ h+  +  +   +++D  aa+  +  +g 
  gi|336252712|ref|YP_004595819.1|  3 RGGGHQGENPHQGQELVTAGTDLADAEAAIVLVHGRGA 40
                                      67777777777666666666666666665554444443 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0021
                                       -GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEE CS
                      Peptidase_S9  62 dserlaitGgSyGGyltgaalnqrpdlFkaavae 95 
                                        ++r+++ G S G  l+   ++++p++++++va 
  gi|336252712|ref|YP_004595819.1| 105 PTDRIMVLGFSQGACLSSEYVARNPQRYGGLVAF 138
                                       579***************************9985 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 3.5e-05
                                       -...---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSS CS
                      Peptidase_S9 141 k...aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkp 191
                                       +   +++p +l +++ D  +p +   + ++ L++ + +v  +i+ + gHgv+++
  gi|336252712|ref|YP_004595819.1| 156 EsdlENTPAFLGCSDSDPHIPEERVHETADVLEELNADVTTRIYEGMGHGVNED 209
                                       345589********************************************9876 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.1   4.3e+03       2      16 ..      31      45 ..      31      74 .. 0.70
   2 !   18.1   0.0   1.2e-06    0.0016      72     114 ..     106     150 ..      92     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.1
                                      EEEEE-STTTCGGGG CS
                     Abhydrolase_1  2 vlvilhGlpgssdvw 16
                                      ++v++hG ++++ + 
  gi|336252712|ref|YP_004595819.1| 31 AIVLVHGRGATARSI 45
                                      589999998866553 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.2e-06
                                       TSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE..CSSCCHHH CS
                     Abhydrolase_1  72 ddkltlvGhSmGGmialayaaeyperVkalvllga..idpaasli 114
                                        d++ ++G+S+G  ++++y a++p+r  +lv+ ++  i  a++++
  gi|336252712|ref|YP_004595819.1| 106 TDRIMVLGFSQGACLSSEYVARNPQRYGGLVAFSGglIGQAIDPD 150
                                       57899*************************999987766666655 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   7.1e-07   0.00098      21     155 ..      34     164 ..      21     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.1e-07
                      Esterase_phd  21 mlhGctqsveefaaGtrmnlladklGvvvlypeqslranaqkcwnwykdtdraGrGeaavvvalvdal..vdehrvd 95 
                                       ++hG   ++       +m    ++ Gv++l p+ ++r+   +   + +  +++  G ++ + a+ da+  +++ ++ 
  gi|336252712|ref|YP_004595819.1|  34 LVHGRGATARSIV---QMGEEIHREGVALLAPQAARRTWYPNS--FLEPVEKNEPGRSSGLQAIEDAIgeANDAGIP 105
                                       5555555554443...366666788999999998888766554..56777777788888999999999334567899 PP

                      Esterase_phd  96 aarvyvaGlsaGaaladllalhypdvfaavalhsGlalGeaadvisaldvmrrGlrqapa 155
                                       + r+ v G+s Ga+l++      p+++  +   sG  +G+a d    ldv  + l ++pa
  gi|336252712|ref|YP_004595819.1| 106 TDRIMVLGFSQGACLSSEYVARNPQRYGGLVAFSGGLIGQAIDPDDYLDV-ESDLENTPA 164
                                       ******************999********************999888887.455665554 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.4e-06    0.0033      69     186 ..      65     186 ..      50     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                              FSH1  69 esraWfrkkde...kneyegleesldavkdyikengp......fdGiiGFSqGaalaallaslleellkeashpslk 136
                                         r+W+ ++     +++  g + +l+a++d+i e +          ++GFSqGa+l++ +++   +         + 
  gi|336252712|ref|YP_004595819.1|  65 ARRTWYPNSFLepvEKNEPGRSSGLQAIEDAIGEANDagiptdRIMVLGFSQGACLSSEYVARNPQR--------YG 133
                                       567888887777777777788888888888887744333333344689********98766544332........23 PP

                              FSH1 137 failvsGfkleepkyeeyy...eedkiqtptLhvlGelDtvvdeerseaLaea 186
                                        ++++sG  + +    + y   e+d  +tp +    ++D  ++eer  + a++
  gi|336252712|ref|YP_004595819.1| 134 GLVAFSGGLIGQAIDPDDYldvESDLENTPAFLGCSDSDPHIPEERVHETADV 186
                                       45666666665555444444533333366666666666666666666665555 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0012       1.6      51      95 ..      87     131 ..      32     147 .. 0.78
   2 !    7.5   0.0    0.0024       3.4     167     209 ..     162     206 ..     148     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHT CS
                     Abhydrolase_3  51 dalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrarde 95 
                                        +l+a++ +  +a ++g+ ++ri+++G S G+ l+   + r  ++
  gi|336252712|ref|YP_004595819.1|  87 SGLQAIEDAIGEANDAGIPTDRIMVLGFSQGACLSSEYVARNPQR 131
                                       5677777778887899******************99888776665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0024
                                       --EEEEEETT-TTHHHH..HHHHHHHHHTT--EEEEEETTEETTG CS
                     Abhydrolase_3 167 pptlvvvaefDplrdeg..eayaerlraagvevelieyegmvHgf 209
                                        p+++ + + Dp   e+   ++a+ l++ + +v+++ yegm Hg+
  gi|336252712|ref|YP_004595819.1| 162 TPAFLGCSDSDPHIPEErvHETADVLEELNADVTTRIYEGMGHGV 206
                                       466667777777665541168999*******************96 PP

>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     3e-06    0.0041      10      69 ..      70     128 ..      61     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3e-06
                            PE-PPE  10 yPasflpvtglksltvdeSvaeGtenLeaairaela...agekvvvfGySqgalvasnekarl 69 
                                       yP+sfl +  +++ + ++  + G++ +e+ai ++++    +++++v+G+Sqga   s++ ar 
  gi|336252712|ref|YP_004595819.1|  70 YPNSFLEP--VEKNEPGR--SSGLQAIEDAIGEANDagiPTDRIMVLGFSQGACLSSEYVARN 128
                                       66666664..33333344..579**********9995555677***********999988775 PP

>> Palm_thioest  Palmitoyl protein thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.8e-05     0.025       2     107 ..      32     146 ..      31     198 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                      Palm_thioest   2 vviwhGldsaesnmqklaeliekligtyvknveigesea..............edrkasffgnlndqveavckk.le 63 
                                       +v++hG ++ + ++ ++ e+i+++ g  v +++ ++  +              e  ++s ++ ++d + ++ ++   
  gi|336252712|ref|YP_004595819.1|  32 IVLVHGRGATARSIVQMGEEIHRE-G--VALLAPQAARRtwypnsflepveknEPGRSSGLQAIEDAIGEANDAgI- 104
                                       789999966666577777777763.3..333332222221222222233322345566666667777766766662. PP

                      Palm_thioest  64 langfhaiGfSQGglflRaliercddkknvrnlislggpqaGvf 107
                                        ++ + ++GfSQG+ +   ++ r + +     l+ ++g   G++
  gi|336252712|ref|YP_004595819.1| 105 PTDRIMVLGFSQGACLSSEYVARNP-QR-YGGLVAFSGGLIGQA 146
                                       5899*******************74.44.799999998877775 PP

>> DUF829  Eukaryotic protein of unknown function (DUF829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.91   1.3e+03      49      86 ..      87     126 ..      39     148 .. 0.74
   2 ?   10.0   0.0   0.00043      0.59     172     224 ..     154     206 ..     147     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.91
                            DUF829  49 saldellellsesqrsey..wpilfhvfsngGpllylall 86 
                                       s+l+++ + + e++ +    ++i++  fs g++l   +++
  gi|336252712|ref|YP_004595819.1|  87 SGLQAIEDAIGEANDAGIptDRIMVLGFSQGACLSSEYVA 126
                                       5666666666666555447788999999998877766655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00043
                            DUF829 172 dlatkplrcpqlylySkaDeviswrdveshaeeaeqrgvkvtakkfedspHva 224
                                       d++++ + +p++  +S++D++i+++ v + a+  e+ + +vt+  +e+  H++
  gi|336252712|ref|YP_004595819.1| 154 DVESDLENTPAFLGCSDSDPHIPEERVHETADVLEELNADVTTRIYEGMGHGV 206
                                       67778888999999************************************985 PP

>> DUF3243  Protein of unknown function (DUF3243)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0028       3.9      12      51 ..      91     130 ..      89     132 .. 0.93
   2 ?    1.5   0.0      0.26   3.6e+02      15      42 ..     196     223 ..     185     224 .] 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHHHHHHTT----HHHHHHHHHHT-----SHH CS
                           DUF3243  12 fLgdrveqaeklGlseetieklAyevGdyLaekvdpknke 51 
                                        ++d++ +a+++G+++++i  l ++ G  L+++  ++n++
  gi|336252712|ref|YP_004595819.1|  91 AIEDAIGEANDAGIPTDRIMVLGFSQGACLSSEYVARNPQ 130
                                       57899******************************99987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHTT----HHHHHHHHHH CS
                           DUF3243  15 drveqaeklGlseetieklAyevGdyLa 42 
                                       +r+ ++   G++e++++ + + v+d L+
  gi|336252712|ref|YP_004595819.1| 196 TRIYEGMGHGVNEDELAFVGEMVADLLS 223
                                       677788889****************996 PP

>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00019      0.26      54      98 ..      81     126 ..      30     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                       TTSS-HHHHHHHHHHHHHHHHH.-TT-EEEEEEETHHHHHHHHHHT CS
                          Cutinase  54 yegseeagakeaaalvqslask.CPdtkivlgGYSqGaqvidnaie 98 
                                        e + ++g ++++ ++ +++ +  P  +i+++G+SqGa +  + ++
  gi|336252712|ref|YP_004595819.1|  81 NEPGRSSGLQAIEDAIGEANDAgIPTDRIMVLGFSQGACLSSEYVA 126
                                       456778999999999999997636**************98776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1550.51
//
Query:       gi|336252713|ref|YP_004595820.1|  [L=208]
Description: Glyoxalase/bleomycin resistance protein/dioxygenase [Halopiger xanaduensis SH-6]
Scores for 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-10   39.2   0.1      1e-09   38.6   0.1    1.3  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    1.4e-05   25.3   0.0    2.5e-05   24.5   0.0    1.6  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
  ------ inclusion threshold ------
      0.086   12.9   0.0       0.21   11.7   0.0    1.7  2  DUF3880       DUF based on E. rectale Gene description (DUF38


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 !   38.6   0.1   1.7e-13     1e-09       2     128 .]      25     145 ..      24     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.7e-13
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC....TS CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkiee....tv 74 
                                        dh+++  ++ e +++FY++ LG+ lv + + +  ++++++ ff+ g+g+i  +  + + ++a ++          v
  gi|336252713|ref|YP_004595820.1|  25 TDHITIWGSNEEDTVEFYQDLLGMPLVLRQP-NLDDPSQTHLFFDTGDGRILTFFVSDDRPSARGQ----RagvgAV 96 
                                       69*****************************.6667*****************************9....3335589 PP

                                       EEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  75 hhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       hh+ f +  +e  ++  + l+eag     + +r  f+++y    rD +G  +e+
  gi|336252713|ref|YP_004595820.1|  97 HHLCFSVEPDEY-EQIMQSLEEAG-HGYNVFDRGIFHSIY---TRDNNGLVIEL 145
                                       999999988777.***********.8888999*******9...89****99996 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   4.3e-09   2.5e-05       1      91 [.      26     120 ..      26     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.3e-09
                                       EEEEEE-S-HHHHHHHHHH.TT-E..ESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT-THHH.TS-EEEEEEE CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvg..pwqryrdepqevdlafallgsgsvqieLieplegpeflae.hgeglhhlay 74 
                                       d+i i+  + e++v+++++llG+    +q+  d+p++ +l f+++g+g +   +++ ++ +   ++ + + +hhl++
  gi|336252713|ref|YP_004595820.1|  26 DHITIWGSNEEDTVEFYQDLLGMPlvLRQPNLDDPSQTHL-FFDTGDGRILTFFVSDDRPSARGQRaGVGAVHHLCF 101
                                       69********************862144555566666666.9*****986555555555554444448888****** PP

                                       EES..-HHHHHHHHCTTTE CS
                      Glyoxalase_4  75 wvd..dldaavarleeqGf 91 
                                        v+  ++++++++lee+G 
  gi|336252713|ref|YP_004595820.1| 102 SVEpdEYEQIMQSLEEAGH 120
                                       *95549*********9864 PP

>> DUF3880  DUF based on E. rectale Gene description (DUF3880)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.1   6.9e+03       4      15 ..      17      28 ..      16      30 .. 0.75
   2 ?   11.7   0.0   3.5e-05      0.21      14      62 ..      69     117 ..      56     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                           DUF3880  4 DsPlltlysksi 15
                                      DsP++t+ +++i
  gi|336252713|ref|YP_004595820.1| 17 DSPFHTTGTDHI 28
                                      899999877655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.5e-05
                           DUF3880  14 siandcnyiftfDkeqyeelkelGvknvyylPLAanverldpleaeaek 62 
                                       +   +  ++f+ D     + +++Gv  v++l + ++++ ++++ ++ e+
  gi|336252713|ref|YP_004595820.1|  69 TGDGRILTFFVSDDRPSARGQRAGVGAVHHLCFSVEPDEYEQIMQSLEE 117
                                       555566789999******************************9988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1525.49
//
Query:       gi|336252714|ref|YP_004595821.1|  [L=209]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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   82.8  13.5    5.2e-13   48.9   2.6    2.1  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.8e-12   45.5   1.4    1.5e-06   27.8   0.1    2.6  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    4.6e-11   42.9   1.9    5.7e-05   22.9   0.1    2.1  2  DAO             FAD dependent oxidoreductase
    9.8e-10   37.7   0.3    3.5e-05   22.7   0.1    2.2  2  HI0933_like     HI0933-like protein
      7e-09   35.4   1.5    4.2e-05   22.9   0.0    2.1  2  FAD_binding_3   FAD binding domain
    5.6e-07   29.0   3.2    5.9e-06   25.6   0.3    2.2  2  FAD_binding_2   FAD binding domain
    7.6e-07   28.6   3.7    2.2e-05   23.7   0.3    2.7  3  GIDA            Glucose inhibited division protein A
    5.5e-06   26.5   0.9     0.0049   16.9   0.1    2.3  2  NAD_binding_9   FAD-NAD(P)-binding
    2.8e-05   24.3   0.0    6.4e-05   23.1   0.0    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00011   21.5   0.2    0.00018   20.8   0.2    1.6  1  Thi4            Thi4 family
    0.00028   20.3   0.2    0.00028   20.3   0.2    1.7  3  FAD_oxidored    FAD dependent oxidoreductase
    0.00064   18.9   1.1      0.062   12.3   0.1    2.1  2  Lycopene_cycl   Lycopene cyclase protein
      0.002   17.4   0.3     0.0037   16.6   0.2    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0036   17.8   0.4      0.019   15.5   0.4    2.1  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.015   14.6   0.1       0.11   11.7   0.0    1.9  2  Amino_oxidase   Flavin containing amine oxidoreductase
       0.02   13.8   3.9       0.83    8.4   0.4    2.2  2  Trp_halogenase  Tryptophan halogenase
      0.032   13.4   0.2        2.2    7.3   0.0    2.1  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.073   13.6   0.0       0.16   12.5   0.0    1.5  1  XdhC_C          XdhC Rossmann 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 !   48.9   2.6   5.3e-16   5.2e-13       2     109 ..      16     122 ..      15     123 .. 0.76
   2 !   46.4   3.3     3e-15     3e-12     183     293 ..      67     171 ..      59     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 5.3e-16
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...HHHHCHHHHCCCCHCCTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias...evvkklnqgielllgeev 75 
                                       +v+v+GgGpAGl+aal+ a++g+++t+++++gt+++   l  +   g+ + +e ++   ++v++++  ++++ geev
  gi|336252714|ref|YP_004595821.1|  16 SVIVVGGGPAGLSAALFTAKNGLETTVFDADGTWMHKAHLFNYLGIGSVGGTEFMEtarQQVDSFG--VDRRQGEEV 90 
                                       79***************************9999998888887766666666656666877778775..777888778 PP

                                       EEEEESC.EEEEETEEECTCEEEEEESEEEE---E CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  76 vkidpgk.kkvklekkkegdeekiaydklvlAtGs 109
                                       ++++ +  ++  + ++++    ++++d++vlAtG+
  gi|336252714|ref|YP_004595821.1|  91 TSVEAADtGDGFVVATED---GEYEADYVVLATGA 122
                                       888744434444433443...37***********8 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 3e-15
                                       HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.EEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 183 kelsaaleealekeGvevklgtsvkeidgnge.kle.vvledgeeidadlvvvavGvrpstelleeklgleldergg 257
                                        e+ +++++++   Gv+ + g++v+ +++ ++ +   vv ++  e++ad+vv+a+G   +++l+ ++lg+  +e + 
  gi|336252714|ref|YP_004595821.1|  67 TEFMETARQQVDSFGVDRRQGEEVTSVEAADTgD-GfVVATEDGEYEADYVVLATGA--NRDLA-DDLGCVFTEEDV 139
                                       57778889999999***********999999853.35788888889*********96..55588.9*********** PP

                                       EE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 258 ivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqq 293
                                       + vd  ++t+v+++ya G+++    +pe +qaA++ 
  gi|336252714|ref|YP_004595821.1| 140 VDVDVEMETSVDNVYATGAMV----RPEEWQAAIAV 171
                                       *******************99....********975 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 !   15.6   0.1   7.4e-06    0.0074       1      27 [.      18      43 ..      17      51 .. 0.87
   2 !   27.8   0.1   1.5e-09   1.5e-06      80     134 ..      66     122 ..      62     125 .. 0.88
   3 ?   -1.6   0.0       1.3   1.3e+03     293     305 .]     145     157 ..     129     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.4e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylil 27
                                      i++G+GPaGl+aa+   k+gle  ++ 
  gi|336252714|ref|YP_004595821.1| 18 IVVGGGPAGLSAALFTAKNGLE-TTVF 43
                                      89*******************6.4565 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 1.5e-09
                       Pyr_redox_3  80 rkealeYlrevaksfelpiklfeeVesvkk..edegfevetsketyeAkkviiAtGe 134
                                       + e++e  r+ ++sf ++ ++ eeV+sv+   +++gf+v t+ ++yeA++v++AtG 
  gi|336252714|ref|YP_004595821.1|  66 GTEFMETARQQVDSFGVDRRQGEEVTSVEAadTGDGFVVATEDGEYEADYVVLATGA 122
                                       667788889999*****************9434577********************5 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.3
                       Pyr_redox_3 293 teetnvpglflaG 305
                                       ++et v++++  G
  gi|336252714|ref|YP_004595821.1| 145 EMETSVDNVYATG 157
                                       6999999999887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   4.6e-07   0.00045       2      29 ..      17      46 ..      16      55 .. 0.93
   2 !   22.9   0.1   5.7e-08   5.7e-05     146     213 ..      67     130 ..      48     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.6e-07
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      v+++GGG +Gls+A++ a+ g  +t+++++
  gi|336252714|ref|YP_004595821.1| 17 VIVVGGGPAGLSAALFTAKNGleTTVFDAD 46
                                      9***************************98 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 5.7e-08
                                       HHHHHHHHHHHHHTT-EEEESECEEEEEEEE.TCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTTCTT CS
                               DAO 146 akltaalaraaealGveilegtevtgleeed.gkvwgverttp.gendaadavVnaaGawsdllgllkel 213
                                        +++   ++++ + Gv+ ++g+evt++e+ d g++  v  +t+ ge  +ad+vV+a+Ga  dl+    +l
  gi|336252714|ref|YP_004595821.1|  67 TEFMETARQQVDSFGVDRRQGEEVTSVEAADtGDGFVV--ATEdGEY-EADYVVLATGANRDLA---DDL 130
                                       56777888889999*************99776776666..7777986.56*********97777...444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   3.5e-08   3.5e-05       2      38 ..      16      52 ..      15      64 .. 0.91
   2 !   13.3   0.0   2.4e-05     0.024     112     164 ..      70     122 ..      62     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.5e-08
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                      +viv+GgG+AGl aA+  ak+g +++++++  +  +K
  gi|336252714|ref|YP_004595821.1| 16 SVIVVGGGPAGLSAALFTAKNGLETTVFDADGTWMHK 52
                                      69***************************98777666 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHHT-EEE-S--EEEEECETTE..EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 112 vdallkelkeagvklrletevksvekeedg.kfrvktkseeeleadklvlAtGG 164
                                       +++  +++++ gv+ r  +ev+sve+ ++g  f v+t +++e+ead++vlAtG 
  gi|336252714|ref|YP_004595821.1|  70 METARQQVDSFGVDRRQGEEVTSVEAADTGdGFVVAT-EDGEYEADYVVLATGA 122
                                       56677899999*************8766541588888.9**************6 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   4.3e-08   4.2e-05       2      34 ..      15      47 ..      14      59 .. 0.88
   2 !   11.5   0.8   0.00013      0.13     112     197 ..      74     151 ..      60     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.3e-08
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                      ++V++VG+GpaGl++al+ ++ G ++++ +   
  gi|336252714|ref|YP_004595821.1| 15 ASVIVVGGGPAGLSAALFTAKNGLETTVFDADG 47
                                      68*************************998765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00013
                                       HHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEE CS
                     FAD_binding_3 112 vehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgiefegeetvyeagvl 188
                                       +++  + g++ r+++ev+s+e+ ++g +  v   e+ge    +a+Y+v a G++   +++lg  f++e+ v     +
  gi|336252714|ref|YP_004595821.1|  74 RQQVDSFGVDRRQGEEVTSVEAADTG-DGFVVATEDGEY---EADYVVLATGANRDLADDLGCVFTEEDVV----DV 142
                                       56677899***************999.899999999999...9*******************999888844....44 PP

                                       EEEEEC-SC CS
                     FAD_binding_3 189 dvlfdadls 197
                                       dv +++ ++
  gi|336252714|ref|YP_004595821.1| 143 DVEMETSVD 151
                                       554444444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.3     6e-09   5.9e-06       2      30 ..      17      45 ..      16      54 .. 0.92
   2 ?    4.3   0.3     0.018        18     138     209 ..      64     129 ..      45     179 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6e-09
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvek 30
                                      viV+G+G AGL+AAl  a++Gl+++v + 
  gi|336252714|ref|YP_004595821.1| 17 VIVVGGGPAGLSAALFTAKNGLETTVFDA 45
                                      9***********************99876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.018
                                       .HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..... CS
                     FAD_binding_2 138 vtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallke 209
                                       v g + +++  +++++ gvd +   e++++    +   G vv+     ++ +++a+ vvlatg+    l++ 
  gi|336252714|ref|YP_004595821.1|  64 VGGTEFMETARQQVDSFGVDRRQGEEVTSVEA-ADTGDGFVVA----TEDGEYEADYVVLATGANRD-LADD 129
                                       56777777777777777777777777777744.4455666666....44557889*******98774.4444 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.3   2.2e-08   2.2e-05       2      46 ..      17      66 ..      16      81 .. 0.76
   2 ?    4.7   0.0     0.013        13     116     150 ..      88     122 ..      68     128 .. 0.77
   3 ?   -0.2   0.0      0.41   4.1e+02     349     391 ..     145     188 ..     131     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.2e-08
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE.....ES-GGGTT--SSSSEEE- CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi.....thkldtiaelsCnpsigg 46
                                      viV+GgG AG+ AAl +a+ G++++ +      ++  ++ +     s+gg
  gi|336252714|ref|YP_004595821.1| 17 VIVVGGGPAGLSAALFTAKNGLETTVFdadgtWMHKAHLFNYLGIGSVGG 66
                                      9*************************988887344444444445555555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.013
                                       S-EEEEEECTTEEEE.EEETTS-EEEECEEEE--TT CS
                              GIDA 116 eeveeliveekkvkg.vvtedgetikakavviatGt 150
                                       eev++++   ++  g vv +++ +++a+ vv+atG+
  gi|336252714|ref|YP_004595821.1|  88 EEVTSVEA-ADTGDGfVVATEDGEYEADYVVLATGA 122
                                       45666644.345555688888899***********8 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.41
                                       TSBBSSSBTEEE-CGGGTB-SHHHHHH..HHHHHHHHHHHHHCTS CS
                              GIDA 349 tLetkkvkgLflAGqinGteGYeEaaa..qGllAGinaarkakgk 391
                                       ++et+ v+++++ G +   e + +a+a   G  A++n+  ++kg+
  gi|336252714|ref|YP_004595821.1| 145 EMETS-VDNVYATGAMVRPEEWQAAIAvgDGAAAALNILSDVKGE 188
                                       67777.899999999988888888887668999999999888875 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   0.0    0.0024       2.4       2      37 ..      19      49 ..      18      55 .. 0.80
   2 !   16.9   0.1   4.9e-06    0.0049     104     155 ..      70     122 ..      67     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0024
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                      +vG+Gp+Gl+++   +++      le t+fd ++++
  gi|336252714|ref|YP_004595821.1| 19 VVGGGPAGLSAALFTAKN-----GLETTVFDADGTW 49
                                      8*********99877776.....6888888887776 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.9e-06
                     NAD_binding_9 104 feellarlpegvtvevhra.evvdleeradgq.avlladgaslaadaVvLAlGh 155
                                       +e++ +++ +++ v+  ++ ev+++e +++g   v+ +++ +++ad+VvLA+G 
  gi|336252714|ref|YP_004595821.1|  70 METARQQV-DSFGVDRRQGeEVTSVEAADTGDgFVVATEDGEYEADYVVLATGA 122
                                       55555555.346677765449*****9999875788899999**********95 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 !   23.1   0.0   6.4e-08   6.4e-05       1      28 [.      19      46 ..      19      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.4e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      +vG+G +Gl+aA + ak+g++ +++++ 
  gi|336252714|ref|YP_004595821.1| 19 VVGGGPAGLSAALFTAKNGLETTVFDAD 46
                                      8*************************85 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   1.8e-07   0.00018      16      49 ..      13      45 ..       1     105 [. 0.87

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.8e-07
                                      TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailer 49
                                       ++ v++vG+G++GL+aa   ak+ +l+++++++
  gi|336252714|ref|YP_004595821.1| 13 SDASVIVVGGGPAGLSAALFTAKN-GLETTVFDA 45
                                      6788********************.**9999986 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   2.8e-07   0.00028       2      30 ..      17      45 ..      16      49 .. 0.91
   2 ?   -2.6   0.1       2.7   2.7e+03     107     136 ..      87     113 ..      68     127 .. 0.49
   3 ?   -3.6   0.1       5.4   5.4e+03     396     415 ..     160     181 ..     147     186 .. 0.53

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.8e-07
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      v+VvGGgpaG+ AA+  a++G ++ + + 
  gi|336252714|ref|YP_004595821.1| 17 VIVVGGGPAGLSAALFTAKNGLETTVFDA 45
                                      9**********************998776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.7
                      FAD_oxidored 107 ntrlvevekegkriesvtveskegrktirA 136
                                       ++++++ve  + + ++ +v++  ++ +++A
  gi|336252714|ref|YP_004595821.1|  87 GEEVTSVEAAD-TGDGFVVAT--EDGEYEA 113
                                       33333333332.333333332..2344444 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.4
                      FAD_oxidored 396 vepvcmalGqAa..GvaAalal 415
                                       v p +++   A+  G+aAal +
  gi|336252714|ref|YP_004595821.1| 160 VRPEEWQAAIAVgdGAAAALNI 181
                                       4555555555541156666655 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   6.2e-05     0.062       2      33 ..      17      46 ..      16      55 .. 0.84
   2 !    5.6   0.1    0.0068       6.8      84     145 ..      64     125 ..      51     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.2e-05
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieas 33
                                      v+v+G+GpAgls A     ak gl+ ++ +a 
  gi|336252714|ref|YP_004595821.1| 17 VIVVGGGPAGLSAALFT--AKNGLETTVFDAD 46
                                      8***********99988..9999988888765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0068
                     Lycopene_cycl  84 vsskrlkeellerlvengvkllea.kvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                       v  +++ e   +++ + gv ++++  v+sve+++ g+  vv  ++ + +a  vv a+g a+++
  gi|336252714|ref|YP_004595821.1|  64 VGGTEFMETARQQVDSFGVDRRQGeEVTSVEAADTGDGFVVATEDGEYEADYVVLATG-ANRD 125
                                       55566777777777778888888736*********999999999999***********.4444 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 !   16.6   0.2   3.7e-06    0.0037      27      64 ..      13      50 ..       5      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.7e-06
                                      ---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                       AlaDh_PNT_C 27 epakvlviGgGvaGlqAiatakglgakVtvlDvrparl 64
                                      + a v+v+GgG aGl+A+   ++ g ++tv+D + + +
  gi|336252714|ref|YP_004595821.1| 13 SDASVIVVGGGPAGLSAALFTAKNGLETTVFDADGTWM 50
                                      5799****************************986655 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   0.4   1.9e-05     0.019       1      35 [.      16      50 ..      16     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      +v+vvGgG  gl +A + a+ g ++tv+++  + +
  gi|336252714|ref|YP_004595821.1| 16 SVIVVGGGPAGLSAALFTAKNGLETTVFDADGTWM 50
                                      699************************99876555 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.23   2.3e+02       2      24 ..      25      47 ..      24      49 .. 0.93
   2 ?   11.7   0.0   0.00011      0.11     222     261 ..      81     121 ..      50     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.23
                                      HHHHHHHHHHHTTEEEEEEESSS CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEard 24
                                      aGL+aA   + +G+++tv+ a++
  gi|336252714|ref|YP_004595821.1| 25 AGLSAALFTAKNGLETTVFDADG 47
                                      9******************9975 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00011
                                       TEEEETSEEEEEEEE..ETTCEEEEETTSTEEEESEEEE-S- CS
                     Amino_oxidase 222 gldirlntrVkeikr..egdgvtvtledgevveaDaVvvTvp 261
                                       g+d r +++V++++    gdg  v +edge  eaD+Vv+++ 
  gi|336252714|ref|YP_004595821.1|  81 GVDRRQGEEVTSVEAadTGDGFVVATEDGEY-EADYVVLATG 121
                                       67778899*******999999*********7.*******986 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0027       2.7       2      22 ..      17      37 ..      16      48 .. 0.83
   2 ?    8.4   0.4   0.00083      0.83     157     215 ..      70     128 ..      64     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0027
                                      EEEE--SHHHHHHHHHHHHHT CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakal 22
                                      +++vGGG+aG  aA   ak +
  gi|336252714|ref|YP_004595821.1| 17 VIVVGGGPAGLSAALFTAKNG 37
                                      89***********99888766 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00083
                                       HHHHHHHHHHCT-EEEE--.EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIII CS
                    Trp_halogenase 157 akfLrrvaearGvtrvegk.vvevqldedgrveslrledgreveadlfiDcsGfrgllie 215
                                        +  r+   + Gv+r++g+ v++v+  ++g+   + +edg+ +ead ++ ++G ++ l +
  gi|336252714|ref|YP_004595821.1|  70 METARQQVDSFGVDRRQGEeVTSVEAADTGDGFVVATEDGE-YEADYVVLATGANRDLAD 128
                                       55567778889*****9972666777667777778999998.***********9998866 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 ?    4.5   0.0     0.017        16       5      41 ..      17      49 ..      13      59 .. 0.81
   2 ?    7.3   0.0    0.0022       2.2     107     167 ..      78     131 ..      63     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.017
                       K_oxygenase  5 ligiGiGpsnLsLailleevkkelkalflerqpefaW 41
                                      +i +G Gp+ Ls a+ ++++   l++ +++   +  W
  gi|336252714|ref|YP_004595821.1| 17 VIVVGGGPAGLSAALFTAKNG--LETTVFD--ADGTW 49
                                      899*********999999888..9999999..55555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0022
                       K_oxygenase 107 sqleeqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevle 167
                                       +++    r geev++ve  +    + + v +     e  e+ea  +vl++G ++ + + l 
  gi|336252714|ref|YP_004595821.1|  78 DSFGVDRRQGEEVTSVEAADTG--DGFVVAT-----EDGEYEADYVVLATGANRDLADDLG 131
                                       4555557889999999999976..4688988.....56789**********9988766655 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00016      0.16       1      64 [.      17     119 ..      17     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG................................-GGG-TT-SE. CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefa................................tkerfpeade. 44 
                                       ++++G+g+ + + a + a+ g+++tv+d++ +                                  +        + 
  gi|336252714|ref|YP_004595821.1|  17 VIVVGGGPAGLSAALFTAKNGLETTVFDADGTWMhkahlfnylgigsvggtefmetarqqvdsfgvD--------Rr 85 
                                       689****************************666578888888888887766666665555555440........04 PP

                                       ..............-EEEE--S-HHHHHHHHHHH CS
                            XdhC_C  45 ..............tavvvlthdhklDaealeaa 64 
                                                     + +vv+t+d +++a+++  a
  gi|336252714|ref|YP_004595821.1|  86 qgeevtsveaadtgDGFVVATEDGEYEADYVVLA 119
                                       5555555566667999999999888877766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 1576.61
//
Query:       gi|336252715|ref|YP_004595822.1|  [L=368]
Description: glutamate--cysteine ligase GCS2 [Halopiger xanaduensis SH-6]
Scores for 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-11   42.6   0.8    1.4e-10   41.0   0.8    1.6  1  GCS2      Glutamate-cysteine ligase family 2(GCS2)


Domain annotation for each model (and alignments):
>> GCS2  Glutamate-cysteine ligase family 2(GCS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.8   7.8e-15   1.4e-10      37     266 ..      30     269 ..      22     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 7.8e-15
                                       EEEE-SSTTEEEEE--SBSSHHHHHHHHHHHHHHHHHHHHHTT-EEE--SB-SS---------------THHHHHGG CS
                              GCS2  37 svvkelpegqvElstapleslaeaaeeisadleelrsvadelGlellglGthPfalrsedevtpkaryrrmleymdr 113
                                       +++ e  e ++E++t p+ s+ae+  e+++ ++ +  +a+e G +l+ l+t  +a++se + ++k r   +  ++  
  gi|336252715|ref|YP_004595822.1|  30 GIDPEFVEPMLEIKTTPCTSMAELRTEFRDRIATVVDAAREQGKRLVPLATPLSASPSEIPYREK-RSTDLQRRIVG 105
                                       566777889******************************************999*******9999.55555555444 PP

                                       ..G.G-S--B-EEEEEEE-SSHHHHH.HHHHHHHTTHHHHHHHH--B-EETTEE-S-SB...-GGGCCTTSTT-CS- CS
                              GCS2 114 vGvlgrqmmvaglhvqvnidssseedVevlrlvrallPvllAlsAnSPfleGrdtgyaS...tRariftqtpqagel 187
                                        G    + ++ag h++ +  s+    V  l+ + a  P ++ l ++S + + r    a    +R+  +++ p+ g+l
  gi|336252715|ref|YP_004595822.1| 106 PGF-DDARVCAGTHIHFEQSSV----VDQLNALTAIDPAFALLTSSSHYRGERILECARpylYRRSCYGACPEQGQL 177
                                       466.8999********986663....668899******999999999998877433322222777889999997777 PP

                                       ---SSHHH.HHHHHHHHTTSTT-SSGG...................G--BSEEEETTTT.EEEEEEEE--...SSHH CS
                              GCS2 188 plafedgaaferyaryaldvpvidvrr..................frlwldirpsslpgttlelrihdttlfPevrl 246
                                           +++    ++ +++ d+  ++  r                  +  w  +r+    + t+e+r  d+ l P  +l
  gi|336252715|ref|YP_004595822.1| 178 WPYVDSV---AEWEQRMDDAFGTFRERaiergvdpdafdeafdpyEACWNPVRLRRAMP-TVEWRSPDAAL-PSQVL 249
                                       7777775...58********99998889****************9899*******9999.**********7.***** PP

                                       HHHHHHHHHHHHHHHHHHH- CS
                              GCS2 247 rallearlldaqpadrldal 266
                                       +  +e+r + aq++ r +a 
  gi|336252715|ref|YP_004595822.1| 250 QLAEEVRSIVAQADARGTAV 269
                                       *************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2700.89
//
Query:       gi|336252716|ref|YP_004595823.1|  [L=390]
Description: peptidase C45 acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase [Halopiger xanaduensis SH-6]
Scores for 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-16   58.8   0.0    9.5e-16   58.2   0.0    1.2  1  AAT            Acyl-coenzyme A:6-aminopenicillanic acid acyl-
     0.0096   15.6   0.0      0.029   14.0   0.0    1.7  1  CBAH           Linear amide C-N hydrolases, choloylglycine hy
  ------ inclusion threshold ------
        2.6    8.9   7.9        5.3    7.9   4.0    2.6  2  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> AAT  Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   1.6e-19   9.5e-16       6     224 ..     133     361 ..     128     363 .. 0.81

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 1.6e-19
                                       ..EEEEEEEE-S-S--EEEEE--S.....SS--EEEESSSS-SEEEEEETTS-EEEE-TTS-TTT-...-------- CS
                               AAT   6 gkllgrNeDldpetlsnrflvvased...sgfaslgyagslpGrtdGiNeaGLavtinllslkklr...akGfpraf 76 
                                       g l+++N+D   + l    +v ++++   +g  +++  g +  + +G+N+ GL+  ++++  +       + ++ ++
  gi|336252716|ref|YP_004595823.1| 133 GPLVLKNRDIAGRGLRPKSIVEQPPIddyHGILTIDTCGTI-SMFKGVNDRGLVAANTYIDSERDDidpEDQLRNGT 208
                                       458999***88888888888888888777777788888888.9999***********999988753222789***** PP

                                       HHHHHHH.--SHHHHHHTHHHHTTTS-S.EEEEEEETTEEEEEEE-SSS-EEEEEESSEEEEE-SS-S-GGGSSS-- CS
                               AAT  77 itRllLekcesveeAvellkeipraagi.nyivldaagnaavveveasskvcsireanealahtNHfvnetleaenq 152
                                       ++R+lLe+c++ve A + l++ p  + +   ++l+++ na+++ev +  + +s  +++ ++++tNHfv+++ +++  
  gi|336252716|ref|YP_004595823.1| 209 VIRMLLEECATVEAARAKLESSPTKHLMgQTLFLADETNAVLLEVDPVAEQISADDGP-VVTRTNHFVISDSTEA-- 282
                                       **********************7554331455677777********************.************9999.. PP

                                       ---HHHHHHHHHHHHHHCSSSSB..HHHHHHHT---STT..TSSSS-......BSSSEEEE...EEE-TTS--EEEE CS
                               AAT 153 nilesSisRlerlqellsqkesa..eeaiellkDredep..ysvlrr...ksfkswenTil...talydlaarkakl 219
                                          esS++R +r  ell++ e    e+   + +D e +p  +s++r      ++  ++ +    ta+++  a ++++
  gi|336252716|ref|YP_004595823.1| 283 ---ESSTKRRRRALELLEELEPLtrEDLWTIARDHEHGPgdDSICRHpepEAGEYATGQLTtasTAVFEGGAPTIEI 356
                                       ...9***************9998899********9998755677876421222222332334448999999999999 PP

                                       EE--T CS
                               AAT 220 vlgnp 224
                                       + gnp
  gi|336252716|ref|YP_004595823.1| 357 ATGNP 361
                                       88887 PP

>> CBAH  Linear amide C-N hydrolases, choloylglycine hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   4.9e-06     0.029      55     125 ..     163     230 ..     135     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.9e-06
                                       EEEEESSSEE.EESEEEETTS-EEEEEE-TTT---BSS--TTSEEEEGGGHHHHHHHH-SSHHHHHHHHTTE CS
                              CBAH  55 GmgtkvesyP.lfvdglNEkGlsiaglylaeyaeykkepkedkvniaagelirwvlenftsveevkeklkkl 125
                                       G+ t+      + + g+N++Gl  a  y     + ++++++   ++  g +ir++le++++ve +++kl++ 
  gi|336252716|ref|YP_004595823.1| 163 GILTIDTCGTiSMFKGVNDRGLVAANTYI----DSERDDIDPEDQLRNGTVIRMLLEECATVEAARAKLESS 230
                                       655543333337899**********9998....55555566777899*********************9874 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.0   0.00088       5.3       8      75 ..      13      79 ..      12      84 .. 0.64
   2 ?    1.6   0.1     0.083     5e+02      40      63 ..     287     310 ..     269     329 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00088
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHHHHHHHHHHT....S--SS-SSTTSTTT CS
                     PSK_trans_fac  8 peverlareLarltgeskteAvrrAleerlerlrreraepllerllallrraaa....kaekedrspdekll 75
                                      pev+  a++ ar++ e+  eAv+ A+ e  + ++  ++   le ll+ ++r ++    +++++   + +++ 
  gi|336252716|ref|YP_004595823.1| 13 PEVDTFAEQ-ARRRAETEREAVEWAVDELESLVD--DRGVDLEPLLEYAERSREslpaRHRRAY--EAMADV 79
                                      678888877.78889***********99888777..5555555555555555553211433333..455555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.083
                                       XXXXXX--HHHHHHHHHHHHHTS- CS
                     PSK_trans_fac  40 lrreraepllerllallrraaaka 63 
                                        rr+ra +lle+l  l r+  ++ 
  gi|336252716|ref|YP_004595823.1| 287 KRRRRALELLEELEPLTREDLWTI 310
                                       333366666666666666555522 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2860.18
//
Query:       gi|336252717|ref|YP_004595824.1|  [L=150]
Description: flagellin domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   60.7   5.2    3.9e-16   59.7   5.2    1.7  1  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> 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 !   59.7   5.2   2.2e-20   3.9e-16       1      61 [.      17      74 ..      17     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.2e-20
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievkidssastgknavsleh 61
                                      +AVSpViGviLmvaitvIlaAvia+fvl + +s  e + +a+++ ++++++++    ++++ 
  gi|336252717|ref|YP_004595824.1| 17 RAVSPVIGVILMVAITVILAAVIATFVLDMgDSMGEGSVNAALDSDVSNEDEE----ITFTL 74
                                      69****************************88888888888887666666654....44332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1051.24
//
Query:       gi|336252718|ref|YP_004595825.1|  [L=350]
Description: integrase protein [Halopiger xanaduensis SH-6]
Scores for complete 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-10   40.9   0.0    6.7e-10   39.0   0.0    1.9  1  Phage_integrase  Phage integrase family
    2.1e-06   27.9   0.1    5.8e-06   26.5   0.1    1.7  1  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.026   15.0   0.1       0.18   12.3   0.1    2.3  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
      0.099   13.0   0.0       0.42   11.0   0.0    1.9  2  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 !   39.0   0.0   1.5e-13   6.7e-10       3     156 ..     127     321 ..     125     336 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.5e-13
                                       HHHHHHHHHHHCCGC.HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEE............EEECSSSS CS
                   Phage_integrase   3 ltedeverllaalee.slkirdklllellyetGlRisEllsLrvkdldlengvilvh............eregKgsk 66 
                                       l+++ ++ +l++le+ + + rd ++++ll++tG+R++ +++L++ dldl+ ++ +v              + +K++ 
  gi|336252718|ref|YP_004595825.1| 127 LKPERAVDILDYLENaQPASRDHIIVMLLWRTGARTGAIRGLDLRDLDLDGSHPRVSgpaihfvhrpdtGTPLKNQE 203
                                       7899999********87788999*********************************************977888877 PP

                                       E..EEEECTHHHHHHHHHHHHHH...CHCCTTTSBSSBET.....................TSSB--HHHHHHHHHH CS
                   Phage_integrase  67 e..ravplseealellkellska...leeaeksellfask.....................rgkplsrqtvrkafkr 117
                                       +  r + +se+ +++l+++++++   +  + ++e l+  +                     rg+p  ++   +  ++
  gi|336252718|ref|YP_004595825.1| 204 KgtRWNRISEKTARYLEDYIEYHrpdVTDDHGREPLITTEygrpagntlrktlyrvtrpcwRGEPCPHERDPDECEA 280
                                       777********************998888888887777766777777777777777778998888877777777777 PP

                                       HHHHCT-S..SC--TTHHHHHHHHHHHHHCTSHHHHHHHHT CS
                   Phage_integrase 118 aveeagie..kpltpHtlRhsfataLleagvdlrvvqkllG 156
                                       ++   + +  ++ +pH+lR    t + ++ v+ rvv++ l+
  gi|336252718|ref|YP_004595825.1| 281 THLDHASKcpSARSPHDLRSGRVTFYRREDVPRRVVKDRLN 321
                                       77665555678999********************9999886 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 !   26.5   0.1   1.3e-09   5.8e-06      13      81 ..      24      98 ..      14      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.3e-09
                                      -S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS-----......-----HHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_1 13 glspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeg......lsatslarrlsalrsFfqflv 81
                                      ++++ T+r+ +++Lr+f++f +e+g+e+l+ l+ +d+ ++  +++e         +  +l+  l+++r+F++f+ 
  gi|336252718|ref|YP_004595825.1| 24 EHAESTRRSEKHRLRAFVQFCDEEGIENLNDLSGRDLYKYRTWRREGHgddrepIKLVTLKGQLASVRRFLRFAA 98
                                      45699***********************************999999779999999******************95 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 ?   12.3   0.1     4e-05      0.18      12      54 ..      23      68 ..      14     102 .. 0.83
   2 ?   -0.2   0.0      0.31   1.4e+03      18      34 ..      82      98 ..      74     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4e-05
                   Phage_int_SAM_4 12 aglserTiksYlsaikrflrflkkk...apeeltkedieaYlnyLa 54
                                      ++ +e+T++s ++ ++ f++f+++    + ++l+ +d+  Y ++ +
  gi|336252718|ref|YP_004595825.1| 23 DEHAESTRRSEKHRLRAFVQFCDEEgieNLNDLSGRDLYKYRTWRR 68
                                      45699*****************966777888999999999998876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.31
                   Phage_int_SAM_4 18 TiksYlsaikrflrflk 34
                                      T k  l  ++rflrf  
  gi|336252718|ref|YP_004595825.1| 82 TLKGQLASVRRFLRFAA 98
                                      77778899******975 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 ?   11.0   0.0   9.3e-05      0.42       7      94 ..      15     108 ..      11     113 .. 0.85
   2 ?   -1.0   0.0       0.5   2.2e+03      47      58 ..     215     226 ..     200     256 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.3e-05
                                       HHHTHHHHTTS-HHHHHHHHHHHHHTTTS-..S-.--TTT--HHHHHHHHHHH.....HHTS---HHHHHHHHHHHH CS
                   Phage_int_SAM_5   7 keyiekkkkkgskgtlrnykstlkhlkkFlkkkd.itfeeidkefleeFedYL.....kkkkglsentiskyfkklk 77 
                                       k y + ++ + +++t r+ k  l+ + +F+ ++   +++++  + l +++++       ++++++  t + ++   +
  gi|336252718|ref|YP_004595825.1|  15 KMYHDAMRDEHAESTRRSEKHRLRAFVQFCDEEGiENLNDLSGRDLYKYRTWRreghgDDREPIKLVTLKGQLASVR 91 
                                       55667777778899****************6666457****************998887788*************** PP

                                       HHHHHHHHTTS--S-HH CS
                   Phage_int_SAM_5  78 avlnkAikegilkknpy 94 
                                       ++l+ A + + +  + y
  gi|336252718|ref|YP_004595825.1|  92 RFLRFAANIDAVPAELY 108
                                       ****9998887777666 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.5
                                       -HHHHHHHHHHH CS
                   Phage_int_SAM_5  47 dkefleeFedYL 58 
                                       + ++le++++Y 
  gi|336252718|ref|YP_004595825.1| 215 TARYLEDYIEYH 226
                                       455556666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2722.22
//
Query:       gi|336252719|ref|YP_004595826.1|  [L=101]
Description: hypothetical protein Halxa_1314 [Halopiger xanaduensis SH-6]
Scores for 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-05   23.0   0.0    0.00038   20.9   0.0    1.9  2  HTH_27        Winged helix DNA-binding domain
     0.0016   18.5   0.1     0.0024   17.9   0.1    1.4  1  HTH_20        Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.017   14.9   0.0    1.1  1  RQC           RQC domain
      0.018   15.2   0.0      0.029   14.6   0.0    1.4  1  PaaX          PaaX-like protein
      0.022   14.8   0.0      0.033   14.2   0.0    1.3  1  HTH_45        Winged helix-turn-helix
      0.023   14.5   0.0      0.033   14.0   0.0    1.2  1  DUF4364       Domain of unknown function (DUF4364)
      0.034   13.7   0.0       0.11   12.0   0.0    1.9  2  HTH_24        Winged helix-turn-helix DNA-binding
      0.046   13.9   0.0      0.077   13.1   0.0    1.5  1  Mrr_N         Mrr N-terminal domain
      0.048   13.7   0.0      0.057   13.5   0.0    1.1  1  Replic_Relax  Replication-relaxation
      0.052   13.5   0.0      0.086   12.8   0.0    1.4  1  PadR          Transcriptional regulator PadR-like family
      0.086   12.8   0.0       0.11   12.4   0.0    1.3  1  YjhX_toxin    Putative toxin of bacterial toxin-antitoxin pai


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 ?   -0.4   0.0         1   1.6e+03      26      43 ..       6      23 ..       5      26 .. 0.85
   2 !   20.9   0.0   2.3e-07   0.00038      27      68 .]      46      84 ..      44      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1
                            HTH_27 26 grlnvedshisyslkkLt 43
                                       ++n  d +i + l++L+
  gi|336252719|ref|YP_004595826.1|  6 PWMNEVDDSILEFLDELE 23
                                      589999999999999997 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.3e-07
                            HTH_27 27 rlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +l+ + s++s  +++L e+GL+e+t   +d++ + +++T+kG
  gi|336252719|ref|YP_004595826.1| 46 MLDKSLSTFSRRMDRLAEHGLLEQT---EDGKGSPYKITEKG 84
                                      6788899***************777...789**********9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   1.5e-06    0.0024      34      60 ..      47      73 ..      14      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                                      HTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 34 ldlskntlsyHLrvLeeagLvevvreg 60
                                      ld s +t s++++ L+e+gL+e+++ g
  gi|336252719|ref|YP_004595826.1| 47 LDKSLSTFSRRMDRLAEHGLLEQTEDG 73
                                      3899*******************9987 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     1e-05     0.017      51     100 ..      42      91 ..      34      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                                       TTTTTTTTS-HHHHHHHHHHHHHTTSEEEE..SSS.BEEE-CCGHHHHTSS CS
                               RQC  51 stfGigkdlskkewrrlirqLiaegyLeedveeyg.vlkltekarevlkge 100
                                         fG+++ +s ++  r ++ L  +g+Le+++++ g  +k+tek+r++l+g+
  gi|336252719|ref|YP_004595826.1|  42 DEFGMLD-KSLSTFSRRMDRLAEHGLLEQTEDGKGsPYKITEKGRAYLSGD 91 
                                       5677764.6778888999*********999997776************997 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.8e-05     0.029      28      70 .]      42      84 ..      23      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                              PaaX 28 rllaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsdkg 70
                                        +  l+ s s+    + Rla++G+l ++++g+ s Y+ ++kg
  gi|336252719|ref|YP_004595826.1| 42 DEFGMLDKSLSTFSRRMDRLAEHGLLEQTEDGKGSPYKITEKG 84
                                      3333333344444446899**********************97 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     2e-05     0.033      34      67 ..      52      89 ..      46      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                            HTH_45 34 kllnkYLdmLvekgli...kk.skekYvlTekGlelle 67
                                      +++++ +d L e gl+   ++ +++ Y++TekG+ +l+
  gi|336252719|ref|YP_004595826.1| 52 STFSRRMDRLAEHGLLeqtEDgKGSPYKITEKGRAYLS 89
                                      67888899********6552236678********9986 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     2e-05     0.033      36      70 ..      54      88 ..      50      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2e-05
                           DUF4364 36 lqqalseLvesglieeeekenktlykiTekGketl 70
                                      ++  ++ L e+gl+e++e+ + + ykiTekG+  l
  gi|336252719|ref|YP_004595826.1| 54 FSRRMDRLAEHGLLEQTEDGKGSPYKITEKGRAYL 88
                                      6677899*************************987 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 ?   -1.5   0.0       1.1   1.8e+03       3      14 ..      10      21 ..       8      27 .. 0.61
   2 ?   12.0   0.0     7e-05      0.11      27      47 ..      47      67 ..      45      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                            HTH_24  3 etdrkILelLqk 14
                                      e d  ILe L +
  gi|336252719|ref|YP_004595826.1| 10 EVDDSILEFLDE 21
                                      555567877765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7e-05
                            HTH_24 27 lglSpstvnrrlkrLeeeGlI 47
                                      l+ S+st +rr++rL e Gl+
  gi|336252719|ref|YP_004595826.1| 47 LDKSLSTFSRRMDRLAEHGLL 67
                                      788**************9997 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.7e-05     0.077      60      86 ..      60      89 ..      48      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.7e-05
                             Mrr_N 60 yLkkagllespkrgv...wkiTekGrevlk 86
                                       L + glle+++ g+   +kiTekGr++l+
  gi|336252719|ref|YP_004595826.1| 60 RLAEHGLLEQTEDGKgspYKITEKGRAYLS 89
                                      68899******9666668*********985 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.5e-05     0.057      24      70 ..      52      89 ..      42     101 .] 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-05
                      Replic_Relax 24 ratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarlla 70
                                      + t +rr+ rL+e+gll+ ++       +gs    Y +t+kG+++l+
  gi|336252719|ref|YP_004595826.1| 52 S-TFSRRMDRLAEHGLLEQTEDG-----KGS---PYKITEKGRAYLS 89
                                      3.489**************6555.....433...8**********93 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.3e-05     0.086      33      73 ..      53      88 ..      38      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.3e-05
                                      HHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                              PadR 33 slYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                      +  + ++rL ++gl+e++++      +   Y++T++Gr++l
  gi|336252719|ref|YP_004595826.1| 53 TFSRRMDRLAEHGLLEQTEDG-----KGSPYKITEKGRAYL 88
                                      5556789*********99775.....3455********998 PP

>> YjhX_toxin  Putative toxin of bacterial toxin-antitoxin pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.9e-05      0.11      63      83 ..      73      93 ..      44      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.9e-05
                        YjhX_toxin 63 kkgkpYritrkGleavraqld 83
                                       kg+pY+it+kG++ + ++ld
  gi|336252719|ref|YP_004595826.1| 73 GKGSPYKITEKGRAYLSGDLD 93
                                      479***********9999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 814.97
//
Query:       gi|336252720|ref|YP_004595827.1|  [L=264]
Description: hypothetical protein Halxa_1315 [Halopiger xanaduensis SH-6]
Scores for 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   12.6   0.5       0.45   10.7   0.1    2.1  2  HTH_28    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 ?   10.7   0.1   2.5e-05      0.45       4      34 ..      34      65 ..      33      66 .. 0.90
   2 ?   -1.2   0.0      0.13   2.3e+03      16      25 ..     254     263 ..     232     264 .] 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.5e-05
                            HTH_28  4 eiikllaaGh.svreaArelgisrrtvyrWik 34
                                      ++i+++ +++   +++A +l + r++++ Wi 
  gi|336252720|ref|YP_004595827.1| 34 RAIEYARKHDvGSSATASALDLPRSRLRTWID 65
                                      78999998878*******************96 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.13
                            HTH_28  16 reaArelgis 25 
                                       ++aAr+lg+ 
  gi|336252720|ref|YP_004595827.1| 254 ADAARRLGTA 263
                                       2389999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2135.44
//
Query:       gi|336252721|ref|YP_004595828.1|  [L=147]
Description: flagellin domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   60.6   6.0    2.9e-16   60.1   6.0    1.6  1  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> 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 !   60.1   6.0   1.6e-20   2.9e-16       1      60 [.      17      74 ..      17     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.6e-20
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievkidssastgknavsle 60
                                      +AVSpViGviLmvaitvIlaAvia+fvl + +s  e + +a++++++++s++ +   ++le
  gi|336252721|ref|YP_004595828.1| 17 RAVSPVIGVILMVAITVILAAVIATFVLDMgDSMGEGTVNAAVDTDVNNSGEIH---FTLE 74
                                      69****************************9999999999***99999888743...4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1155.94
//
Query:       gi|336252722|ref|YP_004595829.1|  [L=61]
Description: hypothetical protein Halxa_1317 [Halopiger xanaduensis SH-6]
Scores for 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:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.31u 0.21s 00:00:00.52 Elapsed: 00:00:00.33
# Mc/sec: 548.81
//
Query:       gi|336252723|ref|YP_004595830.1|  [L=140]
Description: hypothetical protein Halxa_1318 [Halopiger xanaduensis SH-6]
Scores for 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  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 1236.42
//
Query:       gi|336252724|ref|YP_004595831.1|  [L=265]
Description: hypothetical protein Halxa_1319 [Halopiger xanaduensis SH-6]
Scores for 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   3.4      0.012   15.6   3.4    1.9  2  PGF-CTERM  PGF-CTERM motif
      0.074   13.5   0.2       0.12   12.8   0.2    1.3  1  DUF4019    Protein of unknown function (DUF4019)
        0.1   11.4   0.7       0.17   10.7   0.7    1.3  1  DUF1177    Protein of unknown function (DUF1177)


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.5      0.67     4e+03      12      17 ..      31      36 ..      30      38 .. 0.69
   2 ?   15.6   3.4     2e-06     0.012       1      20 [.     240     259 ..     240     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.67
                         PGF-CTERM 12 GLLaaa 17
                                      GL a+a
  gi|336252724|ref|YP_004595831.1| 31 GLVAVA 36
                                      777876 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2e-06
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLa 20 
                                       +PGFGa +A+a+++ a++ a
  gi|336252724|ref|YP_004595831.1| 240 SPGFGAGVAVAAIATAGAAA 259
                                       6**************99776 PP

>> DUF4019  Protein of unknown function (DUF4019)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2     2e-05      0.12      72     103 ..      63      93 ..      46      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                           DUF4019  72 viqfetefenkkqavEtvtlrkeedgkWrvvg 103
                                        i+f++ef+n++ ++Etv ++  ++++W+v g
  gi|336252724|ref|YP_004595831.1|  63 DIEFASEFANNS-STETVDFESYNEEAWQVNG 93 
                                       489*******99.9***************987 PP

>> DUF1177  Protein of unknown function (DUF1177)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.7   2.8e-05      0.17     148     227 ..     103     182 ..      91     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.8e-05
                           DUF1177 148 eGyilkvsedll..dilervtgkepvvlplttqDitPygngvyHlnsilqPavatkaPvvgvAittetvvpGcatga 222
                                       +G +l+vs+d++    ++    ++ +++ ++ +D    +ng   l+++ + +++++  v+ + +t++ vv+ + tga
  gi|336252724|ref|YP_004595831.1| 103 NGTVLEVSDDIVpsATYSAELNQSGTTVDVSSDDFA--DNGTVDLSTVSSDSITSDDEVLSLTLTADPVVSDSVTGA 177
                                       799********9333555666788899999999996..899************************************ PP

                           DUF1177 223 shled 227
                                       ++ + 
  gi|336252724|ref|YP_004595831.1| 178 TNDTV 182
                                       99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2063.84
//
Query:       gi|336252725|ref|YP_004595832.1|  [L=613]
Description: hypothetical protein Halxa_1320 [Halopiger xanaduensis SH-6]
Scores for 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  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1351  (0.0753528); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); 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: 0.62u 0.24s 00:00:00.86 Elapsed: 00:00:00.39
# Mc/sec: 4700.81
//
Query:       gi|336252726|ref|YP_004595833.1|  [L=177]
Description: hypothetical protein Halxa_1321 [Halopiger xanaduensis SH-6]
Scores for 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   12.2   0.1       0.21   10.8   0.0    1.6  2  DUF2099   Uncharacterized protein conserved in archaea (DUF20
       0.43   10.3   2.1       0.43   10.2   0.1    1.9  2  DUF2244   Integral membrane protein (DUF2244)


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 ?   -1.7   0.1      0.15   1.3e+03      75     114 ..       7      44 ..       2      49 .. 0.62
   2 ?   10.8   0.0   2.3e-05      0.21      87     128 ..      98     140 ..      86     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.15
                           DUF2099  75 fGasEilstalkeglidaavivcdgaGtvivtnpelvqgl 114
                                       f+a  +ls a+  g++ a   +    Gt + t++e vq++
  gi|336252726|ref|YP_004595833.1|   7 FAAVVVLSLAVGMGAVAAQENA--TNGTAVETESEDVQAI 44 
                                       5555555555555555444433..3478888888888887 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 2.3e-05
                           DUF2099  87 eglidaavivcdgaGtvivtnpelvqglggris.GlveTePie 128
                                       +++i  av+  +gaG  ++t+ +l qg g+ +s G ve +P++
  gi|336252726|ref|YP_004595833.1|  98 SNTITFAVTDREGAGVAVATRRSLQQGTGAFVSvGTVERNPLK 140
                                       5678899*************************98899999987 PP

>> DUF2244  Integral membrane protein (DUF2244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   4.8e-05      0.43      39     105 ..       5      71 ..       3      81 .. 0.91
   2 ?   -1.6   0.4      0.21   1.9e+03      25      39 ..     153     167 ..     147     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.8e-05
                           DUF2244  39 lpFaglevlalalafrvsarhardrEeitltdeeltvervsprgrerewefnpywvrveleedeeeg 105
                                       ++Fa++ vl la+ + ++a + ++     ++ e+  v+ ++ + r ++we+ p    +++e+d e +
  gi|336252726|ref|YP_004595833.1|   5 FVFAAVVVLSLAVGMGAVAAQENATNGTAVETESEDVQAIDSDTRITDWEYRPGMFTITVEADTETE 71 
                                       68************************9999999999*****9*******************999874 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.21
                           DUF2244  25 vialafllaGawpvl 39 
                                       ++++ f+  Gaw v+
  gi|336252726|ref|YP_004595833.1| 153 AMTVSFAGLGAWYVV 167
                                       456667778888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1453.27
//
Query:       gi|336252727|ref|YP_004595834.1|  [L=268]
Description: hypothetical protein Halxa_1322 [Halopiger xanaduensis SH-6]
Scores for 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   0.2      0.042   14.0   0.1    1.8  1  T4_Rnl2_C    T4 RNA ligase 2 C-terminal
       0.93   10.1   2.8         13    6.3   1.2    2.4  2  Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II


Domain annotation for each model (and alignments):
>> T4_Rnl2_C  T4 RNA ligase 2 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.7e-06     0.042      13      39 ..     166     193 ..     154     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.7e-06
                                       HHGGG--HHHHHHHHHTSS.--STTTHH CS
                         T4_Rnl2_C  13 eierYvtenRLnNviSKig.eitrknfg 39 
                                        +e+Y+  nRL+  iSK+g +i+++ ++
  gi|336252727|ref|YP_004595834.1| 166 LVEEYLAANRLRGRISKMGlQIQKDVIN 193
                                       5899***************888866554 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 ?    6.3   1.2    0.0015        13      67      87 ..      38      58 ..      16      62 .. 0.87
   2 ?    2.8   0.0      0.02   1.8e+02      12      66 ..     153     207 ..     149     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0015
                       Arc_PepC_II 67 vWvtygvPflipitaGfiial 87
                                      vW  + +P ++pi+ G i a 
  gi|336252727|ref|YP_004595834.1| 38 VWFRPELPGIPPIVHGWIAAT 58
                                      9*****************885 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.02
                       Arc_PepC_II  12 vkvkell.kkflflleefeekdgkikrkfisvekeldeelrkelkkykkkglieet 66 
                                       v+vk +l + ++ l+ee+   +  ++ ++ +++ ++++++++e ++  ++gl++++
  gi|336252727|ref|YP_004595834.1| 153 VTVKAMLeDIHGDLVEEYLAANR-LRGRISKMGLQIQKDVINEEAEADERGLMNPK 207
                                       5677766688999****999665.8888999999*********9999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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 0.22s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2221.31
//
Query:       gi|336252728|ref|YP_004595835.1|  [L=389]
Description: hypothetical protein Halxa_1323 [Halopiger xanaduensis SH-6]
Scores for 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      0.031   14.4   0.0    1.3  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.11   12.6   0.0       0.26   11.5   0.0    1.6  1  HTH_28           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.5e-06     0.031      12      50 ..     114     153 ..     108     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.5e-06
                                       HHHHHHHT-SS-EEE.EEETT--HHHHHHCC--TTS-EE- CS
                   Sigma54_activ_2  12 erLeqaaqsklpvfl.tGekGsgkelvArlLhknsgpwle 50 
                                       +rL+++++  +pv + +Ge G+gk+ +A+lL + +++w++
  gi|336252728|ref|YP_004595835.1| 114 TRLQEIVAGPAPVIVvLGEMGAGKTDFAGLLGQLRERWVD 153
                                       79999999999997527*********************97 PP

>> HTH_28  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   2.9e-05      0.26      10      41 ..     345     376 ..     340     379 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.9e-05
                            HTH_28  10 aaGhsvreaArelgisrrtvyrWikryeegGi 41 
                                        +G+s+re+A+ +  s+ tv+ W k  + gG+
  gi|336252728|ref|YP_004595835.1| 345 RQGMSARETAEFVPYSHATVSNWWKEIDDGGE 376
                                       5899********************99888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2883.29
//
Query:       gi|336252729|ref|YP_004595836.1|  [L=127]
Description: hypothetical protein Halxa_1324 [Halopiger xanaduensis SH-6]
Scores for 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:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 962.22
//
Query:       gi|336252730|ref|YP_004595837.1|  [L=154]
Description: hypothetical protein Halxa_1325 [Halopiger xanaduensis SH-6]
Scores for 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   19.8   0.3     0.0009   19.0   0.3    1.4  1  HTH_23        Homeodomain-like domain
     0.0084   15.8   0.0      0.019   14.7   0.0    1.6  1  Sigma70_r4_2  Sigma-70, region 4
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.35   11.0   0.0    1.6  2  HTH_Tnp_1_2   Helix-turn-helix of insertion element transposa


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 !   19.0   0.3   1.5e-07    0.0009      13      37 ..     110     135 ..     105     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-07
                            HTH_23  13 llae.GlsvreIAreLgvsrrTvyrw 37 
                                       l+ +   ++reIA+ Lgv rrTv+ +
  gi|336252730|ref|YP_004595837.1| 110 LYVVqEEPTREIAATLGVDRRTVWDY 135
                                       444447899***************55 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 !   14.7   0.0   3.1e-06     0.019      21      51 ..     110     140 ..     105     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-06
                                       HHHTS---HHHHHHHHT--HHHHHHHHHHHH CS
                      Sigma70_r4_2  21 lryleglsykEIAellgisegtVksrlsRAr 51 
                                       l+ +++ +++EIA+ lg+  +tV  + s+ r
  gi|336252730|ref|YP_004595837.1| 110 LYVVQEEPTREIAATLGVDRRTVWDYWSKIR 140
                                       7799*******************87766665 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 ?   -2.6   0.0      0.97   5.8e+03      96     112 ..      48      64 ..      46      71 .. 0.76
   2 ?   11.0   0.0   5.8e-05      0.35       9      47 ..     101     136 ..      95     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.97
                                       TT--EEEEEEEEE-XXX CS
                       HTH_Tnp_1_2  96 rgeltdkkkveakleda 112
                                       + +lt ++ +e+++e +
  gi|336252730|ref|YP_004595837.1|  48 EYKLTYQNPFEGEIELH 64 
                                       56888899999998876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.8e-05
                                       -HHHHHHHHHHHHHHH--S-HHHHHHHHTS-HHHHHHHH CS
                       HTH_Tnp_1_2   9 takQkkaaellvendyekltldeiaeevgvsrsTlykWk 47 
                                       + +   aa+l v ++     ++eia+ +gv+r+T + + 
  gi|336252730|ref|YP_004595837.1| 101 DGRPAIAAYLYVVQEE---PTREIAATLGVDRRTVWDYW 136
                                       5555667777766554...789**************743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.19s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1260.85
//
Query:       gi|336252731|ref|YP_004595838.1|  [L=84]
Description: hypothetical protein Halxa_1326 [Halopiger xanaduensis SH-6]
Scores for 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:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 725.04
//
Query:       gi|336252732|ref|YP_004595839.1|  [L=117]
Description: hypothetical protein Halxa_1327 [Halopiger xanaduensis SH-6]
Scores for 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   14.3   0.0      0.047   13.9   0.0    1.1  1  DUF4330   Domain of unknown function (DUF4330)
      0.068   12.7   0.0      0.078   12.5   0.0    1.2  1  LptC      Lipopolysaccharide-assembly, LptC-related


Domain annotation for each model (and alignments):
>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.2e-06     0.047      64     115 ..      39      92 ..      30     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-06
                           DUF4330  64 v..peelakvkegektniiirnqPagdveikdvkvlprkvvvpqpdGkvkaled 115
                                       +  ++ ++k+ ege++ + i+ +  g+ ei++++ + +kv v++pdG++++ + 
  gi|336252732|ref|YP_004595839.1|  39 IllTNITFKEFEGEEMDDDIEMNSFGSYEITEISKQYSKVSVENPDGELEIENS 92 
                                       5556777888899*********9************************9988766 PP

>> LptC  Lipopolysaccharide-assembly, LptC-related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.8e-06     0.078      45      83 ..      15      53 ..       6      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.8e-06
                                      XXXXXXX-EEEEEEEEEEETTTTEEEEESEEEEEE-TTS CS
                              LptC 45 ydedGklqyrltadklehypdddqteftnPvliiydegt 83
                                      ydedG+l  ++t+d+l   ++ +++++tn++++ +++++
  gi|336252732|ref|YP_004595839.1| 15 YDEDGELIEEFTSDNLPIPNEGEEILLTNITFKEFEGEE 53
                                      9********************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 880.12
//
Query:       gi|336252733|ref|YP_004595840.1|  [L=539]
Description: hypothetical protein Halxa_1328 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.082   12.7   0.0       0.19   11.5   0.0    1.6  1  HTH_38    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_38  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   1.1e-05      0.19      26      41 ..     380     395 ..     376     396 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.1e-05
                            HTH_38  26 IArrLgrspsTIsREl 41 
                                        A +Lg++p TI+R +
  gi|336252733|ref|YP_004595840.1| 380 LADELGKHPATIYRAI 395
                                       699***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3855.89
//
Query:       gi|336252734|ref|YP_004595841.1|  [L=36]
Description: hypothetical protein Halxa_1329 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00013   21.2   2.6      0.042   13.3   0.1    2.1  2  zf-ribbon_3     zinc-ribbon domain
     0.0011   18.9   0.9       0.29   11.2   0.1    2.1  2  zf-C2H2_6       C2H2-type zinc finger
     0.0036   17.6   0.9     0.0042   17.4   0.9    1.1  1  C1_2            C1 domain
     0.0069   16.2   1.1     0.0082   16.0   1.1    1.2  1  zf-HIT          HIT zinc finger
     0.0074   16.0   2.2       0.12   12.1   0.3    2.1  2  Rubredoxin_2    Rubredoxin metal binding domain
  ------ inclusion threshold ------
      0.015   15.3   0.9      0.016   15.2   0.9    1.1  1  zinc-ribbons_6  zinc-ribbons
      0.017   15.1   0.9        1.6    8.8   0.0    2.1  2  Ogr_Delta       Ogr/Delta-like zinc finger
       0.02   14.7   1.2       0.34   10.7   0.0    2.1  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
      0.031   13.0   0.9      0.031   13.0   0.9    1.0  1  tRNA-synt_1g    tRNA synthetases class I (M)
      0.056   13.6   5.7          1    9.5   0.5    2.1  2  Zn-ribbon_8     Zinc ribbon domain
       0.41   10.7   8.7         14    5.9   0.8    2.9  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
        0.7    9.9   6.2       0.19   11.7   1.3    1.9  2  Nudix_N_2       Nudix N-terminal
        1.7    9.2   4.6         16    6.1   0.2    2.1  2  zf-H2C2_2       Zinc-finger double domain


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 !    8.9   0.3    0.0007      0.97       2      11 ..       1      11 [.       1      14 [. 0.82
   2 !   13.3   0.1     3e-05     0.042       3      16 ..      15      29 ..      13      30 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0007
                       zf-ribbon_3  2 tvrCPnCGa.p 11
                                      +++CP C+a  
  gi|336252734|ref|YP_004595841.1|  1 MTECPVCDAeS 11
                                      799****9966 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3e-05
                       zf-ribbon_3  3 vrCPnCGa.plssdd 16
                                      +rC++CGa ++   d
  gi|336252734|ref|YP_004595841.1| 15 YRCSECGAdLVGRTD 29
                                      79******9998776 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 !    6.9   0.1    0.0047       6.5       2       9 ..       2       9 ..       1      10 [. 0.85
   2 !   11.2   0.1   0.00021      0.29       1       9 [.      14      22 ..      14      24 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0047
                         zf-C2H2_6 2 heCsvCsk 9
                                     +eC+vC++
  gi|336252734|ref|YP_004595841.1| 2 TECPVCDA 9
                                     69****98 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00021
                         zf-C2H2_6  1 vheCsvCsk 9 
                                      v++Cs+C++
  gi|336252734|ref|YP_004595841.1| 14 VYRCSECGA 22
                                      7******97 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.9   3.1e-06    0.0042      19      40 ..       2      22 ..       1      25 [. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.1e-06
                              C1_2 19 fnCsaCgrkidgffYsCseCdf 40
                                      ++C +C+ ++  + Y+CseC  
  gi|336252734|ref|YP_004595841.1|  2 TECPVCDAES-AKVYRCSECGA 22
                                      68*******7.667******75 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.1   5.9e-06    0.0082       5      22 ..       4      23 ..       1      24 [. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.9e-06
                                      -TTT-S..B-SEE-TTT--E CS
                            zf-HIT  5 CgvCgf..pakYkCpkCntr 22
                                      C vC +   + Y+C+ C++ 
  gi|336252734|ref|YP_004595841.1|  4 CPVCDAesAKVYRCSECGAD 23
                                      99****98899******985 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.029        40      17      21 ..       4       8 ..       3      14 .. 0.54
   2 !   12.1   0.3   8.9e-05      0.12       1       8 [.      15      22 ..      15      24 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.029
                      Rubredoxin_2 17 CpsCg 21
                                      Cp C 
  gi|336252734|ref|YP_004595841.1|  4 CPVCD 8 
                                      55554 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.9e-05
                      Rubredoxin_2  1 YvCsqCGf 8 
                                      Y+Cs+CG+
  gi|336252734|ref|YP_004595841.1| 15 YRCSECGA 22
                                      9******8 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.9   1.2e-05     0.016      17      39 ..       2      24 ..       1      27 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                      EE-TTT--EEEEEEE-SSS-S-- CS
                    zinc-ribbons_6 17 yhCeaCqedlkkealCpeCeqel 39
                                      ++C  C+++  k+  C eC+  l
  gi|336252734|ref|YP_004595841.1|  2 TECPVCDAESAKVYRCSECGADL 24
                                      57*****************9876 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 ?    5.5   0.2     0.012        16       1      10 [.       3      12 ..       3      14 .. 0.84
   2 ?    8.8   0.0    0.0012       1.6       1      13 [.      16      28 ..      16      32 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.012
                         Ogr_Delta  1 rCPhCgapaa 10
                                      +CP C a++a
  gi|336252734|ref|YP_004595841.1|  3 ECPVCDAESA 12
                                      6****99876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                         Ogr_Delta  1 rCPhCgapaaart 13
                                      rC +Cga  + rt
  gi|336252734|ref|YP_004595841.1| 16 RCSECGADLVGRT 28
                                      7*******99998 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 ?    3.6   0.2     0.043        59       3       9 ..       3       9 ..       1      13 [. 0.83
   2 ?   10.7   0.0   0.00025      0.34       3      15 ..      16      28 ..      14      33 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.043
                                     E-SSS-- CS
                    zf-C4_Topoisom 3 kCPkCgg 9
                                     +CP C +
  gi|336252734|ref|YP_004595841.1| 3 ECPVCDA 9
                                     8****86 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00025
                                      E-SSS--EEEEEE CS
                    zf-C4_Topoisom  3 kCPkCggdLvlkr 15
                                       C +Cg+dLv ++
  gi|336252734|ref|YP_004595841.1| 16 RCSECGADLVGRT 28
                                      6*********986 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 ?   13.0   0.9   2.3e-05     0.031     137     159 ..       2      24 ..       1      32 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                                       E........-TTS-EE-TTSSB- CS
                      tRNA-synt_1g 137 gtCPkckseeargdqceecgkkl 159
                                        +CP+c +e+a+  +c ecg+ l
  gi|336252734|ref|YP_004595841.1|   2 TECPVCDAESAKVYRCSECGADL 24 
                                       58******************988 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.6    0.0018       2.5      27      39 ..       2      14 ..       1      15 [. 0.82
   2 ?    9.5   0.5   0.00076         1       6      14 ..      15      23 ..      14      33 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                       Zn-ribbon_8 27 taCPeCgsevrrv 39
                                      t+CP C +e  +v
  gi|336252734|ref|YP_004595841.1|  2 TECPVCDAESAKV 14
                                      67*****998887 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00076
                       Zn-ribbon_8  6 YrCeeCghe 14
                                      YrC eCg +
  gi|336252734|ref|YP_004595841.1| 15 YRCSECGAD 23
                                      99****964 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 ?    4.1   5.7     0.036        50       1       8 [.       3      10 ..       3      19 .. 0.75
   2 ?    5.9   0.8    0.0098        14       2      13 ..      17      29 ..      16      34 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.036
                    DNA_ligase_ZBD  1 hCPvCGsa 8 
                                      +CPvC+++
  gi|336252734|ref|YP_004595841.1|  3 ECPVCDAE 10
                                      5****976 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0098
                    DNA_ligase_ZBD  2 CPvCGsavv.Ree 13
                                      C +CG+ +v R++
  gi|336252734|ref|YP_004595841.1| 17 CSECGADLVgRTD 29
                                      669******9976 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3      0.32   4.4e+02      25      29 ..       4       8 ..       3      11 .. 0.70
   2 ?   11.7   1.3   0.00014      0.19       3      22 ..      17      36 .]      17      36 .] 0.95

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.32
                                      ETTTT CS
                         Nudix_N_2 25 CpaCg 29
                                      Cp C+
  gi|336252734|ref|YP_004595841.1|  4 CPVCD 8 
                                      66664 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00014
                                      -TTT--B-EEE--TT-SS-E CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreR 22
                                      Cs+CG+ +  r+ ++++r R
  gi|336252734|ref|YP_004595841.1| 17 CSECGADLVGRTDPEEERGR 36
                                      ***************99987 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 ?    5.8   0.6     0.015        21      16      22 ..       3       9 ..       3      13 .. 0.80
   2 ?    6.1   0.2     0.012        16      13      21 ..      13      21 ..       9      23 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.015
                         zf-H2C2_2 16 eCplCdk 22
                                      eCp+Cd 
  gi|336252734|ref|YP_004595841.1|  3 ECPVCDA 9 
                                      8****95 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.012
                         zf-H2C2_2 13 kpyeCplCd 21
                                      k y C++C+
  gi|336252734|ref|YP_004595841.1| 13 KVYRCSECG 21
                                      569*****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 266.49
//
Query:       gi|336252735|ref|YP_004595842.1|  [L=168]
Description: hypothetical protein Halxa_1330 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.074   13.4   0.0          7    7.0   0.0    2.4  2  Chlam_OMP3  Chlamydia cysteine-rich outer membrane protein 3


Domain annotation for each model (and alignments):
>> Chlam_OMP3  Chlamydia cysteine-rich outer membrane protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0    0.0035        63      36      49 ..      45      58 ..      37      61 .. 0.86
   2 ?    7.0   0.0   0.00039         7      11      32 ..     114     135 ..     109     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0035
                        Chlam_OMP3 36 vdGGcnscnGyvpa 49
                                       dGG +s + yvp 
  gi|336252735|ref|YP_004595842.1| 45 TDGGTDSSERYVPV 58
                                      69***********6 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00039
                        Chlam_OMP3  11 rivdccfedpcapiqcspcesk 32 
                                        i  c  e   a iq + ces 
  gi|336252735|ref|YP_004595842.1| 114 TIAACSIEHGVAGIQLTECESF 135
                                       5889****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1276.93
//
Query:       gi|336252736|ref|YP_004595843.1|  [L=76]
Description: hypothetical protein Halxa_1331 [Halopiger xanaduensis SH-6]
Scores for 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   0.9        2.6    8.4   0.1    2.2  2  zinc_ribbon_9  zinc-ribbon
       0.15   11.9   0.0       0.17   11.8   0.0    1.0  1  FdhE           Protein involved in formate dehydrogenase form


Domain annotation for each model (and alignments):
>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1   0.00029       2.6      11      29 ..       2      19 ..       1      22 [. 0.78
   2 ?    6.1   0.1    0.0015        14      18      28 ..      32      43 ..      23      45 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00029
                     zinc_ribbon_9 11 fVsvspdedsdvlCPhCgg 29
                                      +V ++p+  + + C hC++
  gi|336252736|ref|YP_004595843.1|  2 TVAPWPSAGRST-CLHCDS 19
                                      788988766666.****97 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0015
                     zinc_ribbon_9 18 edsdv.lCPhCg 28
                                      e++ v  CP+C+
  gi|336252736|ref|YP_004595843.1| 32 ENDRVhRCPECD 43
                                      3444447****8 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.9e-05      0.17     208     248 ..      11      50 ..       5      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
                                       TTS-TTT---SS-EEE------C-EEEEEETTTTEEEEEEE CS
                              FdhE 208 RvkCsnCeetkelaylsledekaavkAesCdeChsYlkily 248
                                       R +C +C++    ++ ++ +++++ +   C+eC++Y ++ +
  gi|336252736|ref|YP_004595843.1|  11 RSTCLHCDSFITDRFGRVFGDEND-RVHRCPECDTYARLTR 50 
                                       99********99999999999988.99*********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 566.96
//
Query:       gi|336252737|ref|YP_004595844.1|  [L=46]
Description: hypothetical protein Halxa_1332 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        5.4    6.4   8.1        5.7    6.3   8.1    1.0  1  DUF373           Domain of unknown function (DUF373)
        6.1    6.7   7.1        9.7    6.1   2.9    2.1  2  Adeno_E3_CR2     Adenovirus E3 region protein CR2


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 ?    6.3   8.1   0.00063       5.7     155     196 ..       4      45 ..       2      46 .] 0.92

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00063
                            DUF373 155 ktiLvplGlllliyalllllglpelalaiillllGlylllrG 196
                                       +ti +++Gl l+++++ +l  +++ +l++++ll+Gl+l + G
  gi|336252737|ref|YP_004595844.1|   4 STIAIVVGLGLIVIPIPVLPPFVGTILGVLVLLVGLFLRFLG 45 
                                       57889**************9999**************98877 PP

>> Adeno_E3_CR2  Adenovirus E3 region protein CR2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.9    0.0011       9.7       4      19 ..       4      17 ..       3      22 .. 0.76
   2 ?    3.0   0.1    0.0095        86       6      20 ..      26      40 ..      24      44 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0011
                      Adeno_E3_CR2  4 stiaIivaVvvGlaiI 19
                                      stiaI+v+  +Gl++I
  gi|336252737|ref|YP_004595844.1|  4 STIAIVVG--LGLIVI 17
                                      89999998..577766 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0095
                      Adeno_E3_CR2  6 iaIivaVvvGlaiIi 20
                                      ++ i +V+v l+ ++
  gi|336252737|ref|YP_004595844.1| 26 VGTILGVLVLLVGLF 40
                                      677888887776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 355.00
//
Query:       gi|336252738|ref|YP_004595845.1|  [L=242]
Description: dephospho-CoA kinase-like protein [Halopiger xanaduensis SH-6]
Scores for 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-17   61.7   0.2    1.7e-16   60.9   0.2    1.4  1  AAA_17         AAA domain
    3.8e-10   40.4   0.0    5.8e-10   39.8   0.0    1.3  1  AAA_18         AAA domain
      7e-05   23.0   0.1     0.0001   22.5   0.1    1.2  1  ADK            Adenylate kinase
    0.00012   22.3   0.0    0.00026   21.2   0.0    1.6  1  AAA_33         AAA domain
  ------ inclusion threshold ------
      0.042   13.6   0.2       0.12   12.2   0.2    1.7  1  PEP-utilizers  PEP-utilising enzyme, mobile 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 !   60.9   0.2   4.7e-20   1.7e-16       1     127 [.      41     163 ..      41     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 4.7e-20
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHH....HHHH..HS CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaeki....aeea..kk 71 
                                       +G+PGsGKg+++ +++++ g++++++Gd++r+e +++gl++++d+ + ++  +++   + +ae+     ++ +  ++
  gi|336252738|ref|YP_004595845.1|  41 VGLPGSGKGEAA-TVAREDGIPVVTMGDVVRQETADRGLDPTKDHGKVAQALRDENGPAAIAERSlpmiED-RleDH 115
                                       7***********.*********************************9766666666555555543233133.23466 PP

                                       SEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST- CS
                            AAA_17  72 kgvlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgr 127
                                       ++vlvdg  +    + ++d +++ + e++   +++ +ea+  e++++r+  r+r+ 
  gi|336252738|ref|YP_004595845.1| 116 DTVLVDGIRS----DTEVDVFEERFGEDF---TLVSIEAPF-EVRAERIDARGRDA 163
                                       7799999875....333445555555555...555555555.57777777665554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   1.6e-13   5.8e-10       1     119 [.      38     165 ..      38     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1.6e-13
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       I+  G pG+GK + a   ++  g+     g+++r+  +++gl  + d+ ++ + +r + +  + + + l  + ++le
  gi|336252738|ref|YP_004595845.1|  38 IGTVGLPGSGKGEAATVARED-GIpvvtmGDVVRQETADRGLDPTKDHGKVAQALRDENGPAAIAERSLPMIEDRLE 113
                                       6678**************998.6775777888888888888888888886666666666666777777777777*** PP

                            AAA_18  73 egknlvidghlaeleseaakdikk.....vvLtaspeelleRlekRgyeeak 119
                                       +++++++dg++++ e + + ++ +     v ++a+ e+++eR+ +Rg+   +
  gi|336252738|ref|YP_004595845.1| 114 DHDTVLVDGIRSDTEVDVFEERFGedftlVSIEAPFEVRAERIDARGRDAGE 165
                                       *******************99999***********************77655 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   2.8e-08    0.0001       2     134 ..      41     210 ..      40     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.8e-08
                                       EESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT.....-HHHHHHHHHHH.TTSS--HHHHHHHHHHHHHCHG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                               ADK   2 lGaPgaGKGtqaeklvkkyglahlstGdllRaevksg.....telGkeakevmd.kgelvpdevvvklvkeeleked 72 
                                       +G Pg+GKG  a++++++ g++ ++ Gd++R+e++        + Gk a+++ d +g     e  + +++++le++ 
  gi|336252738|ref|YP_004595845.1|  41 VGLPGSGKGE-AATVAREDGIPVVTMGDVVRQETADRgldptKDHGKVAQALRDeNGPAAIAERSLPMIEDRLEDH- 115
                                       79*******6.56789999**************976423332468999999887257788889999********88. PP

                                       TTTEEEEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                               ADK  73 kkkgfllDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltg........................... 122
                                         +  l+DG  R+ ++ + +ee    +  +  +++++++p ev  eR+                             
  gi|336252738|ref|YP_004595845.1| 116 --DTVLVDGI-RSDTEVDVFEE----RFGEDFTLVSIEAPFEVRAERIDArgrdagedeggeplaarderergfgmd 185
                                       ..889****7.77777788888....455555677888888888888888888899999999999999999999999 PP

                                       .............GSHHHHHHHHHH CS
                                       .............xxxxxxxxxxxx RF
                               ADK 123 .............DneetvkkRlet 134
                                                    D+ e+ ++R++t
  gi|336252738|ref|YP_004595845.1| 186 damaqadvvventDTLEAFHERMRT 210
                                       9998886666666666666666654 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   7.2e-08   0.00026       1     124 [.      37     165 ..      37     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.2e-08
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg......avllssdtlrrrlfgtdqqsktdytrvldr....lyqilnelarkal 67 
                                       ++ +vGlpGsGK   a+ ++++ g      + ++++ t+ r l +t+++ k  ++   ++    + ++   +++++l
  gi|336252738|ref|YP_004595845.1|  37 VIGTVGLPGSGKGEAAT-VAREDGipvvtmGDVVRQETADRGLDPTKDHGKVAQALRDENgpaaIAERSLPMIEDRL 112
                                       5679********99887.79999987666667777777777777754443333222222245557777779**9999 PP

                            AAA_33  68 sagrnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangdd 124
                                       +   +v++d + +s  e + f + +   g  +++v +e++ e+ +eR+ +R ++ ++
  gi|336252738|ref|YP_004595845.1| 113 EDHDTVLVD-GIRSDTEVDVFEERF---GEDFTLVSIEAPFEVRAERIDARGRDAGE 165
                                       887776666.677777776666555...6789*******************998643 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 ?   12.2   0.2   3.2e-05      0.12      32      70 ..      45     122 ..      33     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-05
                                       -TTHHHHHHHHHHTT--EEE--SSHH........................................HH--TEEEEEE CS
                     PEP-utilizers  32 GGmtSHaAivArelgiPaVvgvgeati.......................................elkegdlitvD 69 
                                       G+    aA vAre giP+V   + +++                                       +l+++d++ vD
  gi|336252738|ref|YP_004595845.1|  45 GSGKGEAATVAREDGIPVVTMGDVVRQetadrgldptkdhgkvaqalrdengpaaiaerslpmiedRLEDHDTVLVD 121
                                       677788***********998777777688999999999999999999999999999999999999888888999999 PP

                                       T CS
                     PEP-utilizers  70 g 70 
                                       g
  gi|336252738|ref|YP_004595845.1| 122 G 122
                                       8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1815.36
//
Query:       gi|336252739|ref|YP_004595846.1|  [L=137]
Description: hypothetical protein Halxa_1334 [Halopiger xanaduensis SH-6]
Scores for complete 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-10   41.1   0.3    1.4e-09   38.3   0.3    2.1  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 !   38.3   0.3   7.6e-14   1.4e-09       2     118 ..       9     112 ..       8     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 7.6e-14
                                       EEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH.HHHH CS
                       RNA_binding   2 ievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei.keLl 77 
                                       +e++a v+ TE  ++V++a++n++p+ +       +e  +g      e++ e     ++++++ +ll ++ei +  +
  gi|336252739|ref|YP_004595846.1|   9 VEITAPVYDTEVTSRVADAVANIFPNAD-------LEEEFG------EIRAEA----HSMEHFSDLLHRQEIlDTAR 68 
                                       89***********************885.......677777......445554....999********999853333 PP

                                       HCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS....EEEEEEE CS
                       RNA_binding  78 keleervdekgklylrldKQaaylgklslvegdd....vIkvkik 118
                                        e+     e++++ + l KQaa++++++++ g+      I v+++
  gi|336252739|ref|YP_004595846.1|  69 GEFFA-NREGDTFSFALKKQAAFMDRVNFSVGEPdelgEINVRVR 112
                                       34433.23689******************9888777886666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1091.06
//
Query:       gi|336252740|ref|YP_004595847.1|  [L=326]
Description: hypothetical protein Halxa_1335 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0031   17.2   1.6       0.16   11.6   0.0    3.0  3  YkyA             Putative cell-wall binding lipoprotein
     0.0065   15.4   6.4        0.3    9.9   1.1    2.3  2  Spc7             Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.069   13.6   0.4         17    5.8   0.0    3.2  3  DUF4200          Domain of unknown function (DUF4200)
        0.1   12.6   1.4        1.1    9.3   0.2    2.4  2  Prefoldin_2      Prefoldin subunit
       0.21   11.6   8.5       0.11   12.5   1.1    2.7  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
          4    7.6  12.1        3.3    7.9   1.9    3.2  3  Phage_holin_7_1  Mycobacterial 2 TMS Phage Holin (M2 Hol) Fam


Domain annotation for each model (and alignments):
>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.031        93      64      94 ..      79     109 ..      59     144 .. 0.64
   2 !   11.6   0.0   5.3e-05      0.16      54     124 ..     147     224 ..     135     229 .. 0.72
   3 ?    0.2   0.0      0.17     5e+02      74     100 ..     243     269 ..     238     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.031
                              YkyA  64 eeReellekekesieeakeefekikeeieei 94 
                                       +e +++le+ +e ++ a+ e++  ++++e +
  gi|336252740|ref|YP_004595847.1|  79 SEPRDHLEQAREHLSTAESELDGREDDLEAL 109
                                       5556667777777777777766666666655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.3e-05
                              YkyA  54 klsdealenveeReellekekesieeakeefekikee.ieei...edeelkkeaeelieameer...yeaydklyka 123
                                       +  dea+++ve+R+  le+ + ++++a  e+ +++++ ++e+   +  el++ a++l ++++++    + y++l+  
  gi|336252740|ref|YP_004595847.1| 147 ENLDEAVTTVEDRRATLESTQSAFDAATSELVSLDADrLQELaviDRAELESGASTLGDVLDSQvtlATGYETLLGG 223
                                       5689***************************9999877444444444455555555555554431114556666666 PP

                              YkyA 124 Y 124
                                       Y
  gi|336252740|ref|YP_004595847.1| 224 Y 224
                                       6 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.17
                              YkyA  74 kesieeakeefekikeeieeiedeelk 100
                                       + ++ +ak+ef ++ e++++ ++++ k
  gi|336252740|ref|YP_004595847.1| 243 EMAFTAAKQEFATAAETFSSGKEDAPK 269
                                       567889999999999999999887666 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.4   0.00036       1.1     186     227 ..      68     111 ..      44     129 .. 0.76
   2 !    9.9   1.1    0.0001       0.3     148     204 ..     132     188 ..     125     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00036
                              Spc7 186 lqe.aaeelesid.keeLeelreelaelkaeieekkkelaelqe 227
                                       l++ ++ ++++++ ++ Le++re l+++++e++ ++++l+ l++
  gi|336252740|ref|YP_004595847.1|  68 LENpEEVDFDASEpRDHLEQAREHLSTAESELDGREDDLEALRT 111
                                       444456677777769************************99986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0001
                              Spc7 148 legleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeel 204
                                       le++e+ ++ Le++ e+lde++  +e ++a+le++     +a  el s+d ++L+el
  gi|336252740|ref|YP_004595847.1| 132 LEDVERVNTALESDGENLDEAVTTVEDRRATLESTQSAFDAATSELVSLDADRLQEL 188
                                       567777888999999999999999999999999999999999999999999999987 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0057        17      81     117 ..      84     120 ..      67     122 .. 0.87
   2 ?    2.7   0.1     0.052   1.6e+02      43      94 ..     131     182 ..     126     193 .. 0.73
   3 ?    1.0   0.0      0.18   5.3e+02       9      34 ..     240     265 ..     236     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0057
                           DUF4200  81 eikklkaeietlkseiekleekleeykkYeefLekvv 117
                                        +++++++++t +se++  e+ le +++Y  +Le ++
  gi|336252740|ref|YP_004595847.1|  84 HLEQAREHLSTAESELDGREDDLEALRTYAGVLETLT 120
                                       6789999999999****************99999876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.052
                           DUF4200  43 leedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlks 94 
                                       l ed+++++  l++  ++  +a   +e+ r   ++ ++    +++e++ l +
  gi|336252740|ref|YP_004595847.1| 131 LLEDVERVNTALESDGENLDEAVTTVEDRRATLESTQSAFDAATSELVSLDA 182
                                       5677777777777777777777777777777777777777777777777665 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.18
                           DUF4200   9 fevqealeakkeeiqrleealkqree 34 
                                       +++++a  a+k+e+++  e++++ +e
  gi|336252740|ref|YP_004595847.1| 240 EDAEMAFTAAKQEFATAAETFSSGKE 265
                                       67899***********9999987666 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.087   2.6e+02      62      89 ..      80     107 ..      74     113 .. 0.64
   2 ?    9.3   0.2   0.00036       1.1      57      96 ..     132     171 ..     115     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.087
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  62 evkeeLeerketlekeiktlekqlekle 89 
                                       e +++Le+  e l++  ++l  ++++le
  gi|336252740|ref|YP_004595847.1|  80 EPRDHLEQAREHLSTAESELDGREDDLE 107
                                       5566666666666666666666666665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00036
                                       EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  57 kqdkeevkeeLeerketlekeiktlekqleklekeleelk 96 
                                       ++d+e v++ Le + e+l++ ++t+e++  +le + + + 
  gi|336252740|ref|YP_004595847.1| 132 LEDVERVNTALESDGENLDEAVTTVEDRRATLESTQSAFD 171
                                       689**************************99999887765 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 ?    3.5   0.2     0.022        65      38      80 ..      69     111 ..      46     126 .. 0.87
   2 ?   12.5   1.1   3.7e-05      0.11      19      74 ..     128     183 ..     115     198 .. 0.91
   3 ?   -3.2   0.1       2.7   7.9e+03      31      51 ..     302     322 ..     295     324 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.022
                    CENP-F_leu_zip  38 enqekvileaEtskaevetlkeeieelaeelreleldLvalrs 80 
                                       en e+v  +a + +  +e+ +e++ + ++el   e dL+alr 
  gi|336252740|ref|YP_004595847.1|  69 ENPEEVDFDASEPRDHLEQAREHLSTAESELDGREDDLEALRT 111
                                       7889999999999999999999999999999999999999985 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.7e-05
                    CENP-F_leu_zip  19 adsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleld 74 
                                        d L + ve+ +  le  +en++++++ +E+ +a++e+ ++  +  ++el  l +d
  gi|336252740|ref|YP_004595847.1| 128 DDALLEDVERVNTALESDGENLDEAVTTVEDRRATLESTQSAFDAATSELVSLDAD 183
                                       6889999*************************************999999999876 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.7
                    CENP-F_leu_zip  31 relemseenqekvileaEtsk 51 
                                       r+   + +++e+++   E+++
  gi|336252740|ref|YP_004595847.1| 302 RDPVAARQHREEAEASLEDAR 322
                                       444455555555555555555 PP

>> Phage_holin_7_1  Mycobacterial 2 TMS Phage Holin (M2 Hol) Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.1   1.2e+04      42      51 ..      13      22 ..       8      32 .. 0.67
   2 ?    7.9   1.9    0.0011       3.3      65     104 ..     145     182 ..     111     216 .. 0.67
   3 ?    5.2   1.0    0.0077        23      50      99 ..     253     301 ..     243     310 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.1
                   Phage_holin_7_1 42 vsvlvaaala 51
                                      ++vl++aala
  gi|336252740|ref|YP_004595847.1| 13 GAVLGTAALA 22
                                      5667766665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0011
                   Phage_holin_7_1  65 ttaavdkvvkslediqavlaataqaaedelakvkqvalds 104
                                        +   d++v+++ed +a l++  q+a d  a  + v+ld+
  gi|336252740|ref|YP_004595847.1| 145 DGENLDEAVTTVEDRRATLES-TQSAFDA-ATSELVSLDA 182
                                       47789****************.5666543.3444444444 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0077
                   Phage_holin_7_1  50 lavaavvlrkqikdattaavdkvvkslediqavlaataqaaedelakvkq 99 
                                        a+aa +  + + da+   vd   ++l +    l+++a +  d  a+++ 
  gi|336252740|ref|YP_004595847.1| 253 FATAAETFSSGKEDAPKGLVDYFATALCQ-SGHLESAAGSFADAAAAATE 301
                                       699*************************9.999*9999998888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 2508.27
//
Query:       gi|336252741|ref|YP_004595848.1|  [L=464]
Description: Signal recognition 54 kDa protein [Halopiger xanaduensis SH-6]
Scores for 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-64  215.1   0.1    1.4e-63  214.1   0.1    1.5  1  SRP54          SRP54-type protein, GTPase domain
    2.8e-28   98.4   5.3    2.8e-28   98.4   5.3    3.2  3  SRP_SPB        Signal peptide binding domain
    3.3e-17   62.5   1.6    6.3e-17   61.6   0.2    2.3  2  SRP54_N        SRP54-type protein, helical bundle domain
     0.0011   19.0   0.3       0.26   11.3   0.1    2.5  2  CARD           Caspase recruitment domain
     0.0013   18.8   0.0     0.0042   17.1   0.0    2.0  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0018   17.6   0.4      0.018   14.3   0.0    2.6  3  Zeta_toxin     Zeta toxin
     0.0019   17.8   0.8      0.023   14.3   0.8    2.4  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
     0.0055   17.0   0.0       0.38   11.0   0.0    2.7  2  AAA_22         AAA domain
  ------ inclusion threshold ------
       0.01   15.7   0.1      0.028   14.3   0.1    1.8  1  DUF2202        Uncharacterized protein domain (DUF2202)
       0.02   14.6   0.1      0.063   13.0   0.0    2.0  2  AAA_24         AAA domain
      0.041   13.8   0.0      0.096   12.6   0.0    1.6  1  APS_kinase     Adenylylsulphate kinase
      0.049   13.1   0.0      0.086   12.3   0.0    1.4  1  SMC_N          RecF/RecN/SMC N terminal domain
      0.054   13.3   0.1       0.12   12.2   0.1    1.5  1  KdpC           K+-transporting ATPase, c chain
      0.076   12.2   0.0      0.076   12.2   0.0    2.8  3  ArsA_ATPase    Anion-transporting ATPase
       0.11   12.6   0.0       0.32   11.1   0.0    1.7  1  AAA_33         AAA domain
       0.15   12.5   0.3       0.35   11.3   0.0    1.8  1  Tex_YqgF       Tex protein YqgF-like domain
       0.25   10.9   2.0        1.2    8.7   2.0    2.2  1  AAA_25         AAA domain
        2.6    7.4   8.4        0.1   12.0   1.1    2.2  3  DUF4618        Domain of unknown function (DUF4618)


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 !  214.1   0.1   1.4e-66   1.4e-63       3     196 .]      99     290 ..      97     290 .. 0.99

  Alignments for each domain:
  == domain 1  score: 214.1 bits;  conditional E-value: 1.4e-66
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHH CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeaveka 79 
                                        ill+GlqG+GKTt++aK+a +++++g +++++ +DtfR++A+eQ +++a +++v+++++  ++dp+++a++++e+ 
  gi|336252741|ref|YP_004595848.1|  99 TILLAGLQGSGKTTSAAKMAWWFSTKGLRPAVIQTDTFRPGAYEQAEEMAGRAEVDYYGNPDNDDPVEIARKGLEET 175
                                       79*************************************************************************99 PP

                                       HHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSST CS
                             SRP54  80 keekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakg 156
                                        e  +dv +vDTaGr++ +++l++e+++i+ vv+pd +llvlda++gq a  qa++F+e++gi+gv++tklDg+akg
  gi|336252741|ref|YP_004595848.1| 176 SE--ADVHIVDTAGRHALEDDLIDEIEQIEGVVEPDTSLLVLDAAIGQGAKDQAQQFDESIGIDGVVITKLDGTAKG 250
                                       88..89*********************************************************************** PP

                                       THHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 157 GaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       G+al++++++++ i+f+g+Ge+++d+e+f+p+ ++srllg
  gi|336252741|ref|YP_004595848.1| 251 GGALTAVDQTDSSIAFLGTGEEVQDIERFEPDGFISRLLG 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 ?   -1.2   0.0       3.3   3.3e+03      13      31 ..     287     305 ..     284     319 .. 0.69
   2 !   98.4   5.3   2.8e-31   2.8e-28       1      98 [.     324     426 ..     324     427 .. 0.91
   3 ?    0.4   3.8      0.99   9.9e+02       8      33 ..     424     449 ..     423     458 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.3
                                       HHHCCCCCCHHHHCCC... CS
                           SRP_SPB  13 qikkmGplskllsmiPgms 31 
                                       ++  mG+ls+l++ +   +
  gi|336252741|ref|YP_004595848.1| 287 RLLGMGDLSQLAERVERAM 305
                                       5678999999999876533 PP

  == domain 2  score: 98.4 bits;  conditional E-value: 2.8e-31
                                       SSCTHHHHHHHHHHHCCCCCCHHHHCCC...........H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHH CS
                           SRP_SPB   1 eftlrdlleqlqqikkmGplskllsmiPgmsae......akaeeeaekklkrieaiidSMTkeErdspekllkesRk 71 
                                       +ftl+d+++q++ +++mGpl+++++miPg++         +a++ ++++++ + +i+dSMT++E++ p+  + +s +
  gi|336252741|ref|YP_004595848.1| 324 QFTLHDMQKQMEAMNNMGPLDQVMDMIPGFGGGikdqlpDDAMDVTQERMRSFSVIMDSMTEAEKEYPK-AIGASQI 399
                                       6****************************998865555433448999**********************.6669*** PP

                                       HHHHHHTTS-HHHHHHHHHHHHHHHHH CS
                           SRP_SPB  72 rRiArGsGtsvqevnellkqfeqmkkm 98 
                                       +RiA+GsGts ++v+ell+q+++m+k+
  gi|336252741|ref|YP_004595848.1| 400 ERIAKGSGTSEDQVRELLQQYKMMEKT 426
                                       ************************996 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.99
                                       HHHHHHHHCCCCCCHHHHCCC..... CS
                           SRP_SPB   8 leqlqqikkmGplskllsmiPgmsae 33 
                                        + ++q + mG+ +++  m+  m+++
  gi|336252741|ref|YP_004595848.1| 424 EKTIKQFQGMGSEQEMQRMMKQMQQQ 449
                                       6789999******9999999988766 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 !   61.6   0.2   6.3e-20   6.3e-17       1      75 []       6      83 ..       6      83 .. 0.95
   2 ?   -3.0   0.1       8.8   8.8e+03      15      31 ..     188     200 ..     185     203 .. 0.67

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 6.3e-20
                                      HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                           SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                                      Lg++l+++l kl+gks+i+eed+ee++ke++++L++aDV +++v++l  n+k++a++e+    +  ++ v +iv++eL
  gi|336252741|ref|YP_004595848.1|  6 LGSSLRGTLDKLRGKSRISEEDVEEIVKEIQRSLISADVDISLVQELSGNIKERALEEEPpagTPARDFVLRIVYEEL 83
                                      899**************************************************999955599888999999*****98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.8
                                       SSCGHHHHHHHHHHHHH CS
                           SRP54_N  15 kskideedleealkele 31 
                                       +  + +++++e    +e
  gi|336252741|ref|YP_004595848.1| 188 RHALEDDLIDE----IE 200
                                       55677888888....55 PP

>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00026      0.26      12      45 ..       3      37 ..       1      42 [. 0.87
   2 ?    5.4   0.0     0.019        19      33      56 ..     396     420 ..     371     430 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                                      HHHSS.HHHHHHHHHHHTTSS-HHHHHHHHTSSSH CS
                              CARD 12 verlk.slsglldyLlekkVLteeeeekikakttr 45
                                      +++l+ sl+g ld+L+ k  ++ee+ e+i ++ +r
  gi|336252741|ref|YP_004595848.1|  3 LDDLGsSLRGTLDKLRGKSRISEEDVEEIVKEIQR 37
                                      57788899*********************886555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.019
                                       HHHHHHHHT.SSSHHHHHHHHHHHH CS
                              CARD  33 eeeeekika.kttrlskareLldlv 56 
                                         ++e+i + ++t+++++reLl  +
  gi|336252741|ref|YP_004595848.1| 396 ASQIERIAKgSGTSEDQVRELLQQY 420
                                       568999****************865 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 !   17.1   0.0   4.2e-06    0.0042       9      87 ..     107     247 ..     100     351 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.2e-06
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       G+GKTt aa++a  ++ +glr +++ +D+ ++ +        ++++                               
  gi|336252741|ref|YP_004595848.1| 107 GSGKTTSAAKMAWWFSTKGLRPAVIQTDTFRPGAY-------EQAEemagraevdyygnpdnddpveiarkgleets 176
                                       9***************************9988876.......11112344556777888888888888888888888 PP

                                       ........................................................CCHCCCHHHHHHCHCHHHH.. CS
                                       ........................................................xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ........................................................dlkrllellealgkkkalllk 75 
                                                                                               +                  + 
  gi|336252741|ref|YP_004595848.1| 177 eadvhivdtagrhaleddlideieqiegvvepdtsllvldaaigqgakdqaqqfdeS------------------IG 235
                                       888888888888888888888888888777776666666555444333333333330..................44 PP

                                       EEEEEEEEESS. CS
                                       xxxxxxxxxxxx RF
                              CbiA  76 iagvvlnrvdge 87 
                                       i gvv+++ dg 
  gi|336252741|ref|YP_004595848.1| 236 IDGVVITKLDGT 247
                                       445555555554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.8e-05     0.018      18      58 ..      99     140 ..      89     189 .. 0.76
   2 ?   -0.5   0.0      0.63   6.3e+02      52      83 ..     344     376 ..     326     384 .. 0.82
   3 ?   -1.9   0.1       1.7   1.7e+03      51      89 ..     410     448 ..     409     450 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                        Zeta_toxin  18 lillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelh 58 
                                        ill+G +G+GK++ a++++  +  ++ +  ++++D++R+  
  gi|336252741|ref|YP_004595848.1|  99 TILLAGLQGSGKTTSAAKMAWWFStKGLRPAVIQTDTFRPGA 140
                                       69**************999999887899***********854 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.63
                        Zeta_toxin  52 DdlRelhPeyeeilka.dpkkaseltqkdasel 83 
                                       D++  ++P + + +k+  p++a ++tq+ ++ +
  gi|336252741|ref|YP_004595848.1| 344 DQVMDMIPGFGGGIKDqLPDDAMDVTQERMRSF 376
                                       7888899999876664399*********99987 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.7
                        Zeta_toxin  51 pDdlRelhPeyeeilkadpkkaseltqkdaselvekllq 89 
                                       +D++Rel  +y+ ++k  ++      +++++++++++ q
  gi|336252741|ref|YP_004595848.1| 410 EDQVRELLQQYKMMEKTIKQFQGMGSEQEMQRMMKQMQQ 448
                                       689999999998866655555556667777777777766 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 !   14.3   0.8   2.3e-05     0.023       3     155 ..     100     249 ..      98     265 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                                       EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkeleale 77 
                                       ++l+G  GsGKTt   ++     ++gl+ avi  +    +  ++  +   +   e+   + + +  +d ++ +++ +
  gi|336252741|ref|YP_004595848.1| 100 ILLAGLQGSGKTTSAAKMAwwFSTKGLRPAVIQTDTFRPGAYEQAEEM--AGRAEVDYYGNPDN--DDPVEIARKGL 172
                                       7899**************9998899**********9964433333222..33578888888877..56555555555 PP

                                       HHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHH CS
                              cobW  78 ereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDll 153
                                       e+ ++ dv ++ t G  a    ++ + e+++  ++ d+ + v+Da ++ +  +++++++++ +   d +v++K D  
  gi|336252741|ref|YP_004595848.1| 173 EETSEADVHIVDTAGrHALEDDLIDEIEQIEGVVEPDTSLLVLDA-AIGQGAKDQAQQFDESIGI-DGVVITKLDGT 247
                                       55559**********98888888777999****************.6667777777777777765.999999*9977 PP

                                       CH CS
                              cobW 154 de 155
                                        +
  gi|336252741|ref|YP_004595848.1| 248 AK 249
                                       66 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00038      0.38       6      31 ..      98     123 ..      95     217 .. 0.77
   2 ?    3.1   0.0      0.11   1.1e+02      39      86 ..     395     450 ..     377     455 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00038
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqlde 31 
                                       + +++ G  G+GKTt++++++ ++  
  gi|336252741|ref|YP_004595848.1|  98 QTILLAGLQGSGKTTSAAKMAWWFST 123
                                       67899***************999853 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.11
                            AAA_22  39 rpevvfvtlpsstsskdllrellralglelka........erlsseellealeqal 86 
                                       ++++++  +++s++s+d  rell++++   k+        ++++ ++++++++q+ 
  gi|336252741|ref|YP_004595848.1| 395 GASQIERIAKGSGTSEDQVRELLQQYKMMEKTikqfqgmgSEQEMQRMMKQMQQQG 450
                                       45666667778889999999999999998888999*99999999999999999985 PP

>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.8e-05     0.028      32      82 ..     400     450 ..     373     453 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-05
                           DUF2202  32 lniakseqthtdavksllekYeledpvkederGkfedeelqelYnkLvekg 82 
                                       + iak   t  d+v++ll++Y++ +   ++ +G+ +++e+q + +++ ++g
  gi|336252741|ref|YP_004595848.1| 400 ERIAKGSGTSEDQVRELLQQYKMMEKTIKQFQGMGSEQEMQRMMKQMQQQG 450
                                       67899999999**************999999***************99988 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.3e-05     0.063       3      33 ..      98     135 ..      96     211 .. 0.85
   2 ?   -2.5   0.0       3.6   3.6e+03      48      63 ..     375     390 ..     355     434 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.3e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtek 33 
                                       + il+ G +g+GKTt+a+++       g +p++i+t+ 
  gi|336252741|ref|YP_004595848.1|  98 QTILLAGLQGSGKTTSAAKMawwfstkGLRPAVIQTDT 135
                                       789*****************999999999999998874 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.6
                            AAA_24  48 swedfldevvelaael 63 
                                       s+  ++d ++e ++e+
  gi|336252741|ref|YP_004595848.1| 375 SFSVIMDSMTEAEKEY 390
                                       4444444444444433 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.6e-05     0.096       3      44 ..      98     139 ..      96     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.6e-05
                                       EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTT CS
                        APS_kinase   3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhg 44 
                                        +++l+Gl gsGK+t a +++    +kg +  +++ d+ R g
  gi|336252741|ref|YP_004595848.1|  98 QTILLAGLQGSGKTTSAAKMAWWFSTKGLRPAVIQTDTFRPG 139
                                       699**************************9999999999976 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 ?   12.3   0.0   8.6e-05     0.086       4     102 ..      77     170 ..      74     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.6e-05
                                       EEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--....BTTCSSTTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxx RF
                             SMC_N   4 rleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk....skekasvkk 76 
                                       r++ e+   + g++++lp++++   + G  GSGK+     + + ++   +k lr + ++   ++    +++++ + +
  gi|336252741|ref|YP_004595848.1|  77 RIVYEELVDLIGDSTELPLEEQTILLAGLQGSGKTTSAAKMAWWFS---TKGLRPAVIQTDTFRpgayEQAEEMAGR 150
                                       666677777788999******************************9...4678988888777777776678888888 PP

                                       EEEEEEEEETTEESSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  77 aeveitfdnedkklkiekeevsisrr 102
                                       aev+  + n+d++     + v+i r+
  gi|336252741|ref|YP_004595848.1| 151 AEVDY-YGNPDND-----DPVEIARK 170
                                       88887.5666666.....44555554 PP

>> KdpC  K+-transporting ATPase, c chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012      0.12     133     159 ..     396     422 ..     382     437 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                       HHTHHHHHHHHT--HHHHHHHHHHTEE CS
                              KdpC 133 elQvarvakarglseeeveklvaente 159
                                       + Q++r+ak +g se++v++l++++  
  gi|336252741|ref|YP_004595848.1| 396 ASQIERIAKGSGTSEDQVRELLQQYKM 422
                                       68********************98754 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.7e-05     0.076       3      38 ..      99     134 ..      97     139 .. 0.94
   2 ?   -1.0   0.2      0.82   8.1e+02     152     201 ..     330     380 ..     323     389 .. 0.63
   3 ?    0.1   0.5      0.37   3.7e+02     153     189 ..     414     448 ..     396     451 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.7e-05
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                        il++G  G GKtt++a +a + s kg +  +i tD
  gi|336252741|ref|YP_004595848.1|  99 TILLAGLQGSGKTTSAAKMAWWFSTKGLRPAVIQTD 134
                                       7999******************************99 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.82
                                       HHHHHHHHHHHHHHHHHHCCCSHCHHHHHH.HHHHHHHHHHHHHHHHHHHH CS
                       ArsA_ATPase 152 leklvklkeklsplakqlvkllglggvsie.ealeeleetkeeikkveeil 201
                                       ++k ++  ++++pl + +  + g+gg   +    ++++ t e++++++ i+
  gi|336252741|ref|YP_004595848.1| 330 MQKQMEAMNNMGPLDQVMDMIPGFGGGIKDqLPDDAMDVTQERMRSFSVIM 380
                                       677777788888888887666666666555323345666666666665554 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHH CS
                       ArsA_ATPase 153 eklvklkeklsplakqlvkllglggvsieealeelee 189
                                       ++l++  +++++ +kq++++    +++++++++++++
  gi|336252741|ref|YP_004595848.1| 414 RELLQQYKMMEKTIKQFQGM--GSEQEMQRMMKQMQQ 448
                                       34444444444444444332..122233355555544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00033      0.32       2      35 ..     100     138 ..     100     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                            AAA_33   2 vllvGlpGsGKstlaerl.....lkklgavllssdtlrr 35 
                                       +ll Gl+GsGK+t a ++      k l   ++ +dt+r 
  gi|336252741|ref|YP_004595848.1| 100 ILLAGLQGSGKTTSAAKMawwfsTKGLRPAVIQTDTFRP 138
                                       6899************99666444444488888888665 PP

>> Tex_YqgF  Tex protein YqgF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00036      0.35       2      78 ..     345     421 ..     344     438 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
                                       -EEEEE--STT-EEEEEE-TTS-EEEEEEE--STTT--HHHHHHHHHHHHHHTT--EEEEESSTTHHHHHHHHHHHH CS
                          Tex_YqgF   2 vvlglDPgyrtGcKlavvdetgkvletaviyphepkkkveeakkklkklvkkykveliaiGnGtasreteklvaeli 78 
                                       +v+ + Pg+  G+K  + d+  +v+++++       ++++ea+k+  k +   ++e ia G Gt+  ++ +l+++  
  gi|336252741|ref|YP_004595848.1| 345 QVMDMIPGFGGGIKDQLPDDAMDVTQERMRSFSVIMDSMTEAEKEYPKAIGASQIERIAKGSGTSEDQVRELLQQYK 421
                                       588999******************99999988889999**************************9999998888743 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.0    0.0012       1.2      33      58 ..      97     122 ..      91     221 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                            AAA_25  33 gelallaGapgtGKttlaldlalava 58 
                                       + ++llaG +g+GKtt a  +a   +
  gi|336252741|ref|YP_004595848.1|  97 EQTILLAGLQGSGKTTSAAKMAWWFS 122
                                       6789**************99997665 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.97   9.7e+02     145     174 ..       8      36 ..       3      57 .. 0.50
   2 ?   -3.4   0.2       5.2   5.2e+03      82      93 ..     326     337 ..     294     340 .. 0.57
   3 ?   12.0   1.1    0.0001       0.1      27      74 ..     400     448 ..     381     451 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.97
                           DUF4618 145 elikevleklskkiqkkkekllkslaektl 174
                                         ++  l kl  k +  +e + + ++++++
  gi|336252741|ref|YP_004595848.1|   8 SSLRGTLDKLRGKSRISEEDVEE-IVKEIQ 36 
                                       55555555554444433333222.112222 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.2
                           DUF4618  82 klekLeqqleql 93 
                                       +l+++++q+e++
  gi|336252741|ref|YP_004595848.1| 326 TLHDMQKQMEAM 337
                                       334444444444 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.0001
                           DUF4618  27 keIqdtedstakkvrklLqqyeklktvisileks.skkqleqakaeLqe 74 
                                       + I +   ++  +vr+lLqqy+++++ i+ ++   s+++++++ +++q+
  gi|336252741|ref|YP_004595848.1| 400 ERIAKGSGTSEDQVRELLQQYKMMEKTIKQFQGMgSEQEMQRMMKQMQQ 448
                                       566667778999*****************99987256678888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1334  (0.0744046); expected 358.6 (0.02)
Passed bias filter:                      938  (0.0523175); expected 358.6 (0.02)
Passed Vit filter:                       145  (0.00808746); 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: 0.71u 0.27s 00:00:00.98 Elapsed: 00:00:00.42
# Mc/sec: 3303.35
//
Query:       gi|336252742|ref|YP_004595849.1|  [L=226]
Description: haloacid dehalogenase, type II [Halopiger xanaduensis SH-6]
Scores for complete 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   47.6   0.0    2.5e-12   47.2   0.0    1.3  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.5e-11   45.0   2.8    4.2e-11   43.5   2.8    1.6  1  Hydrolase       haloacid dehalogenase-like hydrolase
    0.00019   21.9   0.4    0.00022   21.7   0.4    1.2  1  HAD             haloacid dehalogenase-like hydrolase
    0.00038   20.5   0.0     0.0013   18.7   0.0    2.0  1  Hydrolase_like  HAD-hyrolase-like


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 !   47.2   0.0   5.6e-16   2.5e-12      35     178 .]      58     197 ..      11     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 5.6e-16
                             HAD_2  35 eelrkliglslrellrklgeseeeeekieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreavee 111
                                       + ++ +++l+ + l + l          e+ ++++ +  +  e++++d+v++ Le L + gy + i ++++ e++e+
  gi|336252742|ref|YP_004595849.1|  58 DAYQPFYELNRDALQYALDAH-G-AAVTEDERDEVLAVYH--ELEVFDDVRDGLEALVDVGYDCYILSNGNPEMLES 130
                                       445555555553333333322.2.2234444344444444..6********************************** PP

                             HAD_2 112 kleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsptDieaakkagikviav 178
                                        +e+ +i++++   ++++++e  KP++e+++    ++++  +e+  v    +D+ +a +ag+++++v
  gi|336252742|ref|YP_004595849.1| 131 LVEHADIDDLLADTISADEIETFKPNAELYRHGAARTGTPIDEIAHVAAGWFDVRGANHAGMQSVWV 197
                                       *****************************************************************98 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   2.8   9.4e-15   4.2e-11       1     210 []       8     191 ..       8     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 9.4e-15
                                       SSEEEEESBTTTBCHH...HHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHH CS
                                       xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttge...psvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkp 74 
                                       ++t+ fD  GTL++ e     + dv++                        a  +r+   +   tf  +   +i   
  gi|336252742|ref|YP_004595849.1|   8 VTTITFDSYGTLVDVEaatAALADVVDDP---------------------DAVSQRWRTRSLAYTFVAN---QIDAY 60 
                                       579**********9997777777777777.....................6666664444333332222...22222 PP

                                       H.HHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHH CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  75 e.wltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaer 150
                                       + + + +      +a  +++ ++g  v  +  + ++v+++ ++l+v++++++ +++L + g++ ++l+++npe+ e+
  gi|336252742|ref|YP_004595849.1|  61 QpFYELN-----RDALQYALDAHGAAVTED--ERDEVLAVYHELEVFDDVRDGLEALVDVGYDCYILSNGNPEMLES 130
                                       2022222.....344444455555555555..********************************************* PP

                                       HHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 151 aanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       + ++++ dd ++ +i++d+ +  kp+ e +++ + + + ++ e+a+V  g  D+ ++  Ag
  gi|336252742|ref|YP_004595849.1| 131 LVEHADiDDLLADTISADEIETFKPNAELYRHGAARTGTPIDEIAHVAAGWFDVRGANHAG 191
                                       ******9999977777777777*************************99999999999887 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.4     5e-08   0.00022       3     155 ..      13     170 ..      11     204 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5e-08
                               HAD   3 fDfDgTLldgdsle.....lllrfllrrgaprl..wralreklllal.....frellrldraglaelleallaglse 67 
                                       fD  gTL+d + ++     +     +  ++     wr+   ++         +  + +l+r++l+ +l+a  a+ +e
  gi|336252742|ref|YP_004595849.1|  13 FDSYGTLVDVEAATaaladV-----VDDPDAVSqrWRTRSLAYTFVAnqidaYQPFYELNRDALQYALDAHGAAVTE 84 
                                       66667888886666434431.....2222211112333333322222333543444555555777777777777778 PP

                               HAD  68 elaaelerfvaevirpklldp..galellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd..rltg 140
                                       +  +e+ + ++e           + le+l    + G+ ++++S+g+ +++e l ++ ++d++la  +  d+   ++ 
  gi|336252742|ref|YP_004595849.1|  85 DERDEVLAVYHELEVFD---DvrDGLEALV---DVGYDCYILSNGNPEMLESLVEHADIDDLLADTISADEieTFKP 155
                                       88888888886666544...2235555555...79******************************888888888888 PP

                               HAD 141 elglegkpvrgegkv 155
                                        ++l+ +  ++ g++
  gi|336252742|ref|YP_004595849.1| 156 NAELYRHGAARTGTP 170
                                       888888888877666 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     3e-07    0.0013       4      50 ..     154     199 ..     152     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3e-07
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESS CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVlt 50 
                                       KP++e+y+  ++++g + +e+  +    + D++gAn aG++sv V +
  gi|336252742|ref|YP_004595849.1| 154 KPNAELYRHGAARTGTPIDEIAHVAAG-WFDVRGANHAGMQSVWVDR 199
                                       9**************************.****************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1631.84
//
Query:       gi|336252743|ref|YP_004595850.1|  [L=81]
Description: hypothetical protein Halxa_1338 [Halopiger xanaduensis SH-6]
Scores for 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  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); 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:                         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: 00:00:00.37
# Mc/sec: 650.93
//
Query:       gi|336252744|ref|YP_004595851.1|  [L=291]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-61  206.9  13.8    3.6e-32  111.8   2.1    2.0  2  Usp              Universal stress protein family
  ------ inclusion threshold ------
       0.12   12.0   0.0        0.2   11.2   0.0    1.4  1  Glyco_trans_4_5  Glycosyl-transferase family 4


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 !  101.0   4.1   8.9e-33     8e-29       4     141 .]       5     137 ..       3     137 .. 0.95
   2 !  111.8   2.1     4e-36   3.6e-32       2     140 ..     148     286 ..     147     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 8.9e-33
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                        IlV+vDgs++s++A+++Ale  ++ ga+l++lhv d+  ++ ++ + + a   e e  e  ++a   +++ae++g+
  gi|336252744|ref|YP_004595851.1|   5 DILVPVDGSDASTAAFDHALEIGADAGATLHVLHVADTALPSLAGLGTDVADALEREGDEIVADA---RDRAEERGI 78 
                                       69****************************************99999999999999988887775...68******* PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +v+++v+ g+p+eei+++a +  adl+V+G++g +g+ +++lG +++yv++ ++ pVl Vr
  gi|336252744|ref|YP_004595851.1|  79 DVVTDVRRGEPREEIVDAAAD--ADLVVMGAHGCHGIGEYVLGTTTDYVINVTETPVLSVR 137
                                       ******************997..***********************************987 PP

  == domain 2  score: 111.8 bits;  conditional E-value: 4e-36
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       y+ IlV++Dgs++ ++A++ A++ a+++ga+l+ll+vid+ +  +++ +de++ e e+  e+  ++a+ ++++a   
  gi|336252744|ref|YP_004595851.1| 148 YEAILVPTDGSDHGTAAVRVAAQVAAHTGATLHLLYVIDELPEVEEPVSDETTTELEENAEAILEAAASTATEAGLD 224
                                       889*************************************************************99999******** PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       +++ +++v +g++ +ei  +a++e +dli +G++g++gl+r l+GS++e++lr+ap+pVl V
  gi|336252744|ref|YP_004595851.1| 225 EASITTTVSSGSVPHEIRTHADAEAVDLIAMGTHGHTGLDRHLIGSFTEQLLRSAPVPVLTV 286
                                       ************************************************************88 PP

>> Glyco_trans_4_5  Glycosyl-transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.2e-05       0.2      46      82 ..      69     110 ..      31     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.2e-05
                   Glyco_trans_4_5  46 llkeladrgikvlea.....kaeelfklalkaDlvvlntvva 82 
                                          ++++rgi v+++       ee +++a++aDlvv+++  +
  gi|336252744|ref|YP_004595851.1|  69 ARDRAEERGIDVVTDvrrgePREEIVDAAADADLVVMGAHGC 110
                                       44577899********9998788999***********97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2099.42
//
Query:       gi|336252745|ref|YP_004595852.1|  [L=293]
Description: hypothetical protein Halxa_1340 [Halopiger xanaduensis SH-6]
Scores for 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-20   72.7   0.0      4e-20   72.2   0.0    1.1  1  EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like


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 !   72.2   0.0   2.2e-24     4e-20       2     164 ..     122     279 ..     119     282 .. 0.91

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 2.2e-24
                        EMC3_TMCO1   2 lvldplirdwvllPivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqe 78 
                                       l l+pl      lP+  v+l ++++t+l+++l++  l d+   ++++ r +elq+r  +++ +gd+ + ++l +++ 
  gi|336252745|ref|YP_004595852.1| 122 LALGPLAA---ALPFPAVVLALAVATTLATTLVRRRL-DRPDASAFRHRTRELQERLAAARARGDEAAAARLGEQRR 194
                                       45566666...9***********************97.*************************************** PP

                        EMC3_TMCO1  79 elmedqsemmmdqmkpmivtmipqiliffwlnsffs..gfvvaklp..fpltgrfksllqrglesldvrfvssiswY 151
                                       +l + q  +++d +k  ++tm++++++f++l++ +    +++a l+  +p++g +  ++    + ++++++ ++ wY
  gi|336252745|ref|YP_004595852.1| 195 DLVGRQALVLTDHLKVLAWTMVLTVPVFLYLSWLVTapAHATAPLVtvAPVLGDIV-WT----ARVVGPVQAWMAWY 266
                                       ***********************************987444444444499999999.99....99************ PP

                        EMC3_TMCO1 152 flcsfglsqiirk 164
                                        lcs+g++ ++r 
  gi|336252745|ref|YP_004595852.1| 267 ALCSLGSNLVVRR 279
                                       ******9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2182.14
//
Query:       gi|336252746|ref|YP_004595853.1|  [L=487]
Description: dihydrolipoyl dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-47  161.7   0.9    4.1e-47  160.8   0.7    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      5e-27   94.3   0.0    8.5e-27   93.6   0.0    1.4  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    1.1e-16   61.1   0.8    2.6e-13   50.3   0.0    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.5e-07   30.9   0.2      3e-05   23.5   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    4.1e-07   29.5   0.0    2.1e-05   23.8   0.0    2.8  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    1.6e-06   27.5   1.0    3.8e-06   26.2   0.1    1.9  2  GIDA            Glucose inhibited division protein A
    0.00038   19.7   4.2       0.66    9.0   0.0    2.4  2  FAD_binding_2   FAD binding domain
     0.0052   16.2   1.1     0.0084   15.5   1.1    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
     0.0081   16.1   1.7       0.82    9.5   0.1    3.1  3  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
       0.13   11.8   0.1       0.25   10.9   0.1    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.15   11.6   7.1        1.1    8.8   2.5    2.7  2  DAO             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 !  160.8   0.7   2.5e-50   4.1e-47       1     280 [.       4     320 ..       4     331 .. 0.88

  Alignments for each domain:
  == domain 1  score: 160.8 bits;  conditional E-value: 2.5e-50
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias................. 57 
                                       +d+vviGgG +  ++a+ +a  g++ +++e   l+g+c ++gc++skal + a+ a+ ++                 
  gi|336252746|ref|YP_004595853.1|   4 YDIVVIGGGSG-SQVATAAADRGLEAAVIErgpLGGACITRGCVPSKALIHRADLADAVRragefgiaadlqdvayg 79 
                                       69*******85.6778899999*******999************************98889**************** PP

                                       ........HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC.......TCEEEEEESEEEE---EEE-BCTCTTC CS
                                       ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ........evvkklnqgielllgeevvkidpgkkkvklekkke.......gdeekiaydklvlAtGssprdlgipGv 119
                                                v +k   + + l ++  v++ +g++++++e +         gd++++  d++vlA Gs+p  ++i+G+
  gi|336252746|ref|YP_004595853.1|  80 eitdaihdTVYEKAARQERALEESDSVALFRGEGRFVDEWTIAvkptddsGDTREVRGDAIVLAVGSRPMVPPIDGL 156
                                       99999997444444444455555568999999999999766668899999*************************** PP

                                       .TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 120 aenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealeke 196
                                        e+v    + l+s++al l+++p+ +++vGgGyiG El  ++  lg +v ++ + +rl ++ d+++sa +++ l + 
  gi|336252746|ref|YP_004595853.1| 157 -EDV----DFLTSDDALFLDEQPDELAIVGGGYIGAELGYFFGALGTDVSMIGRSERLIPGEDDDASAVVTDSLAD- 227
                                       .555....789****************************************************************9. PP

                                       TEEEEESCEEEEEEETTE....EEE..EEETTSCE..EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTS CS
                                       xxxxxxxxxxxxxxxxxx....xxx..xxxxxxxx..xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 197 Gvevklgtsvkeidgnge....kle..vvledgee..idadlvvvavGvrpstelle.eklglelderggivvdefl 264
                                         ++++g ++ e+ + +      ++    ++dge   i+ad +++a+G+rp+t++l  e+  +e+d++g++++d +l
  gi|336252746|ref|YP_004595853.1| 228 YCDLYTGYEAAEVAQGDGggsvTITaePSDDDGEPveIEADELLLATGRRPNTDTLAlEETSVETDDKGYVETDARL 304
                                       59********999988888855222335555555488**************************************** PP

                                       BESSTTEEE-GGGCTE CS
                                       xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 265 rtnvpgiyaiGDvagg 280
                                       +t  +gi+a+GD++g+
  gi|336252746|ref|YP_004595853.1| 305 ETAAEGIWALGDIVGE 320
                                       ************9932 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 !   93.6   0.0   5.2e-30   8.5e-27       1     109 [.     351     459 ..     351     460 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 5.2e-30
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       +p ++ft+p+vasvG te e++++g e++  ++pf+a    l+ + ++gfvK++a   +g++lG+h+vGp+a+ liq
  gi|336252746|ref|YP_004595853.1| 351 MPHAIFTEPQVASVGRTEGELEDEGREYESTTVPFDAAPLGLILGADDGFVKVLAAP-DGEILGCHVVGPQASTLIQ 426
                                       699**************************************************7766.******************* PP

                                       HHHHHHHTT.SBHHHHHTSBSSSSSTGGGGHCH CS
                     Pyr_redox_dim  78 elavaikag.ltvedladtihihPtlsealkea 109
                                       e+ va+  g  tv+d+ad +h+hP lsea+ +a
  gi|336252746|ref|YP_004595853.1| 427 EVVVAMDSGdGTVDDVADPVHVHPALSEAIYTA 459
                                       ******98747******************9776 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.6    0.0022       3.5       2      32 ..       6      35 ..       5      37 .. 0.93
   2 !   50.3   0.0   1.6e-16   2.6e-13       2      77 ..     177     252 ..     176     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0022
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                      +vv+GgG +g  +A+a+a+ g +  v+er++
  gi|336252746|ref|YP_004595853.1|  6 IVVIGGG-SGSQVATAAADRGLEAAVIERGP 35
                                      89**999.8*******************975 PP

  == domain 2  score: 50.3 bits;  conditional E-value: 1.6e-16
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.vesvk 77 
                                       +++vGgGyig El+ ++ +lg +V+++ rs++l +++D++as++++++l +   +++++ +++e+ + + g   +++
  gi|336252746|ref|YP_004595853.1| 177 LAIVGGGYIGAELGYFFGALGTDVSMIGRSERLIPGEDDDASAVVTDSLADY-CDLYTGYEAAEVAQGDGGgSVTIT 252
                                       79**************************************************.*************77766443354 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 ?    3.2   2.4     0.027        44       1      33 [.       7      37 ..       6      42 .. 0.84
   2 !   23.5   0.0   1.8e-08     3e-05     121     305 .]     133     315 ..     129     315 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.027
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                      ++iG+G  G ++a+++ + gle   ++E+g +g
  gi|336252746|ref|YP_004595853.1|  7 VVIGGG-SGSQVATAAADRGLE-AAVIERGPLG 37
                                      577777.69************5.78*****887 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.8e-08
                       Pyr_redox_3 121 etyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgs 197
                                       ++++ + +++A G   +P ++ i G e+    +s +  f + + ++++++Gg+  +++  + + + g +V+++ r++
  gi|336252746|ref|YP_004595853.1| 133 REVRGDAIVLAVGS--RPMVPPIDGLEDVDFLTSDDALFLDEQPDELAIVGGGYIGAELGYFFGALGTDVSMIGRSE 207
                                       56778899*****8..***********9999*********************************************9 PP

                       Pyr_redox_3 198 eiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvk....tedgkkvev.kddvvlatGykp 269
                                        +   e+d    +   + + l+++ +   ++ ++ aev + +    +++++     +dg+ ve+  d+ +latG +p
  gi|336252746|ref|YP_004595853.1| 208 RLIPGEDDDASAV---VTDSLADYCDL--YTGYEAAEVAQGDG-GGSVTITaepsDDDGEPVEIeADELLLATGRRP 278
                                       9988776655444...45555554431..23333444433332.2333333333378999999846677788***** PP

                       Pyr_redox_3 270 dlsflkk..slfeldedgrpvlteeteetnvpglflaG 305
                                       +++ l+     +e+d++g++  t++  et  +g++  G
  gi|336252746|ref|YP_004595853.1| 279 NTDTLALeeTSVETDDKGYV-ETDARLETAAEGIWALG 315
                                       **998764366666666665.56778999999998776 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 ?   -0.5   0.2      0.32   5.2e+02     191     213 ..       3      24 ..       1      33 [. 0.75
   2 !   23.8   0.0   1.3e-08   2.1e-05     133     237 ..     121     218 ..     104     239 .. 0.83
   3 ?    1.8   0.0     0.067   1.1e+02     132     160 ..     250     278 ..     221     291 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
                       K_oxygenase 191 kkriaVvGsGqSaaeifedllrr 213
                                       + +i+V+G+G S+++++  +++r
  gi|336252746|ref|YP_004595853.1|   3 EYDIVVIGGG-SGSQVATAAADR 24 
                                       5689999999.888888877776 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 1.3e-08
                       K_oxygenase 133 ltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifed 209
                                         v+ +d++g+++e++  ++vl+vG++p +P++ + le + +++ s+++l      ++++++a+vG+G  +ae+ + 
  gi|336252746|ref|YP_004595853.1| 121 IAVKPTDDSGDTREVRGDAIVLAVGSRPMVPPI-DGLE-DVDFLTSDDALFLD---EQPDELAIVGGGYIGAELGYF 192
                                       457777899**********************96.6688.6999****999987...799**************9887 PP

                       K_oxygenase 210 llrrqkkvelklvtrsealeplddspfv 237
                                         +  +  +++++ rse+l p +d +  
  gi|336252746|ref|YP_004595853.1| 193 FGALGT--DVSMIGRSERLIPGEDDDAS 218
                                       766555..89999999999998876654 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.067
                       K_oxygenase 132 lltveskdaegeeeelearnlvlgvGtep 160
                                         t e +d++ge  e+ea +l+l++G +p
  gi|336252746|ref|YP_004595853.1| 250 TITAEPSDDDGEPVEIEADELLLATGRRP 278
                                       23333334555555555555555555555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   2.3e-09   3.8e-06       1     150 [.       5     146 ..       5     164 .. 0.82
   2 ?   -0.8   0.1      0.38   6.2e+02       3      28 ..     178     203 ..     176     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.3e-09
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEEEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggiakgllvrEidalggliikaadkagiqfr 75 
                                       d++ViGgG +G+  A aaa +G++ + i   +  + +++ +C ps   i ++ l   +++  g+ + aad + +   
  gi|336252746|ref|YP_004595853.1|   5 DIVVIGGG-SGSQVATAAADRGLEAAVIerGPLGGACITRGCVPSKALIHRADLADAVRR-AGEFGIAADLQDV--- 76 
                                       799***99.6******************988999**************************.78999*******9... PP

                                       EESTTS-CCC-EEEEEE-HHHHHHHHHH..HHHTSTTEEEEES-EEEEEECTTEEEEEEET.TS-EEEECEEEE--T CS
                              GIDA  76 ilNrskGpavralraqvdrelyskevte..klenepnleiieeeveeliveekkvkgvvte.dgetikakavviatG 149
                                               a +++  ++    y+k+ ++  +le+++ + ++++e   ++  +  vk    + d ++++ +a+v+a G
  gi|336252746|ref|YP_004595853.1|  77 --------AYGEITDAIHDTVYEKAARQerALEESDSVALFRGEGRFVDEWTIAVKPTDDSgDTREVRGDAIVLAVG 145
                                       ........667776777777888777642279************999955223333322221456788889999999 PP

                                       T CS
                              GIDA 150 t 150
                                       +
  gi|336252746|ref|YP_004595853.1| 146 S 146
                                       8 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.38
                                       EEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLi 28 
                                        ++GgG  G e  +    lG +v +i
  gi|336252746|ref|YP_004595853.1| 178 AIVGGGYIGAELGYFFGALGTDVSMI 203
                                       79******************999998 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   4.3   0.00064         1       1      33 [.       5      36 ..       5      46 .. 0.87
   2 !    9.0   0.0   0.00041      0.66     150     204 ..     224     279 ..     157     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00064
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      D++ViG+G  G   A++aa++Gl+ av+e ++ 
  gi|336252746|ref|YP_004595853.1|  5 DIVVIGGGS-GSQVATAAADRGLEAAVIERGPL 36
                                      99****998.8888888************9985 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00041
                                       HHHTCTEEEEESEEEEEEEECTT.EEEEEEEEET.TTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 150 sarkagvdfqerteadeLivedg.rvtGavvenp.esgrevrirakavvlatgGfgr 204
                                       s+ +  +d+++ +ea+e+ + dg + +++++e++ ++g+ v+i+a+ ++latg  ++
  gi|336252746|ref|YP_004595853.1| 224 SL-ADYCDLYTGYEAAEVAQGDGgGSVTITAEPSdDDGEPVEIEADELLLATGRRPN 279
                                       33.3339*************887777777777778******************9998 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.1   5.2e-06    0.0084       1      54 [.       5      64 ..       5     110 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.2e-06
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee.......q 54
                                      D+vV+GGg+ G   A aAa +G + +++e+ +  G   t+g v++    + ++       +
  gi|336252746|ref|YP_004595853.1|  5 DIVVIGGGS-GSQVATAAADRGLEAAVIERGPLGGACITRGCVPSKALIHRADladavrrA 64
                                      9*******7.56667899999*********9977777888888776665555555555552 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 ?    4.1   0.2     0.023        37       2      30 ..       6      33 ..       5     105 .. 0.87
   2 !    9.5   0.1    0.0005      0.82       2      35 ..     177     210 ..     176     228 .. 0.86
   3 ?   -0.8   0.0      0.75   1.2e+03     131     165 ..     410     444 ..     401     447 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.023
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                      + viG G  G+++a+++a +gle  ++++
  gi|336252746|ref|YP_004595853.1|  6 IVVIGGGS-GSQVATAAADRGLEAAVIER 33
                                      78999998.**************999987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0005
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseeal 35 
                                       +a++G G +Ga++ + f + g +V ++ +se+ +
  gi|336252746|ref|YP_004595853.1| 177 LAIVGGGYIGAELGYFFGALGTDVSMIGRSERLI 210
                                       69**************************998765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.75
                                       GEEEEEE-SSTTT--EEEEEE-TT--HHHHHHHHH CS
                           3HCDH_N 131 rviglHFfnPpplmkLvEvvrgekTseetvatvve 165
                                       +++g H + P     + Evv + ++ + tv++v +
  gi|336252746|ref|YP_004595853.1| 410 EILGCHVVGPQASTLIQEVVVAMDSGDGTVDDVAD 444
                                       58999*****9999999*********999999875 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 ?   10.9   0.1   0.00015      0.25       3      47 ..     177     221 ..     175     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                                       EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS- CS
                    UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiy 47 
                                       ++++G GY+G+  +  + ++g +v ++  +e+ +     + + ++
  gi|336252746|ref|YP_004595853.1| 177 LAIVGGGYIGAELGYFFGALGTDVSMIGRSERLIPGEDDDASAVV 221
                                       68**********************999988887766666655555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.5   0.00066       1.1       1      36 [.       5      39 ..       5      56 .. 0.93
   2 ?    4.6   0.2     0.013        21       2      48 ..     177     225 ..     176     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00066
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                      d+v+iGGG  G+ +A ++a rg   +++e+g  +g ga
  gi|336252746|ref|YP_004595853.1|  5 DIVVIGGG-SGSQVATAAADRGleAAVIERG-PLG-GA 39
                                      8******9.7*********************.777.54 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.013
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl 48 
                                       ++i+GGG+iG+   y+  + g  V  + +++++  g    +s++++ +l
  gi|336252746|ref|YP_004595853.1| 177 LAIVGGGYIGAELGYFFGALGtdVSMIGRSERLIPGEDDDASAVVTDSL 225
                                       68*********99999866677888887776655577777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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):              11  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3274.19
//
Query:       gi|336252747|ref|YP_004595854.1|  [L=270]
Description: 2,5-didehydrogluconate reductase [Halopiger xanaduensis SH-6]
Scores for 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-52  178.3   0.0    2.2e-50  171.5   0.0    2.0  1  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
      0.029   14.7   0.1        1.5    9.2   0.0    2.7  2  Ish1          Putative stress-responsive nuclear envelope pro


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 !  171.5   0.0   2.5e-54   2.2e-50       2     293 ..       9     255 ..       8     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: 171.5 bits;  conditional E-value: 2.5e-54
                                       EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTS CS
                      Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeik 78 
                                       +glGt +       ++e+  e +r+ale G++++DtA+vY   ++ee++Ge + ++ ++r++++++tK      +++
  gi|336252747|ref|YP_004595854.1|   9 IGLGTYSSD-----NREQWTENVRTALEVGYRHVDTAQVY---ENEEYVGEGIDQADVDRDDIFLSTKT----VHHD 73 
                                       777777666.....57999*********************...**************************....8999 PP

                                       SSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTTT- CS
                      Aldo_ket_red  79 sglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkkkv 155
                                       +  + e++ e+++  l+rLg+d vDll++H+p   ++  ee+l + ++ +++Gk r++G+Snf+ e l++a +  + 
  gi|336252747|ref|YP_004595854.1|  74 VPPESEQVPEAIDGCLERLGVDAVDLLYVHWPSGIYE-HEEILPYYDDAYEAGKTRNVGLSNFTPELLDEAFEVLEA 149
                                       999999*******************************.*************************************** PP

                                       -EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHH CS
                      Aldo_ket_red 156 kivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeel 232
                                       ++ a q+e+++l  l + +l+  +++++  ++ayspl++G+                                ++e+
  gi|336252747|ref|YP_004595854.1| 150 PLFAHQAEMHPL--LPQDELVAHAQEHDYWFVAYSPLAQGAVF-----------------------------DVPEI 195
                                       ************..***************************99.............................5799* PP

                                       HHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHHH CS
                      Aldo_ket_red 233 selakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldell 293
                                       +e+a++h+ ++aq++l+++l    ++ vip+as+ ++le nl+a +l+l+ee+ + +d+++
  gi|336252747|ref|YP_004595854.1| 196 REVAEKHDATPAQVSLAWLLD-HDNVAVIPKASSRDHLEGNLAAADLELDEEDRELIDSID 255
                                       ********************6.566789******************************985 PP

>> Ish1  Putative stress-responsive nuclear envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.019   1.7e+02      28      37 .]     165     174 ..     159     174 .. 0.93
   2 ?    9.2   0.0   0.00017       1.5      11      30 ..     212     232 ..     211     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.019
                              Ish1  28 deLlklardn 37 
                                       deL+++a+++
  gi|336252747|ref|YP_004595854.1| 165 DELVAHAQEH 174
                                       9*******96 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00017
                              Ish1  11 kWLdshGip.vskaastRdeL 30 
                                       +WL +h  + v ++as+Rd+L
  gi|336252747|ref|YP_004595854.1| 212 AWLLDHDNVaVIPKASSRDHL 232
                                       7******66699*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1977.56
//
Query:       gi|336252748|ref|YP_004595855.1|  [L=189]
Description: DoxX family protein [Halopiger xanaduensis SH-6]
Scores for 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   36.7  12.9    4.9e-09   36.7  12.9    2.2  2  DoxX        DoxX
    0.00032   20.7   5.0    0.00051   20.0   5.0    1.3  1  DoxD        TQO small subunit DoxD
  ------ inclusion threshold ------
        1.1    8.0   5.5          2    7.2   5.5    1.5  1  VKG_Carbox  Vitamin K-dependent gamma-carboxylase


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7  12.9   8.2e-13   4.9e-09       2      81 ..      34     129 ..      33     133 .. 0.85
   2 ?    0.1   0.3       0.2   1.2e+03      32      63 ..     132     163 ..     127     165 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 8.2e-13
                              DoxX   2 llllRlllgvlfiahGlqkltg..............fglegtaaslaalglpp..pellaylaalvElvgglllllG 62 
                                       +l+lRl++g+ f+++Gl+kl +               + +  ++ ++ +g +p   e+  +++ +++++ gl+ll+G
  gi|336252748|ref|YP_004595855.1|  34 VLALRLMMGYAFLYAGLGKLLAaepfsaegfllhgvNQASPLVGLFTWMGTTPwfVEIVNVAVPFGQVAIGLGLLVG 110
                                       79*******************998866666666555445558888887777777789999***************** PP

                              DoxX  63 lltRlaAlalavtllvatl 81 
                                        ++RlaA++ a ++ +  +
  gi|336252748|ref|YP_004595855.1| 111 AMVRLAAFFGATMMFMFYF 129
                                       **************98665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.2
                              DoxX  32 slaalglpppellaylaalvElvgglllllGl 63 
                                       + +  gl   +++ +l+ l+  ++g + +lGl
  gi|336252748|ref|YP_004595855.1| 132 WSVEHGLINGDFAYLLVFLAVAAFGAGRILGL 163
                                       55566777777777777777777888777776 PP

>> DoxD  TQO small subunit DoxD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   5.0   8.5e-08   0.00051       1     146 [.      33     169 ..      33     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.5e-08
                              DoxD   1 fllilRlalgliflsagirkkvlkpakLdPnsssyvGgkliefLpqasiikdlleivvlnrsll..vtalvlftlvE 75 
                                       f+l lRl++g  fl+ag+ k +  +    P s++  G+ l + + qas++ +l+  + +++ +   v+  v f+   
  gi|336252748|ref|YP_004595855.1|  33 FVLALRLMMGYAFLYAGLGKLLAAE----PFSAE--GF-LLHGVNQASPLVGLFTWMGTTPWFVeiVNVAVPFG--Q 100
                                       7899*************98877766....66554..44.477799*********99999988752255566677..7 PP

                              DoxD  76 iivGlllliGlltRlsslvafalalgialsayWlgstcedEyqiglllvaaelvliltgsgkl.slDylllk 146
                                       + +Gl ll+G + Rl+++  +++ + +   a W     + + + + llv  ++   + g+g++ +lD+l+ +
  gi|336252748|ref|YP_004595855.1| 101 VAIGLGLLVGAMVRLAAFFGATMMFMFY-FANWSVEHGLINGDFAYLLVFLAVA--AFGAGRIlGLDALIER 169
                                       777888899********87777766555.5999776666666777777666554..3455555599999876 PP

>> VKG_Carbox  Vitamin K-dependent gamma-carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.5   0.00033         2     126     228 ..      25     133 ..       6     158 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00033
                        VKG_Carbox 126 kkksvprwnllilkfqlfivYfyAglaKlns.dWlegaaplklwlfskfkll.ligelleeeidalivswfgllfDl 200
                                       k +s+++w +l l++++   ++yAgl Kl + + +++   l   + + + l+ l++ + +  +   iv ++  +  +
  gi|336252748|ref|YP_004595855.1|  25 KAHSLSAWFVLALRLMMGYAFLYAGLGKLLAaEPFSAEGFLLHGVNQASPLVgLFTWMGTTPWFVEIVNVAVPFGQV 101
                                       67899***********************8651444444443334555555553444466666666666666666778 PP

                        VKG_Carbox 201 livflLllkk.tRilall...lvvvFhllnsi 228
                                       +i+  Ll+ + +R+ a++   ++++F + n+ 
  gi|336252748|ref|YP_004595855.1| 102 AIGLGLLVGAmVRLAAFFgatMMFMFYFANWS 133
                                       88887777651566666522245566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1482.26
//
Query:       gi|336252749|ref|YP_004595856.1|  [L=151]
Description: hypothetical protein Halxa_1344 [Halopiger xanaduensis SH-6]
Scores for complete 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   37.5   0.0    3.1e-09   36.7   0.0    1.4  1  HTH_20    Helix-turn-helix domain
    0.00018   21.3   0.0    0.00037   20.3   0.0    1.5  1  TrmB      Sugar-specific transcriptional regulator TrmB
    0.00088   19.0   0.2     0.0026   17.5   0.0    1.9  3  HTH_IclR  IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.039   13.8   0.0      0.077   12.9   0.0    1.5  1  MarR_2    MarR family
       0.06   13.2   0.1      0.092   12.6   0.1    1.3  1  DUF742    Protein of unknown function (DUF742)
       0.08   13.0   0.0       0.18   11.9   0.0    1.6  1  HTH_7     Helix-turn-helix domain of resolvase
       0.11   12.5   0.0       0.22   11.5   0.0    1.5  1  HTH_11    HTH domain
       0.12   12.3   0.0       0.22   11.4   0.0    1.5  1  HTH_5     Bacterial regulatory protein, arsR family
       0.14   11.7   0.0       0.33   10.5   0.0    1.8  1  HTH_24    Winged helix-turn-helix DNA-binding


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 !   36.7   0.0   1.6e-12   3.1e-09       1      55 [.      15      67 ..      15      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.6e-12
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      d+i++AL++   ++il+ L  +e++t++e+a++ +++ +t ++ ++ L +  Lv 
  gi|336252749|ref|YP_004595856.1| 15 DRIIDALDDDACCDILSVL--EEPMTVKEIADEAEVPLSTTYKKVDRLTDTSLVV 67
                                      689****************..****************************998864 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.9e-07   0.00037      19      54 ..      33      68 ..      29      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.9e-07
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                       ++p+t++eia e++vp s+ Y+ + +L d  lV  
  gi|336252749|ref|YP_004595856.1| 33 LEEPMTVKEIADEAEVPLSTTYKKVDRLTDTSLVVE 68
                                      589***************************999865 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 ?   -2.5   0.0       2.3   4.6e+03       1       7 [.       7      13 ..       7      24 .. 0.71
   2 !   17.5   0.0   1.3e-06    0.0026      15      48 ..      33      66 ..      28      69 .. 0.83
   3 ?   -3.8   0.0       6.2   1.2e+04      16      24 ..     113     121 ..     111     121 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.3
                                      HHHHHHH CS
                          HTH_IclR  1 sldRala 7 
                                      s+dRa++
  gi|336252749|ref|YP_004595856.1|  7 SVDRAAD 13
                                      6888875 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.3e-06
                                      TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                        +++t++e+A+++ +p St++  +  L+   +v
  gi|336252749|ref|YP_004595856.1| 33 LEEPMTVKEIADEAEVPLSTTYKKVDRLTDTSLV 66
                                      6799******************988888877766 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 6.2
                                       BSS-BHHHH CS
                          HTH_IclR  16 pqeltlsel 24 
                                        +e +lsel
  gi|336252749|ref|YP_004595856.1| 113 ERESGLSEL 121
                                       455678886 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   3.9e-05     0.077      18      55 ..      35      74 ..      20      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                                      TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE....E CS
                            MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaGLverr....p 55
                                      ++  +tv+e+a++  ++ s++ + ++rL +  Lv+++    p
  gi|336252749|ref|YP_004595856.1| 35 EP--MTVKEIADEAEVPLSTTYKKVDRLTDTSLVVEEiqlrP 74
                                      34..9*****************************88755534 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.6e-05     0.092      43      86 ..      24      67 ..       6      84 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                            DUF742 43 pehrailrLcreplsVaelaAelklPvgvvrvLlsdLldagllt 86
                                      + + +il   +ep++V e+a e ++P++++   +  L d+ l++
  gi|336252749|ref|YP_004595856.1| 24 DACCDILSVLEEPMTVKEIADEAEVPLSTTYKKVDRLTDTSLVV 67
                                      56789***********************9988888888877665 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 ?   11.9   0.0   9.2e-05      0.18      17      41 ..      32      56 ..      26      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.2e-05
                                      STTTT--STTTSSSS---SSSS--S CS
                             HTH_7 17 LleeGisiskIAkevnisRsTvYRy 41
                                       lee++++++IA+e  +  sT Y++
  gi|336252749|ref|YP_004595856.1| 32 VLEEPMTVKEIADEAEVPLSTTYKK 56
                                      58*********************98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.22       8      51 ..      32      75 ..      28      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                            HTH_11  8 lLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg...vpIesepg 51
                                       L   ++p++ +e+A+e +v  +t ++ +++L+++     +I+ +pg
  gi|336252749|ref|YP_004595856.1| 32 VL---EEPMTVKEIADEAEVPLSTTYKKVDRLTDTSlvvEEIQLRPG 75
                                      44...788************************999855555555555 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 ?   11.4   0.0   0.00011      0.22       9      32 ..      30      53 ..      23      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                      HHHTTSSEEHHHHHHHHTS-HHHH CS
                             HTH_5  9 klLaegelcvcelaeelglsqstv 32
                                       ++ e++++v e+a+e +++ st+
  gi|336252749|ref|YP_004595856.1| 30 LSVLEEPMTVKEIADEAEVPLSTT 53
                                      467899*************99986 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   0.00017      0.33       8      43 ..      29      62 ..      16      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                            HTH_24  8 ILelLqknprisqreLAerlglSpstvnrrlkrLee 43
                                      IL++L++   ++ +e+A++  +++st+ + ++rL++
  gi|336252749|ref|YP_004595856.1| 29 ILSVLEE--PMTVKEIADEAEVPLSTTYKKVDRLTD 62
                                      6777776..89***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.34
# Mc/sec: 1321.68
//
Query:       gi|336252750|ref|YP_004595857.1|  [L=280]
Description: Rhodanese-like protein [Halopiger xanaduensis SH-6]
Scores for 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  140.9   0.0    8.4e-21   74.5   0.0    2.1  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   4.7e-25   8.4e-21       3     106 ..      22     135 ..      20     136 .. 0.76
   2 !   64.7   0.0   5.4e-22   9.7e-18       4     106 ..     168     270 ..     165     271 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 4.7e-25
                         Rhodanese   3 kelkellekgkva....llDvRppeeYek.ghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvv 70 
                                       ++l+++le+++ +    ++DvR+++eY+  gh+pgA+n+++d++++++ +++  l   ++++el    gi++++tvv
  gi|336252750|ref|YP_004595857.1|  22 DWLAARLEAEDEDpqvrVVDVRDAWEYDGiGHVPGAINIPFDSYRDESDVDRGTLPGADAFAELlseaGISPDDTVV 98 
                                       56666665555445566**********************6666666665555555555555555555********** PP

                         Rhodanese  71 vycdgggr.aaaaaallkklGykn.vsvldGGfkawke 106
                                        y+d+ g  aa+   ++ ++G+ + v++ldG ++aw++
  gi|336252750|ref|YP_004595857.1|  99 AYDDTHGVfAARFVLTALEYGH-DdVRLLDGDYSAWNR 135
                                       ********88888666666**5.55***********97 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 5.4e-22
                         Rhodanese   4 elkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel.gidnkktvvvycdgggra 79 
                                        +++ le+g+  ++D+R+++e+e+ h+pgAv + ++   + + +  +  + +e+lle+ gi++++++v+yc+++ r 
  gi|336252750|ref|YP_004595857.1| 168 AVEAALERGA-LFVDTREDHEFEEAHLPGAVRFDWREVIDDETRRLKPEDELEALLEDhGITPDREIVLYCNTARRI 243
                                       5677778887.5*********************99888888888888888888888888*****************7 PP

                         Rhodanese  80 aaaaallkklGyknvsvldGGfkawke 106
                                       + ++  lk+lGy++v +++G++++w e
  gi|336252750|ref|YP_004595857.1| 244 SHTYVVLKALGYEDVAFYEGSLTEWLE 270
                                       777889999**999***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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 0.21s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 2417.77
//
Query:       gi|336252751|ref|YP_004595858.1|  [L=287]
Description: Rhodanese-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-36  125.6   0.5    6.7e-19   68.4   0.0    2.1  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.2   3.5e-19   6.3e-15       2     106 ..      13     126 ..      12     127 .. 0.79
   2 !   68.4   0.0   3.7e-23   6.7e-19       3     105 ..     157     274 ..     156     276 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 3.5e-19
                         Rhodanese   2 akelkellekgkva.....llDvR.ppeeYekghIpgAvnvskdtl.srakkseapllelpeellel.gidnkktvv 70 
                                       a++++e+l++ + +     l+ v  + e+Y++ h pgA+ ++++t+  ++++++   +e++e+ll   g+++++tvv
  gi|336252751|ref|YP_004595858.1|  13 ADWVEERLDEFQDDgsdlrLIEVDvDTEAYDEEHAPGAIGFNWETQlQDQTQRDILEKEDFEDLLGShGVSEDDTVV 89 
                                       67888888666656555667777755556************76654155566667777888888888********** PP

                         Rhodanese  71 vycdgggr.aaaaaallkklGykn.vsvldGGfkawke 106
                                       +y+d+++  aa a++++k++G+ + v++ldGG + w e
  gi|336252751|ref|YP_004595858.1|  90 LYGDNSNWfAAYAYWQFKYYGH-DdVKLLDGGREYWLE 126
                                       ********99999********5.55*******999976 PP

  == domain 2  score: 68.4 bits;  conditional E-value: 3.7e-23
                         Rhodanese   3 kelkellekgkvallDvRppeeY..............ek.ghIpgAvnvskdtlsrakkseapllelpeellelgid 64 
                                       +++++ +e+g   l+DvR+peeY              ++ ghIpgA n+s+   ++ + + +++ el + ++e+gid
  gi|336252751|ref|YP_004595858.1| 157 EDVENAIERGV-PLVDVRSPEEYsgevlappglnetaQRgGHIPGAKNISWAAVTNDDGTFKDSEELEDLYAEEGID 232
                                       67888888875.4**********999999999999995559************************************ PP

                         Rhodanese  65 nkktvvvycdgggraaaaaallkk.lGyknvsvldGGfkawk 105
                                        ++t v yc+ g+r++ a+ +l + lGy++  ++dG++++w 
  gi|336252751|ref|YP_004595858.1| 233 GDETTVAYCRIGERSSVAWFALHElLGYEDTVNYDGSWTEWG 274
                                       **************88888877766**999***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2199.19
//
Query:       gi|336252752|ref|YP_004595859.1|  [L=175]
Description: hypothetical protein Halxa_1347 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   18.4   0.0     0.0026   17.6   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0024   17.9   0.1      0.029   14.5   0.0    2.2  2  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.062   13.0   0.1        3.8    7.3   0.2    2.4  2  HTH_DeoR  DeoR-like helix-turn-helix domain
      0.079   12.6   4.2        0.2   11.3   0.5    2.4  2  RP-C      Replication protein C N-terminal domain


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 !   17.6   0.0   5.8e-07    0.0026      12      63 ..      24      76 ..      23      80 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.8e-07
                                      CHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                              TrmB 12 kvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63
                                      +vY +L+ + ++a+a + ae ++ +++ +  +L++L+++G+ +r ++rp  Yr
  gi|336252752|ref|YP_004595859.1| 24 RVYDVLVgTTDSASAGQFAEWAECSENGARAALEQLVEMGIATRTDSRPATYR 76
                                      79**************************************************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 !   14.5   0.0   6.4e-06     0.029      14      60 ..      24      71 ..      20      72 .. 0.88
   2 ?    1.0   0.0     0.098   4.4e+02       8      20 ..      96     108 ..      87     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.4e-06
                                      HHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 14 rilraL.araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      r+++ L  + + ++a+++ae  ++s n ++  L++L+e g+ ++++++
  gi|336252752|ref|YP_004595859.1| 24 RVYDVLvGTTDSASAGQFAEWAECSENGARAALEQLVEMGIATRTDSR 71
                                      6677777778999****************************9999887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.098
                                       S-HHHHHHHHHHS CS
                            HTH_20   8 ahPvRrrilraLa 20 
                                       a++ R+r++ +La
  gi|336252752|ref|YP_004595859.1|  96 ASELRARLEELLA 108
                                       3455555555553 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 ?    3.0   0.0     0.019        85      16      47 ..      37      68 ..      29      71 .. 0.83
   2 ?    7.3   0.2   0.00085       3.8      29      41 ..     149     161 ..     144     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.019
                          HTH_DeoR 16 sveelvellgvSeaTiRRDLneLeeqglltRt 47
                                      s  + +e  + Se+ +R  L++L+e g+ tRt
  gi|336252752|ref|YP_004595859.1| 37 SAGQFAEWAECSENGARAALEQLVEMGIATRT 68
                                      556677778899999***************97 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00085
                          HTH_DeoR  29 aTiRRDLneLeeq 41 
                                        TiRRD++ L+ +
  gi|336252752|ref|YP_004595859.1| 149 RTIRRDITVLQRA 161
                                       5*******99875 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 ?   11.3   0.5   4.4e-05       0.2      73     140 ..      37     107 ..      34     118 .. 0.71
   2 ?    2.4   0.2     0.025   1.1e+02     149     169 ..     144     164 ..     131     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.4e-05
                              RP-C  73 sNaqLsralglsestlrrhlaaLveaGliirrDs..pngkR...yarrdreGeieeAfGfdLsPllaRaeEle 140
                                       s+ q +++   se   r  l +Lve+G+ +r Ds  ++++R   y r++r  ++  A   d s l+aR+eEl 
  gi|336252752|ref|YP_004595859.1|  37 SAGQFAEWAECSENGARAALEQLVEMGIATRTDSrpATYRRnpsYFRWKRIERL--ADDHDASELRARLEELL 107
                                       788999999*************************54477774444444433333..33446666666666665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.025
                              RP-C 149 erralrrlrerltllrrdiak 169
                                       +  ++r++r+++t+l+r+++ 
  gi|336252752|ref|YP_004595859.1| 144 DLSEWRTIRRDITVLQRAVQR 164
                                       56789999********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1407.52
//
Query:       gi|336252753|ref|YP_004595860.1|  [L=144]
Description: hypothetical protein Halxa_1348 [Halopiger xanaduensis SH-6]
Scores for 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:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1066.90
//
Query:       gi|336252754|ref|YP_004595861.1|  [L=79]
Description: hypothetical protein Halxa_1349 [Halopiger xanaduensis SH-6]
Scores for 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:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 627.34
//
Query:       gi|336252755|ref|YP_004595862.1|  [L=211]
Description: hypothetical protein Halxa_1350 [Halopiger xanaduensis SH-6]
Scores for 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   20.0   1.6       0.03   14.7   0.3    2.3  2  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
      0.082   13.3   2.2         15    6.1   0.1    3.1  3  HEAT_2        HEAT repeats
        1.4    9.1   4.3          1    9.5   0.4    2.5  2  TPR_7         Tetratricopeptide repeat


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 !   14.7   0.3   5.1e-06      0.03      90     133 ..      43      86 ..       7     104 .. 0.83
   2 !    4.6   0.0    0.0068        41      66     111 ..     159     204 ..     146     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.1e-06
                                       HHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  90 egayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerl 133
                                       e   ++e  + +++++ a++e ++ a++ f++ a++E++H e+ 
  gi|336252755|ref|YP_004595862.1|  43 EATADAEHAAWQTFSQWADDEDHDAAREAFETTADEEQGHFETV 86 
                                       55556777778889999999999999999999999999997765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0068
                                       SBBS-------TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTT CS
                      Rubrerythrin  66 ekvreyaeakpkflttaknLeeaiegayaeeeemyrfyeelaekeg 111
                                       ++   ++e  +++ + +++ + a+e a+ + e +y +y e++e +g
  gi|336252755|ref|YP_004595862.1| 159 AQLERATELLEDVCESDEDWDRAEEAATGAIEAAYDEYVENMEAMG 204
                                       5666788888899999999999******************999877 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2    0.0071        43      60      82 ..      49      71 ..       5      76 .. 0.85
   2 ?    0.8   0.0      0.11   6.7e+02      22      42 ..      88     109 ..      75     134 .. 0.61
   3 ?    6.1   0.1    0.0025        15      60      85 ..     161     186 ..     149     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0071
                            HEAT_2 60 dpealpaLkellddddddvvRea 82
                                      +++a++   +++dd+d+d  Rea
  gi|336252755|ref|YP_004595862.1| 49 EHAAWQTFSQWADDEDHDAAREA 71
                                      47799999*****9999999987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                            HEAT_2  22 raLgrignpea....lpaLvelled 42 
                                       ++Lg   n+e+    +paL+e+l+ 
  gi|336252755|ref|YP_004595862.1|  88 EELG---NEEYepqeVPALHEYLRG 109
                                       3333...332222236666666643 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0025
                            HEAT_2  60 dpealpaLkellddddddvvReaAae 85 
                                       +++a ++L++ + +d+d+++ e+Aa 
  gi|336252755|ref|YP_004595862.1| 161 LERATELLEDVCESDEDWDRAEEAAT 186
                                       58899999999999999888887764 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.3      0.16   9.8e+02      10      32 ..      60      80 ..      58      97 .. 0.72
   2 ?    9.5   0.4   0.00017         1       4      34 ..     167     197 ..     164     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.16
                             TPR_7 10 srlGdyeeAielyeqsLaltkdp 32
                                       ++ d++ A e +e     ++++
  gi|336252755|ref|YP_004595862.1| 60 ADDEDHDAAREAFET--TADEEQ 80
                                      567788888888887..555544 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00017
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkdped 34 
                                        L ++++++ d+++A+e  + +++ ++d+++
  gi|336252755|ref|YP_004595862.1| 167 LLEDVCESDEDWDRAEEAATGAIEAAYDEYV 197
                                       5899*****************9999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1522.48
//
Query:       gi|336252756|ref|YP_004595863.1|  [L=173]
Description: hypothetical protein Halxa_1351 [Halopiger xanaduensis SH-6]
Scores for 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  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); 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:                         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 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1266.40
//
Query:       gi|336252757|ref|YP_004595864.1|  [L=90]
Description: hypothetical protein Halxa_1352 [Halopiger xanaduensis SH-6]
Scores for 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  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 687.25
//
Query:       gi|336252758|ref|YP_004595865.1|  [L=277]
Description: hydroxyethylthiazole kinase [Halopiger xanaduensis SH-6]
Scores for complete 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  224.4   1.4    1.6e-66  224.2   1.4    1.0  1  HK            Hydroxyethylthiazole kinase family
    1.6e-06   27.8   0.6    2.1e-06   27.4   0.6    1.1  1  Carb_kinase   Carbohydrate kinase
    1.9e-05   24.2   0.2    2.9e-05   23.6   0.2    1.3  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
      0.038   13.4   0.0      0.056   12.9   0.0    1.4  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


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 !  224.2   1.4   3.5e-70   1.6e-66       1     244 [.      16     260 ..      16     262 .. 0.96

  Alignments for each domain:
  == domain 1  score: 224.2 bits;  conditional E-value: 3.5e-70
                                       HHHHHHH--EEEEE--TTTHHHHHHHHHHHT-EEEE--STTTHHHHHHTSSEEEEE-TT--HHHHHHHHHHHHHHHH CS
                                HK   1 lkklreksPlvhhiTNkVaqnfsANvllAlgaSPimseaeeEvselakianaLllNiGtleekaiealkaAvksake 77 
                                       l++++e +Plvh++TN+V++n++AN +l   a P+m+++e ++ e+a++a+a+l N+G + +++++a+  A+++a+e
  gi|336252758|ref|YP_004595865.1|  16 LETIAESEPLVHSVTNEVTMNDVANLILHWDALPVMADSEGDAGEMAELADAILFNTGQVPDRRVDAMHDAAETANE 92 
                                       67899************************************************************************ PP

                                       TT--EEEE-TTBTTBHHHHHHHHHHHHHS--SEEEEEHHHHHHHHTSSCCSCSSSSSS-SHHHHHHHHHHHHHHTSE CS
                                HK  78 vnrPvvlDPVgvgAtelRrelalellkevklavikGNasEilslaglelkvkGvDskeaataavaavqkvAqklrvv 154
                                       +++P+vlDPVgvgAt++Rr++a++ll+++ +avikGN +Ei +lag+e +vkGv+s    +++  +++++A+ ++++
  gi|336252758|ref|YP_004595865.1|  93 LGTPIVLDPVGVGATATRRSVAEDLLESTDFAVIKGNYGEISALAGVEAEVKGVESVGDYEEIEDTARSLAESTGAI 169
                                       *********************************************************999999999*********** PP

                                       EEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HHHH.HHHTTH CS
                                HK 155 vvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgkeaaa.rsegsg 230
                                       vv++G  Dvv+    vy l  G+e+l+ ++++GC+ g ++aaf +  +d+ +aa+++ l++ +Ag++aa+   +g++
  gi|336252758|ref|YP_004595865.1| 170 VVASGVEDVVATEDAVYRLAVGHEMLSTVVGTGCMVGGTIAAFRGALEDDFTAALHGALAFGLAGERAAEtDYRGPA 246
                                       *****************************************************************87776156788* PP

                                       HHHHHHHHHHHH-- CS
                                HK 231 sFqvelldalsqlt 244
                                       s+++++ d ++ l+
  gi|336252758|ref|YP_004595865.1| 247 SYRTAFHDTVAGLS 260
                                       ******99988775 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.6   4.7e-10   2.1e-06      60     231 ..      57     243 ..      17     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.7e-10
                                       ...--SSS-SEEEE-TT-SSSHCHHH...HCHHHCCCCS-EEEEGGGGGSGGGG.......TTTTSSEEEE--HHHH CS
                       Carb_kinase  60 kileklerldavviGpGLgrdekikk...lleevlekdeplviDAdgLnllaqkne....lserkaeviLTPhkkEf 129
                                          e +e +da++   G   d ++++   + e + e   p+v+D  g    a        l e +   ++  + +E 
  gi|336252758|ref|YP_004595865.1|  57 DAGEMAELADAILFNTGQVPDRRVDAmhdAAETANELGTPIVLDPVGVGATATRRSvaedLLESTDFAVIKGNYGEI 133
                                       34567777888888888777777777444666666666789999888887777766666677788888999999999 PP

                                       HHHCTTTCH........HCCSHHHHHHHHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG.-STTHHHHHHHHH CS
                       Carb_kinase 130 krLlkaivk........keddrlelarelaqklnavvllkgekdvivspegevlinstgssal.akGGsGDvLaGli 197
                                       + L+++  +          ++  ++ar la+  +a+v+  g +dv+++ e++v+ +  g  +l ++ G+G    G i
  gi|336252758|ref|YP_004595865.1| 134 SALAGVEAEvkgvesvgDYEEIEDTARSLAESTGAIVVASGVEDVVAT-EDAVYRLAVGHEMLsTVVGTGCMVGGTI 209
                                       9999988888889987777788899***********************.899999999987652679********** PP

                                       HHHHHCTSSHHHHHHHHHHHHHHHHHHHCCCT-T CS
                       Carb_kinase 198 galLaqneasyeaaiaaawlhgaasdeaaekkgv 231
                                       +a+    e+ + aa+ +a + g a+++aae  ++
  gi|336252758|ref|YP_004595865.1| 210 AAFRGALEDDFTAALHGALAFGLAGERAAETDYR 243
                                       *****************************99877 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.2   6.5e-09   2.9e-05      75     225 ..      83     228 ..      60     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.5e-09
                                       HHHHHHHHHHTTSSEEEE---S.SCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT..---S......SHH CS
                      Phos_pyr_kin  75 ievvaeklkkykvpvVlDPVmv.aksgselleeeavealkeeLlplatvitPNlpEaeaLlg..ekik......tee 142
                                       ++  ae+ ++ ++p+VlDPV v a+  ++ ++e+ +e+          vi  N  E++aL+g   ++k      + e
  gi|336252758|ref|YP_004595865.1|  83 MHDAAETANELGTPIVLDPVGVgATATRRSVAEDLLEST------DFAVIKGNYGEISALAGveAEVKgvesvgDYE 153
                                       5556788888999*******8724444555555555544......46899************663333555555888 PP

                                       HHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHH.HCTSSHH CS
                      Phos_pyr_kin 143 dmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaael.akgesle 218
                                       ++++ a++l++ +   V+  G          +dv+ +++ v++l   +   ++  GtGC +   iaa   a +++  
  gi|336252758|ref|YP_004595865.1| 154 EIEDTARSLAESTGAIVVASGV---------EDVVATEDAVYRLAVGHEMLSTVVGTGCMVGGTIAAFRgALEDDFT 221
                                       9999999999976555554444.........399999999999988888889***************8625566677 PP

                                       HHHHHHH CS
                      Phos_pyr_kin 219 eAvkkAk 225
                                        A++ A 
  gi|336252758|ref|YP_004595865.1| 222 AALHGAL 228
                                       7766665 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 ?   12.9   0.0   1.3e-05     0.056      62     114 ..      77     122 ..      44     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                                       TCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHH CS
                      AP_endonuc_2  62 earreesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaesln 114
                                       ++r    vda+++a+e+a++LG+p++  ++G    g+  ++++  e l es +
  gi|336252758|ref|YP_004595865.1|  77 DRR----VDAMHDAAETANELGTPIVLDPVG---VGATATRRSVAEDLLESTD 122
                                       345....*******************99999...6666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2149.98
//
Query:       gi|336252759|ref|YP_004595866.1|  [L=222]
Description: Thiamine-phosphate pyrophosphorylase [Halopiger xanaduensis SH-6]
Scores for 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-62  209.7   4.0    2.5e-62  209.4   4.0    1.1  1  TMP-TENI  Thiamine monophosphate synthase
    2.9e-07   30.2   8.4    3.8e-07   29.8   8.4    1.1  1  NMO       Nitronate monooxygenase
    0.00017   21.0   4.4     0.0004   19.8   4.4    1.6  1  ThiG      Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
      0.012   14.8   1.4      0.021   14.1   1.4    1.3  1  DHO_dh    Dihydroorotate dehydrogenase
      0.079   12.1   0.6       0.17   11.0   0.6    1.5  1  DUF561    Protein of unknown function (DUF561)


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 !  209.4   4.0     7e-66   2.5e-62       2     181 .]       9     191 ..       8     191 .. 0.97

  Alignments for each domain:
  == domain 1  score: 209.4 bits;  conditional E-value: 7e-66
                          TMP-TENI   2 ylvtdskldkneellevveealkggvtlvqlRekeldarellelaeklaalcrkygvpliindrvdlalavgadgvH 78 
                                       ylvt+++l ++++ le+ve+a++ggv++vqlRek+ dar+++el  ++++l++++gv+li+ndrvd+a a++adgvH
  gi|336252759|ref|YP_004595866.1|   9 YLVTQASLSEGRSTLEIVEAAIAGGVDAVQLREKDTDARRRYELGLEVRELTAEAGVDLIVNDRVDIARAIDADGVH 85 
                                       9**************************************************************************** PP

                          TMP-TENI  79 lgqddlpvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkda...eplgleglkelaealeiP 152
                                       +gq+dlpva ar llg+d+i+G S+++ +ea+eaea+gadY+gvG+i+ T++K+     + +g e+++++a+a++iP
  gi|336252759|ref|YP_004595866.1|  86 VGQSDLPVAVARGLLGSDAIVGCSASTVAEAREAEAEGADYLGVGTIYGTTSKDVDpeqDGVGPERVAAIADAVSIP 162
                                       *****************************************************8654336799************** PP

                          TMP-TENI 153 vvaiGGitlenvaevleagadgvavvsai 181
                                       +v iGGit++n+ +v+eaga gvav+s+i
  gi|336252759|ref|YP_004595866.1| 163 IVGIGGITADNAGSVVEAGATGVAVISEI 191
                                       ***************************97 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   8.4   1.1e-10   3.8e-07      78     234 ..      43     200 ..      20     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.1e-10
                               NMO  78 draekykkeleeaalelnieegvr..fyrkvevvldekvevvsfgfglpteevvarlkeagvvliptissvkearkv 152
                                       d  ++ + el+ +  el  e gv      +v++     ++ v +g  + +  v   l  +++++  ++s+v ear++
  gi|336252759|ref|YP_004595866.1|  43 DTDARRRYELGLEVRELTAEAGVDliVNDRVDIARAIDADGVHVGQSDLPVAVARGLLGSDAIVGCSASTVAEAREA 119
                                       33345677788888899999999988889999999999999****99999*************************** PP

                               NMO 153 earGaDalivqGpeaGGhqGtpevgd..kglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLl 227
                                       ea GaD l v G   G    ++++++  +g  + v+ ++dav+iP++  GGi  + +   +  +GA gv++ +   +
  gi|336252759|ref|YP_004595866.1| 120 EAEGADYLGV-GTIYGTTSKDVDPEQdgVGPER-VAAIADAVSIPIVGIGGIT-ADNAGSVVEAGATGVAVISEITA 193
                                       *******987.6666666665555543255555.789**************96.567789***********999988 PP

                               NMO 228 tkesdak 234
                                       +++  a 
  gi|336252759|ref|YP_004595866.1| 194 ADDPRAA 200
                                       8887664 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   4.4   1.1e-07    0.0004     164     226 ..     149     210 ..     142     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHH CS
                              ThiG 164 kealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafklavea 226
                                       +e +  i + +++P++   Gi ++ +a  ++e Ga++v + + ++ a+dp a  +a+++ave+
  gi|336252759|ref|YP_004595866.1| 149 PERVAAIADAVSIPIVGIGGI-TADNAGSVVEAGATGVAVISEITAADDPRAATEALAQAVET 210
                                       567889999*****9866666.7999***********************************97 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.4   5.8e-06     0.021     234     277 ..     152     192 ..     143     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.8e-06
                                       HHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHH CS
                            DHO_dh 234 irelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalv 277
                                       + ++++ ++  ipi+g+GGi +++ a   +eaGA+ v+v ++++
  gi|336252759|ref|YP_004595866.1| 152 VAAIADAVS--IPIVGIGGI-TADNAGSVVEAGATGVAVISEIT 192
                                       566777777..*********.799**************998875 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.6   4.7e-05      0.17     180     230 ..     154     204 ..     150     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.7e-05
                            DUF561 180 eiskkvslPvicasGlsdvtvplalslgasGiGigsavsklndeeemvall 230
                                       +i+ +vs+P++   G++   +   +++ga G+ + s ++  +d  +  ++l
  gi|336252759|ref|YP_004595866.1| 154 AIADAVSIPIVGIGGITADNAGSVVEAGATGVAVISEITAADDPRAATEAL 204
                                       7999**********************************9988876665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1676.54
//
Query:       gi|336252760|ref|YP_004595867.1|  [L=187]
Description: hypothetical protein Halxa_1355 [Halopiger xanaduensis SH-6]
Scores for 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   12.2   0.0       0.28   11.7   0.0    1.2  1  Copper-bind  Copper binding proteins, plastocyanin/azurin fam


Domain annotation for each model (and alignments):
>> 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 ?   11.7   0.0   1.6e-05      0.28      17      86 ..     105     172 ..      98     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
                                       SEEEEETTE.EEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE.SSEEEEEEET..T CS
                       Copper-bind  17 keitvkkge.kvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfd.eagtYkffCs..P 86 
                                         + v+ ge + t++n++++ HN+ +  +    +v +d++++++et     Ge  ++ f+ +++  ++ C+  P
  gi|336252760|ref|YP_004595867.1| 105 TLVLVEGGEyELTWTNQDGIHHNIAFWDEDR--EVVRDYSTPGNET----LGERETLAFEaTPEMDTYRCEyqP 172
                                       55667777624588999*********98774..7788899998888....7*********55555999998444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1495.16
//
Query:       gi|336252761|ref|YP_004595868.1|  [L=142]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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  117.5   6.1    7.3e-34  117.3   6.1    1.1  1  Usp             Universal stress protein family
  ------ inclusion threshold ------
      0.027   14.7   4.0      0.048   13.9   3.9    1.4  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
       0.32   11.8   6.0       0.44   11.3   4.7    1.9  2  PSK_trans_fac   Rv0623-like transcription factor


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 !  117.3   6.1   1.2e-37   7.3e-34       4     141 .]       2     142 .]       1     142 [] 0.95

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 1.2e-37
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.....HHHHH CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.....akaaa 75 
                                       ++lVa+Dgse +++A+ +A+++ ++   el+ll+v+d  +s +++     +e+ +   + a +++ +     + ++a
  gi|336252761|ref|YP_004595868.1|   2 TVLVAYDGSEPAQQAVTYAFDEYADE--ELVLLRVVDIADSFTEASIQAVEETLADRRKTASEDLREdlreqLVDQA 76 
                                       79*******************99997..7************9999999999999988888888877789**9***** PP

                                       HCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  76 eaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        a +v+ +v++  gdpa+ei+++aee+d+d iVvGs+grsg+sr+llGSv+e+v+r+ap++V+vVr
  gi|336252761|ref|YP_004595868.1|  77 TADDVEYRVETAAGDPAREIVRFAEENDVDHIVVGSHGRSGVSRVLLGSVAERVVRRAPVSVTVVR 142
                                       *****************************************************************8 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 ?   13.9   3.9   8.1e-06     0.048      32     124 ..      45     138 ..      15     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.1e-06
                    baeRF_family10  32 ylgeleeveevegevpgrtktggwk.......sqdrfqrreeeqaerhlkevAellaklleergverlvlgGdeeet 101
                                       ++  +ee+   +++       ++ +         +  ++ +e  +e ++ + A+ +++++ee++v+++v+g + +  
  gi|336252761|ref|YP_004595868.1|  45 SIQAVEETLADRRKTA----SEDLRedlreqlVDQATADDVEYRVETAAGDPAREIVRFAEENDVDHIVVGSHGR-- 115
                                       4444444444444444....44444444488888899999999****************************9865.. PP

                    baeRF_family10 102 aalldrlpkalrarvvgtlplpv 124
                                       + +   l  ++++rvv + p++v
  gi|336252761|ref|YP_004595868.1| 116 SGVSRVLLGSVAERVVRRAPVSV 138
                                       67888999999999999988876 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       0.7   4.2e+03      25      40 ..      13      28 ..       9      40 .. 0.76
   2 ?   11.3   4.7   7.4e-05      0.44      24      64 ..      40      80 ..      36     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.7
                                      XXXXXXXXXXXXXXXX CS
                     PSK_trans_fac 25 kteAvrrAleerlerl 40
                                       ++Av+ A  e+ +++
  gi|336252761|ref|YP_004595868.1| 13 AQQAVTYAFDEYADEE 28
                                      5678888888877665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.4e-05
                                      XXXXXXXXXXXXXXXXXXXXXX--HHHHHHHHHHHHHTS-- CS
                     PSK_trans_fac 24 skteAvrrAleerlerlrreraepllerllallrraaakae 64
                                      s teA  +A+ee+l+ +r+ ++e+l+e+l++ l + a+ ++
  gi|336252761|ref|YP_004595868.1| 40 SFTEASIQAVEETLADRRKTASEDLREDLREQLVDQATADD 80
                                      7799************9988*********998877777333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1056.32
//
Query:       gi|336252762|ref|YP_004595869.1|  [L=364]
Description: peptidase M29 aminopeptidase II [Halopiger xanaduensis SH-6]
Scores for complete 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-69  234.5   0.1    2.3e-69  234.2   0.1    1.0  1  Peptidase_M29  Thermophilic metalloprotease (M29)


Domain annotation for each model (and alignments):
>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.2   0.1   1.3e-73   2.3e-69       2     386 ..       2     339 ..       1     356 [. 0.92

  Alignments for each domain:
  == domain 1  score: 234.2 bits;  conditional E-value: 1.3e-73
                                       HHHHHHHHHHHHHTTT---TT-EEEEEEETT-HHHHHHHHHHHHHTT-SEEEEEEE-HHHHHHHHHHS-TT-TT--- CS
                     Peptidase_M29   2 eeklekyAellvkvglnlqkgqevvinaevealelarlvaeeaykagakkvvvewsdeeltkerlknaseeqleevp 78 
                                       ++++++ Ae++ ++++ l++g++vvi a+  a +l+ +++e + ++ga++v+++ ++ + ++  +  +s+ ++ e+p
  gi|336252762|ref|YP_004595869.1|   2 DPRIREHAEIIANHSVDLEEGDNVVIDAHPVAEDLVVALHEVIGDQGANPVTTTQRTGARQRRAYLRSSDGEF-ETP 77 
                                       67899********************************************************************.778 PP

                                       HHHHHHHHHHHHTT-EEEEEE--.-GGGSTTS-HHHHHHHHHHHHHHHHHHHHHHHTTSS-B-BEE---TTTHHHH- CS
                     Peptidase_M29  79 eweaekleelveegaarlsilae.dpkllkgvdpekiaaaqkarskalkeyreriasgklrWcvvavPteawAkkvf 154
                                       e e     +l+e+ +++++i a+ + ++ ++vdpe +aa+q+a++++l+   er     +rWc++++P +a A+   
  gi|336252762|ref|YP_004595869.1|  78 EHE----LALIENTDVYIAIRASdNVTQTSDVDPETQAAYQQAHQPILE---ERLG---IRWCLTQFPAPANAQ--- 141
                                       888....8***************9*******************999865...5666...9**************... PP

                                       --S-HHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHTT-SEEEEE.ETTEEEEEEE-TTB--EESS CS
                     Peptidase_M29 155 pdleaeealeklwdaifkavrldeedpvaaWeehnaelekrakyLnelkfkeLhyksspgtdLtvglaeghiWigga 231
                                           ae+++e +++++ +av        ++W ++ +++e+ +++L+    +e+++ s   td t+++ +g+  ++  
  gi|336252762|ref|YP_004595869.1| 142 ---LAEMSTEGYENFVWDAVN-------KDWADQRDHQENMVEILDP--ADEVRIVSGDTTDVTMSV-DGNPTLNDH 205
                                       ...89***********99975.......46*****************..9*****************.777777777 PP

                                       ---SSS----SBSS---EEE-EEEEEEEEEEE-SS-EEETTEEEBS-EEEEETTEEEEEE-SB-HHHHHHHTTSSSG CS
                     Peptidase_M29 232 ektkkgiefvaNiPteevftaPdkrgvnGvvratkPlsysGnliegirltFedGkvveakAekGeevLkklletDeg 308
                                       +++        N+P +evftaP  ++v+G v +++Pl+++G++i+++ l+Fe G+vv+ +A+k+e+vL+++l+tD+g
  gi|336252762|ref|YP_004595869.1| 206 GEH--------NLPGGEVFTAPVPDSVEGEVLFDMPLYHQGREITDVYLEFEGGEVVDHSAAKNEDVLTEVLNTDDG 274
                                       776........****************************************************************** PP

                                       GGSEEEEE---TTSHHHHHT-----HHHHHT..TS-EEEEE---GGGB--..-----SHHHHT----S-EEEEE--- CS
                     Peptidase_M29 309 arrLGEvALvpndspisqsgilfyntLfDen..ascHlAlGaaypecleggeelteeelkaaglNdSlihvDfmigs 383
                                       arrLGE+ ++ n+ +i++   ++yn+LfDe+   ++H+A+G+ay +++ +          +++ NdS++hvD mi +
  gi|336252762|ref|YP_004595869.1| 275 ARRLGELGIGMNR-EIDR---FTYNMLFDEKmgDTVHMAVGRAYDDTVGE----------DNEQNDSAVHVD-MIVD 336
                                       *************.****...***********99*************644..........5789********.9988 PP

                                       TT- CS
                     Peptidase_M29 384 edl 386
                                       +  
  gi|336252762|ref|YP_004595869.1| 337 MSE 339
                                       776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2891.94
//
Query:       gi|336252763|ref|YP_004595870.1|  [L=68]
Description: CT1; solute carrier family 6, member 8 [Halopiger xanaduensis SH-6]
Scores for 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:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 603.64
//
Query:       gi|336252764|ref|YP_004595871.1|  [L=340]
Description: hypothetical protein Halxa_1359 [Halopiger xanaduensis SH-6]
Scores for 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  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.36
# Mc/sec: 2842.48
//
Query:       gi|336252765|ref|YP_004595872.1|  [L=220]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-11   43.1   0.0    5.3e-11   42.1   0.0    1.5  1  HTH_10         HTH DNA binding domain
  ------ inclusion threshold ------
      0.092   12.5   0.0       0.14   11.9   0.0    1.2  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal


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 !   42.1   0.0   5.9e-15   5.3e-11       3      52 ..     163     212 ..     162     213 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 5.9e-15
                            HTH_10   3 dkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       d+ql++ ++A   GY+++PRr  ++++A el+ + st+s  Lr+ e ++i
  gi|336252765|ref|YP_004595872.1| 163 DRQLAAMRAARSVGYYEVPRRNGIEAVAAELDCAVSTASALLRRGEANVI 212
                                       9*********************************************9998 PP

>> 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 ?   11.9   0.0   1.5e-05      0.14      25      77 ..     143     193 ..     125     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.5e-05
                                       EEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHH CS
                     Ribo_biogen_C  25 avvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaal 77 
                                       + vd+ W++ ++v+++k+ a ++r+L  + Aa +v Y    + + +EA+aa l
  gi|336252765|ref|YP_004595872.1| 143 VTVDVLWTS-DRVTTTKT-AASDRQLAAMRAARSVGYYEVPRRNGIEAVAAEL 193
                                       578999998.55555555.579*****************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1689.89
//
Query:       gi|336252766|ref|YP_004595873.1|  [L=221]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-20   72.2   0.0    4.4e-20   72.0   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.1e-19   70.9   0.0    1.9e-19   70.1   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    4.1e-16   59.5   0.0    6.3e-16   58.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    9.2e-16   58.3   0.0    2.1e-15   57.2   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    1.4e-13   51.0   0.0    1.9e-13   50.5   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.4e-13   50.3   0.0    4.4e-13   49.5   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.1e-12   47.8   0.0    1.3e-12   47.5   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    9.4e-07   28.6   0.0    1.3e-06   28.2   0.0    1.1  1  NodS             Nodulation protein S (NodS)
    4.3e-06   26.6   0.0    5.6e-06   26.2   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    9.6e-06   25.1   0.0    1.3e-05   24.7   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    4.1e-05   23.3   0.0      6e-05   22.8   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    7.5e-05   22.3   0.0    0.00015   21.3   0.0    1.5  1  MTS              Methyltransferase small domain
     0.0024   18.0   0.0     0.0039   17.3   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
     0.0025   17.3   0.0     0.0035   16.8   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
     0.0025   16.9   0.0     0.0034   16.5   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0044   16.4   0.0     0.0072   15.8   0.0    1.3  1  TehB             Tellurite resistance protein TehB
     0.0049   16.3   0.0     0.0067   15.9   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0097   15.0   0.0      0.014   14.5   0.0    1.2  1  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
      0.014   14.6   0.0      0.019   14.2   0.0    1.1  1  Methyltransf_3   O-methyltransferase
      0.045   13.7   0.0       0.07   13.1   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
      0.072   12.7   0.0      0.095   12.3   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
        0.1   12.6   0.0       0.14   12.1   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.12   12.1   0.0       0.15   11.8   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
       0.25   10.4   0.0       0.31   10.1   0.0    1.2  1  Pox_MCEL         mRNA capping enzyme


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.0   5.9e-23   4.4e-20       2     113 ..      48     156 ..      47     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 5.9e-23
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       ++g rvlD+GCG G    +l + +gp +++v +D+s+e++ +Ar + +++g +nve++++d+++    +e e+fD  
  gi|336252766|ref|YP_004595873.1|  48 ESGDRVLDVGCGPGVNFERLRDAIGPAGQLVAVDYSPEMVAKARDRVERHGWENVEVRRADATAVA--FE-EPFDAA 121
                                       6899************************************************************99..89.9***** PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedpr 113
                                       ++   l  ++d   + e++ + l pgg ++++d+r
  gi|336252766|ref|YP_004595873.1| 122 VATLSLSVMPDVRGAAENVYSHLVPGGSFAVCDVR 156
                                       ********************************998 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0   2.6e-22   1.9e-19       1      97 []      53     148 ..      53     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 2.6e-22
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       vLd+GcG+G + ++l +++g ++++++vD+s+em+++ar r+e++g+ nve++++da+++ fe+  fD+ v++ +l+
  gi|336252766|ref|YP_004595873.1|  53 VLDVGCGPGVNFERLRDAIGpAGQLVAVDYSPEMVAKARDRVERHGWeNVEVRRADATAVAFEE-PFDAAVATLSLS 128
                                       9******************66*****************************************97.*******87788 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       +++  d++ a ++++++L pgG
  gi|336252766|ref|YP_004595873.1| 129 VMP--DVRGAAENVYSHLVPGG 148
                                       876..99**************9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   8.5e-19   6.3e-16       1      98 [.      54     149 ..      54     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 8.5e-19
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       L++GcG G + ++l++++ p  ++++vD+sp+++++a+ +  +++   ++nve++  d+   + ++ fD+ va   l
  gi|336252766|ref|YP_004595873.1|  54 LDVGCGPGVNFERLRDAIgPAGQLVAVDYSPEMVAKARDRVERHG---WENVEVRRADATAVAFEEPFDAAVATLSL 127
                                       8*********************************88888877777...666677766766667778*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGr 98 
                                       ++++d+r + +n++++L+pgG 
  gi|336252766|ref|YP_004595873.1| 128 SVMPDVRGAAENVYSHLVPGGS 149
                                       *********************6 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   2.7e-18   2.1e-15       1      96 []      54     152 ..      54     152 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 2.7e-18
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhh 73 
                                       LdvGcG G ++e l ++    +++v+vD+s+em++ a++++++ g  +ve+++ada+ + fe+  fD+ v++ +l  
  gi|336252766|ref|YP_004595873.1|  54 LDVGCGPGVNFERLRDAIgpaGQLVAVDYSPEMVAKARDRVERHGWeNVEVRRADATAVAFEE-PFDAAVATLSLSV 129
                                       8**************666699**********************999***************99.************* PP

                                       -CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllvi 96 
                                       ++d++ a ++++  L pgG +++
  gi|336252766|ref|YP_004595873.1| 130 MPDVRGAAENVYSHLVPGGSFAV 152
                                       *******************9975 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   2.6e-16   1.9e-13      11     120 ..      40     155 ..      25     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 2.6e-16
                   Methyltransf_23  11 dklerllpklraggrvLdiGcGtGillevlren.gf..svtgvDlspeaveiae...kakkaqkdqfdeqeaaepqg 81 
                                       ++++rl+  l++g rvLd+GcG G + e lr+  g   ++++vD spe+v++a+   +    ++  ++ + ++ ++ 
  gi|336252766|ref|YP_004595873.1|  40 AAIDRLP--LESGDRVLDVGCGPGVNFERLRDAiGPagQLVAVDYSPEMVAKARdrvE----RHGWENVEVRRADAT 110
                                       5677887..99*************99999977657779***************66552....333333332222222 PP

                   Methyltransf_23  82 ......kfdlIvlrevlehvpdppellrqiatllkpgGylllsep 120
                                              fd +v++ +l  +pd+  +  +++++l pgG + ++++
  gi|336252766|ref|YP_004595873.1| 111 avafeePFDAAVATLSLSVMPDVRGAAENVYSHLVPGGSFAVCDV 155
                                       344444**********************************99996 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 !   49.5   0.0     6e-16   4.4e-13      62     156 ..      38     131 ..      33     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 6e-16
                                       HHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTG CS
                              PCMT  62 valalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGye 138
                                         +a++ l l+ g+rvL+vG+G G +   l   +g+ g++v++++++e+v++a+ ++++++ env v+ +D +  ++
  gi|336252766|ref|YP_004595873.1|  38 REAAIDRLPLESGDRVLDVGCGPGVNFERLRDAIGPAGQLVAVDYSPEMVAKARDRVERHGWENVEVRRADATA-VA 113
                                       556788999**************************************************************865.77 PP

                                       GG-SEEEEEESSBBSS-- CS
                              PCMT 139 ekaPYdaihvgaaapeiP 156
                                        + P+da + + +   +P
  gi|336252766|ref|YP_004595873.1| 114 FEEPFDAAVATLSLSVMP 131
                                       888***998887766666 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   1.8e-15   1.3e-12      41     154 ..      43     155 ..      21     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.8e-15
                                       HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-E CS
                   Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsf 117
                                       ++    +g +vlDv +G g    +l d++g  g++v +D++++m+  ++++++++g  n+e   a+a ++ fe+  f
  gi|336252766|ref|YP_004595873.1|  43 DRLPLESGDRVLDVGCGPGVNFERLRDAIGPAGQLVAVDYSPEMVAKARDRVERHGWENVEVRRADATAVAFEE-PF 118
                                       555567899***********999*************************************************85.79 PP

                                       EEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE CS
                   Ubie_methyltran 118 DvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlef 154
                                       D    +  l  ++D   a +++y  l pGG + v ++
  gi|336252766|ref|YP_004595873.1| 119 DAAVATLSLSVMPDVRGAAENVYSHLVPGGSFAVCDV 155
                                       99999999************************99876 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.7e-09   1.3e-06      17     143 ..      25     151 ..      11     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.7e-09
                              NodS  17 dPwrldanefeqerlaqilrlslaqgsiadalevGcaaGalterlapy...ckrltvvdvveeaiararervke..s 88 
                                       d + ++  + e  r a+i rl l+ g+   +l+vGc  G   erl      + +l  vd  +e +a+ar rv++  +
  gi|336252766|ref|YP_004595873.1|  25 DYYAMSERDLEPMREAAIDRLPLESGD--RVLDVGCGPGVNFERLRDAigpAGQLVAVDYSPEMVAKARDRVERhgW 99 
                                       6677889999999**********9997..79************996542236789*****************85337 PP

                              NodS  89 shiswivsdvqqfstdekfdlivvaevlyyiedvaelraavrnlvsllapdgqlv 143
                                        ++    +d + +  +e fd  v +  l  + d   +r+a +n+ s l p+g + 
  gi|336252766|ref|YP_004595873.1| 100 ENVEVRRADATAVAFEEPFDAAVATLSLSVMPD---VRGAAENVYSHLVPGGSFA 151
                                       8899999999999999*******9988877665...79************99875 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   7.5e-09   5.6e-06      34     135 ..      43     144 ..      39     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 7.5e-09
                             GCD14  34 mkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeev 110
                                        +L l+ G +v++ G G g   + +  +++P G+l ++++  + + kar+  ++h+  ++v v+  D+    f+e  
  gi|336252766|ref|YP_004595873.1|  43 DRLPLESGDRVLDVGCGPGVNFERLRDAIGPAGQLVAVDYSPEMVAKARDRVERHGW-ENVEVRRADATAVAFEEPF 118
                                       578899**************************************************7.589************9999 PP

                             GCD14 111 sgkvDavfLD.lPaPweaiphaakal 135
                                       +  v ++ L  +P    a +++ ++l
  gi|336252766|ref|YP_004595873.1| 119 DAAVATLSLSvMPDVRGAAENVYSHL 144
                                       99998888863588888888888887 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.7e-08   1.3e-05      52     133 ..      39     123 ..      13     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.7e-08
                                       HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH-..-EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GG..G- CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraveryd..vkvvglTlSkeqaklakkrvdeldlerkvevklldye..dl 124
                                       + ++++l l+ G+++Ld+GcG G  + r  +  +   + v++  S e  ++a++rv++ +  ++vev+ +d     +
  gi|336252766|ref|YP_004595873.1|  39 EAAIDRLPLESGDRVLDVGCGPGVNFERLRDAIGpaGQLVAVDYSPEMVAKARDRVERHG-WENVEVRRADATavAF 114
                                       56899******************8877655554422689*********************.5678999888752257 PP

                                       ----SEEEE CS
                              CMAS 125 dekvdrvvs 133
                                       +e++d+ v+
  gi|336252766|ref|YP_004595873.1| 115 EEPFDAAVA 123
                                       889998774 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 !   22.8   0.0   8.1e-08     6e-05       5      71 ..      46     112 ..      43     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8.1e-08
                                       ---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCC CS
                   Methyltr_RsmB-F   5 apqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarki 71 
                                        ++ ++++lD+ ++PG     + + + ++g++vAvd + e + +  + ++r g +n+ v +aDa+ +
  gi|336252766|ref|YP_004595873.1|  46 PLESGDRVLDVGCGPGVNFERLRDAIGPAGQLVAVDYSPEMVAKARDRVERHGWENVEVRRADATAV 112
                                       56789**********************************************************9876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0     2e-07   0.00015      24     102 ..      42     122 ..      29     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2e-07
                                       HHHCHCCTCSEEEEET-TTSHHHHHHHHH.TTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-E CS
                               MTS  24 letlpkelsgkvlDlGcGaGvlgaalake.speaevtlvdvdarAlesakenleankle.vevvasdvleeveekkf 98 
                                       ++ lp e  ++vlD+GcG Gv    l ++  p  ++++vd + + ++ a+  +e+++ e vev+  d+++ + e+ f
  gi|336252766|ref|YP_004595873.1|  42 IDRLPLESGDRVLDVGCGPGVNFERLRDAiGPAGQLVAVDYSPEMVAKARDRVERHGWEnVEVRRADATAVAFEEPF 118
                                       67788888999**********88888766257778**********************************99999999 PP

                                       EEEE CS
                               MTS  99 dliv 102
                                       d+ v
  gi|336252766|ref|YP_004595873.1| 119 DAAV 122
                                       9865 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.2e-06    0.0039      19      97 ..      47     157 ..      39     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.2e-06
                                       S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.........HHH..TTEEEECS-CCCSSHHHHHCHCHH CS
                              FtsJ  19 fkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........apl..pgvttiqgditdpetiekikeals 84 
                                       ++ g++v+D+g++PG   + l   +g++g++vavD  p          + +  ++v++ ++d t  + +e +  a+ 
  gi|336252766|ref|YP_004595873.1|  47 LESGDRVLDVGCGPGVNFERLRDAIGPAGQLVAVDYSPEmvakardrvERHgwENVEVRRADATAVAFEEPFDAAVA 123
                                       56899*********************99********76669866544322245677777888887777776665544 PP

                                       H.....................SSEEEEEE--S- CS
                              FtsJ  85 e.....................rkvdlvvsDgap 97 
                                                              + ++ v+D+ p
  gi|336252766|ref|YP_004595873.1| 124 TlslsvmpdvrgaaenvyshlvPGGSFAVCDVRP 157
                                       3555555555555555555555555555555555 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.7e-06    0.0035       5      63 ..      53     112 ..      49     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.7e-06
                                       EEEET-TTSHHHHHHHHH.STTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCH CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkk.nPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkv 63 
                                       vl++GcG G    +l  +  P  ++++++ + ++vak+ +++e+++ +N+++ r da+ v
  gi|336252766|ref|YP_004595873.1|  53 VLDVGCGPGVNFERLRDAiGPAGQLVAVDYSPEMVAKARDRVERHGWENVEVRRADATAV 112
                                       89*******99999976537*************************************654 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.5e-06    0.0034      21      92 ..      40     116 ..      36     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.5e-06
                                       HHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHH CS
                            RrnaAD  21 eIldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpe 92 
                                        ++d l le  + vl++g G+G+  e+L + +    q+v++   +++++  +++++    e+++v  +D+   ++ e
  gi|336252766|ref|YP_004595873.1|  40 AAIDRLPLESGDRVLDVGCGPGVNFERLRDAIgpaGQLVAVDYSPEMVAKARDRVErhGWENVEVRRADATAVAFEE 116
                                       5799999*********************9999999*********************77779****999998877765 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   9.6e-06    0.0072      11     128 ..      30     148 ..      19     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.6e-06
                                       HHHT-----HHHHHHCCCS-S-EEEEES-TTSHHHHHH.HHTT-..EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE CS
                              TehB  11 kkynltathsevveavkivkpgkvldlgcgqgrnslyl.sllgy..dvtawdknensiafleeikekenlknistal 84 
                                          +l ++    ++   + +  +vld+gcg g n   l  ++g   ++ a+d   + +a  ++  e+   +n++ + 
  gi|336252766|ref|YP_004595873.1|  30 SERDLEPMREAAIDRLPLESGDRVLDVGCGPGVNFERLrDAIGPagQLVAVDYSPEMVAKARDRVERHGWENVEVRR 106
                                       44566677777777777778889***********877624566422788**************************** PP

                                       --GGG----S-EEEEEEESSGGGS-GGGHHHHHHHHHHTEEEEE CS
                              TehB  85 ydineaklderydfilstvvlmfleaeripsiienmqectkvgg 128
                                        d  ++ ++e +d  ++t+ l  +    +    en+  +  +gg
  gi|336252766|ref|YP_004595873.1| 107 ADATAVAFEEPFDAAVATLSLSVMP--DVRGAAENVYSHLVPGG 148
                                       ******************9887664..35556667766666666 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     9e-06    0.0067     159     258 ..      47     152 ..      37     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9e-06
                              PrmA 159 vkegeevlDvGtGSGiL..aiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk.eekadviv 231
                                       +++g++vlDvG+G G+    +  a   a + vavD+ +  v  a++ +e+ + e+ +++  + +++++ ee++d  v
  gi|336252766|ref|YP_004595873.1|  47 LESGDRVLDVGCGPGVNfeRLRDAIGPAGQLVAVDYSPEMVAKARDRVERHGWENvEVR-RADATAVAfEEPFDAAV 122
                                       57789**********952234455556899********************998874443.23344443579****** PP

                              PrmA 232 aNILaevliel...aedikklvkeggllil 258
                                       a    +v+ +    ae++++++ +gg++++
  gi|336252766|ref|YP_004595873.1| 123 ATLSLSVMPDVrgaAENVYSHLVPGGSFAV 152
                                       *99888765543338999999999999875 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.9e-05     0.014      62     108 ..      41      87 ..      28     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                                       T-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHH CS
                       Fibrillarin  62 glkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvl 108
                                        +++lp+++g++vL +G + G     + D +g+ g + av++sp ++
  gi|336252766|ref|YP_004595873.1|  41 AIDRLPLESGDRVLDVGCGPGVNFERLRDAIGPAGQLVAVDYSPEMV 87 
                                       57899***************************************986 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.5e-05     0.019      47     111 ..      49     112 ..      26     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                       T--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHH CS
                    Methyltransf_3  47 nakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkv 111
                                       +  rvl++G   G     +  a+ + G+++a+d  +e ++ a++ +++ g++  +e++++da++v
  gi|336252766|ref|YP_004595873.1|  49 SGDRVLDVGCGPGVNFERLRDAIGPAGQLVAVDYSPEMVAKARDRVERHGWE-NVEVRRADATAV 112
                                       5679999999999999999999*****************************7.59******9987 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.3e-05      0.07      13      80 ..      48     115 ..      40     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.3e-05
                   Methyltransf_18  13 ekgsrvaDiGtDHgylpiylv.kegkakkviasDinegplekakeniekagledkievrlsdGleklke 80 
                                       e+g+rv+D+G+  g+    l    g a + +a+D +++ ++ka++ +e++g e ++evr +d  ++  e
  gi|336252766|ref|YP_004595873.1|  48 ESGDRVLDVGCGPGVNFERLRdAIGPAGQLVAVDYSPEMVAKARDRVERHGWE-NVEVRRADATAVAFE 115
                                       57899*******9976555552457899**********************995.699999998776654 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013     0.095      11      42 ..      47      78 ..      39     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                              MetW 11 ikpgsrvldlGcGdGellellkeekqvdgrGl 42
                                      +++g rvld+GcG G  +e l++  +  g+ +
  gi|336252766|ref|YP_004595873.1| 47 LESGDRVLDVGCGPGVNFERLRDAIGPAGQLV 78
                                      57899****************99877666644 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.14      26      83 ..      50     103 ..      37     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                   Methyltransf_32  26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrls 83 
                                         +v+DvG+G g    +l + +     ++v++d + e+v+ka++r e+ g  + ++++
  gi|336252766|ref|YP_004595873.1|  50 GDRVLDVGCGPGVNFERLRD-AIGPAGQLVAVDYSPEMVAKARDRVERHG--W-ENVE 103
                                       5689********99999999.77889**********************99..6.3332 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0002      0.15      76     126 ..      74     122 ..      37     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                       H--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEE CS
                           UPF0020  76 elklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdviv 126
                                         +l+++D  +++v++ar+  e+ g+++ +e++ ada+++   e+ +d+ v
  gi|336252766|ref|YP_004595873.1|  74 AGQLVAVDYSPEMVAKARDRVERHGWEN-VEVRRADATAVA-FEEPFDAAV 122
                                       5579**********************85.899999***999.666787765 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00041      0.31      67     109 ..      52      96 ..      44     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00041
                          Pox_MCEL  67 kvLdldcgkGgDLeKyek..geIsklvatDiaeesieeckeRYnk 109
                                       +vLd++cg G   e+ +   g   +lva+D + e +++++ R ++
  gi|336252766|ref|YP_004595873.1|  52 RVLDVGCGPGVNFERLRDaiGPAGQLVAVDYSPEMVAKARDRVER 96 
                                       7*************9985226789****************99822 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1783.77
//
Query:       gi|336252767|ref|YP_004595874.1|  [L=337]
Description: Threonine aldolase [Halopiger xanaduensis SH-6]
Scores for 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-86  289.0   0.3    4.5e-86  288.7   0.3    1.0  1  Beta_elim_lyase  Beta-eliminating lyase
    2.1e-05   24.0   0.1     0.0073   15.7   0.0    2.8  3  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
       0.28    9.7   0.5       0.39    9.2   0.0    1.5  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.7   0.3   7.6e-90   4.5e-86       1     292 [.       3     286 ..       3     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: 288.7 bits;  conditional E-value: 7.6e-90
                                       E-S-GGG----HHHHHHHHCS----CCCT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEE CS
                   Beta_elim_lyase   1 DLlSDsvtkgteamsdaqaaamlGdesYgedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivt 77 
                                       DL+SD+vt++ + m++a a+a +Gd++Yged+tvn+Le ++ae++gkeaal+vp+Gt++n+i+ ++++ rg+ev+++
  gi|336252767|ref|YP_004595874.1|   3 DLRSDTVTTPDDDMRNAAATADVGDDVYGEDPTVNELETRAAEAVGKEAALYVPSGTMGNQIAARVHTDRGQEVLAD 79 
                                       9**************************************************************************** PP

                                       TT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHH CS
                   Beta_elim_lyase  78 epahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelreva 154
                                       +++h+  +e g+ a+ a+ ++r l++++ G  ++e++ +a  +++ h++ ++l++l++T+n+ gG ++ +e+++++a
  gi|336252767|ref|YP_004595874.1|  80 RKSHVVKYELGGFAQHADLQVRMLETDR-GVPTPEQVDEATVAEDLHRPGTGLLCLENTHNARGGLAIDPEKIAAAA 155
                                       ****************************.**********8888566******************************* PP

                                       HHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH....HHHHHHHHHHHHT- CS
                   Beta_elim_lyase 155 aiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvGgvlafrddeledylaerveqrkylgg 231
                                       + a+++++p+hlDgAR++naa++l+++v+++++ vDsv+++l+K+l+a++G++la++++    +++e++++rk  gg
  gi|336252767|ref|YP_004595874.1| 156 DAARERDVPVHLDGARVFNAATALDVPVSDIVDPVDSVMFCLSKGLGAPIGSMLAGSEE----FVEEARRTRKLFGG 228
                                       ***********************************************************....************** PP

                                       --SSTHHHHH..HHHHHHHHSSTTHHHHHHHHHHHHHHHHHCT--EEECCGTTCCEEEEE. CS
                   Beta_elim_lyase 232 glrqagvlaaleagiraleeglaslerdhktaeqlaeklelvrlaiprrvytqehldyvaa 292
                                       g+rqag++a   +g+ ale+    l+ dh++a+ la++l+++++  +++++t+ +l +v++
  gi|336252767|ref|YP_004595874.1| 229 GMRQAGIVAG--PGLEALENV-DDLAADHENARLLADGLSELEGFDVQEPETNIVLADVSE 286
                                       **********..******987.78899*****************************99976 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 !   15.7   0.0   1.2e-06    0.0073       9      67 ..      20      77 ..      12      85 .. 0.78
   2 ?   -0.5   0.0       0.1     6e+02      98     123 ..     145     170 ..     141     176 .. 0.88
   3 !    4.6   0.0    0.0027        16     207     268 ..     218     276 ..     208     330 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-06
                                      HHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEE CS
                   DegT_DnrJ_EryC1  9 aveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVI 67
                                      a+++ +  + + ++p+v+e+E++ a+ +g++ a+ v sGt ++++a r+   ++g+eV+
  gi|336252767|ref|YP_004595874.1| 20 AATADVGDDVYGEDPTVNELETRAAEAVGKEAALYVPSGTMGNQIAARVH-TDRGQEVL 77
                                      3444444557888********************************98874.44578876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.1
                                       SB-GGGCGGG--TTEEEEEEB-GGGB CS
                   DegT_DnrJ_EryC1  98 nidpaaieaaitertkaIlpVhlyGq 123
                                        idp++i+aa    +   +pVhl G+
  gi|336252767|ref|YP_004595874.1| 145 AIDPEKIAAAADAARERDVPVHLDGA 170
                                       799*******9999999999999886 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0027
                                       CSSCECCSS---B-B-BHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGT CS
                   DegT_DnrJ_EryC1 207 ekryvgevelGynyrlteiqAAiglaqLerldelvarRreiaelykeeLaelegtaelttpk 268
                                       e r + ++ +G  +r   i A  gl+ Le++d+l a  +e+a l+ ++L+eleg+ + ++p+
  gi|336252767|ref|YP_004595874.1| 218 EARRTRKL-FGGGMRQAGIVAGPGLEALENVDDLAAD-HENARLLADGLSELEGFDV-QEPE 276
                                       44555555.79999999999999**********9887.5799***********9844.4443 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 ?    9.2   0.0   6.6e-05      0.39      51     124 ..      33     105 ..      14     182 .. 0.74
   2 ?   -3.0   0.2      0.33     2e+03     367     380 ..     244     257 ..     243     257 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 6.6e-05
                                       -HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST CS
                   Cys_Met_Meta_PP  51 nptrsvleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt 124
                                        pt++ le r a+  g eaal v+sG+   + a +     G+e++++++ +   ++l   ++++  ++v++ +t
  gi|336252767|ref|YP_004595874.1|  33 DPTVNELETRAAEAVGKEAALYVPSGTMGNQIAARVHTDRGQEVLADRKSHVVKYELG-GFAQHADLQVRMLET 105
                                       7*****************************9999999999*****9988766655543.344444444444444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.33
                                       SS-HHHHHHHHHHH CS
                   Cys_Met_Meta_PP 367 iEdvdDliaDlkqa 380
                                       +E+vdDl aD ++a
  gi|336252767|ref|YP_004595874.1| 244 LENVDDLAADHENA 257
                                       7*********8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 2864.62
//
Query:       gi|336252768|ref|YP_004595875.1|  [L=43]
Description: hypothetical protein Halxa_1363 [Halopiger xanaduensis SH-6]
Scores for 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   12.7   4.0       0.12   12.4   4.0    1.1  1  DUF4083   Domain of unknown function (DUF4083)


Domain annotation for each model (and alignments):
>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   4.0   6.5e-06      0.12       7      30 ..      11      33 ..       8      37 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.5e-06
                           DUF4083  7 yliivivLilllvfsftlfiRrvv 30
                                      +  iv++L+ l++fs +l++Rr+v
  gi|336252768|ref|YP_004595875.1| 11 IIAIVLILLALIFFS-YLLLRRTV 33
                                      444555555566666.78899988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 336.55
//
Query:       gi|336252769|ref|YP_004595876.1|  [L=175]
Description: phosphodiesterase [Halopiger xanaduensis SH-6]
Scores for 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-26   91.0   1.3    1.2e-25   90.7   1.3    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.9e-06   27.9   0.5      0.013   16.0   0.0    2.2  2  Metallophos    Calcineurin-like phosphoesterase


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 !   90.7   1.3   1.3e-29   1.2e-25       2     162 ..       3     147 ..       2     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 1.3e-29
                     Metallophos_2   2 klaiiSDlHsnl..daleavlealkevgvdaiihaGDleeeepevleellela.pvlaVrGNnDeevveedvlreaa 75 
                                       ++ai+SD+Hs +  ++  ++l+a++e+  d +ihaGD+  ++  +le+++e + ++ aV+GN D           + 
  gi|336252769|ref|YP_004595876.1|   3 RIAIFSDTHSTVghELEGEALTAAREA--DVVIHAGDF--TSAAALEAFREECdRLFAVHGNAD-----------SG 64 
                                       69*******665226667889999999..********9..88889999999999**********...........99 PP

                     Metallophos_2  76 elgtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdg 152
                                        ++++lpe+++le ag++++++H  + g++ +l+   ++   g+dvvv+GHtH p+v + +++l++nPGs ++pr +
  gi|336252769|ref|YP_004595876.1|  65 AVRDRLPEARVLEEAGVRFAVTHRRE-GGEVGLSMFGRS--RGADVVVSGHTHHPTVVDVEDCLLLNPGSHAQPRGH 138
                                       9***********************94.888888888888..9999******************************99 PP

                     Metallophos_2 153 dpetyaildt 162
                                       +p ++a+l+ 
  gi|336252769|ref|YP_004595876.1| 139 RP-GFAVLEA 147
                                       99.9999986 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-06     0.013       2      75 ..       3      62 ..       2      79 .. 0.71
   2 !   10.2   0.1   8.7e-05      0.78     163     204 .]      82     116 ..      71     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                                      EEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS CS
                       Metallophos  2 rilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe 75
                                      ri++++D+H      +++   ++l  ++   ++d+v++aGD++    le  + e  ++l++       ++GN +
  gi|336252769|ref|YP_004595876.1|  3 RIAIFSDTH---STVGHELEGEALTAAR---EADVVIHAGDFTSAAALEA-FREECDRLFA-------VHGNAD 62
                                      89*******...4444444445554454...56**********9997777.6666555555.......888888 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 8.7e-05
                                       EEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSSE CS
                       Metallophos 163 vivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHvy 204
                                        ++++H+          g+  l  + +  g+d+v+sGHtH++
  gi|336252769|ref|YP_004595876.1|  82 RFAVTHRREG-------GEVGLSMFGRSRGADVVVSGHTHHP 116
                                       5666666666.......888888999999***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1395.13
//
Query:       gi|336252770|ref|YP_004595877.1|  [L=318]
Description: cation diffusion facilitator family transporter [Halopiger xanaduensis SH-6]
Scores for 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-28   97.8   5.7    1.1e-27   97.0   5.7    1.4  1  Cation_efflux  Cation efflux family
    5.5e-07   29.6   0.0    9.6e-07   28.8   0.0    1.4  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
       0.13   12.2   1.9       0.22   11.4   1.9    1.3  1  PKcGMP_CC      Coiled-coil N-terminus of cGMP-dependent prote


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 !   97.0   5.7   1.9e-31   1.1e-27       2     198 ..       9     231 ..       8     232 .. 0.91

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 1.9e-31
                     Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsglll 78 
                                       +++l+an ++a+ ++ + llt+S a+l++ +hs+sd+ ++++ll+++k+  +++++++pfG+g+++++++l ++++l
  gi|336252770|ref|YP_004595877.1|   9 LAALFANGAIAILKFGGFLLTGSPAMLSETYHSISDTGNQIFLLIGIKYGAQEANRTHPFGHGKAQFFYSLLVSVML 85 
                                       689************************************************************************99 PP

                     Cation_efflux  79 lglav.fllleaiqkli............kegereihaglalvvalvslvvnlalllilrragrkl........... 131
                                       +g+a   +  ++++ l               g   ++  + ++v+++++v++ + l++ +++  +            
  gi|336252770|ref|YP_004595877.1|  86 FGIAGwESARHGYDALThggvhraagdvtMLGRTFDPVYVNYAVLIGAIVFETYALWKAYQGISSQmdeygwtslre 162
                                       9999845777888888899999999999988888899999999***************999999889********99 PP

                     Cation_efflux 132 .rsaalkaaalhvlg.DaltslgvlvsalvillfnlksgplaDpvaslligliilysalkllkeslseL 198
                                         s +  + +l +l+ D+++ +g+ +++ +++l+  +++p++D++ +l+igl+++  a+ l++e+ + +
  gi|336252770|ref|YP_004595877.1| 163 aFSKTSDVTTLTALTeDSIALAGAGIALAGVYLTRTTGNPMYDAASALIIGLLLMGFAVALAWENKRLI 231
                                       9444445555555555******************99999*************************98766 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 !   28.8   0.0   1.6e-10   9.6e-07       5      77 ..     240     311 ..     236     313 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.6e-10
                                       HHHHHHHHHTT-SS-EEEEEEEEE-S-.---EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEE CS
                          ZT_dimer   5 eeeeireiiksvpgvkgvhdlrtrksG.skifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHve 77 
                                        e+e+r+i+++ +gv++  d+rt ++G ++++v  ++ +d+ l  +e  e ++++e++++e+ ++v++v+i  e
  gi|336252770|ref|YP_004595877.1| 240 AEDELRAIVTDWDGVTELVDFRTVYFGaEELLVTADVAFDPGLETEEIDERITDLERALREHDDQVRNVYI--E 311
                                       5799***********************77*********************************999877655..4 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 ?   11.4   1.9   3.6e-05      0.22       7      24 ..     288     305 ..     287     307 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                         PKcGMP_CC   7 DERIRELEkrlaekdeEI 24 
                                       DERI +LE++l+e d+ +
  gi|336252770|ref|YP_004595877.1| 288 DERITDLERALREHDDQV 305
                                       9**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); 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):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2282.85
//
Query:       gi|336252771|ref|YP_004595878.1|  [L=138]
Description: hypothetical protein Halxa_1366 [Halopiger xanaduensis SH-6]
Scores for 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:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1108.23
//
Query:       gi|336252772|ref|YP_004595879.1|  [L=727]
Description: DEAD_2 domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-29  101.8   0.0    1.3e-28  100.3   0.0    1.8  1  Helicase_C_2  Helicase C-terminal domain
      2e-20   73.1   0.2    4.2e-20   72.1   0.2    1.5  1  DEAD_2        DEAD_2
    2.3e-07   30.8   0.1    0.00046   20.0   0.0    3.3  3  DEAD          DEAD/DEAH box helicase
    5.1e-07   29.9   0.1    4.1e-05   23.7   0.1    2.3  1  ResIII        Type III restriction enzyme, res subunit
    0.00042   19.7   0.0    0.00084   18.8   0.0    1.6  1  ATPase        KaiC
    0.00058   19.6   0.0     0.0014   18.3   0.0    1.7  1  HBB           Helical and beta-bridge domain
     0.0061   16.2   2.0       0.62    9.6   0.0    3.9  4  AAA_25        AAA domain
  ------ inclusion threshold ------
      0.023   14.2   0.0      0.068   12.6   0.0    1.7  2  PhoH          PhoH-like protein
      0.027   13.6   0.0      0.052   12.7   0.0    1.5  1  DUF815        Protein of unknown function (DUF815)
      0.029   13.3   0.0      0.061   12.2   0.0    1.5  1  AAA_34        P-loop containing NTP hydrolase pore-1
      0.046   13.0   0.3        1.9    7.7   0.0    2.2  2  DUF2075       Uncharacterized conserved protein (DUF2075)
       0.18   10.9   0.3       0.48    9.5   0.1    1.8  2  ArsA_ATPase   Anion-transporting ATPase
        0.8   10.1   3.8        2.7    8.4   3.8    1.8  1  CENP-H        Centromere protein H (CENP-H)


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.0   9.4e-32   1.3e-28       2     159 ..     522     677 ..     521     684 .. 0.91

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 9.4e-32
                      Helicase_C_2   2 lellevvpggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEGi 78 
                                       ++ ++++pg++l+ffp+y   e+ ++rl+++l  ++   ++e      e++ +e+ +  +++a+l+ ++ G+l EG+
  gi|336252772|ref|YP_004595879.1| 522 YDAVRMTPGNTLAFFPNYGEAERYADRLERRLGGDRRIHLDE-PGVAVEELRQEFVA--EDKAVLCTSLWGTLAEGV 595
                                       678999*************************97776666677.899***********..****************** PP

                      Helicase_C_2  79 dfsddllraviivglPfpnpkdpeveakreyldekgk..knsgkewylpealravnQaiGRliRhkdDygaivllDe 153
                                        f +d +  v++vg+P+p+++d + ea +e +d  ++  + +++++ + +++r+ +Qa+GR++R+ dD g+  llD+
  gi|336252772|ref|YP_004595879.1| 596 SFDGDDAHTVLVVGVPYPHLDD-RAEAVQEAYDVAFDgtETGWRYAVEIPTVRKTRQALGRVLRSPDDVGVRALLDR 671
                                       ********************65.5688889999988765677889999***************************** PP

                      Helicase_C_2 154 Rfakee 159
                                       R++++ 
  gi|336252772|ref|YP_004595879.1| 672 RYSRSA 677
                                       **9864 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.2     3e-23   4.2e-20       5     171 ..      72     282 ..      68     287 .. 0.85

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 3e-23
                                       SHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCH........... CS
                            DEAD_2   5 ThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeek........... 70 
                                        h+q++q+v+e + ++    ++e++++v+ +++  +C   +v  e+ ++  +   + l++ +  ++           
  gi|336252772|ref|YP_004595879.1|  72 VHQQMRQFVAEARAIT----REESIRAVVFKGKGSMCHI-DVGYEECQALRD-NTRALVDAERDKQqlerrqrellt 142
                                       699***********95....3578*************54.676655444434.334443333333336778899*** PP

                                       ..................................TTTTTT-SCC..CCHHHHHHHHHHC---CHHHHHHHHHCT--H CS
                            DEAD_2  71 ..................................eekCsffenl..eelkklkkllleevvdiedlvelgeklklCP 111
                                                                         ++ C++++n+  +++++    l+e v + +d++e+ e+++lC 
  gi|336252772|ref|YP_004595879.1| 143 esqeegsggsaadarsavmdelenieerledledQNVCDYYRNNltQDTDDFFGWLFEDVRTPDDIYEYAEQQQLCG 219
                                       *********************************9999****999666666668999********************* PP

                                       HHHHHHHHCCTSEEEEEHHHHTSCCCHHHHH...T..GCGCEEEECTCCCHHHHHHHCC-EEE CS
                            DEAD_2 112 YylsrelledadiiilpYqyLldekireslk...gislknsivilDEAhNiedvceeaasvei 171
                                       Y l +e +e +d++++ Y+ Lld+ ire++    g + ++ i ++DEAhN+ed +++ a  + 
  gi|336252772|ref|YP_004595879.1| 220 YELLKEGIEGVDLVVCNYHHLLDPMIREQFFrwlGRDPEDVIAVFDEAHNVEDAARDHATQHC 282
                                       ****************************9987877799****************999876655 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.3e-07   0.00046       3      83 ..      19      99 ..      17     177 .. 0.80
   2 ?    4.9   0.0     0.014        20      96     146 ..     228     283 ..     207     295 .. 0.70
   3 ?    1.8   0.0      0.13   1.8e+02     160     174 ..     455     470 ..     374     471 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.3e-07
                                      HHHHHHHHHH....TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                      xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  3 iQaeaiplil....gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77
                                       Q+ea++ i     +g++vl +++ G+GKTl  l+p+l+      +++++ ++i +  ++ ++q + +++ ++ + ++r
  gi|336252772|ref|YP_004595879.1| 19 NQREAMDRIHnalvRGQNVLFEGACGTGKTLSSLVPALEVA----REQNKTVVITTNVHQQMRQFVAEARAITREESIR 93
                                      6888888887777799**********************666....5667788999999999999999999888876666 PP

                                      EEEEET CS
                                      xxxxxx RF
                              DEAD 78 vlliig 83
                                      ++++ g
  gi|336252772|ref|YP_004595879.1| 94 AVVFKG 99
                                      664444 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.014
                                       TTCSEEEEEHHHHHH.HHHCTSSH.....CTTEEEEEEETHHHHHHTTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxx.xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  96 ngvdivvgtpgrldd.llstgkln.....lsqvrflVlDEadrlldqgfsdfinril 146
                                       +gvd+vv +   l+d +++++ ++      ++v + V+DEa+++ d  +    +++ 
  gi|336252772|ref|YP_004595879.1| 228 EGVDLVVCNYHHLLDpMIREQFFRwlgrdPEDV-IAVFDEAHNVEDAARDHATQHCS 283
                                       568999999999999666555544433223444.79**********96666666555 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.13
                                       SEEEEEESSBS.HHHH CS
                                       xxxxxxxxxxx.xxxx RF
                              DEAD 160 rqvivlSATlp.kdvk 174
                                         ++++SATl+ +dv+
  gi|336252772|ref|YP_004595879.1| 455 YATVLMSATLQpFDVT 470
                                       459********99986 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 !   23.7   0.1   2.9e-08   4.1e-05       4     146 ..      16     272 ..      14     295 .. 0.64

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.9e-08
                                       E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG...... CS
                            ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef...... 74 
                                       ++e Q ea++++ ++l   r +++l++ a+GtGKTl ++  + +++++++  k++++  ++++ +q+++ +      
  gi|336252772|ref|YP_004595879.1|  16 PYENQREAMDRIHNALV--RGQNVLFEGACGTGKTLSSLVPALEVAREQN--KTVVI--TTNVHQQMRQFVaearai 86 
                                       6899************6..999*********************9999866..66655..556666666444555667 PP

                                       ............................................................................. CS
                            ResIII  75 ............................................................................. 74 
                                                                                                                    
  gi|336252772|ref|YP_004595879.1|  87 treesiravvfkgkgsmchidvgyeecqalrdntralvdaerdkqqlerrqrelltesqeegsggsaadarsavmde 163
                                       77777777777777777777777777777777777777777777777777777777776666666666666666555 PP

                                       .....................GGGTGG....GEEEESSS-B--.................................. CS
                            ResIII  75 .....................kkflseaykeigkkvsgdkkka............................kekdst 102
                                                            +            ++++d++++                             ++ ++
  gi|336252772|ref|YP_004595879.1| 164 lenieerledledqnvcdyyrN------------NLTQDTDDFfgwlfedvrtpddiyeyaeqqqlcgyelLKEGIE 228
                                       5555444433333333222221............2222222224444444444444444555555666666666677 PP

                                       .-SEEEEEHHHHHHTH........HHHTTT-SEE.EEETGGGTTS CS
                            ResIII 103 nkkilvttiqsldadseeeeeeseellrdrfdvi.iiDEaHrlga 146
                                         +++v +++ l  ++  +e+    l+rd +dvi ++DEaH++ +
  gi|336252772|ref|YP_004595879.1| 229 GVDLVVCNYHHLLDPM-IREQFFRWLGRDPEDVIaVFDEAHNVED 272
                                       7777777777777776.3355666666666664437777777766 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   6.1e-07   0.00084       8      92 ..      24     101 ..      21     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.1e-07
                            ATPase   8 lDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegkla 84 
                                       +D+i ++ + +g+ vl  G  GtGKt+ +l  +++ a++ ++++v +t++      +++++++  + +++ +e+++ 
  gi|336252772|ref|YP_004595879.1|  24 MDRI-HNALVRGQNVLFEGACGTGKTLSSLVPALEVARE-QNKTVVITTNV-----HQQMRQFVAEARAITREESIR 93 
                                       7887.6999***************************999.99******865.....566777777777777776666 PP

                            ATPase  85 iidasesa 92 
                                        +    ++
  gi|336252772|ref|YP_004595879.1|  94 AVVFKGKG 101
                                       66555555 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     1e-06    0.0014     129     178 ..     444     495 ..     380     500 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1e-06
                                       CCHH.HHHHHCHCCCCCCTS-SSHHHHHHHHT.....EEE.S..S.GGHCCC CS
                               HBB 129 skal.rflkerlssllmsgtltpleeysdiiGle.aklkkfpspfpkEnliv 178
                                       ++++ +  +e+  ++lms tl+p++  +d++Gle +++  +   fp+En+ +
  gi|336252772|ref|YP_004595879.1| 444 RQVTgQLFEEVYATVLMSATLQPFDVTEDVLGLEdPVTMAYGLQFPEENRRT 495
                                       444425678999*************************************986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00045      0.62      24      61 ..      25      62 ..      15      97 .. 0.85
   2 ?   -0.5   0.2      0.58     8e+02      76     106 ..     123     161 ..     114     190 .. 0.72
   3 ?   -0.4   0.0      0.53   7.4e+02     106     139 ..     498     527 ..     476     533 .. 0.67
   4 ?    1.9   0.1      0.11   1.5e+02      46     111 ..     580     646 ..     579     671 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00045
                            AAA_25 24 wlvkgllpagelallaGapgtGKttlaldlalavatGk 61
                                      + +++ l++g  +l+ Ga gtGKt   l  al+va+ +
  gi|336252772|ref|YP_004595879.1| 25 DRIHNALVRGQNVLFEGACGTGKTLSSLVPALEVAREQ 62
                                      679999*****************************543 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.58
                            AAA_25  76 yvsaEdsedelrrRlravgeal........rddarllvl 106
                                       +v+aE + ++l+rR r+++++         ++dar +v+
  gi|336252772|ref|YP_004595879.1| 123 LVDAERDKQQLERRQRELLTESqeegsggsAADARSAVM 161
                                       689999999999999998877645555555444444444 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.53
                            AAA_25 106 ldlagveslpLfakdrggtlltad.vdaleaaiee 139
                                       +     e  pLfa+dr++++++++ +da+ +a++ 
  gi|336252772|ref|YP_004595879.1| 498 V-----ETPPLFASDRDDPAVQEEvTDAIYDAVRM 527
                                       2.....4689**********766515555555555 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.11
                            AAA_25  46 KttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal......rddarllvldlagv 111
                                       K +l+++l  ++a+G ++ g+      +Vl+v    +   l  R++av ea+      ++ ++ +++ +++v
  gi|336252772|ref|YP_004595879.1| 580 KAVLCTSLWGTLAEGVSFDGD---DAHTVLVVGVPYPH--LDDRAEAVQEAYdvafdgTETGWRYAVEIPTV 646
                                       678999999999*****9993...56788888866666..88888888888877666566677777776666 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.9e-05     0.068       8      55 ..      19      70 ..      15      82 .. 0.77
   2 ?   -2.8   0.0       2.5   3.5e+03     115     133 ..     254     272 ..     249     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.9e-05
                                      HHHHHHHHHH....H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEE CS
                              PhoH  8 eQkeylealk....kndivfaiGpaGtGKtylavalavealkkkkvkriilt 55
                                      +Q+e+++ ++    + + v   G  GtGKt+ +++ a+e+ ++++ + +i t
  gi|336252772|ref|YP_004595879.1| 19 NQREAMDRIHnalvRGQNVLFEGACGTGKTLSSLVPALEVAREQNKTVVITT 70
                                      6777777776555567789999*****************9888775555544 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.5
                                       T--B-SEEEEE-SGGG--H CS
                              PhoH 115 GrTlndafvilDEAQnttk 133
                                       Gr  +d + ++DEA n++ 
  gi|336252772|ref|YP_004595879.1| 254 GRDPEDVIAVFDEAHNVED 272
                                       6667788999******986 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.8e-05     0.052      33     115 ..      17     100 ..      15     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
                            DUF815  33 idkqkealventeqfleglpannvLLwGarGtGK..SslvkallneyaeegLrli..evekedlkelpklvellrer 105
                                       +++q+ea+ +  +++++g   +nvL+ Ga GtGK  Sslv al  + ++++  +i  +v+++  + + +  ++ re+
  gi|336252772|ref|YP_004595879.1|  17 YENQREAMDRIHNALVRG---QNVLFEGACGTGKtlSSLVPALEVAREQNKTVVIttNVHQQMRQFVAEARAITREE 90 
                                       678888888888888877...69***********999*****98877777655542256666666677777778888 PP

                            DUF815 106 perfilfvDD 115
                                       + r ++f   
  gi|336252772|ref|YP_004595879.1|  91 SIRAVVFKGK 100
                                       8999998655 PP

>> AAA_34  P-loop containing NTP hydrolase pore-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.4e-05     0.061     162     195 ..     247     281 ..     201     297 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.4e-05
                            AAA_34 162 eqlveWlgedfdGvi.vfDEchkaknlakseekka 195
                                       eq+ +Wlg+d + vi vfDE+h+++++a ++ ++ 
  gi|336252772|ref|YP_004595879.1| 247 EQFFRWLGRDPEDVIaVFDEAHNVEDAARDHATQH 281
                                       799*****777666549*********998765443 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0013       1.9       3      45 ..      36      76 ..      34     120 .. 0.70
   2 ?    3.3   0.1     0.028        39      86     108 ..     255     280 ..     211     299 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0013
                           DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl 45
                                       vl +G+ GtGKt+  l  + e+   +e++++v+++ N  +++
  gi|336252772|ref|YP_004595879.1| 36 NVLFEGACGTGKTLSSLVPALEV--AREQNKTVVITTNVHQQM 76
                                      57889********9988888888..555555555555544332 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.028
                           DUF2075  86 epkedv.vivDEAhrllt..ksdqae 108
                                       +++edv +++DEAh + +  + ++++
  gi|336252772|ref|YP_004595879.1| 255 RDPEDViAVFDEAHNVEDaaRDHATQ 280
                                       45555527*******99954222222 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00035      0.48       4      38 ..      37      71 ..      35     147 .. 0.91
   2 ?   -3.6   0.0       3.6     5e+03     269     295 ..     206     232 ..     196     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00035
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      +l+ G  G GKt +s   a++++++++k+++i+t 
  gi|336252772|ref|YP_004595879.1| 37 VLFEGACGTGKTLSSLVPALEVAREQNKTVVITTN 71
                                      8999*****************************96 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.6
                                       HHHHHHTTTSEEEEEE--SS-S-SHHH CS
                       ArsA_ATPase 269 keieelfedlevvklplleeEvvGlek 295
                                       ++i+e+ e++++  + ll+e + G++ 
  gi|336252772|ref|YP_004595879.1| 206 DDIYEYAEQQQLCGYELLKEGIEGVDL 232
                                       78999999999*********9999975 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 ?    8.4   3.8     0.002       2.7      20      77 ..     114     173 ..     110     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.002
                            CENP-H  20 qelrelqeeltevekenlrlkrknrelaaellelakekesek..eklkeelekleaelkk 77 
                                       q+lr+ +++l ++e++  +l+r++rel++e +e+ +  ++ +  + +++ele++e+ l++
  gi|336252772|ref|YP_004595879.1| 114 QALRDNTRALVDAERDKQQLERRQRELLTESQEEGSGGSAADarSAVMDELENIEERLED 173
                                       789999*************************76666666666688899999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (727 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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):              13  [number of targets reported over threshold]
# CPU time: 0.76u 0.25s 00:00:01.01 Elapsed: 00:00:00.42
# Mc/sec: 5141.99
//
Query:       gi|336252773|ref|YP_004595880.1|  [L=116]
Description: hypothetical protein Halxa_1368 [Halopiger xanaduensis SH-6]
Scores for 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   14.9   0.1      0.031   14.5   0.1    1.3  1  DUF3247   Protein of unknown function (DUF3247)


Domain annotation for each model (and alignments):
>> DUF3247  Protein of unknown function (DUF3247)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.7e-06     0.031      23      78 ..      29      82 ..      25     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-06
                                      HCTTTT-EEEEEETTS-EEEEEECC---EEEEE-TT--EEEEEEEEEE-SSTT-SE CS
                           DUF3247 23 klldseervaleledGrqlaGtvavrptvqiyrdeqereGvnallrlddlddsseq 78
                                      + l  +erv +  ++G  l+ +v v+    +   + ereG+   lrld++++   +
  gi|336252773|ref|YP_004595880.1| 29 TTLGEDERVEFSADEGAELSVSVDVQEVFPLEDSDLEREGI--SLRLDHVENGIVD 82
                                      568889*********************999999999****8..59****9986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 887.92
//
Query:       gi|336252774|ref|YP_004595881.1|  [L=107]
Description: Rhodanese-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.4   0.1    2.2e-15   57.1   0.1    1.1  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.1   1.2e-19   2.2e-15       1     105 [.       6      99 ..       6     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.2e-19
                         Rhodanese   1 sakelkellekgkva...llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycd 74 
                                       s++ ++e++e+g+ +   l+DvR++++Y++gh+pgA +v                el + + ++  d  + vvvyc 
  gi|336252774|ref|YP_004595881.1|   6 SPETVRERIERGDDDefdLIDVRDADAYDDGHLPGAEHV-------------TIEELEDTVVDR--DWADDVVVYCY 67 
                                       678899999999877999*********************.............888888888888..*********** PP

                         Rhodanese  75 gggraaaaaallkklGykn.vsvldGGfkawk 105
                                        g+ + +aa+l++++G  + v  + GG++aw 
  gi|336252774|ref|YP_004595881.1|  68 VGKTSVQAARLIEEYGDADsVASMAGGYDAWD 99 
                                       *************9**9999***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 815.35
//
Query:       gi|336252775|ref|YP_004595882.1|  [L=97]
Description: SirA-like domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-12   45.5   0.0    7.2e-12   45.0   0.0    1.2  1  TusA      Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0     4e-16   7.2e-12       4      70 .]      31      96 ..      29      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 4e-16
                                      EBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTE.EEEEEE-GCC-EEEEEEE CS
                              TusA  4 DlrGlvCPePllklkkalekleegevlevladdpaatediprfakklgh.elveveeedgeyrivirk 70
                                      D++G+vCP+P +++kk l +le+g+ l   +d+ ++te++p+ +      ++      d +yri++rk
  gi|336252775|ref|YP_004595882.1| 31 DMMGEVCPYPQVEAKKGLQQLESGDLLVQETDHVPCTENVPKAVGDDAEaKVWRS--GDATYRIYLRK 96
                                      99******************************************99888577777..99999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 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:                        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 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 775.85
//
Query:       gi|336252776|ref|YP_004595883.1|  [L=390]
Description: hypothetical protein Halxa_1371 [Halopiger xanaduensis SH-6]
Scores for 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-57  194.0  31.5    4.4e-57  194.0  31.5    1.9  2  Sulf_transp  Sulphur transport


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.4      0.16   2.8e+03     232     243 ..       8      19 ..       3      20 .. 0.79
   2 !  194.0  31.5   2.4e-61   4.4e-57       1     310 []      21     377 ..      21     377 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.16
                       Sulf_transp 232 vlvlGiilGafl 243
                                       + v+Gi lGafl
  gi|336252776|ref|YP_004595883.1|   8 AAVVGIALGAFL 19 
                                       568999999997 PP

  == domain 2  score: 194.0 bits;  conditional E-value: 2.4e-61
                       Sulf_transp   1 rsrfcfagairdivvekdgrllralllaiavaavgfqllaaaglidl.pksafpvvglivGGllFGvGMalaGgCas 76 
                                       ++rfcf++a+rd++  kd+r  + +l a ++++v++++  ++g+++  ++     +  +vGG++FGvGM+ aGgCas
  gi|336252776|ref|YP_004595883.1|  21 KGRFCFVNAFRDFFAYKDSRVTKGVLAATLLTMVFWGIAYQFGYYQGfWTPRWG-LTGLVGGFVFGVGMTYAGGCAS 96 
                                       79*******************************************853665444.899******************* PP

                       Sulf_transp  77 gtlyrvGeGslralitllffilgavalltgilsswleqllestvskeslyetlglsplll..ialllliallllvke 151
                                       gtlyr+GeG+l+ ++tllf+++g++   t +++++ ++ + +  +  + ++++++s l +  +all+  a+ll++++
  gi|336252776|ref|YP_004595883.1|  97 GTLYRAGEGYLQFWLTLLFMGVGYA-GFTVAFPTLESTYFDA-LTFGEGVSLFAYSSLPAglLALLVSGAVLLVYAT 171
                                       *********************9965.4554555555555544.5666666777777554410444444444444444 PP

                       Sulf_transp 152 lrkek...............................lqeae......klektslak..klfrkpwslvlgavllgll 189
                                       l   +                                          +  + ++ +  +  ++pw++ ++a+ + + 
  gi|336252776|ref|YP_004595883.1| 172 LTG-RssvgaalgeradaaefrpaalaapavglrqfA---DgtrayfAGLARAWRNpiEASKQPWDPRTAALGITAA 244
                                       433.224555666666666666666555554443331...1322223223334443224778999999999888877 PP

                       Sulf_transp 190 avlawllsaktgrsfglgftvpgakilqyl..................vlgtskflnwgvvlvlGiilGaflaalls 248
                                       avl w++       + +g+t+p a+++ yl                    g+   ++  +v++  +i+Gaflaa++s
  gi|336252776|ref|YP_004595883.1| 245 AVL-WFTQ-----VSIVGVTGPEARWTGYLlsqvgvdagsfeywgsvlFQGQGVGVTVDMVMIAFVIVGAFLAAVWS 315
                                       777.3332.....222344444444444432222221111111122113355556777899**************** PP

                       Sulf_transp 249 gefkleapkarellaallGGllMGfGarlAgGCniGaglsgiaslslsgwlalvflllGavl 310
                                       g+f+l++pk+r+l  a++GGl MG G+rlA GCniG+++sgia ls+++++a+v++++G+++
  gi|336252776|ref|YP_004595883.1| 316 GDFSLRVPKRRRLPNAVFGGLAMGAGSRLAPGCNIGNIYSGIAELSVHSFIAAVGIVAGVYV 377
                                       ***********************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 3237.33
//
Query:       gi|336252777|ref|YP_004595884.1|  [L=166]
Description: phosphoesterase HXTX [Halopiger xanaduensis SH-6]
Scores for complete 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   60.7   0.1    1.8e-16   60.4   0.1    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    1.2e-07   31.8   0.0    0.00014   21.9   0.0    2.4  3  LigT_PEase       LigT like Phosphoesterase


Domain annotation for each model (and alignments):
>> 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 !   60.4   0.1     2e-20   1.8e-16      25     146 ..      31     151 ..       6     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 2e-20
                   2_5_RNA_ligase2  25 ppHitLlypfvededladlaellsrlaketepfevrldgfgvFeh...kks.vvylsvsdsealqalraallealpe 97 
                                       + H  Ll      ++ ++l++++ r++++++++e+r++g+++F +    +  vvyl v  s+ l+al+a+l+e + +
  gi|336252777|ref|YP_004595884.1|  31 ETHSCLLKRLGDADHVSQLQHRVHRALESAPAVEARITGIDYFADpplGSApVVYLAV-ESPGLEALHADLAETFDA 106
                                       48999999999999*****************************99**97777******.****************** PP

                   2_5_RNA_ligase2  98 agdkedsgeftPHlTiaqsadstsaaelleklaqalpplefevdevall 146
                                        + +e   +++PH+T+a+  d++ a   ++ + ++ +p++++v+e+ ++
  gi|336252777|ref|YP_004595884.1| 107 VDGLEG-ADYVPHVTLARGGDAETA---RRLADREIEPVTWTVSELEFW 151
                                       *99986.*************77775...55556679**********998 PP

>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         1   9.2e+03       9      19 ..      10      20 ..       6      29 .. 0.68
   2 !    7.3   0.0   0.00057       5.1      39      81 ..      37      77 ..      37      84 .. 0.84
   3 !   21.9   0.0   1.6e-08   0.00014      10      78 ..      92     152 ..      86     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1
                                      HHHHHHHHHHH CS
                        LigT_PEase  9 eelarlaaele 19
                                       ++++la+el 
  gi|336252777|ref|YP_004595884.1| 10 GRVRQLADELY 20
                                      56777777776 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00057
                                      EEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC CS
                        LigT_PEase 39 Laflgevdeekvpellealaeiasgaepfelkvdgvglfpsrl 81
                                      L++lg+  ++ v++l  ++ ++ + a+++e +++g+ +f+++ 
  gi|336252777|ref|YP_004595884.1| 37 LKRLGD--ADHVSQLQHRVHRALESAPAVEARITGIDYFADPP 77
                                      899999..6789999999999999999999*********9764 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 1.6e-08
                                       HHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEE CS
                        LigT_PEase  10 elarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfp 78 
                                        l++l+a+l++ + + ++    ++ pH+TLa+ g+      +e  ++la+   ++ep++++v+++  + 
  gi|336252777|ref|YP_004595884.1|  92 GLEALHADLAETFDAVDGLEGADYVPHVTLARGGD------AETARRLADR--EIEPVTWTVSELEFWD 152
                                       6888999999888888887779************9......4677778877..788*******999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1232.51
//
Query:       gi|336252778|ref|YP_004595885.1|  [L=64]
Description: hypothetical protein Halxa_1373 [Halopiger xanaduensis SH-6]
Scores for 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   3.1      0.066   12.9   3.1    1.0  1  DUF2244   Integral membrane protein (DUF2244)


Domain annotation for each model (and alignments):
>> DUF2244  Integral membrane protein (DUF2244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.1   3.7e-06     0.066       2      54 ..       3      57 ..       2      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-06
                           DUF2244  2 kPnrSlsprgflllllalalvslvialafl..laGawpvlpFaglevlalalafr 54
                                       +  Sl  + +l l+l l++v+lvi ++ +  +  aw++ pF+++  la+a+ + 
  gi|336252778|ref|YP_004595885.1|  3 DRRGSLDVETLLKLVLGLIAVLLVIEIVETllSGLAWLLGPFVVIVQLAIAVLIV 57
                                      677799999999999999999999999876535569********99999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 483.45
//
Query:       gi|336252779|ref|YP_004595886.1|  [L=422]
Description: hypothetical protein Halxa_1374 [Halopiger xanaduensis SH-6]
Scores for 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   13.8   0.4       0.12   12.1   0.4    1.9  1  DUF1654       Protein of unknown function (DUF1654)
      0.042   13.7   0.1      0.066   13.0   0.1    1.2  1  DUF4897       Domain of unknown function (DUF4897)
      0.042   13.6   2.3        3.1    7.6   0.3    2.3  2  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr
       0.11   12.4   1.0       0.87    9.4   0.5    2.4  2  DUF3117       Protein of unknown function (DUF3117)


Domain annotation for each model (and alignments):
>> DUF1654  Protein of unknown function (DUF1654)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   2.6e-05      0.12      22      59 ..      88     125 ..      85     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                           DUF1654  22 araavvlrledeseddWerlleeiaeteevelafrdDg 59 
                                       ar +v +r e++s +dWe+l e+i+ + +  +a + D+
  gi|336252779|ref|YP_004595886.1|  88 ARFVVDYRFENDSSGDWEALREDIEANGDTYVADEMDA 125
                                       688999********************999988877776 PP

>> DUF4897  Domain of unknown function (DUF4897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.5e-05     0.066      39     147 ..     116     226 ..     107     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                           DUF4897  39 eqYqkaseetfekylsqlseevgreikvvsl...essateregileveEkavlkglvkvengvvetslgdiklnlag 112
                                       ++Y   + +++++ l++ ++ ++re++++s    + + t+  ++ +v+      +++ ve + +e+      + l++
  gi|336252779|ref|YP_004595886.1| 116 DTYVADEMDAWNRTLEDSANATDREMHLESGaigTDTSTQPRNLGHVQVSFEWVNFAYVELNRIEVGDVLTGIVLSQ 192
                                       67888888999*****************99622234556666777777788888999999888777666678999** PP

                           DUF4897 113 dselvvslPkdaklisvePtPtkivenellWkges 147
                                       d+++ v+ P+   +is +   t+  e+ ++W+g+s
  gi|336252779|ref|YP_004595886.1| 193 DTTMEVYPPEGY-VISEDESSTESNEDSVFWQGDS 226
                                       ******988775.7899999************987 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 ?    5.4   0.1    0.0031        14      66     109 ..      12      55 ..       8      70 .. 0.80
   2 ?    7.6   0.3   0.00069       3.1      95     134 ..     245     284 ..     233     295 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0031
                      Trp_oprn_chp  66 grrvvgvllalagagaavaalslltdpadaaraaaaaatgvasa 109
                                       +++vvg l a+a +ga +aa+ +  +++ a +++++  ++++++
  gi|336252779|ref|YP_004595886.1|  12 ALVVVGCLFAVAPIGAPFAAADAGNGGPNALAQQDEGLSQTQTQ 55 
                                       689********************999998888887554444333 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00069
                      Trp_oprn_chp  95 aaraaa.aaatgvasaaaaveltawpvlalaggvllllagv 134
                                       ++++a+ +  +g+++++ + + +a+ ++ +ag+++ll+a v
  gi|336252779|ref|YP_004595886.1| 245 SNESANaTPNSGASGEQGQGQGPAMRWVIVAGALALLAA-V 284
                                       333343355566666666666666667666655544443.3 PP

>> DUF3117  Protein of unknown function (DUF3117)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.18   8.1e+02       5      40 ..     324     364 ..     323     368 .. 0.67
   2 ?    9.4   0.5   0.00019      0.87       7      29 ..     376     398 ..     374     400 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.18
                           DUF3117   5 tgdGplEvvkegrgivlRvPleGGGRL.....VvelnkeEa 40 
                                       t++Gp     ++ + vlR+  + GGR+     V el  +Ea
  gi|336252779|ref|YP_004595886.1| 324 TSNGPPPELLSNEERVLRLLEQRGGRIkqqavVSELDWTEA 364
                                       55666666667778899999999999744442446666665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00019
                           DUF3117   7 dGplEvvkegrgivlRvPleGGG 29 
                                       dG++Ev + gr+ vl +P eG G
  gi|336252779|ref|YP_004595886.1| 376 DGEIEVFRIGRENVLSLPDEGDG 398
                                       9*******************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3087.04
//
Query:       gi|336252780|ref|YP_004595887.1|  [L=413]
Description: Argininosuccinate synthase [Halopiger xanaduensis SH-6]
Scores for 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-142  474.0   0.0     5e-142  473.8   0.0    1.0  1  Arginosuc_synth  Arginosuccinate synthase
    2.6e-05   23.8   0.0      5e-05   22.9   0.0    1.4  1  QueC             Queuosine biosynthesis protein QueC
     0.0026   16.6   0.0     0.0041   15.9   0.0    1.4  1  tRNA_Me_trans    tRNA methyl transferase
     0.0043   16.8   0.6      0.019   14.7   0.0    2.0  2  Asn_synthase     Asparagine synthase
  ------ inclusion threshold ------
       0.03   13.4   0.0      0.047   12.8   0.0    1.3  1  NAD_synthase     NAD synthase
       0.25   11.6   1.4        2.6    8.4   0.1    2.7  3  SMC_hinge        SMC proteins Flexible Hinge Domain


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 !  473.8   0.0  1.7e-145    5e-142       2     387 ..       6     386 ..       5     387 .. 0.98

  Alignments for each domain:
  == domain 1  score: 473.8 bits;  conditional E-value: 1.7e-145
                   Arginosuc_synth   2 LaysGGlDtsviikllkeklg.eeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikanal 77 
                                       La+sGGlDt+v+++ll+e++g +evi v+vdvGq+ e+++e++e a++l   +++vvDak+ef+ d ++ +++ana+
  gi|336252780|ref|YP_004595887.1|   6 LAFSGGLDTTVCVPLLEEEYGyDEVIGVTVDVGQPAEEFEEAEETAEALDL-DHYVVDAKDEFA-DLCLESVRANAT 80 
                                       9********************899**********************99865.************.9*********** PP

                   Arginosuc_synth  78 YedrYllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeieya 154
                                       Y++ Y+lgtalaRP+iak+++eva++++++ +ahGctGkGnDq+Rfe++ r+ +  l+viaPvRel ltRe+e eya
  gi|336252780|ref|YP_004595887.1|  81 YQG-YPLGTALARPVIAKAILEVAEEQDCDGIAHGCTGKGNDQLRFEAVWRDSD--LEVIAPVRELGLTREWEQEYA 154
                                       ***.*********************************************99877..********************* PP

                   Arginosuc_synth 155 kekgipvevtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeels 231
                                       +e+++pve  +   +siD nl++rs+e+++Ledp+ +ppe+iy++t++p+ +    +e+eiefe+G Pva+dg e++
  gi|336252780|ref|YP_004595887.1| 155 DERDLPVEGGSGGDWSIDTNLWSRSVEGDKLEDPSYVPPEEIYAWTQSPTGDS---QEIEIEFEEGYPVAVDGVEYE 228
                                       *************************************************9876...99******************* PP

                   Arginosuc_synth 232 vlelieklneiagkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvYk 308
                                       ++eli++lne+ag  GvGR+D +edR++glk Re+Ye+paa++L++ah++le l+l++e+++fk+ +++++a+  Y+
  gi|336252780|ref|YP_004595887.1| 229 PVELIQHLNEVAGPYGVGRTDSMEDRMLGLKVRENYEHPAATTLLNAHEALEGLVLTQEEREFKQLIDQRWAKKGYE 305
                                       ***************************************************************************** PP

                   Arginosuc_synth 309 GlwfsPlkealdafiektqervtGtvrvklfkGsvvvlgReseeslYdeelasydeed..efdqkeaeGfikihglq 383
                                       Gl+  Pl +al+ fi++tq+rvtGtv +++  G+++ ++R+s  + Y++e as+d+e+  +++q++a+G++k+hg+q
  gi|336252780|ref|YP_004595887.1| 306 GLVDAPLVSALEGFIAETQKRVTGTVTIRFEGGQARAVARDSTFAAYSAEHASFDTETvgKIKQEDATGVAKYHGFQ 382
                                       *******************************************************8754489**************9 PP

                   Arginosuc_synth 384 akly 387
                                        +l+
  gi|336252780|ref|YP_004595887.1| 383 RRLA 386
                                       9875 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.7e-08     5e-05       4      62 ..       6      64 ..       3      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.7e-08
                                      EE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-G CS
                              QueC  4 vllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildld 62
                                      + +SGGlD t+++ l ++e+  +ev+ +t+d gq  ++e e a++ a++l++ +h ++d +
  gi|336252780|ref|YP_004595887.1|  6 LAFSGGLDTTVCVPLLEEEYgyDEVIGVTVDVGQP-AEEFEEAEETAEALDL-DHYVVDAK 64
                                      569************99997669**********97.5799************.99999986 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.4e-06    0.0041       2      81 ..       3      74 ..       2     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-06
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekv 78
                                      +v+ a+SgG D +v + ll+e++   evigv++ + +            e++++ae+ ae l++ ++vvd ++e+ +  
  gi|336252780|ref|YP_004595887.1|  3 RVALAFSGGLDTTVCVPLLEEEYgyDEVIGVTVDVGQP----------AEEFEEAEETAEALDLDHYVVDAKDEFADLC 71
                                      799*****************996546899999876554..........467889*********************8876 PP

                     tRNA_Me_trans 79 fee 81
                                      +e+
  gi|336252780|ref|YP_004595887.1| 72 LES 74
                                      665 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   6.3e-06     0.019      20      86 ..       4      69 ..       2      88 .. 0.86
   2 ?   -0.4   0.2      0.23   6.9e+02      36      84 ..     319     372 ..     314     378 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.3e-06
                      Asn_synthase 20 vGalLSGGlDSSliaalaarqsk.splktFsigfeekgsdeakyakevaehlgtehtelvlteeelld 86
                                      v++ +SGGlD ++ + l+ ++    ++  ++++   +  +e + a+e+ae+l ++h+ +  +  e++d
  gi|336252780|ref|YP_004595887.1|  4 VALAFSGGLDTTVCVPLLEEEYGyDEVIGVTVDV-GQPAEEFEEAEETAEALDLDHYVVDAKD-EFAD 69
                                      78899***************998889********.899*****************97666544.5665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.23
                      Asn_synthase  36 laarqsksplktFsigf....eekgsdeakyakevaehlgte.htelvlteeel 84 
                                       + a+ +k+   t++i f    + +   ++ +a++ aeh   +  t   +++e++
  gi|336252780|ref|YP_004595887.1| 319 FIAETQKRVTGTVTIRFeggqARAVARDSTFAAYSAEHASFDtETVGKIKQEDA 372
                                       556666778889999995543238889999999999999998445556666665 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.6e-05     0.047      20      84 ..       3      66 ..       1      82 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                                      EEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHH CS
                      NAD_synthase 20 gvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpi 84
                                       v l  SGG+D ++   l  +  g ++v+++ + ++ ++ e+ e+a + ae l+++  ++d k+ 
  gi|336252780|ref|YP_004595887.1|  3 RVALAFSGGLDTTVCVPLLEEEYGYDEVIGVTV-DVGQPAEEFEEAEETAEALDLDHYVVDAKDE 66
                                      678999***************************.999999***************9999998875 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 ?    8.4   0.1   0.00087       2.6       4      44 ..      30      70 ..      28      84 .. 0.84
   2 ?   -3.7   0.0       4.8   1.4e+04      13      29 ..     259     275 ..     258     279 .. 0.72
   3 ?    1.0   0.0      0.17     5e+02       8      43 ..     294     329 ..     287     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00087
                         SMC_hinge  4 vlGrladlievdegyekAveaalgnrlqalvvedeetakki 44
                                      v+G+ +d+ +++e++e A e+a   +l++ vv+ +++   +
  gi|336252780|ref|YP_004595887.1| 30 VIGVTVDVGQPAEEFEEAEETAEALDLDHYVVDAKDEFADL 70
                                      89999****************************99986543 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.8
                         SMC_hinge  13 evdegyekAveaalgnr 29 
                                       +v+e ye + ++ l n+
  gi|336252780|ref|YP_004595887.1| 259 KVRENYEHPAATTLLNA 275
                                       78999998888777665 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.17
                         SMC_hinge   8 ladlievdegyekAveaalgnrlqalvvedeetakk 43 
                                       l+d    ++gye  v+a l ++l+ ++ e+++ ++ 
  gi|336252780|ref|YP_004595887.1| 294 LIDQRWAKKGYEGLVDAPLVSALEGFIAETQKRVTG 329
                                       566656689********************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); 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 0.22s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3121.58
//
Query:       gi|336252781|ref|YP_004595888.1|  [L=500]
Description: Argininosuccinate lyase [Halopiger xanaduensis SH-6]
Scores for 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-59  199.7   0.1    1.6e-58  198.5   0.0    1.6  2  Lyase_1        Lyase
    1.3e-16   61.0   0.6    1.3e-16   61.0   0.6    2.9  4  ASL_C2         Argininosuccinate lyase C-terminal
  ------ inclusion threshold ------
      0.055   13.0   0.0       0.25   10.9   0.0    2.2  1  Phage_fiber_2  Phage tail fibre repeat


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 !  198.5   0.0   2.7e-62   1.6e-58      24     312 .]      50     315 ..      39     315 .. 0.93
   2 ?   -2.7   0.0      0.51     3e+03      65      65 ..     366     366 ..     332     433 .. 0.60

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 2.7e-62
                                       GHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHHHHHHTTHSSG CS
                           Lyase_1  24 lseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnevigellgekve 100
                                       + e+d ++  a    +a+ ++ +  +a +++ ald++  eg+++      +  e+ + a++ ++ e ig       e
  gi|336252781|ref|YP_004595888.1|  50 IFEADLEVDRAHVVMLAEQGIVADDVAGNVLTALDAIEVEGHAG-----LPEGEDVHEAIETAVIERIG-------E 114
                                       55555555556666688999999999999999****99999999.....7899****************.......9 PP

                                       IIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHH CS
                           Lyase_1 101 pndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayae 177
                                         +k ht++S+nD v+  +r+ l++ + e ++++l  L+++l+e a e++d+v++G+Thlq+A+P+t g++  +y +
  gi|336252781|ref|YP_004595888.1| 115 QGGKMHTARSRNDEVAACIRYRLREDVLEAIETTL-ALRESLVEVAAEHADTVMPGYTHLQPAQPITVGHWALSYEA 190
                                       ***************************99777776.7**************************************** PP

                                       HHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHHHHHHH CS
                           Lyase_1 178 alerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglpvkapnsfeavsdrDavvellgalkl 254
                                       a++rd erl e+++r+++++lgg++ +gt +++d+e   + a+ l+ ++g   + +ns++a s+rD+++e++++l++
  gi|336252781|ref|YP_004595888.1| 191 AVRRDTERLLEAYDRINQSPLGGAAFAGTTFDIDRE---RTAELLG-FDG---VVENSMDASSSRDFLLETVQTLST 260
                                       ************************************...99**9*9.***...************************ PP

                                       HHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHHHH CS
                           Lyase_1 255 latsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagrvvG 312
                                        at Ls +aeD+ ++++   g+v ls+ +s+  SSiMP+K+NP++lEl++ vag + G
  gi|336252781|ref|YP_004595888.1| 261 HATTLSGLAEDVVIFAN--RGFVDLSDDYSS-TSSIMPQKKNPDTLELVRAVAGDAAG 315
                                       *****************..***********9.9*******************998765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.51
                                       H CS
                           Lyase_1  65 k 65 
                                       +
  gi|336252781|ref|YP_004595888.1| 366 N 366
                                       1 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.6   9.5e+03      40      63 ..      81     105 ..      60     108 .. 0.47
   2 ?   -3.1   0.0       2.4   1.4e+04      39      58 ..     335     355 ..     330     368 .. 0.55
   3 !   61.0   0.6   2.2e-20   1.3e-16       1      69 []     378     447 ..     378     447 .. 0.77
   4 ?   -2.3   0.2       1.3   7.9e+03      32      55 ..     470     493 ..     459     499 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                                       GG--HHHHHHH-TT--.GGGGGGSS CS
                            ASL_C2  40 eeltleelkeisplle.edveeaLd 63 
                                        +l+  e++  + l e edv+ea++
  gi|336252781|ref|YP_004595888.1|  81 TALDAIEVEGHAGLPEgEDVHEAIE 105
                                       2333333332234455567777665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                                       GGG--HHHHHHH-TT--.GGG CS
                            ASL_C2  39 leeltleelkeisplle.edv 58 
                                       l+ +t  ++++++ + e ++v
  gi|336252781|ref|YP_004595888.1| 335 LQRATTHAWETVDAVTEaSEV 355
                                       555555555555443333333 PP

  == domain 3  score: 61.0 bits;  conditional E-value: 2.2e-20
                                       STTHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH.-...TT--.GGGGGGSSHHHHTT CS
                            ASL_C2   1 FstATdlADyLvrkGlpFReAHeivgravrlaeekgkeleeltleelkei.s...plle.edveeaLdpeasVa 69 
                                       FstAT++AD+L+++GlpFR+AHe+v+ a+++    g + ++l+ ++ + + +   +l++ edv++aLdp++sVa
  gi|336252781|ref|YP_004595888.1| 378 FSTATGVADLLAANGLPFRTAHEMVAVAAEN----GGDYDALEAAAADVLgEpleSLVDpEDVRDALDPAESVA 447
                                       9*****************************9....3333333333333223233266***************96 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.3
                                       HHHTT--GGG--HHHHHHH-TT-- CS
                            ASL_C2  32 aeekgkeleeltleelkeisplle 55 
                                       a++++ +  e+ +++l+ ++++l 
  gi|336252781|ref|YP_004595888.1| 470 AIAADEATLEARIDALEDAHEALR 493
                                       444444444555555554444444 PP

>> Phage_fiber_2  Phage tail fibre repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.1e-05      0.25       4      19 ..     277     292 ..     275     294 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.1e-05
                     Phage_fiber_2   4 qkGivqLssatdStse 19 
                                       ++G+v Ls+ ++Sts+
  gi|336252781|ref|YP_004595888.1| 277 NRGFVDLSDDYSSTSS 292
                                       68*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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 0.23s 00:00:00.78 Elapsed: 00:00:00.38
# Mc/sec: 3935.23
//
Query:       gi|336252782|ref|YP_004595889.1|  [L=54]
Description: lysine biosynthesis protein LysW [Halopiger xanaduensis SH-6]
Scores for 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   18.2   1.8     0.0042   16.7   1.8    1.7  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
     0.0037   16.9   0.5        2.3    8.1   0.0    2.2  2  zinc_ribbon_2    zinc-ribbon domain
     0.0087   16.4   0.3      0.013   15.9   0.3    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
      0.014   15.2   1.0      0.052   13.4   0.0    2.0  2  ADD_ATRX         Cysteine Rich ADD domain
      0.015   15.3   1.3      0.061   13.3   1.4    1.8  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.019   14.3   0.2       0.91    9.0   0.0    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.026   14.5   0.8       0.28   11.3   0.8    1.9  1  DZR              Double zinc ribbon
      0.035   14.1   0.3      0.036   14.1   0.3    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.04   13.7   0.0        6.8    6.6   0.0    2.1  2  zf-HYPF          HypF finger
      0.042   13.4   3.6      0.057   12.9   3.6    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.064   13.4   2.4       0.22   11.7   2.3    1.8  2  Zn-ribbon_8      Zinc ribbon domain
       0.07   13.0   1.5       0.38   10.7   1.5    1.9  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.073   12.7   0.9        4.6    6.9   0.1    2.3  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.086   12.8   2.2        7.3    6.7   0.1    2.2  2  YhfH             YhfH-like protein
        0.1   12.2   2.3       0.89    9.2   0.2    2.1  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.12   12.4   0.9       0.15   12.1   0.9    1.1  1  DUF1451          Zinc-ribbon containing domain
       0.27   11.3   1.2          2    8.5   0.1    2.0  2  zf-C3HC          C3HC zinc finger-like
       0.65   10.0   4.9        1.2    9.2   4.9    1.4  1  Prok-RING_1      Prokaryotic RING finger family 1
        1.3    9.1   4.1        6.6    6.8   0.4    2.0  2  Eapp_C           E2F-associated phosphoprotein


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 !   16.7   1.8   4.5e-06    0.0042       3      25 ..       4      30 ..       3      32 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.5e-06
                                      -SSS--B--....--SSS----SSS-- CS
                    DNA_RNApol_7kD  3 CgeCgaevs....lkkgdpiRCkeCGh 25
                                      C eCgaevs    l+ g+++ C++CG 
  gi|336252782|ref|YP_004595889.1|  4 CVECGAEVSlhddLEVGEIVDCTTCGA 30
                                      ********933344789*********6 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1     0.004       3.8       2      10 ..       4      12 ..       3      16 .. 0.84
   2 !    8.1   0.0    0.0024       2.3       2      10 ..      25      33 ..      25      37 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.004
                     zinc_ribbon_2  2 CpnCGaelq 10
                                      C +CGae++
  gi|336252782|ref|YP_004595889.1|  4 CVECGAEVS 12
                                      999999986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0024
                     zinc_ribbon_2  2 CpnCGaelq 10
                                      C+ CGael+
  gi|336252782|ref|YP_004595889.1| 25 CTTCGAELE 33
                                      999999986 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 !   15.9   0.3   1.3e-05     0.013       6      58 ..       4      52 ..       1      53 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCgastpwfkiaedeaeaekeaieaW 58
                                      C  Cg +  l+ +  v +     v C+ Cga    + +++++ e ++e+ e W
  gi|336252782|ref|YP_004595889.1|  4 CVECGAEVSLHDDLEVGE----IVDCTTCGAELEVVDTEPPVLERAPELEEDW 52
                                      777**********88887....*********5555666666666666666666 PP

>> ADD_ATRX  Cysteine Rich ADD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.27   2.5e+02      13      23 ..       3      13 ..       1      19 [. 0.80
   2 ?   13.4   0.0   5.5e-05     0.052       7      25 ..      18      36 ..      12      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.27
                          ADD_ATRX 13 sCtaCgqqvnh 23
                                      +C  Cg +v +
  gi|336252782|ref|YP_004595889.1|  3 ECVECGAEVSL 13
                                      69999999865 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.5e-05
                          ADD_ATRX  7 eleeivsCtaCgqqvnhfq 25
                                      e  eiv Ct+Cg +++ + 
  gi|336252782|ref|YP_004595889.1| 18 EVGEIVDCTTCGAELEVVD 36
                                      56789*******9998765 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.4   6.4e-05     0.061       4      28 ..       3      31 ..       1      33 [. 0.84
   2 ?    2.9   0.1      0.12   1.1e+02       5      13 ..      25      33 ..      22      38 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.4e-05
                    PhnA_Zn_Ribbon  4 kCplCaSeytY....edgallvCpeCahE 28
                                       C +C++e+++    e g++  C +C+ E
  gi|336252782|ref|YP_004595889.1|  3 ECVECGAEVSLhddlEVGEIVDCTTCGAE 31
                                      6**********777777899999999887 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.12
                    PhnA_Zn_Ribbon  5 CplCaSeyt 13
                                      C  C++e +
  gi|336252782|ref|YP_004595889.1| 25 CTTCGAELE 33
                                      667777654 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00096      0.91       2      11 ..       1      11 [.       1      16 [. 0.83
   2 ?    3.5   0.0     0.054        51      19      26 .]      25      32 ..      23      34 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00096
                       zf-ribbon_3  2 tvrCPnCGa.p 11
                                      +++C +CGa +
  gi|336252782|ref|YP_004595889.1|  1 MTECVECGAeV 11
                                      789*****976 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.054
                       zf-ribbon_3 19 CpyCGtkl 26
                                      C+ CG++l
  gi|336252782|ref|YP_004595889.1| 25 CTTCGAEL 32
                                      66677654 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.8   0.00029      0.28      15      38 ..       4      32 ..       4      47 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                               DZR 15 CseCgtklkavaa.....edrCpsCgekv 38
                                      C eCg++++   +        C  Cg+++
  gi|336252782|ref|YP_004595889.1|  4 CVECGAEVSLHDDlevgeIVDCTTCGAEL 32
                                      66777776633336666666677777654 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 ?   14.1   0.3   3.8e-05     0.036      71     101 ..       2      36 ..       1      45 [. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-05
                                       EEETTTS-EEECHHH.HH....S-TTTSSS-EEEEE CS
                              HypA  71 vrCreCgkefeleek.al....rCpkCgsadveivs 101
                                       ++C eCg+e++l+++ ++     C +Cg+ ++e+v+
  gi|336252782|ref|YP_004595889.1|   2 TECVECGAEVSLHDDlEVgeivDCTTCGA-ELEVVD 36 
                                       58*********88754336667******9.567665 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.015        15      22      33 ..       2      13 ..       1      14 [. 0.83
   2 ?    6.6   0.0    0.0072       6.8      22      33 ..      23      34 ..      21      35 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                                      ---TTTS--EEE CS
                           zf-HYPF 22 isCtnCGPrlsl 33
                                      + C +CG  +sl
  gi|336252782|ref|YP_004595889.1|  2 TECVECGAEVSL 13
                                      5699***99987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0072
                                      ---TTTS--EEE CS
                           zf-HYPF 22 isCtnCGPrlsl 33
                                      + Ct CG  l +
  gi|336252782|ref|YP_004595889.1| 23 VDCTTCGAELEV 34
                                      56*****98875 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   3.6     6e-05     0.057       3      42 ..       4      45 ..       2      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6e-05
                                      ETTTTCEE.CHEETSTTCEE.ESSSSBEEEECCCCCCCHHHH CS
                      TF_Zn_Ribbon  3 CPnCgstn.lveDpergelv.CtdCGlVlednsidegpewre 42
                                      C +Cg +  l  D e ge+v Ct CG+ le  + ++ + +r+
  gi|336252782|ref|YP_004595889.1|  4 CVECGAEVsLHDDLEVGEIVdCTTCGAELEVVDTEPPVLERA 45
                                      ******6659999******66*********998887776665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.3   0.00023      0.22       7      37 ..       3      33 ..       1      35 [. 0.77
   2 ?    8.2   0.1    0.0029       2.8       8      18 ..      25      35 ..      16      43 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgsevr 37
                                      +C eCg e        +  +++ C +Cg+e++
  gi|336252782|ref|YP_004595889.1|  3 ECVECGAEVSLHDDL-EVGEIVdCTTCGAELE 33
                                      6*****999966544.4446666*****9875 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0029
                       Zn-ribbon_8  8 CeeCghefevl 18
                                      C+ Cg e ev+
  gi|336252782|ref|YP_004595889.1| 25 CTTCGAELEVV 35
                                      78888877766 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 ?   10.7   1.5    0.0004      0.38       4      32 ..       4      33 ..       1      36 [. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                                      ESTTTSBEEEEECSCCCE.EEESSSS-EEE CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegkn.feCrqCgYeep 32
                                      C +Cg      +d e+   ++C +Cg+e +
  gi|336252782|ref|YP_004595889.1|  4 CVECGAEVSLHDDLEVGEiVDCTTCGAELE 33
                                      6677777777777777667********976 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0048       4.6       4      16 ..       3      15 ..       1      18 [. 0.82
   2 ?    4.6   0.1     0.027        25       4      14 ..      24      34 ..      21      38 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0048
                            zf_UBZ  4 lCerCgkeipese 16
                                       C +Cg+e++ ++
  gi|336252782|ref|YP_004595889.1|  3 ECVECGAEVSLHD 15
                                      599*******995 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.027
                            zf_UBZ  4 lCerCgkeipe 14
                                       C  Cg+e+++
  gi|336252782|ref|YP_004595889.1| 24 DCTTCGAELEV 34
                                      7*****99876 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0078       7.3      15      22 ..       3      10 ..       1      15 [. 0.85
   2 ?    6.2   0.2     0.011        10      16      24 ..      25      33 ..      24      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0078
                              YhfH 15 kCteCGke 22
                                      +C+eCG e
  gi|336252782|ref|YP_004595889.1|  3 ECVECGAE 10
                                      7*****87 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.011
                              YhfH 16 CteCGkeie 24
                                      Ct+CG e+e
  gi|336252782|ref|YP_004595889.1| 25 CTTCGAELE 33
                                      *****9986 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.081        76       9      17 ..       4      12 ..       3      16 .. 0.85
   2 ?    9.2   0.2   0.00095      0.89       3      20 ..      19      36 ..      17      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.081
                                      -TTT--EEE CS
                   Desulfoferrod_N  9 CevCGniVe 17
                                      C  CG +V 
  gi|336252782|ref|YP_004595889.1|  4 CVECGAEVS 12
                                      999**9996 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00095
                                      TT-EEE-TTT--EEEECC CS
                   Desulfoferrod_N  3 klevYkCevCGniVeVle 20
                                       +e+  C+ CG + eV++
  gi|336252782|ref|YP_004595889.1| 19 VGEIVDCTTCGAELEVVD 36
                                      678889**********86 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.9   0.00015      0.15     116     141 ..       3      31 ..       1      33 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                           DUF1451 116 vCekCgkelalk...kteeippCpkCgat 141
                                       +C +Cg+e++l+   +++ei +C +Cga+
  gi|336252782|ref|YP_004595889.1|   3 ECVECGAEVSLHddlEVGEIVDCTTCGAE 31 
                                       7**********9444589********985 PP

>> zf-C3HC  C3HC zinc finger-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.14   1.3e+02      44      56 ..       2      14 ..       1      20 [. 0.81
   2 ?    8.5   0.1    0.0021         2      42      57 ..      21      36 ..      16      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.14
                           zf-C3HC 44 lkCevCgaslvlk 56
                                       +C++Cga+++l 
  gi|336252782|ref|YP_004595889.1|  2 TECVECGAEVSLH 14
                                      58*******9987 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0021
                           zf-C3HC 42 drlkCevCgaslvlkl 57
                                      +++ C++Cga+l ++ 
  gi|336252782|ref|YP_004595889.1| 21 EIVDCTTCGAELEVVD 36
                                      6899********9983 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 ?    9.2   4.9    0.0012       1.2       5      28 ..       2      30 ..       1      32 [. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                       Prok-RING_1  5 kkCpvCgkelkeedD.....iVvCpeCgt 28
                                      ++C  Cg e++  dD     iV C++Cg+
  gi|336252782|ref|YP_004595889.1|  2 TECVECGAEVSLHDDlevgeIVDCTTCGA 30
                                      58******9988866555559*******8 PP

>> Eapp_C  E2F-associated phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.035        33     124     139 ..       3      18 ..       1      20 [. 0.86
   2 ?    6.8   0.4     0.007       6.6     121     138 ..      21      38 ..      17      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.035
                            Eapp_C 124 kCseCstevavldkde 139
                                       +C eC +ev++ d  e
  gi|336252782|ref|YP_004595889.1|   3 ECVECGAEVSLHDDLE 18 
                                       7**********99866 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.007
                            Eapp_C 121 hpvkCseCstevavldkd 138
                                       + v C++C +e+ v+d++
  gi|336252782|ref|YP_004595889.1|  21 EIVDCTTCGAELEVVDTE 38 
                                       579************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 448.48
//
Query:       gi|336252783|ref|YP_004595890.1|  [L=292]
Description: lysine biosynthesis enzyme LysX [Halopiger xanaduensis SH-6]
Scores for complete 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   96.4   0.0    1.9e-27   96.1   0.0    1.1  1  RimK         RimK-like ATP-grasp domain
      1e-11   45.2   0.0    1.4e-11   44.7   0.0    1.1  1  ATP-grasp_3  ATP-grasp domain
    3.3e-08   33.1   0.0    4.9e-08   32.6   0.0    1.2  1  GSH-S_ATP    Prokaryotic glutathione synthetase, ATP-grasp do
    2.1e-07   30.7   0.3    4.5e-06   26.3   0.1    2.7  2  ATP-grasp    ATP-grasp domain
    4.2e-06   26.4   0.1    0.00012   21.6   0.0    2.6  2  ATP-grasp_5  ATP-grasp domain
    6.9e-06   25.7   0.0    1.3e-05   24.8   0.0    1.7  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
      2e-05   24.0   0.0     0.0053   16.1   0.0    2.5  3  ATPgrasp_ST  Sugar-transfer associated ATP-grasp
  ------ inclusion threshold ------
      0.044   14.2   0.0       0.16   12.4   0.0    2.0  1  Rimk_N       RimK PreATP-grasp domain
       0.46   10.9   2.3       0.86   10.0   0.3    2.5  3  DUF287       Drosophila protein of unknown function, DUF287


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   0.0   9.7e-31   1.9e-27       2     188 .]      88     276 ..      87     276 .. 0.93

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 9.7e-31
                                       H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH......G CS
                              RimK   2 rdKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea......l 72 
                                        dK+k    L ka++++p t++a  +e a + ie++  + P v+K v gs G  +     +++++ +le        
  gi|336252783|ref|YP_004595890.1|  88 ADKVKNSLALEKAGVPTPATKVAFTKESAMEAIEEF--GYPCVLKPVVGSWGRLMAKIDSPDAAEAILEHkatlghY 162
                                       599999999*************************98..6**************999999*********987776663 PP

                                       GG--.EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEE CS
                              RimK  73 keai.lvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaG 148
                                       ++++  vqe++e + ++diRvl  d+e +aa+ r s    + +n  +G+ +++++l++e kel  ka++a++  ++G
  gi|336252783|ref|YP_004595890.1| 163 EHKVfYVQEFVE-KPGRDIRVLATDGEPIAAMVRSSDH--WITNAAKGAETDVFELDDEAKELVQKASDAVGGGLLG 236
                                       333359****97.6789*****************9766..************************************* PP

                                       EEEEEETTEEEEEEEESS--SHHHHHHHT--HHHHHHHHH CS
                              RimK 149 vDllrakrgllvlEvnsspglekiektlgidiakklieai 188
                                       vDl+++++g+ v Evn  ++ + ++  +++d+a  +++++
  gi|336252783|ref|YP_004595890.1| 237 VDLMETEDGYTVHEVNHTVEFKALDGAVETDVAGTVVDWL 276
                                       ************************************9986 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0     7e-15   1.4e-11       1     155 [.      87     252 ..      87     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 7e-15
                                       HTSHHHHHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE............. CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve...... 64 
                                       ++dK+k   +L++agv++P       ++  +e +ee  +++v+Kp+ G+ g  + +++  ++aea++e+++      
  gi|336252783|ref|YP_004595890.1|  87 CADKVKNSLALEKAGVPTPatkvaftKESAMEAIEEFGYPCVLKPVVGSWGRLMAKIDSPDAAEAILEHKAtlghye 163
                                       89******************99998666677777788*******************************999****** PP

                                       ....EEEE---SEEEEEEEEE..SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--E CS
                       ATP-grasp_3  65 ....lvqefieGkplSvsllsd.gekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaG 136
                                            vqef+e     + +l++ ge +  ++ +  ++ +    ++ +G  t++  el++e+ el++++  ++    G
  gi|336252783|ref|YP_004595890.1| 164 hkvfYVQEFVEKPGRDIRVLATdGEPIAAMVRSSDHWIT----NAAKGAETDVF-ELDDEAKELVQKASDAV--GGG 233
                                       **999*****97777777776515556666667777777....899******99.99999999999999999..679 PP

                                       EEEEEEEESS.SEEEEEEE CS
                       ATP-grasp_3 137 yvGvDlvlkdeepyviEvN 155
                                       ++GvDl+ ++++  v EvN
  gi|336252783|ref|YP_004595890.1| 234 LLGVDLMETEDGYTVHEVN 252
                                       ******************9 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   2.5e-11   4.9e-08      12     153 ..     104     241 ..      94     255 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.5e-11
                                       S--EEEES-HHHHHHHHHHHSS.EEEEESS--TTTT-EEE-TT-TTHHHHHH...HHTTTTTS-EEEEE--GGGGG- CS
                         GSH-S_ATP  12 ipktlvskdkeeirafleeqgd.vilKPldgkgGegvfrvkksdpnlksile...llteegkepviaqrylpeikeG 84 
                                       +p t v+  ke+ ++ +ee g   +lKP+ g+ G+ + ++++ d+  ++ile   +l +++++ + +q+++++  + 
  gi|336252783|ref|YP_004595890.1| 104 TPATKVAFTKESAMEAIEEFGYpCVLKPVVGSWGRLMAKIDSPDA-AEAILEhkaTLGHYEHKVFYVQEFVEKPGR- 178
                                       68999999999999999999887****************999765.5677762325667889999******99877. PP

                                       EEEEEEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEET CS
                         GSH-S_ATP  85 DkRillvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvig 153
                                       D R+l  dGepi  a+ R  +++   +n a g++++  el+++ +e+ ++ ++++   G  + G+D+++
  gi|336252783|ref|YP_004595890.1| 179 DIRVLATDGEPIA-AMVR--SSDHWITNAAKGAETDVFELDDEAKELVQKASDAV---GGGLLGVDLME 241
                                       *************.7777..677899********************999877654...55566777764 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.18   3.6e+02     147     162 ..      12      27 ..       7      31 .. 0.88
   2 !   26.3   0.1   2.3e-09   4.5e-06       2     150 ..      98     246 ..      97     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                                       TTCTEEEEEEESS--G CS
                         ATP-grasp 147 edgellvnElapRpHn 162
                                       +d++ll+nEl  R H+
  gi|336252783|ref|YP_004595890.1|  12 KDEKLLLNELRERDHE 27 
                                       5788*********997 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 2.3e-09
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC......GTTCEEEEE-- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal......keekvivEefv 72 
                                       ek+g+p+p   ++ +ke++ ea+ee+g+p+v+K +++g+ G+    + s++ +e +le        +++ ++v efv
  gi|336252783|ref|YP_004595890.1|  98 EKAGVPTPATKVAFTKESAMEAIEEFGYPCVLK-PVVGSWGRLMAKIDSPDAAEAILEHKatlghyEHKVFYVQEFV 173
                                       799******************************.*******************999999878888788888888888 PP

                                       --S.EEEEEEEEEETTC-EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETT CS
                         ATP-grasp  73 pfe.kElsvlvvrsaeGetafypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvled 148
                                       +   + +    v +++Ge  + ++v       i ++     +   +   +a+e+++k+ +++gg G+++v l ++ed
  gi|336252783|ref|YP_004595890.1| 174 EKPgRDI---RVLATDGEPIA-AMVRSSD-HWITNAAKGAETDVFELDDEAKELVQKASDAVGG-GLLGVDLMETED 244
                                       6431444...44467884322.2222221.1222222222222335889999999999999987.999999999988 PP

                                       CT CS
                         ATP-grasp 149 ge 150
                                       g 
  gi|336252783|ref|YP_004595890.1| 245 GY 246
                                       74 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.056   1.1e+02      15      30 ..      66      81 ..      58      94 .. 0.83
   2 !   21.6   0.0   6.1e-08   0.00012      19      55 ..      97     133 ..      87     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.056
                       ATP-grasp_5 15 akelleaygipvvetr 30
                                      a + +eaygipv++++
  gi|336252783|ref|YP_004595890.1| 66 ATQFFEAYGIPVINSH 81
                                      7899********9876 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 6.1e-08
                       ATP-grasp_5  19 leaygipvvetrlassaeeaveaaeeigypvvlKivs 55 
                                       le  g+p++ t++a ++e+a+ea+ee+gyp+vlK v+
  gi|336252783|ref|YP_004595890.1|  97 LEKAGVPTPATKVAFTKESAMEAIEEFGYPCVLKPVV 133
                                       8999******************************765 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 !   24.8   0.0   6.8e-09   1.3e-05       1      93 [.      89     177 ..      89     289 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.8e-09
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       Dk++ + al+k++vp+   + a   t e a+++ +e+gyP+++k+ +g  G+ m  +++ +  ++++++  +     
  gi|336252783|ref|YP_004595890.1|  89 DKVKNSLALEKAGVPTPATKVA--FTKESAMEAIEEFGYPCVLKPVVGSWGRLMAKIDSPDAAEAILEHKATLG--H 161
                                       8999999********9888777..99************************************999999988888..5 PP

                                       HSTS-EEEEE--SSSE CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpk 93 
                                       + +k  +v++++++p 
  gi|336252783|ref|YP_004595890.1| 162 YEHKVFYVQEFVEKPG 177
                                       999999******9983 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.7   5.5e+03     111     136 ..       6      31 ..       5      35 .. 0.84
   2 !   16.1   0.0   2.6e-06    0.0053       8      81 ..      76     145 ..      71     171 .. 0.82
   3 !    5.1   0.0    0.0056        11     227     270 ..     218     259 ..     213     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.7
                       ATPgrasp_ST 111 Lyslggkpdvalveelikqdpelekl 136
                                       Lys   k++++l  el + d+e+ek+
  gi|336252783|ref|YP_004595890.1|   6 LYSRIRKDEKLLLNELRERDHEVEKI 31 
                                       89999999999999999999998887 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.6e-06
                       ATPgrasp_ST   8 rkyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvite 81 
                                       + +N+ + + + +dK+k +  +++ag+++p++ + + +++ ++++e+f   +    v+Kp+ gs+G+ + +i +
  gi|336252783|ref|YP_004595890.1|  76 PVINSHETADICADKVKNSLALEKAGVPTPATKVAFTKESAMEAIEEFGYPC----VLKPVVGSWGRLMAKIDS 145
                                       5689*******************************************97666....9*********98888754 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0056
                       ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNarpglai 270
                                       e+ el+ ka++  +g g+lG+D+  +e++   + E+N+++  + 
  gi|336252783|ref|YP_004595890.1| 218 EAKELVQKASD-AVGGGLLGVDLMETEDG-YTVHEVNHTVEFKA 259
                                       7889*******.99*********999888.9******9987665 PP

>> Rimk_N  RimK PreATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.1e-05      0.16       1      90 [.       1      80 [.       1      83 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.1e-05
                            Rimk_N  1 mkiaiLsrnpelystrrLveaaekrghevevldplrcylkieaekpevyykgekleefdavipR.igasitfygtavlr 78
                                      mk++iL +  +    + L +++++r+heve +d+++ + +i +         e+++++d+v+ R + +s   y+t+   
  gi|336252783|ref|YP_004595890.1|  1 MKVGILYSRIRK-DEKLLLNELRERDHEVEKIDVRKQTFDIGE-------VPEEFADLDIVVDRcLATSRSLYATQ--- 68
                                      888888777664.788899****************99999998.......45788899999999667777777765... PP

                            Rimk_N 79 qFemmgvfvlne 90
                                       Fe+ g++v+n+
  gi|336252783|ref|YP_004595890.1| 69 FFEAYGIPVINS 80
                                      588888888886 PP

>> DUF287  Drosophila protein of unknown function, DUF287
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00043      0.86       8      30 ..      11      33 ..       7      36 .. 0.90
   2 ?   -1.7   0.0       2.1   4.1e+03      31      36 ..      50      55 ..      41      62 .. 0.78
   3 ?   -3.4   0.0         7   1.4e+04      33      41 ..     131     139 ..     131     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00043
                            DUF287  8 dadEkkLLkrivddevvdddvdv 30
                                        dEk+LL+++ + +++++++dv
  gi|336252783|ref|YP_004595890.1| 11 RKDEKLLLNELRERDHEVEKIDV 33
                                      579***************99995 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                            DUF287 31 iDlvvD 36
                                       D+vvD
  gi|336252783|ref|YP_004595890.1| 50 LDIVVD 55
                                      689999 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 7
                            DUF287  33 lvvDsWkkr 41 
                                       +vv sW + 
  gi|336252783|ref|YP_004595890.1| 131 PVVGSWGRL 139
                                       6999**765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); 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:                         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 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2022.38
//
Query:       gi|336252784|ref|YP_004595891.1|  [L=358]
Description: N-acetyl-gamma-glutamyl-phosphate reductase [Halopiger xanaduensis SH-6]
Scores for complete 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   93.1   0.0    3.6e-26   92.0   0.0    1.6  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    5.3e-08   33.2   0.0    8.8e-08   32.4   0.0    1.4  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom


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 !   92.0   0.0     4e-30   3.6e-26       2     120 ..      18     150 ..      17     151 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 4e-30
                                       EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHH CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagv 78 
                                       +++vG++G +G ellrlL+ hp++e+  ++s+s+ aGk + ++++ +  g+ l++++  +++l++vd++f a+p+gv
  gi|336252784|ref|YP_004595891.1|  18 ASVVGGSGFTGGELLRLLAGHPNFEIGEVTSRSK-AGKSVGSVHP-PLRGSGLRFTE--PDDLESVDVLFAATPHGV 90 
                                       579*******************************.**********.999999***99..99**************** PP

                                       HHHHHHHHHHTTSEEEESSSTTTTST..................TSEBE-HHHHGGGGGG CS
                    Semialdhyde_dh  79 skelapklaeagvkviDlssdfRlkd..................davyvlpevnreaikk 120
                                       s+   +++ ++  +++Dls+dfRl++                  +a y lpe+nre+++ 
  gi|336252784|ref|YP_004595891.1|  91 SMGQIDEFFDHADTIVDLSADFRLETeeqydewydgheapeyleKAEYALPEINRENLAG 150
                                       ********************************************************9975 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   9.8e-12   8.8e-08      93     184 .]     232     325 ..     209     325 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 9.8e-12
                                       SEEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCSTTEEEEESS....HCHHSSHHHHTTCSSSEEEEEE CS
                   Semialdhyde_dhC  93 kvsatcvrVPvlrGhseavtiklk..lkdveveeveellaaapevkvvvne....eedrPtpaavaggtnsvsVGRi 163
                                       +v  tc+ V ++rG s++ ++  +  +++ ++ +++   +++ e++v+         ++P p+avag tn + VG +
  gi|336252784|ref|YP_004595891.1| 232 SVAFTCHAVDMIRGASATSHVFPSspVSKGDLWQAYRGCYED-EPFVRMAAggsgVYRYPEPKAVAG-TNLAEVG-F 305
                                       46789******************9888888999999999999.*******99988889********9.9******.* PP

                                       EEETTCTTEEEEEEEEETTTT CS
                   Semialdhyde_dhC 164 rkdemgdeglklvvvgDNllk 184
                                       + d+++++ +++++++DN++k
  gi|336252784|ref|YP_004595891.1| 306 ELDPSNKR-VVVFSAIDNMMK 325
                                       ****9998.*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2657.38
//
Query:       gi|336252785|ref|YP_004595892.1|  [L=290]
Description: acetylglutamate kinase [Halopiger xanaduensis SH-6]
Scores for complete 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-32  113.4   4.8    1.5e-32  113.1   4.8    1.1  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 !  113.1   4.8   8.2e-37   1.5e-32       1     239 [.       1     251 [.       1     253 [. 0.91

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 8.2e-37
                                       TEEEEEE-TT.CCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC........E..HH CS
                         AA_kinase   1 krvVvKlGGs.sltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaa....glrstlee 72 
                                       ++vVvK+GG+ +++++++      ++++a l+e+g+++v+ hGg+  +d+ l+   g ++++ ++      r t+ee
  gi|336252785|ref|YP_004595892.1|   1 MTVVVKVGGArAVDPEGA------LADVASLVEDGEDVVLTHGGSTAVDETLED-LGKEPTYVETpggvVGRFTDEE 70 
                                       79********88886665......88899999999*******************.********99****99****** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE.................HHHTTTCEEECCHHHHH CS
                         AA_kinase  73 agevatrdalaslgerlvaallaaglpavglsaaaldateagr...............degsdgnvesvdaeaieel 134
                                       +++v ++++ ++l+++lv++l ++g++avgls+ +  + e++r               +  ++g++esv+a+ +e+ 
  gi|336252785|ref|YP_004595892.1|  71 TMDVFKMVMPGKLNTDLVESLHNEGVDAVGLSGTDGKLLEGKRksavrvkedgkkkikRGDHSGKIESVNADLLETT 147
                                       ***************************************************************************** PP

                                       HHTT-EEEEES.EEEEETTTE..EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEE.EHHHC CS
                         AA_kinase 135 leagvvpvltg.figldeege..lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpei.svdea 207
                                       l+ g+ pv++  + g    g+    + ++D++aa++A al+A  l++ltdV+G+y ++ ++    ++++   + +e+
  gi|336252785|ref|YP_004595892.1| 148 LAGGYTPVVSVpMLGKEKSGGytAVNADADRAAAAIAGALEA-DLVVLTDVSGIYEDPDDES---TKIDSAaTPEEF 220
                                       *********9834466666669988*****************.56667*******8887777...888888577777 PP

                                       HHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEE CS
                         AA_kinase 208 eesaselatgGmkvkhpaalaaarrggipvvI 239
                                       e+  +e a g m  k+ aa +a+++g   v +
  gi|336252785|ref|YP_004595892.1| 221 EA-VKEAAEGFMTKKVMAAEEALEGGAASVTV 251
                                       77.9999******************9888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2200.64
//
Query:       gi|336252786|ref|YP_004595893.1|  [L=383]
Description: acetylornithine/succinyldiaminopimelate aminotransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-101  339.7   0.0   2.6e-101  339.2   0.0    1.1  1  Aminotran_3      Aminotransferase class-III
     0.0026   17.0   0.0     0.0036   16.5   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.025   13.8   0.0      0.041   13.1   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
      0.028   14.1   0.5        0.4   10.4   0.0    2.2  2  Cupin_6          Cupin
       0.11   12.7   0.0       0.62   10.3   0.0    2.0  2  Asparaginase_C   Glutaminase/Asparaginase C-terminal domain
       0.45   10.1   3.3       0.91    9.1   0.3    2.6  3  PP2C_2           Protein phosphatase 2C


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 !  339.2   0.0  8.7e-105  2.6e-101      11     405 ..      13     375 ..       7     376 .. 0.97

  Alignments for each domain:
  == domain 1  score: 339.2 bits;  conditional E-value: 8.7e-105
                                       EEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-.. CS
                       Aminotran_3  11 lvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgl 87 
                                       + ++++eG yl+ +dg +ylD+ +s+a ++lGh+hP+vv+av+eq+ +l++v    +  e  ++++   ++ +p gl
  gi|336252786|ref|YP_004595893.1|  13 IGLERGEGPYLYTADGTEYLDAGASFACTPLGHCHPAVVDAVQEQVGQLTFVD-SSYPVEARENAYASFVASTPDGL 88 
                                       6789*************************************************.999******************** PP

                                       SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTB CS
                       Aminotran_3  88 dkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypd 164
                                       +   ++nsG+eA+e+AlK+ar+      at  +ki+a + +fHGrt+gal++t++ +kyk+ ++p++ +v +++y d
  gi|336252786|ref|YP_004595893.1|  89 ESAWFCNSGTEANEAALKFARS------ATGESKIVAATRSFHGRTMGALAATWK-DKYKKPYEPLAGDVEFVPYGD 158
                                       **********************......***************************.********************9 PP

                                       GGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTT CS
                       Aminotran_3 165 eevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrT 241
                                                         e l ++ +de+aAvi+EpiqgegG++v+++++l+++re +++ +++l+ DEvqtG+GrT
  gi|336252786|ref|YP_004595893.1| 159 D-----------------EVLADAVDDETAAVILEPIQGEGGINVPPEGYLETARECTDEAGAALVLDEVQTGMGRT 218
                                       3.................45667899*************************************************** PP

                                       SSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHH CS
                       Aminotran_3 242 GklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllenaq 318
                                       G ++A+++agv+pD++t+aK+l++Glp+ av++++ +++     sh sTf+G p+ +a++ a++ ++ ee++  +a+
  gi|336252786|ref|YP_004595893.1| 219 GSMWACQNAGVTPDILTTAKGLGNGLPVGAVAVRDWIADGA--ASHNSTFSGGPVVAAAVDATVSTLVEEEWPAHAA 293
                                       ***************************************99..89******************************** PP

                                       HHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--HHHH CS
                       Aminotran_3 319 elgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitdeei 395
                                       e+g++l ++Le++  ++  i+evRg Gl++++elk  a+   ++  + a ++ +l l+aG++v+rllppl+i +ee+
  gi|336252786|ref|YP_004595893.1| 294 EIGDYLVTELEAALGDD--IREVRGDGLLVGLELKRGAN---RAARDLAMNHQILALPAGRTVLRLLPPLVIGQEEA 365
                                       *************9776..******************99...46889999*************************** PP

                                       HHHHHHHHHH CS
                       Aminotran_3 396 delleilkka 405
                                       d+l+++l ++
  gi|336252786|ref|YP_004595893.1| 366 DQLVDALTAV 375
                                       *****99876 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 !   16.5   0.0   1.2e-06    0.0036      49     266 ..      73     282 ..      43     372 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSE.EEEEEBEE CS
                     Aminotran_1_2  49 leealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsgge.vvryplys 124
                                        e+a a+f+     ++   e+a  + sG+ a+ +al+f+ ++  +++i++ + ++   + ++ +++ +  ++ p+++
  gi|336252786|ref|YP_004595893.1|  73 RENAYASFVA---STPDGLESAWFCNSGTEANEAALKFARSATGESKIVAATRSFHGRTMGALAATWKdKYKKPYEP 146
                                       4778889999...889999999999*******************************************999999775 PP

                                       T.TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHH.HHHHHHHHHHTTEEEEEEETTTTCBSSSSH CS
                     Aminotran_1_2 125 e.edfhldlealeealkeapegnkktkvilvesphNPtGtvatlee.leklldlakkynlllfvDeaYagfvfgsld 199
                                          d +    + +e l++a  +  +t  +++e ++   G   ++e  le+  + +++ ++ l++De+  g+  +  +
  gi|336252786|ref|YP_004595893.1| 147 LaGDVEFVPYGDDEVLADAVDD--ETAAVILEPIQGEGGINVPPEGyLETARECTDEAGAALVLDEVQTGMGRT-GS 220
                                       5644444444444555554433..679************9988887256666777788*********9999888.46 PP

                                       THHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                     Aminotran_1_2 200 avatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsd 266
                                       ++a + n+   p+     + +K +G  G+ vG++++ +++++ +++  ++f    +++aav a +s+
  gi|336252786|ref|YP_004595893.1| 221 MWA-CQNAGVTPD---ILTTAKGLG-NGLPVGAVAVRDWIADGAASHNSTFSGGPVVAAAVDATVST 282
                                       788.889888888...346789998.58888**************9999987755666666555554 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.041      46     167 ..      87     209 ..      50     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                                       T-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHH..HS- CS
                   Beta_elim_lyase  46 gkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdleklea..aik 119
                                       g e a f+ +Gt An+ +lk      ge++iv  +  +h ++ ga+a+    k ++ + + aG++++    +  +++
  gi|336252786|ref|YP_004595893.1|  87 GLESAWFCNSGTEANEAALKFARsATGESKIVAATRSFHGRTMGALAATWKDKYKKPYEPLAGDVEFVPYGDdeVLA 163
                                       779999*************8887789***********************8888999999999999876665442444 PP

                                       -S-TTS-EEEEEEEESSBTTTTTB---HH.HHHHHHHHHHHCT-EEEEE CS
                   Beta_elim_lyase 120 evgaheekiklisltvTnntagGqvvsle.elrevaaiakkygiplhlD 167
                                       +     +++++++l+      gG  v++e +l+ +++ +++ g  l+lD
  gi|336252786|ref|YP_004595893.1| 164 DAV--DDETAAVILEPIQGE-GGINVPPEgYLETARECTDEAGAALVLD 209
                                       433..479999999998885.8887777647888999999999999999 PP

>> Cupin_6  Cupin
   #    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      34      86 ..     122     187 ..      88     243 .. 0.72
   2 ?    2.0   0.1     0.048   1.4e+02     119     154 ..     344     374 ..     271     382 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                           Cupin_6  34 lalhvvlrGscwli.dpasgepvrLsagdvvllpggephvladspgtaplavi............e 86 
                                        ++h  + G++  + +++ ++p +  agdv ++p g+  vlad+ +++++avi            +
  gi|336252786|ref|YP_004595893.1| 122 RSFHGRTMGALAATwKDKYKKPYEPLAGDVEFVPYGDDEVLADAVDDETAAVIlepiqgegginvP 187
                                       67888888988888777777999999********************99998884444433333331 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.048
                           Cupin_6 119 dgsvsdpllaaLPrvlvvaaeeaapelrallellaa 154
                                         ++ +++l+ LP++++      ++e ++l++ l+a
  gi|336252786|ref|YP_004595893.1| 344 ALPAGRTVLRLLPPLVIG-----QEEADQLVDALTA 374
                                       5677899*******9998.....3344444444443 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.58   1.7e+03      38      69 ..     101     131 ..      72     141 .. 0.72
   2 ?   10.3   0.0   0.00021      0.62       7      92 ..     153     238 ..     151     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.58
                                       -HHHHHHHHHHHTTT-EEEEEESSSBS----- CS
                    Asparaginase_C  38 psallealkeakargivvvatsqcpsgsvsns 69 
                                       ++a l+ ++ a+  +  +va+++  +g+++++
  gi|336252786|ref|YP_004595893.1| 101 NEAALKFARSATG-ESKIVAATRSFHGRTMGA 131
                                       4466666666643.445778888888887765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00021
                                       --TT--HHHHHHHHHTT--EEEEE.EBTTTB--H...HHHHHHHHHHTTT-..EEEEEESSSBS-----H.....HH CS
                    Asparaginase_C   7 lhpgmdtkvlkallkkgakGvvle.gtGvGnlps...allealkeakargi..vvvatsqcpsgsvsnseyeagkel 77 
                                       ++p  d++vl  +++ +  +v+le + G G+++      le+++e++++    +v   +q+  g++          +
  gi|336252786|ref|YP_004595893.1| 153 FVPYGDDEVLADAVDDETAAVILEpIQGEGGINVppeGYLETARECTDEAGaaLVLDEVQTGMGRTGSM------WA 223
                                       678899*****************9788****9966789********97754014444566666666555......89 PP

                                       HHHTEEE-TT--HHH CS
                    Asparaginase_C  78 erlgvisaddmtpea 92 
                                       ++  ++++d +t+++
  gi|336252786|ref|YP_004595893.1| 224 CQNAGVTPDILTTAK 238
                                       999999999999987 PP

>> PP2C_2  Protein phosphatase 2C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.17     5e+02     112     155 ..      32      73 ..      23     121 .. 0.78
   2 ?   -1.2   0.1      0.45   1.3e+03      39      50 ..     216     227 ..     201     230 .. 0.85
   3 ?    9.1   0.3    0.0003      0.91      27      77 ..     252     304 ..     245     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.17
                            PP2C_2 112 lqiGDGaivvrdrdgevqllgepdsgeyanqttfltsedaeeel 155
                                       l  G +++    + g  ++   ++++e ++q tf++s+ ++e +
  gi|336252786|ref|YP_004595893.1|  32 LDAGASFA--CTPLGHCHPAVVDAVQEQVGQLTFVDSSYPVEAR 73 
                                       55555555..3577888999999999999999999999887765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.45
                            PP2C_2  39 SerGariaveav 50 
                                       ++ G+++a++ +
  gi|336252786|ref|YP_004595893.1| 216 GRTGSMWACQNA 227
                                       799******976 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0003
                            PP2C_2  27 l.aVaDGaGSakrSerGariaveavvealaelleseeee.....eeallraleaail 77 
                                         ++aDGa S++    G  +++ av  ++++l+e+e++       +     l+++++
  gi|336252786|ref|YP_004595893.1| 252 RdWIADGAASHNSTFSGGPVVAAAVDATVSTLVEEEWPAhaaeiGD----YLVTELE 304
                                       469******************************9999995444322....3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); 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: 00:00:00.39
# Mc/sec: 2937.32
//
Query:       gi|336252787|ref|YP_004595894.1|  [L=372]
Description: N-acetyl-ornithine/N-acetyl-lysine deacetylase [Halopiger xanaduensis SH-6]
Scores for complete 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-24   86.7   0.8    2.3e-24   86.3   0.8    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    6.5e-06   26.0   0.0    1.3e-05   25.0   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain
  ------ inclusion threshold ------
      0.026   14.2   0.3       0.32   10.7   0.2    2.2  1  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 !   86.3   0.8   3.8e-28   2.3e-24       1     205 [.      70     363 ..      70     365 .. 0.87

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 3.8e-28
                                       EEEEES-BSS...TTCGGGSSS.TTSEE..ETTT..EEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEES CS
                                       xxxxxxxxxx...xxxxxxxxx.xxxxx..xxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   1 llgsHlDvVp...eeetdgwtt.pfslt..eedG..klyGrGaddmkggvlaalealralkdegikpkgtivllfqp 69 
                                       ll sH D+Vp   + e ++ ++   +++  ee+G  +l+GrG++d +g ++a+++a+    ++g      + ++ ++
  gi|336252787|ref|YP_004595894.1|  70 LLTSHVDTVPgeiPVEVQSADEdDVEADvaEETGedVLWGRGSVDATGPLAAMAAAA---VRTG------VSFVGVV 137
                                       689*******64222223445566666677777788********************9...4455......99***** PP

                                       TTSSTTTHHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                     Peptidase_M20  70 dEEggrgGakallegleerekvdavfelhieepgileagklaigvv............................... 115
                                        EE++++Ga++l+e   +re++da   ++ +ep++      +i+++                               
  gi|336252787|ref|YP_004595894.1| 138 GEETNSRGARHLVE---DREEPDA---IINGEPSGTT----GITLGyrgflagtyvatsesghtsrpepnaiqhate 204
                                       ***999********...799****...5699999999....556668999*************************** PP

                                       ..................................................................E.EEEEEEEEE CS
                                       ..................................................................x.xxxxxxxxx RF
                     Peptidase_M20 116 ..................................................................k.vevellegg 125
                                                                                                         +  +v++ e  
  gi|336252787|ref|YP_004595894.1| 205 wwtsvedafendeyqpvfervtakpvdidggisddglsvettldvqlrippsldaesvretaeaelEiGTVSWDEPI 281
                                       *************************************************************9988833566666999 PP

                                       SHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHHTTT.EEEEE.EESSG.GCTTSTTTEEEHHHHHHHH CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx.xxxxx.xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 126 apvtln.dsplvkalaeaaeelfgekvelivsgpggtdarffagi.ptvmi.fgpgs.glaHspnEyvdledlekgi 198
                                       +pv+ +   ++++a++ a++e++g +++l+ +  g++d++ +ag   + m  +gpg+ +l H+p+E+++l+++ + +
  gi|336252787|ref|YP_004595894.1| 282 PPVMESpRTEVARAFRVAIREVCG-ETRLVRKT-GTSDMNLYAGAwDCPMAtYGPGNsDLDHAPDERLSLAEFDESV 356
                                       9999999***************99.34555555.9*******8887555555****66******************* PP

                                       HHHHHHH CS
                                       xxxxxxx RF
                     Peptidase_M20 199 kvlarll 205
                                       +vl+r++
  gi|336252787|ref|YP_004595894.1| 357 DVLERVA 363
                                       ***9986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   2.3e-09   1.3e-05       2     102 ..     173     271 ..     172     277 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.3e-09
                                       EB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEE CS
                         M20_dimer   2 ghkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaea 78 
                                       g +G++ g+  ++ ++gH + p+   NAi ++ +  ++ ed  ++ + +  + r t  +  i+gG +   +  e+++
  gi|336252787|ref|YP_004595894.1| 173 GYRGFLAGTYVATSESGHTSRPEP--NAIQHATEWWTSVEDAFENDEYQPVFERVTAKPVDIDGGISDDGLSVETTL 247
                                       5689999999999*******6665..5**************988888999*************************** PP

                                       EEEEEHHHHHHHHHHHHHHHHHHT CS
                         M20_dimer  79 kidiRllpgedpeevleeieeile 102
                                        + +R++p  d+e+v+e+ e+ le
  gi|336252787|ref|YP_004595894.1| 248 DVQLRIPPSLDAESVRETAEAELE 271
                                       ******************999886 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   5.3e-05      0.32      12      86 ..      66     154 ..      58     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.3e-05
                                       SEEEEEEEE--B-TTT.....................TCC...T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEE CS
                     Peptidase_M28  12 devlllgAHyDsvgvg.....................rgp...ifvGAdDnAsgvaalLelarvlaasgsrpkrgvr 64 
                                       d  +ll++H+D+v+ +                       +      G  D   + aa+              + gv 
  gi|336252787|ref|YP_004595894.1|  66 DDSVLLTSHVDTVPGEipvevqsadeddveadvaeetG-EdvlWGRGSVDATGPLAAMAAA---------AVRTGVS 132
                                       67888899999998777777777766666555544431.1333444555655555555332.........34678** PP

                                       EEEESSCSGSSHHHHHHHH.HHC CS
                     Peptidase_M28  65 flffdaEEagllGSkafak.akp 86 
                                       f+ + +EE    G++++++ + +
  gi|336252787|ref|YP_004595894.1| 133 FVGVVGEETNSRGARHLVEdR-E 154
                                       ******************632.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 3131.89
//
Query:       gi|336252788|ref|YP_004595895.1|  [L=304]
Description: Ornithine carbamoyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-53  178.8   0.0    9.7e-53  178.2   0.0    1.3  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    4.5e-52  176.3   0.0    6.7e-52  175.7   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 !  178.2   0.0   1.1e-56   9.7e-53       1     148 []       6     146 ..       6     146 .. 0.99

  Alignments for each domain:
  == domain 1  score: 178.2 bits;  conditional E-value: 1.1e-56
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       rh+l++ d+s++e+ ++l++a+e+k+++++ + ++ l+g+tl+++F++pStRTrvSfe+++++lGg++++l+ ++di
  gi|336252788|ref|YP_004595895.1|   6 RHFLEIGDVSEDELLTILERAEEYKAAQHAGEDHEDLDGQTLGMIFQKPSTRTRVSFETGMTQLGGHAVFLG-EDDI 81 
                                       8***********************************************************************.77** PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       ql+     r+E+l+Dt r+lsryvda+++R++++e++e +a+ya+vpv+N++ +d+ HP+Q+LaDlltire
  gi|336252788|ref|YP_004595895.1|  82 QLG-----RGEPLKDTSRTLSRYVDAVMARVFKHENIEVFAEYADVPVVNGL-TDDAHPCQTLADLLTIRE 146
                                       ***.....78******************************************.****************98 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 !  175.7   0.0   7.5e-56   6.7e-52       2     156 ..     153     301 ..     152     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 7.5e-56
                                       C.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE- CS
                            OTCace   2 glkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytd 78 
                                       g+  a++Gd+ nnva+s + ++a +++d+++++P+g+  d  vle+a++     gg+ t+t+d+ ea++gaDv+ytd
  gi|336252788|ref|YP_004595895.1| 153 GVSAAWIGDG-NNVAQSFVLGCALTDIDLTVATPEGYGIDDRVLERAREL----GGDPTVTHDPDEAAAGADVIYTD 224
                                       8899******.*********************************999998....9********************** PP

                                       -SSETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
                            OTCace  79 vwvsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                                       vw+smg+e+er+ r+++++++qv ++ll++a + a v+HcLPa+rgeE+td+V++s+rsvvf+qaeNrlh++kAll 
  gi|336252788|ref|YP_004595895.1| 225 VWISMGQEDERDVRMQAFEGFQVCADLLERAPE-ASVMHCLPAHRGEEITDDVIESDRSVVFDQAENRLHAQKALLS 300
                                       *****************************9765.9****************************************98 PP

                                       H CS
                            OTCace 156 l 156
                                       +
  gi|336252788|ref|YP_004595895.1| 301 W 301
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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 0.17s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2624.89
//
Query:       gi|336252789|ref|YP_004595896.1|  [L=420]
Description: threonine synthase [Halopiger xanaduensis SH-6]
Scores for 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  238.7   4.7    1.1e-70  238.4   4.7    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
       0.12   12.7   0.1       0.19   12.1   0.1    1.3  1  C1_2      C1 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 !  238.4   4.7   1.2e-74   1.1e-70       2     294 .]      80     387 ..      79     387 .. 0.94

  Alignments for each domain:
  == domain 1  score: 238.4 bits;  conditional E-value: 1.2e-74
                                       GGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaall 77 
                                       t ++g TPl ++prl++e+gv+ l +K E++nptgSfKdRg++  +a +ke  g +++++as+GN+ +alAa++++ 
  gi|336252789|ref|YP_004595896.1|  80 TAQEGATPLYEVPRLEDEIGVDaLRIKHEGMNPTGSFKDRGMTVGVAVAKEL-GVDRLACASTGNTSAALAAYGSRG 155
                                       66899***********************************************.************************ PP

                                       T-EEEEEEETTS-.HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHH.. CS
                              PALP  78 Glkvtivvpadas.pekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEil.. 151
                                       G++  +++pa++  ++k+a+  l+Ga++ ev+g++d+++++++ela+  ++ayl+++  np + eg++tiglEil  
  gi|336252789|ref|YP_004595896.1| 156 GMETLVLLPAGKVaAGKIAQASLHGARILEVDGNFDACLDIVQELAEG-GEAYLLNSL-NPFRLEGQKTIGLEILeg 230
                                       ***********9956*********************************.*********.9**************999 PP

                                       ..HHTTTTEEEEEEE-SSSHHHHHHHHHHHH.......HSTT...-EEEEEEECTTCGGTTCC..S..S.SS..B.S CS
                              PALP 152 ..eqlggkpdavvvpvGgGgliaGiaaglke.......rrpd...vrvigvepegsdalarsl..ragrrvtvpvsd 214
                                         +++g  pd +v+pvG++g+ ++++++++e       +  +   ++++gv++eg++++ +++   a ++ +++  +
  gi|336252789|ref|YP_004595896.1| 231 frDDYGAFPDRIVLPVGNAGNTSALYKAFRElvqagalE--EsevPKLVGVQAEGAAPMVEAIenGADEVRRWDDVE 305
                                       999****************************99776542..1568******************4434455566666* PP

                                       SS.CCSTCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEE CS
                              PALP 215 tiadglavg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrv 288
                                       t a+++++g  +++++a++ ++++++++++v+dee+ ea+r la  egi vep+saa++a+l klr  g +++++rv
  gi|336252789|ref|YP_004595896.1| 306 TRATAIRIGnpVNAPKALPGIRETGGTAISVTDEEITEAQRDLA-GEGIGVEPASAASVAGLrKLRAEGIVDDDERV 381
                                       *********99999999***************************.******************************** PP

                                       EEEE-B CS
                              PALP 289 vviltg 294
                                        ++ tg
  gi|336252789|ref|YP_004595896.1| 382 ACLTTG 387
                                       *99887 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.1e-05      0.19      19      42 ..      22      48 ..       2      51 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                              C1_2 19 fnCsaCgrkidgff...YsCseCdfsl 42
                                       +C  Cg +  +f+   Y+C+eCd  l
  gi|336252789|ref|YP_004595896.1| 22 LECIECGATFAPFEdvrYTCDECDGLL 48
                                      78*******77777788******9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3003.62
//
Query:       gi|336252790|ref|YP_004595897.1|  [L=131]
Description: hypothetical protein Halxa_1385 [Halopiger xanaduensis SH-6]
Scores for 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   16.8   0.9     0.0079   16.2   0.9    1.2  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C


Domain annotation for each model (and alignments):
>> 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 !   16.2   0.9   4.4e-07    0.0079      18      53 ..      67     102 ..      63     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.4e-07
                    CENP-F_leu_zip  18 kadsLkdkvenLerelemseenqekvileaEtskae 53 
                                       +   L+ +v +Ler le+se+ q++++++ E   ae
  gi|336252790|ref|YP_004595897.1|  67 ERTALRARVTALERALETSESRQQEIVTQYERVLAE 102
                                       556899*************************98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1343  (0.0749066); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 998.70
//
Query:       gi|336252791|ref|YP_004595898.1|  [L=256]
Description: glutamine amidotransferase class-I [Halopiger xanaduensis SH-6]
Scores for 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-22   78.8   0.0    5.8e-22   78.4   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
      5e-07   29.7   0.2      1e-05   25.4   0.2    2.3  1  Peptidase_C26  Peptidase C26
     0.0012   17.8   0.0      0.011   14.7   0.0    2.3  1  HTS            Homoserine O-succinyltransferase
  ------ inclusion threshold ------
      0.029   14.2   0.0       0.11   12.3   0.0    1.8  2  DJ-1_PfpI      DJ-1/PfpI family
       0.14   11.7   0.0       0.26   10.9   0.0    1.5  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


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 !   78.4   0.0   1.6e-25   5.8e-22      39     181 ..      42     181 ..      14     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.6e-25
                                       THHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEET CS
                            GATase  39 llknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekekehhggtmrlgdd 110
                                       +  ++dg +v g   s++     +  + e +  a++++iP+LG+C G+Qlla+ +g++v+ +  +e    +++    
  gi|336252791|ref|YP_004595898.1|  42 ETFDFDGAVVTGSRSSVYwdeewIATAAEWVGDAIDRGIPFLGVCWGHQLLAHVLGGTVEDMGAYEVGYSEIEQLG- 117
                                       356899999999999999865666666666667777***************************8888888887666. PP

                                       TTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHH CS
                            GATase 111 etallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpe 181
                                       +++l+ g  +e+++  +H++ev +   +p g e +a++e +  ++++++++  ++gvQFHPE+  ++ ++ 
  gi|336252791|ref|YP_004595898.1| 118 DSRLFDGIAEEFTAFTSHSDEVSE---LPPGAEPLAENEYS--NHGFRKDR--VFGVQFHPEYDTKTAREL 181
                                       46**********************...***********775..79988776..8*********99988654 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.2   2.9e-09     1e-05      97     216 .]      71     172 ..      46     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.9e-09
                     Peptidase_C26  97 LiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnsl 173
                                        +  a++rg+P lg+C G+qll+ +lGGt+      +                +++   +s l + +  ee+   + 
  gi|336252791|ref|YP_004595898.1|  71 WVGDAIDRGIPFLGVCWGHQLLAHVLGGTVEDMGAYEV------------GYSEIEQLGDSRLFDGIA-EEFTAFTS 134
                                       56789***********************9865444322............233444445555555555.58888899 PP

                     Peptidase_C26 174 HhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       H+  ++el ++ +  A  e       ++  +k  v+gvQ+HPE
  gi|336252791|ref|YP_004595898.1| 135 HSDEVSELPPGAEPLAENEY-----SNHGFRKDRVFGVQFHPE 172
                                       99999999999999998864.....344445567999999998 PP

>> HTS  Homoserine O-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     3e-06     0.011      83     249 ..      29     185 ..       2     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-06
                                       HHHHH-B-GGGT.TT--EEEEEE---S-TTS-GGGSTTHHHHHHHHHHHHHHEEEEEEETHHHHHHHHHHH----EE CS
                               HTS  83 hlekfYktfeei.kdekfDgliiTGApveqlefeevkYWeelteildwakenvtstlfiCwaaqaalyylygvekkk 158
                                        l++f  t  e+ ++  fDg ++TG+      + ++++  + +e +  a +     l +Cw+ q  l+++ g + ++
  gi|336252791|ref|YP_004595898.1|  29 SLSEFDVTAGEVpETFDFDGAVVTGSRS--SVYWDEEWIATAAEWVGDAIDRGIPFLGVCWGHQL-LAHVLGGTVED 102
                                       45556666667756679********965..457777787777777777888888899*****887.99********* PP

                                       EEEEEEEEEEEEES.S--GGGTT--SEEEEEEEEEEE--HHHHTT-TTEEEEEEETTTEEEEEEESSSSEEEE-S-T CS
                               HTS 159 lpeKlfGvfehkvlkekspllrgfddeflvphsRytevkeedieekkelevLaeseeaGvsllaskdkrevfvlgHp 235
                                       + +  +G  e + +  +s+l+ g+ +ef++  s   ev+e      ++ e Lae+e +       +++r + v+ Hp
  gi|336252791|ref|YP_004595898.1| 103 MGAYEVGYSEIE-QLGDSRLFDGIAEEFTAFTSHSDEVSEL----PPGAEPLAENEYSNHGF---RKDRVFGVQFHP 171
                                       *******77777.677889***********99999999864....45888899887765544...46677778999* PP

                                       T--TTHHHHHHHHH CS
                               HTS 236 EYdaetLkkEyeRD 249
                                       EYd++t ++  +R 
  gi|336252791|ref|YP_004595898.1| 172 EYDTKTARELVHRK 185
                                       **999987766665 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 ?   12.3   0.0     3e-05      0.11      50     109 ..      33      94 ..       4     117 .. 0.81
   2 ?   -0.9   0.0      0.36   1.3e+03      38      64 ..     222     248 ..     201     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                                       -SEEGGGCTCC.G-SEEEE--BHHHHHHHHTSH..HHHHHHHHHHHTT-EEEEETTTHHHHHH CS
                         DJ-1_PfpI  50 vdaslddvkaa.eyDalvlpGGragperlrene..kvvelvkefaekgklvaaICagpqlLaa 109
                                        d++ ++v    ++D  v+ G r+ + +  e+    + e+v ++ ++g ++  +C g qlLa 
  gi|336252791|ref|YP_004595898.1|  33 FDVTAGEVPETfDFDGAVVTGSRS-SVYWDEEWiaTAAEWVGDAIDRGIPFLGVCWGHQLLAH 94 
                                       4555568888889*********99.66666654447889**********************96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.36
                                       SEEEETTSEEEE-SEEGGGCTCCG-SE CS
                         DJ-1_PfpI  38 eevkgsrGlkvtvdaslddvkaaeyDa 64 
                                       eev+  +G+  t+da l+ +++ e Da
  gi|336252791|ref|YP_004595898.1| 222 EEVRAEEGAVATADADLETAADTEADA 248
                                       688888999999999999888878876 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 ?   10.9   0.0   7.3e-05      0.26      40      92 ..      45      96 ..      18     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.3e-05
                          GATase_3 40 dadlvilpGgkdtiq.dlallresgldeaikeaaeaggpvlgiCGGlqmLGeei 92
                                      d d  ++ G+++ +  d ++ +    +e++ +a+ +g+p lg+C G q+L + +
  gi|336252791|ref|YP_004595898.1| 45 DFDGAVVTGSRSSVYwDEEWIAT--AAEWVGDAIDRGIPFLGVCWGHQLLAHVL 96
                                      46777778887655425555555..8999*******************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1805.40
//
Query:       gi|336252792|ref|YP_004595899.1|  [L=455]
Description: AMP-dependent synthetase and ligase [Halopiger xanaduensis SH-6]
Scores for 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-40  136.4   0.0    1.7e-39  135.6   0.0    1.4  1  AMP-binding  AMP-binding enzyme
  ------ inclusion threshold ------
      0.054   13.8   0.0       0.34   11.2   0.0    2.2  2  FeoA         FeoA 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 !  135.6   0.0   1.9e-43   1.7e-39       2     414 ..      24     452 ..      23     454 .. 0.83

  Alignments for each domain:
  == domain 1  score: 135.6 bits;  conditional E-value: 1.9e-43
                                       HHHHHHSTTSEEEEE...........CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHH CS
                       AMP-binding   2 eeqaaktpdkvalvd...........sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallai 67 
                                       +++a+++pd++a+vd           +    +++Y+el + +++ A  L +lG+  gd+V ++ +n++  +++++a+
  gi|336252792|ref|YP_004595899.1|  24 ARRADRFPDRTAVVDiseerlyapaeTIHEDRVSYAELSRLADATADRLAELGIDAGDTVCLVTRNRVASLALFFAC 100
                                       689*********************99556789********************************************* PP

                                       HHTT-EEEEEETTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCS CS
                       AMP-binding  68 lkaGavvvplnptltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeese 144
                                        ++Ga+ +p++ +lt+ +++  +e  e+ +++   +s++   l + ++ +++v+l  +  ad   +++++  +++s+
  gi|336252792|ref|YP_004595899.1| 101 HRLGATFAPVSHRLTPVTVERPFEVLEPALVV--SESAQ-RDLVRSMPFDRTVTLSELAVADVETDADRSSRTASSD 174
                                       ********************************..44444.3334444444444444433333433444444444444 PP

                                       CTTS-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHH CS
                       AMP-binding 145 ekaekpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilel 221
                                        +++  + ++++++d +++++      G+P  + +s r+l +n+ +     +++l+++d+v  + pl+   gl+   
  gi|336252792|ref|YP_004595899.1| 175 GVDP-RVGDDQTDADRPLLLLHG--DGGRPI-AAYSARSLEWNCIAT--LVTWGLSPRDTVPLVSPLSAHDGLVRVA 245
                                       4432.33556899********95..559**5.5689*******9995..3459999***********9888888*** PP

                                       HHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBH CS
                       AMP-binding 222 llallsGatvvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplsp 297
                                       l +l++G+++ l +    +dp+  l +ie +++t++ag  ++++ l++ s++++         sl+ + +  +++++
  gi|336252792|ref|YP_004595899.1| 246 LPTLYAGGRLLLDRA---FDPGDTLTAIESEEATLFAGRTAAFRDLAAeSKFPE------AADSLERA-FPDASVPA 312
                                       **********99554...5666779*********************99777777......67799995.8******* PP

                                       HHHHHHHHHHTCEEEEEEEEGGGSSECEE...CHCTTTCTSTTS-BEE-TTEEEEEE.-TTTSCBEETTSEEEEEEE CS
                       AMP-binding 298 ellrffralfgeevlegYGlTEttgvvtv...lpleedkkklgsvGkplpgvevkiv.DeetgepvpdgeeGellvr 370
                                       ++l+ +ra+ ++ +  +YG  E+ ++++    ++     + + s Gkp+p+++vk+v D ++g p++   +G+l ++
  gi|336252792|ref|YP_004595899.1| 313 DVLEPYRAHEIP-IARTYGRLECPIALSQtgtDTAASAGTDADSLGKPVPDCRVKLVaDGSDGDPLEGAGTGQLALS 388
                                       *********876.**********999954456555666667899*************99999****99999****** PP

                                       ETTS-SEBTT-HHHHHHHEEE.....................TCCEEEEEEEEEEETTSEEEEEE CS
                       AMP-binding 371 gpgvmkgYlkkpeataeafds.....................egrwlrTGDlgrldedGyleivg 414
                                       gp +  gY ++ + t + +d+                      ++w+ TG   r+de G ++ v+
  gi|336252792|ref|YP_004595899.1| 389 GPILSDGYVGD-ADTDDDVDAgfgtgdrtnekpddtadrgrfADGWFDTGEPFRRDETGCYYRVD 452
                                       **********9.888888876777788888899999*99875467**************998776 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.8e-05      0.34      16      48 ..      63      92 ..      34      97 .. 0.82
   2 ?   -1.2   0.0      0.27   2.5e+03      34      51 ..     360     377 ..     360     388 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.8e-05
                                      EE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS CS
                              FeoA 16 risdedpellrrLremGlvpGarievvarapfg 48
                                      r+    ++++ rL+e+G+  G ++ +v r++ +
  gi|336252792|ref|YP_004595899.1| 63 RL---ADATADRLAELGIDAGDTVCLVTRNRVA 92
                                      33...35678*****************999875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.27
                                       -TT-EEEEEEE-TTS-SE CS
                              FeoA  34 vpGarievvarapfggpl 51 
                                       vp++r+++va++  g+pl
  gi|336252792|ref|YP_004595899.1| 360 VPDCRVKLVADGSDGDPL 377
                                       699*******99889998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3431.09
//
Query:       gi|336252793|ref|YP_004595900.1|  [L=261]
Description: alpha/beta hydrolase fold protein [Halopiger xanaduensis SH-6]
Scores for 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-17   62.5   0.0    7.5e-10   38.9   0.0    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    9.9e-15   55.7  12.6    1.2e-14   55.5  12.6    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
    9.4e-08   31.6   0.0     0.0016   17.8   0.0    2.0  2  Hydrolase_4    Serine aminopeptidase, S33
    0.00031   20.8   0.0    0.00056   20.0   0.0    1.4  1  Abhydrolase_4  TAP-like protein


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 !   38.9   0.0   1.7e-13   7.5e-10       8     131 ..      29     142 ..      21     151 .. 0.83
   2 !   21.8   0.0   2.7e-08   0.00012     206     256 ..     179     241 ..     158     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.7e-13
                                       STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHH CS
                     Abhydrolase_1   8 GlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmGG 84 
                                       Gl+g+s+ w  ++     a   ++ ++ DlrG g+S+++p +    y + ++a dl+++l+   +++ +lvG+ +GG
  gi|336252793|ref|YP_004595900.1|  29 GLGGWSWGWQHAA----VAG-PYEAVVWDLRGTGRSDAPPGP----YDLETLAGDLEAVLAECEIRNAHLVGCGLGG 96 
                                       7777777777722....333.6889***************86....88888************************** PP

                                       HHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHH CS
                     Abhydrolase_1  85 mialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgy 131
                                       ++ala+a    +rV  l l+g+ ++ ++++ + +++ + +pd+++  
  gi|336252793|ref|YP_004595900.1|  97 AVALAAART-SSRVETLSLIGTAAEGSEFDLEPLFASPDDPDALRES 142
                                       ***998876.9***********8888888888888888888887765 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.7e-08
                                       C............THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                     Abhydrolase_1 206 e............lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafleg 256
                                       +            l +v++pt v++gt+D+lvp + + dla+ lp+ + v++++agHla +e+
  gi|336252793|ref|YP_004595900.1| 179 QvaalegfdasdwLVEVTQPTRVFHGTDDGLVPGETGQDLARGLPRGEFVALEGAGHLAMIER 241
                                       233444444445588999*****************************************9986 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5  12.6   2.6e-18   1.2e-14       1     218 [.      22     246 ..      22     248 .. 0.58

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 2.6e-18
                                       EEEE-....-GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS..--HHH.CHHHHHHHCCTT..TTSEEEE CS
                     Abhydrolase_6   1 vlllH....GagssassWlvapLaallaagvhvlapDlpGhGrsdppp..ldled.ladlaalldelaagggpvvlv 70 
                                       v++++    G++s  ++W++a +    a+ ++ ++ Dl+G+Grsd pp  +dle  + dl+a+l+e     ++++lv
  gi|336252793|ref|YP_004595900.1|  22 VVFVPeaglGGWS--WGWQHAAV----AGPYEAVVWDLRGTGRSDAPPgpYDLETlAGDLEAVLAECE--IRNAHLV 90 
                                       7999877334444..44454444....77788899*******88666622555553455588888886..9999*** PP

                                       EETCHHHHHHHHHHCC...EE.EEES-..----TTTS----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHH....CC CS
                     Abhydrolase_6  71 GHSlGGalalaaapla.lvvg.vlldppptalpagllaaalelllallallrllawlsreplprlfladed....ad 141
                                       G  lGGa+alaaa+   +v++  l+ +   a+  ++++  + ++ +  + + +  + ++  l+++f+a+ +      
  gi|336252793|ref|YP_004595900.1|  91 GCGLGGAVALAAARTSsRVETlSLIGT---AAEGSEFDLEPLFASPDDPDALRESLAAG--LSDEFIAEQPdvvdGI 162
                                       ***********7777775555666666...44444433333333322222222122221..2233333333232234 PP

                                       CCHCHCCCGHHHHCC....HHCHTTCCHHTT-TTGC.EEE.CTT-CHHHHCHHCCCH..STTEEETCE...SSS-HH CS
                     Abhydrolase_6 142 aawrarlarlaalla....glgllpaaawadlpvpl.lvl.ggeDplvprllerlla..qagarlpvvlpgaGHlph 210
                                       ++wra  ++ +  ++    +l+ + a++w    ++   v+ g++D lvp    + la  +++ ++ v l+gaGHl +
  gi|336252793|ref|YP_004595900.1| 163 VDWRADGDADREGWDaqvaALEGFDASDWLVEVTQPtRVFhGTDDGLVPGETGQDLArgLPRGEF-VALEGAGHLAM 238
                                       45555555555444432223334556666666666643442677779997766666668899999.99********* PP

                                       HHSHHHHH CS
                     Abhydrolase_6 211 leepdeva 218
                                       +e+ + v+
  gi|336252793|ref|YP_004595900.1| 239 IERSRTVN 246
                                       *7667665 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.5e-07    0.0016      32     112 ..      46     120 ..      39     160 .. 0.87
   2 !   12.1   0.0   1.9e-05     0.083     189     238 ..     194     241 ..     169     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.5e-07
                       Hydrolase_4  32 favyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsa 108
                                       ++ + +D rG Grs+   g   +++++  Dl+a++ + +     ++  l+G  +GG++al+++ + ++ v+ l l++
  gi|336252793|ref|YP_004595900.1|  46 YEAVVWDLRGTGRSDAPPG-PYDLETLAGDLEAVLAECE----IRNAHLVGCGLGGAVALAAARTSSR-VETLSLIG 116
                                       78899**********9999.889********99986665....566788***********99988888.88888888 PP

                       Hydrolase_4 109 Palk 112
                                       +a +
  gi|336252793|ref|YP_004595900.1| 117 TAAE 120
                                       8765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.9e-05
                       Hydrolase_4 189 kitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnEp 238
                                       ++t P+ ++hG++D +v+ e  ++l++ l+  + ++   +g+ H  + E+
  gi|336252793|ref|YP_004595900.1| 194 EVTQPTRVFHGTDDGLVPGETGQDLARGLP--RGEFVALEGAGHLAMIER 241
                                       5678**************************..69**********998885 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.2e-07   0.00056      34      93 ..     196     255 ..     175     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.2e-07
                     Abhydrolase_4  34 aapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLlt 93 
                                       ++p+ ++ ++ D  +P e+++ la+ l++++ v  eg+GH a+++ ++ v++ +  +L++
  gi|336252793|ref|YP_004595900.1| 196 TQPTRVFHGTDDGLVPGETGQDLARGLPRGEFVALEGAGHLAMIERSRTVNDRLLGFLEE 255
                                       67888999*********************************************9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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 0.21s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1935.67
//
Query:       gi|336252794|ref|YP_004595901.1|  [L=925]
Description: alanyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-117  391.6   0.0     7e-117  391.2   0.0    1.1  1  tRNA-synt_2c  tRNA synthetases class II (A)
    4.1e-17   62.9   4.1    1.1e-16   61.6   4.1    1.8  1  DHHA1         DHHA1 domain
      2e-12   47.0   1.1      2e-12   47.0   1.1    1.8  2  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi


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 !  391.2   0.0  1.2e-120    7e-117       1     549 [.      64     605 ..      64     608 .. 0.94

  Alignments for each domain:
  == domain 1  score: 391.2 bits;  conditional E-value: 1.2e-120
                                       HHHHHHHHHHHCTT-EEE----SS-S.SSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGT CS
                      tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpe.ndptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenV 76 
                                       e+re+Fl++Fe++gH+++  ++v ++ +++++l+++A++++f+p+++++e+ p++++++ sQ+ciR++    D++nV
  gi|336252794|ref|YP_004595901.1|  64 EMREAFLSYFEDHGHERIDPYPVAANrWRDDVLLTQASIYDFQPLVTSGETPPPANPLTVSQPCIRMQ----DIDNV 136
                                       89**********************988*****************************************....***** PP

                                       TTSSS--SEEEEEEEEESS..............SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHH CS
                      tRNA-synt_2c  77 GktarHhTfFeMlGnfsfg..............dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiwe 137
                                       Gkt+rH   FeM+++++f+               Y+k+ ++e++  ll  elg d  ++++++ ++ +  +a+++ e
  gi|336252794|ref|YP_004595901.1| 137 GKTGRHTMAFEMMAHHAFNsredaeadyayegeVYWKDHTVELCDGLLE-ELGADITDVTYIEDPWVGggNAGPAIE 212
                                       ***********************************************99.****************9999******* PP

                                       HTTTTEGGGEEEE-HH.....HHEE.ESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEE CS
                      tRNA-synt_2c 138 klvgvpeerilrfgek.....dnfw.emgdtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnr 208
                                        ++++ e ++l+f +       +++ + g+t+  ++++++++++g e+++++++++++++++++ e+++ ++ +++ 
  gi|336252794|ref|YP_004595901.1| 213 VIYRGLEVATLVFMCMeqdpdGEYElKDGNTYSFMDTYIVDTGYGLERWTWMSQGTPTVYEAIYPEMIDFLKDNAGL 289
                                       ***********99654344445676678999*********************************************8 PP

                                       ST.TSHEEEEEEEEEEEEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_2c 209 ee.dgtlkpLpkksidtGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralaf 284
                                       +  d++ +++ + ++  G  ++  v +++ +r   + +++v+v e+   + +          e++++iaDH+r+la+
  gi|336252794|ref|YP_004595901.1| 290 SYtDEESEIVSRAARLSGQLDIDDVDDVEAARGDIAAEIGVSVDELRDLVEP---------LEDIYAIADHCRTLAY 357
                                       8658899999**************************************9999.........799************* PP

                                       HHHTT--SSSSHHHHHHHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCC CS
                      tRNA-synt_2c 285 aladGvvpsnegrgYvlRrllRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakT 361
                                       +l+dG+vpsn+g gY++R++lRr+ r++++ g++++ l++lv++++e l+       e+++++++i+++E e++++T
  gi|336252794|ref|YP_004595901.1| 358 MLGDGIVPSNVGTGYLARMVLRRTKRLCDNAGVDAP-LDELVDMQAERLD------YENRDTIRDIVRTEVEKYRET 427
                                       ************************************.************9......6899***************** PP

                                       HHHHHHHHHHHHHHCCC.CSEEXHHHHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSX CS
                      tRNA-synt_2c 362 lerGlklleelikklkk.kkelsgedafkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekkl 437
                                       lerG + +e l+++ +k ++ ++ e++++Lyd++G+ +d++ eiae+ g++vd+++ ++++++qr+ + + +++ + 
  gi|336252794|ref|YP_004595901.1| 428 LERGGRRVETLAEEYAKkGEPIPTEELIELYDSHGIQPDMVVEIAEDAGAEVDVPDDFYSLVAQRHDTPEGVEAAA- 503
                                       ************998776999***********************************************99888877. PP

                                       XXXXXXXTTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEE CS
                      tRNA-synt_2c 438 ikkdvealkelkkteeflgyeeleaeakvlallkdkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegae 514
                                        +++ e +++l++te+ l+y++ + ++++          + +e+ +   vvLd+T+fY+e+GGq +D+G++++++++
  gi|336252794|ref|YP_004595901.1| 504 ESESDERFADLPETEK-LYYDD-QQRTQFE-----AVVLDVFEREDGYDVVLDQTMFYPEGGGQPADTGTLSTDDTT 573
                                       677889999***9999.99999.4555554.....33455667777788**************************** PP

                                       EEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEX CS
                      tRNA-synt_2c 515 frvkdvqkakgvvlhkgkleegklkvgdkvkaevd 549
                                       ++v+dvq ++gv+lh+++ +     +g+ v+++vd
  gi|336252794|ref|YP_004595901.1| 574 VEVEDVQIEDGVILHRTDAN---PGKGEFVNGQVD 605
                                       ****************9996...667888888887 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   4.1   1.8e-20   1.1e-16       2     134 ..     786     915 ..     785     919 .. 0.85

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 1.8e-20
                                       HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEEC.TCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEE CS
                             DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevk.gvkvlvaevgeewdagalgiaadklksklkkpvivfvak 77 
                                       e++ ee+k+  k++e+lke+la++ a++   +aeev+ g  ++v     ++d++ l+  a+ + +  + +++v+ ++
  gi|336252794|ref|YP_004595901.1| 786 ERFFEEWKDRGKQIEDLKEQLAEARAGGGG-DAEEVDvGEATAVIDR-LDADMDELRATANAISE--EGKIAVLGSG 858
                                       67899******************9988775.6788887444444444.69***************..5577777777 PP

                                       EECTEEEEEEEESSH.SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHHHH CS
                             DHHA1  78 eegdkvkvsarskkd.gvdagelakeaaaklgggGGGH.dlAaGagipaekleealeal 134
                                         g  + +++ + ++ gv+age++ e+aak+gggGGG  d+A+G+g + ++l+eale++
  gi|336252794|ref|YP_004595901.1| 859 ASG--AQFVVSVPDGvGVNAGEVVGELAAKVGGGGGGPaDFAQGGGPNVDELDEALEDA 915
                                       665..77777777667****************************************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 ?   -3.3   0.1       1.8   1.1e+04       9      16 ..     175     182 ..     168     182 .. 0.76
   2 !   47.0   1.1   3.4e-16     2e-12       1      43 [.     707     748 ..     707     749 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.8
                                       .EEEEESS CS
                          tRNA_SAD   9 isvelCgG 16 
                                       + velC G
  gi|336252794|ref|YP_004595901.1| 175 HTVELCDG 182
                                       678***88 PP

  == domain 2  score: 47.0 bits;  conditional E-value: 3.4e-16
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRI 43 
                                       +r++++ + +v++CgGtHv +Tg+Ig +kil+ e++++g+ RI
  gi|336252794|ref|YP_004595901.1| 707 IRLIHVDT-DVQACGGTHVARTGDIGSIKILNTERVQDGVERI 748
                                       69999996.*********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (925 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.79u 0.24s 00:00:01.03 Elapsed: 00:00:00.43
# Mc/sec: 6531.14
//
Query:       gi|336252795|ref|YP_004595902.1|  [L=861]
Description: GAF domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-12   45.5   0.4      9e-12   45.5   0.4    4.5  5  GAF_2        GAF domain
    1.1e-05   26.1   0.1    3.7e-05   24.4   0.1    2.0  1  GAF          GAF domain
    0.00067   19.9   0.9    0.00067   19.9   0.9    3.3  3  PAS_4        PAS fold
  ------ inclusion threshold ------
       0.01   16.0   3.0      0.062   13.5   0.3    2.5  2  TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
      0.085   13.2   0.4        4.3    7.7   0.0    2.9  2  GAF_3        GAF domain


Domain annotation for each model (and alignments):
>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1         1   3.7e+03      57      83 ..      17      44 ..       4      71 .. 0.65
   2 ?   -3.8   0.2       3.9   1.4e+04      40      68 ..     204     232 ..     179     246 .. 0.58
   3 !   45.5   0.4   2.5e-15     9e-12       2     138 .]     336     463 ..     335     463 .. 0.87
   4 ?    1.9   0.5     0.068   2.5e+02      22      77 ..     668     723 ..     611     738 .. 0.57
   5 ?    1.4   0.1       0.1   3.6e+02       4      50 ..     750     806 ..     748     841 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                                      THHHHHHHHTS-EE.ES-GGG-S-HHHH CS
                             GAF_2 57 glvgealrtgrpvi.lndleedpdkkgl 83
                                      +++++a+r+g + +  + +++dp + + 
  gi|336252795|ref|YP_004595902.1| 17 APTEDAAREGAAALeRAATAADPEREPT 44
                                      3788888887655423335555554443 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.9
                                       EES-TTSTT-S-B---TTHHHHHHHHTS- CS
                             GAF_2  40 geaeeefgaaldrplgeglvgealrtgrp 68 
                                       +  e+e   + d   ++ +v ea++t r+
  gi|336252795|ref|YP_004595902.1| 204 ADSEPEREPERDEGEDDEPVDEAAETDRE 232
                                       22222222222223355588888888765 PP

  == domain 3  score: 45.5 bits;  conditional E-value: 2.5e-15
                                       HHHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG- CS
                             GAF_2   2 adleelldlvldelvel.gaalgyillvdddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndleed 77 
                                       +d e l++l++d +ve+ g +++++  v   g+  l++++ a++   ++l++ + +g++gea+rtg ++ ++ l+  
  gi|336252795|ref|YP_004595902.1| 336 HDRERLFELLVDGAVEIlGYEYCWLSTVH-FGE--LVPRATAPAVPADRLESTPVDGPLGEAFRTGASTRIDELDG- 408
                                       7899************66***99877755.255..77888888888999988999***************888666. PP

                                       S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  78 pdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                         +   +   ag+rs  +vP+      +Gvl ++a++ +afde d+ lLe l++++a ++e
  gi|336252795|ref|YP_004595902.1| 409 --RAEIEPPFAGVRSLCSVPV---S-DFGVLRVAAAEANAFDENDVVLLERLCRTAAAVLE 463
                                       ..455555669**********...4.89******************************997 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.068
                                       EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B--....-TTHHHHHHHHTS-EEES-GGG- CS
                             GAF_2  22 lgyillvdddgglrlaawgeaeeefgaaldrpl....geglvgealrtgrpvilndleed 77 
                                       ++y+ l    g+   +++    + +g   dr l    + + + +a+ t +pv l+d++++
  gi|336252795|ref|YP_004595902.1| 668 HSYLELAAKSGK--NEHFDAIADAHGKLDDR-LaaieDVATWDDAADT-EPVALHDVARH 723
                                       333333222222..12222333333333322.1333334478899999.89999996663 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHSS.....EE.....EEEEE-TTS-EEEE....EEEES-TTSTT-S CS
                             GAF_2   4 leelldlvldelvelgaa...lg.....yillvdddgglrla....awgeaeeefgaal 50 
                                       l+el+++v++ ++e++++   ++      ++    d+g+++a    a+++++++  +a+
  gi|336252795|ref|YP_004595902.1| 750 LHELFEFVVRSALEIDSDgddAAapvtvTVGA--TDDGFYVAgdrpAASGTDDGRQEAP 806
                                       89************954433433355334444..3366666666664444444444444 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1     1e-08   3.7e-05       1     131 [.     337     460 ..     337     462 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1e-08
                                       SHHHHHHHHHHHHHHHHTESEEEEEEEEETTEEE.....CEEEEECC......EEEETTSHHHHHHHHHSSSEEEST CS
                               GAF   1 dleelldtvveelrellgadrvalylpdydGlhy.....dipqasrw......lfmkngrgicgqvlatgqplvipd 66 
                                       d+e+l++ +v+ + e+lg++++ l +  + G +                    l+  +++g  g++++tg + +i++
  gi|336252795|ref|YP_004595902.1| 337 DRERLFELLVDGAVEILGYEYCWLST-VHFG-ELvpratA------PavpadrLESTPVDGPLGEAFRTGASTRIDE 405
                                       799*********************98.4555.22233331......233334466666777799************8 PP

                                       GGTSTTHHTT..HHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHH CS
                               GAF  67 stpdprfaqy..nrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvav 131
                                          d+r               g+rs+++vP+ +    +G+l +    +  f+++++ ll+ l++ +a 
  gi|336252795|ref|YP_004595902.1| 406 --LDGRAEIEppF-------AGVRSLCSVPVSD----FGVLRVAAAEAnAFDENDVVLLERLCRTAAA 460
                                       ..55553332332.......58**********9....9*******54458**************9987 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3      0.56     2e+03      34      74 ..       7      48 ..       1      58 [. 0.72
   2 ?   -0.6   0.4      0.43   1.5e+03      29      79 ..     455     505 ..     439     509 .. 0.84
   3 !   19.9   0.9   1.9e-07   0.00067      10     107 ..     529     634 ..     528     637 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.56
                             PAS_4 34 ellGktlaellpee.daarleralrrvlegeepiefleelll 74
                                      +++ +t    +p+e +a++ ++al+r+++  +p ++++++ l
  gi|336252795|ref|YP_004595902.1|  7 RHRSRTILYAAPTEdAAREGAAALERAATAADPEREPTVHPL 48
                                      556666665556664788888999999999999988888765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.43
                             PAS_4  29 gappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeer 79 
                                        ++++++l + ++e+    d+ rler ++r+ ++++ +   +e+l + ++r
  gi|336252795|ref|YP_004595902.1| 455 CRTAAAVLERNWHEMGVVNDRNRLEREVDRLERERDQYAAGTERLANERDR 505
                                       56778888899999877779999*****99999999999999998887776 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 1.9e-07
                             PAS_4  10 vldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyelrll 86 
                                       ++d + +++++Naa   +fg +p++l G ++ e++ ++  ++ ++ l+++l+ +e  + l+ + + ++ r + l+++
  gi|336252795|ref|YP_004595902.1| 529 IVDGEPVIRDVNAAVKTVFGDDPAALDGTPVDEYVVPQGLEERAATLTEALQADEQRQLLDRRETVDGVRDFMLTVV 605
                                       5788999**************************999999**************************888888888888 PP

                             PAS_4  87 Plr........desGevigvlvisrDiTe 107
                                       Pl+        +++G  ++ l++  DiTe
  gi|336252795|ref|YP_004595902.1| 606 PLEraaaadgaARDGSDHAGLLVYEDITE 634
                                       88522222222345666666666666666 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 ?   13.5   0.3   1.7e-05     0.062      15      61 ..     476     522 ..     468     535 .. 0.89
   2 ?    2.0   0.2     0.066   2.4e+02      22      68 ..     636     682 ..     633     700 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                       TMF_TATA_bd  15 erlsseirrlEgElaslkeelerleaerdeareeivklmkeneelke 61 
                                       +rl+ e+ rlE E  ++    erl++erd++++e  +l++ +e++++
  gi|336252795|ref|YP_004595902.1| 476 NRLEREVDRLERERDQYAAGTERLANERDRLAAERDQLLALVEDVNK 522
                                       7999******************************9999999998876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.066
                       TMF_TATA_bd  22 rrlEgElaslkeelerleaerdeareeivklmkeneelkelkkelee 68 
                                       +r+E Ela++ e+ler+++  de  e  +++ ++  el+++++++e+
  gi|336252795|ref|YP_004595902.1| 636 KRRELELAAATERLERVASLLDEDVENPLQVAHSYLELAAKSGKNEH 682
                                       799**************999888888877777777777777766665 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0012       4.3      80     129 .]     419     464 ..     339     464 .. 0.65
   2 ?    2.4   0.2     0.051   1.8e+02      11      75 ..     641     712 ..     640     724 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0012
                             GAF_3  80 draalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                        r++  vP+ +    +Gvl +a  +  afd+ d+ lle l+r +a  +er
  gi|336252795|ref|YP_004595902.1| 419 VRSLCSVPVSD----FGVLRVAAAEANAFDENDVVLLERLCRTAAAVLER 464
                                       34444477777....9*********9********************9997 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.051
                             GAF_3  11 kllvkllgaevgalllldedgnklqvaagw.dgkpalse.....sld.edsalarralssgevvsepsfaee 75 
                                       +l++ + ++e++a ll ++ +n lqva+++ + +++  +     ++  ++ +l +r+++ + v++  ++a++
  gi|336252795|ref|YP_004595902.1| 641 ELAAATERLERVASLLDEDVENPLQVAHSYlELAAKSGKnehfdAIAdAHGKLDDRLAAIEDVATWDDAADT 712
                                       5666677899999989898899********744444433556665536888888888888888877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (861 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); 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):               5  [number of targets reported over threshold]
# CPU time: 0.92u 0.30s 00:00:01.22 Elapsed: 00:00:00.45
# Mc/sec: 5718.85
//
Query:       gi|336252796|ref|YP_004595903.1|  [L=336]
Description: Replication factor C small subunit [Halopiger xanaduensis SH-6]
Scores for 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-23   81.7   0.0    9.9e-23   80.4   0.0    1.7  1  Rep_fac_C        Replication factor C C-terminal domain
    6.5e-20   71.9   0.1    1.2e-17   64.6   0.0    2.2  2  AAA              ATPase family associated with various cellul
    1.9e-15   57.1   0.0    3.5e-11   43.1   0.0    2.2  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    6.4e-07   29.5   0.0    1.5e-06   28.2   0.0    1.6  2  Rad17            Rad17 P-loop domain
    1.1e-06   29.2   0.4     0.0026   18.2   0.0    2.9  3  AAA_16           AAA ATPase domain
    1.2e-06   28.8   1.0    4.2e-06   27.0   0.4    2.2  1  AAA_assoc_2      AAA C-terminal domain
    2.1e-06   27.8   0.1    1.2e-05   25.3   0.0    2.0  2  AAA_14           AAA domain
    3.1e-06   27.0   0.3      4e-05   23.4   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.6e-05   23.6   0.0    7.7e-05   22.5   0.0    1.5  1  DNA_pol3_delta   DNA polymerase III, delta subunit
    3.8e-05   24.0   0.1       0.47   10.7   0.0    2.5  2  AAA_22           AAA domain
    0.00033   20.4   0.0      0.019   14.7   0.0    2.5  1  Sigma54_activat  Sigma-54 interaction domain
     0.0005   19.9   0.0     0.0031   17.4   0.0    2.0  2  AAA_3            ATPase family associated with various cellul
    0.00052   20.6   0.0      0.002   18.7   0.0    2.0  1  AAA_18           AAA domain
    0.00059   19.9   0.0      0.011   15.7   0.0    2.8  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00095   18.6   0.0       0.17   11.3   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0011   18.5   0.0     0.0019   17.7   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
     0.0013   18.7   0.0      0.008   16.2   0.0    2.0  1  ResIII           Type III restriction enzyme, res subunit
     0.0047   16.4   0.0        0.2   11.1   0.0    2.3  2  PhoH             PhoH-like protein
     0.0066   16.2   0.0      0.013   15.3   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0074   16.0   0.9      0.016   14.9   0.1    2.0  2  AAA_30           AAA domain
      0.009   15.8   0.0      0.022   14.5   0.0    1.7  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.016   15.6   0.0      0.037   14.4   0.0    1.7  1  RNA_helicase     RNA helicase
      0.017   14.4   0.0       0.06   12.5   0.0    1.9  2  TIP49            TIP49 P-loop domain
       0.02   14.7   0.8        9.8    5.9   0.0    3.0  3  DEAD             DEAD/DEAH box helicase
       0.03   13.9   0.3        0.1   12.2   0.0    2.1  2  AAA_25           AAA domain
      0.032   14.4   0.0        0.1   12.7   0.0    1.9  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.034   14.0   0.0       0.13   12.2   0.0    1.9  2  NACHT            NACHT domain
      0.038   14.2   0.1       0.11   12.6   0.1    1.9  1  AAA_33           AAA domain
      0.041   14.0   0.0       0.12   12.5   0.0    1.7  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.044   12.8   0.0      0.089   11.8   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
      0.098   12.4   0.0       0.13   12.0   0.0    1.2  1  AAA_11           AAA domain
       0.12   13.2   2.2         28    5.9   0.1    3.7  2  TPR_14           Tetratricopeptide repeat
       0.13   12.4   0.3       0.33   11.1   0.1    1.8  1  TetR_C_12        Bacterial transcriptional repressor C-termin
       0.14   11.6   0.0       0.71    9.3   0.0    2.0  2  TniB             Bacterial TniB protein
       0.14   11.3   0.0       0.23   10.6   0.0    1.3  1  NB-ARC           NB-ARC domain
       0.18   11.9   0.0       0.34   11.0   0.0    1.4  1  Torsin           Torsin
        7.6    7.4   6.1         86    4.1   0.5    3.7  3  TPR_6            Tetratricopeptide repeat


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 !   80.4   0.0     2e-25   9.9e-23       2      88 .]     244     329 ..     243     329 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 2e-25
                                       -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-H CS
                         Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGase 78 
                                       +p+e+ee++ ++  gdf++a++ l++ll+++G+++ d++ qlhr   e  ++pe++ +++le+lge+++r++eGa+e
  gi|336252796|ref|YP_004595903.1| 244 RPEEVEEMVGHAIDGDFTAARAALEDLLTDRGLAGGDVIDQLHRSAWEF-DIPEQATVRLLERLGEVDYRITEGANE 319
                                       79**********99**********************************8.6************************** PP

                                       HHHHHHHHHH CS
                         Rep_fac_C  79 hlqlsallar 88 
                                       +lql+a+la+
  gi|336252796|ref|YP_004595903.1| 320 RLQLEAMLAS 329
                                       ********96 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 !   64.6   0.0   2.4e-20   1.2e-17       2     129 ..      60     175 ..      59     178 .. 0.86
   2 ?    5.2   0.1     0.054        26      66     119 ..     202     252 ..     183     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 2.4e-20
                                       EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHH CS
                               AAA   2 llyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaks 73 
                                       ++ Gp GtGKT++a+a+a+e+       +fle+++s+ +   +    ++i+++ ++     ++ i+f+DE+dal+++
  gi|336252796|ref|YP_004595903.1|  60 MFAGPAGTGKTTAAQAIAREIydddwRENFLELNASDQR--GIDVVRDRIKDFARSSFGGYDHRIIFLDEADALTSD 134
                                       799*****************844433599**********..7888888888887765444488***********999 PP

                                       HTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEE CS
                               AAA  74 rsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkie 129
                                                   +++L + ++++++   ++ +i+ +n+ +++ +++  +R+ +  +
  gi|336252796|ref|YP_004595903.1| 135 A-----------QSALRRTMEQFSN---NTRFILSCNYSSQIIDPIQ-SRCAVFRF 175
                                       9...........*************...699****************.9**98766 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.054
                                       TGGGHHHHHTTCCCHHHHHHHHHHHH.HHHHTTTSSSTEEEEEEESSGGGSTHHH CS
                               AAA  66 EidalaksrsgseseeeervvnqLlt.eldgvkkkeskvivigatnrpdkldpal 119
                                        +dal+ +     +++ ++++n+L + ++ g++ +e++v+ i+at rp+++++ +
  gi|336252796|ref|YP_004595903.1| 202 GVDALVYAA----DGDMRKAINALQAaAVMGETVDEETVFAITATARPEEVEEMV 252
                                       466666666....6677777777764145666667899***********999865 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 !   12.0   0.0   0.00027      0.13       2      47 ..      40      84 ..      39      91 .. 0.89
   2 !   43.1   0.0   7.3e-14   3.5e-11      83     162 ..      98     178 ..      86     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                   DNA_pol3_delta2  2 qeealkilskalksgrlahayLfeGdegigkkelalnlakallcee 47
                                      +e+++  l++ ++++ l h ++f+G++g+gk ++a+++a+++  ++
  gi|336252796|ref|YP_004595903.1| 40 HEDIIPRLKNYVEQDDLPH-LMFAGPAGTGKTTAAQAIAREIYDDD 84
                                      6788999***********9.79******************998765 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 7.3e-14
                   DNA_pol3_delta2  83 ikldqirelieelsrkpre.skkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelk 158
                                         +d +r+ i+++ r+++    ++ii +++a+ +t+ A+ al +t+E  s+n+ fiL  + +++++++i+SRc +++
  gi|336252796|ref|YP_004595903.1|  98 RGIDVVRDRIKDFARSSFGgYDHRIIFLDEADALTSDAQSALRRTMEQFSNNTRFILSCNYSSQIIDPIQSRCAVFR 174
                                       47999*************94579****************************************************** PP

                   DNA_pol3_delta2 159 fspl 162
                                       f +l
  gi|336252796|ref|YP_004595903.1| 175 FTEL 178
                                       *986 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   3.2e-09   1.5e-06       5      69 ..      21      80 ..      18     113 .. 0.87
   2 ?   -2.5   0.0       8.4   4.1e+03      96     116 ..     156     180 ..     132     201 .. 0.63

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.2e-09
                             Rad17  5 enelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskel 69
                                      ++e W+eky+Pe ++e+  h   i  +k++++ d L++     L+ +GP+G gk+t+ + +++e 
  gi|336252796|ref|YP_004595903.1| 21 KTEVWIEKYRPERLDEIKGHEDIIPRLKNYVEQDDLPH-----LMFAGPAGTGKTTAAQAIAREI 80
                                      5799********************************97.....59****************9985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.4
                             Rad17  96 tekesrf....lsqiesfkeleLkd 116
                                       ++  s++    +s++++f+  eL d
  gi|336252796|ref|YP_004595903.1| 156 CNYSSQIidpiQSRCAVFRFTELTD 180
                                       4444433455578888877666665 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   5.3e-06    0.0026       6      53 ..      41      85 ..      36      97 .. 0.82
   2 !    8.6   0.0    0.0046       2.2     116     163 ..      98     147 ..      82     154 .. 0.69
   3 ?   -1.3   0.1       5.3   2.6e+03      86     106 ..     252     272 ..     208     328 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.3e-06
                            AAA_16  6 eeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdgg 53
                                      e+ + +L++++e   +++ + +++ G++G+GK++ +++++r++ +d++
  gi|336252796|ref|YP_004595903.1| 41 EDIIPRLKNYVE---QDDLPHLMFAGPAGTGKTTAAQAIAREIYDDDW 85
                                      666777777777...667799********************9998864 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0046
                            AAA_16 116 a..srllellkrll.allsrderplvlvlDdlqwadeaslqllaaLlrlle 163
                                       +    +++ +k+++ +     ++  +++lD+++ + ++ +++l+ +++  +
  gi|336252796|ref|YP_004595903.1|  98 RgiDVVRDRIKDFArSSFGGYDH-RIIFLDEADALTSDAQSALRRTMEQFS 147
                                       23366777777777655555566.9******************99987655 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 5.3
                            AAA_16  86 ldeaesaeleawrekleeala 106
                                         +a + ++ a+r++le+ l+
  gi|336252796|ref|YP_004595903.1| 252 VGHAIDGDFTAARAALEDLLT 272
                                       444444444444444444444 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 !   27.0   0.4   8.6e-09   4.2e-06       3      43 ..     194     234 ..     192     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 8.6e-09
                                       X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX CS
                       AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeakegk 43 
                                       ++++++dd ++al+ +adGD+Rka+n+L++aa + e+ +++
  gi|336252796|ref|YP_004595903.1| 194 QDIEVTDDGVDALVYAADGDMRKAINALQAAAVMGETVDEE 234
                                       689**************************999887764333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.88   4.2e+02      70      91 ..      34      55 ..       5      65 .. 0.77
   2 !   25.3   0.0   2.6e-08   1.2e-05       6      99 ..      60     156 ..      55     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.88
                            AAA_14 70 lDEiqevpewekalkslvdegk 91
                                      lDEi+  +++   lk++v++++
  gi|336252796|ref|YP_004595903.1| 34 LDEIKGHEDIIPRLKNYVEQDD 55
                                      9*****************9884 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 2.6e-08
                            AAA_14   6 vitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelileklkeekktylflDEiqev.pew 79 
                                       +  G+  +GKTt ++ +++e +    +e++l++n  d+r  +     ++ ++ ++++ + +++++flDE+  + +++
  gi|336252796|ref|YP_004595903.1|  60 MFAGPAGTGKTTAAQAIAREIYddDWRENFLELNASDQRGIDVVRD-RIKDFARSSFGGYDHRIIFLDEADALtSDA 135
                                       5679999***********9999987789*******99998765533.4777777776666899*******987368* PP

                            AAA_14  80 ekalkslvdeg.knldvivtG 99 
                                       ++al++ +++  +n ++i++ 
  gi|336252796|ref|YP_004595903.1| 136 QSALRRTMEQFsNNTRFILSC 156
                                       *********987889998875 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 !   23.4   0.0   8.3e-08     4e-05       2     111 ..      30     146 ..      29     155 .. 0.68
   2 ?   -2.5   0.1       7.7   3.8e+03     110     140 ..     213     243 ..     183     257 .. 0.55

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.3e-08
                            RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakel......g..vklkits..g.. 66 
                                       rP++l+e  g e++  +lk ++e     ++ l h++++Gp G Gktt a+ ia+e+      +   +l+++   g  
  gi|336252796|ref|YP_004595903.1|  30 RPERLDEIKGHEDIIPRLKNYVE-----QDDLPHLMFAGPAGTGKTTAAQAIAREIydddwrEnfLELNASDqrGid 101
                                       99****************99987.....6889*********************997222221111112222211111 PP

                            RuvB_N  67 Pvlekagdlaalltnleekdvlfideihrlsraveevlysamedf 111
                                        v ++ +d+a       ++ ++f+de   l++ ++  l  +me f
  gi|336252796|ref|YP_004595903.1| 102 VVRDRIKDFARSSFGGYDHRIIFLDEADALTSDAQSALRRTMEQF 146
                                       233455566666666666777777777777777777777777766 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.7
                            RuvB_N 110 dfrldivigkGpsarsikldlpkftlvgatt 140
                                       d+r  i   + ++    ++d +    ++at+
  gi|336252796|ref|YP_004595903.1| 213 DMRKAINALQAAAVMGETVDEETVFAITATA 243
                                       4444443333333333333333333344443 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 !   22.5   0.0   1.6e-07   7.7e-05      24     170 ..      86     222 ..      70     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.6e-07
                                       TTTEEEEEEEE-STTS-HHH.HTTTSTTTTSSS.SEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEE CS
                    DNA_pol3_delta  24 kqgfedlnyikfdlnedwiddvleecetlpffs.dkrivvlknpklltkesklnekllkeLeeylsnlpedtlLili 99 
                                       +++f +ln ++  + ++  d  +++    +f++ d ri++l+ +      + l+ + + +L +++++ + +t +il 
  gi|336252796|ref|YP_004595903.1|  86 RENFLELNASDQRGIDVVRD-RIKDFARSSFGGyDHRIIFLDEA------DALTSDAQSALRRTMEQFSNNTRFILS 155
                                       45555666666666665555.55556666776538899999999......568999999****************** PP

                                       ES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                    DNA_pol3_delta 100 apkklderkklvklLkkkatvveaktlkeeelkkwiqkraqelglkiekealelLlelvennlsaikqele 170
                                       ++       ++++ ++++  v+++++l+ + +  ++ ++a+++ ++ +++ ++ L+++  ++++ + ++l+
  gi|336252796|ref|YP_004595903.1| 156 CN----YSSQIIDPIQSRCAVFRFTELTDNAIEAQVREIAADQDIEVTDDGVDALVYAADGDMRKAINALQ 222
                                       **....4568*********************************************************9997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0     0.001      0.48       7      28 ..      58      79 ..      54      88 .. 0.88
   2 !   10.7   0.0   0.00097      0.47      76     128 ..     101     155 ..      82     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.001
                            AAA_22  7 ilvvtGesGtGKTtllrrlleq 28
                                      +l+  G++GtGKTt ++ ++++
  gi|336252796|ref|YP_004595903.1| 58 HLMFAGPAGTGKTTAAQAIARE 79
                                      67889************98875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00097
                            AAA_22  76 eellealeqalrarav...ielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                                       + +++++ + +r+ +    ++++ +DEa+ l + +a + Lr+ ++  + ++++iL 
  gi|336252796|ref|YP_004595903.1| 101 DVVRDRIKDFARSSFGgydHRIIFLDEADAL-TSDAQSALRRTMEQFSNNTRFILS 155
                                       34458888888888889999***********.999999999988888888888886 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.8e-05     0.019      12     118 ..      44     144 ..      36     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHH..HSTTTTS-EEEEETTTS.-TTCHHHHHHEBSSSSSTTTSS CS
                   Sigma54_activat  12 leqikkvaktd..lsvlitGesGtGKellaraihe..askrkekpfvavncaai.peelleseLFGhekGaFtGAek 83 
                                       + ++k+++++d   +++  G  GtGK++ a+ai +    +  +++f+++n ++    ++++ ++   ++ +F G ++
  gi|336252796|ref|YP_004595903.1|  44 IPRLKNYVEQDdlPHLMFAGPAGTGKTTAAQAIAReiYDDDWRENFLELNASDQrGIDVVRDRIKDFARSSFGGYDH 120
                                       5566666666655678899**************995555667899*****997634567777777777777777544 PP

                                       -BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHH CS
                   Sigma54_activat  84 ekkGlfekadgGtlfLDeigelplelQekLlrvlq 118
                                                   ++fLDe   l+ ++Q+ L r ++
  gi|336252796|ref|YP_004595903.1| 121 -----------RIIFLDEADALTSDAQSALRRTME 144
                                       ...........367777777777777777766666 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 !   17.4   0.0   6.5e-06    0.0031       1      88 [.      58     145 ..      58     153 .. 0.92
   2 ?   -0.3   0.0       1.9   9.1e+02      91     116 ..     224     249 ..     211     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.5e-06
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefk.kGpvfanllladeinrapp 76 
                                       h+++ g  G++kt++++a+a+ +  +  r  f  +l  sd  G++v++++ k+f  +  G   + +++ de +  ++
  gi|336252796|ref|YP_004595903.1|  58 HLMFAGPAGTGKTTAAQAIAREIYDDDWRENFL-ELNASDQRGIDVVRDRIKDFARSsFGGYDHRIIFLDEADALTS 133
                                       8999999*******************99*9996.79****************9976516999999************ PP

                             AAA_3  77 ktqsalleamee 88 
                                        +qsal  +me+
  gi|336252796|ref|YP_004595903.1| 134 DAQSALRRTMEQ 145
                                       *******99985 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.9
                             AAA_3  91 vtvegethklpepflvlatqnPieqe 116
                                        +v get + ++ f + at  P e e
  gi|336252796|ref|YP_004595903.1| 224 AAVMGETVDEETVFAITATARPEEVE 249
                                       45778899999999999*99998865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     4e-06     0.002       3      68 ..      61     147 ..      59     183 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4e-06
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf......................gvnlrdvakenglllevdpealdeskrldedkl 57 
                                        +G++G+GKtt a++++++  +                       ++++d a+ +   ++     lde + l  d +
  gi|336252796|ref|YP_004595903.1|  61 FAGPAGTGKTTAAQAIAREI-YdddwrenflelnasdqrgidvvRDRIKDFARSSFGGYDHRIIFLDEADALTSDAQ 136
                                       79**************9993.33344444455555644444444444444444443333333335666666666666 PP

                            AAA_18  58 dklldaleens 68 
                                        +l +++e+ s
  gi|336252796|ref|YP_004595903.1| 137 SALRRTMEQFS 147
                                       66666666555 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 ?   -0.3   0.0         2   9.9e+02      70      92 ..      33      54 ..      31      57 .. 0.87
   2 !   15.7   0.0   2.3e-05     0.011       1      90 [.      58     144 ..      58     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2
                                      EEESGGG--HHHHHHHHHHHHSS CS
                             AAA_5 70 vlDEveraesevlnsLlslleer 92
                                      +lDE++  + +++++L ++ e++
  gi|336252796|ref|YP_004595903.1| 33 RLDEIK-GHEDIIPRLKNYVEQD 54
                                      699**9.9*********999876 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.3e-05
                                       EEEEE--SSSSHHHHHHHGGGGB.....S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEE CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.....nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlD 72 
                                       +++  Gp GtgK++ a+ +a+ +     + ++++ + +++   + ++ r       + +  s++   +   +i++lD
  gi|336252796|ref|YP_004595903.1|  58 HLMFAGPAGTGKTTAAQAIAREIydddwRENFLELNASDQRGIDVVRDR------IKDFARSSFG--GYDHRIIFLD 126
                                       68999******************97764444444443333333333333......3577888887..7799****** PP

                                       SGGG--HHHHHHHHHHHH CS
                             AAA_5  73 EveraesevlnsLlslle 90 
                                       E + + s+++++L + +e
  gi|336252796|ref|YP_004595903.1| 127 EADALTSDAQSALRRTME 144
                                       ***999**9999987766 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00034      0.17      24      44 ..      58      78 ..      34     102 .. 0.82
   2 ?    5.1   0.0     0.026        13     109     133 ..     122     146 ..     117     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlps 44
                                      +l+++Gp+G+GKt  a++++ 
  gi|336252796|ref|YP_004595903.1| 58 HLMFAGPAGTGKTTAAQAIAR 78
                                      89***************9864 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.026
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledg 133
                                       ++fLDE+  +++++  +LR+ +e+ 
  gi|336252796|ref|YP_004595903.1| 122 IIFLDEADALTSDAQSALRRTMEQF 146
                                       89********************986 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 !   17.7   0.0     4e-06    0.0019      35      73 ..      58      96 ..      47     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4e-06
                             AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqt 73
                                      ++++ Gp+GtGKt+ ++ + +++ ++++  ++++++a+ 
  gi|336252796|ref|YP_004595903.1| 58 HLMFAGPAGTGKTTAAQAIAREIYDDDWRENFLELNASD 96
                                      79******************************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 !   16.2   0.0   1.7e-05     0.008      10      62 ..      42      94 ..      29     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-05
                                      HHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEES CS
                            ResIII 10 eaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvp 62
                                      ++i +l++ +++++  +++++ + GtGKT  a +++++++   ++e+fl l  
  gi|336252796|ref|YP_004595903.1| 42 DIIPRLKNYVEQDDLPHLMFAGPAGTGKTTAAQAIAREIYDDDWRENFLELNA 94
                                      55666667776566679******************************997754 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00042       0.2      22      46 ..      59      83 ..      43      94 .. 0.81
   2 ?    2.7   0.1      0.15        72     119     186 ..     119     190 ..     117     199 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00042
                                      EEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH 22 vfaiGpaGtGKtylavalavealkk 46
                                      ++ +GpaGtGKt  a a+a e++ +
  gi|336252796|ref|YP_004595903.1| 59 LMFAGPAGTGKTTAAQAIAREIYDD 83
                                      5678***********9999877665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.15
                                       -SEEEEE-SGGG--HHH...HHHHHTTB-TT-EEEEEE---.-----------THHHHHHTTT-TTEEEEE- CS
                              PhoH 119 ndafvilDEAQnttkeq...mkmfltRlGenskvvvtGdvt.qidlpkgkksGlaealevlknvegieivel 186
                                       ++ +++lDEA  +t+     ++  +  + +n+++++  + + qi  p ++++++   +e  +n  ++++ e+
  gi|336252796|ref|YP_004595903.1| 119 DHRIIFLDEADALTSDAqsaLRRTMEQFSNNTRFILSCNYSsQIIDPIQSRCAVFRFTELTDNAIEAQVREI 190
                                       56789*****99997541115556777788999999877641555556667777777777777666666665 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 !   15.3   0.0   2.6e-05     0.013       3      74 ..      61     131 ..      59     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-05
                   Viral_helicase1   3 vhGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEylll 74 
                                        +G +G GK+t+ + ++r+       r+++  l+++ ++  +    ++++f  +   + + +i++lDE+ +l
  gi|336252796|ref|YP_004595903.1|  61 FAGPAGTGKTTAAQAIAREI-YDDDWRENFLELNASDQRGIDVVRDRIKDFARSSFGGYDHRIIFLDEADAL 131
                                       6799***************4.3335678788888888999999999***********999********9766 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   3.3e-05     0.016      23      45 ..      61      84 ..      52     153 .. 0.83
   2 ?   -1.5   0.1       3.6   1.8e+03     135     137 ..     225     227 ..     185     271 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-05
                            AAA_30 23 ltGpAGtGKttalkal.reaweaa 45
                                        GpAGtGKtta +a+ re+++++
  gi|336252796|ref|YP_004595903.1| 61 FAGPAGTGKTTAAQAIaREIYDDD 84
                                      67*************977887766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.6
                            AAA_30 135 gvl 137
                                       +v+
  gi|336252796|ref|YP_004595903.1| 225 AVM 227
                                       222 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 !   14.5   0.0   4.5e-05     0.022      49      85 ..      58      94 ..      42     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.5e-05
                         IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlfvrved 85
                                       +++ Gp+G+GK+  a a+++e   ++++  f+ +++
  gi|336252796|ref|YP_004595903.1| 58 HLMFAGPAGTGKTTAAQAIAREIYDDDWRENFLELNA 94
                                      57899***********************999988765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.7e-05     0.037       2      35 ..      60      90 ..      59     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.7e-05
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvy 35
                                      ++ Gp+g+GK+t+a+ +a+++    ++++++++ 
  gi|336252796|ref|YP_004595903.1| 60 MFAGPAGTGKTTAAQAIAREIY---DDDWRENFL 90
                                      789*****************99...444444444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.06      53      87 ..      59      96 ..      47     116 .. 0.80
   2 ?   -1.6   0.0       2.4   1.2e+03     281     304 ..     122     145 ..     119     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                      XXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXX CS
                             TIP49 53 vLlaGpsgtGktalaiaiskelged...vpfvalsgse 87
                                      +++aGp+gtGkt  a ai++e+ +d     f  l++s+
  gi|336252796|ref|YP_004595903.1| 59 LMFAGPAGTGKTTAAQAIAREIYDDdwrENFLELNASD 96
                                      789*******************8542224688888876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.4
                                       XXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 281 vlfiDevhmlDiecfsylnrales 304
                                       ++f+De+  l  ++ s l r++e+
  gi|336252796|ref|YP_004595903.1| 122 IIFLDEADALTSDAQSALRRTMEQ 145
                                       79*******************996 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.038        18      17      36 ..      59      78 ..      38      89 .. 0.80
   2 ?    5.9   0.0      0.02       9.8     122     153 ..     120     150 ..     103     159 .. 0.81
   3 ?   -0.2   0.0       1.6   7.5e+02     141     175 ..     213     250 ..     174     251 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.038
                                      EEEEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                              DEAD 17 vlvaaeTGsGKTlaflipvl 36
                                      ++ a++ G+GKT+a++  + 
  gi|336252796|ref|YP_004595903.1| 59 LMFAGPAGTGKTTAAQAIAR 78
                                      67899*********987655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                                       EEEEEEETHHHHHHTTTHHHHHHHHHHSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 122 vrflVlDEadrlldqgfsdfinrilnqlpqit 153
                                        r++ lDEad l ++  +  ++r ++q+++ t
  gi|336252796|ref|YP_004595903.1| 120 HRIIFLDEADALTSD-AQSALRRTMEQFSNNT 150
                                       57889*********8.8999999999996544 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.6
                                       HHHHHHHHSHHHCTTST.TTSE.EEEEESSBS.HHHHH CS
                                       xxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxx.xxxxx RF
                              DEAD 141 finrilnqlpqitcdgk.lqrq.vivlSATlp.kdvkk 175
                                       ++++ +n+l+ +   g+  +++ v +++AT+  ++v++
  gi|336252796|ref|YP_004595903.1| 213 DMRKAINALQAAAVMGEtVDEEtVFAITATARpEEVEE 250
                                       45555666655555555433334899999998888776 PP

>> AAA_25  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       0.1      36      65 ..      59      87 ..      29     199 .. 0.71
   2 ?   -0.7   0.1       1.8   8.6e+02      93     139 ..     226     273 ..     186     304 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                            AAA_25 36 allaGapgtGKttlaldlalavatGkpwlg 65
                                       ++aG+ gtGKtt+a  +a ++  ++ w +
  gi|336252796|ref|YP_004595903.1| 59 LMFAGPAGTGKTTAAQAIAREIYDDD-WRE 87
                                      689****************9998644.654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.8
                            AAA_25  93 vgealrddarllvldlagv.eslpLfakdrggtl...ltadvdaleaaiee 139
                                       v+ +  d ++++++++  + e++    ++ g+++    ta+ +ale+ +++
  gi|336252796|ref|YP_004595903.1| 226 VMGETVDEETVFAITATARpEEVE---EMVGHAIdgdFTAARAALEDLLTD 273
                                       223334555555555443333332...221222222244444555555555 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00021       0.1       5      82 ..      58     133 ..      54     145 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
                                       -EEEE--TTSSHHHHHHHHHHHTT-.....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                             AAA_2   5 silllgptgvGktelakalaellfv.kkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKi 80 
                                        ++++gp g+Gkt +a+a+a+ +   + ++++  ++as+    + v+  ++ +   +    g  ++ i++lDE d  
  gi|336252796|ref|YP_004595903.1|  58 HLMFAGPAGTGKTTAAQAIAREIYDdDWRENFLELNASDQRGIDVVRDRIKDF---ARSSFGGYDHRIIFLDEADAL 131
                                       579*****************998743456788888888888844444444433...333444445569*****9988 PP

                                       -- CS
                             AAA_2  81 hp 82 
                                       ++
  gi|336252796|ref|YP_004595903.1| 132 TS 133
                                       77 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00026      0.13       4      27 ..      60      83 ..      58      92 .. 0.85
   2 ?   -2.2   0.0       7.1   3.5e+03     113     142 ..     226     255 ..     201     275 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                                      EEEC-TTTCHHHHHHHHHHHHCTS CS
                             NACHT  4 ilqGeaGsGKTtLlqklalawaeg 27
                                      +  G+aG GKTt +q +a+++ ++
  gi|336252796|ref|YP_004595903.1| 60 MFAGPAGTGKTTAAQAIAREIYDD 83
                                      568***************998665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.1
                                       HCTTTTT--EEEEEEECCCHHHHCTTSSCE CS
                             NACHT 113 irkkllpeasllltvrpralrdleeqleea 142
                                       + ++ + e ++++++ + + +++ee++ +a
  gi|336252796|ref|YP_004595903.1| 226 VMGETVDEETVFAITATARPEEVEEMVGHA 255
                                       444444555555555555555555555544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00023      0.11       2      22 ..      59      79 ..      59     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                            AAA_33  2 vllvGlpGsGKstlaerllkk 22
                                      +++ G++G+GK+t a+ ++++
  gi|336252796|ref|YP_004595903.1| 59 LMFAGPAGTGKTTAAQAIARE 79
                                      599*************99876 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   0.00024      0.12      19     110 ..      53     159 ..      40     167 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                                       T-SS-.EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H...........HHHHHHT....TTSEEEEEE-T CS
                   Sigma54_activ_2  19 qsklp.vfltGekGsgkelvArlLhknsgpwleifvverlaklp...........ldlleqa....kggtLylkdia 79 
                                       q  lp +  +G++G+gk++ A++++ +   ++   ++ +l ++            +d+  ++    +  +++l + +
  gi|336252796|ref|YP_004595903.1|  53 QDDLPhLMFAGPAGTGKTTAAQAIAREIYDDDWRENFLELNASDqrgidvvrdriKDFARSSfggyDHRIIFLDEAD 129
                                       4445525568**************998655444444444443332355566655533333324444999******** PP

                                       T--HHHHHHHHHHHHHHTTTT-EEEEEEEE- CS
                   Sigma54_activ_2  80 dlskaeqkeLlellakaeksslrlVstsskd 110
                                        l +++q+ L   +++   ++ r++ ++ ++
  gi|336252796|ref|YP_004595903.1| 130 ALTSDAQSALRRTMEQF-SNNTRFILSCNYS 159
                                       ***************99.99*****998765 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 ?   11.8   0.0   0.00018     0.089     117     157 ..      46      84 ..      17     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                             T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyallkeinksd 157
                                       ++++ +++       ++++G+ g+GKtt + a+  ei ++d
  gi|336252796|ref|YP_004595903.1|  46 RLKNYVEQD--DLPHLMFAGPAGTGKTTAAQAIAREIYDDD 84 
                                       555555555..4557899****************9998874 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00027      0.13      19      90 ..      58     187 ..      42     258 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                            AAA_11  19 itliqGPPGtgKTktivellsqll...................................................sr 44 
                                         ++ GP GtgKT++  ++ ++++                                                   s 
  gi|336252796|ref|YP_004595903.1|  58 HLMFAGPAGTGKTTAAQAIAREIYdddwrenflelnasdqrgidvvrdrikdfarssfggydhriifldeadaltSD 134
                                       46899******************877777777777777766666666666666665555555555555444444300 PP

                            AAA_11  45 ......rkseeeksakpriLvCapSNaAvDellerllr.glldsegekykpki 90 
                                             r+ e+  ++++ iL C  S   +D + +r +  ++ + + + ++ ++
  gi|336252796|ref|YP_004595903.1| 135 aqsalrRTMEQFSNNTRFILSCNYSSQIIDPIQSRCAVfRFTELTDNAIEAQV 187
                                       44444333455566666677777777777777777555545555555444444 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.057        28       8      28 ..     205     225 ..     205     237 .. 0.87
   2 ?    4.5   0.1      0.16        79      13      29 ..     256     272 ..     252     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.057
                            TPR_14   8 aeallalGdpdeAiallrral 28 
                                       a +++a Gd ++Ai++l++a 
  gi|336252796|ref|YP_004595903.1| 205 ALVYAADGDMRKAINALQAAA 225
                                       6799***************96 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.16
                            TPR_14  13 alGdpdeAiallrrala 29 
                                         Gd+ +A+a+l+++l 
  gi|336252796|ref|YP_004595903.1| 256 IDGDFTAARAALEDLLT 272
                                       579***********986 PP

>> TetR_C_12  Bacterial transcriptional repressor C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00068      0.33      19      76 ..     233     290 ..     216     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00068
                                       HHHHHHHHH-TT-HHHHHHHHHHHHHHHHHHHHCHHHHHCCTT---SS-HHHHHHHHH CS
                         TetR_C_12  19 elfveAmllarrrpdlrelieetltvLfrqgeralvrtlertgWklraaideearaFW 76 
                                       e  v A++++ r ++++e++ +++   f ++ +al + l+++g      id+  r  W
  gi|336252796|ref|YP_004595903.1| 233 EETVFAITATARPEEVEEMVGHAIDGDFTAARAALEDLLTDRGLAGGDVIDQLHRSAW 290
                                       556789*****************************************99999999988 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0015      0.71      23      58 ..      44      79 ..      23      94 .. 0.84
   2 ?   -0.7   0.0       1.7     8e+02     115     143 ..     115     143 ..     101     154 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                              TniB 23 LeeLleypkrkrmpnlllvGdsnnGKtmivekFarl 58
                                      + +L +y ++++ p+l+++G+  +GKt+ ++  ar+
  gi|336252796|ref|YP_004595903.1| 44 IPRLKNYVEQDDLPHLMFAGPAGTGKTTAAQAIARE 79
                                      4567889999******************99887765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                              TniB 115 lrelkvrvLiiDEihnllagsarkqrefl 143
                                       +  ++ r++ +DE + l +  +++ r+++
  gi|336252796|ref|YP_004595903.1| 115 FGGYDHRIIFLDEADALTSDAQSALRRTM 143
                                       55667899999999988754444444433 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00048      0.23      13      43 ..      51      79 ..      40     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00048
                                      HCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 13 lekdelqslvvalvGmgGvGKttlakqilnk 43
                                      +e+d+l    + + G +G GKtt a+ i ++
  gi|336252796|ref|YP_004595903.1| 51 VEQDDLP--HLMFAGPAGTGKTTAAQAIARE 79
                                      3466666..8999**********99999887 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0007      0.34      38      88 ..      44      91 ..      39     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0007
                                      HHHHHHHHT-SS-SS-EEEEEEE-TTSSHHHHHHHHHHHHSTTGGGSTTEE CS
                            Torsin 38 vksvkaylenekpkkpLvlsfhGwtGtGknfvaeiiaenlyrdGlrsdyvk 88
                                      +  +k y+e+++      l f G +GtGk   a+ ia ++y d  r ++ +
  gi|336252796|ref|YP_004595903.1| 44 IPRLKNYVEQDDLP---HLMFAGPAGTGKTTAAQAIAREIYDDDWRENFLE 91
                                      55666666655432...4789**********************99998876 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       6.3     3e+03      16      32 ..     132     148 ..     127     149 .. 0.79
   2 ?    4.1   0.5      0.18        86       7      25 ..     205     223 ..     205     225 .. 0.87
   3 ?    3.7   0.0      0.24   1.2e+02      14      28 ..     258     272 ..     241     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 6.3
                                       HHHHHHHHHHHHHH-TT CS
                             TPR_6  16 tdkAlealerlikeYPd 32 
                                       t++A  al+r  +++ +
  gi|336252796|ref|YP_004595903.1| 132 TSDAQSALRRTMEQFSN 148
                                       67899999998888876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealer 25 
                                       al y + gd +kA+ al+ 
  gi|336252796|ref|YP_004595903.1| 205 ALVYAADGDMRKAINALQA 223
                                       78899977*********96 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHH CS
                             TPR_6  14 gdtdkAlealerlik 28 
                                       gd ++A++ale+l++
  gi|336252796|ref|YP_004595903.1| 258 GDFTAARAALEDLLT 272
                                       799*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.42
# Mc/sec: 2392.06
//
Query:       gi|336252797|ref|YP_004595904.1|  [L=369]
Description: hypothetical protein Halxa_1392 [Halopiger xanaduensis SH-6]
Scores for 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-09   37.2  21.3    2.6e-07   30.8   9.5    2.6  2  Bactofilin   Polymer-forming cytoskeletal
  ------ inclusion threshold ------
      0.013   14.1  11.0      0.019   13.6  11.0    1.2  1  FapA         Flagellar Assembly Protein A
       0.32   11.1   0.2       0.32   11.1   0.2    4.3  2  Phage_spike  Phage spike trimer


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   8.0   4.5e-05      0.27      30      82 ..      42      94 ..      20      96 .. 0.65
   2 !   30.8   9.5   4.4e-11   2.6e-07       8      86 ..      87     171 ..      81     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                        Bactofilin 30 eakgklvvgeggkvegn.ikaeevvvaGtvkGnveaeekvelkktakveGdika 82
                                      +++g++vv+eg +v+     a++vvv+Gtv+G+vea    +++ ++ v G+++a
  gi|336252797|ref|YP_004595904.1| 42 QTGGTVVVEEGETVDNLeAFAGTVVVDGTVTGDVEAV-AGSIRINGDVGGNVEA 94
                                      5566777777777766446667777777777777777.5555556677777664 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 4.4e-11
                        Bactofilin   8 kikGeleve.gdlridGkveGdi.eakgklvvgeggkvegnika..eevvvaGtvkGnveaee.kvelkktakveGd 79 
                                        + G++e + g++ i+G+v+G++  a+g+l ++eg+++ g+++   ++v ++Gt++G+ e  + +++l ++a + Gd
  gi|336252797|ref|YP_004595904.1|  87 DVGGNVEATgGSVTIAGTVDGSVeAATGSLEIAEGATIGGDLSGgaGSVAIDGTIDGSAELGAdTIRLGDEAAIGGD 163
                                       6789999666*************6569**************9975488***********99999************* PP

                        Bactofilin  80 ika.ksle 86 
                                       +++ + le
  gi|336252797|ref|YP_004595904.1| 164 LRYgGDLE 171
                                       **955555 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6  11.0   3.2e-06     0.019     181     244 ..      56     122 ..      34     161 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-06
                              FapA 181 dpvleikgdV...dlstGnIk.fkGsViikGnVeegmkVkas.gditikGvvesatieAggnItikgGi 244
                                       d+   + g V   +  tG+++ + Gs+ i+G+V  g +V+a+ g++ti G+v+++   A g+++i +G 
  gi|336252797|ref|YP_004595904.1|  56 DNLEAFAGTVvvdGTVTGDVEaVAGSIRINGDV--GGNVEATgGSVTIAGTVDGSVEAATGSLEIAEGA 122
                                       444444444422122246665344566666666..5555554245666666666555556666666554 PP

>> Phage_spike  Phage spike trimer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   5.4e-05      0.32      24      54 .]      56      86 ..      46      86 .. 0.82
   2 ?   -5.2  13.3         3   1.8e+04      29      50 ..     112     135 ..      84     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.4e-05
                                      EEEEEEEEEESSEEEEES-EEEESS-EEETT CS
                       Phage_spike 24 gnLtvgtltvqgGGtikGdithsgGnlssnG 54
                                      +nL+  ++tv  +Gt++Gd+++ +G++  nG
  gi|336252797|ref|YP_004595904.1| 56 DNLEAFAGTVVVDGTVTGDVEAVAGSIRING 86
                                      45555567777779*************9998 PP

  == domain 2  score: -5.2 bits;  conditional E-value: 3
                                       E..EEEESSEEEEES-EEEESS-E CS
                       Phage_spike  29 g..tltvqgGGtikGdithsgGnl 50 
                                       +  +l++ +G+ti Gd++  +G++
  gi|336252797|ref|YP_004595904.1| 112 AtgSLEIAEGATIGGDLSGGAGSV 135
                                       344889999999999996655655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); 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:                         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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2621.81
//
Query:       gi|336252798|ref|YP_004595905.1|  [L=77]
Description: hypothetical protein Halxa_1393 [Halopiger xanaduensis SH-6]
Scores for 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:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 626.16
//
Query:       gi|336252799|ref|YP_004595906.1|  [L=126]
Description: endoribonuclease L-PSP [Halopiger xanaduensis SH-6]
Scores for complete 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-39  134.7   0.1    1.8e-39  134.5   0.1    1.0  1  Ribonuc_L-PSP    Endoribonuclease L-PSP
     0.0095   16.1   0.0      0.012   15.8   0.0    1.2  1  YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endori


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 !  134.5   0.1     2e-43   1.8e-39       2     120 ..       8     124 ..       7     125 .. 0.97

  Alignments for each domain:
  == domain 1  score: 134.5 bits;  conditional E-value: 2e-43
                                       TTSTTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB..-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGG CS
                     Ribonuc_L-PSP   2 eaapaaaapYsqavkagnlvyvsGqlpldpetgelv.egdveeqtrqalenlkavLaaagaslsdvVkvtvFladie 77 
                                       ++apaa+++Ysqa  agnl++++Gqlpl+p +gel  ++ v+eqtrq+len++a+Laa +a+l+dv kvt++l di+
  gi|336252799|ref|YP_004595906.1|   8 DDAPAAVGAYSQATVAGNLLFTAGQLPLTP-NGELLeDAPVAEQTRQCLENVDAILAAEDATLADVCKVTIYLDDID 83 
                                       689**************************8.999998999************************************* PP

                                       GHHHHHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEEE CS
                     Ribonuc_L-PSP  78 dfaevnevyaeafdelkeaParsaveVaaLpkgakvEIeaiav 120
                                       df ++ne+ya +fd++   ParsaveV ++pkga++EIea+a 
  gi|336252799|ref|YP_004595906.1|  84 DFDAMNEAYAAYFDDEP--PARSAVEVGRVPKGAALEIEAVAS 124
                                       ****************5..*********************995 PP

>> YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endoribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-06     0.012      13      45 ..       9      42 ..       3      90 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-06
                                      -----SSSS-SEEEETTEEEE--B--EE.TTEE- CS
                   YjgF_endoribonc 13 kvaaalGayepyaivasflttsfqlpyl.qekll 45
                                      +++aa+Gay   ++ ++ l t++qlp   +++ll
  gi|336252799|ref|YP_004595906.1|  9 DAPAAVGAYSQATVAGNLLFTAGQLPLTpNGELL 42
                                      689***********************86234444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 935.22
//
Query:       gi|336252800|ref|YP_004595907.1|  [L=414]
Description: glycine hydroxymethyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-155  516.9   0.0   3.1e-155  516.7   0.0    1.0  1  SHMT             Serine hydroxymethyltransferase
    5.9e-09   35.6   0.0    9.1e-09   34.9   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    1.6e-05   24.4   0.0     0.0003   20.2   0.0    2.1  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
       0.15   11.3   0.3       0.21   10.9   0.3    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


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 !  516.7   0.0  6.9e-159  3.1e-155       1     399 []       5     383 ..       5     383 .. 0.99

  Alignments for each domain:
  == domain 1  score: 516.7 bits;  conditional E-value: 6.9e-159
                                       HHHHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHH CS
                              SHMT   1 leesdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrake 77 
                                       l+++dp va+++  e+erq++++ +iasen +s+avl a+G+ ltnkyaeGyPG+ryyGGce+vde+e+la++rak 
  gi|336252800|ref|YP_004595907.1|   5 LKDVDPAVADAVAGERERQESTLGMIASENHASEAVLAAQGTALTNKYAEGYPGARYYGGCEHVDEIERLAIERAKS 81 
                                       6899************************************************************************* PP

                                       HCT-STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTS CS
                              SHMT  78 lfkldpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketg 154
                                       l+++d    +vnvqp+sG+qan+ vy a lepg++il+ldl++GGhl+hG +v++     s++l+e+ +y+vd+etg
  gi|336252800|ref|YP_004595907.1|  82 LWGAD----HVNVQPHSGTQANMGVYFAALEPGETILSLDLTHGGHLSHGHHVNF-----SGQLYEVEQYEVDPETG 149
                                       *****....*********************************************9.....***************** PP

                                       SB-HHHHHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESS CS
                              SHMT 155 lidydelekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttth 231
                                       +idyd+l ++a+e+ P +iv+G+say+r +d++r+ eia++v+ay l+d+ahi+Glvaa+v++sP+++ad+vt  th
  gi|336252800|ref|YP_004595907.1| 150 YIDYDKLAEQAREVDPAMIVSGSSAYPREFDWERVGEIAESVDAYHLADIAHITGLVAADVHSSPVDHADFVTGSTH 226
                                       ***************************************************************************** PP

                                       STT-S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHH CS
                              SHMT 232 ktlrGprgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlkn 308
                                       kt+r  rgg+i++               ee ++ ++savfPg qGGPl+h ia+kav+++ea +p f +y+++ ++n
  gi|336252800|ref|YP_004595907.1| 227 KTIRAGRGGIIMCD--------------EEHADDVDSAVFPGSQGGPLMHNIAGKAVGFGEASTPAFEEYAERTVEN 289
                                       *************9..............7999********************************************* PP

                                       HHHHHHHHHHTT-EEGGGS-SSSEEEEEGGGG..TS-HHHHHHHHHHTTEE-EEE--TTS.STTTT-SEEEEESHHH CS
                              SHMT 309 akalaealkekgyklvsgGtdnhlvlvdlrek..gldGkraekvlekvnitankntvPgd.ksalvtsGlrlGtpal 382
                                       a +la+++ ++g +lvsgGtd+hlvlvdlr+   +l+Gk+ae++l +v + +nkntvPg+ +s++vtsG+r+Gtpal
  gi|336252800|ref|YP_004595907.1| 290 AAVLADVFRDRGLSLVSGGTDKHLVLVDLRDShpDLTGKDAEEALAEVGVVVNKNTVPGEtRSPFVTSGVRIGTPAL 366
                                       ******************************873479***************************************** PP

                                       HHTT--HHHHHHHHHHH CS
                              SHMT 383 tsrgfkeedlekvakfi 399
                                       t+rgf+ e++e+v++ i
  gi|336252800|ref|YP_004595907.1| 367 TTRGFGPEEIERVGRCI 383
                                       *************9875 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 !   34.9   0.0     2e-12   9.1e-09      40     353 ..      62     368 ..      37     371 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2e-12
                                       T-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THH.....HHHHH CS
                     Aminotran_1_2  40 ygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasy.....knilr 111
                                       yg +++ +e e   ++ ++       ++  +v+  sG++a+  + +++l+  pg+ il+ d+t++ +     + ++ 
  gi|336252800|ref|YP_004595907.1|  62 YGGCEHVDEIERLAIERAK--SLWGADHV-NVQPHSGTQANMGVYFAALE--PGETILSLDLTHGGHlshghHVNFS 133
                                       6666666666666666666..44456777.***************99998..************9761111134444 PP

                                       HTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEE CS
                     Aminotran_1_2 112 lsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDe 188
                                           ev +y++ ++e+  +d ++l e+ +e    ++    ++v +    + + + + ++e + ++a++  ++ + D 
  gi|336252800|ref|YP_004595907.1| 134 GQLYEVEQYEV-DPETGYIDYDKLAEQARE---VDP---AMIVSG----SSAYPREFDWERVGEIAESVDAYHLADI 199
                                       44455556663.368999999999997777...344...444443....446778889******************* PP

                                       TTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHH CS
                     Aminotran_1_2 189 aYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaa 263
                                       a+ ++   + d   +++   +  + ++++gs  K    aG R G+i ++++ ++ + +++ p+     l+  ++ +a
  gi|336252800|ref|YP_004595907.1| 200 AHITGLVAA-D---VHSSPVD--HaDFVTGSTHKTIR-AG-RGGIIMCDEEHADDVDSAVFPGSQgGPLMHNIAGKA 268
                                       *******92.2...1333333..247********995.46.67*******999999999988777666677778888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSSEEEEEETHH....CHHHHHHHHHHTCTEEEEEG CS
                     Aminotran_1_2 264 lsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgmflltdlsae....takelskkLleevgvyvtpg 335
                                       +   +     +ee ++r  +++ +l d +++ gl+ ++      ++l+dl+ +    t k++ ++L+e  gv+v ++
  gi|336252800|ref|YP_004595907.1| 269 VGFGEASTPAFEEYAERTVENAAVLADVFRDRGLSLVSGGtDKHLVLVDLRDShpdlTGKDAEEALAEV-GVVVNKN 344
                                       888777777***********************8888877655566666777776888888888888888.******* PP

                                       GGGTS......TTEEEEECTTS-H CS
                     Aminotran_1_2 336 tsftv......pgrlRitvAglte 353
                                       t ++       ++ +Ri  ++lt+
  gi|336252800|ref|YP_004595907.1| 345 TVPGEtrspfvTSGVRIGTPALTT 368
                                       ****99999997779999877665 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   6.6e-08    0.0003      27     278 ..      61     342 ..      40     350 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.6e-08
                                       CCT--HHHHHHH....HHHHHHTT-SEE.EEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EE CS
                   Beta_elim_lyase  27 sYgedktvnrLe....davaelfgkeaa.lfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvkl 98 
                                        Yg+ + v ++e    ++++ l g++++ +  ++Gt+An   + + l++ge ++  +  h+     g ++ ++g  l
  gi|336252800|ref|YP_004595907.1|  61 YYGGCEHVDEIErlaiERAKSLWGADHVnVQPHSGTQANMGVYFAALEPGETILSLDLTHGGHLSHGHHVNFSGQ-L 136
                                       555555554444111256677899987625678***************************999999999999886.5 PP

                                       EEE-EBTT....TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HH.HHHHHHHHHHHCT-EEEEEETT CS
                   Beta_elim_lyase  99 rdlknkea....GkmdlekleaaikevgaheekiklisltvTnntagGqvvsle.elrevaaiakkygiplhlDgAR 170
                                        ++++ e     G++d +kl++  +ev     ++++i+           +++ e   ++v +ia++ +   + D A 
  gi|336252800|ref|YP_004595907.1| 137 YEVEQYEVdpetGYIDYDKLAEQAREV-----DPAMIVSGSS-------AYPREfDWERVGEIAESVDAYHLADIAH 201
                                       666554445556***********9993.....4567654433.......3333324577888888888888899999 PP

                                       HHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH.................................. CS
                   Beta_elim_lyase 171 fanaakslgeivkemfsyvDsvtmslkKdllanvGgvlafrddel................................ 215
                                       +   + + +   ++ ++++D vt s  K + a  Gg+++ +++++                                
  gi|336252800|ref|YP_004595907.1| 202 ITGLV-A-ADVHSSPVDHADFVTGSTHKTIRAGRGGIIMCDEEHAddvdsavfpgsqggplmhniagkavgfgeast 276
                                       98755.3.233345679**************************99******************************** PP

                                       .....HHHHHHHHHHHHT---SSTHHHHH..HHHHHHHHSSTTHHHHHH..HHHHHHHHHHHCT--EE CS
                   Beta_elim_lyase 216 ...edylaerveqrkylggglrqagvlaaleagiraleeglaslerdhk..taeqlaeklelvrlaip 278
                                          e+y ++ ve +  l++ +r+ g+  +   g    ++ l  l+++h   t++   e+l++v ++++
  gi|336252800|ref|YP_004595907.1| 277 pafEEYAERTVENAAVLADVFRDRGLSLV--SGGTDKHLVLVDLRDSHPdlTGKDAEEALAEVGVVVN 342
                                       *************************9999..6655555555555554431256666666777766655 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 ?   10.9   0.3   4.7e-05      0.21      91     193 ..     143     246 ..      79     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.7e-05
                                       -B-TTTSSB-GGGCGGG--TTEEEEEEB..-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEE CS
                   DegT_DnrJ_EryC1  91 DvdpdtynidpaaieaaitertkaIlpV..hlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaa 165
                                       +vdp+t  id +++++   e   a ++    +y + +d +++ +ia++ + + + D Ah  G   ++ +   ++ a 
  gi|336252800|ref|YP_004595907.1| 143 EVDPETGYIDYDKLAEQAREVDPAMIVSgsSAYPREFDWERVGEIAESVDAYHLADIAHITGLVAADVHSSPVDHAD 219
                                       79***********999999999776664226788888999**********************999998888888777 PP

                                       EEE-BTTSSS-SSS-EEEEESTHHHHHH CS
                   DegT_DnrJ_EryC1 166 vfSFyptKnlttGeGGavvtndeelaek 193
                                        +     K++ +G GG+++ ++e  a+ 
  gi|336252800|ref|YP_004595907.1| 220 FVTGSTHKTIRAGRGGIIMCDEEH-ADD 246
                                       7777788*********99986654.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2991.84
//
Query:       gi|336252801|ref|YP_004595908.1|  [L=545]
Description: choline/carnitine/betaine transporter [Halopiger xanaduensis SH-6]
Scores for 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-155  517.6  47.4   3.2e-155  517.3  47.4    1.0  1  BCCT      BCCT, betaine/carnitine/choline family transporter


Domain annotation for each model (and alignments):
>> BCCT  BCCT, betaine/carnitine/choline family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  517.3  47.4  1.8e-159  3.2e-155       1     479 [.      27     516 ..      27     521 .. 0.96

  Alignments for each domain:
  == domain 1  score: 517.3 bits;  conditional E-value: 1.8e-159
                              BCCT   1 vflvslliivlfvllalvfpealeevlsslnswilekfgwlylllvllflvfllvlafskygkikLGkddekpefst 77 
                                       vf v  ++ + +v+++l+++e+  e+++ +n+++ ++fgw+yl+++++++ f+l+l+f ++g+ikLG++de pefs+
  gi|336252801|ref|YP_004595908.1|  27 VFGVGFVVAASIVVAFLLREERTLELMEGTNEFLWTSFGWAYLVSMFALVAFVLFLIFGPWGNIKLGDPDEDPEFSF 103
                                       677888999999***************************************************************** PP

                              BCCT  78 lsWfamlfaaglgigllfwgvaEplahylsp.ppga.eagteeaaqeAlaytffhwGlhaWaiyalvalalayfayr 152
                                       l +faml++ag+++g++fwg aE ++hy +p p+++ ea+t+ aa +Al+ytffhwGl+aW+ y+++++ +ayfayr
  gi|336252801|ref|YP_004595908.1| 104 LAYFAMLYSAGIAAGIVFWGPAEAIFHYSTPsPFSGvEAETTGAAVSALQYTFFHWGLSAWSAYVIIGIPIAYFAYR 180
                                       ******************************9446668**************************************** PP

                              BCCT 153 kglpltissalypllg.eringllgkvvDvlavlatvfGvatslGlgvlqinaglselfgieesltvqlaiivvita 228
                                       kg p++is++++p++g ++++g+++k+vD+lav+at+ G+at+lGl   q+  gl++  g++ +   ++++i+ +t+
  gi|336252801|ref|YP_004595908.1| 181 KGAPMRISTIIAPIVGlDNLEGPWAKLVDILAVFATIGGIATTLGLVGNQFLVGLEYAGGVSFGDAGTVLVITGLTV 257
                                       ****************669******************************************99************** PP

                              BCCT 229 latvsavsGldkGikrlSnlnlvlalllllfvllvGptlfilntfvqslgdylqnlvalslatdaaeeae.....ew 300
                                       ++t+s+++G++kGi+r+S +n+ l+ ll ++ +++Gp ++i++  +q+lg+y++++v++sl ++a e+ +     ++
  gi|336252801|ref|YP_004595908.1| 258 AFTISVALGVEKGIRRVSYFNMGLFGLLTVAAFVLGPSVYIMTVGTQALGAYINEFVSMSLFMGASETGGqgadsGF 334
                                       ***************************************************************9988444556669* PP

                              BCCT 301 lasWTvFyWawwiawapfvGlFiAriSrGRtiRefilgvllvptlvtflwftvlGgtaielelegeaelaea...ae 374
                                       + +WTvFyWaww++wapfvGlFiAriSrGRt+R++ ++ +++ t+vt+ wf+ +Ggt+i le +g+ae+  +   + 
  gi|336252801|ref|YP_004595908.1| 335 VGAWTVFYWAWWFSWAPFVGLFIARISRGRTVRQVAATGVVASTAVTIPWFATMGGTSIFLESSGQAEILGTleaWG 411
                                       *******************************************************************9999777789 PP

                              BCCT 375 asveaalfalleqlplgsilsvlavvliiiffvTsaDSatlvlatltsggdenpprkqrvfWgvllgavaavlllag 451
                                        + ++a + l+e+lp g++l+vl++vl+++ffvTsaDS+tl l++lt+gg+++p++ +rv+Wg l+ga+a  l++ag
  gi|336252801|ref|YP_004595908.1| 412 FNEAVAGYPLFEALPAGELLTVLFLVLVTTFFVTSADSSTLALGMLTTGGKRKPSTINRVIWGALMGALASLLMVAG 488
                                       9999************************************************************************* PP

                              BCCT 452 glealqsasiiaalPftlvlllmvvsll 479
                                       g +alq+a+iia+ Pf+++ l++v  ++
  gi|336252801|ref|YP_004595908.1| 489 GTTALQQAAIIAGGPFAVITLVAVGVMI 516
                                       *******************999876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3828.28
//
Query:       gi|336252802|ref|YP_004595909.1|  [L=411]
Description: threonine dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-86  289.3   8.2    5.1e-86  288.7   8.2    1.2  1  PALP      Pyridoxal-phosphate dependent enzyme
    0.00017   21.3   0.1    0.00017   21.3   0.1    3.2  3  ACT       ACT domain
     0.0019   18.8   0.0      0.013   16.1   0.0    2.5  2  ACT_4     ACT 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 !  288.7   8.2   8.5e-90   5.1e-86       4     294 .]      25     311 ..      23     311 .. 0.97

  Alignments for each domain:
  == domain 1  score: 288.7 bits;  conditional E-value: 8.5e-90
                                       CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                              PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlk 80 
                                       ++++TP+ r+ +l + +g+++ lK+E+l+ tgSfK+Rga++ +a+     g ++vv+as+GNh++++A+aa +lG++
  gi|336252802|ref|YP_004595909.1|  25 VVKRTPVERSTSLDDMTGAEVHLKMEHLQWTGSFKTRGAYNKIAQCVADVGVDRVVAASAGNHAQGVALAATKLGVD 101
                                       6899*****************************************555558************************** PP

                                       EEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTT CS
                              PALP  81 vtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggk 157
                                       +tiv+p++a+++kv+++r++Ga+v++vg+d+ +a+a+a+ l  + +   +v+ +d+p++++g+gt+glE++++l ++
  gi|336252802|ref|YP_004595909.1| 102 STIVMPRGAPQAKVDATRSYGADVELVGSDFRDAMAHAKGLVDD-DATEFVHAYDDPAIVAGQGTLGLEMYDDL-PD 176
                                       ********************************************.*****************************.6* PP

                                       EEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHS CS
                              PALP 158 pdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelld 234
                                       +d+vvvp+GgGgli+Gia++++er p++r++gv+++g++++ +slr+g  v++++ dtiadg+a+g  sel+++l++
  gi|336252802|ref|YP_004595909.1| 177 VDTVVVPIGGGGLISGIATAFAERSPETRIVGVQAAGASTVSESLRKGAAVSLDSVDTIADGIATGGISELTLSLIE 253
                                       ***************************************************************************** PP

                                       EEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 235 rlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       ++vde+vtv+d e+++a+ ll +r++ vve ++aa++aa+   +  +++++ +v+ +l+g
  gi|336252802|ref|YP_004595909.1| 254 EHVDEVVTVTDGEIARAVLLLLERAKQVVEGAGAASVAAI-VSDELDVRGE-TVMPLLSG 311
                                       ****************************************.8888888888.88777776 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.074   4.4e+02      12      24 ..     188     200 ..     188     201 .. 0.94
   2 ?   -2.1   0.2      0.59   3.5e+03      26      59 ..     227     260 ..     225     263 .. 0.79
   3 !   21.3   0.1   2.8e-08   0.00017       3      40 ..     336     377 ..     335     408 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.074
                                       THHHHHHHHHHHT CS
                               ACT  12 GlLarvfgaladr 24 
                                       Gl++ +++a+a+r
  gi|336252802|ref|YP_004595909.1| 188 GLISGIATAFAER 200
                                       99*********97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.59
                                       SEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHH CS
                               ACT  26 iNidsieqrssedkvagivfvvivvdeedleevl 59 
                                       +++ds+ +  ++   +gi+ +++   ee+++ev+
  gi|336252802|ref|YP_004595909.1| 227 VSLDSVDTIADGIATGGISELTLSLIEEHVDEVV 260
                                       6778888888888888999999988888888876 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 2.8e-08
                                       EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT....E CS
                               ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedk....v 40 
                                       lrv+  DrPG + +v+g++ad+g Ni+ + + +s ++     
  gi|336252802|ref|YP_004595909.1| 336 LRVRIDDRPGKMEEVSGLIADHGANIRTVRHDRSAPEldvgE 377
                                       78999*************************999977665333 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.96   5.8e+03      17      48 ..      61      92 ..      58     103 .. 0.61
   2 !   16.1   0.0   2.1e-06     0.013       7      70 ..     334     400 ..     328     408 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.96
                             ACT_4 17 kglLaditqviseekan.ivsvnaktrkkdgla 48
                                      +g+ ++i+q +++ +++ +v+ +a ++ ++g+a
  gi|336252802|ref|YP_004595909.1| 61 RGAYNKIAQCVADVGVDrVVAASAGNH-AQGVA 92
                                      678889999998887752444444443.35555 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.1e-06
                             ACT_4   7 vrleveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkdvehLsrviakLr 70 
                                        +l+v   dr+g + +++ +i++++ani+ v+ +        g a++ ++ve + + + + +++++r
  gi|336252802|ref|YP_004595909.1| 334 LKLRVRIDDRPGKMEEVSGLIADHGANIRTVRHDRSAPeldVGEAHLVFQVETSGAGQSRAIVRSIR 400
                                       689*****************************99976677667888888888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3078.71
//
Query:       gi|336252803|ref|YP_004595910.1|  [L=838]
Description: Dimethylglycine dehydrogenase [Halopiger xanaduensis SH-6]
Scores for complete 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-75  254.1   0.0    2.2e-75  253.4   0.0    1.3  1  GCV_T          Aminomethyltransferase folate-binding domain
    1.1e-51  176.5   1.0    1.9e-51  175.7   1.0    1.4  1  DAO            FAD dependent oxidoreductase
    3.7e-16   59.2   0.4    9.3e-16   57.9   0.4    1.8  1  FAO_M          FAD dependent oxidoreductase central domain
    1.8e-15   56.6   0.1    4.8e-15   55.2   0.1    1.8  1  GCV_T_C        Glycine cleavage T-protein C-terminal barrel d
    1.3e-07   31.1   2.5    0.00043   19.5   0.3    2.6  3  FAD_binding_2  FAD binding domain
    9.5e-07   29.1   0.0    6.6e-06   26.3   0.0    2.1  2  SoxG           Sarcosine oxidase, gamma subunit family
    1.5e-06   28.3   0.6    1.6e-05   25.0   0.2    3.0  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    1.9e-05   24.1   3.5      0.012   14.8   0.2    2.3  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      3e-05   24.5   1.3      0.015   15.8   0.4    2.7  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00044   19.6   0.2      0.046   13.0   0.0    2.3  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
     0.0097   15.3   0.2      0.017   14.5   0.2    1.2  1  ThiF           ThiF family
  ------ inclusion threshold ------
      0.039   13.9   3.2        3.5    7.6   0.1    2.7  2  NAD_binding_9  FAD-NAD(P)-binding
      0.057   13.1   0.1       0.11   12.2   0.1    1.4  1  ApbA           Ketopantoate reductase PanE/ApbA
       0.08   12.2   0.2       0.91    8.7   0.1    2.1  2  Thi4           Thi4 family
      0.081   11.6   0.2        3.7    6.2   0.0    2.1  2  HI0933_like    HI0933-like protein
      0.098   11.7   1.4       0.39    9.7   0.3    2.1  2  GIDA           Glucose inhibited division protein A
       0.17   11.1   0.1       0.35   10.1   0.1    1.4  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.34   10.2   3.5       0.23   10.8   0.7    2.0  2  FAD_oxidored   FAD dependent oxidoreductase
       0.36   10.0   2.8        1.7    7.8   0.2    2.2  2  FAD_binding_3  FAD binding domain


Domain annotation for each model (and alignments):
>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.4   0.0   2.3e-78   2.2e-75       2     257 .]     449     726 ..     448     726 .. 0.97

  Alignments for each domain:
  == domain 1  score: 253.4 bits;  conditional E-value: 2.3e-78
                             GCV_T   2 ydrhkalgakfvefagwemPvqYa......................sesikaehlavreaaglfDvShmgkievsGp 56 
                                       y+r+++lga+f + +gwe P++Y+                      s+    eh+avr +++++D+++ + iev+G+
  gi|336252803|ref|YP_004595910.1| 449 YRRQEELGAEFYDSGGWETPQWYEtnealleeydvpdrpdwldrgwSKAQGVEHRAVRDRVAMVDMTTYTGIEVTGD 525
                                       899******************************************99999*************************** PP

                             GCV_T  57 daaalLqrlltndisklkpgkatytlllnedGgvidDlivarldedefllvvnaankekdl.awlekaaekkdldve 132
                                       +a+a+Lqrlltnd++ ++pg+++y++++nedGg+++D++varl+ed++ + + ++n+++++ +wl++ ++++d +v+
  gi|336252803|ref|YP_004595910.1| 526 GATAFLQRLLTNDVD-VSPGRIRYAAMCNEDGGILADVTVARLAEDRYTVFTGGGNSATLHsRWLRE-HAPDDGSVS 600
                                       ***************.778*****************************************9999999.888****** PP

                             GCV_T 133 vedvteelallalqGPkarevlskllgadlselkffsfaevela..ggkkvlvsRtgytGedGfeiyipaeeaeelw 207
                                       v+ ++++++ + + GP +r vls l++adls+ ++f+f++ +++  + ++v+++R++y Ge+G+e+y p e++++lw
  gi|336252803|ref|YP_004595910.1| 601 VRTRDSDMCGIGVFGPDSRAVLSSLVEADLSN-DAFPFYTAQETylESVPVTMLRLSYAGELGWELYAPMEYGARLW 676
                                       *****************************999.99999988888888****************************** PP

                             GCV_T 208 eaLleagkeegvkpaGlgArdtlRlEaglrlyghdldeettPleaglgwa 257
                                       e + +ag e+g+ p+G++A+d+  +E+g+rl+g+d ++e++P+eag+g+a
  gi|336252803|ref|YP_004595910.1| 677 ELIEDAGDEYGIVPMGWAALDSTSMEKGFRLWGTDVTPEYDPYEAGIGFA 726
                                       **********************************************9985 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.7   1.0     2e-54   1.9e-51       3     352 .]      14     383 ..      12     383 .. 0.84

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 2e-54
                                       EEECTSHHHHHHHHHHHHTT...EEEEESSSSTTS.SGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHH CS
                               DAO   3 viiGGGiiGlstAyeLarrg...Vtllekgdiags.gaSgrnsgllhsglrylpeaselarlslealeelreleeel 75 
                                       v++G+G +G+s+Ay+L+r g   V+++++g+ + + g+++++ gl+ +      ++  + r++ ++++++++l+   
  gi|336252803|ref|YP_004595910.1|  14 VVVGAGCVGCSAAYHLTRLGredVVVVDQGPLFETgGSTSHAPGLVFQTG---GNK-LMTRMASYTRRLYEDLD--- 83 
                                       9***************999999********998866**********7743...443.788*************9... PP

                                       SSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTE.EEEEHHHHHHHSTT.ST.TTSEEEEETTEEEEEHHHHH CS
                               DAO  76 gididyrrtGllslaadeeelealdkllallleaglda.elldaeevrelepa.lp.gllgalfypdtgqvdpaklt 149
                                       g    +r +G + +a++e+ ++ l+++ ++++++g++  ell+++ v+++ p+  p  ++g++++p++g +++  + 
  gi|336252803|ref|YP_004595910.1|  84 G----FRTCGGIEVAYTEDRWDFLKRKRERGQSYGIEGgELLSPDAVADRVPQiDPeVIRGGYYVPTDGKAHAVDAS 156
                                       4....9**********99999999999999999***888*****99*******6335888***************** PP

                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTT.CTTTSEEEEEEEE CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gll.keldlpispvrgq 223
                                       aa+a++a+++G+e++  t+vt+le edg +++v  +t+ g++da d v +a+++w  l+ +++    d+p++p+ +q
  gi|336252803|ref|YP_004595910.1| 157 AAMAEQARSAGAEFYGDTTVTDLEVEDGEIQTV--VTDrGTIDA-DEVLVATNIWGPLFgDMVgV--DIPLVPCAHQ 228
                                       *********************************..777798655.77********8888666655..55******** PP

                                       EEEEEECCT.HSTGSGCSEEEEE..EEETTTTEEEEEETTSEEEEEESSE........................... CS
                               DAO 224 vlvlkplse.klvspaailpvpe..tdddgrgvyvtprkdgrvlvGgtad........................... 270
                                       +lv ++l+e +   ++      +   ++++r++y+++    r  +G+  +                           
  gi|336252803|ref|YP_004595910.1| 229 YLVSDELPElAGADREIE----QplLRHQDRSLYFRQHG-ERYGIGSYNHesllvdpediygpekledlgleypslr 300
                                       ****99999333322222....2448999********83.5566777666777777777799999999999999887 PP

                                       ..EETTCSS.TSCSHHHHHHHHHHHHHHSGGG..CGEEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHH CS
                               DAO 271 ..eesgddd.pevdeedidellealrklfPql..gdvlrkwaGlrp.lpdglpligetpgvkglylatGhsghGltl 341
                                         + ++      + +++ ++ ++a+ +l+P+l  ++++++  G+ + +pdg+p++g+t++ +gl+ a  +    +t+
  gi|336252803|ref|YP_004595910.1| 301 efTSEH--FyENTHPDHDQAAYDAACELVPSLrdAEFESAINGMFCfTPDGMPILGPTEEIDGLWWALAI---WVTQ 372
                                       442222..233566666677***********833556689999999779********99999*******9...9999 PP

                                       HHHHHHHHHHH CS
                               DAO 342 apatGkllael 352
                                       + ++G ++a++
  gi|336252803|ref|YP_004595910.1| 373 SGGAGSIVAHW 383
                                       99999999975 PP

>> FAO_M  FAD dependent oxidoreductase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.4   9.9e-19   9.3e-16       5      56 .]     395     446 ..     392     446 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 9.9e-19
                             FAO_M   5 siDlwevDirRFgdlhnnreylrervaesygkvYsipyPreelesgRnlrtS 56 
                                       ++D ++ +i+RF++++++rey+r r+a++y++vY++++Pre+++++R+lr+S
  gi|336252803|ref|YP_004595910.1| 395 RVDATGAHISRFQPHAGSREYTRGRGAQQYQEVYQLIHPREQPQDQRGLRRS 446
                                       5899***********************************************8 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.1   5.1e-18   4.8e-15       1      80 []     749     830 ..     749     830 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 5.1e-18
                           GCV_T_C   1 Rrlvglelddgapllrggepilr..dgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaevvk 75 
                                       R+lv ++ld++ +++  g+p+l+  +++ +G+vT++ y+++++  ia+Ay++a++a++g +ve+   + r++ +v +
  gi|336252803|ref|YP_004595910.1| 749 RKLVPITLDEPGAVVDTGYPVLEpdGDDALGYVTRADYGYSIDAGIAYAYLPAAAAEAGRDVEISYENDRYAGTVRD 825
                                       9********998999*******66455789*********************************************** PP

                           GCV_T_C  76 kpfyD 80 
                                       +p++D
  gi|336252803|ref|YP_004595910.1| 826 EPLFD 830
                                       ****9 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   4.6e-07   0.00043       3      46 ..      14      60 ..      12      76 .. 0.83
   2 !   10.7   0.0    0.0002      0.19     145     203 ..     157     209 ..     129     221 .. 0.87
   3 ?   -2.4   0.0         2   1.9e+03     231     286 ..     513     568 ..     499     593 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.6e-07
                                      EEE--SHHHHHHHHHHHHTTT.-EEEEESSSGGGS..GGGG--S-EE CS
                     FAD_binding_2  3 iViGsGlAGLaAAleaaeaGl.kvavvekeqefgg..atawsqGgid 46
                                      +V+G+G  G++AA+ +++ G+ +v+vv++++ f+   +t  + G ++
  gi|336252803|ref|YP_004595910.1| 14 VVVGAGCVGCSAAYHLTRLGReDVVVVDQGPLFETggSTSHAPGLVF 60
                                      9****************************986543337777777665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0002
                                       HHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----G CS
                     FAD_binding_2 145 arlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfg 203
                                       a+++e+ar+ag +f+  t +++L vedg++ ++v        + +i a+ v++at  +g
  gi|336252803|ref|YP_004595910.1| 157 AAMAEQARSAGAEFYGDTTVTDLEVEDGEIQTVVTD------RGTIDADEVLVATNIWG 209
                                       6899****************************9877......33566888888887666 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2
                                       HHHHCTTSS.EES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH CS
                     FAD_binding_2 231 alalragaa.lnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm 286
                                       +++  +g++  +d +  ++q + t+ v++ +g        +  +Ggil d ++ r+ 
  gi|336252803|ref|YP_004595910.1| 513 DMTTYTGIEvTGDGATAFLQRLLTNDVDVSPGRIR-YAAMCNEDGGILADVTVARLA 568
                                       45555555544555555556666655544444443.335588888888888888876 PP

>> SoxG  Sarcosine oxidase, gamma subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.37   3.5e+02      63     126 ..     508     573 ..     496     576 .. 0.69
   2 !   26.3   0.0     7e-09   6.6e-06      32     146 ..     561     684 ..     547     685 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.37
                              SoxG  63 lasvvdlShgrvlisisGakaeavlakltaiDlsadaFpvGaaaatilgk...vevvilrtgsdafe 126
                                       + ++vd+    + i+++G  a a l++l + D+  +  ++  aa    +    + v++ r ++d + 
  gi|336252803|ref|YP_004595910.1| 508 RVAMVDMT-TYTGIEVTGDGATAFLQRLLTNDVDVSPGRIRYAAMCNEDGgilADVTVARLAEDRYT 573
                                       55666664.46889****************9999887777766655444222234555566666665 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 7e-09
                              SoxG  32 e.svlwlaPdeflvidqegkaa..laalaealae.la..svvdlShgrvlisisGakaeavlakltaiDlsadaFpv 102
                                       + +v  la d+++v  ++g++a    +  +  a+  +  sv         i + G+ ++avl++l+  Dls daFp 
  gi|336252803|ref|YP_004595910.1| 561 DvTVARLAEDRYTVFTGGGNSAtlHSRWLREHAPdDGsvSVRTRDSDMCGIGVFGPDSRAVLSSLVEADLSNDAFPF 637
                                       348888999999999944444433334333444424411344444556789************************** PP

                              SoxG 103 Gaaaatilgkvevvilr...tgsdafevlvfrsFaeslwkaLldasa 146
                                         a++t l+ v v++lr    g+  +e++    +   lw+ + da  
  gi|336252803|ref|YP_004595910.1| 638 YTAQETYLESVPVTMLRlsyAGELGWELYAPMEYGARLWELIEDAGD 684
                                       *************999633378999**************99998865 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 !   25.0   0.2   1.7e-08   1.6e-05       1      67 [.      15      81 ..      15      82 .. 0.85
   2 ?   -1.6   0.0       3.4   3.2e+03      46      67 ..     660     681 ..     654     682 .. 0.84
   3 ?   -2.0   0.0       4.5   4.3e+03       7      29 ..     792     817 ..     792     830 .. 0.63

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.7e-08
                                      EE--SHHHHHHHHHHHCCTE.EEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHHCC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagf.dvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrllre 67
                                      +vGaG  G++aAy+L++ g+ dv+++++++ +    ++ + pg ++++g + +++ +    +rrl+++
  gi|336252803|ref|YP_004595910.1| 15 VVGAGCVGCSAAYHLTRLGReDVVVVDQGPLFETGGSTSHAPGLVFQTGGNKLMT-RMASYTRRLYED 81
                                      8*****************8868*******985555588899********999988.556777777776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.4
                                       CTS---EEETTHHHHCHHHHCC CS
                     NAD_binding_8  46 dygahifhgsgyypnvrrllre 67 
                                       ++g+  +++++y  ++++l+++
  gi|336252803|ref|YP_004595910.1| 660 ELGWELYAPMEYGARLWELIED 681
                                       7899999999999999999875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.5
                                       HHHHHHHHHHCC...TEEEEEE-SSS CS
                     NAD_binding_8   7 sGlvaAylLaka...gfdvlllekrd 29 
                                       +G ++Ayl a a   g+dv++   +d
  gi|336252803|ref|YP_004595910.1| 792 AGIAYAYLPAAAaeaGRDVEISYEND 817
                                       67888888443223499998854444 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 !   14.8   0.2   1.3e-05     0.012     145     176 ..      13      45 ..       4      53 .. 0.87
   2 !    9.7   0.3   0.00047      0.44     184     235 ..     154     205 ..     146     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                                       EEEES-SHHHHHHHHHHHHHT-E.EEEEESSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                       Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgke.vtlveardr 176
                                       +vvvG+G +G+  A +l++lg e v++v++++ 
  gi|336252803|ref|YP_004595910.1|  13 TVVVGAGCVGCSAAYHLTRLGREdVVVVDQGPL 45 
                                       69*******************998999998875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00047
                                       HHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvav 235
                                       ++saa++e+ +  G e++  t+v++++ ++ ++++v +d  +idad v+va+
  gi|336252803|ref|YP_004595910.1| 154 DASAAMAEQARSAGAEFYGDTTVTDLEVEDGEIQTVVTDRGTIDADEVLVAT 205
                                       689999***********************9999999999999********96 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   1.6e-05     0.015       3      32 ..      14      44 ..      12      51 .. 0.85
   2 ?    6.4   0.0     0.014        13      41      78 ..     154     191 ..     150     195 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                                      EEECSSHHHHHHHHHHHHTT.SEEEEEESSS CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelg.kkVtvversd 32
                                      vvvG+G +g+ +A  l++lg  +V vv+ ++
  gi|336252803|ref|YP_004595910.1| 14 VVVGAGCVGCSAAYHLTRLGrEDVVVVDQGP 44
                                      9*******************55788887655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  41 easkilqeklekngievllntkveeiegsedgvesvkl 78 
                                       +as++++e+ +  g e++ +t+v+ +e ++ ++++v++
  gi|336252803|ref|YP_004595910.1| 154 DASAAMAEQARSAGAEFYGDTTVTDLEVEDGEIQTVVT 191
                                       6899***********************99987887876 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 !   13.0   0.0   4.9e-05     0.046       1      32 [.      14      45 ..      14      49 .. 0.93
   2 ?    4.3   0.0     0.022        21     101     132 ..     173     205 ..     146     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgni 32
                                      +++GaG  G +aa++l ++g ed++++++g +
  gi|336252803|ref|YP_004595910.1| 14 VVVGAGCVGCSAAYHLTRLGREDVVVVDQGPL 45
                                      79**************************9976 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.022
                       Pyr_redox_3 101 feeVesvkked.egfevetsketyeAkkviiAt 132
                                       +++V++++ ed e  +v t+++t+ A++v++At
  gi|336252803|ref|YP_004595910.1| 173 DTTVTDLEVEDgEIQTVVTDRGTIDADEVLVAT 205
                                       7889999997615689****************9 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   1.8e-05     0.017      21      50 ..      13      42 ..       7      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                      EEEE--SHHHHHHHHHHHHHTTTEEEEEES CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 21 vllvGaGglGsellknLalsGvgkltlvDn 50
                                      +++vGaG +G+ ++  L ++G + + +vD+
  gi|336252803|ref|YP_004595910.1| 13 TVVVGAGCVGCSAAYHLTRLGREDVVVVDQ 42
                                      79***************************8 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 ?    7.6   0.1    0.0037       3.5       1      36 [.      14      45 ..      14      66 .. 0.85
   2 ?    6.1   0.3     0.011        10     116     153 ..     167     205 ..     151     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0037
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep 36
                                      ++vGaG+ G +++ +L +      + ++ ++d+ ++
  gi|336252803|ref|YP_004595910.1| 14 VVVGAGCVGCSAAYHLTRL----GREDVVVVDQGPL 45
                                      69****************9....5889999998665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
                     NAD_binding_9 116 tvevh.raevvdleeradgqavlladgaslaadaVvLAl 153
                                         e++  ++v+dle ++++ + + +d  +++ad+V +A+
  gi|336252803|ref|YP_004595910.1| 167 GAEFYgDTTVTDLEVEDGEIQTVVTDRGTIDADEVLVAT 205
                                       455552569**********9999**************98 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00011      0.11       2      32 ..      14      45 ..      13      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                      EEES-SHHHHHHHHHHHH.HTHCEEEE-SCHH CS
                              ApbA  2 ailGaGaiGsllaakLak.agadvtlilrsrr 32
                                      +++GaG +G+  a++L++   +dv+++++++ 
  gi|336252803|ref|YP_004595910.1| 14 VVVGAGCVGCSAAYHLTRlGREDVVVVDQGPL 45
                                      69****************77777999998874 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00097      0.91      20      49 ..      13      42 ..       9      62 .. 0.76
   2 ?    0.8   0.0      0.25   2.4e+02      94     143 ..     150     197 ..     138     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00097
                                      EEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 20 vvivGaGssGLtaayylakkpdlkvailer 49
                                       v+vGaG  G +aay l++     v+++++
  gi|336252803|ref|YP_004595910.1| 13 TVVVGAGCVGCSAAYHLTRLGREDVVVVDQ 42
                                      69***************9986667777766 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.25
                                       SEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHH CS
                              Thi4  94 kdaalftstllskvlqlanvkllnavaveDlivregegvaGvvinwtlve 143
                                       ++a+ + + ++ ++   a++  +  ++v Dl v +  +++ vv++  +++
  gi|336252803|ref|YP_004595910.1| 150 AHAVDASAAMAEQARS-AGAEFYGDTTVTDLEVED-GEIQTVVTDRGTID 197
                                       6888888877777777.****************99.78999999887765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.031        29       3      32 ..      13      43 ..      11      47 .. 0.84
   2 ?    6.2   0.0    0.0039       3.7     110     162 ..     154     205 ..     138     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.031
                                      EEEE--SHHHHHHHHHHHHTT-.-EEEE-SS CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgk.rVllleka 32
                                      ++v+G+G  G  aA ++ + g+ +V++++++
  gi|336252803|ref|YP_004595910.1| 13 TVVVGAGCVGCSAAYHLTRLGReDVVVVDQG 43
                                      69***************88776269999986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0039
                                       HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE-- CS
                       HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAt 162
                                       d   a+ +++++ag +++ +t+v+++e e++++ +v t +++++ ad++++At
  gi|336252803|ref|YP_004595910.1| 154 DASAAMAEQARSAGAEFYGDTTVTDLEVEDGEIQTVVT-DRGTIDADEVLVAT 205
                                       445689999*******************9999888888.9************7 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00041      0.39       3      24 ..      14      35 ..      12      56 .. 0.86
   2 ?    0.4   0.0      0.29   2.7e+02     117     148 ..     175     205 ..     172     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00041
                                      EEE-SSHHHHHHHHHHHHTT-- CS
                              GIDA  3 iViGgGhAGceAAlaaarlGak 24
                                      +V+G+G  Gc AA+++ rlG +
  gi|336252803|ref|YP_004595910.1| 14 VVVGAGCVGCSAAYHLTRLGRE 35
                                      8******************975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.29
                                       -EEEEEECTTEEEEEEETTS-EEEECEEEE-- CS
                              GIDA 117 eveeliveekkvkgvvtedgetikakavviat 148
                                       +v++l+ve+++++ vvt++g++  a+ v +at
  gi|336252803|ref|YP_004595910.1| 175 TVTDLEVEDGEIQTVVTDRGTI-DADEVLVAT 205
                                       799**************99975.566666665 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 ?   10.1   0.1   0.00037      0.35      28      59 ..      10      42 ..       3      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00037
                                      --EEEEESTSHHHHHHHHHHHHTT-.EEEEEES CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglga.kVtvlDv 59
                                       a ++v+G+G +G +A+   ++lg  +V+v+D 
  gi|336252803|ref|YP_004595910.1| 10 SAGTVVVGAGCVGCSAAYHLTRLGReDVVVVDQ 42
                                      6889*******************9625887775 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7   0.00024      0.23       3      69 ..      14      84 ..      13     206 .. 0.53
   2 ?   -1.8   0.1       1.6   1.5e+03     288     318 ..     395     425 ..     370     440 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                      FAD_oxidored  3 vVvGGgpaGvaAAiaAaraGa.kvlLveergv..lGGlltsglvatdig..nkaeeqvvtgiareflerlrq 69
                                      vVvG+g  G+ AA+   r G+  v++v++ +    GG ++ + +  + +  nk  +       r+++e l+ 
  gi|336252803|ref|YP_004595910.1| 14 VVVGAGCVGCSAAYHLTRLGReDVVVVDQGPLfeTGGSTSHAPGLVFQTggNKLMT-RMASYTRRLYEDLDG 84
                                      8*******************956888998885226**9998765554442265555.333444444444433 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                      FAD_oxidored 288 ewgfekaeleglapqlyvREsRRivGdyvlt 318
                                       + +  +a+++ ++p+ + RE  R +G  + +
  gi|336252803|ref|YP_004595910.1| 395 RVDATGAHISRFQPHAGSREYTRGRGAQQYQ 425
                                       7778889999*************99988765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0018       1.7       4      31 ..      13      41 ..      10      48 .. 0.87
   2 ?    2.1   0.2     0.099        93     109     147 ..     157     195 ..     150     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0018
                                      EEEE--SHHHHHHHHHHHHTTHH.EEEEE CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvr.vvlve 31
                                      +++VGaG +G ++a  L++ G + vv+v+
  gi|336252803|ref|YP_004595910.1| 13 TVVVGAGCVGCSAAYHLTRLGREdVVVVD 41
                                      589******************98566666 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.099
                                       HHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCT CS
                     FAD_binding_3 109 riLvehaeerglqvrfktevesleqdeegvtaevrdket 147
                                        +++e+a+++g++++ +t v+ le ++ +++++v+d+ t
  gi|336252803|ref|YP_004595910.1| 157 AAMAEQARSAGAEFYGDTTVTDLEVEDGEIQTVVTDRGT 195
                                       689*******************************99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (838 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 5520.23
//
Query:       gi|336252804|ref|YP_004595911.1|  [L=141]
Description: hypothetical protein Halxa_1399 [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.3  16.7    1.9e-15   57.2  16.7    1.0  1  EamA      EamA-like transporter family


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 !   57.2  16.7   1.1e-19   1.9e-15       3     136 ..       9     140 ..       7     141 .] 0.95

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 1.1e-19
                              EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlaf 79 
                                       ++++  + +++w+i+ vl  +++++++p t++++++l+ag l l ++ +++ +l  ++ ++  ll+ ++ l t ++ 
  gi|336252804|ref|YP_004595911.1|   9 AVFFGSITMVTWGIWVVLGNAASESIDPRTAAAISYLVAGPLALGFIIVSDASL-AITARG-GLLAGTAGLFTGIGL 83 
                                       6789999***********************************************.888887.666889999****** PP

                              EamA  80 llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       + ++ +l+ +s +++s + ++  v+++++++++lg  +t++ l+gi++++lGv+l++
  gi|336252804|ref|YP_004595911.1|  84 ISMYVGLSGGSTTIVSTLGAMYFVVAALIGMVVLGDDVTVTRLVGIAFAVLGVVLVT 140
                                       *******************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1048.00
//
Query:       gi|336252805|ref|YP_004595912.1|  [L=382]
Description: FAD dependent oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-50  173.3   0.2    1.2e-50  173.1   0.2    1.0  1  DAO            FAD dependent oxidoreductase
    0.00047   19.5   0.0     0.0042   16.4   0.0    2.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0012   17.7   0.0      0.022   13.5   0.0    2.1  2  HI0933_like    HI0933-like protein
     0.0022   17.3   0.0      0.024   13.9   0.0    2.0  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
     0.0031   17.6   0.0     0.0068   16.5   0.0    1.6  1  SUKH-4         SUKH-4 immunity protein
  ------ inclusion threshold ------
      0.013   14.7   0.3      0.022   14.0   0.3    1.3  1  FAD_binding_3  FAD binding domain
      0.041   13.8   0.2      0.072   13.0   0.2    1.4  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.045   13.4   0.3      0.075   12.7   0.3    1.3  1  ApbA           Ketopantoate reductase PanE/ApbA
      0.085   12.9   0.2      0.085   12.9   0.2    2.6  3  NAD_binding_9  FAD-NAD(P)-binding
       0.13   11.5   0.0       0.21   10.9   0.0    1.4  1  Amino_oxidase  Flavin containing amine oxidoreductase
       0.14   12.2   0.1        0.5   10.4   0.1    1.8  2  DUF1990        Domain of unknown function (DUF1990)
       0.14   11.2   0.7       0.62    9.1   0.1    1.9  2  FAD_binding_2  FAD binding domain
       0.15   11.3   0.4       0.29   10.3   0.0    1.6  2  Thi4           Thi4 family


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.1   0.2   8.4e-54   1.2e-50       1     352 []       9     361 ..       9     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 173.1 bits;  conditional E-value: 8.4e-54
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags.gaSgrnsgllhsglrylpeaselarlslealeelreleee 74 
                                       dvv+iG G +G++t y+La+rg  V+ le+ di+++ g+S++ +++++ ++++ p   ++ +l ++a++++++l+ee
  gi|336252805|ref|YP_004595912.1|   9 DVVVIGVGGMGSATTYHLAERGldVVGLERYDIPHTmGSSHGITRIIRRAYYEHP---DYIPLIERAYDLWDDLAEE 82 
                                       9**********************************77************987777...667**************** PP

                                       HSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT..STTTSEEEEETTEEEEEHHHHH CS
                               DAO  75 lgididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa..lpgllgalfypdtgqvdpaklt 149
                                       +g d+ ++rtG++  + +  +   ++ +l++++e+++++e+l+++ev e++p+  lp+ ++al+ pd+g v p++++
  gi|336252805|ref|YP_004595912.1|  83 TGRDV-LHRTGSIDAGPE--DNVVFEGSLRSCEEHDIPHEVLTSAEVSERFPGydLPEGHKALYQPDGGFVVPEQAI 156
                                       **985.778******854..35668899999999**********99******9876666899*************** PP

                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTTCTTTSEEEEEEEEE CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gllkeldlpispvrgqv 224
                                        + a+aa+a+G+e++ +++v + e + + +++v  +t+  +  +ada V+aaGaw  ++ + l+ l    +p r   
  gi|336252805|ref|YP_004595912.1| 157 VGHAEAAQAAGAEVRARERVLDWEPTPDEGVRV--ETDrDT-YEADAMVLAAGAWNYKFtDALEGL---AVPERQVL 227
                                       ***********************7765666777..555343.357**********77554555545...58988888 PP

                                       EEEEECCTHSTGSGCSEEEEEEEETTTTEEEEE..ETTSEEEEEESSE.....EETTCSS..TSCSHHHHHHHHHHH CS
                               DAO 225 lvlkplseklvspaailpvpetdddgrgvyvtp..rkdgrvlvGgtad.....eesgddd..pevdeedidelleal 292
                                         ++p   ++ +p   +pv     +++ +y +p  +  g +++G  ++     +   +d+   e++ ed + l+e +
  gi|336252805|ref|YP_004595912.1| 228 GWFQPERPATFEP-DSFPVWNLKVPEGRFYGLPiyDVPG-MKLGKYHHfdedvD---PDEydREPNREDERLLREVV 299
                                       8888877777666.5666655677777778888533446.99*99987774433...333555999999999***** PP

                                       HHHSGGG.CGEEEEEEEEEEE.TTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 293 rklfPql.gdvlrkwaGlrpl.pdglpligetpgvkglylatGhsghGltlapatGkllael 352
                                       +++fP+  g+  r  +++ ++ pd+ ++++  p ++ + + +G+sghG+++a ++G++la+l
  gi|336252805|ref|YP_004595912.1| 300 ENYFPEAaGPTMRLATCMFTNsPDEHFILDTLPDHPQVAVGAGFSGHGFKFASVIGEILADL 361
                                       ******63667777779999669********9999*************************97 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 !   16.4   0.0     3e-06    0.0042       1     119 [.       8     219 ..       8     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-06
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.................... 57 
                                       +dvvviG G  G a+  +la+ g++v+ +e +  +++  +  s+ ++++ ++a  ++                    
  gi|336252805|ref|YP_004595912.1|   8 YDVVVIGVGGMGSATTYHLAERGLDVVGLE-RYDIPHT-MGSSHGITRIIRRAYYEHpdyiplieraydlwddlaee 82 
                                       69************************9994.4444443.55556666666666666666667999************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                       Pyr_redox_2  58 ............................................................................. 57 
                                                                                                                    
  gi|336252805|ref|YP_004595912.1|  83 tgrdvlhrtgsidagpednvvfegslrsceehdiphevltsaevserfpgydlpeghkalyqpdggfvvpeqaivgh 159
                                       ***************************************************************************76 PP

                                       .HHHHCHHHHCCCCHCCTCEEEEESC.EEEEETEEECTCEEEEEESEEEE---EEE-BC..TCTTC CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx RF
                       Pyr_redox_2  58 .evvkklnqgielllgeevvkidpgk.kkvklekkkegdeekiaydklvlAtGssprdl..gipGv 119
                                        e    + +g e++++e v++ +p   + v +e     d  ++++d+ vlA G+++ ++   ++G+
  gi|336252805|ref|YP_004595912.1| 160 aEA--AQAAGAEVRARERVLDWEPTPdEGVRVE----TDRDTYEADAMVLAAGAWNYKFtdALEGL 219
                                       533..3344577777777999997773455554....34459**************9996666665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.048        66       1      31 [.       8      38 ..       8      43 .. 0.90
   2 !   13.5   0.0   1.6e-05     0.022     117     164 ..     161     207 ..     153     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.048
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllek 31
                                      +dv+viG G  G  ++ ++a+rg +V+ le+
  gi|336252805|ref|YP_004595912.1|  8 YDVVVIGVGGMGSATTYHLAERGLDVVGLER 38
                                      59**********************9987775 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.6e-05
                                       HHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       +++++ag ++r +++v ++e + d+ +rv+t +++++ead++vlA G 
  gi|336252805|ref|YP_004595912.1| 161 EAAQAAGAEVRARERVLDWEPTPDEGVRVET-DRDTYEADAMVLAAGA 207
                                       567899*************************.9************997 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 ?    0.9   0.0      0.15   2.1e+02       1      32 [.      11      41 ..       9      49 .. 0.83
   2 !   13.9   0.0   1.7e-05     0.024      88     137 ..     160     210 ..     118     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.15
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgni 32
                                      ++iG G  G a+ ++l + gl d++ lE+  i
  gi|336252805|ref|YP_004595912.1| 11 VVIGVGGMGSATTYHLAERGL-DVVGLERYDI 41
                                      689999999999999999999.7888888766 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.7e-05
                       Pyr_redox_3  88 revaksfelpiklfeeVesvkk.edegfevetsketyeAkkviiAtGefdk 137
                                       +e a+    ++++ e+V + ++  deg +vet+++tyeA+  ++A+G +++
  gi|336252805|ref|YP_004595912.1| 160 AEAAQAAGAEVRARERVLDWEPtPDEGVRVETDRDTYEADAMVLAAGAWNY 210
                                       56778888899***********6699*********************9875 PP

>> SUKH-4  SUKH-4 immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.9e-06    0.0068       1      90 [.     221     329 ..     221     334 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.9e-06
                            SUKH-4   1 vtareLeelfGpggvvrlpaeavaawllpeparrfLvevGlPd...............lqllae......eeeaava 56 
                                       v++r++  +f p+++ +++++ ++ w l  p  rf    GlP                +    +       +e++++
  gi|336252805|ref|YP_004595912.1| 221 VPERQVLGWFQPERPATFEPDSFPVWNLKVPEGRFY---GLPIydvpgmklgkyhhfdE----DvdpdeyDREPNRE 290
                                       6899*******************************6...***99*********976651....23445588999999 PP

                            SUKH-4  57 dlelvaaerseelpaeaggllvLGal.....esaslvld 90 
                                       d +l+++  +  +p++ag+ ++L+++     ++ ++ ld
  gi|336252805|ref|YP_004595912.1| 291 DERLLREVVENYFPEAAGPTMRLATCmftnsPDEHFILD 329
                                       9*************************9999999999887 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   1.6e-05     0.022       2      45 ..       8      51 ..       7      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EE CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradgl 45
                                      +dV+++G G  G  ++  L+e+G +vv +e+++  +  + ++g+
  gi|336252805|ref|YP_004595912.1|  8 YDVVVIGVGGMGSATTYHLAERGLDVVGLERYDIPHTMGSSHGI 51
                                      79******************************999988888877 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 ?   13.0   0.2   5.2e-05     0.072       2      30 ..      10      38 ..       9      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.2e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                      v viG G mG+  ++ +a++gl+Vv +++
  gi|336252805|ref|YP_004595912.1| 10 VVVIGVGGMGSATTYHLAERGLDVVGLER 38
                                      89**********************98775 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   5.4e-05     0.075       1      31 [.      10      40 ..      10      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                      ++++G G++Gs   ++La+ g dv+ + r +
  gi|336252805|ref|YP_004595912.1| 10 VVVIGVGGMGSATTYHLAERGLDVVGLERYD 40
                                      689*********************9988865 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 ?    0.7   0.1      0.34   4.7e+02       1      20 [.      11      30 ..      11      46 .. 0.86
   2 ?   12.9   0.2   6.1e-05     0.085     115     154 ..     168     206 ..     155     207 .. 0.81
   3 ?   -2.3   0.1       2.8   3.9e+03       3      10 ..     339     346 ..     337     364 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.34
                     NAD_binding_9  1 aivGaGprGlavlerLlara 20
                                      +++G G  G a++ +L++r 
  gi|336252805|ref|YP_004595912.1| 11 VVIGVGGMGSATTYHLAERG 30
                                      69**************9984 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 6.1e-05
                     NAD_binding_9 115 vtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                        +v+  r++v+d e+++d+   +++d ++++ada vLA G
  gi|336252805|ref|YP_004595912.1| 168 AEVR-ARERVLDWEPTPDEGVRVETDRDTYEADAMVLAAG 206
                                       3333.589***********9999***************99 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.8
                     NAD_binding_9   3 vGaGprGl 10 
                                       vGaG++G 
  gi|336252805|ref|YP_004595912.1| 339 VGAGFSGH 346
                                       9****995 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00015      0.21     218     272 ..     161     214 ..      74     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                                       H..TTTTEEEETSEEEEEEEE.ETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEES CS
                     Amino_oxidase 218 e..elrgldirlntrVkeikr.egdgvtvtledgevveaDaVvvTvplgvlkailfsP 272
                                       e  ++ g ++r ++rV + +   ++gv+v++ d +++eaDa v+++  ++ k   f+ 
  gi|336252805|ref|YP_004595912.1| 161 EaaQAAGAEVRARERVLDWEPtPDEGVRVET-DRDTYEADAMVLAAGAWNYK---FTD 214
                                       14578999********9999988888***96.99999***********9999...555 PP

>> DUF1990  Domain of unknown function (DUF1990)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00036       0.5       9      65 ..     144     204 ..     134     224 .. 0.72
   2 ?   -1.5   0.0       1.7   2.3e+03      91     100 ..     326     335 ..     285     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
                           DUF1990   9 lPagyrvdrarvrlGeg.....eevFerAaeallswemhrlagvrvraeapraaegatvvve 65 
                                       +P+g  v+ +++ +G+      +++  rA+e +l+we  +++gvrv++++++ +++a  v+ 
  gi|336252805|ref|YP_004595912.1| 144 QPDGGFVVPEQAIVGHAeaaqaAGAEVRARERVLDWEPTPDEGVRVETDRDTYEADAM-VLA 204
                                       56666666666667666333323444589********************987777766.333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.7
                           DUF1990  91 FaYgTLpgHp 100
                                       F   TLp+Hp
  gi|336252805|ref|YP_004595912.1| 326 FILDTLPDHP 335
                                       7889999998 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00045      0.62       1      28 [.       9      36 ..       9      50 .. 0.93
   2 ?    0.2   0.0      0.22   3.1e+02     175     204 ..     185     210 ..     151     227 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00045
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEE CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavv 28
                                      Dv+ViG G+ G a ++ +ae+Gl+v+ +
  gi|336252805|ref|YP_004595912.1|  9 DVVVIGVGGMGSATTYHLAERGLDVVGL 36
                                      9***********************9865 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.22
                                       EEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 175 tGavvenpesgrevrirakavvlatgGfgr 204
                                        G+ ve      + +++a+a vla+g+++ 
  gi|336252805|ref|YP_004595912.1| 185 EGVRVE----TDRDTYEADAMVLAAGAWNY 210
                                       344444....33447899********9985 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00021      0.29      18      49 ..       8      38 ..       3      50 .. 0.92
   2 ?   -3.0   0.1       2.4   3.3e+03      50      68 ..     336     354 ..     334     361 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailer 49
                                       Dvv++G G  G +++y la++ +l v+ ler
  gi|336252805|ref|YP_004595912.1|  8 YDVVVIGVGGMGSATTYHLAER-GLDVVGLER 38
                                      69********************.****99997 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.4
                                       SSS--TTTTTTSTTBSEEE CS
                              Thi4  50 svspGGGawlGGqlfsaiv 68 
                                       +v++G G  + G  f  ++
  gi|336252805|ref|YP_004595912.1| 336 QVAVGAGFSGHGFKFASVI 354
                                       5788888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 2949.00
//
Query:       gi|336252806|ref|YP_004595913.1|  [L=383]
Description: Choline monooxygenase [Halopiger xanaduensis SH-6]
Scores for complete 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-18   67.4   7.1    1.5e-16   61.0   7.1    2.2  1  Ring_hydroxyl_A  Ring hydroxylating alpha subunit (catalytic 
    4.4e-16   58.6   0.0    9.5e-16   57.5   0.0    1.5  1  Rieske           Rieske [2Fe-2S] domain
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.34   10.9   0.0    1.7  2  Rieske_2         Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Ring_hydroxyl_A  Ring hydroxylating alpha subunit (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   7.1   2.6e-20   1.5e-16       1     211 [.     201     380 ..     201     383 .] 0.79

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 2.6e-20
                                       HHHHHGGGHHHHHESS-HHHHHHHHHHCCCCCTTTHHHHHHCS-TTS---EEEEE-SSSS-EEEEEES-THHHHHHH CS
                   Ring_hydroxyl_A   1 leellrvaaetldikaNWKlaaEnflEsYHvpvlHpellrallpeeletaeaaeyagfgphgsgsyvgqpgdlrlep 77 
                                       lee++ +++++ ++++NWK++  n++E+ H+++ H++ +r l   + e      ++  + h+  +            
  gi|336252806|ref|YP_004595913.1| 201 LEEYHLARRIVSEVECNWKVFGGNYSECDHCQANHQDWVRDLELLDSE------LEVNDYHWILH------------ 259
                                       689999*******************************84444444444......44444455444............ PP

                                       HHHHHHHHHSHHHHHHHGCHHHHCEEEEEEEETTTEEEE....TTTTEEEEEEESSTT-EEEEEEEEEETT..S-HH CS
                   Ring_hydroxyl_A  78 aaavreldaeaaapelegledeqdrgalhftifPnlsilla..pdhvvifrviPtgpettevelealvppdatasee 152
                                                ++ ++    ++ ++++ a ++  +Pn++++++  +d + ++ + P ++++ +++++++++ ++  +e 
  gi|336252806|ref|YP_004595913.1| 260 --------YQHKEDVDDEMRIHDEHEAKFYYFWPNFTVNMYgtADGYGTYIIDPIDEGRFQLVADYYFADADLSEE- 327
                                       ........333344444566677778889999*******652268899*********************9954333. PP

                                       HHHHHHHHHHHHCSTTHHHHHHHHHHHHHHTTSTTTSBSCCCSCSSHHHHHHHHHHHHH CS
                   Ring_hydroxyl_A 153 lkeelaavvdrtfgvveeeDaelceevQqglrsrgyepgpvlsrqEeavrhFhewvrdr 211
                                        ++e+ + +++     +eeD+el+e++Q+gl+s+++  +  l+++E  v+++h+  ++ 
  gi|336252806|ref|YP_004595913.1| 328 -EAEFVRTSRQ----LQEEDFELVERQQRGLESGAI-AQAQLGPNEHTVHKLHRLAQEA 380
                                       .4777777777....9********************.666679**********976665 PP

>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   1.6e-19   9.5e-16       2      81 ..      52     136 ..      51     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.6e-19
                                       EEEEEEGGGC-.TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGG.SEEE...TT.EEE-TTT--EEETT CS
                            Rieske   2 wvavakesdvp.egdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplse.gkid...ekgvleCpcHgwaydad 73 
                                       wv++ +++ +p  gd+ t ++g+++++v+r++dg++ A+ +vC Hrg  + e   ++   + g+++Cp+H w+yd d
  gi|336252806|ref|YP_004595913.1|  52 WVYAGHANCIPdAGDYFTRNIGDREIIVVRTHDGDIEAFYNVCAHRGSAMVEeTPMTdpgNAGRIKCPYHLWTYDLD 128
                                       99999******99************************************95533332456889************** PP

                                       SBEEE-TT CS
                            Rieske  74 GkvikgPa 81 
                                       G++  +P+
  gi|336252806|ref|YP_004595913.1| 129 GSLASTPK 136
                                       ****9996 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.7e-05      0.34      17      80 ..      68     130 ..      51     146 .. 0.85
   2 ?   -2.5   0.0      0.82   4.9e+03      63      76 ..     300     313 ..     295     322 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.7e-05
                                       EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-B CS
                          Rieske_2  17 vaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGe 80 
                                        +  +++++++++r++++++ A  n++   +++++ +  + d ++   +++P +  ++dL+ G+
  gi|336252806|ref|YP_004595913.1|  68 FTRNIGDREIIVVRTHDGDIEAFYNVCAHRGSAMVEETPMTDPGNAGRIKCPYHLWTYDLD-GS 130
                                       566789*****************************************************94.55 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.82
                                       EEEE-TTT--EEET CS
                          Rieske_2  63 lvvasPlykqkfdL 76 
                                       +++ +P+++ +f+L
  gi|336252806|ref|YP_004595913.1| 300 TYIIDPIDEGRFQL 313
                                       67999*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 3148.75
//
Query:       gi|336252807|ref|YP_004595914.1|  [L=122]
Description: hypothetical protein Halxa_1402 [Halopiger xanaduensis SH-6]
Scores for 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  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); 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:                         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 0.21s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 924.59
//
Query:       gi|336252808|ref|YP_004595915.1|  [L=214]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.0   0.0    2.1e-15   56.2   0.0    1.4  1  HTH_10         HTH DNA binding domain
      3e-10   40.2   0.7    4.2e-10   39.7   0.3    1.4  1  BAT            GAF and HTH_10 associated domain
     0.0014   18.4   0.1     0.0033   17.2   0.1    1.6  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.008   15.8   0.0      0.096   12.4   0.0    2.4  1  Sigma70_r4_2   Sigma-70, region 4
     0.0091   15.5   0.1      0.024   14.2   0.1    1.7  1  Sigma70_r4     Sigma-70, region 4
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.024   14.2   0.0    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.16   12.1   0.0       0.32   11.1   0.0    1.5  1  HTH_3          Helix-turn-helix
       0.19   11.6   0.0       0.49   10.3   0.0    1.6  1  Homeodomain    Homeodomain


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 !   56.2   0.0   9.5e-19   2.1e-15       2      52 ..     157     207 ..     156     208 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 9.5e-19
                            HTH_10   2 TdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       Td q+++l +Aye GYF++PR+++l+eLA+ lGIs++++  ++r+ + +l+
  gi|336252808|ref|YP_004595915.1| 157 TDEQRAALVAAYEEGYFEEPRETSLEELADSLGISPTAVGGRIRRGTGTLV 207
                                       9*******************************************9877776 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.3   1.9e-13   4.2e-10      19     140 ..      19     141 ..       7     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1.9e-13
                               BAT  19 alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtllelt.vsgpslas.tl 93 
                                       ++ +  ++ ve+ +  +++ ++ l ff v+ ad e+++ ++e+ ++v+d  +v++ +++ l++l+ ++g+ l+s + 
  gi|336252808|ref|YP_004595915.1|  19 TIRDCPEASVEVVSHSTTDPETGLFFFLVRNAD-ETFEPTLEADHTVADWLLVDDLGSTRLYRLEhTEGTKLISpMA 94 
                                       55666788899999999999999********99.*******************************777888998677 PP

                               BAT  94 aehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLva 140
                                       +e Gg + +ae +d ++++++++P+++++ ++ e++++   + eL +
  gi|336252808|ref|YP_004595915.1|  95 TELGGLLLRAESNDRGWTVRLHLPDREALAELWERCQDCDISFELHR 141
                                       89***********************************9888888855 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 !   17.2   0.1   1.5e-06    0.0033      18      40 ..     179     201 ..     177     201 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-06
                     HTH_AsnC-type  18 isyaeLAervGlSestvlrRvrr 40 
                                       +s +eLA+ +G+S+++v  R+rr
  gi|336252808|ref|YP_004595915.1| 179 TSLEELADSLGISPTAVGGRIRR 201
                                       699*******************9 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 !   12.4   0.0   4.3e-05     0.096      14      50 ..     159     202 ..     154     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                                       HHHHHHHHHHTS--.......-HHHHHHHHT--HHHHHHHHHHH CS
                      Sigma70_r4_2  14 rqreifllrylegl.......sykEIAellgisegtVksrlsRA 50 
                                       +qr++++  y+eg+       s +E A  lgis+++V  r++R+
  gi|336252808|ref|YP_004595915.1| 159 EQRAALVAAYEEGYfeepretSLEELADSLGISPTAVGGRIRRG 202
                                       67777777777776666666699******************997 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.1e-05     0.024       6      43 ..     157     201 ..     154     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                       -HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4   6 pererevlelrf.......geglTleEIgerlgiSrerVrqiekr 43 
                                       ++++r  l+  +        ++ +leE+++ lgiS  +V  +++r
  gi|336252808|ref|YP_004595915.1| 157 TDEQRAALVAAYeegyfeePRETSLEELADSLGISPTAVGGRIRR 201
                                       899*********99999887888************9888666666 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 ?   14.2   0.0   1.1e-05     0.024      15      40 ..     175     201 ..     173     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                            HTH_24  15 npr.isqreLAerlglSpstvnrrlkr 40 
                                       +pr +s  eLA+ lg+Sp++v  r++r
  gi|336252808|ref|YP_004595915.1| 175 EPReTSLEELADSLGISPTAVGGRIRR 201
                                       6777999**************999987 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.32       8      27 ..     177     196 ..     165     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                       TTHHHHHHHHHHTSSHHHHH CS
                             HTH_3   8 lglsqeeLAeklGvsrstis 27 
                                       +  s+eeLA+ lG+s++++ 
  gi|336252808|ref|YP_004595915.1| 177 RETSLEELADSLGISPTAVG 196
                                       56799************986 PP

>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00022      0.49       8      44 ..     157     195 ..     155     196 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                                       -HHHHHHHHHHHHH..SSS-SHHHHHHHHHHHTS-HHHH CS
                       Homeodomain   8 tkeqleeLeklFee..nrypsaeereeLAkklgLeerqV 44 
                                       t+eq ++L +++ee   + p +   eeLA++lg++ + V
  gi|336252808|ref|YP_004595915.1| 157 TDEQRAALVAAYEEgyFEEPRETSLEELADSLGISPTAV 195
                                       899**********87899****************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1611.34
//
Query:       gi|336252809|ref|YP_004595916.1|  [L=179]
Description: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen [Halopiger xanaduensis SH-6]
Scores for complete 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   60.8   0.0    1.5e-16   60.4   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    8.4e-09   35.3   0.0    1.1e-08   35.0   0.0    1.2  1  Redoxin     Redoxin
      2e-05   24.7   0.0    2.8e-05   24.2   0.0    1.2  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 !   60.4   0.0   2.6e-20   1.5e-16      27     101 ..      46     120 ..      39     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 2.6e-20
                                       EEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHHTT-E CS
                          AhpC-TSA  27 pvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvakaygvl 101
                                        v+l+ ++  +  +C+++++a a++yeef+erg++v+ v +++ e++++++e+++l++pl +D++ +v +a++ +
  gi|336252809|ref|YP_004595916.1|  46 TVLLLLHRDHHAGQCRRQVRAVADRYEEFQERGCQVVSVVPEPRERVREWQERYDLPYPLCADPDATVGEAFEQP 120
                                       6899999999*************************************************************9866 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   1.8e-12   1.1e-08      11     125 ..      27     146 ..       7     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.8e-12
                                       CCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHHTT-TS CS
                           Redoxin  11 lplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgkeglkf 87 
                                       +p a+ d+++++  + +  +v++   +  + + C+++++++++ +e++ e+g +vv vv   ++ v+e+ ++++l++
  gi|336252809|ref|YP_004595916.1|  27 EPVAPADPTTTDGGDPAYETVLLLLHRDHHAGQCRRQVRAVADRYEEFQERGCQVVSVVPEPRERVREWQERYDLPY 103
                                       5667789999999999999999999999************************************************* PP

                                       EEEE-TTSHHHHHTT-TTEEE.GGG.....EEE-EEEEEEETT CS
                           Redoxin  88 pvlsDgsaaftkalGlrleedaseg.....lrtpryavidedg 125
                                       p+ +D++a + +a+  +++     +      r+p+ +v+d ++
  gi|336252809|ref|YP_004595916.1| 104 PLCADPDATVGEAFEQPVRFGPLGRhvdlvGRMPAAVVLDVQD 146
                                       ***************9988887766788877888888877433 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 !   24.2   0.0   4.7e-09   2.8e-05       5      52 ..      70     118 ..      67     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.7e-09
                        AhpC-TSA_2   5 dkpeldaagvklvaigigdps.akkFvkltgfpfelyvDpsaklyqalg 52 
                                       + +e++++g+++v ++ + ++ +++++++ + p++l +Dp+a++ +a++
  gi|336252809|ref|YP_004595916.1|  70 RYEEFQERGCQVVSVVPEPRErVREWQERYDLPYPLCADPDATVGEAFE 118
                                       5799****************66**********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); 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:                         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 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1416.21
//
Query:       gi|336252810|ref|YP_004595917.1|  [L=150]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-09   37.4   1.2    8.4e-09   35.7   1.2    1.9  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.5e-08   33.7   2.5    1.9e-07   31.3   2.5    1.8  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.4e-06   28.3   0.0    1.7e-06   28.0   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0019   18.1   2.1      0.011   15.7   1.3    2.3  2  FR47             FR47-like protein
     0.0046   17.0   0.7      0.022   14.8   0.7    2.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.096   12.8   0.2        0.2   11.8   0.1    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
       0.48   10.2   5.9        1.1    9.0   5.8    1.6  1  PanZ             Acetyltransferase (GNAT) domain, PanZ


Domain annotation for each model (and alignments):
>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   1.2   3.3e-12   8.4e-09       5      75 ..      51     133 ..      20     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 3.3e-12
                                       EEEEEET.........TEEEEEEEEEEES....TCTEEEEE-GGGTTSSHHHHHHHHTTSEEEEE.EEEE..THHHH CS
                    Acetyltransf_7   5 vfVaedd.........gkivGfialslld....aeitrlaVdpeyrgkGiGraLleaaekgiile.qlel..naeka 65 
                                       v+Va d           +i+G+++l++l+    a+i  + V+  +rg+G+GraL+e    g++ e +l+   ++   
  gi|336252810|ref|YP_004595917.1|  51 VLVAGDRrgrgdgsaaARILGTLVLERLEdergAHIAAIGVRRRHRGRGLGRALVER---GLEREgRLTArfDE-GV 123
                                       55554445555555556778888888887888777777*****************95...33322222333222.55 PP

                                       HHHHHHTTEE CS
                    Acetyltransf_7  66 ikfYeklGFe 75 
                                       ++fYe+lGF 
  gi|336252810|ref|YP_004595917.1| 124 RPFYERLGFS 133
                                       66*******6 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.094   2.4e+02      64      82 ..      49      67 ..      14      80 .. 0.78
   2 !   31.3   2.5   7.5e-11   1.9e-07      42     117 .]      67     132 ..      45     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.094
                                      EEEEESGGGTTSSHHHHHH CS
                    Acetyltransf_1 64 eslaVspeyrgkGlGsaLl 82
                                       ++ V+ ++rg+G Gsa  
  gi|336252810|ref|YP_004595917.1| 49 GDVLVAGDRRGRGDGSAAA 67
                                      48999999*****999875 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 7.5e-11
                                       TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  42 geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                        +++G++ l    d  ++ a+i  + V++ +rg+GlG+aL+e  +e  re  +++  +     +++ +++Ye+lGF
  gi|336252810|ref|YP_004595917.1|  67 ARILGTLVLERLED--ERGAHIAAIGVRRRHRGRGLGRALVERGLE--REGRLTA-RF-----DEGVRPFYERLGF 132
                                       45777776666666..9************************99999..6664433.44.....7899********9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   6.8e-10   1.7e-06      41     107 ..      68     133 ..      37     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 6.8e-10
                   Acetyltransf_10  41 kivGvi...elrdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFk 107
                                       +i+G++   +l+d++  hi+ + V++ +rg+G+g+aL+e+ +e+        +lt++ +   +pfYe+lGF 
  gi|336252810|ref|YP_004595917.1|  68 RILGTLvleRLEDERgaHIAAIGVRRRHRGRGLGRALVERGLERE--G----RLTARFDEGVRPFYERLGFS 133
                                       56666645455343358*********************9998883..2....8******************6 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.8   2.1e+03      27      50 ..      51      74 ..      49      80 .. 0.71
   2 !   15.7   1.3   4.4e-06     0.011      10      44 ..      71     106 ..      65     138 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.8
                                      EEE-GGG-SSSHHHHHHHHHHHHH CS
                              FR47 27 lqvlpehrrrGlgsrlvkalakei 50
                                      + v  + r+rG gs  ++ l   +
  gi|336252810|ref|YP_004595917.1| 51 VLVAGDRRGRGDGSAAARILGTLV 74
                                      677788899999888777665555 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.4e-06
                                       --EEEEEEE-TT.SSEEEEEE-GGG-SSSHHHHHHH CS
                              FR47  10 gelaawilrkdg.gelgalqvlpehrrrGlgsrlvk 44 
                                       g l+ ++l+ +    + a+ v+  hr+rGlg+ lv+
  gi|336252810|ref|YP_004595917.1|  71 GTLVLERLEDERgAHIAAIGVRRRHRGRGLGRALVE 106
                                       567777777766478******************996 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.7   8.7e-06     0.022       3     125 ..      18     132 ..      17     134 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.7e-06
                                       EEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEE.TTEEEEEEEEEEEEEEETT..EEEEEEEE CS
                    Acetyltransf_9   3 relteedldevlellkyaFqdeespleeireyfrklleesrvlgaed.ngelvgqlallplelnvpG..ktlkaagv 76 
                                       r++t +d  ev ++l++a  +  +         + +++ ++vl+a d  g+  g++a+  l   v +  +  + a +
  gi|336252810|ref|YP_004595917.1|  18 RSATADDALEVRRILDAAMLEPGDV--------EARIDAGDVLVAGDrRGRGDGSAAARILGTLVLErlEDERGAHI 86 
                                       6666666666666666666666655........356677777777766444444444444433332224667889** PP

                                       EEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSHHHHHTTT- CS
                    Acetyltransf_9  77 tgVavapehrgrgvlskLlaraleemreegqplsllfPssipiYrrfGy 125
                                       ++++v   hrgrg+ ++L++r le+    + +  +  +  +p+Y+r+G+
  gi|336252810|ref|YP_004595917.1|  87 AAIGVRRRHRGRGLGRALVERGLEREG--RLTARFDEGV-RPFYERLGF 132
                                       ***********************9744..3444445555.677777777 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 ?   11.8   0.1     8e-05       0.2      24      51 ..      83     110 ..      66     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8e-05
                   Acetyltransf_CG  24 vldfthTeVpeelrGkGiAkkLvkaald 51 
                                         ++  + V  ++rG+G++++Lv++ l+
  gi|336252810|ref|YP_004595917.1|  83 GAHIAAIGVRRRHRGRGLGRALVERGLE 110
                                       55677899***************99876 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.8   0.00043       1.1      47      90 ..      67     112 ..      22     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00043
                              PanZ  47 dRlLgAvkveledk..eaelsdlcVRevTRrRGVgsyLleearrqa 90 
                                       +R Lg   +e+ ++   a++  + VR+  R RG g+ L+e+ +++ 
  gi|336252810|ref|YP_004595917.1|  67 ARILGTLVLERLEDerGAHIAAIGVRRRHRGRGLGRALVERGLERE 112
                                       6999999888755523689*********************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1069.20
//
Query:       gi|336252811|ref|YP_004595918.1|  [L=102]
Description: hypothetical protein Halxa_1406 [Halopiger xanaduensis SH-6]
Scores for 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   3.2       0.14   11.8   3.2    1.2  1  CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like


Domain annotation for each model (and alignments):
>> 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 ?   11.8   3.2     8e-06      0.14     112     181 ..       7      74 ..       2      93 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8e-06
                         CPP1-like 112 vapaesvpalllalglgasiyflnrKek.klgravlltlvgLvvGlllGsllasllqvdvalsglsseell 181
                                       + +a++  +l+   ++++  y   r+ +   +rav+ +++ +v+G +lG++    l++ val+ +++ + +
  gi|336252811|ref|YP_004595918.1|   7 FIAASNAATLVTGGAVATLAYRAFRRTGsPALRAVAAGFAIIVAGSVLGGVAHL-LRS-VALGVAIQSS-F 74 
                                       44455533444444555555655555553789*****************97655.444.4444444444.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 777.09
//
Query:       gi|336252812|ref|YP_004595919.1|  [L=160]
Description: cytidyltransferase-related domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-15   58.1   0.0    1.3e-15   57.8   0.0    1.1  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.025   14.5   0.0      0.057   13.3   0.0    1.6  2  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 !   57.8   0.0   1.4e-19   1.3e-15       2     143 .]      20     149 ..      19     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.4e-19
                                       EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHH CS
                   CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevlk 78 
                                       a GtFD++H GH ++le+a++ ++e l v+v+ +++  +k  p+++ ++R +++ +++ vd++    p +     ++
  gi|336252812|ref|YP_004595919.1|  20 AQGTFDILHPGHVHYLEEAAAAGDE-LHVIVARADNIAHKPDPVMPDAQRRDTVAALEAVDYARLGHPEDFSV-PIE 94 
                                       78***********************.999999988888888*******************************9.9** PP

                                       HTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHHH CS
                   CTP_transf_like  79 klkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkirer 143
                                        ++pd  +lv+g+d++ d   ++++   l++ ++ +++++       l+++ +t  +Ss++i++r
  gi|336252812|ref|YP_004595919.1|  95 AIDPD--VLVLGHDQHHD---ERDVSAMLAEWGIDCRVER----ASGLDPDGET-LVSSSEIKAR 149
                                       *****..**********9...99*************9777....4446666666.7999999875 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.3e-06     0.057       5      39 ..      14      48 ..      10      77 .. 0.85
   2 ?   -1.8   0.0      0.29   2.6e+03     120     140 ..     104     124 ..      91     144 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-06
                           FAD_syn  5 degavvtlGnFDGvHlGHqallkkaveaakekglp 39
                                      +   vv+ G FD +H GH + l++a +a +e ++ 
  gi|336252812|ref|YP_004595919.1| 14 EPTRVVAQGTFDILHPGHVHYLEEAAAAGDELHVI 48
                                      56789********************9999887765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.29
                           FAD_syn 120 Gkkregdvellkelgaklgfe 140
                                       G++++ d ++++++ a+ g++
  gi|336252812|ref|YP_004595919.1| 104 GHDQHHDERDVSAMLAEWGID 124
                                       444444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 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:                        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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1165.91
//
Query:       gi|336252813|ref|YP_004595920.1|  [L=205]
Description: hypothetical protein Halxa_1408 [Halopiger xanaduensis SH-6]
Scores for 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-05   22.3   4.1    0.00013   21.5   2.4    2.1  2  SHOCT     Short C-terminal domain
  ------ inclusion threshold ------
      0.027   14.5   0.4       0.05   13.7   0.4    1.5  1  DUF1707   Domain of unknown function (DUF1707)
       0.16   12.0   0.3       0.26   11.3   0.3    1.3  1  GvpG      Gas vesicle protein G


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   2.4   2.2e-08   0.00013       5      26 ..     147     168 ..     143     168 .. 0.91
   2 !    4.1   0.2    0.0069        41       4      14 ..     164     174 ..     164     174 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.2e-08
                             SHOCT   5 kLkeLyarGeIteEEFeakKak 26 
                                        Lk+ y++Ge++e+EFe++ ++
  gi|336252813|ref|YP_004595920.1| 147 DLKAKYENGELSEDEFERRLEE 168
                                       69*****************875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0069
                             SHOCT   4 ekLkeLyarGe 14 
                                       ++L e++a+Ge
  gi|336252813|ref|YP_004595920.1| 164 RRLEERLANGE 174
                                       69********8 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   8.3e-06      0.05      14      35 ..     147     168 ..     137     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.3e-06
                           DUF1707  14 lLrealaeGrLtldEfdeRlea 35 
                                        L++ +++G L+ dEf++Rle+
  gi|336252813|ref|YP_004595920.1| 147 DLKAKYENGELSEDEFERRLEE 168
                                       5999***************986 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   4.4e-05      0.26      39      62 ..     147     170 ..     141     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.4e-05
                              GvpG  39 aLqqeLdaGeIdeeeFdrrEeelL 62 
                                       +L+ + ++Ge +e+eF+rr ee L
  gi|336252813|ref|YP_004595920.1| 147 DLKAKYENGELSEDEFERRLEERL 170
                                       7999**************966655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1585.58
//
Query:       gi|336252814|ref|YP_004595921.1|  [L=795]
Description: helicase c2 [Halopiger xanaduensis SH-6]
Scores for 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  115.5   0.0    5.7e-33  114.5   0.0    1.4  1  Helicase_C_2   Helicase C-terminal domain
    1.9e-06   27.6   0.0    7.1e-06   25.8   0.0    2.0  1  DEAD_2         DEAD_2
    6.6e-05   22.7   0.0       0.13   12.0   0.0    2.4  2  DEAD           DEAD/DEAH box helicase
     0.0011   19.1   0.0      0.023   14.7   0.0    2.1  2  ResIII         Type III restriction enzyme, res subunit
     0.0013   18.2   0.0     0.0026   17.2   0.0    1.4  1  PhoH           PhoH-like protein
     0.0045   16.3   0.0      0.036   13.3   0.0    2.0  2  DUF2075        Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.054   13.2   0.0       0.12   12.1   0.0    1.5  1  HBB            Helical and beta-bridge domain
      0.062   13.6   0.0       0.25   11.7   0.0    1.9  1  AAA_19         AAA domain
      0.082   12.6   0.0        1.2    8.8   0.0    2.3  2  AAA_30         AAA domain
       0.19   11.2   0.0       0.29   10.6   0.0    1.2  1  UvrD-helicase  UvrD/REP helicase N-terminal domain


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.5   0.0   3.2e-36   5.7e-33       6     160 ..     607     758 ..     603     768 .. 0.93

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 3.2e-36
                      Helicase_C_2   6 evvpggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEGidfsd 82 
                                       + vpg+vlv +pSy+  e ++ +l+++ + k i +  ++++e +e++ +e+ +  ++g++l+ ++rG+l EG+d+s+
  gi|336252814|ref|YP_004595921.1| 607 ARVPGNVLVGMPSYAEAEWAAGVLEDRVDGKPILLDASTDDEATESLKSEFFA--GEGKVLVTSLRGTLTEGVDYSG 681
                                       569************************9877777777779999**********..********************** PP

                      Helicase_C_2  83 dllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeRfakee 159
                                       d+l a +++g+P  n+++p++ea r+ +d+ ++ +++ ++ + +a+r+ +QaiGR+iR+ +D g+ vllDeR+a+++
  gi|336252814|ref|YP_004595921.1| 682 DRLAAAVVCGVPIVNTSSPRTEAVRRAYDDAFG-DGFTYALTIPAVRKARQAIGRVIRSPEDVGVRVLLDERYARDS 757
                                       *********************************.****************************************977 PP

                      Helicase_C_2 160 i 160
                                       +
  gi|336252814|ref|YP_004595921.1| 758 W 758
                                       4 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   3.9e-09   7.1e-06      71     170 ..     200     312 ..      70     318 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.9e-09
                                       TTTTTT-SCC..........CCHHHH......HHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHH CS
                            DEAD_2  71 eekCsffenl..........eelkkl......kkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqy 131
                                       +e C+f+ +                +       +++++++++ edlv+   k+++CP+ ++ ++l +++++i  Y  
  gi|336252814|ref|YP_004595921.1| 200 TEYCPFYAQYledlpeedseG----DaaeavpYDFTTAGMITPEDLVARSVKHGTCPHSVMGAALGHVEVVIGNYYH 272
                                       666777766665665543321....122334567788899999********************************** PP

                                       HTSCCCHHHHH.T..GCGCEEEECTCCCHHHHHHHCC-EE CS
                            DEAD_2 132 Lldekireslk.gislknsivilDEAhNiedvceeaasve 170
                                        +d+ +  s++  +    + v+ DEAh +e  +++++s  
  gi|336252814|ref|YP_004595921.1| 273 AFDPTTTGSFTgALLDDSTFVVCDEAHMLEPRVRDLVSDG 312
                                       **********954445556899********9999988865 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   7.2e-05      0.13       6      72 ..      23      88 ..      19     107 .. 0.86
   2 !    8.1   0.0    0.0012       2.1      96     135 ..     261     303 ..     240     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-05
                                      HHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  6 eaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk 72
                                       ai+++ +gg  +v+++ G+GKT+++l + ++ v +  +++  ++++++  ++  +q  ++l+++ +
  gi|336252814|ref|YP_004595921.1| 23 TAIEAARDGGYTVVEGACGTGKTMIALTAGIDLVRD-PDTDYERVFVLTSVKQQLRQFEEDLETINE 88
                                      68999999***********************99955.888888999999999999999998888766 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0012
                                       TTCSEEEEEHHHHHHHHHCTSSH...CTTEEEEEEETHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
                              DEAD  96 ngvdivvgtpgrlddllstgkln...lsqvrflVlDEadrlld 135
                                        +v++v+g+    +d ++tg+++   l++ +f+V DEa++l  
  gi|336252814|ref|YP_004595921.1| 261 GHVEVVIGNYYHAFDPTTTGSFTgalLDDSTFVVCDEAHMLEP 303
                                       56999*****9999999999998899*************9975 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 !   14.7   0.0   1.3e-05     0.023       6      80 ..      15      89 ..      10     116 .. 0.73
   2 ?    1.9   0.0      0.11   1.9e+02     128     144 ..     285     301 ..     258     320 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                      HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTGG CS
                            ResIII  6 eyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee..kflflvprkslleqtleefkkflse 80
                                      e Q + ie  +e+   ++    +++ a+GtGKT++a+ +   l +  + +  ++++l   k+ l q +e+++ + ++
  gi|336252814|ref|YP_004595921.1| 15 EPQVDGIETAIEAA--RDGGYTVVEGACGTGKTMIALTAGIDLVRDPDTDyeRVFVLTSVKQQLRQFEEDLETINEN 89
                                      55666666666554..233445699***********66555555544433459999999999999999998877765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                                       HHTTT-SEEEEETGGGT CS
                            ResIII 128 llrdrfdviiiDEaHrl 144
                                       +l d + ++++DEaH l
  gi|336252814|ref|YP_004595921.1| 285 ALLDDSTFVVCDEAHML 301
                                       56677789*******76 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.4e-06    0.0026      12      54 ..      24      68 ..      15      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                                      HHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT..TS-SEEEE CS
                              PhoH 12 ylealkkndivfaiGpaGtGKtylavalavealkk..kkvkriil 54
                                      ++ea ++   +++ G  GtGKt++a++++++++++   +++r+ +
  gi|336252814|ref|YP_004595921.1| 24 AIEAARDGGYTVVEGACGTGKTMIALTAGIDLVRDpdTDYERVFV 68
                                      5566666778999********************985566666644 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0     2e-05     0.036       4      44 ..      34      75 ..      32      90 .. 0.80
   2 ?    0.2   0.0      0.19   3.4e+02      88     101 ..     289     302 ..     263     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                           DUF2075  4 vlVtGvaGtGKtvvllnllael.eddeeertavylsvNhplv 44
                                       +V+G+ GtGKt+++l++  +l +d + ++++v+++ + +++
  gi|336252814|ref|YP_004595921.1| 34 TVVEGACGTGKTMIALTAGIDLvRDPDTDYERVFVLTSVKQQ 75
                                      58*******************987888888888887765544 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.19
                           DUF2075  88 kedvvivDEAhrll 101
                                       + ++v++DEAh l 
  gi|336252814|ref|YP_004595921.1| 289 DSTFVVCDEAHMLE 302
                                       5679*******875 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.5e-05      0.12     139     176 ..     525     571 ..     511     577 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.5e-05
                                       HCCCCCCTS-SSHHHHHHHHT.............EEE.S..S.GGHC CS
                               HBB 139 lssllmsgtltpleeysdiiGle.........aklkkfpspfpkEnl 176
                                          +lms tl+p++++++++Gl+          + +++   fp+En+
  gi|336252814|ref|YP_004595921.1| 525 GGGILMSATLEPMDAFTEVTGLQyiereedrpVVERRYGLHFPAENR 571
                                       5679******************9754444443345778888888876 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   0.00014      0.25       3     122 ..      23     309 ..      22     318 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                            AAA_19   3 eave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.......... 68 
                                        a+e a   +  +v +  GtGKT +  ++   lv+  + + e++ +++  ++  ++ +e l++++++          
  gi|336252814|ref|YP_004595921.1|  23 TAIEaARDGGYTVVEGACGTGKTMIALTAGIDLVRDPDTDYERVFVLTSVKQQLRQFEEDLETINENlpddwcpvsg 99 
                                       577768889999*************9999989999999999***********9999999998877767777666664 PP

                            AAA_19  69 ............................................atTiHrlal........................ 77 
                                                                                           +                        
  gi|336252814|ref|YP_004595921.1| 100 ltlvgkadvcpynrektagfddgnvydrcetlrdrtrdlvgeggD-------Ttaqnlaararsqqigladsgsqgg 169
                                       444444444444444444444444444433333333333333332.......0333333466666666666666666 PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|336252814|ref|YP_004595921.1| 170 tanyletageptpyppdlpeygeggpvgaeteycpfyaqyledlpeedsegdaaeavpydfttagmitpedlvarsv 246
                                       66666666666666666666666666666666666666666666666666666666666666666666666666666 PP

                            AAA_19  78 .........................ldfddlltealelleeaeeekklqeeellivDEfqdvdelqyrLl 122
                                                                 +fd+++  + ++     +   l + + ++ DE+ ++++    L+
  gi|336252814|ref|YP_004595921.1| 247 khgtcphsvmgaalghvevvignyyHAFDPTT--TGSF-----TGALLDDSTFVVCDEAHMLEPRVRDLV 309
                                       66666666666666555555555444444444..2222.....223343333666666666666666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00066       1.2       9      57 ..      24      74 ..      18      91 .. 0.63
   2 ?    0.9   0.0      0.18   3.3e+02      83     105 ..     284     306 ..     246     322 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00066
                            AAA_30  9 avealltsgdrvavltGpAGtGKttalkal.reaweaag...grviglAptgk 57
                                      a+ea+  +g  ++v++G+ GtGKt++  ++  +++++     +rv++l++ ++
  gi|336252814|ref|YP_004595921.1| 24 AIEAARDGG--YTVVEGACGTGKTMIALTAgIDLVRDPDtdyERVFVLTSVKQ 74
                                      565555555..8************86433324444444334455666555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
                            AAA_30  83 rarlepgtllivDEagmvdtkql 105
                                        a l+++t ++ DEa m+  +  
  gi|336252814|ref|YP_004595921.1| 284 GALLDDSTFVVCDEAHMLEPRVR 306
                                       3567889**********976654 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 ?   10.6   0.0   0.00016      0.29      12      52 ..      30      70 ..      20      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                                      -SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEE CS
                     UvrD-helicase 12 lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvT 52
                                       gg ++ve + G+GKT +     + l++   ++ +r++v+T
  gi|336252814|ref|YP_004595921.1| 30 DGGYTVVEGACGTGKTMIALTAGIDLVRDPDTDYERVFVLT 70
                                      588999**********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.69u 0.22s 00:00:00.90 Elapsed: 00:00:00.41
# Mc/sec: 5826.56
//
Query:       gi|336252815|ref|YP_004595922.1|  [L=321]
Description: abortive infection protein [Halopiger xanaduensis SH-6]
Scores for complete 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-11   44.7   7.9    1.3e-11   44.7   7.9    2.3  2  CPBP      CPBP intramembrane metalloprotease


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 ?   -3.1   2.6      0.57     1e+04      58      58 ..      42      42 ..       9      98 .. 0.57
   2 !   44.7   7.9   7.4e-16   1.3e-11      10      91 ..     142     244 ..     132     245 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.57
                                      H CS
                              CPBP 58 s 58
                                      +
  gi|336252815|ref|YP_004595922.1| 42 A 42
                                      1 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 7.4e-16
                                       H.......HHHHHHHHHHHHHTTCHHHHHHHH..S-HHHHHHHHHHHHHCSGGG...............HHHHHHHH CS
                              CPBP  10 l.......alllapllEEllfRglllqllqer.gsstlailissilFglaHlpn...............gpsvllaa 63 
                                       +       +  + +++EE+++Rg+l+++l+   ++   a ++ ++++g++H+p                g+ +++++
  gi|336252815|ref|YP_004595922.1| 142 VavvagatINAVFAFGEEFGWRGVLQTALAPLgFW--RASAVVGFFWGVWHAPIviegynfpnepvvgvGVMTVACI 216
                                       322233334455667*****************888..****************9888888777777766555699** PP

                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              CPBP  64 laGlvlgylylktgsllaaillHallnl 91 
                                       ++  v++y++l  +s+la++++H+ +n+
  gi|336252815|ref|YP_004595922.1| 217 AMAPVYTYVTLAARSVLAPAVFHGTFNA 244
                                       ***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2501.76
//
Query:       gi|336252816|ref|YP_004595923.1|  [L=79]
Description: hypothetical protein Halxa_1411 [Halopiger xanaduensis SH-6]
Scores for 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:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 699.87
//
Query:       gi|336252817|ref|YP_004595924.1|  [L=198]
Description: hypothetical protein Halxa_1412 [Halopiger xanaduensis SH-6]
Scores for complete 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  167.9   0.1      2e-49  167.5   0.1    1.2  1  DUF1684   Protein of unknown function (DUF1684)


Domain annotation for each model (and alignments):
>> DUF1684  Protein of unknown function (DUF1684)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.5   0.1   1.1e-53     2e-49       2     140 .]      42     191 ..      41     191 .. 0.96

  Alignments for each domain:
  == domain 1  score: 167.5 bits;  conditional E-value: 1.1e-53
                                       C--S-EE----GGGEEEEEEEE-CCEEEEEEEBSSSSCEEEEEEEEEEEEETTEE........EEEEEECTT.-CSS CS
                           DUF1684   2 eFegleyfepdpawrveaelepadepeevevetstgeeveyervgevefelegkg........eLtvyreee.ekea 69 
                                       +F+gl+yfepdp++rv a+ + +d+pe v+++t++g+e +y rv+++ef+le ++        eL++yr e+ ++e+
  gi|336252817|ref|YP_004595924.1|  42 DFDGLDYFEPDPDYRVVATATVHDDPEVVRMDTTAGREMRYLRVATLEFDLERDDedledgtyELAAYRLESpNEEQ 118
                                       7**************************************************765567888899******999999** PP

                                       EEEEEEECCCCTTC-TT-EEEEE--TTTTT..EEEEEEGGGEB--HHHHTTTS--BB--GGGEESS---SSEE CS
                           DUF1684  70 lfvpfrDatsgketYgggRyleleakkada..gtvvlDfNrAynppcAysdafsCPlppeeNrLdvaveAGek 140
                                       lf+pfrD+t+g+++Y+ggRy+el+++++ +  +++vlDfN+Ay+p+cAys++f CPlppeeN+L+va+ AGe+
  gi|336252817|ref|YP_004595924.1| 119 LFIPFRDKTTGQQSYEGGRYMELAPDRDLEdgDELVLDFNLAYTPFCAYSETFDCPLPPEENWLEVAIAAGER 191
                                       **************************9988999***************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1699.26
//
Query:       gi|336252818|ref|YP_004595925.1|  [L=226]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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   84.4   0.0    1.1e-23   83.7   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    6.6e-20   71.6   0.0    1.3e-19   70.7   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.7e-15   57.2   0.0    2.1e-15   56.8   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
      1e-13   51.4   0.0    1.3e-13   51.1   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    4.9e-11   42.4   0.0      1e-10   41.3   0.0    1.4  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.8e-11   43.0   0.0    9.6e-11   42.3   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    0.00013   22.0   0.0    0.00022   21.2   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
    0.00015   21.1   0.0    0.00022   20.6   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00033   20.3   0.0    0.00054   19.6   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
    0.00043   19.3   0.0    0.00095   18.2   0.0    1.6  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0012   18.4   0.0     0.0033   17.0   0.0    1.7  1  MTS              Methyltransferase small domain
     0.0022   17.3   0.0     0.0031   16.9   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
     0.0031   17.4   0.0     0.0099   15.7   0.0    1.7  1  Methyltransf_8   Hypothetical methyltransferase
     0.0034   17.1   0.0     0.0059   16.4   0.0    1.6  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0047   16.7   0.0        0.8    9.4   0.0    2.3  2  N6_N4_Mtase      DNA methylase
  ------ inclusion threshold ------
       0.02   14.0   0.0      0.034   13.2   0.0    1.3  1  Fibrillarin      Fibrillarin
      0.035   14.2   0.0       0.44   10.6   0.0    2.0  2  FtsJ             FtsJ-like methyltransferase
       0.16   11.3   0.0       0.31   10.4   0.0    1.5  2  PrmA             Ribosomal protein L11 methyltransferase (Prm


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 !   83.7   0.0   1.1e-26   1.1e-23       1      96 []      43     138 ..      43     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 1.1e-26
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhve 75 
                                       Ld+GcG+G+  +al ++   +rv+g+D s+em + a   + +++  v +vv+d+ +lpf+d+s+D v+s e++ + +
  gi|336252818|ref|YP_004595925.1|  43 LDLGCGSGYAGRALRDNKdaGRVYGLDGSPEMARNAAGYTDDPE--VGYVVGDFDSLPFADDSIDHVWSMEAFYYAA 117
                                       8**************555569************99988888888..9****************************** PP

                                       CHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllvi 96 
                                       dp+ +l+e+aR+L+pgG++++
  gi|336252818|ref|YP_004595925.1| 118 DPHNTLREVARILRPGGTFYC 138
                                       ******************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0   1.3e-22   1.3e-19       1      97 []      42     134 ..      42     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 1.3e-22
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vLdlGcG+G   +al ++  +++v+g+D s+em ++a+     ++++v +v+gd+++lpf+d+s+D v+s+ a+ + 
  gi|336252818|ref|YP_004595925.1|  42 VLDLGCGSGYAGRALRDNKDAGRVYGLDGSPEMARNAAGYT--DDPEVGYVVGDFDSLPFADDSIDHVWSMEAFYYA 116
                                       9***************99659******************99..5789***********************8889886 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                          d +++l+e+ar+L+pgG
  gi|336252818|ref|YP_004595925.1| 117 A--DPHNTLREVARILRPGG 134
                                       6..66799***********9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   2.1e-18   2.1e-15       4     117 ..      39     146 ..      37     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 2.1e-18
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g +vlDlGCG+G+ + +l ++  + ++v+G+D s+e+ + A   +++ +   v   +gd+ +l+  ++d+++D + s
  gi|336252818|ref|YP_004595925.1|  39 GDTVLDLGCGSGYAGRALRDN-KDAGRVYGLDGSPEMARNAAGYTDDPE---VGYVVGDFDSLP--FADDSIDHVWS 109
                                       679****************64.46789**************99877554...5699********..*********** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedprllae 117
                                        e++++ adp ++l+e+ r l+pgg + ++    +++
  gi|336252818|ref|YP_004595925.1| 110 MEAFYYAADPHNTLREVARILRPGGTFYCAVNYYEEN 146
                                       *************************998665442222 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   1.4e-16   1.3e-13       7     164 ..      25     181 ..      16     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.4e-16
                   Methyltransf_23   7 eelsdklerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae.....kakkaqkdqfdeqea 76 
                                       + ++++l+r++   ++g  vLd+GcG+G+  + lr+n     v+g D spe+   a+            +  d ++ 
  gi|336252818|ref|YP_004595925.1|  25 HTAKHALARMP--VEPGDTVLDLGCGSGYAGRALRDNKDagRVYGLDGSPEMARNAAgytddP--EVGYVVGDFDSL 97 
                                       45666777776..68999******************97668*********9888876666442..333333333577 PP

                   Methyltransf_23  77 aepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllse..plaslkedrllldwlylvpagrhisffsarsl 151
                                       ++ ++++d + ++e ++   dp+ +lr +a++l+pgG +++ +  + ++ ++ ++ ++++ + ++      +++ ++
  gi|336252818|ref|YP_004595925.1|  98 PFADDSIDHVWSMEAFYYAADPHNTLREVARILRPGGTFYCAVnyYEENVHSHEWQENIAVEMTR------WDRGQY 168
                                       77999**********************************99995566666777776666666665......9***** PP

                   Methyltransf_23 152 kelleeaGlevve 164
                                       +e++++aGl v e
  gi|336252818|ref|YP_004595925.1| 169 REAFRDAGLHVAE 181
                                       *********9876 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0     1e-13     1e-10      34     151 ..      23     138 ..      19     149 .. 0.86
   2 ?   -2.6   0.0       2.8   2.8e+03     200     218 ..     164     182 ..     143     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1e-13
                                       HHHH..HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TT CS
                   Ubie_methyltran  34 lWkk..fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanae 108
                                        W++      ++ v +g +vlD+ +G+g    +l d  ++ g+v +lD +++m + +      +   ++ +++++  
  gi|336252818|ref|YP_004595925.1|  23 HWHTakHALARMPVEPGDTVLDLGCGSGYAGRALRD-NKDAGRVYGLDGSPEMARNAAG---YTDDPEVGYVVGDFD 95 
                                       5655435567889999************87777766.5789**********99766654...444569********* PP

                                       T-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran 109 eLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                        Lpf dds D v     +   +D +++L+e+ r+l+pGG++++
  gi|336252818|ref|YP_004595925.1|  96 SLPFADDSIDHVWSMEAFYYAADPHNTLREVARILRPGGTFYC 138
                                       ************9999999***********************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.8
                                       -HHHHHHHHHHTTEEEEEE CS
                   Ubie_methyltran 200 dqetlkeliedaGfksvey 218
                                       d+ +++e ++daG++ +e 
  gi|336252818|ref|YP_004595925.1| 164 DRGQYREAFRDAGLHVAEQ 182
                                       6667888999999988765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   9.6e-14   9.6e-11       1      99 []      43     136 ..      43     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 9.6e-14
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++GcG+G   ral+++    +++g+D sp++  +a+  + + e     + +++ l  +d    +s D v++ +++ 
  gi|336252818|ref|YP_004595925.1|  43 LDLGCGSGYAGRALRDNKDAGRVYGLDGSPEMARNAAGYTDDPE-VGYVVGDFDSLPFAD----DSIDHVWSMEAFY 114
                                       8********************************44444444444.444555555554444....5************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                       + +d++ +l+++++ L+pgG +
  gi|336252818|ref|YP_004595925.1| 115 YAADPHNTLREVARILRPGGTF 136
                                       ********************75 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   2.2e-07   0.00022      26      68 ..      39      79 ..      25      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.2e-07
                   Methyltransf_32 26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekae 68
                                        tv+D+G+G gY +++l +  ++   +v+g+d + e++++a 
  gi|336252818|ref|YP_004595925.1| 39 GDTVLDLGCGSGYAGRALRD--NKDAGRVYGLDGSPEMARNAA 79
                                      679*****************..44589*********9998876 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.2e-07   0.00022      43     163 ..      19     137 ..      11     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--.EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEE CS
                              CMAS  43 LeeAqlaKldlileklelkpGmtlLdiGcGWGslvrraverydv.kvvglTlSkeqaklakkrvdeldlerkvevkl 118
                                       +ee   +  +++l ++ ++pG+t+Ld+GcG G+  r   ++ d+ +v gl  S e a+ a    d+ ++       +
  gi|336252818|ref|YP_004595925.1|  19 MEERHWHTAKHALARMPVEPGDTVLDLGCGSGYAGRALRDNKDAgRVYGLDGSPEMARNAAGYTDDPEV----GYVV 91 
                                       66677778899*********************9998888777765799999888877777666665553....3334 PP

                                       S-GGG---...--SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEE CS
                              CMAS 119 ldyedlde...kvdrvvsvgafehvgkenydtffkklkkllkedGlll 163
                                        d+  l+     +d+v s++af     + + +  +++ ++l+++G++ 
  gi|336252818|ref|YP_004595925.1|  92 GDFDSLPFaddSIDHVWSMEAFYYA-ADPH-NTLREVARILRPGGTFY 137
                                       4555554311366666666666432.2233.33566777777777765 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   5.4e-07   0.00054      10     102 ..      35     130 ..      26     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.4e-07
                              MetW  10 likpgsrvldlGcGdGellellkeekqv.dgrGleldeegvaecvakG....lsviqgdldkdlenfedksfdyvvl 81 
                                        ++pg +vldlGcG G   + l+++k+  + +Gl+ + e   ++        +  + gd   d   f+d+s d v  
  gi|336252818|ref|YP_004595925.1|  35 PVEPGDTVLDLGCGSGYAGRALRDNKDAgRVYGLDGSPEMARNAAGYTddpeVGYVVGDF--DSLPFADDSIDHVWS 109
                                       499***********************9746899998877766554332111133444444..446799999999999 PP

                              MetW  82 sqtlqatrnpkevldellrig 102
                                         ++    +p++ l+e+ ri 
  gi|336252818|ref|YP_004595925.1| 110 MEAFYYAADPHNTLREVARIL 130
                                       999999999999999999985 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 !   18.2   0.0   9.6e-07   0.00095     115     215 ..      38     136 ..      19     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.6e-07
                                       TT-EEEEET-TTSHHHHHHH.HCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEE CS
                    Methyltransf_9 115 kgrtildvGcgnGyhlwrmv.gegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsm 189
                                        g t+ld+Gcg+Gy    +   ++a  v G+d s        a   + ++d ++  +    + lp   ++ d v+sm
  gi|336252818|ref|YP_004595925.1|  38 PGDTVLDLGCGSGYAGRALRdNKDAGRVYGLDGSPEMARN--A-AGY-TDDPEVGYVVGDFDSLPFaDDSIDHVWSM 110
                                       4789**********8755542568999******9875433..2.223.355555556567999**8678******** PP

                                       S-GGG-S-HHHHHHHHHCTEEEEEEE CS
                    Methyltransf_9 190 GvlyhrrsPldhllqlkdqlvkgGel 215
                                         +y+   P ++l+++   l+ gG++
  gi|336252818|ref|YP_004595925.1| 111 EAFYYAADPHNTLREVARILRPGGTF 136
                                       ***********************986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.3e-06    0.0033      24      72 ..      31      79 ..      25     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.3e-06
                                      HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHH CS
                               MTS 24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesak 72
                                      l  +p e  ++vlDlGcG G+ g al ++++  +v  +d + +  + a 
  gi|336252818|ref|YP_004595925.1| 31 LARMPVEPGDTVLDLGCGSGYAGRALRDNKDAGRVYGLDGSPEMARNAA 79
                                      56788889999*****************999999999998876555444 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.1e-06    0.0031      40     197 ..      16     171 ..       5     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.1e-06
                                       HHHHHTTHHHHHHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE.-HHHHHHHHHHS-----TTEEE CS
                    Methyltransf_2  40 nkglqessslvakkvleafdleglkslvDvGGGtGalakaivsayPtikvivfD.lpeVveaAkehlsageeervef 115
                                        +g++e    +ak++l+ + +e+  +++D+G G+G + +a   +    +v  +D  pe +++A  +   + +++v +
  gi|336252818|ref|YP_004595925.1|  16 DRGMEERHWHTAKHALARMPVEPGDTVLDLGCGSGYAGRALRDNKDAGRVYGLDgSPEMARNAAGY---TDDPEVGY 89 
                                       58999999999******************************9998888877777447777777777...99****** PP

                                       EES-TTTS-----SEEE.EESSGGG.S-HHHHHHHHHHHHHH--TT-EEEEEE----TTS---HHHHHHHHHHHHCS CS
                    Methyltransf_2 116 vgGdffkdslPeaDail.lkrvlhD.wsdekcvklLkrvkkalpagGkvivveavlgadpsgeletelvdlimlvqt 190
                                       v Gdf   slP aD  +  ++ +   +  ++ ++ L++v + l++gG    +    +++ +++  +e +++ m    
  gi|336252818|ref|YP_004595925.1|  90 VVGDFD--SLPFADDSIdHVWSMEAfYYAADPHNTLREVARILRPGGTFYCAVNYYEENVHSHEWQENIAVEMTRWD 164
                                       ****86..***887543134433331345567788999999999999998877777777777777777788888888 PP

                                       S-----H CS
                    Methyltransf_2 191 eGkeRte 197
                                        G+ R++
  gi|336252818|ref|YP_004595925.1| 165 RGQYREA 171
                                       8887765 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.9e-06    0.0099     108     157 ..      89     139 ..      30     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.9e-06
                                       EEES-TTS-S--TT-EEEEEEES--.-SS-HHHHHHHHHHHEEEEEEEEEE CS
                    Methyltransf_8 108 vvacdlakvPledesvdvavfclsl.mgtnladflkeanrvlkvGGllkva 157
                                        v+ d+  +P +d+s+d +    ++  + + ++ l+e+ r+l++GG ++ a
  gi|336252818|ref|YP_004595925.1|  89 YVVGDFDSLPFADDSIDHVWSMEAFyYAADPHNTLREVARILRPGGTFYCA 139
                                       367899***********77655554268899****************9987 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 !   16.4   0.0   5.9e-06    0.0059      65     115 ..      30      79 ..      14     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.9e-06
                                       HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHH CS
                              PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeak 115
                                       al  + +++g+ vL++G+GsGy    l    ++ grv +++ ++e++++a 
  gi|336252818|ref|YP_004595925.1|  30 ALARMPVEPGDTVLDLGCGSGYAGRALRD-NKDAGRVYGLDGSPEMARNAA 79 
                                       44445599**************9888765.588899999999999988775 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0008       0.8     186     213 ..      33      60 ..      26      79 .. 0.75
   2 ?    4.9   0.0     0.018        18      35      60 ..     119     144 ..     109     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0008
                                       HHHS-TT-EEEETT-TTTHHHHHHHHTT CS
                       N6_N4_Mtase 186 klstkkgdivlDpFaGSGtTavaakelg 213
                                       ++  ++gd+vlD  +GSG+ ++a +  +
  gi|336252818|ref|YP_004595925.1|  33 RMPVEPGDTVLDLGCGSGYAGRALRDNK 60 
                                       666789****************998765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHEEEEEEEEEEE-CCC CS
                       N6_N4_Mtase  35 lekvlkevrrvLkddgsifiniddse 60 
                                        ++ l+ev r+L ++g++++ + + e
  gi|336252818|ref|YP_004595925.1| 119 PHNTLREVARILRPGGTFYCAVNYYE 144
                                       57899*************99876655 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.5e-05     0.034      61     110 ..      29      77 ..      16      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.5e-05
                                       TT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHH CS
                       Fibrillarin  61 kglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlre 110
                                       + l+++p+++g+ vL lG +sG +   + D  +  g+vy+++ sp + r+
  gi|336252818|ref|YP_004595925.1|  29 HALARMPVEPGDTVLDLGCGSGYAGRALRDNKD-AGRVYGLDGSPEMARN 77 
                                       56889*************************876.9***********9997 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00044      0.44      11      58 ..      29      78 ..      20     110 .. 0.73
   2 ?    1.2   0.0      0.36   3.5e+02     122     135 ..     127     140 ..     120     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00044
                                      HHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS....H CS
                              FtsJ 11 eidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm....a 58
                                      ++++++  ++pg+tv+Dlg++ G     l  +  a g+v+++D  p     a
  gi|336252818|ref|YP_004595925.1| 29 HALARMP-VEPGDTVLDLGCGSGYAGRALRDNKDA-GRVYGLDGSPEmarnA 78
                                      5666777.789************999999999765.*******966534440 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.36
                                       CCCCECCCEEEECC CS
                              FtsJ 122 lkllkpggtfvlki 135
                                        ++l+pggtf + +
  gi|336252818|ref|YP_004595925.1| 127 ARILRPGGTFYCAV 140
                                       479********987 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00031      0.31     159     176 ..      36      53 ..      24      80 .. 0.72
   2 ?   -3.7   0.0         6     6e+03     196     215 ..     139     158 ..     125     165 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                              PrmA 159 vkegeevlDvGtGSGiLa 176
                                       v++g++vlD+G+GSG   
  gi|336252818|ref|YP_004595925.1|  36 VEPGDTVLDLGCGSGYAG 53 
                                       8999***********654 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6
                              PrmA 196 AvkvakeNaelNkveaklev 215
                                       Av+  +eN++  + ++++ v
  gi|336252818|ref|YP_004595925.1| 139 AVNYYEENVHSHEWQENIAV 158
                                       55555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1665.92
//
Query:       gi|336252819|ref|YP_004595926.1|  [L=192]
Description: hypothetical protein Halxa_1414 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00028   20.3   0.0    0.00037   19.9   0.0    1.1  1  ATPase     KaiC
  ------ inclusion threshold ------
      0.032   14.8   0.1      0.072   13.6   0.0    1.6  2  SIP        Siderophore-interacting protein
      0.051   14.2   0.0       0.14   12.8   0.0    1.8  1  Dabb       Stress responsive A/B Barrel Domain
        3.3    7.3   5.8        3.4    7.3   1.7    2.9  2  EF-hand_5  EF hand


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.3e-08   0.00037      51     189 ..      45     184 ..      36     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.3e-08
                            ATPase  51 gvfvtveepaedlrenakslGwdlekleeegklaiidasesaeesaee..kdkedleelieelaeaikeika.krvv 124
                                        + +++  +a+++r++ +  ++d e  e  + l i   ++ ++ +a +     +d++ +++++++ +++     r+ 
  gi|336252819|ref|YP_004595926.1|  45 FLVISTRTTAREVRQKLEYYDVDEECAEILDTLSIERGYSRRKSDAVHyvAAPDDIDGIVSQIESFLADNDGkLRLS 121
                                       57899999***************99999999999999999998877779999*************999887637*** PP

                            ATPase 125 iDsitglayeekeavaReilrqlvrvlkklgvTail.vsekssseeaaggygveefivdgvivLdl 189
                                        Ds+t lay++ ++ a e + ++++ l++++ + ++ vse +++ e + +++    + dgvi Ld 
  gi|336252819|ref|YP_004595926.1| 122 FDSVTELAYYAGDEAAIEAVERILELLEEYDAVGLFhVSEEPHDPEIVDRFR--A-LFDGVIDLDE 184
                                       ***********************************96666555544444443..3.5588888875 PP

>> SIP  Siderophore-interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.4   1.1e+04      92     115 ..      70      93 ..      67      93 .. 0.73
   2 ?   13.6   0.0   1.6e-05     0.072       5      38 ..     130     162 ..     126     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.4
                               SIP  92 vkalRrhlvkergldrkqvaamgY 115
                                       + ++ + l  erg+ r++ +a+ Y
  gi|336252819|ref|YP_004595926.1|  70 CAEILDTLSIERGYSRRKSDAVHY 93 
                                       556666777889999988887766 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.6e-05
                               SIP   5 llagDeTAlPAiaaiLeelpadaqvravievpda 38 
                                       ++agDe+A+ A+++iLe l ++  +  +++v+++
  gi|336252819|ref|YP_004595926.1| 130 YYAGDEAAIEAVERILELL-EEYDAVGLFHVSEE 162
                                       689***************9.77777777777765 PP

>> Dabb  Stress responsive A/B Barrel Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.2e-05      0.14      59      89 ..     120     150 ..     102     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                                       EEESSHHHHHHHHTSHHHHHHHHHHHHTEEE CS
                              Dabb  59 seFeseedlkaYlehpahvefvelvkplvek 89 
                                         F+s+ +l++Y+++ a  e+ve++ +l+e+
  gi|336252819|ref|YP_004595926.1| 120 LSFDSVTELAYYAGDEAAIEAVERILELLEE 150
                                       57**************************996 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.14   6.4e+02      10      16 ..     112     118 ..     112     118 .. 0.85
   2 ?    7.3   1.7   0.00077       3.4       8      19 ..     180     191 ..     178     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.14
                                       SS-SSCE CS
                         EF-hand_5  10 lNgDGkI 16 
                                       +++DGk+
  gi|336252819|ref|YP_004595926.1| 112 ADNDGKL 118
                                       69***96 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00077
                                       H-SS-SSCE-HH CS
                         EF-hand_5   8 iDlNgDGkIske 19 
                                       iDl+ DG I+++
  gi|336252819|ref|YP_004595926.1| 180 IDLDEDGSIDAD 191
                                       9*********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1571.19
//
Query:       gi|336252820|ref|YP_004595927.1|  [L=260]
Description: hypothetical protein Halxa_1415 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        2.2    8.0   5.4        3.3    7.4   0.3    2.9  3  DUF3515   Protein of unknown function (DUF3515)


Domain annotation for each model (and alignments):
>> DUF3515  Protein of unknown function (DUF3515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2     0.012   2.2e+02      29      55 ..      14      41 ..       4      62 .. 0.75
   2 ?   -0.8   0.0     0.062   1.1e+03      45      82 ..      59      97 ..      44      98 .. 0.80
   3 ?    7.4   0.3   0.00018       3.3      26      76 ..     202     254 ..     188     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.012
                           DUF3515 29 lasvpApkadsaeCaallaalPdelg.d 55
                                      + + +Ap+a+  +C+   + lP  l+ d
  gi|336252820|ref|YP_004595927.1| 14 VRESQAPEATVFDCERDFETLPPALAeD 41
                                      34678*****************999634 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.062
                           DUF3515 45 llaalPdelgdlrraeladpap.agtaaWgepegeevvl 82
                                      l ++ P+ l+++ +++l+   p +g  +W+++ + +vvl
  gi|336252820|ref|YP_004595927.1| 59 LPDDAPTLLARYASSDLTIGMPgDGSIVWTRQTEPPVVL 97
                                      557789999999999998877745788999998888887 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00018
                           DUF3515  26 pvalasvpApkadsaeCaallaa..lPdelgdlrraeladpapagtaaWgepe 76 
                                        va ++++  +a++ +Caa+ +a  lP+ ++ l++ + +d  p+ +  W+e+ 
  gi|336252820|ref|YP_004595927.1| 202 AVARGETDFADATELACAAIKHAieLPAPFAALDTDAYRDHGPEYAVRWAEKT 254
                                       5777788888999999****886559***********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.43u 0.19s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2187.49
//
Query:       gi|336252821|ref|YP_004595928.1|  [L=396]
Description: hypothetical protein Halxa_1416 [Halopiger xanaduensis SH-6]
Scores for 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-32  111.2   4.2    5.6e-16   59.0   0.0    2.7  3  DUF2072        Zn-ribbon containing protein
  ------ inclusion threshold ------
       0.19   11.8   1.3       0.37   10.8   1.3    1.4  1  DUF1451        Zinc-ribbon containing domain
        0.2   11.7   0.3       0.32   11.0   0.3    1.3  1  HypA           Hydrogenase/urease nickel incorporation, metal
       0.22   11.7   3.1       0.46   10.6   3.1    1.5  1  Zn-ribbon_8    Zinc ribbon domain
       0.38   10.7   1.0       0.66   10.0   1.0    1.4  1  zf-C2HC_2      zinc-finger of a C2HC-type
       0.72    9.9   3.1          2    8.4   3.1    1.7  1  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi
        1.2    9.0   5.0        2.3    8.1   5.0    1.5  1  zinc_ribbon_2  zinc-ribbon domain
        7.7    7.2   5.1        2.8    8.6   0.6    2.2  2  zf-C2H2        Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.5   1.5e-17   3.3e-14       1      53 [.       2      54 ..       2     132 .. 0.72
   2 ?   -3.1   0.2       3.9   8.7e+03      57      62 ..     217     222 ..     189     260 .. 0.50
   3 !   59.0   0.0   2.5e-19   5.6e-16      75     132 ..     335     392 ..     270     393 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1.5e-17
                           DUF2072  1 PHkCtkCekvfedgskeilkGCpsCGgkkFlyvkeeekkedvseekeelvaea 53
                                      PH+Ct+C+++f dgske+l+GCp CGg+kF++    + +++ s+++ ++++ a
  gi|336252821|ref|YP_004595928.1|  2 PHQCTNCGRTFPDGSKEMLSGCPDCGGNKFQFTPSGSGSNSGSAATGSSDTAA 54
                                      9*******************************887776655554444333333 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.9
                           DUF2072  57 ieevld 62 
                                       +++v+ 
  gi|336252821|ref|YP_004595928.1| 217 RSDVVS 222
                                       222222 PP

  == domain 3  score: 59.0 bits;  conditional E-value: 2.5e-19
                           DUF2072  75 ekekaekekeeedrvesvrilepGsYelNlekLlerdelvmalkeegkYvvdlpsvlk 132
                                       e + +e ++e ++++es++i++pG+YelNl++L++r+e +++l+e+g+Yv+d+p++ +
  gi|336252821|ref|YP_004595928.1| 335 EPSIEELREELNKQFESIKIVNPGQYELNLMELYNREEYIISLQEDGRYVIDVPDSWR 392
                                       45567788999******************************************98765 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.3   0.00017      0.37     116     144 ..       4      32 ..       3      35 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                           DUF1451 116 vCekCgkelalkkteeippCpkCgateFr 144
                                       +C++Cg++    + e ++ Cp+Cg+++F+
  gi|336252821|ref|YP_004595928.1|   4 QCTNCGRTFPDGSKEMLSGCPDCGGNKFQ 32 
                                       6***************************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 ?   11.0   0.3   0.00014      0.32      72      99 ..       4      33 ..       1      39 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                      EETTTS-EEECHHH..HHS-TTTSSS-EEE CS
                              HypA 72 rCreCgkefeleek..alrCpkCgsadvei 99
                                      +C++Cg++f   +k     Cp+Cg++++++
  gi|336252821|ref|YP_004595928.1|  4 QCTNCGRTFPDGSKemLSGCPDCGGNKFQF 33
                                      7*********665434558******99886 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.1   0.00021      0.46       7      35 ..       4      30 ..       3      32 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.e 35
                                      +C++Cg++f    +   + l  CP+Cg+ +
  gi|336252821|ref|YP_004595928.1|  4 QCTNCGRTFPDGSK---EMLSGCPDCGGnK 30
                                      6********94443...33555*****955 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 ?   10.0   1.0   0.00029      0.66       4      12 ..       4      12 ..       3      13 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00029
                         zf-C2HC_2  4 pCpkCgRsF 12
                                      +C +CgR+F
  gi|336252821|ref|YP_004595928.1|  4 QCTNCGRTF 12
                                      9******** 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 ?    8.4   3.1   0.00089         2      12      48 ..       4      38 ..       2      39 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00089
                                      E-TTTTTTSEETTE.......E-TTTTTSSEEE-HHHH CS
                         Anti-TRAP 12 kCdaCngsGkiepeeprasl.eCPkCsGkglipTaqGq 48
                                      +C +C   G+  p+  +  l  CP+C+G+++  T  G+
  gi|336252821|ref|YP_004595928.1|  4 QCTNC---GRTFPDGSKEMLsGCPDCGGNKFQFTPSGS 38
                                      45555...55555533333326*********9998885 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   5.0     0.001       2.3       2      20 ..       5      27 ..       4      30 .. 0.96

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.001
                     zinc_ribbon_2  2 CpnCGaelqdnakF....CpyCG 20
                                      C+nCG++ +d++k     Cp CG
  gi|336252821|ref|YP_004595928.1|  5 CTNCGRTFPDGSKEmlsgCPDCG 27
                                      **********************9 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.6    0.0012       2.8       1      12 [.       3      14 ..       3      17 .. 0.90
   2 ?    0.2   0.3      0.57   1.3e+03       3       7 ..      23      27 ..      23      36 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0012
                                      EEETTTTEEESS CS
                           zf-C2H2  1 ykCpdCgksFkr 12
                                      ++C+ Cg++F++
  gi|336252821|ref|YP_004595928.1|  3 HQCTNCGRTFPD 14
                                      79********86 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.57
                                      ETTTT CS
                           zf-C2H2  3 CpdCg 7 
                                      CpdCg
  gi|336252821|ref|YP_004595928.1| 23 CPDCG 27
                                      ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1156  (0.0644765); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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):               8  [number of targets reported over threshold]
# CPU time: 0.73u 0.26s 00:00:00.99 Elapsed: 00:00:00.39
# Mc/sec: 3063.14
//
Query:       gi|336252822|ref|YP_004595929.1|  [L=134]
Description: hypothetical protein Halxa_1417 [Halopiger xanaduensis SH-6]
Scores for 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-45  152.7   0.5    2.9e-45  152.4   0.5    1.1  1  DUF2073   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2073  Uncharacterized protein conserved in archaea (DUF2073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   0.5   1.6e-49   2.9e-45       1     105 []      27     132 ..      27     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 1.6e-49
                           DUF2073   1 lekmtsmekirlildkvkegkivvlEkgLtpeeeakliettmeeikpdeFsGieietypkkek.dkgllekllgkke 76 
                                       +++m++mekir+ild v++g+iv+lE+gLtp+ee++lie+tm+ei+pdeF+Gieietypk+ + d++ll++++g +e
  gi|336252822|ref|YP_004595929.1|  27 MQDMATMEKIRMILDGVHDGNIVILEEGLTPDEESRLIEVTMSEISPDEFNGIEIETYPKSGTrDSSLLGRIMGGDE 103
                                       689**********************************************************9989************ PP

                           DUF2073  77 seerltvigPanqlktlkkdkdlisalvs 105
                                       s+ +ltvigPanq++tl+kd++lisalvs
  gi|336252822|ref|YP_004595929.1| 104 SDAKLTVIGPANQIETLHKDETLISALVS 132
                                       ***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1094.41
//
Query:       gi|336252823|ref|YP_004595930.1|  [L=212]
Description: small GTP-binding protein [Halopiger xanaduensis SH-6]
Scores for 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   56.5   0.0    3.6e-15   56.0   0.0    1.2  1  MMR_HSR1      50S ribosome-binding GTPase
    1.4e-11   44.3   0.4     0.0001   21.9   0.0    3.2  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    5.9e-08   32.4   0.1    0.00015   21.3   0.1    2.5  3  Arf           ADP-ribosylation factor family
    9.4e-06   25.2   0.1    6.3e-05   22.5   0.1    2.2  1  FeoB_N        Ferrous iron transport protein B
    1.7e-05   24.8   0.0       0.16   11.9   0.0    2.2  2  RsgA_GTPase   RsgA GTPase
    0.00011   21.6   0.0    0.00019   20.8   0.0    1.3  1  Septin        Septin
    0.00017   21.6   0.0     0.0003   20.8   0.0    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    0.00023   20.4   0.0    0.00038   19.7   0.0    1.3  1  NB-ARC        NB-ARC domain
    0.00035   20.1   0.0      0.072   12.5   0.0    2.2  2  SRPRB         Signal recognition particle receptor beta subun
    0.00087   19.7   0.1      0.021   15.2   0.0    2.3  2  AAA           ATPase family associated with various cellular 
      0.001   18.7   0.0       0.43   10.2   0.0    2.5  2  Ras           Ras family
     0.0011   19.6   0.0      0.004   17.7   0.0    2.0  1  AAA_18        AAA domain
     0.0013   18.9   0.0      0.012   15.8   0.0    2.1  2  Roc           Ras of Complex, Roc, domain of DAPkinase
     0.0015   18.3   0.0     0.0028   17.4   0.0    1.7  1  AAA_24        AAA domain
     0.0048   17.3   0.0     0.0088   16.4   0.0    1.6  1  AAA_16        AAA ATPase domain
     0.0049   17.1   0.4       0.02   15.2   0.4    2.0  1  AAA_28        AAA domain
     0.0053   16.7   0.0      0.011   15.6   0.0    1.8  1  ATPase_2      ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
       0.01   15.9   0.0       0.89    9.6   0.0    2.3  2  Dynamin_N     Dynamin family
      0.011   16.1   0.0      0.017   15.5   0.0    1.4  1  RNA_helicase  RNA helicase
      0.012   16.2   0.0      0.017   15.6   0.0    1.4  1  ABC_tran      ABC transporter
      0.024   14.2   0.5        6.6    6.3   0.1    2.4  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.036   13.7   0.2      0.089   12.4   0.2    1.7  1  AAA_25        AAA domain
      0.038   13.7   0.0      0.074   12.8   0.0    1.5  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.064   13.2   0.0       0.11   12.5   0.0    1.3  1  NACHT         NACHT domain
       0.12   11.7   0.0        0.2   11.1   0.0    1.4  1  TniB          Bacterial TniB protein
       0.13   11.4   0.0       0.21   10.6   0.0    1.3  1  Parvo_NS1     Parvovirus non-structural protein NS1
       0.14   12.5   0.0       0.28   11.4   0.0    1.7  1  AAA_22        AAA domain
       0.16   11.3   0.0        1.2    8.4   0.0    2.1  1  Gtr1_RagA     Gtr1/RagA G protein conserved region


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   5.7e-18   3.6e-15       1     114 []      26     169 ..      26     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 5.7e-18
                                       EEEEEESTTSSHHHHHHHHHTS.....TEEESSSTTSSSSE.EEEEEE....ETTEEEEEEECGGC........... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.....kaivsdkpgtTrdi.negrvk....lkgkeielvDtpGl........... 56 
                                       +++i+G pN+GK+tL n++ ++     +   s+ p  Tr   ++++v+     k+  i +vDtpG+           
  gi|336252823|ref|YP_004595930.1|  26 RIGIYGPPNAGKTTLANRIARDwtgdaVGTESHVPHETRRArRKENVEierdGKKVTIDIVDTPGVttkvdyeeftd 102
                                       69*****************97444433457799*****99944445655443223679*******866666555555 PP

                                       .......SS.HHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  57 .......ie.gaseekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                              i  + +  +g+++a++ l+e +d +++v+d++e+ +++++  l  ++e+++ p+++ +nk
  gi|336252823|ref|YP_004595930.1| 103 emdeddaIRrSREATEGVAEAMHWLREdVDGVIYVLDSAEDPITQVNTMLIGIIESRDLPVLIFANK 169
                                       54444433323333337777777777779********88889****999999999999999999997 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 !   18.4   0.1   1.9e-06    0.0012       5      80 ..      26      91 ..      22     106 .. 0.79
   2 !   21.9   0.0   1.6e-07    0.0001      93     188 ..     130     207 ..     121     212 .] 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                                      EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSS CS
                          GTP_EFTU  5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGH 80
                                       igi g  ++GKtTL  r+  +   ++  +e           ++E +r      +++++e+++kk +i ++DtPG 
  gi|336252823|ref|YP_004595930.1| 26 RIGIYGPPNAGKTTLANRIARDWTGDAVGTE--------SHVPHETRRAR--RKENVEIERDGKKVTIDIVDTPGV 91
                                      699*****************98888777444........34678888765..5677777777*************4 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.6e-07
                                       T-SEEEEEEETTTBSTHHHHHHH.HHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTE CS
                          GTP_EFTU  93 vlDgavlvvdaveGvepqteevl.rlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekev 168
                                        +Dg++ v+d++e++ +q +++l  ++ ++++p+ +f NK+D  ++++k+i ++  q+                   
  gi|336252823|ref|YP_004595930.1| 130 DVDGVIYVLDSAEDPITQVNTMLiGIIESRDLPVLIFANKIDLDDSSVKRIEDAFPQHK------------------ 188
                                       68************99999987526888999*************999999888776443.................. PP

                                       EEEEEBTTTTBTHHHHHHHH CS
                          GTP_EFTU 169 pvvfgSalkgegvktlleal 188
                                         ++ Sa++g++++++ + +
  gi|336252823|ref|YP_004595930.1| 189 -TIPLSAKEGDNMDEVYDNI 207
                                       .4555555555555555555 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0016         1       3      41 ..      13      51 ..      11      92 .. 0.85
   2 ?   -1.5   0.0       2.2   1.4e+03     161     174 ..     117     130 ..     111     131 .. 0.83
   3 !   21.3   0.1   2.4e-07   0.00015      80     131 ..     129     176 ..     123     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                                      HHHHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHSSCEE CS
                               Arf  3 silaklklkkkelrilllGLDnaGKtTilkklkleelvt 41
                                      ++ ++l++++   ri + G  naGKtT+ +++  + + +
  gi|336252823|ref|YP_004595930.1| 13 RVTDRLFSEQEPKRIGIYGPPNAGKTTLANRIARDWTGD 51
                                      6778899988889999*************9998876555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                                       TBTHHHHHHHHHHH CS
                               Arf 161 geglkeglewlses 174
                                        eg+ e+++wl e+
  gi|336252823|ref|YP_004595930.1| 117 TEGVAEAMHWLRED 130
                                       699********876 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 2.4e-07
                                       TTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS CS
                               Arf  80 ektdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpeal 131
                                       e++d+vi+v+Dsa+ + +++ ++ L  ++   e ++ ++l++aNK+Dl ++ 
  gi|336252823|ref|YP_004595930.1| 129 EDVDGVIYVLDSAE-DPITQVNTMLIGII---ESRDLPVLIFANKIDLDDSS 176
                                       579*********97.56777777776666...567889**********8764 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 !   22.5   0.1   9.9e-08   6.3e-05       3     155 ..      27     206 ..      25     207 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.9e-08
                                       EEEEESTTSSHHHHHHHHHT..TSEEEEESTTSSSEEEEEEEEE........TTEEEEEEE----.....SSS.... CS
                            FeoB_N   3 valvGnpnvGkttlfnaltg..akqkvgNwpGvtvekkegklkl........kgkeveivDlPGi.....Ysl.... 60 
                                       + + G pn+Gkttl n+++   +   vg  + v  e ++++ k         k+ +++ivD PG+     Y+     
  gi|336252823|ref|YP_004595930.1|  27 IGIYGPPNAGKTTLANRIARdwTGDAVGTESHVPHETRRARRKEnveierdgKKVTIDIVDTPGVttkvdYEEftde 103
                                       7789*************986222355666555555544443333233333334467899*****9555554337766 PP

                                       ........SSSSHHHHHHHHH.HHCTSSSEEEEEEEGGG..HHHHHHHHHHHHHTT.SSEEEEEETHHHHHHTTEEE CS
                            FeoB_N  61 ........sayseeekvardf.lleeepdvvvnvvdatn..lernLyLtlqllelg.vpvvlalnmideaekkgiei 125
                                                +    e va+ +  l+e++d v+ v+d+++  + +  ++++ ++e + +pv++  n+id  +++  +i
  gi|336252823|ref|YP_004595930.1| 104 mdeddairRSREATEGVAEAMhWLREDVDGVIYVLDSAEdpITQVNTMLIGIIESRdLPVLIFANKIDLDDSSVKRI 180
                                       666666543333334555443156999*********9865577777777888887548999999****999998888 PP

                                       -HHHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N 126 dlkkLsekLgvpvvktsakkkegieellka 155
                                       + +  +     + +++sak++++++e+ ++
  gi|336252823|ref|YP_004595930.1| 181 EDAFPQ----HKTIPLSAKEGDNMDEVYDN 206
                                       765433....46778888888888887765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00025      0.16      90     162 ..      15      92 ..       4      97 .. 0.67
   2 !   10.9   0.0   0.00048      0.31      32      98 ..     145     208 ..     124     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                                       HHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTE.....EEESS-SS CS
                       RsgA_GTPase  90 leelkellkdktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegg.....lliDtPGf 161
                                       +++l ++ + k + + G+  +GK+tL n+++ + +     + ++  +     ++ e +e++++g      ++DtPG+
  gi|336252823|ref|YP_004595930.1|  15 TDRLFSEQEPKRIGIYGPPNAGKTTLANRIARDWTGDAVGTESHVPHETRRARRKENVEIERDGkkvtiDIVDTPGV 91 
                                       5667777777888899***************98443333333333333333455667778776633333599****8 PP

                                       S CS
                       RsgA_GTPase 162 r 162
                                       +
  gi|336252823|ref|YP_004595930.1|  92 T 92 
                                       6 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00048
                                       HHHHHHHHH.HHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCT CS
                       RsgA_GTPase  32 lnlldrfLv.laeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellk 98 
                                         +++ +L+ ++e+++++++i  nKiDl +++   +++++++ +   +++ +sak++++++e+ ++++
  gi|336252823|ref|YP_004595930.1| 145 ITQVNTMLIgIIESRDLPVLIFANKIDLDDSSV--KRIEDAFPQH--KTIPLSAKEGDNMDEVYDNIA 208
                                       3445555552789999************88766..8888888887..888899999999999988776 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.9e-07   0.00019       9      80 ..      29      99 ..      26     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.9e-07
                                      EEEBTTSSCCCCCCTTSSSS------------------S-EEEEEEEEETTCEEEEEEEE---BSSSSSHHC CS
                            Septin  9 vvGesglGkttlintlfetdlieeekleeasekkkktveikkkkvvieedgvklnltviDtpgfGdavdnsk 80
                                      + G    Gkttl n + ++   ++  +e++   +++    +k++v+ie dg k+++ ++Dtpg   +vd ++
  gi|336252823|ref|YP_004595930.1| 29 IYGPPNAGKTTLANRIARDWTGDAVGTESH-VPHETRRARRKENVEIERDGKKVTIDIVDTPGVTTKVDYEE 99
                                      5688889********998887777555433.34555556678999*******************99999765 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 !   20.8   0.0   4.7e-07    0.0003      56     103 ..     161     210 ..     126     212 .] 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.7e-07
                      MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare...pnsvviSaekelnldeLkekiwee 103
                                       +p+l++ NKiDl +++++++++     ++++++Sa+++ n+de+ ++i e+
  gi|336252823|ref|YP_004595930.1| 161 LPVLIFANKIDL-DDSSVKRIEDAfpqHKTIPLSAKEGDNMDEVYDNIAEY 210
                                       699********9.6666677776443389*****************99876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   5.9e-07   0.00038       2      43 ..       8      47 ..       7      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.9e-07
                                      HHHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  2 eksvekviekLlekdelqslvvalvGmgGvGKttlakqilnk 43
                                      ++s+ +v ++L+ ++e++   ++++G +  GKttla+ i ++
  gi|336252823|ref|YP_004595930.1|  8 KDSISRVTDRLFSEQEPK--RIGIYGPPNAGKTTLANRIARD 47
                                      57899*************..9******************988 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 !   12.5   0.0   0.00011     0.072       5      59 ..      26      91 ..      22     112 .. 0.64
   2 ?    5.5   0.0     0.016        10      73     123 ..     128     171 ..     120     185 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                      EEEEE-STTSSHHHHHHHHHHS.....S---B---SS-EEETTG.........GGTT-SEEEETT- CS
                             SRPRB  5 avllvGlsdsGKTslftrLttd.....svkktvtSqessaalkv......ksekgskltliDfPGh 59
                                      ++ + G+ ++GKT+l +r+  d       +++ +  e+  a +       ++ k+ +++++D PG 
  gi|336252823|ref|YP_004595930.1| 26 RIGIYGPPNAGKTTLANRIARDwtgdaVGTESHVPHETRRARRKenveieRDGKKVTIDIVDTPGV 91
                                      56699****************965544222222333333333334444444556667778999995 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.016
                                       HGGEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TT CS
                             SRPRB  73 ksslkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqe 123
                                       ++ + g+++v+DS+ dp  +++v  +l+ i+         +++li  nK +
  gi|336252823|ref|YP_004595930.1| 128 REDVDGVIYVLDSAEDP--ITQVNTMLIGIIESRD-----LPVLIFANKID 171
                                       56799*********998..6777777777654433.....56666666655 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   3.3e-05     0.021       3      22 ..      29      48 ..      27      86 .. 0.85
   2 ?    2.3   0.1      0.33   2.1e+02      64     117 ..     104     175 ..     100     191 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.3e-05
                                      EESSTTSSHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel 22
                                      +yGpp  GKT+la+ +a+++
  gi|336252823|ref|YP_004595930.1| 29 IYGPPNAGKTTLANRIARDW 48
                                      7****************986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.33
                                       EETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS....................SSTEEEEEEESSGGGSTH CS
                               AAA  64 iDEidalaksrsgseseeeervvnqLlteldgvkkk....................eskvivigatnrpdkldp 117
                                       +DE da+ +sr  +++e   +++  L + +dgv                       ++++ v++ +n++d  d+
  gi|336252823|ref|YP_004595930.1| 104 MDEDDAIRRSR--EATEGVAEAMHWLREDVDGVIYVldsaedpitqvntmligiieSRDLPVLIFANKIDLDDS 175
                                       46666666666..5555555555556555555544466666666666555555555555677777777665555 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0      0.01       6.4       6      57 ..      31      90 ..      26     108 .. 0.59
   2 !   10.2   0.0   0.00067      0.43      97     158 ..     155     209 ..     121     211 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.01
                                      ESTTSSHHHHHHHHHHSSCSSSC..TTTSSEE......EEEEEEEETTEEEEEEEEEETT CS
                               Ras  6 GdsavGKtslllrfvkdkFkeey..esTigvd......fytkeievdgkevkleiwDTAG 57
                                      G  + GKt+l +r ++d   +    es +  +      + + eie dgk+v+++i DT G
  gi|336252823|ref|YP_004595930.1| 31 GPPNAGKTTLANRIARDWTGDAVgtESHVPHEtrrarrKENVEIERDGKKVTIDIVDTPG 90
                                      55566777777665554332222001112112222222334456667***********99 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00067
                                       HHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHHHHHHHH CS
                               Ras  97 ikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAktnenveeafeellr 158
                                       i +   +++p+++ +nK+Dl+++ + + e++  + +++    +  SAk+  n++e+++++++
  gi|336252823|ref|YP_004595930.1| 155 IIES--RDLPVLIFANKIDLDDSSVKRIEDA--FPQHKT---IPLSAKEGDNMDEVYDNIAE 209
                                       3333..469************8544444443..444444...458***********999876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   6.2e-06     0.004       1      59 [.      27     111 ..      27     147 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.2e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskr..lgf...........................gvnlrdvakenglllevdpealde 48 
                                       I++ G+p +GKttla+++++   +                               + +d++   g  + vd e  + 
  gi|336252823|ref|YP_004595930.1|  27 IGIYGPPNAGKTTLANRIARDwtG-DavgteshvphetrrarrkenveierdgKKVTIDIVDTPGVTTKVDYE--EF 100
                                       89****************665320.133334444445555555555688888766667777777777777777..55 PP

                            AAA_18  49 skrldedkldk 59 
                                       ++++ded   +
  gi|336252823|ref|YP_004595930.1| 101 TDEMDEDDAIR 111
                                       55555555332 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.8e-05     0.012       2      66 ..      27      91 ..      26     101 .. 0.89
   2 ?    0.8   0.0      0.84   5.4e+02      82     119 ..     133     171 ..     116     172 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-05
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SG CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGq 66
                                      + + G  ++GKt+l++r+ +d   +   +   v   t+++ + ++ve +++ kkv+++i Dt G 
  gi|336252823|ref|YP_004595930.1| 27 IGIYGPPNAGKTTLANRIARDWTGDAVGTESHVPHETRRARRKENVEIERDGKKVTIDIVDTPGV 91
                                      56789****************99999999999999999998899999999************985 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.84
                                       EEEEEEEGHHH..HCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                               Roc  82 lailvydsrss..enlkeWlkelkkvagkspvilvgnkiD 119
                                        +i+v+ds ++  +++++ l  + + +++ pv++ +nkiD
  gi|336252823|ref|YP_004595930.1| 133 GVIYVLDSAEDpiTQVNTMLIGIIE-SRDLPVLIFANKID 171
                                       5666666555422344433333322.3456999999**99 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.4e-06    0.0028       2      22 ..      24      44 ..      23     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.4e-06
                            AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                      +++i iyGp+ +GKTtla+++
  gi|336252823|ref|YP_004595930.1| 24 PKRIGIYGPPNAGKTTLANRI 44
                                      689***************998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.4e-05    0.0088      21      62 ..      21      58 ..       5     189 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-05
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcdq 62
                                      +++p  + ++G++  GK++l+++++r +++d + +      +
  gi|336252823|ref|YP_004595930.1| 21 EQEPKRIGIYGPPNAGKTTLANRIARDWTGDAVGT----ESH 58
                                      45558899**********************93222....222 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   3.1e-05      0.02       1      40 [.      26      73 ..      26     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-05
                            AAA_28  1 kivitGgestGKTtlleaLaar......gyp.vv.pEaareileekla 40
                                      +i i G++ +GKTtl++++a++      g++ +v +E+ r   +e+ +
  gi|336252823|ref|YP_004595930.1| 26 RIGIYGPPNAGKTTLANRIARDwtgdavGTEsHVpHETRRARRKENVE 73
                                      5789****************7766666666633356766666666654 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 !   15.6   0.0   1.8e-05     0.011      17      48 ..      21      52 ..       8     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
                          ATPase_2 17 repneiyfiYGpegsGKtaLlkeiienledkd 48
                                      +++ + + iYGp + GKt+L ++i+       
  gi|336252823|ref|YP_004595930.1| 21 EQEPKRIGIYGPPNAGKTTLANRIARDWTGDA 52
                                      44455567***************998765444 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.077        49       1      19 [.      27      45 ..      27      48 .. 0.87
   2 ?    9.6   0.0    0.0014      0.89     100     147 ..      80     149 ..      57     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.077
                                      EEEEEBTTTTHHHHHHHHH CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLl 19
                                      i + G  ++GK++++n + 
  gi|336252823|ref|YP_004595930.1| 27 IGIYGPPNAGKTTLANRIA 45
                                      6788999*********997 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0014
                                       S-SEEEEE---B-SSSGTTS.....................HHHHHHH.STTEEEEEEEETTS-CCC-CH CS
                         Dynamin_N 100 vkgltlvDlPGldsvnkrdq.....................elvkeyi.kkadiilavtsanhdlsnsea 147
                                       + ++ +vD+PG++   + ++                     + +++ + ++ d +++v+++  d  ++ +
  gi|336252823|ref|YP_004595930.1|  80 KVTIDIVDTPGVTTKVDYEEftdemdeddairrsreategvAEAMHWLrEDVDGVIYVLDSAEDPITQVN 149
                                       56789*******9977766678999999999999999998866666666899999999877766555544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   2.7e-05     0.017       3      26 ..      29      52 ..      27     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-05
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkkl 26
                                      +yGp++ GK+tla+++a++++++ 
  gi|336252823|ref|YP_004595930.1| 29 IYGPPNAGKTTLANRIARDWTGDA 52
                                      8******************98655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   2.7e-05     0.017      10      63 ..      23      73 ..      16     152 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.7e-05
                                      TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigv 63
                                      e ++++i G+  aGK+tL++ +a+    t + +  +++  +e +++  rke   
  gi|336252823|ref|YP_004595930.1| 23 EPKRIGIYGPPNAGKTTLANRIARDW--TGDAVGTESHVPHE-TRRARRKENVE 73
                                      5689*******************985..55555444444433.33333333322 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 ?    5.9   0.0     0.014       8.7       3      23 ..      27      47 ..      25      55 .. 0.83
   2 ?    6.3   0.1      0.01       6.6      92     161 ..     119     179 ..     115     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                                      EEEEESTTCCHHHHHHHHHCT CS
                              cobW  3 tvltGflGsGKTtLlnhllen 23
                                      +++ G++ +GKTtL n++ ++
  gi|336252823|ref|YP_004595930.1| 27 IGIYGPPNAGKTTLANRIARD 47
                                      57899**********999865 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.01
                                       TTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSE...EEEE-HHHHCHC..HHH CS
                              cobW  92 GlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadl...lvlnKtDlldeeallek 161
                                       G+ae++ +         +  +d+v++v+D++  e+  ++ ++ +   ++  dl   +  nK+Dl d++  +++
  gi|336252823|ref|YP_004595930.1| 119 GVAEAMHW--------LREDVDGVIYVLDSA--EDPITQVNTMLIGIIESRDLpvlIFANKIDLDDSS--VKR 179
                                       55555555........36789*********4..46777788888888888886322667****98777..334 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00014     0.089      38      69 ..      29      63 ..      23     149 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                            AAA_25 38 laGapgtGKttlaldlalavatGkpwlg.....pvap 69
                                      ++G+p +GKttla  +a +++ +    g     p+++
  gi|336252823|ref|YP_004595930.1| 29 IYGPPNAGKTTLANRIARDWTGDA--VGteshvPHET 63
                                      79******************9433..23344344333 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   0.00012     0.074      35      59 ..      26      50 ..       7      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                            RuvB_N 35 hvllyGpPGlGkttlakiiakelgv 59
                                       + +yGpP  Gkttla+ ia++   
  gi|336252823|ref|YP_004595930.1| 26 RIGIYGPPNAGKTTLANRIARDWTG 50
                                      5779****************98755 PP

>> NACHT  NACHT domain
   #    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       5      31 ..      29      55 ..      25      77 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                                      EEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                             NACHT  5 lqGeaGsGKTtLlqklalawaegklpq 31
                                      + G++  GKTtL+ ++a++w  +    
  gi|336252823|ref|YP_004595930.1| 29 IYGPPNAGKTTLANRIARDWTGDAVGT 55
                                      7899999*************9877555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00031       0.2      32      69 ..      21      58 ..       5      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                              TniB 32 rkrmpnlllvGdsnnGKtmivekFarlhppekdedaek 69
                                      +++++ + ++G++n GKt+++++ ar+ + +   ++++
  gi|336252823|ref|YP_004595930.1| 21 EQEPKRIGIYGPPNAGKTTLANRIARDWTGDAVGTESH 58
                                      55667799***************999877666555555 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 ?   10.6   0.0   0.00033      0.21     117     136 ..      27      46 ..      14      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       +++yGp+n Gkt la+ Ia+
  gi|336252823|ref|YP_004595930.1|  27 IGIYGPPNAGKTTLANRIAR 46 
                                       89***************996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00044      0.28      10      38 ..      29      76 ..      21     174 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                            AAA_22 10 vtGesGtGKTtllrrlleqldeeakaee...................e 38
                                      ++G++ +GKTtl++r+++  + +a  +e                   +
  gi|336252823|ref|YP_004595930.1| 29 IYGPPNAGKTTLANRIARDWTGDAVGTEshvphetrrarrkenveieR 76
                                      89*************998655444444456666666665554444441 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 ?    8.4   0.0    0.0019       1.2      74     126 ..     128     175 ..      27     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0019
                         Gtr1_RagA  74 frnvgvliyVfDvesreleedletlkeilealrqyspeakvfvlihKmDliqe 126
                                        ++v+ +iyV+D+     e+ +++ +++l  + + s+++ v ++ +K+Dl ++
  gi|336252823|ref|YP_004595930.1| 128 REDVDGVIYVLDSA----EDPITQVNTMLIGIIE-SRDLPVLIFANKIDLDDS 175
                                       457889******99....8888888888888776.899**********98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 1602.47
//
Query:       gi|336252824|ref|YP_004595931.1|  [L=564]
Description: cell division control protein 6-like protein [Halopiger xanaduensis SH-6]
Scores for 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   83.8   0.1    1.5e-23   82.5   0.1    1.7  1  Cdc6_C           CDC6, C terminal winged helix domain
    1.7e-09   38.3   0.3    1.4e-08   35.3   0.0    2.5  2  AAA_16           AAA ATPase domain
    2.4e-09   37.7   0.1     0.0021   18.5   0.0    2.5  2  AAA              ATPase family associated with various cellul
    9.2e-09   35.7   0.1    3.2e-06   27.5   0.0    2.6  2  AAA_22           AAA domain
    0.00054   19.7   0.0     0.0017   18.1   0.0    1.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00065   19.2   0.2     0.0054   16.2   0.0    2.3  2  TniB             Bacterial TniB protein
     0.0026   16.9   0.0     0.0064   15.7   0.0    1.6  2  DUF815           Protein of unknown function (DUF815)
     0.0027   17.4   0.0     0.0065   16.2   0.0    1.6  1  Sigma54_activat  Sigma-54 interaction domain
     0.0065   16.4   0.2       0.15   11.9   0.0    2.4  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0069   15.5   0.0      0.012   14.7   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
     0.0072   16.5   0.1        5.1    7.2   0.1    2.4  2  AAA_2            AAA domain (Cdc48 subfamily)
     0.0082   16.7   0.1      0.027   15.0   0.0    1.9  2  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.012   15.5   0.0       0.11   12.4   0.0    2.2  2  Rad17            Rad17 P-loop domain
      0.016   14.0   0.4        1.3    7.8   0.0    2.2  2  AAA_32           AAA domain
      0.027   15.0   0.0      0.093   13.2   0.0    1.9  1  ABC_tran         ABC transporter
      0.036   13.3   0.0      0.075   12.2   0.0    1.5  1  TIP49            TIP49 P-loop domain
      0.039   14.3   1.0      0.099   13.0   0.3    2.0  1  AAA_assoc_2      AAA C-terminal domain
       0.04   13.4   0.0      0.066   12.7   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.058   13.2   0.0       0.17   11.7   0.0    1.8  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
      0.087   12.5   0.1       0.31   10.8   0.0    2.0  2  AAA_24           AAA domain
      0.093   12.9   2.9       0.13   12.5   0.5    2.2  2  MutS_III         MutS domain III
      0.094   12.5   0.7        8.3    6.1   0.0    2.7  3  DEAD             DEAD/DEAH box helicase
        0.1   11.8   0.1       0.33   10.1   0.0    1.7  2  KAP_NTPase       KAP family P-loop domain
       0.11   11.7   0.0       0.17   11.0   0.0    1.3  1  NB-ARC           NB-ARC domain
       0.11   12.9   0.0       0.24   11.8   0.0    1.6  1  RNA_helicase     RNA helicase
       0.15   12.2   0.0        1.2    9.3   0.0    2.2  2  AAA_lid_10       AAA lid domain
       0.52   10.6   2.6         14    6.0   0.2    2.6  2  ABC_tran_CTD     ABC transporter C-terminal domain


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 !   82.5   0.1   2.3e-26   1.5e-23       1      82 [.     460     539 ..     460     541 .. 0.96

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 2.3e-26
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L a++ll++ +g +++ tgev++ Yk+lCe+ ++d+ltqr+v dl+seL+mlgi+++ ++skGr +grt++isL+v+
  gi|336252824|ref|YP_004595931.1| 460 LFAIILLEK-NGVHSINTGEVFNIYKRLCEEIDADVLTQRRVTDLISELDMLGIVNAVVVSKGR-YGRTKEISLSVP 534
                                       7799*9999.*****************************************************9.***********9 PP

                                       CHHHH CS
                            Cdc6_C  78 pddvl 82 
                                        ++ +
  gi|336252824|ref|YP_004595931.1| 535 LEETE 539
                                       99876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   2.1e-11   1.4e-08       2     161 ..      66     323 ..      65     335 .. 0.68
   2 ?   -1.6   0.1       4.6   3.1e+03      83     103 ..     408     427 ..     354     461 .. 0.48

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.1e-11
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqala 77 
                                       l+ R +++++++++l ++ +g++ +++l++G  G+GK++ ++ + ++le +     +   + +  +++y+    + +
  gi|336252824|ref|YP_004595931.1|  66 LPHRSDQINKMATILVAALRGETpSNILIYGKTGTGKTASAKFVSKELEST----SQKYSVPC--DVEYINCEVTDT 136
                                       789*************99999999************************999....66666666..555644333333 PP

                            AAA_16  78 reellrqlldeaesaeleawrekleeala................................................ 106
                                       + ++l+ql+++  +++ e+ ++++++                                                   
  gi|336252824|ref|YP_004595931.1| 137 QYRVLAQLANKFIEKNKERIDDRIDSLEDllgaieeyeagndpsadeselfdypdeladapddpnvstgadnpdtpn 213
                                       44566666666333333333333333222556666777788889999999999999999999999999999999999 PP

                            AAA_16 107 ..............................................avpelagaea...................sr 118
                                                                                     +        +                    r
  gi|336252824|ref|YP_004595931.1| 214 espvetegyedgdtagdsgatadgaaepshplastpfdsvaeiearI--------EsleedkdsfedvpmtgwptDR 282
                                       99999999999988888777766666666666666555443333320........1333333344555666655566 PP

                            AAA_16 119 llellkrllallsrderplvlvlDdlqwadeaslql.laaLlrl 161
                                       +++++ +++++ +r    +v+ lD+++++ e s +  l++L r 
  gi|336252824|ref|YP_004595931.1| 283 VYNVFFDAVDYDER---VVVIMLDEIDKLVEKSGDDtLYNLSRM 323
                                       66665555544443...699999999988887766668877766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.6
                            AAA_16  83 rqlldeaesaeleawreklee 103
                                       r+l+   ++ el a r + e+
  gi|336252824|ref|YP_004595931.1| 408 RALDLLRTAGEL-AERSQAET 427
                                       222222122222.22222222 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 !   18.5   0.0   3.1e-06    0.0021       1      33 [.      92     135 ..      92     170 .. 0.58
   2 !   16.6   0.1   1.2e-05     0.008      48     113 ..     285     345 ..     257     362 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.1e-06
                                       EEEESSTTSSHHHHHHHHHHHH...........THEEEEEETTT CS
                               AAA   1 vllyGppGtGKTllakavakel...........gvefleisgse 33 
                                       +l+yG  GtGKT+ ak v kel           +ve+++ ++++
  gi|336252824|ref|YP_004595931.1|  92 ILIYGKTGTGKTASAKFVSKELestsqkysvpcDVEYINCEVTD 135
                                       699******************83333322222223333333333 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GG CS
                               AAA  48 elfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pd 113
                                       ++f +a     + +++++DEid+l++++       +++++  L ++ +++++  s+v +ig++n+    d
  gi|336252824|ref|YP_004595931.1| 285 NVFFDAVDYDeRVVVIMLDEIDKLVEKS-------GDDTLYNLSRMNSELEN--SRVSIIGISNDlkfTD 345
                                       45555444443459*************9.......88889999888888888..589*******955444 PP

>> AAA_22  AAA 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   3.2e-06       4      84 ..      88     172 ..      85     193 .. 0.82
   2 ?    5.3   0.1     0.035        23      92     117 ..     297     324 ..     283     341 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 4.8e-09
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka....erlss 75 
                                       t + ++++G +GtGKT +++ + ++l+  ++  +  + +v ++++ +  ++  +l +l++++ +++k+    + +s+
  gi|336252824|ref|YP_004595931.1|  88 TPSNILIYGKTGTGKTASAKFVSKELESTSQK-YsVPCDVEYINCEVTDTQYRVLAQLANKFIEKNKEriddRIDSL 163
                                       66789*********************654443.34777888**********************99888777766777 PP

                            AAA_22  76 eellealeq 84 
                                       e+ll a+e+
  gi|336252824|ref|YP_004595931.1| 164 EDLLGAIEE 172
                                       777777666 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.035
                            AAA_22  92 ielliiDEaqhlr..s.eealeeLrslln 117
                                       ++++++DE+++l   s ++ l +L+++ n
  gi|336252824|ref|YP_004595931.1| 297 VVVIMLDEIDKLVekSgDDTLYNLSRM-N 324
                                       47*********9876368888888443.3 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 !   18.1   0.0   2.5e-06    0.0017      20      67 ..      77     123 ..      57     138 .. 0.82
   2 ?   -3.1   0.0       8.9   5.9e+03      87     105 ..     299     318 ..     295     323 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.5e-06
                            RuvB_N  20 kifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgP 67 
                                       + +i  a  r+e+   +l+yG  G Gkt+ ak ++kel+++ +  s P
  gi|336252824|ref|YP_004595931.1|  77 A-TILVAALRGETPSNILIYGKTGTGKTASAKFVSKELESTSQKYSVP 123
                                       3.34446689*****************************999988887 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.9
                            RuvB_N  87 vlfideihrlsr.aveevly 105
                                       v+++dei +l + + ++ ly
  gi|336252824|ref|YP_004595931.1| 299 VIMLDEIDKLVEkSGDDTLY 318
                                       7899***9986514566777 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.1e-06    0.0054      17     101 ..      71     155 ..      59     172 .. 0.74
   2 ?   -0.2   0.1      0.84   5.6e+02     120     142 ..     297     319 ..     292     342 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.1e-06
                              TniB  17 keilerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppe.kdedaekvpvlvvqappkpdekrlyaaiLe 92 
                                       ++i ++   L+++ + + ++n+l++G++ +GKt+ + kF +++ ++ +++ +  ++v ++++  + ++ r  a++ +
  gi|336252824|ref|YP_004595931.1|  71 DQINKMATILVAALRGETPSNILIYGKTGTGKTASA-KFVSKELEStSQKYSVPCDVEYINCEVTDTQYRVLAQLAN 146
                                       45555555566677788889*************865.677666555156777899********99999999999888 PP

                              TniB  93 algaplkar 101
                                       ++ ++ k+r
  gi|336252824|ref|YP_004595931.1| 147 KFIEKNKER 155
                                       887765433 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.84
                              TniB 120 vrvLiiDEihnllagsarkqref 142
                                       v v+++DEi++l++ s ++    
  gi|336252824|ref|YP_004595931.1| 297 VVVIMLDEIDKLVEKSGDDTLYN 319
                                       67899******997666554444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.7e-06    0.0064      35      81 ..      71     117 ..      58     156 .. 0.79
   2 ?   -3.2   0.0       5.7   3.8e+03      90     119 ..     315     344 ..     307     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.7e-06
                            DUF815  35 kqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg 81 
                                       +q +++ +   + l+g++ +n+L++G+ GtGK +  k++ +e+++++
  gi|336252824|ref|YP_004595931.1|  71 DQINKMATILVAALRGETPSNILIYGKTGTGKTASAKFVSKELESTS 117
                                       566677777778899*************************9998765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.7
                            DUF815  90 edlkelpklvellrerperfilfvDDLsFe 119
                                       ++l +l+++ ++l++++  +i    DL F+
  gi|336252824|ref|YP_004595931.1| 315 DTLYNLSRMNSELENSRVSIIGISNDLKFT 344
                                       568999999999999999999999999997 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.8e-06    0.0065      16      53 ..      81     120 ..      67     139 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.8e-06
                                       HHHC..TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
                   Sigma54_activat  16 kkva..ktdlsvlitGesGtGKellaraiheaskrkekpf 53 
                                        ++   +t++++li G++GtGK+  a+ + ++ + +++++
  gi|336252824|ref|YP_004595931.1|  81 VAALrgETPSNILIYGKTGTGKTASAKFVSKELESTSQKY 120
                                       3333225679******************998666555543 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 !   11.9   0.0   0.00023      0.15      13      52 ..      82     121 ..      68     187 .. 0.70
   2 ?    1.9   0.0      0.26   1.7e+02     105     145 ..     283     320 ..     252     340 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                          ATPase_2  13 eilerepneiyfiYGpegsGKtaLlkeiienledkdkyvi 52 
                                         l+ e+ + ++iYG  g GKta  k + ++le+ +++  
  gi|336252824|ref|YP_004595931.1|  82 AALRGETPSNILIYGKTGTGKTASAKFVSKELESTSQKYS 121
                                       4568899999**************9999999877665333 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.26
                          ATPase_2 105 aielllekikkkgkkiiiiiDelqklidlglngaellvkeL 145
                                         + +++++  + + ++i++De+ kl++   ++  + +++L
  gi|336252824|ref|YP_004595931.1| 283 VYNVFFDAVDYDERVVVIMLDEIDKLVE---KSGDDTLYNL 320
                                       556778888889899***********93...3334444444 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 !   14.7   0.0   1.8e-05     0.012     107     160 ..      65     120 ..      51     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                             T2SSE 107 dlgaeealkekiaevlrkavr..erglilvsGgTgsGKttllyallkeinksderi 160
                                       +l  + ++ +k+a +l +a+r  +  +il+ G Tg+GKt ++  + ke+++++++ 
  gi|336252824|ref|YP_004595931.1|  65 ELPHRSDQINKMATILVAALRgeTPSNILIYGKTGTGKTASAKFVSKELESTSQKY 120
                                       555566677788888888886224579*********************99986665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0     0.009         6       4      34 ..      90     119 ..      87     174 .. 0.81
   2 !    7.2   0.1    0.0077       5.1      65      83 ..     292     311 ..     248     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.009
                                       --EEEE--TTSSHHHHHHHHHHHTT-....- CS
                             AAA_2   4 isilllgptgvGktelakalaellfvkkekk 34 
                                       ++il+ g+tg+Gkt  ak +++ l+  +++k
  gi|336252824|ref|YP_004595931.1|  90 SNILIYGKTGTGKTASAKFVSKELES-TSQK 119
                                       79**************9999999995.4433 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0077
                                       HHHTTS.EEEEETGGG---- CS
                             AAA_2  65 gaeegG.ivllDEidKihpk 83 
                                        ++e+  +++lDEidK  +k
  gi|336252824|ref|YP_004595931.1| 292 DYDERVvVIMLDEIDKLVEK 311
                                       444544699*******9995 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     4e-05     0.027       1      58 [.      92     160 ..      92     182 .. 0.63
   2 ?   -2.3   0.0       8.9   5.9e+03      28      85 ..     377     435 ..     367     450 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..........gvnlrdvakenglllevdpe.aldeskrldedkld 58 
                                       Il+ G+ G+GKt  ak +sk+l++          ++ +++ +++ +++   + + ++ e++++++d + 
  gi|336252824|ref|YP_004595931.1|  92 ILIYGKTGTGKTASAKFVSKELEStsqkysvpcdVEYINCEVTDTQYRVLAQLAnKFIEKNKERIDDRI 160
                                       99*******************977788555555544444444444443332222455555555555444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.9
                            AAA_18  28 lrdvakenglllevdpe...aldeskrldedkldklldaleenss.aleegknlvidghlae 85 
                                        +dva+++g l e+  +   a+  ++    +   ++ld+l+ + + a++++   +++ h+ +
  gi|336252824|ref|YP_004595931.1| 377 RSDVAFKGGALSEDVIPlcaAFAAQEH---GDARRALDLLRTAGElAERSQAETIVEEHVRQ 435
                                       567777777666666663332222222...22233333333333343333333367766655 PP

>> Rad17  Rad17 P-loop 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      26      93 ..      71     137 ..      57     158 .. 0.78
   2 ?    0.0   0.0         1   6.8e+02      93     182 ..     383     475 ..     368     478 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                             Rad17  26 kkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqksdfk 93 
                                        +i+++ + l a    + + +i Li G +G gk+   k +skel    ++++ p  +   + +++d++
  gi|336252824|ref|YP_004595931.1|  71 DQINKMATILVAALRGETPSNI-LIYGKTGTGKTASAKFVSKELESTSQKYSVPCDVEYINCEVTDTQ 137
                                       5677777777777777776665.799***************************999887777777664 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1
                             Rad17  93 kgltekesrflsqiesfkeleLkdakyl..klqklGddl.rtdkklilvedlP.nkfyrdsdalrevirkylrssea 165
                                       kg    e+  ++++++f   e  da+     l+  G+ + r++ + i+ e +   + ++++d++ ev+r+  + s+ 
  gi|336252824|ref|YP_004595931.1| 383 KGGALSED-VIPLCAAFAAQEHGDARRAldLLRTAGELAeRSQAETIVEEHVRqAQDKIELDRVVEVVRTLPTQSKL 458
                                       55555555.67788888777777776531145666766524444555555555677788999*******99999998 PP

                             Rad17 166 lplilviteieslegdn 182
                                       + + +++ e + +  +n
  gi|336252824|ref|YP_004595931.1| 459 VLFAIILLEKNGVHSIN 475
                                       77777777777777776 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0019       1.3      32      69 ..      91     131 ..      82     175 .. 0.77
   2 ?    4.2   0.2     0.022        15     479     510 ..     408     439 ..     403     442 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0019
                            AAA_32  32 NifvlGesgtGrtt...lvkrlleeiakkeptpdDwcYvnn 69 
                                       Ni + G++gtG+t    +v++ le++++k ++p D+ Y+n 
  gi|336252824|ref|YP_004595931.1|  91 NILIYGKTGTGKTAsakFVSKELESTSQKYSVPCDVEYINC 131
                                       9***********9622267788999999999*******974 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.022
                            AAA_32 479 eiadllrEAdywakkegaevveaehVekAlee 510
                                       +  dllr A  +a++++ae++ +ehV++A ++
  gi|336252824|ref|YP_004595931.1| 408 RALDLLRTAGELAERSQAETIVEEHVRQAQDK 439
                                       6789*************************765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00014     0.093      13      80 ..      91     165 ..      84     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.........H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........x RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.........e 80 
                                        + i G++G+GK+  +k ++++l+ t+ +  +   d+++++ e+++ + +vl q ++ f e+ ++e+         +
  gi|336252824|ref|YP_004595931.1|  91 NILIYGKTGTGKTASAKFVSKELESTSQKYSV-PCDVEYINCEVTDTQYRVLAQLANKFIEK-NKERiddridsleD 165
                                       6789********************99998744.6899999**************98888887.66654433433330 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011     0.075      42      96 ..      83     136 ..      71     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  42 likekklaGravLlaGpsgtGktalaiaiskelg.edvpfvalsgsevyslevkkt 96 
                                        ++ ++     +L+ G++gtGkta a  +skel  ++ ++ +    e   +ev  t
  gi|336252824|ref|YP_004595931.1|  83 ALRGETP--SNILIYGKTGTGKTASAKFVSKELEsTSQKYSVPCDVEYINCEVTDT 136
                                       5555443..379*********************84555666666666667777666 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 ?   13.0   0.3   0.00015     0.099      15      56 ..     398     438 ..     386     449 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                                       XXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX CS
                       AAA_assoc_2  15 laeladGDaRkaLnlLElaaeaaeakegkieitledleealq 56 
                                        a+  +GDaR+aL lL +a e ae+ ++ ++i +e++++a +
  gi|336252824|ref|YP_004595931.1| 398 FAAQEHGDARRALDLLRTAGELAER-SQAETIVEEHVRQAQD 438
                                       455558*************999986.8899999999998765 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 ?   12.7   0.0   9.9e-05     0.066      34      61 ..      90     117 ..      73     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.9e-05
                             AAA_7  34 kpvllvGptGtGKtviikdllkkldkek 61 
                                        ++l++G+tGtGKt+ +k + k+l++++
  gi|336252824|ref|YP_004595931.1|  90 SNILIYGKTGTGKTASAKFVSKELESTS 117
                                       689**************99999998433 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 ?   11.7   0.0   0.00025      0.17      15      64 ..      85     135 ..      71     323 .. 0.72
   2 ?   -2.0   0.0       4.1   2.7e+03      80      97 ..     425     442 ..     383     469 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                   DNA_pol3_delta2  15 sgrlahayLfeGdegigkkelalnlakallceeknetkpcg.ecksckkie 64 
                                       +g+    +L++G++g+gk ++a+ ++k+l +++++ + pc+ e  +c+  +
  gi|336252824|ref|YP_004595931.1|  85 RGETPSNILIYGKTGTGKTASAKFVSKELESTSQKYSVPCDvEYINCEVTD 135
                                       46667789**************************99999984445555544 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.1
                   DNA_pol3_delta2  80 ersikldqirelieelsr 97 
                                        ++i  +++r+ +++++ 
  gi|336252824|ref|YP_004595931.1| 425 AETIVEEHVRQAQDKIEL 442
                                       234444444444444332 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00046      0.31       3      21 ..      90     108 ..      88     179 .. 0.89
   2 ?   -1.9   0.1       3.5   2.3e+03      63      85 ..     294     316 ..     249     329 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                            AAA_24   3 lkiliyGpsgiGKTtlake 21 
                                        +iliyG+ g+GKT +ak 
  gi|336252824|ref|YP_004595931.1|  90 SNILIYGKTGTGKTASAKF 108
                                       589***********99985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.5
                            AAA_24  63 ladyktlviDtideleelclaev 85 
                                       +++  ++ +D id+l+e   +++
  gi|336252824|ref|YP_004595931.1| 294 DERVVVIMLDEIDKLVEKSGDDT 316
                                       34455677788988888766655 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       2.2   1.5e+03      42      64 ..      57      78 ..      53     183 .. 0.44
   2 ?   12.5   0.5    0.0002      0.13      44     187 ..     249     510 ..     243     511 .. 0.47

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.2
                                      H--BS-HHHHHHHHHHHHHT..T CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III 42 lqPltdleeInaRldaVeelene 64
                                      l+P+  ++e+ +R d +  +  +
  gi|336252824|ref|YP_004595931.1| 57 LRPSYTPHELPHRSDQINKMA-T 78
                                      566666666666666665432.1 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0002
                                       -BS-HHHHHHHHHHHHHT................................TT.HHHHHHHHTT--.....-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx..............................xxxxxxxxxxxxxxxx.....xxxxxxx RF
                          MutS_III  44 PltdleeInaRldaVeele..............................neelreelrellrrlp.....DleRlls 85 
                                       P+ +++eI+aR++  ee +                                 + +e+ +l+++++     +l R+ s
  gi|336252824|ref|YP_004595931.1| 249 PFDSVAEIEARIESLEEDKdsfedvpmtgwptdrvynvffdavdydervVVIMLDEIDKLVEKSGddtlyNLSRMNS 325
                                       66677777777777776332344444444443333333333222222221111111112222211222223444444 PP

                                       HHHTT---HHHHHHHHHHHH........................................HHHTTTTT---SSTHHH CS
                                       xxxxxxxxxxxxxxxxxxxx........................................xxxxxxxxxxxxxxxxx RF
                          MutS_III  86 rislgkakardlkallealk........................................aleelvallekeklaes 122
                                       ++ +++++   +  + + lk                                        +                
  gi|336252824|ref|YP_004595931.1| 326 ELENSRVS---IIGISNDLKftdfldprvksslgeeeivfppydanqlrdilehrsdvafK---------------- 383
                                       44333222...11111111122222222222222222222222111111111122222220................ PP

                                       HH................................HHHH..HHHHHHB-SS--SSGGGS--B-T.............. CS
                                       xx................................xxxx..xxxxxxxxxxxxxxxxxxxxxxx.............. RF
                          MutS_III 123 ee................................esla..elleeaideeplalekegedlra.............. 151
                                                                          +la  +   e+i+ee  ++ +++ +l+               
  gi|336252824|ref|YP_004595931.1| 384 -GgalsedviplcaafaaqehgdarraldllrtaGELAerSQA-ETIVEEHVRQAQDKIELDRvvevvrtlptqskl 458
                                       .022223333444444444444443333333332223321222.346666666666666666699999999999999 PP

                                       ................HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHH CS
                                       ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III 152 ................iealeqelfqelleeveealerlrrlaealaeLDvl 187
                                                       ++ +  +++++l+ee+++ + + rr++++++eLD+l
  gi|336252824|ref|YP_004595931.1| 459 vlfaiillekngvhsiNTGEVFNIYKRLCEEIDADVLTQRRVTDLISELDML 510
                                       999999999999999766666999********9999***************8 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.013       8.3      15      31 ..      90     106 ..      71     153 .. 0.84
   2 ?    3.8   0.1     0.067        44     121     155 ..     296     329 ..     281     344 .. 0.73
   3 ?   -2.7   0.0       6.5   4.3e+03      68     107 ..     484     522 ..     477     547 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                                       CEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaf 31 
                                        ++l+ ++TG+GKT+ +
  gi|336252824|ref|YP_004595931.1|  90 SNILIYGKTGTGKTASA 106
                                       699***********975 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.067
                                       TEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 121 qvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                       +v ++ lDE+d+l +++  d++ + l+++++  ++
  gi|336252824|ref|YP_004595931.1| 296 RVVVIMLDEIDKLVEKSGDDTLYN-LSRMNSELEN 329
                                       566889*********966666666.6666544444 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.5
                                       HHHTTTSTSEEEEEETTSSHHHHHHHHH.TT.CSEEEEEHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxx RF
                              DEAD  68 kkfkkyidlrvlliiggvaardqlskld.ng.vdivvgtpgr 107
                                       k+++++id  v   +++ + +d +s+ld  g v+ vv   gr
  gi|336252824|ref|YP_004595931.1| 484 KRLCEEIDADV---LTQRRVTDLISELDmLGiVNAVVVSKGR 522
                                       44555544333...3445555555555532356666665555 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 ?   10.1   0.0   0.00049      0.33       3      49 ..      71     136 ..      69     177 .. 0.71
   2 ?   -1.9   0.0       2.3   1.5e+03     167     187 ..     290     310 ..     252     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00049
                        KAP_NTPase   3 lyasaladilseptl..atpivvgLygkWGsGKssllnkledelkefa..................k 49 
                                         ++++a+il+   l  +tp+ + +ygk G+GK++  +++ +el++ +                   
  gi|336252824|ref|YP_004595931.1|  71 DQINKMATILVAA-LrgETPSNILIYGKTGTGKTASAKFVSKELESTSqkysvpcdveyincevtdT 136
                                       5789999999955.5689*************************999865555555555555555552 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.3
                        KAP_NTPase 167 tLdalqkrlVvviDdLDrcet 187
                                       + d  ++ +V+ +D++D +  
  gi|336252824|ref|YP_004595931.1| 290 AVDYDERVVVIMLDEIDKLVE 310
                                       5555677889999***98755 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00025      0.17      18      82 ..      89     154 ..      69     173 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                                       SCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTE...EEEEEEESXXHHHHHHHXXHHHHHCCCTT CS
                            NB-ARC  18 lqslvvalvGmgGvGKttlakqilnksdevegrFds...vawvvvsktdkseeiletilkeLslsedd 82 
                                       +    + ++G+ G GKt  ak + ++++++ +++ +   v ++    td+++++l ++++++ +++++
  gi|336252824|ref|YP_004595931.1|  89 PS--NILIYGKTGTGKTASAKFVSKELESTSQKYSVpcdVEYINCEVTDTQYRVLAQLANKFIEKNKE 154
                                       33..688***************************9622245557777888899999999888776544 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   0.00036      0.24       1      39 [.      92     124 ..      92     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00036
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnp 39 
                                       i++yG++g+GK+  ak ++k+l++++      + ys ++
  gi|336252824|ref|YP_004595931.1|  92 ILIYGKTGTGKTASAKFVSKELESTS------QKYSVPC 124
                                       789**************999998554......3344444 PP

>> AAA_lid_10  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.6   1.1e+03      20      53 ..     105     141 ..      84     150 .. 0.74
   2 ?    9.3   0.0    0.0018       1.2      45      80 ..     387     422 ..     368     437 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.6
                                       --------...-----------------------HHH CS
                        AAA_lid_10  20 sailieae...eekkqklPenvkkvrlkisddaieia 53 
                                       sa+++ +e   +++k ++P +v  ++ +++d   ++ 
  gi|336252824|ref|YP_004595931.1| 105 SAKFVSKElesTSQKYSVPCDVEYINCEVTDTQYRVL 141
                                       444444445556778999******9999998766555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0018
                                       ------HHHHHHHHHHT-TTTTHHHHHHHHHHHHHH CS
                        AAA_lid_10  45 isddaieiasrkvAsvsgdarrAlkiCkrAvEiaek 80 
                                       +s+d+i + +   A+  gdarrAl + + A E+ae+
  gi|336252824|ref|YP_004595931.1| 387 LSEDVIPLCAAFAAQEHGDARRALDLLRTAGELAER 422
                                       799*******************************97 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 ?    3.8   0.2       0.1        69      10      42 ..     153     185 ..     147     197 .. 0.74
   2 ?    6.0   0.2     0.022        14      11      28 ..     254     271 ..     251     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.1
                      ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdpek 42 
                                        e+++++I++LE  + ++e+  a ++  +d+ +
  gi|336252824|ref|YP_004595931.1| 153 KERIDDRIDSLEDLLGAIEEYEAGNDPSADESE 185
                                       4899**************995554444466655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.022
                      ABC_tran_CTD  11 eeleaeIeaLEeeiaele 28 
                                       +e+ea+Ie+LEe++ + e
  gi|336252824|ref|YP_004595931.1| 254 AEIEARIESLEEDKDSFE 271
                                       689*********998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); 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: 0.71u 0.25s 00:00:00.96 Elapsed: 00:00:00.41
# Mc/sec: 4080.86
//
Query:       gi|336252825|ref|YP_004595932.1|  [L=155]
Description: hypothetical protein Halxa_1420 [Halopiger xanaduensis SH-6]
Scores for 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   15.4   1.6      0.017   15.0   1.6    1.2  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
       0.17   12.1   0.0        6.4    7.0   0.0    2.5  2  DUF4115     Domain of unknown function (DUF4115)


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.6   1.9e-06     0.017       2      24 ..       1      22 [.       1      24 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      ++RR+ L +++A++ +  l+gc+
  gi|336252825|ref|YP_004595932.1|  1 MNRRTVLAATGAVGLGS-LAGCL 22
                                      89************776.55554 PP

>> DUF4115  Domain of unknown function (DUF4115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0   0.00071       6.4      48      64 ..      36      52 ..      34      62 .. 0.81
   2 ?    2.6   0.0     0.017   1.6e+02      50      63 ..     121     134 ..     117     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00071
                           DUF4115 48 gavevsvnGkpvdllgy 64
                                      g ++v+vnG+p+dl  +
  gi|336252825|ref|YP_004595932.1| 36 GTIDVTVNGEPIDLEAP 52
                                      6789*********9874 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.017
                           DUF4115  50 vevsvnGkpvdllg 63 
                                       + ++vnG +vd+  
  gi|336252825|ref|YP_004595932.1| 121 IAFTVNGDEVDPTE 134
                                       679********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1159.77
//
Query:       gi|336252826|ref|YP_004595933.1|  [L=317]
Description: peptidase S26B, signal peptidase [Halopiger xanaduensis SH-6]
Scores for complete 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-05   25.1   0.4    3.3e-05   23.8   0.4    1.8  1  Peptidase_S24  Peptidase S24-like


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 !   23.8   0.4   1.8e-09   3.3e-05       2      45 ..      98     169 ..      97     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.8e-09
                                       XXSSTTCCTXXTTXEEEEECTS..........................---TTSEEEEEETTCE..-EEEEE CS
                     Peptidase_S24   2 vpGdSMeptlldGdlilVdkfs..........................epkrGdivvfrlpgee..eayiKr 45 
                                       v+++SM p ++ Gdli++  ++                            ++Gd+++fr +g e  +  i+r
  gi|336252826|ref|YP_004595933.1|  98 VESESMVPNMQKGDLIFITDSDrfvgddpvegtgvvtlataretgyekFNRPGDVIIFRPDGSEyeTPVIHR 169
                                       89****************9777899**************************************977777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2575.34
//
Query:       gi|336252827|ref|YP_004595934.1|  [L=520]
Description: DNA-directed DNA polymerase [Halopiger xanaduensis SH-6]
Scores for 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-12   46.6   0.0    3.8e-12   46.0   0.0    1.2  1  DNA_pol_E_B    DNA polymerase alpha/epsilon subunit B
      1e-10   42.0   3.0    2.7e-10   40.7   3.0    1.6  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    5.1e-10   40.2   0.6    9.3e-10   39.3   0.6    1.4  1  Metallophos    Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
       0.19   11.8   0.0       0.37   10.8   0.0    1.4  1  DUF1249        Protein of unknown function (DUF1249)


Domain annotation for each model (and alignments):
>> 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 !   46.0   0.0   8.6e-16   3.8e-12       5     203 ..     271     464 ..     268     472 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 8.6e-16
                                       ES--S-TT---...-HHHHHHHHHHH.HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHHTTS- CS
                       DNA_pol_E_B   5 sglnldndnrs...leaLrkiLqgyapeesppdvlilaGnfvdaahkaiasskvstdekkenfdalalllsilesll 78 
                                       s++++ ++++     + + ++L   +  +  ++ l+laG +v+      ++ +    +  +  +  +++++ l+++ 
  gi|336252827|ref|YP_004595934.1| 271 SDVHVGSEEFMedaWNRFADWLHTEQ--ARNVEYLLLAGDMVEGVGVYPDQDEE--LDIIDIYEQYEAFSEHLKKVP 343
                                       55555544444455556666776666..77777777777777733222222221..233333333344444455555 PP

                                       TTSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EEESHHHH CS
                       DNA_pol_E_B  79 ekttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkreslkesnt 155
                                          ++v++Pg  D++   + Pq+ +++  l +i +     ++v+NPs++++++v v+++ +  ++++ +e  +e++ 
  gi|336252827|ref|YP_004595934.1| 344 GDLEIVMIPGNHDAVRL-AEPQPGFDEE-LREIMSAH-DPEIVSNPSTVTVEGVSVLMYHGVSLDEVIAELPEEKA- 416
                                       7778************9.*******777.66666654.47******************************999999. PP

                                       HS-HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEEE-- CS
                       DNA_pol_E_B 156 dverlrklvktildqrhlaPlaptlrpvswdkddalvleplPdvlvlp 203
                                       + +  +k++ ++l+ rh+aP +        +++d lv++++Pd++  +
  gi|336252827|ref|YP_004595934.1| 417 SYDDPHKAMYQLLKKRHVAPQFGGHTRLAPEEKDYLVIDEVPDIFHTG 464
                                       6*******************************************9876 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 !   40.7   3.0     6e-14   2.7e-10       3     150 ..     267     489 ..     265     504 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 6e-14
                     Metallophos_2   3 laiiSDlH........snldaleavlealkevgvdaiihaGD....................leeeepe.vleelle 50 
                                        a+iSD+H        ++ ++ + +l+  ++ +v+++++aGD                    +  e+ e + e l++
  gi|336252827|ref|YP_004595934.1| 267 AALISDVHvgseefmeDAWNRFADWLHTEQARNVEYLLLAGDmvegvgvypdqdeeldiidiY--EQYEaFSEHLKK 341
                                       689*******999999888888888999999999********766666666655555543321..222313333344 PP

                     Metallophos_2  51 la....pvlaVrGNnD......eev.veedvlreaaelgtdl.peeaelelagekvlliHgdpl............. 102
                                             ++++++GN+D      ++  ++e++ +    ++ ++  +  +++++g++vl++Hg  l             
  gi|336252827|ref|YP_004595934.1| 342 -VpgdlEIVMIPGNHDavrlaePQPgFDEELREIMSAHDPEIvSNPSTVTVEGVSVLMYHGVSLdeviaelpeekas 417
                                       .25888**********776664222455555555555555554488999999*********988************* PP

                     Metallophos_2 103 .....................gvkdalaellke...aeegsdvvvcGHtHvpevekeggvlvvnPGsvgepr 150
                                                            g++ +la+  k+    +e+ d++  GH H+ +  k ++vl +n G  + + 
  gi|336252827|ref|YP_004595934.1| 418 yddphkamyqllkkrhvapqfGGHTRLAPEEKDylvIDEVPDIFHTGHVHKLGFGKYHNVLAINSGCWQAQT 489
                                       *********************666666666666664558888************************987764 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.6   2.1e-13   9.3e-10       4     203 ..     268     468 ..     266     469 .. 0.68

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 2.1e-13
                                       EEEESBTB...TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.............HHHHHHHHHHHHHHHH. CS
                       Metallophos   4 lvigDlHl...algggqlddllkllddllreekpdlvllaGDlvdrg.............dlekellellaalvky. 63 
                                       ++i+D+H+   +  +  +++++++l+  +++ ++ ++llaGD v++              d+ + ++ + +      
  gi|336252827|ref|YP_004595934.1| 268 ALISDVHVgseEFMEDAWNRFADWLHTEQAR-NVEYLLLAGDMVEGVgvypdqdeeldiiDIYEQYEAFSE----Hl 339
                                       689********9999**********666666.9*********88886688888677766633332333333....13 PP

                                       .....TSEEEEEC-TTS.........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEE CS
                       Metallophos  64 .....pipvylllGNHe.........gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspe 126
                                            +  +++++GNH+         gf+eel +             +d e ++n+  +   +    vl +hG    
  gi|336252827|ref|YP_004595934.1| 340 kkvpgDLEIVMIPGNHDavrlaepqpGFDEELREIMSA---------HDPEIVSNPSTVTVEGV--SVLMYHGV--- 402
                                       334668888********666655555555555555332.........22455566666664444..66666666... PP

                                       ETHHHHHHHHHHHSCHHHHCC.....HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEE CS
                       Metallophos 127 llvsldklgslnleleapepg.....dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvis 198
                                          sld++  +  e  a+ ++     +++lk+              H+ +   +g++   ++ +d+l + +v  +++
  gi|336252827|ref|YP_004595934.1| 403 ---SLDEVIAELPEEKASYDDphkamYQLLKK-------------RHVAPQ-FGGHTRLAPEEKDYLVIDEVPDIFH 462
                                       ...55555555555555555567778999999.............788888.7777777777778888888777777 PP

                                       .ESSSS CS
                       Metallophos 199 .GHtHv 203
                                        GH+H+
  gi|336252827|ref|YP_004595934.1| 463 tGHVHK 468
                                       7**997 PP

>> DUF1249  Protein of unknown function (DUF1249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   8.2e-05      0.37      53      98 ..     390     433 ..     377     439 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.2e-05
                           DUF1249  53 kkpkltvRlYhDArmaEvlsaqqhrrlkarydypnkkmhqldeKlq 98 
                                       +   ++v +Yh + + Ev++  +  + ka+yd p k+m+ql +K  
  gi|336252827|ref|YP_004595934.1| 390 TVEGVSVLMYHGVSLDEVIA--ELPEEKASYDDPHKAMYQLLKKRH 433
                                       55678999***********9..7778899***********999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); 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:                         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 0.26s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3719.11
//
Query:       gi|336252828|ref|YP_004595935.1|  [L=112]
Description: transcriptional regulator TrmB [Halopiger xanaduensis SH-6]
Scores for 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-09   36.3   0.2    6.7e-09   35.7   0.2    1.3  1  HTH_20        Helix-turn-helix domain
    3.1e-07   30.2   0.0    4.2e-07   29.7   0.0    1.3  1  TrmB          Sugar-specific transcriptional regulator TrmB
    4.2e-07   29.7   0.1    7.1e-07   29.0   0.1    1.3  1  MarR_2        MarR family
    5.8e-06   26.2   0.0    6.9e-05   22.7   0.0    2.1  2  PadR          Transcriptional regulator PadR-like family
    2.8e-05   24.0   0.0    4.6e-05   23.3   0.0    1.3  1  HTH_11        HTH domain
    9.6e-05   22.3   0.1    0.00015   21.7   0.1    1.3  1  HTH_Crp_2     Crp-like helix-turn-helix domain
    0.00014   21.7   0.0    0.00021   21.1   0.0    1.3  1  HTH_5         Bacterial regulatory protein, arsR family
     0.0018   17.8   0.2     0.0071   15.9   0.2    1.9  1  HTH_24        Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.022   15.1   0.0      0.038   14.3   0.0    1.3  1  Rrf2          Transcriptional regulator
       0.03   14.2   0.0      0.038   13.8   0.0    1.3  1  HxlR          HxlR-like helix-turn-helix
      0.048   13.7   0.0       0.06   13.4   0.0    1.2  1  Replic_Relax  Replication-relaxation
       0.05   13.6   0.0      0.079   12.9   0.0    1.3  1  HTH_36        Helix-turn-helix domain
      0.056   13.4   0.0      0.087   12.8   0.0    1.3  1  MarR          MarR family
      0.062   13.1   0.0      0.099   12.5   0.0    1.3  1  HTH_IclR      IclR helix-turn-helix domain
      0.065   12.9   0.1       0.12   12.0   0.1    1.4  1  GntR          Bacterial regulatory proteins, gntR family
      0.066   13.4   0.0      0.089   12.9   0.0    1.4  1  FUR           Ferric uptake regulator family
      0.067   12.8   0.0      0.082   12.5   0.0    1.1  1  ArsR          ArsR 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 !   35.7   0.2   6.3e-12   6.7e-09       2      57 ..      19      73 ..      18      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 6.3e-12
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                       ++ +L++    +il+ L  + ++ta+el er+ +s+ t++++L+ Le+agLve++
  gi|336252828|ref|YP_004595935.1| 19 AALALLGDDYAQEILAVL-IENPATAKELTERCPGSRVTIYRRLNRLEDAGLVETE 73
                                      56788999**********.***********************************86 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0     4e-10   4.2e-07      15      55 ..      33      73 ..      26      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4e-10
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      la+l + pata+e+ e+   +r ++Y+ L++Led+GlVe+e
  gi|336252828|ref|YP_004595935.1| 33 LAVLIENPATAKELTERCPGSRVTIYRRLNRLEDAGLVETE 73
                                      578899*********************************87 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.1   6.7e-10   7.1e-07      10      54 ..      32      73 ..      30      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 6.7e-10
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +La+L  +p    t++el++r+  s+ ++ r+l+rL++aGLve++
  gi|336252828|ref|YP_004595935.1| 32 ILAVLIENP---ATAKELTERCPGSRVTIYRRLNRLEDAGLVETE 73
                                      7999****9...6******************************98 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.35   3.6e+02       7      20 ..       9      22 ..       7      29 .. 0.81
   2 !   22.7   0.0   6.6e-08   6.9e-05       1      65 [.      32      88 ..      32      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.35
                                      CS-EEHHHHHHHHH CS
                              PadR  7 eqpsyGyeiikele 20
                                      ++ ++G+ei  +l+
  gi|336252828|ref|YP_004595935.1|  9 RENEHGLEIDAALA 22
                                      5778*****98886 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 6.6e-08
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEE CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrl 65
                                      iLa+l e+p    + +kel+e+  g    s  ++Y+ L+rLe+ glve+e +  ++g     Yrl
  gi|336252828|ref|YP_004595935.1| 32 ILAVLIENP----ATAKELTERCPG----SRVTIYRRLNRLEDAGLVETEIRIRSDGNHCERYRL 88
                                      788888888....778999999999....999******************999988888888887 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   4.3e-08   4.6e-05       3      49 ..      30      79 ..      29      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.3e-08
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.....vpIese 49
                                      + il  L+e+    +++eL e+   Sr t++r++ +Le++g     ++I s+
  gi|336252828|ref|YP_004595935.1| 30 QEILAVLIENP--ATAKELTERCPGSRVTIYRRLNRLEDAGlveteIRIRSD 79
                                      67999998888..7***************************88877777776 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 !   21.7   0.1   1.4e-07   0.00015      16      60 ..      31      77 ..      18      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.4e-07
                                      C....EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES CS
                         HTH_Crp_2 16 g....eielpltqeelAsmlGltretvsrilseLkreglisrgrriril 60
                                      +     ie p t +el +++  +r+t+ r l++L+++gl++++  iri+
  gi|336252828|ref|YP_004595935.1| 31 EilavLIENPATAKELTERCPGSRVTIYRRLNRLEDAGLVETE--IRIR 77
                                      234467899********************************76..4443 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 !   21.1   0.0     2e-07   0.00021       6      47 .]      31      72 ..      29      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2e-07
                                      HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      +IL  L e+++++ el+e    s+ t+ + L++L++aGLVe+
  gi|336252828|ref|YP_004595935.1| 31 EILAVLIENPATAKELTERCPGSRVTIYRRLNRLEDAGLVET 72
                                      79**************************************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 !   15.9   0.2   6.7e-06    0.0071       2      48 .]      26      71 ..      25      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.7e-06
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      d++  +IL +L +np  + +eL er+  S+ t+ rrl+rLe++Gl++
  gi|336252828|ref|YP_004595935.1| 26 DDYAQEILAVLIENP-ATAKELTERCPGSRVTIYRRLNRLEDAGLVE 71
                                      566778999999977.8999*************************96 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.6e-05     0.038       8      57 ..      27      72 ..      25      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.6e-05
                                      HHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2  8 eyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      +ya  +l++L +++     +++e+ er   s++ + + l++L+ aglv++
  gi|336252828|ref|YP_004595935.1| 27 DYAQEILAVLIENPA----TAKELTERCPGSRVTIYRRLNRLEDAGLVET 72
                                      567777777776665....78***************************98 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.6e-05     0.038       2      53 ..      24      74 ..      23     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-05
                                      HHSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE CS
                              HxlR  2 iggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierev 53
                                      +g+ +   il  l++ +   +el++++p+ s+ ++ +rL +Le  gl+e e+
  gi|336252828|ref|YP_004595935.1| 24 LGDDYAQEILAVLIENPATAKELTERCPG-SRVTIYRRLNRLEDAGLVETEI 74
                                      677778889*******************9.89999*************9875 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.7e-05      0.06      11      60 ..      42      87 ..      33     109 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-05
                      Replic_Relax 11 Ttrqiarllfashra.....tarrrLarLrelgllsr.lrkrvggarggsepyvYa 60
                                      T++ +++       +     t++rrL+rL++ gl+++ +r r     +g +  +Y 
  gi|336252828|ref|YP_004595935.1| 42 TAKELTER------CpgsrvTIYRRLNRLEDAGLVETeIRIR----SDGNHCERYR 87
                                      55555555......3333448****************76655....2222333444 PP

>> HTH_36  Helix-turn-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     0.079      27      55 .]      42      70 ..      35      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      + + l +r+  s+ T++r ++ Le++G++
  gi|336252828|ref|YP_004595935.1| 42 TAKELTERCPGSRVTIYRRLNRLEDAGLV 70
                                      778999*********************85 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.3e-05     0.087      16      48 ..      39      71 ..      32      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.3e-05
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlie 48
                                      +p++ +eL ++   s+ t+ r l rLe++Gl+e
  gi|336252828|ref|YP_004595935.1| 39 NPATAKELTERCPGSRVTIYRRLNRLEDAGLVE 71
                                      578999*************************98 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 ?   12.5   0.0   9.4e-05     0.099       8      50 ..      32      72 ..      29      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.4e-05
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      iL  l e p   t +el +r+  ++ t +R L+ L+  G+ve+
  gi|336252828|ref|YP_004595935.1| 32 ILAVLIENPA--TAKELTERCPGSRVTIYRRLNRLEDAGLVET 72
                                      7777777777..59***************************96 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00012      0.12      28      57 ..      44      73 ..      40      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglverr 57
                                      +eL ++   sr t+ + L+rLe +glve +
  gi|336252828|ref|YP_004595935.1| 44 KELTERCPGSRVTIYRRLNRLEDAGLVETE 73
                                      799999999******************976 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.4e-05     0.089      41      60 ..      53      72 ..      31      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.4e-05
                                      -HHHHHHHHHHHHHTTSEEE CS
                               FUR 41 slaTVYrtLklleeaglvke 60
                                      s  T+Yr L+ le+aglv++
  gi|336252828|ref|YP_004595935.1| 53 SRVTIYRRLNRLEDAGLVET 72
                                      788***************74 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.8e-05     0.082      11      83 ..      21      95 ..      15     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.8e-05
                              ArsR 11 lqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEsqWrmpepgekpekeYhtsYskvqa 83
                                      l +++++  ++++  l ++  t++el+e++  +     + l+ L+ ++l+E+  r+ + g++ e+ Y+ + +k+ +
  gi|336252828|ref|YP_004595935.1| 21 LALLGDDYAQEILAVLIENPATAKELTERCPGSrvtIYRRLNRLEDAGLVETEIRIRSDGNHCER-YRLAVEKITV 95
                                      6677888999******************996554445689****************998888775.7777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 865.21
//
Query:       gi|336252829|ref|YP_004595936.1|  [L=250]
Description: hypothetical protein Halxa_1424 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.022   13.5   0.0      0.031   13.0   0.0    1.1  1  DUF1887   Domain of unknown function (DUF1887)


Domain annotation for each model (and alignments):
>> DUF1887  Domain of unknown function (DUF1887)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.7e-06     0.031      32     118 ..      39     125 ..      25     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-06
                           DUF1887  32 livteaq..kekanrlekvlkekgidveifeledevdleeleeslkglleelkaaeevvlNvtgGtklmalgayevf 106
                                       l+ +++   ++  +rl + l  +gi+v + e++   d+  +  ++  ++++++ ++ v +Nv+ G kl  +ga  + 
  gi|336252829|ref|YP_004595936.1|  39 LLADDEAaeASYHDRLVEDLSDHGITVHTREIDF-GDMYDVLGEITTIVDDYR-DDIVRVNVSSGPKLADIGAALAC 113
                                       5555544346778899999***********9965.578888899*********.9999*************997665 PP

                           DUF1887 107 RskhkrIfyvet 118
                                         + +  +yv +
  gi|336252829|ref|YP_004595936.1| 114 MATDASGYYVHP 125
                                       566666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1973.32
//
Query:       gi|336252830|ref|YP_004595937.1|  [L=204]
Description: regulatory protein TetR [Halopiger xanaduensis SH-6]
Scores for complete 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-13   50.9   6.4    3.1e-13   50.0   6.4    1.5  1  TetR_C_6   BetI-type transcriptional repressor, C-terminal
    1.9e-08   33.9   0.0    3.5e-08   33.1   0.0    1.5  1  TetR_N     Bacterial regulatory proteins, tetR family
    1.7e-06   28.2   0.8    4.9e-06   26.8   0.2    2.2  3  TetR_C_24  Tetracyclin repressor-like, C-terminal domain
    3.8e-05   23.7   0.6    0.00011   22.2   0.3    2.0  2  TetR_C_27  Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.013   15.6   0.7      0.028   14.4   0.7    1.6  1  TetR_C_7   AefR-like transcriptional repressor, C-terminal do
      0.099   12.5   0.0       0.14   12.0   0.0    1.2  1  RLL        RNA transcription, translation and transport facto


Domain annotation for each model (and alignments):
>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   6.4     1e-16   3.1e-13       2     113 ..      86     199 ..      85     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1e-16
                                       HHHHHHHHHCCSTHSHHHH..HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSTHHHHH CS
                          TetR_C_6   2 rerlraileallpldqerr..aelavwlafwaeaardpelaelqrenyarlrsnlrallaelaegglradadaeaaA 76 
                                       +e l+ ++e +lp++ +++  +++ +  a+ ++a++d+ ++e+++++++ +r++ +++++++ e+g+++d+d+e+aA
  gi|336252830|ref|YP_004595937.1|  86 QEHLETLIEYALPDEFDDDhlDFAGAIEALRGQAPHDETYQEQFAAADEFYRRLTAEVIRDGIEQGVFRDVDPERAA 162
                                       7999*********54444333699999************************************************** PP

                                       HHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHH CS
                          TetR_C_6  77 erlaAlidGLwlraalapeeldaeraralvrrhldal 113
                                       + ++  ++G   + ++a+ + + ++ar+ +++++++ 
  gi|336252830|ref|YP_004595937.1| 163 AFIVTTVHGARNQRVTADTDDPVRAARQELEAYVRTR 199
                                       *********************************9875 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 !   33.1   0.0   1.2e-11   3.5e-08       2      46 ..      19      63 ..      18      64 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.2e-11
                                      HHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                            TetR_N  2 ldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                      ++a+ e + ++Gy+++t+++I ++   sk+++Y++++sK+eLl a
  gi|336252830|ref|YP_004595937.1| 19 MEATYEALRKHGYSELTIQRIGDEFPKSKSLIYQHYDSKDELLVA 63
                                      6899**************************************987 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.87   2.6e+03      40      61 ..      74      95 ..      48     112 .. 0.56
   2 !   26.8   0.2   1.7e-09   4.9e-06      37      86 ..     122     171 ..      82     174 .. 0.88
   3 ?   -2.3   0.0       1.7   5.1e+03      37      56 ..     178     197 ..     172     201 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.87
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                         TetR_C_24 40 hreeiralrreyerllrdliee 61
                                      +   i a  ++ +++l+ lie 
  gi|336252830|ref|YP_004595937.1| 74 ADLPIDAEFDDAQEHLETLIEY 95
                                      4444555555555566665554 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 1.7e-09
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHHHHHHHHHC CS
                         TetR_C_24  37 spehreeiralrreyerllrdlieeGvaagefedldpklaalailgmlnw 86 
                                       ++ ++e+++a  + y+rl +++i++G+++g+f+d+dp+ aa +i++++++
  gi|336252830|ref|YP_004595937.1| 122 DETYQEQFAAADEFYRRLTAEVIRDGIEQGVFRDVDPERAAAFIVTTVHG 171
                                       56788999999999999***************************998875 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.7
                                       -HHHHHHHHHHHHHHHHHHH CS
                         TetR_C_24  37 spehreeiralrreyerllr 56 
                                       +++  + +ra r+e+e+ +r
  gi|336252830|ref|YP_004595937.1| 178 TADTDDPVRAARQELEAYVR 197
                                       55666677777877777766 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 ?   -2.0   0.0       1.2   3.7e+03      39      50 ..      83      94 ..      68     109 .. 0.68
   2 !   22.2   0.3   3.8e-08   0.00011      37      95 ..     128     183 ..     122     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                                      HHHHHHHHHHHH CS
                         TetR_C_27 39 evvekhieelee 50
                                      + +++h+e+l+e
  gi|336252830|ref|YP_004595937.1| 83 DDAQEHLETLIE 94
                                      444444444443 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 3.8e-08
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT-STT--HHHHHHHHHHHSGGGTSHHHHHHHGG CS
                         TetR_C_27  37 elevvekhieeleeqlaeIireGvaaGeFkaadpeaaaravfdatarfhhPalaaewsd 95 
                                       ++++++++ ++l    ae+ir+G+++G F+  dpe+aa  +++ +    +  + a+ +d
  gi|336252830|ref|YP_004595937.1| 128 QFAAADEFYRRL---TAEVIRDGIEQGVFRDVDPERAAAFIVTTVHGARNQRVTADTDD 183
                                       555555555554...589********************999987766666655555555 PP

>> TetR_C_7  AefR-like transcriptional repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.7   9.4e-06     0.028      29     103 ..     118     191 ..     107     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.4e-06
                                       HHHT-HHHHCCHHHT.T----HHHHHHHHHHHHTTSB-SS-HHHHHHHHHHHHHHHHTHHHHHH------HHHHH CS
                          TetR_C_7  29 eaerfPelarafyeagpgrveealaayLeaavaaGrLridDpelAAeqflgllkgelfwprlfgveeppseeeie 103
                                       +a+++    ++ ++a  + +++  a+++++  ++G  r  Dpe+AA+  +  ++g   +++   +++p+ ++++e
  gi|336252830|ref|YP_004595937.1| 118 QAPHDETYQEQ-FAAADEFYRRLTAEVIRDGIEQGVFRDVDPERAAAFIVTTVHGARNQRVTADTDDPVRAARQE 191
                                       56665444444.55548888888899***************************************9998888776 PP

>> RLL  RNA transcription, translation and transport factor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.6e-05      0.14      63     124 ..      69     128 ..      51     157 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.6e-05
                               RLL  63 lkdlecpieienk..ekkeevldwLlslAvkleYkDnadkieelkkklkqksklekkkseqeeq 124
                                       l+++e ++ i+ +  +++e  l+ L+++A+ +e+ D++ ++    ++l++++ ++++    +eq
  gi|336252830|ref|YP_004595937.1|  69 LEQFEADLPIDAEfdDAQE-HLETLIEYALPDEFDDDHLDFAGAIEALRGQAPHDETY---QEQ 128
                                       4555544444444415455.9***************9977777777666665554332...222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); 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):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 1758.48
//
Query:       gi|336252831|ref|YP_004595938.1|  [L=145]
Description: hypothetical protein Halxa_1426 [Halopiger xanaduensis SH-6]
Scores for 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:                       282  (0.0157287); 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:                         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 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1104.54
//
Query:       gi|336252832|ref|YP_004595939.1|  [L=392]
Description: aspartate kinase [Halopiger xanaduensis SH-6]
Scores for complete 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  159.4   2.7    1.1e-46  159.4   2.7    1.7  2  AA_kinase  Amino acid kinase family
    1.9e-13   50.0   0.0    8.7e-07   28.6   0.0    2.5  2  ACT_7      ACT domain
    2.9e-07   30.1   2.5      0.064   13.0   0.0    3.5  3  ACT        ACT domain
    0.00087   19.8   0.0        1.7    9.3   0.0    2.7  2  ACT_4      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 !  159.4   2.7   2.4e-50   1.1e-46       1     240 [.       1     226 [.       1     227 [. 0.92
   2 ?   -0.8   0.1      0.22   9.7e+02       9      82 ..     262     322 ..     260     343 .. 0.62

  Alignments for each domain:
  == domain 1  score: 159.4 bits;  conditional E-value: 2.4e-50
                                       TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHHTCCCCCHHHC....E..HHHHHH CS
                         AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllalksglssgelaaglrstleeagev 76 
                                       +rvV K+GG+sl+++e+  ++r+a+ iaa++e+g++++vV ++ gs+td ll+    ++ +e++             
  gi|336252832|ref|YP_004595939.1|   1 MRVVAKFGGTSLGSGER--IDRAADSIAAAVEDGHEIAVVASAmGSTTDDLLDD-ITFETDEAD------------- 61 
                                       79***************..***********************************.888888888............. PP

                                       HHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE......HHHTTTCEEECCHHHHHHHTT.-EEEEESEEE CS
                         AA_kinase  77 atrdalaslgerlvaallaaglpavglsaaaldateagr....degsdgnvesvdaeaieelleag.vvpvltgfig 148
                                         r++++s+ger + ++l+a+l+++g++a  l + ++++    de    +ve  +++a e   e++ vvpv+tgf +
  gi|336252832|ref|YP_004595939.1|  62 --RAQIVSMGERTSVRMLKAALASRGIDAVFLEPGSENWpvitDEYGEVDVEATQQRAREVAAEMDeVVPVITGFLA 136
                                       ..5***************************************7555555555555444444445544********** PP

                                       EETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHC CS
                         AA_kinase 149 ldeege...lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvk 222
                                         ++g    lgrg+sDt+a++ +++++Ad+++i+tdV+GV++ dp++v+ ar + eisvde+++    l+  G++v+
  gi|336252832|ref|YP_004595939.1| 137 EGPDGSittLGRGGSDTTAVMMGKYMDADEVVIVTDVEGVMTGDPNVVEGARNVGEISVDELRN----LSFRGAEVV 209
                                       ****************************************************************....********* PP

                                       HHHHHHHHHCTT-EEEEE CS
                         AA_kinase 223 hpaalaaarrggipvvIt 240
                                        p+al    ++  +v+++
  gi|336252832|ref|YP_004595939.1| 210 APSALSYKDGK-LDVRVV 226
                                       *****999887.998886 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.22
                                       TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHHHHHH CS
                         AA_kinase   9 GssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevatrdal 82 
                                       G ++ ++++ ++++l e +a+    + ++  V +g  ++ +++++ ++ ++ e+++        + ev+ rd+l
  gi|336252832|ref|YP_004595939.1| 262 GRAIRNESG-VFNHLSEALAES---DVNIDAVASGMDTVTFYIDE-AEAERAENIL--------HREVIARDEL 322
                                       556664444.455555555555...66666777777777777777.5555555552........3444444444 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.1e-07   0.00095       3      65 .]     252     314 ..     250     314 .. 0.93
   2 !   28.6   0.0   1.9e-10   8.7e-07       3      62 ..     328     387 ..     326     389 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.1e-07
                                       EEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE.-SS-EEEEEEGGGHHHHHHHHHH CS
                             ACT_7   3 edgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS.tyrtdyiLVpeedlekAveaLhe 65 
                                       e+  ++l+v g  ++   +G+   l+++Lae +++i +++   +t  + ++e+++e+A ++Lh+
  gi|336252832|ref|YP_004595939.1| 252 ERPLACLTVAGRAIRN-ESGVFNHLSEALAESDVNIDAVAsGMDTVTFYIDEAEAERAENILHR 314
                                       567899******9988.***********************9999******************96 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.9e-10
                                       EEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE.-SS-EEEEEEGGGHHHHHHH CS
                             ACT_7   3 edgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS.tyrtdyiLVpeedlekAvea 62 
                                       ++ +++++v g+ lp  ++Giv+ +++pLae+ I +  +  ++++  ++V+ ed ek +e+
  gi|336252832|ref|YP_004595939.1| 328 DSPIAVVRVTGGELPN-QPGIVSDIVTPLAEERIHLQDVItSATSVALFVEWEDREKTLEI 387
                                       67899*********99.*******************98888***************99875 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.029   1.3e+02      28      59 ..      38      66 ..      36      67 .. 0.86
   2 !   12.5   0.1     2e-05     0.092       8      59 ..     266     312 ..     265     314 .. 0.86
   3 !   13.0   0.0   1.4e-05     0.064       7      46 ..     341     375 ..     340     392 .] 0.75

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.029
                                      EEEEEEEEESTTECEEEEEEEEEEHHHHHHHH CS
                               ACT 28 idsieqrssedkvagivfvvivvdeedleevl 59
                                      ++s+  ++++d    + ++++++de+d ++++
  gi|336252832|ref|YP_004595939.1| 38 VASAMGSTTDD---LLDDITFETDEADRAQIV 66
                                      67888888888...999**********99986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2e-05
                                       ESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHH CS
                               ACT   8 pDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevl 59 
                                       +++ G+++ ++ ala+ ++Nid + ++ +     + +f ++++++e++e++l
  gi|336252832|ref|YP_004595939.1| 266 RNESGVFNHLSEALAESDVNIDAVASGMD-----TVTFYIDEAEAERAENIL 312
                                       5889*********************9988.....678888888888777775 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 1.4e-05
                                       EESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEE CS
                               ACT   7 vpDrPGlLarvfgaladrgiNidsieqrssedkvagivfv 46 
                                       +p++PG+ +++ + la+  i +  + ++ +     + + +
  gi|336252832|ref|YP_004595939.1| 341 LPNQPGIVSDIVTPLAEERIHLQDVITSAT-----SVALF 375
                                       79*****************99888888877.....44444 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00038       1.7      14      40 ..     266     292 ..     263     301 .. 0.87
   2 !    7.4   0.0    0.0015       6.5      15      43 ..     343     371 ..     339     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00038
                             ACT_4  14 edrkglLaditqviseekanivsvnak 40 
                                       ++++g+++ ++++++e+++ni +v + 
  gi|336252832|ref|YP_004595939.1| 266 RNESGVFNHLSEALAESDVNIDAVASG 292
                                       79********************99865 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0015
                             ACT_4  15 drkglLaditqviseekanivsvnaktrk 43 
                                       +++g+++di++ ++ee++++++v +++++
  gi|336252832|ref|YP_004595939.1| 343 NQPGIVSDIVTPLAEERIHLQDVITSATS 371
                                       99********************9998864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); 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):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2864.08
//
Query:       gi|336252833|ref|YP_004595940.1|  [L=48]
Description: hypothetical protein Halxa_1428 [Halopiger xanaduensis SH-6]
Scores for 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-05   22.3   2.5    9.9e-05   22.2   2.5    1.1  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
      0.006   16.5   1.9      0.033   14.1   1.9    1.9  1  zinc_ribbon_4  zinc-ribbon domain
  ------ inclusion threshold ------
      0.013   15.4   3.6       0.79    9.7   0.1    2.4  2  zf-C2HC_2      zinc-finger of a C2HC-type
       0.05   13.7   3.7        2.4    8.4   0.3    2.1  2  Zn-ribbon_8    Zinc ribbon domain


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 !   22.2   2.5   2.2e-08   9.9e-05      10      45 ..       5      41 ..       1      42 [. 0.83

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.2e-08
                     Zn_Tnp_IS1595 10 LealrWpngfvCPhCgsrkayrikt.rglfqCkeCrk 45
                                      L +l+ + g+ CPhC+s++   i + +gl +C +C++
  gi|336252833|ref|YP_004595940.1|  5 LRSLCRRLGVQCPHCASARTVGIPAtPGLRRCLACGE 41
                                      66666677899*******88888777*********86 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.9   7.4e-06     0.033       3      36 .]      14      44 ..      13      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.4e-06
                     zinc_ribbon_4  3 itCpsCkakyeiddeklpakgvkvrCskCghvFr 36
                                      ++Cp+C +++++    +pa+ +  rC +Cg++F+
  gi|336252833|ref|YP_004595940.1| 14 VQCPHCASARTVG---IPATPGLRRCLACGESFN 44
                                      79*********95...7**************996 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 ?    6.4   0.9     0.002       8.8       3       8 ..      14      19 ..      14      20 .. 0.93
   2 ?    9.7   0.1   0.00018      0.79       2      15 ..      33      46 ..      32      48 .] 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.002
                         zf-C2HC_2  3 vpCpkC 8 
                                      v+Cp+C
  gi|336252833|ref|YP_004595940.1| 14 VQCPHC 19
                                      8***** PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00018
                         zf-C2HC_2  2 lvpCpkCgRsFnpd 15
                                      l+ C  Cg sFn++
  gi|336252833|ref|YP_004595940.1| 33 LRRCLACGESFNES 46
                                      789999******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 ?    8.4   0.3   0.00053       2.4      27      35 ..      14      23 ..       3      26 .. 0.72
   2 ?    6.8   0.3    0.0017       7.5       7      16 ..      35      44 ..      35      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00053
                       Zn-ribbon_8 27 taCPeCgs.e 35
                                      ++CP+C s +
  gi|336252833|ref|YP_004595940.1| 14 VQCPHCASaR 23
                                      56****9854 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0017
                       Zn-ribbon_8  7 rCeeCghefe 16
                                      rC +Cg+ f+
  gi|336252833|ref|YP_004595940.1| 35 RCLACGESFN 44
                                      8******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 366.30
//
Query:       gi|336252834|ref|YP_004595941.1|  [L=453]
Description: Tryptophanase [Halopiger xanaduensis SH-6]
Scores for 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-76  256.5   0.1    4.2e-76  256.0   0.1    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    2.3e-05   23.9   0.4    0.00014   21.3   0.4    2.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.0   0.1   4.7e-80   4.2e-76       1     292 [.      42     413 ..      42     414 .. 0.98

  Alignments for each domain:
  == domain 1  score: 256.0 bits;  conditional E-value: 4.7e-80
                                       E-S-GGG----HHHHHHH.HCS----CCCT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEE CS
                   Beta_elim_lyase   1 DLlSDsvtkgteamsdaq.aaamlGdesYgedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeeviv 76 
                                       DLl+Ds   gt+amsdaq aa+  Gde+Y++++++ rLe av++++g e++++++qG++A+++l+ +ll   e  + 
  gi|336252834|ref|YP_004595941.1|  42 DLLTDS---GTGAMSDAQwAALLRGDEAYAGSRSFDRLESAVRDVMGVEHVVPTHQGRGAENVLYGTLLSDAEDAV- 114
                                       9*****...************************************************************6655555. PP

                                       ETT-HHHHSSTTHHHHCC--EEEEE-EBTT..........TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB CS
                   Beta_elim_lyase  77 tepahihfdetgaiaelagvklrdlknkea..........GkmdlekleaaikevgaheekiklisltvTnntagGq 143
                                         p+++hfd+t+a+++ +g++++d++ + a          G+++le+ +a+++evga  ++i+l++ t+Tnn+a+Gq
  gi|336252834|ref|YP_004595941.1| 115 -VPNNTHFDTTRAHVANQGAEPVDCPVDGAhdpdleapfkGNFSLERARALVDEVGA--DRIPLVIQTITNNSAAGQ 188
                                       .489***********************99999*************************..****************** PP

                                       ---HHHHHHHHHHHHHCT-EEEEEETTHHHHH.............HHHTS-CHHHHTTSSEEEEESSSTT--SS-EE CS
                   Beta_elim_lyase 144 vvsleelrevaaiakkygiplhlDgARfanaa.............kslgeivkemfsyvDsvtmslkKdllanvGgv 207
                                       +vs+++ r+v+++a++ + ++++D++Rfa++a             ++++ei++e + y+D v+ms+kKd+l+n Gg+
  gi|336252834|ref|YP_004595941.1| 189 PVSVANTRRVRDFADEIDATFVIDACRFAENAyfvqqredefaaeTEIAEIAREQLGYADAVVMSGKKDGLVNTGGF 265
                                       ***************************************************************************** PP

                                       EEE-HH.........................................HHHHHHHHHHHHT---SSTHHHHH...... CS
                   Beta_elim_lyase 208 lafrddel.....................................edylaerveqrkylggglrqagvlaa...... 241
                                       +a++d+el                                       y+a rveq+++lg+ lr+agv++       
  gi|336252834|ref|YP_004595941.1| 266 VATDDEELferckqrailyegfptyggmagrdleamavglreaveRSYVADRVEQVRTLGSLLRDAGVPIYepvggh 342
                                       ******99********************************************************************* PP

                                       ..............................HHHHHHHHSSTTHHHHHHHHHHHHHHHHHCT--EEECCGTTCCEEEE CS
                   Beta_elim_lyase 242 ............................leagiraleeglaslerdhktaeqlaeklelvrlaiprrvytqehldyv 290
                                                                   +e g+r +e+g          a   ae+ elvrla+prr+y  eh+d+v
  gi|336252834|ref|YP_004595941.1| 343 avyldaaaalphleadafpgqalvcelyREGGVRGVELG--------SFAFPDAERPELVRLAVPRRTYHREHFDHV 411
                                       **************************************9........6788889999*******************9 PP

                                       E. CS
                   Beta_elim_lyase 291 aa 292
                                       a+
  gi|336252834|ref|YP_004595941.1| 412 AE 413
                                       97 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 !   21.3   0.4   1.6e-08   0.00014      12     195 ..      59     278 ..      50     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.6e-08
                                       HHHTSS-SSS.SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EE CS
                   DegT_DnrJ_EryC1  12 evlksgwlts.gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakp 87 
                                       ++l+++      +  +++E+a+++ +gv+h++++  G  A  +++  l  +++d V+   + F +t + v++ ga+p
  gi|336252834|ref|YP_004595941.1|  59 ALLRGDEAYAgSRSFDRLESAVRDVMGVEHVVPTHQGRGAENVLYGTLLSDAEDAVVPNNTHFDTTRAHVANQGAEP 135
                                       55666655552566799******************************9999999999888889999*********** PP

                                       EEE-B-TT.........TSSB-GGGCGGG--TTE........EEEEEB-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1  88 vfvDvdpd.........tynidpaaieaaitert........kaIlpVhlyGqva...dmdalkaiaakhglkvieD 144
                                       v + vd +           n + ++++a++ e          + I+   ++Gq++   +  ++++ a++ +  ++ D
  gi|336252834|ref|YP_004595941.1| 136 VDCPVDGAhdpdleapfKGNFSLERARALVDEVGadriplviQTITNNSAAGQPVsvaNTRRVRDFADEIDATFVID 212
                                       *8777643112222333688999999999998888888999999999999999762225567888899999999999 PP

                                       -TT.-TT-EETT.................EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHH CS
                   DegT_DnrJ_EryC1 145 aAh.AlGatykg.................kkvGalgdaavfSFyptKnlttGeGGavvtndeelaekar 195
                                       a+  A  a + +                 +   +lg a ++ + ++K   +  GG v t+deel e+++
  gi|336252834|ref|YP_004595941.1| 213 ACRfAENAYFVQqredefaaeteiaeiarE---QLGYADAVVMSGKKDGLVNTGGFVATDDEELFERCK 278
                                       987344455544677888888777665522...344455566668888888888999999999888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3453.40
//
Query:       gi|336252835|ref|YP_004595942.1|  [L=121]
Description: hypothetical protein Halxa_1430 [Halopiger xanaduensis SH-6]
Scores for 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  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 868.93
//
Query:       gi|336252836|ref|YP_004595943.1|  [L=376]
Description: ThiB subfamily ABC transporter periplasmic binding protein [Halopiger xanaduensis SH-6]
Scores for 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-22   79.2   0.0      4e-22   78.8   0.0    1.1  1  SBP_bac_6   Bacterial extracellular solute-binding protein
      4e-10   40.0   0.0    5.5e-10   39.5   0.0    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    1.2e-07   31.7   0.3    1.9e-07   31.1   0.3    1.2  1  SBP_bac_11  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.018   15.0   0.0    1.3  1  SBP_bac_1   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   8.9e-26     4e-22      22     225 ..     125     332 ..     123     356 .. 0.91

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 8.9e-26
                         SBP_bac_6  22 glfqpldpanlpnvnkdfaeeglkdpdgkyypygvgplvlavnkdrlkgrpvPksWaDLldPeykgkvalpgnngsd 98 
                                       +lf+ l+ ++l++v +  +e ++ dp g+  p+++g+l+l++++  l+   +P s++ Ll+ ey+      +++ sd
  gi|336252836|ref|YP_004595943.1| 125 ELFESLERDRLDRVGRLRDELTVDDPGGRVLPFDTGYLSLVYDERDLESG-PPDSFDGLLESEYERALLAQDPRSSD 200
                                       68999999*******87779999999*********************766.6************************* PP

                         SBP_bac_6  99 lfealllalykdfgedgvkkllrnlkanlhpaq...mvkaagslesgepavsvvpyffadilpekkkgk...nlkvv 169
                                       +  a+ll +    gedg+++++r+l++n+   +   ++ + ++  +ge   s+v+ +++d + +   ++     +v 
  gi|336252836|ref|YP_004595943.1| 201 PGLAFLLWTIAAAGEDGYREYWRALRDNGLRLAgswTDAYRNRYLEGE--GSMVVSYSTDRVGAAAAERplaLHQVA 275
                                       ******************************999999999999999**9..9**************999966555788 PP

                         SBP_bac_6 170 wPedGalvspifmlvkkg.kkkelakafidfllspevqailakaggvfPvvtnpavl 225
                                         ed ++ +++f++v ++  +kela++f+dflls ++qa +a+ + +fP+v+++ v+
  gi|336252836|ref|YP_004595943.1| 276 MLEDAGYRNTEFAAVFADgARKELAYEFLDFLLSSTAQAEIAARNVQFPAVADASVD 332
                                       9999**********************************************8444443 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   1.2e-13   5.5e-10      85     270 ..     153     332 ..     124     342 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.2e-13
                                       ---EEEEEEE-EEEEEHHHHHHS.---BHHHHHHHHHHHHHH-SEGG---G......GGGGGTHHETTEE---H..H CS
                         SBP_bac_8  85 ygvPyasetpyvliynkdllekaedpktwdellaaakklkgkfglpdpasg......wlqaallakdgksldddggk 155
                                         +P++++    l+y++  le   +p+++d+ll+   ++ +++ l++++ +      +l+++  a +g++       
  gi|336252836|ref|YP_004595943.1| 153 RVLPFDTGY-LSLVYDERDLESG-PPDSFDGLLE--SEY-ERALLAQDPRSsdpglaFLLWTIAA-AGED------- 216
                                       568*****7.8**********98.**********..999.5555543332213444488888888.6554....... PP

                                       HH.HHHHHHHHHHHHTT-EE.-S...--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE...--S--EEEEEEEEE CS
                         SBP_bac_8 156 dglkealellkklkdngkty.dtg.adavsefanGevaftingswdiaaaqkagkklgai...vpkqgsfaggkgla 227
                                            ++e+++ l+dng  + +++ +++ + + +Ge  +++++s d   a++a+ +l+     ++ ++   ++++ a
  gi|336252836|ref|YP_004595943.1| 217 ----GYREYWRALRDNGLRLaGSWtDAYRNRYLEGEGSMVVSYSTDRVGAAAAERPLALHqvaMLEDAGYRNTEFAA 289
                                       ....48999********9665455478999************999999999888777644322679*********** PP

                                       EBTTS-HHHHHHHHHHHHHTTSHHHHHHHH.HH---BS-S-TTT CS
                         SBP_bac_8 228 vpknaknedlaAldFlkwltspenqaalae.ktgyipvnksaal 270
                                       v+++   ++l A +Fl +l+s+ +qa+ a  + +++ v +++ +
  gi|336252836|ref|YP_004595943.1| 290 VFADGARKEL-AYEFLDFLLSSTAQAEIAArNVQFPAVADASVD 332
                                       *********9.****************99856666666665554 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.3   4.3e-11   1.9e-07      95     225 ..     178     317 ..     157     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4.3e-11
                                       SHHHHHHSS-..-EEEE--T-TTTTHH.H.HHHGGG--...HHHHHHHHHTEEEEESSHHHHHHH.HHTTT-SEEEE CS
                        SBP_bac_11  95 gwadLlkpgl..klavadPttspsGlaal.alleaaga...qellkalekkvvklgessrqllta.veageadagiv 164
                                       +++ Ll  +    l   dP++s  Gla l  +++aag    +e+++al+++  +l++s ++++     +ge  ++++
  gi|336252836|ref|YP_004595943.1| 178 SFDGLLESEYerALLAQDPRSSDPGLAFLlWTIAAAGEdgyREYWRALRDNGLRLAGSWTDAYRNrYLEGEGSMVVS 254
                                       555566665542477889***99999777688888888899****************999999887999******** PP

                                       EHHHH...H..HSTTSSEEE.E--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHH CS
                        SBP_bac_11 165 yesea...kaaengdkleav.ylpeglnldpldypaavlkkaakreaAraFlafLrspeaqailr 225
                                       y ++    +aae++  l+ v  l +  + + ++++a+ +++a ++e A +Fl+fL+s+ aqa ++
  gi|336252836|ref|YP_004595943.1| 255 YSTDRvgaAAAERPLALHQVaMLEDAGY-RNTEFAAVFADGA-RKELAYEFLDFLLSSTAQAEIA 317
                                       *996656566689999999966677777.6899988666655.9*****************9765 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   4.1e-06     0.018     231     315 .]     244     314 ..     144     314 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.1e-06
                                       H.TTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHH CS
                         SBP_bac_1 231 e.aGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFld 306
                                       + +Ge  m +++++++         v++aa+ +++  +  va+    +++++   ++   a++++ + +e A +Fld
  gi|336252836|ref|YP_004595943.1| 244 YlEGEGSMVVSYSTDR---------VGAAAAERPLALHQ-VAM---LEDAGYR--NTEFAAVFADGARKELAYEFLD 305
                                       3389999999999993.........33333333333333.222...2334444..9********************* PP

                                       HHTSHHHHH CS
                         SBP_bac_1 307 fllspeaqa 315
                                       flls+ aqa
  gi|336252836|ref|YP_004595943.1| 306 FLLSSTAQA 314
                                       *****9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2723.26
//
Query:       gi|336252837|ref|YP_004595944.1|  [L=374]
Description: hypothetical protein Halxa_1432 [Halopiger xanaduensis SH-6]
Scores for 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  104.3  37.0    1.7e-29  103.0  37.0    1.5  1  AI-2E_transport  AI-2E family transporter
     0.0015   18.8  15.4     0.0015   18.8  15.4    3.4  3  DUF456           Protein of unknown function (DUF456)


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0  37.0   1.9e-33   1.7e-29       6     325 ..      26     333 ..      21     335 .. 0.88

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 1.9e-33
                   AI-2E_transport   6 vllllllalypfiselllplliAlvlayllnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvplliaqltql 82 
                                       v ll ++    ++ e+l ++l+Al +ay+l p+  +L +rg+  ++a+++ +++ +v +v ++  ++    ++l   
  gi|336252837|ref|YP_004595944.1|  26 VALLGIVTGAILL-EVLGTILFALTVAYVLLPLQGWLVRRGLTEWVAAAAATVIGFVGAVAVFSPIA----VTLYFR 97 
                                       3334444444444.5999******************************9999888887777776666....666666 PP

                   AI-2E_transport  83 vkslpayidslqnilnelpslleelenliqalkqslskilsnilssilnsllsllasllglilslvlvllllfflll 159
                                       v+++  +i++l + +     +         +   ++s++ + +++++ +++ +++ sl+ l+++++l+l llf lll
  gi|336252837|ref|YP_004595944.1|  98 VDEITSIIEGLPEAVPITAFNI--------TYTIEASEVQAFVVDYLSSIAATFALSLPVLAIKFALFLTLLFALLL 166
                                       6666666666665555444333........34578899999999999999999************************ PP

                   AI-2E_transport 160 dgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvglanliPy 236
                                       + +   +  +  +p+++r+ v a++ ++ +tl +++  q+ +++++ ++++ ++++l ++ +l+lai++ +++++P+
  gi|336252837|ref|YP_004595944.1| 167 EADSAGRAAIAPIPREYRDVVYALATRARETLYAIYVLQLATSVATLLIAYPVFWLLDYEMSLTLAIIAAILQFVPI 243
                                       ***************************************************************************** PP

                   AI-2E_transport 237 iGavivlipiaiialltgg.ikevlivlivvllvqliegnilePklmgkrlglhplvillsllaggklfGlvGlila 312
                                       +G+ + +  ia++ ++ g   ++vli++++++l+  + +  ++P+l ++++gl+  + ++ + +g+  +G++G+ ++
  gi|336252837|ref|YP_004595944.1| 244 VGPSVLVGLIAVYHVTAGEiAAAVLIAVFGLVLIGWLPDIAVRPRLARRSAGLPGSLYFIGFTGGLFTLGPIGIVVG 320
                                       *******************77889999************************************************** PP

                   AI-2E_transport 313 vpltavikailea 325
                                       ++++av+ ++++ 
  gi|336252837|ref|YP_004595944.1| 321 PLIVAVFVEAVDL 333
                                       ********99985 PP

>> DUF456  Protein of unknown function (DUF456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   7.9   0.00011      0.95      64     123 ..      24      86 ..       7      98 .. 0.60
   2 ?   -1.1   0.4      0.23   2.1e+03      72      94 ..     139     163 ..     119     177 .. 0.51
   3 !   18.8  15.4   1.7e-07    0.0015       7      97 ..     245     331 ..     237     339 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                            DUF456  64 ligaivGaivGffllpplGlllgpflgaflg....EllrarkdlreAlkaalgalvGfllgtlv 123
                                        ++a++G++ G++ll +lG +l ++  a++      +l++r  l+e ++aa ++++Gf+  ++v
  gi|336252837|ref|YP_004595944.1|  24 GVVALLGIVTGAILLEVLGTILFALTVAYVLlplqGWLVRR-GLTEWVAAAAATVIGFVGAVAV 86 
                                       244555555555566699*9999999999872221334444.6666667777777777666554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.23
                            DUF456  72 ivGff..llpplGlllgpflgaflg 94 
                                       i+ +f   lp+l + +  fl+ +++
  gi|336252837|ref|YP_004595944.1| 139 IAATFalSLPVLAIKFALFLTLLFA 163
                                       3333321122333333333333333 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 1.7e-07
                            DUF456   7 GtllilaglllyalltgfaelgwlflavllvlallglvldylapalgakraGaskrgligaivGaivGffllpplGl 83 
                                       G+ ++++ +++y+++ g  e+   +l++++ l+l+g++ d+++  + a+r  +   +    ++G   G+f l+p+G+
  gi|336252837|ref|YP_004595944.1| 245 GPSVLVGLIAVYHVTAG--EIAAAVLIAVFGLVLIGWLPDIAVRPRLARRSAGLPGS--LYFIGFTGGLFTLGPIGI 317
                                       88999999999999855..7999*************************998887777..5688888899999***** PP

                            DUF456  84 llgpflgaflgEll 97 
                                       ++gp++ a+++E +
  gi|336252837|ref|YP_004595944.1| 318 VVGPLIVAVFVEAV 331
                                       ************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 2742.25
//
Query:       gi|336252838|ref|YP_004595945.1|  [L=227]
Description: hypothetical protein Halxa_1433 [Halopiger xanaduensis SH-6]
Scores for 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-18   66.0  36.8    3.8e-18   65.7  36.8    1.1  1  DUF5518          Family of unknown function (DUF5518)
  ------ inclusion threshold ------
       0.43   10.7   3.5       0.49   10.5   0.9    2.2  2  PT-VENN          Pre-toxin domain with VENN motif
        4.1    7.3  20.4         32    4.5   0.6    3.8  3  Rick_17kDa_Anti  Glycine zipper 2TM domain


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7  36.8   6.4e-22   3.8e-18       3     118 .]       9     117 ..       7     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 6.4e-22
                           DUF5518   3 aaliGavvaivlslllglllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllvlll....gl 75 
                                        a+iGavv ivls++++          ++++gG+vaG+l+g ds++ga+aGa+aG+i+++pv++++++ll     g+
  gi|336252838|ref|YP_004595945.1|   9 HAVIGAVVGIVLSFIPF----------STVIGGAVAGFLEGPDSRAGAIAGAVAGVIAFVPVAAVAVLLLGflgfGM 75 
                                       69***************..........***********************************55555555558999* PP

                           DUF5518  76 vaaigglagfvallvalllvvllllvvllvilgaiGGaiGgll 118
                                       + a++++ gf+++++a+l++ +l++++++v+l+++GG++G++l
  gi|336252838|ref|YP_004595945.1|  76 GVAAAPFEGFAVAAFAVLVF-ALIVLLYTVGLSLLGGYLGAYL 117
                                       ************99999999.********************97 PP

>> PT-VENN  Pre-toxin domain with VENN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.23   1.4e+03      21      28 ..      10      17 ..       4      21 .. 0.55
   2 ?   10.5   0.9   8.2e-05      0.49      16      41 ..      26      53 ..      22      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.23
                           PT-VENN 21 GlaGgvvg 28
                                      +++G+vvg
  gi|336252838|ref|YP_004595945.1| 10 AVIGAVVG 17
                                      44444443 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 8.2e-05
                           PT-VENN 16 stlaaGlaGgvvg..gtladavaGaeag 41
                                      st+++G+++g     ++ a a+aGa ag
  gi|336252838|ref|YP_004595945.1| 26 STVIGGAVAGFLEgpDSRAGAIAGAVAG 53
                                      89999988887777************99 PP

>> Rick_17kDa_Anti  Glycine zipper 2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.6    0.0054        32       3      10 ..      10      17 ..       6      21 .. 0.57
   2 ?    0.9  12.6      0.07   4.2e+02      12      36 ..      28      55 ..      26      56 .. 0.77
   3 ?    4.3   0.0    0.0062        37       4      19 ..     108     124 ..     106     136 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0054
                   Rick_17kDa_Anti  3 aliGAaaG 10
                                      a+iGA++G
  gi|336252838|ref|YP_004595945.1| 10 AVIGAVVG 17
                                      44444444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.07
                   Rick_17kDa_Anti 12 vaGaaigg...gggrvlGavvGAaaGav 36
                                      v+G+a++g   g ++++Ga++GA+aG +
  gi|336252838|ref|YP_004595945.1| 28 VIGGAVAGfleGPDSRAGAIAGAVAGVI 55
                                      5666666667678999999999999976 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0062
                   Rick_17kDa_Anti   4 liGAaaGgvaGaai.gg 19 
                                       l+G+ +G+++ +   g+
  gi|336252838|ref|YP_004595945.1| 108 LLGGYLGAYLAREYpGK 124
                                       67788888887777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 1690.96
//
Query:       gi|336252839|ref|YP_004595946.1|  [L=385]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for complete 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-90  303.9  36.0    2.3e-90  302.8  36.0    1.5  1  FecCD     FecCD transport family
     0.0022   17.5  19.9      0.008   15.7  19.9    1.9  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 !  302.8  36.0   2.5e-94   2.3e-90       3     312 .]      40     378 ..      37     378 .. 0.95

  Alignments for each domain:
  == domain 1  score: 302.8 bits;  conditional E-value: 2.5e-94
                             FecCD   3 llllllslllgavkispsevfeallgka...............................dsleaeivlelrlprvla 48 
                                       +++ ++ +++ga+++s+ e ++al++ +                                s++  iv+++rlprvl+
  gi|336252839|ref|YP_004595946.1|  40 FISGFVQISFGAYSMSFGEAWRALFDTTvlfdyrwllnfllgeglletltgyragelpeLSTATHIVWNIRLPRVLT 116
                                       56778899999999999999999998888888888888888888888777777777777666666************ PP

                             FecCD  49 allvGaaLavaGallQtvtrNpLadPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkr 125
                                       a++vG+ L+v+Ga++Q+vtrN+La+P ilG+ssga+l+++l+l+++  s  +  lpl+a +g+++a+llv+++a ++
  gi|336252839|ref|YP_004595946.1| 117 AIIVGVNLSVSGAIFQAVTRNELASPFILGVSSGAGLMILLVLTVF--SGLTTILPLIAAIGGAIAFLLVYVIA-WN 190
                                       ********************************************96..667779********************.** PP

                             FecCD 126 kgasplkliLaGiavsallsaltsllllll.neealesilfwllGslsgaswskvllllvllllllllllllarkld 201
                                       +g+sp++l+LaG++vs++++++ +++ +++ + + +++++ wl Gsl g++w++v ++l+++++++ l++l +r+l+
  gi|336252839|ref|YP_004595946.1| 191 HGTSPVRLVLAGVIVSTVFGSFQTAMFVFTdDIAVVQQAISWLNGSLTGVNWQHVRIALPWSAVSVGLAYLSSRQLN 267
                                       ****************************99788899***************************************** PP

                             FecCD 202 llalgdetAkslGvnvervrllllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGalllll 278
                                       +l lg++tA+slG++vervr+ l  +++l++a+++a++G+++FvGLivPh++r +vg+d+rkl++ ++++G +l+++
  gi|336252839|ref|YP_004595946.1| 268 VLLLGEQTASSLGMSVERVRFGLSGIAVLAAAASIAVAGIVSFVGLIVPHVVRNVVGSDYRKLMIGCVFVGPALMIV 344
                                       ***************************************************************************** PP

                             FecCD 279 adllarlllsptelpvgivtaliGapffiylllr 312
                                       ad+ arl+lsp++lpvgivt liG+p+f+yl++r
  gi|336252839|ref|YP_004595946.1| 345 ADVGARLALSPVQLPVGIVTGLIGGPYFLYLMRR 378
                                       ********************************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 !   15.7  19.9     9e-07     0.008      81     223 ..     196     340 ..     113     354 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9e-07
                             ABC-3  81 kedtaigivlsvfla...lglvlvslikkskvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfd 154
                                          ++ g+++s++++    ++++++    + ++  s+L G++ +++ + + + +  +av + l+ l  ++l ++ + 
  gi|336252839|ref|YP_004595946.1| 196 VRLVLAGVIVSTVFGsfqTAMFVFTDDIAVVQQAISWLNGSLTGVNWQHVRIALPWSAVSVGLAYLSSRQLNVLLLG 272
                                       33467788888877532246666665555889999****************************************** PP

                             ABC-3 155 eelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglv 223
                                       e++A + g+sv+++++ l  + +la ++++ ++G++  +  li+P ++   ++++ ++l+i  + +g  
  gi|336252839|ref|YP_004595946.1| 273 EQTASSLGMSVERVRFGLSGIAVLAAAASIAVAGIVSFVG-LIVPHVVRNVVGSDYRKLMIGCVFVGPA 340
                                       **********************************998777.578***************9999888855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2895.83
//
Query:       gi|336252840|ref|YP_004595947.1|  [L=302]
Description: Iron-chelate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-31  109.2   0.0    2.9e-31  108.8   0.0    1.2  1  ABC_tran        ABC transporter
    1.4e-11   44.8   3.9    9.3e-06   25.7   0.4    2.2  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    1.1e-10   41.4   0.3    2.3e-08   33.7   0.3    2.1  1  SMC_N           RecF/RecN/SMC N terminal domain
    1.5e-05   24.7   0.0    2.9e-05   23.7   0.0    1.4  1  AAA_29          P-loop containing region of AAA domain
    0.00015   21.6   0.0     0.0009   19.1   0.0    1.8  2  AAA_15          AAA ATPase domain
    0.00041   19.3   0.4      0.026   13.3   0.0    2.6  2  ABC_ATPase      Predicted ATPase of the ABC class
     0.0005   20.6   0.0    0.00077   20.0   0.0    1.3  1  AAA_23          AAA domain
     0.0012   18.5   0.6     0.0021   17.7   0.0    1.7  2  AAA_25          AAA domain
     0.0023   18.2   1.6      0.017   15.4   1.6    2.1  1  AAA_22          AAA domain
     0.0024   18.0   1.7     0.0058   16.8   0.1    2.4  2  AAA_33          AAA domain
     0.0061   16.5   0.5      0.017   15.1   0.1    1.8  2  NACHT           NACHT domain
     0.0069   16.3   0.4      0.016   15.1   0.4    1.5  1  RsgA_GTPase     RsgA GTPase
     0.0073   16.7   0.8      0.014   15.8   0.8    1.7  1  AAA_16          AAA ATPase domain
     0.0079   15.9   0.4      0.014   15.1   0.4    1.6  1  AAA_30          AAA domain
  ------ inclusion threshold ------
      0.013   16.0   0.0      0.029   14.8   0.0    1.7  2  AAA             ATPase family associated with various cellula
      0.043   13.5   0.2       0.28   10.9   0.0    2.0  2  AAA_24          AAA domain
      0.047   13.3   0.0       0.11   12.1   0.0    1.6  1  SRP54           SRP54-type protein, GTPase domain
      0.052   13.6   0.0        0.1   12.6   0.0    1.4  1  TsaE            Threonylcarbamoyl adenosine biosynthesis prot
      0.067   13.2   0.0       0.22   11.6   0.0    1.8  2  AAA_14          AAA domain
      0.087   12.0   0.0       0.15   11.2   0.0    1.3  1  TIP49           TIP49 P-loop domain
      0.095   12.2   0.0       0.31   10.5   0.0    1.7  2  RecA            recA bacterial DNA recombination protein
       0.12   12.1   0.5        2.8    7.6   0.0    2.1  2  ATP_bind_1      Conserved hypothetical ATP binding protein
       0.13   12.9   0.0       0.36   11.4   0.0    1.8  1  AAA_18          AAA domain
       0.13   11.8   0.2       0.32   10.6   0.0    1.7  2  cobW            CobW/HypB/UreG, nucleotide-binding domain
       0.15   11.8   0.1        0.3   10.8   0.1    1.5  1  Cytidylate_kin  Cytidylate kinase
       0.17   11.8   0.3        2.2    8.2   0.0    2.1  2  NTPase_1        NTPase
       0.17   12.3   0.0       0.32   11.4   0.0    1.5  1  RNA_helicase    RNA helicase
       0.17   11.0   0.1       0.36   10.0   0.1    1.4  1  NB-ARC          NB-ARC domain
       0.29   11.2   0.5          2    8.5   0.1    2.1  2  MMR_HSR1        50S ribosome-binding GTPase


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   4.7e-34   2.9e-31       4     136 ..      50     195 ..      47     196 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 4.7e-34
                                       EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                          ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                        sl++ eg+++a++G+nG+GKStLlk +a++++ ++G++lldg d++e e++++ +++g l+qe+     ltv+e  
  gi|336252840|ref|YP_004595947.1|  50 ESLSVPEGQVTALIGPNGSGKSTLLKGIARQVSLESGSVLLDGSDIHELEKKEFARKLGLLSQENVSPGSLTVEELv 126
                                       589*************************************************************888888999999* PP

                                       ................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                       e+++ +++a++  g ++l++t +     sLSgGqkq v +a++l+++ ++lllDEpt
  gi|336252840|ref|YP_004595947.1| 127 fhgryphrgffesttdEDEAAVDRAIALAGVDHLRETEL----DSLSGGQKQLVWIAMVLAQETDVLLLDEPT 195
                                       ************998888888******************....*****************************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 !   25.7   0.4   1.5e-08   9.3e-06       1      21 [.      59      79 ..      59     117 .. 0.81
   2 !   20.5   0.2   5.7e-07   0.00036     226     293 ..     157     222 ..     116     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.5e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldl 21
                                      +++liGpNgsGKS+LL+ +  
  gi|336252840|ref|YP_004595947.1| 59 VTALIGPNGSGKSTLLKGIAR 79
                                      69****************953 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 5.7e-07
                            AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvi 293
                                        ++ +e+ +++lS G+k+l   ++++l++    ++ll+DEp ++L+ + + +++e++++l++  ++ ++
  gi|336252840|ref|YP_004595947.1| 157 VDHLRETELDSLSGGQKQL-VWIAMVLAQET--DVLLLDEPTTFLDVHHQLEVMEIVEALRDySDVTIV 222
                                       5788999************.88888888777..9*************9998888888777765556555 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 !   33.7   0.3   3.8e-11   2.3e-08      24     196 ..      57     223 ..      48     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 3.8e-11
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsi 99 
                                        ++ta++GpNGSGKs ll  i    + +s + l     sd ih+    ++ ++a+   ++++e+ +  + + ee++ 
  gi|336252840|ref|YP_004595947.1|  57 GQVTALIGPNGSGKSTLLKGIARQVSLESGSVLLDG--SD-IHE---LEKKEFARKLGLLSQENVSpGSLTVEELVF 127
                                       579******************666666655443322..22.444...333344443333444444436789999999 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                         r  + g  e + ++ e+       l    ++   + ++LSgG+k+Lv +a+++A    + + + llDe    LD 
  gi|336252840|ref|YP_004595947.1| 128 HGRYPHRGFFESTTDEDEAAVDRAIALAGVDHLretELDSLSGGQKQLVWIAMVLA----QETDVLLLDEPTTFLDV 200
                                       9999999999999999998887666665544441114568**************98....567799*********** PP

                                       HHHHHHHHHHHHHCTTSEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 174 knvkkvaellkeksknaQfivis 196
                                       ++  +v e++++ ++ + + ++ 
  gi|336252840|ref|YP_004595947.1| 201 HHQLEVMEIVEALRDYSDVTIVL 223
                                       **********9999888776664 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 !   23.7   0.0   4.7e-08   2.9e-05      12      40 ..      47      75 ..      43      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.7e-08
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllD 40
                                      +dg+++++ + ++t l+Gp+GsGKSTll 
  gi|336252840|ref|YP_004595947.1| 47 IDGESLSVPEGQVTALIGPNGSGKSTLLK 75
                                      577888887555***************95 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.4e-06    0.0009      25      75 ..      59     105 ..      46     113 .. 0.77
   2 ?    0.7   0.0      0.54   3.3e+02     287     332 ..     142     194 ..      93     213 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-06
                            AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenisesk 75 
                                       +t liG+N+sGKS++l+ +    + +    +  + ++ +d+++ e++++ +
  gi|336252840|ref|YP_004595947.1|  59 VTALIGPNGSGKSTLLKGIARQVSLE----SGSVLLDGSDIHELEKKEFAR 105
                                       9****************996666555....566777777777777766655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.54
                            AAA_15 287 k................ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEP 332
                                                        +  e++l+  + G+++l+++++ ++            ++ll++EP
  gi|336252840|ref|YP_004595947.1| 142 DedeaavdraialagvdHLRETELDSLSGGQKQLVWIAMVLAQET---------DVLLLDEP 194
                                       055555555555666656678999999*********998765322.........34556665 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 !   13.3   0.0   4.2e-05     0.026     240     268 ..      52      81 ..      26      83 .. 0.90
   2 ?    3.3   0.1     0.046        28     324     351 ..     169     196 ..     159     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.2e-05
                                       EEE-SS.EEEEEE-TTSSHHHHHHHHHHCC CS
                        ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAlekGv 268
                                       + +p+G vt+++G++  GKsTLL+ +++ v
  gi|336252840|ref|YP_004595947.1|  52 LSVPEGqVTALIGPNGSGKSTLLKGIARQV 81 
                                       789*********************998765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.046
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDts 351
                                       SG   q ++i+  l  ++++lL+DE t+
  gi|336252840|ref|YP_004595947.1| 169 SGGQKQLVWIAMVLAQETDVLLLDEPTT 196
                                       8889999999999999999999999876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.2e-06   0.00077      19      39 ..      57      77 ..      46     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.2e-06
                            AAA_23 19 kgltlItGpNGaGKTTildAi 39
                                        +t+++GpNG+GK+T+l  i
  gi|336252840|ref|YP_004595947.1| 57 GQVTALIGPNGSGKSTLLKGI 77
                                      579***************988 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.3e-06    0.0021      30      61 ..      54      87 ..      37     160 .. 0.88
   2 ?   -2.7   0.1       5.9   3.6e+03     169     188 ..     207     226 ..     173     228 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.3e-06
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava..tGk 61
                                      +p+g +++l+G+ g+GK+tl+  +a  v+  +G+
  gi|336252840|ref|YP_004595947.1| 54 VPEGQVTALIGPNGSGKSTLLKGIARQVSleSGS 87
                                      69*********************99999865555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.9
                            AAA_25 169 vealeriarrtgaavllvhH 188
                                       +e +e +++  +++++lv H
  gi|336252840|ref|YP_004595947.1| 207 MEIVEALRDYSDVTIVLVLH 226
                                       33344444555666666666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.6   2.8e-05     0.017       6     113 ..      58     214 ..      55     230 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.8e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka.......... 70 
                                       ++++++G+ G+GK+tll+ +++q          +++ v+ + +     + k+++r+l    +++ +           
  gi|336252840|ref|YP_004595947.1|  58 QVTALIGPNGSGKSTLLKGIARQVSL-------ESGSVLLDGSDIHelEKKEFARKLGLLSQENVSPgsltveelvf 127
                                       7899******************9853.......23333222222224445555555555555544445555555555 PP

                            AAA_22  71 .........................erlsseellealeqalrarav............ielliiDEaqh.lr...s. 105
                                                                + +  ++l+e+  + l+  ++            + +l++DE    l+   + 
  gi|336252840|ref|YP_004595947.1| 128 hgryphrgffesttdedeaavdraiALAGVDHLRETELDSLSGGQKqlvwiamvlaqeTDVLLLDEPTTfLDvhhQl 204
                                       55555555666666666666666663333333333333333333333444333566666777777766645454323 PP

                            AAA_22 106 ..eealeeLr 113
                                         +e++e Lr
  gi|336252840|ref|YP_004595947.1| 205 evMEIVEALR 214
                                       3344444443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       5.7   3.5e+03     105     126 ..       5      26 ..       4      31 .. 0.78
   2 !   16.8   0.1   9.4e-06    0.0058       1      33 [.      59     104 ..      59     235 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.7
                            AAA_33 105 etdeetlkeRlakRaangddrs 126
                                       +t++et ++R+++  a++ ++ 
  gi|336252840|ref|YP_004595947.1|   5 HTSPETDADRNRATDAEEPTDE 26 
                                       7899999999999988876655 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 9.4e-06
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg....avllssdt.........l 33 
                                       ++ l+G++GsGKstl+++++++       vll+  +         +
  gi|336252840|ref|YP_004595947.1|  59 VTALIGPNGSGKSTLLKGIARQVSlesgSVLLDGSDihelekkefA 104
                                       5679***************998777776777776664554444440 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.7e-05     0.017       2      24 ..      59      81 ..      58      87 .. 0.88
   2 ?   -1.4   0.0       3.1   1.9e+03      72      88 ..     176     192 ..     139     223 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-05
                                      CEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                      + +l G++GsGK+tLl+++a++ 
  gi|336252840|ref|YP_004595947.1| 59 VTALIGPNGSGKSTLLKGIARQV 81
                                      6789***************9875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.1
                                       CHHHHCCSCCCEEEEEE CS
                             NACHT  72 vwavllelperlLlilD 88 
                                       vw+ ++  +e  +l+lD
  gi|336252840|ref|YP_004595947.1| 176 VWIAMVLAQETDVLLLD 192
                                       44444444444444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   2.5e-05     0.016      98     130 ..      56      88 ..      49      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                                       TTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgev 130
                                       ++++++l+G+ G GKStL++ ++ + +l+ g+v
  gi|336252840|ref|YP_004595947.1|  56 EGQVTALIGPNGSGKSTLLKGIARQVSLESGSV 88 
                                       679*******************99998887765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.8   2.2e-05     0.014      23      63 ..      56      96 ..      49     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.2e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      +++++ l+G+ G+GKs+l++ ++r+++ + g +l    d +
  gi|336252840|ref|YP_004595947.1| 56 EGQVTALIGPNGSGKSTLLKGIARQVSLESGSVLLDGSDIH 96
                                      447899******************99998777766666655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   2.2e-05     0.014      18      49 ..      57      88 ..      50     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrv 49
                                       +v++l Gp G+GK+t+lk++++ +  + g+v
  gi|336252840|ref|YP_004595947.1| 57 GQVTALIGPNGSGKSTLLKGIARQVSLESGSV 88
                                      4699*****************87776664444 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 ?   14.8   0.0   4.7e-05     0.029       3      35 ..      62      96 ..      60     154 .. 0.77
   2 ?   -2.0   0.0       7.3   4.5e+03      59      66 ..     186     193 ..     158     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-05
                                      EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelg..vefleisgsell 35
                                      l+Gp G GK++l k +a++++  +  + ++gs++ 
  gi|336252840|ref|YP_004595947.1| 62 LIGPNGSGKSTLLKGIARQVSleSGSVLLDGSDIH 96
                                      89*****************8522334555555554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.3
                                       SEEEEEET CS
                               AAA  59 psilfiDE 66 
                                       + +l++DE
  gi|336252840|ref|YP_004595947.1| 186 TDVLLLDE 193
                                       35666666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00046      0.28       3      42 ..      58      94 ..      56     116 .. 0.77
   2 ?    0.4   0.1      0.75   4.7e+02     109     133 ..     204     229 ..     200     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00046
                            AAA_24  3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadk 42
                                      +  +++Gp+g+GK+tl+k +   +  + +e G+  ld+ +
  gi|336252840|ref|YP_004595947.1| 58 QVTALIGPNGSGKSTLLKGI---ARQVSLESGSVLLDGSD 94
                                      6689*************999...55556666666555555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.75
                            AAA_24 109 eefrrllkklqelrk.nvifiahekt 133
                                        e+++++++l+++ + +++++ h  +
  gi|336252840|ref|YP_004595947.1| 204 LEVMEIVEALRDYSDvTIVLVLHDIE 229
                                       689999********9******99766 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00018      0.11       3      39 ..      59      95 ..      57      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      v++l+G++G+GK t l  +a++++ e  +vll   D+
  gi|336252840|ref|YP_004595947.1| 59 VTALIGPNGSGKSTLLKGIARQVSLESGSVLLDGSDI 95
                                      789***********************99999988886 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00017       0.1      19      46 ..      57      84 ..      41      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                                      TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrglakalgve 46
                                      g+v +L G+ G+GK+tl +g+a+++ +e
  gi|336252840|ref|YP_004595947.1| 57 GQVTALIGPNGSGKSTLLKGIARQVSLE 84
                                      7899*******************98764 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00035      0.22       3      49 ..      58     103 ..      56     123 .. 0.72
   2 ?   -1.4   0.0       3.6   2.2e+03      63      76 ..     184     197 ..     152     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49 
                                       ++ ++ G+  +GK+tllk ++++    ++  + ++  d ++ +++++
  gi|336252840|ref|YP_004595947.1|  58 QVTALIGPNGSGKSTLLKGIARQVS-LESGSVLLDGSDIHELEKKEF 103
                                       7889****************99877.445555555555555555444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                            AAA_14  63 ekktylflDEiqev 76 
                                       +++ +l+lDE    
  gi|336252840|ref|YP_004595947.1| 184 QETDVLLLDEPTTF 197
                                       46778888886655 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00024      0.15      50      94 ..      57     101 ..      47     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevk 94 
                                       G++  l Gp+g+Gk+ l  +i+++++ +   v l gs+++ le k
  gi|336252840|ref|YP_004595947.1|  57 GQVTALIGPNGSGKSTLLKGIARQVSLESGSVLLDGSDIHELEKK 101
                                       6777899********************************988865 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0005      0.31      50     103 ..      54     109 ..      45     126 .. 0.75
   2 ?   -1.2   0.0       1.8   1.1e+03      40      95 ..     147     206 ..     139     238 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                                       EETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS..----H.HHHHHTT- CS
                              RecA  50 lpkGriieiyGpessGkttlalhaiaeaqkkggvaafidae..haldp.kyakklGv 103
                                       +p+G+++ + Gp+ sGk+tl   +  ++  ++g ++++d    h l+  ++a+klG+
  gi|336252840|ref|YP_004595947.1|  54 VPEGQVTALIGPNGSGKSTLLKGIARQVSLESG-SVLLDGSdiHELEKkEFARKLGL 109
                                       8******************95555445555555.55666533488875269999997 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                                       HHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT.....T--EEEEESS----H CS
                              RecA  40 aldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkk.....ggvaafidaehaldp 95 
                                       a+d a+ + G+ + r +e+  + s+G+  l   a++ aq++     +  ++f+d+ h l++
  gi|336252840|ref|YP_004595947.1| 147 AVDRAIALAGVDHLRETELD-SLSGGQKQLVWIAMVLAQETdvlllDEPTTFLDVHHQLEV 206
                                       56667777777777776664.3455555555444444444411111344667777777764 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 ?    7.6   0.0    0.0046       2.8       2      22 ..      63      83 ..      62      92 .. 0.81
   2 ?    2.8   0.1      0.14        87      78     142 ..     174     238 ..     160     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0046
                        ATP_bind_1  2 vGpaGsGKttfvgalseilel 22
                                      +Gp GsGK+t+ + ++  ++l
  gi|336252840|ref|YP_004595947.1| 63 IGPNGSGKSTLLKGIARQVSL 83
                                      8**********9998876655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.14
                        ATP_bind_1  78 sldwldeelekeeddyllfDtPGQielfthseslakiveeLes.efalvvvyLvDsqrltdptkfi 142
                                       +l w++  l  +e+d ll+D P     + h  +  +ive+L   +  ++v++L D + ++  ++++
  gi|336252840|ref|YP_004595947.1| 174 QLVWIAMVL-AQETDVLLLDEPTTFLDVHHQLEVMEIVEALRDySDVTIVLVLHDIEQAARYADYL 238
                                       555666666.55778888888877666666667777999999988888888999988887777776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00058      0.36       3      33 ..      62      90 ..      61     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00058
                            AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvak 33
                                      l G+ G+GK+tl k +++    + ++++v+ 
  gi|336252840|ref|YP_004595947.1| 62 LIGPNGSGKSTLLKGIARQV--SLESGSVLL 90
                                      89**************9986..555555544 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 ?   10.6   0.0   0.00051      0.32       2      25 ..      59      82 ..      58     108 .. 0.83
   2 ?   -2.0   0.0       3.8   2.3e+03     107     152 ..     143     188 ..     131     210 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00051
                                      EEEEEESTTCCHHHHHHHHHCT-- CS
                              cobW  2 vtvltGflGsGKTtLlnhllenra 25
                                      vt l G+ GsGK+tLl+ + ++ +
  gi|336252840|ref|YP_004595947.1| 59 VTALIGPNGSGKSTLLKGIARQVS 82
                                      7899************99987655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.8
                                       HHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHH CS
                              cobW 107 ksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDl 152
                                       ++++ +d  +a+  +++l + e ++ + +++ql    +++   tD+
  gi|336252840|ref|YP_004595947.1| 143 EDEAAVDRAIALAGVDHLRETELDSLSGGQKQLVWIAMVLAQETDV 188
                                       5577788888888888886666666667777777777776666665 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00048       0.3       2      25 ..      61      84 ..      60      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00048
                                      EEE-STTSSHHHHHHHHHHHHT-E CS
                    Cytidylate_kin  2 aiDGPagsGKssvaralaeklglk 25
                                      a+ GP gsGKs++ + +a++++l+
  gi|336252840|ref|YP_004595947.1| 61 ALIGPNGSGKSTLLKGIARQVSLE 84
                                      677****************99864 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0035       2.2       4      24 ..      62      82 ..      59     108 .. 0.80
   2 ?    1.5   0.1      0.41   2.5e+02     122     156 ..     191     225 ..     178     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0035
                                      EE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellk 24
                                      + Gp G+GK+Tl+k ++++++
  gi|336252840|ref|YP_004595947.1| 62 LIGPNGSGKSTLLKGIARQVS 82
                                      679*************99874 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.41
                                       HTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE-- CS
                          NTPase_1 122 Lksekpvlavihrrkdlalveeirerkdvkvfevt 156
                                       L++ + +l v h+ +  ++ve +r+ +dv+++ v 
  gi|336252840|ref|YP_004595947.1| 191 LDEPTTFLDVHHQLEVMEIVEALRDYSDVTIVLVL 225
                                       55777777787887789999999999999988775 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   0.00052      0.32       3      25 ..      62      84 ..      60     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00052
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkk 25
                                      l Gp+g GKStl k +a++++ +
  gi|336252840|ref|YP_004595947.1| 62 LIGPNGSGKSTLLKGIARQVSLE 84
                                      78***************999844 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00058      0.36      18      44 ..      57      81 ..      49      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00058
                                      SCSEEEEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC 18 lqslvvalvGmgGvGKttlakqilnks 44
                                       q  v al G  G+GK+tl+k i ++ 
  gi|336252840|ref|YP_004595947.1| 57 GQ--VTALIGPNGSGKSTLLKGIARQV 81
                                      45..889**************999884 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0032         2       3      23 ..      61      81 ..      59      96 .. 0.86
   2 ?    0.8   0.0      0.83   5.1e+02      45      86 ..     185     229 ..     154     248 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0032
                                      EEEESTTSSHHHHHHHHHTST CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltgek 23
                                      a++G   +GKStL++ + +++
  gi|336252840|ref|YP_004595947.1| 61 ALIGPNGSGKSTLLKGIARQV 81
                                      89*************998875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.83
                                       TEEEEEEECGGCSSHHHHHH...HHHHHHHHHHCTSEEEEEEETT CS
                          MMR_HSR1  45 gkeielvDtpGliegaseek...glgkaflaleeadlillvvdas 86 
                                       ++++ l+D p  + + + +    ++ +a+++  ++ ++l++ d++
  gi|336252840|ref|YP_004595947.1| 185 ETDVLLLDEPTTFLDVHHQLevmEIVEALRDYSDVTIVLVLHDIE 229
                                       467788888886433333441234444444444455555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2157.90
//
Query:       gi|336252841|ref|YP_004595948.1|  [L=400]
Description: ferrichrome-binding protein [Halopiger xanaduensis SH-6]
Scores for complete 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-14   53.9   0.1    2.7e-14   53.3   0.1    1.2  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 !   53.3   0.1   1.5e-18   2.7e-14      46     233 ..     135     343 ..      89     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1.5e-18
                                       ESSSB-HHHHHHH--SEEEE-GGG.........GGGHHHHHHHS-EEE----TTS......HHHHHHHHHHHHHTT- CS
                      Peripla_BP_2  46 adgeidvEklaalkPDlvilskgl......gltdedeellksgiptvivessntg......eslkeqiralgellgl 110
                                       + ++ d E   +++PD+v++++++         +++ e++++ +p +    ++        +  +e ++ +++++++
  gi|336252841|ref|YP_004595948.1| 135 SARNYDKEIFYEVDPDVVLADPRMlqfysnWSDEDMAEIEENVAPILGSYIRFDYegeepyYTMYELFERIATIFQR 211
                                       5556666888899**********99999985566666777777777765444444448899**************** PP

                                       HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE........EEEE-TTSTTTHHHHTS--EESTTT--STT- CS
                      Peripla_BP_2 111 edeaeklvaeidsklaaaksaidsekpkpvlvfggade......ggyvvagsnsyigdlldalgieniaaeskksey 181
                                        +++e++v  +d+ ++ ++s+++    ++v+vf  + +      ++  +    ++    +++lg+++++ae + +  
  gi|336252841|ref|YP_004595948.1| 212 RAQYEAWVDLHDEFIDGIESDLPDGEGPTVAVFWRGIDaeagefQPAPIHEKRND-ARSFRDLGFRDAFAEAGLDPD 287
                                       *************************999999998888888888666666555555.555666******9999999** PP

                                       EEE-HHHHHHH--SEEEEEEH....HHHT-S--HHHHT-SHHHHTSHHHHTT-EEE CS
                      Peripla_BP_2 182 eeisaEqilasdpdvifvsgr....aeadnktgleflkenpllaelpAvkngrVya 233
                                       + ++ E++l  dpd+i  +       ++ +++++e l+ + ++++l Av+ng+V++
  gi|336252841|ref|YP_004595948.1| 288 GAVGYETLLDLDPDYIAAYNLssmtGDEWRSQVVEPLEDHSTASRLSAVQNGNVVR 343
                                       ****************9999988896777899**********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3141.27
//
Query:       gi|336252842|ref|YP_004595949.1|  [L=446]
Description: hypothetical protein Halxa_1437 [Halopiger xanaduensis SH-6]
Scores for 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-19   69.4   5.4    5.1e-19   69.4   5.4    2.2  2  MacB_PCD      MacB-like periplasmic core domain
    4.6e-15   55.9   0.8    4.6e-15   55.9   0.8    3.0  3  FtsX          FtsX-like permease family


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   5.4   5.7e-23   5.1e-19       1     179 [.      21     265 ..      21     283 .. 0.65
   2 ?   -3.7   2.4       1.4   1.3e+04       9      20 ..     324     336 ..     322     357 .. 0.76

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 5.7e-23
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgk...........gsgeslsdpdvealrrevpv 66 
                                       s+lt LG++iG+aavia+v+lg++lqa v  +is  ++  +++ ++           g ++ +s++d+e+l+ + ++
  gi|336252842|ref|YP_004595949.1|  21 SALTTLGVVIGIAAVIAFVTLGASLQAGVIGDIS-PDDRRNLYGWAaepdteggplaGAQPVFSQDDLEELEGRDEI 96 
                                       89*******************************9.543344655554556677777777777******988533349 PP

                          MacB_PCD  67 eavapvv.....tvrgggsgeeevtvvg.vd..pdyfkvfglklaeGrffteadlrggpnvvvigeelaerlf.... 131
                                       ea+  +      +v++g+  e+ ++  g v+  p+y +       eGr+ + ++++ g+ ++v++ ++a + f    
  gi|336252842|ref|YP_004595949.1|  97 EAAYGYAtiqtqAVSNGD--EQVAQGDGfVAsgPSYIR-------EGRLAEGRQFEMGESEAVLNPAAAGQ-Fednv 163
                                       998887655443223333..433344444221234555.......4444444445669999**********.88999 PP

                          MacB_PCD 132 pvGdtirl.......kpftVvGvledpp....gsgsalg...ddavylp....lttlqrrs................ 174
                                        vGd++++        +++VvG+ ++++          g   ++++y+p    +t     +                
  gi|336252842|ref|YP_004595949.1| 164 SVGDELTVtflggqqATVEVVGITDTSEglspF--E--GfeaAPRIYVPtepyYT-----Eqaaglgigtgggsdng 231
                                       9************9999******8554323221..2..2446999****554422.....22334444445555555 PP

                          MacB_PCD 175 .............................itvrl 179
                                                                    i+v++
  gi|336252842|ref|YP_004595949.1| 232 anggdggdggggngnesgtaqggqprylaIVVEA 265
                                       5556666666666666666666666666655544 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.4
                          MacB_PCD   9 aiGvaaviaiv.s 20 
                                       ++G+aa++++v s
  gi|336252842|ref|YP_004595949.1| 324 IVGIAAISLVVgS 336
                                       6888888888843 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.081   7.3e+02      29      44 ..      24      39 ..      17      58 .. 0.53
   2 ?    0.5   0.6     0.097   8.7e+02      20      39 ..     322     341 ..     303     348 .. 0.62
   3 !   55.9   0.8   5.1e-19   4.6e-15       2      96 .]     352     439 ..     351     439 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.081
                              FtsX 29 tlvalviGlglgllaa 44
                                      t ++ viG+++ +++ 
  gi|336252842|ref|YP_004595949.1| 24 TTLGVVIGIAAVIAFV 39
                                      3344444422222221 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.097
                              FtsX  20 lllteillitlvalviGlgl 39 
                                        +++ i++i+lv   iG+++
  gi|336252842|ref|YP_004595949.1| 322 NFIVGIAAISLVVGSIGIAN 341
                                       34444455555555555444 PP

  == domain 3  score: 55.9 bits;  conditional E-value: 5.1e-19
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivllll 78 
                                       reigi++a+G+ +++vl+l+lte+++++++++++G++lgl+a +l       ++  + l++  +++ v++++++++l
  gi|336252842|ref|YP_004595949.1| 352 REIGIMKAVGAQNRDVLGLFLTEAVVLGVIGAILGTALGLAAGYL------GVWY-IDLPLVYPYEYVALAVAVGIL 421
                                       9**************************************999887......2223.89******************* PP

                              FtsX  79 lallagllsiskilkkep 96 
                                       + ++agl++++++++++p
  gi|336252842|ref|YP_004595949.1| 422 VGVVAGLYPAWRAARTDP 439
                                       ***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 3586.57
//
Query:       gi|336252843|ref|YP_004595950.1|  [L=260]
Description: phosphonate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-33  115.1   0.0    4.9e-33  114.5   0.0    1.2  1  ABC_tran     ABC transporter
    1.7e-07   30.9   0.1     0.0015   18.0   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    5.7e-05   22.8   0.1    5.7e-05   22.8   0.1    1.7  1  AAA_29       P-loop containing region of AAA domain
    5.8e-05   23.0   0.3        0.2   11.4   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0011   19.3   0.3     0.0026   18.2   0.2    1.6  1  AAA_16       AAA ATPase domain
     0.0021   18.0   0.1     0.0052   16.7   0.0    1.6  2  RsgA_GTPase  RsgA GTPase
     0.0061   16.8   0.4       0.08   13.2   0.1    2.2  2  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.026   15.0   0.0       0.04   14.4   0.0    1.2  1  AAA_23       AAA domain
       0.04   14.0   0.1       0.43   10.7   0.0    2.3  2  MMR_HSR1     50S ribosome-binding GTPase
      0.045   13.3   1.9       0.24   10.9   1.9    2.2  1  AAA_25       AAA domain
      0.062   13.0   0.5       0.16   11.6   0.5    1.9  1  AAA_30       AAA domain
      0.067   13.3   1.0       0.28   11.3   1.0    2.0  1  AAA_33       AAA domain
      0.096   11.7   0.0       0.16   10.9   0.0    1.3  1  DUF3987      Protein of unknown function (DUF3987)
       0.17   11.6   0.0       0.32   10.7   0.0    1.4  1  AAA_24       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 !  114.5   0.0   3.8e-36   4.9e-33       1     136 [.      40     188 ..      40     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 3.8e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l+ vsl++ +g+ +ai+G++G+GKStL++l+  l +pteG++ +dg+d+ +    ++++     +g+++q+ +l p+
  gi|336252843|ref|YP_004595950.1|  40 LDGVSLDVPRGSYTAIMGPSGSGKSTLMNLVGCLDTPTEGTVVVDGADVAQlgdrERTRLRGTTVGFVFQTFNLMPR 116
                                       789*************************************************996666667789************* PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       l++ en             ++++++ ++l+++gl + +d+     p++LSgGq+qrvalaral+++p ++l+DEp+
  gi|336252843|ref|YP_004595950.1| 117 LNALENvalpqlfrgvdreTRRDRARDLLERVGLGDRADHL----PNELSGGQRQRVALARALVNDPAIVLADEPS 188
                                       ****************9877788899999999999955555....5*****************************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 !   10.8   0.1   0.00019      0.24      25      42 ..      51      68 ..      41      73 .. 0.87
   2 !   18.0   0.0   1.2e-06    0.0015     134     211 ..     158     232 ..     117     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                                      SEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlld 42
                                      s tai+Gp GSGKs l++
  gi|336252843|ref|YP_004595950.1| 51 SYTAIMGPSGSGKSTLMN 68
                                      689***********9986 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.2e-06
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklv 209
                                       +++LSgG+++ vala       v+  +++l De   +LD    + v +l+ e ++  + +iv+++++++ e+a+++v
  gi|336252843|ref|YP_004595950.1| 158 PNELSGGQRQRVALARA----LVNDPAIVLADEPSGNLDTDTEADVLDLFAEFHDAgTTMIVVTHERHVAERAERIV 230
                                       459*******9988754....57788899**********************98887799****************99 PP

                                       EE CS
                                       xx RF
                             SMC_N 210 gv 211
                                        +
  gi|336252843|ref|YP_004595950.1| 231 HL 232
                                       76 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 !   22.8   0.1   4.5e-08   5.7e-05      11      39 ..      39      67 ..      38      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.5e-08
                            AAA_29 11 tfdghtieidlkgatlltGpsGsGKSTll 39
                                       +dg ++++ + + t ++GpsGsGKSTl+
  gi|336252843|ref|YP_004595950.1| 39 ALDGVSLDVPRGSYTAIMGPSGSGKSTLM 67
                                      5678888897555***************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 !   10.3   0.1   0.00035      0.45       2      22 ..      53      73 ..      52     113 .. 0.80
   2 !   11.4   0.0   0.00015       0.2     195     298 ..     137     219 ..     109     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                      +++ Gp gsGKS+L+ +  +l
  gi|336252843|ref|YP_004595950.1| 53 TAIMGPSGSGKSTLMNLVGCL 73
                                      7999***********988777 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00015
                            AAA_21 195 veielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLH 271
                                       ++++++dl+e++ l +++d++                  ++elS G+++  al+ al  ++   +++l DEp  +L+
  gi|336252843|ref|YP_004595950.1| 137 RRDRARDLLERVGLGDRADHL------------------PNELSGGQRQRVALARALVNDP---AIVLADEPSGNLD 192
                                       344566666666677777776..................567********9*******999...************* PP

                            AAA_21 272 PkllrrllellkelsrngaQviltTHS 298
                                           + +l+l+ e ++ g+  i++TH 
  gi|336252843|ref|YP_004595950.1| 193 TDTEADVLDLFAEFHDAGTTMIVVTHE 219
                                       ****************9*********6 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   0.2     2e-06    0.0026      20     107 ..      48     173 ..      29     216 .. 0.48

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-06
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekd.................ggiflrgkcdqlesa............. 66 
                                          r++++ + G+sG+GKs+l++ +   l +                  +             +             
  gi|336252843|ref|YP_004595950.1|  48 P--RGSYTAIMGPSGSGKSTLMNLVGC-LDTPtegtvvvdgadvaqlgdR-------------Ertrlrgttvgfvf 108
                                       3..33899**************87773.3333332233333333333330.............23233333333333 PP

                            AAA_16  67 ..ipysalaqalareellrqlldeaesaeleawrekleeala.......................a 107
                                           + + ++al++   l ql +  +   +++ ++ l+e+++                        
  gi|336252843|ref|YP_004595950.1| 109 qtFNLMPRLNALEN-VALPQLFRGVDRETRRDRARDLLERVGlgdradhlpnelsggqrqrvalaR 173
                                       22111234555522.444444444333233333333444444566444433333333333333330 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.1e-06    0.0052      99     119 ..      50      70 ..      36      84 .. 0.85
   2 ?   -2.6   0.0       3.5   4.5e+03      65     100 ..     199     236 ..     189     239 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.1e-06
                                       TSEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinal 119
                                       ++ ++++G+SG GKStL+n +
  gi|336252843|ref|YP_004595950.1|  50 GSYTAIMGPSGSGKSTLMNLV 70 
                                       67899**************65 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHTTSEEEE--TTTH..TTHHHHHHHCTTS CS
                       RsgA_GTPase  65 leelkeelealgyevllvsaktk..egleelkellkdk 100
                                       + +l +e++++g+++++v  +++  e +e++ +ll++k
  gi|336252843|ref|YP_004595950.1| 199 VLDLFAEFHDAGTTMIVVTHERHvaERAERIVHLLDGK 236
                                       55666667777777666655543336666676666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   6.2e-05      0.08       7      25 ..      52      70 ..      48      89 .. 0.89
   2 ?    1.7   0.0      0.23     3e+02      52     123 ..     136     211 ..     121     226 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.2e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrl 25
                                       ++++G+sG+GK+tl++ +
  gi|336252843|ref|YP_004595950.1| 52 YTAIMGPSGSGKSTLMNLV 70
                                      689************9875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.23
                            AAA_22  52 sskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLrsllnlsr 120
                                       +++d +r+ll+ +gl+  a  l   el   + ++ + ara    +++++ DE    l+   ++++l  + ++++   
  gi|336252843|ref|YP_004595950.1| 136 TRRDRARDLLERVGLGDRADHL-PNELSgGQRQRVALARALvndPAIVLADEPSGnLDtdtEADVLDLFAEFHD--- 208
                                       7888899999999998888333.333333555555555555566678888886555654322555555544444... PP

                            AAA_22 121 kgv 123
                                        g+
  gi|336252843|ref|YP_004595950.1| 209 AGT 211
                                       444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.1e-05      0.04      21      37 ..      52      68 ..      22      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                            AAA_23 21 ltlItGpNGaGKTTild 37
                                       t+I Gp G+GK+T+++
  gi|336252843|ref|YP_004595950.1| 52 YTAIMGPSGSGKSTLMN 68
                                      699************98 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00033      0.43       3      18 ..      54      69 ..      52     113 .. 0.92
   2 ?    1.0   0.0      0.34   4.3e+02      65      90 ..     215     240 ..     160     256 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                                      EEEESTTSSHHHHHHH CS
                          MMR_HSR1  3 aivGrpNvGKStLina 18
                                      ai+G + +GKStL+n 
  gi|336252843|ref|YP_004595950.1| 54 AIMGPSGSGKSTLMNL 69
                                      89************95 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHCTSEEEEEEETTTTCS CS
                          MMR_HSR1  65 glgkaflaleeadlillvvdaseekl 90 
                                        ++++ +  e+a+ i++++d + e +
  gi|336252843|ref|YP_004595950.1| 215 VVTHERHVAERAERIVHLLDGKIERI 240
                                       23334444556888888888443334 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.9   0.00019      0.24      30      50 ..      47      67 ..      32     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +p+g+ ++++G++g+GK+tl 
  gi|336252843|ref|YP_004595950.1| 47 VPRGSYTAIMGPSGSGKSTLM 67
                                      69*****************95 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   0.00013      0.16      20      50 ..      52      82 ..      47     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvi 50
                                      ++++ Gp G+GK+t+++ +  + +  +g+v+
  gi|336252843|ref|YP_004595950.1| 52 YTAIMGPSGSGKSTLMNLVGCLDTPTEGTVV 82
                                      7899*************99877777755555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.0   0.00022      0.28       4     114 ..      55     225 ..      53     230 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                            AAA_33   4 lvGlpGsGKstlaerl..lkklg...avllssdt........................................... 32 
                                       + G++GsGKstl   +  l   +   +v+++  +                                           
  gi|336252843|ref|YP_004595950.1|  55 IMGPSGSGKSTLMNLVgcLDT-PtegTVVVDGADvaqlgdrertrlrgttvgfvfqtfnlmprlnalenvalpqlfr 130
                                       57**********987653222.2355666665555777777555555555555555555555555444443333322 PP

                            AAA_33  33 ....lrrrlfgtdqqskt................dytrvldrlyqiln...elarkalsagrnvildat..nlsrre 84 
                                           +            t                +  ++ ++l + ++   +lar      + v++d +  nl+ ++
  gi|336252843|ref|YP_004595950.1| 131 gvdrE------------TrrdrardllervglgdRADHLPNELSGGQRqrvALARALVNDPAIVLADEPsgNLDTDT 195
                                       22220............122233344444444432222333333333300033333333333333344444666666 PP

                            AAA_33  85 rarflklarrlgvpvrivvvetdeetlkeR 114
                                        a++l l+ +++ + + ++v t e+  +eR
  gi|336252843|ref|YP_004595950.1| 196 EADVLDLFAEFHDAGTTMIVVTHERHVAER 225
                                       666666655555555555555555555555 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013      0.16      37      56 ..      51      70 ..      41      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                           DUF3987 37 LytlvvapsGerKSpvdklv 56
                                       yt++++psG++KS++++lv
  gi|336252843|ref|YP_004595950.1| 51 SYTAIMGPSGSGKSTLMNLV 70
                                      59***************997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00025      0.32       6      23 ..      54      77 ..      50     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                            AAA_24  6 liyGpsgiGKTtlakel......g 23
                                      +i+Gpsg+GK+tl++        +
  gi|336252843|ref|YP_004595950.1| 54 AIMGPSGSGKSTLMNLVgcldtpT 77
                                      79***********99775544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 1945.01
//
Query:       gi|336252844|ref|YP_004595951.1|  [L=266]
Description: peptidase S26B, signal peptidase [Halopiger xanaduensis SH-6]
Scores for 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-07   28.7   2.4    1.2e-06   28.4   1.1    1.7  2  Peptidase_S24  Peptidase S24-like


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 !   28.4   1.1   6.5e-11   1.2e-06       2      45 ..      89     160 ..      88     162 .. 0.92
   2 ?   -3.6   0.0      0.63   1.1e+04      53      65 ..     199     212 ..     195     213 .. 0.53

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 6.5e-11
                                       XXSSTTCCTXXTTXEEEEECTS..........................---TTSEEEEEETTCE..-EEEEE CS
                     Peptidase_S24   2 vpGdSMeptlldGdlilVdkfs..........................epkrGdivvfrlpgee..eayiKr 45 
                                       ++++SMep ++ Gdl++V  ++                            ++Gd+vvfr +g++  +  i+r
  gi|336252844|ref|YP_004595951.1|  89 IESGSMEPNMNTGDLVFVVATDrfvgdesvadtgvvtlengresgyetFDRSGDVVVFRPDGNDsrTPVIHR 160
                                       89*****************777899***********************9**************977666666 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.63
                                       EEEE.SST.TSTEE CS
                     Peptidase_S24  53 rvllasnn.eyppl 65 
                                        v +  nn +y+++
  gi|336252844|ref|YP_004595951.1| 199 FVTKGDNNgMYDQV 212
                                       34444455678776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2193.99
//
Query:       gi|336252845|ref|YP_004595952.1|  [L=222]
Description: hypothetical protein Halxa_1440 [Halopiger xanaduensis SH-6]
Scores for 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   14.1   7.2      0.052   13.4   7.2    1.4  1  TAT_signal   TAT (twin-arginine translocation) pathway signal


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   7.2   2.9e-06     0.052       2      25 ..       8      32 ..       7      33 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-06
                        TAT_signal  2 lSRRdFLKgsAAaa.AAaalggcaa 25
                                      ++RR +LK+s+A+  A++a+++ a+
  gi|336252845|ref|YP_004595952.1|  8 VTRRRLLKASGATVvAGGAFASTAS 32
                                      89********999979999999987 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:                      253  (0.0141112); 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):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.19s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1911.69
//
Query:       gi|336252846|ref|YP_004595953.1|  [L=235]
Description: ribose-5-phosphate isomerase A [Halopiger xanaduensis SH-6]
Scores for 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-63  212.7   0.0    3.2e-63  212.4   0.0    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    9.3e-07   28.9   0.3    3.9e-05   23.6   0.1    2.2  2  DeoRC           DeoR C terminal sensor domain
  ------ inclusion threshold ------
      0.037   13.4   0.1       0.13   11.6   0.0    1.9  3  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 !  212.4   0.0   5.4e-67   3.2e-63       2     173 .]      55     229 ..      54     229 .. 0.97

  Alignments for each domain:
  == domain 1  score: 212.4 bits;  conditional E-value: 5.4e-67
                                       EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEET......TS-EE--TTS-HHHHHHHHHTEEEEEEEEEG CS
                    Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevde......dlnliKGgGgallrEKivaaaakkfiviade 72 
                                       g+ptS+q+++la e+gipl++ld+ve++dlaiDGaD+v +      + +l+KGgG+a+ rEK+v+aaa++f+v+ad 
  gi|336252846|ref|YP_004595953.1|  55 GIPTSFQSRQLALEVGIPLTDLDAVETVDLAIDGADQVVDdadspaHGALVKGGGAAHAREKLVDAAAERFVVVADP 131
                                       8*************************************998999999****************************** PP

                                       GGBESSTTSS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHT CS
                    Rib_5-P_isom_A  73 sKlveklgkfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelks 149
                                       +Kl ++l+  +vP+eVlp a++ va++l++l gg+p+lR a++kdgpvvTdngnl+lD++f ++i++p++l+++l++
  gi|336252846|ref|YP_004595953.1| 132 TKLADALE-RSVPIEVLPDAHSVVADRLSEL-GGDPTLRDAERKDGPVVTDNGNLVLDCEF-GRIDNPDALAARLSR 205
                                       *******6.9*******************75.*****************************.5788*********** PP

                                       STTEEEESEE-S--SEEEEEETTC CS
                    Rib_5-P_isom_A 150 ipGVvetGlFlgladkvlvgkedg 173
                                       +pGVve+GlF++lad+ +vg edg
  gi|336252846|ref|YP_004595953.1| 206 LPGVVEHGLFVDLADATYVGLEDG 229
                                       ********************9987 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   6.5e-09   3.9e-05       4      40 ..       9      45 ..       7      54 .. 0.92
   2 ?    3.5   0.0      0.01        62     123     140 ..     118     135 ..      95     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.5e-09
                             DeoRC  4 eeKrrIAkaAaeliedgdtifldaGtTtlelaraLae 40
                                      ++Krr +++Aae +edgd+++l++G+Tt++ ++a+ e
  gi|336252846|ref|YP_004595953.1|  9 AAKRRAGERAAEEVEDGDVVALGTGSTTAYAIEAIGE 45
                                      68****************************9999876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.01
                             DeoRC 123 lieaarrvillaDssKfg 140
                                       + +aa+r +++aD +K+ 
  gi|336252846|ref|YP_004595953.1| 118 VDAAAERFVVVADPTKLA 135
                                       33567888999****986 PP

>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.2e-05      0.13       4      36 ..      14      43 ..      11      53 .. 0.82
   2 ?   -3.0   0.0      0.65   3.9e+03     173     196 ..     106     128 ..     101     141 .. 0.66
   3 ?   -2.6   0.0      0.48   2.9e+03     162     180 ..     181     199 ..     179     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.2e-05
                                      HHHHHCTT--TTEEEEE-SBTTBT.HHHHHHHHH CS
                         CoA_trans  4 aaeavakeikdGmtvavGGFglig.iPealiaal 36
                                      a e++a+e++dG++va+G    +g + +++i+a+
  gi|336252846|ref|YP_004595953.1| 14 AGERAAEEVEDGDVVALG----TGsTTAYAIEAI 43
                                      7799999***********....776666888887 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.65
                                       TTHSHHHHHHEEEEEEEEEEEECT CS
                         CoA_trans 173 nfnkpaiaeaakvtileveeivek 196
                                       ++++ a+a   k ++++ e++v +
  gi|336252846|ref|YP_004595953.1| 106 KGGGAAHA-REKLVDAAAERFVVV 128
                                       55555555.667888888888743 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.48
                                       TCSEESSGGGHTTHSHHHH CS
                         CoA_trans 162 egnlvfeksagnfnkpaia 180
                                        gnlv +++ g +++p++ 
  gi|336252846|ref|YP_004595953.1| 181 NGNLVLDCEFGRIDNPDAL 199
                                       5899999999999888854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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 0.19s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 2057.16
//
Query:       gi|336252847|ref|YP_004595954.1|  [L=298]
Description: hypothetical protein Halxa_1442 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0027   17.8  21.6     0.0027   17.8  21.6    3.0  3  DUF5518   Family of unknown function (DUF5518)


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8  21.6   1.5e-07    0.0027       2     113 ..      17     134 ..      16     139 .. 0.73
   2 ?   -6.9  15.2         1   1.8e+04      39      74 ..     183     216 ..     169     259 .. 0.54
   3 ?   -1.1   0.8      0.11     2e+03      55      66 ..     243     254 ..     236     282 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-07
                           DUF5518   2 raaliGavvaivlslllg........lllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllv 70 
                                       r a++ ++++++++++++         ++++++s  +ll++G+++Gy + ++  +  +aG+ +G  g+i +++++ +
  gi|336252847|ref|YP_004595954.1|  17 RVAILIGLATVPVTVASAwgpvadslGTVGDSVSDGALLLAGVLTGYYYSSRPTETRYAGIWTGRAGSIGLVLVFCA 93 
                                       6788899999999999999999988878889999999***************************9999988666666 PP

                           DUF5518  71 lllglvaaigglagfvallvalllvvllllvvllvilgaiGGa 113
                                        +++++   ggl+ ++a+++  +++   l++v++v++ ++ ++
  gi|336252847|ref|YP_004595954.1|  94 SVVAAIVSDGGLGAAIAVILSPVVI--GLIIVFTVLVTMLTAV 134
                                       6654444445555444444444444..4555555555444443 PP

  == domain 2  score: -6.9 bits;  conditional E-value: 1
                           DUF5518  39 GylaggdskdgavaGalaGligaipvlvlllvlll.g 74 
                                       Gyl+   ++++  aG+++  +++i+v+v+++++l   
  gi|336252847|ref|YP_004595954.1| 183 GYLV---IQSASGAGIVISTLAVIVVTVFSFAALGiL 216
                                       5555...445566677777777777766655555431 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.11
                           DUF5518  55 laGligaipvlv 66 
                                       +aG++g ++++v
  gi|336252847|ref|YP_004595954.1| 243 VAGVLGYLIATV 254
                                       344444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); 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:                         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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2144.97
//
Query:       gi|336252848|ref|YP_004595955.1|  [L=137]
Description: hypothetical protein Halxa_1443 [Halopiger xanaduensis SH-6]
Scores for 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:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1036.61
//
Query:       gi|336252849|ref|YP_004595956.1|  [L=145]
Description: hypothetical protein Halxa_1444 [Halopiger xanaduensis SH-6]
Scores for 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:                       283  (0.0157845); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1163.87
//
Query:       gi|336252850|ref|YP_004595957.1|  [L=55]
Description: hypothetical protein Halxa_1445 [Halopiger xanaduensis SH-6]
Scores for 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-05   24.5   1.5    2.6e-05   24.4   1.5    1.1  1  DUF1931        Domain of unknown function (DUF1931)
     0.0012   19.1   0.1     0.0018   18.5   0.1    1.5  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
  ------ inclusion threshold ------
      0.064   13.6   0.0      0.064   13.6   0.0    1.2  1  Histone        Core histone H2A/H2B/H3/H4
       0.19   12.0   0.4       0.23   11.7   0.4    1.1  1  Glutaredoxin   Glutaredoxin


Domain annotation for each model (and alignments):
>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   1.5   5.7e-09   2.6e-05      14      53 ..      16      55 .]       3      55 .] 0.89

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.7e-09
                                      -HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS CS
                           DUF1931 14 dkedlkrisdfVekklydLllvaeenAkangrdviepaDL 53
                                      dk+ ++++ d +++++++Ll+ a ++A+an r++++p+DL
  gi|336252850|ref|YP_004595957.1| 16 DKNVASDFYDALDEEVDELLEDAARRAEANDRKTVQPRDL 55
                                      49999**********************************8 PP

>> 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 !   18.5   0.1     4e-07    0.0018      29      61 ..      23      55 .]       3      55 .] 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4e-07
                                      HHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHH CS
                     CBFD_NFYB_HMF 29 iaecveefieelaseAaeickkekrKtikaehi 61
                                      +++++ e + el++ Aa+++++++rKt+++ ++
  gi|336252850|ref|YP_004595957.1| 23 FYDALDEEVDELLEDAARRAEANDRKTVQPRDL 55
                                      5778899999********************997 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.4e-05     0.064     100     124 ..      31      55 .]       5      55 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHHHHTTXSEEXHHHH CS
                           Histone 100 lvelfeeAnllakhaKRvTitpkDi 124
                                         el+e+A++ a+ + R+T++p+D+
  gi|336252850|ref|YP_004595957.1|  31 VDELLEDAARRAEANDRKTVQPRDL 55 
                                       579*********************6 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   5.1e-05      0.23      14      44 ..       9      41 ..       8      50 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.1e-05
                                      HHHHHHHHTTGGEEEEEGCCSH..HHHHHHHHH CS
                      Glutaredoxin 14 kakrlLkelgvkfeeidvdkde..eireelkel 44
                                      ++k++L++++v+ +++d +++e  e+ e+  ++
  gi|336252850|ref|YP_004595957.1|  9 AVKEALDDKNVASDFYDALDEEvdELLEDAARR 41
                                      89******************8766555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 480.79
//
Query:       gi|336252851|ref|YP_004595958.1|  [L=259]
Description: 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR) carboxylase [Halopiger xanaduensis SH-6]
Scores for 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-13   48.5   2.8    6.8e-13   48.5   2.8    1.6  2  AIRC      AIR carboxylase
  ------ inclusion threshold ------
      0.033   14.1   0.0      0.051   13.5   0.0    1.2  1  TraB      TraB family
      0.035   14.0   0.0      0.052   13.4   0.0    1.2  1  DUF1463   Protein of unknown function (DUF1463)
       0.04   14.2   0.9      0.071   13.4   0.9    1.5  1  DUF2267   Uncharacterized conserved protein (DUF2267)


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 ?   -2.4   0.0      0.68   3.1e+03      38      52 ..      52      66 ..      38      80 .. 0.57
   2 !   48.5   2.8   1.5e-16   6.8e-13       2     129 ..     120     250 ..     119     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.68
                                      TSHHHHHHHHHHCHT CS
                              AIRC 38 rtpeelleyaeeaee 52
                                      +tp++++++ae+a e
  gi|336252851|ref|YP_004595958.1| 52 KTPAQVVALAETALE 66
                                      455555555555433 PP

  == domain 2  score: 48.5 bits;  conditional E-value: 1.5e-16
                                       EEEEESSGGGHHHHHHHHHHHHHTT-EE....EEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHH CS
                              AIRC   2 VgiimGSdsDlevmkkaaeilkelgvey....evrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvas 74 
                                       Vg++++ + D +v+ +a +++ + g ++    ++ v+   rt +++ ++ e       +++I++AG++ +Lp v+a+
  gi|336252851|ref|YP_004595958.1| 120 VGLVTAGTVDQPVADEAEAVCVDAGATVdrvdDIGVAALDRTLDQVDRLRE------ADMLIVAAGREGALPTVIAG 190
                                       889999999999999999999998876633345778888888888777654......689***************** PP

                                       HSSS-EEEEEE--...STTCCHHHHHHHHT--TTS--EE-SST..HHHHHHHHHHHHHTT CS
                              AIRC  75 lttlPVigvPvks...kalkgldsllSivqmPsgvpvatvaig..kaknAallAaqilal 129
                                       l+++PVigvPv+s      +g  +l  ++q ++ ++v+++++g   +++A l+A +i a+
  gi|336252851|ref|YP_004595958.1| 191 LVDTPVIGVPVSSgygYGGDGEAALSGMLQSCTVMSVVNIDAGfvAGAQATLIARTIDAA 250
                                       ************94323579999******************9998888999999888765 PP

>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.1e-05     0.051      51     136 ..      51     137 ..      34     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                              TraB  51 dtdeatqkelaklkllpdgktlsdllseelyarlqkalakrglplaaldkmkPwllalllslaelakkkagld..pe 125
                                        + +a++ +la+ +l ++++ l  +ls+e++a+l++a+ +  +p a +d++     +ll++++++  ++++l+    
  gi|336252851|ref|YP_004595958.1|  51 GKTPAQVVALAETALETTDRALLTRLSDEQFAALEEAIPE-TVPDATFDRWSS---SLLIRTPDY--ERPSLEatVG 121
                                       366899999*******************************.9***88887666...999999999..6666642222 PP

                              TraB 126 l.....vDrylaktak 136
                                       l     vD+++a++a+
  gi|336252851|ref|YP_004595958.1| 122 LvtagtVDQPVADEAE 137
                                       2555678888888886 PP

>> DUF1463  Protein of unknown function (DUF1463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.2e-05     0.052      33      81 ..      36      85 ..      16     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                           DUF1463 33 issedknlpvislrdpktvvyvfdl.evskgsldyklltklsdeqfyeld 81
                                      +  + +++p   l + kt + v  l e ++ + d  llt+lsdeqf  l+
  gi|336252851|ref|YP_004595958.1| 36 ARQQRRGIPEAILAEGKTPAQVVALaETALETTDRALLTRLSDEQFAALE 85
                                      5566789999999999999999887588999***************8765 PP

>> DUF2267  Uncharacterized conserved protein (DUF2267)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   1.6e-05     0.071      20      64 ..      61     109 ..      48     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHHTTS-HHHHHHHHTTS-HHHHHHHHTT--TTS....- CS
                           DUF2267  20 AeratravLrtLrdrlteeeaadlaaqLPeelrgllrdgwppve....p 64 
                                       Ae+a++++ r+L  rl+ e+ a l+++ Pe + ++ +d w+ +     p
  gi|336252851|ref|YP_004595958.1|  61 AETALETTDRALLTRLSDEQFAALEEAIPETVPDATFDRWSSSLlirtP 109
                                       99**************************************875576553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); 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):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2057.38
//
Query:       gi|336252852|ref|YP_004595959.1|  [L=49]
Description: hypothetical protein Halxa_1447 [Halopiger xanaduensis SH-6]
Scores for 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   0.5       0.02   14.9   0.5    1.2  1  DZR              Double zinc ribbon
      0.031   14.6   1.2      0.035   14.5   1.2    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.036   14.4   0.3      0.036   14.4   0.3    1.0  1  DUF3268          zinc-finger-containing domain
        0.2   11.8   2.8       0.44   10.7   2.8    1.6  1  Zn-ribbon_8      Zinc ribbon 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 ?   14.9   0.5   4.4e-06      0.02      15      38 ..       4      36 ..       2      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.4e-06
                               DZR 15 CseCgtklkavaa.........edrCpsCgekv 38
                                      C++Cg+++++  a          ++C+sC++ +
  gi|336252852|ref|YP_004595959.1|  4 CNHCGAHVSERFArvfadergeIHACVSCSANA 36
                                      ********977779*******99******9875 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 ?   14.5   1.2   7.7e-06     0.035       5      42 ..       3      39 ..       1      48 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.7e-06
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCgastpwfk 42
                                       C++Cg      ++   + e+g+  +C  C a+   + 
  gi|336252852|ref|YP_004595959.1|  3 KCNHCGAHVSERFARVFADERGEIHACVSCSAN-AGIA 39
                                      7*************9999999999999999992.2222 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3     8e-06     0.036       3      46 ..       2      42 ..       1      49 [] 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8e-06
                           DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkCdayvgvhkgt 46
                                       +C++CG++v  + a+ ++ + ++g  ++ C +C a  g+ + +
  gi|336252852|ref|YP_004595959.1|  2 PKCNHCGAHVSERFAR-VF-ADERG-EIHACVSCSANAGIAEAA 42
                                      58*******9988776.56.34444.6899********997654 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.8   9.7e-05      0.44       7      35 ..       3      35 ..       2      37 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.7e-05
                       Zn-ribbon_8  7 rCeeCghefe.vlqsis..daplta.CPeCgse 35
                                      +C+ Cg     ++++++  ++ +++ C +C ++
  gi|336252852|ref|YP_004595959.1|  3 KCNHCGAHVSeRFARVFadERGEIHaCVSCSAN 35
                                      7****965544777777535559999****875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 421.92
//
Query:       gi|336252853|ref|YP_004595960.1|  [L=83]
Description: Excinuclease ABC C subunit domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   60.1   0.1    2.1e-16   59.9   0.1    1.0  1  GIY-YIG   GIY-YIG catalytic domain


Domain annotation for each model (and alignments):
>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.1   1.2e-20   2.1e-16       2      75 ..       5      75 ..       4      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 1.2e-20
                                      -EEEEEEETTT--EEEEEESSHHHHHHHHHHHHHHT--S-HS.STEEEEEEEE----HHHHHHHHHHHHHHTTS CS
                           GIY-YIG  2 ggvYiirskenkliYvGstknlekRlkqHnagkkakytrkkgkkpfeliileifptksealelEkklikkyksn 75
                                      ++vY++++ ++ l Y+G+t++le+R  +H ag++akytr+  ++p+el + e f ++s a+++E+++++ ++++
  gi|336252853|ref|YP_004595960.1|  5 HVVYVLECADGTL-YTGYTTDLERRVAEHDAGEGAKYTRG--RTPVELQYHERFASRSAAMSREYEIKQLSRTE 75
                                      79**********7.*************************8..****************************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 644.82
//
Query:       gi|336252854|ref|YP_004595961.1|  [L=205]
Description: NADPH-dependent FMN reductase [Halopiger xanaduensis SH-6]
Scores for complete 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-31  109.4   0.0    1.6e-31  109.1   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    5.6e-11   42.5   0.0    7.4e-11   42.1   0.0    1.3  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
      0.083   13.1   0.0       0.15   12.3   0.0    1.3  1  Flavodoxin_5  Flavodoxin domain


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 !  109.1   0.0   2.7e-35   1.6e-31       2     153 ..       6     147 ..       5     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 2.7e-35
                                       EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEE CS
                           FMN_red   2 kilvisGSlrkgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadalii 78 
                                        +l+++GSlr++s+tr++++++++a++ +gae++l+dl++++lp  ++d d +    ++ d++e+++ +++ada+ +
  gi|336252854|ref|YP_004595961.1|   6 SVLAVNGSLRAESYTRTALRYVLRAAEDRGAETTLLDLREYDLP--VYDPDVDD--REQGDAREVKRLVREADAVAL 78 
                                       59******************************************..***99965..899****************** PP

                                       EEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEEEETSH CS
                           FMN_red  79 vtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraavavgka 153
                                       +tP+Y+gsysg+lKn+ D+++     +e ++  v+l+a +gg + g  +  +lr   + ++ +v+p+ +v +++a
  gi|336252854|ref|YP_004595961.1|  79 GTPVYHGSYSGALKNFHDYCG----FDEYEDTTVGLLASAGGGSYG-STLDHLRITVRGVHGWVLPH-QVGIRNA 147
                                       ********************8....9****9999999777664444.78999******99******9.8888775 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   1.2e-14   7.4e-11       3     103 ..       7      98 ..       5     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.2e-14
                                       EEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTT.CHHHHHHHHHHHHCS CS
                      Flavodoxin_2   3 iLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeek.padveseqiekllaa 78 
                                       +L +n++ r  +s ++ +++ +++a+e+ g +e t +dL +  lpv ++       + ++  + d+++ +   +++a
  gi|336252854|ref|YP_004595961.1|   7 VLAVNGSLRA-ESYTRTALRYVLRAAEDRG-AETTLLDLREYDLPVYDP-------DVDDReQGDAREVK-RLVREA 73 
                                       89*******9.5******************.9****************9.......33333259999999.****** PP

                                       SEEEEEEE-BTTB--HHHHHHHHHH CS
                      Flavodoxin_2  79 daivlqfPlwwfgvPailKgwiDrv 103
                                       da+ l++P++  +++ +lK++ D+ 
  gi|336252854|ref|YP_004595961.1|  74 DAVALGTPVYHGSYSGALKNFHDYC 98 
                                       **********************986 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.5e-05      0.15      38      65 ..      67      94 ..      54      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                      Flavodoxin_5 38 sedlesydavvigasvyygkllpelakF 65
                                      +  + ++dav +g++vy+g+ +++l++F
  gi|336252854|ref|YP_004595961.1| 67 KRLVREADAVALGTPVYHGSYSGALKNF 94
                                      4567899*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1453.12
//
Query:       gi|336252855|ref|YP_004595962.1|  [L=466]
Description: phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain I [Halopiger xanaduensis SH-6]
Scores for 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-38  130.9   0.0    4.8e-38  130.0   0.0    1.4  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.8e-23   82.9   0.0    3.1e-23   82.1   0.0    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
      5e-23   81.7   0.2      5e-23   81.7   0.2    2.1  2  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    7.8e-16   58.0   0.1    2.3e-15   56.5   0.1    1.9  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 !  130.0   0.0   1.1e-41   4.8e-38       3     132 ..       5     133 ..       3     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 1.1e-41
                                       GBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEE.EB- CS
                         PGM_PMM_I   3 kfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillg.llp 78 
                                       +fgt+G+R      e+t+  v+ +gqa+a+yl+ e+++++vv+G+D+R +sr +ae+la++l anG++vi+ +  +p
  gi|336252855|ref|YP_004595962.1|   5 SFGTDGWRATLD--EFTAPRVRMVGQAVATYLRDEGRDAPVVIGYDARETSRGFAEELARVLCANGFDVIVPErDRP 79 
                                       7********998..689************************************************************ PP

                                       HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHC CS
                         PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiie 132
                                       tP v++ai + ++++g+ itaSHnppeyng+K+++ +G+p+ p+v+++I+++++
  gi|336252855|ref|YP_004595962.1|  80 TPLVAHAIVERDLAGGLAITASHNPPEYNGVKFIPDDGAPALPAVTDAIADRLA 133
                                       **************************************************9876 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 !   82.1   0.0   6.9e-27   3.1e-23       5     111 ..     268     369 ..     264     374 .. 0.87

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 6.9e-27
                                       HHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBS CS
                       PGM_PMM_III   5 llallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeat 81 
                                        +a l +ylle+    g   ++tv+t+ +++rva+++g +++e++vG+k+v++ + e++a++GgEeSg++ ++ +++
  gi|336252855|ref|YP_004595962.1| 268 FFAALYDYLLED--DAGP-AIRTVSTTFLIDRVAEAHGETVHEVPVGFKWVAQGIAEHDALVGGEESGGFTIRGHVR 341
                                       567888999885..4344.8********************************************************* PP

                                       S--HHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                       PGM_PMM_III  82 tkDGilaallvleilaetgkslselleell 111
                                       +kDG+l+all++++ a++  +l+e +++ll
  gi|336252855|ref|YP_004595962.1| 342 EKDGVLMALLAAAMHADE--PLDERVDRLL 369
                                       **************9986..5666555444 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 ?   -1.3   0.2      0.77   3.5e+03      80      97 ..     115     133 ..      52     134 .. 0.74
   2 !   81.7   0.2   1.1e-26     5e-23      13     102 ..     169     259 ..     155     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.77
                                       GGG-.SEEEEE-TTS-BEE CS
                        PGM_PMM_II  80 kega.dlglafDgDaDRlg 97 
                                       ++ga  l +++D  aDRl+
  gi|336252855|ref|YP_004595962.1| 115 DDGApALPAVTDAIADRLA 133
                                       4455566778888888875 PP

  == domain 2  score: 81.7 bits;  conditional E-value: 1.1e-26
                                       HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG-..SEEE CS
                        PGM_PMM_II  13 seaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkega..dlgl 87 
                                       ++    sgl+v++d++hG+g+++++ ll+++g+ + +l++e+dp+f+++ap+p + e+l++li+lv ++ga  +lg+
  gi|336252855|ref|YP_004595962.1| 169 TDDVDLSGLTVAYDAMHGSGRGTTDALLERAGASLECLRCERDPEFGGGAPEPAP-ENLEALIDLVTDDGAgpELGV 244
                                       55566789***********************************************.*************9999**** PP

                                       EE-TTS-BEEEEETT CS
                        PGM_PMM_II  88 afDgDaDRlgvvder 102
                                       a+DgDaDR+++v+++
  gi|336252855|ref|YP_004595962.1| 245 ANDGDADRIAIVTPE 259
                                       ************864 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 !   56.5   0.1   5.2e-19   2.3e-15      12      68 ..     392     457 ..     380     463 .. 0.78

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 5.2e-19
                                       ..EECCCCCTTH.........HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHH CS
                        PGM_PMM_IV  12 vvaalaallkva.........sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaee 68 
                                       v+++l++   +a         ++++g k  l+dG++l +RpSGTep+lrvy+Ea++++++a+l e+
  gi|336252855|ref|YP_004595962.1| 392 VLEDLEDEIPDAvagtdvegvNTADGFKLQLADGSWLLIRPSGTEPVLRVYAEASDEDRVAELLEA 457
                                       555555555555555666677899**************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3388.15
//
Query:       gi|336252856|ref|YP_004595963.1|  [L=607]
Description: hypothetical protein Halxa_1451 [Halopiger xanaduensis SH-6]
Scores for 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   15.9   0.1      0.029   14.7   0.1    1.6  1  EndoU_bacteria  Bacterial EndoU nuclease
       0.15   12.4   2.1       0.37   11.1   2.1    1.7  1  GAT             GAT domain
       0.45   10.9   3.0       0.72   10.3   0.2    2.4  2  RXLR            RXLR phytopathogen effector protein, Avirulen


Domain annotation for each model (and alignments):
>> EndoU_bacteria  Bacterial EndoU nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   4.8e-06     0.029      69     124 ..     527     587 ..     510     588 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.8e-06
                    EndoU_bacteria  69 Pdtwsaekildaveeaaenknstesqang....vvvggesdG.vkirvvvenggivtayPd 124
                                       P + s+ +i +a+ +a e+ ++t++ + +       + +++G  +i+v+++ng+++tayP 
  gi|336252856|ref|YP_004595963.1| 527 PNSMSERDISKAIYKALEDTETTPQDSFKfskfDQSFVDRTGvSEIEVIIRNGNVRTAYPT 587
                                       8899*******************9965559999777777788678*******99******6 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.1   6.2e-05      0.37       9      64 ..     391     449 ..     388     451 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.2e-05
                               GAT   9 emLsstepd.eellenellkeLyetckamqpriqklieet...adeedllaelLqlNDeL 64 
                                       +mL+ + ++  e ++ + +++L +  k +q  iq++++ +   ad+  l+++ +q+ND L
  gi|336252856|ref|YP_004595963.1| 391 QMLARYGEGdLEADHLQQMNKLLDDGKMVQADIQQMMGMLetkADNP-LIEDTIQANDLL 449
                                       8999997555677789999*******************995455555.**********88 PP

>> RXLR  RXLR phytopathogen effector protein, Avirulence activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00012      0.72      21     113 ..     190     277 ..     177     291 .. 0.67
   2 ?    0.1   0.3      0.17   9.9e+02      28      88 ..     351     427 ..     337     435 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                              RXLR  21 asaastkkdqktvavvskssgeaesrdaadkRfLRshkae.eddeeseeraagknlldvfvekklkkmlanekyakk 96 
                                       a+++s+k+     ++ s+++ +    ++ad++ L   +   + ++ ++ ra  +++l +     ++ +l+  ++a  
  gi|336252856|ref|YP_004595963.1| 190 AASSSAKA-----TIKSTDTAQDVGSRLADTKALKALDRVsDAKKAAKGRAT-ARILLAVDGDAAEPLLSQADTAGG 260
                                       22222222.....2223333334678999*****999855244444555555.55555599**************** PP

                              RXLR  97 lFreWkanGftlkdies 113
                                       ++r W++++    d++s
  gi|336252856|ref|YP_004595963.1| 261 AYRLWQQQRAMDADVDS 277
                                       ********999999876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.17
                              RXLR  28 kdqktvavvskss....geaesrdaadkRfLRshkae..........eddeeseeraagknlld..vfvekklkkml 88 
                                       +dq tv  ++++s    + ++s+da++++ L   +++          e d e+  +++ ++lld    v++ +++m+
  gi|336252856|ref|YP_004595963.1| 351 RDQLTVVNSRSDSfdanQFVKSTDADSRQVLERVDDAttrqmlarygEGDLEADHLQQMNKLLDdgKMVQADIQQMM 427
                                       45555555555555665556666677777774434222344455555666666666666666666655566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); 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:                         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 0.26s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4361.93
//
Query:       gi|336252857|ref|YP_004595964.1|  [L=145]
Description: hypothetical protein Halxa_1452 [Halopiger xanaduensis SH-6]
Scores for 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:                       350  (0.0195214); 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:                         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: 1076.28
//
Query:       gi|336252858|ref|YP_004595965.1|  [L=231]
Description: hypothetical protein Halxa_1453 [Halopiger xanaduensis SH-6]
Scores for 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  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); 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:                         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 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1741.20
//
Query:       gi|336252859|ref|YP_004595966.1|  [L=170]
Description: hypothetical protein Halxa_1454 [Halopiger xanaduensis SH-6]
Scores for 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  (170 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:                        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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1347.65
//
Query:       gi|336252860|ref|YP_004595967.1|  [L=178]
Description: hypothetical protein Halxa_1455 [Halopiger xanaduensis SH-6]
Scores for 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  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); 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:                         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 0.18s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1580.15
//
Query:       gi|336252861|ref|YP_004595968.1|  [L=123]
Description: hypothetical protein Halxa_1456 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.078   11.5   0.2      0.087   11.4   0.2    1.1  1  Terminase_GpA   Phage terminase large subunit (GpA)
       0.73    9.9   3.2        1.8    8.7   3.2    1.9  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


Domain annotation for each model (and alignments):
>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   9.7e-06     0.087     188     230 ..      18      69 ..       8      81 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.7e-06
                     Terminase_GpA 188 lyeesdqrryyvpCphCgelqels..fer......lkwpege.aeekaryvC 230
                                       ++ + d+ +yy+ Cp+Cg+   l+   ++      l+ +e+e + +++++ C
  gi|336252861|ref|YP_004595968.1|  18 AWHQDDDGNYYIDCPECGSAATLMnvVKHgrcngyLNQQEDEtDVDETAMDC 69 
                                       6788899************998653233333333322233333555555555 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 ?    8.7   3.2    0.0002       1.8       2       9 ..      31      38 ..      30      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0002
                    DNA_ligase_ZBD  2 CPvCGsav 9 
                                      CP+CGsa+
  gi|336252861|ref|YP_004595968.1| 31 CPECGSAA 38
                                      ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1061.71
//
Query:       gi|336252862|ref|YP_004595969.1|  [L=170]
Description: serine O-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-14   50.9   8.4    9.9e-09   34.6   0.4    3.3  4  Hexapep     Bacterial transferase hexapeptide (six repeats)
    2.4e-07   30.4   8.1    9.2e-07   28.5   1.8    3.1  2  Hexapep_2   Hexapeptide repeat of succinyl-transferase
    0.00011   22.6   0.0    0.00018   21.8   0.0    1.4  1  SATase_N    Serine acetyltransferase, N-terminal
  ------ inclusion threshold ------
      0.036   14.4   2.6      0.069   13.5   2.6    1.4  1  Bactofilin  Polymer-forming cytoskeletal


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 ?    3.0   0.0      0.02        89      16      34 ..      62      80 ..      58      82 .. 0.62
   2 !   18.8   0.8   2.2e-07   0.00098       5      36 .]      75     108 ..      65     108 .. 0.91
   3 !   34.6   0.4   2.2e-12   9.9e-09       1      35 [.     117     151 ..     117     152 .. 0.95
   4 ?   -3.0   0.1       1.6   7.1e+03      28      34 ..     154     160 ..     154     162 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.02
                                      EETTEEE-TTEEEETTEEE CS
                           Hexapep 16 iggnVkIGdnvkIgagvvi 34
                                      ++ +V+I++ + +g+ v+i
  gi|336252862|ref|YP_004595969.1| 62 LLTGVEIHPAADLGRRVTI 80
                                      5566666666666666666 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.2e-07
                                       ETTEEE-T..TEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   5 GsnvlIgp..faviggnVkIGdnvkIgagvvigg 36 
                                       G  v+I++  ++vig+ ++IGd+v+  +gv++gg
  gi|336252862|ref|YP_004595969.1|  75 GRRVTIDHgmGVVIGETAEIGDDVHMYHGVTLGG 108
                                       7778888888*********************997 PP

  == domain 3  score: 34.6 bits;  conditional E-value: 2.2e-12
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +++++++v+Ig++a+++g+++IG+++ +gag+v++
  gi|336252862|ref|YP_004595969.1| 117 HPTVEDGVQIGANATLLGDITIGEDAAVGAGSVVT 151
                                       5789*****************************98 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.6
                                       EETTEEE CS
                           Hexapep  28 Igagvvi 34 
                                       +++g+++
  gi|336252862|ref|YP_004595969.1| 154 VEPGATV 160
                                       5677776 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 ?    3.7   0.5     0.011        51      14      31 ..      86     105 ..      74     107 .. 0.63
   2 !   28.5   1.8   2.1e-10   9.2e-07       4      34 .]     120     152 ..     119     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.011
                                       -EES..EEE-TT-EE-TT-E CS
                         Hexapep_2  14 agiG..vslGdncvvgaGvv 31 
                                        +iG   ++Gd+++ + Gv+
  gi|336252862|ref|YP_004595969.1|  86 VVIGetAEIGDDVHMYHGVT 105
                                       34444456677766666665 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 2.1e-10
                                       E-TT-EE-TT-EE.S.EEE-TT-EE-TT-EE-S CS
                         Hexapep_2   4 IGdnCliGanagi.G.vslGdncvvgaGvvita 34 
                                       ++d + iGana+  G +++G+++ vgaG+v+ta
  gi|336252862|ref|YP_004595969.1| 120 VEDGVQIGANATLlGdITIGEDAAVGAGSVVTA 152
                                       89**********6666****************7 PP

>> SATase_N  Serine acetyltransferase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     4e-08   0.00018      71     103 ..       3      35 ..       1      36 [. 0.94

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4e-08
                                       HHHHHHHHHHHHH-TT---THHHHHH-HHHHHH CS
                          SATase_N  71 eaaraDlkAvlerDpAcksylepllyfKGFhAl 103
                                       +++r+D++A++erDpA+k +le+ l + G hA+
  gi|336252862|ref|YP_004595969.1|   3 RRLREDVRAMCERDPAAKGCLEVALAYPGVHAV 35 
                                       6799***************************97 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.6   1.5e-05     0.069      29      95 ..      80     152 ..      75     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                        Bactofilin  29 ieakgklvvgeggkvegnika.eevvvaGtvkG....nveaeekvelkktakveGdika.ksleieegavfeG 95 
                                       i+++  +v+ge++++  +++  + v++ G  +       ++e+ v++ ++a++ Gdi+  +  ++  g v+++
  gi|336252862|ref|YP_004595969.1|  80 IDHGMGVVIGETAEIGDDVHMyHGVTLGGDTNEpvkrHPTVEDGVQIGANATLLGDITIgEDAAVGAGSVVTA 152
                                       6667789**************666******7752222667999***************955566777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1348.31
//
Query:       gi|336252863|ref|YP_004595970.1|  [L=222]
Description: phosphodiesterase [Halopiger xanaduensis SH-6]
Scores for complete 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  113.0   0.0    1.9e-32  112.7   0.0    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    6.6e-13   49.6   0.4    9.3e-12   45.9   0.4    2.0  1  Metallophos    Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.062   12.6   0.3       0.24   10.7   0.1    1.9  2  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 !  112.7   0.0   3.2e-36   1.9e-32       1     163 [.       1     185 [.       1     187 [. 0.84

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 3.2e-36
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepe.vleellelapvlaVrGNnD............ 62 
                                       Mk+++iSD+H+n+ ale+vle++  v  d++++aGD+  ++  p  +++el+e+ +v +V GN+D            
  gi|336252863|ref|YP_004595970.1|   1 MKVGLISDVHGNRVALETVLEEMPPV--DKLLCAGDVvgYNPWPAdCVDELRER-EVPTVMGNHDaavagdapfrfn 74 
                                       **************************..********977666665488888885.***************9999999 PP

                     Metallophos_2  63 ......eev.veedvlreaaelgtdlp.eeaelelagekvlliHgdpl........gvkdalaellkeaeegsdvvv 123
                                               + ++e++++ + e+  dlp e+ e++    ++ l+Hg+p+         +++++++++     ++dv+v
  gi|336252863|ref|YP_004595970.1|  75 gmaragV-EhAKEQLSEGQLEWLADLPaERTECD---GRIKLVHGHPDdpdrytryTYPEEFSARMLG---DEDVLV 144
                                       9877633.25788889999999999986666666...58*******9888885555444444444444...455*** PP

                     Metallophos_2 124 cGHtHvpevekeggvlvvnPGsvgeprdgdpe.tyaildtd 163
                                       +GHtHv++v+k  + +vvnPGsvg+prdgdp+ +ya++d++
  gi|336252863|ref|YP_004595970.1| 145 LGHTHVQGVRKYAEGIVVNPGSVGQPRDGDPRaGYAVVDLE 185
                                       **************************************997 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.4   1.5e-15   9.3e-12       1     203 [.       1     150 [.       1     151 [. 0.77

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1.5e-15
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCH CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegf 77 
                                       +++ +i+D+H     g+  +l+++l++ +    +d +l+aGD+v  ++++ ++++ l++         +++GNH+  
  gi|336252863|ref|YP_004595970.1|   1 MKVGLISDVH-----GNRVALETVLEEMP---PVDKLLCAGDVVGYNPWPADCVDELREREV-----PTVMGNHD-- 62 
                                       799*******.....**********9994...55**********************655544.....69******.. PP

                                       HHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHH. CS
                       Metallophos  78 eeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepgdewlkd. 153
                                                     +++  +    fn++  a+      k +l  G                          ewl+d 
  gi|336252863|ref|YP_004595970.1|  63 --------------AAVAGDAPFRFNGMARAGVEHA--KEQLSEGQ------------------------LEWLADl 99 
                                       ..............3333344456788888886666..77777777........................9999999 PP

                                       ..HHHHTTCSEEEEEESSESS.CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 154 ..lekrekadwvivlgHsply.rgsgylfgdealedllkkygvdlvisGHtHv 203
                                          + + ++++++v+gH   + r+  y++++e  +     ++ d+ + GHtHv
  gi|336252863|ref|YP_004595970.1| 100 paERTECDGRIKLVHGHPDDPdRYTRYTYPEEFSA--RMLGDEDVLVLGHTHV 150
                                       55555555555555555555599999999999999..5566667888899997 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.13   7.9e+02       7      45 ..       2      38 ..       1      62 [. 0.78
   2 ?   10.7   0.1     4e-05      0.24     213     257 .]     142     194 ..     136     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.13
                                      EEEEEE--TT-GGGHHHHHHHHHHH--SEEEEES----- CS
                     Metallophos_3  7 kvlaisdlkgevellerlveviedkdpDllvlvGdlvka 45
                                      kv  isd++g+   le ++e ++   +D l+  Gd+v+ 
  gi|336252863|ref|YP_004595970.1|  2 KVGLISDVHGNRVALETVLEEMP--PVDKLLCAGDVVGY 38
                                      56668899999888888877665..58999999999875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4e-05
                                       EEEE-SS--EE.EEETTEEEEE--BG...GGTE....EEEEETTTTEEEEEE- CS
                     Metallophos_3 213 vvvvghavkeh.eelgktlvvnPGal...eeGd....favvdleekkveleqv 257
                                       v v gh++ +   +  + +vvnPG++   ++Gd    +avvdle   v++++v
  gi|336252863|ref|YP_004595970.1| 142 VLVLGHTHVQGvRKYAEGIVVNPGSVgqpRDGDpragYAVVDLEAMTVDTGRV 194
                                       67789988777799999*******9933335657777************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1674.41
//
Query:       gi|336252864|ref|YP_004595971.1|  [L=94]
Description: hypothetical protein Halxa_1459 [Halopiger xanaduensis SH-6]
Scores for 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   2.9       0.19   12.0   2.9    1.3  1  DUF4418   Domain of unknown function (DUF4418)


Domain annotation for each model (and alignments):
>> DUF4418  Domain of unknown function (DUF4418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.9     1e-05      0.19      37      83 ..      45      90 ..      43      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1e-05
                           DUF4418 37 aelgvGivllvlgllalfvkkkklrrglsiavillgvlviliptvli 83
                                      a l++G+++++ g++ ++ k++  r+++ + v+++g+lv+l++++++
  gi|336252864|ref|YP_004595971.1| 45 ALLIIGVAMTLSGIAEVLPKNR-RRAAIVFRVTAIGILVVLVVRSVV 90
                                      6789******************.9999999************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 686.01
//
Query:       gi|336252865|ref|YP_004595972.1|  [L=196]
Description: IMP cyclohydrolase [Halopiger xanaduensis SH-6]
Scores for 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-65  218.1   0.0    9.1e-65  217.8   0.0    1.0  1  IMP_cyclohyd  IMP cyclohydrolase-like protein


Domain annotation for each model (and alignments):
>> IMP_cyclohyd  IMP cyclohydrolase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.8   0.0   5.1e-69   9.1e-65       1     189 [.       2     185 ..       2     187 .. 0.96

  Alignments for each domain:
  == domain 1  score: 217.8 bits;  conditional E-value: 5.1e-69
                                       ---SEEEEEEETTEE.EEEEEEE-SS---EEEEEETTEEEEEE-TGGGGGT-TTSSEEEEEEE....TTEEEEESST CS
                      IMP_cyclohyd   1 YvGRfivvgksedgkavaaYrvssRSfpnrnrvfredkirveptdeeklednpyiiYncvrvl....ddkavvtNGs 73 
                                       YvGRf+vvg++     v aYrvssRSfpnr+ ++red+++v ptd +  +dnpy++Ync+rv+    +++a  +NGs
  gi|336252865|ref|YP_004595972.1|   2 YVGRFVVVGPE-----VGAYRVSSRSFPNRKLTEREDALTVGPTDDAPETDNPYVSYNCLRVVetptGETAAFGNGS 73 
                                       9**********.....*****************************77778*************999899******** PP

                                       HHHHHHHHHHTSB-HHHHHHHHHHHH-S--STT---EEEEEE-.SS.EEEEEEETTEEEEEE--..TTS-EEEESSS CS
                      IMP_cyclohyd  74 qtdtiaeklekgltardalalsLlaldyEkDdynTPRiagvvk.eeeaalgivksdallvekvelkagegtliatYe 149
                                       ++d+iaekle+g++ardal++sLlaldyEkDdy+TPRia+ +  + ea +g+v++dallve+v+    e+tl+atYe
  gi|336252865|ref|YP_004595972.1|  74 HVDPIAEKLELGYPARDALTESLLALDYEKDDYDTPRIAATIGdDGEALIGTVRKDALLVETVD----EPTLVATYE 146
                                       ******************************************95556*****************....********* PP

                                       --S-EE-----SSHHHHHHHHHHGGGSS-EEEEEEEEESS CS
                      IMP_cyclohyd 150 kgepkeveleaedaeeaaeelweslefenkVslavavide 189
                                       k++p+++++eae+aeeaa+e+++ lefe++V++a++++++
  gi|336252865|ref|YP_004595972.1| 147 KNAPEAFDFEAETAEEAAREAYD-LEFEHAVCAAGVARTD 185
                                       ***********************.**********998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1533.83
//
Query:       gi|336252866|ref|YP_004595973.1|  [L=262]
Description: hypothetical protein Halxa_1461 [Halopiger xanaduensis SH-6]
Scores for 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   14.2  23.0        3.2    8.0   8.6    3.9  2  HNH       HNH endonuclease
        1.2    9.0   6.1        5.4    7.0   0.3    3.0  3  NinF      NinF protein


Domain annotation for each model (and alignments):
>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.4   0.00056         5       1      46 [.     121     179 ..     121     180 .. 0.65
   2 ?    8.0   8.6   0.00035       3.2       1      45 [.     200     256 ..     200     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00056
                               HNH   1 CeyCgrkfhksealevdHiipis...............qggaddieNlqllCksCHnkkhd 46 
                                       C++Cg       +l  +H++  +               +  + +ie +  lC +CH++ h 
  gi|336252866|ref|YP_004595973.1| 121 CTRCGTDTV--ACLDFHHVDTAAkemavgkmvtygygkERLREEIEKCDVLCANCHRQIHY 179
                                       666666632..3577777776665555555544444423667779*************995 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00035
                               HNH   1 CeyCgrkfhksealevdHiipis..............qggaddieNlqllCksCHnkkh 45 
                                       Ce+C++  h   +l  +Hi   +              + ++++ie ++ lC +CH+ +h
  gi|336252866|ref|YP_004595973.1| 200 CERCDES-HP-ACLDFHHIGDEKestvatlvsnsrsiDRIQTEIERCRILCANCHRVEH 256
                                       8999988.44.37999999888878888877776655599999*************998 PP

>> NinF  NinF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1      0.78     7e+03      15      25 ..     115     126 ..     113     138 .. 0.67
   2 ?    7.0   0.3    0.0006       5.4      18      29 ..     168     179 ..     154     187 .. 0.79
   3 ?    4.5   0.1    0.0036        32      17      25 ..     245     253 ..     227     258 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.78
                              NinF  15 veRaL.CanCsk 25 
                                       ++R   C  C+ 
  gi|336252866|ref|YP_004595973.1| 115 IKRKRgCTRCGT 126
                                       556656888875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0006
                              NinF  18 aLCanCskkLev 29 
                                        LCanC ++++ 
  gi|336252866|ref|YP_004595973.1| 168 VLCANCHRQIHY 179
                                       48*******995 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0036
                              NinF  17 RaLCanCsk 25 
                                       R LCanC +
  gi|336252866|ref|YP_004595973.1| 245 RILCANCHR 253
                                       568****76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2080.36
//
Query:       gi|336252867|ref|YP_004595974.1|  [L=252]
Description: hypothetical protein Halxa_1462 [Halopiger xanaduensis SH-6]
Scores for complete 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-06   28.5   0.1    4.8e-06   27.1   0.1    1.7  1  Rhodanese   Rhodanese-like domain
      0.005   16.6   2.1     0.0084   15.9   2.1    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   5.3e-10   4.8e-06      12     105 ..      80     161 ..      71     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 5.3e-10
                         Rhodanese  12 gkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr.aaaaaallk 87 
                                       +++++ D+R +++Ye+ hI gA              ++   ++p ++ +     ++++v+yc   ++ +   aa l 
  gi|336252867|ref|YP_004595974.1|  80 QEARVADARGSDQYEQAHIAGAPLS---------SAPDGVSNDPIADWP----TDDRIVTYCGCPHHlSGLRAASLI 143
                                       444589****************888.........344444444444444....49********99996666677777 PP

                         Rhodanese  88 klGyknvsvldGGfkawk 105
                                         Gy++v+ +d Gf+aw 
  gi|336252867|ref|YP_004595974.1| 144 DNGYEEVYAIDEGFQAWI 161
                                       8**999***********6 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.1   9.4e-07    0.0084       2      24 ..       1      23 [.       1      25 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.4e-07
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      ++RR+FL  ++++a + ++g ++
  gi|336252867|ref|YP_004595974.1|  1 MNRRTFLALGGVTALGSVAGCLG 23
                                      89******999998666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 2203.15
//
Query:       gi|336252868|ref|YP_004595975.1|  [L=451]
Description: NADH:flavin oxidoreductase/NADH oxidase [Halopiger xanaduensis SH-6]
Scores for 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-39  134.9   0.0    4.2e-34  118.3   0.0    2.1  2  Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase famil
     0.0024   17.0   0.0     0.0055   15.8   0.0    1.5  1  Dus           Dihydrouridine synthase (Dus)
  ------ inclusion threshold ------
       0.02   14.3   0.0      0.044   13.3   0.0    1.5  1  His_biosynth  Histidine biosynthesis protein
      0.062   12.7   0.0       0.11   11.9   0.0    1.3  1  NMO           Nitronate monooxygenase


Domain annotation for each model (and alignments):
>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   0.0   9.4e-38   4.2e-34       4     222 ..       6     231 ..       3     243 .. 0.85
   2 !   14.6   0.0   3.2e-06     0.014     281     335 ..     334     392 ..     256     398 .. 0.73

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 9.4e-38
                                       S-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-.SCTTSEE-SSGGGH CS
                      Oxidored_FMN   4 kPikignmtLknRivmapmtrlraldkgnvledlaaeyysqraeipvtliiteaafvnpksg.gfdnapgiwdeeqi 79 
                                        P++ig  ++ nR++ ap+   +++ ++  + d++++  ++ a  +v+li  +a+ v  ++g + ++  +++d   +
  gi|336252868|ref|YP_004595975.1|   6 DPVEIGGCEIPNRLYRAPLLECAGNGPD--AVDALIDDLEPAAASGVGLICQGATIVRGEGGcAAPGMTRVHDPAFV 80 
                                       6******************999999999..44689999999*******************99999************ PP

                                       HHHHHHHHHHHHTT-EEEEEEE--GGGS..SCSTCEC............SS.ESSSSSTTT-..........S...C CS
                      Oxidored_FMN  80 eewrklteavhengskvvvqlwhlGreakseyladqe..........vdspsdpvaldaqee.........esaeev 137
                                         ++ lt+ +h++g+ ++vql h+G ++    +a+ +          v      +      +         + +   
  gi|336252868|ref|YP_004595975.1|  81 SRLERLTDRIHDHGGRIFVQLEHGGLRSMETWHAEYRrehpdleqlaV------S------NppwqlrlldRLGFLS 145
                                       *************************99854444444422224432221......1......1223334556777778 PP

                                       S.-EE--HHHHHHHHHHHHHHHHHHHHTT-SEEEEEE-CTSHHHHHH-TTT----STTSSSHHHHHHHHHHHHHHHH CS
                      Oxidored_FMN 138 y.kkeltkeeikqliqefveAAkraieAgfDgVeihganGYLlnqFlspksnkrtDeygGslenRarFllevvdaVk 213
                                       y ++ l+ +e+ +l  +f +AA+ a++Ag+Dg+   gan  +++qFlsp +n+r+De+gGs e R+ Fl  v d+++
  gi|336252868|ref|YP_004595975.1| 146 YdPHVLSTDEVYDLAADFGRAAAHAVDAGYDGIHLSGANMGIVQQFLSPFYNRRSDEFGGSPEARLEFLALVHDEIR 222
                                       889************************************************************************** PP

                                       HHH-SSSEE CS
                      Oxidored_FMN 214 eavgeervg 222
                                       +++g   ++
  gi|336252868|ref|YP_004595975.1| 223 DRAGDVPLM 231
                                       **9975555 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.2e-06
                                       THHHHHHCCCHSSEEEE-SS--SHHHHHHHHHT....TS-SEEEESTHHHH-TTHHHHH CS
                      Oxidored_FMN 281 ekntefvkevwkkplitvgriadeekaaeivae....geadLvamgRefladpdlvekl 335
                                       e +   v+e+++ p+++ g+i d  +++  +         d+v+m+R+f a+p l  +l
  gi|336252868|ref|YP_004595975.1| 334 EDFCRRVREQVSIPVLAEGGIRDRAQMDRLLGAadaaPACDMVGMARPFYAEPRLGARL 392
                                       3677899***************9999987765522224569*************99887 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.2e-06    0.0055     175     243 ..     337     410 ..     320     417 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-06
                                       HHHHHHH-SS-EEEESS--SHHHHHHHH....HHH--SEEEESCHHCCSTTHHHHHHHHHHSC------.HHHH CS
                               Dus 175 IkevkqavsipviaNGdIkdaedaqail....eetGadgvmigrgalgnPwlfaestavktgeaepapp.laee 243
                                        + v+++vsipv+a G+I+d+ ++++ l    +   +d v ++r  + +P l a+  + + + + ++p  ++e 
  gi|336252868|ref|YP_004595975.1| 337 CRRVREQVSIPVLAEGGIRDRAQMDRLLgaadAAPACDMVGMARPFYAEPRLGARLLETDANADPENPRvVCES 410
                                       678**********************999333234578999999999****999985466666666666556665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.7e-06     0.044      61      94 ..     333     366 ..     329     388 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.7e-06
                                       HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHC CS
                      His_biosynth  61 nldlveeiaeevfipvqvGGGIrsledveellea 94 
                                       n d  ++++e+v+ipv   GGIr+  ++++ll a
  gi|336252868|ref|YP_004595975.1| 333 NEDFCRRVREQVSIPVLAEGGIRDRAQMDRLLGA 366
                                       5677788999999999999999999999998865 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.4e-05      0.11     186     212 ..     338     364 ..     332     375 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                               NMO 186 pqvldavdiPviAaGGiidrrgvaaaL 212
                                        +v++ v+iPv+A GGi dr +++  L
  gi|336252868|ref|YP_004595975.1| 338 RRVREQVSIPVLAEGGIRDRAQMDRLL 364
                                       57999****************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3231.16
//
Query:       gi|336252869|ref|YP_004595976.1|  [L=79]
Description: hypothetical protein Halxa_1464 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.43   10.2   3.1        1.9    8.1   0.2    2.3  2  zf_UBZ    Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2    0.0069   1.2e+02       4      13 ..      23      32 ..      21      36 .. 0.84
   2 ?    8.1   0.2   0.00011       1.9       2      10 ..      53      61 ..      52      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0069
                            zf_UBZ  4 lCerCgkeip 13
                                      +C+ C  e++
  gi|336252869|ref|YP_004595976.1| 23 TCSTCEIEME 32
                                      7****99886 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00011
                            zf_UBZ  2 tylCerCgk 10
                                      ++ C+rCg+
  gi|336252869|ref|YP_004595976.1| 53 QFNCPRCGQ 61
                                      799*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.24s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 656.03
//
Query:       gi|336252870|ref|YP_004595977.1|  [L=347]
Description: alcohol dehydrogenase GroES domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-28   97.7   1.1    5.2e-28   97.1   0.3    1.7  2  ADH_N            Alcohol dehydrogenase GroES-like domain
    1.3e-20   73.7   0.4    2.1e-20   73.0   0.4    1.4  1  ADH_zinc_N       Zinc-binding dehydrogenase
    1.7e-08   35.6   1.0    2.9e-08   34.8   1.0    1.4  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
  ------ inclusion threshold ------
       0.01   15.8   0.9       0.09   12.7   0.5    2.2  2  TP_methylase     Tetrapyrrole (Corrin/Porphyrin) Methylases
      0.046   13.5   0.1      0.069   12.9   0.1    1.3  1  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.3   1.4e-31   5.2e-28       2     109 .]      31     140 ..      30     140 .. 0.97
   2 ?   -2.6   0.0       1.4   4.9e+03      46      63 ..     163     180 ..     158     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 1.4e-31
                                       TEEEEEEEEEEE-HHHHHHHTTS..TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkgg..kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkeg 76 
                                       ++vl++v+ ag C++D hi++g+  +  ++ lp++lGHE +G+v+e+g+ev+ ++ Gd V+++p+++cg C+ C+ g
  gi|336252870|ref|YP_004595977.1|  31 DQVLVEVEGAGWCQTDNHIIEGMwaDYAPQDLPMTLGHENAGIVAETGEEVTLVEEGDPVICHPVQTCGICRPCRLG 107
                                       79********************988889999********************************************** PP

                                       -GGG-TTBEETTTSS-SSSBSEEEECGGGEEEE CS
                             ADH_N  77 eenlCeeakllgvsldGgfaeyvvvpekklvkl 109
                                       e+ +Ce+ ++ g+++dGgfae + ++e+ +++l
  gi|336252870|ref|YP_004595977.1| 108 EDMYCENSAFNGLTTDGGFAEFLQTNERAVIPL 140
                                       ***************************999975 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                                       ESTT-CS--TT-EEEE-S CS
                             ADH_N  46 vgpevkklkvGdrVvvep 63 
                                       + ++v++l+ Gd  vv  
  gi|336252870|ref|YP_004595977.1| 163 AKKAVDELNPGDACVVIG 180
                                       567888999999988754 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.4     6e-24   2.1e-20       1     128 [.     183     309 ..     183     311 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 6e-24
                                       HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaal 76 
                                       g+G++++q++ a+ a  + avd+++e lela++lGa +++n+ e+dl +++++lt++eg++ v+++vG+ +t  aa 
  gi|336252870|ref|YP_004595977.1| 183 GLGHIGLQCLEAMSAaDILAVDVKDEALELAEDLGARHTVNSAEEDLADAVADLTDDEGAQQVLDFVGADETTGAAP 259
                                       89****************************************555******************************** PP

                                       HCEEEEEEEEECSCTSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                        ADH_zinc_N  77 kllkpgGrlvvvGggkgeeefdlrnlllkeksilGsllgslreefkealdll 128
                                       ++++ gG   ++G g++    + + l+  e s++G+l+g+   e++e+++l+
  gi|336252870|ref|YP_004595977.1| 260 DIVAAGGDHHIIGYGGHIH-EPCQALVDGEFSFKGTLVGQ-YAELQELVALV 309
                                       *************955555.799999**************.89999999987 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   1.0   8.1e-12   2.9e-08       1     133 []     216     344 ..     216     344 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 8.1e-12
                                       TT-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEE..EE----.S-EEE-CHHHCTTT- CS
                      ADH_zinc_N_2   1 lGAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrl..vsiggpplsaallkpakkrkgr 71 
                                       lGA + +++ +ed++    + t+ eg + vld vg +++  a+ ++++ gG+   + +gg      + +p +    +
  gi|336252870|ref|YP_004595977.1| 216 LGARHTVNSAEEDLAdavaDLTDDEGAQQVLDFVGADETTGAAPDIVAAGGDHhiIGYGG-----HIHEPCQALVDG 287
                                       8******99999999999999999***********777779999***6668862255555.....466666655555 PP

                                       EEEE--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  72 svkyeflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                        ++++  + +  +  a+ l+el+al++ G ++ + + +++l++++   ++le++   G+ V+
  gi|336252870|ref|YP_004595977.1| 288 EFSFKGTL-VG-Q-YAE-LQELVALVDRGDVELRTE-RYDLADINAVAERLEHNEIEGRAVV 344
                                       55555555.33.3.688.*****************8.6********************9997 PP

>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.12   4.2e+02      76      93 ..      75      92 ..      69     100 .. 0.86
   2 ?   12.7   0.5   2.5e-05      0.09       5      72 ..     177     245 ..     175     286 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
                      TP_methylase 76 lragkdVvllvsGDPlvy 93
                                      +++g++V l+  GDP + 
  gi|336252870|ref|YP_004595977.1| 75 AETGEEVTLVEEGDPVIC 92
                                      678999*********986 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.5e-05
                      TP_methylase   5 VGvGpGdpellTvrAlralktadvvlgddsr.aleilldllaeel..eleapmgkekepleea....yeeiaeal 72 
                                       V +G+G+  ++ +  l+a+ +ad+++ d +  ale+++dl a+ +  ++e++ +        +     +e a+++
  gi|336252870|ref|YP_004595977.1| 177 VVIGIGGLGHIGLQCLEAMSAADILAVDVKDeALELAEDLGARHTvnSAEEDLADA------VadltDDEGAQQV 245
                                       669**********************9888558*******99886554222222222......1222244444444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.9e-05     0.069      13      84 ..     183     255 ..     172     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                   Methyltransf_31  13 GtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.lekl.ledekfDlilsnevl 84 
                                       G G+++++   e+ + a++  +D + ea+elA+   +++ ++ +e   +d+ + l  +  +++  D++ ++e+ 
  gi|336252870|ref|YP_004595977.1| 183 GLGHIGLQCL-EAMSAADILAVDVKDEALELAEDLGARHTVNSAEEDLADAVAdLTDDeGAQQVLDFVGADETT 255
                                       789*******.9999*******************9999999999988888877777666555777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2608.02
//
Query:       gi|336252871|ref|YP_004595978.1|  [L=354]
Description: amidohydrolase 2 [Halopiger xanaduensis SH-6]
Scores for 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-41  141.5   4.7    5.6e-41  141.2   4.7    1.1  1  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.2   4.7   3.1e-45   5.6e-41       1     291 []      12     320 ..      12     320 .. 0.93

  Alignments for each domain:
  == domain 1  score: 141.2 bits;  conditional E-value: 3.1e-45
                                       EEEEEEE..SHHH...................CCCCCCGGCTSCCCHHHHHCHHTSSECCCEHCHHHHHHHHTSHHC CS
                      Amidohydro_2   1 iDvHaHllppeaa...................irddgepngfdpeerlafmkragvdpqlaspeallvlnaaagiar 58 
                                       iD+H+Hl+++ ++                   ++  +++    +++++++ k    ++  + +  + v + +++ ++
  gi|336252871|ref|YP_004595978.1|  12 IDAHVHLWDATEEniqheggeefiqcfydyhtTFTPEDR----QWSMEEYRKYGAERMVEDMFGNAAVDMGIFQPTY 84 
                                       9********9999************99987744433333....4666677777777777777*************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHCTTCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGH.... CS
                      Amidohydro_2  59 avivaalcrgannrvlaeaakrpdrfvggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrld.... 131
                                         ++++++++++++ +++a+++p rfv  + ++p+d+++ +++le+  e + + Gv+l+++ + d+ +g rld    
  gi|336252871|ref|YP_004595978.1|  85 LTDFYEEGFNTTEQNAELADEYPERFVLNGSFDPRDGDEGLEYLEELHETYDVPGVKLYTAEWRDESKGWRLDdeea 161
                                       ***************************************************************99999999999999 PP

                                       HHHHHHHHHHT-EEE.EE....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHH CS
                      Amidohydro_2 132 rpifealeelglpvd.ihtGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrp 207
                                        +++e++++lg+     h G      ++ ++   +a++  +++++a  fP+l++++ H G p  rl ++ +++a+ +
  gi|336252871|ref|YP_004595978.1| 162 FRFLEKCADLGIENIhAHKG------PTIRPLNRDAFDVADVDDAASSFPELNFIVEHVGLP--RLDDFCWIAAQEN 230
                                       9***********87669988......************************************..************* PP

                                       HCCEEECCGHHHSSEEECCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHH........SSHHH CS
                      Amidohydro_2 208 nvyvklsglytellyfdspladppalarlieavgpdrilfGsDyPhptleaepealalldlval........lsdee 276
                                       nvy  l  +++  + +  p  + +++++l+ ++g+drilfGsDy  +++++ +e++ +++ +++         + e 
  gi|336252871|ref|YP_004595978.1| 231 NVYGGLAVAAP--FAQNRPGKFSEIMSELLWWLGEDRILFGSDYALWNPDWLVEEVMEAEFLQEhrmeygveWDLET 305
                                       ***99999888..899****************************************999988889************ PP

                                       HHHHHTHHHHHHCTB CS
                      Amidohydro_2 277 rekilggNAarlygl 291
                                       ++k++g+NAa+ly++
  gi|336252871|ref|YP_004595978.1| 306 KKKVMGENAAELYDI 320
                                       *************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2768.36
//
Query:       gi|336252872|ref|YP_004595979.1|  [L=282]
Description: hypothetical protein Halxa_1467 [Halopiger xanaduensis SH-6]
Scores for 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-17   61.5   0.1    2.2e-16   59.8   0.1    1.9  1  FeS_assembly_P  Iron-sulfur cluster assembly protein


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.1   1.2e-20   2.2e-16       1      72 [.      17      88 ..      17      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1.2e-20
                                      HHHHHHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--SSTT-T..THHHHHHHHHHHHC.STT--EEEE CS
                    FeS_assembly_P  1 keavlaaLrtVtDPelgvdlvslglvreidieggkVsvditltypacs..laeairadaeaalralpgvevveV 72
                                      ++av++ L+ VtDPel++++v+l  + +i+i+g++V+v +tl+++ cs  +a +++ da++ +++lp   v+e+
  gi|336252872|ref|YP_004595979.1| 17 RAAVRDRLDRVTDPELDRSIVELEYIDAIEIDGDRVTVEFTLPTAWCSpaFAWMMAVDARDEVESLPA--VEEA 88
                                      689**********************************************999****************..6555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2192.13
//
Query:       gi|336252873|ref|YP_004595980.1|  [L=391]
Description: Water Stress and Hypersensitive response domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-13   51.7   0.0    2.7e-08   34.3   0.0    2.6  2  LEA_2     Late embryogenesis abundant protein
  ------ inclusion threshold ------
       0.16   12.1   0.0       0.28   11.3   0.0    1.3  1  DUF3426   Protein of unknown function (DUF3426)


Domain annotation for each model (and alignments):
>> LEA_2  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0     3e-12   2.7e-08       2      95 ..      55     145 ..      54     150 .. 0.90
   2 !   14.7   0.0   3.7e-06     0.033       1      83 [.     212     300 ..     212     313 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 3e-12
                                       EEEEESSS.S-EEEEEEEEEEEESSSEEEEEEECE-EEESSSCEEEEEEEEEEEHHHHHHHHHHHH..HCCSEEEEE CS
                             LEA_2   2 lrvrNPNs.fgvrydgleldlsyngqrlasgtspqgfsqpargtttlevpvsvsaddlarelrallagevgleleyt 77 
                                       + ++NPN+ ++++  +le+dls n++ la ++s++g+ +p++++t  e++  + +++l++++++++   +++  +++
  gi|336252873|ref|YP_004595980.1|  55 VWIDNPNPgIELDDVTLEYDLSMNDVDLA-NGSVDGVAVPSGNST-TEIRTDMRYQQLPSWWASHV--RNDEVSALE 127
                                       669*****9***999**************.***************.89999*******99999999..788889999 PP

                                       EEEEEE.EEETTTSCEEE CS
                             LEA_2  78 lrgrlkvlgkpilgsvtv 95 
                                       ++++++   +p+ gs+++
  gi|336252873|ref|YP_004595980.1| 128 ADVTAHASLGPFSGSPSY 145
                                       999999888888888776 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.7e-06
                                       EEEEEESSSS-EEEEEEEEEEEESSSEEE........EEEECE-EEESSSCEEEEEEEEEEEHHHHHHHHHHHH..H CS
                             LEA_2   1 tlrvrNPNsfgvrydgleldlsyngqrla........sgtspqgfsqpargtttlevpvsvsaddlarelrallage 69 
                                       t++v NPN  +++   l+ + ++n++ +a             +  ++p++gt+++++ +++ +dd++++++ ++   
  gi|336252873|ref|YP_004595980.1| 212 TFEVHNPNAYPLPTPALTGEMEFNDRMVAqwdaheveLLDAASDTTIPPQGTREITFVAEMENDDIVSWFATHV--D 286
                                       5789*********************777722211110333444556666666666666**************99..5 PP

                                       CCSEEEEEEEEEEE CS
                             LEA_2  70 vgleleytlrgrlk 83 
                                       +++ ++ ++r+ l 
  gi|336252873|ref|YP_004595980.1| 287 NEEFTDAEMRAQLA 300
                                       66666666666554 PP

>> DUF3426  Protein of unknown function (DUF3426)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.1e-05      0.28      38     134 ..     181     272 ..     161     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.1e-05
                           DUF3426  38 plgcelppprdielisiessslrekageanlvlegtlrNradkpqalpaleltLtDaqgqvvarrvlspaeyllanq 114
                                       p +  ++p  +i++ + e  +++e   e  l l++++ N  ++p + pal  ++   ++++va+   ++ e+l a  
  gi|336252873|ref|YP_004595980.1| 181 PQQELVEPTVEIRDTDAEWGEVTENRTE--LHLTFEVHNPNAYPLPTPALTGEM-EFNDRMVAQWDAHEVELLDA-- 252
                                       5555678888999999999999877776..5**********************7.5899*****99999999876.. PP

                           DUF3426 115 aantglapgseipfalvlev 134
                                       a+ t+++p+++ ++++v e 
  gi|336252873|ref|YP_004595980.1| 253 ASDTTIPPQGTREITFVAEM 272
                                       56999***998777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3108.10
//
Query:       gi|336252874|ref|YP_004595981.1|  [L=172]
Description: hypothetical protein Halxa_1469 [Halopiger xanaduensis SH-6]
Scores for 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   36.7   0.0      5e-09   36.5   0.0    1.0  1  CGI-121   Kinase binding protein CGI-121
  ------ inclusion threshold ------
      0.069   13.4   0.1       0.12   12.7   0.1    1.4  1  PGDYG     PGDYG protein
       0.16   11.7   0.0       0.23   11.1   0.0    1.2  1  Stk19     Serine-threonine protein kinase 19


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 !   36.5   0.0   8.4e-13     5e-09      19     161 ..      27     167 ..      11     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 8.4e-13
                                       HCTT-EEE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT.-S-EEEEEEE CS
                           CGI-121  19 aeldfafldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdk.ttsllvvkvs 94 
                                        ++ +   da+++ ++ h+  Av  a  a  rg+   ++   Eil++  + ++I  al  +g+++  ++++++v  +
  gi|336252874|ref|YP_004595981.1|  27 HDVTIQAFDARYVADRRHVERAVELADRAIDRGENVARNRAVEILLYAAGRRQIDRALA-MGVDEGeNRAVVLVDSQ 102
                                       56667789**************************************************9.*****988889999998 PP

                                       SS......S--HHHHHHHHHHHS-SEEE--SHHHHHH--HHHHHHHTT--..TT---SSHHHHHHHHHHHHHT CS
                           CGI-121  95 ss......eadeeevlkslkevvegelvpleeeleeltdwkkikkiYklneleeekeeevkeledlvvsaval 161
                                       s       e+ + ++l++l++ ve +++     le+  d +++ +++ ++  ++e+e++  +l +lv ++val
  gi|336252874|ref|YP_004595981.1| 103 SGrgsggnESAAIADLADLEAFVERTPT-----LES-PDEATLCEFFEIT--DAEREATDASLAALVRERVAL 167
                                       8866655555555555566666665444.....444.89***********..6677788888*****999997 PP

>> PGDYG  PGDYG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.9e-05      0.12       9      71 ..      14      89 ..       9     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                             PGDYG  9 daivtg..etGdrWvvsrerfdakyvalkpg...........larGeagayrnrPievla.kemdeafsiarsaagd 71
                                      d  vt+  e Gd+  v  + fda+yva + +           ++rGe++a rnr +e+l    +++++  a ++++d
  gi|336252874|ref|YP_004595981.1| 14 DSFVTAinEIGDKHDVTIQAFDARYVADRRHveraveladraIDRGENVA-RNRAVEILLyAAGRRQIDRALAMGVD 89
                                      6667763367***************9988777888999999999999998.89999887515567777777777666 PP

>> Stk19  Serine-threonine protein kinase 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.9e-05      0.23      42     128 ..      73     163 ..      62     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.9e-05
                             Stk19  42 laqsptkvereleelirkgklrklvingrgkdisklg...evlvltedyeklikesseleeeek.vlekFlellken 114
                                       +a ++ +++r l+  +++g+ r +v+  ++++  + g    ++    d+e+ ++++ +le+  + +l +F e+ +++
  gi|336252874|ref|YP_004595981.1|  73 YAAGRRQIDRALAMGVDEGENRAVVLVDSQSGRGSGGnesAAIADLADLEAFVERTPTLESPDEaTLCEFFEITDAE 149
                                       467899*******************99999775533356699***********999999876664789999999988 PP

                             Stk19 115 ptalsisasslsee 128
                                        +a+  s ++l +e
  gi|336252874|ref|YP_004595981.1| 150 REATDASLAALVRE 163
                                       88887766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1302.25
//
Query:       gi|336252875|ref|YP_004595982.1|  [L=787]
Description: ski2-type helicase [Halopiger xanaduensis SH-6]
Scores for 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-23   81.2   0.0    1.4e-22   80.3   0.0    1.4  1  DEAD             DEAD/DEAH box helicase
    4.9e-09   36.7   1.8      1e-08   35.6   0.2    2.4  2  HHH_5            Helix-hairpin-helix domain
    6.8e-08   32.7   0.0    1.4e-07   31.7   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
    1.7e-07   31.6   0.0    1.7e-06   28.3   0.0    2.5  2  Helicase_C       Helicase conserved C-terminal domain
    0.00033   20.4   0.0      0.001   18.9   0.0    1.8  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
  ------ inclusion threshold ------
      0.038   13.9   0.0        1.9    8.5   0.0    3.3  2  HHH              Helix-hairpin-helix motif
        0.8   10.1   5.1       0.47   10.9   0.8    2.6  2  FCD              FCD 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 !   80.3   0.0   5.3e-26   1.4e-22       2     170 ..      27     183 ..      26     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 5.3e-26
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       + Qaea+++   +g+++++a +T+sGKT+++++ +l++v     ++g kal+++P+r+La +   +++ + ++ +  
  gi|336252875|ref|YP_004595982.1|  27 PPQAEAVEAGAtEGDSLVAAVPTASGKTMIAALSMLSAV-----QRGGKALYIVPLRALASEKKAEFEAYEEF-G-- 95 
                                       679*****9994566677788***************999.....6788*********************9994.4.. PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                       v + +   ++++  + l ++ divv+t +++d+l+++g   ls+++++V DE++ + d +++++++  l++l++ + 
  gi|336252875|ref|YP_004595982.1|  96 VTAGVATGNYESTSDWL-ATKDIVVATSEKVDSLVRNGADWLSDLTCVVSDEVHLIDDRNRGPTLEVTLAKLRKLNP 171
                                       44444555677777778.99***************989977*******************************87766 PP

                                       TSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxx RF
                              DEAD 155 dgklqrqvivlSATlp 170
                                       d +    +++lSAT+ 
  gi|336252875|ref|YP_004595982.1| 172 DLQ----TVALSATVG 183
                                       644....*******86 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       2.6   6.7e+03      23      34 ..     500     512 ..     495     519 .. 0.69
   2 !   35.6   0.2   4.1e-12     1e-08       3      55 ..     683     734 ..     681     736 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.6
                                       --SHHHHHHS.-H CS
                             HHH_5  23 iesvedlaaa.dv 34 
                                       ++s +dla++ d+
  gi|336252875|ref|YP_004595982.1| 500 FTSAADLAEQnDR 512
                                       8899****98333 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 4.1e-12
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS.-HHHHHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGi.GkktAeriilel 55 
                                       eL sv G+G+k+A++l++aGie ++dl +ad+  +  +  + GkktAe+i++ +
  gi|336252875|ref|YP_004595982.1| 683 ELVSVGGVGRKRARRLYEAGIEEPADLRNADKGVILNV--LkGKKTAENILENA 734
                                       799**********************************9..77********9866 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 !   31.7   0.0   5.4e-11   1.4e-07       3     169 ..      24     182 ..      22     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 5.4e-11
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       el++ Q+ea+e+ +     ++   ++ + +T +GKT++aa  + +  + g+  k+l +vp ++l +  + ef+ + +
  gi|336252875|ref|YP_004595982.1|  24 ELYPPQAEAVEAGA-----TEGDSLVAAVPTASGKTMIAALSMLSAVQRGG--KALYIVPLRALASEKKAEFEAYEE 93 
                                       57778888888877.....556688999********************999..9*********************** PP

                                       G....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......T CS
                            ResIII  80 eaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......s 149
                                         +++  ++ +g+ ++  +    +k+i+v+t +++d+        +     +   +++ DE+H + + +       +
  gi|336252875|ref|YP_004595982.1|  94 FGVTA--GVATGNYEST-SDWLATKDIVVATSEKVDSLV-----RNGADWLSDLTCVVSDEVHLIDDRNrgptlevT 162
                                       *9854..4444444444.455699***************.....33444444555********99998456666666 PP

                                       THHHHHT---SEEEEEESS- CS
                            ResIII 150 wreilekfkeavllglTATp 169
                                         ++ + +++   ++l+AT 
  gi|336252875|ref|YP_004595982.1| 163 LAKLRKLNPDLQTVALSATV 182
                                       66667777778999999996 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 ?   -2.0   0.0       1.7   4.4e+03       9      49 ..      61     104 ..      54     110 .. 0.63
   2 !   28.3   0.0   6.8e-10   1.7e-06      10     111 .]     243     387 ..     234     387 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.7
                                       HHHHTTTTSEEEEEESSHH.HHHHHHHH..HHHTTSTEEEESTT CS
                        Helicase_C   9 llkleeeggkilifvntid.rlekvkll..lekkgikvavlhge 49 
                                       +l+  ++ggk+l +v+ +    ek   +   e++g+++ v +g+
  gi|336252875|ref|YP_004595982.1|  61 MLSAVQRGGKALYIVPLRAlASEKKAEFeaYEEFGVTAGVATGN 104
                                       34678999999999999995333333332235557777766665 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 6.8e-10
                                       HHHTTTTSEEEEEESSHHHH.............HHHHHH....................HHHT.........TSTEE CS
                        Helicase_C  10 lkleeeggkilifvntidrl.............ekvkll....................lekk.........gikva 44 
                                       l   +egg +l+fvn+++++             e    l                    +  +         +  +a
  gi|336252875|ref|YP_004595982.1| 243 L---QEGGSSLVFVNSRRNAeaaarrlgkvasrE----LtpeeedqlaelaeeirddsdT--EtskdladcvERGSA 310
                                       4...778888888888885522233333333330....1344333334444444444441..033456677789999 PP

                                       EESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEE....ESSSS......SSHHHHHHHHTTSSSTT CS
                        Helicase_C  45 vlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVi....nfdlp......rnvtsyiqriGRtgRag 111
                                        +h+ l++ +r  + ++f++   +v+ at  ++ G++ p  ++++    +fd+        +v +++q++GR+gR g
  gi|336252875|ref|YP_004595982.1| 311 FHHAGLSSTQRSIVEDAFRDRLLKVISATPTLAAGVNTPARRVIVrdwrRFDPSaggmapLDVLEVHQMMGRAGRPG 387
                                       ***************************************777777777777777776666668************75 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 !   18.9   0.0   3.9e-07     0.001       3      31 ..     684     714 ..     683     725 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.9e-07
                   DNA_pol_lambd_f   3 FtkvyGVGpktAkkwyakGirtledlra..k 31 
                                       + +v GVG+k+A+++y++Gi    dlr+  k
  gi|336252875|ref|YP_004595982.1| 684 LVSVGGVGRKRARRLYEAGIEEPADLRNadK 714
                                       67899**********************9543 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00075       1.9      12      29 ..     683     700 ..     683     701 .. 0.90
   2 ?    1.3   0.0      0.14   3.6e+02      20      29 ..     723     732 ..     723     733 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00075
                                       HHHTSTT-SHHHHHHHHH CS
                               HHH  12 eLlalPGVGpktAeaIls 29 
                                       eL+++ GVG+k+A++ ++
  gi|336252875|ref|YP_004595982.1| 683 ELVSVGGVGRKRARRLYE 700
                                       899***********9875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.14
                                       SHHHHHHHHH CS
                               HHH  20 GpktAeaIls 29 
                                       G+ktAe Il+
  gi|336252875|ref|YP_004595982.1| 723 GKKTAENILE 732
                                       99******96 PP

>> FCD  FCD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   0.00018      0.47      16      74 ..     269     330 ..     259     357 .. 0.84
   2 ?   -0.3   0.3      0.54   1.4e+03      13      42 ..     650     679 ..     648     686 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                               FCD  16 laarratdadlaeleellealeeaaa...egdleefaeadraFHralaeaagnpvlaellee 74 
                                        a r  t++++++l el+e++++ ++   ++dl++ +e   aFH a ++ +++    +++++
  gi|336252875|ref|YP_004595982.1| 269 VASRELTPEEEDQLAELAEEIRDDSDtetSKDLADCVERGSAFHHAGLSSTQRSIVEDAFRD 330
                                       578999********************988999999***********9999998888866554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.54
                               FCD  13 aarlaarratdadlaeleellealeeaaae 42 
                                       aa+  ar +++++  + +e+ ++ e  +++
  gi|336252875|ref|YP_004595982.1| 650 AAESLAREIDSEWTVAVREARARVEHGVGD 679
                                       8999*****************999987664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (787 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.66u 0.24s 00:00:00.90 Elapsed: 00:00:00.40
# Mc/sec: 5844.77
//
Query:       gi|336252876|ref|YP_004595983.1|  [L=414]
Description: MgtE integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-26   91.8  11.3    6.6e-26   91.1  11.3    1.3  1  MgtE      Divalent cation transporter
    3.9e-14   53.1   2.2    3.9e-14   53.1   2.2    2.3  3  MgtE_N    MgtE intracellular N domain
    1.7e-07   31.6   5.4    0.00059   20.2   0.6    3.0  3  CBS       CBS domain
  ------ inclusion threshold ------
       0.12   12.6   0.0        0.4   10.9   0.0    1.9  1  FliG_M    FliG middle domain
       0.13   12.5   0.0       0.81    9.9   0.0    2.2  2  FliG_C    FliG C-terminal domain


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 !   91.1  11.3   1.8e-29   6.6e-26       1     123 [.     286     407 ..     286     408 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 1.8e-29
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTSS-GG.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHH CS
                              MgtE   1 iPvilglgGnlgaqlasristalhlgelekk.lkkvllkelrvvlllgvilgllifllalllgwslllalvvglalv 76 
                                       +Pv++g+gGn+g+q++++++++++l++++ +   + +++e++++  +g+i g+l++l+a ++ +s+ll+lv+g+++v
  gi|336252876|ref|YP_004595983.1| 286 MPVVAGMGGNAGTQSMAVTVRGIALDQISLStGGRAVVNEIVAGAANGLITGVLVALIASVFNQSPLLGLVLGVSMV 362
                                       8***************************88888******************************************** PP

                                       HHHHHHHHH..HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  77 lvllaaallilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                       l+l++a ++  g+++plll k+g DP+++a+ ++t+++D+lg+++++
  gi|336252876|ref|YP_004595983.1| 363 LNLVIAGFF--GTIIPLLLDKIGKDPATSATIFITTMTDVLGFFIFL 407
                                       *********..*********************************996 PP

>> MgtE_N  MgtE intracellular N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   2.2   1.1e-17   3.9e-14      20     101 ..      20     101 ..       3     102 .. 0.94
   2 ?   -1.2   0.0      0.86   3.1e+03      25      41 ..     181     197 ..     172     201 .. 0.65
   3 ?   -1.9   0.1       1.4   5.1e+03      68      91 ..     215     238 ..     208     242 .. 0.67

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.1e-17
                                       HHHHHS-HHHHHHHHCTS-CCCCCHHHHCS-HHHHHHHHCCS-HHHHHHHHCCCHHHHHHHHHHCS-HHHHHHHHHH CS
                            MgtE_N  20 allrllpkeeaaevleeldedlqeeliealsdeelaelleeldsDdaadlleelpeekveellsaldeeereeieel 96 
                                       a +++l++ ++ ev+  l+e ++++l+e+l+++ l+e++  ld+D+aad+le  +e ++  +l++lde +re++e l
  gi|336252876|ref|YP_004595983.1|  20 AEFERLSRRRQREVFYLLPETVRRSLVEDLDPDGLREFVRRLDPDEAADVLELTDESTRTDVLRHLDESRREKVEFL 96 
                                       56899************************************************************************ PP

                                       CTS-T CS
                            MgtE_N  97 lsYpe 101
                                       l++++
  gi|336252876|ref|YP_004595983.1|  97 LEFSP 101
                                       **986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.86
                                       S-HHHHHHHHCTS-CCC CS
                            MgtE_N  25 lpkeeaaevleeldedl 41 
                                       +p+e+ +ev+ e +e+ 
  gi|336252876|ref|YP_004595983.1| 181 VPDEDVVEVFREHPESS 197
                                       45666666666655544 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.4
                                       HHHCCCHHHHHHHHHHCS-HHHHH CS
                            MgtE_N  68 dlleelpeekveellsaldeeere 91 
                                       dll+ ++ee +e l + +  +e e
  gi|336252876|ref|YP_004595983.1| 215 DLLRVVEEEATETLYEFTGVQEEE 238
                                       777777888777777766555555 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       2.1   7.4e+03      47      56 ..      77      86 ..      77      87 .. 0.85
   2 !   12.6   0.0   3.9e-05      0.14       5      44 ..     108     151 ..     104     153 .. 0.82
   3 !   20.2   0.6   1.6e-07   0.00059      19      55 ..     184     220 ..     169     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.1
                                      EHHHHHHHHH CS
                               CBS 47 tlrDllrall 56
                                      t++D+lr l 
  gi|336252876|ref|YP_004595983.1| 77 TRTDVLRHLD 86
                                      899***9986 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.9e-05
                                       SBSSCEEEETTSBHHHHHHHHH..HHTSSEEE.E.EETTTBEEE CS
                               CBS   5 mtrdvvtvppdttleealelmr..ekgvsrlP.V.VdedgklvG 44 
                                       m  d+vtv  d +le ++++    e+g +r+P + V +dg+l G
  gi|336252876|ref|YP_004595983.1| 108 MDLDYVTVEIDRDLEAVAQRVQrfEEGTGRIPlIfVTDDGELAG 151
                                       55599*************9986456779***9565599***998 PP

  == domain 3  score: 20.2 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  19 eealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       e+++e +re+  s++ V+d+dg + G+++ +Dllr++
  gi|336252876|ref|YP_004595983.1| 184 EDVVEVFREHPESSVAVLDDDGTIMGVIHAEDLLRVV 220
                                       8999***888889*********999**********87 PP

>> FliG_M  FliG middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011       0.4      22      47 ..      60      85 ..      57      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                      TS-HHHHHHHHHTS-HHHHHHHHHHH CS
                            FliG_M 22 yLdpeqAAevLseLpeelraevirri 47
                                      +Ldp+ AA+vL+  +e  r++v+r +
  gi|336252876|ref|YP_004595983.1| 60 RLDPDEAADVLELTDESTRTDVLRHL 85
                                      79********************9976 PP

>> FliG_C  FliG C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00023      0.81      25      72 ..      47      94 ..      40     104 .. 0.90
   2 ?   -0.7   0.0      0.46   1.6e+03      13      46 ..     166     200 ..     162     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00023
                                      GGS-HHHHHHHHTTS-HHHHHHHHCTS-HHHHHHHHTTS-HHHHHHHH CS
                            FliG_C 25 vrlddraiqrllrevdkedLalaLkgaseelrekilsnmSkraaemlr 72
                                       +ld++++++++r +d+++ a  L  ++e  r  +l+ + + ++e+++
  gi|336252876|ref|YP_004595983.1| 47 EDLDPDGLREFVRRLDPDEAADVLELTDESTRTDVLRHLDESRREKVE 94
                                      689************************************999999886 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.46
                                       HHHHHHS-GGGG.GGS-HHHHHHHHTTS-HHHHHH CS
                            FliG_C  13 eirkkmftfedl.vrlddraiqrllrevdkedLal 46 
                                       eir+++     +  +++d+++ +++re ++ ++a+
  gi|336252876|ref|YP_004595983.1| 166 EIREHVHETPAVrYDVPDEDVVEVFREHPESSVAV 200
                                       677777777777788999********999887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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 0.24s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 3252.50
//
Query:       gi|336252877|ref|YP_004595984.1|  [L=138]
Description: phosphate transporter [Halopiger xanaduensis SH-6]
Scores for complete 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-12   47.6  10.3    1.2e-12   47.6  10.3    1.3  1  PHO4      Phosphate transporter family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6  10.3   6.5e-17   1.2e-12       3     105 ..      26     124 ..      24     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 6.5e-17
                              PHO4   3 anDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselm.lgmlaallgaavwll 78 
                                       an  +  fa+++g++a+++++A+++ +++ ++Ga+++G++++et++  ++d        ++ l+++a ll+aa+++ 
  gi|336252877|ref|YP_004595984.1|  26 ANSNSPPFAPAIGANAISTMRAAFVIGLLATAGALMQGGSISETVGADLID-----GVAITpLAATAGLLTAATFMG 97 
                                       799999********************************************4.....3344459************** PP

                              PHO4  79 latvlglPvStthslvGaliGaalaae 105
                                       +  ++++P+  +++++Ga++G++l ++
  gi|336252877|ref|YP_004595984.1|  98 IGIYTRYPIPAAFATTGAMVGVGLGLG 124
                                       ***********************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1174.47
//
Query:       gi|336252878|ref|YP_004595985.1|  [L=521]
Description: Alkaline phosphatase [Halopiger xanaduensis SH-6]
Scores for 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-76  256.3   5.0    6.9e-76  255.8   5.0    1.2  1  Alk_phosphatase  Alkaline phosphatase
    0.00094   18.6   1.1     0.0012   18.3   0.1    1.6  2  Metalloenzyme    Metalloenzyme superfamily
  ------ inclusion threshold ------
      0.054   13.1   0.2       0.14   11.7   0.2    1.8  1  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
       0.14   12.2   0.2       0.42   10.7   0.2    1.8  1  EF-hand_6        EF-hand domain


Domain annotation for each model (and alignments):
>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.8   5.0   1.5e-79   6.9e-76       2     414 ..      38     431 ..      37     433 .. 0.85

  Alignments for each domain:
  == domain 1  score: 255.8 bits;  conditional E-value: 1.5e-79
                                       SEEEEEEETT-SHHHHHHHHHHHCHCTCSSSTTS.TTGGG-SEEEEEESSECSTTSSGHHHHHHHHHHSSBTBTT-B CS
                   Alk_phosphatase   2 knvilligDGmgvstvtaaRslkeqakdklgeetllamdrfplvglsktyavdkqvtDSaataTAyacgvktyngai 78 
                                        nvi+ligDGmg   + ++  ++++            ++ +  vg ++t +   +vtDSaa++TA+a+g k++ng++
  gi|336252878|ref|YP_004595985.1|  38 ENVIVLIGDGMGFDPIEVTSVVHGDL----------SLQSMTGVGYTRTNSRSGEVTDSAAAGTALATGHKAFNGQV 104
                                       6****************998887773..........44556679********************************* PP

                                       SB-TTS....T-B---HHHHHHHTT-EEEEEEEEETTSHHHHTTTTTBSSTTSSSHHHSTCCCHHTTS-SHHHHHHH CS
                   Alk_phosphatase  79 gvdaaa....gkevksvleaAkkaGkstGlVtTtritdAtPaalvahvesRkwkedaavpaealeegkkdiaeqlik 151
                                       +v  +       ++ + le A+++Gk+tGlV+Ttrit+AtPa + +hv +R    d++            ia+q ++
  gi|336252878|ref|YP_004595985.1| 105 SVRGDEdyedPTPLVTQLELAQAQGKATGLVSTTRITHATPAVYASHVPDR----DME----------AAIAQQYVE 167
                                       **888766556778899**********************************....333..........56889**** PP

                                       CST-SEEEEESCGGGSBCSBCTSSTCCT.SBHHHHHCCTTCEEE-SHHHHHHHCTSTSSCEEEESSSSSCS-CCCSC CS
                   Alk_phosphatase 152 akkidvllGGGrkeffpaeyatdGerkdGrnlieeakkkgyqyvsdrkeLlkakeenvkplLGLFadgdlkveldrd 228
                                         ++dvl+GGGr+ef            d   l ++a+++gy+++ d ++L +a+ ++   lLGLF+d+++ + ldrd
  gi|336252878|ref|YP_004595985.1| 168 S-DVDVLMGGGRREF-----------DD--ALLDRARNAGYEVLFDESDLEAASGDR---LLGLFDDSHITYTLDRD 227
                                       9.*************...........45..9999**********************9...***************** PP

                                       TCCE--HHHHHHHHHHHHTTSTT-EEEEEEETCHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHCHHCTTEEEEEEES CS
                   Alk_phosphatase 229 eatdPsLkemtevAiklLsknekGFFLlVEGsrIDhaaHendavgalsEvvefdeAvkaalefakkeketlvvvTaD 305
                                       e++ PsL  mt +A++ L+  ++GFFL+VEG+rIDha+H nd+   + E++efd  v+ ale+a+  ++tlvvv +D
  gi|336252878|ref|YP_004595985.1| 228 ESI-PSLPAMTAAAVDRLEGGDDGFFLMVEGGRIDHAEHGNDIQTTVAETKEFDAVVDWALEYAEGRDDTLVVVASD 303
                                       ***.************************************************************************* PP

                                       SEESEEEESTTST...T..TTSEECCEET.TTSSEE..................CEEECCSTT.....BTTB..... CS
                   Alk_phosphatase 306 Hshvfsfggyttr...gesvlglepllaa.dkkpvl..................lllYgngeetke..lkgvredvt 358
                                       H++    gg+ t+   g s + +e++ +a  +++ +                   +  ++++ +++  + g+++   
  gi|336252878|ref|YP_004595985.1| 304 HET----GGLATGndyG-SPIDAEAIRNArASNAAIaesieggkpvretveahvDVDLTDEDVARIedVVGADDPYA 375
                                       ***....7777774432.34455555555233333367777888888876665523333333333323445555555 PP

                                       HHHHTSTT....EEE..SSHTEE-SSEEEEEESTTGGGGSCEEECCHHHHHHHHHC CS
                   Alk_phosphatase 359 akeskeadyrkraavpltseeHtgedvavfAygpkaelvrGvqeqteiakvlaaal 414
                                        +++ +a ++ +  v + s+ Htg   +v+A g   + ++G +  t++  +++a+l
  gi|336252878|ref|YP_004595985.1| 376 LSNELGAVVSDHLGVSWASNVHTGPAQTVMAAGADVDPFNGWIHHTDLSVTVTALL 431
                                       55666666****************************************99998765 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.79   3.5e+03       2      16 ..      39      53 ..      38      60 .. 0.80
   2 !   18.3   0.1   2.6e-07    0.0012     117     187 ..     234     306 ..     211     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.79
                                      EEEEEEETTBB---- CS
                                      xxxxxxxxxxxxxxx RF
                     Metalloenzyme  2 kvvlvvlDGlGeapa 16
                                      +v++++ DG+G  p 
  gi|336252878|ref|YP_004595985.1| 39 NVIVLIGDGMGFDPI 53
                                      6899*******8776 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.6e-07
                                       HHHHHHHHHHH.CC.-S..EEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-.SSB- CS
                                       xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                     Metalloenzyme 117 vevaekaldailsgkfd..lvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtA.DHgn 187
                                        +++ +a+d ++ g  d  +++v     D + H +d++ t+a  +++D+ v   l+  e  d++lvv+A DH +
  gi|336252878|ref|YP_004595985.1| 234 PAMTAAAVDRLEGG-DDgfFLMVEGGRIDHAEHGNDIQTTVAETKEFDAVVDWALEYAEGRDDTLVVVAsDHET 306
                                       56788999999555.56789999999********************************9877776665449976 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   3.1e-05      0.14     170     236 ..     244     308 ..      40     379 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
                                       T...SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EE CS
                      Phosphodiest 170 l...ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGmad 236
                                       l   ++  +l+v    +D++ H  G d  ++ ++ ++ D++++  le+++ r   ++t ++++SDH  + 
  gi|336252878|ref|YP_004595985.1| 244 LeggDDGFFLMVEGGRIDHAEH--GNDIQTTVAETKEFDAVVDWALEYAEGR---DDTLVVVASDHETGG 308
                                       2345777899999999******..9898889999******************...***********4444 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   9.5e-05      0.42       7      27 ..     478     498 ..     474     501 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.5e-05
                         EF-hand_6   7 klfDkdgdGkidaeElrkalr 27 
                                       k++D+dg+G +d+ ++ ++l 
  gi|336252878|ref|YP_004595985.1| 478 KALDRDGNGVVDYGDVLSILE 498
                                       789*************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3875.80
//
Query:       gi|336252879|ref|YP_004595986.1|  [L=81]
Description: hypothetical protein Halxa_1474 [Halopiger xanaduensis SH-6]
Scores for complete 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-20   73.5   4.7      2e-20   73.3   4.7    1.1  1  Fer4_15   4Fe-4S single cluster domain
    6.6e-06   26.6   1.0    1.2e-05   25.7   1.0    1.4  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.041   13.7   1.6        3.2    7.7   0.1    2.4  2  Fer4      4Fe-4S binding domain
      0.067   13.3   0.2       0.44   10.7   0.2    2.0  1  Fer4_19   Divergent 4Fe-4S mono-cluster
       0.23   11.6   1.6        2.7    8.2   0.2    2.3  2  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   4.7   5.5e-24     2e-20       1      66 []       3      71 ..       3      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 5.5e-24
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaeg....evpddeeeaaqeAaraCPvdAIrv 66
                                      V++D+d Cig+++Cvae++ + e+++ g+a++  d +e+++g    evpdd e +a++Aar+CPvdAI +
  gi|336252879|ref|YP_004595986.1|  3 VEFDEDVCIGMFQCVAEWDAFEENKSTGKADLA-DSEEVEDGvfvrEVPDDAELDAKFAARTCPVDAIKI 71
                                      89****************988888889***877.67888888**************************87 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 !   25.7   1.0   3.4e-09   1.2e-05       2      57 ..       6      70 ..       5      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3.4e-09
                           Fer4_13  2 DrdtCiacgaCvelaPdvFeeddeggasvvaeqpts..........eeekadaeeAadaCPvesIg 57
                                      D+d Ci+  +Cv+   d Fee++  g++  a+ ++           ++ + da+ Aa +CPv++I+
  gi|336252879|ref|YP_004595986.1|  6 DEDVCIGMFQCVAEW-DAFEENKSTGKADLADSEEVedgvfvrevpDDAELDAKFAARTCPVDAIK 70
                                      8899********875.99*************9544444455555559999***************8 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2    0.0058        21       1      10 [.       3      12 ..       3      12 .. 0.89
   2 ?    7.7   0.1    0.0009       3.2      16      24 .]      62      70 ..      61      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0058
                                      EEEETTTSSS CS
                              Fer4  1 vvideekCig 10
                                      v++de+ Cig
  gi|336252879|ref|YP_004595986.1|  3 VEFDEDVCIG 12
                                      579******8 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0009
                                      HHSTTTEEE CS
                              Fer4 16 evCPvgAIt 24
                                        CPv+AI+
  gi|336252879|ref|YP_004595986.1| 62 RTCPVDAIK 70
                                      57******6 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 ?   10.7   0.2   0.00012      0.44       6      32 ..       1      26 [.       1      74 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                           Fer4_19  6 itiednrelCihsgnCvkglpevFdpk 32
                                      +++e+++++Ci+  +Cv  + + F+ +
  gi|336252879|ref|YP_004595986.1|  1 MKVEFDEDVCIGMFQCVA-EWDAFEEN 26
                                      5899*************9.55566555 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2   0.00077       2.7       1      11 [.       2      12 ..       2      21 .. 0.79
   2 ?    2.6   0.1     0.044   1.6e+02      17      24 .]      62      69 ..      61      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00077
                            Fer4_6  1 vveidpdkCig 11
                                      +ve+d+d Cig
  gi|336252879|ref|YP_004595986.1|  2 KVEFDEDVCIG 12
                                      79********6 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.044
                            Fer4_6 17 rvCPegai 24
                                      r CP +ai
  gi|336252879|ref|YP_004595986.1| 62 RTCPVDAI 69
                                      78***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 620.34
//
Query:       gi|336252880|ref|YP_004595987.1|  [L=304]
Description: Malate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-40  136.5   0.4    9.9e-40  135.9   0.4    1.3  1  Ldh_1_N   lactate/malate dehydrogenase, NAD binding domain
    1.3e-29  103.3   0.0      2e-29  102.7   0.0    1.3  1  Ldh_1_C   lactate/malate dehydrogenase, alpha/beta C-terminal


Domain annotation for each model (and alignments):
>> 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 !  135.9   0.4   1.1e-43   9.9e-40       1     141 []       2     143 ..       2     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 135.9 bits;  conditional E-value: 1.1e-43
                                       EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHH..HHHHHHHHHHHCHCCSTS-EEEEESSGGGGTTESEEEE CS
                           Ldh_1_N   1 vkvavvGaaGgiGqslalllankkladelaLlDiake..kleGvaldlshistflsvkvkvsekeeealkdadvvvi 75 
                                       +kv+vvGaaG++G++ a+++a +++adel+L+Di+++  ++ G+a+d++h++++  +++ ++++ +e+++++dvvvi
  gi|336252880|ref|YP_004595987.1|   2 TKVSVVGAAGTVGAAAAYNIALRDVADELVLVDIPDKedDTIGQAADVNHGAAYD-SNTTIRQGGYEDTAGSDVVVI 77 
                                       69********************************9887899************99.99999**************** PP

                                       --S-SS-TTTTHHHHHHHHHHHHHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
                           Ldh_1_N  76 tagvprkpGetRddLlkvNakIvkeiveaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                                       tag+pr+pG+tR dL  +Na I+++i++++a+++++ + +  sNPvd+l+++l++ ++  +++vig
  gi|336252880|ref|YP_004595987.1|  78 TAGIPRQPGQTRIDLAGDNAPIMEDIGSSLAEHNDDFVTVTTSNPVDLLNRHLYESGERAREKVIG 143
                                       ****************************************************************98 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.7   0.0   2.2e-33     2e-29       2     163 ..     147     303 ..     146     304 .] 0.93

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 2.2e-33
                                       HHHHHHHHHHHHHHHTS-GGGEE--EEBSSSTETTEEHHHHHT...TSTTSTHHHHHHHHHHHHHHHHHHHHHHTTS CS
                           Ldh_1_C   2 tLDivRaktflaekagvtprsvkvtViGgHsgvtiipllsqvk...ellklsekqleeliervqnggdevvkakkGa 75 
                                       +LD++R+++++ae+++   ++v++t++G+H++ + +p++s v    + l++++ ++eel e+ q  + +v+++k   
  gi|336252880|ref|YP_004595987.1| 147 RLDSARFRYVIAERFDAPVQNVEATILGEHGDAQ-VPVFSKVRvngQDLEFDDAEKEELLEELQTSAMNVIEKK--- 219
                                       7*******************************66.66666655111557899**********************... PP

                                       SSS-HHHHHHHHHHHHHHHTTHTEEEEEEEEEESCCCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHHHHH CS
                           Ldh_1_C  76 gsatlsmAvAgakfveallrdtkeilsagvyldgevglkdqeieyfsvPvvlgknGvekvleilklndfeeekleks 152
                                       g++  + A+ +   vea+lrdt+e+l+ +v l+ge+g +d     f+vP+ lg +Gve+++e   l++fe+++l ++
  gi|336252880|ref|YP_004595987.1| 220 GATQWGPATGVGHTVEAILRDTGEVLPCSVKLEGEYGHED---AAFGVPCKLGSDGVEEIVE-WGLTEFERNQLGEA 292
                                       9***************************************...7******************.99************ PP

                                       HHHHHHHHHHH CS
                           Ldh_1_C 153 vkeLkkeiekg 163
                                       +++L +++ek+
  gi|336252880|ref|YP_004595987.1| 293 AEKLSEQYEKI 303
                                       *******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2248.30
//
Query:       gi|336252881|ref|YP_004595988.1|  [L=154]
Description: hypothetical protein Halxa_1476 [Halopiger xanaduensis SH-6]
Scores for 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-37  127.2   4.8    4.5e-37  127.1   4.8    1.0  1  LDcluster4       SLOG cluster4 family
    3.8e-07   30.3   0.1    6.7e-07   29.5   0.1    1.4  1  Lysine_decarbox  Possible lysine decarboxylase
    0.00043   19.6   3.6     0.0006   19.1   3.6    1.2  1  DNA_processg_A   DNA recombination-mediator protein A


Domain annotation for each model (and alignments):
>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.1   4.8   7.5e-41   4.5e-37       3     130 ..       2     127 ..       1     152 [. 0.87

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 7.5e-41
                        LDcluster4   3 kigVmGsaeteakeealelaeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdii 79 
                                        ++V+G +   +++e+  +ae++Gr++A +g+++++Ggr+G+mea+++Gak +gG+t+Gilp++++ e +n+yvd++
  gi|336252881|ref|YP_004595988.1|   2 RVSVIGGGI--ITDEEAAIAEAVGRELAARGHTVVCGGRGGTMEAVCRGAKAEGGTTIGILPSADTAE-ANDYVDVP 75 
                                       699*****9..89999***********************************************66666.7778**** PP

                        LDcluster4  80 iyTGlglagRnlilvlssdvviaiggrsGTlsEialaleegkpvivlkgt..d 130
                                       i+TGlg+a Rn ++ l  d+via++g++GT +E+ +a  +++pv+ l ++  +
  gi|336252881|ref|YP_004595988.1|  76 IATGLGHA-RNALVPLNGDAVIALSGGVGTFTELGFAGIYDRPVVGLATHdvS 127
                                       *******9.**************************************944431 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   1.1e-10   6.7e-07       1      69 [.      42     108 ..      42     111 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.1e-10
                                       HHHHHHHHHHTTS-EEEEEECCHHHHHCCTTT-SEEEEESSHHHHHHHHHHHESEEEE-S-SHHHHHHH CS
                   Lysine_decarbox   1 meavakgaleaggrviGiipkillaeeapneevnelvivedmeeRkealveladafvilPGGiGTleEl 69 
                                       meav +ga   gg++iGi p++  ae   n++v+  + +   + R++     +da+++l GG+GT+ El
  gi|336252881|ref|YP_004595988.1|  42 MEAVCRGAKAEGGTTIGILPSADTAEA--NDYVDVPIATGLGHARNALVPLNGDAVIALSGGVGTFTEL 108
                                       9*****************998887665..9999999999999************************997 PP

>> DNA_processg_A  DNA recombination-mediator protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   3.6     1e-07    0.0006      45     104 ..       3      62 ..       1      70 [. 0.95

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-07
                    DNA_processg_A  45 vaiVGtRkaseygkevakklakelaeagitivSGlAlGiDaaahraaleaggktvavlgt 104
                                       v+++G   ++++  ++a+ + +ela +g+t+v G+  G  +a  r+a ++gg+t+++l++
  gi|336252881|ref|YP_004595988.1|   3 VSVIGGGIITDEEAAIAEAVGRELAARGHTVVCGGRGGTMEAVCRGAKAEGGTTIGILPS 62 
                                       8999999***************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); 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:                         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 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1202.41
//
Query:       gi|336252882|ref|YP_004595989.1|  [L=144]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-14   52.5   0.0    6.5e-14   52.0   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.6e-12   47.6   0.0    2.3e-12   47.1   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    8.2e-12   45.4   0.0      1e-11   45.1   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    9.1e-07   29.0   0.0    1.3e-06   28.5   0.0    1.4  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00029   20.7   0.0    0.00065   19.6   0.0    1.6  1  FR47             FR47-like protein
  ------ inclusion threshold ------
      0.024   14.1   0.0      0.032   13.6   0.0    1.1  1  GNAT_acetyltr_2  GNAT acetyltransferase 2
      0.051   13.3   0.0      0.067   12.9   0.0    1.1  1  NodA             Nodulation protein A (NodA)
       0.12   13.1   0.0       0.12   13.0   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
       0.14   12.3   0.1        0.2   11.8   0.1    1.2  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


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 !   52.0   0.0   3.2e-17   6.5e-14      35     111 ..      55     134 ..      46     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 3.2e-17
                   Acetyltransf_10  35 vaeeggkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFk 107
                                       v+e  +++vG++++  dg+   +is ++V+p+++gqG+g++++ a+e+++e++ +  +  vn      +fYe++G++
  gi|336252882|ref|YP_004595989.1|  55 VHEPTDEVVGMGRIvGDGGtvyQISDMAVHPDHQGQGLGTRIMAALESYLEEAAPP-DAYVNLMADVDGFYERFGYE 130
                                       566679********99999*******************************999877.******************** PP

                   Acetyltransf_10 108 avge 111
                                       ++ +
  gi|336252882|ref|YP_004595989.1| 131 ETRP 134
                                       9976 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   1.2e-15   2.3e-12       7      76 .]      53     131 ..      39     131 .. 0.69

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.2e-15
                                       EEEET..TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH.....TTSEEE.....EEEEEE.THHHHHH CS
                    Acetyltransf_7   7 Vaedd..gkivGfialslld...aeitrlaVdpeyrgkGiGraLlea.....aekgii.....leqlel.naekaik 67 
                                       Va ++  +++vG+ +++ ++   ++i  +aV+p+++g+G+G+++++a     +    +       +++l ++    +
  gi|336252882|ref|YP_004595989.1|  53 VAVHEptDEVVGMGRIVGDGgtvYQISDMAVHPDHQGQGLGTRIMAAlesylE----EaappdA-YVNLmAD--VDG 122
                                       5556677889998888888787666667*****************98333221....0222211.2233222..345 PP

                                       HHHHTTEEE CS
                    Acetyltransf_7  68 fYeklGFee 76 
                                       fYe++G+ee
  gi|336252882|ref|YP_004595989.1| 123 FYERFGYEE 131
                                       *******96 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0     5e-15     1e-11      29     117 .]      44     129 ..      11     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 5e-15
                                       HSTTC.EEEEEEET..TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTE.SEEEEEE CS
                    Acetyltransf_1  29 sleae.gllvaeed..geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegi.kkivlav 101
                                        l+++ +++va ++  +e++G+ ++  +      v+ i ++aV+p+++g+GlG++ + ale +++e    ++ ++  
  gi|336252882|ref|YP_004595989.1|  44 GLPNSlFGVVAVHEptDEVVGMGRIVGDGG---TVYQISDMAVHPDHQGQGLGTRIMAALESYLEEAAPpDA-YVNL 116
                                       346777777777776688*****8887777...9****************************9998855344.6644 PP

                                       ETTEHHHHHHHHHTTE CS
                    Acetyltransf_1 102 eedndaairlYeklGF 117
                                        +d     ++Ye++G+
  gi|336252882|ref|YP_004595989.1| 117 MADV---DGFYERFGY 129
                                       4443...89*****98 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   6.6e-10   1.3e-06      72     127 ..      74     131 ..      51     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 6.6e-10
                                       EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT..T--EEEE--SSHHHHHTTT-EE CS
                    Acetyltransf_9  72 kaagvtgVavapehrgrgvlskLlaraleemree..gqplsllfPssipiYrrfGyei 127
                                       +++++++ av+p+h+g+g+ ++++a++  +++e    +  + l++   ++Y+rfGye 
  gi|336252882|ref|YP_004595989.1|  74 TVYQISDMAVHPDHQGQGLGTRIMAALESYLEEAapPDAYVNLMADVDGFYERFGYEE 131
                                       6789***************************99966677888***999********96 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.3e-07   0.00065      23      80 ..      77     132 ..      65     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.3e-07
                                       SEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  23 elgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                       +++ + v+p+h+++Glg+r+ +al   + e+   + ++v+   +    +ye+ G+e+ 
  gi|336252882|ref|YP_004595989.1|  77 QISDMAVHPDHQGQGLGTRIMAALESYLEEA-APPDAYVNLMAD-VDGFYERFGYEET 132
                                       57889*******************9988773.345555555433.4688888888875 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.6e-05     0.032     101     127 ..      81     107 ..      74     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                   GNAT_acetyltr_2 101 iAvhpelqkmGYGsralellekyyegk 127
                                       +Avhp+ q++G G+r++  le+y+e+ 
  gi|336252882|ref|YP_004595989.1|  81 MAVHPDHQGQGLGTRIMAALESYLEEA 107
                                       7**********************9986 PP

>> NodA  Nodulation protein A (NodA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.4e-05     0.067      86     137 ..      77     129 ..      66     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                              NodA  86 elGlyavrpdleglgighs.ievllpvlkelgvPfafgtvrkalrkhverlvr 137
                                       ++  +av+pd +g+g+g + + +l   l+e   P a+  +  ++  ++er+  
  gi|336252882|ref|YP_004595989.1|  77 QISDMAVHPDHQGQGLGTRiMAALESYLEEAAPPDAYVNLMADVDGFYERFGY 129
                                       566689*************56667778999999*****************974 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.3e-05      0.12      52     112 ..      48     108 ..       1     130 [. 0.64

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.3e-05
                    Acetyltransf_3  52 egyg.waivlkdtgv.iGsvglrdleeedeeaelg.ymlapsfwgkGyateavralleyafeel 112
                                       + +g  a+ +++t++ +G+ ++    +     +++ + ++p+++g+G++t  ++al  y+ e  
  gi|336252882|ref|YP_004595989.1|  48 SLFGvVAV-HEPTDEvVGMGRIVGDGGT--VYQISdMAVHPDHQGQGLGTRIMAALESYLEEAA 108
                                       33553333.4555444888877733222..266663778999**************99996554 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 ?   11.8   0.1   9.9e-05       0.2      20      54 ..      71     105 ..      53     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.9e-05
                   Acetyltransf_CG  20 rkegvldfthTeVpeelrGkGiAkkLvkaalddar 54 
                                       +++ v+++    V++ ++G+G++ +++ a   + +
  gi|336252882|ref|YP_004595989.1|  71 DGGTVYQISDMAVHPDHQGQGLGTRIMAALESYLE 105
                                       56679999******************988766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1174.96
//
Query:       gi|336252883|ref|YP_004595990.1|  [L=267]
Description: hypothetical protein Halxa_1478 [Halopiger xanaduensis SH-6]
Scores for complete 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   50.9   1.3    1.8e-13   50.4   1.3    1.2  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
  ------ inclusion threshold ------
      0.011   15.8   1.0      0.026   14.5   1.0    1.6  1  DZR            Double zinc ribbon
      0.063   13.2   0.8       0.11   12.4   0.8    1.4  1  Prok-RING_1    Prokaryotic RING finger family 1
       0.56    9.9   4.1        2.2    8.0   4.1    1.9  1  zf-RRN7        Zinc-finger of RNA-polymerase I-specific TFIIB
        1.6    8.5   5.8        5.1    7.0   5.7    1.9  1  zinc_ribbon_2  zinc-ribbon domain
        2.4    8.0  11.4        2.9    7.7  11.4    1.3  1  SPX            SPX domain
        2.9    7.0  11.4        3.6    6.7  11.4    1.2  1  SOG2           RAM signalling pathway protein


Domain annotation for each model (and alignments):
>> 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 !   50.4   1.3   7.1e-17   1.8e-13       2      39 ..      29      64 ..      28      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 7.1e-17
                     Auto_anti-p27  2 kmgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaC 39
                                      +m++lLlkG+tM++++C +Cg PL++  ++g+++C++C
  gi|336252883|ref|YP_004595990.1| 29 RMSDLLLKGATMTNTHCGTCGDPLFK--QDGTTFCPSC 64
                                      8*************************..67999***** PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.0     1e-05     0.026      12      36 ..      42      66 ..      37      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                               DZR 12 arfCseCgtklkavaaedrCpsCge 36
                                      +  C++Cg +l ++   ++CpsC+ 
  gi|336252883|ref|YP_004595990.1| 42 NTHCGTCGDPLFKQDGTTFCPSCHG 66
                                      568********99999*******85 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 ?   12.4   0.8   4.5e-05      0.11       3      27 ..      41      65 ..      39      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.5e-05
                       Prok-RING_1  3 tgkkCpvCgkelkeedDiVvCpeCg 27
                                      t+++C  Cg++l ++d    Cp C 
  gi|336252883|ref|YP_004595990.1| 41 TNTHCGTCGDPLFKQDGTTFCPSCH 65
                                      799*********************5 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 ?    8.0   4.1   0.00088       2.2       7      28 ..      45      65 ..      40      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00088
                           zf-RRN7  7 CgvCgcrsftlddGfyyCrrCh 28
                                      Cg+Cg    +  dG+++C +Ch
  gi|336252883|ref|YP_004595990.1| 45 CGTCGD-PLFKQDGTTFCPSCH 65
                                      777777.55679*********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 ?    7.0   5.7     0.002       5.1       2      20 ..      45      66 ..      43      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.002
                     zinc_ribbon_2  2 CpnCGael..qdnakFCpyC.G 20
                                      C  CG +l  qd+ +FCp C G
  gi|336252883|ref|YP_004595990.1| 45 CGTCGDPLfkQDGTTFCPSChG 66
                                      888999999459********66 PP

>> SPX  SPX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  11.4    0.0011       2.9      70     177 ..      88     185 ..       6     254 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                               SPX  70 aaadesgnsaadasssepkdeaeslprrsplsrssrssssygglvssppsansssssddssesnpadsssssssses 146
                                       a ades+++a+das+++ + e  s+++ +  ++ +  +++ ++ +s +p++ +ss++d+++ +           s+s
  gi|336252883|ref|YP_004595990.1|  88 AGADESAAAATDASAQSIDVE--SPSDADAAAGTGAAETASTAGTSAEPDRTDSSGTDERDRPA----------SAS 152
                                       333333333333333333333..33333333333333332222222222222222222222222..........111 PP

                               SPX 147 esssssspsllrrlfs..esesreeksersyet 177
                                       ++ s +s+ + rr+++   +e+ +e+++rs+ t
  gi|336252883|ref|YP_004595990.1| 153 SERSRESTDRSRRTQQagNAEEPSESQSRSPAT 185
                                       111111111111111111122222222222222 PP

>> SOG2  RAM signalling pathway protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  11.4    0.0014       3.6     212     339 ..      21     193 ..       2     243 .. 0.39

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0014
                              SOG2 212 t..RhagsfsaqdveqGaalt..plrsd.qipfnl...........................srsrrssssgnsasp 256
                                       +  R+a+   +  + +Ga +t     +  ++ f+                            +              
  gi|336252883|ref|YP_004595990.1|  21 KaeREATQRMSDLLLKGATMTntHCGTCgDPLFKQdgttfcpschgnpdavegtdleaqpaeE-------------- 83 
                                       255888777777777888888443333334444337777788888888766655443222220.............. PP

                              SOG2 257 aangaqsetsersasssg.vqssasstPlgegstsppgalsrqslsttgststltsssksrs............... 317
                                       ++ +a  + s  +a+ ++ +qs    +P  +++ + +ga++++  st g +++++  ++s                 
  gi|336252883|ref|YP_004595990.1|  84 SPGAAGADESAAAAT-DAsAQSIDVESPSDADAAAGTGAAETA--STAGTSAEPDRTDSSGTderdrpasassersr 157
                                       222222222222222.222444444444444444443221111..11111222222222111112233222211112 PP

                              SOG2 318 ........ssrsnt.....nasastprslattpa........p 339
                                               +   ++      +s+s++rs     a         
  gi|336252883|ref|YP_004595990.1| 158 estdrsrrT---QQagnaeEPSESQSRSP----AtaadrrgqE 193
                                       222221111...11110112222222222....1112233332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1520  (0.0847788); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 1915.49
//
Query:       gi|336252884|ref|YP_004595991.1|  [L=385]
Description: multicopper oxidase type 2 [Halopiger xanaduensis SH-6]
Scores for 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-30  104.1  12.6    1.1e-19   70.6   1.6    3.2  2  Cu-oxidase_2  Multicopper oxidase
    1.1e-22   80.3   7.7    8.6e-19   67.7   1.8    2.6  2  Cu-oxidase_3  Multicopper oxidase
    1.1e-13   51.6   0.1    2.8e-13   50.3   0.0    1.7  2  Cu-oxidase    Multicopper oxidase
    0.00035   20.6   0.0       0.23   11.6   0.0    2.8  2  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
      0.029   14.2   3.9      0.049   13.5   3.9    1.3  1  TAT_signal    TAT (twin-arginine translocation) pathway signa


Domain annotation for each model (and alignments):
>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   3.6   1.5e-12   5.2e-09      29     136 ..     114     208 ..      96     209 .. 0.83
   2 !   70.6   1.6   2.9e-23   1.1e-19       5     127 ..     244     353 ..     235     356 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.5e-12
                                       TTSSEEEEEETTEEEEEEEEE-SSS.-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEEEE CS
                      Cu-oxidase_2  29 sentnvitlpkgevveiviqnntkl.pHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwvair 104
                                       s   ++i++ +g+ +e++++n++    H++H+HG++    +                +  +    ++v pg++ ++ 
  gi|336252884|ref|YP_004595991.1| 114 SVPGPIIRTTEGNDIEVTLDNTDADhAHTLHFHGVRKTWEN----------------DGVPTTTGITVGPGEKHTYS 174
                                       55678999999**************9********9544432................22344677999********* PP

                                       EES.S-EEEEEEESSH..HHHHTT-EEEEEEECH CS
                      Cu-oxidase_2 105 fkadnpGvwllHCHil..wHldqGmalqfvvrpd 136
                                       + a+ pG  l+HCH +   H d+Gm++ f v+p+
  gi|336252884|ref|YP_004595991.1| 175 IPANVPGTHLYHCHYQthRHIDMGMYGIFRVDPK 208
                                       ****************9999**********9986 PP

  == domain 2  score: 70.6 bits;  conditional E-value: 2.9e-23
                                       SCCCCCCCEEEEEEEEEEEETCCTTTSSEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCS CS
                      Cu-oxidase_2   5 klptllqltsgneeaseitngeefsentnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpks 81 
                                       ++p+++++  g++ ++     + ++e+ ++i +++g++v++ + n + + HP+H H h+f+++++++g+        
  gi|336252884|ref|YP_004595991.1| 244 RKPDVFTIN-GKSLPR-----TLHPEDGSPIIVDHGDTVRLHMVNAGYMSHPMHTHNHRFRLVEKDGGQ-------- 306
                                       445555555.333222.....47789*******************************************........ PP

                                       SGCCGSSCBSEEEE-TTEEEEEEEES..S-EEEEEEESSHHHHHTT- CS
                      Cu-oxidase_2  82 ynlenpvrrdtvqvppggwvairfkad.npGvwllHCHilwHldqGm 127
                                       +   ++ ++d +++ p ++ +i+f+ad  pG +l+HCH   H+ +G 
  gi|336252884|ref|YP_004595991.1| 307 VPEAAQYEQDITNIAPAERHTIEFEADaEPGIYLMHCHKVDHAMNGN 353
                                       555677799*****************98***************9995 PP

>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   1.8   2.4e-22   8.6e-19      23     117 ..     114     208 ..     111     209 .. 0.94
   2 !   15.2   0.4   4.5e-06     0.016      16     107 ..     247     352 ..     235     361 .. 0.69

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 2.4e-22
                                       SSBS-EEEEETT-EEEEEEEE-S.SS-B-EEEET--S-GG.....GSCSGGG-B-TT-EEEEEEE--S-SEEEEEEE CS
                      Cu-oxidase_3  23 qfpgptievregdtvvvnvtNkl.dentsihwhGlqqrktswmDGvpgvtqcpiqpgesftyrftvkqqagtlwYhs 98 
                                       ++pgp i+ +eg++++v++ N   d+  ++h+hG++  ++   DGvp  t   + pge+ ty+++++   gt++Yh 
  gi|336252884|ref|YP_004595991.1| 114 SVPGPIIRTTEGNDIEVTLDNTDaDHAHTLHFHGVRKTWE--NDGVPTTTGITVGPGEKHTYSIPANV-PGTHLYHC 187
                                       68*******************987999*********9999..**************************.******** PP

                                       --TT.HHH.TT-EEEEEEE-H CS
                      Cu-oxidase_3  99 hlsl.qqa.aGlaGaiiiedk 117
                                       h+++ ++  +G++G++ +++k
  gi|336252884|ref|YP_004595991.1| 188 HYQThRHIdMGMYGIFRVDPK 208
                                       ****65558*********986 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.5e-06
                                       EEEEECTSSB........S-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.......GSCSGG.....G-B-T CS
                      Cu-oxidase_3  16 evitvNgqfp........gptievregdtvvvnvtNkldentsihwhGlqqrktswmDG..vpgvtq.....cpiqp 77 
                                       +v t+Ng+ +        g  i v+ gdtv+++++N+   +  +h h  + r    +DG  vp  +q       i+p
  gi|336252884|ref|YP_004595991.1| 247 DVFTINGKSLprtlhpedGSPIIVDHGDTVRLHMVNAGYMSHPMHTHNHRFRLV-EKDGgqVPEAAQyeqdiTNIAP 322
                                       56666666552333333355689*************985555555555555444.44995644444422222469** PP

                                       T-EEEEEEE--S-SEEEEEEE--TTHHHTT CS
                      Cu-oxidase_3  78 gesftyrftvkqqagtlwYhshlslqqaaG 107
                                        e+ t +f+++ + g ++ h h   + ++G
  gi|336252884|ref|YP_004595991.1| 323 AERHTIEFEADAEPGIYLMHCHKVDHAMNG 352
                                       **********************98887776 PP

>> Cu-oxidase  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.3   4.8e+03      59     116 ..     160     169 ..     115     196 .. 0.58
   2 !   50.3   0.0   7.8e-17   2.8e-13       2     150 ..     216     354 ..     215     360 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
                                       SGGGEEEEETTEEEEEEEESSS-BEEEEETSB-EEEEEETCETTSEEEESCEEE-TTE CS
                        Cu-oxidase  59 latltvepgktyrlriinvsaddslnfsIeGHkltVvevDgvyvepvevdsldIavGq 116
                                       ++                                                 + +++G+
  gi|336252884|ref|YP_004595991.1| 160 TT------------------------------------------------GITVGPGE 169
                                       22................................................33333333 PP

  == domain 2  score: 50.3 bits;  conditional E-value: 7.8e-17
                                       EEEEEEEEETCBCTTSCBC.HSSCHCHHHHHTT--SEEEETTBSS.......CTTTTSGGGEEEEETTEEEEEEEES CS
                        Cu-oxidase   2 eyvitlsDwyhkdakelekellasgkapadtppvpdavlingkggfnatladkdgaslatltvepgktyrlriinvs 78 
                                       ey++t++Dw     + l ++++ ++ +++     pd ++ingk+ +  tl +    +   + v++g+t+rl+++n++
  gi|336252884|ref|YP_004595991.1| 216 EYFFTVKDWD----SRLNRQYAGEDVDYSTRDRKPDVFTINGKSLPR-TLHP---EDGSPIIVDHGDTVRLHMVNAG 284
                                       6889999993....44455577777777777888********66544.6555...56899****************9 PP

                                       SS-BEEEEETSB-EEEEEETCETTS...EEEESCEEE-TTEEEEEEEEE-SSSEEEEEEEEGSSSCHHHHTTSEE CS
                        Cu-oxidase  79 addslnfsIeGHkltVvevDgvyve...pvevdsldIavGqrysvlvtanqapgnYwivasgrsnlieafengta 150
                                        + s+++  ++H++ +ve Dg  v    ++e+d  +Ia+++r ++ ++a+++pg Y +++    ++ ++  ng+a
  gi|336252884|ref|YP_004595991.1| 285 YM-SHPMHTHNHRFRLVEKDGGQVPeaaQYEQDITNIAPAERHTIEFEADAEPGIYLMHC----HKVDHAMNGNA 354
                                       98.689999*************999899********************************....44566666655 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   6.5e-05      0.23      40      96 ..     123     191 ..     118     196 .. 0.75
   2 !    6.0   0.0    0.0036        13      66      94 ..     317     345 ..     266     359 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.5e-05
                      Cupredoxin_1  40 kagekvklkiknkdktp.eefesed...........lgeekvlapgktttitiaplkpGeYeftcdmhm 96 
                                        +g  ++++++n+d+   +++ ++              +  ++ pg+++t  i++  pG++ ++c ++ 
  gi|336252884|ref|YP_004595991.1| 123 TEGNDIEVTLDNTDADHaHTLHFHGvrktwendgvpTTTGITVGPGEKHTYSIPANVPGTHLYHCHYQT 191
                                       67889999999999994455555555555555555534445889**********************986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0036
                      Cupredoxin_1  66 eekvlapgktttitiap.lkpGeYeftcdm 94 
                                       + +++ap + +ti++++  +pG Y ++c  
  gi|336252884|ref|YP_004595991.1| 317 I-TNIAPAERHTIEFEAdAEPGIYLMHCHK 345
                                       3.89***********86258********84 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.9   1.4e-05     0.049       2      25 ..      12      34 ..      11      35 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      lSRR F  +++++a A+al+gc++
  gi|336252884|ref|YP_004595991.1| 12 LSRREFVAATGVGA-ATALAGCTS 34
                                      79*****9777775.777888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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: 0.53u 0.21s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2912.44
//
Query:       gi|336252885|ref|YP_004595992.1|  [L=831]
Description: helicase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-23   82.0   0.0      9e-22   77.5   0.0    2.6  2  Helicase_C     Helicase conserved C-terminal domain
    4.6e-23   82.2   0.0    1.1e-22   80.9   0.0    1.7  1  ERCC4          ERCC4 domain
    2.2e-15   56.9   0.0    6.5e-15   55.3   0.0    1.7  1  DEAD           DEAD/DEAH box helicase
    1.1e-12   48.4   0.0      3e-12   46.9   0.0    1.8  1  ResIII         Type III restriction enzyme, res subunit
    1.1e-08   35.6   0.9    1.8e-07   31.6   0.2    3.0  2  HHH_5          Helix-hairpin-helix domain
    1.4e-08   34.7   0.6    7.4e-08   32.4   0.2    2.4  2  HHH_2          Helix-hairpin-helix motif
      1e-05   25.1   0.5     0.0016   18.2   0.1    3.0  2  HHH            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.011   15.9   0.3      0.088   13.0   0.0    2.6  2  Helicase_C_2   Helicase C-terminal domain
      0.039   14.5   0.0       0.19   12.4   0.0    2.3  1  5_3_exonuc     5'-3' exonuclease, C-terminal SAM fold
      0.062   13.1   0.4         19    5.1   0.0    3.0  2  MEDS           MEDS: MEthanogen/methylotroph, DcmR Sensory do
      0.089   13.2   0.1       0.32   11.4   0.1    1.9  1  MtrB           Tetrahydromethanopterin S-methyltransferase su
       0.12   12.9   0.0       0.32   11.5   0.0    1.7  1  OAM_dimer      Dimerisation domain of d-ornithine 4,5-aminomu
       0.29   10.4   9.5        0.8    9.0   2.2    2.4  2  DUF4407        Domain of unknown function (DUF4407)
       0.36   10.2   6.5       0.25   10.7   3.0    2.2  2  DUF4618        Domain of unknown function (DUF4618)
        1.4    9.6   6.9       0.26   12.0   0.2    3.2  3  RsbRD_N        RsbT co-antagonist protein rsbRD N-terminal do
        7.2    6.8   9.4        4.4    7.5   1.3    2.6  2  TolA_bind_tri  TolA binding protein trimerisation


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 ?    1.3   0.0      0.39   4.3e+02      11      62 ..      60     115 ..      50     155 .. 0.74
   2 !   77.5   0.0     8e-25     9e-22      10     109 ..     367     472 ..     357     474 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.39
                                       HHTTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  11 kleeeggkilifvntidrlek.vklllekk...gikvavlhgelpqnereeileqf 62 
                                        lee+ggk+l+ ++t+  +++ +++ +e     + +++v++g+ + ++r e+ ++ 
  gi|336252885|ref|YP_004595992.1|  60 RLEEVGGKSLMLAPTKPLVQQhADFYREALqipDEEIVVFTGDVSPDDRAETWQEA 115
                                       67999************8877655553333556899999*********99988766 PP

  == domain 2  score: 77.5 bits;  conditional E-value: 8e-25
                                       HHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTT......STHHHHHHHHHHHHTTSSSEEEESGGGTSS CS
                        Helicase_C  10 lkleeeggkilifvntidrlek.vklllekkgikvavlhge......lpqnereeileqfnkgesdvLiatdvaerG 79 
                                       l   e g+++++f++++d++e  +++l e+++ k  v +g+      ++q e++e+l++f++ge+ vL++t+vae+G
  gi|336252885|ref|YP_004595992.1| 367 L-GLEGGERVIVFTESRDTAEAlTDFLSESFDAKRFVGQGDregsdgMTQTEQQEVLDEFRAGEFEVLVSTSVAEEG 442
                                       3.568899**********99988899977776666666666999999****************************** PP

                                       STSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  80 idipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       +d+p+v+lV ++++  +  + iqr+GRtgR
  gi|336252885|ref|YP_004595992.1| 443 LDVPEVDLVLFYEPVPTAIRSIQRKGRTGR 472
                                       ****************************** PP

>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.0   9.8e-26   1.1e-22       2     154 ..     620     740 ..     619     742 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 9.8e-26
                                       EGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHH..CCSHH CS
                             ERCC4   2 Dsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasi..kdgrl 76 
                                       D+re   +i + l ++ ++ev  etl +gdy ++   +++               v+verks+ d+v+s+   d++ 
  gi|336252885|ref|YP_004595992.1| 620 DQREMDANIARDLSRRDEIEVSLETLDVGDY-VL---SDR---------------VVVERKSVADFVDSLvgGDRSV 677
                                       9999888888885666669************.**...9**...............***************65558** PP

                                       HHHHHHHHH.H-SEEEEEEES-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHHH CS
                             ERCC4  77 eeqvsrlkrngykkpillvegldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaewl 153
                                       +eq+  ++r +y++pi++veg+  y ++               i++++i +aL++l++df+ s+l+tes+ +t e+l
  gi|336252885|ref|YP_004595992.1| 678 FEQIGAMAR-HYSRPIVVVEGEGLYEQRD--------------IHPNAIRGALSSLAVDFDASVLRTESEDDTTELL 739
                                       *********.****************998..............********************************99 PP

                                       H CS
                             ERCC4 154 a 154
                                       a
  gi|336252885|ref|YP_004595992.1| 740 A 740
                                       7 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0   5.8e-18   6.5e-15      13     168 ..      35     178 ..      25     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 5.8e-18
                                       TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  13 gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaard 89 
                                        +++ lv+ +TG GKT++ l+   +++    ++ g k l+++Pt+ L++q+++ +++ ++  d ++++++g+v+ +d
  gi|336252885|ref|YP_004595992.1|  35 ANHHTLVCLPTGLGKTTVSLLVTARRL----EEVGGKSLMLAPTKPLVQQHADFYREALQIPDEEIVVFTGDVSPDD 107
                                       46899*******************999....67888************************88866667788888888 PP

                                       HHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT.TTHHHHHHHHHHSHHHCTTSTTTSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  90 qlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq.gfsdfinrilnqlpqitcdgklqrqvivl 165
                                         ++  +++ +v++tp+ + + l   +++l +v+ + +DE++r   +  +    +r ++  +        +  v  +
  gi|336252885|ref|YP_004595992.1| 108 RAETW-QEATVVMATPQVIENDLVGSRISLAEVTHITFDECHRATGDyAYNYIAERYHEDAK--------KPLVTGM 175
                                       88888.**************966567889**************9998677777777777763........1226666 PP

                                       ESS CS
                                       xxx RF
                              DEAD 166 SAT 168
                                       SA 
  gi|336252885|ref|YP_004595992.1| 176 SAS 178
                                       665 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 !   46.9   0.0   2.7e-15     3e-12      23     169 ..      35     179 ..      19     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 2.7e-15
                                       TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEESSS-B-- CS
                            ResIII  23 rdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke...igkkvsgdkkka 96 
                                        +++ l+ ++TG GKT v++ +++r l++ +  k l+l+p+k l++q  + +++ l+ +++e    +++vs d + +
  gi|336252885|ref|YP_004595992.1|  35 ANHHTLVCLPTGLGKTTVSLLVTARRLEEVGG-KSLMLAPTKPLVQQHADFYREALQIPDEEivvFTGDVSPDDRAE 110
                                       578999*************7777776666553.**********************9999988777777788888777 PP

                                       .......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT-....--SEEEEEESS- CS
                            ResIII  97 kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekf....keavllglTATp 169
                                            +++ ++++t q + +d+        + +  +   i +DE+Hr++++ +++ i+e +    k+ ++ g++A p
  gi|336252885|ref|YP_004595992.1| 111 ---TWQEATVVMATPQVIENDL-----VGSRISLAEVTHITFDECHRATGDYAYNYIAERYhedaKKPLVTGMSASP 179
                                       ...899****************.....888888899999***********989999955542333669999999987 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0         1   1.1e+03      33      50 ..     735     752 ..     708     752 .. 0.79
   2 !   31.6   0.2   1.6e-10   1.8e-07       5      53 ..     774     821 ..     772     823 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1
                                       -HHHHHTSTTS-HHHHHH CS
                             HHH_5  33 dveeLakipGiGkktAer 50 
                                       ++e La+i G  ++tA+r
  gi|336252885|ref|YP_004595992.1| 735 TTELLATIAGREQETADR 752
                                       3566999*********98 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1.6e-10
                                       HTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5   5 lsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                        s+  iGp+tA++ll+  +++ve  + a+++eL+++ G+G+ tAeri +
  gi|336252885|ref|YP_004595992.1| 774 ASIAEIGPVTARSLLEE-FGTVEGAMIATEDELQEADGVGQVTAERIRE 821
                                       58899************.*****99999*******************76 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.4   4.9e+03      48      61 ..     307     320 ..     291     321 .. 0.82
   2 !   32.4   0.2   6.6e-11   7.4e-08       7      53 ..     775     821 ..     771     825 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.4
                             HHH_2  48 AqsivefFeneknr 61 
                                        ++++++F+ ++n+
  gi|336252885|ref|YP_004595992.1| 307 VEAVRRYFDRQRNQ 320
                                       57899****99998 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 6.6e-11
                             HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsive 53 
                                       +I ++G  tA+ L ++F++++  + a+++eL+e d++G+++A+ i+e
  gi|336252885|ref|YP_004595992.1| 775 SIAEIGPVTARSLLEEFGTVEGAMIATEDELQEADGVGQVTAERIRE 821
                                       7999*****************************************97 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.045        51      15      29 ..     775     789 ..     774     790 .. 0.85
   2 !   18.2   0.1   1.4e-06    0.0016       3      29 ..     795     821 ..     793     822 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.045
                                       TSTT-SHHHHHHHHH CS
                               HHH  15 alPGVGpktAeaIls 29 
                                       ++  +Gp tA++ l+
  gi|336252885|ref|YP_004595992.1| 775 SIAEIGPVTARSLLE 789
                                       6778*******9986 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.4e-06
                                       HHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   3 eglipasreeLlalPGVGpktAeaIls 29 
                                       eg + a+++eL++  GVG  tAe+I++
  gi|336252885|ref|YP_004595992.1| 795 EGAMIATEDELQEADGVGQVTAERIRE 821
                                       566669*******************87 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 ?   -0.7   0.0       1.2   1.4e+03      14     127 ..     302     342 ..     289     371 .. 0.51
   2 ?   13.0   0.0   7.8e-05     0.088      10      82 ..     373     447 ..     364     454 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                      Helicase_C_2  14 vffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEGidfsddllravii 90 
                                       v ++S                                                                        
  gi|336252885|ref|YP_004595992.1| 302 VETQS------------------------------------------------------------------------ 306
                                       44444........................................................................ PP

                      Helicase_C_2  91 vglPfpnpkdpeveakreyldekgk...........knsgkewylpea 127
                                                   vea r+y+d++++           +++ ++   +ea
  gi|336252885|ref|YP_004595992.1| 307 ------------VEAVRRYFDRQRNqarssgaskasQRMVSDPRVREA 342
                                       ............455555555555433333333332222333333333 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.8e-05
                      Helicase_C_2  10 ggvlvffpSyklleevverlkeeleskkieifvee........keesrekvleeykekkkkgaillavcrGklsEGi 78 
                                       ++v+vf+ S ++ e ++++l+e+ ++k++  +           ++ ++++vl+e+++  ++  +l+++      EG+
  gi|336252885|ref|YP_004595992.1| 373 ERVIVFTESRDTAEALTDFLSESFDAKRFVGQ--GdregsdgmTQTEQQEVLDEFRA--GEFEVLVSTS--VAEEGL 443
                                       689********************987766433..233678888999***********..9999999998..999*** PP

                      Helicase_C_2  79 dfsd 82 
                                       d+++
  gi|336252885|ref|YP_004595992.1| 444 DVPE 447
                                       *985 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 ?   12.4   0.0   0.00017      0.19      21      53 ..     774     807 ..     753     824 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                        5_3_exonuc  21 pGvpgiGektAakLlkeygsleeilenld.elke 53 
                                         ++ iG+ tA +Ll+e+g++e+ + +++ el+e
  gi|336252885|ref|YP_004595992.1| 774 ASIAEIGPVTARSLLEEFGTVEGAMIATEdELQE 807
                                       56899*****************987766535544 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2      0.02        22      39     109 ..     227     293 ..     221     322 .. 0.83
   2 ?    5.1   0.0     0.017        19      24      61 ..     368     405 ..     366     434 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.02
                              MEDS  39 tldelrealrkagldvdaalesgqleildaeetylrgggfdpermlealrralakaladgyaglrvigemt 109
                                       ++ e+r+ l  +++  +++++ ++l i+++++   ++ + d ++m ++l++ +++ + +g++g+ + +e+ 
  gi|336252885|ref|YP_004595992.1| 227 EVLEIRDTL--NEVIKERLEKLKELGIASSTQ--PDQSQKDLNKMRAELQQLINNDQSEGFEGMSIHAEVM 293
                                       667888888..444478899999999999998..89999999**********************9999875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.017
                              MEDS  24 glargekvlyvasastldelrealrkagldvdaalesg 61 
                                       gl+ ge+v++++++++++e++  + ++  d+ +++  g
  gi|336252885|ref|YP_004595992.1| 368 GLEGGERVIVFTESRDTAEALTDFLSESFDAKRFVGQG 405
                                       89***********9999998888888899999988777 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00029      0.32      33      73 ..     501     541 ..     497     547 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                              MtrB  33 pvleeidkLekiaddlvnsLdpetallesypgRektlviaG 73 
                                       ++++e+ +L+ +addl + Ld +++ l  ++g e++    G
  gi|336252885|ref|YP_004595992.1| 501 EMENELRELKGMADDLAEELDDSQQALTDFDGNEEQRSSDG 541
                                       67899***************************999877666 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 ?   11.5   0.0   0.00029      0.32      29      58 ..     183     213 ..     178     215 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                                       HHHHHHHHHCTTSEEEEEEEEEEEET.TEEE CS
                         OAM_dimer  29 eeAAlelakkmGledpeVvhkeelhe.eftf 58 
                                       eeA le+++++Gle++eV++ e+ +  eft+
  gi|336252885|ref|YP_004595992.1| 183 EEAILEVCENLGLEEVEVMTEEDADVsEFTH 213
                                       7999*********************999996 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.2   0.00071       0.8     120     239 ..     228     345 ..     202     354 .. 0.84
   2 ?    5.4   0.8     0.009        10     130     195 ..     483     559 ..     448     645 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00071
                           DUF4407 120 akelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaq 196
                                       + e++++l++  +++l++l++   a +++ d+ +++l++ rae+q+ +++++++g +g+    +++k ++a     +
  gi|336252885|ref|YP_004595992.1| 228 VLEIRDTLNEVIKERLEKLKELGIASSTQPDQSQKDLNKMRAELQQLINNDQSEGFEGMSIHAEVMKLRQAVTLVET 304
                                       5677788888899******************************************9999999999999999999999 PP

                           DUF4407 197 aelaelkakldatarlaalraelaeleaerakeraasqaaaaa 239
                                       + ++++++    + +++++r+  a+ +++r  +  + ++a ++
  gi|336252885|ref|YP_004595992.1| 305 QSVEAVRRY--FDRQRNQARSSGASKASQRMVSDPRVREAMRK 345
                                       999999999..66666666666666666666666555555554 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.009
                           DUF4407 130 a...........ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.gtgttgvaGkgpaakekkaqlda 194
                                       a           ++ + +e+e+++++l++  d + ++ld+ +++++   dg+  +    g  G+ ++  ek +   +
  gi|336252885|ref|YP_004595992.1| 483 AedtrdeayfwiSRRREKEMENELRELKGMADDLAEELDDSQQALT-DFDGNEeQRSSDGASGDAASRGEKSEVKVD 558
                                       04455566777789999**************************999.667766533334455555555554443333 PP

                           DUF4407 195 a 195
                                       a
  gi|336252885|ref|YP_004595992.1| 559 A 559
                                       3 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.0   0.00022      0.25      24     113 ..     223     316 ..     209     320 .. 0.82
   2 ?   -0.2   0.1       0.5   5.6e+02     202     225 ..     499     522 ..     480     533 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                           DUF4618  24 eLvkeIqdtedstakkvrklLqqyeklktvisileksskkqleqakaeLqeweekeek...klekLeqqleqlnakv 97 
                                       +L +e+ ++ d+  + +++ L++ + l+ ++s+  ++s+k+l++++aeLq++ ++ ++   +  +++ ++ +l + v
  gi|336252885|ref|YP_004595992.1| 223 DLPDEVLEIRDTLNEVIKERLEKLKELGIASSTQPDQSQKDLNKMRAELQQLINNDQSegfEGMSIHAEVMKLRQAV 299
                                       677888888899999999********************************986554441115667899********* PP

                           DUF4618  98 qklq.eelnvLstYkDk 113
                                       + ++ + ++ ++ Y D+
  gi|336252885|ref|YP_004595992.1| 300 TLVEtQSVEAVRRYFDR 316
                                       98761569999999997 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.5
                           DUF4618 202 ieeleeeipeLkaeveqLqaqaee 225
                                        +e+e+e+ eLk   ++L+++  +
  gi|336252885|ref|YP_004595992.1| 499 EKEMENELRELKGMADDLAEELDD 522
                                       333333333333333333333332 PP

>> RsbRD_N  RsbT co-antagonist protein rsbRD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00023      0.26      37      99 ..     231     299 ..     200     302 .. 0.77
   2 ?   -1.2   0.2       3.1   3.4e+03      34      64 ..     499     535 ..     489     550 .. 0.48
   3 ?   -1.9   0.1       4.8   5.4e+03      37      65 ..     727     752 ..     703     777 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                           RsbRD_N  37 lreqlrelldallaalas.....eql.dleseeeeelrealdelsrsRarqgftpsetasfvfaLKeal 99 
                                       +r++l+e++++ l+ l++     +++ d+++++ +++r+ l++l+++    gf+ + + ++v+ L++a+
  gi|336252885|ref|YP_004595992.1| 231 IRDTLNEVIKERLEKLKElgiasSTQpDQSQKDLNKMRAELQQLINNDQSEGFEGMSIHAEVMKLRQAV 299
                                       444444444444444444444436668****************************************98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.1
                           RsbRD_N  34 eaelreqlrel...ldallaalaseql...dleseee 64 
                                       e+e++++lrel    d l++ l+++q+   d++++ee
  gi|336252885|ref|YP_004595992.1| 499 EKEMENELRELkgmADDLAEELDDSQQaltDFDGNEE 535
                                       3443333333211144444444443333444444444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.8
                           RsbRD_N  37 lreqlrelldallaalaseqldleseeee 65 
                                       lr ++++  ++lla++a  ++   + + +
  gi|336252885|ref|YP_004595992.1| 727 LRTESEDDTTELLATIAGREQ---ETADR 752
                                       777777777777766664222...23333 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 ?    3.1   1.5      0.09     1e+02      19      44 ..     249     274 ..     234     280 .. 0.73
   2 ?    7.5   1.3    0.0039       4.4      28      73 ..     500     545 ..     496     548 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.09
                     TolA_bind_tri  19 lllelqqqlealqqelreLRGqiEel 44 
                                       l +   +q ++ q++l+++R ++++l
  gi|336252885|ref|YP_004595992.1| 249 LGIASSTQPDQSQKDLNKMRAELQQL 274
                                       44555678888899999999888886 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0039
                     TolA_bind_tri  28 ealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkleagg 73 
                                       +++++elreL+G  ++l+ +l++ ++   d+  + ++r++   +g 
  gi|336252885|ref|YP_004595992.1| 500 KEMENELRELKGMADDLAEELDDSQQALTDFDGNEEQRSSDGASGD 545
                                       5799********************9988888777777766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (831 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1272  (0.0709465); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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):              16  [number of targets reported over threshold]
# CPU time: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.46
# Mc/sec: 5419.52
//
Query:       gi|336252886|ref|YP_004595993.1|  [L=166]
Description: hypothetical protein Halxa_1481 [Halopiger xanaduensis SH-6]
Scores for 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:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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: 1237.90
//
Query:       gi|336252887|ref|YP_004595994.1|  [L=229]
Description: metallophosphoesterase [Halopiger xanaduensis SH-6]
Scores for complete 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   39.1   0.0    1.4e-09   38.7   0.0    1.2  1  Metallophos    Calcineurin-like phosphoesterase
      9e-07   29.2   0.0    1.4e-06   28.6   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
       0.14   11.5   0.0       0.19   11.0   0.0    1.2  1  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


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 !   38.7   0.0   2.4e-13   1.4e-09       3     173 ..      26     181 ..      25     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.4e-13
                                       EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH CS
                       Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfee 79 
                                       + v+gD+H     g+ d+l++l++ l      dl +++GDlv  g+ +k++l+ ++   +    +  ++GN e    
  gi|336252887|ref|YP_004595994.1|  26 VYVVGDVH-----GCPDALERLFSTLEFG-SSDLAIFVGDLVRKGPDSKAVLDRVKSSPQ----LRSVRGNNE---- 88 
                                       789*****.....**********999777.99999999***********99999888888....7********.... PP

                                       HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE.CEEE.THHHHHHHHHHHSCHHHHCC.HHHHHH CS
                       Metallophos  80 ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg.spel.lvsldklgslnleleapepg.dewlkd 153
                                         + + +  ++ +++ +sd ++ + lp a   +g    l++hGg +p + l + ++ + l+++ ++ ++    ++ d
  gi|336252887|ref|YP_004595994.1|  89 --QKLLDGRAELPALDESDRQYIESLPTAISWEG---NLVVHGGvDPSRpLLEHSNGDLLTMRSPNGDGYdGPFWFD 160
                                       ..44555555557777777888888888885555...8999999755557677777777777777777668677777 PP

                                       HHHHTTCSEEEEEESSESS....C CS
                       Metallophos 154 lekrekadwvivlgHsply....r 173
                                          +  + + +++gH  l+    r
  gi|336252887|ref|YP_004595994.1| 161 ---EYADGPRVFFGHTVLEepleR 181
                                       ...688888888888877755552 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 !   28.6   0.0   2.3e-10   1.4e-06       3     100 ..      26     127 ..      25     177 .. 0.65

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.3e-10
                     Metallophos_2   3 laiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepe.vleellelapvlaVrGNnD.....eevveedvl 71 
                                       + ++ D+H+  dale++++ l+  + d+ i++GDl  ++ + + vl+++++  +++ VrGNn+     ++++  ++ 
  gi|336252887|ref|YP_004595994.1|  26 VYVVGDVHGCPDALERLFSTLEFGSSDLAIFVGDLvrKGPDSKaVLDRVKSSPQLRSVRGNNEqklldGRAELPALD 102
                                       5799******************************9553333333666666666**********55443333455555 PP

                     Metallophos_2  72 reaaelgtdlpeeaelelagekvlliHgd 100
                                       ++  ++ ++lp++   e +    l++Hg 
  gi|336252887|ref|YP_004595994.1| 103 ESDRQYIESLPTAISWE-G---NLVVHGG 127
                                       55555555555444444.2...4677775 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.3e-05      0.19       8      53 ..      26      71 ..      21     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
                                      EEEEE--TT-GGGHHHHHHHHHHH--SEEEEES-----HHHHHHHH CS
                     Metallophos_3  8 vlaisdlkgevellerlveviedkdpDllvlvGdlvkaeakadeye 53
                                      v  + d++g  + lerl  ++e  ++Dl ++vGdlv+++  ++   
  gi|336252887|ref|YP_004595994.1| 26 VYVVGDVHGCPDALERLFSTLEFGSSDLAIFVGDLVRKGPDSKAVL 71
                                      667889*****************************99877666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1785.33
//
Query:       gi|336252888|ref|YP_004595995.1|  [L=767]
Description: polyphosphate kinase [Halopiger xanaduensis SH-6]
Scores for 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-73  244.5   0.7    1.5e-72  242.5   0.4    2.1  3  PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
    5.1e-66  221.4   0.0    3.8e-64  215.3   0.0    2.3  2  PP_kinase_C    Polyphosphate kinase C-terminal domain 2
    1.9e-65  220.3   3.1    3.9e-65  219.2   3.1    1.6  1  PP_kinase      Polyphosphate kinase middle domain
    2.6e-36  124.2   0.0    8.3e-36  122.6   0.0    1.9  1  PP_kinase_N    Polyphosphate kinase N-terminal domain
    1.7e-15   57.1   0.0    4.3e-07   29.9   0.1    2.5  2  PLDc_2         PLD-like domain
  ------ inclusion threshold ------
       0.04   13.5   3.2      0.042   13.4   0.4    2.2  2  MR_MLE_C       Enolase C-terminal domain-like


Domain annotation for each model (and alignments):
>> 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 ?   -3.9   0.0       2.9   8.8e+03      34      52 ..     292     310 ..     292     318 .. 0.84
   2 !  242.5   0.4   5.1e-76   1.5e-72       1     165 [.     408     573 ..     408     575 .. 0.98
   3 ?   -1.2   0.0      0.44   1.3e+03      12      68 ..     581     639 ..     576     643 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.9
                                       TTEEEEEEEES-S-S--HH CS
                     PP_kinase_C_1  34 pkvlaikitlYrvakdski 52 
                                       p+v+ + ++l+rv++++++
  gi|336252888|ref|YP_004595995.1| 292 PDVEIVDTALFRVTRNAEV 310
                                       6788899999999999887 PP

  == domain 2  score: 242.5 bits;  conditional E-value: 5.1e-76
                                       SHHHHHHHS-EEEECTTB-S.CHHHHHHHHHHC-TTEEEEEEEES-S-S--HHHHHHHHHHHTT-EEEEEES--SSS CS
                     PP_kinase_C_1   1 sifeairkkdillhhPyesf.esvvelleeAaedpkvlaikitlYrvakdskivkaLieAaengkqvtvlvElkArf 76 
                                       sif++ir++d+l+hhPy+ f ++v+++leeAa+dp+vlaik ++Yr+a+dskiv++LieAa+ngkqv+v+vElkArf
  gi|336252888|ref|YP_004595995.1| 408 SIFDVIRDRDVLVHHPYHAFeDTVQRFLEEAANDPDVLAIKAAIYRTASDSKIVETLIEAARNGKQVAVMVELKARF 484
                                       69******************889****************************************************** PP

                                       --HHHHHHHHHHHHHT-EEEE--TT--B--EEEEEEE---S---EEEEEESS-SS---SS-EEEEEEEE--HHHHHH CS
                     PP_kinase_C_1  77 deenNiewakkleeagvkvvygvvglkvhaklllvvrreeeklrryvhlgtGnynektaklYtDlslltadeelged 153
                                       deenN+ewakklee+g++v+yg+ g+k+h+k+ lvvr+e+++++ y h+gtGny+++tak Y+Dl+lltad+++g+d
  gi|336252888|ref|YP_004595995.1| 485 DEENNLEWAKKLEEEGIHVAYGTIGYKTHTKTSLVVREEDDGVQLYSHIGTGNYHSETAKQYEDLGLLTADRDIGQD 561
                                       ***************************************************************************** PP

                                       HHHHHHHHTT-- CS
                     PP_kinase_C_1 154 veklfnvltgks 165
                                       + ++fn++tg+s
  gi|336252888|ref|YP_004595995.1| 562 LVRVFNYFTGHS 573
                                       ********9986 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.44
                                       EEECTTB-SCHHHHHHHHHHC-TTE...EEEEEEES-S-S--HHHHHHHHHHHTT-EEEE CS
                     PP_kinase_C_1  12 llhhPyesfesvvelleeAaedpkv...laikitlYrvakdskivkaLieAaengkqvtv 68 
                                       ll  P +  e +v+l++eAae  +     +i + + r+ +d ++v+ L +A  +g ++  
  gi|336252888|ref|YP_004595995.1| 581 LLVAPGNMRERFVDLVREAAERARNgedARIVLKVNRL-EDPELVRELYAASMAGVDIDL 639
                                       67777777889999999998765541114455555555.467888888888888877665 PP

>> 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 ?    3.7   0.0     0.012        37      38      61 ..     455     478 ..     425     487 .. 0.85
   2 !  215.3   0.0   1.3e-67   3.8e-64       1     166 [.     581     746 ..     581     752 .. 0.98

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.012
                       PP_kinase_C  38 ledkeiidkLyeAsqaGVkikliv 61 
                                        +d++i++ L+eA++ G ++ ++v
  gi|336252888|ref|YP_004595995.1| 455 ASDSKIVETLIEAARNGKQVAVMV 478
                                       5799*************9999998 PP

  == domain 2  score: 215.3 bits;  conditional E-value: 1.3e-67
                       PP_kinase_C   1 LlvaplnlrekllelidreieaakagkkakiilklNsledkeiidkLyeAsqaGVkiklivrgicclrpgvkglsen 77 
                                       Llvap n+re++++l+++ +e+a++g++a+i+lk+N led e++++Ly+As aGV+i+livr+ic+lrpg +++se+
  gi|336252888|ref|YP_004595995.1| 581 LLVAPGNMRERFVDLVREAAERARNGEDARIVLKVNRLEDPELVRELYAASMAGVDIDLIVRDICRLRPGLEDVSET 657
                                       89*************************************************************************** PP

                       PP_kinase_C  78 ikvisivdrfLEhaRiyifenggeeevyisSaDlmtRnldrRvevlvpvedeklkkelkeilelqlkDnvkarelde 154
                                       i+v+s+v+rfLEh+Ri++f+ ggee+++ +SaD+m+Rnld+Rve+++p+ed++l+++l+e+le+ l+D+ + +++++
  gi|336252888|ref|YP_004595995.1| 658 ITVHSVVGRFLEHSRIFYFRAGGEERYFTGSADWMERNLDNRVEAVAPIEDPRLQSRLDEVLETLLADTRNRWVMRS 734
                                       ***************************************************************************** PP

                       PP_kinase_C 155 dgeykkvkekee 166
                                       dg+y++++++  
  gi|336252888|ref|YP_004595995.1| 735 DGSYERCRQRVD 746
                                       ******998544 PP

>> PP_kinase  Polyphosphate kinase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.2   3.1   1.3e-68   3.9e-65       2     202 .]     201     398 ..     200     398 .. 0.96

  Alignments for each domain:
  == domain 1  score: 219.2 bits;  conditional E-value: 1.3e-68
                                       HHHHHHHHHHHTTGGG---EE--TTTS-----TT-EEEEEEEESST-SS-..EEEEEE--TTS-SEEEE-T.TSS-. CS
                         PP_kinase   2 qkefleeyFeeevfpvLtplavdpshpfpflsnkslnlavelrkkekeekekefalvkvPsvlpRfielppeeegke 78 
                                       +++ +++yFe+ v+p Ltpl +dp+hpfpf+sn+sl+lav+ r+++  +++ +f +vk+P++  Rf++l  e +g+ 
  gi|336252888|ref|YP_004595995.1| 201 ERREVRDYFESSVLPTLTPLTFDPAHPFPFISNQSLSLAVLTRERS--GDDLTFSRVKIPRNQVRFVQL-GEGDGDD 274
                                       6889**************************************9984..44469****************.6678888 PP

                                       EEEEHHHHHHCCHHHH-TTSEEEEEEEEEEE-SSS----.---.-------------------EEEEETT--HHHHC CS
                         PP_kinase  79 rfilledvIeanldelFpgyevleaylfrvtRnadleidedeaedlleeiekeLkkRrrgevvRLeveaempeellk 155
                                       r++lle+v+++nld lFp++e+++++lfrvtRna++  de+ aedl+e++e+ L++Rr++ vvRLe+e+e pe++++
  gi|336252888|ref|YP_004595995.1| 275 RYVLLEEVVRENLDLLFPDVEIVDTALFRVTRNAEVRRDEEVAEDLIEMVEEVLEERRFATVVRLEIEQEPPEQIRE 351
                                       ***************************************************************************** PP

                                       CHTTTT---TTT.EEEE-S--GGGGGCS...--TTTSSS----B--H CS
                         PP_kinase 156 fLlkeleldeedvyeidgpldltdlmklvgkdrpeLkyppftpqtpp 202
                                       +L +el+ld+++v+e+ gpld +d+++l++ drpeL+ p++tpq +p
  gi|336252888|ref|YP_004595995.1| 352 ILTRELDLDDREVFELAGPLDYRDFFELADLDRPELRLPEWTPQSHP 398
                                       ****************************99**************986 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 !  122.6   0.0   2.8e-39   8.3e-36       1     107 []      86     192 ..      86     192 .. 0.99

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 2.8e-39
                                       XXXHHHHHHHHHHHHHHHHH-TTS-HHHHHHHHHHHHHHHHHHHHHCCHHHHH.HTT-..-----------HHHHHH CS
                       PP_kinase_N   1 ylnRelSwLkFneRVLeeAedervplleRlkFlaIfssNlDEFfmvRvaslkrqleakvekksedgltpeeqlkais 77 
                                       ylnRelS L+F++RVL+eA de++plleR+kFlaIf++N+DEF++ Rv++lk+q++a+++++++dg+tp+eq++++ 
  gi|336252888|ref|YP_004595995.1|  86 YLNRELSELAFQRRVLHEAIDEKNPLLERVKFLAIFTKNVDEFIRKRVGGLKQQIAAGITEETPDGRTPREQWREVL 162
                                       89*************************************************************************** PP

                                       HHHHHHHHHHHHHHHHTHHHHHHHTTEEE. CS
                       PP_kinase_N  78 eeveelveeqekileeellpeLaeegikll 107
                                       +e++el+e+q +++++e+ p+La+egi ++
  gi|336252888|ref|YP_004595995.1| 163 DETHELLERQAACYRDEIEPALADEGIDIV 192
                                       ***************************985 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   1.4e-10   4.3e-07      15     131 ..     450     568 ..     444     570 .. 0.84
   2 !   24.7   0.0   5.8e-09   1.7e-05      12     131 ..     611     721 ..     595     723 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.4e-10
                            PLDc_2  15 atyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetllgslHaKlylidg 91 
                                       a+y   sd++i++ l++aa++g++v +++     +a++ + +++ e++++l e+g+ v   +      H+K+ l+ +
  gi|336252888|ref|YP_004595995.1| 450 AIYRTASDSKIVETLIEAARNGKQVAVMVEL---KARFDE-ENNLEWAKKLEEEGIHVAYGTI-GYKTHTKTSLVVR 521
                                       56677899**********************9...667755.5555555555******997542.3568****99964 PP

                            PLDc_2  92 k.......tvivGSsNltkrgldlnlElnvviedkelakeleeeFer 131
                                       +       +  +G+ N+  +  ++  +l++ + d+++ + l + F++
  gi|336252888|ref|YP_004595995.1| 522 EeddgvqlYSHIGTGNYHSETAKQYEDLGLLTADRDIGQDLVRVFNY 568
                                       44789999999******************************999986 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 5.8e-09
                            PLDc_2  12 idiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetllgslHaKlyl 88 
                                       i + +  +  d+e++++l++a+  gv++ +++++      ++ ++ l   +e ++ + v  r+   l+   H+ ++ 
  gi|336252888|ref|YP_004595995.1| 611 IVLKVNRL-EDPELVRELYAASMAGVDIDLIVRD-----ICRLRPGLEDVSETITVHSVVGRF---LE---HSRIFY 675
                                       55666667.899*********************9.....788899999999998877777554...35...****** PP

                            PLDc_2  89 id...gktvivGSsNltkrgldlnlElnvviedkelakeleeeFer 131
                                       ++   ++  ++GS+ + +r+ld + E+   ied++l+++l+e  e 
  gi|336252888|ref|YP_004595995.1| 676 FRaggEERYFTGSADWMERNLDNRVEAVAPIEDPRLQSRLDEVLET 721
                                       *999899********************************9998775 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 ?   13.4   0.4   1.4e-05     0.042      16      72 ..     445     499 ..     429     504 .. 0.83
   2 ?   -0.6   0.1      0.26   7.8e+02      27      56 ..     589     618 ..     572     641 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                                       SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGG CS
                          MR_MLE_C  16 ravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleel 72 
                                        a+K  + +   a d + v+ + ea+ +g++v +mv+  +++d +  +++a++lee 
  gi|336252888|ref|YP_004595995.1| 445 LAIKAAIYR--TASDSKIVETLIEAARNGKQVAVMVELKARFDEENNLEWAKKLEEE 499
                                       567777555..699****************************************874 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHHHTTTSTSEEEEE-TTT CS
                          MR_MLE_C  27 vaedvervravreavgpgddvdlmvDanqa 56 
                                       +++ v+ vr++ e++ +g+d+++++ +n  
  gi|336252888|ref|YP_004595995.1| 589 RERFVDLVREAAERARNGEDARIVLKVNRL 618
                                       566677777777777777777777666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (767 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.42
# Mc/sec: 5432.28
//
Query:       gi|336252889|ref|YP_004595996.1|  [L=93]
Description: hypothetical protein Halxa_1484 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.42   11.1   2.3         12    6.4   0.2    2.1  2  PP2C_C    Protein serine/threonine phosphatase 2C, C-terminal


Domain annotation for each model (and alignments):
>> PP2C_C  Protein serine/threonine phosphatase 2C, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0022        39      17      50 ..       6      39 ..       3      47 .. 0.79
   2 ?    6.4   0.2   0.00067        12      16      37 ..      68      89 ..      64      93 .] 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0022
                            PP2C_C 17 avkkEkeldekleervkeiiekeekkeeldlekv 50
                                      a+++E++ d+ l++  +++ + ++++++ +++++
  gi|336252889|ref|YP_004595996.1|  6 AQDNETDQDADLDQAAANVADLAQEQNQANVNSL 39
                                      7788888999999999999997777777777665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00067
                            PP2C_C 16 eavkkEkeldekleervkeiie 37
                                      + ++++++l++++e+ v+ +++
  gi|336252889|ref|YP_004595996.1| 68 QGIEQDADLEQEIERIVQGALN 89
                                      5689999999999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 759.56
//
Query:       gi|336252890|ref|YP_004595997.1|  [L=414]
Description: hypothetical protein Halxa_1486 [Halopiger xanaduensis SH-6]
Scores for 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   42.2   3.8    8.1e-11   42.2   3.8    2.4  2  Glyco_trans_2_3  Glycosyl transferase family group 2
  ------ inclusion threshold ------
      0.091   12.6   7.4       0.74    9.6   7.4    2.0  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> 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 ?   -3.9   4.4       1.2   1.1e+04     158     191 ..       6      39 ..       2      46 .. 0.64
   2 !   42.2   3.8     9e-15   8.1e-11      26     181 ..     147     300 ..     130     357 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.2
                   Glyco_trans_2_3 158 ylgsllwsalplhlallllfsllalalvllllll 191
                                       ++  ll + + +++a+lll++l+a +++l +l+l
  gi|336252890|ref|YP_004595997.1|   6 FANPLLGALVAVLWAGLLLYGLSAGWWLLEALVL 39 
                                       4555666666677788999999887776644444 PP

  == domain 2  score: 42.2 bits;  conditional E-value: 9e-15
                   Glyco_trans_2_3  26 pevaivqgpvlv.mnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalqevggwdgdessvsEDf 101
                                       p+++ivq+   + + ++++ + + +++   +   +++   +l  ++  +G g+++r+s+ ++v +wd   ++++ED+
  gi|336252890|ref|YP_004595997.1| 147 PDADIVQFTEKPiYTGSRLAYLCEVFRVGYQLEQLGFH--RLRYPLYAWGGGIAVRASLEDAV-TWD--ARTITEDT 218
                                       66666666655423455555555555543333333333..34458999**********88888.***..99****** PP

                   Glyco_trans_2_3 102 dmglrlqrkG.yrvrfvpeslvkekspltlraalrQrkRwayGceleklil.......lvrllgylgsllwsalplh 170
                                       ++  r++++G +  r+ + + ++ + p+++r  +rQr+Rw+ G      i+       + r+l y++ ++w   pl 
  gi|336252890|ref|YP_004595997.1| 219 NFIWRAAAAGdLSYRLLDTR-FRNQAPPSVRQLIRQRRRWISGT-----IAdghilprRYRPLYYTRVVVWGLSPLV 289
                                       **********6666777755.**********************5.....3344222222333333333333333332 PP

                   Glyco_trans_2_3 171 lallllfslla 181
                                        +++l +sl++
  gi|336252890|ref|YP_004595997.1| 290 PLVALAASLAP 300
                                       22222222222 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 ?    9.6   7.4   8.3e-05      0.74     153     228 ..     184     258 ..      56     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 8.3e-05
                   Glyco_tranf_2_3 153 ralgvltln.GsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwv 228
                                       ++l+ + ++ G g ++r+++ ++  ++d+   +t+D     r+ +ag  ++ + +   r + p+s+ ++i+qr+Rw+
  gi|336252890|ref|YP_004595997.1| 184 HRLRYPLYAwGGGIAVRASLEDAV-TWDA-RTITEDTNFIWRAAAAGDLSYRLLDTRFRNQAPPSVRQLIRQRRRWI 258
                                       6666644444999***********.****.999999988888889998888899999*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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 0.21s 00:00:00.71 Elapsed: 00:00:00.35
# Mc/sec: 3531.10
//
Query:       gi|336252891|ref|YP_004595998.1|  [L=196]
Description: dolichol kinase-like protein [Halopiger xanaduensis SH-6]
Scores for 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:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1687.74
//
Query:       gi|336252892|ref|YP_004595999.1|  [L=590]
Description: glycyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for complete 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-23   83.1   0.1    2.6e-23   82.0   0.1    1.6  1  HGTP_anticodon  Anticodon binding domain
    1.7e-09   37.9   0.0    1.1e-08   35.3   0.0    2.1  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
      0.002   17.5   0.3          2    7.9   0.0    2.4  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.019   15.2   0.1       0.48   10.7   0.0    2.8  3  Ribosomal_L32p  Ribosomal L32p protein family
      0.052   13.7   0.4        9.8    6.4   0.0    2.5  2  Zn-ribbon_8     Zinc ribbon domain
      0.055   13.0   2.2          1    8.9   2.2    2.6  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.11   12.3   1.5         12    5.8   0.1    2.5  2  zinc_ribbon_2   zinc-ribbon domain
       0.17   11.6   1.7        1.1    8.9   0.0    2.3  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.48   10.4   1.6        6.7    6.7   0.1    2.4  2  Prok-RING_1     Prokaryotic RING finger family 1
        1.2    9.3   2.5         17    5.6   0.0    2.4  2  zf-ACC          Acetyl-coA carboxylase zinc finger 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 !   82.0   0.1   1.5e-26   2.6e-23       2      93 ..     488     579 ..     488     580 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 1.5e-26
                                       EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHH..TEEEEEETTT CS
                    HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelek..gtvtvrdrdt 76 
                                       v v pl++ ++el e a+++ ++Lr+ g++v +d ++++ig+++r+ d++g+pf+v+v++++le+   tvtvr+rdt
  gi|336252892|ref|YP_004595999.1| 488 VGVFPLQS-DDELVEQAQEIVDDLREVGLSVTYD-DSGNIGRRYRRQDEVGTPFCVTVDFETLEEeeTTVTVRERDT 562
                                       6799***9.777*******************998.69**************************75569********* PP

                                       CEEEEEETTHHHHHHHH CS
                    HGTP_anticodon  77 reqervsldelveklke 93 
                                       +eq r+++del+e l++
  gi|336252892|ref|YP_004595999.1| 563 TEQKRLPVDELPETLSA 579
                                       ************99875 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 !   35.3   0.0   5.9e-12   1.1e-08      12     175 ..     171     459 ..     165     463 .. 0.56

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 5.9e-12
                                       EE-SSSHHHH.HHHHH.HHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHHHHH CS
                                       xxxxxxxxxx.xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                      tRNA-synt_2b  12 iLkPtneetf.velir.devlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslrdlik 85 
                                       +L+P+  +++ ve  r +e +r ++LP+ ++qi++ yR+E s  r ++R reF+q + + f+  e +++d l++++ 
  gi|336252892|ref|YP_004595999.1| 171 YLRPETAQGIfVEFPRlKEYAR-NQLPFGVTQIGRAYRNEISPRRSIIRTREFTQAELEYFVDpETDSPD-LSKVED 245
                                       7888888875145544134334.44****************9788******************5555544.333333 PP

                                       HHHHHHHHT......T.SCEEEEEE.GTTSC.............................................. CS
                                       xxxxxxxxx......xxxxxxxxxx.xxxxx.............................................. RF
                      tRNA-synt_2b  86 aisriferl......glefraiiel.msaks.............................................. 109
                                       +  +++ +       g e r +i++  s +                                               
  gi|336252892|ref|YP_004595999.1| 246 VEVTLYPASeqnkedGEEIRTTIGDaVS-EGiigdewvayflgvakpwydavgvdmdrfrfrqhlsgerahyaadcw 321
                                       3333333331113334444555555311.224556666666666666666666666666666666666666666666 PP

                                       ............................................................................B CS
                                       ............................................................................x RF
                      tRNA-synt_2b 110 ............................................................................a 110
                                                                                                                   +
  gi|336252892|ref|YP_004595999.1| 322 daeseidgnwiemagfayrgdydlskhgehaddrftifkqydepktveratvdpdmsylgpefggdaqavvqkledL 398
                                       66666666666665555555555555555555555555555555555555555555555555555555444444444 PP

                                       TTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEEEEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 111 dykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimicaaigveRllsai 175
                                        + d+  f+  + ++t ++e+  +   +t++s     +   e++++ +++++  ++gv Rl+  +
  gi|336252892|ref|YP_004595999.1| 399 AARDRSAFDGDTVEITLEGETHEVPTEKTGFSV----EEQTEAGEHITPHVVEPSFGVDRLVYTV 459
                                       444444444444445555555555544444332....2223446666666666666666666555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0011         2       3      13 ..      96     106 ..      94     111 .. 0.78
   2 !    7.5   0.0    0.0016       2.8       4      11 ..     138     146 ..     132     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0011
                       zf-ribbon_3   3 vrCPnCGa.pls 13 
                                       v+CP+CG+ + +
  gi|336252892|ref|YP_004595999.1|  96 VECPECGEsH-R 106
                                       89*****966.5 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0016
                       zf-ribbon_3   4 rCPnCGa.p 11 
                                        CP+CGa +
  gi|336252892|ref|YP_004595999.1| 138 VCPSCGAgL 146
                                       477777644 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00027      0.48      26      50 ..      95     119 ..      92     123 .. 0.85
   2 ?   -1.1   0.0       1.3   2.3e+03      41      46 ..     138     143 ..     136     152 .. 0.73
   3 ?    0.2   0.0      0.53   9.5e+02      28      46 ..     433     451 ..     425     457 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                                       EEEETTTCCEECTTC-BTTTTBSSS CS
                    Ribosomal_L32p  26 lvecpncgelklpHrvcpscGyYkg 50 
                                       lvecp+cge +++ +v+ + + Y+ 
  gi|336252892|ref|YP_004595999.1|  95 LVECPECGESHRADHVVEDNTEYED 119
                                       89*************9999877665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                                       -BTTTT CS
                    Ribosomal_L32p  41 vcpscG 46 
                                       vcpscG
  gi|336252892|ref|YP_004595999.1| 138 VCPSCG 143
                                       677776 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.53
                                       EETTTCCEECTTC-BTTTT CS
                    Ribosomal_L32p  28 ecpncgelklpHrvcpscG 46 
                                       e ++ ge++ pH+v ps G
  gi|336252892|ref|YP_004595999.1| 433 EQTEAGEHITPHVVEPSFG 451
                                       556789********98866 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0055       9.8      23      34 ..      92     103 ..      81     108 .. 0.67
   2 ?    4.8   0.1     0.017        30      26      34 ..     136     144 ..     127     149 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0055
                       Zn-ribbon_8  23 dapltaCPeCgs 34 
                                       d+ l++CPeCg+
  gi|336252892|ref|YP_004595999.1|  92 DDMLVECPECGE 103
                                       445666****97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.017
                       Zn-ribbon_8  26 ltaCPeCgs 34 
                                       + +CP+Cg+
  gi|336252892|ref|YP_004595999.1| 136 ELVCPSCGA 144
                                       445777776 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.2   0.00056         1       3      27 ..      98     144 ..      96     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00056
                                       ETTTTCEEC.....................HEE.TSTTCEEESSSSB CS
                      TF_Zn_Ribbon   3 CPnCgstnl.....................veD.pergelvCtdCGl 27 
                                       CP+Cg ++                      ve+  ++ elvC++CG+
  gi|336252892|ref|YP_004595999.1|  98 CPECGESHRadhvvednteyedaeslpipeVEEvIAEYELVCPSCGA 144
                                       9999998866899999999999999999985557999********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 ?    4.9   0.2     0.012        22       2       9 ..      98     105 ..      97     110 .. 0.76
   2 ?    5.8   0.1    0.0067        12      16      22 ..     139     145 ..     132     147 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.012
                     zinc_ribbon_2   2 CpnCGael 9  
                                       Cp+CG+ +
  gi|336252892|ref|YP_004595999.1|  98 CPECGESH 105
                                       88888876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0067
                     zinc_ribbon_2  16 CpyCGtp 22 
                                       Cp CG++
  gi|336252892|ref|YP_004595999.1| 139 CPSCGAG 145
                                       5555554 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 ?    0.9   0.7       0.2   3.7e+02      24      31 ..      98     105 ..      96     105 .. 0.84
   2 ?    8.9   0.0   0.00064       1.1      16      29 ..     131     144 ..     127     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.2
                     zf-NADH-PPase  24 CpaCgleh 31 
                                       Cp Cg+ h
  gi|336252892|ref|YP_004595999.1|  98 CPECGESH 105
                                       99999877 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00064
                     zf-NADH-PPase  16 aeggwarvCpaCgl 29 
                                       + +++ +vCp+Cg+
  gi|336252892|ref|YP_004595999.1| 131 VIAEYELVCPSCGA 144
                                       789*********96 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 ?    6.7   0.1    0.0038       6.7      18      30 ..      93     105 ..      85     109 .. 0.76
   2 ?    2.1   0.1       0.1   1.8e+02      22      28 ..     138     144 ..     134     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0038
                       Prok-RING_1  18 dDiVvCpeCgtpy 30 
                                       d +V CpeCg ++
  gi|336252892|ref|YP_004595999.1|  93 DMLVECPECGESH 105
                                       33688*****986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.1
                       Prok-RING_1  22 vCpeCgt 28 
                                       vCp Cg+
  gi|336252892|ref|YP_004595999.1| 138 VCPSCGA 144
                                       9****98 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 ?    2.9   0.8     0.068   1.2e+02       3       9 ..      97     103 ..      96     104 .. 0.83
   2 ?    5.6   0.0    0.0094        17       4      17 ..     139     152 ..     138     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.068
                            zf-ACC   3 KCpsCge 9  
                                        Cp+Cge
  gi|336252892|ref|YP_004595999.1|  97 ECPECGE 103
                                       6****98 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0094
                            zf-ACC   4 CpsCgemlykkeLe 17 
                                       CpsCg+ l  + +e
  gi|336252892|ref|YP_004595999.1| 139 CPSCGAGLAGQAVE 152
                                       9***9998766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 4383.40
//
Query:       gi|336252893|ref|YP_004596000.1|  [L=284]
Description: CBS domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-33  114.8   6.7    6.9e-11   42.4   0.1    4.1  4  CBS       CBS domain
  ------ inclusion threshold ------
       0.79    9.8   2.8       0.91    9.7   0.3    2.3  3  DUF2288   Protein of unknown function (DUF2288)


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 !   21.5   0.0   2.7e-08   0.00024       1      52 [.       3      59 ..       3      62 .. 0.86
   2 !   40.9   0.5   2.3e-14   2.1e-10       4      56 ..      70     120 ..      65     121 .. 0.94
   3 !   11.2   0.0   4.4e-05      0.39      13      54 ..     142     183 ..     130     185 .. 0.75
   4 !   42.4   0.1   7.7e-15   6.9e-11       1      56 [.     229     283 ..     229     284 .] 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.7e-08
                                      HHHHSBS..SCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTT.BEEEEEEHHHHH CS
                               CBS  1 Vgdimtr..dvvtvppdttleealelmrekgvsrlPVV..dedg.klvGivtlrDll 52
                                      V+d mt+  dvvtv    t +++le + e  +s++PVV   +dg ++ G++++  l+
  gi|336252893|ref|YP_004596000.1|  3 VADAMTPreDVVTVELPGTRSDVLEYLQEQPFSSVPVVkpTDDGpEYRGLISRNALI 59
                                      567766666******************6666********9778889******98887 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 2.3e-14
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       +m +dv+t + dt le+++++m+e g +r+PVV  dg++ Givt +D++ a++
  gi|336252893|ref|YP_004596000.1|  70 LMDEDVPTTTADTALEDVARTMVEQGARRVPVV--DGEFEGIVTVTDVVHAIA 120
                                       599***********************99*****..799***********9986 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 4.4e-05
                                       ETTSBHHHHHHHHHHHTSSEEEE.EETTTBEEEEEEHHHHHHH CS
                               CBS  13 ppdttleealelmrekgvsrlPV.VdedgklvGivtlrDllra 54 
                                       ++ t+l  a +++  ++v    V +d+dg+  Gi+t  D+l++
  gi|336252893|ref|YP_004596000.1| 142 YEGTPLPVAERELSYANVPYA-VaLDDDGRMSGILTVVDVLEV 183
                                       566778888888833335444.645***************985 PP

  == domain 4  score: 42.4 bits;  conditional E-value: 7.7e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       Vg++m++dvvtv+ ++++ ea+++m+++++ ++  V ++  lvGiv + D+l+al 
  gi|336252893|ref|YP_004596000.1| 229 VGEFMSDDVVTVSANASIQEAAQRMISNDIEQIAMVTGEQ-LVGIVCDIDILEALY 283
                                       89************************999****7774555.************995 PP

>> DUF2288  Protein of unknown function (DUF2288)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.78     7e+03      62      74 ..     124     136 ..     111     141 .. 0.50
   2 ?   -2.0   0.0      0.44   3.9e+03      32      53 ..     152     173 ..     147     189 .. 0.71
   3 ?    9.7   0.3    0.0001      0.91      22      65 ..     232     275 ..     230     281 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.78
                                       E--HHHHHHHHHH CS
                           DUF2288  62 kvseeqasewnee 74 
                                       ++++ ++++w++e
  gi|336252893|ref|YP_004596000.1| 124 QPTDGTVEAWASE 136
                                       3444444444433 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.44
                                       SSS-HHHHHHHHHTT-HHHHHH CS
                           DUF2288  32 eeldLvevavaiaeDdkaavea 53 
                                       +el   +v +a+a Dd  +++ 
  gi|336252893|ref|YP_004596000.1| 152 RELSYANVPYAVALDDDGRMSG 173
                                       6777788888888888766655 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0001
                                       HHTT-EEEE-SSS-HHHHHHHHHTT-HHHHHHHHHTTSEEE--H CS
                           DUF2288  22 fargavivVaeeldLvevavaiaeDdkaaveawleegllakvse 65 
                                       f ++ v++V+++  + e+a+++ ++d ++++    e+l+  v +
  gi|336252893|ref|YP_004596000.1| 232 FMSDDVVTVSANASIQEAAQRMISNDIEQIAMVTGEQLVGIVCD 275
                                       56899**************************9999999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2094.61
//
Query:       gi|336252894|ref|YP_004596001.1|  [L=55]
Description: hypothetical protein Halxa_1490 [Halopiger xanaduensis SH-6]
Scores for 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:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 408.75
//
Query:       gi|336252895|ref|YP_004596002.1|  [L=164]
Description: DoxX family protein [Halopiger xanaduensis SH-6]
Scores for 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-14   53.7  14.4      1e-13   51.6  10.1    2.2  2  DoxX       DoxX
    8.3e-05   22.8   0.2    0.00089   19.5   0.1    2.0  2  HR_lesion  HR-like lesion-inducing
  ------ inclusion threshold ------
        1.1    9.5   4.6         45    4.3   2.6    2.5  2  YtpI       YtpI-like protein


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6  10.1   1.7e-17     1e-13       2      85 .]      37     118 ..      36     118 .. 0.98
   2 !    4.4   0.1    0.0098        59      27      59 ..     129     161 ..     121     164 .] 0.83

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.7e-17
                              DoxX   2 llllRlllgvlfiahGlqkltgfglegtaaslaalglpppellaylaalvElvgglllllGlltRlaAlalavtllv 78 
                                        l++R+l+g+++  +Gl+ +   +le+ta++ +  g+p+p   + l +++ ++gg++++lG+++ la +alav+llv
  gi|336252895|ref|YP_004596002.1|  37 FLVARILFGGTLAFTGLNHFL--DLESTAGYAEMKGVPAPKASVALSGFALVFGGVGIVLGVFPALAGAALAVFLLV 111
                                       599******************..****************************************************** PP

                              DoxX  79 atltvhr 85 
                                       at t+h+
  gi|336252895|ref|YP_004596002.1| 112 ATPTMHD 118
                                       *****95 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0098
                              DoxX  27 egtaaslaalglpppellaylaalvElvgglll 59 
                                       ++++++l+++gl+ + l+++ + ++E   +++l
  gi|336252895|ref|YP_004596002.1| 129 TEMTQFLKNVGLLGASLAVIGISALEWPYAVGL 161
                                       578999***************999997666555 PP

>> HR_lesion  HR-like lesion-inducing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.06   3.6e+02       6      41 ..      38      73 ..      34      86 .. 0.80
   2 !   19.5   0.1   1.5e-07   0.00089      74     137 ..      89     149 ..      78     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.06
                         HR_lesion  6 fiGrvlfasvfllsawqdyaefgadggpaekalkPk 41
                                      ++ r+lf  +  ++  +++ ++++  g ae +  P+
  gi|336252895|ref|YP_004596002.1| 38 LVARILFGGTLAFTGLNHFLDLESTAGYAEMKGVPA 73
                                      57899****************999888887766555 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.5e-07
                         HR_lesion  74 glggLlfilgsslgaylLllyqaiatvvlydfynydldtkeflrlllkfvqnlalvGaLLffvg 137
                                       g+g +l ++    ga  L++++ +at+ ++df+    +++  ++ +++f++n+ l+Ga L  +g
  gi|336252895|ref|YP_004596002.1|  89 GVGIVLGVFPALAGAA-LAVFLLVATPTMHDFWAAPEEQR--QTEMTQFLKNVGLLGASLAVIG 149
                                       5566666666677775.678999*********98776665..5899************998776 PP

>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   2.6    0.0075        45      34      59 ..      40      65 ..      38     105 .. 0.84
   2 ?    3.2   2.1     0.017     1e+02      32      68 ..      74     111 ..      65     118 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0075
                              YtpI 34 asialGlflilfginqllllestval 59
                                      a+i++G  l++ g+n +l lest ++
  gi|336252895|ref|YP_004596002.1| 40 ARILFGGTLAFTGLNHFLDLESTAGY 65
                                      68888999999999999998888765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.017
                              YtpI  32 akasialGlflilfgin.qllllestvalvvgavflvl 68 
                                        kas+al+ f ++fg +  +l    ++a +  avfl++
  gi|336252895|ref|YP_004596002.1|  74 PKASVALSGFALVFGGVgIVLGVFPALAGAALAVFLLV 111
                                       57777777777777766455555555555556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1278.89
//
Query:       gi|336252896|ref|YP_004596003.1|  [L=195]
Description: hypothetical protein Halxa_1492 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.069   13.2   0.0        4.3    7.4   0.0    2.2  2  BsuPI     Intracellular proteinase inhibitor


Domain annotation for each model (and alignments):
>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0    0.0037        67       1      23 [.      75      97 ..      75     104 .. 0.86
   2 ?    7.4   0.0   0.00024       4.3      67      98 ..     137     180 ..     126     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0037
                                      EEEEEEEEE-SS-EEEEEEEEE- CS
                             BsuPI  1 lelaleaeasgeavelaltvtNe 23
                                      +e++ +++a+g++ve+++t  N 
  gi|336252896|ref|YP_004596003.1| 75 VETDRAVYARGDPVEITVTFRNR 97
                                      58999***************997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00024
                                       EE-TT-EEEEEEEE............S.---SEEEEEEEEE--E CS
                             BsuPI  67 tlepgesatyeetwd...........e.dlepGeYtleaelvae 98 
                                       +++ ge +  + tw+           +  ++pGeY++ea+++++
  gi|336252896|ref|YP_004596003.1| 137 SFRGGERKRATVTWNgrlertdeqheSvVPKPGEYEIEAFVATH 180
                                       5677778888888888888888776425899********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1441.66
//
Query:       gi|336252897|ref|YP_004596004.1|  [L=51]
Description: hypothetical protein Halxa_1493 [Halopiger xanaduensis SH-6]
Scores for 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:                       128  (0.00713927); expected 358.6 (0.02)
Passed bias filter:                      120  (0.00669307); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); 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 0.21s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 406.69
//
Query:       gi|336252898|ref|YP_004596005.1|  [L=461]
Description: oligopeptide/dipeptide ABC transporter ATPase [Halopiger xanaduensis SH-6]
Scores for 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  112.2   0.0      4e-32  111.6   0.0    1.3  1  ABC_tran     ABC transporter
    4.1e-18   65.7   0.1    9.2e-18   64.5   0.1    1.6  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
      2e-06   27.4   0.0    2.8e-06   26.9   0.0    1.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00047   20.6   0.0    0.00086   19.7   0.0    1.6  1  AAA_16       AAA ATPase domain
     0.0036   17.6   0.3      0.031   14.5   0.3    2.2  1  AAA_22       AAA domain
     0.0088   15.9   0.1        1.8    8.3   0.0    2.5  3  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.024   14.4   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.022   15.2   0.0      0.098   13.1   0.0    1.9  2  AAA          ATPase family associated with various cellular a
      0.025   14.5   0.0      0.046   13.6   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
      0.055   13.2   0.0      0.089   12.5   0.0    1.3  1  PRK          Phosphoribulokinase / Uridine kinase family
      0.082   12.6   0.0      0.087   12.5   0.0    1.3  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
       0.11   12.5   0.1       0.21   11.6   0.1    1.5  1  AAA_5        AAA domain (dynein-related subfamily)


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 !  111.6   0.0   2.6e-35     4e-32       2     136 ..      65     215 ..      64     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 2.6e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       ++vs+++++ge++++vGe+G+GKStL +++++ll+pt G+i ++g+dl e   + l++ r+e+++++q+  ++l+p+
  gi|336252898|ref|YP_004596005.1|  65 DDVSFDVRRGETLGLVGESGCGKSTLGRTILRLLEPTDGTIAFKGEDLAEmsgEALREKRAEMQMIFQDpqASLDPR 141
                                       89************************************************99999**************8889**** PP

                                       SBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +tv++                ++++++++l+k+gl+  +    +++p+ +SgGq+qrv laral  +p+++++DEp 
  gi|336252898|ref|YP_004596005.1| 142 MTVGRIieepmrahdmlddeGREARAKELLEKVGLDPHH---YERHPHAFSGGQRQRVNLARALSVDPDFVVCDEPV 215
                                       **9999999*****9998877888899999999998844...45569*****************************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.1   6.1e-21   9.2e-18       1      60 [.     267     327 ..     267     330 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 6.1e-21
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpf 60 
                                       vE +++++lf++p+HPYT+aLl+s+p +d++k+ +   ++ge+ps+ + ++GC+F++RCp 
  gi|336252898|ref|YP_004596005.1| 267 VELADKEELFENPQHPYTEALLESIPIPDPRKRnARGVLEGEVPSPVNPPSGCRFRTRCPR 327
                                       8********************************778889********************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 !   26.9   0.0   1.9e-09   2.8e-06      28     205 ..      78     254 ..      60     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.9e-09
                                       EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvk 104
                                        +vG+ G+GKs l   il +L  ++     + k +dl   s e  + k+ae++++f++++++    ++++++ r ++
  gi|336252898|ref|YP_004596005.1|  78 GLVGESGCGKSTLGRTILRLLEPTDG--TIAFKGEDLAEMSGEALREKRAEMQMIFQDPQAS---LDPRMTVGRIIE 149
                                       58***************999986554..4455667777777889999**************9...8999******99 PP

                                       TTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 105 rkgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                       +  + + ++++ e +++  +elle++g++++       ++SgG+++ v la  +++   +p  +++ De  +aLD +
  gi|336252898|ref|YP_004596005.1| 150 EPMRAHDMLDD-EGREARAKELLEKVGLDPHhyerhphAFSGGQRQRVNLARALSV---DP-DFVVCDEPVSALDVS 221
                                       99997766665.6889999***********99999999**********99988765...44.499************ PP

                                       HHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                             SMC_N 175 nvkkvaellkekskn..aQfivislreemleka 205
                                         ++v + +++ +++    ++ i+++  ++++ 
  gi|336252898|ref|YP_004596005.1| 222 IQAQVLNTMDQLQDEfgLTYLFIAHDLSVIRHI 254
                                       ********9999988444566666666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   5.8e-07   0.00086      10      63 ..      62     112 ..      56     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.8e-07
                            AAA_16  10 eqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                       +++ ++  +vr+g  e + l+GesG+GKs+l r++lr le ++  +++ k ++l
  gi|336252898|ref|YP_004596005.1|  62 KAVDDVSFDVRRG--ETLGLVGESGCGKSTLGRTILRLLEPTD-GTIAFKGEDL 112
                                       5555555567777..56889****************9888885.4444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.3   2.1e-05     0.031      10      39 ..      79     101 ..      72     250 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeer 39 
                                       ++GesG+GK+tl r++l+ l+         
  gi|336252898|ref|YP_004596005.1|  79 LVGESGCGKSTLGRTILRLLEP-------T 101
                                       89****************9953.......2 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 !    8.3   0.0    0.0012       1.8       3      23 ..      78      98 ..      77     151 .. 0.75
   2 ?    5.2   0.0     0.011        16     229     301 ..     180     250 ..     138     252 .. 0.82
   3 ?   -3.0   0.0       3.3     5e+03     171     218 ..     330     377 ..     326     396 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                            AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                      +l+G  g+GKS+L +++  l 
  gi|336252898|ref|YP_004596005.1| 78 GLVGESGCGKSTLGRTILRLL 98
                                      69***************8874 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                            AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                        +e+ ++ +S G+++   l+ al  ++   ++++ DEp + L+ ++++ +l  +++l++  g   ++  H+ ++
  gi|336252898|ref|YP_004596005.1| 180 HYERHPHAFSGGQRQRVNLARALSVDP---DFVVCDEPVSALDVSIQAQVLNTMDQLQDeFGLTYLFIAHDLSV 250
                                       556667788999999999999999999...9***********************99988766666766666655 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.3
                            AAA_21 171 ifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlre 218
                                       ++ +y+  ++e+  ++ ++r +k++ +e+++  + e++ ++ d+++ e
  gi|336252898|ref|YP_004596005.1| 330 APERYALTDEEWAHTRAFMRAVKRRTFEPTAAADLEREFFDGDLPSGE 377
                                       566777888888888888999999999998888888888888777766 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   1.6e-05     0.024      13      50 ..      65     102 ..      62     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                            AAA_29  13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                       d+ ++++++ ++  l+G+sG GKSTl   i  lL p+ 
  gi|336252898|ref|YP_004596005.1|  65 DDVSFDVRRGETLGLVGESGCGKSTLGRTILRLLEPTD 102
                                       55677777555777************888888887765 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 ?   13.1   0.0   6.6e-05     0.098       3      53 ..      79     134 ..      77     149 .. 0.73
   2 ?   -0.8   0.0       1.3     2e+03      84     100 ..     221     245 ..     186     273 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-05
                                       EESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSSSTTHHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel..........gvefleisgsellskyvgesekkirelfkea 53 
                                       l+G  G+GK++l + + + l          g ++ e+sg  l+     e+ ++++++f++ 
  gi|336252898|ref|YP_004596005.1|  79 LVGESGCGKSTLGRTILRLLeptdgtiafkGEDLAEMSGEALR-----EKRAEMQMIFQDP 134
                                       89*****************955444333333446666666666.....8888999999874 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHTTTS........S CS
                               AAA  84 rvvnqLlteldgvkkk........e 100
                                       ++++q l+ +d+++++         
  gi|336252898|ref|YP_004596005.1| 221 SIQAQVLNTMDQLQDEfgltylfiA 245
                                       5889999999999987433333330 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.1e-05     0.046      80     120 ..      54      95 ..      42     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                                       EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       + v  ++ +++++++  ++  +t  lvG+SG GKStL  ++l
  gi|336252898|ref|YP_004596005.1|  54 IDVGRERVKAVDDVSFDVRRgETLGLVGESGCGKSTLGRTIL 95 
                                       5566667788889998888779**************977765 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     6e-05     0.089       3      68 ..      78     136 ..      76     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6e-05
                               PRK   3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspea 68 
                                       g+ g+SG+Gk+t+ r++  +++ +         ++f   d ae++ e+ ++kra+ +++ f +p+a
  gi|336252898|ref|YP_004596005.1|  78 GLVGESGCGKSTLGRTILRLLEPTD------GTIAFKGEDLAEMSGEALREKRAE-MQMIFQDPQA 136
                                       899****************999333......347788888888888888777776.7777777776 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 ?   12.5   0.0   5.8e-05     0.087       6      42 ..      66     102 ..      61     400 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.8e-05
                                       HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   6 DalfpivqGqrtlipgafgvGktvisqslskqsnsdd 42 
                                       D+ f + +G++++++g++g+Gk+++ +++++  + +d
  gi|336252898|ref|YP_004596005.1|  66 DVSFDVRRGETLGLVGESGCGKSTLGRTILRLLEPTD 102
                                       6778999*******************99998766554 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 ?   11.6   0.1   0.00014      0.21       4      23 ..      79      98 ..      76     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                      EE--SSSSHHHHHHHGGGGB CS
                             AAA_5  4 LvGppGtgKselaerlaaal 23
                                      LvG++G+gKs+l + ++++l
  gi|336252898|ref|YP_004596005.1| 79 LVGESGCGKSTLGRTILRLL 98
                                      9*****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3366.70
//
Query:       gi|336252899|ref|YP_004596006.1|  [L=406]
Description: oligopeptide/dipeptide ABC transporter ATPase [Halopiger xanaduensis SH-6]
Scores for 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-26   93.0   0.0    3.5e-26   92.4   0.0    1.3  1  ABC_tran     ABC transporter
    1.2e-19   70.6   0.4    2.3e-19   69.7   0.4    1.5  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    1.5e-05   24.9   0.1    0.00014   21.8   0.0    2.0  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
  ------ inclusion threshold ------
      0.038   13.4   0.0       0.15   11.5   0.0    1.7  2  SMC_N        RecF/RecN/SMC N terminal domain
      0.064   13.3   0.0       0.12   12.4   0.0    1.4  1  AAA_5        AAA domain (dynein-related subfamily)
       0.15   11.6   0.1        1.3    8.5   0.0    2.1  2  AAA_25       AAA domain
       0.21   11.5   0.0       0.35   10.8   0.0    1.3  1  RsgA_GTPase  RsgA GTPase


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 !   92.4   0.0   1.4e-29   3.5e-26       2     136 ..      28     201 ..      27     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 1.4e-29
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG....................B-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx....................xxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke....................qel 54 
                                       + +s++++ege+v++vGe+GaGKS   + l++l++      +Gei+++g+ +                      +++
  gi|336252899|ref|YP_004596006.1|  28 DGISFTVREGEIVGLVGESGAGKSVASMSLLRLVESpgeiVAGEITYKGETIFGleegpdgelrerddvlseeeIRT 104
                                       789*********************99999999998656666777766666666566666666666666666888888 PP

                                       HHCCHCEEEE-SS..--S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHH CS
                                       xxxxxxxxxxxxx..xxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  55 eslrkeigvlpqe..pqlfpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkq 115
                                       ++  +ei+v++q+  ++l+p  tv+ +              e+++e+ ++l+++g+++ ++++ ++ p+++SgG++q
  gi|336252899|ref|YP_004596006.1| 105 RIRGNEIAVIFQDpmESLNPVFTVGGQlrefielnrglgkdEARREAIDMLREVGIPD-PEERYEEYPHQFSGGMRQ 180
                                       9999*********9999*******999************9999999************.888889************ PP

                                       HHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 116 rvalarallkkpkllllDEpt 136
                                       rv +a+al+++p+l+++DEpt
  gi|336252899|ref|YP_004596006.1| 181 RVLIAMALACEPSLIIADEPT 201
                                       ********************9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.4     9e-23   2.3e-19       1      65 []     253     317 ..     253     317 .. 0.99

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 9e-23
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE++p+++lf++ +HPYT aLl+s+pr+dr  ++le i+g+ p++   ++GC+F+pRCp a+e C
  gi|336252899|ref|YP_004596006.1| 253 VEQAPVDELFHDTKHPYTDALLDSIPRPDRTVEQLEPIEGTMPEAISPPSGCRFHPRCPDAREVC 317
                                       8**************************************************************99 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 ?    1.1   0.1      0.11   2.7e+02       2      22 ..      40      60 ..      39     105 .. 0.69
   2 !   21.8   0.0   5.3e-08   0.00014     168     302 ..      98     237 ..      77     238 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.11
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       +l+G  g+GKS     l  l
  gi|336252899|ref|YP_004596006.1| 40 VGLVGESGAGKSVASMSLLRL 60
                                      689*********887777444 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 5.3e-08
                            AAA_21 168 llnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer.......gvvflengdgqelparel 237
                                         +  +  + ++++  ++q+ + sl++v+     l+e++el+     ++ +r        v + +++ ++e  ++++
  gi|336252899|ref|YP_004596006.1|  98 SEEEIRTRIRGNEIAVIFQDPMESLNPVFTVGGQLREFIELNRGLGKDEARReaidmlrEVGIPDPEERYEEYPHQF 174
                                       444555555555555555555555555555555555554444333333333367777778888888999******** PP

                            AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                       S G+++   ++ al+  +   sl++ DEp + L+  +   +++l++el++  g+ +i +TH+  ++
  gi|336252899|ref|YP_004596006.1| 175 SGGMRQRVLIAMALACEP---SLIIADEPTTALDVTVEGQIIDLVDELQEkYGTSFIWVTHDMGVV 237
                                       ******967777777666...************************888888**********98776 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 ?   -0.9   0.1      0.35   8.9e+02      26      39 ..      39      52 ..      30      61 .. 0.81
   2 ?   11.5   0.0   5.8e-05      0.15     135     208 ..     148     243 ..      68     253 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.35
                                      EEEEEESTTSSHHH CS
                                      xxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsn 39
                                      +  +vG+ G+GKs 
  gi|336252899|ref|YP_004596006.1| 39 IVGLVGESGAGKSV 52
                                      56799*******95 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.8e-05
                                       T........................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHC CS
                                       x........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e........................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeks 187
                                                                ++SgG ++ v +a+ +A    +p +l + De   aLD +   ++ +l++e +
  gi|336252899|ref|YP_004596006.1| 148 RreaidmlrevgipdpeeryeeyphQFSGGMRQRVLIAMALAC---EP-SLIIADEPTTALDVTVEGQIIDLVDELQ 220
                                       044444444444444466777777799***8888877777775...44.6999*********************999 PP

                                       TT..SEEEEE-SSHHHCCC-SCE CS
                                       xx..xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 188 kn..aQfivislreemlekadkl 208
                                       ++  + fi ++++ +++++    
  gi|336252899|ref|YP_004596006.1| 221 EKygTSFIWVTHDMGVVAEICDR 243
                                       987789******99998876433 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   4.5e-05      0.12       4      47 ..      42      85 ..      39     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.5e-05
                                      EE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B-- CS
                             AAA_5  4 LvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrrei 47
                                      LvG++G gKs  +++l+++++++ e+v++   ++ e+++g  e 
  gi|336252899|ref|YP_004596006.1| 42 LVGESGAGKSVASMSLLRLVESPGEIVAGEITYKGETIFGLEEG 85
                                      9***************************9999988888886654 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00052       1.3      30      89 ..      34      93 ..      19     114 .. 0.83
   2 ?    0.5   0.0      0.15   3.8e+02     165     188 ..     209     232 ..     178     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00052
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrR 89
                                      +++ge++ l+G +g+GK+++ ++l   v   G+ ++g++ + +g +++   E++  elr+R
  gi|336252899|ref|YP_004596006.1| 34 VREGEIVGLVGESGAGKSVASMSLLRLVEsPGEIVAGEI-TYKGETIFGLEEGPDGELRER 93
                                      578999*****************9987776677777744.567777777777777777766 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.15
                            AAA_25 165 vgalvealeriarrtgaavllvhH 188
                                       +g++++ ++++++++g  ++ v H
  gi|336252899|ref|YP_004596006.1| 209 EGQIIDLVDELQEKYGTSFIWVTH 232
                                       29999************9999999 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00014      0.35      80     114 ..      17      52 ..       5      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                       EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHH CS
                       RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKSt 114
                                       ++++a t ++++ ++  +++ +++ lvG+SG+GKS 
  gi|336252899|ref|YP_004596006.1|  17 FFTQAGTVRAVDGISFTVREgEIVGLVGESGAGKSV 52 
                                       5677888999999999999989************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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 0.27s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3131.62
//
Query:       gi|336252900|ref|YP_004596007.1|  [L=331]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-32  111.7  11.6    4.6e-32  111.2   8.6    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.044   13.8   0.0      0.044   13.8   0.0    3.3  4  OppC_N        N-terminal TM domain of oligopeptide transport 


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 ?    1.1   0.0     0.031   2.8e+02     144     174 ..      28      57 ..      15      63 .. 0.75
   2 !  111.2   8.6   5.2e-36   4.6e-32       1     184 [.     144     330 ..     144     331 .] 0.96

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.031
                      BPD_transp_1 144 ailgydyseisnggvlalviavlllnlvadi 174
                                        + ++d+++   g++++++++++   +++d+
  gi|336252900|ref|YP_004596007.1|  28 RTVMRDTTARW-GLYVIATVLLITAYTLVDA 57 
                                       45566777777.8888888888888888875 PP

  == domain 2  score: 111.2 bits;  conditional E-value: 5.2e-36
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       g+++G++a+ ++++++d+ll++ i++++++P+++l+i++++  +++++  + + +++ +++ +++ ++r+ir+++l+
  gi|336252900|ref|YP_004596007.1| 144 GTIVGAVAG-YYGGWVDDLLMRAIETVYAIPPLILIIVFTV--FVSGGSPDVMYAIVGVGVAFIPVFARIIRSEVLS 217
                                       7899*****.************************9999996..588888899999********************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                       ++++d++eaara G++++ i+ ++v+Pn++ p++  + l++g  +   + ++flg    +g +  ++ +g +++   
  gi|336252900|ref|YP_004596007.1| 218 VREMDYIEAARAAGVKDRNIILRHVIPNSFAPVLVYATLQIGVTILIVAGISFLG----FGAQPPTPDWGEMLNTSH 290
                                       *******************************************************....***************666 PP

                      BPD_transp_1 155 ..........nggvlalviavlllnlvadilqrlldprvr 184
                                                 +++ la+ i ++ +nl+ d lq++ldpr+ 
  gi|336252900|ref|YP_004596007.1| 291 symhsnvwlsIWPGLAIMITIMGFNLFGDGLQDALDPRIN 330
                                       **************************************86 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.9e-06     0.044       3      33 ..      23      53 ..      21      87 .. 0.83
   2 ?   -1.6   0.8      0.32   2.8e+03      24      32 ..     176     184 ..     175     212 .. 0.53
   3 ?   -2.1   0.0      0.44     4e+03      21      33 ..     260     272 ..     258     289 .. 0.67
   4 ?   -0.2   0.0      0.12     1e+03      19      36 ..     304     321 ..     303     329 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-06
                            OppC_N  3 wqdawrrFkrNklAvvglvilllllliaifa 33
                                      w+ ++r   r+ +A  gl +++++lli ++ 
  gi|336252900|ref|YP_004596007.1| 23 WRNTLRTVMRDTTARWGLYVIATVLLITAYT 53
                                      9**************************8874 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.32
                            OppC_N  24 llllliaif 32 
                                       +l++++ +f
  gi|336252900|ref|YP_004596007.1| 176 ILIIVFTVF 184
                                       333333333 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.44
                            OppC_N  21 villlllliaifa 33 
                                       v +l+++ i++++
  gi|336252900|ref|YP_004596007.1| 260 VTILIVAGISFLG 272
                                       4456677777775 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.12
                            OppC_N  19 glvilllllliaifaPli 36 
                                       gl+i +++  + +f++ +
  gi|336252900|ref|YP_004596007.1| 304 GLAIMITIMGFNLFGDGL 321
                                       89*******999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); 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:                         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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.35
# Mc/sec: 2795.98
//
Query:       gi|336252901|ref|YP_004596008.1|  [L=332]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for complete 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-41  142.4   9.0    1.3e-41  142.4   9.0    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.28   10.9   0.0    1.6  1  HTH_psq       helix-turn-helix, Psq domain
        2.7    8.6   5.3        1.4    9.6   1.3    2.2  2  Renin_r       Renin receptor-like protein


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 ?   -0.6   0.3      0.15   9.1e+02      26      43 ..      11      28 ..       4     114 .. 0.68
   2 !  142.4   9.0   2.2e-45   1.3e-41       2     184 ..     117     327 ..     116     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.15
                      BPD_transp_1 26 vllslPsfvlaillvlvf 43
                                      + +++P+++ + ++++v+
  gi|336252901|ref|YP_004596008.1| 11 FAQAIPVLIGISIITFVL 28
                                      444455544222222222 PP

  == domain 2  score: 142.4 bits;  conditional E-value: 2.2e-45
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.............................vilsil 49 
                                       i+lGilaa +rn ++d+++r++  ++ s+Psf+++i+l+l+f                                  +
  gi|336252901|ref|YP_004596008.1| 117 IPLGILAAKRRNEPFDHVSRIVALIGVSTPSFWIGIMLILLFgvqlgwfpssdlvypwwppdayghdgyleHAVETV 193
                                       8**********************************************************************88899* PP

                      BPD_transp_1  50 ghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggav 126
                                        hl lp+i+l++l++a ++r+ r ++++sl+ ++v++ara+G+++++i+rk+++  a  piit ++l++  +lggav
  gi|336252901|ref|YP_004596008.1| 194 RHLLLPMIALGTLQMATLMRVERTQMIDSLQGEYVKLARAYGVPERTILRKHAFQVAQLPIITIVGLNLSTALGGAV 270
                                       ***************************************************************************** PP

                      BPD_transp_1 127 lleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       l+ef+++ +Glg+l+ eai + dy++i+ g++ +++ ++++ ++++di ++++dprv+
  gi|336252901|ref|YP_004596008.1| 271 LTEFVFNINGLGRLFYEAIVQLDYQLIM-GITMIIATMFVIGVIITDIAYAYIDPRVT 327
                                       ****************************.***************************97 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 ?   10.9   0.0   4.7e-05      0.28      21      35 ..     229     244 ..     228     246 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.7e-05
                           HTH_psq  21 kAArkYgiPrsTLw.r 35 
                                       k+Ar Yg+P +T+  +
  gi|336252901|ref|YP_004596008.1| 229 KLARAYGVPERTILrK 244
                                       89**********9855 PP

>> Renin_r  Renin receptor-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.27   1.6e+03      65      82 ..      17      34 ..      11      37 .. 0.81
   2 ?    9.6   1.3   0.00024       1.4      46      81 ..     289     324 ..     279     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.27
                           Renin_r 65 lvlaliaivvalasmdPg 82
                                      +++ + +i+++la+m Pg
  gi|336252901|ref|YP_004596008.1| 17 VLIGISIITFVLANMTPG 34
                                      45677889999****998 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00024
                           Renin_r  46 kyssdYpaiFniiLwlvvvlvlaliaivvalasmdP 81 
                                        ++ dY  i  i + +  ++v+ +i++ +a a +dP
  gi|336252901|ref|YP_004596008.1| 289 IVQLDYQLIMGITMIIATMFVIGVIITDIAYAYIDP 324
                                       5788*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2485.15
//
Query:       gi|336252902|ref|YP_004596009.1|  [L=558]
Description: ABC transporter periplasmic protein [Halopiger xanaduensis SH-6]
Scores for 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-70  235.9   3.1    8.9e-70  235.5   3.1    1.1  1  SBP_bac_5   Bacterial extracellular solute-binding proteins, 
  ------ inclusion threshold ------
       0.18   11.7   3.6       0.36   10.7   3.6    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.5   3.1   9.9e-74   8.9e-70       2     374 ..     110     468 ..     109     470 .. 0.93

  Alignments for each domain:
  == domain 1  score: 235.5 bits;  conditional E-value: 9.9e-74
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       ++p +A+ ++e ++Dg+ty f + +g++F++G+++tA+Dv++sf   ++ +t+  +++ +     i+++ea+ddy++
  gi|336252902|ref|YP_004596009.1| 110 LEPKIADGMPE-EQDGTTYVFQIQEGIQFHNGDEVTASDVAHSFTAPVEEETQNAATYAM-----IESAEAIDDYQL 180
                                       79******988.********************************************9999.....************ PP

                                       EEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTTSCSSSSEE CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgggkpkldri 155
                                       ++ l++ + +f ++++ v+  +     +  +++ + +n++p+g+GP+++++f+pg++++l+r +dYw+  +p+++ i
  gi|336252902|ref|YP_004596009.1| 181 EVSLEHEYGPFTMMTMGVNVVPE----DARTEDREAFNTDPIGSGPFQFADFQPGEYVELQRWDDYWDDPQPYVETI 253
                                       ********************999....999999**********************************99******** PP

                                       EEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS- CS
                         SBP_bac_5 156 efkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyAiD 232
                                       +f+  pd+++r+a++++G+ d++  +p++++++++ ++g+ + + s ++++ ylafN++     d++vR+A+++ + 
  gi|336252902|ref|YP_004596009.1| 254 RFEAAPDDANRVAQVLAGDTDVIDTVPATEWDEVESEDGVRI-HGSRSPSYMYLAFNCNEGQTTDPDVRRAVAHSFS 329
                                       ******************************************.********************************** PP

                                       HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH.......SHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEE CS
                         SBP_bac_5 233 reeivkavlegyatpansllppsspgadeeykpayka.......ydpekAkklLkeaGykdgdggglrekklkltll 302
                                        +++v+  l+  a +  s++p+      ++  p  ++       ydp++A++lL++aG ++++             +
  gi|336252902|ref|YP_004596009.1| 330 MQQFVEDHLGAAADALVSPIPELTNEEGGWEFPT-DEwadqmpeYDPDQAEQLLNDAGVPNDW----------EPRI 395
                                       ********99999999999887555444433332.225779999*******************..........8999 PP

                                       EETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHH...HHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTC CS
                         SBP_bac_5 303 lasgspaekaiaeliqqqlkkiGikvevktvdwa...atylervkdgdfdmillgwgadypdpdnflnpflsssg 374
                                       +a+++ +++a+ae i + l+++G  ++v+++++a    ty  + ++ d+ m+llgw+++ pdpd ++++++++s+
  gi|336252902|ref|YP_004596009.1| 396 IAPEGGPREALAERIGSRLNEVGYGADVQGMSFAtlvDTY-VTGNADDYEMYLLGWTGG-PDPDVYYYNLFHESQ 468
                                       *******************************887575333.4689************98.999999999999876 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.6   4.1e-05      0.36       3      22 ..       9      28 ..       8      31 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.1e-05
                        TAT_signal  3 SRRdFLKgsAAaaAAaalgg 22
                                      +RR  L +++A+ AAa +g 
  gi|336252902|ref|YP_004596009.1|  9 TRRRVLAAGGAVSAAAIAGC 28
                                      7************9986554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 4273.53
//
Query:       gi|336252903|ref|YP_004596010.1|  [L=139]
Description: hypothetical protein Halxa_1499 [Halopiger xanaduensis SH-6]
Scores for 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-17   63.5   0.0    2.5e-17   63.2   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 !   63.2   0.0   1.4e-21   2.5e-17       3     101 ..      12     119 ..      10     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.4e-21
                                       EEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE.EEECTTT......EE-S-EEEEEEEEEEEE..TT.. CS
                            DUF296   3 hvlrlepGediveaieefarkrgiraacvlsaiGavsnvt.rladgee......kllgrfeilslsGtilp..dg.. 68 
                                       +v++le+G d+ ++ie++a + +  aa++ +a+Gav++++  ++d++e      ++++++e+ +++G+++   d+  
  gi|336252903|ref|YP_004596010.1|  12 YVASLETGADWRAEIESLADDVEADAAWF-TALGAVQDAElWFYDQDEceyypiEFDEPLEVAGCVGNVSLldDDrf 87 
                                       899**************************.**********************99999**************863389 PP

                                       EEEEEEEEETTSEEEEEEEEEE.EEEEEEEEEE CS
                            DUF296  69 lHlhvslagedgqvvgGhlaegplvaattvevv 101
                                       +H h++l++++g++++Ghl e+ +v a+ v++ 
  gi|336252903|ref|YP_004596010.1|  88 AHTHAVLSDDEGTTYAGHLNEA-TVWAGEVHMR 119
                                       *********99*********77.8767766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1146.52
//
Query:       gi|336252904|ref|YP_004596011.1|  [L=1233]
Description: DNA polymerase II large subunit [Halopiger xanaduensis SH-6]
Scores for 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 1322.4   0.0          0 1319.9   0.0    1.8  2  PolC_DP2        DNA polymerase II large subunit DP2
     0.0078   16.2  16.0       0.85    9.7   0.1    3.5  3  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.094   12.7  16.3        5.4    7.1   0.1    2.6  2  zinc-ribbons_6  zinc-ribbons
       0.19   11.8  18.1        2.4    8.3   0.5    2.9  2  DZR             Double zinc ribbon


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 ! 1319.9   0.0         0         0       1     864 []       7     985 ..       7     985 .. 0.96
   2 ?   -0.1   0.3     0.034   1.5e+02     618     674 ..    1149    1209 ..    1118    1231 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1319.9 bits;  conditional E-value: 0
                          PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirelekelsreevalkiakeia 77 
                                       +Yf++le++l+ea+++ae+a+++g dpk+evEip+A+d+adRve++lgi+gvaer+rele e+sree+al++a+++a
  gi|336252904|ref|YP_004596011.1|   7 QYFQTLESRLDEAFDVAETAKQRGGDPKPEVEIPTARDMADRVENILGIDGVAERVRELEGEMSREEAALELAEDFA 83 
                                       6**************************************************************************** PP

                          PolC_DP2  78 egkvgeaeskeeavdkavrtalalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaDy 154
                                       eg+vg++e+k+ +v+ avrta+alltegvvaAP+eGi+kv+i +nddgte+++vyyaGPiRsaGGtaqalsvLvaDy
  gi|336252904|ref|YP_004596011.1|  84 EGRVGDYETKAGKVEGAVRTAVALLTEGVVAAPIEGIDKVEILENDDGTEFVNVYYAGPIRSAGGTAQALSVLVADY 160
                                       ***************************************************************************** PP

                          PolC_DP2 155 vrkklgldrykpreeeieRyveEielYervaslqyspsdeeirlivknipveidGeatedeevsgyrdlervetnrv 231
                                       +r+ +g+d++k+r+eeieRy+eEi lY++ ++lqy+p+d+e+++i+k++p+++dGeat+deevsg+rdlerv+tn++
  gi|336252904|ref|YP_004596011.1| 161 TRALVGIDQFKARDEEIERYAEEIALYDKETGLQYTPKDKETKFIAKHMPIMLDGEATGDEEVSGFRDLERVDTNSA 237
                                       ***************************************************************************** PP

                          PolC_DP2 232 RGGmllvlaeGialkakKikkkvkklklegWewleelika............ekeekkeeeeek............. 283
                                       RGGm+lv+aeGialka+Ki++++++l+  +W+wl++li++            +          +             
  gi|336252904|ref|YP_004596011.1| 238 RGGMCLVMAEGIALKAPKIQRYTRNLDEVDWPWLQDLIDGtyyddagdeeseD----------Eaddadeesaddgd 304
                                       ****************************************8888776654331..........02233344667888 PP

                          PolC_DP2 284 ...................kevkpkekylrdliaGRpvlshpsrkGGfRLrYGRsrntglatagihPatmelldefl 341
                                                          ++v++++k+lrdliaGRpv+shp+++GGfRLrYGR+rn+g+atag+hPa+m+l+d+fl
  gi|336252904|ref|YP_004596011.1| 305 daaaedaddgtesdepqgpPRVDKSKKFLRDLIAGRPVFSHPCAEGGFRLRYGRARNHGFATAGVHPAAMHLVDDFL 381
                                       8889999999999999999********************************************************** PP

                          PolC_DP2 342 avGtqlkverPgKaaavvpvdsiegPtvklknGdvvriddveealeikkeveeildlGeiLvayGeflennhpLvpa 418
                                       a+Gtq+k+erPgKaa+vvpvdsiegPtvkl+nGdv+ridd e+alei++ ve+ildlGe+Lv+yGef+ennhpL+pa
  gi|336252904|ref|YP_004596011.1| 382 ATGTQIKTERPGKAAGVVPVDSIEGPTVKLANGDVRRIDDPEDALEIRNGVEKILDLGEYLVNYGEFVENNHPLAPA 458
                                       ***************************************************************************** PP

                          PolC_DP2 419 syveewwiqelekaaakkeaee........kpsaeealelseeldvpLhPkytylwhdisveelekLaeavaekkkl 487
                                       sy++eww+q+le+a+a+++a e         p+ eea+e++ e+d+pLhP+ytylwhdisv+ +++La avae ++ 
  gi|336252904|ref|YP_004596011.1| 459 SYTYEWWVQDLEAAGADVQALEddpridleFPDPEEAVEWAVEYDAPLHPEYTYLWHDISVDAFCNLAAAVAEGRIE 535
                                       *******************9999*****9999*****************************************9977 PP

                          PolC_DP2 488 ...........eeeklvleleeevkeiLekllvehkvke..ekivieealallkslgldleeeklekeeek...... 545
                                                  +++ lvle++++v ++Le++++eh+++e  ++i i++++++++++g++ +++  + +  +      
  gi|336252904|ref|YP_004596011.1| 536 qdgdgsvngngDDSILVLEHDDAVADALETIVLEHRQREgeDRIEIDDWRPFVRTVGCEPRQAVADGA--Alepdpd 610
                                       99*******998899*********************9862256888***********98885555433..1235566 PP

                          PolC_DP2 546 ............................................dalelvnelsglevrekaptrigaRmGRPeKsk 578
                                                                                   +a+e+vne++++evre++ptrig+RmGRPeKs+
  gi|336252904|ref|YP_004596011.1| 611 grgeeperepdtdpeeptvelertwtdddlserartwgheaegdNAIEAVNEVAPFEVRERSPTRIGNRMGRPEKSE 687
                                       778889999******************************************************************** PP

                          PolC_DP2 579 eRkmkpavhvLfpigeaggkrrsvkeaakk.......kgeieveiarrkCkkCgketlearCeeCgekteeklvCkk 648
                                       +R+++pavh+Lfpigeagg++r+v++aak+        g +ev+++r++C++C++et+++rC++C+++te+ ++C++
  gi|336252904|ref|YP_004596011.1| 688 SRDLSPAVHTLFPIGEAGGTQRNVADAAKHaetmqdtPGIVEVQVGRQRCPDCDTETFKNRCPDCNARTEPDYRCPD 764
                                       *****************************668999988999************************************ PP

                          PolC_DP2 649 ceeeve.eek....cekcekeakavkkkkidlkellekaleklgereekleelkgvkgltskekipEpleKgilRak 720
                                       c+e+ e +++    c++ce e ++v+ ++id++e++++ale++gere+++e lkgvkgl s++k+pEp+eKgilRak
  gi|336252904|ref|YP_004596011.1| 765 CDERLEpDDAgrveCDRCEVEGTCVEPREIDVNEEFRSALESVGERENAFEILKGVKGLSSTNKVPEPIEKGILRAK 841
                                       ***99855558889*************************************************************** PP

                          PolC_DP2 721 hdvsvfkdgtvRyDmtdlplthfrpkeigvsveklrelGYteDieGkplesedqivelkvqDivlsedaaeyllkva 797
                                       hdvs+fkdgtvRyDmtdlp+t++r++e++v+v +l+ lGY+ Di+G+pl++edq++elkvqDivls++aae+++k+a
  gi|336252904|ref|YP_004596011.1| 842 HDVSTFKDGTVRYDMTDLPVTAVRASELDVDVGQLQALGYDADIHGEPLTHEDQLIELKVQDIVLSDGAAEHMIKTA 918
                                       ***************************************************************************** PP

                          PolC_DP2 798 kfvDdlLeklyglerfYnvekkedLiGklviglaPHtsagvlgRiiGftkasvgyahPyfHaakRRn 864
                                       +f+DdlLe++ygle+fY++++++dL+G+lv+g+aPHtsa+++gR+iGft+a+vgyahPyfHaakRRn
  gi|336252904|ref|YP_004596011.1| 919 DFIDDLLEQYYGLEPFYKIDDRQDLVGELVFGMAPHTSAATVGRVIGFTSAAVGYAHPYFHAAKRRN 985
                                       ******************************************************************9 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.034
                          PolC_DP2  618 rrkCkkCgke....tlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkkkid 674 
                                        +++C +Cg++     l+ +C+eCg +++ +++  ++++ ++++     e + + ++k++++
  gi|336252904|ref|YP_004596011.1| 1149 ETRCLDCGEKfrrmPLTGECRECGGQVNLTVHQGSVNKYMQTAIQVAEEYDCRDYTKQRLE 1209
                                        5567777654111134456777777777755555555544433333333333333344333 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 !    6.4   1.8    0.0019       8.6      62      95 ..     726     755 ..     707     758 .. 0.74
   2 !    7.5   2.8   0.00087       3.9      68     108 ..     757     797 ..     754     799 .. 0.80
   3 !    9.7   0.1   0.00019      0.85      69     102 ..    1148    1182 ..    1123    1189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0019
                                       EEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  62 LeieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                         +e +  + rC +C++e+ ++    rCp+C+++
  gi|336252904|ref|YP_004596011.1| 726 GIVEVQVGRQRCPDCDTETFKN----RCPDCNAR 755
                                       4578888899******887755....8****985 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00087
                                       --EEEETTTS-EEECHHH.HHS-TTTSSS-EEEEESSSEEEE CS
                              HypA  68 pvkvrCreCgkefeleek.alrCpkCgsadveivsGeellvk 108
                                       +  +rC +C+++ e +++ +++C +C+ ++ ++v+ +e+ v+
  gi|336252904|ref|YP_004596011.1| 757 EPDYRCPDCDERLEPDDAgRVECDRCEVEG-TCVEPREIDVN 797
                                       6789**********9876789*****9976.56677777765 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00019
                                        -EEEETTTS-EEECHHHHHS-TTTSSS.-EEEEES CS
                              HypA   69 vkvrCreCgkefeleekalrCpkCgsa.dveivsG 102 
                                         ++rC +Cg++f+    + +C +Cg++ ++++ +G
  gi|336252904|ref|YP_004596011.1| 1148 QETRCLDCGEKFRRMPLTGECRECGGQvNLTVHQG 1182
                                        5789********97654679****99767888777 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  12.2    0.0015       6.5       2      40 ..     736     770 ..     734     788 .. 0.89
   2 ?    7.1   0.1    0.0012       5.4      14      49 ..    1147    1185 ..    1135    1192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0015
                                       --SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S--- CS
                    zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqedlkkealCpeCeqele 40 
                                        Cp+C++e+ k+     C  C+++ +    Cp+C+++le
  gi|336252904|ref|YP_004596011.1| 736 RCPDCDTETFKNR----CPDCNARTEPDYRCPDCDERLE 770
                                       6****99987665....********************98 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0012
                                        SSEEE-TTT--EEEEEEE...-SSS-S---EEEETTEEE CS
                    zinc-ribbons_6   14 geqyhCeaCqedlkkeal...CpeCeqelevlkaCgavd 49  
                                         ++++C  C e++++ +l   C eC+ +++     g+v+
  gi|336252904|ref|YP_004596011.1| 1147 RQETRCLDCGEKFRRMPLtgeCRECGGQVNLTVHQGSVN 1185
                                        47899******8887654333999998888777666665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  11.5    0.0027        12       1      48 [.     737     782 ..     728     783 .. 0.80
   2 ?    8.3   0.5   0.00053       2.4      11      40 ..    1148    1177 ..    1143    1180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0027
                               DZR   1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvdpearf...CpeC 48 
                                       Cp C +e    ++ C++C+++ ++    +rCp C+e ++p+++    C+ C
  gi|336252904|ref|YP_004596011.1| 737 CPDCDTE--TFKNRCPDCNARTEP---DYRCPDCDERLEPDDAGrveCDRC 782
                                       8888887..445679999999876...899999999998888766678887 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00053
                               DZR   11 darfCseCgtklkavaaedrCpsCgekvdp 40  
                                        +   C +Cg+k ++++    C +Cg +v++
  gi|336252904|ref|YP_004596011.1| 1148 QETRCLDCGEKFRRMPLTGECRECGGQVNL 1177
                                        5667*********9999********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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):               4  [number of targets reported over threshold]
# CPU time: 0.95u 0.29s 00:00:01.24 Elapsed: 00:00:00.46
# Mc/sec: 8058.24
//
Query:       gi|336252905|ref|YP_004596012.1|  [L=406]
Description: hypothetical protein Halxa_1501 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.078   13.3   1.4        2.9    8.2   0.3    3.3  3  Calycin_like  Calycin-like beta-barrel domain
        0.9    9.7   3.0        8.2    6.6   0.1    3.6  3  Fn3-like      Fibronectin type III-like domain
          3    7.9  12.3         15    5.7   0.4    4.3  4  Big_1         Bacterial Ig-like domain (group 1)


Domain annotation for each model (and alignments):
>> Calycin_like  Calycin-like beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3   0.00048       2.9      56     110 ..      45     102 ..      34     113 .. 0.66
   2 ?   -0.7   0.0      0.27   1.6e+03      93     112 ..     211     239 ..     173     248 .. 0.52
   3 ?    1.6   0.0     0.055   3.3e+02      20      57 ..     272     307 ..     250     347 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00048
                                       EEEEEE-SSSSSBEEEEEEEEE-TT--E....EEEEEEEEE.ETTEEEEEEEEE...E CS
                      Calycin_like  56 dnvkvtkeggsyttfsgsqkltlagggdaee.atvslsGti.sgkklnltitikvk.d 110
                                       d v vt++++ +++++  +  ++ +  ++ee ++ +l Gti sg+  ++ti i+ + +
  gi|336252905|ref|YP_004596012.1|  45 DTVDVTENETATVNVTVGDANEIPVRFGDEErLNYKLAGTIdSGDSETVTIRIDPSaT 102
                                       5677888886666666655555555555555699*******66666666777764343 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.27
                                       E.........EEETTEEEEEEEEE..ETT CS
                      Calycin_like  93 G.........tisgkklnltitikvkdga 112
                                       +         t+ ++   +t+t++ +d a
  gi|336252905|ref|YP_004596012.1| 211 ApgvfvltesTTVNESGVATVTFDLGDHA 239
                                       22233333334444444445555554444 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.055
                                       -B-S-EEEEEE-SSS-EEEEEE-GG.G------EEEEE CS
                      Calycin_like  20 sdadakvtitknedgtvnlsLknfsfgelplGditvdn 57 
                                       s a+a +t++ ++  +v+l ++  ++   +l  + v+ 
  gi|336252905|ref|YP_004596012.1| 272 SAANADITLENESSASVTLDVDAEAG--AELDAVLVSP 307
                                       22225555555555666655554443..4444444444 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.15   8.8e+02      27      42 ..      47      62 ..      43      84 .. 0.74
   2 ?    6.6   0.1    0.0014       8.2      29      46 ..      85     117 ..      79     142 .. 0.65
   3 ?    0.0   0.1      0.16   9.5e+02      28      46 ..     279     297 ..     276     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.15
                                      EEE-TT-EEEEEEEEE CS
                          Fn3-like 27 veLapGesktvtftld 42
                                      v++   e++tv++t+ 
  gi|336252905|ref|YP_004596012.1| 47 VDVTENETATVNVTVG 62
                                      7788888888888875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0014
                                       E-TT-EEEEEEEEECGG...............G CS
                          Fn3-like  29 LapGesktvtftldrkd...............l 46 
                                       +  G+s+tvt+++d+++               l
  gi|336252905|ref|YP_004596012.1|  85 IDSGDSETVTIRIDPSAtadsespisvagdasL 117
                                       6789***********994555555555555555 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.16
                                       EE-TT-EEEEEEEEECGGG CS
                          Fn3-like  28 eLapGesktvtftldrkdl 46 
                                       +L+   s+ vt+++d+++ 
  gi|336252905|ref|YP_004596012.1| 279 TLENESSASVTLDVDAEAG 297
                                       6888889999999998874 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 ?    5.7   0.4    0.0025        15       5      21 ..      53      69 ..      51      70 .. 0.90
   2 ?   -1.8   0.1      0.55   3.3e+03      25      53 ..      92     120 ..      89     124 .. 0.71
   3 ?    5.6   0.2    0.0027        16      25      52 ..     206     233 ..     202     234 .. 0.83
   4 ?    2.2   0.2     0.031   1.9e+02      36      51 ..     311     327 ..     284     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0025
                             Big_1  5 dtntltatvkDangnpv 21
                                      +t+t+++tv Dan  pv
  gi|336252905|ref|YP_004596012.1| 53 ETATVNVTVGDANEIPV 69
                                      799**********9998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.55
                             Big_1  25 tVtfsvsggalsassgtTdanGkatvtlt 53 
                                       tVt++++ +a++ s++     G a+ +++
  gi|336252905|ref|YP_004596012.1|  92 TVTIRIDPSATADSESPISVAGDASLEVS 120
                                       78888888777777776666677766665 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0027
                             Big_1  25 tVtfsvsggalsassgtTdanGkatvtl 52 
                                       +V +s++g  +++ s+t +++G+atvt+
  gi|336252905|ref|YP_004596012.1| 206 QVRLSAPGVFVLTESTTVNESGVATVTF 233
                                       57777777666699************97 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.031
                             Big_1  36 s.assgtTdanGkatvt 51 
                                       + +s++t d+nG+a+v 
  gi|336252905|ref|YP_004596012.1| 311 VrESTATVDENGTARVA 327
                                       357999********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2815.77
//
Query:       gi|336252906|ref|YP_004596013.1|  [L=112]
Description: hypothetical protein Halxa_1502 [Halopiger xanaduensis SH-6]
Scores for 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   17.9   0.1      0.004   17.2   0.0    1.4  2  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0044   16.7   1.9       0.12   12.1   0.1    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
  ------ inclusion threshold ------
      0.022   13.5   0.3      0.029   13.2   0.3    1.1  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
      0.054   13.2   1.3      0.093   12.4   1.3    1.3  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.054   13.5   1.3       0.13   12.3   1.3    1.7  1  DZR             Double zinc ribbon
      0.063   13.3   1.1        8.1    6.6   0.5    2.4  2  Rubredoxin      Rubredoxin
        0.2   11.8   3.5       0.46   10.7   3.2    1.8  1  Zn-ribbon_8     Zinc ribbon domain
       0.38   10.7   7.9        6.3    6.8   1.3    3.1  3  HalOD2          Halobacterial output domain 2
       0.48   10.2   5.1       0.82    9.5   1.1    2.3  2  zinc_ribbon_2   zinc-ribbon 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 ?   -2.8   0.0       3.1   6.1e+03      21      28 ..      15      22 ..       3      28 .. 0.53
   2 !   17.2   0.0     2e-06     0.004      63      97 ..      69     104 ..      35     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.1
                                      TT..EEEE CS
                              HypA 21 aaarkvtk 28
                                      +a+++v+ 
  gi|336252906|ref|YP_004596013.1| 15 EAVEEVHD 22
                                      33344444 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 2e-06
                                       EEEEE--EEEETTTS-EEECHHH.HHS-TTTSSS-E CS
                              HypA  63 eieevpvkvrCreCgkefeleek.alrCpkCgsadv 97 
                                       e+ e ++  rC eCg+ +++++    +Cp+Cg+++ 
  gi|336252906|ref|YP_004596013.1|  69 EFGEAHLMWRCMECGQMGDIDDGlPDECPNCGTERE 104
                                       466788999**********99744458*****9875 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   6.1e-05      0.12      10      24 ..      72      86 ..      69      89 .. 0.83
   2 ?    4.2   0.2     0.018        36      17      21 ..      96     100 ..      95     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.1e-05
                      Rubredoxin_2 10 sakwfGrCpsCgsWn 24
                                       a +++rC +Cg+++
  gi|336252906|ref|YP_004596013.1| 72 EAHLMWRCMECGQMG 86
                                      5678********987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.018
                      Rubredoxin_2  17 CpsCg 21 
                                       Cp+Cg
  gi|336252906|ref|YP_004596013.1|  96 CPNCG 100
                                       77777 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   1.5e-05     0.029     507     533 ..      76     108 ..      69     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                                       EEEETT.--EESS.....SB-TTT--BE..EEE CS
                              NRDD 507 idvCnecgykgei.....ekCpkCgseee.vev 533
                                       + +C+ecg+ g i     ++Cp+Cg e+e + +
  gi|336252906|ref|YP_004596013.1|  76 MWRCMECGQMGDIddglpDECPNCGTEREnLMY 108
                                       568******99988999999*****88776555 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 ?   12.4   1.3   4.7e-05     0.093       2      24 ..      78     100 ..      77     102 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.7e-05
                                       B-SSS--B----SSS----SSS- CS
                    DNA_RNApol_7kD   2 iCgeCgaevslkkgdpiRCkeCG 24 
                                        C+eCg+   ++ g p  C +CG
  gi|336252906|ref|YP_004596013.1|  78 RCMECGQMGDIDDGLPDECPNCG 100
                                       5*********************9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.3   6.7e-05      0.13      29      49 .]      77     100 ..      50     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                               DZR  29 drCpsCgekvdpearf...CpeCG 49 
                                        rC++Cg++ d ++     Cp+CG
  gi|336252906|ref|YP_004596013.1|  77 WRCMECGQMGDIDDGLpdeCPNCG 100
                                       566666666666665555566665 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.012        24      14      41 ..      56      83 ..      53      90 .. 0.81
   2 ?    6.6   0.5    0.0041       8.1      31      45 ..      92     104 ..      89     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.012
                                      TTBBGGGTB-TT--GGGS-TT-BBTTTB CS
                        Rubredoxin 14 akGdpdegiapgTkFedlPddWvCPdCg 41
                                      a+G   e+   g +F +    W+C +Cg
  gi|336252906|ref|YP_004596013.1| 56 AEGMSVEHARSGHEFGEAHLMWRCMECG 83
                                      5677777788888888888999999998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0041
                                       S-TT-BBTTTB-BGG CS
                        Rubredoxin  31 lPddWvCPdCgveke 45 
                                       lPd  +CP+Cg e+e
  gi|336252906|ref|YP_004596013.1|  92 LPD--ECPNCGTERE 104
                                       566..4*****9987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.2   0.00023      0.46       7      35 ..      78     102 ..      76     107 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                       Zn-ribbon_8   7 rCeeCghefevlqsisdaplta.CPeCgse 35 
                                       rC eCg    ++  i d+ l++ CP+Cg e
  gi|336252906|ref|YP_004596013.1|  78 RCMECG----QMGDI-DDGLPDeCPNCGTE 102
                                       899999....33334.5567777****984 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.15     3e+02      15      31 ..      32      50 ..      29      69 .. 0.82
   2 ?    6.8   1.3    0.0032       6.3      31      39 ..      76      84 ..      51      87 .. 0.90
   3 ?    5.5   0.2     0.008        16       1      10 [.      92     101 ..      92     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.15
                            HalOD2 15 rhGdglGe..GyrqLGayv 31
                                      ++G+ lG+  G ++ G +v
  gi|336252906|ref|YP_004596013.1| 32 KDGNELGHvrGLEKSGFFV 50
                                      6899999888999999887 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0032
                            HalOD2 31 vWkCtrCGe 39
                                      +W+C +CG+
  gi|336252906|ref|YP_004596013.1| 76 MWRCMECGQ 84
                                      7*******7 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.008
                            HalOD2   1 rPekCseCsl 10 
                                       +P++C++C+ 
  gi|336252906|ref|YP_004596013.1|  92 LPDECPNCGT 101
                                       59******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 ?    2.1   0.2     0.085   1.7e+02       2       6 ..      79      83 ..      78      85 .. 0.59
   2 ?    9.5   1.1   0.00041      0.82       2       8 ..      96     102 ..      95     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.085
                     zinc_ribbon_2  2 CpnCG 6 
                                      C +CG
  gi|336252906|ref|YP_004596013.1| 79 CMECG 83
                                      55555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00041
                     zinc_ribbon_2   2 CpnCGae 8  
                                       CpnCG+e
  gi|336252906|ref|YP_004596013.1|  96 CPNCGTE 102
                                       7777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 848.70
//
Query:       gi|336252907|ref|YP_004596014.1|  [L=97]
Description: small CPxCG-related zinc finger protein [Halopiger xanaduensis SH-6]
Scores for 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   21.4   0.0    0.00025   21.0   0.0    1.2  1  HypA           Hydrogenase/urease nickel incorporation, metal
     0.0015   17.9   1.2        0.6    9.6   0.3    2.4  2  zf-ribbon_3    zinc-ribbon domain
     0.0042   17.1   2.0          1    9.5   0.7    2.3  2  Rubredoxin     Rubredoxin
     0.0093   15.7   3.9       0.18   11.6   0.6    2.2  2  Rubredoxin_2   Rubredoxin metal binding domain
  ------ inclusion threshold ------
      0.021   14.9   0.1      0.028   14.5   0.1    1.3  1  PRC            PRC-barrel domain
      0.021   14.8   0.3      0.029   14.4   0.3    1.4  1  DZR            Double zinc ribbon
      0.056   13.2   4.3       0.44   10.3   0.6    2.1  2  zinc_ribbon_2  zinc-ribbon domain
       0.17   12.0   3.1       0.41   10.8   3.2    1.6  1  Zn-ribbon_8    Zinc ribbon domain
       0.21   11.3   0.0       0.29   10.9   0.0    1.2  1  Gar1           Gar1/Naf1 RNA binding region
       0.75    9.8   4.4       0.52   10.3   2.8    1.6  2  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi
       0.76    9.6   7.5        8.8    6.2   8.0    2.3  2  HscB_4_cys     Co-chaperone HscB tetracysteine metal binding 
       0.99    9.4   6.8        3.6    7.6   0.5    2.6  3  HalOD2         Halobacterial output domain 2


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 !   21.0   0.0   1.7e-07   0.00025      32      98 ..      21      90 ..      12      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.7e-07
                                      EEETTCT--HHHHHHHHHHHHCC.TTT..T-EEEEEEE--EEEETTTS-EEECHHH.HHS-TTTSSS-EE CS
                              HypA 32 evGelsgvepeaLefafellaegtvle..gaeLeieevpvkvrCreCgkefeleek.alrCpkCgsadve 98
                                      ++G+++g++++ L   ++   +g  +e  ++  ++ e ++  rC eCg+ ++le++   +Cp+Cg+++ e
  gi|336252907|ref|YP_004596014.1| 21 KIGQIRGIDEDGLYISLRDGIQGLSVEhvRSGQQFGEAELMWRCWECGEMGRLEDDvPDECPNCGAEREE 90
                                      689999999998888887777776666123446688999*************98766568*****98765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0032       4.7       4      10 ..      63      69 ..      61      78 .. 0.79
   2 !    9.6   0.3    0.0004       0.6       4      10 ..      80      86 ..      79      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0032
                       zf-ribbon_3  4 rCPnCGa 10
                                      rC++CG+
  gi|336252907|ref|YP_004596014.1| 63 RCWECGE 69
                                      8*****8 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0004
                       zf-ribbon_3  4 rCPnCGa 10
                                      +CPnCGa
  gi|336252907|ref|YP_004596014.1| 80 ECPNCGA 86
                                      6888887 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0044       6.5      15      41 ..      42      68 ..      38      74 .. 0.87
   2 !    9.5   0.7   0.00067         1      30      46 ..      76      90 ..      73      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0044
                                      TBBGGGTB-TT--GGGS-TT-BBTTTB CS
                        Rubredoxin 15 kGdpdegiapgTkFedlPddWvCPdCg 41
                                      +G   e++  g +F +    W+C +Cg
  gi|336252907|ref|YP_004596014.1| 42 QGLSVEHVRSGQQFGEAELMWRCWECG 68
                                      677889999999**************8 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00067
                                      GS-TT-BBTTTB-BGGG CS
                        Rubredoxin 30 dlPddWvCPdCgvekeq 46
                                      d+Pd+  CP+Cg+e+e+
  gi|336252907|ref|YP_004596014.1| 76 DVPDE--CPNCGAEREE 90
                                      78885..******9975 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.6   0.00012      0.18      10      24 ..      57      71 ..      54      74 .. 0.84
   2 ?    5.3   0.1     0.011        17      17      22 ..      81      86 ..      80      92 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                      Rubredoxin_2 10 sakwfGrCpsCgsWn 24
                                       a +++rC +Cg+++
  gi|336252907|ref|YP_004596014.1| 57 EAELMWRCWECGEMG 71
                                      6789********987 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.011
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp+Cg+
  gi|336252907|ref|YP_004596014.1| 81 CPNCGA 86
                                      666654 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.9e-05     0.028      11      32 ..      11      30 ..       4      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                                      T-EEEETTSSEEEEEEEEEEET CS
                               PRC 11 GkeVytedGeklGkVkDvvide 32
                                      G +VytedG+k+G +  +  de
  gi|336252907|ref|YP_004596014.1| 11 GATVYTEDGTKIGQIRGI--DE 30
                                      99*************987..54 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   1.9e-05     0.029      28      49 .]      61      85 ..      19      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                               DZR 28 edrCpsCgekvdpearf...CpeCG 49
                                      + rC++Cge+  +e+ +   Cp+CG
  gi|336252907|ref|YP_004596014.1| 61 MWRCWECGEMGRLEDDVpdeCPNCG 85
                                      6678888888888887777788887 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.4   0.00034      0.51       1      22 [.      63      87 ..      63      87 .. 0.85
   2 ?   10.3   0.6   0.00029      0.44       2       8 ..      81      87 ..      80      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00034
                     zinc_ribbon_2  1 fCpnCGaelq.dnakF..CpyCGtp 22
                                      +C++CG+    ++++   Cp+CG++
  gi|336252907|ref|YP_004596014.1| 63 RCWECGEMGRlEDDVPdeCPNCGAE 87
                                      699999999658888899****986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00029
                     zinc_ribbon_2  2 CpnCGae 8 
                                      CpnCGae
  gi|336252907|ref|YP_004596014.1| 81 CPNCGAE 87
                                      8888887 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.2   0.00027      0.41       7      35 ..      63      87 ..      61      92 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgse 35
                                      rC eCg e  +l    d+ + +CP+Cg+e
  gi|336252907|ref|YP_004596014.1| 63 RCWECG-EMGRL---EDDVPDECPNCGAE 87
                                      899999.55544...4555555*****95 PP

>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00019      0.29      44      65 ..       5      26 ..       1      28 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                                      -B--BTT-EEEETT--EEEE-- CS
                              Gar1 44 kkvldfnsilflenktqiGkVd 65
                                         l f++ +++e++t+iG++ 
  gi|336252907|ref|YP_004596014.1|  5 RSQLTFGATVYTEDGTKIGQIR 26
                                      46799***************96 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 ?   -3.3   0.0         6     9e+03      42      49 ..      14      21 ..      13      22 .. 0.77
   2 ?   10.3   2.8   0.00035      0.52       8      37 ..      59      85 ..      53      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6
                                      EE-HHHHH CS
                         Anti-TRAP 42 ipTaqGqk 49
                                      + T++G k
  gi|336252907|ref|YP_004596014.1| 14 VYTEDGTK 21
                                      56999987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00035
                                      HCEEE-TTTTTTSEETTE......E-TTTT CS
                         Anti-TRAP  8 eLEtkCdaCngsGkiepeeprasleCPkCs 37
                                      eL   C++C   G+ e +      eCP+C+
  gi|336252907|ref|YP_004596014.1| 59 ELMWRCWECGEMGRLEDD---VPDECPNCG 85
                                      777789999999998888...6669****8 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   8.0    0.0059       8.8       2      25 ..      63      86 ..      63      88 .. 0.84
   2 ?    2.7   0.4     0.076   1.1e+02       3       9 ..      81      87 ..      78      91 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0059
                                      B-SSS--B--SS-S---B-TTT-- CS
                        HscB_4_cys  2 rCWnCGgpgapgrgdefFCpqCRA 25
                                      rCW CG+ g   +  +  Cp C A
  gi|336252907|ref|YP_004596014.1| 63 RCWECGEMGRLEDDVPDECPNCGA 86
                                      8*****998888887888999955 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.076
                                      -SSS--B CS
                        HscB_4_cys  3 CWnCGgp 9 
                                      C nCG  
  gi|336252907|ref|YP_004596014.1| 81 CPNCGAE 87
                                      7788875 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.7   4.1e+03      14      28 ..      16      32 ..      12      35 .. 0.66
   2 ?    7.6   0.5    0.0024       3.6      31      40 ..      61      70 ..      51      73 .. 0.83
   3 ?    5.0   0.3     0.015        22       2      10 ..      78      86 ..      77      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.7
                            HalOD2 14 trhGdglGe..GyrqLG 28
                                      t +G   G+  G+++ G
  gi|336252907|ref|YP_004596014.1| 16 TEDGTKIGQirGIDEDG 32
                                      66777777666666555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0024
                            HalOD2 31 vWkCtrCGev 40
                                      +W+C +CGe+
  gi|336252907|ref|YP_004596014.1| 61 MWRCWECGEM 70
                                      7*******85 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.015
                            HalOD2  2 PekCseCsl 10
                                      P++C++C+ 
  gi|336252907|ref|YP_004596014.1| 78 PDECPNCGA 86
                                      99*****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 725.97
//
Query:       gi|336252908|ref|YP_004596015.1|  [L=308]
Description: 2-dehydropantoate 2-reductase [Halopiger xanaduensis SH-6]
Scores for 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  118.0   1.0    4.2e-34  117.4   1.0    1.3  1  ApbA_C    Ketopantoate reductase PanE/ApbA C terminal
    3.1e-30  104.8   0.1    5.3e-30  104.1   0.1    1.4  1  ApbA      Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.028   13.9   0.9      0.044   13.2   0.4    1.4  2  DUF4392   Domain of unknown function (DUF4392)


Domain annotation for each model (and alignments):
>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   1.0   7.1e-38   4.2e-34       4     124 ..     182     301 ..     179     302 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 7.1e-38
                            ApbA_C   4 larweKllinaainpltalldckngellespelralvrallkEalavaeaegvelseerleeaveavlektaanrsS 80 
                                       ++ weK ++na in++tal+   ng++le+p +++++ra+ +E  +va+a+ v+++  ++ +a+e+v+e taan+sS
  gi|336252908|ref|YP_004596015.1| 182 RRLWEKAAVNAGINAITALTATENGAVLEAP-ANDVARAATRETARVARACDVRVPNREALAAMERVAEHTAANTSS 257
                                       679*************************777.9*********************99999****************** PP

                            ApbA_C  81 MlqDveagrktEidyinGavvklAeklgvetPvnellyellkal 124
                                       M+qDv+agr+tEid+inG++v +A + g+e+P+n++l++l++a 
  gi|336252908|ref|YP_004596015.1| 258 MRQDVLAGRRTEIDAINGYIVDRAGERGLEVPTNRTLTALVRAW 301
                                       *****************************************986 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   0.1   8.9e-34   5.3e-30       2     150 ..       4     152 ..       3     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 8.9e-34
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETT..CEEEEEECEEECCH..SCCCCS-ESEEEE CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseg..geeilrppealsae..ekselepidlviv 74 
                                       ++ GaG++Gsl+++ La+  +dvtl++r++++ a+++ Glrl++ +  g    ++p++++++  ++  ++++dl iv
  gi|336252908|ref|YP_004596015.1|   4 LVFGAGSLGSLVGGLLAR-EYDVTLVGREDHVTAVRESGLRLEDGTddGALEGETPTTTRPTatTDGRNQEADLAIV 79 
                                       699*************88.99*************************664444444444444477778999******* PP

                                       -SSGGGHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE-EEEEEETTEEEECS--EEEEEES CS
                              ApbA  75 tvKayqteealeeikplldpntvvlllqNGlgheeelrealpkprvlggvtthgatregpgevhhagkgeikigel 150
                                       +vKa++t++a+++++    +  +vl+lqNGlg+ee+l+ +l + +vl+g+ t ga  +gpg+v  +g gei++g+ 
  gi|336252908|ref|YP_004596015.1|  80 AVKAFDTQAAADALATGSFD--AVLSLQNGLGNEEQLANRL-DVPVLAGTATYGALLRGPGRVACTGVGEITLGAR 152
                                       **********9999988777..5******************.66*****************************986 PP

>> DUF4392  Domain of unknown function (DUF4392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.66   3.9e+03     101     113 ..      63      75 ..      17     102 .. 0.56
   2 ?   13.2   0.4   7.3e-06     0.044      64     170 ..     163     271 ..     158     286 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.66
                           DUF4392 101 pllelqdrsaeaa 113
                                       p+++ + r++ea 
  gi|336252908|ref|YP_004596015.1|  63 PTATTDGRNQEAD 75 
                                       2223333333333 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.3e-06
                           DUF4392  64 laraLqalgkkvvivtdelnekiveaaveqgvlktevpllelqdrsaeaaivfltkdgdkkeaeaeelleklkp..d 138
                                       ++raL a g + ++ td + +   +aav++g+   +  +++ +    ea ++ ++  ++ + a   ++ ++  p  +
  gi|336252908|ref|YP_004596015.1| 163 IGRALTAAGLETTVATDMPRRLWEKAAVNAGINAITALTATENGAVLEAPANDVARAATRETARVARACDVRVPnrE 239
                                       78***************88888888899998877774334444444444444444444444444555555554567* PP

                           DUF4392 139 hliaiErpGraadGnyynmrgeniselvapld 170
                                       +l a+Er+ + +  n+ +mr   +     ++d
  gi|336252908|ref|YP_004596015.1| 240 ALAAMERVAEHTAANTSSMRQDVLAGRRTEID 271
                                       ********************998877766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2289.74
//
Query:       gi|336252909|ref|YP_004596016.1|  [L=120]
Description: nitrogen-fixing NifU domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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    1.8e-13   50.4   0.0    1.4  1  NifU      NifU-like domain


Domain annotation for each model (and alignments):
>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0     1e-17   1.8e-13      11      66 ..      25      81 ..      10      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1e-17
                                      GG--GG--EEEEEEEETT..EEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EE CS
                              NifU 11 PaLasdGGdielvdvdeg..vVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeV 66
                                      P+++++GG+  + d+d +  +V + l GaCsgC  s +t+ ++i++++ +e+pe+++V
  gi|336252909|ref|YP_004596016.1| 25 PQIQMHGGSAAIQDLDREtgEVSIALGGACSGCGISPMTI-QAIKSRMVKEIPEIEQV 81
                                      9***********99988888********************.9**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 904.64
//
Query:       gi|336252910|ref|YP_004596017.1|  [L=105]
Description: hypothetical protein Halxa_1506 [Halopiger xanaduensis SH-6]
Scores for 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   14.5   0.0      0.039   13.8   0.0    1.3  1  DUF5605   Domain of unknown function (DUF5605)
      0.081   11.9   0.2        4.8    6.0   0.0    2.0  2  DUF2891   Protein of unknown function (DUF2891)


Domain annotation for each model (and alignments):
>> DUF5605  Domain of unknown function (DUF5605)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.3e-06     0.039      10      67 ..      10      70 ..       5      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-06
                           DUF5605 10 eeyyliYfgferprerefelpegsrykveviDtWnmtieelpgvf...egkvrveLPgrpy 67
                                      e+ y +Yf + ++ +++     + ry  e++ + +  + +  + f   +g++rveLP+ py
  gi|336252910|ref|YP_004596017.1| 10 EDKYANYFPELQQAYKNAFNRMNDRYDSELVHAIDQQVLNESEPFyegDGEFRVELPENPY 70
                                      677889999999999998888888***********99988888888888***********9 PP

>> DUF2891  Protein of unknown function (DUF2891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0013        11     224     262 ..       5      41 ..       2      43 .. 0.85
   2 ?    6.0   0.0   0.00054       4.8     178     225 ..      42      89 ..      41     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0013
                           DUF2891 224 pkeefakwleaflpklaekeatllepaevsdrtDgkiaH 262
                                       ++e+f++  ++++p+l++  ++ +   +++dr D +++H
  gi|336252910|ref|YP_004596017.1|   5 DPEKFEDKYANYFPELQQAYKNAF--NRMNDRYDSELVH 41 
                                       6799*************9966665..5689*******99 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.00054
                           DUF2891 178 eleelieekakrfyakdkdapaalEPsgddFLSpaLeeadlmrrvlpk 225
                                       ++++++ ++++ fy+ d + +++l  + +d LS+ L+e +  + vl++
  gi|336252910|ref|YP_004596017.1|  42 AIDQQVLNESEPFYEGDGEFRVELPENPYDRLSGVLVEEERFETVLET 89 
                                       57789999***************99999************99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 819.95
//
Query:       gi|336252911|ref|YP_004596018.1|  [L=135]
Description: hypothetical protein Halxa_1507 [Halopiger xanaduensis SH-6]
Scores for 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  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 0.36u 0.19s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 1171.40
//
Query:       gi|336252912|ref|YP_004596019.1|  [L=271]
Description: hypothetical protein Halxa_1508 [Halopiger xanaduensis SH-6]
Scores for 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   14.6   1.8      0.055   13.8   1.8    1.3  1  OmpH           Outer membrane protein (OmpH-like)
       0.11   13.0   1.7       0.21   12.1   1.2    1.6  2  FadA           Adhesion protein FadA
       0.31   11.2   2.1       0.35   11.0   0.1    2.1  3  GIT1_C         G protein-coupled receptor kinase-interacting 
       0.37   11.1  12.8        4.3    7.7   2.7    3.7  4  DUF4164        Domain of unknown function (DUF4164)
       0.43   11.2   3.1        2.8    8.6   1.7    2.5  2  Syntaxin-6_N   Syntaxin 6, N-terminal
          1    9.9   6.2         20    5.7   0.2    3.0  3  ZapB           Cell division protein ZapB
        1.1    9.6   8.3       0.28   11.5   4.3    1.9  2  THOC7          Tho complex subunit 7
        1.5    9.4   7.7       0.24   11.9   2.3    2.4  2  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.8   2.5e-05     0.055      22      96 ..     141     222 ..     124     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS........-HHHHHH.....HHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  22 eqlekkfkklqaeleakekelqklqeelqkkakkle.......keekeqe.....lqkkeqelqqkqqqkaqelqkk 86 
                                       +    ++++lq++lea+++ l++l+++l+   + l        +     +     lq+k ++l+++ +q +  ++++
  gi|336252912|ref|YP_004596019.1| 141 TTRRFEAERLQEALEAEAERLETLVADLDPIVAWLRstaaeslQ-----QygfdeLQAKHDRLEEFCEQLETGIEER 212
                                       33344558889999999999999999997555444257544333.....356677**********999999999999 PP

                                       HHHHHHHHHH CS
                              OmpH  87 qqellkpild 96 
                                       q+ l++p+ +
  gi|336252912|ref|YP_004596019.1| 213 QERLQEPVRE 222
                                       9999988765 PP

>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.6   8.1e+03      37      51 ..      22      36 ..      10      42 .. 0.62
   2 ?   12.1   1.2   9.5e-05      0.21      12      91 ..     137     218 ..     129     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.6
                              FadA 37 kkelkakieeklakl 51
                                       +e+++++ ++++  
  gi|336252912|ref|YP_004596019.1| 22 VTEQRESVADRIDAF 36
                                      455666666666554 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 9.5e-05
                              FadA  12 Lekkeeqrykke..kakaeaaaaklakkkelkakieeklakleadsevrfykdeYkellkeyksllkelekeikeke 86 
                                       +e +++ r++ e  ++++ea+a++l+   +  + i + l+  +a+s  ++  de + +  +++++ ++le+ i+e++
  gi|336252912|ref|YP_004596019.1| 137 IEAATTRRFEAErlQEALEAEAERLETLVADLDPIVAWLRSTAAESLQQYGFDELQAKHDRLEEFCEQLETGIEERQ 213
                                       66777778766522699************************66666666667************************* PP

                              FadA  87 kkian 91 
                                       +++++
  gi|336252912|ref|YP_004596019.1| 214 ERLQE 218
                                       *9875 PP

>> GIT1_C  G protein-coupled receptor kinase-interacting protein 1 C term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.9   4.3e+03      37      44 ..      21      28 ..       7      45 .. 0.47
   2 ?   11.0   0.1   0.00016      0.35      29      93 ..     149     216 ..     131     228 .. 0.80
   3 ?   -2.6   0.1       2.5   5.6e+03      72      84 ..     253     264 ..     237     268 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.9
                            GIT1_C 37 caerIqsa 44
                                      c+   ++ 
  gi|336252912|ref|YP_004596019.1| 21 CVTEQRES 28
                                      22222222 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00016
                            GIT1_C  29 ekkesfvpcaerIqsaVqdlvalfp..enlseetlrt.aLkqLtssaerLqeeCeelqeaeseskedi 93 
                                       + +e+    aer ++ V+dl  +++   +++ e+l++   ++L+++  rL+e Ce+l++  +e +e +
  gi|336252912|ref|YP_004596019.1| 149 RLQEALEAEAERLETLVADLDPIVAwlRSTAAESLQQyGFDELQAKHDRLEEFCEQLETGIEERQERL 216
                                       556778889***********9999987888999999966******************99444444443 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.5
                            GIT1_C  72 aerLqeeCeelqe 84 
                                       + r+  eC+++++
  gi|336252912|ref|YP_004596019.1| 253 C-RICRECQRTVR 264
                                       3.67778887765 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.095   2.1e+02      30      67 ..       8      45 ..       3      48 .. 0.70
   2 ?    7.7   2.7    0.0019       4.3      16      47 ..     135     164 ..     120     170 .. 0.82
   3 ?    6.3   0.0    0.0052        12       4      34 ..     189     219 ..     187     229 .. 0.87
   4 ?   -3.6   0.0       6.4   1.4e+04      60      74 ..     247     261 ..     245     263 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.095
                           DUF4164 30 aerkrdeleaeiealgedrsRLaeeLdqaearaarlee 67
                                      +e ++ ++ + +e ++e r+  a+++d+ e  aar+ e
  gi|336252912|ref|YP_004596019.1|  8 TETATTDVHRALECVTEQRESVADRIDAFESFAARVRE 45
                                      45566777778888888888888888877766666654 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0019
                           DUF4164  16 aldsLEkavdrrleaerkrdeleaeiealged 47 
                                       a+  +E+a +rr+eaer +++leae e+l+  
  gi|336252912|ref|YP_004596019.1| 135 AV--IEAATTRRFEAERLQEALEAEAERLETL 164
                                       44..79**********************9875 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0052
                           DUF4164   4 keleaaltrLeaaldsLEkavdrrleaerkr 34 
                                       +el+a  +rLe+  ++LE+ +++r e+ ++ 
  gi|336252912|ref|YP_004596019.1| 189 DELQAKHDRLEEFCEQLETGIEERQERLQEP 219
                                       57889999****************9998865 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 6.4
                           DUF4164  60 araarleevnrEvsr 74 
                                       a ++rl +++rE +r
  gi|336252912|ref|YP_004596019.1| 247 ATLTRLCRICRECQR 261
                                       567888899999876 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 ?    1.0   0.0      0.29   6.5e+02      40      71 ..       9      40 ..       2      61 .. 0.75
   2 ?    8.6   1.7    0.0012       2.8      14      95 ..     122     205 ..     110     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.29
                      Syntaxin-6_N 40 detrteLrkalrsiewdledLeetvriveknp 71
                                      + ++t++++al+ + ++ e   + +++ e+  
  gi|336252912|ref|YP_004596019.1|  9 ETATTDVHRALECVTEQRESVADRIDAFESFA 40
                                      56778888888888888888888887777654 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0012
                      Syntaxin-6_N  14 lnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpsk..fkidekelsrrrafv 88 
                                       l ++++  ++ +    ++ ++++ e +++++ L+++ + +e+ + dL+  v+ +++  ++   +   +el+ +++ +
  gi|336252912|ref|YP_004596019.1| 122 LTTNATWTAELKTAVIEAATTRRFEAERLQEALEAEAERLETLVADLDPIVAWLRSTAAEslQQYGFDELQAKHDRL 198
                                       444444444444333333345899***************************99988664334566667777777666 PP

                      Syntaxin-6_N  89 eevreev 95 
                                       ee+ e++
  gi|336252912|ref|YP_004596019.1| 199 EEFCEQL 205
                                       6666655 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.79   1.8e+03      43      64 ..      14      35 ..       3      36 .. 0.75
   2 ?    5.7   0.2    0.0089        20      45      70 ..     144     169 ..     125     170 .. 0.73
   3 ?    5.2   1.0     0.013        29      36      63 ..     190     217 ..     178     224 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.79
                              ZapB 43 eleeeneqlkeereawqerlkk 64
                                       + + +e   e+re++ +r+++
  gi|336252912|ref|YP_004596019.1| 14 DVHRALECVTEQRESVADRIDA 35
                                      4557778888999999999985 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0089
                              ZapB  45 eeeneqlkeereawqerlkkLLgkle 70 
                                       + e e+l+e  ea  erl++L++ l+
  gi|336252912|ref|YP_004596019.1| 144 RFEAERLQEALEAEAERLETLVADLD 169
                                       36788899999999999999998876 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.013
                              ZapB  36 elkeenreleeeneqlkeereawqerlk 63 
                                       el+ + ++lee  eql++  e+ qerl+
  gi|336252912|ref|YP_004596019.1| 190 ELQAKHDRLEEFCEQLETGIEERQERLQ 217
                                       4444444444444444444444444443 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.86   1.9e+03      33      59 ..      17      43 ..       3      46 .. 0.67
   2 ?   11.5   4.3   0.00013      0.28      31     100 ..     133     218 ..      99     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.86
                             THOC7 33 steeeleqlkedllldfaafelsierl 59
                                      +  e + + +e++  ++ afe+  +r+
  gi|336252912|ref|YP_004596019.1| 17 RALECVTEQRESVADRIDAFESFAARV 43
                                      455666777888888888888887775 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00013
                             THOC7  31 a..............esteeeleqlkedllldfaafelsie..rlqllakanerereryeaekeeieseieavreei 91 
                                                      e+ +e+le+  e+l++ +a ++  ++  r+ + ++  +   ++++a+++++e+ +e++++ i
  gi|336252912|ref|YP_004596019.1| 133 KtavieaattrrfeaERLQEALEAEAERLETLVADLDPIVAwlRSTAAESLQQYGFDELQAKHDRLEEFCEQLETGI 209
                                       355555554444444445555555555555555555555559999999999999*********************** PP

                             THOC7  92 eelkaqLee 100
                                       ee +++L+e
  gi|336252912|ref|YP_004596019.1| 210 EERQERLQE 218
                                       *******98 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.6   3.5e+03      18      33 ..      25      40 ..      10      72 .. 0.56
   2 ?   11.9   2.3   0.00011      0.24      32      82 ..     112     163 ..     104     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.6
                     T7SS_ESX_EspC 18 khdevaaeiasavaaa 33
                                      + ++va++i++  + a
  gi|336252912|ref|YP_004596019.1| 25 QRESVADRIDAFESFA 40
                                      4445555555444433 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                     T7SS_ESX_EspC  32 aa.agasaavldshGpicaatndavaaaeaarraagealaaasteLadkLra 82 
                                       a  +++ a  l++  +++a++++av +a ++rr ++e+l++a++  a++L +
  gi|336252912|ref|YP_004596019.1| 112 AEfSRDIAVALTTNATWTAELKTAVIEAATTRRFEAERLQEALEAEAERLET 163
                                       33367888999999*****************************999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); 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):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2025.90
//
Query:       gi|336252913|ref|YP_004596020.1|  [L=317]
Description: hypothetical protein Halxa_1509 [Halopiger xanaduensis SH-6]
Scores for 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  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); 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:                         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 0.21s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2410.46
//
Query:       gi|336252914|ref|YP_004596021.1|  [L=254]
Description: PHP domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   77.9   0.3    1.9e-21   75.5   0.2    2.1  2  PHP_C     PHP-associated
    2.8e-05   24.5   0.0    6.5e-05   23.3   0.0    1.5  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 ?   -0.5   0.0      0.11     1e+03       6      19 ..      53      66 ..      50      68 .. 0.87
   2 !   75.5   0.2   2.1e-25   1.9e-21       1      56 []     141     205 ..     141     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.11
                             PHP_C  6 rArrfAeklglpgt 19
                                      rA+++A ++gl g+
  gi|336252914|ref|YP_004596021.1| 53 RAAELAPEYGLIGI 66
                                      8*********9887 PP

  == domain 2  score: 75.5 bits;  conditional E-value: 2.1e-25
                             PHP_C   1 geaNrrArrfAeklglpgtgGSDAHrleeVGrayTef....eepia.....tpdelleairegrt 56 
                                       g++NrrAr+fA+++g+p +g+SDAH+l++VG+ayTe+    +++++     +  el+eai egrt
  gi|336252914|ref|YP_004596021.1| 141 GYRNRRARTFARRRGYPEIGASDAHYLPNVGKAYTEVivtpDAENPtradiDGGELVEAILEGRT 205
                                       69************************************9874444444544449*********98 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   7.3e-09   6.5e-05       1      74 [.      10     117 ..      10     185 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 7.3e-09
                                       EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                               PHP   1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse.... 73 
                                       d+HvH++ s   g   +e +++ a++ gl+ + iTDh+++ + +++++ a    + g+  i G+e++ + ++     
  gi|336252914|ref|YP_004596021.1|  10 DFHVHSDDSYD-GHEPVELILEHAADIGLDGVVITDHDEIGESLRAAELA---PEYGLIGIPGVEVSTKHGHLlaig 82 
                                       79*******65.55556******************************999...445899999999655555445555 PP

                                       ................................... CS
                                       ..................................x RF
                               PHP  74 ..................................k 74 
                                                                         +
  gi|336252914|ref|YP_004596021.1|  83 veerpepgrpvgetvqtvrdlggiaivphpfqrsR 117
                                       55555555555555555555555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1979.71
//
Query:       gi|336252915|ref|YP_004596022.1|  [L=492]
Description: phosphoesterase RecJ domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-19   69.3   1.2      1e-18   68.0   1.2    1.7  1  DHHA1     DHHA1 domain
  ------ inclusion threshold ------
      0.014   15.7   0.4      0.055   13.7   0.4    2.0  1  DHH       DHH family
      0.062   13.5   0.0       0.15   12.3   0.0    1.6  1  PGDYG     PGDYG protein


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 !   68.0   1.2   1.8e-22     1e-18       7     138 .]     355     487 ..     350     487 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.8e-22
                                       HHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHG....BTTCEEEEEEEE CS
                             DHHA1   7 erkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklkskl....kkpvivfvakee 79 
                                        r  l+++  +l+e +  +++e++ ++     +   ++++  + ++ +++gi+a++   +      kp+++f+ k++
  gi|336252915|ref|YP_004596022.1| 355 ARTLLRNHRRNLSEGIDLVTREGVTHE-----DNVQWFHAG-DRIRETIVGIVAGMAMGNEgisrSKPIVAFAQKND 425
                                       555566666667888888888888876.....777777777.9**************9966677455*********9 PP

                                       CTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHHH CS
                             DHHA1  80 gdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGagipaekleealealeeai 138
                                       +  vkvsar + +    g+d++ ++ ea++++ g GGGHd AaGa++p+++ ee++e ++e++
  gi|336252915|ref|YP_004596022.1| 426 E-AVKVSARGTHSlvrkGLDLSVVMGEASRAVDGDGGGHDVAAGATVPIGREEEFVEMADEIV 487
                                       9.*********99**********************************************9976 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   9.2e-06     0.055       7      58 ..      28     115 ..      24     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.2e-06
                                       ECSSSHHHHHH.HHHHHH................................CECS--TCGGCGCCHHCCCSE.EEEEE CS
                                       xxxxxxxxxxx.xxxxxx................................xxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                               DHH   7 hknpDtDsigS.aialan................................llvDhneksqavegeakeeae.dviii 49 
                                         + D+D+++S aia ++                                l  D+++ + + +g+ ++ ++ + +i 
  gi|336252915|ref|YP_004596022.1|  28 ASHIDADGLTSaAIAAQAleraaisfetvfekqldedaiadiaatdydtvLFTDFGSGQLDIIGDREDAGDfTPVIA 104
                                       6899*******777777777777777777777777777777777777777699999999999998776666245777 PP

                                       E-S---S..S- CS
                                       xxxxxxx..xx RF
                               DHH  50 DHHrlge..ef 58 
                                       DHH++++  + 
  gi|336252915|ref|YP_004596022.1| 105 DHHQPADreTE 115
                                       99999854422 PP

>> PGDYG  PGDYG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.5e-05      0.15      12      66 ..     378     432 ..     371     450 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                             PGDYG  12 vtgetGdrWvvsrerfdakyvalkpglarGeagayrnrPievlakemdeafsiar 66 
                                       vt e   +W    +r  +  v + +g+a+G++g  r +Pi+ +a++ dea++++ 
  gi|336252915|ref|YP_004596022.1| 378 VTHEDNVQWFHAGDRIRETIVGIVAGMAMGNEGISRSKPIVAFAQKNDEAVKVSA 432
                                       56666778999999999999******************************99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.52u 0.21s 00:00:00.73 Elapsed: 00:00:00.36
# Mc/sec: 4047.00
//
Query:       gi|336252916|ref|YP_004596023.1|  [L=249]
Description: Uroporphyrinogen III synthase HEM4 [Halopiger xanaduensis SH-6]
Scores for 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-42  146.1   2.4    1.3e-42  145.8   2.4    1.0  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 !  145.8   2.4     7e-47   1.3e-42       4     230 ..      25     238 ..      22     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 145.8 bits;  conditional E-value: 7e-47
                                       HHHHHHTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEESS CS
                              HEM4   4 aealearGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealkreeedvkalaslkvaavG 80 
                                       +++le++Gaep+  P++ +e+       +a+ +    ++ d+++ftS+++ e ++ea         ++ + +v+a+G
  gi|336252916|ref|YP_004596023.1|  25 VALLEELGAEPIPDPMLAVEA------TDATPR----SDADYVVFTSKTGAELVSEAGW-------KSGEETVCAIG 84 
                                       789******************......444443....579*************999988.......778889***** PP

                                       HHHHHHHHHTT---SEE-..SSSHHHHGGGS-.---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHH CS
                              HEM4  81 paTaraLeelglrvdlvpseegtaegLaeelaeslagkrvlllrgeiarddlaegLeergaevdevevYetvpaeee 157
                                       paTa+aL++ g+ vdlvp+ ++t+ gL+++l+ ++ g rv + r++++++ l egLe +ga v+e ++Y+ v++e+ 
  gi|336252916|ref|YP_004596023.1|  85 PATADALRAEGYAVDLVPE-AFTSSGLVAALEDRVDGARVEVARSDHGSPVLLEGLEDAGAYVHETILYRLVRPEGS 160
                                       ******************9.*************9999**********************************777665 PP

                                       HHHHHHHHHTT--SEEEESSHHHHHHHHHH-S-HH......HHHCTSEEEEESHHHHHHHHHTT---SEEETS--HH CS
                              HEM4 158 peelkealkagevdavvftSpstvrnllellkdeg......delkevkvaaiGptTaealkklglkvdvvaeeptae 228
                                         e  e+  ag++d+ +ftS+ tv+++le++ ++g      ++l++++v +iG+ T+e+++++g+ vd+va+e+t e
  gi|336252916|ref|YP_004596023.1| 161 G-ESAELAAAGDLDVACFTSSLTVEHFLEAAAERGirddalAGLETATVGVIGEPTRETAEDCGIDVDLVASEATFE 236
                                       5.55666669***********************99****************************************99 PP

                                       HH CS
                              HEM4 229 gl 230
                                        l
  gi|336252916|ref|YP_004596023.1| 237 RL 238
                                       87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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 0.20s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 2150.28
//
Query:       gi|336252917|ref|YP_004596024.1|  [L=271]
Description: uroporphyrin-III C-methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-55  188.1   0.6    2.5e-55  187.7   0.6    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 !  187.7   0.6   1.4e-59   2.5e-55       1     212 [.      12     223 ..      12     224 .. 0.94

  Alignments for each domain:
  == domain 1  score: 187.7 bits;  conditional E-value: 1.4e-59
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       ++ylVG GpGdp llTvrA ++l++adv+l d+   ++i+  l++e+    +  gk ++ +++++ ei+++l+e++r
  gi|336252917|ref|YP_004596024.1|  12 TVYLVGSGPGDPGLLTVRAKALLEDADVILHDRLPGPKIIGMLPDER---CEYVGKHAQGERTTQSEINDRLVEYAR 85 
                                       59*******************************77*****9888775...44445555667888************* PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.....lpglake 149
                                       +gk+Vv+l++GD +v+g+g+e++e l++  +g+++ev+PGv+s+ aa+a +gip+t+++ ++sv+     ++++++e
  gi|336252917|ref|YP_004596024.1|  86 DGKKVVRLKGGDSFVFGRGGEEAEYLAN--HGVPFEVVPGVTSAIAAPAVVGIPVTHRDHASSVSfvtghEDPTKDE 160
                                       ****************************..****************************************888899* PP

                      TP_methylase 150 eereleallangdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                       ++ ++e l+++g+t+v+l+++++l++  ++L+ea +  +t pva+ver+++++++v +gtle++
  gi|336252917|ref|YP_004596024.1| 161 SAVDWESLAEAGGTIVVLMGVKRLPDYTAALREAgMSSET-PVALVERGTWPEQQVATGTLETI 223
                                       **********************************988855.********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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 0.21s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 2344.11
//
Query:       gi|336252918|ref|YP_004596025.1|  [L=396]
Description: porphobilinogen deaminase [Halopiger xanaduensis SH-6]
Scores for 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-66  222.4   0.5    1.7e-52  177.9   0.2    2.1  2  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    5.3e-09   36.3   0.0    1.3e-08   35.1   0.0    1.6  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
  ------ inclusion threshold ------
      0.021   13.7   0.0       0.39    9.5   0.0    2.1  2  DUF917           Protein of unknown function (DUF917)


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 !  177.9   0.2   2.9e-56   1.7e-52       1     150 [.       7     159 ..       7     166 .. 0.95
   2 !   42.8   0.0   6.8e-15   4.1e-11     151     199 ..     214     263 ..     201     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 177.9 bits;  conditional E-value: 2.9e-56
                    Porphobil_deam   1 irigtRkSkLAlaqaelvaeaLke.eeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKD 76 
                                       +r++tR+S+LA+ qa+lv+eaL++ + eve+vt++t+GD+i+d+ ++++g++g+F++el+e++leg++d a+hS+KD
  gi|336252918|ref|YP_004596025.1|   7 LRLATRGSTLARRQATLVKEALEDrRYEVELVTVETTGDQIRDELIHQLGKTGAFVRELDERVLEGDLDGAIHSMKD 83 
                                       699*******************6644559************************************************ PP

                    Porphobil_deam  77 lptelpeglelaavlkredprDvlvv..kssleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkld 150
                                       +pte+p++l++aav++r  p Dvlv+  +s+leelpega+vgTsSlRR+aql + r dl+v++lRGnvdtRl+kl 
  gi|336252918|ref|YP_004596025.1|  84 MPTEQPDDLVTAAVPERGRPGDVLVTpdSSTLEELPEGATVGTSSLRRRAQLLSERDDLQVEPLRGNVDTRLEKLL 159
                                       *************************975449*******************************************95 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 6.8e-15
                    Porphobil_deam 151 egeydaiiLAaAGLkRlgleeri.sevlspeellpavgQGalavevrked 199
                                       e+eydai+LA AGL+R gl++ +  + l++++++pa+gQGalav++ +++
  gi|336252918|ref|YP_004596025.1| 214 ETEYDAIVLAHAGLERSGLAHYVdYQELPTSTFVPAPGQGALAVTATDGE 263
                                       469******************996445*****************988764 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 !   35.1   0.0   2.1e-12   1.3e-08       4      52 ..     281     328 ..     279     350 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.1e-12
                                       HHHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S-EEE CS
                   Porphobil_deamC   4 vlaERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglksavee 52 
                                        ++ER++l+eL+GGC +P+G ya+v+++  +  + +v ++dg++s+   
  gi|336252918|ref|YP_004596025.1| 281 TTVERTILAELGGGCIAPVGIYAVVQGEY-VHADVTVFDRDGEESVTGA 328
                                       699*********************99655.9***********8754433 PP

>> DUF917  Protein of unknown function (DUF917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.012        71      11      88 ..       7      88 ..       3      98 .. 0.75
   2 ?    9.5   0.0   6.6e-05      0.39      38     120 ..     233     313 ..     215     321 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.012
                                      HHTTTT-SS-HHHHHHHHTT-SBTT-.-EEEE-GGG--S...EE..EEEEEEE-HHH.HTT-SS-HH....HHHHHHHH CS
                            DUF917 11 avLGtGGGGspysgylllrqaleegk.svrvvsldelpd...dalvvvvgamGsptv.ieeklpsgdelleavealekl 84
                                        L+t G   +  ++ l+++ale ++ +v++v+++   d   d+l+   g  G+    + e++++gd l  a+++++++
  gi|336252918|ref|YP_004596025.1|  7 LRLATRGSTLARRQATLVKEALEDRRyEVELVTVETTGDqirDELIHQLGKTGAFVReLDERVLEGD-LDGAIHSMKDM 84
                                      55777777778889999******88669*******99999999999999999997651455555544.77788888776 PP

                                      HT-- CS
                            DUF917 85 lgrk 88
                                        ++
  gi|336252918|ref|YP_004596025.1| 85 PTEQ 88
                                      6555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 6.6e-05
                                       EEEE-GGG--SEE..EEEEEEE-HHHHTT-SS-HH....HHHHHHHHHT--EEEEE-SSSSCCHHHHHHHHHHHHT- CS
                            DUF917  38 vrvvsldelpddalvvvvgamGsptvieeklpsgdelleavealekllgrkidavislEiGGlNglvallaaaklgl 114
                                          v+ +elp ++ +v++   G+ +v++    + +++  a+++    ++++++ +i +E+GG+  ++++ + a ++ 
  gi|336252918|ref|YP_004596025.1| 233 AHYVDYQELPTST-FVPAPGQGALAVTATDGETARDIQSAIDHPRSRVETTVERTILAELGGG-CIAPVGIYAVVQG 307
                                       5779999***998.7778889*****************************************5.5556555555555 PP

                                       EEESB- CS
                            DUF917 115 pvvDaD 120
                                         v aD
  gi|336252918|ref|YP_004596025.1| 308 EYVHAD 313
                                       555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.35
# Mc/sec: 3423.34
//
Query:       gi|336252919|ref|YP_004596026.1|  [L=121]
Description: globin [Halopiger xanaduensis SH-6]
Scores for 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-23   81.8   0.2    4.6e-23   81.7   0.2    1.0  1  Bac_globin   Bacterial-like globin
    0.00013   21.9   0.2     0.0003   20.7   0.2    1.7  1  Protoglobin  Protoglobin
  ------ inclusion threshold ------
        0.1   12.8   0.3        1.1    9.5   0.1    2.3  2  Imm74        Immunity protein 74


Domain annotation for each model (and alignments):
>> Bac_globin  Bacterial-like globin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.2   7.7e-27   4.6e-23       1     119 [.       4     116 ..       4     118 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 7.7e-27
                                       -HHHHHTHHHHHHHHHHHHHHHHHT-CCCCCCGGGTTSSHHHHHHHHHHHHHHHTTSSSHHHHHHSS-.HHHHHTTS CS
                        Bac_globin   1 tlydaiGgeatveelvdrfYervdedeeealseifsgtdlegsreklveFlvqalgGPelYverrGhPrlrkrHapf 77 
                                       tlyd +Gge+++ ++vdrfY+rv +de+    + f+  d++++r+++ +F+  + gGP  Y+   G   +++ H  +
  gi|336252919|ref|YP_004596026.1|   4 TLYDRLGGEDAIAQVVDRFYDRVMADEQ--VAHYFEDVDMQKQRAHQTQFISSVTGGPVEYT---GEE-MEAAHEEM 74 
                                       79**************************..999****************************6...998.******** PP

                                       --BHHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHH CS
                        Bac_globin  78 eitaaerdawlkhlaeAleetgvssedreeklellealahaa 119
                                       +i +a++ a++ hl + l+e +v +edr++ le +e  ++++
  gi|336252919|ref|YP_004596026.1|  75 GISPADFKAIATHLDDTLAEFDVGEEDRQAVLEAIESYRDDI 116
                                       ***********************************9988765 PP

>> Protoglobin  Protoglobin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2   4.9e-08    0.0003      30      80 ..      12      61 ..       8     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.9e-08
                                      HHCHHHHHHHHHHHHCTSHHHHHHHCHHCHHHHHHHHHHHHHHHCCCSSCC CS
                       Protoglobin 30 ealipavvdafYekllsfpetarifetssqierlkdflksyllklfsgpfd 80
                                      e++i +vvd+fY++++  ++ a++fe+   +++ ++++ +++++++ gp+ 
  gi|336252919|ref|YP_004596026.1| 12 EDAIAQVVDRFYDRVMADEQVAHYFED-VDMQKQRAHQTQFISSVTGGPVE 61
                                      6899***********************.88888888888999988888842 PP

>> Imm74  Immunity protein 74
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.062   3.7e+02      44      70 ..      66      92 ..      62      97 .. 0.80
   2 ?    9.5   0.1   0.00019       1.1      53      72 ..      96     115 ..      84     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.062
                             Imm74 44 eWdaPhesepitkeerqeIveaiekef 70
                                      e +a+he+  i++++  +I     + +
  gi|336252919|ref|YP_004596026.1| 66 EMEAAHEEMGISPADFKAIATHLDDTL 92
                                      67999*********9999877666655 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00019
                             Imm74  53 pitkeerqeIveaiekeftk 72 
                                        +++e+rq+++eaie ++++
  gi|336252919|ref|YP_004596026.1|  96 DVGEEDRQAVLEAIESYRDD 115
                                       689*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 978.32
//
Query:       gi|336252920|ref|YP_004596027.1|  [L=778]
Description: Nitric-oxide reductase [Halopiger xanaduensis SH-6]
Scores for 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-59  200.9  48.9    3.2e-59  200.9  48.9    1.5  2  COX1      Cytochrome C and Quinol oxidase polypeptide I
     0.0071   16.6   2.6     0.0071   16.6   2.6    2.6  2  DUF2871   Protein of unknown function (DUF2871)


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       0.3   2.7e+03     158     168 ..     226     236 ..     220     254 .. 0.40
   2 !  200.9  48.9   3.6e-63   3.2e-59       6     431 ..     277     721 ..     273     722 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHH CS
                              COX1 158 avlatailill 168
                                       +v+a+++l+  
  gi|336252920|ref|YP_004596027.1| 226 SVIAMVLLVGG 236
                                       22222222211 PP

  == domain 2  score: 200.9 bits;  conditional E-value: 3.6e-63
                                       HHHHHHHHHHHHHHHHHHHHHHCTCT...............-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH CS
                              COX1   6 ylilalvlllvggllgllirlqlafp...............dletynqlrtlHgnlmiflfatpfilgfgnylvpll 67 
                                       +++++ +l+++++llg l++++++                 + + ++ +rt+H+ l i+++at + lg+g++l+pll
  gi|336252920|ref|YP_004596027.1| 277 FVLIGALLFFAQTLLGGLLAHYYVERddffglhefigidilQILPWSIARTWHVDLGILWIATIW-LGAGLFLAPLL 352
                                       789999*****************6433333333344444445588********************.*********** PP

                                       HCTSS-S-HHHHHHHHHHHHHHHHHHHHHHH...CS..........S-STTTTTTTC.SHHHHHHHHHHHHHHHHH. CS
                              COX1  68 lgardlafprlnalsfwlvvlgvvllllsll...ga..........attgwteYaplsevdlwllglllvvvssll. 130
                                       +g+++  +   ++ ++ ++++ +v++l+++    ++          +++g  eY++   +++w+ gll++    +l 
  gi|336252920|ref|YP_004596027.1| 353 TGREPRKQALYVKGLIGALLVVAVGALAGIWlgiNNffdgqlwwllGNEGL-EYLE--IGRVWQAGLLVG----FLg 422
                                       *********9988888866666666555554444225667799999****5.***9..**********99....443 PP

                                       HHHHHHHHHHH..HHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT-SSSCE-HHHHHHHHHHH CS
                              COX1 131 gainfivtilk..rrapgmtvaklplfvwavlatailillalpvlalalllllldrslgkffspgdplldqhlfWff 205
                                       + + +++ + +   r+p   +a  +++   v+a   ++ll+++++ ++  +++              ++ ++++W++
  gi|336252920|ref|YP_004596027.1| 423 WTALVARGFKPllDREPRYGLA--HMI---VYAGGSIGLLFMAGFLYTPRTNI--------------VVTEFWRWWV 480
                                       5556666665543445544444..444...77888888899999999988988..............9********* PP

                                       HTHHH.HHHHHHHHHHHHHHHHHHHT..SCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTH CS
                              COX1 206 gHpeV.yililpalgivyyilpkfag..rplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfsllia 279
                                       +H++V +++++++l++++  l+ + +  r+  ++k+++++++l++  ++++  HH+++ glpe++  +gsvfs++++
  gi|336252920|ref|YP_004596027.1| 481 VHMWVeGVFEFFILVVISLTLVSM-NllRKKSAEKAVIFQAALVMGSGIIGVSHHYWWAGLPEVWLPIGSVFSTIEF 556
                                       ***********************9.559999********************************************** PP

                                       HHHHHCCCHHHHCC..TTS-CH.C..HHHHHHHHHHHHHH.HHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTH CS
                              COX1 280 vPsglkvfnwlatl..wrgsir.f..ktpmlfflgfavlf.iigGltGvllalpsvnyvvhntywvvaHfHlvllga 350
                                       vP+++ ++  l+    + g+ + f  + +++f+++++v++ +++G+ G++++lp + y+  +ty++vaH+H +++ga
  gi|336252920|ref|YP_004596027.1| 557 VPLLFILYEALGQYraVDGASKdFpyRMVFYFIVASSVWNfFGAGVIGFFINLPVISYFQSGTYLTVAHAHGAMFGA 633
                                       *****8888877777744444444459999999999***************************************** PP

                                       HHHHHHHHHHHHHHHHH.SB--HHHHHHHHHHHHHHHHHHHHH.HHHHHHHTTHB.........SSSST--SCCCCH CS
                              COX1 351 vvfllfaaiyyllpklt.grmlserlaklhfwllfiGlvlmfl.pmhilGllgmp.........rraadyksfletv 416
                                       ++fl++++ +y+l   t    +ser   ++fwl ++Gl+lm + +++++G+l +          +r+     ++++ 
  gi|336252920|ref|YP_004596027.1| 634 FGFLAMGMAVYILRVTTrESHWSERRLTWSFWLCNVGLALMLFlSLLPVGFLQLEtaftqgyaaARSL----EFYSG 706
                                       *************666655588******************9999********7774555444433333....45566 PP

                                       HHCHHHHHHHHHHHH CS
                              COX1 417 pelqplnvlrtiggv 431
                                         +q+l +lr+ g++
  gi|336252920|ref|YP_004596027.1| 707 GLIQTLFWLRMPGDT 721
                                       79999****999986 PP

>> DUF2871  Protein of unknown function (DUF2871)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.8     0.032   2.9e+02      42      86 ..     481     527 ..     442     541 .. 0.72
   2 !   16.6   2.6   7.9e-07    0.0071      13      98 ..     597     689 ..     586     707 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.032
                           DUF2871  42 tHllvLGfvvfLlvlllekl...fklseekkfkkffivYniglvltvv 86 
                                       +H+ v G++ f+++++++ +   ++l ++k+ +k  ++++++lv+  +
  gi|336252920|ref|YP_004596027.1| 481 VHMWVEGVFEFFILVVISLTlvsMNLLRKKSAEK-AVIFQAALVMGSG 527
                                       5777777765544444332211266666666666.7788888877554 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 7.9e-07
                           DUF2871  13 ilgllsGvfyReftklneftgktqLsvvHtHllvLGfvvfLlvllleklfkls......eekkfkkffivYniglvl 83 
                                       ++g     f+ ++  ++ f++ t L+v H+H  ++G + fL + +   +++++      +e+++++ f++ n+gl+l
  gi|336252920|ref|YP_004596027.1| 597 FFGAGVIGFFINLPVISYFQSGTYLTVAHAHGAMFGAFGFLAMGMAVYILRVTtreshwSERRLTWSFWLCNVGLAL 673
                                       444433336678888999*************999999988865443333333311123468999************9 PP

                           DUF2871  84 tvv.mmlvrGilqvlg 98 
                                       ++   +l  G+lq+  
  gi|336252920|ref|YP_004596027.1| 674 MLFlSLLPVGFLQLET 689
                                       9751566789998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (778 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.25s 00:00:00.91 Elapsed: 00:00:00.40
# Mc/sec: 5823.94
//
Query:       gi|336252921|ref|YP_004596028.1|  [L=390]
Description: integral membrane sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.3   0.0    3.3e-15   56.6   0.0    1.3  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.1e-08   34.9   3.0    2.4e-08   33.7   3.0    1.6  1  HisKA_4TM    Archaeal 4TM region of histidine kinase
    1.9e-08   34.3   0.0    4.8e-08   33.0   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain
    7.1e-05   22.8   1.0    0.00014   21.8   0.2    1.9  2  HisKA        His Kinase A (phospho-acceptor) domain
    0.00077   19.3   0.0     0.0014   18.5   0.0    1.3  1  HATPase_c_5  GHKL domain
     0.0082   15.8   0.2      0.016   14.9   0.2    1.4  1  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain
     0.0097   15.7   0.0      0.018   14.9   0.0    1.3  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
       0.59    8.3   0.9       0.85    7.8   0.9    1.2  1  OATP         Organic Anion Transporter Polypeptide (OATP) fam
        3.3    8.1   4.5        3.2    8.1   3.3    1.6  1  2TM          2TM domain
        4.4    7.5   9.5        1.3    9.2   4.9    2.2  2  DUF4381      Domain of unknown function (DUF4381)


Domain annotation for each model (and alignments):
>> 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 !   56.6   0.0   1.8e-18   3.3e-15       7     110 ..     274     372 ..     270     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.8e-18
                                       HHHHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHH CS
                         HATPase_c   7 rqiisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivk 82 
                                        +++ nl+ Nav+++  + ++++v++++  d+++i++ DnG+Gip ++++ lf++         +g+ +GlGl++v+
  gi|336252921|ref|YP_004596028.1| 274 ARVFGNLLVNAVEHNDaERPRVSVTVEPGPDTVRIEIVDNGPGIPDAEVDALFDRIEG------RGSSHGLGLYLVQ 344
                                       57999*********44477777888885448**********************99999......789********** PP

                                       HHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  83 klvelmgGeiwvesepgrGttftftlpl 110
                                       +lv+ ++G++++ ++   G+ f ++lp 
  gi|336252921|ref|YP_004596028.1| 345 QLVTGFDGSVELVETGSDGSVFAVELPA 372
                                       ****9*******888899****999986 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   3.0   1.4e-11   2.4e-08      44     163 ..      62     189 ..      19     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.4e-11
                         HisKA_4TM  44 lglvyagyrlastdlpaeqewtvlvwslgGavvvgavigltvlvrllegrtiaePvfvvlvaaevGavaGllaGyla 120
                                        g+ ++gy+l+ +dl+  +   ++ w lg a v+  +  +   + ++     a  v  +  a+ +Ga  Gll G  +
  gi|336252921|ref|YP_004596028.1|  62 AGISFGGYWLRDADLSPSRYPRIAGWILGSALVFLLINVAL--IAVMPPESWALVVGWLRWAVALGAGVGLLIGCIE 136
                                       37889*************999*****998777765554444..5556666677778888889999999********* PP

                         HisKA_4TM 121 araradasrakris..........dalafvndlirhdlrndlvvirgyaeaie 163
                                       ara + +  a+r++          d l ++n+++rh++ n  +vi+gya  ++
  gi|336252921|ref|YP_004596028.1| 137 ARAIERSLAAERAAlraahleeqrDYLDYLNTVLRHEVLNAATVINGYASLLR 189
                                       *99765433333322222333333889**********************9876 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   2.7e-11   4.8e-08      39     110 ..     280     348 ..     273     361 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.7e-11
                       HATPase_c_2  39 actNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslkegGrGlalikglvD 110
                                       +++Naveh+  e+p  +v+v++e +++++++e+ D+Gpg  d+e  +    +  ++ + ++G+Gl+l+++lv 
  gi|336252921|ref|YP_004596028.1| 280 LLVNAVEHNDAERP--RVSVTVEPGPDTVRIEIVDNGPGiPDAEVDALF--DRIEGRGSSHGLGLYLVQQLVT 348
                                       589***********..7777777****************8888854444..44569***************96 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.78   1.4e+03      26      44 ..     150     166 ..     137     172 .. 0.67
   2 !   21.8   0.2   7.9e-08   0.00014       6      61 ..     167     222 ..     162     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.78
                                       HHHC..T-HSSCHHHHHHH CS
                             HisKA  26 aLkregklteelkeyleti 44 
                                       aL+   +  ee+++yl+ +
  gi|336252921|ref|YP_004596028.1| 150 ALRA--AHLEEQRDYLDYL 166
                                       3333..4568999988866 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 7.9e-08
                                       HHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA   6 lagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdl 61 
                                          + HE  +  ++i g+a++L+re+++t++ +e  e++ +e++ +  +++d++ l
  gi|336252921|ref|YP_004596028.1| 167 NTVLRHEVLNAATVINGYASLLRREAATTDQHREWAEIVMDESDEMATVIDDVRVL 222
                                       56789********************999*************************866 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   7.5e-07    0.0014       7      87 ..     274     356 ..     269     370 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.5e-07
                       HATPase_c_5   7 cvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg....ekkkle.sskskkeehGiGlksireiv 78 
                                        +++gnlL NA+e  ++   e++ +++tv+   +++ i+i  +  g    e + l+   + +++ hG+Gl  ++++v
  gi|336252921|ref|YP_004596028.1| 274 ARVFGNLLVNAVEHNDA---ERPRVSVTVEPGPDTVRIEIVDNGPGipdaEVDALFdRIEGRGSSHGLGLYLVQQLV 347
                                       689**********8766...379*************9998877666555566777735588999************* PP

                       HATPase_c_5  79 kkykgnlsi 87 
                                          +g++++
  gi|336252921|ref|YP_004596028.1| 348 TGFDGSVEL 356
                                       ****99873 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   8.9e-06     0.016       5      43 ..     155     194 ..     152     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.9e-06
                            SPOB_a   5 eikelkeliklL.rsqRHDflNhLQvIsGylqLgkydkae 43 
                                       +++e+++++++L  ++RH+ lN   vI Gy  L + + a+
  gi|336252921|ref|YP_004596028.1| 155 HLEEQRDYLDYLnTVLRHEVLNAATVINGYASLLRREAAT 194
                                       5789999*****8899*****************9988875 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 !   14.9   0.0     1e-05     0.018      10      54 ..     280     326 ..     273     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                       HATPase_c_3  10 lvdNsld...AdaenvkievnknrgktgeivieDdGkGmseeelknal 54 
                                       l+ N+++   A+  +v+++v+  + +t +i i D+G G++ +e++  +
  gi|336252921|ref|YP_004596028.1| 280 LLVNAVEhndAERPRVSVTVEPGP-DTVRIEIVDNGPGIPDAEVDALF 326
                                       566776443388889******997.79*****************9876 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 ?    7.8   0.9   0.00048      0.85     334     386 ..      50     105 ..      47     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00048
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 334 lltGvvvipgaalGillgGllvkklklsakk...laklvlvvsllsllllllllfl 386
                                       +l+Gvv+ + + +Gi +gG+ ++   ls+++   +a ++l ++l+ ll+ ++l+++
  gi|336252921|ref|YP_004596028.1|  50 FLIGVVTTLPFLAGISFGGYWLRDADLSPSRyprIAGWILGSALVFLLINVALIAV 105
                                       799**************************875558999999999999998888765 PP

>> 2TM  2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.3    0.0018       3.2      17      53 ..      92     135 ..      79     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0018
                               2TM  17 lvvYlivniflilinl.gsswf......lw.pilfWgiglllhal 53 
                                       ++v+l++n+ li++ +   sw+       w ++l+ g+gll+  +
  gi|336252921|ref|YP_004596028.1|  92 ALVFLLINVALIAV-MpPESWAlvvgwlRWaVALGAGVGLLIGCI 135
                                       689***********.443344433333344488999****99766 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3      0.49   8.8e+02      12      36 ..      78     102 ..      71     106 .. 0.57
   2 ?    9.2   4.9   0.00073       1.3      11      90 ..     107     202 ..     101     208 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.49
                           DUF4381  12 vswwPpapGwwlllaalllllllvl 36 
                                       +s  P   Gw l  a+++ll+ ++l
  gi|336252921|ref|YP_004596028.1|  78 PSRYPRIAGWILGSALVFLLINVAL 102
                                       5667888896666644444333333 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00073
                           DUF4381  11 pvswwPpapGwwlllaalllllllvlalwllrrrkrn...............rreAlreLaalr.adeadakellaa 71 
                                       p++ w + +Gw   ++al + + l+++    r   r                +r+ l+ L+++   +  +a++++  
  gi|336252921|ref|YP_004596028.1| 107 PPESWALVVGWLRWAVALGAGVGLLIGCIEARAIERSlaaeraalraahleeQRDYLDYLNTVLrHEVLNAATVING 183
                                       677899****9888866666444444444445333332344444555555555555555555556666777777777 PP

                           DUF4381  72 lselLkrvalayypreeva 90 
                                        ++lL+r a ++++  e+a
  gi|336252921|ref|YP_004596028.1| 184 YASLLRREAATTDQHREWA 202
                                       7777777776666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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 0.22s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3038.07
//
Query:       gi|336252922|ref|YP_004596029.1|  [L=424]
Description: glutamate-1-semialdehyde 2,1-aminomutase [Halopiger xanaduensis SH-6]
Scores for complete 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-68  231.6   0.0    1.5e-68  231.3   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
  ------ inclusion threshold ------
      0.031   13.4   0.0      0.047   12.9   0.0    1.2  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 !  231.3   0.0   1.7e-72   1.5e-68       9     373 ..      32     393 ..      25     424 .] 0.88

  Alignments for each domain:
  == domain 1  score: 231.3 bits;  conditional E-value: 1.7e-72
                                       SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT- CS
                       Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapk 85 
                                        +++++k++G  + d+dg+ry+D v +  +++lGh  P+ v+a  +q a+     +  + +e  ++lae +++++p 
  gi|336252922|ref|YP_004596029.1|  32 YPFFVQKGDGGHVIDADGNRYIDWVMGLGPLLLGHDLPEPVQAGIQQKASE--GPMYGTPTEIEVDLAEFVVRHVPS 106
                                       5699***********************************999988877766..45568899999************9 PP

                                       ..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-T CS
                       Aminotran_3  86 gldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlky 162
                                        ++k+ ++nsG+eA+ +A++lar       +t ++ki+  +g++HG    +l  +++     ++  p++++++++ +
  gi|336252922|ref|YP_004596029.1| 107 -VEKIRFVNSGTEATTSAVRLARG------YTGRNKIVVNQGGYHGAQESTLVEGDH-----ENPRPSSAGIPQAFA 171
                                       .***********************......9*********************98888.....778899999999999 PP

                                       TBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTT CS
                       Aminotran_3 163 pdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfG 239
                                       + +  +++n+      +e ++++ +++ d++aAv++Epi g+ G+v +++++ + lr+++++h+ lli+DEv tGf 
  gi|336252922|ref|YP_004596029.1| 172 EHTLPVPFND------EESVREVFEEHGDDIAAVLTEPILGNYGIVQPEDGYHEFLRDITEEHGSLLIFDEVITGFR 242
                                       9999999999......778999999***************************************************9 PP

                                       TTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHHHTTH CS
                       Aminotran_3 240 rTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiieeekl 313
                                         G   A  ++gv+pDl+t++K ++gG+p+ a+ ++ae+ + ++p++   +++Tf+G p+ +a+ l++l+ ++e+++
  gi|336252922|ref|YP_004596029.1| 243 VGGLGCAQSEFGVTPDLTTFGKIIGGGFPVGAIGGRAEIIENFTPSGdvfQAGTFSGHPVTMAAGLETLQFAAENDV 319
                                       99988999999**********************************999***************************** PP

                                       HHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC..............HHHHHHHHHCTEE CS
                       Aminotran_3 314 lenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke..............keilkkakekGvl 373
                                        ++++++g++l+egLee+ +++    +v g   m+ + ++ + e+ +              + +  ++ke+Gv 
  gi|336252922|ref|YP_004596029.1| 320 YDHVNDIGDRLREGLEEIVADQAPEYTVAGTDSMFKVIFTRDGEAPKnaadvknaetdrwrRIFWGQMKEQGVF 393
                                       ******************98875555666666677776666665444566666666666654455666666666 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 ?   12.9   0.0   5.3e-06     0.047     169     361 ..     220     418 ..     179     419 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.3e-06
                                       HHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHH CS
                     Aminotran_1_2 169 eleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrk 245
                                        l+   d++++++ ll++De+  gf  g l+ ++  ++v ++     +++++K  G  G+ vG+i g a++++  + 
  gi|336252922|ref|YP_004596029.1| 220 FLR---DITEEHGSLLIFDEVITGFRVGGLGCAQSEFGVTPD-----LTTFGKIIG-GGFPVGAIGGRAEIIENFTP 287
                                       344...559*******************99665557777776.....55******9.5999**************99 PP

                                       HHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS......TEEEECCSCSSEEEEEETHH CS
                     Aminotran_1_2 246 lsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael......glkvlasqsgmflltdlsae 315
                                           f   + ++ ++++aa   +l+ +   ++  +++++  ++lr++L+e+      + +v + +s + ++   + e
  gi|336252922|ref|YP_004596029.1| 288 SGDVFQAgTFSGHPVTMAAGLETLQFA-AENDVYDHVNDIGDRLREGLEEIvadqapEYTVAGTDSMFKVIFTRDGE 363
                                       999888887778888887777777776.5555556666666677777766666677656665555544444444444 PP

                                       ..........CHHHHHHH...........HHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHHHHHHH CS
                     Aminotran_1_2 316 ..........takelskk...........LleevgvyvtpgtsftvpgrlRitvAglteeeleelve 361
                                                 +      +           + e+ gv +++ ++f+++    +++ g+tee++e+ +e
  gi|336252922|ref|YP_004596029.1| 364 apknaadvknA------EtdrwrrifwgqMKEQ-GVFLSQ-NQFECQF---VSY-GHTEEDVERTLE 418
                                       44666555553......0444444788868888.999999.9999988...999.999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3174.45
//
Query:       gi|336252923|ref|YP_004596030.1|  [L=558]
Description: ammonium transporter [Halopiger xanaduensis SH-6]
Scores for complete 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-94  317.4  38.0    1.3e-94  317.2  38.0    1.0  1  Ammonium_transp  Ammonium Transporter Family
    5.6e-34  116.8   1.0    7.8e-34  116.3   0.1    1.8  2  P-II             Nitrogen regulatory protein P-II
  ------ inclusion threshold ------
       0.71    9.8   5.8       0.19   11.7   0.2    2.6  2  PsbY             Photosystem II protein Y (PsbY)


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 !  317.2  38.0   2.2e-98   1.3e-94       2     399 .]      21     406 ..      20     406 .. 0.93

  Alignments for each domain:
  == domain 1  score: 317.2 bits;  conditional E-value: 2.2e-98
                                       HHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-TTTTSCCGC CS
                   Ammonium_transp   2 flllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfignlglsaagvq 78 
                                       ++l++++l++fm+agfa+leag+vrsknv n l+knll + v+v +++l+G ++         g++   g+s +++q
  gi|336252923|ref|YP_004596030.1|  21 WILVATFLIFFMHAGFAMLEAGQVRSKNVANQLTKNLLTWSVGVTVFFLIGATVE--------GIVAGNGVS-FQFQ 88 
                                       9*************************************************96554........333332443.3444 PP

                                       CTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--.-SSSTTT CS
                   Ammonium_transp  79 detlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvliDfAgstv 155
                                        ++  + + +l+ ++fa+ta+tivsgava r+k+ ay+++ +ll+ ++yp+v+ ++w+   +++   v++DfAg+++
  gi|336252923|ref|YP_004596030.1|  89 SDAA-SWMDWLYGAVFAMTAATIVSGAVAGRAKLRAYVTYTFLLAAVIYPVVTGLTWAGSHLAYGDVVFHDFAGGMI 164
                                       4333.44569************************************************555555555559******* PP

                                       THHHHHHHHHHHHHHHS-STTTTG..TTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH......HHH CS
                   Ammonium_transp 156 VHlvggvagLaaalvlgkregrfe..gkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrara.....raav 225
                                       VH +gg+agL+aa+vlg+r +r++  g+++ i+gh+l+fa lGtl+L+fgW+gFN+G+++ + + a       r+a+
  gi|336252923|ref|YP_004596030.1| 165 VHGMGGIAGLTAAWVLGPRMDRYNsdGTANVIPGHSLTFAALGTLILAFGWYGFNVGTSAIIGESAFLgdqlgRVAL 241
                                       ************************999********************************9999999888999***** PP

                                       HHHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTC- CS
                   Ammonium_transp 226 tTllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklkid 302
                                       tT++A+a+ga++a l+ +lk+gk+++l++anG+lAGl+AiTa  ++   wgA+++G +Ag++  l++ ++++ lkid
  gi|336252923|ref|YP_004596030.1| 242 TTTVAMACGAMGAGLVAWLKTGKVDTLYVANGLLAGLAAITAIPDTTAWWGAFVVGGLAGIQLPLVFGFVEQYLKID 318
                                       ***************************************************************************** PP

                                       CTTHHHHHHHHHHHHHHHHHHHHTSHHHCSSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB CS
                   Ammonium_transp 303 DsldvvavHgvgGiwGllavgifaaekvvaskisggllsgegkqlvvqligilvilayafvvtlilllllklllgLr 379
                                       D++ v++vHg +G++G+l+  ++aa+          ++++  + +++q+ig+ vi+++++  t +++++ kl+ + r
  gi|336252923|ref|YP_004596030.1| 319 DVCAVFPVHGSAGVLGTLLFPFVAAPG---------VVESIPNAFIAQAIGVGVITVWTVFATGLIWFVFKLTGQAR 386
                                       ***********************9996.........567777889******************************** PP

                                       --HHHHHHSHHHHHHSSSSB CS
                   Ammonium_transp 380 vseeeeevglDvaehgetay 399
                                       vs+e e  glDv+ehg  +y
  gi|336252923|ref|YP_004596030.1| 387 VSPEHERDGLDVSEHGVDTY 406
                                       ***************97766 PP

>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       2.4   1.4e+04      77      93 ..     353     369 ..     345     373 .. 0.49
   2 !  116.3   0.1   1.3e-37   7.8e-34       1     102 []     450     551 ..     450     551 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.4
                                       HH-SSSTTSEEEEEEEE CS
                              P-II  77 aaktgeiGDGkiFvlpv 93 
                                       a+  + iG G i v  v
  gi|336252923|ref|YP_004596030.1| 353 AFIAQAIGVGVITVWTV 369
                                       55555555555544333 PP

  == domain 2  score: 116.3 bits;  conditional E-value: 1.3e-37
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       ++aiirp+kl evk+aL+++g ++ltvt+v+GrG+q  +++  rg+ey+v+l +kvk+e vv d  +++vv+ai +a
  gi|336252923|ref|YP_004596030.1| 450 VTAIIRPDKLGEVKKALAEVGAPSLTVTNVSGRGSQPAKKGQWRGEEYTVDLHQKVKIECVVADIPADEVVDAIGEA 526
                                       79*************************************************************************** PP

                                       H-SSSTTSEEEEEEEESEEEETTTT CS
                              P-II  78 aktgeiGDGkiFvlpveevirirtg 102
                                       a+tge+GDGkiFv+pve+++++rtg
  gi|336252923|ref|YP_004596030.1| 527 ANTGEPGDGKIFVIPVESAYQVRTG 551
                                       ************************8 PP

>> PsbY  Photosystem II protein Y (PsbY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   1.2      0.25   1.5e+03       6      19 ..     132     145 ..     131     146 .. 0.89
   2 ?   11.7   0.2   3.2e-05      0.19       9      34 ..     206     231 ..     203     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHHHH CS
                              PsbY   6 LiVLaPillAagWA 19 
                                        +V+ P++  + WA
  gi|336252923|ref|YP_004596030.1| 132 AAVIYPVVTGLTWA 145
                                       689**********9 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PsbY   9 LaPillAagWAlfNIgkaAlkQlqkf 34 
                                       L+ ++lA gW  fN+g+ A+ ++  f
  gi|336252923|ref|YP_004596030.1| 206 LGTLILAFGWYGFNVGTSAIIGESAF 231
                                       6679***************9888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); 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:                         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: 0.55u 0.21s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 4382.06
//
Query:       gi|336252924|ref|YP_004596031.1|  [L=337]
Description: Porphobilinogen synthase [Halopiger xanaduensis SH-6]
Scores for 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-142  471.9   0.0     1e-141  471.7   0.0    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 !  471.7   0.0  5.6e-146    1e-141       2     315 ..       5     334 ..       4     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 471.7 bits;  conditional E-value: 5.6e-146
                                       --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE- CS
                              ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvp 78 
                                       +r+rrlr++  +r lv+et+l+++d+i+p+fv+ +++e+ +i+smpg++r+++de+v++vee++++g++av+lFg+p
  gi|336252924|ref|YP_004596031.1|   5 HRPRRLRQDG-VRGLVSETSLEPTDFIAPVFVDATTDERVPIESMPGHERVPIDEAVARVEEVLETGVEAVMLFGIP 80 
                                       79****9876.9***************************************************************** PP

                                       SS-BSS-GGGGSTTSHHHHHHHHHHHH-TTSEEEEEE-STTTBSS-SSSEEESS...................EEHH CS
                              ALAD  79 eekdeegsealnedglvqrairaikeevpelvvitDvclceytshGhcgileeke..................vdnd 137
                                       e+kd+eg++a+ edg+vq+a+r++ +e ++ +vitDvclceyt+hGhcg lee+                   vdnd
  gi|336252924|ref|YP_004596031.1|  81 ESKDPEGTRAWVEDGVVQEATRRVTAE-TDAYVITDVCLCEYTTHGHCGPLEEELrgedhehgpacdhdptltVDND 156
                                       *************************99.899********************754456778899************** PP

                                       HHHHHHHHHHHHHHHCT-SEEEE-S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--T CS
                              ALAD 138 etlellakvavsqaeaGadivapSdmmDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrk 214
                                       ++le la++avs+aeaGad+vapS+mmDg+v+aire Ld++g+e+v+i+sY+aKy SafYgPFrdaa+ apsfgdr+
  gi|336252924|ref|YP_004596031.1| 157 AALESLARTAVSHAEAGADMVAPSSMMDGMVGAIREGLDDEGYEHVPIMSYAAKYESAFYGPFRDAADGAPSFGDRR 233
                                       ***************************************************************************** PP

                                       TTSB-TT-HHHHHHHHHHHHHTT-SBEEEES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHH CS
                              ALAD 215 tYqmdpansrealreveldleeGADivmvKPalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvv 291
                                       +Yqmdpansreal+ev+ld eeGAD++mvKPal+ylDi+++v++efd+pvaay+vSGEYam++aaae+gwld ++v+
  gi|336252924|ref|YP_004596031.1| 234 HYQMDPANSREALQEVRLDAEEGADVMMVKPALPYLDIVSAVRREFDHPVAAYNVSGEYAMLHAAAEKGWLDLEEVA 310
                                       ***************************************************************************** PP

                                       HHHHHHHHHTT-SEEEETTHHHHH CS
                              ALAD 292 lEsllsikRAGadliltYfakeva 315
                                        EsllsikRAGadliltYfa++va
  gi|336252924|ref|YP_004596031.1| 311 RESLLSIKRAGADLILTYFAEDVA 334
                                       **********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2567.70
//
Query:       gi|336252925|ref|YP_004596032.1|  [L=66]
Description: hypothetical protein Halxa_1521 [Halopiger xanaduensis SH-6]
Scores for 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:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 526.18
//
Query:       gi|336252926|ref|YP_004596033.1|  [L=272]
Description: transcriptional regulator TrmB [Halopiger xanaduensis SH-6]
Scores for 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   74.4   0.4    9.4e-21   73.5   0.1    1.7  2  TrmB            Sugar-specific transcriptional regulator TrmB
    6.2e-05   22.3   0.1    8.5e-05   21.8   0.1    1.2  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    0.00018   21.9   0.4     0.0095   16.4   0.1    2.7  2  HTH_27          Winged helix DNA-binding domain
    0.00092   19.4   0.0      0.082   13.1   0.0    2.3  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0021   17.9   2.2     0.0025   17.6   0.3    2.1  3  MarR_2          MarR family
      0.006   16.4   0.0       0.31   10.9   0.0    2.5  2  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.038   14.5   3.0        2.3    8.8   0.1    3.4  3  RuvA_C          RuvA, C-terminal domain
      0.049   14.0   0.0        0.1   13.0   0.0    1.5  1  Rrf2            Transcriptional regulator
      0.067   13.0   0.0       0.33   10.7   0.0    2.2  3  LexA_DNA_bind   LexA DNA binding domain
      0.075   12.9   0.1       0.19   11.6   0.1    1.7  1  HTH_23          Homeodomain-like domain
       0.12   12.5   0.3       0.34   11.0   0.0    1.8  2  HTH_20          Helix-turn-helix domain
       0.13   12.3   0.0       0.28   11.2   0.0    1.6  1  PadR            Transcriptional regulator PadR-like family
       0.13   12.3   0.0        1.5    8.9   0.0    2.3  2  DUF2250         Uncharacterized protein conserved in archaea 
       0.15   11.9   0.1        0.2   11.4   0.1    1.2  1  MCPVI           Minor capsid protein VI


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 !   73.5   0.1   7.3e-24   9.4e-21       1      67 [.      13      79 ..      13      80 .. 0.98
   2 ?   -2.7   0.0       4.3   5.5e+03      26      50 ..     140     164 ..     130     173 .. 0.60

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 7.3e-24
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                      L++lGL+eyEa++++aL +  + ta+ei++ ++vprs+vY+++++L +kGlVe+++  p+ Yrav++
  gi|336252926|ref|YP_004596033.1| 13 LEELGLTEYEARCFVALTRISKGTAREISQVADVPRSRVYDTVERLDRKGLVEVQQTDPREYRAVPV 79
                                      789**************************************************************97 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.3
                                       CHHCCCTTSSCHCHHHHHHHHHHCT CS
                              TrmB  26 deiaeelgvprskvYevLrsLedkG 50 
                                         +  ++ v    + e+Lrs  ++G
  gi|336252926|ref|YP_004596033.1| 140 HYLVAATSVVDREIREALRSAAERG 164
                                       4444555555556667777666666 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   6.6e-08   8.5e-05       2      61 ..     115     176 ..     114     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.6e-08
                                       EEEESSHHHHHHHHHHHHHH-SSEE..EEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS--- CS
                    Regulator_TrmB   2 vwvvksretvierieelIesAenel..ivslpselLeelreeliaaaergvtVllliypded 61 
                                       +w ++++e v +r+  ++e+A++ +  +v+++s   +e+re l++aaergvtV++ + +++ 
  gi|336252926|ref|YP_004596033.1| 115 MWSITQKEHVTDRVVTFLEEADETVhyLVAATSVVDREIREALRSAAERGVTVYVEVPTEDV 176
                                       799*********************9555777777779******************9988444 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 ?    3.1   0.0      0.11   1.4e+02      32      49 ..       3      20 ..       1      31 [. 0.79
   2 !   16.4   0.1   7.4e-06    0.0095      16      59 ..      32      76 ..      25      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.11
                            HTH_27 32 dshisyslkkLtekGLve 49
                                      +s++ +++ +L+e GL e
  gi|336252926|ref|YP_004596033.1|  3 SSSAEEAVGALEELGLTE 20
                                      78899***********94 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 7.4e-06
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLv.ertgdeadrre 59
                                        + ++++++++ +v  s +   +++L +kGLv ++++d+++ r+
  gi|336252926|ref|YP_004596033.1| 32 ISKGTAREISQVADVPRSRVYDTVERLDRKGLVeVQQTDPREYRA 76
                                      567899***************************888888866665 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 ?    3.7   0.0     0.055        71      37      56 ..       4      23 ..       2      25 .. 0.91
   2 !   13.1   0.0   6.4e-05     0.082      26      56 ..      38      68 ..      32      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.055
                                      HHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress 37 ssVsemlkkLekdGyveyek 56
                                      ss+ e +  Le+ G+ eye 
  gi|336252926|ref|YP_004596033.1|  4 SSAEEAVGALEELGLTEYEA 23
                                      89****************85 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.4e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdGyveyek 56
                                       +++++ +v  s V  ++++L+++G+ve+++
  gi|336252926|ref|YP_004596033.1| 38 REISQVADVPRSRVYDTVERLDRKGLVEVQQ 68
                                      689*************************985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.1   1.4e+03      36      54 ..       4      22 ..       1      25 [. 0.79
   2 !   17.6   0.3     2e-06    0.0025      15      57 ..      30      71 ..      16      76 .. 0.77
   3 ?   -2.8   0.0       4.7     6e+03      14      44 ..     132     159 ..     127     170 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                                      HHHHHHHHHHHHTTSEEEE CS
                            MarR_2 36 savsrilkrLvaaGLverr 54
                                      s++  ++  L++ GL e++
  gi|336252926|ref|YP_004596033.1|  4 SSAEEAVGALEELGLTEYE 22
                                      6777789999****99887 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2e-06
                                      HCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE.ESS CS
                            MarR_2 15 grrpgrdltvgelarrlglsksavsrilkrLvaaGLverr.pgp 57
                                       r   +  t++e+ +  ++++s+v  +++rL ++GLve + ++p
  gi|336252926|ref|YP_004596033.1| 30 TRISKG--TAREISQVADVPRSRVYDTVERLDRKGLVEVQqTDP 71
                                      444432..9*****************************995544 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.7
                                       HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2  14 Lgrrpgrdltvgelarrlglsksavsrilkr 44 
                                       L  +++   tv  l++++ +    +  +l+ 
  gi|336252926|ref|YP_004596033.1| 132 LEEADE---TVHYLVAATSVVDREIREALRS 159
                                       555555...5555555555444444444444 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 ?    3.0   0.0     0.069        89      30      50 ..       1      21 [.       1      23 [. 0.91
   2 !   10.9   0.0   0.00024      0.31      20      49 ..      36      65 ..      27      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.069
                                      S-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 30 lpkStvhRlLqtLvelGyveq 50
                                      +p S++   +  L+elG+ e+
  gi|336252926|ref|YP_004596033.1|  1 MPSSSAEEAVGALEELGLTEY 21
                                      799**************9886 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00024
                                      BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyve 49
                                      t +e+++ +++p+S v+  +  L + G+ve
  gi|336252926|ref|YP_004596033.1| 36 TAREISQVADVPRSRVYDTVERLDRKGLVE 65
                                      789**************************9 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0018       2.3       3      22 ..       6      25 ..       4      43 .. 0.85
   2 ?    1.9   0.1      0.24   3.1e+02      20      37 ..      97     113 ..      94     115 .. 0.80
   3 ?    2.3   0.0      0.19   2.4e+02      19      45 ..     134     159 ..     121     165 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                                      HHHHHHHHHHCTS-HHHHHH CS
                            RuvA_C  3 ledaveALlaLGYkekeaek 22
                                       e+av AL+ LG +e ea+ 
  gi|336252926|ref|YP_004596033.1|  6 AEEAVGALEELGLTEYEARC 25
                                      69*************99985 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.24
                                       HHHHHHHHHC-TTS-HHH CS
                            RuvA_C  20 aekAvakvlanpgasvee 37 
                                       ae A+++v+ +p+a+ +e
  gi|336252926|ref|YP_004596033.1|  97 AENALQQVE-EPNAPDDE 113
                                       899*****9.88888776 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHC-TTS-.HHHHHHHHHCC CS
                            RuvA_C  19 eaekAvakvlanpgas.veelIraALkl 45 
                                       ea+++v+ +   +++s v+  Ir+AL++
  gi|336252926|ref|YP_004596033.1| 134 EADETVHYL--VAATSvVDREIREALRS 159
                                       455555555..34455667789999986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.8e-05       0.1       8      58 ..      20      67 ..      17      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.8e-05
                                      HHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2  8 eyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      ey  ++ + L++ +++   +++ei++  ++++s +   +++L ++glv+++
  gi|336252926|ref|YP_004596033.1| 20 EYEARCFVALTRISKG---TAREISQVADVPRSRVYDTVERLDRKGLVEVQ 67
                                      6667777777777774...69***************************987 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 ?   -3.5   0.0       7.1     9e+03      41      56 ..       4      19 ..       3      22 .. 0.73
   2 ?   10.7   0.0   0.00026      0.33      28      64 ..      37      72 ..      34      73 .. 0.84
   3 ?   -2.5   0.0       3.7   4.7e+03      29      43 ..     187     201 ..     185     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.1
                                      HHHHHHHHHHHHTTSE CS
                     LexA_DNA_bind 41 saveehLkaLerKGyi 56
                                      s++ee   aLe  G+ 
  gi|336252926|ref|YP_004596033.1|  4 SSAEEAVGALEELGLT 19
                                      6788888888887765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00026
                                      HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG-CC CS
                     LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyierdpgkpR 64
                                       rei++   +   s v    ++L rKG++e++++ pR
  gi|336252926|ref|YP_004596033.1| 37 AREISQVADVP-RSRVYDTVERLDRKGLVEVQQTDPR 72
                                      67777777776.67788999***************99 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.7
                                       HHHHHHHTS-.HHHH CS
                     LexA_DNA_bind  29 reiaralglkSpsav 43 
                                       +ei  a  l+S++ v
  gi|336252926|ref|YP_004596033.1| 187 AEIVVAADLESTNHV 201
                                       799999999999977 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00015      0.19      16      46 ..      32      63 ..      19      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                            HTH_23 16 e.GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                        + + reI++  +v+r+ vy  ++r  ++Gl
  gi|336252926|ref|YP_004596033.1| 32 IsKGTAREISQVADVPRSRVYDTVERLDRKGL 63
                                      346699********************988986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       8.4   1.1e+04      47      55 ..      12      20 ..       4      22 .. 0.74
   2 ?   11.0   0.0   0.00026      0.34      26      57 ..      36      67 ..      28      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.4
                                      HHHHCTTEE CS
                            HTH_20 47 vLeeagLve 55
                                      +Lee gL e
  gi|336252926|ref|YP_004596033.1| 12 ALEELGLTE 20
                                      788888865 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00026
                                      -HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 26 taselaerldlskntlsyHLrvLeeagLvevv 57
                                      ta e+ +  d++++ +++ ++ L + gLvev+
  gi|336252926|ref|YP_004596033.1| 36 TAREISQVADVPRSRVYDTVERLDRKGLVEVQ 67
                                      899***************************96 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.28      23      54 ..      40      71 ..      30      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                      STT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S CS
                              PadR 23 segllelseGslYpaLkrLekeglvesewees 54
                                      ++ + ++  +++Y++ +rL ++glve ++++ 
  gi|336252926|ref|YP_004596033.1| 40 ISQVADVPRSRVYDTVERLDRKGLVEVQQTDP 71
                                      4566788999****************998875 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 ?    1.2   0.0       0.3   3.9e+02      35      57 ..       2      24 ..       1      35 [. 0.80
   2 ?    8.9   0.0    0.0012       1.5      17      55 ..      29      67 ..      14      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.3
                           DUF2250 35 pleevrellkkLeelGLlerveg 57
                                      p + ++e++ +LeelGL e+  +
  gi|336252926|ref|YP_004596033.1|  2 PSSSAEEAVGALEELGLTEYEAR 24
                                      6677889999*******987655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0012
                           DUF2250 17 lkkanvdYaksiakeleipleevrellkkLeelGLlerv 55
                                      l+++    a+ i++  ++p+++v + +++L + GL+e +
  gi|336252926|ref|YP_004596033.1| 29 LTRISKGTAREISQVADVPRSRVYDTVERLDRKGLVEVQ 67
                                      55666667999*************************965 PP

>> MCPVI  Minor capsid protein VI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00016       0.2      75     138 ..      30      98 ..      26     166 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX.....XXXXXXXXXXXXXXXX CS
                             MCPVI  75 envadlagetlsalvDigrlkvqkdleklkrkalGeerpatqeeleaL.....iaaldpkdeeavkqge 138
                                        +++++ ++ +s + D+ r +v + +e+l rk+l e +++  +e +a+        ++ +++  ++++e
  gi|336252926|ref|YP_004596033.1|  30 TRISKGTAREISQVADVPRSRVYDTVERLDRKGLVEVQQTDPREYRAVpvdtaCRRIREDYDSRINAAE 98 
                                       5678999*****************************999988886543111114455555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1981.18
//
Query:       gi|336252927|ref|YP_004596034.1|  [L=154]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-14   53.0   0.0    4.3e-14   52.8   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.1e-08   34.5   0.0    2.6e-08   34.1   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    7.9e-06   25.8   0.0    9.5e-06   25.6   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0018   18.2   0.0     0.0028   17.6   0.0    1.2  1  FR47             FR47-like protein
     0.0077   16.3   0.1      0.099   12.8   0.0    2.0  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 !   52.8   0.0   1.2e-17   4.3e-14      14     117 .]      23     143 ..       5     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 1.2e-17
                                       HHHHHHHHHHHHHHHHSTTCEEEEEEET................TEEEEEEEEEEEET.TSTTEEEEEEEEESGGGT CS
                    Acetyltransf_1  14 ppnedaseeefeesfsleaegllvaeed................geliGfisllkipd.ekggvayieslaVspeyr 73 
                                         + d+s +e+  +  +e  +l+ ++ d                +el++ +++l     +++++a++++l+V++ +r
  gi|336252927|ref|YP_004596034.1|  23 QLWTDRSPDEVLAWTGDEQYRLFGGYVDdgsdvadadetgresePELVAVAGVLVTHVlHHTRRAWLYDLVVDEPRR 99 
                                       5566666666666655555555554444456666666666665577999998887777989**************** PP

                                       TSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  74 gkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                       g+G+G+ +le++e +a e+g++++ la   + +a++++Ye  G+
  gi|336252927|ref|YP_004596034.1| 100 GQGYGTVMLEEVESWADEQGCDAVALASPRSKEATHEFYEARGY 143
                                       ************************9999999********99997 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   7.4e-12   2.6e-08      16      76 .]      74     145 ..      44     145 .. 0.66

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 7.4e-12
                                       EEEEEEEES.....TCTEE...EEE-GGGTTSSHHHHHHHHTT.....SEEEEEEEEE.THH....HHHHHHHHTTE CS
                    Acetyltransf_7  16 Gfialslld.....aeitr...laVdpeyrgkGiGraLleaae.....kgiileqlel.nae....kaikfYeklGF 74 
                                       G ++ +++      a   +   l+Vd+  rg+G+G+ +le +e     +g+  +   l + +    ++++fYe  G+
  gi|336252927|ref|YP_004596034.1|  74 GVLV-THVLhhtrrA---WlydLVVDEPRRGQGYGTVMLEEVEswadeQGCDAV--ALaS-PrskeATHEFYEARGY 143
                                       3222.2222343333...145599***************962334456898533..4422.223434566******* PP

                                       EE CS
                    Acetyltransf_7  75 ee 76 
                                       e+
  gi|336252927|ref|YP_004596034.1| 144 ER 145
                                       95 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.6e-09   9.5e-06      37     111 ..      71     148 ..      33     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.6e-09
                   Acetyltransf_10  37 eeggkivGviel.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavg 110
                                        + g +v ++   +++  ++ l+Vd+  rgqG+g+ +le+ve+ a+++g    +l    s+ +  +fYe  G+++ g
  gi|336252927|ref|YP_004596034.1|  71 AVAGVLVTHVLHhTRRAWLYDLVVDEPRRGQGYGTVMLEEVESWADEQGCDAvALASPRSKeATHEFYEARGYERWG 147
                                       4456777777665677799*****************************99988555555554899********9876 PP

                   Acetyltransf_10 111 e 111
                                        
  gi|336252927|ref|YP_004596034.1| 148 Y 148
                                       5 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.9e-07    0.0028      12      78 ..      76     144 ..      71     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.9e-07
                                       EEEEEEE-TT.SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHH.HHHHHHT-E CS
                              FR47  12 laawilrkdg.gelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsi.rlyeklGfe 78 
                                       l++ +l+      l+ l v++  r++G+g+++ +++     e+g ++++++ +  +++  ++ye+ G+e
  gi|336252927|ref|YP_004596034.1|  76 LVTHVLHHTRrAWLYDLVVDEPRRGQGYGTVMLEEVESWADEQGCDAVALASPRSKEAThEFYEARGYE 144
                                       6777787777799***************************************99887752699999998 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 ?    2.6   0.0     0.042   1.5e+02      17      55 ..      48      86 ..      35      89 .. 0.76
   2 !   12.8   0.0   2.8e-05     0.099      24      61 ..      86     123 ..      81     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.042
                   Acetyltransf_CG 17 YevrkegvldfthTeVpeelrGkGiAkkLvkaalddare 55
                                      Y +++++v d + T  + e +   +A+ Lv+++l ++r+
  gi|336252927|ref|YP_004596034.1| 48 YVDDGSDVADADETGRESEPELVAVAGVLVTHVLHHTRR 86
                                      5556666777777777777777779**********9997 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.8e-05
                   Acetyltransf_CG  24 vldfthTeVpeelrGkGiAkkLvkaalddareeglkvv 61 
                                       +  ++  +V+e  rG+G++  + +++  +a e+g   v
  gi|336252927|ref|YP_004596034.1|  86 RAWLYDLVVDEPRRGQGYGTVMLEEVESWADEQGCDAV 123
                                       5678999************************9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1150.28
//
Query:       gi|336252928|ref|YP_004596035.1|  [L=107]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-11   41.5  13.8    3.4e-07   29.8   5.0    2.3  2  Fer4      4Fe-4S binding domain
    6.9e-10   39.4   1.8    7.1e-05   23.3   0.4    2.2  2  Fer4_7    4Fe-4S dicluster domain
    3.6e-08   33.4   4.8    5.5e-08   32.9   4.8    1.3  1  Fer4_9    4Fe-4S dicluster domain
      3e-07   30.5  17.7    2.7e-05   24.2   7.4    2.1  2  Fer4_10   4Fe-4S dicluster domain
      3e-06   27.0  13.6      4e-05   23.5   5.3    2.3  2  Fer4_6    4Fe-4S binding domain
    6.3e-06   26.2  10.3    4.5e-05   23.5  10.4    2.0  2  Fer4_21   4Fe-4S dicluster domain
    7.2e-06   26.8   4.7    0.00029   21.7   1.1    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
    1.3e-05   25.6   1.1      0.024   15.2   0.5    2.2  2  Fer4_17   4Fe-4S dicluster domain
     0.0001   22.7   6.4     0.0033   17.8   6.7    2.1  2  Fer4_8    4Fe-4S dicluster domain
    0.00033   20.6  11.1     0.0093   16.0   4.1    2.5  2  Fer4_2    4Fe-4S binding domain
    0.00064   20.0   1.6    0.00064   20.0   1.6    2.2  2  Fer4_4    4Fe-4S binding domain
    0.00075   19.7   3.1    0.00075   19.7   3.1    2.0  2  Fer4_18   4Fe-4S dicluster domain
     0.0023   18.7   4.1     0.0023   18.7   4.1    2.3  2  Fer4_3    4Fe-4S binding domain
     0.0024   18.0   0.1      0.003   17.6   0.1    1.1  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
     0.0075   16.8  14.1       0.24   11.9  14.1    2.6  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


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 !   17.0   1.5   3.1e-06    0.0037       2      23 ..      40      61 ..      39      62 .. 0.91
   2 !   29.8   5.0   2.8e-10   3.4e-07       4      24 .]      80     100 ..      78     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.1e-06
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                       +d + C + GaC e CPv++ 
  gi|336252928|ref|YP_004596035.1| 40 AVDFDICLADGACLEDCPVDVF 61
                                      69*****************986 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 2.8e-10
                                       ETTTSSS-THHHHHSTTTEEE CS
                              Fer4   4 deekCigCGaCvevCPvgAIt 24 
                                       +e  Ci C++Cv+vCPv+AI+
  gi|336252928|ref|YP_004596035.1|  80 NETQCIDCMLCVDVCPVDAID 100
                                       7889***************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 !   15.7   0.0   1.4e-05     0.016      28      52 .]      32      60 ..       2      60 .. 0.69
   2 !   23.3   0.4   5.9e-08   7.1e-05       1      20 [.      83     102 ..      62     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                            Fer4_7 28 t....ekveidpekClgCgaCvavCPtga 52
                                            +v++d + Cl  gaC + CP+++
  gi|336252928|ref|YP_004596035.1| 32 LgihgTHVAVDFDICLADGACLEDCPVDV 60
                                      133337889*****************986 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 5.9e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaield 20 
                                       +Ci C  Cv++Cpv+ai++d
  gi|336252928|ref|YP_004596035.1|  83 QCIDCMLCVDVCPVDAIDVD 102
                                       58888888888888888765 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   4.8   4.6e-11   5.5e-08       6      51 .]      50      99 ..      44      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 4.6e-11
                            Fer4_9  6 gaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkgai 51
                                      gaC e Cp +v++  + ++  + +++ +    ++Ci+C+ Cv++Cp +ai
  gi|336252928|ref|YP_004596035.1| 50 GACLEDCPVDVFEWVDTPGHPESERKADpaneTQCIDCMLCVDVCPVDAI 99
                                      78**********99999999998887779999***************987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   7.4   2.3e-08   2.7e-05       1      56 []      38      95 ..      38      95 .. 0.82
   2 !   17.9   2.6     2e-06    0.0024       5      26 ..      80     101 ..      76     107 .] 0.80

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.3e-08
                           Fer4_10  1 kvvidddtCirCgkCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +v +d d C+  g+C + CP+d+  + +     +se +a+  +  +C++c  Cv++CP
  gi|336252928|ref|YP_004596035.1| 38 HVAVDFDICLADGACLEDCPVDVfeWVDTPGHPESERKADPANETQCIDCMLCVDVCP 95
                                      577899****************99755555555666666666889************9 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2e-06
                           Fer4_10   5 dddtCirCgkCvkaCPadltsv 26 
                                       ++ +Ci C  Cv++CP+d+  v
  gi|336252928|ref|YP_004596035.1|  80 NETQCIDCMLCVDVCPVDAIDV 101
                                       6789*************66444 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   1.2    0.0016         2       2      23 ..      39      60 ..      38      61 .. 0.87
   2 !   23.5   5.3   3.3e-08     4e-05       5      24 .]      80      99 ..      79      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                            Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                                      v++d d C+  g+C   CP ++
  gi|336252928|ref|YP_004596035.1| 39 VAVDFDICLADGACLEDCPVDV 60
                                      6788899************876 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 3.3e-08
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      ++  Ci+C+ Cv+vCP +ai
  gi|336252928|ref|YP_004596035.1| 80 NETQCIDCMLCVDVCPVDAI 99
                                      6788*************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 !    8.0   0.4    0.0027       3.2      32      55 ..      37      59 ..      32      63 .. 0.84
   2 !   23.5  10.4   3.7e-08   4.5e-05       3      58 ..      41     100 ..      39     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0027
                           Fer4_21 32 tvlkvvedeCvGCnlCssvCPved 55
                                      t+++v  d C +   C++ CPv d
  gi|336252928|ref|YP_004596035.1| 37 THVAVDFDICLADGACLEDCPV-D 59
                                      677888999************9.4 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 3.7e-08
                           Fer4_21   3 idedkCigCgkCliaCedtshqai....eidak.tvlkvvedeCvGCnlCssvCPvedcie 58 
                                       +d d C+  g Cl  C+    + +    + +++ +  +  e +C+ C lC++vCPv d+i+
  gi|336252928|ref|YP_004596035.1|  41 VDFDICLADGACLEDCPVDVFEWVdtpgHPESErKADPANETQCIDCMLCVDVCPV-DAID 100
                                       68899************9999999554422233134477899*************9.8886 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 ?    6.6   0.1     0.013        15       2      18 ..      46      62 ..      45      82 .. 0.72
   2 !   21.7   1.1   2.4e-07   0.00029       1      20 [.      83     102 ..      83     107 .] 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
                           Fer4_16  2 CgtCgkCaevCPtnaik 18
                                      C   g+C+e CP+++++
  gi|336252928|ref|YP_004596035.1| 46 CLADGACLEDCPVDVFE 62
                                      555689*******9987 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.4e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++C  C++vCP++ai+ +
  gi|336252928|ref|YP_004596035.1|  83 QCIDCMLCVDVCPVDAIDVD 102
                                       6****************977 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0011       1.3      43      60 ..      43      60 ..       5      61 .. 0.82
   2 !   15.2   0.5     2e-05     0.024      41      58 ..      79      96 ..      63      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                           Fer4_17 43 aslCieCgeCerkCPqgl 60
                                      ++ C+  g C ++CP ++
  gi|336252928|ref|YP_004596035.1| 43 FDICLADGACLEDCPVDV 60
                                      678************875 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2e-05
                           Fer4_17 41 ekaslCieCgeCerkCPq 58
                                       +  +Ci C +C+ +CP 
  gi|336252928|ref|YP_004596035.1| 79 ANETQCIDCMLCVDVCPV 96
                                      466799999999999996 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00057      0.68      45      65 .]      40      60 ..       4      60 .. 0.70
   2 !   17.8   6.7   2.8e-06    0.0033       2      64 ..      43      97 ..      42      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00057
                            Fer4_8 45 eealwsCttcgaCtevCpvgi 65
                                      +  ++ C++ gaC e Cpv++
  gi|336252928|ref|YP_004596035.1| 40 AVDFDICLADGACLEDCPVDV 60
                                      556788************976 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.8e-06
                            Fer4_8  2 lekCieCgaCqsaCpv.lrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      ++ C   gaC + Cpv + ++ + + +++ e+++ +  ++         +C  c+ C++vCpv+
  gi|336252928|ref|YP_004596035.1| 43 FDICLADGACLEDCPVdVFEWVDTPGHPESERKA-DPANE--------TQCIDCMLCVDVCPVD 97
                                      5679999********6455566888888888888.33333........58************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 !    8.5   0.6    0.0019       2.2       2      21 ..      38      57 ..      37      58 .. 0.90
   2 !   16.0   4.1   7.8e-06    0.0093       6      21 ..      80      95 ..      76      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0019
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      +v+vd d+C++ gaC+  CP
  gi|336252928|ref|YP_004596035.1| 38 HVAVDFDICLADGACLEDCP 57
                                      789******9879******9 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.8e-06
                            Fer4_2  6 dtdrCigCgaCvsaCP 21
                                      ++  Ci C  Cv++CP
  gi|336252928|ref|YP_004596035.1| 80 NETQCIDCMLCVDVCP 95
                                      5556************ PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.4      0.87     1e+03       8      16 ..      50      58 ..      44      60 .. 0.71
   2 !   20.0   1.6   5.4e-07   0.00064       4      16 ..      84      96 ..      72      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.87
                            Fer4_4  8 gsCvaaCPq 16
                                      g+C   CP+
  gi|336252928|ref|YP_004596035.1| 50 GACLEDCPV 58
                                      677777885 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 5.4e-07
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      Ci+C+ Cv++CP+
  gi|336252928|ref|YP_004596035.1| 84 CIDCMLCVDVCPV 96
                                      ************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 ?    1.7   0.3      0.23   2.8e+02      58      75 ..      43      60 ..      12      62 .. 0.79
   2 !   19.7   3.1   6.3e-07   0.00075      53      80 ..      76     104 ..      62     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.23
                           Fer4_18 58 agdcidcescvkvcPtgi 75
                                         c++ ++c++ cP+++
  gi|336252928|ref|YP_004596035.1| 43 FDICLADGACLEDCPVDV 60
                                      556899999999999876 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 6.3e-07
                           Fer4_18  53 rkekgagdcidcescvkvcPtg.idirkG 80 
                                          +++++cidc  cv+vcP++ id+  G
  gi|336252928|ref|YP_004596035.1|  76 ADPANETQCIDCMLCVDVCPVDaIDVDAG 104
                                       34567889************954888766 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.6      0.16   1.9e+02       5      14 ..      50      59 ..      45      60 .. 0.77
   2 !   18.7   4.1   1.9e-06    0.0023       1      15 []      84      98 ..      84      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.16
                            Fer4_3  5 gaCvevCPvg 14
                                      gaC+e CPv+
  gi|336252928|ref|YP_004596035.1| 50 GACLEDCPVD 59
                                      79**99**96 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.9e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C++Cv+vCPv+A
  gi|336252928|ref|YP_004596035.1| 84 CIDCMLCVDVCPVDA 98
                                      9************98 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.5e-06     0.003      21      90 ..      27      99 ..      18     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.5e-06
                                      SS--SEEESSTTHHHHTHHHHHS-THHHH-TTS-EEEEETT...TTSSEEEEE-CCC--S--HHHHH-TT--E CS
                            ETF_QO 21 dqpvhLklkdaevavkvnlekyagpeqryCPagvyeivede...eakekklqinaqnCvhCktCdikdpsqni 90
                                      d+p  L ++ ++vav+  +   +g +   CP  v+e+v++    e++ k    n ++C+ C  C    p + i
  gi|336252928|ref|YP_004596035.1| 27 DEPEELGIHGTHVAVDFDICLADGACLEDCPVDVFEWVDTPghpESERKADPANETQCIDCMLCVDVCPVDAI 99
                                      678888899899999999999999999***********9764224555666789999*****99666666665 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 !   11.9  14.1    0.0002      0.24       1      58 []      41     101 ..      41     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                           Fer4_13   1 VDrdtCiacgaCvelaP.dvFeeddegga..svvaeqptseeekadaeeAadaCPvesIgv 58 
                                       VD d C a+gaC e +P dvFe  d  g+  s  +++p +e++  d++  +d CPv++I v
  gi|336252928|ref|YP_004596035.1|  41 VDFDICLADGACLEDCPvDVFEWVDTPGHpeSERKADPANETQCIDCMLCVDVCPVDAIDV 101
                                       78899************99***998877622555568999999****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 755.60
//
Query:       gi|336252929|ref|YP_004596036.1|  [L=54]
Description: hypothetical protein Halxa_1525 [Halopiger xanaduensis SH-6]
Scores for 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   14.1   0.1      0.042   14.0   0.1    1.2  1  E3_UbLigase_RBR  E3 Ubiquitin Ligase RBR C-terminal domain


Domain annotation for each model (and alignments):
>> E3_UbLigase_RBR  E3 Ubiquitin Ligase RBR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.3e-06     0.042      54      77 ..      19      42 ..       3      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-06
                   E3_UbLigase_RBR 54 gqaglCelHYkEyLvelinenkld 77
                                       + glCe H++E+L el +  +l+
  gi|336252929|ref|YP_004596036.1| 19 LKVGLCEEHFRERLQELAEADGLE 42
                                      468*************98877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 401.29
//
Query:       gi|336252930|ref|YP_004596037.1|  [L=299]
Description: PHP domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-05   24.0   0.0    4.5e-05   23.8   0.0    1.3  1  PHP       PHP domain
     0.0041   16.8   0.1       0.01   15.6   0.1    1.6  1  PHP_C     PHP-associated


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 !   23.8   0.0     5e-09   4.5e-05       1      74 [.      34     107 ..      34     278 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5e-09
                                       EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                               PHP   1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse.... 73 
                                       dlHvHt  s  dg+l+  e+ ++a++ g + +a+TDh+ l+ + e + +      +g++++ G+e+ v+ d +    
  gi|336252930|ref|YP_004596037.1|  34 DLHVHTMRS--DGSLERAEVPAAARRAGVEVVALTDHDRLQPVAEPIVER-----DGVTIVNGIELRVEVDADtadr 103
                                       89***9988..4566678***********************999999555.....58********999887765555 PP

                                       .... CS
                                       ...x RF
                               PHP  74 ...k 74 
                                          +
  gi|336252930|ref|YP_004596037.1| 104 gddR 107
                                       5550 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.1e-06      0.01       8      25 ..     260     277 ..     256     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-06
                             PHP_C   8 rrfAeklglpgtgGSDAH 25 
                                       +r+ e++gl +tgGSDAH
  gi|336252930|ref|YP_004596037.1| 260 ERAIERHGLLATGGSDAH 277
                                       6889************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2201.92
//
Query:       gi|336252931|ref|YP_004596038.1|  [L=95]
Description: hypothetical protein Halxa_1527 [Halopiger xanaduensis SH-6]
Scores for complete 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   24.9   0.0    3.2e-05   24.1   0.0    1.4  1  DUF2795   Protein of unknown function (DUF2795)


Domain annotation for each model (and alignments):
>> DUF2795  Protein of unknown function (DUF2795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.8e-09   3.2e-05       2      43 ..      11      57 ..      10      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.8e-09
                           DUF2795  2 kgadyPatKdeLveyArrngA.....pdevleaLeaLPdreYespae 43
                                      ++ dyPat +eL+  + ++       ++ v + L++++ +++e+p++
  gi|336252931|ref|YP_004596038.1| 11 DDYDYPATTEELIADCGEHTLelpngSEQVCDVLDRIESETFETPED 57
                                      578**************999667777*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 676.85
//
Query:       gi|336252932|ref|YP_004596039.1|  [L=341]
Description: hypothetical protein Halxa_1528 [Halopiger xanaduensis SH-6]
Scores for 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  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2509.43
//
Query:       gi|336252933|ref|YP_004596040.1|  [L=64]
Description: hypothetical protein Halxa_1529 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        3.6    7.7   6.2         11    6.1   0.3    2.3  2  GvpG      Gas vesicle protein G


Domain annotation for each model (and alignments):
>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3    0.0006        11      43      60 ..       5      22 ..       2      24 .. 0.90
   2 ?    4.1   1.6    0.0026        47      51      69 ..      40      60 ..      21      64 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0006
                              GvpG 43 eLdaGeIdeeeFdrrEee 60
                                      ++ +G+ de+e++rrE++
  gi|336252933|ref|YP_004596040.1|  5 AMSMGAYDEDEHERREQQ 22
                                      789*************86 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0026
                              GvpG 51 eeeFdrrE..eelLdrLeale 69
                                      e e+d  E  eelLd+ e+++
  gi|336252933|ref|YP_004596040.1| 40 EVEYDSGEstEELLDQFEQIK 60
                                      446776664478999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 482.32
//
Query:       gi|336252934|ref|YP_004596041.1|  [L=324]
Description: hypothetical protein Halxa_1530 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0002   22.0   2.5     0.0074   17.0   2.5    2.3  1  CxxCxxCC  Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
        2.6    8.2   5.8        3.7    7.7   0.3    2.4  2  CMD       Carboxymuconolactone decarboxylase family


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 !   17.0   2.5   8.2e-07    0.0074       1      83 [.       4     162 ..       4     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.2e-07
                          CxxCxxCC   1 eCkeCgaCCkelkvklteedlerlkaaevaeeeeeskkiak.................................... 41 
                                       +C++C+ CC ++++    +d +  ++    ++++++++ a                                     
  gi|336252934|ref|YP_004596041.1|   4 HCEGCAGCCMDWRPLTDGDDASGGRRRAALDDDDDATREAIdgdpnfvpltrdevraflehgmaaaltprfwkaade 80 
                                       6*********8888888888777766655555444444333589999999999999999999999999999999999 PP

                          CxxCxxCC  42 ........................................adgrCvfldeetklCkiYeeR..pkicrlfpasekee 76 
                                                                               +   Cvfld++t +C+i++    p  c ++p +  + 
  gi|336252934|ref|YP_004596041.1|  81 aeaveidgyevasvadrpvffvglrkppkpvapfgrkdetWLPTCVFLDPTTLQCRIHNGElyPAECGAYPTH--NL 155
                                       ************************************9999999***************96556********95..44 PP

                          CxxCxxCC  77 llaraet 83 
                                        l  +++
  gi|336252934|ref|YP_004596041.1| 156 ALEQETE 162
                                       4444444 PP

>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3   0.00041       3.7      55      84 ..      53      82 ..      51      83 .. 0.92
   2 ?    2.7   0.9     0.015   1.3e+02      21      83 ..     221     288 ..     207     290 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00041
                                      --HHHHHHHHHHHHHHHSHHHHHHHHHHHH CS
                               CMD 55 vteeeiaevlaqaaayagwpaaraAlaaae 84
                                      +t++e+++ l ++ a+a +p++++A++ ae
  gi|336252934|ref|YP_004596041.1| 53 LTRDEVRAFLEHGMAAALTPRFWKAADEAE 82
                                      79*********************9998887 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.015
                                       S-HHHH.HHHHHHHHHHTT-HHHH.HHHHHHHHHTT--H...HHHHHHHHHHHHHH.SHHHHHHHHHHH CS
                               CMD  21 Ldpker.eLialavsaangceyCv.daHtraAleaGvte...eeiaevlaqaaaya.gwpaaraAlaaa 83 
                                       L++ +r e + +a++ + g +  + d+H+++ +e+ + +   +e +++  +  ++   w++ r A+ aa
  gi|336252934|ref|YP_004596041.1| 221 LTREDRaECLGVAAASSAGTVA-IsDYHYERGKERALEAmatDETDDAESWVGPAIrEWERRREAATAA 288
                                       5555554778899999999999.5599999966665555444555555555444433677777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2491.15
//
Query:       gi|336252935|ref|YP_004596042.1|  [L=80]
Description: hypothetical protein Halxa_1531 [Halopiger xanaduensis SH-6]
Scores for 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:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 572.95
//
Query:       gi|336252936|ref|YP_004596043.1|  [L=614]
Description: helicase c2 [Halopiger xanaduensis SH-6]
Scores for 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-21   76.1   0.0    5.2e-21   75.6   0.0    1.2  1  Helicase_C_2   Helicase C-terminal domain
    5.3e-06   26.2   0.0    8.7e-06   25.5   0.0    1.3  1  DEAD_2         DEAD_2
    7.6e-05   23.0   0.0    0.00029   21.1   0.0    1.9  1  AAA_22         AAA domain
      9e-05   22.5   0.0      0.034   14.2   0.0    2.7  3  ResIII         Type III restriction enzyme, res subunit
    0.00033   20.4   0.2       0.72    9.5   0.0    2.4  2  AAA_30         AAA domain
    0.00035   20.4   0.0       0.14   11.9   0.0    2.4  2  DEAD           DEAD/DEAH box helicase
     0.0028   18.1   0.2      0.028   14.8   0.1    2.6  2  AAA_16         AAA ATPase domain
  ------ inclusion threshold ------
       0.02   15.3   0.1      0.046   14.2   0.1    1.5  1  OrsD           Orsellinic acid/F9775 biosynthesis cluster pro
       0.02   14.3   0.0      0.034   13.5   0.0    1.2  1  Mg_chelatase   Magnesium chelatase, subunit ChlI
      0.037   14.2   0.0       0.11   12.7   0.0    1.7  2  DXP_redisom_C  1-deoxy-D-xylulose 5-phosphate reductoisomeras
      0.046   13.2   0.0      0.086   12.3   0.0    1.4  1  PhoH           PhoH-like protein
      0.075   13.0   0.1       0.15   12.0   0.1    1.4  1  PRO8NT         PRO8NT (NUC069), PrP8 N-terminal domain
        0.1   13.0   0.0       0.26   11.6   0.0    1.6  1  AAA_19         AAA domain
       0.16   11.2   0.0        3.7    6.7   0.0    2.2  2  DUF2075        Uncharacterized conserved protein (DUF2075)


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.0     4e-24   5.2e-21       2     170 ..     385     541 ..     384     542 .. 0.89

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 4e-24
                      Helicase_C_2   2 lellevvp.ggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEG 77 
                                       ++l++  p ++ l+  +Sy++ e++++ l++ +  ++i++ +   +  r++ lee+k+ +++  ++l+v   k+ E 
  gi|336252936|ref|YP_004596043.1| 385 VRLMQRHPdEKGLIHAHSYDIQERLADLLRDFGVGERIRVHD---RDGRDAALEEWKA-SNDPDVFLSV---KMEEA 454
                                       566777775778999****************99766666655...699**********.7888888888...7**** PP

                      Helicase_C_2  78 idfsddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeR 154
                                       +d+++dl+r  ++++ Pf n+ d +v+ + e        ++ + wy + alr+v Qa+GR++R  dD+ga +l D+ 
  gi|336252936|ref|YP_004596043.1| 455 LDLKGDLCRWQVLCKAPFLNTGDSRVAHRLE--------EGQWAWYYRTALRTVIQACGRVVRAPDDHGATYLADSS 523
                                       **************************99976........3569********************************** PP

                      Helicase_C_2 155 fak..eeireklpkwlre 170
                                       + +  e+ r  +p+w++e
  gi|336252936|ref|YP_004596043.1| 524 LLDlfERARTDMPDWFEE 541
                                       *988899999****9986 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   6.8e-09   8.7e-06     107     171 ..     131     191 ..     121     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 6.8e-09
                                       CT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHHT..GCGCEEEECTCCCHHHHHHHCC-EEE CS
                            DEAD_2 107 lklCPYylsrelledadiiilpYqyLldekireslkgislknsivilDEAhNiedvceeaasvei 171
                                       ++ CPY++ r+++++ +i  +  +y+++    e ++    k  +v++DEAh + + +e  a +++
  gi|336252936|ref|YP_004596043.1| 131 KHRCPYFSDRAIASNREIAAMTLAYFMQTAGSEVFR----KRDVVVVDEAHGLAEWAEMYATIQL 191
                                       688*************************99999886....899***********99998888776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.3e-07   0.00029       7     112 ..      36     189 ..      31     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.3e-07
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelka............ 70 
                                       +++v +++G+GK++l+r ++  +  + +ae  +++ +++t p+ + ++d+ + +ll +l++ + +            
  gi|336252936|ref|YP_004596043.1|  36 VVLVRAPTGSGKSLLARAVAGCARTVDDAEPSEASGAYYTTPQVSQLDDVaADDLLADLNVIRGKsnyscilpnern 112
                                       678899***********************9999999999999999999999999999999988889999******** PP

                            AAA_22  71 ...............................erlsseell.ealeqalrarav..ielliiDEaqhlrs..eealee 111
                                                                      ++ +  ++  +++ q + +     + ++++DEa+ l    +e++ +
  gi|336252936|ref|YP_004596043.1| 113 tpvnqapcvrergydcsvkhrcpyfsdraiaSNREIAAMTlAYFMQTAGSEVFrkRDVVVVDEAHGL-AewAEMYAT 188
                                       ***************************976644444444444444444444337999*********9.446777776 PP

                            AAA_22 112 L 112
                                       +
  gi|336252936|ref|YP_004596043.1| 189 I 189
                                       6 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 !   14.2   0.0   2.6e-05     0.034       5      42 ..      16      52 ..      13      60 .. 0.90
   2 ?    5.1   0.0     0.016        21     132     146 ..     167     181 ..     141     194 .. 0.80
   3 ?   -2.0   0.0       2.4     3e+03      42      78 ..     381     417 ..     377     446 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                                      -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHH CS
                            ResIII  5 reyQeeaienlleklkskrdkrglikmaTGtGKTlvaa 42
                                      r  Qe+a++++++++   ++  +l+ ++TG+GK+l+a 
  gi|336252936|ref|YP_004596043.1| 16 RGNQEQALRDIRDAFA-AGNDVVLVRAPTGSGKSLLAR 52
                                      678************9.*****************9884 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                                       T-SEEEEETGGGTTS CS
                            ResIII 132 rfdviiiDEaHrlga 146
                                       + dv+++DEaH l++
  gi|336252936|ref|YP_004596043.1| 167 KRDVVVVDEAHGLAE 181
                                       678********9987 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.4
                                       HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII  42 aklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       a++i rl++ ++ ek l+ +++ ++ e++ + +++f 
  gi|336252936|ref|YP_004596043.1| 381 ARTIVRLMQRHPDEKGLIHAHSYDIQERLADLLRDFG 417
                                       6789999999999999999**9999999998777765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00056      0.72       5      41 ..      18      57 ..      14      77 .. 0.77
   2 !    8.5   0.1    0.0011       1.5      63      98 ..     143     177 ..     138     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00056
                            AAA_30  5 eQaaave...alltsgdrvavltGpAGtGKttalkalrea 41
                                      +Q++a++    + + g+ v+++ +p G+GK+ + +a++  
  gi|336252936|ref|YP_004596043.1| 18 NQEQALRdirDAFAAGNDVVLVRAPTGSGKSLLARAVAGC 57
                                      566665411155677778**************99999765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0011
                            AAA_30  63 aeelgieastiakllkrlkgrarlepgtllivDEag 98 
                                       a + +i+a+t+a ++++ ++ + ++++++++vDEa 
  gi|336252936|ref|YP_004596043.1| 143 ASNREIAAMTLAYFMQTAGS-EVFRKRDVVVVDEAH 177
                                       566789*********66664.678889*******95 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00011      0.14       4      31 ..      19      51 ..      16      77 .. 0.80
   2 !    6.0   0.0     0.007       8.9     118     136 ..     164     182 ..     141     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      HHHHHHHHH.....TTCEEEEEESTTSSHHHHH CS
                                      xxxxxxxxx.....xxxxxxxxxxxxxxxxxxx RF
                              DEAD  4 Qaeaiplil.....gggdvlvaaeTGsGKTlaf 31
                                      Q++a+  i      g++ vlv+a+TGsGK+l +
  gi|336252936|ref|YP_004596043.1| 19 QEQALRDIRdafaaGNDVVLVRAPTGSGKSLLA 51
                                      66777777666664556788**********976 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.007
                                       HCTTEEEEEEETHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              DEAD 118 nlsqvrflVlDEadrlldq 136
                                        +++  ++V+DEa++l ++
  gi|336252936|ref|YP_004596043.1| 164 VFRKRDVVVVDEAHGLAEW 182
                                       4778889*********998 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   0.1   2.2e-05     0.028       4      45 ..      15      55 ..      13     184 .. 0.85
   2 ?    0.1   0.0      0.74   9.5e+02      61     107 ..     208     266 ..     200     330 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.2e-05
                            AAA_16  4 GReeeleqLlsalervrsgrpelvllsGesGvGKsslvrell 45
                                      +R+++ ++L+++ ++ ++g   +vl++ + G+GKs l+r+++
  gi|336252936|ref|YP_004596043.1| 15 YRGNQEQALRDIRDAFAAGN-DVVLVRAPTGSGKSLLARAVA 55
                                      58888889999888777777.8*****************998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.74
                            AAA_16  61 dqlesaipysa.laqalareellrqlldeaesaeleawrekleeala............a 107
                                       d+ e+a++y+  laq+++r +    l++++ s +  + r++l+e ++            +
  gi|336252936|ref|YP_004596043.1| 208 DDVERAVRYAEnLAQTCTR-RKDDLLAQDSLSPAEVRERDRLQELIGeldwfvsdyrdpQ 266
                                       5667888888888888866.3335555555555555555556655555555555555540 PP

>> OrsD  Orsellinic acid/F9775 biosynthesis cluster protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   3.6e-05     0.046      64     101 ..     101     140 ..      74     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-05
                              OrsD  64 eaeavslpsaesepipgLpvy..eGyrCrakakCkyltrs 101
                                       ++  + lp+  + p+++ p+   +Gy C +k +C+y + +
  gi|336252936|ref|YP_004596043.1| 101 SNYSCILPNERNTPVNQAPCVreRGYDCSVKHRCPYFSDR 140
                                       4557899************98789************9865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.6e-05     0.034       8      58 ..      19      70 ..      16      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                      Mg_chelatase  8 qeeakraleia.aaGgHnlllvGppGsGKtmlakrlpsllpplseeealeva 58
                                      qe+a r ++ a aaG+  +l+  p GsGK++la+++++    ++++e  e++
  gi|336252936|ref|YP_004596043.1| 19 QEQALRDIRDAfAAGNDVVLVRAPTGSGKSLLARAVAGCARTVDDAEPSEAS 70
                                      5555555544428999999999**************9998888888877765 PP

>> DXP_redisom_C  1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       8.5   1.1e+04      30      51 ..      69      90 ..      68      94 .. 0.84
   2 ?   12.7   0.0   8.6e-05      0.11      43      73 ..     300     330 ..     295     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.5
                                      E--GTTTTS-HHHHCT-SHHHH CS
                     DXP_redisom_C 30 asGGpfrklkleeleevtveea 51
                                      asG  +++ + ++l++v +++ 
  gi|336252936|ref|YP_004596043.1| 69 ASGAYYTTPQVSQLDDVAADDL 90
                                      8999999999999999988775 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.6e-05
                                       HCT-SHHHHHS-SS----HHHHHHHHHSHHH CS
                     DXP_redisom_C  43 leevtveealkhPnWsmGkkitvdsatlmNk 73 
                                       ++ +++e+ l+h  W+ G+k ++ sat++Nk
  gi|336252936|ref|YP_004596043.1| 300 IKPMNPEKYLQHTVWDRGNKFALLSATILNK 330
                                       5678999***********************9 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.7e-05     0.086       8      40 ..      18      55 ..      14      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                                      HHHHHHHHHH.....H-SEEEEE--TTSSTTHHHHHHH CS
                              PhoH  8 eQkeylealk.....kndivfaiGpaGtGKtylavala 40
                                      +Q+++l+ ++      nd+v + +p+G+GK++la a+a
  gi|336252936|ref|YP_004596043.1| 18 NQEQALRDIRdafaaGNDVVLVRAPTGSGKSLLARAVA 55
                                      678888888777777899****************9887 PP

>> PRO8NT  PRO8NT (NUC069), PrP8 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00012      0.15      73     128 ..     168     223 ..     145     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                       -----B-HHHHHHHHHHHHHHHHHHHHTTS------SS-S-SSS----H.HHHHHH CS
                            PRO8NT  73 neiprviepvylaqwstmwiamrrekrdrrhfkrlrfppfddeeppldyadnildv 128
                                        ++  v e + la+w++m+++++   r       lr+p  dd e+ + ya+n++++
  gi|336252936|ref|YP_004596043.1| 168 RDVVVVDEAHGLAEWAEMYATIQLGPRTVPFWDDLRVPEIDDVERAVRYAENLAQT 223
                                       356677888899****************************************9875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.26       4     115 ..      29     180 ..      26     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                            AAA_19   4 avealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelre.rlaalgaeatTiHrlal.. 77 
                                       a  a+ ++v+lv a+ G+GK+ + +++  ++  + + +p e   + +t   +++l + + + l+a+ + i + ++  
  gi|336252936|ref|YP_004596043.1|  29 AF-AAGNDVVLVRAPTGSGKSLLARAVAGCARTVDDAEPSEASGAYYTTPQVSQLDDvAADDLLADLNVIRGKSNys 104
                                       44.78899***********************************9*9**99999999944456677766666555567 PP

                            AAA_19  78 ......................................ldfddlltealelleeaeeekklqeeellivDEfqdvd 115
                                                                               + ++  ++l+++ +++ ++ ++++++++vDE+  + 
  gi|336252936|ref|YP_004596043.1| 105 cilpnerntpvnqapcvrergydcsvkhrcpyfsdraiASNREIAAMTLAYFMQTAGSEVFRKRDVVVVDEAHGLA 180
                                       77777777777777778888888888888888888775444444445555555888999998888******97766 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.072        92       3      25 ..      36      58 ..      34     105 .. 0.76
   2 ?    6.7   0.0    0.0029       3.7      82     104 ..     161     183 ..     129     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.072
                           DUF2075  3 vvlVtGvaGtGKtvvllnllael 25
                                      vvlV+  +G+GK++++ +++  +
  gi|336252936|ref|YP_004596043.1| 36 VVLVRAPTGSGKSLLARAVAGCA 58
                                      8999999********98887655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0029
                           DUF2075  82 ekkeepkedvvivDEAhrlltks 104
                                        ++  +k dvv+vDEAh l + +
  gi|336252936|ref|YP_004596043.1| 161 GSEVFRKRDVVVVDEAHGLAEWA 183
                                       46667899*********998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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):              14  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 3975.87
//
Query:       gi|336252937|ref|YP_004596044.1|  [L=38]
Description: hypothetical protein Halxa_1533 [Halopiger xanaduensis SH-6]
Scores for 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   0.1       0.11   12.1   0.1    1.0  1  gpUL132   Glycoprotein UL132


Domain annotation for each model (and alignments):
>> gpUL132  Glycoprotein UL132
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.9e-06      0.11      40      68 ..       6      34 ..       3      38 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.9e-06
                           gpUL132 40 hnvrnneimkvlailfyivtgtsifsfia 68
                                      + vr n+  k++a+lf ++t ts++++ a
  gi|336252937|ref|YP_004596044.1|  6 QAVRMNKRNKIIAVLFALLTATSMIAMPA 34
                                      579********************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 293.00
//
Query:       gi|336252938|ref|YP_004596045.1|  [L=378]
Description: hypothetical protein Halxa_1534 [Halopiger xanaduensis SH-6]
Scores for 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-49  165.9   0.0    2.2e-47  161.4   0.0    2.1  2  Met_10           Met-10+ like-protein
    6.6e-05   23.5   0.0    0.00018   22.1   0.0    1.8  1  Methyltransf_25  Methyltransferase domain
    0.00011   21.8   0.0    0.00016   21.3   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00043   19.9   0.0     0.0017   17.9   0.0    1.8  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.019   14.0   0.0      0.028   13.4   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.023   14.1   0.0      0.031   13.6   0.0    1.2  1  DNA_methylase    C-5 cytosine-specific DNA methylase
      0.023   14.6   1.3      0.089   12.7   1.3    2.0  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
      0.056   12.8   0.0      0.096   12.1   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.071   13.8   0.0       0.24   12.1   0.0    2.0  1  Methyltransf_11  Methyltransferase domain
       0.11   12.1   0.0        0.2   11.3   0.0    1.3  1  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 !  161.4   0.0   1.2e-50   2.2e-47       2     180 ..     111     291 ..     110     296 .. 0.96
   2 ?    2.4   0.0     0.063   1.1e+02     178     199 .]     304     325 ..     299     325 .. 0.93

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 1.2e-50
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-S....BTTTTB--EEEEEES-.SEEEEEETTEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsev....egefRtfelevlaGsdstetihkEngcr 73 
                                       ++++iG vv++ ++e+  + +++++e++l+ + +  +vl +++      +g++R+++ ++laG+ +tetih+E+g+r
  gi|336252938|ref|YP_004596045.1| 111 SWAVIGSVVLVTVPEDCPD-ETEMAEALLELHgEADSVLADEGVAndgqAGTYREPRTRLLAGERDTETIHTEHGTR 186
                                       79**************999.999****************9987666666899************************* PP

                                       EEEETTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-T CS
                            Met_10  74 fklDvskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkve 150
                                       + lD +kv+fs++++aEr+r+  +   +e V d+fAGiG+f++p+a+   + rv a ++nP++++yl en  lN+v+
  gi|336252938|ref|YP_004596045.1| 187 YGLDPAKVMFSPGNQAERARMGDISGADEHVFDMFAGIGYFTLPMAR--AGARVTASEINPTAFRYLLENAVLNEVD 261
                                       **********************************************9..8888************************ PP

                                       TCEEEEES-GGG---TT-EEEEEE--TTTG CS
                            Met_10 151 kvvkpileDgrevireqladrvvmnlpksa 180
                                       ++v+++++D+r+++ e  adrvvm++  sa
  gi|336252938|ref|YP_004596045.1| 262 DRVEAYMTDCRDLAGEIEADRVVMGYYGSA 291
                                       **************************9877 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.063
                                       TTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 178 ksaieFldkvlaalkdggvihy 199
                                       ++a +Fl+++++al  ggv+hy
  gi|336252938|ref|YP_004596045.1| 304 DEARDFLEHAFEALVPGGVVHY 325
                                       6799*****************9 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     1e-07   0.00018       1      97 []     217     321 ..     217     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1e-07
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEE..... CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvs..... 70 
                                       v d+ +G G +tl +a+++  a+vt+ +i++++ ++  e+a  +++  +ve +  d++dl  e  + D vv+     
  gi|336252938|ref|YP_004596045.1| 217 VFDMFAGIGYFTLPMARAG--ARVTASEINPTAFRYLLENAVLNEVddRVEAYMTDCRDLAGEI-EADRVVMgyygs 290
                                       78999*************5..********************99999**************9665.778888754444 PP

                                       ESTGG......G.SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  71 sgalh......h.lsdedlekalkeiarvLkpgG 97 
                                       +          h +  ++++++l++++++L pgG
  gi|336252938|ref|YP_004596045.1| 291 A---DgtdadgHgTRSDEARDFLEHAFEALVPGG 321
                                       0...144455555778889999999999999999 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 !   21.3   0.0   9.1e-08   0.00016       3      67 ..     216     280 ..     214     306 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9.1e-08
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkl 67 
                                        + D+f+G G  +  +a+ + +v a+ein+       +Na + +v+d++   + d+ +l  +++ 
  gi|336252938|ref|YP_004596045.1| 216 HVFDMFAGIGYFTLPMARAGARVTASEINPTAFRYLLENAVLNEVDDRVEAYMTDCRDLAGEIEA 280
                                       689*****************************************************998766655 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   9.6e-07    0.0017      32     103 ..     214     285 ..     207     326 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.6e-07
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivs 103
                                       +++v D+ +G+G+ ++ +a++  +  vt+ +++  A +   en+  n+++  ve++ +d+ + + e + d +v+
  gi|336252938|ref|YP_004596045.1| 214 DEHVFDMFAGIGYFTLPMARAGAR--VTASEINPTAFRYLLENAVLNEVDdrVEAYMTDCRDLAGEIEADRVVM 285
                                       5689****************8877..9***********************9***********999999999997 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 ?   13.4   0.0   1.6e-05     0.028     201     250 ..     213     262 ..     207     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                   tRNA_U5-meth_tr 201 skgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidn 250
                                       +++ +++++ G G f+l++ar   +v a+ei  ++    + n   n++d+
  gi|336252938|ref|YP_004596045.1| 213 ADEHVFDMFAGIGYFTLPMARAGARVTASEINPTAFRYLLENAVLNEVDD 262
                                       5667899*************************************999986 PP

>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.8e-05     0.031       3      42 ..     217     255 ..     216     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                       EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH- CS
                     DNA_methylase   3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanf 42 
                                       ++d+faGiG f+l +++ag   v asei+++a+  +  n 
  gi|336252938|ref|YP_004596045.1| 217 VFDMFAGIGYFTLPMARAG-ARVTASEINPTAFRYLLENA 255
                                       68*****************.788999******98877776 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 ?   12.7   1.3     5e-05     0.089       4      40 ..      17      67 ..      16      73 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-05
                                      EEGGGHHHHHHHHHHTT-B-TTS--EEE..............TTEEEEEB- CS
                            Trm5_N  4 VpkkegEkvRkkLlekglLdrnyKIksd..............ddylyIPvk 40
                                      V+k+ +E+++  L+++g+ d ++++++                d + +Pv+
  gi|336252938|ref|YP_004596045.1| 17 VEKRRAETAIESLRAEGVYDDDRRVRAArgrrdaapaddddnPDKVALPVT 67
                                      99***********************98655555555555544445555555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.4e-05     0.096     161     231 ..     213     284 ..     206     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.4e-05
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevals..eellkeekadviv 231
                                       ++e+v+D+ +G G  ++  a+ ga +v+a  i++ A +   eNa lN+v++++e +++  ++l  e +ad +v
  gi|336252938|ref|YP_004596045.1| 213 ADEHVFDMFAGIGYFTLPMARAGA-RVTASEINPTAFRYLLENAVLNEVDDRVEAYMTdcRDLAGEIEADRVV 284
                                       6789*****************998.699*************************99753224555467777666 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.24       5      55 ..     222     274 ..     218     324 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                       -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCT CS
                   Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaekl 55 
                                       +G G+++ ++a++garv++ ++++++ ++  e+a+ +++  +ve    d+++l
  gi|336252938|ref|YP_004596045.1| 222 AGIGYFTLPMARAGARVTASEINPTAFRYLLENAVLNEVddRVEAYMTDCRDL 274
                                       699************************99999999998877777777777765 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011       0.2      40     100 ..     212     271 ..     195     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                       HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES- CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkeda 100
                                       + +++v D+faG G   l  + R  +++++ e +++a++ l en    +++++++++  d 
  gi|336252938|ref|YP_004596045.1| 212 GADEHVFDMFAGIGYFTLP-MARAGARVTASEINPTAFRYLLENAVLNEVDDRVEAYMTDC 271
                                       56789**********9995.78999*******************99888888777766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2912.34
//
Query:       gi|336252939|ref|YP_004596046.1|  [L=398]
Description: NMD3 family protein [Halopiger xanaduensis SH-6]
Scores for complete 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-64  217.4   0.1    2.4e-64  217.1   0.1    1.1  1  NMD3           NMD3 family
    0.00046   20.4   0.4      0.043   14.1   0.0    3.1  3  Rpr2           RNAse P Rpr2/Rpp21/SNM1 subunit domain
     0.0036   17.3   5.9       0.17   11.9   3.8    3.0  2  DZR            Double zinc ribbon
     0.0053   16.4   4.4       0.65    9.8   0.1    3.5  3  zinc_ribbon_2  zinc-ribbon domain
  ------ inclusion threshold ------
      0.037   13.4   4.4        3.9    7.0   0.2    3.4  3  zf-ribbon_3    zinc-ribbon domain
      0.039   14.1   5.3       0.21   11.8   0.7    3.0  3  PknG_rubred    Protein kinase G rubredoxin domain
      0.054   13.6   1.7        5.3    7.2   1.0    2.9  2  FYVE           FYVE zinc finger
      0.087   13.0   0.1       0.27   11.4   0.0    1.9  1  DUF2703        Domain of unknown function (DUF2703)
       0.13   12.4   1.7        4.1    7.6   0.0    3.2  3  NOB1_Zn_bind   Nin one binding (NOB1) Zn-ribbon like
       0.22   11.2   6.5        2.4    7.8   0.1    3.4  3  zf_UBZ         Ubiquitin-Binding Zinc Finger
       0.27   11.6   3.7         11    6.5   0.1    3.4  3  GFA            Glutathione-dependent formaldehyde-activating 
        6.8    6.7  21.9        2.3    8.2   0.1    4.5  6  Nudix_N_2      Nudix N-terminal
        9.2    6.5   8.6         29    4.9   0.7    3.3  3  UPF0547        Uncharacterised protein family UPF0547


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 !  217.1   0.1   1.7e-67   2.4e-64       1     243 []       8     256 ..       8     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 217.1 bits;  conditional E-value: 1.7e-67
                              NMD3   1 CcrCGkei.........eeling........lCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseel 60 
                                       C+rCG+++         +    +        lC++C+++++d+++++++i+v+vC++Cg+++++++Wv+     +++
  gi|336252939|ref|YP_004596046.1|   8 CPRCGDPVpersasdatD----PlrpgaeveLCDACYFEDFDFVDAPDRIDVRVCSQCGAVHQGNRWVDI---GAQD 77 
                                       ********7766655441....155678889************************************776...999* PP

                              NMD3  61 laeclkklvekgLkvseeveevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprC 137
                                       +++++ + v+++L v+ +v +v ++ v++e   +++ +++i++++ ++g vrg   t +++ev+v+vk++rq+C+rC
  gi|336252939|ref|YP_004596046.1|  78 YTDIAIEKVSEALGVHVDVADVAWQ-VEPE---QVD-ENTIRMHCFFTGVVRG---TPVEEEVTVPVKISRQTCQRC 146
                                       *************************.****...888.99************88...7889***************** PP

                              NMD3 138 sriaggyyeaivQvRqk.relteeehkrtfelleqli....lkhdahafiskikevkeGlDfyfgsksaArklvefl 209
                                        riag+yy+++vQ+R++ r++t ee +r++e++++++    +++d++af+++i ev++Gl++++++++ ++k+++++
  gi|336252939|ref|YP_004596046.1| 147 GRIAGDYYASTVQIRAEdRTPTGEETDRAEEIAHRVVadmeATGDRNAFVTEIGEVDDGLNIKVSTNKIGKKIANKM 223
                                       ****************************************99*********************************** PP

                              NMD3 210 ksevggkvkeseklvsedkksgkevyrltysvrl 243
                                        +e+gg+v+++e+lv+ed++ g+evyr+t++vrl
  gi|336252939|ref|YP_004596046.1| 224 IEEFGGTVNDAETLVTEDED-GNEVYRVTFAVRL 256
                                       ********************.***********97 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 ?   -0.1   0.1      0.86   1.2e+03      44      54 ..       4      14 ..       2      40 .. 0.77
   2 ?    2.1   0.0      0.18   2.4e+02      40      54 ..      50      64 ..      45      73 .. 0.84
   3 !   14.1   0.0   3.1e-05     0.043      19      72 ..     114     167 ..      95     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.86
                                      CCTB-TTT--B CS
                              Rpr2 44 krtvCkkCgsv 54
                                      +r +C +Cg  
  gi|336252939|ref|YP_004596046.1|  4 SRAFCPRCGDP 14
                                      58899999875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.18
                                      SSTCCCTB-TTT--B CS
                              Rpr2 40 ppsvkrtvCkkCgsv 54
                                      p+ +  +vC++Cg+v
  gi|336252939|ref|YP_004596046.1| 50 PDRIDVRVCSQCGAV 64
                                      6788899*****987 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E CS
                              Rpr2  19 alsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkk 72 
                                       ++++++   +r    ++++ +p +++r++C++Cg +      ++v+++ + ++ 
  gi|336252939|ref|YP_004596046.1| 114 RMHCFFTGVVRGTPVEEEVTVPVKISRQTCQRCGRIAGDYYASTVQIRAEDRTP 167
                                       567778888888888999*******************99999999997655543 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   3.8   0.00013      0.17      11      36 ..       4      63 ..       1      70 [. 0.79
   2 ?    2.8   0.0     0.086   1.2e+02      28      36 ..     140     148 ..     123     155 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                               DZR 11 darfCseCgtklkavaa..................................edrCpsCge 36
                                      +  fC++Cg ++++ +a                                   ++C++Cg+
  gi|336252939|ref|YP_004596046.1|  4 SRAFCPRCGDPVPERSAsdatdplrpgaevelcdacyfedfdfvdapdridVRVCSQCGA 63
                                      567*********988889***********7777777777777777777777777777776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.086
                               DZR  28 edrCpsCge 36 
                                        ++C +Cg+
  gi|336252939|ref|YP_004596046.1| 140 RQTCQRCGR 148
                                       445555554 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00047      0.65       1      12 [.       7      18 ..       3      20 .. 0.75
   2 ?    4.7   0.1     0.019        26       2       7 ..      58      63 ..      54      68 .. 0.63
   3 ?    1.3   0.1      0.22   3.1e+02       2       6 ..     143     147 ..     140     149 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00047
                     zinc_ribbon_2  1 fCpnCGaelqdn 12
                                      fCp+CG +++++
  gi|336252939|ref|YP_004596046.1|  7 FCPRCGDPVPER 18
                                      677777777765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.019
                     zinc_ribbon_2  2 CpnCGa 7 
                                      C++CGa
  gi|336252939|ref|YP_004596046.1| 58 CSQCGA 63
                                      666665 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.22
                     zinc_ribbon_2   2 CpnCG 6  
                                       C +CG
  gi|336252939|ref|YP_004596046.1| 143 CQRCG 147
                                       66666 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0029       3.9       4      14 ..       7      17 ..       4      21 .. 0.75
   2 ?    5.8   0.1    0.0069       9.6       4      11 ..      57      64 ..      53      67 .. 0.74
   3 ?   -0.4   0.0      0.59   8.2e+02      12      23 ..     136     147 ..     133     149 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0029
                       zf-ribbon_3  4 rCPnCGaplss 14
                                      +CP+CG p+ +
  gi|336252939|ref|YP_004596046.1|  7 FCPRCGDPVPE 17
                                      8*****96554 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0069
                       zf-ribbon_3  4 rCPnCGap 11
                                       C++CGa+
  gi|336252939|ref|YP_004596046.1| 57 VCSQCGAV 64
                                      58888883 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.59
                       zf-ribbon_3  12 lssddnvCpyCG 23 
                                       ++ + ++C  CG
  gi|336252939|ref|YP_004596046.1| 136 VKISRQTCQRCG 147
                                       566667788887 PP

>> PknG_rubred  Protein kinase G rubredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   0.00015      0.21      89     127 ..       2      47 ..       1      60 [. 0.81
   2 ?   -1.9   0.1       2.4   3.4e+03      93     100 ..      56      63 ..      52      65 .. 0.83
   3 ?    3.4   0.1     0.057        79      86     103 ..     135     151 ..     120     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                       -GGG-B-TTT--B-S.---SS-.....---SEEE-TTT-.-EEE-S CS
                       PknG_rubred  89 pEskRfCwrCGrpvG.Rseker.....kgaseGtCpkCg.spysFl 127
                                       +Es+ fC rCG pv  Rs ++      +ga+  +C  C  + ++F+
  gi|336252939|ref|YP_004596046.1|   2 SESRAFCPRCGDPVPeRSASDAtdplrPGAEVELCDACYfEDFDFV 47 
                                       79************54888876666768999999999953667776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.4
                                       -B-TTT-- CS
                       PknG_rubred  93 RfCwrCGr 100
                                       R C++CG+
  gi|336252939|ref|YP_004596046.1|  56 RVCSQCGA 63 
                                       88999996 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.057
                                       S---GGG-B-TTT--B-S CS
                       PknG_rubred  86 pvvpEskRfCwrCGrpvG 103
                                       p v+ s+ +C rCGr  G
  gi|336252939|ref|YP_004596046.1| 135 P-VKISRQTCQRCGRIAG 151
                                       4.567999******9887 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.0    0.0039       5.3      25      64 ..       5      63 ..       1      67 [. 0.53
   2 ?    3.5   0.0     0.056        77      24      37 ..     139     152 ..     130     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0039
                                      -EE-TTT--EE-STTS-EEE.EE...................GGGTEEEEEEE-HHHHH CS
                              FYVE 25 rhhCrlCGkvvCekCssklvall...................ekeaeeksvrvCkeCla 64
                                      r  C  CG+ v e+  s  ++ l                    ++ ++ +vrvC++C a
  gi|336252939|ref|YP_004596046.1|  5 RAFCPRCGDPVPERSASDATDPLrpgaevelcdacyfedfdfVDAPDRIDVRVCSQCGA 63
                                      556666666666433333332223333333333333333333588888899****9976 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.056
                                       --EE-TTT--EE-S CS
                              FYVE  24 rrhhCrlCGkvvCe 37 
                                        r  C+ CG++  +
  gi|336252939|ref|YP_004596046.1| 139 SRQTCQRCGRIAGD 152
                                       6889******9765 PP

>> DUF2703  Domain of unknown function (DUF2703)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.27      21      94 ..      79     152 ..      75     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                           DUF2703  21 TgktleeavkelkeaLealgievelekvelseeelareflesntilingrpleell..gvevkeelCescgelsGe 94 
                                       T+ ++e++ + l    + ++++ ++e ++++e+ ++ + +   t  + g+p+ee +   v+ + ++C+ cg+++G+
  gi|336252939|ref|YP_004596046.1|  79 TDIAIEKVSEALGVHVDVADVAWQVEPEQVDENTIRMHCFF--TGVVRGTPVEEEVtvPVKISRQTCQRCGRIAGD 152
                                       56667777777777777777777777888888888855333..3457899999877456777899********998 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 ?    7.6   0.0     0.003       4.1      21      32 ..       3      14 ..       1      25 [. 0.81
   2 ?    1.0   0.2      0.35   4.8e+02      10      31 ..      35      63 ..      32      70 .. 0.70
   3 ?    0.3   0.0      0.58     8e+02      20      31 ..     137     148 ..     130     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.003
                      NOB1_Zn_bind 21 mtkkFCpkCGnk 32
                                       ++ FCp+CG +
  gi|336252939|ref|YP_004596046.1|  3 ESRAFCPRCGDP 14
                                      5799******86 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.35
                      NOB1_Zn_bind 10 rChaCfk....vt...kdmtkkFCpkCGn 31
                                       C aC+     ++    + + + C++CG 
  gi|336252939|ref|YP_004596046.1| 35 LCDACYFedfdFVdapDRIDVRVCSQCGA 63
                                      69999875555223335578889999995 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.58
                      NOB1_Zn_bind  20 dmtkkFCpkCGn 31 
                                       + +++ C++CG 
  gi|336252939|ref|YP_004596046.1| 137 KISRQTCQRCGR 148
                                       568999****96 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0017       2.4       4      14 ..       7      17 ..       4      21 .. 0.87
   2 ?    1.7   0.1      0.14   1.9e+02       4      10 ..      57      63 ..      54      65 .. 0.85
   3 ?    3.2   0.4     0.047        65       3      10 ..     141     148 ..     139     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0017
                            zf_UBZ  4 lCerCgkeipe 14
                                      +C+rCg ++pe
  gi|336252939|ref|YP_004596046.1|  7 FCPRCGDPVPE 17
                                      8********98 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                            zf_UBZ  4 lCerCgk 10
                                      +C++Cg+
  gi|336252939|ref|YP_004596046.1| 57 VCSQCGA 63
                                      8****97 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.047
                            zf_UBZ   3 ylCerCgk 10 
                                       ++C+rCg+
  gi|336252939|ref|YP_004596046.1| 141 QTCQRCGR 148
                                       79****96 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0078        11      48      63 ..       4      19 ..       1      32 [. 0.78
   2 ?    0.6   0.2      0.51     7e+02      42      58 ..      48      64 ..      31      72 .. 0.78
   3 ?    3.2   0.0     0.083   1.1e+02       4      28 ..     142     166 ..     137     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0078
                               GFA 48 trsfCpeCgsplysee 63
                                      +r fCp+Cg p+  ++
  gi|336252939|ref|YP_004596046.1|  4 SRAFCPRCGDPVPERS 19
                                      689********99543 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.51
                               GFA 42 dsgnkvtrsfCpeCgsp 58
                                      d  ++++ ++C++Cg+ 
  gi|336252939|ref|YP_004596046.1| 48 DAPDRIDVRVCSQCGAV 64
                                      5667788899****975 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.083
                               GFA   4 hCsdCrkasgsaftanavvkaeale 28 
                                        C++C +++g  +++ + ++ae+ +
  gi|336252939|ref|YP_004596046.1| 142 TCQRCGRIAGDYYASTVQIRAEDRT 166
                                       5999999999999999999988866 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0017       2.3       2      13 ..       7      18 ..       6      26 .. 0.83
   2 ?   -2.7   0.1       4.1   5.7e+03      25      28 ..      36      39 ..      34      41 .. 0.77
   3 ?    6.5   0.4    0.0056       7.7      24      32 ..      57      65 ..      52      66 .. 0.92
   4 ?   -3.9   0.0       9.8   1.4e+04      17      25 ..     109     117 ..     107     117 .. 0.83
   5 ?    6.6   0.4    0.0051       7.1       7      31 ..     125     149 ..     125     150 .. 0.85
   6 ?   -1.8   0.2       2.2     3e+03      11      23 ..     163     175 ..     161     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0017
                                      B-TTT--B-EEE CS
                         Nudix_N_2  2 FCsqCGtpvelr 13
                                      FC+ CG pv  r
  gi|336252939|ref|YP_004596046.1|  7 FCPRCGDPVPER 18
                                      9*******9655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.1
                                      ETTT CS
                         Nudix_N_2 25 CpaC 28
                                      C+aC
  gi|336252939|ref|YP_004596046.1| 36 CDAC 39
                                      9999 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0056
                                      EETTTTEEE CS
                         Nudix_N_2 24 vCpaCgtih 32
                                      vC++Cg++h
  gi|336252939|ref|YP_004596046.1| 57 VCSQCGAVH 65
                                      9*****999 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 9.8
                                       T-SS-EEEE CS
                         Nudix_N_2  17 gDnreRlvC 25 
                                       ++n  R  C
  gi|336252939|ref|YP_004596046.1| 109 DENTIRMHC 117
                                       689999999 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0051
                                       --B-EEE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2   7 GtpvelripdgDnreRlvCpaCgti 31 
                                       Gtpve ++    +  R +C++Cg i
  gi|336252939|ref|YP_004596046.1| 125 GTPVEEEVTVPVKISRQTCQRCGRI 149
                                       778888888888889********98 PP

  == domain 6  score: -1.8 bits;  conditional E-value: 2.2
                                       EEE--TT-SS-EE CS
                         Nudix_N_2  11 elripdgDnreRl 23 
                                       e r+p g++  R+
  gi|336252939|ref|YP_004596046.1| 163 EDRTPTGEETDRA 175
                                       6799*****9985 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   0.7     0.021        29       3      12 ..       8      17 ..       7      19 .. 0.89
   2 ?    3.9   0.2     0.041        56      12      21 ..      53      62 ..      53      66 .. 0.88
   3 ?    0.8   0.1       0.4   5.5e+02       9      21 ..     135     147 ..     133     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.021
                           UPF0547  3 CPeCeakvPv 12
                                      CP+C  +vP+
  gi|336252939|ref|YP_004596046.1|  8 CPRCGDPVPE 17
                                      9999999996 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.041
                           UPF0547 12 vaaqfCphCG 21
                                      +++++C+ CG
  gi|336252939|ref|YP_004596046.1| 53 IDVRVCSQCG 62
                                      689******9 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.4
                           UPF0547   9 kvPvaaqfCphCG 21 
                                       +v+++ q C  CG
  gi|336252939|ref|YP_004596046.1| 135 PVKISRQTCQRCG 147
                                       58899999*99*9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2813.78
//
Query:       gi|336252940|ref|YP_004596047.1|  [L=293]
Description: protease htpX [Halopiger xanaduensis SH-6]
Scores for 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-44  151.6   0.0    3.6e-44  150.9   0.0    1.3  1  Peptidase_M48  Peptidase family M48
    3.9e-10   39.4   0.3    1.2e-08   34.5   0.0    2.2  2  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.013   15.3   0.0       0.02   14.7   0.0    1.3  1  SprT-like      SprT-like family
      0.023   15.0   0.5      0.023   15.0   0.5    2.2  2  DUF996         Protein of unknown function (DUF996)
      0.084   13.1   0.1       0.19   12.0   0.1    1.6  1  DUF4157        Domain of unknown function (DUF4157)


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 !  150.9   0.0     1e-47   3.6e-44       4     195 ..      74     286 ..      71     287 .. 0.88

  Alignments for each domain:
  == domain 1  score: 150.9 bits;  conditional E-value: 1e-47
                                       SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   4 eaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrh 79 
                                        ++l++++e+l ++a+l  p++kv+vv+s+  NAFa+g+++++  + +t+g++ ++l+eeel++Vl+HEl+H+k+r+
  gi|336252940|ref|YP_004596047.1|  74 YPQLHATIERLSQQADL--PKPKVAVVDSQVPNAFATGRNQKNaAVCVTTGIM-TTLNEEELEGVLAHELAHVKNRD 147
                                       579**************..*********************9999*********.*********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT.......HHHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  80 svvslivsllasillllglallisraeedaagafldalavliglliillfl.......alSRkrEyqADeagvellk 149
                                       ++v++i s l++i++++++  ++   ++  +g +++   v+++l+++l+ +       alSR+rEy AD+ ++ ++ 
  gi|336252940|ref|YP_004596047.1| 148 MMVMTIASFLSTIAFMIVRWGAFFG-GGHGRGRQGGGGIVVAILVSLLVWIisyllirALSRYREYAADRGAAAITG 223
                                       **************99998644433.33333333333344444455554446668999******************* PP

                                       .HHHHHHHHHHHHHHTT--S---HHHH.................HHS-SS--HHHHHHHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 150 rakdlvraliklakdlerqdvsaslrs.................ellstHPplleRiqalkel 195
                                       ++ +l++al+k++ +++++++++  ++                  l+stHPp+++Ri++l++l
  gi|336252940|ref|YP_004596047.1| 224 NPSALASALMKISGRMDKVPKDDMREEaemnaffiipiksgvvgRLFSTHPPTEKRIEQLRSL 286
                                       ***********************99999********************************986 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   3.4e-12   1.2e-08     104     226 ..      38     162 ..      15     163 .. 0.87
   2 ?    3.0   0.1     0.014        49       8      35 ..     186     213 ..     183     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 3.4e-12
                     Peptidase_M56 104 illliWivgalilllyliaallvlkkrfvrklgklraeelkeaLkeakeemqlkrnikirlsssidsPavlgllkp. 179
                                       +++ ++++g + l+ y     l l++   r  ++ +  +l   ++  +++  l ++   ++ s++ + + +g  +  
  gi|336252940|ref|YP_004596047.1|  38 FVVFVVLFGGMSLVQYYFSDTLTLRSMGARTVSADEYPQLHATIERLSQQADLPKPKVAVVDSQVPNAFATGRNQKn 114
                                       67888999999999999999999998877777777777789999999999999999999999999998888875532 PP

                     Peptidase_M56 180 .rIvlPadflkklsdeeleyillHElaHlkrkDllvnllvavlqclfw 226
                                         + + + ++++l++eele +l+HElaH+k++D++v  ++ +l+ + +
  gi|336252940|ref|YP_004596047.1| 115 aAVCVTTGIMTTLNEEELEGVLAHELAHVKNRDMMVMTIASFLSTIAF 162
                                       2799999************************************99976 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.014
                     Peptidase_M56   8 iaaaiavllvlllrrilrrllsaiaaYa 35 
                                       + a ++ llv+++ ++l r ls  ++Ya
  gi|336252940|ref|YP_004596047.1| 186 VVAILVSLLVWIISYLLIRALSRYREYA 213
                                       5677788999999999999999999986 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.7e-06      0.02      40      77 ..      88     145 ..      43     152 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-06
                         SprT-like  40 r....................atvrhhasIeLseklldsrsedrllntLaHElcHlal 77 
                                                             +++++a +   + ++++ +e++l+ +LaHEl+H+ +
  gi|336252940|ref|YP_004596047.1|  88 AdlpkpkvavvdsqvpnafatGRNQKNAAVCVTTGIMTTLNEEELEGVLAHELAHVKN 145
                                       14444444444444444444444566789999999********************876 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.7      0.11   3.8e+02      29      58 ..      22      51 ..       9      68 .. 0.49
   2 ?   15.0   0.5   6.4e-06     0.023      27     104 ..     146     224 ..     136     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.11
                            DUF996 29 aliafilsiialvvailalllvlgalatal 58
                                      al+ + +++ia ++  +++ +vl+  ++ +
  gi|336252940|ref|YP_004596047.1| 22 ALYIVFAGVIAAYMGSFVVFVVLFGGMSLV 51
                                      223333333333333444444444444433 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 6.4e-06
                            DUF996  27 snaliafilsiialvvailalllvlgalatalelpgleeaaslilllllvliiay.vlliisavflkksyellgkrt 102
                                       +++++++i+s+ ++++++++  ++++   ++ +++g   + ++il++llv+ii y ++  +s +  + + +  +++t
  gi|336252940|ref|YP_004596047.1| 146 RDMMVMTIASFLSTIAFMIVRWGAFFGGGHGRGRQGGGGIVVAILVSLLVWIISYlLIRALSRYREYAADRGAAAIT 222
                                       789999*********************************999*********99993444566666665555555566 PP

                            DUF996 103 gv 104
                                       g+
  gi|336252940|ref|YP_004596047.1| 223 GN 224
                                       65 PP

>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.4e-05      0.19      40      74 ..     118     145 ..      95     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.4e-05
                           DUF4157  40 AfTlgndivfaageyqpesaagrellaHELtHvvq 74 
                                        +T+g    +       ++++ + +laHEL+Hv  
  gi|336252940|ref|YP_004596047.1| 118 CVTTGIMTTL-------NEEELEGVLAHELAHVKN 145
                                       4444444444.......34555679********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1120  (0.0624686); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2212.72
//
Query:       gi|336252941|ref|YP_004596048.1|  [L=88]
Description: hypothetical protein Halxa_1537 [Halopiger xanaduensis SH-6]
Scores for 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   12.1   0.0       0.16   11.7   0.0    1.2  1  Tetraspanin   Tetraspanin family
        0.3   11.1   3.9        1.6    8.7   0.1    2.1  2  SecE          SecE/Sec61-gamma subunits of protein translocat


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.8e-05      0.16      42     107 ..       7      72 ..       3      87 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.8e-05
                                       ...........XXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX--HHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                       Tetraspanin  42 saedpailaillivvGvllfllgflG.cigalkenkcllltfsllllvlfllelaagi.lgfvfsdka 107
                                         e +a+++ +l+++G++lf+ +  G   g+l+     ll+ +++ ++l+++ ++  + l++v++d +
  gi|336252941|ref|YP_004596048.1|   7 LIEIAAAVTSVLLMLGAMLFIGTAYGgTNGTLNPDGAQLLVGVIVGFILLMTAVG--VgLAYVLNDPE 72 
                                       56778889999******99998888835556666666665555555555555444..44788888873 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 ?    8.7   0.1   0.00018       1.6      17      42 ..       2      27 ..       1      27 [. 0.95
   2 ?    3.2   1.2    0.0097        87      27      46 ..      48      67 ..      43      71 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00018
                                      CHCCHHHHHHHHHHHHHHHHHHHHHH CS
                              SecE 17 PtrkEllkttvvVlvfvvimglflfl 42
                                      P r++l+ ++++V  + +++g+ lf+
  gi|336252941|ref|YP_004596048.1|  2 PEREQLIEIAAAVTSVLLMLGAMLFI 27
                                      99********************9996 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0097
                                      HHHHHHHHHHHHHHHHHHHH CS
                              SecE 27 vvVlvfvvimglflflvDlv 46
                                      +v + f+++m++++ ++ +v
  gi|336252941|ref|YP_004596048.1| 48 GVIVGFILLMTAVGVGLAYV 67
                                      56666777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 615.20
//
Query:       gi|336252942|ref|YP_004596049.1|  [L=151]
Description: hypothetical protein Halxa_1538 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        3.9    7.4   8.8       0.26   11.2   0.9    2.5  3  GRA6      Granule antigen protein (GRA6)


Domain annotation for each model (and alignments):
>> GRA6  Granule antigen protein (GRA6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3     0.026   4.7e+02     159     176 ..      26      43 ..      13      50 .. 0.80
   2 ?   11.2   0.9   1.5e-05      0.26     153     205 ..      51      98 ..      42     105 .. 0.59
   3 ?   -1.2   0.0     0.092   1.7e+03      73     102 ..     117     147 ..     114     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.026
                              GRA6 159 vlaasvalltafflrrsg 176
                                        + a+vall a  l r++
  gi|336252942|ref|YP_004596049.1|  26 AVVAVVALLGASVLVRTS 43 
                                       456789999999999987 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 1.5e-05
                              GRA6 153 rliGavvlaasvalltafflrrsgrrapgePrgendgndagdnagnrenegrg 205
                                        +iG+vvla    +l        +rr++g+ r  + g+   d   + +  g g
  gi|336252942|ref|YP_004596049.1|  51 AVIGSVVLAGIALAL-----VVLSRRSAGDSRAPTRGDADADADPDADGTGGG 98 
                                       588888888765555.....345888888877555555444444333333333 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.092
                              GRA6  73 vnssalg.Ggqgdslaeaddetsdvaegdvd 102
                                       v+s  l+ G q  +l e +de+ + a +d  
  gi|336252942|ref|YP_004596049.1| 117 VESGGLArGEQTRALQEIQDEADELAGSDDP 147
                                       6666666477888999999999999888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1130.49
//
Query:       gi|336252943|ref|YP_004596050.1|  [L=364]
Description: DNA primase large subunit [Halopiger xanaduensis SH-6]
Scores for 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-34  117.1   0.0    1.4e-33  116.4   0.0    1.3  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 !  116.4   0.0   7.9e-38   1.4e-33       2     217 ..     139     327 ..     138     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 7.9e-38
                                       EEEEEHHHHHHHTT-G........GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HH CS
                   DNA_primase_lrg   2 fykvpfedvldlvkrr........rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederek 70 
                                       +y++++ +++ l+++         +++l++G + +++++l++ll+e++r r+ ++l + +  ++  +    e+e + 
  gi|336252943|ref|YP_004596050.1| 139 EYRIDVGTYVPLAEDLwedgwrlvNQPLDRGAVPVDESDLLTLLREAIRTRIDDGLPF-EVPDAIADA--LEEEAAA 212
                                       57777777777777334457888899*******************************9.333333322..3333335 PP

                                       HHHHHCT--.............TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHH CS
                   DNA_primase_lrg  71 leellealsesyvaedvqeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldei 147
                                       ++++l  l                  +++id+++ ++fPpCm++ll++++k++hl+h++r+++t+Fl +ig+++dei
  gi|336252943|ref|YP_004596050.1| 213 VRDVLADLD----------------LTREIDTVVPDLFPPCMKALLDQIQKGEHLPHHSRFAITAFLTSIGMTTDEI 273
                                       777777777................45568*********************************************** PP

                                       HCCCHCHST..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S.-HHHH.HHHHHHH CS
                   DNA_primase_lrg 148 lelwkeaftrteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahg.Cpfrhdpdklktl 217
                                       ++l + +      +F +  +ry+ +h+ G + + t+ysp+sC+++         +++g C+   ++d+l ++
  gi|336252943|ref|YP_004596050.1| 274 VDLYRVN-----SSFGEeMTRYQTDHIRG-DTSPTEYSPPSCATM---------QSYGdCV---NKDDLCEQ 327
                                       ******8.....9****9999********.9**************.........9*****7...55665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2806.60
//
Query:       gi|336252944|ref|YP_004596051.1|  [L=289]
Description: alpha/beta hydrolase fold protein [Halopiger xanaduensis SH-6]
Scores for 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-26   93.1   0.0    5.6e-24   85.2   0.0    2.0  1  Abhydrolase_1  alpha/beta hydrolase fold
    7.4e-22   79.0   7.8    8.8e-22   78.8   7.8    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    6.9e-18   64.8   0.0    1.8e-17   63.4   0.0    1.5  1  Hydrolase_4    Serine aminopeptidase, S33
    0.00017   21.7   0.0    0.00028   20.9   0.0    1.3  1  Abhydrolase_4  TAP-like protein
     0.0014   18.2   0.0      0.012   15.1   0.0    2.3  3  Peptidase_S9   Prolyl oligopeptidase family
     0.0016   18.2   0.0       0.72    9.6   0.0    2.2  2  Abhydrolase_5  Alpha/beta hydrolase family
     0.0088   15.6   0.0      0.079   12.5   0.0    2.0  2  DLH            Dienelactone hydrolase family
  ------ inclusion threshold ------
      0.018   14.7   0.0      0.032   13.9   0.0    1.3  1  FSH1           Serine hydrolase (FSH1)
      0.022   13.8   0.0       0.98    8.5   0.0    2.0  2  DUF2048        Abhydrolase domain containing 18
      0.032   14.4   0.0      0.045   13.9   0.0    1.3  1  Patatin        Patatin-like phospholipase
      0.034   14.1   0.0       0.28   11.1   0.1    2.0  2  UPF0227        Uncharacterised protein family (UPF0227)
       0.11   11.2   0.0       0.16   10.6   0.0    1.2  1  Ndr            Ndr family
       0.16   11.2   0.2         14    4.9   0.2    2.2  2  LIP            Secretory lipase


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 !   85.2   0.0   4.1e-27   5.6e-24       2     256 ..      26     272 ..      25     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 4.1e-27
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB...............CHHSHHHHHHHHH CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacin..............ddygtasvaddld 64 
                                       ++v+l+Gl+ + ++w+    ++   +d+++vi++D rG g+S++++ +                  y++  +a+dl+
  gi|336252944|ref|YP_004596051.1|  26 PVVLLQGLGFGRWMWRW---QREALRDKYQVIAPDTRGTGRSDAGLPPLLprlpgrlrtpllsrFGYSIEGLAADLE 99 
                                       89***********9776...5555566*******************98889***********99999********** PP

                                       HHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHH CS
                     Abhydrolase_1  65 rildalgddkltlvGhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpag 141
                                       ++l+  g+++ ++vG S+GGm+a +ya eyp   ++l+ll++  ++  ++ a    + + +  + g   d +r ++ 
  gi|336252944|ref|YP_004596051.1| 100 AVLEDAGVRSAHIVGASLGGMVAQQYAVEYPR-ASSLTLLCT--SHGGPDAAPIPEDVRQQLLAGGGDGDRKRLRDS 173
                                       *******************************8.9********..444444444444444444444444444444444 PP

                                       HHHHCCSCHHHHHHHHHHHHHHHCHHHCCHH.HHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEE CS
                     Abhydrolase_1 142 plladelaaleqrhrlvdalkfpdkskrfps.sgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvi 217
                                       +   ++ ++++ +         p  ++r+ +  + ++a ++a+ a+++        ++ + +rl +   v +ptl++
  gi|336252944|ref|YP_004596051.1| 174 MRPVFSERFTNRN---------PHLMDRIVEwRREQDAGGPARIAQGAA-----VSNFDVADRLAS---VRVPTLIM 233
                                       4444444444444.........888888887555556666666665443.....333333344333...445***** PP

                                       EETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                     Abhydrolase_1 218 sgtsDplvppkaledlaqllpkkrlvvisdagHlafleg 256
                                       +gt+D++vpp + + la+ +p+++l++++++ H+ f e+
  gi|336252944|ref|YP_004596051.1| 234 HGTDDRVVPPANARLLAERIPDAELEHVDGGSHCFFVER 272
                                       ***********************************9987 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   7.8   6.3e-25   8.8e-22       1     219 [.      27     278 ..      27     279 .. 0.65

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 6.3e-25
                                       EEEE--GC.....GCHHHH.HHHHCCTCEEEEE--TTSTS-........GGCS..............--HHH.CHHH CS
                     Abhydrolase_6   1 vlllHGagssassWlvapL.aallaagvhvlapDlpGhGrs........dppp..............ldled.ladl 53 
                                       v+ll G+g+++++W   ++ +++l++ ++v+apD +G+Grs        +                 ++ e  +adl
  gi|336252944|ref|YP_004596051.1|  27 VVLLQGLGFGRWMW---RWqREALRDKYQVIAPDTRGTGRSdaglppllP--RlpgrlrtpllsrfgYSIEGlAADL 98 
                                       89************...55477778889***********66444333331..0344444444555345555556888 PP

                                       HHHHCCTT..TTSEEEEEETCHHHHHHHHHHCC.....EE..EEES-..----TTTS----TTHHHHHH....TT-C CS
                     Abhydrolase_6  54 aalldelaagggpvvlvGHSlGGalalaaapla...lvvg..vlldppptalpagllaaalelllalla....llrl 121
                                       +a+l++ +   + +++vG SlGG++a++   +a   ++++   ll++   + + +++a+++e +++ l        +
  gi|336252944|ref|YP_004596051.1|  99 EAVLEDAG--VRSAHIVGASLGGMVAQQ---YAveyPRASslTLLCT---SHGGPDAAPIPEDVRQQLLagggDGDR 167
                                       99999995..7888**************...5555555556999999...555555444444444333312223333 PP

                                       CCCH.CCH.S-HSCCCCHHH..C..CCCHCHCCCGHH.....HHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHHHC CS
                     Abhydrolase_6 122 lawl.sre.plprlfladed..a..daawrarlarla.....allaglgllpaaawadlpvpllvl.ggeDplvprl 186
                                        +++ s++  ++++f + ++  +   ++wr+  +++      + +a   +  a+++a ++vp+l++ g++D++vp+ 
  gi|336252944|ref|YP_004596051.1| 168 KRLRdSMRpVFSERFTNRNPhlMdrIVEWRREQDAGGpariaQGAAVSNFDVADRLASVRVPTLIMhGTDDRVVPPA 244
                                       333322112222244443333322355555555555533232444444466799*********998679999***** PP

                                       HHCCCH..STTEEETCE...SSS-HHHHSHHHHHH CS
                     Abhydrolase_6 187 lerlla..qagarlpvvlpgaGHlphleepdevae 219
                                        +rlla  +++a+l + + g++H+++ e+ d+v+e
  gi|336252944|ref|YP_004596051.1| 245 NARLLAerIPDAEL-EHVDGGSHCFFVERDDRVNE 278
                                       99****999*****.9***********88899986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   1.3e-20   1.8e-17      30     239 .]      49     273 ..      44     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 1.3e-20
                       Hydrolase_4  30 qGfavyalDhrGhGrse.............gkrg.hvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliall 92 
                                         ++v+a D rG Grs+               r   +++f   ++ laa +e+v e+ + +   ++G S+GG++a++
  gi|336252944|ref|YP_004596051.1|  49 DKYQVIAPDTRGTGRSDaglppllprlpgrL-RTpLLSRFGYSIEGLAADLEAVLEDAGVRSAHIVGASLGGMVAQQ 124
                                       579************************7642.2236778888899999999999999999999************** PP

                       Hydrolase_4  93 yllrypdkvaglilsaPalkikaklk.appllklllkllgkllpklqv....snnlkadslsrdpevvaayeadplv 164
                                       y+ +yp+  + l l ++  + +   + +  + + ll   g    + ++          ++  r+p+ ++++ +    
  gi|336252944|ref|YP_004596051.1| 125 YAVEYPR-ASSLTLLCTSHGGPDAAPiPEDVRQQLLAGGGD-GDRKRLrdsmRPVFSERFTNRNPHLMDRIVEWRRE 199
                                       *******.778999999988887766444444443333332.22333334555577889999*******99999988 PP

                       Hydrolase_4 165 .hgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnEpd 239
                                          +  +r+++++     ++ +r a++++P+l++hG++D+vv+p+++r l+er++  d +l+  +g+ H  + E+d
  gi|336252944|ref|YP_004596051.1| 200 qDAGGPARIAQGAAVSNFDVADRLASVRVPTLIMHGTDDRVVPPANARLLAERIP--DAELEHVDGGSHCFFVERD 273
                                       8999***************************************************..9**************9986 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     2e-07   0.00028      32      93 ..     225     286 ..     209     289 .] 0.89

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2e-07
                     Abhydrolase_4  32 kgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLlt 93 
                                        + +p+L++ ++ D ++P++ a+ la+++++a+l  v+g+ H+++ + ++ v++ + ++L++
  gi|336252944|ref|YP_004596051.1| 225 SVRVPTLIMHGTDDRVVPPANARLLAERIPDAELEHVDGGSHCFFVERDDRVNESLLSFLAE 286
                                       4469*****************************************999******99999986 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.5   3.4e+03       5      26 ..      42      62 ..      38      64 .. 0.74
   2 ?    0.0   0.0      0.36     5e+02      67      82 ..     111     126 ..     104     132 .. 0.79
   3 !   15.1   0.0   8.5e-06     0.012     125     168 ..     209     252 ..     175     284 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
                                      HHHHHHHCCT-EEEEE--TTSS CS
                      Peptidase_S9  5 selqlladrGyvvvvanirGsg 26
                                      ++ + l    y v++++ rG+g
  gi|336252944|ref|YP_004596051.1| 42 WQREAL-RDKYQVIAPDTRGTG 62
                                      556666.567999999999998 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.36
                                       EEEEETHHHHHHHHHH CS
                      Peptidase_S9  67 aitGgSyGGyltgaal 82 
                                        i G+S GG+++   +
  gi|336252944|ref|YP_004596051.1| 111 HIVGASLGGMVAQQYA 126
                                       699*******987655 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 8.5e-06
                                       HHHHHHHHHH-CGGG--.---EEEEEEETT-SSS-THHHHHHHHH CS
                      Peptidase_S9 125 eegykelspyspldnvk.aypplLlihGlaDdrvppaealklvaa 168
                                        +g  ++s+ + +d+++ + +p+L++hG+ D  vppa+a  l+++
  gi|336252944|ref|YP_004596051.1| 209 AQG-AAVSNFDVADRLAsVRVPTLIMHGTDDRVVPPANARLLAER 252
                                       333.3677777777777899******************9988876 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0049       6.7      53      86 ..     104     137 ..      90     147 .. 0.76
   2 !    9.6   0.0   0.00052      0.72      93     143 ..     220     269 ..     210     275 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0049
                     Abhydrolase_5  53 apklekfvvgGhslGGvvasrfaaeeekiegvvf 86 
                                         +++   + G slGG+va ++a e  +  ++ +
  gi|336252944|ref|YP_004596051.1| 104 DAGVRSAHIVGASLGGMVAQQYAVEYPRASSLTL 137
                                       4457778899*************98766555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00052
                     Abhydrolase_5  93 kdelselskkvlsivgteDgvlnvkslekakkflpkdtkvvsieGgnhagf 143
                                        d l +  +++l + gt+D v++  +++  ++++p d+++ +++Gg h+ f
  gi|336252944|ref|YP_004596051.1| 220 ADRLASVRVPTLIMHGTDDRVVPPANARLLAERIP-DAELEHVDGGSHCFF 269
                                       678889999*************************9.6899********988 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.21   2.9e+02      97     122 ..     107     132 ..      90     188 .. 0.81
   2 !   12.5   0.0   5.7e-05     0.079     140     199 ..     223     278 ..     213     283 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.21
                               DLH  97 tkkvgvvGfCmGGalalllaaevpev 122
                                       +    +vG  +GG +a ++a e p++
  gi|336252944|ref|YP_004596051.1| 107 VRSAHIVGASLGGMVAQQYAVEYPRA 132
                                       4556789999**********998765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.7e-05
                               DLH 140 aakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsresyne 199
                                        a + +p l+++g+ D ++p +++  l+e +    +d+el+  +g  H F+ ++++  ne
  gi|336252944|ref|YP_004596051.1| 223 LASVRVPTLIMHGTDDRVVPPANARLLAERI----PDAELEHVDGGSHCFFVERDDRVNE 278
                                       567899***********************99....9999999**********99987776 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.3e-05     0.032     159     198 ..     225     263 ..     204     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-05
                              FSH1 159 kiqtptLhvlGelDtvvdeerseaLaeafknsskvlkHpg 198
                                       ++++ptL ++G++D vv++++++ Lae + + +++ + +g
  gi|336252944|ref|YP_004596051.1| 225 SVRVPTLIMHGTDDRVVPPANARLLAERIPD-AELEHVDG 263
                                       579*************************999.66555555 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.022        30     170     202 ..     102     134 ..      91     152 .. 0.80
   2 ?    8.5   0.0   0.00071      0.98     297     345 ..     231     279 ..     158     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.022
                           DUF2048 170 lereGyGplgltGlSmGGhmaslaasnwpkplv 202
                                       le  G     + G S+GG+ a+  a  +p+  +
  gi|336252944|ref|YP_004596051.1| 102 LEDAGVRSAHIVGASLGGMVAQQYAVEYPRASS 134
                                       55667778889****************999765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00071
                           DUF2048 297 ivvaAkdDayvpresvaslqeiwpgsevryldgGHvsayllkkklfrka 345
                                        ++  +dD+ vp  + + l e  p++e +++dgG   +++ + +   ++
  gi|336252944|ref|YP_004596051.1| 231 LIMHGTDDRVVPPANARLLAERIPDAELEHVDGGSHCFFVERDDRVNES 279
                                       356789****************************999999998876655 PP

>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.3e-05     0.045       9      81 ..      86     194 ..      84     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                           Patatin   9 rgafslgalka.....LkkelgerfdiisGtSaGAiia....................................lll 44 
                                       r  +s++ l+a     L +++g r  +i+G+S G+++a                                    l+ 
  gi|336252944|ref|YP_004596051.1|  86 RFGYSIEGLAAdleavL-EDAGVRSAHIVGASLGGMVAqqyaveyprassltllctshggpdaapipedvrqqlLAG 161
                                       55578888888877788.9********************************99999999999999999999985555 PP

                           Patatin  45 algrdpaalvddlrnlllnkifdrdl.....lirelaanlaa 81 
                                       +  +d+++l+d +r ++++++++r++     +         +
  gi|336252944|ref|YP_004596051.1| 162 GGDGDRKRLRDSMRPVFSERFTNRNPhlmdrI---------V 194
                                       55599999999999999999999996555531.........2 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0002      0.28      45      77 ..      94     126 ..      84     135 .. 0.86
   2 ?    0.6   0.0      0.34   4.7e+02     131     150 ..     224     243 ..     187     272 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                           UPF0227  45 alkeleklvaelgddnillvGssLGGyyatrlg 77 
                                       +++ le+++++ g ++  +vG sLGG +a+  +
  gi|336252944|ref|YP_004596051.1|  94 LAADLEAVLEDAGVRSAHIVGASLGGMVAQQYA 126
                                       67889999********************98766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.34
                           UPF0227 131 lkrperilvllskqDevldy 150
                                       +  ++++l++++++D v++ 
  gi|336252944|ref|YP_004596051.1| 224 ASVRVPTLIMHGTDDRVVPP 243
                                       5668999*********9986 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00012      0.16      81     122 ..      90     131 ..      83     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                                       -HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGG CS
                               Ndr  81 slddladqllavldhfklksviglGvgaGAyilarfalkhpe 122
                                       s+++la +l+avl+   ++s+  +G+  G  +  ++a+++p 
  gi|336252944|ref|YP_004596051.1|  90 SIEGLAADLEAVLEDAGVRSAHIVGASLGGMVAQQYAVEYPR 131
                                       89**************************************95 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2    0.0098        14      76     112 ..      87     123 ..      81     128 .. 0.92
   2 ?    3.9   0.0      0.02        28     215     241 ..     227     253 ..     208     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0098
                               LIP  76 wGYSgGslAsawAaelqpeYAPelelvGaalGgfvan 112
                                       +GYS  +lA+   a+l        ++vGa lGg+va+
  gi|336252944|ref|YP_004596051.1|  87 FGYSIEGLAADLEAVLEDAGVRSAHIVGASLGGMVAQ 123
                                       9********************************9986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.02
                               LIP 215 qiPvlvyhgvidelipikdakklaknw 241
                                       ++P l++hg+ d ++p  +a+ la+  
  gi|336252944|ref|YP_004596051.1| 227 RVPTLIMHGTDDRVVPPANARLLAERI 253
                                       689***************999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2260.78
//
Query:       gi|336252945|ref|YP_004596052.1|  [L=104]
Description: hypothetical protein Halxa_1541 [Halopiger xanaduensis SH-6]
Scores for 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-26   91.8   0.8    3.3e-26   91.4   0.8    1.2  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.8   1.8e-30   3.3e-26       2      75 .]      22      95 ..      21      95 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 1.8e-30
                            HalOD1  2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75
                                       e++s+a+v+a+aa+ + dp  l+pLyda+DpdAL+aL+a++++ ++ ++++++Ftyeg++V Vr dg+i++e+
  gi|336252945|ref|YP_004596052.1| 22 GERASEAIVTAIAALVDDDPASLSPLYDAVDPDALNALVAHARRADDAGTHELRFTYEGFDVGVRTDGRIQIED 95
                                      5899*******************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 811.49
//
Query:       gi|336252946|ref|YP_004596053.1|  [L=118]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   57.2   0.0    1.5e-15   56.7   0.0    1.2  1  HTH_10    HTH DNA binding domain
     0.0011   18.9   0.0     0.0013   18.6   0.0    1.2  1  BAT       GAF and HTH_10 associated domain


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 !   56.7   0.0   1.6e-19   1.5e-15       3      52 ..      51     100 ..      50     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 1.6e-19
                            HTH_10   3 dkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       ++qle+l lAye GYFd+PRr+tl++LA   GI++++l  +Lr+  ++l+
  gi|336252946|ref|YP_004596053.1|  51 PAQLEALELAYERGYFDEPRRATLEDLAAGVGITRQSLAGRLRRGHRNLL 100
                                       68******************************************999987 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.4e-07    0.0013       6      58 ..       5      57 ..       2      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-07
                               BAT  6 Leleirdeddvlval.aaeldcrveleglvprsdgevlvfftvdgadpeevrda 58
                                      +e++++ ++++l al a+  d ++el+++vp+  g++  +++++ga+p++++++
  gi|336252946|ref|YP_004596053.1|  5 VEFTVDGDEFPLGALfASLPDVAIELDRIVPT-TGSLCPYVWIRGASPAQLEAL 57
                                      89**********98746677999********5.5689***********998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 957.39
//
Query:       gi|336252947|ref|YP_004596054.1|  [L=247]
Description: DNA polymerase sliding clamp [Halopiger xanaduensis SH-6]
Scores for 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-09   35.4   0.1    1.3e-08   34.6   0.1    1.4  1  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    2.1e-05   24.7   0.0    6.4e-05   23.1   0.0    1.9  2  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
  ------ inclusion threshold ------
      0.094   12.1   0.0       0.16   11.4   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 !   34.6   0.1   2.2e-12   1.3e-08       7     101 ..       6      99 ..       1     112 [. 0.90

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.2e-12
                                       SSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTST CS
                            PCNA_N   7 eqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcan 83 
                                       + a  l   l+++  lv+e  +  +++G++++a+D + v +v l+l + +fe+y  D  l +gv+l+ l  i  +a+
  gi|336252947|ref|YP_004596054.1|   6 VSAETLTSALDSVSVLVDECKIHLEEDGLEIRAVDPANVGMVDLSLDAAAFESYEADGGL-IGVDLSRLEDIAGMAE 81 
                                       5567788899***********************************************987.8*************** PP

                                       TTSEEEEEEETTSSEEEE CS
                            PCNA_N  84 nedsvtlkaedeadtlal 101
                                         + + l+ ++e+ +l +
  gi|336252947|ref|YP_004596054.1|  82 SGQLIQLELDEETRKLHI 99 
                                       ******999998877765 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 ?   -2.5   0.0      0.91   5.4e+03      49      76 ..      66      93 ..      59      99 .. 0.74
   2 !   23.1   0.0   1.1e-08   6.4e-05      65     127 ..     180     242 ..     121     243 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.91
                                      TEEEEEEE--BEESSSGGGCBEEEESS- CS
                            PCNA_C 49 iGsasivlkqvkdvdkeeeavklelkep 76
                                      iG     l++   ++++ + ++lel+e 
  gi|336252947|ref|YP_004596054.1| 66 IGVDLSRLEDIAGMAESGQLIQLELDEE 93
                                      6666667788888888888999988875 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 1.1e-08
                                       GGGCBEEEESS-EEEEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTC.EEEEEEE-B CS
                            PCNA_C  65 eeeavklelkepvtltfalkYlaeftkatsLservtlslssevPlvveykikdv.gllayllak 127
                                        e+ + l++  p +  f+l+Yl ++ ka +   +vtl+l +e P+++ +  +++ g ++y+la+
  gi|336252947|ref|YP_004596054.1| 180 REDLIDLQA-GPAHSLFSLDYLKDMNKAIPSDAEVTLHLGEEFPVKMFFGFAEGqGQVTYMLAP 242
                                       455566654.477888*********************************998863667777776 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05      0.16       3      52 ..      13      62 ..      11      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                              Rad9  3 ralqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyeke 52
                                       al ++s + de  ++ +edgle+r+v+ ++ + + + l  + F++ye +
  gi|336252947|ref|YP_004596054.1| 13 SALDSVSVLVDECKIHLEEDGLEIRAVDPANVGMVDLSLDAAAFESYEAD 62
                                      678999*****************************************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1894.49
//
Query:       gi|336252948|ref|YP_004596055.1|  [L=89]
Description: hypothetical protein Halxa_1544 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.064   13.4   0.0      0.081   13.1   0.0    1.1  1  PYRIN     PAAD/DAPIN/Pyrin domain


Domain annotation for each model (and alignments):
>> PYRIN  PAAD/DAPIN/Pyrin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.5e-06     0.081      30      68 ..      48      87 ..      40      89 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-06
                                      HTTHCCHCT.-SHHHHHHHHHHHHTCCCCHHHHHHHHHHT CS
                             PYRIN 30 siprgelek.adrvdladlLvehygedaavevtlkvleki 68
                                      ++ +g++e  +d++ +  l+++h ged+a e + ++ eki
  gi|336252948|ref|YP_004596055.1| 48 EVRTGKVEGgDDWEVTSVLIEKHVGEDKAEEQAEEIVEKI 87
                                      67799****8888888888999*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 710.20
//
Query:       gi|336252949|ref|YP_004596056.1|  [L=144]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-34  119.4   2.3    1.9e-34  119.2   2.3    1.0  1  Usp             Universal stress protein family
     0.0045   17.2   0.7     0.0069   16.6   0.7    1.6  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
      0.066   13.5   0.0      0.079   13.3   0.0    1.2  1  OmpH            Outer membrane protein (OmpH-like)
       0.13   12.7   1.3          2    8.9   1.2    2.6  2  pPIWI_RE_Y      pPIWI_RE three-gene island domain Y


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 !  119.2   2.3   4.3e-38   1.9e-34       1     141 []       1     144 []       1     144 [] 0.93

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 4.3e-38
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.....HH CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.....ak 72 
                                       m  ++lV+vD+s+ s++Ale+Ale   +++a++++lhvidp +   +++++ e++e+  + +++++e  +     a+
  gi|336252949|ref|YP_004596056.1|   1 MATHVLVPVDDSDPSDAALEFALED--QHDARITALHVIDPADLRDSPTLEMESAEDYGDFRLQQQEFSEqilddAE 75 
                                       7789********************6..45589*************999999999999888777776655578999** PP

                                       HHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  73 aaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++a++ g + e+++++g +a++ +e+a+e+++d iV+Gs+gr+g sr+llGSv+e v+r+ap+pV++Vr
  gi|336252949|ref|YP_004596056.1|  76 ERAREYGTSIETDQVVGAVADAVVEYADEHGVDRIVIGSHGRTGASRVLLGSVAETVARRAPVPVTIVR 144
                                       ********************************************************************8 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 !   16.6   0.7   1.5e-06    0.0069      68     124 ..      86     140 ..      21     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-06
                    baeRF_family10  68 qaerhlkevAellaklleergverlvlgGdeeetaalldrlpkalrarvvgtlplpv 124
                                        +++ + +vA++++++++e+gv+r+v+g + +  a     l  ++++ v+ + p+pv
  gi|336252949|ref|YP_004596056.1|  86 ETDQVVGAVADAVVEYADEHGVDRIVIGSHGRTGA--SRVLLGSVAETVARRAPVPV 140
                                       5789999*********************9876544..44577777777777777775 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.8e-05     0.079      58     115 ..      52     111 ..      22     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHTT-SEEE CS
                              OmpH  58 keekeqelqkkeqelqqkqqqkaqelqkkqqe..llkpildkinkaikevakekgydlvl 115
                                       ++e++ +++ ++qe+ ++   +a+e +++     ++++++  + +a+ e+a e+g+d ++
  gi|336252949|ref|YP_004596056.1|  52 SAEDYGDFRLQQQEFSEQILDDAEERAREYGTsiETDQVVGAVADAVVEYADEHGVDRIV 111
                                       66777779999999999666666777776666444459******************9886 PP

>> pPIWI_RE_Y  pPIWI_RE three-gene island domain Y
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.2   0.00044         2      77     134 ..       2      60 ..       1     104 [. 0.78
   2 ?    0.1   0.0      0.22   9.7e+02       3      20 ..      92     109 ..      90     139 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00044
                        pPIWI_RE_Y  77 adevlldeedelptqlclElaleyagdsearqtaeqvlreafrr...creagsqesYtafR 134
                                       a  vl+  +d  p++++lE ale  ++++ar ta +v+  a  r     e++s+e+Y  fR
  gi|336252949|ref|YP_004596056.1|   2 ATHVLVPVDDSDPSDAALEFALE--DQHDARITALHVIDPADLRdspTLEMESAEDYGDFR 60 
                                       567899999999**********9..667778888888866543311122446666676666 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.22
                        pPIWI_RE_Y   3 rrvatAllrlaeawdlrs 20 
                                       + va+A++++a+  ++++
  gi|336252949|ref|YP_004596056.1|  92 GAVADAVVEYADEHGVDR 109
                                       677888888777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1085.40
//
Query:       gi|336252950|ref|YP_004596057.1|  [L=191]
Description: phage SPO1 DNA polymerase-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-38  132.4   0.0    1.7e-38  132.1   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 !  132.1   0.0   9.3e-43   1.7e-38       1     151 [.      39     180 ..      39     185 .. 0.95

  Alignments for each domain:
  == domain 1  score: 132.1 bits;  conditional E-value: 9.3e-43
                                       HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCC CS
                               UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaei 77 
                                       pg gp +a+v++vGeaPg +e + g+pF+grag++l+++l+++g +r     +++y+tn+vk rpp+nr +p+ +ei
  gi|336252950|ref|YP_004596057.1|  39 PGVGPLSADVMLVGEAPGGQEVKRGEPFVGRAGKQLDRALESIGYDR-----RDCYVTNLVKVRPPENR-DPHVDEI 109
                                       799********************************************.....*****************.******* PP

                                       TCCHHHHHHHHHHHHSSEEEEESHHHHHH....HHHHSCESCCCSCT..SEEEEES-SSTTTTTTTTSHHHHHHHHH CS
                               UDG  78 kacaplleeeiellkprlivllGktaakall..geklgklrgklleak.irvlplphPsplnrnffksnpelkaeaw 151
                                       +a +p le+eie++ p+++v +G  a   +l  +e++++l+g+ +e++   v+p++hP+++++        +k +a+
  gi|336252950|ref|YP_004596057.1| 110 EAWRPVLEAEIERVDPTVLVPMGSFATAEILdtDETITDLHGREFERNgRLVIPSFHPAAALYD------RSKVDAI 180
                                       *****************************989899************99**************9......5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1510.98
//
Query:       gi|336252951|ref|YP_004596058.1|  [L=81]
Description: hypothetical protein Halxa_1547 [Halopiger xanaduensis SH-6]
Scores for 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  (81 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:                        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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 676.76
//
Query:       gi|336252952|ref|YP_004596059.1|  [L=260]
Description: ribosomal RNA large subunit methyltransferase E [Halopiger xanaduensis SH-6]
Scores for 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-56  189.3   0.0    7.5e-56  189.0   0.0    1.1  1  FtsJ             FtsJ-like methyltransferase
    3.3e-12   46.2   0.5    3.3e-12   46.2   0.5    1.8  2  TRAM             TRAM domain
    4.7e-05   23.2   0.0    0.00028   20.7   0.0    1.9  1  Methyltransf_31  Methyltransferase domain
    0.00032   21.4   0.0    0.00072   20.2   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.041   13.7   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
      0.033   14.0   0.0       0.29   10.9   0.0    2.1  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.044   13.4   0.0      0.085   12.4   0.0    1.4  1  MaoC_dehydratas  MaoC like domain
        0.1   12.0   0.2       0.15   11.4   0.2    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


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 !  189.0   0.0   3.3e-59   7.5e-56       1     177 []      16     196 ..      16     196 .. 0.97

  Alignments for each domain:
  == domain 1  score: 189.0 bits;  conditional E-value: 3.3e-59
                                       CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHH.....TTEEEECS-CCC CS
                              FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmapl.....pgvttiqgditd 72 
                                       yrsR+ayKL ++d+  +++++g++vvDlgaaPGgw qv+++++g++g+vv+vDlq ++p+     ++v+ti+gd t+
  gi|336252952|ref|YP_004596059.1|  16 YRSRAAYKLKQLDDLENVIDRGDAVVDLGAAPGGWLQVAAEKVGPEGRVVGVDLQRIKPFdddinERVETIRGDMTE 92 
                                       9********************************************************777665688*********** PP

                                       SSHHHHHCHCHHHSSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHH CS
                              FtsJ  73 petiekikealserkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlk 149
                                       ++t++++ +a +  kvd vvsD+ap++sg  +ld++++++L+++a+e+al+ll++gg fv+k+f+g++++++ ++++
  gi|336252952|ref|YP_004596059.1|  93 ERTRDRVIDAAE-GKVDAVVSDMAPNMSGEYSLDQARSLHLARQAFETALELLDTGGDFVVKVFEGPDVDDFRADVE 168
                                       ********9875.5*************************************************************** PP

                                       CCEEEEEEEE-SS--CCG-EEEEEEEEC CS
                              FtsJ 150 kfFekvsvvkPkssrsesseeflvcrgf 177
                                       + F++v+ + Pk+sr esse++++++g+
  gi|336252952|ref|YP_004596059.1| 169 EEFQYVRATSPKASRDESSEVYFIAKGR 196
                                       *************************985 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       4.1   9.1e+03      39      52 ..      47      58 ..      37      67 .. 0.62
   2 !   46.2   0.5   1.5e-15   3.3e-12       3      60 ..     202     255 ..     200     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.1
                                      T..TEEEEEEEEEE CS
                              TRAM 39 pgIGdfVeVkItkv 52
                                      p  G +++V  +kv
  gi|336252952|ref|YP_004596059.1| 47 P--GGWLQVAAEKV 58
                                      5..55555555554 PP

  == domain 2  score: 46.2 bits;  conditional E-value: 1.5e-15
                                       XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEE CS
                              TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGe 60 
                                         G ++eV++++++ +eg+gi+ ++ g+ +fvp +++  G++VeV+I++vk+++ +++
  gi|336252952|ref|YP_004596059.1| 202 RPGDELEVEITDVG-NEGDGIASVE-GYRLFVPATEE--GETVEVRIDDVKPNFGFAQ 255
                                       679***********.**********.***********..*****************97 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.2e-07   0.00028       2     129 ..      35     174 ..      34     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.2e-07
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled...... 72 
                                       d+g  v+DlG++ G  + ++ae++gp+++vvG+D +         n      ++ve  +gd++e  +   d      
  gi|336252952|ref|YP_004596059.1|  35 DRGDAVVDLGAAPGGWLQVAAEKVGPEGRVVGVDLQRIKPFDDDIN------ERVETIRGDMTEERTR--Drvidaa 103
                                       67889*****************************986544444443......6788888888885532..3445577 PP

                   Methyltransf_31  73 .ekfDlilsnevl...........naladpdkileeiervlkpggilliedpr..llaelpakveeeskay 129
                                         k+D ++s+ +              l    +++e + ++l +gg +++  +     ++++a veee ++ 
  gi|336252952|ref|YP_004596059.1| 104 eGKVDAVVSDMAPnmsgeysldqaRSLHLARQAFETALELLDTGGDFVVKVFEgpDVDDFRADVEEEFQYV 174
                                       77888888884444444444455566666667777888888888888877776555666667777776654 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.2e-07   0.00072       1      73 [.      40     115 ..      40     148 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.2e-07
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG.......BSSSTTTEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvefvqgdaed.......lpfedgsfDlvv 69 
                                       v+dlG+ +G +++ +a+++g +++v+gvD++   ++     ++    +ve ++gd+++       ++ ++g++D+vv
  gi|336252952|ref|YP_004596059.1|  40 VVDLGAAPGGWLQVAAEKVGpEGRVVGVDLQR--IKPFDDDIN---ERVETIRGDMTEertrdrvIDAAEGKVDAVV 111
                                       89*****************66********985..445555552...2566666666332222255678999****** PP

                                       EEST CS
                   Methyltransf_25  70 ssga 73 
                                       s +a
  gi|336252952|ref|YP_004596059.1| 112 SDMA 115
                                       9544 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.8e-05     0.041      16      57 ..      30      74 ..      13     181 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                   Methyltransf_23 16 llpklraggrvLdiGcGtGillevlren.gf..svtgvDlspeav 57
                                      l    ++g  v+d+G++ G +l+v++e+ g    v+gvDl +++ 
  gi|336252952|ref|YP_004596059.1| 30 LENVIDRGDAVVDLGAAPGGWLQVAAEKvGPegRVVGVDLQRIKP 74
                                      4444578889***************776477899******87633 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 ?   10.9   0.0   0.00013      0.29      67     107 ..      28      70 ..       9     114 .. 0.81
   2 ?    0.6   0.0      0.18   4.1e+02     167     208 ..     195     236 ..     188     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                                       HHTT..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESB CS
                              PCMT  67 elle..lkkgarvLevGsGsGyltavlarlvgekgrvvsieri 107
                                       + le  +++g+ v+++G+  G    v a+ vg++grvv+++ +
  gi|336252952|ref|YP_004596059.1|  28 DDLEnvIDRGDAVVDLGAAPGGWLQVAAEKVGPEGRVVGVDLQ 70 
                                       44556799*******************************9843 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.18
                                       EEEEEEESBSSSEEEEEEEEETTTEEEEEEEEEE---B-BCC CS
                              PCMT 167 GrlvvPvgeeeeQvlklvdkkadgkvvikkleevrfvpltdk 208
                                       Grl +Pv +  e +++  d  ++g  + + +   +fvp+t++
  gi|336252952|ref|YP_004596059.1| 195 GRLTAPVRPGDELEVEITDVGNEGDGIASVEGYRLFVPATEE 236
                                       99*******99999999999999999999999999**99975 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.8e-05     0.085      78     107 ..     190     218 ..     174     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.8e-05
                                       EEEEEEEE-S--BTTCEEEEEEEEEEEEEE CS
                   MaoC_dehydratas  78 vgeikvrFtkpVlpgdtlkvelevvgkrdv 107
                                       + + k r t+pV+pgd+l+ve++ vg+ ++
  gi|336252952|ref|YP_004596059.1| 190 YFIAKGRLTAPVRPGDELEVEITDVGN-EG 218
                                       55667899****************994.34 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   6.9e-05      0.15     152     195 ..      27      72 ..      25     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.9e-05
                              PrmA 152 lealeklvkegeevlDvGtG.SGiLaiaaakLgak.kvvavDiDev 195
                                       l  le+++ +g+ v+D+G+   G L +aa k+g + +vv+vD+  +
  gi|336252952|ref|YP_004596059.1|  27 LDDLENVIDRGDAVVDLGAApGGWLQVAAEKVGPEgRVVGVDLQRI 72 
                                       5679**************873579*********8648*****9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 00:00:00.40
# Mc/sec: 1970.75
//
Query:       gi|336252953|ref|YP_004596060.1|  [L=59]
Description: CopG/Arc/MetJ family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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   20.7   1.5    0.00074   19.4   0.1    2.1  2  RHH_1     Ribbon-helix-helix protein, copG family
     0.0043   17.2   0.0     0.0043   17.2   0.0    1.1  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 !   19.4   0.1   8.3e-08   0.00074       2      37 ..       4      41 ..       3      43 .. 0.93
   2 ?    1.2   0.1     0.044     4e+02       9      20 ..      42      53 ..      40      57 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.3e-08
                                      EEEEEEHHHHHHHHHHHHHHT..SSHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg..rSrSelIReAlreyl 37
                                      +s+ +++ell+ Ld ++ + g  ++rS++IR+ +r  l
  gi|336252953|ref|YP_004596060.1|  4 ISVEIPQELLDDLDDHVGDDGkfVNRSDAIRASIRKTL 41
                                      89***************99998************9866 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.044
                                      HHHHHHHHHHHH CS
                             RHH_1  9 ellerLdelarr 20
                                      ++++++de+ +r
  gi|336252953|ref|YP_004596060.1| 42 DIMDEIDERHDR 53
                                      789999998666 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 !   17.2   0.0   4.8e-07    0.0043       6      47 ..       4      46 ..       1      56 [. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.8e-07
                             RHH_8  6 vtinlgvvDLgqiDlLv.eeGfYsnRtDlirtairaqLakhdd 47
                                      +++ + +  L  +D  v ++G + nR+D ir++ir+ L+  d+
  gi|336252953|ref|YP_004596060.1|  4 ISVEIPQELLDDLDDHVgDDGKFVNRSDAIRASIRKTLDIMDE 46
                                      55555555555665444389******************87765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 486.09
//
Query:       gi|336252954|ref|YP_004596061.1|  [L=789]
Description: Sec-independent periplasmic protein translocase [Halopiger xanaduensis SH-6]
Scores for 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-74  248.4  37.6    1.5e-41  142.5  14.7    2.6  3  TatC      Sec-independent protein translocase protein (TatC)


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.5  14.7   8.4e-46   1.5e-41       4     207 .]      25     242 ..      22     242 .. 0.90
   2 ?   -2.2   0.0      0.17   3.1e+03      14      39 ..     341     367 ..     336     423 .. 0.72
   3 !  110.3  15.7   6.3e-36   1.1e-31       4     207 .]     507     746 ..     504     746 .. 0.82

  Alignments for each domain:
  == domain 1  score: 142.5 bits;  conditional E-value: 8.4e-46
                                       HHHHHHHHHHHHHHHHHHHHHHH.THHHHHHHCCHHHHC.C.....TTS-EE--SSS-HHHHHHHHHHHHHHHHSHH CS
                              TatC   4 eeLrkrlirallavaiafiitfv.faeeliafllepleeae.....eevelivlspleafllklkvslvaglvlasP 74 
                                        + +++l +++++++i+fi +f+ +   + +fl +  +++      +++++i+ +p+e++ll+ k+++++g++la+P
  gi|336252954|ref|YP_004596061.1|  25 SSAQTHLQKVFIVFVIGFIGSFYaLRVFVWDFLKATAKAEMsqeigQATDIITRTPFEVILLQAKIGMLIGVILAIP 101
                                       5567899**************85233333446665544442455554599*************************** PP

                                       HHHHHHHCCCTTTTS--........-STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT....TTTSSTTEEHHH CS
                              TatC  75 vilyqlwafvapgLykh........errlvlvfliaslllfllGaafayfvvlplvlkfll....seevepllslse 139
                                        +ly    f + +L+++         + ++  + ++s++lf++G+ +ay v++p++++fl+    +++v+p + ++e
  gi|336252954|ref|YP_004596061.1| 102 ALLY----FSRDALRERgvhsvvpvSKWYAAALGLISITLFCVGVGYAYGVFFPFAFDFLAtisyEAGVNPHWGITE 174
                                       ****....********999999**99***********************************9998888999****** PP

                                       HHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S.SHHHHHHHHHH CS
                              TatC 140 ylsfvlllllafgiaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltPpdvisqlllavP 207
                                       + +f++ll+l fg+a +lPl +  la++++vs+et+r+k+r+ai++i v++a+++Ppd+++ +++a+P
  gi|336252954|ref|YP_004596061.1| 175 FTQFTVLLTLSFGLAAQLPLAMSALAYTEIVSYETFRDKWRHAIIAITVFGAMFSPPDPFTLVMWALP 242
                                       ******************************************************************99 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHH.THHHHHHHCCHHH CS
                              TatC  14 llavaiafiitfv.faeeliafllepl 39 
                                       +++++ia+++++v +    i++l+ p+
  gi|336252954|ref|YP_004596061.1| 341 AIGLVIAAVVGLVaLIGYTIKVLQSPV 367
                                       566666666665433444566666665 PP

  == domain 3  score: 110.3 bits;  conditional E-value: 6.3e-36
                                       HHHHHHHHHHHHHHHHHHHHHHH.THHHHHHHCCHHHHC..C..............................TTS-E CS
                              TatC   4 eeLrkrlirallavaiafiitfv.faeeliafllepleea.e..............................eevel 48 
                                       ++L ++ i+++ +++ ++  tf+ +++  + ++l+ + +  +                                  +
  gi|336252954|ref|YP_004596061.1| 507 DSLTSKTIYIVGVFMAVLGGTFLaLYQGGFGIILAQFVDRvPnealaevadgneayltedmtteatiqllqdL-GLV 582
                                       6788899998888888888888534444444555554444344555556555555555555444443333220.335 PP

                                       E--SSS-HHHHHHHHHHHHHHHHSHHHHHHHHHCCC.TTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHH CS
                              TatC  49 ivlspleafllklkvslvaglvlasPvilyqlwafv.apgLykherrlvlvfliaslllfllGaafayfvvlplvlk 124
                                       ++l+p+e++++++kvs ++g+v ++P+i+y  w    + gL   + r++lv+ +a ++ f lG+++++++++p+v++
  gi|336252954|ref|YP_004596061.1| 583 VALEPVEVLIFMVKVSTILGFVSVLPLICYWGWPAAkERGLVTGDSRIFLVWGLALFAGFGLGIFLGFYWIAPAVIS 659
                                       5*****************************9997662579************************************* PP

                                       HHT....TTTSSTTEEHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S.S CS
                              TatC 125 fll....seevepllslseylsfvlllllafgiaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltPpd 197
                                       +l+    ++++e  ++++++ ++v++++l++g++F++ + ++l++  g+vs++t+ +++r a+v+++ +aa+ +P+ 
  gi|336252954|ref|YP_004596061.1| 660 YLItdalANGMEVSYRINSFSWLVIYTTLGVGFLFNVVVTMALFHIGGIVSYRTMLERWRPAVVGVFAIAAFASPKG 736
                                       ***76664555778*************************************************************** PP

                                       HHHHHHHHHH CS
                              TatC 198 visqlllavP 207
                                       ++++llla+P
  gi|336252954|ref|YP_004596061.1| 737 ILTMLLLAIP 746
                                       *********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (789 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); 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: 0.70u 0.26s 00:00:00.96 Elapsed: 00:00:00.40
# Mc/sec: 5850.30
//
Query:       gi|336252955|ref|YP_004596062.1|  [L=363]
Description: Sec-independent periplasmic protein translocase [Halopiger xanaduensis SH-6]
Scores for 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-37  128.0  18.1    5.3e-37  127.7  18.1    1.1  1  TatC      Sec-independent protein translocase protein (TatC)
  ------ inclusion threshold ------
       0.02   13.0  15.0      0.025   12.7  15.0    1.0  1  AF-4      AF-4 proto-oncoprotein
          1   10.1  11.6        1.8    9.3  11.6    1.3  1  IMUP      Immortalisation up-regulated protein


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7  18.1   8.8e-41   5.3e-37       1     206 [.     133     344 ..     133     344 .. 0.93

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 8.8e-41
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHCCHHHHC..CTT.S-EE--SSS-HHHHHHHHHHHHHHHHSHHH CS
                              TatC   1 ehLeeLrkrlirallavaiafiitfvfaeeliafllepleea.eee.velivlspleafllklkvslvaglvlasPv 75 
                                       +h+ee+  rl  +ll+   +++i+++fa++ i+++++ +  a +ee     v++ple  l+++k+s ++g+++a+P 
  gi|336252955|ref|YP_004596062.1| 133 DHIEEMILRLAVVLLFGTAGTAIGLLFASDAISYIWTDVFPAaAEEvPPPHVYHPLELWLTRIKLSALLGIMVALPT 209
                                       7********************************9998877764432123349************************* PP

                                       HHHHHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT...TTTSSTTEEHHHHHHHHHHHHH CS
                              TatC  76 ilyqlwafvapgLykherrlvlvfliaslllfllGaafayfvvlplvlkfll...seevepllslseylsfvlllll 149
                                       ++y+ + f++pgLy+her+++l ++++s++l  +G++f+y++vlp+++++++   + ++  ++ l++ ++++++l+ 
  gi|336252955|ref|YP_004596062.1| 210 FVYECYLFMRPGLYPHERKYYLAAVPTSVVLAGIGMVFSYVLVLPVLFQYFTyyaEGSAAIAYALGDTFDLIITLTG 286
                                       ***************************************************98864445567*************** PP

                                       HHHHHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S..SHHHHHHHHH CS
                              TatC 150 afgiaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltP.pdvisqlllav 206
                                       +  i+F++Pl+++l++++g+ ++++l++kr y++ ++l +++++t  p+ +  +l+a+
  gi|336252955|ref|YP_004596062.1| 287 FLAIVFQIPLFIMLAIMMGVTTRRWLAQKRLYFWAAFLGLSFMFTFdPSGMAPILVAI 344
                                       *********************************************9999999999986 PP

>> AF-4  AF-4 proto-oncoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  15.0   4.1e-06     0.025     463     509 ..      37      85 ..       3      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-06
                              AF-4 463 esahsssaeSeSsSeSeSSS..eSDSesEssssdseanepprtatpepe 509
                                        + + ++a+S+S S+SeSSS  + DS+s+s+ss  +an+  +t+tp  e
  gi|336252955|ref|YP_004596062.1|  37 TPPEDEGADSGSGSDSESSSsaNADSDSDSNSSAATANDDDETETPPVE 85 
                                       55667788888888888877335799999**************999544 PP

>> IMUP  Immortalisation up-regulated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  11.6   0.00031       1.8      45      81 ..      41      77 ..      32      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00031
                              IMUP 45 rhghgkssssdsssssssssdsdaeakphaagskkhk 81
                                       +g   +s sds ssss+ +dsd+++ + aa++++ +
  gi|336252955|ref|YP_004596062.1| 41 DEGADSGSGSDSESSSSANADSDSDSNSSAATANDDD 77
                                      4566677888888888889999999999999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 2655.74
//
Query:       gi|336252956|ref|YP_004596063.1|  [L=717]
Description: Nitrate reductase [Halopiger xanaduensis SH-6]
Scores for 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-50  171.2   0.0    4.6e-50  170.8   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    2.5e-15   56.5   0.1    7.1e-14   51.8   0.1    2.5  1  Molydop_binding  Molydopterin dinucleotide binding domain
    3.5e-06   26.9   2.1    9.5e-06   25.5   2.1    1.8  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.8   0.0   7.7e-54   4.6e-50       2     431 ..      61     478 ..      61     479 .. 0.87

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 7.7e-54
                                       --S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEE CS
                     Molybdopterin   2 lkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfyd 78 
                                       l +P+vR   r +G++v+ + ++Ale  a+ l+   ++ gp+ va+ +sg+ + +e+ ++l kl++  +g  + +yd
  gi|336252956|ref|YP_004596063.1|  61 LARPLVR---R-DGDLVPTTLETALERAAEGLEGALDEAGPEGVAVLGSGQQT-NEAAYALGKLARGGFG--TPYYD 130
                                       679****...9.****************************************9.****************..9**** PP

                                       CCGGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC.-EEEEECSS CS
                     Molybdopterin  79 wyadlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkk.akvivigpr 150
                                        +  l++asa+     ++gsd +  + +     d+ +++  ++wG+N++  +p++  r +++   ++  ++iv++p 
  gi|336252956|ref|YP_004596063.1| 131 ANTTLCMASAVtayyDAFGSD-APPPTYD----DIPEAETHLVWGANPAAAHPVM-FRWINQSADAEdSELIVVDPI 201
                                       **********98887777777.5566666....**********************.666666666667********* PP

                                       B-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHH CS
                     Molybdopterin 151 yaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarel 227
                                        +e++  ad+++++ pg d+ala a    +++ + vd+ef++  t g++ ++  l     e +++  +v ++ +++ 
  gi|336252956|ref|YP_004596063.1| 202 ESETADVADLHVPLEPGGDLALARAVLARVVETGRVDEEFVAAATEGFDDLRAELPD--AEAAAERAGVSIEDVDRI 276
                                       ***99*******************************************999877654..445677777888888888 PP

                                       HHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCC CS
                     Molybdopterin 228 arnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvksl 304
                                       a+ + +     +  +G+g+n++ +g+a+  a+i L+l++gn + pg+g+++l+Gq + +g+++  ++   + + ++ 
  gi|336252956|ref|YP_004596063.1| 277 AAALEDP---TLCYWGMGINQSVNGTAASGALIDLCLATGNLR-PGSGPFSLTGQANSMGTRVCSSKG--TWPGHRP 347
                                       7766654...56*****************************96.6********988777766555555..4444444 PP

                                       TT......HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESC CS
                     Molybdopterin 305 ke......ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgr 375
                                                    ++  +  l+  p+   v   ++++  ++++++ + +np+   +d+ +v ++l    ++vv d +
  gi|336252956|ref|YP_004596063.1| 348 FDdpehrrAVADHWNVPEPRLPADPGPGPVGIVDAIG-DDVEAVFAVATNPVAGMPDATRVREHL-EDAFLVVQDAF 422
                                       447764443333444556789999999999999****.5**********************8888.56788999*** PP

                                       SSHHHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                     Molybdopterin 376 ltstalyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                        ++ta+ aD++LPaatw E  +++tn+e+ +++ ++a+++p   k+d + + a+ +
  gi|336252956|ref|YP_004596063.1| 423 RSETAELADVVLPAATWGESAGTTTNMERTVSRVRAATETPSGIKTDLELIGAIGD 478
                                       ***************************************************99975 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.1   1.2e-17   7.1e-14       1     111 []     586     698 ..     586     698 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.2e-17
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT..--TT-EE.............EEEETTEEEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpepevveinpedAaalG..ikdGdlV.............evesrrGsvevr 62 
                                       l+L+tgr++d +++++rtr++      ep+v++++p++A al   ++ G++V             +v srr sv+vr
  gi|336252956|ref|YP_004596063.1| 586 LTLTTGRRPDAYNTGVRTRED------EPPVARVSPATAVALAdeLEGGERVdaavqddddaqygRVVSRRASVTVR 656
                                       78****************998......5679999999999885559999999666666666677779********** PP

                                       EEEESSB-TTEEEEESSHCC.....S-GHCTS--SCSTTT--CSTT-EE CS
                   Molydop_binding  63 akvtervrpGvvfmpfgwweagekggnaNaltddatdplsgtpefksva 111
                                       ++++e+++ Gvv++p ++++       +N+lt +++dp s++p+fk++a
  gi|336252956|ref|YP_004596063.1| 657 VETDESIPDGVVWLPIHHPA-------VNDLTLPDVDPRSKEPNFKQCA 698
                                       *******************9.......********************96 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   2.1   1.6e-09   9.5e-06       3      48 ..       4      51 ..       2      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.6e-09
                                      EEEEE-SSBTT--EEEEEEETTEEE...EEEE-TTSTTTTT---HHHHT CS
                    Molybdop_Fe4S4  3 vvktaCpyCgvgCglevhvkdgkiv...kvegdpdhpvnegrlCvKGrt 48
                                       v+t+C  C vgCg  v+ + ++++    v+gd +hpvn+g +C +G t
  gi|336252956|ref|YP_004596063.1|  4 LVPTTCMRCAVGCG-HVQRPVEQGYgldVVRGDASHPVNNGLACQRGVT 51
                                      589***********.444444444445799*****************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (717 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.38
# Mc/sec: 5637.77
//
Query:       gi|336252957|ref|YP_004596064.1|  [L=460]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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-26   92.2  69.8    5.6e-19   68.3  35.2    2.1  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.063   13.1   0.0       0.13   12.1   0.0    1.4  1  PapC_C    PapC C-terminal 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 !   68.3  35.2   6.2e-23   5.6e-19       2     272 ..      40     330 ..      39     331 .. 0.79
   2 !   37.9  26.6     1e-13   9.4e-10      31     178 ..     300     450 ..     296     457 .. 0.89

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 6.2e-23
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.ll 77 
                                        +++f+ +++  ++gp++      + g+s+  +gll+++  l+ +++ +p+G+++++ G+++ +l+ l l+++g + 
  gi|336252957|ref|YP_004596064.1|  40 TFGFFVGFAGVVLFGPVAA-EFEGAMGLSGLLLGLLVAAPQLTGSLLRIPFGAWVEKTGAKKPFLVLLGLSIVGmGG 115
                                       5899999999999*****9.899***************************************999999999999544 PP

                             MFS_1  78 lll.fa.........sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggll 144
                                       ll+ +a         ++++l+++l  l+G g  a f++g a ++ w+p  ++g +++ +++  + ++++  +l +  
  gi|336252957|ref|YP_004596064.1| 116 LLVlLAtagadgltmAHYPLVFLLGSLSGCGI-ATFSVGTAQTSYWYPSAKQGTVLAAFGGLGNTSPAIFTILVPTA 191
                                       44444344556677777889999999999996.9*********************************6666666655 PP

                             MFS_1 145 asslgWravfyilaivsllafvlfllllpeepperkrkspkeee.....kgtgpaplvp...awkallkdpvl...w 210
                                       ++++g + ++ +   +++++  + + + ++ p     k++ e++     +   +++l+p   a+++++    +   w
  gi|336252957|ref|YP_004596064.1| 192 LAAVGLTTTYAVWFCFLVVGTAVYARYAVDAPYFQFSKRGLEDGearrrAEARGQELFPggdALGSIREAARIprtW 268
                                       55999888888888888888777777776666666666666665555564444444444777555555555444449 PP

                             MFS_1 211 illialllfffgfsglltllplylqevlglsglllaglllallalvgail.allagrlsdrlg 272
                                       +l++ +++ f gf +l+t+lp+y q+ +gl    +agll al++ +  ++ ++ +g+lsdr+g
  gi|336252957|ref|YP_004596064.1| 269 SLVALFFVSFGGFLALTTWLPSYWQSFHGLE-SRTAGLLTALGFTLLSAAvRIGGGALSDRIG 330
                                       *******************************.45555555555444444449999******87 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 1e-13
                             MFS_1  31 pseigllltl.yalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw.lllvlrvlqGlgagalfpa 105
                                         ++gll++l ++l++a+  + +G+lsdr+G   + ++++++ a+g+++l++ ++ + l l++ +l G+g+g++ +a
  gi|336252957|ref|YP_004596064.1| 300 SRTAGLLTALgFTLLSAAVRIGGGALSDRIGGEGTAIASFATIAVGAAILIV-AHDFvLALAATMLLGAGMGVASAA 375
                                       66899999998999999999999***********************777775.55555******************* PP

                             MFS_1 106 gaaliadwfpkeergraigllsagfslGailgpllggllasslg...Wravfyilaivsllafvlfllllpeeppe 178
                                       +  l+ +++p+   g a gl+++  ++G  + p+l gl++++ g   + a f++  +++l+a+ l   l++ +p++
  gi|336252957|ref|YP_004596064.1| 376 VFQLVPKYVPD-AVGGASGLVGGIGAFGGFVVPPLLGLFVDLRGvsgYAAGFVVYLVLGLVALGLSSHLYRIKPVS 450
                                       ***********.****************************999988888889999999999877777888777765 PP

>> PapC_C  PapC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.4e-05      0.13      12      39 ..      87     121 ..      85     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.4e-05
                                       --TT-EEEETTSSS.......-EEB-CCCEEEEEC CS
                            PapC_C  12 lPfGAevtdeengk.......vgiVgqgGqvylrg 39 
                                       +PfGA v+  + +k       ++iVg gG + l +
  gi|336252957|ref|YP_004596064.1|  87 IPFGAWVEKTGAKKpflvllgLSIVGMGGLLVLLA 121
                                       9*********9888******88*******998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3425.51
//
Query:       gi|336252958|ref|YP_004596065.1|  [L=589]
Description: Ferredoxin--nitrite reductase [Halopiger xanaduensis SH-6]
Scores for 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-47  159.0   0.1    3.4e-31  107.9   0.0    2.4  2  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    2.4e-35  120.2   0.1    2.7e-16   59.2   0.0    3.2  2  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
  ------ inclusion threshold ------
      0.073   13.2   0.5       0.98    9.6   0.0    2.4  2  DGC           DGC domain


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   5.7e-35   3.4e-31       2     155 ..     139     293 ..     138     297 .. 0.94
   2 !   48.4   0.0   1.2e-16   6.9e-13       6     152 ..     406     549 ..     403     554 .. 0.92

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 5.7e-35
                                       SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdeke 78 
                                       g+++rn+++cp  g  +e+ +++ +l +++e+el ++ +  ++PrKf+i+vsgc+  c++  +nDig+ + +k+   
  gi|336252958|ref|YP_004596065.1| 139 GDTMRNISGCPLHG-KAEEFVESGPLLERFEEELRGDDALANMPRKFNISVSGCRVGCAQDSINDIGFEPATKEIDG 214
                                       899***********.89999*************************************************99885333 PP

                                       E...EEEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHH CS
                                       x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  79 i...gfnilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekve 152
                                       +   gfn+ +GGglg ++++++t+ + +fv +e+ +ev ++ ve+y d+g+r+nr k R + + +++G+ek+re +e
  gi|336252958|ref|YP_004596065.1| 215 EevrGFNVRIGGGLGGRQPRAATPLD-VFVRPENAYEVGRGFVELYHDYGNRQNRSKNRARFFADDWGMEKIRETLE 290
                                       3578**********************.7************************************************7 PP

                                       HCC CS
                                       xxx RF
                           NIR_SIR 153 eel 155
                                       ee+
  gi|336252958|ref|YP_004596065.1| 291 EEY 293
                                       764 PP

  == domain 2  score: 48.4 bits;  conditional E-value: 1.2e-16
                                       CCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                           NIR_SIR   6 rnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei... 79 
                                       r  ++c+g+++c  al++t+  ++++ ++l ++ + ++   K K+  sgc  +c+++ + Digl g+   +  +   
  gi|336252958|ref|YP_004596065.1| 406 RGAMACTGTEFCSIALTETKARMARMLRWLNKNVDLPDDVGKIKMHYSGCTADCGQAMTADIGLQGMRARKDGEmve 482
                                       67899*************************************************************97654444478 PP

                                       EEEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  80 gfnilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekve 152
                                        f i vGGg+g++++    +     +p++e   ++++++e y+    ++ ++ + ++ +ve +G e+++e +e
  gi|336252958|ref|YP_004596065.1| 483 AFDIGVGGGVGEEPSFVDWIQ--QRIPADEAPGAIRNLLEAYA----AHRKEGQTFRQWVEATGQEQLIEFCE 549
                                       *************99888777..68******************....*********************99886 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   3.6e-19   2.1e-15       5      68 ..      57     129 ..      53     130 .. 0.90
   2 !   59.2   0.0   4.4e-20   2.7e-16       4      65 ..     330     391 ..     328     393 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 3.6e-19
                      NIR_SIR_ferr   5 dgkgyymvrlrvpnGritaeqlraladia..........ekygsgeirlTtrQnlqlhgvpeedleeileeLae 68 
                                       + ++y+m+rl+  +G++ + qlr++ ++a           ++g+g i+lTtrQ++qlh+++ ed++ei+e+L++
  gi|336252958|ref|YP_004596065.1|  57 Q-EEYFMMRLTNASGILEPGQLRRIGEVArdyakgpvenPEFGNGWIDLTTRQSIQLHWLKLEDIPEIWEKLEA 129
                                       5.4566***********************88888888555********************************98 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 4.4e-20
                      NIR_SIR_ferr   4 kdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeilee 65 
                                       ++g+g+ +v+l+vp Gr+ ae + +lad+a++ygsgeirlT rQn ++ +vp e+++++l+e
  gi|336252958|ref|YP_004596065.1| 330 QKGDGMKYVGLSVPIGRLPAEDAIELADLADEYGSGEIRLTRRQNPVIVDVPHEEVDDLLAE 391
                                       5678999****************************************************997 PP

>> DGC  DGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00016      0.98      53      77 ..     185     209 ..     170     215 .. 0.83
   2 ?    0.9   0.1     0.083   4.9e+02      58      73 ..     454     469 ..     450     474 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00016
                               DGC  53 iiaidGCpleCakkilekagvkpde 77 
                                        i + GC + Ca+  +++ g++p+ 
  gi|336252958|ref|YP_004596065.1| 185 NISVSGCRVGCAQDSINDIGFEPAT 209
                                       699******************9986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.083
                               DGC  58 GCpleCakkilekagv 73 
                                       GC+ +C + ++++ g+
  gi|336252958|ref|YP_004596065.1| 454 GCTADCGQAMTADIGL 469
                                       **********999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 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:                        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: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 4427.58
//
Query:       gi|336252959|ref|YP_004596066.1|  [L=120]
Description: hypothetical protein Halxa_1555 [Halopiger xanaduensis SH-6]
Scores for 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  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 943.93
//
Query:       gi|336252960|ref|YP_004596067.1|  [L=118]
Description: hypothetical protein Halxa_1556 [Halopiger xanaduensis SH-6]
Scores for 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  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 951.57
//
Query:       gi|336252961|ref|YP_004596068.1|  [L=299]
Description: hypothetical protein Halxa_1557 [Halopiger xanaduensis SH-6]
Scores for 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-11   43.2   1.5    4.8e-11   42.9   1.5    1.3  1  Asn_synthase     Asparagine synthase
    4.6e-09   35.5   0.0    4.2e-06   25.8   0.0    2.3  2  tRNA_Me_trans    tRNA methyl transferase
    1.7e-08   33.9   0.0    2.9e-08   33.1   0.0    1.3  1  NAD_synthase     NAD synthase
    8.2e-06   25.5   0.0    4.5e-05   23.0   0.0    2.0  2  QueC             Queuosine biosynthesis protein QueC
     0.0011   18.7   0.0     0.0026   17.5   0.0    1.6  1  ATP_bind_3       PP-loop family
     0.0092   16.1   0.1      0.016   15.3   0.1    1.4  1  QueH             Epoxyqueuosine reductase QueH
  ------ inclusion threshold ------
      0.012   14.9   0.1      0.021   14.2   0.1    1.3  1  Arginosuc_synth  Arginosuccinate synthase
       0.12   12.4   0.0       0.24   11.4   0.0    1.5  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa


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 !   42.9   1.5   2.1e-14   4.8e-11       7     136 ..      19     143 ..      13     261 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.1e-14
                      Asn_synthase   7 edaVkrrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlte.. 81 
                                       e+  +  l a+  v + +SGG+DSS++aa+a+  +  ++ + +++ e+    e++ ak+va+++g++h  + ++e  
  gi|336252961|ref|YP_004596068.1|  19 EA-ARADLAARDGVLVAFSGGVDSSAVAAIARDALGDDAIACTAKSETLPEAELEDAKRVADEIGIRHEIVSFSEle 94 
                                       44.445777888899999****************************999******************9887665422 PP

                      Asn_synthase  82 .eelldalpdviyhleepfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYp 136
                                        +++++  +d +yh+ ++  +++        + a+++gv  v  G  aD   +G++
  gi|336252961|ref|YP_004596068.1|  95 sDDFVENDDDRCYHCRTMRLGEM-------LETAREHGVETVCDGTNADDPGAGHR 143
                                       28899999999999999877776.......77788888888888888777666665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.9e-09   4.2e-06       3      72 ..      31      92 ..      29     132 .. 0.83
   2 !    7.6   0.0   0.00065       1.5     169     191 ..     161     183 ..     148     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.9e-09
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeq.gyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfek 72
                                      v+va+SgGVDSs +aa+ +++ g + i+++ k          e   e++l+da+rva+++gi++e+v+f++
  gi|336252961|ref|YP_004596068.1| 31 VLVAFSGGVDSSAVAAIARDAlGDDAIACTAKS---------ETLPEAELEDAKRVADEIGIRHEIVSFSE 92
                                      99*********9988888876256666665443.........23457899******************987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00065
                     tRNA_Me_trans 169 geltKeevrkiAkeaglavaekk 191
                                       + +tK+evr+iA++++l+va+k+
  gi|336252961|ref|YP_004596068.1| 161 HGITKDEVRAIAAHYDLSVADKP 183
                                       6789*****************98 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.3e-11   2.9e-08      19      83 ..      29      92 ..      12     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.3e-11
                                      SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HH CS
                      NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikp 83
                                      +gv++  SGGvDSs vaa+a++alg++ ++a    s++ +e ++eda+ +a+++gi+ + ++ ++
  gi|336252961|ref|YP_004596068.1| 29 DGVLVAFSGGVDSSAVAAIARDALGDD-AIACTAKSETLPEAELEDAKRVADEIGIRHEIVSFSE 92
                                      7999********************766.56777779*********************99988765 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0     2e-08   4.5e-05       2      64 ..      31      93 ..      30     102 .. 0.90
   2 ?   -0.5   0.0      0.32   7.2e+02     150     185 ..     150     189 ..     143     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2e-08
                                      EEEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGG CS
                              QueC  2 avvllSGGlDSttvlalakke.gkevealtfdYgqrhkkeleaakkiakelgveehkildldll 64
                                      ++v +SGG+DS++v+a+a+++ g+  +a t + +   ++ele ak++a+e+g+ +h+i++ + l
  gi|336252961|ref|YP_004596068.1| 31 VLVAFSGGVDSSAVAAIARDAlGDDAIACTAKSETLPEAELEDAKRVADEIGI-RHEIVSFSEL 93
                                      5899**************9873699999****9999*****************.***9998766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.32
                                       S--EEE-TTTT..--HHHHHHHHHHTT..HHHHH-B-STT CS
                              QueC 150 kkieieaPlid..lsKaeivklgkelg..vpleetlsCYe 185
                                       +++ ++ Pl++  ++K e+ +++++++  v  + +++C +
  gi|336252961|ref|YP_004596068.1| 150 EELDVHSPLLAhgITKDEVRAIAAHYDlsVADKPSMACLS 189
                                       6789999998544899999999998885566677888865 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.2e-06    0.0026       2     108 ..      31     137 ..      30     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.2e-06
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H.....HHCTT CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv.....akkkg 73 
                                       vlvA+SgG+DS a   ++ +     g +++a++   ++ +e+  e e  k+++++++i++ei +++        ++ 
  gi|336252961|ref|YP_004596068.1|  31 VLVAFSGGVDSSAVAAIARDAL---GDDAIACTAKSETLPEA--ELEDAKRVADEIGIRHEIVSFSElesddFVEND 102
                                       79***********999888874...44677777766666655..5556799999********999987655422334 PP

                                       STCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHH CS
                        ATP_bind_3  74 knleeaARelRYevlkealkkegievlllAhhadD 108
                                       +      R++R   + e+++++g+e ++ + +adD
  gi|336252961|ref|YP_004596068.1| 103 DDRCYHCRTMRLGEMLETAREHGVETVCDGTNADD 137
                                       4455579*****999999*********99999999 PP

>> QueH  Epoxyqueuosine reductase QueH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   7.1e-06     0.016      79     109 ..     100     130 ..      68     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.1e-06
                              QueH  79 kekgeRCekCyelrLektaelAkengfdaft 109
                                       ++ ++RC +C ++rL +  e+A+e+g+++++
  gi|336252961|ref|YP_004596068.1| 100 ENDDDRCYHCRTMRLGEMLETAREHGVETVC 130
                                       45679**********************9986 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   9.2e-06     0.021       2      59 ..      33      90 ..      32     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.2e-06
                   Arginosuc_synth  2 LaysGGlDtsviikllkeklgeeviavavdvGq.eeedldevkekalklgavksvvvDa 59
                                      +a+sGG+D s + ++ ++ lg++ ia+++     +e +l+ +k+ a ++g  +  +v  
  gi|336252961|ref|YP_004596068.1| 33 VAFSGGVDSSAVAAIARDALGDDAIACTAKSETlPEAELEDAKRVADEIGIRH-EIVSF 90
                                      69*************************9986543889*************854.44443 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.24       3     114 ..      32     140 ..      30     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                       EEE--SSCTCHHHHHHHHHHCTTHE.EEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THH CS
                       PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpvp.vvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssly 78 
                                        v++sgG ds+++  +a+ a+ +      ++ +   +  +e  +++++++g+r ++++  e +++ +++++   +  
  gi|336252961|ref|YP_004596068.1|  32 LVAFSGGVDSSAVAAIARDALGDDAiACTAKSETLPEAELEDAKRVADEIGIRHEIVSFSELESDDFVENDD--DRC 106
                                       699*******************97615555555555666899***********5555555444555555552..333 PP

                                       HCHHHHHHTHHHHHHHHHCTTECEEE----CCCTTT CS
                       PAPS_reduct  79 eeaaeriaKveplkkaLekldedalltGaRrdesks 114
                                        +  +r +++ ++ ++ ++++ +++  G  +d++ +
  gi|336252961|ref|YP_004596068.1| 107 YH--CRTMRLGEMLETAREHGVETVCDGTNADDPGA 140
                                       44..799*********************99999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 2481.97
//
Query:       gi|336252962|ref|YP_004596069.1|  [L=325]
Description: oxidoreductase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-25   88.2   0.0    2.5e-24   86.4   0.0    2.0  3  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
  ------ inclusion threshold ------
      0.036   14.7   0.0      0.077   13.6   0.0    1.6  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> 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 !   86.4   0.0   2.8e-28   2.5e-24      10     120 .]      10     120 ..       1     120 [. 0.92
   2 ?   -2.9   0.0       1.3   1.2e+04      24      54 ..     127     157 ..     122     166 .. 0.58
   3 ?   -2.8   0.0       1.3   1.1e+04      26      44 ..     206     223 ..     194     252 .. 0.65

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 2.8e-28
                                       HHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHT CS
                      GFO_IDH_MocA  10 kigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngtheelakaalea 85 
                                        i++k + p  e+  ++ev+a+ ++d eraea+a++fg++ +y+ +e+l +++++dav++  pn+ h+e +k+ + a
  gi|336252962|ref|YP_004596069.1|  10 GIARKAFLPGIEP-TEHEVTAVASRDLERAEAFADEFGIDdCYEGYEALIEESDVDAVYIPLPNEFHAEWTKKTADA 85 
                                       4566666677777.788************************************************************ PP

                                       T-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  86 gkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       g++vl+EKPl+ + +ea+e+v+ +e++g++++ g+
  gi|336252962|ref|YP_004596069.1|  86 GIDVLCEKPLTVDAAEAREVVAHCEERGVTLMEGF 120
                                       ******************************99875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                                       TTEEEEEEECSSHHHHHHHHHHTTHEEESSH CS
                      GFO_IDH_MocA  24 rleevvalldpdaeraeavaesfgveaysdl 54 
                                       r+e+   l +++ e  + v +sf+++ + + 
  gi|336252962|ref|YP_004596069.1| 127 RTERALELASEELEDVRSVTASFKFPLFGSP 157
                                       4444455555566666666666666666555 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.3
                                       EEEEEEECSSHHHHHHHHH CS
                      GFO_IDH_MocA  26 eevvalldpdaeraeavae 44 
                                       +e++++l+ + ++a+ +  
  gi|336252962|ref|YP_004596069.1| 206 TELAGILEYHDASARIA-S 223
                                       47888888888777754.3 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 ?   13.6   0.0   8.6e-06     0.077      13      64 ..      10      63 ..       4      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.6e-06
                                      HHHHHHHHTTS..-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SE CS
                     F420_oxidored 13 alasgllaaga..qpheivvansrnpekaeelaeelgvkvtavdneeaaeeadv 64
                                      ++a+++   g   ++he++ ++sr+ e+ae++a+e+g++ +   +e ++ee+dv
  gi|336252962|ref|YP_004596069.1| 10 GIARKAFLPGIepTEHEVTAVASRDLERAEAFADEFGIDDCYEGYEALIEESDV 63
                                      566666666766778**********************99888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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 0.18s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2811.83
//
Query:       gi|336252963|ref|YP_004596070.1|  [L=226]
Description: hypothetical protein Halxa_1559 [Halopiger xanaduensis SH-6]
Scores for 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-31  109.4   0.0    8.4e-31  107.8   0.0    1.7  1  ThuA      Trehalose utilisation


Domain annotation for each model (and alignments):
>> ThuA  Trehalose utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.8   0.0   4.7e-35   8.4e-31      12     210 .]      14     224 ..       3     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 4.7e-35
                                       SHHHH-...HHHHHH-HHHT-EEEEETTS.G--HHHHHT-SEEEEE-G..GS-HHHHHH.HHHHHHTT-EEEEEGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThuA  12 rhdsieaaieaieklgkengfevdatedaavfteenLaqydvvvflstegevldaaqeaalqryveaGgGfvglhsA 88 
                                        h+  e++ e++ ++g ++  +v++t+d +++++   + yd+++   t + +l+++q++ l ++v++GgG++g+h A
  gi|336252963|ref|YP_004596070.1|  14 FHKIDEKGPELVDAVGDAA--DVTTTTDRDELAALPHSAYDLLIDYLT-DSTLTDDQQEGLLEFVRNGGGYLGVHCA 87 
                                       6777777888888888755..555556555577766799******999.58999999999***************** PP

                                       GS.....H..................HHH.HH-SEEEEET............TSGGGTT--.SEEEEEEEEE-..S- CS
                                       xxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                              ThuA  89 adaeersk..................wfsgLiGarfvghppvqeatvkvedrshpateglpeewertdewYnf..kp 145
                                       ad +   +                    s L+G++f +hp+++e  v+++  +hp+t+g++ +++++de Y++  ++
  gi|336252963|ref|YP_004596070.1|  88 ADLQSTPPsdpdanevlekrdepipeLRS-LVGGHFLDHPEQAEFGVDIV-ADHPVTAGVE-DFSVHDEPYQVdaDE 161
                                       **665322335666777777889995555.**********8888888876.7********5.9*********84433 PP

                                       --SE...EEEEE...............ETE...TTEEEEEE----TTSGGG-HHHHHHHHHHHHHC CS
                                       xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThuA 146 nprg.vhvlatvdestydpngadhPiaWcreydgkGrvFytalGhteesyeepefrkhllgglkWa 210
                                         ++ +++la++d+ + d   +d+PiaW r  +g Grv y ++Ght+e+++++ fr +l++++ W+
  gi|336252963|ref|YP_004596070.1| 162 GADSdLTILARMDHPDPD--FEDYPIAWVR-TEGDGRVCYISIGHTDEALRSDGFRGLLRNAISWT 224
                                       233369999999777654..48*******9.5699******************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 1933.94
//
Query:       gi|336252964|ref|YP_004596071.1|  [L=197]
Description: hypothetical protein Halxa_1560 [Halopiger xanaduensis SH-6]
Scores for 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  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.39u 0.19s 00:00:00.58 Elapsed: 00:00:00.34
# Mc/sec: 1745.59
//
Query:       gi|336252965|ref|YP_004596072.1|  [L=197]
Description: hypothetical protein Halxa_1561 [Halopiger xanaduensis SH-6]
Scores for 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   0.0      0.042   13.7   0.0    1.8  2  MarR_2     MarR family
      0.025   13.0   0.0      0.031   12.7   0.0    1.1  1  DUF505     Protein of unknown function (DUF505)
      0.056   13.3   0.0        0.1   12.4   0.0    1.5  1  HTH_IclR   IclR helix-turn-helix domain
       0.11   12.7   0.1       0.44   10.8   0.1    2.2  1  DUF4148    Domain of unknown function (DUF4148)
       0.11   12.5   0.0       0.18   11.8   0.0    1.4  1  HTH_Crp_2  Crp-like helix-turn-helix domain


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 ?   -2.0   0.0      0.97   3.5e+03      23      38 ..      88     103 ..      69     108 .. 0.56
   2 ?   13.7   0.0   1.2e-05     0.042       4      54 ..     111     160 ..     109     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.97
                                       EHHHHHHHHTSSHHHH CS
                            MarR_2  23 tvgelarrlglsksav 38 
                                       + +e ar l  ++s+v
  gi|336252965|ref|YP_004596072.1|  88 RTTEWARVLLSEPSRV 103
                                       4445555555555555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.2e-05
                                       -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       tp++  +Laa ++ +   lt++ +a  +g s+  v+r+l +L+a+G+v ++
  gi|336252965|ref|YP_004596072.1| 111 TPMDDEILAAFHDTGLA-LTPSVVAFNTGFSRKEVNRRLIELEAHGFVDKV 160
                                       55555677777777764.8*****************************876 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.6e-06     0.031     467     530 ..     109     173 ..      83     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.6e-06
                            DUF505 467 fltryelkvlkkiPkrgvsve.elveevdeleeeevrealeklearglvevlpdgnvvlTeaGel 530
                                       ++t ++ ++l+   + g ++  ++v+  ++  ++ev++ l +lea g+v+  + g++ l + Ge+
  gi|336252965|ref|YP_004596072.1| 109 WMTPMDDEILAAFHDTGLALTpSVVAFNTGFSRKEVNRRLIELEAHGFVDKVERGKYRLARRGER 173
                                       68999999999999888776526777779*******************************99986 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 ?   12.4   0.0   2.9e-05       0.1       7      50 ..     116     159 ..     116     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.9e-05
                                       HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       +iL a+  ++ +lt s +A +tg ++  v R L  L+ +G+v +
  gi|336252965|ref|YP_004596072.1| 116 EILAAFHDTGLALTPSVVAFNTGFSRKEVNRRLIELEAHGFVDK 159
                                       59****************************************86 PP

>> DUF4148  Domain of unknown function (DUF4148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00012      0.44      21      46 ..     122     157 ..      36     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                           DUF4148  21 a..........ahskspkTRAqVraELaqaeaaGyl 46 
                                                  + ++++ +R +V + L ++ea G+ 
  gi|336252965|ref|YP_004596072.1| 122 HdtglaltpsvVAFNTGFSRKEVNRRLIELEAHGFV 157
                                       15555566777789********************76 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 ?   11.8   0.0   5.1e-05      0.18      19      58 ..     125     166 ..      92     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
                                       EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EE CS
                         HTH_Crp_2  19 elpltqeelAsmlGltretvsrilseLkreglis.rgrr.ir 58 
                                        l lt    A   G +r  v+r l eL+ +g ++  +r+  r
  gi|336252965|ref|YP_004596072.1| 125 GLALTPSVVAFNTGFSRKEVNRRLIELEAHGFVDkVERGkYR 166
                                       4788889999999********************963433355 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.41u 0.19s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 1725.90
//
Query:       gi|336252966|ref|YP_004596073.1|  [L=133]
Description: hypothetical protein Halxa_1562 [Halopiger xanaduensis SH-6]
Scores for 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  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1023.50
//
Query:       gi|336252967|ref|YP_004596074.1|  [L=117]
Description: hypothetical protein Halxa_1563 [Halopiger xanaduensis SH-6]
Scores for 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-07   30.1  50.7     0.0013   18.6   4.1    4.9  5  DUF326    Domain of Unknown Function (DUF326)
  ------ inclusion threshold ------
      0.086   12.3   1.5        0.4   10.1   1.1    1.9  2  HDOD      HDOD domain
        0.1   12.9   0.1        0.1   12.9   0.1    2.0  2  GAT       GAT domain


Domain annotation for each model (and alignments):
>> DUF326  Domain of Unknown Function (DUF326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   9.2   9.7e-07    0.0058       4      19 ..      15      30 ..      15      32 .. 0.93
   2 !    4.8   5.8    0.0051        30       9      19 ..      27      37 ..      27      38 .. 0.93
   3 ?   -1.1   0.8      0.35   2.1e+03       6      12 ..      45      51 ..      43      52 .. 0.53
   4 !   14.0   7.1   6.1e-06     0.037       8      21 .]      79      92 ..      79      92 .. 0.94
   5 !   18.6   4.1   2.2e-07    0.0013       2      19 ..      95     112 ..      95     114 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.7e-07
                                      HHHHHHHHHHHHHHHH CS
                            DUF326  4 ckkCAkaCrkCAkaCr 19
                                      +++C++ C +CA+aC+
  gi|336252967|ref|YP_004596074.1| 15 MQECIDSCLECAQACE 30
                                      79*************8 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0051
                                      HHHHHHHHHHH CS
                            DUF326  9 kaCrkCAkaCr 19
                                      +aC+ CA++C+
  gi|336252967|ref|YP_004596074.1| 27 QACEWCADECA 37
                                      79********6 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.35
                                      HHHHHHH CS
                            DUF326  6 kCAkaCr 12
                                      +C + Cr
  gi|336252967|ref|YP_004596074.1| 45 ECLRLCR 51
                                      4445566 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 6.1e-06
                                      HHHHHHHHHHHHHG CS
                            DUF326  8 AkaCrkCAkaCrkc 21
                                      A+aC++CA++C+++
  gi|336252967|ref|YP_004596074.1| 79 ADACEECADECEQH 92
                                      89*********987 PP

  == domain 5  score: 18.6 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHHHHHHHHH CS
                            DUF326   2 khckkCAkaCrkCAkaCr 19 
                                       +hc+ CA+  r+CA+ Cr
  gi|336252967|ref|YP_004596074.1|  95 EHCQVCADVLRDCAETCR 112
                                       6****************8 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.1   6.6e-05       0.4      87     177 ..      10     104 ..       1     106 [. 0.74
   2 ?    3.2   0.1    0.0088        53     102     134 ..      78     111 ..      70     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.6e-05
                                       .-SS-HHHHHHHHHHHHHHHHHHHHHTT-S-HHHHHHHHHTTTHHHHHHHHHS....HHHHHHHHHHHHHH---HHH CS
                              HDOD  87 eegadlkklwehslavAlvarelaeelgledpeeaflaGLLhdiGklvllsll....peeleellekvaeeelslle 159
                                       +e+ ++++  + +l++A +++  a+e+  e +e a +  L +d+ +lv l++     +  ++  ++++ +++++  +
  gi|336252967|ref|YP_004596074.1|  10 SEDEEMQECIDSCLECAQACEWCADECADEGEEMAECLRLCRDVADLVSLHARfmarNSGYSSDVAAITADACEECA 86 
                                       46889******************************************988754111134455555556666666666 PP

                                       HHHHHHSS-HHHHHHHHH CS
                              HDOD 160 aeeellgtdhaevGaall 177
                                        e e   ++h++v a +l
  gi|336252967|ref|YP_004596074.1|  87 DECEQHDAEHCQVCADVL 104
                                       666677777777777665 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0088
                                       HHHHHHHHHHHTT-S-HHHHHHHH.HTTTHHHHH CS
                              HDOD 102 vAlvarelaeelgledpeeaflaG.LLhdiGklv 134
                                       +A +++e a+e++++d+e + +++  L+d+ + +
  gi|336252967|ref|YP_004596074.1|  78 TADACEECADECEQHDAEHCQVCAdVLRDCAETC 111
                                       7899999999999999888766544888887766 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.8e-05       0.1      19      76 ..       8      65 ..       2      66 .. 0.91
   2 ?    0.1   0.3      0.18   1.1e+03      23      36 ..     101     114 ..      80     117 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                               GAT 19 ellenellkeLyetckamqpriqklieetadeedllaelLqlNDeLnnvlerYerlkk 76
                                       ++e+e ++e  ++c +  +     ++e ade + +ae+L+l  ++  +++ + r+++
  gi|336252967|ref|YP_004596074.1|  8 HVSEDEEMQECIDSCLECAQACEWCADECADEGEEMAECLRLCRDVADLVSLHARFMA 65
                                      57899***************999999999*************************9986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.18
                               GAT  23 nellkeLyetckam 36 
                                        ++l + +etc++m
  gi|336252967|ref|YP_004596074.1| 101 ADVLRDCAETCRNM 114
                                       57888889999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 869.26
//
Query:       gi|336252968|ref|YP_004596075.1|  [L=126]
Description: hypothetical protein Halxa_1564 [Halopiger xanaduensis SH-6]
Scores for 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-10   39.4  24.7    1.3e-05   24.7   8.9    2.3  2  SPW       SPW repeat
  ------ inclusion threshold ------
       0.04   13.3   3.4      0.058   12.7   3.1    1.4  1  ThrE      Putative threonine/serine exporter


Domain annotation for each model (and alignments):
>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   7.8   2.7e-08   0.00024       4      43 ..      12      49 ..      11      52 .. 0.90
   2 !   24.7   8.9   1.4e-09   1.3e-05       4      45 ..      68     109 ..      65     115 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.7e-08
                               SPW  4 nlllGlwlivSPWvlGfsattgaawnnvivGavvavLala 43
                                      n+llG wliv+  vl   ++  a wn+v vGa+vavLa +
  gi|336252968|ref|YP_004596075.1| 12 NCLLGCWLIVAAAVLA--PSGIARWNDVLVGAAVAVLAGY 49
                                      8**************9..55569**************965 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.4e-09
                               SPW   4 nlllGlwlivSPWvlGfsattgaawnnvivGavvavLalafa 45 
                                       + +lG wl+v+P+vlG    + a wn+v vG v+a ++ + a
  gi|336252968|ref|YP_004596075.1|  68 VAVLGGWLVVAPFVLGLGRAQPALWNDVAVGTVIASFGGYNA 109
                                       78*********************************9998655 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.1   6.5e-06     0.058     113     183 ..      17      87 ..       8     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-06
                              ThrE 113 laaglaaaafallfggdwidflvaflagllggllrlllakrglnsfvleavaaflasllallavslglgln 183
                                          ++aaa++a+   ++w+d+lv +++++l+g+ +  +++r+ +s v  ++ a+l ++l ++ + lglg  
  gi|336252968|ref|YP_004596075.1|  17 CWLIVAAAVLAPSGIARWNDVLVGAAVAVLAGYNYVDVRDRRSPSAVGACLVAVLGGWLVVAPFVLGLGRA 87 
                                       4567788888888899*******************************************998888766433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 999.93
//
Query:       gi|336252969|ref|YP_004596076.1|  [L=651]
Description: glycoside hydrolase 15-like protein [Halopiger xanaduensis SH-6]
Scores for 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-49  166.6   0.0    1.1e-43  149.7   0.0    2.1  2  Glyco_hydro_15  Glycosyl hydrolases family 15
     0.0018   18.7   0.6      0.051   14.2   0.2    3.4  3  TPR_4           Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.047   14.0   0.1          7    7.0   0.0    2.7  2  TPR_12          Tetratricopeptide repeat
       0.11   12.6   0.7        8.5    6.8   0.1    2.8  2  TPR_2           Tetratricopeptide repeat
       0.79    9.9   3.3        4.9    7.4   0.1    3.5  4  TPR_9           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.7   0.0   2.9e-47   1.1e-43       5     348 ..     249     558 ..     245     565 .. 0.94
   2 !   15.0   0.0   2.2e-06    0.0078     400     445 ..     565     610 ..     560     613 .. 0.93

  Alignments for each domain:
  == domain 1  score: 149.7 bits;  conditional E-value: 2.9e-47
                                       HHHHHCBCSTTSSBTTS-TT-B-S-S-BSSS.........B--SEEHHHHHHHHHHHH.......HHHHHTTT-HCC CS
                    Glyco_hydro_15   5 dlylrnvktlilleqnpvtGlliASpstsdp.........DYrytWvRDsvyvilavwglgyrdedrakayeleqsl 72 
                                       dl +r+   l+ll+ +  tG++ A+p+ts+p         DYry W+RD+++++ a+ +l   +e+r++ +     +
  gi|336252969|ref|YP_004596076.1| 249 DLAVRSSLVLKLLIHRE-TGAVCAAPTTSLPediggvrnwDYRYNWIRDAAFTVRALSELDHLEEARSYFELCLDHC 324
                                       67778888889999999.9****************************************9999********999999 PP

                                       HHHHHHHHHHHHHHCTS-BTTB-TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHHHCTTHCHCCCC CS
                    Glyco_hydro_15  73 vklmrglleamvrqagkvekfketqstkgLhakyftktgstvvGddewghlQlDatslyllalaqmtasglqiistl 149
                                        +     +  +++ +g   +f+e+ ++   h++++ ++ +++vG+ + ++ QlD++++ +lal++ +  g  + s+ 
  gi|336252969|ref|YP_004596076.1| 325 SRHDPAEMPPVYSLHGG-SDFEERVLD---HLEGYRGSAPVRVGNAARDQHQLDVYGELVLALYESVRYGEPMRSDD 397
                                       9988888*********8.99*******...*********************************************** PP

                                       HHHHTHHHHHHHHHHHTTS-EE-TTS--ECEEHH..HHHHHHHHHHHHHHHHHHC.T-HHHHCCHHHHHHHHHHHHH CS
                    Glyco_hydro_15 150 devafvqnlvdYieaayktpdfglWEenqgeselnassvgmakAlleaideadlf.gakgdaqlvektkdeilnklq 225
                                       ++v  v+ lvdY+ + +++pd g+WE++ + +++++s+v+ + Al+++i++a+++ g+++  + +++ +d++   + 
  gi|336252969|ref|YP_004596076.1| 398 WPV--VRDLVDYVVEGWDEPDAGIWEVRTDPEHFVYSKVMCWTALDRGIELAEAAdGVDAPLERWRTARDDVRAAI- 471
                                       ***..************************************************98345667777************. PP

                                       STTT..GGGEETTCCECECSCH.....HHHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHH CS
                    Glyco_hydro_15 226 gkygckrgfwplfntylildgsfaedkeqvqeyrealdasllllpelyfvpaddvdeeyqnpqsprllaqslyilds 302
                                            +rg  ++ n +++ +g+           ++ lda+ ll+p ++f p+dd          +r+  ++++ +d+
  gi|336252969|ref|YP_004596076.1| 472 ----LERGVSEETNSFVQSFGD-----------ADTLDAANLLVPVVGFLPPDD----------DRVRRTIDATIDR 523
                                       ....******************...........9********************..........************* PP

                                       HHHHSGGGTT-STTS--SBTT--CGSSSBSCT--BHHHHHHHHHHH CS
                    Glyco_hydro_15 303 llsegflavgeldplvrRysedvkpdklglsGrpyylctlwtvetl 348
                                       l ++        d+lvrRy+ d   d+l +  +p+ ++ +w v  l
  gi|336252969|ref|YP_004596076.1| 524 LATD--------DGLVRRYEGD---DGLPGVDNPFVVSAFWLVTAL 558
                                       9998........456*****99...689*************66554 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.2e-06
                                       HHHHHHHHHHHHHS-TTS---SEE-TTT--EESSTT-HHHHHHHHH CS
                    Glyco_hydro_15 400 eeladliveaveednslgvLteevdvylgeliraqpllfsealllr 445
                                        e ++ + ++ e +  lg+L e vd ++ge++++ p+++s++ ll+
  gi|336252969|ref|YP_004596076.1| 565 DEARERFESILEYASPLGLLGEAVDPDDGEQRGNYPQAYSHIGLLN 610
                                       578999999*********************************9997 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       0.5   1.8e+03       8      21 ..     301     314 ..     297     315 .. 0.85
   2 !   14.2   0.2   1.4e-05     0.051       3      25 ..     550     572 ..     548     573 .. 0.89
   3 ?   -2.1   0.0       2.6   9.4e+03      13      21 ..     595     603 ..     595     606 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.5
                             TPR_4   8 ArallalGdldeAr 21 
                                        ral +l +l+eAr
  gi|336252969|ref|YP_004596076.1| 301 VRALSELDHLEEAR 314
                                       68999********9 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.4e-05
                             TPR_4   3 allaLArallalGdldeAralle 25 
                                        + +L  al+++G+ deAr+ +e
  gi|336252969|ref|YP_004596076.1| 550 SAFWLVTALALAGRTDEARERFE 572
                                       6789***************9987 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.6
                             TPR_4  13 alGdldeAr 21 
                                       ++G++++A 
  gi|336252969|ref|YP_004596076.1| 595 QRGNYPQAY 603
                                       69*****96 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.019        69      54      75 ..     303     324 ..     301     326 .. 0.77
   2 ?    7.0   0.0    0.0019         7       9      33 ..     554     578 ..     546     582 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.019
                            TPR_12  54 lyralgryeeAlelleealaia 75 
                                       ++++l+++eeA++++e +l+ +
  gi|336252969|ref|YP_004596076.1| 303 ALSELDHLEEARSYFELCLDHC 324
                                       6778888899999988888765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0019
                            TPR_12   9 laavlrrlgrydeAlellekaleia 33 
                                       l ++l+ +gr deA+e +e  le a
  gi|336252969|ref|YP_004596076.1| 554 LVTALALAGRTDEARERFESILEYA 578
                                       5666777777777777777777755 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0024       8.5      10      31 ..     303     324 ..     302     327 .. 0.85
   2 ?    3.2   0.1     0.033   1.2e+02      10      30 ..     557     577 ..     556     579 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0024
                             TPR_2  10 ayyklgdyeeAleafekAleld 31 
                                       a+ +l+++eeA+ +fe +l ++
  gi|336252969|ref|YP_004596076.1| 303 ALSELDHLEEARSYFELCLDHC 324
                                       678899**********999876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.033
                             TPR_2  10 ayyklgdyeeAleafekAlel 30 
                                       a++ +g+ +eA+e fe  le+
  gi|336252969|ref|YP_004596076.1| 557 ALALAGRTDEARERFESILEY 577
                                       67889**********998886 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.26   9.4e+02      28      66 ..      63     101 ..      61     104 .. 0.84
   2 ?    7.4   0.1    0.0014       4.9      38      62 ..     303     327 ..     291     332 .. 0.79
   3 ?   -1.1   0.0       0.6   2.1e+03      42      58 ..     457     473 ..     453     496 .. 0.80
   4 ?   -2.3   0.0       1.4   5.1e+03       8      38 ..     568     602 ..     558     613 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.26
                             TPR_9  28 dpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                                       +++ +rdR  +l+   ++++++a L  ++ +a++ + a+
  gi|336252969|ref|YP_004596076.1|  63 SVQRYRDRTNVLETTFRTAGGAATLTDFVPVAEAGESAD 101
                                       5677999999999999*************8887766665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0014
                             TPR_9  38 llaqlGclsaAladLeaylalapda 62 
                                       +l +l++l++A+  +e +l+++   
  gi|336252969|ref|YP_004596076.1| 303 ALSELDHLEEARSYFELCLDHCSRH 327
                                       6889******************744 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.6
                             TPR_9  42 lGclsaAladLeaylal 58 
                                       l+++++A++d  a++  
  gi|336252969|ref|YP_004596076.1| 457 LERWRTARDDVRAAILE 473
                                       899999**999998854 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.4
                             TPR_9   8 eedweralavverllll....aPddpeerrdRGll 38 
                                       +e++e  l+++  l ll    +Pdd e r    ++
  gi|336252969|ref|YP_004596076.1| 568 RERFESILEYASPLGLLgeavDPDDGEQRGNYPQA 602
                                       44444444444444444444455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 4766.32
//
Query:       gi|336252970|ref|YP_004596077.1|  [L=525]
Description: Vitamin K epoxide reductase [Halopiger xanaduensis SH-6]
Scores for 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-15   54.9   6.7    9.1e-15   54.9   6.7    3.1  3  VKOR        Vitamin K epoxide reductase family
    3.1e-05   23.5  48.7     0.0015   18.0   6.7    5.3  5  SPW         SPW repeat
  ------ inclusion threshold ------
       0.53   10.5   3.1        4.1    7.6   0.1    2.8  2  Holin_SPP1  SPP1 phage holin


Domain annotation for each model (and alignments):
>> VKOR  Vitamin K epoxide reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   3.5         3   1.8e+04      76      76 ..     154     154 ..      97     191 .. 0.54
   2 !   54.9   6.7   1.5e-18   9.1e-15       3     123 ..     216     342 ..     214     343 .. 0.89
   3 ?    2.8   4.0     0.021   1.2e+02      39      76 ..     384     442 ..     372     496 .. 0.61

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 3
                                       H CS
                              VKOR  76 l 76 
                                       l
  gi|336252970|ref|YP_004596077.1| 154 L 154
                                       1 PP

  == domain 2  score: 54.9 bits;  conditional E-value: 1.5e-18
                                       HHHHHHHHHHHHHHHHHHHH...HT---SS-SSSS..HHHHHCSTTSEETTEEHHHHHHHHHHHHHHHHHS-..... CS
                              VKOR   3 llvlalvGllvsiyltleklglktsssaalCdissvsCdkvlnSpyasilgvplsllGllayalvlllalapl.... 75 
                                       l++l+++G+++s+y+++ +lg+++s  ++   i +  ++++l+S+ ++++ v+ + lG++ay++ +l+++++     
  gi|336252970|ref|YP_004596077.1| 216 LIALGVFGFFASWYMAAFQLGYIESVWDP---IYGSGTEQILTSRISEAFPVSDAGLGAVAYSIEALMGFMGDrrrw 289
                                       799*****************988444444...333459*********************************99**** PP

                                       ...HHHHHHHHHH..HHHHHHHHHHHHHHTTS----HHHHHHHHHHHHHHHHH CS
                              VKOR  76 ...lwlllllgsl..agvvfslyLiylslfvigalCpyClvsavlsllllvla 123
                                          +w+++++g++  +   + + L++++ + +g++C++Cl+sa+ +l +++l+
  gi|336252970|ref|YP_004596077.1| 290 rtmPWMVAFFGVVviPLGFVQVLLVIMQPIMVGTWCTLCLLSAFGMLWMIALT 342
                                       ********99999866777778899999******************9999886 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.021
                                       .HHHHHCSTTSEET...TEEHHHHHHHHHHHHHHHHHS-...................H CS
                              VKOR  39 sCdkvlnSpyasil...gvplsllGllayalvlllalapl..................l 76 
                                       s+  + +Sp+++ +    +p++llG++a  + l+l+ +                    +
  gi|336252970|ref|YP_004596077.1| 384 STRPIGDSPVSEPFwgvSIPWTLLGAMALGAWLMLSPTVFgttglmadsshlagalivS 442
                                       5566678999987554458********88888877543335555555555444333330 PP

>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   5.6   7.4e-05      0.44       3      43 ..      97     136 ..      95     139 .. 0.88
   2 !    6.3   3.9    0.0012       7.1       3      46 ..     148     190 ..     146     192 .. 0.84
   3 ?   -2.2   0.3      0.54   3.2e+03       5      17 ..     217     229 ..     215     234 .. 0.75
   4 !   11.3   3.0   3.3e-05      0.19       4      45 ..     409     448 ..     408     451 .. 0.84
   5 !   18.0   6.7   2.6e-07    0.0015       3      41 ..     458     495 ..     456     498 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.4e-05
                               SPW   3 anlllGlwlivSPWvlGfsattgaawnnvivGavvavLala 43 
                                       a+  lG+wl++    +G+ +   ++wn+v+ G+v+++La a
  gi|336252970|ref|YP_004596077.1|  97 AVISLGAWLVATAPAFGYESA-PVFWNSVVSGLVLIALAGA 136
                                       67789*******99***9876.89**************965 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0012
                               SPW   3 anlllGlwlivSPWvlGfsattgaawnnvivGavvavLalafaa 46 
                                       an  +Glwl+++P  +  ++t++a  n+  vG +v+++++   +
  gi|336252970|ref|YP_004596077.1| 148 ANGFVGLWLVFAPIAFS-APTAAAYANSGLVGTMVITFSVLIVM 190
                                       67889********6665.88889999999******999987766 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.54
                               SPW   5 lllGlwlivSPWv 17 
                                        +lG++ +++ W 
  gi|336252970|ref|YP_004596077.1| 217 IALGVFGFFASWY 229
                                       5788988888885 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 3.3e-05
                               SPW   4 nlllGlwlivSPWvlGfsattgaawnnvivGavvavLalafa 45 
                                       +++lG+wl++SP v+G  +t  +a ++  +Ga+++ + ++++
  gi|336252970|ref|YP_004596077.1| 409 AMALGAWLMLSPTVFG--TTGLMADSSHLAGALIVSFTVIAT 448
                                       589*************..444588899999999999988876 PP

  == domain 5  score: 18.0 bits;  conditional E-value: 2.6e-07
                               SPW   3 anlllGlwlivSPWvlGfsattgaawnnvivGavvavLa 41 
                                       +n+ l+ wli++PW+l  ++t  aa+n+ ++G++va+L+
  gi|336252970|ref|YP_004596077.1| 458 LNVPLAGWLIAAPWLLAGVPT-IAAINAAVAGLLVAILS 495
                                       5677889*********65666.5889***********97 PP

>> Holin_SPP1  SPP1 phage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1   0.00069       4.1       3      57 ..      89     142 ..      87     148 .. 0.83
   2 ?    2.1   0.6     0.038   2.3e+02      11      50 ..     406     448 ..     402     449 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00069
                        Holin_SPP1   3 dkgtlvrt.illllallnqlltilGknplpideealytaitlvftvataivawyKN 57 
                                       +k+t+v++ ++ l a l ++  ++G ++ p+  +++ + ++l+ + +++i+  y+N
  gi|336252970|ref|YP_004596077.1|  89 TKETWVQYaVISLGAWLVATAPAFGYESAPVFWNSVVSGLVLIALAGATIY--YEN 142
                                       799***983556778888899*************99999999999999996..555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.038
                        Holin_SPP1  11 illllallnqll...tilGknplpideealytaitlvftvata 50 
                                       +l+++al + l+   t++G + l  d++ l  a+ + ftv+++
  gi|336252970|ref|YP_004596077.1| 406 LLGAMALGAWLMlspTVFGTTGLMADSSHLAGALIVSFTVIAT 448
                                       5666666666667789***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3729.46
//
Query:       gi|336252971|ref|YP_004596078.1|  [L=339]
Description: short-chain dehydrogenase/reductase SDR [Halopiger xanaduensis SH-6]
Scores for 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  147.6   0.2    3.9e-43  147.2   0.2    1.1  1  adh_short     short chain dehydrogenase
    1.4e-30  106.6   0.1    1.7e-30  106.3   0.1    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    7.8e-15   55.2   0.2    1.1e-14   54.8   0.2    1.2  1  KR            KR domain
  ------ inclusion threshold ------
       0.14   11.6   0.3       0.39   10.1   0.3    1.8  1  Epimerase     NAD dependent epimerase/dehydratase family


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 !  147.2   0.2   8.7e-47   3.9e-43       1     186 [.       8     195 ..       8     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 147.2 bits;  conditional E-value: 8.7e-47
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       +vv+vtGas+G+Gra+a+++a++Gak+ +++r e+ le + + ++++g +a+a++++v+d ++vea+ e++++ +g+
  gi|336252971|ref|YP_004596078.1|   8 NVVVVTGASAGVGRATARAFAERGAKLGLLARGEDGLEGARADVEDAGGEAIAVPTNVSDPDAVEAAAETVEDAFGP 84 
                                       69*************************************************************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       +dv vnNA ++ ++p++e+++++++rv ev + g+++ t+a+l+ m  + +G+Iv+v+S  +  + + ++aY+ +K+
  gi|336252971|ref|YP_004596078.1|  85 IDVWVNNAMVSVFSPAAEMTADDYRRVTEVTYLGYVHGTQAALERMRPRDEGTIVQVGSALAYRGIPLQSAYCGAKH 161
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHGGGT..EEEEEEEESSBSSHH CS
                         adh_short 155 avagltrslakelaptg..irvnavaPGlvdTdm 186
                                       a++g+t+s++ el  +   ++ ++v+ ++++T+ 
  gi|336252971|ref|YP_004596078.1| 162 AIQGYTESVRTELIHDDcdVQLSMVQMPAMNTPQ 195
                                       *************999988999999999999975 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 !  106.3   0.1   3.8e-34   1.7e-30       1     163 [.      14     178 ..      14     227 .. 0.90

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 3.8e-34
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvn 75 
                                       Ga  g+Gra+A+a+ae+Ga++ l  ++e++ + + +++++++g+++ ++++V+d+++vea++e+v++ fg +D+ vn
  gi|336252971|ref|YP_004596078.1|  14 GASAGVGRATARAFAERGAKLGLLARGEDGlEGARADVEDAGGEAIaVPTNVSDPDAVEAAAETVEDAFGPIDVWVN 90 
                                       899***************************88888888888888856****************************** PP

                                       -----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHH CS
                      adh_short_C2  76 nagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalea 150
                                       na ++    +p++e++ ++++r+ +v   ++++ ++aal+ m+++  g iv + s  a r++p ++ay+ aK+a+++
  gi|336252971|ref|YP_004596078.1|  91 NAMVSVF--SPAAEMTADDYRRVTEVTYLGYVHGTQAALERMRPRdeGTIVQVGSALAYRGIPLQSAYCGAKHAIQG 165
                                       *****99..*******************************9987778****************************** PP

                                       HHHHHHHHHGGGT CS
                      adh_short_C2 151 ltrylAvelgpkg 163
                                        t ++  el ++ 
  gi|336252971|ref|YP_004596078.1| 166 YTESVRTELIHDD 178
                                       **99988887765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.2   2.4e-18   1.1e-14       2     165 ..       9     172 ..       8     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 2.4e-18
                                       EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                                KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78 
                                       ++++tG+  g+G+++ar  ae+ga+ l ll+R +   e +    a +e+ g e  +v+  vsd+davea+ e++++ 
  gi|336252971|ref|YP_004596078.1|   9 VVVVTGASAGVGRATARAFAERGAK-LGLLARGEDGLEGA---RADVEDAGGEAIAVPTNVSDPDAVEAAAETVEDA 81 
                                       579********************95.99999995444444...4778999*************************** PP

                                       SS---EEEE---------TTT--HHHHHHHHTTT....THHHHHHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHH CS
                                KR  79 eppikGvihaAgvlrdklleemtaedleqvlapK....vkGawnLhelledesldffvlfSSiagllgsagqanYaa 151
                                       ++pi   ++ A+v+  ++ +emta+d+++v++      v+G++   e +++++   +v + S+ +  g + q++Y  
  gi|336252971|ref|YP_004596078.1|  82 FGPIDVWVNNAMVSVFSPAAEMTADDYRRVTEVTylgyVHGTQAALERMRPRDEGTIVQVGSALAYRGIPLQSAYCG 158
                                       ******************************9975333377888877788889999********************** PP

                                       HHHHHHHHHHHHHH CS
                                KR 152 aNaflDalaeyrrs 165
                                       a + + ++ e+ r+
  gi|336252971|ref|YP_004596078.1| 159 AKHAIQGYTESVRT 172
                                       *9999988877655 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   8.7e-05      0.39       1      61 [.      10      76 ..      10     172 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.7e-05
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHH CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfk 61
                                      ++VtGa+  +G+a+++a++e+g ++  l+r +++ + ar +          v  ++ d++a+e++ +
  gi|336252971|ref|YP_004596078.1| 10 VVVTGASAGVGRATARAFAERGAKLGLLARGEDGLEGARADVEdaggeaIAVPTNVSDPDAVEAAAE 76
                                      68*********************99999999665555544444667777566666666665555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2612.96
//
Query:       gi|336252972|ref|YP_004596079.1|  [L=401]
Description: glutamate--cysteine ligase GCS2 [Halopiger xanaduensis SH-6]
Scores for 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  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 3280.02
//
Query:       gi|336252973|ref|YP_004596080.1|  [L=166]
Description: hypothetical protein Halxa_1569 [Halopiger xanaduensis SH-6]
Scores for 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-26   91.9   1.8    4.9e-26   91.6   1.8    1.1  1  DUF892    Domain of unknown function (DUF892)
  ------ inclusion threshold ------
       0.04   14.5   1.3       0.87   10.3   0.2    2.7  2  SlyX      SlyX
      0.041   14.1   0.0       0.06   13.6   0.0    1.3  1  GDH_N     Glutamate dehydrogenase N terminal


Domain annotation for each model (and alignments):
>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   1.8   8.3e-30   4.9e-26       1     151 [.       5     153 ..       5     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 8.3e-30
                                       ..HHHHHHHHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-------.-HHHHTT CS
                            DUF892   1 tleelfvdeLrDlyaaEkqllkalpkmakaaespeLkaaleqHleeTegqierLeqvferlgesasekkcdamegli 77 
                                       tle+lf  +L+ +y++E+  +++l++ma  a s++L++++ +H eeT +q+erLe+vf++lg ++ +    +++gl+
  gi|336252973|ref|YP_004596080.1|   5 TLEDLFGYQLQHAYYVERTHVELLDEMATDAPSDDLADRFATHREETARQVERLEDVFAALGRRPHASRARSADGLA 81 
                                       699******************************************************************89988887 PP

                                       T-----------THHHHHHH...HHHHHHHHHHHHHHHHHHHHHCTT-H.HHHHHHHHHHHHHHHHHHHHHHHHH CS
                            DUF892  78 aegqelieeaaedeslkdaaliaaaqavehyEiAsYgtLialAeqlgek.eaaklLeqtleeekatdekltelae 151
                                          + l ++aa++ ++ d +    +   e++Ei +Y+tL++lA +l ++ ++++ Le++l+ee++t + l++l  
  gi|336252973|ref|YP_004596080.1|  82 DS-RHLRDDAAGEPTVPDDL--ELGLLAERLEIRCYETLVRLAGRLAYAdDVVEPLETNLAEERETLQALEALEA 153
                                       65.55666656666666666..6999********************9976999*****************99855 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.037   2.2e+02      29      53 ..      51      75 ..      16      89 .. 0.75
   2 ?   10.3   0.2   0.00015      0.87       4      38 ..     116     150 ..     114     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.037
                                      HHHHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX 29 qqqqidrlqrqlrllaerlkelees 53
                                       ++q++rl+  +++l +r  + +++
  gi|336252973|ref|YP_004596080.1| 51 TARQVERLEDVFAALGRRPHASRAR 75
                                      4566666666666666666555544 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   4 rleeLEiklafqedtieeLndvvaeqqqqidrlqr 38 
                                        l++L  +la+ +d++e L   +ae ++++++l++
  gi|336252973|ref|YP_004596080.1| 116 TLVRLAGRLAYADDVVEPLETNLAEERETLQALEA 150
                                       6788999*********************9999987 PP

>> GDH_N  Glutamate dehydrogenase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     1e-05      0.06      10      61 ..      32      84 ..      25     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                             GDH_N 10 sskaaakdvakr.alvvdvearqavslepvfaalrkryPaarqsevqalaaaf 61
                                      ++ a++ d a+r a   + +arq   le vfaal +r  a+r   +  la++ 
  gi|336252973|ref|YP_004596080.1| 32 ATDAPSDDLADRfATHREETARQVERLEDVFAALGRRPHASRARSADGLADSR 84
                                      5667888888883455677899999****************999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1269.26
//
Query:       gi|336252974|ref|YP_004596081.1|  [L=200]
Description: hypothetical protein Halxa_1570 [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.8   0.7    1.4e-14   54.4   0.7    1.9  1  DUF892     Domain of unknown function (DUF892)
  ------ inclusion threshold ------
      0.032   14.3   0.5      0.088   12.9   0.3    1.9  2  DASH_Dad3  DASH complex subunit Dad3


Domain annotation for each model (and alignments):
>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.7   1.5e-18   1.4e-14       2     153 ..       7     172 ..       6     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.5e-18
                                       .HHHHHHHHHHHHHHHHHHHHHHHHHH...........HH-SS.HHHHHHHHHHHHHHHHHHHHHHHHHHHTT---- CS
                            DUF892   2 leelfvdeLrDlyaaEkqllkalpkma...........kaaes.peLkaaleqHleeTegqierLeqvferlgesas 66 
                                       +++ ++ eL+ ly++E++l + l++++           +++e  ++L+ a ++H e+T +++er+e+ f++lge+++
  gi|336252974|ref|YP_004596081.1|   7 PRDALTAELERLYYVERKLRDELETLSsdvaidtlddlRELECrEQLQYAVDRHREQTDRHVERIERAFDALGEEPD 83 
                                       6777888888888888887777776651111111111134455589999**************************** PP

                                       ---.-HHHHTTT-----------THHHHHHH...HHHHHHHHHHHHHHHHHHHHHCTT-...HHHHHHHHHHHHHHH CS
                            DUF892  67 ekkcdamegliaegqelieeaaedeslkdaaliaaaqavehyEiAsYgtLialAeqlge...keaaklLeqtleeek 140
                                       ++  +  +glia+ +++ +  + ++ l+ ++ i    ++e  E ++Y+  + +A +l++   + +++ Le++++ e 
  gi|336252974|ref|YP_004596081.1|  84 TRRVPELDGLIADKEKFNNV-VLNDGLRPLFYIETVLKLEAIECTAYERTMGIAGALEDdagDAVVDALEKNYDDEC 159
                                       ****************9998.77777*********************************6666999*********** PP

                                       HHHHHHHHHHHHH CS
                            DUF892 141 atdekltelaesl 153
                                       +  + ++ la+ +
  gi|336252974|ref|YP_004596081.1| 160 DLRSEIDSLADGE 172
                                       *999999999865 PP

>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   9.8e-06     0.088      15      49 ..      18      52 ..       8      57 .. 0.82
   2 ?   -2.5   0.0      0.63   5.7e+03      22      34 ..     161     173 ..     146     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.8e-06
                         DASH_Dad3 15 LaenlktLaselkeLasnsteeildgLReLErkig 49
                                      L    ++L +el++L+s  + ++ld+LReLE +  
  gi|336252974|ref|YP_004596081.1| 18 LYYVERKLRDELETLSSDVAIDTLDDLRELECREQ 52
                                      55555789***********************8765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.63
                         DASH_Dad3  22 LaselkeLasnst 34 
                                       L se+++La+ ++
  gi|336252974|ref|YP_004596081.1| 161 LRSEIDSLADGEA 173
                                       7788888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1594.56
//
Query:       gi|336252975|ref|YP_004596082.1|  [L=108]
Description: hypothetical protein Halxa_1571 [Halopiger xanaduensis SH-6]
Scores for 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:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 831.71
//
Query:       gi|336252976|ref|YP_004596083.1|  [L=260]
Description: MOSC domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-14   52.8   0.0    5.1e-14   52.2   0.0    1.5  1  MOSC_N    MOSC N-terminal beta barrel domain
      5e-07   29.8   0.0    7.3e-07   29.3   0.0    1.3  1  MOSC      MOSC domain


Domain annotation for each model (and alignments):
>> MOSC_N  MOSC N-terminal beta barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   5.7e-18   5.1e-14       1      93 [.       1      92 [.       1     139 [. 0.89

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 5.7e-18
                            MOSC_N  1 sarvssLyvyPiKsckgvslseaevtaaGllalDReflvvdedGkfltqrrePrlalirteldeedglLtltapgrkdl 79
                                      +a++++L vyP+K+++g++l++a + + G +  DRef++ d+ G++++ +r  r++ ++t++d  +  L+l+ap+++  
  gi|336252976|ref|YP_004596083.1|  1 MAQLERLRVYPVKGLDGIDLESASILEGGTVEYDREFALFDDGGEVINGKRTDRVHDLETDFDPATRELVLEAPDGERR 79
                                      6899**************************************************************************9 PP

                            MOSC_N 80 evslakakasleev 93
                                       + la++++  e++
  gi|336252976|ref|YP_004596083.1| 80 RFALADEADR-ERA 92
                                      9999854433.333 PP

>> MOSC  MOSC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   8.1e-11   7.3e-07      14      88 ..     124     215 ..     118     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 8.1e-11
                                       EEETHHHHHHHHHS..GGG.GG-STTTT--SEEES-............-TTT-BTT-E.EEETT............. CS
                              MOSC  14 lisresldalneelkegrs.veldpgrfreNivvggaaa.....feEdtwkelrigdrrfrlggacsRcqmvnvdqe 84 
                                       ++s++ +++++++++e++   e + +r+r+Ni ++g +a     f  d+   ++i   r++ +++c+Rc +++ d++
  gi|336252976|ref|YP_004596083.1| 124 VVSTATVRQVASWFDEEGMtLEGARRRIRANIEISGVPAfwedrFVGDEAPAFEIEGIRLEGVTPCGRCVVPQRDPD 200
                                       7999**********777668666779********8878856666666667777777779****************** PP

                                       ..............E CS
                              MOSC  85 tga...........r 88 
                                       tg+           +
  gi|336252976|ref|YP_004596083.1| 201 TGEpiekfqqrfveK 215
                                       **9888753333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.22s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1925.11
//
Query:       gi|336252977|ref|YP_004596084.1|  [L=130]
Description: hypothetical protein Halxa_1573 [Halopiger xanaduensis SH-6]
Scores for 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:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1029.30
//
Query:       gi|336252978|ref|YP_004596085.1|  [L=319]
Description: hypothetical protein Halxa_1574 [Halopiger xanaduensis SH-6]
Scores for 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-57  193.0  19.3    7.8e-57  192.7  19.3    1.1  1  DUF368    Domain of unknown function (DUF368)


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 !  192.7  19.3   4.3e-61   7.8e-57       1     230 [.      24     279 ..      24     295 .. 0.93

  Alignments for each domain:
  == domain 1  score: 192.7 bits;  conditional E-value: 4.3e-61
                            DUF368   1 mGaAdvvPGvSGGtiAlitGiYeelieslksinlealklllra.......rlkaalkkinlkfLlalvlGivvsilv 70 
                                       mG+Ad++PGvSGGt+Al++G+Y +li++++++++ ++ ++l++       ++++al +++l+fL++l +G+v+++++
  gi|336252978|ref|YP_004596085.1|  24 MGTADALPGVSGGTVALLLGFYGRLIAAVTALTPGRIITVLSGyhpdrrtNAREALLELDLQFLVPLGVGMVTAVVL 100
                                       9*********************************99999998889998888899999******************** PP

                            DUF368  71 lakllsyllekypillwslffGlilasvvvlikevkkwsvkkiialllglaiallltvlepveteeslvfvflaGai 147
                                       +a+++s+l  ++p++++++f+Gli+as+v+l ++++  s ++++a+++g+ +all+++  ++   ++ +++++aGa+
  gi|336252978|ref|YP_004596085.1| 101 IADIVSSLASTHPLPMFGFFTGLIAASAVTLGRSLEFASRTHVAAAIVGAGLALLVAADLVALPGSGPLVIVVAGAL 177
                                       ******************************************************999988777788*********** PP

                            DUF368 148 aicAmilPGiSGSfiLlllGlYelllealkeld...................vkvllvfllGavvGllsfsrvlsal 205
                                       a++AmilPG+SGS+iL+llG+Y  l ++l+ ++                    +++++f++G vvGl++++rv++a+
  gi|336252978|ref|YP_004596085.1| 178 AVSAMILPGVSGSLILILLGQYVFLSSELSAFVgaigdvvldggstaaavgpGTTVVLFVVGGVVGLVTIARVVRAA 254
                                       *********************************88888877777776664443669********************* PP

                            DUF368 206 lkkyrsltlavliGlmlGslrkvwp 230
                                       l++ r+ltl++l+ l+ Gs+ + ++
  gi|336252978|ref|YP_004596085.1| 255 LERRRNLTLVFLVSLIAGSVPAPLH 279
                                       *******************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2525.64
//
Query:       gi|336252979|ref|YP_004596086.1|  [L=688]
Description: DNA mismatch repair protein MutS domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-09   37.1   0.6      5e-09   36.5   0.1    1.6  2  MutS_V          MutS domain V
    6.7e-08   33.0   5.3    1.1e-07   32.3   0.4    3.1  3  HHH_5           Helix-hairpin-helix domain
    1.8e-05   24.4   0.8     0.0013   18.5   0.1    3.2  2  HHH             Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.017   14.9   0.0       0.32   10.8   0.0    2.2  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
       0.13   12.6   0.0       0.51   10.7   0.0    2.0  2  Transposase_20  Transposase IS116/IS110/IS902 family
       0.26   11.7   0.9       0.62   10.5   0.0    2.1  2  AAA             ATPase family associated with various cellula


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.6   1.1e+04      84     108 ..     270     294 ..     270     296 .. 0.85
   2 !   36.5   0.1   1.7e-12     5e-09       2     126 ..     489     610 ..     488     632 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.6
                                       ESTS-SS-HHHHHHHHHHHHHHHHH CS
                            MutS_V  84 DElGRGtstydGlaialavaeylle 108
                                       DEl R t+++d l  a + ae +++
  gi|336252979|ref|YP_004596086.1| 270 DELDRLTTAVDDLDAAASAAESVAN 294
                                       8999999999999999999888765 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 1.7e-12
                                       EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TT CS
                            MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatek 78 
                                       l+ G n +Gk + l  va +v+la++G  vpae ae++ +d ++    ++ +l  g  +F   + E a  l +  e 
  gi|336252979|ref|YP_004596086.1| 489 LLSGVNSGGKTSTLDLVASVVVLAHMGLPVPAEGAELRRFDDLHYHAKTQGTLDAG--AFESTVREFAD-LAQGGEG 562
                                       789*****************************************998888777665..799999**998.67899** PP

                                       SEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-G.GGGGH CS
                            MutS_V  79 slvilDElGRGtstydGlaialavaeyllekikaktlfatHyh.eltkl 126
                                       slv++DEl   t       i   ++e l e + a+++f  H   e+ ++
  gi|336252979|ref|YP_004596086.1| 563 SLVLVDELESITEPGASAKIIAGILEALEE-NGATAVFVSHLAgEIREM 610
                                       ********99999988999999****9987.899999999975244444 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.4   3.7e-11   1.1e-07       3      51 ..       2      49 ..       1      53 [. 0.95
   2 ?   -3.3   0.0       4.9   1.5e+04      27      43 ..     115     132 ..     106     134 .. 0.60
   3 ?    1.8   0.2      0.12   3.7e+02      19      56 ..     547     591 ..     539     592 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3.7e-11
                                      HHHTSTT--HHHHHHHHTTT--SHH.HHHHS-HHHHHTSTTS-HHHHHHH CS
                             HHH_5  3 eLlsvsGiGpktAlallsaGiesve.dlaaadveeLakipGiGkktAeri 51
                                      eL s++G+G+ktA+al +   + +e +l a dv+++a++pGi++ +A ri
  gi|336252979|ref|YP_004596086.1|  2 ELESIPGVGEKTARALSEL--DDPErALRAGDVATIATAPGISQGRAARI 49
                                      799***************9..***989**********************9 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.9
                                       HHHHHS.-HHHHHTSTTS CS
                             HHH_5  27 edlaaa.dveeLakipGi 43 
                                       e+l ++ d + La++ G+
  gi|336252979|ref|YP_004596086.1| 115 EALEREpDSDVLAALEGV 132
                                       344444566778888887 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.12
                                       HTTT--SHHHHHHS...-...HHHHHTS..TTS-HHHHHHHHHHHH CS
                             HHH_5  19 lsaGiesvedlaaa...d...veeLaki..pGiGkktAeriilelk 56 
                                        s+ ++ ++dla+    +   v+eL +i  pG ++k    i+++l+
  gi|336252979|ref|YP_004596086.1| 547 EST-VREFADLAQGgegSlvlVDELESItePGASAKIIAGILEALE 591
                                       455.66677777764441556999***9999******999999997 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   4.5e-07    0.0013      12      27 ..       2      17 ..       2      19 .. 0.93
   2 ?    2.7   0.1     0.046   1.4e+02       7      28 ..      29      50 ..      24      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.5e-07
                                      HHHTSTT-SHHHHHHH CS
                               HHH 12 eLlalPGVGpktAeaI 27
                                      eL+++PGVG+ktA+a 
  gi|336252979|ref|YP_004596086.1|  2 ELESIPGVGEKTARAL 17
                                      8************995 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.046
                                      TSSHHHHHTSTT-SHHHHHHHH CS
                               HHH  7 pasreeLlalPGVGpktAeaIl 28
                                      + +++ +++ PG+   +A +I+
  gi|336252979|ref|YP_004596086.1| 29 AGDVATIATAPGISQGRAARIA 50
                                      567889999*********9996 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 ?    1.6   0.0     0.064   1.9e+02       2      20 ..     488     506 ..     487     529 .. 0.86
   2 ?   10.8   0.0   0.00011      0.32     255     297 ..     559     602 ..     553     607 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.064
                            AAA_21   2 nvliGpNgsGKSnLLdald 20 
                                       ++l G N+ GK++ Ld+  
  gi|336252979|ref|YP_004596086.1| 488 ALLSGVNSGGKTSTLDLVA 506
                                       6778***********9875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                            AAA_21 255 lkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTH 297
                                        ++gsl+l+DE+E+  +P + ++++ ++l++l++nga  ++++H
  gi|336252979|ref|YP_004596086.1| 559 GGEGSLVLVDELESITEPGASAKIIaGILEALEENGATAVFVSH 602
                                       4566****************999999****************** PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00017      0.51       4      37 ..       3      35 ..       2      50 .. 0.89
   2 ?   -3.9   0.0         6   1.8e+04      26      43 ..     118     135 ..     115     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                    Transposase_20  4 LesipGiGpvtaaallaeigdlrrfksakqlaay 37
                                      LesipG+G+ ta a l+e++d++r  +a ++a  
  gi|336252979|ref|YP_004596086.1|  3 LESIPGVGEKTARA-LSELDDPERALRAGDVATI 35
                                      89*********877.89*******9999988876 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6
                    Transposase_20  26 rrfksakqlaayaGlapv 43 
                                       +r ++++ laa+ G+ p 
  gi|336252979|ref|YP_004596086.1| 118 EREPDSDVLAALEGVEPL 135
                                       677889999999999986 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 ?   -2.1   0.3       1.6   4.7e+03      65      94 ..     270     302 ..     270     311 .. 0.61
   2 ?   10.5   0.0   0.00021      0.62       2      94 ..     489     591 ..     488     612 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
                                       ETGGGHHHHH...TTCCCHHHHHHHHHHHHHHH CS
                               AAA  65 DEidalaksr...sgseseeeervvnqLlteld 94 
                                       DE+d+l+++    + ++s  e+ + +qL  ++ 
  gi|336252979|ref|YP_004596086.1| 270 DELDRLTTAVddlDAAASAAESVANDQLRDAIR 302
                                       666776666655555555556666666666555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00021
                                       EEESSTTSSHHHHHHHHHHHH............THEEEEEETTTCSSS.............STTHHHHHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavakel............gvefleisgsellsk.............yvgesekkirelfkea 53 
                                       ll+G    GKT++   va+ +            g+e+ +                        g+ e+ +re+ + a
  gi|336252979|ref|YP_004596086.1| 489 LLSGVNSGGKTSTLDLVASVVvlahmglpvpaeGAELRR--------FddlhyhaktqgtlDAGAFESTVREFADLA 557
                                       89999999***********96444433333333222333........1334444446666678999********999 PP

                                       HHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHH CS
                               AAA  54 kekakpsilfiDEidalaksrsgseseeeervvnqLlteld 94 
                                       +  +  s +++DE++++++         + ++++ +l++l+
  gi|336252979|ref|YP_004596086.1| 558 QGGE-GSLVLVDELESITEPG------ASAKIIAGILEALE 591
                                       8886.8***********8766......56666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (688 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); 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:                         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 0.23s 00:00:00.79 Elapsed: 00:00:00.37
# Mc/sec: 5529.88
//
Query:       gi|336252980|ref|YP_004596087.1|  [L=55]
Description: hypothetical protein Halxa_1576 [Halopiger xanaduensis SH-6]
Scores for complete 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-07   31.2   0.1    2.7e-07   30.7   0.1    1.3  1  DUF1059   Protein of unknown function (DUF1059)


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.1   1.5e-11   2.7e-07      12      50 ..      11      49 ..       2      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.5e-11
                           DUF1059 12 dCgfeitaeteeEvlrkvaeHakaaHglteippelveki 50
                                       C+f+i+ ++ +Ev r v++H++++H+    +++l   i
  gi|336252980|ref|YP_004596087.1| 11 SCQFRIRSSSSDEVERLVRAHVRMVHNGRIDRADLERGI 49
                                      6**************************999999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 428.81
//
Query:       gi|336252981|ref|YP_004596088.1|  [L=363]
Description: oxidoreductase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-22   79.3   0.0    7.8e-22   78.4   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    2.2e-06   28.3   0.1    4.9e-06   27.2   0.1    1.5  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
  ------ inclusion threshold ------
      0.029   13.7   0.0      0.063   12.6   0.0    1.7  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.064   13.5   0.2       0.18   12.1   0.2    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.079   13.0   0.0       0.18   11.8   0.0    1.7  1  GFO_IDH_MocA_C   Oxidoreductase family, C-terminal alpha/beta


Domain annotation for each model (and alignments):
>> 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 !   78.4   0.0   2.2e-25   7.8e-22       3     117 ..       5     117 ..       3     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 2.2e-25
                                       EEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHH CS
                      GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheela 79 
                                        +i+G+G i++ +    n++++ ++++a  d + eraea a+++g+e   ++e+ll dp+id++i  tp++ h+ ++
  gi|336252981|ref|YP_004596088.1|   5 AGIVGCGTIADAYC-EANDRFDSYRIAACADLERERAEATAAEYGLE-ARSVEDLLVDPDIDIAINLTPPTAHAGVI 79 
                                       79***********9.99******************************.789************************** PP

                                       HHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EE CS
                      GFO_IDH_MocA  80 kaaleagkhvllEKPlattveeakelvelaekkgklvs 117
                                       ++alea  hv  EKPlat++e+a++++e+a+++g +v+
  gi|336252981|ref|YP_004596088.1|  80 LQALEADTHVYTEKPLATDLEDAEAVLETADERGLRVG 117
                                       **********************************9986 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 !   27.2   0.1   1.4e-09   4.9e-06       1     113 [.       9     115 ..       9     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.4e-09
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHH CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvl 77 
                                       G+G+i+ a +e+ +r  s   ++++a+ad +   + + +  ++   +  +++dl+ ++d+d+ + +++++a a+++l
  gi|336252981|ref|YP_004596088.1|   9 GCGTIADAYCEANDRFDS---YRIAACADLE--RERAEATAAEYGLEARSVEDLLVDPDIDIAINLTPPTAHAGVIL 80 
                                       9**********9888886...7999999988..33444456777788999*************************** PP

                                       HHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--. CS
                     NAD_binding_3  78 kaLkagkdvvtankgaladealyeeLreaaeangak 113
                                       +aL+a+ +v t  k + +d++  e+ +e a + g +
  gi|336252981|ref|YP_004596088.1|  81 QALEADTHVYTE-KPLATDLEDAEAVLETADERGLR 115
                                       ********9885.44444899999999999888765 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 ?   12.6   0.0   1.8e-05     0.063      38     107 ..       4      75 ..       1     109 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                                       EEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH..CHHHHTCEECSHHHHHHH-SEEEE-S--STTTTT CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgm.kviaydrskkkee..eeeelgvelvsleellaesDivslhlpltpetrh 107
                                       t Gi+G+G I+ a  +    f+  ++ a    +++++  +++e+g+e  s+e+ll + Di  ++++ltp t h
  gi|336252981|ref|YP_004596088.1|   4 TAGIVGCGTIADAYCEANDRFDSyRIAACADLERERAeaTAAEYGLEARSVEDLLVDPDI-DIAINLTPPTAH 75 
                                       89*******************9967777666555444568999999*********98885.566666666655 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 ?   12.1   0.2   5.1e-05      0.18       3      98 ..       7      91 ..       5     115 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.1e-05
                                      EE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGG CS
                   Sacchrp_dh_NADP  3 iiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppis 81
                                      i+G+G ++ a  e   r +++  +i  a+ ++e+ +a+a      ++  + l a  +e++L+    + d+ +nl+pp+ 
  gi|336252981|ref|YP_004596088.1|  7 IVGCGTIADAYCEANDRFDSY--RI-AACADLERERAEA------TAAEYGLEARSVEDLLVD--PDIDIAINLTPPTA 74
                                      788888888877766666666..44.4455555533333......334566777777775555..355*********** PP

                                      HHHHHHHHHHHT-EEEE CS
                   Sacchrp_dh_NADP 82 sldvlkaCietgvhyvd 98
                                      ++ v+  ++e+ +h+ +
  gi|336252981|ref|YP_004596088.1| 75 HAGVILQALEADTHVYT 91
                                      **************987 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.9e-05      0.18      32      71 ..     158     201 ..     132     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.9e-05
                                       CGGSH....HCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.S CS
                    GFO_IDH_MocA_C  32 wkrrk....kksgGvlgdlgiHdiDllqwLfGqppsvvaalgrm 71 
                                       w+ ++    +++gG l d+g +    l+ L+G+  +v+ a+gr 
  gi|336252981|ref|YP_004596088.1| 158 WHPNPdlyyQEGGGPLFDMGPYYVGALIALLGPAERVTGATGRA 201
                                       44444557899**************************9999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2936.57
//
Query:       gi|336252982|ref|YP_004596089.1|  [L=587]
Description: chaperonin Cpn60/TCP-1 [Halopiger xanaduensis SH-6]
Scores for 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-133  445.2   0.4   3.2e-133  444.9   0.4    1.1  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.025   14.3   0.0      0.069   12.9   0.0    1.7  1  DUF3509     Protein of unknown function (DUF3509)


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 !  444.9   0.4  3.6e-137  3.2e-133       1     488 [.      55     547 ..      55     550 .. 0.96

  Alignments for each domain:
  == domain 1  score: 444.9 bits;  conditional E-value: 3.6e-137
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++++ttlGP+G+ Kmlv + g vvvTnDGa +lk+lei +P+a+ +ve+ae+q+  vGDGTtt+v+L+g+Ll++a
  gi|336252982|ref|YP_004596089.1|  55 VAETLRTTLGPNGRHKMLVGRQGRVVVTNDGANVLKNLEIADPVARAVVEVAEAQEAVVGDGTTTAVLLTGALLDAA 131
                                       6899************************************************************************* PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       ++l+++g+hptt+++gy +a+  a + L+e+  e  ++  d+e+L++vart++++++++++ ++++ l+v A +++ 
  gi|336252982|ref|YP_004596089.1| 132 ASLLEDGLHPTTVVSGYGTAVRFARDRLDEY--ETGVDRGDDETLRAVARTAVTNDWDDASIDRFAYLAVSAARAV- 205
                                       *******************************..55555669********************************777. PP

                                       CCSEECSCCCEECCCCEECECTTSEEESEEEESS--SST...........TSSCEEECEEEEEESS-BS--HHCCHH CS
                        Cpn60_TCP1 155 enekeldlgrikvvkieggsledselveGlvldkgvlsp...........dmpkklenakvllldvsLeiektetkt 220
                                           +++  +i  +++ g  le sel++Glv+d + +s+             +++ ++a+++l+d+++  ++ ++ t
  gi|336252982|ref|YP_004596089.1| 206 ----DFETASIARKSYAGAPLEASELIDGLVVDLDASSTtierdrdgrtrAADRSATDARIALVDHEIGVQEADAVT 278
                                       ....499999**************************99977777766655558888********************* PP

                                       HCCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--E CS
                        Cpn60_TCP1 221 tvvlsdaeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGata 297
                                       t +++d++ele+l+++e+++  +++++  + gv+v+vcq+++d+ + ++l+++g+++++r+++++++ la+atGa+a
  gi|336252982|ref|YP_004596089.1| 279 TPTVTDPDELERLRESEREERSRVVDRCRDRGVDVLVCQQSVDERIRETLEREGLVVAERTRRDEFDALAAATGAQA 355
                                       ***************************************************************************** PP

                                       BSCGGGGGCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHE..E CS
                        Cpn60_TCP1 298 vssledltpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedek..v 372
                                         s++dl+++ +G a++ve+++ig   ++++ +++s ++a++llrg t +v+de+ r ++d+l v++++ +d++  v
  gi|336252982|ref|YP_004596089.1| 356 TYSIADLDESTIGRAGTVERRTIGASPVLVVANCPSDAHASLLLRGGTPQVADETRRIVDDCLAVTASVARDGGgaV 432
                                       ***********************************************************************86444* PP

                                       EETTTCHHHHHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTT CS
                        Cpn60_TCP1 373 vpGGGatelelakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesg 449
                                       vpGGGat ++la+ l++ya++ +++eqla++afa ALe+ip+tLa+NaG dpi+v+a+lra+h++g+  +g+d+ +g
  gi|336252982|ref|YP_004596089.1| 433 VPGGGATPMALAQDLSRYASRFDKREQLAVDAFATALESIPRTLATNAGRDPIDVVAELRAEHDAGRSAAGVDA-NG 508
                                       *************************************************************************7.88 PP

                                       CEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEX CS
                        Cpn60_TCP1 450 eiidlveagvvDplkvkrqalksAteaastiLrideiik 488
                                        i d  + gv++p +v  + l +A+ea + iLrid ++ 
  gi|336252982|ref|YP_004596089.1| 509 GIADTADIGVLEPRAVLDRTLAAAFEATAAILRIDGVLA 547
                                       89*********************************9986 PP

>> DUF3509  Protein of unknown function (DUF3509)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.7e-06     0.069      29      83 ..     442     495 ..     434     498 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.7e-06
                           DUF3509  29 TLrdedgvvvrRvlsaaQlndkrqLedvvdairrdLaieaGelpvdviaaLqsqa 83 
                                       +L ++ ++ ++R   ++Ql+   +++ ++++i r La +aG+ p+dv+a L+ ++
  gi|336252982|ref|YP_004596089.1| 442 ALAQDLSRYASRFDKREQLAV-DAFATALESIPRTLATNAGRDPIDVVAELRAEH 495
                                       666666777777777778764.57999************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 4199.73
//
Query:       gi|336252983|ref|YP_004596090.1|  [L=423]
Description: formamidase [Halopiger xanaduensis SH-6]
Scores for 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-156  519.1   0.0   6.2e-156  518.9   0.0    1.0  1  FmdA_AmdA  Acetamidase/Formamidase family


Domain annotation for each model (and alignments):
>> FmdA_AmdA  Acetamidase/Formamidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.9   0.0  3.4e-160  6.2e-156       2     373 .]       8     399 ..       7     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 518.9 bits;  conditional E-value: 3.4e-160
                         FmdA_AmdA   2 vdlskpaaeq.eeklhNRwHpdipavaevkpgetvkvecldwtdgqiknndsaddvrtvdlkkvHeltgPvevegAe 77 
                                       vd++ p+++q   + +NRwHpdipav+e +pg+t+++e+ldwt+gqi++nd+a++vr+vdl++vH+l+gPvev+gAe
  gi|336252983|ref|YP_004596090.1|   8 VDVDAPPDDQpGANPFNRWHPDIPAVVEADPGDTMRLEALDWTGGQIRDNDDANEVRDVDLSQVHYLAGPVEVNGAE 84 
                                       788888888845789************************************************************** PP

                         FmdA_AmdA  78 pGDllvveildievleea.ewGytgifdkenggGflkdafpeaakaiwdlegiyassrqipgvrfrglphpGllGta 153
                                       pGDll ve ld+++l+++ e+G+tg+f+++nggGfl+d+fp+aak+iwdl+g + ssr++p+vr++g++hpGl G+a
  gi|336252983|ref|YP_004596090.1|  85 PGDLLKVEFLDMGPLNDRaEFGFTGTFSQQNGGGFLTDHFPNAAKSIWDLDGYTVSSRHVPDVRYEGKIHPGLAGCA 161
                                       **************987669********************************************************* PP

                         FmdA_AmdA 154 pskelldswnareeeliek.................ralallpepkeallgklee.eaekvaaegartvpprengGn 212
                                       ps+ell++wn+re+el+e+                 +++a++p++++al+g+++  eae++a+e+artvppre+gGn
  gi|336252983|ref|YP_004596090.1| 162 PSQELLEEWNERERELMERhaedpdsiqnhptgeaePPVANPPTTEGALMGEMDPdEAEEAAEEAARTVPPREHGGN 238
                                       ******************9**********************************777********************* PP

                         FmdA_AmdA 213 mDiknlsrGskvylPVkveGaklsvGDlHfsqGDGEisfcgaiemsgvvtlkvevikggmeklgiknpiflpeevep 289
                                       +Dik+ls Gs+vy+PV+v+Gak+ +GD+H+sqGDGEi+fcgaiem+++v++k++++++gmeklg+++pif+p++  p
  gi|336252983|ref|YP_004596090.1| 239 HDIKDLSIGSTVYFPVYVDGAKFALGDFHASQGDGEITFCGAIEMAAYVDVKFDLVEDGMEKLGVDHPIFEPGHRGP 315
                                       ***************************************************************************** PP

                         FmdA_AmdA 290 ryseylsfeGisvdesgkqhyldltvAyrnallraieyLkkfGytkeqaylllsvapvegrisgivdiPnvvatlal 366
                                       ++++y++f G+sv+e+g+q+yld ++Ayr+a l+ai+yLk+fGyt +qa ++l++ pvegr sg+vd+Pn++ tlal
  gi|336252983|ref|YP_004596090.1| 316 TFEDYVTFCGYSVTEDGEQRYLDSHTAYRRASLQAIDYLKQFGYTGQQALHILGTVPVEGRQSGVVDVPNACSTLAL 392
                                       ***************************************************************************** PP

                         FmdA_AmdA 367 PldiFdf 373
                                       P   F+f
  gi|336252983|ref|YP_004596090.1| 393 PKGAFEF 399
                                       **99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2828.64
//
Query:       gi|336252984|ref|YP_004596091.1|  [L=376]
Description: cell division control protein 6-like protein [Halopiger xanaduensis SH-6]
Scores for 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-14   53.1   0.1    1.2e-11   45.3   0.0    2.7  2  AAA_16           AAA ATPase domain
    4.9e-10   39.8   0.0      1e-09   38.8   0.0    1.5  1  AAA_22           AAA domain
    9.3e-06   26.1   0.0    2.4e-05   24.8   0.0    1.7  1  AAA              ATPase family associated with various cellul
    1.3e-05   24.8   0.0    0.00039   20.0   0.0    2.2  2  AAA_7            P-loop containing dynein motor region
    0.00074   19.3   0.0     0.0025   17.6   0.0    1.9  1  MarR_2           MarR family
    0.00084   19.2   0.0     0.0016   18.3   0.0    1.5  1  AAA_11           AAA domain
     0.0009   19.2   0.0     0.0032   17.4   0.0    2.0  1  Cdc6_C           CDC6, C terminal winged helix domain
      0.001   18.0   0.0      0.037   12.9   0.0    2.3  2  AAA_35           AAA-like domain
     0.0013   18.9   0.0     0.0031   17.7   0.0    1.8  1  AAA_33           AAA domain
     0.0016   17.6   0.0     0.0025   16.9   0.0    1.2  1  T2SSE            Type II/IV secretion system protein
      0.002   17.9   0.0        1.3    8.7   0.0    2.6  2  IstB_IS21        IstB-like ATP binding protein
     0.0029   17.4   0.0     0.0044   16.8   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0039   16.0   0.0        1.1    7.9   0.0    2.2  2  AAA_32           AAA domain
      0.004   17.2   0.0       0.01   16.0   0.0    1.7  1  TIP49_C          TIP49 AAA-lid domain
     0.0051   16.6   0.2      0.014   15.1   0.0    1.8  1  AAA_30           AAA domain
     0.0059   17.1   0.1      0.014   15.8   0.1    1.7  1  HTH_27           Winged helix DNA-binding domain
     0.0062   15.7   0.0      0.029   13.5   0.0    1.9  2  DUF815           Protein of unknown function (DUF815)
     0.0065   16.4   0.0      0.015   15.2   0.0    1.6  1  NTPase_1         NTPase
     0.0066   16.2   0.0      0.012   15.4   0.0    1.3  1  Sigma54_activat  Sigma-54 interaction domain
     0.0074   16.2   0.0      0.018   14.9   0.0    1.7  1  NACHT            NACHT domain
      0.008   16.2   0.1      0.092   12.8   0.1    2.3  1  AAA_14           AAA domain
     0.0092   16.5   0.0      0.023   15.2   0.0    1.8  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.023   14.1   0.0    1.5  1  TniB             Bacterial TniB protein
      0.016   15.5   0.0      0.036   14.4   0.0    1.5  1  AAA_19           AAA domain
      0.016   14.5   0.0      0.031   13.5   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.027   14.3   0.0      0.099   12.5   0.0    1.8  2  Bac_DnaA         Bacterial dnaA  protein
       0.03   13.6   0.0      0.047   12.9   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.034   14.6   0.0      0.075   13.4   0.0    1.6  1  RNA_helicase     RNA helicase
       0.05   13.5   0.0       0.08   12.9   0.0    1.5  1  Rad17            Rad17 P-loop domain
      0.063   13.5   0.0       0.17   12.1   0.0    1.7  1  AAA_28           AAA domain
      0.075   12.0   0.0       0.15   11.0   0.0    1.4  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
      0.081   12.6   0.0       0.16   11.7   0.0    1.5  1  AAA_24           AAA domain
      0.099   12.4   0.0       0.19   11.5   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
        0.1   13.0   0.1       0.63   10.5   0.0    2.2  2  AAA_17           AAA domain
       0.12   12.4   0.0       0.22   11.5   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.13   11.6   0.0        0.2   10.9   0.0    1.2  1  Septin           Septin
       0.14   11.8   0.0       0.37   10.4   0.0    1.7  2  SRP54            SRP54-type protein, GTPase domain
       0.18   10.7   0.0       0.28   10.0   0.0    1.2  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.19   11.0   0.0        2.5    7.3   0.0    2.1  2  KAP_NTPase       KAP family P-loop domain


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   2.5e-14   1.2e-11       2      82 ..      32     111 ..      31     180 .. 0.72
   2 ?   -1.8   0.0       7.5   3.5e+03     120     125 ..     319     324 ..     257     366 .. 0.56

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.5e-14
                            AAA_16   2 lvGReeeleqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysalaqa 75 
                                       +  Re+++e L+ al+ +vr +rp +v+++G++G+GK++ +++l++++ ++  ++ ++r +c+ +  a++ys++ ++
  gi|336252984|ref|YP_004596091.1|  32 FKHREAQTESLTYALRpAVRGSRPLNVMVRGPPGTGKTTAIQKLFDEVGAQtsDVRTIRVNCQVN--ATRYSVFSRL 106
                                       567*************66666667**********************99999877999********..7777777777 PP

                            AAA_16  76 lareell 82 
                                       + + + +
  gi|336252984|ref|YP_004596091.1| 107 F-E-GTF 111
                                       7.3.343 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.5
                            AAA_16 120 lellkr 125
                                       +e++ +
  gi|336252984|ref|YP_004596091.1| 319 YEAFHE 324
                                       222222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   2.2e-12     1e-09       8     121 ..      58     173 ..      51     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.2e-12
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.erlsseelleale 83 
                                       ++v G++GtGKTt +++l+++  ++    + ++++++v++++  ++ +++++l++ + +     ++ s + l+ +++
  gi|336252984|ref|YP_004596091.1|  58 VMVRGPPGTGKTTAIQKLFDEVGAQ----TSDVRTIRVNCQVNATRYSVFSRLFEGTFDYEPPsSGISFKKLFGQIA 130
                                       6889*****************9644....46******************999998876433335899******9999 PP

                            AAA_22  84 qalraravielliiDEaqhlr.seealeeLrsllnl....srk 121
                                       + l + +++ ++ +D++ +l+ ++ea  +L sll         
  gi|336252984|ref|YP_004596091.1| 131 EKLVEEDKVLVVALDDVNYLFyENEASDTLYSLLRAheeyPGA 173
                                       999999999***********99788888887777755444444 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 !   24.8   0.0   5.2e-08   2.4e-05       1     125 [.      58     197 ..      58     203 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.2e-08
                                       EEEESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTCSSS..................STTHHHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelg.....vefleisgsellsk..................yvgesekkirelfkeak 54 
                                       v++ GppGtGKT++++ +  e+g     v+ +++++                               ++++lf ++ 
  gi|336252984|ref|YP_004596091.1|  58 VMVRGPPGTGKTTAIQKLFDEVGaqtsdVRTIRVNCQVNATRysvfsrlfegtfdyeppsS----GISFKKLFGQIA 130
                                       5788*****************8633433556666665555336778889999999755532....334444444444 PP

                                       HTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS..GGGSTHHHHSTTSS CS
                               AAA  55 eka....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr..pdkldpallrgRfd 125
                                       ek     k  ++ +D++  l+ ++      e+++++  Ll++ +++    +k+ v++++ +   d +d+    +R++
  gi|336252984|ref|YP_004596091.1| 131 EKLveedKVLVVALDDVNYLFYEN------EASDTLYSLLRAHEEYPG--AKIGVVVVSSDpaLDVIDELD--SRVQ 197
                                       4334443569***********999......667777777777777766..466666666664344444433..3555 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 !   20.0   0.0   8.5e-07   0.00039      34      77 ..      56      99 ..      36     108 .. 0.81
   2 ?    2.4   0.0      0.22     1e+02      99     132 ..     137     170 ..     133     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.5e-07
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanq 77
                                       +v++ Gp GtGKt+ i++l++++  ++  + ti ++ q +a++
  gi|336252984|ref|YP_004596091.1| 56 LNVMVRGPPGTGKTTAIQKLFDEVGAQTSDVRTIRVNCQVNATR 99
                                      369*****************************999999998876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.22
                             AAA_7  99 gkklvvFvDDlnmpakekygaqppiellRqlldy 132
                                        k lvv +DD+n    e+  + +   llR + +y
  gi|336252984|ref|YP_004596091.1| 137 DKVLVVALDDVNYLFYENEASDTLYSLLRAHEEY 170
                                       67899************************99877 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.5e-06    0.0025       1      62 []     294     357 ..     294     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.5e-06
                                       TT--HHHHHHHHHHHCTTTSEEEHHHHHH....HHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                            MarR_2   1 lgltpaqarvLaaLgrrpgrdltvgelar....rlglsksavsrilkrLvaaGLverrpgpeDkRa 62 
                                       +glt +++ +L ++++r+g+   +g++ +    r++l   + s i+++L + GL+  +  + D+R+
  gi|336252984|ref|YP_004596091.1| 294 SGLTDTERALLEVIAHRDGE--QAGDIYEafheRTDLGYTRYSEIVNKLDQLGLIDAEYTDVDGRG 357
                                       79*****************5..8999999888899********************77744458885 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.6e-06    0.0016      13      76 ..      49     108 ..      36     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.6e-06
                            AAA_11  13 alsese..itliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr 76 
                                       a++ s    +++ GPPGtgKT++i +l+ ++       ++ s  + i v  + Na    + +rl++
  gi|336252984|ref|YP_004596091.1|  49 AVRGSRplNVMVRGPPGTGKTTAIQKLFDEV------GAQTSDVRTIRVNCQVNATRYSVFSRLFE 108
                                       44444455689*****************999......34555555555555556555555555555 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 !   17.4   0.0     7e-06    0.0032      36      83 ..     327     373 ..     315     374 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7e-06
                                       ---HHHHHHHHHHHHHTTSEEEEEEE-.CC.C-EEEEEEESSSCHHHHH CS
                            Cdc6_C  36 pltqrevsdllseLemlgilelekssk.GrregrtrkisLnvdpddvle 83 
                                        l  +++s+++++L+ lg++++e     Gr  gr+r  sL+++++ vl+
  gi|336252984|ref|YP_004596091.1| 327 DLGYTRYSEIVNKLDQLGLIDAEYTDVdGR--GRSRSLSLSYEKEAVLN 373
                                       5789*******************6654255..9***********99975 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.11        49      34      69 ..      58      95 ..      38     107 .. 0.82
   2 !   12.9   0.0     8e-05     0.037     123     158 ..     134     169 ..     119     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                            AAA_35 34 irikapkkmGKtSLlarilakakqq..gyktvsldlql 69
                                      + +++p  +GKt  ++++ +++ +q  +++t+ +++q 
  gi|336252984|ref|YP_004596091.1| 58 VMVRGPPGTGKTTAIQKLFDEVGAQtsDVRTIRVNCQV 95
                                      7899***************9865553378888888875 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8e-05
                            AAA_35 123 keidkplvLaldevdrlfeypeiakdflslLRswhe 158
                                        e dk lv+ald+v+ lf ++e ++ + slLR+  e
  gi|336252984|ref|YP_004596091.1| 134 VEEDKVLVVALDDVNYLFYENEASDTLYSLLRAHEE 169
                                       456899**************************9766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   6.8e-06    0.0031       2      32 ..      58      88 ..      58     232 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.8e-06
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdt 32
                                      v++ G+pG+GK+t +++l  + ga++ +  t
  gi|336252984|ref|YP_004596091.1| 58 VMVRGPPGTGKTTAIQKLFDEVGAQTSDVRT 88
                                      799***************9999866544444 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 !   16.9   0.0   5.4e-06    0.0025     106     163 ..      30      89 ..      11      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.4e-06
                             T2SSE 106 ddlgaeealkekiaevlrkavr..erglilvsGgTgsGKttllyallkeinksderivtv 163
                                       +++  +ea++e +  +lr avr  +  +++v G+ g+GKtt +  l  e+ +++  + t+
  gi|336252984|ref|YP_004596091.1|  30 ETFKHREAQTESLTYALRPAVRgsRPLNVMVRGPPGTGKTTAIQKLFDEVGAQTSDVRTI 89 
                                       56677899999*********97435689*********************99987766665 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 ?    6.4   0.0     0.014       6.6      46      62 ..      54      70 ..      18      99 .. 0.78
   2 !    8.7   0.0    0.0028       1.3      95     137 ..     125     167 ..     118     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                         IstB_IS21 46 kkenivllGpsGvGKsh 62
                                      +  n+++ Gp+G+GK+ 
  gi|336252984|ref|YP_004596091.1| 54 RPLNVMVRGPPGTGKTT 70
                                      5569***********95 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0028
                         IstB_IS21  95 rdgklaralkrllkvdllilDdlgllpldqaeaellfeviekr 137
                                         g++a++l +  kv ++ lDd+ +l  +++++ +l+ ++ + 
  gi|336252984|ref|YP_004596091.1| 125 LFGQIAEKLVEEDKVLVVALDDVNYLFYENEASDTLYSLLRAH 167
                                       568999999999***************************9865 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 !   16.8   0.0   9.7e-06    0.0044       2      39 ..      59      91 ..      58     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.7e-06
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegk 39
                                      +v G pG GK+t+i+kl+++     v+ +t  ++t ++
  gi|336252984|ref|YP_004596091.1| 59 MVRGPPGTGKTTAIQKLFDE-----VGAQTSDVRTIRV 91
                                      799***************99.....4555455555444 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0025       1.1      31      57 ..      56      82 ..      36      88 .. 0.87
   2 ?    5.8   0.0     0.011       5.1     481     512 ..     254     285 ..     237     286 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0025
                            AAA_32 31 YNifvlGesgtGrttlvkrlleeiakk 57
                                       N+ v G++gtG+tt++++l +e+ ++
  gi|336252984|ref|YP_004596091.1| 56 LNVMVRGPPGTGKTTAIQKLFDEVGAQ 82
                                      599*****************9998665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.011
                            AAA_32 481 adllrEAdywakkegaevveaehVekAleeke 512
                                       +dllr A   a+++++++ve+++Ve+A+e+ +
  gi|336252984|ref|YP_004596091.1| 254 IDLLRRAGLNAEMRASRTVERQDVEEAYEKSK 285
                                       79**************************9876 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.2e-05      0.01      16      62 ..     235     282 ..     218     282 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-05
                           TIP49_C  16 eAldlLakigtetS.LRYaiqLltpasilakkrkkkevevedveevee 62 
                                       + l++ a++   ++ LR  i Ll  a + a++r +++ve +dvee++e
  gi|336252984|ref|YP_004596091.1| 235 DTLEYVAELTADSGdLRVGIDLLRRAGLNAEMRASRTVERQDVEEAYE 282
                                       667777777766655*******************************96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     3e-05     0.014      15      41 ..      52      79 ..      43      98 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-05
                            AAA_30 15 tsgdrvavltGpAGtGKttalkal.rea 41
                                      +s+ + +++ Gp+GtGKtta+++l  e+
  gi|336252984|ref|YP_004596091.1| 52 GSRPLNVMVRGPPGTGKTTAIQKLfDEV 79
                                      4555567899***********9984443 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 !   15.8   0.1   3.1e-05     0.014       1      59 [.     296     357 ..     296     364 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.1e-05
                            HTH_27   1 ltrqqalvLhlir...hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre 59 
                                       lt  ++++L++i+   +++++++ ++ ++r++++++ +s++++kL   GL+  +  + d+r 
  gi|336252984|ref|YP_004596091.1| 296 LTDTERALLEVIAhrdGEQAGDIYEAFHERTDLGYTRYSEIVNKLDQLGLIDAEYTDVDGRG 357
                                       5778999******66666666777***************************55555567775 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   6.3e-05     0.029      30      88 ..      32      92 ..      10     108 .. 0.87
   2 ?   -0.7   0.0       1.4   6.2e+02      95     125 ..     126     156 ..     122     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.3e-05
                            DUF815 30 LvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlieve 88
                                      ++  ++q e+l+   +  ++g +  nv++ G  GtGK + ++ l+ e+ +++  +r i v+
  gi|336252984|ref|YP_004596091.1| 32 FKHREAQTESLTYALRPAVRGSRPLNVMVRGPPGTGKTTAIQKLFDEVGAQTsdVRTIRVN 92
                                      5667899999999999*******************************99988788888876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                            DUF815  95 lpklvellrerperfilfvDDLsFeeeeeey 125
                                       + ++ e+l e+++ +++ +DD+ +   e+e+
  gi|336252984|ref|YP_004596091.1| 126 FGQIAEKLVEEDKVLVVALDDVNYLFYENEA 156
                                       5689999999999********9875444433 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.2e-05     0.015       1      30 [.      57      86 ..      57     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-05
                                      EEEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkv 30
                                      +v++ GppG+GKtT ++k+ +++  +   v
  gi|336252984|ref|YP_004596091.1| 57 NVMVRGPPGTGKTTAIQKLFDEVGAQTSDV 86
                                      58999***************9995544444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.5e-05     0.012      20      71 ..      53     107 ..      33     111 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                                       TSSS-EEEECSTTSSHHHHHHHHHH..HSTTTTS-EEEEETTTS.-TTCHHHHHH CS
                   Sigma54_activat  20 ktdlsvlitGesGtGKellaraihe..askrkekpfvavncaai.peelleseLF 71 
                                       + +l+v+++G  GtGK++  +++++    + ++ + ++vnc    ++  + s+LF
  gi|336252984|ref|YP_004596091.1|  53 SRPLNVMVRGPPGTGKTTAIQKLFDevGAQTSDVRTIRVNCQVNaTRYSVFSRLF 107
                                       3459********************9444456677999****84413334455555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     4e-05     0.018       3      95 ..      58     152 ..      56     185 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-05
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C........ CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse........ 71 
                                       v+++G++G GKTt +qkl ++  +++ +  +    + ++++   ++   +s+   lf+   + + p+s         
  gi|336252984|ref|YP_004596091.1|  58 VMVRGPPGTGKTTAIQKLFDEVGAQTSDVRT----IRVNCQVNATR---YSVFSRLFEGTFDYEPPSSGisfkklfg 127
                                       799*****************99988865532....22222222222...2444444444444444444444445555 PP

                                       .CHHHHCCSCCCEEEEEE-STT-SS CS
                             NACHT  72 .vwavllelperlLlilDglDelvt 95 
                                        + + l+e  + l+  lD++++l  
  gi|336252984|ref|YP_004596091.1| 128 qIAEKLVEEDKVLVVALDDVNYLFY 152
                                       5555555555555555666666665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1    0.0002     0.092       5      83 ..      58     160 ..      55     196 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0002
                            AAA_14   5 lvitGaRrvGKTtllkqlikell..vkkesilyinldderd..............kkladpe.........klleli 56 
                                       ++++G+  +GKTt +++l++e    +++ +++ +n++ + +              +     e         kl   i
  gi|336252984|ref|YP_004596091.1|  58 VMVRGPPGTGKTTAIQKLFDEVGaqTSDVRTIRVNCQVNATrysvfsrlfegtfdY-----EppssgisfkKLFGQI 129
                                       789****************9988877777888888888777555555444444330.....1333444333555566 PP

                            AAA_14  57 lek.lkeekktylflDEiqev...pewekal 83 
                                        ek ++e+k  ++ lD + ++   +e++++l
  gi|336252984|ref|YP_004596091.1| 130 AEKlVEEDKVLVVALDDVNYLfyeNEASDTL 160
                                       6653444566667788887765554444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     5e-05     0.023       1      44 [.      58     105 ..      58     186 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf....gvnlrdvakenglllevdpe 44 
                                       +++ G+pG+GKtt  + L ++ g     ++ +r +++ n ++++v+  
  gi|336252984|ref|YP_004596091.1|  58 VMVRGPPGTGKTTAIQKLFDEVGAqtsdVRTIRVNCQVNATRYSVFSR 105
                                       6899**************776544566766666666666666666655 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     5e-05     0.023      26     180 ..      46     201 ..      30     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-05
                              TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkara 102
                                       L  + + +r+ n+++ G++ +GKt+ ++k  ++  +++    + v+ + v++  +++    +++++e       ++ 
  gi|336252984|ref|YP_004596091.1|  46 LRPAVRGSRPLNVMVRGPPGTGKTTAIQKLFDEVGAQT----SDVRTIRVNCQVNATRYSVFSRLFEGTFDYEPPSS 118
                                       4455678999*******************998877766....56677778888888888888888887766555555 PP

                              TniB 103 rvs..kle.qqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgne..lkipivlvGteealralrt.Dp 173
                                        +s  kl  q + +l +e kv v+ +D ++ l   + ++  ++  +l+   +    ki +v+v  + al+++++ D+
  gi|336252984|ref|YP_004596091.1| 119 GISfkKLFgQIAEKLVEEDKVLVVALDDVNYLF-YENEASDTLYSLLRAHEEYpgAKIGVVVVSSDPALDVIDElDS 194
                                       443213331445566677777777778777665.4444555555555554442225677777777777777753355 PP

                              TniB 174 qlasRFe 180
                                        ++s F+
  gi|336252984|ref|YP_004596091.1| 195 RVQSVFR 201
                                       5555555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.8e-05     0.036       4      38 ..      49      83 ..      47     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.8e-05
                            AAA_19  4 avealkekvllvtaGpGtGKTrvlkhivallvelg 38
                                      av+ ++  +++v ++pGtGKT+ +++   ++ +++
  gi|336252984|ref|YP_004596091.1| 49 AVRGSRPLNVMVRGPPGTGKTTAIQKLFDEVGAQT 83
                                      55566667899*************99988776655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.8e-05     0.031      11      47 ..      50      86 ..      40     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.8e-05
                        Zeta_toxin 11 psqerPklillgGqpGAGKselaellkdelerqgnvv 47
                                      ++++rP  +++ G pG GK++++++l de+++q + v
  gi|336252984|ref|YP_004596091.1| 50 VRGSRPLNVMVRGPPGTGKTTAIQKLFDEVGAQTSDV 86
                                      6789************************999555444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.5   1.6e+03      37      68 ..      58      89 ..      30      98 .. 0.80
   2 ?   12.5   0.0   0.00022     0.099     100     199 ..     141     245 ..     123     257 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.5
                                      EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EE CS
                          Bac_DnaA 37 lfiygevGlGktHLlkaignevlenapelrvv 68
                                      +++ g+ G Gkt  ++ +  ev +++++ r +
  gi|336252984|ref|YP_004596091.1| 58 VMVRGPPGTGKTTAIQKLFDEVGAQTSDVRTI 89
                                      57789999****99999999998888888765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00022
                                       EEEEE-GGGGTT-HHHHHHHHHHHHHHHT....TT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHH CS
                          Bac_DnaA 100 vLliDDiqflagkektqeelfhtfnalle....egkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrl 172
                                       v+ +DD+++l + ++  + l+ ++ a  e    +   vv+ssD +   ++el++r++s f+    v     d+   +
  gi|336252984|ref|YP_004596091.1| 141 VVALDDVNYLFYENEASDTLYSLLRAHEEypgaKIGVVVVSSDPALDVIDELDSRVQSVFRPE-DVYFPVYDQPEIV 216
                                       3446*******************99987732212346899********************864.4455566777788 PP

                                       HHHHHHHHHTT--..--TTHHHHHHHH-- CS
                          Bac_DnaA 173 ailkkkieaekle..vpeevlefiaervt 199
                                       +il+ ++++   +  + ++ le++ae   
  gi|336252984|ref|YP_004596091.1| 217 DILEERVKRGFHDgvIGRDTLEYVAELTA 245
                                       99999998766656689999999987654 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0001     0.047       4      44 ..      58     100 ..      56     145 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                           DUF2075   4 vlVtGvaGtGKtvvllnllael..eddeeertavylsvNhplv 44 
                                       v+V+G +GtGKt    +l+ e+  ++++ +  +v   vN    
  gi|336252984|ref|YP_004596091.1|  58 VMVRGPPGTGKTTAIQKLFDEVgaQTSDVRTIRVNCQVNATRY 100
                                       78********************554444444444444444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00016     0.075       1      26 [.      58      83 ..      58     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00016
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                      +++ Gp+g+GK+t++++L +++  + 
  gi|336252984|ref|YP_004596091.1| 58 VMVRGPPGTGKTTAIQKLFDEVGAQT 83
                                      6899***************9998665 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   0.00017      0.08      48      75 ..      58      85 ..      26     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00017
                             Rad17 48 LLisGPsGCgkstvvkvLskelgiklre 75
                                      +++ GP+G gk+t+++ L  e g +  +
  gi|336252984|ref|YP_004596091.1| 58 VMVRGPPGTGKTTAIQKLFDEVGAQTSD 85
                                      4789***************999998755 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   0.00038      0.17       2      25 ..      58      82 ..      57     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00038
                            AAA_28  2 ivitGgestGKTtlleaLaar.gyp 25
                                      +++ G+++tGKTt +++L ++ g +
  gi|336252984|ref|YP_004596091.1| 58 VMVRGPPGTGKTTAIQKLFDEvGAQ 82
                                      7889*************98655544 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00034      0.15      36      81 ..      59     110 ..      41     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                             AAA_6  36 apaGpagtGKtEtvkdLakalakq.....vvvfncs.dqldykslgkifkGl 81 
                                        + Gp gtGKt ++++L  +++ q     ++ +nc+ ++  y+  +++f+G 
  gi|336252984|ref|YP_004596091.1|  59 MVRGPPGTGKTTAIQKLFDEVGAQtsdvrTIRVNCQvNATRYSVFSRLFEGT 110
                                       679**************99999872222246789984567789999999995 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00034      0.16       2      22 ..      55      75 ..      54     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00034
                            AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                      +l++++ Gp+g+GKTt + +l
  gi|336252984|ref|YP_004596091.1| 55 PLNVMVRGPPGTGKTTAIQKL 75
                                      57899************9998 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 ?   11.5   0.0   0.00041      0.19      14      61 ..      37      83 ..      28      95 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00041
                            RuvB_N 14 kvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl 61
                                      + +e+l+ +++ a  r++    v++ GpPG Gktt  + + +e+g++ 
  gi|336252984|ref|YP_004596091.1| 37 AQTESLTYALRPAV-RGSRPLNVMVRGPPGTGKTTAIQKLFDEVGAQT 83
                                      55566666666665.455555799***********9999999988775 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0014      0.63       2      21 ..      62      81 ..      61      85 .. 0.90
   2 ?   -0.8   0.0       4.1   1.9e+03      87     125 ..     187     225 ..     166     231 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0014
                                      E-TTSSHHHHHHHHHHHHTE CS
                            AAA_17  2 GgPGsGKgtqceklvekygf 21
                                      G+PG GK+t+++kl +++g 
  gi|336252984|ref|YP_004596091.1| 62 GPPGTGKTTAIQKLFDEVGA 81
                                      9*************998875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 4.1
                                       EEEESSHHHHHHHH..SEEEE.EE--HHHHHHHHHHHTTS CS
                            AAA_17  87 gfldglpkevleelkpdaiil.leadpeeilerrlkdrtr 125
                                       + +d+l++ v+  + p+ + + ++++pe i++ + ++ +r
  gi|336252984|ref|YP_004596091.1| 187 DVIDELDSRVQSVFRPEDVYFpVYDQPE-IVDILEERVKR 225
                                       5678899999999999777774666666.55544444444 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00048      0.22       3      47 ..      35      85 ..      33      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00048
                                      SHHHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT--..- CS
                              TsaE  3 seeetealgkklakal....gdvilLeGdLGaGKTtlvrglakalgve..e 47
                                      +e++te+l  +l  a+       ++ +G+ G+GKTt +++l  ++g +  +
  gi|336252984|ref|YP_004596091.1| 35 REAQTESLTYALRPAVrgsrPLNVMVRGPPGTGKTTAIQKLFDEVGAQtsD 85
                                      57888888888888776443334********************99986444 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00043       0.2       5      33 ..      56      84 ..      52     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00043
                                      EEEEEEEBTTSSCCCCCCTTSSSS----- CS
                            Septin  5 ftlmvvGesglGkttlintlfetdlieee 33
                                      +++mv G  g+Gktt i+ lf +   +++
  gi|336252984|ref|YP_004596091.1| 56 LNVMVRGPPGTGKTTAIQKLFDEVGAQTS 84
                                      89*******************98766654 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00082      0.37       3      28 ..      57      82 ..      55      93 .. 0.82
   2 ?   -2.7   0.0       8.3   3.8e+03     120     143 ..     306     329 ..     282     342 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00082
                                      EEEEEESTTSSHHHHHHHHHHHHHHT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkke 28
                                       +++ G+ G+GKTt++ KL + + ++
  gi|336252984|ref|YP_004596091.1| 57 NVMVRGPPGTGKTTAIQKLFDEVGAQ 82
                                      58999**************8776665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.3
                                       EEETTBHTHHHHHHHHHHHHSSCS CS
                             SRP54 120 vldattgqeavkqakaFkeavgit 143
                                       v+    g++a    +aF+e+++++
  gi|336252984|ref|YP_004596091.1| 306 VIAHRDGEQAGDIYEAFHERTDLG 329
                                       777778888888899999988875 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 ?   10.0   0.0   0.00061      0.28      16      43 ..      56      83 ..      43      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00061
                     TrwB_AAD_bind 16 qhilivGttGsGKtqalekllrairarg 43
                                        +++ G  G+GKt+a++kl +++ a+ 
  gi|336252984|ref|YP_004596091.1| 56 LNVMVRGPPGTGKTTAIQKLFDEVGAQT 83
                                      67899*****************998876 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 ?    7.3   0.0    0.0054       2.5      17      47 ..      50      82 ..      35     107 .. 0.79
   2 ?    0.9   0.0      0.45   2.1e+02     155     182 ..     120     147 ..      95     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0054
                        KAP_NTPase 17 l..atpivvgLygkWGsGKssllnkledelkef 47
                                      +  ++p+ v++ g+ G+GK++ ++kl de   +
  gi|336252984|ref|YP_004596091.1| 50 VrgSRPLNVMVRGPPGTGKTTAIQKLFDEVGAQ 82
                                      3458999*********************98766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.45
                        KAP_NTPase 155 teveelladmektLdalqkrlVvviDdL 182
                                        + ++l+ +++++L +++k lVv +Dd 
  gi|336252984|ref|YP_004596091.1| 120 ISFKKLFGQIAEKLVEEDKVLVVALDDV 147
                                       566789999*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 2496.59
//
Query:       gi|336252985|ref|YP_004596092.1|  [L=150]
Description: hypothetical protein Halxa_1581 [Halopiger xanaduensis SH-6]
Scores for 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-22   79.5   4.2    2.9e-22   79.2   4.2    1.1  1  DUF2267   Uncharacterized conserved protein (DUF2267)


Domain annotation for each model (and alignments):
>> DUF2267  Uncharacterized conserved protein (DUF2267)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   4.2   1.6e-26   2.9e-22       2     116 ..      22     133 ..      21     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 1.6e-26
                                       HHHHHHHHHHHT---HHHHHHHHHHHHHHHHTTS-HHHHHHHHTTS-HHHHHHHHTT--TTS-----SHHHHHHHHH CS
                           DUF2267   2 defleevqerlgledreeAeratravLrtLrdrlteeeaadlaaqLPeelrgllrdgwppvepgkrfdreeflerva 78 
                                       ++f++ vq +++l+d+++A++at+avL +L++rl+e   +++  +LP e+ + l +g      g+rfd +efler+ 
  gi|336252985|ref|YP_004596092.1|  22 HDFYGSVQFEADLADEADARDATQAVLSALGERLDETRLQRIDGELPAEIGDHLVEGA----SGRRFDYDEFLERIT 94 
                                       68*******************************************************9....899************ PP

                                       HTS......EHHHHHHHHHHHHHHHS-HHHHHHHHHTS- CS
                           DUF2267  79 eelg.vdpedaeqaaraVfaalkealsegeiedvaaqLP 116
                                       e+++ +d  ++e +a+aV+ +  e++s++e e ++++L 
  gi|336252985|ref|YP_004596092.1|  95 ERADrADTGEPEALAQAVVGTALEHISDEEAEGLRDRLE 133
                                       ***4366666*************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1076.26
//
Query:       gi|336252986|ref|YP_004596093.1|  [L=140]
Description: hypothetical protein Halxa_1582 [Halopiger xanaduensis SH-6]
Scores for 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-23   81.0   7.0    1.1e-22   80.6   7.0    1.1  1  DUF2267   Uncharacterized conserved protein (DUF2267)
  ------ inclusion threshold ------
      0.051   13.1   0.1      0.058   12.9   0.1    1.1  1  PSD1      Protein of unknown function (DUF1553)
       0.12   12.6   0.2        1.3    9.1   0.1    2.0  2  CHDCT2    CHDCT2 (NUC038) domain
       0.18   12.4   6.1        4.1    8.1   0.1    2.8  2  MgtE_N    MgtE intracellular N domain
       0.64    9.8   4.2        1.7    8.4   0.3    2.4  2  TruB_C    tRNA Pseudouridine synthase II, C terminal


Domain annotation for each model (and alignments):
>> DUF2267  Uncharacterized conserved protein (DUF2267)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   7.0     3e-26   1.1e-22       3     114 ..       5     113 ..       3     117 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 3e-26
                                       HHHHHHHHHHT-.--HHHHHHHHHHHHHHHHTTS-HHHHHHHHTTS-HHHHHHHHTT--TTS-----SHHHHHHHHH CS
                           DUF2267   3 efleevqerlgl.edreeAeratravLrtLrdrlteeeaadlaaqLPeelrgllrdgwppvepgkrfdreeflerva 78 
                                       e+le v++r+   +d+e A +atravL+tL++rl+ +ea+dlaaqLP +l + l+ g+     g+rf++eef+ r+ 
  gi|336252986|ref|YP_004596093.1|   5 ELLETVSDRAAAdADEESADDATRAVLQTLGERLSADEARDLAAQLPGDLSQHLTGGE----SGQRFSEEEFVSRID 77 
                                       899******999789******************************************9....899************ PP

                                       HTS.....EHHHHHHHHHHHHHHHS-HHHHHHHHHT CS
                           DUF2267  79 eelgvdpedaeqaaraVfaalkealsegeiedvaaq 114
                                       +++++++   e+aa +V+ ++ ea++e e++ v ++
  gi|336252986|ref|YP_004596093.1|  78 RRMDTTELHGEEAATTVLGTVLEAVDESERAAVVDR 113
                                       ***999999*********************999876 PP

>> PSD1  Protein of unknown function (DUF1553)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.6e-05     0.058      86     177 ..      15     107 ..       8     124 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                              PSD1  86 kaseealeadpenrllaraprrRleaeqirDsllavsglldekvggpsvkpyqpkekyeeskgeelyrRslylf... 159
                                       +a++++++ad + r + +    Rl+a++ rD + ++ g l++++ g +  +  ++e+ ++    ++ rR+  +    
  gi|336252986|ref|YP_004596093.1|  15 AADADEESADDATRAVLQTLGERLSADEARDLAAQLPGDLSQHLTGGESGQRFSEEEFVS----RIDRRMDTTElhg 87 
                                       456777888999*****************************9977764444433333332....1222222222222 PP

                              PSD1 160 ..vkrsvppplleaFdapdr 177
                                          + +v  ++lea d+++r
  gi|336252986|ref|YP_004596093.1|  88 eeAATTVLGTVLEAVDESER 107
                                       22233333335555554444 PP

>> CHDCT2  CHDCT2 (NUC038) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.027        98     113     151 ..      15      55 ..       2      60 .. 0.68
   2 ?    9.1   0.1   0.00037       1.3      88     134 ..      58     104 ..      31     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.027
                            CHDCT2 113 esaagnknanavlekvLnqleelLs..dmkadvsrlpatls 151
                                        + a++++a +  + vL++l e Ls  + +   ++lp  ls
  gi|336252986|ref|YP_004596093.1|  15 AADADEESADDATRAVLQTLGERLSadEARDLAAQLPGDLS 55 
                                       34567889999999******999973223333456776666 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00037
                            CHDCT2  88 ekvgslaqrfaelellaeshqkllkesaagnknanavlekvLnqlee 134
                                        + g+  qrf+e e+++   +++ +   +g+++a++vl +vL+ ++e
  gi|336252986|ref|YP_004596093.1|  58 LTGGESGQRFSEEEFVSRIDRRMDTTELHGEEAATTVLGTVLEAVDE 104
                                       3446779*************************************998 PP

>> MgtE_N  MgtE intracellular N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.8    0.0074        26      31      77 ..       4      54 ..       1      60 [. 0.48
   2 ?    8.1   0.1    0.0011       4.1      28      68 ..      93     133 ..      73     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0074
                                      HHHHCTS-CCCCCHHHHCS-HHHHHHHH....CCS-HHHHHHHHCCCHHHH CS
                            MgtE_N 31 aevleeldedlqeeliealsdeelaell....eeldsDdaadlleelpeek 77
                                      ae+le ++++ +++  e+  d+  +++l    e l++D+a dl  +lp + 
  gi|336252986|ref|YP_004596093.1|  4 AELLETVSDRAAADADEESADDATRAVLqtlgERLSADEARDLAAQLPGDL 54
                                      444444444444444444433333333311115667777777777777665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0011
                                       HHHHHHHCTS-CCCCCHHHHCS-HHHHHHHHCCS-HHHHHH CS
                            MgtE_N  28 eeaaevleeldedlqeeliealsdeelaelleeldsDdaad 68 
                                         ++ vle +de++++ +++++++    ell+e d+D  +d
  gi|336252986|ref|YP_004596093.1|  93 TVLGTVLEAVDESERAAVVDRFDRYGFGELLAETDADADVD 133
                                       56678999999999999999999999999999988887665 PP

>> TruB_C  tRNA Pseudouridine synthase II, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.3     0.038   1.4e+02       5      15 ..      37      47 ..      36      48 .. 0.90
   2 ?    8.4   0.3   0.00049       1.7       2      33 ..      81     112 ..      80     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.038
                                      E--HHHHHHHH CS
                            TruB_C  5 dvteaeArdlr 15
                                      +++++eArdl+
  gi|336252986|ref|YP_004596093.1| 37 RLSADEARDLA 47
                                      699******97 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00049
                                       EEEE--HHHHHHHHTT---B-----S-EEEE- CS
                            TruB_C   2 prrdvteaeArdlrhGrrLeaagikgvvAaia 33 
                                       +  ++  +eA+  + G  Lea+  ++ +A+++
  gi|336252986|ref|YP_004596093.1|  81 DTTELHGEEAATTVLGTVLEAVDESERAAVVD 112
                                       5678899***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1044.45
//
Query:       gi|336252987|ref|YP_004596094.1|  [L=88]
Description: hypothetical protein Halxa_1583 [Halopiger xanaduensis SH-6]
Scores for 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   18.8   1.9     0.0014   18.8   1.9    2.0  2  Halo_GVPC       Halobacterial gas vesicle protein C (GVPC) re
     0.0026   17.2   5.6       0.11   11.9   0.2    2.0  2  HBM             Helical bimodular sensor domain
  ------ inclusion threshold ------
      0.015   15.2   7.9      0.026   14.4   7.9    1.4  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
      0.018   15.7   1.0      0.046   14.4   1.0    1.6  1  Cytochrom_B562  Cytochrome b562
      0.033   14.8   7.5       0.24   12.0   1.6    2.1  2  DUF883          Bacterial protein of unknown function (DUF883
      0.042   13.7   0.5      0.095   12.5   0.0    1.7  2  SCAB_CC         Coiled-coil regions of plant-specific actin-b
      0.063   12.6   2.5      0.079   12.3   2.5    1.2  1  DUF3450         Protein of unknown function (DUF3450)
      0.069   13.1   0.1      0.077   12.9   0.1    1.2  1  PBP-Tp47_c      Penicillin-binding protein Tp47 domain C
      0.097   13.2   5.7        5.9    7.5   5.7    2.1  1  YtxH            YtxH-like protein
       0.24   11.8   4.6        3.9    7.9   0.1    2.5  3  DUF2564         Protein of unknown function (DUF2564)
       0.27   11.6   5.9          1    9.8   0.1    2.9  3  MT0933_antitox  MT0933-like antitoxin protein
        0.8    9.0   6.9       0.86    8.9   6.9    1.0  1  CorA            CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> Halo_GVPC  Halobacterial gas vesicle protein C (GVPC) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.9   9.5e-07    0.0014       6      25 ..      19      37 ..      16      40 .. 0.90
   2 ?   -1.7   0.0       2.5   3.7e+03      22      27 ..      78      83 ..      74      86 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.5e-07
                         Halo_GVPC  6 aaIaafreefdatqdaFeaY 25
                                      a+ ++ re++++t+daF++Y
  gi|336252987|ref|YP_004596094.1| 19 AD-DDVREDIRETTDAFADY 37
                                      56.89*************** PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                         Halo_GVPC 22 FeaYad 27
                                       e+Y++
  gi|336252987|ref|YP_004596094.1| 78 VEDYRE 83
                                      477887 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   1.3    0.0011       1.6     170     207 ..       3      40 ..       1      47 [. 0.93
   2 !   11.9   0.2   7.2e-05      0.11     172     210 ..      49      87 ..      40      88 .] 0.93

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHH-GG.GHHHHHHHHHHHHHHHHH CS
                               HBM 170 taldaalaeldqlrqalasdpraalqqlesalskYRaa 207
                                       ++l++a+ +l++ ++ +++d r+++ + ++a + Y ++
  gi|336252987|ref|YP_004596094.1|   3 EQLQQARDDLEEAAKSADDDVREDIRETTDAFADYVRS 40 
                                       79********************************9765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.2e-05
                                       HHHHHHHHHHHHHH-GG.GHHHHHHHHHHHHHHHHHHHH CS
                               HBM 172 ldaalaeldqlrqalasdpraalqqlesalskYRaaleq 210
                                       ld+ l++l q+r++ +++ +++++ + + ++ YR++++q
  gi|336252987|ref|YP_004596094.1|  49 LDERLNTLRQVRERTDGNTEDKVESAIETVEDYREQVDQ 87 
                                       8999*********************************97 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   7.9   1.7e-05     0.026      88     172 ..       3      87 ..       1      88 [] 0.60

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                                       HCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..-----SSSHHHHHHHTS- CS
                    Apolipoprotein  88 adaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaphaeeveerlssrveelrekle 164
                                       ++++++++ l++ a+ + + +++ + ++ + +a yv +  ++ ++ l+e  ++l++  e+   + +++ve + e++e
  gi|336252987|ref|YP_004596094.1|   3 EQLQQARDDLEEAAKSADDDVREDIRETTDAFADYVRSDTAPDHAILDERLNTLRQVRERTDGNTEDKVESAIETVE 79 
                                       45555555555555555555555555556666666666666666666666666666677777777777777777777 PP

                                       TTSHHHHH CS
                    Apolipoprotein 165 eqaeelre 172
                                       ++ e++ +
  gi|336252987|ref|YP_004596094.1|  80 DYREQVDQ 87 
                                       77776654 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.0   3.1e-05     0.046      23      96 ..       3      84 ..       1      87 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                    Cytochrom_B562 23 eelkkalkelraaaedakeatpsklekdseeqkdY........qeGldklidqldkaealakagkleeakaalkelkdl 93
                                      e+l++a ++l++aa++a     +++++    ++dY        ++ ld+ +++l ++++  + +  +++++a+++++d+
  gi|336252987|ref|YP_004596094.1|  3 EQLQQARDDLEEAAKSADDDVREDIRETTDAFADYvrsdtapdHAILDERLNTLRQVRERTDGNTEDKVESAIETVEDY 81
                                      78999999**************999997777777733333333678********************************* PP

                    Cytochrom_B562 94 rke 96
                                      r++
  gi|336252987|ref|YP_004596094.1| 82 REQ 84
                                      986 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 ?   12.0   1.6   0.00016      0.24      34      71 ..       3      40 ..       1      48 [. 0.76
   2 ?    6.8   0.5    0.0068        10      38      68 ..      51      81 ..      46      88 .] 0.48

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                            DUF883 34 erleerlerarerlrdaeeavaerakeaaeaaddyVre 71
                                      e+l+++ +++ e+++ a ++v+e ++e  +a  dyVr 
  gi|336252987|ref|YP_004596094.1|  3 EQLQQARDDLEEAAKSADDDVREDIRETTDAFADYVRS 40
                                      45666666667777777778999999999999999986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0068
                            DUF883 38 erlerarerlrdaeeavaerakeaaeaaddy 68
                                      erl+++r+  +++  + ++++++a+e+++dy
  gi|336252987|ref|YP_004596094.1| 51 ERLNTLRQVRERTDGNTEDKVESAIETVEDY 81
                                      4444444444444445555555555554444 PP

>> SCAB_CC  Coiled-coil regions of plant-specific actin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.77   1.1e+03      30      35 ..      10      15 ..       1      34 [. 0.45
   2 ?   12.5   0.0   6.4e-05     0.095       7      41 ..      46      80 ..      42      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.77
                           SCAB_CC 30 ddvees 35
                                      dd+ee+
  gi|336252987|ref|YP_004596094.1| 10 DDLEEA 15
                                      222221 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.4e-05
                           SCAB_CC  7 dvllkkLrdvLeslrgrvaGknkddveesismvea 41
                                      + +l +  + L ++r+r +G + d+ve +i  ve 
  gi|336252987|ref|YP_004596094.1| 46 HAILDERLNTLRQVRERTDGNTEDKVESAIETVED 80
                                      5667777799*********************9985 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.5   5.3e-05     0.079      76     154 ..       4      79 ..       1      85 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.3e-05
                           DUF3450  76 sqeqeiasleeqieeieeierelvpllekmidrLeqfveldlPflleeRqarlakLkelmdradvslaekyrrvlea 152
                                       +++q +++lee  +++    +++   ++++ d+  ++v++d+ +     ++rl+ L+++ +r+d ++++k++  +e+
  gi|336252987|ref|YP_004596094.1|   4 QLQQARDDLEEAAKSA---DDDVREDIRETTDAFADYVRSDTAPDHAILDERLNTLRQVRERTDGNTEDKVESAIET 77 
                                       4555555555554444...4577788999******************************************999997 PP

                           DUF3450 153 yq 154
                                        +
  gi|336252987|ref|YP_004596094.1|  78 VE 79 
                                       65 PP

>> PBP-Tp47_c  Penicillin-binding protein Tp47 domain C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.2e-05     0.077      30      77 ..      12      59 ..       2      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                        PBP-Tp47_c 30 ikdqalkkaekitvevkeasgsyGeflrvdlkgnygdlgakmqavkwt 77
                                      ++++a ++ +++  +++e+++++ +++r d   +++ l  ++++++  
  gi|336252987|ref|YP_004596094.1| 12 LEEAAKSADDDVREDIRETTDAFADYVRSDTAPDHAILDERLNTLRQV 59
                                      55555555579************************9999998887654 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.7    0.0039       5.9      33      53 ..       4      42 ..       1      88 [] 0.46

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0039
                              YtxH 33 kaddlkekakelleeakeka..................k 53
                                      ++++++++++e++++a + +                  +
  gi|336252987|ref|YP_004596094.1|  4 QLQQARDDLEEAAKSADDDVredirettdafadyvrsdT 42
                                      455555555555444444443333333233334444440 PP

>> DUF2564  Protein of unknown function (DUF2564)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.1     0.019        29      36      54 ..       3      21 ..       1      40 [. 0.75
   2 ?   -0.4   0.0         1   1.5e+03      45      70 ..      34      59 ..      24      68 .. 0.65
   3 ?    7.9   0.1    0.0026       3.9      23      48 ..      63      88 .]      55      88 .] 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.019
                           DUF2564 36 qAiedAreqlssaeehatg 54
                                      + +++Ar++l++a++ a +
  gi|336252987|ref|YP_004596094.1|  3 EQLQQARDDLEEAAKSADD 21
                                      5688999999999888754 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1
                           DUF2564 45 lssaeehatgvdeeFleeseqlldka 70
                                      +++  + +t  d++ l+e  ++l ++
  gi|336252987|ref|YP_004596094.1| 34 FADYVRSDTAPDHAILDERLNTLRQV 59
                                      55555566666777777777776654 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0026
                           DUF2564 23 TmsmdpdqlesAtqAiedAreqlssa 48
                                      T    +d +esA + +ed req ++a
  gi|336252987|ref|YP_004596094.1| 63 TDGNTEDKVESAIETVEDYREQVDQA 88
                                      777889****************9986 PP

>> MT0933_antitox  MT0933-like antitoxin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.9     0.071   1.1e+02      14      40 ..       7      33 ..       2      42 .. 0.54
   2 ?    9.8   0.1   0.00067         1      26      48 ..      59      81 ..      56      82 .. 0.91
   3 ?    5.9   0.2      0.01        16      20      41 ..      69      88 .]      69      88 .] 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.071
                    MT0933_antitox 14 kvdqgiDKAgdavddktGgKysdkIdk 40
                                      ++ + ++ A++ +dd   ++  +  d 
  gi|336252987|ref|YP_004596094.1|  7 QARDDLEEAAKSADDDVREDIRETTDA 33
                                      444445556666665555555555544 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00067
                    MT0933_antitox 26 vddktGgKysdkIdkgqdaakda 48
                                      v ++t g   dk++++ ++++d+
  gi|336252987|ref|YP_004596094.1| 59 VRERTDGNTEDKVESAIETVEDY 81
                                      889***************99986 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.01
                    MT0933_antitox 20 DKAgdavddktGgKysdkIdkg 41
                                      DK + a++  t ++y +++d++
  gi|336252987|ref|YP_004596094.1| 69 DKVESAIE--TVEDYREQVDQA 88
                                      88889999..9999*****997 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   6.9   0.00058      0.86     127     217 ..       2      87 ..       1      88 [] 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00058
                              CorA 127 lekleeeldeledeledstkkeilrelaqlr.rrlvklrralapnrevlkrllakaddkllddedkeylrdlldele 202
                                       +e+l + +d+le+   +s +++ ++++ +     + ++r+  ap  ++l+++l+ ++    +++d     + +d++e
  gi|336252987|ref|YP_004596094.1|   2 TEQLQQARDDLEEAA-KSADDDVREDIRETTdAFADYVRSDTAPDHAILDERLN-TLRQVRERTD----GNTEDKVE 72 
                                       589999999999999.6666666666666551569999****************.7777777777....89****** PP

                              CorA 203 rllemlealrerles 217
                                       +++e++e +re++++
  gi|336252987|ref|YP_004596094.1|  73 SAIETVEDYREQVDQ 87 
                                       ************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1186  (0.0661498); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); 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):              12  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 635.29
//
Query:       gi|336252988|ref|YP_004596095.1|  [L=253]
Description: hypothetical protein Halxa_1584 [Halopiger xanaduensis SH-6]
Scores for 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  143.2   0.5    5.3e-20   72.4   0.0    2.2  2  DUF4397     Domain of unknown function (DUF4397)
  ------ inclusion threshold ------
      0.022   14.6   3.6      0.046   13.6   3.6    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
      0.049   13.4   0.0       0.29   10.9   0.0    2.0  2  AlgF        Alginate O-acetyl transferase AlgF
       0.12   12.2   1.7        1.4    8.8   0.2    2.1  2  DUF4493     Domain of unknown function (DUF4493)


Domain annotation for each model (and alignments):
>> DUF4397  Domain of unknown function (DUF4397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.0   1.2e-23   5.3e-20       1      95 [.      56     146 ..      56     150 .. 0.90
   2 !   69.6   0.1     9e-23     4e-19       1      85 [.     149     228 ..     149     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 1.2e-23
                           DUF4397   1 AtvrvvhaspdapsvDvyvngkkvlknvaygdvtgylqvpaGqytielnpagnkikagttvallnvditleagteyt 77 
                                       A vrv+h spdap+vDvyv+ ++vl++v+yg++++yl+v++G+yt++++p+g+    +t++   + ++t+ +g  yt
  gi|336252988|ref|YP_004596095.1|  56 AAVRVAHFSPDAPNVDVYVDWTRVLEDVPYGEISPYLEVEPGTYTVTITPTGDP---ETKA--FEGEVTVGEGF-YT 126
                                       78**************************************************93...4455..5666******6.** PP

                           DUF4397  78 vaavgsa..aalellvledd 95 
                                       vaa+g++  +++++ vl+d 
  gi|336252988|ref|YP_004596095.1| 127 VAAIGELgaDTFRPEVLTDA 146
                                       *******9999999999985 PP

  == domain 2  score: 69.6 bits;  conditional E-value: 9e-23
                           DUF4397   1 AtvrvvhaspdapsvDvyvngkkvlknvaygdvtgylqvpaGqytielnpagnkikagttvallnvditleagteyt 77 
                                       A vr +haspdap+vDvy++g++++ ++++g+ t+y+ vpaG+y ++l+pag+      ++++++ d ++eagt+yt
  gi|336252988|ref|YP_004596095.1| 149 ALVRAFHASPDAPAVDVYADGEPLFADLSFGESTNYVAVPAGSYALSLRPAGDA-----ETVVAEFDAPVEAGTAYT 220
                                       789*************************************************92.....34579************* PP

                           DUF4397  78 vaavgsaa 85 
                                       + a+g ++
  gi|336252988|ref|YP_004596095.1| 221 ASAIGYLE 228
                                       ****9873 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.6     1e-05     0.046       2      24 ..       3      25 ..       2      27 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      +SRR+ LK  ++a+ ++a+ g +
  gi|336252988|ref|YP_004596095.1|  3 VSRRTALKSLGVAGGLTAASGTV 25
                                      8*****************99976 PP

>> AlgF  Alginate O-acetyl transferase AlgF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.15   6.8e+02      30      73 ..      57     103 ..      47     108 .. 0.76
   2 ?   10.9   0.0   6.5e-05      0.29      24      72 ..     144     195 ..     123     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.15
                              AlgF  30 FvRvlnasee..evevsv.GetklksvsplqssdfkflpaGkyqaqv 73 
                                        vRv   s +  +v+v v     l++v  ++ s +  + +G+y++ +
  gi|336252988|ref|YP_004596095.1|  57 AVRVAHFSPDapNVDVYVdWTRVLEDVPYGEISPYLEVEPGTYTVTI 103
                                       56666666432267777755566899999999**********99987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 6.5e-05
                              AlgF  24 APkgsaFvRvlnaseeevevsv...GetklksvsplqssdfkflpaGkyqaq 72 
                                         +gsa vR++ as +  +v v   Ge    ++s ++s+++  +paG+y + 
  gi|336252988|ref|YP_004596095.1| 144 TDAGSALVRAFHASPDAPAVDVyadGEPLFADLSFGESTNYVAVPAGSYALS 195
                                       5689**********9887777666999999*******************876 PP

>> DUF4493  Domain of unknown function (DUF4493)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2    0.0003       1.4      46      91 ..      81     127 ..      29     130 .. 0.70
   2 ?    2.9   0.1     0.019        85      52      86 ..     180     217 ..     151     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0003
                           DUF4493  46 syatyaelpeaieLpvGtYtvkaesg.dssaagfdkpyyeGsetftv 91 
                                       +   y e+   +e+++GtYtv+++   d+++++f+  +  G+   tv
  gi|336252988|ref|YP_004596095.1|  81 EDVPYGEISPYLEVEPGTYTVTITPTgDPETKAFEGEVTVGEGFYTV 127
                                       444566665559***********965488999999888888776666 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.019
                           DUF4493  52 elpeaieLpvGtYtvkaesg...dssaagfdkpyyeGs 86 
                                       e  + + +p+G+Y ++       +++ a+fd+p+ +G+
  gi|336252988|ref|YP_004596095.1| 180 ESTNYVAVPAGSYALSLRPAgdaETVVAEFDAPVEAGT 217
                                       44445889********98775556666******98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1893.80
//
Query:       gi|336252989|ref|YP_004596096.1|  [L=688]
Description: UvrABC system protein B [Halopiger xanaduensis SH-6]
Scores for 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-32  109.2   0.0    3.5e-31  107.2   0.0    2.1  1  UvrB_inter   UvrB interaction domain
    1.2e-18   66.6   0.1    2.9e-18   65.4   0.1    1.7  1  UvrB         Ultra-violet resistance protein B
    6.1e-17   62.0   0.1    1.5e-16   60.7   0.1    1.7  1  Helicase_C   Helicase conserved C-terminal domain
    1.4e-09   37.4   6.5    1.4e-09   37.4   6.5    2.9  3  UVR          UvrB/uvrC motif
    7.6e-09   35.8   0.0    5.8e-08   32.9   0.0    2.2  2  ResIII       Type III restriction enzyme, res subunit
      0.001   18.9   0.1      0.009   15.8   0.0    2.6  3  DEAD         DEAD/DEAH box helicase
     0.0087   16.4   0.2        6.8    7.0   0.0    2.9  3  AAA_19       AAA domain
  ------ inclusion threshold ------
       0.01   15.5   0.0       0.24   11.1   0.0    2.7  3  AAA_30       AAA domain
      0.013   15.5   0.1      0.039   14.0   0.0    1.9  2  UB2H         Bifunctional transglycosylase second domain
      0.032   14.3   0.1      0.032   14.3   0.1    2.9  4  DUF87        Helicase HerA, central domain
        0.3   11.5   1.0        3.2    8.2   0.0    3.2  5  AAA          ATPase family associated with various cellular a
        0.4   10.5   2.2       0.49   10.2   0.2    2.2  2  Cofilin_ADF  Cofilin/tropomyosin-type actin-binding protein


Domain annotation for each model (and alignments):
>> UvrB_inter  UvrB interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.2   0.0   2.3e-34   3.5e-31       1      91 []     175     264 ..     175     264 .. 0.99

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 2.3e-34
                        UvrB_inter   1 lelkvgqkidreellrkLvelqYerndvelkrGtFrvrGdtveifpasaeevairieffgdeiesireidpltgksl 77 
                                       l+l+vgq++ r+ell++Lv+l+Yerndv++++GtFrvrGdtvei+p++ +++a+r+e++gdei+++ ++dpl+g+++
  gi|336252989|ref|YP_004596096.1| 175 LRLEVGQEVGRDELLKQLVDLNYERNDVDFTQGTFRVRGDTVEIYPMY-GRYAVRVELWGDEIDRMVKVDPLEGETK 250
                                       78**********************************************.7*************************** PP

                        UvrB_inter  78 ekleeitifPakhf 91 
                                        + +++ + Pa+h+
  gi|336252989|ref|YP_004596096.1| 251 GDQQAVLVHPAEHY 264
                                       *************9 PP

>> UvrB  Ultra-violet resistance protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.1     2e-21   2.9e-18       1      42 [.     566     607 ..     566     608 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 2e-21
                                       EE-SS--HHHHHHHHHHHHHHHHHHHHHHHHT------XXXX CS
                              UvrB   1 lYADkiTdSMkkAideTerRReiQeaYNeehgItPktikKki 42 
                                       lYAD+ +++M++Ai+eT+rRR+iQ+++Neehg  P+ti+K+i
  gi|336252989|ref|YP_004596096.1| 566 LYADEPSNAMEAAIEETRRRRRIQQEFNEEHGFEPTTIEKEI 607
                                       8***************************************98 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 !   60.7   0.1     1e-19   1.5e-16       9     109 ..     452     558 ..     444     560 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1e-19
                                       HH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTST CS
                        Helicase_C   9 ll.kleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidip 83 
                                        + ++ e+++++l+ + t++++e+ +++l e+ g+ va++h e+ + er ei+++ + ge+dvL+  + + +G+dip
  gi|336252989|ref|YP_004596096.1| 452 RIdERIERDERTLVTTLTKRMAEDlTEYL-EEAGVDVAYMHDETDTLERHEIIRSLRLGEIDVLVGINLLREGLDIP 527
                                       344556999*************9977777.7779******************************************* PP

                                       TESEEEESSSS.....SSHHHHHHHHTTSSS CS
                        Helicase_C  84 kvnlVinfdlp.....rnvtsyiqriGRtgR 109
                                       +v+lV ++d++     r+ t+++q +GR++R
  gi|336252989|ref|YP_004596096.1| 528 EVSLVGILDADqegflRSETTLVQTMGRAAR 558
                                       ***********77777778***********9 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       5.6   8.3e+03       6      13 ..     270     277 ..     269     277 .. 0.84
   2 ?   -2.6   0.2       3.6   5.4e+03       9      17 ..     573     581 ..     572     583 .. 0.82
   3 !   37.4   6.5   9.1e-13   1.4e-09       3      35 ..     636     668 ..     634     669 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.6
                               UVR   6 eLeeemee 13 
                                       +Le++m+e
  gi|336252989|ref|YP_004596096.1| 270 KLERAMDE 277
                                       89999987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.6
                               UVR   9 eemeeAaen 17 
                                       ++me A+e+
  gi|336252989|ref|YP_004596096.1| 573 NAMEAAIEE 581
                                       68****998 PP

  == domain 3  score: 37.4 bits;  conditional E-value: 9.1e-13
                               UVR   3 likeLeeemeeAaenedFEkAAklRDqinalkk 35 
                                        ++eLe++m+eAa+n++FE+AA +RD+i+++++
  gi|336252989|ref|YP_004596096.1| 636 YVDELEQQMQEAASNLEFELAADIRDRIREVRE 668
                                       679***************************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 !   32.9   0.0   3.9e-11   5.8e-08       5     118 ..      30     135 ..      26     156 .. 0.72
   2 ?    0.0   0.0       0.5   7.4e+02     134     147 ..     345     361 ..     273     413 .. 0.60

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.9e-11
                                       -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
                            ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflsea 81 
                                          Q eaie+l+e +  ++  +  +   TG+GKT +   +ie+++k      +l+++++k+l  q++eef+++++e+
  gi|336252989|ref|YP_004596096.1|  30 AGDQPEAIEQLAEGFR-QGMDKQTLLGVTGSGKTNTVSWVIEEIQK-----PTLVIAHNKTLAAQLYEEFRNLFPEN 100
                                       5579***********9.88888888899*****************9.....8**********************998 PP

                                       ...GEEEESSS-B--.......-SEEEEEHHHHHHTH CS
                            ResIII  82 ykeigkkvsgdkkkakekdstnkkilvttiqsldads 118
                                       + e   +vs   + + e   ++++ ++ +  s++ ++
  gi|336252989|ref|YP_004596096.1| 101 AVE--YFVSYYDYYQPEAYVEQTDTYIDKDASINDEI 135
                                       744..33333333332333345555555555555555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.5
                                       S...EEEEETGGGTTS. CS
                            ResIII 134 d...viiiDEaHrlgak 147
                                       +   + ++DE+H +  +
  gi|336252989|ref|YP_004596096.1| 345 PddfLTVVDESHQTLPQ 361
                                       24557789999988665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     6e-06     0.009       4      74 ..      33     100 ..      31     153 .. 0.76
   2 ?   -1.2   0.0      0.97   1.4e+03     126     139 ..     351     364 ..     348     416 .. 0.42
   3 ?   -3.0   0.0       3.7   5.5e+03      58      83 ..     467     492 ..     452     517 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6e-06
                                       HHHHHHHHHTT.....CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTS CS
                                       xxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   4 Qaeaiplilgg.....gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyi 74 
                                       Q eai+++ +g     ++  + + TGsGKT   +  v++++       ++ +l+++  + La q ++++++++ + 
  gi|336252989|ref|YP_004596096.1|  33 QPEAIEQLAEGfrqgmDKQTLLGVTGSGKTNTVSW-VIEEI-------QKPTLVIAHNKTLAAQLYEEFRNLFPEN 100
                                       667777777554444455667889*******9665.55454.......4567******************998753 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.97
                                       EEETHHHHHHTTTH CS
                                       xxxxxxxxxxxxxx RF
                              DEAD 126 VlDEadrlldqgfs 139
                                       V+DE ++ l q ++
  gi|336252989|ref|YP_004596096.1| 351 VVDESHQTLPQIRG 364
                                       66666666655222 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHHHHTTTSTSEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  58 eLaeqtlnnlkkfkkyidlrvlliig 83 
                                        L++ ++++l+++++++++ v  +  
  gi|336252989|ref|YP_004596096.1| 467 TLTKRMAEDLTEYLEEAGVDVAYMHD 492
                                       35555555555555555544443322 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0046       6.8      14      66 ..      52      97 ..      44     165 .. 0.60
   2 ?   -2.5   0.0       3.8   5.7e+03      54      54 ..     297     297 ..     269     359 .. 0.58
   3 !    6.1   0.2    0.0087        13      35      78 ..     457     540 ..     442     648 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0046
                            AAA_19 14 lvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalg 66
                                       +++  G+GKT ++  +++++++ +       l++a ++  a +l e+ ++l 
  gi|336252989|ref|YP_004596096.1| 52 TLLGVTGSGKTNTVSWVIEEIQKPT-------LVIAHNKTLAAQLYEEFRNLF 97
                                      578999*********9999887654.......566666666666666665544 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.8
                            AAA_19  54 A 54 
                                       A
  gi|336252989|ref|YP_004596096.1| 297 A 297
                                       2 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0087
                            AAA_19  35 velggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal.................................. 77 
                                       +e+     e+ l+ ++t+r a+ l+e l+++g++   +H  +                                   
  gi|336252989|ref|YP_004596096.1| 457 IERD----ERTLVTTLTKRMAEDLTEYLEEAGVDVAYMHDETDtlerheiirslrlgeidvlvginllregldipev 529
                                       3333....899*****************9999996656643223444444666666666666666666666666666 PP

                            AAA_19  78 ..........l 78 
                                                  
  gi|336252989|ref|YP_004596096.1| 530 slvgildadqE 540
                                       66555443331 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.24       5      81 ..      32     110 ..      29     158 .. 0.69
   2 ?    0.2   0.0      0.36   5.4e+02      39      80 ..     454     497 ..     448     540 .. 0.65
   3 ?   -0.8   0.0      0.69     1e+03      32      82 ..     547     618 ..     544     655 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                            AAA_30   5 eQaaaveallts...gdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelg..ieastiakl 76 
                                       +Q +a+e+l+++   g   ++l G+ G+GKt +++ + e ++   ++ +++A++++ A++L ee+   ++ + ++ +
  gi|336252989|ref|YP_004596096.1|  32 DQPEAIEQLAEGfrqGMDKQTLLGVTGSGKTNTVSWVIEEIQ---KPTLVIAHNKTLAAQLYEEFRnlFPENAVEYF 105
                                       688888888765111445789************999888777...67899**********99987644465556555 PP

                            AAA_30  77 lkrlk 81 
                                       ++ ++
  gi|336252989|ref|YP_004596096.1| 106 VSYYD 110
                                       55555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.36
                            AAA_30  39 reaweaaggrviglAptgkaAkvLae...elgieastiakllkrl 80 
                                        e +e++ +r ++ + t+++A++L+e   e+g++ + ++  +++l
  gi|336252989|ref|YP_004596096.1| 454 DERIERD-ERTLVTTLTKRMAEDLTEyleEAGVDVAYMHDETDTL 497
                                       5555544.4778889999999999962225555444444444333 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.69
                            AAA_30  32 ttalkalreaweaaggrviglAptgkaAkvLa...............eelgieastiakllkrlk......g 82 
                                       tt+++++ +a+++ +g+v+++A +   A + a               ee g+e  ti+k + +++      +
  gi|336252989|ref|YP_004596096.1| 547 TTLVQTMGRAARNVNGKVVLYADEPSNAMEAAieetrrrrriqqefnEEHGFEPTTIEKEIGETNlpgsktD 618
                                       677777777777777778877755555544443355555555555555777777777777766666555440 PP

>> UB2H  Bifunctional transglycosylase second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.6e-05     0.039       1      43 [.     177     219 ..     177     220 .. 0.96
   2 ?   -3.3   0.0       6.6   9.8e+03       5      36 ..     390     417 ..     387     421 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                              UB2H   1 LypGaalsaaqleqeLellgYrkvsnvtrpGeyavsgnriell 43 
                                       L+ G+++ +++l + L +l+Y +++   ++G+++v+g+++e++
  gi|336252989|ref|YP_004596096.1| 177 LEVGQEVGRDELLKQLVDLNYERNDVDFTQGTFRVRGDTVEIY 219
                                       789*********************9999*************97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.6
                              UB2H   5 aalsaaqleqeLellgYrkvsnvtrpGeyavs 36 
                                       ++l+ +++e+  +++ Y +    ++pG+y+++
  gi|336252989|ref|YP_004596096.1| 390 RPLTFEEFEEKTDQTLYVS----ATPGDYERE 417
                                       5666666666666666654....478888775 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.1e-05     0.032      28      51 ..      53      75 ..      51      84 .. 0.87
   2 ?   -0.7   0.0      0.85   1.3e+03     152     183 ..     266     299 ..     229     322 .. 0.72
   3 ?   -2.6   0.1       3.1   4.7e+03     138     147 ..     445     454 ..     371     501 .. 0.51
   4 ?   -2.1   0.1       2.3   3.4e+03     140     151 ..     634     645 ..     563     680 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                             DUF87 28 ilgsTGsGKSntvavLleellekk 51
                                       lg TGsGK+ntv+  +ee+  k+
  gi|336252989|ref|YP_004596096.1| 53 LLGVTGSGKTNTVSWVIEEIQ-KP 75
                                      59*****************98.54 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.85
                             DUF87 152 kekeelrklknqaiarlldkledllrkggsf..s 183
                                       + +++l+++ +++++ l ++++++ rkg  +  +
  gi|336252989|ref|YP_004596096.1| 266 IPETKLERAMDEIREDLDSRISYFERKGDMIaaQ 299
                                       5666888999999999999999999998877432 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.1
                             DUF87 138 ssdepvekll 147
                                       ++d+++ ++ 
  gi|336252989|ref|YP_004596096.1| 445 QIDDLMDRID 454
                                       2222222222 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.3
                             DUF87 140 depveklleelk 151
                                       +++v +l+++++
  gi|336252989|ref|YP_004596096.1| 634 ARYVDELEQQMQ 645
                                       233333333333 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 ?    8.2   0.0    0.0021       3.2       3      35 ..      53      85 ..      52     153 .. 0.83
   2 ?   -2.3   0.0       3.6   5.4e+03      65      82 ..     234     253 ..     231     259 .. 0.67
   3 ?   -2.6   0.1       4.7     7e+03      73      91 ..     452     470 ..     440     481 .. 0.48
   4 ?   -2.3   0.0       3.8   5.6e+03      54      83 ..     558     586 ..     534     595 .. 0.45
   5 ?   -2.2   0.0       3.6   5.3e+03      29      51 ..     622     649 ..     601     664 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0021
                                      EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelgvefleisgsell 35
                                      l G  G GKT +++ v++e++ + l i   + l
  gi|336252989|ref|YP_004596096.1| 53 LLGVTGSGKTNTVSWVIEEIQKPTLVIAHNKTL 85
                                      789*****************9888887777766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                                       ETGGGHHHHH..TTCCCHHH CS
                               AAA  65 DEidalaksr..sgseseee 82 
                                       DEid+++k +  +g++++++
  gi|336252989|ref|YP_004596096.1| 234 DEIDRMVKVDplEGETKGDQ 253
                                       9*****99887644444444 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.7
                                       HHTTCCCHHHHHHHHHHHH CS
                               AAA  73 srsgseseeeervvnqLlt 91 
                                       + +++ +++e+++v +L +
  gi|336252989|ref|YP_004596096.1| 452 RIDERIERDERTLVTTLTK 470
                                       1122222333444444433 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 3.8
                                       HHTSTSEEEEEETGGGHHHHHTTCCCHHHH CS
                               AAA  54 kekakpsilfiDEidalaksrsgseseeee 83 
                                       ++ +++++l  DE  + +++   +e++ ++
  gi|336252989|ref|YP_004596096.1| 558 RNVNGKVVLYADEPSNAMEAA-IEETRRRR 586
                                       222233444444433333333.22333333 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 3.6
                                       EETTTCSSS.....STTHHHHHHHHHHH CS
                               AAA  29 isgsellsk.....yvgesekkirelfk 51 
                                       +sg++l ++     yv e e++++e  +
  gi|336252989|ref|YP_004596096.1| 622 VSGKSLEDEddaarYVDELEQQMQEAAS 649
                                       4444444334445555555555554443 PP

>> Cofilin_ADF  Cofilin/tropomyosin-type actin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00033      0.49      13      62 ..      64     115 ..      58     125 .. 0.77
   2 ?   -2.4   0.1       2.7   4.1e+03      22      63 ..     458     494 ..     452     501 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00033
                                       .SSEEEEEEECTTTEEEEEESS-....HHHHHHHHHHTTT-EEEEEEEEEECCS CS
                       Cofilin_ADF  13 ktkyilfkidddkeeivveeege....tyeelreelpeseprYavydveyehdd 62 
                                       + ++++ +i++ +  +v+ + ++     yee+r+ +pe+ + Y v  ++y  ++
  gi|336252989|ref|YP_004596096.1|  64 TVSWVIEEIQKPT--LVIAHNKTlaaqLYEEFRNLFPENAVEYFVSYYDYYQPE 115
                                       6789999998765..666663345599******************999998766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.7
                                       ECTTTEEEEEESS-HHHHHHHHHHTTT-EEEEEEEEEECCSE CS
                       Cofilin_ADF  22 dddkeeivveeegetyeelreelpeseprYavydveyehdde 63 
                                       + d+ ++v   ++   e+l+e l+e     a +dv y+hd++
  gi|336252989|ref|YP_004596096.1| 458 ERDERTLVTTLTKRMAEDLTEYLEE-----AGVDVAYMHDET 494
                                       4555555555555555888888888.....667888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (688 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.71u 0.26s 00:00:00.97 Elapsed: 00:00:00.42
# Mc/sec: 4872.58
//
Query:       gi|336252990|ref|YP_004596097.1|  [L=183]
Description: hypothetical protein Halxa_1586 [Halopiger xanaduensis SH-6]
Scores for 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   15.0   0.3      0.038   13.5   0.3    1.9  1  EF-hand_5  EF hand
      0.019   15.0   0.1      0.039   14.0   0.0    1.6  2  PapC_N     PapC N-terminal domain


Domain annotation for each model (and alignments):
>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   4.3e-06     0.038       8      19 ..     100     111 ..     100     111 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-06
                                       H-SS-SSCE-HH CS
                         EF-hand_5   8 iDlNgDGkIske 19 
                                       +D+NgDG I++e
  gi|336252990|ref|YP_004596097.1| 100 VDTNGDGAIDRE 111
                                       6*********98 PP

>> PapC_N  PapC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.75   6.8e+03      45      48 ..      59      62 ..      42      81 .. 0.52
   2 ?   14.0   0.0   4.3e-06     0.039      22      52 ..     150     180 ..     134     183 .] 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.75
                                      EEEE CS
                            PapC_N 45 qeve 48
                                      q+v+
  gi|336252990|ref|YP_004596097.1| 59 QTVQ 62
                                      2222 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.3e-06
                                       TT-SS-SEEEEEEEEETTEEEEEEEEEEEEC CS
                            PapC_N  22 kgnavlpGeYrvdvyvNgkeigrqevefkae 52 
                                        +n+ +pGeY v+v++N++++ + ++e++a+
  gi|336252990|ref|YP_004596097.1| 150 VNNPSEPGEYAVEVTLNEEQTVEGTIEITAD 180
                                       568899********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1495.88
//
Query:       gi|336252991|ref|YP_004596098.1|  [L=408]
Description: hypothetical protein Halxa_1587 [Halopiger xanaduensis SH-6]
Scores for 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-134  448.2  14.2   2.5e-134  448.0  14.2    1.0  1  ArsP_2    Putative, 10TM heavy-metal exporter
  ------ inclusion threshold ------
        3.3    7.0   6.5       0.26   10.6   1.2    1.9  2  CCB1      Cofactor assembly of complex C subunit B


Domain annotation for each model (and alignments):
>> ArsP_2  Putative, 10TM heavy-metal exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.0  14.2  2.8e-138  2.5e-134       3     361 .]       5     394 ..       3     394 .. 0.96

  Alignments for each domain:
  == domain 1  score: 448.0 bits;  conditional E-value: 2.8e-138
                            ArsP_2   3 reilleslsDaflqvsafvavtlliysllslkkdeklvellekseklqvliaallGllPGCGGAivvitlyvrgkvs 79 
                                        ++llesl+D+++qvsafva+t+l++ l+++++d++l  ++e++e+lqvl+++llGl+PGCGGAi+v++lyvrg+vs
  gi|336252991|ref|YP_004596098.1|   5 LTVLLESLRDGYVQVSAFVAITVLAFGLIQYRTDGALLAAIEDNERLQVLFGGLLGLTPGCGGAIIVMPLYVRGTVS 81 
                                       6789************************************************************************* PP

                            ArsP_2  80 FgavvAvLtatmGDaAFlllalkPkaalivlaialvvgivsGlvvnaih...................dedflrpkv 137
                                       Fg+vvA+L+at+GD+AF++lal+P+aal+++aia+++++++G++v++++                   d++++++  
  gi|336252991|ref|YP_004596098.1|  82 FGTVVATLGATAGDSAFVILALAPEAALYAYAIAFAASVATGYLVDSVGlgvsrvdaavarlspnattDGGTVVNGG 158
                                       *******************************************************************9999999999 PP

                            ArsP_2 138 aeeeee.dassaaaskaeek.......letklsklakvlWllllvpalivall..........lafqvdveallsle 196
                                       +  +++ d+ + a+++a+e+       + t ls+la+vlW++++v++l+++ l          la+++ ++ l+   
  gi|336252991|ref|YP_004596098.1| 159 VGPNPAhDYGGPAPTHAHETgpdrrsrVLTPLSHLAHVLWWVAAVAGLVLGSLylfrggpevpLATGLGFDGLF--- 232
                                       99998879999*****999999*******************************777766666666666666666... PP

                            ArsP_2 197 eksiellgavlavlslllwaltreleeekevvsedekiksake.lqkaaqdtsfvtvWvivafllfElvvvltgvdl 272
                                           +++g+++a+lsl+l++++r++ +e+e++++++++ks ++ l++aa++tsfvtvWv+vafl++E++v+ltg+++
  gi|336252991|ref|YP_004596098.1| 233 ----TVVGIAGALLSLYLYVVGRHYVGEGEIARARDSFKSIYDtLTHAAMETSFVTVWVLVAFLVYEYAVLLTGLNV 305
                                       ....9*************************************99********************************* PP

                            ArsP_2 273 aallaalgvlaplvgvliGllPGCgPqilvtslYleGaiPlsaqianaisnDGDALFPaialapkaAlvAtlYsaiP 349
                                       aal++++gvlap++++++Gl+PGCgPqil++s+Y+eG +P+sa++anai++DGDALFP++a+++kaA+vA++Y+++P
  gi|336252991|ref|YP_004596098.1| 306 AALASTAGVLAPIGAAVVGLIPGCGPQILLASVYAEGGLPFSALTANAIAQDGDALFPLLAVDAKAAVVASIYNFLP 382
                                       ***************************************************************************** PP

                            ArsP_2 350 Alivgyayyfll 361
                                       A+ivg+a+++l+
  gi|336252991|ref|YP_004596098.1| 383 AVIVGVALHLLW 394
                                       *********997 PP

>> CCB1  Cofactor assembly of complex C subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.2   2.9e-05      0.26      61     123 ..      46     110 ..      14     116 .. 0.88
   2 ?   -3.1   0.4      0.49   4.4e+03      81     100 ..     297     316 ..     294     324 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.9e-05
                              CCB1  61 vdaeketvtfeGlv..apslflAifLtllaalgllclaLVlsilvpelgnlflllvllsPlAgvf 123
                                        d+e+ +v f Gl+   p  + Ai+++ l + g+++++ V+++l  + g   +++++l+P A ++
  gi|336252991|ref|YP_004596098.1|  46 EDNERLQVLFGGLLglTPGCGGAIIVMPLYVRGTVSFGTVVATLGATAGDSAFVILALAPEAALY 110
                                       4889999999998533799999***************************************9988 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.49
                              CCB1  81 AifLtllaalgllclaLVls 100
                                       A++Lt l + +l++ a Vl+
  gi|336252991|ref|YP_004596098.1| 297 AVLLTGLNVAALASTAGVLA 316
                                       88999999999999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 3446.93
//
Query:       gi|336252992|ref|YP_004596099.1|  [L=167]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-16   58.0   0.0    1.1e-15   57.6   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.3e-14   53.1   0.0    3.9e-14   52.9   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.2e-13   50.4   0.0    3.3e-13   49.9   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.6e-07   31.4   0.1    3.1e-07   31.1   0.1    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    2.2e-06   27.5   0.0    3.3e-06   27.0   0.0    1.2  1  FR47             FR47-like protein
    7.2e-06   26.2   0.0    9.4e-06   25.8   0.0    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    9.8e-05   22.4   0.1     0.0049   17.0   0.1    2.3  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00083   19.5   0.5     0.0012   19.1   0.5    1.3  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.044   12.8   0.1      0.055   12.5   0.1    1.3  1  DUF2156          Uncharacterised conserved protein (DUF2156)


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 !   57.6   0.0   5.7e-19   1.1e-15      11     115 ..      43     152 ..      19     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 5.7e-19
                   Acetyltransf_10  11 etfkefispealrerieegealllvaeeggkivGvi..el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdg 84 
                                       +t++e   ++al+  +++  + +lvae++g++vG+    + +d++ + +++V+p+++  Gig+aL e+++e +++ +
  gi|336252992|ref|YP_004596099.1|  43 RTIDEWYGDDALETALSKAGTAFLVAERDGEVVGFThgVVtEDEGDVLRMAVHPDHQNEGIGTALHERLCEDLQDFN 119
                                       344555556999999999999*************99854457788****************************9888 PP

                   Acetyltransf_10  85 ikl..eltvnaspyavpfYeklGFkavgeeqee 115
                                        +   ++ + ++   ++fYe++GF+++ge ++e
  gi|336252992|ref|YP_004596099.1| 120 MERmrAIDLASNEGGREFYERQGFERTGEGTVE 152
                                       888899*********************987766 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0     2e-17   3.9e-14      28     117 .]      58     143 ..      21     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 2e-17
                                       HHSTTC.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEET CS
                    Acetyltransf_1  28 fsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlavee 103
                                       +s  a+  +lvae+dge++Gf  +    d    ++ + ++aV+p++++ G+G+aL e l e + + + +++ +   +
  gi|336252992|ref|YP_004596099.1|  58 LS-KAGtAFLVAERDGEVVGFTHGVVTED----EGDVLRMAVHPDHQNEGIGTALHERLCEDLQDFNMERMRAIDLA 129
                                       33.44548888************999999....79999****************************99998554558 PP

                                       TEHHHHHHHHHTTE CS
                    Acetyltransf_1 104 dndaairlYeklGF 117
                                       +n++ +++Ye+ GF
  gi|336252992|ref|YP_004596099.1| 130 SNEGGREFYERQGF 143
                                       8************9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0   1.6e-16   3.3e-13       4      76 .]      64     145 ..      61     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.6e-16
                                       EEEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHH.H.......TTSEEEEE.EEEE.THHHHHHH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLle.a.......aekgiile.qlel.naekaikf 68 
                                        ++Vae+dg++vGf   ++++  ++  r+aV+p++++ GiG+aL e +       +   ++      l ++e  ++f
  gi|336252992|ref|YP_004596099.1|  64 AFLVAERDGEVVGFTHGVVTEdeGDVLRMAVHPDHQNEGIGTALHErLcedlqdfN---MERMrAIDLaSNEGGREF 137
                                       699***********99999887777777****************994333332221...22122234433346778* PP

                                       HHHTTEEE CS
                    Acetyltransf_7  69 YeklGFee 76 
                                       Ye+ GFe+
  gi|336252992|ref|YP_004596099.1| 138 YERQGFER 145
                                       ******95 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.1   1.6e-10   3.1e-07       2     138 .]       8     144 ..       7     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.6e-10
                    Acetyltransf_3   2 LlLrplteeDlealfelrsdpevmry..lpepltleeaeewlera.waeeseeegygwaivlkdtgviGsv.glrdl 74 
                                       + +rp+t eD e++ +++ d    +y  l  ++ +   +ew+ +  +++   + g  +++ ++d++v+G+  g+   
  gi|336252992|ref|YP_004596099.1|   8 IEIRPATLEDREGIRAVARDTWHDTYdeLDADTIDRTIDEWYGDDaLETALSKAGTAFLVAERDGEVVGFThGVVTE 84 
                                       689**********97655543333343322233334445555543666666677788***9999978****777755 PP

                    Acetyltransf_3  75 eeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       +e      l + ++p++++ G++t   + l+e + ++ ++er++a   ++Ne+ +  +e+ Gfe
  gi|336252992|ref|YP_004596099.1|  85 DEG---DVLRMAVHPDHQNEGIGTALHERLCEDL-QDFNMERMRAIDLASNEGGREFYERQGFE 144
                                       555...689*************************.9999***********************97 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.6e-09   3.3e-06       9      80 ..      74     146 ..      67     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.6e-09
                                       T--EEEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47   9 lgelaawilrkdggelgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfeki 80 
                                       ++    +++++d g +  + v+p+h+++G g+ l + l +++   + + + ++  asN+  +++ye+ Gfe  
  gi|336252992|ref|YP_004596099.1|  74 VVGFTHGVVTEDEGDVLRMAVHPDHQNEGIGTALHERLCEDLQDfNMERMRAIDLASNEGGREFYERQGFERT 146
                                       555667889999********************************88899999999***************975 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   4.7e-09   9.4e-06       1     139 [.      10     148 ..      10     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.7e-09
                    Acetyltransf_4   1 iraateeDakeilaiyaeyvvnt..aitfeyevssveefe..kflealdsekeyvflvae.sdrivGyaylgqfkkr 72 
                                       ir at+eD + i+a+  +  + t  +++ +    +++e      le   s+    flvae ++++vG   ++     
  gi|336252992|ref|YP_004596099.1|  10 IRPATLEDREGIRAVARDTWHDTydELDADTIDRTIDEWYgdDALETALSKAGTAFLVAErDGEVVGFTHGVVT--- 83 
                                       7889999999999988664332223455444445554433246677666888999************9999844... PP

                    Acetyltransf_4  73 akdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgi 139
                                        +d+   l + + + d ++eg+g +l++ l + l+  n+e++ a   ++ne   +f+++ GFe +g+
  gi|336252992|ref|YP_004596099.1|  84 -EDEGDVLRMAV-HPDHQNEGIGTALHERLCEDLQDFNMERMRAIDLASNEGGREFYERQGFERTGE 148
                                       .46778889999.589****************************9999***************9886 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.4e-06    0.0049       1     126 [.       9     144 ..       9     146 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.4e-06
                                       .EEEE-GGGHHHHHHHHHHHTT----H.........HHHHHHHHHHTTS...........EEEEEEETTEEEEEEEE CS
                    Acetyltransf_9   1 eirelteedldevlellkyaFqdeespl.......eeireyfrkllees...........rvlgaedngelvgqlal 59 
                                       eir++t ed +++ ++ +  ++d+ ++l              ++ ++++            +l+ae++ge+vg  + 
  gi|336252992|ref|YP_004596099.1|   9 EIRPATLEDREGIRAVARDTWHDTYDELdadtidrT-----IDEWYGDDaletalskagtAFLVAERDGEVVGFTHG 80 
                                       6999*******************9999997666441.....333333221111233335689999999999997765 PP

                                       EEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT...T--EEEE--SS..HHHHHTTT-E CS
                    Acetyltransf_9  60 lplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemree...gqplsllfPss..ipiYrrfGye 126
                                       +             + v   av+p+h+++g+ ++L +r+ e++++    + + + l   +  +++Y+r G+e
  gi|336252992|ref|YP_004596099.1|  81 VVT--EDE------GDVLRMAVHPDHQNEGIGTALHERLCEDLQDFnmeRMRAIDLASNEggREFYERQGFE 144
                                       433..234......4555668**********99999999998877511123333344444224677777776 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.5   5.8e-07    0.0012      26     132 ..      16     127 ..       3     140 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.8e-07
                    Acetyltransf_6  26 tdpedleallelfraqwarr.....pdvfadpltraflrdllaalaargalrlyvlrldgrpvAvalglrsgdrlyy 97 
                                       +d+e ++a+ +  ++ +         d   d+++     d+l++  ++    ++v++ dg++v++  g++ +d    
  gi|336252992|ref|YP_004596099.1|  16 EDREGIRAVARDTWHDTYDEldadtIDRTIDEWYG---DDALETALSKAGTAFLVAERDGEVVGFTHGVVTEDEGDV 89 
                                       45555555544444433333432223333344433...3444444444466799*********************** PP

                    Acetyltransf_6  98 wlggydpelaklspgllllweliedaae...eGlrrfd 132
                                       + ++++p++   ++g+ l+ +l ed+ +   e +r +d
  gi|336252992|ref|YP_004596099.1|  90 LRMAVHPDHQNEGIGTALHERLCEDLQDfnmERMRAID 127
                                       ************************99884444555555 PP

>> DUF2156  Uncharacterised conserved protein (DUF2156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.8e-05     0.055     175     267 ..      59     150 ..       5     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                                       HHHTSEEEEEEE.TTEEEEEEEEEEECTTTEEEEEEEEE-TT.STTHHHHHHHHHHHHCHHTT-SEEEEEEE..... CS
                           DUF2156 175 ddldlrglvvrdeegrivAftsfeplngkdglsldlmRrdpdapnGlmefliaelaeelkeegveyvsLgfaplagl 251
                                        +++   lv+++ +g++v+ft+++ +  ++g +l +  +     +G+ ++l  +l+e l++ ++e++   +  la+ 
  gi|336252992|ref|YP_004596099.1|  59 SKAGTAFLVAER-DGEVVGFTHGVVTE-DEGDVLRMAVHPDHQNEGIGTALHERLCEDLQDFNMERMR--AIDLASN 131
                                       455677788888.*************9.56666666655555679**********9999999999988..3333333 PP

                                       .............HHHHHH CS
                           DUF2156 252 .gerega..gllerllrll 267
                                        g re    + +er ++++
  gi|336252992|ref|YP_004596099.1| 132 eGGREFYerQGFERTGEGT 150
                                       3333332335555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1281.06
//
Query:       gi|336252993|ref|YP_004596100.1|  [L=98]
Description: translation initiation factor SUI1 [Halopiger xanaduensis SH-6]
Scores for complete 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   64.2   0.0    1.8e-17   63.6   0.0    1.3  1  SUI1      Translation initiation factor SUI1
    0.00093   19.5   0.0     0.0015   18.8   0.0    1.5  1  Img2      Mitochondrial large subunit ribosomal protein (Img2
  ------ inclusion threshold ------
       0.18   11.1   0.0       0.33   10.3   0.0    1.4  1  HEM4      Uroporphyrinogen-III synthase HemD


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 !   63.6   0.0     3e-21   1.8e-17       2      77 .]      24      95 ..      23      95 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 3e-21
                              SUI1  2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygvp 77
                                      ++++++r+e+r+  K vT+v+g+++ + +++++a++lk+ ++++g+v++ g   i++QGd+r++v +lL e+ g++
  gi|336252993|ref|YP_004596100.1| 24 QQQLRLRTESRRYDKPVTIVEGFDLSKSEIEDVASDLKSSLGTGGTVTE-G--HIELQGDHRDRVPDLLRER-GFK 95
                                      799*******************************************944.5..5*****************9.985 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 !   18.8   0.0   2.4e-07    0.0015      35      80 .]      18      94 ..       5      94 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.4e-07
                              Img2 35 GDiaalredLrkalee.....lvkvne..........................vtgkieikGdrveevkkfLeskgF 80
                                      GD++  +++Lr   e+      v++ e                          ++g+ie++Gd++++v + L+++gF
  gi|336252993|ref|YP_004596100.1| 18 GDLETSQQQLRLRTESrrydkPVTIVEgfdlskseiedvasdlksslgtggtvTEGHIELQGDHRDRVPDLLRERGF 94
                                      5555555555555554333331333333444444444455555555555555599*********************9 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   5.5e-05      0.33     105     145 ..      54      98 .]      46      98 .] 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.5e-05
                                       HHHGGGS-.---E.EEEEE....-SS.S--HHHHHHHHHTTEEEEE CS
                              HEM4 105 egLaeelaeslag.krvll....lrgeiarddlaegLeergaevde 145
                                       e++a+ l++sl+  ++v      l+g ++rd++++ L+erg++v+e
  gi|336252993|ref|YP_004596100.1|  54 EDVASDLKSSLGTgGTVTEghieLQG-DHRDRVPDLLRERGFKVQE 98 
                                       56666666666665554445556899.5****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); 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:                         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: 00:00:00.40
# Mc/sec: 740.22
//
Query:       gi|336252994|ref|YP_004596101.1|  [L=222]
Description: hypothetical protein Halxa_1590 [Halopiger xanaduensis SH-6]
Scores for 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-25   87.9   0.0    4.8e-25   87.5   0.0    1.2  1  DUF192       Uncharacterized ACR, COG1430
  ------ inclusion threshold ------
       0.56   10.7   7.3        9.4    6.7   0.0    2.7  3  GOLD_2       Golgi-dynamics membrane-trafficking
        2.5    7.3   9.3        2.6    7.3   9.3    1.1  1  BUD22        BUD22
        3.2    5.8  11.7        3.8    5.6  11.7    1.0  1  Nop14        Nop14-like family


Domain annotation for each model (and alignments):
>> DUF192  Uncharacterized ACR, COG1430
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.0   1.1e-28   4.8e-25       2      95 ..     110     217 ..     109     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 1.1e-28
                                       EEEEE-SHHHHHHTTTT-----TTEEEEEEECCEEEEEE--TT--S-EEEEEE-TTSBEEEEEEEE-TT.....-.. CS
                            DUF192   2 tvevAdteeerarGLmgreslpedegmlfvfdkerehsfwMkntripLdiifldadgriveieealkpq.....s.. 71 
                                       t+ +Adt e r+ GL+ +e+lped+gmlfv+++ +e++f+M+++ + +dii+ dadg+i+++++a +p      +  
  gi|336252994|ref|YP_004596101.1| 110 TAAIADTSELRYLGLSDTEELPEDRGMLFVYESVEEREFVMREMSFGIDIIYADADGTITSVHHAPEPEpgedgEse 186
                                       7899************************************************************9988866655055 PP

                                       .......ECEEEEEETTHHHHHT--TT-EEE CS
                            DUF192  72 .......vryvLElpaGaakklgikpGdrle 95 
                                               +yvLE++ +++++ ++++Gd le
  gi|336252994|ref|YP_004596101.1| 187 ehtypgeGQYVLEVNYEWTAERDVSEGDVLE 217
                                       6666666999******************997 PP

>> GOLD_2  Golgi-dynamics membrane-trafficking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   4.0     0.011        48      42      91 ..      56     108 ..      30     120 .. 0.74
   2 ?   -0.8   0.0      0.46     2e+03      30      60 ..     152     182 ..     142     188 .. 0.72
   3 ?    6.7   0.0    0.0021       9.4     103     121 ..     185     203 ..     168     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
                            GOLD_2  42 atskavsvkvsesddeedeeeeee...eekveeedvekgsvkaakprldeivp 91 
                                       ++s + s + +esdde++ e e+e   +e++ +e+ e + v++a p  de+  
  gi|336252994|ref|YP_004596101.1|  56 TESASESGDGNESDDENESEGENEsdgDESTVHENYETTDVTVATPDGDELGS 108
                                       45556667778888887766655545556777777888888888888777655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.46
                            GOLD_2  30 diGfGvyfewteatskavsvkvsesddeede 60 
                                       ++ fG+   +++a+ +  sv+ +   +  ++
  gi|336252994|ref|YP_004596101.1| 152 EMSFGIDIIYADADGTITSVHHAPEPEPGED 182
                                       5789999999999999999987654443333 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0021
                            GOLD_2 103 aGsheypGrGvyllkfdns 121
                                       +  h+ypG+G y+l ++  
  gi|336252994|ref|YP_004596101.1| 185 SEEHTYPGEGQYVLEVNYE 203
                                       567***********98755 PP

>> BUD22  BUD22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   9.3   0.00058       2.6     194     251 ..      38      94 ..      23     191 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00058
                             BUD22 194 eededdedaeedeedeeaeerelaqydgllasddededeyneetdeesseesdssdss 251
                                       + de+d  +++ +  +++e ++++++ +  +sdde+e+e ++e+d ++s   ++ +++
  gi|336252994|ref|YP_004596101.1|  38 STDETDGTDGT-DGTDGDETESASESGDGNESDDENESEGENESDGDESTVHENYETT 94 
                                       11111111111.1112222222222222122333333322222222222222222222 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  11.7   0.00084       3.8     338     399 ..      28      88 ..      16     133 .. 0.42

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.00084
                             Nop14 338 kglka......taeeeeeededdfeedddlveseseeeeeeeeedeeeeedeeeeeeeeededdlsdl 399
                                       +g ++      t+e ++ +  d  + d+++++ses + +   e+d+e+e++     e+e+d d++   
  gi|336252994|ref|YP_004596101.1|  28 SGASTdeagnsTDETDGTDGTDGTDGDETESASESGDGN---ESDDENESEG----ENESDGDESTVH 88 
                                       444222122111111122222222222222222222221...1111111111....222222221111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1723.10
//
Query:       gi|336252995|ref|YP_004596102.1|  [L=600]
Description: UvrABC system protein C [Halopiger xanaduensis SH-6]
Scores for complete 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  142.2   0.0    2.5e-41  141.2   0.0    1.5  1  UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
    8.6e-13   48.7   0.1    2.7e-12   47.1   0.1    1.9  1  HHH_5       Helix-hairpin-helix domain
    9.2e-12   44.2   0.2    8.4e-09   34.9   0.1    2.7  2  HHH         Helix-hairpin-helix motif
      1e-09   38.3   0.0    3.2e-09   36.8   0.0    1.8  1  HHH_2       Helix-hairpin-helix motif
    2.2e-09   36.7   2.3    5.4e-09   35.5   2.3    1.7  1  UVR         UvrB/uvrC motif
    5.7e-09   36.1   0.0    1.1e-08   35.3   0.0    1.5  1  GIY-YIG     GIY-YIG catalytic domain
     0.0012   19.4   0.1       0.65   10.6   0.0    3.0  3  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
     0.0023   18.2   0.0      0.019   15.2   0.0    2.4  2  HHH_3       Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.013   14.2   0.0      0.021   13.6   0.0    1.3  1  FbpA        Fibronectin-binding protein A N-terminus (FbpA)
      0.041   14.2   0.1        0.4   11.1   0.0    2.4  2  IMS_HHH     IMS family HHH motif
       0.06   13.7   0.0       0.49   10.8   0.0    2.4  2  HHH_8       Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.2   0.0   1.5e-44   2.5e-41       3     154 .]     390     534 ..     388     534 .. 0.91

  Alignments for each domain:
  == domain 1  score: 141.2 bits;  conditional E-value: 1.5e-44
                                       HTT-SS---EEEEEEEEEETTTEEEEEEEEEETTEE-GGG-EEEEEE.-SS--HHHHHHHHHHHHHTTS.......- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                        UvrC_HhH_N   3 llglkekpkriecyDiShiqgtntvgsmvvfedgkpkkseyRkfkiksvkegdDyaamrevlrRrfkrllke..fsk 77 
                                       +l+++ + +rie++D+Sh qg+++vgs v+f dg+++k +yR+ k++  +++dDy  mr +l+ r +r+ ++  +++
  gi|336252995|ref|YP_004596102.1| 390 ALEID-SARRIEGFDVSHAQGKSAVGSDVTFVDGSAEKADYRRKKLT--DQNDDYDNMRALLEWRARRAVEDrdDRP 463
                                       67777.589**************************************..679****************998844567 PP

                                       --SEEEESSSHHHHHHHHHHHHHTT----EEEEES............SSSEEEE--TT-HHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrC_HhH_N  78 lPdLiliDGGkgqlnaakevleelglkipvvglaKdkkrktrakaeereeevlelkkssealkllqrirdeaHrfAI 154
                                        PdL+liDGG+gql+aa+++l+++g+++p v+laK ++r  +    +re   ++ + + + l+llqr+rdeaHrfA+
  gi|336252995|ref|YP_004596102.1| 464 DPDLLLIDGGQGQLEAARDALADVGWDVPAVALAKAEERVVTP---DRE---FSWPDDAPHLHLLQRVRDEAHRFAV 534
                                       77*********************************76664444...477...9***********************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 !   47.1   0.1   1.7e-15   2.7e-12       4      55 ..     548     598 ..     545     599 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.7e-15
                                       HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                             HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilel 55 
                                       L +v+G+Gp+t ++ll   ++sve + +a+ e+L ++pGiG+ktAe i+  l
  gi|336252995|ref|YP_004596102.1| 548 LDDVEGVGPETRKRLLGR-FGSVENVREASLEDLRSVPGIGEKTAETIKSRL 598
                                       789*************99.*****************************9877 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0045       7.4      13      28 ..     548     563 ..     548     564 .. 0.83
   2 !   34.9   0.1   5.2e-12   8.4e-09       1      29 [.     568     596 ..     568     597 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0045
                                       HHTSTT-SHHHHHHHH CS
                               HHH  13 LlalPGVGpktAeaIl 28 
                                       L +++GVGp+t  + l
  gi|336252995|ref|YP_004596102.1| 548 LDDVEGVGPETRKRLL 563
                                       668********88765 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 5.2e-12
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIls 29 
                                       s+e++++as+e+L ++PG+G+ktAe I s
  gi|336252995|ref|YP_004596102.1| 568 SVENVREASLEDLRSVPGIGEKTAETIKS 596
                                       689***********************986 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   1.9e-12   3.2e-09      10      53 ..     553     596 ..     551     599 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.9e-12
                             HHH_2  10 hVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsive 53 
                                        VG +t k L  rF+s+++ ++asle+L +v++iGe++A+ i++
  gi|336252995|ref|YP_004596102.1| 553 GVGPETRKRLLGRFGSVENVREASLEDLRSVPGIGEKTAETIKS 596
                                       69**************************************9986 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   2.3   3.3e-12   5.4e-09       7      34 ..     204     231 ..     199     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.3e-12
                               UVR   7 LeeemeeAaenedFEkAAklRDqinalk 34 
                                       L++eme Aae+++FE+AA lRD+++ ++
  gi|336252995|ref|YP_004596102.1| 204 LRREMEAAAEDQNFERAANLRDRLETVQ 231
                                       9***********************9776 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   6.6e-12   1.1e-08       2      78 .]      17      89 ..      16      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 6.6e-12
                                      -EEEEEEETTT--EEEEEESSHHHHHHHHHHHHHHT--S-HS.STEEEEEEEE----HHHHHHHHHHHHHHTTSSSS CS
                           GIY-YIG  2 ggvYiirskenkliYvGstknlekRlkqHnagkkakytrkkgkkpfeliileifptksealelEkklikkyksnkyn 78
                                       gvY++r+ e  l YvG++ +l++R +++   ++a+++r   ++  + i + + +t+++al lE+ lik++++ +yn
  gi|336252995|ref|YP_004596102.1| 17 PGVYQFREDETTL-YVGKAVDLRSRVGSYADPRSARIRRM--VQRADGIEIAVTDTETQALLLEANLIKRHQP-RYN 89
                                      59*******9997.************************97..9999***************************.998 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 ?   -2.9   0.0       6.4     1e+04      54      74 ..     428     448 ..     420     456 .. 0.74
   2 !   10.6   0.0    0.0004      0.65      22      47 ..     550     575 ..     542     581 .. 0.89
   3 ?    5.8   0.0     0.013        21      19      33 ..     579     593 ..     575     598 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.4
                        5_3_exonuc  54 kklkekLeenkeearlskkLa 74 
                                       + +++kL++++++ + ++ L 
  gi|336252995|ref|YP_004596102.1| 428 DYRRKKLTDQNDDYDNMRALL 448
                                       347899999999888777776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0004
                        5_3_exonuc  22 GvpgiGektAakLlkeygsleeilen 47 
                                        v+g+G+ t ++Ll ++gs+e++ e+
  gi|336252995|ref|YP_004596102.1| 550 DVEGVGPETRKRLLGRFGSVENVREA 575
                                       69********************9984 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.013
                        5_3_exonuc  19 nipGvpgiGektAak 33 
                                       ++  vpgiGektA +
  gi|336252995|ref|YP_004596102.1| 579 DLRSVPGIGEKTAET 593
                                       6788*********76 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.99   1.6e+03      46      63 ..     548     565 ..     545     567 .. 0.78
   2 !   15.2   0.0   1.2e-05     0.019      41      63 ..     575     597 ..     569     599 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.99
                             HHH_3  46 Llkvkglgpktfeqlagf 63 
                                       L +v+g+gp+t  +l g+
  gi|336252995|ref|YP_004596102.1| 548 LDDVEGVGPETRKRLLGR 565
                                       668999999998887765 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.2e-05
                             HHH_3  41 ksreeLlkvkglgpktfeqlagf 63 
                                       +s+e+L +v+g+g+kt e ++ +
  gi|336252995|ref|YP_004596102.1| 575 ASLEDLRSVPGIGEKTAETIKSR 597
                                       46667777777777777776665 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 ?   13.6   0.0   1.3e-05     0.021     146     231 ..     498     583 ..     491     598 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                                       SSXSXXBSTTXBXXXSXXXSXBXTT..SXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH.... CS
                              FbpA 146 qsrvReilpgekYelPpsqdklnPl..eaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsa 220
                                       + + R + p +++ +P+    l  l    +e+ +f    ++  +d vk+ ++ ++G++p++ + ll r g  + +++
  gi|336252995|ref|YP_004596102.1| 498 KAEERVVTPDREFSWPDDAPHLHLLqrVRDEAHRFAVQYHQTVRDEVKTVLDDVEGVGPETRKRLLGRFG--SVENV 572
                                       5567*******************9984334434777777778899*************************..66668 PP

                                       ........... CS
                              FbpA 221 kelseedlerl 231
                                       +e+s edl+++
  gi|336252995|ref|YP_004596102.1| 573 REASLEDLRSV 583
                                       88888888766 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.81   1.3e+03      14      27 ..     549     563 ..     548     567 .. 0.77
   2 ?   11.1   0.0   0.00024       0.4      12      28 ..     579     595 ..     575     598 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.81
                           IMS_HHH  14 tkipGiGgklgek.L 27 
                                        ++ G+G+ + ++ L
  gi|336252995|ref|YP_004596102.1| 549 DDVEGVGPETRKRlL 563
                                       5677********955 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00024
                           IMS_HHH  12 pitkipGiGgklgekLe 28 
                                       +++++pGiG k++e ++
  gi|336252995|ref|YP_004596102.1| 579 DLRSVPGIGEKTAETIK 595
                                       89***********9876 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.5   2.4e+03      40      62 ..     542     561 ..     526     563 .. 0.70
   2 ?   10.8   0.0    0.0003      0.49      44      64 ..     576     595 ..     568     599 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.5
                                       S-HHHHTTHCTTSTT--HHHHHH CS
                             HHH_8  40 eeitsleeeltklpgiGkkiaak 62 
                                       +e+++    l ++ g+G+ ++++
  gi|336252995|ref|YP_004596102.1| 542 DEVKT---VLDDVEGVGPETRKR 561
                                       44555...3788*****999876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0003
                                       HHTTHCTTSTT--HHHHHHHH CS
                             HHH_8  44 sleeeltklpgiGkkiaakie 64 
                                       sle+ l+++pgiG+k+a+ i+
  gi|336252995|ref|YP_004596102.1| 576 SLED-LRSVPGIGEKTAETIK 595
                                       4455.*************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4183.69
//
Query:       gi|336252996|ref|YP_004596103.1|  [L=256]
Description: hypothetical protein Halxa_1592 [Halopiger xanaduensis SH-6]
Scores for 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  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); 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:                         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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1809.20
//
Query:       gi|336252997|ref|YP_004596104.1|  [L=116]
Description: hypothetical protein Halxa_1593 [Halopiger xanaduensis SH-6]
Scores for 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:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 927.84
//
Query:       gi|336252998|ref|YP_004596105.1|  [L=314]
Description: ABC transporter-like protein [Halopiger xanaduensis SH-6]
Scores for 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  100.7   0.0    1.6e-28   99.9   0.0    1.4  1  ABC_tran     ABC transporter
    6.2e-10   39.4   0.1    8.7e-06   25.8   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.1e-09   37.9   0.0    7.1e-09   36.3   0.0    1.9  2  DUF4162      Domain of unknown function (DUF4162)
    6.5e-06   26.0   0.0    1.1e-05   25.2   0.0    1.3  1  AAA_30       AAA domain
     0.0021   17.1   0.0     0.0044   16.1   0.0    1.4  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.003   17.0   0.0       0.84    9.0   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0046   17.5   0.1     0.0082   16.7   0.1    1.3  1  AAA_23       AAA domain
     0.0095   15.8   0.0      0.016   15.2   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.026   14.3   0.0      0.052   13.3   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.047   14.1   0.1      0.086   13.2   0.0    1.5  2  AAA_16       AAA ATPase domain
      0.066   12.8   0.0       0.18   11.4   0.0    1.7  1  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 !   99.9   0.0     1e-31   1.6e-28       1     136 [.      23     161 ..      23     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1e-31
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+++s++++ege+ +++G+nGaGKSt +++++   +pt+G++++ g d +  + ++ r++ gvlp+  +  ++lt+r
  gi|336252998|ref|YP_004596105.1|  23 LEDLSFEVREGEVFGFLGPNGAGKSTTINVILDFIRPTAGRVEVLGMDAQA-NSREIRSRTGVLPEGVETYDRLTAR 98 
                                       689***********************************************9.89999******************** PP

                                       HH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++         +d+++e++l+++gl +  d+++      +S+G+ qr++la+al+ +p+ll+lDEp+
  gi|336252998|ref|YP_004596105.1|  99 QHlefaieskGADDDPETLLERVGLLDAIDKKA----GGYSKGMAQRLMLAMALVGEPDLLILDEPS 161
                                       ******999888899************888888....*****************************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 !   11.7   0.1    0.0001      0.16       2      26 ..      36      69 ..      35     113 .. 0.64
   2 !   25.8   0.0   5.3e-09   8.7e-06     238     297 ..     135     191 ..     100     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl.........d 26
                                       ++ GpNg+GKS+ +  +  + r          +
  gi|336252998|ref|YP_004596105.1| 36 FGFLGPNGAGKSTTINVILDFIRPtagrvevlgM 69
                                      5789***********9885544335555555554 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 5.3e-09
                            AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       S G+ + l l+ al   +   +ll++DEp +gL+P   r+  ++++e++++ga v++++H
  gi|336252998|ref|YP_004596105.1| 135 SKGMAQRLMLAMALVGEP---DLLILDEPSTGLDPNGAREMRDIVREENARGATVFFSSH 191
                                       777777755555555555...9***********************999999********* PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.3   5.3e+03      30      56 ..      89     120 ..      63     127 .. 0.61
   2 !   36.3   0.0   4.4e-12   7.1e-09       3      80 ..     217     305 ..     216     306 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.3
                                       -EEEE-TT..S-EEEEE-..-.---------- CS
                           DUF4162  30 veeveeeg..gelelkle..d.eeaanellka 56 
                                       ve+ ++ +  ++le+ +e  + ++++++ll++
  gi|336252998|ref|YP_004596105.1|  89 VETYDRLTarQHLEFAIEskGaDDDPETLLER 120
                                       55554444444566665543446666666665 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 4.4e-12
                                       HHHHHTTS.-SSEEEEE...-------.....---EEE..E-TT.S-EEEEE-------------.----EEEEEEE CS
                           DUF4162   3 leeiKrsy.gknrieve...adaeellee...pgveev..eeeg.gelelkledeeaanellkal.tsgveirsFee 68 
                                       +e +++s  g++ ++v+    d+e+l+++   p+v+ v  e e+  +++++++ + ++ ++l +l ++gve+r F+ 
  gi|336252998|ref|YP_004596105.1| 217 VEGLRDSVgGGTSLRVTvdrLDDEALQAVrslPDVSNVvvEGEDpPTITVQVQADGSKTAVLGELeDRGVEVRDFST 293
                                       67788899566666688766445555444555888888444444778******************77********** PP

                                       E---HHHHHHHH CS
                           DUF4162  69 eePsLndIFiek 80 
                                       +e+sL+d+F  +
  gi|336252998|ref|YP_004596105.1| 294 REASLEDVFQSY 305
                                       *********776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   6.8e-09   1.1e-05      20     121 ..      35     188 ..      28     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.8e-09
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Laeelgi...eastiakllkrlk........... 81 
                                       v    Gp G+GK+t+++++ + ++   grv +l   ++a  + ++  +g+     +t ++l+ r+            
  gi|336252998|ref|YP_004596105.1|  35 VFGFLGPNGAGKSTTINVILDFIRPTAGRVEVLGMDAQANSReIRSRTGVlpeGVETYDRLTARQHlefaieskgad 111
                                       66678*********************99*********998877******988889999999988889********** PP

                            AAA_30  82 .................................grarlepgtllivDEagmv....dtkqlaallkaaekagakvil 121
                                                                        ++a + + +lli DE +      +++++++++++ +++ga+v +
  gi|336252998|ref|YP_004596105.1| 112 ddpetllervglldaidkkaggyskgmaqrlmlAMALVGEPDLLILDEPSTGldpnGAREMRDIVREENARGATVFF 188
                                       ********************************976778888*******99988888999999999999999999987 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 !   16.1   0.0   2.7e-06    0.0044      11      68 ..      15      72 ..       4      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.7e-06
                                      -SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--- CS
                              MeaB 11 erpeakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPs 68
                                      + +ea+  le l+ +  + +v G+ G  GaGkst+++ +   +r    rv vl +D  
  gi|336252998|ref|YP_004596105.1| 15 QGSEATLALEDLSFEVREGEVFGFLGPNGAGKSTTINVILDFIRPTAGRVEVLGMDAQ 72
                                      5568888899999999999***********************************9975 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 !    6.0   0.0    0.0045       7.3      29      44 ..      38      53 ..      26      61 .. 0.85
   2 !    9.0   0.0   0.00052      0.84     137     212 ..     130     206 ..      78     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0045
                                      EEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 29 ivGpNGSGKsnlldAi 44
                                       +GpNG+GKs  ++ i
  gi|336252998|ref|YP_004596105.1| 38 FLGPNGAGKSTTINVI 53
                                      57********988776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00052
                                       S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvt 212
                                         gG  + +a  L++A+  v    l +lDe    LD +  +++ ++++e++ + a ++  s+  e++e +   vg+ 
  gi|336252998|ref|YP_004596105.1| 130 KAGGYSKGMAQRLMLAMALVGEPDLLILDEPSTGLDPNGAREMRDIVREENARgATVFFSSHIMEQVEAVCDRVGIL 206
                                       56888889999*************************************87766599999999999998887777765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1     5e-06    0.0082      12      39 ..      25      53 ..      16      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5e-06
                            AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAi 39
                                      d +++  +  ++ + GpNGaGK+T ++ i
  gi|336252998|ref|YP_004596105.1| 25 DLSFEVrEGEVFGFLGPNGAGKSTTINVI 53
                                      44444466689*************99877 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.6e-06     0.016      88     121 ..      21      55 ..       8      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.6e-06
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                        +le+l+ ++++ ++  ++G+ G+GKSt in++l 
  gi|336252998|ref|YP_004596105.1|  21 LALEDLSFEVREgEVFGFLGPNGAGKSTTINVILD 55 
                                       568899999988899****************9976 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   0.0   3.2e-05     0.052      17      40 ..      28      51 ..      21      64 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllD 40
                                      +e+++ +++ + Gp+G+GKST + 
  gi|336252998|ref|YP_004596105.1| 28 FEVREGEVFGFLGPNGAGKSTTIN 51
                                      55554448899**********885 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   5.3e-05     0.086      22     107 ..      33     132 ..      15     199 .. 0.70
   2 ?   -3.5   0.0       7.4   1.2e+04     144     160 ..     234     250 ..     230     256 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipy....sa.laqalareellrqlldeaes 91 
                                       g  e+  + G+ G GKs+ ++ +l+ ++ + g +  l  +++ ++++i+     ++  +++ +r +  + l+ + es
  gi|336252998|ref|YP_004596105.1|  33 G--EVFGFLGPNGAGKSTTINVILDFIRPTAGRVevLGMDAQANSREIRSrtgvLPeGVETYDRLTARQHLEFAIES 107
                                       4..566689***************99999955555455555555444322344467788888888888888888888 PP

                            AAA_16  92 aeleawrekleeala.........a 107
                                       + +++++e+l+e+++          
  gi|336252998|ref|YP_004596105.1| 108 KGADDDPETLLERVGlldaidkkaG 132
                                       9999999999998886554333330 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.4
                            AAA_16 144 lqwadeaslqllaaLlr 160
                                       ++++d++ lq+ ++L +
  gi|336252998|ref|YP_004596105.1| 234 VDRLDDEALQAVRSLPD 250
                                       57778888888777765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.18      19      49 ..      26      56 ..       9      60 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      l+f+  e ++   +GpN AGKst+++ i d+
  gi|336252998|ref|YP_004596105.1| 26 LSFEVREGEVFGFLGPNGAGKSTTINVILDF 56
                                      44444566666779************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2407.63
//
Query:       gi|336252999|ref|YP_004596106.1|  [L=336]
Description: ABC-2 type transporter [Halopiger xanaduensis SH-6]
Scores for 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-57  192.5  16.3    1.2e-56  192.2  16.3    1.1  1  ABC2_membrane_2  ABC-2 family transporter protein
    4.1e-08   32.7  18.1    4.1e-08   32.7  18.1    2.1  2  ABC2_membrane_3  ABC-2 family transporter protein
    3.5e-07   30.4  12.3    3.5e-07   30.4  12.3    1.9  2  ABC2_membrane_4  ABC-2 family transporter protein
    1.2e-06   28.2  14.1    1.2e-06   28.2  14.1    2.4  2  ABC2_membrane_5  ABC-2 family transporter protein
    0.00039   19.9  14.8    0.00039   19.9  14.8    1.6  2  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
       0.14   11.8   0.0       0.21   11.2   0.0    1.2  1  Thymidylate_kin  Thymidylate kinase


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 !  192.2  16.3   3.9e-60   1.2e-56       2     288 .]      38     336 .]      37     336 .] 0.96

  Alignments for each domain:
  == domain 1  score: 192.2 bits;  conditional E-value: 3.9e-60
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                       a+akk+frd++rs++f++l+++++ + v ++   ++ +++ ++a+a+ ea++ +                     vs
  gi|336252999|ref|YP_004596106.1|  38 AVAKKDFRDSIRSWVFWGLSIFFFTLLVSVTGAISYFGDEIAQAGATTEALVLF---------------------VS 93 
                                       89**********************999**************************7.....................33 PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgiv 155
                                       +i+ ++ip+ia+++g+++iagE+e+g++k+lLs+P+sR+++llgK++g++a+   + ++l++++ la ++++++  +
  gi|336252999|ref|YP_004596106.1|  94 QITRLVIPLIAIVLGWKSIAGERESGSIKILLSLPHSRKDVLLGKLLGRSAV---LSISLTIGFALAAVVVAVVLGS 167
                                       4***************************************************...********************** PP

                   ABC2_membrane_2 156 laledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp...... 226
                                       +++ d++ l++++++++l  +++++++ lSs +rs++ a a++ g+f++++++++ + +++  l++   ++      
  gi|336252999|ref|YP_004596106.1| 168 FDVVDYVSLLAMAIIYGL--AYTSITVSLSSMTRSTTLAGAAMAGVFLLFYLVWNALQSAFQLLMSRGLISgvsytr 242
                                       ******************..89**********************************99997777665555599999* PP

                   ABC2_membrane_2 227 .................qeindflsllsptsayntllneilagsdlna...............lgstatnllillll 271
                                                        + + +f+++++p++a++ ++  +++ ++ n                ++ ++++++illl+
  gi|336252999|ref|YP_004596106.1| 243 evtlldgsteqrtaerlPDWALFVDMIDPGNAFQNAITVLSSAGGSNLgtaypeyyfpdglpfYLENWFSFVILLLW 319
                                       ******************************************9987779**************************** PP

                   ABC2_membrane_2 272 lavllvlgyvlFkrkDl 288
                                       ++v++++++++F+r Dl
  gi|336252999|ref|YP_004596106.1| 320 IVVPIAIALYRFDRVDL 336
                                       **************997 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 ?   -4.0   4.3         2   5.8e+03     210     262 ..      52      74 ..      43     109 .. 0.47
   2 !   32.7  18.1   1.4e-11   4.1e-08     181     345 .]     107     329 ..      79     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2
                   ABC2_membrane_3 210 ilgdflvyllqlllilllafglgipfgnlglllllfllfglayialgyllssl 262
                                       +++ + +++++ll+                               ++ ++s++
  gi|336252999|ref|YP_004596106.1|  52 VFWGLSIFFFTLLVS------------------------------VTGAISYF 74 
                                       333333333333332..............................22222222 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 1.4e-11
                   ABC2_membrane_3 181 v...siveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll...afgl...gipfgnlglllllfllf 248
                                           si+ E+es+ ++++l+ + s+   +l+k+lg  +v  ++l + ++l   ++++   ++++ ++++ll + +++
  gi|336252999|ref|YP_004596106.1| 107 LgwkSIAGERESGSIKILLSLPHSRKDVLLGKLLGRSAVLSISLTIGFALaavVVAVvlgSFDVVDYVSLLAMAIIY 183
                                       234489**************************************998886444333355578888************ PP

                   ABC2_membrane_3 249 glayialgyllsslfknsetaqilifivilllsgffgglfp..........ledlp.................salk 298
                                       glay++++  lss++++++ a +++  v+ll+ +++ +l +          ++ ++                 + l 
  gi|336252999|ref|YP_004596106.1| 184 GLAYTSITVSLSSMTRSTTLAGAAMAGVFLLFYLVWNALQSafqllmsrglISGVSytrevtlldgsteqrtaERLP 260
                                       ******************88888888888855555444422211111123333333666777777878888887777 PP

                   ABC2_membrane_3 299 wifsiiPffapglgllrli........tgdplwe...................illsliilalfavvylllall 345
                                        ++ ++ +  pg+++ + i        +     +                    + s++il+l +vv +++al+
  gi|336252999|ref|YP_004596106.1| 261 DWALFVDMIDPGNAFQNAItvlssaggS-----NlgtaypeyyfpdglpfyleNWFSFVILLLWIVVPIAIALY 329
                                       7888887777777777777555465440.....144566678888999999999*************9999986 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 !   30.4  12.3   1.2e-10   3.5e-07      17     172 ..      58     209 ..      49     235 .. 0.74
   2 ?   -0.8   0.1      0.42   1.3e+03     138     158 ..     307     328 ..     290     333 .. 0.65

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.2e-10
                   ABC2_membrane_4  17 llvlaallvpllallyf.nllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrt 92 
                                       ++++ +l+ +  a+ yf   +++ g+ ++ ++++ ++  t  l++pli ++++  +i  E++++ +k Ll +P sr+
  gi|336252999|ref|YP_004596106.1|  58 IFFFTLLVSVTGAISYFgDEIAQAGATTEALVLFVSQI-T-RLVIPLIAIVLGWKSIAGERESGSIKILLSLPHSRK 132
                                       55666666666677788556788888888888875544.3.479********************************* PP

                   ABC2_membrane_4  93 klllaKliv.llllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvllkksy.vl 167
                                        +ll+Kl+   ++ls+ l++ ++l++v++a+++g++  +v   ++ll + +++gl  + +++    l+++++s  ++
  gi|336252999|ref|YP_004596106.1| 133 DVLLGKLLGrSAVLSISLTIGFALAAVVVAVVLGSF--DVVDYVSLLAMAIIYGLAYTSITV---SLSSMTRSTtLA 204
                                       ******986257788888888889999999999965..556777888877777775544333...344444443133 PP

                   ABC2_membrane_4 168 plilt 172
                                       + +++
  gi|336252999|ref|YP_004596106.1| 205 GAAMA 209
                                       33333 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.42
                   ABC2_membrane_4 138 lkkclelgllvffavlpi.ial 158
                                       l  ++ +++l++ +v+pi ial
  gi|336252999|ref|YP_004596106.1| 307 LENWFSFVILLLWIVVPIaIAL 328
                                       4455556666666666653444 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 !   28.2  14.1     4e-10   1.2e-06      42     166 ..      98     223 ..      41     242 .. 0.79
   2 ?   -1.7   0.6       0.6   1.8e+03     180     193 ..     310     323 ..     302     331 .. 0.49

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 4e-10
                   ABC2_membrane_5  42 ilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitllll.iiavlikgnvtisevl 117
                                       +++++i+i+l  ++++ ++ s++ k+ll+LP +rk++   K l+   +  i++ i+++l+ +++ ++ g++++ + +
  gi|336252999|ref|YP_004596106.1|  98 LVIPLIAIVLGWKSIAGERESGSIKILLSLPHSRKDVLLGKLLGRSAVLSISLTIGFALAaVVVAVVLGSFDVVDYV 174
                                       345667777788*******************************987777777777777761568899999******* PP

                   ABC2_membrane_5 118 lsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaifs 166
                                         ++++++++l++++i+  l  ++   +   ++++ +f++++l+ + ++
  gi|336252999|ref|YP_004596106.1| 175 SLLAMAIIYGLAYTSITVSLSSMTRSTTLAGAAMAGVFLLFYLVWNALQ 223
                                       ******************9999999666666666666666555554444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.6
                   ABC2_membrane_5 180 yilliillviilll 193
                                       +++++ill+ i++ 
  gi|336252999|ref|YP_004596106.1| 310 WFSFVILLLWIVVP 323
                                       44444443333332 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9  14.8   1.3e-07   0.00039       3     174 ..      36     217 ..      34     239 .. 0.78
   2 ?   -3.9   0.9       2.4   7.3e+03     193     200 ..     312     319 ..     297     329 .. 0.43

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.3e-07
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgn...lgnsedglnrpgllffsvlflafsaltsv..... 71 
                                       ++a+ k++f+  +r+++   l+ ++++ll+++     +++   +  ++++ +++ +lf s ++  ++ l+++     
  gi|336252999|ref|YP_004596106.1|  36 VRAVAKKDFRDSIRSWVFWGLSIFFFTLLVSVTGAISYFGdeiA--QAGATTEALVLFVSQITRLVIPLIAIvlgwk 110
                                       78999***********9999999999999999999999964431..4444444444444444444444444311111 PP

                     ABC2_membrane  72 apvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrf.....flflllllltala 143
                                       ++  ere g+++ +l+ p  s+++++l+k+l+  +v  +  +i ++++ ++v + l +f     + +l+++++++la
  gi|336252999|ref|YP_004596106.1| 111 SIAGERESGSIKILLSLPH-SRKDVLLGKLLGRSAVLSISLTIGFALAAVVVAVVLGSFdvvdyVSLLAMAIIYGLA 186
                                       3899***************.***********998888888888777777777555542233356999********** PP

                     ABC2_membrane 144 asslgllisalapsfedasqlaslvllplll 174
                                        +s+ + +s++++s   a+  +  v+l++ l
  gi|336252999|ref|YP_004596106.1| 187 YTSITVSLSSMTRSTTLAGAAMAGVFLLFYL 217
                                       **************************99987 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.4
                     ABC2_membrane 193 aylnPlty 200
                                       + +  l +
  gi|336252999|ref|YP_004596106.1| 312 SFVILLLW 319
                                       11111111 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.1e-05      0.21      71     131 ..     216     274 ..     190     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.1e-05
                                       HHHHHHHHTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEE.SSHHHH CS
                   Thymidylate_kin  71 ekikpalkqgktvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflld.vdpeva 131
                                        +++ al++ + + ++R l+S++ Y+     +d +  ++  e     Pd+ +++d +dp +a
  gi|336252999|ref|YP_004596106.1| 216 YLVWNALQSAFQLLMSRGLISGVSYTREVTLLDGSTEQRTAER---LPDWALFVDmIDPGNA 274
                                       47899**********************8777777777777777...79******97787666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1133  (0.0631937); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2192.38
//
Query:       gi|336253000|ref|YP_004596107.1|  [L=695]
Description: DNA ligase [Halopiger xanaduensis SH-6]
Scores for 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-107  358.6   0.0     4e-107  358.0   0.0    1.3  1  DNA_ligase_aden  NAD-dependent DNA ligase adenylation domain
    3.9e-30  103.6   2.9    3.9e-30  103.6   2.9    2.1  2  DNA_ligase_OB    NAD-dependent DNA ligase OB-fold domain
    2.6e-20   72.3   0.5    2.7e-19   69.0   0.1    2.5  2  HHH_2            Helix-hairpin-helix motif
    3.1e-16   59.7   0.0      3e-07   31.0   0.1    2.6  2  HHH_5            Helix-hairpin-helix domain
    4.2e-13   49.5   0.0    7.8e-13   48.6   0.0    1.5  1  BRCT             BRCA1 C Terminus (BRCT) domain
    1.7e-05   24.7   1.8    1.7e-05   24.7   1.8    3.0  3  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
    0.00042   20.0   0.3        2.7    8.0   0.0    4.4  4  HHH              Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.011   16.3   0.0      0.082   13.5   0.0    2.4  2  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold
      0.014   15.7   0.0         13    6.2   0.0    3.6  2  HHH_8            Helix-hairpin-helix domain
      0.069   12.7   0.1       0.13   11.8   0.1    1.3  1  E1-E2_ATPase     E1-E2 ATPase
       0.17   11.8   0.7          4    7.3   0.3    2.9  3  YebG             YebG protein


Domain annotation for each model (and alignments):
>> DNA_ligase_aden  NAD-dependent DNA ligase adenylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  358.0   0.0  2.5e-110    4e-107       2     318 .]      32     340 ..      31     340 .. 0.98

  Alignments for each domain:
  == domain 1  score: 358.0 bits;  conditional E-value: 2.5e-110
                                       HHHHHHHHHHHHHHHHHHHHHCTT-SSC-HCHHHHHHHHHHHHHHHSGGG--TTSCCG-SSSS--CTS-EEE-SS-- CS
                   DNA_ligase_aden   2 eakkeleelrellrkydyeYyvldePlvsDaeyDrllkelkelEekfPelitpdSPtqrvgaeleaefkkveHeapl 78 
                                       ea+++++ lre +r++d +Yyv+++P+v D  yD+l+++l++lE++f +l +pdSPt+ vg e+   f++veH ap+
  gi|336253000|ref|YP_004596107.1|  32 EAREQIALLREAIREHDRRYYVENDPIVADRAYDALFTRLQALEDEF-DLSHPDSPTRSVGGEPIEGFDTVEHVAPM 107
                                       678999****************************************9.9************999999********** PP

                                       ---EEE-SHHHHHHHHHHHHHHSSS--S-EEEEEEEESSEEEEEEEETTEEEEEEE-TTSSEEEB-HHHHCT-TTS- CS
                   DNA_ligase_aden  79 lSLdnafdedelkaflerieealgnkekvayvvelKiDGlavsllYengvlvraatRGdGttGedvtaNvktiksiP 155
                                       lS+dn+ d++++++f++r+++++g+     yv+e+K DG+++ ++Ye+g l+ra+tRGdG++G+dvt+N++ti s+P
  gi|336253000|ref|YP_004596107.1| 108 LSIDNSGDAADVREFDDRVRREVGEVD---YVCEPKFDGVSMEFVYEDGRLERAVTRGDGREGDDVTRNARTIGSVP 181
                                       *********************998766...9********************************************** PP

                                       SB-SSSS--SEEEEEEEEE--HHHHHHHHHHHHHCT----SSHHHHHHHHHT-SSHHHHHTS--EEEEEEEEEEESS CS
                   DNA_ligase_aden 156 lklkvdnlpeelevRGEvylrkedFeklNeerleegeklfaNpRNaAaGslRqldpkitakrkLkliayglglveke 232
                                       ++l+ d  p  l vRGEvy++k++F++ N+er+e+ge +faNpRNa aG++Rqldp ++a+r+L+++++++   e++
  gi|336253000|ref|YP_004596107.1| 182 QRLHGD-YPDFLAVRGEVYMPKDAFQAHNRERIERGEDPFANPRNATAGTIRQLDPSVVAERPLEVFFFDVL--EAT 255
                                       *****8.****************************************************************9..677 PP

                                       ---.SBHHHHHHHHHHCT--B-TT-EEECSHHHHHHHHHHHHHHGGGSSS-EEEEEEEESBHHHHHHH-EETSCESS CS
                   DNA_ligase_aden 233 elevktqsealkvlkklglkvseelklvksieevleyieelekkRdeleyeiDGvVvkvdelalqeeLGftakaPrw 309
                                       +le +++ + l+ + ++gl+v++++++vk+i+e ++y +++ + Rd+l+yeiDGvV+kvd+++ +eeLG ta++ r+
  gi|336253000|ref|YP_004596107.1| 256 DLE-DSHRDELERFPDWGLRVNDRVEVVKDIDEAIDYRDRMLEVRDDLNYEIDGVVIKVDDRDAREELGRTARHDRY 331
                                       788.9************************************************************************ PP

                                       EEEEE---C CS
                   DNA_ligase_aden 310 AiAyKfpae 318
                                       A AyKfpa+
  gi|336253000|ref|YP_004596107.1| 332 AYAYKFPAR 340
                                       *******96 PP

>> DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         3   4.9e+03      46      59 ..     270     283 ..     264     286 .. 0.81
   2 !  103.6   2.9   2.4e-33   3.9e-30       2      75 ..     344     417 ..     343     420 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3
                                       XXXXXXXXXXXXXX CS
                     DNA_ligase_OB  46 rkdirigdtVvvek 59 
                                       ++++r++d+V v k
  gi|336253000|ref|YP_004596107.1| 270 DWGLRVNDRVEVVK 283
                                       6799******9977 PP

  == domain 2  score: 103.6 bits;  conditional E-value: 2.4e-33
                                       --XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     DNA_ligase_OB   2 tkledievqVGRtGaltpvAeLepvelaGttVsratLhnedeierkdirigdtVvvekaGdvIPevvgvvlekr 75 
                                       t + di vqVGRtG++tpvA Lepv+++G+tVsra+Lhn +eie k++++gdtV v++aGdvIP v +vv+++ 
  gi|336253000|ref|YP_004596107.1| 344 TPIADIAVQVGRTGRVTPVALLEPVDVGGVTVSRASLHNPEEIEAKNVNVGDTVRVQRAGDVIPYVAEVVEKSS 417
                                       7899*****************************************************************99876 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.34   5.6e+02      12      52 ..     472     514 ..     465     520 .. 0.75
   2 !   69.0   0.1   1.7e-22   2.7e-19       2      63 ..     528     592 ..     527     593 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.34
                             HHH_2  12 GektAklLakr..FksldaLkkasleeLlevddiGeeiAqsiv 52 
                                       Gek  ++L+ +   +s+  L + + e+L+ +++ Ge+  ++ v
  gi|336253000|ref|YP_004596107.1| 472 GEKSVRQLVDAglLESVADLYELEREDLTDLEGWGETSTENLV 514
                                       555566664433368999999999*********9998877765 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 1.7e-22
                             HHH_2   2 llfaLGIrhVGektAklLakrFksldaLkkasl...eeLlevddiGeeiAqsivefFeneknrel 63 
                                       +l+aLGI+hVG +tA++La++F++++a ++a +   e L +vdd+Ge++A++i+efF++e+n e 
  gi|336253000|ref|YP_004596107.1| 528 FLSALGIPHVGPTTARELAREFGTFEAVREAAVtdpEHLETVDDVGETVAAQIHEFFTSEANAEA 592
                                       899***************************96533389***********************9986 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1   1.8e-10     3e-07       3      55 ..     464     517 ..     462     519 .. 0.94
   2 !   26.0   0.0   6.6e-09   1.1e-05       1      53 [.     528     582 ..     528     584 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.8e-10
                                       HHHTSTT--HHHHHHHHTTT.--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsaG.iesvedlaaadveeLakipGiGkktAeriilel 55 
                                       + l+++G+G+k ++ l++aG  esv+dl ++++e+L+++ G G+   e++++e+
  gi|336253000|ref|YP_004596107.1| 464 DGLDLEGLGEKSVRQLVDAGlLESVADLYELEREDLTDLEGWGETSTENLVEEI 517
                                       6689***************9899*****************************97 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 6.6e-09
                                       -HHHHTSTT--HHHHHHHHTTT--SHHHHHHS...-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5   1 feeLlsvsGiGpktAlallsaGiesvedlaaa...dveeLakipGiGkktAeriil 53 
                                       f + l+++ +Gp tA+ l++  ++++e++ +a   d+e L ++ ++G+  A +i +
  gi|336253000|ref|YP_004596107.1| 528 FLSALGIPHVGPTTARELARE-FGTFEAVREAavtDPEHLETVDDVGETVAAQIHE 582
                                       67789****************.*******9986778999************99976 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   4.8e-16   7.8e-13       6      79 .]     613     685 ..     608     685 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 4.8e-16
                                       TTTEEEEEEESTSSHHHHHHHHHHHHTTCEEESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEETHHHHHHH CS
                              BRCT   6 fhgckfvitgvldnftrdeleelikehGGkvttevskktthlvvgepesrslkylealklnipivheewlldci 79 
                                       ++g++fv+tg+l+++tr e++e+++ hG+  t++vs +t++lvvge+  +++k   a ++ +piv+ +++ +++
  gi|336253000|ref|YP_004596107.1| 613 LEGLTFVFTGSLEGMTRGEAQETVEAHGANATSSVSGNTDYLVVGEN-PGQTKRDDAEANDVPIVDADEFRELL 685
                                       89*********************************************.*********************99875 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 ?    0.7   1.2      0.34   5.6e+02       9      20 ..     126     137 ..     124     138 .. 0.88
   2 ?   -2.2   0.1       2.7   4.3e+03       8      19 ..     280     292 ..     280     292 .. 0.86
   3 !   24.7   1.8   1.1e-08   1.7e-05       1      27 []     426     451 ..     426     451 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.34
                    DNA_ligase_ZBD   9 vvReegeaiyRC 20 
                                       v Re ge++y C
  gi|336253000|ref|YP_004596107.1| 126 VRREVGEVDYVC 137
                                       67999*****99 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.7
                    DNA_ligase_ZBD   8 avvReegeai.yR 19 
                                       +vv+  +eai yR
  gi|336253000|ref|YP_004596107.1| 280 EVVKDIDEAIdYR 292
                                       589999***9887 PP

  == domain 3  score: 24.7 bits;  conditional E-value: 1.1e-08
                    DNA_ligase_ZBD   1 hCPvCGsavvReegeaiyRCtn.lsCpA 27 
                                       hCPvC+sa++R  ++ i++Ct+ l C A
  gi|336253000|ref|YP_004596107.1| 426 HCPVCDSAIER--DGPIAFCTGgLACDA 451
                                       9********98..78******77***87 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.1   1.8e+03      15      27 ..     467     479 ..     466     482 .. 0.80
   2 ?    4.7   0.1     0.018        30      10      22 ..     496     508 ..     493     511 .. 0.92
   3 ?    1.1   0.0      0.26   4.2e+02      16      27 ..     534     545 ..     532     547 .. 0.80
   4 !    8.0   0.0    0.0016       2.7       9      30 .]     562     583 ..     557     583 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.1
                                       TSTT-SHHHHHHH CS
                               HHH  15 alPGVGpktAeaI 27 
                                       +l+G G+k  ++ 
  gi|336253000|ref|YP_004596107.1| 467 DLEGLGEKSVRQL 479
                                       79******98765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.018
                                       HHHHHTSTT-SHH CS
                               HHH  10 reeLlalPGVGpk 22 
                                       re+L++l+G+G+ 
  gi|336253000|ref|YP_004596107.1| 496 REDLTDLEGWGET 508
                                       79*********85 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.26
                                       STT-SHHHHHHH CS
                               HHH  16 lPGVGpktAeaI 27 
                                       +P VGp tA+  
  gi|336253000|ref|YP_004596107.1| 534 IPHVGPTTAREL 545
                                       666******975 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0016
                                       SHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   9 sreeLlalPGVGpktAeaIlsy 30 
                                       ++e L+++  VG+ +A +I+++
  gi|336253000|ref|YP_004596107.1| 562 DPEHLETVDDVGETVAAQIHEF 583
                                       67889**************997 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 ?   -1.3   0.0         2   3.3e+03      23      46 ..     468     493 ..     461     521 .. 0.55
   2 ?   13.5   0.0     5e-05     0.082      22      49 ..     533     564 ..     530     612 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2
                        5_3_exonuc  23 vpgiGektAakLlke..ygsleeile 46 
                                        +g Gek   +L+     +s+++++e
  gi|336253000|ref|YP_004596107.1| 468 LEGLGEKSVRQLVDAglLESVADLYE 493
                                       67888988888886522355555555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5e-05
                        5_3_exonuc  22 GvpgiGektAakLlkeygsleeilenl....d 49 
                                       G+p +G+ tA +L +e+g+ e++ e++    +
  gi|336253000|ref|YP_004596107.1| 533 GIPHVGPTTARELAREFGTFEAVREAAvtdpE 564
                                       9***********************97633221 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.03        48       6      62 ..     483     544 ..     477     549 .. 0.59
   2 ?    6.2   0.0    0.0081        13      41      67 ..     559     584 ..     551     585 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.03
                                       HHHHHHHHHHHHCT--.....CCCHHHHHHHHCCCCC-SS.-HHHHTTHCTTSTT--HHHHHH CS
                             HHH_8   6 daLeeladllelkged.....pfrvraYrrAaraiealpe.eitsleeeltklpgiGkkiaak 62 
                                        +Le  adl+el++ed      +   +  + ++ iea  e ++ +    +  +p++G+ +a++
  gi|336253000|ref|YP_004596107.1| 483 GLLESVADLYELEREDltdleGWGETSTENLVEEIEASREpPLPDFLS-ALGIPHVGPTTARE 544
                                       567778888888776533333455555555555555555555555543.57777777777765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0081
                                       -HHHHTTHCTTSTT--HHHHHHHHHHH CS
                             HHH_8  41 eitsleeeltklpgiGkkiaakieeil 67 
                                       ++t+ e +l+ ++ +G+ +aa+i+e+ 
  gi|336253000|ref|YP_004596107.1| 559 AVTDPE-HLETVDDVGETVAAQIHEFF 584
                                       566644.599***************96 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   7.9e-05      0.13      14      48 ..     382     417 ..     372     421 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.9e-05
                                       S-EEEEGGG--TTSEEEEET.T-B--SEEEEEEE-S CS
                      E1-E2_ATPase  14 teeeidakelvpGDivllka.gdrvpaDgrivegsa 48 
                                       + eei+ak++++GD v ++  gd++p  +++ve s+
  gi|336253000|ref|YP_004596107.1| 382 NPEEIEAKNVNVGDTVRVQRaGDVIPYVAEVVEKSS 417
                                       5689*************9755******999999876 PP

>> YebG  YebG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3    0.0025         4      26      57 ..     290     322 ..     280     328 .. 0.84
   2 ?    0.8   0.0      0.28   4.5e+02      18      34 ..     583     599 ..     574     603 .. 0.88
   3 ?   -2.8   0.0       3.6   5.8e+03      21      45 ..     664     688 ..     657     691 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHHHHHHHHHHHHSTT--HHHH.HHH CS
                              YebG  26 DayDkmLdladeLaelLeqselgldeeqa.Eel 57 
                                       D +D+mL++ d L+  ++  ++++d+++a Eel
  gi|336253000|ref|YP_004596107.1| 290 DYRDRMLEVRDDLNYEIDGVVIKVDDRDArEEL 322
                                       889********************9997542665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.28
                                       XXXHHHHHHHHHHHHHH CS
                              YebG  18 tftsKkeADayDkmLdl 34 
                                        fts ++A+a D +L+ 
  gi|336253000|ref|YP_004596107.1| 583 FFTSEANAEAVDAILEH 599
                                       69*************96 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YebG  21 sKkeADayDkmLdladeLaelLeqs 45 
                                        + +A+a D     ade++elL+++
  gi|336253000|ref|YP_004596107.1| 664 KRDDAEANDVPIVDADEFRELLAER 688
                                       5678888888888899999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (695 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.62u 0.24s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 5136.48
//
Query:       gi|336253001|ref|YP_004596108.1|  [L=125]
Description: ferredoxin [Halopiger xanaduensis SH-6]
Scores for 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-11   43.1   0.5    1.7e-10   40.7   0.5    1.9  1  Fer2      2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.5   9.4e-15   1.7e-10       4      76 ..      14     102 ..      12     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 9.4e-15
                                       TTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE.CTT.SSSSTHHHHHTTEE......... CS
                              Fer2   4 dgkevevevadgettlldaaeenggidipysCggggCgtClvevlegev.qsd.etelegeeldegkl......... 69 
                                       d++++++ v ++et +l+ ae++ ++++p++C+ g+CgtC+ ++l+         t  e    de++          
  gi|336253001|ref|YP_004596108.1|  14 DRERRTIAVRADET-VLEGAERA-DVALPFGCRTGACGTCTGRLLSVGGtD-AtGTNSEPTTVDEAFDyrrppralk 87 
                                       678999*9*99**9.*******9.*******************99644432.2333444333333333456666666 PP

                                       ........EEGGGSE CS
                              Fer2  70 ........rlaCqti 76 
                                               +l C + 
  gi|336253001|ref|YP_004596108.1|  88 drhraagyVLLCIAA 102
                                       666666666777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.39u 0.19s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1041.52
//
Query:       gi|336253002|ref|YP_004596109.1|  [L=469]
Description: selenium-binding protein [Halopiger xanaduensis SH-6]
Scores for complete 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-197  657.2   0.1   1.5e-197  657.0   0.1    1.0  1  SBP56      56kDa selenium binding protein (SBP56)
  ------ inclusion threshold ------
      0.036   13.3   0.0       0.19   11.0   0.0    2.0  2  Lactonase  Lactonase, 7-bladed beta-propeller


Domain annotation for each model (and alignments):
>> SBP56  56kDa selenium binding protein (SBP56)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  657.0   0.1  1.6e-201  1.5e-197       2     453 ..      24     468 ..      23     469 .] 0.98

  Alignments for each domain:
  == domain 1  score: 657.0 bits;  conditional E-value: 1.6e-201
                             SBP56   2 kadPgyasPkeai.kapreklayvaaleanteiekpDalavvdvdpesetyskvvhrvelpnlgdelhhfGWnaCss 77 
                                       +++Pgya+P++ai +++reklayv++l+++t++++pD++avvd+dp+s+ty+++v+r+elpn+gdelhhfGWnaCss
  gi|336253002|ref|YP_004596109.1|  24 HEGPGYATPQAAIeEGEREKLAYVMSLYVGTDVDAPDFVAVVDLDPDSDTYCEIVDRIELPNRGDELHHFGWNACSS 100
                                       689**********99************************************************************99 PP

                             SBP56  78 .chaedaskerrylivPglrssriyvvdtktdprkpklvkviepeevaektglsrphtvhClpegeilisalgdaeG 153
                                        ch   +  err+livPg rssri+v+d   d+r+p+l  viepeev+e  +ls+phtvhC+p+geilis+lgda+G
  gi|336253002|ref|YP_004596109.1| 101 sCH--MEGLERRHLIVPGQRSSRIHVIDAA-DRRNPELETVIEPEEVFE-YDLSAPHTVHCIPDGEILISMLGDADG 173
                                       687..55679******************98.*****************9.6************************** PP

                             SBP56 154 egkggillldketfevkgrWekdrekqelaYDfwyqlrkdvmvsseWgaPkafekGldledleegkyGkrlhvwdle 230
                                       + +gg+l l+++ fe+ grWe ++e  e++YD+wyq+r++vmvsseW+aPk++  G+dled+eeg+yG+rlh+wd+e
  gi|336253002|ref|YP_004596109.1| 174 DLPGGFLELNDD-FEIEGRWEPPGE-IEMNYDYWYQPRQNVMVSSEWAAPKTYYPGFDLEDVEEGNYGHRLHFWDWE 248
                                       ************.********9987.89************************************************* PP

                             SBP56 231 erkllqtidlgeegqlvlevrflhdPkkaegfvgvvLsssvfrfykeedekweaekvieipakkvegeelpelpglv 307
                                       e++++qtidlgeeg ++levrflh+P++++gfvg++Lss++f+f+++  ++++aekvi+++++++  +++p  p+l 
  gi|336253002|ref|YP_004596109.1| 249 EGTVEQTIDLGEEGLIPLEVRFLHTPESTHGFVGAALSSNIFHFWRDRTGEYRAEKVIDFEDREHPDWDMPV-PALP 324
                                       ********************************************************************9997.**** PP

                             SBP56 308 tDillslDDrflyvsnWltGdlrqydisdpkkPkltgqvrlGGiirkaehpavkgrkleggPqmvelslDGkrlYvt 384
                                       tDil+s+DDr+l+ snWl+Gd+++ydisdp++P++++++++GG++ +   ++v+gr+l++gPqm++lslDGkrlY+t
  gi|336253002|ref|YP_004596109.1| 325 TDILISMDDRYLFGSNWLHGDVWMYDISDPANPRRADSLSVGGTFGDV--QEVQGRELSAGPQMIQLSLDGKRLYWT 399
                                       ********************************************9866..789************************ PP

                             SBP56 385 nsLysawddqfypelvkkgsvllkidvdtekGglsldknflvdfgkepegparahevryegGDassDiy 453
                                       +sL+s+wd+qfyp++ ++gsv+lk+dvd+++G+++ld++flvd+g+ p+gparahe+r+++GD++sD++
  gi|336253002|ref|YP_004596109.1| 400 TSLFSSWDEQFYPQEGERGSVMLKADVDPRNGTMELDEDFLVDWGECPDGPARAHEIRWPDGDCTSDVW 468
                                       ********************************************************************* PP

>> Lactonase  Lactonase, 7-bladed beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.11   9.5e+02      88     158 ..     101     165 ..      96     170 .. 0.57
   2 ?   11.0   0.0   2.1e-05      0.19     200     291 ..     274     368 ..     269     372 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.11
                                       EEEEEE-TTSSEEEEEETTTTEEEEEEB.TTSEBESECEEEE.....SSTTT-SSTTEEEEEE-TTSSEEE CS
                         Lactonase  88 pchlsvdedgkllavAnYsggsvsvfpldadgslkeasqvlkhegsgpnperqesphaHsvvldpdgkfll 158
                                       +ch+++  ++++l+v    +++++v++ ++  +++ ++ v+  e + +   + + + +H v+  pdg+ l+
  gi|336253002|ref|YP_004596109.1| 101 SCHMEG-LERRHLIVPGQRSSRIHVIDAADRRNPELET-VI--EPEEVF--EYDLSAPHTVHCIPDGEILI 165
                                       566665.3344455555566677776666555555553.33..222232..35677888888888887665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.1e-05
                                       TTSSEEEEEETTTTEEEEEEEE-TTTEEEEEEEEESS-TSS-S-.....--EEEEEE-TTSSEEEEEETSSTEEEEE CS
                         Lactonase 200 pdgkiaYvvnELsstvsvfsydeatgaleelqtvstlpegftgk.....nsaaeIrlspdgkflyvSnRgadsiavf 271
                                       p+ ++ +v   Lss++  f  d  tg+ +  + ++    ++ +      + + +I +s d+++l+ Sn ++  ++++
  gi|336253002|ref|YP_004596109.1| 274 PESTHGFVGAALSSNIFHFWRD-RTGEYRAEKVIDFEDREHPDWdmpvpALPTDILISMDDRYLFGSNWLHGDVWMY 349
                                       5667778888888888888777.677555555444443322222223437899************************ PP

                                       EE-TTT--EEEEEEEE-SSS CS
                         Lactonase 272 avdeadgtltlveevstegk 291
                                       ++ ++  + +  +  s++g+
  gi|336253002|ref|YP_004596109.1| 350 DI-SDPANPRRADSLSVGGT 368
                                       **.66678888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.36
# Mc/sec: 3856.93
//
Query:       gi|336253003|ref|YP_004596110.1|  [L=140]
Description: ferredoxin [Halopiger xanaduensis SH-6]
Scores for 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   46.1   1.1      3e-11   43.1   1.1    2.1  1  Fer2      2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.016   15.2   0.1      0.037   14.1   0.1    1.6  1  Fer2_4    2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   1.1   3.3e-15     3e-11       4      56 ..      11      65 ..       9     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 3.3e-15
                                      TTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE..CTT..S CS
                              Fer2  4 dgkevevevadgettlldaaeenggidipysCggggCgtClvevlegev..qsd..e 56
                                      dg++ ++++++ e+ +ldaa+++ g+ +py+C+ g+C tC+ ++le +   +++   
  gi|336253003|ref|YP_004596110.1| 11 DGRTETIDAPESES-VLDAAQRA-GVRLPYDCRKGTCITCVGRLLEVDGegEREatD 65
                                      89************.*******9.*********************877744322222 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 ?   14.1   0.1   4.1e-06     0.037      12      63 ..      16      60 ..       5      68 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-06
                            Fer2_4 12 evtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepn 63
                                      ++ +pe ++v++A++++gv++p  c +g           C   l ev+ge+ 
  gi|336253003|ref|YP_004596110.1| 16 TIDAPESESVLDAAQRAGVRLPYDCRKG-------TCITCVGRLLEVDGEGE 60
                                      6889******************999983.......33334444566666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1090.55
//
Query:       gi|336253004|ref|YP_004596111.1|  [L=487]
Description: Na+/H+ antiporter NhaC [Halopiger xanaduensis SH-6]
Scores for complete 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-59  201.9  37.3    1.6e-52  178.6  19.4    2.1  2  Na_H_antiporter  Na+/H+ antiporter family
  ------ inclusion threshold ------
      0.062   13.6  10.7       0.16   12.3   1.0    3.3  2  Gate             Nucleoside recognition


Domain annotation for each model (and alignments):
>> Na_H_antiporter  Na+/H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   9.9   1.9e-13   1.7e-09     131     264 ..      55     186 ..      24     186 .. 0.84
   2 !  178.6  19.4   1.8e-56   1.6e-52       1     303 []     172     464 ..     172     464 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.9e-13
                   Na_H_antiporter 131 alaglivatllelaslseidkllnrGiksmlgaililllAwgiggvlealgvteslvsslakgvvskgllplilflv 207
                                       a+agl   +  ++ +++++ + + r i + l+ailil++ + +     + g + sl+   ++++ ++ +lp+ ++++
  gi|336253004|ref|YP_004596111.1|  55 AFAGLFGRYYFGY-DWDQLYDGIGRSILMGLQAILILFVIYMLIASWIDSGTIPSLMYYGLEFLSPQIFLPF-TIII 129
                                       4555555555565.777788888888889999*******9999999999999*****999999988888887.5677 PP

                   Na_H_antiporter 208 allvafatGtswgtigIilpiavplaaklgisllalvraveaggtlgdhlsPisdtt 264
                                       +++vafa+G+sw t g ++  ++ ++a lgi ++ +++av++g+  gd  sP+sdtt
  gi|336253004|ref|YP_004596111.1| 130 SAVVAFAIGSSWTTAGTLGVAMIGIGAGLGIPEPMTAGAVLSGAYTGDKNSPLSDTT 186
                                       889*****************************************************8 PP

  == domain 2  score: 178.6 bits;  conditional E-value: 1.8e-56
                   Na_H_antiporter   1 vavfgdkssplsdtvgliagilktdlieeiaalgmlvqsipanvysifallvvglvvl...llrdigamlraeaear 74 
                                       +a+ gdk splsdt++l+a++++tdl+++i+a  m   + +a+ +s+++++++gl +     ++ i ++++ + +++
  gi|336253004|ref|YP_004596111.1| 172 GAYTGDKNSPLSDTTNLAAAVTNTDLMDHIRA--MRPGTAIAFAISLLLFVLLGLNASgtiPADRIAEIQGGLSSSY 246
                                       6999***************************4..************************8888889999999999998 PP

                   Na_H_antiporter  75 eleekeltklpiavliiltlskmpytgalalvaivkafivalafqntdvatalvvgalaglivatllelaslseidk 151
                                        +++ +++  p++ +++l++ + p++++l +++++ ++ + +++q+  +a+a+      g+  +t++ l     +d+
  gi|336253004|ref|YP_004596111.1| 247 AISPITFL--PLVLTFALAFYGLPALPSLGAGIFA-GVGITTVVQGKGFAAAWS-VVHYGTEPETGVDL-----TDE 314
                                       99888888..********************99999.******************.88899*********.....*** PP

                   Na_H_antiporter 152 llnrG.iksmlgaililllAwgiggvlealgvteslvsslakgvvskgllplilflvallvafatGtswgtigIilp 227
                                       ll  G +++ +++++i+++A+++gg+l+++gv++++  ++ +++ s++ l++ + + + +++f+ ++++++i+++++
  gi|336253004|ref|YP_004596111.1| 315 LLASGgLEGSIWVVTIVVAALALGGILQETGVLAAIAYHIGRAISSVFGLTFGTAVGTVAMNFFSAEQYMAIVVPGM 391
                                       ***************************************************************************** PP

                   Na_H_antiporter 228 iavplaaklgisllalvraveaggtlgdhlsPisdttilsstglnadhidhvsytqlpyallvapitailllvfGi 303
                                       ++ +l++++++++++l+ravea+gt +++++P+++++++++++l    + +++y +++++ +++p+++i+++++G+
  gi|336253004|ref|YP_004596111.1| 392 TLQNLYDEYDLESRNLSRAVEAAGTTTSAFVPWGSGGVFMASAL---DVPVLQYAPYYFFGILSPFVLIGMGLTGW 464
                                       ********************************************...9***************************9 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   3.0    0.0056        50       4     104 ..      86     232 ..      83     241 .. 0.66
   2 ?   12.3   1.0   1.8e-05      0.16       3      59 ..     326     382 ..     324     426 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0056
                              Gate   4 agpiillasiliwflssssllgrigkllepvfap.lgqeldwkatvslltgfa..akevvvgtlgtly......... 68 
                                       a+ i++++ +li    +s+ +  +  +   +++p +   l+  +++s ++ fa  +  + +gtlg+ +         
  gi|336253004|ref|YP_004596111.1|  86 AILILFVIYMLIASWIDSGTIPSLMYYGLEFLSPqIF--LPFTIIISAVVAFAigSSWTTAGTLGVAMigigaglgi 160
                                       6666666666666666666666666665566666555..55555555555555546677777777777788888888 PP

                              Gate  69 .....................................tsalgellqgfdtpks.alafllfvllytpcvatlav 104
                                                                            ++  +++  +  t ++ a+++llfvll   +  t+++
  gi|336253004|ref|YP_004596111.1| 161 pepmtagavlsgaytgdknsplsdttnlaaavtntdlMDHIRAM--RPGTAIAfAISLLLFVLLGLNASGTIPA 232
                                       88888888888888888888888888888998853332222222..5666666778999999998888777776 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.8e-05
                              Gate   3 kagpiillasiliwflssssllgrigkllepvfap.lgqeldwkatvslltgfaakev 59 
                                        +++i+++a++l ++l+++++l++i+  ++  ++  +g    + a+ +  ++f++ e 
  gi|336253004|ref|YP_004596111.1| 326 WVVTIVVAALALGGILQETGVLAAIAYHIGRAISSvFG-LTFGTAVGTVAMNFFSAEQ 382
                                       589*********************99999999888777.4445666666677775543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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 0.25s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3367.90
//
Query:       gi|336253005|ref|YP_004596112.1|  [L=291]
Description: Non-specific serine/threonine protein kinase [Halopiger xanaduensis SH-6]
Scores for 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-60  202.4   0.1    2.6e-59  200.0   0.0    1.8  2  RIO1            RIO1 family
    8.4e-11   42.2   0.3    6.1e-05   23.1   0.0    2.7  2  APH             Phosphotransferase enzyme family
    3.4e-05   23.3   0.0    0.00021   20.7   0.0    1.9  2  Pkinase         Protein kinase domain
    0.00029   20.2   0.2     0.0041   16.5   0.0    2.4  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
      0.008   15.0   0.0      0.013   14.3   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
  ------ inclusion threshold ------
       0.05   13.1   0.1      0.091   12.3   0.1    1.5  1  VQ              VQ motif


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 ?    0.0   0.2      0.19   5.6e+02      16      43 ..      36      63 ..      25      73 .. 0.81
   2 !  200.0   0.0   8.6e-63   2.6e-59       1     184 [.      96     273 ..      96     277 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.19
                                      EEE-S---SS-HHHHCTTTSTTSTCG-- CS
                              RIO1 16 KiyktstteFkkrkkyvsgekrfkdrks 43
                                      +i +   +eF++ ++++++  +fk ++s
  gi|336253005|ref|YP_004596112.1| 36 RIARKRDREFNQFQERIKDADQFKVEQS 63
                                      567778899999999**99999998765 PP

  == domain 2  score: 200.0 bits;  conditional E-value: 8.6e-63
                                       EEEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEE CS
                              RIO1   1 nVyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpie 77 
                                       nVyha   d++eva+K+y++++++F++++ y +g++rf+      +++++v +w++kE +nL+r+++agv+vP+pi+
  gi|336253005|ref|YP_004596112.1|  96 NVYHALG-DDREVAVKVYRINASNFRQMRDYLEGDPRFEGL--GGKKKDVVLAWTKKELANLRRAKKAGVRVPEPIA 169
                                       7***977.7788***************************76..8999****************************** PP

                                       EETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEE CS
                              RIO1  78 lkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQave 154
                                        +r+vlvme+ig+++ +a++l +v+  e+ e++y+ + e+mr+ly  agl+H+DLSeyNv++de+++v+ID++Qav+
  gi|336253005|ref|YP_004596112.1| 170 SERNVLVMEYIGNEDGRAKRLGEVQ-IENPETAYRVMREYMRRLY-SAGLIHGDLSEYNVVFDEGQLVLIDLGQAVT 244
                                       *************************.66777888888889*****.******************************* PP

                                       TTSTTHHHHHHHHHHHHHHHHHTTC----- CS
                              RIO1 155 ldhpnalefLerDveniikfFrrkgvekvd 184
                                       ++hpn+ +fLerD+en++ fF+r+g++ +d
  gi|336253005|ref|YP_004596112.1| 245 VHHPNSCDFLERDCENVASFFSRQGMD-TD 273
                                       ************************998.34 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.4e-06    0.0042       4      84 ..      88     187 ..      87     197 .. 0.74
   2 !   23.1   0.0     2e-08   6.1e-05     149     198 ..     201     244 ..     182     289 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.4e-06
                                       EE--.SSCEEEEEEETT--EEEEEE-TT.S-HHHHHHHHH.........................HHHHHHHTT-B- CS
                               APH   4 elsggasnrtylvttpagryvlrrnppa.raaeeirreva.........................llrlLakagvpv 54 
                                       +ls g +  +y+  ++++++++++++    + +++r++++                          lr   kagv+v
  gi|336253005|ref|YP_004596112.1|  88 PLSTGKEANVYHALGDDREVAVKVYRINaSNFRQMRDYLEgdprfeglggkkkdvvlawtkkelaNLRRAKKAGVRV 164
                                       678899999***************666655555555555566666666666666666666664448888889999** PP

                                       -B-CTTBS-EEETTEEEEEEE----EE-SS CS
                               APH  55 Pevlagdtddeeigllfalieyvpgrsllr 84 
                                       Pe++a       +++ ++++ey++ ++ + 
  gi|336253005|ref|YP_004596112.1| 165 PEPIA-------SERNVLVMEYIGNEDGRA 187
                                       *****.......677788999998887766 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 2e-08
                                       HHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                               APH 149 eeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedagl 198
                                       + +v+++  ++l    +++l+HgDl+  N+++d +++ v  +iD++ a++
  gi|336253005|ref|YP_004596112.1| 201 AYRVMREYMRRLY---SAGLIHGDLSEYNVVFD-EGQLV--LIDLGQAVT 244
                                       2235555555555...8****************.55555..****99975 PP

>> Pkinase  Protein kinase domain
   #    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       9      35 ..      91     115 ..      85     127 .. 0.80
   2 !   20.7   0.0   7.2e-08   0.00021      71     153 ..     171     250 ..     142     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.12
                                       EESSEEEEEEEETTTTEEEEEEEEECH CS
                           Pkinase   9 eGsfGkVykaveketgkivAvKkikke 35 
                                       +G+ ++Vy a+   ++++vAvK+ + +
  gi|336253005|ref|YP_004596112.1|  91 TGKEANVYHAL--GDDREVAVKVYRIN 115
                                       79999*****9..8999*****87654 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 7.2e-08
                                       SEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEE CS
                           Pkinase  71 delylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlake 147
                                       ++ +lv+ey+ +++   + +r g ++ e+ +   + + e ++ l+s+g+iH Dl   N+ +d +g+l ++D+G a  
  gi|336253005|ref|YP_004596112.1| 171 ERNVLVMEYIGNED--GRAKRLGEVQIENPETAYRVMREYMRRLYSAGLIHGDLSEYNVVFD-EGQLVLIDLGQAVT 244
                                       455789***99885..344444556666666666667778899*******************.************99 PP

                                       SSSSCS CS
                           Pkinase 148 lesssk 153
                                       +++ ++
  gi|336253005|ref|YP_004596112.1| 245 VHHPNS 250
                                       998765 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.7     5e+03     160     182 ..       8      28 ..       5      49 .. 0.68
   2 !   16.5   0.0   1.4e-06    0.0041      60     170 ..     149     243 ..     145     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.7
                               Kdo 160 eiwliDldkarlrlradrwrekd 182
                                       e  l+Dl+ a++  ++d w+e d
  gi|336253005|ref|YP_004596112.1|   8 EYGLVDLEEAET--PGDEWEEID 28 
                                       566778876654..456666555 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.4e-06
                               Kdo  60 rEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkavgrliaklhr 136
                                       +E+++l+r ++agv+vp+p+a++        r +l++e + +    ++ l +   ++ e  ++ ++     +++l +
  gi|336253005|ref|YP_004596112.1| 149 KELANLRRAKKAGVRVPEPIASE--------RNVLVMEYIGNEDGRAKRLGE---VQIENPETAYRVMREYMRRLYS 214
                                       79******************986........679******999888888886...888899999999999******* PP

                               Kdo 137 agvnHadlyaknillqqeeeeeaeiwliDldkar 170
                                       ag+ H+dl   n+ +++++     ++liDl +a 
  gi|336253005|ref|YP_004596112.1| 215 AGLIHGDLSEYNVVFDEGQ-----LVLIDLGQAV 243
                                       *****************97.....*****98875 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.2e-06     0.013     320     367 ..     210     250 ..     201     263 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-06
                    Pkinase_fungal 320 rsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddss 367
                                       r+L+  ag++H D Se+N+++       e + +LiDL  a+++++++s
  gi|336253005|ref|YP_004596112.1| 210 RRLY-SAGLIHGDLSEYNVVFD------EGQLVLIDLGQAVTVHHPNS 250
                                       89**.****************9......8899********99997665 PP

>> VQ  VQ motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1     3e-05     0.091       5      17 ..     110     122 ..     106     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                                VQ   5 tvvhtdasnFRal 17 
                                       +v++++asnFR++
  gi|336253005|ref|YP_004596112.1| 110 KVYRINASNFRQM 122
                                       9**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); 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:                         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 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2132.49
//
Query:       gi|336253006|ref|YP_004596113.1|  [L=546]
Description: 5'-nucleotidase [Halopiger xanaduensis SH-6]
Scores for 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-47  159.6   0.0    1.2e-46  158.9   0.0    1.4  1  5_nucleotid_C  5'-nucleotidase, C-terminal domain
  ------ inclusion threshold ------
      0.057   13.9   1.2       0.11   13.1   0.4    1.8  2  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> 5_nucleotid_C  5'-nucleotidase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.9   0.0   1.3e-50   1.2e-46       1     157 [.     352     507 ..     352     508 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 1.3e-50
                                       EEEEESSB....---HHTS--HHHHHHHHHHTGSTT--EEEEEGGG----B..TTTEEEHHHHHHHS-S--EEEEEE CS
                     5_nucleotid_C   1 vigtttveldgrdlalrtgetnlgnliadalraaagadialangggiradl..paGditvkdlltvlpfgntlvvve 75 
                                       vig+t+v+ld+r+ ++r  e+n+gn++ad +r+ ++ad+a++ngggir+d   +aG+it++ ++++lpf n+++++e
  gi|336253006|ref|YP_004596113.1| 352 VIGETAVDLDTRRETVRQAESNFGNWLADLIREDVDADVAIQNGGGIRSDQlyEAGEITRGMIVDILPFPNYTTKLE 428
                                       79*********999***********************************655899********************** PP

                                       EEHHHHHHHHHH.HTTTTTS--TT-EEEESEEEEE-TTS-TT--EEEESSS-BEEE--TTSEEEEEEEHHHHTTGGG CS
                     5_nucleotid_C  76 ltGaqlkeaLenesvsaskaasgrflqvsGlrytydlskpagervtslsvtvngkpldddktYkvatnsylasggdg 152
                                       +tG+ lk+a+e+  v+a +++ grf+qvsGl+++yd++++ag+rv++l  tv g+p+d ++tY + tn++la+ggdg
  gi|336253006|ref|YP_004596113.1| 429 ITGEALKAAIEH-GVGAVEDGHGRFPQVSGLSFVYDPDAEAGQRVQEL--TVGGEPVDLEATYELGTNDFLAGGGDG 502
                                       ***********8.99*********************************..66************************* PP

                                       -HHHH CS
                     5_nucleotid_C 153 fsmlk 157
                                       ++ml+
  gi|336253006|ref|YP_004596113.1| 503 YEMLA 507
                                       ***96 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   1.2e-05      0.11      54     106 ..     214     267 ..     186     276 .. 0.79
   2 ?   -3.5   0.0       1.6   1.4e+04      63      83 ..     425     445 ..     423     445 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                       .T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT---HHHHHHHHH.TT-EEE CS
                     CoA_binding_2  54 epvdlvdvftppeatpeivkealalgakavwlqpgsedeeaaelaee.agirvv 106
                                       ++ d v v+ p +a++++v +++++ga  ++  +++ ++ea ela++ +gi+vv
  gi|336253006|ref|YP_004596113.1| 214 SVGDDVEVLEPTAAAEAVVADLQDEGADLIVALSHIASPEAEELAAAvDGIDVV 267
                                       34457999***************************************9999966 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.6
                                       S-HHHHGGGHHHHHHH--SEE CS
                     CoA_binding_2  63 tppeatpeivkealalgakav 83 
                                       t+ e+t e +k+a++ g+ av
  gi|336253006|ref|YP_004596113.1| 425 TKLEITGEALKAAIEHGVGAV 445
                                       667888999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 4114.10
//
Query:       gi|336253007|ref|YP_004596114.1|  [L=442]
Description: tryptophanyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-22   77.9   0.0      3e-21   76.0   0.0    1.8  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)


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 !   76.0   0.0   1.7e-25     3e-21       4     292 ..      85     364 ..      82     365 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 1.7e-25
                                       S--EEEEEEETSSS-BGGGHHHHHHHHHHHH.TTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHT CS
                      tRNA-synt_1b   4 rplrvysGidPTgklHlGylvplkklvelqk.aghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakg 79 
                                       +p ++++G  P+g++HlG+++pl    ++q+  g +v++ + D + ++ + +  +  ++ +++++       +la+g
  gi|336253007|ref|YP_004596114.1|  85 EPHAIVTGRGPSGPMHLGHVLPLYLAKRFQQkTGATVYVPLSDDEKFLAKDQ--SFASIGEHTRDNLRD---ILAVG 156
                                       67899*************************989**************99999..899999999999999...***** PP

                                       CHTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS.... CS
                      tRNA-synt_1b  80 ldpekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkad.... 152
                                       +dpe++++ + ++  +   +  +  +l+k+ + +++ +        e+ +  ++g+  Yp  qa   ll +      
  gi|336253007|ref|YP_004596114.1| 157 FDPERTRIAVDTADADV--VYPIAVRLAKHLTPATVEAVYG-----EQ-D--TVGLQFYPAVQATHLLLPQLVdgrq 223
                                       ********998765554..4455556777665555555544.....33.4..7888899999999999988777888 PP

                                       ..EEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHC CS
                      tRNA-synt_1b 153 ..lvpgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavt 227
                                         lvp   DQ+ ++++ rd+a +       +kp +l+ ++l++l+G  KmS+S +   I L+d++e++ + i++   
  gi|336253007|ref|YP_004596114.1| 224 ptLVPIAVDQDPHVRVCRDVAAKEALP--VAKPGALLGRFLPSLEGPGKMSSSGDAPSIGLTDDPETIAETIRNHAY 298
                                       88******************9887655..89***********************999***************97555 PP

                                       STTC...SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 228 dsde...evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                       + ++   e ++ + + + ++  l+++l  + + ++ +++e ++++++ +++  g+lk+ + e +  +l
  gi|336253007|ref|YP_004596114.1| 299 TGGRstlEEHREKGGDPTVDV-LFQYLRFFFEPDD-EALEGIAERYRAGELLSGELKEFAIERITDFL 364
                                       555559999************.*******999998.9**********************999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 3657.43
//
Query:       gi|336253008|ref|YP_004596115.1|  [L=176]
Description: phosphodiesterase [Halopiger xanaduensis SH-6]
Scores for 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-31  108.7   0.5    3.8e-31  108.5   0.5    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    0.00016   22.2   4.1    0.00048   20.7   4.1    1.8  1  Metallophos    Calcineurin-like phosphoesterase


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 !  108.5   0.5   4.2e-35   3.8e-31       1     162 [.       1     155 [.       1     158 [. 0.86

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 4.2e-35
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellelapvlaVrGNnDeev.veedvlreaae 76 
                                       M+++iiSD+H+n++a e+++e+++e+gv+ ++h+GD+  ++p  l +l++ ++v+ V GNnD+e+   ++  +    
  gi|336253008|ref|YP_004596115.1|   1 MNVGIISDTHDNVAAAERAAEIFAEEGVEVVVHCGDF--IAPPLLPALED-FEVHGVLGNNDGEIaGLHAAFDDLGS 74 
                                       9************************************..***99999999.6**********444433444444444 PP

                     Metallophos_2  77 lgtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgd 153
                                        ++ +   a le++g +++++Hg+    k+++++l+ +  e  d+v++GH H++ +++ g ++++nPG   +   ++
  gi|336253008|ref|YP_004596115.1|  75 ESELHGRFASLEFDGLSFAVLHGE---SKAEVEALAAA--EAYDFVCYGHHHERDLTENGRTTLLNPGGHFPTIPDE 146
                                       4444468899999**********8...67777777766..7778*****************************9999 PP

                     Metallophos_2 154 petyaildt 162
                                       ++t+ai+dt
  gi|336253008|ref|YP_004596115.1| 147 HRTVAIVDT 155
                                       99*****98 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   4.1   5.4e-08   0.00048       1     130 [.       1     121 [.       1     158 [. 0.64

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.4e-08
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS.. CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe.. 75 
                                       +++ +i+D+H      + ++++++ + +++e ++ +v+++GD++    l+  l+++          v+ +lGN +  
  gi|336253008|ref|YP_004596115.1|   1 MNVGIISDTH-----DNVAAAERAAEIFAEE-GVEVVVHCGDFIAPPLLPA-LEDF---------EVHGVLGNNDge 61 
                                       7899******.....**********999777.***********99997777.6666.........56999*****55 PP

                                       ......CHHHHHHHHHHHHHHHHHHHEHH.HCEEETSEEEEEETTE...........EEEEEEESECEEETHH CS
                       Metallophos  76 ......gfeeellnkygylgifsepwrsd.aevfnnlplaslgsgs...........lkvlllhGgspellvs 130
                                             +        +++lg  se++ ++ +  f++l  a+l++ s            + ++++G+     ++
  gi|336253008|ref|YP_004596115.1|  62 iaglhaA--------FDDLGSESELHGRFaSLEFDGLSFAVLHGESkaevealaaaeAYDFVCYGH-----HH 121
                                       5544441........444444433333333344444444444333333333444444467777777.....22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1317.62
//
Query:       gi|336253009|ref|YP_004596116.1|  [L=185]
Description: KH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   51.1   0.7    1.8e-07   30.8   0.1    2.3  2  KH_1      KH domain
    3.2e-05   23.7   2.2     0.0046   16.8   0.1    2.5  2  KH_2      KH domain
    0.00014   21.9   0.0    0.00022   21.3   0.0    1.3  1  KH_8      Krr1 KH1 domain
     0.0081   16.0   3.0        1.8    8.5   0.3    3.1  3  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 !   30.8   0.1   4.1e-11   1.8e-07       3      52 ..       3      48 ..       1      78 [. 0.77
   2 !   18.8   0.1   2.3e-07     0.001       9      61 ..     100     144 ..      98     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 4.1e-11
                                      EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE CS
                              KH_1  3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG 52
                                       +++P++ +g +IG gG++ +eI++e  ++ +++ se++   +  v+  G
  gi|336253009|ref|YP_004596116.1|  3 HVKIPQDRIGVLIGEGGETMREIEAEAEVRLDID-SENG---SVAVETVG 48
                                      689**********************99*****87.6664...44444444 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.3e-07
                                       GHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHH CS
                              KH_1   9 slvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAk 61 
                                       ++ gr+IG  G++   ++e tga +++  +       +++ i+G+pe+v++ +
  gi|336253009|ref|YP_004596116.1| 100 RQKGRLIGEEGRTRELMEELTGADVVIY-G-------STLGIIGTPEQVDAVR 144
                                       678**********99888989*****76.4.......48********998765 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1     1e-06    0.0046      33      59 ..       8      34 ..       3      52 .. 0.74
   2 !    6.0   0.2    0.0023        10      34      58 ..     100     124 ..      96     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-06
                                      ESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                              KH_2 33 esqpgivIGkgGsnikkigkelrkdie 59
                                        + g++IG gG+++++i++e++ +++
  gi|336253009|ref|YP_004596116.1|  8 QDRIGVLIGEGGETMREIEAEAEVRLD 34
                                      6799****************9998885 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0023
                                       SCHHHHHTGGGHHHHHHHHHHHHHH CS
                              KH_2  34 sqpgivIGkgGsnikkigkelrkdi 58 
                                        q+g++IG +G++ + +++  + d+
  gi|336253009|ref|YP_004596116.1| 100 RQKGRLIGEEGRTRELMEELTGADV 124
                                       69*********99888888887777 PP

>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   4.8e-08   0.00022      20      81 .]      20      78 ..      13      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.8e-08
                              KH_8 20 ekikklleekklklevdlkerslkvsTtekTrDPyiilkardlikLisrgvpleeakkvleD 81
                                      e+++++ +e +++l++d +++s+ v+T     DP   lk+ ++++ i+rg + e a ++leD
  gi|336253009|ref|YP_004596116.1| 20 ETMREIEAEAEVRLDIDSENGSVAVETV---GDPVLGLKGPEIVRAIGRGFAPEDALRLLED 78
                                      6788888999****************97...6*****************************9 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.3   0.00039       1.8      33      52 ..       4      23 ..       2      27 .. 0.89
   2 ?   -0.6   0.0      0.27   1.2e+03      17      31 ..      28      42 ..      22      66 .. 0.59
   3 !    6.5   0.0    0.0017       7.8      38      50 ..     100     112 ..      85     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00039
                              KH_4 33 lnvegedlGrvIGkrGrtld 52
                                      +++ ++ +G++IG  G+t++
  gi|336253009|ref|YP_004596116.1|  4 VKIPQDRIGVLIGEGGETMR 23
                                      78999************975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.27
                              KH_4 17 evevteeeeeeevei 31
                                      e ev++++++e+ ++
  gi|336253009|ref|YP_004596116.1| 28 EAEVRLDIDSENGSV 42
                                      333333333334444 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0017
                              KH_4  38 edlGrvIGkrGrt 50 
                                        ++Gr+IG +Grt
  gi|336253009|ref|YP_004596116.1| 100 RQKGRLIGEEGRT 112
                                       578*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1479.12
//
Query:       gi|336253010|ref|YP_004596117.1|  [L=555]
Description: thermosome [Halopiger xanaduensis SH-6]
Scores for 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-175  585.1  15.0   1.2e-175  584.9  15.0    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.37   11.4   3.7        8.6    7.0   0.0    3.6  3  P-II        Nitrogen regulatory protein P-II


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 !  584.9  15.0  1.3e-179  1.2e-175       1     489 [.      37     522 ..      37     524 .. 0.99

  Alignments for each domain:
  == domain 1  score: 584.9 bits;  conditional E-value: 1.3e-179
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a+ v+ttlGPkGmdKmlv++ g+vvvTnDG+t+l+e++i+hPaa ++ve+ae+q++evGDGTt++v++ageLl++a
  gi|336253010|ref|YP_004596117.1|  37 VAESVRTTLGPKGMDKMLVDSTGNVVVTNDGVTLLSEMDIDHPAADMIVEVAETQEDEVGDGTTSAVVIAGELLSQA 113
                                       6899************************************************************************* PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       e+l+++++h tt+ +gy++a+e+a eaL+ei  +i+++e+d+e+L ++a+t++++k  ++ ++ l++lvv+Av+++ 
  gi|336253010|ref|YP_004596117.1| 114 EELLEQDIHATTLAQGYREAAEEATEALEEI--AIDVDEDDDEILHQIAATAMTGKGAENARDLLANLVVEAVQAVA 188
                                       *******************************..8899999*********************************9987 PP

                                       CCSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHH CS
                        Cpn60_TCP1 155 enekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeele 231
                                       ++ + +d ++ikv+k+ ggs+e+selveG+++dk+ +s +mp   e+a v+++d  Lei++te++++v+++d+++le
  gi|336253010|ref|YP_004596117.1| 189 DD-EGIDTDNIKVEKVVGGSVENSELVEGVIVDKERVSDSMPYFAEDADVAIIDGDLEIKETEIDAEVNVTDPDQLE 264
                                       66.69************************************************************************ PP

                                       HHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC CS
                        Cpn60_TCP1 232 klekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpee 308
                                       +++++ee+ql+e+ e i++ g++vv++ +gidd+a+h+la++gi+a+rrvk +d  +la+atGat+v+s++dl++++
  gi|336253010|ref|YP_004596117.1| 265 QFLEQEEQQLKEMAEGIADVGADVVFVDGGIDDMAQHYLAQEGIIAVRRVKSSDQTQLARATGATPVTSVDDLSEDD 341
                                       ***************************************************************************** PP

                                       -EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHH CS
                        Cpn60_TCP1 309 lGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelak 385
                                       lG a++v +++i  ++ +++e+v++++++t++lrg t++v+dei raied+l vv+ ++ed+kv++GGGa e+ l+ 
  gi|336253010|ref|YP_004596117.1| 342 LGFAGSVAQKEIAGDQRIFVEDVDEARSVTLILRGGTEHVIDEIDRAIEDSLGVVRTTLEDGKVLAGGGAPEVNLSL 418
                                       ***************************************************************************** PP

                                       HHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEE CS
                        Cpn60_TCP1 386 klkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDp 462
                                       +l++ya+sv g+eqla+eafa+ALevip+tLaeNaGldpi+ l +lra h+ g+ ++g+d+ +g++id+ e+gv++p
  gi|336253010|ref|YP_004596117.1| 419 ALRDYADSVGGREQLAVEAFADALEVIPRTLAENAGLDPIDSLVELRADHDGGNSSAGLDAYTGDTIDMAEEGVYEP 495
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHCEEEEEXX CS
                        Cpn60_TCP1 463 lkvkrqalksAteaastiLrideiika 489
                                       l+vk+qa++sAteaa ++Lrid++i a
  gi|336253010|ref|YP_004596117.1| 496 LRVKTQAIESATEAAVMLLRIDDVIAA 522
                                       *************************97 PP

>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.068   6.1e+02      69      87 ..      79      99 ..      36     106 .. 0.82
   2 ?    1.8   0.1     0.041   3.7e+02      47      82 ..     135     167 ..     113     170 .. 0.72
   3 ?    7.0   0.0   0.00096       8.6      76      97 ..     347     368 ..     308     371 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.068
                                      HHHHHHHHHH-SSS..TTSEE CS
                              P-II 69 kvveaiikaaktge..iGDGk 87
                                       + ++i+++a+t+e  +GDG 
  gi|336253010|ref|YP_004596117.1| 79 PAADMIVEVAETQEdeVGDGT 99
                                      46788999998876669**95 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.041
                                       EEEEEEEEEEEEEEEEEGGGHHHHHHHHHHHH-SSS CS
                              P-II  47 eyevellpkvkleivvsdedvekvveaiikaaktge 82 
                                       e ++e l+ + +++   ded ++++++i  +a tg+
  gi|336253010|ref|YP_004596117.1| 135 EEATEALEEIAIDV---DEDDDEILHQIAATAMTGK 167
                                       44444555555544...78999**********9997 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.00096
                                       HHH-SSSTTSEEEEEEEESEEE CS
                              P-II  76 kaaktgeiGDGkiFvlpveevi 97 
                                       ++a+++  GD +iFv +v+e+ 
  gi|336253010|ref|YP_004596117.1| 347 SVAQKEIAGDQRIFVEDVDEAR 368
                                       68899999***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3867.00
//
Query:       gi|336253011|ref|YP_004596118.1|  [L=331]
Description: Ornithine cyclodeaminase [Halopiger xanaduensis SH-6]
Scores for 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-93  312.0   1.4    4.1e-93  311.8   1.4    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
  ------ inclusion threshold ------
      0.038   14.0   0.0      0.072   13.1   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.053   14.3   0.2       0.13   13.1   0.1    1.8  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.068   13.4   1.4        2.1    8.6   0.1    2.6  2  TrkA_N           TrkA-N domain


Domain annotation for each model (and alignments):
>> 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 !  311.8   1.4   9.1e-97   4.1e-93       4     316 ..       4     316 ..       1     318 [. 0.96

  Alignments for each domain:
  == domain 1  score: 311.8 bits;  conditional E-value: 9.1e-97
                                       EEE-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTT..EEEEEEEEEETTTC CS
                   OCD_Mu_crystall   4 avltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagre..llgvKlvnshpenk 78 
                                        +l   +v e+ +l+++++aveeaf +++ g  ++p + + e ++++g+++ mpayl + +  ++gvK+vn+hp+n+
  gi|336253011|ref|YP_004596118.1|   4 LLLDSDAVDEHAQLAAVIDAVEEAFGAFERGDTQMPAKSYIELPQYNGDFRSMPAYLDTGDwdAAGVKWVNVHPDNP 80 
                                       56677889************************************************99877779************* PP

                                       CC.TSSSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS-- CS
                   OCD_Mu_crystall  79 ks.glptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldi 154
                                       ++  lptv ++++ +dpet +pla+md+t+lt +RT+A++ava+ yLa +das l+i+GaGvq++tqlea+++v+++
  gi|336253011|ref|YP_004596118.1|  81 AEhDLPTVLGTMIYSDPETAFPLAIMDGTMLTMKRTGAAAAVATDYLALEDASSLGIVGAGVQSYTQLEAISEVRQL 157
                                       *99************************************************************************** PP

                                       SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--S CS
                   OCD_Mu_crystall 155 kevriydrdeeaaekfaenlqefefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkte 231
                                       +ev + d dee  ++f+e+ +   f+v+  +    ++  +d++ tvT+ + pi+  + v++ +hina+gada gk+e
  gi|336253011|ref|YP_004596118.1| 158 EEVVVADQDEERVQRFVETYED-RFDVRGGS-IS-EAGHCDVLSTVTPVRDPIVGSDDVGEHTHINAIGADAAGKHE 231
                                       *********************7.88888643.44.4579************************************** PP

                                       B-HHHHHCCEEEESHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHH CS
                   OCD_Mu_crystall 232 LdddilkradifvdseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaak 308
                                       L dd+l+ a+i++d+ +q +++Gei+v+  +gvl ++++ ae+ge + G k+GRt +  +t+fds+Gla++Dvaaa+
  gi|336253011|ref|YP_004596118.1| 232 LADDLLQAARIVIDDHEQCTHSGEINVPYGEGVLTDEDIYAEIGELVVGAKDGRTAETGVTVFDSTGLAIQDVAAAR 308
                                       ***************************************************************************** PP

                                       HHHHHHCC CS
                   OCD_Mu_crystall 309 lvyeraee 316
                                       +vye+a++
  gi|336253011|ref|YP_004596118.1| 309 VVYENASD 316
                                       *****987 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.6e-05     0.072      14      97 ..     134     215 ..     122     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                                       EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-S CS
                      Shikimate_DH  14 kvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepi 89 
                                          ++GaG  +   ++++++  ++++vvva  + er+++++e +++  +  ++  +++    ++dv+ + t  ++pi
  gi|336253011|ref|YP_004596118.1| 134 SLGIVGAGVQSYTQLEAISEVrQLEEVVVADQDEERVQRFVETYEDR-FD-VRGGSIS-EAGHCDVLSTVTPVRDPI 207
                                       5679**************996599********************766.32.2333333.345788888888888888 PP

                                       B-HHHHHC CS
                      Shikimate_DH  90 lekeevee 97 
                                       + +++v e
  gi|336253011|ref|YP_004596118.1| 208 VGSDDVGE 215
                                       88887765 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 ?   -3.8   0.0         4   1.8e+04      25      39 ..      14      28 ..      10      43 .. 0.64
   2 ?   13.1   0.1     3e-05      0.13       3      48 ..     135     179 ..     134     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4
                                      TEEEEEEECSSHHHH CS
                      GFO_IDH_MocA 25 leevvalldpdaera 39
                                      +++++a++d  +e+ 
  gi|336253011|ref|YP_004596118.1| 14 HAQLAAVIDAVEEAF 28
                                      456666666655554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3e-05
                                       EEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTH CS
                      GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgv 48 
                                        +i+GaG   + +l+++ e ++leevv + d+d+er +++ e+++ 
  gi|336253011|ref|YP_004596118.1| 135 LGIVGAGVQSYTQLEAISEVRQLEEVV-VADQDEERVQRFVETYED 179
                                       59******************8888887.************777654 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00047       2.1       3      39 ..     137     175 ..     135     189 .. 0.87
   2 ?    3.1   0.1     0.025   1.1e+02      12      59 ..     231     275 ..     222     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00047
                                       EES-SHHHHHHHHHHHH.TT.EEEEEEESSHHHHHHHHH CS
                            TrkA_N   3 iiGlGrvGrslaeeLse.gg.kdvvvidkdeerveelre 39 
                                       i+G+G   ++ +e +se ++ ++vvv d+deerv+++ e
  gi|336253011|ref|YP_004596118.1| 137 IVGAGVQSYTQLEAISEvRQlEEVVVADQDEERVQRFVE 175
                                       89999999999999999888977***********99754 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.025
                                       HHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTT CS
                            TrkA_N  12 slaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeag 59 
                                       +la+ L ++ +  +vid+ +e++ +  e ++++  g  tde++ +e+g
  gi|336253011|ref|YP_004596118.1| 231 ELADDLLQAAR--IVIDD-HEQCTHSGEINVPYGEGVLTDEDIYAEIG 275
                                       68999999774..77877.67999999999************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2452.77
//
Query:       gi|336253012|ref|YP_004596119.1|  [L=480]
Description: sugar transporter [Halopiger xanaduensis SH-6]
Scores for 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-131  437.6  19.4   6.1e-131  437.4  19.4    1.0  1  Sugar_tr         Sugar (and other) transporter
    5.6e-45  153.8  70.5    8.8e-36  123.5  39.8    2.0  2  MFS_1            Major Facilitator Superfamily
    1.1e-07   30.7   3.4    1.1e-07   30.7   3.4    2.1  2  TRI12            Fungal trichothecene efflux pump (TRI12)
    0.00065   18.1   7.4      0.011   14.1   0.5    3.0  2  OATP             Organic Anion Transporter Polypeptide (OATP)
    0.00073   18.2  37.0    0.00084   18.0   4.8    4.1  4  MFS_2            MFS/sugar transport protein
  ------ inclusion threshold ------
       0.34    9.7  13.5      0.072   11.9   0.3    2.9  2  MFS_1_like       MFS_1 like family
       0.89    9.6  11.6      0.032   14.2   4.2    2.6  2  Gly-zipper_Omp   Glycine zipper
        4.7    7.0   9.7       0.28   11.0   3.2    2.4  2  Gly-zipper_YMGG  YMGG-like Gly-zipper


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.4  19.4  2.7e-134  6.1e-131       1     451 [.      20     458 ..      20     459 .. 0.95

  Alignments for each domain:
  == domain 1  score: 437.4 bits;  conditional E-value: 2.7e-134
                                       HHHHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHH CS
                          Sugar_tr   1 valvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkk 77 
                                       va +aal gllfg+dtgvi++++  +   + + +++   s +  s+  g+ivs ++vGai+G+ f+g l+dr+GR+ 
  gi|336253012|ref|YP_004596119.1|  20 VAALAALNGLLFGFDTGVISGAMLYIRETF-ELATVLGVSLD-PSLIEGVIVSGAMVGAILGAAFGGRLADRLGRRR 94 
                                       6789****************9998888433.33444444455.689******************************* PP

                                       HHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  78 slliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilva 154
                                        +l++av+f++g++++a+a+   +ve+li+gR++ GigvG+asv+ P+yisEi+p+k+Rg lvsl+ql +t+Gil+a
  gi|336253012|ref|YP_004596119.1|  95 LILVGAVVFFVGSLIMAIAP---TVEILILGRIIDGIGVGFASVVGPLYISEISPPKIRGSLVSLNQLTVTTGILIA 168
                                       ********************...9***************************************************** PP

                                       HHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHH CS
                          Sugar_tr 155 aifglglnktsnadgwrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrgeedadrelaeekdsl 231
                                       ++++++++  ++   wr++lgl ++pa +l++++lf+P SPr+l+e+g+e +a+evl + r e ++d+el e+k+++
  gi|336253012|ref|YP_004596119.1| 169 YVVNYAFSAGGD---WRWMLGLGMLPAAVLFVGMLFMPASPRWLYEQGREADAREVLTRTRVEHQVDDELREIKETI 242
                                       ************...********************************************9999*************9 PP

                                       HHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH..HHHHHHHHHHHHHHHHH CS
                          Sugar_tr 232 eaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks..llvtiivgvvnfvatfv 306
                                       + e    + s++ ll+ +  r  l++gv+l++fqq+tGin +myy+pti+e++g++++  +l+t+++gvvn++ t+v
  gi|336253012|ref|YP_004596119.1| 243 RTE----SGSLRDLLQPWI-RPMLIVGVGLAVFQQVTGINTVMYYAPTILESTGFEDTasILATVGIGVVNVALTVV 314
                                       999....678999999865.999****************************************************** PP

                                       HHHHHHHS-SHHHHHHHHHHHHHHHHHHH...HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTT CS
                          Sugar_tr 307 aiflvdrfGRRtllllGaagmaicfvilg.ivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqs 382
                                       a++l+dr+GRR+lll+G+ gm++++ +lg    l++ ++  + + va+  ++l++a+fa+g+gpv+w+++sE++p++
  gi|336253012|ref|YP_004596119.1| 315 AVLLIDRTGRRPLLLTGLGGMTVMLGVLGaVFYLPGLSG--VVGWVATGSLMLYVAFFAIGLGPVFWLMISEIYPME 389
                                       *****************************6666777777..8*********************************** PP

                                       THHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGGG CS
                          Sugar_tr 383 vRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeieel 451
                                       +R++a+ +++++nw an+l+sl+f  +++  g+ ++f+++++l +++++f++  vpetkgr+leeie++
  gi|336253012|ref|YP_004596119.1| 390 FRGTAMGVVTVLNWAANLLVSLTFLRLVDVFGQSGTFWLYGALSLAALVFCYRLVPETKGRSLEEIEAD 458
                                       ******************************************************************986 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5  39.8   3.9e-39   8.8e-36       2     351 ..      25     408 ..      24     410 .. 0.77
   2 !   44.3  22.7   4.9e-15   1.1e-11       2     187 ..     266     457 ..     265     476 .. 0.85

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 3.9e-39
                             MFS_1   2 llaaflsalarsilgpalplalaedlg........ispsei.gllltlyalgaavaslplGrlsdrfGrrrvlllgl 69 
                                       +l ++l +++ ++++ a+  ++ e++         ++ps i g ++++ ++ga++++ ++Grl+dr+Grrr++l+g+
  gi|336253012|ref|YP_004596119.1|  25 ALNGLLFGFDTGVISGAML-YIRETFElatvlgvsLDPSLIeGVIVSGAMVGAILGAAFGGRLADRLGRRRLILVGA 100
                                       5778999***********9.*****99766666665555542559999***************************** PP

                             MFS_1  70 llfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllas 146
                                       ++f++g+l++++a+++ +l+++r++ G+g g++  +g  +i++++p++ rg+ ++l ++++  G+++++++  ++++
  gi|336253012|ref|YP_004596119.1| 101 VVFFVGSLIMAIAPTVEILILGRIIDGIGVGFASVVGPLYISEISPPKIRGSLVSLNQLTVTTGILIAYVVNYAFSA 177
                                       ******88888767777***********************************************************9 PP

                             MFS_1 147 slgWravfyilaivsllafvlfllllpeepperkrkspkeee....................kgtgpaplvpawkal 203
                                        + Wr++  +  + ++++fv ++l++p++p+    +  + +                     k t +++  + ++ l
  gi|336253012|ref|YP_004596119.1| 178 GGDWRWMLGLGMLPAAVLFV-GMLFMPASPRWLYEQGREADArevltrtrvehqvddelreiKETIRTESGS-LRDL 252
                                       999**************999.447776666666666666665888888888777666655553333333333.5555 PP

                             MFS_1 204 lkdpvlwillialllf....ffgfsglltllplylqevlgls.glllaglllallalvgailallagrlsdrlgrrr 275
                                       l +    +l++++ l+     +g+++++++ p++  e  g+  +   + l+   +++v+++l ++a  l+dr+grr+
  gi|336253012|ref|YP_004596119.1| 253 LQPWIRPMLIVGVGLAvfqqVTGINTVMYYAPTI-LESTGFEdT--ASILATVGIGVVNVALTVVAVLLIDRTGRRP 326
                                       55443323444444442233445555*******7.*******52..333235555556666688888888*****99 PP

                             MFS_1 276 rlllallllllaa..lglallavtssavllll....vlvliGfglgfvfpsllalasdlappeeagtasglfntags 346
                                        ll +l+++++++  lg ++  +  s v++++    +++ + f++    p ++ ++s+ +p e +gta+g++++++ 
  gi|336253012|ref|YP_004596119.1| 327 LLLTGLGGMTVMLgvLGAVFYLPGLSGVVGWVatgsLMLYVAFFAIGLGPVFWLMISEIYPMEFRGTAMGVVTVLNW 403
                                       9999999987654115555555558888888899865555777666669************************9998 PP

                             MFS_1 347 lggal 351
                                       ++ +l
  gi|336253012|ref|YP_004596119.1| 404 AANLL 408
                                       77665 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 4.9e-15
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.ll 77 
                                        la+f   +++++++  +p ++ e+ g+  ++  l++++ +++ +++++++  l+dr Grr++ll+gl ++ ++ ++
  gi|336253012|ref|YP_004596119.1| 266 GLAVFQQVTGINTVMYYAP-TILESTGFEDTASILATVGIGVVNVALTVVAVLLIDRTGRRPLLLTGLGGMTVMlGV 341
                                       57889999999999*****.999****999998889999***********************************888 PP

                             MFS_1  78 lll.f.......a.....sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllg 141
                                       l++ f       +     +++ +l+v+ +  Glg     p+   +i++++p e rg a+g++++ + ++ +l  l  
  gi|336253012|ref|YP_004596119.1| 342 LGAvFylpglsgVvgwvaTGSLMLYVAFFAIGLG-----PVFWLMISEIYPMEFRGTAMGVVTVLNWAANLLVSLTF 413
                                       8888667766551455557788999999999999.....788899******************************** PP

                             MFS_1 142 gllasslgWravfyilaivsllafvlfllllpeepperkrkspkee 187
                                         l++ +g +++f++ +++sl a+v+  ++ ++++++ +  +++e 
  gi|336253012|ref|YP_004596119.1| 414 LRLVDVFGQSGTFWLYGALSLAALVF--CYRLVPETKGRSLEEIEA 457
                                       ***********************887..555555555555444444 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   3.4   4.8e-11   1.1e-07      92     237 ..      77     223 ..      50     229 .. 0.75
   2 !    4.8   2.9    0.0034       7.6      63     124 ..     279     346 ..     226     401 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 4.8e-11
                             TRI12  92 avsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgvaagpag.asplfvgelmsnktkflg 167
                                        +     grl+dr+grr ++++  ++ +vg+++ + a  ++ l+    + g+  g a    pl++ e+   k +   
  gi|336253012|ref|YP_004596119.1|  77 ILGAAFGGRLADRLGRRRLILVGAVVFFVGSLIMAIAPTVEILILGRIIDGIGVGFASvVGPLYISEISPPKIRG-S 152
                                       33344579***********************************************997257******98877653.3 PP

                             TRI12 168 llivsipvvvtsglspyl.gqrlaiqgswrwifyiyiitsaiavllivvwyyppsfaql..hgkkvrkreela 237
                                       l+ +   +v+t  l  y+    ++  g+wrw++ + ++ +  avl++ + + p s + l  +g+ +  re l+
  gi|336253012|ref|YP_004596119.1| 153 LVSLNQLTVTTGILIAYVvNYAFSAGGDWRWMLGLGMLPA--AVLFVGMLFMPASPRWLyeQGREADAREVLT 223
                                       4445555666666667761567899*******99887765..6677777777777666622588888888776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0034
                             TRI12  63 sasalpnilqdvgqsensslfstlwttgqavsilvmg.rltdrfgrrpfvi.....lthilglvgaiv 124
                                            p il+  g  +  s+++t+      v++ v+   l dr grrp+++     +t +lg++ga+ 
  gi|336253012|ref|YP_004596119.1| 279 VMYYAPTILESTGFEDTASILATVGIGVVNVALTVVAvLLIDRTGRRPLLLtglggMTVMLGVLGAVF 346
                                       4556799***************9988888888877661579*******99733333477888888875 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 !    6.0   1.7    0.0014       3.1      37      85 ..      64     112 ..      29     117 .. 0.94
   2 !   14.1   0.5   4.9e-06     0.011     132     350 ..     116     318 ..     111     350 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0014
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP  37 tsgliassneignillilfvsYfggrghrPrwigigallmalgslllal 85 
                                         g+i+s+  +g+il ++f + +++r  r r+i +ga+++ +gsl++a+
  gi|336253012|ref|YP_004596119.1|  64 IEGVIVSGAMVGAILGAAFGGRLADRLGRRRLILVGAVVFFVGSLIMAI 112
                                       569********************************************97 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.9e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 132 vllfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllklyvdidseisltpkd 208
                                       v +++l+ ++ GiG      +G  Yi + + +k    ++++ + + + G  +++++ +++                d
  gi|336253012|ref|YP_004596119.1| 116 VEILILGRIIDGIGVGFASVVGPLYISEISPPKIRGSLVSLNQLTVTTGILIAYVVNYAFSA------------GGD 180
                                       56899*****************************9999999999999999999999886655............246 PP

                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 209 prWvgaWWlgflilgvllllaai.plffFPkelpkkkeerakkkseeesaekkeekkkkeksksseeeelkslkdfp 284
                                        rW+    lg  +l +++l++ + ++ + P+ l ++ +e+++++  ++++  +++ +++ ++ +++    ++  ++ 
  gi|336253012|ref|YP_004596119.1| 181 WRWM----LGLGMLPAAVLFVGMlFMPASPRWLYEQGREADAREVLTRTR-VEHQVDDELREIKET--IRTESGSLR 250
                                       5665....555555555555543033445555655555554444444332.233333333333333..223333333 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                              OATP 285 kalkrllknpifllvilssvfeillvaGfitFlpkylEtq.Fslsas.eAnlltGvvvipgaalGill 350
                                         l   ++  + + v l+   ++++++ ++ + p  lE+  F+ +as  A++ +Gvv++   ++ +ll
  gi|336253012|ref|YP_004596119.1| 251 DLLQPWIRPMLIVGVGLAVFQQVTGINTVMYYAPTILESTgFEDTASiLATVGIGVVNVALTVVAVLL 318
                                       344444444455557788888899**************754*99998469999******999998875 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   4.8   3.8e-07   0.00084     264     338 ..      67     140 ..      16     145 .. 0.83
   2 ?    2.9   1.2     0.014        31     240     276 ..     160     199 ..     152     210 .. 0.69
   3 !   11.5   7.5   3.5e-05     0.079     203     342 ..     239     385 ..     222     389 .. 0.70
   4 ?    2.7   1.4     0.017        38     257     308 ..     391     442 ..     385     452 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.8e-07
                             MFS_2 264 fllvv.tisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpwsm 338
                                       + +   +++a+lg+++  +la rlg+++++l+ga++ +v+++++ ++    + ++++  +i g+gvg+a ++ +  
  gi|336253012|ref|YP_004596119.1|  67 VIVSGaMVGAILGAAFGGRLADRLGRRRLILVGAVVFFVGSLIMAIA--PTVEILILGRIIDGIGVGFASVVGPLY 140
                                       444545*****************************************..445566778899999999888877655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.014
                             MFS_2 240 lgvlnglllYyltyvlgngsaasvfllvvtisal...lgi 276
                                       ++ +  l +Y+++y   +g +  ++l++ +++a+   +g+
  gi|336253012|ref|YP_004596119.1| 160 TVTTGILIAYVVNYAFSAGGDWRWMLGLGMLPAAvlfVGM 199
                                       4566778889999999999999999998888888433333 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 3.5e-05
                             MFS_2 203 ekteqkeklslleqlkevfrnraflillllfllaalalgvlnglllYyltyvlg.ngsaasvfllvv.tisal..lg 275
                                       ++t ++e++sl++ l+   r     +l++++ la++ ++ + + ++Yy+  +l+ +g++ +++ l++  i+++  + 
  gi|336253012|ref|YP_004596119.1| 239 KETIRTESGSLRDLLQPWIRP----MLIVGVGLAVFQQVTGINTVMYYAPTILEsTGFEDTASILATvGIGVVnvAL 311
                                       556666666666666666666....67777778889999**************998887666666662333336588 PP

                             MFS_2 276 iplwqplakrlgkkntyllga.lltivllvlvlll......qpsnlllflvllviagfgvgvaallpwsmladv 342
                                       ++++  l  r g++ + l g+  +t++l+vl  ++      +   ++++  l++ + f++++++ ++w m++++
  gi|336253012|ref|YP_004596119.1| 312 TVVAVLLIDRTGRRPLLLTGLgGMTVMLGVLGAVFylpglsGVVGWVATGSLMLYVAFFAIGLGPVFWLMISEI 385
                                       888889999***99776654313333333333333367*99777777777777777777778889999999876 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.017
                             MFS_2 257 ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvll 308
                                        g+a+ v++++  +++ll+++ + +l+  +g   t+ l  +l ++ lv+++ 
  gi|336253012|ref|YP_004596119.1| 391 RGTAMGVVTVLNWAANLLVSLTFLRLVDVFGQSGTFWLYGALSLAALVFCYR 442
                                       4556666666667777777777777777777774444433333333333333 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   0.3   3.2e-05     0.072     263     354 ..      66     157 ..      60     167 .. 0.82
   2 ?    0.1   7.2      0.12   2.8e+02     242     359 ..     277     403 ..     160     409 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                        MFS_1_like 263 GslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvs 339
                                       G++v   +v+ i    f+ +l ++lG ++l++++ +++++  l++ai   + ++++  ++ gi +g   +++  y+s
  gi|336253012|ref|YP_004596119.1|  66 GVIVSGAMVGAILGAAFGGRLADRLGRRRLILVGAVVFFVGSLIMAIAPTVEILILGRIIDGIGVGFASVVGPLYIS 142
                                       55556666777777788999999999999999999999999999999998999999999999999999999999999 PP

                        MFS_1_like 340 kiapksleatgqgll 354
                                       +i p+++++ + +l 
  gi|336253012|ref|YP_004596119.1| 143 EISPPKIRGSLVSLN 157
                                       999999998887765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.12
                        MFS_1_like 242 giienFlflYLkelgasntllGslvalgv.vaeiplfffaeklleklGhvklliiallayilrfllyaii....... 310
                                       + +  ++   L++ g+  t +++l ++g  v ++ l ++a  l++++G + ll+++l  +++ + +++++       
  gi|336253012|ref|YP_004596119.1| 277 NTVMYYAPTILESTGFEDT-ASILATVGIgVVNVALTVVAVLLIDRTGRRPLLLTGLGGMTVMLGVLGAVfylpgls 352
                                       4555566666777777654.45555555335678899999*******************999999998888999998 PP

                        MFS_1_like 311 .enawlvlpievLhgisfgllwaaa.veyvskiapksleatgqgllsglyf 359
                                         + w++    +L+ + f++  + +    +s+i p++ ++t +g+++ l +
  gi|336253012|ref|YP_004596119.1| 353 gVVGWVATGSLMLYVAFFAIGLGPVfWLMISEIYPMEFRGTAMGVVTVLNW 403
                                       888888888888888777776554303457899999999999999998877 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.8       4.3   9.7e+03       4      18 ..      22      36 ..      21      42 .. 0.52
   2 ?   14.2   4.2   1.4e-05     0.032       2      33 ..      71     104 ..      70     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.3
                    Gly-zipper_Omp  4 aiGAaaGaliGgavg 18
                                      a+ A+ G l+G  +g
  gi|336253012|ref|YP_004596119.1| 22 ALAALNGLLFGFDTG 36
                                      445666666666555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.4e-05
                    Gly-zipper_Omp   2 GaaiGAaaGaliGg.avg...grgtGaliGAavGaa 33 
                                       Ga++GA++Ga++Gg       gr + +l+GA+v  +
  gi|336253012|ref|YP_004596119.1|  71 GAMVGAILGAAFGGrL-AdrlGRRRLILVGAVV-FF 104
                                       9************952.335589999****965.55 PP

>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.5       3.6   8.1e+03      18      33 ..      28      41 ..      21      42 .. 0.47
   2 ?   11.0   3.2   0.00012      0.28       9      34 ..      70     101 ..      68     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.6
                                      XXXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG 18 GaliGsgggkGAaiGA 33
                                      G l+G ++  G + GA
  gi|336253012|ref|YP_004596119.1| 28 GLLFGFDT--GVISGA 41
                                      55555333..444444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00012
                                       XXXXXXXXXXXXXX...XXXXXX....XXXXXX CS
                   Gly-zipper_YMGG   9 iGAaaGAvvGaliG...sgggkG....AaiGAa 34 
                                        GA +GA++Ga++G   +  + G     ++GA+
  gi|336253012|ref|YP_004596119.1|  70 SGAMVGAILGAAFGgrlA-DRLGrrrlILVGAV 101
                                       589999999999994421.22235555677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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):               8  [number of targets reported over threshold]
# CPU time: 0.71u 0.27s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 3108.57
//
Query:       gi|336253013|ref|YP_004596120.1|  [L=255]
Description: hypothetical protein Halxa_1609 [Halopiger xanaduensis SH-6]
Scores for complete 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-67  227.4   0.1    1.6e-67  227.2   0.1    1.0  1  DUF2071   Uncharacterized conserved protein (COG2071)
    1.2e-05   25.0   0.1    3.8e-05   23.4   0.1    1.9  1  ADC       Acetoacetate decarboxylase (ADC)


Domain annotation for each model (and alignments):
>> DUF2071  Uncharacterized conserved protein (COG2071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.2   0.1   1.8e-71   1.6e-67       2     211 ..      27     245 ..      26     246 .. 0.96

  Alignments for each domain:
  == domain 1  score: 227.2 bits;  conditional E-value: 1.8e-71
                           DUF2071   2 qeWrdllflhwpvdpealapllPaglelDtfdGkayvslvpFrmedvrvrglpavpglstfpelNvRtYvrdkegrr 78 
                                       ++Wr+ lf+hwp++p+al+p lP+ l+l+t++G+a++s++pF++++v++rg p+ +++  fpelNvRtYvr+ + ++
  gi|336253013|ref|YP_004596120.1|  27 MTWRHGLFVHWPISPDALRPQLPDPLALETWEGDAWISVLPFVLVNVGLRGSPSATRIA-FPELNVRTYVRY-RDDP 101
                                       89***************************************************999999.**********87.789* PP

                           DUF2071  79 GVvFlsldadrllivlvarllfglpYvtarmrveeeegeveyksrr.............sparfaatyrptaeveea 142
                                       G++F+s+d+ ++l++++a + ++lp+++a+m+v+ +e+ ++++srr             ++  f+atyrp+++++++
  gi|336253013|ref|YP_004596120.1| 102 GLFFFSVDVGNPLVAAAAGQ-TRLPVRYAQMHVSGSETGISFSSRRtdvnpatagepdrESGWFSATYRPDGDAFRP 177
                                       *************7776666.8************999******9999**********999999************** PP

                           DUF2071 143 epgsleeflteryrlYtrrrgrlleyeveHepwplqeaellelentlleaaglplkpsseplvlyspgv 211
                                       ep++le++lter+r+Y+ ++g +l++ev+Hepwplq+ae++++entl+ea+glp  p+++p+++y++++
  gi|336253013|ref|YP_004596120.1| 178 EPDTLEYWLTERRRFYAPANGDVLTAEVSHEPWPLQPAEVTIHENTLFEADGLPV-PTESPIAYYCDEL 245
                                       ******************************************************8.9779******985 PP

>> ADC  Acetoacetate decarboxylase (ADC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   4.2e-09   3.8e-05      17      91 ..      22     111 ..       7     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.2e-09
                                       E......EEEEEEEEEEE-HHHHHTTSBTTEEECS.TSEEEEEEEEEEEECTTTC........EEEEEEEEEEEEET CS
                               ADC  17 y......naealtvsyrtdpeaaaallPepLelae.rplvavyfaeypdssfggg........qYneagivvpvryg 78 
                                       +       +++l v+++ +p+a++  lP+pL l+  ++ +++ +  +  +++g           + e+ +   vry+
  gi|336253013|ref|YP_004596120.1|  22 PhltsmtWRHGLFVHWPISPDALRPQLPDPLALETwEGDAWISVLPFVLVNVGLRgspsatriAFPELNVRTYVRYR 98 
                                       133455699**************************9888888888888888887788899999************** PP

                                       TEEEEEEEEEEES CS
                               ADC  79 gkegayilvlwvd 91 
                                       + +g++++++ v 
  gi|336253013|ref|YP_004596120.1|  99 DDPGLFFFSVDVG 111
                                       *******998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1799.55
//
Query:       gi|336253014|ref|YP_004596121.1|  [L=308]
Description: transcription factor TFIIB cyclin-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-23   82.4   1.6    4.6e-14   52.2   0.4    2.3  2  TFIIB           Transcription factor TFIIB repeat
    1.9e-10   40.1   4.6      3e-10   39.4   4.6    1.3  1  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.013   15.5   1.1      0.028   14.5   1.1    1.4  1  DZR             Double zinc ribbon
      0.026   14.6   0.0      0.041   13.9   0.0    1.2  1  RB_B            Retinoblastoma-associated protein B domain
       0.11   12.5   1.5       0.27   11.2   1.5    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.27   11.4   3.3        3.4    7.9   0.2    2.6  2  Zn-ribbon_8     Zinc ribbon domain
       0.88    9.8   4.0       0.36   11.0   0.6    2.0  2  HNH             HNH endonuclease


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 !   52.2   0.4   1.8e-17   4.6e-14       1      65 [.     129     193 ..     129     199 .. 0.95
   2 !   29.2   0.0   2.8e-10   7.1e-07       2      71 .]     224     295 ..     223     295 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.8e-17
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlq 65 
                                       i r+ ++l L++ V+++A  l++ a ++++ +Grs +g aAA++y  cr   v+rt  ei +v++
  gi|336253014|ref|YP_004596121.1| 129 IRRVNAQLSLSDSVREQACALFESAQSDGLFQGRSLEGFAAAAIYATCRTRSVARTIDEITAVAR 193
                                       678999********************************************************997 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 2.8e-10
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTS..S--HHHHHHHSS--SHHH CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeev..krtqkeissvlqVsekti 71 
                                       +r a++le    V+++A e a+  +e + + Gr p g+a+ cly A++  e+    tq+  ++v+ V+ +ti
  gi|336253014|ref|YP_004596121.1| 224 PRYAAKLEVGSAVERRAREHANALSEAGQIGGRNPSGVAGGCLYKATQEREEwpTVTQAAAADVADVAPVTI 295
                                       6889*******************************************9888722345666677777777765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   4.6   1.2e-13     3e-10       2      43 .]      15      53 ..      14      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.2e-13
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      +CP+C+++     +  +e+vC++CGlV  ++ +d gpewr f
  gi|336253014|ref|YP_004596121.1| 15 VCPECNGRL---RETDTETVCEECGLVTTEDAVDRGPEWRSF 53
                                      7******94...444489**********************87 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.1   1.1e-05     0.028      10      38 ..      11      39 ..       6      43 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                               DZR 10 pdarfCseCgtklkavaaedrCpsCgekv 38
                                      +   +C+eC+ +l+++ +e++C +Cg  +
  gi|336253014|ref|YP_004596121.1| 11 NLTSVCPECNGRLRETDTETVCEECGLVT 39
                                      55679*********9999*******9665 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 ?   13.9   0.0   1.6e-05     0.041      15      84 ..     127     194 ..     119     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                              RB_B  15 vrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrk 84 
                                         +r++ ++L+ls+++re++  lfe +  ++  l++ R l+ +  +a+Y++++  +  ++  ei +  r 
  gi|336253014|ref|YP_004596121.1| 127 AEIRRVNAQLSLSDSVREQACALFESA--QSDGLFQGRSLEGFAAAAIYATCRTRSVARTIDEITAVARA 194
                                       46889999****************985..8899****************************999887665 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 ?   11.2   1.5   0.00011      0.27      28      59 ..      14      42 ..       6      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                    OrfB_Zn_ribbon 28 SktCseCgsknkealsgrtfkCpnCgfeadrD 59
                                      S  C+eC  +++e  ++ + +C++Cg++   D
  gi|336253014|ref|YP_004596121.1| 14 S-VCPECNGRLRE--TDTETVCEECGLVTTED 42
                                      4.6**********..***********987655 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0013       3.4      23      37 ..       9      24 ..       3      26 .. 0.78
   2 ?    4.3   0.3     0.017        43      24      35 ..      27      39 ..      22      44 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0013
                       Zn-ribbon_8 23 daplta.CPeCgsevr 37
                                       ++lt  CPeC++++r
  gi|336253014|ref|YP_004596121.1|  9 NSNLTSvCPECNGRLR 24
                                      5568888*****9987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.017
                       Zn-ribbon_8 24 apltaCPeCgs.e 35
                                      + +t+C eCg  +
  gi|336253014|ref|YP_004596121.1| 27 DTETVCEECGLvT 39
                                      45777****9755 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.6   0.00014      0.36      26      43 ..       5      22 ..       2      26 .. 0.84
   2 ?   -2.2   0.2       1.9   4.9e+03       1       5 [.      32      36 ..      32      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                               HNH 26 gaddieNlqllCksCHnk 43
                                      ++++ +Nl+ +C++C+ +
  gi|336253014|ref|YP_004596121.1|  5 DSNSNSNLTSVCPECNGR 22
                                      567899**********87 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                               HNH  1 CeyCg 5 
                                      Ce+Cg
  gi|336253014|ref|YP_004596121.1| 32 CEECG 36
                                      999*8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2209.81
//
Query:       gi|336253015|ref|YP_004596122.1|  [L=702]
Description: MCM family protein [Halopiger xanaduensis SH-6]
Scores for complete 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-92  308.6   0.0    2.8e-92  307.9   0.0    1.3  1  MCM              MCM P-loop domain
    6.6e-37  126.2   0.2    1.1e-36  125.4   0.2    1.4  1  MCM_OB           MCM OB domain
    1.1e-28   99.5   0.4    2.4e-28   98.4   0.4    1.6  1  MCM_lid          MCM AAA-lid domain
    9.1e-10   38.3   0.0      1e-05   25.1   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.6e-09   37.1   0.9    3.6e-09   37.1   0.9    2.8  2  MCM_N            MCM N-terminal domain
    3.9e-06   26.9   0.0    1.1e-05   25.5   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00055   20.4   1.4     0.0019   18.6   0.1    2.4  2  AAA_16           AAA ATPase domain
      0.001   18.8   0.1       0.02   14.6   0.1    2.3  1  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.031   14.7   0.1       0.16   12.4   0.0    2.4  2  AAA              ATPase family associated with various cellul
      0.035   14.0   0.0       0.14   12.0   0.0    2.0  1  AAA_3            ATPase family associated with various cellul
      0.038   13.7   0.2      0.094   12.4   0.2    1.6  1  AAA_30           AAA domain
      0.062   13.7   0.2        1.3    9.4   0.0    2.6  2  DUF5631          Family of unknown function (DUF5631)
        2.3    8.1   4.7        8.7    6.2   0.3    3.4  4  SurA_N_2         SurA N-terminal 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 !  307.9   0.0     2e-95   2.8e-92       2     222 ..     267     489 ..     266     491 .. 0.97

  Alignments for each domain:
  == domain 1  score: 307.9 bits;  conditional E-value: 2e-95
                                       HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHH CS
                               MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyve 78 
                                       ++ei ++++++d++e+++ siapsiyg+++ k a++lqlf+gv+k+l+d++++rgd ++ll+gdpgt+Ksq+L y++
  gi|336253015|ref|YP_004596122.1| 267 KKEIYNISNRDDVYEQMIGSIAPSIYGYDQEKLAMILQLFSGVTKQLPDGSRIRGDLHMLLIGDPGTGKSQMLGYIQ 343
                                       6899************************************************************************* PP

                                       HHSSSEEEEESSSSSSSHSSSEEEEES..SSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEE CS
                               MCM  79 klapravytsgkgssaagLtaavvrde..etgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisia 153
                                       ++apr+vytsgkgss+agLtaa vrd+  + ++++leaGalvlad+G++++De+dkm+ edrsa+hEa+Eqq+is++
  gi|336253015|ref|YP_004596122.1| 344 NIAPRSVYTSGKGSSSAGLTAAAVRDDfgDGQQWTLEAGALVLADQGIAAVDELDKMRPEDRSAMHEALEQQKISVS 420
                                       **************************8334567******************************************** PP

                                       SSSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHH CS
                               MCM 154 KaGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivs 222
                                       KaGi+atL++r+s+l Aanpk+gr+d+ +++ e+i+l++al+srFDlif++ D++deekD++laehi++
  gi|336253015|ref|YP_004596122.1| 421 KAGINATLKSRCSLLGAANPKYGRFDQYEPIGEQIDLEPALISRFDLIFTVTDQPDEEKDKNLAEHILT 489
                                       *******************************************************************97 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   0.2   8.2e-40   1.1e-36       2     124 ..     103     228 ..     102     230 .. 0.96

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 8.2e-40
                                       XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-HHH-EEE-GGGSE CS
                            MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCeskdpfkleteksk 73 
                                       +R++rs ++++lv+v+Giv +a++v+pk++ a+fec+ cg+ ++v     +++eP++C  + Ce+++pf+++ ++s+
  gi|336253015|ref|YP_004596122.1| 103 IREIRSPDMNTLVEVRGIVRKATDVRPKIEDAAFECQLCGTLTRVpqssgDFQEPHEC--QGCERQGPFQVNFDQSE 177
                                       8***************************************98888899988999****..99*************** PP

                                       EEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                            MCM_OB  74 fvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                       fvd qkl++QEspe +  Ge+P+sl+v++edd++ +v+PGd+v+ tG++r 
  gi|336253015|ref|YP_004596122.1| 178 FVDSQKLRIQESPEGLRGGETPQSLDVHVEDDITGEVTPGDHVSATGVLRL 228
                                       ************************************************986 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.4   1.7e-31   2.4e-28       1      86 [.     527     611 ..     527     612 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 1.7e-31
                                       HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHH CS
                           MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedve 77 
                                       ellrkYia+a+++++P+++e+a+e+++++Yv+lR++ +d+ +  +p+t+R+Le+l+RLseA+A++rls++v+e+d++
  gi|336253015|ref|YP_004596122.1| 527 ELLRKYIAFAKQNCHPRMTEAAREAIRDFYVDLRSKGTDE-DAPVPVTARKLEALVRLSEASARVRLSDTVEESDAN 602
                                       68*********************************99766.99********************************** PP

                                       HHHHHHHHH CS
                           MCM_lid  78 eairllkes 86 
                                       ++i++++++
  gi|336253015|ref|YP_004596122.1| 603 RVIEIVRSC 611
                                       ******987 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00017      0.24      21      49 ..     321     349 ..     318     360 .. 0.88
   2 !   25.1   0.0   7.2e-09     1e-05      96     159 ..     378     441 ..     363     476 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                      Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsllppl 49 
                                       G  ++ll+G pG+GK+ +   ++++ p+ 
  gi|336253015|ref|YP_004596122.1| 321 GDLHMLLIGDPGTGKSQMLGYIQNIAPRS 349
                                       7889*************999999999875 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 7.2e-09
                      Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                       + + G++ la +G+  +DEl +++ +   ++ e le++++++s+a  +++  +r+ l+ a+Np 
  gi|336253015|ref|YP_004596122.1| 378 TLEAGALVLADQGIAAVDELDKMRPEDRSAMHEALEQQKISVSKAGINATLKSRCSLLGAANPK 441
                                       7889**********************************************************94 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.9   2.6e-12   3.6e-09       3      73 ..      14      75 ..      12     104 .. 0.91
   2 ?    2.6   1.6      0.14     2e+02      21      85 ..     482     561 ..     461     642 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.6e-12
                             MCM_N  3 kFedFLeefkddsededgekkYrdqlqemaer...ekttLevdlddLaafdeeLaeailenpkeylplleealk 73
                                      +Fe+F++++            Y ++++++a++   e+++L vd++dL+ +d++La+  l++p++   + eeal+
  gi|336253015|ref|YP_004596122.1| 14 SFEQFFRNY------------YDNEIKQLAQQypnEQRSLHVDWQDLYRYDPDLADDFLNQPEQLQRYAEEALR 75
                                      799999999............888999988887879************************************97 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                             MCM_N  21 e.......kkYrdqlqemaerekttLevdlddLaafde........eLae.ailenpkeylplleealkevvkklep 81 
                                       +       + Y  +l +  +++ t+Lev+ d + +  e        eL +  i    + ++p + ea++e +++++ 
  gi|336253015|ref|YP_004596122.1| 482 NlaehiltTNYAGELTT-QREQMTSLEVSNDEIDEMTEqvdpeidaELLRkYIAFAKQNCHPRMTEAAREAIRDFYV 557
                                       25666666777777777.55677999999999999955566688885555156666778889999999999988776 PP

                             MCM_N  82 sykd 85 
                                       +   
  gi|336253015|ref|YP_004596122.1| 558 DLRS 561
                                       4443 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 !   25.5   0.0   7.9e-09   1.1e-05       1     138 []     324     465 ..     324     465 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 7.9e-09
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEE...E--TT--HHHHH--B--.........--------G-SEEEEESG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyv...qltrdtteedlkgrreikngttslvdsplvraaregeilvlDEv 74 
                                       ++lL+G+pGtgKs++  ++     r+v +      ++++t++ ++     ++++  l+ ++lv       i+ +DE+
  gi|336253015|ref|YP_004596122.1| 324 HMLLIGDPGTGKSQMLGYIQNIAPRSVYTSgkgSSSAGLTAAAVRDDFG-DGQQWTLEAGALV--LADQGIAAVDEL 397
                                       78*********************88877652224456667777666666.3666677888888..77889******* PP

                                       GG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..........-TT-TTHHHHTT- CS
                             AAA_5  75 eraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.........rslnelspalrsRf 138
                                       +++++e  ++++  le++++++ + g     k+       +++++anp +         +++ +l pal+sRf
  gi|336253015|ref|YP_004596122.1| 398 DKMRPEDRSAMHEALEQQKISVSKAGINATLKSR-----CSLLGAANPKYgrfdqyepiGEQIDLEPALISRF 465
                                       *********************9988888877775.....9********9988888888888889999999998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.3e-06    0.0019      24     125 ..     318     414 ..     296     422 .. 0.77
   2 ?   -0.1   0.2      0.78   1.1e+03      73      76 ..     549     552 ..     442     671 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                            AAA_16  24 p....elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaelea 96 
                                              +ll+G++G+GKs ++  +++ + ++  ++++gk  ++      + l+ a+ r + + +  + + +a +  
  gi|336253015|ref|YP_004596122.1| 318 RirgdLHMLLIGDPGTGKSQMLGYIQNIAPRS--VYTSGKGSSS------AGLTAAAVR-DDFGDGQQWTLEAGALV 385
                                       14445899******************877777..7799999999......556666645.77777777777777777 PP

                            AAA_16  97 wrekleealaavpelagaeasrllellkr 125
                                        +++  +a+ + ++++++++s+++e+l +
  gi|336253015|ref|YP_004596122.1| 386 LADQGIAAVDELDKMRPEDRSAMHEALEQ 414
                                       77777788888999999999999998875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.78
                            AAA_16  73 aqal 76 
                                        +a+
  gi|336253015|ref|YP_004596122.1| 549 REAI 552
                                       2222 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.4e-05      0.02      20     143 ..     320     440 ..     309     447 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                                       TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-..BEHHHHHTTT CS
                   Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAeke..kkGlfekadg 94 
                                       + dl++l+ G+ GtGK+ +   i +  +r+     +   ++ ++ l ++     ++  F + ++   ++G++  ad+
  gi|336253015|ref|YP_004596122.1| 320 RGDLHMLLIGDPGTGKSQMLGYIQNIAPRSV---YTSGKGSSSAGLTAA----AVRDDFGDGQQWtlEAGALVLADQ 389
                                       5678999999999999999999998888654...455566666666666....3455666555541145******** PP

                                       SEEEEETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEESS CS
                   Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqegev..ervGsskeikvdvriiaatne 143
                                       G+  +De+ ++ +e  + + ++l+++++  ++ G +++ k  + ++ a+n 
  gi|336253015|ref|YP_004596122.1| 390 GIAAVDELDKMRPEDRSAMHEALEQQKIsvSKAGINATLKSRCSLLGAANP 440
                                       ***********************9997522699999999999999998875 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 ?   12.4   0.0   0.00011      0.16       1     110 [.     325     439 ..     325     472 .. 0.70
   2 ?   -3.4   0.0       8.7   1.2e+04      77      96 ..     635     654 ..     625     678 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                       EEEESSTTSSHHHHHHHHHHHHTHEE.EEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.........TSEEEEEETG CS
                               AAA   1 vllyGppGtGKTllakavakelgvef.leisgsellskyvgesekkirelfkeakeka.........kpsilfiDEi 67 
                                       +ll+G pGtGK+ +   + + + +++  + +gs+      g +++ +r+ f + ++           ++ i  +DE+
  gi|336253015|ref|YP_004596122.1| 325 MLLIGDPGTGKSQMLGYIQNIAPRSVyTSGKGSSS----AGLTAAAVRDDFGDGQQWTleagalvlaDQGIAAVDEL 397
                                       89*************99999986544144444444....4889999999998876655666779997779******* PP

                                       GGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..........SSTEEEEEEES CS
                               AAA  68 dalaksrsgseseeeervvnqLlteldgvkkk..........eskvivigatn 110
                                       d++ +++            +++ ++l+++k +          +s++ ++ga+n
  gi|336253015|ref|YP_004596122.1| 398 DKMRPED-----------RSAMHEALEQQKISvskaginatlKSRCSLLGAAN 439
                                       ***9988...........33333333333333222333334445555555555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.7
                                       CCCHHHHHHHHHHHHHHHHT CS
                               AAA  77 seseeeervvnqLlteldgv 96 
                                       ++++++ + ++qL++ ++++
  gi|336253015|ref|YP_004596122.1| 635 KSQRDRIKNLKQLISDIEEE 654
                                       34445555555555555544 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 ?   12.0   0.0    0.0001      0.14       1     112 [.     324     440 ..     324     449 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpd..llPsdilGtevfeeke..kefefkkGpvf.an..lllade 70 
                                       h+ll g PG++k ++   + ++   +     +t+      + ++ + v ++    +++++++G+++ a+  +  +de
  gi|336253015|ref|YP_004596122.1| 324 HMLLIGDPGTGKSQMLGYIQNIAPRS----VYTSGkgSSSAGLTAAAVRDDFGdgQQWTLEAGALVlADqgIAAVDE 396
                                       67777777777776655554443322....233320023445555555554323478888888865233337778** PP

                             AAA_3  71 inrappktqsalleameerqvtvege..thklpepflvlatqnP 112
                                       +++  p  +sa+ ea+e+++++v+++  + +l++   +l + nP
  gi|336253015|ref|YP_004596122.1| 397 LDKMRPEDRSAMHEALEQQKISVSKAgiNATLKSRCSLLGAANP 440
                                       ********************998765115678888888877777 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   6.8e-05     0.094      17     119 ..     321     419 ..     316     428 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.8e-05
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtll 92 
                                       gd+ ++l G +GtGK+ +l+ +++++ ++   +  g ++ g  A+++++++g      ++++ +  g+  l+++ + 
  gi|336253015|ref|YP_004596122.1| 321 GDLHMLLIGDPGTGKSQMLGYIQNIAPRSvYTSGKGSSSAGLTAAAVRDDFGD----GQQWTLEA-GALVLADQGIA 392
                                       567789*******************9999556667888888888888888883....12222111.22344555677 PP

                            AAA_30  93 ivDEagmvdtkqlaallkaaekagakv 119
                                        vDE   +  ++  a+ +a+e+++++v
  gi|336253015|ref|YP_004596122.1| 393 AVDELDKMRPEDRSAMHEALEQQKISV 419
                                       777777777777666666666666555 PP

>> DUF5631  Family of unknown function (DUF5631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00098       1.3      25      71 ..       1      47 [.       1      56 [. 0.93
   2 ?    1.2   0.1      0.36     5e+02      33      77 ..     506     551 ..     496     554 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00098
                           DUF5631 25 lakaaaagtgvldeEvdllrehldtirkqvlaaYPdvdaalvlnwlL 71
                                      +a+a a ++ ++d+  + +r+  d+  kq+ ++YP+ +  l ++w+ 
  gi|336253015|ref|YP_004596122.1|  1 MAQAQAGNSELVDSFEQFFRNYYDNEIKQLAQQYPNEQRSLHVDWQD 47
                                      68999999*********************************99*985 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.36
                           DUF5631  33 tgvldeEvdllrehld.tirkqvlaaYPdvdaalvlnwlLLAaiea 77 
                                         v ++E+d + e++d +i +++l +Y    +++    +  Aa ea
  gi|336253015|ref|YP_004596122.1| 506 LEVSNDEIDEMTEQVDpEIDAELLRKYIAFAKQNCHPRMTEAAREA 551
                                       568899***9999998689999**9998888777777776666665 PP

>> SurA_N_2  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.5       4.1   5.6e+03      56      74 ..      19      37 ..      16      44 .. 0.69
   2 ?    1.7   0.0      0.16   2.2e+02      98     138 ..     407     447 ..     404     449 .. 0.85
   3 ?    6.2   0.3    0.0063       8.7      76     128 ..     474     527 ..     470     541 .. 0.86
   4 ?   -2.2   0.0       2.5   3.4e+03     126     141 ..     612     629 ..     592     631 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.1
                          SurA_N_2 56 fqqaveearqqlqqqlgen 74
                                      f++ ++++ +ql+qq+ ++
  gi|336253015|ref|YP_004596122.1| 19 FRNYYDNEIKQLAQQYPNE 37
                                      7777888888888776544 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.16
                          SurA_N_2  98 lleqeaeklGltvsdeelqdaiqgnpaikqsFqpetGkFdk 138
                                        + +++e+ +++vs++ +++++++   +  +  p+ G+Fd+
  gi|336253015|ref|YP_004596122.1| 407 AMHEALEQQKISVSKAGINATLKSRCSLLGAANPKYGRFDQ 447
                                       6789999*****************77767767799999997 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0063
                          SurA_N_2  76 deseedeaqlreqvldqlvseklleqeaeklGltvsdeelqdaiqg.npaikqs 128
                                       +++ee++++l e +l++    +l +q  +   l+vs++e++++ ++ +p+i ++
  gi|336253015|ref|YP_004596122.1| 474 QPDEEKDKNLAEHILTTNYAGELTTQREQMTSLEVSNDEIDEMTEQvDPEIDAE 527
                                       467788899*************************************99987665 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 2.5
                          SurA_N_2 126 kqs..FqpetGkFdkekl 141
                                        q     petG+Fd++ +
  gi|336253015|ref|YP_004596122.1| 612 LQDigVDPETGEFDADIV 629
                                       444444599*****9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (702 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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: 0.73u 0.24s 00:00:00.97 Elapsed: 00:00:00.42
# Mc/sec: 5050.90
//
Query:       gi|336253016|ref|YP_004596123.1|  [L=212]
Description: hypothetical protein Halxa_1612 [Halopiger xanaduensis SH-6]
Scores for 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-25   87.0   0.8    8.9e-25   86.6   0.0    1.6  2  DUF502    Protein of unknown function (DUF502)
     0.0075   16.7   1.7      0.013   16.0   1.7    1.2  1  FtsX      FtsX-like permease family


Domain annotation for each model (and alignments):
>> DUF502  Protein of unknown function (DUF502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2      0.74   6.6e+03      32      38 ..      19      25 ..      12      41 .. 0.58
   2 !   86.6   0.0   9.9e-29   8.9e-25       4     106 .]      69     172 ..      66     172 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.74
                            DUF502 32 riPlvks 38
                                       iPlv +
  gi|336253016|ref|YP_004596123.1| 19 TIPLVAT 25
                                      4555543 PP

  == domain 2  score: 86.6 bits;  conditional E-value: 9.9e-29
                            DUF502   4 lllillvGllasnligrkllklgerllkriPlvksiYsalkqvvetfsseekksfrevvlveyprkglwalgFvtge 80 
                                       + l ll+G++a+ + gr + + ++++++ iP v+++Y+++++ +++++++++++f+ev lve+p++g+++lgF+t  
  gi|336253016|ref|YP_004596123.1|  69 FGLFLLIGFVAEYTPGRYISQRVHQTMETIPGVSTVYESVRRASKILADDDTDQFKEVKLVEFPHEGAYMLGFLTAV 145
                                       67899************************************************************************ PP

                            DUF502  81 tegelatk.geedlvaVfvPtspnpts 106
                                       t+++++++  +ed+v+++vP  pnpt+
  gi|336253016|ref|YP_004596123.1| 146 TPDDIEQSvASEDMVTIMVPLGPNPTT 172
                                       *999*99899***************96 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.7   1.4e-06     0.013      10      91 ..       6      87 ..       5      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                              FtsX 10 lGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagllsi 88
                                      +G+k++ v ++++t  l+ tlv l++ + + l ++ ++  ++l  + +  +   ++l+t++ +++l+ll+  +a + + 
  gi|336253016|ref|YP_004596123.1|  6 IGVKRWLVNGIVITIPLVATLVVLLVVFDFVLGVLSPVIEGVLYAWPNEPPRAVVQLLTLASLFGLFLLIGFVAEYTPG 84
                                      8**************************999999999**********99**********************999866666 PP

                              FtsX 89 ski 91
                                      + i
  gi|336253016|ref|YP_004596123.1| 85 RYI 87
                                      655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1605.77
//
Query:       gi|336253017|ref|YP_004596124.1|  [L=76]
Description: hypothetical protein Halxa_1613 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0073   16.0   0.3       0.31   10.8   0.1    2.2  2  zf-CSL    CSL zinc finger


Domain annotation for each model (and alignments):
>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.0    0.0028        50      14      31 ..       7      25 ..       1      31 [. 0.62
   2 !   10.8   0.1   1.7e-05      0.31      20      39 ..      39      59 ..      37      75 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0028
                                      TTEEEEEE.TTSSEEEEEH CS
                            zf-CSL 14 eesyyypC.RCgdeFelte 31
                                       +     C  Cg  +  te
  gi|336253017|ref|YP_004596124.1|  7 PDRMIAACtHCGALYAATE 25
                                      4445566777777777666 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 1.7e-05
                                      EETTSSE.EEEEHHHHHTT.. CS
                            zf-CSL 20 pCRCgde.Felteedleegae 39
                                       CRCg++ F   +e+l e+a+
  gi|336253017|ref|YP_004596124.1| 39 GCRCGGTtFTKVNEELLENAT 59
                                      5*******8777666666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 580.31
//
Query:       gi|336253018|ref|YP_004596125.1|  [L=276]
Description: 2,5-didehydrogluconate reductase [Halopiger xanaduensis SH-6]
Scores for 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-59  200.2   0.0    3.7e-47  160.9   0.0    2.0  2  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
       0.01   16.2   0.1        2.6    8.4   0.0    3.2  3  HTH_Tnp_1     Transposase
       0.15   11.6   0.0       0.23   11.0   0.0    1.2  1  IP_trans      Phosphatidylinositol transfer protein


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 !  160.9   0.0   6.2e-51   3.7e-47       2     197 ..      19     197 ..      18     202 .. 0.98
   2 !   37.8   0.0     2e-13   1.2e-09     230     292 ..     201     261 ..     196     263 .. 0.96

  Alignments for each domain:
  == domain 1  score: 160.9 bits;  conditional E-value: 6.2e-51
                                       EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTS CS
                      Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeik 78 
                                       lglGtwq ++     ++e +e +r+ale G++++DtA++Y    +e  +G  ++++ ++re+v++atKv      + 
  gi|336253018|ref|YP_004596125.1|  19 LGLGTWQNED-----PDECAESVRTALETGYRHIDTAQAY---DNEGAVGDGIAAADVDREDVFLATKV------WI 81 
                                       899***9885.....7************************...**************************......** PP

                                       SSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTTT- CS
                      Aldo_ket_red  79 sglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkkkv 155
                                       ++l ++++ e  +esl rLg+dyvDll++H+p ++++  ee+l+a++el++eG+i ++GvSnf  eq+e+a +    
  gi|336253018|ref|YP_004596125.1|  82 DNLAHDDVLETARESLDRLGVDYVDLLYVHWPSREYD-AEETLSAFDELYDEGLIENVGVSNFLPEQVEEAVELCDA 157
                                       *************************************.*********************************99999* PP

                                       -EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTT CS
                      Aldo_ket_red 156 kivavqveynllreleeegllelckkkgvpliaysplggGll 197
                                       +i a+qve ++l  l + +++e+c  +++ ++ yspl++G+ 
  gi|336253018|ref|YP_004596125.1| 158 PIFANQVELHPL--LPQDEIREVCDTHDIEVVGYSPLARGAV 197
                                       ************..*************************985 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 2e-13
                                       HHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                      Aldo_ket_red 230 eelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                       +e++e+a++h+vs aq++l++a   ++++++ip++ + ++++dn+++l l+l+ ++v+++d++
  gi|336253018|ref|YP_004596125.1| 201 PEIREVAEKHDVSEAQVSLAWAR--EKGVTAIPKSASEDHIRDNFESLTLELDVDDVETIDAI 261
                                       6899*******************..************************************98 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.018   1.1e+02      13      34 ..      33      54 ..      28      56 .. 0.87
   2 ?   -0.4   0.0      0.24   1.4e+03      21      35 ..     170     184 ..     163     186 .. 0.83
   3 ?    8.4   0.0   0.00043       2.6      24      46 ..     201     224 ..     194     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.018
                         HTH_Tnp_1 13 ariVreslepgksvsevArrhg 34
                                      a+ Vr +le+g+++ ++A+ ++
  gi|336253018|ref|YP_004596125.1| 33 AESVRTALETGYRHIDTAQAYD 54
                                      5679**************9876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.24
                         HTH_Tnp_1  21 epgksvsevArrhgv 35 
                                        p+  ++ev+  h++
  gi|336253018|ref|YP_004596125.1| 170 LPQDEIREVCDTHDI 184
                                       5788999****9998 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00043
                         HTH_Tnp_1  24 ksvsevArrhgvspnqLy.kWrrq 46 
                                         ++evA++h+vs++q + +W r+
  gi|336253018|ref|YP_004596125.1| 201 PEIREVAEKHDVSEAQVSlAWARE 224
                                       6799***********976456665 PP

>> IP_trans  Phosphatidylinositol transfer protein
   #    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     112     163 ..      76     127 ..      66     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.9e-05
                                       EEEEESSSS--SSTT---HHHHTT-EEEEE-TT-GGG-GGG--GGG-TTT-- CS
                          IP_trans 112 etvhkedngtqeNvfnlskeelkkreveviDivndkisskdykeeedptlfk 163
                                        t +  dn  +++v++   e+l +  v+++D+   + +s++y++ee ++ f 
  gi|336253018|ref|YP_004596125.1|  76 ATKVWIDNLAHDDVLETARESLDRLGVDYVDLLYVHWPSREYDAEETLSAFD 127
                                       5677779999************************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2117.27
//
Query:       gi|336253019|ref|YP_004596126.1|  [L=85]
Description: hypothetical protein Halxa_1615 [Halopiger xanaduensis SH-6]
Scores for 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-08   33.1  18.6    6.5e-08   32.7  18.6    1.2  1  BofA           SigmaK-factor processing regulatory protein Bo
  ------ inclusion threshold ------
       0.71   10.4   3.8       0.94   10.0   3.8    1.2  1  GTA_holin_3TM  Holin of 3TMs, for gene-transfer release


Domain annotation for each model (and alignments):
>> BofA  SigmaK-factor processing regulatory protein BofA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7  18.6   7.3e-12   6.5e-08       5      75 .]      10      79 ..       5      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 7.3e-12
                              BofA  5 llllvikllk..kplkillkllinavlGlvlLflvNllgavfglhipiNlitaliagflGipGvilLillklf 75
                                      l+l+++ +l     ++++  +++nav+Glv+Lfl+    avfgl +++ +i + i++++G+pG +l++ll+lf
  gi|336253019|ref|YP_004596126.1| 10 LVLVLAAVLGasTLIQTVRPFIVNAVVGLVVLFLAQ---AVFGLNVAVTPIALVIVAIGGFPGSLLVLLLSLF 79
                                      333333333345889999999***************...9******************************997 PP

>> GTA_holin_3TM  Holin of 3TMs, for gene-transfer release
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.8    0.0001      0.94      64     120 ..      21      84 ..      11      85 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0001
                     GTA_holin_3TM  64 dgfnrrwRPllgyvtlalllwai.........vldPllaaaialglalvPepLwwllggvvgfyfv 120
                                       +++ +  RP+++ ++++l+++ +         ++ P+  a ++++++++P +L+ ll+++ g++fv
  gi|336253019|ref|YP_004596126.1|  21 STLIQTVRPFIVNAVVGLVVLFLaqavfglnvAVTPI--ALVIVAIGGFPGSLLVLLLSLFGVAFV 84 
                                       6677788***998666655554445788888899999..788888999***********9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 639.57
//
Query:       gi|336253020|ref|YP_004596127.1|  [L=107]
Description: hypothetical protein Halxa_1616 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.004   17.1   0.6     0.0045   16.9   0.6    1.0  1  7TMR-DISM_7TM    7TM diverse intracellular signalling
     0.0071   15.7   1.3     0.0089   15.4   1.3    1.0  1  MBOAT            MBOAT, membrane-bound O-acyltransferase fami
  ------ inclusion threshold ------
      0.014   15.1   0.1      0.014   15.1   0.1    1.1  1  DUF4131          Domain of unknown function (DUF4131)
      0.028   13.6   0.2      0.032   13.5   0.2    1.1  1  Herpes_LMP1      Herpesvirus latent membrane protein 1 (LMP1)
      0.045   11.7   0.9      0.047   11.6   0.9    1.1  1  DUF4175          Domain of unknown function (DUF4175)
       0.21   12.6   0.6        2.3    9.3   0.0    2.1  2  Conotoxin        Conotoxin
        0.5   10.3   6.0       0.64    9.9   6.0    1.1  1  DUF2721          Protein of unknown function (DUF2721)


Domain annotation for each model (and alignments):
>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6   1.8e-06    0.0045      96     144 ..      11      59 ..       4      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-06
                     7TMR-DISM_7TM  96 llklllllavllsllllllpllpyteslslaqllallvillllligika 144
                                       l ++l +l +l++ll+ll+ +lp++ ++s++++++++++ll++++g++ 
  gi|336253020|ref|YP_004596127.1|  11 LGRALHALQFLVLLLVLLFVALPHDNAWSILFAVLIVLLLLATAVGLWR 59 
                                       5677888888988899998899999999998777777777777777764 PP

>> MBOAT  MBOAT, membrane-bound O-acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.3   3.5e-06    0.0089     264     304 ..      13      52 ..       8      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.5e-06
                             MBOAT 264 kkfklnkslatlatFlfsAvwHglalgyliwfvlrvllllv 304
                                       ++++   +l +l+++lf+A+ H+ a+  +++ vl+vllll+
  gi|336253020|ref|YP_004596127.1|  13 RALHALQFLVLLLVLLFVALPHDNAW-SILFAVLIVLLLLA 52 
                                       577888899*****************.8888******9996 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   5.4e-06     0.014      15      65 ..      20      70 ..      11     107 .] 0.58

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.4e-06
                           DUF4131 15 llllllllllrrrprrrvllllllllllallgfalrapqpnandlsqlles 65
                                      +l lll+ll+   p+   + +l+++l+++ll +++  +++   d + ++++
  gi|336253020|ref|YP_004596127.1| 20 FLVLLLVLLFVALPHDNAWSILFAVLIVLLLLATAVGLWRRPADGDGQAHL 70
                                      333333333333677777777777777777777777766666666666654 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 ?   13.5   0.2   1.2e-05     0.032     147     210 ..      21      90 ..       4      97 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXX...XXXXXXXX..XXXXXXXXXX-EE-S-- CS
                       Herpes_LMP1 147 ffldlilliialylqqnwwtllvdllwlllflail..iwmy...yhgqrhsd..ehhhddslphpqqatdd 210
                                       ++l l+ll +al  ++n w++l  +l +ll+la    +w       gq h    +    d +  p qa+ d
  gi|336253020|ref|YP_004596127.1|  21 LVLLLVLLFVALP-HDNAWSILFAVLIVLLLLATAvgLWRRpadGDGQAHLGtaDDITSDPFADPGQAAKD 90 
                                       2344566666665.456677777777666666655015543211346666431133344555566676666 PP

>> DUF4175  Domain of unknown function (DUF4175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.9   1.8e-05     0.047      13      79 ..      16      81 ..       5      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.8e-05
                           DUF4175 13 vlalflalsllglwqllpdllrlalllafalallaalvlplrrfrwPtraealrrlerasglphrPl 79
                                       ++ fl+l+l+ l+ +lp+   + +l+a++++ll+++   +  +r+P + +  ++l  a ++   P 
  gi|336253020|ref|YP_004596127.1| 16 HALQFLVLLLVLLFVALPHDNAWSILFAVLIVLLLLAT-AVGLWRRPADGDGQAHLGTADDITSDPF 81
                                      46678999999999999999988888887777666666.6677899******999999998888886 PP

>> Conotoxin  Conotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.9      0.34   8.8e+02       6      23 ..      21      35 ..      17      37 .. 0.47
   2 ?    9.3   0.0   0.00089       2.3       3      33 ..      41      73 ..      39      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.34
                                      XXXXXXXXXXXXXXXXXX CS
                         Conotoxin  6 vlivavLllttlvtadld 23
                                      +++ +vLl   +v+ ++d
  gi|336253020|ref|YP_004596127.1| 21 LVLLLVLL---FVALPHD 35
                                      33333333...4455554 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00089
                                      XXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXX CS
                         Conotoxin  3 LtcvlivavLllt..tlvtadldgdqpadrkak 33
                                      L  vliv++Ll t   l   ++dgd++a++  +
  gi|336253020|ref|YP_004596127.1| 41 LFAVLIVLLLLATavGLWRRPADGDGQAHLGTA 73
                                      6679*********76667778888888876555 PP

>> 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   6.0   0.00025      0.64      59     112 ..       3      56 ..       1      59 [. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00025
                           DUF2721  59 Rarlirrailllvlsallvvlvvlllflsallsldlsllaailfvlalllllvs 112
                                       R+++irr++  +  ++ ++vl+ +llf++   ++ +s+l a+l vl ll+++v+
  gi|336253020|ref|YP_004596127.1|   3 RLECIRRSLGRALHALQFLVLLLVLLFVALPHDNAWSILFAVLIVLLLLATAVG 56 
                                       999*************************33335555555555555544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 806.94
//
Query:       gi|336253021|ref|YP_004596128.1|  [L=175]
Description: hypothetical protein Halxa_1617 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.054   13.2   0.0      0.086   12.6   0.0    1.3  1  DUF2299   Uncharacterized conserved protein (DUF2299)
       0.27   11.7   2.2         18    6.0   0.2    2.5  2  LRV       Leucine rich repeat variant


Domain annotation for each model (and alignments):
>> DUF2299  Uncharacterized conserved protein (DUF2299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.6e-06     0.086      14     127 ..      20     136 ..       9     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.6e-06
                                       EE--...-TTEEEEEEEE-STT..-EEEEEEETT-SSEEEEEEEEE--HHHHHHHHHS-HHHHHHHHHHHHHHHTTT CS
                           DUF2299  14 eevp...danaefhilveppqpggvvvdvikpkgksdvvvvgmgvkvseehkkalsslkeeerkeflselkrdLlrl 87 
                                       +e++   +++ ef + v+       ++ +ik + k  v vvg    ++ e  ++l   +  +r+e+ls++   L++ 
  gi|336253021|ref|YP_004596128.1|  20 QEITahtQEETEFNLQVTLSS---LPIHLIKEEPKGPVRVVGR-SGLDSERARRLVR-DDGQRAELLSQIGPVLATT 91 
                                       444444577778888887777...6888888888866666664.4667775555554.6778999999999888877 PP

                                       T-EEEEE-TTS--......-EEEEEEEEEGGG--HHHHHHHHHHH CS
                           DUF2299  88 cvdfqlipqdeel.....pqsiqvskeiykdgltknelldavkrv 127
                                       +  ++++ +++        +++q    iy dg ++++l+d+v+ +
  gi|336253021|ref|YP_004596128.1|  92 PGFYTFLDEESRGcelreAETLQMEHRIYPDGASQQALMDSVMAI 136
                                       76666666665435668889*********************9976 PP

>> LRV  Leucine rich repeat variant
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2    0.0021        18       7      24 ..      56      73 ..      55      75 .. 0.93
   2 ?    5.1   0.1    0.0038        34       6      16 ..     147     157 ..     146     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0021
                               LRV  7 VArrPdlPpeaLerLahD 24
                                      V+ r+ l++e+ +rL++D
  gi|336253021|ref|YP_004596128.1| 56 VVGRSGLDSERARRLVRD 73
                                      899**************9 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0038
                               LRV   6 aVArrPdlPpe 16 
                                        +A++P++P+e
  gi|336253021|ref|YP_004596128.1| 147 LAASNPQTPRE 157
                                       69*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1258.57
//
Query:       gi|336253022|ref|YP_004596129.1|  [L=688]
Description: DEAD/DEAH box helicase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-22   77.6   0.0      2e-21   76.6   0.0    1.5  1  DEAD        DEAD/DEAH box helicase
    3.8e-15   56.2   0.0    9.2e-15   54.9   0.0    1.7  1  Helicase_C  Helicase conserved C-terminal domain
    3.1e-10   40.3   0.0    5.6e-10   39.5   0.0    1.4  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 !   76.6   0.0   3.3e-25     2e-21       2     170 ..     228     397 ..     227     402 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 3.3e-25
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.STS CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.idl 76 
                                       ++Q+ ++++ l +g+d +v  +T++GKTl+  ++ +++v+    + + k+l+++P+ +La+q +++++    + +d 
  gi|336253022|ref|YP_004596129.1| 228 PVQSLSVENGLfDGDDQMVVSATATGKTLVGEMAGINRVL----NGKGKMLFLVPLVALANQKYEDFQDEYGHlVD- 299
                                       789999999998999************************6....57779******************988887344. PP

                                       EEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  77 rvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqit 153
                                        v+  +g ++  d+ +++d ++d++vgt + +d+ l+tgk ++ ++ ++V+DE+++l +++++  ++ ++++l + t
  gi|336253022|ref|YP_004596129.1| 300 -VSIRVGASRIADNGNQFDPNADVIVGTYEGIDHALRTGK-DMGDIGTVVIDEVHTLKEEDRGHRLDGLISRL-KYT 373
                                       .666699999*****************************9.********************************.577 PP

                                       TTSTTT.......SEEEEEESSBS CS
                                       xxxxxx.......xxxxxxxxxxx RF
                              DEAD 154 cdgklq.......rqvivlSATlp 170
                                       c+++++        q i lSAT+ 
  gi|336253022|ref|YP_004596129.1| 374 CEQRAKrrddyggAQWIYLSATVG 397
                                       777744478888888*******86 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 !   54.9   0.0   1.5e-18   9.2e-15      12     109 ..     449     547 ..     436     549 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1.5e-18
                                       HTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEE CS
                        Helicase_C  12 leeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlV 88 
                                       ++  +g+++if+n+++r++  ++  +k ++++a++h+ l  + r+++ +qf ++e   +++t +++ G+d+p  ++V
  gi|336253022|ref|YP_004596129.1| 449 SKGYRGQTIIFTNSRRRCH--EIS-RKLEYSSAPYHAGLDYKRRKKVERQFGEQELSAVVTTAALAAGVDFPASQVV 522
                                       566799************5..555.5558************************************************ PP

                                       EESSSS....SSHHHHHHHHTTSSS CS
                        Helicase_C  89 infdlp....rnvtsyiqriGRtgR 109
                                       ++  +      +v++++q+ GR+gR
  gi|336253022|ref|YP_004596129.1| 523 FDSLAMgiewLSVQEFHQMLGRAGR 547
                                       987777777677************* 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 !   39.5   0.0   9.4e-14   5.6e-10      27     169 ..     244     396 ..     215     398 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 9.4e-14
                                       EEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEESSS-B--... CS
                            ResIII  27 glikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayke...igkkvsgdkkkakek 99 
                                        +++ aT tGKTlv  ++ i r+l+ ++  k+lflvp  +l +q +e+f++ +   ++    +g +   d+    ++
  gi|336253022|ref|YP_004596129.1| 244 QMVVSATATGKTLVGeMAGINRVLNGKG--KMLFLVPLVALANQKYEDFQDEYGHLVDVsirVGASRIADN---GNQ 315
                                       57899*******************9766..************************99876444333322222...445 PP

                                       ....-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T..............TTHHHHHT---... CS
                            ResIII 100 dstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk..............swreilekfke... 159
                                       ++ n++++v t++ +d ++      ++ ++ + +  ++iDE+H l++++              +         e   
  gi|336253022|ref|YP_004596129.1| 316 FDPNADVIVGTYEGIDHAL------RTGKDMGDIGTVVIDEVHTLKEEDrghrldglisrlkyTC--------Eqra 378
                                       799****************......7788888999************844444444444343311........0222 PP

                                       ........SEEEEEESS- CS
                            ResIII 160 ........avllglTATp 169
                                               a +++l+AT 
  gi|336253022|ref|YP_004596129.1| 379 krrddyggAQWIYLSATV 396
                                       234445668888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (688 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 4791.94
//
Query:       gi|336253023|ref|YP_004596130.1|  [L=847]
Description: methyl-accepting chemotaxis sensory transducer [Halopiger xanaduensis SH-6]
Scores for complete 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  103.0  26.8    1.5e-29  103.0  26.8    4.9  5  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
    4.2e-09   36.6   1.7    4.2e-09   36.6   1.7    5.2  5  HAMP            HAMP domain
    1.9e-07   31.1   0.4    1.9e-07   31.1   0.4    4.1  4  dCache_1        Cache domain
  ------ inclusion threshold ------
      0.016   14.1  29.8     0.0068   15.3   5.5    3.6  3  Spc7            Spc7 kinetochore protein
      0.031   14.3  22.7       0.29   11.2   0.5    5.4  5  DUF1664         Protein of unknown function (DUF1664)
      0.081   13.2  31.4        1.3    9.3   0.4    6.7  6  DUF948          Bacterial protein of unknown function (DUF948
       0.16   12.0  33.8       0.12   12.4   2.4    5.4  5  Laminin_II      Laminin Domain II
       0.18   10.4  30.9       0.01   14.5   7.9    2.3  2  AAA_13          AAA domain
       0.63    9.6  21.0       0.12   11.9   2.3    4.3  5  Fzo_mitofusin   fzo-like conserved region
       0.98   10.2  31.6      0.081   13.6   0.8    5.2  5  DUF2203         Uncharacterized conserved protein (DUF2203)
        6.1    7.0  14.4         15    5.7   0.2    4.0  5  Fib_alpha       Fibrinogen alpha/beta chain family
        6.5    6.0  29.7       0.89    8.8   5.9    3.9  4  CorA            CorA-like Mg2+ transporter protein
        8.8    6.8   6.5        8.5    6.8   0.3    3.8  3  Syntaxin_2      Syntaxin-like protein


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.64   8.8e+02      95     141 ..     342     388 ..     324     411 .. 0.54
   2 !    7.5   4.6    0.0024       3.3      86     157 ..     418     489 ..     409     494 .. 0.61
   3 !    5.6   0.3    0.0092        13     137     169 ..     490     522 ..     487     525 .. 0.83
   4 !  103.0  26.8   1.1e-32   1.5e-29       3     170 ..     527     698 ..     522     700 .. 0.93
   5 ?    2.3   5.1     0.092   1.3e+02      98     151 ..     689     742 ..     687     750 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.64
                                       H..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH CS
                         MCPsignal  95 iieiqkeindsvesleetrqrveegselveetgealkeiveavaeva 141
                                       i ++ +   d +e  e  r+r+e++++ +ee++e+ ++  ++ +  +
  gi|336253023|ref|YP_004596130.1| 342 IDRMRRSLRDRLEEAERERERAESALQDAEEAREEAEQARAESEAFS 388
                                       44444444455555555555555555555555544444333333333 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0024
                                       HHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  86 qaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsas 157
                                       + ++ ++++ +e ++ ++d  ++l  tr  ++   e +++t+e + e+ +a ++va++vq+ia  ++ qs  
  gi|336253023|ref|YP_004596130.1| 418 DESEAMATIAAEFNAMMDDIEATLAATRAFADAVDEAADSTAEGVVEVRSASEQVATSVQQIADGADRQSGQ 489
                                       444444445555555566666666666666666666666677777777777777777777777777777655 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0092
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 137 vaevadlvqeiaaaseeqsasieevnqaveeva 169
                                        + +  +++++++++ee++a++++v++  e+ a
  gi|336253023|ref|YP_004596130.1| 490 LTTIGGEIDDLSTTTEEIAATASDVATLAERTA 522
                                       5778899999**********9999999887766 PP

  == domain 4  score: 103.0 bits;  conditional E-value: 1.1e-32
                                       HHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHH CS
                         MCPsignal   3 laeeaseeAeeg....gkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAd 75 
                                       +a+e+ ++A +g    + e a +v+++e++e + + i d++e i e+a+ TN+LALNA iEAARA  +  GFaVVAd
  gi|336253023|ref|YP_004596130.1| 527 AARESATSAIDGmnaiEDEAAAAVDEVEQLEAEIDAIDDLLEFIREVAQETNMLALNANIEAARADAADAGFAVVAD 603
                                       5677777777776666778888999**************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  76 EVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaase 152
                                       EV++LAe ++ aa ++e+ ++++  + +++++++ +t  r+      ve++  +++ei+e +ae +d +q+i++a++
  gi|336253023|ref|YP_004596130.1| 604 EVKSLAEDTQGAADDVEERLERVRGQAEQVAAVVRQTDARIGDHRGAVEDAIGSIEEISEYAAETNDGIQQISSATQ 680
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHH CS
                         MCPsignal 153 eqsasieevnqaveevak 170
                                       +q+a+ +e+ +  + v++
  gi|336253023|ref|YP_004596130.1| 681 QQAAATQEIVSMADDVTA 698
                                       ********9887777665 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.092
                                       ............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  98 iqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaas 151
                                       i+   +d++++ eet  ++++++  +ee +++l +++++++ ++++ +e+a a+
  gi|336253023|ref|YP_004596130.1| 689 IVSMADDVTAISEETSAEAQTAAAAAEEQTSSLTDVSHTATALSEQARELADAV 742
                                       445555666666666666666666666666666666666666666666666555 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   1.7   3.1e-12   4.2e-09       2      53 .]     300     351 ..     299     351 .. 0.96
   2 !    7.9   1.4    0.0029       3.9      15      52 ..     400     438 ..     389     439 .. 0.86
   3 ?    1.3   0.3      0.33   4.6e+02      12      40 ..     471     500 ..     470     519 .. 0.70
   4 ?   -1.1   0.3       1.8   2.5e+03       9      33 ..     622     648 ..     621     650 .. 0.77
   5 ?   -3.0   0.0       7.4     1e+04      13      28 ..     731     748 ..     730     753 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 3.1e-12
                                       HHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHHH CS
                              HAMP   2 larrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLre 53 
                                       + r++  +Lr L++ a++i +Gdl+++++ ++ DE+GeL r++++M+++Lr+
  gi|336253023|ref|YP_004596130.1| 300 VGRTTAGSLRHLSERAAAIEDGDLEESVESDRSDELGELHRSIDRMRRSLRD 351
                                       5799999*******************************************96 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0029
                                       HHHHHHTTTBTSSTCCTTSSSH.HHHHHHHHHHHHHHHH CS
                              HAMP  15 raarriaaGdldtrlpvsgrDE.iGeLarafNaMldrLr 52 
                                       +a+r+ a+Gdl+ rl+ +   E ++++a+ fNaM+d ++
  gi|336253023|ref|YP_004596130.1| 400 EAMRACADGDLTRRLESDDESEaMATIAAEFNAMMDDIE 438
                                       57888889******9998888878***********9987 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.33
                                       HHHHHHHHHTTT......BTSSTCCTTSSSHHHHH CS
                              HAMP  12 rLaraarriaaG......dldtrlpvsgrDEiGeL 40 
                                       ++a+++++ia+G      +l+t      + Ei++L
  gi|336253023|ref|YP_004596130.1| 471 QVATSVQQIADGadrqsgQLTTI-----GGEIDDL 500
                                       77888999999866666655554.....4444444 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHTT..TBTSSTCCTTS CS
                              HAMP   9 PLrrLaraarriaa..Gdldtrlpvsg 33 
                                       +L+r++ +a+++aa   + d+r+ +++
  gi|336253023|ref|YP_004596130.1| 622 RLERVRGQAEQVAAvvRQTDARIGDHR 648
                                       699999999999975557777777655 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 7.4
                                       HHHHHHHHTT..TBTSST CS
                              HAMP  13 Laraarriaa..Gdldtr 28 
                                       L+++ar++a+  G ++++
  gi|336253023|ref|YP_004596130.1| 731 LSEQARELADavGKFEVS 748
                                       788999999756666655 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.4   1.4e-10   1.9e-07       3     246 ..      46     262 ..      44     265 .. 0.79
   2 ?   -2.4   0.1       2.3   3.2e+03      15      48 ..     423     453 ..     415     484 .. 0.63
   3 ?   -0.6   1.0      0.69   9.5e+02      14      68 ..     489     540 ..     464     573 .. 0.54
   4 ?    3.3   0.3     0.043        59       9      44 ..     606     639 ..     599     701 .. 0.63

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.4e-10
                          dCache_1   3 ieeqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvyl 79 
                                       +e+++e ql + a+  a+ +++++ds  + +  l ++++++++          +r ++++ l  + ++   ++g y+
  gi|336253023|ref|YP_004596130.1|  46 LESDVESQLVSDAQKDASRLDTWFDSTGRYVDSLVRSSTFRNG----------DRFAVADSLYRMTDRT-AFDGAYY 111
                                       78999********************************999874..........7889999999998876.6999999 PP

                          dCache_1  80 vdadGqviassdpssppnleg.tddpadrdwykealaggggkpvisdpyvdqtggkpvitiavpiyddsgkfiGvla 155
                                       v+ + + +   + +++  leg    +a  d + +a ++++ ++++s+p    +g   +++i +   d       +++
  gi|336253023|ref|YP_004596130.1| 112 VNYETGEVD-AKSGTDAALEGgQVSDAVDDRLATATESPS-QVTFSEPFETEDGRPAMLVIGMSSADH------AVV 180
                                       987766665.455555566665333333344555555555.999****97777456999999999873......7** PP

                          dCache_1 156 adldldnlqd.llsniklgetgyvfivdsdGniiahpd.kdllgknlrdelkaqealekalakiesgvssvklngee 230
                                       + +dl +l++ ++ +   +    v +vd++G+ +   d ++ll+++ +d          +  ++ sg++s++ +g e
  gi|336253023|ref|YP_004596130.1| 181 GLVDLGSLSQyMVGTDA-S--DDVVVVDQSGTTVLAADrSRLLQEDAIDPT-------EI--GTGSGTTSFDAGGTE 245
                                       **********6666443.3..47********88888885667776666653.......44..8899*********99 PP

                          dCache_1 231 ylva.yapip.tglgWyl 246
                                         va ya ++ ++++W+l
  gi|336253023|ref|YP_004596130.1| 246 T-VAgYAGLEtEQQDWTL 262
                                       9.999******99****9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
                          dCache_1  15 aeqlanniedvldslenlaetlasnpslqdllee 48 
                                       + ++a+++++ +d +e+   tla + +++d+++e
  gi|336253023|ref|YP_004596130.1| 423 MATIAAEFNAMMDDIEA---TLAATRAFADAVDE 453
                                       56777777777777774...55555555555543 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.69
                          dCache_1  14 laeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksil 68 
                                       ++++++ +i+d  ++ e +a t    ++++ l+e   r++ a res++++++ ++
  gi|336253023|ref|YP_004596130.1| 489 QLTTIGGEIDDLSTTTEEIAATA---SDVATLAERTARTSSAARESATSAIDGMN 540
                                       33333333333333333333333...22444443333335666666666655544 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.043
                          dCache_1   9 eqllglaeqlanniedvldslenlaetlasnpslqd 44 
                                       ++l +  +++a+++e+ l++++ +ae++a    +++
  gi|336253023|ref|YP_004596130.1| 606 KSLAEDTQGAADDVEERLERVRGQAEQVAAV--VRQ 639
                                       5677788999*****************9874..332 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   7.4    0.0063       8.7     189     257 ..     323     388 ..     302     398 .. 0.65
   2 ?    3.2   3.5     0.025        34     183     281 ..     469     566 ..     413     587 .. 0.42
   3 ?   15.3   5.5     5e-06    0.0068     149     289 ..     571     710 ..     564     729 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0063
                              Spc7 189 aaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervl 257
                                        +e++es  ++eL el++++++    ++   ++l+e ++++e+ e+++++++e ++e+e++ ae+e + 
  gi|336253023|ref|YP_004596130.1| 323 LEESVESDRSDELGELHRSIDRMRRSLR---DRLEEAERERERAESALQDAEEAREEAEQARAESEAFS 388
                                       2334445557777777777777777776...77788888888888888888888888888777777664 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.025
                              Spc7 183 leklqeaaeeles...idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelke.qkseleeeiaeaer 255
                                        e+  + ++++++    ++ +L ++  e+++l+++ e    e+a   +++++l+e+ + +++  ++++ ++i   + 
  gi|336253023|ref|YP_004596130.1| 469 SEQVATSVQQIADgadRQSGQLTTIGGEIDDLSTTTE----EIAATASDVATLAERTARTSSaARESATSAIDGMNA 541
                                       2222222222222211344455555555444444444....222222222222222222222022223333332222 PP

                              Spc7 256 vleeckgwsesevsrlkeevkaleel 281
                                        +e +     +ev++l++e +a+++l
  gi|336253023|ref|YP_004596130.1| 542 -IEDEAAAAVDEVEQLEAEIDAIDDL 566
                                       .2333344445555555555555444 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 5e-06
                              Spc7 149 egleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelael 225
                                        ++ ++ ++L+ + +   +  ++ ++ +a + +e+++l e  +  ++  +e+Le +r + +++ a +++  +++ + 
  gi|336253023|ref|YP_004596130.1| 571 REVAQETNMLALNANIEAARADAADAGFAVVADEVKSLAEDTQGAADDVEERLERVRGQAEQVAAVVRQTDARIGDH 647
                                       566666677777777667777888899999**********887766666**************************** PP

                              Spc7 226 qeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivsl 289
                                       +  +e+   +iee++e  +e+++ i++  + ++ ++   ++e+ ++ + v a+ e+t  +  ++
  gi|336253023|ref|YP_004596130.1| 648 RGAVEDAIGSIEEISEYAAETNDGIQQISSATQ-QQAAATQEIVSMADDVTAISEETSAEAQTA 710
                                       **************************9999988.66778899************9998776655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3     0.064        88      47      96 ..     332     384 ..     321     398 .. 0.61
   2 ?    5.9   0.2    0.0088        12      54     114 ..     420     480 ..     406     496 .. 0.61
   3 ?    6.4   0.4    0.0063       8.7      55     121 ..     498     564 ..     479     567 .. 0.86
   4 ?   11.2   0.5   0.00021      0.29      44     121 ..     599     676 ..     588     680 .. 0.90
   5 ?    1.4   1.0      0.22   3.1e+02      68      99 ..     686     717 ..     666     748 .. 0.43

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.064
                           DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqkeisk...eikeevtevredl 96 
                                       s +l ++  s+ + +r L +r+++ +++ +  + + +   e +ee +++r + 
  gi|336253023|ref|YP_004596130.1| 332 SDELGELHRSIDRMRRSLRDRLEEAERERERAESALQdaeEAREEAEQARAES 384
                                       66788888899999999999998888776665544430003333333333333 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0088
                           DUF1664  54 seslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       se++a+   ++++ +d ++++l ++ + + +++e  ++  e++ e+++ +e+v + v++++
  gi|336253023|ref|YP_004596130.1| 420 SEAMATIAAEFNAMMDDIEATLAATRAFADAVDEAADSTAEGVVEVRSASEQVATSVQQIA 480
                                       4555555555666666666666666655555555555555555555555555555555543 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0063
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       ++l++t +++++    v +  + ++++s++ +e  t++ +++++i+++  +  + ve+le++++ i+
  gi|336253023|ref|YP_004596130.1| 498 DDLSTTTEEIAATASDVATLAERTARTSSAARESATSAIDGMNAIEDEAAAAVDEVEQLEAEIDAID 564
                                       67888999999999999999999****************************************9996 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00021
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       + v+ +++++ e+ + + ++ ++r++rv  + ++++++ +++++ + + r+ +++    +e+++e   + +  +++i
  gi|336253023|ref|YP_004596130.1| 599 AVVADEVKSLAEDTQGAADDVEERLERVRGQAEQVAAVVRQTDARIGDHRGAVEDAIGSIEEISEYAAETNDGIQQI 675
                                       6788999999999999***************************************9999999999999998888888 PP

                           DUF1664 121 e 121
                                       +
  gi|336253023|ref|YP_004596130.1| 676 S 676
                                       6 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.22
                           DUF1664  68 idrvdkkldeqkeiskeikeevtevredlsei 99 
                                        +++ +  d++++is+e+++e +++    +e 
  gi|336253023|ref|YP_004596130.1| 686 TQEIVSMADDVTAISEETSAEAQTAAAAAEEQ 717
                                       22233333333333333333333333333333 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 ?   -3.1   0.0         7   9.7e+03      58      77 ..      53      72 ..      50      78 .. 0.84
   2 ?   -0.1   0.0      0.83   1.1e+03      28      67 ..     335     374 ..     286     403 .. 0.74
   3 ?    7.4   3.0    0.0037       5.1      20      87 ..     440     507 ..     421     519 .. 0.77
   4 ?    5.1   0.6      0.02        27      24      85 ..     521     578 ..     514     583 .. 0.79
   5 ?    9.3   0.4   0.00097       1.3      31      74 ..     594     637 ..     579     643 .. 0.61
   6 ?    1.7   5.3      0.23   3.2e+02      29      85 ..     683     736 ..     649     740 .. 0.51

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7
                            DUF948 58 elledvneklekvdplteav 77
                                      +l++d ++   ++d+++++ 
  gi|336253023|ref|YP_004596130.1| 53 QLVSDAQKDASRLDTWFDST 72
                                      68899999999***999876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.83
                            DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvnekl 67 
                                       l e+ ++i+ +++ ++  l+e+e+  + ++  l+d +e  
  gi|336253023|ref|YP_004596130.1| 335 LGELHRSIDRMRRSLRDRLEEAERERERAESALQDAEEAR 374
                                       4566666666666666666666666666666666665544 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0037
                            DUF948  20 vllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       +l   +  +d++ ++ +++ + v ++   +e++ + v++++++  +++ ++ ++  ++ dl+++ +e+
  gi|336253023|ref|YP_004596130.1| 440 TLAATRAFADAVDEAADSTAEGVVEVRSASEQVATSVQQIADGADRQSGQLTTIGGEIDDLSTTTEEI 507
                                       44555666677777777777888888888888888888888888888888888888888888887765 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.02
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                        ++t ++a+++ ++  + +++i +e+++++++v++    ++ +++++d l e ++++++  +
  gi|336253023|ref|YP_004596130.1| 521 TARTSSAARESATSAIDGMNAIEDEAAAAVDEVEQ----LEAEIDAIDDLLEFIREVAQETN 578
                                       56777888888888888899999999999999998....88899999999998888887765 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.00097
                            DUF948  31 aaatieelekqvdpilkevedllakvnelledvneklekvdplt 74 
                                       a a  +++ ++v+++ ++++++ + v+e le v+++ e+v +++
  gi|336253023|ref|YP_004596130.1| 594 ADAGFAVVADEVKSLAEDTQGAADDVEERLERVRGQAEQVAAVV 637
                                       44455555566666666666666666666666666666665555 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.23
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                        +a++ i ++ ++v++i++e   + a++++ ++  +e++ ++  + + +  l+e+ +
  gi|336253023|ref|YP_004596130.1| 683 AAATQEIVSMADDVTAISEE---TSAEAQTAAAAAEEQTSSLTDVSHTATALSEQAR 736
                                       22233333333333333333...3334444444555566666666555555555555 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.07        96      10      47 ..     361     398 ..     326     415 .. 0.58
   2 ?    5.0   1.0     0.017        24      11      78 ..     426     493 ..     416     509 .. 0.69
   3 ?    8.0   3.8    0.0019       2.6       9      95 ..     504     589 ..     495     596 .. 0.60
   4 ?   12.4   2.4   8.7e-05      0.12       4      87 ..     601     684 ..     599     691 .. 0.88
   5 ?    1.2   6.3      0.24   3.3e+02       5      66 ..     658     723 ..     657     751 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  10 etakevleqlaplsqnlentkeklseinrsveetnekv 47 
                                       e a++ l++ ++  ++ e+ +++ + + r +eet ++ 
  gi|336253023|ref|YP_004596130.1| 361 ERAESALQDAEEAREEAEQARAESEAFSRRLEETADDY 398
                                       33334444444444444444444444444444444444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.017
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II  11 takevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                       +a+e  + + ++++ l  t++ +  +++ ++ t e v +   a +++ +sv+++   a++   +l ++
  gi|336253023|ref|YP_004596130.1| 426 IAAEFNAMMDDIEATLAATRAFADAVDEAADSTAEGVVEVRSASEQVATSVQQIADGADRQSGQLTTI 493
                                       56666667777777777777777777777777777777777777777777777777777666666655 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0019
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH. CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeas 85 
                                        e ++++ +++a l++++ +t++ + e ++s     + +++     + A ++v +Le +++ + d l+ +++  ++ 
  gi|336253023|ref|YP_004596130.1| 504 TEEIAATASDVATLAERTARTSSAARESATS---AIDGMNAIEDEAAAAVDEVEQLEAEIDAIDDLLEFIREVAQET 577
                                       3344445555555555555555555555555...6667777777777788888888888887777777777665554 PP

                                       ....HHHHHHHH CS
                        Laminin_II  86 ss..lsdnisei 95 
                                       +   l +ni+  
  gi|336253023|ref|YP_004596130.1| 578 NMlaLNANIEAA 589
                                       434477777654 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 8.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                       +a+e+++ a+ ++    +++++le+++ +++++++ v++t++ + d   a++dA  s+ ++ + a +  d ++++  
  gi|336253023|ref|YP_004596130.1| 601 VADEVKSLAEDTQGAADDVEERLERVRGQAEQVAAVVRQTDARIGDHRGAVEDAIGSIEEISEYAAETNDGIQQISS 677
                                       6899999******************************************************9999888777777776 PP

                                       HHHH... CS
                        Laminin_II  81 leeasss 87 
                                         +++++
  gi|336253023|ref|YP_004596130.1| 678 ATQQQAA 684
                                       6666544 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.24
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXX.XXXXXXXXXXXXXXXX-- CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklsei...nrsveetnekvk.dankairdArrsvkkLek 66 
                                       ++e++e a+e+ + ++++s  +++  +  +ei   +++v  + e+ + +a++a + A+++ + L+ 
  gi|336253023|ref|YP_004596130.1| 658 IEEISEYAAETNDGIQQISSATQQQAAATQEIvsmADDVTAISEETSaEAQTAAAAAEEQTSSLTD 723
                                       567778888888888888777777665555551114444444444444455555555555555543 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   7.9   7.6e-06      0.01     284     465 ..     331     516 ..     312     523 .. 0.80
   2 ?    1.8  15.6     0.054        75     307     464 ..     533     714 ..     512     750 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.6e-06
                            AAA_13 284 kqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesv 360
                                         ++L +l  ++++++++l ++l+++  e ++ + + +d ee+++eae+ +++ ++ +r+le+  ++  + +     
  gi|336253023|ref|YP_004596130.1| 331 RSDELGELHRSIDRMRRSLRDRLEEAERERERAESALQDAEEAREEAEQARAESEAFSRRLEETADDYGEAMRACAD 407
                                       46789999999999999999***999988777777888899**************************9998876444 PP

                            AAA_13 361 kaki..esikklvaeineliakhNekvanleeekeeak...kklelhlveeleseldeykkkykklekaieklekel 432
                                        + +   +  ++ +++ ++ a++N++++++e+  ++ +   +++    + +  + + e  ++ +++++++++  + +
  gi|336253023|ref|YP_004596130.1| 408 GDLTrrLESDDESEAMATIAAEFNAMMDDIEATLAATRafaDAVDE-AADSTAEGVVEVRSASEQVATSVQQIADGA 483
                                       4444234466777777778889********9876544411033333.34445555668999**************** PP

                            AAA_13 433 keeeaelkkleeeikeLekqlrdekpaaeeink 465
                                       + ++ +l ++ +ei +L ++++++  +a+++++
  gi|336253023|ref|YP_004596130.1| 484 DRQSGQLTTIGGEIDDLSTTTEEIAATASDVAT 516
                                       ***************************999876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.054
                            AAA_13 307 kavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakie.................. 365
                                       ++++d     +a e++ + + +e e+le++++++ + le  r e++++ ++  ++a+ie                  
  gi|336253023|ref|YP_004596130.1| 533 TSAID---GMNAIEDEAAAAVDEVEQLEAEIDAIDDLLEFIR-EVAQETNMLALNANIEaaradaadagfavvadev 605
                                       33333...2233455555555566666666666655555544.6666666666666665555555577777778877 PP

                            AAA_13 366 ............sikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklek 430
                                                    +++ ++++  + ++  + v + +++  + + ++e  + +   +e++ey  + ++  ++i+++++
  gi|336253023|ref|YP_004596130.1| 606 kslaedtqgaadDVEERLERVRGQAEQVAAVVRQTDARIGDHRGAVEDAIGS--IEEISEYAAETNDGIQQISSATQ 680
                                       7777777666664444444444444444444444444444444444443333..46677777777777888899999 PP

                            AAA_13 431 elkeeeaelkkleeeikeLekqlrdekpaaeein 464
                                       +++++++e+  +++++ ++ ++++ e ++a+  +
  gi|336253023|ref|YP_004596130.1| 681 QQAAATQEIVSMADDVTAISEETSAEAQTAAAAA 714
                                       9999999999999999998888888887776544 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.6    0.0029         4      94     157 ..     326     389 ..     313     399 .. 0.72
   2 ?    1.1   0.1      0.18   2.5e+02      90     146 ..     467     522 ..     453     533 .. 0.82
   3 ?    0.7   0.1      0.25   3.4e+02     104     141 ..     544     580 ..     524     593 .. 0.57
   4 ?   -3.8   0.1       5.8   8.1e+03     105     136 ..     607     638 ..     602     642 .. 0.62
   5 ?   11.9   2.3   8.9e-05      0.12      84     156 ..     672     746 ..     660     748 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0029
                     Fzo_mitofusin  94 qvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfee 157
                                       +v+++ s  + +l++++d+++++l+++++e e+e e+ e++ + a+  r++a++ ++e e+f++
  gi|336253023|ref|YP_004596130.1| 326 SVESDRSDELGELHRSIDRMRRSLRDRLEEAERERERAESALQDAEEAREEAEQARAESEAFSR 389
                                       5556666666777777888888888888888888888888877777777777777777777765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.18
                     Fzo_mitofusin  90 ncshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkas 146
                                       + s+qv   +++  +   +q+ +  +++  ei++l+++ e+++++ +   +l +++ 
  gi|336253023|ref|YP_004596130.1| 467 SASEQVATSVQQIADGADRQSGQL-TTIGGEIDDLSTTTEEIAATASDVATLAERTA 522
                                       568889888888888888888765.67999*************99999999988875 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.25
                     Fzo_mitofusin 104 arlcqqvdetekeleeeikelekeiekleevqkkakll 141
                                       ++  ++vde+e +le+ei++++  +e + ev ++ ++l
  gi|336253023|ref|YP_004596130.1| 544 DEAAAAVDEVE-QLEAEIDAIDDLLEFIREVAQETNML 580
                                       44444444443.35555555555555555555555544 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 5.8
                     Fzo_mitofusin 105 rlcqqvdetekeleeeikelekeiekleevqk 136
                                        l ++ + + +++ee++++++ + e++++v +
  gi|336253023|ref|YP_004596130.1| 607 SLAEDTQGAADDVEERLERVRGQAEQVAAVVR 638
                                       55566666666777777777766666666555 PP

  == domain 5  score: 11.9 bits;  conditional E-value: 8.9e-05
                     Fzo_mitofusin  84 vsltsancshq..vqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfe 156
                                       +++ s++ ++q   +qe+ s+ + +++ ++et++e ++  ++ e++ ++l +v+++a +l ++a +l+  + kfe
  gi|336253023|ref|YP_004596130.1| 672 IQQISSATQQQaaATQEIVSMADDVTAISEETSAEAQTAAAAAEEQTSSLTDVSHTATALSEQARELADAVGKFE 746
                                       4455555555522579*****************************************************999997 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   2.8     0.032        45      15      71 ..     338     393 ..     330     405 .. 0.53
   2 ?    6.1   0.1     0.013        17       6      80 ..     428     501 ..     425     504 .. 0.89
   3 ?   13.6   0.8   5.9e-05     0.081      14      95 ..     499     578 ..     496     599 .. 0.87
   4 ?    2.3   0.4      0.19   2.7e+02      14      72 ..     604     661 ..     591     677 .. 0.64
   5 ?    2.3   3.8      0.19   2.6e+02       6      65 ..     666     724 ..     664     749 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.032
                           DUF2203  15 lkelleelr.alrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeiee 71 
                                       l++ ++++r +lr++lee+e+e e+a+  ++ ++a+e+++e e+++ae e++ +++ee
  gi|336253023|ref|YP_004596130.1| 338 LHRSIDRMRrSLRDRLEEAERERERAE--SALQDAEEAREEAEQARAESEAFSRRLEE 393
                                       444444444123333333332222222..22334666666666666666666666665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                           DUF2203   6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdle 80 
                                       +e na++  ++ +l++ ra ++ + e++++ +e   e + s+ ++ +++++++++ +++   +++ +G e+ dl+
  gi|336253023|ref|YP_004596130.1| 428 AEFNAMMDDIEATLAATRAFADAVDEAADSTAEGVVEVR-SASEQVATSVQQIADGADRQSGQLTTIGGEIDDLS 501
                                       57799999999*******999999999999999998875.5589999***********************99985 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 5.9e-05
                           DUF2203  14 llkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleaglvDFpakl 90 
                                        l+ ++ee++a+++++++l+e+ ++++++a+ ++a+++   ++++e+e+ ++v+e+e+l +e+  ++  l++F  ++
  gi|336253023|ref|YP_004596130.1| 499 DLSTTTEEIAATASDVATLAERTARTSSAAR-ESATSAIDGMNAIEDEAAAAVDEVEQLEAEIDAID-DLLEFIREV 573
                                       6788999***********9999998888865.458899999*************************7.788998888 PP

                           DUF2203  91 dgeev 95 
                                        +e+ 
  gi|336253023|ref|YP_004596130.1| 574 AQETN 578
                                       77765 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.19
                           DUF2203  14 llkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieel 72 
                                       ++k+l e+ + +++++ee+ e+++ + ++ ++   ++  a++   +  +e+++  iee+
  gi|336253023|ref|YP_004596130.1| 604 EVKSLAEDTQGAADDVEERLERVRGQAEQVAAV-VRQTDARIGDHRGAVEDAIGSIEEI 661
                                       566777777777777777777666666665432.5555555555555555555555554 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.19
                           DUF2203   6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieel 65 
                                       +e n+ ++++++ +++ +a+++e+ +++++++++++e+++++  a   +a+ ee ++++ ++
  gi|336253023|ref|YP_004596130.1| 666 AETNDGIQQISSATQQQAAATQEIVSMADDVTAISEETSAEAqtA---AAAAEEQTSSLTDV 724
                                       577888899999999999999999999999999988876554332...33333333333332 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 ?    2.6   0.2       0.1   1.4e+02      28      81 ..     337     390 ..     332     404 .. 0.67
   2 ?   -1.7   0.0       2.2   3.1e+03      30      84 ..     427     481 ..     420     493 .. 0.56
   3 ?    5.7   0.2     0.011        15      33     125 ..     493     586 ..     487     592 .. 0.71
   4 ?   -2.0   0.0       2.7   3.8e+03      33      63 ..     612     642 ..     601     661 .. 0.57
   5 ?    4.5   2.3     0.026        35      26     101 ..     661     735 ..     638     742 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.1
                                       CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikk 81 
                                       + ++++++  ++l+++lee++++ + ae+  ++ ++  +e+++  ++++   ++
  gi|336253023|ref|YP_004596130.1| 337 ELHRSIDRMRRSLRDRLEEAERERERAESALQDAEEAREEAEQARAESEAFSRR 390
                                       556666666677888888888888888888888888777777766655444444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikkssk 84 
                                         +++  ++++e +l+  +     ++e   ++ + + e  + +++  + ++++++
  gi|336253023|ref|YP_004596130.1| 427 AAEFNAMMDDIEATLAATRAFADAVDEAADSTAEGVVEVRSASEQVATSVQQIAD 481
                                       5555556666666666666666666666665555555555555544555555544 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.011
                                       CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHH.HHHHHHHHCCCHHHHHHHCCHHHHH CS
                         Fib_alpha  33 vkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvik.ksskeleeeilrlketidaqesnir 105
                                       +  ++++l  + eei+ + +++ +l +++  +  ++ +s++      n+i+ + +  ++ e+++l+++ida    ++
  gi|336253023|ref|YP_004596130.1| 493 IGGEIDDLSTTTEEIAATASDVATLAERTARTSSAARESATSAidgMNAIEdEAAAAVD-EVEQLEAEIDAIDDLLE 568
                                       55678889999999999998888888777666666655555544445555515666777.99999999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 106 vLqnvlesneqkiqkLeqdi 125
                                       ++++v +  e ++  L+ +i
  gi|336253023|ref|YP_004596130.1| 569 FIREVAQ--ETNMLALNANI 586
                                       9999975..45566666666 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2.7
                                       CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHH CS
                         Fib_alpha  33 vkkdlekleneleeisnstkeaeelvkeikd 63 
                                       ++   +++e++le+++ + +++  +v++++ 
  gi|336253023|ref|YP_004596130.1| 612 TQGAADDVEERLERVRGQAEQVAAVVRQTDA 642
                                       4444455555555555555555555555544 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.026
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe 101
                                       +++y  ++++ ++++ +  ++ +  t+e+ ++  +++ + +e+ ++++    + ++ +++l  +++     +++q 
  gi|336253023|ref|YP_004596130.1| 661 ISEYAAETNDGIQQISSATQQQAAATQEIVSMADDVTAISEETSAEAQTAAAAAEEQTSSLT-DVSHTATALSEQA 735
                                       67888899999999999999999999999999999999988888888888888888888887.6666666666655 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   5.9   0.00065      0.89     126     224 ..     307     400 ..     293     404 .. 0.78
   2 ?   -0.6   0.0      0.49   6.8e+02     176     221 ..     412     457 ..     409     462 .. 0.63
   3 ?    6.8   3.0    0.0026       3.6      93     233 ..     453     585 ..     443     589 .. 0.67
   4 ?    2.6   2.9     0.049        68      92     221 ..     617     741 ..     594     745 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00065
                              CorA 126 llekleeeldeledel.edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldel 201
                                        l++l+e+   +ed   e+s + +  +el +l+r++ ++rr+l++  e   ++ + ++++   +      ++ ++e+
  gi|336253023|ref|YP_004596130.1| 307 SLRHLSERAAAIEDGDlEESVESDRSDELGELHRSIDRMRRSLRDRLEEA-ERER-ERAESALQ----DAEEAREEA 377
                                       57888888888888766888888899999999999999999998888888.6666.22222222....3579***** PP

                              CorA 202 erllemlealrerleslqdtyss 224
                                       e++  ++ea ++rle   d y  
  gi|336253023|ref|YP_004596130.1| 378 EQARAESEAFSRRLEETADDYGE 400
                                       **************999998865 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.49
                              CorA 176 rllakaddkllddedkeylrdlldelerllemlealrerleslqdt 221
                                       r+l+++d+++  ++ +  ++ ++d++e  l  + a ++ ++   d+
  gi|336253023|ref|YP_004596130.1| 412 RRLESDDESEAMATIAAEFNAMMDDIEATLAATRAFADAVDEAADS 457
                                       5566566666666666667777777777777777666666666655 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0026
                              CorA  93 evikrlkdeggkpkspgellyrlldeivdrlfellekleeeldeledel.edstkkeilrelaqlrrrlvklrrala 168
                                       e+++++ +   +++s++e ++  +++i+d  +++  +l +   e++d    +++ +  ++++a+l +r ++  +a++
  gi|336253023|ref|YP_004596130.1| 453 EAADSTAEGVVEVRSASEQVATSVQQIADGADRQSGQLTTIGGEIDDLStTTEEIAATASDVATLAERTARTSSAAR 529
                                       55555555556788888889999999999999999888888888888774445555555555555555555544444 PP

                              CorA 169 pnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtyssllserlNrv 233
                                          e  ++ ++    + ++de+        de+e+l+ +++a+ ++le +++  + +    lN +
  gi|336253023|ref|YP_004596130.1| 530 ---ESATSAID--GMNAIEDEA----AAAVDEVEQLEAEIDAIDDLLEFIREVAQETNMLALNAN 585
                                       ...44444455..333444444....799999999999999999999999988877776666655 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.049
                              CorA  92 devikrlkdeggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaq.lrrrlvklrral 167
                                       d+v +rl+ + +++      + r  d+ + +++ ++e+    ++e+++     ++++ +++++   +++++  ++++
  gi|336253023|ref|YP_004596130.1| 617 DDVEERLE-RVRGQAEQVAAVVRQTDARIGDHRGAVEDAIGSIEEISEYA--AETNDGIQQISSaTQQQAAATQEIV 690
                                       55555555.32333333344444444444455555555555555555555..5555555555552667788888888 PP

                              CorA 168 apnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdt 221
                                       +   +v  ++ +  +++ + ++++   ++  + l+ ++ +++al+e+++ l d+
  gi|336253023|ref|YP_004596130.1| 691 SMADDVT-AISE--ETSAEAQTAAAAAEEQTSSLTDVSHTATALSEQARELADA 741
                                       8888888.7777..3333333333356777777777888888888888888876 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.9   1.2e+03      28      89 ..     342     401 ..     330     408 .. 0.58
   2 ?   -0.5   0.1       1.2   1.6e+03      48      51 ..     520     523 ..     472     591 .. 0.56
   3 ?    6.8   0.3    0.0061       8.5      33      68 ..     652     687 ..     619     719 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.9
                        Syntaxin_2  28 teelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkdfkealqeFqki 89 
                                        +++r++l++  ee+ +  ++ ++ l++ ++  +  +  q + + e  ++ ++e    + ++
  gi|336253023|ref|YP_004596130.1| 342 IDRMRRSLRDRLEEAERERERAESALQDAEEAREEAE--QARAESEAFSRRLEETADDYGEA 401
                                       4456666666666666666666666666666655554..55555555555555555555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                        Syntaxin_2  48 ktne 51 
                                       +t +
  gi|336253023|ref|YP_004596130.1| 520 RTAR 523
                                       2222 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0061
                        Syntaxin_2  33 eklhelieeinelikktnellkklsqldnsssdsqq 68 
                                       e +  +ieei+e + +tn+ ++++s+ ++++   +q
  gi|336253023|ref|YP_004596130.1| 652 EDAIGSIEEISEYAAETNDGIQQISSATQQQAAATQ 687
                                       6667799*******************9999876644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (847 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2533  (0.141279); expected 358.6 (0.02)
Passed bias filter:                      927  (0.0517039); expected 358.6 (0.02)
Passed Vit filter:                       147  (0.00819901); expected 17.9 (0.001)
Passed Fwd filter:                        73  (0.00407162); 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: 1.76u 0.34s 00:00:02.10 Elapsed: 00:00:00.59
# Mc/sec: 4317.60
//
Query:       gi|336253024|ref|YP_004596131.1|  [L=391]
Description: Fe3+-hydroxamate ABC transporter periplasmic component-like protein [Halopiger xanaduensis SH-6]
Scores for 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-22   78.5   0.2    7.3e-22   78.1   0.2    1.3  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.078   12.9   1.9       0.12   12.3   1.9    1.3  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
        0.2   11.7   0.0       0.52   10.3   0.0    1.6  1  TP6A_N        Type IIB DNA topoisomerase


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 !   78.1   0.2   1.2e-25   7.3e-22      58     236 ..     154     351 ..      85     353 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 1.2e-25
                                       H--SEEEE-GGG...GGGHHHHHHHS-EEE----TTS...........HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                      Peripla_BP_2  58 lkPDlvilskglgltdedeellksgiptvivessntg...........eslkeqiralgellgledeaeklvaeids 123
                                       ++P  +i   ++ ++d+++++++ g+p++       +             l+e ++ l+e++++++++e++++ +d+
  gi|336253024|ref|YP_004596131.1| 154 MDPNFLINRGDW-DQDDIDQIESMGAPFFGNSI---FsrdygwhdyefLTLYEAFEKLAEVFQEQERYEAFASLHDG 226
                                       567777777777.99999999999999975321...123455899999***************************** PP

                                       HHHHHHHTS-TT...-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--....STT-EEE-HHHHHHH-- CS
                      Peripla_BP_2 124 klaaaksaidse..kpkpvlvfggadeggyvvagsnsyigdlldalgieniaaesk....kseyeeisaEqilasdp 194
                                         +++++ ++ e   p+ ++v+  +d+ +y ++ + +   +  ++lg+ ++++e +    ++++++i+ E++l+ dp
  gi|336253024|ref|YP_004596131.1| 227 FQDEVEAIVPPEdeRPDVAIVWPAGDDTFYPYTIDEGTSYKQWRDLGVGDALSEAGvsdfTDDRGTIDYENLLEIDP 303
                                       ************888888999999999888888888888888999*********99********************* PP

                                       SEEEEEEH......HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-H CS
                      Peripla_BP_2 195 dvifvsgr......aeadnktgleflkenpllaelpAvkngrVyalds 236
                                       dv++ +g       +e+++++++++++++ ++++l+Av+ng+Vy+ ++
  gi|336253024|ref|YP_004596131.1| 304 DVLVLRGPsneslsDEEFQNQVVAEMENHNVASDLTAVQNGDVYRGGP 351
                                       ********************************************9876 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.9     2e-05      0.12       3      25 ..       8      30 ..       8      31 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                      +RR  L++sA +a A++ +gc++
  gi|336253024|ref|YP_004596131.1|  8 TRRAILRTSATVAGAGLIAGCTS 30
                                      79*******************86 PP

>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   8.7e-05      0.52      26      43 ..     368     385 ..     356     388 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.7e-05
                                       HHHHHHGGGS-SSHHHHH CS
                            TP6A_N  26 RdiYYrdvelFksQaesd 43 
                                       Rd+Y  d+elF++Q++sd
  gi|336253024|ref|YP_004596131.1| 368 RDLYGVDEELFDRQEVSD 385
                                       9****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2837.01
//
Query:       gi|336253025|ref|YP_004596132.1|  [L=317]
Description: Iron-chelate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-31  107.3   0.0    1.2e-30  106.8   0.0    1.2  1  ABC_tran      ABC transporter
    1.5e-13   51.2   0.9    1.2e-05   25.3   0.2    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.4e-11   44.3   0.2    4.4e-09   36.1   0.2    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    3.6e-06   26.6   0.0    8.9e-06   25.4   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
    8.5e-06   24.8   0.1       0.02   13.7   0.0    2.9  2  ABC_ATPase    Predicted ATPase of the ABC class
    1.2e-05   25.8   0.1    2.4e-05   24.8   0.1    1.7  1  AAA_16        AAA ATPase domain
    1.2e-05   25.6   0.0    3.8e-05   24.0   0.0    1.7  1  AAA_22        AAA domain
    5.7e-05   23.0   0.0    0.00031   20.6   0.0    1.9  2  AAA_15        AAA ATPase domain
    0.00027   21.5   0.0    0.00037   21.1   0.0    1.4  1  AAA_23        AAA domain
    0.00057   19.8   0.1      0.032   14.0   0.0    2.2  2  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.001   19.3   0.0     0.0024   18.0   0.0    1.7  1  AAA_33        AAA domain
     0.0012   18.2   0.0      0.002   17.4   0.0    1.4  1  Zeta_toxin    Zeta toxin
     0.0015   18.2   0.6       0.02   14.5   0.6    2.5  1  AAA_25        AAA domain
     0.0019   17.9   0.1     0.0049   16.6   0.1    1.9  1  AAA_30        AAA domain
     0.0022   17.9   0.0     0.0045   16.9   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
     0.0025   18.4   0.0     0.0079   16.7   0.0    1.9  1  AAA_18        AAA domain
     0.0042   17.3   0.0       0.01   16.1   0.0    1.6  1  HD            HD domain
     0.0055   16.1   0.1        3.2    7.1   0.0    2.2  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0072   16.3   0.1      0.017   15.1   0.0    1.6  1  Rad17         Rad17 P-loop domain
     0.0085   15.9   0.0      0.016   15.0   0.0    1.3  1  MukB          MukB N-terminal
  ------ inclusion threshold ------
       0.02   15.3   0.0       0.05   14.0   0.0    1.6  1  AAA           ATPase family associated with various cellular 
      0.022   14.8   0.0      0.053   13.5   0.0    1.6  2  AAA_14        AAA domain
      0.028   14.0   0.0      0.047   13.3   0.0    1.3  1  AAA_27        AAA domain
      0.028   13.9   0.0      0.052   13.0   0.0    1.4  1  AviRa         RRNA methyltransferase AviRa
      0.055   12.7   0.0       0.08   12.2   0.0    1.2  1  DUF2813       Protein of unknown function (DUF2813)
      0.055   13.7   0.0       0.13   12.5   0.0    1.7  1  AAA_28        AAA domain
      0.083   12.9   0.0        0.2   11.6   0.0    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
      0.093   13.1   0.0       0.16   12.3   0.0    1.4  1  RNA_helicase  RNA helicase
        0.1   12.1   0.0       0.17   11.4   0.0    1.3  1  AAA_7         P-loop containing dynein motor region
        0.1   12.7   0.0       0.68   10.0   0.0    2.1  2  MMR_HSR1      50S ribosome-binding GTPase
       0.17   11.7   0.0        0.3   11.0   0.0    1.4  1  APS_kinase    Adenylylsulphate kinase
       0.18   11.0   0.0       0.32   10.1   0.0    1.4  1  DUF815        Protein of unknown function (DUF815)


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 !  106.8   0.0   2.2e-33   1.2e-30       5     136 ..      78     222 ..      74     223 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 2.2e-33
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                        l++ ege++a+vG+nG+GKSt+lk+l+++l+p+ G ++l+g+dl++ ++++l +e+g l+qe+   +++tv++   
  gi|336253025|ref|YP_004596132.1|  78 RLDVPEGEITALVGPNGSGKSTMLKALSKHLEPDTGVVRLRGEDLQSFDRPELARELGLLSQENDSVSGITVEDLvy 154
                                       689*********************************************************************999** PP

                                       ...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                      e++e +e+al+  g ++l+d+ +     +LSgGqkq   +a++l+++ ++lllDEpt
  gi|336253025|ref|YP_004596132.1| 155 hgryphrgffdsvspEDREAVERALELAGVEHLRDSEL----GQLSGGQKQLAWIAMVLAQDTDILLLDEPT 222
                                       *************9888888******************....*****************************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 !   24.3   0.0   4.4e-08   2.4e-05       1      37 [.      86     116 ..      86     121 .. 0.86
   2 !   25.3   0.2   2.1e-08   1.2e-05     230     292 ..     188     248 ..     148     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4.4e-08
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdels 37 
                                       +++l+GpNgsGKS+ L+al       +++e++t + +
  gi|336253025|ref|YP_004596132.1|  86 ITALVGPNGSGKSTMLKAL------SKHLEPDTGVVR 116
                                       79*****************......888888887766 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 2.1e-08
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQv 292
                                       ++  + +lS G+k+l a ++++l+++   ++ll+DEp ++L+ + + r+le +++l++ +g+ v
  gi|336253025|ref|YP_004596132.1| 188 RDSELGQLSGGQKQL-AWIAMVLAQDT--DILLLDEPTTFLDLHHQFRVLETIRQLNEeKGVTV 248
                                       44567899*******.********998..9*********************9977766556655 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 !   36.1   0.2   7.9e-12   4.4e-09      24     201 ..      84     255 ..      76     272 .. 0.66

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 7.9e-12
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEE.EEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkka.eveitfdnedkklkiekeevsi 99 
                                        ++ta+vGpNGSGKs +l A++  L  ++   + + + +dl +     ++ + a e+ ++ +++d+      + +++
  gi|336253025|ref|YP_004596132.1|  84 GEITALVGPNGSGKSTMLKALSKHLEPDTG--VVRLRGEDLQSF----DRPELArELGLLSQENDSV-----SGITV 149
                                       4699*****************999986544..334444555443....3334440445543444444.....44555 PP

                                       EEEEETTSE.EEEEETTEEE-H.HHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTT CS
                                       xxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkge.seykingkevtk.kevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeid 168
                                       +  v+++    + +++  + +  + v++ le ag++        +LSgG+k+L+ +a+++A    + + + llDe  
  gi|336253025|ref|YP_004596132.1| 150 EDLVYHGRYpHRGFFDSVSPEDrEAVERALELAGVEHLrdselgQLSGGQKQLAWIAMVLA----QDTDILLLDEPT 222
                                       554444444322333333332225566666666665544455559**************98....67889******* PP

                                       TTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 169 aaLDeknvkkvaellkeksknaQfivislreem 201
                                         LD ++  +v e +++ +++  + v  + +++
  gi|336253025|ref|YP_004596132.1| 223 TFLDLHHQFRVLETIRQLNEEKGVTVAVVLHDI 255
                                       ****************99988777666555554 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 !   25.4   0.0   1.6e-08   8.9e-06      16      50 ..      78     112 ..      71     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.6e-08
                            AAA_29  16 tieidlkg.atlltGpsGsGKSTllDAiqalLvpak 50 
                                       ++++ + g +t l+Gp+GsGKST+l A++  L p++
  gi|336253025|ref|YP_004596132.1|  78 RLDVPE-GeITALVGPNGSGKSTMLKALSKHLEPDT 112
                                       556654.45*******************99888876 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 !   13.7   0.0   3.6e-05      0.02     240     266 ..      79     106 ..      69     110 .. 0.91
   2 !    6.4   0.1     0.006       3.4     323     413 ..     195     270 ..     185     291 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                                       EEE-SS.EEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAlek 266
                                       + +p+G +t++vG++  GKsT+L+Al+k
  gi|336253025|ref|YP_004596132.1|  79 LDVPEGeITALVGPNGSGKSTMLKALSK 106
                                       56899********************986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.006
                                       --HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-G CS
                        ABC_ATPase 323 ASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsg 399
                                        SG   q a+i+  l  ++++lL+DE t+   l +     q            +++ +r+l ++ gv++ +v   ++
  gi|336253025|ref|YP_004596132.1| 195 LSGGQKQLAWIAMVLAQDTDILLLDEPTTFLDLHH-----QFR----------VLETIRQLNEEKGVTVAVVLHDIS 256
                                       57778888888888888888888888776444333.....222..........356778888888888888888888 PP

                                       CCTTT-SEEEEEET CS
                        ABC_ATPase 400 dyldvAdtvilmee 413
                                       +  + Ad  i+m++
  gi|336253025|ref|YP_004596132.1| 257 QAARFADYLIAMRD 270
                                       88888888888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   4.2e-08   2.4e-05      23      88 ..      83     137 ..      71     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.2e-08
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                       ++e++ l+G+ G+GKs+++++l ++le d   ++r + ++l          q ++r el r+l+  
  gi|336253025|ref|YP_004596132.1|  83 EGEITALVGPNGSGKSTMLKALSKHLEPDT-GVVRLRGEDL----------QSFDRPELARELGLL 137
                                       4589*************************5.5555555555..........335555555555544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   6.8e-08   3.8e-05       6     128 ..      85     251 ..      82     256 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6.8e-08
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelka........... 70 
                                        i++++G+ G+GK+t l+ l + l         +p++  v l ++  ++++ + el+r+lgl   +           
  gi|336253025|ref|YP_004596132.1|  85 EITALVGPNGSGKSTMLKALSKHL---------EPDTGVVRLRGED-LQSFdRPELARELGLLSQEndsvsgitved 151
                                       6899********************.........8999999999999.7788799999999987777999******** PP

                            AAA_22  71 ............................erlsseell.ealeqalrarav...........ielliiDEaqh.lr.. 104
                                                                   e +  e+l+ + l q +  ++            + +l++DE    l+  
  gi|336253025|ref|YP_004596132.1| 152 lvyhgryphrgffdsvspedreaveralELAGVEHLRdSELGQLSGGQKQlawiamvlaqdTDILLLDEPTTfLDlh 228
                                       *************************9998888888888888888877777888888999999*******99977797 PP

                            AAA_22 105 .seealeeLrsllnlsrkgvqliLv 128
                                        + ++le++r+l +  +kgv++ +v
  gi|336253025|ref|YP_004596132.1| 229 hQFRVLETIRQLNE--EKGVTVAVV 251
                                       66*******99999..999988776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   5.6e-07   0.00031      23      47 ..      85     108 ..      74     143 .. 0.79
   2 ?    0.1   0.0       0.9   5.1e+02     293     351 ..     191     240 ..     157     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.6e-07
                            AAA_15  23 eeltvliGkNnsGKSsilealdlFl 47 
                                       e +t l+G+N+sGKS+ l+al + l
  gi|336253025|ref|YP_004596132.1|  85 E-ITALVGPNGSGKSTMLKALSKHL 108
                                       3.9******************7655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.9
                            AAA_15 293 plnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkel 351
                                       +l + + G+++l ++++ ++         ++++ill++EP + L   +q  + ++++ l
  gi|336253025|ref|YP_004596132.1| 191 ELGQLSGGQKQLAWIAMVLA---------QDTDILLLDEPTTFLDLHHQFRVLETIRQL 240
                                       55566667777777776543.........346899999998777666666666666655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   6.6e-07   0.00037      18      39 ..      83     104 ..      65     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 6.6e-07
                            AAA_23  18 skgltlItGpNGaGKTTildAi 39 
                                       +  +t+++GpNG+GK+T l A+
  gi|336253025|ref|YP_004596132.1|  83 EGEITALVGPNGSGKSTMLKAL 104
                                       5579****************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 !   14.0   0.0   5.8e-05     0.032       2      21 ..      90     109 ..      89     117 .. 0.89
   2 ?    3.7   0.0     0.084        47      77     143 ..     200     266 ..     191     270 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-05
                        ATP_bind_1   2 vGpaGsGKttfvgalseile 21 
                                       vGp GsGK+t+ +als++le
  gi|336253025|ref|YP_004596132.1|  90 VGPNGSGKSTMLKALSKHLE 109
                                       8*****************97 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.084
                        ATP_bind_1  77 esldwldeelekeeddyllfDtPGQielfthseslakiveeLes.efalvvvyLvDsqrltdptkfis 143
                                       ++l w++  l  +++d ll+D P       h     + +++L++ ++ +v+v+L D   ++  ++++ 
  gi|336253025|ref|YP_004596132.1| 200 KQLAWIAMVL-AQDTDILLLDEPTTFLDLHHQFRVLETIRQLNEeKGVTVAVVLHDISQAARFADYLI 266
                                       5677888888.66778889999964433333333444788999999**********998888777765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.3e-06    0.0024       3      33 ..      88     163 ..      86     261 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-06
                            AAA_33   3 llvGlpGsGKstlaerllkklg....avllssdt.........................................l 33 
                                        lvG++GsGKst ++ l k+l     +v+l+  +                                         +
  gi|336253025|ref|YP_004596132.1|  88 ALVGPNGSGKSTMLKALSKHLEpdtgVVRLRGEDlqsfdrpelarelgllsqendsvsgitvedlvyhgryphrgF 163
                                       68***************99998888899999888666666666666666666555555555555555555555551 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.6e-06     0.002      19      57 ..      87     125 ..      72     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.6e-06
                        Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57 
                                         l+G  G+GKs+++++l + le++ +vvrl + dl+++
  gi|336253025|ref|YP_004596132.1|  87 TALVGPNGSGKSTMLKALSKHLEPDTGVVRLRGEDLQSF 125
                                       56899******************************9987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.6   3.5e-05      0.02      30      56 ..      81     107 ..      75     255 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-05
                            AAA_25  30 lpagelallaGapgtGKttlaldlala 56 
                                       +p+ge+++l+G+ g+GK+t++  l+ +
  gi|336253025|ref|YP_004596132.1|  81 VPEGEITALVGPNGSGKSTMLKALSKH 107
                                       69******************9887755 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   8.8e-06    0.0049      19      48 ..      85     114 ..      79     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.8e-06
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggr 48 
                                        +++l+Gp G+GK+t+lkal +++e + g 
  gi|336253025|ref|YP_004596132.1|  85 EITALVGPNGSGKSTMLKALSKHLEPDTGV 114
                                       4899****************9999977444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     8e-06    0.0045      98     131 ..      83     116 ..      73     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8e-06
                                       TTSEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevs 131
                                       ++++++lvG+ G GKSt+++al  +le  tg v+
  gi|336253025|ref|YP_004596132.1|  83 EGEITALVGPNGSGKSTMLKALSKHLEPDTGVVR 116
                                       5799*********************999999886 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.4e-05    0.0079       3      24 ..      89     110 ..      88     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.4e-05
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf 24 
                                       l G+ G+GK+t+ k+Lsk+l+ 
  gi|336253025|ref|YP_004596132.1|  89 LVGPNGSGKSTMLKALSKHLEP 110
                                       89*****************744 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.8e-05      0.01       3      74 ..     228     295 ..     227     304 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHH...HHHCTCCHHHHHHHHHHHHHHHHHH CS
                                HD   3 eHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekk...eeefekflaHekvgaeilrevekrl 74 
                                        H ++V++ +r+l e+ g       + +a  lHDi         + +    e+++  +  e+v++++l +v++++
  gi|336253025|ref|YP_004596132.1| 228 HHQFRVLETIRQLNEEKG-------VTVAVVLHDISQAARFADYLIAmrdGELYDWGPPEEIVTEQLLADVFEVE 295
                                       7*****************.......***********999776555556544447777788999999999888887 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0     0.007       3.9      27      48 ..      89     110 ..      84     133 .. 0.84
   2 !    7.1   0.0    0.0057       3.2      90     151 ..     195     262 ..     176     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.007
                      Mg_chelatase  27 lvGppGsGKtmlakrlpsllpp 48 
                                       lvGp GsGK+ + k+l++ l p
  gi|336253025|ref|YP_004596132.1|  89 LVGPNGSGKSTMLKALSKHLEP 110
                                       89**********9999887755 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0057
                      Mg_chelatase  90 lvGggskpkpGeislah.nGvLfLDElpef.....krkvlevLRePledgevtisrakakvefparfq 151
                                       l Gg+++    ++ la+ + +L+LDE + f     + +vle++R+  e++ vt++   ++++  arf 
  gi|336253025|ref|YP_004596132.1| 195 LSGGQKQLAWIAMVLAQdTDILLLDEPTTFldlhhQFRVLETIRQLNEEKGVTVAVVLHDISQAARFA 262
                                       55666677777777776257999999877644333569*****************9999999999884 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     3e-05     0.017      39      71 ..      78     110 ..      71     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-05
                             Rad17  39 vLesrkkriLLisGPsGCgkstvvkvLskelgi 71 
                                        L+  + +i  + GP G gkst++k Lsk l +
  gi|336253025|ref|YP_004596132.1|  78 RLDVPEGEITALVGPNGSGKSTMLKALSKHLEP 110
                                       555555678889*****************9865 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.9e-05     0.016      27      60 ..      85     118 ..      77     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.9e-05
                                       HHHHHHS--SHHHHHHHHHHHHHHS--TTT---- CS
                              MukB  27 lvttlsGgnGaGksttmaafvtaliPdlsllhfr 60 
                                        +t+l G nG+Gkst++ a+   l Pd  ++++r
  gi|336253025|ref|YP_004596132.1|  85 EITALVGPNGSGKSTMLKALSKHLEPDTGVVRLR 118
                                       58*************************9998877 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 ?   14.0   0.0   8.9e-05      0.05       3      35 ..      89     123 ..      87     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.9e-05
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCS CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsell 35 
                                       l+Gp G GK+++ ka+ k+l+  + ++++ g +l 
  gi|336253025|ref|YP_004596132.1|  89 LVGPNGSGKSTMLKALSKHLEpdTGVVRLRGEDLQ 123
                                       89*****************9644667888777765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.5e-05     0.053       3      44 ..      85     125 ..      83     150 .. 0.76
   2 ?   -2.6   0.0       9.6   5.4e+03      66      76 ..     214     224 ..     199     266 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.5e-05
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdk 44 
                                       +i +++G+  +GK+t+lk l k+l  ++  ++ +  +d +  
  gi|336253025|ref|YP_004596132.1|  85 EITALVGPNGSGKSTMLKALSKHLE-PDTGVVRLRGEDLQSF 125
                                       7899****************98887.6667777666665543 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9.6
                            AAA_14  66 tylflDEiqev 76 
                                        +l+lDE    
  gi|336253025|ref|YP_004596132.1| 214 DILLLDEPTTF 224
                                       45666664433 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.4e-05     0.047      25      48 ..      83     106 ..      73     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.4e-05
                            AAA_27  25 eadlhliyGpNEAGKstalrAisd 48 
                                       e +++ ++GpN +GKst+l+A+s+
  gi|336253025|ref|YP_004596132.1|  83 EGEITALVGPNGSGKSTMLKALSK 106
                                       6678889**************987 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.2e-05     0.052     162     213 ..      67     120 ..      22     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.2e-05
                             AviRa 162 eaeke..vdivitDlPYGelvswqgeseepvkqlleslaavldpeesvvaviad 213
                                       + + e  vd    D+P Ge+++  g ++++ +++l++l++ l+p+++vv +  +
  gi|336253025|ref|YP_004596132.1|  67 PGSDEtiVDCTRLDVPEGEITALVGPNGSGKSTMLKALSKHLEPDTGVVRLRGE 120
                                       4444445788889***********************************987655 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.08      22      61 ..      84     123 ..      76     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                           DUF2813  22 eentvLiGENaWGKSSLldALslilnvekelyqFtlkDFh 61 
                                        e t+L+G N  GKS +l+ALs  l++++ + + + +D  
  gi|336253025|ref|YP_004596132.1|  84 GEITALVGPNGSGKSTMLKALSKHLEPDTGVVRLRGEDLQ 123
                                       57899***********************999988888865 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   0.00023      0.13       3      23 ..      88     111 ..      86     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00023
                            AAA_28   3 vitGgestGKTtlleaLaar...g 23 
                                       +++G+ ++GK+t+l+aL+++   +
  gi|336253025|ref|YP_004596132.1|  88 ALVGPNGSGKSTMLKALSKHlepD 111
                                       799***************986553 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 ?   11.6   0.0   0.00036       0.2       4      24 ..      89     109 ..      87     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00036
                                       EE--SSSSHHHHHHHGGGGBS CS
                             AAA_5   4 LvGppGtgKselaerlaaaln 24 
                                       LvGp G+gKs++ + l++ l+
  gi|336253025|ref|YP_004596132.1|  89 LVGPNGSGKSTMLKALSKHLE 109
                                       9****************9994 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00029      0.16       3      23 ..      89     109 ..      87     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00029
                      RNA_helicase   3 lyGpsgeGKStlakeLakall 23 
                                       l+Gp+g GKSt+ k L+k+l+
  gi|336253025|ref|YP_004596132.1|  89 LVGPNGSGKSTMLKALSKHLE 109
                                       79*************999987 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    0.0003      0.17      35      61 ..      86     112 ..      76     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                             AAA_7  35 pvllvGptGtGKtviikdllkkldkek 61 
                                        + lvGp G+GK++++k l k+l++++
  gi|336253025|ref|YP_004596132.1|  86 ITALVGPNGSGKSTMLKALSKHLEPDT 112
                                       5679******************99875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0012      0.68       3      22 ..      88     107 ..      86     123 .. 0.87
   2 ?   -0.0   0.0       1.6     9e+02      45      87 ..     212     257 ..     188     285 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                                       EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge 22 
                                       a+vG   +GKSt+++al++ 
  gi|336253025|ref|YP_004596132.1|  88 ALVGPNGSGKSTMLKALSKH 107
                                       89***************985 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.6
                                       TEEEEEEECGGCSSHHHHHHHHHHHHHHHHC...TSEEEEEEETTT CS
                          MMR_HSR1  45 gkeielvDtpGliegaseekglgkaflalee...adlillvvdase 87 
                                       +++i l+D p  + + + + ++ +++++l+e   + +++++ d+s+
  gi|336253025|ref|YP_004596132.1| 212 DTDILLLDEPTTFLDLHHQFRVLETIRQLNEekgVTVAVVLHDISQ 257
                                       4677777877754334444445555555333234566666666662 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00053       0.3       5      53 ..      87     138 ..      83     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00053
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHH....TTTTTTT--SSH CS
                        APS_kinase   5 vwltGlsgsGKstianalekkLvekgisvylLdGdnv....RhgLnkdLgfse 53 
                                         l G  gsGKst+ +al+k+L+ + + v++L G+ +    R +L ++Lg  +
  gi|336253025|ref|YP_004596132.1|  87 TALVGPNGSGKSTMLKALSKHLEPD-TGVVRLRGEDLqsfdRPELARELGLLS 138
                                       5689*****************9865.567889999885556778999998754 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00057      0.32      58      95 ..      89     125 ..      82     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00057
                            DUF815  58 LwGarGtGKSslvkallneyaeegLrlievekedlkel 95 
                                       L+G  G+GKS+++kal ++++ ++  ++ ++ edl+++
  gi|336253025|ref|YP_004596132.1|  89 LVGPNGSGKSTMLKALSKHLEPDT-GVVRLRGEDLQSF 125
                                       89**************99998765.5667777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); 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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2032.32
//
Query:       gi|336253026|ref|YP_004596133.1|  [L=368]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-84  282.7  37.9    3.8e-84  282.3  37.9    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 !  282.3  37.9   2.1e-88   3.8e-84       2     312 .]      34     361 ..      23     361 .. 0.95

  Alignments for each domain:
  == domain 1  score: 282.3 bits;  conditional E-value: 2.1e-88
                             FecCD   2 lllllllslllgavkispsevfeallgka...................dsleaeivlelrlprvlaallvGaaLava 59 
                                       ++++ l+ +++g++++++ e ++a+++ a                    s ++ +v+++rlprv++a+++G  Lav+
  gi|336253026|ref|YP_004596133.1|  34 TVVAGLVQVSFGSYSMTIGEAWRAVVDPAvvfnrqawnaflfggelpeMSRNSIVVWNIRLPRVFVAIIAGTTLAVS 110
                                       578889999*****************9999997766666666666665555555*********************** PP

                             FecCD  60 GallQtvtrNpLadPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLa 136
                                       Ga++Q+vtrN+La+P +lG+ssga+++++++l+++  s  +  lpl+a lg+ +a+l+v+l+a ++ g+sp++l+La
  gi|336253026|ref|YP_004596133.1| 111 GAIFQAVTRNELASPFVLGVSSGAGFAVLATLVVF--SGLAPLLPLIAALGGTIAFLVVYLIA-WKDGTSPVRLVLA 184
                                       *********************************97..555568********************.************* PP

                             FecCD 137 Giavsallsaltsllllll.neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAks 212
                                       G++v++++++l + l +++ +   +++++ wl+Gsl g  w++v ++ + ++++++l+++ ar+l++l lg++tA+s
  gi|336253026|ref|YP_004596133.1| 185 GVIVNMVFQSLQQGLFFFAdDIGVVQTAIAWLTGSLTGTGWDEVRIATIPAIIAIVLAMAGARQLNVLLLGEQTARS 261
                                       ******************9777899**************************************************** PP

                             FecCD 213 lGvnvervrllllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsp 289
                                       lG++ve vr+ll  +++l+++va++++G+++F GL+vPhi+r  vg+d+r+l++ + ++G +l+++ad+ arl+l  
  gi|336253026|ref|YP_004596133.1| 262 LGMRVEMVRFLLSGVAILAASVAISVAGIVSFFGLVVPHIVRNTVGSDYRQLMVGCLFAGPALMVAADVGARLALGG 338
                                       ***************************************************************************** PP

                             FecCD 290 telpvgivtaliGapffiylllr 312
                                       +++pvg+vt l+G+p+f+yl+++
  gi|336253026|ref|YP_004596133.1| 339 VQMPVGVVTGLLGGPYFLYLMRK 361
                                       *********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2535.69
//
Query:       gi|336253027|ref|YP_004596134.1|  [L=147]
Description: Cupin 2 barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   64.8   0.3    6.4e-18   64.2   0.3    1.3  1  Cupin_2          Cupin domain
    6.6e-10   38.8   0.0    9.3e-10   38.3   0.0    1.2  1  Cupin_1          Cupin
    4.5e-06   26.6   0.0    6.1e-06   26.2   0.0    1.2  1  AraC_binding     AraC-like ligand binding domain
    0.00017   21.5   0.0    0.00023   21.1   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
     0.0026   17.9   0.0     0.0035   17.5   0.0    1.1  1  CENP-C_C         Mif2/CENP-C like
  ------ inclusion threshold ------
      0.012   15.3   0.1      0.019   14.7   0.1    1.3  1  Cupin_3          Protein of unknown function (DUF861)
      0.024   14.8   0.0      0.034   14.3   0.0    1.2  1  ARD              ARD/ARD' family


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 !   64.2   0.3   2.5e-21   6.4e-18       3      70 ..      69     135 ..      67     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 2.5e-21
                                       EEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   3 velppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       ++l+pG++ p h+ + e +  yVleGe ++ + +ee+e++aGds+++pag  H++rN+gdep  +l+ 
  gi|336253027|ref|YP_004596134.1|  69 FVLEPGADVPKHTNDVE-HEQYVLEGEYVVGIADEEYEVTAGDSLLIPAGAVHWYRNEGDEPGAFLCA 135
                                       789**************.**********************************************9985 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   3.6e-13   9.3e-10      35     112 ..      66     135 ..      61     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 3.6e-13
                                       EEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEEE CS
                           Cupin_1  35 aarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavaiv 111
                                       + r++lepg+ ++ h++   +  +yvl+Ge  vg++ ++        ++++Gd + +Pag vh+  n gdep+  + 
  gi|336253027|ref|YP_004596134.1|  66 IRRFVLEPGADVPKHTN-DVEHEQYVLEGEYVVGIADEEY-------EVTAGDSLLIPAGAVHWYRNEGDEPGAFLC 134
                                       557888***********.99999*************9997.......9*********************99987665 PP

                                       E CS
                           Cupin_1 112 v 112
                                       +
  gi|336253027|ref|YP_004596134.1| 135 A 135
                                       5 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 !   26.2   0.0   2.4e-09   6.1e-06      12      68 ..      73     129 ..      66     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.4e-09
                                       TT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSE CS
                      AraC_binding  12 pdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedg 68 
                                       p+ ++p+h+ d  + +yv+eG+  + +++++y++++Gd +L+p g +H y+ +++++
  gi|336253027|ref|YP_004596134.1|  73 PGADVPKHTNDVEHEQYVLEGEYVVGIADEEYEVTAGDSLLIPAGAVHWYRNEGDEP 129
                                       5566788888877779*************************************9984 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.9e-08   0.00023      62     129 ..      63     129 ..      56     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.9e-08
                   MannoseP_isomer  62 ryqvkritvkPgeklslqkhhhraeh.WvvvkGtakvtvddevlllkenestyiplgaihrlenpGkip 129
                                       ++ ++r +++Pg+   + kh    eh   v++G   v + de++++++ +s  ip+ga+h   n G  p
  gi|336253027|ref|YP_004596134.1|  63 HFAIRRFVLEPGAD--VPKHTNDVEHeQYVLEGEYVVGIADEEYEVTAGDSLLIPAGAVHWYRNEGDEP 129
                                       799*********97..568888888844689*********************************99865 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.4e-06    0.0035      27      78 ..      78     129 ..      62     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-06
                                       EEE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE-SSS- CS
                          CENP-C_C  27 kknskkatlvFyViqGrvevtvsktsfvigkgsvFqvPagneysieNklnke 78 
                                       +k+ ++     yV++G+  v + ++++ ++ g++ ++Pag     +N++++ 
  gi|336253027|ref|YP_004596134.1|  78 PKHTNDVEHEQYVLEGEYVVGIADEEYEVTAGDSLLIPAGAVHWYRNEGDEP 129
                                       56677777778*******************************9999988775 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 ?   14.7   0.1   7.4e-06     0.019      30      60 ..      89     118 ..      76     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.4e-06
                                       EEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                           Cupin_3  30 yileGevkvtpeggetvelraGDlvvlpkgl 60 
                                       y+leGe  v     e++e+ aGD++ +p+g 
  gi|336253027|ref|YP_004596134.1|  89 YVLEGEYVVGI-ADEEYEVTAGDSLLIPAGA 118
                                       9**********.99***************97 PP

>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-05     0.034      88     136 ..      80     123 ..      77     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                               ARD  88 hlhedeeirliveGtgyFdvrskdeawirvlvekGDLivlPagiyhrFt 136
                                       h+ + e   +++eG+  ++v   de++    v++GD +++Pag  h++ 
  gi|336253027|ref|YP_004596134.1|  80 HTNDVEHEQYVLEGE--YVVGIADEEYE---VTAGDSLLIPAGAVHWYR 123
                                       555556667788776..9*********9...****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1169.09
//
Query:       gi|336253028|ref|YP_004596135.1|  [L=64]
Description: cold-shock DNA-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-20   72.3   0.1    2.4e-20   72.1   0.1    1.0  1  CSD       'Cold-shock' DNA-binding domain
  ------ inclusion threshold ------
      0.039   13.6   2.2      0.049   13.3   2.2    1.2  1  OB_RNB    Ribonuclease B OB domain
       0.14   12.1   0.2       0.18   11.7   0.2    1.4  1  S1-like   S1-like


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.1     4e-24   2.4e-20       2      65 ..       3      63 ..       2      64 .] 0.97

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 4e-24
                                      EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                               CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                      +GtV  fn+  g+GFI++ed d+dvF+H+ +i g +   L+egqe eFe+++  kgp+A+nV +
  gi|336253028|ref|YP_004596135.1|  3 QGTVDFFNDTGGYGFIETEDADEDVFFHMEDIGGPD---LEEGQELEFEIEQAPKGPRATNVER 63
                                      8********************************999...***********************75 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.2   8.2e-06     0.049       8      28 ..      13      33 ..       4      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.2e-06
                                      SS-EEEEECT.TEEEEE-HHH CS
                            OB_RNB  8 kGFGFlipdegkeDifippeq 28
                                       G+GF+++++ +eD+f + e+
  gi|336253028|ref|YP_004596135.1| 13 GGYGFIETEDADEDVFFHMED 33
                                      59**************87766 PP

>> S1-like  S1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   3.1e-05      0.18      14      47 ..      14      52 ..       3      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
                           S1-like 14 tfGfv.....DeevfFqrsvvkGrlpkvgdrVlveAvyn 47
                                       +Gf+     De+vfF+++ + G+  + g   ++e  + 
  gi|336253028|ref|YP_004596135.1| 14 GYGFIetedaDEDVFFHMEDIGGPDLEEGQELEFEIEQA 52
                                      58888777778********99999888887777765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 491.52
//
Query:       gi|336253029|ref|YP_004596136.1|  [L=154]
Description: AsnC family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for complete 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   53.7   0.4    1.8e-14   53.0   0.4    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    2.2e-10   40.2   1.6    3.7e-10   39.5   1.6    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    1.1e-08   34.9   0.1    2.5e-08   33.7   0.1    1.6  1  HTH_11           HTH domain
    2.5e-06   27.3   0.1    9.1e-06   25.5   0.0    1.9  2  MarR_2           MarR family
    8.3e-06   25.5   0.0    1.5e-05   24.7   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
    1.1e-05   25.6   0.1    5.8e-05   23.2   0.1    2.0  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    2.1e-05   24.3   0.0    4.4e-05   23.3   0.0    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
    4.4e-05   23.5   0.1    9.9e-05   22.3   0.0    1.6  1  HTH_20           Helix-turn-helix domain
    0.00022   20.8   0.2    0.00042   19.9   0.2    1.5  1  Sigma70_r4_2     Sigma-70, region 4
    0.00023   21.5   0.0    0.00045   20.5   0.0    1.4  1  Rrf2             Transcriptional regulator
    0.00065   19.4   0.1     0.0048   16.6   0.1    2.1  2  HTH_DeoR         DeoR-like helix-turn-helix domain
     0.0022   18.0   0.0     0.0041   17.1   0.0    1.4  1  HTH_Mga          M protein trans-acting positive regulator (M
     0.0029   17.5   0.5      0.018   15.0   0.3    2.4  2  HTH_12           Ribonuclease R winged-helix domain
     0.0032   17.4   0.1     0.0068   16.4   0.1    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0034   17.0   0.1     0.0056   16.3   0.1    1.4  1  GntR             Bacterial regulatory proteins, gntR family
     0.0042   17.2   0.1     0.0075   16.4   0.1    1.3  1  HTH_28           Helix-turn-helix domain
     0.0055   16.3   0.0     0.0091   15.6   0.0    1.4  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
     0.0057   16.7   0.2      0.013   15.5   0.2    1.5  1  Put_DNA-bind_N   Putative DNA-binding protein N-terminus
     0.0062   16.6   0.1       0.11   12.6   0.1    2.1  2  DUF2250          Uncharacterized protein conserved in archaea
     0.0068   16.2   0.5      0.013   15.4   0.1    1.6  2  Nuc_N            Nuclease N terminal
     0.0076   16.7   0.0      0.015   15.7   0.0    1.5  1  HTH_27           Winged helix DNA-binding domain
     0.0077   16.1   0.0      0.014   15.3   0.0    1.4  1  MarR             MarR family
  ------ inclusion threshold ------
      0.013   15.3   0.2      0.022   14.5   0.2    1.3  1  HTH_23           Homeodomain-like domain
      0.013   15.0   0.5      0.026   14.1   0.5    1.4  1  Sigma70_r4       Sigma-70, region 4
       0.02   14.8   0.1      0.038   13.9   0.1    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
       0.15   12.0   0.0       0.23   11.4   0.0    1.3  1  Phage_antitermQ  Phage antitermination protein Q
       0.17   11.8   0.3       0.37   10.6   0.3    1.5  1  HTH_10           HTH DNA binding domain


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 !   53.0   0.4   2.7e-17   1.8e-14       1      48 []       6      54 ..       6      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 2.7e-17
                            HTH_24  1 ldetdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ld  dr+IL +Lq+++r +s  e+Aer++ S+stv++r++rLe+eG+Ik
  gi|336253029|ref|YP_004596136.1|  6 LDAVDREILYALQEEARnLSSGEIAERTDASSSTVRKRIQRLESEGVIK 54
                                      7999********************************************8 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 !   39.5   1.6   5.5e-13   3.7e-10       1      42 []       6      48 ..       6      48 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 5.5e-13
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaR.isyaeLAervGlSestvlrRvrrLe 42
                                      LD++Dr IL aLqe aR +s  e+Aer+  S stv++R++rLe
  gi|336253029|ref|YP_004596136.1|  6 LDAVDREILYALQEEARnLSSGEIAERTDASSSTVRKRIQRLE 48
                                      8**************8879***********************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.1   3.7e-11   2.5e-08       3      54 ..      11      67 ..      10      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 3.7e-11
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg......vpIesepgrGY 54
                                      + il  L e+  ++s+ e+Ae+++ S +tvr++I++Le+ g      + I+ +++ GY
  gi|336253029|ref|YP_004596136.1| 11 REILYALQEEARNLSSGEIAERTDASSSTVRKRIQRLESEGvikgysANIDYTKS-GY 67
                                      579999*888888****************************88888888877777.77 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.4e-08   9.1e-06       5      52 ..       8      54 ..       4      61 .. 0.90
   2 ?   -1.8   0.0       4.5     3e+03       8      28 ..      83     102 ..      80     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.4e-08
                                      HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                        ++ +L+aL  + + +l+ ge+a+r++ s s+v ++++rL++ G + 
  gi|336253029|ref|YP_004596136.1|  8 AVDREILYALQEEAR-NLSSGEIAERTDASSSTVRKRIQRLESEGVIK 54
                                      567889****99996.5****************************985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.5
                                       HHHHHHHHCTTTSEEEHHHHH CS
                            MarR_2   8 arvLaaLgrrpgrdltvgela 28 
                                        + L ++ + pg  ++v+el+
  gi|336253029|ref|YP_004596136.1|  83 GDYLDEVLDIPGV-VSVQELV 102
                                       5788899999995.6999985 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 !   24.7   0.0   2.2e-08   1.5e-05       7      49 ..      12      54 ..      11      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.2e-08
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +iL al e+++ l+  e+A+rt+ + Stv+  +q L+ +G ++
  gi|336253029|ref|YP_004596136.1| 12 EILYALQEEARNLSSGEIAERTDASSSTVRKRIQRLESEGVIK 54
                                      5999***********************************9875 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 !   23.2   0.1   8.8e-08   5.8e-05      12      52 ..      13      53 ..      12      57 .. 0.94
   2 ?   -1.4   0.0       4.2   2.8e+03      44      54 ..     125     135 ..     121     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8.8e-08
                                      HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                       +Y l+ee    +  ++aer + s s+V + +++Le++G +
  gi|336253029|ref|YP_004596136.1| 13 ILYALQEEARNLSSGEIAERTDASSSTVRKRIQRLESEGVI 53
                                      68************************************965 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.2
                                       HHHHHTTSEEE CS
                    Fe_dep_repress  44 kkLekdGyvey 54 
                                       ++L+++G+ ++
  gi|336253029|ref|YP_004596136.1| 125 QELSDMGLTIT 135
                                       68999999765 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 !   23.3   0.0   6.6e-08   4.4e-05       5      45 ..      11      53 ..      10      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.6e-08
                                      HHHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  5 lkILklLae..gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      ++IL++L+e  ++l+++e+ae ++ s stv+    +L+ +G++
  gi|336253029|ref|YP_004596136.1| 11 REILYALQEeaRNLSSGEIAERTDASSSTVRKRIQRLESEGVI 53
                                      59********99***************************9998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.5e-07   9.9e-05      11      56 ..       9      55 ..       6      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.5e-07
                                      HHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 11 vRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      v r+il aL  +a+ l+ +e+aer d s +t++++++ Le+ g +++
  gi|336253029|ref|YP_004596136.1|  9 VDREILYALqEEARNLSSGEIAERTDASSSTVRKRIQRLESEGVIKG 55
                                      678999999889999***************************99975 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 !   19.9   0.2   6.4e-07   0.00042      26      49 ..      23      46 ..       5      48 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.4e-07
                                      ---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 26 glsykEIAellgisegtVksrlsR 49
                                      +ls  EIAe+++ s++tV++r++R
  gi|336253029|ref|YP_004596136.1| 23 NLSSGEIAERTDASSSTVRKRIQR 46
                                      699********************9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   6.8e-07   0.00045      18      56 ..      16      54 ..       7      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.8e-07
                                      HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      a++ee + +ss eiaer++ s s ++k +++L+ +g++k
  gi|336253029|ref|YP_004596136.1| 16 ALQEEARNLSSGEIAERTDASSSTVRKRIQRLESEGVIK 54
                                      66777778*****************************98 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 !   16.6   0.1   7.2e-06    0.0048      11      45 ..      20      54 ..      10      57 .. 0.83
   2 ?    0.0   0.0       1.1   7.4e+02       7      21 ..      88     102 ..      82     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.2e-06
                          HTH_DeoR 11 qqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                      + + ls  e++e+ + S  T+R+ ++ Le +g+++
  gi|336253029|ref|YP_004596136.1| 20 EARNLSSGEIAERTDASSSTVRKRIQRLESEGVIK 54
                                      45789999************************974 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.1
                          HTH_DeoR   7 ellkqqgklsveelv 21 
                                       e l   g +sv+elv
  gi|336253029|ref|YP_004596136.1|  88 EVLDIPGVVSVQELV 102
                                       67888899*****98 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 !   17.1   0.0   6.1e-06    0.0041       9      56 ..      12      60 ..       9      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.1e-06
                           HTH_Mga  9 kLlelLteneksltldelakeLglseltlqsdiseLnel.Fpeelsivi 56
                                      ++l +L e+++ l+  e+a++++ s++t++++i+ L ++ +++ +s +i
  gi|336253029|ref|YP_004596136.1| 12 EILYALQEEARNLSSGEIAERTDASSSTVRKRIQRLESEgVIKGYSANI 60
                                      6888999999**************************9888888877776 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 !   15.0   0.3   2.7e-05     0.018       2      50 ..      12      55 ..      11      84 .. 0.87
   2 ?   -0.2   0.0       1.5   9.6e+02      19      33 ..     123     137 ..     105     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-05
                            HTH_12  2 eILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrr 50
                                      eIL  l+e+ + ++++eiae       d +  +vR r++ le +g ++ 
  gi|336253029|ref|YP_004596136.1| 12 EILYALQEEARNLSSGEIAER-----TDASSSTVRKRIQRLESEGVIKG 55
                                      8******************86.....4566799************9974 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.5
                            HTH_12  19 iaeeLkkrgydiger 33 
                                       ia+eL + g  i ++
  gi|336253029|ref|YP_004596136.1| 123 IAQELSDMGLTITDE 137
                                       888888888777655 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 !   16.4   0.1     1e-05    0.0068      20      53 ..      22      55 ..       7      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-05
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisr 53
                                       +l+  e+A++  ++ +tv + +++L+ eg+i+ 
  gi|336253029|ref|YP_004596136.1| 22 RNLSSGEIAERTDASSSTVRKRIQRLESEGVIKG 55
                                      479999**************************93 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   8.5e-06    0.0056      24      54 ..      24      53 ..       7      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.5e-06
                                      ---HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 24 LPsereLaaefgVsrttvReALrrLeaeglv 54
                                      L s  e+a++ + s +tvR+ ++rLe+eg++
  gi|336253029|ref|YP_004596136.1| 24 L-SSGEIAERTDASSSTVRKRIQRLESEGVI 53
                                      7.788************************97 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   0.1   1.1e-05    0.0075      14      41 ..      25      52 ..      13      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                            HTH_28 14 svreaArelgisrrtvyrWikryeegGi 41
                                      s  e+A++   s++tv++ i+r+e++G+
  gi|336253029|ref|YP_004596136.1| 25 SSGEIAERTDASSSTVRKRIQRLESEGV 52
                                      6788**********************95 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 !   15.6   0.0   1.4e-05    0.0091       2      56 ..       6      56 ..       5      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                      HrcA_DNA-bdg  2 LtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegv 56
                                      L +v +eil aL    +++ r + + eiAe  +  + tvR  +q L + g+++g 
  gi|336253029|ref|YP_004596136.1|  6 LDAVDREILYAL----QEEARNLSSGEIAERTDASSSTVRKRIQRLESEGVIKGY 56
                                      778889999988....67889999************************9999986 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.9e-05     0.013      17      46 ..      14      42 ..      11      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                                      HHHHHHTT--EE-HHHHHHHCTS-HHHHHH CS
                    Put_DNA-bind_N 17 LeelkeegveriSSteLaealgvtaaqvRK 46
                                      L +l+ee   + SS e+ae+++ ++++vRK
  gi|336253029|ref|YP_004596136.1| 14 LYALQEE-ARNLSSGEIAERTDASSSTVRK 42
                                      6667766.799******************9 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 !   12.6   0.1   0.00017      0.11       3      58 ..       3      59 ..       1      65 [. 0.85
   2 ?    2.0   0.0      0.33   2.2e+02      36      52 ..     117     133 ..     106     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                           DUF2250  3 eleedelalkvlkhlkkanvdYa.ksiakeleipleevrellkkLeelGLlervegk 58
                                      e+e d ++ ++l+ l++   + +   ia++++++ + vr+ +++Le+ G ++ ++++
  gi|336253029|ref|YP_004596136.1|  3 EYELDAVDREILYALQEEARNLSsGEIAERTDASSSTVRKRIQRLESEGVIKGYSAN 59
                                      67788888999999988777765158*************************999876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.33
                           DUF2250  36 leevrellkkLeelGLl 52 
                                          ++ + ++L ++GL 
  gi|336253029|ref|YP_004596136.1| 117 DRDITPIAQELSDMGLT 133
                                       5679999********95 PP

>> Nuc_N  Nuclease N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.9e-05     0.013      27      55 ..      26      55 ..      21      58 .. 0.87
   2 ?   -2.7   0.0       8.2   5.4e+03       2      13 ..      96     107 ..      95     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                             Nuc_N 27 sakvkeaHkaSKAkiQsrIsklEkeG.vkg 55
                                      s+ + e  +aS   +  rI++lE+eG +kg
  gi|336253029|ref|YP_004596136.1| 26 SGEIAERTDASSSTVRKRIQRLESEGvIKG 55
                                      567888889*****************8887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.2
                             Nuc_N   2 dsvsdiakGvev 13 
                                       +sv++++ G e 
  gi|336253029|ref|YP_004596136.1|  96 VSVQELVTGEEN 107
                                       799999888875 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 !   15.7   0.0   2.3e-05     0.015       3      48 ..       8      53 ..       6      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-05
                            HTH_27  3 rqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                      ++++ +L  ++++ r  +  ++++r++ ++s++ + + +L+  G++
  gi|336253029|ref|YP_004596136.1|  8 AVDREILYALQEEARNLSSGEIAERTDASSSTVRKRIQRLESEGVI 53
                                      67899******99999999*************************99 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.1e-05     0.014      14      47 ..      20      53 ..      11      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                                      HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR 14 eqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      e  +ls  e+a++   s+stv + + rLe +G i
  gi|336253029|ref|YP_004596136.1| 20 EARNLSSGEIAERTDASSSTVRKRIQRLESEGVI 53
                                      45679999************************98 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   3.3e-05     0.022       9      46 ..      12      52 ..      11      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-05
                            HTH_23  9 rillllae...GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      +il++l+e    ls  eIA++ + s +Tv++ ++r + eG+
  gi|336253029|ref|YP_004596136.1| 12 EILYALQEearNLSSGEIAERTDASSSTVRKRIQRLESEGV 52
                                      5788888778899**********************977995 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5   3.8e-05     0.026       5      43 ..       6      46 ..       5      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-05
                                      S-HHHHHHHHHHH..TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  5 Lpererevlelrf..geglTleEIgerlgiSrerVrqiekr 43
                                      L++ +re+l+      ++l+  EI+er + S ++Vr ++ r
  gi|336253029|ref|YP_004596136.1|  6 LDAVDREILYALQeeARNLSSGEIAERTDASSSTVRKRIQR 46
                                      7777899999999666666667***************9876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.7e-05     0.038       4      53 ..       4      54 ..       1      69 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-05
                                      CHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB  4 lGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      + L   + ++  aL  +  +++  eiae+++ + s+v + +++Le+ G+++
  gi|336253029|ref|YP_004596136.1|  4 YELDAVDREILYALQeEARNLSSGEIAERTDASSSTVRKRIQRLESEGVIK 54
                                      667777777777888677889999************************997 PP

>> Phage_antitermQ  Phage antitermination protein Q
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00035      0.23      77     114 ..      22      61 ..       7      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                   Phage_antitermQ  77 fgvskraiarklkisekevrkklq..kaegfiegclaald 114
                                        ++s  +ia++ + s+++vrk++q   +eg+i+g+ a +d
  gi|336253029|ref|YP_004596136.1|  22 RNLSSGEIAERTDASSSTVRKRIQrlESEGVIKGYSANID 61 
                                       5789999****************94458999*99877665 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00055      0.37      19      49 ..      19      49 ..      17      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00055
                            HTH_10 19 dyPRrvtlkeLAkelGIskstlsehLrkaes 49
                                      ++ R+ ++ e+A++ + s st+ +++++ es
  gi|336253029|ref|YP_004596136.1| 19 EEARNLSSGEIAERTDASSSTVRKRIQRLES 49
                                      578999*********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1203.45
//
Query:       gi|336253030|ref|YP_004596137.1|  [L=499]
Description: NADH dehydrogenase (quinone) [Halopiger xanaduensis SH-6]
Scores for 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-39  133.6  19.2    7.8e-39  133.6  19.2    1.7  1  Proton_antipo_M  Proton-conducting membrane transporter
    4.1e-10   39.6   0.9    4.1e-10   39.6   0.9    3.3  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 !  133.6  19.2   8.7e-43   7.8e-39       1     226 [.     112     331 ..     112     342 .. 0.93

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 8.7e-43
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       a++++l+  ++ +++l +  Lig  ++++++ +A+  +  ++ ++s +L  ++++l + +gt+++  ++  le  ++
  gi|336253030|ref|YP_004596137.1| 112 ADHVALFAAAWLAMGLLMAGLIGHVRDWEQARAAGALARRYFVASSAVLAGSLAVLAWEAGTTSISGIFGGLE-EVS 187
                                       6788899999*************************************************************54.445 PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavssneisqlllil 153
                                           l+++  +++++l+ sa++p+h Wl  + + aPtp sal+ A+  v+ag+ ll+r+++l+a    +i++ +++l
  gi|336253030|ref|YP_004596137.1| 188 ATVGLVAAGGIVLAALIQSALFPFHGWLLSS-MTAPTPASALMhAG-FVNAGGVLLTRFSPLVA-DHLAIMSAVVVL 261
                                       555567788999*******************.***********777.*****************.999********* PP

                   Proton_antipo_M 154 aiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyer 226
                                       +++s+llg  + l+qtd+Kr l+ S+++++G+m++++++ ++   +aai+hl++h++ ka lFl +g+++ e 
  gi|336253030|ref|YP_004596137.1| 262 GAVSALLGQAMLLVQTDVKRKLGSSTMAQMGFMILQCGL-GFF--AAAIAHLVLHGFYKAYLFLSSGAAVEEA 331
                                       ***************************************.666..9********************9987764 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 !   39.6   0.9   4.6e-14   4.1e-10      17      55 ..      59      97 ..      57      99 .. 0.96
   2 ?   -2.3   0.2      0.56   5.1e+03      17      31 ..     248     262 ..     245     267 .. 0.76
   3 ?   -0.8   0.5      0.18   1.7e+03      15      31 ..     373     389 ..     371     393 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 4.6e-14
                   Proton_antipo_N 17 llDklsalmllvvtfvsllvhlYSigYMaddegyqRFfa 55
                                       +D+l+a+  +vvtf s +vh YS  YMa+d+   RFfa
  gi|336253030|ref|YP_004596137.1| 59 VVDGLTAVLWVVVTFFSGIVHSYSRRYMAGDRDLERFFA 97
                                      69************************************8 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.56
                   Proton_antipo_N  17 llDklsalmllvvtf 31 
                                         D l ++ ++vv +
  gi|336253030|ref|YP_004596137.1| 248 VADHLAIMSAVVVLG 262
                                       568899988888876 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.18
                   Proton_antipo_N  15 gfllDklsalmllvvtf 31 
                                       g+ +D+ ++l l+vv +
  gi|336253030|ref|YP_004596137.1| 373 GLSFDSGTILTLVVVLT 389
                                       7899999****999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3341.85
//
Query:       gi|336253031|ref|YP_004596138.1|  [L=858]
Description: hypothetical protein Halxa_1627 [Halopiger xanaduensis SH-6]
Scores for complete 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-269  896.5   0.0   1.8e-269  896.3   0.0    1.0  1  DUF2309   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2309  Uncharacterized protein conserved in bacteria (DUF2309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  896.3   0.0  9.8e-274  1.8e-269       1     752 []      46     811 ..      46     811 .. 0.95

  Alignments for each domain:
  == domain 1  score: 896.3 bits;  conditional E-value: 9.8e-274
                           DUF2309   1 veeaaevipplwPlktfvahNplhgledlpfeeavaelaklfgarlylseeeyrealaegrideedLeaaeeeleee 77 
                                       +e+aae++ ++wPl +fv+ Npl+g+ed+pf++av+e+++lfg+r+y++ + +r+a ++g+id+++Le++ e+ + +
  gi|336253031|ref|YP_004596138.1|  46 IERAAERVGSVWPLYSFVTANPLSGFEDRPFHRAVDEAESLFGGRGYPHPDVFRKARERGQIDSDVLEDELEARGID 122
                                       789*******************************************************************5455444 PP

                           DUF2309  78 etlaelldaltged.........ldelvdeqlikllaaflDegqaawslpkrekglyaawrelakhdlslellllke 145
                                       +++++ll+++++ d         ++e+vd++l+k+laaflDegqa+w++p+re+g+yaawr++a +d +++      
  gi|336253031|ref|YP_004596138.1| 123 RDPETLLEEMAEADaardadaddATETVDRVLSKWLAAFLDEGQAKWPMPNREEGFYAAWRSVAPYDGDVP------ 193
                                       44444444444444444455666************************************************...... PP

                           DUF2309 146 lrkvlaelpedpeeaiaealeelgipeeeweaylealllalpGWagliryreeqpeaelqgeepaslvdllairLll 222
                                         +   +lpe+++ea++++l ++   e++w+++ e++++alpGW+g+i++r +++++ +q+e+p++l+d+la+rL+l
  gi|336253031|ref|YP_004596138.1| 194 GCDDPGDLPETATEALESVLGDYP--EDRWTDIAEHHFAALPGWTGFIKQRVDDETDPWQAEYPITLRDYLAVRLTL 268
                                       5677788**************987..*************************************************** PP

                           DUF2309 223 eaalleevakeklsleeleaaaaleelaeeergklwleAlErsyreellealaaeseseeaa...erpeaqavfCiD 296
                                       + +l ++++ ++ ++ + +   a ++++   + ++wl+A+E+syre+lle+++ + + +++a   +rp+aq+vfCiD
  gi|336253031|ref|YP_004596138.1| 269 ADLLDAPIEPANDERGADAGDGADDSEEVLPIPEIWLTAWEKSYRERLLEQIDGSVTDPADAdksSRPAAQLVFCID 345
                                       *******99999888888888899999999**********************9888877777778************ PP

                           DUF2309 297 vRseslRRhLEevgpeveTlGfAGFFGvpiayqgldkeeeealcPvlltPkhlvkeeakeeeeaekakrkrrlkaal 373
                                       +Rse +RRh+E +g+ +eT+G+AGFFGvp++y+g+d+++  ++cP++++++h+v +++++ e+++k++r++ l +a+
  gi|336253031|ref|YP_004596138.1| 346 TRSEIIRRHIEDQGS-YETHGYAGFFGVPMRYRGYDAKADVDACPPIVDAEHRVVDRPDDPETTAKRDRWKGLATAT 421
                                       ***************.************************************************************* PP

                           DUF2309 374 ekllkelkrsllssfllvealGllyalkllaktlaprraarlkeklkakleekeetklkldkeseee.......... 440
                                       +k++k+lk +++++f +ve  G +y+ +++a+tlap++ a+l++++++++ +++e      + ++++          
  gi|336253031|ref|YP_004596138.1| 422 RKHFKRLKANAVAAFPFVEGGGAAYGSAMAARTLAPSAIASLESAVADRVPSRHEFCSPAIDYDDHDdhshadhdlp 498
                                       **************************************************99998766555555545689******* PP

                           DUF2309 441 .gltleeqvelveaaLraigLtenfAplVllvGHgSsseNNpheaaldCGACgGrsGgvnARvlAallNdpeVRegL 516
                                        g++le++v ++e+a+ ++g+t +fA+lV+++GH+S+++NNp++++ldCGAC+G++Gg+nARvlA+++Ndp+V+++L
  gi|336253031|ref|YP_004596138.1| 499 qGMSLEQKVGYAENAFALMGWT-EFARLVVFAGHASETTNNPFDSSLDCGACAGNPGGPNARVLATICNDPDVQAEL 574
                                       *********************7.9***************************************************** PP

                           DUF2309 517 aergieIPedTvFvaalhnTttDevelfdldllpashrealeklkadleeagelaaaeRarrlesaeakk.ekaeae 592
                                       +erg++IP+dTvF+a++hnTttDe++lfd  ++p+shre+le+l+adle+a++ aaaeR+++++++++ + e+a ae
  gi|336253031|ref|YP_004596138.1| 575 RERGFHIPDDTVFLAGEHNTTTDEITLFDG-AVPESHREDLEQLRADLERAQAGAAAERLESMTDETDVDpEEAVAE 650
                                       ****************************65.69******************************99888779****** PP

                           DUF2309 593 verraedwsevRPEwglagnaafiigrReltrgldLdgraFLhsYdwrqDpdgklLeniltaplvVaqwInleYYfS 669
                                       ver+a+dw+e+RPEwglagna+f+ig+Relt++ +LdgraFLhsYdw++Dp+g++Le+i+t+plvV+qwIn +YYf+
  gi|336253031|ref|YP_004596138.1| 651 VERKAADWAETRPEWGLAGNASFVIGPRELTDDENLDGRAFLHSYDWTTDPEGDALEAIMTGPLVVTQWINNQYYFA 727
                                       ***************************************************************************** PP

                           DUF2309 670 tvdnevyGsGsKvlhnvvgriGVmeGnggDLrtGLplQsvhdgdr.eiHePlRLlvvieapreaierilarheavre 745
                                       tvdn vyGsGsKv++n  g++GV++GnggDL+tGLplQs++ +d+  +H+PlRL++vi+ap e++++il+rh++v+e
  gi|336253031|ref|YP_004596138.1| 728 TVDNGVYGSGSKVTQNALGNVGVVQGNGGDLMTGLPLQSLQLSDDeSYHQPLRLTAVIHAPVERVTDILQRHDEVAE 804
                                       ****************************************998888******************************* PP

                           DUF2309 746 lvdngWl 752
                                       l+dngW+
  gi|336253031|ref|YP_004596138.1| 805 LLDNGWI 811
                                       ******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (858 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); 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: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.45
# Mc/sec: 5676.65
//
Query:       gi|336253032|ref|YP_004596139.1|  [L=72]
Description: hypothetical protein Halxa_1628 [Halopiger xanaduensis SH-6]
Scores for 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   13.5   2.4      0.025   13.4   2.4    1.0  1  LptF_LptG        Lipopolysaccharide export system permease Lp
      0.074   13.1  10.9       0.71   10.0   1.8    2.1  2  YqzM             YqzM-like protein
       0.45   10.0   9.7       0.94    8.9   9.8    1.5  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
        1.8    8.0   8.8          3    7.3   2.0    2.1  2  MtrF             Tetrahydromethanopterin S-methyltransferase,
        3.3    7.8   5.8          4    7.5   0.2    2.2  2  FixQ             Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> LptF_LptG  Lipopolysaccharide export system permease LptF/LptG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.4     7e-06     0.025     279     329 ..      16      70 ..       4      72 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-06
                         LptF_LptG 279 placlvfaliaaplglvkrrggrglr....lliaillfvlyyvllslgkalaeng 329
                                         ++ v ++i+++  +v+   g g+r    l++++llf+++y+++++  +l +++
  gi|336253032|ref|YP_004596139.1|  16 GAFVAVIFVIGLATLAVLSPAGIGARelggLVVGFLLFMVVYFISITIHQLEKRE 70 
                                       556778888999988888888888888999**********999999999988876 PP

>> YqzM  YqzM-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.8    0.0002      0.71      16      36 ..       6      27 ..       4      32 .. 0.80
   2 ?    8.3   2.1   0.00067       2.4      20      39 ..      45      64 ..      43      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0002
                              YqzM 16 DSgvGFv.vsFgFFavlFiIAt 36
                                       S vGF  + ++F av+F+I+ 
  gi|336253032|ref|YP_004596139.1|  6 ESDVGFYyAVGAFVAVIFVIGL 27
                                      78999973578899******96 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00067
                              YqzM 20 GFvvsFgFFavlFiIAtvik 39
                                      G vv+F+ F+v+++I + i+
  gi|336253032|ref|YP_004596139.1| 45 GLVVGFLLFMVVYFISITIH 64
                                      789*************9998 PP

>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   9.8   0.00026      0.94     239     274 ..      16      52 ..       5      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00026
                   LPG_synthase_TM 239 allllillaltlvgalpplPgGlGvrEaal.alllal 274
                                       ++ +++++++ l+++++++P+G+G+rE +  ++ + l
  gi|336253032|ref|YP_004596139.1|  16 GAFVAVIFVIGLATLAVLSPAGIGARELGGlVVGFLL 52 
                                       334499*********************8763555555 PP

>> MtrF  Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.7     0.004        14      46      59 ..      14      28 ..       5      31 .. 0.79
   2 ?    7.3   2.0   0.00082         3      35      58 ..      36      59 ..      34      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.004
                              MtrF 46 aiGfvlAllLvv.lP 59
                                      a+G ++A+++v+ l+
  gi|336253032|ref|YP_004596139.1| 14 AVGAFVAVIFVIgLA 28
                                      78*********9776 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00082
                              MtrF 35 SGvsatgivGfaiGfvlAllLvvl 58
                                      +G+ a ++ G+++Gf+l ++   +
  gi|336253032|ref|YP_004596139.1| 36 AGIGARELGGLVVGFLLFMVVYFI 59
                                      79**************99887655 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.4     0.039   1.4e+02       6      24 ..       8      26 ..       5      30 .. 0.77
   2 ?    7.5   0.2    0.0011         4      14      29 ..      50      65 ..      46      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.039
                              FixQ  6 lrgfadswgllflvllfyg 24
                                       +gf + +g ++ v++ +g
  gi|336253032|ref|YP_004596139.1|  8 DVGFYYAVGAFVAVIFVIG 26
                                      5788888888888888777 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0011
                              FixQ 14 gllflvllfygvviya 29
                                      +llf+v+ f+ + i+ 
  gi|336253032|ref|YP_004596139.1| 50 FLLFMVVYFISITIHQ 65
                                      89**********9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 535.43
//
Query:       gi|336253033|ref|YP_004596140.1|  [L=262]
Description: carbonic anhydrase [Halopiger xanaduensis SH-6]
Scores for 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-26   92.1   0.0    5.8e-26   91.6   0.0    1.1  1  Pro_CA     Carbonic anhydrase
  ------ inclusion threshold ------
      0.032   14.6   0.3        0.1   12.9   0.2    1.9  2  TetR_C_11  Tetracyclin repressor-like, C-terminal domain


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 !   91.6   0.0   6.5e-30   5.8e-26       2     152 ..      68     221 ..      67     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 6.5e-30
                                       EEEEETTTTS-HHHHTTS.-TTSEEEEEETTG---TT...-HHHHHHHHHHHHTS--SEEEEEEETT-HHHHHHHS. CS
                            Pro_CA   2 lvigCsDSRvppelitda.gpGdlFvvrnvgnlvppa...dssvlaaleyAvevlkvkhivVlGHskCGavkaalk. 73 
                                       + i+CsDSRvp+e+++++ +pG +F+  n+gn v ++   +  v + + y ++++++    V+GH++CGav+aa++ 
  gi|336253033|ref|YP_004596140.1|  68 VAICCSDSRVPQEHMWGVdHPGAVFTPSNIGNQVWDEddgERIVDGGILYPIHHTETAVAAVVGHTGCGAVTAAYRv 144
                                       78**************86379*************99966555679***************************99999 PP

                                       .HHCCSTTSSHHHHHHHHHHHHHHH..CHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHTTS-EEEEE CS
                            Pro_CA  74 .aekseeeagaidkwlekirealek..veeelesekekearerlleeenVaeqlenLlekpvvreavekgklkvhGl 147
                                        +  +    + +dkw+e++ +++e+   + + +++ ++e++ ++l+e nV++q+e L+e + + +     +++++G 
  gi|336253033|ref|YP_004596140.1| 145 aTGGDMPGPQGVDKWVEMLVPVVEEaiESGAVDADADEETVVNRLVEYNVNRQVEFLREAEEIPD-----DVAIYGF 216
                                       75555667899*************964344444555999999999**************987774.....4689999 PP

                                       EEETT CS
                            Pro_CA 148 vydle 152
                                       vyd++
  gi|336253033|ref|YP_004596140.1| 217 VYDFQ 221
                                       99875 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.4   1.3e+04      96     111 ..      97     112 ..      89     112 .. 0.76
   2 ?   12.9   0.2   1.1e-05       0.1      53      92 ..     156     195 ..     125     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.4
                         TetR_C_11  96 ltgeplddafaerlvd 111
                                       ++ + +d+++ er+vd
  gi|336253033|ref|YP_004596140.1|  97 IGNQVWDEDDGERIVD 112
                                       5667789999999998 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.1e-05
                         TetR_C_11  53 leprraalravlrrAvarGelradadvelvldlllgplly 92 
                                       ++ + + l  v++ A++ G ++adad e+v+  l+   + 
  gi|336253033|ref|YP_004596140.1| 156 VDKWVEMLVPVVEEAIESGAVDADADEETVVNRLVEYNVN 195
                                       6678889999********************9988776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1903.19
//
Query:       gi|336253034|ref|YP_004596141.1|  [L=338]
Description: 2-alkenal reductase [Halopiger xanaduensis SH-6]
Scores for 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-42  141.6   0.1    1.3e-41  140.8   0.1    1.4  1  ADH_N_2       N-terminal domain of oxidoreductase
    1.7e-23   83.0   0.0    2.4e-23   82.5   0.0    1.2  1  ADH_zinc_N    Zinc-binding dehydrogenase
    1.2e-09   39.3   0.0    2.2e-09   38.4   0.0    1.4  1  ADH_zinc_N_2  Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> ADH_N_2  N-terminal domain of oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.8   0.1   2.2e-45   1.3e-41       1     107 [.       5     111 ..       5     112 .. 0.98

  Alignments for each domain:
  == domain 1  score: 140.8 bits;  conditional E-value: 2.2e-45
                           ADH_N_2   1 kqwvlkkrpegaptesdfeleeeelpelkdGevlvralylSvDPymRgrmndaksyvepvelgdvmrggavgeVveS 77 
                                       +qw+l++rp+g+pt+++f+l++++ pe+++Gevlv++ly SvDPymRgrm+d++sy+ep+++gd+m++g vgeVv+S
  gi|336253034|ref|YP_004596141.1|   5 RQWRLASRPTGEPTRENFDLVTVDRPEPGPGEVLVKTLYQSVDPYMRGRMRDEESYAEPWDVGDPMQAGIVGEVVQS 81 
                                       89*************************************************************************** PP

                           ADH_N_2  78 knpdfkvGdlVvgllgwqdyavsdgkglek 107
                                       +++df +Gd+V+g+l w+++av+d+++l++
  gi|336253034|ref|YP_004596141.1|  82 EADDFDEGDVVTGNLLWAEHAVADADELRP 111
                                       **************************9986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.0   4.1e-27   2.4e-23       1     128 [.     157     291 ..     157     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 4.1e-27
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakk.lGadevinykea.dlverikeltggegvdvvfecvGsgatleaa 75 
                                       +vG+ a q+A+ +Ga+v+++++seek++ + + lG d++inyke+ dl+++++e++ ++gvd++f+ vG g   +a 
  gi|336253034|ref|YP_004596141.1| 157 AVGSVAGQIARLSGARVVGTAGSEEKIDWLTDeLGFDAAINYKETdDLEAAVAEAC-PDGVDAYFDNVG-GPITDAV 231
                                       69***************************9999***********************.99**********.******* PP

                                       HHCEEEEEEEEECSC..TSSEEE.....EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                        ADH_zinc_N  76 lkllkpgGrlvvvGg..gkgeee.....fdlrnlllkeksilGsllgslreefkealdll 128
                                         ll+ + r++v+G   +++e+e      +l++l+  + ++ G+l+g++++++ eal+ l
  gi|336253034|ref|YP_004596141.1| 232 WPLLNVDARVAVCGQisLYNETEvptgpRKLSKLIESRARVEGFLVGDYQSRWGEALESL 291
                                       ***************999999995555555555**********************99876 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   3.7e-13   2.2e-09       1     130 [.     190     328 ..     190     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 3.7e-13
                                       TT-SEEEETT.STTHH...HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----........S-EEE-CHHH CS
                      ADH_zinc_N_2   1 lGAdevidyr.tedfe...aatggegvDvvldtvggealleaslkvlpggGrlvsiggpp.......lsaallkpak 66 
                                       lG+d +i+y+ t+d+e   a+++++gvD+ +d+vgg+ + +a++ +l+  +r+ + g+ +       ++++ +k++k
  gi|336253034|ref|YP_004596141.1| 190 LGFDAAINYKeTDDLEaavAEACPDGVDAYFDNVGGPIT-DAVWPLLNVDARVAVCGQ-IslyneteVPTGPRKLSK 264
                                       8*********99999999988899*************99.*******88799966664.335777776666666666 PP

                                       CTTT-EEEE--GGG...-...-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSE CS
                      ADH_zinc_N_2  67 krkgrsvkyeflfsmkas..aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGK 130
                                          + + ++e ++ + ++  +  ++le l ++i++  l+ + + v ++e+a++A+  l +g  +GK
  gi|336253034|ref|YP_004596141.1| 265 LI-ESRARVEGFL-VGDYqsRWGEALESLSEFIQQDDLHYRENVVDGFENAPDAFLGLFEGENIGK 328
                                       33.4444444444.34446745555******************99********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2452.28
//
Query:       gi|336253035|ref|YP_004596142.1|  [L=285]
Description: alpha/beta hydrolase fold protein [Halopiger xanaduensis SH-6]
Scores for 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-16   59.7   0.0    5.6e-16   58.9   0.0    1.5  1  Abhydrolase_1  alpha/beta hydrolase fold
    2.3e-11   44.8  10.2    2.9e-11   44.4  10.2    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    3.9e-06   26.3   0.0      1e-05   24.9   0.0    1.6  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.018   14.7   0.0       0.02   14.5   0.0    1.2  1  Esterase       Putative esterase


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 !   58.9   0.0   1.3e-19   5.6e-16       2     128 ..      45     161 ..      44     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1.3e-19
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       +lv++hG pgs  + a   l +a  ++g +vi++  +G+g+S+p+p+      ++ + add + + d lg++++++ 
  gi|336253035|ref|YP_004596142.1|  45 PLVFHHGVPGSCALGAV--LSYAARQRGVRVIAPSRPGYGRSDPRPD---G--TLETWADDCRHLADELGLESFAVA 114
                                       89***********9888..99999888*******************9...4..66667******************* PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHH CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdff 128
                                       G+S GG  ala+a ++p+rV a  +++a   +    e  + ++++fp+ +
  gi|336253035|ref|YP_004596142.1| 115 GFSGGGPPALAVADRFPDRVTAAGAVSA---PVPETEGPLASLARFPRVL 161
                                       ***********************99999...5555666666666666655 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4  10.2   6.5e-15   2.9e-11       1     192 [.      46     255 ..      46     280 .. 0.55

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 6.5e-15
                                       EEEE--GC.....GCHHHHHHHHCCT.CEEEEE--TTSTS-GGCS....--HHHCHHHHHHHCCTT..TTSEEEEEE CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaag.vhvlapDlpGhGrsdppp....ldledladlaalldelaagggpvvlvGH 72 
                                       +++ HG   ++s+ l a L ++++++ v+v+ap++pG+Grsdp+p     ++  ++d+++l+del+     + + G 
  gi|336253035|ref|YP_004596142.1|  46 LVFHHG--VPGSCALGAVLSYAARQRgVRVIAPSRPGYGRSDPRPdgtlETW--ADDCRHLADELG--LESFAVAGF 116
                                       799***..6668886667755555557************7766664444666..677799999995..8888***** PP

                                       TCHHHHHHHHHHCC.........EE..EEES-...----TTTS----TTHH...HHHHTT-C...CCCHCCH..... CS
                     Abhydrolase_6  73 SlGGalalaaapla.......lvvg..vlldppp.talpagllaaalelll...allallrl...lawlsre..... 128
                                       S GG  ala   +a          +   + +p p t +p++ la+++++l    + ++ll++   +a+++       
  gi|336253035|ref|YP_004596142.1| 117 SGGGPPALA---VAdrfpdrvT--AagAVSAPVPeTEGPLASLARFPRVLGialRCTRLLARrrgDAFVVDQltern 188
                                       *********...5555465322..13355555333333333333333333322222222222223555522222222 PP

                                       ..S-HSCCCCHHHCCCCHCHCCCGHHHHCCHHC....HTTCCHHTT-TTGCEEECTT-C...HHHHCHHCCCH CS
                     Abhydrolase_6 129 ..plprlfladedadaawrarlarlaallaglg....llpaaawadlpvpllvlggeDp...lvprllerlla 192
                                         +++ ++++    d + + ++++  a + + +    +  +++ +d+p+++ ++g+eD+   l p  +er  a
  gi|336253035|ref|YP_004596142.1| 189 idDVTAQIVG---HDFRTGLADRPSGAVRESQFlagdWSLPEPEPDVPTTV-WHGTEDEnvpLEP--VERVYA 255
                                       3322223333...23444444444444444333333355677888888887.6589999444333..444444 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   2.3e-09     1e-05       7     216 ..      46     256 ..      41     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.3e-09
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGh 83 
                                       +v+ HG+  ++   a l +a  ++G+ v+a    G+Grs+++      ++++ dD++ + +++      + + + G 
  gi|336253035|ref|YP_004596142.1|  46 LVFHHGVPGSCALGAVLSYAARQRGVRVIAPSRPGYGRSDPRPD--GTLETWADDCRHLADELG----LESFAVAGF 116
                                       79999********9**************************7776..689999****99988887....45699**** PP

                       Hydrolase_4  84 SmGGliallyllrypdkva.glilsaPalkikaklk.appllklllkllgkllpklqv..snnlkadslsrdpevva 156
                                       S GG  al++++r pd+v+ +  +saP+ + + +l  + ++ +    +lg +l+  ++   ++ +a  + + +e+  
  gi|336253035|ref|YP_004596142.1| 117 SGGGPPALAVADRFPDRVTaAGAVSAPVPETEGPLAsLARFPR----VLGIALRCTRLlaRRRGDAFVVDQLTERNI 189
                                       ******************98999*****988877533333333....333333322221122223322333333333 PP

                       Hydrolase_4 157 ayeadplvhgkitvrlllelldamkrleeraakit.......lPllllhGeaDkvvdpeasrelyer 216
                                          + ++v+ +++++l+     a+ + +  a +++       +P+ + hG++D+ v+ e+ +++y+ 
  gi|336253035|ref|YP_004596142.1| 190 DDVTAQIVGHDFRTGLADRPSGAVRESQFLAGDWSlpepepdVPTTVWHGTEDENVPLEPVERVYAD 256
                                       34445566888888888888888888888888888777777799**********9999999888865 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.5e-06      0.02     117     152 ..     111     146 ..      91     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.5e-06
                                       EEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-C CS
                          Esterase 117 ravaGqSmGGlgALilalkhpdrFgsvssfSpivnp 152
                                        avaG+S GG  AL +a + pdr + +++ S++v  
  gi|336253035|ref|YP_004596142.1| 111 FAVAGFSGGGPPALAVADRFPDRVTAAGAVSAPVPE 146
                                       69*****************************88755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1940.87
//
Query:       gi|336253036|ref|YP_004596143.1|  [L=63]
Description: hypothetical protein Halxa_1632 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.086   12.5   3.3        0.1   12.3   3.3    1.0  1  DUF2244     Integral membrane protein (DUF2244)
        0.2   11.8   2.2       0.21   11.7   2.2    1.2  1  SLATT_3     SMODS and SLOG-associating 2TM effector domain 3


Domain annotation for each model (and alignments):
>> DUF2244  Integral membrane protein (DUF2244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.3   1.1e-05       0.1      12      57 ..       7      52 ..       2      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
                           DUF2244 12 flllllalalvslvialafllaGawpvlpFaglevlalalafrvsa 57
                                      +l+l++al +++lv      l G+ ++l Fa++++ +l++a+ ++ 
  gi|336253036|ref|YP_004596143.1|  7 LLVLIAALLALILVEIGEGKLTGLLALLAFAAIALSVLGYALIAVL 52
                                      57788888888888888888*********************98876 PP

>> SLATT_3  SMODS and SLOG-associating 2TM effector domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.2   2.3e-05      0.21      23      60 ..       3      40 ..       1      57 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                           SLATT_3 23 rlrlvllvvAAlaaalslkvgsvdlaallaalafllal 60
                                      r++ +l+++AAl+a++ +++g+++l+ lla+laf++ +
  gi|336253036|ref|YP_004596143.1|  3 RTDSLLVLIAALLALILVEIGEGKLTGLLALLAFAAIA 40
                                      788899***************************98644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 469.54
//
Query:       gi|336253037|ref|YP_004596144.1|  [L=267]
Description: ABC-2 type transporter [Halopiger xanaduensis SH-6]
Scores for 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-30  105.1  15.4    4.1e-30  104.8  15.4    1.2  1  ABC2_membrane  ABC-2 type transporter


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 !  104.8  15.4   2.3e-34   4.1e-30       3     209 ..       6     216 ..       4     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 2.3e-34
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgn.lgnsedglnr........pgllffsvlflafsalts 70 
                                       ++al++re+l+++r+p  +++ + i+ +l++ vfg++ g+ + ++              pgl++  ++ +a + ++s
  gi|336253037|ref|YP_004596144.1|   6 FRALFRREVLRFVRRPKNTFMPPAITNVLYFAVFGLILGGrI-DEIA---GfpyilfivPGLIVLGAISNA-FENAS 77 
                                       899************************************422.3333...135579999************.99999 PP

                     ABC2_membrane  71 vapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaassl 147
                                        +++  r ++ + + l+spl s +++v+a+v+++++++l++++i+ ++  ++v + +++++++++++++++ ++ +l
  gi|336253037|ref|YP_004596144.1|  78 FSIFHGRWNEYIHETLTSPL-SYAEMVVAYVAASAVRGLIVGVIIAVVGRLFVPISIEHGLFLVATMVIITALFAGL 153
                                       9999999*************.********************************9999999999************** PP

                     ABC2_membrane 148 gllisalapsfedasqlaslvllpllllsGffipidsm.pkwlqwiaylnPltyavealrsnl 209
                                       g++ + +a++f+d +++ +++l pl++++ +f+++++  + w   i+ +nP++y+v+++r++l
  gi|336253037|ref|YP_004596144.1| 154 GIIGGLVARDFDDLTVMNQFILRPLVFFGAVFYSLETFeQAWQVQISLVNPMVYMVDSVRYGL 216
                                       **************************************5456667***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1957.59
//
Query:       gi|336253038|ref|YP_004596145.1|  [L=337]
Description: phosphonate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-30  106.0   0.0    3.3e-30  105.4   0.0    1.3  1  ABC_tran     ABC transporter
    1.1e-14   55.0   2.7    7.8e-10   39.0   0.1    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.3e-09   38.6   0.0    4.6e-09   36.9   0.0    1.9  2  DUF4162      Domain of unknown function (DUF4162)
     0.0006   19.6   0.0     0.0014   18.3   0.0    1.6  1  AAA_30       AAA domain
     0.0052   17.3   0.4      0.011   16.3   0.1    1.6  2  AAA_23       AAA domain
     0.0088   15.8   0.1        2.4    7.9   0.0    2.3  2  IstB_IS21    IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.012   15.1   0.0        1.7    8.0   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
      0.018   14.9   0.0      0.036   14.0   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.023   14.4   0.0        1.8    8.2   0.0    2.1  2  AAA_15       AAA ATPase domain
      0.041   13.6   0.1       0.41   10.3   0.0    2.1  2  AAA_24       AAA domain
      0.047   13.4   0.0      0.097   12.4   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.048   13.4   0.0       0.27   11.0   0.0    1.9  2  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.074   13.1   0.1       0.19   11.8   0.1    1.7  1  MMR_HSR1     50S ribosome-binding GTPase
        0.1   12.5   0.0        0.2   11.5   0.0    1.5  1  ATPase_2     ATPase domain predominantly from Archaea
       0.12   12.3   0.2        1.6    8.6   0.0    2.4  2  NTPase_1     NTPase
       0.15   11.7   0.0       0.26   10.9   0.0    1.3  1  SRP54        SRP54-type protein, GTPase domain
       0.27   10.9   1.2        1.2    8.8   0.3    2.2  2  FlbD         Flagellar and Swarming motility proteins


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 !  105.4   0.0   3.1e-33   3.3e-30       1     137 []      20     164 ..      20     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 3.1e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+++sl+++ege  +++G+nGaGK+t++++l gl+++t Ge ++ g d++  + +++r  ig  pqe ++++   ++
  gi|336253038|ref|YP_004596145.1|  20 LQELSLTVEEGEFFGLLGPNGAGKTTFINTLVGLVRKTGGEARVFGYDVEA-DYREARDAIGLAPQEFNVDRFFPIK 95 
                                       6899***********************************************.999************8888888888 PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       e              e+ e+++++l+++g+ ++++++       LSgG+k+r+ laral+++p+ll+lDEpta
  gi|336253038|ref|YP_004596145.1|  96 EVlmhkagyhgipedEAAERADEVLKRVGIYDKRNERF----DWLSGGMKRRLLLARALVTDPDLLILDEPTA 164
                                       88888********9999999*****************9....*****************************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 !   15.8   0.5   9.1e-06    0.0095       1      22 [.      32      53 ..      32      74 .. 0.82
   2 !   39.0   0.1   7.4e-13   7.8e-10     220     297 ..     119     193 ..      69     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.1e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      + +l GpNg+GK++++ +l +l
  gi|336253038|ref|YP_004596145.1| 32 FFGLLGPNGAGKTTFINTLVGL 53
                                      6789***************888 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 7.4e-13
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296
                                        +  +   d ++  ++ lS G+kr l l+ al  ++   +ll++DEp +g + +l + l+el+ el+++g+ v+ltT
  gi|336253038|ref|YP_004596145.1| 119 VLKRVGIYDKRNERFDWLSGGMKRRLLLARALVTDP---DLLILDEPTAGVDVQLRHDLWELVTELNEEGTTVLLTT 192
                                       444555667889999**********66666666655...9***********************999999******** PP

                            AAA_21 297 H 297
                                       H
  gi|336253038|ref|YP_004596145.1| 193 H 193
                                       * PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.1   5.4e+03      32      61 ..     158     186 ..     147     195 .. 0.64
   2 !   36.9   0.0   4.4e-12   4.6e-09       2      80 ..     218     301 ..     218     302 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.1
                                       EEE-TTS-EEEEE--------------.--- CS
                           DUF4162  32 eveeeggelelkledeeaanellkalt.sgv 61 
                                       +++e + ++ ++l+  ++  el ++l+ +g+
  gi|336253038|ref|YP_004596145.1| 158 ILDEPTAGVDVQLR--HDLWELVTELNeEGT 186
                                       55555556667777..468888888851444 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 4.4e-12
                                       -HHHHHTTS-SSEEEEE.-------.....---EEEE-TTS-EEEEE--.-----------.----EEEEEEEE--- CS
                           DUF4162   2 tleeiKrsygknrieve.adaeellee...pgveeveeeggelelkled.eeaanellkal.tsgveirsFeeeePs 72 
                                       t++e+K++ g+++i v+ + a ++      +  +e + +g++le++++d +++a++ll+ l ++g+ei  +e ++ s
  gi|336253038|ref|YP_004596145.1| 218 TPDELKER-GTDTISVRlESAPSMTPDvsaEYAHETTLDGDRLEVRVDDgGSTAPRLLNDLeAKGYEIADLEITRTS 293
                                       68999999.99999999644444443333233666677779********************77************** PP

                                       HHHHHHHH CS
                           DUF4162  73 LndIFiek 80 
                                       L++IF+ +
  gi|336253038|ref|YP_004596145.1| 294 LEEIFVDL 301
                                       *****976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.4e-06    0.0014      17     120 ..      29     189 ..      19     193 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.4e-06
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaag.................grviglAptgkaAkvLa.......eelgi. 68 
                                       +  +  l Gp G+GKtt +++l+ ++++ g                 ++ iglAp++   ++         +++g  
  gi|336253038|ref|YP_004596145.1|  29 EGEFFGLLGPNGAGKTTFINTLVGLVRKTGgearvfgydveadyreaRDAIGLAPQEFNVDRFFpikevlmHKAGYh 105
                                       44577899*********************779999999999999888888999998888877554555555333434 PP

                            AAA_30  69 ......eastiakllkrlk......................grarlepgtllivDE.agmvdtkqlaal...lkaae 113
                                             +a++ +++lkr +                      +ra +++ +lli DE ++ vd +  ++l   +++++
  gi|336253038|ref|YP_004596145.1| 106 gipedeAAERADEVLKRVGiydkrnerfdwlsggmkrrlllARALVTDPDLLILDEpTAGVDVQLRHDLwelVTELN 182
                                       44666678888888877778889999999999999999999777788889999999434466655555400044444 PP

                            AAA_30 114 kagakvi 120
                                       ++g++v+
  gi|336253038|ref|YP_004596145.1| 183 EEGTTVL 189
                                       4566665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     1e-05     0.011      17      38 ..      27      49 ..      13      62 .. 0.79
   2 ?   -2.7   0.0       6.6     7e+03      58      93 ..     282     312 ..     258     332 .. 0.48

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                            AAA_23 17 F.skgltlItGpNGaGKTTildA 38
                                        +  ++ + GpNGaGKTT+++ 
  gi|336253038|ref|YP_004596145.1| 27 VeEGEFFGLLGPNGAGKTTFINT 49
                                      444468999***********985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.6
                            AAA_23  58 feksdveiesegkvkay.veltfenkdgrytrsiere 93 
                                       +e +d ei+   + +++ v+lt + +     r+++r+
  gi|336253038|ref|YP_004596145.1| 282 YEIADLEITRT-SLEEIfVDLTRSED-----RTVTRS 312
                                       33333333221.22222233332222.....223333 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 ?    5.6   0.0     0.012        12      38      65 ..      20      48 ..       6      69 .. 0.79
   2 !    7.9   0.0    0.0023       2.4     106     149 ..     151     193 ..     139     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.012
                         IstB_IS21 38 Latlsf.iekkenivllGpsGvGKshlai 65
                                      L++ls  +e+ e + llGp G+GK+ +  
  gi|336253038|ref|YP_004596145.1| 20 LQELSLtVEEGEFFGLLGPNGAGKTTFIN 48
                                      444443267889999*********97755 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0023
                         IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnl 149
                                       ++ +dllilD+  +  +d + +++l+e++ +  e  ++++ +  
  gi|336253038|ref|YP_004596145.1| 151 VTDPDLLILDEP-TAGVDVQLRHDLWELVTELNEEGTTVLLTTH 193
                                       5678*******7.5789***************999888775554 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 ?    8.0   0.0    0.0016       1.7      25      44 ..      31      50 ..      12      58 .. 0.83
   2 ?    5.1   0.0     0.013        14     136     204 ..     135     200 ..      87     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                      +f  ++GpNG+GK+ +++ +
  gi|336253038|ref|YP_004596145.1| 31 EFFGLLGPNGAGKTTFINTL 50
                                      57889**********99876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.013
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlek 204
                                        LSgG k      Ll+A   v    l +lDe  a  D + ++ + el+ e +++ + ++ +++  e  e+
  gi|336253038|ref|YP_004596145.1| 135 WLSGGMKR----RLLLARALVTDPDLLILDEPTAGVDVQLRHDLWELVTELNEEgTTVLLTTHYIEEAER 200
                                       68888776....68888888888899***********************999885777777775544444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.4e-05     0.036      89     122 ..      19      53 ..       6      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-05
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       +l+el+  +++ ++  l+G+ G+GK+t+in+l++ 
  gi|336253038|ref|YP_004596145.1|  19 ALQELSLTVEEgEFFGLLGPNGAGKTTFINTLVGL 53 
                                       5677777777768999****************985 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0017       1.8      12      44 ..      18      51 ..      16      90 .. 0.86
   2 ?    4.3   0.0     0.026        28     322     364 ..     152     193 ..     106     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0017
                            AAA_15 12 Rslkdveidlsee.ltvliGkNnsGKSsileald 44
                                      R+l++ ++ ++e  +  l G+N++GK+++++ l 
  gi|336253038|ref|YP_004596145.1| 18 RALQELSLTVEEGeFFGLLGPNGAGKTTFINTLV 51
                                      7788888888877788899***********9886 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.026
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +++++l+++EP a    q+   l++l  el +++   v++tTH
  gi|336253038|ref|YP_004596145.1| 152 TDPDLLILDEPTAGVDVQLRHDLWELVTELNEEGT-TVLLTTH 193
                                       4679**************************99997.9****** 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   0.00039      0.41       7      22 ..      35      50 ..      32      84 .. 0.79
   2 ?    0.8   0.0      0.33   3.5e+02     106     135 ..     169     198 ..     165     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
                            AAA_24  7 iyGpsgiGKTtlakel 22
                                      + Gp+g+GKTt++++l
  gi|336253038|ref|YP_004596145.1| 35 LLGPNGAGKTTFINTL 50
                                      89************99 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.33
                            AAA_24 106 elaeefrrllkklqelrknvifiahektrk 135
                                       +l++++++l++ l+e + +v ++ h  ++ 
  gi|336253038|ref|YP_004596145.1| 169 QLRHDLWELVTELNEEGTTVLLTTHYIEEA 198
                                       5788999****************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 ?   12.4   0.0   9.2e-05     0.097      18      41 ..      26      49 ..      12      56 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.2e-05
                            AAA_29 18 eidlkgatlltGpsGsGKSTllDA 41
                                      ++++ +++ l Gp+G+GK+T++  
  gi|336253038|ref|YP_004596145.1| 26 TVEEGEFFGLLGPNGAGKTTFINT 49
                                      4443348889***********965 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   0.00025      0.27       2      29 ..      36      63 ..      35      78 .. 0.80
   2 ?   -0.1   0.0      0.63   6.7e+02      90     144 ..     153     204 ..     129     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvav 29
                                      +Gp G+GKttf+++l+ +++++g + +v
  gi|336253038|ref|YP_004596145.1| 36 LGPNGAGKTTFINTLVGLVRKTGGEARV 63
                                      7***************999998776655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.63
                        ATP_bind_1  90 eddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisg 144
                                       + d+l++D P     ++++ +l+++v eL++e+   +++L+ +++++++  ++++
  gi|336253038|ref|YP_004596145.1| 153 DPDLLILDEPTAGVDVQLRHDLWELVTELNEEG---TTVLLTTHYIEEAERLCDR 204
                                       447777777777777888999999999999755...4556666776666666555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00018      0.19       3      25 ..      34      56 ..      32      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                      EEEESTTSSHHHHHHHHHTSTEE CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltgekai 25
                                      +++G   +GK+t+in+l+g + +
  gi|336253038|ref|YP_004596145.1| 34 GLLGPNGAGKTTFINTLVGLVRK 56
                                      799**************995444 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   0.00019       0.2       8      67 ..      20      78 ..      17     130 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                          ATPase_2  8 lkeleeilerepneiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesisklde 67
                                      l+el   +e+   e+  + Gp g GKt++++ ++    +  ++ +++ ++++ ++ +  d 
  gi|336253038|ref|YP_004596145.1| 20 LQELSLTVEE--GEFFGLLGPNGAGKTTFINTLVGLVrKTGGEARVFGYDVEADYREARDA 78
                                      5666655555..6677788***************99845566799**99999887765554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0015       1.6       4      27 ..      35      58 ..      33      78 .. 0.86
   2 ?    0.3   0.1      0.56   5.9e+02      94     155 ..     152     216 ..     142     227 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                                      EE--TTSSHHHHHHHHHHHH...G CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkssg 27
                                      + Gp G GKtT+++ ++ l+++ g
  gi|336253038|ref|YP_004596145.1| 35 LLGPNGAGKTTFINTLVGLVRKTG 58
                                      569**************9999886 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.56
                                       HHH-EEEE--..-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE- CS
                          NTPase_1  94 seadviviDE..iGkmElkskkfkeaveevLksekpvlavihrrk.dlalveeirerkdvkvfev 155
                                       +++d++++DE   G      + + e v+e+ ++++ vl + h  +  ++l +++   ++++ ++v
  gi|336253038|ref|YP_004596145.1| 152 TDPDLLILDEptAGVDVQLRHDLWELVTELNEEGTTVLLTTHYIEeAERLCDRVAIMNEGRKVTV 216
                                       56666666663223222233456667777777888888888877767777777776666655555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00025      0.26       6      38 ..      35      67 ..      31      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      l+G++GaGKTt +  L  l++k g ++ +   D
  gi|336253038|ref|YP_004596145.1| 35 LLGPNGAGKTTFINTLVGLVRKTGGEARVFGYD 67
                                      79***************9999998777666665 PP

>> FlbD  Flagellar and Swarming motility proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.6   6.3e+02      42      56 ..     114     128 ..     112     130 .. 0.85
   2 ?    8.8   0.3    0.0011       1.2       4      41 ..     178     217 ..     177     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.6
                              FlbD  42 Esvdeviervieyrr 56 
                                       E +dev++rv  y +
  gi|336253038|ref|YP_004596145.1| 114 ERADEVLKRVGIYDK 128
                                       99********88876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                              FlbD   4 ltrlnge..efvlNadlIetieetPDTvItLtnGkkyvVk 41 
                                       +t ln+e  +++l  ++Ie  e   D v ++ +G+k+ V 
  gi|336253038|ref|YP_004596145.1| 178 VTELNEEgtTVLLTTHYIEEAERLCDRVAIMNEGRKVTVA 217
                                       788887554999************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2339.05
//
Query:       gi|336253039|ref|YP_004596146.1|  [L=392]
Description: peptidase M50 [Halopiger xanaduensis SH-6]
Scores for complete 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-24   85.9   4.7    1.8e-12   47.5   0.7    2.5  2  CBS             CBS domain
    1.5e-15   57.1   5.5    3.8e-08   32.9   0.1    3.2  3  Peptidase_M50   Peptidase family M50
    0.00033   20.3   1.3    0.00033   20.3   1.3    2.3  3  Peptidase_M50B  Peptidase M50B-like
      0.002   18.4   0.7      0.002   18.4   0.7    2.2  2  DUF3267         Putative zincin peptidase
  ------ inclusion threshold ------
        6.6    6.0  10.1       0.14   11.5   1.9    2.0  2  ThrE            Putative threonine/serine exporter


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 !   39.6   0.2   1.4e-13   5.2e-10       1      52 [.     252     308 ..     252     311 .. 0.86
   2 !   47.5   0.7   5.1e-16   1.8e-12       1      54 [.     320     372 ..     320     374 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.4e-13
                                       HHHHSBS..SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT...BEEEEEEHHHHH CS
                               CBS   1 Vgdimtr..dvvtvppdttleealelmrekgvsrlPVVdedg...klvGivtlrDll 52 
                                       V+dimt+  d++tv p++++++++++m +++++++PV++ dg   +lvG+vtl+D  
  gi|336253039|ref|YP_004596146.1| 252 VSDIMTPasDLHTVEPEASIADLIRRMFSERHTGYPVIERDGagdRLVGLVTLTDAR 308
                                       89**99988*****************6577789*****55555599*********65 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 5.1e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V+d+mt+d+ t+ pd++   a+++mr ++++rl+VV e+g lvG+++++D++ a
  gi|336253039|ref|YP_004596146.1| 320 VEDVMTTDLETIAPDSDAMAAIDRMRANDIGRLLVV-ENGDLVGLISRTDVMTA 372
                                       89***********************7777*******.8999**********987 PP

>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   1.5   4.6e-09   1.6e-05       2     107 ..      69     139 ..      68     147 .. 0.90
   2 !   32.9   0.1   1.1e-11   3.8e-08     188     247 ..     151     208 ..     141     212 .. 0.80
   3 ?   -2.2   0.0      0.55     2e+03      97     109 ..     219     246 ..     214     334 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4.6e-09
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeaka 78 
                                       ++l l++ vv+HElGH l+A++ g+ +++                    i+l+ +GG+ ++ ++ ++          
  gi|336253039|ref|YP_004596146.1|  69 AALGLFVGVVLHELGHSLTARRYGFPIDS--------------------ITLWLFGGVAQFTEMPED---------- 115
                                       578899*********************99....................9999****9999999955.......... PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  79 flkkspwqrllivlAGplanfilailvfv 107
                                              q+++i++AGp++ ++++++ + 
  gi|336253039|ref|YP_004596146.1| 116 -----WRQEFAIAIAGPIVSVLVGVVSYG 139
                                       .....45****************999875 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 1.1e-11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 188 lssflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglall 247
                                       +  +l++la+++v+L+ +N+lP +++DGg++l+a+l + r  p  + ++++a+   ++ +
  gi|336253039|ref|YP_004596146.1| 151 ARFVLAYLAILNVALAGFNMLPAFPMDGGRVLRAFLARSR--PYAKATQQAASVGKFFAV 208
                                       457899*****************************99877..776666666665555444 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.55
                                       XXXXXXXXXXXX...............- CS
                                       xxxxxxxxxxxx...............x RF
                     Peptidase_M50  97 anfilailvfvv...............p 109
                                       +n+il  ++f+v                
  gi|336253039|ref|YP_004596146.1| 219 VNIILVGVAFFVyiaasseaqqvtmkaA 246
                                       6777777777775444433333333330 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.91   3.3e+03     120     154 ..      21      55 ..       9      61 .. 0.63
   2 !   20.3   1.3   9.3e-08   0.00033      23      90 ..      75     143 ..      55     173 .. 0.80
   3 ?   -0.5   0.3      0.22   7.8e+02      97     131 ..     202     236 ..     179     278 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.91
                    Peptidase_M50B 120 llllgallllvlllaedelleflllflgvflllgs 154
                                        ll++ l++ ++ ++ +++ e+l  +lg+ +++ +
  gi|336253039|ref|YP_004596146.1|  21 FLLVLPLFAYLIGVQIEQVSEVLNAVLGAGISVDA 55 
                                       34444444455555556777777777777776655 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 9.3e-08
                    Peptidase_M50B  23 lvvffHElGHalaalLtGgrvkgielhsdesGvtvtrg..pgglgqiltllaGYlgpallGlllillsas 90 
                                       + v++HElGH l+a   G  +++i+l    +Gv+  +   + + + +++++aG++ + l+G++   l + 
  gi|336253039|ref|YP_004596146.1|  75 VGVVLHELGHSLTARRYGFPIDSITLWLF-GGVAQFTEmpEDWRQEFAIAIAGPIVSVLVGVVSYGLFSV 143
                                       5699**********************985.6788777778888899***************997766544 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.22
                    Peptidase_M50B  97 lvllvllllvllllvrnlfglvlllllgallllvl 131
                                       ++ ++++l+ ++ +++ +  +++ +++++ +++ +
  gi|336253039|ref|YP_004596146.1| 202 VGKFFAVLMGIFGIIPPVNIILVGVAFFVYIAASS 236
                                       33444444444444444433333333333333332 PP

>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.7   5.5e-07     0.002       1      94 [.      73     170 ..      73     176 .. 0.76
   2 ?   -0.3   0.3      0.35   1.3e+03      37      73 ..     192     225 ..     179     247 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.5e-07
                           DUF3267   1 llvlvilHEllHglffklfgkkpkkkvkfgi.klliayatsseallskkqfiiillaPfvll..gilllllalllps 74 
                                       l+v+v+lHEl H l+ +++g +   ++++++ + ++ ++  +e    +++f i+   P+v +  g++ + l+ ++p 
  gi|336253039|ref|YP_004596146.1|  73 LFVGVVLHELGHSLTARRYGFP-IDSITLWLfGGVAQFTEMPEDW--RQEFAIAIAGPIVSVlvGVVSYGLFSVTPA 146
                                       5899**************9775.6666665656677777777777..8899999999*8644237777777777775 PP

                           DUF3267  75 stl....llllllalnaagsagDl 94 
                                              +l+ l++ln+a++   +
  gi|336253039|ref|YP_004596146.1| 147 GLDgarfVLAYLAILNVALAGFNM 170
                                       444899999999999999987765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.35
                           DUF3267  37 yatsseallskkqfiiillaPfvllgilllllalllp 73 
                                       ya ++++ +s  +f  +l+  f ++   +++ ++l+ 
  gi|336253039|ref|YP_004596146.1| 192 YAKATQQAASVGKFFAVLMGIFGII---PPVNIILVG 225
                                       6666666666666666666544443...333333322 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.9   3.9e-05      0.14     123     199 ..      55     135 ..      36     139 .. 0.85
   2 ?   -1.4   1.3      0.35   1.2e+03     139     192 ..     199     255 ..     181     257 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.9e-05
                              ThrE 123 allfggdwidflvaflagllggllrlllakrglnsfvleavaaflasllallavsl....glglnpdaiiigsillL 195
                                       a+ +g++++ f +a+++gl++g++ + l ++ + + + + + +++  l++ +a  +    ++ ++++++i+g i+ +
  gi|336253039|ref|YP_004596146.1|  55 AVTAGANPWIFGLAAALGLFVGVVLHELGHSLTARRYGFPIDSITLWLFGGVAQFTempeDWRQEFAIAIAGPIVSV 131
                                       5677**********************************************9999975565556779*********99 PP

                              ThrE 196 vPGl 199
                                       + G+
  gi|336253039|ref|YP_004596146.1| 132 LVGV 135
                                       9887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.35
                              ThrE 139 agllggllrlllakrglnsfvleavaaflasllallavs....lglglnpdaiiigsi 192
                                       a+ +g ++  l+  +g+++ v+ ++ ++ a +++++a s    ++++  ++ ++++ i
  gi|336253039|ref|YP_004596146.1| 199 AASVGKFFAVLMGIFGIIPPVNIILVGV-AFFVYIAASSeaqqVTMKAAFQDVTVSDI 255
                                       4455555555555555555555444443.33333333332222222333455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2914.51
//
Query:       gi|336253040|ref|YP_004596147.1|  [L=80]
Description: hypothetical protein Halxa_1636 [Halopiger xanaduensis SH-6]
Scores for 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-06   26.0   0.1    1.8e-05   24.5   0.0    1.7  2  TrmB            Sugar-specific transcriptional regulator TrmB
    6.9e-05   22.7   0.1    8.6e-05   22.3   0.1    1.2  1  MarR_2          MarR family
    0.00021   21.1   0.0    0.00029   20.7   0.0    1.2  1  MarR            MarR family
    0.00096   19.6   0.0     0.0013   19.1   0.0    1.2  1  HTH_27          Winged helix DNA-binding domain
     0.0027   17.5   0.4      0.004   16.9   0.4    1.2  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.032   14.1   0.1      0.046   13.6   0.1    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
       0.04   14.1   0.0      0.054   13.7   0.0    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.059   13.4   0.1      0.089   12.9   0.1    1.3  1  HTH_20          Helix-turn-helix domain


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 ?   -0.8   0.0      0.63   1.4e+03      53      68 .]       4      19 ..       2      19 .. 0.84
   2 !   24.5   0.0   8.1e-09   1.8e-05      13      57 ..      28      72 ..      22      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.63
                                      EEESSTTTEEEE--HH CS
                              TrmB 53 erekgrpklYravdpe 68
                                      e+++++p+   +++pe
  gi|336253040|ref|YP_004596147.1|  4 ETQQRSPTEIDPLPPE 19
                                      7788999999999997 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 8.1e-09
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      vYl L + g at++++++ lg  +  + +vL+ L+  GlVer   
  gi|336253040|ref|YP_004596147.1| 28 VYLFLESTGGATVTDLHRSLGMQKMAILSVLEALSAQGLVERTGT 72
                                      899999***********************************9854 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   3.8e-08   8.6e-05      13      54 ..      31      70 ..      20      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.8e-08
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +L   +g   tv++l r lg+ k a+  +l+ L+a+GLver+
  gi|336253040|ref|YP_004596147.1| 31 FLESTGG--ATVTDLHRSLGMQKMAILSVLEALSAQGLVERT 70
                                      5666677..8******************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.3e-07   0.00029      12      50 ..      32      70 ..      21      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.3e-07
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      l++ g+++v++L + lg++k+++  vl +L  +Gl+eR+
  gi|336253040|ref|YP_004596147.1| 32 LESTGGATVTDLHRSLGMQKMAILSVLEALSAQGLVERT 70
                                      77899*********************************7 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 !   19.1   0.0     6e-07    0.0013      16      54 ..      35      73 ..      27      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6e-07
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                                       ++++ +dl++ l +++ +i ++l++L ++GLvertg e
  gi|336253040|ref|YP_004596147.1| 35 TGGATVTDLHRSLGMQKMAILSVLEALSAQGLVERTGTE 73
                                      567889*****************************9876 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 !   16.9   0.4   1.8e-06     0.004      11      51 ..      30      70 ..      27      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-06
                                      T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      ++ e +++ t+++l+r +g+ k +    L  L  +G+ve+ 
  gi|336253040|ref|YP_004596147.1| 30 LFLESTGGATVTDLHRSLGMQKMAILSVLEALSAQGLVERT 70
                                      577889999******************************97 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 ?   13.6   0.1   2.1e-05     0.046       6      46 ..      26      68 ..      21      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                                      HHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  6 kILklLae..gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      k+++l  e  g ++v++l + lg+ + ++   L +L  +GLVe
  gi|336253040|ref|YP_004596147.1| 26 KLVYLFLEstGGATVTDLHRSLGMQKMAILSVLEALSAQGLVE 68
                                      677888887899******************************8 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 ?   13.7   0.0   2.4e-05     0.054      18      53 ..      37      72 ..      34      80 .] 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-05
                    B-block_TFIIIC 18 GitqsdLakeskqdprslfyrlksLekkgLIvkqsi 53
                                      G t +dL++++++ +  + ++l +L+ +gL+++  +
  gi|336253040|ref|YP_004596147.1| 37 GATVTDLHRSLGMQKMAILSVLEALSAQGLVERTGT 72
                                      99*****************************99765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     4e-05     0.089      20      59 ..      33      72 ..      27      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-05
                                      STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 20 araegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                       + +g+t+++l++ l++ k  +   L++L+  gLve++++
  gi|336253040|ref|YP_004596147.1| 33 ESTGGATVTDLHRSLGMQKMAILSVLEALSAQGLVERTGT 72
                                      56789********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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):               8  [number of targets reported over threshold]
# CPU time: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 713.24
//
Query:       gi|336253041|ref|YP_004596148.1|  [L=176]
Description: 50S ribosomal protein L10e [Halopiger xanaduensis SH-6]
Scores for 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-32  110.1   0.0    8.9e-32  109.9   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 !  109.9   0.0     5e-36   8.9e-32       2     132 .]      13     166 ..      12     166 .. 0.96

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 5e-36
                                       XSSXXBSSSXXSSTSXX.XSXXXXXESX...........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EE CS
                     Ribosomal_L16   2 krkkyrKsrkryirgvs.tkgtklefgd...........ygLvalekgqltaealeaariainrylkkkrgk...kl 63 
                                       ++++y++++  yi+g + +k+ + ++gd           ++L+++e+ q+++  lea r+ +nr++ k+ g+   k+
  gi|336253041|ref|YP_004596148.1|  13 SKPAYTRRE--YITGIPgSKIAQHKMGDvskdpedypiqISLITEEEVQIRHGSLEASRLSANRHMLKNAGEnnyKM 87 
                                       5789*****..***************************999****************************999***** PP

                                       XXSXXXXEEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE..TTXX.XSHHHHHHHHHHHHTSSSX CS
                     Ribosomal_L16  64 wirvfphhpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei..kagv.neeiakealrraasKlpik 128
                                       ++r+fphh+++++     ag+dR+++G+    Gk+ g++ar+ +g+ if++  +  v ++e ak+a+rra +K++ +
  gi|336253041|ref|YP_004596148.1|  88 ILRKFPHHVIRENkqatgAGADRVSDGMrqafGKIVGTAARIDEGERIFTVwcD--VdDAEFAKDAFRRAYNKISPP 162
                                       ***************************************************641..54899**************** PP

                                       EEEE CS
                     Ribosomal_L16 129 tkiv 132
                                       ++iv
  gi|336253041|ref|YP_004596148.1| 163 CRIV 166
                                       **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1558.94
//
Query:       gi|336253042|ref|YP_004596149.1|  [L=73]
Description: hypothetical protein Halxa_1638 [Halopiger xanaduensis SH-6]
Scores for 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:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.18s 00:00:00.55 Elapsed: 00:00:00.33
# Mc/sec: 654.65
//
Query:       gi|336253043|ref|YP_004596150.1|  [L=292]
Description: RimK domain-containing protein ATP-grasp [Halopiger xanaduensis SH-6]
Scores for 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-22   79.1   0.0    4.3e-22   78.6   0.0    1.1  1  RimK             RimK-like ATP-grasp domain
    5.5e-12   45.4   0.0    8.2e-12   44.9   0.0    1.2  1  GSH-S_ATP        Prokaryotic glutathione synthetase, ATP-gras
    2.5e-06   27.6   0.0    4.7e-06   26.7   0.0    1.4  1  ATP-grasp_3      ATP-grasp domain
    1.4e-05   24.5   0.0      0.008   15.5   0.0    2.2  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
     0.0042   16.6   0.0      0.009   15.6   0.0    1.5  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
     0.0047   16.1   0.0      0.024   13.8   0.0    1.8  2  TTL              Tubulin-tyrosine ligase family
     0.0082   16.0   0.0      0.018   14.9   0.0    1.5  2  ATPgrasp_TupA    TupA-like ATPgrasp
  ------ inclusion threshold ------
      0.042   13.9   0.3      0.061   13.3   0.3    1.3  1  R2K_3            ATP-grasp domain, R2K clade family 3
      0.067   12.7   0.0       0.12   11.8   0.0    1.4  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   2.2e-25   4.3e-22       2     175 ..      84     271 ..      83     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 2.2e-25
                                       H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-..-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH...... CS
                              RimK   2 rdKlkslklLakakikvpntalardeedaekliekik.lrfPvvvKsvegsqGikvvlakkeqklkqvlea...... 71 
                                       r+K+  l+ L +a+++vp++  + +++   +l + ++ ++ PvvvK   ++ G++v  a++ ++   + +       
  gi|336253043|ref|YP_004596150.1|  84 RNKAEVLARLERADLPVPKSVYVSNDVGEAELTDVFErFEPPVVVKPNSTTRGVGVAKAHDLDSFLGICDYlslvhd 160
                                       899999***************9999999999999998899************************9999887665655 PP

                                       ....GGG--EEEEE--SS-SEEEEEEEETTEEEEEEEEE.....--SSS----TTTT-EEEE----HHHHHHHHHHH CS
                              RimK  72 ....lkeailvqeyieeaenediRvlvvddevvaalrrv.....skeGdFRsnlhrGgvaeklqlseeekelAikaa 139
                                            + + lvqey+      d Rv+v+++e v+a++r+       eG+++ n+hrG++a  ++l +e +elA  +a
  gi|336253043|ref|YP_004596150.1| 161 ykatGDRSFLVQEYLPD--AVDYRVMVLEGEYVGAVERRlpddaVTEGQWKHNVHRGAKATGVELPDEHRELAEAVA 235
                                       554334556*****975..589***************9744443589****************************** PP

                                       HHCT-SEEEEEEEEETTEEEEEEEESS--SHHHHHH CS
                              RimK 140 kamelvvaGvDllrakrgllvlEvnsspglekiekt 175
                                        a+e+ ++GvDll++++ l+v E n+ p +++  k+
  gi|336253043|ref|YP_004596150.1| 236 AALEIPFLGVDLLETEDRLVVNETNARPTIDEATKY 271
                                       ****************************99887665 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   4.1e-15   8.2e-12      23     153 ..     114     249 ..      99     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 4.1e-15
                                       HHHHHHHHHSS.EEEEESS--TTTT-EEE-TT-TTHH.....HHHHHHTTTTTS-EEEEE--GGGGG-EEEEEEETT CS
                         GSH-S_ATP  23 eirafleeqgd.vilKPldgkgGegvfrvkksdpnlk.....silellteegkepviaqrylpeikeGDkRillvdG 93 
                                       e++++ e+ +  v++KP + + G gv + ++ d+ l+     s++  + ++g + +++q+ylp++   D R+++++G
  gi|336253043|ref|YP_004596150.1| 114 ELTDVFERFEPpVVVKPNSTTRGVGVAKAHDLDSFLGicdylSLVHDYKATGDRSFLVQEYLPDAV--DYRVMVLEG 188
                                       555555554444*****************999876543333378888899999***********97..7******** PP

                                       EE-SEEEEEE-....-SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEET CS
                         GSH-S_ATP  94 epigyalaRvp....aegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvig 153
                                       e +g+  +R+p    +eg+ + n++ g++a+ +el +++re+ae++a +L+   + f G+D+++
  gi|336253043|ref|YP_004596150.1| 189 EYVGAVERRLPddavTEGQWKHNVHRGAKATGVELPDEHRELAEAVAAALE---IPFLGVDLLE 249
                                       ****55556883333478999***************************997...6788888875 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   2.4e-09   4.7e-06       3     159 ..      85     264 ..      83     265 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.4e-09
                                       SHHHHHHHHTTT.S---..........-EESS--....SSSEEEEESS-------B--SS--TTE............ CS
                       ATP-grasp_3   3 dKlktykkLkeagvkvP......tkleaeeleee....ekklvvKprdGaggesvrvveekeeaeaaieeve..... 64 
                                       +K ++  +L++a ++vP      + + ++el+ +    e ++vvKp +   g +v ++++ ++   ++++++     
  gi|336253043|ref|YP_004596150.1|  85 NKAEVLARLERADLPVPksvyvsNDVGEAELTDVferfEPPVVVKPNSTTRGVGVAKAHDLDSFLGICDYLSlvhdy 161
                                       8999*************988887556666665557777999***********************9999999955555 PP

                                       ........EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET.................TEEEEEEES----HHHHH CS
                       ATP-grasp_3  65 ........lvqefieGkplSvsllsdgekvlvlavnrqliekaeke.............fvyaGnvtpietelkeev 120
                                               lvqe++           d+ + +v+++  ++++  e++             +v +G  +    el +e 
  gi|336253043|ref|YP_004596150.1| 162 katgdrsfLVQEYL----------PDAVDYRVMVLEGEYVGAVERRlpddavtegqwkhNVHRGAKATGV-ELPDEH 227
                                       56666666666665..........4444444444444444444444444444456666699999988777.99**** PP

                                       HHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS-- CS
                       ATP-grasp_3 121 velaeevvekleglaGyvGvDlvlkdeepyviEvNPRlt 159
                                       +elae v ++l     ++GvDl+ +++ ++v E N+R+t
  gi|336253043|ref|YP_004596150.1| 228 RELAEAVAAAL--EIPFLGVDLLETEDRLVVNETNARPT 264
                                       ***********..5689********************98 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     4e-06     0.008       9      80 ..      73     143 ..      67     150 .. 0.87
   2 !    7.0   0.0    0.0015       3.1     222     283 ..     223     279 ..     180     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4e-06
                       ATPgrasp_ST   9 kyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvit 80 
                                        +N+ + + +  +K  +   ++ra l+vpk  + +++    +el ++ +++e+ vv+Kp+ +  G G+ ++ 
  gi|336253043|ref|YP_004596150.1|  73 WLNDHETVLTSRNKAEVLARLERADLPVPK-SVYVSNDVGEAELTDVFERFEPPVVVKPNSTTRGVGVAKAH 143
                                       58999999999****999999*********.55666667778899999***999**************9875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0015
                       ATPgrasp_ST 222 iPnweevlelaakaaeklpglgylGwDivldeekgplllElNarpglaivqiangegllprl 283
                                        P  +e+ ela  +a+  +++  lG+D+  +e++ +++ E Narp ++     ++ g  +rl
  gi|336253043|ref|YP_004596150.1| 223 LP--DEHRELAEAVAA-ALEIPFLGVDLLETEDR-LVVNETNARPTIDE-ATKYEPGFYDRL 279
                                       44..466788888888.88999******999999.**********9987.566666666665 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 !   15.6   0.0   4.5e-06     0.009       4     181 ..      95     268 ..      93     276 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.5e-06
                                       HTT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGG...HHHHHHHHHTT....-S CS
                   Dala_Dala_lig_C   4 aaGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseee...lkeaieeafky....de 73 
                                       +a+lpv++ v + ++  + e    l++v e++  pv+VKp  +   vGv+k++  +    + ++++    y    d+
  gi|336253043|ref|YP_004596150.1|  95 RADLPVPKSVYVSNDVGEAE----LTDVFERFEPPVVVKPNSTTRGVGVAKAHDLDSflgICDYLSLVHDYkatgDR 167
                                       66777777777665544443....58999***********************9988622234455444333333389 PP

                                       CEEEEE--.ESEEEEEEEEETSSCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHT CS
                   Dala_Dala_lig_C  74 kvlvEeai.egreievavlgneklevsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykal 149
                                       + lv e++ ++ +  v vl+     v  v+++ +++++ + + k+  ++      ++l++e     +ela  + +al
  gi|336253043|ref|YP_004596150.1| 168 SFLVQEYLpDAVDYRVMVLE--GEYVGAVERRLPDDAVTEGQWKHNVHRGAKATGVELPDEH----RELAEAVAAAL 238
                                       99******9**********9..5567888888999999999999854666666666666665....45666666777 PP

                                       T--SEEEEEEEEETTTEEEEEEEESS---STT CS
                   Dala_Dala_lig_C 150 dlrGlaRvDfflteegeivlnEvNtlPGfTei 181
                                       ++  l  vD++ t e+++v+nE N  P + e 
  gi|336253043|ref|YP_004596150.1| 239 EIPFL-GVDLLET-EDRLVVNETNARPTIDEA 268
                                       77654.4897655.889999999999977665 PP

>> TTL  Tubulin-tyrosine ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   1.2e-05     0.024      55     110 ..     113     176 ..      82     178 .. 0.90
   2 ?   -0.3   0.0      0.24   4.7e+02     256     280 ..     258     282 ..     242     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                                       HHHHTTTS--S-B----SS---XX------BSSTHHHHHH.........HH..SSS-EEEEB--S CS
                               TTL  55 aefveeaekeesntwIvKpsasarGkgirvfnkledikki.........vsqsqkeplvvqkYie 110
                                       ae+ + +e+ e   ++vKp +  rG g+   ++l++++ i         ++   +++++vq+Y+ 
  gi|336253043|ref|YP_004596150.1| 113 AELTDVFERFEP-PVVVKPNSTTRGVGVAKAHDLDSFLGIcdylslvhdYKATGDRSFLVQEYLP 176
                                       577888999999.99************************9********99999**********96 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.24
                                       XXXXXX..XXXXXXXXXXXXXXXXX CS
                               TTL 256 EvNasPdlksttkldaelkeelidd 280
                                       E Na P++ ++tk+ + ++++l d+
  gi|336253043|ref|YP_004596150.1| 258 ETNARPTIDEATKYEPGFYDRLADA 282
                                       89*****************999875 PP

>> ATPgrasp_TupA  TupA-like ATPgrasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.2   8.4e+03      56      73 ..     123     140 ..     114     147 .. 0.74
   2 !   14.9   0.0   8.9e-06     0.018     178     222 ..     219     265 ..     203     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.2
                     ATPgrasp_TupA  56 kesiViKpthdsGsrgvl 73 
                                       + ++V+Kp   + ++gv 
  gi|336253043|ref|YP_004596150.1| 123 EPPVVVKPNSTTRGVGVA 140
                                       567999999888777775 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 8.9e-06
                     ATPgrasp_TupA 178 ekpgvleemielAetisse..ipfvRvDlyksgdkvyfGElTfkpgn 222
                                        + +  +e  elAe ++    ipf+ vDl+ ++d++++ E   +p  
  gi|336253043|ref|YP_004596150.1| 219 TGVELPDEHRELAEAVAAAleIPFLGVDLLETEDRLVVNETNARPTI 265
                                       555566788899999998777*****************998888764 PP

>> R2K_3  ATP-grasp domain, R2K clade family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   3.1e-05     0.061      68     173 ..     120     252 ..      72     261 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                             R2K_3  68 eaeeepvFvkprgdklfggvV..........lrefeelralaakledtevlvsevvrfsaEwRvFvvdGevvaasrY 134
                                       e+ e pv vkp  ++   gv           + ++ +l+   + + d ++lv e+ + +  +Rv v+ Ge v+a + 
  gi|336253043|ref|YP_004596150.1| 120 ERFEPPVVVKPNSTTRGVGVAkahdldsflgICDYLSLVHDYKATGDRSFLVQEYLPDAVDYRVMVLEGEYVGAVER 196
                                       3366666666666662222223233222222225555554444444****************************999 PP

                             R2K_3 135 r.....kanddpdl.............epdlaafaeavralvgappfyvlDvavtad 173
                                       r      +++++++             + + +++aeav+a+  + pf  +D+  t+d
  gi|336253043|ref|YP_004596150.1| 197 RlpddaVTEGQWKHnvhrgakatgvelPDEHRELAEAVAAAL-EIPFLGVDLLETED 252
                                       988988677777778877777778888888888*****9999.7*******988876 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 ?   11.8   0.0   6.2e-05      0.12       4      99 ..      88     185 ..      85     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.2e-05
                                       HHHHHHHHTT-BBSSEECSSBSS.HHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHH.HHHHHHHHHH CS
                       CPSase_L_D2   4 sakealkkinvpvvpssaapvet.leealaiakeigyPviikaafglGGkGmrvarneeelaelvk.kalaeakaaf 78 
                                       +  + l++++ pv +s+ +  +  + e +++ +++  Pv++k+  +  G G   a++ + +  ++   +l +   a 
  gi|336253043|ref|YP_004596150.1|  88 EVLARLERADLPVPKSVYVSNDVgEAELTDVFERFEPPVVVKPNSTTRGVGVAKAHDLDSFLGICDyLSLVHDYKAT 164
                                       556788999*******9996443145668999*****************************9999735777778899 PP

                                       STS-EEEEE--SSSEEEEEEE CS
                       CPSase_L_D2  79 gnkqvlvekslkgpkeiEvev 99 
                                       g+++ lv+++l    ++ v v
  gi|336253043|ref|YP_004596150.1| 165 GDRSFLVQEYLPDAVDYRVMV 185
                                       999999999997765555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2278.60
//
Query:       gi|336253044|ref|YP_004596151.1|  [L=133]
Description: heat shock protein Hsp20 [Halopiger xanaduensis SH-6]
Scores for complete 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-20   73.0   0.0    1.5e-20   72.5   0.0    1.2  1  ArsA_HSP20  HSP20-like domain found in ArsA
    5.6e-10   39.3   0.1    1.1e-08   35.1   0.1    2.0  1  HSP20       Hsp20/alpha crystallin family
    6.4e-07   29.6   1.1    7.4e-07   29.4   1.1    1.2  1  GvpH        GvpH
  ------ inclusion threshold ------
       0.04   14.3   0.0      0.058   13.8   0.0    1.2  1  PIH1_CS     PIH1 CS-like domain


Domain annotation for each model (and alignments):
>> 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 !   72.5   0.0   3.3e-24   1.5e-20       1      63 []      56     121 ..      56     121 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 3.3e-24
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkignfrRq....itLPsvlarkevtsAkfedgvLeIrF 63 
                                       dde+++++dLP+v+k++i+l+++g++LtI++g+++Rq    ++LP++++++++ sA++++gvLe+ F
  gi|336253044|ref|YP_004596151.1|  56 DDEIRVVADLPGVEKDNIELECDGKTLTISAGSDHRQyderVSLPTRVNEHTA-SATYNNGVLEVVF 121
                                       79*************************************************66.***********98 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1   2.5e-12   1.1e-08       1      91 [.      51     127 ..      51     132 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.5e-12
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslk 77 
                                       di+e+++e++v +d+pg++k++++++ ++++++++++ +        +      r+++ +++LP  v++++ +a+++
  gi|336253044|ref|YP_004596151.1|  51 DIHETDDEIRVVADLPGVEKDNIELECDGKTLTISAGSD--------H------RQYDERVSLPTRVNEHTASATYN 113
                                       789**********************************99........3......67********************* PP

                                       TTEEEEEEEBSS-- CS
                             HSP20  78 dGvLtvtvpkkepe 91 
                                       +GvL+v  +  e+ 
  gi|336253044|ref|YP_004596151.1| 114 NGVLEVVFDPAEES 127
                                       *****988777665 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   1.1   1.6e-10   7.4e-07      89     169 ..      47     127 ..      10     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.6e-10
                              GvpH  89 sihvetrasddsdelvvvadlpGvtdedvdvaletdeqaltlrvddd...vverlvld.dpdvaitdltlrnqvlel 161
                                         hv+    +  de+ vvadlpGv  ++++  le+d ++lt++ + d     er+ l  + +   ++ t +n vle+
  gi|336253044|ref|YP_004596151.1|  47 DTHVDIH--ETDDEIRVVADLPGVEKDNIE--LECDGKTLTISAGSDhrqYDERVSLPtRVNEHTASATYNNGVLEV 119
                                       4566654..45689**********999876..7888********998333469***962567778899********* PP

                              GvpH 162 rlarseds 169
                                          ++e+s
  gi|336253044|ref|YP_004596151.1| 120 VFDPAEES 127
                                       99999987 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.3e-05     0.058      31      87 ..      57     114 ..      46     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                           PIH1_CS  31 kelaieielPllksikevklrvgerrleleskk..akyfLslkLpYpvdedkveAkFvk 87 
                                       +e+++  +lP++ +  +++l+ + ++l + + +   +y  +++Lp +v+e  ++A++++
  gi|336253044|ref|YP_004596151.1|  57 DEIRVVADLPGV-EKDNIELECDGKTLTISAGSdhRQYDERVSLPTRVNEHTASATYNN 114
                                       68899999****.7899************8887789*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); 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 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1018.61
//
Query:       gi|336253045|ref|YP_004596152.1|  [L=361]
Description: glyceraldehyde-3-phosphate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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   64.2   0.0    1.6e-17   63.6   0.0    1.3  1  Gp_dh_C        Glyceraldehyde 3-phosphate dehydrogenase, C-te
    1.8e-09   37.8   0.0    4.1e-09   36.6   0.0    1.7  1  DapB_N         Dihydrodipicolinate reductase, N-terminus
    0.00013   22.2   0.0    0.00033   20.9   0.0    1.7  1  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 
     0.0013   18.2   0.3       0.11   11.8   0.2    2.3  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
     0.0027   18.4   0.4      0.064   13.9   0.4    2.8  2  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
  ------ inclusion threshold ------
      0.049   14.5   0.2       0.14   12.9   0.1    1.9  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
       0.13   12.5   0.1       0.32   11.3   0.1    1.6  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 !   63.6   0.0   6.1e-21   1.6e-17       1     157 [.     145     299 ..     145     300 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 6.1e-21
                                       HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT..CSSEEEE-THHHHHHHHSGGGTTTEEEE CS
                           Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa..eniiptstgaakavglVlpelkgkldgl 75 
                                       L +++  l++ +gi+k+++t+v++  ++    D     +  r++++   ++++ ++++++++v++V+pe   ++d++
  gi|336253045|ref|YP_004596152.1| 145 LSRFLAPLHETYGIDKARVTLVRRGGDP----D-----QTGRGPINDtvPDPVSIPSHHGPDVQTVFPE--LDIDTI 210
                                       678999**********************....5.....7789***9989*******************8..579*** PP

                                       EEEESSSSEEEEEEEEEESST.S-HHHHHHHHHHHHH....TTTTTTEEEEHSHHHGGGGTTGCS..SEEEEGGGCE CS
                           Gp_dh_C  76 AvrVPtpnvsvvdlvveleke.vtveevnaalkeaae....galkgilsyteeelvssDlvgdph..ssifdaketi 145
                                        ++VPt+ ++v+ + v+le++   v++v ++++++ +     +  gi +  + + ++ D  + +    ++  + e+i
  gi|336253045|ref|YP_004596152.1| 211 GLKVPTTMMHVHAVNVTLEDDpDGVDDVRDLFRAEDRlltiPEYAGIDGAGTLKDFAMDAGRPRGdiWENCIWGESI 287
                                       *******************99567************9*9999999**************99988778999******* PP

                                       EETTTEEEEEEE CS
                           Gp_dh_C 146 vveenlvkvvaw 157
                                       ++++++++ +++
  gi|336253045|ref|YP_004596152.1| 288 TLQGRDLYCMQA 299
                                       *******99997 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   1.6e-12   4.1e-09       1      95 [.       2     105 ..       2     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.6e-12
                                       EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHH............HHSSSS--S-BEBSSHHHHH CS
                            DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdag............ellglgklgvavtddleevl 65 
                                       i+v+++G+ G++Gk+v++av++++d+++ ++ +r++ ++++  a             ++ g++++g+ +  + ++++
  gi|336253045|ref|YP_004596152.1|   2 IRVGINGY-GTIGKRVADAVRAQPDMTVRGVAKRSP-DYVAVGAAeadypvyaadedRADGFREIGIDLAGTADDLV 76 
                                       79******.*************************99.55555555788999999998899999************** PP

                                       HH-SEEEE-S-HHHHHHHHHHHHHTT-EEE CS
                            DapB_N  66 ekadvliDFTtpeavlenlklalekgvklV 95 
                                       +++dv++D T p++v +  + ++e++  + 
  gi|336253045|ref|YP_004596152.1|  77 AESDVIVDAT-PSGVGAENRPLYERHDTPA 105
                                       **********.9999888888888754443 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 !   20.9   0.0   1.3e-07   0.00033       1      32 [.       2      33 ..       2      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.3e-07
                                      CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE- CS
                           Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaind 32
                                      ++v+inG+G IG+ v+ a+ ++++++v  + +
  gi|336253045|ref|YP_004596152.1|  2 IRVGINGYGTIGKRVADAVRAQPDMTVRGVAK 33
                                      69*************************99987 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 !   11.8   0.2   4.3e-05      0.11      38      68 ..       3      34 ..       2      48 .. 0.82
   2 !    4.4   0.0    0.0082        21      52     100 ..      40      87 ..      37     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.3e-05
                                      EEEEES-SHHHHHHHHHHH.HTT-EEEEESSS CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk.afgmkviaydrs 68
                                      +vGi G+G IG++va+ ++ + +m v ++ ++
  gi|336253045|ref|YP_004596152.1|  3 RVGINGYGTIGKRVADAVRaQPDMTVRGVAKR 34
                                      69**************9996778988887665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0082
                                       HHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S- CS
                      2-Hacid_dh_C  52 akrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlp 100
                                       a  +++ +  v+a d  +   + ++e g++l+ + ++l+aesD+++ ++p
  gi|336253045|ref|YP_004596152.1|  40 AVGAAEADYPVYAADEDRA--DGFREIGIDLAgTADDLVAESDVIVDATP 87 
                                       5567777888999998866..5689999988889***********98877 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 !   13.9   0.4   2.5e-05     0.064       1      69 [.       8      88 ..       8      94 .. 0.70
   2 ?    0.4   0.0       0.4     1e+03      76      95 ..     296     315 ..     292     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                                      --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TT..............HHHHHT-..-CB---HHHHHHHHS-EE CS
                     NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrd.sllskd..............rkallas..ealtldlddliahldpdv 62
                                      G+G+iG++v++++++q++   +++++va+r+ + ++                r+  +++   +l    ddl+a  + dv
  gi|336253045|ref|YP_004596152.1|  8 GYGTIGKRVADAVRAQPD---MTVRGVAKRSpDYVAVGaaeadypvyaadedRADGFREigIDLAGTADDLVA--ESDV 81
                                      99***************7...7888888888544444466666666665555444443311355666677777..9999 PP

                                      EEE-S-- CS
                     NAD_binding_3 63 vVEcass 69
                                      +V++++s
  gi|336253045|ref|YP_004596152.1| 82 IVDATPS 88
                                      9999986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.4
                                       HHHHHHTTEEEE-S--CGGG CS
                     NAD_binding_3  76 vlkaLkagkdvvtankgala 95 
                                         +a+ +  dvv  n++a+ 
  gi|336253045|ref|YP_004596152.1| 296 CMQAIHQEADVVPENVDAIR 315
                                       57999***********9985 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 ?   12.9   0.1   5.6e-05      0.14       1      73 [.       2      89 ..       2     108 .. 0.82
   2 ?   -1.6   0.0       1.9   4.8e+03      48      75 ..     116     144 ..      95     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS..................HHHHHTCT CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd..................leelladp 61
                                      +rv+i G+G ig++ + +++++ ++  v ++ ++++      a++ + ++y+                    ++l+a  
  gi|336253045|ref|YP_004596152.1|  2 IRVGINGYGTIGKRVADAVRAQ-PDMTVRGVAKRSPDYVAVGAAEADYPVYAAdedradgfreigidlagtADDLVA-- 77
                                      69**************777666.*****************99*******9998777777777777776666666666.. PP

                                      TESEEEE-S-GG CS
                      GFO_IDH_MocA 62 eidavivatpng 73
                                      e d+++ atp+g
  gi|336253045|ref|YP_004596152.1| 78 ESDVIVDATPSG 89
                                      667777777765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                                       HE.EESSHHHHHTCTTESEEEE-S-GGGH CS
                      GFO_IDH_MocA  48 ve.aysdleelladpeidavivatpngth 75 
                                       +e +++  ++ ++ +++d++ v++ n+t+
  gi|336253045|ref|YP_004596152.1| 116 AEvSFNARANFAEAEDADYARVVSCNTTG 144
                                       44455666677777889999999988876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00012      0.32       3      63 ..       6      69 ..       4      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                      EES-SHHHHHHHHHHHH.TTEEEEEEESSHHH..HHHHHHTTSEEEES-TTSHHHHHHTTGGGE CS
                            TrkA_N  3 iiGlGrvGrslaeeLse.ggkdvvvidkdeer..veelreeglevvvgdatdeevLeeagieka 63
                                      i G+G++G+++a+ +++   + v ++ k+     +  ++e  ++v+ +d  + +  +e+gi+ a
  gi|336253045|ref|YP_004596152.1|  6 INGYGTIGKRVADAVRAqPDMTVRGVAKRSPDyvAVGAAEADYPVYAADEDRADGFREIGIDLA 69
                                      77***************55577999998874422444455569*****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2732.50
//
Query:       gi|336253046|ref|YP_004596153.1|  [L=357]
Description: glyceraldehyde-3-phosphate dehydrogenase, type I [Halopiger xanaduensis SH-6]
Scores for 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-62  208.6   0.0    4.9e-62  208.2   0.0    1.2  1  Gp_dh_C     Glyceraldehyde 3-phosphate dehydrogenase, C-termi
    6.7e-34  116.3   0.0    1.3e-33  115.3   0.0    1.5  1  Gp_dh_N     Glyceraldehyde 3-phosphate dehydrogenase, NAD bin
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.043   13.9   0.0    2.0  2  DapB_N      Dihydrodipicolinate reductase, N-terminus
      0.032   14.2   0.0      0.055   13.5   0.0    1.4  1  ADH_zinc_N  Zinc-binding dehydrogenase


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 !  208.2   0.0   1.1e-65   4.9e-62       1     158 []     169     325 ..     169     325 .. 0.99

  Alignments for each domain:
  == domain 1  score: 208.2 bits;  conditional E-value: 1.1e-65
                                       HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTTCSSEEEE-THHHHHHHHSGGGTTTEEEEEE CS
                           Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaaeniiptstgaakavglVlpelkgkldglAv 77 
                                       +ap+akvl+++fgi++gl+ttvhayt++Q+++Dgps ++ rr+raaaeniipt+tgaa a ++Vlpel+gkldg+A+
  gi|336253046|ref|YP_004596153.1| 169 VAPVAKVLDEEFGIESGLLTTVHAYTGTQSIVDGPS-SKRRRGRAAAENIIPTTTGAAIAATEVLPELEGKLDGMAI 244
                                       59*********************************9.899************************************* PP

                                       EESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHHTTTTTTEEEEHSHHHGGGGTTGCSSEEEEGGGCEEETTTEEEE CS
                           Gp_dh_C  78 rVPtpnvsvvdlvvelekevtveevnaalkeaaegalkgilsyteeelvssDlvgdphssifdaketivveenlvkv 154
                                       rVP+pn+s++d++v+le++vt+ee  +a+++aa+++l gil+yt+ee+vs+D++g p ss +d ++++v+e+ lvkv
  gi|336253046|ref|YP_004596153.1| 245 RVPVPNGSITDFTVDLEEDVTKEELEEAFRDAADNELAGILGYTDEEIVSRDIIGLPFSSYVDLEASMVLEDGLVKV 321
                                       ***************************************************************************** PP

                                       EEEE CS
                           Gp_dh_C 155 vawy 158
                                       ++wy
  gi|336253046|ref|YP_004596153.1| 322 LTWY 325
                                       ***9 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 !  115.3   0.0   2.9e-37   1.3e-33       2     100 ..      17     114 ..      16     115 .. 0.97

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 2.9e-37
                                       EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-HHHHHHHHHEETTTEC-SS-EEEETTEEEETTEEEEEE--SSG CS
                           Gp_dh_N   2 kvainGfGRIGrlvlralleekelevvaindltdletlayllkyDsvhgrfkgeveaeeealvvngkkikvlaekdp 78 
                                       ++++nGfGRIGr+vlra l+++++e+vaind++d+++++yll+yDsvhgr++ +v+ ++++l++++++i++l+e+dp
  gi|336253046|ref|YP_004596153.1|  17 RIGLNGFGRIGRNVLRASLSDDNVEIVAINDVMDADDMEYLLRYDSVHGRLD-DVSRDGDTLHIGDREIELLSERDP 92 
                                       8*************************************************97.6999******************** PP

                                       GGS-CHHHTSSEEEE-SSS--S CS
                           Gp_dh_N  79 eelpwkelgvdlVvestGvftd 100
                                       ++lpw+el++d+ +e+tG+f++
  gi|336253046|ref|YP_004596153.1|  93 AQLPWDELDIDVAFEATGLFRT 114
                                       ********************86 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.5e-06     0.043       2      35 ..      17      49 ..      16      73 .. 0.85
   2 ?   -2.8   0.0       1.4   6.4e+03      16      46 ..     269     299 ..     267     319 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.5e-06
                                      EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETT CS
                            DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrk 35
                                      +++++G+ Gr+G++v++a  +++++e+va  d  
  gi|336253046|ref|YP_004596153.1| 17 RIGLNGF-GRIGRNVLRASLSDDNVEIVAINDVM 49
                                      89*****.********************987764 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.4
                                       HHHHHHHSTTEEEEEEEETTCSTTTTTBHHH CS
                            DapB_N  16 vvkaveeaedlelvaavdrkeselegkdage 46 
                                       + +a ++a+d el++ +  +++e++++d+  
  gi|336253046|ref|YP_004596153.1| 269 LEEAFRDAADNELAGILGYTDEEIVSRDIIG 299
                                       5667777888888888888888888777754 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.2e-05     0.055      57     100 ..     100     144 ..      61     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                                       SSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC.TSSEEEEEHH CS
                        ADH_zinc_N  57 egvdvvfecvGsgatleaalkllkpgGrlvvvGg.gkgeeefdlr 100
                                        ++dv+fe++G  +t+++a + l  g   vv+ + +kge+e++++
  gi|336253046|ref|YP_004596153.1| 100 LDIDVAFEATGLFRTYDDAAQHLEAGADKVVISApPKGEKEVPMF 144
                                       489*****************************9977777778776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2616.56
//
Query:       gi|336253047|ref|YP_004596154.1|  [L=402]
Description: phosphoglycerate kinase [Halopiger xanaduensis SH-6]
Scores for complete 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-99  333.9   0.0    1.4e-99  333.6   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 !  333.6   0.0  7.8e-104   1.4e-99       7     377 ..      12     389 ..       7     390 .. 0.90

  Alignments for each domain:
  == domain 1  score: 333.6 bits;  conditional E-value: 7.8e-104
                                       TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHHHTT-E CS
                               PGK   7 kgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsellgkeV 83 
                                       +g+++lvR+D+N+p+++ g+++d++r+ ++++T+ +lle++++v +l+H+grp g+++ +sl+++a+ L++ l+++V
  gi|336253047|ref|YP_004596154.1|  12 AGQQLLVRIDINAPVED-GVVQDNRRFARHAETLAELLENDHAVAVLAHQGRP-GRDTFVSLEQHADILADHLDRDV 86 
                                       5899***********86.***********************************.89********************* PP

                                       EEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTT..TTT-H.......HHHHHHHHT-SEEEE--GGGTTS--TTT CS
                               PGK  84 kfvedvvgeeveeaiaelkegevllLeNvrfykeE..eknde.......elakklasladvyVnDAFgtahrahaSt 151
                                        fv d++ge++ +ai++l++g+vl+LeN r+ +eE  e  +e       e++++la  +d+yVnDA+++ahr+haS+
  gi|336253047|ref|YP_004596154.1|  87 DFVADTFGEDALTAIDDLESGDVLVLENARMCDEElpE--EEpevkaetEFVQTLAPEFDAYVNDAYSAAHRSHASL 161
                                       ********************************999542..2223444458*************************** PP

                                       THHHHCSEEEE-HHHHHHHHHHHHHHHS-.-SSEEEEEEES-HHHCHHHHHHHTTT-SEEEEETCHHHHHHHHTT-B CS
                               PGK 152 vgiakvlsaaaGllmekElealskvlenp.erplvailGGakvsdkikvienLlekvdkliigGgmantFlkaqgle 227
                                       vg++ v++a+aG++me+E++a s++ e++ + p++++lGG+k +d i vie++ ++vd++ +gG +   Fl+a+g++
  gi|336253047|ref|YP_004596154.1| 162 VGFPLVMDAYAGRVMEAEYTANSAIQEQEfDGPVTMVLGGTKAEDLIPVIERVDDTVDRFCLGGIVGELFLRAAGHD 238
                                       *******99*************9998654269********************************************* PP

                                       -TTSS--G........GGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EEEEE-HHHHHH CS
                               PGK 228 igkslvee........dklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipedemalDigpktiel 296
                                       +g ++  +        d+ e+++++le++   g++++l  D++++++ +   +   +ve+i++++ +lD+g++t+++
  gi|336253047|ref|YP_004596154.1| 239 VGYDVEGTeffdhqweDHQETIERVLEEY---GDRLHLASDLAYEDDGE---RAEEAVEDIEKETSYLDVGSDTADE 309
                                       **776633233333434577777777776...69***********9532...2345789****************** PP

                                       HHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GG.GSSEEESSSHHHH CS
                               PGK 297 faeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklglad.kvshvStGGgAsL 372
                                       +a  ++e++ v+++G++Gvfe e+fa+GT  +++a+ae+  +++s++GGgd+ + +e++gl++ ++ hvS +GgA++
  gi|336253047|ref|YP_004596154.1| 310 YAGLVRESEAVFVKGALGVFEDERFADGTVDVLSAIAET--DCFSVIGGGDTSRSIEMYGLEEdDFGHVSVAGGAYV 384
                                       **************************************7..47*****************97769************ PP

                                       HHHCT CS
                               PGK 373 elLeg 377
                                       ++L+g
  gi|336253047|ref|YP_004596154.1| 385 RALTG 389
                                       ***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2888.34
//
Query:       gi|336253048|ref|YP_004596155.1|  [L=281]
Description: hypothetical protein Halxa_1644 [Halopiger xanaduensis SH-6]
Scores for 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   12.8   0.0      0.058   12.5   0.0    1.1  1  DUF2048        Abhydrolase domain containing 18
      0.061   12.6   0.0       0.13   11.5   0.0    1.5  1  CcmH           Cytochrome C biogenesis protein
      0.074   13.1   0.7       0.12   12.4   0.1    1.6  2  CoA_binding_3  CoA-binding domain


Domain annotation for each model (and alignments):
>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.7e-06     0.058     180     271 ..      81     255 ..      78     277 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.7e-06
                           DUF2048 180 ltGlSmGGhm.aslaasnwpkplv..lvpclswstasavfteGvlsksiawdvLekqledgnyrerl.......... 243
                                       +tGlS+ G     + a + p+ +   ++ ++s + a +++t+  l+  +  d+Le  l+dg + erl          
  gi|336253048|ref|YP_004596155.1|  81 VTGLSVVGQTdIDVRAFVNPHTAFgaVLMLVSTAIAGVTYTTSNLRGGVGRDALEAALSDGAFAERLvrsygewiey 157
                                       6788876654145556566655535488899999*********************************8888887777 PP

                           DUF2048 244 ......................................................................stasdaa 250
                                                                                                             s  + ++
  gi|336253048|ref|YP_004596155.1| 158 naavtavndvlvtitvllivdsfvfvvvgigvgaadlspigvwtsfagltlvlgylthvayqmdhvgsvgSSEDPTT 234
                                       77777777777777777777777777777777777777777777777777777777777777777666664444444 PP

                           DUF2048 251 aeekaakldeakerkaekeal 271
                                       a     +l +  +r++ ++al
  gi|336253048|ref|YP_004596155.1| 235 ATFDGVRLSKGATRGQSHDAL 255
                                       444444444444444444444 PP

>> CcmH  Cytochrome C biogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.2e-05      0.13      62     116 ..     131     185 ..     120     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.2e-05
                                       HHHHHHT--HHHHHHHHHHHHTTT-EE---XXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CcmH  62 remlkaGksdeeivdylvarYGdfVlykPpvkastllLWlgPllllllgllvlll 116
                                       r+ l+a  sd    + lv+ YG+++ y+  v+a + +L  + +ll++  ++++++
  gi|336253048|ref|YP_004596155.1| 131 RDALEAALSDGAFAERLVRSYGEWIEYNAAVTAVNDVLVTITVLLIVDSFVFVVV 185
                                       567888889999999****************************999999888776 PP

>> CoA_binding_3  CoA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1     2e-05      0.12       6      98 ..      54     150 ..      51     167 .. 0.81
   2 ?   -1.7   0.1      0.43   2.6e+03      46      59 ..     195     209 ..     151     225 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                     CoA_binding_3   6 Yqswrgrsllrlllrvlsawllvllllallsfslk..dafSRlwlaywavvglvllivsrllvravlrrlrrngrne 80 
                                       Yq+ r+r    +++ +l a+ll ++++++ + +++  d+  R ++   ++ g+vl++vs +++  + +    +g++ 
  gi|336253048|ref|YP_004596155.1|  54 YQVERLREIDAKAIEILKANLLIIGVFVTGLSVVGqtDIDVRAFVNPHTAFGAVLMLVSTAIAGVTYTTSNLRGGVG 130
                                       9************************98887777765689********************999976666555567777 PP

                     CoA_binding_3  81 rrvv..avgggeelakqira 98 
                                       r ++  a + g+++++ +r+
  gi|336253048|ref|YP_004596155.1| 131 RDALeaALSDGAFAERLVRS 150
                                       77766677777777777666 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.43
                     CoA_binding_3  46 lwlaywa.vvglvll 59 
                                       + ++ w+ ++gl+l+
  gi|336253048|ref|YP_004596155.1| 195 SPIGVWTsFAGLTLV 209
                                       334555434444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); 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:                         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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2035.26
//
Query:       gi|336253049|ref|YP_004596156.1|  [L=325]
Description: leucyl aminopeptidase [Halopiger xanaduensis SH-6]
Scores for 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-12   44.9   0.0    7.1e-11   41.5   0.0    1.9  2  Peptidase_M29    Thermophilic metalloprotease (M29)
  ------ inclusion threshold ------
       0.93    9.6   4.2         11    6.1   0.1    3.0  3  Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_Yhc


Domain annotation for each model (and alignments):
>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.015   1.4e+02       7      54 ..      13      60 ..       8      68 .. 0.85
   2 !   41.5   0.0     8e-15   7.1e-11     183     348 ..     127     287 ..     121     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.015
                                      HHHHHHHHTTT---TT-EEEEEEETT-HHHHHHHHHHHHHTT-SEEEE CS
                     Peptidase_M29  7 kyAellvkvglnlqkgqevvinaevealelarlvaeeaykagakkvvv 54
                                        A+ +v+ +l+l+++++ v+ ++ +  +  ++++e a + +    +v
  gi|336253049|ref|YP_004596156.1| 13 TAARTAVEQCLELESDESCVVVTDDKREPIGEVLYEVASEITDDATIV 60
                                      5699**************************999999998876665555 PP

  == domain 2  score: 41.5 bits;  conditional E-value: 8e-15
                                       HHHHHHHHHHHHHHHHHHHTT-SEEEEE.ETTEEEEEEE-TTB--EESS---SSS----SBSS---EEE-EEEEEEE CS
                     Peptidase_M29 183 aaWeehnaelekrakyLnelkfkeLhyksspgtdLtvglaeghiWiggaektkkgiefvaNiPteevftaPdkrgvn 259
                                       a+++++ +e e+ ++  +    +e++++++ gtd+t  l  ++ W   +++  ++   ++N+P +evf++P+  +++
  gi|336253049|ref|YP_004596156.1| 127 ADYDRIREECERMVDRVSG--ADEVRVTTDRGTDITFAL-GDRDWFDDTGDV-SEPGAFSNLPAGEVFISPE--SAE 197
                                       5788899999999999999..99****************.778888888885.7888999***********6..689 PP

                                       EEEE-SS-EEETTEEEBS-EEEE..ETTEEEEEE-SB-HHHHHHHT.TSSSGGGSEEEEE---TTSHHHHHT----- CS
                     Peptidase_M29 260 GvvratkPlsysGnliegirltF..edGkvveakAekGeevLkkll.etDegarrLGEvALvpndspisqsgilfyn 333
                                       G+++ +  +  +G l eg +l+F  edG v+e++ ++    +++   e+ + a  L E+ +++n   ++    l+ +
  gi|336253049|ref|YP_004596156.1| 198 GTYVVDGTMRPHGLLEEGQELEFvvEDGLVTEISDDEIRRQVEEAAeEVGDAAYNLAELGIGTNV-GVTD---LVGS 270
                                       *************9999887776669*******9999888887777256777778*********9.9999...**** PP

                                       HHHHHT..TS-EEEEE- CS
                     Peptidase_M29 334 tLfDen..ascHlAlGa 348
                                       +L+De+  +++H+A+G+
  gi|336253049|ref|YP_004596156.1| 271 VLLDEKaaGTVHIAIGD 287
                                       ******9999******7 PP

>> Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3     0.031   2.8e+02      56      85 ..       9      38 ..       3      59 .. 0.72
   2 ?    6.1   0.1    0.0012        11      96     126 ..     127     156 ..     116     158 .. 0.87
   3 ?    1.8   0.0     0.025   2.2e+02      98     118 ..     232     252 ..     225     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.031
                   Spore_YhcN_YlaJ 56 dydgetaqniaqrverlegVedarvlvtgn 85
                                      +++++ a  +++++ +le+ e + v++ ++
  gi|336253049|ref|YP_004596156.1|  9 ADRRTAARTAVEQCLELESDESCVVVTDDK 38
                                      556666677777777777777777776665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0012
                   Spore_YhcN_YlaJ  96 sdnekvkkkVketVekvvddiknVyVvtdpd 126
                                       +d + ++++ ++ V+ v +   +V+V+td+ 
  gi|336253049|ref|YP_004596156.1| 127 ADYDRIREECERMVDRVSGA-DEVRVTTDRG 156
                                       788999************99.********85 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.025
                   Spore_YhcN_YlaJ  98 nekvkkkVketVekvvddikn 118
                                        ++++++V+e++e+v d  +n
  gi|336253049|ref|YP_004596156.1| 232 DDEIRRQVEEAAEEVGDAAYN 252
                                       689**********99887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2397.11
//
Query:       gi|336253050|ref|YP_004596157.1|  [L=328]
Description: hypothetical protein Halxa_1646 [Halopiger xanaduensis SH-6]
Scores for 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   24.1   0.0    7.9e-05   22.6   0.0    1.8  1  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.085   12.9   2.8        2.2    8.4   0.4    2.5  2  DZR             Double zinc ribbon
       0.65   10.3   2.5       0.57   10.4   0.2    2.2  3  Se-cys_synth_N  Selenocysteine synthase N terminal


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 !   22.6   0.0   1.3e-08   7.9e-05       2      52 ..      20      79 ..      19      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.3e-08
                                      HHHHHHS-HHHHHHHHHH.........STCTTB-HHHHHHHHTS-HHH.HHHHHHHHHHCT CS
                            HTH_20  2 qiaeALahPvRrrilraL.........araegltaselaerldlsknt.lsyHLrvLeeag 52
                                      +++ AL++P R +ilra+         + +  + +s l ++++++++   +yHL++L +  
  gi|336253050|ref|YP_004596157.1| 20 DAFAALGNPIRVEILRAFleraqaegeSAEPVVRFSTLRKTVGIRDSGqFRYHLEQL-RGQ 79
                                      789***************9996666655555566667777778999999********.555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1    0.0092        55      14      31 ..     126     147 ..     116     153 .. 0.73
   2 ?    8.4   0.4   0.00036       2.2      15      37 ..     191     240 ..     187     247 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0092
                               DZR  14 fCseCgtklkavaa....edrC 31 
                                        C++Cgt+ +a  +    e +C
  gi|336253050|ref|YP_004596157.1| 126 ACGRCGTAARASYRdgvlEVTC 147
                                       6889998887555466666666 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00036
                               DZR  15 CseCgtklkavaa...........................edrCpsCgek 37 
                                       CseC +++++  +                             rC++Cg+ 
  gi|336253050|ref|YP_004596157.1| 191 CSECYSPVEPGIRllegcdtetdtdddatpttvdgrsvrfTARCDACGAG 240
                                       666666655333355555555555667999999*******9******985 PP

>> Se-cys_synth_N  Selenocysteine synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   9.6e-05      0.57      14      39 ..      16      41 ..      14      41 .. 0.90
   2 ?   -2.6   0.0       1.2     7e+03      12      26 ..     251     265 ..     249     266 .. 0.83
   3 ?   -3.3   0.1       1.9   1.1e+04      26      37 ..     304     311 ..     295     312 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.6e-05
                    Se-cys_synth_N 14 learallaalpRalvrdavrafLdrc 39
                                      le +++ aal+ +  ++ +rafL+r+
  gi|336253050|ref|YP_004596157.1| 16 LEPADAFAALGNPIRVEILRAFLERA 41
                                      6678999*****************96 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.2
                    Se-cys_synth_N  12 talearallaalpRa 26 
                                       t++++  l  + +R+
  gi|336253050|ref|YP_004596157.1| 251 THPRVESLYHRRGRP 265
                                       789999999999997 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.9
                    Se-cys_synth_N  26 alvrdavrafLd 37 
                                       a     vra +d
  gi|336253050|ref|YP_004596157.1| 304 AQ----VRATID 311
                                       44....555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2582.83
//
Query:       gi|336253051|ref|YP_004596158.1|  [L=360]
Description: peptidase M23 [Halopiger xanaduensis SH-6]
Scores for 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-21   75.4   0.1    1.5e-20   73.2   0.0    1.9  2  Peptidase_M23  Peptidase family M23


Domain annotation for each model (and alignments):
>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.0   8.5e-25   1.5e-20      13      90 ..     221     316 ..     216     320 .. 0.91
   2 ?   -1.0   0.0      0.12   2.1e+03      62      73 ..     348     359 ..     342     360 .] 0.75

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 8.5e-25
                                       T-EEEESSSEEEEEEEEET...............TT.EEEEEEEECTCEEEEEEEESEES..S-TTEEE-TTCEEEE CS
                     Peptidase_M23  13 gtpVlAaadGtVvfagkke...............gy.Gnvviidhgdgystlyahlskis..vkegqkVkaGqvIGt 71 
                                       g+p+lA+adG+Vv  ++++               ++ Gn+v+idh++g +++ ahl++ s  v++g++V++Gq+I++
  gi|336253051|ref|YP_004596158.1| 221 GEPILAPADGVVVSTRNDHrdyhrtngwmdplqrSIlGNHVVIDHENGEYSVLAHLQQGSvaVEPGERVERGQQIAR 297
                                       89**********999995558999*********9667*********************665588************* PP

                                       EBSTSSCSSSEEEEEEEET CS
                     Peptidase_M23  72 vgstgrstgphLhfeirkn 90 
                                        g++g++t+phLhf+++++
  gi|336253051|ref|YP_004596158.1| 298 CGNSGNTTEPHLHFHLQDR 316
                                       **************99864 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.12
                                       EE-TTCEEEEEB CS
                     Peptidase_M23  62 kVkaGqvIGtvg 73 
                                       +V aGq +++vg
  gi|336253051|ref|YP_004596158.1| 348 YVHAGQRVAHVG 359
                                       588888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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 0.21s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2761.22
//
Query:       gi|336253052|ref|YP_004596159.1|  [L=224]
Description: Zn-finger protein-like protein [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.044   14.2   1.4      0.073   13.5   0.5    1.9  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.11   13.0  11.7       0.59   10.6   1.2    3.3  3  DraK_HK_N        DraK Histidine Kinase N-terminal domain
       0.14   12.1   4.1       0.75    9.8   4.1    2.1  1  zinc_ribbon_4    zinc-ribbon domain
       0.14   11.6   0.1       0.14   11.6   0.1    2.3  2  zf-ribbon_3      zinc-ribbon domain
       0.15   12.0   0.3       0.29   11.1   0.3    1.4  1  zf-DNL           DNL zinc finger
       0.25   11.5   3.0        9.9    6.4   0.1    2.5  2  Zn-ribbon_8      Zinc ribbon domain
        2.8    7.8   4.3        7.9    6.3   4.3    1.8  1  zinc_ribbon_5    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 ?   13.5   0.5   2.9e-05     0.073       5      43 ..      16      52 ..      14      70 .. 0.81
   2 ?   -3.8   0.0         7   1.8e+04      51      60 ..     121     130 ..     117     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigq..cvyCadCgastpwfki 43
                                      pCP C  + + +++ ++++e+g   +v C +Cg +    + 
  gi|336253052|ref|YP_004596159.1| 16 PCPSCSPELETVHEVLTASEGGGtvTVRCSECGHV----HK 52
                                      9*************9999998889*********92....22 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7
                   Lar_restr_allev  51 ekeaieaWNr 60 
                                        +e++ +W r
  gi|336253052|ref|YP_004596159.1| 121 VDEIATVWSR 130
                                       5789999976 PP

>> DraK_HK_N  DraK Histidine Kinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.41   1.1e+03      68      85 ..      27      44 ..      21      45 .. 0.74
   2 ?   10.6   1.2   0.00023      0.59      27      63 ..      56      92 ..      53     112 .. 0.81
   3 ?    7.4   1.1    0.0023         6      31      61 ..     131     168 ..      98     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.41
                                      EEEEEEE-TTS-EEEEEE CS
                         DraK_HK_N 68 visatargesgetVtvee 85
                                      v ++ + +e g+tVtv  
  gi|336253052|ref|YP_004596159.1| 27 VHEVLTASEGGGTVTVRC 44
                                      556667889999999975 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00023
                                      HHTS---HHHHTTT-SS-SEEEEE-TT-.--B-S--- CS
                         DraK_HK_N 27 aagepitaelLeeqvpgdryvvVripggtpieaGedp 63
                                      ++++++t +++ +q ++   + V++p+++++e+G++ 
  gi|336253052|ref|YP_004596159.1| 56 EQEREVTLDVVVSQDDESFTANVTTPEDETVEVGDEF 92
                                      578999*****99999999********99*****765 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0023
                                       ---HHHHTTT-SS-S.......EEEEE-TT-.--B-S- CS
                         DraK_HK_N  31 pitaelLeeqvpgdr.......yvvVripggtpieaGe 61 
                                       ++++ ++   v +++       +++V++pg+ ++e+G+
  gi|336253052|ref|YP_004596159.1| 131 EVDNVAVNVTVHPQDgrrddsrSITVHVPGDYEFEVGA 168
                                       5555556665555555667777********99*****4 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.1   0.00029      0.75      17      34 ..      33      50 ..      15      52 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00029
                     zinc_ribbon_4 17 eklpakgvkvrCskCghv 34
                                      +   +++v vrCs Cghv
  gi|336253052|ref|YP_004596159.1| 33 ASEGGGTVTVRCSECGHV 50
                                      44457789*********8 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   2.5      0.65   1.7e+03       5       8 ..      17      20 ..      15      20 .. 0.71
   2 ?   11.6   0.1   5.5e-05      0.14       2      15 ..      41      56 ..      40      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.65
                       zf-ribbon_3  5 CPnC 8 
                                      CP+C
  gi|336253052|ref|YP_004596159.1| 17 CPSC 20
                                      8887 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.5e-05
                       zf-ribbon_3  2 tvrCPnCGa.p.lssd 15
                                      tvrC++CG+ + ++++
  gi|336253052|ref|YP_004596159.1| 41 TVRCSECGHvHkVQPE 56
                                      89*******7766665 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00011      0.29      12      40 ..      25      53 ..      14      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                            zf-DNL 12 rsskeiskkaYekGvVivqCpgCknrHli 40
                                       + +e+   +   G+V v+C++C + H +
  gi|336253052|ref|YP_004596159.1| 25 ETVHEVLTASEGGGTVTVRCSECGHVHKV 53
                                      4668888888899************9976 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.4      0.01        26      23      36 ..      11      24 ..       4      28 .. 0.68
   2 ?    6.4   0.1    0.0039       9.9       7      16 ..      43      52 ..      37      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.01
                       Zn-ribbon_8 23 dapltaCPeCgsev 36
                                      d+ +t+CP+C  e+
  gi|336253052|ref|YP_004596159.1| 11 DRVPTPCPSCSPEL 24
                                      445677****5465 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0039
                       Zn-ribbon_8  7 rCeeCghefe 16
                                      rC eCgh++ 
  gi|336253052|ref|YP_004596159.1| 43 RCSECGHVHK 52
                                      89****9876 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.3    0.0031       7.9      24      36 ..      40      52 ..      14      53 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0031
                     zinc_ribbon_5 24 kkVrCakCaevFd 36
                                      + VrC  C++v  
  gi|336253052|ref|YP_004596159.1| 40 VTVRCSECGHVHK 52
                                      579*******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1632.55
//
Query:       gi|336253053|ref|YP_004596160.1|  [L=319]
Description: hypothetical protein Halxa_1649 [Halopiger xanaduensis SH-6]
Scores for 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-10   38.3  21.8    8.8e-09   35.1  21.8    2.0  1  SBF_like  SBF-like CPA transporter family (DUF4137)
    5.6e-08   32.7  12.1    5.6e-08   32.7  12.1    2.2  3  SBF       Sodium Bile acid symporter family
  ------ inclusion threshold ------
        2.5    8.6   5.2        5.9    7.4   0.4    2.8  3  Tox-WTIP  Toxin with a conserved tryptophan and TIP tripeptid


Domain annotation for each model (and alignments):
>> SBF_like  SBF-like CPA transporter family (DUF4137)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1  21.8   1.5e-12   8.8e-09       5     312 ..      15     298 ..      11     299 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.5e-12
                          SBF_like   5 lllilvillAslvPvfakaggtikaeyvikygValiFllsGlslsteellanlrnwrlhllvll.isflltplivla 80 
                                       l+++++ l + ++P +a+   +   + +i ++Va + + s   +++ +l    rn+ + ++  l + +lltpl    
  gi|336253053|ref|YP_004596160.1|  15 LVVLAATLAGVVAPTLAA---P--LQPTIPALVAGLIFTSFYGFDSAALTGRGRNVSVPVVLSLgCLYLLTPLA--- 83 
                                       444555555566666666...3..456888999999999999*************9998776651667888865... PP

                          SBF_like  81 lvsllkaaldpelliGllllaalPtTvssnvvmtsqAgGnealalceavignllGvfltPalvqlllsgssvsvdya 157
                                       l+++++++l+ +ll+G+l++ a+P T  s+++ t+ +gGn +la + a+++ l+++++ P l+ l+   s+v++ + 
  gi|336253053|ref|YP_004596160.1|  84 LYPVAATVLSGDLLLGVLIVLAAPLTAGSSIIWTRLSGGNALLATVIALVSLLIAPLAMPSLIALFA-DSTVDIAAS 159
                                       56666677899*******************************************************9.689****** PP

                          SBF_like 158 evlkklllsvllPlvvGqvlqkifpklvkrlkkllkkvdslvlllivytsfstafaqgaftsvshiillvifnvall 234
                                       e+l +l++ +l     G +l   +p+  +  ++ l  ++ +++ +++y  +  +   ga++ ++   +  + + al 
  gi|336253053|ref|YP_004596160.1| 160 EILVDLGAIILG----GGLLAVFVPDD-AISDDRLDAFSLATIGILIYAGVGAS--GGAIDVLELAFVSGLAVAALG 229
                                       ***999997653....55555556654.55688999999999999999998877..666644444333333333333 PP

                          SBF_like 235 LllvvlvillllarllklskedeiavlfcgsaKslalgvplisvlfgsnpqlgllllPlllyhliqlvvaavlvsrl 311
                                       L + +  +   +  + +l   d i+vlf  s K l+++v ++  +fg+    g ++  +  +h++q +v++ lv rl
  gi|336253053|ref|YP_004596160.1| 230 LSAGL--AY--VLYARGLRSDDCISVLFSSSMKNLSVSV-MVGAMFGG----GAIVAGITAFHVVQQIVSSSLVHRL 297
                                       33333..22..3345578899*****************9.56778987....789999999*************998 PP

                          SBF_like 312 r 312
                                       +
  gi|336253053|ref|YP_004596160.1| 298 A 298
                                       6 PP

>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.22   1.3e+03      20      68 ..       4      47 ..       1      59 [. 0.61
   2 !   32.7  12.1   9.4e-12   5.6e-08      29     133 ..      68     164 ..      57     205 .. 0.84
   3 ?   -1.3   0.1      0.25   1.5e+03     132     145 ..     260     273 ..     207     306 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.22
                               SBF 20 lkellkrpkalllglvlqw..vikPllmfilakillrdlklepelavGlil 68
                                      l++++++++ ll+ l +++  v+ P+l+  l      ++   p l++Gli 
  gi|336253053|ref|YP_004596160.1|  4 LRKVVRSQRSLLVVLAATLagVVAPTLAAPLQP----TI---PALVAGLIF 47
                                      667777766666666665532456666655555....33...566666665 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 9.4e-12
                               SBF  29 alllglvlqwvikPllmfilakillrdlklepelavGlilvglapggam.snvwtylakGdlelsvvlvalstllai 104
                                       +++l+l + +++ Pl  +  a ++     l+  l++G+++v +ap +a+ s++wt l++G+  l++v+ ++s l+a+
  gi|336253053|ref|YP_004596160.1|  68 PVVLSLGCLYLLTPLALYPVAATV-----LSGDLLLGVLIVLAAPLTAGsSIIWTRLSGGNALLATVIALVSLLIAP 139
                                       7999***********999999933.....6788*************9862699************************ PP

                               SBF 105 lltPlllyllaksleqttlkvpieeivks 133
                                       l +P l++l+a s     ++++++ei+  
  gi|336253053|ref|YP_004596160.1| 140 LAMPSLIALFADST----VDIAASEILVD 164
                                       *************9....55555555332 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.25
                               SBF 132 ksvlivviiPliaG 145
                                       +sv ++v+  +  G
  gi|336253053|ref|YP_004596160.1| 260 LSVSVMVGAMFGGG 273
                                       23333333333333 PP

>> Tox-WTIP  Toxin with a conserved tryptophan and TIP tripeptide motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4   0.00098       5.9      55      71 ..      26      42 ..      23      44 .. 0.88
   2 ?   -3.4   0.0       2.4   1.4e+04      44      53 ..     196     205 ..     189     206 .. 0.78
   3 ?    2.6   0.1      0.03   1.8e+02      37      54 ..     226     244 ..     220     247 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00098
                          Tox-WTIP 55 mlPSLlPpLWptiPaNl 71
                                      ++P L+ pL ptiPa +
  gi|336253053|ref|YP_004596160.1| 26 VAPTLAAPLQPTIPALV 42
                                      58************965 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.4
                          Tox-WTIP  44 GvgYliYRgv 53 
                                        +g liY gv
  gi|336253053|ref|YP_004596160.1| 196 TIGILIYAGV 205
                                       4678999998 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.03
                          Tox-WTIP  37 akvvaavGvgYliY.RgvR 54 
                                       a+ + ++G +Y++Y Rg+R
  gi|336253053|ref|YP_004596160.1| 226 AALGLSAGLAYVLYaRGLR 244
                                       5667799*******99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); 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:                         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 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 2436.58
//
Query:       gi|336253054|ref|YP_004596161.1|  [L=224]
Description: protein-L-isoaspartate O-methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-62  210.7   0.0    2.2e-62  210.5   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.2e-06   29.1   0.0    2.5e-06   28.1   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    5.3e-05   23.1   0.0    7.1e-05   22.6   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    0.00012   21.3   0.0    0.00016   20.9   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00014   21.3   0.0    0.00021   20.7   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00019   21.2   0.0    0.00033   20.4   0.0    1.3  1  GCD14            tRNA methyltransferase complex GCD14 subunit
  ------ inclusion threshold ------
      0.016   14.4   0.0      0.022   13.9   0.0    1.1  1  Fibrillarin      Fibrillarin
       0.02   14.6   0.0      0.028   14.2   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)
      0.025   14.5   0.0       0.04   13.8   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
      0.054   13.5   0.0      0.082   12.9   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.089   12.3   0.0       0.14   11.7   0.0    1.2  1  DOT1             Histone methylation protein DOT1
       0.13   12.1   0.0       0.15   11.9   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
       0.16   11.5   0.0       0.26   10.8   0.0    1.2  1  MTS              Methyltransferase small domain
        0.2   11.9   0.2        0.2   11.9   0.2    2.0  2  DUF2795          Protein of unknown function (DUF2795)


Domain annotation for each model (and alignments):
>> 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 !  210.5   0.0   1.7e-65   2.2e-62      12     205 ..      32     222 ..      22     224 .] 0.96

  Alignments for each domain:
  == domain 1  score: 210.5 bits;  conditional E-value: 1.7e-65
                                       HTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHH CS
                              PCMT  12 kkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevGsGsGylt 88 
                                       +++ +++d+v+eale+v+R+efvp   + +aY d pl+ig ++tiSaphmva++ + l+l++g++vLe+G+G+Gy++
  gi|336253054|ref|YP_004596161.1|  32 AHR-VADDRVLEALEDVPRHEFVPPDRRGEAYADRPLPIGDGQTISAPHMVAVMADRLDLEPGDEVLEIGTGCGYHA 107
                                       455.799******************9999************************************************ PP

                                       HHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS--HHHHHTEEE CS
                              PCMT  89 avlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiPealidQLke 165
                                       av+a++vg++  v s+e+ ++l+e+a+++l++ ++ ++ v++gDGr+G++e+aPYda +++ a+ e+Pe+ ++Q+ +
  gi|336253054|ref|YP_004596161.1| 108 AVTAEIVGPEN-VYSVEYGEQLAEQARARLEEIGYGEIDVRIGDGRNGWAEQAPYDAAYFTCATAELPEPVVEQVRP 183
                                       **********9.***************************************************************** PP

                                       EEEEEEEESBSSSEEEEEEEEETTTEEEEEEEEEE---B- CS
                              PCMT 166 GGrlvvPvgeeeeQvlklvdkkadgkvvikkleevrfvpl 205
                                       GGr+++Pvg +++Q+l ++dk+adg+++ ++   vrfv +
  gi|336253054|ref|YP_004596161.1| 184 GGRILAPVG-TGRQTLVQADKRADGSLERTEHGGVRFVQM 222
                                       *********.****************************76 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.9e-09   2.5e-06       1      84 [.      96     180 ..      96     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.9e-09
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       vL++G+G G +++  a+ +g ++v+ v++ e++ e+ar+r+ee g+ +++++ gd ++   e++ +D+ + + a   
  gi|336253054|ref|YP_004596161.1|  96 VLEIGTGCGYHAAVTAEIVGPENVYSVEYGEQLAEQARARLEEIGYgEIDVRIGDGRNGWAEQAPYDAAYFTCATAE 172
                                       9*****************999********************999999***********99999*******9755655 PP

                                       SSHHHHHH CS
                   Methyltransf_25  77 lsdedlek 84 
                                       l+++ +e+
  gi|336253054|ref|YP_004596161.1| 173 LPEPVVEQ 180
                                       77665543 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   5.5e-08   7.1e-05       3      86 ..      92     172 ..      90     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.5e-08
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDli 78 
                                        g +vl++G+G G+ + + ae +gp  +v+++++ e+  e+Ar+++++ g+ ++ +++gd  +   +   ++++D  
  gi|336253054|ref|YP_004596161.1|  92 PGDEVLEIGTGCGYHAAVTAEIVGP-ENVYSVEYGEQLAEQARARLEEIGYGEIDVRIGDGRNgWAE---QAPYDAA 164
                                       5789****************76666.88********************************9886553...3778877 PP

                   Methyltransf_31  79 lsnevlna 86 
                                          ++ + 
  gi|336253054|ref|YP_004596161.1| 165 YFTCATAE 172
                                       66655544 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.2e-07   0.00016      19      80 ..      81     146 ..      73     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.2e-07
                                       HHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEE CS
                            RrnaAD  19 ineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkv 80 
                                       ++   d l+le+ ++vleig+G G   +  a+++  ++v ++E  e+La+  +++l+   ++ + v
  gi|336253054|ref|YP_004596161.1|  81 VAVMADRLDLEPGDEVLEIGTGCGYHAAVTAEIVgpENVYSVEYGEQLAEQARARLEeiGYGEIDV 146
                                       5566899***********************************************998665666655 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   1.6e-07   0.00021      53     112 ..      83     143 ..      76     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.6e-07
                                       HHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--.EEEEEES-HHHHHHHHHHHHTS-SSS CS
                              CMAS  53 lileklelkpGmtlLdiGcGWGslvrraverydv.kvvglTlSkeqaklakkrvdeldler 112
                                       ++ ++l+l+pG+++L+iG+G G+ +  ++e  +  +v ++   ++ a++a++r++e++  +
  gi|336253054|ref|YP_004596161.1|  83 VMADRLDLEPGDEVLEIGTGCGYHAAVTAEIVGPeNVYSVEYGEQLAEQARARLEEIGYGE 143
                                       6789*******************999999988753899****9999*********999754 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.6e-07   0.00033      29      87 ..      81     138 ..      73     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.6e-07
                             GCD14  29 isliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefre 87 
                                       ++++  +L+l+pG  v+e GtG g  +   a  v+P  +++++e+ eq ae+ar  ++e
  gi|336253054|ref|YP_004596161.1|  81 VAVMADRLDLEPGDEVLEIGTGCGYHAAVTAEIVGPE-NVYSVEYGEQLAEQARARLEE 138
                                       6788899*******************99999999997.79*************988776 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.7e-05     0.022      63     107 ..      85     128 ..      77     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                                       -S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHH CS
                       Fibrillarin  63 lkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprv 107
                                        ++l +++g++vL +G++ G  ++  ++ivg+e  vy+ve+ ++ 
  gi|336253054|ref|YP_004596161.1|  85 ADRLDLEPGDEVLEIGTGCGYHAAVTAEIVGPE-NVYSVEYGEQL 128
                                       567889*************************76.79****98765 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.2e-05     0.028      17      74 ..      83     141 ..      76     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                            DUF938  17 vLksylaktte.rvLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelal 74 
                                       v+ + l+ +   +vLEi++G G HA+  A+ + + +  + ++ e+l e  +a ++e++ 
  gi|336253054|ref|YP_004596161.1|  83 VMADRLDLEPGdEVLEIGTGCGYHAAVTAEIVGPENVYSVEYGEQLAEQARARLEEIGY 141
                                       5555555433237*******************999999999999999999998888776 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.1e-05      0.04      13      81 ..      91     158 ..      85     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                   Methyltransf_18  13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkee 81 
                                       e+g+ v+ iGt  gy ++  ++    ++v+ ++  e+  e+a++ +e+ g+  +i+vr++dG +   e+
  gi|336253054|ref|YP_004596161.1|  91 EPGDEVLEIGTGCGYHAAVTAEIVGPENVYSVEYGEQLAEQARARLEEIGY-GEIDVRIGDGRNGWAEQ 158
                                       568999*******************************************99.57********9887755 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.4e-05     0.082      13      78 ..      81     141 ..      75     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.4e-05
                   Methyltransf_32  13 vakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78 
                                       va ++++  + ++  +v+++G G gY + v a      + +v++++  e+l+e+a++r e++g  +
  gi|336253054|ref|YP_004596161.1|  81 VAVMADR-LDLEPGDEVLEIGTGCGYHAAVTAE--IVGPENVYSVEYGEQLAEQARARLEEIG--Y 141
                                       4444444.35577899**************999..54699******************99998..4 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.14      28      88 ..      78     138 ..      74     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHH CS
                              DOT1  28 peflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkee 88 
                                       p++++ + d+++l++ d  +++G G G     +a  vg ++ + vE  ++ +e a+++ ee
  gi|336253054|ref|YP_004596161.1|  78 PHMVAVMADRLDLEPGDEVLEIGTGCGYHAAVTAEIVGPENVYSVEYGEQLAEQARARLEE 138
                                       6789999*********************************************999887665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.15      20      62 ..      90     155 ..      20     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlren.gf.svtgvDlspeaveiae.....................k 62 
                                       l++g +vL+iG+G G+ + v +e  g  +v+ v+  +++ e a+                      
  gi|336253054|ref|YP_004596161.1|  90 LEPGDEVLEIGTGCGYHAAVTAEIvGPeNVYSVEYGEQLAEQARarleeigygeidvrigdgrngW 155
                                       57788**********888888665366789999998888888777777777774444333333331 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0002      0.26      22      94 ..      83     156 ..      80     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                                       HHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST CS
                               MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve 94 
                                       ++++ l+ e  ++vl +G+G G+ +a+ a+     +v  v+   +  e a++ le+ +   ++v+  d+ + ++
  gi|336253054|ref|YP_004596161.1|  83 VMADRLDLEPGDEVLEIGTGCGYHAAVTAEIVGPENVYSVEYGEQLAEQARARLEEIGYGeIDVRIGDGRNGWA 156
                                       788999999999*******************99999******99999999999999887778888888888776 PP

>> DUF2795  Protein of unknown function (DUF2795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00015       0.2       8      38 ..      22      52 ..      17      56 .. 0.89
   2 ?   -3.5   0.2       9.8   1.3e+04      11      19 ..     126     134 ..     126     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                           DUF2795  8 atKdeLveyArrngApdevleaLeaLPdreY 38
                                      a ++  v+   +  A+d+vleaLe+ P+ e+
  gi|336253054|ref|YP_004596161.1| 22 AARERMVRTVAHRVADDRVLEALEDVPRHEF 52
                                      67888899999999*************9998 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.8
                           DUF2795  11 deLveyArr 19 
                                       ++L+e+Ar 
  gi|336253054|ref|YP_004596161.1| 126 EQLAEQARA 134
                                       689999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.34
# Mc/sec: 1952.16
//
Query:       gi|336253055|ref|YP_004596162.1|  [L=253]
Description: protein-L-isoaspartate(D-aspartate) O-methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-36  126.1   0.0    2.1e-36  125.7   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.9e-08   33.7   0.0    4.2e-08   33.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.4e-05   24.7   0.0    2.2e-05   24.1   0.0    1.3  1  MTS              Methyltransferase small domain
    2.3e-05   25.0   0.1    5.6e-05   23.8   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.022   15.5   0.0      0.058   14.1   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
      0.029   13.8   0.0      0.044   13.2   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.034   14.4   0.1      0.074   13.3   0.0    1.6  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.038   13.6   0.0      0.072   12.7   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.039   13.2   0.0      0.061   12.6   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.049   12.8   0.0      0.064   12.4   0.0    1.2  1  Fibrillarin      Fibrillarin
      0.052   13.3   0.1      0.093   12.5   0.1    1.3  1  Met_10           Met-10+ like-protein
      0.079   13.1   0.1       0.18   12.0   0.1    1.5  1  ACP_syn_III_C    3-Oxoacyl-[acyl-carrier-protein (ACP)] synth


Domain annotation for each model (and alignments):
>> 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 !  125.7   0.0   1.4e-39   2.1e-36      12     191 ..      18     192 ..       7     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: 125.7 bits;  conditional E-value: 1.4e-39
                                       HTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHH CS
                              PCMT  12 kkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevGsGsGylt 88 
                                       +k v+++++va a+++v+R+efv++  +++aY d   ++ +++ + ap++ a++l+ l+l++g +vL vG+G Gy +
  gi|336253055|ref|YP_004596162.1|  18 AKDVLRDEAVAVAMRDVPRHEFVDD--ERAAYADREHEV-FGTRVLAPSTAARMLQALDLEEGHSVLIVGAGVGYTA 91 
                                       567899*******************..89*******988.678899******************************* PP

                                       HHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS--HHHHHTEEE CS
                              PCMT  89 avlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiPealidQLke 165
                                       av a+l ge   v +i+  + lv ea+ nl   ++e v v   DG  G +e+aP+d+i++ aaa + P+al +QL++
  gi|336253055|ref|YP_004596162.1|  92 AVAAELAGEAN-VHAIDIARPLVYEARGNLASAGYEGVLVDRRDGADGLPEYAPFDRILLEAAAVDPPRALRKQLAD 167
                                       ********988.99*************************************************************** PP

                                       EEEEEEEESBSSSEEEEEEEEETTTE CS
                              PCMT 166 GGrlvvPvgeeeeQvlklvdkkadgk 191
                                        Grlv+P g +++Q+l++v  ++d +
  gi|336253055|ref|YP_004596162.1| 168 DGRLVLPRG-SQSQRLEVVTADGDRE 192
                                       *********.9******999887655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   2.8e-11   4.2e-08       4     136 ..      77     226 ..      72     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.8e-11
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlil 79 
                                       g +vl +G+G G+ + ++a el  +a+v+ iDi    +  Ar n+++ g++ v + + d  + l++    ++fD il
  gi|336253055|ref|YP_004596162.1|  77 GHSVLIVGAGVGYTAAVAA-ELAGEANVHAIDIARPLVYEARGNLASAGYEGVLVDRRDGADgLPEY---APFDRIL 149
                                       6678889************.77778****************************************73...68***** PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedpr..........................llaelpakveeeskaye 130
                                            +a  dp+ +l++    l ++g+l++   +                          ++ e+ + ve++++a+e
  gi|336253055|ref|YP_004596162.1| 150 LE---AAAVDPPRALRK---QLADDGRLVLPRGSqsqrlevvtadgdrerrgpvafdpllVEGEQSGAVERNRTARE 220
                                       98...667999999998...999999999988887777777777777777766666666666666666666666666 PP

                   Methyltransf_31 131 vvegak 136
                                       +ve+a+
  gi|336253055|ref|YP_004596162.1| 221 DVEHAQ 226
                                       666666 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.5e-08   2.2e-05       9     101 ..      53     148 ..      49     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.5e-08
                                       TSTTTTS--HHHHH.HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EE CS
                               MTS   9 gvFskdklDkGskl.LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.ve 83 
                                        vF ++ l   ++  +l++l+ e+ ++vl +G+G+G+ +a++a+   ea+v+++d+    +  a+ nl++ + e v 
  gi|336253055|ref|YP_004596162.1|  53 EVFGTRVLAPSTAArMLQALDLEEGHSVLIVGAGVGYTAAVAAELAGEANVHAIDIARPLVYEARGNLASAGYEgVL 129
                                       56666666666543399*****99*************************************************9777 PP

                                       EEE-STTTTSTT.S-EEEE CS
                               MTS  84 vvasdvleevee.kkfdli 101
                                       v  +d+ + ++e + fd i
  gi|336253055|ref|YP_004596162.1| 130 VDRRDGADGLPEyAPFDRI 148
                                       7788888888742456666 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   3.7e-08   5.6e-05       1      84 [.      80     163 ..      80     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.7e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       vL +G+G G +++ +a+  g+a+v+++Di+  ++ +ar +++++g+  v + + d  d   e + fD +++  a  +
  gi|336253055|ref|YP_004596162.1|  80 VLIVGAGVGYTAAVAAELAGEANVHAIDIARPLVYEARGNLASAGYeGVLVDRRDGADGLPEYAPFDRILLE-AAAV 155
                                       789*******9999999999***********************999888888899988555778*****994.4333 PP

                                       SSHHHHHH CS
                   Methyltransf_25  77 lsdedlek 84 
                                        +++ l+k
  gi|336253055|ref|YP_004596162.1| 156 DPPRALRK 163
                                       33444444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.9e-05     0.058       1      47 [.      81     127 ..      81     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.9e-05
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennn 47 
                                       L +G+G+G ++++ +e   +++++++Di +  +  a+  la+ + + 
  gi|336253055|ref|YP_004596162.1|  81 LIVGAGVGYTAAVAAELAGEANVHAIDIARPLVYEARGNLASAGYEG 127
                                       569******************************99999888877654 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.9e-05     0.044     151     207 ..      68     123 ..      55     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                              PrmA 151 clealeklvkegeevlDvGtGSGiL.aiaaakLgakkvvavDiDevAvkvakeNaelN 207
                                        l+al+  ++eg++vl vG+G G   a+aa + g ++v+a+Di    v  a+ N++  
  gi|336253055|ref|YP_004596162.1|  68 MLQALD--LEEGHSVLIVGAGVGYTaAVAAELAGEANVHAIDIARPLVYEARGNLASA 123
                                       455555..67899**********76268888889************9*9999998765 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 ?   13.3   0.0     5e-05     0.074      44     101 ..      44     110 ..      15     134 .. 0.79
   2 ?   -3.4   0.0       7.3   1.1e+04      10      36 ..     169     193 ..     169     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                                       H......TTTCEEEEE--TTTHHHHHHHH.HTTS..SEEEE-SSGGGHHHHHHHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  44 a......lgvrfeaialdaenyeavLaal.lkeg..dlvvnlsppissldvlkaCietgvhyvdtsi 101
                                               ++ f ++ l ++  + +L+al l+eg   l+v + + + ++  ++++ e+ vh +d++ 
  gi|336253055|ref|YP_004596162.1|  44 RaayadrEHEVFGTRVLAPSTAARMLQALdLEEGhsVLIVGAGVGYTAAVAAELAGEANVHAIDIAR 110
                                       13334447888***********************99999*************************664 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.3
                                       HHHHHHHHHCTCCT-GEEEEEESSHHH CS
                   Sacchrp_dh_NADP  10 Gqavaellarhfdvdaeitvadrskek 36 
                                       G+ v++  ++++ +  e++ ad ++e+
  gi|336253055|ref|YP_004596162.1| 169 GRLVLPRGSQSQRL--EVVTADGDRER 193
                                       66777777777777..88888888876 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 ?   12.7   0.0   4.8e-05     0.072       2      87 ..      70     152 ..      69     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                                       HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgge 78 
                                       ++L+++e+  +l + a+ G   +  ael + +++v A+d+ +  + +   nl   g + + v + D+         +
  gi|336253055|ref|YP_004596162.1|  70 QALDLEEGHSVLIVGAGVGYTAAVAAEL-AGEANVHAIDIARPLVYEARGNLASAGYEGVLVDRRDGADGLPEY--A 143
                                       57999999****9999998877777777.999**************************9999888887653333..4 PP

                                       .EEEEEEEE CS
                   Methyltr_RsmB-F  79 lfDriLlDa 87 
                                        fDriLl+a
  gi|336253055|ref|YP_004596162.1| 144 PFDRILLEA 152
                                       5******98 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.1e-05     0.061      53     109 ..      67     124 ..      62     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                                       HHHTTTT--TT-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS- CS
                              CMAS  53 lileklelkpGmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeld 109
                                       ++l+ l+l++G+ +L +G+G G+++  a+e   +++v ++ + +     a+ ++++++
  gi|336253055|ref|YP_004596162.1|  67 RMLQALDLEEGHSVLIVGAGVGYTAAVAAELAgEANVHAIDIARPLVYEARGNLASAG 124
                                       67999*********************99986525888888877766666666666665 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.3e-05     0.064      59     105 ..      65     110 ..      21     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                                       HHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSH CS
                       Fibrillarin  59 ilkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsp 105
                                         + l+ l +++g++vL +Ga+ G t++  +++ g e+ v+a++ + 
  gi|336253055|ref|YP_004596162.1|  65 AARMLQALDLEEGHSVLIVGAGVGYTAAVAAELAG-EANVHAIDIAR 110
                                       456688899*************************9.999***99875 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   6.2e-05     0.093      93     132 ..      67     108 ..      61     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-05
                                       HHHTT..--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES CS
                            Met_10  93 rlakl..veegevVvdvfAGiGpfaipiakyskakrvlaidl 132
                                       r+ +    eeg  V+ v AG+G+ a ++a ++ +  v aid+
  gi|336253055|ref|YP_004596162.1|  67 RMLQAldLEEGHSVLIVGAGVGYTAAVAAELAGEANVHAIDI 108
                                       444443589********************************8 PP

>> 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 ?   12.0   0.1   0.00012      0.18      56      85 ..      64      93 ..      60      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                      HHHHHHHTTSS-TT-EEEEEEEETTTEEEE CS
                     ACP_syn_III_C 56 aLdeaveegklkpgdlvllvgfGaGltwga 85
                                      + +++++  +l++g+ vl+vg+G+G+t + 
  gi|336253055|ref|YP_004596162.1| 64 TAARMLQALDLEEGHSVLIVGAGVGYTAAV 93
                                      5567788889*****************775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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):              12  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2067.15
//
Query:       gi|336253056|ref|YP_004596163.1|  [L=710]
Description: response regulator receiver modulated GAF sensor protein [Halopiger xanaduensis SH-6]
Scores for 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  111.7  10.9    2.9e-32  111.7  10.9    2.9  2  BAT           GAF and HTH_10 associated domain
    1.1e-25   90.6   7.7    1.5e-14   54.5   0.9    2.6  2  GAF_2         GAF domain
    1.3e-22   80.1   0.0    3.3e-22   78.8   0.0    1.7  1  Response_reg  Response regulator receiver domain
    6.6e-20   70.7   0.1    2.1e-19   69.0   0.1    2.0  1  HTH_10        HTH DNA binding domain
    3.1e-09   37.3   0.2    0.00041   20.7   0.0    2.9  2  GAF_3         GAF domain
      5e-06   26.8   0.3    4.1e-05   23.8   0.0    2.6  3  OKR_DC_1_N    Orn/Lys/Arg decarboxylase, N-terminal domain
    2.4e-05   24.9   0.1    0.00035   21.2   0.0    2.5  2  GAF           GAF domain
  ------ inclusion threshold ------
       0.39   10.9   2.3       0.89    9.7   0.1    2.2  2  RasGAP_C      RasGAP C-terminus


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.1       0.3   6.7e+02      18      89 ..     352     423 ..     341     430 .. 0.77
   2 !  111.7  10.9   1.3e-35   2.9e-32       1     146 [.     494     636 ..     494     644 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.3
                               BAT  18 valaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtlleltvsgpsl 89 
                                        +la++   r++   +++++   +++ + +d a ++++rd a   + ve vr   e++d  ++e  +++++ 
  gi|336253056|ref|YP_004596163.1| 352 ERLADTDRYRFAWLATTDDEPPAPTAWAGIDAAYVDRIRDDAPYSPEVELVRDALETNDVRVVENVLEDDTW 423
                                       466666666666666666666677788888999999999999999999999999999999999988877765 PP

  == domain 2  score: 111.7 bits;  conditional E-value: 1.3e-35
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       D+++eLel+++d++ +l+++++++d+ v+leg+++r+d+  + f+++    ++++ ++++d  +v++v+ vs++dd+
  gi|336253056|ref|YP_004596163.1| 494 DSRLELELRCTDPRMLLNRVTERVDGPVALEGVIDRGDE-IVTFVSAPT--TAAIPELVADKASVTSVSEVSDGDDE 567
                                       899********************************9996.889****99..569*********************** PP

                               BAT  78 tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrerer 146
                                       +l+e+tv+ +++++ l  +++ +r+a  edg ++l++evP++++ Rs+ve ++e+yp++eL arre++ 
  gi|336253056|ref|YP_004596163.1| 568 SLFEVTVEPTPFFEILRGYDVALRTAIGEDGATTLTLEVPQRVEPRSLVESIAETYPETELEARRETTT 636
                                       ******************************************************************985 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   1.0   2.9e-13   6.4e-10       3     138 .]     160     298 ..     158     298 .. 0.74
   2 !   54.5   0.9   6.6e-18   1.5e-14       2     137 ..     341     482 ..     340     483 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 2.9e-13
                                       HHHHHHHHHHHHHHHS.S..EE.EEEEE-TTS-EEEEEEEES-TTSTT-S-B--..-TTHHHHHHHHTS-EEES-GG CS
                             GAF_2   3 dleelldlvldelvel.gaalg.yillvdddgglrlaawgeaeeefgaaldrpl..geglvgealrtgrpvilndle 75 
                                       +  e+++ ++d++ ++ ++ l+  ++++  +g+l+ aa++  +      +   +  ge+ v++a+ +g + + +dle
  gi|336253056|ref|YP_004596163.1| 160 SKAEIYRSAVDTAGDIlDVPLAvAYAFDPTAGRLERAAATDSQTLAEPVA--TMqrGESRVWDAFSEGDSAYYEDLE 234
                                       6789***********66988772555555666655444444444444444..33348888***************99 PP

                                       G....-S-HHHHH.HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  76 e....dpdkkglp.aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                            ++ ++++p  +  + rs+l+vPl   g ++Gvl   +++ ++fde+  elL  la+    a++
  gi|336253056|ref|YP_004596163.1| 235 CdevaEAGQDPAPtPRTDRGRSELIVPL---G-THGVLIARTEDADGFDETMTELLHILAANTEAALD 298
                                       94555444455554455555555*****...9.*******9999999**************9999885 PP

  == domain 2  score: 54.5 bits;  conditional E-value: 6.6e-18
                                       HHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B....---TTHHHHHHHHTS-EEES- CS
                             GAF_2   2 adleelldlvldelvelg.aalgyillvdddgglrlaawgeaeeefgaaldr....plgeglvgealrtgrpvilnd 73 
                                       a+ ee+ ++v+++l++++  ++++++  dd++     aw++ ++   +++++    +++  lv +al+t+   ++++
  gi|336253056|ref|YP_004596163.1| 341 ATREEIESIVCERLADTDrYRFAWLATTDDEPP-APTAWAGIDAAYVDRIRDdapySPEVELVRDALETNDVRVVEN 416
                                       7899*************77********887764.355999999999888888643244666**************** PP

                                       GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  74 leedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       + ed+ +++ +  a   g+++ lavPl++++r  Gvl++   + +a    ++++L+el+e+i+ ai
  gi|336253056|ref|YP_004596163.1| 417 VLEDDTWNRRRkeALTYGFQTVLAVPLVDDERQRGVLVVHVGGADAIGGGERDVLSELGETIGHAI 482
                                       6665555555544****************99********9999999*******************9 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   1.5e-25   3.3e-22       1     105 [.       7     112 ..       7     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 1.5e-25
                                       EEEESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlle..eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpvi 75 
                                       vl+vd++p +++l +++le  +e + +   a++++ealell+++++d+i+ D +mp m+Glell+++re+dp+lp i
  gi|336253056|ref|YP_004596163.1|   7 VLVVDNEPGFAALAEEMLEreREAI-DAVPATSADEALELLEQRAIDCIVSDYEMPAMSGLELLERVREDDPDLPFI 82 
                                       89*****************755666.77789********************************************** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpe 105
                                       ++t++++ee+a ea+ ag+ ++l+K    e
  gi|336253056|ref|YP_004596163.1|  83 LFTGRGSEEVASEAIAAGVTQYLQKGTGDE 112
                                       *************************87665 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.1   9.4e-23   2.1e-19       1      52 [.     650     701 ..     650     702 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 9.4e-23
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT+kqle+l++A+ +G+F++PR++t ++LA +l +s++t+++hLr+a++kl+
  gi|336253056|ref|YP_004596163.1| 650 LTEKQLEALQAAHYSGFFEWPRETTGEDLAATLSVSAPTYHYHLRAAQRKLV 701
                                       9*************************************************98 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   2.6e-05     0.058       3     123 ..     162     293 ..     160     299 .. 0.79
   2 !   20.7   0.0   1.8e-07   0.00041      74     127 ..     429     482 ..     349     484 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse..sldedsalarralssgevvsepsfaeedg 77 
                                        e++ ++++ + ++l++  ++ + +d+   +l +aa++d +   +   ++ ++++  + a+s+g  ++  + ++ + 
  gi|336253056|ref|YP_004596163.1| 162 AEIYRSAVDTAGDILDVPLAVAYAFDPTAGRLERAAATDSQTLAEPvaTMQRGESRVWDAFSEGDSAYYEDLECDEV 238
                                       689999**********************99*******9777666556566699999999999999888855555222 PP

                             GAF_3  78 .............lpdraalavPLvagrqviGvlalastkprafdaedlelleslArqi 123
                                                     ++r+ l+vPL +     Gvl +++ +   fd++ +ell  lA+ +
  gi|336253056|ref|YP_004596163.1| 239 aeagqdpaptprtDRGRSELIVPLGT----HGVLIARTEDADGFDETMTELLHILAANT 293
                                       2222333333444578**********....9************************9866 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.8e-07
                             GAF_3  74 eedglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                       e+ ++  + +lavPLv+ ++ +Gvl+++  +  a++  +++ l++l+  i+ ai
  gi|336253056|ref|YP_004596163.1| 429 EALTYGFQTVLAVPLVDDERQRGVLVVHVGGADAIGGGERDVLSELGETIGHAI 482
                                       234467899********99********************************999 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.8e-08   4.1e-05      14     111 .]      27     128 ..      13     128 .. 0.83
   2 ?   -2.3   0.0       2.3   5.2e+03       5      44 ..     140     176 ..     137     197 .. 0.73
   3 ?   -1.7   0.0       1.5   3.4e+03      74     110 ..     651     688 ..     645     689 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.8e-08
                        OKR_DC_1_N  14 ekegfevvgvtstdDllsvieqnsriaavvlsvd...deaaelldeirernedlPvFllaetrtsedvpadvlreid 87 
                                       e+e ++ v +ts d++l+++eq  +i+++v +++    +  ell+ +re  +dlP  l++ + ++e ++  + + ++
  gi|336253056|ref|YP_004596163.1|  27 EREAIDAVPATSADEALELLEQ-RAIDCIVSDYEmpaMSGLELLERVREDDPDLPFILFTGRGSEEVASEAIAAGVT 102
                                       3455667889***********9.89***********9999*******************998899999999999999 PP

                        OKR_DC_1_N  88 gfiel..ledtpefiarqieaaakkY 111
                                       ++++    +++   +a+qi  a+++Y
  gi|336253056|ref|YP_004596163.1| 103 QYLQKgtGDEQYTLLANQITNAVSQY 128
                                       *999943444455689*******999 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.3
                        OKR_DC_1_N   5 airelaealekegfevvgvtstdDllsvieqnsriaavvl 44 
                                       + ++  + l+++++++++++s     +++++  + a+ +l
  gi|336253056|ref|YP_004596163.1| 140 RYERTLTTLHETTRDLMRAESKA---EIYRSAVDTAGDIL 176
                                       55666778889999999999998...55555555555555 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.5
                        OKR_DC_1_N  74 tsedvpadvlreidgfiel.ledtpefiarqieaaakk 110
                                       t+++++a   ++ +gf+e+  e+t e++a  ++ +a  
  gi|336253056|ref|YP_004596163.1| 651 TEKQLEALQAAHYSGFFEWpRETTGEDLAATLSVSAPT 688
                                       66666666777788999998899999998887766655 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.28   6.2e+02       4     132 ..     163     296 ..     160     297 .. 0.55
   2 !   21.2   0.0   1.6e-07   0.00035      42     109 ..     378     457 ..     343     482 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHTESEEEEEE..EEETTEEECEEEEECC.....EEEETTSHHHHHHHHHSSSEEESTGGTSTTH CS
                               GAF   4 elldtvveelrellgadrvalyl..pdydGlhydipqasrw.....lfmkngrgicgqvlatgqplvipdstpdprf 73 
                                       e+ + +v++++++l++  +++y   p++  l+      s+        m+ g++++  ++++g++   +d+  d+  
  gi|336253056|ref|YP_004596163.1| 163 EIYRSAVDTAGDILDVPLAVAYAfdPTAGRLERAAATDSQTlaepvATMQRGESRVWDAFSEGDSAYYEDLECDEV- 238
                                       5677778888888888877777654433333221222222222233344445556667777777777776432222. PP

                                       HTT..HHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHH CS
                               GAF  74 aqy..nrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvava 132
                                       a++      + +    rs l vPl  +    G+l +  +++  f++   ell  la+  + a
  gi|336253056|ref|YP_004596163.1| 239 AEAgqDPAPTPRTDRGRSELIVPLGTH----GVLIARTEDAdGFDETMTELLHILAANTEAA 296
                                       111233334445555667788888764....6666666444578888888888887766655 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.6e-07
                                       C...............EEEETTSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEE CS
                               GAF  42 w...............lfmkngrgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwG 103
                                       w               ++ ++++ ++  +l+t+++ v++++ +d+ +++  rr+ +  +g++++l+vPlv+d++  G
  gi|336253056|ref|YP_004596163.1| 378 WagidaayvdrirddaPYSPEVE-LVRDALETNDVRVVENVLEDDTWNR--RRKEALTYGFQTVLAVPLVDDERQRG 451
                                       23333333333333322222233.35689***********99*******..999*****************9999** PP

                                       EEEEEE CS
                               GAF 104 llvlhn 109
                                       +lv+h 
  gi|336253056|ref|YP_004596163.1| 452 VLVVHV 457
                                       ****96 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0004      0.89      24      82 ..     111     171 ..     106     202 .. 0.88
   2 ?   -0.0   0.3       0.4   8.9e+02      19      44 ..     318     343 ..     307     350 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0004
                          RasGAP_C  24 ennyqellneIakdirnkgrlrekrkeElesleetlktLseknnyl...esqlesYkayien 82 
                                       + +y  l n+I++ + + +   e r++E  + e tl+tL+e ++ l   es+ e Y++ +++
  gi|336253056|ref|YP_004596163.1| 111 DEQYTLLANQITNAVSQYRAETELRESER-RYERTLTTLHETTRDLmraESKAEIYRSAVDT 171
                                       679*************************6.6899********99874446778888887776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.4
                          RasGAP_C  19 gvisrennyqellneIakdirnkgrl 44 
                                       + ++r n+ +e++ eI++ i++  ++
  gi|336253056|ref|YP_004596163.1| 318 EELTRLNHINEIVREINHGIAQAATR 343
                                       56899999999999999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (710 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 4976.99
//
Query:       gi|336253057|ref|YP_004596164.1|  [L=793]
Description: methyl-accepting chemotaxis sensory transducer [Halopiger xanaduensis SH-6]
Scores for 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-41  140.2  25.5    5.7e-41  140.2  25.5    5.9  6  MCPsignal     Methyl-accepting chemotaxis protein (MCP) signa
    4.9e-08   33.2  16.0    7.5e-06   26.2   0.1    5.2  5  HAMP          HAMP domain
    1.1e-06   28.6   0.4    1.1e-06   28.6   0.4    5.1  5  dCache_1      Cache domain
     0.0021   18.2  27.9     0.0021   18.2  27.9    5.4  4  ATP-synt_B    ATP synthase B/B' CF(0)
     0.0096   16.0  12.0     0.0096   16.0  12.0    5.6  5  TPR_MLP1_2    TPR/MLP1/MLP2-like protein
  ------ inclusion threshold ------
       0.15   12.7   7.8        8.6    7.1   0.0    4.5  5  SnoaL_2       SnoaL-like domain
       0.34   11.2  51.9       0.75   10.1   1.1    8.2  9  DUF948        Bacterial protein of unknown function (DUF948)
       0.43   10.7  45.2        0.6   10.2   0.0    5.3  4  Mod_r         Modifier of rudimentary (Mod(r)) protein
       0.54   10.1   4.8        2.9    7.7   0.1    3.9  4  SnoaL         SnoaL-like polyketide cyclase
       0.86    9.5  10.6        3.6    7.4   0.2    5.3  6  DASH_Dam1     DASH complex subunit Dam1
        4.4    7.5  41.0      0.029   14.6   3.5    5.3  6  Fib_alpha     Fibrinogen alpha/beta chain family
        4.8    7.2  57.3      0.041   13.9   6.9    6.6  7  Laminin_II    Laminin Domain II


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.4      0.72   1.1e+03      86     126 ..      65     105 ..      49     146 .. 0.63
   2 ?    2.6   1.5     0.073   1.1e+02      98     161 ..     320     386 ..     315     401 .. 0.77
   3 ?    0.1   3.0      0.41   6.1e+02     111     160 ..     371     420 ..     357     437 .. 0.47
   4 ?    1.1  25.6       0.2     3e+02       2     162 ..     388     549 ..     387     551 .. 0.89
   5 !  140.2  25.5   3.8e-44   5.7e-41       1     171 [.     542     726 ..     542     727 .. 0.98
   6 !    6.1   4.9     0.006         9     131     169 ..     721     759 ..     718     762 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.72
                                       HHHHHHHHHH..............HHHHHHHHHHHHHHHHH CS
                         MCPsignal  86 qaakeiealiieiqkeindsvesleetrqrveegselveet 126
                                       +aa+  ++ i + +++ nd +  ++++++ +++  ++ + +
  gi|336253057|ref|YP_004596164.1|  65 NAAEREADGIDKFVQDRNDNTVEISNSVNLANTDKSQLRAS 105
                                       33333444566666777777777777777776666655544 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.073
                                       ............HHHHHHHHHHHHHHHHHC...CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  98 iqkeindsvesleetrqrveegselveetg...ealkeiveavaevadlvqeiaaaseeqsasieev 161
                                       i +++n+s+e ++   + +eeg  +ve  +   +++ ++    a++ d++qe  + +e+q++ +e  
  gi|336253057|ref|YP_004596164.1| 320 ISRDVNNSLEEMTGYAEAIEEGNLEVEIDQsriDEFGQLGGLFARIRDTLQERLTEVEQQAQEAERA 386
                                       6899*****************9888765550015566677889999999999999999999877654 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 111 etrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasiee 160
                                       e  ++ve+ ++++e+++e+ +   +++++ +++ qe +a +e +s+ +ee
  gi|336253057|ref|YP_004596164.1| 371 ERLTEVEQQAQEAERAREQAEVSKAEAQQAKAEAQEAKAEAEALSQHLEE 420
                                       33344444444444444443333333444444444444444333333333 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHH CS
                         MCPsignal   2 dlaeeaseeAeeggkevanvvkqmeeieks.skeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEV 77 
                                       + ae ++ eA++ + e +++ ++ e+++++  ++  +  + i+  ad      L  a E     e Gr F     ++
  gi|336253057|ref|YP_004596164.1| 388 EQAEVSKAEAQQAKAEAQEAKAEAEALSQHlEEKADEYRQSIEAAADGDLTRRLETASESEAMTEIGRAFNEMLTDI 464
                                       578899999999999999999999999999444566677888888888888889999999999999*********** PP

                                       HHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  78 rkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeq 154
                                        ++  r +  a+++++   e+++ +++  +s  e+ + +ee s  +e+ +e+l + ++++++++++v+eia++s+  
  gi|336253057|ref|YP_004596164.1| 465 EAMVVRIQTVANQVDEKSSEVTASTEEIRASSGEVAESIEEISAGAETQNEKLTTAAAEMSDLSATVEEIASSSNTV 541
                                       ******************9****999999999999999999999999999999999999999999999999999999 PP

                                       HHHHHHHH CS
                         MCPsignal 155 sasieevn 162
                                       +  +e+ +
  gi|336253057|ref|YP_004596164.1| 542 ADQSEQAA 549
                                       99888865 PP

  == domain 5  score: 140.2 bits;  conditional E-value: 3.8e-44
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                         MCPsignal   1 sdlaeeaseeAeeggkevanvvkqmeeieks..............skeisdiieVideiadQTNlLALNAaiEAARA 63 
                                       +d +e+a e+ +eg++  ++vv+qm+ ie++              ++ i +++e id+ia+ TN+LALNA+iEAA A
  gi|336253057|ref|YP_004596164.1| 542 ADQSEQAAERGQEGQEAASDVVEQMDRIESKavdtaeematlqeeVERIGEVVELIDQIAEETNMLALNASIEAATA 618
                                       57899999999*******************9********************************************** PP

                                       CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH CS
                         MCPsignal  64 GeqGrGFaVVAdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaev 140
                                       Ge+G+GFaVVA+EV++LAe++a+a++e+e+l++ +++ ++++++ + e r  +e g e++++t ++l++iv+++++ 
  gi|336253057|ref|YP_004596164.1| 619 GEAGDGFAVVANEVKSLAEETAEATEEVEDLVETVEASTESVADDMFEMRDGIEDGRETIDRTVDTLESIVDSIDDA 695
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 141 adlvqeiaaaseeqsasieevnqaveevakv 171
                                       ++ +q i+ a+++q+ s++ev++ v+ +a+v
  gi|336253057|ref|YP_004596164.1| 696 NAGIQSINDATDDQADSAQEVSSMVDDIAAV 726
                                       **************************99987 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 131 keiveavaevadlvqeiaaaseeqsasieevnqaveeva 169
                                        +i++  ++ ad+ q+++aa+eeq+++i++++++ e ++
  gi|336253057|ref|YP_004596164.1| 721 DDIAAVSEQTADEAQNVSAAAEEQTSAISQISDSAESLS 759
                                       6789999999***********************998765 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1     5e-09   7.5e-06       2      53 .]     320     371 ..     319     371 .. 0.95
   2 !   13.2   1.1   5.9e-05     0.088      15      52 ..     427     465 ..     426     466 .. 0.89
   3 ?    1.1   0.1      0.36   5.4e+02      11      31 ..     515     533 ..     492     538 .. 0.80
   4 ?   -1.9   0.1       3.1   4.6e+03       9      37 ..     589     621 ..     587     623 .. 0.69
   5 ?   -2.0   0.1       3.4   5.1e+03      12      44 ..     750     772 ..     744     777 .. 0.58

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5e-09
                                       HHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHHH CS
                              HAMP   2 larrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLre 53 
                                       ++r + ++L++++  a++i +G+l++ ++ s+ DE+G+L+  f + +d L+e
  gi|336253057|ref|YP_004596164.1| 320 ISRDVNNSLEEMTGYAEAIEEGNLEVEIDQSRIDEFGQLGGLFARIRDTLQE 371
                                       7888999****************************************99985 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.9e-05
                                       HHHHHHTTTBTSSTCCTTSSSH.HHHHHHHHHHHHHHHH CS
                              HAMP  15 raarriaaGdldtrlpvsgrDE.iGeLarafNaMldrLr 52 
                                       +++++ a+Gdl+ rl++ +  E + e++rafN+Ml+ ++
  gi|336253057|ref|YP_004596164.1| 427 QSIEAAADGDLTRRLETASESEaMTEIGRAFNEMLTDIE 465
                                       6788999**********8888878***********9886 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHTTTBTSSTCCT CS
                              HAMP  11 rrLaraarriaaGdldtrlpv 31 
                                       ++L++aa++++  dl++++++
  gi|336253057|ref|YP_004596164.1| 515 EKLTTAAAEMS--DLSATVEE 533
                                       47888888888..88887665 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHTTT....BTSSTCCTTSSSHH CS
                              HAMP   9 PLrrLaraarriaaG....dldtrlpvsgrDEi 37 
                                       ++ ++++ +++ia+      l+++++  +  E 
  gi|336253057|ref|YP_004596164.1| 589 RIGEVVELIDQIAEEtnmlALNASIEAATAGEA 621
                                       678888888888875566677777777666665 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 3.4
                                       HHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHH CS
                              HAMP  12 rLaraarriaaGdldtrlpvsgrDEiGeLaraf 44 
                                       +++++a+++++          +  E+  L + f
  gi|336253057|ref|YP_004596164.1| 750 QISDSAESLSE----------RAQELQSLTAHF 772
                                       45555555554..........356666666666 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.4   7.3e-10   1.1e-06       3     246 ..      55     282 ..      53     285 .. 0.70
   2 ?    0.6   2.2      0.27     4e+02       8      53 ..     404     457 ..     397     476 .. 0.67
   3 ?   -0.4   1.2      0.55   8.2e+02      15      52 ..     471     509 ..     462     567 .. 0.62
   4 !    5.9   0.6    0.0064       9.5       9      77 ..     630     702 ..     626     717 .. 0.64
   5 ?   -1.4   2.2       1.1   1.7e+03      16      66 ..     728     774 ..     721     789 .. 0.49

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 7.3e-10
                          dCache_1   3 ieeqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksn.pdisgvy 78 
                                       +e++aee ll+ ae+ a+ i+ +++ ++ ++  ++++ +l++           ++++l+a l+++l++  ++++++ 
  gi|336253057|ref|YP_004596164.1|  55 VESDAEETLLNAAEREADGIDKFVQDRNDNTVEISNSVNLAN----------TDKSQLRASLRTYLEALpDSVHAIH 121
                                       6889******************************99855543..........4788899999999988834669**9 PP

                          dCache_1  79 lvdadGqviassdpssppnleg.tddpadrdwykealaggg.gkpvisdpy.vdqtggkpvitiavpiyddsgkfiG 152
                                       +++ +++ + +s+  +    eg t d + r+w  ++ a+g+ g++   +py v  + g+  i +++p+     +   
  gi|336253057|ref|YP_004596164.1| 122 YYSMENDEVEVSTQFN---REGdTVDETTRPWAVDIDAFGSsGDVRSFEPYdV--D-GEKRIGFISPVAG---QDDH 189
                                       9999888888888774...444489*******999999998878888889933..4.99*********65...4556 PP

                          dCache_1 153 vlaadldldnlqdllsniklgetgyvfivdsdGniiahpd......kdllgknlrdelkaqealekalakiesgvss 223
                                       ++++ ++l++ ++ll + ++++ g++ +v  +G+i           +++l+++l+  +   +al  ++ + + +   
  gi|336253057|ref|YP_004596164.1| 190 AIVLVINLEERSELLTS-PIDG-GEIEVVATNGQITLAETtgtilnESFLMGDLSHLED--GALRPRVDQVTAENDV 262
                                       78888888888996664.3444.677777777766554221233334467776655443..4566664444444443 PP

                          dCache_1 224 vklngeeylvayapip..tglgWyl 246
                                           g+++ v +a++p  + ++W +
  gi|336253057|ref|YP_004596164.1| 263 ---VGDDQ-VVVATVPlsE-KDWDV 282
                                       ...35556.4444444435.88855 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.27
                          dCache_1   8 eeqllglaeqlanniedvldslenlaetlasnpslqdlleepnra.........n 53 
                                        +++++ ae l++++e++ d+++++ e  a + +l + le  +            
  gi|336253057|ref|YP_004596164.1| 404 AQEAKAEAEALSQHLEEKADEYRQSIE-AAADGDLTRRLETASESeamteigraF 457
                                       5678888999999******99996555.556788888887655434433333333 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.55
                          dCache_1  15 aeqlanniedvldslenlaetl.asnpslqdlleepnra 52 
                                       ++++an+++++  ++++++e + as+ +++++ ee+++ 
  gi|336253057|ref|YP_004596164.1| 471 IQTVANQVDEKSSEVTASTEEIrASSGEVAESIEEISAG 509
                                       566666666666666666666655555566655555432 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.0064
                          dCache_1   9 eqllglaeqlan...niedvldslenlaetlasn.....pslqdlleepnraneasreslqallksilksnpdisgv 77 
                                       +++++lae++a+   ++ed ++++e+++e +a +       + d+ e ++r    + + l+++++si ++n++i+++
  gi|336253057|ref|YP_004596164.1| 630 NEVKSLAEETAEateEVEDLVETVEASTESVADDmfemrDGIEDGRETIDR----TVDTLESIVDSIDDANAGIQSI 702
                                       555566666555333788889999999999988743332224444444443....5666666666666666666665 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 1.1
                          dCache_1  16 eqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallks 66 
                                       eq+a++ ++v + +e ++  +++ ++ +++l+e      +  +sl+a++++
  gi|336253057|ref|YP_004596164.1| 728 EQTADEAQNVSAAAEEQTSAISQISDSAESLSERA----QELQSLTAHFET 774
                                       45555555555555555555555444444444332....233444444333 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 ?    0.8   0.4      0.32   4.8e+02      52      77 ..      56      81 ..      48     114 .. 0.56
   2 !   18.2  27.9   1.4e-06    0.0021      23     126 ..     364     471 ..     361     476 .. 0.87
   3 ?   -1.1   0.4       1.3   1.9e+03      47      81 ..     637     649 ..     608     681 .. 0.61
   4 ?   -3.6   9.9       7.5   1.1e+04      39     101 ..     702     763 ..     683     782 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.32
                        ATP-synt_B 52 llaeaeqqlkeAraeAaeiiknAkke 77
                                        +++e+ l+ A++eA+ i k ++++
  gi|336253057|ref|YP_004596164.1| 56 ESDAEETLLNAAEREADGIDKFVQDR 81
                                      33455555666666666555544444 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.4e-06
                        ATP-synt_B  23 plkkvLdkReekIadeiaeAeerrkeaaallaeaeqql...keAraeAaeiiknAkkeaeklkeeieaeaeaeaerl 96 
                                       +++++L++R  +++++ +eAe++r++a+  +aea+q++   +eA+aeA+ + ++ +++a + ++ iea+a  +++r+
  gi|336253057|ref|YP_004596164.1| 364 RIRDTLQERLTEVEQQAQEAERAREQAEVSKAEAQQAKaeaQEAKAEAEALSQHLEEKADEYRQSIEAAADGDLTRR 440
                                       6899************************999999998722256799*****************************99 PP

                        ATP-synt_B  97 kesAaa.eIeqekdralaeLreqvvalavqi 126
                                        e+A + e ++e  ra +e+  ++ a+ v i
  gi|336253057|ref|YP_004596164.1| 441 LETASEsEAMTEIGRAFNEMLTDIEAMVVRI 471
                                       9998653788888888888888888887765 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.3
                        ATP-synt_B  47 keaaallaeaeqqlkeAraeAaeiiknAkkeaekl 81 
                                       +e+a+                      A++e e l
  gi|336253057|ref|YP_004596164.1| 637 EETAE----------------------ATEEVEDL 649
                                       11111......................22222222 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 7.5
                        ATP-synt_B  39 iaeAeerrkeaaallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAa 101
                                       i++A   ++++a+  ++  +  + +  + a+  +n+ ++ae++  + + + + +ae+l e A+
  gi|336253057|ref|YP_004596164.1| 702 INDATDDQADSAQEVSSMVDDIAAVSEQTADEAQNVSAAAEEQTSA-ISQISDSAESLSERAQ 763
                                       4444444444444444444444444444444444444444443332.2344444444444443 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  12.0   6.5e-06    0.0096      46     108 ..     370     432 ..     350     435 .. 0.91
   2 ?    3.0   3.7     0.068     1e+02      51      88 ..     481     518 ..     438     529 .. 0.44
   3 ?    3.3   8.5     0.055        82       3      81 ..     527     605 ..     525     620 .. 0.89
   4 !    6.0   1.3    0.0081        12      64     110 ..     630     676 ..     610     697 .. 0.75
   5 !    5.9  11.1    0.0084        13      18     106 ..     693     770 ..     676     784 .. 0.45

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.5e-06
                        TPR_MLP1_2  46 erelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelsel 108
                                       ++ l++ +++++e +++re+++  kae++++kaea++akae e+  +++ee+ +e+++ ++ +
  gi|336253057|ref|YP_004596164.1| 370 QERLTEVEQQAQEAERAREQAEVSKAEAQQAKAEAQEAKAEAEALSQHLEEKADEYRQSIEAA 432
                                       5678889999************************************************99875 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.068
                        TPR_MLP1_2  51 khaedvkelqalreelnelkaeiaelkaeaesakaele 88 
                                       k +e + + +++r+ + e+ + i+e+ a ae+ +++l 
  gi|336253057|ref|YP_004596164.1| 481 KSSEVTASTEEIRASSGEVAESIEEISAGAETQNEKLT 518
                                       22233333334444444444444444444444444444 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.055
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       l++  eei+s ++  +++ +++++  ++ ++ a+ + e  ++ e+  v  ae++ +lq+  e++ e+ + i ++ +e
  gi|336253057|ref|YP_004596164.1| 527 LSATVEEIASSSNTVADQSEQAAERGQEGQEAASDVVEQMDRIESKAVDTAEEMATLQEEVERIGEVVELIDQIAEE 603
                                       56778999999************************************************999999999999998887 PP

                        TPR_MLP1_2  80 ae 81 
                                        +
  gi|336253057|ref|YP_004596164.1| 604 TN 605
                                       65 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0081
                        TPR_MLP1_2  64 eelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselek 110
                                       +e+++l +e ae+++e+e++ +++e+s+es +    e+++ +++ ++
  gi|336253057|ref|YP_004596164.1| 630 NEVKSLAEETAEATEEVEDLVETVEASTESVADDMFEMRDGIEDGRE 676
                                       67788888888888888888888888888877766666666665554 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.0084
                        TPR_MLP1_2  18 eeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesw 94 
                                       ++a+a +q++ +    qa++a+e               v++++a+ e+ ++  + ++ + +e  sa ++++ s es+
  gi|336253057|ref|YP_004596164.1| 693 DDANAGIQSINDATDDQADSAQEVSS-----------MVDDIAAVSEQTADEAQNVSAAAEEQTSAISQISDSAESL 758
                                       44444444444444444444444444...........4444444444444444444444444444444444444444 PP

                        TPR_MLP1_2  95 eeqkeelekels 106
                                       +e+ +el++  +
  gi|336253057|ref|YP_004596164.1| 759 SERAQELQSLTA 770
                                       444444443333 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0057       8.6      34      83 ..      97     142 ..      65     174 .. 0.78
   2 ?   -2.6   0.0         6   8.9e+03      42      74 ..     361     393 ..     352     412 .. 0.76
   3 ?   -0.7   0.1       1.6   2.3e+03      38      72 ..     452     486 ..     412     503 .. 0.64
   4 ?    6.6   0.1    0.0078        12      40      91 ..     514     565 ..     493     574 .. 0.83
   5 ?   -1.8   0.1       3.2   4.8e+03      33      67 ..     643     677 ..     610     708 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0057
                                       ESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEETTSSE CS
                           SnoaL_2  34 rGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgtipatgrg 83 
                                       + + ++ra +r++++a+pd  + ih    ++d+v v+ ++      +g++
  gi|336253057|ref|YP_004596164.1|  97 TDKSQLRASLRTYLEALPDSVHAIHYYSMENDEVEVSTQFNR----EGDT 142
                                       567899*********************999999988877763....3332 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6
                                       HHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEE CS
                           SnoaL_2  42 ffralfaafpdlrfeihdvvadgdrvavewtvt 74 
                                        f++ ++++ ++  e+++ +++ +r+  + +v+
  gi|336253057|ref|YP_004596164.1| 361 LFARIRDTLQERLTEVEQQAQEAERAREQAEVS 393
                                       678888888888889999999999888887776 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEE CS
                           SnoaL_2  38 airaffralfaafpdlrfeihdvvadgdrvavewt 72 
                                       +i ++f +++  ++ + ++i+ v+ + d+   e+t
  gi|336253057|ref|YP_004596164.1| 452 EIGRAFNEMLTDIEAMVVRIQTVANQVDEKSSEVT 486
                                       34445566666666666666666555554444444 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0078
                                       HHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEETTSSEEEEEEEEE CS
                           SnoaL_2  40 raffralfaafpdlrfeihdvvadgdrvavewtvtgtipatgrgvtvrgvdv 91 
                                        + ++++ a+++dl  ++++++ + ++va + +  ++++ +g++   ++v+ 
  gi|336253057|ref|YP_004596164.1| 514 NEKLTTAAAEMSDLSATVEEIASSSNTVADQSEQAAERGQEGQEAASDVVEQ 565
                                       5567788889**********************99999999999988877765 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 3.2
                                       EESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEE CS
                           SnoaL_2  33 lrGreairaffralfaafpdlrfeihdvvadgdrv 67 
                                       ++  e++ + ++a  +++ d  fe++d ++dg++ 
  gi|336253057|ref|YP_004596164.1| 643 TEEVEDLVETVEASTESVADDMFEMRDGIEDGRET 677
                                       44445555555555556666666666666666544 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 ?   -0.1   0.0      0.75   1.1e+03      21      54 ..      64      97 ..      29     124 .. 0.62
   2 ?    1.3   3.7      0.27     4e+02      27      79 ..     382     434 ..     303     442 .. 0.77
   3 ?   10.1   1.1    0.0005      0.75      32      84 ..     447     499 ..     436     503 .. 0.88
   4 ?    7.2   5.2     0.004         6      21      88 ..     468     535 ..     466     554 .. 0.85
   5 ?    4.5   2.9     0.028        42      25      87 ..     521     583 ..     515     585 .. 0.80
   6 ?    3.9   1.4     0.042        63      33      85 ..     557     605 ..     548     612 .. 0.72
   7 ?    9.6   3.9   0.00072       1.1      19      86 ..     627     694 ..     605     704 .. 0.56
   8 ?    8.3   1.7    0.0018       2.6      33      84 ..     676     730 ..     664     732 .. 0.68
   9 ?    7.0   4.0    0.0047       7.1      24      88 ..     702     766 ..     695     767 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.75
                            DUF948 21 llklkktldeaaatieelekqvdpilkevedlla 54
                                      l+ +++ +d + +++++ ++++ +i++ v+ + +
  gi|336253057|ref|YP_004596164.1| 64 LNAAEREADGIDKFVQDRNDNTVEISNSVNLANT 97
                                      3334555566666666666666666666665444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.27
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavad 79 
                                        +++a+++ e+ + ++++   e++++ a++++l + ++ek ++  + +ea+ad
  gi|336253057|ref|YP_004596164.1| 382 EAERAREQAEVSKAEAQQAKAEAQEAKAEAEALSQHLEEKADEYRQSIEAAAD 434
                                       33445555555557777778888888888888888888888877777777765 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0005
                            DUF948  32 aatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                       +++++e+++  +++l+++e+++  +++++++v ek+ +v + te+++  +  v
  gi|336253057|ref|YP_004596164.1| 447 SEAMTEIGRAFNEMLTDIEAMVVRIQTVANQVDEKSSEVTASTEEIRASSGEV 499
                                       46789999***********************************9998877766 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.004
                            DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       +++++ +++++ +   e++  +++i   + ++ + ++e+ ++ + + ek+ +  +++ dl+++v+e+ 
  gi|336253057|ref|YP_004596164.1| 468 VVRIQTVANQVDEKSSEVTASTEEIRASSGEVAESIEEISAGAETQNEKLTTAAAEMSDLSATVEEIA 535
                                       566777788888888888888888888888888888888889999******************99875 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.028
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       +  ++ ++at+ee+ +  + + +++e++ +  +e +e  ++ +e++d++ +++ d++e +++l
  gi|336253057|ref|YP_004596164.1| 521 AAEMSDLSATVEEIASSSNTVADQSEQAAERGQEGQEAASDVVEQMDRIESKAVDTAEEMATL 583
                                       56788999********************99999977777777777777777777777777666 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.042
                            DUF948  33 atieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                       ++  ++ +q+d i  ++ d+ +++ +    ++e++e++ +++e + +++e  +
  gi|336253057|ref|YP_004596164.1| 557 EAASDVVEQMDRIESKAVDTAEEMAT----LQEEVERIGEVVELIDQIAEETN 605
                                       56667778888888888888888777....67777777777777777776654 PP

  == domain 7  score: 9.6 bits;  conditional E-value: 0.00072
                            DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       vv +++k++++e+a++ ee+e+ v+ +   +e + + + e+ +++++  e++d+ ++ ++ + +s+ +
  gi|336253057|ref|YP_004596164.1| 627 VVANEVKSLAEETAEATEEVEDLVETVEASTESVADDMFEMRDGIEDGRETIDRTVDTLESIVDSIDD 694
                                       33334444444444444444444444444444444444446666666666666666666665555544 PP

  == domain 8  score: 8.3 bits;  conditional E-value: 0.0018
                            DUF948  33 atieelekqvdpi...lkevedllakvnelledvneklekvdplteavadlgesv 84 
                                       +ti+ + + +++i   ++++++ ++ +n+ ++d  +  ++v ++++ +a ++e+ 
  gi|336253057|ref|YP_004596164.1| 676 ETIDRTVDTLESIvdsIDDANAGIQSINDATDDQADSAQEVSSMVDDIAAVSEQT 730
                                       4444444444444000466777889999999999999999999999999999875 PP

  == domain 9  score: 7.0 bits;  conditional E-value: 0.0047
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       +++  d  a++ +e+ + vd i   +e++ ++++++ +  +e++ ++ ++ ++++ l+e  +el+
  gi|336253057|ref|YP_004596164.1| 702 INDATDDQADSAQEVSSMVDDIAAVSEQTADEAQNVSAAAEEQTSAISQISDSAESLSERAQELQ 766
                                       55666777777888888888888888888888888888888888888888888888888888876 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 ?    7.8  15.1    0.0023       3.4      30     119 ..     368     458 ..     348     474 .. 0.75
   2 ?   -2.1   9.0       2.5   3.7e+03      17      62 ..     530     575 ..     456     620 .. 0.47
   3 ?   10.2   0.0    0.0004       0.6      19      89 ..     633     704 ..     629     710 .. 0.85
   4 ?    4.2   4.6     0.029        43      27      83 ..     712     768 ..     700     783 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0023
                             Mod_r  30 qlkeekeella..eneslaeknlsl.epeleelrselqekleelkelekefeekeqeldellqkfspdallarLqta 103
                                       +l+e+++e+++  ++ + a+++ +  + e ++ ++e qe+  e+++l++ +eek  e+ + ++   +  l +rL+ta
  gi|336253057|ref|YP_004596164.1| 368 TLQERLTEVEQqaQEAERAREQAEVsKAEAQQAKAEAQEAKAEAEALSQHLEEKADEYRQSIEAAADGDLTRRLETA 444
                                       3444444443300344556666666688**********************************************998 PP

                             Mod_r 104 vaeaeeeSealaeefl 119
                                        +e+e ++e     f 
  gi|336253057|ref|YP_004596164.1| 445 -SESEAMTEI-GRAFN 458
                                       .788888775.55555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.5
                             Mod_r  17 klealvktlpevkqlkeekeellaeneslaeknlslepeleelrse 62 
                                        +e++++++++v ++ e+  e  +e ++ a++  ++ +++e +  +
  gi|336253057|ref|YP_004596164.1| 530 TVEEIASSSNTVADQSEQAAERGQEGQEAASDVVEQMDRIESKAVD 575
                                       1222222223333333333333333333333333333333333333 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0004
                             Mod_r  19 ealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellq 89 
                                       ++l++++ + ++++++  e ++a++es+a++  + ++ +e+ r+ +  + ++l+++ ++ ++ ++  +++ +
  gi|336253057|ref|YP_004596164.1| 633 KSLAEETaEATEEVEDLVETVEASTESVADDMFEMRDGIEDGRETIDRTVDTLESIVDSIDDANAGIQSIND 704
                                       6677766477999*******************************************9999998877776665 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.029
                             Mod_r  27 evkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqe 83 
                                       + +++ +  +++ a  e++a++  +     ee+ s +++  +++++l+++ +e+++ 
  gi|336253057|ref|YP_004596164.1| 712 SAQEVSSMVDDIAAVSEQTADEAQNVSAAAEEQTSAISQISDSAESLSERAQELQSL 768
                                       444444444444444455554444444455555555555555555555555555443 PP

>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0019       2.9      27      78 ..      86     137 ..      61     146 .. 0.81
   2 ?   -1.2   0.0       1.1   1.6e+03      43      73 ..     446     476 ..     411     485 .. 0.76
   3 ?    0.2   0.0      0.42   6.3e+02      37      72 ..     507     542 ..     490     550 .. 0.84
   4 ?   -1.1   0.2         1   1.5e+03      30      62 ..     647     679 ..     623     686 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0019
                                       EEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEE CS
                             SnoaL  27 vvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltft 78 
                                       v+  n+++  ++ ++++ra +++ ++a+PD  ++++    e+d v +  +f+
  gi|336253057|ref|YP_004596164.1|  86 VEISNSVNLANTDKSQLRASLRTYLEALPDSVHAIHYYSMENDEVEVSTQFN 137
                                       5555555566777899*****************************9988875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHCTTCEEEEEEEEEETTEEEE CS
                             SnoaL  43 frafveelfkafPDlkvevedlvaegdkvaa 73 
                                         ++++e  +af ++ +++e +v+   +va 
  gi|336253057|ref|YP_004596164.1| 446 ESEAMTEIGRAFNEMLTDIEAMVVRIQTVAN 476
                                       5678889999999999999999998877775 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.42
                                       ECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEE CS
                             SnoaL  37 arGlegfrafveelfkafPDlkvevedlvaegdkva 72 
                                       + G+e   + +++  ++++Dl+ +ve++ ++  +va
  gi|336253057|ref|YP_004596164.1| 507 SAGAETQNEKLTTAAAEMSDLSATVEEIASSSNTVA 542
                                       5688888899999999***********999988887 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1
                                       TCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEE CS
                             SnoaL  30 hnpeeeparGlegfrafveelfkafPDlkveve 62 
                                       ++ +e++  + e++++ + e+++ + D + +++
  gi|336253057|ref|YP_004596164.1| 647 EDLVETVEASTESVADDMFEMRDGIEDGRETID 679
                                       223335555555666666666666665555554 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.68     1e+03       8      32 ..     520     544 ..     514     549 .. 0.75
   2 ?    1.6   0.1      0.16   2.4e+02       9      34 ..     577     602 ..     569     607 .. 0.82
   3 ?   -2.6   0.0       3.4   5.1e+03       6      25 ..     633     652 ..     629     659 .. 0.68
   4 ?    2.3   0.0     0.098   1.5e+02       8      35 ..     671     698 ..     666     702 .. 0.88
   5 ?   -2.2   0.0       2.6   3.8e+03       9      30 ..     710     731 ..     702     739 .. 0.76
   6 ?    7.4   0.2    0.0024       3.6       3      31 ..     746     774 ..     744     778 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.68
                         DASH_Dam1   8 LaDsletLdknledLqqihesLsdf 32 
                                        a ++++L++ +e++ + +++++d 
  gi|336253057|ref|YP_004596164.1| 520 AAAEMSDLSATVEEIASSSNTVADQ 544
                                       5678999999999999888888775 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.16
                         DASH_Dam1   9 aDsletLdknledLqqihesLsdfNe 34 
                                       a++++tL++ +e++ ++ e +++  e
  gi|336253057|ref|YP_004596164.1| 577 AEEMATLQEEVERIGEVVELIDQIAE 602
                                       78999999999999998888877665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.4
                         DASH_Dam1   6 aeLaDsletLdknledLqqi 25 
                                       ++La++ ++ ++ +edL ++
  gi|336253057|ref|YP_004596164.1| 633 KSLAEETAEATEEVEDLVET 652
                                       66777777777777777655 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.098
                         DASH_Dam1   8 LaDsletLdknledLqqihesLsdfNeS 35 
                                       ++D  et+d+ ++ L++i +s++d N +
  gi|336253057|ref|YP_004596164.1| 671 IEDGRETIDRTVDTLESIVDSIDDANAG 698
                                       678999*****************99965 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 2.6
                         DASH_Dam1   9 aDsletLdknledLqqihesLs 30 
                                       aDs +++++ ++d+  ++e+ +
  gi|336253057|ref|YP_004596164.1| 710 ADSAQEVSSMVDDIAAVSEQTA 731
                                       7999999999999988888755 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.0024
                         DASH_Dam1   3 pafaeLaDsletLdknledLqqihesLsd 31 
                                        a+++++Ds e L+++ ++Lq+++ + ++
  gi|336253057|ref|YP_004596164.1| 746 SAISQISDSAESLSERAQELQSLTAHFET 774
                                       6899******************9987765 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 ?   -2.3   0.2       3.1   4.6e+03      34      79 ..      75     120 ..      62     135 .. 0.60
   2 ?    4.2   5.5      0.03        45      39      99 ..     368     431 ..     357     446 .. 0.58
   3 ?    4.5   0.5     0.024        36      25      91 ..     449     515 ..     443     520 .. 0.82
   4 ?    5.4   3.8     0.013        19      35     116 ..     512     592 ..     498     607 .. 0.57
   5 ?   -0.6   0.0       0.9   1.3e+03      30      57 ..     636     663 ..     627     673 .. 0.48
   6 ?   14.6   3.5   1.9e-05     0.029      22     126 ..     667     770 ..     664     778 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.1
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvi 79 
                                       +k +++ +++  eisns + a++  ++++ slr   +  +d+ ++i
  gi|336253057|ref|YP_004596164.1|  75 DKFVQDRNDNTVEISNSVNLANTDKSQLRASLRTYLEALPDSVHAI 120
                                       4555555555666666666666666666666666666555554444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.03
                                       CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHHHHHHHC CS
                         Fib_alpha  39 kleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrlketida 99 
                                       +l+++l+e++++ +eae+  ++ + s +e+q+ k++    +   + +s++lee+  +++++i a
  gi|336253057|ref|YP_004596164.1| 368 TLQERLTEVEQQAQEAERAREQAEVSKAEAQQAKAEAqeaKAEAEALSQHLEEKADEYRQSIEA 431
                                       3555555555555555555555555555544444443222444555666666666666666654 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.024
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeil 91 
                                       ++++  + +++ l+++e  + +i+   ++++e ++e++ s++e  +s+ +  + i+++s   e++ +
  gi|336253057|ref|YP_004596164.1| 449 AMTEIGRAFNEMLTDIEAMVVRIQTVANQVDEKSSEVTASTEEIRASSGEVAESIEEISAGAETQNE 515
                                       6788888999999999999999999999999999999999999888888778888887776666555 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.013
                                       HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHH CS
                         Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvl 111
                                       ++ ekl+   +e+s+ + ++ee+ ++ +++  + ++ ++   +  ++ ++++ e++ r++ + +++ +++  Lq+ +
  gi|336253057|ref|YP_004596164.1| 512 TQNEKLTTAAAEMSDLSATVEEIASSSNTVADQSEQAAE-RGQEGQEAASDVVEQMDRIESKAVDTAEEMATLQEEV 587
                                       444444444444444444444444443333333333333.3444455555555577799999999999999999988 PP

                                       HHHHH CS
                         Fib_alpha 112 esneq 116
                                       e+  +
  gi|336253057|ref|YP_004596164.1| 588 ERIGE 592
                                       87654 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.9
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeel 57 
                                        +++ +  e++e+ +e+++ st+++ + 
  gi|336253057|ref|YP_004596164.1| 636 AEETAEATEEVEDLVETVEASTESVADD 663
                                       3334444444455555555555444444 PP

  == domain 6  score: 14.6 bits;  conditional E-value: 1.9e-05
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketid 98 
                                       ++d +++ ++++++++++le+ +++i + +  ++++  +++d+  ++q+ ++  d +   s+++ + e +++ +   
  gi|336253057|ref|YP_004596164.1| 667 MRDGIEDGRETIDRTVDTLESIVDSIDDANAGIQSINDATDDQADSAQEVSSMVDDIAAVSEQTAD-EAQNVSAAAE 742
                                       77888888999****************************************977777777777777.99999***** PP

                                       CCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  99 aqesnirvLqnvlesneqkiqkLeqdid 126
                                       +q s i ++ +  es++++ q+L++  +
  gi|336253057|ref|YP_004596164.1| 743 EQTSAISQISDSAESLSERAQELQSLTA 770
                                       *********9999999999999987655 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.5      0.43   6.5e+02      33      71 ..      64     102 ..      50     119 .. 0.62
   2 ?   -0.4   6.4       0.7     1e+03      14      70 ..     371     424 ..     360     443 .. 0.52
   3 ?    7.4   7.6    0.0027       4.1       1      96 [.     393     493 ..     393     494 .. 0.77
   4 ?   13.9   6.9   2.7e-05     0.041       4      84 ..     467     547 ..     464     565 .. 0.91
   5 ?    5.5   1.7      0.01        16       5      58 ..     566     619 ..     562     634 .. 0.87
   6 ?   10.2   0.9   0.00039      0.58       5      66 ..     643     704 ..     628     708 .. 0.77
   7 ?    4.0   6.5     0.032        48       4      73 ..     698     767 ..     692     783 .. 0.56

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.43
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II  33 lseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       l+ ++r+++ +++ v+d n  +++ ++sv   +    qL
  gi|336253057|ref|YP_004596164.1|  64 LNAAEREADGIDKFVQDRNDNTVEISNSVNLANTDKSQL 102
                                       455556666666666666666666666665444444444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.7
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTT CS
                        Laminin_II  14 evleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapq 70 
                                       e l  +++ +q+ e+ +e+++  +++    ++   +a++a ++A+  +++Le++a++
  gi|336253057|ref|YP_004596164.1| 371 ERLTEVEQQAQEAERAREQAEVSKAE---AQQAKAEAQEAKAEAEALSQHLEEKADE 424
                                       33333333333333333333332222...2233335555556666666666666654 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0027
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX--TTTTTG CS
                        Laminin_II   1 skelaaeanetakevleqlaplsqnlentkekls....einrsveetnekvk.dankairdArrsvkkLeklapqLl 72 
                                       sk+ a++a+  a+e ++  ++lsq le+  +++      +++  + t  +   + ++a+ + +r+  ++   ++ ++
  gi|336253057|ref|YP_004596164.1| 393 SKAEAQQAKAEAQEAKAEAEALSQHLEEKADEYRqsieAAADG-DLTRRLETaSESEAMTEIGRAFNEMLTDIEAMV 468
                                       6788888888888888888888888877666654111044444.5555544468899******************** PP

                                       GGHHHHHHHHHH....HHHHHHHHH CS
                        Laminin_II  73 dklkelkqleeasss.lsdniseik 96 
                                        +++++ ++ +++ss + ++ +ei+
  gi|336253057|ref|YP_004596164.1| 469 VRIQTVANQVDEKSSeVTASTEEIR 493
                                       ********99999989*******99 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 2.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                       ++  ++  a++v e+  ++ + +e+++++  e+++s+ee+ + ++  n+ +  A  ++++L  +++++ +  +++  
  gi|336253057|ref|YP_004596164.1| 467 MVVRIQTVANQVDEKSSEVTASTEEIRASSGEVAESIEEISAGAETQNEKLTTAAAEMSDLSATVEEIASSSNTVAD 543
                                       6677889999**********************************************************988777777 PP

                                       HHHH CS
                        Laminin_II  81 leea 84 
                                       ++e+
  gi|336253057|ref|YP_004596164.1| 544 QSEQ 547
                                       7665 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.01
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdAr 58 
                                       ++ ++++a+ + e +a l++++e++ e ++ i++ +eetn ++ +a+   + A+
  gi|336253057|ref|YP_004596164.1| 566 MDRIESKAVDTAEEMATLQEEVERIGEVVELIDQIAEETNMLALNASIEAATAG 619
                                       6788999*********************************99988877766666 PP

  == domain 6  score: 10.2 bits;  conditional E-value: 0.00039
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-- CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLek 66 
                                        +e+++ ++ v++ ++ ++ ++ ++++ ++  ++++++t + +++    i+dA+  ++ ++ 
  gi|336253057|ref|YP_004596164.1| 643 TEEVEDLVETVEASTESVADDMFEMRDGIEDGRETIDRTVDTLESIVDSIDDANAGIQSIND 704
                                       45667777777777888888888888888888899999999999999999999988887776 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.032
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGG CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLld 73 
                                        ++++n+ +    +  +++s  ++ + +  ++ +++++++ + +++ + ai + ++s   L + a++L +
  gi|336253057|ref|YP_004596164.1| 698 GIQSINDATDDQADSAQEVSSMVDDIAAVSEQTADEAQNVSAAAEEQTSAISQISDSAESLSERAQELQS 767
                                       4555555555555555555555555555555555555555555555555555555555555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (793 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3282  (0.183055); expected 358.6 (0.02)
Passed bias filter:                      920  (0.0513135); expected 358.6 (0.02)
Passed Vit filter:                       213  (0.0118802); expected 17.9 (0.001)
Passed Fwd filter:                       135  (0.0075297); 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: 2.52u 0.40s 00:00:02.92 Elapsed: 00:00:00.65
# Mc/sec: 3659.16
//
Query:       gi|336253058|ref|YP_004596165.1|  [L=264]
Description: NH(3)-dependent NAD(+) synthetase [Halopiger xanaduensis SH-6]
Scores for 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-81  271.8   0.0    4.4e-81  271.6   0.0    1.0  1  NAD_synthase   NAD synthase
    8.1e-05   21.6   0.0      0.011   14.6   0.0    2.2  2  tRNA_Me_trans  tRNA methyl transferase
     0.0043   16.8   0.1        1.6    8.6   0.1    3.6  4  HTH_23         Homeodomain-like domain
  ------ inclusion threshold ------
      0.043   13.2   0.1       0.32   10.4   0.1    2.5  2  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
      0.047   13.8   0.0       0.13   12.4   0.0    1.6  2  FLYWCH_N       FLYWCH-type zinc finger-containing protein
      0.084   12.4   0.0       0.28   10.6   0.0    1.8  2  QueC           Queuosine biosynthesis protein QueC


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 !  271.6   0.0   1.5e-84   4.4e-81       3     242 .]      16     257 ..      14     257 .. 0.98

  Alignments for each domain:
  == domain 1  score: 271.6 bits;  conditional E-value: 1.5e-84
                                       HHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE- CS
                      NAD_synthase   3 eelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievkti 79 
                                       e++++f+ e v+ aga+g+vlGlSGG+DS+l+++l+v+alg+env++l+lP +vsse ++ da  +a++l+i + +i
  gi|336253058|ref|YP_004596165.1|  16 EHITEFISERVDAAGADGAVLGLSGGIDSTLTGYLTVEALGPENVHGLVLPAHVSSEGNMSDAERVAQELDITYDVI 92 
                                       57899************************************************************************ PP

                                       --HHHHHHHHHHHHHHH.-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS- CS
                      NAD_synthase  80 dikpivrafeqelkeak.edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaell 155
                                       +i+piv  + +++ ea+ +  a gN +aR+R++++y +an++++lv+gTgn+sE++vGyfTkyGDga+d  pi++l+
  gi|336253058|ref|YP_004596165.1|  93 EIEPIVDQLLSAYPEAEgDREAVGNARARVRAVLNYLVANHESRLVVGTGNRSEAAVGYFTKYGDGAVDCHPIGNLY 169
                                       ***********999998788999****************************************************** PP

                                       HHHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHHHH CS
                      NAD_synthase 156 KtevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpaevvekiekl 231
                                       K +v++La++++vPe++  k  +A+L+++qtDe+eLgi+Y++lD iL   v+   s   +++ +e+++e+ve++ ++
  gi|336253058|ref|YP_004596165.1| 170 KGQVRQLARHVGVPEELAAKTATAELWADQTDEDELGISYETLDSILAtHVDGPLSVAATARLLEVQEETVERVRSM 246
                                       ************************************************99*************************** PP

                                       HHHTGGGGSSS CS
                      NAD_synthase 232 vkksehKrklp 242
                                       +++sehKr++p
  gi|336253058|ref|YP_004596165.1| 247 YERSEHKRNVP 257
                                       ********987 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.5e-06     0.011       4      71 ..      35      95 ..      33     143 .. 0.80
   2 !    4.8   0.0    0.0034        10     166     186 ..     163     183 ..     160     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.5e-06
                     tRNA_Me_trans  4 vvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfe 71
                                      v +lSgG+DS+++ +l  e+    +v g++l  + +         +e +++daerva++l+i ++v+++e
  gi|336253058|ref|YP_004596165.1| 35 VLGLSGGIDSTLTGYLTVEALgpENVHGLVLPAHVS---------SEGNMSDAERVAQELDITYDVIEIE 95
                                      579************998886567899999887666.........556889**************99976 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0034
                     tRNA_Me_trans 166 fPlgeltKeevrkiAkeagla 186
                                        P+g+l K +vr++A++ g++
  gi|336253058|ref|YP_004596165.1| 163 HPIGNLYKGQVRQLARHVGVP 183
                                       6***************99886 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.88   2.6e+03      21      31 ..      79      89 ..      78      90 .. 0.85
   2 ?   -1.4   0.0      0.77   2.3e+03      20      31 ..     173     184 ..     170     185 .. 0.85
   3 ?    3.3   0.0     0.026        77      25      40 ..     203     218 ..     203     223 .. 0.85
   4 !    8.6   0.1   0.00053       1.6      19      43 ..     225     249 ..     224     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.88
                            HTH_23 21 reIAreLgvsr 31
                                      +++A+eL++++
  gi|336253058|ref|YP_004596165.1| 79 ERVAQELDITY 89
                                      689*****985 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.77
                            HTH_23  20 vreIAreLgvsr 31 
                                       vr+ Ar+ gv++
  gi|336253058|ref|YP_004596165.1| 173 VRQLARHVGVPE 184
                                       7999*****985 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.026
                            HTH_23  25 reLgvsrrTvyrwlkr 40 
                                       +eLg+s+ T++ +l +
  gi|336253058|ref|YP_004596165.1| 203 DELGISYETLDSILAT 218
                                       69********999875 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.00053
                            HTH_23  19 svreIAreLgvsrrTvyrwlkryre 43 
                                       sv++ Ar+L v + Tv r+++ y++
  gi|336253058|ref|YP_004596165.1| 225 SVAATARLLEVQEETVERVRSMYER 249
                                       8999*****************9964 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 ?   -1.7   0.0      0.66     2e+03      30      40 ..     173     183 ..     173     185 .. 0.80
   2 ?   10.4   0.1   0.00011      0.32      19      47 ..     214     243 ..     206     243 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.66
                      HTH_Tnp_ISL3  30 vkavArqlgvS 40 
                                       v++ Ar++gv 
  gi|336253058|ref|YP_004596165.1| 173 VRQLARHVGVP 183
                                       5789****995 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00011
                      HTH_Tnp_ISL3  19 yilellles.rsvkavArqlgvSwtTVwri 47 
                                        il+ + ++  sv+a Ar+l v + TV+r+
  gi|336253058|ref|YP_004596165.1| 214 SILATHVDGpLSVAATARLLEVQEETVERV 243
                                       6899999999******************96 PP

>> FLYWCH_N  FLYWCH-type zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.4     1e+04      41      57 ..      62      78 ..      51      90 .. 0.55
   2 ?   12.4   0.0   4.2e-05      0.13      47     104 ..     197     255 ..     189     257 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.4
                          FLYWCH_N 41 klvLltaskedgdgvds 57
                                       lvL +  +++g+  d+
  gi|336253058|ref|YP_004596165.1| 62 GLVLPAHVSSEGNMSDA 78
                                      44444444444444444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.2e-05
                          FLYWCH_N  47 askedgdgvdskpkevhCvlsLemsdPdtlastlqiLpa.eeqegavqpapqapeqkrs 104
                                       a + d+d+ + + +    +l+  + +P ++a t ++L++ ee ++ v++  + +e+kr+
  gi|336253058|ref|YP_004596165.1| 197 ADQTDEDELGISYETLDSILATHVDGPLSVAATARLLEVqEETVERVRSMYERSEHKRN 255
                                       567789999999999************************99999***********9987 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.4e-05      0.28       2      62 ..      34      95 ..      33     117 .. 0.87
   2 ?   -1.4   0.0      0.45   1.4e+03     157     179 ..     164     186 ..     160     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.4e-05
                                      EEEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-G CS
                              QueC  2 avvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildld 62
                                      av+ lSGG+DSt   +l  ++   ++v+ l +  +   + +++ a+++a+el++    +++++
  gi|336253058|ref|YP_004596165.1| 34 AVLGLSGGIDSTLTGYLTVEALgpENVHGLVLPAHVSSEGNMSDAERVAQELDI-TYDVIEIE 95
                                      8999********99888888765699*******9999****************9.88888876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.45
                                       TTTT--HHHHHHHHHHTTHHHHH CS
                              QueC 157 PlidlsKaeivklgkelgvplee 179
                                       P+ +l K ++ +l+ ++gvp e+
  gi|336253058|ref|YP_004596165.1| 164 PIGNLYKGQVRQLARHVGVPEEL 186
                                       88899999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1974.02
//
Query:       gi|336253059|ref|YP_004596166.1|  [L=177]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-27   95.6   0.0    4.7e-27   95.4   0.0    1.1  1  Acetyltransf_3  Acetyltransferase (GNAT) domain
    1.4e-13   51.1   0.1    1.8e-13   50.7   0.1    1.2  1  Acetyltransf_1  Acetyltransferase (GNAT) family
    4.4e-12   46.4   0.0      5e-12   46.2   0.0    1.0  1  Acetyltransf_4  Acetyltransferase (GNAT) domain
      2e-07   30.8   0.0    6.9e-07   29.0   0.0    1.7  1  Acetyltransf_8  Acetyltransferase (GNAT) domain
    0.00031   21.1   0.0     0.0005   20.5   0.0    1.4  1  Acetyltransf_7  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.055   13.3   0.1       0.11   12.3   0.1    1.5  1  TetR_N          Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   0.0   1.6e-30   4.7e-27       1     138 []      11     146 ..      11     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 1.6e-30
                    Acetyltransf_3   1 RLlLrplteeDlealfelrsdpevmry.lpe.pltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdle 75 
                                       R+ Lrp++e+Dle l    +dp+v+r  ++  p + +++++++e++  +   +++++++iv  d + +G++g++ +e
  gi|336253059|ref|YP_004596166.1|  11 RVDLRPIEEDDLEFLQTKINDPRVWRGiGRArPVNGAQERDFFENVVCD---DDSVNLLIV-ADAEPVGTIGFHTIE 83 
                                       788************8779******963444699**********99776...488999996.55537********** PP

                    Acetyltransf_3  76 eedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       +e ++aelgy++ap+++ +Gy++ a++ l+ey f++lgl+r+ a++ + NeaS+++le++Gf+
  gi|336253059|ref|YP_004596166.1|  84 WEARRAELGYWVAPEHHEQGYGSAATELLVEYGFDHLGLHRIAARVFECNEASQALLESVGFT 146
                                       **************************************************************6 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.1   6.1e-17   1.8e-13      22     117 .]      50     145 ..      25     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 6.1e-17
                                       HHHHHH.HHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TESE CS
                    Acetyltransf_1  22 eefees.fsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gikk 96 
                                       ++f+e    ++++  l++  d e++G+i+++ i + + ++a++ +++V+pe++ +G+Gsa  e l+e+ +++ g+++
  gi|336253059|ref|YP_004596166.1|  50 RDFFENvVCDDDSVNLLIVADAEPVGTIGFHTIEW-EARRAEL-GYWVAPEHHEQGYGSAATELLVEYGFDHlGLHR 124
                                       33333325556666666778889************.5666666.********************************* PP

                                       EEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  97 ivlaveedndaairlYeklGF 117
                                       i + v+e n+a+++l+e +GF
  gi|336253059|ref|YP_004596166.1| 125 IAARVFECNEASQALLESVGF 145
                                       ****************99**9 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   1.7e-15     5e-12       2     155 .]      15     166 ..      14     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.7e-15
                    Acetyltransf_4   2 raateeDakeilaiyaeyvvntaitfeyevssveefekfleal.dsekeyvflvaesdrivGyaylgqfkkrakdwk 77 
                                       r ++e+D++ ++   ++++v + i++   v+ ++e   f e++   + +  +l+  + + vG+     +++  +   
  gi|336253059|ref|YP_004596166.1|  15 RPIEEDDLEFLQTKINDPRVWRGIGRARPVNGAQER-DFFENVvCDDDSVNLLIVADAEPVGTIGFHTIEW--EARR 88 
                                       678888888888888888888888888877777664.4777775577788888888999************..**** PP

                    Acetyltransf_4  78 aelsvylaerdnnkeglgrelidaleqvl.keqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiDm 153
                                       ael +++a     ++g+g++  ++l+++     +++++ a+++  ne+s+++++++GF+ +g  +++  + g++ D 
  gi|336253059|ref|YP_004596166.1|  89 AELGYWVA-PEHHEQGYGSAATELLVEYGfDHLGLHRIAARVFECNEASQALLESVGFTPEGVHRDAEFIDGEYQDT 164
                                       *******9.679****************88*********************************************** PP

                    Acetyltransf_4 154 iw 155
                                       +w
  gi|336253059|ref|YP_004596166.1| 165 HW 166
                                       99 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   2.3e-10   6.9e-07       3     142 ..      19     150 ..      18     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.3e-10
                                       GGGHHHHHHHCTSCCCHHHH-----H..HHHHHHHHHHC.STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS---T CS
                    Acetyltransf_8   3 eaDlellhrWmnrprvaewweeagtl..eevrellakldadphsepliglldgepvgyfeiYwakedelaeyydaep 77 
                                       e+Dle l++ +n+prv +  + a ++  +++r++ +++  d++s  l++  d epvg + +  ++ +       a+ 
  gi|336253059|ref|YP_004596166.1|  19 EDDLEFLQTKINDPRVWRGIGRARPVngAQERDFFENVVCDDDSVNLLIVADAEPVGTIGFHTIEWE-------ARR 88 
                                       78**********************9888999*****9999*******************99765544.......555 PP

                                       T-EEEEEEESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEE CS
                    Acetyltransf_8  78 gdrGiHlligeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekeke 142
                                         +G  +++++ e++++g+++a  + lv+y f++ +  r+ +     Ne++ +lle++Gf++e+ 
  gi|336253059|ref|YP_004596166.1|  89 AELG--YWVAP-EHHEQGYGSAATELLVEYGFDHLGLHRIAARVFECNEASQALLESVGFTPEGV 150
                                       5555..79996.5669********************************************99875 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.7e-07    0.0005       6      75 ..      67     146 ..      48     147 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.7e-07
                                       EEEEETTEEEEEEEEEEES...TCTEE....EEE-GGGTTSSHHHHHHHH......TTSEEE.EEEEEE...THHHH CS
                    Acetyltransf_7   6 fVaeddgkivGfialslld...aeitr....laVdpeyrgkGiGraLlea......aekgii.leqlel...naeka 65 
                                       +Va  d ++vG+i+++ ++       r     +V+pe++ +G+G+a  e+       + g++ +  +++   n+ ++
  gi|336253059|ref|YP_004596166.1|  67 IVA--DAEPVGTIGFHTIEweaR---RaelgYWVAPEHHEQGYGSAATELlveygfDHLGLHrI-AARVfecNE-AS 136
                                       233..589999999999985531...2455689************9888543333321332221.112222222.56 PP

                                       HHHHHHTTEE CS
                    Acetyltransf_7  66 ikfYeklGFe 75 
                                       +++ e+ GF+
  gi|336253059|ref|YP_004596166.1| 137 QALLESVGFT 146
                                       7788998887 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 ?   12.3   0.1   3.8e-05      0.11       3      25 ..     106     128 ..     106     129 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.8e-05
                                       HHHHHHHHHHHTTT--HHHHHHH CS
                            TetR_N   3 daArelfaerGydattvreIAkr 25 
                                       +aA el+ e+G+d +++ +IA+r
  gi|336253059|ref|YP_004596166.1| 106 SAATELLVEYGFDHLGLHRIAAR 128
                                       59*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1385.38
//
Query:       gi|336253060|ref|YP_004596167.1|  [L=283]
Description: hypothetical protein Halxa_1656 [Halopiger xanaduensis SH-6]
Scores for 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  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); 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 0.19s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2220.87
//
Query:       gi|336253061|ref|YP_004596168.1|  [L=270]
Description: restriction endonuclease [Halopiger xanaduensis SH-6]
Scores for 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   94.8   0.2    4.6e-27   94.3   0.2    1.2  1  Mrr_cat    Restriction endonuclease
    4.7e-15   55.6   0.5    6.3e-15   55.2   0.5    1.2  1  Mrr_cat_2  Restriction endonuclease


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.2   5.1e-31   4.6e-27       1     114 [.      18     131 ..      18     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 5.1e-31
                                       HTTT-TTCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--T..S-B-HHHHHHHHHHCTT CS
                           Mrr_cat   1 ldkmspkeFeklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKryk..nkvgvkeVqeligalkk 75 
                                       l++m+ ++Fe++va+l+ ++G+k + ++++s+D+  D++a+k+  +++r ++qaKry+  n+vg ++V+e ++  ++
  gi|336253061|ref|YP_004596168.1|  18 LQAMDNEKFEHFVADLWSRHGWK-TVVSQQSRDKSLDVLAEKETPYHQRHAIQAKRYQeeNNVGGPKVSEYASLRDQ 93 
                                       578*******************9.99*******************************7679**************** PP

                                       S..SEEEEEESS-B-HHHHHHHHTT--EEEE-HHHHHHH CS
                           Mrr_cat  76 rgadkgifvttsdftkaAreeaeelnkieLldgdeLael 114
                                         ad +++vtts+ft +Are  +   +++L+dgd+L+e+
  gi|336253061|ref|YP_004596168.1|  94 FDADVAVVVTTSGFTVDARERSKT-LNVKLIDGDDLVEM 131
                                       ***********************9.8***********98 PP

>> Mrr_cat_2  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.5   7.1e-19   6.3e-15       3     123 ..      22     141 ..      20     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 7.1e-19
                         Mrr_cat_2   3 dpayaee.fkeVwlwkewpeekrlgkkDtGIDlVake.rkegeywAIQcKfYaedekiqkedidsFlsasgkkkftk 77 
                                       d++  e+ ++++w+ ++w++  +++++D+  D+ a++    ++ +AIQ+K+Y+e++++  ++++++ s+ ++   + 
  gi|336253061|ref|YP_004596168.1|  22 DNEKFEHfVADLWSRHGWKTVVSQQSRDKSLDVLAEKeTPYHQRHAIQAKRYQEENNVGGPKVSEYASLRDQFDADV 98 
                                       555556659***************************9777899************************9998877665 PP

                         Mrr_cat_2  78 rliisTtdkwsknaeealknqkipvkridledLeeseidwsklslg 123
                                       +++ +Tt+ ++ +a e    ++++vk+id +dL e  +  ++l+l 
  gi|336253061|ref|YP_004596168.1|  99 AVV-VTTSGFTVDARER--SKTLNVKLIDGDDLVEMVVQADALDLV 141
                                       555.59999*******9..899*************99988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2164.04
//
Query:       gi|336253062|ref|YP_004596169.1|  [L=322]
Description: NAD-dependent epimerase/dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-32  112.2   0.2    1.1e-31  110.2   0.2    1.8  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.1e-22   78.7   0.0    8.6e-21   74.7   0.0    2.5  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    9.5e-16   57.7   0.3    1.9e-15   56.8   0.3    1.4  1  RmlD_sub_bind    RmlD substrate binding domain
    2.3e-10   40.1   0.0    2.6e-08   33.3   0.0    2.2  2  NAD_binding_4    Male sterility protein
      2e-08   34.3   0.8    2.8e-08   33.9   0.8    1.2  1  NAD_binding_10   NAD(P)H-binding
    2.8e-08   33.1   0.0    3.9e-08   32.6   0.0    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.5e-06   26.8   0.1    0.00022   20.5   0.1    2.9  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    0.00029   20.4   0.3     0.0033   16.9   0.2    2.5  2  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.047   13.2   0.2        0.2   11.2   0.0    2.1  3  NmrA             NmrA-like family
       0.09   12.7   0.1        0.3   11.0   0.1    1.9  1  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 !  110.2   0.2     6e-35   1.1e-31       1     177 [.      25     204 ..      25     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 6e-35
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       +lVtGatG +Gs +v++l+++g +v+g+dr+   ++++ ++++++  +dlt+++ + + + e++pdav+hlAa++++
  gi|336253062|ref|YP_004596169.1|  25 ALVTGATGDVGSWVVDRLADRGTHVVGIDRE---QPEGVRANADFRAVDLTEQAPTWETICEVEPDAVVHLAAISDP 98 
                                       59*****************************...5555566668**********99999999*************** PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGT........SCSSSSBSTCSTTS----SSHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYG........kdaeqpkeettltgplkpnspYaaaK 146
                                        ++  +  +++e+n+  t+n+l+aa + gv  ++  sS ++YG        +++  p +et    + +p   Y+++K
  gi|336253062|ref|YP_004596169.1|  99 LDNPAT--RVFENNVTSTYNVLQAAGREGV-DVVWSSSQATYGalfagrgwRPDALPIDETH---EQRPADSYGLSK 169
                                       **7666..899*******************.************7776665533334667777...669********* PP

                                       HHHHHHHHHHHHHHT-EEEEEEESEEESTT....S CS
                         Epimerase 147 lageklveayaaqyglnaiilrlfnlyGpr....n 177
                                       ++ge++++a a+ y+++++++r+ +++ p     +
  gi|336253062|ref|YP_004596169.1| 170 RCGEEIARATARGYDISVTTIRPATIFTPEkvraR 204
                                       *****************************944322 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 !   74.7   0.0   4.8e-24   8.6e-21       1     179 [.      26     191 ..      26     207 .. 0.87
   2 ?    0.7   0.0      0.16   2.8e+02     307     324 ..     284     301 ..     275     305 .. 0.82

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 4.8e-24
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG +G +Gs+++++L ++g +v+gi+r + +                 + n  +  +Dlt+++   + + ev+pd
  gi|336253062|ref|YP_004596169.1|  26 LVTGATGDVGSWVVDRLADRGTHVVGIDREQPEGV---------------RANADFRAVDLTEQAPTWETICEVEPD 87 
                                       9**************************99877643...............23456899******************* PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-........SSSSB-TTS- CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkv........qevpqtEttp 146
                                       +v++LAA s      + + +++e+nv+ t+++L+a+ + g    v ++ +S+   YG +        ++ p++Et+ 
  gi|336253062|ref|YP_004596169.1|  88 AVVHLAAISDPLD--NPATRVFENNVTSTYNVLQAAGREG----VDVVWSSSQATYGALfagrgwrpDALPIDETHE 158
                                       *******997654..3445899**************8877....5799*********99776655444799****** PP

                                       ----SHHHHHHHHHHHHHHHHHHHH---EEEEE CS
                     GDP_Man_Dehyd 147 fyPrsPYaaaKlyadwivvnyreayglfavngi 179
                                        +P   Y+ +K   + i+++  + y++ +++ +
  gi|336253062|ref|YP_004596169.1| 159 QRPADSYGLSKRCGEEIARATARGYDISVTTIR 191
                                       ***************************999876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                                       -B-THHHHHHH----SS- CS
                     GDP_Man_Dehyd 307 lgdaskakeeLgWkpkvs 324
                                       +  ++ka   LgW+p+ s
  gi|336253062|ref|YP_004596169.1| 284 ALSNAKAAAMLGWEPTHS 301
                                       56789**********976 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 !   56.8   0.3     1e-18   1.9e-15       3     154 ..      25     198 ..      23     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1e-18
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT............T--TTSHHHHHHHHHHH--SEEEE------HHHH CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre............eldltdaeavaellkeakpdvvvnaAAytavDka 67 
                                        lvtGa+G +Gs ++++la +g++v++++re            ++dlt+++   e++ e++pd+vv++AA    D  
  gi|336253062|ref|YP_004596169.1|  25 ALVTGATGDVGSWVVDRLADRGTHVVGIDREqpegvranadfrAVDLTEQAPTWETICEVEPDAVVHLAAIS--DPL 99 
                                       69********************************************************************86..677 PP

                                       HHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGG....GS-S-....TTS-B-TTS----SSHHHHHHHHHHHHH CS
                     RmlD_sub_bind  68 EseeeaayavnaeavealAeaaaavgalLihvStDy....VFdGe....kkrpYeeddetsPlnvYGrtKlaGEqav 136
                                        +   + ++ n++++ ++ +aa + g+ ++  S+       F G+     + p  e++e+ P   YG +K  GE+  
  gi|336253062|ref|YP_004596169.1| 100 DNPATRVFENNVTSTYNVLQAAGREGVDVVWSSSQAtygaLFAGRgwrpDALPIDETHEQRPADSYGLSKRCGEEIA 176
                                       8889999**************************986223367777887777789*********************99 PP

                                       HHH-S....SEEEEEE-SEESS CS
                     RmlD_sub_bind 137 laagk....kalivRtswvyge 154
                                       +a+       ++ +R + ++  
  gi|336253062|ref|YP_004596169.1| 177 RATARgydiSVTTIRPATIFTP 198
                                       9955411125566777777755 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0097        17       1      22 [.      27      48 ..      27      54 .. 0.87
   2 !   33.3   0.0   1.5e-11   2.6e-08      70     209 ..      67     199 ..      54     222 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0097
                                      EE-TTSHHHHHHHHHHHHHS-. CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpe 22
                                      +TGaTG +G+ ++ +L ++ ++
  gi|336253062|ref|YP_004596169.1| 27 VTGATGDVGSWVVDRLADRGTH 48
                                      7***************988765 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 1.5e-11
                                       TSGGGG--HHHHHHHHH.H--EEEE--SS-S..STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE..GGGTTS CS
                     NAD_binding_4  70 seprlGLseedlqelae.evdviihsaAtvn.fdepykellrvNveGtrevlelakklkklkvllhvST..ayvnge 142
                                          +l  ++ ++++++e e d+++h aA  + +d+p  ++++ Nv++t +vl+ a +      ++  S+   y +  
  gi|336253062|ref|YP_004596169.1|  67 RAVDLTEQAPTWETICEvEPDAVVHLAAISDpLDNPATRVFENNVTSTYNVLQAAGRE-GV-DVVWSSSqaTYGALF 141
                                       55555556777888865478********98757889*****************99844.44.688888853333333 PP

                                       -TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.- CS
                     NAD_binding_4 143 regeveekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.e 209
                                         + ++            +   ++++++  ++ Y  sK ++E++ r+++r  ++ v+ +Rp +i + e
  gi|336253062|ref|YP_004596169.1| 142 AGRGWRP----------DALPIDETHEQRPADSYGLSKRCGEEIARATARGYDISVTTIRPATIFTpE 199
                                       4433322..........356677888899999********************************9851 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 !   33.9   0.8   1.6e-11   2.8e-08       1     182 [.      29     239 ..      29     241 .. 0.67

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.6e-11
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT.HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-..SEEEES---TCC. CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.peklaeleaeeglevvegdvtdvedlaealkga..daVvsalggggk. 73 
                                       GAtG vG+ +v++l++rg ++v+ + R+ pe +      ++++   +d+t+++   e++  +  daVv  ++ ++  
  gi|336253062|ref|YP_004596169.1|  29 GATGDVGSWVVDRLADRG-THVVGIDREqPEGVR-----ANADFRAVDLTEQAPTWETICEVepDAVVHLAAISDPl 99 
                                       9****************6.888888554244444.....67888888888776666666544237887777665555 PP

                                       HHHH..........HHHHHHHHHHCT--EEEEEEETTTTSGCGCH........HHHHHHH.CCHHHHHHHHHHHHHH CS
                    NAD_binding_10  74 deeg..........aknivdaakeagvkRfvlvsaigvgdevpge........fgewnke.llkaylaakraaeell 131
                                       d+ +          + n+++aa ++gv  +   s +  g   +g+         +e+ ++    +y   kr  ee+ 
  gi|336253062|ref|YP_004596169.1| 100 DNPAtrvfennvtsTYNVLQAAGREGVDVVWSSSQATYGALFAGRgwrpdalpIDETHEQrPADSYGLSKRCGEEIA 176
                                       33334556666678*************7666666555554333321111111122222221345555889*****99 PP

                                       HH....SSSEEEEEEE-CEE-ST--SEEEEETTSS--........--EEEHHHHHHHHHHHCT CS
                    NAD_binding_10 132 ra....sgldwTivrpggLtdepttkyrvvekgepfk........ggsisradVAdvlvavld 182
                                       ra     ++  T +rp+ +   ++ + r +e++ +++        g+ +  +dVA+ + a+l+
  gi|336253062|ref|YP_004596169.1| 177 RAtargYDISVTTIRPATIFTPEKVRARPAEDDSDLTtaessgdfGSYVDVRDVARMVEAALA 239
                                       99554448889********99999999999877766534444444578999999999988886 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 !   32.6   0.0   2.2e-11   3.9e-08       1     188 [.      26     202 ..      26     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.2e-11
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegv..dvvihlas 75 
                                       +vtG++G +G+ +v +L +++     +v+ ++ +++      + n + +  +D+t+++   e + +v  d+v+hla+
  gi|336253062|ref|YP_004596169.1|  26 LVTGATGDVGSWVVDRLADRGT----HVVGIDREQPE---GVRANAD-FRAVDLTEQAPTWETICEVepDAVVHLAA 94 
                                       69******************96....55555554444...2344444.8899**9987666665554338******* PP

                         3Beta_HSD  76 lvdvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdE....eleyeslhqdaype 148
                                       ++d        ++ + nv  T nvl+a+ + gv v v+ Ss    g  + g   +   +    ++++e+ + d y  
  gi|336253062|ref|YP_004596169.1|  95 ISDPLD-NPATRVFENNVTSTYNVLQAAGREGVDV-VWSSSQATYGALFAGRGWR--PDalpiDETHEQRPADSYGL 167
                                       ***999.67777*********************85.7888776666655565555..2201113345666899**** PP

                         3Beta_HSD 149 sKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkl 188
                                       sK+  E++  ++       g ++    +Rpa+i+ + + +
  gi|336253062|ref|YP_004596169.1| 168 SKRCGEEIARATAR-----GYDISVTTIRPATIFTPEKVR 202
                                       ******98766555.....66999999*******998765 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   1.2e-07   0.00022       2     123 ..      26     129 ..      25     139 .. 0.76
   2 ?    1.2   0.0     0.094   1.7e+02     133     155 ..     160     182 ..     157     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-07
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T- CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkv 78 
                                       lvtGa+G +Gs +v++++++  +  + ++r+  +  + + ++           +      d+++++   +++ e+++
  gi|336253062|ref|YP_004596169.1|  26 LVTGATGDVGSWVVDRLADRGTHV-VGIDREQPEGVRANADF-----------R----AVDLTEQAPTWETICEVEP 86 
                                       899999999999999999887654.44455544444333333...........3....4577788877777777*** PP

                                       SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEE CS
                   Polysacc_synt_2  79 dvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkv 123
                                       d+v+h AA+     +++ ++ ++++Nv++t nv++aa + gv+ v
  gi|336253062|ref|YP_004596169.1|  87 DAVVHLAAISD--PLDNPATRVFENNVTSTYNVLQAAGREGVDVV 129
                                       ********975..56888999********************9744 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.094
                                       S--SHHHHHHHHHHHHHHHGGG- CS
                   Polysacc_synt_2 133 nPtnvmGatKrlaekllqalake 155
                                       +P + +G++Kr+ e ++ a+a+ 
  gi|336253062|ref|YP_004596169.1| 160 RPADSYGLSKRCGEEIARATARG 182
                                       79999**********99988765 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   1.8e-06    0.0033       2      64 ..      24      77 ..      23     135 .. 0.72
   2 ?   -0.8   0.0       0.5   8.9e+02     156     189 ..     172     202 ..     162     208 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-06
                                      EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHH CS
                         adh_short  2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreev 64
                                      ++lvtGa++ +G  ++++la +G +vv +dr++ +  ++ + ++         +vD+t+++ +
  gi|336253062|ref|YP_004596169.1| 24 TALVTGATGDVGSWVVDRLADRGTHVVGIDREQPEGVRANADFR---------AVDLTEQAPT 77
                                      79******************************998855555544.........4444444444 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                         adh_short 156 vagltrslakelaptgirvnavaPGlvdTdmake 189
                                        + ++r+ a+    + i+v+++ P+ + T+ + +
  gi|336253062|ref|YP_004596169.1| 172 GEEIARATAR---GYDISVTTIRPATIFTPEKVR 202
                                       4444444443...456999999999998876655 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011       0.2       2      32 ..      26      56 ..      25      83 .. 0.88
   2 ?   -2.3   0.0       1.5   2.7e+03       3      19 ..     117     133 ..     102     138 .. 0.62
   3 ?   -1.5   0.0      0.82   1.5e+03     178     196 ..     223     240 ..     187     268 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdt 32
                                      lv+GaTG  G+ vv+ l+++g +v  + R++
  gi|336253062|ref|YP_004596169.1| 26 LVTGATGDVGSWVVDRLADRGTHVVGIDREQ 56
                                      79*********************98887776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                                       ESSTTSHHHHHHHHHHH CS
                              NmrA   3 viGaTGrqGksvvrall 19 
                                       v+ a+Gr G  vv+ + 
  gi|336253062|ref|YP_004596169.1| 117 VLQAAGREGVDVVWSSS 133
                                       45556666666665554 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.82
                                       -EE-HHHHHHHHHHHHHHH CS
                              NmrA 178 vlldaeeDiGafvikilkd 196
                                        ++ +++D++++v ++l  
  gi|336253062|ref|YP_004596169.1| 223 SYV-DVRDVARMVEAALAA 240
                                       344.777888877777654 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00017       0.3       2      35 ..      24      56 ..      23     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                                      EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS. CS
                                KR  2 tylitGGlGgLGlelarwlaekgarhlvllsRsa 35
                                      t l+tG++G +G  +++ la++g  h+v + R++
  gi|336253062|ref|YP_004596169.1| 24 TALVTGATGDVGSWVVDRLADRGT-HVVGIDREQ 56
                                      579*******************95.666666764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2270.89
//
Query:       gi|336253063|ref|YP_004596170.1|  [L=164]
Description: hypothetical protein Halxa_1659 [Halopiger xanaduensis SH-6]
Scores for complete 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   48.1   0.5    2.4e-12   47.2   0.5    1.5  1  AAA_33           AAA domain
      1e-08   35.8   0.1    8.6e-05   23.1   0.0    2.3  2  AAA_18           AAA domain
    4.2e-07   29.7   0.0    9.7e-06   25.2   0.0    2.0  1  KTI12            Chromatin associated protein KTI12
    2.8e-06   27.6   0.0    1.2e-05   25.6   0.0    2.0  2  AAA_22           AAA domain
    3.9e-05   24.1   0.0    5.8e-05   23.5   0.0    1.5  1  AAA_16           AAA ATPase domain
    7.9e-05   22.6   0.0    0.00018   21.5   0.0    2.0  1  NTPase_1         NTPase
    0.00012   22.0   0.0       0.23   11.3   0.0    2.4  2  dNK              Deoxynucleoside kinase
    0.00036   20.8   0.2    0.00074   19.8   0.2    2.0  1  AAA_28           AAA domain
    0.00045   20.1   0.2      0.017   15.0   0.3    2.0  2  CPT              Chloramphenicol phosphotransferase-like prot
    0.00072   19.3   0.0     0.0026   17.5   0.0    1.8  1  AAA_30           AAA domain
     0.0016   18.5   0.0     0.0045   17.0   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0025   17.1   0.0      0.014   14.7   0.0    2.1  2  Zeta_toxin       Zeta toxin
     0.0026   17.6   0.0       0.06   13.2   0.0    2.5  1  APS_kinase       Adenylylsulphate kinase
     0.0034   17.0   0.0     0.0051   16.4   0.0    1.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.004   17.6   0.0     0.0077   16.7   0.0    1.5  1  AAA              ATPase family associated with various cellul
      0.005   16.6   0.0     0.0095   15.7   0.0    1.5  2  PRK              Phosphoribulokinase / Uridine kinase family
     0.0077   16.6   0.0     0.0085   16.4   0.0    1.2  1  AAA_19           AAA domain
      0.008   16.6   0.0       0.18   12.2   0.0    2.2  2  AAA_17           AAA domain
     0.0088   16.1   0.0      0.011   15.8   0.0    1.2  1  AAA_14           AAA domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.022   14.7   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
      0.012   15.7   0.0      0.018   15.1   0.0    1.5  1  MMR_HSR1         50S ribosome-binding GTPase
      0.016   15.6   0.0      0.023   15.1   0.0    1.3  1  RNA_helicase     RNA helicase
      0.018   14.8   0.0       0.27   10.9   0.0    2.1  2  Thymidylate_kin  Thymidylate kinase
      0.022   15.3   0.0      0.025   15.1   0.0    1.4  1  ABC_tran         ABC transporter
      0.022   14.5   0.0      0.076   12.8   0.0    1.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.022   14.5   0.0      0.038   13.8   0.0    1.3  1  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.03   14.2   0.0      0.089   12.7   0.0    1.8  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.034   13.5   0.0      0.052   12.9   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.035   14.1   0.0      0.055   13.5   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.047   13.2   0.1      0.082   12.4   0.1    1.4  1  Lactamase_B_2    Beta-lactamase superfamily domain
      0.049   13.4   0.0       0.07   12.8   0.0    1.5  1  AAA_24           AAA domain
      0.054   13.4   0.0      0.054   13.4   0.0    1.2  1  ATPase_2         ATPase domain predominantly from Archaea
      0.066   12.8   0.1        0.1   12.2   0.1    1.5  1  AAA_25           AAA domain
      0.067   13.1   0.0      0.095   12.6   0.0    1.3  1  NACHT            NACHT domain
      0.088   12.5   0.0        0.3   10.8   0.1    1.9  2  IstB_IS21        IstB-like ATP binding protein
      0.097   12.2   0.0       0.47    9.9   0.0    1.9  2  AAA_7            P-loop containing dynein motor region
        0.1   11.7   0.0       0.14   11.1   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
       0.11   11.7   0.0       0.13   11.4   0.0    1.2  1  NB-ARC           NB-ARC domain
       0.11   13.0   0.0       0.21   12.0   0.0    1.5  1  AAA_23           AAA domain
       0.11   12.1   0.0        0.2   11.3   0.0    1.5  1  Guanylate_kin    Guanylate kinase
       0.12   11.3   0.0       0.17   10.8   0.0    1.2  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.13   12.2   0.0       0.17   11.8   0.0    1.2  1  Rad17            Rad17 P-loop domain
        0.2   11.9   0.0       0.38   11.0   0.0    1.5  1  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.21   11.2   0.0       0.61    9.7   0.0    1.7  2  SRP54            SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.5   5.8e-15   2.4e-12       1     125 [.       2     113 ..       2     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 5.8e-15
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvil 75 
                                       +v+++G+pG+GK+tl  r+ k+l    v +  +++ ++l  +d          ++r+y++l e+ar+  +a+  +++
  gi|336253063|ref|YP_004596170.1|   2 IVVICGPPGAGKTTLTNRVRKRLEarDVPVPVPVAVETLHSDDF---------SSRTYERLYERARD--AAADVTLV 67 
                                       589*********************9999999999*999996655.........45678888777754..44445888 PP

                            AAA_33  76 datnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaang.ddr 125
                                       d t+ +r+ + +f+ l       vr v+v+++ et+ eR++ Ra++  ++ 
  gi|336253063|ref|YP_004596170.1|  68 DGTFYRREWQTQFRTLPD-----VRFVHVTASLETCLERNRTRADPIeEQG 113
                                       999988888888888874.....89*******************9842444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.1e-07   8.6e-05       1      25 [.       3      34 ..       3      69 .. 0.73
   2 !   11.1   0.1    0.0011      0.43      96     115 ..      78     107 ..      41     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.1e-07
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.......g 25
                                      ++++G+pG+GKttl+++++krl+         
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRKRLEArdvpvpvP 34
                                      79*******************94445555541 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0011
                            AAA_18  96 k..........vvLtaspeelleRlekRgy 115
                                       +          v++tas e++leR ++R  
  gi|336253063|ref|YP_004596170.1|  78 TqfrtlpdvrfVHVTASLETCLERNRTRAD 107
                                       23355666777*****************85 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.4e-08   9.7e-06       3     147 ..       2     131 ..       1     144 [. 0.82

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.4e-08
                                       EEEEE--TTSSHHHHHHHHHHHHHHTT--EEE.E-THHHH.TTSSS--GGGHHHHHHHHHHHHHHHHTT.SEEEE-S CS
                             KTI12   3 LvvltGlPssGKstrakeLakaleeekrsvvv.iddeslgiekdsykdsakekalRsslrsavkrdLskekvVIvDs 78 
                                       +vv++G P +GK+t++++++k le+++  v v +  e+l+  +d++ +  +e+    +  +a        +v+ vD 
  gi|336253063|ref|YP_004596170.1|   2 IVVICGPPGAGKTTLTNRVRKRLEARDVPVPVpVAVETLH--SDDFSSRTYERLYERARDAA-------ADVTLVDG 69 
                                       79*************************9998845567766..88888888887655444433.......47889999 PP

                                       ---SHHHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHHHHTT-S..S-HHHHHHHHHH---TTSS-GGG CS
                             KTI12  79 lnyikgfRYeLyciakaakttlcvvyvvapldvlvkwneereekeeyekelldaLiqRyeePdsknrWD 147
                                       + y    R+e     +     +  v+v+a+l++++++n  r+++  +e++ +  + + ++ePd ++  D
  gi|336253063|ref|YP_004596170.1|  70 TFY----RREWQTQFRTLP-DVRFVHVTASLETCLERNRTRADP--IEEQGVHVVHREFDEPDAEVTID 131
                                       986....777777777664.67789*****************99..999999999999****9987666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.9e-08   1.2e-05       7      49 ..       2      37 ..       1     117 [. 0.75
   2 ?   -0.1   0.0       2.5     1e+03      19      66 ..      92     143 ..      92     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.9e-08
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49
                                      i+v++G++G+GKTtl +r++++l+++       +  v v +++
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKRLEAR-------DVPVPVPVAV 37
                                      789********************753.......2222333333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.5
                            AAA_22  19 Ttllrrlleqldeeakaee.erpevv..fvtlpsst.sskdllrellralgl 66 
                                       T +l++ le++  +a++ e ++++vv  +++ p  + + ++ ++ + +a+g+
  gi|336253063|ref|YP_004596170.1|  92 TASLETCLERNRTRADPIEeQGVHVVhrEFDEPDAEvTIDTDRQSIPEATGR 143
                                       5677777777777766666788888877777777778888888888888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.4e-07   5.8e-05      26     106 ..       2      85 ..       1     149 [. 0.70

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.4e-07
                            AAA_16  26 lvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipysalaqalareellrqlldeaesaelea 96 
                                       +v++ G++G GK++l ++++++le++       + + + + d++ s+++y  l + + r +  +++   + +  +++
  gi|336253063|ref|YP_004596170.1|   2 IVVICGPPGAGKTTLTNRVRKRLEARdvpvpvPVAVETLHSDDF-SSRTYERLYERA-R-DAAADVTLVDGTFYRRE 75 
                                       699***********************776664355566666666.556776666666.5.55555555566667777 PP

                            AAA_16  97 wrekleeala 106
                                       w++++++   
  gi|336253063|ref|YP_004596170.1|  76 WQTQFRTLPD 85 
                                       7777766544 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   4.3e-07   0.00018       2      30 ..       3      31 ..       2     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.3e-07
                                      EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                      v+i GppG GKtTl ++v + l+ ++v+v
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRKRLEARDVPV 31
                                      789**********************9998 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   0.00056      0.23       2      26 ..       4      28 ..       3      41 .. 0.85
   2 !    8.2   0.0    0.0049         2     119     149 ..      79     111 ..      62     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00056
                                      EEEESTTSSHHHHHHHHHCCSTCEE CS
                               dNK  2 vveGnIgaGKstlvklLskklgvkv 26
                                      v+ G+ gaGK+tl+++ +k+l+   
  gi|336253063|ref|YP_004596170.1|  4 VICGPPGAGKTTLTNRVRKRLEARD 28
                                      78999***************98654 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0049
                                       HCCH.-SE.EEEEE--HHHHHHHHHHCTTCCCT CS
                               dNK 119 elak.pdl.liYLkasletclerikkRgreeek 149
                                       ++ + pd+ ++++ asletcler + R++  e+
  gi|336253063|ref|YP_004596170.1|  79 QFRTlPDVrFVHVTASLETCLERNRTRADPIEE 111
                                       4444455449***************99998765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   1.8e-06   0.00074       2      26 ..       3      31 ..       2     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.8e-06
                            AAA_28  2 ivitGgestGKTtlleaLaar....gypv 26
                                      +vi G++++GKTtl+++  +r    ++pv
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRKRlearDVPV 31
                                      8**************87775543335444 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.14        58       2      26 ..       1      25 [.       1      47 [. 0.83
   2 !   15.0   0.3   4.2e-05     0.017      86     172 ..      65     147 ..      40     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.14
                                      -EEEEEE-TTSSHHHHHHHHHHHSS CS
                               CPT  2 riilLnGgsssGKsslaralqevld 26
                                      +i+++ G + +GK++l++ +++ l+
  gi|336253063|ref|YP_004596170.1|  1 MIVVICGPPGAGKTTLTNRVRKRLE 25
                                      58999***********998877666 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.2e-05
                                       EEEEE--TTTHHHHHHHHHHHTTS-EEEEEEE--HHHHHHHHHHHTS..SSTTHHHHHTTGGGTT---SEEEETTSS CS
                               CPT  86 vivDdvilekewlvdllrrllsgldvllVGvrcplevlerRelergd..RepGlaalqaeavHagaeyDlevDtsak 160
                                        +vD  +  +ew +  + r l   dv +V v ++le   +R++ r+d   e+G+  +++e    +    + +Dt  +
  gi|336253063|ref|YP_004596170.1|  65 TLVDGTFYRREW-QTQF-RTL--PDVRFVHVTASLETCLERNRTRADpiEEQGVHVVHRE--FDEPDAEVTIDTDRQ 135
                                       368999999999.5555.455..5999********************7777888877777..455556778899988 PP

                                       -HHHHHHHHHTT CS
                               CPT 161 tpeecArairer 172
                                          e   +i ++
  gi|336253063|ref|YP_004596170.1| 136 SIPEATGRILTA 147
                                       888888777765 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   6.4e-06    0.0026      20      81 ..       2      58 ..       1      70 [. 0.70

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.4e-06
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk 81
                                      ++v+ Gp+G+GKtt+ + +r+ +ea+  +v    p   a ++L  + ++ ++t ++l +r +
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKRLEARDVPV----PVPVAVETLHSD-DFSSRTYERLYERAR 58
                                      67999*******************998555....445555666644.666666666665555 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 !   17.0   0.0   1.1e-05    0.0045       2      95 ..       3      90 ..       2     119 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-05
                                      EEEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal..nreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76
                                      v++ GppG gK++l+ r+ ++l  ++  + v     t  +d + +r +           l++ ar   ++++++D+ + 
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRKRLeaRDVPVPVPVAVETLHSDDFSSRTY---------ERLYERARdaAADVTLVDGTF- 71
                                      7899******************76444444444444444444444443.........555555555555555555555. PP

                                      --HHHHHHHHHHHHSSEEE CS
                             AAA_5 77 aesevlnsLlslleerrll 95
                                       ++e++  + +l + r ++
  gi|336253063|ref|YP_004596170.1| 72 YRREWQTQFRTLPDVRFVH 90
                                      5555555555555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.5e-05     0.014      18      45 ..       2      29 ..       1      65 [. 0.86
   2 ?    0.8   0.1      0.62   2.5e+02      79     111 ..      45      78 ..      36     137 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.5e-05
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgn 45
                                      ++++ G pGAGK++l + ++++le+++ 
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKRLEARDV 29
                                      6899******************986554 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.62
                        Zeta_toxin  79 daselvekllqeaiengyni.ivegtlrspdvvk 111
                                       ++s+  e+l + a ++  ++ +v+gt+   ++  
  gi|336253063|ref|YP_004596170.1|  45 FSSRTYERLYERARDAAADVtLVDGTFYRREWQT 78 
                                       5555556666666666666545666665555443 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00015      0.06       4      33 ..       2      31 ..       1     137 [. 0.94

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00015
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--E CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisv 33
                                      +v + G  g+GK+t++n++ k+L+++ + v
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKRLEARDVPV 31
                                      7899*******************9987655 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 !   16.4   0.0   1.3e-05    0.0051       2      28 ..       2      28 ..       1      57 [. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                                      EEEEEESTTCCHHHHHHHHHCT--SS- CS
                              cobW  2 vtvltGflGsGKTtLlnhllenraglk 28
                                      ++v++G++G+GKTtL n++ ++ + ++
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKRLEARD 28
                                      689*************99986655555 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 !   16.7   0.0   1.9e-05    0.0077       1      33 [.       3      35 ..       3      70 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.9e-05
                                      EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTT CS
                               AAA  1 vllyGppGtGKTllakavakelgvefleisgse 33
                                      v+++GppG GKT+l + v k l+++ + + ++ 
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRKRLEARDVPVPVPV 35
                                      5789****************9975533333332 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.3e-05    0.0095       1      49 [.       2      51 ..       2      83 .. 0.68
   2 ?   -2.1   0.0       6.6   2.7e+03      33      68 ..      91     126 ..      70     129 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-05
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvk.aaeiegdsflrldraekdle 49
                                      ++ ++g+ GaGktt++++++k+++   v+ ++ +    +++ d     +e
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKRLEARDVPvPVPVAVETLHSDDFSSRTYE 51
                                      6789********************99988223334444444433333333 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.6
                               PRK  33 iegdsflrldraekdleleerkrakekevsflspea 68 
                                       ++   ++ l+r   ++ + e+++ +  + +f++p+a
  gi|336253063|ref|YP_004596170.1|  91 VTASLETCLERNRTRADPIEEQGVHVVHREFDEPDA 126
                                       444444445555555555556666666666666655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.1e-05    0.0085      12      69 ..       2      76 ..       1     141 [. 0.62

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.1e-05
                            AAA_19 12 vllvtaGpGtGKTrvlkhivallvelggvkp......eeillvaftgrAakelrerlaalgae............a 69
                                      ++++ ++pG GKT++++ + + l+++  v++      e++    f +r  ++l er + + a+             
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKRLEARD-VPVpvpvavETLHSDDFSSRTYERLYERARDAAADvtlvdgtfyrreW 76
                                      57899********87776666665555.554445544444445578888888888886666654555444444441 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00044      0.18       2      19 ..       7      24 ..       6      31 .. 0.88
   2 ?    2.2   0.0      0.54   2.2e+02      69     118 ..      60     101 ..      41     113 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00044
                                      E-TTSSHHHHHHHHHHHH CS
                            AAA_17  2 GgPGsGKgtqceklveky 19
                                      G+PG+GK+t+ +++ +++
  gi|336253063|ref|YP_004596170.1|  7 GPPGAGKTTLTNRVRKRL 24
                                      9************99887 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.54
                                       HHSSEEEEEE-S.EEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHH CS
                            AAA_17  69 akkkgvlvdghp.rikeqagfldglpkevleelkpdaiilleadpeeiler 118
                                       a+ +  lvdg + r ++q +         +++l    ++ + a+ e++ler
  gi|336253063|ref|YP_004596170.1|  60 AAADVTLVDGTFyRREWQTQ---------FRTLPDVRFVHVTASLETCLER 101
                                       35566788876513333333.........4455334566677777777666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.6e-05     0.011       4     107 ..       2     101 ..       1     123 [. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-05
                            AAA_14   4 ilvitGaRrvGKTtllkqlikell...vkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                       i+vi G+  +GKTtl +++ k+l    v     + + +  e++ + + +++ +e + e++++    + + D   + +
  gi|336253063|ref|YP_004596170.1|   2 IVVICGPPGAGKTTLTNRVRKRLEardV----PVPVPVAVETLHSDDFSSRTYERLYERARDAAADVTLVDGTFYRR 74 
                                       89*************9999877765443....344433333333222222234445554444577899********* PP

                            AAA_14  78 ewekalkslvdegknldvivtGSnskllsk 107
                                       ew++  + l d +    v vt S+   l +
  gi|336253063|ref|YP_004596170.1|  75 EWQTQFRTLPDVR---FVHVTASLETCLER 101
                                       ********99988...78899998887766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.3e-05     0.022     101     125 ..       2      26 ..       1      32 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.3e-05
                                       EEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpelel 125
                                       ++v++G+ G+GK+tL n+++ +le+
  gi|336253063|ref|YP_004596170.1|   2 IVVICGPPGAGKTTLTNRVRKRLEA 26 
                                       689***************9988765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   4.4e-05     0.018       2      22 ..       3      33 ..       2     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.4e-05
                                      EEEEESTTSSHHHHHHHHHT..........S CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg..........e 22
                                      v+i G p +GK+tL n+  +           
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRKrleardvpvpV 33
                                      89***************98744444444440 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   5.7e-05     0.023       1      23 [.       3      25 ..       3      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.7e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakall 23
                                      ++++Gp+g GK+tl++++ k+l+
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRKRLE 25
                                      689**************888887 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00067      0.27       3      24 ..       7      28 ..       5      34 .. 0.88
   2 ?    2.0   0.0      0.35   1.4e+02     108     140 ..      73     107 ..      44     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00067
                                      ESTTSSHHHHHHHHHHHHHHTT CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeeg 24
                                      G  GaGKtt ++ +++rl+++ 
  gi|336253063|ref|YP_004596170.1|  7 GPPGAGKTTLTNRVRKRLEARD 28
                                      677***************9986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.35
                                       HHHGGGTTS.E-SEEEEEE.SSHHHHHTSCCTTSS CS
                   Thymidylate_kin 108 lslnedvll.kPdltflld.vdpevalkRlakrde 140
                                       ++  ++ ++  Pd+ f     + e++l+R ++r+ 
  gi|336253063|ref|YP_004596170.1|  73 RREWQTQFRtLPDVRFVHVtASLETCLERNRTRAD 107
                                       44444445559999877554789999999999987 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   6.2e-05     0.025      13      37 ..       2      26 ..       1     139 [. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.2e-05
                                      EEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkp 37
                                      +v+i G+ GaGK+tL + + + l+ 
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKRLEA 26
                                      689************9988877765 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   0.00019     0.076      36      59 ..       3      26 ..       2      41 .. 0.86
   2 ?   -0.7   0.0       2.6     1e+03      99     122 ..      48      71 ..      35     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00019
                            RuvB_N 36 vllyGpPGlGkttlakiiakelgv 59
                                      v+++GpPG Gkttl++ + k l++
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRKRLEA 26
                                      7899***********999888876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.6
                            RuvB_N  99 aveevlysamedfrldivigkGps 122
                                        + e ly    d + d+++ +G+ 
  gi|336253063|ref|YP_004596170.1|  48 RTYERLYERARDAAADVTLVDGTF 71 
                                       566888888899999988888764 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 ?   13.8   0.0   9.3e-05     0.038       1      26 [.       5      30 ..       5      34 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.3e-05
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrs 26
                                      ++Gp+G+GKtt+++++ + le+r  +
  gi|336253063|ref|YP_004596170.1|  5 ICGPPGAGKTTLTNRVRKRLEARDVP 30
                                      79****************99998655 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 ?   12.7   0.0   0.00022     0.089       1      30 [.       2      31 ..       2      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00022
                              MobB  1 vlgivgksgsGKTtLleklipelkarglrv 30
                                      ++ i+g  g+GKTtL +++ + l+ar++ v
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKRLEARDVPV 31
                                      6889*********************99876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00013     0.052      25      92 ..       3      68 ..       2      77 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpfraphhsaskaalvG 92
                                      ++++GppG+GKt l +r+ + l + +    + v +++++ + ++ ++ + +r ++  +++a++++lv 
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRKRLEARDVPVPVPV-AVETLHS-DDFSSRTYERLYERARDAAADVTLVD 68
                                      5789*************9987765544333333.2333333.44444555556666666666666665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00013     0.055      22      52 ..       3      33 ..       1     103 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00013
                                      EEEEESTTSSHHHHHHHHHHHTT------TT CS
                              TsaE 22 ilLeGdLGaGKTtlvrglakalgveevkSPT 52
                                      +++ G+ GaGKTtl+  + k l+ ++v  P 
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRKRLEARDVPVPV 33
                                      788999****************998776665 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 ?   12.4   0.1    0.0002     0.082     152     181 ..      55      93 ..      37     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                                       HHHCT..-SEEEEE-S-SSTTHHHH.......HHT---S CS
                     Lactamase_B_2 152 erlgg..adllllditayeddemir.......hmgHltp 181
                                       er ++  ad++l+d+t+y+ ++  +       + +H+t 
  gi|336253063|ref|YP_004596170.1|  55 ERARDaaADVTLVDGTFYRREWQTQfrtlpdvRFVHVTA 93 
                                       44444449**************98899999998888876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00017      0.07       5      22 ..       3      20 ..       1      83 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++i Gp+g+GKTtl ++ 
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRV 20
                                      79************9988 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 ?   13.4   0.0   0.00013     0.054      22      57 ..       2      37 ..       1     128 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                          ATPase_2 22 iyfiYGpegsGKtaLlkeiienledkdkyviyyial 57
                                      i++i Gp g GKt+L +++ ++le  d  v    a+
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKRLEARDVPVPVPVAV 37
                                      89*****************99999887755544444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00025       0.1      36     107 ..       3      68 ..       1     117 [. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                            AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvld 107
                                       ++++G+pg+GKttl+  +  + ++ + ++    p +++V  ++ +d  +++ +Rl++  +++   a+++++d
  gi|336253063|ref|YP_004596170.1|   3 VVICGPPGAGKTTLTNRV-RKRLEARDVPV---PVPVAVETLHSDDFSSRTYERLYERARDA--AADVTLVD 68 
                                       6899*********98665.44444443322...46888888898998888888888666555..34444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00023     0.095       2      30 ..       2      30 ..       1      60 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegklp 30
                                      +v++ G++G GKTtL  ++   + +++ p
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKRLEARDVP 30
                                      5899**************99998887755 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 ?   10.8   0.1   0.00073       0.3      50      65 ..       3      18 ..       1      69 [. 0.89
   2 ?   -1.0   0.0       3.2   1.3e+03      20      45 ..     130     155 ..     119     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00073
                         IstB_IS21 50 ivllGpsGvGKshlai 65
                                      +v++Gp+G+GK+ l+ 
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTN 18
                                      79**********9986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.2
                         IstB_IS21  20 edidfraarsldkrkvkeLatlsfie 45 
                                        d d ++ +++  r++++L +  +i+
  gi|336253063|ref|YP_004596170.1| 130 IDTDRQSIPEATGRILTALEGWGWID 155
                                       47899999999999*****9999997 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 ?    9.9   0.0    0.0012      0.47      36      61 ..       3      28 ..       1      60 [. 0.86
   2 ?    0.2   0.0       1.2   4.7e+02     133     154 ..      69      91 ..      63     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                             AAA_7 36 vllvGptGtGKtviikdllkkldkek 61
                                      v+++Gp G GKt++++++ k+l+ ++
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRKRLEARD 28
                                      7899*************999998654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.2
                             AAA_7 133 ggwYdr.kklefkeikdvqlvaa 154
                                       g +Y r  +++f+++ dv +v  
  gi|336253063|ref|YP_004596170.1|  69 GTFYRReWQTQFRTLPDVRFVHV 91 
                                       78999944679*******99875 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 ?   11.1   0.0   0.00036      0.14     131     157 ..       2      28 ..       1      89 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00036
                             T2SSE 131 lilvsGgTgsGKttllyallkeinksd 157
                                       ++++ G+ g GKttl++ + k ++++d
  gi|336253063|ref|YP_004596170.1|   2 IVVICGPPGAGKTTLTNRVRKRLEARD 28 
                                       6899*************9999998874 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00032      0.13      22      43 ..       2      23 ..       1      56 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                                      EEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 22 vvalvGmgGvGKttlakqilnk 43
                                      +v + G +G GKttl + + + 
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKR 23
                                      899*************999876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00052      0.21      21      35 ..       2      16 ..       1      21 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00052
                            AAA_23 21 ltlItGpNGaGKTTi 35
                                      +++I+Gp GaGKTT+
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTL 16
                                      689***********9 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0005       0.2       5      45 ..       3      44 ..       1      63 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0005
                                      EEEESTTTSSHHHHHHHHHHHSTTTEE.E--EEESS---TTS CS
                     Guanylate_kin  5 vvlvgpsgaGksslkkaLlselpekfg.vsvshtTrdprkge 45
                                      vv+ gp gaGk +l + + ++l+ ++  v+v+    +   ++
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRKRLEARDVpVPVPVAVETLHSDD 44
                                      89************************8899997766665555 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 ?   10.8   0.0   0.00042      0.17      32      62 ..       3      33 ..       1      45 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                                      EEEEE-TTSSHHHHHHHHHHHHHCTT--EEE CS
                              MeaB 32 vGltGvPGaGkstlvealglelrrrGkrvav 62
                                      v + G PGaGk tl++++  +l +r   v v
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRKRLEARDVPVPV 33
                                      6689******************999887766 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   0.00041      0.17      47      71 ..       2      26 ..       1      54 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00041
                             Rad17 47 iLLisGPsGCgkstvvkvLskelgi 71
                                      i++i+GP+G gk+t  + + k l  
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKRLEA 26
                                      789***********99988887754 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00094      0.38       2      21 ..       3      22 ..       2      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00094
                                      EEEESSTTSSHHHHHHCHCT CS
                               Roc  2 vvlvGdsgvGKtsllkrfve 21
                                      vv++G  g+GKt+l +r+ +
  gi|336253063|ref|YP_004596170.1|  3 VVICGPPGAGKTTLTNRVRK 22
                                      799*************9875 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0015      0.61       3      28 ..       2      27 ..       1      41 [. 0.84
   2 ?   -1.1   0.0       3.1   1.2e+03      70      91 ..      48      69 ..      29      94 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                                      EEEEEESTTSSHHHHHHHHHHHHHHT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkke 28
                                      +++++G+ GaGKTt + ++ ++l+++
  gi|336253063|ref|YP_004596170.1|  2 IVVICGPPGAGKTTLTNRVRKRLEAR 27
                                      6899************9999888776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.1
                                      HHHHHHHHHHHHTTSSEEEEEE CS
                             SRP54 70 avakeavekakeekidvvlvDT 91
                                       + ++  e+a++  +dv lvD 
  gi|336253063|ref|YP_004596170.1| 48 RTYERLYERARDAAADVTLVDG 69
                                      4455666778888888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        44  (0.00245412); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 1153.50
//
Query:       gi|336253064|ref|YP_004596171.1|  [L=338]
Description: hypothetical protein Halxa_1660 [Halopiger xanaduensis SH-6]
Scores for 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   11.5   2.7       0.37   10.7   2.7    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.7   2.1e-05      0.37       3      22 ..      20      39 ..      19      44 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.1e-05
                        TAT_signal  3 SRRdFLKgsAAaaAAaalgg 22
                                      +RR++LK+s +a A+ ++g+
  gi|336253064|ref|YP_004596171.1| 20 TRRTLLKASSGALALPVVGA 39
                                      8********77777777774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2681.93
//
Query:       gi|336253065|ref|YP_004596172.1|  [L=349]
Description: Chloromuconate cycloisomerase [Halopiger xanaduensis SH-6]
Scores for 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-42  145.2   0.2    2.9e-42  144.7   0.2    1.3  1  MR_MLE_C   Enolase C-terminal domain-like
    1.6e-12   47.7   0.0    2.6e-12   47.0   0.0    1.3  1  MR_MLE_N   Mandelate racemase / muconate lactonizing enzyme, 
     0.0012   18.0   0.0     0.0021   17.3   0.0    1.3  1  MAAL_C     Methylaspartate ammonia-lyase C-terminus
  ------ inclusion threshold ------
      0.047   13.9   0.0       0.11   12.7   0.0    1.5  1  Enolase_N  Enolase, N-terminal domain
        0.1   12.1   0.1       0.98    8.9   0.0    2.2  3  HMGL-like  HMGL-like


Domain annotation for each model (and alignments):
>> 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 !  144.7   0.2   8.2e-46   2.9e-42       3     206 ..     147     336 ..     145     349 .] 0.83

  Alignments for each domain:
  == domain 1  score: 144.7 bits;  conditional E-value: 8.2e-46
                                       HHHHHHHHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGTESEEES CS
                          MR_MLE_C   3 aeearelvaeqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeldllwlEE 79 
                                       +e+ +  + e+g+ ++K+k+g    ++d+e v+ +r+++ p+  vdl+vDan+aw++++A+ ++++l+e+dl+++E+
  gi|336253065|ref|YP_004596172.1| 147 REKTET-ALERGYGRLKVKLGT---DRDIEIVETIRDVA-PE--VDLFVDANEAWTPREAVARIERLAEYDLEFVEQ 216
                                       555555.4457********887...6************9.74..6******************************** PP

                                       SSSTTTHHHHHHHHHHHHSSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBS CS
                          MR_MLE_C  80 PvppeddleglaelrarasipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHs 156
                                       Pvp+e+ +egl+ + +r+++piaa+Es+ +++d+ ++  a+ +di++++++++gG+ ear+++  a+a+g++v++++
  gi|336253065|ref|YP_004596172.1| 217 PVPAEN-PEGLRFVYERSPLPIAADESCVTLEDVPRI--ADRCDIANLKLMKCGGLREARRMISTARAHGLEVMLGC 290
                                       ****75.********555*******************..7899********************************** PP

                                       CS.SHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEEC CS
                          MR_MLE_C 157 gs.gglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtv 206
                                       ++ ++ + aa++hla  ++ ++     l      +e   + +++ dGr+++
  gi|336253065|ref|YP_004596172.1| 291 MTeSDASIAAACHLAPLLDYADLDGALL-----LAEDPYDGVPMPDGRIDL 336
                                       9769**********99986443333333.....334444445555555555 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   7.2e-16   2.6e-12       9     114 ..      13     122 ..       6     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 7.2e-16
                                       EEEEEC.EEEETTEEEEEEEEEEEEEEECTTEEEEEEEE-STT...GHHHHHHHHHHHHHHHHTTSBTTHHHHHHHH CS
                          MR_MLE_N   9 eavklr.PvqlavttvqkqslvlvkietseGvvGigeatsvgg...raetikaelddhlapllvgkdaanisdlaql 81 
                                        a +l+ P+ ++++t+++ ++v+v++e  +G vGig a++      +a t++a l d la      d ++++ + + 
  gi|336253065|ref|YP_004596172.1|  13 HALPLEyPFGISRGTRSETEVVTVHVEDGDGNVGIGAAGPSAHygeTAATVEAVLPDLLAVVEDVGDTHQLERIERR 89 
                                       5667788*****************************99876643337777777777655444434588999999999 PP

                                       HHHHCSSCHHHHHHHHHHHHHHHHHHTTSBHHH CS
                          MR_MLE_N  82 lkravlgnmsAkaaidmAlwDlkakalnlplad 114
                                       +   v  n +A+ a+ +A +Dl ak+l++pl+ 
  gi|336253065|ref|YP_004596172.1|  90 MRETVERNPAARTAVSIACHDLVAKRLEVPLYR 122
                                       9999999***********************986 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.7e-07    0.0021     140     213 ..     235     305 ..     226     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.7e-07
                            MAAL_C 140 velvaDeWcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvsarvsvhva 213
                                       + + aDe c tled+ + +d+  +d+  +k    Gg++++   +  ++ +g++++lG    e d+s  ++ h+a
  gi|336253065|ref|YP_004596172.1| 235 LPIAADESCVTLEDVPRIADR--CDIANLKLMKCGGLREARRMISTARAHGLEVMLGC-MTESDASIAAACHLA 305
                                       5689*************9986..9*******************************985.568888877777765 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.9e-05      0.11     106     130 ..      99     123 ..      56     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHHHHHHHHHHHTS-HHHH CS
                         Enolase_N 106 NailavSlAvakaaAkakelplyry 130
                                        a +avS+A+    Ak +e+plyry
  gi|336253065|ref|YP_004596172.1|  99 AARTAVSIACHDLVAKRLEVPLYRY 123
                                       46789*******************9 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.8   6.4e+03     174     200 ..      83     110 ..      71     112 .. 0.61
   2 ?    0.1   0.0      0.13   4.8e+02     150     185 ..     172     207 ..     160     216 .. 0.66
   3 ?    8.9   0.0   0.00027      0.98     116     153 ..     269     306 ..     253     318 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHS-..GGGEEEEEB- CS
                         HMGL-like 174 Pneaaelisalkervk.dkvilsvHcHn 200
                                        + + +++++ +er +  ++++s+ cH+
  gi|336253065|ref|YP_004596172.1|  83 LERIERRMRETVERNPaARTAVSIACHD 110
                                       4455556666666655666666666665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.13
                                       HHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHH CS
                         HMGL-like 150 evveaaeeaGatriniaDtvGvltPneaaelisalk 185
                                       e+ve+++++ +    + D  ++ tP+ea ++i++l+
  gi|336253065|ref|YP_004596172.1| 172 EIVETIRDVAPEVDLFVDANEAWTPREAVARIERLA 207
                                       555555666555555666666666666666666654 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00027
                                       HHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHH CS
                         HMGL-like 116 akkaeeavkaarslgkdvelsledasrtdleflaevve 153
                                       +++a++++  ar +g +v l+++++s+++++ ++ ++ 
  gi|336253065|ref|YP_004596172.1| 269 LREARRMISTARAHGLEVMLGCMTESDASIAAACHLAP 306
                                       6899**************************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2756.61
//
Query:       gi|336253066|ref|YP_004596173.1|  [L=340]
Description: hypothetical protein Halxa_1662 [Halopiger xanaduensis SH-6]
Scores for 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-72  240.8   0.2    1.1e-71  240.3   0.2    1.1  1  DUF1611    Domain of unknown function (DUF1611_C) P-loop doma
    4.4e-31  107.0   0.0      8e-30  102.9   0.0    2.2  2  DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-li


Domain annotation for each model (and alignments):
>> 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 !  240.3   0.2   1.2e-75   1.1e-71       3     199 ..     136     333 ..     134     334 .. 0.97

  Alignments for each domain:
  == domain 1  score: 240.3 bits;  conditional E-value: 1.2e-75
                           DUF1611   3 adgkarevkakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgiliagegvvldavvvdfvaGaveglv 79 
                                        +g a ev+a+++l+vGTdc++GK+tt++el++ ++++G++aa+++Tgqtgi+i g+g ++d+vv+df+aGave+++
  gi|336253066|ref|YP_004596173.1| 136 SEGVAGEVDADVILTVGTDCSTGKMTTTMELARNARDAGYDAAVIPTGQTGIMIEGWGNPIDRVVSDFTAGAVEEMI 212
                                       5677889********************************************************************** PP

                           DUF1611  80 kkaaeeeepdlilveGQgsLthpaysgvtlglLlGsqPdalvLchrpgrkhirglpeialppleeeieliealaakk 156
                                       ++  + e+ d+++veGQgs++hpays+vt+g+L+G++Pd lvLch++g+++i+g+++++lpp++++++l+e+l+a+ 
  gi|336253066|ref|YP_004596173.1| 213 LEKGN-EH-DYLFVEGQGSIVHPAYSAVTCGILHGAMPDKLVLCHNAGQETIHGYESFELPPISTYVDLYERLSAPV 287
                                       **996.88.******************************************************************99 PP

                           DUF1611 157 ...kvvgislNtknlseeeakealeeleeelglpvvdpvregaekl 199
                                          ++++ ++Nt++l++++a++a++e+++el+ p++d++r+  +++
  gi|336253066|ref|YP_004596173.1| 288 sdaEIAAGAINTSDLEDDAAEDAVAEYADELDAPATDVIRFDTDAV 333
                                       999*************************************988875 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 !  102.9   0.0   8.9e-34     8e-30       2      94 .]      36     129 ..      35     129 .. 0.98
   2 ?    1.6   0.0     0.036   3.3e+02      17      49 ..     161     192 ..     149     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 8.9e-34
                         DUF1611_N   2 ekaGkdagelldd.rgipvvssleealaagaevlviGiapeggklpeswreavkeAleaGldvvsGlHerLsddpel 77 
                                       ++aG++++++++d +++p+v+  ++ +a ++++l+iGi p gg ++eswre+v++Ale+G+d+vsGlH++L++d+e+
  gi|336253066|ref|YP_004596173.1|  36 DNAGERVADFVPDvQDAPIVEGTDDLEADEIDTLLIGISPIGGEFDESWREDVETALERGCDIVSGLHYFLAEDEEF 112
                                       789************************************************************************** PP

                         DUF1611_N  78 aalakkkgvkiiDvRkp 94 
                                       a+la+++g+++ DvRkp
  gi|336253066|ref|YP_004596173.1| 113 ARLAEEHGCELRDVRKP 129
                                       ***************98 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.036
                         DUF1611_N  17 ipvvssleealaagaevlviGiapeggklpesw 49 
                                        + ++   +a +ag+++ vi+++  g ++ e w
  gi|336253066|ref|YP_004596173.1| 161 TTTMELARNARDAGYDAAVIPTGQTGIMI-EGW 192
                                       5566777777999*********9999887.555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2676.34
//
Query:       gi|336253067|ref|YP_004596174.1|  [L=320]
Description: hypothetical protein Halxa_1663 [Halopiger xanaduensis SH-6]
Scores for 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-36  123.5   1.4    6.6e-36  123.5   1.4    2.5  1  acVLRF1          Actinobacteria/chloroflexi VLRF1 release fac
    7.8e-08   32.7   0.3    7.8e-08   32.7   0.3    2.1  1  baeRF_family10   Bacterial archaeo-eukaryotic release factor 
    4.4e-06   27.0   0.1    8.9e-05   22.8   0.0    2.2  2  eRF1_2           eRF1 domain 2
     0.0022   17.9   5.7     0.0022   17.9   5.7    1.5  2  ERM              Ezrin/radixin/moesin family
     0.0038   17.3  16.5      0.075   13.1   8.0    3.5  3  DUF1192          Protein of unknown function (DUF1192)
     0.0046   16.3   4.2     0.0046   16.3   4.2    1.8  2  DUF3450          Protein of unknown function (DUF3450)
     0.0053   16.0   3.2     0.0088   15.3   3.2    1.2  1  Taxilin          Myosin-like coiled-coil protein
     0.0069   15.8   1.5      0.029   13.7   1.2    1.9  2  GAS              Growth-arrest specific micro-tubule binding
     0.0094   16.0   6.3     0.0094   16.0   6.3    1.9  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
  ------ inclusion threshold ------
      0.011   15.1  10.2      0.011   15.1  10.2    2.0  2  Tropomyosin      Tropomyosin
      0.026   14.6   2.7      0.037   14.1   1.3    1.8  2  DUF1664          Protein of unknown function (DUF1664)
      0.032   14.3   3.4      0.054   13.6   3.4    1.4  1  ADIP             Afadin- and alpha -actinin-Binding
      0.037   14.4   0.7      0.072   13.5   0.7    1.4  1  YlqD             YlqD protein
      0.037   12.7   0.4       0.05   12.3   0.4    1.2  1  AAA_13           AAA domain
      0.064   13.7   7.2          3    8.4   2.3    2.6  2  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
      0.089   13.0   9.2       0.16   12.2   9.2    1.4  1  ATG16            Autophagy protein 16 (ATG16)
       0.11   11.0   2.0      0.093   11.3   0.9    1.3  1  FapA             Flagellar Assembly Protein A
       0.11   12.3   0.4       0.19   11.6   0.4    1.4  1  DUF724           Protein of unknown function (DUF724)
       0.14   11.5  10.5       0.11   11.9   3.3    2.3  2  TraF_2           F plasmid transfer operon, TraF, protein
       0.16   11.0   1.6       0.27   10.3   1.6    1.4  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.17   10.1   3.4      0.099   10.8   1.4    1.5  2  EzrA             Septation ring formation regulator, EzrA
       0.17   11.1   5.3       0.11   11.9   3.2    1.5  2  Dynamitin        Dynamitin
        0.2   10.5   4.8       0.34    9.7   4.8    1.4  1  Spc7             Spc7 kinetochore protein
       0.21   10.7   6.4       0.37    9.8   6.4    1.3  1  PDCD7            Programmed cell death protein 7
       0.21    9.7   1.9        1.9    6.6   1.3    2.0  2  HSP70            Hsp70 protein
       0.24   10.8   5.2       0.42   10.0   5.2    1.4  1  Golgin_A5        Golgin subfamily A member 5
       0.25   11.4   3.1       0.63   10.1   3.1    1.6  1  DUF1515          Protein of unknown function (DUF1515)
       0.34   11.0  19.1       0.11   12.6   2.4    3.1  2  bZIP_2           Basic region leucine zipper
        0.4   10.7   7.5        7.1    6.7   6.8    2.4  1  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
       0.43   10.5   6.9        9.4    6.2   0.9    3.7  4  Prefoldin        Prefoldin subunit
       0.58    8.9   4.5       0.85    8.4   4.5    1.2  1  Nup188_C         Nuclear pore protein NUP188 C-terminal domai
        0.6   10.0   6.0        1.2    9.1   6.0    1.4  1  Ax_dynein_light  Axonemal dynein light chain
          1    9.9  17.2        1.8    9.1  13.5    2.5  2  APG6_N           Apg6 coiled-coil region
        1.4    9.1  18.5        2.5    8.2  14.4    2.3  2  Tropomyosin_1    Tropomyosin like
        1.4    9.4   5.4         16    6.0   0.1    2.7  2  LPP              Lipoprotein leucine-zipper
        2.6    8.4   5.4         15    6.0   0.4    2.5  2  TSC22            TSC-22/dip/bun family
        2.8    6.6   6.8        4.1    6.0   6.8    1.2  1  HAUS5            HAUS augmin-like complex subunit 5
        3.5    7.9   5.9        3.9    7.8   1.5    2.4  2  Spc24            Spc24 subunit of Ndc80
        4.6    6.0   5.4        1.5    7.6   2.4    1.6  2  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
        4.8    7.1  10.1        2.1    8.2   6.5    2.2  2  Phage_Mu_Gam     Bacteriophage Mu Gam like protein
        5.8    6.8  11.9         22    4.9   3.3    2.8  2  DivIC            Septum formation initiator
        5.9    7.2   7.1       0.96    9.8   3.5    1.5  1  OmpH             Outer membrane protein (OmpH-like)
        7.4    7.1  16.6         17    5.9   4.3    3.5  3  DUF4140          N-terminal domain of unknown function (DUF41
        7.8    4.9   8.8        1.4    7.4   5.2    1.5  2  FUSC             Fusaric acid resistance protein family
        8.2    7.1  15.7         23    5.7   0.1    3.0  3  DUF883           Bacterial protein of unknown function (DUF88


Domain annotation for each model (and alignments):
>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   1.4   1.7e-38   6.6e-36       2     130 .]     185     318 ..     184     318 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 1.7e-38
                           acVLRF1   2 rlgvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae.. 76 
                                       r+++++vr+++fa+g++e+ge+v+++++++dv+g++++GG+Sq+Rf+R r++q+d++l++++e++++ +++++++  
  gi|336253067|ref|YP_004596174.1| 185 RYALAVVRTDLFALGIYEDGERVDYRGFESDVKGSHSKGGFSQARFERLRNEQIDEHLDECRETLEEYVGAQAQSgr 261
                                       799******************************************************************65555566 PP

                           acVLRF1  77 .....vvlgGdrslvaevled..arlaplatlareelldvpdprravLedavrraravrve 130
                                            ++l+G+r +v+++ ++  ++l+p at+a++   +++dp + +Leda++++++++++
  gi|336253067|ref|YP_004596174.1| 262 aavdrLFLVGQRGVVDTLVDEsgPELEPDATAAVD---ATGDP-KPALEDAHHSFWTTELH 318
                                       78889*************9996566**********...*****.*************9986 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 !   32.7   0.3     2e-10   7.8e-08      14     107 ..     184     282 ..     181     310 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2e-10
                    baeRF_family10  14 erygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellaklleerg.. 88 
                                        ry++++v+ + ++l  ++ ge +  +++e++v+g + +gg  sq+rf+r + eq+++hl+e  e+l++++  +   
  gi|336253067|ref|YP_004596174.1| 184 GRYALAVVRTDLFALGIYEDGERVDYRGFESDVKGSHSKGGF-SQARFERLRNEQIDEHLDECRETLEEYVGAQAqs 259
                                       69****************************************.***************************9877666 PP

                    baeRF_family10  89 ....verlvlgGdeeetaalldr 107
                                           v+rl+l+G++ + + l+d 
  gi|336253067|ref|YP_004596174.1| 260 graaVDRLFLVGQRGVVDTLVDE 282
                                       7889*********9888888776 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0       0.6   2.4e+02      37      61 ..      73      97 ..      70     115 .. 0.84
   2 !   22.8   0.0   2.2e-07   8.9e-05       3      68 ..     187     252 ..     185     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.6
                                      STTBSCCCCHHHHHHHHHHHHHHHH CS
                            eRF1_2 37 krGgqsarrfeRlreekleeflkkv 61
                                      ++Gg + rr eRlr ++le  l+++
  gi|336253067|ref|YP_004596174.1| 73 GAGGVEIRRRERLRGRRLEDVLDRL 97
                                      579**************99988765 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 2.2e-07
                                       EEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                            eRF1_2   3 glivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaanka 68 
                                       +l v+  ++  +g+ ++  +   + +e++v + h +Gg s++rfeRlr+e+++e l++  e ++++
  gi|336253067|ref|YP_004596174.1| 187 ALAVVRTDLFALGIYEDGERVDYRGFESDVKGSHSKGGFSQARFERLRNEQIDEHLDECRETLEEY 252
                                       666666666666666666666667899*******************************99998876 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   5.7   5.5e-06    0.0022       8     110 ..      11      71 ..       9     135 .. 0.62
   2 ?   -2.1   0.0         7   2.8e+03     183     199 ..     234     250 ..     215     263 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.5e-06
                               ERM   8 releerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerkl 84 
                                       +el+er+ +l++e+++ +e  + + e+  + a+ +++aeee ++Le + a++e e                      
  gi|336253067|ref|YP_004596174.1|  11 AELKERIDELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGEL--------------------- 66 
                                       45555555555555555555555555555555555555555555555555555555..................... PP

                               ERM  85 reaeleaarleeeserkeeeaerLke 110
                                                            e+  +
  gi|336253067|ref|YP_004596174.1|  67 ---------------------EQVDD 71 
                                       .....................54444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7
                               ERM 183 kskrlqeqLkeLksele 199
                                       +++++ e+L+e ++ le
  gi|336253067|ref|YP_004596174.1| 234 RNEQIDEHLDECRETLE 250
                                       44555555555444444 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   8.0   0.00019     0.075      19      53 ..       7      41 ..       2      45 .. 0.87
   2 !    7.8   0.3    0.0083       3.3      23      40 ..      53      70 ..      51      75 .. 0.85
   3 ?   -1.1   0.0         5     2e+03      45      57 ..     256     268 ..     249     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00019
                           DUF1192 19 lLSveELeerIalLeaEIaRleaaiakkkasraAA 53
                                      lL+ +EL+erI +Le+E +Rl++  ++ ++ ra A
  gi|336253067|ref|YP_004596174.1|  7 LLGRAELKERIDELEDETDRLRERYEAESERRAEA 41
                                      5899**********************999999866 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0083
                           DUF1192 23 eELeerIalLeaEIaRle 40
                                      + Le+rIa+Le E + ++
  gi|336253067|ref|YP_004596174.1| 53 NRLEDRIAQLEGELEQVD 70
                                      669**********99876 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 5
                           DUF1192  45 kkkasraAAealF 57 
                                       +++++raA + lF
  gi|336253067|ref|YP_004596174.1| 256 QAQSGRAAVDRLF 268
                                       67899*****999 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   4.2   1.1e-05    0.0046      33      92 ..      11      70 ..       9      75 .. 0.96
   2 ?   -2.8   0.0         8   3.2e+03      45      60 ..     237     252 ..     216     261 .. 0.50

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                           DUF3450 33 aqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92
                                      a+  ++id+l+de++ l ++y+a +e+ ++++  +++ e+ v+ +e +ia+le ++e+++
  gi|336253067|ref|YP_004596174.1| 11 AELKERIDELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQVD 70
                                      7889*****************************************************997 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8
                           DUF3450  45 ekqellaeyralkeel 60 
                                       + +e+l+e r+  ee 
  gi|336253067|ref|YP_004596174.1| 237 QIDEHLDECRETLEEY 252
                                       2233444444433333 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   3.2   2.2e-05    0.0088     249     302 ..      13      66 ..      11      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                           Taxilin 249 mtkktkklEketnlwkskfektnkallemaeertekkkeieklkkkiqkLeklc 302
                                       +++ + +lE+et+++++++e+  +  +e+a  r+e ++e+++l+ +i +Le   
  gi|336253067|ref|YP_004596174.1|  13 LKERIDELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGEL 66 
                                       788999********************************************9765 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 !   13.7   1.2   7.2e-05     0.029      27     116 ..      16     109 ..      11     132 .. 0.68
   2 ?   -0.3   0.0       1.5   5.8e+02     127     171 ..     210     255 ..     208     264 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.2e-05
                               GAS  27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkq....slknlkarlkelek 99 
                                        I++l +e  +l+++ e+ + + +e++   ++ +e+++++e  +++L+ +l++ + d +      ++ + r ++le+
  gi|336253067|ref|YP_004596174.1|  16 RIDELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQVDDDGAggveIRRRERLRGRRLED 92 
                                       58899999999999999999999999999999999999999999999999999988865111133333444455555 PP

                               GAS 100 elkdlkwehevleqrfe 116
                                        l +l+ +    e  ++
  gi|336253067|ref|YP_004596174.1|  93 VLDRLESFRSDAEGALT 109
                                       55555555555554444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                               GAS 127 kkfeaaiqevqqktglknllLek.klkalqeelEkkeaqleevlaa 171
                                       + fe+ ++  + k g+ +   e+ + ++++e l++  + lee++ a
  gi|336253067|ref|YP_004596174.1| 210 RGFESDVKGSHSKGGFSQARFERlRNEQIDEHLDECRETLEEYVGA 255
                                       5666667777777777666666656677777777777777777655 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   6.3   2.4e-05    0.0094      26      83 ..      12      69 ..       9      74 .. 0.94
   2 ?   -2.0   0.1         9   3.6e+03     101     113 ..     238     250 ..     228     263 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.4e-05
                        TPR_MLP1_2 26 klqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesa 83
                                      +l+e + + ++++ +  ++Ye e    ae++++ q++ ee+n+l+++ia+l+ e+e++
  gi|336253067|ref|YP_004596174.1| 12 ELKERIDELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQV 69
                                      7899999999********************************************9987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 9
                        TPR_MLP1_2 101 lekelselekrie 113
                                       ++++l+e+++ +e
  gi|336253067|ref|YP_004596174.1| 238 IDEHLDECRETLE 250
                                       2222222222222 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1  10.2   2.9e-05     0.011       2      57 ..      16      71 ..      15      77 .. 0.94
   2 ?   -1.8   0.1       4.2   1.7e+03     217     231 ..     232     246 ..     228     259 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.9e-05
                       Tropomyosin  2 klkqveeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeelertee 57
                                      ++ ++e+e+d+ +er e+  ++ +ea +++++ae+Ev  l+ ri +le ele++++
  gi|336253067|ref|YP_004596174.1| 16 RIDELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQVDD 71
                                      78899***********************************************9987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.2
                       Tropomyosin 217 kekykaiseeLdqtl 231
                                       + ++++i+e+Ld+  
  gi|336253067|ref|YP_004596174.1| 232 RLRNEQIDEHLDECR 246
                                       555666666665433 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.3   9.4e-05     0.037      61     121 ..      10      70 ..       5      72 .. 0.93
   2 ?   -1.9   0.0       7.9   3.2e+03      69      83 ..     236     250 ..     232     261 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.4e-05
                           DUF1664  61 krhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       + +L++rid+++++ d   e  ++ +e  +e+ +  +e +e+v+ +++ + +le++le+++
  gi|336253067|ref|YP_004596174.1|  10 RAELKERIDELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQVD 70 
                                       789******************************************************9986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.9
                           DUF1664  69 drvdkkldeqkeisk 83 
                                       +++d++lde+ e+ +
  gi|336253067|ref|YP_004596174.1| 236 EQIDEHLDECRETLE 250
                                       566777777776654 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.4   0.00013     0.054      55     116 ..      10      71 ..       7      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00013
                              ADIP  55 reslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklkneke 116
                                       r +l+e+i +le e +rl+ ++e  +++ ++ +r  + ++++ + le ++++le  l +  +
  gi|336253067|ref|YP_004596174.1|  10 RAELKERIDELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQVDD 71 
                                       6789999*******************************************999988877655 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.7   0.00018     0.072      24      87 ..      12      70 ..       9      77 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00018
                              YlqD 24 qlqaqieqldkelqqLefqakrlikeikkqsaq..qieeiqeqvekekserlekkkqllqqleqvq 87
                                      +l+++i++l+ e         rl +  + +s++  +++++++++e+e ++++++++ql+ +leqv+
  gi|336253067|ref|YP_004596174.1| 12 ELKERIDELEDET-------DRLRERYEAESERraEAARARQEAEEEVNRLEDRIAQLEGELEQVD 70
                                      4445555555555.......555444444444333889999***********************96 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   0.00013      0.05     287     347 ..      12      69 ..       1     112 [. 0.58

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            AAA_13 287 rLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaK 347
                                       +L+++i+++e ++++l e+++a s++   + +++++++e+++e + le+++ +l+ +le+ 
  gi|336253067|ref|YP_004596174.1|  12 ELKERIDELEDETDRLRERYEAESER---RAEAARARQEAEEEVNRLEDRIAQLEGELEQV 69 
                                       45555555555555444444443332...12234444444444444444444444444443 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 ?    8.4   2.3    0.0075         3      11      59 ..      11      54 ..       9      55 .. 0.82
   2 ?    8.3   0.9     0.008       3.2      19      66 ..      47      99 ..      42      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0075
                       Cep57_MT_bd 11 eaLaevlkeLedEfehlklelqelaaqynaldpslgkrkRkdLaeelee 59
                                       +L+e + eLedE + l+ +++  +++  +       r R++ +ee+++
  gi|336253067|ref|YP_004596174.1| 11 AELKERIDELEDETDRLRERYEAESERRAEAA-----RARQEAEEEVNR 54
                                      58*******************99888877776.....777777777665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.008
                       Cep57_MT_bd 19 eLedEfehlklelqelaaqynaldpsl....gkrkRkdLa.eeleelvkrlEa 66
                                      e e+E+  l  + ++l+ ++++ d+      + r+R+ L  ++le++++rlE+
  gi|336253067|ref|YP_004596174.1| 47 EAEEEVNRLEDRIAQLEGELEQVDDDGaggvEIRRRERLRgRRLEDVLDRLES 99
                                      7799********************98878888999999963789999999995 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   9.2   0.00041      0.16      96     158 ..       9      71 ..       4      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00041
                             ATG16  96 srgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqD 158
                                        r+el++r+ el++e ++l+e+ ++++er ae+ + r++ e++++++e++++++e  ++++ D
  gi|336253067|ref|YP_004596174.1|   9 GRAELKERIDELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQVDD 71 
                                       689***************************************************999999988 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.9   0.00023     0.093     340     408 ..      11      73 ..       2      85 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                              FapA 340 keleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeel 408
                                       +el+e++ ele+e+++l+++++  ++ +      +e     ++++e+ ++l++++++le el+++++  
  gi|336253067|ref|YP_004596174.1|  11 AELKERIDELEDETDRLRERYEAESERR------AEAARARQEAEEEVNRLEDRIAQLEGELEQVDDDG 73 
                                       5666666666666666666655444433......34446677777777777777777777777776654 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00047      0.19      99     147 ..      19      67 ..       2     110 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00047
                            DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqla 147
                                       +l de ++l+e+ ++  ++ +e++ +++++eee++ le +i++le +l+
  gi|336253067|ref|YP_004596174.1|  19 ELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELE 67 
                                       3445555555555555555555555555566666666666666655554 PP

>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.3   0.00027      0.11      35      83 ..      12      74 ..       8      80 .. 0.72
   2 ?    3.8   0.6     0.081        32      40      82 ..      90     132 ..      76     140 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                            TraF_2 35 nlvDkiDdlsdildgleaavnaasad.............etq.vdeaaddlnalLedlggdgy 83
                                      +l ++iD+l+d++d+l++  +a+s++             e++ +++++++l+++Le++++dg 
  gi|336253067|ref|YP_004596174.1| 12 ELKERIDELEDETDRLRERYEAESERraeaararqeaeeEVNrLEDRIAQLEGELEQVDDDGA 74
                                      567788888888886666655555555666667776666555899999999999999999983 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.081
                            TraF_2  40 iDdlsdildgleaavnaasadetq.vdeaaddlnalLedlggdg 82 
                                       ++d+ d+l+++++++++a  +  + +d++ ddl+++L dl gd 
  gi|336253067|ref|YP_004596174.1|  90 LEDVLDRLESFRSDAEGALTTV-VaADADRDDLDGDLTDLLGDR 132
                                       3333344444444444444333.36**************98886 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 ?   10.3   1.6   0.00068      0.27      35      99 ..       7      68 ..       4     112 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00068
                             Atg14 35 ksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeiee 99
                                      ++ +++lk++i++++ +++   +l+++ + ++++  e    +++ +e++++l+d++ ql  e+e+
  gi|336253067|ref|YP_004596174.1|  7 LLGRAELKERIDELEDETD---RLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQ 68
                                      5566777777777777666...5666666666666666666666666666666666666555543 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.4   0.00025     0.099     276     333 ..      13      70 ..       8      75 .. 0.60
   2 ?   -2.8   0.0       3.3   1.3e+03      78      93 ..     236     251 ..     227     260 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS CS
                              EzrA 276 veeelktieeeidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlk 333
                                        +e ++++e+e d L +  e+E e + e  +  +e +e++++le+ + +l+ el++++
  gi|336253067|ref|YP_004596174.1|  13 LKERIDELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQVD 70 
                                       4555666666666666666666666666666666666666666666666666666654 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.3
                                       HHHHHT-GGGT--S-S CS
                              EzrA  78 peieellfeaeelldk 93 
                                       ++i+e+l e+ e l++
  gi|336253067|ref|YP_004596174.1| 236 EQIDEHLDECRETLEE 251
                                       2333333333333333 PP

>> Dynamitin  Dynamitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.2   0.00027      0.11      93     178 ..      13     103 ..       9     126 .. 0.78
   2 ?   -2.2   0.0       4.9     2e+03     124     145 ..     231     252 ..     212     266 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                         Dynamitin  93 leqklqRLqrEveeleeEvekakeaakes....eeeeldpvelaeqleslqkqLeel.eellgedsaasltdaqeal 164
                                       l +++  L  E  +l+e +e+ +e ++e+    +e e+++  l +++++l+ +Le++ ++ +g     + ++ ++++
  gi|336253067|ref|YP_004596174.1|  13 LKERIDELEDETDRLRERYEAESERRAEAararQEAEEEVNRLEDRIAQLEGELEQVdDDGAGGVEIRRRERLRGRR 89 
                                       67899999999999999999988888777777777777888899999999999999954444444444777788888 PP

                         Dynamitin 165 akrllsqleefkes 178
                                        + +l++le+f++ 
  gi|336253067|ref|YP_004596174.1|  90 LEDVLDRLESFRSD 103
                                       88888888888754 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.9
                         Dynamitin 124 eeldpvelaeqleslqkqLeel 145
                                       e+l ++++ e+l++ ++ Lee 
  gi|336253067|ref|YP_004596174.1| 231 ERLRNEQIDEHLDECRETLEEY 252
                                       5555566666666666666665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.8   0.00087      0.34     171     234 ..      12      71 ..       9     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00087
                              Spc7 171 eleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleelee 234
                                       el+e+ +ele+e ++l+e++e  es  ++e + +r+e   +++e++++++++a+l+ +le++++
  gi|336253067|ref|YP_004596174.1|  12 ELKERIDELEDETDRLRERYEA-ESERRAEAARARQE---AEEEVNRLEDRIAQLEGELEQVDD 71 
                                       6778888888888888887754.66566666666654...556666777888888888887765 PP

>> PDCD7  Programmed cell death protein 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.4   0.00094      0.37      48     134 ..      10      94 ..       5     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00094
                             PDCD7  48 kkelqeklalLedaerleelkrklerrkkkRarrkrrkeerkeekkekeerraereakidkWrrkqiqeveekkkeq 124
                                       ++el+e++++Led+  +++l+++ e+ +++Ra   r+++e++ee ++ e r+a++e + ++  ++    ve +++e+
  gi|336253067|ref|YP_004596174.1|  10 RAELKERIDELEDE--TDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQVDDDGAGGVEIRRRER 84 
                                       689999*****886..5789*****************************************9999999999999998 PP

                             PDCD7 125 elkeaadavL 134
                                          +  ++vL
  gi|336253067|ref|YP_004596174.1|  85 LRGRRLEDVL 94 
                                       7777777776 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.3    0.0047       1.9     493     549 ..      14      70 ..       8     114 .. 0.74
   2 ?    1.6   0.0      0.15        60     285     334 ..     217     271 ..     206     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0047
                                       EEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHG CS
                             HSP70 493 eitieaseglseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeea 549
                                       +++i++ e+ ++   e+ + ++e+ ae+ ++++ea e+ n++e+ + +le++le+  
  gi|336253067|ref|YP_004596174.1|  14 KERIDELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQVD 70 
                                       556666667777777778888888888888888888888888888888888887763 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.15
                                       TTEEEEEEEEHHHHHHHHHHHHHHTHHHHHHHHH.....HCTEEGGGCSEEEEES CS
                             HSP70 285 dgkdlseklsRakfeelvedllertlepvekalk.....daklkkeeidevvlvG 334
                                       +g + ++ +s a+fe+l ++ +++ l+ +++ l+     +a+     +d + lvG
  gi|336253067|ref|YP_004596174.1| 217 KGSHSKGGFSQARFERLRNEQIDEHLDECRETLEeyvgaQAQSGRAAVDRLFLVG 271
                                       47899999************99999999999996222225666677888888887 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.2    0.0011      0.42      74     135 ..      10      71 ..       4     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                         Golgin_A5  74 rtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleeelvrska 135
                                       r+el++  ++ + e++ lre+ +   e+ +e  +a++e+e+e++rl++ +  le el ++  
  gi|336253067|ref|YP_004596174.1|  10 RAELKERIDELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQVDD 71 
                                       7888888888999******************************************9998755 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.1    0.0016      0.63       4      63 ..      11      73 ..       8      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0016
                           DUF1515  4 agvlqqlgtllaevkelredlk.rsedrsdasrakm..yrkmdelvervtalegsvvklkadi 63
                                      a +++++++l  e   lre    +se r++a+ra+    + ++ l +r++ leg + ++++d 
  gi|336253067|ref|YP_004596174.1| 11 AELKERIDELEDETDRLRERYEaESERRAEAARARQeaEEEVNRLEDRIAQLEGELEQVDDDG 73
                                      5677888999999999**998768*******9997511567889999**********999995 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.0    0.0014      0.57      28      50 ..      11      33 ..       7      36 .. 0.92
   2 ?   12.6   2.4   0.00028      0.11      27      52 ..      45      70 ..      38      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0014
                                      HHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2 28 eeleervkeLeeeNaqLrqkveq 50
                                      +el+er+ eLe e ++Lr+++e+
  gi|336253067|ref|YP_004596174.1| 11 AELKERIDELEDETDRLRERYEA 33
                                      79******************986 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00028
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2 27 eeeleervkeLeeeNaqLrqkveqLe 52
                                       +e ee+v++Le ++aqL+ ++eq+ 
  gi|336253067|ref|YP_004596174.1| 45 RQEAEEEVNRLEDRIAQLEGELEQVD 70
                                      5899*******************985 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   6.8     0.018       7.1      12      66 ..      15      69 ..      14      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.018
                        TMF_DNA_bd 12 eqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleel 66
                                      e+I++L  E  +L+    ++++   +     +e+e+e+++l++++++le ele+ 
  gi|336253067|ref|YP_004596174.1| 15 ERIDELEDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQV 69
                                      6899999999999999999999999999999999999999999999999999986 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2      0.17        67      87     108 ..      11      32 ..      10      37 .. 0.80
   2 ?    6.2   0.9     0.024       9.4      85     117 ..      37      69 ..      33      72 .. 0.89
   3 ?    0.8   0.0       1.1   4.5e+02      20      43 ..      88     111 ..      80     116 .. 0.79
   4 ?   -0.1   0.0         2   8.1e+02      15      34 ..     233     254 ..     226     275 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  87 eelekqlekleeeleklkdqit 108
                                       +el++ +++le+e + l+++++
  gi|336253067|ref|YP_004596174.1|  11 AELKERIDELEDETDRLRERYE 32 
                                       5788888888888888888875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  85 kleelekqlekleeeleklkdqittleanlaql 117
                                       + +e+ +++++ eee++ l d+i +le +l+q+
  gi|336253067|ref|YP_004596174.1|  37 RRAEAARARQEAEEEVNRLEDRIAQLEGELEQV 69 
                                       778999999*****************9999987 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHTT.-TT-EEEE CS
                         Prefoldin  20 eelektletlktlkkedegkevlv 43 
                                       ++le++l++l++++   eg++++v
  gi|336253067|ref|YP_004596174.1|  88 RRLEDVLDRLESFRSDAEGALTTV 111
                                       578999999999999888888776 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 2
                                       HHHHH..HHHHHHHHHHHHHTT CS
                         Prefoldin  15 lkeai..eelektletlktlkk 34 
                                       l+ ++  e+l++++etl+++  
  gi|336253067|ref|YP_004596174.1| 233 LRNEQidEHLDECRETLEEYVG 254
                                       5443322568888888887765 PP

>> Nup188_C  Nuclear pore protein NUP188 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.5    0.0021      0.85     308     361 ..      10      61 ..       5      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHT-HHHHHHHB---SHHHHHHHHS---.SS-S-SSHHHHHHHH CS
                          Nup188_C 308 aasvkedvefwlssrklLrerlvplgerelelarkkaedesskaenrLeekvva 361
                                       +a++ke ++++  +   Lrer  + +er +e ar ++e  +++  nrLe+++ +
  gi|336253067|ref|YP_004596174.1|  10 RAELKERIDELEDETDRLRERYEAESERRAEAARARQE--AEEEVNRLEDRIAQ 61 
                                       6899*****************************99999..88999*****9965 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 ?    9.1   6.0    0.0029       1.2     129     186 ..      11      67 ..       7      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0029
                   Ax_dynein_light 129 keLeeekeelekqvaelkaklealekrekerrqeeekkheeeieflkksnqqlkeqle 186
                                       +eL+e+ +ele++   l++++ea+ +r +e  +++ ++ eee++ l+    ql+ +le
  gi|336253067|ref|YP_004596174.1|  11 AELKERIDELEDETDRLRERYEAESERRAEAARAR-QEAEEEVNRLEDRIAQLEGELE 67 
                                       57899999999999999999999888888776654.5667899999999999998887 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  13.5    0.0046       1.8      34     124 ..      12      99 ..       7     108 .. 0.85
   2 ?    1.6   0.1      0.93   3.7e+02      24      70 ..     205     252 ..     201     266 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0046
                            APG6_N  34 klkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelql 110
                                       +lk++ +e    ++e+++l+e++e+ ++ ++e+ +  +e+e+e  +le+ +a+le ele+++++ +  ++ ++  +l
  gi|336253067|ref|YP_004596174.1|  12 ELKERIDEL---EDETDRLRERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQVDDDGAGGVEIRRRERL 85 
                                       556665554...57999999999999999*********************************999999999999999 PP

                            APG6_N 111 elleleeeldslea 124
                                          +le+ ld le+
  gi|336253067|ref|YP_004596174.1|  86 RGRRLEDVLDRLES 99 
                                       99999998888876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.93
                            APG6_N  24 erdaYeeflkklkkekkeeekqdeeleeleee.leklekeeeelleeL 70 
                                       er +Y+ f++ +k ++++   ++   e+l++e +++  +e +e lee 
  gi|336253067|ref|YP_004596174.1| 205 ERVDYRGFESDVKGSHSKGGFSQARFERLRNEqIDEHLDECRETLEEY 252
                                       788899999999877555332344444444333555555555555554 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  14.4    0.0063       2.5      39      98 ..      12      75 ..      10     120 .. 0.69
   2 ?    2.5   0.1      0.38   1.5e+02      43      63 ..     234     254 ..     226     265 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0063
                     Tropomyosin_1 39 sLtkknqqleeevekleeklkeakekaeesekkktnne....altrkiqlLEeeleesdkkLke 98
                                      +L++++++le+e ++l e+ +   e   e++++++++e     l+ +i +LE ele+ d + + 
  gi|336253067|ref|YP_004596174.1| 12 ELKERIDELEDETDRLRERYEAESERRAEAARARQEAEeevnRLEDRIAQLEGELEQVDDDGAG 75
                                      6777888888888888888777777777777666666666666777888888888887766555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.38
                     Tropomyosin_1  43 knqqleeevekleeklkeake 63 
                                       +n+q++e +++  e+l+e+  
  gi|336253067|ref|YP_004596174.1| 234 RNEQIDEHLDECRETLEEYVG 254
                                       677888888888888877654 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.4      0.23        91      11      41 ..      12      45 ..      11      49 .. 0.68
   2 ?    6.0   0.1      0.04        16       7      29 ..      50      72 ..      46      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.23
                               LPP 11 qLkskvdqlssdvnsakaaaqa...akeEAaRAN 41
                                      +Lk+ +d+l+++++ +++  +a    ++EAaRA 
  gi|336253067|ref|YP_004596174.1| 12 ELKERIDELEDETDRLRERYEAeseRRAEAARAR 45
                                      6888999999997777765554111566888885 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.04
                               LPP  7 sqVsqLkskvdqlssdvnsakaa 29
                                      ++V++L++ ++ql+ +++++ ++
  gi|336253067|ref|YP_004596174.1| 50 EEVNRLEDRIAQLEGELEQVDDD 72
                                      68***************999987 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.4     0.037        15      18      42 ..      12      29 ..      11      39 .. 0.63
   2 ?    4.1   0.6      0.15        59      14      33 ..      50      69 ..      48      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.037
                             TSC22 18 vLkekIkeLeernseleeENslLka 42
                                      +Lke+I eLe++  +l+       +
  gi|336253067|ref|YP_004596174.1| 12 ELKERIDELEDETDRLR-------E 29
                                      36666666666655554.......3 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.15
                             TSC22 14 EeVevLkekIkeLeernsel 33
                                      EeV+ L ++I+ Le + +++
  gi|336253067|ref|YP_004596174.1| 50 EEVNRLEDRIAQLEGELEQV 69
                                      99*********999887775 PP

>> HAUS5  HAUS augmin-like complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   6.8      0.01       4.1      70     109 ..      33      72 ..      10      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.01
                             HAUS5  70 skaeeresaaaereelekeverLraeirrldkeleareee 109
                                        + e+r +aa+ r+e+e+ev+rL + i++l+ ele+++++
  gi|336253067|ref|YP_004596174.1|  33 AESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQVDDD 72 
                                       567788889999***********************99875 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.3      0.48   1.9e+02      15      43 ..      12      40 ..       9      47 .. 0.53
   2 ?    7.8   1.5    0.0097       3.9       6      42 ..      38      74 ..      33     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.48
                             Spc24 15 dleselesleselaelkeeleeleeesee 43
                                      +l++ +++le e ++l+e++e  +e + e
  gi|336253067|ref|YP_004596174.1| 12 ELKERIDELEDETDRLRERYEAESERRAE 40
                                      45555555666666666555554444444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0097
                             Spc24  6 kfriakelsdleselesleselaelkeeleeleeese 42
                                      + ++a + +++e+e+++le + a+l+ ele++++ + 
  gi|336253067|ref|YP_004596174.1| 38 RAEAARARQEAEEEVNRLEDRIAQLEGELEQVDDDGA 74
                                      667899999*********************9988765 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.4    0.0038       1.5     176     230 ..      13      70 ..       9     101 .. 0.76
   2 ?   -1.9   0.1       2.9   1.1e+03     173     203 ..     228     258 ..     224     267 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0038
                        Fmp27_WPPW 176 leeRleeleeqiekleekleelelkseke...deelkeeieelekeikelkeklefle 230
                                       l+eR++ele++ ++l+e+ e  ++++ +    ++e +ee+++le+ i++l+ +le ++
  gi|336253067|ref|YP_004596174.1|  13 LKERIDELEDETDRLRERYEAESERRAEAaraRQEAEEEVNRLEDRIAQLEGELEQVD 70 
                                       7899999999999999999887777777555556666666666666666655555554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.9
                        Fmp27_WPPW 173 kelleeRleeleeqiekleekleelelksek 203
                                       ++  + R e+++e++++++e+lee+   + +
  gi|336253067|ref|YP_004596174.1| 228 ARFERLRNEQIDEHLDECRETLEEYVGAQAQ 258
                                       5566779999999999999999998777666 PP

>> Phage_Mu_Gam  Bacteriophage Mu Gam like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.5    0.0053       2.1      16      56 ..      28      68 ..      10      69 .. 0.71
   2 ?   -2.3   0.1       9.5   3.8e+03      40      61 ..     235     256 ..     231     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0053
                                      HHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH CS
                      Phage_Mu_Gam 16 releeieaeaneeiaaikekleaeleplkkeieylesllkq 56
                                      re  e+e+e  +e a++++++e+e+++l+++i++le++l+q
  gi|336253067|ref|YP_004596174.1| 28 RERYEAESERRAEAARARQEAEEEVNRLEDRIAQLEGELEQ 68
                                      3334445555566677779*******************997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.5
                                       CHHHHHHHHHHHHHHHHHHHCT CS
                      Phage_Mu_Gam  40 leplkkeieylesllkqYaean 61 
                                       +e++++  ++  ++l++Y+ a+
  gi|336253067|ref|YP_004596174.1| 235 NEQIDEHLDECRETLEEYVGAQ 256
                                       5677788888888888887665 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   4.6      0.13        53      34      55 ..      11      32 ..      10      48 .. 0.58
   2 ?    4.9   3.3     0.056        22      25      54 ..      44      72 ..      35      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                                      HHHHHHHHHHHHHHCC-XXXXX CS
                             DivIC 34 aklkaeneeLeaevkdLksded 55
                                      a+lk++++eLe+e ++L+  ++
  gi|336253067|ref|YP_004596174.1| 11 AELKERIDELEDETDRLRERYE 32
                                      4677777777777777765333 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.056
                                      HHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                             DivIC 25 eiaalqaelaklkaeneeLeaevkdLksde 54
                                       +++ ++e+++l +++++Le e+++  +d+
  gi|336253067|ref|YP_004596174.1| 44 ARQEAEEEVNRLEDRIAQLEGELEQV-DDD 72
                                      5678899999*************999.555 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.5    0.0024      0.96      30      76 ..      12      62 ..       9      98 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0024
                                      HHHHHHHHHHHHHHHHHHHHHHHTTTS......-HHHHHHHHHHHHHHHHHH CS
                              OmpH 30 klqaeleakekelqklqeelqkkakkl.e....keekeqelqkkeqelqqkq 76
                                      +l++ ++++e+e ++l+e+++++++   e    ++e+e+e++++e+++ q +
  gi|336253067|ref|YP_004596174.1| 12 ELKERIDELEDETDRLRERYEAESERRaEaaraRQEAEEEVNRLEDRIAQ-L 62
                                      45556666666666666666644444333444456666664444444444.2 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 ?    5.6   2.7     0.054        21      68      95 ..      11      38 ..       9      41 .. 0.89
   2 ?    5.9   4.3     0.043        17      57      87 ..      42      72 ..      34      75 .. 0.68
   3 ?    1.0   0.0       1.5   5.8e+02      47      80 ..     223     255 ..     215     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.054
                           DUF4140 68 kalraeleeledelaaledelaaaearl 95
                                      ++l+++++elede ++l+++ +a ++r+
  gi|336253067|ref|YP_004596174.1| 11 AELKERIDELEDETDRLRERYEAESERR 38
                                      689****************999988876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.043
                           DUF4140 57 vpnreaeeeelkalraeleeledelaalede 87
                                         r+++eee+++l++++ +le el++++d+
  gi|336253067|ref|YP_004596174.1| 42 ARARQEAEEEVNRLEDRIAQLEGELEQVDDD 72
                                      3445555556888888888888888888775 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.5
                           DUF4140  47 atildvqvervpnreaeeeelkalraeleelede 80 
                                          ++ ++er  n++++e+ l++ r++lee   +
  gi|336253067|ref|YP_004596174.1| 223 GGFSQARFERLRNEQIDEH-LDECRETLEEYVGA 255
                                       5566778888888888887.99988888886554 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   5.2    0.0034       1.4     269     361 ..      14     114 ..       3     116 .. 0.60
   2 ?   -2.8   0.1       4.3   1.7e+03     272     291 ..     239     258 ..     225     283 .. 0.41

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0034
                              FUSC 269 aaaaealeaalaalrarlralrrale...adadtaalllarlaellaelaqllaslraleaaiaa.....arraerl 337
                                       ++  ++le++ ++lr+r +a +++++    +++ a++ + rl +++a+l   l++++++ a++++     + r +rl
  gi|336253067|ref|YP_004596174.1|  14 KERIDELEDETDRLRERYEAESERRAeaaRARQEAEEEVNRLEDRIAQLEGELEQVDDDGAGGVEirrreRLRGRRL 90 
                                       44566677777777777755555555233444444444555555555555555555555555555877777777778 PP

                              FUSC 338 arhrdhlaallnglraalaillag 361
                                       ++  d+l+ +++ + +al++++a+
  gi|336253067|ref|YP_004596174.1|  91 EDVLDRLESFRSDAEGALTTVVAA 114
                                       888888888888888888888775 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.3
                              FUSC 272 aealeaalaalrarlralrr 291
                                        e+l++ +++l++ + a+ +
  gi|336253067|ref|YP_004596174.1| 239 DEHLDECRETLEEYVGAQAQ 258
                                       12222222222222211111 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 ?    4.7   8.6      0.12        47       2      55 ..      12      67 ..      11      78 .. 0.78
   2 ?   -0.6   0.1       5.4   2.1e+03      39      59 ..      89     109 ..      61     120 .. 0.58
   3 ?    5.7   0.1     0.057        23      24      64 ..     225     266 ..     218     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.12
                            DUF883  2 eleaeleslladleellkeaadeage..eaeelRerleerlerarerlrdaeeava 55
                                      el++ +++l ++++ l ++ ++e+++  ea+++R+++ee+++r+ +r++++e +++
  gi|336253067|ref|YP_004596174.1| 12 ELKERIDELEDETDRLRERYEAESERraEAARARQEAEEEVNRLEDRIAQLEGELE 67
                                      57788999999999999987777766115556677899999**9999999988776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 5.4
                            DUF883  39 rlerarerlrdaeeavaerak 59 
                                       rle++ +rl+  + +++    
  gi|336253067|ref|YP_004596174.1|  89 RLEDVLDRLESFRSDAEGALT 109
                                       455555555555555554444 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.057
                            DUF883  24 eageeaeelR.erleerlerarerlrdaeeavaerakeaaea 64 
                                        ++   e+lR e+++e+l++ re+l++   a a++ ++a+++
  gi|336253067|ref|YP_004596174.1| 225 FSQARFERLRnEQIDEHLDECRETLEEYVGAQAQSGRAAVDR 266
                                       56777888985689************9999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1620  (0.0903564); expected 358.6 (0.02)
Passed bias filter:                     1117  (0.0623013); expected 358.6 (0.02)
Passed Vit filter:                       265  (0.0147805); expected 17.9 (0.001)
Passed Fwd filter:                        65  (0.00362541); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.79u 0.31s 00:00:01.10 Elapsed: 00:00:00.46
# Mc/sec: 2109.27
//
Query:       gi|336253068|ref|YP_004596175.1|  [L=131]
Description: hypothetical protein Halxa_1664 [Halopiger xanaduensis SH-6]
Scores for 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   12.3   0.0          8    6.3   0.0    2.4  2  PSD2      Protein of unknown function (DUF1585)


Domain annotation for each model (and alignments):
>> PSD2  Protein of unknown function (DUF1585)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0    0.0035        63      33      52 ..      39      58 ..      36      60 .. 0.89
   2 ?    6.3   0.0   0.00044         8       2      36 ..      83     112 ..      82     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0035
                              PSD2 33 YAlGRgleasDrcaveeiva 52
                                      YA G gle+ D++ v ++++
  gi|336253068|ref|YP_004596175.1| 39 YASGEGLEPLDSPLVMKLES 58
                                      **************998876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00044
                              PSD2   2 GesfegpaeLkqlLlarsdqfarclaeklltYAlG 36 
                                       G+++++p  L+++ lar+++     a++ll+YA G
  gi|336253068|ref|YP_004596175.1|  83 GTEIRNPPALQEVFLARRER-----ARQLLEYAGG 112
                                       89999999999999776666.....5677777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 990.05
//
Query:       gi|336253069|ref|YP_004596176.1|  [L=406]
Description: hypothetical protein Halxa_1665 [Halopiger xanaduensis SH-6]
Scores for 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   15.2  30.1      0.014   15.2  30.1    4.5  4  Collagen        Collagen triple helix repeat (20 copies)
      0.016   14.7   4.4      0.032   13.7   4.4    1.5  1  DUF4349         Domain of unknown function (DUF4349)
      0.055   13.5   1.8        0.1   12.6   1.8    1.5  1  PilJ            Type IV pili methyl-accepting chemotaxis tran
      0.089   13.4   2.3        0.4   11.3   2.3    2.3  1  SlyX            SlyX
       0.13   10.8   3.6       0.17   10.4   3.6    1.2  1  FUSC            Fusaric acid resistance protein family
       0.14   12.4   4.4        0.2   11.9   3.2    1.7  2  ABC_tran_CTD    ABC transporter C-terminal domain
       0.15   12.1   1.9        0.2   11.6   1.9    1.2  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
       0.24   12.3   3.3       0.38   11.7   3.3    1.3  1  PRKG1_interact  cGMP-dependent protein kinase interacting dom
       0.37    9.6   2.2       0.51    9.2   2.2    1.2  1  Spc7            Spc7 kinetochore protein
        1.1    9.6   3.4        2.4    8.6   2.9    1.8  1  CLZ             C-terminal leucine zipper domain of cyclic nu


Domain annotation for each model (and alignments):
>> Collagen  Collagen triple helix repeat (20 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.4   8.6        10   1.8e+04      12      31 ..     180     199 ..     166     204 .. 0.34
   2 ?   15.2  30.1   7.6e-06     0.014       6      59 ..     205     258 ..     196     259 .. 0.91
   3 ?    1.4  29.7      0.15   2.7e+02       3      56 ..     229     281 ..     228     318 .. 0.68
   4 ?    0.2  17.6      0.36   6.5e+02      12      48 ..     358     394 ..     346     406 .] 0.42

  Alignments for each domain:
  == domain 1  score: -5.4 bits;  conditional E-value: 10
                                       XXXXXXX-----XXXXEEEE CS
                          Collagen  12 pGppGkrGepGeaGekGekG 31 
                                        Gpp +rG++ ++  +G+ G
  gi|336253069|ref|YP_004596176.1| 180 GGPPADRGPNATTPGAGNGG 199
                                       12222233333322222222 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 7.6e-06
                                       XXXXXXXXXXXXX-----XXXXEEEE-TTSS-----------------BB--XX CS
                          Collagen   6 pGepGppGppGkrGepGeaGekGekGpaGekGppGaaGkpGapGekGeaGapge 59 
                                       +G++ ppG++G++ +pG+aG++ ++G+aG++ ppG+aG++ +pG++G++ +pg+
  gi|336253069|ref|YP_004596176.1| 205 AGNQTPPGQAGNQTPPGQAGNQTPPGQAGNQTPPGQAGNQTPPGQAGNQTPPGQ 258
                                       69999999999999**********************************999998 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.15
                                       XXXXXXXXXXXXXXXX-----XXXXEEEE-TTSS-----------------BB- CS
                          Collagen   3 pGepGepGppGppGkrGepGeaGekGekGpaGekGppGaaGkpGapGekGeaGa 56 
                                       pG++G++ ppG++G++ +pG+aG++ ++G+a ++  pG++G+p ++G+  ++Ga
  gi|336253069|ref|YP_004596176.1| 229 PGQAGNQTPPGQAGNQTPPGQAGNQTPPGQADNQ-TPGNQGPPDTAGNGAAPGA 281
                                       5666666666666666666666666666655332.3444444444444444433 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.36
                                       XXXXXXX-----XXXXEEEE-TTSS------------ CS
                          Collagen  12 pGppGkrGepGeaGekGekGpaGekGppGaaGkpGap 48 
                                        G +G+ G++G++ ++ ++G++G+ G+  + G+ G++
  gi|336253069|ref|YP_004596176.1| 358 DGDNGTGGNSGNSDQSSNSGNSGNGGNSENSGNGGNN 394
                                       2333333333333333333333333333333333332 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   4.4   1.8e-05     0.032      77     138 ..      77     139 ..      44     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                           DUF4349  77 rstsaeDVTeqyvDleaRlkaleasedrllallekaksv.edlleiereLsevqaeieslegq 138
                                        +++ e VT+++ DleaRl++le+++++l++  ++++   + + ++  e+s  +  ie+ e +
  gi|336253069|ref|YP_004596176.1|  77 AEQRDEIVTDRVDDLEARLATLETEREQLRSEDNRTGAYqARMTRLAVEISALERSIEQTEPR 139
                                       4666777***********************998886655156888888999999999888755 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.8   5.8e-05       0.1      35     102 ..      72     140 ..      65     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.8e-05
                              PilJ  35 agaydaaearaqlretiaqfdrtlaalrlgdpapgllvpae.avraqleaveqlWqelkkpaeaalaqq 102
                                         +  a+++ + +++++++++++la l+   ++ +  + ++ a +a++ ++  + ++l++++e+    +
  gi|336253069|ref|YP_004596176.1|  72 YENAAAEQRDEIVTDRVDDLEARLATLETEREQLRSEDNRTgAYQARMTRLAVEISALERSIEQTEPRA 140
                                       444567899999******************99988888888*********************5544433 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.3   0.00023       0.4       2      59 ..      85     145 ..      84     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHT-XXXXXXXXXXXX CS
                              SlyX   2 eerleeLEiklafqedtieeLndvvae...qqqqidrlqrqlrllaerlkeleessgasea 59 
                                        +r+++LE +la +e   e+L  +  +    q +++rl  ++ +l++ +++ e+++++++ 
  gi|336253069|ref|YP_004596176.1|  85 TDRVDDLEARLATLETEREQLRSEDNRtgaYQARMTRLAVEISALERSIEQTEPRAAEAGV 145
                                       58*******************7765542228999****************99999887665 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.6   9.5e-05      0.17     179     266 ..      69     160 ..       7     187 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.5e-05
                              FUSC 179 geegaeareaararlaadil.alealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavp 254
                                       ++  + a  ++r +++ d + +lea ++ +++e +++r + ++  + ++rm++l   +s+l+r  ++   + a+a  
  gi|336253069|ref|YP_004596176.1|  69 EAAYENAAAEQRDEIVTDRVdDLEARLATLETEREQLRSEDNRTGAYQARMTRLAVEISALERSIEQTEPRAAEAGV 145
                                       33333333445555554444268888888888888888888888888888888888888888888777665555533 PP

                              FUSC 255 e...laallaelaal 266
                                       +   l++l   + al
  gi|336253069|ref|YP_004596176.1| 146 DnkrLETLRSNASAL 160
                                       323344443333332 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 ?   11.9   3.2   0.00011       0.2      10      61 ..      88     137 ..      77     139 .. 0.89
   2 ?    6.8   0.2    0.0044       7.9       7      46 ..     116     153 ..     110     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                      ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeely 61 
                                        + lea+++ LE+e ++l  e +  + y  ++++++l  e+ +le  +e+ +
  gi|336253069|ref|YP_004596176.1|  88 VDDLEARLATLETEREQLRSEDNRTGAY--QARMTRLAVEISALERSIEQTE 137
                                       578*****************99999966..688**************99976 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0044
                      ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdpeklael 46 
                                       q ++ +l  eI aLE  i++ e + a+++   d ++l  l
  gi|336253069|ref|YP_004596176.1| 116 QARMTRLAVEISALERSIEQTEPRAAEAG--VDNKRLETL 153
                                       66777888999999999999999999988..566666655 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 ?   11.6   1.9   0.00011       0.2      58     118 ..      78     141 ..      50     162 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                    CENP-F_leu_zip  58 keeieelaeelreleldLvalrsekeeLeke...lqkkqervseLeslnsslenlleekEqekv 118
                                       ++  e  + +  +le+ L++l  e+e+L  e       q r+  L    s le+ +e+ E   +
  gi|336253069|ref|YP_004596176.1|  78 EQRDEIVTDRVDDLEARLATLETEREQLRSEdnrTGAYQARMTRLAVEISALERSIEQTEPRAA 141
                                       3444455678888888888888888888765222566799999999999999999998886544 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.3   0.00021      0.38      13      92 ..      88     166 ..      68     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                    PRKG1_interact  13 nerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkiseleeelkeleeLraenqrLkdE 89 
                                        + L ++L +le e ++l+se +++    q ++++ +  +++ +r+ +++e +++e   ++k le Lr++ + L d 
  gi|336253069|ref|YP_004596176.1|  88 VDDLEARLATLETEREQLRSEDNRTG-AYQARMTRLAVEISALERSIEQTEPRAAEAGVDNKRLETLRSNASALADD 163
                                       34566666666666666666666654.3455777777777777788888999999999999*************998 PP

                    PRKG1_interact  90 ngA 92 
                                       + A
  gi|336253069|ref|YP_004596176.1| 164 DVA 166
                                       755 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.2   0.00029      0.51     160     233 ..      79     151 ..      60     178 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00029
                              Spc7 160 kqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleele 233
                                       ++ e +++ +++le++ a+le e e+l+++ +  +   ++++  l  e+++l+  ie+ + + ae   + ++le
  gi|336253069|ref|YP_004596176.1|  79 QRDEIVTDRVDDLEARLATLETEREQLRSEDNR-TGAYQARMTRLAVEISALERSIEQTEPRAAEAGVDNKRLE 151
                                       555555666666666666666666666665544.3334555566666666666666555544444433332222 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 ?    8.6   2.9    0.0014       2.4      13      56 ..      66     111 ..      64     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0014
                               CLZ  13 glLDee..aakagaeqkeleekverLessLeaLqtrlarLlaeyes 56 
                                       g+++ +  +a+a++  + + ++v+ Le++L +L+t  ++L +e + 
  gi|336253069|ref|YP_004596176.1|  66 GMFEAAyeNAAAEQRDEIVTDRVDDLEARLATLETEREQLRSEDNR 111
                                       66777743455556667799****************9999887543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1141  (0.0636399); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                       131  (0.0073066); 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):              10  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.45
# Mc/sec: 2694.71
//
Query:       gi|336253070|ref|YP_004596177.1|  [L=225]
Description: ArsR family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-21   73.7   0.2      5e-17   61.5   0.1    2.5  2  HTH_5           Bacterial regulatory protein, arsR family
    3.4e-15   55.8   1.8    4.5e-12   45.8   0.3    2.5  2  HTH_20          Helix-turn-helix domain
    3.6e-14   52.4   0.2    6.8e-06   25.9   0.0    2.3  2  TrmB            Sugar-specific transcriptional regulator TrmB
    5.2e-13   48.7   0.6    2.7e-07   30.3   0.1    2.4  2  MarR_2          MarR family
    2.5e-09   36.5   0.6    5.1e-07   29.1   0.3    3.0  2  HTH_24          Winged helix-turn-helix DNA-binding
      4e-09   36.3   0.4    0.00011   22.0   0.1    2.5  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    5.8e-09   35.8   0.1    2.5e-06   27.3   0.0    2.4  2  MarR            MarR family
      6e-07   29.7   0.0     0.0069   16.7   0.0    2.5  2  Rrf2            Transcriptional regulator
    1.2e-06   28.2   1.5      0.024   14.4   0.1    3.1  2  HTH_IclR        IclR helix-turn-helix domain
    3.4e-06   27.1   0.0    0.00014   22.0   0.0    2.2  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    1.4e-05   25.1   3.0    0.00025   21.1   0.0    3.0  2  DprA_WH         DprA winged helix domain
    2.6e-05   24.6   0.3    0.00066   20.1   0.1    2.4  2  HTH_27          Winged helix DNA-binding domain
    3.5e-05   23.7   0.0    8.9e-05   22.4   0.0    1.7  1  HTH_11          HTH domain
    4.7e-05   23.2   0.0       0.11   12.3   0.0    2.2  2  DUF742          Protein of unknown function (DUF742)
    5.9e-05   22.9   0.4     0.0024   17.8   0.0    3.3  3  PadR            Transcriptional regulator PadR-like family
     0.0002   21.0   0.2       0.26   11.0   0.0    2.9  2  GntR            Bacterial regulatory proteins, gntR family
    0.00041   20.4   0.1        0.1   12.7   0.0    2.4  2  DUF2250         Uncharacterized protein conserved in archaea 
     0.0015   18.3   0.0     0.0052   16.6   0.0    1.9  1  HTH_10          HTH DNA binding domain
     0.0016   18.2   0.0      0.012   15.4   0.0    2.3  2  LexA_DNA_bind   LexA DNA binding domain
     0.0016   17.9   0.0     0.0038   16.7   0.0    1.6  1  HTH_CodY        CodY helix-turn-helix domain
     0.0029   17.4   0.0      0.065   13.1   0.0    2.3  2  HxlR            HxlR-like helix-turn-helix
     0.0049   16.5   0.0      0.011   15.4   0.0    1.5  1  DDRGK           DDRGK domain
      0.005   16.6   0.2      0.036   13.9   0.2    2.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
     0.0051   16.8   0.0       0.82    9.8   0.0    2.5  2  FeoC            FeoC like transcriptional regulator
     0.0055   16.5   0.0       0.49   10.3   0.0    2.6  2  IF2_N           Translation initiation factor IF-2, N-termina
  ------ inclusion threshold ------
      0.014   15.3   2.0        2.2    8.3   0.0    2.7  2  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.016   15.1   0.0      0.033   14.1   0.0    1.6  1  HTH_36          Helix-turn-helix domain
      0.017   15.4   0.2        0.1   12.9   0.0    2.2  2  DUF2513         Hypothetical protein (DUF2513)
      0.019   14.9   0.0       0.48   10.4   0.0    2.5  2  Cdc6_C          CDC6, C terminal winged helix domain
      0.027   14.1   0.1        3.2    7.4   0.0    2.3  2  SMC_ScpB        Segregation and condensation complex subunit 
      0.039   13.9   0.0        4.4    7.4   0.0    2.4  2  HTH_45          Winged helix-turn-helix
      0.055   13.1   0.0        0.3   10.7   0.0    2.1  2  ArsR            ArsR transcriptional regulator
       0.06   13.0   0.0       0.25   11.0   0.0    2.0  2  RP-C            Replication protein C N-terminal domain
      0.065   13.0   0.0       0.21   11.4   0.0    1.9  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.075   13.1   0.8       0.19   11.8   0.2    2.0  2  GPP34           Golgi phosphoprotein 3 (GPP34)
      0.077   12.8   0.1       0.23   11.2   0.1    1.8  1  HTH_38          Helix-turn-helix domain
      0.082   13.1   0.0       0.39   10.9   0.0    1.9  2  HTH_34          Winged helix DNA-binding domain
       0.11   12.1   0.0        4.5    6.9   0.0    2.4  2  HTH_47          winged helix-turn-helix
       0.16   12.4   0.1       0.41   11.1   0.0    1.7  1  FaeA            FaeA-like protein
       0.16   12.3   1.5        0.2   12.0   0.1    1.8  1  TetR_C_11       Tetracyclin repressor-like, C-terminal domain
       0.37   10.8   7.6       0.51   10.4   0.3    3.0  2  BLACT_WH        Beta-lactamase associated winged helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.1   1.1e-19     5e-17       1      47 []      12      58 ..      12      58 .. 0.97
   2 !    9.9   0.0    0.0015      0.64       7      46 ..     168     207 ..     166     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1.1e-19
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      +++R++IL+lLa+++++v+e++e+lg+s+ +v +HL+kL++aGL+e+
  gi|336253070|ref|YP_004596177.1| 12 NENRRRILRLLARKPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIES 58
                                      589******************************************86 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0015
                                       HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       +L + ++++++v++l+ee++ ++  v + L  + ++G+V+
  gi|336253070|ref|YP_004596177.1| 168 LLASIRSEPKSVGDLSEEIDAPREVVAELLESMADEGIVR 207
                                       56677889**************999999999999999996 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.3     1e-14   4.5e-12       2      57 ..       5      59 ..       4      63 .. 0.95
   2 !    9.0   0.1    0.0033       1.4      14      61 .]     167     213 ..     161     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1e-14
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                       ++++L+++ Rrrilr+L  +++  ++e+ e l++s++ +  HLr+Le+agL+e+ 
  gi|336253070|ref|YP_004596177.1|  5 ALLDLLGNENRRRILRLL-ARKPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIESH 59
                                      5789**************.**********************************975 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0033
                                       HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       ++l+ + r e+ ++++l e++d ++  +   L+ +++ g+v++++ g+
  gi|336253070|ref|YP_004596177.1| 167 DLLASI-RSEPKSVGDLSEEIDAPREVVAELLESMADEGIVRRTERGW 213
                                       556666.99***********************************9987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0     5e-08   2.2e-05      16      62 ..      20      67 ..      18      72 .. 0.87
   2 !   25.9   0.0   1.6e-08   6.8e-06      10      57 ..     161     211 ..     158     219 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5e-08
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklY 62
                                       Ll+++p  ++ei+e lgv+   v e Lr+Led+Gl+e    + +++Y
  gi|336253070|ref|YP_004596177.1| 20 RLLARKPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIESHVDEqRRKY 67
                                      699***********************************9875545566 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.6e-08
                                       CCCHCHHHH...HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB  10 EakvYlaLl...klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57 
                                       E+++Y+ Ll   +++p+++ +++ee++ pr  v e L+s+ d G+V+r ++
  gi|336253070|ref|YP_004596177.1| 161 ESRIYADLLasiRSEPKSVGDLSEEIDAPREVVAELLESMADEGIVRRTER 211
                                       99*******99999*********************************9875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.1   6.3e-10   2.7e-07       7      59 ..      15      63 ..       8      66 .. 0.89
   2 !   16.4   0.0   1.4e-05    0.0062       7      54 ..     165     209 ..     161     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 6.3e-10
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSS CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeD 59
                                       +r+L  L+r p   + v+e+ ++lg+s+ av  +l++L++aGL+e   + e 
  gi|336253070|ref|YP_004596177.1| 15 RRRILRLLARKP---CYVTEISEYLGVSPKAVIEHLRKLEDAGLIESHVD-EQ 63
                                      589********9...9*****************************97644.44 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                        a++La ++ +p    +vg+l ++ + ++  v  +l+ + + G v+r+
  gi|336253070|ref|YP_004596177.1| 165 YADLLASIRSEPK---SVGDLSEEIDAPREVVAELLESMADEGIVRRT 209
                                       689*********8...*****************************997 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 !   29.1   0.3   1.2e-09   5.1e-07       2      48 .]      12      57 ..      11      57 .. 0.93
   2 ?    3.9   0.0     0.091        40      19      48 .]     178     207 ..     174     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.2e-09
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +e++r+IL+lL ++p    +e++e lg+Sp +v ++l++Le++GlI+
  gi|336253070|ref|YP_004596177.1| 12 NENRRRILRLLARKPC-YVTEISEYLGVSPKAVIEHLRKLEDAGLIE 57
                                      799**********775.589**************************7 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.091
                            HTH_24  19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       s  +L+e+++ ++  v + l+ + +eG+++
  gi|336253070|ref|YP_004596177.1| 178 SVGDLSEEIDAPREVVAELLESMADEGIVR 207
                                       6679************************96 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 !   22.0   0.1   2.6e-07   0.00011      20      53 ..      25      60 ..       4      77 .. 0.68
   2 !   12.1   0.0   0.00034      0.15      21      55 ..     176     211 ..     143     219 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.6e-07
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglis..r 53
                                       p   +e++++lG+++  v   l++L+++gli+   
  gi|336253070|ref|YP_004596177.1| 25 KPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIEshV 60
                                      377779**************************9642 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00034
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis.rgr 55 
                                       p +  +l++ + + re v  +l  + +eg+++ ++r
  gi|336253070|ref|YP_004596177.1| 176 PKSVGDLSEEIDAPREVVAELLESMADEGIVRrTER 211
                                       778889**************************4344 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   5.8e-09   2.5e-06       7      50 ..      17      59 ..      12      66 .. 0.84
   2 ?    6.0   0.0     0.026        11      15      51 ..     174     210 ..     167     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 5.8e-09
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      +iLr+l++  p++v+e+ + lgvs+ +v + l++Le++Glie+ 
  gi|336253070|ref|YP_004596177.1| 17 RILRLLAR-KPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIESH 59
                                      67777765.689*****************************986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.026
                                       STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  15 qgplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                       ++p sv +L + +   +  v ++l  + ++G ++R+ 
  gi|336253070|ref|YP_004596177.1| 174 SEPKSVGDLSEEIDAPREVVAELLESMADEGIVRRTE 210
                                       578899*****************************85 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.6e-05    0.0069      23      57 ..      24      58 ..      17      60 .. 0.90
   2 !   10.5   0.0    0.0014      0.59      19      57 ..     170     208 ..     162     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.6e-05
                                      CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvks 57
                                      ++p+ ++ei+e  ++sp+ +   l+kL+ agl++s
  gi|336253070|ref|YP_004596177.1| 24 RKPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIES 58
                                      457899****************************9 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0014
                                       HSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2  19 keeeeepvsseeiaerqnispsylekilakLrkaglvks 57 
                                       +  ++ep s+ +++e+ + ++++++ +l+ ++ +g+v+ 
  gi|336253070|ref|YP_004596177.1| 170 ASIRSEPKSVGDLSEEIDAPREVVAELLESMADEGIVRR 208
                                       4445567899***************************74 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 !   14.4   0.1   5.5e-05     0.024       7      49 ..      17      57 ..       3      59 .. 0.85
   2 !   11.6   0.0   0.00041      0.18       7      51 ..     167     209 ..     164     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.5e-05
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +iL++la+ p    ++e+++ +g+++ +v  +L+ L+  G++e
  gi|336253070|ref|YP_004596177.1| 17 RILRLLARKPCY--VTEISEYLGVSPKAVIEHLRKLEDAGLIE 57
                                      577777777775..***************************98 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00041
                                       HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                       ++L  ++++p   ++ +l+++++ p+  v  lL ++  +G+v++ 
  gi|336253070|ref|YP_004596177.1| 167 DLLASIRSEPK--SVGDLSEEIDAPREVVAELLESMADEGIVRRT 209
                                       56666666666..6*****************************85 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 !   22.0   0.0   3.2e-07   0.00014      15      55 ..      20      59 ..      16      62 .. 0.85
   2 ?    2.8   0.0      0.32   1.4e+02      24      53 ..     178     207 ..     170     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.2e-07
                                      HHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress 15 tlseekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                      +l   +k+  +++++e L+vsp  V e l+kLe++G++e +
  gi|336253070|ref|YP_004596177.1| 20 RLL-ARKPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIESH 59
                                      555.5777889**************************9865 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.32
                                       -HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress  24 ktkdlaerLnvspssVsemlkkLekdGyve 53 
                                       ++ dl+e+++     V e l+ ++++G v 
  gi|336253070|ref|YP_004596177.1| 178 SVGDLSEEIDAPREVVAELLESMADEGIVR 207
                                       6889***********************986 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   5.8e-07   0.00025      12      58 ..      13      59 ..       2      62 .. 0.92
   2 ?    3.4   0.0      0.19        84      10      46 ..     161     197 ..     154     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.8e-07
                           DprA_WH 12 dlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlverl 58
                                      + +rr+L +L+  P+ v ++++ +g+++ +v  +L  LE aGl+e++
  gi|336253070|ref|YP_004596177.1| 13 ENRRRILRLLARKPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIESH 59
                                      789******************************************98 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.19
                           DprA_WH  10 lddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaL 46 
                                        +   + +La + +eP +v +L+++  +p ++v+ +L
  gi|336253070|ref|YP_004596177.1| 161 ESRIYADLLASIRSEPKSVGDLSEEIDAPREVVAELL 197
                                       566778899999*************999876666555 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 !   20.1   0.1   1.5e-06   0.00066       9      61 ..      19      68 ..      12      71 .. 0.80
   2 ?    2.2   0.0      0.59   2.6e+02      16      52 ..     174     210 ..     166     212 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.5e-06
                            HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekr 61
                                      L+l++  r +   ++++++l v+  ++++ l+kL+ +GL+e+  de  rr  +
  gi|336253070|ref|YP_004596177.1| 19 LRLLA--RKPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIESHVDE-QRRKYF 68
                                      66666..5555669**************************999997.444444 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.59
                            HTH_27  16 rrrkkladlcgrlnvedshisyslkkLtekGLvertg 52 
                                        ++k+  dl++  +     +++ l+ +   G v rt+
  gi|336253070|ref|YP_004596177.1| 174 SEPKSVGDLSEEIDAPREVVAELLESMADEGIVRRTE 210
                                       6666666666666666666667777766666665554 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0     2e-07   8.9e-05       2      48 ..      15      58 ..      14      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2e-07
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIes 48
                                      ++ il+lL  ar+p    e++e+L+vS ++v  ++++Le++g  Ies
  gi|336253070|ref|YP_004596177.1| 15 RRRILRLL--ARKPCYVTEISEYLGVSPKAVIEHLRKLEDAG-LIES 58
                                      67899999..88889***************************.5555 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0031       1.3      43      91 ..      13      62 ..       6      74 .. 0.84
   2 !   12.3   0.0   0.00026      0.11      52      89 ..     172     210 ..     148     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0031
                            DUF742 43 pehrailrLcre.plsVaelaAelklPvgvvrvLlsdLldaglltvrapv 91
                                      +++r+ilrL ++ p  V e++ +l +   +v   l  L dagl++++   
  gi|336253070|ref|YP_004596177.1| 13 ENRRRILRLLARkPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIESHVDE 62
                                      67899***9988799*********99777777778999999999988765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00026
                            DUF742  52 cre.plsVaelaAelklPvgvvrvLlsdLldaglltvra 89 
                                       +r+ p+sV +l+ e++ P  vv  Ll +++d g ++  +
  gi|336253070|ref|YP_004596177.1| 172 IRSePKSVGDLSEEIDAPREVVAELLESMADEGIVRRTE 210
                                       33359****************************998765 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.6e-06    0.0024       1      68 [.      18      73 ..      18      79 .. 0.79
   2 ?   -0.1   0.0         2   8.9e+02      16      43 ..     127     154 ..     119     157 .. 0.68
   3 ?   -1.5   0.0       5.8   2.5e+03      37      51 ..     196     210 ..     192     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.6e-06
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHC CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTda 68
                                      iL ll+++p y +ei + l          s+  +   L++Le+ gl+es+ +e+    +rky++++++
  gi|336253070|ref|YP_004596177.1| 18 ILRLLARKPCYVTEISEYLGV--------SPKAVIEHLRKLEDAGLIESHVDEQ----RRKYFHIARN 73
                                      788888888888887765544........45567789*************9885....9*****9875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2
                                       HHHHHCCSTT-CCTTHHHHHHHHHHHHH CS
                              PadR  16 ikeleelsegllelseGslYpaLkrLek 43 
                                        ++le+ ++ + +  +G+l ++L+r ++
  gi|336253070|ref|YP_004596177.1| 127 LEQLENELSLAQRWVQGRLCDVLDRISE 154
                                       5666666666677778888888888765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 5.8
                                       HHHHHHHTTSEEEEE CS
                              PadR  37 aLkrLekeglvesew 51 
                                       +L+++ +eg+v +++
  gi|336253070|ref|YP_004596177.1| 196 LLESMADEGIVRRTE 210
                                       688899999998765 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0    0.0006      0.26      28      57 ..      30      59 ..      27      62 .. 0.93
   2 ?    6.6   0.3     0.014       5.9      26      59 ..     178     211 ..     160     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0006
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglverr 57
                                       e+++ +gVs   v e Lr+Le +gl+e++
  gi|336253070|ref|YP_004596177.1| 30 TEISEYLGVSPKAVIEHLRKLEDAGLIESH 59
                                      6999***********************986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.014
                                       -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR  26 sereLaaefgVsrttvReALrrLeaeglverrqg 59 
                                       s+ +L++e++  r +v e L   + eg+v r  +
  gi|336253070|ref|YP_004596177.1| 178 SVGDLSEEIDAPREVVAELLESMADEGIVRRTER 211
                                       577899***********************99765 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 !   12.7   0.0   0.00023       0.1      13      55 ..      18      59 ..       8      73 .. 0.83
   2 ?    5.3   0.0      0.05        22      29      57 ..     183     211 ..     176     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00023
                           DUF2250 13 vlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerv 55
                                      +l+ l+  ++ Y   i+++l ++ + v e l+kLe++GL+e  
  gi|336253070|ref|YP_004596177.1| 18 ILRLLA-RKPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIESH 59
                                      555554.46789999*************************964 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.05
                           DUF2250  29 akeleipleevrellkkLeelGLlerveg 57 
                                       ++e+++p+e v ell+++ + G++ r e+
  gi|336253070|ref|YP_004596177.1| 183 SEEIDAPREVVAELLESMADEGIVRRTER 211
                                       678999******************99885 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.2e-05    0.0052      25      48 ..      28      51 ..      24      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
                            HTH_10 25 tlkeLAkelGIskstlsehLrkae 48
                                       + e+++ lG+s+ ++ ehLrk e
  gi|336253070|ref|YP_004596177.1| 28 YVTEISEYLGVSPKAVIEHLRKLE 51
                                      5789*****************976 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 !   15.4   0.0   2.7e-05     0.012      28      59 ..      29      59 ..      17      65 .. 0.87
   2 ?   -0.5   0.0       2.5   1.1e+03      42      60 ..     192     210 ..     176     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                     LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyierd 59
                                      + ei++ lg++ p+av ehL++Le  G+ie  
  gi|336253070|ref|YP_004596177.1| 29 VTEISEYLGVS-PKAVIEHLRKLEDAGLIESH 59
                                      789******96.*****************976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHTTSEE-GG CS
                     LexA_DNA_bind  42 aveehLkaLerKGyierdp 60 
                                        v+e L+ ++  G+++r++
  gi|336253070|ref|YP_004596177.1| 192 VVAELLESMADEGIVRRTE 210
                                       4788899999999999985 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 !   16.7   0.0   8.7e-06    0.0038       9      37 ..      31      59 ..      27      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.7e-06
                          HTH_CodY  9 kiaDriGitrsvivnaLrkLesaGiiesr 37
                                      +i++ +G+    ++  LrkLe aG+ies 
  gi|336253070|ref|YP_004596177.1| 31 EISEYLGVSPKAVIEHLRKLEDAGLIESH 59
                                      6888899999999**************96 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00015     0.065       3      56 ..      11      63 ..       9      69 .. 0.87
   2 ?    1.7   0.0      0.53   2.3e+02      11      52 ..     169     209 ..     163     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                                      HSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESS CS
                              HxlR  3 ggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevype 56
                                      g+  +  il+ l +++   +e+++ l ++s k  +++Lr+Le  glie +v ++
  gi|336253070|ref|YP_004596177.1| 11 GNENRRRILRLLARKPCYVTEISEYL-GVSPKAVIEHLRKLEDAGLIESHVDEQ 63
                                      55556789999999************.9*******************9988665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.53
                                       HHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEE CS
                              HxlR  11 lvellkgkkRfselkralpkisqkmLaqrLreLeqdgliere 52 
                                       l ++ + +k  ++l++++ + ++++ a+ L  +  +g++ r+
  gi|336253070|ref|YP_004596177.1| 169 LASIRSEPKSVGDLSEEI-DAPREVVAELLESMADEGIVRRT 209
                                       566677788889999999.8899****************997 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.4e-05     0.011     110     158 ..      23      72 ..      13      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.4e-05
                                       H-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-T.T--EEE--- CS
                             DDRGK 110 ekKvvlleelavkfklktqevierikeLeeqgsltGvlDd.rGkyiyitd 158
                                        +K + ++e++  ++++ + vie +++Le+ g ++  +D+ r ky +i  
  gi|336253070|ref|YP_004596177.1|  23 ARKPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIESHVDEqRRKYFHIAR 72 
                                       579999*********************************95679999975 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 !   13.9   0.2   8.3e-05     0.036       6      42 .]      16      51 ..      16      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.3e-05
                     HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      r+IL++L + +   ++e++e +G+S+ +v++ +r+Le
  gi|336253070|ref|YP_004596177.1| 16 RRILRLLARKP-CYVTEISEYLGVSPKAVIEHLRKLE 51
                                      78999998775.679*********************8 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.094        41      11      47 ..      23      59 ..      20      66 .. 0.85
   2 !    9.8   0.0    0.0019      0.82      16      49 ..     178     211 ..     169     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.094
                              FeoC 11 ergrvslkeLsrhfkaspealeamLeqwvrkGrvekv 47
                                      +r+   + e+s ++ +sp+a+   L  ++  G +e +
  gi|336253070|ref|YP_004596177.1| 23 ARKPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIESH 59
                                      57778899*************9999999999988865 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0019
                              FeoC  16 slkeLsrhfkaspealeamLeqwvrkGrvekvaa 49 
                                       s+++Ls + +a  e +  +Le +   G v+++++
  gi|336253070|ref|YP_004596177.1| 178 SVGDLSEEIDAPREVVAELLESMADEGIVRRTER 211
                                       89***************************99887 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0011      0.49       6      28 ..      29      50 ..      25      61 .. 0.89
   2 ?    3.6   0.0      0.14        59       2      28 ..     175     200 ..     174     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                             IF2_N  6 VyeLAkeLgvkskevikkLfkel 28
                                      V e+ + Lgv++k vi++L k l
  gi|336253070|ref|YP_004596177.1| 29 VTEISEYLGVSPKAVIEHLRK-L 50
                                      889****************76.5 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.14
                             IF2_N   2 skirVyeLAkeLgvkskevikkLfkel 28 
                                       + ++V +L +e+  + + v + L +++
  gi|336253070|ref|YP_004596177.1| 175 EPKSVGDLSEEIDAPREVVAELL-ESM 200
                                       679*********98766666655.545 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 ?    8.3   0.0    0.0049       2.2      21      39 ..      34      52 ..      17      54 .. 0.90
   2 ?    5.9   0.2     0.027        12      37      60 .]     197     220 ..     194     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0049
                                      HHHTS-HHHHHHHHHHHHH CS
                             HTH_1 21 eeLglsqpavsrqikrLEe 39
                                      e Lg+s++av  ++++LE+
  gi|336253070|ref|YP_004596177.1| 34 EYLGVSPKAVIEHLRKLED 52
                                      679***************8 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.027
                                       HHHHHTS-SEEESSSEEEE-HHHH CS
                             HTH_1  37 LEeelgvpLfeRtgrglrLTeaGe 60 
                                       LE+  ++ ++ Rt rg++LT ++e
  gi|336253070|ref|YP_004596177.1| 197 LESMADEGIVRRTERGWELTTEAE 220
                                       888899999***********9986 PP

>> HTH_36  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   7.5e-05     0.033      29      55 .]      30      56 ..      16      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.5e-05
                            HTH_36 29 etlakrlglsknTvsraikeLeqlGyi 55
                                        +++ lg+s + v+ ++++Le++G+i
  gi|336253070|ref|YP_004596177.1| 30 TEISEYLGVSPKAVIEHLRKLEDAGLI 56
                                      57999********************98 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00023       0.1      33      65 ..      34      66 ..      13      79 .. 0.79
   2 ?   -0.6   0.1       3.8   1.7e+03       3      28 ..     113     138 ..     112     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00023
                           DUF2513 33 aidgyskeeiiyhlkllaeagLieaekkkakss 65
                                      +  g+s + +i+hl++l++agLie+  ++++ +
  gi|336253070|ref|YP_004596177.1| 34 EYLGVSPKAVIEHLRKLEDAGLIESHVDEQRRK 66
                                      566788999****************99998887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.8
                           DUF2513   3 dmdlvRdiLltleeletkeeslddee 28 
                                       d d   ++L +le+le+ e++l+ ++
  gi|336253070|ref|YP_004596177.1| 113 DTDDLDELLHALEDLEQLENELSLAQ 138
                                       56666789999999999988887654 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 ?   10.4   0.0    0.0011      0.48      37      76 ..      38      78 ..      27      83 .. 0.75
   2 ?    1.7   0.0      0.58   2.5e+02      42      60 ..     193     211 ..     187     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                                      --HHHHHHHHHHHHHTTSEEEEEEE-CC.C.-EEEEEEESS CS
                            Cdc6_C 37 ltqrevsdllseLemlgileleksskGrre.grtrkisLnv 76
                                      ++ + v ++l++Le+ g++e+++  + r++    r ++L v
  gi|336253070|ref|YP_004596177.1| 38 VSPKAVIEHLRKLEDAGLIESHVDEQRRKYfHIARNVRLEV 78
                                      678899****************9966666666666666655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHTTSEEEEEE CS
                            Cdc6_C  42 vsdllseLemlgileleks 60 
                                       v +ll  +++ gi++++++
  gi|336253070|ref|YP_004596177.1| 193 VAELLESMADEGIVRRTER 211
                                       7899************988 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 ?    7.4   0.0    0.0073       3.2      95     129 ..      24      61 ..      16      76 .. 0.73
   2 ?    4.4   0.0     0.059        26      11      63 ..     174     219 ..     164     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0073
                          SMC_ScpB  95 kqpvtraeieeiRGvnsdsvv...rtLlerglieekgr 129
                                       ++p+  +ei+e  Gv+ ++v+   r+L + glie++  
  gi|336253070|ref|YP_004596177.1|  24 RKPCYVTEISEYLGVSPKAVIehlRKLEDAGLIESHVD 61 
                                       78999999****99996665411167778899998773 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.059
                          SMC_ScpB  11 geplsleeLakilelskeeveealeeLkeeyeeedrglelvevaggyrlvtkp 63 
                                       +ep s+ +L++ +++ +e v+e+le++++e       + ++++++g++l+t++
  gi|336253070|ref|YP_004596177.1| 174 SEPKSVGDLSEEIDAPREVVAELLESMADEG------I-VRRTERGWELTTEA 219
                                       5678888888888777777777777777775......2.45555555555544 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.11        50      11      50 ..      18      61 ..      16      71 .. 0.81
   2 ?    7.4   0.0      0.01       4.4       6      61 ..     163     218 ..     161     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                            HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli....k 50
                                      IL+ + ++    T+i      s k + + L +L + gli    +
  gi|336253070|ref|YP_004596177.1| 18 ILRLLARKPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIeshvD 61
                                      7888888888899999999999999**************54432 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.01
                            HTH_45   6 eIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTek 61 
                                        I+ad+L +i+++ ++   +  + +   +++ + L+ + ++g+++ ++  ++lT +
  gi|336253070|ref|YP_004596177.1| 163 RIYADLLASIRSEPKSVGDLSEEIDAPREVVAELLESMADEGIVRRTERGWELTTE 218
                                       699*********************************************99999975 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00068       0.3       9      60 ..       5      59 ..       1      75 [. 0.86
   2 ?   -0.9   0.0       2.4   1.1e+03     112     133 ..     167     188 ..     145     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00068
                              ArsR  9 pllqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEsq 60
                                      +ll ++++e+ +++++ l ++ +  +e++e+lg +   v e l+ L+ ++liEs+
  gi|336253070|ref|YP_004596177.1|  5 ALLDLLGNENRRRILRLLARKPCYVTEISEYLGVSpkaVIEHLRKLEDAGLIESH 59
                                      689999***************************8844466777777789999985 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.4
                              ArsR 112 kiekeveegntsisdlsrklgl 133
                                       ++ + ++++ +s++dls++++ 
  gi|336253070|ref|YP_004596177.1| 167 DLLASIRSEPKSVGDLSEEIDA 188
                                       4555566666666666666554 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 ?   11.0   0.0   0.00058      0.25      76     104 ..      31      59 ..      28      85 .. 0.81
   2 ?   -1.5   0.0       3.9   1.7e+03      76     101 ..     181     206 ..     167     210 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00058
                              RP-C  76 qLsralglsestlrrhlaaLveaGliirr 104
                                       ++s++lg+s++++ +hl++L +aGli   
  gi|336253070|ref|YP_004596177.1|  31 EISEYLGVSPKAVIEHLRKLEDAGLIESH 59 
                                       6899*********************9755 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.9
                              RP-C  76 qLsralglsestlrrhlaaLveaGli 101
                                       +Ls++++ +++ + ++l ++++ G++
  gi|336253070|ref|YP_004596177.1| 181 DLSEEIDAPREVVAELLESMADEGIV 206
                                       56666666777777777777777766 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 ?   11.4   0.0   0.00047      0.21       8      45 ..      21      57 ..      15      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00047
                          HTH_DeoR  8 llkqqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                      ll  +  + v+e++e+lgvS++ +   L++Le +gl++
  gi|336253070|ref|YP_004596177.1| 21 LL-ARKPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIE 57
                                      44.456789**************************986 PP

>> GPP34  Golgi phosphoprotein 3 (GPP34)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1         1   4.4e+02     112     112 ..      82      82 ..       4     162 .. 0.52
   2 ?   11.8   0.2   0.00043      0.19      48     112 ..     142     213 ..     117     224 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1
                             GPP34 112 f 112
                                        
  gi|336253070|ref|YP_004596177.1|  82 P 82 
                                       0 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00043
                             GPP34  48 ggrvv.vids......rptgdplldealklikaserprsvktwvdlls..ksvrervakgLvdkGilrtekrrf 112
                                       +gr++ v+d       + ++  + + +l+ i+ s +p+sv ++ +     + v ++++++++d+Gi+r+ +r +
  gi|336253070|ref|YP_004596177.1| 142 QGRLCdVLDRisenvgTGPESRIYADLLASIR-S-EPKSVGDLSEEIDapREVVAELLESMADEGIVRRTERGW 213
                                       45555555555544333445668888888887.4.347899988666678899999**************9986 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00053      0.23       7      34 ..      12      40 ..      10      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00053
                            HTH_38  7 leeReeIerllaeG.lslreIArrLgrsp 34
                                       e+R++I rlla++ + + eI  +Lg+sp
  gi|336253070|ref|YP_004596177.1| 12 NENRRRILRLLARKpCYVTEISEYLGVSP 40
                                      689*********9989999*********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 ?   10.9   0.0   0.00089      0.39      14      54 ..      26      66 ..      17      72 .. 0.85
   2 ?   -1.1   0.0       4.9   2.1e+03      33      53 ..     119     139 ..     109     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00089
                            HTH_34 14 eadfvelkealeatdgnLsvhlkkLekagYievdkefkgkk 54
                                          +e++e l+++  +   hl+kLe+ag ie + + + +k
  gi|336253070|ref|YP_004596177.1| 26 PCYVTEISEYLGVSPKAVIEHLRKLEDAGLIESHVDEQRRK 66
                                      566789**************************999999887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.9
                            HTH_34  33 vhlkkLekagYievdkefkgk 53 
                                         l++Le+ +++e ++++ ++
  gi|336253070|ref|YP_004596177.1| 119 ELLHALEDLEQLENELSLAQR 139
                                       668899999999999888777 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0      0.01       4.5      50      77 ..      30      57 ..      27      58 .. 0.93
   2 ?    2.5   0.0      0.24     1e+02      48      77 ..     178     207 ..     174     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.01
                                      HHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 50 ldiAeriglpfdrvaaiaraLaeaglla 77
                                       +i+e +g++ ++v++ +r+L++agl++
  gi|336253070|ref|YP_004596177.1| 30 TEISEYLGVSPKAVIEHLRKLEDAGLIE 57
                                      5899**********************97 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.24
                                       EHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47  48 sLldiAeriglpfdrvaaiaraLaeaglla 77 
                                       s+ d++e+i++p + va++++++a++g+++
  gi|336253070|ref|YP_004596177.1| 178 SVGDLSEEIDAPREVVAELLESMADEGIVR 207
                                       566999*********************997 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00093      0.41       5      46 ..      18      57 ..      14      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00093
                                      HHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                              FaeA  5 IleylnsikapckTreiAdalglsaYQaRyYLeqLekegkik 46
                                      Il  l +   pc  +ei + lg+s   +   L +Le +g i+
  gi|336253070|ref|YP_004596177.1| 18 ILRLLAR--KPCYVTEISEYLGVSPKAVIEHLRKLEDAGLIE 57
                                      5666665..9*****************************997 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00045       0.2       8      75 ..     142     208 ..     140     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00045
                         TetR_C_11   8 rgDLrallralaealaspragallrallaeaqrdpelaealrerlleprraalravlrrAvarGelra 75 
                                       +g L  +l+++ e++ + +++++ ++lla ++++p+    l e  ++  r+ ++++l+  ++ G +r 
  gi|336253070|ref|YP_004596177.1| 142 QGRLCDVLDRISENVGTGPESRIYADLLASIRSEPKSVGDLSE-EIDAPREVVAELLESMADEGIVRR 208
                                       688999***********99******************999999.889999*************98886 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3    0.0012      0.51      25      43 ..      43      61 ..      41      65 .. 0.83
   2 ?    4.0   0.0      0.11        49      27      47 .]     195     213 ..     188     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
                          BLACT_WH 25 vlahLeKLeeeGkVkregd 43
                                      v+ hL+KLe+ G+++++ d
  gi|336253070|ref|YP_004596177.1| 43 VIEHLRKLEDAGLIESHVD 61
                                      899***********98655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.11
                          BLACT_WH  27 ahLeKLeeeGkVkregdkgkW 47 
                                         Le + +eG V+r++  + W
  gi|336253070|ref|YP_004596177.1| 195 ELLESMADEGIVRRTE--RGW 213
                                       568999********99..577 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1680.07
//
Query:       gi|336253071|ref|YP_004596178.1|  [L=252]
Description: hypothetical protein Halxa_1667 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.039   13.8   2.7       0.29   11.0   0.1    2.2  2  DUF2062   Uncharacterized protein conserved in bacteria (DUF2
       0.49   10.7  16.0       0.26   11.6  12.8    1.9  2  DUF456    Protein of unknown function (DUF456)


Domain annotation for each model (and alignments):
>> DUF2062  Uncharacterized protein conserved in bacteria (DUF2062)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   3.2e-05      0.29      98     147 ..     140     189 ..     104     190 .. 0.82
   2 ?    2.8   0.7     0.011        98     108     136 ..     213     241 ..     193     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.2e-05
                           DUF2062  98 eelglewlleslleiglplllGslilglilallgYflvlllwrlyrrrrr 147
                                       + ++ +++l+ ll +g+ ll+G+++l +++ ++g f++ +l+ l+  +rr
  gi|336253071|ref|YP_004596178.1| 140 QYFSPKEFLAMLLVVGAGLLVGWTVLPVAGRMIGMFATAFLVGLLASKRR 189
                                       344448999999*****************************999988875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.011
                           DUF2062 108 slleiglplllGslilglilallgYflvl 136
                                       +++  ++++l+ ++ +gl+++l+gY++ +
  gi|336253071|ref|YP_004596178.1| 213 AVAGSAQAVLAVGATVGLVATLVGYYFGR 241
                                       44455556666677889999999999876 PP

>> DUF456  Protein of unknown function (DUF456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  12.8   2.9e-05      0.26      64     133 ..     151     218 ..     148     226 .. 0.74
   2 ?   -2.1   5.3      0.47   4.2e+03      45      74 ..     204     233 ..     193     241 .. 0.38

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                            DUF456  64 ligaivGaivGffllpplGlllgpflgaflgEllrarkdlreAlkaalgalvGfllgtlvklvlallmlv 133
                                       l++ ++G++vG  +lp++G ++g+f++afl+ ll+++++      +a g+ vG + ++++++++a++  +
  gi|336253071|ref|YP_004596178.1| 151 LLVVGAGLLVGWTVLPVAGRMIGMFATAFLVGLLASKRRY--LELTAAGISVGAVSSLVTHAFFAVAGSA 218
                                       567789**************************99988553..3344556666777777777666665444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.47
                            DUF456  45 ldylapalgakraGaskrgligaivGaivG 74 
                                         ++  a++a +  a+   ++ga+vG+++ 
  gi|336253071|ref|YP_004596178.1| 204 SSLVTHAFFAVAGSAQAVLAVGATVGLVAT 233
                                       333333333333333333333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 1971.39
//
Query:       gi|336253072|ref|YP_004596179.1|  [L=79]
Description: hypothetical protein Halxa_1668 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.87   10.1   6.6        2.3    8.7   6.6    1.7  1  DUF202    Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.6   0.00013       2.3      16      60 ..       8      71 ..       5      76 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00013
                            DUF202 16 tslalialglallrffl...................tgepsalgkilglilivlgiltllvglv 60
                                      +++++ialg++ll + +                   t     + ++ gl+li++gi+t l++++
  gi|336253072|ref|YP_004596179.1|  8 MGILAIALGVGLLSLARrfyprlefgadtmetirllTALIVGILVLTGLGLIAVGIVTPLTAAH 71
                                      8999*********998877777766665544333222222222344478888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 595.32
//
Query:       gi|336253073|ref|YP_004596180.1|  [L=421]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Halopiger xanaduensis SH-6]
Scores for 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-59  199.3   0.2    1.3e-58  197.8   0.2    1.7  2  Asparaginase    Asparaginase, N-terminal
    1.7e-26   92.7   0.0    1.2e-25   89.9   0.0    2.1  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
      1e-17   63.2   0.0    1.8e-17   62.4   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 !  197.8   0.2   2.1e-62   1.3e-58       2     187 ..      86     278 ..      85     282 .. 0.95
   2 ?   -1.8   0.0      0.33     2e+03     140     166 ..     345     371 ..     340     393 .. 0.77

  Alignments for each domain:
  == domain 1  score: 197.8 bits;  conditional E-value: 2.1e-62
                                       EEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.-S CS
                      Asparaginase   2 vlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.yd 77 
                                       + +++tGGTias++d+++ga++ +++ae++l+a+p+l+  a+++ +++ani S+nm+p  w++laea++e++e  +d
  gi|336253073|ref|YP_004596180.1|  86 ISLISTGGTIASTVDYRTGAVTAQFDAEDVLRAVPDLAGRANYRGRVVANILSENMEPPIWRELAEAVREEIEAgAD 162
                                       889*********************************************************************666** PP

                                       EEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE..... CS
                      Asparaginase  78 gfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk..... 149
                                       g+Vv+hGTDT++y+A+aL++ml++ ++p+v+tGsqr++++++sD ++N ++A+ +a s+   a+vlv+++g+     
  gi|336253073|ref|YP_004596180.1| 163 GVVVMHGTDTMQYSAAALAFMLET-PVPIVFTGSQRSADRPSSDNVMNAVSAVEAAKSD--CAEVLVCMHGSesddv 236
                                       ************************.*******************************987..9*************** PP

                                       ..EEETTTEEE-BSSSSS-EEETTT--SEEE..ETTEEEESE CS
                      Asparaginase 150 ..llranrvtKvhtssldaFespnlgplaev..egskvkvnk 187
                                         l+r++rv+K hts++daFe++ +++l++v  e+++v++++
  gi|336253073|ref|YP_004596180.1| 237 caLHRGTRVRKNHTSRRDAFETIGAESLGTVdyETETVEFRR 278
                                       *****************************9965566666665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.33
                                       SECEEEETTEEEETTTEEE-BSSSSS- CS
                      Asparaginase 140 agvlvvfngkllranrvtKvhtsslda 166
                                        g +vv+  ++l+++ + +v  + +d 
  gi|336253073|ref|YP_004596180.1| 345 DGTTVVMTSQCLEGRVCDRVYDTGRDL 371
                                       688999999999999888877666665 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.17     1e+03      15      30 ..     152     167 ..     113     196 .. 0.80
   2 !   89.9   0.0   2.1e-29   1.2e-25       2     109 ..     298     403 ..     297     406 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.17
                                       HHHHHHHTT--EEEEE CS
                    Asparaginase_C  15 vlkallkkgakGvvle 30 
                                        +++ +++ga+Gvv+ 
  gi|336253073|ref|YP_004596180.1| 152 AVREEIEAGADGVVVM 167
                                       3444558888888876 PP

  == domain 2  score: 89.9 bits;  conditional E-value: 2.1e-29
                                       EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHH CS
                    Asparaginase_C   2 VvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkele 78 
                                       V++lk++pgmd+++l+ +  +g +G+++egtG G+++++l++ ++e+++ g+ vv+tsqc++g+v + +y++g++l 
  gi|336253073|ref|YP_004596180.1| 298 VELLKFTPGMDPQFLDVV--EGSEGLIIEGTGLGHVHTDLIPRIEELIEDGTTVVMTSQCLEGRVCDRVYDTGRDLL 372
                                       99**************44..8******************************************************** PP

                                       HHTEEE-TT--HHHHHHHHHHHCTT---HHH CS
                    Asparaginase_C  79 rlgvisaddmtpeaarikLmlllgkgldpae 109
                                       ++gvi+a+d  p +a +kLm++l +  d +e
  gi|336253073|ref|YP_004596180.1| 373 DAGVIEAGDTLPGTAKVKLMWALENSADVEE 403
                                       *************************999887 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0   2.9e-21   1.8e-17       1      55 []       1      51 [.       1      51 [. 0.97

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 2.9e-21
                                      --TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
                            GatD_N  1 ievGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                                      +++GD+++v +++r+yeG+++P+s   +dd++v+KL+ GYN+G++ +e+  +e+l
  gi|336253073|ref|YP_004596180.1|  1 MNPGDRVRVDREDRTYEGVVLPSS---TDDHLVVKLEGGYNVGVDRDEA-AVEVL 51
                                      689*********************...**********************.99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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: 00:00:00.40
# Mc/sec: 3193.64
//
Query:       gi|336253074|ref|YP_004596181.1|  [L=313]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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   39.8   0.6    5.4e-09   36.3   0.1    2.3  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    5.3e-05   23.3   0.4       0.11   12.6   0.0    2.9  3  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00025   21.1   0.1    0.00064   19.8   0.1    1.7  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    0.00059   19.7   1.4     0.0012   18.8   1.4    1.5  1  PknH_C           PknH-like extracellular domain
    0.00092   19.6   0.0      0.002   18.5   0.0    1.6  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0023   18.6   0.6     0.0023   18.6   0.6    2.4  2  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0024   17.8   0.0      0.013   15.4   0.0    2.1  3  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.014   15.1   0.0       0.03   14.1   0.0    1.5  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
       0.04   14.5   0.1      0.097   13.2   0.1    1.7  1  FoP_duplication  C-terminal duplication domain of Friend of P
      0.083   13.5   0.0       0.26   11.9   0.0    1.8  1  DUF883           Bacterial protein of unknown function (DUF88
       0.16   12.1   0.0        1.6    8.8   0.0    2.0  2  Acetyltransf_4   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 !   36.3   0.1   3.3e-12   5.4e-09       9     109 ..      19     119 ..      11     127 .. 0.81
   2 ?    1.5   0.0      0.21   3.4e+02      13      51 ..     183     221 ..     170     286 .. 0.63

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 3.3e-12
                                       HHHTHHHHHHHHHHHHHHHHHSTTC...EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHH CS
                    Acetyltransf_1   9 vesffppnedaseeefeesfsleae...gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLl 82 
                                        ++++   +d   +++++++++e++    +++ae dge +G +++ +  +   ++a+  ++ V+ e+r+kG+ ++L 
  gi|336253074|ref|YP_004596181.1|  19 SDIWTDRGGDYIPRIYHDWLEDEPGqgkKTFLAEIDGEAAGIVQAVMLSE---DEAWFQGMRVAAEHRRKGVSTRLN 92 
                                       44555555555556699999998888889999******************...99********************** PP

                                       HHHHHHHHHTTESEEEEEEETTEHHHH CS
                    Acetyltransf_1  83 ealeerareegikkivlaveedndaai 109
                                       ea+ e+are+g++   + ++++n a+ 
  gi|336253074|ref|YP_004596181.1|  93 EACFEWAREHGATVARVMIFSWNAASF 119
                                       **********99666555678887775 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHHSTTCEEEE.EEETTEEEEEEEEE CS
                    Acetyltransf_1  13 fppnedaseeefeesfsleaegllv.aeedgeliGfisll 51 
                                       ++ +  +++ + e++ +l +e+ ++ +e ++ l+G +  +
  gi|336253074|ref|YP_004596181.1| 183 EESWAVRELTR-EDFDRLADESAVFaVESEDGLAGAAYRS 221
                                       44455555555.6666667774444377777788887333 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0042       6.9       1      60 [.       2      64 ..       2      68 .. 0.78
   2 !   12.6   0.0   6.5e-05      0.11      79     113 ..      76     110 ..      70     130 .. 0.78
   3 ?    0.1   0.0      0.49   7.9e+02       3      55 ..     189     216 ..     182     231 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0042
                                      .EEEE-GGGHHHHHHHHHHHTT----H......HHHHHHHHHHTTS.EEEEEEETTEEEEEEEEE CS
                    Acetyltransf_9  1 eirelteedldevlellkyaFqdeespl....eeireyfrkllees.rvlgaedngelvgqlall 60
                                      +ir++t +d+++v+++ +  + d+  ++    +  + ++++  +++ ++++ae +ge +g ++++
  gi|336253074|ref|YP_004596181.1|  2 NIRRATHDDYEAVADFTSDIWTDRGGDYipriY--HDWLEDEPGQGkKTFLAEIDGEAAGIVQAV 64
                                      59*************************976432..344444444434999999999999998876 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.5e-05
                                       EEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE- CS
                    Acetyltransf_9  79 VavapehrgrgvlskLlaraleemreegqplsllf 113
                                         va+ehr++gv ++L ++ +e +re+g++++  +
  gi|336253074|ref|YP_004596181.1|  76 MRVAAEHRRKGVSTRLNEACFEWAREHGATVARVM 110
                                       5699*************************997544 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.49
                                       EEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEE CS
                    Acetyltransf_9   3 relteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvg 55 
                                       relt ed+d                         +l +es v+ +e+++ l+g
  gi|336253074|ref|YP_004596181.1| 189 RELTREDFD-------------------------RLADESAVFAVESEDGLAG 216
                                       444444444.........................4444444444444444444 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 !   19.8   0.1   3.9e-07   0.00064       5      60 ..      52     106 ..      48     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.9e-07
                   Acetyltransf_CG   5 tldegeevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglkv 60 
                                       ++d ge +++++     e++  f+   V  e+r+kG+  +L +a++++are+g +v
  gi|336253074|ref|YP_004596181.1|  52 EID-GEAAGIVQAVMLSEDEAWFQGMRVAAEHRRKGVSTRLNEACFEWAREHGATV 106
                                       455.6666777776777889999999***************************998 PP

>> PknH_C  PknH-like extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.4   7.2e-07    0.0012      52     113 ..     217     277 ..     191     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.2e-07
                                       -SSBHHHHTTS---EEEEEEEE-SSTT-SEEEEEEEEE-SSHHHHHHHHHHHHHHHHTTTT.- CS
                            PknH_C  52 sageesvYggsgvtavagqtlrdsaddgaslvsqavvafptadaAqaffaalaaqwrrCag.v 113
                                       +a ++ +Y+ + v ++ g + +d+++ ++ +++ +v a+ + daA+a+faa a+  + C+  +
  gi|336253074|ref|YP_004596181.1| 217 AAYRSRTYERT-VDDAEGDSSEDEPTTET-WAEYGVGAWNSVDAARALFAAIARDAADCGAdK 277
                                       34445678877.77766666666666666.6****************************9953 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.2e-06     0.002       3      49 ..      46      99 ..      44     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                                      EEEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH....T CS
                    Acetyltransf_7  3 gevfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea....a 49
                                      +++f+ae dg+  G + ++ l+   a+  ++ V+ e+r+kG+ ++L ea    a
  gi|336253074|ref|YP_004596181.1| 46 KKTFLAEIDGEAAGIVQAVMLSedeAWFQGMRVAAEHRRKGVSTRLNEAcfewA 99
                                      56788****999999888888765455555****************99633431 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.6   1.4e-06    0.0023       4     137 ..       3     127 ..       1     128 [. 0.79
   2 ?    0.7   0.2      0.47   7.6e+02      16      40 ..     153     188 ..     139     232 .. 0.51

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                    Acetyltransf_3   4 LrplteeDlealfelrsdpevmrylpepltleeaeewlerawaeeseeeg.ygwaivlkdtgviGsvglrdleeede 79 
                                       +r++t +D+ea++ + sd  + r  + ++ +   ++wle+  ++   ++g  +++  + d+++ G+v    l+e++ 
  gi|336253074|ref|YP_004596181.1|   3 IRRATHDDYEAVADFTSDIWTDR--GGDYIPRIYHDWLED--EP---GQGkKTFLA-EIDGEAAGIVQAVMLSEDEA 71 
                                       79999999999999888755554..557888889999995..23...333223555.44554699998887777765 PP

                    Acetyltransf_3  80 eaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                        +  g+++a ++++kG+ t   +a+ e+a +e+g++  ++ i   N aS+   +  G+
  gi|336253074|ref|YP_004596181.1|  72 -WFQGMRVAAEHRRKGVSTRLNEACFEWA-REHGATVARVMIFSWNAASFGATRANGY 127
                                       .999*************************.8888****************99999887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.47
                    Acetyltransf_3  16 felrsdpe.vmrylpe..........pltleeaeew 40 
                                       +++ sdp+  +ry ++           l +ee+++ 
  gi|336253074|ref|YP_004596181.1| 153 YRVSSDPTaAWRYWTHsdarehldglGLAPEESWAV 188
                                       346788886667644422222233222222222222 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   8.2e-06     0.013      28      95 ..      43     115 ..      23     130 .. 0.84
   2 ?   -2.4   0.0       2.6   4.2e+03      28      46 ..     200     218 ..     184     227 .. 0.67
   3 ?   -1.8   0.0       1.7   2.7e+03      68      93 ..     258     284 ..     253     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.2e-06
                   Acetyltransf_10  28 egealllvaeeggkivGvi...el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp 95 
                                        + +++++ae +g+ +G++    l +d+   + + V+ e+r++G++++L ea+ e a+++g  + ++ + + +
  gi|336253074|ref|YP_004596181.1|  43 GQGKKTFLAEIDGEAAGIVqavMLsEDEAWFQGMRVAAEHRRKGVSTRLNEACFEWAREHGATVaRVMIFSWN 115
                                       5678899***********976445555559***************************9999888888877655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                   Acetyltransf_10  28 egealllvaeeggkivGvi 46 
                                       + e  ++++e ++ ++G++
  gi|336253074|ref|YP_004596181.1| 200 ADESAVFAVESEDGLAGAA 218
                                       5666688888888899987 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.7
                   Acetyltransf_10  68 igkaLleaveeeaekdgikl.eltvna 93 
                                        ++aL+ a+ + a ++g  + ++ + +
  gi|336253074|ref|YP_004596181.1| 258 AARALFAAIARDAADCGADKtRVLIPE 284
                                       6999*****999999988876666655 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.8e-05      0.03      21      87 ..      21      96 ..       2     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                              PanZ 21 Iy........paqsaealeaalteegalfaarFNdRlLgAvk.veledkeaelsdlcVRevTRrRGVgsyLleear 87
                                      I+        p+ +++ le +  ++++ f a       g v+ v l+++ea+ + ++V ++ Rr+GV+ +L e + 
  gi|336253074|ref|YP_004596181.1| 21 IWtdrggdyiPRIYHDWLEDEPGQGKKTFLAEIDGEAAGIVQaVMLSEDEAWFQGMRVAAEHRRKGVSTRLNEACF 96
                                      66666666677778888888888888888888888888888548999***********************987654 PP

>> FoP_duplication  C-terminal duplication domain of Friend of PRMT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.9e-05     0.097      43      62 ..     137     161 ..     120     177 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.9e-05
                   FoP_duplication  43 kkkpltkeeLDaeLDaYmg.....k 62 
                                       +++p+t  +LDaeLD Y        
  gi|336253074|ref|YP_004596181.1| 137 QPDPATDADLDAELDGYRVssdptA 161
                                       6899*************98555440 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 ?   11.9   0.0   0.00016      0.26      47      80 ..     267     300 ..     252     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                            DUF883  47 lrdaeeavaerakeaaeaaddyVrenPwqavGiA 80 
                                       +rda++  a++++  + ++ +yV + P++ vGi+
  gi|336253074|ref|YP_004596181.1| 267 ARDAADCGADKTRVLIPETPRYVTDAPYAGVGIS 300
                                       7899999*************************97 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0     0.001       1.6      37     141 ..      34     134 ..       3     138 .. 0.84
   2 ?    1.0   0.0      0.25   4.1e+02      44      67 ..     199     221 ..     160     231 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.001
                    Acetyltransf_4  37 fekflealdsekeyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnien 113
                                       ++ +le+   +++  fl++ +++ +G+ +++ +     d+++   + +a    + +g+   l +a+ + ++e + + 
  gi|336253074|ref|YP_004596181.1|  34 YHDWLEDEPGQGKKTFLAEIDGEAAGIVQAVMLSE---DEAWFQGMRVA-AEHRRKGVSTRLNEACFEWAREHGATV 106
                                       67899998344466677777**********95555...9999999***9.689************************ PP

                    Acetyltransf_4 114 llaeiaspnensiqfhkalGFelvgifk 141
                                           i+s n++s     a G+e +++f+
  gi|336253074|ref|YP_004596181.1| 107 ARVMIFSWNAASFGATRANGYEPLAEFR 134
                                       **************9******9998887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.25
                    Acetyltransf_4  44 ldsekeyvflvaesdrivGyaylg 67 
                                       l ++++ vf v+ +d ++G ay +
  gi|336253074|ref|YP_004596181.1| 199 L-ADESAVFAVESEDGLAGAAYRS 221
                                       2.77899************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2276.26
//
Query:       gi|336253075|ref|YP_004596182.1|  [L=94]
Description: MoaD family protein [Halopiger xanaduensis SH-6]
Scores for 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-19   69.3   0.5    3.6e-19   69.2   0.5    1.0  1  ThiS          ThiS family
  ------ inclusion threshold ------
      0.027   14.6   1.6       0.54   10.5   0.4    2.1  2  Flagellin_IN  Flagellin hook IN motif


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 !   69.2   0.5   4.1e-23   3.6e-19       2      77 .]       6      94 .]       5      94 .] 0.97

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 4.1e-23
                                      EETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG..........TTTTEEEEETTEEEGC.CTTTSB--TTCE CS
                              ThiS  2 llfaelrelag..eeelelaegstvaelleaLgerypela..........lerrvavavNgeivpr.lwldtelkdgDe 67
                                      +lfa l e +g    +++ a g+tv+++l+aL +++ el+          l+ +++v++Ng++v++ ++l+tel +gDe
  gi|336253075|ref|YP_004596182.1|  6 KLFADLAERTGdkHVTVDAAAGDTVGDALDALLAEHAELEgrvldeegddLRSQINVLRNGTNVREeEGLETELEEGDE 84
                                      89*********998999999****************9999**********99**************88*********** PP

                                      EEEEESTTC- CS
                              ThiS 68 vailppVaGG 77
                                      +a++ppV+GG
  gi|336253075|ref|YP_004596182.1| 85 LALFPPVSGG 94
                                      *********9 PP

>> Flagellin_IN  Flagellin hook IN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4     6e-05      0.54      12      29 ..      17      36 ..      12      37 .. 0.81
   2 ?    3.3   0.0     0.011        97      24      39 ..      54      69 ..      52      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6e-05
                                      -..EEEEECTTTBCHHHHHH CS
                      Flagellin_IN 12 t..vtisvkagdtlddiada 29
                                      +  vt++++agdt++d+ da
  gi|336253075|ref|YP_004596182.1| 17 DkhVTVDAAAGDTVGDALDA 36
                                      2359************9887 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.011
                                      HHHHHHHHHHCCTTTE CS
                      Flagellin_IN 24 ddiadaINavssktGV 39
                                      dd++++IN   ++t+V
  gi|336253075|ref|YP_004596182.1| 54 DDLRSQINVLRNGTNV 69
                                      79******88888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 751.19
//
Query:       gi|336253076|ref|YP_004596183.1|  [L=447]
Description: TrkA-C domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-06   28.2   0.5    1.9e-05   24.4   0.1    2.5  2  TrkA_C    TrkA-C domain
  ------ inclusion threshold ------
      0.071   13.0   0.1       0.84    9.5   0.1    2.5  2  PDZ_6     PDZ domain


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 ?    1.2   0.0     0.037   3.3e+02      48      65 ..     292     309 ..     282     317 .. 0.72
   2 !   24.4   0.1   2.1e-09   1.9e-05       3      67 ..     343     405 ..     341     406 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.037
                                       -TT-EEEEEEEHHHHHHH CS
                            TrkA_C  48 eeGDvllvvgspsdlael 65 
                                       ++GDv +v+++ +d a+l
  gi|336253076|ref|YP_004596183.1| 292 TAGDVATVAVDADDAAAL 309
                                       678888888888887776 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2.1e-09
                                       EEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T...-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   3 evtvpagsplvGktlkelnlrargvlvvairRg...geliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                        + ++a+s l+G  ++   l+   vlvva+ R    + + +p  d +Le+GD+ +v+g p++l++++e
  gi|336253076|ref|YP_004596183.1| 343 TLPIDADSGLAGEAVGS--LP---VLVVALERAgdgDPVALPAADVRLEAGDTAYVLGRPDALRRIAE 405
                                       67899************..97...6*****88879566666666*******************99876 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   9.4e-05      0.84       2      53 ..     102     152 ..     101     153 .. 0.91
   2 ?   -0.1   0.0     0.095   8.5e+02      37      52 ..     329     344 ..     323     346 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 9.4e-05
                             PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallrgsagesvvlv 53 
                                       + a ++ ++A+ AG r GD++       + +++++dv +llr sag+ v+++
  gi|336253076|ref|YP_004596183.1| 102 IAALVASGIAADAGRRTGDYLAREMFLVTAPRTINDVGQLLR-SAGRVVSVE 152
                                       567788899*********************************.999999886 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.095
                             PDZ_6  37 dvaallrgsagesvvl 52 
                                       ++++llr+++++ ++l
  gi|336253076|ref|YP_004596183.1| 329 ELVSLLRTANDTVTTL 344
                                       899****999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3594.57
//
Query:       gi|336253077|ref|YP_004596184.1|  [L=419]
Description: hypothetical protein Halxa_1673 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0049   16.7   0.3      0.038   13.8   0.1    2.5  2  TrkA_C        TrkA-C domain
  ------ inclusion threshold ------
      0.079   12.5   9.3       0.13   11.8   9.3    1.2  1  5TM-5TMR_LYT  5TMR of 5TMR-LYT


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 ?   -0.7   0.0      0.15   1.3e+03      43      51 ..     229     238 ..     224     241 .. 0.56
   2 !   13.8   0.1   4.2e-06     0.038      24      66 ..     358     410 ..     347     412 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.15
                                       T.T-B--TT- CS
                            TrkA_C  43 g.dtvLeeGD 51 
                                       g + ++++GD
  gi|336253077|ref|YP_004596184.1| 229 GdEVTIRAGD 238
                                       3355666666 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.2e-06
                                       HH.S-EEEEEE.........-T-EEES--TT-B--TT-EEEEEEEHHHHHHHH CS
                            TrkA_C  24 ar.gvlvvair.........RggeliipsgdtvLeeGDvllvvgspsdlaelr 66 
                                       ++  v ++a r         R+g+++ p+ + +Le GD+ +vvg+   ++++ 
  gi|336253077|ref|YP_004596184.1| 358 ENpEVQILAARrresdtdgrRRGWVFAPGLERRLEVGDEAFVVGPEGLVDAVL 410
                                       55566777775344444442448**********************99999886 PP

>> 5TM-5TMR_LYT  5TMR of 5TMR-LYT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   9.3   1.5e-05      0.13      52     120 ..      11      85 ..       7      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
                      5TM-5TMR_LYT  52 vvaGllgGplvGliagliaglhRyl....lgGftalacgisti.lagllaGlihrklkrrr.kkltvlvalligl 120
                                       +  Gll G +++l+ag ++ l+Ry+    l Gf+ ++ ++s+  + g l+Gl+   + ++    + vlv+l+++l
  gi|336253077|ref|YP_004596184.1|  11 IYLGLLTGIVPALVAGSLGFLVRYFtgvtLPGFGVVVLSLSIAsVQGGLMGLVEPTIAQSPrLLVAVLVVLMLSL 85 
                                       578**********************76666677777766665415799999999999964444445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3161.44
//
Query:       gi|336253078|ref|YP_004596185.1|  [L=394]
Description: TrkA-N domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-26   92.6   0.9    3.1e-26   91.9   0.9    1.3  1  TrkA_N        TrkA-N domain
    1.1e-12   47.8   3.7    1.1e-12   47.8   3.7    2.4  2  Ion_trans_2   Ion channel
    0.00012   21.4   0.4     0.0002   20.7   0.4    1.4  1  Ion_trans     Ion transport protein
  ------ inclusion threshold ------
      0.013   15.3   0.1      0.024   14.4   0.1    1.3  1  IRK           Inward rectifier potassium channel transmembran
      0.048   14.0   0.8       0.12   12.7   0.8    1.6  1  NTP_transf_3  MobA-like NTP transferase 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 !   91.9   0.9   8.6e-30   3.1e-26       2     116 .]     253     366 ..     252     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 8.6e-30
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanil 78 
                                       +++G+G++++ +++eL ++ +++vv+ +d ++++el+++ ++vv gd++de+ Le+a+ie+a ++++at++d+  +l
  gi|336253078|ref|YP_004596185.1| 253 LVLGYGELTEPIVDELAANDREFVVVTTD-AAADELADRDVPVVTGDPSDEAPLERAKIERAAGILVATNEDARDAL 328
                                       79****************7767*****98.79********************************************* PP

                                       HHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  79 avllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                       a+l+a++l pk +i+a a d+e+ ++l+ +gad+visp
  gi|336253078|ref|YP_004596185.1| 329 AILTARQLAPKTRIVAAATDRENTKKLEHAGADAVISP 366
                                       ************************************98 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.55     2e+03      50      70 ..      15      36 ..      11      44 .. 0.47
   2 !   47.8   3.7   2.9e-16   1.1e-12       3      73 ..     150     224 ..     148     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.55
                                      ---HHH.HHHHHHHHHHHHHHH CS
                       Ion_trans_2 50 agrlft.ivyillGlalfalfl 70
                                      ++rl++  v+i+l l++ +l +
  gi|336253078|ref|YP_004596185.1| 15 WQRLLSiRVTIVLALTVAVLSV 36
                                      5566653333333333333333 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 2.9e-16
                                       HHHTCHHHHHHHHT......T.---HHHHHHHHHHHHTTS----SSTT.---.--HHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2   3 lllvlifgaviysl..eegwe.kwsfldalYfsfvtltTiGYGdivpe.tda.grlftivyillGlalfalflavl 73 
                                       ll v ++g++  +   e++ e   ++lda+Yf+++t +T+GYGdi+p+ + +  +lft+ +++lG+a f++++  l
  gi|336253078|ref|YP_004596185.1| 150 LLGVQAYGTIGAYAlrEDF-EgISNILDAFYFTLITSSTVGYGDITPDqGSTeAMLFTMSVLVLGVASFGIAIGAL 224
                                       6667788888777775344.4378************************6555569***************998765 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.4   5.7e-08    0.0002     140     222 ..     144     214 ..     120     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.7e-08
                                       HHHHHHHHHHHHHTTSCCCCCCSCCSTSSSTTTSSS.SSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHH CS
                         Ion_trans 140 vlfifaligvqlfkgklreknecaktwenpnngntn.Fdnfftallwlfrlmttegwgdilyatldekskvaliyfv 215
                                       ++  fal+gvq +           + ++++   +++  +n+++a+++++ + +t+g+gdi+++  + +   a+++ +
  gi|336253078|ref|YP_004596185.1| 144 IAAGFALLGVQAY----------GTIGAYALREDFEgISNILDAFYFTLITSSTVGYGDITPDQGSTE---AMLFTM 207
                                       6678*********..........33444444444444888*************************999...888888 PP

                                       HHHHHHH CS
                         Ion_trans 216 ifiilgs 222
                                       ++++lg+
  gi|336253078|ref|YP_004596185.1| 208 SVLVLGV 214
                                       8888875 PP

>> IRK  Inward rectifier potassium channel transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   6.7e-06     0.024      80     134 ..     169     223 ..     164     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.7e-06
                               IRK  80 anvksftsallfslEtqttigyGsrvvteeCpeailllviqsivgllidavlvgi 134
                                       + ++++++a+ f+l t  t+gyG  ++ +  +ea+l+ +  +++g++   + +g+
  gi|336253078|ref|YP_004596185.1| 169 EGISNILDAFYFTLITSSTVGYGDITPDQGSTEAMLFTMSVLVLGVASFGIAIGA 223
                                       568999******************************9999999998877666666 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 ?   12.7   0.8   3.3e-05      0.12      19     109 ..     253     348 ..     249     375 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.3e-05
                                       HCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHH........HHHHHHHHHH.SSS CS
                      NTP_transf_3  19 lplggkpllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgpl........aslaaalraaadad 87 
                                       l lg   l e ++d l+a   +e vvv+ d   +++la+++v+vv+ +++++ pl        a+++ a ++    d
  gi|336253078|ref|YP_004596185.1| 253 LVLGYGELTEPIVDELAAN-DREFVVVTTDA-AADELADRDVPVVTGDPSDEAPLerakieraAGILVATNED-ARD 326
                                       5666667788889999987.47777777775.56789***************999777777778888888886.689 PP

                                       CEEEEETT-TT--HHHHHHHHH CS
                      NTP_transf_3  88 avlvlacDmPlltpelverlla 109
                                       a+++l++ +   ++ +v++ ++
  gi|336253078|ref|YP_004596185.1| 327 ALAILTARQLAPKTRIVAAATD 348
                                       9999998888777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2833.43
//
Query:       gi|336253079|ref|YP_004596186.1|  [L=474]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-17   62.6   3.6    7.2e-17   61.7   3.6    1.5  1  HPP       HPP family
    6.9e-06   26.6   0.5    0.00072   20.1   0.1    2.8  3  Usp       Universal stress protein family


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 !   61.7   3.6     8e-21   7.2e-17       1     117 [.      67     186 ..      67     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 8e-21
                               HPP   1 liaslGAsavllfavpesplaqPrnvvgGhlisalvGvaiaklfgl......sllwlaaalavalaialmlltrtlh 71 
                                       l+++l++ ++ lfa pe +++ P+++vgG +++al+G+++++++g+      +++ + aal+++++ a+++++++ +
  gi|336253079|ref|YP_004596186.1|  67 LFPPLASGTYTLFADPEGRYSDPWTFVGGMTVGALCGWVALAVVGElglhsgTVSAAGAALGIFFTGACTWALDLEE 143
                                       79**************************************999999999998556569******************* PP

                               HPP  72 PPagAtaliavlgkeikelgwafllvpvllgslllvlvalllnn.ls 117
                                       P a +tal+++++++    ++a++l  ++++s++++++ +++++ + 
  gi|336253079|ref|YP_004596186.1| 144 PTAFSTALLVLVTGN---ARLAYVLG-LVVSSAFVAATFVVWRDrFY 186
                                       **************8...58889888.88999999999999987444 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1     8e-08   0.00072      16     122 ..     219     330 ..     201     337 .. 0.67
   2 !    3.8   0.0    0.0087        78       3      41 ..     352     390 ..     350     407 .. 0.79
   3 ?   -2.0   0.0      0.51   4.6e+03     102     129 ..     430     458 ..     414     467 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8e-08
                                       HHHHHHHHHHHHH.CTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHHHCTTCEEEEEEEES CS
                               Usp  16 kkAlewAlelaka.rgaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaaeaggvkvevvveeg 89 
                                       + ++++A+ela a   ++++l   +   +++++s a+++  e   e   a +++++  + +   + +v+v  + +  
  gi|336253079|ref|YP_004596186.1| 219 ETVARFAAELAGAhEAGKVVLFETVYQGDDDSSSPAEPDGDERTTETVDAVERLAEelESRYDVPCEVIVAGDDRRE 295
                                       6789*********6666666666666666555555555544444444444444333336666666666666666677 PP

                                       SHHHHHHHHHHHTTSSEEEEESCC..SSTTTTCSS CS
                               Usp  90 dpaeeilevaeeedadliVvGsrg..rsglsrlll 122
                                       + a+  l++a+e+++dliV+      r+gls ++ 
  gi|336253079|ref|YP_004596186.1| 296 PSARLVLQTAREQNCDLIVTPYAEddRGGLSPFIR 330
                                       7788889************9766655666666655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0087
                                       SEEEEEE-.SSHHHHHHHHHHHHHHHHCTSEEEEEEEEES CS
                               Usp   3 krIlVavD.gseeskkAlewAlelakargaelillhvidp 41 
                                       + +lV+v    +++++ +++Al+la ++  ++ ++++i+ 
  gi|336253079|ref|YP_004596186.1| 352 RQVLVPVRgAGDTARAMVDFALRLAGRT-QPVGVCTCIKR 390
                                       789****9445666699*********96.47777777765 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.51
                                       TTSSEEEEESCC.SSTTTTCSSBHHHHHH CS
                               Usp 102 edadliVvGsrg.rsglsrlllGSvseyv 129
                                        ++d + +Gs+  rs+ sr++   + e+v
  gi|336253079|ref|YP_004596186.1| 430 SQYDVVFLGSSTdRSAASRFVSPPTFEKV 458
                                       57899999987658888887766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3526.25
//
Query:       gi|336253080|ref|YP_004596187.1|  [L=85]
Description: hypothetical protein Halxa_1676 [Halopiger xanaduensis SH-6]
Scores for 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   59.6   0.4    3.1e-16   59.4   0.4    1.1  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.4   1.8e-20   3.1e-16       1      69 [.      16      79 ..      16      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 1.8e-20
                            HalOD1  1 deespstaVveavaavegvdptelep.LydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdg 69
                                      +++sps a+++a+aa+e+v+p+ l+  Ly +iDp ALd+L+a+      ++ + vsF+ ++y + ++++ 
  gi|336253080|ref|YP_004596187.1| 16 SNTSPSSAIIAAIAAIENVNPMHLDLvLYRHIDPTALDTLVAT------DERIAVSFSLDDYLISIEGSD 79
                                      579*********************988****************......56799************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 636.29
//
Query:       gi|336253081|ref|YP_004596188.1|  [L=272]
Description: transcriptional regulator TrmB [Halopiger xanaduensis SH-6]
Scores for 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-20   70.6   0.2      3e-19   68.7   0.0    2.2  3  TrmB            Sugar-specific transcriptional regulator TrmB
      9e-05   21.8   0.1    0.00012   21.4   0.1    1.2  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
      0.002   18.2   1.1      0.015   15.4   0.1    2.9  3  HTH_20          Helix-turn-helix domain
     0.0023   17.9   0.0     0.0055   16.7   0.0    1.7  1  E2F_TDP         E2F/DP family winged-helix DNA-binding domain
     0.0032   17.3   0.5      0.035   14.0   0.1    2.6  3  MarR_2          MarR family
  ------ inclusion threshold ------
      0.019   14.8   0.2      0.053   13.3   0.1    2.0  2  HTH_IclR        IclR helix-turn-helix domain
      0.065   13.2   0.0       0.19   11.7   0.0    1.8  1  Cdc6_C          CDC6, C terminal winged helix domain
       0.11   12.5   0.0       0.47   10.4   0.0    2.1  2  PadR            Transcriptional regulator PadR-like family


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 !   68.7   0.0   1.3e-22     3e-19       1      65 [.      14      78 ..      14      81 .. 0.97
   2 ?   -3.2   0.0       3.7   8.3e+03      20      29 ..     203     212 ..     202     216 .. 0.84
   3 ?   -2.8   0.0       2.6   5.9e+03      43      53 ..     256     266 ..     255     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1.3e-22
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE- CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYrav 65
                                      Lq+lGL+eyEa+++ aL +l + ta++i+e ++vpr++vY+++r Le+ GlVe+++++p+ Yr v
  gi|336253081|ref|YP_004596188.1| 14 LQELGLQEYEARCFMALTQLSSGTAKDIHELSEVPRTRVYDAVRVLESQGLVEVQHSNPQQYRSV 78
                                      89************************************************************976 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.7
                                       HCCCHHCHHC CS
                              TrmB  20 lgpatadeia 29 
                                       +g+at++eia
  gi|336253081|ref|YP_004596188.1| 203 HGRATVNEIA 212
                                       6889999997 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.6
                                       HHHHHHCTSEE CS
                              TrmB  43 LrsLedkGlVe 53 
                                       Lr+L++ Gl  
  gi|336253081|ref|YP_004596188.1| 256 LRRLVSSGLAA 266
                                       89999999975 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   5.4e-08   0.00012       1      69 [.     119     187 ..     119     244 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 5.4e-08
                                       -EEEESSHHHHHHHHHHHHHH-SSEEEE.EE-GGGH.HHHHHHHHHHHHTT-EEEEEESS----GGGSSSS CS
                    Regulator_TrmB   1 avwvvksretvierieelIesAeneliv.slpselL.eelreeliaaaergvtVllliypdedleeldlee 69 
                                       +vw  ++ e++ +r  +lIesAe+e+ +  ++ ++L e+l + l++a +rgv++ll   +  ++ +++lee
  gi|336253081|ref|YP_004596188.1| 119 EVWSLTGHEAIESRTIDLIESAESEVALlVVDERILsETLYSALADASDRGVSTLLGGQT--AEITERLEE 187
                                       58999********************96516677777456889************997776..333333333 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   6.6e-06     0.015      26      58 ..      37      69 ..      13      72 .. 0.89
   2 ?   -0.9   0.0      0.82   1.8e+03       6      27 ..     161     179 ..     156     212 .. 0.58
   3 ?   -0.7   0.0      0.69   1.6e+03      45      61 .]     256     272 .]     251     272 .] 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.6e-06
                                      -HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 26 taselaerldlskntlsyHLrvLeeagLvevvr 58
                                      ta++++e+ +++++ +++ +rvLe+ gLvev+ 
  gi|336253081|ref|YP_004596188.1| 37 TAKDIHELSEVPRTRVYDAVRVLESQGLVEVQH 69
                                      8999999999********************975 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.82
                                       HHS-HHHHHHHHHHSTCTTB-H CS
                            HTH_20   6 ALahPvRrrilraLaraeglta 27 
                                       ALa+ + r++  +L   +g+ta
  gi|336253081|ref|YP_004596188.1| 161 ALADASDRGVSTLL---GGQTA 179
                                       66666666666666...33333 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.69
                                       HHHHHHCTTEEEECTEE CS
                            HTH_20  45 LrvLeeagLvevvregr 61 
                                       Lr L++ gL  v ++gr
  gi|336253081|ref|YP_004596188.1| 256 LRRLVSSGLAAVDDPGR 272
                                       799999**999999987 PP

>> E2F_TDP  E2F/DP family winged-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.5e-06    0.0055      37      66 ..      43      72 ..       6      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.5e-06
                           E2F_TDP 37 kdekvkkRRiYDilNVLealglieKeskne 66
                                      +  +v + R+YD++ VLe+ gl+e ++ n 
  gi|336253081|ref|YP_004596188.1| 43 ELSEVPRTRVYDAVRVLESQGLVEVQHSNP 72
                                      44589999***************9887654 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.5e-05     0.035      23      56 ..      37      71 ..       7      77 .. 0.82
   2 ?   -3.0   0.0       3.2   7.3e+03      22      28 ..     206     212 ..     199     220 .. 0.72
   3 ?    0.2   0.0      0.32   7.2e+02      41      51 ..     255     265 ..     252     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE.ES CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverr.pg 56
                                      t++++ +   +++ +v  +++ L+++GLve + ++
  gi|336253081|ref|YP_004596188.1| 37 TAKDIHELSEVPRTRVYDAVRVLESQGLVEVQhSN 71
                                      9*****************************98555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.2
                                       EEHHHHH CS
                            MarR_2  22 ltvgela 28 
                                        tv+e+a
  gi|336253081|ref|YP_004596188.1| 206 ATVNEIA 212
                                       5788876 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.32
                                       HHHHHHHTTSE CS
                            MarR_2  41 ilkrLvaaGLv 51 
                                       +l+rLv+ GL 
  gi|336253081|ref|YP_004596188.1| 255 LLRRLVSSGLA 265
                                       79*******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 ?   13.3   0.1   2.4e-05     0.053      19      49 ..      36      66 ..      24      69 .. 0.82
   2 ?   -3.7   0.0       4.8   1.1e+04      38      48 ..     255     265 ..     255     268 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                                      -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyve 49
                                       t +++++ + +p++ v+  ++ L+ +G+ve
  gi|336253081|ref|YP_004596188.1| 36 GTAKDIHELSEVPRTRVYDAVRVLESQGLVE 66
                                      3889**************************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.8
                                       HHHHHHHTTSE CS
                          HTH_IclR  38 lLqtLvelGyv 48 
                                       lL+ Lv  G+ 
  gi|336253081|ref|YP_004596188.1| 255 LLRRLVSSGLA 265
                                       78889988886 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 ?   11.7   0.0   8.4e-05      0.19      34      72 ..      44      78 ..      37      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.4e-05
                                      -----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEE CS
                            Cdc6_C 34 vdpltqrevsdllseLemlgileleksskGrregrtrki 72
                                      ++ + +++v+d ++ Le++g++e+++s       ++r +
  gi|336253081|ref|YP_004596188.1| 44 LSEVPRTRVYDAVRVLESQGLVEVQHS----NPQQYRSV 78
                                      566778*******************99....44566655 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00021      0.47      23      53 ..      41      71 ..      31      78 .. 0.81
   2 ?   -2.5   0.0       2.3   5.2e+03      14      25 ..     180     191 ..     178     199 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                                      STT-CCTTHHHHHHHHHHHHHTTSEEEEEE- CS
                              PadR 23 segllelseGslYpaLkrLekeglvesewee 53
                                      +++l e+  +++Y+a + Le +glve + ++
  gi|336253081|ref|YP_004596188.1| 41 IHELSEVPRTRVYDAVRVLESQGLVEVQHSN 71
                                      456678999****************988765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                                       HHHHHHHCCSTT CS
                              PadR  14 eiikeleelseg 25 
                                       ei+++lee +  
  gi|336253081|ref|YP_004596188.1| 180 EITERLEEEFPS 191
                                       788888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1971.60
//
Query:       gi|336253082|ref|YP_004596189.1|  [L=105]
Description: hypothetical protein Halxa_1678 [Halopiger xanaduensis SH-6]
Scores for 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   0.2      0.013   15.5   0.2    1.9  1  HTH_20    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 !   15.5   0.2   7.5e-07     0.013       1      59 [.       8      73 ..       8      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.5e-07
                                      HHHHHHHS-HHHHHHHHHH..........STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  1 dqiaeALahPvRrrilraL..........araegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      d++++AL++  Rrr+l aL           ++ + t+se  + l +sk   + HL +L++ gL+e +r 
  gi|336253082|ref|YP_004596189.1|  8 DRLFDALTDVHRRRLLFALidhnpqdvseLPDVPWTLSESEAVL-TSK--HHVHLPKLADYGLIEWERD 73
                                      689****************9999999999999999999999988.554..5679**********98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 762.17
//
Query:       gi|336253083|ref|YP_004596190.1|  [L=217]
Description: Deoxyribose-phosphate aldolase [Halopiger xanaduensis SH-6]
Scores for 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-09   35.9   1.3    7.7e-09   35.5   1.3    1.1  1  DeoC      DeoC/LacD family aldolase
  ------ inclusion threshold ------
      0.019   15.1   2.9      0.048   13.8   2.9    1.6  1  CRA_rpt   Cytoplasmic repetitive antigen (CRA) like repeat


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 !   35.5   1.3   8.6e-13   7.7e-09       6     232 ..      10     205 ..       6     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 8.6e-13
                                       ECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEET CS
                              DeoC   6 vDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvde 82 
                                       +D++v+  + t +       d++++ +ea++ g +a    + v   a    +   a++v++++g+   + k      
  gi|336253083|ref|YP_004596190.1|  10 IDHTVLGPETTTA-------DVRTVLDEAAEYGMNACIPPYAVEEAADYAPDVTLATVVGFPHGQNEPELK------ 73 
                                       6777766666666.......9**************97766666666666666799*********9988888...... PP

                                       TCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEE.EEE-CTTBSSTTCHHHHHHHHHH CS
                              DeoC  83 vasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplile.lylrdeaikdekvdpdlvaeAar 158
                                         +  +a+++GAd+++vv+++  ++++e+  + ae++++ +a      ++i+e ++l d++    k      ++A +
  gi|336253083|ref|YP_004596190.1|  74 RREGVRAWQAGADELDVVINVGRLKAGEDDVVRAELAEIVAA-VPIPVKVIIEtALLSDAE----K------RRACE 139
                                       445559*********************************975.578899999955555555....4......79*** PP

                                       HHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTSSHHHHHHHHHHHHH..HHTH..CEEEESHH CS
                              DeoC 159 vsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGvseedfletvedAvk..eaga..sGvlsGRa 231
                                       +++ ++a+ +K++++ +   a+ ed+e +++      +p v+ sGGv         ++Av+  eaga  +G++sG +
  gi|336253083|ref|YP_004596190.1| 140 AAVAADAKMVKTSTGFADGGAELEDVELMREY-----LP-VKASGGV------GSYDEAVAmlEAGAerIGASSGVE 204
                                       ***************77777777888777765.....67.9******......788888887899999999999977 PP

                                       H CS
                              DeoC 232 i 232
                                       i
  gi|336253083|ref|YP_004596190.1| 205 I 205
                                       6 PP

>> CRA_rpt  Cytoplasmic repetitive antigen (CRA) like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.9   5.3e-06     0.048       9      31 ..     125     147 ..     124     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.3e-06
                           CRA_rpt   9 EaakvAEAEKrkAAEAakvaEae 31 
                                       E+a    AEKr+A EAa +a a+
  gi|336253083|ref|YP_004596190.1| 125 ETALLSDAEKRRACEAAVAADAK 147
                                       7888899**********999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1601.36
//
Query:       gi|336253084|ref|YP_004596191.1|  [L=348]
Description: translation initiation factor, aIF-2BII family [Halopiger xanaduensis SH-6]
Scores for 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-75  252.9   0.1    3.8e-75  252.7   0.1    1.0  1  IF-2B          Initiation factor 2 subunit family
  ------ inclusion threshold ------
       0.01   15.5   0.6        2.2    8.1   0.3    3.5  3  PEP-utilizers  PEP-utilising enzyme, mobile domain
      0.019   15.6   7.4          5    7.9   3.6    3.3  3  DUF2849        Protein of unknown function (DUF2849)
       0.16   11.5   2.3       0.82    9.3   0.1    3.0  3  PRP4           pre-mRNA processing factor 4 (PRP4) like
        0.2   11.9   0.3        3.1    8.0   0.0    2.5  3  BtrH_N         Butirosin biosynthesis protein H, N-terminal


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 !  252.7   0.1   1.1e-78   3.8e-75       2     282 .]      30     321 ..      29     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 252.7 bits;  conditional E-value: 1.1e-78
                                       S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHH CS
                             IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakks 78 
                                       +rG+++ia aa+e+l+  ++++++++ a ++e+lr a+++L ++rPtavsl na+r++l+      + ++v+e + s
  gi|336253084|ref|YP_004596191.1|  30 IRGAATIADAAAEALAVQAERSEAETPAAFREQLRAAARTLYETRPTAVSLPNALRYVLRG----MEGETVSELRGS 102
                                       89**********************************************************3....5799******** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHH CS
                             IF-2B  79 liekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLv 155
                                         +++ e+ ++ e+a+   g+i+a+++ dgd+++T+c+s  +l+ ++aa +++k+++ iv E+rPr qG+ ta +L+
  gi|336253084|ref|YP_004596191.1| 103 TTSRAAEFRDDLEQAQATLGEIGANRLRDGDVVMTHCHSTDALSCIEAALEDGKHIEAIVKETRPRKQGHITARQLR 179
                                       ***************************************************************************** PP

                                       HTTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGS CS
                             IF-2B 156 qagipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedi 232
                                       + g+pvtli+d+a++  ++   d v+vGAd+i+++G+++nkiGTs lAv A+e+ +pv+v+a+++k+++ + +++ +
  gi|336253084|ref|YP_004596191.1| 180 ELGVPVTLIVDNAARRYLDD-ADHVLVGADSIAADGSVINKIGTSGLAVNARERGVPVMVAAQTIKLHPDTMTGHTV 255
                                       ********************.******************************************************** PP

                                       SXXBEXTHHHHEETTEESSTT................TEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 233 fieerdpeellnitgeriaee................elkvvnpafDvtPpelItliITevGvlpp 282
                                        ie+rd++e+l+ +++                      l v npafDvtPp+ +++i+Te G +pp
  gi|336253084|ref|YP_004596191.1| 256 AIEMRDEHEVLPEDERAEIVGdgtdssaepaadddddGLTVENPAFDVTPPRHVDAIVTERGQFPP 321
                                       ************99865433379****************************************998 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 ?    2.7   0.1     0.028     1e+02      41      69 ..     177     206 ..     129     214 .. 0.82
   2 ?    8.1   0.3   0.00061       2.2      35      57 ..     222     244 ..     204     262 .. 0.80
   3 ?   -0.1   0.0      0.22     8e+02      23      32 ..     308     317 ..     298     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.028
                                       HHHHTT--EEE--SSHH.HH--T.EEEEEE CS
                     PEP-utilizers  41 vArelgiPaVvgvgeatielkeg.dlitvD 69 
                                         relg+P+ + v++a +++ ++ d + v 
  gi|336253084|ref|YP_004596191.1| 177 QLRELGVPVTLIVDNAARRYLDDaDHVLVG 206
                                       5699******99999999888888888775 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00061
                                       HHHHHHHHHHTT--EEE--SSHH CS
                     PEP-utilizers  35 tSHaAivArelgiPaVvgvgeat 57 
                                       tS  A+ Are g+P+ v ++ ++
  gi|336253084|ref|YP_004596191.1| 222 TSGLAVNARERGVPVMVAAQTIK 244
                                       8999**************99986 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.22
                                       GEEEEEES-- CS
                     PEP-utilizers  23 kaaGivterG 32 
                                       ++ +ivterG
  gi|336253084|ref|YP_004596191.1| 308 HVDAIVTERG 317
                                       799******9 PP

>> DUF2849  Protein of unknown function (DUF2849)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.6    0.0014         5      26      80 ..      12      67 ..       3      72 .. 0.75
   2 ?    7.6   0.0    0.0017       6.2       3      20 ..     124     141 ..     123     180 .. 0.71
   3 ?   -1.4   0.0       1.1     4e+03      27      61 ..     270     304 ..     248     313 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0014
                           DUF2849 26 laeAavl..eeadealaalaaaaaaeqevvgvyladveeeedgvepahlREriRaaG 80
                                      ++ A  +  +++d a++++  aa+ ++ + ++ ++++e+ ++  +pa +RE++Raa 
  gi|336253084|ref|YP_004596191.1| 12 VTVAPAVaeTADDIAEMRIRGAATIADAAAEALAVQAER-SEAETPAAFREQLRAAA 67
                                      555555534667778888888888899999999999998.6678**********975 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0017
                           DUF2849   3 vTAnrLldGevvyltadg 20 
                                       + AnrL+dG+vv  + ++
  gi|336253084|ref|YP_004596191.1| 124 IGANRLRDGDVVMTHCHS 141
                                       67**********765444 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.1
                           DUF2849  27 aeAavleeadealaalaaaaaaeqevvgvyladve 61 
                                       ++A+++ + +++ a+ aa + ++   v+  ++dv+
  gi|336253084|ref|YP_004596191.1| 270 ERAEIVGDGTDSSAEPAADDDDDGLTVENPAFDVT 304
                                       56888877777777777777777777777777766 PP

>> PRP4  pre-mRNA processing factor 4 (PRP4) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00023      0.82       3      14 ..     176     187 ..     175     187 .. 0.94
   2 ?   -2.3   0.0      0.97   3.5e+03       6      13 ..     230     237 ..     230     238 .. 0.87
   3 ?    0.3   0.1      0.15   5.2e+02      14      19 ..     331     336 ..     331     342 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00023
                              PRP4   3 rrLRelGEPitL 14 
                                       r+LRelG P+tL
  gi|336253084|ref|YP_004596191.1| 176 RQLRELGVPVTL 187
                                       79*********8 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.97
                              PRP4   6 RelGEPit 13 
                                       Re+G P+ 
  gi|336253084|ref|YP_004596191.1| 230 RERGVPVM 237
                                       9***9985 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.15
                              PRP4  14 LFGEth 19 
                                       LFGEt 
  gi|336253084|ref|YP_004596191.1| 331 LFGETT 336
                                       9***95 PP

>> BtrH_N  Butirosin biosynthesis protein H, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.18   6.4e+02      53      85 ..      34      66 ..      19      80 .. 0.82
   2 ?    8.0   0.0   0.00088       3.1      54     111 ..     147     204 ..     130     215 .. 0.83
   3 ?   -1.9   0.0         1   3.7e+03      88     101 ..     232     245 ..     229     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                            BtrH_N 53 gdlekrlakrlglkvevketkdpeeawkalkee 85
                                      + +   +a+ l ++ e++e ++p++  ++l+++
  gi|336253084|ref|YP_004596191.1| 34 ATIADAAAEALAVQAERSEAETPAAFREQLRAA 66
                                      4788899999*************9999999875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00088
                            BtrH_N  54 dlekrlakrlglkvevketkdpeeawkalkeeLdaGrpvivqvdvyyLpYlpkesrlh 111
                                        +e+ l +  +++  vket+  ++++ + ++  + G pv + vd++   Yl +  ++ 
  gi|336253084|ref|YP_004596191.1| 147 CIEAALEDGKHIEAIVKETRPRKQGHITARQLRELGVPVTLIVDNAARRYLDDADHVL 204
                                       567778888889999999*999*****999999******************9666654 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1
                            BtrH_N  88 aGrpvivqvdvyyL 101
                                       +G pv+v++   +L
  gi|336253084|ref|YP_004596191.1| 232 RGVPVMVAAQTIKL 245
                                       78999998877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); 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 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2483.04
//
Query:       gi|336253085|ref|YP_004596192.1|  [L=273]
Description: hypothetical protein Halxa_1681 [Halopiger xanaduensis SH-6]
Scores for 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   64.2   8.5    2.8e-17   63.8   8.5    1.1  1  DUF63           Membrane protein of unknown function DUF63
  ------ inclusion threshold ------
       0.21   11.4   0.2       0.21   11.4   0.2    2.9  3  Phage_Coat_Gp8  Phage major coat protein, Gp8


Domain annotation for each model (and alignments):
>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   8.5   3.1e-21   2.8e-17      41     267 ..      28     269 ..      13     273 .] 0.84

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 3.1e-21
                             DUF63  41 llkklkikidekfvlatipyvilgsslRvveDagllkpplsyllitPliyflvflitlavlliskklekk.lkkdyk 116
                                       ll  l+  + ++ v++  p++++gs+l v+   + +   + +l+ +P +y++ ++++ +v ++   l+   l+ + +
  gi|336253085|ref|YP_004596192.1|  28 LLWALEPPVTDRTVISFAPWMMFGSTLQVLYRLEAFPDSIAVLFTAPSVYLVTAIVAGLVWVVGIFLQAGgLQPTIE 104
                                       5555566788999***************************************************9999999999999 PP

                             DUF63 117 klyaavGvvlvlvvlllLl...lteevvnlevlllvlllaavltalvllllrklk..lellsdklnlllllahllDa 188
                                       +++ ++G+  ++v++++++   ++    +++ +++ +++a ++tal ++ l  +   + +++  +  l+++++ +D+
  gi|336253085|ref|YP_004596192.1| 105 RVVGVAGTGFFVVFAMFIVlsgWNAGSFSPFWPVIAVVVAGIVTALAWVALGLWFtdVAATTGATGALVVFGQTIDG 181
                                       9999988888777777766668788888888888888888888888888877776356677788999********** PP

                             DUF63 189 satfvgidllgYvEqHvvpsfLidl.........tGtalvmyplkllvlipvlyildkevkeeeelrnlvklailvl 256
                                        +t vg ++lg  E+ ++ ++++++         +G+ + ++ +k+++ + vl +++++v+ee +  + ++  + ++
  gi|336253085|ref|YP_004596192.1| 182 VSTAVGYAVLGSSEEVPLSRAILEVgkslptaeyIGAGWLFVLVKVVLALVVLGLFKEYVEEEPRQARTILGLLAAI 258
                                       *****************999998643332222228999*************************9977777777999* PP

                             DUF63 257 GlaPgiRnllr 267
                                       Gl+Pg+ n+l 
  gi|336253085|ref|YP_004596192.1| 259 GLGPGVHNTLL 269
                                       ********985 PP

>> Phage_Coat_Gp8  Phage major coat protein, Gp8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.4       1.4   1.3e+04      33      41 ..      79      87 ..      78      88 .. 0.61
   2 ?    3.4   1.4    0.0074        66      29      42 ..     136     148 ..     132     151 .. 0.75
   3 ?   11.4   0.2   2.4e-05      0.21      22      49 ..     213     241 ..     208     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.4
                                      HHHHHHHHH CS
                    Phage_Coat_Gp8 33 vvvvvAtlg 41
                                      v+ +vA+l+
  gi|336253085|ref|YP_004596192.1| 79 VTAIVAGLV 87
                                      455677775 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0074
                                       HHHHHHHHHHHHHH CS
                    Phage_Coat_Gp8  29 WavVvvvvvAtlgI 42 
                                       W+v+  vvvA+++ 
  gi|336253085|ref|YP_004596192.1| 136 WPVI-AVVVAGIVT 148
                                       8865.678899985 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHH.HHHHHHHHHHHHHHHHH CS
                    Phage_Coat_Gp8  22 teligyaWavV.vvvvvAtlgIkLFKKFs 49 
                                        e+ig  W  V v vv A +++ LFK ++
  gi|336253085|ref|YP_004596192.1| 213 AEYIGAGWLFVlVKVVLALVVLGLFKEYV 241
                                       59******977367999*********886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2048.16
//
Query:       gi|336253086|ref|YP_004596193.1|  [L=296]
Description: PfkB domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-50  169.5   4.8    1.3e-49  169.2   4.8    1.1  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 !  169.2   4.8     7e-54   1.3e-49       3     300 ..       3     282 ..       1     284 [. 0.89

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 7e-54
                                       EEEEEEEEEEEEEEECSSH.TTSEE.EESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTE CS
                              PfkB   3 kvvviGealidliavsekl.egelv.evktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegv 77 
                                       +v++ G+++ d+ + +++l e++     ++ ++s GG++aNvA ala l +d+ +ig vGdD+ G   ++ l+++gv
  gi|336253086|ref|YP_004596193.1|   3 RVLSAGHVNWDVTLRVDRLpEADGEaSIRSQRQSGGGSAANVAAALAGLEVDAGLIGSVGDDDNGVLARRDLESAGV 79 
                                       68899***************777777*************************************************** PP

                                       EETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHH CS
                              PfkB  78 dtdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaea 154
                                       d ++v+i+e  +t++++++vd dge  ++ n+g +++  +ee   de  + +ad++++ +    + p+++ + +++a
  gi|336253086|ref|YP_004596193.1|  80 DLEGVRIVEAGQTAVKYLLVDDDGEVAVLGNDGVNEAVGPEEI--DERRIRNADHVHLTS----QRPDTAAAIARTA 150
                                       *********************99*****************876..**************9....6666666666666 PP

                                       HHHTTE..EEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGG CS
                              PfkB 155 aknggt..fdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGk 229
                                        ++g t  fdp  +         ++ e+la ad+l++n++El+al++ +     e +   +       + v v++G+
  gi|336253086|ref|YP_004596193.1| 151 NEAGVTvsFDPGRRLG-----DRDYGEALAAADVLFANDRELAALLEDE----YEYVGSDFD-----DRIVAVKHGS 213
                                       6666655555554433.....468*********************9999....333333333.....59******** PP

                                       GEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCSC CS
                              PfkB 230 eGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiaslp 300
                                       +Ga v + +g++ +p  + v++vDt GAGD+f++gf+a +l+  ++e+al++ana++al++ ++ga++ +p
  gi|336253086|ref|YP_004596193.1| 214 DGAEVHTPTGSYVHPG-FDVDAVDTAGAGDAFAAGFIATWLTDGDVERALEYANACGALTAGREGARS-AP 282
                                       ******9999999999.78***********************************************96.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2242.33
//
Query:       gi|336253087|ref|YP_004596194.1|  [L=99]
Description: hypothetical protein Halxa_1683 [Halopiger xanaduensis SH-6]
Scores for 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-20   72.7   2.2    2.8e-20   72.4   2.2    1.2  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   2.2   1.5e-24   2.8e-20       2      75 .]      25      98 ..      24      98 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 1.5e-24
                            HalOD1  2 eespstaVveavaavegvdptelep.LydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75
                                       e+ps+a ++a+a+++++d+t+ ++ Lyd++Dp+ALdaLf++++++ +r+ + v+F+++g++VtVr d+ +eV p
  gi|336253087|ref|YP_004596194.1| 25 GEPPSIAAATALARYNDEDVTAASTqLYDYVDPEALDALFDDTCTRGSRSVAAVEFDVDGVRVTVRPDR-VEVAP 98
                                      69*********************666***************************************9998.99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 779.16
//
Query:       gi|336253088|ref|YP_004596195.1|  [L=242]
Description: Uridine phosphorylase [Halopiger xanaduensis SH-6]
Scores for complete 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-47  161.5   2.4    2.3e-47  161.2   2.4    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 !  161.2   2.4   1.3e-51   2.3e-47       1     230 [.      16     233 ..      16     238 .. 0.93

  Alignments for each domain:
  == domain 1  score: 161.2 bits;  conditional E-value: 1.3e-51
                                       CEEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEE CS
                         PNP_UDP_1   1 kiaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriG 77 
                                       +ia+i g+pg+v+ +a++  +e +   ++r++k+v  t++g+  +i+stGiG+p+aa +a  ++    gv++++r+G
  gi|336253088|ref|YP_004596195.1|  16 DIALIPGDPGRVDRIADH-CDEAETVAQNREYKLVNATYEGRDLTICSTGIGCPSAA-IAIEEMAN-VGVETFVRVG 89 
                                       69****************.9999999999****************************.77777777.46******** PP

                                       EEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESES CS
                         PNP_UDP_1  78 taGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgf 154
                                       t G+l++++++GD+++++ a   +g+s+         y  ++y+a +d + +++l+ +ae ++ +vh+G++a+ d f
  gi|336253088|ref|YP_004596195.1|  90 TTGALQSEIEIGDMIVATGAAKNEGTSK--------RYEDAEYPAVPDYDVLSALVDSAETNDEDVHVGPIASDDAF 158
                                       ****************************........99*************************************** PP

                                       S-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHHH CS
                         PNP_UDP_1 155 yaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaaknaaalll 230
                                       yaet+++++ +++ g  +veME+aav++lAr+ g++++ai++v  ++++g+ +  + +e+ e  ++a++n+ ++++
  gi|336253088|ref|YP_004596195.1| 159 YAETDEYVADWEDAGLLCVEMEAAAVFTLARRKGLRAGAICTVDGNLVEGTQKGTD-TEDDELPDKAKNNVGRAID 233
                                       *******************************************8888886666665.8888888888888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1976.11
//
Query:       gi|336253089|ref|YP_004596196.1|  [L=76]
Description: hypothetical protein Halxa_1685 [Halopiger xanaduensis SH-6]
Scores for 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   16.5   1.8     0.0046   16.5   1.8    1.1  1  Fzo_mitofusin  fzo-like conserved region


Domain annotation for each model (and alignments):
>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.8   2.6e-07    0.0046      22      55 ..      28      61 ..       8      76 .] 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.6e-07
                     Fzo_mitofusin 22 slgvlvvggvvlravgWrvialslalygllYlyE 55
                                       ++ +v ++vv r+ gW v a  l+++g++  y 
  gi|336253089|ref|YP_004596196.1| 28 VVVWVVAATVVFRTAGWPVTAYYLVVFGGVLGYS 61
                                      567789999*******************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 586.86
//
Query:       gi|336253090|ref|YP_004596197.1|  [L=405]
Description: hypothetical protein Halxa_1686 [Halopiger xanaduensis SH-6]
Scores for 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  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3246.74
//
Query:       gi|336253091|ref|YP_004596198.1|  [L=296]
Description: hypothetical protein Halxa_1687 [Halopiger xanaduensis SH-6]
Scores for 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   2.6       0.21   11.6   0.3    2.4  2  DZR          Double zinc ribbon
  ------ inclusion threshold ------
      0.064   12.7   3.1       0.92    9.0   0.0    3.1  3  zf-ribbon_3  zinc-ribbon domain
       0.55   10.1   6.4       0.32   10.9   0.6    2.7  3  zf-C3HC4_3   Zinc finger, C3HC4 type (RING finger)
        4.9    6.8  10.9        3.4    7.3   3.9    3.3  3  RecR         RecR protein
        8.8    6.3   8.3        1.6    8.7   0.7    2.5  3  Prok-RING_4  Prokaryotic RING finger family 4


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 !   11.6   0.3   5.9e-05      0.21       8      39 ..      20      71 ..      16      74 .. 0.88
   2 !    6.5   0.1    0.0023       8.3      28      48 ..     222     242 ..     198     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.9e-05
                               DZR  8 lppdarfCseCgtklkavaa....................edrCpsCgekvd 39
                                      l+ d+r+C +Cg++ + +++                     ++C+sC ++++
  gi|336253091|ref|YP_004596198.1| 20 LERDDRTCRRCGADGDDPSTlrcypvgdvplegavhesalVTVCSSCFTALQ 71
                                      67899*********987777899999*********************88766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0023
                               DZR  28 edrCpsCgekvdpearfCpeC 48 
                                        drC  C e++  e   Cp C
  gi|336253091|ref|YP_004596198.1| 222 LDRCHGCLEPLGDEVDRCPIC 242
                                       788999999999998889988 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00026      0.92      10      25 ..      18      33 ..      17      33 .. 0.87
   2 ?    0.0   0.1      0.17   6.2e+02      16      22 ..      60      66 ..      53      66 .. 0.76
   3 ?    1.9   0.1     0.045   1.6e+02       3       8 ..     237     242 ..     235     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00026
                       zf-ribbon_3 10 aplssddnvCpyCGtk 25
                                      a+l+ dd++C  CG++
  gi|336253091|ref|YP_004596198.1| 18 AVLERDDRTCRRCGAD 33
                                      4789**********85 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.17
                       zf-ribbon_3 16 dnvCpyC 22
                                      ++vC +C
  gi|336253091|ref|YP_004596198.1| 60 VTVCSSC 66
                                      5677777 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.045
                       zf-ribbon_3   3 vrCPnC 8  
                                        rCP C
  gi|336253091|ref|YP_004596198.1| 237 DRCPIC 242
                                       59**99 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 ?   -0.6   0.1      0.34   1.2e+03       2      20 ..      24      42 ..      23      45 .. 0.73
   2 ?    0.7   0.0      0.13   4.7e+02      24      33 ..      61      70 ..      55      77 .. 0.77
   3 ?   10.9   0.6   8.9e-05      0.32      26      44 ..     225     243 ..     222     248 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.34
                                      GSB-TTTSSSBS-EEETTE CS
                        zf-C3HC4_3  2 deeCviClerprnvvllpC 20
                                      d++C  C     +   l+C
  gi|336253091|ref|YP_004596198.1| 24 DRTCRRCGADGDDPSTLRC 42
                                      6788888887777777776 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.13
                                      EE-HHHHHHH CS
                        zf-C3HC4_3 24 vlCeeCaekl 33
                                       +C++C++ l
  gi|336253091|ref|YP_004596198.1| 61 TVCSSCFTAL 70
                                      5788888877 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 8.9e-05
                                       -HHHHHHHHHTT-B-TTT- CS
                        zf-C3HC4_3  26 CeeCaekllkrkkkCpiCr 44 
                                       C+ C+e l ++ ++CpiC 
  gi|336253091|ref|YP_004596198.1| 225 CHGCLEPLGDEVDRCPICD 243
                                       ********99********6 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.099   3.5e+02      17      23 ..      25      31 ..      21      36 .. 0.86
   2 ?    0.3   0.0      0.15   5.3e+02      16      24 ..      60      68 ..      57      71 .. 0.85
   3 ?    7.3   3.9   0.00094       3.4      26      40 .]     234     248 ..     219     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.099
                                      EE-TTT- CS
                              RecR 17 rhCsrCg 23
                                      r C+rCg
  gi|336253091|ref|YP_004596198.1| 25 RTCRRCG 31
                                      6899998 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.15
                                      -EE-TTT-- CS
                              RecR 16 vrhCsrCgn 24
                                      v+ Cs C++
  gi|336253091|ref|YP_004596198.1| 60 VTVCSSCFT 68
                                      678****96 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00094
                                       ESSSS-CCCCSTTSE CS
                              RecR  26 teedlCaICsdprRD 40 
                                       +e d C+IC  +rRD
  gi|336253091|ref|YP_004596198.1| 234 DEVDRCPICDLERRD 248
                                       6889**********9 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 ?   -3.8   0.4       3.6   1.3e+04      21      25 ..      27      31 ..      27      42 .. 0.53
   2 ?    2.2   0.0     0.045   1.6e+02      20      29 ..      62      71 ..      56      76 .. 0.86
   3 ?    8.7   0.7   0.00043       1.6      21      38 ..     225     244 ..     222     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.6
                       Prok-RING_4 21 CkeCf 25
                                      C++C 
  gi|336253091|ref|YP_004596198.1| 27 CRRCG 31
                                      66663 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.045
                       Prok-RING_4 20 vCkeCfdskd 29
                                      vC +Cf + +
  gi|336253091|ref|YP_004596198.1| 62 VCSSCFTALQ 71
                                      9*****9876 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00043
                       Prok-RING_4  21 CkeCfdsk..dlssCPlCqr 38 
                                       C+ C++    +  +CP+C  
  gi|336253091|ref|YP_004596198.1| 225 CHGCLEPLgdEVDRCPICDL 244
                                       9****99865666*****74 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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 0.20s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2488.64
//
Query:       gi|336253092|ref|YP_004596199.1|  [L=256]
Description: hypothetical protein Halxa_1688 [Halopiger xanaduensis SH-6]
Scores for 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   65.9   0.1    3.4e-18   65.2   0.1    1.4  1  DUF1508   Domain of unknown function (DUF1508)


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 !   65.2   0.1   1.9e-22   3.4e-18       1      48 []     202     250 ..     202     250 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 1.9e-22
                                       ETTTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCEEE CS
                           DUF1508   1 DknGefrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaeveD 48 
                                       D+++e+r+rL+++Ng+++a+ +egY+++++a+++ +sV++ ap+a v D
  gi|336253092|ref|YP_004596199.1| 202 DRADEWRWRLVHWNGNIVADsGEGYTTRSNAKRAARSVMRTAPTARVTD 250
                                       789******************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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 0.21s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 2228.96
//
Query:       gi|336253093|ref|YP_004596200.1|  [L=246]
Description: hypothetical protein Halxa_1689 [Halopiger xanaduensis SH-6]
Scores for 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-23   82.0   0.0    4.6e-23   81.6   0.0    1.2  1  DUF547    Protein of unknown function, DUF547


Domain annotation for each model (and alignments):
>> DUF547  Protein of unknown function, DUF547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.0   2.6e-27   4.6e-23       5     123 .]      45     172 ..      41     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 2.6e-27
                            DUF547   5 sreeklAfwiNlYNalvlhaileyg...pesnvkrlslfkkaayniggqslslddIehgiLrkn.....lsrlkkka 73 
                                       +re klAfw+N YNa+    + e       ++  r++++ + ++ ++g  lsl+dIehg+Lr++     l       
  gi|336253093|ref|YP_004596200.1|  45 TREGKLAFWLNCYNAYAQLRLEEDPgllEGGRLARWKFVARDRIPVAGAWLSLNDIEHGLLRSSkhpwgL------G 115
                                       5899***********9877776443676666799*****************************9666553......1 PP

                            DUF547  74 .......rderrkyaleqpdprihfaLvcgsascpplriytaerleeqLeaaaeeFl 123
                                              ++ +r++ le+ dprihfaL+ g    pp+ +y++++++++L+   e Fl
  gi|336253093|ref|YP_004596200.1| 116 ylprpfpSSFERRFRLEECDPRIHFALTRGIENRPPITVYSPADVDDDLDVDVEWFL 172
                                       44445588999***************************************9998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1785.72
//
Query:       gi|336253094|ref|YP_004596201.1|  [L=341]
Description: hypothetical protein Halxa_1690 [Halopiger xanaduensis SH-6]
Scores for 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-48  165.0  28.1    2.9e-48  164.7  28.1    1.0  1  AI-2E_transport  AI-2E family transporter
  ------ inclusion threshold ------
        1.3    9.1   0.0        1.3    9.1   0.0    3.1  3  CrgA             Cell division protein CrgA
        9.1    5.8  12.6        3.4    7.3   0.8    2.5  2  SUR7             SUR7/PalI family


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.7  28.1   4.8e-52   2.9e-48       5     325 ..      10     324 ..       6     326 .. 0.94

  Alignments for each domain:
  == domain 1  score: 164.7 bits;  conditional E-value: 4.8e-52
                   AI-2E_transport   5 lvllllllalypfiselllplliAlvlayllnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvplliaqltq 81 
                                        + ll++++ ++++ +++  +l+A++la++l p  ++L ++ ++ +++++++++++++ ++l+++l++ l+++ ++ 
  gi|336253094|ref|YP_004596201.1|  10 ALVLLFAYLSWQLVTPFVQYVLAAILLAFVLYPGQRRL-ENHIPSSISAFILVVFAVLGFILPFVLVIALVAEDAAM 85 
                                       333444444444444999999*****************.************************************** PP

                   AI-2E_transport  82 lvkslpayidslqnilnelpslleelenliqalkqslskilsnilssilnsllsllasllglilslvlvllllffll 158
                                       +++sl  ++ +l++i +e++ ++        ++  +++ ++++i    l+  ++ ++ l+  ++ l l l+ll++ll
  gi|336253094|ref|YP_004596201.1|  86 MLESLDPSTFQLSDIEEEIQAETGMS----VNISETIAGSAEQIGTVALERTTEWFGVLTHALIGLGLALFLLYYLL 158
                                       ******99999999999999888888....5999******************************************* PP

                   AI-2E_transport 159 ldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvglanliP 235
                                       +dg+ l+  i+++ p +  +    +  el+++++++l g+vl+a+i+g++++igl + g+p a ++++++++++liP
  gi|336253094|ref|YP_004596201.1| 159 KDGDDLLGWIRSTTPLP-DDVQHDLYDELAEVMWAVLAGHVLIAIIQGFIAGIGLFATGIPNAAFWTFVMIILALIP 234
                                       ****************9.77777888999999********************************************* PP

                   AI-2E_transport 236 yiGavivlipiaiialltggikevlivlivvllvqliegnilePklmgkrlglhplvillsllaggklfGlvGlila 312
                                       +iG+++v+ p++ ++l+tg +  +++++++ ++++ + + +l+P+++ + ++l+p++i+l +l+g+  fG++Gl+++
  gi|336253094|ref|YP_004596201.1| 235 LIGSFLVWGPAVGYLLVTGEPVLAVVLFLYSTVIVGVSDDYLRPIVVDRYAQLNPAIIILGVLGGIYAFGVMGLFFG 311
                                       ***************************************************************************** PP

                   AI-2E_transport 313 vpltavikailea 325
                                       ++l++++ a+l++
  gi|336253094|ref|YP_004596201.1| 312 PVLLGALLATLDV 324
                                       *********9986 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.15   9.1e+02      32      59 ..      54      83 ..      22      94 .. 0.64
   2 ?    9.1   0.0   0.00022       1.3      27      57 ..     130     160 ..     111     172 .. 0.83
   3 ?   -1.3   0.5       0.4   2.4e+03      29      46 ..     218     235 ..     206     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.15
                              CrgA 32 rwyvpvmlglmllGll..wlvvyYlageei 59
                                      ++ + +++ + +lG +  +++v  l +e+ 
  gi|336253094|ref|YP_004596201.1| 54 SISAFILVVFAVLGFIlpFVLVIALVAEDA 83
                                      445556666666765422344444433333 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00022
                              CrgA  27 akpsprwyvpvmlglmllGllwlvvyYlage 57 
                                        +++ +w+ ++  +l+ lGl+  ++yYl ++
  gi|336253094|ref|YP_004596201.1| 130 LERTTEWFGVLTHALIGLGLALFLLYYLLKD 160
                                       567899**********************876 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.4
                              CrgA  29 psprwyvpvmlglmllGl 46 
                                       p+  ++  vm+ l l+ l
  gi|336253094|ref|YP_004596201.1| 218 PNAAFWTFVMIILALIPL 235
                                       566778888888888766 PP

>> SUR7  SUR7/PalI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   5.3      0.01        63     114     174 ..      20      80 ..       6      98 .. 0.68
   2 ?    7.3   0.8   0.00056       3.4      96     165 ..     170     241 ..      95     310 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.01
                              SUR7 114 alfilhiialvlsfislvvgllaic.vspdnsrllsflnlllsvlsflatllaalldtllfv 174
                                       + +++ ++  vl +i+l + l     +  ++ +  s+ +++l v+++l  +l ++l+++l++
  gi|336253094|ref|YP_004596201.1|  20 WQLVTPFVQYVLAAILLAFVLYPGQrRLENHIP-SSISAFILVVFAVLGFILPFVLVIALVA 80 
                                       444444444444444444433333124556666.9***********************9987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00056
                              SUR7  96 d...lPsnlrktlsklnnltkalfilhiialvlsfislvv...gllai.cvspdnsrllsflnlllsvlsflatlla 165
                                           lP++++++l     l +++++++   + + +i  ++   gl+a  +    n  + +f++++l+++ ++ ++l 
  gi|336253094|ref|YP_004596201.1| 170 SttpLPDDVQHDLYD--ELAEVMWAVLAGHVLIAIIQGFIagiGLFATgI---PNAAFWTFVMIILALIPLIGSFLV 241
                                       044599999999976..777777777655555555544441224555433...555557777777776666555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); 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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2404.83
//
Query:       gi|336253095|ref|YP_004596202.1|  [L=352]
Description: hypothetical protein Halxa_1691 [Halopiger xanaduensis SH-6]
Scores for 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   22.2   3.2      0.003   18.0   0.2    2.6  2  DUF4350         Domain of unknown function (DUF4350)
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.028   13.9   0.0    1.6  1  ABC_transp_aux  ABC-type uncharacterized transport system


Domain annotation for each model (and alignments):
>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   3.3e-07     0.003      29      69 .]     116     159 ..      89     159 .. 0.85
   2 !    4.3   0.3    0.0061        54      28      65 ..     233     274 ..     214     277 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.3e-07
                           DUF4350  29 daleg...edgtllvvapdlrlteeelaallewvarGntlvlaa 69 
                                        al++     + l+vv p+ r+t++e++ + e+  +G+++++aa
  gi|336253095|ref|YP_004596202.1| 116 VALAEtlqDADALIVVEPGTRYTSAEADVVSEFEGAGGRVMVAA 159
                                       455444446779******************************96 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0061
                           DUF4350  28 fdaleg...edgtllvvapdlrlteeela.allewvarGntl 65 
                                       fda ++   e++tll ++ +   +e+++a +    +++Gnt+
  gi|336253095|ref|YP_004596202.1| 233 FDAPTPvvsEETTLLTTTATTEHSENRVAdEYGVVARSGNTV 274
                                       444444565999999999998888866662556666699988 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.1e-06     0.028     188     232 ..     120     163 ..      26     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.1e-06
                    ABC_transp_aux 188 dilpedidvlviakptkdlseeelykldqflmnGgkllvfldpva 232
                                       ++l +d d+l++++p ++++  e + +++f  +Gg+++v++ p +
  gi|336253095|ref|YP_004596202.1| 120 ETL-QDADALIVVEPGTRYTSAEADVVSEFEGAGGRVMVAAGPET 163
                                       445.799********************************998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2545.62
//
Query:       gi|336253096|ref|YP_004596203.1|  [L=337]
Description: peptidase S49 [Halopiger xanaduensis SH-6]
Scores for complete 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   64.3   1.0      3e-10   40.2   0.4    2.3  2  Peptidase_S49  Peptidase family S49
    1.8e-07   31.2   0.4      1e-05   25.5   0.4    2.3  1  CLP_protease   Clp protease
  ------ inclusion threshold ------
      0.038   13.3   0.1          6    6.1   0.0    2.4  2  ECH_1          Enoyl-CoA hydratase/isomerase
      0.052   13.8   0.0       0.11   12.8   0.0    1.5  1  OKR_DC_1_N     Orn/Lys/Arg decarboxylase, N-terminal domain
       0.14   11.7   0.2       0.23   10.9   0.2    1.3  1  DUF2884        Protein of unknown function (DUF2884)


Domain annotation for each model (and alignments):
>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.4   8.5e-14     3e-10       4      49 ..     106     151 ..     103     157 .. 0.92
   2 !   22.5   0.0   2.4e-08   8.8e-05      87     153 ..     173     240 ..     164     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 8.5e-14
                                       HTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEEEEE CS
                     Peptidase_S49   4 kakkPvvasaenvaaSggYylasaadkivanpstivgsiGvitqll 49 
                                       ++++Pvva ++++ aSggYy+ + +d+i+++ps+ vgsiGv +  +
  gi|336253096|ref|YP_004596203.1| 106 AEEMPVVANVQSTGASGGYYMIAPSDEIYVSPSSTVGSIGVRATYT 151
                                       6899*************************************98766 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.4e-08
                                       HHHHHHHHHHHHHHHHHHHHHTS-HHHH.HCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHCHC CS
                     Peptidase_S49  87 ilqrlldetyqqFvqtVaknRnlsveqv.dkiAegrvltgqqAlklgLvdelgtvddavaeleelakv 153
                                        ++r ++++ q F+ +V ++R+ + e    ++  ++ +tg + +++gL+de+g  d a+ +++e a++
  gi|336253096|ref|YP_004596203.1| 173 EIKRQVEKMKQTFIGSVMEHRGDDLELSeTELSYAKTYTGMESVENGLADEIGDRDVAIGSAAERAGL 240
                                       57899****************95554331467888****************************99887 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.4   2.8e-09     1e-05      18     181 ..      50     227 ..      47     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.8e-09
                                       EEEEES-BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHS..SS-EEEEEEEEEETHHHHH CS
                      CLP_protease  18 iiflgseiddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyi..kpdvsticlGlaaSmgsll 92 
                                       +i + ++i+++va+ ++  L  + ++++++ ++l ++spGG vta+ ++y ++     + +v+  +  ++aS g  +
  gi|336253096|ref|YP_004596203.1|  50 VIEMDRSITESVADGVTDDLREARENESIDAVVLQVDSPGGGVTASESLYLAVDRTaeEMPVVANVQSTGASGGYYM 126
                                       6788999*****************************************99888766334444444556666666555 PP

                                       HH............TS-TTGEEE...ETTEEEEES-TEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHH CS
                      CLP_protease  93 la............agekgkRfa...lpnarimihqPlggaqgqasdieieaeellkikerlneilakhtgqsleki 154
                                       +a             g+ g R+    +p ++ mi      ++ +  +i+++   ++k+k++ +  + +h g +le  
  gi|336253096|ref|YP_004596203.1| 127 IApsdeiyvspsstVGSIGVRATytdMPMSEGMIATGPDKVGSNEAEIKRQ---VEKMKQTFIGSVMEHRGDDLELS 200
                                       43222222222222577777865444899*****99999999999999866...67899****************** PP

                                       HHHHCSTEEEEHHHHHHHTSSSEE-SS CS
                      CLP_protease 155 ekdldrdtflsaeeAveyGLideviek 181
                                       e++l+  +  + +e ve GL+de+ ++
  gi|336253096|ref|YP_004596203.1| 201 ETELSYAKTYTGMESVENGLADEIGDR 227
                                       ************************875 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0043        16       5      47 ..      47      84 ..      44      90 .. 0.87
   2 ?    6.1   0.0    0.0017         6      87     122 ..     107     142 ..      92     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0043
                                      TEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEE CS
                             ECH_1  5 gvaviklnrPeavNalsaelltEliqalekleddksvravvLt 47
                                      +vavi ++r      +++ + + +++ l ++++++s+ avvL 
  gi|336253096|ref|YP_004596203.1| 47 TVAVIEMDRS-----ITESVADGVTDDLREARENESIDAVVLQ 84
                                      7899999998.....999999999999999***********97 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0017
                                       SSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE CS
                             ECH_1  87 vpkpviaavnGaaigGGlelalacDiviaadnasfg 122
                                        ++pv+a v+  ++ GG  +    D ++++ ++  g
  gi|336253096|ref|YP_004596203.1| 107 EEMPVVANVQSTGASGGYYMIAPSDEIYVSPSSTVG 142
                                       589*******************99999998877655 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.1e-05      0.11      27      72 ..      67     117 ..      51     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                        OKR_DC_1_N  27 dDllsvieqnsriaavvlsvd......deaaelldeirernedlPvFllaet 72 
                                       dDl   +++n +i+avvl+vd       +++ l  +++++ e++Pv + +++
  gi|336253096|ref|YP_004596203.1|  67 DDL-REARENESIDAVVLQVDspgggvTASESLYLAVDRTAEEMPVVANVQS 117
                                       444.446778*****************9******************998874 PP

>> DUF2884  Protein of unknown function (DUF2884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   6.5e-05      0.23     135     198 ..     171     235 ..     156     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.5e-05
                           DUF2884 135 dkefeqeieelveesiGsilsalgsemlesegdn.leafeqrmeklgekieeeveeqakalekka 198
                                       + e+ +++e++ +++iGs++++ g+ +  se +   ++  + me++++ +  e+  ++ a+   a
  gi|336253096|ref|YP_004596203.1| 171 EAEIKRQVEKMKQTFIGSVMEHRGDDLELSETELsYAKTYTGMESVENGLADEIGDRDVAIGSAA 235
                                       67999*******************99877776645888899999999999999888887776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.54u 0.21s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2497.92
//
Query:       gi|336253097|ref|YP_004596204.1|  [L=456]
Description: FO synthase subunit 2 [Halopiger xanaduensis SH-6]
Scores for 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-17   62.2   0.6    1.7e-16   61.0   0.2    1.9  2  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 ?   -2.9   0.0      0.42   7.5e+03      29      39 ..      56      66 ..      21      82 .. 0.52
   2 !   61.0   0.2   9.7e-21   1.7e-16       2     164 ..      86     291 ..      85     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.42
                                      HHHHHHHHHHH CS
                                      xxxxxxxxxxx RF
                       Radical_SAM 29 lsveeileevk 39
                                      + +e++le ++
  gi|336253097|ref|YP_004596204.1| 56 RRKERVLEAAD 66
                                      22233333333 PP

  == domain 2  score: 61.0 bits;  conditional E-value: 9.7e-21
                                       EEESEESS--TTTSCCTT.......HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTH.HHHHHH CS
                                       xxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet.......vrregrgrslsveeileevkelkaekg.vkevilgggepllypdf.veller 69 
                                       +vt +Cn +C fC+++          ++e  g +++++e  e+vk + +e+g  +++ ++g +p +  d+ +++l+ 
  gi|336253097|ref|YP_004596204.1|  86 NVTTACNVGCLFCNFKDAahtfereTEMETAGFTKTPDESREIVKDA-VERGiYEVCSVSGLHPAFALDEeHRELLD 161
                                       6899************99*****************************.9***8888888888887764440333444 PP

                                       HHHTC.............................CCTEEEEEEECSSCHG.........HHHHHHHHHTT-SEEE.E CS
                                       xxxxx.............................xxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxx.x RF
                       Radical_SAM  70 lakla.............................vpgiritvetngtlpd.........eeklerllelgvdrvs.l 107
                                       +   +                             v+g++++  t++             ee+ +rl+++g+d+v   
  gi|336253097|ref|YP_004596204.1| 162 A---HpnpkevnykppavyetspgtyvdqisamnVDGVHVHSMTPEEAYHarrgtdwsyEEVFRRLKDAGLDTVPgT 235
                                       4...2446****************************************99********************6666505 PP

                                       EEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 108 gleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeeleell 164
                                        +e++ +e v++ ++ ++ + +++lea+e+++++g+   + +i+ ++ en++++  +l
  gi|336253097|ref|YP_004596204.1| 236 AAEILVEE-VRDVICpGKIGTDDWLEAMEAAANVGLG-MTATIMYGHVENEAHRALHL 291
                                       55666666.****************************.**************976555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3502.30
//
Query:       gi|336253098|ref|YP_004596205.1|  [L=883]
Description: methyl-accepting chemotaxis sensory transducer [Halopiger xanaduensis SH-6]
Scores for 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-40  137.6  56.1    2.5e-39  134.8  24.3    5.3  6  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
    6.5e-07   29.4   2.4    6.5e-07   29.4   2.4    3.2  2  dCache_1         Cache domain
    3.8e-06   27.0  31.2     0.0018   18.3   2.8    5.3  5  Laminin_II       Laminin Domain II
    3.6e-05   23.9  36.4      0.022   15.0   2.6    6.7  4  DUF948           Bacterial protein of unknown function (DUF94
    0.00079   19.6  10.6       0.13   12.5   0.2    3.5  3  Med30            Mediator complex subunit 30
     0.0018   18.3   4.7     0.0018   18.3   4.7    4.9  4  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
     0.0018   17.9  10.6       0.61    9.8   0.0    5.2  5  RPW8             Arabidopsis broad-spectrum mildew resistance
     0.0022   18.0  28.6       0.48   10.5   1.7    5.5  5  DUF1664          Protein of unknown function (DUF1664)
     0.0033   16.4  17.9     0.0033   16.4  17.9    2.9  3  CALCOCO1         Calcium binding and coiled-coil domain (CALC
     0.0046   16.7  27.7       0.34   10.6   0.2    4.6  4  Laminin_I        Laminin Domain I
     0.0082   16.5   0.8     0.0082   16.5   0.8    6.4  4  HAMP             HAMP domain
     0.0096   16.4  24.8      0.041   14.3   2.1    5.9  4  NPV_P10          Nucleopolyhedrovirus P10 protein
  ------ inclusion threshold ------
       0.01   14.7  33.3       0.12   11.3   7.6    3.4  3  Spc7             Spc7 kinetochore protein
      0.022   15.4  16.7        3.3    8.4   0.1    5.4  6  YabA             Initiation control protein YabA
      0.026   14.4  14.4        1.2    9.0   0.5    5.2  7  Sec34            Sec34-like family
      0.038   12.7  30.5       0.15   10.7  11.3    2.3  2  AAA_13           AAA domain
      0.047   13.3   8.5       0.22   11.1   0.6    3.2  3  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
      0.059   13.8   0.5      0.059   13.8   0.5    4.9  5  TSNAXIP1_N       Translin-associated factor X-interacting N-t
      0.083   12.9   2.0       0.16   12.0   2.0    1.5  1  Antimicrobial24  Frog antimicrobial peptide
      0.087   12.8   0.0      0.087   12.8   0.0    4.1  2  Rootletin        Ciliary rootlet component, centrosome cohesi
       0.12   11.3  16.3        1.1    8.2   1.7    3.5  3  Ran-binding      RanGTP-binding protein
       0.12   12.1   2.4       0.17   11.6   0.2    2.4  1  DUF2913          Protein of unknown function (DUF2913)
       0.16   11.8   7.7         24    4.8   0.0    5.6  6  DASH_Duo1        DASH complex subunit Duo1
       0.17   11.3  28.9        1.2    8.5   2.7    4.3  5  HMMR_N           Hyaluronan mediated motility receptor N-term
       0.23   11.8  32.9      0.049   13.9   2.0    6.7  7  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.43   10.7   0.1       0.43   10.7   0.1    3.5  2  bZIP_1           bZIP transcription factor
       0.45   10.9  27.9      0.028   14.8   3.5    4.0  3  DUF4200          Domain of unknown function (DUF4200)
       0.46   11.2  30.1        2.6    8.8   1.6    5.6  5  DUF2203          Uncharacterized conserved protein (DUF2203)
       0.65   10.1  40.8       0.75    9.9   3.6    4.8  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.86    9.4   4.7         28    4.6   0.4    4.1  3  DASH_Dam1        DASH complex subunit Dam1
        1.3    9.0  18.6        2.2    8.3   0.4    5.0  5  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
        1.4    7.9  23.7        3.7    6.5  10.4    3.1  2  AIP3             Actin interacting protein 3
        1.6    8.1  20.1       0.51    9.7   2.2    3.6  4  Mce4_CUP1        Cholesterol uptake porter CUP1 of Mce4, puta
        1.7    7.8  15.0       0.41    9.8   0.3    4.1  5  TMPIT            TMPIT-like protein
        1.9    9.0  23.8       0.59   10.6   1.4    5.9  7  Spectrin         Spectrin repeat
        1.9    8.6  31.2       0.18   11.9   0.8    4.4  4  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
        2.1    8.5  16.4        4.8    7.4   1.4    4.8  5  Fib_alpha        Fibrinogen alpha/beta chain family
        3.1    6.4  14.8        3.7    6.1   1.4    3.7  3  Dor1             Dor1-like family
        3.1    8.6   6.2        6.6    7.5   0.0    4.2  3  Occludin_ELL     Occludin homology domain
        3.3    7.8  20.6        1.9    8.6   1.4    4.4  3  Mod_r            Modifier of rudimentary (Mod(r)) protein
        4.7    7.5  30.6        1.7    8.9   1.4    5.5  6  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        4.8    6.8  22.5        2.5    7.7   1.7    4.9  5  Syntaxin         Syntaxin
        6.2    6.3  17.5         14    5.2   0.1    5.1  5  Fzo_mitofusin    fzo-like conserved region
        6.5    5.5  30.6        1.2    7.9   3.8    3.4  3  DUF812           Protein of unknown function (DUF812)


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       6.6   2.7e+03     122     157 ..      97     132 ..      58     140 .. 0.65
   2 ?    0.3   0.1       1.3   5.3e+02      98     147 ..     403     452 ..     395     463 .. 0.76
   3 !    9.0   3.1    0.0028       1.1     113     167 ..     478     536 ..     433     539 .. 0.67
   4 !   12.9   6.4   0.00017     0.071      97     165 ..     494     569 ..     486     578 .. 0.49
   5 !  134.8  24.3   6.3e-42   2.5e-39       8     171 ..     583     750 ..     573     751 .. 0.90
   6 ?    6.1   5.0     0.021       8.8     110     166 ..     738     794 ..     736     799 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.6
                                       HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 122 lveetgealkeiveavaevadlvqeiaaaseeqsas 157
                                       + +e +ea+++ v av+ v+   +ei+ +se+ + +
  gi|336253098|ref|YP_004596205.1|  97 TLAEEQEAMSSEVYAVHYVDLWTEEITHSSEDGAVG 132
                                       223346778888888888888888888888876654 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.3
                                       ............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  98 iqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqei 147
                                       + +e ++ ++ le ++  +e + e+++e++++ ++++e+ ++ a++  ++
  gi|336253098|ref|YP_004596205.1| 403 MRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEFGDV 452
                                       56677777888888888888888888888888888888888777766665 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHHHHHCCHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 113 rqrveegselveetgealkeiveavaev....adlvqeiaaaseeqsasieevnqavee 167
                                        +  +  +e  e t  ++++++e v++v    +  v+ei +as e s+s+ee+++a + 
  gi|336253098|ref|YP_004596205.1| 478 ATAFNGMLEDLEATIVDIQDLAEDVDRVsadvTGRVEEIERASGEVSESAEEIATATAD 536
                                       44444455666777777777777776651111557899999999999999999999765 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 0.00017
                                       ................HHHHHHHHHHHHHHHHHCCHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  97 eiqkeindsves...leetrqrveegselveetgeal....keiveavaevadlvqeiaaaseeqsasieevnqav 165
                                       +iq   +d+ ++   ++  ++++e +s +v+e++e++    ++ +++  ev  ++++++a++ee+++++++v++  
  gi|336253098|ref|YP_004596205.1| 494 DIQDLAEDVDRVsadVTGRVEEIERASGEVSESAEEIatatADQSDRFREVYGEMNDLSATVEEIASTADDVASVS 569
                                       4444333333330003333333344444443333333000033455666777777777777777777777776554 PP

  == domain 5  score: 134.8 bits;  conditional E-value: 6.3e-42
                                       HHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHH CS
                         MCPsignal   8 seeAeeg....gkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkL 80 
                                       ++e +++    +   +++ +q+ +++++ ++i +i++ id+ia+QTNlLALNA+iEAA AGe+G+GFaVVA+EV++L
  gi|336253098|ref|YP_004596205.1| 583 TGEIRTEmdrlEDRADEITEQVAQLDEEMDQIREIVDLIDDIAEQTNLLALNASIEAAGAGEEGDGFAVVANEVKSL 659
                                       3333333333366677888888888888************************************************* PP

                                       HHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  81 Aersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsas 157
                                       Ae++ +a++e+++li  +++ + ++v+ ++  r++v+eg+  v++  ea+  i+e+v+e ++ vq i+ a++eq+++
  gi|336253098|ref|YP_004596205.1| 660 AEETGEATQEVDELIGSVEESVAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEEANAGVQSINDATDEQARA 736
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHH CS
                         MCPsignal 158 ieevnqaveevakv 171
                                       +e v + v+e +++
  gi|336253098|ref|YP_004596205.1| 737 SERVVTMVDEATEI 750
                                       ******99998876 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 110 eetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqave 166
                                       e +++ v+e++e+ eet+++ +++++a++e +++v++++a ++ +++ +++  ++++
  gi|336253098|ref|YP_004596205.1| 738 ERVVTMVDEATEISEETKDETENVAAAAEEQTATVSDVSAGTQSLTEMADDLRTSLD 794
                                       567888999999999999999999999999999999999999999988888877765 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   2.4   1.6e-09   6.5e-07       6     248 ..      50     282 ..      47     283 .. 0.76
   2 ?   -2.3   0.7       7.3     3e+03      17      17 ..     444     444 ..     387     544 .. 0.54

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.6e-09
                          dCache_1   6 qaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallks.........ilksnpd 73 
                                       +++ +++  a + an++ d++ds+e ++++l+s   l d+          s+++++++l +         ++ ++ d
  gi|336253098|ref|YP_004596205.1|  50 NVQAEMELNAVGEANDFADWIDSQEESVRMLSSYGVLTDG----------SDAEIESTLAEeqeamssevYAVHYVD 116
                                       68899**************************998877664..........444455555442221111222222333 PP

                          dCache_1  74 i..sgvylvdadGqv.......iassdpssppnleg....tddpadrdw.ykealaggggkpvisdpyvdqtggkpv 136
                                       +  ++++  ++dG v                           d++ +++ y+ a+++    +v+sd+y   + g+  
  gi|336253098|ref|YP_004596205.1| 117 LwtEEITHSSEDGAVgtniqdlN------------LtlhvRTDDRISEFdYRGAMNDD---VVYSDVYE-RD-GEQL 176
                                       34457777778888833322220............23455444445555699999988...99*****4.36.9999 PP

                          dCache_1 137 itiavpiyddsgkfiGvlaadldldnlqd.llsniklgetgyvfivd.sdGniiahpdkdllgknlrdelkaqeale 211
                                       +++  ++  ++g    ++++ +++++  d + + i  ++ +++ +vd ++G + ++ +++ ++   r+ +++     
  gi|336253098|ref|YP_004596205.1| 177 VAFFGKVAETNGD--TAVMIEISASEMADgFADPI--DG-QHTEVVDtGKGVVEFSGNETAIQAPYREGAES--YVV 246
                                       99999****99*9..**************555555..44.79*****99*********99999999988886..899 PP

                          dCache_1 212 kalakiesgvssvklngeeylvayapiptglgWylvv 248
                                       +a+a+ e  +  v++++ +  vaya i+  ++W lv+
  gi|336253098|ref|YP_004596205.1| 247 DAVANQEHASGIVEYDDTDEVVAYADIER-TDWALVS 282
                                       999999999999*****9999******95.9****98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.3
                          dCache_1  17 q 17 
                                       +
  gi|336253098|ref|YP_004596205.1| 444 R 444
                                       2 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.69   2.8e+02      25      69 ..     399     443 ..     390     456 .. 0.63
   2 ?    4.9   0.2     0.062        25       9      63 ..     471     525 ..     467     533 .. 0.81
   3 !   18.3   2.8   4.3e-06    0.0018       9      96 ..     538     625 ..     525     630 .. 0.71
   4 !   13.6   2.7   0.00013     0.053       1      71 [.     656     726 ..     656     737 .. 0.92
   5 ?    3.1   4.8      0.21        88       3      75 ..     721     793 ..     719     804 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.69
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
                        Laminin_II  25 nlentkeklseinrsveetnekvkdankairdArrsvkkLeklap 69 
                                        le ++ +l++  +++e  +++++++++  ++Arr+   L + ++
  gi|336253098|ref|YP_004596205.1| 399 SLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLE 443
                                       455566666666666666666666666666666666655555444 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.062
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkk 63 
                                       ne ++e+    +++ ++le t  +++ ++++v+++ ++v    + i+ A+ +v++
  gi|336253098|ref|YP_004596205.1| 471 NEALAEIATAFNGMLEDLEATIVDIQDLAEDVDRVSADVTGRVEEIERASGEVSE 525
                                       6677788888889999999999999999999999999999888888888888875 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 4.3e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH. CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeas 85 
                                       ++   ev   +++ls+ +e++ + +  +++  e   + ++da++a+ + r+++  Le  a+++ +++ +l++  ++ 
  gi|336253098|ref|YP_004596205.1| 538 SDRFREVYGEMNDLSATVEEIASTADDVASVSETAADRADDASEATGEIRTEMDRLEDRADEITEQVAQLDEEMDQI 614
                                       44556777778888888888888888888776666677778888888888888888888888888877777777775 PP

                                       ..HHHHHHHHH CS
                        Laminin_II  86 sslsdniseik 96 
                                         + d i+ i 
  gi|336253098|ref|YP_004596205.1| 615 REIVDLIDDIA 625
                                       55666666555 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 0.00013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II   1 skelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       +k+la+e  e ++ev e +  +++ + +t +++ +++++v+e +++v+d  +ai+   ++v + +  ++ +
  gi|336253098|ref|YP_004596205.1| 656 VKSLAEETGEATQEVDELIGSVEESVAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEEANAGVQSI 726
                                       5999***************************************************9999999887766665 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.21
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGH CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldkl 75 
                                       + ++++n+ + e  +  + + + +++  e  +e +++ e++ + +++ + ++ d++   + L++ a++L   l
  gi|336253098|ref|YP_004596205.1| 721 AGVQSINDATDEQARASERVVTMVDEATEISEETKDETENVAAAAEEQTATVSDVSAGTQSLTEMADDLRTSL 793
                                       5677777777777777888888888888888888888888888888888888888888888888888886555 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 ?    1.7   0.1      0.75   3.1e+02      28      78 ..     404     457 ..     396     467 .. 0.80
   2 ?    2.7  10.4      0.38   1.5e+02      45      85 ..     491     531 ..     462     640 .. 0.61
   3 !   15.0   2.6   5.4e-05     0.022      24      87 ..     663     726 ..     648     728 .. 0.53
   4 ?    2.9   5.1      0.32   1.3e+02      34      75 ..     739     784 ..     721     797 .. 0.41

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.75
                            DUF948  28 ldeaaatieele...kqvdpilkevedllakvnelledvneklekvdplteava 78 
                                        +e+++ i++le    ++++  +e++++ +++++l+e +++k ++   +++ +a
  gi|336253098|ref|YP_004596205.1| 404 RRELESYIDDLEaskADAEASKEEAAEARREAERLAERLERKAAEFGDVMNDAA 457
                                       45566666666655589999999******************9999999887765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.38
                            DUF948  45 ilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                       ++ +++dl + v ++ +dv++++e++++   +v + +e ++
  gi|336253098|ref|YP_004596205.1| 491 TIVDIQDLAEDVDRVSADVTGRVEEIERASGEVSESAEEIA 531
                                       44444444444444444444444444433333333333332 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 5.4e-05
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                        ++  +e+ + i ++e+ v +++ e++++ ++v e ++ v + +e++d++ e+v+++ + v+++
  gi|336253098|ref|YP_004596205.1| 663 TGEATQEVDELIGSVEESVAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEEANAGVQSI 726
                                       2444455555555555555666666666666666555555666666666666666666666555 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.32
                            DUF948  34 tieelekqvdpilkevedllakvne....lledvneklekvdplte 75 
                                       ++ ++ +++++i++e++d +++v +     ++ v++ ++  ++lte
  gi|336253098|ref|YP_004596205.1| 739 RVVTMVDEATEISEETKDETENVAAaaeeQTATVSDVSAGTQSLTE 784
                                       3333333333333333333333333000033333333333333333 PP

>> Med30  Mediator complex subunit 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.089        36      86     132 ..     407     454 ..     395     457 .. 0.83
   2 !   12.5   0.2   0.00031      0.13      46     138 ..     523     618 ..     491     628 .. 0.60
   3 ?    7.3   1.1     0.013       5.2      50     136 ..     695     791 ..     654     795 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.089
                             Med30  86 Lipyvdee.kskreerkkseevkqlkeerkelleklkeknkqLkeimd 132
                                       L  y d+   sk++++ ++ee+ ++  e + l e+l+ k +++ ++m+
  gi|336253098|ref|YP_004596205.1| 407 LESYIDDLeASKADAEASKEEAAEARREAERLAERLERKAAEFGDVMN 454
                                       5557777757888888889999********************999997 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00031
                             Med30  46 rkkklqeqlrqlkvlfkkLrliYekckencqgleevp.iesLipyvdeekskreerk.k.....seevkqlkeerke 115
                                        ++  +e   +   +  + r +Y ++++ ++ +ee+    + +  v+e+ ++r++   +     + e+  l+++ +e
  gi|336253098|ref|YP_004596205.1| 523 VSESAEEIATATADQSDRFREVYGEMNDLSATVEEIAsTADDVASVSETAADRADDAsEatgeiRTEMDRLEDRADE 599
                                       55555666666667778999999999999999997776444555555553444433302111113344455555555 PP

                             Med30 116 lleklkeknkqLkeimdqlrkll 138
                                       ++e++++ ++++ +i    r+++
  gi|336253098|ref|YP_004596205.1| 600 ITEQVAQLDEEMDQI----REIV 618
                                       555555555555555....4444 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.013
                             Med30  50 lqeqlrqlkvlfkkLrliYekckencqgle.........evpiesLipyvdee.kskreerkkseevkqlkeerkel 116
                                       ++e +  +    +++  i e+++e+ +g++            +e  + +vde  +   e ++++e+v  + ee+   
  gi|336253098|ref|YP_004596205.1| 695 VDEGTAVVDDGIEAIDAIAEQVEEANAGVQsindatdeqARASERVVTMVDEAtEISEETKDETENVAAAAEEQTAT 771
                                       44444444455555555555555555544433333332222378999999999677788888899999999999999 PP

                             Med30 117 leklkeknkqLkeimdqlrk 136
                                       +  +++ ++ L e+ d lr 
  gi|336253098|ref|YP_004596205.1| 772 VSDVSAGTQSLTEMADDLRT 791
                                       ******************97 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 !   18.3   4.7   4.4e-06    0.0018      22     120 ..     396     495 ..     390     504 .. 0.77
   2 ?    2.4   5.8      0.37   1.5e+02      17     122 ..     504     616 ..     495     620 .. 0.65
   3 ?   -0.8   1.5       3.4   1.4e+03      23      93 ..     653     720 ..     649     733 .. 0.63
   4 ?    6.4   1.9     0.021       8.6      34      79 ..     752     797 ..     728     806 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.4e-06
                    CENP-F_leu_zip  22 LkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsek..eeLekelqkkqerv 96 
                                       L d  e + rele    ++e+ + +aE sk+e+ + + e e+lae+l++  +++ ++ ++    + ++ l +  +  
  gi|336253098|ref|YP_004596205.1| 396 LGDSLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEFGDVMNDAaaGDFTRRLDEDVDN- 471
                                       88999*********************************************99999988553114566666554443. PP

                    CENP-F_leu_zip  97 seLeslnsslenlleekEqekvqm 120
                                       + L ++   ++ +le++E+  v +
  gi|336253098|ref|YP_004596205.1| 472 EALAEIATAFNGMLEDLEATIVDI 495
                                       555556666666666666555544 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.37
                    CENP-F_leu_zip  17 rkadsLkdkvenLerelemseenqekvileaEtskaevet.......lkeeieelaeelreleldLvalrsekeeLe 86 
                                       r ++ + ++ve++er   ++ e+ e++ +   ++     +       l + +ee+a++  +  +  ++     ++  
  gi|336253098|ref|YP_004596205.1| 504 RVSADVTGRVEEIERASGEVSESAEEIATATADQSDRFREvygemndLSATVEEIASTADDVASVSETAADRADDAS 580
                                       55677788888888887776666666665554444433331112222666666666666666555555556777777 PP

                    CENP-F_leu_zip  87 kelqkkqervseLeslnsslenlleekEqekvqmke 122
                                       +   + + +++ Le +  ++++++ ++ +e+ q++e
  gi|336253098|ref|YP_004596205.1| 581 EATGEIRTEMDRLEDRADEITEQVAQLDEEMDQIRE 616
                                       778888888888888888888888888888777766 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3.4
                    CENP-F_leu_zip  23 kdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkq 93 
                                        + v++L  e  ++ ++ +++i  +E+s ae     +ei++++e+  e ++ +++  +  + +++++++ +
  gi|336253098|ref|YP_004596205.1| 653 ANEVKSLAEETGEATQEVDELIGSVEESVAET---VAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEEAN 720
                                       56677777777777777777777777765543...456666666666655555555555555555555555 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.021
                    CENP-F_leu_zip  34 emseenqekvileaEtskaevetlkeeieelaeelreleldLvalr 79 
                                       e+ + + e+v   aE++ a+v+ + +  + l+e   +l++ L+a+ 
  gi|336253098|ref|YP_004596205.1| 752 EETKDETENVAAAAEEQTATVSDVSAGTQSLTEMADDLRTSLDAFD 797
                                       4445677999*****************************9999875 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       2.4   9.7e+02      35      74 ..     405     444 ..     398     448 .. 0.83
   2 !    9.8   0.0    0.0015      0.61      26      69 ..     477     520 ..     472     530 .. 0.86
   3 ?    4.3   0.0     0.076        31      14      63 ..     528     578 ..     525     592 .. 0.84
   4 ?    2.2   0.4      0.32   1.3e+02      49      80 ..     588     619 ..     581     632 .. 0.66
   5 ?    4.1   0.1     0.087        35      14      60 ..     679     725 ..     650     755 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.4
                              RPW8  35 krLestleritPvvkeieklnkeldrpreeieeLkklLek 74 
                                       ++Les + +++ + ++ e  ++e  + r e e+L ++Le+
  gi|336253098|ref|YP_004596205.1| 405 RELESYIDDLEASKADAEASKEEAAEARREAERLAERLER 444
                                       6799999999999999999999997777799***999986 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                              RPW8  26 ksldfksilkrLestleritPvvkeieklnkeldrpreeieeLk 69 
                                        ++ f+ +l++Le+t+ +i+ + ++++++++++  + eeie+  
  gi|336253098|ref|YP_004596205.1| 477 IATAFNGMLEDLEATIVDIQDLAEDVDRVSADVTGRVEEIERAS 520
                                       56789999*************************99999999765 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.076
                              RPW8  14 gellkaileakkksldfksilkrLestleritPvvkeieklnkel.drpre 63 
                                       +e++ a  +++++  ++   +++L +t+e+i+   +++ ++++   dr ++
  gi|336253098|ref|YP_004596205.1| 528 EEIATATADQSDRFREVYGEMNDLSATVEEIASTADDVASVSETAaDRADD 578
                                       56777888888888999999**********************999787764 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.32
                              RPW8  49 keieklnkeldrpreeieeLkklLekaekLVe 80 
                                       +e+++l+++ d+ +e++ +L +++++  ++V 
  gi|336253098|ref|YP_004596205.1| 588 TEMDRLEDRADEITEQVAQLDEEMDQIREIVD 619
                                       56777777777777777777777766666654 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.087
                              RPW8  14 gellkaileakkksldfksilkrLestleritPvvkeieklnkeldr 60 
                                       +++++ + e  +   +++      ++ +e+i  + +++e+ n+ +++
  gi|336253098|ref|YP_004596205.1| 679 ESVAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEEANAGVQS 725
                                       34444444444444444444444444445555555555555544444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.18        73      52      96 ..     395     442 ..     392     458 .. 0.61
   2 !    7.6   0.5    0.0092       3.7      49     118 ..     494     563 ..     471     569 .. 0.78
   3 !    9.1   2.2    0.0032       1.3      42     104 ..     564     626 ..     559     635 .. 0.58
   4 !   10.5   1.7    0.0012      0.48      37     109 ..     657     729 ..     647     735 .. 0.79
   5 ?    5.3   4.0     0.047        19      42     113 ..     708     782 ..     707     796 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.18
                           DUF1664  52 qvseslaatkrhLssridrvdkkldeq...keiskeikeevtevredl 96 
                                       q+ +sl++ +r+L+s id ++++  +    ke ++e ++e +++ e l
  gi|336253098|ref|YP_004596205.1| 395 QLGDSLETMRRELESYIDDLEASKADAeasKEEAAEARREAERLAERL 442
                                       677899999999999999988765444000344444444444444444 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0092
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                       +++++ e++ ++  + + r++++++   e++e ++ei+   ++ ++  +e+  +++ ++++ve+++s+ +
  gi|336253098|ref|YP_004596205.1| 494 DIQDLAEDVDRVSADVTGRVEEIERASGEVSESAEEIATATADQSDRFREVYGEMNDLSATVEEIASTAD 563
                                       4667778888888888888888888888888888888888888888888888888888888888877655 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0032
                           DUF1664  42 avesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedve 104
                                        v+svs+   +  ++ +++  ++  ++dr++++ de +e  ++++ee++++re ++ i++  e
  gi|336253098|ref|YP_004596205.1| 564 DVASVSETAADRADDASEATGEIRTEMDRLEDRADEITEQVAQLDEEMDQIREIVDLIDDIAE 626
                                       455555555555555555666666666666666666666666666666666666655555444 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.0012
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkea 109
                                       +sl++   + +++++++  s+++   +  ++idr+ +++de +++  +  e ++++ e+++e +  v+s+++a
  gi|336253098|ref|YP_004596205.1| 657 KSLAEETGEATQEVDELIGSVEESVAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEEANAGVQSINDA 729
                                       5677777777888888888888888888888888888888888888888888888888888888888888765 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.047
                           DUF1664  42 avesvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                       a++ +++q+e+     +s++++ ++ ++  +rv + +de +eis+e+k+e ++v    +e    v+ v++  ++l
  gi|336253098|ref|YP_004596205.1| 708 AIDAIAEQVEEANagvQSINDATDEQARASERVVTMVDEATEISEETKDETENVAAAAEEQTATVSDVSAGTQSL 782
                                       566666777766644456667777777777888888888888888888887777777666666666666555555 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 !   16.4  17.9   8.1e-06    0.0033      34     248 ..     398     620 ..     394     636 .. 0.82
   2 ?    4.2  10.7      0.04        16      62     168 ..     584     704 ..     578     737 .. 0.74
   3 ?   -1.3  10.6       1.9   7.6e+02      18     149 ..     645     790 ..     637     798 .. 0.43

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.1e-06
                          CALCOCO1  34 nrLeeclreraeLlqaqeaanrqrekekeeykrdreeldrerkelesrveelkeelkesre.kveeleekqkelerl 109
                                         Le  +re +  +   ea++ + e  kee  ++r+e +r  + le++ +e  + ++ +   + ++   +    +++
  gi|336253098|ref|YP_004596205.1| 398 DSLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEFGDVMNDAAAgDFTRRLDED-VDNEA 473
                                       5799999**********************************************999887652444443333.34456 PP

                          CALCOCO1 110 seelaeeksalleakeesearirELEeDiktltqralekEteLeRlkerak.......kalaqrkeeeaerkqlqak 179
                                        +e+a  ++ +le  e+  + i++L eD+  ++  +  +  e+eR   ++         a+a + +   e     ++
  gi|336253098|ref|YP_004596205.1| 474 LAEIATAFNGMLEDLEATIVDIQDLAEDVDRVSADVTGRVEEIERASGEVSesaeeiaTATADQSDRFREVYGEMND 550
                                       67889999999**********************************88777767767666677777777777778899 PP

                          CALCOCO1 180 leqseeelrslskelqelrnslaerdtqvlqLqdtittltqkLtt.AqrkeaenEallkelrslqerlaa 248
                                       l+++ ee+ s + ++ ++ ++ a+r+ ++ +   +i t  ++L++ A+  + +  +l +e+  ++e +  
  gi|336253098|ref|YP_004596205.1| 551 LSATVEEIASTADDVASVSETAADRADDASEATGEIRTEMDRLEDrADEITEQVAQLDEEMDQIREIVDL 620
                                       **************************99999999998888888651555555566777888888887654 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.04
                          CALCOCO1  62 eeykrdreeldrerkelesrveelkeelkesre.................kveeleekqkelerlseelaeeksall 121
                                        e +++ ++l+++  e+ ++v++l ee+ + re                 +    ++   e+ +  +++a+e + l+
  gi|336253098|ref|YP_004596205.1| 584 GEIRTEMDRLEDRADEITEQVAQLDEEMDQIREivdliddiaeqtnllalNASIEAAGAGEEGDGFAVVANEVKSLA 660
                                       578899999******************************99976655554333333344556666678999999999 PP

                          CALCOCO1 122 eakeesearirELEeDiktltqralekEteLeRlkerakkalaqrke 168
                                       e+++e ++ + EL   i ++ + + e  +e++R++e++   +a   +
  gi|336253098|ref|YP_004596205.1| 661 EETGEATQEVDEL---IGSVEESVAETVAEIDRMREQVDEGTAVVDD 704
                                       9999999988886...888899999************9955544444 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.9
                          CALCOCO1  18 egtdmLLVvPrAelLqnrLeeclreraeLlqaqeaanrqrekekeeykrdreeldrerkelesrveelkeelkesre 94 
                                       eg+++  V    + L +   e+ +e  eL+   e   +++ +   e  r re+ d+  + + + +e + + +++++e
  gi|336253098|ref|YP_004596205.1| 645 EGDGFAVVANEVKSLAEETGEATQEVDELIGSVE---ESVAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEE 718
                                       4555555555555566666666666666665532...2222222223333333333333333322222222222222 PP

                          CALCOCO1  95 .................kveeleekqkelerlseelaeeksalleakeesearirELEeDiktltqralekE 149
                                                          e++ +   e++++see+++e +  ++a+ee++a + ++    ++lt+ a +  
  gi|336253098|ref|YP_004596205.1| 719 anagvqsindatdeqarASERVVTMVDEATEISEETKDETENVAAAAEEQTATVSDVSAGTQSLTEMADDLR 790
                                       222222233244433333344444445555555555555555555555555555555555555555554444 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.2   0.00084      0.34      19      75 ..     398     454 ..     390     459 .. 0.75
   2 ?    6.9   0.1     0.011       4.6     184     235 ..     480     531 ..     462     541 .. 0.82
   3 !    9.7   3.5    0.0015      0.63      40     114 ..     539     613 ..     528     617 .. 0.86
   4 ?   -0.6   8.2       2.1   8.5e+02      60     149 ..     678     768 ..     651     795 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00084
                         Laminin_I  19 anledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvna 75 
                                        +le ++ eL+++    +a k ++e +++e  +   e+e+L++++++  a+  +v +
  gi|336253098|ref|YP_004596205.1| 398 DSLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEFGDVMN 454
                                       567788888888888888888888888888888888888888888887777666655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                         Laminin_I 184 eyeakLsDlrelleeAaaktrdanrlnlanqanlreiekkkeevseeknqle 235
                                        ++  L+Dl++ +   ++ + d++r ++ +  + +eie+   evse+ +++ 
  gi|336253098|ref|YP_004596205.1| 480 AFNGMLEDLEATIVDIQDLAEDVDRVSADVTGRVEEIERASGEVSESAEEIA 531
                                       5888899999999999999999999999999999999999999999887764 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0015
                         Laminin_I  40 skieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlneneea 114
                                       ++     +e+++L   +ee +  a  v    ++   +++++++ + e  ++  +l+d + ei+e+va+l+e+ ++
  gi|336253098|ref|YP_004596205.1| 539 DRFREVYGEMNDLSATVEEIASTADDVASVSETAADRADDASEATGEIRTEMDRLEDRADEITEQVAQLDEEMDQ 613
                                       5555555789999999***********9999***************************************97665 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.1
                         Laminin_I  60 qkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlne..neealpssklseelaeaqrlLeel 134
                                        + + ++ a+   +++++++ +    +  e+i ++a++++e+++ v+ +n   +e+a +s+    +  ea+ + ee 
  gi|336253098|ref|YP_004596205.1| 678 EESVAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEEANAGVQSINDatDEQARASERVVTMVDEATEISEET 754
                                       33444444555555555555555555666677777777777777777777777777777777777777777777766 PP

                         Laminin_I 135 rsRd.ftkqleeaeae 149
                                         +d +++  ++ae++
  gi|336253098|ref|YP_004596205.1| 755 --KDeTENVAAAAEEQ 768
                                       ..55344444444443 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.8     2e-05    0.0082       2      49 ..     318     366 ..     317     370 .. 0.90
   2 ?    2.5   0.2      0.48     2e+02      38      52 ..     394     408 ..     364     409 .. 0.70
   3 !   13.6   2.2   0.00016     0.064      15      52 ..     451     489 ..     435     490 .. 0.90
   4 ?   -1.0   0.2       5.8   2.4e+03      16      16 ..     571     571 ..     548     609 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2e-05
                                       HHHTTHHHHHHHHHHHHHHTTTBTSSTCCT.TSSSHHHHHHHHHHHHHH CS
                              HAMP   2 larrilrPLrrLaraarriaaGdldtrlpv.sgrDEiGeLarafNaMld 49 
                                       l r++ r +  La+ a ++++Gd d  +++  + DE+G++  af+  ++
  gi|336253098|ref|YP_004596205.1| 318 LGRTTARAMDDLAADATALSRGDTDIEIDDdGRVDEVGQVRTAFEGIRQ 366
                                       67999999999*******************99************97766 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHHHHHH CS
                              HAMP  38 GeLarafNaMldrLr 52 
                                       G+L+ ++++M+++L+
  gi|336253098|ref|YP_004596205.1| 394 GQLGDSLETMRRELE 408
                                       899999999999986 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00016
                                       HHHHHHTTTBTSSTCCTTSSSH.HHHHHHHHHHHHHHHH CS
                              HAMP  15 raarriaaGdldtrlpvsgrDE.iGeLarafNaMldrLr 52 
                                       ++++  aaGd++ rl+++ ++E ++e+a afN Ml+ L+
  gi|336253098|ref|YP_004596205.1| 451 DVMNDAAAGDFTRRLDEDVDNEaLAEIATAFNGMLEDLE 489
                                       56788889**************89************997 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 5.8
                                       H CS
                              HAMP  16 a 16 
                                       +
  gi|336253098|ref|YP_004596205.1| 571 T 571
                                       1 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.0      0.31   1.3e+02      24      52 ..     482     510 ..     464     573 .. 0.66
   2 !   14.3   2.1    0.0001     0.041       9      52 ..     586     629 ..     584     640 .. 0.87
   3 ?    5.7   4.9     0.049        20      14      64 ..     700     750 ..     665     762 .. 0.79
   4 ?    1.1   0.2       1.4   5.7e+02      18      64 ..     738     785 ..     734     797 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.31
                           NPV_P10  24 qqqvddvqenlpdvtelnekLdaqsaqLa 52 
                                       +  ++d+++ + d+++l e +d+ sa ++
  gi|336253098|ref|YP_004596205.1| 482 NGMLEDLEATIVDIQDLAEDVDRVSADVT 510
                                       55555666666666666666666655544 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.0001
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLa 52 
                                       Ir++   ++d+ d + +qv++++e++ ++ e+ + +d++++q +
  gi|336253098|ref|YP_004596205.1| 586 IRTEMDRLEDRADEITEQVAQLDEEMDQIREIVDLIDDIAEQTN 629
                                       999***********************************999854 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.049
                           NPV_P10  14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                       + vdd ++a+++  ++v+e    v+ +n+  d+q+ + + + t v++ ++i
  gi|336253098|ref|YP_004596205.1| 700 AVVDDGIEAIDAIAEQVEEANAGVQSINDATDEQARASERVVTMVDEATEI 750
                                       457888888888888888888888888888888888888888888877766 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 1.4
                           NPV_P10  18 dkVdalqqqvddvqenlpd.vtelnekLdaqsaqLaeletkvenIqdi 64 
                                       ++V  + ++ ++++e+ +d ++++ +  ++q+a++ ++++  ++ +++
  gi|336253098|ref|YP_004596205.1| 738 ERVVTMVDEATEISEETKDeTENVAAAAEEQTATVSDVSAGTQSLTEM 785
                                       555555566667777766624557788888999988888766555554 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   4.2     0.027        11     198     277 ..     404     483 ..     395     499 .. 0.66
   2 ?   11.3   7.6   0.00029      0.12     157     281 ..     494     617 ..     470     632 .. 0.57
   3 ?    9.3   7.1    0.0011      0.45     160     279 ..     665     786 ..     649     798 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.027
                              Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkee 274
                                       + eLe++ ++l++ ka+ e+ k+e ae +++ e+l+e++e  +++  +++++ a+ + +++  ++++++ + ++ + 
  gi|336253098|ref|YP_004596205.1| 404 RRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEFGDVMNDAAAGDFTRRLDEDVDNEALAEIATA 480
                                       45777777777777788888888888888888888888777777777777776666666666666666555555555 PP

                              Spc7 275 vka 277
                                       ++ 
  gi|336253098|ref|YP_004596205.1| 481 FNG 483
                                       555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00029
                              Spc7 157 lLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleele 233
                                        +++  e +d++  +++ + +e+e+   +  e aee+++ + ++   +re +   ++++++  +e+a+  +++++++
  gi|336253098|ref|YP_004596205.1| 494 DIQDLAEDVDRVSADVTGRVEEIERASGEVSESAEEIATATADQSDRFRE-VYGEMNDLSATVEEIASTADDVASVS 569
                                       55555666666666666666666666666666666666544444444332.22223333333336666666666666 PP

                              Spc7 234 ekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleel 281
                                       e+ ++ ++  se+  ei+ + + le + +  +++v +l ee++++ e+
  gi|336253098|ref|YP_004596205.1| 570 ETAADRADDASEATGEIRTEMDRLEDRADEITEQVAQLDEEMDQIREI 617
                                       666666666666666666666666666666666666666666666554 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0011
                              Spc7 160 kqeeeldellpeleeekaeleeeleklqeaaeelesid...keeLeelreelaelkaeieekkkelaelqeqleele 233
                                       +  +e+del  ++ee  ae  +e+++++e+++e +++     e + ++ e+++e++a +++ ++ ++e  +  e++ 
  gi|336253098|ref|YP_004596205.1| 665 EATQEVDELIGSVEESVAETVAEIDRMREQVDEGTAVVddgIEAIDAIAEQVEEANAGVQSINDATDEQARASERVV 741
                                       45677888888888888888888888888888888855013344455566666666666666666666666666666 PP

                              Spc7 234 ekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkale 279
                                       + ++e++e  +e+++e+++      e++  + s+vs+ ++++ ++ 
  gi|336253098|ref|YP_004596205.1| 742 TMVDEATEISEETKDETENVAAAA-EEQTATVSDVSAGTQSLTEMA 786
                                       666666655555555555444444.455667777777777766665 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0081       3.3       6      57 ..     396     447 ..     394     468 .. 0.87
   2 ?    0.3   0.0       2.6   1.1e+03       4      34 ..     496     526 ..     470     552 .. 0.43
   3 ?    0.9   0.0       1.7   6.9e+02       5      52 ..     508     555 ..     493     575 .. 0.50
   4 ?    7.4   0.4     0.017       6.9       9      52 ..     575     618 ..     569     643 .. 0.80
   5 ?    1.9   0.2      0.88   3.6e+02       9      52 ..     655     695 ..     650     720 .. 0.62
   6 ?    3.7   0.8      0.23        94      15      76 ..     724     785 ..     706     788 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0081
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXX CS
                              YabA   6 lfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeek 57 
                                       l d+le++ ++le+  ++le+ k++ ++  ee ae + e e+l erle++ +
  gi|336253098|ref|YP_004596205.1| 396 LGDSLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAA 447
                                       66899******************************************65544 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   4 kelfdkleeleeqleelleeleelkeelael 34 
                                       ++l + +++++ +++  +ee+e+   e++e 
  gi|336253098|ref|YP_004596205.1| 496 QDLAEDVDRVSADVTGRVEEIERASGEVSES 526
                                       2222222222222222222222222222222 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                       +++ ++ee+e+  +e++e+ ee+ +++a+  ++ +e+  e + l  ++
  gi|336253098|ref|YP_004596205.1| 508 DVTGRVEEIERASGEVSESAEEIATATADQSDRFREVYGEMNDLSATV 555
                                       334444555555555555555555554444444444444444444444 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                       + ++ +e ++e+ +e+++l+++  e++e+ a+L  e +++re +
  gi|336253098|ref|YP_004596205.1| 575 RADDASEATGEIRTEMDRLEDRADEITEQVAQLDEEMDQIREIV 618
                                       55667788999999999999999999999999999999999988 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.88
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                       ++++l e+++e ++e++el  +++e + e     +e +++re++
  gi|336253098|ref|YP_004596205.1| 655 EVKSLAEETGEATQEVDELIGSVEESVAET---VAEIDRMREQV 695
                                       566666666666666666655555555443...34555555544 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA  15 eqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarl 76 
                                       +++++ ++e ++  e+++++++e +e++ e +   e+++ + ++++++ +++s g ++L+++
  gi|336253098|ref|YP_004596205.1| 724 QSINDATDEQARASERVVTMVDEATEISEETKDETENVAAAAEEQTATVSDVSAGTQSLTEM 785
                                       45666667777788899999999999999999999999999999999999999999999875 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       4.4   1.8e+03      13      52 ..     401     440 ..     396     454 .. 0.50
   2 ?    3.2   0.1      0.18        74      15      58 ..     509     552 ..     471     563 .. 0.44
   3 ?    2.7   0.0      0.26   1.1e+02       9      61 ..     517     569 ..     510     577 .. 0.73
   4 ?    7.3   0.7      0.01       4.1       7      76 ..     557     626 ..     548     637 .. 0.75
   5 ?    0.6   0.0       1.2   4.7e+02      21      51 ..     665     696 ..     649     730 .. 0.43
   6 ?    5.4   0.4     0.039        16       3      64 ..     693     754 ..     679     760 .. 0.88
   7 ?    9.0   0.5    0.0029       1.2       6      72 ..     731     797 ..     726     801 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.4
                             Sec34  13 delleqtdealeqLeeleekfksvsektsslheaceqlle 52 
                                       +++ +++++  ++Le  + + ++ +e+  + ++++e+l e
  gi|336253098|ref|YP_004596205.1| 401 ETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAE 440
                                       3444444444444444444444444444444444444443 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.18
                             Sec34  15 lleqtdealeqLeeleekfksvsektsslheaceqlleeqkrle 58 
                                       +  +++e+++   e++e+ +++++ t + +++  +++ e ++l+
  gi|336253098|ref|YP_004596205.1| 509 VTGRVEEIERASGEVSESAEEIATATADQSDRFREVYGEMNDLS 552
                                       23333333333333333333444444433333344444444444 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.26
                             Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleela 61 
                                       e+   e+ e+++e+ +  ++ +++f++v  ++++l+++ e++ +  +++ +++
  gi|336253098|ref|YP_004596205.1| 517 ERASGEVSESAEEIATATADQSDRFREVYGEMNDLSATVEEIASTADDVASVS 569
                                       55566777788888888888888888888888888888888887777666655 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.01
                             Sec34   7 skeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldp 76 
                                       +  ++ d++ +  ++a +  ++ +e   ++ +++ +l++++++++e+  +l+e  ++i+e ++  +++ +
  gi|336253098|ref|YP_004596205.1| 557 EIASTADDVASVSETAADRADDASEATGEIRTEMDRLEDRADEITEQVAQLDEEMDQIREIVDLIDDIAE 626
                                       5556677777778888888888888888888888888888888888888888888888887766555555 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 1.2
                             Sec34  21 ealeqLeeleekfks.vsektsslheaceqll 51 
                                       ea ++++el  ++++ v+e   +++++ eq+ 
  gi|336253098|ref|YP_004596205.1| 665 EATQEVDELIGSVEEsVAETVAEIDRMREQVD 696
                                       44444444443333202222222222222222 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.039
                             Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeei 64 
                                       +q+++ ++ +d+ +e +d++ eq+ee +  ++s+++ t +  +a+e++++  ++ +e++ee 
  gi|336253098|ref|YP_004596205.1| 693 EQVDEGTAVVDDGIEAIDAIAEQVEEANAGVQSINDATDEQARASERVVTMVDEATEISEET 754
                                       677777888888899999*********************99999999999999999988875 PP

  == domain 7  score: 9.0 bits;  conditional E-value: 0.0029
                             Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFe 72 
                                       +++ +  +++++ +dea e  ee +++ ++v++  ++  ++  ++ + +++l+e+a+++++ L+ F+
  gi|336253098|ref|YP_004596205.1| 731 DEQARASERVVTMVDEATEISEETKDETENVAAAAEEQTATVSDVSAGTQSLTEMADDLRTSLDAFD 797
                                       5677888999*******************************************************97 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  13.7    0.0029       1.2     269     470 ..     403     614 ..     394     626 .. 0.58
   2 ?   10.7  11.3   0.00037      0.15     278     453 ..     608     793 ..     605     802 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0029
                            AAA_13 269 rkaaLeahFddefeekqerLekliekveskkselleklkavsdeasensafeed...keelkaea..ealeeqLkgl 340
                                       ++ +Le+++dd  e+++++ e  +e+ +++++ ++e+l++  +++ +++    +     ++++++  ++ +e+L ++
  gi|336253098|ref|YP_004596205.1| 403 MRRELESYIDD-LEASKADAEASKEEAAEARR-EAERLAERLERKAAEFGDVMNdaaAGDFTRRLdeDVDNEALAEI 477
                                       67789999998.66667777777777776654.45667666665433332211112233333333223444556666 PP

                            AAA_13 341 qraleaKrkepfk.svelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlv......eelese 410
                                         a +   +++ +  v+++++++++++++ +v+   e i++    v++ +ee ++a+ +    +       ++l + 
  gi|336253098|ref|YP_004596205.1| 478 ATAFNGMLEDLEAtIVDIQDLAEDVDRVSADVTGRVEEIERASGEVSESAEEIATATADQSDRFRevygemNDLSAT 554
                                       66666666666552355777777777777777777777777777777777777777666555444334444455555 PP

                            AAA_13 411 ldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                       ++e  ++ ++++   e + ++++++++++ +++ e+  Le +  ++++ ++++ +e+ ++
  gi|336253098|ref|YP_004596205.1| 555 VEEIASTADDVASVSETAADRADDASEATGEIRTEMDRLEDRADEITEQVAQLDEEMDQI 614
                                       555555555555555555666666666666666666666666666666666666666554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00037
                            AAA_13 278 ddefeekqerLekliekveskkselleklkavsde.......asensa.feedkeelkaeaealeeqLkglqralea 346
                                       d+e+++ ++++ +li++++++++ ll+ l+a +++       +   +a  +++++ l +e+ + +++ ++l   +e+
  gi|336253098|ref|YP_004596205.1| 608 DEEMDQ-IREIVDLIDDIAEQTN-LLA-LNASIEAagageegD--GFAvVANEVKSLAEETGEATQEVDELIGSVEE 679
                                       555554.9999999999999984.544.445554435444321..22223344555555555555556666666666 PP

                            AAA_13 347 Krkepfksve.l.esvkaki...esikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykk 416
                                        + e +++++ + e+v++ +   + + +++++i e++++ N+ v+++++++ e + + e+ +  v e+++  +e k+
  gi|336253098|ref|YP_004596205.1| 680 SVAETVAEIDrMrEQVDEGTavvDDGIEAIDAIAEQVEEANAGVQSINDATDEQARASERVVtmVDEATEISEETKD 756
                                       665555544322233333323347899999999999*****999988777665555555543225666555567889 PP

                            AAA_13 417 kykklekaieklekelkeeeaelkkleeeikeLekql 453
                                       + +++++a+e+ ++ +++ +a ++ l e + +L+++l
  gi|336253098|ref|YP_004596205.1| 757 ETENVAAAAEEQTATVSDVSAGTQSLTEMADDLRTSL 793
                                       9999999999999999999999999999999999877 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3      0.56   2.3e+02      84     127 ..     398     441 ..     373     449 .. 0.79
   2 ?   11.1   0.6   0.00055      0.22      10     113 ..     493     613 ..     486     624 .. 0.73
   3 ?    4.1   0.1     0.078        32      11     119 ..     648     762 ..     641     799 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.56
                     PI3K_P85_iSH2  84 eklqenleqlksrlkelhsskekLeedlkqqkeeereleReina 127
                                       ++l++  ++l+s ++ l++sk++ e + ++ +e  re eR   +
  gi|336253098|ref|YP_004596205.1| 398 DSLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAER 441
                                       45666677888888899999999999999999998888886554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00055
                     PI3K_P85_iSH2  10 gdleklseklrevskqlqekskeydqlkeeynkiseeiqlkr.qaleaFneaikmFeeqiklqekfskeaq...... 79 
                                        d++ l+e+  +vs +++ + +e ++ + e ++  eei++    + + F+e+    ++  ++ e++ + a+      
  gi|336253098|ref|YP_004596205.1| 493 VDIQDLAEDVDRVSADVTGRVEEIERASGEVSESAEEIATATaDQSDRFREVYGEMNDLSATVEEIASTADdvasvs 569
                                       6999***********************************998456789*****999*********999995454455 PP

                     PI3K_P85_iSH2  80 .........ehEie.klqenleqlksrlkelhsskekLeedlkq 113
                                                  E   ++ + +++l++r +e+ ++ ++L+e++ q
  gi|336253098|ref|YP_004596205.1| 570 etaadraddASEATgEIRTEMDRLEDRADEITEQVAQLDEEMDQ 613
                                       55555555533333355555555555555555555555555443 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.078
                     PI3K_P85_iSH2  11 dleklseklrevskqlqekskeydql....keeynkiseeiqlkrqaleaFneaikmFeeqiklqekfskeaq.... 79 
                                         ++++++ + + ++  e ++e d+l     e+  ++  ei+ +r ++    e + +  + i+ ++ + ++++    
  gi|336253098|ref|YP_004596205.1| 648 GFAVVANEVKSLAEETGEATQEVDELigsvEESVAETVAEIDRMREQV---DEGTAVVDDGIEAIDAIAEQVEeana 721
                                       567888888999999999999999872222466666777777777655...58888888888888888888754444 PP

                     PI3K_P85_iSH2  80 .ehEieklqenleqlksrlkelhsskekLeedlkqqkeeer 119
                                         + i++ ++  +++ +r+ ++ ++  +++e+ k ++e+  
  gi|336253098|ref|YP_004596205.1| 722 gVQSINDATDEQARASERVVTMVDEATEISEETKDETENVA 762
                                       47788888889999999999999999999999999998765 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   0.00014     0.059      41      99 ..     397     455 ..     395     460 .. 0.90
   2 ?    6.0   0.0     0.037        15      43     102 ..     473     532 ..     471     542 .. 0.86
   3 ?    2.1   0.3      0.61   2.5e+02      55     110 ..     548     607 ..     545     619 .. 0.70
   4 ?   -0.4   0.1       3.7   1.5e+03      71     111 .]     655     692 ..     648     697 .. 0.49
   5 ?   -0.9   0.5       5.2   2.1e+03      73      80 ..     748     755 ..     706     790 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00014
                        TSNAXIP1_N  41 kdlLseIKkEYelyiahllesqreaqylkaklktlsessdkraleleekreelraleke 99 
                                       +d L++++ E e yi+ l+ s+ +a+++k++ +++ +++++ a  le+k +e+ ++ ++
  gi|336253098|ref|YP_004596205.1| 397 GDSLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEFGDVMND 455
                                       56799********************************************8887766655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.037
                        TSNAXIP1_N  43 lLseIKkEYelyiahllesqreaqylkaklktlsessdkraleleekreelralekeska 102
                                        L+eI   +  +++ l+ ++ + q l++ +  +s++ + r+ e+e++  e+++  +e ++
  gi|336253098|ref|YP_004596205.1| 473 ALAEIATAFNGMLEDLEATIVDIQDLAEDVDRVSADVTGRVEEIERASGEVSESAEEIAT 532
                                       5999******************************************98887766665554 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.61
                        TSNAXIP1_N  55 iahllesqreaqylkaklktlsessdkraleleek....reelralekeskalleeidkl 110
                                       ++ l  + +e    +  ++++se+++ ra++ +e+    r+e+ +le +++++ e++ +l
  gi|336253098|ref|YP_004596205.1| 548 MNDLSATVEEIASTADDVASVSETAADRADDASEAtgeiRTEMDRLEDRADEITEQVAQL 607
                                       566677777777777777777777776666666554445677777777777777777665 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 3.7
                        TSNAXIP1_N  71 klktlsessdkraleleekreelralekeskalleeidklr 111
                                       ++k+l+e++ +  +e++e    + ++e+ +++  +eid++r
  gi|336253098|ref|YP_004596205.1| 655 EVKSLAEETGEATQEVDEL---IGSVEESVAETVAEIDRMR 692
                                       4555555555444444444...4444444444444444443 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 5.2
                        TSNAXIP1_N  73 ktlsessd 80 
                                       +++se+++
  gi|336253098|ref|YP_004596205.1| 748 TEISEETK 755
                                       22222222 PP

>> Antimicrobial24  Frog antimicrobial peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.0   0.00039      0.16       2      15 ..     292     305 ..     291     306 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00039
                   Antimicrobial24   2 LvSSIGkALGGLLv 15 
                                       L SS+G+ LGGL+v
  gi|336253098|ref|YP_004596205.1| 292 LTSSVGRSLGGLIV 305
                                       78***********8 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   2.6      0.57   2.3e+02      85     132 ..     402     449 ..     398     458 .. 0.85
   2 ?   12.8   0.0   0.00021     0.087      89     172 ..     480     563 ..     454     573 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.57
                         Rootletin  85 klaqvnslLreqleearqaneaLtedlqkltkdwerlreeleqkekew 132
                                       ++ ++ + + ++le++++  ea +e++   +++ erl+e le+k +e+
  gi|336253098|ref|YP_004596205.1| 402 TMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEF 449
                                       556666778889999999999999999999999999999999999988 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00021
                         Rootletin  89 vnslLreqleearqaneaLtedlqkltkdwerlreeleqkekewreeeeafneylssehsrllsLWrevvavrrqfs 165
                                         + + e+le++    + L ed++++++d++   ee+e+ + e  e  e++++   ++ +r  +   e++ +   ++
  gi|336253098|ref|YP_004596205.1| 480 AFNGMLEDLEATIVDIQDLAEDVDRVSADVTGRVEEIERASGEVSESAEEIATATADQSDRFREVYGEMNDLSATVE 556
                                       3333458899999999********************************************************99999 PP

                         Rootletin 166 elksate 172
                                       e+ s+++
  gi|336253098|ref|YP_004596205.1| 557 EIASTAD 563
                                       9988765 PP

>> Ran-binding  RanGTP-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.037        15      83     140 ..     434     492 ..     392     499 .. 0.80
   2 ?    8.2   1.7    0.0027       1.1      46     152 ..     541     642 ..     516     647 .. 0.78
   3 ?    6.2   2.6     0.011       4.4      28     127 ..     666     777 ..     656     790 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.037
                       Ran-binding  83 saveLtksLkkeieelgerleeaaekeekskk.keeekeelkkviedikeLLkrieeai 140
                                       +a +L+++L+++  e+g+ +++aa+   +++  ++ ++e+l+++ ++ + +L+++e +i
  gi|336253098|ref|YP_004596205.1| 434 EAERLAERLERKAAEFGDVMNDAAAGDFTRRLdEDVDNEALAEIATAFNGMLEDLEATI 492
                                       67889999************99998887655557778899999*********9999887 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0027
                       Ran-binding  46 rkeleklqkkLeskikiispaidLieliaarGntsLesaveLtksLkkeieelgerleeaaekeekskkkeeekeel 122
                                        +e+    ++L+  ++ i+++ d +  ++       + a e t ++++e+++l++r +e++e+        + +ee+
  gi|336253098|ref|YP_004596205.1| 541 FREVYGEMNDLSATVEEIASTADDVASVSETAADRADDASEATGEIRTEMDRLEDRADEITEQVA------QLDEEM 611
                                       5566677788888888888888889999999999999999********************98777......455566 PP

                       Ran-binding 123 kkviedikeLLkrieeaiPllnL..alttsGa 152
                                       +++ ++i +L+++i e++ ll L  ++ ++Ga
  gi|336253098|ref|YP_004596205.1| 612 DQI-REIVDLIDDIAEQTNLLALnaSIEAAGA 642
                                       665.5677899999999999766436777775 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.011
                       Ran-binding  28 aikqvsrllkkvpedkk.erkeleklqkkLeskikiispaidLieliaar...GntsLesaveLtksLkkeieelge 100
                                       a ++v +l+ +v+e+ + + +e++++++++++   ++   i+ i+ ia +    n+  +s  + t++  +  e++ +
  gi|336253098|ref|YP_004596205.1| 666 ATQEVDELIGSVEESVAeTVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQveeANAGVQSINDATDEQARASERVVT 742
                                       788999999999987652568*****************998888888876444777788888888877777777777 PP

                       Ran-binding 101 rleeaaekeekskk........keeekeelkkvie 127
                                        ++ea+e +e++k+         ee+++++++v +
  gi|336253098|ref|YP_004596205.1| 743 MVDEATEISEETKDetenvaaaAEEQTATVSDVSA 777
                                       77777776665554555665555555555555555 PP

>> DUF2913  Protein of unknown function (DUF2913)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00042      0.17      72     183 ..     591     699 ..     582     703 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00042
                           DUF2913  72 aqLkalleriseqykevaeeekeldskleallaeleekewvvitdeevvdklkldsdgqeslvvcakqleqhfdeeg 148
                                       + L+++  +i eq +++ ee  ++  ++ +l++++ e+  ++  ++++++    + ++   ++v+a+++++  +e g
  gi|336253098|ref|YP_004596205.1| 591 DRLEDRADEITEQVAQLDEEMDQI-REIVDLIDDIAEQTNLLALNASIEA--AGAGEEGDGFAVVANEVKSLAEETG 664
                                       678888999999999999988888.*************************..99999999***************** PP

                           DUF2913 149 elikpislyvrgdeaefvelafaaglllskvtdkk 183
                                       e ++ +  ++ + e+ ++e +++ + +  +v++ +
  gi|336253098|ref|YP_004596205.1| 665 EATQEVDELIGSVEESVAETVAEIDRMREQVDEGT 699
                                       *************************9999998765 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.9   7.9e+02       8      36 ..     399     427 ..     397     433 .. 0.82
   2 ?    4.8   0.0     0.058        24       7      41 ..     472     506 ..     469     507 .. 0.90
   3 ?   -2.0   0.0       7.9   3.2e+03      21      56 ..     528     564 ..     521     568 .. 0.63
   4 ?    1.8   0.2      0.49     2e+02       1      21 [.     606     626 ..     599     632 .. 0.89
   5 ?    1.6   0.0      0.58   2.4e+02      10      41 ..     668     699 ..     661     704 .. 0.85
   6 ?    1.3   0.1      0.74     3e+02       7      35 ..     707     735 ..     692     759 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.9
                         DASH_Duo1   8 qLrkinevienviesLkkaksniervket 36 
                                       +L+++++ +e++i++L+++k + e  ke 
  gi|336253098|ref|YP_004596205.1| 399 SLETMRRELESYIDDLEASKADAEASKEE 427
                                       78999999**********99988776665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.058
                         DASH_Duo1   7 eqLrkinevienviesLkkaksniervketvestn 41 
                                       e L +i ++++++ e+L+++  +i+ ++e v+ ++
  gi|336253098|ref|YP_004596205.1| 472 EALAEIATAFNGMLEDLEATIVDIQDLAEDVDRVS 506
                                       7899************************9998765 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 7.9
                         DASH_Duo1  21 esLkkak.sniervketvestntLLdkWirIlsqteh 56 
                                       e++ +a+ ++ +r+ e   ++n L  +  +I s +++
  gi|336253098|ref|YP_004596205.1| 528 EEIATATaDQSDRFREVYGEMNDLSATVEEIASTADD 564
                                       5555555566667777777777776666666666655 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.49
                         DASH_Duo1   1 aLekEleqLrkinevienvie 21 
                                       +L +E++q+r+i + i+++ e
  gi|336253098|ref|YP_004596205.1| 606 QLDEEMDQIREIVDLIDDIAE 626
                                       689999******999998876 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.58
                         DASH_Duo1  10 rkinevienviesLkkaksniervketvestn 41 
                                       +++ e i +v+es  ++  +i+r+ e+v++  
  gi|336253098|ref|YP_004596205.1| 668 QEVDELIGSVEESVAETVAEIDRMREQVDEGT 699
                                       6778899********************98755 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.74
                         DASH_Duo1   7 eqLrkinevienviesLkkaksniervke 35 
                                       e ++ i e +e  ++  +++++ +++ ++
  gi|336253098|ref|YP_004596205.1| 707 EAIDAIAEQVEEANAGVQSINDATDEQAR 735
                                       33444444444444444444444444444 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.8    0.0047       1.9     229     286 ..     400     457 ..     395     502 .. 0.84
   2 ?    0.2   0.1         1   4.2e+02     227     266 ..     486     525 ..     461     545 .. 0.57
   3 ?    8.5   2.7     0.003       1.2     220     298 ..     535     613 ..     514     619 .. 0.83
   4 ?    0.8   0.4      0.67   2.7e+02     279     322 ..     653     696 ..     646     703 .. 0.75
   5 ?    6.7   4.6     0.011       4.5     231     310 ..     704     782 ..     689     804 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0047
                            HMMR_N 229 lleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdln 286
                                       l+    el++ ++ le  k d ++++e ++e+ +e e L + Le k+ e+   ++d+ 
  gi|336253098|ref|YP_004596205.1| 400 LETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEFGDVMNDAA 457
                                       6677789*****************************************9999999875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1
                            HMMR_N 227 eklleyieelsnvseqlekykldiaqleellkekndeies 266
                                       e l++ i  ++ ++e +++ + d++   e ++ +  e+++
  gi|336253098|ref|YP_004596205.1| 486 EDLEATIVDIQDLAEDVDRVSADVTGRVEEIERASGEVSE 525
                                       4455555555555555555555555555555555544443 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.003
                            HMMR_N 220 ieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekckllekek 296
                                       +++    ++   +++ ls++ e++     d+a++ e+++ ++d+ ++   +++ + + l+ ++++ +e++ +l++e 
  gi|336253098|ref|YP_004596205.1| 535 ADQSDRFREVYGEMNDLSATVEEIASTADDVASVSETAADRADDASEATGEIRTEMDRLEDRADEITEQVAQLDEEM 611
                                       4444555777789999999999999999**********************************************999 PP

                            HMMR_N 297 ee 298
                                       ++
  gi|336253098|ref|YP_004596205.1| 612 DQ 613
                                       85 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.67
                            HMMR_N 279 skqvkdlnekckllekekeelvreeeekeqtlsaEleelkeklk 322
                                        ++vk+l e+  +  +e +el+   ee   +  aE++ ++e+++
  gi|336253098|ref|YP_004596205.1| 653 ANEVKSLAEETGEATQEVDELIGSVEESVAETVAEIDRMREQVD 696
                                       46677777777777777777777777777888888888877765 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.011
                            HMMR_N 231 eyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekckllekekeelvreeeeke 307
                                       + ie + +++eq+e  +  ++++++  +e+++  e + + ++e ++ +s+++kd +e++    +e+  +v+     +
  gi|336253098|ref|YP_004596205.1| 704 DGIEAIDAIAEQVEEANAGVQSINDATDEQARASERVVTMVDEATE-ISEETKDETENVAAAAEEQTATVSDVSAGT 779
                                       5689999******************************999999888.99999***9999998888777777665555 PP

                            HMMR_N 308 qtl 310
                                       q+l
  gi|336253098|ref|YP_004596205.1| 780 QSL 782
                                       444 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 ?    0.5   0.1       1.9   7.6e+02      76      93 ..     399     416 ..     397     419 .. 0.88
   2 ?    1.3   0.1         1   4.2e+02      46      74 ..     481     509 ..     469     542 .. 0.55
   3 ?    4.3   0.7      0.13        51      35      88 ..     512     569 ..     484     575 .. 0.69
   4 ?   13.9   2.0   0.00012     0.049      31      90 ..     571     630 ..     565     636 .. 0.61
   5 ?    5.1   1.4      0.07        29      32      81 ..     652     702 ..     649     718 .. 0.73
   6 ?    4.7   0.5     0.092        37      39      90 ..     681     732 ..     679     735 .. 0.87
   7 ?    2.3   2.7      0.51   2.1e+02      30      84 ..     734     789 ..     717     795 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.9
                           BLOC1_2  76 eLeeavseLDeyskeLEa 93 
                                       +Le++  eL++y+ +LEa
  gi|336253098|ref|YP_004596205.1| 399 SLETMRRELESYIDDLEA 416
                                       79999999*******997 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1
                           BLOC1_2  46 lekkleklnekyeelqpylqqidqiekqv 74 
                                       ++  le+l+++   +q + + +d++ ++v
  gi|336253098|ref|YP_004596205.1| 481 FNGMLEDLEATIVDIQDLAEDVDRVSADV 509
                                       44444444444444444444444444333 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.13
                           BLOC1_2  35 kykklkdvaaslekklekl....nekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                       ++++++++  ++++++e++      +++ +++   +++++ ++v+e+ ++++ + + s
  gi|336253098|ref|YP_004596205.1| 512 RVEEIERASGEVSESAEEIatatADQSDRFREVYGEMNDLSATVEEIASTADDVASVS 569
                                       5555555555555555544111156677888888899999999999999988776665 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 0.00012
                           BLOC1_2  31 aasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyske 90 
                                       +a+ + ++ ++++ ++++++++l+ + +e+ +++ q+d+  +q++e+ ++++ + e +  
  gi|336253098|ref|YP_004596205.1| 571 TAADRADDASEATGEIRTEMDRLEDRADEITEQVAQLDEEMDQIREIVDLIDDIAEQTNL 630
                                       566666666666666666666666666666666666666666666666655555555544 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.07
                           BLOC1_2  32 asekykklkdvaaslekkleklnekye.elqpylqqidqiekqvteLeeav 81 
                                       +++++k+l++++ ++++++++l    e ++++ + +id++ +qv+e +++v
  gi|336253098|ref|YP_004596205.1| 652 VANEVKSLAEETGEATQEVDELIGSVEeSVAETVAEIDRMREQVDEGTAVV 702
                                       567788888888888888888866555488888888888888888755554 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.092
                           BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyske 90 
                                       +++ +a++ +  e+++e  + ++  ++ id+i +qv+e  + v+ ++  + e
  gi|336253098|ref|YP_004596205.1| 681 VAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEEANAGVQSINDATDE 732
                                       678899999999999999999****************999999999888776 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.51
                           BLOC1_2  30 eaasekykklkdvaaslekklek.lnekyeelqpylqqidqiekqvteLeeavseL 84 
                                        +ase++  + d+a +++++ ++ +++  ++ +++   + ++ + +++L+e+++ L
  gi|336253098|ref|YP_004596205.1| 734 ARASERVVTMVDEATEISEETKDeTENVAAAAEEQTATVSDVSAGTQSLTEMADDL 789
                                       57899999999999999998876155556699999****************99987 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1     0.001      0.43      26      57 ..     588     619 ..     587     624 .. 0.91
   2 ?   -1.7   0.0       8.1   3.3e+03      39      59 ..     653     673 ..     649     678 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkeve 57 
                                        e+++Le+r+++++++ ++L +e++++++ v+
  gi|336253098|ref|YP_004596205.1| 588 TEMDRLEDRADEITEQVAQLDEEMDQIREIVD 619
                                       6899***********************99876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 8.1
                                       HHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  39 ekeNksLkseleelkkevekL 59 
                                        +e ksL++e +e + ev++L
  gi|336253098|ref|YP_004596205.1| 653 ANEVKSLAEETGEATQEVDEL 673
                                       567777888887777777766 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.9     0.003       1.2       4      58 ..     403     457 ..     400     506 .. 0.86
   2 ?   14.8   3.5     7e-05     0.028       7     114 ..     515     622 ..     512     627 .. 0.92
   3 ?    0.6   0.2       1.7   7.1e+02      68     105 ..     660     697 ..     653     704 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.003
                           DUF4200   4 kkremfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkend 58 
                                        +re++ +   lea k++ +  +e+++++++e e+  ++le+++++f   +++  
  gi|336253098|ref|YP_004596205.1| 403 MRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEFGDVMNDAA 457
                                       599********************************************99998865 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 7e-05
                           DUF4200   7 emfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeik 83 
                                       e++++  ++++  eei++    +++r +e++ + + l  ++++      +  + ++ a  +a++ ++++ e   e+ 
  gi|336253098|ref|YP_004596205.1| 515 EIERASGEVSESAEEIATATADQSDRFREVYGEMNDLSATVEEIASTADDVASVSETAADRADDASEATGEIRTEMD 591
                                       6777888899999**************************************************************** PP

                           DUF4200  84 klkaeietlkseiekleekleeykkYeefLe 114
                                       +l++  +++ ++ ++l+e++++ ++  +  +
  gi|336253098|ref|YP_004596205.1| 592 RLEDRADEITEQVAQLDEEMDQIREIVDLID 622
                                       *******************999877666555 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.7
                           DUF4200  68 aeeerklkkekeaeikklkaeietlkseiekleeklee 105
                                       aee  ++++e ++ i   ++++++  +ei+++ e+++e
  gi|336253098|ref|YP_004596205.1| 660 AEETGEATQEVDELIGSVEESVAETVAEIDRMREQVDE 697
                                       55555666677777777777777777888888888765 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.4     0.079        32      23      77 ..     401     450 ..     392     470 .. 0.51
   2 ?    5.9   0.4     0.049        20       8      74 ..     488     553 ..     476     557 .. 0.61
   3 ?    8.8   1.6    0.0064       2.6      13      90 ..     549     624 ..     541     634 .. 0.70
   4 ?    2.3   0.8      0.63   2.6e+02      14      57 ..     655     697 ..     610     716 .. 0.53
   5 ?    6.6   4.0      0.03        12       5      71 ..     716     784 ..     714     798 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.079
                           DUF2203  23 ralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevk 77 
                                        ++r+ele+  ++le++ka+ae+      ++e +e++ e+e+l e++e+  +e  
  gi|336253098|ref|YP_004596205.1| 401 ETMRRELESYIDDLEASKADAEA-----SKEEAAEARREAERLAERLERKAAEFG 450
                                       45566666666666666666443.....333333333344444444333333333 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.049
                           DUF2203   8 AnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGv 74 
                                        +a++  +++l e++ ++ ++++ ++ee+e+a+ e ++s a+e +++ +  +++++e+  e+++l +
  gi|336253098|ref|YP_004596205.1| 488 LEATIVDIQDLAEDVDRVSADVTGRVEEIERASGEVSES-AEEIATATADQSDRFREVYGEMNDLSA 553
                                       345666666666666666666666666666666665443.555556666666677777666666555 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0064
                           DUF2203  13 pllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleaglvDFpak 89 
                                         l+ ++ee++++++++++++e  ++  ++a+ ++  e ++e+++le++++e++e++ +l  e+ +++  +vD   +
  gi|336253098|ref|YP_004596205.1| 549 NDLSATVEEIASTADDVASVSETAADRADDAS-EATGEIRTEMDRLEDRADEITEQVAQLDEEMDQIR-EIVDLIDD 623
                                       56778888888888888888777666666644.44677778888888888888888888877777663.55666555 PP

                           DUF2203  90 l 90 
                                       +
  gi|336253098|ref|YP_004596205.1| 624 I 624
                                       5 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.63
                           DUF2203  14 llkelleelralrkeleeleeeleeakaeaekseaaeleaelee 57 
                                       ++k+l ee  ++++e+ el  ++ee+ ae+   e  +++++++e
  gi|336253098|ref|YP_004596205.1| 655 EVKSLAEETGEATQEVDELIGSVEESVAETV-AEIDRMREQVDE 697
                                       3444444444444444444444444444432.224444444444 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.03
                           DUF2203   5 leeAnalLpllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeiee 71 
                                       +eeAna ++ +++ ++e +++ +++ ++++e +e+++e++ ++   a++++e ++  + +++ ++ ++e
  gi|336253098|ref|YP_004596205.1| 716 VEEANAGVQSINDATDEQARASERVVTMVDEATEISEETKDETenVAAAAEEQTATVSDVSAGTQSLTE 784
                                       79****************************999999998766655444455555555555555555555 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.6    0.0018      0.75      58     109 ..     399     450 ..     394     458 .. 0.88
   2 ?    9.1   7.1    0.0031       1.3      15     124 ..     497     609 ..     484     632 .. 0.45
   3 ?    6.5   7.1      0.02       8.2       5     114 ..     585     697 ..     581     701 .. 0.85
   4 ?    3.5   6.7      0.17        71       2      91 ..     715     804 ..     714     814 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0018
                        TPR_MLP1_2  58 elqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelsele 109
                                       +l+++r el+++ ++++  ka+ae+ k+e +e++ + e+  e+le++ +e+ 
  gi|336253098|ref|YP_004596205.1| 399 SLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEFG 450
                                       78999**********************************9999999998875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0031
                        TPR_MLP1_2  15 eekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesa...kaele 88 
                                       + +e+ ++  + +   +e+ ++   e  ++ e+  +  a++++  +++  e+n+l a+++e+ + a+++   +++ +
  gi|336253098|ref|YP_004596205.1| 497 DLAEDVDRVSADVTGRVEEIERASGEVSESAEEIATATADQSDRFREVYGEMNDLSATVEEIASTADDVasvSETAA 573
                                       44444444444444444444444444444444444444444444444444444444444444444433300023333 PP

                        TPR_MLP1_2  89 eseesweeqkeelekelselekriedlneqNklLhd 124
                                             +e   e+++e++ le r ++++eq + L +
  gi|336253098|ref|YP_004596205.1| 574 DRADDASEATGEIRTEMDRLEDRADEITEQVAQLDE 609
                                       333344444445555555555555555555433333 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.02
                        TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreel...nelkaeiaelka 78 
                                       + ++e+++l+++++e ++++++l e++ + +ei+    +  e+  ++  +++ e + + ee    + + +e+++l +
  gi|336253098|ref|YP_004596205.1| 585 EIRTEMDRLEDRADEITEQVAQLDEEMDQIREIVDLIDDIAEQTNLLALNASIEAAGAGEEGdgfAVVANEVKSLAE 661
                                       6789*********************************9999987666655555555555553333999999999999 PP

                        TPR_MLP1_2  79 eaesakaeleeseesweeqkeelekelselekried 114
                                       e  +a++e++e   s ee   e   e++ +++++++
  gi|336253098|ref|YP_004596205.1| 662 ETGEATQEVDELIGSVEESVAETVAEIDRMREQVDE 697
                                       999************************999999998 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.17
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       +++++++ ++s+++  +e++++ + + + + + +ei +e ++  e+     +e++ +++++ +  ++l++ + +l++
  gi|336253098|ref|YP_004596205.1| 715 QVEEANAGVQSINDATDEQARASERVVTMVDEATEISEETKDETENVAAAAEEQTATVSDVSAGTQSLTEMADDLRT 791
                                       67888899999999999999999999999*************9999999999************************* PP

                        TPR_MLP1_2  79 eaesakaeleese 91 
                                       ++++     ee e
  gi|336253098|ref|YP_004596205.1| 792 SLDAFDVGSEERE 804
                                       *999888777776 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       5.1   2.1e+03      11      31 ..     484     504 ..     473     507 .. 0.78
   2 ?    3.4   0.0      0.17        68       3      34 ..     539     570 ..     538     573 .. 0.89
   3 ?    4.6   0.4     0.068        28       4      34 ..     596     626 ..     593     629 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.1
                         DASH_Dam1  11 sletLdknledLqqihesLsd 31 
                                        le+L++ + d+q++ e++++
  gi|336253098|ref|YP_004596205.1| 484 MLEDLEATIVDIQDLAEDVDR 504
                                       578999999999999888876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.17
                         DASH_Dam1   3 pafaeLaDsletLdknledLqqihesLsdfNe 34 
                                       ++f+e   ++++L++ +e++ ++ +++++++e
  gi|336253098|ref|YP_004596205.1| 539 DRFREVYGEMNDLSATVEEIASTADDVASVSE 570
                                       57999999***************999998887 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.068
                         DASH_Dam1   4 afaeLaDsletLdknledLqqihesLsdfNe 34 
                                       +  e+++++++Ld+ ++++ +i + ++d  e
  gi|336253098|ref|YP_004596205.1| 596 RADEITEQVAQLDEEMDQIREIVDLIDDIAE 626
                                       55799999***********999998888766 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1       0.7   2.9e+02      32     117 ..     392     490 ..     386     495 .. 0.53
   2 ?    8.3   0.4    0.0053       2.2      18      99 ..     481     560 ..     465     571 .. 0.76
   3 ?    5.7   1.7     0.034        14      22      90 ..     548     621 ..     535     640 .. 0.54
   4 ?    4.9   0.4     0.063        26      36      92 ..     652     711 ..     648     731 .. 0.70
   5 ?   -0.5   1.3       2.9   1.2e+03      77     101 ..     748     772 ..     699     799 .. 0.43

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.7
                      Baculo_PEP_C  32 ilaqlatlldaietqLnalsedlksllaeldt..........rldtlltnLtdalnalq....dtlrneLt.nlnsi 93 
                                       + +ql   l+++ ++L++  +dl+++ a+ ++          + + l+++L+++ +++     d+   + t  l+ +
  gi|336253098|ref|YP_004596205.1| 392 VPGQLGDSLETMRRELESYIDDLEASKADAEAskeeaaearrEAERLAERLERKAAEFGdvmnDAAAGDFTrRLDED 468
                                       55677777777777777777777776666666555555555544444455554444444222233333333234555 PP

                      Baculo_PEP_C  94 ltnLlssvtNinstLnnllqalnn 117
                                       + n +  ++ i ++ n++l++l++
  gi|336253098|ref|YP_004596205.1| 469 VDNEA--LAEIATAFNGMLEDLEA 490
                                       55433..55555555555555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0053
                      Baculo_PEP_C  18 LtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsil 94 
                                       ++ +L+++ +  v i  +la+++d +   ++   e++++++ e+++  ++ +t+  d+  ++  ++  e++ l + +
  gi|336253098|ref|YP_004596205.1| 481 FNGMLEDLEATIVDI-QDLAEDVDRVSADVTGRVEEIERASGEVSESAEEIATATADQSDRFR-EVYGEMNDLSATV 555
                                       577888888888888.88999999999988888888888888888877777777777777776.5566666666666 PP

                      Baculo_PEP_C  95 tnLls 99 
                                        +++s
  gi|336253098|ref|YP_004596205.1| 556 EEIAS 560
                                       66665 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.034
                      Baculo_PEP_C  22 LnairlqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalq...dtlrneLtnl 90 
                                       +n++ +   +i a  a +++++ ++  + ++d +++  e++t   rl++ ++++t+++++l    d++r+  + +
  gi|336253098|ref|YP_004596205.1| 548 MNDLSATVEEI-ASTADDVASVSETAADRADDASEATGEIRTemdRLEDRADEITEQVAQLDeemDQIREIVDLI 621
                                       44443333333.444444444444444444444445555555555677777777777777775555555544444 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.063
                      Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlns 92 
                                       +a+ +++++++ ++ ++++ +l+ ++++ ++++++++++   ++      ++  ++++++
  gi|336253098|ref|YP_004596205.1| 652 VANEVKSLAEETGEATQEVDELIGSVEESVAETVAEIDRMREQVDegtAVVDDGIEAIDA 711
                                       678888888888999999999999999999999999988888887665334444444433 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 2.9
                      Baculo_PEP_C  77 nalqdtlrneLtnlnsiltnLlssv 101
                                        +++++ + e +n+ +   + ++ v
  gi|336253098|ref|YP_004596205.1| 748 TEISEETKDETENVAAAAEEQTATV 772
                                       2233333333333333333222222 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  10.4     0.009       3.7      71     218 ..     492     615 ..     386     628 .. 0.40
   2 ?    4.0   6.6     0.055        22      59     206 ..     622     792 ..     616     804 .. 0.44

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.009
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXX CS
                              AIP3  71 iepldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrdLavl 147
                                       i  ++++ + +d+  a+++ +++e++++  + ++s++e+++ +++++ +  +   ++++l+a ++e+ s   d+a++
  gi|336253098|ref|YP_004596205.1| 492 IVDIQDLAEDVDRVSADVTGRVEEIERASGEVSESAEEIATATADQSDRFREVYGEMNDLSATVEEIASTADDVASV 568
                                       12233333333333333333333333333222222222222222222222222222344444444444444444444 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 148 rqlysefkseikeslselrekakkvkeaslastkkssnrayiekgkkkLseesdklvtkvddLqDlvedlr 218
                                        ++ ++  ++ +e   e+r+++++++                        +++d++ ++v  L+  ++++r
  gi|336253098|ref|YP_004596205.1| 569 SETAADRADDASEATGEIRTEMDRLE------------------------DRADEITEQVAQLDEEMDQIR 615
                                       44444444444444444444444444........................333333333333333333333 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.055
                                       XXXXXXX.XXXXX..................XXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXX CS
                              AIP3  59 sdvkdrs.vLsLn..................iepldevkkhideslaslskelkelkssiesqkaslqevserqeea 116
                                       +d+ +++ +L Ln                   ++++++ ++  e ++++ + + ++++s+ ++ a++++++e+  e 
  gi|336253098|ref|YP_004596205.1| 622 DDIAEQTnLLALNasieaagageegdgfavvANEVKSLAEETGEATQEVDELIGSVEESVAETVAEIDRMREQVDEG 698
                                       55555443666776666666666666655443344444444444555555555555555555555555544444444 PP

                                       XXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........XXXX.XXXXXXH CS
                              AIP3 117 akekaseslakkelkaqlkevqslrrdLavlrqlysefkseikeslselrekakkvk........easlastkkssn 185
                                       ++   + +      +a  ++v++ +  ++++    +e+ +  +  ++ + e a+++         +++ a  +++++
  gi|336253098|ref|YP_004596205.1| 699 TAVVDDGIE---AIDAIAEQVEEANAGVQSINDATDEQARASERVVTMVDE-ATEISeetkdeteNVAAAAEEQTAT 771
                                       444433322...344444444444445555544444433333333332222.2222212222222222233333444 PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 186 rayiekgkkkLseesdklvtk 206
                                        + +++g ++L e +d+l t 
  gi|336253098|ref|YP_004596205.1| 772 VSDVSAGTQSLTEMADDLRTS 792
                                       444455555555555544444 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 ?    9.7   2.2    0.0013      0.51      16     118 ..     471     573 ..     463     583 .. 0.94
   2 ?    0.3   0.3      0.93   3.8e+02      38      75 ..     591     628 ..     584     696 .. 0.66
   3 ?   -1.6   0.0       3.6   1.5e+03      22      66 ..     652     696 ..     647     711 .. 0.79
   4 ?    6.1   4.4     0.016       6.6      39     132 ..     704     793 ..     696     802 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                         Mce4_CUP1  16 natLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveq 92 
                                       n+ L  +a+A++G  e l  +++d++++ +++++   +++  ++e+++++   +++a+++ +a ++ +   r +  +
  gi|336253098|ref|YP_004596205.1| 471 NEALAEIATAFNGMLEDLEATIVDIQDLAEDVDRVSADVTGRVEEIERASGEVSESAEEIATATADQSDRFREVYGE 547
                                       778999*********************************************************************** PP

                         Mce4_CUP1  93 qaeLdalllaavglsntgadllerng 118
                                        ++L+a + +++++++++a++ e+  
  gi|336253098|ref|YP_004596205.1| 548 MNDLSATVEEIASTADDVASVSETAA 573
                                       *****************999877665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.93
                         Mce4_CUP1  38 tdlnevLdelNprlpqlredireladladvYadaapdl 75 
                                       ++l++  de+ +++ ql e++ ++ ++ d+ +d+a++ 
  gi|336253098|ref|YP_004596205.1| 591 DRLEDRADEITEQVAQLDEEMDQIREIVDLIDDIAEQT 628
                                       56666677777888888888888888888888877764 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.6
                         Mce4_CUP1  22 vaeALeGrGerlGesltdlnevLdelNprlpqlredireladlad 66 
                                       va+ ++ + e+ Ge++++++e++  +++++ +  ++i ++ +  d
  gi|336253098|ref|YP_004596205.1| 652 VANEVKSLAEETGEATQEVDELIGSVEESVAETVAEIDRMREQVD 696
                                       677788888999**********99999999888888887776555 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.016
                         Mce4_CUP1  39 dlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsntgadlle 115
                                       d+ e +d++ ++++++++ +++++d++d  a a++ +++++d+a+  s+  +++ ++++a+  + + + +++    +
  gi|336253098|ref|YP_004596205.1| 704 DGIEAIDAIAEQVEEANAGVQSINDATDEQARASERVVTMVDEATEISEETKDETENVAAAAEEQTATVSDV----S 776
                                       556789999****************************************99**9999999988776655443....3 PP

                         Mce4_CUP1 116 rngdnLirlaadlrptl 132
                                       ++ ++L+++a+dlr  l
  gi|336253098|ref|YP_004596205.1| 777 AGTQSLTEMADDLRTSL 793
                                       45556666666666555 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3      0.32   1.3e+02       8      61 ..     397     450 ..     394     497 .. 0.72
   2 ?    9.8   0.3     0.001      0.41       4      87 ..     541     623 ..     538     635 .. 0.84
   3 ?    1.5   0.2      0.35   1.4e+02      13      87 ..     655     728 ..     647     739 .. 0.61
   4 ?    2.1   1.6      0.23        92      19      85 ..     710     775 ..     667     782 .. 0.56
   5 ?    2.6   1.1      0.16        64      24      87 ..     715     777 ..     706     810 .. 0.49

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.32
                             TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk 61 
                                        +++++++ + ++y+ +le  ++  ++ ++e+++ ++++++l ++l++  ++ +
  gi|336253098|ref|YP_004596205.1| 397 GDSLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEFG 450
                                       566777777888888899999999999999999999999999999988777754 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.001
                             TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80 
                                       ++e+  e+++l++t +e+ ++ +++++  ++ + +++  ++   e+++++++l+ ++ +e  e+v++l+ee++++++
  gi|336253098|ref|YP_004596205.1| 541 FREVYGEMNDLSATVEEIASTADDVASVSETAADRADDASEATGEIRTEMDRLEDRA-DEITEQVAQLDEEMDQIRE 616
                                       567788999999999999999999999999999999999999999999999999996.6888999999999999999 PP

                             TMPIT  81 vlkeves 87 
                                       +++ +++
  gi|336253098|ref|YP_004596205.1| 617 IVDLIDD 623
                                       8875554 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.35
                             TMPIT  13 eleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeves 87 
                                       e+++ a+e  + ++e+ +l+ ++ +++++   ++ ++++++++ ++ v ++  e+++ ++e+++e+++ ++++++
  gi|336253098|ref|YP_004596205.1| 655 EVKSLAEETGEATQEVDELIGSVEESVAETVAEIDRMREQVDEGTAVV-DDGIEAIDAIAEQVEEANAGVQSIND 728
                                       333344444555555555666666666666666666666666655443.57777888888888888777776655 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.23
                             TMPIT  19 keykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkev 85 
                                       + + +++ee ++  +++  ++++q +  +++ +++++ ++  +ee+++e+e++++  +e+++++++v
  gi|336253098|ref|YP_004596205.1| 710 DAIAEQVEEANAGVQSINDATDEQARASERVVTMVDEATEI-SEETKDETENVAAAAEEQTATVSDV 775
                                       33444555555555555555555555555555555544433.4555566666666666666555555 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.16
                             TMPIT  24 kleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeves 87 
                                       ++ee ++  +++  ++++q +  +++ +++++ ++  +ee+++e+e++++  +e+++++++v++
  gi|336253098|ref|YP_004596205.1| 715 QVEEANAGVQSINDATDEQARASERVVTMVDEATEI-SEETKDETENVAAAAEEQTATVSDVSA 777
                                       444444444444444444444444444444443332.334444444444444444444444332 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.93   3.8e+02       9      24 ..      62      77 ..      60     122 .. 0.86
   2 ?    0.1   0.1       2.7   1.1e+03      39      70 ..     406     441 ..     389     455 .. 0.49
   3 ?    3.6   0.3      0.23        95       3      97 ..     439     528 ..     437     543 .. 0.54
   4 ?    3.3   0.1      0.28   1.1e+02      27      82 ..     486     545 ..     470     569 .. 0.48
   5 ?   10.6   1.4    0.0014      0.59      20     100 ..     527     608 ..     522     613 .. 0.85
   6 ?    5.3   0.8     0.068        28      26      99 ..     660     733 ..     652     738 .. 0.86
   7 ?    0.4   0.3       2.3   9.4e+02      59     103 ..     749     793 ..     733     795 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.93
                                      HHHHHHHHHHHHHHHH CS
                          Spectrin  9 dadeleeWieekeell 24
                                      +a+++ +Wi+ +ee +
  gi|336253098|ref|YP_004596205.1| 62 EANDFADWIDSQEESV 77
                                      799*********9987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.7
                                       HHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                          Spectrin  39 llk....khkaleaelaaqqervkalnelaekllde 70 
                                        l+    +++a +a+ +a +e+  +    ae+l+++
  gi|336253098|ref|YP_004596205.1| 406 ELEsyidDLEASKADAEASKEEAAEARREAERLAER 441
                                       222222244444444444444444444444444333 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTTHTTHHHH CS
                          Spectrin   3 lqqfaqdadeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaekl.ldeghsaseei 78 
                                        ++++++a+e+ + ++++ +   +++l +d+++ +al +  +a+   l++ +  + ++++lae++        s+++
  gi|336253098|ref|YP_004596205.1| 439 AERLERKAAEFGDVMNDAAAGDFTRRLDEDVDN-EALAEIATAFNGMLEDLEATIVDIQDLAEDVdR-----VSADV 509
                                       567788888888888887443334444444433.555555555555555555555555555555521.....13445 PP

                                       HHHHHHHHHHHHHHHHHHH CS
                          Spectrin  79 eerleelnerWeeLkelaa 97 
                                       + r+ee++++  e++e a+
  gi|336253098|ref|YP_004596205.1| 510 TGRVEEIERASGEVSESAE 528
                                       5555555544444444443 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.28
                                       SSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHTTHTTHHHHHHHH CS
                          Spectrin  27 edlgkdleevqallkkhkaleaelaaqqervkaln....elaeklldeghsaseeieerl 82 
                                       edl+ ++ ++q+l ++ +++ a+++ + e++++      e ae+++++  ++s++ +e  
  gi|336253098|ref|YP_004596205.1| 486 EDLEATIVDIQDLAEDVDRVSADVTGRVEEIERASgevsESAEEIATATADQSDRFREVY 545
                                       334444445555555555555555544444444444444444444444333333333332 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.0014
                                       HHHHH.CCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  20 keell.ssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkel 95 
                                       +ee++ ++ d +    ev   ++++ a  +e+a+  + v ++ e+a + +d   +a+ ei++ ++ l++r +e+ e+
  gi|336253098|ref|YP_004596205.1| 527 AEEIAtATADQSDRFREVYGEMNDLSATVEEIASTADDVASVSETAADRADDASEATGEIRTEMDRLEDRADEITEQ 603
                                       5566634455577788888889999999***********************************************99 PP

                                       HHHHH CS
                          Spectrin  96 aaerk 100
                                       +a+ +
  gi|336253098|ref|YP_004596205.1| 604 VAQLD 608
                                       99765 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.068
                                       CSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  26 sedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaer 99 
                                        e+ g+  +ev +l+   ++  ae  a+ +r+++  + +++++d g +a ++i e++ee n   +++ ++++e+
  gi|336253098|ref|YP_004596205.1| 660 AEETGEATQEVDELIGSVEESVAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEEANAGVQSINDATDEQ 733
                                       57888999999999999999999999999999999999999999999999999999999999999999988876 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  59 alnelaeklldeghsaseeieerleelnerWeeLkelaaerkqkL 103
                                       ++ e  ++ +++   a+ee +++++++    ++L e+a++ + +L
  gi|336253098|ref|YP_004596205.1| 749 EISEETKDETENVAAAAEEQTATVSDVSAGTQSLTEMADDLRTSL 793
                                       344444444555577778888888888888888888887766666 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       3.9   1.6e+03      60      83 ..     400     423 ..     388     457 .. 0.51
   2 ?    7.0   4.0     0.015       5.9      17     141 ..     485     606 ..     468     632 .. 0.64
   3 ?   11.9   0.8   0.00043      0.18      68     121 ..     653     706 ..     649     708 .. 0.88
   4 ?    5.0   9.2     0.059        24      49     144 ..     691     790 ..     689     792 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.9
                         ApoLp-III  60 lkevkkkieetadklseenPevkk 83 
                                       l+ ++ ++e   d+l++++++++ 
  gi|336253098|ref|YP_004596205.1| 400 LETMRRELESYIDDLEASKADAEA 423
                                       444444444444444443222221 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.015
                         ApoLp-III  17 lpsqeevvetiKensenlvdqlkqvikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQ 93 
                                       l + e +   i++ +e  vd++++      ee+ ++s+e+ e+ +e+ ++ +   d ++e   e++  ++++ e++ 
  gi|336253098|ref|YP_004596205.1| 485 LEDLEATIVDIQDLAED-VDRVSADVTGRVEEIERASGEVSESAEEIATATADQSDRFREVYGEMN-DLSATVEEIA 559
                                       44555566666655554.455555555556788888888888888888888888888888444443.3444444444 PP

                         ApoLp-III  94 sgvqslvkesqklaeslkensqeakeklakaikqayddaveaaqklak 141
                                       s    +++ s+++a +  ++++ea+ ++++ +  + d a e ++++a+
  gi|336253098|ref|YP_004596205.1| 560 STADDVASVSETAADR-ADDASEATGEIRTEMDRLEDRADEITEQVAQ 606
                                       4444444444444444.4555667777888888888888777777764 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00043
                         ApoLp-III  68 eetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslkensqeakekl 121
                                       ++ +++l ee  e++++++el  +v ++v ++v e + + e+++e ++ + +++
  gi|336253098|ref|YP_004596205.1| 653 ANEVKSLAEETGEATQEVDELIGSVEESVAETVAEIDRMREQVDEGTAVVDDGI 706
                                       566889999**********************************99988887766 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.059
                         ApoLp-III  49 lkkksdeleealkevkkkieetadklseenPevk..kkaqelqekvQsgvqslvkesqklaeslkensqeakeklak 123
                                       + ++ de + ++++  ++i  +a++++e+n++v+    a++ q+   ++v ++v e+ ++ e+ k++++++ +  ++
  gi|336253098|ref|YP_004596205.1| 691 MREQVDEGTAVVDDGIEAIDAIAEQVEEANAGVQsiNDATDEQARASERVVTMVDEATEISEETKDETENVAAAAEE 767
                                       56677888899*********************99334778888889999********************99999999 PP

                         ApoLp-III 124 aikqaydda..veaaqklakqLk 144
                                        +  ++d    +++++++a+ L+
  gi|336253098|ref|YP_004596205.1| 768 QTATVSDVSagTQSLTEMADDLR 790
                                       88888886522567777777665 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 ?    2.9   0.1      0.27   1.1e+02      22     125 ..     396     502 ..     394     508 .. 0.63
   2 ?    1.9   0.0      0.57   2.3e+02      30      72 ..     478     520 ..     471     543 .. 0.44
   3 ?    7.4   1.4     0.012       4.8      37     123 ..     541     622 ..     527     638 .. 0.52
   4 ?    1.7   0.1      0.65   2.6e+02      78     113 ..     662     697 ..     651     715 .. 0.66
   5 ?    2.0   2.9      0.55   2.2e+02      29      99 ..     677     742 ..     667     796 .. 0.51

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.27
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHCCCHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkd.....ndnvikksskeleeeilrl 93 
                                       l d l++++++++  +++le + ++++ s++ea e  +e +   ++ ++++++     nd +  +++++l+e++   
  gi|336253098|ref|YP_004596205.1| 396 LGDSLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEfgdvmNDAAAGDFTRRLDEDV--- 469
                                       56778888899999999999999998888888888877766665555555555555556777777777777433... PP

                                       HHHHHCCH.HHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  94 ketidaqe.snirvLqnvlesneqkiqkLeqdi 125
                                       +++  a++ +  + + + le+  ++iq+L +d+
  gi|336253098|ref|YP_004596205.1| 470 DNEALAEIaTAFNGMLEDLEATIVDIQDLAEDV 502
                                       333333333444444555555555556665555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.57
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqksk 72 
                                        + ++  le+le ++ +i++  +++++++ +++  ++e ++ +
  gi|336253098|ref|YP_004596205.1| 478 ATAFNGMLEDLEATIVDIQDLAEDVDRVSADVTGRVEEIERAS 520
                                       4444444444444444444444444444444443333333332 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.012
                                       HCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHH CS
                         Fib_alpha  37 lekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvles 113
                                        +++  e++++s + +e+ ++  ++ ++ + +   ++d ++++ ++++e++ + ++  ++i++q+ ++    + +++
  gi|336253098|ref|YP_004596205.1| 541 FREVYGEMNDLSATVEEIASTADDVASVSETAADRADDASEATGEIRTEMD-RLEDRADEITEQVAQLD---EEMDQ 613
                                       455555566666666666666666666666666666666666666666666.44444444443333333...33222 PP

                                       HHHHHHHHHH CS
                         Fib_alpha 114 neqkiqkLeq 123
                                         ++i +L  
  gi|336253098|ref|YP_004596205.1| 614 I-REIVDLID 622
                                       2.22333333 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHH CS
                         Fib_alpha  78 vikksskeleeeilrlketidaqesnirvLqnvles 113
                                        + + ++e++e i  ++e++ +++ +i  +++ +++
  gi|336253098|ref|YP_004596205.1| 662 ETGEATQEVDELIGSVEESVAETVAEIDRMREQVDE 697
                                       455666666666666777777777777666666654 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.55
                                       CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHC CS
                         Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketida 99 
                                       +e++v ++++++ +  e++ + t  +++ +++i+ + ++ ++ +++    ++++++  + e++r  e++++
  gi|336253098|ref|YP_004596205.1| 677 VEESVAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEEANAG----VQSINDATD-EQARASERVVT 742
                                       5555555555555555555555555555555554444333333332....222222222.22222222222 PP

>> Dor1  Dor1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.73     3e+02      62     114 ..     400     454 ..     363     513 .. 0.51
   2 ?    4.8   2.6     0.023       9.4      43      81 ..     578     616 ..     466     636 .. 0.69
   3 ?    6.1   1.4    0.0091       3.7       6      90 ..     667     759 ..     663     784 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.73
                              Dor1  62 ledLvlklpkLteectrfskkaeeisek....rkenkllldkheqllellelPqlmd 114
                                       le+++ +l+      + ++++ae + e+    r+e++ l ++ e+     e + +m+
  gi|336253098|ref|YP_004596205.1| 400 LETMRRELESYIDDLEASKADAEASKEEaaeaRREAERLAERLERK--AAEFGDVMN 454
                                       3333333333333333333333333333222255554444444432..234444444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.023
                              Dor1  43 daaealeairqelediraqledLvlklpkLteectrfsk 81 
                                       da ea+ +ir+e++++++  +++ +++ +L+ee+ ++++
  gi|336253098|ref|YP_004596205.1| 578 DASEATGEIRTEMDRLEDRADEITEQVAQLDEEMDQIRE 616
                                       334455556666666666666666666666655544433 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0091
                              Dor1   6 skpleelek.epelLaeeaeeilaqiqdLarknyktlidaa.ealeairqelediraqledLvlkl...pkLteect 77 
                                       +++++el   + e++ae+ +ei++ + +++ +   +++d + ea++ai +++e+ +a ++++ + +    + +e ++
  gi|336253098|ref|YP_004596205.1| 667 TQEVDELIGsVEESVAETVAEIDRMREQVDEGT--AVVDDGiEAIDAIAEQVEEANAGVQSINDATdeqARASERVV 741
                                       5667777655899***************99875..5555543999***************99999943345677888 PP

                              Dor1  78 rfskkaeeisek.....r 90 
                                        ++++a+eise+      
  gi|336253098|ref|YP_004596205.1| 742 TMVDEATEISEEtkdetE 759
                                       8899*******9654322 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2         5     2e+03      26      69 ..     402     445 ..     398     453 .. 0.72
   2 ?    7.5   0.0     0.016       6.6      15      96 ..     539     618 ..     529     623 .. 0.84
   3 ?   -0.6   0.1       5.5   2.2e+03      28      71 ..     713     749 ..     706     771 .. 0.50

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 5
                      Occludin_ELL  26 elhaeleevskkfseLerelkelkegskeykkieeeilqeykkl 69 
                                       ++ +ele++ ++++  +++ +++ke+  e ++ +e++ ++++++
  gi|336253098|ref|YP_004596205.1| 402 TMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERK 445
                                       46677777777777777778877777777777777777777665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.016
                      Occludin_ELL  15 aeFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLsh 91 
                                       + F++ Y e ++l a +ee++++  ++ +  ++++++ +  ++++ ei  e  +l+   +  e  +++ +L e+++ 
  gi|336253098|ref|YP_004596205.1| 539 DRFREVYGEMNDLSATVEEIASTADDVASVSETAADRADDASEATGEIRTEMDRLE--DRADEITEQVAQLDEEMDQ 613
                                       57999999999999999999999999999999999999999999999999999995..4555666778888888888 PP

                      Occludin_ELL  92 iKkli 96 
                                       i++ +
  gi|336253098|ref|YP_004596205.1| 614 IREIV 618
                                       87766 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 5.5
                      Occludin_ELL  28 haeleevskkfseLerelkelkegskeykkieeeilqeykklkk 71 
                                        +++ee+++ ++ +++ ++e+++ s+       +++    + ++
  gi|336253098|ref|YP_004596205.1| 713 AEQVEEANAGVQSINDATDEQARASE-------RVVTMVDEATE 749
                                       34444445555555555555444444.......44433333332 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 ?    6.3   0.9     0.024       9.6      31     104 ..     396     469 ..     391     493 .. 0.83
   2 ?    8.6   1.4    0.0046       1.9       8     126 ..     495     612 ..     489     651 .. 0.55
   3 ?    0.4   3.9       1.6   6.4e+02      36     118 ..     675     758 ..     652     798 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.024
                             Mod_r  31 lkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspdallarLqtav 104
                                       l +++e ++ e es  ++  +++ + e  ++e +e++ e+++l +++e+k +e  +++++       +rL + v
  gi|336253098|ref|YP_004596205.1| 396 LGDSLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEFGDVMNDAAAGDFTRRLDEDV 469
                                       56678889999999999888889999999999999999999999999999999988887777776666666655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0046
                             Mod_r   8 Lqelledeeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqel 84 
                                       +q+l ed + ++a v  + +v++++ +  e+ ++ e++a +  ++ ++++e+  e+++   +++e+ ++ ++  +  
  gi|336253098|ref|YP_004596205.1| 495 IQDLAEDVDRVSADV--TGRVEEIERASGEVSESAEEIATATADQSDRFREVYGEMNDLSATVEEIASTADDVASVS 569
                                       566666666666655..355666666666666666666666666666555555555555555555555555555555 PP

                             Mod_r  85 dellqkfspd.allarLqtavaeaeeeSealaeeflegeield 126
                                       +++ ++ +++  +    +t++++ e+ ++++ e++ + ++e+d
  gi|336253098|ref|YP_004596205.1| 570 ETAADRADDAsEATGEIRTEMDRLEDRADEITEQVAQLDEEMD 612
                                       5555444444234444555555555555555555443333332 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.6
                             Mod_r  36 eellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspd.allarLqtavaeaeeeS 111
                                        +++++  ++  +    +++++e  + + + +e ++++ +++ee ++  +++ + ++++  + +r+ t v+ea e S
  gi|336253098|ref|YP_004596205.1| 675 GSVEESVAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEEANAGVQSINDATDEQaRASERVVTMVDEATEIS 751
                                       33333333332322233556666666677777778888888888888888888777776346667777777777777 PP

                             Mod_r 112 ealaeef 118
                                       e+  +e 
  gi|336253098|ref|YP_004596205.1| 752 EETKDET 758
                                       7766654 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 ?    7.3   1.4     0.013       5.5      46     101 ..     398     453 ..     394     455 .. 0.89
   2 ?   -0.1   0.1       2.6   1.1e+03      53      92 ..     471     511 ..     468     532 .. 0.69
   3 ?    2.1   0.1      0.54   2.2e+02      70     103 ..     521     554 ..     486     573 .. 0.48
   4 ?    8.9   1.4    0.0042       1.7      29     100 ..     539     614 ..     534     621 .. 0.72
   5 ?    1.5   2.9      0.83   3.4e+02      31      92 ..     656     718 ..     646     738 .. 0.39
   6 ?    1.5   6.2      0.81   3.3e+02      40     102 ..     711     773 ..     679     777 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  46 eelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                       ++l + r el   I  + ++k+dae+ ++e++e   e ++l ++l+   ae+ +++
  gi|336253098|ref|YP_004596205.1| 398 DSLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEFGDVM 453
                                       6778889999999999****************************999999987766 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.6
                                       HHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  53 NelskeIgkakkkk.edaeeliaevkelkeelkaleaelke 92 
                                       Ne+ +eI+ a +   ed e+ i ++++l e++++++a+++ 
  gi|336253098|ref|YP_004596205.1| 471 NEALAEIATAFNGMlEDLEATIVDIQDLAEDVDRVSADVTG 511
                                       66667777777644777777777777777777777766554 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.54
                                       CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                      Seryl_tRNA_N  70 eeliaevkelkeelkaleaelkeleaelekllla 103
                                        e+ ++++e+ + +++ +++ +e+  e+++l ++
  gi|336253098|ref|YP_004596205.1| 521 GEVSESAEEIATATADQSDRFREVYGEMNDLSAT 554
                                       2233333444444444444444444444444333 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0042
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekl 100
                                       d++ e++ ++  l +++ee+ +    ++   + a ++     e + e++ e++ l ++ +++++++++l++e++++
  gi|336253098|ref|YP_004596205.1| 539 DRFREVYGEMNDLSATVEEIASTADDVASVSETAADRAddasEATGEIRTEMDRLEDRADEITEQVAQLDEEMDQI 614
                                       566666666666666666666666655544444443334456888899999********************99987 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.83
                                       HHHHHHHHHHHHHHHHHHH.HHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  31 lleldekrrelqveleelq.aerNelskeIgkakkkkedaeeliaevkelkeelkaleaelke 92 
                                       + +l e+  e+ +e++el  +   +++++++++ +  e+ +e  a v++  e ++a+ ++++e
  gi|336253098|ref|YP_004596205.1| 656 VKSLAEETGEATQEVDELIgSVEESVAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEE 718
                                       333333333333333333212222333333333333333333333333333333333333332 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.81
                                       HHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Seryl_tRNA_N  40 elqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklll 102
                                       ++  ++ee++a   +++ +  +  ++ e    +++e+ e++ee+k+ +++++++ +e+++ ++
  gi|336253098|ref|YP_004596205.1| 711 AIAEQVEEANAGVQSINDATDEQARASERVVTMVDEATEISEETKDETENVAAAAEEQTATVS 773
                                       45556677777777777777777777799999*******************999999987765 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.3      0.25     1e+02       6     104 ..     352     453 ..     348     458 .. 0.71
   2 ?    5.1   0.1     0.038        16      31     115 ..     473     556 ..     462     559 .. 0.81
   3 ?    5.9   0.7     0.023       9.3       3      75 ..     543     614 ..     538     620 .. 0.65
   4 ?    7.7   1.7    0.0061       2.5       5      94 ..     653     742 ..     649     749 .. 0.87
   5 ?    1.7   0.3      0.43   1.7e+02      14      79 ..     743     807 ..     736     816 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.25
                          Syntaxin   6 keveeikkeiekleeevkklkkqneesktstraksvklkkrmesdikeikkraesvkarLeaLdksnkenekksgeg 82 
                                       +ev ++++  e +++ +    +q + +  +   +    ++   ++ ++ ++  +++++ ++ L+ s +++e++++e+
  gi|336253098|ref|YP_004596205.1| 352 DEVGQVRTAFEGIRQYLGTAAAQADAIARQEFDDPALERDVPGQLGDSLETMRRELESYIDDLEASKADAEASKEEA 428
                                       57777777777777777777777776666555554414444456667777888899999999999999999999898 PP

                          Syntaxin  83 savdRirksqtaaLrkk...lkevm 104
                                       + + R ++ +++ L++k   + +vm
  gi|336253098|ref|YP_004596205.1| 429 AEARREAERLAERLERKaaeFGDVM 453
                                       8899999999988887633355555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.038
                          Syntaxin  31 esktstraksvklkkrmesdikeikkraesvkarLeaLdksnkenekksgegsavdRirksqtaaLrkklkevmtey 107
                                        + +  +a++  + +++e++i +i+  ae+v +       +++e e+ sge s ++    + ta  + +++ev  e 
  gi|336253098|ref|YP_004596205.1| 473 ALAEIATAFNG-MLEDLEATIVDIQDLAEDVDRVSADVTGRVEEIERASGEVSESAEEIATATADQSDRFREVYGEM 548
                                       45555555555.78899999999999999999999999999999999999999999999999999999999999999 PP

                          Syntaxin 108 nelrekir 115
                                       n+l ++++
  gi|336253098|ref|YP_004596205.1| 549 NDLSATVE 556
                                       98887765 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.023
                          Syntaxin   3 effkeveeikkeiekleeevkklkkqneesktstraksvklkkrmesdikeikkraesvkarLeaLdksnken 75 
                                       e++ e+++++  +e++++  +++ +  e+     +  s     ++ +++++ + ra+++ +++ +Ld+++++ 
  gi|336253098|ref|YP_004596205.1| 543 EVYGEMNDLSATVEEIASTADDVASVSETAADRADDASE-ATGEIRTEMDRLEDRADEITEQVAQLDEEMDQI 614
                                       455666666666666666666666666666655555555.666777777777777777777777777776655 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0061
                          Syntaxin   5 fkeveeikkeiekleeevkklkkqneesktstraksvklkkrmesdikeikkraesvkarLeaLdksnkenekksge 81 
                                        +ev+++ +e+ + ++ev++l  + ees++ t a+  ++++++++ ++ +    e++ a  e+ +++n+  ++ + +
  gi|336253098|ref|YP_004596205.1| 653 ANEVKSLAEETGEATQEVDELIGSVEESVAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEEANAGVQSINDA 729
                                       57999************************999999999******************************999998877 PP

                          Syntaxin  82 gsavdRirksqta 94 
                                       +  ++R ++ +++
  gi|336253098|ref|YP_004596205.1| 730 TDEQARASERVVT 742
                                       7777776665554 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.43
                          Syntaxin  14 eiekleeevkklkkqneesktstraksvklkkrmesdikeikkraesvkarLeaLdksnkenekks 79 
                                        +++ +e  ++ k+++e++ ++ ++++  + +++++ +++ ++ a+++++ L+a+d  ++e e+  
  gi|336253098|ref|YP_004596205.1| 743 MVDEATEISEETKDETENVAAAAEEQTA-TVSDVSAGTQSLTEMADDLRTSLDAFDVGSEERETDG 807
                                       5555566666777778888888777777.89999999****************9999988887655 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.033        14     106     159 ..     396     449 ..     390     451 .. 0.89
   2 ?    0.3   0.0       1.1   4.6e+02     115     151 ..     496     533 ..     468     547 .. 0.60
   3 ?    3.4   0.7      0.12        51      98     142 ..     585     632 ..     566     639 .. 0.72
   4 ?   -0.2   0.1       1.6   6.6e+02     105     134 ..     665     694 ..     654     708 .. 0.59
   5 ?    4.0   1.0     0.078        32      96     156 ..     737     797 ..     714     799 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.033
                     Fzo_mitofusin 106 lcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfeeqy 159
                                       l  + +++++ele+ i++le++ +  e+ +++a   r +a++l+++Le+ ++++
  gi|336253098|ref|YP_004596205.1| 396 LGDSLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEF 449
                                       5667788999*************************************9987776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.1
                     Fzo_mitofusin 115 keleeeikelekeie.kleevqkkakllrnkasllese 151
                                       ++l e++++++++++ ++ee+++ +  + + a+++++ 
  gi|336253098|ref|YP_004596205.1| 496 QDLAEDVDRVSADVTgRVEEIERASGEVSESAEEIATA 533
                                       55666666666666436666666666666666666554 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.12
                     Fzo_mitofusin  98 elsstfarlcqqvdete...keleeeikelekeiekleevqkkakllr 142
                                       e+ + ++rl+ + de +   ++l+ee++++++ ++ ++++ ++ +ll 
  gi|336253098|ref|YP_004596205.1| 585 EIRTEMDRLEDRADEITeqvAQLDEEMDQIREIVDLIDDIAEQTNLLA 632
                                       666777777776665541115688899999998998998888888776 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.6
                     Fzo_mitofusin 105 rlcqqvdetekeleeeikelekeiekleev 134
                                       + +q+vde   ++ee+++e  +ei+++ e 
  gi|336253098|ref|YP_004596205.1| 665 EATQEVDELIGSVEESVAETVAEIDRMREQ 694
                                       445555555555555555555555555433 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.078
                     Fzo_mitofusin  96 qqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfe 156
                                        +++ +++++ ++ ++et++e e+  ++ e++ +++ +v+   + l + a  l+++L++f+
  gi|336253098|ref|YP_004596205.1| 737 SERVVTMVDEATEISEETKDETENVAAAAEEQTATVSDVSAGTQSLTEMADDLRTSLDAFD 797
                                       456777888888999999****************************************996 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.8    0.0029       1.2     334     469 ..     395     534 ..     356     556 .. 0.78
   2 ?    5.5   3.6     0.016       6.3     340     406 ..     570     638 ..     547     643 .. 0.58
   3 ?    3.6   6.9      0.06        24     324     403 ..     677     756 ..     635     767 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0029
                            DUF812 334 elqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktl.ellpdaeen..iekLqalvea 407
                                       +l + +e++++++e++ +++++ +++ +  +ee+ e ++e e+l++ ++ k   + + ++da +    ++L ++v++
  gi|336253098|ref|YP_004596205.1| 395 QLGDSLETMRRELESYIDDLEASKADAEASKEEAAEARREAERLAERLERKAAEFgDVMNDAAAGdfTRRLDEDVDN 471
                                       56778999999999999999999999999999999999999999999999876662566664443337899999997 PP

                            DUF812 408 saqrlvelakqWe...khRvplieeyrelkesksekekeaerkleeikklrekmkevaeelrqke 469
                                           l e+a+ ++   +  ++ i ++++l e  ++  ++   ++eei++   ++ e aee+++  
  gi|336253098|ref|YP_004596205.1| 472 E--ALAEIATAFNgmlEDLEATIVDIQDLAEDVDRVSADVTGRVEEIERASGEVSESAEEIATAT 534
                                       5..467777766622266677899999999999999999999*****999999999999887654 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.016
                            DUF812 340 eeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpd..aeeniekLqalve 406
                                       e++  +++  +e   ++++++ ++e+ ++e  e+ ++l +e++  + +++l++d   ++n+ +L+a +e
  gi|336253098|ref|YP_004596205.1| 570 ETAADRADDASEATGEIRTEMDRLEDRADEITEQVAQLDEEMDQIREIVDLIDDiaEQTNLLALNASIE 638
                                       333444444555555556666666666666666666666666666666666666545556666666665 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.06
                            DUF812 324 lkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniek 400
                                       +++   e ++e+ ++ e++++  + +++ i+++++  +qvee+    ++ n  + ++ +  ++++ ++++a e  e+
  gi|336253098|ref|YP_004596205.1| 677 VEESVAETVAEIDRMREQVDEGTAVVDDGIEAIDAIAEQVEEANAGVQSINDATDEQARASERVVTMVDEATEISEE 753
                                       2333333444444444455555566788899999999999999999999*******************999887666 PP

                            DUF812 401 Lqa 403
                                        + 
  gi|336253098|ref|YP_004596205.1| 754 TKD 756
                                       555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (883 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1773  (0.0988901); expected 358.6 (0.02)
Passed bias filter:                      733  (0.0408835); expected 358.6 (0.02)
Passed Vit filter:                       157  (0.00875676); expected 17.9 (0.001)
Passed Fwd filter:                       107  (0.00596798); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 1.95u 0.34s 00:00:02.29 Elapsed: 00:00:00.55
# Mc/sec: 4804.23
//
Query:       gi|336253099|ref|YP_004596206.1|  [L=349]
Description: SAICAR synthetase [Halopiger xanaduensis SH-6]
Scores for 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-25   87.7   0.0    4.3e-24   85.5   0.0    1.8  1  SAICAR_synt  SAICAR synthetase
  ------ inclusion threshold ------
      0.031   14.4   0.0      0.066   13.3   0.0    1.6  1  DUF4110      Domain of unknown function (DUF4110)


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 !   85.5   0.0   4.8e-28   4.3e-24      20     250 ..      25     284 ..      16     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 4.8e-28
                                       EEEEESEEEECCC.TEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE........................... CS
                       SAICAR_synt  20 llvakDrisAfdv.vlkeeipgKGkvltqlsafwfeklek..ipnhliksld........pe............... 70 
                                        +v++D+ s+fd+ +++++ip+KG+ l+++ a+ fe+le+  +p+h+   ++         e               
  gi|336253099|ref|YP_004596206.1|  25 SFVFTDDYSVFDWgKMPDQIPEKGASLCTMGAYNFELLESegVPTHYRGVVEhgadngenGEvvsleeassppwema 101
                                       689*********63799**********************558***98855556666665500555556667778888 PP

                                       .................-SSSEEEEE-EEEESEEEEEEEE-.-HHH.......HH....HH..T--TT-EEEEEEEE CS
                       SAICAR_synt  71 ................qlegrsmlvkklkmlpvEvvvRgyl.tGslwkeykksgkvcgirlpeglkegeklpepift 130
                                                        +++ +  + +  ++p+E+v+R+ +  Gs ++  ++ +  +g+ +++   e   l epi++
  gi|336253099|ref|YP_004596206.1| 102 idltqvpdlpnegreyDYDSYHEAAGENYLIPLEIVFRNRVpVGSSLRRRTEPAD-HGLDFESWPDEPVDLAEPIVE 177
                                       888889999999998878888888999999********97648***999888888.9****9999************ PP

                                       EEE--CCCT.S-EE-HHHHH.HTT-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--. CS
                       SAICAR_synt 131 pstKaeegehDeniseeevvealgteeeaeeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevl 207
                                       +stK eeg  D  +++ee+  ++g +++++ +e++al+v+++++e a++ g+   D K+E      +ge+ +aD v 
  gi|336253099|ref|YP_004596206.1| 178 FSTKYEEG--DRYLEREEADYIAG-TADVDALEDVALEVNRIVTEQAESAGLDHQDGKIECLYY--QGEIRVADVVG 249
                                       *******8..9********98888.88**********************************998..7********** PP

                                       STTTEEEEETTT.....GGGB-STHHHHTT-STHHHHHHHHHH CS
                       SAICAR_synt 208 tpDssRfwdaetyeegkeqeslDKqfvRdwleeveekwkekle 250
                                       t D  Rf  + t        +l K+++R++ ++++ +w + +e
  gi|336253099|ref|YP_004596206.1| 250 TFDENRFSYEGT--------QLSKEVLRQYHKRTQPEWVQAVE 284
                                       *******99888........99*********999999988765 PP

>> DUF4110  Domain of unknown function (DUF4110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.3e-06     0.066      12      46 ..     264     299 ..     258     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.3e-06
                           DUF4110  12 pgEslrdFfaRTseeWqelaieslkekgaek.kseK 46 
                                         E lr++ +RT+ eW++++ + ++e+++e+ ++ K
  gi|336253099|ref|YP_004596206.1| 264 SKEVLRQYHKRTQPEWVQAVEQAKAEAKREDvADWK 299
                                       679****************99999888776655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2712.53
//
Query:       gi|336253100|ref|YP_004596207.1|  [L=241]
Description: hypothetical protein Halxa_1696 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00013   21.4   8.0    0.00013   21.4   8.0    3.3  3  SPW             SPW repeat
  ------ inclusion threshold ------
        3.1    7.5  25.0        1.1    9.0   7.2    2.8  3  Trp_oprn_chp    Tryptophan-associated transmembrane protein (
        5.4    7.1   7.5         12    6.0   0.5    3.0  2  Fumarate_red_C  Fumarate reductase subunit C


Domain annotation for each model (and alignments):
>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.2      0.66   3.9e+03      27      27 ..      44      44 ..      26      64 .. 0.58
   2 ?    2.3   6.4     0.021   1.3e+02       2      43 ..     126     165 ..     125     169 .. 0.78
   3 !   21.4   8.0   2.2e-08   0.00013       2      45 ..     181     223 ..     180     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.66
                               SPW 27 a 27
                                      a
  gi|336253100|ref|YP_004596207.1| 44 A 44
                                      1 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.021
                               SPW   2 WanlllGlwlivSPWvlGfsattgaawnnvivGavvavLala 43 
                                       ++  ++G+++++S+ v  f+ t  + ++nv +Ga  avLa +
  gi|336253100|ref|YP_004596207.1| 126 GLTAAIGAFVMASTAV--FTITEWMGIHNVLIGATMAVLASI 165
                                       5667888888888866..456667889************975 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 2.2e-08
                               SPW   2 WanlllGlwlivSPWvlGfsattgaawnnvivGavvavLalafa 45 
                                       +++ llG+w++++P+vlG+s    ++  n ++G+++a+L+l+ a
  gi|336253100|ref|YP_004596207.1| 181 GVLALLGAWTAAAPFVLGVSRP-LVMQINGVAGVLIAILSLGSA 223
                                       7899**************7655.8899999**********9875 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 ?    9.0   7.2   0.00019       1.1      49     139 ..      27     138 ..      17     149 .. 0.70
   2 ?    6.0   6.7    0.0015         9      45      92 ..     154     201 ..     148     212 .. 0.88
   3 ?   -0.5   0.1      0.16   9.5e+02      69      92 ..     210     233 ..     204     240 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00019
                      Trp_oprn_chp  49 AlvllAaavAvlavrglgrrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaavelta........ 117
                                       A ++ A++vA  ++  ++ ++ g+l++ + +++++++ls  +d+   a+ a+++a+g ++++++ +  +        
  gi|336253100|ref|YP_004596207.1|  27 ASAIAASIVAFSLTSAIAAVASGMLTLFVLIIVGFTVLSQGSDDWGPAQPAQSSAAGSSRQHKTGKSNDkqnrtgll 103
                                       55677899999999999999999999999999999999999999999988887767766666666622244455567 PP

                      Trp_oprn_chp 118 .............wpvlalaggvllllagvllllr 139
                                                      vla  ++ l+++ g++++++
  gi|336253100|ref|YP_004596207.1| 104 drisvtgvtnrdgTIVLAERAAGLTAAIGAFVMAS 138
                                       77777889999994444444444444444444433 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0015
                      Trp_oprn_chp  45 ltalAlvllAaavAvlavrglgrrvvgvllalagagaavaalslltdp 92 
                                       l    +++lA++ A+ + +    +v++ +lal+ga++a+a++ l +++
  gi|336253100|ref|YP_004596207.1| 154 LIGATMAVLASIHALRISQDKPIIVLAGVLALLGAWTAAAPFVLGVSR 201
                                       6678899*******************************9998877665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.16
                      Trp_oprn_chp  69 vvgvllalagagaavaalslltdp 92 
                                       v gvl+a++++g a+  l+  +++
  gi|336253100|ref|YP_004596207.1| 210 VAGVLIAILSLGSAYGILQTSRSS 233
                                       567777777777777666665554 PP

>> Fumarate_red_C  Fumarate reductase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.4    0.0083        50      17      52 ..      15      50 ..      13      73 .. 0.88
   2 ?    6.0   0.5     0.002        12      39      74 ..     176     211 ..     174     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0083
                    Fumarate_red_C 17 knpfYrfYmlrEatavlvalfalvlllgllaLaqge 52
                                      +n fYr+ m   a+a+++ + a+ l+  ++a+a+g 
  gi|336253100|ref|YP_004596207.1| 15 QNTFYRASMSFTASAIAASIVAFSLTSAIAAVASGM 50
                                      578999999999999999999999999999999874 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.002
                    Fumarate_red_C  39 lvlllgllaLaqgeaayeafleflqnPlvlllniia 74 
                                       +++l+g+laL  + +a + f+  +++Plv+ +n +a
  gi|336253100|ref|YP_004596207.1| 176 IIVLAGVLALLGAWTAAAPFVLGVSRPLVMQINGVA 211
                                       6899*****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 1785.79
//
Query:       gi|336253101|ref|YP_004596208.1|  [L=135]
Description: hypothetical protein Halxa_1698 [Halopiger xanaduensis SH-6]
Scores for complete 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-29  102.6   1.2    1.9e-29  102.4   1.2    1.0  1  DUF2267   Uncharacterized conserved protein (DUF2267)


Domain annotation for each model (and alignments):
>> DUF2267  Uncharacterized conserved protein (DUF2267)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4   1.2     1e-33   1.9e-29       2     121 ..       4     123 ..       3     124 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 1e-33
                                       HHHHHHHHHHHT---HHHHHHHHHHHHHHHHTTS-HHHHHHHHTTS-HHHHHHHHTT--TTS-----SHHHHHHHHH CS
                           DUF2267   2 defleevqerlgledreeAeratravLrtLrdrlteeeaadlaaqLPeelrgllrdgwppvepgkrfdreeflerva 78 
                                       def++ vq++++le++++++ at+avL+tL++ +t++ea d+a+qLP el+ +++d+++    g+ +dreef+erv 
  gi|336253101|ref|YP_004596208.1|   4 DEFYGLVQQAGHLESTDRTQAATEAVLETLGETMTGGEAGDVAEQLPTELASVIEDADH---DGAGYDREEFVERVG 77 
                                       79*******************************************************85...4779*********** PP

                                       HTS........EHHHHHHHHHHHHHHHS-HHHHHHHHHTS-HHHHT CS
                           DUF2267  79 eelg...vdpedaeqaaraVfaalkealsegeiedvaaqLPkdlre 121
                                       e+l+    + +daeq a aV++al+ al++ge+e++++qL  +l  
  gi|336253101|ref|YP_004596208.1|  78 EHLRgadLESDDAEQYADAVTDALAVALTGGELENLKSQLDSGLHP 123
                                       ***877677888****************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 969.40
//
Query:       gi|336253102|ref|YP_004596209.1|  [L=54]
Description: hypothetical protein Halxa_1699 [Halopiger xanaduensis SH-6]
Scores for 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   15.1   0.8        1.4    9.0   0.1    2.1  2  DUF2116   Uncharacterized protein containing a Zn-ribbon (DUF
       0.11   12.6   3.0       0.32   11.1   1.8    2.1  1  YHS       YHS domain


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 ?    5.1   0.1    0.0025        22       6      14 ..      12      20 ..      10      27 .. 0.85
   2 ?    9.0   0.1   0.00016       1.4      18      29 ..      40      51 ..      35      54 .] 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0025
                           DUF2116  6 CivCGkaIp 14
                                      C vCG+++ 
  gi|336253102|ref|YP_004596209.1| 12 CRVCGTPVA 20
                                      9******86 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00016
                           DUF2116 18 sfCsekCqeeye 29
                                       fCs++C e +e
  gi|336253102|ref|YP_004596209.1| 40 YFCSDDCLETWE 51
                                      69*******998 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.8   3.6e-05      0.32      26      40 ..      39      53 ..      13      54 .] 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.6e-05
                               YHS 26 YyFcSegCkdkFede 40
                                       yFcS+ C++  e++
  gi|336253102|ref|YP_004596209.1| 39 HYFCSDDCLETWEAD 53
                                      49*******987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.52
# Mc/sec: 314.60
//
Query:       gi|336253103|ref|YP_004596210.1|  [L=57]
Description: hypothetical protein Halxa_1700 [Halopiger xanaduensis SH-6]
Scores for 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:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 429.71
//
Query:       gi|336253104|ref|YP_004596211.1|  [L=319]
Description: formyltetrahydrofolate deformylase [Halopiger xanaduensis SH-6]
Scores for complete 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  148.9   0.0    1.8e-43  148.4   0.0    1.2  1  Formyl_trans_N  Formyl transferase
    2.5e-09   37.0   0.2    5.1e-09   36.0   0.2    1.5  1  ACT_6           ACT domain
    1.6e-05   24.6   0.1    7.9e-05   22.3   0.1    2.2  2  ACT             ACT domain
    9.4e-05   22.9   0.1    0.00025   21.6   0.1    1.7  1  ACT_4           ACT domain


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 !  148.4   0.0     4e-47   1.8e-43       2     181 .]      93     267 ..      92     267 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 4e-47
                                       EEEEEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCT CS
                    Formyl_trans_N   2 kivvlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkel 78 
                                       +i+vl+++++++l+al +a  + +l+ad+ +v++n+d+++    ae+ + p++++  +k ++    e+el++ l+e+
  gi|336253104|ref|YP_004596211.1|  93 QIAVLVTKESHCLEALFEAWANDELGADIGVVIGNHDDLQ--PLAEQYDVPFHDIGDEKGRQ---NEDELIDLLEEY 164
                                       69**************************************..899**********9987655...59********** PP

                                       T-SEEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE CS
                    Formyl_trans_N  79 kadlivlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkve 155
                                        adlivla ym++l++++v +++ +i+n+HpSLLP+f+Ga+a+++al +G++++Gvt h+v+ +lD+G+i+ q + +
  gi|336253104|ref|YP_004596211.1| 165 DADLIVLARYMRILSPNVVFRYEDRIINVHPSLLPAFPGAEAYRQALDEGVRVAGVTAHYVTTDLDQGPIITQRAFD 241
                                       ***************************************************************************** PP

                                       --TT--HHHHHHHHHHHHHHHHHHHH CS
                    Formyl_trans_N 156 iiaedtkeeleqrvadaehkalveal 181
                                       +  + +++e+++r + +e  al+ea+
  gi|336253104|ref|YP_004596211.1| 242 VPDDADLDEMKRRGQPLEADALLEAV 267
                                       *********************99986 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.2   1.1e-12   5.1e-09       5      75 ..      11      83 ..      11      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.1e-12
                             ACT_6  5 itvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgped..alarlekaLlflakelgltvef 75
                                      itv+G+d +Gl+a +ts+l e g+ni D+ qav  g +   l v+ +e   +++ l+++L+ l  +lgl+v++
  gi|336253104|ref|YP_004596211.1| 11 ITVIGEDDTGLIANVTSLLFERGINIEDLDQAVRDGVFRMYLAVDTSEMvcTEETLRADLHDLGDDLGLDVKV 83
                                      9**********************************************8888*******************987 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   1.8e-08   7.9e-05       2      45 ..      10      51 ..       9      72 .. 0.80
   2 ?   -2.3   0.0      0.89     4e+03      45      61 ..     121     137 ..     116     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.8e-08
                                      EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEE CS
                               ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivf 45
                                       + v  +D  Gl+a v+++l +rgiNi+ + q+  +     ++ 
  gi|336253104|ref|YP_004596211.1| 10 EITVIGEDDTGLIANVTSLLFERGINIEDLDQAVRDGV--FRMY 51
                                      578999***************************99873..3333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.89
                                       EEEEEEEHHHHHHHHHH CS
                               ACT  45 fvvivvdeedleevlea 61 
                                       + v++++++dl+ + e+
  gi|336253104|ref|YP_004596211.1| 121 IGVVIGNHDDLQPLAEQ 137
                                       55889999999998886 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   5.5e-08   0.00025       7      55 ..       9      55 ..       8      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.5e-08
                             ACT_4  7 vrleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitve 55
                                      ++++v++ed++gl+a++t+++ e ++ni+++      +dg++++ + v 
  gi|336253104|ref|YP_004596211.1|  9 TEITVIGEDDTGLIANVTSLLFERGINIEDLDQAV--RDGVFRMYLAVD 55
                                      689********************************..589***999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2246.14
//
Query:       gi|336253105|ref|YP_004596212.1|  [L=104]
Description: hypothetical protein Halxa_1702 [Halopiger xanaduensis SH-6]
Scores for complete 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   79.5   0.5    2.2e-22   79.1   0.5    1.2  1  HalOD1     Halobacterial output domain 1
  ------ inclusion threshold ------
      0.096   12.5   0.0       0.13   12.1   0.0    1.2  1  AbiJ_NTD5  AbiJ N-terminal domain 5


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.5   2.5e-26   2.2e-22       2      74 ..      29     101 ..      28     102 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 2.5e-26
                            HalOD1   2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVe 74 
                                       ++s+ +++++++a+++g dp +l+ Lyd iDpd L+++fa+++ +++r++g+vsF+ + ye+tV+++g ++V+
  gi|336253105|ref|YP_004596212.1|  29 DDSLAETIIATIADLSGSDPAALDRLYDRIDPDSLETIFAPANGSATRDSGRVSFRLDVYEITVHASGAVVVT 101
                                       7899********************************************************************8 PP

>> AbiJ_NTD5  AbiJ N-terminal domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.5e-05      0.13      47      82 ..      23      59 ..      15      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                         AbiJ_NTD5 47 slsf.gDdDYegnvldvlekllsedpenLkeleeyle 82
                                      s ++ gDd+ +++++ +++ l ++dp++L+ l + ++
  gi|336253105|ref|YP_004596212.1| 23 SHDWtGDDSLAETIIATIADLSGSDPAALDRLYDRID 59
                                      778999************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 787.27
//
Query:       gi|336253106|ref|YP_004596213.1|  [L=167]
Description: hypothetical protein Halxa_1703 [Halopiger xanaduensis SH-6]
Scores for 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   31.8   2.0    1.6e-07   30.9   2.0    1.5  1  SHOCT     Short C-terminal domain
    1.2e-06   28.5   3.2    2.5e-06   27.4   3.2    1.6  1  DUF1707   Domain of unknown function (DUF1707)


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   2.0   1.7e-11   1.6e-07       1      27 [.     101     127 ..     101     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.7e-11
                             SHOCT   1 daLekLkeLyarGeIteEEFeakKakL 27 
                                       daLe+L+ +ya+G ++++EFe++ + L
  gi|336253106|ref|YP_004596213.1| 101 DALERLRTRYADGDLSDAEFERRLETL 127
                                       89*********************9866 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   3.2   2.8e-10   2.5e-06       9      49 ..     100     140 ..      95     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.8e-10
                           DUF1707   9 eravelLrealaeGrLtldEfdeRleaalaArtrgeLaalv 49 
                                       e+a+e+Lr+ +a+G L+ +Ef++Rle+  + +t ++ ++ +
  gi|336253106|ref|YP_004596213.1| 100 EDALERLRTRYADGDLSDAEFERRLETLVETETIADVERYL 140
                                       789*********************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1411  (0.0786993); expected 358.6 (0.02)
Passed bias filter:                      914  (0.0509789); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1279.03
//
Query:       gi|336253107|ref|YP_004596214.1|  [L=83]
Description: phosphoribosylformylglycinamidine synthase, purS [Halopiger xanaduensis SH-6]
Scores for complete 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-26   92.2   0.0    1.9e-26   92.1   0.0    1.0  1  PurS      Phosphoribosylformylglycinamidine (FGAM) synthase
  ------ inclusion threshold ------
      0.033   13.6   0.0      0.035   13.5   0.0    1.1  1  DUF2184   Uncharacterized protein conserved in bacteria (DUF2
      0.092   13.2   0.6        0.1   13.1   0.6    1.1  1  SIMPL     Protein of unknown function (DUF541)


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 !   92.1   0.0   3.1e-30   1.9e-26       2      77 .]       6      80 ..       5      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 3.1e-30
                                      EEEEEEE-TTS--HHHHHHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEEEE CS
                              PurS  2 akveVtlKkgvlDpqGkavkkalkslgyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyeiel 77
                                      a+v+V+lK+gvlDp++++ k+al++lg+e  ed+r + ++e++leae++++a+e+++em+e+lLaNp i+dy +e+
  gi|336253107|ref|YP_004596214.1|  6 ATVTVRLKRGVLDPEAETTKQALERLGFE-LEDLRSADRFEVDLEAESADAARERADEMAERLLANPTIHDYDVEV 80
                                      89**************************9.*******************************************986 PP

>> DUF2184  Uncharacterized protein conserved in bacteria (DUF2184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.9e-06     0.035      22      69 ..      19      66 ..       7      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.9e-06
                           DUF2184 22 ketakvkligasygytvqElraaqalGrsLdtrkadaarraadkkink 69
                                      +e  + k++   +g+++++lr+a ++  +L+++ adaar  ad++ ++
  gi|336253107|ref|YP_004596214.1| 19 PEAETTKQALERLGFELEDLRSADRFEVDLEAESADAARERADEMAER 66
                                      56667788889999*****************************98766 PP

>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   1.7e-05       0.1      80     146 ..       4      67 ..       1      82 [. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                             SIMPL  80 yeasqsltvkfrdldklgevldaavkaaneingvsfslsde...delrdeareeAvkdArakAealAkal 146
                                       y+a+ ++++k   ld  +e  ++a      ++ + f+l+d    d  + ++ +e  ++Ar++A+++A+ l
  gi|336253107|ref|YP_004596214.1|   4 YTATVTVRLKRGVLDPEAETTKQA------LERLGFELEDLrsaDRFEVDLEAESADAARERADEMAERL 67 
                                       544444444332233322233233......455777777332347778899999**************55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 627.90
//
Query:       gi|336253108|ref|YP_004596215.1|  [L=229]
Description: phosphoribosylformylglycinamidine synthase 1 [Halopiger xanaduensis SH-6]
Scores for complete 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-42  145.7   0.0    1.6e-42  145.4   0.0    1.1  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
    8.6e-08   32.2   0.0    1.1e-07   31.8   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
    6.7e-05   22.6   0.0    0.00011   21.9   0.0    1.4  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
     0.0002   21.2   0.0    0.00028   20.8   0.0    1.2  1  DJ-1_PfpI      DJ-1/PfpI family
  ------ inclusion threshold ------
        0.1   12.3   0.1       0.17   11.6   0.1    1.2  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 !  145.4   0.0   4.6e-46   1.6e-42       3     231 ..       2     208 ..       1     217 [. 0.92

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 4.6e-46
                          GATase_5   3 kvailreeGvngeyemaaafekaGfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklr 79 
                                        vai+r+ G+n+++++a+a+e+ G +a+ v  +d l +     d  +++lpGGfsygD l +g+++a+s        
  gi|336253108|ref|YP_004596215.1|   2 TVAIIRFGGSNCDRDAARALEHLGIDAEIVWHEDGLPE-----DTTGIVLPGGFSYGDYLRAGAMAARSPI-----V 68 
                                       69****************************99998776.....589******************9996665.....5 PP

                          GATase_5  80 ealekflnredtlaLGiCnGfqlLvklglvpggeieeaeksptltrNksgrfesrlvsv.vvsekspsvfl.kgmeg 154
                                       +++++  ++ +  +LG+CnG q+ ++ gl  g          ++t N+s rf+++ v++ v  +++p+ +  +++e+
  gi|336253108|ref|YP_004596215.1|  69 AEVREAASE-GVPVLGVCNGAQIGCESGLTEG----------AFTTNESARFQCEHVYLrVERDDTPWTAAyEEGEV 134
                                       566665566.9999*****************9..........9****************889999****9989**** PP

                          GATase_5 155 lslpvahGeGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvlalmpHpervve 231
                                       +++p+ahGeGr ++  +e l+ele++  + +rY+de+g++    ++NPNgS++++ag+  +   v +lmpHper++ 
  gi|336253108|ref|YP_004596215.1| 135 IEVPIAHGEGRYEI-RDERLDELEEEDRILFRYCDENGET--GPEVNPNGSKHNVAGVLGDRDTVAVLMPHPERATL 208
                                       **************.7789*****************9987..5578****************************875 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   3.1e-11   1.1e-07      14     128 ..      18     141 ..      10     177 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3.1e-11
                                       HHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.........TTTHHHHHHHHCTSTS-EEEETHHH CS
                            GATase  14 vhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.........vegkieaikearenkiPiLGICLGm 81 
                                       ++al +lg++ e+v+++    e        +gi+++gG+ +           +   ++ ++ea+++++P+LG+C G 
  gi|336253108|ref|YP_004596215.1|  18 ARALEHLGIDAEIVWHEDGLPED------TTGIVLPGGFSYGDylragamaaRSPIVAEVREAASEGVPVLGVCNGA 88 
                                       799************99777776......79********999999766654433333345555558*********** PP

                                       HHHHHHTTT....EEEEEECEEEEEEEEEEEETTT..CGGTTTTSEEEEEEEE CS
                            GATase  82 Qllaiefgr....kvvkekekehhggtmrlgddet..allyglknevierhrH 128
                                       Q+ +++       ++ +  +++      r++ d+t    +y++++++++   H
  gi|336253108|ref|YP_004596215.1|  89 QIGCESGLTegafTTNESARFQCEHVYLRVERDDTpwTAAYEEGEVIEVPIAH 141
                                       *9766533344444445555555556666665555665555555555555555 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 !   21.9   0.0   3.1e-08   0.00011      25      90 ..      26      93 ..       3     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.1e-08
                          GATase_3 25 vrvrfvplkdeslgedadlvilpGgkdt...iqdlallresgldeaikeaaeaggpvlgiCGGlqmLGe 90
                                      ++ ++v  +++ l+ed   ++lpGg+++   +++ a++++s +  +++eaa++g+pvlg+C G q+ +e
  gi|336253108|ref|YP_004596215.1| 26 IDAEIVW-HEDGLPEDTTGIVLPGGFSYgdyLRAGAMAARSPIVAEVREAASEGVPVLGVCNGAQIGCE 93
                                      5555666.7899999**********9751116677889999************************9666 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 !   20.8   0.0   7.7e-08   0.00028      59     119 ..      38     103 ..      16     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7.7e-08
                                       CCG-SEEEE--BHHHHHHHHTSH.....HHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE- CS
                         DJ-1_PfpI  59 aaeyDalvlpGGragperlrene.....kvvelvkefaekgklvaaICagpqlLaaagvlkgrrvT 119
                                       +++   +vlpGG +  ++lr+ +      +v+ v+e+a++g +v  +C g+q+  + g+ +g  +T
  gi|336253108|ref|YP_004596215.1|  38 PEDTTGIVLPGGFSYGDYLRAGAmaarsPIVAEVREAASEGVPVLGVCNGAQIGCESGLTEGAFTT 103
                                       567789************997653333378999********************9999998775444 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.7e-05      0.17      98     117 ..      71      90 ..      62      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                     Peptidase_C26  98 iraalergvPilgiCrGlql 117
                                       +r+a ++gvP+lg+C G q+
  gi|336253108|ref|YP_004596215.1|  71 VREAASEGVPVLGVCNGAQI 90 
                                       7899**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1612.58
//
Query:       gi|336253109|ref|YP_004596216.1|  [L=1008]
Description: multi-sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for 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-21   75.4   0.1      1e-13   51.2   0.1    2.7  2  PAS           PAS fold
      1e-19   70.7   0.0    2.9e-12   46.8   0.0    2.7  2  PAS_9         PAS domain
    4.7e-18   65.8  12.0    8.9e-12   45.5   0.7    3.1  2  GAF_2         GAF domain
    1.4e-16   60.0   0.0    1.9e-07   31.0   0.0    3.0  2  PAS_8         PAS domain
    1.4e-13   51.0   8.4    3.5e-08   33.7   0.4    4.6  4  PAS_4         PAS fold
    1.6e-11   44.7   0.0    3.3e-11   43.7   0.0    1.5  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
      2e-10   41.4   1.7    1.7e-07   32.0   0.1    3.1  2  GAF           GAF domain
    5.5e-10   39.4   0.0    9.3e-06   25.9   0.0    2.6  2  PAS_3         PAS fold
      2e-06   28.1   1.4    5.9e-06   26.7   0.3    2.4  3  GAF_3         GAF domain
    0.00018   21.2   0.0    0.00046   19.8   0.0    1.7  1  HisKA_4TM     Archaeal 4TM region of histidine kinase
    0.00044   20.4   0.9       0.18   12.0   0.1    4.1  3  PAS_7         PAS fold
     0.0054   16.9   0.0      0.021   15.0   0.0    2.0  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
       0.14   12.0   0.0        0.8    9.6   0.0    2.2  3  MEKHLA        MEKHLA domain
       0.58   10.2   6.3      0.077   13.0   0.5    2.6  3  HisKA         His Kinase A (phospho-acceptor) domain
        2.2    8.6   4.8          2    8.8   0.1    3.2  3  YqaH          Uncharacterized YqaH-like


Domain annotation for each model (and alignments):
>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.1   8.7e-17     1e-13       2     113 .]     329     448 ..     328     448 .. 0.88
   2 !   21.4   0.0   1.5e-07   0.00019       4      84 ..     623     706 ..     620     725 .. 0.75

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 8.7e-17
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH..........HHHHHHHHHHHH CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda..........elaelleqlleq 68 
                                       + +ai+e+  d++  +D  gr++ vN+a++e +G++r +++g +++  + ++++a            a ++ +++++
  gi|336253109|ref|YP_004596216.1| 329 RTEAIVETVGDGVYSLDSAGRFVTVNDAMTEVTGYERVDLVGAHISTIL-TDESAerrrkriralSSAGRVDNHERD 404
                                       679*******************************************555.555666889888888888889999999 PP

                                       TT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  69 geesrageisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ge   a+e+++++rdgr +++e++a+ ++  g+   g +g++rdi
  gi|336253109|ref|YP_004596216.1| 405 GEAIAAYEVTLETRDGRRVPCEINAALTGPDGDL-EGTVGIVRDI 448
                                       9999999999999************988877765.5********8 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.5e-07
                                       HHHHHHSSSEEEEEE..TTSB..EEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCC CS
                               PAS   4 raileslpdpifvvD..edgr..ilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrage 76 
                                        a++e+ pd+ ++    e+g+  +  vN+a+e l+G++++ ++g++l + i+++d++  a ++ ++ + g+  +++ 
  gi|336253109|ref|YP_004596216.1| 623 AALFENVPDAAVIAHhtESGEpiVEAVNPAFEHLFGYEADNLVGEPLDERIVPPDRSAAAMAINRRSNRGSVVETEG 699
                                       566666666666665444443214459*****************************999999999999999999988 PP

                                       EEEECTTS CS
                               PAS  77 isfklrdg 84 
                                       ++++  dg
  gi|336253109|ref|YP_004596216.1| 700 KRRTA-DG 706
                                       88877.43 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   2.4e-15   2.9e-12       2     104 .]     339     450 ..     338     450 .. 0.86
   2 !   21.3   0.0     2e-07   0.00024       9      85 ..     640     717 ..     630     748 .. 0.64

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 2.4e-15
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk............kerevev 66 
                                       dg+   ++ gr + +N+a+ +++Gy + +++g +i++++   +e++er r+ ++++++               ++ev
  gi|336253109|ref|YP_004596216.1| 339 DGVYSLDSAGRFVTVNDAMTEVTGYERVDLVGAHISTIL--TDESAERRRKRIRALSSagrvdnherdgeAIAAYEV 413
                                       566666799******************************..666666666666666666777********99***** PP

                             PAS_9  67 vlirkngetfwvlltaspvkdd.dgelvgiivilrDite 104
                                       +l +++g++++++++a+    + dg l g ++i+rDi++
  gi|336253109|ref|YP_004596216.1| 414 TLETRDGRRVPCEINAALT--GpDGDLEGTVGIVRDISD 450
                                       ****************877..4489999999******96 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2e-07
                             PAS_9   9 pdg.ril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkng.etfwvllt 81 
                                       ++g +i+  +N+a++ l+Gy ++ ++g ++++ +  +p++     a+ ++  + ++ e e   ++ +g + f+  ++
  gi|336253109|ref|YP_004596216.1| 640 ESGePIVeAVNPAFEHLFGYEADNLVGEPLDERI-VPPDRSAAAMAINRRSNRgSVVETEGKRRTADGlRDFM--IR 713
                                       55569999**************************.33333333333333333345666666666666654444..77 PP

                             PAS_9  82 aspv 85 
                                       ++pv
  gi|336253109|ref|YP_004596216.1| 714 VVPV 717
                                       7777 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   3.0   1.4e-08   1.7e-05       3     138 .]     180     319 ..     175     319 .. 0.68
   2 !   45.5   0.7   7.4e-15   8.9e-12       3     138 .]     480     607 ..     478     607 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.4e-08
                                       HHHHHHHHHHHHHHHSS..EEEEEEE-TTS-EEEE..........EEEES-TTSTT-S-B....---TTHHHHHHHH CS
                             GAF_2   3 dleelldlvldelvelgaalgyillvdddgglrla..........awgeaeeefgaaldr....plgeglvgealrt 65 
                                       ++  ++ ++++++v+ +  ++ +l  dddg+  +a           + ++++++ a +d+     +g+gl+++a+  
  gi|336253109|ref|YP_004596216.1| 180 EIAAIVTAATEHVVD-DPLAALYLRTDDDGH--IAtgdrtaserlEPVGTTPRLEAVADDvrrvGPGDGLLWRAYTA 253
                                       344445555555555.533344444556666..334455555566333444444444433443466***9******* PP

                                       TS-EEES-GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  66 grpvilndleedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                        +p++++d+    d+ ++p  + + ++ +  Pl   g  +G l++++  + ++d+  ++lL  la+++  a++
  gi|336253109|ref|YP_004596216.1| 254 AEPTVVADITP--DHTPHP-IADATGTVALQPL---G-EHGLLAVGSGPETDLDAVAVHLLGVLAATAEAALD 319
                                       ********555..355566.55666788*****...8.9******9999999*****************9996 PP

  == domain 2  score: 45.5 bits;  conditional E-value: 7.4e-15
                                       HHHHHHHHHHHHHHH.SS..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG-S CS
                             GAF_2   3 dleelldlvldelve.lgaalgyillvdddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndleedp 78 
                                       + ee++ l+l++++e l ++++++ + +++  ++ a ++e +ee       +++eg++g+ ++tg+   ++d+++++
  gi|336253109|ref|YP_004596216.1| 480 TREEIYALTLEAAEEvLHFDACVVDVAEGESLVKKAISSEIDEEYARTM--SIDEGIAGKTYQTGQTYRIADVAASE 554
                                       789************559*****99988655444458888888888888..88*******************99955 PP

                                       -HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  79 dkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       d   +p +   +rs l+vP+   g   Gv+  ++++p+afd+ed el+e+l +++a a++
  gi|336253109|ref|YP_004596216.1| 555 DA--AP-ESDEFRSALSVPI---G-ETGVFQAVSTDPDAFDAEDAELAELLLSHVADALD 607
                                       44..33.66999********...8.89*******************************96 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   6.9e-09   8.2e-06       1      58 [.     328     388 ..     328     397 .. 0.85
   2 !   31.0   0.0   1.6e-10   1.9e-07       2      53 ..     621     678 ..     620     690 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.9e-09
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrplle..d 58 
                                       er +a++e++ dg+  +d +g r+v vN+a+ e +Gy+  dl g+ + ++l++   +++  +
  gi|336253109|ref|YP_004596216.1| 328 ERTEAIVETVGDGVYSLDsAG-RFVTVNDAMTEVTGYErVDLVGAHISTILTDESAERRrkR 388
                                       7899**************555.5********************9999988888888877443 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.6e-10
                             PAS_8   2 rlralfesspdgiavvd...lgd.rivdvNqaalellGys.adlkgellg.qllpvlr 53 
                                       r+ alfe++pd+ +++     g+  +  vN+a+++l+Gy+ + l ge+l+ +++p  r
  gi|336253109|ref|YP_004596216.1| 621 RFAALFENVPDAAVIAHhteSGEpIVEAVNPAFEHLFGYEaDNLVGEPLDeRIVPPDR 678
                                       899********88886644333378999************999999999866666554 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.4   1.7e+03      34      61 ..     163     190 ..     154     208 .. 0.85
   2 !   33.7   0.4     3e-11   3.5e-08       2     110 .]     335     453 ..     334     453 .. 0.85
   3 !   18.5   0.1   1.5e-06    0.0018       2      88 ..     627     717 ..     626     725 .. 0.78
   4 ?   -1.9   0.1       3.4     4e+03      95     110 .]     736     751 ..     730     751 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                             PAS_4  34 ellGktlaellpeedaarleralrrvle 61 
                                       e+l +t +ell +e+aa+++++++++ e
  gi|336253109|ref|YP_004596216.1| 163 EALQETTHELLRAESAAEIAAIVTAATE 190
                                       6788999999999999999999988765 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 3e-11
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.... 74 
                                       + + d+++ ld+ gr++ +N a+ e+ g+++ +l+G +   +l++e+a+r +  +r++ + + +++ +e        
  gi|336253109|ref|YP_004596216.1| 335 ETVGDGVYSLDSAGRFVTVNDAMTEVTGYERVDLVGAHISTILTDESAERRRKRIRALSSAG-RVDNHERDGEaiaa 410
                                       67899****************************************99999999998877766.44444433334666 PP

                             PAS_4  75 ........pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                               +g+++++e+++     ++G+  g+++i+rDi++r+r
  gi|336253109|ref|YP_004596216.1| 411 yevtletrDGRRVPCEINAALT-GPDGDLEGTVGIVRDISDRKR 453
                                       7777789999999999999876.8******************97 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 1.5e-06
                             PAS_4   2 dslpdalavl....dpdgrvlyaNaaaaelfgappeellGktlae.llpeedaarleralrrvlegeepiefleell 73 
                                       +++pda ++     + +  v+++N+a+++lfg++++ l+G++l e ++p+ d+ + + a++r    + ++e++  ++
  gi|336253109|ref|YP_004596216.1| 627 ENVPDAAVIAhhteSGEPIVEAVNPAFEHLFGYEADNLVGEPLDErIVPP-DRSAAAMAINRRSNRGSVVETEGKRR 702
                                       666666666666555556799***********************746666.88888888888888888888888888 PP

                             PAS_4  74 lpgeerhyelrllPl 88 
                                       + ++ r + +r++P+
  gi|336253109|ref|YP_004596216.1| 703 TADGLRDFMIRVVPV 717
                                       878888888888887 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 3.4
                             PAS_4  95 vigvlvisrDiTerrr 110
                                       v  ++++ +DiT+r+r
  gi|336253109|ref|YP_004596216.1| 736 VERTVGLYTDITDRKR 751
                                       7788999*******97 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 !   43.7   0.0   2.7e-14   3.3e-11       5     109 ..     876     990 ..     873     993 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 2.7e-14
                                       HHHHHHHHHHHHHHHHHS.TTTEEEEEEEE........EE.....TEEEEEEEESSSSSTTHHHTGTCSTTCHHCST CS
                         HATPase_c   5 rLrqiisnlvdNavkfat.kageieveika........se.....ddlvisveDnGiGipkedlkklfekfsqddst 67 
                                        L+ +i ++++Nav+++   a++ie++++          e     + +++s+ D+G+Gip e++ +l e    d++ 
  gi|336253109|ref|YP_004596216.1| 876 YLETAIFQVLENAVEHNDsAAPTIEIRLSDasagdgsgGEnggpdEMVTLSIADDGPGIPDEERALLQE----DREI 948
                                       57889999********4458999******87766655501556668*******************4444....3334 PP

                                       CHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  68 krggggtGlGlsivkklvelmgGeiwvesepgrGttftftlp 109
                                       ++    +GlGl +v+ +v++ gG++ ++ ++ rGt + ++lp
  gi|336253109|ref|YP_004596216.1| 949 TQLRHASGLGLWLVNWVVSQSGGQLAFRANQPRGTVVDIRLP 990
                                       4456899*********8888*******9999******99998 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.2    0.0053       6.4       4     124 ..     180     332 ..     162     340 .. 0.59
   2 !   32.0   0.1   1.4e-10   1.7e-07       2     133 .]     481     606 ..     480     606 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0053
                                       HHHHHHHHHHHHHHTESEEEEEE.EEETTEEECEEEEECC.....................EEEETTSHHHHHHHHH CS
                               GAF   4 elldtvveelrellgadrvalyl.pdydGlhydipqasrw.....................lfmkngrgicgqvlat 58 
                                       e++++v++  +++++   +alyl +d dG h  i  ++r                       +  +g+g+  ++++ 
  gi|336253109|ref|YP_004596216.1| 180 EIAAIVTAATEHVVDDPLAALYLrTDDDG-H--IATGDRTaserlepvgttprleavaddvRRVGPGDGLLWRAYTA 253
                                       56677777777777777788888766777.3..33333333222233322222222222212222255555599999 PP

                                       SSSEEESTGG..TSTTHHTT.....HHHHHHHHTTESEEEEEEEEE....TTEEEEEEEEEESSS...CSHHHHHHH CS
                               GAF  59 gqplvipdst..pdprfaqy.....nrrdllenmgirsslvvPlvn....dgelwGllvlhnpsp...pftreelel 121
                                        +p v++d+t  ++p +  +       ++ l+++g  ++ + P ++      +l+G+l+++ + +     ++ ele 
  gi|336253109|ref|YP_004596216.1| 254 AEPTVVADITpdHTP-HPIAdatgtVALQPLGEHGLLAVGSGPETDldavAVHLLGVLAATAEAAldrAVRERELER 329
                                       9*******8764222.3333356786678888888888888888865455555888888877444333345555555 PP

                                       HHH CS
                               GAF 122 lqv 124
                                        ++
  gi|336253109|ref|YP_004596216.1| 330 TEA 332
                                       555 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 1.4e-10
                                       HHHHHHHHHHHHHHHHTESEEEEEEEEETTEEE...CEEEEECC...EEEETTSHHHHHHHHHSSSEEESTGGTSTT CS
                               GAF   2 leelldtvveelrellgadrvalylpdydGlhy...dipqasrw...lfmkngrgicgqvlatgqplvipdstpdpr 72 
                                       +ee+ + ++e ++e+l  d +++    ++G       i+ + +      m+ ++gi+g++++tgq+ +i+d++++++
  gi|336253109|ref|YP_004596216.1| 481 REEIYALTLEAAEEVLHFDACVVD--VAEGESLvkkAISSEIDEeyaRTMSIDEGIAGKTYQTGQTYRIADVAASED 555
                                       6999*******************4..47773224452333333344567777999****************988888 PP

                                       HHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHHH CS
                               GAF  73 faqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvaval 133
                                        a+       e  ++rs+l+vP+       G++++++++p  f+ e+ el++ l ++va al
  gi|336253109|ref|YP_004596216.1| 556 AAP-------ESDEFRSALSVPIGE----TGVFQAVSTDPdAFDAEDAELAELLLSHVADAL 606
                                       888.......6789*********97....69******99999****************9876 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00034       0.4       2      50 ..     351     397 ..     350     445 .. 0.76
   2 !   25.9   0.0   7.8e-09   9.3e-06       4      63 ..     649     706 ..     646     708 .. 0.97

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge 50 
                                       ++v++++ e++Gy++ +l g   ++  ++  e  er r+ + ++ + g+
  gi|336253109|ref|YP_004596216.1| 351 VTVNDAMTEVTGYERVDLVGA--HISTILTDESAERRRKRIRALSSAGR 397
                                       799******************..88888888889999998887775444 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 7.8e-09
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdG 63 
                                       v++++e+++Gy+++ l g    + +++ p Dr+ +  a+++  ++g+++e+e ++r++dG
  gi|336253109|ref|YP_004596216.1| 649 VNPAFEHLFGYEADNLVGE--PLDERIVPPDRSAAAMAINRRSNRGSVVETEGKRRTADG 706
                                       89*****************..**************************************9 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.1   4.9e+03       3      37 ..     179     211 ..     177     239 .. 0.71
   2 ?   -2.9   0.0       6.7   8.1e+03      96     123 ..     287     314 ..     245     320 .. 0.80
   3 !   26.7   0.3   4.9e-09   5.9e-06       3     129 .]     482     608 ..     480     608 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.1
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqva 37 
                                        e+++++  ++ ++++   +al+l+++d    ++a
  gi|336253109|ref|YP_004596216.1| 179 AEIAAIVTAATEHVVDDPLAALYLRTDDD--GHIA 211
                                       67888888889999999999999999773..3333 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.7
                             GAF_3  96 GvlalastkprafdaedlelleslArqi 123
                                       G+la++s ++ ++da+ ++ll  lA+ +
  gi|336253109|ref|YP_004596216.1| 287 GLLAVGSGPETDLDAVAVHLLGVLAATA 314
                                       7888888887788888888887777655 PP

  == domain 3  score: 26.7 bits;  conditional E-value: 4.9e-09
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagw.dgkpalsesldedsalarralssgevvsepsfae.edg 77 
                                       +e+++ +l+++ ++l+++++++ + +++ + ++ a+++   ++   +++ +d+  a  ++++g+ +  +++a+ ed+
  gi|336253109|ref|YP_004596216.1| 482 EEIYALTLEAAEEVLHFDACVVDVAEGE-SLVKKAISSeIDEEYA-RTMSIDEGIAGKTYQTGQTYRIADVAAsEDA 556
                                       79999*****************777744.5555555553455544.488899***********98766555442444 PP

                             GAF_3  78 ....lpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                            + r+al vP+       Gv  + st+p afdaed+el e l +++a a++r
  gi|336253109|ref|YP_004596216.1| 557 apesDEFRSALSVPIGE----TGVFQAVSTDPDAFDAEDAELAELLLSHVADALDR 608
                                       11115567778887777....********************************997 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.9e-07   0.00046     125     163 ..     744     782 ..     737     783 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.9e-07
                         HisKA_4TM 125 adasrakrisdalafvndlirhdlrndlvvirgyaeaie 163
                                       +d +  kr  + l  +n ++rhdlrn++++i+g ae+++
  gi|336253109|ref|YP_004596216.1| 744 TDITDRKRQQQQLEILNRVLRHDLRNGMNIIDGCAEELA 782
                                       577778999999***********************9975 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00015      0.18       2     114 ..     335     455 ..     334     456 .. 0.77
   2 ?   -1.0   0.0       1.6   1.9e+03      17      43 ..     646     671 ..     642     704 .. 0.82
   3 ?    3.6   0.1      0.06        72     101     115 .]     740     754 ..     738     754 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellryn...aergefgagdveaeverrlaaaragkp 75 
                                       e + +G+  +D+++r v++N+ + e+ ++ +  + vg++++++l      ++r+ ++a +++  v++  +  +a ++
  gi|336253109|ref|YP_004596216.1| 335 ETVGDGVYSLDSAGRFVTVNDAMTEVTGYERVDL-VGAHISTILTDEsaeRRRKRIRALSSAGRVDNHERDGEAIAA 410
                                       78899************************99888.********9876322344444455566666666666777788 PP

                             PAS_7  76 hsfererpdgrvievrgnpl......pdgGfVttytDiTerrrae 114
                                       + +  e++dgr +  + n+       +  G+V +  Di++r+r +
  gi|336253109|ref|YP_004596216.1| 411 YEVTLETRDGRRVPCEINAAltgpdgDLEGTVGIVRDISDRKRMQ 455
                                       889999999999877777665684434469999999999999875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                             PAS_7  17 LvawNrrylelldlpeelvqvgvplee 43 
                                       + a+N  + +l+++ ++ + vg pl+e
  gi|336253109|ref|YP_004596216.1| 646 VEAVNPAFEHLFGYEADNL-VGEPLDE 671
                                       5688999999999998888.8887765 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.06
                             PAS_7 101 VttytDiTerrraee 115
                                       V  ytDiT+r+r+++
  gi|336253109|ref|YP_004596216.1| 740 VGLYTDITDRKRQQQ 754
                                       678*********986 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.7e-05     0.021      29     110 ..      32     113 ..      15     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                                       ESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE.E.SSTSHHHHHHHHHCTESEEEESSG- CS
                      Response_reg  29 aedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil.t.ahseeedavealkagaddflsKpfd 103
                                       + +++++l+ l   + d++++   +p+ +  +l+++ir++  ++p+++  t a ++ee a +++ agad+++     
  gi|336253109|ref|YP_004596216.1|  32 VGTAADCLAALS--SADCVVIGGPLPDGSPATLCTRIRAQCGDVPIVVApTaADGSEELAGNVIAAGADGYVPRSQG 106
                                       444444444444..469************************9999888725566669***************98887 PP

                                       HHHHHHH CS
                      Response_reg 104 peeLlka 110
                                        + L ++
  gi|336253109|ref|YP_004596216.1| 107 VAMLATR 113
                                       7777666 PP

>> MEKHLA  MEKHLA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.9   5.8e+03      57      80 ..     105     128 ..     104     134 .. 0.82
   2 ?   -2.5   0.0       3.5   4.2e+03      51     100 ..     350     399 ..     313     402 .. 0.67
   3 ?    9.6   0.0   0.00067       0.8      26     117 ..     618     713 ..     593     718 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.9
                            MEKHLA  57 aaldllettweeltdlpsrksaep 80 
                                       ++ ++l t++++l + +sr s  +
  gi|336253109|ref|YP_004596216.1| 105 QGVAMLATRLHDLLQAQSRSSSAD 128
                                       68899***********99988664 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.5
                            MEKHLA  51 fnyaNqaaldllettweeltdlpsrksaepeekeeRealLekvaeqgfve 100
                                       f+  N a  ++  ++ ++l+  +   ++ +e+ e R++ ++++   g v+
  gi|336253109|ref|YP_004596216.1| 350 FVTVNDAMTEVTGYERVDLVGAHISTILTDESAERRRKRIRALSSAGRVD 399
                                       44455555566666667777777777777666666666666666666655 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00067
                            MEKHLA  26 aeelakaLfe..apfavlshslkad.pvfnyaNqaaldllettweeltdlpsrksaepeekeeRealLekvaeqgfv 99 
                                       +++  +aLfe   + av++h +++  p+    N a  +l+ ++ ++l+  p+++ + p+++++ +  +++  ++g v
  gi|336253109|ref|YP_004596216.1| 618 ERDRFAALFEnvPDAAVIAHHTESGePIVEAVNPAFEHLFGYEADNLVGEPLDERIVPPDRSAAAMAINRRSNRGSV 694
                                       5667788998644568999999985599999999999*****************99999999999************ PP

                            MEKHLA 100 enysGvrisstG.rrfsie 117
                                        + +G r +++G r f+i+
  gi|336253109|ref|YP_004596216.1| 695 VETEGKRRTADGlRDFMIR 713
                                       ***********95557665 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       6.5   7.7e+03      22      37 ..     160     177 ..     159     192 .. 0.54
   2 ?   -2.6   0.0       4.8   5.8e+03      41      57 ..     320     336 ..     304     340 .. 0.54
   3 ?   13.0   0.5   6.4e-05     0.077       6      59 ..     760     814 ..     755     824 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.5
                                       HHHHHHHC....T-HSSC CS
                             HisKA  22 gnaeaLkre..gklteel 37 
                                       +++eaL+++  + l+ e 
  gi|336253109|ref|YP_004596216.1| 160 AALEALQETthELLRAES 177
                                       567777776553333333 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHHHHHHHH CS
                             HisKA  41 letiesearrldhlved 57 
                                        ++ e+e +r +++ve+
  gi|336253109|ref|YP_004596216.1| 320 RAVRERELERTEAIVET 336
                                       33334455577777665 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 6.4e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHC...T-HSSCHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA   6 lagvaHELrtPLsailgnaeaLkre.gklteelkeyletiesearrldhlvedlL 59 
                                          + H+Lr+ ++ i g ae L ++ ++   e +ey  +i++ a+ l+ l e  +
  gi|336253109|ref|YP_004596216.1| 760 NRVLRHDLRNGMNIIDGCAEELADRlADDGTEAAEYATIIRERADDLLGLAEKTR 814
                                       56799*****************9988666799999**********9998877765 PP

>> YqaH  Uncharacterized YqaH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0017         2      35      75 ..     435     476 ..     417     479 .. 0.81
   2 ?   -2.1   0.1       4.2     5e+03      22      42 ..     596     615 ..     590     617 .. 0.79
   3 ?   -0.4   0.1       1.2   1.4e+03      29      66 ..     781     817 ..     758     835 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                              YqaH  35 egDfegaielagsivvlskDlkr.lehkekvvrLyeiaskfa 75 
                                       +gD eg++ +   i ++ +  +  ++h+ k+ +L+e+as++ 
  gi|336253109|ref|YP_004596216.1| 435 DGDLEGTVGIVRDISDRKRMQHElVAHEAKIANLHEVASRLD 476
                                       89999999998888887775554157889**********985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.2
                              YqaH  22 eeLvselLaealkegDfegai 42 
                                       e L+s  +a+al   Dfe  i
  gi|336253109|ref|YP_004596216.1| 596 ELLLSH-VADALDRFDFEAEI 615
                                       556777.99********9765 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.2
                              YqaH  29 LaealkegDfegaielagsivvlskDlkrlehkekvvr 66 
                                       La+ l + D  +a e a+ i  ++ Dl  l++k + v+
  gi|336253109|ref|YP_004596216.1| 781 LADRLAD-DGTEAAEYATIIRERADDLLGLAEKTRAVE 817
                                       5555554.556788999999999***999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1008 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); 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: 0.78u 0.25s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 6515.03
//
Query:       gi|336253110|ref|YP_004596217.1|  [L=365]
Description: hypothetical protein Halxa_1707 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0044   17.4   0.1     0.0082   16.5   0.1    1.4  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 !   16.5   0.1   4.6e-07    0.0082      10     140 ..      68     208 ..      62     240 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.6e-07
                                       -....-TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC.CC CS
                                       x....xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Radical_SAM  10 r....CsfCarpet....vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla.vp 76 
                                       +    C+ C         ++    + + ++e  le+ +e++ +   +   i ++g  l+ ++   +++r+++    +
  gi|336253110|ref|YP_004596217.1|  68 AraggCTMCGYVAEsvdgGSVSHEALMDQIEVCLEHEEENA-DEPaGLIKIYTSGSFLDEREVGAETRRAIADTfGD 143
                                       44444888888874343333333333444444444446664.33324444556777888888888888888888999 PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHH.TCTSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklm.nrghtfeevlealeklrea 140
                                         ri+ve+ +  +d+ek++ + + g  + v++gle+a+d+ v+  + n+  +f ++ +a+  +++a
  gi|336253110|ref|YP_004596217.1| 144 RDRIVVESLPDFVDREKIADFTQHGlDTDVAIGLETATDR-VRHDCvNKYFDFADFEDACAEAAAA 208
                                       9************************9999***********.4444403333455555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2684.99
//
Query:       gi|336253111|ref|YP_004596218.1|  [L=67]
Description: hypothetical protein Halxa_1708 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00021   21.4   0.7       0.39   10.9   0.1    2.2  2  Zn-ribbon_8     Zinc ribbon domain
    0.00041   20.2   0.6       0.09   12.7   0.1    2.2  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
     0.0017   17.8   0.5        1.6    8.3   0.1    2.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0078   16.1   3.1      0.071   13.0   3.1    2.1  1  Nudix_N_2       Nudix N-terminal
     0.0099   15.6   0.6       0.11   12.1   0.6    1.9  1  TackOD1         Thaumarchaeal output domain 1
  ------ inclusion threshold ------
      0.012   15.3   2.6        1.4    8.7   0.1    2.2  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.013   15.5   3.5      0.081   13.0   3.5    2.0  1  Rubredoxin      Rubredoxin
      0.013   15.4   0.6       0.46   10.5   0.1    2.2  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.022   14.2   0.3        0.8    9.2   0.0    2.3  2  zf-ribbon_3     zinc-ribbon domain
      0.029   14.4   0.1      0.037   14.0   0.1    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.034   13.7   0.6       0.36   10.5   0.1    2.1  2  GATA            GATA zinc finger
      0.035   13.8   2.3        2.5    7.9   0.5    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.054   13.2   0.5        1.6    8.5   0.1    2.1  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.059   13.5   0.2        5.7    7.1   0.0    2.2  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
      0.065   13.3   0.8        3.8    7.6   0.0    2.1  2  Elf1            Transcription elongation factor Elf1 like
       0.18   11.7   1.7       0.72    9.8   1.2    1.8  3  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.32   10.7   0.1       0.32   10.7   0.1    2.4  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII


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 !   10.9   0.1   0.00037      0.39      14      33 ..       7      26 ..       5      29 .. 0.91
   2 !    9.1   0.1    0.0013       1.4       4      35 ..      45      56 ..      44      65 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
                       Zn-ribbon_8 14 efevlqsisdapltaCPeCg 33
                                       fe+l++ +d+++ +C +Cg
  gi|336253111|ref|YP_004596218.1|  7 PFERLREKFDKSELQCRQCG 26
                                      7*****999**********9 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                       Zn-ribbon_8  4 YeYrCeeCghefevlqsisdapltaCPeCgs.e 35
                                      Y + C  Cg                     + e
  gi|336253111|ref|YP_004596218.1| 45 YRFVCPTCG---------------------AiE 56
                                      555566665.....................444 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 !   12.7   0.1   8.5e-05      0.09      17      32 ..      17      30 ..      11      33 .. 0.74
   2 !    6.3   0.0    0.0086       9.1      20      31 ..      44      56 ..      36      60 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.5e-05
                                      SCCCEEEESSSS-EEE CS
                    RNA_POL_M_15KD 17 kegknfeCrqCgYeep 32
                                      k+   + CrqCgY  +
  gi|336253111|ref|YP_004596218.1| 17 KSE--LQCRQCGYLDE 30
                                      333..78******766 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0086
                                      CE.EEESSSS-EE CS
                    RNA_POL_M_15KD 20 kn.feCrqCgYee 31
                                      ++ f C +Cg++e
  gi|336253111|ref|YP_004596218.1| 44 NYrFVCPTCGAIE 56
                                      5578899999887 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0016       1.6      15      31 ..      15      31 ..       6      33 .. 0.83
   2 !    8.1   0.1    0.0017       1.8      19      28 ..      46      55 ..      41      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                                      TSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon 15 pergelvCtdCGlVled 31
                                      ++  el C  CG++ ed
  gi|336253111|ref|YP_004596218.1| 15 FDKSELQCRQCGYLDED 31
                                      7888999*******998 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0017
                                      CEEESSSSBE CS
                      TF_Zn_Ribbon 19 elvCtdCGlV 28
                                       +vC+ CG++
  gi|336253111|ref|YP_004596218.1| 46 RFVCPTCGAI 55
                                      5899999986 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   3.1   6.7e-05     0.071       3      31 ..      22      55 ..      21      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.7e-05
                                      -TTT--B-E...EE--TT-SS-..EEEETTTTEE CS
                         Nudix_N_2  3 CsqCGtpve...lripdgDnre..RlvCpaCgti 31
                                      C+qCG   e   +++   +nr   R+vCp Cg+i
  gi|336253111|ref|YP_004596218.1| 22 CRQCGYLDEdggWQVTTSGNRInyRFVCPTCGAI 55
                                      888987766677888888888555********99 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.6   0.00011      0.11      80     101 ..      39      60 ..       8      63 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                           TackOD1  80 ksghlnvrevCpkCkSidieeq 101
                                       +++++n+r vCp C++i+++e 
  gi|336253111|ref|YP_004596218.1|  39 SGNRINYRFVCPTCGAIETKEM 60 
                                       4789*************99986 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 ?    6.8   0.4    0.0052       5.4      18      29 ..      16      27 ..      15      30 .. 0.89
   2 ?    8.7   0.1    0.0014       1.4      23      32 ..      48      57 ..      46      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0052
                     A2L_zn_ribbon 18 eqgylvCieCga 29
                                      ++++l+C  Cg+
  gi|336253111|ref|YP_004596218.1| 16 DKSELQCRQCGY 27
                                      689********8 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0014
                     A2L_zn_ribbon 23 vCieCgasfp 32
                                      vC+ Cga+++
  gi|336253111|ref|YP_004596218.1| 48 VCPTCGAIET 57
                                      9*******97 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.5   7.6e-05     0.081       2      42 ..      20      54 ..      19      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-05
                                      EEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB- CS
                        Rubredoxin  2 yeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgv 42
                                      ++C+ Cgy  d++ G++       T+ + +   +vCP+Cg+
  gi|336253111|ref|YP_004596218.1| 20 LQCRQCGYL-DEDGGWQV-----TTSGNRINYRFVCPTCGA 54
                                      69******7.88888876.....588889999*******98 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 ?    3.8   0.1     0.053        56      38      45 ..      20      27 ..       8      31 .. 0.73
   2 ?   10.5   0.1   0.00043      0.46      17      27 ..      45      55 ..      33      66 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.053
                     Zn_Tnp_IS1595 38 fqCkeCrk 45
                                      +qC+ C++
  gi|336253111|ref|YP_004596218.1| 20 LQCRQCGY 27
                                      56777764 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00043
                     Zn_Tnp_IS1595 17 ngfvCPhCgsr 27
                                       +fvCP Cg  
  gi|336253111|ref|YP_004596218.1| 45 YRFVCPTCGAI 55
                                      46*******65 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.071        75      19      24 ..      22      27 ..      16      31 .. 0.67
   2 ?    9.2   0.0   0.00076       0.8       5      11 ..      49      55 ..      47      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.071
                       zf-ribbon_3 19 CpyCGt 24
                                      C  CG+
  gi|336253111|ref|YP_004596218.1| 22 CRQCGY 27
                                      666665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00076
                       zf-ribbon_3  5 CPnCGap 11
                                      CP CGa+
  gi|336253111|ref|YP_004596218.1| 49 CPTCGAI 55
                                      9***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 ?   14.0   0.1   3.5e-05     0.037      65      98 ..      14      58 ..       4      64 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                                      EEE--EEEETTTS-EEECHHHHH...........S-TTTSSS-EE CS
                              HypA 65 eevpvkvrCreCgkefeleekal...........rCpkCgsadve 98
                                      +  + +++Cr+Cg+  e    ++            Cp+Cg+ +++
  gi|336253111|ref|YP_004596218.1| 14 KFDKSELQCRQCGYLDEDGGWQVttsgnrinyrfVCPTCGAIETK 58
                                      5567899******766644432346788889999******97654 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.17   1.8e+02       1       5 [.      22      26 ..      11      29 .. 0.81
   2 ?   10.5   0.1   0.00034      0.36       1      16 [.      49      64 ..      49      67 .] 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.17
                              GATA  1 CsnCg 5 
                                      C++Cg
  gi|336253111|ref|YP_004596218.1| 22 CRQCG 26
                                      67776 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00034
                              GATA  1 CsnCgttkTplWRrgp 16
                                      C  Cg+++T+++R g 
  gi|336253111|ref|YP_004596218.1| 49 CPTCGAIETKEMRLGS 64
                                      99***********985 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.5    0.0024       2.5       2       9 ..      21      28 ..      21      35 .. 0.87
   2 ?    5.8   0.0     0.011        11       2      22 ..      48      54 ..      47      59 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0024
                      Rubredoxin_2  2 vCsqCGfe 9 
                                      +C+qCG+ 
  gi|336253111|ref|YP_004596218.1| 21 QCRQCGYL 28
                                      7*****95 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.011
                      Rubredoxin_2  2 vCsqCGfesakwfGrCpsCgs 22
                                      v              Cp Cg+
  gi|336253111|ref|YP_004596218.1| 48 V--------------CPTCGA 54
                                      4..............666665 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 ?    3.5   0.1     0.057        60      38      53 ..      13      28 ..       8      29 .. 0.76
   2 ?    8.5   0.1    0.0015       1.6      42      53 ..      44      55 ..      33      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.057
                    zinc_ribbon_10 38 eeleevkyrCpkCgal 53
                                      e++++ + +C +Cg l
  gi|336253111|ref|YP_004596218.1| 13 EKFDKSELQCRQCGYL 28
                                      6777778889999875 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0015
                    zinc_ribbon_10 42 evkyrCpkCgal 53
                                      + +++Cp Cga+
  gi|336253111|ref|YP_004596218.1| 44 NYRFVCPTCGAI 55
                                      459******985 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   0.0      0.03        32      13      24 ..      16      27 ..       6      29 .. 0.83
   2 ?    7.1   0.0    0.0054       5.7      14      23 ..      44      53 ..      32      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.03
                          zf-Mss51 13 khvdfeCpdCGi 24
                                       + +++C +CG+
  gi|336253111|ref|YP_004596218.1| 16 DKSELQCRQCGY 27
                                      56789******7 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0054
                          zf-Mss51 14 hvdfeCpdCG 23
                                      + +f Cp CG
  gi|336253111|ref|YP_004596218.1| 44 NYRFVCPTCG 53
                                      6789*****9 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.026        28      38      53 ..      12      27 ..       8      39 .. 0.81
   2 ?    7.6   0.0    0.0036       3.8      16      34 ..      41      59 ..      34      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.026
                              Elf1 38 dkkekiaevsCkvCge 53
                                       +k ++ e++C++Cg 
  gi|336253111|ref|YP_004596218.1| 12 REKFDKSELQCRQCGY 27
                                      566678999*****85 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0036
                              Elf1 16 kklptkFdCpfCnheksve 34
                                      ++++ +F Cp C++ ++ e
  gi|336253111|ref|YP_004596218.1| 41 NRINYRFVCPTCGAIETKE 59
                                      568899******9987655 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 ?    4.6   0.2     0.028        30      40      54 ..      13      27 ..       7      32 .. 0.75
   2 ?    9.8   1.2   0.00069      0.72      30      54 ..      21      54 ..      20      58 .. 0.91
   3 ?    5.0   0.1     0.021        22      31      40 ..      49      58 ..      47      66 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.028
                    OrfB_Zn_ribbon 40 ealsgrtfkCpnCgf 54
                                      e+ ++ +++C++Cg+
  gi|336253111|ref|YP_004596218.1| 13 EKFDKSELQCRQCGY 27
                                      456788899999986 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00069
                    OrfB_Zn_ribbon 30 tCseCgsknke.........alsgrtfkCpnCgf 54
                                      +C +Cg+ +++         ++ + +f+Cp Cg+
  gi|336253111|ref|YP_004596218.1| 21 QCRQCGYLDEDggwqvttsgNRINYRFVCPTCGA 54
                                      69********99**999999999999******97 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.021
                    OrfB_Zn_ribbon 31 CseCgsknke 40
                                      C+ Cg++ ++
  gi|336253111|ref|YP_004596218.1| 49 CPTCGAIETK 58
                                      9999998877 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 ?    0.8   2.2      0.38   4.1e+02       6      11 ..      21      26 ..      17      34 .. 0.76
   2 ?   10.7   0.1   0.00031      0.32       3      12 ..      45      54 ..      44      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.38
                           zf-RRN7  6 pCgvCg 11
                                      +C +Cg
  gi|336253111|ref|YP_004596218.1| 21 QCRQCG 26
                                      566665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00031
                           zf-RRN7  3 kgppCgvCgc 12
                                      ++++C++Cg+
  gi|336253111|ref|YP_004596218.1| 45 YRFVCPTCGA 54
                                      799******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 494.93
//
Query:       gi|336253112|ref|YP_004596219.1|  [L=658]
Description: PAS/PAC sensor protein [Halopiger xanaduensis SH-6]
Scores for 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-49  165.2  15.1    9.6e-49  165.2  15.1    3.7  3  BAT       GAF and HTH_10 associated domain
    2.1e-25   89.0   0.0      2e-23   82.6   0.1    2.7  2  PAS_9     PAS domain
    2.6e-19   68.7   0.0    5.6e-19   67.7   0.0    1.6  1  HTH_10    HTH DNA binding domain
    3.7e-16   59.1   0.0    7.7e-12   45.2   0.0    2.5  2  PAS       PAS fold
    1.6e-14   54.1   2.2    3.9e-10   39.9   0.1    3.1  3  PAS_4     PAS fold
    4.9e-10   39.6   0.0    2.6e-09   37.3   0.0    2.3  3  PAS_3     PAS fold
    7.7e-08   32.2   0.0    0.00014   21.8   0.0    3.0  2  PAS_8     PAS domain
  ------ inclusion threshold ------
       0.01   16.1   1.7       0.01   16.1   1.7    3.0  4  GAF_2     GAF domain
      0.095   12.7   0.0       0.22   11.5   0.0    1.5  1  HTH_11    HTH domain
        0.1   12.9   0.1       0.27   11.6   0.1    1.8  1  GAF_3     GAF domain


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   2.7     0.037        66      20      66 ..      78     123 ..      65     150 .. 0.71
   2 ?   -3.5   3.9       4.7   8.4e+03      55     119 ..     267     329 ..     229     334 .. 0.57
   3 !  165.2  15.1   5.3e-52   9.6e-49       1     155 [.     427     587 ..     427     588 .. 0.99

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.037
                               BAT  20 laaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldave 66 
                                       + + +    e++  v+r++++++  f+ + ++ e+v+d a dl + e
  gi|336253112|ref|YP_004596219.1|  78 VRTVALEDAEYDARVHRDEDGATIVFESTAES-ETVADPAGDLADPE 123
                                       45555566789988888888888888877756.89999998887765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.7
                               BAT  55 vrdaaedldavedvrvvseeddgtlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpg 119
                                       v d +e l+    ++v + +d    le++v  + +a+  a  G+ + +     g+ +++ +v  g
  gi|336253112|ref|YP_004596219.1| 267 VLDRVEGLVRDVTASVAGSTDR-GDLEAAV-CERIAEESAYDGVWIGERNPATGTIDVRSRVDAG 329
                                       3344443333333333333333.5666666.5556666666666666666666666666666555 PP

  == domain 3  score: 165.2 bits;  conditional E-value: 5.3e-52
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsd........gevlvfftvdgadpeevrdaaedldavedvr 69 
                                       Davv++ele+rd+++++val+a++dcr+e++++v+r++        ++++++ftv+ga+++e++daa++l++v d+r
  gi|336253112|ref|YP_004596219.1| 427 DAVVAVELEVRDRQVAPVALSADADCRLEYRRSVHRTGetsdgdgqERTTSLFTVTGASAAELTDAAAELPNV-DCR 502
                                       99***********************************999****9999*************************.*** PP

                               BAT  70 vvseeddgtlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrerer 146
                                       +v e+++g+l+el+  +++l+ +l+e+G+++r++eaedgra++++e+P++a+vRs+ve+le+ry++++++++++r+r
  gi|336253112|ref|YP_004596219.1| 503 IVVERENGCLIELER-DDDLVGWLSERGVRTRAIEAEDGRASVTLELPRSANVRSIVEGLEDRYEGTDVRSFQQRDR 578
                                       **************7.9************************************************************ PP

                               BAT 147 pvrtrrefr 155
                                       + +tr+ef+
  gi|336253112|ref|YP_004596219.1| 579 SGDTRQEFA 587
                                       *******96 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.054        97       9      29 ..      31      51 ..      24      54 .. 0.83
   2 !   82.6   0.1   1.1e-26     2e-23       1     104 []     143     249 ..     143     249 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.054
                             PAS_9  9 pdgrilyaNeaalrllGyspe 29
                                       dg+i yaN aa++ +G +pe
  gi|336253112|ref|YP_004596219.1| 31 VDGTIAYANGAARDAFGIDPE 51
                                      79*999***********8776 PP

  == domain 2  score: 82.6 bits;  conditional E-value: 1.1e-26
                             PAS_9   1 pdgili...dnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkn 72 
                                       p+gi i   d +d++++y+Nea  +++Gys +ev+g++++ l+  +++p+a  +++aa+++ r  + +ve++++rk+
  gi|336253112|ref|YP_004596219.1| 143 PVGITIsdpDREDNPLVYVNEAYQEITGYSYDEVVGRNCRFLQggDSNPDAIAEMAAAIDEDR--PVTVELENYRKD 217
                                       67888866666777999**********************************************..************ PP

                             PAS_9  73 getfwvlltaspvkdddgelvgiivilrDite 104
                                       g++fw+++t++pv++d ge++ ++++++D+t+
  gi|336253112|ref|YP_004596219.1| 218 GTEFWNEVTIAPVRNDAGEVTNYVGFQNDVTA 249
                                       ******************************95 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.0   3.1e-22   5.6e-19       1      52 [.     594     645 ..     594     646 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 3.1e-22
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT++ql +l+ Ay  GYF++PR +t +eLA+ +++s++t++ehLr ae kl 
  gi|336253112|ref|YP_004596219.1| 594 LTERQLDALRRAYLGGYFEWPRPTTGEELAQSMDVSRPTFHEHLRTAEAKLC 645
                                       9*************************************************96 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00015      0.26       7      51 ..      20      64 ..      17      91 .. 0.79
   2 !   45.2   0.0   4.3e-15   7.7e-12       4     113 .]     136     247 ..     135     247 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                      HHHSSSEEEEEETTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBS CS
                               PAS  7 leslpdpifvvDedgrilyvNaaaeellGlsr.eevlgkslldlih 51
                                      le   +p+++v  dg i y+N aa++ +G+++ + ++  s l +++
  gi|336253112|ref|YP_004596219.1| 20 LERVVAPVVAV-VDGTIAYANGAARDAFGIDPeSGACEPSTLASWP 64
                                      55666789999.9******************966666666666665 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 4.3e-15
                                       HHHHHHSSSEEEEEE...TTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   4 raileslpdpifvvD...edgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       ++ le +p++i + D   ed   +yvN+a++e++G+s +ev+g++   ++   d+   ++++ + +++  e r + +
  gi|336253112|ref|YP_004596219.1| 136 ERALEEAPVGITISDpdrEDNPLVYVNEAYQEITGYSYDEVVGRNCR-FLQGGDS--NPDAIAEMAAAIDEDRPVTV 209
                                       6899***********9999999************************9.7777777..9****************999 PP

                                       EEEC..TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfkl..rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        ++   +dg++++ ev+ +pvr+  ge++ ++g+ +d+
  gi|336253112|ref|YP_004596219.1| 210 ELENyrKDGTEFWNEVTIAPVRNDAGEVTNYVGFQNDV 247
                                       9999999****************************997 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1     7e-05      0.13      14      85 ..      32     107 ..      22     120 .. 0.72
   2 !   39.9   0.1   2.2e-13   3.9e-10       1     110 []     139     252 ..     139     252 .. 0.90
   3 ?   -3.0   0.0       4.9   8.8e+03      55      74 ..     419     438 ..     407     448 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7e-05
                             PAS_4  14 dgrvlyaNaaaaelfgappee..llGktlaellpee...daarleralrrvlegeepiefleelllpgeerhyelrl 85 
                                       dg++ yaN aa++ fg++pe+  +  +tla+ +p       + +   +r v+ +++ ++   +++ +g++ ++e ++
  gi|336253112|ref|YP_004596219.1|  32 DGTIAYANGAARDAFGIDPESgaCEPSTLAS-WPSLeaaIEETVVGTVRTVALEDAEYDARVHRDEDGATIVFESTA 107
                                       9******************972255666666.555447666777777777777776666666666699999998876 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 2.2e-13
                             PAS_4   1 ldslpdalavldpdgr...vlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll 74 
                                       l+  p+++++ dpd      +y+N+a++e+ g++ +e++G+ ++ l   ++ ++  + +++++++++p++ + e  +
  gi|336253112|ref|YP_004596219.1| 139 LEEAPVGITISDPDREdnpLVYVNEAYQEITGYSYDEVVGRNCRFLQGGDSNPDAIAEMAAAIDEDRPVTVELENYR 215
                                       57788888888887755559************************655566*********************999988 PP

                             PAS_4  75 .pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        +g e + e+++ P+r++ Gev  ++++  D+T+r++
  gi|336253112|ref|YP_004596219.1| 216 kDGTEFWNEVTIAPVRNDAGEVTNYVGFQNDVTARKE 252
                                       89999999**************************985 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.9
                             PAS_4  55 alrrvlegeepiefleelll 74 
                                          rvl++++++  + e+++
  gi|336253112|ref|YP_004596219.1| 419 ETSRVLATDAVVAVELEVRD 438
                                       55789999999988888776 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.7   4.8e+03       2      18 ..      36      52 ..      35      60 .. 0.89
   2 ?   -3.7   0.0       8.9   1.6e+04      72      87 ..      90     105 ..      86     107 .. 0.67
   3 !   37.3   0.0   1.4e-12   2.6e-09       2      88 ..     159     243 ..     158     244 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.7
                             PAS_3  2 iyvserveeilGyspee 18
                                       y++++ ++ +G++pe+
  gi|336253112|ref|YP_004596219.1| 36 AYANGAARDAFGIDPES 52
                                      699***********996 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8.9
                             PAS_3  72 arvirdengkpvrvig 87 
                                       arv+rde+g  + + +
  gi|336253112|ref|YP_004596219.1|  90 ARVHRDEDGATIVFES 105
                                       6777888887665555 PP

  == domain 3  score: 37.3 bits;  conditional E-value: 1.4e-12
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +yv+e+++ei+Gys +e+ g+  +++ l   +  + + +++++a+++++p+++e    rkdG+ +w e ++ ++r++
  gi|336253112|ref|YP_004596219.1| 159 VYVNEAYQEITGYSYDEVVGR--NCRFLQGGDSNPDAIAEMAAAIDEDRPVTVELENYRKDGTEFWNEVTIAPVRND 233
                                       89*******************..9999999999******************************************** PP

                             PAS_3  79 ngkpvrvigv 88 
                                        g+++ ++g+
  gi|336253112|ref|YP_004596219.1| 234 AGEVTNYVGF 243
                                       *******997 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0036       6.5      14      39 ..      28      51 ..      17      75 .. 0.78
   2 !   21.8   0.0   7.8e-08   0.00014       5      54 ..     137     189 ..     134     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0036
                             PAS_8 14 iavvdlgdrivdvNqaalellGysad 39
                                      +avvd  ++i ++N aa + +G +++
  gi|336253112|ref|YP_004596219.1| 28 VAVVD--GTIAYANGAARDAFGIDPE 51
                                      45566..55*************7644 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 7.8e-08
                             PAS_8   5 alfesspdgiavvdlgdr...ivdvNqaalellGys.adlkgellgqllpvlrp 54 
                                        ++e +p+gi + d ++    +v+vN+a++e++Gys +++ g  + ++l++ ++
  gi|336253112|ref|YP_004596219.1| 137 RALEEAPVGITISDPDREdnpLVYVNEAYQEITGYSyDEVVGRNC-RFLQGGDS 189
                                       568999*****9884442446***************999999988.55544444 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.9   8.8e+03      55      77 ..      61      89 ..      18     108 .. 0.48
   2 ?   -2.8   0.0       4.1   7.3e+03      59      71 ..     197     209 ..     132     237 .. 0.51
   3 ?   16.1   1.7   5.7e-06      0.01       5     137 ..     289     415 ..     285     416 .. 0.62
   4 ?   -3.0   0.0       4.6   8.2e+03      48      77 ..     612     640 ..     589     652 .. 0.59

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.9
                                      -TTH.HHHHHHH.....TS-EEES-GGG- CS
                             GAF_2 55 gegl.vgealrt.....grpvilndleed 77
                                      ++ + ++ a+++      r v l+d e d
  gi|336253112|ref|YP_004596219.1| 61 ASWPsLEAAIEEtvvgtVRTVALEDAEYD 89
                                      33332333333322222345555554444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.1
                                       HHHHHHHTS-EEE CS
                             GAF_2  59 vgealrtgrpvil 71 
                                       ++ a+ + rpv +
  gi|336253112|ref|YP_004596219.1| 197 MAAAIDEDRPVTV 209
                                       3455555566554 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 5.7e-06
                                       HHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEE........EEEES-TTSTT-S-B--.-TTHHHHHHHHTS-EE CS
                             GAF_2   5 eelldlvldelvelg.aalgyillvdddgg.lrla........awgeaeeefgaaldrpl.geglvgealrtgrpvi 70 
                                        +l  +v+++++e    + ++i++ ++++g ++++        a+ ++ +++ +++  p  g+ +++ al +     
  gi|336253112|ref|YP_004596219.1| 289 GDLEAAVCERIAEESaYDGVWIGERNPATGtIDVRsrvdagasAADGPVDRDADSI--PAdGDHPAAAALSS----- 358
                                       56666677777663225566777766555432222334443223333333333333..22233344444444..... PP

                                       ES-GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  71 lndleedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                        +d++          g ++ +s +a+Pl++++  +Gvl++  ++  + de++ ++L++la+ ia  i
  gi|336253112|ref|YP_004596219.1| 359 -DDVAV---------GTVDGASLAAFPLRYNEIEYGVLTVRLADGTDVDERESAILSALARAIASGI 415
                                       .33333.........77888888*******878*******9999999****************9877 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 4.6
                                       T-S-B---TTHHHHHHHHTS-EEES-GGG- CS
                             GAF_2  48 aaldrplgeglvgealrtgrpvilndleed 77 
                                       + +++  ge  +++++   rp+++++l++ 
  gi|336253112|ref|YP_004596219.1| 612 EWPRPTTGEE-LAQSMDVSRPTFHEHLRTA 640
                                       4442222333.4666666677777776654 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.22      15      43 ..     616     644 ..     612     647 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                            HTH_11  15 pisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                       p +geeLA+ ++vSr t + ++++ e+++
  gi|336253112|ref|YP_004596219.1| 616 PTTGEELAQSMDVSRPTFHEHLRTAEAKL 644
                                       58***************999999888876 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00015      0.27      56     127 ..     351     415 ..     322     417 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                             GAF_3  56 larralssgevvsepsfaeedglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                        a++alss+ v++++  +      ++++ a PL+  +  +Gvl ++  ++ + d+++ + l++lAr ia++i
  gi|336253112|ref|YP_004596219.1| 351 PAAAALSSDDVAVGTV-D------GASLAAFPLRYNEIEYGVLTVRLADGTDVDERESAILSALARAIASGI 415
                                       4555555555554433.3......367777*****99*********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (658 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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):              10  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4457.19
//
Query:       gi|336253113|ref|YP_004596220.1|  [L=70]
Description: hypothetical protein Halxa_1710 [Halopiger xanaduensis SH-6]
Scores for 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-11   43.2  19.9    5.4e-11   42.5  19.9    1.4  1  DUF1328   Protein of unknown function (DUF1328)
  ------ inclusion threshold ------
          4    7.6  10.2       0.58   10.3   0.6    2.1  2  DUF2973   Protein of unknown function (DUF2973)


Domain annotation for each model (and alignments):
>> DUF1328  Protein of unknown function (DUF1328)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5  19.9     6e-15   5.4e-11       1      39 []      28      66 ..      28      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 6e-15
                           DUF1328  1 liFLviAliAgvLGFgGiagaaagiAkiLFfiFlvlfvi 39
                                      ++F+v+A+iA+++G++G+ag++++iA+i+++iF++l+++
  gi|336253113|ref|YP_004596220.1| 28 IVFFVLAIIAAAVGARGVAGVSMEIARIFVLIFIILAIV 66
                                      89***********************************98 PP

>> DUF2973  Protein of unknown function (DUF2973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.6   6.5e-05      0.58       6      33 ..      26      53 ..      23      55 .. 0.86
   2 ?    1.5   4.1     0.035   3.1e+02       5      18 ..      55      68 ..      52      70 .] 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.5e-05
                           DUF2973  6 YilaftvlaflAvanLirslitlsadsq 33
                                      ++++f+vla++A a+  r++  +s++  
  gi|336253113|ref|YP_004596220.1| 26 WAIVFFVLAIIAAAVGARGVAGVSMEIA 53
                                      4789*******************99976 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.035
                           DUF2973  5 lYilaftvlaflAv 18
                                      +++l+f++la++A+
  gi|336253113|ref|YP_004596220.1| 55 IFVLIFIILAIVAL 68
                                      899********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1160  (0.0646996); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 526.90
//
Query:       gi|336253114|ref|YP_004596221.1|  [L=645]
Description: aldehyde ferredoxin oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-118  395.4   2.1   3.1e-118  395.1   2.1    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    5.1e-72  241.9   0.0    7.8e-72  241.3   0.0    1.3  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.1   2.1  3.5e-122  3.1e-118       4     382 .]     228     624 ..     225     624 .. 0.94

  Alignments for each domain:
  == domain 1  score: 395.1 bits;  conditional E-value: 3.5e-122
                                       HHHHHHHHHSH.HHH...HHHHH-GGGHHHHHHHTT---BTTTTB.S--T...........TGGGGSHHHHHHHTEE CS
                            AFOR_C   4 kkiqkeiksspqvta...elrkyGTaelvnianetgalptknfqe.gtfe...........kaekisgealeekylv 65 
                                       ++++++i++s++++    +l+k+GT++l+n+++e++ lpt+n ++ +t +           + e++sge+++e++lv
  gi|336253114|ref|YP_004596221.1| 228 QQAMQVIQESDVTAPnegGLSKFGTNVLMNLTEEMSGLPTRNGKYtSTRDaredgfagdefDSEQVSGENVRENILV 304
                                       688999999995554889***************************66643455666666555599************ PP

                                       EE.E-TT-SS--EEEEE.......ET....EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHH CS
                            AFOR_C  66 knegCfsCpiaCgrevkveegkk.vk....vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiaf 137
                                       ++  C+sCp+aC++ev+v++  k  +    +e +eye+++alG+n g ++ + i+ + ++c+++G+Dti++Gn++a+
  gi|336253114|ref|YP_004596221.1| 305 DEPTCHSCPVACKKEVEVQTMHKgEEmnvrTESYEYESAFALGPNSGHTERDDIALMIDRCNDMGVDTIEVGNMMAM 381
                                       **88**************9998855599**9********************************************** PP

                                       HHHHHHTTSS-HHHHTS----TT-THHHHHHHHHHHTT-T.THHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GG CS
                            AFOR_C 138 amelyekGllkkedtdglelefgdaeallellekiAkreg.igdllAeGvkrlaeklgaeelamhvkGlelpaydpr 213
                                       ame++e+G l++ d+   ++++gd e++++++e+iA+re  ++dllAeG+ r+ae+++a+e +  vkG+ +paydpr
  gi|336253114|ref|YP_004596221.1| 382 AMEMTEEGKLEDLDH---DMDWGDSEEMVDMIERIAHRETdLADLLAEGADRIAEQMDAHENSLAVKGQTIPAYDPR 455
                                       **********98776...89********************************************************* PP

                                       G-HHHHHHHHH-TTSS-SGGG-THHHH.....S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH...... CS
                            AFOR_C 214 gakgmalaYatsnrGacHlrayliale.....ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlel 285
                                       ++kgm+++YatsnrGacHlr+y+ a+e     ekvdp+e+egk+el++ fqdl+a+ ds+ +Ckf++       +e+
  gi|336253114|ref|YP_004596221.1| 456 CMKGMGIGYATSNRGACHLRGYTPAAEilgipEKVDPYEWEGKGELTAEFQDLHAISDSFDICKFNAF---AEGIEE 529
                                       *******************************************************************4...456999 PP

                                       HHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHT--HHHS---HHHHHS--.-SSTTTT---..-HHHHHHHHH CS
                            AFOR_C 286 yakllsavtGidvteeellkaGeRiynleRlfnlreGltrkddtlperlleepl.kegpakgkvledeleemldeyY 361
                                       y+ +++ +tG+dv+e+el++aGeR+ynleR++n+ +G++ +dd+lp+r+l++ +  +g ++g+++  ele m++eyY
  gi|336253114|ref|YP_004596221.1| 530 YVLQYNGMTGLDVSEDELMEAGERVYNLERYYNNLAGFDGSDDSLPDRFLPDGIpGQGASEGEHC--ELEPMKEEYY 604
                                       **************************************************999955888899998..9********* PP

                                       HHHT--TTS---HHHHHHCT- CS
                            AFOR_C 362 elrGWdetGvPtketlkrLgL 382
                                         rGW  +Gv+  e+l++L++
  gi|336253114|ref|YP_004596221.1| 605 DYRGWV-DGVVPDEKLDELDI 624
                                       ******.************97 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.3   0.0   8.8e-76   7.8e-72       2     196 ..      10     209 ..       9     211 .. 0.96

  Alignments for each domain:
  == domain 1  score: 241.3 bits;  conditional E-value: 8.8e-76
                                       EEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE- CS
                            AFOR_N   2 kilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaks 78 
                                       +++r+dLs+g + +e++++e a+ky+G rgl++k+++++  p+vdpl+p+n l+f+ Gpl+gt++++sgr++v++ks
  gi|336253114|ref|YP_004596221.1|  10 RVARIDLSDGDVAYESIDDEDAKKYIGARGLGVKYVFEQ-GPDVDPLGPDNLLAFMNGPLSGTQVTMSGRIAVCTKS 85 
                                       899***********************************6.599********************************** PP

                                       TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS..... CS
                            AFOR_N  79 PltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd..... 150
                                       Pltgt+++s+ Gg+ ga+lk++G+d++ +eG+a++pvy ++ed++ve++da++lwg++++e+ +a++ee++      
  gi|336253114|ref|YP_004596221.1|  86 PLTGTVTDSHQGGWSGARLKWSGFDGLLFEGQADEPVYAFVEDGEVELRDASHLWGMGFHEARDAIEEEVDGsygkn 162
                                       ********************************************************************555456668 PP

                                       .EEEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE CS
                            AFOR_N 151 .kvaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvr 196
                                        +++ iGp Gen+vr+A+i+ +d+ra grgG+G+v gsKnlka+vv+
  gi|336253114|ref|YP_004596221.1| 163 lSIMGIGPGGENQVRYATIMNEDDRASGRGGVGCVAGSKNLKAVVVK 209
                                       9999***************66699**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 4773.22
//
Query:       gi|336253115|ref|YP_004596222.1|  [L=134]
Description: hypothetical protein Halxa_1712 [Halopiger xanaduensis SH-6]
Scores for complete 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   41.4   0.9    1.6e-10   40.9   0.9    1.2  1  HTH_20    Helix-turn-helix domain
    5.9e-06   26.0   0.1    9.5e-06   25.3   0.1    1.3  1  HTH_IclR  IclR helix-turn-helix domain
    1.8e-05   24.5   0.0    2.7e-05   24.0   0.0    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB
    4.6e-05   23.1   0.0    5.5e-05   22.8   0.0    1.1  1  ArsR      ArsR transcriptional regulator
     0.0011   18.8   0.1     0.0018   18.1   0.1    1.4  1  MarR_2    MarR family
     0.0011   18.5   0.0      0.002   17.7   0.0    1.4  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.027   14.8   0.0      0.044   14.1   0.0    1.3  1  Rrf2      Transcriptional regulator
      0.033   14.0   0.0      0.044   13.6   0.0    1.2  1  HTH_5     Bacterial regulatory protein, arsR family
      0.055   13.6   0.0      0.067   13.3   0.0    1.2  1  FUR       Ferric uptake regulator family
      0.068   13.1   0.1        0.1   12.5   0.1    1.2  1  HTH_11    HTH domain
      0.071   13.2   1.9       0.65   10.1   1.9    2.3  1  DprA_WH   DprA winged 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 !   40.9   0.9   9.9e-14   1.6e-10       3      57 ..      24      77 ..      22      79 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 9.9e-14
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      ++ AL++   r+il a  ++e lta+el e++d++ +t+++ ++ L ea+Lve +
  gi|336253115|ref|YP_004596222.1| 24 VLAALDDDACRAILEAT-SDESLTATELSEQCDIPTSTAYRKVEMLTEADLVEER 77
                                      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 !   25.3   0.1   5.8e-09   9.5e-06      13      50 ..      39      76 ..      34      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 5.8e-09
                                      CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 13 aeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      a+ ++ lt +el++++++p St++R +  L+e  +ve 
  gi|336253115|ref|YP_004596222.1| 39 ATSDESLTATELSEQCDIPTSTAYRKVEMLTEADLVEE 76
                                      4567779****************************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 !   24.0   0.0   1.7e-08   2.7e-05      20      55 ..      42      77 ..      32      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.7e-08
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                       +++ta+e++e+ ++p s++Y+ ++ L +++lVe +
  gi|336253115|ref|YP_004596222.1| 42 DESLTATELSEQCDIPTSTAYRKVEMLTEADLVEER 77
                                      6889*****************************987 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   3.4e-08   5.5e-05      10      84 ..      24     100 ..      16     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.4e-08
                              ArsR  10 llqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEsqWrmpepgekpekeYhtsYskvqa 83 
                                       +l ++d++  + ++e+ s+e lt++el+e+++     + + +++L +++l+E++ r+   + k   eY+ s++ v +
  gi|336253115|ref|YP_004596222.1|  24 VLAALDDDACRAILEATSDESLTATELSEQCDIPtstAYRKVEMLTEADLVEERVRINT-SGKHATEYRRSFDDVVV 99 
                                       79999*************************996632366789***************99.566788******99876 PP

                              ArsR  84 n 84 
                                       +
  gi|336253115|ref|YP_004596222.1| 100 S 100
                                       6 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   1.1e-06    0.0018       8      54 ..      34      77 ..      23      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      + +L a  ++    lt++el + ++++ s++ r ++ L +a Lve+r
  gi|336253115|ref|YP_004596222.1| 34 RAILEATSDES---LTATELSEQCDIPTSTAYRKVEMLTEADLVEER 77
                                      44555555555...9*****************************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 !   17.7   0.0   1.2e-06     0.002      14      48 .]      41      75 ..      34      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                            HTH_24 14 knprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       + +++ +eL+e+++++ st  r ++ L+e+ l++
  gi|336253115|ref|YP_004596222.1| 41 SDESLTATELSEQCDIPTSTAYRKVEMLTEADLVE 75
                                      4899***************************9996 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.7e-05     0.044      17      57 ..      37      76 ..      31      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                                      HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      L++ ++e+ ++++e++e+ +i+ s + + +++L++a+lv+ 
  gi|336253115|ref|YP_004596222.1| 37 LEATSDES-LTATELSEQCDIPTSTAYRKVEMLTEADLVEE 76
                                      55666665.******************************85 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 ?   13.6   0.0   2.7e-05     0.044       6      46 ..      35      75 ..      30      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                                      HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       IL + ++++l+++el+e+ +++ st  +   +L ea+LVe
  gi|336253115|ref|YP_004596222.1| 35 AILEATSDESLTATELSEQCDIPTSTAYRKVEMLTEADLVE 75
                                      68999999********************************8 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.1e-05     0.067      27      61 ..      43      77 ..      35     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.1e-05
                                      HHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEE CS
                               FUR 27 eevykelkeedpeislaTVYrtLklleeaglvkel 61
                                      e+++    +e+ +i  +T Yr +++l+ea+lv+e 
  gi|336253115|ref|YP_004596222.1| 43 ESLTATELSEQCDIPTSTAYRKVEMLTEADLVEER 77
                                      566666678999********************863 PP

>> HTH_11  HTH 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       0.1       9      42 ..      37      71 ..      34      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-05
                            HTH_11  9 Lleargp.isgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      L ++ +  +++ eL+e+ ++ ++t +r ++ L+e+
  gi|336253115|ref|YP_004596222.1| 37 LEATSDEsLTATELSEQCDIPTSTAYRKVEMLTEA 71
                                      54555556**********************99664 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.9    0.0004      0.65       7      42 ..      26      61 ..      12      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0004
                           DprA_WH  7 epplddlerrvLaaLgpePvhvDqLvrrtglpaaev 42
                                      ++ +dd  r++L+a + e+++  +L++++ +p+++ 
  gi|336253115|ref|YP_004596222.1| 26 AALDDDACRAILEATSDESLTATELSEQCDIPTSTA 61
                                      4456888899***********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 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:                        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):              11  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1001.80
//
Query:       gi|336253116|ref|YP_004596223.1|  [L=238]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-21   73.4   0.1    1.5e-20   72.8   0.1    1.3  1  HTH_10         HTH DNA binding domain
  ------ inclusion threshold ------
       0.05   13.2   0.1        2.3    7.8   0.0    2.2  2  GerE           Bacterial regulatory proteins, luxR family
      0.064   13.0   0.1       0.26   11.1   0.1    1.9  1  LexA_DNA_bind  LexA DNA binding domain
       0.14   11.8   0.0       0.32   10.6   0.0    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.14   12.0   0.0       0.35   10.8   0.0    1.7  1  Homeodomain    Homeodomain


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 !   72.8   0.1   4.1e-24   1.5e-20       1      52 [.     179     230 ..     179     231 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 4.1e-24
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LTd+qlevl +A++mGYF+ P+r+++ e+A+elGI+ +t++ehL +a+ kl+
  gi|336253116|ref|YP_004596223.1| 179 LTDRQLEVLETAHRMGYFEHPKRANAGEVAEELGITSTTFTEHLAAAQTKLL 230
                                       9*************************************************97 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.02        71       2      12 ..     178     188 ..     177     191 .. 0.88
   2 ?    7.8   0.0   0.00064       2.3      22      45 ..     206     229 ..     203     231 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.02
                                       SS-HHHHHHHH CS
                              GerE   2 sLskRErevLr 12 
                                       +L++R++evL+
  gi|336253116|ref|YP_004596223.1| 178 TLTDRQLEVLE 188
                                       7*********8 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00064
                                       HHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE  22 eIAeelniSekTVkvhksnimkKL 45 
                                       e+Aeel+i  +T + h++ +++KL
  gi|336253116|ref|YP_004596223.1| 206 EVAEELGITSTTFTEHLAAAQTKL 229
                                       89*********************8 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   0.1   7.3e-05      0.26       2      53 ..     177     228 ..     176     233 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.3e-05
                                       X---HHHHHHHHHHHHHHHHHSS-..--HHHHHHHHTS-.HHHHHHHHHHHHHT CS
                     LexA_DNA_bind   2 kkLTerQrevldlikasieetgyp..PsireiaralglkSpsaveehLkaLerK 53 
                                       + LT+rQ evl+  ++ +    +p      e+a++lg++S+ +  ehL+a ++K
  gi|336253116|ref|YP_004596223.1| 177 STLTDRQLEVLETAHR-MGYFEHPkrANAGEVAEELGITST-TFTEHLAAAQTK 228
                                       579********98765.44444541134569********76.688999998777 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 ?   10.6   0.0   8.8e-05      0.32      17      39 ..     201     223 ..     197     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.8e-05
                            HTH_24  17 risqreLAerlglSpstvnrrlk 39 
                                       r +  e+Ae+lg++++t +++l 
  gi|336253116|ref|YP_004596223.1| 201 RANAGEVAEELGITSTTFTEHLA 223
                                       56778***************996 PP

>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.7e-05      0.35       4      42 ..     176     216 ..     174     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.7e-05
                                       SSSS-HHHHHHHHHHHHH..SSS-SHHHHHHHHHHHTS-HH CS
                       Homeodomain   4 RttftkeqleeLeklFee..nrypsaeereeLAkklgLeer 42 
                                       R t+t+ qle+Le++ ++   ++p+++   e A++lg++ +
  gi|336253116|ref|YP_004596223.1| 176 RSTLTDRQLEVLETAHRMgyFEHPKRANAGEVAEELGITST 216
                                       99***************87799***************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1674.63
//
Query:       gi|336253117|ref|YP_004596224.1|  [L=49]
Description: hypothetical protein Halxa_1714 [Halopiger xanaduensis SH-6]
Scores for 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-10   40.4   1.8    2.8e-10   40.1   1.8    1.1  1  Zn-ribbon_8      Zinc ribbon domain
    5.1e-05   22.8   0.6      0.049   13.2   0.1    2.1  2  Sgf11            Sgf11 (transcriptional regulation protein)
    6.2e-05   22.5   1.0     0.0035   16.9   0.4    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
    8.9e-05   22.4   4.4      0.046   13.8   0.1    2.2  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
    0.00027   21.1   1.1     0.0082   16.4   1.1    2.0  1  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
     0.0003   20.6   0.0    0.00043   20.1   0.0    1.3  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
    0.00032   20.0   1.6       0.17   11.3   0.0    2.2  2  zf-ribbon_3      zinc-ribbon domain
    0.00033   20.6   0.7    0.00043   20.3   0.7    1.2  1  DZR              Double zinc ribbon
    0.00039   20.3   1.3      0.092   12.7   0.3    2.2  2  YhfH             YhfH-like protein
    0.00046   19.5   0.1       0.39   10.2   0.0    2.1  2  zf_Rg            Reverse gyrase zinc finger
    0.00069   19.2   2.7       0.19   11.5   0.3    2.1  2  zinc_ribbon_2    zinc-ribbon domain
    0.00075   19.5   4.9       0.11   12.6   0.7    2.2  2  UPF0547          Uncharacterised protein family UPF0547
    0.00092   18.7   5.0     0.0075   15.8   0.5    2.1  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0011   18.8   2.8       0.19   11.7   0.5    2.2  2  zf-dskA_traR     Prokaryotic dksA/traR C4-type zinc finger
     0.0012   18.8   0.7      0.099   12.7   0.0    2.1  2  Nop10p           Nucleolar RNA-binding protein, Nop10p family
     0.0018   18.3   0.5      0.002   18.2   0.5    1.1  1  Elf1             Transcription elongation factor Elf1 like
      0.003   17.3   0.9       0.47   10.2   0.1    2.1  2  YacG             DNA gyrase inhibitor YacG
     0.0033   17.3   2.9       0.13   12.3   0.5    2.2  2  DUF1610          Domain of unknown function (DUF1610)
     0.0034   17.7   1.3       0.97    9.9   0.2    2.1  2  zf-IS66          zinc-finger binding domain of transposase IS
     0.0034   17.4   1.4      0.095   12.8   0.1    2.0  2  CpXC             CpXC protein
      0.004   17.2   0.7      0.004   17.1   0.7    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.004   17.1   1.1      0.017   15.1   1.1    1.8  1  zinc-ribbons_6   zinc-ribbons
     0.0053   16.6   1.6       0.13   12.2   1.4    2.0  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0058   17.3   0.3        2.1    9.1   0.0    2.1  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
     0.0064   16.4   1.1       0.72    9.9   0.1    2.2  2  Ogr_Delta        Ogr/Delta-like zinc finger
     0.0093   15.9   0.3      0.015   15.2   0.3    1.3  1  zinc_ribbon_4    zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.6   1.8       0.53   10.1   0.1    2.1  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
      0.011   15.7   2.1       0.64   10.0   0.2    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.012   15.4   0.8       0.43   10.5   1.0    2.0  2  Prok-RING_4      Prokaryotic RING finger family 4
      0.012   15.4   0.9      0.073   12.9   0.9    1.9  1  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
      0.013   15.4   3.2       0.22   11.5   0.8    2.2  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.013   15.5   0.4          4    7.5   0.1    2.1  2  Rubredoxin       Rubredoxin
      0.017   14.8   0.3        1.3    8.7   0.3    2.2  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
      0.017   15.1   0.5      0.019   15.0   0.5    1.1  1  Zn_Tnp_IS91      Transposase zinc-binding domain
      0.019   15.2   0.4      0.023   15.0   0.4    1.3  1  DUF2072          Zn-ribbon containing protein
      0.022   14.1   2.2      0.067   12.5   2.7    1.5  2  zf-TFIIB         Transcription factor zinc-finger
      0.022   15.0   1.6        1.5    9.2   0.1    2.1  2  zf-LITAF-like    LITAF-like zinc ribbon domain
      0.027   14.4   1.0      0.075   13.0   0.9    1.6  2  RNHCP            RNHCP domain
       0.03   14.3   1.4        3.7    7.5   0.1    2.1  2  Nudix_N_2        Nudix N-terminal
      0.031   14.4   3.3       0.77    9.9   0.3    2.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
      0.033   14.0   1.6      0.076   12.8   1.6    1.6  1  zf-HYPF          HypF finger
      0.042   13.7   1.3        4.8    7.1   0.1    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.052   13.9   1.5          6    7.3   0.1    2.0  2  DUF983           Protein of unknown function (DUF983)
      0.062   13.0   0.6      0.063   13.0   0.6    1.1  1  zf-DNA_Pol       DNA Polymerase alpha zinc finger
       0.07   12.7   1.5        3.2    7.4   0.1    2.1  2  zf_C2H2_10       C2H2 type zinc-finger
      0.077   13.4   0.4      0.095   13.1   0.4    1.2  1  DUF4379          Probable Zinc-ribbon domain
      0.078   13.1   2.0       0.13   12.5   0.4    1.8  2  Acetone_carb_G   Acetone carboxylase gamma subunit
      0.078   11.5   0.7      0.076   11.6   0.7    1.0  1  Terminase_GpA    Phage terminase large subunit (GpA)
       0.08   13.6   0.7        2.2    9.0   0.1    2.0  2  FYDLN_acid       Protein of unknown function (FYDLN_acid)
       0.09   13.7   0.5         13    6.9   0.1    2.2  2  zf-C2H2_4        C2H2-type zinc finger
       0.09   12.8   1.8        4.1    7.5   0.3    2.1  2  DUF2116          Uncharacterized protein containing a Zn-ribb
      0.091   12.6   2.3        1.1    9.1   0.1    2.1  2  Rad50_zn_hook    Rad50 zinc hook motif
      0.093   12.6   3.1       0.46   10.4   3.2    1.9  2  Cys_rich_CPXG    Cysteine-rich CPXCG
        0.1   12.3   4.0        3.7    7.3   0.3    2.1  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.11   12.9   2.6       0.21   12.0   2.6    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.14   11.9   1.0       0.27   11.0   1.0    1.5  1  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.17   11.5   2.1        9.9    5.9   0.0    2.2  2  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
       0.38   10.9   3.1        5.8    7.0   0.1    2.0  2  TerY_C           TerY-C metal binding domain
       0.62   10.0   4.1        4.3    7.3   0.3    2.1  2  DUF3797          Domain of unknown function (DUF3797)
        0.7   10.2   5.7         12    6.3   1.5    2.1  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase


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 !   40.1   1.8   9.4e-13   2.8e-10       1      37 [.       1      38 [.       1      40 [. 0.95

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 9.4e-13
                       Zn-ribbon_8  1 MPiYeYrCeeCghefevlqsisdaplta.CPeCgsevr 37
                                      M  Ye+ C eCg+e ev  s+ +a l + CP Cg++v 
  gi|336253117|ref|YP_004596224.1|  1 MSRYEFTCPECGQEIEVNESMREATLSHgCPVCGADVS 38
                                      889*******************************9886 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   0.00017     0.049       3      17 ..       4      18 ..       2      18 .. 0.84
   2 !    8.3   0.0    0.0057       1.7       7      21 ..      30      44 ..      25      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                                      -EEE-TTTSSEEEGG CS
                             Sgf11  3 eyvtCpnCgRqiaas 17
                                        +tCp Cg++i  +
  gi|336253117|ref|YP_004596224.1|  4 YEFTCPECGQEIEVN 18
                                      579********9865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0057
                                      -TTTSSEEEGGGHHH CS
                             Sgf11  7 CpnCgRqiaasRFAp 21
                                      Cp Cg +++   FA+
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADVSEAAFAA 44
                                      *************97 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4   1.2e-05    0.0035       3      16 ..       6      19 ..       5      23 .. 0.84
   2 ?    4.6   0.0     0.082        25       5      17 ..      30      42 ..      27      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-05
                            zf_UBZ  3 ylCerCgkeipese 16
                                      ++C++Cg+ei+++e
  gi|336253117|ref|YP_004596224.1|  6 FTCPECGQEIEVNE 19
                                      9**********995 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.082
                            zf_UBZ  5 CerCgkeipesel 17
                                      C+ Cg+ ++e+++
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADVSEAAF 42
                                      ******9999865 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 !   13.8   0.1   0.00015     0.046       1      13 [.       7      19 ..       7      26 .. 0.82
   2 !   10.6   0.8    0.0015      0.45       2       9 ..      30      37 ..      29      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00015
                    DNA_ligase_ZBD  1 hCPvCGsavvRee 13
                                      +CP+CG++++ +e
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIEVNE 19
                                      7*******99555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0015
                    DNA_ligase_ZBD  2 CPvCGsav 9 
                                      CPvCG+ v
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADV 37
                                      *****987 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 !   16.4   1.1   2.7e-05    0.0082       2      43 ..       5      39 ..       4      49 .] 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.7e-05
                           zf-Di19  2 sftCPyCgkeltvkeLveHvedeHrveskevvCPvCaekvtk 43
                                      +ftCP Cg+e++v+e ++       +++ ++ CPvC + v++
  gi|336253117|ref|YP_004596224.1|  5 EFTCPECGQEIEVNESMR-------EATLSHGCPVCGADVSE 39
                                      7**********9887665.......5555667****988775 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 !   20.1   0.0   1.4e-06   0.00043       2      31 ..       3      34 ..       2      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.4e-06
                    Zn_ribbon_SprT  2 kyvYrCtgCgreythhlsirrhn..YrCrrCk 31
                                      +y+ +C+ Cg+e++++ s r ++  + C+ C+
  gi|336253117|ref|YP_004596224.1|  3 RYEFTCPECGQEIEVNESMREATlsHGCPVCG 34
                                      9********************99********7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00058      0.17       4      11 ..       7      15 ..       5      22 .. 0.72
   2 !    8.2   0.3    0.0055       1.6       5      13 ..      30      38 ..      29      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00058
                       zf-ribbon_3  4 rCPnCGa.p 11
                                      +CP+CG+ +
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQeI 15
                                      788888855 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0055
                       zf-ribbon_3  5 CPnCGa.pls 13
                                      CP CGa + s
  gi|336253117|ref|YP_004596224.1| 30 CPVCGAdV-S 38
                                      9****966.5 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.7   1.4e-06   0.00043      14      41 ..       7      40 ..       2      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.4e-06
                               DZR 14 fCseCgtklkavaa......edrCpsCgekvdpe 41
                                      +C+eCg++++  ++      ++ Cp Cg++v++ 
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIEVNESmreatlSHGCPVCGADVSEA 40
                                      8*******9855559999999********99875 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.3   0.00031     0.092      15      24 ..       7      16 ..       6      24 .. 0.88
   2 ?    6.9   0.0      0.02       6.1      16      27 ..      30      41 ..      27      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00031
                              YhfH 15 kCteCGkeie 24
                                      +C+eCG+eie
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIE 16
                                      7*******97 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.02
                              YhfH 16 CteCGkeieEqa 27
                                      C+ CG +  E a
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADVSEAA 41
                                      *******99975 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0062       1.9       6      19 ..       4      17 ..       1      20 [. 0.84
   2 !   10.2   0.0    0.0013      0.39       1      19 [.      21      39 ..      21      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0062
                             zf_Rg  6 feklCPNCgGdisd 19
                                      +e  CP Cg +i+ 
  gi|336253117|ref|YP_004596224.1|  4 YEFTCPECGQEIEV 17
                                      5678******9986 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0013
                             zf_Rg  1 MikavfeklCPNCgGdisd 19
                                      M +a ++++CP Cg d+s+
  gi|336253117|ref|YP_004596224.1| 21 MREATLSHGCPVCGADVSE 39
                                      6778899*********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 !   11.5   0.3   0.00064      0.19       2      11 ..       8      17 ..       7      20 .. 0.80
   2 !    8.2   0.1     0.007       2.1       2      10 ..      30      38 ..      29      41 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00064
                     zinc_ribbon_2  2 CpnCGaelqd 11
                                      Cp+CG e++ 
  gi|336253117|ref|YP_004596224.1|  8 CPECGQEIEV 17
                                      9999999974 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.007
                     zinc_ribbon_2  2 CpnCGaelq 10
                                      Cp CGa ++
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADVS 38
                                      777777665 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.7   0.00037      0.11       2      13 ..       7      18 ..       7      20 .. 0.88
   2 !    9.0   0.2    0.0049       1.5       3      14 ..      30      41 ..      29      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00037
                           UPF0547  2 vCPeCeakvPva 13
                                      +CPeC +++ v+
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIEVN 18
                                      7*******9776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0049
                           UPF0547  3 CPeCeakvPvaa 14
                                      CP C a v++aa
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADVSEAA 41
                                      **********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 !   15.8   0.5   2.5e-05    0.0075      17      33 ..       3      19 ..       2      25 .. 0.83
   2 ?    5.4   0.4     0.045        13       3       8 ..      30      35 ..      28      41 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-05
                                      TTCEEESSSSBEEEECC CS
                      TF_Zn_Ribbon 17 rgelvCtdCGlVledns 33
                                      r e++C++CG  +e n 
  gi|336253117|ref|YP_004596224.1|  3 RYEFTCPECGQEIEVNE 19
                                      889*******9999775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.045
                                      ETTTTC CS
                      TF_Zn_Ribbon  3 CPnCgs 8 
                                      CP+Cg 
  gi|336253117|ref|YP_004596224.1| 30 CPVCGA 35
                                      999986 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 !   11.7   0.5   0.00063      0.19       3      14 ..       4      16 ..       2      18 .. 0.85
   2 ?    7.7   0.1     0.011       3.3       3      16 ..      26      40 ..      22      40 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00063
                      zf-dskA_traR  3 ygs.CeeCGEpIp 14
                                      y++ C eCG++I 
  gi|336253117|ref|YP_004596224.1|  4 YEFtCPECGQEIE 16
                                      7788********6 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.011
                      zf-dskA_traR  3 ygs.CeeCGEpIpea 16
                                      +++ C +CG ++ ea
  gi|336253117|ref|YP_004596224.1| 26 LSHgCPVCGADVSEA 40
                                      5567******99986 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 ?    6.7   0.2     0.025       7.4      19      29 ..       7      17 ..       4      22 .. 0.79
   2 !   12.7   0.0   0.00033     0.099       5      30 ..      15      40 ..      14      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.025
                                      B-TTT-SB-B- CS
                            Nop10p 19 vcpecggptks 29
                                      +cpecg++ ++
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIEV 17
                                      8*****99876 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00033
                                      -EE-TTT--EESSSB-TTT-SB-B-S CS
                            Nop10p  5 lrkcgkcrvYTLkkvcpecggptksa 30
                                      ++++++ r+ TL++ cp cg+++  a
  gi|336253117|ref|YP_004596224.1| 15 IEVNESMREATLSHGCPVCGADVSEA 40
                                      5677788889***********98877 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.5   6.6e-06     0.002      21      56 ..       5      38 ..       2      49 .] 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.6e-06
                              Elf1 21 kFdCpfCnheksvevkldkkekiaevsCkvCgesfe 56
                                      +F+Cp C++e  +ev+ + +e + +  C vCg++++
  gi|336253117|ref|YP_004596224.1|  5 EFTCPECGQE--IEVNESMREATLSHGCPVCGADVS 38
                                      7*********..899888888899999*****9765 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1    0.0016      0.47       2      15 ..       7      20 ..       6      24 .. 0.86
   2 ?    6.3   0.1     0.027       7.9       3      12 ..      30      39 ..      28      47 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0016
                              YacG  2 kCPtCkkevewsee 15
                                      +CP C++e+e++e+
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIEVNES 20
                                      7*********9986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.027
                              YacG  3 CPtCkkevew 12
                                      CP+C+++v+ 
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADVSE 39
                                      *****99975 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.5   0.00042      0.13      16      23 ..       5      12 ..       4      13 .. 0.91
   2 ?    5.6   0.1     0.053        16      16      23 ..      27      34 ..      22      35 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00042
                           DUF1610 16 vFpCPNCG 23
                                      +F CP+CG
  gi|336253117|ref|YP_004596224.1|  5 EFTCPECG 12
                                      6******* PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.053
                           DUF1610 16 vFpCPNCG 23
                                      ++ CP CG
  gi|336253117|ref|YP_004596224.1| 27 SHGCPVCG 34
                                      688****9 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 !    9.9   0.2    0.0032      0.97       3      19 ..       7      21 ..       5      25 .. 0.73
   2 ?    7.5   0.1     0.019       5.5       4      17 ..      30      43 ..      27      48 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0032
                           zf-IS66  3 tCpcCGgllkpigedrv 19
                                      tCp+CG++  ++ e   
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEI-EVNES-M 21
                                      7*****984.66555.4 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.019
                           zf-IS66  4 CpcCGgllkpiged 17
                                      Cp CG+++++++  
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADVSEAAFA 43
                                      *****988888776 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   0.00032     0.095      37      53 ..       5      21 ..       2      28 .. 0.85
   2 ?    5.1   0.1     0.075        22      35      48 ..      25      38 ..      19      47 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00032
                              CpXC 37 eatCpkCgatakleapl 53
                                      e+tCp+Cg++++++ ++
  gi|336253117|ref|YP_004596224.1|  5 EFTCPECGQEIEVNESM 21
                                      89********9998776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.075
                              CpXC 35 lfeatCpkCgatak 48
                                       +++ Cp Cga+++
  gi|336253117|ref|YP_004596224.1| 25 TLSHGCPVCGADVS 38
                                      567889***99875 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 !   17.1   0.7   1.3e-05     0.004      69      95 ..       4      36 ..       1      46 [. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-05
                                      -EEEETTTS-EEECHH..HHH.....S-TTTSSS CS
                              HypA 69 vkvrCreCgkefelee..kal.....rCpkCgsa 95
                                       +++C eCg+e+e++e  + +      Cp Cg+ 
  gi|336253117|ref|YP_004596224.1|  4 YEFTCPECGQEIEVNEsmR-EatlshGCPVCGAD 36
                                      6899*********877442.1356669*****86 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.1   5.7e-05     0.017       2      31 ..       7      42 ..       6      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.7e-05
                                      --SSS-S--EE-S......SEEE-TTT--EEEEEEE CS
                    zinc-ribbons_6  2 kCpeCqqelekrg......eqyhCeaCqedlkkeal 31
                                      +CpeC qe+e ++       +  C  C +d+++ a+
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIEVNEsmreatLSHGCPVCGADVSEAAF 42
                                      7*******9966658888777889999999988775 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 !   12.2   1.4   0.00045      0.13      30      54 ..       7      35 ..       2      37 .. 0.84
   2 !   10.2   0.1    0.0019      0.56      23      41 ..      22      43 ..      13      49 .] 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00045
                    OrfB_Zn_ribbon 30 tCseCgsknke....alsgrtfkCpnCgf 54
                                      tC+eCg++ +     + ++  + Cp Cg+
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIEVnesmREATLSHGCPVCGA 35
                                      8*****99998777777777888999997 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0019
                    OrfB_Zn_ribbon 23 npayTSktCseCgsknke...a 41
                                       +a  S  C++Cg+ ++e   a
  gi|336253117|ref|YP_004596224.1| 22 REATLSHGCPVCGADVSEaafA 43
                                      4455699*******99985442 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 !    9.1   0.0     0.007       2.1       4      11 ..       7      14 ..       5      24 .. 0.82
   2 ?    7.0   0.0     0.032       9.6       3      11 ..      28      36 ..      26      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.007
                           zf-ISL3  4 rCPnCgsk 11
                                      +CP+Cg+ 
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQE 14
                                      8*****97 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.032
                           zf-ISL3  3 hrCPnCgsk 11
                                      h CP Cg+ 
  gi|336253117|ref|YP_004596224.1| 28 HGCPVCGAD 36
                                      88*****86 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 !    9.9   0.1    0.0024      0.72       1      14 [.       7      20 ..       7      27 .. 0.83
   2 ?    6.0   0.1      0.04        12       2       8 ..      30      36 ..      29      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0024
                         Ogr_Delta  1 rCPhCgapaaarts 14
                                      +CP+Cg+++ +  s
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIEVNES 20
                                      6******9887665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.04
                         Ogr_Delta  2 CPhCgap 8 
                                      CP Cga 
  gi|336253117|ref|YP_004596224.1| 30 CPVCGAD 36
                                      *****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 !   15.2   0.3   4.9e-05     0.015       3      32 ..       6      34 ..       5      36 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.9e-05
                     zinc_ribbon_4  3 itCpsCkakyeiddeklpakgvkvrCskCg 32
                                      +tCp+C+ + e++++ +++++ +  C+ Cg
  gi|336253117|ref|YP_004596224.1|  6 FTCPECGQEIEVNES-MREATLSHGCPVCG 34
                                      79************7.9************9 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 ?   10.1   0.1    0.0018      0.53       3      12 ..       7      16 ..       5      23 .. 0.82
   2 ?    5.4   0.2     0.054        16       4      11 ..      30      37 ..      27      39 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0018
                                      E-SSS--EEE CS
                    zf-C4_Topoisom  3 kCPkCggdLv 12
                                      +CP+Cg+++ 
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIE 16
                                      8*****9875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.054
                                      -SSS--EE CS
                    zf-C4_Topoisom  4 CPkCggdL 11
                                      CP Cg+d+
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADV 37
                                      *****986 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 ?   10.0   0.2    0.0021      0.64      19      29 ..       6      17 ..       2      26 .. 0.79
   2 ?    6.5   0.1     0.028       8.2      21      31 ..      30      42 ..      19      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0021
                     Zn_Tnp_IS1595 19 fvCPhCgsr.ka 29
                                      f+CP Cg + ++
  gi|336253117|ref|YP_004596224.1|  6 FTCPECGQEiEV 17
                                      99*****88765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.028
                     Zn_Tnp_IS1595 21 CPhCgsr..kayr 31
                                      CP Cg +  +a +
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADvsEAAF 42
                                      *****88765555 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 ?    5.9   0.1     0.039        12      32      42 ..       7      17 ..       1      21 [. 0.75
   2 ?   10.5   1.0    0.0014      0.43      21      42 ..       8      39 ..       7      42 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.039
                       Prok-RING_4 32 sCPlCqrrisk 42
                                      +CP C ++i+ 
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIEV 17
                                      8****999965 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0014
                       Prok-RING_4 21 CkeCfdskdls..........sCPlCqrrisk 42
                                      C eC ++ + +          +CP+C   +s+
  gi|336253117|ref|YP_004596224.1|  8 CPECGQEIEVNesmreatlshGCPVCGADVSE 39
                                      8888888766666777778899****998865 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 ?   12.9   0.9   0.00024     0.073      24      49 ..       6      39 ..       2      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00024
                                      EE-HHHHHHHHH........TT-B-TTT--B--E CS
                        zf-C3HC4_3 24 vlCeeCaekllk........rkkkCpiCrrpiek 49
                                      ++C eC ++++          ++ Cp+C +++++
  gi|336253117|ref|YP_004596224.1|  6 FTCPECGQEIEVnesmreatLSHGCPVCGADVSE 39
                                      58******998788999999999*****999876 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8   0.00073      0.22      21      30 .]       7      16 ..       4      16 .. 0.90
   2 ?    4.5   0.1      0.12        35       5      12 ..      30      37 ..      25      38 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00073
                    PhnA_Zn_Ribbon 21 vCpeCahEwe 30
                                       CpeC+ E+e
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIE 16
                                      6********7 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.12
                    PhnA_Zn_Ribbon  5 CplCaSey 12
                                      Cp C++++
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADV 37
                                      99999886 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1     0.013         4      34      42 ..       5      13 ..       4      18 .. 0.84
   2 ?    6.7   0.0     0.024       7.3      36      43 ..      29      36 ..      24      42 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.013
                                      T-BBTTTB- CS
                        Rubredoxin 34 dWvCPdCgv 42
                                      +++CP+Cg 
  gi|336253117|ref|YP_004596224.1|  5 EFTCPECGQ 13
                                      699****96 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.024
                                      BBTTTB-B CS
                        Rubredoxin 36 vCPdCgve 43
                                       CP+Cg++
  gi|336253117|ref|YP_004596224.1| 29 GCPVCGAD 36
                                      5****987 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 ?    8.7   0.3    0.0044       1.3       6      17 ..       8      19 ..       8      37 .. 0.61
   2 ?    5.3   0.2     0.051        15       6      11 ..      30      35 ..      29      40 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0044
                     zf-NADH-PPase  6 CgrCGaptepae 17
                                      C+ CG++ e++e
  gi|336253117|ref|YP_004596224.1|  8 CPECGQEIEVNE 19
                                      888888887765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.051
                     zf-NADH-PPase  6 CgrCGa 11
                                      C+ CGa
  gi|336253117|ref|YP_004596224.1| 30 CPVCGA 35
                                      777776 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 ?   15.0   0.5   6.4e-05     0.019      39      77 ..       5      47 ..       1      49 [] 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.4e-05
                       Zn_Tnp_IS91 39 ryeCeeCghekivyfsCks...rh.CpsCqkkateewlekqqe 77
                                      ++ C+eCg+e  v  s ++    h Cp C++  +e   +++q+
  gi|336253117|ref|YP_004596224.1|  5 EFTCPECGQEIEVNESMREatlSHgCPVCGADVSEAAFAAKQQ 47
                                      678*****99888888875222345******999988877765 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.4   7.7e-05     0.023       3      28 ..       7      36 ..       5      48 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.7e-05
                           DUF2072  3 kCtkCekvfed....gskeilkGCpsCGgk 28
                                       C +C++++e     +++++ +GCp+CG  
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIEVnesmREATLSHGCPVCGAD 36
                                      699***999851112356799*******75 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.7   0.00023     0.067       2      26 ..       8      34 ..       7      34 .. 0.90
   2 ?    5.2   0.2     0.043        13       2      12 ..      30      40 ..      29      44 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00023
                          zf-TFIIB  2 CPkCqdele..eserggveidyCpqCr 26
                                      CP C++e e  es r   + + Cp C+
  gi|336253117|ref|YP_004596224.1|  8 CPECGQEIEvnESMREATLSHGCPVCG 34
                                      *****998877888899*********7 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.043
                          zf-TFIIB  2 CPkCqdelees 12
                                      CP+C+++  e+
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADVSEA 40
                                      ****9987665 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 ?    9.2   0.1     0.005       1.5      56      67 ..       5      16 ..       1      19 [. 0.59
   2 ?    5.7   0.2     0.059        18      55      66 ..      26      37 ..      20      40 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.005
                     zf-LITAF-like 56 ehyCpnCgallg 67
                                      e +Cp+Cg+ + 
  gi|336253117|ref|YP_004596224.1|  5 EFTCPECGQEIE 16
                                      456666666655 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.059
                     zf-LITAF-like 55 vehyCpnCgall 66
                                        h Cp Cga +
  gi|336253117|ref|YP_004596224.1| 26 LSHGCPVCGADV 37
                                      579999999865 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.9   0.00025     0.075       3      29 ..       5      33 ..       3      38 .. 0.72
   2 ?    4.3   0.1      0.13        39       5      20 ..      29      44 ..      25      49 .] 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00025
                             RNHCP  3 sftCeeCgkeveklaagsa.krnH.CpsC 29
                                      +ftC eCg+e+e +++  + +  H Cp C
  gi|336253117|ref|YP_004596224.1|  5 EFTCPECGQEIEVNESMREaTLSHgCPVC 33
                                      7********9987765443133445**99 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.13
                             RNHCP  5 tCeeCgkeveklaags 20
                                       C  Cg++v+++a  +
  gi|336253117|ref|YP_004596224.1| 29 GCPVCGADVSEAAFAA 44
                                      5888999998776655 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   0.1     0.012       3.7       3      11 ..       8      16 ..       7      25 .. 0.87
   2 ?    6.3   0.1     0.031       9.3       3      11 ..      30      38 ..      28      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.012
                                      -TTT--B-E CS
                         Nudix_N_2  3 CsqCGtpve 11
                                      C++CG+++e
  gi|336253117|ref|YP_004596224.1|  8 CPECGQEIE 16
                                      9****9987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.031
                                      -TTT--B-E CS
                         Nudix_N_2  3 CsqCGtpve 11
                                      C+ CG+ v+
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADVS 38
                                      999999887 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 ?    9.9   0.3    0.0026      0.77      14      29 ..       3      18 ..       1      28 [. 0.78
   2 ?    7.1   0.1      0.02         6      11      29 ..      22      38 ..      14      49 .] 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0026
                          zf-Mss51 14 hvdfeCpdCGiptycs 29
                                      + +f+Cp+CG  + ++
  gi|336253117|ref|YP_004596224.1|  3 RYEFTCPECGQEIEVN 18
                                      679*******776655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.02
                          zf-Mss51 11 apkhvdfeCpdCGiptycs 29
                                       ++  ++ Cp CG  +  s
  gi|336253117|ref|YP_004596224.1| 22 REATLSHGCPVCGADV--S 38
                                      56788899*****765..3 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.6   0.00025     0.076       1      30 [.       7      36 ..       7      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00025
                                      --HHHHHHHC-TTSTTTT-TT---TTTS-- CS
                           zf-HYPF  1 lCedClrEykdpldRRfhaqfisCtnCGPr 30
                                      +C++C +E++  ++ R       C+ CG  
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIEVNESMREATLSHGCPVCGAD 36
                                      6***************************76 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   0.1     0.016       4.8       1       9 [.       6      14 ..       6      17 .. 0.79
   2 ?    5.5   0.1      0.05        15       3      17 ..      30      46 ..      28      48 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.016
                           TFIIS_C  1 akCpkCgsr 9 
                                      ++Cp+Cg++
  gi|336253117|ref|YP_004596224.1|  6 FTCPECGQE 14
                                      579999875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.05
                           TFIIS_C  3 CpkCgsr..eayffqlQ 17
                                      Cp Cg +  ea f  +Q
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADvsEAAFAAKQ 46
                                      ****9753377777666 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.035        10      10      22 ..       7      19 ..       3      25 .. 0.83
   2 ?    7.3   0.1      0.02         6       7      21 ..      26      40 ..      21      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.035
                            DUF983 10 aCeaCgldlshar 22
                                      +C++Cg++++  +
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIEVNE 19
                                      7*******98765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.02
                            DUF983  7 vadaCeaCgldlsha 21
                                      + + C++Cg+d s a
  gi|336253117|ref|YP_004596224.1| 26 LSHGCPVCGADVSEA 40
                                      6788*******9876 PP

>> zf-DNA_Pol  DNA Polymerase alpha zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.6   0.00021     0.063      13      59 ..       2      40 ..       1      49 [] 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00021
                                      --EEEE-TTT--EEEE-SSS--S.SEEEETTEEEET..TT--B--HH CS
                        zf-DNA_Pol 13 eplelrCpsCkeefefegvfesaeeekvtasglrCsnesCkaslsta 59
                                      ++ e++Cp+C++e+e+++ +++a   ++++    C+   C a +s+a
  gi|336253117|ref|YP_004596224.1|  2 SRYEFTCPECGQEIEVNESMREA---TLSHG---CP--VCGADVSEA 40
                                      5789***************9999...33333...43..344444444 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 ?    7.4   0.1     0.011       3.2       2      10 ..       5      13 ..       5      15 .. 0.84
   2 ?    4.6   0.1     0.078        23       3       9 ..      28      34 ..      27      37 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.011
                        zf_C2H2_10  2 efsCPKCqe 10
                                      ef CP C+ 
  gi|336253117|ref|YP_004596224.1|  5 EFTCPECGQ 13
                                      79*****86 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.078
                        zf_C2H2_10  3 fsCPKCq 9 
                                      + CP C+
  gi|336253117|ref|YP_004596224.1| 28 HGCPVCG 34
                                      99****7 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   0.00032     0.095      29      56 .]       5      33 ..       1      33 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00032
                           DUF4379 29 wWkCakCgh..eWeasvsnrtkgsskCpkC 56
                                        +C++Cg+  e ++s+++ t +++ Cp C
  gi|336253117|ref|YP_004596224.1|  5 EFTCPECGQeiEVNESMREATLSHG-CPVC 33
                                      668*****85577888999999999.**** PP

>> Acetone_carb_G  Acetone carboxylase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   0.00042      0.13      76      90 ..       4      18 ..       1      28 [. 0.87
   2 ?    1.0   0.1       1.5   4.5e+02      78      87 ..      28      37 ..      19      46 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00042
                                      EEEE-TTT--EEEEE CS
                    Acetone_carb_G 76 rEyycPecgtllevE 90
                                      +E+ cPecg+ +ev 
  gi|336253117|ref|YP_004596224.1|  4 YEFTCPECGQEIEVN 18
                                      7************96 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.5
                                      EE-TTT--EE CS
                    Acetone_carb_G 78 yycPecgtll 87
                                      + cP cg+ +
  gi|336253117|ref|YP_004596224.1| 28 HGCPVCGADV 37
                                      5699999765 PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.7   0.00025     0.076     196     240 ..       3      40 ..       1      48 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                     Terminase_GpA 196 ryyvpCphCgelqelsferlkwpegeaeekaryvCphcgslieeh 240
                                       ry+  Cp+Cg+++e++      +++ +e +  + Cp cg  ++e+
  gi|336253117|ref|YP_004596224.1|   3 RYEFTCPECGQEIEVN------ESM-REATLSHGCPVCGADVSEA 40 
                                       89***********998......233.6778889999999888776 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 ?    9.0   0.1    0.0073       2.2      27      44 ..       6      23 ..       1      29 [. 0.80
   2 ?    4.1   0.1      0.25        75      29      45 ..      30      46 ..      27      49 .] 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0073
                        FYDLN_acid 27 ivcpkcgeefepeevlks 44
                                       +cp+cg+e+e++e +++
  gi|336253117|ref|YP_004596224.1|  6 FTCPECGQEIEVNESMRE 23
                                      58**********998654 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.25
                        FYDLN_acid 29 cpkcgeefepeevlksr 45
                                      cp cg+ ++ +++++++
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADVSEAAFAAKQ 46
                                      9*****99999984443 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 ?    6.9   0.1     0.044        13       1       9 [.       6      14 ..       6      22 .. 0.84
   2 ?    5.4   0.0      0.14        41       3      10 ..      30      37 ..      28      42 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.044
                         zf-C2H2_4  1 fkCpiCgks 9 
                                      f+Cp Cg+ 
  gi|336253117|ref|YP_004596224.1|  6 FTCPECGQE 14
                                      89****975 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.14
                         zf-C2H2_4  3 CpiCgksF 10
                                      Cp+Cg+  
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADV 37
                                      ****9876 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 ?    7.5   0.3     0.014       4.1       6      19 ..       8      21 ..       7      24 .. 0.93
   2 ?    5.1   0.1     0.074        22       6      13 ..      30      37 ..      26      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.014
                           DUF2116  6 CivCGkaIpldesf 19
                                      C+ CG+ I+ +es+
  gi|336253117|ref|YP_004596224.1|  8 CPECGQEIEVNESM 21
                                      ************86 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.074
                           DUF2116  6 CivCGkaI 13
                                      C+vCG+ +
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADV 37
                                      *****876 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 ?    4.7   0.3     0.092        27      21      31 ..       7      17 ..       2      24 .. 0.79
   2 ?    9.1   0.1    0.0037       1.1      18      28 ..      27      36 ..      16      45 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.092
                                      E-TTT--EE-H CS
                     Rad50_zn_hook 21 cCPlCgRelde 31
                                       CP Cg+e++ 
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIEV 17
                                      7******9875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0037
                                      -SEE-TTT--E CS
                     Rad50_zn_hook 18 akgcCPlCgRe 28
                                      ++  CP+Cg +
  gi|336253117|ref|YP_004596224.1| 27 SH-GCPVCGAD 36
                                      44.6*****87 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.2    0.0015      0.46       2      31 ..       7      34 ..       6      40 .. 0.83
   2 ?    4.4   0.3      0.11        34       3      10 ..      30      37 ..      28      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0015
                     Cys_rich_CPXG  2 qCPyCgeeievlvDlsagdqeYieDCqvCC 31
                                      +CP Cg+eie  v+ s  + +    C+vC 
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQEIE--VNESMREATLSHGCPVCG 34
                                      7*****9876..678888999999999996 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.11
                     Cys_rich_CPXG  3 CPyCgeei 10
                                      CP Cg+ +
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADV 37
                                      99998765 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 ?    7.3   0.3     0.012       3.7       4      11 ..       5      12 ..       2      16 .. 0.60
   2 ?    6.7   0.4      0.02       5.9       7      13 ..      30      36 ..      30      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.012
                           zf-RRN7  4 gppCgvCg 11
                                      ++ C++Cg
  gi|336253117|ref|YP_004596224.1|  5 EFTCPECG 12
                                      56666665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.02
                           zf-RRN7  7 CgvCgcr 13
                                      C+vCg++
  gi|336253117|ref|YP_004596224.1| 30 CPVCGAD 36
                                      *****93 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 ?   12.0   2.6    0.0007      0.21       6      43 ..       8      42 ..       6      49 .] 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0007
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCgastpwfki 43
                                      CP Cg++ ++ +s r +        C  Cga  +++ +
  gi|336253117|ref|YP_004596224.1|  8 CPECGQEIEVNESMREATL---SHGCPVCGADVSEAAF 42
                                      *************999987...8889999**3233322 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 ?   11.0   1.0   0.00089      0.27      19      52 ..       2      35 ..       1      37 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00089
                    zinc_ribbon_10 19 nryalICskChshnGlapkeeleevkyrCpkCga 52
                                      +ry   C++C     + ++ + ++++  Cp Cga
  gi|336253117|ref|YP_004596224.1|  2 SRYEFTCPECGQEIEVNESMREATLSHGCPVCGA 35
                                      6899999999999999988888889999999996 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 ?    5.3   0.6     0.049        15      13      17 ..       8      12 ..       7      15 .. 0.85
   2 ?    5.9   0.0     0.033       9.9      13      21 ..      30      38 ..      28      47 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.049
                           zf-tcix 13 CpkCG 17
                                      Cp+CG
  gi|336253117|ref|YP_004596224.1|  8 CPECG 12
                                      ***** PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.033
                           zf-tcix 13 CpkCGtyNG 21
                                      Cp CG+   
  gi|336253117|ref|YP_004596224.1| 30 CPVCGADVS 38
                                      *****9755 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 ?    7.0   0.1     0.019       5.8     102     117 ..       5      20 ..       2      27 .. 0.74
   2 ?    5.4   0.3     0.064        19      75      86 ..      28      39 ..      20      46 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.019
                            TerY_C 102 eatCpwCgkevkfgea 117
                                       e tCp Cg+e++++e+
  gi|336253117|ref|YP_004596224.1|   5 EFTCPECGQEIEVNES 20 
                                       5689999999888754 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.064
                            TerY_C 75 pgCPhCgnalaf 86
                                       gCP Cg+ ++ 
  gi|336253117|ref|YP_004596224.1| 28 HGCPVCGADVSE 39
                                      589999987764 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3     0.015       4.3      15      22 ..       7      14 ..       2      27 .. 0.72
   2 ?    4.6   0.3     0.097        29      16      22 ..      30      36 ..      26      40 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.015
                           DUF3797 15 qCPeCgNn 22
                                       CPeCg +
  gi|336253117|ref|YP_004596224.1|  7 TCPECGQE 14
                                      7****964 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.097
                           DUF3797 16 CPeCgNn 22
                                      CP+Cg +
  gi|336253117|ref|YP_004596224.1| 30 CPVCGAD 36
                                      ****976 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 ?    6.2   0.2     0.042        13       2      11 ..       4      13 ..       3      14 .. 0.84
   2 ?    6.3   1.5     0.039        12       6      11 ..      30      35 ..      27      36 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.042
                                      EEE--TTTT- CS
                    Prim_Zn_Ribbon  2 khspCPvCGG 11
                                      ++  CP CG 
  gi|336253117|ref|YP_004596224.1|  4 YEFTCPECGQ 13
                                      8999*****5 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.039
                                      -TTTT- CS
                    Prim_Zn_Ribbon  6 CPvCGG 11
                                      CPvCG+
  gi|336253117|ref|YP_004596224.1| 30 CPVCGA 35
                                      *****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 355.45
//
Query:       gi|336253118|ref|YP_004596225.1|  [L=150]
Description: pyridoxamine 5'-phosphate oxidase-like FMN-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-16   59.4   0.0    4.9e-16   59.0   0.0    1.2  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    5.8e-05   23.2   0.0    7.5e-05   22.8   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.025   14.1   0.0    1.4  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   8.2e-20   4.9e-16       2     141 .]      11     143 ..      10     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 8.2e-20
                                       HHHHHHHHHC-SEEEEEEEETTEEEEEEEEEEEETTE..EEEE.EET.TSHCCHCCCT--.ECEEEEE.EEEEEE-S CS
                      Pyridox_ox_2   2 reeilalLdegevgrlafvddgepvilPvnyvvdgds..lyfh.gak.gsrlaaalrgap.vcvvvte.vdglvlar 72 
                                       +eei+++L ++e+g+l++++ +ep+++P++y++d+d+  +y++  ++  s++ + l+ +p +  vv+  +d+     
  gi|336253118|ref|YP_004596225.1|  11 DEEIDDFLGRHETGVLSLARTDEPYAIPISYGYDEDDreFYMRlVSTpDSEKREFLSSSPqARLVVYTeADS----- 82 
                                       79********************************76667****75556999999999666666665551555..... PP

                                       EGGEEEEEEEEEEEEEEEE--HHH...HHHHCCCHHHHHSTTTGGCSB---CCCCCTEEEEEEEEEEEEEEE CS
                      Pyridox_ox_2  73 sfnslnyrSVvvrGraeevtdeee...kaealellvekivpgrwenlrpptrkelkatsvlrlkieevsgrr 141
                                       +     yrSV+++G++ee+ d+++   ++ a+ + +++ + + w++ +    k+l+  +++r+ ++++ grr
  gi|336253118|ref|YP_004596225.1|  83 T-----YRSVIATGTLEEI-DPADltpDQIAQYGEAKRPLFEIWAEGK----KDLNI-ELYRFVPDSLNGRR 143
                                       5.....*************.5544111334444444444444466554....66665.99999999999996 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.3e-08   7.5e-05       2      86 ..      11      98 ..       9     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.3e-08
                                      HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTT..TEEEEEEETTSHHHHHHHHH-EEEEEEEETT..GSEEEE CS
                    Putative_PNPOx  2 deelreflaeskavvlATvdedGrPnvspvllkagdgr..dgivfatnadsrklrnleenprvallfldde..lgrgvr 76
                                      dee+ +fl +++++vl+ ++ d  P++ p+++ ++ ++   ++ + +  ds+k + l + p++ l+++ ++  ++r+v 
  gi|336253118|ref|YP_004596225.1| 11 DEEIDDFLGRHETGVLSLARTDE-PYAIPISYGYDEDDreFYMRLVSTPDSEKREFLSSSPQARLVVYTEAdsTYRSVI 88
                                      679****************9888.***********9997777778999***********************99999999 PP

                                      EEEEEEEESC CS
                    Putative_PNPOx 77 ieGtaelvsd 86
                                        Gt e +++
  gi|336253118|ref|YP_004596225.1| 89 ATGTLEEIDP 98
                                      9***999876 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 ?   14.1   0.0   4.2e-06     0.025       5     120 ..      13     137 ..      10     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-06
                     Pyrid_ox_like   5 klkelvkdiktamLttteadgklksrPMatqkveedgdlwf..ltkkdsdkvkeirkdsqvnlafsdeskkkyvsv. 78 
                                       ++ + +  ++t+ L + + +++  + P +   +e+d +++   ++  ds+k + ++  +q+ l++  e +++y sv 
  gi|336253118|ref|YP_004596225.1|  13 EIDDFLGRHETGVLSLAR-TDEPYAIPISYGYDEDDREFYMrlVSTPDSEKREFLSSSPQARLVVYTEADSTYRSVi 88 
                                       67788889999****997.778999*****99999999996448999**************************8873 PP

                     Pyrid_ox_like  79 .sGtae......vvedr.akieelWspvvkawfpegkddpnltlikvtpe 120
                                        +Gt+e      +  d+ a+  e   p++++w  egk+d n+ l ++ p+
  gi|336253118|ref|YP_004596225.1|  89 aTGTLEeidpadLTPDQiAQYGEAKRPLFEIWA-EGKKDLNIELYRFVPD 137
                                       367765211111333433677788888888887.9999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1118.41
//
Query:       gi|336253119|ref|YP_004596226.1|  [L=140]
Description: hypothetical protein Halxa_1716 [Halopiger xanaduensis SH-6]
Scores for 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  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1109.76
//
Query:       gi|336253120|ref|YP_004596227.1|  [L=85]
Description: hypothetical protein Halxa_1717 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.16   12.1   0.0       0.19   11.8   0.0    1.1  1  Apocytochr_F_C  Apocytochrome F, C-terminal


Domain annotation for each model (and alignments):
>> Apocytochr_F_C  Apocytochrome F, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     1e-05      0.19      19      72 ..      26      79 ..      15      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1e-05
                                      EESSEEEEEEETSTSEEE-EEEESSS-BS--ST-EE-TT-BSC------EEEEE CS
                    Apocytochr_F_C 19 eekggtevtietedgeavvetipaGpelivsegqevkagealtndPnvGGfGqk 72
                                      e++++ +v+ e+  +++ +e++  Gp++ ++e   v +g+  t +P v  f qk
  gi|336253120|ref|YP_004596227.1| 26 EHREDGTVASEDWTATVSSEKVDIGPSMSLTEVTVVFEGNEETLEPLVDKFAQK 79
                                      5556677888888888999********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 652.25
//
Query:       gi|336253121|ref|YP_004596228.1|  [L=110]
Description: branched-chain amino acid transport [Halopiger xanaduensis SH-6]
Scores for 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   8.7    3.1e-15   56.1   8.7    1.1  1  AzlD      Branched-chain amino acid transport protein (AzlD)


Domain annotation for each model (and alignments):
>> AzlD  Branched-chain amino acid transport protein (AzlD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   8.7   1.7e-19   3.1e-15       2      96 ..      18     104 ..      17     107 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1.7e-19
                              AzlD   2 llaillmalvtyltRylplllfrrlklppwlqrllryvPiavLaaliapellaetgklsaslglarllaalvavlva 78 
                                       + +il+m++vt+lt++ +++l+r+++l+++l+  l+++P a+ +a++ p+l a         g+a++ aa +++lv+
  gi|336253121|ref|YP_004596228.1|  18 VGVILAMTAVTVLTKVGGIWLVRHVELSERLEAGLSVLPGAIVIAVLGPDLAAG--------GPAEWGAAWLVLLVM 86 
                                       679*************************************************88........9************** PP

                              AzlD  79 lltrnlllsilvGmavya 96 
                                       ++t n+ll+ ++G++ ++
  gi|336253121|ref|YP_004596228.1|  87 WRTENILLALIAGVVGVV 104
                                       *************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 826.55
//
Query:       gi|336253122|ref|YP_004596229.1|  [L=258]
Description: AzlC family protein [Halopiger xanaduensis SH-6]
Scores for 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-39  133.6  11.5    5.9e-39  133.6  11.5    1.6  2  AzlC      AzlC protein


Domain annotation for each model (and alignments):
>> AzlC  AzlC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6  11.5   3.3e-43   5.9e-39       1     136 []      49     188 ..      49     188 .. 0.94
   2 ?   -2.1   0.2      0.27   4.8e+03      55      62 ..     222     229 ..     199     251 .. 0.53

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 3.3e-43
                              AzlC   1 PillgylpvgiafGvlavqaglsvweavlmSllvfAGsaqfaavgllaagasllaivlttllvNlRhllyglslapk 77 
                                       Pi+lg+  +giafGvla qaglsv ea+lmS++v AG++q++av+l+a   ++++iv+t++ +NlR+ l+g++l+p+
  gi|336253122|ref|YP_004596229.1|  49 PIALGVGGYGIAFGVLADQAGLSVAEAALMSATVLAGASQIIAVELWADPLPIATIVFTVFAINLRYSLMGAALQPW 125
                                       9**********************************************9888************************** PP

                              AzlC  78 lkklsrlkrlllaflltDetfalasar....klsrayflglglllylawvlgtllGallgsll 136
                                       +++ls  + +  +++++De++al++++    + + a++lg g++++++wv++t+lGa++g ++
  gi|336253122|ref|YP_004596229.1| 126 FRRLSPSQVYGSLYFMADENWALTMRDlksgSGRGAFLLGSGIAIWVFWVGSTILGAVAGGVV 188
                                       **99888887777***********97666553349*************************875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.27
                              AzlC  55 aivlttll 62 
                                       ++ l t++
  gi|336253122|ref|YP_004596229.1| 222 VASLGTAV 229
                                       22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1999.96
//
Query:       gi|336253123|ref|YP_004596230.1|  [L=66]
Description: hypothetical protein Halxa_1722 [Halopiger xanaduensis SH-6]
Scores for 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    8.9   7.7         10    6.7   0.5    1.9  2  DUF202    Domain of unknown function (DUF202)
        5.2    7.4  11.4        3.7    7.9   2.6    2.2  2  YiaAB     yiaA/B two helix domain


Domain annotation for each model (and alignments):
>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.5    0.0011        10      21      54 ..       9      42 ..       5      46 .. 0.74
   2 ?    6.3   7.7    0.0015        13      19      59 ..      27      66 .]      19      66 .] 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0011
                            DUF202 21 ialglallrffltgepsalgkilglilivlgilt 54
                                      ++++++l r   + +p++++  lg++l+++++++
  gi|336253123|ref|YP_004596230.1|  9 AGFDAVLERRNDRTGPQWAALFLGVLLLLAALAV 42
                                      6788888887778888888888888877777665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0015
                            DUF202 19 alialglallrffltgepsalgkilglilivlgiltllvgl 59
                                      a+++lg++ll   l  + s+ g + gl+ +v+gi+++++g+
  gi|336253123|ref|YP_004596230.1| 27 AALFLGVLLLLAALAVGASS-GLWYGLTVAVFGIALVAYGF 66
                                      45666666666555666666.8****************996 PP

>> YiaAB  yiaA/B two helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.7    0.0036        33       6      21 ..      26      41 ..      23      46 .. 0.89
   2 ?    7.9   2.6   0.00041       3.7       1      17 [.      49      65 ..      49      66 .] 0.95

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0036
                             YiaAB  6 wlsfllalvlllvGlw 21
                                      w++++l+++lll+ l+
  gi|336253123|ref|YP_004596230.1| 26 WAALFLGVLLLLAALA 41
                                      9*********999886 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00041
                             YiaAB  1 figqswlsfllalvlll 17
                                      ++g+++++f++alv+++
  gi|336253123|ref|YP_004596230.1| 49 WYGLTVAVFGIALVAYG 65
                                      9**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 506.26
//
Query:       gi|336253124|ref|YP_004596231.1|  [L=94]
Description: MoaD family protein [Halopiger xanaduensis SH-6]
Scores for 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   65.7   0.2      5e-18   65.5   0.2    1.0  1  ThiS      ThiS family
  ------ inclusion threshold ------
       0.11   12.4   0.1        1.1    9.1   0.0    2.1  2  Ub-Mut7C  Mut7-C ubiquitin


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 !   65.5   0.2   5.5e-22     5e-18       2      77 .]       6      94 .]       5      94 .] 0.98

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 5.5e-22
                                      EETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG..........TTTTEEEEETTEEEGC.CTTTSB--TTCE CS
                              ThiS  2 llfaelrelag..eeelelaegstvaelleaLgerypela..........lerrvavavNgeivpr.lwldtelkdgDe 67
                                      ++fa+ r+++g  e++  ++ ++tv+++l+aL+ +y++l            ++++ v+ Ng++v + ++  t+l +gD+
  gi|336253124|ref|YP_004596231.1|  6 RFFATFRDAVGdkERTRTVDADATVGDVLAALEDEYEGLDgrlltddgeaVREQLSVLKNGRNVAHmEGPATALDEGDV 84
                                      8*************************************************99**************99*********** PP

                                      EEEEESTTC- CS
                              ThiS 68 vailppVaGG 77
                                      v+++ppVaGG
  gi|336253124|ref|YP_004596231.1| 85 VSVFPPVAGG 94
                                      *********9 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00013       1.1       3      42 ..       2      37 ..       1      38 [. 0.86
   2 ?    1.3   0.0     0.035   3.1e+02      60      75 ..      74      89 ..      58      92 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00013
                          Ub-Mut7C  3 titfrfyaeLndflprarreralavafdeaatvkhviEal 42
                                      +i++rf+a+ +d +  ++r+r     +d  atv++v+ al
  gi|336253124|ref|YP_004596231.1|  2 EIDLRFFATFRDAVGDKERTR----TVDADATVGDVLAAL 37
                                      699****************99....667789999988776 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.035
                          Ub-Mut7C 60 gfshiledGdrvavyp 75
                                      g+   l +Gd v v p
  gi|336253124|ref|YP_004596231.1| 74 GPATALDEGDVVSVFP 89
                                      3556788999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 682.34
//
Query:       gi|336253125|ref|YP_004596232.1|  [L=116]
Description: hypothetical protein Halxa_1724 [Halopiger xanaduensis SH-6]
Scores for 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:                       375  (0.0209158); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 935.72
//
Query:       gi|336253126|ref|YP_004596233.1|  [L=118]
Description: hypothetical protein Halxa_1725 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        4.9    5.6  22.4        5.4    5.5  22.4    1.1  1  TFIIF_alpha  Transcription initiation factor IIF, alpha subun
        6.9    6.6  20.5        9.5    6.2  20.5    1.3  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)


Domain annotation for each model (and alignments):
>> TFIIF_alpha  Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  22.4    0.0006       5.4     294     373 ..      22     102 ..      18     118 .] 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0006
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXX CS
                       TFIIF_alpha 294 ndpeeredkkseEeeekkeieqdedeeekeee.kkeeegklskkkkkakklkkkkkekdkkdSddeedsddsDidee 369
                                       n+ +e e  + +E+ee +++   + e e+e e ++e +g++s ++ ++++  +++ +++ ++S+++++s++sD++ e
  gi|336253126|ref|YP_004596233.1|  22 NETNETEGGAGNETEETGNDTGIGTETENETEnETEIGGNESDNETENETAIGNETGNESNESNESNESNESDDELE 98 
                                       566666666666666666665555555555441458899**********************************9988 PP

                                       XXXX CS
                       TFIIF_alpha 370 dsvs 373
                                       +  +
  gi|336253126|ref|YP_004596233.1|  99 AEEG 102
                                       7765 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  20.5    0.0011       9.5      30     113 ..      20     103 ..       4     117 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0011
                       Trypan_PARP  30 gpedkgltkggkgkekgtkvsdddtngtdpepepepepepe.pepepepepetepeeepepepepepepepepepep 105
                                       g ++   t gg g+ +  + ++d   gt++e e e+e e    e + e e+et   +e+ +e++   e +   e + 
  gi|336253126|ref|YP_004596233.1|  20 GGNETNETEGGAGN-ETEETGNDTGIGTETENETENETEIGgNESDNETENETAIGNETGNESNESNESNESNESDD 95 
                                       555666799****5.666777888899***99999999964156667777777777666666666667777777777 PP

                       Trypan_PARP 106 epepepga 113
                                       e e e g+
  gi|336253126|ref|YP_004596233.1|  96 ELEAEEGT 103
                                       77777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 841.61
//
Query:       gi|336253127|ref|YP_004596234.1|  [L=280]
Description: inorganic polyphosphate/ATP-NAD kinase [Halopiger xanaduensis SH-6]
Scores for 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-39  134.0   1.3    1.2e-37  129.7   0.5    2.0  2  NAD_kinase    ATP-NAD kinase
    0.00077   19.8   0.2      0.011   16.2   0.2    2.3  1  Secretin_N    Bacterial type II/III secretion system short do
  ------ inclusion threshold ------
       0.13   12.9   3.3       0.26   12.0   0.9    2.5  2  CW_binding_2  Putative cell wall binding repeat 2


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 !    3.2   0.0     0.007        42       2      36 ..       5      39 ..       4      49 .. 0.64
   2 !  129.7   0.5     2e-41   1.2e-37      79     290 ..      59     266 ..      52     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.007
                                      EEEEESSCGGTCSHHHHHHHHHHHCT-..EEEEEC CS
                        NAD_kinase  2 vgivvnpikkeaieraeevarwLldalsrvlevtv 36
                                      vgiv+++++  a e+a+ ++++L +    v +v++
  gi|336253127|ref|YP_004596234.1|  5 VGIVAQRNNARAQELAQTLVDTLEREYEGVATVVD 39
                                      89999999866666666666666665224444443 PP

  == domain 2  score: 129.7 bits;  conditional E-value: 2e-41
                                       SSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEE.EEEEETTE. CS
                        NAD_kinase  79 vdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevld.avimrskge 154
                                        d+++ +GGDGT l+var++   + P+lgvn+G +gfl  + p++a+e+ ++l+ +  ++e+ e  + a ++ s + 
  gi|336253127|ref|YP_004596234.1|  59 RDFVVSIGGDGTLLFVAREVG--ATPILGVNLGEVGFLNAVAPDDAREVVTELVGRLRETESLEGRKlARLQASGA- 132
                                       69*******************..8*******************************888887777444245555554. PP

                                       .....EEEEEEESSEEEEEESSSSS-EE..EEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEE CS
                        NAD_kinase 155 ediadiviensvlnevviirgpgstlie..lelyvdtelleadqldglivstPtGstayslsaGgplisPgvlaili 229
                                            +  ++ +lnevv++  ++ +     +++++d++  ++ ++dg++v+tPtGstay ls Ggpl++P+ +a l+
  gi|336253127|ref|YP_004596234.1| 133 --DGSWTLDP-ALNEVVVHGPRRGHGGGatIDVEIDGQRYTTSRADGVLVATPTGSTAYNLSEGGPLVQPAADA-LV 205
                                       ..35677777.5*******99999988788********************************************.88 PP

                                       EEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEE CS
                        NAD_kinase 230 vpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkkfkli 290
                                       v  +++++   p+Vv+++ +++++v+s ++a ++ dG+++ el+p  +v++ ++d+++ l+
  gi|336253127|ref|YP_004596234.1| 206 VTQMAAADGMPPLVVDPDAEITLTVSSAETAYAISDGHDRRELEPPATVSIAVADEPVTLV 266
                                       999999999*********************************************9998776 PP

>> Secretin_N  Bacterial type II/III secretion system short domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   1.8e-06     0.011       7      63 ..      12     151 ..       8     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-06
                                       SSS-HHHHHHHHHHHCCTT.......................................................... CS
                        Secretin_N   7 kyasaadlasiLrellgggggesas.................................................... 31 
                                       ++a+a++la++L + l+ + ++ a+                                                    
  gi|336253127|ref|YP_004596234.1|  12 NNARAQELAQTLVDTLEREYEGVATvvdeltgaaidadgvpipamgdrdfvvsiggdgtllfvarevgatpilgvnl 88 
                                       68899999999999998777777779999999999999999999999999999999999999999999999999999 PP

                                       ......................................SSTT-TTSEEEEETTTTEEEEEECH CS
                        Secretin_N  32 ...............................sgassqsgallgkggrvvadprtNsllvrgsp 63 
                                                                      +g + +  +++g +g+++ dp+ N ++v g+ 
  gi|336253127|ref|YP_004596234.1|  89 gevgflnavapddarevvtelvgrlreteslEGRKLARLQASGADGSWTLDPALNEVVVHGPR 151
                                       9999999999999999999999999999999*****************************996 PP

>> CW_binding_2  Putative cell wall binding repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.21   1.2e+03      18      39 ..      34      53 ..       8      87 .. 0.65
   2 ?   12.0   0.9   4.4e-05      0.26      11      61 ..     187     267 ..     166     277 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.21
                                      EEETTHHHHHHHHHHHHHT--E CS
                      CW_binding_2 18 latgfaDALsaaalaakknaPi 39
                                      +at   D L++aa+ a  + Pi
  gi|336253127|ref|YP_004596234.1| 34 VATV-VDELTGAAIDAD-GVPI 53
                                      3333.788888888874.5665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHEEET......THHHHHHHHHHHHHT--EEEE-.TSSS.-.HHHH.HHH...................... CS
                      CW_binding_2  11 aaaiakalatg......faDALsaaalaakknaPiLLtd.kldtal.kalk.sat...................... 56 
                                       a ++++    g       aDAL+++ +aa++++P L +d +  + +  +++ ++t                      
  gi|336253127|ref|YP_004596234.1| 187 AYNLSE----GgplvqpAADALVVTQMAAADGMPPLVVDpDA-E-ItLTVSsAETayaisdghdrreleppatvsia 257
                                       333333....33444335***************999998532.2.22223323333445555555555555555555 PP

                                       .....EEEES CS
                      CW_binding_2  57 .....vyilG 61 
                                            v+++G
  gi|336253127|ref|YP_004596234.1| 258 vadepVTLVG 267
                                       5555544555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); 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: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2198.16
//
Query:       gi|336253128|ref|YP_004596235.1|  [L=398]
Description: circadian clock protein KaiC [Halopiger xanaduensis SH-6]
Scores for 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-50  170.4   0.0    4.5e-50  170.1   0.0    1.1  1  ATPase         KaiC
    4.5e-06   26.2   0.0      0.019   14.3   0.0    2.2  2  DnaB_C         DnaB-like helicase C terminal domain
    4.8e-06   26.3   0.0      8e-06   25.6   0.0    1.3  1  AAA_25         AAA domain
    1.7e-05   23.6   0.1    2.5e-05   23.1   0.1    1.2  1  GvpD           GvpD gas vesicle protein
    0.00021   21.1   0.0    0.00057   19.7   0.0    1.7  1  AAA_24         AAA domain
    0.00032   20.6   0.0    0.00077   19.3   0.0    1.6  1  MEDS           MEDS: MEthanogen/methylotroph, DcmR Sensory do
  ------ inclusion threshold ------
      0.012   14.9   0.1       0.02   14.2   0.1    1.4  1  Rad51          Rad51
      0.042   13.3   0.0       0.11   12.0   0.0    1.6  2  RecA           recA bacterial DNA recombination protein
       0.11   12.3   0.0       0.16   11.6   0.0    1.3  1  AAA_30         AAA domain
       0.15   10.9   0.0       0.23   10.3   0.0    1.2  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
       0.17   11.3   0.0       0.28   10.6   0.0    1.2  1  PhoH           PhoH-like protein


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.1   0.0   2.8e-53   4.5e-50       3     229 ..     173     394 ..     171     396 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.1 bits;  conditional E-value: 2.8e-53
                            ATPase   3 tgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdleklee 79 
                                        g+eglD++++gG+pe++ +   G++GtGKt+f+lqFl +g+e+ g+p vf+++ee+ + +  +a++ G  ++++ +
  gi|336253128|ref|YP_004596235.1| 173 LGVEGLDRMIQGGVPERSLMVAIGSAGTGKTTFGLQFLNHGLER-GDPAVFIALEESRQRVLDSAREKGYAFDEFLA 248
                                       69***************************************999.******************************** PP

                            ATPase  80 egklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlkklg 155
                                        ++lai+d+   +        +++l ++ +el + ++e++a+r+v+Ds++ l + +++ a+ R+++ +++r lk+ g
  gi|336253128|ref|YP_004596235.1| 249 DDRLAIVDLDPVEM-------TNSLASIRNELPRLVDEFGAERLVLDSVSLLeMMYDDRAKRRNEIYEFARGLKEAG 318
                                       *********99965.......699****************************9999********************* PP

                            ATPase 156 vTailvsekssseeaaggygveefivdgvivLdlkeiee..elvRtleivkmRgtkhskkehpfeIteegikvlee 229
                                       vTa+l+se+  ++  ++++g+ e++ d v+v+++ + ++  e++  +ei k+R ++hs+++ p+e t++gi+v+++
  gi|336253128|ref|YP_004596235.1| 319 VTALLTSEAAAENPYNSRHGIVEYLTDAVFVMQYVRPDDfrETRLAIEIQKIRDANHSREKKPYELTDDGISVYQQ 394
                                       **************************************99899999****************************97 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 !   14.3   0.0   1.2e-05     0.019       3      63 ..     172     232 ..     171     240 .. 0.83
   2 !    9.7   0.0    0.0003      0.49     111     163 ..     263     316 ..     241     320 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                       XSSTHHHHHHCTS.BXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHH CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C   3 stgfkdLDkltsG.lqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeql 63 
                                       + g + LD++++G + +  l++  + +++Gkt++ l++ ++  + +  p +++ le s++++
  gi|336253128|ref|YP_004596235.1| 172 ELGVEGLDRMIQGgVPERSLMVAIGSAGTGKTTFGLQFLNHGLE-RGDPAVFIALEESRQRV 232
                                       678899**9997626677888888***************99886.56689999999998876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0003
                                       SXCHHHHHHHHHHHHHHTTEEEEEEEEGGGTBTS.CSSSCCCHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 111 altvseirskarrlkkekglgliviDyLqlmegs.eekenreqevseisrsLka 163
                                       + ++++ir+++ rl  e g + +v+D + l+e    ++ +r++e+ e +r+Lk+
  gi|336253128|ref|YP_004596235.1| 263 TNSLASIRNELPRLVDEFGAERLVLDSVSLLEMMyDDRAKRRNEIYEFARGLKE 316
                                       4578899*************************87555789************97 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   4.9e-09     8e-06      24     153 ..     180     292 ..     162     326 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.9e-09
                            AAA_25  24 wlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal.. 97 
                                         ++g +p+ +l + +G  gtGKtt+ l+   + + +G+           + +++++E+s++++   +r+ g a+  
  gi|336253128|ref|YP_004596235.1| 180 RMIQGGVPERSLMVAIGSAGTGKTTFGLQFLNHGLeRGD-----------PAVFIALEESRQRVLDSAREKGYAFde 245
                                       5788889**************************996666...........689********9999999988877766 PP

                            AAA_25  98 .rddarllvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsr 153
                                         +d+rl+++dl+ v + +           l++  ++l + ++e  g++ +v+D++s 
  gi|336253128|ref|YP_004596235.1| 246 fLADDRLAIVDLDPVeMTNS----------LASIRNELPRLVDE-FGAERLVLDSVSL 292
                                       55588888888876633333..........34555668888888.6788899998875 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   1.5e-08   2.5e-05      13     211 ..     192     390 ..     180     398 .] 0.72

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.5e-08
                              GvpD  13 llikGaPGtGktlftlrgld.vlrresdvlyvs.....trvddetvseay.fsgeaeldktalldllkdpleldldv 82 
                                       ++  G  GtGkt+f l++l+  l+r ++ ++++      rv d++ +  y f++  + d+ a++dl  dp+e+    
  gi|336253128|ref|YP_004596235.1| 192 MVAIGSAGTGKTTFGLQFLNhGLERGDPAVFIAleesrQRVLDSAREKGYaFDEFLADDRLAIVDL--DPVEMTNS- 265
                                       5567***************8369********97444335788888888884444445559999998..99988544. PP

                              GvpD  83 dvPiekldlesllefvdeiaaiatkliialdsw...elvyeylaerydsPediktvkndlvvlaresgvrlvlvlet 156
                                          i     + l   vd  +  a++l++  ds    e++y+  a+r +   +i      l    +e+gv  +l +e+
  gi|336253128|ref|YP_004596235.1| 266 LASI----RNELPRLVD--EFGAERLVL--DSVsllEMMYDDRAKRRN---EIYEFARGL----KEAGVTALLTSEA 327
                                       4555....467888899..556788775..663001344444444444...344444444....5999999999999 PP

                              GvpD 157 aansr.......leyivdGvvtl.nvkeddrgrlrrdlrleklrGvrignrlqPftladGkfk 211
                                       aa+++       +ey+ d v  +  v+ dd   +r  + ++k+r  +     +P+ l+d    
  gi|336253128|ref|YP_004596235.1| 328 AAENPynsrhgiVEYLTDAVFVMqYVRPDDFRETRLAIEIQKIRDANHSREKKPYELTDDGIS 390
                                       9876533334557*******999679********************9999999*999986655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.5e-07   0.00057       5      92 ..     192     308 ..     189     320 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.5e-07
                            AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel............... 59 
                                       ++ +G++g+GKTt+ +++       g+ ++fi +e++ +++ +   ++  ++++fl +                   
  gi|336253128|ref|YP_004596235.1| 192 MVAIGSAGTGKTTFGLQFlnhglerGDPAVFIALEESRQRVLDSAREKGYAFDEFLADDRLAivdldpvemtnslas 268
                                       5779********************99999***999988888877777666777777654444666778888888888 PP

                            AAA_24  60 .......aaeladyktlviDtideleelclaevirqneka 92 
                                                ++ + + lv+D+++ le + ++ ++r+ne+ 
  gi|336253128|ref|YP_004596235.1| 269 irnelprLVDEFGAERLVLDSVSLLEMMYDDRAKRRNEIY 308
                                       8888876334444699***************999999984 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.7e-07   0.00077      19      75 ..     208     264 ..     205     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.7e-07
                              MEDS  19 pfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrg 75 
                                       +f+  gl+rg++ + +a +++++++++  r++g + d++l+ ++l i+d + + +++
  gi|336253128|ref|YP_004596235.1| 208 QFLNHGLERGDPAVFIALEESRQRVLDSAREKGYAFDEFLADDRLAIVDLDPVEMTN 264
                                       79*********88888888******************************99765554 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.2e-05      0.02      16      56 ..     168     208 ..     162     317 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                       S-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHH CS
                             Rad51  16 llqlttGskklDelLgGGietgsiteifGefrsGktqlcht 56 
                                       l ++  G + lD++++GG++  s+   +G  ++Gkt +  +
  gi|336253128|ref|YP_004596235.1| 168 LPRIELGVEGLDRMIQGGVPERSLMVAIGSAGTGKTTFGLQ 208
                                       66788999****************************99876 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.4e-05      0.11      34      93 ..     171     229 ..     159     257 .. 0.82
   2 ?   -2.5   0.0       1.7   2.7e+03      76     103 ..     312     339 ..     307     365 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.4e-05
                                       E--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS--- CS
                              RecA  34 issGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehal 93 
                                       i  G  +ld  +  GG+p+  ++   G+  +Gktt+ l+ + +  ++g  a+fi  e + 
  gi|336253128|ref|YP_004596235.1| 171 IELGVEGLDRMIQ-GGVPERSLMVAIGSAGTGKTTFGLQFLNHGLERGDPAVFIALEESR 229
                                       5667777887775.********999*****************************999765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                                       HHHHTT--EEEEESS----HHHHHHTT- CS
                              RecA  76 eaqkkggvaafidaehaldpkyakklGv 103
                                       +  k++gv+a++ +e a +  y  + G+
  gi|336253128|ref|YP_004596235.1| 312 RGLKEAGVTALLTSEAAAENPYNSRHGI 339
                                       5568999999999999999999999887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.16      18      77 ..     189     247 ..     181     292 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                            AAA_30  18 drvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakll 77 
                                       + ++v+ G AGtGKtt   +  ++  ++g + + +A ++   +vL  +   +++  +++l
  gi|336253128|ref|YP_004596235.1| 189 RSLMVAIGSAGTGKTTFGLQFLNHGLERGDPAVFIALEESRQRVLDSA-REKGYAFDEFL 247
                                       56899**********986555555555666667777777666666633.33555555555 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 ?   10.3   0.0   0.00014      0.23      14      48 ..     188     222 ..     185     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                     TrwB_AAD_bind  14 etqhilivGttGsGKtqalekllrairargdraiv 48 
                                       e++ ++ +G++G+GKt+   ++l++  +rgd a+ 
  gi|336253128|ref|YP_004596235.1| 188 ERSLMVAIGSAGTGKTTFGLQFLNHGLERGDPAVF 222
                                       5667889***********************99885 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00017      0.28      18      38 ..     188     208 ..     178     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00017
                                       H-SEEEEE--TTSSTTHHHHH CS
                              PhoH  18 kndivfaiGpaGtGKtylava 38 
                                       + ++++aiG+aGtGKt + ++
  gi|336253128|ref|YP_004596235.1| 188 ERSLMVAIGSAGTGKTTFGLQ 208
                                       67899***********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2941.07
//
Query:       gi|336253129|ref|YP_004596236.1|  [L=113]
Description: hypothetical protein Halxa_1728 [Halopiger xanaduensis SH-6]
Scores for 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:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 851.81
//
Query:       gi|336253130|ref|YP_004596237.1|  [L=144]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-32  110.7   4.3      9e-32  110.5   4.3    1.0  1  Usp             Universal stress protein family
  ------ inclusion threshold ------
      0.051   13.6   0.1      0.078   13.0   0.1    1.3  1  DNA_photolyase  DNA photolyase


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 !  110.5   4.3     1e-35     9e-32       1     140 [.       1     138 [.       1     139 [. 0.97

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 1e-35
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my++Il ++Dgs++++ ++ +A++ a +r+a++++l v+d+ra+   +d + +  ++ le +++e+  + a+++a++
  gi|336253130|ref|YP_004596237.1|   1 MYETILFPTDGSDHAETVAAHAIDIATTRNAAVHVLSVVDDRAFLVLDDDRVADVRSDLEASAREATDA-AATRAAD 76 
                                       9****************************************************9999999999988765.5****** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       ++ +ve+ ve g+pae i+++a+e+++dliV+G++g +  +  ++GSvs++v+r a++pVl V
  gi|336253130|ref|YP_004596237.1|  77 HDLDVETAVETGNPAECIVDYADEHGIDLIVMGTSG-DDYENNVVGSVSQRVVRTASVPVLTV 138
                                       ************************************.999*********************87 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   8.7e-06     0.078      16     113 ..      22     127 ..      18     138 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.7e-06
                                       HHHHHHCTTSEEEEEEEE-HH...HHTCG...S-CHHHHHHHHHHHHHHHHHH.....HHTT--EEEEESSHHHHHH CS
                    DNA_photolyase  16 ALaaAaasgepvipvfvldpe...kahkl...rvgaarvdfllesLadLdeeL.....relgirLvvrrgdpadvlp 81 
                                       A+  A ++++ v+++ v+d++       l   rv++ r d+ +   ++ d++      ++l+++  v +g+pa++++
  gi|336253130|ref|YP_004596237.1|  22 AIDIATTRNAAVHVLSVVDDRaflV---LdddRVADVRSDLEASAREATDAAAtraadHDLDVETAVETGNPAECIV 95 
                                       5556777778888888888884321...2445667777766555555555555544446677999999********* PP

                                       HHHHHCTECEEEEE---SHHHHHHHHHHHHHH CS
                    DNA_photolyase  82 elakelgasavvanreyepdererdeavkeal 113
                                       ++a e+g++ +v+ ++ + +e +    v +++
  gi|336253130|ref|YP_004596237.1|  96 DYADEHGIDLIVMGTSGDDYENNVVGSVSQRV 127
                                       *************9999999998888776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1142.33
//
Query:       gi|336253131|ref|YP_004596238.1|  [L=475]
Description: hypothetical protein Halxa_1730 [Halopiger xanaduensis SH-6]
Scores for 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   13.3   0.1       0.29   11.5   0.0    2.0  2  ParBc        ParB-like nuclease domain
        1.8    9.1   5.9       0.15   12.5   0.7    2.0  2  YadA_head    Head domain of trimeric autotransporter adhesin


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 ?   -3.0   0.0         1   9.4e+03      65      80 ..      72      86 ..      66      91 .. 0.67
   2 ?   11.5   0.0   3.2e-05      0.29      32      69 ..     358     405 ..     318     423 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1
                             ParBc 65 glkevpvivleiddee 80
                                      + +++ viv+  +d++
  gi|336253131|ref|YP_004596238.1| 72 R-SPINVIVRGETDQI 86
                                      4.67888888877776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.2e-05
                             ParBc  32 k.........kGllqPiivrktrqgryeiiaG.erRlrAakrlglkev 69 
                                       +         +Gll P+i+ + +   y i +G erRl Aa  + l+  
  gi|336253131|ref|YP_004596238.1| 358 TvdaftahmiAGLLYPVIAVGLPVAAYAIASGlERRLDAALAASLSLA 405
                                       04444445559*********************88*****988876554 PP

>> YadA_head  Head domain of trimeric autotransporter adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   1.7e-05      0.15      12      24 ..     142     154 ..     141     157 .. 0.92
   2 ?   -4.0   0.4         2   1.8e+04      18      24 ..     383     389 ..     382     389 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                         YadA_head  12 nAtAsGdnSiAiG 24 
                                       nAtA++++S+AiG
  gi|336253131|ref|YP_004596238.1| 142 NATAEANGSTAIG 154
                                       9************ PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2
                         YadA_head  18 dnSiAiG 24 
                                       +++iA G
  gi|336253131|ref|YP_004596238.1| 383 AYAIASG 389
                                       5666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3462.52
//
Query:       gi|336253132|ref|YP_004596239.1|  [L=75]
Description: DNA-directed RNA polymerase subunit H [Halopiger xanaduensis SH-6]
Scores for complete 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-25   88.9   0.7    1.6e-25   88.7   0.7    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
     0.0072   16.5   2.2        1.1    9.5   2.2    2.2  1  DUF3006         Protein of unknown function (DUF3006)


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 !   88.7   0.7   1.8e-29   1.6e-25       1      73 []       2      73 ..       2      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 1.8e-29
                                      ..-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                    RNA_pol_Rpb5_C  1 vnitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                      v++++HelvP+h+vl+ee  +e+l++++i++++LPki+++Dp++   +++ Gdv+kI+r+s+t+++av+YRlV
  gi|336253132|ref|YP_004596239.1|  2 VDVSQHELVPEHTVLEEETLEEVLDEYDIDRTDLPKIKRNDPALP-DEAEVGDVIKIVRDSRTTDQAVVYRLV 73
                                      689*****************************************7.59************************9 PP

>> DUF3006  Protein of unknown function (DUF3006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   2.2   0.00012       1.1      11      41 ..      14      58 ..       8      71 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
                           DUF3006 11 AVleled.getid...........iprsd..LpegakeGdvLeie 41
                                       Vle e  +e++d           i+r+d  Lp++a+ Gdv++i 
  gi|336253132|ref|YP_004596239.1| 14 TVLEEETlEEVLDeydidrtdlpkIKRNDpaLPDEAEVGDVIKIV 58
                                      577777777777777744444444444433366777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 574.14
//
Query:       gi|336253133|ref|YP_004596240.1|  [L=524]
Description: RNA polymerase subunit beta [Halopiger xanaduensis SH-6]
Scores for complete 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  171.6   0.1    1.8e-50  171.3   0.1    1.1  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    5.4e-27   94.7   0.1    8.2e-27   94.1   0.1    1.2  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    8.6e-24   83.5   0.0    1.6e-23   82.6   0.0    1.5  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3


Domain annotation for each model (and alignments):
>> 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 !  171.3   0.1     3e-54   1.8e-50       2     202 ..      21     402 ..      20     403 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.3 bits;  conditional E-value: 3e-54
                                       TTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBXE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1   2 LvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltYs 78 
                                       L++ +  SFn+f++  ++++++e+++i ++   ++ +e ++++++++r+  P v+e+d+se+ +yP+earlrn+tYs
  gi|336253133|ref|YP_004596240.1|  21 LAEHHYRSFNAFLNRGMQEVVDEKETIDTDIGDKEGEEPVHVELGDVRVVTPRVREADGSEELLYPQEARLRNITYS 97 
                                       788999*************************99877777************************************** PP

                                       EEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1  79 aplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqek 155
                                       ap+++++  v  e+ +++  +++e +iG++P+M+ s++c++ + s+eelve++E+p d+GGyFi+nG+e+v++  e+
  gi|336253133|ref|YP_004596240.1|  98 APVFMEMSIVKGEEGDERVVDSTETKIGRMPIMVGSEKCNIAGFSDEELVEIGEDPADPGGYFIVNGSERVLMTSED 174
                                       ***********9999************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|336253133|ref|YP_004596240.1| 175 lapnkilaeydtkygdeiqvaktfsqrrgyralvlcertrdgllevsfpsvsgsinfvtlvralglesdeeivhkvs 251
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|336253133|ref|YP_004596240.1| 252 ndpevvkymlenleeaevqteeeaiealgkrvasgqgknyqlkranyvidryllphlhedgvdeedvrinkahylcr 328
                                       ***************************************************************************** PP

                                       ...........................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHH CS
                                       ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1 156 ...........................laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpit 202
                                                                  + G+L+++lfr++l+kl+rdvk +l++   ++++l+++ +v+++ +t
  gi|336253133|ref|YP_004596240.1| 329 maeacfelalgrreaddkdhyankrlkVSGDLMKDLFRTALNKLARDVKYQLERANMRNRQLSVSTVVRSDVLT 402
                                       *********************************************************************99876 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 !   94.1   0.1   1.4e-30   8.2e-27      13     190 .]     177     355 ..     167     355 .. 0.84

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 1.4e-30
                                       SSSE.............SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSS CS
                    RNA_pol_Rpb2_2  13 knki.............satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericyd 76 
                                       +nki             +a+  s +  +r++vl +++ ++ l ++ +s+   i++v + +Algl sd+eI+ +++  
  gi|336253133|ref|YP_004596240.1| 177 PNKIlaeydtkygdeiqVAKTFSQRRGYRALVLCERTRDGLLEVSFPSVSGSINFVTLVRALGLESDEEIVHKVS-- 251
                                       45555555555555556677777888899999999999999**********************************.. PP

                                       STTHHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSST.C CS
                    RNA_pol_Rpb2_2  77 sedsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglsesl.e 152
                                        +d+++ + +le+  e++e+qt+eea++ +gk+va ++g++ +l++a  ++         +r+ l+ hl  +    e
  gi|336253133|ref|YP_004596240.1| 252 -NDPEVVKYMLEN-LEEAEVQTEEEAIEALGKRVASGQGKNYQLKRANYVI---------DRYLLP-HLHEDGVDeE 316
                                       .677776655555.566789****************************996.........8*****.**88765404 PP

                                       HH...HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                    RNA_pol_Rpb2_2 153 nkr.lkaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                         r  ka+++  m+++ ++l+lgrre DD+Dh++nkR++
  gi|336253133|ref|YP_004596240.1| 317 DVRiNKAHYLCRMAEACFELALGRREADDKDHYANKRLK 355
                                       56789********************************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 !   82.6   0.0   2.7e-27   1.6e-23       1      66 [.     423     485 ..     423     487 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 2.7e-27
                    RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLalla 66 
                                       q++dr+n++  lshlrr++s+   ls+++ ++e+Rdlh+++wGri p+eTPEG+ncGlvk++a+ +
  gi|336253133|ref|YP_004596240.1| 423 QLVDRTNYMGVLSHLRRLRSP---LSRSQPHFEARDLHATQWGRIGPSETPEGPNCGLVKNFAQAV 485
                                       899******************...**************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); 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:                         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 0.26s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3548.64
//
Query:       gi|336253134|ref|YP_004596241.1|  [L=609]
Description: DNA-directed RNA polymerase subunit B [Halopiger xanaduensis SH-6]
Scores for complete 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-128  429.5   0.0   1.6e-128  429.1   0.0    1.1  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    1.9e-29  101.9   0.1    3.5e-29  101.1   0.1    1.5  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
      4e-21   75.1   0.4    7.3e-21   74.2   0.4    1.4  1  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    4.3e-10   40.0   5.4    1.3e-09   38.5   5.4    1.9  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
     0.0077   16.1   0.8      0.015   15.2   0.8    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.18   12.0   0.1       0.35   11.0   0.1    1.4  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
       0.41   10.8   2.5       0.72   10.1   2.5    1.4  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
        1.6    8.2   3.4         17    5.0   0.1    2.3  2  zf-ribbon_3     zinc-ribbon 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 !  429.1   0.0  7.2e-132  1.6e-128       2     390 .]     140     512 ..     139     512 .. 0.96

  Alignments for each domain:
  == domain 1  score: 429.1 bits;  conditional E-value: 7.2e-132
                                       HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SE CS
                    RNA_pol_Rpb2_6   2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalG 78 
                                       a  +p++eh+ spri++ a m kq+lg+ s+n+  r +++ +ll+++q  +vkt+ + e+++        +++ ++ 
  gi|336253134|ref|YP_004596241.1| 140 AGMIPYPEHNASPRITMGAGMIKQSLGLPSANYRIRPDTRQHLLHYPQLSMVKTQ-TTEQIG--------YDDRPAA 207
                                       7789***************************************************.999999........9****** PP

                                       EEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.....-SS-GGGS-TTS CS
                    RNA_pol_Rpb2_6  79 qnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.....seealkkLdedG 150
                                       qn+vVAvmsyeG+niEDa+++n+++v+r +++s+++++ye e r++++g+e+ ++ ++++     +e+a+++LdedG
  gi|336253134|ref|YP_004596241.1| 208 QNFVVAVMSYEGFNIEDALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRFEIPSQDvrgarGEDAYAHLDEDG 284
                                       **************************************************99998888879**************** PP

                                       B--SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT-- CS
                    RNA_pol_Rpb2_6 151 ivrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvn 227
                                       +v++++ev e+++l gk+  ++ ++ +e   +     +   + ++ts++++sge+gvVd+v++        + ++++
  gi|336253134|ref|YP_004596241.1| 285 LVNPETEVDENSVLLGKT--SPPRFLEEPDDMGGLSPQ---KRRETSVTMRSGESGVVDTVTL-------MEGEDGS 349
                                       *****************8..899999766666555555...5679******************.......6888999 PP

                                       EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSS CS
                    RNA_pol_Rpb2_6 228 klvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaale 304
                                       kl kv v+++R +++GDKfasrhGqKGvv+ ++pqeDmPf+e+G v+D+vlNP+++PSRmt+g++lE++ gk ++le
  gi|336253134|ref|YP_004596241.1| 350 KLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTESGLVPDLVLNPHALPSRMTVGHILEMIGGKLGSLE 426
                                       ***************************************************************************** PP

                                       SS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT CS
                    RNA_pol_Rpb2_6 305 gkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpysllt 381
                                       g++vd+t+F g++e++++e Leeag+e+sGke++y+G+tGek+eaeifvGvi+y+kL+h+v++K+haRs+Gp+++lt
  gi|336253134|ref|YP_004596241.1| 427 GRRVDGTPFLGEDEDKLREGLEEAGFESSGKETMYSGVTGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRGPVQVLT 503
                                       ***************************************************************************** PP

                                       --B-SCGGG CS
                    RNA_pol_Rpb2_6 382 qQPlgGkaq 390
                                       +QP++G+a+
  gi|336253134|ref|YP_004596241.1| 504 RQPTEGRAR 512
                                       *******96 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 !  101.1   0.1   1.5e-32   3.5e-29       1      86 [.     514     605 ..     514     606 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 1.5e-32
                                       BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHH CS
                    RNA_pol_Rpb2_7   1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafklL 71 
                                       GGlr+GEMErd+ i++Gaa++Lkerl+++SD+  + +c +c++ a++n      +C+++++e++i+++e+++afklL
  gi|336253134|ref|YP_004596241.1| 514 GGLRIGEMERDVFIGHGAAMTLKERLLDESDREYIPICANCGMSAVENveqrrvYCPNCDEETDIHEIEMSYAFKLL 590
                                       9*********************************************99***************************** PP

                                       HHHHHHTTBEEEEES CS
                    RNA_pol_Rpb2_7  72 lqeLqslgialklll 86 
                                       l+e+++lgia++l+l
  gi|336253134|ref|YP_004596241.1| 591 LDEMKALGIAPRLEL 605
                                       ***********9975 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 !   74.2   0.4   3.2e-24   7.3e-21       1      62 []      10      71 ..      10      71 .. 0.99

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 3.2e-24
                                      EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE-S CS
                    RNA_pol_Rpb2_4  1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiVe 62
                                      V+vNG+l+G++ +p++l+e++Re RR g++se v+++++++++ev i+ D+GR++RPl++Ve
  gi|336253134|ref|YP_004596241.1| 10 VYVNGSLVGTHPNPNELAEQIREARRIGDVSEMVNVSVKDRTREVIINADAGRARRPLLVVE 71
                                      9************************************************************7 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 !   38.5   5.4   5.6e-13   1.3e-09       1      58 []      92     132 ..      92     132 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 5.6e-13
                                       HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEES-G CS
                    RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcEIhP 58 
                                       +ddL+++g +E++DaeEEe++++a++++dl+++                 +TH+EI+P
  gi|336253134|ref|YP_004596241.1|  92 FDDLVDHGYIEFIDAEEEEDILVAVDEDDLTEK-----------------HTHLEIDP 132
                                       9*****************************776.................79999999 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 !   15.2   0.8   6.7e-06     0.015      30      57 ..     550     577 ..     549     578 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.7e-06
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfead 57 
                                        C++Cg    e++++r+++CpnC  e d
  gi|336253134|ref|YP_004596241.1| 550 ICANCGMSAVENVEQRRVYCPNCDEETD 577
                                       5**********************98765 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   0.1   0.00016      0.35       5      33 ..     545     576 ..     542     588 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                      NOB1_Zn_bind   5 kswvlrChaCfkvt.kd..mtkkFCpkCGnkt 33 
                                       ++++  C  C     ++  +++++Cp+C ++t
  gi|336253134|ref|YP_004596241.1| 545 REYIPICANCGMSAvENveQRRVYCPNCDEET 576
                                       899*******87553334599*******9966 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 ?   10.1   2.5   0.00032      0.72      18      40 .]     551     573 ..     549     573 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00032
                     Auto_anti-p27  18 CpvCgvPLmrdrkggkvyCvaCd 40 
                                       C +Cg+  +++ ++ +vyC++Cd
  gi|336253134|ref|YP_004596241.1| 551 CANCGMSAVENVEQRRVYCPNCD 573
                                       **********9999********7 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   0.5     0.025        56      18      24 ..     550     556 ..     549     557 .. 0.86
   2 ?    5.0   0.1    0.0074        17       3      10 ..     567     574 ..     566     577 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.025
                       zf-ribbon_3  18 vCpyCGt 24 
                                       +C++CG+
  gi|336253134|ref|YP_004596241.1| 550 ICANCGM 556
                                       8*****6 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0074
                       zf-ribbon_3   3 vrCPnCGa 10 
                                       v+CPnC++
  gi|336253134|ref|YP_004596241.1| 567 VYCPNCDE 574
                                       79****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4453.11
//
Query:       gi|336253135|ref|YP_004596242.1|  [L=975]
Description: DNA-directed RNA polymerase subunit A' [Halopiger xanaduensis SH-6]
Scores for complete 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-112  376.1   0.0   3.8e-112  374.7   0.0    1.7  2  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    2.4e-68  229.6   0.3    3.8e-68  228.9   0.3    1.3  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    7.8e-32  109.4   0.0    1.8e-31  108.3   0.0    1.7  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    2.2e-28   99.2   0.0      4e-28   98.3   0.0    1.4  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    2.1e-26   92.9   0.0    4.1e-26   92.0   0.0    1.5  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
     0.0087   16.1   0.0      0.025   14.6   0.0    1.8  1  HTH_3           Helix-turn-helix


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 !  374.7   0.0  1.3e-115  3.8e-112       2     312 .]       7     382 ..       6     382 .. 0.95
   2 ?   -2.1   0.0      0.62   1.9e+03     258     289 ..     716     747 ..     705     758 .. 0.76

  Alignments for each domain:
  == domain 1  score: 374.7 bits;  conditional E-value: 1.3e-115
                                       E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLak 78 
                                       k+i +i+fg+++pee+r++S++++ +a+t++++  +P ++Gl+D+rlg+id  leC+tCgk++ +C+ghfGhieLa+
  gi|336253135|ref|YP_004596242.1|   7 KDIGSINFGLMEPEEYREMSATKIITADTYDDDG-FPIDMGLMDPRLGVIDPGLECKTCGKHSGSCNGHFGHIELAA 82 
                                       7899****************************95.****************************************** PP

                                       EEE-HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHH..HHHCSSSCCCCHHHHHHHHCCS-BE-SSSSB-EEE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                    RNA_pol_Rpb1_1  79 Pvfhigffklilkilecvckecskllldeekkkllsklk..krekleelkkrlkaieelckkinlcekCgavqpkl. 152
                                       Pv+h+gf+kli+++l+ +c+ecs+lll+e +++ +  +   +r+  ++l++  ka  +  +k++ c +Cg +q  + 
  gi|336253135|ref|YP_004596242.1|  83 PVIHVGFTKLIRRLLRGTCRECSRLLLTEDERDEFRGQLdeSRKLGRDLNDVTKAAIRQARKKDRCPFCGEIQYDId 159
                                       *****************************998877665533555568899999**9**************9666667 PP

                                       ...............EEETTEEEEEESSSST.............................................. CS
                                       ...............xxxxxxxxxxxxxxxx.............................................. RF
                    RNA_pol_Rpb1_1 153 ...............eeegeklkaalkkske.............................................. 168
                                                      +e+++++ aa++ +++                                              
  gi|336253135|ref|YP_004596242.1| 160 hekpttyyevqqvltSEYSQQIAAAMQGEEDgermspdelaeetdidlgrvneilsgsfrpresqrkaiekaldidl 236
                                       7777778888888899***********9999********************************************** PP

                                       ..SCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHHHHHHH CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 169 ..eekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDlteklrdiik 243
                                         e+++kl+++++++++++i+ded+evlg++s++srPew+iltvlPVpP+++RPs++ld+g+rsedDlt+kl+dii+
  gi|336253135|ref|YP_004596242.1| 237 teEDTNKLMPSDIRDWFEDIPDEDIEVLGIDSDRSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDLTHKLVDIIR 313
                                       *8888************************************************************************ PP

                                       HHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 244 rNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrfRgnL 312
                                       +N+r+++++e+gap+liie+ +elLQ+hv+t++dneisg++pa+++s+rplk+lsqrLkGKeGrfRg+L
  gi|336253135|ref|YP_004596242.1| 314 INQRFMENREAGAPQLIIEDLWELLQYHVTTFMDNEISGTPPARHRSGRPLKTLSQRLKGKEGRFRGSL 382
                                       *******************************************************************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.62
                                       STCHHHHHHHHHHHHHHCC-TTSSSSSEEBST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 258 eliieeekelLQehvatlfdneisglkpatqk 289
                                       + +i++  + +Qe ++++ +ne ++l+  t  
  gi|336253135|ref|YP_004596242.1| 716 DETIDDAYDRVQELIEAYENNELESLPGRTID 747
                                       56789999999**********99988765555 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 !  228.9   0.3   1.3e-71   3.8e-68       1     166 []     384     550 ..     384     550 .. 0.99

  Alignments for each domain:
  == domain 1  score: 228.9 bits;  conditional E-value: 1.3e-71
                                       SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT CS
                    RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkak 77 
                                       Gkrv++saR+vispdp+l+l+evgvP +vak +t +  vte n +  r++v+ngpe +Pga+yv+r dg++ k+++k
  gi|336253135|ref|YP_004596242.1| 384 GKRVNFSARTVISPDPTLSLNEVGVPDRVAKEMTQTMNVTERNLEDARRFVANGPEAHPGANYVRRPDGRRLKVTEK 460
                                       9**************************************************************************99 PP

                                       -S.CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SS CS
                    RNA_pol_Rpb1_2  78 kr.klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqs 153
                                       +  +la+++e g+ v+rh+ dgd+v++NRqPsLh++simah+v v+++kt+rln++v+ +yNaDFDGDemn+h  q+
  gi|336253135|ref|YP_004596242.1| 461 NCeALAEKVEAGWEVNRHLVDGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQN 537
                                       9867************************************************************************* PP

                                       HHHHHHHHHCSBT CS
                    RNA_pol_Rpb1_2 154 eearaEaeelllv 166
                                       eearaEa+ l+ v
  gi|336253135|ref|YP_004596242.1| 538 EEARAEARVLMRV 550
                                       **********975 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 !  108.3   0.0   6.1e-35   1.8e-31       1     108 []     730     836 ..     730     836 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 6.1e-35
                                       HHHHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEE CS
                    RNA_pol_Rpb1_4   1 ieeaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqn 77 
                                       ie++e+ ++le+lpg++ +e++e+ki++ l++ard+ag+ia ++ +++N+ ++M++sGa+Gs++n++q+ag +Gqq+
  gi|336253135|ref|YP_004596242.1| 730 IEAYEN-NELESLPGRTIDETLEMKIMQTLSRARDNAGNIADEHFDDENPAVVMANSGARGSMLNLTQMAGAVGQQA 805
                                       678888.***************************************77***************************** PP

                                       BTTBSS--SSTSCSSTTSSSSESSTTTSSEE CS
                    RNA_pol_Rpb1_4  78 vegkripkgfsgrtlphfkkidespesrGFv 108
                                       v+g+ri++g+++rtl h++++d s+e++GFv
  gi|336253135|ref|YP_004596242.1| 806 VRGERINRGYEDRTLSHYEPNDLSAEAHGFV 836
                                       ******************************8 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 !   98.3   0.0   1.3e-31     4e-28       1     156 [.     553     704 ..     553     705 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 1.3e-31
                                       CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESS.SEBEEHHHHHHCCCH CS
                    RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkp.kelwtgkqtfsrilp 76 
                                       +ilsp+ g+ +ig +QD+++G+yllT ++  +++ +a+ ll+    +   ++  ++ i    k+ wtg ++fs +lp
  gi|336253135|ref|YP_004596242.1| 553 QILSPRFGENIIGAIQDHISGMYLLTADNPRFNETQALDLLRATRID---ELPEPSGIDDEgKPFWTGYDVFSELLP 626
                                       79******************************************665...33455567777888************* PP

                                       CCCCEEEE.SSSSSTSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCEB- CS
                    RNA_pol_Rpb1_3  77 neinyerk.neekdgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyllqsgfti 152
                                       +++n+e + +    ++v+i++g+l++G+i +  vg +  g+++++++k yg ++++ f++ ++ l+++ +++ gf+i
  gi|336253135|ref|YP_004596242.1| 627 DDLNLEFTgT-V-GDQVVIEDGQLVEGTIAEDEVG-EFGGEIVDTITKIYGNTRARIFINEVSTLAMRAIMHFGFSI 700
                                       *******743.3.489*******************.999************************************** PP

                                       TGGG CS
                    RNA_pol_Rpb1_3 153 gigD 156
                                       gi+D
  gi|336253135|ref|YP_004596242.1| 701 GIDD 704
                                       ***9 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 !   92.0   0.0   1.4e-29   4.1e-26       1      66 [.     843     908 ..     843     959 .. 0.92

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 1.4e-29
                                       B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                       GL++ efffh+mggReGL+DtAv+T++sGYlqRrl++al ++  +yd+tvr+++ +ivqf +gedg
  gi|336253135|ref|YP_004596242.1| 843 GLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYDGTVRDTSDTIVQFEFGEDG 908
                                       9****************************************************************9 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.4e-06     0.025      10      54 ..     194     238 ..     192     238 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.4e-06
                                       HHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                             HTH_3  10 lsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54 
                                       +s  eLAe++++    ++ i +G  +P+ +  k+++kaL+++l+e
  gi|336253135|ref|YP_004596242.1| 194 MSPDELAEETDIDLGRVNEILSGSFRPRESQRKAIEKALDIDLTE 238
                                       6778*************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (975 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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: 0.75u 0.28s 00:00:01.03 Elapsed: 00:00:00.45
# Mc/sec: 6543.65
//
Query:       gi|336253136|ref|YP_004596243.1|  [L=407]
Description: DNA-directed RNA polymerase subunit A'' [Halopiger xanaduensis SH-6]
Scores for complete 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-54  185.2   0.3    1.8e-54  185.0   0.3    1.1  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5


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 !  185.0   0.3     1e-58   1.8e-54      44     265 ..      35     337 ..       7     339 .. 0.90

  Alignments for each domain:
  == domain 1  score: 185.0 bits;  conditional E-value: 1e-58
                                       EETTSEEEETTS-EEESSGGGTS...........B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5  44 vkyddtvrnsggeivqflygedg...........lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvp 109
                                        + d tv +++                        v+p + vG+++aQSiGePgTQlt+nTFH+aGva+  vt+G+p
  gi|336253136|ref|YP_004596243.1|  35 GRTDATVEDADE----------LakavesryvdtRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLP 101
                                       444444444433..........033333333333999999************************************* PP

                                       HHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSE.................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................... RF
                    RNA_pol_Rpb1_5 110 rlkeilnvskniksksltvllvdeeakelekakkvkkaiek.................................... 150
                                       rl e++++ k+  ++++tv+l de+a+e+eka++v  +ie                                     
  gi|336253136|ref|YP_004596243.1| 102 RLIELVDARKTPDTPMMTVYLEDEYATEREKAHEVVWNIEAtkilalgdvstnvadmrvqislnedtlrermiepee 178
                                       *********************************999999999999******************************** PP

                                       .............................................CBTTEEEEEEEEEEEEEEETEEEEEEECS--H CS
                                       .............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 151 .............................................gikkikrilvkeaekgkeeekelvletegvnl 182
                                                                                    gi++i+r++++++e  + + +e+vl teg ++
  gi|336253136|ref|YP_004596243.1| 179 vaeiiednlgvkaiqqgtqiqfgpeepsyrdllqlveelreitfkGIEDISRVVIRREEMDHGD-EEFVLYTEGSAF 254
                                       ********************************************************99988888.89********** PP

                                       HHHTTSTTTBETTTEEESSHHHHHHHHCHHHHHHHHHHHHHHHHHHTTS.---HHHHHHHHHHHTTTSS---SSTTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 183 sevlkveevvdageilsndiaeileilgieaarkallkeiqevykvqgv.svndrHlelivdqmtkkgeivavnrsG 258
                                        +vl++e+ vda+++++n+i+ei + lgieaar+a+++e ++++++qg+ +vn rHl+l++d+mt +gei +++r+G
  gi|336253136|ref|YP_004596243.1| 255 GDVLEIEG-VDASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLdDVNVRHLMLVADIMTNRGEIESIGRHG 330
                                       ********.***************************************945************************** PP

                                       HCCSSSH CS
                                       xxxxxxx RF
                    RNA_pol_Rpb1_5 259 inkaels 265
                                       i  ++ s
  gi|336253136|ref|YP_004596243.1| 331 ISGSKDS 337
                                       *987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2968.73
//
Query:       gi|336253137|ref|YP_004596244.1|  [L=159]
Description: NusA family KH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-11   43.0   0.1    2.1e-10   40.5   0.0    2.0  2  KH_5      NusA-like KH domain
    1.2e-10   41.0   0.1    8.1e-05   22.4   0.0    2.2  2  KH_2      KH domain
    9.1e-08   31.9   0.1     0.0009   19.1   0.0    2.2  2  KH_4      KH domain
    0.00054   19.7   0.0      0.019   14.7   0.0    2.3  2  KH_1      KH domain


Domain annotation for each model (and alignments):
>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   4.6e-14   2.1e-10       2      69 .]      51     112 ..      50     112 .. 0.97
   2 ?    0.1   0.0      0.19   8.6e+02      19      32 ..     129     142 ..     117     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 4.6e-14
                              KH_5   2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVki 69 
                                       ++r +v+V s++     +G+++g  G+ +k  +++  +  +++ve  +D++ f+anal+Pa v +V+i
  gi|336253137|ref|YP_004596244.1|  51 DDRLIVVVSSGQ-----LGEAIGPDGRTVKRFEEQV-DASVRLVEDADDPEAFVANALAPAAVYNVTI 112
                                       799*********.....*******************.***************************9986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.19
                              KH_5  19 vGaivgkkGsrika 32 
                                        G ++g +G+ i++
  gi|336253137|ref|YP_004596244.1| 129 RGVAIGSNGRTIET 142
                                       58899999999975 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.8e-08   8.1e-05      24      63 ..      51      90 ..      28      99 .. 0.87
   2 !   17.0   0.0   8.8e-07    0.0039       5      59 ..      97     152 ..      93     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.8e-08
                                      SCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHT CS
                              KH_2 24 anrviiviresqpgivIGkgGsnikkigkelrkdiekleg 63
                                       +r+i+v+ ++q g +IG  G+++k+ ++++   ++ +e+
  gi|336253137|ref|YP_004596244.1| 51 DDRLIVVVSSGQLGEAIGPDGRTVKRFEEQVDASVRLVED 90
                                      389******************************9999887 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 8.8e-07
                                       HHHHHTECETEEEEEEECCSCEEEEEEE.ESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                              KH_2   5 slaveikkagvskveIertanrviivir.esqpgivIGkgGsnikkigkelrkdie 59 
                                       ++a+ ++ a v +v I ++ + v +v+  ++  g++IG +G++i++ +  +++ ++
  gi|336253137|ref|YP_004596244.1|  97 FVANALAPAAVYNVTISENGDTVAYVEVaTEDRGVAIGSNGRTIETARRLAKRHFG 152
                                       566666777888999988778888886526789****************9998875 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1     8e-05      0.36       4      52 ..      28      75 ..      25      76 .. 0.74
   2 !   19.1   0.0     2e-07    0.0009      15      58 ..     105     147 ..      95     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8e-05
                              KH_4  4 vedilkalvddpeevevtee.eeeeeveielnvegedlGrvIGkrGrtld 52
                                      +++ +++  d  ++v+ +++ + ++++++ + v++ +lG  IG +Grt++
  gi|336253137|ref|YP_004596244.1| 28 IRQTVDGAGD--ANVNADADaDAADDDRLIVVVSSGQLGEAIGPDGRTVK 75
                                      5555555444..34555555567899**********************86 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2e-07
                              KH_4  15 peevevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylv 58 
                                       ++  +vt++ e+ +++  ++v++ed G+ IG +Grt+   + l+
  gi|336253137|ref|YP_004596244.1| 105 AAVYNVTIS-ENGDTVAYVEVATEDRGVAIGSNGRTIETARRLA 147
                                       345678887.55678999*******************8766665 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.3e-06     0.019       4      41 ..      56      92 ..      52     123 .. 0.80
   2 ?    2.9   0.0     0.022        97       4      23 ..     122     141 ..     119     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.3e-06
                                      EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT. CS
                              KH_1  4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksede 41
                                      + v s + g  IG+ G+++k+ +e+  a++++++ +++
  gi|336253137|ref|YP_004596244.1| 56 VVVSSGQLGEAIGPDGRTVKRFEEQVDASVRLVE-DAD 92
                                      67889999999*************87*****984.332 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.022
                                       EEEGGGHHHHHHTGGGHHHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnIk 23 
                                       ++v ++  g  IG +G++I 
  gi|336253137|ref|YP_004596244.1| 122 VEVATEDRGVAIGSNGRTIE 141
                                       67788888999*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1175.75
//
Query:       gi|336253138|ref|YP_004596245.1|  [L=142]
Description: 30S ribosomal protein S23 (S12) [Halopiger xanaduensis SH-6]
Scores for 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-50  167.8   0.4    6.8e-50  167.5   0.4    1.1  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 !  167.5   0.4   3.8e-54   6.8e-50       1     113 [.      27     140 ..      27     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 167.5 bits;  conditional E-value: 3.8e-54
                                       --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE- CS
                   Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGi 77 
                                       r+++++++ksd+legapq rG+vlekv++eak+PnsA+Rk+vrv+Likngk+vtaf+pg+ga++f+dEhdev+++Gi
  gi|336253138|ref|YP_004596245.1|  27 RRARGLREKSDPLEGAPQGRGIVLEKVGIEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGAISFIDEHDEVTIAGI 103
                                       678899*********************************************************************** PP

                                       -......BTTSTTEEEEBETS---TSSSTTTTT---- CS
                   Ribosom_S12_S23  78 rrk.gkavkDlpGvrykvvkvagvslkalskykkekp 113
                                       +++ g+a++Dl+Gv+ykv kv+gv lk+l+++++ekp
  gi|336253138|ref|YP_004596245.1| 104 GGAkGRAMGDLSGVNYKVDKVNGVALKELVRGNAEKP 140
                                       9988*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1123.47
//
Query:       gi|336253139|ref|YP_004596246.1|  [L=202]
Description: 30S ribosomal protein S7 [Halopiger xanaduensis SH-6]
Scores for 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-36  124.1   4.2    4.2e-36  123.8   4.2    1.0  1  Ribosomal_S7  Ribosomal protein S7p/S5e
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.18   11.8   0.0    1.3  1  DUF2420       Protein of unknown function (DUF2420)


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 !  123.8   4.2   4.7e-40   4.2e-36      13     149 .]      57     202 .]      48     202 .] 0.94

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 4.7e-40
                                       ---SSTTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBE CS
                      Ribosomal_S7  13 lpdpkynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGaty 85 
                                       ++ +k + ++ve++in+lm+    +Gkk++  + v++a++i++e+t+++p++vl++A+en++Pr+e+ ++++GG+++
  gi|336253139|ref|YP_004596246.1|  57 KQFKKSQISIVERFINRLMQteenTGKKQKTLNAVREAFEIVHERTEDNPIQVLVTAVENAAPREETVRLKYGGISV 133
                                       445568999******************************************************************** PP

                                       EEEEEE-HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                      Ribosomal_S7  86 qvpvevrpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                       + +v+v+p+Rr+++Al++++e++   ++++ ++++e++a++li Aa+ +   +av+++ee +r+A a+r
  gi|336253139|ref|YP_004596246.1| 134 PKAVDVAPQRRVDQALKFLAEGVyndSFKTATPVEEAIANQLIGAANYDvqTYAVSQKEEKERVAAAAR 202
                                       ***********************88888888899**************999***************987 PP

>> DUF2420  Protein of unknown function (DUF2420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     2e-05      0.18      43      80 ..      70     105 ..      49     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                           DUF2420  43 eL.dltltEdnvynkdislndilsifkiLkenskseedv 80 
                                        +  l+ tE+n+  k+ +ln + + f+i +e++  e d+
  gi|336253139|ref|YP_004596246.1|  70 FInRLMQTEENTGKKQKTLNAVREAFEIVHERT--E-DN 105
                                       4457899**************************..3.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 1712.97
//
Query:       gi|336253140|ref|YP_004596247.1|  [L=254]
Description: hypothetical protein Halxa_1740 [Halopiger xanaduensis SH-6]
Scores for 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  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1897.63
//
Query:       gi|336253141|ref|YP_004596248.1|  [L=728]
Description: translation elongation factor aEF-2 [Halopiger xanaduensis SH-6]
Scores for 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-65  218.3   0.3    1.1e-64  217.5   0.3    1.4  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    3.5e-24   84.9   0.0    1.1e-23   83.3   0.0    1.9  1  EFG_IV       Elongation factor G, domain IV
    5.8e-24   83.9   0.1    6.8e-23   80.5   0.0    2.6  2  EFG_C        Elongation factor G C-terminus
    7.2e-22   77.3   0.4    2.4e-21   75.6   0.4    2.0  1  EFG_II       Elongation Factor G, domain II
    8.4e-19   67.7   1.7    9.7e-18   64.3   0.8    3.0  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    2.9e-05   24.1   0.3    0.00021   21.4   0.1    2.5  2  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.041   13.7   0.0      0.092   12.6   0.0    1.6  1  RF3_C        Class II release factor RF3, C-terminal domain
      0.087   12.7   0.2        1.3    8.9   0.0    2.7  3  RsgA_GTPase  RsgA GTPase
       0.17   11.5   0.0       0.39   10.3   0.0    1.5  1  Ras          Ras family


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 !  217.5   0.3   5.6e-68   1.1e-64       1     193 [.      19     258 ..      19     259 .. 0.91

  Alignments for each domain:
  == domain 1  score: 217.5 bits;  conditional E-value: 5.6e-68
                                       TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.T.TCSSEEEEEE CS
                          GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.k.etkkylinli 75 
                                       ++irni+i++hvDhGKtTL+d+Ll+ +g+is+  e+a+e+ ++Dt ++E+ergiTi++a++s+  + e++++linli
  gi|336253141|ref|YP_004596248.1|  19 ENIRNIAIAAHVDHGKTTLSDNLLAGAGMISD--ETAGEQLAMDTEEDEQERGITIDAANVSMThEyEGENHLINLI 93 
                                       589*****************************..77888999**********************6269********* PP

                                       EESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  76 DtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsr 152
                                       DtPGHvdF  +v+r++r++Dga++vvdaveG +pqte+vlr+al+egv++ +fiNK+Drl++el+e +ee++++l +
  gi|336253141|ref|YP_004596248.1|  94 DTPGHVDFGGDVTRAMRAVDGALVVVDAVEGAMPQTETVLRQALREGVKPTLFINKVDRLISELQEGPEEMQERLLS 170
                                       ***************************************************************************77 PP

                                       H..............HHHHHHHHHTTTTTEEEEEEBTTTTBTHH................................. CS
                          GTP_EFTU 153 k..............eeklekygekgekevpvvfgSalkgegvk................................. 182
                                       +              ++++e+ +++  ++ +v fgSal ++gv+                                 
  gi|336253141|ref|YP_004596248.1| 171 VirdvnelirgmteeMDDIEDWTVSV-EDGTVGFGSALYKWGVSmpsmqrtgmdfaeimelerndkrqelhektpls 246
                                       77888777777777644444444444.5889**********999999999999999999999999999999999998 PP

                                       .HHHHHHHHHSH CS
                          GTP_EFTU 183 .tllealvellp 193
                                         +l+++ e++p
  gi|336253141|ref|YP_004596248.1| 247 dVVLDMVCEHFP 258
                                       779999998887 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 !   83.3   0.0   5.3e-27   1.1e-23      10     118 ..     511     615 ..     503     618 .. 0.94

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 5.3e-27
                                       SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESE CS
                            EFG_IV  10 rkpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdv 86 
                                        +p++er+e l++ +g+d++ ++ + +i       +n+++d+tkg+q+++e++e+v++G++eal++Gpla+epv++ 
  gi|336253141|ref|YP_004596248.1| 511 DMPEQERREALQD-AGMDKDTSQNVETIHG-----TNILIDDTKGIQHLNETMELVVEGLEEALDNGPLANEPVQGT 581
                                       5788888999999.9*************99.....8***************************************** PP

                                       EEEEEEEE--T..TTC-HHHHHHHHCHHHHHHHH CS
                            EFG_IV  87 kvtLldgslhe..vdsseaafkpaarralkeall 118
                                        ++L+d++lhe  +++++a+++pa+r a+++al 
  gi|336253141|ref|YP_004596248.1| 582 LIRLHDARLHEdtIHRGPAQVIPAVREAVHNALI 615
                                       *******************************986 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 ?   -0.1   0.0      0.47   9.4e+02      20      44 ..     170     194 ..     161     197 .. 0.82
   2 !   80.5   0.0   3.4e-26   6.8e-23       2      87 ..     621     705 ..     620     707 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.47
                                       CHHHHHHH.CT-EEEEEEEE.TTEEE CS
                             EFG_C  20 kvisdlss.rrGeiedmeqdasgrvi 44 
                                        vi d+++  rG  e+m+ + +++++
  gi|336253141|ref|YP_004596248.1| 170 SVIRDVNElIRGMTEEMDDI-EDWTV 194
                                       6899999999********99.87765 PP

  == domain 2  score: 80.5 bits;  conditional E-value: 3.4e-26
                                       EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEE CS
                             EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgY 78 
                                       +lEP+++v i+vp++++g++ ++++ rrG++ dm q+ ++ +++e+ +P+ e+igfa+++rs+T+G++s+++e +g+
  gi|336253141|ref|YP_004596248.1| 621 MLEPMQDVRIDVPNDHMGAASGEIQGRRGRVDDMYQE-GDLMVVEGIAPVGEMIGFASDIRSATEGRASWNTENAGF 696
                                       79***********************************.*************************************** PP

                                       EE--HHHHH CS
                             EFG_C  79 eevpgdkld 87 
                                       e +  ++++
  gi|336253141|ref|YP_004596248.1| 697 EVMSDSLQR 705
                                       **9988776 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 !   75.6   0.4   1.2e-24   2.4e-21       1      74 [.     387     460 ..     387     461 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 1.2e-24
                            EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                       ++ePvi+ ++e+++ +d  kl + L+++++EDpt++++ +e+T+e ++sG GelHle++++r++++ ++ v++g
  gi|336253141|ref|YP_004596248.1| 387 ISEPVITKSVEAQNMDDLPKLIETLRQVSKEDPTIQININEDTGEHLISGQGELHLEVITQRIEKNQGIPVNTG 460
                                       689********************************************************************998 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 !   64.3   0.8   4.9e-21   9.7e-18       1      73 [.     307     373 ..     307     374 .. 0.97
   2 ?    0.3   0.0      0.47   9.4e+02      32      55 ..     616     638 ..     597     642 .. 0.80

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 4.9e-21
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       G++a grv+sGtl+kG+e+++  ++t +k    r++s+  f++ e+e+v++++aG+i+a+ gl+da i+G+t+
  gi|336253141|ref|YP_004596248.1| 307 GEIASGRVFSGTLEKGQELYV--SGTAGK---NRVQSVGIFMGGEREEVDEVPAGNIAALTGLKDA-IAGSTV 373
                                       89*******************..9999**...*********************************8.****98 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.47
                                       EEEEEEEEEETEEESEEETTSEEE CS
                       GTP_EFTU_D2  32 vtrissletfhededeavaganaG 55 
                                        ++i+ le + +d++++v+ ++ G
  gi|336253141|ref|YP_004596248.1| 616 NGKIKMLEPM-QDVRIDVPNDHMG 638
                                       5666666666.99*******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 !   21.4   0.1     1e-07   0.00021       2     112 ..      24     147 ..      23     149 .. 0.60
   2 ?   -1.3   0.0       1.1   2.2e+03      38      97 ..     534     557 ..     510     592 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1e-07
                                       EEEEESTTSSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEE....ETTEEEEEEECGGCSS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg................ekaivsdkpgtTrdinegrvk....lkgkeielvDtpGlie 58 
                                       +ai+ +   GK+tL   l+                 ++ + +++ g T+d     ++     +++ i+l+DtpG ++
  gi|336253141|ref|YP_004596248.1|  24 IAIAAHVDHGKTTLSDNLLAgagmisdetageqlamDTEEDEQERGITIDAANVSMTheyeGENHLINLIDTPGHVD 100
                                       777888889******999854445555555544332244556667888888777666453222356********665 PP

                                       HHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEE CS
                          MMR_HSR1  59 gaseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvl 112
                                           + ++++a+   + +d +l+vvda e+ + + +  l + l+e  kp +l +
  gi|336253141|ref|YP_004596248.1| 101 ---FGGDVTRAM---RAVDGALVVVDAVEGAMPQTETVLRQALREGVKP-TLFI 147
                                       ...222344444...458********99554444444445555544444.4444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                                       EEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHH CS
                          MMR_HSR1  38 egrvklkgkeielvDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldeel 97 
                                        +++  +g++i + Dt G i                                 ++l+e++
  gi|336253141|ref|YP_004596248.1| 534 VETI--HGTNILIDDTKG-I---------------------------------QHLNETM 557
                                       2222..255566666666.3.................................3333332 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 ?   12.6   0.0   4.6e-05     0.092      11      78 ..     392     459 ..     381     488 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                                       EEEEEEESSGGGHHHHHHHHHHHHHCT.SSEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEE CS
                             RF3_C  11 lfarvrlkdplkrkqlrkgleqLaeEG.avqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrl 78 
                                       + ++v++++     +l + l+q+++E  ++q+  +e ++ e +++  G+L +eV+++R+++  g++v++
  gi|336253141|ref|YP_004596248.1| 392 ITKSVEAQNMDDLPKLIETLRQVSKEDpTIQININE-DTGEHLISGQGELHLEVITQRIEKNQGIPVNT 459
                                       556788888888899999*****9997478887777.5666677778*************999988865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         1     2e+03     154     160 ..      91      97 ..       9     103 .. 0.53
   2 ?    8.9   0.0   0.00066       1.3      16      79 ..     112     175 ..     105     204 .. 0.67
   3 ?   -0.4   0.0      0.46   9.1e+02     128     164 ..     518     553 ..     508     555 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1
                                       EEESS-S CS
                       RsgA_GTPase 154 lliDtPG 160
                                        liDtPG
  gi|336253141|ref|YP_004596248.1|  91 NLIDTPG 97 
                                       4677777 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00066
                                       --EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH..HHHHHHHHHHHTTSEE CS
                       RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee..eleelkeelealgyev 79 
                                       vd +l+vv ++  e  + + + +L +a ++g++p++ +nK+D l +e     ee++e+l ++  +v
  gi|336253141|ref|YP_004596248.1| 112 VDGALVVVDAV--EGAMPQTETVLRQALREGVKPTLFINKVDRLISELqeGPEEMQERLLSVIRDV 175
                                       78888888777..45566778999******************655444243445555544444444 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.46
                                       S--------------SEEEEEETTTEEEESS-SSSS- CS
                       RsgA_GTPase 128 gevseklgrGkhTTtavellelaegglliDtPGfrel 164
                                       +e  ++ g  k T+++ve ++   + l+ Dt G+++l
  gi|336253141|ref|YP_004596248.1| 518 REALQDAGMDKDTSQNVETIHGT-NILIDDTKGIQHL 553
                                       555566778899********999.999999***9987 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00019      0.39      26      82 ..      66     122 ..      59     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                                       SSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETT CS
                               Ras  26 eeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvydit 82 
                                       +e   Ti +++ + + e++g++  +++ DT G  +f    +  +r ++g+l+v d  
  gi|336253141|ref|YP_004596248.1|  66 QERGITIDAANVSMTHEYEGENHLINLIDTPGHVDFGGDVTRAMRAVDGALVVVDAV 122
                                       5566799999******************************************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (728 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.41
# Mc/sec: 5316.28
//
Query:       gi|336253142|ref|YP_004596249.1|  [L=459]
Description: Seryl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-29  100.9  10.0      9e-29   99.9  10.0    1.5  1  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
      6e-27   94.8   0.0    1.1e-26   93.9   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
     0.0078   15.9   0.3      0.011   15.4   0.3    1.2  1  LUC7            LUC7 N_terminus
  ------ inclusion threshold ------
       0.02   13.6   3.0      0.031   12.9   3.0    1.2  1  FapA            Flagellar Assembly Protein A
      0.052   13.6   1.6      0.098   12.7   1.6    1.5  1  LidA_Long_CC    LidA long coiled-coil domain
       0.13   11.6   1.1       0.19   11.0   1.1    1.2  1  Vps54_N         Vacuolar-sorting protein 54, of GARP complex
       0.17   11.0   5.2       0.25   10.4   5.2    1.2  1  Atg14           Vacuolar sorting 38 and autophagy-related sub
       0.21   11.9   3.2       0.38   11.1   3.2    1.4  1  OmpH            Outer membrane protein (OmpH-like)
       0.28   10.6   6.2       0.43   10.0   5.6    1.5  1  Golgin_A5       Golgin subfamily A member 5
       0.32   11.4  10.7         30    5.1   6.2    3.4  2  V-SNARE         Vesicle transport v-SNARE protein N-terminus
       0.38    9.4   5.0       0.54    9.0   5.0    1.2  1  HAUS5           HAUS augmin-like complex subunit 5
       0.49   10.1   3.7       0.72    9.6   3.7    1.2  1  AAA_11          AAA domain
        1.3    9.1  15.4       0.12   12.4  10.2    2.0  2  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
        1.5    9.1   4.4        2.8    8.2   4.4    1.4  1  zf-C4H2         Zinc finger-containing protein
        1.9    9.0  15.4       0.51   10.8   0.7    3.1  3  ZapB            Cell division protein ZapB
        2.2    8.8   6.9        4.1    7.8   6.9    1.4  1  CENP-H          Centromere protein H (CENP-H)
          3    8.0   9.2        9.5    6.4   7.3    2.6  2  DUF4363         Domain of unknown function (DUF4363)
        7.4    5.2   6.4         10    4.7   6.4    1.1  1  HlyD_2          HlyD family secretion protein
        7.5    6.6   8.1        1.6    8.8   4.7    1.6  2  UPF0242         Uncharacterised protein family (UPF0242) N-te


Domain annotation for each model (and alignments):
>> 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 !   99.9  10.0   9.5e-32     9e-29       1     108 []       1     109 [.       1     109 [. 0.98

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 9.5e-32
                                       ---HHHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT..S-TCCCCCC CS
                      Seryl_tRNA_N   1 MLDiklirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk..edaeeliae 75 
                                       MLD  ++renp++v+e+l +R +++ d+de+lelde++rel+++ +el++erNe++ +Igk+ +++  e++ee i+e
  gi|336253142|ref|YP_004596249.1|   1 MLDRTYLRENPDEVREALDNR-DADVDLDEILELDERWRELKARGDELRHERNEITSKIGKLVAENkeEEREEAIQE 76 
                                       *********************.5889*************************************99999********* PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHHHCTS---- CS
                      Seryl_tRNA_N  76 vkelkeelkaleaelkeleaeleklllaiPNip 108
                                       ++elk+e++++e e +e++++l++ +l+iPN+p
  gi|336253142|ref|YP_004596249.1|  77 SRELKAEIEDVESEADEIREDLNQRMLEIPNVP 109
                                       *******************************98 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 !   93.9   0.0   1.1e-29   1.1e-26       7     178 ..     232     418 ..     221     419 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 1.1e-29
                                       TSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeasldds 79 
                                       +++++ L Pt+e ++++++ + +l + +LPlk  ++++ +R+E+     ++rG++Rv++F++ + + f+ +++++d 
  gi|336253142|ref|YP_004596249.1| 232 DEEDLWLCPTAEVPVTNMYANDILLQDDLPLKHQAYTPNFRREAGehgtETRGIVRVHQFNKVELVNFVEPENSYDR 308
                                       4689******************99********************778999*************************** PP

                                       HHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETT.........TSEEEEEEEEEEEETHHHHHTTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  80 lrdlikaisriferlglefraiielmsaksadykdkkefeavses.........ltkgieigtiqklgtrlserlga 147
                                       l++l+++++++++rl l++r++++++++  +++ ++ ++e++ +           ++ +e++t+++ ++ +++r g+
  gi|336253142|ref|YP_004596249.1| 309 LEELLEEAEEVLRRLDLPYRVLELCTGDLGFKATKQIDLEVWAPAddmedgpeeGGRWLEVSTASNFEDFQARRSGL 385
                                       *****************************************************99********************** PP

                                       EEECTTS.SEEEEEEEEEE.EEHHHHHHHHHHH CS
                                       xxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxx RF
                      tRNA-synt_2b 148 tvldenn.reksvimicaa.igveRllsaileq 178
                                       ++  e   + +  ++++a+ +++ R++ aile 
  gi|336253142|ref|YP_004596249.1| 386 RYRPERHeSAEYLHTLNASgLAIPRVMVAILEY 418
                                       **988874678899999999***********96 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   1.2e-05     0.011     123     179 ..      46     102 ..      15     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                       ..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                              LUC7 123 kkqeqlkeleekiekllaeaeelgeeGkVdeaqklmkeveelkeekeeleqqyeaaa 179
                                       +  ++ +e+++ki kl+ae +e  +e  ++e+ +l +e+e++++e +e++++ ++ +
  gi|336253142|ref|YP_004596249.1|  46 ELRHERNEITSKIGKLVAENKEEEREEAIQESRELKAEIEDVESEADEIREDLNQRM 102
                                       5677889******************************************99988765 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.0   3.3e-05     0.031     333     417 ..      31     103 ..      20     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                              FapA 333 pelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeele 409
                                       +el+e+ +el+ +  el+ e +++++ki kl +        ++k+e+ ++++++  +lk e+e++e e +e+ e l+
  gi|336253142|ref|YP_004596249.1|  31 LELDERWRELKARGDELRHERNEITSKIGKLVA--------ENKEEEREEAIQESRELKAEIEDVESEADEIREDLN 99 
                                       578888899999999999999999999999998........4577999999999999999***99999999999999 PP

                              FapA 410 skkeeaki 417
                                       ++     +
  gi|336253142|ref|YP_004596249.1| 100 QR----ML 103
                                       88....33 PP

>> LidA_Long_CC  LidA long coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.6    0.0001     0.098     127     177 .]      49     100 ..      23     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                                       HHT---.B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHT- CS
                      LidA_Long_CC 127 klkpei.mtvkklvhhnkklEleehkekkeelkqrseelqkeilelanqiak 177
                                       + + ei + + klv +nk++E ee  ++  elk+++e+ ++e +e+++ +++
  gi|336253142|ref|YP_004596249.1|  49 HERNEItSKIGKLVAENKEEEREEAIQESRELKAEIEDVESEADEIREDLNQ 100
                                       555454145899*******************************999988776 PP

>> Vps54_N  Vacuolar-sorting protein 54, of GARP complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.1    0.0002      0.19      19      95 ..      26     103 ..      15     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                           Vps54_N  19 eLkklpddelsyesiekevkklksqhdvvskklsqlilekreef.vkelseveeiekelkesvvickngrraLdlak 94 
                                        L+++ + +    ++ +  ++l+++ + +++k+ +l+ e++ee   + ++e +e++ e++++  +  ++r+ L++ +
  gi|336253142|ref|YP_004596249.1|  26 DLDEILELDERWRELKARGDELRHERNEITSKIGKLVAENKEEErEEAIQESRELKAEIEDVESEADEIREDLNQRM 102
                                       57777777778888999999******************99876515669************************9977 PP

                           Vps54_N  95 k 95 
                                        
  gi|336253142|ref|YP_004596249.1| 103 L 103
                                       5 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 ?   10.4   5.2   0.00027      0.25      22      97 ..      35     105 ..      19     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                             Atg14  22 erlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97 
                                       er  el+ r   l++e++++ +ki k++++++     e++ +   +  +elk++i+d +++  e++++l q+  ei
  gi|336253142|ref|YP_004596249.1|  35 ERWRELKARGDELRHERNEITSKIGKLVAENK-----EEEREEAIQESRELKAEIEDVESEADEIREDLNQRMLEI 105
                                       567789999999***************99999.....5566666778899*******************9987665 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.2    0.0004      0.38      27      87 ..      39     102 ..      13     109 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHH...HHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  27 kfkklqaeleakekelqklqeelqkkakklekeekeqe...lqkkeqelqqkqqqkaqelqkkq 87 
                                       + k++ +el+ +++e+++++ +l +++k++e+ee+ qe   l+++ ++++ ++++ +++l+++ 
  gi|336253142|ref|YP_004596249.1|  39 ELKARGDELRHERNEITSKIGKLVAENKEEEREEAIQEsreLKAEIEDVESEADEIREDLNQRM 102
                                       4578888899999999999999986555532444444444455555555555554456666665 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.6   0.00046      0.43      24      74 ..      59     109 ..      39     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
                         Golgin_A5  24 ekliasLkegsgeeglesstalsaeldelkqerdllreelqklnqqieqlr 74 
                                        kl+a+ ke++ ee+++ s++l+ae++++++e d +re+l++ + +i ++ 
  gi|336253142|ref|YP_004596249.1|  59 GKLVAENKEEEREEAIQESRELKAEIEDVESEADEIREDLNQRMLEIPNVP 109
                                       699***************************************999987765 PP

>> 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 ?    5.1   6.2     0.032        30       6      52 ..      52     109 ..      47     115 .. 0.66
   2 ?    4.2   0.1     0.058        55      30      46 ..     309     325 ..     304     331 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.032
                           V-SNARE   6 aeiksklarlsslag.e..........erkaalreiekkldeaeelldqMelEvrnlp 52 
                                       +ei+sk+++l  ++  e          e ka + ++e++ de++e l+q  lE+ n+p
  gi|336253142|ref|YP_004596249.1|  52 NEITSKIGKLVAENKeEereeaiqesrELKAEIEDVESEADEIREDLNQRMLEIPNVP 109
                                       5666666666655553422234444446677777888999999999999888888887 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.058
                           V-SNARE  30 iekkldeaeelldqMel 46 
                                       +e+ l+eaee+l++++l
  gi|336253142|ref|YP_004596249.1| 309 LEELLEEAEEVLRRLDL 325
                                       7999***********98 PP

>> HAUS5  HAUS augmin-like complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.0   0.00057      0.54      69     112 ..      58     107 ..      29     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00057
                             HAUS5  69 g......skaeeresaaaereelekeverLraeirrldkeleareeelsr 112
                                              +k+eere+a++e +el++e+e   +e  +++++l++r++e+ +
  gi|336253142|ref|YP_004596249.1|  58 IgklvaeNKEEEREEAIQESRELKAEIEDVESEADEIREDLNQRMLEIPN 107
                                       1334444899************************************9865 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.7   0.00076      0.72     115     194 ..      29     104 ..       5     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00076
                            AAA_11 115 krlekeekaqlakeiskeleklakelrafeeeeekeklkkskekskskleqerrklkkerkelskeleeaeesleee 191
                                       + le  e+++  k   +el+ +++e+ ++      + ++++ke++++++ qe+r+lk+e++++++e +e++e l++ 
  gi|336253142|ref|YP_004596249.1|  29 EILELDERWRELKARGDELRHERNEITSKIG----KLVAENKEEEREEAIQESRELKAEIEDVESEADEIREDLNQR 101
                                       4444444555555555555555555544433....57899**********************************999 PP

                            AAA_11 192 vld 194
                                       +l+
  gi|336253142|ref|YP_004596249.1| 102 MLE 104
                                       986 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 ?   12.4  10.2   0.00012      0.12      14      82 ..      46     112 ..      26     124 .. 0.85
   2 ?   -3.0   0.2         7   6.6e+03     105     115 ..     308     318 ..     300     324 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                    CENP-F_leu_zip  14 eserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsek 82 
                                       e +++ + +  k+ +L +e  + ee++e++i e  + kae+e +++e +e++e l++  l++ ++  e 
  gi|336253142|ref|YP_004596249.1|  46 ELRHERNEITSKIGKLVAE--NKEEEREEAIQESRELKAEIEDVESEADEIREDLNQRMLEIPNVPHES 112
                                       4577788888899999886..678999******************************999999987775 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7
                    CENP-F_leu_zip 105 slenlleekEq 115
                                        le+llee+E+
  gi|336253142|ref|YP_004596249.1| 308 RLEELLEEAEE 318
                                       34455555544 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.4    0.0029       2.8      11     113 ..      32     138 ..      27     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0029
                           zf-C4H2  11 eleklknklakevealekeekcleey..kkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakkl 85 
                                       el++   +l++  ++l++e++ +++   k   e+ e+E+++ ++e r ++a i+++Es   e +e+ ++++ ++ ++
  gi|336253142|ref|YP_004596249.1|  32 ELDERWRELKARGDELRHERNEITSKigKLVAENKEEEREEAIQESRELKAEIEDVESEADEIREDLNQRMLEIPNV 108
                                       55555566666666666666666543113345667889999999999999999999999999999999999999999 PP

                           zf-C4H2  86 yeeykklkeevnelrse..lglekledlee 113
                                        +e  +l  +  ++ ++   g + l+d  e
  gi|336253142|ref|YP_004596249.1| 109 PHESVPLGVDERHNVEDrrWGFDDLRDVPE 138
                                       999888865444444443477777777554 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7   0.00054      0.51      36      68 ..      32      64 ..      27      67 .. 0.77
   2 ?    2.8   5.9      0.18   1.7e+02      14      57 ..      71     100 ..      64     126 .. 0.62
   3 ?   -0.5   0.1       1.9   1.8e+03      57      68 ..     304     315 ..     288     324 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00054
                              ZapB 36 elkeenreleeeneqlkeereawqerlkkLLgk 68
                                      el e+ rel++  ++l++er+++++++ kL+++
  gi|336253142|ref|YP_004596249.1| 32 ELDERWRELKARGDELRHERNEITSKIGKLVAE 64
                                      678888888888888888888888888888764 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.18
                              ZapB  14 qkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeerea 57 
                                       ++ai++ ++L+ eie+++ e  e  e  +              +
  gi|336253142|ref|YP_004596249.1|  71 EEAIQESRELKAEIEDVESEADEIREDLN--------------Q 100
                                       34555555555555555555544444433..............3 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.9
                              ZapB  57 awqerlkkLLgk 68 
                                       +  +rl+ LL++
  gi|336253142|ref|YP_004596249.1| 304 NSYDRLEELLEE 315
                                       444555555554 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 ?    7.8   6.9    0.0044       4.1      13      80 ..      28      96 ..      16     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0044
                            CENP-H 13 sellklsqelrelqeeltevekenlrlkrknrelaael.lelakekesekeklkeelekleaelkksrq 80
                                       e+l+l +  rel+++ +e++ e+ +++ k  +l+ae  +e+++e+ +e+ +lk+e+e +e+e ++ r+
  gi|336253142|ref|YP_004596249.1| 28 DEILELDERWRELKARGDELRHERNEITSKIGKLVAENkEEEREEAIQESRELKAEIEDVESEADEIRE 96
                                      6899999999****************************56777777777799*********99988775 PP

>> DUF4363  Domain of unknown function (DUF4363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   7.3      0.01       9.5      15      97 ..       8      88 ..       4      93 .. 0.86
   2 ?   -1.0   0.0         2   1.9e+03       8      24 ..     303     319 ..     297     325 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.01
                           DUF4363 15 sekleeleeaienedweeakekleelekeWekkkkklsifiehdeldeietslaklkayietedkeealaelaelkfll 93
                                       e+ +e++ea++n d +   +++ el ++W++ k     + +h e +ei+ ++ kl a  ++e++eea+ e +elk  +
  gi|336253142|ref|YP_004596249.1|  8 RENPDEVREALDNRDADVDLDEILELDERWRELKARGDEL-RH-ERNEITSKIGKLVAENKEEEREEAIQESRELKAEI 84
                                      5667899999999999999999999999999998888765.44.4589******************************* PP

                           DUF4363 94 ehik 97
                                      e ++
  gi|336253142|ref|YP_004596249.1| 85 EDVE 88
                                      9886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2
                           DUF4363   8 kkstdelsekleeleea 24 
                                       ++s+d+l+e lee+ee 
  gi|336253142|ref|YP_004596249.1| 303 ENSYDRLEELLEEAEEV 319
                                       57788888888888775 PP

>> HlyD_2  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   6.4     0.011        10     101     164 ..      24      85 ..       9     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.011
                            HlyD_2 101 eklkekletlnerikeienneaieniekdiekldreInvlekdikesiknedikkieelKeeln 164
                                       + +  ++ +l+er  e++      +++++ +++ ++I +l+++ ke+ ++e+i+   elK+e++
  gi|336253142|ref|YP_004596249.1|  24 DVDLDEILELDERWRELKARG--DELRHERNEITSKIGKLVAENKEEEREEAIQESRELKAEIE 85 
                                       3455677789********999..999************************************97 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 ?    8.8   4.7    0.0017       1.6      66     146 ..      19     104 ..       5     133 .. 0.70
   2 ?   -3.0   0.1         7   6.6e+03      83     100 ..     305     322 ..     289     329 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                           UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkee.....ldakeeelerlkeenqqLqekleaiaedfeelk 137
                                       ++   + +   + elde  ++ +    el++e +e   +      ++keee e+  +e  +L+ + e++  + +e +
  gi|336253142|ref|YP_004596249.1|  19 DNRDADVDLDEILELDERWRELKARGDELRHERNEITSKigklvAENKEEEREEAIQESRELKAEIEDVESEADEIR 95 
                                       55555555666667776666666666666666666666677777788888888888888888888888888888888 PP

                           UPF0242 138 leleeqLae 146
                                        +l++++ e
  gi|336253142|ref|YP_004596249.1|  96 EDLNQRMLE 104
                                       888877654 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7
                           UPF0242  83 glktkeealeelqeeeee 100
                                       +++  ee lee++e  ++
  gi|336253142|ref|YP_004596249.1| 305 SYDRLEELLEEAEEVLRR 322
                                       333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1280  (0.0713927); expected 358.6 (0.02)
Passed bias filter:                      770  (0.0429472); expected 358.6 (0.02)
Passed Vit filter:                       148  (0.00825478); 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):              19  [number of targets reported over threshold]
# CPU time: 0.74u 0.25s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 3077.63
//
Query:       gi|336253143|ref|YP_004596250.1|  [L=149]
Description: hypothetical protein Halxa_1743 [Halopiger xanaduensis SH-6]
Scores for 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   12.7   0.0       0.17   11.6   0.0    1.5  1  Sigma70_r4_2  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.3e-06      0.17      11      48 ..      92     129 ..      90     134 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.3e-06
                                       S-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2  11 LperqreifllryleglsykEIAellgisegtVksrls 48 
                                       L+e + ++f+l+ +++++ + +Ae l++s + V+ ++ 
  gi|336253143|ref|YP_004596250.1|  92 LTEPEMRVFVLYGWFDMDAERAAEPLDCSAADVEAYVE 129
                                       889999***************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 00:00:00.41
# Mc/sec: 1082.84
//
Query:       gi|336253144|ref|YP_004596251.1|  [L=402]
Description: TrkA-C domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-20   72.6   3.0    1.2e-12   47.4   0.2    2.6  2  TrkA_C    TrkA-C domain
    1.7e-17   63.6   7.2    4.3e-08   33.5   0.4    2.4  2  PhoU      PhoU domain
     0.0011   18.4   2.9       0.79    9.0   0.0    3.1  3  PhoU_div  Protein of unknown function DUF47
  ------ inclusion threshold ------
      0.089   13.2   0.8         14    6.1   0.2    2.3  2  CLZ       C-terminal leucine zipper domain of cyclic nucleoti
      0.097   13.4   3.5       0.22   12.2   0.1    3.0  4  KfrA_N    Plasmid replication region DNA-binding N-term


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 !   47.4   0.2   3.5e-16   1.2e-12       5      67 ..     133     197 ..     129     200 .. 0.94
   2 !   25.3   0.2   2.8e-09     1e-05       1      68 [.     329     399 ..     329     401 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 3.5e-16
                                       EEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   5 tvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       +v+++s +v++tl++++l+ + gv+v+a+rRg ++l++p+++t  +++Dv l+ g+  ++ +++e
  gi|336253144|ref|YP_004596251.1| 133 VVDPDSVYVDRTLADIDLESEtGVRVIALRRGdDWLLNPGPETAVRANDVALLRGPELAIGDVCE 197
                                       799*****************************************************999988887 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 2.8e-09
                                       CEEEEEE--GGGTTSBHHHHTHHHH..S-EEEEEE-T..-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar..gvlvvairRg..geliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                       +v+v+v++gs l+G+ +   ++++      ++airR+  g+l++ + d +++ GDvl+  g++ + a+++el
  gi|336253144|ref|YP_004596251.1| 329 IVRVAVDEGSDLDGTDIVA-GVPDTesTMSIIAIRRPedGWLLVGDADVEIQGGDVLISKGTRTAAAAFEEL 399
                                       689****************.888888*******************************999999998888876 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   1.5   1.4e-11   5.1e-08       1      88 [.      24     107 ..      24     108 .. 0.91
   2 !   33.5   0.4   1.2e-11   4.3e-08       2      87 ..     225     306 ..     224     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.4e-11
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlER 77 
                                       l +m++++e  +d++++a+ +  +++a ev+++++++d le++ +  l+   a+r+p   d ++l  +l i+     
  gi|336253144|ref|YP_004596251.1|  24 LVEMKDTAELLIDLSYSAVLHSSEDIATEVLRLEERMDVLEMRARMGLMM--ATRSPD--DAEQLAPVLGIVGAADD 96 
                                       579*****************************************888664..558887..6799999********** PP

                                       HHHHHHHHHHH CS
                              PhoU  78 igDhavniaer 88 
                                       i+D a +ia+ 
  gi|336253144|ref|YP_004596251.1|  97 ISDAAGDIAKV 107
                                       *********97 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 1.2e-11
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HGG-SHHHHHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealak.rqplaedlrellsllriardlER 77 
                                        +m++++e ++d+a++a+  + + la+ev++++ e+d+le ++e   l+a+a  ++p+a  lr    l+++ +  E 
  gi|336253144|ref|YP_004596251.1| 225 VHMKNLSELAVDLAYSAVLFDSEALAEEVRNLEVEVDALESRFEAWTLRAAADaSDPVA--LRG---LIHLGSATEV 296
                                       68***************777777****************************55599986..455...9********* PP

                                       HHHHHHHHHH CS
                              PhoU  78 igDhavniae 87 
                                       i+D a +i+e
  gi|336253144|ref|YP_004596251.1| 297 ISDAAIDISE 306
                                       ********98 PP

>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.2    0.0005       1.8     145     206 ..      44     106 ..      18     110 .. 0.70
   2 !    9.0   0.0   0.00022      0.79     136     206 ..     226     306 ..     200     309 .. 0.78
   3 ?   -2.2   0.1      0.61   2.2e+03     126     166 ..     321     361 ..     315     365 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0005
                          PhoU_div 145 lskkdiveeieslEdeiDqlqrklikklfsred.asnplevlllveiieklenvsdraedvad 206
                                       +s +di+ e+ +lE+++D l+ + +  l+          +   +  i+     +sd+a d+a+
  gi|336253144|ref|YP_004596251.1|  44 HSSEDIATEVLRLEERMDVLEMRARMGLMMATRsPDDAEQLAPVLGIVGAADDISDAAGDIAK 106
                                       34449******************9999998444034444555677888888888888888875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00022
                          PhoU_div 136 eleklletalskk.........diveeieslEdeiDqlqrklik.klfsredasnplevlllveiieklenvsdrae 202
                                        ++ l e a++           +++ee+ +lE e+D l+ +     l    das p++   l+++    e++sd+a 
  gi|336253144|ref|YP_004596251.1| 226 HMKNLSELAVDLAysavlfdseALAEEVRNLEVEVDALESRFEAwTLRAAADASDPVALRGLIHLGSATEVISDAAI 302
                                       44444444444444455555559****************998662566699*************************9 PP

                          PhoU_div 203 dvad 206
                                       d+++
  gi|336253144|ref|YP_004596251.1| 303 DISE 306
                                       9986 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.61
                          PhoU_div 126 aiealaevieeleklletalskkdiveeieslEdeiDqlqr 166
                                       a+e+ +e+i ++  + +++l++ div  + + E  + ++ +
  gi|336253144|ref|YP_004596251.1| 321 AVEESDEIIVRVAVDEGSDLDGTDIVAGVPDTESTMSIIAI 361
                                       56778888888888889999999999999999988776665 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 ?    6.1   0.2    0.0039        14      14      47 ..      34      67 ..      27      77 .. 0.82
   2 ?    5.1   0.0    0.0079        28      25      48 ..     245     268 ..     235     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0039
                               CLZ 14 lLDeeaakagaeqkeleekverLessLeaLqtrl 47
                                      l+D +  +     +++ + v rLe+++++L++r 
  gi|336253144|ref|YP_004596251.1| 34 LIDLSYSAVLHSSEDIATEVLRLEERMDVLEMRA 67
                                      677775555578999***************9985 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0079
                               CLZ  25 eqkeleekverLessLeaLqtrla 48 
                                       + + l e v++Le +++aL+ r++
  gi|336253144|ref|YP_004596251.1| 245 DSEALAEEVRNLEVEVDALESRFE 268
                                       456778888999999999988886 PP

>> KfrA_N  Plasmid replication region DNA-binding N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.2   4.5e+03      68     105 ..      27      64 ..       8      69 .. 0.53
   2 ?   -0.4   0.1      0.51   1.8e+03      55      67 ..     116     130 ..      79     137 .. 0.65
   3 ?   12.2   0.1   6.1e-05      0.22      51     110 ..     207     269 ..     191     274 .. 0.84
   4 ?   -1.9   0.0       1.5   5.3e+03      57      83 ..     302     329 ..     291     336 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                            KfrA_N  68 laalwqaaleeaeeelaaaraelqaaraaleaeraeae 105
                                       +++ ++ + ++  +++ +  ++++ +   le++ + +e
  gi|336253144|ref|YP_004596251.1|  27 MKDTAELLIDLSYSAVLHSSEDIATEVLRLEERMDVLE 64 
                                       44444444444444444455555555555555444443 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.51
                            KfrA_N  55 aa..pelPealaeal 67 
                                       +a  ++lPea+++++
  gi|336253144|ref|YP_004596251.1| 116 EAmrAALPEAVETLV 130
                                       223447777777766 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 6.1e-05
                            KfrA_N  51 laaraa..pelPealaeal.laalwqaaleeaeeelaaaraelqaaraaleaeraeaearvee 110
                                       ++a+++  p+l  a+ + + ++ l + a+++a +++    ++l+++ + le e++++e+r e+
  gi|336253144|ref|YP_004596251.1| 207 PSADVPdiPDLERAVDTIVhMKNLSELAVDLAYSAVLFDSEALAEEVRNLEVEVDALESRFEA 269
                                       3333333578888998888***************************************99986 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.5
                            KfrA_N  57 pelPealaeal.laalwqaaleeaeeel 83 
                                        +++e + + + ++ + q a+ee +e +
  gi|336253144|ref|YP_004596251.1| 302 IDISEGVLRDIdVHPVVQMAVEESDEII 329
                                       4777888888899999999999999844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3103.61
//
Query:       gi|336253145|ref|YP_004596252.1|  [L=85]
Description: hypothetical protein Halxa_1745 [Halopiger xanaduensis SH-6]
Scores for 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  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 620.77
//
Query:       gi|336253146|ref|YP_004596253.1|  [L=132]
Description: CrcB-like protein [Halopiger xanaduensis SH-6]
Scores for 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-22   78.7   5.0    3.6e-22   78.5   5.0    1.1  1  CRCB      CrcB-like protein, Camphor Resistance (CrcB)
  ------ inclusion threshold ------
        2.7    8.3   5.0        2.3    8.5   0.4    2.5  2  DUF3956   Protein of unknown function (DUF3956)


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 !   78.5   5.0     4e-26   3.6e-22       2      91 ..      20     120 ..      19     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 4e-26
                                       HHHHHHHHHHHHHHHH.HHHHBE..BHHHHHHHHHHHHHHHHHHH.........HHTTTHHHHHS-SHHHHHHHHHH CS
                              CRCB   2 lvalggalGallRyllssllnkr..plgtlavNvlGsfllgllla.........llttGflGglTTfStfvlelvsl 67 
                                       +v+ gga+Ga+lR+ +s ++ ++  p+ tlavNvlGsf+ +l +          ll+tG++G++TTfS+f++e+v+l
  gi|336253146|ref|YP_004596253.1|  20 VVGTGGAIGAILRHQVSLRCSSErfPWPTLAVNVLGSFVFALSIFagagdaalrLLGTGICGSFTTFSSFSVETVRL 96 
                                       5889************88888879*9**************995555667777778********************** PP

                                       HHHT-HHHHHHHHHHHHHHHHHHH CS
                              CRCB  68 leegellaallyvllsvvlgllav 91 
                                        e+g+   a+++++ ++vl+l+ +
  gi|336253146|ref|YP_004596253.1|  97 YERGDRRLAVANAAGNLVLSLAGI 120
                                       ****99999999999999999755 PP

>> DUF3956  Protein of unknown function (DUF3956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.5     0.046   4.1e+02      35      44 ..      71      80 ..      47      81 .. 0.87
   2 ?    8.5   0.4   0.00025       2.3      13      25 ..     112     124 ..     105     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.046
                           DUF3956 35 aLivLGiPiC 44
                                      aL+ LG  iC
  gi|336253146|ref|YP_004596253.1| 71 ALRLLGTGIC 80
                                      7999999999 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00025
                           DUF3956  13 lLvlsvAGiEiAR 25 
                                        Lvls+AGi +AR
  gi|336253146|ref|YP_004596253.1| 112 NLVLSLAGIGLAR 124
                                       59**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 965.46
//
Query:       gi|336253147|ref|YP_004596254.1|  [L=148]
Description: CrcB-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.3   5.5    1.9e-15   57.0   5.5    1.1  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 !   57.0   5.5     1e-19   1.9e-15       2      92 ..      19     122 ..      18     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 1e-19
                                       HHHHHHHHHHHHHHHH.HHHHBEBHHHHHHHHHHHHHHHHHHH..............HHTTTHHHHHS-SHHHHHHH CS
                              CRCB   2 lvalggalGallRyllssllnkrplgtlavNvlGsfllgllla..............llttGflGglTTfStfvlel 64 
                                       l+a+gg++G+ lRy+++++l + p +++avN +Gsf+lgl+++              ++ttGfl++lTT+Stf+l++
  gi|336253147|ref|YP_004596254.1|  19 LIAVGGFAGSNLRYFVDGVLPAIP-AVVAVNAAGSFCLGLFAYeaqsigllerrsrlVFTTGFLSSLTTYSTFALQT 94 
                                       799*************88776668.***************999999988888888877******************* PP

                                       HHHHHHT-HHHHHHHHHHHHHHHHHHHH CS
                              CRCB  65 vslleegellaallyvllsvvlgllavv 92 
                                       +  +   e l  +  v++++ lg++ v+
  gi|336253147|ref|YP_004596254.1|  95 ALEAGPAEPLLLAGIVAANYGLGFAGVL 122
                                       9987666788888999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1208.56
//
Query:       gi|336253148|ref|YP_004596255.1|  [L=306]
Description: cation diffusion facilitator family transporter [Halopiger xanaduensis SH-6]
Scores for 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-41  141.9   8.1    2.6e-41  141.6   8.1    1.1  1  Cation_efflux  Cation efflux family
    6.6e-17   61.4   1.5    1.3e-16   60.5   1.5    1.5  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
      0.037   14.3   3.5      0.047   13.9   2.6    1.6  2  EI24           Etoposide-induced protein 2.4 (EI24)
      0.055   14.2   0.0       0.18   12.6   0.0    1.9  1  ASL_C2         Argininosuccinate lyase C-terminal
        0.2   11.8   0.0       0.34   11.0   0.0    1.3  1  DUF2634        Protein of unknown function (DUF2634)


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 !  141.6   8.1   7.2e-45   2.6e-41       4     198 ..      23     212 ..      21     213 .. 0.98

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 7.2e-45
                     Cation_efflux   4 sllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllg 80 
                                       ++l n++  l+e++vgl ++S+al+ada hs++dlv+++++l+  + s  +pd+++p G+ r+e+l al++g+++ +
  gi|336253148|ref|YP_004596255.1|  23 NVLGNAVKILFEGFVGLTFGSVALVADAAHSVADLVASVVVLVWGRSSFDEPDATHPHGHARIEPLTALFVGAVISL 99 
                                       78999999********************************************************************* PP

                     Cation_efflux  81 lavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsa 157
                                       l+++ll+++ q +i  g++++ + l+l+ +++s+v ++++++++  ++++l+s++l+a a + l+D++ts++++v++
  gi|336253148|ref|YP_004596255.1| 100 LGLNLLYDSAQGII-YGVEVEFNVLLLAALGFSIVDMYLVYRYTELVNERLESTSLAALATDCLNDIYTSVAAVVGV 175
                                       **************.************************************************************** PP

                     Cation_efflux 158 lvillfnlksgplaDpvaslligliilysalkllkeslseL 198
                                        ++l++     pl+Dp+a+ l++l+++y + ++++e++  L
  gi|336253148|ref|YP_004596255.1| 176 CGVLFG----FPLLDPIAGGLVSLLVVYQGIEIARENVDYL 212
                                       *****7....588*************************988 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 !   60.5   1.5   3.6e-20   1.3e-16       3      78 ..     219     293 ..     217     294 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 3.6e-20
                                       ..HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                          ZT_dimer   3 eeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                       +e ++ei+e+++s+p+v+gvhdl + + G  + v++h+evdgd++ +eaH+i  e+ +r++ ++++v d  +H++P
  gi|336253148|ref|YP_004596255.1| 219 PEQRAEITEALRSHPDVEGVHDLTVFYDGVVLEVEVHVEVDGDMPFREAHDIESELVDRLR-AIDDVGDAHVHLDP 293
                                       5789********************************************************8.788**********9 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.97   3.5e+03     145     173 ..      12      47 ..       9      50 .. 0.68
   2 ?   13.9   2.6   1.3e-05     0.047      28     123 ..      91     199 ..      35     232 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.97
                                       HHHHHHHCTHHHHHHHH.......HHHHHHTTSCCH CS
                              EI24 145 errallerrrayflgfG.......llvslllliPll 173
                                       +rra++++    +lg +       ++ +++ +++l+
  gi|336253148|ref|YP_004596255.1|  12 DRRAFVRASGVNVLGNAvkilfegFVGLTFGSVALV 47 
                                       567777777777777766666666777777777776 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHH..-.......TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHCCTTSHH.....H CS
                              EI24  28 llfllllvlll..w.......vllasllvllllllplwlfplvalllaapfygllaekvekrhlglvksla.....e 90 
                                       l++++++ ll+          ++  + + + +lll+++ f++v ++l+  +++l+ e++e+  l   ++la     +
  gi|336253148|ref|YP_004596255.1|  91 LFVGAVISLLGlnLlydsaqgIIYGVEVEFNVLLLAALGFSIVDMYLVYRYTELVNERLESTSL---AALAtdclnD 164
                                       33333333333330344334344444455667777788899*******************9665...3333444544 PP

                                       HHHHHHHHHHHHHHHHHH.HH.TTHHH....HHHH CS
                              EI24  91 slkslllllllllvllpl.li.Pvvglilspllls 123
                                        ++s+++++ +  vl+ + l+ P+ g ++s+l+ +
  gi|336253148|ref|YP_004596255.1| 165 IYTSVAAVVGVCGVLFGFpLLdPIAGGLVSLLVVY 199
                                       44455555555557777766679999988887754 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.1e-05      0.18      15      31 ..     261     277 ..     258     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.1e-05
                                       TS-HHHHHHHHHHHHHH CS
                            ASL_C2  15 GlpFReAHeivgravrl 31 
                                       ++pFReAH i +++v +
  gi|336253148|ref|YP_004596255.1| 261 DMPFREAHDIESELVDR 277
                                       89************987 PP

>> DUF2634  Protein of unknown function (DUF2634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.5e-05      0.34      68     105 .]     219     256 ..     207     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.5e-05
                           DUF2634  68 seikreiteaLlvnpriesvdnfsfekekddlkvsftv 105
                                       +e + eiteaL  +p++e+v ++++  ++  l+v+++v
  gi|336253148|ref|YP_004596255.1| 219 PEQRAEITEALRSHPDVEGVHDLTVFYDGVVLEVEVHV 256
                                       577899***********************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2428.96
//
Query:       gi|336253149|ref|YP_004596256.1|  [L=318]
Description: beta-lactamase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-24   85.5   6.4    6.7e-24   85.0   6.4    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.4e-07   31.2   0.5    6.2e-07   29.1   0.3    2.0  2  Lactamase_B_2  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 !   85.0   6.4   7.4e-28   6.7e-24       8     197 .]      42     236 ..      36     236 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 7.4e-28
                                       EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHC CS
                       Lactamase_B   8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfm 84 
                                       +y++ +d+g  ++ +G++t  +r++++l  l+++ +++ av +TH HlDH+Gg+g l+e+ +++ ++v++++++l+ 
  gi|336253149|ref|YP_004596256.1|  42 AYIL-DDDGPAVVESGIGTNHERILEALEELDIDREELAAVAVTHIHLDHAGGAGFLAEKCPNADVYVPDVGASLLA 117
                                       6666.9*********************************************************************** PP

                                       HHHHHHHHHCCHH........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS CS
                       Lactamase_B  85 eeaddaasrkgll........lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall 153
                                       + ++  a+ k +          +++ + + +v +e++d++++g ++l v+  pgh  +++++e++  + +ftGDa  
  gi|336253149|ref|YP_004596256.1| 118 DPGKLVAGTKNAVgdqwefyvEPEPIPEDRIVGIEDGDTIDLGAHELRVHEAPGHAFHQVIFEDPANDAVFTGDAAG 194
                                       ***9999999999***************************************************************9 PP

                                       ..SHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 154 ..agetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                         ++e++ri +      ++ + d e++l++l+ +a+ +++vl+++H
  gi|336253149|ref|YP_004596256.1| 195 iwVPEQERIVE----TSPPSDFDLEQCLADLETIAEIDPDVLLYTH 236
                                       88999999999....9****************************99 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 !   29.1   0.3   6.9e-11   6.2e-07      28     129 ..      75     196 ..      53     208 .. 0.73
   2 ?   -1.0   0.0      0.12   1.1e+03      45      73 ..     219     249 ..     213     289 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 6.9e-11
                                       ..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT...............TTEEEEE CS
                     Lactamase_B_2  28 lppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee...............pavnvhe 89 
                                        ++++aV +th H DH  g+ +l+e +p+ +++y+p+  ++ l++ ++  a  ++               p+ +++ 
  gi|336253149|ref|YP_004596256.1|  75 REELAAVAVTHIHLDHAGGAGFLAEKCPN-ADVYVPDVGASLLADPGKLVAGTKNavgdqwefyvepepiPEDRIVG 150
                                       3689*********************9995.89**99655555555554444444466677777777777999***** PP

                                       E-TTSEEEECSTTEEEEEEEE-EE--C......TCCE-TTTSEEEE CS
                     Lactamase_B_2  90 ldwgesfelgdggleitatparhksgr......rldrnagdtlGlr 129
                                       ++ g++++lg ++l+++  p + +++       +++  +gd++G +
  gi|336253149|ref|YP_004596256.1| 151 IEDGDTIDLGAHELRVHEAPGHAFHQVifedpaNDAVFTGDAAGIW 196
                                       *********9999888888888888885444333333334444444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.12
                                       GGGGCCCCC--EE..EEEEEEHHHHHHCCTT CS
                     Lactamase_B_2  45 aglltlrelrpkk..lplyapkgvlavlean 73 
                                       a+l t++e+ p+   ++ ++p++v+ +le  
  gi|336253149|ref|YP_004596256.1| 219 ADLETIAEIDPDVllYTHFGPRDVGNDLEGA 249
                                       6777777777755655556777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2356.37
//
Query:       gi|336253150|ref|YP_004596257.1|  [L=666]
Description: Long-chain-fatty-acid--CoA ligase [Halopiger xanaduensis SH-6]
Scores for 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-94  314.8   0.0      8e-94  314.6   0.0    1.0  1  AMP-binding  AMP-binding enzyme


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 !  314.6   0.0   4.4e-98     8e-94       3     422 ..      26     533 ..      24     534 .. 0.81

  Alignments for each domain:
  == domain 1  score: 314.6 bits;  conditional E-value: 4.4e-98
                                       HHHHHSTTSEEEEE..................CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHH CS
                       AMP-binding   3 eqaaktpdkvalvd..................sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewv 61 
                                       ++a+++ ++ a  +                   ge +t++Y+e+++ v+rlAag+r lGv++gdr++i++ +++ew 
  gi|336253150|ref|YP_004596257.1|  26 ASAERNANRAAQRYkggiydrsltdsvlpaatPGEFRTISYAEMRDIVRRLAAGFRDLGVERGDRIGIFANTRMEWA 102
                                       55666666666655555556666666666677789****************************************** PP

                                       HHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCC CS
                       AMP-binding  62 vallailkaGavvvplnptltaeelayiledseakvliatvdsel.leklleaaakleavklvivldadellkeeel 137
                                         ++a+l aGavv ++++++++e ++y+l+d +a  ++  v++++ le++l+++++l   +l+ +++ d+l+ ++ +
  gi|336253150|ref|YP_004596257.1| 103 QCDFALLGAGAVVTTVYTGSSEEKVEYLLDDPDANGVV--VENRElLERVLAVEDSL---DLEFIVSIDDLEGHDAA 174
                                       **************************************..99999999999999876...44444554454444334 PP

                                       CHCCCCSCTTS................-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH..HHHC CS
                       AMP-binding 138 keeeeseekae................kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk..letr 196
                                       + ++                       + + ++++  ddla +iYTSGTTGkPKGV l+hrn+ +nv +++  + +r
  gi|336253150|ref|YP_004596257.1| 175 ERDDVFT---LadlyergdeafdletyQ-TWVDAPAMDDLASLIYTSGTTGKPKGVRLTHRNFRSNVNQVHrrFAPR 247
                                       3333333...123457788999999953.46668999*****************************99988774444 PP

                                       ...SCCTT.......T-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHH CS
                       AMP-binding 197 ...fklke.......ddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrv 263
                                          +   +       +++ +s+lplah+f+ +++ ++ ++ Ga+v +++  ++l+     e+++  ++t+ ++vPrv
  gi|336253150|ref|YP_004596257.1| 248 pdrD---DdvptldeTSRAVSYLPLAHVFERTAGHFVLFATGASVAYAESPDTLQ-----EDFSLVEPTTATSVPRV 316
                                       3221...2456777799******************************99776655.....8999999********** PP

                                       HHHH...........HHCCCHHCHHHHC........................................CGTT.-SEE CS
                       AMP-binding 264 leal...........lesgalkaakkak........................................dlss.lrlv 288
                                       +e++                   ak  k                                         l++ ++l+
  gi|336253150|ref|YP_004596257.1| 317 YEKIydrireqasesP-------AK--KrifewatdvgvayqetdepgpllrakrtladklvfstvreALGGnIELL 384
                                       ****777544322110.......12..13466666667777777888888888888888888888888888889999 PP

                                       EEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE....T CS
                       AMP-binding 289 llggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvp....d 361
                                       ++gg++lspel + ++a +  +++egYGlTEt++v++ ++++++ +k+g++G+p+ +ve++i  e+     +    +
  gi|336253150|ref|YP_004596257.1| 385 ISGGGSLSPELCQLYHAMGL-PIHEGYGLTETSPVIS-VNPPGE-VKIGTIGPPVVDVEIAID-ESVADQAAfaddP 457
                                       9***********99999876.5**************9.675555.79***************4.442333335677* PP

                                       TSEEEEEEEETTS-SEBTT-HHHHHHHEEE...............TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 362 geeGellvrgpgvmkgYlkkpeataeafds...............egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       ge+Gellvrgp+v++gY++kp at ++f++               +g+w+rTGD++++++d yle+ +R+k++++l
  gi|336253150|ref|YP_004596257.1| 458 GEVGELLVRGPNVTRGYWNKPGATDRSFTDdigeseatvmadgeaSGQWFRTGDVVHRRPDDYLEFRDRAKQILVL 533
                                       ****************************988999********963356************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (666 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 4566.95
//
Query:       gi|336253151|ref|YP_004596258.1|  [L=200]
Description: MgtE integral membrane protein [Halopiger xanaduensis SH-6]
Scores for complete 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   76.8  13.2    1.8e-21   76.8  13.2    1.7  2  MgtE      Divalent cation transporter


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 ?   -1.4   0.0      0.16   2.9e+03      78      82 ..      33      37 ..      17      54 .. 0.47
   2 !   76.8  13.2   9.9e-26   1.8e-21       1     123 [.      65     193 ..      65     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.16
                                      HHHHH CS
                              MgtE 78 vllaa 82
                                      +l+a+
  gi|336253151|ref|YP_004596258.1| 33 LLIAM 37
                                      11111 PP

  == domain 2  score: 76.8 bits;  conditional E-value: 9.9e-26
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTSS-GG.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.....CTSHHHHH CS
                              MgtE   1 iPvilglgGnlgaqlasristalhlgelekk.lkkvllkelrvvlllgvilgllifllalllgw....slllalvvg 72 
                                       +Pv++g++Gnlg+++ +r+st+lhlg+le + ++  ++ ++ +vl l++++++l+++  + +g     +l l++++ 
  gi|336253151|ref|YP_004596258.1|  65 VPVMIGTAGNLGSIMCARLSTQLHLGTLEFSpANPGIRANVGAVLGLAATVFVLLGIASWAIGAllggTLGLGTLLV 141
                                       6***************************99999***********************999987776666777777777 PP

                                       HHHHHHHHHHHHH...HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  73 lalvlvllaaall.ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                       +++v  +l+a+ + i+ ++ ++++++lg+DPd  +iP++t + D++g+l+l+
  gi|336253151|ref|YP_004596258.1| 142 ITMVSGMLLAVWVvIVSTVSVYVSYQLGYDPDDTTIPVVTNVCDITGVLILF 193
                                       778887777777788888888******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1442.86
//
Query:       gi|336253152|ref|YP_004596259.1|  [L=190]
Description: MgtE integral membrane protein [Halopiger xanaduensis SH-6]
Scores for complete 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-20   73.8   6.8    1.5e-20   73.8   6.8    1.7  2  MgtE             Divalent cation transporter
     0.0037   17.8   4.1     0.0099   16.5   4.1    1.7  1  Transmemb_17     Predicted membrane protein
  ------ inclusion threshold ------
        0.2   11.3  19.3       0.67    9.6  19.3    1.7  1  Yip1             Yip1 domain
       0.35    9.6   2.3       0.46    9.1   2.3    1.2  1  Clostridium_P47  Clostridium P-47 protein


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 ?   -0.6   0.0      0.36   1.6e+03      71      84 ..      18      31 ..       4      41 .. 0.52
   2 !   73.8   6.8   3.5e-24   1.5e-20       2     123 ..      52     180 ..      51     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.36
                                      HHHHHHHHHHHHHH CS
                              MgtE 71 vglalvlvllaaal 84
                                      + ++lv+ l+a +l
  gi|336253152|ref|YP_004596259.1| 18 ILVSLVAGLFAGTL 31
                                      22222222222222 PP

  == domain 2  score: 73.8 bits;  conditional E-value: 3.5e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHTTSS-GG..HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HT-.CTSHHHHH CS
                              MgtE   2 PvilglgGnlgaqlasristalhlgelekk..lkkvllkelrvvlllgvilgllifllall....lgwslllalvvg 72 
                                       P++l+++G ++  l +r+s++lh+g ++++  ++  l++ +++ +l+g+i++++i++la++    lg +  l+ +v 
  gi|336253152|ref|YP_004596259.1|  52 PAFLATRGGVYGSLGARLSSGLHQGIIDPEfeWNGPLRNAILASFLNGMIVSVFIAVLAWVvllvLGRNGNLLELVI 128
                                       9999*********************9988877767777777776666666666666666541111555666666677 PP

                                       HHHHHHHHHHHHH..HHHHHHHHH..HTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  73 lalvlvllaaallilgvllplllw..klglDPdnaaiPlltalgDllgtlllv 123
                                       + +v++ll+a  + lgvll+++++  ++glDPdn+++P++t++gD++g+++l+
  gi|336253152|ref|YP_004596259.1| 129 ILFVAALLSAFAM-LGVLLTVIFKgyRRGLDPDNVIGPVVTTVGDVFGVVFLL 180
                                       7666666666555.6777776664339***********************997 PP

>> Transmemb_17  Predicted membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   4.1   2.2e-06    0.0099      37      92 ..      99     154 ..      89     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.2e-06
                      Transmemb_17  37 ldvvllvlllllEvlRlylgykgNltekvpelalfllltlpvllplvyllllqtyv 92 
                                        ++v +++++l+ v+ l lg+ gNl e v+ l++  ll++++ l++++ ++++ y+
  gi|336253152|ref|YP_004596259.1|  99 GMIVSVFIAVLAWVVLLVLGRNGNLLELVIILFVAALLSAFAMLGVLLTVIFKGYR 154
                                       5788899999999999******************************9999888776 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  19.3   0.00015      0.67      29     141 ..      17     179 ..      10     190 .] 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
                              Yip1  29 lalltlllgllas.....lnlgqtlasg......................................eevqgltlssl 62 
                                       ++l++l+ gl+a+      ++++ ++s                                       e+   l++   
  gi|336253152|ref|YP_004596259.1|  17 VILVSLVAGLFAGtllgtETMRNGIESVpglllllpaflatrggvygslgarlssglhqgiidpefEWNGPLRN--- 90 
                                       45555555555554444433333333335555555555555555555555555555666654444444433333... PP

                              Yip1  63 lgaiiggylglllgllllalllhliakllggkgsfkqtlsvvgyallPlilgaliaillllllgt............ 127
                                         ai++++l + +  +++a+l +++  +lg +g++ +++ ++  a+l +++++l  +l +++ g+            
  gi|336253152|ref|YP_004596259.1|  91 --AILASFLNGMIVSVFIAVLAWVVLLVLGRNGNLLELVIILFVAALLSAFAMLGVLLTVIFKGYrrgldpdnvigp 165
                                       ..355666666677777777777777777**************************9999999999*********999 PP

                              Yip1 128 llllvgllaliWsl 141
                                       +++ vg+++++  l
  gi|336253152|ref|YP_004596259.1| 166 VVTTVGDVFGVVFL 179
                                       66666665555433 PP

>> Clostridium_P47  Clostridium P-47 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.3    0.0001      0.46     371     422 ..     100     149 ..      93     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0001
                   Clostridium_P47 371 vilgvivavigsvagavggkvkslvdkiiiaiivaiiagiivaiqeiiedvi 422
                                       +i++v++av++ v+  v+g+  +l++ +ii  ++a++++   a+  ++  vi
  gi|336253152|ref|YP_004596259.1| 100 MIVSVFIAVLAWVVLLVLGRNGNLLELVIILFVAALLSAF--AMLGVLLTVI 149
                                       79**********************************9954..5555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1433.10
//
Query:       gi|336253153|ref|YP_004596260.1|  [L=80]
Description: hypothetical protein Halxa_1753 [Halopiger xanaduensis SH-6]
Scores for 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:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 611.60
//
Query:       gi|336253154|ref|YP_004596261.1|  [L=192]
Description: hypothetical protein Halxa_1754 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00072   18.8   0.5      0.006   15.8   0.1    1.9  2  UT          Urea transporter
  ------ inclusion threshold ------
      0.015   15.0   0.1      0.029   14.1   0.1    1.4  1  Sensor_TM1  Sensor N-terminal transmembrane domain
        0.2   10.9   0.9       0.44    9.8   0.9    1.5  1  CorA        CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> UT  Urea transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1     1e-06     0.006     169     220 ..      72     123 ..      33     126 .. 0.87
   2 ?    1.3   0.0     0.025   1.5e+02     198     237 ..     141     180 ..     133     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-06
                                       HHCCT---HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHTT--HHHHH CS
                                UT 169 gqVffldnvlaGllillallissriaallallGsllgllaalllgapleaiy 220
                                       + V++l+ ++ G ++ ++ ++++r a+++a l+++++l++++l+ a++ +i+
  gi|336253154|ref|YP_004596261.1|  72 SVVIGLPMLVEGGVMEIGTFLATRPAFFVANLAMAVALVVGILYVADFREIQ 123
                                       448999*****************************************99885 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHHHTT--HHHHHCTCCCHHHHHHHHHCTT CS
                                UT 198 allGsllgllaalllgapleaiysGlwGyNavLtaiAlgg 237
                                       +++ +++++l+ l+ +++ ++   +l   + v ta+A+gg
  gi|336253154|ref|YP_004596261.1| 141 GIAFATAAVLMTLWGRVAWDEPWLDLCQVSVVFTAMAIGG 180
                                       4445566777788889999999999999999999999998 PP

>> Sensor_TM1  Sensor N-terminal transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   4.8e-06     0.029      18      39 ..     100     121 ..      94     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.8e-06
                        Sensor_TM1  18 llnLlaLvvLvaGiLYlnqfRd 39 
                                       + nL+  v+Lv+GiLY+ +fR+
  gi|336253154|ref|YP_004596261.1| 100 VANLAMAVALVVGILYVADFRE 121
                                       56999999*************8 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.9   7.4e-05      0.44     125     165 ..      12      52 ..       7      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 7.4e-05
                              CorA 125 ellekleeeldeledeledstkkeilrelaqlrrrlvklrr 165
                                       +++e+l e+l+ le+++++s ++ ++r++++l  rl + r 
  gi|336253154|ref|YP_004596261.1|  12 ATIEDLYEQLETLEETVDTSDERTEVRRTMRLVNRLSHNRA 52 
                                       6899999**********999999999999999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1097  (0.0611858); expected 358.6 (0.02)
Passed bias filter:                      782  (0.0436165); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 1471.49
//
Query:       gi|336253155|ref|YP_004596262.1|  [L=410]
Description: iron transport protein [Halopiger xanaduensis SH-6]
Scores for 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   47.1   0.0    3.9e-12   46.3   0.0    1.5  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.014   15.3   0.2      0.027   14.3   0.2    1.5  1  TAT_signal    TAT (twin-arginine translocation) pathway signa


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 !   46.3   0.0   4.3e-16   3.9e-12      10     234 ..      86     349 ..      68     352 .. 0.71

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 4.3e-16
                                       HHHHHTT-GGGEEEB-GGG--GGGGGGT.........TS-BSBESSSB-HHHHHHH--SEEEE-GGG.........G CS
                      Peripla_BP_2  10 eillalGatdkvvgvdtttsdpldadklee.......aivevgadgeidvEklaalkPDlvilskgl......gltd 73 
                                       +++lalG +d + +  +  ++   ++kl         +   + +++ +  Ekl +l+ D+ i+++         ++ 
  gi|336253155|ref|YP_004596262.1|  86 DMVLALGRSDDMNAMFAPEYHQGLYRKLTRhfdgisiDWEGLYNSWPPKKEKLYELDSDVHIADPAKvatadgWDNN 162
                                       56666666666666666655555555554455333333344445555555999999999999999985544443444 PP

                                       GGHHHHHHHS-EEE----TTS.............HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.. CS
                      Peripla_BP_2  74 edeellksgiptvivessntg.............eslkeqiralgellgledeaeklvaeidsklaaaksaidse.. 135
                                       +  e+ ++ +p +    s t              + l e +  +++llg+ +++e+l++ +ds ++ + ++ + e  
  gi|336253155|ref|YP_004596262.1| 163 DVQEIAEKVAPWFGNALSGTNrtppegwkdqyeyYTLWEIFGRVAQLLGEDERYEALASVHDSMVQTIAEKRPPEsg 239
                                       4444444445555555555559999999999888899999999********************************96 PP

                                       .-EEEEEEEETTE....EEEE-TTSTTTHHHHT..S--EESTTT--......STT-EEE-HHHHHHH--SEEEEEEH CS
                      Peripla_BP_2 136 kpkpvlvfggade..ggyvvagsnsyigdllda..lgieniaaesk......kseyeeisaEqilasdpdvifvsgr 202
                                        p+++lv+ ++ e  +g+ +  +n+ + + +++  +g+ ++++e        ++ + + + E +l++dpdv+++ g+
  gi|336253155|ref|YP_004596262.1| 240 RPTAALVLFSSSEdhKGWGYK-MNHPGYYAAHTrpMGVTDTLSEAFgggygeSGRNMPFDYELLLEADPDVLLILGS 315
                                       555555555555533333333.3333333333347999999555446999988999999****************** PP

                                       ..HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 203 ..aeadnktgleflkenpllaelpAvkngrVyal 234
                                         a  + +++ + l+++++++el+Avk+g+Vya 
  gi|336253155|ref|YP_004596262.1| 316 mtAYFNPDEIRKTLENHEVASELTAVKEGNVYAQ 349
                                       86666678888889999***************85 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2     3e-06     0.027       3      25 ..      12      34 ..      10      35 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-06
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                      +RR  +K ++A++ +++++gca+
  gi|336253155|ref|YP_004596262.1| 12 TRRGYIKHGGAVMGGGLFAGCAS 34
                                      8********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3085.84
//
Query:       gi|336253156|ref|YP_004596263.1|  [L=120]
Description: hypothetical protein Halxa_1756 [Halopiger xanaduensis SH-6]
Scores for 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   14.1   5.1      0.033   14.1   5.1    1.8  2  PLDc_N    Phospholipase_D-nuclease N-terminal
      0.041   14.2   0.7      0.054   13.8   0.7    1.1  1  DUF4499   Domain of unknown function (DUF4499)


Domain annotation for each model (and alignments):
>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.5      0.25   2.3e+03      30      30 ..      13      13 ..       1      30 [. 0.58
   2 ?   14.1   5.1   3.6e-06     0.033      18      39 ..      35      56 ..      19      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.25
                            PLDc_N 30 P 30
                                      P
  gi|336253156|ref|YP_004596263.1| 13 P 13
                                      2 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.6e-06
                            PLDc_N 18 sklaWllvilflPvlGailYll 39
                                      +++ W+ + +++P++G+++Yl+
  gi|336253156|ref|YP_004596263.1| 35 PRAKWTAITFLIPLFGFFIYLF 56
                                      4778*****************8 PP

>> DUF4499  Domain of unknown function (DUF4499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7     6e-06     0.054      38      84 ..       5      49 ..       2      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6e-06
                           DUF4499 38 llrlgfvlavliHvlEalyalklckkkgisnaaalkWflqTlllGfa 84
                                      ll +++++ ++ H+   ++a++ ++++g++  a   W++ T+l+ ++
  gi|336253156|ref|YP_004596263.1|  5 LLAVIVGIPLAWHLGLTAVAYYDAGRVGLEPRAK--WTAITFLIPLF 49
                                      7888999999********************9999..******86444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 913.26
//
Query:       gi|336253157|ref|YP_004596264.1|  [L=378]
Description: acetyl-CoA acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-76  255.1   3.4    9.7e-76  254.5   3.4    1.3  1  Thiolase_N     Thiolase, N-terminal domain
    7.8e-43  145.0   0.1      2e-42  143.7   0.1    1.8  2  Thiolase_C     Thiolase, C-terminal domain
    4.5e-06   26.4   0.9    1.1e-05   25.1   0.9    1.7  1  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
      0.056   13.3   6.7        0.2   11.5   0.1    2.6  3  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


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 !  254.5   3.4   2.2e-79   9.7e-76       2     259 ..       6     247 ..       5     248 .. 0.94

  Alignments for each domain:
  == domain 1  score: 254.5 bits;  conditional E-value: 2.2e-79
                                       EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSCHHHHHHHHTTS-TTSE CS
                        Thiolase_N   2 vivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqniarqaalkagipeevp 77 
                                       v+++a+rtp gk  g+++d+++e+L+  ++ ++l+++g++ ee+d++++G+  q  ++g+n+ar +al +++ e vp
  gi|336253157|ref|YP_004596264.1|   6 VVAAAVRTPQGKEDGVFADVRSEDLSVPLIDEILAETGLSGEEIDDLMWGCAQQRgEQGNNVARVIALLSELGEAVP 82 
                                       7999***************************************************889999**************** PP

                                       EEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSE CS
                        Thiolase_N  78 avtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneeh 154
                                       a+t+n+ c+S+++av+ aa++iaag+ d+v+agGvEsms++++ e++    + ++ d + ++ l            +
  gi|336253157|ref|YP_004596264.1|  83 ATTINRWCASSMQAVMSAADAIAAGNRDAVLAGGVESMSRVQMGENMG-SIHPRMADLYNVGEL------------Q 146
                                       *********************************************933.345556666666555............7 PP

                                       HHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-B CS
                        Thiolase_N 155 mGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkp 231
                                       mG+tae++a++++isRe+qde+A++s+q+a++a+++g+F++eivP+++++     tv++de++r+++t ekLa+l +
  gi|336253157|ref|YP_004596264.1| 147 MGMTAEKVAEEHDISREQQDEYAARSQQRAVEATEDGRFAEEIVPIETED----GTVEEDEGLRPGTTKEKLAELPT 219
                                       9*********************************************9998....46********************* PP

                                       SSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 232 aFkkeGtvtAgnasqisDGaaavllmse 259
                                       +Fk++Gtvt gnasqisDGaaa+l++se
  gi|336253157|ref|YP_004596264.1| 220 VFKSDGTVTPGNASQISDGAAALLVTSE 247
                                       *************************998 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.1   5.1e+03      26      43 ..      33      50 ..      31      52 .. 0.85
   2 !  143.7   0.1   4.5e-46     2e-42       2     121 ..     256     375 ..     255     377 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                                      HHHHHHHHHHT--GGGES CS
                        Thiolase_C 26 yaikkvlkkagltvedid 43
                                      + i ++l ++gl+ e+id
  gi|336253157|ref|YP_004596264.1| 33 PLIDEILAETGLSGEEID 50
                                      56889999*****99998 PP

  == domain 2  score: 143.7 bits;  conditional E-value: 4.5e-46
                                       --SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH CS
                        Thiolase_C   2 kplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaial 78 
                                       ++la++ +  ++gvdp+ +g+gP++a++ +l+++g +v+d d +E+nEAFa+q+L++  +l++d+e +NvnGGaia+
  gi|336253157|ref|YP_004596264.1| 256 EILAEVGANNVAGVDPTVMGIGPVPATRGLLERNGREVDDYDQVELNEAFASQTLYCRDELGVDPEIFNVNGGAIAI 332
                                       67999999********************************************************************* PP

                                       -B-TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEE CS
                        Thiolase_C  79 GHPlGasGaRivvtllselkkeggklgvaalCigggqgvalvi 121
                                       GHPlGasGaR+ vtl++el+++gg lg+a+lC g gqg+a+ +
  gi|336253157|ref|YP_004596264.1| 333 GHPLGASGARLPVTLINELRRRGGGLGLATLCVGFGQGAAIEF 375
                                       ***************************************9866 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 !   25.1   0.9   2.5e-09   1.1e-05     162     206 ..      77     121 ..      50     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.5e-09
                                       HT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE--- CS
                     ketoacyl-synt 162 lglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvelll 206
                                       lg   p+ t+   C+Ss  av  a +++ +g+ d++laGGve + 
  gi|336253157|ref|YP_004596264.1|  77 LGEAVPATTINRWCASSMQAVMSAADAIAAGNRDAVLAGGVESMS 121
                                       5556688899999****99999999*****************876 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   0.1   4.5e-05       0.2       3      40 ..      86     123 ..      85     134 .. 0.92
   2 ?    5.1   0.1    0.0046        20      52      72 ..     235     258 ..     226     264 .. 0.78
   3 ?   -3.3   0.3       1.9   8.4e+03      48      57 ..     363     372 ..     361     372 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                                       EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGC CS
                       ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlski 40 
                                       +n  C++ ++a+  A+++i++g+   vL  g e +s++
  gi|336253157|ref|YP_004596264.1|  86 INRWCASSMQAVMSAADAIAAGNRDAVLAGGVESMSRV 123
                                       6778********************************95 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0046
                                       B-EEEEEEEEEEE...SSSSCEEE CS
                       ACP_syn_III  52 fGDGAgAvvleas...eeegaril 72 
                                        +DGA+A++++ +   e+++ +il
  gi|336253157|ref|YP_004596264.1| 235 ISDGAAALLVTSEafaEDHDLEIL 258
                                       68********99877666665555 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.9
                                       HHTTB-EEEE CS
                       ACP_syn_III  48 tavlfGDGAg 57 
                                        +v fG GA+
  gi|336253157|ref|YP_004596264.1| 363 LCVGFGQGAA 372
                                       6999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2890.80
//
Query:       gi|336253158|ref|YP_004596265.1|  [L=234]
Description: hypothetical protein Halxa_1758 [Halopiger xanaduensis SH-6]
Scores for 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   12.1   0.1      0.087   11.8   0.1    1.2  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.9e-06     0.087     268     316 ..     163     214 ..      99     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.9e-06
                                       HT--GGGG...-HHH......HHHHHHHHHT----HHHHHHHHHHHHHHHHH CS
                            AFOR_C 268 lglCkfts...eaeerldlelyakllsavtGidvteeellkaGeRiynleRl 316
                                         +C+f +     +++++ +++ak+l  v G+d++ ee l+a eRi  + R 
  gi|336253158|ref|YP_004596265.1| 163 GAMCDFFTaeeLDDVMYEATEVAKFLLEVEGVDLSVEEELEAEERISSVMRE 214
                                       469***99999888999*****************************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); 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: 0.43u 0.19s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1961.18
//
Query:       gi|336253159|ref|YP_004596266.1|  [L=191]
Description: hypothetical protein Halxa_1759 [Halopiger xanaduensis SH-6]
Scores for 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  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1505.65
//
Query:       gi|336253160|ref|YP_004596267.1|  [L=245]
Description: biotin/lipoate A/B protein ligase [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.094   12.6   0.0       0.14   12.1   0.0    1.2  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.7e-06      0.14      29     129 ..      68     171 ..      53     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-06
                                       EEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHH..HHHHHHHHHHHH......HHTT-TTEEEETTTEEEE CS
                     BPL_LplA_LipB  29 vrrqtgGrnvwhspkgeltyslllspeqktfqnrvlely..vsllvlavlealgyrdskpgiegipvfikwpnDlyv 103
                                       v+r +gGr+v  +  g++t++++  +    f++  +++y   ++ v ++l  lg  +++ +  ++ +   +   l v
  gi|336253160|ref|YP_004596267.1|  68 VERDVGGRAVAYD--GDATLAFARAEPVADFRRGTTARYerLTDDVKRALADLGVATERGEPDDSFCP--GTHSLSV 140
                                       78999***99999..9*******999999999999999955444444444445423478899999999..9999999 PP

                                       .....TTEEEEEEEEEEEETTS-EEEEEEEE CS
                     BPL_LplA_LipB 104 .....ngrKlaGiavtstrgktlhhivigvg 129
                                            + rK+ Gia++++  + + +++++v+
  gi|336253160|ref|YP_004596267.1| 141 egpagERRKIVGIAQRVRQDAAVGAGIVLVD 171
                                       99999**************999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1864.26
//
Query:       gi|336253161|ref|YP_004596268.1|  [L=305]
Description: hypothetical protein Halxa_1761 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0058   16.8   0.0      0.012   15.7   0.0    1.6  1  Peptidase_M23  Peptidase family M23


Domain annotation for each model (and alignments):
>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     7e-07     0.012      43      89 ..      98     146 ..      53     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7e-07
                                       TCEEEEEEEESEESS-TTEEE-TTCEEEEEBSTSSCS...SSEEEEEEEE CS
                     Peptidase_M23  43 dgystlyahlskisvkegqkVkaGqvIGtvgstgrst...gphLhfeirk 89 
                                       dg++ +++h++  +v++g++V++G+ +G+    g  +    +hLh  +r 
  gi|336253161|ref|YP_004596268.1|  98 DGLTARILHVEP-TVEAGDRVRRGESLGRLVRAGFFApwvDNHLHLGFRG 146
                                       567788888888.8********************87778899***99984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       177  (0.00987227); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2395.75
//
Query:       gi|336253162|ref|YP_004596269.1|  [L=478]
Description: proteinase inhibitor I4 serpin [Halopiger xanaduensis SH-6]
Scores for 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-107  359.4   0.0     3e-107  359.2   0.0    1.0  1  Serpin    Serpin (serine protease inhibitor)


Domain annotation for each model (and alignments):
>> Serpin  Serpin (serine protease inhibitor)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.2   0.0  1.7e-111    3e-107       3     370 ..      85     474 ..      83     475 .. 0.95

  Alignments for each domain:
  == domain 1  score: 359.2 bits;  conditional E-value: 1.7e-111
                                       HHHHHHHHHHHHHHHSTTSSEEE-HHHHHHHHHHHHHTB-HHHHHHHHHHHTGCCHCHHHHHHHHHHHHHHHCS... CS
                            Serpin   3 ntkfaldlfkalskekpskNiifSPlsistaLallllGakgetaeellevLglnesdeeelhealekllsrlne... 76 
                                       n +f++dl+ +l++++p++N++fSP+s+s+aLa+++ Ga++eta+e++++L+++  + e+lh a+++l  +l++   
  gi|336253162|ref|YP_004596269.1|  85 NVAFSFDLLARLRATTPDENLFFSPYSVSVALAMTYGGARDETATEMADALHYE-LEGESLHGAFGSLEAELEQrne 160
                                       779**************************************************6.889999***********999** PP

                                       ..................SGGTSEEEEEEEEEEEETTSEB-HHHHHHHHHHHS-EEEEE-TTTHHH.HHHHHHHHHH CS
                            Serpin  77 ..................seekdkelkianglfvekglklkeeflklakklykaevesvdfkddee.arkkINswve 134
                                                         +++ + ++++an+++ +++++l+e++++l++ +y++    vdf+++++ ar++IN wve
  gi|336253162|ref|YP_004596269.1| 161 dgrtvetagqtdeeneedEDDLGFQISSANAVWPDESFQLDEAYVDLLEAHYGSGQHRVDFSGSPDeARREINGWVE 237
                                       **************99887778899**************************************************** PP

                                       HHTTTSSSSSSSTTSS-TTECEEEEEEEEEEEEBSS--BGGGEEEEEEESSSSEEEEEEEEEEEEEEEEEEETTTTE CS
                            Serpin 135 kqTngkIkdllsegsidsdtrlvlvNaiyFkGkWeepFqpeatreekFyvnegekvkvpmMsqegkfkyaedeelna 211
                                       ++Tn++I+dlls+++++++trlvl+Na+yF+++We+ F + +t+  +F + +g++++v+mM+q+ +++yae    + 
  gi|336253162|ref|YP_004596269.1| 238 ERTNDRIEDLLSASAVNRTTRLVLTNAVYFRAAWEHDFASASTEPAPFAGIDGSETEVEMMHQTTELPYAEIG--GH 312
                                       *********************************************************************9988..** PP

                                       EEEEEEBGG.SEEEEEEEESSTTT.HHHHHHHHSHHHHHHHHHHGEEEEEEEEEEEE-EEEEEEEEHHHHHHHTTHC CS
                            Serpin 212 kvlelpYkg.nlsmlillPdeekg.leelekkltaerleewlsklkmkkekeevslPkfkieesidlkevLqklGlk 286
                                       +++elpY++ ++sm+++lP   +g +e++e++lt++rl ++l++ ++ +++  +++Pkf ie++++l   ++klG++
  gi|336253162|ref|YP_004596269.1| 313 QLVELPYANdDTSMVVILPA--EGeFESFEESLTTDRLATMLEETSRPRVD--LTMPKFGIESKFELAAEMKKLGME 385
                                       *******877*********7..666*********************99888..************************ PP

                                       GGGSTTTB.BTTTBSS..SSEEEEEEEEEEEEEESSSEEEEEEEEE....ECCTTCS-SSCEEEEECSEEEEEEEET CS
                            Serpin 287 dlFseneadlsgiskk..eplfvsevlhkafievnEeGteaaaata....vatllskksspvefkvdrPFlfliree 357
                                       ++F   +ad+sg++++  + l ++e++h++fiev+E+Gtea+aata    +      + ++ve++vdrPFlf ir++
  gi|336253162|ref|YP_004596269.1| 386 RAFG-RDADFSGMVESdgSGLSIDEIVHQSFIEVDEDGTEASAATAvvmgTDGSGGGPADRVEMTVDRPFLFYIRDR 461
                                       ****.*********667799*************************9665423445567899**************** PP

                                       TTTEEEEEEEESS CS
                            Serpin 358 ktgliLFlGkvvn 370
                                       +t+++LF+G++v+
  gi|336253162|ref|YP_004596269.1| 462 PTETPLFVGRIVD 474
                                       ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.35
# Mc/sec: 4120.11
//
Query:       gi|336253163|ref|YP_004596270.1|  [L=463]
Description: Unspecific monooxygenase [Halopiger xanaduensis SH-6]
Scores for complete 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-85  288.1   0.0    1.4e-85  287.9   0.0    1.0  1  p450      Cytochrome P450
     0.0049   16.8   0.2      0.012   15.6   0.2    1.6  1  Sdh5      Flavinator of succinate dehydrogenase


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.9   0.0   1.5e-89   1.4e-85       1     436 [.      23     434 ..      23     455 .. 0.90

  Alignments for each domain:
  == domain 1  score: 287.9 bits;  conditional E-value: 1.5e-89
                                       --SESEHHCCHCHHHHTTTCCHHHHHHHHHHHH-SEEEEE.ETTEEEEEEESHHHHHHHHCTSTTTTCEESSHHHHH CS
                              p450   1 Ppgptplplvgnllqlgrkeelhevlrklqkkygpifrlk.lgskpvvvlsgpeavkevlikkgeefsgrpdealla 76 
                                       Pp  + lp++gn +ql    e    +++++++ g+++ l+ lg  ++  +++p++++++l+++++ f +    a l+
  gi|336253163|ref|YP_004596270.1|  23 PPTHEGLPVIGNTHQLVL--EQGGLYEDAAER-GDVVELRiLGFGEFYQVNHPDLAEHILVDDRDRFRK----ASLS 92 
                                       788889**********95..444446688888.8899887256699*****************744444....4443 PP

                                       .HHHHTTTTSSSTTCGHHHHHHHHHHHHHHHTSHSTTTHHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHH CS
                              p450  77 .tsrkpfkgkgvlfangekwkklRrfltptltsfgklsleelveeeaedlveklrkkagesselditellskaaldv 152
                                           +  +g+g+++++g+ w+++R ++ p++ ++++  + ++++ ea+   +++ +ka+ +    + + +   +l +
  gi|336253163|ref|YP_004596270.1|  93 rDDLGDLLGQGLVLSEGDLWERQRERIQPAFYMDQIADYADVMTAEARAAADEWGEKATVN----VEREMKALTLGI 165
                                       03356889**************************666*********************999....99********** PP

                                       HHHHHHSSHHHTTTSSHHHHHHHHHHHHHHHHHCHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              p450 153 igsilFgarfdlledeklselvkaveelssllskssvqllllfpllkylptkllrklkeavkklkdlldklieerre 229
                                       + + +Fg+++d +e    +++v++ +e  + ++++   +  l p  k++p +++r++++  +++++l+++++  rr+
  gi|336253163|ref|YP_004596270.1| 166 LVKAMFGSEID-YEAAGIPDIVAKLQEPGEPVKQP---IARLVP--KWVPIPMWRRYERGIREMEGLIEAFVDRRRA 236
                                       ***********.99999999999999997766443...355555..899***************************9 PP

                                       CHCHCSCSSCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHH CS
                              p450 230 tldsakksrrdfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidev 306
                                       +  ++   r d+l+ ll a+ ++ ge ++s++ l+ +++++lfaG++Tt+++l+++ ++La++P+v+++l  E++ v
  gi|336253163|ref|YP_004596270.1| 237 EGPET---RDDLLSRLLTAT-DEAGE-TMSERLLRDELMTFLFAGHETTATALTFTWLLLAQHPDVERRLVDELEAV 308
                                       99999...99*********7.88887.************************************************** PP

                                       C.CTTTT-HHHHCCT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS CS
                              p450 307 l.gdkreptyddlqklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPee 382
                                       l gd  + t +d+ +l+y++av++E++Rl+p+vp ++pRe+t++++++gy+ip+G +v ++ +++hrd+ ++++P +
  gi|336253163|ref|YP_004596270.1| 309 LdGD--RATVADVPDLEYTEAVLREAMRLYPPVP-SIPRETTEPLTLGGYSIPEGATVAPMQWTIHRDERFWDEPLT 382
                                       *555..48**************************.****************************************** PP

                                       --GGGGB-TTSCTESSCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHEEEE CS
                              p450 383 FdpeRFldekgnskrksfaflPFGaGpRnCiGerlArmelklflatlLqnFeve 436
                                       Fdp+RFl +++  +r++ a++PFGaGpR CiG+++A +e  l+latl +++   
  gi|336253163|ref|YP_004596270.1| 383 FDPDRFLGDEA--ERPDLAYFPFGAGPRRCIGQQFALVEGTLILATLARRYHPV 434
                                       *********98..5*********************************9999755 PP

>> Sdh5  Flavinator of succinate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   1.3e-06     0.012       6      48 ..     213     255 ..     212     256 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-06
                                       HHH.--SSHHHHHTTTTHHHHHTTT--HHHHHHHHHHHTS--H CS
                              Sdh5   6 yrsrrRGmlElDllLgrFaekhlatlseeeldaferLLdleDp 48 
                                       +r   RG++E++ l++ F++++ a+  e+  d ++rLL+  D 
  gi|336253163|ref|YP_004596270.1| 213 WRRYERGIREMEGLIEAFVDRRRAEGPETRDDLLSRLLTATDE 255
                                       66678*********************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 3520.92
//
Query:       gi|336253164|ref|YP_004596271.1|  [L=166]
Description: phenylacetic acid degradation-like protein [Halopiger xanaduensis SH-6]
Scores for 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    3.6e-13   49.7   0.0    1.4  1  4HBT      Thioesterase superfamily
    2.4e-05   24.5   0.0    4.8e-05   23.5   0.0    1.5  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 !   49.7   0.0     4e-17   3.6e-13       4      72 ..      75     143 ..      73     150 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 4e-17
                                       B-HHHHHHHHHHHHHHHHHHTTST..TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEE CS
                              4HBT   4 vhgGvylallDeaagaalrslggr..gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrd 72 
                                       +hgG  ++llD+a+g+alr+         +++++l++++lrp++ +  lt++a+v+r+g+++ v e+ v +
  gi|336253164|ref|YP_004596271.1|  75 IHGGIAATLLDTAGGLALRTEIENpfAASIATINLNVNYLRPATGD--LTATANVVRAGSSVGVSEIVVES 143
                                       8*********************************************..****************9998876 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   5.4e-09   4.8e-05      47     101 ..      74     130 ..      33     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5.4e-09
                                       SB-HHHHHHHHHHHHHHHHHHHS-T..TEEEEEEEEEEEE-S---S-EEEEEE-TTS CS
                           DUF4442  47 tvHAiAicnlaElamGllaeatlpd..thrwipkgmevdYlakatgdltavaelepe 101
                                        +H++ +++l+++a Gl + + +++   + +   + +v+Yl++atgdlta+a++ ++
  gi|336253164|ref|YP_004596271.1|  74 DIHGGIAATLLDTAGGLALRTEIENpfAASIATINLNVNYLRPATGDLTATANVVRA 130
                                       589999*****************998777777889*****************98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 1361.83
//
Query:       gi|336253165|ref|YP_004596272.1|  [L=633]
Description: Nitrous-oxide reductase [Halopiger xanaduensis SH-6]
Scores for 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-31  107.7   0.2    1.1e-30  105.8   0.2    2.0  2  nos_propeller_2  Nitrous oxide reductase propeller repeat 2
    4.4e-31  106.6   0.4    3.7e-29  100.4   0.1    3.3  3  nos_propeller    Nitrous oxide reductase propeller repeat
    2.5e-08   34.0   0.0    5.7e-08   32.8   0.0    1.6  1  Cupredoxin_1     Cupredoxin-like domain
    3.5e-07   29.8   4.0    5.4e-07   29.2   4.0    1.3  1  TAT_signal       TAT (twin-arginine translocation) pathway si
    2.8e-06   27.2   0.0    6.5e-06   26.0   0.0    1.6  1  COX2             Cytochrome C oxidase subunit II, periplasmic


Domain annotation for each model (and alignments):
>> 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 !  105.8   0.2     3e-34   1.1e-30       1      70 []     179     247 ..     179     247 .. 0.99
   2 ?   -1.8   0.0       1.2   4.2e+03       6      26 ..     331     349 ..     328     352 .. 0.81

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 3e-34
                   nos_propeller_2   1 iPNvqaiHGlrvqkvPktkyvfangEfrvPlpndGrdlddpekyvslfsaidaetmevawqviVdGNLDn 70 
                                       iPN+q++HG+++  +P+tkyvf++gEfrvP+pndGrdl+dp++y+s+++aid+etm+v+w+v+VdGN+Dn
  gi|336253165|ref|YP_004596272.1| 179 IPNQQGTHGACCL-LPDTKYVFGVGEFRVPMPNDGRDLTDPDSYTSTIAAIDPETMNVEWEVLVDGNMDN 247
                                       8***********9.9******************************************************9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                   nos_propeller_2   6 aiHGlrvqkvPktkyvfangE 26 
                                       + HG+ v   P+ ky +a+g 
  gi|336253165|ref|YP_004596272.1| 331 SPHGVSVT--PDNKYAIASGK 349
                                       56999887..9****999985 PP

>> nos_propeller  Nitrous oxide reductase propeller repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.24   8.6e+02      19      56 ..     146     182 ..     131     185 .. 0.77
   2 ?    1.5   0.0     0.081   2.9e+02      13      32 ..     331     350 ..     328     354 .. 0.88
   3 !  100.4   0.1     1e-32   3.7e-29       1      71 []     425     497 ..     425     497 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.24
                     nos_propeller  19 kepdGkylvalnKlskdrflpvGplkpeneqLidisge 56 
                                       ++ dG++ ++  K + +r++++  +  e++ ++di ++
  gi|336253165|ref|YP_004596272.1| 146 NDYDGRWAFVNDK-ANGRMARINLKYFETDAIVDIPNQ 182
                                       4678999998888.689999999999999999999765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.081
                     nos_propeller  13 aaegdtkepdGkylvalnKl 32 
                                       +++g +++pd ky +a  Kl
  gi|336253165|ref|YP_004596272.1| 331 SPHGVSVTPDNKYAIASGKL 350
                                       578999**********9997 PP

  == domain 3  score: 100.4 bits;  conditional E-value: 1e-32
                     nos_propeller   1 kvdvhYniGHlsaaegdtkepdGkylvalnKlskdrflpvGplkpeneqLidisgek..mklladaptlgEPH 71 
                                       k+dvhYn+GHl a+e+ t++p+G++l++lnKlskdrfl+vGp+kpen+qLi i +++  m+l++d+p ++EPH
  gi|336253165|ref|YP_004596272.1| 425 KIDVHYNPGHLIASESYTADPQGDWLISLNKLSKDRFLNVGPQKPENDQLIYIGDDEegMQLVKDTPSYAEPH 497
                                       79***************************************************987777************** PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   1.6e-11   5.7e-08      18      94 ..     534     613 ..     525     628 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.6e-11
                      Cupredoxin_1  18 aaektveitvkdggfePskievkagekvklkiknkdktp...eefesedlgeekvlapgktttitiaplkpGeYeft 91 
                                       +++++v++  + ++f   +++v++g +v+++++n  +tp   +++ +++ +++ +lap++t ++t+++++pG Y ++
  gi|336253165|ref|YP_004596272.1| 534 DGRAHVKMYSTRNEFGLHEVTVQEGDEVTMTVTNIEQTPdilHSLAIPEHDINIKLAPQETREVTFTADEPGVYWMY 610
                                       55677888899999************************9999********************************999 PP

                      Cupredoxin_1  92 cdm 94 
                                       c +
  gi|336253165|ref|YP_004596272.1| 611 CAF 613
                                       984 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   4.0   1.5e-10   5.4e-07       4      25 ..      30      51 ..      27      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.5e-10
                        TAT_signal  4 RRdFLKgsAAaaAAaalggcaa 25
                                      RRdF+K++AAa+A++ l+gc++
  gi|336253165|ref|YP_004596272.1| 30 RRDFMKAGAAAGAMGSLAGCTG 51
                                      ********************97 PP

>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.8e-09   6.5e-06      55     113 ..     560     622 ..     522     629 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.8e-09
                              COX2  55 kirllvt....aedvlhsfavpslgvkvdavpGrlnqvsllidreGvfyGqcselcGvnhssm 113
                                       ++ + vt    + d+lhs a+p   + +   p    +v++++d +Gv++  c+ +c ++h  m
  gi|336253165|ref|YP_004596272.1| 560 EVTMTVTnieqTPDILHSLAIPEHDINIKLAPQETREVTFTADEPGVYWMYCAFFCSALHLEM 622
                                       4555554222167***********************************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); 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:                         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 0.17s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 5553.86
//
Query:       gi|336253166|ref|YP_004596273.1|  [L=289]
Description: hypothetical protein Halxa_1766 [Halopiger xanaduensis SH-6]
Scores for 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   14.3   1.0      0.044   13.4   0.1    1.8  2  DUF5336   Family of unknown function (DUF5336)


Domain annotation for each model (and alignments):
>> DUF5336  Family of unknown function (DUF5336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.4e-06     0.044      80     123 ..     100     144 ..      72     154 .. 0.81
   2 ?   -1.5   0.1     0.093   1.7e+03     135     148 ..     191     204 ..     178     207 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-06
                           DUF5336  80 avvllLlagLlAgvslLPkqksktavaAvls.vlgfLlvlaevin 123
                                       +v++  lag  A+vs+LP +k +++++A+l  ++++++ +a++i+
  gi|336253166|ref|YP_004596273.1| 100 PVAFIGLAGASAAVSVLPSGKLERGLVALLGgTVAIFGTMAAIIQ 144
                                       47788899********************98437788877777776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.093
                           DUF5336 135 wvvlvlallqaaaA 148
                                        +v+++all  a+A
  gi|336253166|ref|YP_004596273.1| 191 LLVVAVALLAVAVA 204
                                       44555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2245.50
//
Query:       gi|336253167|ref|YP_004596274.1|  [L=460]
Description: parallel beta-helix repeat-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-54  184.7  15.0    3.2e-53  180.5  14.2    2.0  2  NosD        Periplasmic copper-binding protein (NosD)
    1.6e-30  106.1  16.6    1.1e-22   80.6   3.4    2.9  3  Beta_helix  Right handed beta helix region
    1.6e-07   30.9  11.9     0.0023   17.3   0.2    2.6  2  DUF1565     Protein of unknown function (DUF1565)
    0.00031   20.2   2.0    0.00064   19.2   2.0    1.5  1  eIF-6       eIF-6 family


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0042        19      97     148 ..     134     185 ..     101     191 .. 0.63
   2 !  180.5  14.2   7.2e-57   3.2e-53       8     236 ..     185     403 ..     179     408 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0042
                              NosD  97 nNtisnnen.yGillsdssnntisnNtisnnnkGiflensssntitgNriesn 148
                                       n+ + ++ +  G+l+++ss  t+s+ + ++ + G+++ + ++ t++++ i++ 
  gi|336253167|ref|YP_004596274.1| 134 NSGLDKSAGdSGVLVNGSS-ATLSELRLTEIAFGVWIGSVDDATVEDSLIAGR 185
                                       3333333336777777777.458888888888888888888888888877765 PP

  == domain 2  score: 180.5 bits;  conditional E-value: 7.2e-57
                              NosD   8 devlvsa.rgngiqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnes 83 
                                       +e + +  rgngi+l++s+++ei nn+i+++rdgi++++++++  +gnt+++ ryG+h+++s++n++ dnt+++n+ 
  gi|336253167|ref|YP_004596274.1| 185 REDVQTVqRGNGIHLWESTDAEIHNNSITTVRDGIYYQWAEGVHAEGNTMWDMRYGVHYMYSNDNRLVDNTAFDNDV 261
                                       444333369******************************************************************** PP

                              NosD  84 GialmsssnntlenNtisnnen...yGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGillls 157
                                       G+alm s++ tlenNt+ nn++   +Gill+d +++ i +N+++ n++G++++n+++n++ +N + +n +iG+++++
  gi|336253167|ref|YP_004596274.1| 262 GFALMVSKGLTLENNTAVNNDGtsgHGILLKDVEDSAIVGNEVVGNDNGLYVYNAQDNRLADNLVLEN-EIGVHVTA 337
                                       *********************99*********************************************.******** PP

                              NosD 158 ssegntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydgeDadgDGigDtpYeindgviDy 234
                                       +s +  + +N+Fi n + +  +++++ +Wn t+            +GNyW+d + +D d+DG+++  +++ + v  +
  gi|336253167|ref|YP_004596274.1| 338 GSANAVVAGNSFIANDQAAFAETTSQAHWNATD------------RGNYWADARTTDLDEDGVSELRHQPAGAV-EK 401
                                       *********************************............***********************999887.77 PP

                              NosD 235 lp 236
                                       l+
  gi|336253167|ref|YP_004596274.1| 402 LV 403
                                       66 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.12   5.5e+02      15      54 ..      96     135 ..      84     141 .. 0.73
   2 !   80.6   3.4   2.4e-26   1.1e-22       1     143 [.     144     290 ..     144     293 .. 0.96
   3 !   32.5   4.1   1.5e-11   6.9e-08      70     147 ..     287     362 ..     283     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.12
                                       SEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT CS
                        Beta_helix  15 nntisnsggyGiylrgssnvvienneiannsgsGiyilgs 54 
                                       n+t+  + +++  ++g++n ++ +    + + +G++i++s
  gi|336253167|ref|YP_004596274.1|  96 NVTVAAVERDAAVIDGGENGTVVEIAADDVTLEGVWIRNS 135
                                       6777777888888888888666645555588888888875 PP

  == domain 2  score: 80.6 bits;  conditional E-value: 2.4e-26
                                       -SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES.......-SS-SEEE-TT-S-EEES-EEE---SE CS
                        Beta_helix   1 sgisingssnvtiknntisnsggyGiylrgssnvvienneian.......nsgsGiyilgssnntisnntisdnngg 70 
                                       sg+++ngss  t++   ++++ + G+++++ +++++e++ ia+       ++g+Gi++ +s+++ i+nn+i+    +
  gi|336253167|ref|YP_004596274.1| 144 SGVLVNGSSA-TLSELRLTEI-AFGVWIGSVDDATVEDSLIAGredvqtvQRGNGIHLWESTDAEIHNNSITTVR-D 217
                                       699*******.*********7.*****************************************************.* PP

                                       EE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-S...SEEEE CS
                        Beta_helix  71 gialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnk...gaGia 143
                                       gi++++a ++  e+n+++d +  G++ +ys++n++ +N++ +n   G+ ++ s+ ++t +nNt++nn+   g+Gi 
  gi|336253167|ref|YP_004596274.1| 218 GIYYQWAEGVHAEGNTMWDMRY-GVHYMYSNDNRLVDNTAFDND-VGFALMVSK-GLTLENNTAVNNDgtsGHGIL 290
                                       ********************76.*********************.*********.************977777774 PP

  == domain 3  score: 32.5 bits;  conditional E-value: 1.5e-11
                                       EEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT CS
                        Beta_helix  70 ggialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvg 146
                                        gi l++   + i +ne+  n++ G+y++++++n++ +N + +n+  G++++++s+n +v +N++  n++a++a ++
  gi|336253167|ref|YP_004596274.1| 287 HGILLKDVEDSAIVGNEVVGNDN-GLYVYNAQDNRLADNLVLENE-IGVHVTAGSANAVVAGNSFIANDQAAFAETT 361
                                       58999999*************88.*********************.*********9999*********988886555 PP

                                       - CS
                        Beta_helix 147 s 147
                                       s
  gi|336253167|ref|YP_004596274.1| 362 S 362
                                       4 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   5.1e-07    0.0023      74     195 ..      96     221 ..      74     269 .. 0.76
   2 !   15.3   7.2   2.1e-06    0.0093     113     225 ..     258     359 ..     251     381 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.1e-07
                           DUF1565  74 kvgp.lisgggddlsgvqnvtiv..laneatiaGvtitNp...nilkgtgvliesasakianNtitgniadGievsi 144
                                       +v +  ++  +  ++g++n t+v   a+ +t+ Gv i+N    + + + gvl++++sa++++  +t+ ia G+    
  gi|336253167|ref|YP_004596274.1|  96 NVTVaAVERDAAVIDGGENGTVVeiAADDVTLEGVWIRNSgldKSAGDSGVLVNGSSATLSELRLTE-IAFGVWIGS 171
                                       555545666677778888888873357899**********775448889999999999999999999.699999999 PP

                           DUF1565 145 yeaktgaggniisGns.ilfeknGiaisgasaavenkienNiivkNliGvva 195
                                        +    + +  i+G + ++  ++G +i+  + +    i+nN i+  + G+  
  gi|336253167|ref|YP_004596274.1| 172 VD-DATVEDSLIAGREdVQTVQRGNGIHLWEST-DAEIHNNSITTVRDGIYY 221
                                       96.888999999998844444445555555444.558999988887777754 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.1e-06
                           DUF1565 113 lkgtgvliesa.sakianNtitgniadGievsiyeaktgaggniisGnsilfeknGiaisgasaavenkienNiivk 188
                                        +++g ++  + + +++nNt  +n  dG + +   + +++ +  i+Gn++  + nG+   +a+    n++ +N++ +
  gi|336253167|ref|YP_004596274.1| 258 DNDVGFALMVSkGLTLENNTAVNN--DGTSGHGI-LLKDVEDSAIVGNEVVGNDNGLYVYNAQ---DNRLADNLVLE 328
                                       45666666555589999**99885..99999999.589999****************987665...56********* PP

                           DUF1565 189 NliGvvanalalDlGsgsegsaGnNifsnnaeaDini 225
                                       N iGv ++a     Gs+ +  aG N f +n +a    
  gi|336253167|ref|YP_004596274.1| 329 NEIGVHVTA-----GSANAVVAG-NSFIANDQAAFAE 359
                                       *****9554.....667776677.7777776665555 PP

>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   2.0   1.4e-07   0.00064      47     112 ..     293     360 ..     266     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-07
                                       -BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHHHHHH---EEE--SS--..HHHHEEE-SSEEEE-G CS
                             eIF-6  47 tiagsrlvGslvvgNsngllvpstvtdeeleklkeslkleverleekltA..lGNvilaNDkvAlvhp 112
                                        +++s +vG  vvgN+ngl v +   ++  ++l  + ++ v++   + +A  +GN ++aND++A+ ++
  gi|336253167|ref|YP_004596274.1| 293 DVEDSAIVGNEVVGNDNGLYVYNAQDNRLADNLVLENEIGVHVTAGSANAvvAGNSFIANDQAAFAET 360
                                       6899*****************99888888887765555666667777776336***********8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.56u 0.22s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3393.28
//
Query:       gi|336253168|ref|YP_004596275.1|  [L=327]
Description: sulfate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-28   99.6   0.0    3.4e-28   98.9   0.0    1.3  1  ABC_tran  ABC transporter
      4e-11   43.3   0.1    6.9e-07   29.4   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
  ------ inclusion threshold ------
      0.036   13.5   0.1        4.6    6.6   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
      0.065   13.7   0.3       0.11   12.9   0.3    1.3  1  AAA_23    AAA domain
       0.11   11.2   0.0       0.17   10.7   0.0    1.1  1  DLIC      Dynein light intermediate chain (DLIC)


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 !   98.9   0.0   9.5e-32   3.4e-28       1     137 []      18     160 ..      18     160 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 9.5e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+  s+++  g++ +++G nGaGK+tL++ll g+ +p+eG+i++ g d+ e   +++r+++++lp+++ + p +t r
  gi|336253168|ref|YP_004596275.1|  18 LDGPSFTVPSGSTFGVLGTNGAGKTTLFELLVGHDRPDEGRIEVGGIDVAE-AGHRVRERVAFLPEHAGFPPAMTGR 93 
                                       57789**********************************************.9999*******************99 PP

                                       HH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       e            +++e+i++al+++gl + +d+ v    + +S G+ +r+ la+al+ +p++l+lDEpta
  gi|336253168|ref|YP_004596275.1|  94 EVldvharirgltNQRERIDDALETVGLADAADRAV----EGYSNGMGRRLGLAAALIADPPVLVLDEPTA 160
                                       99**********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 !   11.9   0.1   3.9e-05      0.14       4      21 ..      33      50 ..      31      73 .. 0.81
   2 !   29.4   0.0   1.9e-10   6.9e-07     228     297 ..     123     190 ..      74     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                            AAA_21  4 liGpNgsGKSnLLdaldl 21
                                      + G Ng+GK++L+++l +
  gi|336253168|ref|YP_004596275.1| 33 VLGTNGAGKTTLFELLVG 50
                                      78*************955 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1.9e-10
                            AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTH 297
                                       d  ++ +   S G+ r l+l++al++++   ++l++DEp +gL+P+ ++ + + +++l r +++ ++l++H
  gi|336253168|ref|YP_004596275.1| 123 DAADRAVEGYSNGMGRRLGLAAALIADP---PVLVLDEPTAGLDPRGVAAFHQTIERLGReTDTTIVLSSH 190
                                       4455556667****************99...**************999999999966666699******** 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 ?    4.7   0.1    0.0049        18      28      42 ..      32      46 ..      20      50 .. 0.83
   2 ?    6.6   0.0    0.0013       4.6     151     198 ..     142     188 ..     136     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0049
                                      EEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxx RF
                             SMC_N 28 aivGpNGSGKsnlld 42
                                       ++G NG+GK+ l++
  gi|336253168|ref|YP_004596275.1| 32 GVLGTNGAGKTTLFE 46
                                      589********9987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0013
                                       HHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 151 fAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislr 198
                                       +A   +   p+ +lDe  a LD + v+++ + +++   ++   ++ l+
  gi|336253168|ref|YP_004596275.1| 142 LAAALIADPPVLVLDEPTAGLDPRGVAAFHQTIERLGRETDTTIV-LS 188
                                       5666677789************************98877655433.33 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   3.2e-05      0.11      21      38 ..      30      47 ..      18      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                            AAA_23 21 ltlItGpNGaGKTTildA 38
                                       + + G NGaGKTT+++ 
  gi|336253168|ref|YP_004596275.1| 30 TFGVLGTNGAGKTTLFEL 47
                                      57789***********96 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.6e-05      0.17      21      55 ..      24      58 ..      19      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.6e-05
                              DLIC 21 klPsgksvlvlGedgsGkttliaklqGveeekkGr 55
                                       +Psg +  vlG +g+Gkttl   l G + +  Gr
  gi|336253168|ref|YP_004596275.1| 24 TVPSGSTFGVLGTNGAGKTTLFELLVGHDRPDEGR 58
                                      579************************99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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 0.26s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2469.24
//
Query:       gi|336253169|ref|YP_004596276.1|  [L=306]
Description: hypothetical protein Halxa_1769 [Halopiger xanaduensis SH-6]
Scores for 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   92.2  21.1    1.1e-24   87.3  21.1    2.0  1  ABC2_membrane_2  ABC-2 family transporter protein
     0.0029   17.2   1.3      0.011   15.3   1.5    1.8  1  ABC2_membrane_5  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.34   10.0  10.5       0.42    9.7  10.5    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein


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 !   87.3  21.1   1.8e-28   1.1e-24       2     285 ..      46     303 ..      45     306 .] 0.87

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 1.8e-28
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                       ++a+ E r +vr r+ ++lt++++ + + l+ ++ ++  +++++  ++ ++                          
  gi|336253169|ref|YP_004596276.1|  46 VVAETEYRLAVRGRWAIALTAIFAAFALGLTTFSGASV-SPEGFERTVGSLAV------------------------ 97 
                                       6899999999*************999555555554444.44555555554444........................ PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgiv 155
                                        ++  l+p++a++f++d+i+g ke+g l  l+s+Pv R+ i++g + g++++   +a a+++++ +a ++ l     
  gi|336253169|ref|YP_004596276.1|  98 -LAVYLVPLVALAFSYDVIVGRKESGWLQTLFSLPVDRAWIVVGAAAGRAVV---LASATIIGFGVAGGFLLREYGL 170
                                       .68899**********************************************...9999999999999999998888 PP

                   ABC2_membrane_2 156 laledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindf 232
                                         ++++ ++++ +v l+l  vfla+g+l+S++ar+++ a+ ++l  ++ ++++ +++++g++ +l   +        
  gi|336253169|ref|YP_004596276.1| 171 DGFDAYATFMLGAVGLGL--VFLAVGVLVSTLAREKTHALGVSLLAWAWFVLVHDLLALGLIGALELSET---AVSA 242
                                       89999*************..99**************************************8888776655...6888 PP

                   ABC2_membrane_2 233 lsllsptsayntllneilagsdlna........lgstatnllilllllavllvlgyvlFkr 285
                                       ++l +pt ++++l+   l  +++           +st+   ++ll+++av++++++ + +r
  gi|336253169|ref|YP_004596276.1| 243 MLLANPTGVFRALVLGSLGAGGNAGfasvlaesGLSTGVLSGALLAWIAVPIAIAALAIRR 303
                                       99**********99888888865559*******9********************9976655 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 !   15.3   1.5   1.8e-06     0.011      39     162 ..      98     221 ..      60     260 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-06
                   ABC2_membrane_5  39 ifsilslvisiililttlsyDek.....skwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgn 110
                                       + ++l+++++      ++syD       s+w + l++LPv+r  iV     + +++ ++a++i++ ++  ++++ ++
  gi|336253169|ref|YP_004596276.1|  98 LAVYLVPLVA-----LAFSYDVIvgrkeSGWLQTLFSLPVDRAWIVVGAAAGRAVVLASATIIGFGVA--GGFLLRE 167
                                       3333333333.....3455554333334************************************8887..4566666 PP

                   ABC2_membrane_5 111 ..vtisevllsiliglv.ialiflaivlPlyfkfgvekgrivliiiifgiifllv 162
                                         ++  ++  ++++g v ++l+fla+   +   +  ek+  + + + + ++f+lv
  gi|336253169|ref|YP_004596276.1| 168 ygLDGFDAYATFMLGAVgLGLVFLAVGVLVS-TLAREKTHALGVSLLAWAWFVLV 221
                                       4644445555555544425666666544444.44446666655555555555444 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 ?    9.7  10.5     7e-05      0.42     146     279 ..      74     225 ..      50     299 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 7e-05
                   ABC2_membrane_3 146 nvestqleeel.snvasflvgliliilifitasfiav...siveEkesrikelqlvsgvsplqywlskilgdflvyl 218
                                       ++++++  + + +++++++ +l+++ + +++++ +a+    iv  kes+ ++ +++ +v+++ ++++   g ++v +
  gi|336253169|ref|YP_004596276.1|  74 GLTTFSGASVSpEGFERTVGSLAVLAVYLVPLVALAFsydVIVGRKESGWLQTLFSLPVDRAWIVVGAAAGRAVVLA 150
                                       555555533334555555555444444444444444411157********************************999 PP

                   ABC2_membrane_3 219 lqlllilllafgl.....gipfgnlglll.llfllfglayialgyllsslfknsetaqilifivil........l 279
                                         +++ +++a g+     g++ ++  +++ l  +  gl+++a+g l+s+l +  + a ++ ++ +         l
  gi|336253169|ref|YP_004596276.1| 151 SATIIGFGVAGGFllreyGLDGFDAYATFmLGAVGLGLVFLAVGVLVSTLAREKTHALGVSLLAWAwfvlvhdlL 225
                                       999999988777777856555555555666999999**************9998888776555555333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2523.82
//
Query:       gi|336253170|ref|YP_004596277.1|  [L=192]
Description: NosL family protein [Halopiger xanaduensis SH-6]
Scores for complete 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-40  138.7   0.5    1.7e-40  138.4   0.5    1.0  1  NosL      NosL


Domain annotation for each model (and alignments):
>> NosL  NosL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.4   0.5   9.3e-45   1.7e-40       1     129 [.      43     189 ..      43     191 .. 0.94

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 9.3e-45
                              NosL   1 pveltaeaecdvCgMliaehpgpkgqifyed.....edepakFcstrdlfafllepeerk.eikaiyvtDmsavdw. 70 
                                       p++lt++++cd CgM++a+h gp+gq+fy+d     +d pa+F+s+++l+a ++++ +r+ e +a++vtD+s+vd+ 
  gi|336253170|ref|YP_004596277.1|  43 PIALTDGQACDACGMTVADHYGPAGQLFYADgypedRDGPARFDSVHELVAAHAAQARRGrELRAAFVTDYSSVDYd 119
                                       789****************************887545***************999999998**************** PP

                              NosL  71 ...........esp.daeafidakkalyVvgsdveGaMGpelvpFsdeadAeaFaaehgGkvlrfedvtee 129
                                                      +ae f+da+ a +Vv+   eGaMG+++vpFs+++dAeaFaaehgG+v+++e+++++
  gi|336253170|ref|YP_004596277.1| 120 lderegttyisS-HvRAEDFTDATAASFVVDGGIEGAMGEDVVPFSSTDDAEAFAAEHGGSVATWEELSSD 189
                                       *********744.369***************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1431.41
//
Query:       gi|336253171|ref|YP_004596278.1|  [L=53]
Description: hypothetical protein Halxa_1771 [Halopiger xanaduensis SH-6]
Scores for 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  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       170  (0.00948185); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 397.71
//
Query:       gi|336253172|ref|YP_004596279.1|  [L=53]
Description: hypothetical protein Halxa_1772 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.56    9.9   4.2       0.58    9.8   4.2    1.0  1  DUF2244   Integral membrane protein (DUF2244)


Domain annotation for each model (and alignments):
>> DUF2244  Integral membrane protein (DUF2244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.2   3.2e-05      0.58       8      58 ..       2      52 ..       1      53 [] 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 3.2e-05
                           DUF2244  8 sprgflllllalalvslvialafllaGawpvlpFaglevlalalafrvsar 58
                                      ++r++++l+++ ++++lv+++  ++ Ga++ ++ +gl  + l++  +++ar
  gi|336253172|ref|YP_004596279.1|  2 NQRHLRWLYVVGIAFNLVAMASAASTGAMLYAVTFGLVTVYLGARYWMIAR 52
                                      7899*****************************999999999988887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.42
# Mc/sec: 378.53
//
Query:       gi|336253173|ref|YP_004596280.1|  [L=192]
Description: isochorismatase hydrolase [Halopiger xanaduensis SH-6]
Scores for 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  167.9   0.0    2.7e-49  167.7   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 !  167.7   0.0   1.5e-53   2.7e-49       1     173 [.      10     186 ..      10     188 .. 0.99

  Alignments for each domain:
  == domain 1  score: 167.7 bits;  conditional E-value: 1.5e-53
                   Isochorismatase   1 talvviDmqndfv.eegvkeseeisavveninkllkaarkagipviftrdvhe...leevkgdlderkaaphfkpgt 73 
                                       ta+vv+Dmqn+f+ ++g    ++ ++++e i+ l+++ar+ag   +ftrdvh+   +e+ ++ ++ +++ +h+ +g+
  gi|336253173|ref|YP_004596280.1|  10 TAIVVVDMQNGFChPDGSLYAPGSERAIEPIAALVERAREAGASLLFTRDVHPpeqFEDAHYYDEFEQWGEHVLEGS 86 
                                       79*************************************************************************** PP

                   Isochorismatase  74 tgaelvpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaa 150
                                       ++ae+v+el++ + d vv+K++++af++t+l+ +L+++gi+++v++G  ++vCV++t  +a  l++++++v+D+++a
  gi|336253173|ref|YP_004596280.1|  87 WDAEIVDELPVEAADNVVEKHTYDAFYNTELEGWLNARGIDDLVICGTLANVCVLHTGGSAGLLDFRPILVEDCIGA 163
                                       ***************************************************************************** PP

                   Isochorismatase 151 lspelhdaalkrlkqafatvitt 173
                                       ++ +++++al++++  f++v+  
  gi|336253173|ref|YP_004596280.1| 164 IEDDHKEYALEHAEWLFGEVVEG 186
                                       ********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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 0.21s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1413.63
//
Query:       gi|336253174|ref|YP_004596281.1|  [L=602]
Description: hypothetical protein Halxa_1774 [Halopiger xanaduensis SH-6]
Scores for 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   14.2   0.0      0.044   13.6   0.0    1.3  1  Peptidase_M76  Peptidase M76 family
       0.16   11.9   0.0        0.3   11.0   0.0    1.4  1  Peptidase_M78  IrrE N-terminal-like domain
        1.6    8.3   3.1          3    7.5   3.1    1.3  1  DUF4956        Domain of unknown function (DUF4956)


Domain annotation for each model (and alignments):
>> Peptidase_M76  Peptidase M76 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.3e-06     0.044      45      87 ..     176     219 ..     128     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-06
                     Peptidase_M76  45 qaggfspee.gillcenrlrskehledtlahElvhayDdlrakv 87 
                                       + g ++p+e +i++++n+  + e  e +l hElvha  d r+++
  gi|336253174|ref|YP_004596281.1| 176 VGGYYEPTEdRIVIVSNTPDTPELNEVVLGHELVHALQDQRFDL 219
                                       34457777657****************************99976 PP

>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     5e-05       0.3      20      57 ..     177     215 ..     146     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5e-05
                     Peptidase_M78  20 gfrfdnsetkvivlnsn.hsptrqrftlaHElgHlllhh 57 
                                       g ++++ e++++++++  ++p+  + +l+HEl H+l ++
  gi|336253174|ref|YP_004596281.1| 177 GGYYEPTEDRIVIVSNTpDTPELNEVVLGHELVHALQDQ 215
                                       444555579999999999****************98665 PP

>> DUF4956  Domain of unknown function (DUF4956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.1    0.0005         3      31      58 ..      10      37 ..       4      37 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0005
                           DUF4956 31 vgvfavvlllasvevsiglglGLfgvls 58
                                      v+v++ ++ll+ v v++g+glG+fg ls
  gi|336253174|ref|YP_004596281.1| 10 VAVVVALVLLTVVGVGLGVGLGVFGPLS 37
                                      566667777888*************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); 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:                         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 0.23s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 4492.53
//
Query:       gi|336253175|ref|YP_004596282.1|  [L=521]
Description: hypothetical protein Halxa_1775 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0084   15.9   0.0      0.013   15.2   0.0    1.2  1  Peptidase_M76    Peptidase M76 family
     0.0087   16.8   0.0      0.019   15.7   0.0    1.5  1  Glyco_hydro_20b  Glycosyl hydrolase family 20, domain 2
  ------ inclusion threshold ------
      0.096   12.9   0.0       0.33   11.2   0.0    2.0  2  DUF4157          Domain of unknown function (DUF4157)


Domain annotation for each model (and alignments):
>> Peptidase_M76  Peptidase M76 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.2e-06     0.013      46      88 ..     141     183 ..     121     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-06
                     Peptidase_M76  46 aggfspeegillcenrlrskehledtlahElvhayDdlrakvd 88 
                                        +g+  + +i+++++   + +  ++tl+hElvha  d r+ ++
  gi|336253175|ref|YP_004596282.1| 141 VQGYYVDDRIVIVTDDSDEIRIDRRTLVHELVHALQDQRFGLE 183
                                       467888999*****************************99877 PP

>> Glyco_hydro_20b  Glycosyl hydrolase family 20, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.2e-06     0.019      29      92 ..     422     483 ..     405     486 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.2e-06
                   Glyco_hydro_20b  29 eeaadeat.adllaevlkaatgirlteakepgkgdirllalkdaelgaEgYrLavdedtitiegk 92 
                                       e++ad++  a + +++l+ ++g + ++a+++ +gd++  + +d+e  a++YrL+v+ dt+ i g+
  gi|336253175|ref|YP_004596282.1| 422 ESEADADEfATAYRSLLE-THGGDRVDADAATAGDVY--RIPDDEPFAGAYRLTVTGDTVEIVGA 483
                                       455555552556677777.*****************9..58999******************997 PP

>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.5e-05      0.33      38      77 ..     141     179 ..     123     181 .. 0.80
   2 ?   -3.5   0.0       2.1   1.3e+04      35      45 ..     445     455 ..     444     459 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.5e-05
                           DUF4157  38 AqAfTlgndivfaageyqpesaagrellaHELtHvvqqre 77 
                                       +q + + + iv+  +  + e + +r++l HEL+H  q ++
  gi|336253175|ref|YP_004596282.1| 141 VQGYYVDDRIVIVTDD-SDEIRIDRRTLVHELVHALQDQR 179
                                       5666677788885444.8888999*************986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.1
                           DUF4157  35 algAqAfTlgn 45 
                                       +++A+A T g+
  gi|336253175|ref|YP_004596282.1| 445 RVDADAATAGD 455
                                       57999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 4107.94
//
Query:       gi|336253176|ref|YP_004596283.1|  [L=400]
Description: Quinolinate phosphoribosyl transferase [Halopiger xanaduensis SH-6]
Scores for complete 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   60.6   0.0    2.1e-16   60.2   0.0    1.2  1  QRPTase_C   Quinolinate phosphoribosyl transferase, C-termina
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.041   13.9   0.0    2.0  2  QRPTase_N   Quinolinate phosphoribosyl transferase, N-termina
       0.19   12.2   0.0       0.52   10.7   0.0    1.8  1  NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N


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 !   60.2   0.0   3.5e-20   2.1e-16       2     169 .]     115     304 ..     114     304 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 3.5e-20
                                       HHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSS..HHHH CS
                         QRPTase_C   2 AtltarmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaags..ivea 69 
                                       At++ ++  aa +  v +++ R  +P +++  ++A+l++G d          l+ +   +++++ + ++g+  + ea
  gi|336253176|ref|YP_004596283.1| 115 ATAALEARLAAPDSLVLSFGARHVHPSIAATVERAALLAGLDgfshvaaGEILDREASGTMPHALMFCFGEgnQAEA 191
                                       89999999999999**************************999988777777888999***********86669*** PP

                                       HHHHHHHHTTTSE..EEEEESSHHHHHHHHHHT.....-SEEEEES--H..HHHHHHHHHH.HHHSTT....SEEEE CS
                         QRPTase_C  70 vksvreavdkevk..ievevesleeleevleae.....adiimLDnfsv..eelkkaveel.keknkr....vliev 132
                                       +++++eav++ v+    v++  +e+ e  l+ae      d++++D+  +   ++++++ e+ +e + r    v i++
  gi|336253176|ref|YP_004596283.1| 192 WTAFDEAVPEDVPriALVDTFWDEKSESLLAAEtlgddLDGVRIDTTGSrrGDFRHIIREVrWELDARghedVDIFC 268
                                       **********9999889**************99888889********776699*****99989999999999***** PP

                                       ESS--TTTHHHHHCTT-SEEEECHHCHTB----EEEE CS
                         QRPTase_C 133 SGgvtlenveeyaksgvdvisvgalthsvkalDislk 169
                                       SGg+  e ++++++   d ++vg+ ++++ ++D+sl+
  gi|336253176|ref|YP_004596283.1| 269 SGGLDPEAIRNLRDVA-DGFGVGSHITGADSVDFSLD 304
                                       ***************9.******************97 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 ?   13.9   0.0   6.8e-06     0.041      29      87 ..      55     110 ..      28     112 .. 0.91
   2 ?   -3.4   0.0       1.8   1.1e+04      49      59 ..     367     377 ..     364     380 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-06
                                       EE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHHH CS
                         QRPTase_N  29 vvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLnllqr 87 
                                       v+ G++ ++ +fe   ++ v++l +DG+ +  g  +l+ieG++ ++ + E  +L +l++
  gi|336253176|ref|YP_004596283.1|  55 VFTGVKDVATLFEGR-SVDVDAL-PDGQLFDGG-PVLRIEGPYLEFAELETSLLGFLSQ 110
                                       789999999999999.9999998.******766.99********************986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.8
                                       EESS-TT-EEE CS
                         QRPTase_N  49 ellvkDGerve 59 
                                       e+lv+DGe v+
  gi|336253176|ref|YP_004596283.1| 367 EPLVRDGEIVR 377
                                       67899**9987 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 ?   10.7   0.0   8.8e-05      0.52      88     124 ..      72     108 ..      60     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.8e-05
                        NAPRTase_N  88 evaveeeevvfpgepeirveGpwieaillEtplLaiv 124
                                        v +  ++  f+g p +r+eGp +e   lEt lL  +
  gi|336253176|ref|YP_004596283.1|  72 DVDALPDGQLFDGGPVLRIEGPYLEFAELETSLLGFL 108
                                       3444556779***********************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3004.95
//
Query:       gi|336253177|ref|YP_004596284.1|  [L=203]
Description: AMMECR1 domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-40  137.5   0.0    3.7e-40  137.3   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 !  137.3   0.0   2.1e-44   3.7e-40       1     166 []      22     191 ..      22     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 137.3 bits;  conditional E-value: 2.1e-44
                                       HHHHHHHHHHHTTSS-S-H.H---HHHHSEEEEEEEEE..EE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS CS
                           AMMECR1   1 lklareaieealkeekkle.eeakeelkekaglFVtlk..ekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRF 74 
                                       ++larea+e++++++++ +  + +e+++e++g+FV+l+  +++g+LRGC G +++ ++L++ ++++A++aA eD++ 
  gi|336253177|ref|YP_004596284.1|  22 VELAREAVESYVQHGQREQpGSMREAFYERTGAFVRLEstRGRGSLRGCAGGYRSGDQLGHVIVDAAIEAASEDSCG 98 
                                       689*************999899999*************888888********************************* PP

                                       ----HHHHTTEEEEEEEE---EE--..GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS-TT CS
                           AMMECR1  75 spvtaeElpeleveVsvLtepepiv..ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKaglrpd 149
                                       s+v+++Elp+l+v+V+ ++++   +  l+dle+g+hG+ i+  ++ ++l+P+v+ve+gw+++e+l++++rKa+l p 
  gi|336253177|ref|YP_004596284.1|  99 SEVSPSELPNLTVSVCTVKNVVLTDdpLADLEIGTHGVAIDG-GEGGWLYPTVPVENGWSPREYLDRTCRKAKLAPG 174
                                       *********************777455799**********86.799******************************9 PP

                                       CCCSTTSEEEEE-EEEE CS
                           AMMECR1 150 ewkdseikltryevekf 166
                                       +w+++++ +t +e+++f
  gi|336253177|ref|YP_004596284.1| 175 AWQNDDVVVTLFEGQVF 191
                                       9************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1639.30
//
Query:       gi|336253178|ref|YP_004596285.1|  [L=111]
Description: hypothetical protein Halxa_1778 [Halopiger xanaduensis SH-6]
Scores for 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   14.6   1.6      0.046   13.8   1.6    1.4  1  DprA_WH   DprA winged helix domain


Domain annotation for each model (and alignments):
>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.6   2.6e-06     0.046       7      35 ..       9      37 ..       3      38 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-06
                           DprA_WH  7 epplddlerrvLaaLgpePvhvDqLvrrt 35
                                      + +++d +r+v a+L+ e +++D+L++r+
  gi|336253178|ref|YP_004596285.1|  9 LLADTDRRRAVAALLETETTTIDALSERL 37
                                      56789*********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 826.35
//
Query:       gi|336253179|ref|YP_004596286.1|  [L=102]
Description: hypothetical protein Halxa_1779 [Halopiger xanaduensis SH-6]
Scores for 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-24   83.5   2.5    1.3e-23   83.0   2.5    1.2  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   2.5   7.2e-28   1.3e-23       1      74 [.      25      96 ..      25      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 7.2e-28
                            HalOD1  1 deespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVe 74
                                      d+e++++aV++av++v+gv pt+l+pLy++iDpdALd +f+    +++ ++++v+F+y+++eV+V++  +++V+
  gi|336253179|ref|YP_004596286.1| 25 DNEPITVAVIDAVSRVAGVAPTALPPLYETIDPDALDGVFDA--GSSDGESVRVAFSYADHEVVVQGGPRVTVT 96
                                      689***************************************..6667788*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 767.54
//
Query:       gi|336253180|ref|YP_004596287.1|  [L=124]
Description: hypothetical protein Halxa_1780 [Halopiger xanaduensis SH-6]
Scores for 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-24   83.9   1.4      1e-23   83.3   1.2    1.4  1  HalOD1         Halobacterial output domain 1
  ------ inclusion threshold ------
      0.074   12.6   0.1      0.088   12.3   0.1    1.4  1  DUF1833        Domain of unknown function (DUF1833)
      0.097   13.2   3.2       0.28   11.7   3.2    1.7  1  Cadherin-like  Cadherin-like beta sandwich domain


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   1.2   1.7e-27     1e-23       2      70 ..      10      78 ..       9      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 1.7e-27
                            HalOD1  2 eespstaVveavaavegvdptel.epLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdge 70
                                      +es++++ v+a+a++++vdp++l +pLyda+Dp+AL+aLfa++a+g+ ++ g+++F+y++y+VtV  dg+
  gi|336253180|ref|YP_004596287.1| 10 DESLTVQLVQAIADAADVDPVDLsPPLYDAVDPEALEALFAPTASGT-TRRGRIEFSYAEYRVTVSVDGD 78
                                      89*********************777****************77665.6679*************99985 PP

>> DUF1833  Domain of unknown function (DUF1833)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.5e-05     0.088      87     136 ..      54     102 ..       7     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                           DUF1833  87 egaavservieltyraylstdlnaphveapielkvkdvsvdalkvsatag 136
                                        g+ + + +ie  y  y +t +     e+pi+++v d + ++ ++ ++a+
  gi|336253180|ref|YP_004596287.1|  54 SGTTRRG-RIEFSYAEYRVTVSVDGDSETPITITVSDADDETTRIRSRAQ 102
                                       5778888.9***********9988888******************99986 PP

>> Cadherin-like  Cadherin-like beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.2   4.7e-05      0.28      43      81 ..      56      96 ..       2     100 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.7e-05
                     Cadherin-like 43 tvngvaveeg.....stetkdvsLneGrnk..ieikvtaedgsttr 81
                                      t++      +      +++ +vs+ +G+++  i+i+v ++d++ttr
  gi|336253180|ref|YP_004596287.1| 56 TTRRG----RiefsyAEYRVTVSV-DGDSEtpITITVSDADDETTR 96
                                      22222....244435778888888.5988899*********99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 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:                        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 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 934.63
//
Query:       gi|336253181|ref|YP_004596288.1|  [L=223]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-16   60.1   2.3    3.3e-16   59.5   2.3    1.2  1  BAT       GAF and HTH_10 associated domain
    6.5e-09   35.5   0.1    1.1e-08   34.7   0.1    1.4  1  HTH_10    HTH DNA binding domain
     0.0074   16.4   0.0      0.015   15.4   0.0    1.5  1  HTH_AraC  Bacterial regulatory helix-turn-helix proteins, Ara
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.028   14.7   0.0    1.4  1  UPF0122   Putative helix-turn-helix protein, YlxM / p13 like
      0.045   13.6   0.1       0.12   12.2   0.0    1.8  2  MarR_2    MarR family
        0.1   12.6   0.0       0.31   11.0   0.0    1.8  1  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR
       0.21   11.7   0.1       0.61   10.2   0.1    1.7  2  AgrD      Staphylococcal AgrD protein


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   2.3   1.3e-19   3.3e-16       7     146 ..       6     147 ..       6     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.3e-19
                               BAT   7 eleirdeddvlv.alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtllel 82 
                                       e+++  e+++l+ +laa+ +  ve e++v++ ++ ++ +f+v+g+d  +++daa+d +++  +r++++ d ++l+++
  gi|336253181|ref|YP_004596288.1|   6 EFHVPAEAFALAeTLAAAPELVVETERVVAT-EEVLTPYFWVSGDDGVAFEDAAADDPSIRHLRHIDDVDRASLYRA 81 
                                       78899999999989****************6.55799**************************************** PP

                               BAT  83 tvs..gpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrerer 146
                                       +++   +s++ ++a+ G+t+ +a+a++++++l +++ ++  + ++ e+++e+    +L++  er  
  gi|336253181|ref|YP_004596288.1|  82 EWTenVESIVYAYATVGATILEASAQGDEWELSIRFNNRDRLDQFREYCDEHDIPFQLTQLYERAH 147
                                       *9833468888**************************************99877777776666655 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.1   4.3e-12   1.1e-08       1      52 [.     156     206 ..     156     207 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 4.3e-12
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT kq e+l +A emGY+ ++ +v+l ++A+ l Is+++ls +L++  ++li
  gi|336253181|ref|YP_004596288.1| 156 LTRKQHEALVTAWEMGYY-RSTDVSLTDVADSLEISQQSLSRRLQRGYENLI 206
                                       9*****************.678***********************9988887 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 !   15.4   0.0   5.8e-06     0.015       6      31 ..     175     200 ..     174     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.8e-06
                                       SCT--HHHHHHHTTSSHHHHHHHHHH CS
                          HTH_AraC   6 stnltiediAdelgfSrsyFsrlFkk 31 
                                       st+ +++d+Ad l +S++ +sr++++
  gi|336253181|ref|YP_004596288.1| 175 STDVSLTDVADSLEISQQSLSRRLQR 200
                                       7999*******************997 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.1e-05     0.028      26      60 ..     170     204 ..     153     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                           UPF0122  26 lelyyadDlSlsEiAeefnvsrqavydnikrtekl 60 
                                       +  y   D Sl+++A+  ++s+q+++  ++r  + 
  gi|336253181|ref|YP_004596288.1| 170 MGYYRSTDVSLTDVADSLEISQQSLSRRLQRGYEN 204
                                       4457789*******************999987655 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.4   8.8e+03       5      18 ..      10      23 ..      10      29 .. 0.64
   2 ?   12.2   0.0   4.9e-05      0.12      20      44 ..     173     200 ..     148     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.4
                                      HHHHHHHHHHHCTT CS
                            MarR_2  5 paqarvLaaLgrrp 18
                                      pa+a +La+  ++ 
  gi|336253181|ref|YP_004596288.1| 10 PAEAFALAETLAAA 23
                                      67777888854444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.9e-05
                                       S...EEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2  20 r...dltvgelarrlglsksavsrilkr 44 
                                       +   d++ +++a+ l +s++++sr+l+r
  gi|336253181|ref|YP_004596288.1| 173 YrstDVSLTDVADSLEISQQSLSRRLQR 200
                                       144479********************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 ?   11.0   0.0   0.00012      0.31      15      36 ..     179     200 ..     176     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                       SHHHHHHHHTS-HHHHHHHHHH CS
                             HTH_1  15 sftrAAeeLglsqpavsrqikr 36 
                                       s+t  A+ L +sq ++sr+++r
  gi|336253181|ref|YP_004596288.1| 179 SLTDVADSLEISQQSLSRRLQR 200
                                       89999***************97 PP

>> AgrD  Staphylococcal AgrD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.8   4.5e+03      30      40 ..       3      13 ..       2      18 .. 0.74
   2 ?   10.2   0.1   0.00024      0.61      30      45 .]     129     144 ..     127     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.8
                              AgrD 30 ifDEvEVPkEL 40
                                      +f E  VP E 
  gi|336253181|ref|YP_004596288.1|  3 LFGEFHVPAEA 13
                                      68899999996 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00024
                              AgrD  30 ifDEvEVPkELTkLyE 45 
                                       + DE ++P  LT+LyE
  gi|336253181|ref|YP_004596288.1| 129 YCDEHDIPFQLTQLYE 144
                                       89*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1635.16
//
Query:       gi|336253182|ref|YP_004596289.1|  [L=111]
Description: hypothetical protein Halxa_1782 [Halopiger xanaduensis SH-6]
Scores for 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   1.1       0.01   15.9   1.1    2.1  1  HTH_20    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 !   15.9   1.1   5.7e-07      0.01       3      60 ..       7      82 ..       5      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.7e-07
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHH.....T.............S-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerl.....d.............lskntlsyHLrvLeeagLvevvreg 60
                                      +++AL+hP Rr   +aLa+   +t+ ++  ++     +             +  + ++ H+  Le+agL+e   ++
  gi|336253182|ref|YP_004596289.1|  7 LFRALSHPYRRHAIAALASTNSMTLRDVSNTVvsrtyGapltdvpsdavtdVYLSLVHVHVPLLEDAGLLEYDPHR 82
                                      79***************888888888888888765551444445555555599999**************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 788.00
//
Query:       gi|336253183|ref|YP_004596290.1|  [L=495]
Description: OB-fold tRNA/helicase-type nucleic acid binding protein [Halopiger xanaduensis SH-6]
Scores for 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-32  109.0   8.5    2.4e-13   49.9   0.5    3.5  3  tRNA_anti-codon  OB-fold nucleic acid binding domain
    1.8e-14   53.4   3.7    5.4e-06   26.2   0.1    3.3  3  REPA_OB_2        Replication protein A OB domain
    8.1e-11   42.1   0.1    0.00019   21.2   0.0    3.2  3  CDC24_OB3        Cell division control protein 24, OB domain 
    0.00015   21.7   0.2        2.9    8.0   0.0    3.4  3  SSB              Single-strand binding protein family
     0.0032   17.3   0.0       0.85    9.5   0.0    2.7  2  POT1PC           ssDNA-binding domain of telomere protection 
     0.0042   17.3   0.1       0.43   10.8   0.0    2.8  3  tRNA_anti_2      OB-fold nucleic acid binding domain
     0.0048   16.6   0.9        7.1    6.2   0.1    3.4  3  DUF4131          Domain of unknown function (DUF4131)
     0.0089   15.8   0.0         12    5.6   0.0    3.1  3  Rep_fac-A_C      Replication factor-A C terminal domain
  ------ inclusion threshold ------
      0.034   14.2   0.1       0.27   11.3   0.0    2.4  2  DUF4539          Domain of unknown function (DUF4539)


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 !   49.6   0.2   1.5e-16     3e-13       5      75 ..      81     153 ..      72     154 .. 0.89
   2 !   49.9   0.5   1.2e-16   2.4e-13       1      70 [.     179     255 ..     179     261 .. 0.95
   3 !   13.0   0.1   3.7e-05     0.074       2      42 ..     287     332 ..     286     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.5e-16
                                       EEEEEEE...EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEE CS
                   tRNA_anti-codon   5 Grvtsis...drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveeiel 75 
                                       G+v++ +   + + g+v+++++ D+tg++++ +++e a++  e+l+eG+v+rv+Gr+k+   g +e++v+e+e+
  gi|336253183|ref|YP_004596290.1|  81 GEVRTFErdgEDEDGRVVNVEVADETGSVRAAFWDEHAEAAIEELEEGQVLRVKGRPKEGFSG-VEVSVDEVEP 153
                                       55555558888889*************************************************.*******996 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 1.2e-16
                                       EEEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelel 68 
                                       V+++G v ++         d+s+gkv+++ + D+tgr++v+l++ e+ +la +l++G+ v+v  G+vk+r+g+ lel
  gi|336253183|ref|YP_004596290.1| 179 VNLVGVVLDTDsvrtfdrdDGSEGKVSNLAVGDETGRVRVTLWD-EQADLATELEPGTTVEVVdGYVKERDGN-LEL 253
                                       6788888888888899999*************************.****************************.*** PP

                                       EE CS
                   tRNA_anti-codon  69 kv 70 
                                       +v
  gi|336253183|ref|YP_004596290.1| 254 HV 255
                                       98 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 3.7e-05
                                       EEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHH CS
                   tRNA_anti-codon   2 tvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatkl 42 
                                        +aG v+s          d+s+g v +i ++D t+ i+v l+ e+    
  gi|336253183|ref|YP_004596290.1| 287 DLAGVVRSADpkrtfdrdDGSEGQVRNIRVQDATDDIRVALWGEK---A 332
                                       578999999999999999************************933...3 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00011      0.21      37      89 ..      95     148 ..      72     151 .. 0.76
   2 !   15.0   0.1   8.7e-06     0.017      11      63 ..     177     227 ..     168     250 .. 0.86
   3 !   26.2   0.1   2.7e-09   5.4e-06       4      73 ..     277     343 ..     275     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                         REPA_OB_2  37 lkkreltlvDesgasvevtlWgkeaekfe..sseepvvalkgvkvsdFggrslsl 89 
                                        +  ++++ De+g sv+ ++W+++ae      +e +v+ +kg   + F+g ++s+
  gi|336253183|ref|YP_004596290.1|  95 GRVVNVEVADETG-SVRAAFWDEHAEAAIeeLEEGQVLRVKGRPKEGFSGVEVSV 148
                                       4456889999998.7********99884434699****************99986 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 8.7e-06
                         REPA_OB_2  11 sivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaek 63 
                                       s v ++gvv +++ v+++ + +++ e k  +l + De+g+ v+vtlW+++a+ 
  gi|336253183|ref|YP_004596290.1| 177 SNVNLVGVVLDTDSVRTFDRDDGS-EGKVSNLAVGDETGR-VRVTLWDEQADL 227
                                       56899**********999998888.9************96.9*******9875 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 2.7e-09
                         REPA_OB_2   4 lenvekdsivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepvva 73 
                                       +e+ve +++vD+ gvv+s+++ +++ + +++ e + r++ + D +   ++v+lWg++a+  + +  + va
  gi|336253183|ref|YP_004596290.1| 277 IEEVEIGQTVDLAGVVRSADPKRTFDRDDGS-EGQVRNIRVQDATD-DIRVALWGEKADI-DIGPGDEVA 343
                                       8999*****************9999988888.***********986.7********8863.555555555 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 !   13.3   0.0   2.5e-05     0.049       1      65 [.      63     131 ..      63     135 .. 0.79
   2 !   21.2   0.0   9.7e-08   0.00019       1      65 [.     171     237 ..     171     254 .. 0.83
   3 ?    3.8   0.0      0.02        40      13      67 ..     290     344 ..     280     363 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
                         CDC24_OB3   1 DLrekmlnvtLlGrvvai.....freknsekkkmdryslrieDttGaidatlweeagklhfkrlrvGhlv 65 
                                       D+++ m +   +++v  i     f e+++e++  ++ +++++D+tG+++a+ w+e ++ +  +l+ G+++
  gi|336253183|ref|YP_004596290.1|  63 DIEPGMEEAKFVAKVLSIgevrtF-ERDGEDEDGRVVNVEVADETGSVRAAFWDEHAEAAIEELEEGQVL 131
                                       677777777888888888887543.5666556666679*****************999988899999986 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 9.7e-08
                         CDC24_OB3   1 DLrekmlnvtLlGrvvai.....freknsekkkmdryslrieDttGaidatlweeagklhfkrlrvGhlv 65 
                                       DL    +nv L+G+v +      f ++++++ + ++++l + D+tG +++tlw+e + l+   l++G +v
  gi|336253183|ref|YP_004596290.1| 171 DLSLGLSNVNLVGVVLDTdsvrtF-DRDDGS-EGKVSNLAVGDETGRVRVTLWDEQADLATE-LEPGTTV 237
                                       5666778*********99997655.444444.45556******************9999999.****998 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.02
                         CDC24_OB3  13 Grvvai.....freknsek.kkmdryslrieDttGaidatlweeagklhfkrlrvGhlvll 67 
                                       G+v        f+ +++++  +++  ++r++D t +i+++lw e   +++ ++++G+ v l
  gi|336253183|ref|YP_004596290.1| 290 GVVRSAdpkrtFD-RDDGSeGQVR--NIRVQDATDDIRVALWGE---KADIDIGPGDEVAL 344
                                       5555555554343.3333424555..9***************88...33444667766666 PP

>> SSB  Single-strand binding protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0017       3.4      44      77 ..     103     136 ..      91     142 .. 0.90
   2 !    8.0   0.0    0.0014       2.9      45      76 ..     211     242 ..     190     267 .. 0.82
   3 ?    1.7   0.0      0.14   2.7e+02      41      61 ..     314     334 ..     302     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0017
                                       EEEEEEEEEEEEHHHHHHHHHH--TT-EEEEEEE CS
                               SSB  44 deetewhrvvvfgklaevvaeylkkGslvyveGr 77 
                                        +et  +r +++++ ae + e l+ G+ + v+Gr
  gi|336253183|ref|YP_004596290.1| 103 ADETGSVRAAFWDEHAEAAIEELEEGQVLRVKGR 136
                                       678888999************************9 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0014
                                       EEEEEEEEEEEHHHHHHHHHH--TT-EE.EEEE CS
                               SSB  45 eetewhrvvvfgklaevvaeylkkGslv.yveG 76 
                                       +et  +rv++++++a++++e l++G+ v +v+G
  gi|336253183|ref|YP_004596290.1| 211 DETGRVRVTLWDEQADLATE-LEPGTTVeVVDG 242
                                       678889***********999.*****9934555 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.14
                                       CCEEEEEEEEEEEEEHHHHHH CS
                               SSB  41 gekdeetewhrvvvfgklaev 61 
                                        + +++t+ +rv+++g+ a++
  gi|336253183|ref|YP_004596290.1| 314 IRVQDATDDIRVALWGEKADI 334
                                       567899***********9875 PP

>> POT1PC  ssDNA-binding domain of telomere protection protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.012        23      82     103 ..     112     133 ..      90     135 .. 0.89
   2 !    9.5   0.0   0.00043      0.85      79     121 ..     216     255 ..     148     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.012
                                       EE-HHHHHHHTTT--TT-EEEE CS
                            POT1PC  82 tlydehaefarenlkpgdfvrL 103
                                         +dehae a e+l++g+++r 
  gi|336253183|ref|YP_004596290.1| 112 AFWDEHAEAAIEELEEGQVLRV 133
                                       57********999******997 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00043
                                       EEEEE-HHHHHHHTTT--TT-EEEEEEEEEEE-TTS.-EEEEE CS
                            POT1PC  79 lqitlydehaefarenlkpgdfvrLrNvhiklgrkgsklegfl 121
                                       + +tl+de+a++a e l+pg+ v      +  +r+g +le+++
  gi|336253183|ref|YP_004596290.1| 216 VRVTLWDEQADLATE-LEPGTTVEVVDGYV-KERDG-NLELHV 255
                                       78*************.******98766555.23333.566655 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 !   10.8   0.0   0.00021      0.43      17      78 ..      72     137 ..      61     151 .. 0.82
   2 ?    3.1   0.0     0.053   1.1e+02      44      74 ..     210     239 ..     198     257 .. 0.70
   3 ?   -3.8   0.0       7.6   1.5e+04      44      72 ..     317     342 ..     314     344 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                       tRNA_anti_2  17 elkkavwvrGeisnlk...rkasg.hvYftLkDekakisavifrsraaklkftledGmkVlvkgrl 78 
                                       ++  +v   Ge+  ++   + + g  v ++  De+ +++a+++ ++a++   +le+G+ + vkgr+
  gi|336253183|ref|YP_004596290.1|  72 KFVAKVLSIGEVRTFErdgEDEDGrVVNVEVADETGSVRAAFWDEHAEAAIEELEEGQVLRVKGRP 137
                                       56666777899999986543334448999***************999887789***********97 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.053
                       tRNA_anti_2  44 kDekakisavifrsraaklkftledGmkVlv 74 
                                        De+ +++++++ ++a  l ++le G++V v
  gi|336253183|ref|YP_004596290.1| 210 GDETGRVRVTLWDEQA-DLATELEPGTTVEV 239
                                       4788899999998766.67788999998865 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 7.6
                       tRNA_anti_2  44 kDekakisavifrsraaklkftledGmkV 72 
                                       +D++  i+++++ ++a   ++++  G++V
  gi|336253183|ref|YP_004596290.1| 317 QDATDDIRVALWGEKA---DIDIGPGDEV 342
                                       5766678899998655...4455556655 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.024        47     102     133 ..     103     138 ..      63     139 .. 0.76
   2 !    6.2   0.1    0.0036       7.1      59     128 ..     172     239 ..     161     246 .. 0.69
   3 ?    3.0   0.1     0.035        70      56     128 ..     274     344 ..     268     345 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.024
                           DUF4131 102 kpvsgrvlvtvpkspae....glrpGdrlrltgrlk 133
                                       ++ +g+v+    +++ae    +l+ G++lr++gr+k
  gi|336253183|ref|YP_004596290.1| 103 ADETGSVRAAFWDEHAEaaieELEEGQVLRVKGRPK 138
                                       556677777666666667999*************97 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0036
                           DUF4131  59 lsqllesgqeviveGvv..aslpeltgsgtrfvlevervlsagktkpvsgrvlvtvpkspae...glrpGdrlrl 128
                                       ls  l+    v ++Gvv  ++ +++ ++ +  + +    +s+ +  + +grv+vt+ +++a    +l+pG ++ +
  gi|336253183|ref|YP_004596290.1| 172 LSLGLS---NVNLVGVVldTDSVRTFDRDDGSEGK----VSNLAVGDETGRVRVTLWDEQADlatELEPGTTVEV 239
                                       454444...35566666333334444444466666....456678889**********************99976 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.035
                           DUF4131  56 andlsqllesgqeviveGvv..aslpeltgsgt.rfvlevervlsagktkpvsgrvlvtvpkspae.glrpGdrlrl 128
                                       +++++ +   gq+v + Gvv  a  p++t +++   + +    +++ + ++++  ++v + +++a  ++ pGd+++l
  gi|336253183|ref|YP_004596290.1| 274 STPIEEVEI-GQTVDLAGVVrsA-DPKRTFDRDdGSEGQ----VRNIRVQDATDDIRVALWGEKADiDIGPGDEVAL 344
                                       455555555.9999999999644.455555555488888....568899999999****999999999****99986 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 !    5.6   0.0    0.0061        12      55      80 ..      97     122 ..      93     144 .. 0.83
   2 ?    4.5   0.0     0.014        27      57      77 ..     206     226 ..     203     238 .. 0.90
   3 ?    1.4   0.0      0.12   2.3e+02      57      77 ..     313     333 ..     310     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0061
                                       EEEEEEE-SS-EEEEEEEHHHHHHHH CS
                       Rep_fac-A_C  55 ilsikvsDstgqlwvtlFneaaekll 80 
                                       +++++v+D+tg++++  ++e+ae  +
  gi|336253183|ref|YP_004596290.1|  97 VVNVEVADETGSVRAAFWDEHAEAAI 122
                                       689*******************9866 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.014
                                       EEEEE-SS-EEEEEEEHHHHH CS
                       Rep_fac-A_C  57 sikvsDstgqlwvtlFneaae 77 
                                       ++ v D+tg+++vtl++e+a 
  gi|336253183|ref|YP_004596290.1| 206 NLAVGDETGRVRVTLWDEQAD 226
                                       6789***************96 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.12
                                       EEEEE-SS-EEEEEEEHHHHH CS
                       Rep_fac-A_C  57 sikvsDstgqlwvtlFneaae 77 
                                       +i+v+D+t++++v l+ e+a 
  gi|336253183|ref|YP_004596290.1| 313 NIRVQDATDDIRVALWGEKAD 333
                                       689***************997 PP

>> DUF4539  Domain of unknown function (DUF4539)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.27      10      59 ..      80     160 ..      72     188 .. 0.74
   2 ?   -0.4   0.0      0.62   1.2e+03      22      41 ..     205     224 ..     179     239 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                           DUF4539  10 iksintlnslgd......alvtlkDptGeidgtihrkvleeygkdlsvGavllLk...................... 58 
                                       i +++t +++g+      + v ++D+tG++++++  +  e   ++l+ G vl  k                      
  gi|336253183|ref|YP_004596290.1|  80 IGEVRTFERDGEdedgrvVNVEVADETGSVRAAFWDEHAEAAIEELEEGQVLRVKgrpkegfsgvevsvdevepdpd 156
                                       55555555555556677899*******************************98887777777777555555555555 PP

                           DUF4539  59 ...q 59 
                                          +
  gi|336253183|ref|YP_004596290.1| 157 tevD 160
                                       5444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.62
                           DUF4539  22 alvtlkDptGeidgtihrkv 41 
                                         + + D+tG ++ t+  + 
  gi|336253183|ref|YP_004596290.1| 205 SNLAVGDETGRVRVTLWDEQ 224
                                       56778999**9999986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3529.64
//
Query:       gi|336253184|ref|YP_004596291.1|  [L=143]
Description: transcription factor CBF/NF-Y/histone domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-27   93.1   0.3      4e-13   49.4   0.1    2.0  2  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    4.7e-16   59.3   0.7    2.3e-11   44.2   0.1    2.0  2  Histone        Core histone H2A/H2B/H3/H4
    5.1e-07   29.8   1.1    7.4e-05   22.8   0.1    2.1  2  CENP-T_C       Centromere kinetochore component CENP-T histon
    0.00026   21.3   0.9    0.00057   20.2   0.3    1.8  2  CENP-S         CENP-S protein
  ------ inclusion threshold ------
      0.016   15.3   2.1       0.28   11.4   0.3    2.3  2  TAF            TATA box binding protein associated factor (TA
      0.028   14.5   0.9      0.066   13.3   0.3    1.7  2  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
      0.039   14.0   0.3        4.5    7.4   0.0    2.1  2  TFIID-18kDa    Transcription initiation factor IID, 18kD subu
      0.068   13.3   2.0       0.22   11.6   0.1    2.0  2  DUF1931        Domain of unknown function (DUF1931)


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 !   42.0   0.0   3.7e-14   8.3e-11       2      60 ..       4      62 ..       3      64 .. 0.98
   2 !   49.4   0.1   1.8e-16     4e-13       2      62 ..      75     136 ..      74     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 3.7e-14
                                      XXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHH CS
                     CBFD_NFYB_HMF  2 eLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaeh 60
                                      eLP a+v++I++   ++ +++ dA + +a  ++e  +ela  Aae++++++rKt++ae+
  gi|336253184|ref|YP_004596291.1|  4 ELPFAPVDTIIRRNAGDLRVSADASKELATRIQEHGSELAIDAAERATEDGRKTLMAED 62
                                      8*********************************************************9 PP

  == domain 2  score: 49.4 bits;  conditional E-value: 1.8e-16
                                       XXXHHHHHHHHHCC.TTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHH CS
                     CBFD_NFYB_HMF   2 eLPiarvkkImksd.pdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehik 62 
                                       eLP+a+v++I +   +d  +++ dA++ +a+++e ++  +a+ Aa ++++++r+ti++++i+
  gi|336253184|ref|YP_004596291.1|  75 ELPVAPVDRIARLEiDDRYRVSMDARVALADILEAYADNVAESAAILAHHADRRTITEDDIE 136
                                       8*************999999****************************************97 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.1e-05     0.047      65     123 ..       5      62 ..       2      65 .. 0.88
   2 !   44.2   0.1     1e-14   2.3e-11      56     127 ..      70     138 ..      64     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHH CS
                           Histone  65 lpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkD 123
                                       lpfa v + i+ ++  dlr+sa+a+  l++ +  +  el+ +A+  a +  R+T++++D
  gi|336253184|ref|YP_004596291.1|   5 LPFAPVDTIIR-RNAGDLRVSADASKELATRIQEHGSELAIDAAERATEDGRKTLMAED 62 
                                       66666444455.5999*****************************************99 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 1e-14
                                       HXXSXXSXHHHHHHHHH.HHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHH CS
                           Histone  56 kstdlliqklpfaRvvr.eivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlA 127
                                       ++ dl+ + +p++R+ r ei       +r+s +a +al+ +lEa+   ++e A++la ha R+Tit  Di+++
  gi|336253184|ref|YP_004596291.1|  70 DKDDLELPVAPVDRIARlEIDD----RYRVSMDARVALADILEAYADNVAESAAILAHHADRRTITEDDIETY 138
                                       568999999*****99988888....********************************************987 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0052        12      20      70 ..      13      63 ..       7      71 .. 0.91
   2 !   22.8   0.1   3.3e-08   7.4e-05       7      72 ..      75     137 ..      69     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0052
                          CENP-T_C 20 fakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDv 70
                                      + ++++   +++++a k l +  +++ + ++ D +  a   gRKt+ ++D 
  gi|336253184|ref|YP_004596291.1| 13 IIRRNAGDLRVSADASKELATRIQEHGSELAIDAAERATEDGRKTLMAEDF 63
                                      5677789999************************************99995 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 3.3e-08
                          CENP-T_C   7 slPaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvil 72 
                                        lP+a v ++a+        + +++ +a  al  +++ + + v+e  +  a+Ha R+ti e+D+++
  gi|336253184|ref|YP_004596291.1|  75 ELPVAPVDRIARLEID---DRYRVSMDARVALADILEAYADNVAESAAILAHHADRRTITEDDIET 137
                                       4899999999987644...589*****************************************986 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.4   3.1e+03      43      65 ..      40      62 ..      12      65 .. 0.61
   2 !   20.2   0.3   2.5e-07   0.00057      20      66 ..      89     135 ..      78     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.4
                            CENP-S 43 enlakDLeaFakHAkRstittdD 65
                                      ++la D    a   +R+t  ++D
  gi|336253184|ref|YP_004596291.1| 40 SELAIDAAERATEDGRKTLMAED 62
                                      44455555555556666666666 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 2.5e-07
                            CENP-S  20 aekeveatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDv 66 
                                        + + +++ ++  al+++  + ++n+a+   + a+HA R tit dD+
  gi|336253184|ref|YP_004596291.1|  89 IDDRYRVSMDARVALADILEAYADNVAESAAILAHHADRRTITEDDI 135
                                       4566788999999*********************************7 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 ?    3.6   0.1     0.033        73      21      61 ..      23      63 ..      12      66 .. 0.90
   2 ?   11.4   0.3   0.00013      0.28      23      62 ..      97     136 ..      86     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.033
                                      B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHH CS
                               TAF 21 LsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDv 61
                                      +s++a+++La  +++   e + +aa       R++L ++D+
  gi|336253184|ref|YP_004596291.1| 23 VSADASKELATRIQEHGSELAIDAAERATEDGRKTLMAEDF 63
                                      6899***********99999999999999999999999997 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHH CS
                               TAF  23 deaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvd 62 
                                        +a  +La+ +e    ++++ aa   +h+ R+++t +D++
  gi|336253184|ref|YP_004596291.1|  97 MDARVALADILEAYADNVAESAAILAHHADRRTITEDDIE 136
                                       5677788888888889999********************8 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.81   1.8e+03      40      65 ..      40      76 ..      24      81 .. 0.59
   2 ?   13.3   0.3   2.9e-05     0.066      30      64 ..     102     136 ..      93     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.81
                       TFIID-31kDa 40 ssvLedAkvlaehakkke...........vslddvrl 65
                                      s++  dA   a++ ++k+           v+ dd++l
  gi|336253184|ref|YP_004596291.1| 40 SELAIDAAERATEDGRKTlmaedfgvetvVDKDDLEL 76
                                      4444555555555555555555555555566666665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.9e-05
                       TFIID-31kDa  30 qLldfayrytssvLedAkvlaehakkkevslddvr 64 
                                        L d+   y  +v e A +la+ha++++++ dd++
  gi|336253184|ref|YP_004596291.1| 102 ALADILEAYADNVAESAAILAHHADRRTITEDDIE 136
                                       689******************************97 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.011        26      33      61 ..      36      64 ..      18      76 .. 0.82
   2 ?    7.4   0.0     0.002       4.5      26      60 ..     101     135 ..      89     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.011
                                      HHHHHHHHHHHHC-XXXX...XXXXXXXX CS
                       TFIID-18kDa 33 rgyliellqqaakvaklrgsrkitlEDll 61
                                      +++  el + aa+ a ++g++ +  ED+ 
  gi|336253184|ref|YP_004596291.1| 36 QEHGSELAIDAAERATEDGRKTLMAEDFG 64
                                      56667999*******************85 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXX CS
                       TFIID-18kDa  26 qlledlvrgyliellqqaakvaklrgsrkitlEDl 60 
                                         l d+++ y  ++ + aa +a++ ++r it +D+
  gi|336253184|ref|YP_004596291.1| 101 VALADILEAYADNVAESAAILAHHADRRTITEDDI 135
                                       56899**************************9998 PP

>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   9.8e-05      0.22       6      53 ..      16      63 ..      11      72 .. 0.92
   2 ?    1.0   0.2      0.18   4.1e+02      21      53 ..     103     135 ..      81     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.8e-05
                                      HHHHS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS CS
                           DUF1931  6 reaagLdvdkedlkrisdfVekklydLllvaeenAkangrdviepaDL 53
                                      r+a +L v  +  k++   ++++  +L++ a e+A+++gr++ + +D 
  gi|336253184|ref|YP_004596291.1| 16 RNAGDLRVSADASKELATRIQEHGSELAIDAAERATEDGRKTLMAEDF 63
                                      77889*************************************999997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS CS
                           DUF1931  21 isdfVekklydLllvaeenAkangrdviepaDL 53 
                                       + d++e+  +++++ a   A+   r +i + D+
  gi|336253184|ref|YP_004596291.1| 103 LADILEAYADNVAESAAILAHHADRRTITEDDI 135
                                       567888888888888888888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1076.98
//
Query:       gi|336253185|ref|YP_004596292.1|  [L=342]
Description: histone deacetylase superfamily [Halopiger xanaduensis SH-6]
Scores for 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-80  269.3   0.2    7.2e-80  268.7   0.2    1.2  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.7   0.2     4e-84   7.2e-80       1     305 [.      18     305 ..      18     307 .. 0.94

  Alignments for each domain:
  == domain 1  score: 268.7 bits;  conditional E-value: 4e-84
                                       SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiaskll 77 
                                       hpe+p+Rl+ai e+l+++ g+       +++ +++ + +++vH++eY+e++e+ + + + +               +
  gi|336253185|ref|YP_004596292.1|  18 HPETPDRLRAIRERLKKKHGVE-----YVDADPVDIDTIAAVHDREYVESVEQFCADGGGD---------------W 74 
                                       8****************96742.....5899*********************999775443...............7 PP

                                       SSSTHCTTTCCHHHHHHHHHHHHHHHHHHTTSS..SEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHH..CC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                     Hist_deacetyl  78 dddtpvspktlkaallavgavleavdavlsgsv..kaafvlvrPpgHHakaseasGFClvNnvaiaikylqa..khe 150
                                       d dt +  +t++a++++ g ++ av+a l+g    k+ f + rPpgHHa  ++a+GFC+vNn+a+a++++ +  ++ 
  gi|336253185|ref|YP_004596292.1|  75 DPDTSAVAETWDAIRHSSGLACWAVEAALEGATgrKTPFSIGRPPGHHAVVDDAMGFCFVNNAAVAAQHALDhdEYD 151
                                       899**************************9988767779999****************************6644788 PP

                                       SS-EEEEE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 151 lkrvailDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfe 227
                                       ++rva++D+DvHhGnGt+++fy+++dv+++SiH+  +++yPgtga++++geg+g+g+++n+p+++gtgde yl++ e
  gi|336253185|ref|YP_004596292.1| 152 IDRVAVVDWDVHHGNGTQDIFYEREDVFFVSIHE--KGLYPGTGAIDEIGEGDGHGTTMNIPMPAGTGDEAYLAAAE 226
                                       99********************************..788************************************** PP

                                       HCHHHHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G..EEEEE-S---HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 228 eilrpvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkvk.kvvllleGGYnlealaravtav 303
                                         +  +le+++ dl+lvsaGfDa+++dp+++++ls+e y+ lt++l+++ad+++  + ++leGGY l+ la +v++v
  gi|336253185|ref|YP_004596292.1| 227 GPIATALEAHDIDLLLVSAGFDAHRHDPISRIRLSTEAYALLTDRLRTIADNCDaALAFVLEGGYGLDVLADSVAMV 303
                                       ***************************************************9955******************9998 PP

                                       HH CS
                                       xx RF
                     Hist_deacetyl 304 ls 305
                                        +
  gi|336253185|ref|YP_004596292.1| 304 HE 305
                                       66 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2683.74
//
Query:       gi|336253186|ref|YP_004596293.1|  [L=463]
Description: CCA-adding protein [Halopiger xanaduensis SH-6]
Scores for 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-45  152.4   0.0    7.6e-45  151.8   0.0    1.3  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    5.2e-13   49.1   0.0    9.7e-13   48.2   0.0    1.5  1  NTP_transf_2     Nucleotidyltransferase domain
     0.0019   18.4   0.0      0.011   15.9   0.0    2.0  1  SMODS            Second Messenger Oligonucleotide or Dinucleo


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 !  151.8   0.0   1.3e-48   7.6e-45       2     112 ..     168     276 ..     167     277 .. 0.98

  Alignments for each domain:
  == domain 1  score: 151.8 bits;  conditional E-value: 1.3e-48
                                       HHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEETT CS
                   tRNA_NucTransf2   2 evrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDPv 78 
                                       +vrl K+flkgig+YGs+l+++GfsGYl+Ellv+eyg+f+++leaa +w+p+v++d+e + +  ++fd+plvviDP+
  gi|336253186|ref|YP_004596293.1| 168 DVRLAKQFLKGIGAYGSDLRTRGFSGYLTELLVCEYGGFRDLLEAAVDWHPQVELDPEVHGR--ETFDDPLVVIDPT 242
                                       8*******************************************************999999..9************ PP

                                       EEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGG CS
                   tRNA_NucTransf2  79 DpkRNvaaalsleklaefilaareflkkpseeff 112
                                       Dp+RNvaa++s +++a+f+++arefl++p  e+f
  gi|336253186|ref|YP_004596293.1| 243 DPERNVAAVCSPDNVARFQHYAREFLAEPAVEYF 276
                                       *********************************9 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.0   1.6e-16   9.7e-13      10      94 ..      55     152 ..      38     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.6e-16
                                       HHTTTSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH............HHHEHHHHHHHHCCCEEECTTEEEEE CS
                      NTP_transf_2  10 elepvakvvlfGSyarGtalkg.SDiDllvvlpeevsre............kkeegleklaeiikfleellglevdl 73 
                                       +l p+a+v  +GS+ar+t+ +g  DiD++v +p e +re            + +eg e++ae++++   + g  vd+
  gi|336253186|ref|YP_004596293.1|  55 DLCPDADVLQVGSTARNTWISGdRDIDIFVRFPPELDREtleqyglevghaTLPEGHEEYAEHPYVKGTVEGFDVDV 131
                                       34459**********************************************9999********************** PP

                                       ECEEECCCCTEEEEEECEEEH CS
                      NTP_transf_2  74 vtrekledpllvksileerpl 94 
                                       v++  le+   ++s+++++p+
  gi|336253186|ref|YP_004596293.1| 132 VPCFRLESATEIRSAVDRTPF 152
                                       *****************9987 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.9e-06     0.011      47     135 ..      60     139 ..      17     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-06
                             SMODS  47 aesllvGSyardTaikpvsdkdmlfeldvdllvvvnevegdepsdlleklkkalkktyksseirqdrqvvvvelnei 123
                                       a+ l+vGS ar+T i +  d d+ ++++ +l  ++ e      +  le  +++l +  +   +  +++ v  +++++
  gi|336253186|ref|YP_004596293.1|  60 ADVLQVGSTARNTWISGDRDIDIFVRFPPELDRETLE------QYGLEVGHATLPEGHE---EYAEHPYVKGTVEGF 127
                                       56799***********888888888888765444444......3335555555533332...357799999999*** PP

                             SMODS 124 kidvvPavenkd 135
                                       ++dvvP+++ ++
  gi|336253186|ref|YP_004596293.1| 128 DVDVVPCFRLES 139
                                       *******98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3303.33
//
Query:       gi|336253187|ref|YP_004596294.1|  [L=154]
Description: hypothetical protein Halxa_1787 [Halopiger xanaduensis SH-6]
Scores for 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-25   88.3   0.0    4.9e-25   88.1   0.0    1.0  1  PDDEXK_5  PD-(D/E)XK endonuclease


Domain annotation for each model (and alignments):
>> PDDEXK_5  PD-(D/E)XK endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.0   2.7e-29   4.9e-25       4     137 ..      15     144 ..      12     145 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 2.7e-29
                                       HHHHHHHHHHHHHHHHHTT-EEEEESSTTSS-SEEEEETTEEEEEEEEE-EEETTTSCEEEE-CEEEESSSSEEEEE CS
                          PDDEXK_5   4 kdkGDiaeakaiadllkkgysVltPvgdhlpyDLvadkdgklyriQvKyawleeksgqlrvknrstktdkngvhrkk 80 
                                       +++G ++ea   ++ + ++  +l+P+ d++pyDLv++ +g+++riQ+K+a +++++g++++++ st+ +  g+ r++
  gi|336253187|ref|YP_004596294.1|  15 QKRGQATEAILRSAFVVRDIPILVPAYDNEPYDLVVEVGGRFHRIQCKTA-YRKSEGTVAFETVSTRKRGDGYDRED 90 
                                       789***********************************************.88888********************* PP

                                       --CCS-SEEEEEETTTTEEEEEEHHHHHTSSSEEEE--STS-SS--GGGGGBT-THH CS
                          PDDEXK_5  81 YkkedfDflavyleeidkvyyvpletrknydseihlrevekkskeepsaqiakdfev 137
                                       Y+ +  +++avy + +d++y++ ++++   + ++++r  e+k+++   +++a+d+++
  gi|336253187|ref|YP_004596294.1|  91 YD-GRAEYFAVYDPVNDSCYLISVSDAA--TGKMEIRFREPKNGQRVGINWAEDYRL 144
                                       **.9***********************9..999999*******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1222.60
//
Query:       gi|336253188|ref|YP_004596295.1|  [L=196]
Description: molybdenum cofactor synthesis domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-33  113.3   0.0      9e-33  113.0   0.0    1.1  1  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.0     5e-37     9e-33       1     144 []      25     173 ..      25     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 5e-37
                                       EEEEE-HHHH...TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHH..HHHHHTS.SEEEEESS-SSSTT CS
                     MoCF_biosynth   1 avitvGdell...sgkieDtngpllaellkelgvevskytvvpDdeeeikeal..laaleea.dviittGGtGptpd 71 
                                       +++tv+++++   + + +D  g+++ e +++ g+ev+++ +v+Dd+++i+ a+  l a ++  dv++ttGGtG+t+d
  gi|336253188|ref|YP_004596295.1|  25 GIVTVSSSRAqadEADPDDPGGDTIRECFEDEGHEVQERVLVRDDYSAIRTAVrgLVA-RRDiDVVLTTGGTGVTAD 100
                                       689999999966555558999********************************76555.3336************** PP

                                       --HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE.....TTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  72 Dvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsrav.....gktiigLPGspkavkealeeillpale 143
                                       Dv pea++ lfe+el+gf+e+fr +s ++     v++ a+ sra+     ++++++LPGs++a+++a ee+++p+ +
  gi|336253188|ref|YP_004596295.1| 101 DVSPEATSSLFERELPGFGELFRSLSWEE-----VGTRAMASRATagiavDTPVFCLPGSKSACRTACEELIVPEAP 172
                                       ****************************9.....999999********97777*******************99987 PP

                                       H CS
                     MoCF_biosynth 144 h 144
                                       h
  gi|336253188|ref|YP_004596295.1| 173 H 173
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1405.73
//
Query:       gi|336253189|ref|YP_004596296.1|  [L=309]
Description: OB-fold tRNA/helicase-type nucleic acid binding protein [Halopiger xanaduensis SH-6]
Scores for 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   13.9   0.1       0.18   11.8   0.0    2.1  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.053   13.4   0.0       0.13   12.1   0.0    1.6  1  RMI1_C           Recq-mediated genome instability protein 1, 
       0.15   12.5   0.6       0.24   11.9   0.6    1.3  1  Notch            LNR 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 ?   11.8   0.0   3.1e-05      0.18      22      75 ..     105     155 ..      85     156 .. 0.85
   2 ?   -3.1   0.0       1.4   8.2e+03      22      45 ..     220     242 ..     216     247 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.1e-05
                                       EEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEE CS
                   tRNA_anti-codon  22 dlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveeiel 75 
                                        l D tg+i+ + +    ++ + +l+eG v++ +  v+  ++g +++k ++ ++
  gi|336253189|ref|YP_004596296.1| 105 LLGDPTGTIKFTKWA---KSDLPTLEEGGVYELRNVVTDEYQGRYSVKLNSTTV 155
                                       589************...****************9999998888****998765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                                       EEEETTEEEEEEEETHHHHHHHTT CS
                   tRNA_anti-codon  22 dlrDgtgriqvvlfreeatklaen 45 
                                       +++Dg +  +v++++ +at+ +  
  gi|336253189|ref|YP_004596296.1| 220 VVDDGIDAHEVIFDK-DATEELTG 242
                                       567777777777777.77666655 PP

>> RMI1_C  Recq-mediated genome instability protein 1, C-terminal OB-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.2e-05      0.13      46      82 ..     216     252 ..     200     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
                            RMI1_C  46 qlkakisDGsaildvdlssevlteligfspaelkesl 82 
                                       ++ka+++DG ++ +v ++++  +el g+s +e k ++
  gi|336253189|ref|YP_004596296.1| 216 RIKAVVDDGIDAHEVIFDKDATEELTGLSLEEAKDMA 252
                                       6899***************************976654 PP

>> Notch  LNR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6     4e-05      0.24       2      22 ..     187     206 ..     186     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4e-05
                             Notch   2 eqCsaeeyCaekfgdgvCDee 22 
                                       ++C++e +C +  ++g+C+e+
  gi|336253189|ref|YP_004596296.1| 187 KRCPKE-DCTRVLQNGRCNEH 206
                                       69**98.************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2252.19
//
Query:       gi|336253190|ref|YP_004596297.1|  [L=211]
Description: hypothetical protein Halxa_1790 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.46   10.6   2.7       0.49   10.5   0.5    2.0  2  Fn3-like  Fibronectin type III-like domain


Domain annotation for each model (and alignments):
>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.12   2.1e+03      56      69 ..      72      85 ..      59      87 .. 0.62
   2 ?   10.5   0.5   2.7e-05      0.49      33      64 ..     115     147 ..     113     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.12
                                      EE--SCEEEEEEES CS
                          Fn3-like 56 wvvepGeytvlvgt 69
                                       v ++G++ v+ g+
  gi|336253190|ref|YP_004596297.1| 72 VVDPTGTFFVYAGQ 85
                                      23345666666664 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 2.7e-05
                                       -EEEEEEEEECGGG-EEETT.TTEEE--SCEEE CS
                          Fn3-like  33 esktvtftldrkdlsvwdee.kqkwvvepGeyt 64 
                                       e  tv++++ +++ +v+d++ +++wvve+ e t
  gi|336253190|ref|YP_004596297.1| 115 EDGTVNVSVRPENIAVVDDDtRDRWVVETAERT 147
                                       5669**************972578****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1630.10
//
Query:       gi|336253191|ref|YP_004596298.1|  [L=235]
Description: phospholipase/carboxylesterase [Halopiger xanaduensis SH-6]
Scores for 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-18   66.1   0.0    2.1e-17   63.7   0.0    1.9  1  Abhydrolase_2  Phospholipase/Carboxylesterase
    3.1e-07   29.9   0.1     0.0026   17.1   0.0    2.8  2  Hydrolase_4    Serine aminopeptidase, S33
    6.3e-07   29.1   0.0    0.00099   18.6   0.0    2.3  1  Peptidase_S9   Prolyl oligopeptidase family
    0.00013   21.7   0.0    0.00046   19.9   0.0    1.7  1  FSH1           Serine hydrolase (FSH1)
    0.00087   20.0   5.9      0.014   16.0   1.1    2.1  2  Abhydrolase_6  Alpha/beta hydrolase family
     0.0014   18.2   0.0     0.0031   17.1   0.0    1.5  1  DLH            Dienelactone hydrolase family
  ------ inclusion threshold ------
      0.017   15.0   0.1        2.3    8.0   0.0    2.2  2  Abhydrolase_3  alpha/beta hydrolase fold
      0.024   14.3   0.0        2.8    7.5   0.0    2.5  2  Abhydrolase_1  alpha/beta hydrolase fold
      0.048   13.3   0.0      0.063   12.9   0.0    1.3  1  Esterase       Putative esterase


Domain annotation for each model (and alignments):
>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0   1.1e-20   2.1e-17       9     213 ..      33     229 ..      29     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.1e-20
                                       -SS---EEEEEE--TT--SHHHHHHHH.TT--TTEEEEEE---EEE-GGGTT-EEE-SS-B--SSTTS-B-HHHHHH CS
                     Abhydrolase_2   9 pkdkaqavviflHGlGdsghawaeaakteaalpnikfifphgpelpvtlnggmrmpaWfdlvglspekkedeagikk 85 
                                       p+ +a+a++i++HG G++++++ + +           +  hg + +  +        W++  + +p +  +e     
  gi|336253191|ref|YP_004596298.1|  33 PALAAEAALILCHGRGATAQGVVNLFD---------PVYRHGVAVLAPQAERS---RWYPKPASAPRA-DNEPWLTS 96 
                                       677899******************999.........46677777555555555...5**********9.788899** PP

                                       HHHHHHHHHHHHHHTT--GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGG..GTT..TTS-GGG.... CS
                     Abhydrolase_2  86 saekleelidaelkkgipssriiigGFSqGaalalylaltlpkklggivafsgalplsq..kle..ssatavt.... 154
                                       s+e + + ++a  +  ip +r++igGFSqGa +a + +   p ++gg   +sg+lp +    +   +     +    
  gi|336253191|ref|YP_004596298.1|  97 SVECVAAALEAAREIDIPPERTVIGGFSQGACVAAEFVRRNPRRYGGLCCLSGVLPGAVddDWTigEGS---Gddpl 170
                                       *******************************************************97641134311222...12346 PP

                                       GG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS--HHHHHHHHHHH CS
                     Abhydrolase_2 155 kklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHsideeemqdikefl 213
                                         +p+l ++ge+Dp ++    +++   l+++   v+ ++y + +H+   +e+ +i+  l
  gi|336253191|ref|YP_004596298.1| 171 ERTPVLFGYGEDDPHLDPERVARTVRTLENAGATVDERVYSDTGHEVTDDEFDAIAALL 229
                                       79**************************************************9998766 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.3e-06    0.0026       3     110 ..      37     150 ..      36     156 .. 0.83
   2 !    8.8   0.0   0.00044      0.89     191     237 ..     172     220 ..     165     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
                       Hydrolase_4   3 pkavvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse........gkrghvpsfddyvdDlaafvekvke 71 
                                       ++a+++l+HG++ +++ + +l++   ++G+av+a  +    rs         ++    p +++ v+ +aa++e+++e
  gi|336253191|ref|YP_004596298.1|  37 AEAALILCHGRGATAQGVVNLFDPVYRHGVAVLAPQAE---RSRwypkpasaPRADNEPWLTSSVECVAAALEAARE 110
                                       5799*******************************987...666777888844444556668889999999999996 PP

                       Hydrolase_4  72 eh.pelplfllGhSmGGliallyllrypdkvaglilsaPa 110
                                          p ++ ++ G S G+ +a++++ r+p+++ gl + + +
  gi|336253191|ref|YP_004596298.1| 111 IDiPPERTVIGGFSQGACVAAEFVRRNPRRYGGLCCLSGV 150
                                       551555888999*****************99999988765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00044
                       Hydrolase_4 191 tlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyHellnE 237
                                       ++P+l+ +Ge+D+  dpe  ++++++l  +   +  ++y    He+  +
  gi|336253191|ref|YP_004596298.1| 172 RTPVLFGYGEDDPHLDPERVARTVRTLENAgaTVDERVYSDTGHEVTDD 220
                                       69******************88888888874455568999999998755 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     5e-07   0.00099     142     194 ..     171     223 ..      95     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5e-07
                                       ---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHH CS
                      Peptidase_S9 142 aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprak 194
                                       + +p+L+  G+ D    p+  ++ v++L+++g +v+ +++ d gH v +++  
  gi|336253191|ref|YP_004596298.1| 171 ERTPVLFGYGEDDPHLDPERVARTVRTLENAGATVDERVYSDTGHEVTDDEFD 223
                                       359******************************************99887765 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.3e-07   0.00046      73     202 ..      78     217 ..      67     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.3e-07
                              FSH1  73 Wfrkkde...kneyegleesldavkdyikengp......fdGiiGFSqGaalaallaslleellkeashpslkfail 140
                                       W+ k++     ++   l  s+++v+ ++++  +       + i GFSqGa++aa  +    +        ++  + +
  gi|336253191|ref|YP_004596298.1|  78 WYPKPASaprADNEPWLTSSVECVAAALEAAREidippeRTVIGGFSQGACVAAEFVRRNPR--------RYGGLCC 146
                                       666655555555555677888888888888555222233457889********988765443........3557899 PP

                              FSH1 141 vsGfkleepkyeeyy....eedki.qtptLhvlGelDtvvdeerseaLaeafkns....skvlkHpggHfv 202
                                       +sG  +   + +++      +d++ +tp+L+ +Ge+D   d+er  + +++ +n      + ++ + gH v
  gi|336253191|ref|YP_004596298.1| 147 LSGVLPGAVDDDWTIgegsGDDPLeRTPVLFGYGEDDPHLDPERVARTVRTLENAgatvDERVYSDTGHEV 217
                                       9***9988886666665556677789*********************999999987666556666667765 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.1   7.1e-06     0.014       1      95 [.      41     149 ..      41     163 .. 0.57
   2 !    6.4   0.6    0.0061        12     163     219 ..     167     227 ..     152     228 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.1e-06
                                       EEEE--GC.....GCHHHHHHHHCCTCEEEEE--...TTST.S-GGCS--HHH.....CHHH.HHHHCCTT.....T CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDl...pGhG.rsdpppldled.....ladl.aalldelaa...gg 64 
                                       ++l+HG g++a +  v  + + +++gv+vlap++   + +  +++ p  d e+     + ++ aa+l++ ++    +
  gi|336253191|ref|YP_004596298.1|  41 LILCHGRGATAQGV-VNLFDPVYRHGVAVLAPQAersRWYPkPASAPRADNEPwltssV-ECvAAALEAAREidiPP 115
                                       69****99865555.34558888999********5333331211222222222322321.22244444444444366 PP

                                       TSEEEEEETCHHHHHHHHHHCC....EE..EEES- CS
                     Abhydrolase_6  65 gpvvlvGHSlGGalalaaapla..lvvg..vlldp 95 
                                        + v+ G S+G+ +a+++++    +  g  + l++
  gi|336253191|ref|YP_004596298.1| 116 ERTVIGGFSQGACVAAEFVRRNprR-YGglCCLSG 149
                                       666**************76666542.223444444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0061
                                       CCHHTT-TTGCEEECTT-CHHHHCHHCCCH......STTEEET.CE...SSS-HHHHSHHHHHH CS
                     Abhydrolase_6 163 aaawadlpvpllvlggeDplvprllerlla......qagarlp.vvlpgaGHlphleepdevae 219
                                        ++++++pv++   g++Dp++ +   r ++       aga+++  v+ ++GH + ++e d++a+
  gi|336253191|ref|YP_004596298.1| 167 DDPLERTPVLFGY-GEDDPHLDPE--RVARtvrtleNAGATVDeRVYSDTGHEVTDDEFDAIAA 227
                                       5677777777766.7888866622..3333111333355555479999****999966699987 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.6e-06    0.0031     141     189 ..     169     217 ..      93     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.6e-06
                               DLH 141 akikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaF 189
                                       +   +p+l+ +ge D++ + + v ++  +l++a+++++  vY++ gH  
  gi|336253191|ref|YP_004596298.1| 169 PLERTPVLFGYGEDDPHLDPERVARTVRTLENAGATVDERVYSDTGHEV 217
                                       55679******************************************65 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0011       2.3      53      94 ..      98     139 ..      83     157 .. 0.77
   2 ?    5.1   0.0    0.0088        18     166     209 ..     172     217 ..     146     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHH CS
                     Abhydrolase_3  53 laalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrard 94 
                                       ++ +  ++e a e+ + p+r v++G S G+  aa  ++r  +
  gi|336253191|ref|YP_004596298.1|  98 VECVAAALEAAREIDIPPERTVIGGFSQGACVAAEFVRRNPR 139
                                       444445555555799*******************99887655 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0088
                                       ---EEEEEETT-TTHH..HHHHHHHHHHHTT--EEEEEETTEETTG CS
                     Abhydrolase_3 166 lpptlvvvaefDplrd..egeayaerlraagvevelieyegmvHgf 209
                                         p+l   +e Dp  d  + +++ + l+ ag  v+ ++y+++ H++
  gi|336253191|ref|YP_004596298.1| 172 RTPVLFGYGEDDPHLDpeRVARTVRTLENAGATVDERVYSDTGHEV 217
                                       56899999999999983345688999******************86 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0014       2.8       3     106 ..      41     149 ..      39     163 .. 0.61
   2 ?    4.2   0.0     0.014        29     212     256 ..     173     221 ..     160     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0014
                                       EEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.........CHHSHHHHHHHHHHHHHHCT CS
                     Abhydrolase_1   3 lvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacin........ddygtasvaddldrildalg 71 
                                       l+++hG ++++    +  l++   ++g  v+++    + + +++ + +         +  +   va+ l+++++   
  gi|336253191|ref|YP_004596298.1|  41 LILCHGRGATAQGVVN--LFDPVYRHGVAVLAPQAERSRWYPKPASAPRadnepwltS--SVECVAAALEAAREIDI 113
                                       6666666666666555..5555555555555543332222222222222333344322..33338899999988766 PP

                                       TSSEE.EEEETHHHHHHHHHHHHHGGGEEEEEEESE CS
                     Abhydrolase_1  72 ddklt.lvGhSmGGmialayaaeyperVkalvllga 106
                                         + t + G+S+G  +a+++  ++p r  +l +l++
  gi|336253191|ref|YP_004596298.1| 114 PPERTvIGGFSQGACVAAEFVRRNPRRYGGLCCLSG 149
                                       666665999****************99888877777 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.014
                                       SEEEEEEETTCSSSCH.HHHHHHHHCHTS....EEEEEEETCSSSHHHHS CS
                     Abhydrolase_1 212 aptlvisgtsDplvpp.kaledlaqllpk....krlvvisdagHlafleg 256
                                        p+l+ +g++Dp  +p ++ +  + l  +    + ++v+sd+gH +  ++
  gi|336253191|ref|YP_004596298.1| 173 TPVLFGYGEDDPHLDPeRVARTVRTL-ENagatVDERVYSDTGHEVTDDE 221
                                       399999******99996777777766.444789***********997766 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.2e-05     0.063      90     152 ..      89     153 ..      50     228 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                                       CCCCHCHHHHTHHHHHHHHHCSEECCC..EEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-C CS
                          Esterase  90 gaeayetfltqeLlplldanfrtapdg..ravaGqSmGGlgALilalkhpdrFgsvssfSpivnp 152
                                        +e + t   + ++  l+a ++++     +++ G+S+G+ +A     ++p r+g   ++S+++  
  gi|336253191|ref|YP_004596298.1|  89 DNEPWLTSSVECVAAALEAAREIDIPPerTVIGGFSQGACVAAEFVRRNPRRYGGLCCLSGVLPG 153
                                       445566666666777777777666555559999***************************88533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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 0.30s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1639.24
//
Query:       gi|336253192|ref|YP_004596299.1|  [L=324]
Description: Glyoxalase/bleomycin resistance protein/dioxygenase [Halopiger xanaduensis SH-6]
Scores for 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   91.8   3.2    2.1e-12   47.4   0.2    2.2  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
     0.0006   20.1   1.3       0.29   11.4   0.1    2.9  2  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
  ------ inclusion threshold ------
        4.8    7.3   5.9         39    4.3   0.8    3.3  3  Glyoxalase_3  Glyoxalase-like domain


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 !   47.4   0.2   3.5e-16   2.1e-12       1     128 []       7     135 ..       7     135 .. 0.80
   2 !   45.2   0.3   1.6e-15   9.6e-12      22     128 .]     184     277 ..     182     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 3.5e-16
                                       EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEE.ETTTSEEEEEEEECCTTSCTHHCCBSCTSEE CS
                        Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdnteeteglriaff.haggghielvlneapsgaakhvkkieetvhh 76 
                                       gi+hv+ +vgd+++++dFY + LG+ l  +t+n e     + +f+  ag+    ++ +  p+g++ +v+k+  +v+ 
  gi|336253192|ref|YP_004596299.1|   7 GIHHVTGIVGDAQQAVDFYVGTLGLALDTQTVNFEDILQHHLYFGdAAGTPGTVFTVFADPHGDPGRVGKP--QVER 81 
                                       79******************************733333334444414455555556666666666666333..699* PP

                                       EEEEEEEHCHHHHHHHHHHHTT....GEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  77 vafialdvedvgkaldrlkeag....vkvvaepgrhyfgalysfyfrDpdGillei 128
                                       v f++ d    + + drl+e++    ++  ++++r+ f+ ++ + f+Dp G +le+
  gi|336253192|ref|YP_004596299.1|  82 VSFLVPDGSL-EYWRDRLREHDialeGEDGEPLERERFDERVLR-FEDPVGTRLEL 135
                                       ******9765.***********888889999***********99.*******9996 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 1.6e-15
                                       HHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHCHHHHHHHHHHHTT CS
                        Glyoxalase  22 vLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdvedvgkaldrlkeag 98 
                                        LGf+   +td     e +r+++  +  +++ ++++ea  g++        t+hhva+++ +++d++++ + ++e+g
  gi|336253192|ref|YP_004596299.1| 184 TLGFEYEAETD-----ERVRYRAPCDRATVVDVLDREASFGREGIG-----THHHVAVRVEEEDDLYEWRKLFDERG 250
                                       68888888888.....899998888888899999999888888887.....79************************ PP

                                       GEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  99 vkvvaepgrhyfgalysfyfrDpdGillei 128
                                       + v+++ +rh+f++ly   +r+p+G+l+e+
  gi|336253192|ref|YP_004596299.1| 251 YDVSRVKDRHFFHSLY---VREPGGVLFEL 277
                                       ****************...*********96 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   4.9e-05      0.29       1      96 [.       9     108 ..       9     201 .. 0.87
   2 !    6.1   0.2    0.0021        13      60      96 ..     217     256 ..     201     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.9e-05
                                       EEEEEE-S-HHHHHHHHHH.TT-E.ESS--E.EET.TTTEEEEEEEETTEEEEEEEESSTT-THHHTS-EEEEEEEE CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvg.pwqryrdepq.evdlafallgsgsvqieLieplegpeflaehgeglhhlayw 75 
                                       +++  +V D ++av+++ ++lG+   +q++++e+  +++l+f ++ +++  +  + +++  ++ + +++++  + + 
  gi|336253192|ref|YP_004596299.1|   9 HHVTGIVGDAQQAVDFYVGTLGLAlDTQTVNFEDIlQHHLYFGDAAGTPGTVFTVFADPHGDPGRVGKPQVERVSFL 85 
                                       79999*****************9855677888876578899999999886666666666667778899999999999 PP

                                       ES-..HHHHHHHHCTTTEEEEEE CS
                      Glyoxalase_4  76 vdd..ldaavarleeqGfevvqk 96 
                                       v d  l+   +rl+e+++++  +
  gi|336253192|ref|YP_004596299.1|  86 VPDgsLEYWRDRLREHDIALEGE 108
                                       97655888888888888886554 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0021
                                       -THHHTS-EEEEEEEEE...S-HHHHHHHHCTTTEEEEEE CS
                      Glyoxalase_4  60 eflaehgeglhhlaywv...ddldaavarleeqGfevvqk 96 
                                       +f +e+ +  hh+a++v   ddl +  + ++e+G+ v   
  gi|336253192|ref|YP_004596299.1| 217 SFGREGIGTHHHVAVRVeeeDDLYEWRKLFDERGYDVSRV 256
                                       566667777899****9544599999999******98754 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.8    0.0065        39       1      32 [.       8      39 ..       8      53 .. 0.79
   2 ?   -0.2   0.0      0.16   9.3e+02      89     116 ..      92     125 ..      76     127 .. 0.80
   3 ?    3.2   0.1     0.014        82      49     106 ..     133     196 ..     120     273 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0065
                      Glyoxalase_3  1 lDHvvlavpdleeaaarfarrlGftvtpggeh 32
                                      ++Hv+ +v+d ++a++ +  +lG+ ++   + 
  gi|336253192|ref|YP_004596299.1|  8 IHHVTGIVGDAQQAVDFYVGTLGLALDTQTVN 39
                                      69**********************99876655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.16
                      Glyoxalase_3  89 dataarlraaGvd......eagrrvrpdggdlrw 116
                                       + +++rlr++ ++      e+++r r d++ lr+
  gi|336253192|ref|YP_004596299.1|  92 EYWRDRLREHDIAlegedgEPLERERFDERVLRF 125
                                       6677888887777778778999999999999998 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.014
                      Glyoxalase_3  49 lEllavdpeapaperprlfgld...rlakgeglhtlalrtddidataarlraaGvd...eagrr 106
                                       lEl++  p++ ++ + +++ ++   + a+  glh++ + + +  ata +l+  G++   e+ +r
  gi|336253192|ref|YP_004596299.1| 133 LELVGGSPAEIEAAAVEPWTAGpipDDAAIRGLHGVSALSVNPYATASTLETLGFEyeaETDER 196
                                       6777777777766666666666666445678999999999999999999999998765433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 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:                        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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2384.14
//
Query:       gi|336253193|ref|YP_004596300.1|  [L=141]
Description: CopG-like DNA-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   20.4   0.1    0.00035   20.4   0.1    2.4  2  RHH_1           Ribbon-helix-helix protein, copG family
     0.0063   16.1   0.1      0.012   15.2   0.1    1.4  1  DUF3562         Protein of unknown function (DUF3562)
  ------ inclusion threshold ------
      0.013   16.1   0.0      0.028   14.9   0.0    1.6  1  CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin sys


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 !   20.4   0.1   5.8e-08   0.00035       2      38 ..       8      44 ..       7      45 .. 0.97
   2 ?   -1.9   1.5      0.61   3.6e+03      10      19 ..     124     133 ..     117     136 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.8e-08
                                      EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyle 38
                                      +s+r+ e+  e L+ +a++r+ S S+++R+++ +++e
  gi|336253193|ref|YP_004596300.1|  8 ISFRVNEDAFESLQDIAEERDISLSAVFRDYVDQLVE 44
                                      89*******************************9987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.61
                                       HHHHHHHHHH CS
                             RHH_1  10 llerLdelar 19 
                                       ++ +Ldel +
  gi|336253193|ref|YP_004596300.1| 124 EVLLLDELDE 133
                                       4445666655 PP

>> DUF3562  Protein of unknown function (DUF3562)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     2e-06     0.012       2      31 ..      14      43 ..      13      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-06
                           DUF3562  2 ddvdeiiqaiAeetdaPeelVsrlyedava 31
                                      +d +e++q iAee+d+   +V r y d++ 
  gi|336253193|ref|YP_004596300.1| 14 EDAFESLQDIAEERDISLSAVFRDYVDQLV 43
                                      6899**********************9875 PP

>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   4.8e-06     0.028      40      76 ..       3      39 ..       1      42 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.8e-06
                    CopG_antitoxin 40 kktksislrlpedlLealkekAnkrdvpyqslikell 76
                                       k+k+is+r++ed  e+l+  A++rd++ +   ++++
  gi|336253193|ref|YP_004596300.1|  3 NKNKTISFRVNEDAFESLQDIAEERDISLSAVFRDYV 39
                                      5899************************999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      766  (0.0427241); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1118.17
//
Query:       gi|336253194|ref|YP_004596301.1|  [L=151]
Description: superfamily II helicase-like protein [Halopiger xanaduensis SH-6]
Scores for 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:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1333.41
//
Query:       gi|336253195|ref|YP_004596302.1|  [L=431]
Description: hypothetical protein Halxa_1795 [Halopiger xanaduensis SH-6]
Scores for 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   11.4  18.3      0.041   13.7   3.8    4.0  2  DUF2238   Predicted membrane protein (DUF2238)


Domain annotation for each model (and alignments):
>> DUF2238  Predicted membrane protein (DUF2238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   6.6     0.067   1.2e+03      75     116 ..     107     150 ..      13     156 .. 0.84
   2 ?   13.7   3.8   2.3e-06     0.041      58     138 ..     311     397 ..     266     399 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.067
                           DUF2238  75 vrel..llrkkklrkwllllavlvvlaisalYEliEwlvalllg 116
                                       v+e+  ++  +  ++++++l+vl++la++ ++ + +w++ ++lg
  gi|336253195|ref|YP_004596302.1| 107 VVEIdrFTAVRMNHAFAIALVVLTTLAAAGAWNVAQWVADVTLG 150
                                       2232213333333568999999999************9988876 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.3e-06
                           DUF2238  58 kYDrlvHfaqGlllalvvrelllrkkkl.......rkwllllavlvvlaisalYEliEwlvalllggeaaeaflGtq 127
                                       ++D l H +   ++a + + +++ +  +        ++l+++++++vla++ ++El+E+ +   +    + + + +q
  gi|336253195|ref|YP_004596302.1| 311 QWDSLTHTMSASVVAAAGYAVVRAIDLYtdevhfpPAMLFTFILVFVLAFGVVWELFEFGIDWSAR-VLGIDAVVSQ 386
                                       57778887777776655444433333333333565569*********************9988877.5555555666 PP

                           DUF2238 128 GdiWDaqkDml 138
                                       + + D+  D++
  gi|336253195|ref|YP_004596302.1| 387 HGLSDTIVDLV 397
                                       66889988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.20s 00:00:00.70 Elapsed: 00:00:00.36
# Mc/sec: 3593.11
//
Query:       gi|336253196|ref|YP_004596303.1|  [L=286]
Description: aldo/keto reductase [Halopiger xanaduensis SH-6]
Scores for 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-61  207.3   0.0    3.8e-59  200.3   0.0    2.0  1  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
      0.037   14.1   0.0      0.084   13.0   0.0    1.5  1  DpaA_N        Dipicolinate synthase subunit A N-terminal doma


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 !  200.3   0.0   4.2e-63   3.8e-59       1     292 [.      22     284 ..      22     286 .] 0.97

  Alignments for each domain:
  == domain 1  score: 200.3 bits;  conditional E-value: 4.2e-63
                                       .EEEE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE... CS
                      Aldo_ket_red   1 elglGtwqlgsk....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv... 70 
                                       +lg+G+++l ++     + ++++a e++++a++ G+ ++DtA++Yg+g se+l+ +a+ +    r++v++atK    
  gi|336253196|ref|YP_004596303.1|  22 RLGFGAMRLCGEdiigAPDDEDTAREVVQHAVDLGVDLIDTADSYGPGVSERLIRQAIGD----RDDVLVATKAgll 94 
                                       59*******9999**99999999*************************************....************* PP

                                       --SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHH CS
                      Aldo_ket_red  71 dlrdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqle 147
                                       ++r +++ +++ ++ ir+++ +sl rLgtd++Dl+++Hrpd ++p +e+ +++++el++ G++ ++GvSn+sveqle
  gi|336253196|ref|YP_004596303.1|  95 RNREGDWLAHGDPDYIRNQVLTSLDRLGTDTIDLYQFHRPDEDVP-YEDSIQTFAELQDDGLVDQVGVSNVSVEQLE 170
                                       *********************************************.******************************* PP

                                       HHHHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HH CS
                      Aldo_ket_red 148 kakkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsk 224
                                        a   + v++++vq++ynl  ++ ++ +le+c+++++++i++ p+ g  l+g                         
  gi|336253196|ref|YP_004596303.1| 171 TA--REHVDVATVQNRYNLD-DRSSADVLEVCEDEDIGFIPWAPIDGDDLDGH------------------------ 220
                                       99..***************9.*************************9999944........................ PP

                                       HHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                      Aldo_ket_red 225 nldaaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                            + l+e+a +h+ +  q+al+++l ++ v+ +ipg+s +e+le n++a +l ls++ev++l  +
  gi|336253196|ref|YP_004596303.1| 221 ----GDVLDEIADDHDATRRQVALAWLLDHSDVVLPIPGTSDPEHLESNVAATQLSLSDDEVQRLTDV 284
                                       ....4589*******************************************************99865 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 ?   13.0   0.0   9.4e-06     0.084      55      86 ..     249     281 ..     227     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.4e-06
                                       EE--TT-BETTTEE-BSS-SS-EE-.HHHHHTS CS
                            DpaA_N  55 iilPvpgtkdggeintpfseeklsl.eellekl 86 
                                       ++lP+pgt+d +++++++++++lsl ++ ++ l
  gi|336253196|ref|YP_004596303.1| 249 VVLPIPGTSDPEHLESNVAATQLSLsDDEVQRL 281
                                       79***********************87766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2420.63
//
Query:       gi|336253197|ref|YP_004596304.1|  [L=660]
Description: xenobiotic-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-41  142.0   0.1    3.5e-41  141.7   0.1    1.1  1  ABC_membrane  ABC transporter transmembrane region
    1.5e-34  119.5   0.0    2.4e-34  118.8   0.0    1.3  1  ABC_tran      ABC transporter
    0.00099   18.4   0.0     0.0018   17.6   0.0    1.3  1  Zeta_toxin    Zeta toxin
     0.0033   17.7   0.2      0.016   15.5   0.2    2.1  1  AAA_22        AAA domain
     0.0048   17.3   0.9      0.013   15.9   0.9    1.7  1  AAA_16        AAA ATPase domain
     0.0068   16.3   0.0      0.014   15.2   0.0    1.5  1  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0095   15.7   0.1      0.022   14.5   0.1    1.6  1  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.015   14.8   0.3       0.37   10.2   0.1    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.023   14.6   0.0      0.043   13.7   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
       0.03   14.1   0.9      0.055   13.2   0.0    1.9  1  AAA_29        P-loop containing region of AAA domain
      0.068   13.4   0.1       0.14   12.4   0.1    1.5  1  HR_lesion     HR-like lesion-inducing
      0.068   13.3   0.0       0.15   12.2   0.0    1.5  1  AAA_33        AAA domain
      0.075   13.1   0.1       0.16   12.1   0.1    1.5  1  DUF87         Helicase HerA, central domain
      0.077   12.7   0.0       0.14   11.9   0.0    1.4  1  AAA_24        AAA domain
      0.082   13.5   0.0       0.24   12.0   0.0    1.8  1  AAA_18        AAA domain
        0.1   12.7   0.0       0.27   11.3   0.0    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
       0.16   10.7   0.1       0.29    9.9   0.1    1.3  1  ABC_ATPase    Predicted ATPase of the ABC class


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 !  141.7   0.1   3.3e-44   3.5e-41       3     268 ..      36     322 ..      34     328 .. 0.95

  Alignments for each domain:
  == domain 1  score: 141.7 bits;  conditional E-value: 3.3e-44
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHH...............HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   3 liillailagvlsplfplvlgrildtlldkgdpet...............ealnvysllllllglaqfilallqsyl 64 
                                       ++++l +++ ++s++ p++lg  +d ++ + ++ +                +l + + l+++ +l+ ++++l++  +
  gi|336253197|ref|YP_004596304.1|  36 VGLVLNLIQRGASLVPPFILGVAIDAVFNQTQA-YelpllpaawipgdraGQLWLSFGLIIGSYLLLAVSSLARGLC 111
                                       6899************************85444.359999999999999888888899999**************** PP

                                       HHHHHHHHHHHHHHHHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSH CS
                      ABC_membrane  65 lnvtgerlskrlrrklfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgw 141
                                       + + + r+++++r+ +++k+ r++m+ff++ ++Gel+s l+ndvs+++ ++ + ++  ++  ++++g+ ++++yl+w
  gi|336253197|ref|YP_004596304.1| 112 MDYFSHRVMHDVRTTTYRKLQRLDMGFFESEDTGELMSVLNNDVSNFERFFDDAFVRATRIAAVLLGVTAILVYLNW 188
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 142 kltlvllailpliilvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagi 218
                                       +l+lv+l+ lpl+++ + ++ ++++++ +   +av+ +++ +e  l g++ +k+ + eey++e+  + + ++ ++++
  gi|336253197|ref|YP_004596304.1| 189 QLALVTLSALPLLAVGTLLYHRLVEPAYDAIRSAVGSMNTRLENNLGGMQLIKSTATEEYENERVRDVSWDYFESNW 265
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.......SSTHHHHHHHHHHHH CS
                      ABC_membrane 219 kkaianglligitqllgllsyalalwfGttlvisg.......elsvgdlvvflslfa 268
                                       ++++++ +  + +++l+++++ +++++G+++  sg       elsvg+lv+fl ++ 
  gi|336253197|ref|YP_004596304.1| 266 WRIKLELFYHPGSRFLTNVAFGMTFLVGGVWLVSGppgpftgELSVGTLVTFLFMSQ 322
                                       ********************************9999999999******999987665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   0.0   2.3e-37   2.4e-34       1     137 []     419     568 ..     419     568 .. 0.93

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 2.3e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk+vs++ ++ge+va+vG +GaGKSt+lkll++l++ +eG i++dg dl++ +l slr++ig+++qe+ lf ++ +r
  gi|336253197|ref|YP_004596304.1| 419 LKDVSFEAEPGETVALVGATGAGKSTVLKLLLRLYDVDEGAIRIDGYDLRDVTLASLRESIGYVSQETYLFGGT-IR 494
                                       79***********************************************************************9.** PP

                                       HH................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       en                ++ +e+++++++l   +  dt v++++  +SgGq+qr+++ar+++ +p++l++DE+t+
  gi|336253197|ref|YP_004596304.1| 495 ENiaygrfdatdeeireaAKIAEAHEFIERLPEGY--DTQVGERGVRVSGGQRQRISIARTVVGDPDILIFDEATS 568
                                       ********988776655555555888888888777..99999********************************96 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.7e-06    0.0018      18      56 ..     431     469 ..     418     498 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.7e-06
                        Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56 
                                        + l+G++GAGKs++++ll +  + +++++r+d+ dlR 
  gi|336253197|ref|YP_004596304.1| 431 TVALVGATGAGKSTVLKLLLRLYDVDEGAIRIDGYDLRD 469
                                       57899*****************************99996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.5e-05     0.016       8      38 ..     432     468 ..     427     630 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee......e 38 
                                       ++++G +G+GK+t+l+ ll+ +d ++ a +      +
  gi|336253197|ref|YP_004596304.1| 432 VALVGATGAGKSTVLKLLLRLYDVDEGAIRidgydlR 468
                                       689*******************987766655444441 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.9   1.3e-05     0.013      23     127 ..     427     598 ..     416     627 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                            AAA_16  23 rp.elvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqllde......... 88 
                                       +p e v l+G+ G GKs++++ llr +  d+ +i + g   +         ++ a   +e +  + +e         
  gi|336253197|ref|YP_004596304.1| 427 EPgETVALVGATGAGKSTVLKLLLRLYDVDEgAIRIDGYDLRD--------VTLAS-LRESIGYVSQEtylfggtir 494
                                       44689*******************9888774133355555444........11111.22444444444444444444 PP

                            AAA_16  89 ...............aesaeleawrekleeala............................................ 106
                                                       e+a+ ++++e++e+  +                                            
  gi|336253197|ref|YP_004596304.1| 495 eniaygrfdatdeeiREAAKIAEAHEFIERLPEgydtqvgergvrvsggqrqrisiartvvgdpdilifdeatsavd 571
                                       44444444323333333333333333333333366666656555555555555555555555555555555444444 PP

                            AAA_16 107 ......avpelagaeasrllellkrll 127
                                             ++++l++ +a r    +++ l
  gi|336253197|ref|YP_004596304.1| 572 tetemlIQRSLDRLSADRTTFIIAHRL 598
                                       444444444444444455555555555 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   0.0   1.3e-05     0.014       3      26 ..     433     467 ..     432     521 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                            AAA_21   3 vliGpNgsGKSnLLdaldllarl...........d 26 
                                       +l+G+ g+GKS++L++l  l ++           +
  gi|336253197|ref|YP_004596304.1| 433 ALVGATGAGKSTVLKLLLRLYDVdegairidgydL 467
                                       79******************987655555443330 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   2.1e-05     0.022      19     108 ..     430     577 ..     423     588 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g.grviglAptgkaAkvLaeelgieastiakllkrlk............ 81 
                                        +++l+G+ G+GK+t+lk l ++++ + g  r+ g+       + L+e++g  ++ +  +  + +            
  gi|336253197|ref|YP_004596304.1| 430 ETVALVGATGAGKSTVLKLLLRLYDVDeGaIRIDGYDLRDVTLASLRESIGYVSQETYLFGGTIReniaygrfdatd 506
                                       57899***************999998855677778888888888888888887777766666666666666666666 PP

                            AAA_30  82 ............................................grarlepgtllivDEagmvdtkqlaal 108
                                                                                   +r+ + + ++li DEa  +  ++++ l
  gi|336253197|ref|YP_004596304.1| 507 eeireaakiaeahefierlpegydtqvgergvrvsggqrqrisiARTVVGDPDILIFDEATSAVDTETEML 577
                                       66666666666666777777777777777777777777777776555556667777777766655555555 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 ?    2.7   0.0     0.069        73      26      42 ..     431     447 ..     418     461 .. 0.82
   2 ?   10.2   0.1   0.00035      0.37     138     209 ..     541     608 ..     450     614 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.069
                                       EEEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlld 42 
                                         a+vG+ G+GKs +l 
  gi|336253197|ref|YP_004596304.1| 431 TVALVGATGAGKSTVLK 447
                                       5689*********9986 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00035
                                       -HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 138 SgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklv 209
                                       SgG+++ +++a       v    + ++De  +a D +    + + l++ s +   ++i++r  ++++adk++
  gi|336253197|ref|YP_004596304.1| 541 SGGQRQRISIAR----TVVGDPDILIFDEATSAVDTETEMLIQRSLDRLSADRTTFIIAHRLSTIRDADKIL 608
                                       666666555543....3445555889******************************************9986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.1e-05     0.043      91     130 ..     420     460 ..     409     468 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       ++++ + +  +t++lvG +G+GKSt+++ ll   ++  g++
  gi|336253197|ref|YP_004596304.1| 420 KDVSFEAEPgETVALVGATGAGKSTVLKLLLRLYDVDEGAI 460
                                       555555555599****************9987666666555 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 ?   13.2   0.0   5.2e-05     0.055      16      39 ..     423     446 ..     418     451 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-05
                            AAA_29  16 tieidlkgatlltGpsGsGKSTll 39 
                                       ++e ++ +++ l+G++G+GKST+l
  gi|336253197|ref|YP_004596304.1| 423 SFEAEPGETVALVGATGAGKSTVL 446
                                       5677777799************97 PP

>> HR_lesion  HR-like lesion-inducing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00013      0.14      61     113 ..      70     156 ..      55     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                         HR_lesion  61 dikhlvaaliilkglggLlfilgsslgaylLllyqaiatvvlydfynydldt......................... 112
                                       ++  l aa i     g L+  +g ++g+ylLl+   +a  +  d++ +++ +                         
  gi|336253197|ref|YP_004596304.1|  70 ELPLLPAAWIPGDRAGQLWLSFGLIIGSYLLLAVSSLARGLCMDYFSHRVMHdvrtttyrklqrldmgffesedtge 146
                                       55566667777777899*******************************98765565666555555555555555555 PP

                         HR_lesion 113 .........k 113
                                                +
  gi|336253197|ref|YP_004596304.1| 147 lmsvlnndvS 156
                                       5555544443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.15       2      47 ..     432     481 ..     432     524 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                            AAA_33   2 vllvGlpGsGKstlaerllkklg....avllssdtlrrrlfgtdqqsktd 47 
                                       v lvG+ G+GKst+++ ll+  +    a++++  +lr+   ++ ++s+ +
  gi|336253197|ref|YP_004596304.1| 432 VALVGATGAGKSTVLKLLLRLYDvdegAIRIDGYDLRDVTLASLRESIGY 481
                                       568***************97666778899999999998444455665554 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   0.00015      0.16      26      45 ..     432     451 ..     429     459 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                             DUF87  26 lAilgsTGsGKSntvavLle 45 
                                       +A +g TG+GKS+  ++Ll+
  gi|336253197|ref|YP_004596304.1| 432 VALVGATGAGKSTVLKLLLR 451
                                       799***************97 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.14       4      79 ..     431     571 ..     429     588 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                            AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie..swedfldevvel................... 59 
                                        ++++G  g+GK+t++k l     + d+++G+ ++d+ ++ d++  s+ + + +v +                    
  gi|336253197|ref|YP_004596304.1| 431 TVALVGATGAGKSTVLKLL---LRLYDVDEGAIRIDGYDLRDVTlaSLRESIGYVSQEtylfggtireniaygrfda 504
                                       589****************...8899*************99996664444333333335555555555555555555 PP

                            AAA_24  60 ...............................................aaeladyktlviDtidelee 79 
                                                                                      ++   d ++l++D ++ +++
  gi|336253197|ref|YP_004596304.1| 505 tdeeireaakiaeahefierlpegydtqvgergvrvsggqrqrisiaRTVVGDPDILIFDEATSAVD 571
                                       5555555555556566665555555555555555555555555555555555555555555555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00023      0.24       1      31 [.     432     470 ..     432     533 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf........gvnlrdv 31 
                                       ++l G+ G+GK+t+ k L ++  +        g+ lrdv
  gi|336253197|ref|YP_004596304.1| 432 VALVGATGAGKSTVLKLLLRLYDVdegairidGYDLRDV 470
                                       6899**************776344666667776666554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.27       2      21 ..     432     451 ..     431     472 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                       EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                       va+vG + +GKSt+++ l++
  gi|336253197|ref|YP_004596304.1| 432 VALVGATGAGKSTVLKLLLR 451
                                       9**************99986 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 ?    9.9   0.1   0.00028      0.29     300     353 ..     516     570 ..     503     601 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00028
                                       E--TTTB---CCC--ST.TEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-H CS
                        ABC_ATPase 300 vDispFinnLPegkdtt.kfstedASGStsqAanimealeagakllLiDEDtsAt 353
                                       ++   Fi++LPeg dt+        SG   q  +i++ +  + ++l++DE tsA+
  gi|336253197|ref|YP_004596304.1| 516 AEAHEFIERLPEGYDTQvGERGVRVSGGQRQRISIARTVVGDPDILIFDEATSAV 570
                                       56789************66667799*****************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.39
# Mc/sec: 5022.88
//
Query:       gi|336253198|ref|YP_004596305.1|  [L=148]
Description: hypothetical protein Halxa_1798 [Halopiger xanaduensis SH-6]
Scores for 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   13.3   0.1       0.18   11.9   0.1    1.8  1  HTH_20    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 ?   11.9   0.1     1e-05      0.18       1      55 [.      16      89 ..      16      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1e-05
                                      HHHHHHHS-HHHHHHHHHH.STCTTB-HHHHHHHH.....T.............S-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  1 dqiaeALahPvRrrilraL.araegltaselaerl.....d.............lskntlsyHLrvLeeagLve 55
                                      d+i+e+La++ Rr +l aL  r+++  +s lae++     d             +  +++  H+ +L++ag v+
  gi|336253198|ref|YP_004596305.1| 16 DTILELLANRRRRYLLYALrGREDPIELSTLAEQVagwehDvhpdevekneyksVYVSSVQCHVPKLADAGVVD 89
                                      689****************99*************9755442666677777777788888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1098.69
//
Query:       gi|336253199|ref|YP_004596306.1|  [L=163]
Description: hypothetical protein Halxa_1799 [Halopiger xanaduensis SH-6]
Scores for 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-28   96.8   0.0    7.9e-28   96.5   0.0    1.2  1  DUF192           Uncharacterized ACR, COG1430
  ------ inclusion threshold ------
      0.084   12.8   5.2       0.14   12.1   5.2    1.4  1  CDP-OH_P_tran_2  CDP-alcohol phosphatidyltransferase 2


Domain annotation for each model (and alignments):
>> DUF192  Uncharacterized ACR, COG1430
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   0.0   8.8e-32   7.9e-28       1      96 []      53     160 ..      53     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 8.8e-32
                                       EEEEEE-SHHHHHHTTTT-----TTEEEEEEECCEEEEEE--TT--S-EEEEEE-TTSBEEEEEEEE-TT...-... CS
                            DUF192   1 itvevAdteeerarGLmgreslpedegmlfvfdkerehsfwMkntripLdiifldadgriveieealkpq...s... 71 
                                       i+vevAdt +e+++GL+ ++sl+++ gmlfv+++e++++++M+++ +p+di+f+ ad++i+ ie+a +p    +   
  gi|336253199|ref|YP_004596306.1|  53 IDVEVADTRQEQYTGLSDHDSLEPGAGMLFVHSSEDDRTYVMREMDFPIDIVFIGADREITGIEHARAPEpseDges 129
                                       68****************************************************************99996651555 PP

                                       ......ECEEEEEETTHHHHHT--TT-EEE. CS
                            DUF192  72 ......vryvLElpaGaakklgikpGdrlei 96 
                                             +++vLE+p+G+a+++g+ +Gd++ei
  gi|336253199|ref|YP_004596306.1| 130 lqytgrAKWVLEVPRGYANETGMAVGDEVEI 160
                                       555555777*******************986 PP

>> CDP-OH_P_tran_2  CDP-alcohol phosphatidyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.2   1.6e-05      0.14       3      24 ..      14      35 ..       9      35 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                   CDP-OH_P_tran_2  3 vlPllllvglfaAlLityPWlt 24
                                      vl ll++v+l+ A  +++PW++
  gi|336253199|ref|YP_004596306.1| 14 VLVLLVGVVLVQAGYVSAPWHI 35
                                      99******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1330.54
//
Query:       gi|336253200|ref|YP_004596307.1|  [L=654]
Description: xenobiotic-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-46  157.0   1.2    9.3e-46  156.7   1.2    1.1  1  ABC_membrane   ABC transporter transmembrane region
    7.4e-38  130.2   0.0    1.5e-37  129.1   0.0    1.6  1  ABC_tran       ABC transporter
    8.3e-05   22.9   0.1    0.00038   20.7   0.1    2.0  1  AAA_22         AAA domain
    0.00048   20.1   0.0    0.00097   19.1   0.0    1.4  1  RsgA_GTPase    RsgA GTPase
    0.00059   19.7   0.0     0.0016   18.3   0.0    1.7  1  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
     0.0019   18.0   0.1     0.0034   17.1   0.1    1.4  1  AAA_24         AAA domain
     0.0019   18.8   0.0     0.0047   17.5   0.0    1.8  1  AAA_18         AAA domain
     0.0021   18.5   0.2      0.005   17.2   0.2    1.7  1  AAA_16         AAA ATPase domain
     0.0047   17.0   0.5      0.013   15.6   0.5    1.7  1  DUF2107        Predicted membrane protein (DUF2107)
     0.0052   16.3   1.1       0.14   11.5   0.2    2.1  2  SMC_N          RecF/RecN/SMC N terminal domain
     0.0064   15.8   0.0      0.014   14.7   0.0    1.4  1  Zeta_toxin     Zeta toxin
  ------ inclusion threshold ------
      0.012   15.3   0.1      0.036   13.8   0.1    1.7  1  AAA_29         P-loop containing region of AAA domain
      0.018   14.8   0.2      0.048   13.4   0.2    1.7  1  AAA_30         AAA domain
      0.035   14.3   0.2       0.09   12.9   0.0    1.8  1  AAA_33         AAA domain
      0.038   13.7   0.0       0.28   10.8   0.1    2.4  2  Guanylate_kin  Guanylate kinase
      0.063   13.8   0.0       0.13   12.7   0.0    1.5  1  AAA_23         AAA domain
      0.095   13.1   0.0       0.68   10.4   0.0    2.3  1  AAA            ATPase family associated with various cellular
       0.11   12.5   0.1       0.67   10.0   0.0    2.2  2  AAA_5          AAA domain (dynein-related subfamily)
       0.15   10.8   0.2       0.27   10.0   0.2    1.4  1  ABC_ATPase     Predicted ATPase of the ABC class
       0.16   11.2   0.3       0.29   10.4   0.3    1.3  1  DUF1385        Protein of unknown function (DUF1385)
       0.18   11.9   0.0       0.43   10.7   0.0    1.7  1  MMR_HSR1       50S ribosome-binding GTPase
       0.19   11.1   0.0       0.35   10.2   0.0    1.3  1  Mg_chelatase   Magnesium chelatase, subunit ChlI
       0.54   10.0   4.9       0.82    9.5   0.1    2.8  3  DUF2157        Predicted membrane protein (DUF2157)


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 !  156.7   1.2   1.2e-48   9.3e-46       2     274 .]      41     340 ..      40     340 .. 0.94

  Alignments for each domain:
  == domain 1  score: 156.7 bits;  conditional E-value: 1.2e-48
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHH..................HHHHHHHHHHHHHH...HHHHHH CS
                      ABC_membrane   2 iliillailagvlsplfplvlgrildtlldkgdpet..................ealnvysllllllg...laqfil 57 
                                       i++il++ +a +l++l p+ l+  ld ++ + + ++                  ++l +++l++ +++   ++ + +
  gi|336253200|ref|YP_004596307.1|  41 IVGILASTVARILDLLPPIMLAVALDAVFRN-EVDSyagalpfggglvepyipaTQLGQFYLTIGVIAgafFFGATF 116
                                       6899*************************95.55555999**************66666666665555111566667 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane  58 allqsyllnvtgerlskrlrrklfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvggli 134
                                        +l+++ +n  ++++ +++r+++++k+ r++m ff ++++Ge++s l+ndv++l+ +l++ +  +f+  +++vg+ +
  gi|336253200|ref|YP_004596307.1| 117 HWLRNWGFNAFAQNIQHDIRTDTYDKMQRLNMDFFADKQTGEMMSILSNDVNRLERFLNDGMNSLFRMAVMIVGIGV 193
                                       79*************************************************************************** PP

                                       HHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHH CS
                      ABC_membrane 135 vmfylgwkltlvllailpliilvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekale 211
                                       ++f ++w+l+lv l  +pli+ +++++ ki+++      ++v+k++s +e  l gi+++k+ + eey+ e+ e+ ++
  gi|336253200|ref|YP_004596307.1| 194 ILFAYNWQLALVALLPVPLIAGFTYLFVKIIQPKYAAVRSTVGKVNSRLENNLGGIQVIKSSTTEEYESERVEDVSQ 270
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.......SSTHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 212 eakkagikkaianglligitqllgllsyalalwfGttlvisg.......elsvgdlvvflslfailfgal 274
                                       ++  a++ ++ ++  +++ +++l+ + +++++++G+ +v +g       +ls g++vvf+++   +++++
  gi|336253200|ref|YP_004596307.1| 271 DYFDANWDAIETRIKFFPGLRVLAGIGFVVTFLVGGLWVFQGppgpftgTLSEGEFVVFILYTQRFIWPM 340
                                       ******************************************99999999************99999986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.1   0.0     2e-40   1.5e-37       2     137 .]     403     551 ..     402     551 .. 0.96

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 2e-40
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +++++++  ge++a+vG++GaGKSt+lkll+++++ +eG i++dg+d+++ +leslr +ig+++q+++lf+++ v+e
  gi|336253200|ref|YP_004596307.1| 403 DDIDFTVAGGETLALVGPTGAGKSTVLKLLLRMYDVDEGAITVDGQDIRDVTLESLRDSIGYVSQDTFLFYGT-VEE 478
                                       89***********************************************************************.*** PP

                                       H................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       n                ++ +e+++++++l + +  dt v++++ +LSgGq+qr+++ara+lk+p++l+lDE+t+
  gi|336253200|ref|YP_004596307.1| 479 NikygtfdadredvveaAKMAEAHDFIQNLPDGY--DTEVGERGVKLSGGQRQRISIARAILKDPDILVLDEATS 551
                                       ******9999888887777777999999999888..999**********************************96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   4.9e-07   0.00038       8     103 ..     415     553 ..     410     583 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.9e-07
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee........................................erpevv. 43 
                                       l+++G++G+GK+t+l+ ll+ +d ++ a +                                         +++   
  gi|336253200|ref|YP_004596307.1| 415 LALVGPTGAGKSTVLKLLLRMYDVDEGAITvdgqdirdvtleslrdsigyvsqdtflfygtveenikygtFDADREd 491
                                       799********************999998898888888888888888888876666666666655444442222224 PP

                            AAA_22  44 fvtlpsstsskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.l 103
                                        v++++  +  d+ ++l   ++ e  +   +   l   + ++ + ara    + +l++DEa   +
  gi|336253200|ref|YP_004596307.1| 492 VVEAAKMAEAHDFIQNLPDGYDTEVGE---RGVKLSgGQRQRISIARAIlkdPDILVLDEATSdV 553
                                       555555556666666666666666666...33334334444444444445567788888887744 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.2e-06   0.00097      68     130 ..     379     443 ..     361     456 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHTTSEEEE--TTTH.TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  68 lkeelealgyevllvsaktk.egleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       l+    +++y+ ++   +++ + ++++   +++ +t +lvG++G+GKSt+++ ll   ++  g++
  gi|336253200|ref|YP_004596307.1| 379 LEVSAGRVEYDRVTFGYDDEeTIVDDIDFTVAGgETLALVGPTGAGKSTVLKLLLRMYDVDEGAI 443
                                       55566667777666666655156789**999999*******************998877776666 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 !   18.3   0.0   2.1e-06    0.0016       3      76 ..     416     484 ..     415     504 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.1e-06
                            AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryrygl 76 
                                       +l+Gp g+GKS++L++l  + +      +++ +  +g++ir+++ ++ ++++ + ++ ++ + ++ + +++yg 
  gi|336253200|ref|YP_004596307.1| 416 ALVGPTGAGKSTVLKLLLRMYD-----VDEGAITVDGQDIRDVTLESLRDSIGYVSQDTFLFYGTVEENIKYGT 484
                                       79***************99987.....57777777778888888888888888888888887777777777764 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   4.4e-06    0.0034       5      87 ..     415     562 ..     412     575 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.4e-06
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie..swedfldevvel.................... 59 
                                       ++++Gp g+GK+t++k l     + d+++G+  +d+ ++ d++  s+ d + +v ++                    
  gi|336253200|ref|YP_004596307.1| 415 LALVGPTGAGKSTVLKLL---LRMYDVDEGAITVDGQDIRDVTleSLRDSIGYVSQDtflfygtveenikygtfdad 488
                                       789***************...99*****************9978855555555555566777766666666666666 PP

                            AAA_24  60 ..............................................aaeladyktlviDtideleelclaevir 87 
                                                                                     +a l+d ++lv+D ++  ++  ++++i+
  gi|336253200|ref|YP_004596307.1| 489 redvveaakmaeahdfiqnlpdgydtevgergvklsggqrqrisiaRAILKDPDILVLDEATSDVDTETEMLIQ 562
                                       66666668888888888888888888888888888888888888888888888888888887766666666655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.1e-06    0.0047       3      70 ..     417     515 ..     415     571 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.1e-06
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf........................gvnlrdvakenglllevdpe...aldeskrl 52 
                                       l G+ G+GK+t+ k L ++  +                        g++++d++   g+++e+ ++   + d+++++
  gi|336253200|ref|YP_004596307.1| 417 LVGPTGAGKSTVLKLLLRMYDVdegaitvdgqdirdvtleslrdsiGYVSQDTFLFYGTVEENIKYgtfDADREDVV 493
                                       89**************88744477778899888899999999999999999999999999999999999999***** PP

                            AAA_18  53 dedkldklldaleenss....a 70 
                                       +  k+++++d +++ ++     
  gi|336253200|ref|YP_004596307.1| 494 EAAKMAEAHDFIQNLPDgydtE 515
                                       ********99999987766551 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   6.4e-06     0.005      19     154 ..     408     560 ..     396     597 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.4e-06
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipy.....sa.laqalareellrqllde 88 
                                       + +g+ e + l+G+ G GKs++++ llr +  d+ +i++ g+  +    +++     s+ ++++ ++  ++  ++++
  gi|336253200|ref|YP_004596307.1| 408 TVAGG-ETLALVGPTGAGKSTVLKLLLRMYDVDEgAITVDGQDIRD---VTLeslrdSIgYVSQDTF-LFYGTVEEN 479
                                       55565.8999*****************9777774377777777666...222222222223333322.333333333 PP

                            AAA_16  89 aesaeleawrekleeala.....................avpelagaeasrllellkrllallsrderplvlvlDdl 144
                                        +   ++a+re   ea++                      + +l+g   +r +  ++r++  l   ++p +lvlD++
  gi|336253200|ref|YP_004596307.1| 480 IKYGTFDADREDVVEAAKmaeahdfiqnlpdgydtevgeRGVKLSGG--QRQRISIARAI--L---KDPDILVLDEA 549
                                       44444444444444444444445555555445555332322222222..44444444444..2...23446666655 PP

                            AAA_16 145 q.wadeaslql 154
                                         ++d+++ +l
  gi|336253200|ref|YP_004596307.1| 550 TsDVDTETEML 560
                                       54555555555 PP

>> DUF2107  Predicted membrane protein (DUF2107)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.5   1.6e-05     0.013      25      69 ..     178     224 ..     172     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                           DUF2107  25 lvrllnlEvpavGvllilLaynetlALlTfiavtaii..tlvlvrai 69 
                                       +  l+ + v  vG+ +il ayn  lAL+ ++ v  i+  t ++v++i
  gi|336253200|ref|YP_004596307.1| 178 MNSLFRMAVMIVGIGVILFAYNWQLALVALLPVPLIAgfTYLFVKII 224
                                       66678899999**********************99972244566655 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 ?    3.2   0.0     0.064        50      27      42 ..     415     430 ..     403     435 .. 0.86
   2 !   11.5   0.2   0.00019      0.14     135     209 ..     507     591 ..     431     598 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.064
                                       EEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlld 42 
                                        a+vGp G+GKs +l 
  gi|336253200|ref|YP_004596307.1| 415 LALVGPTGAGKSTVLK 430
                                       589*********9985 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00019
                                       T..............CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-S CS
                                       x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e..............lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivisl 197
                                       +               LSgG+++ +++a   Ai   k   + +lDe  +  D +    + + ++e  ++   + i++
  gi|336253200|ref|YP_004596307.1| 507 NlpdgydtevgergvKLSGGQRQRISIAR--AI--LKDPDILVLDEATSDVDTETEMLIQRSIDELAEDRTTFAIAH 579
                                       05555555555555589*****9887764..44..4566689*********************************** PP

                                       SHHHCCC-SCEE CS
                                       xxxxxxxxxxxx RF
                             SMC_N 198 reemlekadklv 209
                                       r  ++++ad+++
  gi|336253200|ref|YP_004596307.1| 580 RLSTIRDADQIL 591
                                       ********9986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.8e-05     0.014      21      56 ..     417     452 ..     413     463 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                        Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56 
                                       l+G +GAGKs++++ll +  + +++++++d+ d+R 
  gi|336253200|ref|YP_004596307.1| 417 LVGPTGAGKSTVLKLLLRMYDVDEGAITVDGQDIRD 452
                                       899*******************************97 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 ?   13.8   0.1   4.6e-05     0.036      17      39 ..     405     429 ..     399     433 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                            AAA_29  17 ieidlkg..atlltGpsGsGKSTll 39 
                                       i+++++g  +  l+Gp+G+GKST+l
  gi|336253200|ref|YP_004596307.1| 405 IDFTVAGgeTLALVGPTGAGKSTVL 429
                                       556666666889***********97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   6.1e-05     0.048      18      51 ..     412     447 ..     405     566 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.1e-05
                            AAA_30  18 drvavltGpAGtGKttalkalreaweaa.g.grvig 51 
                                         + +l+Gp G+GK+t+lk l ++++ + g  +v g
  gi|336253200|ref|YP_004596307.1| 412 GETLALVGPTGAGKSTVLKLLLRMYDVDeGaITVDG 447
                                       457899***************999987733344444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012      0.09       4      59 ..     417     476 ..     415     485 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            AAA_33   4 lvGlpGsGKstlaerllkklg....avllssdtlrrrlfgtdqqsktdytrvldrlyqil 59 
                                       lvG+ G+GKst+++ ll+  +    a++++  ++r+   ++ ++s+ + ++ ++ +y+++
  gi|336253200|ref|YP_004596307.1| 417 LVGPTGAGKSTVLKLLLRMYDvdegAITVDGQDIRDVTLESLRDSIGYVSQDTFLFYGTV 476
                                       89**************99888888899999999888555566777777766666666655 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.8   3.8e+03      61      87 ..      22      50 ..      14      67 .. 0.65
   2 ?   10.8   0.1   0.00036      0.28       4      94 ..     414     497 ..     411     501 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.8
                                      HHHHTTTEEEEEE..ETTEEEEEEHHHHH CS
                     Guanylate_kin 61 kdiskneflEaae..fsgnlygtsveaie 87
                                      +++ k+ flE+++      + g   +++ 
  gi|336253200|ref|YP_004596307.1| 22 ENPMKRLFLEYGRdyAFPAIVGILASTVA 50
                                      57888999999986223344455555555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00036
                                       EEEEESTTTSSHHHHHHHHHHHSTTTEEE--EEESS---TTS-TTTSEEE--HHHHHHHH...HTTTEEEEEEETTE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfgvsvshtTrdprkgevdGkdYyFvskeemekdi...skneflEaaefsgn 77 
                                       ++ lvgp+gaGks++ k Ll+ +    g  ++   +d+r           v+ e++   i   s++ fl ++++++n
  gi|336253200|ref|YP_004596307.1| 414 TLALVGPTGAGKSTVLKLLLRMYDVDEG-AITVDGQDIRD----------VTLESLRDSIgyvSQDTFLFYGTVEEN 479
                                       788*****************99987776.33444455555..........777777766544477888888886666 PP

                                       E.EEEEHHHHHHHHHTTS CS
                     Guanylate_kin  78 l.ygtsveaieevlekgk 94 
                                       + ygt  +  e v e +k
  gi|336253200|ref|YP_004596307.1| 480 IkYGTFDADREDVVEAAK 497
                                       447887777777777666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017      0.13      15      37 ..     405     430 ..     394     441 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                            AAA_23  15 idF...skgltlItGpNGaGKTTild 37 
                                       idF   +    +++Gp+GaGK+T+l 
  gi|336253200|ref|YP_004596307.1| 405 IDFtvaGGETLALVGPTGAGKSTVLK 430
                                       788887777789***********997 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   0.0   0.00088      0.68       2      38 ..     416     472 ..     415     590 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00088
                                       EEESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSS..................S CS
                               AAA   2 llyGppGtGKTllakavakelgve..fleisgsellsk..................y 38 
                                        l+Gp G GK+++ k + +  +v+   ++++g ++++                   +
  gi|336253200|ref|YP_004596307.1| 416 ALVGPTGAGKSTVLKLLLRMYDVDegAITVDGQDIRDVtleslrdsigyvsqdtflF 472
                                       599*****************8654347888888888444444444455555555551 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 ?   10.0   0.0   0.00086      0.67       3      23 ..     416     436 ..     414     481 .. 0.83
   2 ?   -0.9   0.1       1.9   1.5e+03      57      89 ..     532     561 ..     512     579 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00086
                                       EEE--SSSSHHHHHHHGGGGB CS
                             AAA_5   3 lLvGppGtgKselaerlaaal 23 
                                        LvGp+G gKs++ + l++++
  gi|336253200|ref|YP_004596307.1| 416 ALVGPTGAGKSTVLKLLLRMY 436
                                       69****************998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                                       --------G-SEEEEESGGG--HHHHHHHHHHH CS
                             AAA_5  57 splvraaregeilvlDEveraesevlnsLlsll 89 
                                       s++    + ++ilvlDE +   s+v  +  +l+
  gi|336253200|ref|YP_004596307.1| 532 SIARAILKDPDILVLDEAT---SDVDTETEMLI 561
                                       44444556999*****988...66655555555 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 ?   10.0   0.2   0.00034      0.27     300     352 ..     499     552 ..     484     592 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00034
                                       E--TTTB---CCC--ST.TEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS- CS
                        ABC_ATPase 300 vDispFinnLPegkdtt.kfstedASGStsqAanimealeagakllLiDEDtsA 352
                                       ++   Fi+nLP g dt+      + SG   q  +i++a+  + ++l++DE ts 
  gi|336253200|ref|YP_004596307.1| 499 AEAHDFIQNLPDGYDTEvGERGVKLSGGQRQRISIARAILKDPDILVLDEATSD 552
                                       56789***********966667789*************************9985 PP

>> DUF1385  Protein of unknown function (DUF1385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   0.00037      0.29     139     187 ..     182     227 ..     160     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00037
                           DUF1385 139 flllvlivsilvfslvgasslllrvllrllllpvvagisYelirlagks 187
                                       f + v+iv+i v+ +  +   +   l+ ll +p++ag +Y ++++++ +
  gi|336253200|ref|YP_004596307.1| 182 FRMAVMIVGIGVILF-AY--NWQLALVALLPVPLIAGFTYLFVKIIQPK 227
                                       668899999999666.23..36677788999*************98865 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00055      0.43       2      22 ..     415     435 ..     414     486 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00055
                                       EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                        a+vG + +GKSt+++ l++ 
  gi|336253200|ref|YP_004596307.1| 415 LALVGPTGAGKSTVLKLLLRM 435
                                       699**************9973 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00045      0.35      15      43 ..     405     433 ..     397     455 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00045
                      Mg_chelatase  15 leiaaaGgHnlllvGppGsGKtmlakrlp 43 
                                       ++ ++aGg  l lvGp G+GK+ + k l 
  gi|336253200|ref|YP_004596307.1| 405 IDFTVAGGETLALVGPTGAGKSTVLKLLL 433
                                       56789*****************9988765 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       1.4   1.1e+03      63      85 ..      95     118 ..      92     136 .. 0.65
   2 ?    9.5   0.1    0.0011      0.82      34      81 ..     173     219 ..     152     256 .. 0.74
   3 ?    0.9   0.2      0.44   3.5e+02      56      89 ..     275     316 ..     272     363 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                           DUF2157  63 rlvkfllllvllllslllg.avlw 85 
                                       +l +f l ++++++++++g  + w
  gi|336253200|ref|YP_004596307.1|  95 QLGQFYLTIGVIAGAFFFGaTFHW 118
                                       556666666666666666644444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                           DUF2157  34 f....leallvlGalllglGlilfvAanWqglsrlvkfllllvllllslllg 81 
                                       f    ++ l+ ++++++g+G+ilf A+nWq    l+ ++ll v+l++ +   
  gi|336253200|ref|YP_004596307.1| 173 FlndgMNSLFRMAVMIVGIGVILF-AYNWQ----LALVALLPVPLIAGFTYL 219
                                       34455889*************975.99**7....555666666666666555 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.44
                           DUF2157  56 anWqglsrlvkf.....llllvllllslllg.avlwrdr..r 89 
                                       anW+++   +kf     +l+ + +++++l+g +++ + +   
  gi|336253200|ref|YP_004596307.1| 275 ANWDAIETRIKFfpglrVLAGIGFVVTFLVGgLWVFQGPpgP 316
                                       789999888888444444555566666666656666655453 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); 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: 0.70u 0.26s 00:00:00.96 Elapsed: 00:00:00.41
# Mc/sec: 4838.64
//
Query:       gi|336253201|ref|YP_004596308.1|  [L=115]
Description: hypothetical protein Halxa_1801 [Halopiger xanaduensis SH-6]
Scores for 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:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); 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 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 962.29
//
Query:       gi|336253202|ref|YP_004596309.1|  [L=247]
Description: Creatininase [Halopiger xanaduensis SH-6]
Scores for 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  237.0   1.0    2.3e-70  236.8   1.0    1.0  1  Creatininase  Creatinine amidohydrolase
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.21   11.5   0.0    1.3  1  Alba          Alba


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.8   1.0   2.6e-74   2.3e-70       3     240 ..       6     232 ..       4     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 236.8 bits;  conditional E-value: 2.6e-74
                      Creatininase   3 ltwpeveealkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTisl 79 
                                        tw++v++   ++d+a++PvGstEqHGph+plgtD+l+aea+a++ +++++ +++ +P++p+G++eeh++fpGT+++
  gi|336253202|ref|YP_004596309.1|   6 ATWTDVRDC--DSDLAVVPVGSTEQHGPHAPLGTDVLTAEAIADAGCDRIDREVVRAPAVPVGIAEEHRQFPGTMWV 80 
                                       69******9..99*************************************999************************ PP

                      Creatininase  80 spetliavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaaeaaee 156
                                       s++t+++++r+ +esla+hGf+r+v+vngHggn++al+e+  ++++  d +a+         a+ +++ e      +
  gi|336253202|ref|YP_004596309.1|  81 SEDTFRNYVREAVESLAHHGFDRVVIVNGHGGNVDALREVGGTITRSADTDAY---------AVPFTWFE-----AV 143
                                       **********************************************9966653.........33333432.....34 PP

                      Creatininase 157 seeeegggHAgelEtSlmlalrpelVrmdraedpeeaklakeg.....vstaedaeelspsGvlGdpskataekGea 228
                                        e+ +++gH+g+lEt+l+ +l p+lVr+dr+e++++ +++++g     ++ a d  e++++Gv+Gdp + +a +Ge+
  gi|336253202|ref|YP_004596309.1| 144 GEHASDMGHGGPLETALLRHLEPDLVREDRIEEAQAGAADRWGewvsyANLAYDSAEFTENGVVGDPDDGDARRGEE 220
                                       4555599***********************************9********************************** PP

                      Creatininase 229 lleaaveelael 240
                                       lle a+++la+l
  gi|336253202|ref|YP_004596309.1| 221 LLELAADALARL 232
                                       **********97 PP

>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.3e-05      0.21       3      32 ..      78     106 ..      76     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.3e-05
                                       EEE-STS-HHHHHHHHHHHHTHTTESEEEE CS
                              Alba   3 iyVsskspimsyvkralklLsnkkeeeVvl 32 
                                       + Vs  + +++yv++a++ L +++++ Vv+
  gi|336253202|ref|YP_004596309.1|  78 MWVSE-DTFRNYVREAVESLAHHGFDRVVI 106
                                       66888.99************9999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2025.65
//
Query:       gi|336253203|ref|YP_004596310.1|  [L=156]
Description: hypothetical protein Halxa_1803 [Halopiger xanaduensis SH-6]
Scores for 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   12.5   0.1        0.6   10.1   0.0    2.2  2  Phe_tRNA-synt_N  Aminoacyl tRNA synthetase class II, N-termin


Domain annotation for each model (and alignments):
>> Phe_tRNA-synt_N  Aminoacyl tRNA synthetase class II, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   3.3e-05       0.6      38      60 ..      13      35 ..       8      40 .. 0.88
   2 ?   -1.0   0.0     0.094   1.7e+03      51      61 ..      93     103 ..      78     119 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.3e-05
                                      HHHCCHHHHCCCCCCCCCHHHCC CS
                   Phe_tRNA-synt_N 38 aGkliNelKqeieealeerkeel 60
                                      +G+++Ne ++++e++l+e+ ++l
  gi|336253203|ref|YP_004596310.1| 13 FGEAANEMREDVESSLAEAWAAL 35
                                      8*****************98887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.094
                                       CCCCCHHHCCH CS
                   Phe_tRNA-synt_N  51 ealeerkeele 61 
                                       + +++ +e++e
  gi|336253203|ref|YP_004596310.1|  93 AEIADLEEAIE 103
                                       44444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1109.11
//
Query:       gi|336253204|ref|YP_004596311.1|  [L=122]
Description: hypothetical protein Halxa_1804 [Halopiger xanaduensis SH-6]
Scores for 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  136.6   0.0    4.7e-40  136.5   0.0    1.0  1  DHNA      Dihydroneopterin aldolase


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 !  136.5   0.0   2.6e-44   4.7e-40       2     107 ..       8     113 ..       7     114 .. 0.96

  Alignments for each domain:
  == domain 1  score: 136.5 bits;  conditional E-value: 2.6e-44
                                       HHHHHHHHHHHHHHHHHHHHTT-EESTTTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-S..TS-EE--TTT CS
                              DHNA   2 drerAvFEagiklgalyHqfvGtPvseesaeslekaieesielQPfvedvkvkidrekleeklee..fgYteLtgem 76 
                                       + e A+FEagik+g+lyHqf+GtP+s++sa+s+e+a+ee+ie+QP+++dv+v+++r++le++l++   +YteLtg++
  gi|336253204|ref|YP_004596311.1|   8 TGEAACFEAGIKFGTLYHQFAGTPLSPHSAASIETAMEEAIENQPHCTDVTVEVQRDALEAELADsaADYTELTGRF 84 
                                       6799*********************************************************99886667******** PP

                                       EEEEEEEEETTEEEEEEEEEETTTTEEEEEE CS
                              DHNA  77 ldveitvkyeeaevkarleyieeldYplmkv 107
                                       l+vei+v+ye++ev++r+++  e++Yplm+v
  gi|336253204|ref|YP_004596311.1|  85 LEVEIVVDYEGCEVVTRMAM--EDGYPLMTV 113
                                       ********************..*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 911.38
//
Query:       gi|336253205|ref|YP_004596312.1|  [L=247]
Description: NAD-dependent epimerase/dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-26   91.4   0.0    7.5e-26   91.1   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.1e-13   49.9   0.0    2.9e-13   49.5   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.7e-13   49.7   0.0    8.3e-13   48.1   0.0    1.6  2  NAD_binding_4    Male sterility protein
    2.5e-12   47.1   0.0    4.4e-12   46.3   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    2.4e-11   43.3   0.2    1.8e-07   30.6   0.1    2.7  3  Polysacc_synt_2  Polysaccharide biosynthesis protein
    9.2e-11   41.7   0.0    2.8e-10   40.1   0.0    1.9  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.9e-05   22.1   0.0    0.00016   20.9   0.0    1.5  1  RmlD_sub_bind    RmlD substrate binding domain
    9.2e-05   22.1   0.0    0.00017   21.3   0.0    1.4  1  NmrA             NmrA-like family


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 !   91.1   0.0   3.3e-29   7.5e-26       1     172 [.       5     176 ..       5     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 3.3e-29
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       +l+tGa+G +G a++  l+++ ye+  ldr++      ++   e+v +d+td++a++++++  ++davihlA+   +
  gi|336253205|ref|YP_004596312.1|   5 VLLTGAAGRVGDAILGGLADE-YEWRLLDRDPP----TEDYPGEFVVADITDDEAVREAME--GIDAVIHLAGDPRP 74 
                                       699****************96.9********33....3333349*****************..********999999 PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSS...SS.....BSTCSTTS--..--SSHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdae...qp.....keettltgpl..kpnspYaa 144
                                       +a +++   ++ +n+ gt++++eaa +agv+++ f+sS +  G  ++   +p     +++++l+g    +p + Y++
  gi|336253205|ref|YP_004596312.1|  75 DAPWDS---VLTNNIDGTQTVFEAAVDAGVEKVAFASSNHAVGHYETeerTPemyraDDDYLLDGTElpRPGNLYGV 148
                                       998888...777*******************************76665544678888777777766569******** PP

                                       HHHHHHHHHHHHHHHHT-EEEEEEESEE CS
                         Epimerase 145 aKlageklveayaaqyglnaiilrlfnl 172
                                       +K+age+l ++y+++++l+++++r+ nl
  gi|336253205|ref|YP_004596312.1| 149 SKAAGESLGRYYHDEHDLSVVCVRIGNL 176
                                       *************************998 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 !   49.5   0.0   1.3e-16   2.9e-13       3     136 ..       8     132 ..       6     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 1.3e-16
                         3Beta_HSD   3 tGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdv 79 
                                       tG+aG +G a+   L ++    e r lD   +p++ +        +++ +D+td + ++ea+eg+d+vihl  + d 
  gi|336253205|ref|YP_004596312.1|   8 TGAAGRVGDAILGGLADEY---EWRLLDR--DPPTEDYPG-----EFVVADITDDEAVREAMEGIDAVIHL--AGDP 72 
                                       6666666666666665554...4555553..233322222.....26778*********************..5688 PP

                         3Beta_HSD  80 agkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslge...eilngdEel 136
                                       +     d++ + n+ GT++v ea+v+agv+++ + Ss  +vg   ++e   e+ ++d++ 
  gi|336253205|ref|YP_004596312.1|  73 RPDAPWDSVLTNNIDGTQTVFEAAVDAGVEKVAFASSNHAVGHYETEErtpEMYRADDDY 132
                                       8889**************************************954433111455555555 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.39   8.7e+02       1      17 [.       7      23 ..       7      28 .. 0.84
   2 !   48.1   0.0   3.7e-16   8.3e-13      78     212 ..      52     182 ..      49     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.39
                                      EE-TTSHHHHHHHHHHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLL 17
                                      lTGa G +G  +l  L 
  gi|336253205|ref|YP_004596312.1|  7 LTGAAGRVGDAILGGLA 23
                                      8*********9997765 PP

  == domain 2  score: 48.1 bits;  conditional E-value: 3.7e-16
                                       HHHHHHHHHH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS-H CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepykellrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekvye 153
                                       +e+++e +e +d++ih a++ + d+p + +l  N++Gt+ v+e a        + + S+  +v  ++++e + ++y+
  gi|336253205|ref|YP_004596312.1|  52 DEAVREAMEGIDAVIHLAGDPRPDAPWDSVLTNNIDGTQTVFEAAVDAGVE-KVAFASSnHAVGHYETEERTPEMYR 127
                                       78999****************************************987776.8999999644444444444455554 PP

                                       ......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSS CS
                     NAD_binding_4 154 egekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgeskt 212
                                           ++ ++ ++ ++l    n Y  sKa++E l r ++++++l vv vR++++t +  +
  gi|336253205|ref|YP_004596312.1| 128 ----ADDDYLLDGTELPRPGNLYGVSKAAGESLGRYYHDEHDLSVVCVRIGNLTEDHPP 182
                                       ....77788889999999999********************************995444 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 !   46.3   0.0     2e-15   4.4e-12       1     157 [.       9     188 ..       9     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 2e-15
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk.... 73 
                                       GA G+vG +++  l+++  +e ++l R+p   + ++     e v++d+td e+++ea++g+daV+  +g  +     
  gi|336253205|ref|YP_004596312.1|   9 GAAGRVGDAILGGLADE--YEWRLLDRDPPTED-YPG----EFVVADITDDEAVREAMEGIDAVIHLAGDPRPdapw 78 
                                       9***********99988..9*********9977.553....89*************************988885555 PP

                                       ..HHHH......HHHHHHHHHHCT--EEEEEEETTTTS..GCGCHHHHHHHH............CCHHHH.HHHHHH CS
                    NAD_binding_10  74 ..deeg......aknivdaakeagvkRfvlvsaigvgd..evpgefgewnke............llkayl.aakraa 127
                                                   ++++ +aa  agv+++ + s+ ++    e++++++e+++               ++ +   k+a 
  gi|336253205|ref|YP_004596312.1|  79 dsV--LtnnidgTQTVFEAAVDAGVEKVAFASSNHAVGhyETEERTPEMYRAdddylldgtelpRPGNLYgVSKAAG 153
                                       440..1555677********************976643123334444433321222222222112233343334444 PP

                                       HHHHHH....SSSEEEEEEE-CEE-S.T--SEEEE CS
                    NAD_binding_10 128 eellra....sgldwTivrpggLtde.pttkyrvv 157
                                       e l r      +l  + vr g Lt++ p+ +y+ +
  gi|336253205|ref|YP_004596312.1| 154 ESLGRYyhdeHDLSVVCVRIGNLTEDhPPIDYERG 188
                                       44333244449999999999999988458888765 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.2   4.5e+02       1      17 [.       5      21 ..       5      35 .. 0.84
   2 !   30.6   0.1   7.9e-11   1.8e-07      59     132 ..      45     113 ..      39     118 .. 0.94
   3 !    8.7   0.0   0.00037      0.82     133     171 ..     141     176 ..     139     180 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.2
                                      EEEETTTSHHHHHHHHH CS
                   Polysacc_synt_2  1 vlvtGagGsiGselvrq 17
                                      vl+tGa+G +G +++  
  gi|336253205|ref|YP_004596312.1|  5 VLLTGAAGRVGDAILGG 21
                                      899********998765 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 7.9e-11
                                       .E--TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGS CS
                   Polysacc_synt_2  59 vigdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAv 132
                                       v++d++d e +++a+e  ++d+v+h A     P  +  + +++++N+ gt++v eaa++agv+kv + S+  Av
  gi|336253205|ref|YP_004596312.1|  45 VVADITDDEAVREAME--GIDAVIHLAGD---PRPDAPWDSVLTNNIDGTQTVFEAAVDAGVEKVAFASSNHAV 113
                                       89**************..*********86...88999999******************************9998 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00037
                                       S--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EE CS
                   Polysacc_synt_2 133 nPtnvmGatKrlaekllqalakeseekktkfvvvRfGNV 171
                                       +P n++G++K++ e l   +++e+   +  +v+vR GN 
  gi|336253205|ref|YP_004596312.1| 141 RPGNLYGVSKAAGESLGRYYHDEH---DLSVVCVRIGNL 176
                                       799**************9999998...89*********6 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 !   40.1   0.0   1.3e-13   2.8e-10      54     182 ..      42     175 ..       6     187 .. 0.83
   2 ?   -2.6   0.0       1.2   2.7e+03     302     322 ..     220     240 ..     211     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.3e-13
                                       EEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEG CS
                     GDP_Man_Dehyd  54 lklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaSts 130
                                        +++ +D+tD ++++++++ +  d+v++LA+    d  +++   ++ +n+ Gt++++ea+ ++g+e   ++ +aS+ 
  gi|336253205|ref|YP_004596312.1|  42 GEFVVADITDDEAVREAMEGI--DAVIHLAGDPRPDAPWDS---VLTNNIDGTQTVFEAAVDAGVE---KVAFASSN 110
                                       57999*************998..9***************97...8999****************97...67789*99 PP

                                       GGG-S-SSSS.B-TT............S-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-E CS
                     GDP_Man_Dehyd 131 EvYGkvqevp.qtEt............tpfyPrsPYaaaKlyadwivvnyreayglfavngilfn 182
                                          G+ +      E                +P + Y+++K++ + + + y+++++l +v  ++ n
  gi|336253205|ref|YP_004596312.1| 111 HAVGHYETEErTPEMyradddylldgtELPRPGNLYGVSKAAGESLGRYYHDEHDLSVVCVRIGN 175
                                       9999997444144523344445555525558***************************9999888 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.2
                                       --SB--B-THHHHHHH----S CS
                     GDP_Man_Dehyd 302 evdlllgdaskakeeLgWkpk 322
                                       + d+ +  +++a+  Lg++p+
  gi|336253205|ref|YP_004596312.1| 220 DNDRKYYSIDRARAVLGYEPQ 240
                                       667778888999999999997 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 !   20.9   0.0   7.2e-08   0.00016       3     138 ..       5     159 ..       3     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 7.2e-08
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...........T--TTSHHHHHHHHHHH--SEEEE------HHHHH CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre...........eldltdaeavaellkeakpdvvvnaAAytavDkaE 68 
                                       +l+tGa G +G ++   la  ++e   l+r+            +d+td eav+e+++    d+v+++A   + D+  
  gi|336253205|ref|YP_004596312.1|   5 VLLTGAAGRVGDAILGGLAD-EYEWRLLDRDpptedypgefvVADITDDEAVREAMEG--IDAVIHLAGDPRPDAP- 77 
                                       89************999985.46888888888899******99*************99..788*****99999975. PP

                                       HSHHHHHHHHTHHHHHHHHHHHHCT-EEE.EEEEGGGS-S-......TTS-B-TTS-........---SSHHHHHHH CS
                     RmlD_sub_bind  69 seeeaayavnaeavealAeaaaavgalLi.hvStDyVFdGe......kkrpYeedde........tsPlnvYGrtKl 130
                                          ++    n ++++++ eaa  +g+  + + S+     G+      +++ Y+ dd         + P n+YG +K+
  gi|336253205|ref|YP_004596312.1|  78 --WDSVLTNNIDGTQTVFEAAVDAGVEKVaFASSNHAV-GHyeteerTPEMYRADDDylldgtelPRPGNLYGVSKA 151
                                       ..5566777999*************9766155555432.3334667744446666543333333389********** PP

                                       HHHHHHHH CS
                     RmlD_sub_bind 131 aGEqavla 138
                                       aGE   + 
  gi|336253205|ref|YP_004596312.1| 152 AGESLGRY 159
                                       ***87665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   7.4e-08   0.00017       1     117 [.       5     124 ..       5     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7.4e-08
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG.. CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy.. 75 
                                       +l +Ga+Gr G ++   l+ ++++ r l Rd+ +e      + + e+v +d+ d+e ++ea++g d+v+   g    
  gi|336253205|ref|YP_004596312.1|   5 VLLTGAAGRVGDAILGGLA-DEYEWRLLDRDPPTE------DYPGEFVVADITDDEAVREAMEGIDAVIHLAGDPrp 74 
                                       6789999999999998765.689999999999876......6799***************************96599 PP

                                       ........S-HHHHHHHHHHHHHHHS-SEEEEEE---GG.GT.SSS---T CS
                              NmrA  76 ........skeiedgkklvdAakeaGvkhfiySslgddndrsnaeepavp 117
                                                ++i+  +++ +Aa+ aGv+++ ++s   ++ +++ ee   +
  gi|336253205|ref|YP_004596312.1|  75 dapwdsvlTNNIDGTQTVFEAAVDAGVEKVAFASSNHAVGHYETEERTPE 124
                                       9999*9999999999999****************9999999988775555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); 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 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1869.70
//
Query:       gi|336253206|ref|YP_004596313.1|  [L=39]
Description: hypothetical protein Halxa_1806 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.008   16.1   0.9      0.056   13.4   0.9    1.9  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
  ------ inclusion threshold ------
      0.051   13.5   0.2      0.052   13.5   0.2    1.0  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> 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 !   13.4   0.9   6.3e-06     0.056       2      39 ..       5      36 ..       4      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-06
                            zf-FCS  2 vkkrCwfCkkyikgkpeftyvlendgvvgqFCStsCld 39
                                      v+ +C+ C+ ++k  p+       +    +FCS  C+ 
  gi|336253206|ref|YP_004596313.1|  5 VSVTCNECGDEFKAYPD------ANAADREFCSPACAL 36
                                      6789********99998......99999********86 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 ?   13.5   0.2   5.8e-06     0.052      28      55 ..       6      37 ..       2      39 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.8e-06
                    OrfB_Zn_ribbon 28 SktCseCgsknke....alsgrtfkCpnCgfe 55
                                      S tC+eCg + k     + ++r+f  p+C +e
  gi|336253206|ref|YP_004596313.1|  6 SVTCNECGDEFKAypdaNAADREFCSPACALE 37
                                      99********9999999999999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.30u 0.24s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 324.76
//
Query:       gi|336253207|ref|YP_004596314.1|  [L=204]
Description: hypothetical protein Halxa_1807 [Halopiger xanaduensis SH-6]
Scores for 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-18   64.8   4.1      6e-18   64.3   4.1    1.3  1  DUF309    Domain of unknown function (DUF309)


Domain annotation for each model (and alignments):
>> DUF309  Domain of unknown function (DUF309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   4.1   3.3e-22     6e-18       1      58 [.       5      64 ..       5      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 3.3e-22
                            DUF309  1 leeaielfnegeffeaHEvlEelWkeagep..erkllqglIqlAvAlyhlrrgnvrgakr 58
                                      l+++++ +n+g++++aH+++E+ W e +++  +++ll+glIqlA+A++h+ ++n+ ga+ 
  gi|336253207|ref|YP_004596314.1|  5 LRAGAAIYNDGYYHAAHDAWEDRWLECEDGtdDERLLHGLIQLAAAVHHAHERNWVGAVG 64
                                      68999*******************666665589*************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1562.21
//
Query:       gi|336253208|ref|YP_004596315.1|  [L=365]
Description: peptidase M29 aminopeptidase II [Halopiger xanaduensis SH-6]
Scores for 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-62  209.0   0.0    1.1e-61  208.8   0.0    1.0  1  Peptidase_M29  Thermophilic metalloprotease (M29)


Domain annotation for each model (and alignments):
>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.8   0.0   6.3e-66   1.1e-61       2     387 ..       2     341 ..       1     357 [. 0.91

  Alignments for each domain:
  == domain 1  score: 208.8 bits;  conditional E-value: 6.3e-66
                                       HHHHHHHHHHHHHTTT---TT-EEEEEEETT-HHHHHHHHHHHHHTT-SEEEEEEE-HHHHHHHHHHS-TT-TT--- CS
                     Peptidase_M29   2 eeklekyAellvkvglnlqkgqevvinaevealelarlvaeeaykagakkvvvewsdeeltkerlknaseeqleevp 78 
                                       +e++++ A++lv+ ++++++g++vv+++  +a+ela +vae++ ++ga+ + + + + e+t+++l  a++ +++e p
  gi|336253208|ref|YP_004596315.1|   2 DERVREHADVLVDWSARVEAGDDVVLSVGPDAHELAVAVAEKLGERGANLLAT-YGSGEITRAYL-RAHDGDFDENP 76 
                                       7899*********************************************9999.*******9855.68899****** PP

                                       HHHHHHHHHHHHTT-EEEEEE--.-GGGSTTS-HHHHHHHHHHHHHHHHHHHHHHHTTSS-B-BEE---TTTHHHH- CS
                     Peptidase_M29  79 eweaekleelveegaarlsilae.dpkllkgvdpekiaaaqkarskalkeyreriasgklrWcvvavPteawAkkvf 154
                                       + e    ++l+e+++++ls+ +  ++++ ++v+ +   a+++ar++++      +a+ + rW+ +  Pt+++A+   
  gi|336253208|ref|YP_004596315.1|  77 AHE----RALFENADVYLSLGGGrNTSATADVPGDTRRAYSNARTEIR------EARFDARWVSTVHPTRSLAQ--- 140
                                       ***....**************999********9888777777777664......3456789*************... PP

                                       --S-HHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHTT-SEEEEE.ETTEEEEEEE-TTB--EESS CS
                     Peptidase_M29 155 pdleaeealeklwdaifkavrldeedpvaaWeehnaelekrakyLnelkfkeLhyksspgtdLtvglaeghiWigga 231
                                          +a++a+e++ d+ ++a+        ++We+  +e+++ ++ L++   +e+++ s+ gtdLt+ + +++   ++a
  gi|336253208|ref|YP_004596315.1| 141 ---QANMAYEEYQDFAYDAIL-------RDWESLADEMANMKDLLDA--GSEVRLVSD-GTDLTMAIDDRTAVNSAA 204
                                       ...*************99976.......56*****************..99*****66.********7777766666 PP

                                       ---SSS----SBSS---EEE-EEEEEEEEEEE-SS-EEETTEEEBS-EEEEETTEEEEEE-SB-HHHHHHHTTSSSG CS
                     Peptidase_M29 232 ektkkgiefvaNiPteevftaPdkrgvnGvvratkPlsysGnliegirltFedGkvveakAekGeevLkklletDeg 308
                                       + +    +   N+P++evftaP +  ++G v+++ P+ ++G+ ++++rl+F dG+vv++ Ae+Geev+ ++letD+g
  gi|336253208|ref|YP_004596315.1| 205 SVA----YDSHNLPSGEVFTAPYA--TEGEVTFDVPMTLRGEAVRNVRLEFDDGEVVDYGAEQGEEVISEILETDDG 275
                                       665....7788***********86..79************************************************* PP

                                       GGSEEEEE---TTSHHHHHT-----HHHHHT..TS-EEEEE---GGGB--..-----SHHHHT----S-EEEEE--- CS
                     Peptidase_M29 309 arrLGEvALvpndspisqsgilfyntLfDen..ascHlAlGaaypecleggeelteeelkaaglNdSlihvDfmigs 383
                                       arrLGE+ ++ n+  i+q   ++ n+LfDe+   ++HlAlG+ay  cl +ge+           N+S++hvD mi +
  gi|336253208|ref|YP_004596315.1| 276 ARRLGELGIGMNR-GIDQ---YTDNILFDEKmgETVHLALGRAYDACLPEGES----------GNESAVHVD-MITD 337
                                       *************.****...**************************999876..........9********.**98 PP

                                       TT-E CS
                     Peptidase_M29 384 edld 387
                                       +  d
  gi|336253208|ref|YP_004596315.1| 338 MSED 341
                                       8763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2878.39
//
Query:       gi|336253209|ref|YP_004596316.1|  [L=241]
Description: hypothetical protein Halxa_1809 [Halopiger xanaduensis SH-6]
Scores for complete 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-50  171.3   8.9    1.6e-50  171.3   8.9    1.4  2  Vut_1     Putative vitamin uptake transporter


Domain annotation for each model (and alignments):
>> Vut_1  Putative vitamin uptake transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.36   6.5e+03      36      75 ..      22      27 ..       7      39 .. 0.46
   2 !  171.3   8.9   9.2e-55   1.6e-50       2     150 .]      55     223 ..      54     223 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.36
                             Vut_1 36 anllalillllalllpaealesvfgltprivlasliaylv 75
                                      +                                  +a+++
  gi|336253209|ref|YP_004596316.1| 22 V----------------------------------AALVT 27
                                      1..................................12222 PP

  == domain 2  score: 171.3 bits;  conditional E-value: 9.2e-55
                             Vut_1   2 aGvllfpltflitdiisevyGkkaarkvvllgflanllalillllalllpa.......ealesvfgltprivlasli 71 
                                       +++l+++ltfl++d+++e+yG++aa+ vv++gfl+n+++l+l++ ++++pa        a+e+ +g ++++v++sl+
  gi|336253209|ref|YP_004596316.1|  55 GAALAYALTFLASDCYTELYGRRAAQIVVNVGFLLNFIVLALVWSTIAAPAapssvdpGAFETALGASTNVVIGSLL 131
                                       789***********************************************9999999999***************** PP

                             Vut_1  72 aylvsqlldvyvfhrlkkltkgkklwlrnigStlvsqlvdtlifvtiaflg.............eqlleiilsqyli 135
                                       ay+vsq++dv vfhr+++ t+ ++lwlrnigSt++sq++dt+ifv++af++             ++ll++i++qyl+
  gi|336253209|ref|YP_004596316.1| 132 AYVVSQNWDVIVFHRIREATGARMLWLRNIGSTATSQAIDTVIFVSVAFAIapavlgvgavlptNVLLSLIVGQYLL 208
                                       *************************************************88************************** PP

                             Vut_1 136 kllialldtplvylv 150
                                       k++ialldtp+vy+v
  gi|336253209|ref|YP_004596316.1| 209 KFAIALLDTPIVYAV 223
                                       *************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1785.54
//
Query:       gi|336253210|ref|YP_004596317.1|  [L=64]
Description: cold-shock DNA-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-19   67.6   0.1      7e-19   67.5   0.1    1.0  1  CSD       'Cold-shock' DNA-binding domain
  ------ inclusion threshold ------
      0.052   13.2   1.9      0.073   12.8   1.9    1.3  1  OB_RNB    Ribonuclease B OB domain
      0.076   13.0   0.2      0.086   12.8   0.2    1.3  1  S1-like   S1-like


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.1   1.2e-22     7e-19       2      65 ..       3      63 ..       2      64 .] 0.97

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 1.2e-22
                                      EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                               CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                      +G V  fn+  g+GFI++ed d+dvF+H+ ++ g +   L+eg e+eF++++  kgp+A+nVt+
  gi|336253210|ref|YP_004596317.1|  3 KGNVDFFNDTGGYGFISTEDADEDVFFHMEDVGGPD---LEEGTEIEFDIEQAPKGPRATNVTR 63
                                      79******************************9999...***********************97 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.9   1.2e-05     0.073       8      28 ..      13      33 ..       8      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                                      SS-EEEEECT.TEEEEE-HHH CS
                            OB_RNB  8 kGFGFlipdegkeDifippeq 28
                                       G+GF+++++ +eD+f + e+
  gi|336253210|ref|YP_004596317.1| 13 GGYGFISTEDADEDVFFHMED 33
                                      59**************87766 PP

>> S1-like  S1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.4e-05     0.086      14      48 ..      14      53 ..       3      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                           S1-like 14 tfGfv.....DeevfFqrsvvkGrlpkvgdrVlveAvynp 48
                                       +Gf+     De+vfF+++ v G+  + g  ++++  + p
  gi|336253210|ref|YP_004596317.1| 14 GYGFIstedaDEDVFFHMEDVGGPDLEEGTEIEFDIEQAP 53
                                      58888777779**********9998888887777665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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):               3  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 517.96
//
Query:       gi|336253211|ref|YP_004596318.1|  [L=91]
Description: transcriptional regulator PadR family protein [Halopiger xanaduensis SH-6]
Scores for 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   48.9   0.1    5.7e-13   48.6   0.1    1.1  1  PadR      Transcriptional regulator PadR-like family
     0.0013   18.7   0.0     0.0017   18.3   0.0    1.2  1  HTH_45    Winged helix-turn-helix
     0.0028   17.4   0.0     0.0036   17.1   0.0    1.2  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
  ------ inclusion threshold ------
      0.063   13.4   0.0      0.071   13.3   0.0    1.1  1  FUR       Ferric uptake regulator family
        0.1   12.5   0.0       0.14   12.1   0.0    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB
       0.11   12.4   0.3        3.1    7.8   0.1    2.5  2  MarR_2    MarR family


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 !   48.6   0.1   1.9e-16   5.7e-13       2      74 ..      12      79 ..      11      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.9e-16
                                      HHHH..CCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  2 Lall..eeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      L+++  ++qp  G ++++e+e +++   ++++G+lYp+L++L ++glve+ + +    ++++yY++ d+G ++++
  gi|336253211|ref|YP_004596318.1| 12 LYVIagADQP-SGQDVKDEIESYYSA--DINHGRLYPNLDTLVNKGLVEKGQLD----RRTNYYEISDQGVQAIE 79
                                      7777534466.8***********976..***********************998....7***********99987 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.6e-07    0.0017      26      74 ..      33      86 ..      22      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.6e-07
                            HTH_45 26 mykanLsykllnkYLdmLvekgli.....kkskekYvlTekGlelleklkelee 74
                                       y+a+++  +l   Ld+Lv+kgl+     + +++ Y++ ++G + +e+ +e e+
  gi|336253211|ref|YP_004596318.1| 33 YYSADINHGRLYPNLDTLVNKGLVekgqlDRRTNYYEISDQGVQAIEERREWER 86
                                      599********************98887778999**********9999888765 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 !   17.1   0.0   1.2e-06    0.0036      52      88 ..      43      79 ..      26      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                           DUF1495 52 rynsessLielGLveeeeeseglklYklteeGieive 88
                                       y + + L+++GLve+ + ++ +++Y+++++G +  e
  gi|336253211|ref|YP_004596318.1| 43 LYPNLDTLVNKGLVEKGQLDRRTNYYEISDQGVQAIE 79
                                      5777789********9999*************98765 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.4e-05     0.071      24      74 ..      21      72 ..       7      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                                      BEHHHHHHHHH.HTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS CS
                               FUR 24 lsaeevykelk.eedpeislaTVYrtLklleeaglvkelefedgesryelak 74
                                      +s ++v +e++   + +i    +Y +L++l + glv++ +++  +++ye+++
  gi|336253211|ref|YP_004596318.1| 21 PSGQDVKDEIEsYYSADINHGRLYPNLDTLVNKGLVEKGQLDRRTNYYEISD 72
                                      677889999983456789999****************************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.6e-05      0.14      32      63 ..      36      69 ..      23      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.6e-05
                                      TTSSCHCHHHHHHHHHHCTSEEEES.ST.TTEEE CS
                              TrmB 32 lgvprskvYevLrsLedkGlVerek.gr.pklYr 63
                                      +++ + + Y  L  L++kGlVe+ +  r +++Y+
  gi|336253211|ref|YP_004596318.1| 36 ADINHGRLYPNLDTLVNKGLVEKGQlDRrTNYYE 69
                                      6788999***************988544244555 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1     0.001       3.1      41      61 ..      46      64 ..       2      65 .. 0.66
   2 ?   -2.0   0.0       1.2   3.6e+03      24      37 ..      75      88 ..      70      89 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.001
                                      HHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 41 ilkrLvaaGLverrpgpeDkR 61
                                       l+ Lv +GLve+     D+R
  gi|336253211|ref|YP_004596318.1| 46 NLDTLVNKGLVEKGQL--DRR 64
                                      6888999999997744..888 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                                      HHHHHHHHTSSHHH CS
                            MarR_2 24 vgelarrlglsksa 37
                                      v+++++r   ++++
  gi|336253211|ref|YP_004596318.1| 75 VQAIEERREWERQY 88
                                      56777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 691.53
//
Query:       gi|336253212|ref|YP_004596319.1|  [L=152]
Description: DNA binding protein, Tfx family [Halopiger xanaduensis SH-6]
Scores for 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-31  106.8   0.0    5.7e-31  106.3   0.0    1.2  1  TFX_C         DNA_binding protein, TFX, C-term
      1e-06   28.2   0.2      2e-06   27.2   0.2    1.5  1  Sigma70_r4    Sigma-70, region 4
    2.2e-05   24.4   0.0    5.2e-05   23.2   0.0    1.6  1  HTH_19        Helix-turn-helix domain
      4e-05   23.9   2.8    8.9e-05   22.8   2.8    1.6  1  HTH_31        Helix-turn-helix domain
    0.00019   20.9   0.1    0.00028   20.4   0.1    1.3  1  GerE          Bacterial regulatory proteins, luxR family
    0.00052   20.0   0.2     0.0011   19.0   0.2    1.5  1  HTH_3         Helix-turn-helix
     0.0031   17.2   0.1     0.0054   16.4   0.1    1.4  1  Sigma70_r4_2  Sigma-70, region 4
     0.0066   16.2   0.1      0.012   15.4   0.1    1.4  1  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.021   14.9   0.0    1.4  1  HTH_7         Helix-turn-helix domain of resolvase
      0.023   14.7   0.1      0.044   13.8   0.1    1.4  1  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.045   13.5   0.1      0.082   12.7   0.1    1.4  1  HTH_38        Helix-turn-helix domain
      0.045   14.1   0.2       0.17   12.2   0.0    2.0  2  TAL_effector  TAL effector repeat
      0.047   13.2   0.1      0.086   12.4   0.1    1.4  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.061   13.2   0.2       0.17   11.8   0.2    1.7  1  MarR_2        MarR family
      0.072   13.2   0.1       0.11   12.6   0.1    1.2  1  RepB          RepB plasmid partitioning protein
      0.096   12.7   0.0       0.16   12.0   0.0    1.4  1  HTH_37        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TFX_C  DNA_binding protein, TFX, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.0   5.1e-34   5.7e-31       1      83 []      66     148 ..      66     148 .. 0.99

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 5.1e-34
                                       SS-HHHHHHHH---EEEEE--GGGHHHHHHHHHHHHHHHS-S----HHHHHHHHHHH-SSS-----SSS-EEEEESS CS
                             TFX_C   1 AreTlaflealdapvlvtieeGtdlfdipkiiyaeadkagikvkydtieLikllreeapeaikgrvvkedlevyite 77 
                                       AreT+af+eal+apv+v +++Gtdl+d+p+++y+++d+ag+kv+y++++L+k+++++a+ a++gr+v ++l + +t+
  gi|336253212|ref|YP_004596319.1|  66 ARETVAFAEALRAPVRVRVPAGTDLYDVPDLVYEACDEAGVKVDYTAPDLMKVVSDSAGSAVSGREVSTPLIIGVTS 142
                                       9**************************************************************************** PP

                                       SSSEEE CS
                             TFX_C  78 dGeirv 83 
                                       +G +rv
  gi|336253212|ref|YP_004596319.1| 143 NGMVRV 148
                                       ****98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.2   1.8e-09     2e-06       4      48 ..      20      63 ..      19      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.8e-09
                                      HS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  4 sLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48
                                      +L+ r+ +vl lr ++g ++++I+  lg Sr  V++ie+ A+++L
  gi|336253212|ref|YP_004596319.1| 20 VLTYRQAQVLALR-ERGISQADIAGALGTSRANVSSIESSARENL 63
                                      6999********9.8999************************998 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   4.7e-08   5.2e-05       7      52 ..      30      76 ..      29      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.7e-08
                            HTH_19  7 aReelgltqeelaerlgisrskisaiEngkkdvps.aelllkiaeal 52
                                      a +e+g++q+++a+ lg+sr+  s iE+  +++++ a++  ++aeal
  gi|336253212|ref|YP_004596319.1| 30 ALRERGISQADIAGALGTSRANVSSIESSARENLEkARETVAFAEAL 76
                                      6789************************9777888788888877775 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   2.8   7.9e-08   8.9e-05       9      60 ..      31      82 ..      22      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.9e-08
                            HTH_31  9 lReraGLsqeevAerlgvsestlsrlEq.Grrgrpspavlealaralgldpae 60
                                      lR ++G+sq++ A++lg s++ +s +E+ +r+++ + +   a+a+al++++  
  gi|336253212|ref|YP_004596319.1| 31 LR-ERGISQADIAGALGTSRANVSSIESsARENLEKARETVAFAEALRAPVRV 82
                                      55.569**********************5555455888***********9865 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   2.5e-07   0.00028       2      43 ..      20      61 ..      19      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.5e-07
                                      SS-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHH CS
                              GerE  2 sLskRErevLrllaeGksnkeIAeelniSekTVkvhksnimk 43
                                      +L+ R+++vL+l   G s  +IA +l+ S  +V++  s++ +
  gi|336253212|ref|YP_004596319.1| 20 VLTYRQAQVLALRERGISQADIAGALGTSRANVSSIESSARE 61
                                      8********************************997777665 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   9.4e-07    0.0011       5      32 ..      31      58 ..      28      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.4e-07
                                      HHHTTHHHHHHHHHHTSSHHHHHHHHTT CS
                             HTH_3  5 RkqlglsqeeLAeklGvsrstisriEnG 32
                                      + ++g+sq+++A +lG sr+ +s iE+ 
  gi|336253212|ref|YP_004596319.1| 31 LRERGISQADIAGALGTSRANVSSIESS 58
                                      446***********************97 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 !   16.4   0.1   4.8e-06    0.0054      11      45 ..      21      54 ..      19      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.8e-06
                                      S-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHH CS
                      Sigma70_r4_2 11 LperqreifllryleglsykEIAellgisegtVks 45
                                      L+ rq +++ l ++ g s+++IA  lg+s ++V s
  gi|336253212|ref|YP_004596319.1| 21 LTYRQAQVLAL-RERGISQADIAGALGTSRANVSS 54
                                      7889*******.69******************977 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.1e-05     0.012       7      32 ..      25      50 ..      21      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                            HTH_23  7 RlrillllaeGlsvreIAreLgvsrr 32
                                       +++l l  +G+s+++IA +Lg sr 
  gi|336253212|ref|YP_004596319.1| 25 QAQVLALRERGISQADIAGALGTSRA 50
                                      4677777777**************97 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 ?   14.9   0.0   1.9e-05     0.021      10      36 ..      24      50 ..      16      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                                      HHGGGGSSTTTT--STTTSSSS---SS CS
                             HTH_7 10 dinrvvkLleeGisiskIAkevnisRs 36
                                      ++++v++L+e Gis ++IA ++++sR+
  gi|336253212|ref|YP_004596319.1| 24 RQAQVLALRERGISQADIAGALGTSRA 50
                                      479***********************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 ?   13.8   0.1   3.9e-05     0.044      19      41 ..      33      55 ..      18      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-05
                                      EEEHHHHHHHHHTTSSHHHHHHH CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsri 41
                                      e  ++q+++A  lG++r  vs i
  gi|336253212|ref|YP_004596319.1| 33 ERGISQADIAGALGTSRANVSSI 55
                                      4469****************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 ?   12.7   0.1   7.3e-05     0.082      14      35 ..      29      50 ..      25      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-05
                            HTH_38 14 erllaeGlslreIArrLgrsps 35
                                       +l+++G s+++IA  Lg s+ 
  gi|336253212|ref|YP_004596319.1| 29 LALRERGISQADIAGALGTSRA 50
                                      5799***************986 PP

>> TAL_effector  TAL effector repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.17      13      28 ..      27      42 ..      25      42 .. 0.87
   2 ?   -2.5   0.0         6   6.7e+03       5      11 ..      65      71 ..      65      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                      HHHHHHHTT--HHHHH CS
                      TAL_effector 13 hgpaLrqrGfSradIV 28
                                      +  aLr+rG S+adI+
  gi|336253212|ref|YP_004596319.1| 27 QVLALRERGISQADIA 42
                                      5679***********5 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6
                                      HHHHHHH CS
                      TAL_effector  5 QALeAVl 11
                                      +A+e+V+
  gi|336253212|ref|YP_004596319.1| 65 KARETVA 71
                                      699**96 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 ?   12.4   0.1   7.7e-05     0.086      14      35 ..      32      53 ..      29      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.7e-05
                            HTH_24 14 knprisqreLAerlglSpstvn 35
                                      ++ +isq+++A +lg S+++v+
  gi|336253212|ref|YP_004596319.1| 32 RERGISQADIAGALGTSRANVS 53
                                      5679***************998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00015      0.17       4      41 ..      22      55 ..      19      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                      -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHH CS
                            MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsri 41
                                      t  qa+vLa L+ r+   ++++++a +lg s+++vs i
  gi|336253212|ref|YP_004596319.1| 22 TYRQAQVLA-LRERG---ISQADIAGALGTSRANVSSI 55
                                      667777774.77776...9****************976 PP

>> RepB  RepB plasmid partitioning 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      0.11      12      52 ..      26      65 ..      23      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.5e-05
                              RepB 12 rfaarleerGvdreeiasalgldkqtvskmvaraipegica 52
                                      + +  l+erG ++++ia alg++++ v +++  +++e++++
  gi|336253212|ref|YP_004596319.1| 26 AQVLALRERGISQADIAGALGTSRANV-SSIESSARENLEK 65
                                      56788**********************.6667777777754 PP

>> HTH_37  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   0.00014      0.16      27      53 ..      31      57 ..      20      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                      HHHCT--HHHHHHHHT--HHHHHHHHT CS
                            HTH_37 27 iekrelsqseaaqllgiaqPkvsrllr 53
                                      +++r++sq+++a +lg+++++vs+++ 
  gi|336253212|ref|YP_004596319.1| 31 LRERGISQADIAGALGTSRANVSSIES 57
                                      5789*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1112.84
//
Query:       gi|336253213|ref|YP_004596320.1|  [L=161]
Description: TRAM domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   34.6   0.0      2e-08   34.1   0.0    1.2  1  TRAM         TRAM domain
  ------ inclusion threshold ------
      0.026   15.2   6.6       0.55   10.9   6.7    2.1  2  FYDLN_acid   Protein of unknown function (FYDLN_acid)
       0.28    9.4   3.2       0.29    9.4   3.2    1.1  1  CDC45        CDC45-like protein


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   3.3e-12     2e-08       3      61 ..      50     105 ..      48     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 3.3e-12
                                       XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61 
                                       + G+++e  + + +   g g+Grt++g++v+v+g lp    ++ V+It+v+++ +r+e 
  gi|336253213|ref|YP_004596320.1|  50 KSGEEVELDIVDMH-ESGAGVGRTEDGFIVLVDGLLP--ECRARVEITQVHSNHARAET 105
                                       679***********.**********************..******************96 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 ?    2.1   0.0     0.052   3.1e+02       5      29 ..      27      51 ..      25      72 .. 0.83
   2 ?   10.9   6.7   9.2e-05      0.55      30      92 ..      85     142 ..      83     155 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.052
                        FYDLN_acid  5 elGtKriCpscgakFYDLnkdPivc 29
                                      ++G K  C++ ++   DL+ +P+ +
  gi|336253213|ref|YP_004596320.1| 27 DRGGKEWCQHYSQPIEDLKTQPVKS 51
                                      6899999**9999999******976 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.2e-05
                        FYDLN_acid  30 pkcgeefepeevlksraaaaeaeeakkkkeeeedeedeeeeedvsdedadeeeeedddddvdl 92 
                                       p+c + +e+++v +s++a+ae+ e+     + ++e d+++ +++   dad++e+++dd+++++
  gi|336253213|ref|YP_004596320.1|  85 PECRARVEITQV-HSNHARAETLEQ--LPMDGDEEGDDADSDAD--GDADADEAAADDESEET 142
                                       899999999999.566666665555..44444444455544444..44444444345542222 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.2   4.9e-05      0.29     118     172 ..      98     150 ..      47     158 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 4.9e-05
                             CDC45 118 eereayealeeeeesdeedeeeeeeddddeeeeeeeeedeedeeedeeeskkkrk 172
                                       +++   e+le+ + + +e+  ++ ++d  +++ + +e + +de+e+++++++ r+
  gi|336253213|ref|YP_004596320.1|  98 SNHARAETLEQLPMDGDEE-GDDADSDA-DGDADADEAAADDESEETDRKSRARE 150
                                       3444555555555553222.22222222.22333333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1266.76
//
Query:       gi|336253214|ref|YP_004596321.1|  [L=263]
Description: Electron transfer flavoprotein alpha/beta-subunit [Halopiger xanaduensis SH-6]
Scores for 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-40  136.5   1.9    8.7e-40  136.5   1.9    1.4  2  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 !  136.5   1.9   4.8e-44   8.7e-40       4     181 ..      24     212 ..      21     213 .. 0.94
   2 ?   -3.6   0.0       0.5     9e+03      73      87 ..     244     258 ..     242     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 136.5 bits;  conditional E-value: 4.8e-44
                                       EE-EC.CCCE-HHHHHHHHHHHHHHHH.HT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS-...-CCH CS
                               ETF   4 laehgvdgklnpvdlealeaArrlkek.aggevtavvvGppeaeealrealaamGadkvilvddpalagy...daea 76 
                                       +ae+  ++ ln++d +a+e+A++l+e+    ev+ v++Gp+ +e+++r+ala +Gad++i v+d+al+++   d  a
  gi|336253214|ref|YP_004596321.1|  24 IAERYLGADLNEWDDYAVEEAVQLQEAgIADEVVTVTIGPEDCEQTIRQALA-KGADRAIRVWDDALEEFdllDVGA 99 
                                       7899999*******************96339*********************.*****************7777889 PP

                                       HHHHHHHHHHHC--SEEEEESSCC.H..HHHHHHHHHHCT-EEEEEESEEEE..ETCCEEEEEECCCCTEEEEEE-T CS
                               ETF  77 takalaalikkedpdlvlagatai.g..kqvaprlAalLgvplitdvtelev..eggkltvtRpieggnglaevvea 148
                                         ++l a+i++edpdlvl+g ++  +  + ++  +A+ Lg+ +++ v +le   egg++ v+R++eg  g++e +e+
  gi|336253214|ref|YP_004596321.1| 100 KRELLGAVIAEEDPDLVLTGVQSGdDnfGATGVSVAEALGYEWAAVVNHLEHdfEGGTASVRRELEG--GVEELTEV 174
                                       99**********************66***********************887446677*********..******** PP

                                       SSSEEEEE-TTSS--.....--S-TT---EEEE--HHH CS
                               ETF 149 dlpavltvrpgafep.....aaimaakkkeveevevad 181
                                       +lpavltv++g++ep     ++i++a++ke+ +v +ad
  gi|336253214|ref|YP_004596321.1| 175 ELPAVLTVQTGINEPryaslRGIRQAQRKELDVVGLAD 212
                                       *********************************99887 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.5
                                       -CCHHHHHHHHHHHH CS
                               ETF  73 daeatakalaalikk 87 
                                       dae+ta  la+l+++
  gi|336253214|ref|YP_004596321.1| 244 DAEQTATELADLLRD 258
                                       788888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1940.93
//
Query:       gi|336253215|ref|YP_004596322.1|  [L=317]
Description: Electron transfer flavoprotein subunit alpha [Halopiger xanaduensis SH-6]
Scores for 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-36  121.8   0.1    1.7e-35  120.9   0.1    1.5  1  ETF_alpha  Electron transfer flavoprotein FAD-binding domain
    4.4e-33  114.7   3.0    6.6e-33  114.1   3.0    1.2  1  ETF        Electron transfer flavoprotein domain
  ------ inclusion threshold ------
      0.032   13.4   0.1        1.1    8.4   0.0    2.2  2  PBP_like   PBP superfamily domain


Domain annotation for each model (and alignments):
>> ETF_alpha  Electron transfer flavoprotein FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   0.1   2.8e-39   1.7e-35       1      84 []     196     279 ..     196     279 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 2.8e-39
                                       .-TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTTTSS-CCCB-SSSS-----S-EEEES----HHH CS
                         ETF_alpha   1 vdLeeakvvvsgGrGlkskenlelleelaealgaavgasRavvdagwipeerqvGqtGktvaPklyiavGisGaiqh 77 
                                       vd+++a+v+vs+GrG++++enl+l+ +laeal+a+v+ sR++vd+gw+p++rqvGq+Gk+v+P++yia+GisGa+qh
  gi|336253215|ref|YP_004596322.1| 196 VDISDADVLVSVGRGIEEEENLDLIFDLAEALDATVSSSRPIVDNGWLPKNRQVGQSGKVVTPDVYIAIGISGAVQH 272
                                       699************************************************************************** PP

                                       HGGGTT- CS
                         ETF_alpha  78 laGmkes 84 
                                       +aGmk s
  gi|336253215|ref|YP_004596322.1| 273 VAGMKGS 279
                                       ****987 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   3.0   1.1e-36   6.6e-33       2     180 ..       5     175 ..       4     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 1.1e-36
                                       EEEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHH CS
                               ETF   2 lvlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeata 78 
                                       l +a+h+ +g+l++v+ e+l+a+rrl++++gg++++ v+    +++  +  l   G+d v+ vd  +  ++++  +a
  gi|336253215|ref|YP_004596322.1|   5 LAVADHR-RGELRDVSYELLTAGRRLADETGGDLHVAVISG--TVDDFASKLDREGVDVVHTVDYGE--EFNHGVYA 76 
                                       7899**8.*********************999999999988..45559**********999998775..5799**** PP

                                       HHHHHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEE CS
                               ETF  79 kalaalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpavlt 155
                                       +a+ +l   + p+ vla+++  g ++ap +A  L+vp++tdv++le +g++lt+tR+++gg++  ++ e++ pav+t
  gi|336253215|ref|YP_004596322.1|  77 QAITQLYDRLAPQYVLAPNSVNGLDYAPAVATALDVPIVTDVVGLETDGETLTATREMYGGKVE-TTSELEGPAVVT 152
                                       ***************************************************************9.************ PP

                                       E-TTSS----S-TT---EEEE--HH CS
                               ETF 156 vrpgafepaaimaakkkeveeveva 180
                                       +r   +++  +++++ +++e ++v+
  gi|336253215|ref|YP_004596322.1| 153 IRGAEWPA--AEGTGDAAIEAADVT 175
                                       ******99..578888888888875 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00018       1.1     103     173 ..      43     112 ..      42     119 .. 0.92
   2 ?    2.6   0.0      0.01        62      19      42 ..     183     206 ..     167     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00018
                                       SHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCCETTCCECCCGG-HCCCCCCECTTCE-EEEEE CS
                          PBP_like 103 SGtrdlfdellkkegiskssikgyaqearshlavaaaVaagradvgvgieavaeelkgldfvplaeerydl 173
                                       SGt d f ++l +eg++     +y+ e+++h+  a+a+ +     ++    + ++++gld+ p    ++d+
  gi|336253215|ref|YP_004596322.1|  43 SGTVDDFASKLDREGVDVVHTVDYG-EEFNHGVYAQAITQLYDRLAPQYVLAPNSVNGLDYAPAVATALDV 112
                                       9***********************8.*********************99999999******9988877775 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.01
                                       -HHHHHHHHHTTS-SEEEESS--- CS
                          PBP_like  19 GsggGlkalrageadiagshlldk 42 
                                        +++G++ ++ g +di+ +++l +
  gi|336253215|ref|YP_004596322.1| 183 STVNGFEEVAGGDVDISDADVLVS 206
                                       4689**************999843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2477.96
//
Query:       gi|336253216|ref|YP_004596323.1|  [L=924]
Description: methyl-accepting chemotaxis sensory transducer [Halopiger xanaduensis SH-6]
Scores for 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-34  117.4  60.5    8.7e-34  116.8  24.1    4.5  4  MCPsignal      Methyl-accepting chemotaxis protein (MCP) sign
    1.2e-10   41.6  13.8    7.2e-09   35.9   0.0    5.0  6  HAMP           HAMP domain
    0.00026   21.2  41.5     0.0057   16.9   3.3    6.5  6  DUF948         Bacterial protein of unknown function (DUF948)
      0.002   17.1   4.2      0.002   17.1   4.2    2.5  2  LMBR1          LMBR1-like membrane protein
  ------ inclusion threshold ------
      0.021   14.8  48.6       0.15   12.0   3.3    6.0  6  Laminin_II     Laminin Domain II
      0.096   11.6  46.5       0.21   10.4  12.8    3.5  3  Spc7           Spc7 kinetochore protein
       0.22   11.5  33.5      0.026   14.5   2.5    5.5  7  DUF1664        Protein of unknown function (DUF1664)
       0.34   11.1   1.1        1.3    9.2   1.1    2.0  1  GM_CSF         Granulocyte-macrophage colony-stimulating fact
       0.57   10.9  38.0       0.21   12.3   3.1    5.2  5  DUF2203        Uncharacterized conserved protein (DUF2203)
        1.3    7.3  44.3      0.025   13.0  23.0    2.2  2  MAD            Mitotic checkpoint protein
        1.5    9.0  12.9        0.6   10.2   1.0    4.1  4  Med9           RNA polymerase II transcription mediator compl
        2.2    8.7  16.2         33    4.9   0.0    5.4  4  Syntaxin_2     Syntaxin-like protein
        3.1    8.1  40.9        2.2    8.5   1.4    5.8  5  Seryl_tRNA_N   Seryl-tRNA synthetase N-terminal domain
        3.2    7.5  63.3      0.034   14.0  15.5    3.4  3  ERM            Ezrin/radixin/moesin family
        3.7    6.7  28.8        0.2   10.8   3.0    4.3  5  TMPIT          TMPIT-like protein
        4.7    7.1   6.2        6.3    6.7   0.3    2.9  2  XH             XH domain
        4.9    7.3  26.8        2.5    8.3   3.4    4.7  5  Fib_alpha      Fibrinogen alpha/beta chain family
        7.5    7.1  27.1        1.6    9.3   1.5    6.2  6  NPV_P10        Nucleopolyhedrovirus P10 protein
        7.5    6.2  39.0        3.4    7.3  13.8    3.9  3  TMP_2          Prophage tail length tape measure protein


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   9.6     0.017        16     113     169 ..     417     473 ..     350     475 .. 0.74
   2 !   11.2  13.9   0.00026      0.25      82     168 ..     435     521 ..     426     527 .. 0.53
   3 !  116.8  24.1   9.3e-37   8.7e-34       6     171 ..     530     699 ..     525     700 .. 0.92
   4 ?    3.8   4.4     0.048        45     112     164 ..     689     741 ..     687     750 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 113 rqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveeva 169
                                       +++ e  +e+++e ++ ++ei +++aev++  +e+a+asee +as+eev +a  +va
  gi|336253216|ref|YP_004596323.1| 417 ESENEAMTEIAAEFNDMIAEIEATTAEVKSFATEVATASEEVTASSEEVRSASGQVA 473
                                       445556677888888888999999999999999999999999999999988887776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00026
                                       HHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  82 ersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasi 158
                                       ++   ++ e+++  +e+   ++++++s ee+r+   + +e ++e  e   +  ++ ++v+++++ ++++ ee++as+
  gi|336253216|ref|YP_004596323.1| 435 AEIEATTAEVKSFATEVATASEEVTASSEEVRSASGQVAESIQEISEGADRQNDSLQSVTQEMNGLSTTIEEIAASS 511
                                       45555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                                       HHHHHHHHHH CS
                         MCPsignal 159 eevnqaveev 168
                                       ++v++  e+ 
  gi|336253216|ref|YP_004596323.1| 512 NQVAELAERT 521
                                       5555544443 PP

  == domain 3  score: 116.8 bits;  conditional E-value: 9.3e-37
                                       HHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHH CS
                         MCPsignal   6 easeeAeeg....gkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVr 78 
                                       ea +eA eg    ++  + +v+++e +e++ ++i d++e i+e+a+QTN+LALNA iEA R   + +GF+ VA+EV+
  gi|336253216|ref|YP_004596323.1| 530 EAAQEAIEGmqeiETDSESAVEEIERLEEEMAQIDDLLEFITEVAEQTNMLALNANIEASRSSSSNEGFSAVAGEVK 606
                                       55555555522226666789********************************************************* PP

                                       HHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  79 kLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqs 155
                                       +LAe + +aa +ie+ +++i+++++++++ ++ t  rv+e ++ ve++++al ei++ ++e ++ vqei+ as+eq+
  gi|336253216|ref|YP_004596323.1| 607 ELAEDTREAAADIEDRLEQIKEQTDRTATEVQRTSDRVSEHTDSVERAADALDEIADYATETNTGVQEISNASDEQA 683
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHH CS
                         MCPsignal 156 asieevnqaveevakv 171
                                       as ++v   v+ va++
  gi|336253216|ref|YP_004596323.1| 684 ASTQQVVAMVDDVAAI 699
                                       ******9999998875 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.048
                                       HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 112 trqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqa 164
                                       ++  v+  + ++e+t ++ +++++a++e ++ ++e+++++ e+++ +++ +++
  gi|336253216|ref|YP_004596323.1| 689 VVAMVDDVAAIAEQTSSESETVAAAAEEQTTALTEVSRSAGELANRASHLSET 741
                                       44445555555555555555555555555555555555555555544444443 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   7.6e-12   7.2e-09       3      52 ..     315     364 ..     313     365 .. 0.95
   2 !   10.6   1.1   0.00058      0.55      15      52 ..     400     438 ..     399     439 .. 0.91
   3 ?    0.2   0.1         1   9.8e+02      12      51 ..     471     504 ..     470     526 .. 0.67
   4 ?   -2.8   0.0       9.5     9e+03      10      21 ..     553     564 ..     549     566 .. 0.85
   5 ?   -2.6   0.0       8.1   7.6e+03       9      24 ..     650     663 ..     643     670 .. 0.77
   6 ?   -2.8   0.0       9.5     9e+03       8      31 ..     726     751 ..     722     755 .. 0.68

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 7.6e-12
                                       HHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                              HAMP   3 arrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                        ++++r++ rL++ a+r+ +Gdld++l+  + D iG+L   f+ M+d+L+
  gi|336253216|ref|YP_004596323.1| 315 GWNTSRSIDRLTTKAARMEEGDLDVDLDSPRIDSIGRLYDGFDSMRDSLQ 364
                                       57899********************************************8 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00058
                                       HHHHHHTTTBTSSTCCTTSSSH.HHHHHHHHHHHHHHHH CS
                              HAMP  15 raarriaaGdldtrlpvsgrDE.iGeLarafNaMldrLr 52 
                                       ++++  a+Gdl++r ++++ +E + e+a+ fN+M+ +++
  gi|336253216|ref|YP_004596323.1| 400 DVMQTAADGDLTARMDPESENEaMTEIAAEFNDMIAEIE 438
                                       68999************9999978**********99986 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1
                                       HHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHH CS
                              HAMP  12 rLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrL 51 
                                       ++a+++++i++G  ++       D +  + + +N +++ +
  gi|336253216|ref|YP_004596323.1| 471 QVAESIQEISEGADRQN------DSLQSVTQEMNGLSTTI 504
                                       56777778887755555......55555555555555544 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 9.5
                                       HHHHHHHHHHHT CS
                              HAMP  10 LrrLaraarria 21 
                                       ++rL++ +++i+
  gi|336253216|ref|YP_004596323.1| 553 IERLEEEMAQID 564
                                       899*****9998 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 8.1
                                       HHHHHHHHHHHHTTTB CS
                              HAMP   9 PLrrLaraarriaaGd 24 
                                       +++r a+a ++ia  d
  gi|336253216|ref|YP_004596323.1| 650 SVERAADALDEIA--D 663
                                       5778888888888..3 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 9.5
                                       HHHHHHHHHHHHHTTT..BTSSTCCT CS
                              HAMP   8 rPLrrLaraarriaaG..dldtrlpv 31 
                                       r+  +La  a ++++   +++t+ +v
  gi|336253216|ref|YP_004596323.1| 726 RSAGELANRASHLSETldNFETDADV 751
                                       55567888888888866677777665 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 ?    3.8   0.4     0.071        67      26      79 ..     354     407 ..     299     414 .. 0.81
   2 !    7.7   0.6    0.0045       4.3      49      85 ..     423     459 ..     408     463 .. 0.79
   3 !   10.5   1.3    0.0006      0.57      32      88 ..     462     518 ..     458     519 .. 0.87
   4 ?    1.1   0.3       0.5   4.7e+02      42      84 ..     539     577 ..     520     587 .. 0.57
   5 !   16.9   3.3     6e-06    0.0057      24      84 ..     605     665 ..     598     677 .. 0.66
   6 ?    3.5   4.3      0.09        84      24      88 ..     675     739 ..     670     740 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.071
                            DUF948  26 ktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavad 79 
                                       + +d++++++++  +++++  +e+e++ a++++l + ++ k ++   +++ +ad
  gi|336253216|ref|YP_004596323.1| 354 DGFDSMRDSLQTQIEETTQAREEAEAARAEAERLNDHLEAKADEYSDVMQTAAD 407
                                       345555555555556667777899999999999999999999999999999886 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0045
                            DUF948  49 vedllakvnelledvneklekvdplteavadlgesvs 85 
                                       ++++ a+ n++ ++++  +++v+++ ++va+++e v 
  gi|336253216|ref|YP_004596323.1| 423 MTEIAAEFNDMIAEIEATTAEVKSFATEVATASEEVT 459
                                       6788888899999999999999999999999998875 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0006
                            DUF948  32 aatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       ++ +++   qv + ++e+ +  +  n+ l+ v+++++ + + +e++a  +++v+el 
  gi|336253216|ref|YP_004596323.1| 462 SEEVRSASGQVAESIQEISEGADRQNDSLQSVTQEMNGLSTTIEEIAASSNQVAELA 518
                                       677888889999999999999999999999999999999999999999999999885 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.5
                            DUF948  42 vdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                       +++i +++e +++++++    ++e+++++d l e + +++e+ 
  gi|336253216|ref|YP_004596323.1| 539 MQEIETDSESAVEEIER----LEEEMAQIDDLLEFITEVAEQT 577
                                       44444444444444444....5556666666665555555544 PP

  == domain 5  score: 16.9 bits;  conditional E-value: 6e-06
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                       +k++++ ++++ +++e+++++i ++++++ ++v+++ + v+e++++v++  +a+ ++++  
  gi|336253216|ref|YP_004596323.1| 605 VKELAEDTREAAADIEDRLEQIKEQTDRTATEVQRTSDRVSEHTDSVERAADALDEIADYA 665
                                       5666667777777777777777777777777777777777777777777777766665544 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.09
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       +++  de aa+ +++   vd +   +e++ ++++++++  +e++ ++ ++  ++++l++  s+l+
  gi|336253216|ref|YP_004596323.1| 675 ISNASDEQAASTQQVVAMVDDVAAIAEQTSSESETVAAAAEEQTTALTEVSRSAGELANRASHLS 739
                                       566778889999999999999999999999999999999999**************999999986 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   4.2   2.1e-06     0.002     165     323 ..     296     558 ..     291     589 .. 0.65
   2 ?    2.6   7.4     0.055        52     195     328 ..     591     720 ..     578     735 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.1e-06
                             LMBR1 165 slantwGlvllilllGyGl.velPrslwr...........................................eiksd 197
                                           t G+vlli l G G+   + rs+ r                                           e++++
  gi|336253216|ref|YP_004596323.1| 296 GTFATAGAVLLIGLVGAGFgWNTSRSIDRlttkaarmeegdldvdldspridsigrlydgfdsmrdslqtqiEETTQ 372
                                       566899*************5466788888*******************************************9**** PP

                             LMBR1 198 ldeelkklyfeaaklntekeeae..............................................reledllk 228
                                         ee +++++ea++ln+ +e +                                                       
  gi|336253216|ref|YP_004596323.1| 373 AREEAEAARAEAERLNDHLEAKAdeysdvmqtaadgdltarmdpeseneamteiaaefndmiaeieattA------- 442
                                       ****************999999945555555555555555555555555555555333333333333331....... PP

                             LMBR1 229 evkklrksisesdplrkyleeilk.......................kvPeeiaeklks.................. 264
                                                              +                       +          +                  
  gi|336253216|ref|YP_004596323.1| 443 -----------------------EvksfatevataseevtasseevrS----------Asgqvaesiqeisegadrq 486
                                       .......................0222222222222222222222220..........0222222222333333334 PP

                             LMBR1 265 ............nenkteeslaklekqlikalqkrertekqwkrllekale.lediiknksskekefksses 323
                                                   + + t e++a + +q+ +  +++++t ++ +++ ++a+e +++i  +++s+ +e++++e+
  gi|336253216|ref|YP_004596323.1| 487 ndslqsvtqemnGLSTTIEEIAASSNQVAELAERTAETGERGREAAQEAIEgMQEIETDSESAVEEIERLEE 558
                                       444555655575556688888888888888889999998888888888843244455555555444444433 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.055
                             LMBR1 195 ksdldeelkklyfeaaklntekeeaereledllkevkklrksisesdp.lrkyleeilkkvPeeiaeklksnenkte 270
                                       +s+++e ++++  e+++l ++  ea  ++ed l+++k++++++  + +  ++ ++e  ++v    a+       + +
  gi|336253216|ref|YP_004596323.1| 591 SSSSNEGFSAVAGEVKELAEDTREAAADIEDRLEQIKEQTDRTATEVQrTSDRVSEHTDSVERA-AD----ALDEIA 662
                                       7888889999999999999999999999999999999999999777753446666666655442.22....222233 PP

                             LMBR1 271 eslakle...kqlikalqkrertekqwkrllekalelediiknksskekefkssessrrge 328
                                       ++ ++ +   +++ +a+ +++ + +q   +++ +    +i+++ ss+++ +    +++++ 
  gi|336253216|ref|YP_004596323.1| 663 DYATETNtgvQEISNASDEQAASTQQVVAMVDDV---AAIAEQTSSESETVAAAAEEQTTA 720
                                       3333333122456666666777777777777766...788888888888877766644443 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.3      0.32     3e+02      35      70 ..     362     397 ..     354     407 .. 0.77
   2 ?   11.4   5.5   0.00025      0.24       9      95 ..     420     507 ..     413     507 .. 0.77
   3 ?    9.1   7.5    0.0013       1.2       5     101 ..     483     576 ..     480     581 .. 0.87
   4 ?    7.7   2.0    0.0036       3.4       2      58 ..     529     585 ..     528     597 .. 0.92
   5 ?   12.0   3.3   0.00016      0.15       4      61 ..     601     658 ..     598     668 .. 0.76
   6 ?    1.7   5.6      0.25   2.4e+02       9      68 ..     683     735 ..     657     751 .. 0.42

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.32
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTT CS
                        Laminin_II  35 einrsveetnekvkdankairdArrsvkkLeklapq 70 
                                       ++++++eet++  ++a  a ++A+r   +Le +a++
  gi|336253216|ref|YP_004596323.1| 362 SLQTQIEETTQAREEAEAARAEAERLNDHLEAKADE 397
                                       577888888888888888888888888888888775 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsv....kkLeklapqLldklkelkql 81 
                                       ne ++e+ +  +++ +++e t +++++++++v+   e+v ++++ +r+A+ +v    +++ + a++  d l+++ q 
  gi|336253216|ref|YP_004596323.1| 420 NEAMTEIAAEFNDMIAEIEATTAEVKSFATEVATASEEVTASSEEVRSASGQVaesiQEISEGADRQNDSLQSVTQE 496
                                       78888888889999999999999999999999999999999999999887655222256777788888888888777 PP

                                       HHH...HHHHHHHH CS
                        Laminin_II  82 eeassslsdnisei 95 
                                        ++   ls  i+ei
  gi|336253216|ref|YP_004596323.1| 497 MNG---LSTTIEEI 507
                                       777...88888876 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       a+  n+++++v + +++ls+ +e++ ++ +++++ +e+t e  +   +a ++A + ++++e   +  ++ +++l++ 
  gi|336253216|ref|YP_004596323.1| 483 ADRQNDSLQSVTQEMNGLSTTIEEIAASSNQVAELAERTAETGERGREAAQEAIEGMQEIETDSESAVEEIERLEEE 559
                                       667799**************************************************************999999988 PP

                                       HHH...HHHHHHHHHHHHHH CS
                        Laminin_II  82 eeassslsdniseikelIaq 101
                                         +   + d ++ i e  +q
  gi|336253216|ref|YP_004596323.1| 560 MAQ---IDDLLEFITEVAEQ 576
                                       777...55555555555444 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0036
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdAr 58 
                                       +e a+ea e ++e++ + +   +++e+++e++ +i++ +e ++e++++ n+    A+
  gi|336253216|ref|YP_004596323.1| 529 REAAQEAIEGMQEIETDSESAVEEIERLEEEMAQIDDLLEFITEVAEQTNMLALNAN 585
                                       6889**********************************************9988886 PP

  == domain 5  score: 12.0 bits;  conditional E-value: 0.00016
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsv 61 
                                       +a e++e a+ + e  a+++ +le++ke+  + +++v++t + v++ +  ++ A ++ 
  gi|336253216|ref|YP_004596323.1| 601 VAGEVKELAEDTREAAADIEDRLEQIKEQTDRTATEVQRTSDRVSEHTDSVERAADAL 658
                                       6778888888888888888888888888888888888888888887777666665554 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.25
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TT CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekla 68 
                                         ++++v + + ++++  e+t+++ +++++        +++ ++a+ +++rs  +L + a
  gi|336253216|ref|YP_004596323.1| 683 AASTQQVVAMVDDVAAIAEQTSSESETVAAA-------AEEQTTALTEVSRSAGELANRA 735
                                       2223333333333333333333333333333.......3333333333333333333333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   4.2      0.23   2.2e+02     203     250 ..     358     405 ..     353     433 .. 0.68
   2 ?    9.3  17.5    0.0005      0.47     137     302 ..     423     586 ..     419     594 .. 0.84
   3 ?   10.4  12.8   0.00022      0.21     153     283 ..     575     704 ..     566     727 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.23
                              Spc7 203 elreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeei 250
                                       ++r++l+++ +e  + ++e +  +++ e+l++ +e+ ++++s++++  
  gi|336253216|ref|YP_004596323.1| 358 SMRDSLQTQIEETTQAREEAEAARAEAERLNDHLEAKADEYSDVMQTA 405
                                       567777777777777777777777777777777777777777766654 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0005
                              Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelae 210
                                       + ++  + ++ ++++e+  +++++   e+ ++ +e+++  +e+++   +  e  +e+++    ++++L+++ +e++ 
  gi|336253216|ref|YP_004596323.1| 423 MTEIAAEFNDMIAEIEATTAEVKSFATEVATASEEVTASSEEVRSASGQVAESIQEISEgadRQNDSLQSVTQEMNG 499
                                       56777888888999999999999999999999999999999999998888887666665543779************ PP

                              Spc7 211 lkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkiv 287
                                       l+++ie    e+a   +q++el+e+ +e+ e+ +e+ +e  e  + +e   ++  +e++rl+ee+ ++++l+++ i+
  gi|336253216|ref|YP_004596323.1| 500 LSTTIE----EIAASSNQVAELAERTAETGERGREAAQEAIEGMQEIETDSESAVEEIERLEEEMAQIDDLLEF-IT 571
                                       ******....******************999999988888889999999********************99987.44 PP

                              Spc7 288 slsgstleltyrsel 302
                                       ++ ++t  l+++ ++
  gi|336253216|ref|YP_004596323.1| 572 EVAEQTNMLALNANI 586
                                       555555555555555 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00022
                              Spc7 153 edkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeql 229
                                       e+ ++L+ + +   +   + +e ++++  e+++l e  +e ++  +++Le+++e+ ++  +e+++ +++++e ++ +
  gi|336253216|ref|YP_004596323.1| 575 EQTNMLALNANIEASRSSSSNEGFSAVAGEVKELAEDTREAAADIEDRLEQIKEQTDRTATEVQRTSDRVSEHTDSV 651
                                       55555555555555566667778899999*******999977777******************************** PP

                              Spc7 230 eeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltg 283
                                       e+ +++++e+++  +e+++ ++e  +  +e+   s+++v ++ + v a+ e+t 
  gi|336253216|ref|YP_004596323.1| 652 ERAADALDEIADYATETNTGVQEISNASDEQAA-STQQVVAMVDDVAAIAEQTS 704
                                       **********************99999997665.55667778888888888776 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.51   4.8e+02      68     104 ..     356     392 ..     347     407 .. 0.70
   2 ?    1.2   0.2      0.39   3.7e+02      64     106 ..     410     451 ..     380     458 .. 0.62
   3 ?   14.5   2.5   2.8e-05     0.026      37     111 ..     445     519 ..     439     524 .. 0.92
   4 ?    3.0   1.5       0.1        99      76     121 ..     519     564 ..     511     579 .. 0.76
   5 ?    8.4   2.3    0.0023       2.2      43     121 ..     598     676 ..     588     678 .. 0.82
   6 ?    6.8   5.6    0.0068       6.4      39     113 ..     619     696 ..     612     702 .. 0.81
   7 ?    3.2   1.5     0.087        83      69     120 ..     673     724 ..     666     747 .. 0.51

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.51
                           DUF1664  68 idrvdkkldeqkeiskeikeevtevredlseigedve 104
                                        d++ ++l+ q+e +++ +ee +++r + +++++ +e
  gi|336253216|ref|YP_004596323.1| 356 FDSMRDSLQTQIEETTQAREEAEAARAEAERLNDHLE 392
                                       5667777777777777777777777777777666554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.39
                           DUF1664  64 Lssridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                                       L++r+d  +++ ++++ei++e ++ ++e++  ++e+++  ++v
  gi|336253216|ref|YP_004596323.1| 410 LTARMDP-ESENEAMTEIAAEFNDMIAEIEATTAEVKSFATEV 451
                                       5555544.33446666666666666666666666665544444 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2.8e-05
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       +s++  v++ s++++  se+++++  + ++ i+++ +  d q++  +++++e++ ++  ++ei   +++v e+ e
  gi|336253216|ref|YP_004596323.1| 445 KSFATEVATASEEVTASSEEVRSASGQVAESIQEISEGADRQNDSLQSVTQEMNGLSTTIEEIAASSNQVAELAE 519
                                       6888899999999*******************************************************9998766 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.1
                           DUF1664  76 deqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       + ++e+ +  +e  +e+ e+++ei++d+es  e +e le+++++i+
  gi|336253216|ref|YP_004596323.1| 519 ERTAETGERGREAAQEAIEGMQEIETDSESAVEEIERLEEEMAQID 564
                                       5556666666777778888888888888888888888888888876 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0023
                           DUF1664  43 vesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                        + v+ +++++ e+ +++  ++++r++++ ++ d ++   + +++ v+e  + +++  + ++++ +  ++ ++ +++
  gi|336253216|ref|YP_004596323.1| 598 FSAVAGEVKELAEDTREAAADIEDRLEQIKEQTDRTATEVQRTSDRVSEHTDSVERAADALDEIADYATETNTGVQE 674
                                       56677788888888899999999999999999999999999999999999999999999999998888888887777 PP

                           DUF1664 120 ie 121
                                       i+
  gi|336253216|ref|YP_004596323.1| 675 IS 676
                                       75 PP

  == domain 6  score: 6.8 bits;  conditional E-value: 0.0068
                           DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvd...kkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                       ++d +e++ +q ++  +++++t ++ s++ d+v+   + lde ++ ++e++  v+e+++  +e     ++v ++v +
  gi|336253216|ref|YP_004596323.1| 619 IEDRLEQIKEQTDRTATEVQRTSDRVSEHTDSVEraaDALDEIADYATETNTGVQEISNASDEQAASTQQVVAMVDD 695
                                       6788899999999999******9999988777761115677788888999999999999999999999999999876 PP

                           DUF1664 113 l 113
                                       +
  gi|336253216|ref|YP_004596323.1| 696 V 696
                                       5 PP

  == domain 7  score: 3.2 bits;  conditional E-value: 0.087
                           DUF1664  69 drvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       +++ +  deq++ ++++ + v++v    +++++++e+v +a e+  + l+++
  gi|336253216|ref|YP_004596323.1| 673 QEISNASDEQAASTQQVVAMVDDVAAIAEQTSSESETVAAAAEEQTTALTEV 724
                                       4444444444555555544454444444455555554444444433333333 PP

>> GM_CSF  Granulocyte-macrophage colony-stimulating factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.1    0.0014       1.3       3      53 ..     635     685 ..     633     722 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                                       X----TTT-TTHHHHHHHHHHHHHHH----HHHHTSEEEEESS--BSSS-- CS
                            GM_CSF   3 trspspvtrpwkhvdaikealsllnessdlaavlneevevvseefdlqept 53 
                                       t+   ++ r ++h d+++ a + l+e  d a++ n  v+ +s+  d q  +
  gi|336253216|ref|YP_004596323.1| 635 TEVQRTSDRVSEHTDSVERAADALDEIADYATETNTGVQEISNASDEQAAS 685
                                       5667788999*********************************99988765 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.9    0.0018       1.7      21      80 ..     369     448 ..     356     452 .. 0.68
   2 ?    9.5   0.5    0.0017       1.6       8      79 ..     430     500 ..     428     510 .. 0.61
   3 ?   12.3   3.1   0.00022      0.21       7      96 ..     492     579 ..     488     583 .. 0.84
   4 ?    6.1   3.3     0.019        18      14      72 ..     604     661 ..     598     675 .. 0.70
   5 ?    1.0   2.1       0.7   6.6e+02      23      57 ..     683     733 ..     665     755 .. 0.42

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                           DUF2203  21 elralrkeleeleeeleeakaeaekse....................aaeleaeleeleaeieelveeieelGvevk 77 
                                       e  ++r+e+e +++e e+ +++ e+++                     ++++++++e++ae++++++eie++ +evk
  gi|336253216|ref|YP_004596323.1| 369 ETTQAREEAEAARAEAERLNDHLEAKAdeysdvmqtaadgdltarmdPESENEAMTEIAAEFNDMIAEIEATTAEVK 445
                                       4444444444444444444444333333444455777778888877788889999********************** PP

                           DUF2203  78 dle 80 
                                       +++
  gi|336253216|ref|YP_004596323.1| 446 SFA 448
                                       985 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0017
                           DUF2203   8 AnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdl 79 
                                        n+++ +++ +++e+++ ++e+++++ee++++++e ++ +  + +++++e+++ +++  + ++++  e+ +l
  gi|336253216|ref|YP_004596323.1| 430 FNDMIAEIEATTAEVKSFATEVATASEEVTASSEEVRSAS-GQVAESIQEISEGADRQNDSLQSVTQEMNGL 500
                                       5788999999999999999999999999988888876554.3444444444444444444444433333333 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00022
                           DUF2203   7 eAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleagl 83 
                                         ++ +  l+ ++ee++a  ++++el+e+ +e+ ++ + ++a+e+ + ++e+e+  e++veeie+l  e+ +++  l
  gi|336253216|ref|YP_004596323.1| 492 SVTQEMNGLSTTIEEIAASSNQVAELAERTAETGERGR-EAAQEAIEGMQEIETDSESAVEEIERLEEEMAQID-DL 566
                                       55667778899999999999999999999999999875.4588889999***********************97.78 PP

                           DUF2203  84 vDFpakldgeevl 96 
                                       ++F +++ +++ +
  gi|336253216|ref|YP_004596323.1| 567 LEFITEVAEQTNM 579
                                       9999998887655 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.019
                           DUF2203  14 llkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieel 72 
                                       ++kel e+ r++++++e++ e+++e++++++++  ++   +++e ++++e++ + ++e+
  gi|336253216|ref|YP_004596323.1| 604 EVKELAEDTREAAADIEDRLEQIKEQTDRTATE-VQRTSDRVSEHTDSVERAADALDEI 661
                                       689999999999999999999999999987654.5555555555555555554444443 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.7
                           DUF2203  23 ralrkeleeleeeleeakaeaekse................aaeleaelee 57 
                                       +a ++++  ++++++++ +++++++                 ++ + el++
  gi|336253216|ref|YP_004596323.1| 683 AASTQQVVAMVDDVAAIAEQTSSESetvaaaaeeqttalteVSRSAGELAN 733
                                       444444444444444444333322222111111111111113333333333 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7  25.0      0.73   6.9e+02      17     208 ..     369     572 ..     358     580 .. 0.69
   2 ?   13.0  23.0   2.7e-05     0.025      10     223 ..     523     745 ..     515     747 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.73
                               MAD  17 elkqkelehkrarielekkasalkrqleeesdrnq.....elqkrikllekreeeke.....ealreqiElarlkkk 83 
                                       e  q   e + ar+e+e+    l+ + +e sd +q     +l++r+    ++e+  e     + + ++iE   +  k
  gi|336253216|ref|YP_004596323.1| 369 ETTQAREEAEAARAEAERLNDHLEAKADEYSDVMQtaadgDLTARMDPESENEAMTEiaaefNDMIAEIEATTAEVK 445
                                       44444455555555555554444444444444433222227888888777777544411112456688888877655 PP

                               MAD  84 .nlealnkkekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqliqqle 159
                                        + +++  + +e +++ +e+r  + ++ + ++e  + + +q+  l++ ++e++ l    ++  +  +++ +l +   
  gi|336253216|ref|YP_004596323.1| 446 sFATEVATASEEVTASSEEVRSASGQVAESIQEISEGADRQNDSLQSVTQEMNGLSTTIEEIAASSNQVAELAERTA 522
                                       156789999999999**********************************************9999999999996665 PP

                               MAD 160 kkqkelaeaeqrikeLefeiqs.qeddslivknskselaripelekeler 208
                                       +  +   ea q   e  +ei+   e+  ++++  ++e+a+i +l + + +
  gi|336253216|ref|YP_004596323.1| 523 ETGERGREAAQEAIEGMQEIETdSESAVEEIERLEEEMAQIDDLLEFITE 572
                                       55555555555555555666663667778999999999999999766555 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.7e-05
                               MAD  10 aleqlknelkqkelehkrarielekkasalkrqleeesdrnqelqkrikllekreeekeealreqiElarlkkknl. 85 
                                       +  +  +e +q+++e  ++     + a +  + leee+++  +l++ i+++ ++   +  al+++iE +r+   n+ 
  gi|336253216|ref|YP_004596323.1| 523 ETGERGREAAQEAIEGMQEIETDSESAVEEIERLEEEMAQIDDLLEFITEVAEQT--NMLALNANIEASRSSSSNEg 597
                                       555566888999999988887777777888999***************9998765..56789999999998776652 PP

                               MAD  86 .....ealnkkekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqliqq 157
                                             ++++++++  +  a++++  +++k+++ + +++++++   +se++  +e+   +ld+    ++e++  +q+
  gi|336253216|ref|YP_004596323.1| 598 fsavaGEVKELAEDTREAAADIEDRLEQIKEQTDRTATEVQRTSDRVSEHTDSVERAADALDEIADYATETNTGVQE 674
                                       22221467778888888899999999999999********************************************* PP

                               MAD 158 lekkqkelaeaeqrikeLefeiqs....qeddslivknsksel.aripelekelerlreenkklnelkenk 223
                                         ++++e a++ q++  +   ++      +++s+ v ++ +e+   + e+ +   +l ++ ++l+e+ +n 
  gi|336253216|ref|YP_004596323.1| 675 ISNASDEQAASTQQVVAMVDDVAAiaeqTSSESETVAAAAEEQtTALTEVSRSAGELANRASHLSETLDNF 745
                                       **************98887766655553455667777777777799*******************998885 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       6.8   6.4e+03      40      62 ..     365     387 ..     351     396 .. 0.49
   2 ?    2.0   0.1      0.24   2.3e+02      44      70 ..     475     501 ..     432     526 .. 0.66
   3 ?   10.2   1.0   0.00063       0.6      38      74 ..     532     568 ..     530     573 .. 0.93
   4 ?    2.9   0.1      0.12   1.1e+02      21      46 ..     609     634 ..     598     660 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.8
                              Med9  40 elirelpgidrsveeqeaeieel 62 
                                       ++i+e     +  e   ae e l
  gi|336253216|ref|YP_004596323.1| 365 TQIEETTQAREEAEAARAEAERL 387
                                       33333333333333444444444 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.24
                              Med9  44 elpgidrsveeqeaeieeleeqlakKr 70 
                                       ++++i++  + q++ +++  +++    
  gi|336253216|ref|YP_004596323.1| 475 SIQEISEGADRQNDSLQSVTQEMNGLS 501
                                       333344444455555444444443333 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00063
                              Med9  38 arelirelpgidrsveeqeaeieeleeqlakKrelLk 74 
                                       a e+i+ +++i+   e+  +eie lee++a+  +lL+
  gi|336253216|ref|YP_004596323.1| 532 AQEAIEGMQEIETDSESAVEEIERLEEEMAQIDDLLE 568
                                       789****************************999996 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.12
                              Med9  21 skdletktgelrhkLkkarelirelp 46 
                                       ++d+  +++++ ++L++++e+ +   
  gi|336253216|ref|YP_004596323.1| 609 AEDTREAAADIEDRLEQIKEQTDRTA 634
                                       67888899999999999999987654 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.035        33       5      63 ..     346     405 ..     343     439 .. 0.80
   2 ?    4.5   0.5     0.046        43      12      64 ..     441     501 ..     428     521 .. 0.58
   3 ?    0.2   0.2         1   9.6e+02      14      61 ..     513     558 ..     500     592 .. 0.59
   4 ?    0.3   6.2         1   9.4e+02      11      66 ..     622     685 ..     551     747 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.035
                        Syntaxin_2   5 lqkinsnvstleklvkqLgtk.kdteelreklhelieeinelikktnellkklsqldnss 63 
                                       + +i ++   +++++++L+t+  +t++ re+++  + e+ +l    +++  + s + ++ 
  gi|336253216|ref|YP_004596323.1| 346 IDSIGRLYDGFDSMRDSLQTQiEETTQAREEAEAARAEAERLNDHLEAKADEYSDVMQTA 405
                                       7789999999***********668********9999999999888888877777766655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.046
                        Syntaxin_2  12 vstleklvkqLgtkkd.....teelr...eklhelieeinelikktnellkklsqldnsss 64 
                                       + + +++ + + t+ +     +ee+r    ++ e+i+ei+e + + n++l++++q  n +s
  gi|336253216|ref|YP_004596323.1| 441 TAEVKSFATEVATASEevtasSEEVRsasGQVAESIQEISEGADRQNDSLQSVTQEMNGLS 501
                                       4444455555555533333334444444456677777777777777777777766665555 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1
                        Syntaxin_2  14 tleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldn 61 
                                       +  +l +        e+ re ++e ie ++e+ ++ ++ ++++++l++
  gi|336253216|ref|YP_004596323.1| 513 QVAELAERTAE--TGERGREAAQEAIEGMQEIETDSESAVEEIERLEE 558
                                       44444443222..23455555566666666666666655555555554 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 1
                        Syntaxin_2  11 nvstleklvkqLgtk....kdteelr......eklhelieeinelikktnellkklsqldnsssds 66 
                                        + +++++++   t        +++       e++ +  +ei + +++tn  ++++s+ ++ +  s
  gi|336253216|ref|YP_004596323.1| 622 RLEQIKEQTDRTATEvqrtS--DRVSehtdsvERAADALDEIADYATETNTGVQEISNASDEQAAS 685
                                       33444444444444432211..11112233336667777777777777777777777777666555 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 ?    8.5   1.4    0.0023       2.2      49      93 ..     357     401 ..     339     407 .. 0.88
   2 ?    4.8   1.3     0.033        31      52      99 ..     419     467 ..     409     481 .. 0.59
   3 ?    7.8   7.3     0.004       3.7      23     100 ..     482     563 ..     470     571 .. 0.88
   4 ?    2.1   2.5      0.24   2.3e+02      46      77 ..     606     638 ..     581     662 .. 0.47
   5 ?    2.7   1.8      0.15   1.4e+02      50     103 ..     666     723 ..     646     728 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  49 qaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkel 93 
                                        + r +l+ +I++  ++ e+ae+ +ae++ l++ l+a+ +e +++
  gi|336253216|ref|YP_004596323.1| 357 DSMRDSLQTQIEETTQAREEAEAARAEAERLNDHLEAKADEYSDV 401
                                       56788999****************************999988776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.033
                                       HHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  52 rNelskeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaelek 99 
                                        Ne+  eI+   ++  +++e+  aevk+  +e++++++e+++ ++e+ +
  gi|336253216|ref|YP_004596323.1| 419 ENEAMTEIAAEFNDMiAEIEATTAEVKSFATEVATASEEVTASSEEVRS 467
                                       4555555555555555666666666666666666666666665555543 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.004
                                       CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  23 edkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkelea 95 
                                       +++ + d+l ++ +++  l +++ee+ a +N++++  ++  + +    e a+e i+ ++e+ ++ + + +e + le+
  gi|336253216|ref|YP_004596323.1| 482 GADRQNDSLQSVTQEMNGLSTTIEEIAASSNQVAELAERTAETGergrEAAQEAIEGMQEIETDSESAVEEIERLEE 558
                                       566677999999**********************9999999999999***********************9999999 PP

                                       HHHHH CS
                      Seryl_tRNA_N  96 elekl 100
                                       e+ ++
  gi|336253216|ref|YP_004596323.1| 559 EMAQI 563
                                       99775 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCH CS
                      Seryl_tRNA_N  46 eelqaerNelskeIgkakkkk.edaeeliaevk 77 
                                        el +   e+++ I+   ++  e++++   ev+
  gi|336253216|ref|YP_004596323.1| 606 KELAEDTREAAADIEDRLEQIkEQTDRTATEVQ 638
                                       222222222222222222221133333333333 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.15
                                       HHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                      Seryl_tRNA_N  50 aerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekllla 103
                                       +e N+  +eI++a++++    ++  +++++v+++ e+++  +++++++ +e++++l++
  gi|336253216|ref|YP_004596323.1| 666 TETNTGVQEISNASDEQaastQQVVAMVDDVAAIAEQTSSESETVAAAAEEQTTALTE 723
                                       6777778889999988886667777788888888888888888888888888887765 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0  19.5      0.67   6.4e+02      25     138 ..     364     477 ..     351     492 .. 0.67
   2 ?    3.7  17.0     0.048        45      26     128 ..     474     575 ..     469     618 .. 0.73
   3 ?   14.0  15.5   3.6e-05     0.034       7     134 ..     616     743 ..     607     804 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.67
                               ERM  25 qeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserk 101
                                       q + +e ++  e+ +  + +ae+  + Le+ka e    +q  +          e+ ++ ++e  +e++++  e e+ 
  gi|336253216|ref|YP_004596323.1| 364 QTQIEETTQAREEAEAARAEAERLNDHLEAKADEYSDVMQTAADGDLTARMDPESENEAMTEIAAEFNDMIAEIEAT 440
                                       33344444444444444444444455667777777777777777777777777888888889999999999999999 PP

                               ERM 102 eeeaerLkeeleeareaeeeakekllealstpskses 138
                                        +e++   +e+  a e+ +  +e+++ a+ + ++s++
  gi|336253216|ref|YP_004596323.1| 441 TAEVKSFATEVATASEEVTASSEEVRSASGQVAESIQ 477
                                       9999999999999999999999998888888865544 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.048
                               ERM  26 eaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserke 102
                                       e  +e  e a++ + +++ + +e++ L+   +e+ +  ++++e ae+++e+ e+  + ++ea + ++++e +se   
  gi|336253216|ref|YP_004596323.1| 474 ESIQEISEGADRQNDSLQSVTQEMNGLSTTIEEIAASSNQVAELAERTAETGERGREAAQEAIEGMQEIETDSESAV 550
                                       6678888899999999999999******************************************************* PP

                               ERM 103 eeaerLkeeleeareaeeeakeklle 128
                                       ee erL+ee+ ++ + +e  +e + e
  gi|336253216|ref|YP_004596323.1| 551 EEIERLEEEMAQIDDLLEFITE-VAE 575
                                       ********99998887743332.222 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3.6e-05
                               ERM   7 kreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerk 83 
                                        + +e+rL+q++e+++++  + ++  +++ +   + +ra  + ++ +  a+e ++  q++  ++ +++++ +++ + 
  gi|336253216|ref|YP_004596323.1| 616 AADIEDRLEQIKEQTDRTATEVQRTSDRVSEHTDSVERAADALDEIADYATETNTGVQEISNASDEQAASTQQVVAM 692
                                       56799************************************************************************ PP

                               ERM  84 lreaeleaarleeeserkeeeaerLkeeleeareaeeeakekllealstps 134
                                       ++++ + a++  +ese  ++ ae+  + l e+ ++  e +++  ++++t  
  gi|336253216|ref|YP_004596323.1| 693 VDDVAAIAEQTSSESETVAAAAEEQTTALTEVSRSAGELANRASHLSETLD 743
                                       *****************9999999999999999998776666655555552 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   2.0       0.1        97      14     113 ..     363     465 ..     351     471 .. 0.55
   2 ?    9.4   0.6    0.0006      0.56       5      86 ..     428     508 ..     424     510 .. 0.89
   3 ?   10.8   3.0   0.00022       0.2       3      91 ..     489     576 ..     487     593 .. 0.89
   4 ?    6.0   3.1    0.0065       6.1       8      82 ..     606     686 ..     595     697 .. 0.64
   5 ?    1.6   0.8      0.14   1.4e+02       6      61 ..     695     750 ..     673     772 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.1
                             TMPIT  14 leetakeykqkleelsklqs...kcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeves 87 
                                       l+++ +e +q  ee ++      ++  +++ +  +++++ ++  + + +++ + e+e e ++e  +e + +++e+e+
  gi|336253216|ref|YP_004596323.1| 363 LQTQIEETTQAREEAEAARAeaeRLNDHLEAKADEYSDVMQTAADGDLTARMDPESENEAMTEIAAEFNDMIAEIEA 439
                                       34444444444444444444000444444444444444444444444444455566666777777777788888888 PP

                             TMPIT  88 llpkknglylklvlGnvnvsllnkqd 113
                                       +  + +++  ++   + +v++ +++ 
  gi|336253216|ref|YP_004596323.1| 440 TTAEVKSFATEVATASEEVTASSEEV 465
                                       86666777777777777777766665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0006
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkv 81 
                                       +e+++ + e+e+t  e+k+   e+++  ++++ + ++ +    ++ +s++++++ + +++++ ++++++e++  +++
  gi|336253216|ref|YP_004596323.1| 428 AEFNDMIAEIEATTAEVKSFATEVATASEEVTASSEEVRSASGQVAESIQEISEGA-DRQNDSLQSVTQEMNGLSTT 503
                                       577888899999****************************************9996.68999999999999999999 PP

                             TMPIT  82 lkeve 86 
                                       ++e++
  gi|336253216|ref|YP_004596323.1| 504 IEEIA 508
                                       99886 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00022
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79 
                                       +++++++e++ l++t +e+ ++++++++l ++++++ ++ ++ ++e  + +++++++ +e+  ee+e+l+ee+++++
  gi|336253216|ref|YP_004596323.1| 489 SLQSVTQEMNGLSTTIEEIAASSNQVAELAERTAETGERGREAAQEAIEGMQEIETD-SESAVEEIERLEEEMAQID 564
                                       578999*************************************************99.589999***********99 PP

                             TMPIT  80 kvlkevesllpk 91 
                                         l+ + ++  +
  gi|336253216|ref|YP_004596323.1| 565 DLLEFITEVAEQ 576
                                       998877666444 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0065
                             TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkeelker 78 
                                       ++ +++ +e+a  ++ +le+++++ +++++e+++ + r++e ++s+++   +++      +e+++ v+e+++  +e+
  gi|336253216|ref|YP_004596323.1| 606 KELAEDTREAAADIEDRLEQIKEQTDRTATEVQRTSDRVSEHTDSVERAADALDeiadyaTETNTGVQEISNASDEQ 682
                                       33344445566667778888888888888888888888888888888887776544444455555555555555555 PP

                             TMPIT  79 kkvl 82 
                                        ++ 
  gi|336253216|ref|YP_004596323.1| 683 AAST 686
                                       5444 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.14
                             TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk 61 
                                       +++  +++ +++ +++ +  ee ++  +++s+++ +  +r+++l+++l++++++++
  gi|336253216|ref|YP_004596323.1| 695 DVAAIAEQTSSESETVAAAAEEQTTALTEVSRSAGELANRASHLSETLDNFETDAD 750
                                       34444455555666667777777777777777777777777777777777777643 PP

>> XH  XH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.1      0.22   2.1e+02      66     126 ..     516     575 ..     493     579 .. 0.83
   2 ?    6.7   0.3    0.0066       6.3      80     123 ..     652     694 ..     606     702 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.22
                                XH  66 kLkeLkeeyGeevykaVtkallelneynpsgryivselWnfkegrkAtlkevvdvllkqlk 126
                                       +L e  +e Ge+  +a ++a++ ++e++++    v+e+  ++e+  A++ ++++++++  +
  gi|336253216|ref|YP_004596323.1| 516 ELAERTAETGERGREAAQEAIEGMQEIETDSESAVEEIERLEEE-MAQIDDLLEFITEVAE 575
                                       5666678999999**************99999999999777665.7999999999987655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0066
                                XH  80 kaVtkallelneynpsgryivselWnfkegrkAtlkevvdvllk 123
                                       +  ++al e+ +y ++  + v+e+ n  +++ A+ ++vv+++ +
  gi|336253216|ref|YP_004596323.1| 652 ERAADALDEIADYATETNTGVQEISNASDEQAASTQQVVAMV-D 694
                                       344789*********************************954.4 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 ?   -1.2   0.2       2.3   2.1e+03      51      65 ..     381     395 ..     351     444 .. 0.47
   2 ?    2.6   0.3      0.15   1.4e+02      26      84 ..     423     481 ..     417     492 .. 0.51
   3 ?    8.3   3.4    0.0027       2.5      31     124 ..     491     585 ..     483     594 .. 0.73
   4 ?    7.2   0.9    0.0057       5.3      23      78 ..     602     657 ..     600     667 .. 0.82
   5 ?    4.5   1.1     0.039        37      25      90 ..     660     724 ..     655     747 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHHH CS
                         Fib_alpha  51 tkeaeelvkeikdsl 65 
                                         eae+l  +++ + 
  gi|336253216|ref|YP_004596323.1| 381 RAEAERLNDHLEAKA 395
                                       333333322222222 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.15
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikkssk 84 
                                       +++   ++++ ++++e + +e+++  +e+ + ++e++ s +e  + + +  + i+++s+
  gi|336253216|ref|YP_004596323.1| 423 MTEIAAEFNDMIAEIEATTAEVKSFATEVATASEEVTASSEEVRSASGQVAESIQEISE 481
                                       44445555555555555555555555555555555555544444444444455555444 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0027
                                       CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHCCCHHHHHHHCCHHH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn....dnvikksskeleeeilrlketidaqesn 103
                                       ++v+++++ l  ++eei+ s++++ el +++ ++ ++  + +++     +++ ++s++ +e ei+rl+e++ +    
  gi|336253216|ref|YP_004596323.1| 491 QSVTQEMNGLSTTIEEIAASSNQVAELAERTAETGERGREAAQEAiegmQEIETDSESAVE-EIERLEEEMAQIDDL 566
                                       7899*************************99999888777777763344666666777777.777777777666666 PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 104 irvLqnvlesneqkiqkLeqd 124
                                       ++++++v e+   ++  L+ +
  gi|336253216|ref|YP_004596323.1| 567 LEFITEVAEQ--TNMLALNAN 585
                                       6666666554..345555555 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0057
                                       HHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  23 qdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnv 78 
                                       ++ +++  +d+++  +++e++le+i+++t  + + v++++d + e+  s +    +
  gi|336253216|ref|YP_004596323.1| 602 AGEVKELAEDTREAAADIEDRLEQIKEQTDRTATEVQRTSDRVSEHTDSVERAADA 657
                                       5666777889999999*************************999999887765544 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.039
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeei 90 
                                        + +y +++++ ++++ n  +e + st+++  +v ++  + +++ ++++    + ++ ++ l  e+
  gi|336253216|ref|YP_004596323.1| 660 EIADYATETNTGVQEISNASDEQAASTQQVVAMVDDVAAIAEQTSSESETVAAAAEEQTTALT-EV 724
                                       345566666666666666666666666666666666666655555555544444444444444.33 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3      0.76   7.1e+02      37      54 ..     384     401 ..     356     456 .. 0.55
   2 ?    8.2   0.6    0.0036       3.4      14      61 ..     452     507 ..     446     520 .. 0.58
   3 ?    2.7   0.8      0.19   1.8e+02      28      66 ..     530     568 ..     500     584 .. 0.62
   4 ?    3.2   0.2      0.13   1.2e+02      21      63 ..     599     642 ..     595     648 .. 0.79
   5 ?    9.3   1.5    0.0017       1.6      15      63 ..     629     677 ..     617     683 .. 0.87
   6 ?    0.5   0.9      0.92   8.7e+02      18      56 ..     687     726 ..     679     750 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.76
                           NPV_P10  37 vtelnekLdaqsaqLael 54 
                                        + ln++L+a +++  ++
  gi|336253216|ref|YP_004596323.1| 384 AERLNDHLEAKADEYSDV 401
                                       444555555554444433 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0036
                           NPV_P10  14 kavddkVdalqqqvddvqenl.pdvtelnekLdaqsaqLaelet.......kvenI 61 
                                       +  ++ V+a +++v + + ++ + ++e++e  d+q+++L+++ +       ++e+I
  gi|336253216|ref|YP_004596323.1| 452 ATASEEVTASSEEVRSASGQVaESIQEISEGADRQNDSLQSVTQemnglstTIEEI 507
                                       55566666666666555555413456666666666666666555222222266666 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.19
                           NPV_P10  28 ddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                       +  qe ++ ++e+++  ++  ++++ le+++ +I+d+L 
  gi|336253216|ref|YP_004596323.1| 530 EAAQEAIEGMQEIETDSESAVEEIERLEEEMAQIDDLLE 568
                                       445555666666666666666666666666666666665 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.13
                           NPV_P10  21 dalqqqvddvqenlpdv.telnekLdaqsaqLaeletkvenIqd 63 
                                       +a+  +v++++e+ ++   +++++L+++ +q +   t+v+  +d
  gi|336253216|ref|YP_004596323.1| 599 SAVAGEVKELAEDTREAaADIEDRLEQIKEQTDRTATEVQRTSD 642
                                       57788899999988764157999999999999999999987655 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.0017
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       ++d   + +q   d+v+e    v+   + Ld++++  +e +t v++I++
  gi|336253216|ref|YP_004596323.1| 629 QTDRTATEVQRTSDRVSEHTDSVERAADALDEIADYATETNTGVQEISN 677
                                       3566678889999**********************************86 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 0.92
                           NPV_P10  18 dkVdalqqqvddvqenlpd.vtelnekLdaqsaqLaelet 56 
                                       ++V a+ + v+ ++e+     + + +  ++q+++L+e++ 
  gi|336253216|ref|YP_004596323.1| 687 QQVVAMVDDVAAIAEQTSSeSETVAAAAEEQTTALTEVSR 726
                                       5677777777666665543034466677777777777765 PP

>> TMP_2  Prophage tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   3.4       2.4   2.3e+03     151     191 ..     421     460 ..     371     476 .. 0.70
   2 ?    4.1  14.3     0.035        33      69     196 ..     451     580 ..     417     587 .. 0.64
   3 ?    7.3  13.8    0.0036       3.4      89     197 ..     611     722 ..     597     728 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.4
                             TMP_2 151 ervakaaaelekatGqsvdetakelaklakdPvkaaeklne 191
                                       e ++++aae+++ +  ++++t++e +++a++ + a+e+++ 
  gi|336253216|ref|YP_004596323.1| 421 EAMTEIAAEFND-MIAEIEATTAEVKSFATEVATASEEVTA 460
                                       445555555554.5555666666666666665555555443 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.035
                             TMP_2  69 lisPltlaAaavgalalAyykgakearefnkaliltGnaaGlTasqLeamaesiaeaggtqaaaaealaalastGki 145
                                       + ++   ++a+   +  A  + a++ +e+ +     + +    +++++ ++ +i+e++ + +++ae++   a+tG+ 
  gi|336253216|ref|YP_004596323.1| 451 VATASEEVTASSEEVRSASGQVAESIQEISEGADRQNDSLQSVTQEMNGLSTTIEEIAASSNQVAELAERTAETGER 527
                                       44444434444445555555555555555555555555666667778888888888888888889999999999999 PP

                             TMP_2 146 ggeqlervakaaaelekatGqsvdetakelakla..kdPvkaaeklneqlhfL 196
                                       g+e+ +++++   e+e    ++v+e+ +  +++a  +d ++ +++++eq ++L
  gi|336253216|ref|YP_004596323.1| 528 GREAAQEAIEGMQEIETDSESAVEEIERLEEEMAqiDDLLEFITEVAEQTNML 580
                                       99999999999999998888888876433333321146667777777776666 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0036
                             TMP_2  89 kgakearefnkaliltGnaaGlTasqLeamaesiaeaggtqaaaaealaalastGkiggeqlervakaaaelekatG 165
                                       + ++ a +++  l ++ ++++ Ta ++++ +++++e + ++++aa+al ++a+ +  +++ ++++++a  e ++ t+
  gi|336253216|ref|YP_004596323.1| 611 DTREAAADIEDRLEQIKEQTDRTATEVQRTSDRVSEHTDSVERAADALDEIADYATETNTGVQEISNASDEQAASTQ 687
                                       556778889999999*************************************9999999999998888777666665 PP

                             TMP_2 166 q...svdetakelaklakdPvkaaeklneqlhfLt 197
                                       q    vd++a+  ++ +++    a++ +eq   Lt
  gi|336253216|ref|YP_004596323.1| 688 QvvaMVDDVAAIAEQTSSESETVAAAAEEQTTALT 722
                                       51113445555555555555555555556665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (924 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2225  (0.124101); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                       146  (0.00814323); expected 17.9 (0.001)
Passed Fwd filter:                        91  (0.00507558); 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: 2.06u 0.39s 00:00:02.45 Elapsed: 00:00:00.60
# Mc/sec: 4639.52
//
Query:       gi|336253217|ref|YP_004596324.1|  [L=280]
Description: polyprenyl synthetase [Halopiger xanaduensis SH-6]
Scores for 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-54  182.7   0.0    7.8e-54  182.4   0.0    1.0  1  polyprenyl_synt  Polyprenyl synthetase


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 !  182.4   0.0   4.3e-58   7.8e-54       3     230 ..      26     240 ..      24     264 .. 0.90

  Alignments for each domain:
  == domain 1  score: 182.4 bits;  conditional E-value: 4.3e-58
                                       HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTC CS
                   polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvG 79 
                                        l+e ++++  +gGKr+Rp++++la+e ++    + e+a + ++ +el+h+asLv+DDi+D se+RRG p+a +++G
  gi|336253217|ref|YP_004596324.1|  26 TLNEEVRHVALSGGKRVRPMVTVLACETVG---GTAEDAVEFGVGIELVHNASLVIDDIIDRSELRRGTPSAWAEFG 99 
                                       67888899999*******************...35689*************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCH CS
                   polyprenyl_synt  80 nklAindgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfa 156
                                          Ai ++d ll+ af l++      ++++++++++++++ +G++ +l+++        +++ey++  ++KT++lf+
  gi|336253217|ref|YP_004596324.1| 100 YGPAIIASDGLLGEAFSLFSAD----PDATRVVADAMVELGIGEATELSAK---PE---NEAEYMTLARRKTGALFR 166
                                       ******************9987....89********************555...23...3689************** PP

                                       HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HH CS
                   polyprenyl_synt 157 lpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspe 230
                                       ++++l+a++a+ ++ ++eal ++++++G+aFQi+DD+lD ++dpe+lgKp+g D + ++ +++ ++ l+ ++++
  gi|336253217|ref|YP_004596324.1| 167 AAAELGAIAADSEPVTVEALGEYAERVGIAFQIRDDVLDAVSDPEELGKPTGHDAALERPSVVQVTDLTPEEAN 240
                                       ***********99999**************************************************99933322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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: 00:00:00.40
# Mc/sec: 2089.72
//
Query:       gi|336253218|ref|YP_004596325.1|  [L=378]
Description: hypothetical protein Halxa_1818 [Halopiger xanaduensis SH-6]
Scores for 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-119  397.6   6.2   6.1e-119  397.4   6.2    1.0  1  DUF373    Domain of unknown function (DUF373)
  ------ inclusion threshold ------
        1.3    9.3   7.6         12    6.1   7.7    2.0  1  EI24      Etoposide-induced protein 2.4 (EI24)


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 !  397.4   6.2  6.8e-123  6.1e-119       2     334 ..       2     342 ..       1     343 [. 0.96

  Alignments for each domain:
  == domain 1  score: 397.4 bits;  conditional E-value: 6.8e-123
                            DUF373   2 tLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvg 78 
                                       +LvlcvD+DdDlgrk+g++tPv+Gr+ v+eaa++la++dPeDSDvN++f++++vyd+L +++e+vevavvtG+e+ +
  gi|336253218|ref|YP_004596325.1|   2 LLVLCVDLDDDLGRKTGFTTPVIGRDPVEEAAIALATEDPEDSDVNVIFQGLHVYDDLDERDESVEVAVVTGNEDGD 78 
                                       79*************************************************************************** PP

                            DUF373  79 veadrkiaeqldevlsklea..d.saivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyllkkalkdpe 152
                                       v a+r++ +++d+vl++l++  d  a v++DGa+Desv+p+i+srv++d+v+rVvV+q++n+Es+yy++k++l+dpe
  gi|336253218|ref|YP_004596325.1|  79 VAANREVGDEVDTVLASLSTaeDvTALVITDGAQDESVIPVIRSRVPIDGVRRVVVRQAQNLESMYYTIKQVLDDPE 155
                                       ******************99764799*************************************************** PP

                            DUF373 153 lrktiLvplGlllliyallll...lglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvv 226
                                       +r t+L+plG+llliy+l+l+   l++p+++l++ ++llGlyl+ rG++l ++l++++e++++sl++gr t+++yvv
  gi|336253218|ref|YP_004596325.1| 156 TRGTVLIPLGILLLIYPLALIgsaLEMPGFVLGTTSALLGLYLISRGLRLGDRLDTAVERARRSLYAGRTTLLAYVV 232
                                       ***************************************************************************** PP

                            DUF373 227 allllligiisgyislesvss.asvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpfl 302
                                       a++l+++g +sg+++le+v++ ++ + +  ++++a++yg+++wla+a++t+slg+i+dey+++  +  +r+l++pf+
  gi|336253218|ref|YP_004596325.1| 233 AAALFVLGGVSGTNELEAVREsTAGEVSAPVMLAALVYGSIQWLAAAGVTTSLGQITDEYIAG--SLEWRYLNAPFY 307
                                       ********************97444555555666689************************65..59********** PP

                            DUF373 303 vlaiglvlygasaylls...lsilalslvvgivva 334
                                       v++i+lvl+++sa++l+   +s+la++l++g++++
  gi|336253218|ref|YP_004596325.1| 308 VVSIALVLRAVSAFFLDrvaISYLAAALTAGTLLG 342
                                       ***************999999*******9999886 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   7.7    0.0013        12       6     122 ..     147     349 ..     143     359 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0013
                                       HHHHTS.TTTHHHHHHHHHHHHHHHHHHHHHHH....................................-....... CS
                              EI24   6 lglllsspkllallllplllnlllfllllvlll....................................w....... 39 
                                       ++++l++p+ +  +l+pl + ll++ l+l+                                               
  gi|336253218|ref|YP_004596325.1| 147 IKQVLDDPETRGTVLIPLGILLLIYPLALIGSAlempgfvlgttsallglylisrglrlgdrldtaverArrslyag 223
                                       7899********************99665555577777666666666665555555555444444433304444444 PP

                                       ..TTHHHHHHHHHHHHH...............................................HHHHHHHHHHHHH CS
                              EI24  40 ..vllasllvllllllp...............................................lwlfplvalllaa 67 
                                         +             +                                               ++   +v+  l++
  gi|336253218|ref|YP_004596325.1| 224 rtT-------------LlayvvaaalfvlggvsgtneleavrestagevsapvmlaalvygsiqWLAAAGVTTSLGQ 287
                                       442.............0222222222233466667888888888888888887777777777754444466666666 PP

                                       HHHHHHHHHHHH.HH...CCTTSHH.....HHHHHHHHHHHHHHHHHHH.HHTTHHH....HHH CS
                              EI24  68 pfygllaekvekrhl...glvksla.....eslkslllllllllvllpl.liPvvglilsplll 122
                                       +  + +a  +e r+l     v s+a      s+++l ++ ++ l + ++ + +++g i+s+l++
  gi|336253218|ref|YP_004596325.1| 288 ITDEYIAGSLEWRYLnapFYVVSIAlvlraVSAFFLDRVAISYLAAALTaG-TLLG-IASTLAF 349
                                       666666666666554444233333333333333333333333333222222.3333.3444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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 0.21s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2870.62
//
Query:       gi|336253219|ref|YP_004596326.1|  [L=200]
Description: hypothetical protein Halxa_1819 [Halopiger xanaduensis SH-6]
Scores for 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  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); 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:                         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 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1510.33
//
Query:       gi|336253220|ref|YP_004596327.1|  [L=331]
Description: Radical SAM domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   27.9   2.7    0.00026   21.4   0.2    2.8  2  Radical_SAM  Radical SAM superfamily
    0.00011   22.3   0.1     0.0002   21.5   0.1    1.4  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.07   13.4   0.1       0.16   12.2   0.1    1.6  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 !   21.4   0.2   4.4e-08   0.00026       6     106 ..      22     124 ..      18     128 .. 0.90
   2 !    5.5   0.2    0.0033        20      65     164 ..     141     276 ..     133     279 .. 0.54

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.4e-08
                                       EESS-.-TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.CCTE CS
                                       xxxxx.xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                       Radical_SAM   6 gCnlr.CsfCarpet..vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.vpgi 78 
                                        C +r C +C+ +e     +++++ +++ve+ ++ + e+ +++++ +  ++ggep    d +  +++l k +  ++ 
  gi|336253220|ref|YP_004596327.1|  22 YCDQRdCFYCPLGENrkNVTNVYANERQVEDDEDVITEA-KRMDALGTSITGGEPQEALDRTCHYLELLKDEfGEDH 97 
                                       588888***********99999*****************.7999*************99999999999999988899 PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvs 106
                                       ++++ t  t   +e ++rl e+g+d + 
  gi|336253220|ref|YP_004596327.1|  98 HTHLYTGITGG-RENMRRLSEAGLDEIR 124
                                       99999888887.***********99875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0033
                                       HHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH.........................H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................x RF
                       Radical_SAM  65 ellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaadde.........................k 116
                                       e+++ +a++  +g++ ++e++g++ +ee+le l+e   d  +++    +                           +
  gi|336253220|ref|YP_004596327.1| 141 EDILYIARE--EGLTPAFEIPGIRAEEEFLEFLDEGAADFCNVNEFEMSQGnyrrmqdqgfelkedhmsavegsreD 215
                                       444455555..699999999999997777777777555555555444444411144444444444333333333333 PP

                                       HHHHHTCTSHH...................HHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 117 vlklmnrghtf...................eevlealeklreagikrvvdrivglpGendeeleell 164
                                       +l+ m                          ++++  ++ r+  +++v+d  +++ G + ++ e ++
  gi|336253220|ref|YP_004596327.1| 216 ILEVM-----GdheqvyfctsvfkdaaqhrRRLKRMARNVRRE-FDDVTDDGTLVYGKTYADPERFA 276
                                       44444.....033335666666666665544444444444444.66677777777777777666665 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 !   21.5   0.1   3.4e-08    0.0002       6      90 ..      21     106 ..       6     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.4e-08
                           Fer4_14   6 sgCn.lsCkgCd...nketwks.elgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkee 77 
                                       + C    C  C    n+++  +  +++ q+e+++ +++  ++++++++ g ++tGGeP   e  +  ++ ++ lk+e
  gi|336253220|ref|YP_004596327.1|  21 GYCDqRDCFYCPlgeNRKNVTNvYANERQVEDDE-DVI--TEAKRMDALGTSITGGEPQ--EALDRTCHYLELLKDE 92 
                                       5554135777767775555544155666666666.666..5888888899*********..7899************ PP

                           Fer4_14  78 y.pekkiwletngt 90 
                                       + ++++ +l+t+ t
  gi|336253220|ref|YP_004596327.1|  93 FgEDHHTHLYTGIT 106
                                       *888*******976 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 ?   12.2   0.1   2.7e-05      0.16       5      95 ..      12     106 ..       9     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                           Fer4_12   5 Gvrlslfvsg.Cnl.sCkgCfnketwsfk...sgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelv 76 
                                       G+ ++lfv g C+   C +C   e ++     + +e + e  e +i+++k     g +++GGEP +    +     +
  gi|336253220|ref|YP_004596327.1|  12 GGKMVLFVYGyCDQrDCFYCPLGENRKNVtnvYANERQVEDDEDVITEAKRMDALGTSITGGEPQE--ALDRTCHYL 86 
                                       778889976659865899996555544441116666677888899999999999**********99..666666666 PP

                           Fer4_12  77 kevkeekp.ekdiwlytgyt 95 
                                       + +k e+  +    lytg t
  gi|336253220|ref|YP_004596327.1|  87 ELLKDEFGeDHHTHLYTGIT 106
                                       77777776555566777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2391.18
//
Query:       gi|336253221|ref|YP_004596328.1|  [L=107]
Description: hypothetical protein Halxa_1821 [Halopiger xanaduensis SH-6]
Scores for 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   17.2   0.4     0.0047   16.9   0.4    1.2  1  HypA           Hydrogenase/urease nickel incorporation, metal
  ------ inclusion threshold ------
      0.011   15.8   0.3      0.014   15.5   0.3    1.1  1  ArfGap         Putative GTPase activating protein for Arf
      0.028   14.1   2.8        3.1    7.6   0.2    2.2  2  Rubredoxin_2   Rubredoxin metal binding domain
      0.031   14.9   0.0       0.04   14.6   0.0    1.1  1  zinc-ribbon_6  zinc-ribbon domain
      0.037   14.0   0.6        1.2    9.1   0.1    2.4  2  Nudix_N_2      Nudix N-terminal
      0.052   13.1   7.0        1.3    8.6   0.6    2.9  3  TF_Zn_Ribbon   TFIIB zinc-binding
      0.075   12.6   0.3          5    6.8   0.1    2.2  2  zf_UBZ         Ubiquitin-Binding Zinc Finger
      0.098   12.1   0.2       0.11   11.9   0.2    1.1  1  DUF1258        Protein of unknown function (DUF1258)
       0.24   11.2   3.6       0.36   10.6   3.6    1.3  1  zinc_ribbon_2  zinc-ribbon domain
       0.44   10.7   2.0        1.2    9.3   2.0    1.7  1  Zn-ribbon_8    Zinc ribbon 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 !   16.9   0.4   2.6e-06    0.0047      66     104 ..      12      48 ..       1      53 [. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-06
                                       EE--EEEETTTS-EEECHHHHHS-TTTSSS-EEEEESSS CS
                              HypA  66 evpvkvrCreCgkefeleekalrCpkCgsadveivsGee 104
                                        ++v++ C++Cg+  + +  +l C++Cgs +++  + e+
  gi|336253221|ref|YP_004596328.1|  12 ATSVSFVCDDCGRVHNRN--NLPCNNCGSMSLSAAADED 48 
                                       467999******666655..589******9998776665 PP

>> ArfGap  Putative GTPase activating protein for Arf
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.3   7.8e-06     0.014      30      76 ..      13      59 ..       8      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.8e-06
                                      TTTEEE-HHHHHHHCCS.TTT--EEETTTS---HHHHHHHHHTCHHH CS
                            ArfGap 30 nlgvflCieCsgvHrslgvhiskvrsltldkwedeelellkalgNkk 76
                                      +   f+C++C  vH   +   +++ s++l+   de+++  +++ +++
  gi|336253221|ref|YP_004596328.1| 13 TSVSFVCDDCGRVHNRNNLPCNNCGSMSLSAAADEDIDNTQEIDEEE 59
                                      5668**********************************999887766 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0017       3.1       1      12 [.      17      28 ..      17      29 .. 0.87
   2 ?    6.8   0.2     0.003       5.4       3      11 ..      33      41 ..      32      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0017
                      Rubredoxin_2  1 YvCsqCGfesak 12
                                      +vC++CG ++++
  gi|336253221|ref|YP_004596328.1| 17 FVCDDCGRVHNR 28
                                      8******98875 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.003
                      Rubredoxin_2  3 CsqCGfesa 11
                                      C++CG+ s 
  gi|336253221|ref|YP_004596328.1| 33 CNNCGSMSL 41
                                      9****9875 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.2e-05      0.04       2      51 ..      17      67 ..      16      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                     zinc-ribbon_6  2 feCeqCgqllffenssClkCgaalgfapeelellaleeaee.eewrslaek 51
                                      f C+ Cg+    +n  C++Cg++   a+ ++++   +e +e e+wr + ++
  gi|336253221|ref|YP_004596328.1| 17 FVCDDCGRVHNRNNLPCNNCGSMSLSAAADEDIDNTQEIDEeESWRIVRDA 67
                                      99******9999*********987777888888877777665888877765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00066       1.2      23      32 ..      17      26 ..       4      27 .. 0.93
   2 ?    3.0   0.1     0.054        97       3       9 ..      33      39 ..      32      53 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00066
                                      EEETTTTEEE CS
                         Nudix_N_2 23 lvCpaCgtih 32
                                      +vC++Cg +h
  gi|336253221|ref|YP_004596328.1| 17 FVCDDCGRVH 26
                                      69*******9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.054
                                      -TTT--B CS
                         Nudix_N_2  3 CsqCGtp 9 
                                      C++CG+ 
  gi|336253221|ref|YP_004596328.1| 33 CNNCGSM 39
                                      8999975 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.6   0.00073       1.3      16      28 ..      13      25 ..       2      29 .. 0.80
   2 ?    7.7   0.7    0.0014       2.6      15      29 ..      26      40 ..      26      63 .. 0.80
   3 ?   -2.6   0.0       2.3   4.1e+03      11      18 ..      63      70 ..      59      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00073
                                      STTCEEESSSSBE CS
                      TF_Zn_Ribbon 16 ergelvCtdCGlV 28
                                       +  +vC dCG V
  gi|336253221|ref|YP_004596328.1| 13 TSVSFVCDDCGRV 25
                                      55679******98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0014
                                      TSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon 15 pergelvCtdCGlVl 29
                                      ++r++l C +CG++ 
  gi|336253221|ref|YP_004596328.1| 26 HNRNNLPCNNCGSMS 40
                                      5899999*****996 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.3
                                      CHEETSTT CS
                      TF_Zn_Ribbon 11 lveDperg 18
                                      +v+D++rg
  gi|336253221|ref|YP_004596328.1| 63 IVRDASRG 70
                                      79999997 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0028         5       2      10 ..      16      24 ..      15      26 .. 0.88
   2 ?    4.0   0.0     0.021        38       2      19 ..      30      47 ..      29      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0028
                            zf_UBZ  2 tylCerCgk 10
                                      +++C++Cg+
  gi|336253221|ref|YP_004596328.1| 16 SFVCDDCGR 24
                                      79*****97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.021
                            zf_UBZ  2 tylCerCgkeipeselqE 19
                                      + +C  Cg++ ++++ +E
  gi|336253221|ref|YP_004596328.1| 30 NLPCNNCGSMSLSAAADE 47
                                      679******998887666 PP

>> DUF1258  Protein of unknown function (DUF1258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   6.3e-05      0.11      13      38 ..      13      39 ..       6      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.3e-05
                           DUF1258 13 fsthkfcnkcGkvvakse.kcelcggk 38
                                       s+ ++c++cG+v ++++  c+ cg+ 
  gi|336253221|ref|YP_004596328.1| 13 TSVSFVCDDCGRVHNRNNlPCNNCGSM 39
                                      6999********88766536****974 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.6    0.0002      0.36       2      21 ..      19      38 ..      18      39 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                      C  CG+ +  n+  C +CG+
  gi|336253221|ref|YP_004596328.1| 19 CDDCGRVHNRNNLPCNNCGS 38
                                      999****************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 ?    9.3   2.0   0.00066       1.2       6      35 ..      17      40 ..      16      44 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00066
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs.e 35
                                      + C++Cg+++++        + +C +Cgs  
  gi|336253221|ref|YP_004596328.1| 17 FVCDDCGRVHNRN-------NLPCNNCGSmS 40
                                      89*****777632.......566*****966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 789.38
//
Query:       gi|336253222|ref|YP_004596329.1|  [L=374]
Description: hypothetical protein Halxa_1822 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.058   13.2   0.0       0.11   12.3   0.0    1.4  1  HTH_IclR  IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.1e-06      0.11      10      42 ..     314     346 ..     312     355 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.1e-06
                                       CT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHH CS
                          HTH_IclR  10 dalaeapqeltlselArrtglpkStvhRlLqtL 42 
                                       ++l + +++++ + + ++tg++ ++v+ lL+ +
  gi|336253222|ref|YP_004596329.1| 314 RMLKRNGGRMKQAAIVNETGWSNAKVSQLLSQM 346
                                       579999************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2862.84
//
Query:       gi|336253223|ref|YP_004596330.1|  [L=418]
Description: hypothetical protein Halxa_1823 [Halopiger xanaduensis SH-6]
Scores for 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   14.9   0.9      0.069   13.8   0.9    1.5  1  MDMPI_N   Mycothiol maleylpyruvate isomerase N-terminal domai


Domain annotation for each model (and alignments):
>> MDMPI_N  Mycothiol maleylpyruvate isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.9   3.8e-06     0.069      65     134 ..      76     157 ..      34     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-06
                           MDMPI_N  65 alvtaad............aeavdlaaslapeallaafraavtrlaaalaalppdaiadrlgipggprslgeflrtr 129
                                       al  a+d            + + d+a +++ ea+++a    ++ + +al++ ++dai++ + + ++++++  ++++ 
  gi|336253223|ref|YP_004596330.1|  76 ALANADDklridheqyvivESEFDEASADEREAMIEAAYNRTQNRTEALEERERDAIEAYVAGEQSETEVLGTIARN 152
                                       33333334555555666679999**************************************99999999999***** PP

                           MDMPI_N 130 lvEav 134
                                        +Eav
  gi|336253223|ref|YP_004596330.1| 153 YHEAV 157
                                       ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3164.70
//
Query:       gi|336253224|ref|YP_004596331.1|  [L=163]
Description: flagellin domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   37.7   2.5    4.6e-09   37.1   2.5    1.3  1  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> 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 !   37.1   2.5   2.6e-13   4.6e-09       2      79 ..      15      86 ..      14      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.6e-13
                           Pilin_N  2 AVSpViGviLmvaitvIlaAviaafvlglasneekapqasievkidssastgknavslehkgGdsidtkdlkivlnse 79
                                       VS+V+G iL+++i v +a+vi   v     ++e+ +++++e + ds+ st    +++eh  Gd+id  +l+i++  +
  gi|336253224|ref|YP_004596331.1| 15 SVSSVVGTILLLVIAVSVAGVILIGVSTW--TPESPAMTAFELSADSDRST----ITIEHRVGDTIDVRELSITVIVD 86
                                      6*************999999999888887..67777778887777777777....*************9999987554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1216.93
//
Query:       gi|336253225|ref|YP_004596332.1|  [L=207]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-25   87.2   0.0    1.4e-24   86.5   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.3e-24   86.7   0.0    1.9e-24   86.2   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    6.1e-19   68.3   0.0    3.1e-14   52.9   0.0    2.1  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    7.3e-19   68.1   0.0    8.7e-19   67.8   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    2.3e-15   57.1   0.0    3.3e-15   56.6   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    3.4e-15   56.3   0.0    4.8e-15   55.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    6.9e-07   29.2   0.0    8.7e-07   28.9   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      3e-05   23.1   0.0      4e-05   22.7   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
    3.1e-05   23.2   0.0    3.9e-05   22.9   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    4.8e-05   22.1   0.0    6.1e-05   21.8   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
    0.00032   20.4   0.0    0.00041   20.0   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
    0.00042   19.9   0.0     0.0017   18.0   0.0    1.8  1  MTS              Methyltransferase small domain
     0.0038   16.5   0.0     0.0057   16.0   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0041   16.2   0.0     0.0064   15.6   0.0    1.4  1  DREV             DREV methyltransferase
      0.005   16.2   0.0       0.01   15.1   0.0    1.4  1  Methyltransf_2   O-methyltransferase domain
  ------ inclusion threshold ------
      0.035   13.3   0.0      0.093   11.9   0.0    1.6  2  Methyltransf_33  Histidine-specific methyltransferase, SAM-de
      0.057   13.4   0.0      0.075   13.0   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.058   13.5   0.0      0.074   13.1   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
      0.064   12.8   0.0      0.077   12.5   0.0    1.1  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
      0.074   12.9   0.0       0.44   10.4   0.0    1.9  1  Methyltransf_8   Hypothetical methyltransferase
       0.13   11.8   0.0       0.17   11.5   0.0    1.1  1  NodS             Nodulation protein S (NodS)


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 !   86.5   0.0   1.6e-27   1.4e-24       1      95 [.      50     144 ..      50     145 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 1.6e-27
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       LdvGcGtG  +e l +++ +v+++D s+ +l++a +k  ++ + v f+++dae+lpf+ ++fD+v+ss +++++++p
  gi|336253225|ref|YP_004596332.1|  50 LDVGCGTGFATEGLLEHVDEVYALDQSEHQLEQAYAKFGKRAPPVHFHRGDAERLPFATDTFDVVWSSGSIEYWPNP 126
                                       8*********************************99999998899******************************** PP

                                       HHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                         al+e++RvLkpgG ++
  gi|336253225|ref|YP_004596332.1| 127 ILALREFRRVLKPGGQVL 144
                                       ***************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.0   2.3e-27   1.9e-24       1      97 []      49     141 ..      49     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 2.3e-27
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vLd+GcGtG  t+ l++++   +v+++D se +le+a +++ ++ + v+f++gdae+lpf+ ++fD+v+ssg+++++
  gi|336253225|ref|YP_004596332.1|  49 VLDVGCGTGFATEGLLEHV--DEVYALDQSEHQLEQAYAKFGKRAPPVHFHRGDAERLPFATDTFDVVWSSGSIEYW 123
                                       9*****************9..9**********************9*************************999***8 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +++    al+e++rvLkpgG
  gi|336253225|ref|YP_004596332.1| 124 PNPI--LALREFRRVLKPGG 141
                                       8665..68***********9 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   3.6e-17   3.1e-14      41     152 ..      39     146 ..       4     155 .. 0.81
   2 !   13.5   0.1   3.9e-05     0.033     189     218 ..     157     186 ..     151     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 3.6e-17
                                       HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-E CS
                   Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsf 117
                                        l       +vlDv +Gtg  +  l+++v+e   v  lD +e+ L+++ +k  +++   ++f  ++ae+Lpf  d+f
  gi|336253225|ref|YP_004596332.1|  39 GLLDLEDDMTVLDVGCGTGFATEGLLEHVDE---VYALDQSEHQLEQAYAKFGKRAP-PVHFHRGDAERLPFATDTF 111
                                       3444455679******************985...8899************9988764.8****************** PP

                                       EEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
                   Ubie_methyltran 118 DvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvl 152
                                       Dvv  s  +   ++   aL+e +rvlkpGG+++v+
  gi|336253225|ref|YP_004596332.1| 112 DVVWSSGSIEYWPNPILALREFRRVLKPGGQVLVV 146
                                       ********************************997 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.9e-05
                                       HHHHHHHHHS--HHHHHHHHHHTTEEEEEE CS
                   Ubie_methyltran 189 ryLvesirafPdqetlkeliedaGfksvey 218
                                       +yL++si  f d+ + +++++ aGf+ v++
  gi|336253225|ref|YP_004596332.1| 157 QYLADSIMLFYDEYEADAMFKTAGFEDVKH 186
                                       8**************************986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.0     1e-21   8.7e-19       2     122 ..      44     158 ..      43     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1e-21
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       +++++vlD+GCGtG+ t  l e +    ev+ +D se+ +e+A ++  k     v+F++gd+e l+  ++ ++fD++
  gi|336253225|ref|YP_004596332.1|  44 EDDMTVLDVGCGTGFATEGLLEHVD---EVYALDQSEHQLEQAYAKFGKRAP-PVHFHRGDAERLP--FATDTFDVV 114
                                       689******************7653...6****************9998888.6************..99******* PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedprllaelpakv 122
                                        s + + + ++p  +l+e  rvlkpgg +l+  p+  ++++a+ 
  gi|336253225|ref|YP_004596332.1| 115 WSSGSIEYWPNPILALREFRRVLKPGGQVLVVGPNYPDNVLAQY 158
                                       *******************************9999433333333 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   3.8e-18   3.3e-15       1      99 []      50     143 ..      50     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 3.8e-18
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       L++GcGtG  ++ lle+    e++++D s++++e+a +k+ kr +     v++   d++ l+   ++fD+v++s+ +
  gi|336253225|ref|YP_004596332.1|  50 LDVGCGTGFATEGLLEH--VDEVYALDQSEHQLEQAYAKFGKRAP----PVHFHRGDAERLPFAtDTFDVVWSSGSI 120
                                       8****************..**************999999999987....67777777665555578*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGrl 99 
                                       ++++++  +l+++r++LkpgG++
  gi|336253225|ref|YP_004596332.1| 121 EYWPNPILALREFRRVLKPGGQV 143
                                       *********************85 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   5.6e-18   4.8e-15      14     164 ..      38     185 ..      21     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 5.6e-18
                   Methyltransf_23  14 erllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdl 85 
                                       + ll+ l+ ++ vLd+GcGtG  +e l e++ +v++ D+s+++ e a       a+  +++  d++  ++  ++fd+
  gi|336253225|ref|YP_004596332.1|  38 LGLLD-LEDDMTVLDVGCGTGFATEGLLEHVDEVYALDQSEHQLEQAYakfgkRAPPVHFHRGDAERLPFATDTFDV 113
                                       44555.78999**********99999999999*********99998889988877778888888888888999**** PP

                   Methyltransf_23  86 IvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGlev 162
                                       + ++ ++e  p+p  +lr +++ lkpgG +l+  p+ +   d+ l ++l++      + f+++ +   +++ aG+e+
  gi|336253225|ref|YP_004596332.1| 114 VWSSGSIEYWPNPILALREFRRVLKPGGQVLVVGPNYP---DNVLAQYLAD----SIMLFYDEYEADAMFKTAGFED 183
                                       ***********************************854...4444444443....3558999999999999999998 PP

                   Methyltransf_23 163 ve 164
                                       v+
  gi|336253225|ref|YP_004596332.1| 184 VK 185
                                       85 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 !   28.9   0.0     1e-09   8.7e-07      55     171 ..      27     145 ..      11     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1e-09
                                       EE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES CS
                              PCMT  55 tiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvg 131
                                        i    m a al ll+l++ + vL+vG+G+G+ t  l + v e+    +++++++  e+a ++  k +   v+++ g
  gi|336253225|ref|YP_004596332.1|  27 FIWTEEMRADALGLLDLEDDMTVLDVGCGTGFATEGLLEHVDEVY---ALDQSEHQLEQAYAKFGKRAP-PVHFHRG 99 
                                       5667789***************************99999999888...999999999999999988765.799**** PP

                                       -GGGTTGGG-SEEEEEESSBBSS--HHHH......HTEEEEEEEEE CS
                              PCMT 132 DGrkGyeekaPYdaihvgaaapeiPeali......dQLkeGGrlvv 171
                                       D +    ++  +d+++ + + +  P++++      + Lk+GG+++v
  gi|336253225|ref|YP_004596332.1| 100 DAERLPFATDTFDVVWSSGSIEYWPNPILalrefrRVLKPGGQVLV 145
                                       9988777788899999999999999876522222246888888766 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 !   22.7   0.0   4.7e-08     4e-05     116     216 ..      46     144 ..      29     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.7e-08
                                       T-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES- CS
                    Methyltransf_9 116 grtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsmGv 191
                                       + t+ldvGcg+G+    ++ e+ + v  +d se  l q  a  k+     ++h      e+lp  +++fd+v+s G 
  gi|336253225|ref|YP_004596332.1|  46 DMTVLDVGCGTGFATEGLL-EHVDEVYALDQSEHQLEQ--AYAKFGKRAPPVHFHRGDAERLPFaTDTFDVVWSSGS 119
                                       579*********9887666.788999******998886..5667777777777777789****889*********** PP

                                       GGG-S-HHHHHHHHHCTEEEEEEEE CS
                    Methyltransf_9 192 lyhrrsPldhllqlkdqlvkgGelv 216
                                       + +   P+  l++++  l+ gG+++
  gi|336253225|ref|YP_004596332.1| 120 IEYWPNPILALREFRRVLKPGGQVL 144
                                       **********************986 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   4.5e-08   3.9e-05      12      76 ..      27      92 ..      20     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.5e-08
                                      EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.TCC CS
                            RrnaAD 12 flknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.kde 76
                                      f++ + + +++l  l+le+++tvl++g G+G+ Te L++ +++v +l + e+ ++   +k+   ++
  gi|336253225|ref|YP_004596332.1| 27 FIWTEEMRADALGLLDLEDDMTVLDVGCGTGFATEGLLEHVDEVYALDQSEHQLEQAYAKFGkRAP 92
                                      88888899999999********************************99888777776666654445 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 !   21.8   0.0   7.2e-08   6.1e-05     120     220 ..      48     148 ..      35     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.2e-08
                   Methyltransf_29 120 tvlDvGCgvasfgayllsr..dvltlslapkDeheaqvqfaLeRgvpailavlgtkrlpyPsrsfdlihCsrCridw 194
                                       tvlDvGCg    +  ll++  +v +l  + +   +a  +f   R  p       ++rlp+ + +fd++  s   i++
  gi|336253225|ref|YP_004596332.1|  48 TVLDVGCGTGFATEGLLEHvdEVYALDQSEHQLEQAYAKFG-KRAPPVHFHRGDAERLPFATDTFDVVWSS-GSIEY 122
                                       89******987777888753367787777777777777776.6888999999999************9866.68999 PP

                   Methyltransf_29 195 teedgilllevdRvlRpgGyfvlsap 220
                                         +  + l e  Rvl+pgG  ++ +p
  gi|336253225|ref|YP_004596332.1| 123 WPNPILALREFRRVLKPGGQVLVVGP 148
                                       999****************8877776 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   4.8e-07   0.00041      12     112 ..      44     150 ..      34     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.8e-07
                              MetW  12 kpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvak.G.....lsviqgdldkdlenfedksfdyvvls 82 
                                       ++  +vld+GcG G   e l e+ + + + l+++e+ + ++ ak G     ++ ++gd++     f+ ++fd+v  s
  gi|336253225|ref|YP_004596332.1|  44 EDDMTVLDVGCGTGFATEGLLEHVD-EVYALDQSEHQLEQAYAKfGkrappVHFHRGDAE--RLPFATDTFDVVWSS 117
                                       67889*********99987766433.5688999999999998875233333666666665..568999********* PP

                              MetW  83 qtlqatrnpkevldellri...grraivsfPnf 112
                                        ++    np   l+e  r+   g +++v  Pn+
  gi|336253225|ref|YP_004596332.1| 118 GSIEYWPNPILALREFRRVlkpGGQVLVVGPNY 150
                                       **************9988855577999999997 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    0.0017      30     101 ..      44     114 ..      35     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
                                       CTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEE CS
                               MTS  30 elsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdli 101
                                       e + +vlD+GcG+G+ +  l+++ +e  v ++d++ + le a + + + +  v+++  d+    ++ + fd++
  gi|336253225|ref|YP_004596332.1|  44 EDDMTVLDVGCGTGFATEGLLEHVDE--VYALDQSEHQLEQAYAKFGKRAPPVHFHRGDAERlPFATDTFDVV 114
                                       45678***************999988..9**********************9****99986623445667776 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.6e-06    0.0057      54     106 ..      37      88 ..      31     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.6e-06
                                       HHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHH CS
                              CMAS  54 ileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvd 106
                                       +l+ l+l++ mt+Ld+GcG G  +    e+ d +v +l  S+ q ++a +++ 
  gi|336253225|ref|YP_004596332.1|  37 ALGLLDLEDDMTVLDVGCGTGFATEGLLEHVD-EVYALDQSEHQLEQAYAKFG 88 
                                       67889****************99988888844.89999999999888877665 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   7.5e-06    0.0064      94     131 ..      45      82 ..      33     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.5e-06
                              DREV  94 edkklldlGaGdGeitkrvaptfeevyatelsetmrdr 131
                                       +d ++ld+G G G  t+ + ++++evya + se+  ++
  gi|336253225|ref|YP_004596332.1|  45 DDMTVLDVGCGTGFATEGLLEHVDEVYALDQSEHQLEQ 82 
                                       5789**************************99976655 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05      0.01      52     209 ..      35     181 ..      27     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                                       HHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-H.HHHHHHHHHS-----TTEEEEES-TTTS---. CS
                    Methyltransf_2  52 kkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlp.eVveaAkehlsageeervefvgGdffkdslP. 126
                                       +++l   dle   +++DvG GtG + +   ++  ++    +D + +  e+A  ++  + ++ v+f+ Gd    +lP 
  gi|336253225|ref|YP_004596332.1|  35 ADALGLLDLEDDMTVLDVGCGTGFATEGLLEHVDEV--YALDQSeHQLEQAYAKF-GKRAPPVHFHRGDAE--RLPf 106
                                       5788899999999**********9999999887654..55665426778888774.567899*******76..9**7 PP

                                       --SEEEEESS...GGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS---HHHHHHHHHHHHCSS-----HHHH CS
                    Methyltransf_2 127 eaDaillkrv...lhDwsdekcvklLkrvkkalpagGkvivveavlgadpsgeletelvdlimlvqteGkeRteaey 200
                                        +D + +++    +  w +      L++ ++ l++gG+v+vv    ++ p++ l+++l d iml+       +e e 
  gi|336253225|ref|YP_004596332.1| 107 ATDTFDVVWSsgsIEYWPN--PILALREFRRVLKPGGQVLVV---GPNYPDNVLAQYLADSIMLFY------DEYEA 172
                                       7788777765111333433..345689*************98...678889999999999999998......67777 PP

                                       HHHHHHCT- CS
                    Methyltransf_2 201 eellseaGf 209
                                        +++++aGf
  gi|336253225|ref|YP_004596332.1| 173 DAMFKTAGF 181
                                       788888887 PP

>> Methyltransf_33  Histidine-specific methyltransferase, SAM-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011     0.093      62     119 ..      46      97 ..      31     102 .. 0.86
   2 ?   -1.8   0.0       1.6   1.4e+03     194     194 ..     158     158 ..     125     188 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                   Methyltransf_33  62 aatlvelGsGsseKtrlLLealeaaekeltYvplDvseeaLeealealaaeypsleve 119
                                       + t+++ G+G++  t+ LLe++++       ++lD se++Le+a ++  ++ p ++++
  gi|336253225|ref|YP_004596332.1|  46 DMTVLDVGCGTGFATEGLLEHVDEV------YALDQSEHQLEQAYAKFGKRAPPVHFH 97 
                                       3499******************866......9**************999988888765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                   Methyltransf_33 194 Y 194
                                       Y
  gi|336253225|ref|YP_004596332.1| 158 Y 158
                                       3 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.8e-05     0.075      23      69 ..      43      85 ..      18     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.8e-05
                   Methyltransf_32 23 esgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaek 69
                                       ++++tv+DvG+G g+ +  l      +  +v+++d +e+  e+a +
  gi|336253225|ref|YP_004596332.1| 43 LEDDMTVLDVGCGTGFATEGLLE----HVDEVYALDQSEHQLEQAYA 85
                                      46789****************99....4669*********9998865 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.7e-05     0.074      20      72 ..      44     103 ..       5     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.7e-05
                                       -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS..........HHHTTEEEECS-CCC CS
                              FtsJ  20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm..........aplpgvttiqgditd 72 
                                       + ++tv+D+g+++G  ++ ll+++     v+a+D+ +           +  p v++++gd  +
  gi|336253225|ref|YP_004596332.1|  44 EDDMTVLDVGCGTGFATEGLLEHVD---EVYALDQSEHqleqayakfgKRAPPVHFHRGDAER 103
                                       25588******************84...6******9887888886664444899999999854 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     9e-05     0.077      55     162 ..      45     149 ..      30     188 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9e-05
                   Methyltransf_PK  55 evkvaldcGaGiGrvtknlLlkllskvDlvepvekflekakeelaeekkkvgkvyvvglqeftP.eegrYdliWiqW 130
                                       +  ++ld+G+G G  t+ lL +++ +v  ++  e+ le+a  ++++  +     +  g  e  P + + +d++W   
  gi|336253225|ref|YP_004596332.1|  45 DDMTVLDVGCGTGFATEGLL-EHVDEVYALDQSEHQLEQAYAKFGK--RAPPVHFHRGDAERLPfATDTFDVVWSSG 118
                                       55689************987.6889999999999999999999988..444445566655555526899*****999 PP

                   Methyltransf_PK 131 cvghLtDedlvaflkrckkalkpnG.livvken 162
                                        +   ++  l+  l+   + lkp+G ++vv  n
  gi|336253225|ref|YP_004596332.1| 119 SIEYWPNPILA--LREFRRVLKPGGqVLVVGPN 149
                                       88888876554..67777788888833455555 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00051      0.44     101     156 ..      89     145 ..       8     149 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00051
                                       SS-SSTTEEES-TTS-S--TT-EEEEEEES---S.S-HHHHHHHHHHHEEEEEEEEE CS
                    Methyltransf_8 101 lvavnervvacdlakvPledesvdvavfclslmg.tnladflkeanrvlkvGGllkv 156
                                         a+  +    d  ++P + ++ dv+    s+    n    l+e +rvlk+GG + v
  gi|336253225|ref|YP_004596332.1|  89 KRAPPVHFHRGDAERLPFATDTFDVVWSSGSIEYwPNPILALREFRRVLKPGGQVLV 145
                                       34444566778999***********99999985426778889***********8766 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.17      46     141 ..      48     142 ..      29     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                              NodS  46 dalevGcaaGalterlapyckrltvvdvveeaiararervke.sshiswivsdvqqfs.tdekfdlivvaevlyyie 120
                                        +l+vGc +G  te l  + + +  +d  e+ +++a  +  + ++ + ++  d +++  +++ fd++  +  + y  
  gi|336253225|ref|YP_004596332.1|  48 TVLDVGCGTGFATEGLLEHVDEVYALDQSEHQLEQAYAKFGKrAPPVHFHRGDAERLPfATDTFDVVWSSGSIEYWP 124
                                       69**********************************9998652789*********9973578999998877665554 PP

                              NodS 121 dvaelraavrnlvsllapdgq 141
                                       +      a+r++ ++l+p+gq
  gi|336253225|ref|YP_004596332.1| 125 NPI---LALREFRRVLKPGGQ 142
                                       432...356666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1490.68
//
Query:       gi|336253226|ref|YP_004596333.1|  [L=110]
Description: ATP synthase H subunit [Halopiger xanaduensis SH-6]
Scores for 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-05   24.5  20.4    3.3e-05   24.0  20.4    1.3  1  ATP-synt_B      ATP synthase B/B' CF(0)
      7e-05   23.2  25.3    0.00011   22.6  25.3    1.3  1  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
     0.0013   18.2  13.3     0.0013   18.2  13.3    2.2  2  vATP-synt_E     ATP synthase (E/31 kDa) subunit
     0.0013   19.2  20.6      0.059   13.9  20.0    2.1  1  V-ATPase_G      Vacuolar (H+)-ATPase G subunit
     0.0062   16.4  12.5      0.012   15.5  12.5    1.5  1  HrpE            HrpE/YscL/FliH and V-type ATPase subunit E
      0.008   16.8  17.7       0.42   11.2   7.0    2.1  2  DUF883          Bacterial protein of unknown function (DUF883
  ------ inclusion threshold ------
       0.01   15.9  16.2       0.43   10.7   0.9    2.0  2  DivIVA          DivIVA protein
      0.022   14.1  26.1       0.24   10.8  19.5    2.0  2  DUF3552         Domain of unknown function (DUF3552)
      0.058   13.2   6.4      0.064   13.1   6.4    1.1  1  PIN_8           PIN like domain
      0.072   12.3   2.4      0.059   12.5   1.3    1.4  1  dCache_2        Cache domain
       0.08   12.8  22.5       0.11   12.3  22.5    1.2  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
        0.3   10.0   8.7       0.34    9.8   8.7    1.1  1  DUF3435         Protein of unknown function (DUF3435)
        0.4   10.0  11.4       0.44    9.8  11.4    1.1  1  DUF4407         Domain of unknown function (DUF4407)
       0.43   10.1   5.0       0.46   10.0   5.0    1.1  1  Inositol_P      Inositol monophosphatase family
       0.49   11.0  10.8        1.6    9.3   0.6    2.3  2  YtxH            YtxH-like protein
       0.61    9.0   6.6       0.67    8.9   6.6    1.0  1  Histidinol_dh   Histidinol dehydrogenase
       0.71    9.2  13.4       0.79    9.1  13.4    1.0  1  GBP_C           Guanylate-binding protein, C-terminal domain
       0.74    9.2  15.6       0.86    9.0  15.6    1.0  1  Golgin_A5       Golgin subfamily A member 5
       0.74    9.7  16.3       0.21   11.5   5.2    2.1  2  Remorin_C       Remorin, C-terminal region
       0.88    9.5  20.9        1.1    9.2  20.9    1.1  1  Merozoite_SPAM  Merozoite surface protein (SPAM)
       0.99    9.2  13.4       0.81    9.5   1.8    2.1  2  CdvA            CdvA-like coiled-coil domain
          1    9.5  12.8        2.2    8.4   8.7    2.5  2  Caudo_TAP       Caudovirales tail fibre assembly protein, lam
        1.3    8.8   8.0        1.2    9.0   0.8    2.0  2  Peptidase_M41   Peptidase family M41
        1.6    7.1  12.7        1.8    6.9  12.7    1.0  1  Borrelia_P83    Borrelia P83/100 protein
        2.4    8.5  12.9        3.5    8.0  12.9    1.3  1  OmpH            Outer membrane protein (OmpH-like)
          7    4.7  12.5        8.5    4.4  12.5    1.0  1  HSP70           Hsp70 protein


Domain annotation for each model (and alignments):
>> 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 !   24.0  20.4   4.7e-08   3.3e-05      35     122 ..       6      94 ..       3     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.7e-08
                        ATP-synt_B  35 IadeiaeAeerrkea.aallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqekdr 110
                                       + + i++Ae  ++e  a++++++ ++ +eAr +A+ei+ +A +ea++lke + +ea++e+++  e   +e e+e+++
  gi|336253226|ref|YP_004596333.1|   6 VLERIQSAESDADEIvAQAEQDRDERIAEARERAEEIRTEADQEAQELKERRLEEAREEIDQECERVLEEGEREREA 82 
                                       67788888888887526667777788999999999999999999999999999999999999999999999999999 PP

                        ATP-synt_B 111 alaeLreqvval 122
                                       + +  r++v ++
  gi|336253226|ref|YP_004596333.1|  83 LADRARDRVDEV 94 
                                       988888888877 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 !   22.6  25.3   1.6e-07   0.00011       5     100 ..       5     100 ..       1     102 [. 0.97

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.6e-07
                                       HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2   5 rllkeLaerEaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaq 81 
                                        +l+ + + E++ d+ + +A ++  +++++A+  A+ i +eA+++a++l+++  +e +ee+ ++ e++ +++e e +
  gi|336253226|ref|YP_004596333.1|   5 EVLERIQSAESDADEIVAQAEQDRDERIAEARERAEEIRTEADQEAQELKERRLEEAREEIDQECERVLEEGERERE 81 
                                       699************************************************************************** PP

                                       HHHHHHHCSHHHHHHHHHH CS
                      V-ATPase_G_2  82 avrkraearlqqAvelilk 100
                                       a+  ra +r+++  +++++
  gi|336253226|ref|YP_004596333.1|  82 ALADRARDRVDEVTDHVVE 100
                                       ************9999985 PP

>> 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 ?    2.7   1.7       0.1        72      15      36 ..      11      32 ..       5      34 .. 0.59
   2 !   18.2  13.3   1.9e-06    0.0013       5      52 ..      34      81 ..      32     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                                      HHHHHHHHHHHHHHHHHHHHCH CS
                       vATP-synt_E 15 akaeeefeiekaklveeeeeki 36
                                      ++ae ++++++a+++++  e+i
  gi|336253226|ref|YP_004596333.1| 11 QSAESDADEIVAQAEQDRDERI 32
                                      4566666666666666655555 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.9e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH CS
                       vATP-synt_E  5 eAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkk 52
                                      eA+e+AeeI+++a++e+++ k++  ee++e+i+++ e    + e++++
  gi|336253226|ref|YP_004596333.1| 34 EARERAEEIRTEADQEAQELKERRLEEAREEIDQECERVLEEGERERE 81
                                      9************************************99888887775 PP

>> 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 !   13.9  20.0   8.5e-05     0.059      11      93 ..      12      94 ..       5      99 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.5e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSH.HHHHHHHHHHHSSHHHHHHHHHHHH CS
                        V-ATPase_G 11 qAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgs.eeelekkieketeekikelkesvkk 88
                                      +AE +A+eiv++A +++ +r+ +A+e Ae Ei     ++ +e+ke + e++ +  ++  +++ +e e++ + l++ ++ 
  gi|336253226|ref|YP_004596333.1| 12 SAESDADEIVAQAEQDRDERIAEARERAE-EIRTEADQEAQELKERRLEEAREeIDQECERVLEEGEREREALADRARD 89
                                      7*************************995.7888777777777776655542212333344444444454555555544 PP

                                      HHHHH CS
                        V-ATPase_G 89 nkeav 93
                                      + ++v
  gi|336253226|ref|YP_004596333.1| 90 RVDEV 94
                                      44444 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5  12.5   1.7e-05     0.012      28     100 ..      24      96 ..       5     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                              HrpE  28 eslrarellaeArlqAeqllaqarekaeellevaveqAeaqFWeqAnalLrglqqeRealeeqlltaveqLLs 100
                                       +++  +e +aeAr  Ae++  +a + a+el e   e+A  +  ++ + +L++  +eReal +++  +v+++  
  gi|336253226|ref|YP_004596333.1|  24 AEQDRDERIAEARERAEEIRTEADQEAQELKERRLEEAREEIDQECERVLEEGEREREALADRARDRVDEVTD 96 
                                       334456779*******************************************************999999754 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 !   11.2   7.0   0.00061      0.42       5      52 ..       8      55 ..       5      57 .. 0.88
   2 !   10.2   6.8    0.0013       0.9      20      69 ..      49      98 ..      46     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00061
                            DUF883  5 aeleslladleellkeaadeageeaeelRerleerlerarerlrdaee 52
                                      + ++s+ +d++e++ +a+++ +e ++e+Rer+ee  ++a +++++++e
  gi|336253226|ref|YP_004596333.1|  8 ERIQSAESDADEIVAQAEQDRDERIAEARERAEEIRTEADQEAQELKE 55
                                      56899999*************************999999999998876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0013
                            DUF883 20 eaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaaddyV 69
                                      ea++  ++ +ee+Re+++++ er+ e+ ++ +ea+a+ra++ ++++ d V
  gi|336253226|ref|YP_004596333.1| 49 EAQELKERRLEEAREEIDQECERVLEEGEREREALADRARDRVDEVTDHV 98
                                      677888999*******************************9998877766 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  11.5    0.0022       1.5      71     115 ..      12      56 ..       5      64 .. 0.73
   2 ?   10.7   0.9   0.00062      0.43      74     122 ..      56     104 ..      53     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0022
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  71 vaqetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaee 115
                                       +a++ a+e+ a+a++  +  i+eA+++ae+i  ea +ea++++e+
  gi|336253226|ref|YP_004596333.1|  12 SAESDADEIVAQAEQDRDERIAEARERAEEIRTEADQEAQELKER 56 
                                       577778888888888888888888888888888888888887654 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00062
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  74 etaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeieelkrq 122
                                       +  ee++++  +e+e +++e e + e++ + a+++++++++ + el ++
  gi|336253226|ref|YP_004596333.1|  56 RRLEEAREEIDQECERVLEEGEREREALADRARDRVDEVTDHVVELFQE 104
                                       566999999*******************************999888665 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.4    0.0026       1.8      27      46 ..       8      27 ..       3      31 .. 0.88
   2 ?   10.8  19.5   0.00034      0.24      25      88 ..      28      92 ..      25     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0026
                           DUF3552 27 kkiaeAeeeAkkiieeAkke 46
                                      ++i++Ae++A++i+++A+++
  gi|336253226|ref|YP_004596333.1|  8 ERIQSAESDADEIVAQAEQD 27
                                      689**************997 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00034
                           DUF3552 25 aekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklree.lekelkerrnelqrlekRll 88
                                       +++iaeA+e+A++i  eA +eA+++k+  l ea+eei +  e  le+  +er++  +r  +R+ 
  gi|336253226|ref|YP_004596333.1| 28 RDERIAEARERAEEIRTEADQEAQELKERRLEEAREEIDQECERvLEEGEREREALADRARDRVD 92
                                      5789**********************************865444145555666655556555554 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   6.4   9.3e-05     0.064      57     145 ..      23     109 ..       3     110 .] 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.3e-05
                             PIN_8  57 kayedlekeleklkkaaekkleealkkwakkkaldteelrkelkkqleelkeelkaeleelkksskadkeedpilkk 133
                                       +a +d  + +++++++ae+ ++ea+++ ++ k+ + ee+r+e++++ e++ ee ++e e+l ++ ++ +  d++ + 
  gi|336253226|ref|YP_004596333.1|  23 QAEQDRDERIAEARERAEEIRTEADQEAQELKERRLEEAREEIDQECERVLEEGEREREALADRARDRV--DEVTDH 97 
                                       233344455666666677666666666666666669999999999999999999777777777777776..****** PP

                             PIN_8 134 leellegkigea 145
                                       + el+++ + ++
  gi|336253226|ref|YP_004596333.1|  98 VVELFQEDVHAQ 109
                                       ******999765 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.3   8.6e-05     0.059       4      63 ..      45     104 ..      42     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.6e-05
                          dCache_2   4 dfkeeiekleeetikerkellksevdsaielieyeknsleeslkesLksrveeaysiaee 63 
                                       ++ +e+++l+e++++e +e++ +e +++ e  e+e++ l ++++ ++++ +++++++++e
  gi|336253226|ref|YP_004596333.1|  45 EADQEAQELKERRLEEAREEIDQECERVLEEGEREREALADRARDRVDEVTDHVVELFQE 104
                                       677999************************************************999876 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  22.5   0.00016      0.11      73     170 ..      11     106 ..       5     110 .] 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                       HHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..--- CS
                    Apolipoprotein  73 qrlapyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaphaeeve 149
                                       q  ++ ++e+ +++++d +e     ++ aee+r+++++++++lk+r    +ee+r++++++ e + e+ + + e++ 
  gi|336253226|ref|YP_004596333.1|  11 QSAESDADEIVAQAEQDRDERIAEARERAEEIRTEADQEAQELKER---RLEEAREEIDQECERVLEEGEREREALA 84 
                                       5567777888888888888888888888888888888887777775...4578888888888888888888888888 PP

                                       --SSSHHHHHHHTS-T.TSHHH CS
                    Apolipoprotein 150 erlssrveelreklee.qaeel 170
                                       +r+++rv+e+ + + e   e++
  gi|336253226|ref|YP_004596333.1|  85 DRARDRVDEVTDHVVElFQEDV 106
                                       8888888888777655344555 PP

>> DUF3435  Protein of unknown function (DUF3435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   8.7   0.00049      0.34     287     354 ..       3      70 ..       2     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00049
                           DUF3435 287 dpelqelkrkreelkkeleakygqvakakgtelyeelekakrelrnerqrlrrelkkkireeFkeeqp 354
                                       +pe+ e+++  e+ ++e+ a+++q ++++ +e+ e++e+ ++e  +e q+l+++  +++ree ++e  
  gi|336253226|ref|YP_004596333.1|   3 RPEVLERIQSAESDADEIVAQAEQDRDERIAEARERAEEIRTEADQEAQELKERRLEEAREEIDQECE 70 
                                       58899999999999999999999999999999999999999999999999999999999999888754 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  11.4   0.00064      0.44     114     198 ..      11      97 ..       3     109 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00064
                           DUF4407 114 eeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalr.aeaqkeldgtk....gtgttgvaGkgpaa 185
                                       + ++++a+e+ +q +++ ++++ae++++ +++++e d+  ++l++ r +ea++e+d+++     +g    + +++ a
  gi|336253226|ref|YP_004596333.1|  11 QSAESDADEIVAQAEQDRDERIAEARERAEEIRTEADQEAQELKERRlEEAREEIDQECervlEEG---EREREALA 84 
                                       556778899999999997777777777777666666665555544332555555555553222544...44555555 PP

                           DUF4407 186 kekkaqldaaqae 198
                                       +++++  d+ +  
  gi|336253226|ref|YP_004596333.1|  85 DRARDRVDEVTDH 97 
                                       5555555555554 PP

>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.0   0.00067      0.46      10      77 ..      10      77 ..       3     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00067
                                      HHHHH.HHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCC CS
                        Inositol_P 10 velaa.kagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakge 77
                                      +++a   a e++++++++++  i e   e++e++ t+ad++++el   +l+e +++ +   e  l++ge
  gi|336253226|ref|YP_004596333.1| 10 IQSAEsDADEIVAQAEQDRDERIAEAR-ERAEEIRTEADQEAQELKERRLEEAREEIDQECERVLEEGE 77
                                      4444449**********7766666666.79**********************99999888888888887 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   3.7     0.021        14      34      72 ..      10      55 ..       3      57 .. 0.73
   2 ?    9.3   0.6    0.0024       1.6      24      66 ..      59     101 ..      56     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.021
                              YtxH 34 addlkekakelleeakeka.......kekaedlkekvkekadelke 72
                                       + +  +a+e++ +a++         +e+ae+++++++++a+elke
  gi|336253226|ref|YP_004596333.1| 10 IQSAESDADEIVAQAEQDRderiaeaRERAEEIRTEADQEAQELKE 55
                                      44555555555555555557777888999**************998 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0024
                              YtxH  24 ketRkdlkekaddlkekakelleeakekakekaedlkekvkek 66 
                                       +e R+++ ++++ + e  ++  e ++++a+++++++++ v e 
  gi|336253226|ref|YP_004596333.1|  59 EEAREEIDQECERVLEEGEREREALADRARDRVDEVTDHVVEL 101
                                       4778888888888888887777777777777777776666555 PP

>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   6.6   0.00098      0.67       7      85 ..       9      90 ..       3     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00098
                                      --HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSS..S.SGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC CS
                     Histidinol_dh  7 dseeveetvkeiledvreeGdealleytekFDkv..k.kleslrvseeeieealekldeelkealeeaaenirkfheaq 82
                                      + +++e+  +ei+++ +++ de + e  e+ +++  + ++e+ +++e+++eea e++d+e ++ lee  ++ ++ + + 
  gi|336253226|ref|YP_004596333.1|  9 RIQSAESDADEIVAQAEQDRDERIAEARERAEEIrtEaDQEAQELKERRLEEAREEIDQECERVLEEGEREREALADRA 87
                                      5677889999**********************9975345588999*********************9999888888877 PP

                                      --- CS
                     Histidinol_dh 83 kes 85
                                      +++
  gi|336253226|ref|YP_004596333.1| 88 RDR 90
                                      753 PP

>> GBP_C  Guanylate-binding protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  13.4    0.0011      0.79     206     287 ..      11      92 ..       5     102 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                             GBP_C 206 ieaeqakaeaaeaekelleekqkeeeqrmeakeksleehvkqLke.kleeereklleeqerllekklkeqeellkeg 281
                                       + ae    e + ++++   e+ +e ++r e+ + + ++++++Lke +lee re++ +e er+le+ ++e e+l    
  gi|336253226|ref|YP_004596333.1|  11 QSAESDADEIVAQAEQDRDERIAEARERAEEIRTEADQEAQELKErRLEEAREEIDQECERVLEEGEREREALAD-R 86 
                                       444444455444444555555566666677777777777778876379****************99999887654.4 PP

                             GBP_C 282 fkeeae 287
                                        + +++
  gi|336253226|ref|YP_004596333.1|  87 ARDRVD 92 
                                       444555 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  15.6    0.0012      0.86      63     154 ..      10     100 ..       2     109 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                         Golgin_A5  63 lqklnqqieqlrtelqdleaqqqaeaeslreqlqel...eeqleeerkakeeveaelerlkeelryleeelvrskat 136
                                       +q++++  +++ ++    e+ + + + ++re+ +e+    +q ++e k+++ +e+  e++++e +++ ee  r+++ 
  gi|336253226|ref|YP_004596333.1|  10 IQSAESDADEIVAQ---AEQDRDERIAEARERAEEIrteADQEAQELKERR-LEEAREEIDQECERVLEEGEREREA 82 
                                       44444444444444...4444444455555555555000555554444444.7888899****************** PP

                         Golgin_A5 137 lqsrikdrekeieklrnq 154
                                       l  r +dr +e+ +   +
  gi|336253226|ref|YP_004596333.1|  83 LADRARDRVDEVTDHVVE 100
                                       *********999876555 PP

>> Remorin_C  Remorin, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   5.2    0.0003      0.21      62     101 ..       6      45 ..       3      50 .. 0.90
   2 ?    3.2   4.8      0.11        79      47      94 ..      50      97 ..      44     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0003
                         Remorin_C  62 lknklariekkAeekRasaeakrreeelktkekankirst 101
                                       + ++++++e  A+e  a+ae+ r+e ++++ e+a++ir++
  gi|336253226|ref|YP_004596333.1|   6 VLERIQSAESDADEIVAQAEQDRDERIAEARERAEEIRTE 45 
                                       5678999******************************986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.11
                         Remorin_C 47 leeklEkkrakaleklknklariekkAeekRasaeakrreeelktkek 94
                                       +e  E++ ++a e++ ++ +r+ ++ e  R++   + r  + ++++ 
  gi|336253226|ref|YP_004596333.1| 50 AQELKERRLEEAREEIDQECERVLEEGEREREALADRARDRVDEVTDH 97
                                      445557888899999999999999999999999999998888877765 PP

>> Merozoite_SPAM  Merozoite surface protein (SPAM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  20.9    0.0016       1.1      22     100 ..       6      83 ..       3     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0016
                    Merozoite_SPAM  22 lLeevkitsedkediakEnedvveeeeeedleekedeeeEteeeeteekneeeieeetedeedE.eeveEeeekeee 97 
                                       +Le+++ +++d ++i+   e+  +e   e +e+ e++ +E + +e +e +e   ee  e+ ++E e v Ee e  e 
  gi|336253226|ref|YP_004596333.1|   6 VLERIQSAESDADEIVAQAEQDRDERIAEARERAEEIRTEAD-QEAQELKERRLEEAREEIDQEcERVLEEGER-ER 80 
                                       8****************9999999999*************99.7777777877777777777775666664444.33 PP

                    Merozoite_SPAM  98 edk 100
                                       e  
  gi|336253226|ref|YP_004596333.1|  81 EAL 83 
                                       333 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   6.5     0.074        51       4      55 ..       5      56 ..       3      62 .. 0.88
   2 ?    9.5   1.8    0.0012      0.81      18      59 ..      60     101 ..      54     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.074
                              CdvA  4 kALeeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledq 55
                                       +Le + s      + +++ ++  +e +++ +e+a+e++ + +++ +el++ 
  gi|336253226|ref|YP_004596333.1|  5 EVLERIQSAESDADEIVAQAEQDRDERIAEARERAEEIRTEADQEAQELKER 56
                                      6799999999999999999999999999**********99999999999986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                              CdvA  18 styeeikekleealkklkekakelkeklkkrlkeledqiksl 59 
                                       ++ eei ++ e+ l++ ++++++l+++ + r++e+ d + +l
  gi|336253226|ref|YP_004596333.1|  60 EAREEIDQECERVLEEGEREREALADRARDRVDEVTDHVVEL 101
                                       66799*******************************998876 PP

>> Caudo_TAP  Caudovirales tail fibre assembly protein, lambda gpK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   8.7    0.0032       2.2      58      98 ..      13      55 ..       4      62 .. 0.81
   2 ?    1.4   0.2      0.47   3.3e+02      61      89 ..      70      98 ..      61     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0032
                         Caudo_TAP 58 dk..keeqiqqAeqekqqllaqAseqiaplqdavdlgiatdeE 98
                                      ++  ++e ++qAeq +++++a+A+e+ +++++++d +    +E
  gi|336253226|ref|YP_004596333.1| 13 AEsdADEIVAQAEQDRDERIAEARERAEEIRTEADQEAQELKE 55
                                      3355999**************************9988766665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.47
                         Caudo_TAP 61 eeqiqqAeqekqqllaqAseqiaplqdav 89
                                      e   ++ e+e+++l + A++++ + +d v
  gi|336253226|ref|YP_004596333.1| 70 ERVLEEGEREREALADRARDRVDEVTDHV 98
                                      5567788999********99999988865 PP

>> Peptidase_M41  Peptidase family M41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.6    0.0079       5.4     125     167 ..      27      69 ..      11      72 .. 0.80
   2 ?    9.0   0.8    0.0017       1.2     138     179 ..      59     100 ..      55     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0079
                                       ---.------SS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTH CS
                     Peptidase_M41 125 flgkelkkekelseetaeeideevkelveeayerakeileekr 167
                                          +++++++e +ee+++e d+e +el e++ e+a+e + ++ 
  gi|336253226|ref|YP_004596333.1|  27 DRDERIAEARERAEEIRTEADQEAQELKERRLEEAREEIDQEC 69 
                                       244678899999***********************99998765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHH CS
                     Peptidase_M41 138 eetaeeideevkelveeayerakeileekreelealaeaLle 179
                                       ee +eeid+e ++++ee  ++ +++  + r+++++++++++e
  gi|336253226|ref|YP_004596333.1|  59 EEAREEIDQECERVLEEGEREREALADRARDRVDEVTDHVVE 100
                                       57789*******************************998876 PP

>> Borrelia_P83  Borrelia P83/100 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  12.7    0.0027       1.8     277     360 ..      14      92 ..       2     107 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0027
                      Borrelia_P83 277 eekkreiekaqkeikkkdeeakkakdakaedlkkeskaeekeaedkeleakkereevaeDlqkikeevkakktseae 353
                                       e    ei   q e + +de +  a+++ ae+++ e+ +e +e   ke   ++ ree+ ++  ++ ee++ ++ ++a+
  gi|336253226|ref|YP_004596333.1|  14 ESDADEIVA-QAE-QDRDERIAEARER-AEEIRTEADQEAQE--LKERRLEEAREEIDQECERVLEEGEREREALAD 85 
                                       344444433.444.3345555556665.66666666655555..444444456667777777777777777777777 PP

                      Borrelia_P83 354 daidssn 360
                                        a+d + 
  gi|336253226|ref|YP_004596333.1|  86 RARDRVD 92 
                                       7766554 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  12.9    0.0051       3.5      19     103 ..      12      96 ..       5     105 .. 0.45

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  19 aaqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkqqellkpil 95 
                                       +a+++ ++  ++ +++ +++ +e ++ +ee+ ++a ++++e ke+ l++ ++e+ q+ ++  +e ++++++l ++  
  gi|336253226|ref|YP_004596333.1|  12 SAESDADEIVAQAEQDRDERIAEARERAEEIRTEADQEAQELKERRLEEAREEIDQECERVLEEGEREREALADRAR 88 
                                       33333444444444444444444444444444333332122333335555555555555555555555555555555 PP

                                       HHHHHHHH CS
                              OmpH  96 dkinkaik 103
                                       d+++++++
  gi|336253226|ref|YP_004596333.1|  89 DRVDEVTD 96 
                                       55555544 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  12.5     0.012       8.5     507     595 ..      10     100 ..       5     105 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHCHHH.HHHHHHH.HHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHH CS
                             HSP70 507 iekmvkdaeesaee.dkkkkea.ieakneaeelvyslekkleeeaekvseaekekvesaieeLkeeleeeekeeiea 581
                                       i++ ++da+e  ++ ++ + e+ +ea+++aee+ ++++++ +e +e   e+++e+++++ e + ee+e+e ++   +
  gi|336253226|ref|YP_004596333.1|  10 IQSAESDADEIVAQaEQDRDERiAEARERAEEIRTEADQEAQELKERRLEEAREEIDQECERVLEEGEREREALADR 86 
                                       55555566554333033333332599999999999999999999999999999999999999999998888777777 PP

                                       HHHHHHHHHHHHHH CS
                             HSP70 582 kteelkkvvekiae 595
                                       +++++++v+ +++e
  gi|336253226|ref|YP_004596333.1|  87 ARDRVDEVTDHVVE 100
                                       78888877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2447  (0.136483); expected 358.6 (0.02)
Passed bias filter:                      782  (0.0436165); expected 358.6 (0.02)
Passed Vit filter:                       140  (0.00780858); 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):              26  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 776.64
//
Query:       gi|336253227|ref|YP_004596334.1|  [L=746]
Description: V-type ATPase 116 kDa subunit [Halopiger xanaduensis SH-6]
Scores for complete 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   82.7  10.6    5.1e-11   41.3   1.8    5.1  5  V_ATPase_I       V-type ATPase 116kDa subunit family
     0.0011   18.9   0.9        0.2   11.6   0.2    2.3  2  Prefoldin_2      Prefoldin subunit
     0.0019   18.5   1.9       0.13   12.6   0.1    2.9  2  FlaC_arch        Flagella accessory protein C (FlaC)
     0.0054   15.5   0.6      0.069   11.9   0.1    2.0  2  Tektin           Tektin family
  ------ inclusion threshold ------
       0.07   13.6   6.2        1.6    9.2   2.6    2.6  2  DUF4140          N-terminal domain of unknown function (DUF41
      0.074   13.3   2.4        3.4    8.0   0.1    2.4  2  Spc24            Spc24 subunit of Ndc80
      0.081   12.5   2.1       0.39   10.2   0.4    2.1  2  MscS_porin       Mechanosensitive ion channel porin domain
      0.093   12.0   0.4        1.6    8.0   0.2    2.1  2  DUF3450          Protein of unknown function (DUF3450)
       0.11   12.4   0.4       0.77    9.7   0.0    2.1  2  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
       0.15   12.1   6.1        1.8    8.6   0.5    2.3  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.16   12.0   1.1        6.7    6.8   0.2    2.3  2  DUF1664          Protein of unknown function (DUF1664)
       0.36    9.7   2.8       0.85    8.4   0.2    2.0  2  Spc7             Spc7 kinetochore protein
       0.62    9.9   6.3       0.44   10.4   1.8    2.1  2  Apolipoprotein   Apolipoprotein A1/A4/E domain
       0.67   10.2   5.4        2.8    8.2   1.5    2.7  2  XhlA             Haemolysin XhlA
          1    8.7   2.5        1.3    8.3   0.1    2.0  2  Helo_like_N      Fungal N-terminal domain of STAND proteins
        2.1    7.9   6.3         13    5.2   6.3    1.9  1  Filament         Intermediate filament protein
        2.3    8.1   4.5         18    5.2   0.3    2.1  2  Ax_dynein_light  Axonemal dynein light chain
        5.4    7.4   5.2         24    5.4   0.4    2.5  2  CCDC-167         Coiled-coil domain-containing protein 167


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 ?   -1.5   0.0      0.43   4.3e+02      62     104 ..      83     118 ..      27     128 .. 0.56
   2 !   10.2   0.0   0.00013      0.12     230     332 ..     198     298 ..     188     314 .. 0.75
   3 !   41.3   1.8   5.1e-14   5.1e-11     337     459 ..     348     460 ..     316     464 .. 0.83
   4 ?   -0.4   0.1       0.2     2e+02     513     537 ..     492     516 ..     491     526 .. 0.86
   5 !   31.6   0.1   4.4e-11   4.4e-08     763     811 ..     689     737 ..     597     739 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.43
                        V_ATPase_I  62 sleapeekeldeleeelekleeelkelnenleklkkelnelve 104
                                       +l+++        e++le++ ++++el+++ ++++++l++++e
  gi|336253227|ref|YP_004596334.1|  83 QLDENW-------ENRLEEIRTRVNELDDQRSDVRDDLRQVEE 118
                                       333333.......344444444444444444444444333333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00013
                        V_ATPase_I 230 fgaklyelpeseeereeklkeveeriedlekvleqteealkevleeiakeleewklkvkkekai..yhtLnlfnldv 304
                                       ++ + +e+p++e++ +  ++++e+r +dle+ le+ +    ++l+ei ++  ++ l+v+ e +i    +   +++ +
  gi|336253227|ref|YP_004596334.1| 198 VEFTRHEVPDTEKSPSAYVDDLESRKADLESRLEEID----AELAEIRRKEGSFLLQVESELSIevQRAEAPLQFAT 270
                                       6677888999999999999999999999988886655....555666666666666666655441144445677789 PP

                        V_ATPase_I 305 tkkvliaegWvpkeeleeiqkalkeate 332
                                       t + ++aegW+p++e +++++al++a  
  gi|336253227|ref|YP_004596334.1| 271 TGRAFVAEGWIPTDEYDRLRSALRDAVG 298
                                       99**********************9874 PP

  == domain 3  score: 41.3 bits;  conditional E-value: 5.1e-14
                        V_ATPase_I 337 svpsilneietketpPTyfrtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalll 413
                                        v+   + ++  ++pPT  +     + f  +v+a   ++Y E+ p++f   tFP  F+ M GD+G Gll +++++++
  gi|336253227|ref|YP_004596334.1| 348 AVTDGGSAVTMGDEPPTVQNNPGPARPFEVLVQAVNRPKYSELDPTIFLFLTFPAFFGFMIGDFGYGLLYVAIGAYM 424
                                       55555556666789**************************************************************9 PP

                        V_ATPase_I 414 vlkekklkkkkkdeilemlfsgRYiillmGlfsiYtGliYNdifsk 459
                                        ++    ++k        + s   + +  Glf +  G+iY +if++
  gi|336253227|ref|YP_004596334.1| 425 ATQF---DSK-------GITSLGGVAIWAGLFTMLFGIIYGEIFGL 460
                                       7654...443.......23333345677899999999999999976 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.2
                        V_ATPase_I 513 mKlsvilGviqMlfgvllslvNaly 537
                                       m +sv+ G++++ +g++l ++++l 
  gi|336253227|ref|YP_004596334.1| 492 MVVSVLAGIVHLNIGYILDFYENLS 516
                                       779***************9987765 PP

  == domain 5  score: 31.6 bits;  conditional E-value: 4.4e-11
                        V_ATPase_I 763 ilfavfavltvavLllmeglsafLHaLRLhWVEfqsKFykgdGykFepf 811
                                       ++ ++ +v+  +v+l + ++sa L a+RL+ VEf +KFy g G k+epf
  gi|336253227|ref|YP_004596334.1| 689 LGGLIILVVGHIVVLALGVTSAGLQAVRLEYVEFFNKFYDGGGEKYEPF 737
                                       4445556777789999********************************9 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.2    0.0002       0.2      60     100 ..      81     121 ..      77     124 .. 0.90
   2 ?    5.5   0.0     0.016        16      69      96 ..     214     241 ..     194     247 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelkeelq 100
                                       + ++ e+ e+r+e++ +++++l +q ++++ +l++++e ++
  gi|336253227|ref|YP_004596334.1|  81 RGQLDENWENRLEEIRTRVNELDDQRSDVRDDLRQVEERIN 121
                                       56788999******************************997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  69 erketlekeiktlekqleklekeleelk 96 
                                       +  ++le + + le++le++ +el+e++
  gi|336253227|ref|YP_004596334.1| 214 AYVDDLESRKADLESRLEEIDAELAEIR 241
                                       4444444444444444444444444443 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 !   12.6   0.1   0.00013      0.13       5      40 ..      88     123 ..      86     142 .. 0.80
   2 ?    4.1   0.1     0.062        61       2      28 ..     216     242 ..     215     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                         FlaC_arch   5 lEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                        En+l+++ t+++ + ++ +++++++ +++e+++++
  gi|336253227|ref|YP_004596334.1|  88 WENRLEEIRTRVNELDDQRSDVRDDLRQVEERINRV 123
                                       69*******************************554 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.062
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsk 28 
                                       +d+lE++  +l+++le + +e+ e++ 
  gi|336253227|ref|YP_004596334.1| 216 VDDLESRKADLESRLEEIDAELAEIRR 242
                                       677888888888888888888887764 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1     7e-05     0.069     226     283 ..      65     122 ..      39     124 .. 0.86
   2 ?    1.8   0.1     0.082        82      43      77 ..     207     241 ..     199     272 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7e-05
                            Tektin 226 aidsilkqtandlraqaeavnealrkrieetedaknkleeqlkkvleeiaelekniee 283
                                       a++s+l  +  d++ q+ + +e  ++r+ee++   n+l +q++ v++++ ++e+ i++
  gi|336253227|ref|YP_004596334.1|  65 ALESTLDLADADVEPQRGQLDENWENRLEEIRTRVNELDDQRSDVRDDLRQVEERINR 122
                                       689999999*********************************************9986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.082
                            Tektin  43 dsnkrLeeRiediefwkeeLekeleelkeeieaLe 77 
                                       d++k+ ++ ++d+e  k  Le  lee+++e  ++ 
  gi|336253227|ref|YP_004596334.1| 207 DTEKSPSAYVDDLESRKADLESRLEEIDAELAEIR 241
                                       55566666666666666666666666666555443 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 ?    9.2   2.6    0.0016       1.6      51      96 ..      76     121 ..      53     123 .. 0.77
   2 ?    4.9   0.1     0.035        35      52      93 ..     198     242 ..     190     247 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0016
                           DUF4140  51 dvqvervpnreaeeeelkalraeleeledelaaledelaaaearla 96 
                                       dv+ +r + +e+ e++l+++r +++el d++++++d+l+ +e+r++
  gi|336253227|ref|YP_004596334.1|  76 DVEPQRGQLDENWENRLEEIRTRVNELDDQRSDVRDDLRQVEERIN 121
                                       4555555555666668***************************997 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.035
                           DUF4140  52 vqvervpnreaeee..e.lkalraeleeledelaaledelaaaea 93 
                                       v+++r + +++e++  + ++ l+++   le +l+++++ela ++ 
  gi|336253227|ref|YP_004596334.1| 198 VEFTRHEVPDTEKSpsAyVDDLESRKADLESRLEEIDAELAEIRR 242
                                       455554444444445645778888888888888888777776654 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0034       3.4      21      69 ..      86     135 ..      80     166 .. 0.82
   2 ?    4.6   0.3     0.038        38      13      42 ..     216     245 ..     208     267 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0034
                             Spc24  21 esleselaelkeeleeleeesee.keservedetllklklYrsLGielek 69 
                                       e+ e++l+e +++++el++++++ +++ r+ +e + ++  + +LGi+l+ 
  gi|336253227|ref|YP_004596334.1|  86 ENWENRLEEIRTRVNELDDQRSDvRDDLRQVEERINRVAPFAELGIDLDL 135
                                       56789999***********99995444445599*************9964 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.038
                             Spc24  13 lsdleselesleselaelkeeleeleeese 42 
                                       ++dles   +les+l+e  +el+e+ +++ 
  gi|336253227|ref|YP_004596334.1| 216 VDDLESRKADLESRLEEIDAELAEIRRKEG 245
                                       578899999999999999999999888765 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4   0.00039      0.39      79     139 ..      62     123 ..      50     132 .. 0.89
   2 ?    1.3   0.1      0.21   2.1e+02      84     125 ..     220     240 ..     203     258 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00039
                        MscS_porin  79 sleeLeqrllqtssqlqelqeqlaq.lnsqlvelqtrperaqqqltearqrlqeirnrLnst 139
                                       + ++Le+ l+ + ++++ ++ ql +  +++l e++tr +++  q ++ r  l +++ r+n  
  gi|336253227|ref|YP_004596334.1|  62 TVRALESTLDLADADVEPQRGQLDEnWENRLEEIRTRVNELDDQRSDVRDDLRQVEERINRV 123
                                       7789*******************76279*****************************99876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.21
                        MscS_porin  84 eqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltea 125
                                       e+r ++ +s+l+e  ++la                     e 
  gi|336253227|ref|YP_004596334.1| 220 ESRKADLESRLEEIDAELA---------------------EI 240
                                       2222222222222222222.....................22 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0016       1.6      23      62 ..      83     122 ..      64     127 .. 0.89
   2 ?    1.8   0.0      0.12   1.2e+02      61      93 ..     210     242 ..     177     257 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                           DUF3450  23 keaekavaaaaqsqkkidklddekqellaeyralkeeles 62 
                                       +  e++ +  +++ +++++ldd+++++ +++r+++e++++
  gi|336253227|ref|YP_004596334.1|  83 QLDENWENRLEEIRTRVNELDDQRSDVRDDLRQVEERINR 122
                                       56788999999************************99876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.12
                           DUF3450  61 eslevyneqlerlvasqeqeiasleeqieeiee 93 
                                       +s ++y + le+  a++e+++++++ +++ei++
  gi|336253227|ref|YP_004596334.1| 210 KSPSAYVDDLESRKADLESRLEEIDAELAEIRR 242
                                       444555555555555555555555555555544 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 ?    0.3   0.2       0.6     6e+02     108     140 ..      87     119 ..      56     125 .. 0.66
   2 ?    9.7   0.0   0.00077      0.77      93     150 ..     198     253 ..     181     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.6
                       EMP24_GP25L 108 akkekletleselkkleekldsikreqkylrer 140
                                       + ++ le++ +++++l+++ ++++++++  +er
  gi|336253227|ref|YP_004596334.1|  87 NWENRLEEIRTRVNELDDQRSDVRDDLRQVEER 119
                                       336666666666666666666666666555554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00077
                       EMP24_GP25L  93 fdievgseasdykdsakkekletleselkkleekldsikreqkylrereerlrdtnes 150
                                       ++++  +e++ +++  ++  +++les+   le++l++i  e+  +r++e ++  ++es
  gi|336253227|ref|YP_004596334.1| 198 VEFTR-HEVP-DTEKSPSAYVDDLESRKADLESRLEEIDAELAEIRRKEGSFLLQVES 253
                                       45554.4554.477788*********************************99888887 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 ?    8.6   0.5    0.0018       1.8      83     116 ..      86     119 ..      57     128 .. 0.80
   2 ?    5.8   0.7     0.013        13      96     134 ..     216     254 ..     200     263 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
                    CENP-F_leu_zip  83 eeLekelqkkqervseLeslnsslenlleekEqe 116
                                       e+ e+ l++ + rv+eL+  +s+++  l++ E+ 
  gi|336253227|ref|YP_004596334.1|  86 ENWENRLEEIRTRVNELDDQRSDVRDDLRQVEER 119
                                       677899************************9986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                    CENP-F_leu_zip  96 vseLeslnsslenlleekEqekvqmkeeskaaveeLqtq 134
                                       v++Les++ +le+ lee  +e ++++ +  + + + +++
  gi|336253227|ref|YP_004596334.1| 216 VDDLESRKADLESRLEEIDAELAEIRRKEGSFLLQVESE 254
                                       788888888888888888888777766665555555544 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0067       6.7      74     112 ..      83     122 ..      54     125 .. 0.59
   2 ?    3.5   0.0     0.068        68      54      80 ..     216     242 ..     205     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0067
                           DUF1664  74 kldeqke.iskeikeevtevredlseigedvesvkeaveg 112
                                       +lde+ e   +ei+  v+e+ ++ s++++d+++v+e ++ 
  gi|336253227|ref|YP_004596334.1|  83 QLDENWEnRLEEIRTRVNELDDQRSDVRDDLRQVEERINR 122
                                       3444433134566677777777777777777777666654 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.068
                           DUF1664  54 seslaatkrhLssridrvdkkldeqke 80 
                                        ++l++ k +L+sr++++d++l e  +
  gi|336253227|ref|YP_004596334.1| 216 VDDLESRKADLESRLEEIDAELAEIRR 242
                                       5789999*************9988765 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2   0.00086      0.85     201     258 ..      63     121 ..      52     129 .. 0.84
   2 ?    1.2   0.2      0.14   1.4e+02     169     241 ..     216     242 ..     196     264 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00086
                              Spc7 201 Leelreelaelkaeieekkkelael.qeqleeleekieelkeqkseleeeiaeaervle 258
                                       +++l ++l+ ++a++e ++ +l+e  +++lee++++++el++q+s++++++++ e+ ++
  gi|336253227|ref|YP_004596334.1|  63 VRALESTLDLADADVEPQRGQLDENwENRLEEIRTRVNELDDQRSDVRDDLRQVEERIN 121
                                       677888999999999999999977538899*******************9999887665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                              Spc7 169 lpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelke 241
                                       +++le++ka+le++le++ ++ +e+                                              + 
  gi|336253227|ref|YP_004596334.1| 216 VDDLESRKADLESRLEEIDAELAEI----------------------------------------------RR 242
                                       3344444444444444443333333..............................................33 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.8   0.00045      0.44      40      99 ..      64     122 ..      53     163 .. 0.84
   2 ?    1.4   0.2      0.25   2.5e+02      45      65 ..     218     238 ..     200     265 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCC CS
                    Apolipoprotein  40 arlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeqlav 99 
                                       ++l++ l+ + a +ep+r ++ e+++ +lee+r r++++ +++ + ++ d+++++e++  
  gi|336253227|ref|YP_004596334.1|  64 RALESTLDLADADVEPQRGQLDENWENRLEEIRTRVNELDDQRSD-VRDDLRQVEERINR 122
                                       567888899999999*******************99998888855.67777777776654 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.25
                                       HHHHHHHHCCCCHHHHHHCCC CS
                    Apolipoprotein  45 eleevrarlepyrdevqeqlg 65 
                                       +le+ +a le++++e+ ++l+
  gi|336253227|ref|YP_004596334.1| 218 DLESRKADLESRLEEIDAELA 238
                                       333333333333333333332 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.5    0.0028       2.8      10      43 ..      89     122 ..      86     124 .. 0.89
   2 ?    2.6   0.1      0.16   1.6e+02      19      45 ..     215     241 ..     205     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0028
                              XhlA  10 etkldnleervdkleekaaeaeekiknleedlkk 43 
                                       e++l+++ +rv++l++  + ++  + ++ee++++
  gi|336253227|ref|YP_004596334.1|  89 ENRLEEIRTRVNELDDQRSDVRDDLRQVEERINR 122
                                       8999999999999999999999999999999997 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.16
                              XhlA  19 rvdkleekaaeaeekiknleedlkkle 45 
                                        vd+le ++a  e++++++  +l+++ 
  gi|336253227|ref|YP_004596334.1| 215 YVDDLESRKADLESRLEEIDAELAEIR 241
                                       589999999999999999999999885 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.4      0.57   5.7e+02     160     186 ..      86     112 ..      83     124 .. 0.68
   2 ?    8.3   0.1    0.0013       1.3     148     191 ..     212     255 ..     192     267 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.57
                       Helo_like_N 160 sdLeehLedideklealtekseeasee 186
                                       ++ e++Le+i +++++l +++++ +++
  gi|336253227|ref|YP_004596334.1|  86 ENWENRLEEIRTRVNELDDQRSDVRDD 112
                                       567899999999999999666555333 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0013
                       Helo_like_N 148 leeykeliedttsdLeehLedideklealtekseeaseedeael 191
                                        + y + +e+ ++dLe++Le+id  l+++ +k+ +   + e+el
  gi|336253227|ref|YP_004596334.1| 212 PSAYVDDLESRKADLESRLEEIDAELAEIRRKEGSFLLQVESEL 255
                                       556777788999*****************988877665555555 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   6.3     0.013        13      29     138 ..      65     242 ..      61     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                                       XXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........... CS
                          Filament  29 eLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyeke........... 94 
                                       +Le+ +       ++++ +l+e +e+ lee+r +++el  +r+ ++ +l++++e ++++    e             
  gi|336253227|ref|YP_004596334.1|  65 ALESTLDLADADVEPQRGQLDENWENRLEEIRTRVNELDDQRSDVRDDLRQVEERINRVAPFAELGidldllsgyet 141
                                       57777777777788999999**********************************99999876666688999999999 PP

                                       .........................................................XXXXXXXXXXXXXXXXXXXX CS
                          Filament  95 .........................................................lnkreevEaelkalrkdlde 114
                                                                                                   r+ev ++ k+    +d+
  gi|336253227|ref|YP_004596334.1| 142 idvvvgegrvdaiedaleasdeirayetftggdvvavaaaptddaganpiddalvgvEFTRHEVPDTEKSPSAYVDD 218
                                       99999999999966666666666666666666666666666666666666666555544555555555555599999 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 115 atlarvdLekkvesLkeelaflkk 138
                                       +  +++dLe+++e++  ela  ++
  gi|336253227|ref|YP_004596334.1| 219 LESRKADLESRLEEIDAELAEIRR 242
                                       999999999999999999987665 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 ?    4.3   0.4     0.034        33     118     157 ..      82     121 ..      76     124 .. 0.88
   2 ?    5.2   0.3     0.018        18     126     172 ..     214     260 ..     201     267 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.034
                   Ax_dynein_light 118 eqgkselekkikeLeeekeelekqvaelkaklealekrek 157
                                        q  ++ e++++e++++++el +q ++++  l+++e+r +
  gi|336253227|ref|YP_004596334.1|  82 GQLDENWENRLEEIRTRVNELDDQRSDVRDDLRQVEERIN 121
                                       5677899999************************999876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.018
                   Ax_dynein_light 126 kkikeLeeekeelekqvaelkaklealekrekerrqeeekkheeeie 172
                                       + + +Le++k++le++++e++a+l++++++e   + + e++ + e++
  gi|336253227|ref|YP_004596334.1| 214 AYVDDLESRKADLESRLEEIDAELAEIRRKEGSFLLQVESELSIEVQ 260
                                       45889**********************99998877777777666665 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 ?    3.7   0.5     0.079        79       4      30 ..      97     123 ..      91     129 .. 0.88
   2 ?    5.4   0.4     0.024        24       6      28 ..     216     238 ..     202     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.079
                          CCDC-167   4 seIdkleeklascrerLeaverrlrke 30 
                                       + +++l+++ +++r++L +ve r++++
  gi|336253227|ref|YP_004596334.1|  97 TRVNELDDQRSDVRDDLRQVEERINRV 123
                                       5688999****************9876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.024
                          CCDC-167   6 IdkleeklascrerLeaverrlr 28 
                                       +d+le + a+++ rLe+++ +l 
  gi|336253227|ref|YP_004596334.1| 216 VDDLESRKADLESRLEEIDAELA 238
                                       67777777777777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (746 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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):              18  [number of targets reported over threshold]
# CPU time: 0.81u 0.28s 00:00:01.09 Elapsed: 00:00:00.49
# Mc/sec: 4595.77
//
Query:       gi|336253228|ref|YP_004596335.1|  [L=91]
Description: H+transporting two-sector ATPase C subunit [Halopiger xanaduensis SH-6]
Scores for 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-13   49.4   8.0    5.4e-13   49.1   8.0    1.2  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 !   49.1   8.0     3e-17   5.4e-13       2      59 ..      31      88 ..      30      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 3e-17
                                      HHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_C  2 gaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivali 59
                                      +a++avGl+al+sG++   +g+a+++a+a++ +lf+  li+ +++e++ +++L+v +i
  gi|336253228|ref|YP_004596335.1| 31 AAAIAVGLAALASGYAERGIGAAAVGALAEDDDLFVPGLIMTVLPETLVILALVVVFI 88
                                      8********************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 696.34
//
Query:       gi|336253229|ref|YP_004596336.1|  [L=195]
Description: V-type proton ATPase subunit E [Halopiger xanaduensis SH-6]
Scores for complete 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-41  142.0  10.1    2.1e-41  141.6  10.1    1.2  1  vATP-synt_E      ATP synthase (E/31 kDa) subunit
     0.0057   14.7   1.6     0.0061   14.6   1.6    1.0  1  V_ATPase_I       V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
      0.088   12.0   1.7       0.12   11.6   1.7    1.1  1  DUF3535          Domain of unknown function (DUF3535)
       0.16   11.6   1.7       0.24   11.1   1.7    1.3  1  Peptidase_C58    Yersinia/Haemophilus virulence surface antig
       0.23   11.8   9.0       0.41   11.0   9.0    1.5  1  OmpH             Outer membrane protein (OmpH-like)
       0.28    9.9  10.3       0.36    9.5  10.3    1.1  1  HAUS5            HAUS augmin-like complex subunit 5
        0.3   10.8   7.5       0.22   11.2   0.3    2.6  2  Nbl1_Borealin_N  Nbl1 / Borealin N terminal
        0.4   10.2   9.6       0.57    9.7   9.6    1.2  1  HAUS-augmin3     HAUS augmin-like complex subunit 3
       0.49   11.0  14.5       0.23   12.0  12.1    1.7  1  V-ATPase_G       Vacuolar (H+)-ATPase G subunit
        2.1    6.4   8.0        2.4    6.2   8.0    1.1  1  HSP70            Hsp70 protein
        3.6    7.5  13.1        5.7    6.8  13.1    1.3  1  MRP-S26          Mitochondrial ribosome subunit S26
        4.1    7.4  13.3        2.9    7.9   7.0    2.5  3  Phasin           Poly(hydroxyalcanoate) granule associated pr
        6.1    7.5  15.8        2.7    8.7   2.2    2.8  2  DUF883           Bacterial protein of unknown function (DUF88


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 !  141.6  10.1   1.5e-44   2.1e-41       1     199 []       9     193 ..       9     193 .. 0.95

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 1.5e-44
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       vATP-synt_E   1 fIrqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleev 77 
                                       +Ir+eA+++AeeI+a++e  ++++ + ++e++e  +eea  +  +++++ +++ +S+a+++a++k+L+ar++vl ev
  gi|336253229|ref|YP_004596336.1|   9 DIREEAHARAEEIRAEGESRADEIESAAEEDAEATLEEAEREVDREIDQLREQRLSSAKLEAKQKRLEARRDVLGEV 85 
                                       69*************************************************************************** PP

                                       HHHHHHHHHHHTTSHHCCCCHHHHHHCCCCCCC-.SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEE CS
                       vATP-synt_E  78 feeaekkLaeveedkdeYkellkkLivqalvkle.epevivrarkeDaelveealdkaaeeykaktkkktvevagde 153
                                       +e++e++La ++ ++  ++el++ L+ +a  ++  +++v+v++r++D+el+e++     e+ +     + +e ag++
  gi|336253229|ref|YP_004596336.1|  86 REQVEEELASLDGNT--REELTRALLEAAGTEFDaGDDVSVYGREDDRELIESI----LEDDAF----DGYEYAGER 152
                                       ***************..****************9899****************6....333222....347889999 PP

                                       SSEBTTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                       vATP-synt_E 154 edfledvlGGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                            d+lGGvv+e+ +++++vnnT++++Le v+e++l++i+++LF
  gi|336253229|ref|YP_004596336.1| 153 -----DCLGGVVVESDQSRVRVNNTFDSVLEDVWEDNLQAISNRLF 193
                                       .....****************************************9 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 !   14.6   1.6   4.4e-06    0.0061      36     146 ..      11     119 ..       4     177 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.4e-06
                        V_ATPase_I  36 erklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavleka 112
                                        ++ +   eei+ + +  +   e+e+  e++ e++l+e e+e+++  ++l+e++ ++ kl++++++l+  + vl ++
  gi|336253229|ref|YP_004596336.1|  11 REEAHARAEEIRAEGESRAD--EIESAAEEDAEATLEEAEREVDREIDQLREQRLSSAKLEAKQKRLEARRDVLGEV 85 
                                       45555555666663333333..34789999999******************************************** PP

                        V_ATPase_I 113 kefleee.eeeeeeeeseeeeeekeeeeeeeseee 146
                                       +e +eee ++ + + ++ee +++  e+  +e+++ 
  gi|336253229|ref|YP_004596336.1|  86 REQVEEElASLDGN-TREELTRALLEAAGTEFDAG 119
                                       ****9985444444.33333333333333444444 PP

>> DUF3535  Domain of unknown function (DUF3535)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.7   8.4e-05      0.12     198     300 ..       5     108 ..       2     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                           DUF3535 198 lsltrlrqecqdllatlesvg..klpklavvvqgeaekaftleqaeklvttdyekllkslslkqkllaek.qLeerr 271
                                       ++++ +r+e+++  + ++ +g  +  +++   +++a    tle+ae+ v+ ++++l ++  +++kl a++  Le+rr
  gi|336253229|ref|YP_004596336.1|   5 TVVEDIREEAHARAEEIRAEGesRADEIESAAEEDA--EATLEEAEREVDREIDQLREQRLSSAKLEAKQkRLEARR 79 
                                       667888999999999999999666666666666665..99******************9999999999886788888 PP

                           DUF3535 272 rrlqaaieeakeeqealhvrvqaalAgAl 300
                                         l +  e+++ee ++l+ +++  l  Al
  gi|336253229|ref|YP_004596336.1|  80 DVLGEVREQVEEELASLDGNTREELTRAL 108
                                       88888888999999999988877777766 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 ?   11.1   1.7   0.00017      0.24      51     116 ..      23      94 ..       8     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                                       .HHHHHHHHHHHHHHHHHHHHH.HTT-SSHHHHHHH..HHHHHTT-EE-S--EEEE.......--S-HHHHH CS
                     Peptidase_C58  51 skgqsraaeiqslysikklqll.sqrakaqdqqfqatdtwlkeaglepseeelklg.....evagavsaenv 116
                                       ++g+sra+ei+s+ ++   ++l + + + + + +q+++++l++a le++++ l+ +     ev ++v++e +
  gi|336253229|ref|YP_004596336.1|  23 AEGESRADEIESAAEEDAEATLeEAEREVDREIDQLREQRLSSAKLEAKQKRLEARrdvlgEVREQVEEELA 94 
                                       3678999***998877776666045555666667*******************9999888888888877655 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   9.0    0.0003      0.41      23     103 ..       9      90 ..       2     115 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHH CS
                              OmpH  23 qlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkqqellk..pildk 97 
                                       ++ +++ ++++e++a++++  +++e   ++ ++++ ee+e+e++++ ++l++ q+    +l++kq+ l +   +l +
  gi|336253229|ref|YP_004596336.1|   9 DIREEAHARAEEIRAEGESRADEIESAAEEDAEATLEEAEREVDREIDQLRE-QRLSSAKLEAKQKRLEArrDVLGE 84 
                                       4444444444444444444444444333222222267777777777777777.666666666666554332245555 PP

                                       HHHHHH CS
                              OmpH  98 inkaik 103
                                       +++ ++
  gi|336253229|ref|YP_004596336.1|  85 VREQVE 90 
                                       554443 PP

>> HAUS5  HAUS augmin-like complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5  10.3   0.00026      0.36      82     168 ..      11     111 ..       5     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00026
                             HAUS5  82 reelekeverLraeirrldkeleareee.....lsreeaevkraldeisdsrhrqvlLeaydqqceeaakilaedtk 153
                                       ree+++  e++rae +    e+e++ ee     l++ e+ev+r +d+ +++r   + Lea +++ e+ + +l e + 
  gi|336253229|ref|YP_004596336.1|  11 REEAHARAEEIRAEGESRADEIESAAEEdaeatLEEAEREVDREIDQLREQRLSSAKLEAKQKRLEARRDVLGEVRE 87 
                                       89999999999999999999998765543333367779999************************************ PP

                             HAUS5 154 rlqeqvqqlrdaer.........k 168
                                       +++e +++l+   r          
  gi|336253229|ref|YP_004596336.1|  88 QVEEELASLDGNTReeltralleA 111
                                       *********999994444444441 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 ?   11.2   0.3   0.00016      0.22       3      35 ..       4      36 ..       2      40 .. 0.89
   2 ?    2.4   1.9     0.089   1.2e+02       3      24 ..      41      62 ..      39      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                   Nbl1_Borealin_N  3 ealLenfdlEveeRirrlraelelllktlrnrf 35
                                      +++ e+   E++ R++++rae e+ +++++++ 
  gi|336253229|ref|YP_004596336.1|  4 DTVVEDIREEAHARAEEIRAEGESRADEIESAA 36
                                      67789999*******************999875 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.089
                   Nbl1_Borealin_N  3 ealLenfdlEveeRirrlrael 24
                                      ea Le+ + Ev+  i +lr++ 
  gi|336253229|ref|YP_004596336.1| 41 EATLEEAEREVDREIDQLREQR 62
                                      78899999***********985 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   9.6   0.00041      0.57      70     153 ..      26     110 ..       2     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00041
                      HAUS-augmin3  70 evilee.eeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaetna 145
                                       e+ ++e e +++e+ e+ l+e+++e ++ + +l +  +  a+l+ ++++le++ +   ++ ++ +eel++   +t++
  gi|336253229|ref|YP_004596336.1|  26 ESRADEiESAAEEDAEATLEEAEREVDREIDQLREQRLSSAKLEAKQKRLEARRDVLGEVREQVEEELASLDGNTRE 102
                                       33333303457899*************************************************************** PP

                      HAUS-augmin3 146 vLqqltee 153
                                       +L++ + e
  gi|336253229|ref|YP_004596336.1| 103 ELTRALLE 110
                                       **987654 PP

>> 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 ?   12.0  12.1   0.00017      0.23      12      88 ..      25     102 ..      21     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHSHHHHHHHHHHHHSSHHHHHHHHHHH CS
                        V-ATPase_G  12 AEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefk.ekeaeklgseeelekkieketeekikelkesvk 87 
                                        E +A+ei ++A ++ ++ l +A+ e  +Ei++ r+++    k e +++ l ++ ++  ++++++ee++++l+ +++
  gi|336253229|ref|YP_004596336.1|  25 GESRADEIESAAEEDAEATLEEAEREVDREIDQLREQRLSSAKlEAKQKRLEARRDVLGEVREQVEEELASLDGNTR 101
                                       5899**********************************888773456667888999999**********99987765 PP

                                       H CS
                        V-ATPase_G  88 k 88 
                                       +
  gi|336253229|ref|YP_004596336.1| 102 E 102
                                       4 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   8.0    0.0017       2.4     519     589 ..      10      78 ..       1     105 [. 0.74

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHHHHHHHHHH CS
                             HSP70 519 eedkkkkeaieakneaeelvyslekkleeeaekvseaekekvesaieeLkeeleeeekeeieakteelkkv 589
                                        +++++++a e ++e e+ ++++e++ ee+ae+  e+++++v+++i++L+e+    +++++eak+++l++ 
  gi|336253229|ref|YP_004596336.1|  10 IREEAHARAEEIRAEGESRADEIESAAEEDAEATLEEAEREVDREIDQLREQR--LSSAKLEAKQKRLEAR 78 
                                       46677777889999999999999999999999999999999999999999985..3344455555554443 PP

>> MRP-S26  Mitochondrial ribosome subunit S26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  13.1    0.0041       5.7      42     140 ..       9     104 ..       3     115 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0041
                           MRP-S26  42 slrelfk...eevekeeeeelkkeseekaeeeeeefkellaiNdewNaelaelReerlkkeaeekkeeilerieeke 115
                                        +re+ +   ee++ e e++ ++e+e  aee+    + l +   e  +e+ +lRe+rl++ + e k+++le+  + +
  gi|336253229|ref|YP_004596336.1|   9 DIREEAHaraEEIRAEGESR-ADEIESAAEED--AEATLEEAEREVDREIDQLREQRLSSAKLEAKQKRLEARRDVL 82 
                                       56666665544444444444.55666666666..556778889999****************999999999888777 PP

                           MRP-S26 116 qkeeekkekaeeevlqekeesktFI 140
                                           e +e++eee+  +  ++ + +
  gi|336253229|ref|YP_004596336.1|  83 G---EVREQVEEELASLDGNTREEL 104
                                       7...555555566555555555555 PP

>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   7.0    0.0021       2.9      56     113 ..       4      61 ..       1      77 [. 0.86
   2 ?    4.0   4.4     0.034        47      47     108 ..      43     105 ..      38     112 .. 0.72
   3 ?   -2.6   0.0       3.9   5.4e+03      63      73 ..     170     180 ..     159     192 .. 0.42

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0021
                            Phasin  56 eekleevresvkskveevkekaeeqwdklekafdervakaLsrlgvpsredveaLsar 113
                                       ++ +e++re++++++ee++++ e++ d++e+a +e  +++L++ +    +++++L+++
  gi|336253229|ref|YP_004596336.1|   4 DTVVEDIREEAHARAEEIRAEGESRADEIESAAEEDAEATLEEAEREVDREIDQLREQ 61 
                                       667899****************************************99****999763 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.034
                            Phasin  47 lekktkkvaeekleevr.esvkskveevkekaeeqwdklekafdervakaLsrlgvpsredve 108
                                       + ++++++++ +++++r ++++s+  e+k+k  e+ + +   + e+v++ L +l+  +re++ 
  gi|336253229|ref|YP_004596336.1|  43 TLEEAEREVDREIDQLReQRLSSAKLEAKQKRLEARRDVLGEVREQVEEELASLDGNTREELT 105
                                       556677888888888885566666667777777777777777888899999999999998875 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.9
                            Phasin  63 resvkskveev 73 
                                       +++ +s +e+v
  gi|336253229|ref|YP_004596336.1| 170 NNTFDSVLEDV 180
                                       22222222222 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 ?    8.7   2.2     0.002       2.7      29      65 ..       7      43 ..       2      43 .. 0.82
   2 ?    4.1   9.7     0.052        72       6      62 ..      31      89 ..      29     118 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.002
                            DUF883 29 aeelRerleerlerarerlrdaeeavaerakeaaeaa 65
                                      +e++Re++++r+e+ r++ +  +++++  a+e aea+
  gi|336253229|ref|YP_004596336.1|  7 VEDIREEAHARAEEIRAEGESRADEIESAAEEDAEAT 43
                                      6789999999999999999999999998888887775 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.052
                            DUF883  6 el.eslladleellkeaadeageeaeelRerl..eerlerarerlrdaeeavaerakeaa 62
                                      e+  ++ +d+e+ l+ea++e ++e+++lRe+   +++le+ ++rl+ a+++v  +++e +
  gi|336253229|ref|YP_004596336.1| 31 EIeSAAEEDAEATLEEAEREVDREIDQLREQRlsSAKLEAKQKRLE-ARRDVLGEVREQV 89
                                      663345789********************97411334455555554.4444333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1895  (0.105695); expected 358.6 (0.02)
Passed bias filter:                      789  (0.0440069); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); 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):              13  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 1354.97
//
Query:       gi|336253230|ref|YP_004596337.1|  [L=349]
Description: V-type ATP synthase subunit C [Halopiger xanaduensis SH-6]
Scores for 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-82  275.4   5.9    9.1e-82  275.2   5.9    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 !  275.2   5.9   5.1e-86   9.1e-82       1     335 [.      11     344 ..      11     345 .. 0.95

  Alignments for each domain:
  == domain 1  score: 275.2 bits;  conditional E-value: 5.1e-86
                                       HHHHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--......SSSHHHHHHHHHHHHHHHTTTGGGGS- CS
                    vATP-synt_AC39   1 leArvramrsglLteedyenLlqcesledvkryLketdYgnfladel.seplsrsdiekalreklarefnklreqap 76 
                                       ++Arvr +r++l+++edy++L+++   ++++r+++e++Y+ + ++el ++ ++++ ie+al+++la++f++l+++a+
  gi|336253230|ref|YP_004596337.1|  11 VNARVRSRRAKLFDDEDYRKLVRM-GPSEIARFMEESEYERE-INELgARFSGVDLIEYALNRNLAKHFQDLLDWAE 85 
                                       69*******************555.*****************.56666***************************** PP

                                       H.HHHHHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SSSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHH CS
                    vATP-synt_AC39  77 gpsrefldyllyrydidNvklllrgklsgdldleeleeklhplgelsaldldklieaksveelyeallgtpyakyle 153
                                       g ++++++ +l+++d++Nvk+++rg+++ d+++e ++ +l+ +gel+  +ld+l+e + +e+++e l++t y+++l+
  gi|336253230|ref|YP_004596337.1|  86 GRLYDLISRYLRKFDVWNVKTIIRGIYT-DTPAEGIQTDLIRAGELDDATLDRLLEVDEIEDVVELLSDTIYYEPLS 161
                                       **88************************.8999******************************************** PP

                                       HHHCC...--SHHHHHHHHHHHHHHHHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS.......T...- CS
                    vATP-synt_AC39 154 ealdeleetgdleiienaLdkayledllkfckklggetaeilreilgfeiDlrniniilrskkyg.elskedrkkll 229
                                       e l+e+eetg+l ++enaLd+ ++e+ll+   + ++  ++ + e+l++eiD+rn +++lr+ ++g +l ++ +   +
  gi|336253230|ref|YP_004596337.1| 162 EGLEEFEETGTLVPLENALDREFYEHLLDDLGRPEEGPEAKYVEFLEAEIDFRNARNALRLARSGaDLDPAAY---Y 235
                                       ******************************776665555779***********************77777767...* PP

                                       -SS-.S--HHHHHHHHTT-G.....GG.GGSSTSSTTGGGTT-...-S.HHHHHHHHHHHHHHHHHT.TTSSSTSTH CS
                    vATP-synt_AC39 230 ipgg.slypeglealaeaedveellaalkyteygelleealee...agslksledaldealvkllkk.afrqqfsvg 301
                                       i gg  +++++l++l++  d++el++ + +++yg+ l+ al++   a+sl ++e+ald+al++++++ +  ++ sv 
  gi|336253230|ref|YP_004596337.1| 236 IAGGvLFDESELSRLVA--DYDELVDHIDDSRYGDRLSGALDQlrdADSLIQFEHALDAALLEYADTlSSIYPVSVS 310
                                       ****************4..6*******************9999**8888**************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHT--SHHHHG CS
                    vATP-synt_AC39 302 vfyaYlklkeqEirnlrwIaegiaqglpkekIre 335
                                       ++++Y+++ke+E++n+r+Ia+g++ gl++++I+e
  gi|336253230|ref|YP_004596337.1| 311 AVLSYILAKEREVENIRAIARGREVGLDESEIEE 344
                                       ********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 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:                        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 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2643.55
//
Query:       gi|336253231|ref|YP_004596338.1|  [L=110]
Description: V-type ATP synthase subunit F [Halopiger xanaduensis SH-6]
Scores for 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   56.5   0.1      3e-15   56.3   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 !   56.3   0.1   1.7e-19     3e-15       1      90 [.       5      98 ..       5      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.7e-19
                                      EEEEESHHHHHHHHHTTCEEEE....CSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCS.SSSEEEEES CS
                        ATP-synt_F  1 iavIGdedtvtgfrlaGvgeve....vtdeeeieealkelleredigiilitekiaeeirelideykee.alPaileIP 74
                                      iav+G+ +++tgfrlaGv+ +e    +++  ++ +a++++l+++d+gi++++++ +e +++ +++  e+ + P++++I 
  gi|336253231|ref|YP_004596338.1|  5 IAVVGSPEFTTGFRLAGVRRFEnvpdDEKGTDLDDAVTDVLNDDDVGIVVMHDDDLEYLSRGVRQDVETsVEPVVVTIG 83
                                      8*********************99999999******************************9998877777********8 PP

                                      CSCCGGSHH.CHHHHHH CS
                        ATP-synt_F 75 skegpydee.kdsvrkk 90
                                      s +g    + +d++++ 
  gi|336253231|ref|YP_004596338.1| 84 SGTGGG--GlRDQIKRA 98
                                      877744..448888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 834.60
//
Query:       gi|336253232|ref|YP_004596339.1|  [L=587]
Description: V-type ATP synthase subunit alpha [Halopiger xanaduensis SH-6]
Scores for 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-92  308.0   0.0    4.3e-92  307.6   0.0    1.1  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    1.8e-39  134.4   0.1    3.1e-39  133.6   0.1    1.4  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    1.1e-11   45.1   3.9    1.1e-11   45.1   3.9    2.3  3  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
  ------ inclusion threshold ------
      0.027   14.8   0.0       0.08   13.2   0.0    1.8  1  AAA_22           AAA domain
       0.15   12.1   0.3         16    5.7   0.0    2.8  3  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
       0.15   12.4   0.0       0.45   10.9   0.0    1.7  1  Npun_R1517       Npun R1517


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 !  307.6   0.0   1.4e-95   4.3e-92       1     213 []     219     440 ..     219     440 .. 0.98

  Alignments for each domain:
  == domain 1  score: 307.6 bits;  conditional E-value: 1.4e-95
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imk 70 
                                       G+rv D lfp+++G++ +ipg fg Gktv +q+l+k+s++d +++y+g+Gergne++ev+e+fpe      g+ +m+
  gi|336253232|ref|YP_004596339.1| 219 GQRVQDGLFPLAKGGTAAIPGPFGSGKTVTQQQLAKWSDAD-IVVYIGCGERGNEMTEVIEDFPElpdpqtGNpLMA 294
                                       9************************************9888.************************99976337*** PP

                                       GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  71 rtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                       rt+l+antsn+pvaare +iytgit+AEy+rd+g++v l+ads+srwaeA+reis rl+emp+++gypayl+a l++
  gi|336253232|ref|YP_004596339.1| 295 RTCLIANTSNMPVAARESCIYTGITIAEYYRDMGYDVALMADSTSRWAEAMREISSRLEEMPGEEGYPAYLAAALSE 371
                                       ***************************************************************************** PP

                                       HHTTSEEE...TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 148 lyERagka...pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       +yERagk+   + ++Gs+++v avsp+ggDfs+pvt++tl+i+++f+ Ld +la+r+hfP+in+  S+S
  gi|336253232|ref|YP_004596339.1| 372 FYERAGKFqlmNGDEGSISVVGAVSPPGGDFSEPVTQNTLRIVKTFWALDADLAERRHFPSINWNESYS 440
                                       ********9887889*****************************************************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 !  133.6   0.1     1e-42   3.1e-39       1     120 [.      93     209 ..      93     210 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 1e-42
                                       EETTS-BHHHHHHHHTS.BE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-.EEEE CS
                   ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgs.fierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkv.egkv 75 
                                       yDG+qrpL+ +++k+g+ f++rGv++p +d ek+wef+ +v++gd+v++gd++G+v+et +i+hk+mvpp+   g+v
  gi|336253232|ref|YP_004596339.1|  93 YDGVQRPLDVLEDKMGTaFLDRGVDAPGIDLEKQWEFTAEVEEGDEVEPGDVVGVVPETVTIDHKVMVPPDYeGGEV 169
                                       9*********************************************************************983567* PP

                                       EEE--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEE CS
                   ATP-synt_ab_Xtn  76 keiaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkek 120
                                       ++i+ +ge+tve+t+ae++++e    e++++q+wPvr++rp  +k
  gi|336253232|ref|YP_004596339.1| 170 TSIE-SGEFTVEETVAELSSGE----EIQMHQEWPVREARPAGNK 209
                                       **98.**************776....8**************9876 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 !   45.1   3.9   3.7e-15   1.1e-11       2      69 .]      17      77 ..      16      77 .. 0.94
   2 ?   -3.9   0.0         6   1.8e+04      56      66 ..     130     140 ..     129     141 .. 0.79
   3 ?   -2.3   0.1       2.2   6.5e+03      32      46 ..     471     485 ..     465     501 .. 0.52

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 3.7e-15
                                      EEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  2 vqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                       +v+Gpvv + +  +    +++++ v+  +  ++l+g++++++++   ++v+++t+G+ +G++V++TG
  gi|336253232|ref|YP_004596339.1| 17 ESVSGPVVTATDLDA---RMNDVVYVG--D--EGLMGEVIEIEGNLTTIQVYEETSGVGPGEPVENTG 77
                                      68********66666...*********..9..***********************************9 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6
                                       STTBBTTSEEE CS
                     ATP-synt_ab_N  56 tdGlsrGteVk 66 
                                       t  +++G+eV+
  gi|336253232|ref|YP_004596339.1| 130 TAEVEEGDEVE 140
                                       56789999998 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.2
                                       CSTEEEEEEEEEETT CS
                     ATP-synt_ab_N  32 fgtlllgvalnlged 46 
                                       +++ l++ ++ +g d
  gi|336253232|ref|YP_004596339.1| 471 EEDELQEIVQLVGKD 485
                                       344445555544443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.7e-05      0.08       6      54 ..     233     274 ..     230     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.7e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.ssk 54 
                                       g  ++ G+ G+GKT++ ++l+++ d         + vv++ + + + + +
  gi|336253232|ref|YP_004596339.1| 233 GTAAIPGPFGSGKTVTQQQLAKWSD--------ADIVVYIGCGERGnEMT 274
                                       66799******************97........67777888877765555 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 ?   -2.5   0.0       1.9   5.6e+03      64      80 ..      48      64 ..      46      65 .. 0.84
   2 ?    5.7   0.0    0.0053        16      45      66 ..     126     147 ..     115     149 .. 0.87
   3 ?    3.2   0.0      0.03        89      18      39 ..     303     324 ..     292     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.9
                                      EEEEEEEHHHHHHHHHH CS
                         QRPTase_N 64 lleieGnarallsaERv 80
                                      ++eieGn+ ++  +E +
  gi|336253232|ref|YP_004596339.1| 48 VIEIEGNLTTIQVYEET 64
                                      789*****999988865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0053
                                       TTEEEESS-TT-EEETTEEEEE CS
                         QRPTase_N  45 glevellvkDGervekgdvlle 66 
                                       + e++++v++G++ve+gdv+  
  gi|336253232|ref|YP_004596339.1| 126 QWEFTAEVEEGDEVEPGDVVGV 147
                                       568999*************975 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.03
                                       EEEEEEESSSEEE-SHHHHHHH CS
                         QRPTase_N  18 akaeiiakeegvvaGlevaeev 39 
                                       +++ + a+e++++ G+++ae  
  gi|336253232|ref|YP_004596339.1| 303 SNMPVAARESCIYTGITIAEYY 324
                                       567799***********99864 PP

>> Npun_R1517  Npun R1517
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00015      0.45      34      69 ..     526     561 ..     518     563 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                        Npun_R1517  34 lldalseGedeylesleasvkiqevaelkasPemrr 69 
                                       +l a+   +de +e+l+a v + e+ +++a+P++ r
  gi|336253232|ref|YP_004596339.1| 526 MLQAIKTFNDEAFEALDAGVPVDEIQDIDAAPRLNR 561
                                       577888899***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 4429.50
//
Query:       gi|336253233|ref|YP_004596340.1|  [L=469]
Description: V-type ATP synthase subunit beta [Halopiger xanaduensis SH-6]
Scores for 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-66  221.8   0.0    1.2e-65  221.2   0.0    1.3  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    5.5e-14   52.4   1.2    1.5e-13   51.0   1.2    1.8  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
     0.0013   18.8   0.5     0.0042   17.2   0.5    2.0  1  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 !  221.2   0.0   1.9e-69   1.2e-65       1     213 []     129     351 ..     129     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 221.2 bits;  conditional E-value: 1.9e-69
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS........S.EEEEEEESEEHHHHHHHHHHCHHSSG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........x.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd........d.aiiyvgiGergnevaevleefpegti 68 
                                       G++++D + ++v+Gq++ i++++g+++++++ ++++q++          + a+i+ ++G  ++e++e++++f+++++
  gi|336253233|ref|YP_004596340.1| 129 GVSAIDGMNTLVRGQKLPIFSGSGLPHNELALQIARQATVPeeegeggsEfAVIFGAMGITQEEANEFMDDFERTGA 205
                                       899**********************************8666999****878************************** PP

                                       GGGEEEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  69 mkrtvlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgak 144
                                       ++r+v+++n +++p+++r  ++++++t+AEy++  ++++vl+i++++++++eAlrei+++ +e+p+++gyp+y++++
  gi|336253233|ref|YP_004596340.1| 206 LERSVVFMNLADDPAVERQVTPRLALTTAEYLAFeKDYHVLVILTDMTNYCEALREIGAAREEVPGRRGYPGYMYTD 282
                                       *********************************9899**************************************** PP

                                       HHHHHTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 145 laslyERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       la+lyERag+++ + Gsvt++++++++g+D ++p+++ t +it+g+iv+d++l ++++ P+invl S+S
  gi|336253233|ref|YP_004596340.1| 283 LAQLYERAGRIEGKDGSVTQIPILTMPGDDDTHPIPDLTGYITEGQIVMDRDLNSQGIEPPINVLPSLS 351
                                       *******************************************************************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 !   51.0   1.2   2.6e-17   1.5e-13       1      69 []       7      72 ..       7      72 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.6e-17
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      i++++Gp+v +e ++    g+++++e+e ++ g+ l+g++l+ +e+ V ++v+++t G++r++ V+++G
  gi|336253233|ref|YP_004596340.1|  7 ITEISGPLVFAEVDEP--VGYDEIVEIETPQ-GETLRGQVLESSEGIVSIQVFEGTGGIDRNASVRFLG 72
                                      89*********99999..9999999999888.***********************************98 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.5   7.1e-07    0.0042       3      82 ..       2      59 ..       1      89 [. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.1e-07
                        HAS-barrel  3 evigests.sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalate 80
                                      +++++ t  s++++++e +++v++ e Veie+p+ge + G+v+  ++g                       ++ ++++e
  gi|336253233|ref|YP_004596340.1|  2 KEYQTITEiSGPLVFAEVDEPVGYDEIVEIETPQGETLRGQVLESSEG-----------------------IVSIQVFE 57
                                      689999999*********************************998884.......................44444444 PP

                        HAS-barrel 81 dt 82
                                      +t
  gi|336253233|ref|YP_004596340.1| 58 GT 59
                                      44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3459.43
//
Query:       gi|336253234|ref|YP_004596341.1|  [L=115]
Description: hypothetical protein Halxa_1834 [Halopiger xanaduensis SH-6]
Scores for 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:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 941.30
//
Query:       gi|336253235|ref|YP_004596342.1|  [L=67]
Description: hypothetical protein Halxa_1835 [Halopiger xanaduensis SH-6]
Scores for 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  100.5   0.4    4.5e-29  100.4   0.4    1.0  1  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
     0.0012   19.1   0.3     0.0016   18.8   0.3    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0026   17.2   0.6       0.32   10.5   0.1    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0049   16.5   3.4          1    9.1   0.5    2.2  2  zinc_ribbon_2    zinc-ribbon domain
      0.005   16.2   2.3       0.56    9.7   0.2    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0056   16.5   1.2       0.87    9.5   0.1    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
     0.0062   16.2   0.6        1.9    8.3   0.0    2.3  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.007   16.4   0.1       0.01   15.9   0.1    1.2  1  CpXC             CpXC protein
     0.0093   16.1   1.2       0.53   10.5   1.2    2.1  1  DUF2387          Probable metal-binding protein (DUF2387)
  ------ inclusion threshold ------
      0.011   15.7   2.9        1.6    8.8   0.5    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.014   15.4   0.2      0.019   15.0   0.2    1.3  1  DZR              Double zinc ribbon
      0.015   15.4   0.8       0.92    9.7   0.3    2.3  2  Zn-ribbon_8      Zinc ribbon domain
      0.016   15.6   1.4       0.09   13.2   0.0    2.1  2  zf-IS66          zinc-finger binding domain of transposase IS
      0.047   13.4   0.9        3.5    7.4   0.1    2.1  2  Ribosomal_S27e   Ribosomal protein S27
      0.074   13.1   0.6        0.3   11.2   0.6    1.8  1  Elf1             Transcription elongation factor Elf1 like
       0.11   12.1   2.8          1    9.1   0.1    2.2  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.12   11.5   0.5        1.7    7.7   0.0    1.9  2  GcpE             GcpE protein
       0.21   11.7   2.3        2.8    8.0   0.2    2.1  2  Zn_Tnp_IS91      Transposase zinc-binding domain
       0.42   10.6   2.4        3.7    7.5   2.4    2.0  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.72    9.8   5.7        7.2    6.6   0.3    2.4  2  zinc_ribbon_4    zinc-ribbon domain
       0.91    9.7   5.5         12    6.1   1.2    2.1  2  UPF0547          Uncharacterised protein family UPF0547
        5.8    6.8   8.6          1    9.2   0.8    2.5  2  zf-HYPF          HypF finger


Domain annotation for each model (and alignments):
>> 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 !  100.4   0.4   5.6e-32   4.5e-29       1      63 []       7      67 .]       7      67 .] 0.97

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 5.6e-32
                    zinc_ribbon_13  1 kCpKCgnteaevkevaatGsglskifdvqnkkfitvsCknCgYtelYkaetsegknilDlllg 63
                                      +CpKCg+te+e++e+a+tGsglsk+fd+qn+kf++vsC+nCgY+elY+ ++s   n++Dl+lg
  gi|336253235|ref|YP_004596342.1|  7 GCPKCGHTETEMDEIATTGSGLSKMFDIQNRKFMVVSCTNCGYSELYRGQSSG--NMVDLFLG 67
                                      5*************************************************999..9*****97 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 !   18.8   0.3   1.9e-06    0.0016       6      36 ..       8      49 ..       4      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.9e-06
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigq...........cvyCadCga 36
                                      CP Cg+ ++   +  ++ ++             +v+C++Cg+
  gi|336253235|ref|YP_004596342.1|  8 CPKCGHTETEMDEIATTGSGLSkmfdiqnrkfmVVSCTNCGY 49
                                      ********999999988876669******************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 !   10.5   0.1    0.0004      0.32       3      15 ..       8      20 ..       6      26 .. 0.84
   2 ?    5.7   0.0     0.013        10      21      27 ..      43      49 ..      33      62 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0004
                                      ETTTTCEECHEET CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDp 15
                                      CP+Cg+t+++ D+
  gi|336253235|ref|YP_004596342.1|  8 CPKCGHTETEMDE 20
                                      *******998884 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                                      EESSSSB CS
                      TF_Zn_Ribbon 21 vCtdCGl 27
                                       Ct+CG+
  gi|336253235|ref|YP_004596342.1| 43 SCTNCGY 49
                                      4777764 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.5    0.0013         1      16      21 ..       8      13 ..       2      14 .. 0.69
   2 !    8.2   0.1    0.0024         2      16      21 ..      44      49 ..      35      50 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                     zinc_ribbon_2 16 CpyCGt 21
                                      Cp+CG+
  gi|336253235|ref|YP_004596342.1|  8 CPKCGH 13
                                      777776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0024
                     zinc_ribbon_2 16 CpyCGt 21
                                      C++CG+
  gi|336253235|ref|YP_004596342.1| 44 CTNCGY 49
                                      777775 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.2   0.00068      0.56       5      10 ..       8      13 ..       2      19 .. 0.65
   2 !    6.5   0.2     0.007       5.7      18      24 ..      43      49 ..      40      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00068
                       zf-ribbon_3  5 CPnCGa 10
                                      CP+CG+
  gi|336253235|ref|YP_004596342.1|  8 CPKCGH 13
                                      555555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.007
                       zf-ribbon_3 18 vCpyCGt 24
                                       C++CG+
  gi|336253235|ref|YP_004596342.1| 43 SCTNCGY 49
                                      6999997 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 !    9.5   0.1    0.0011      0.87       3      11 ..       8      16 ..       6      23 .. 0.89
   2 ?    6.3   0.1     0.011       8.7      29      36 ..      42      49 ..      34      56 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                           TFIIS_C  3 CpkCgsrea 11
                                      CpkCg++e+
  gi|336253235|ref|YP_004596342.1|  8 CPKCGHTET 16
                                      ******997 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                           TFIIS_C 29 ykCtkCgh 36
                                      + Ct+Cg+
  gi|336253235|ref|YP_004596342.1| 42 VSCTNCGY 49
                                      66777775 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 !    8.3   0.0    0.0023       1.9      18      31 ..       2      15 ..       1      16 [. 0.84
   2 !    6.4   0.1     0.009       7.3      23      31 ..      43      51 ..      36      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0023
                     A2L_zn_ribbon 18 eqgylvCieCgasf 31
                                      +++++ C++Cg ++
  gi|336253235|ref|YP_004596342.1|  2 KDDERGCPKCGHTE 15
                                      689999*****876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.009
                     A2L_zn_ribbon 23 vCieCgasf 31
                                      +C +Cg+s+
  gi|336253235|ref|YP_004596342.1| 43 SCTNCGYSE 51
                                      699***997 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.3e-05      0.01       3      48 ..       8      52 ..       7      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                              CpXC  3 CpaCgkefeaeiwtsidadedpelkeklldgslfeatCpkCgatak 48
                                      Cp+Cg++ e+e+ ++ ++ +      ++ + ++  + C +Cg++  
  gi|336253235|ref|YP_004596342.1|  8 CPKCGHT-ETEMDEIATTGSGLSKMFDIQNRKFMVVSCTNCGYSEL 52
                                      *****85.78999******99999******************9875 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   1.2   0.00065      0.53      11      45 ..       8      56 ..       8      64 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00065
                           DUF2387 11 CPrC....semD........kirmweede..veyrECvsCgftdelsek 45
                                      CP+C     emD          +m++ ++    ++ C++Cg+++  + +
  gi|336253235|ref|YP_004596342.1|  8 CPKCghteTEMDeiattgsgLSKMFDIQNrkFMVVSCTNCGYSELYRGQ 56
                                      888843333677444444433368876663356899******9977666 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 ?    8.8   0.5     0.002       1.6      19      28 ..       6      17 ..       2      39 .. 0.78
   2 ?    8.1   0.1    0.0032       2.6      20      32 ..      42      55 ..      28      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.002
                     Zn_Tnp_IS1595 19 fvCPhCgsr..k 28
                                      + CP+Cg++  +
  gi|336253235|ref|YP_004596342.1|  6 RGCPKCGHTetE 17
                                      56*****98544 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0032
                     Zn_Tnp_IS1595 20 v.CPhCgsrkayri 32
                                      v C +Cg++++yr 
  gi|336253235|ref|YP_004596342.1| 42 VsCTNCGYSELYRG 55
                                      44**********85 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   2.3e-05     0.019       9      37 ..       2      50 ..       1      57 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                               DZR  9 ppdarfCseCgtklkavaa....................edrCpsCgek 37
                                      ++d r C++Cg++  ++ +                       C +Cg++
  gi|336253235|ref|YP_004596342.1|  2 KDDERGCPKCGHTETEMDEiattgsglskmfdiqnrkfmVVSCTNCGYS 50
                                      578899******977666688899***************9*******96 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   0.3    0.0011      0.92      26      36 ..       4      16 ..       1      19 [. 0.69
   2 ?    4.6   0.0     0.042        35       8      12 ..      44      48 ..      27      60 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                       Zn-ribbon_8 26 lta.CPeCgs.ev 36
                                      ++  CP+Cg+ e+
  gi|336253235|ref|YP_004596342.1|  4 DERgCPKCGHtET 16
                                      4455****99665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.042
                       Zn-ribbon_8  8 CeeCg 12
                                      C++Cg
  gi|336253235|ref|YP_004596342.1| 44 CTNCG 48
                                      66666 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 ?   13.2   0.0   0.00011      0.09       1      32 [.       5      41 ..       5      43 .. 0.68
   2 ?    1.5   0.3      0.48   3.9e+02       3       9 ..      43      49 ..      42      55 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                           zf-IS66  1 prtCpcCGg.l..lkpigedrvr...eeldipPakfrV 32
                                      +r Cp+CG+ +  +++i+++  +     +di   kf V
  gi|336253235|ref|YP_004596342.1|  5 ERGCPKCGHtEteMDEIATT-GSglsKMFDIQNRKFMV 41
                                      578******66776666555.33566777777777776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.48
                           zf-IS66  3 tCpcCGg 9 
                                      +C +CG 
  gi|336253235|ref|YP_004596342.1| 43 SCTNCGY 49
                                      5888885 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.025        21      10      22 ..       8      20 ..       6      24 .. 0.78
   2 ?    7.4   0.1    0.0044       3.5       2      15 ..      36      49 ..      35      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.025
                                      -TTTS-EEEEESS CS
                    Ribosomal_S27e 10 CpdCenetvvFsh 22
                                      Cp+C+++ +  + 
  gi|336253235|ref|YP_004596342.1|  8 CPKCGHTETEMDE 20
                                      ******9986665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0044
                                      S--EEEEE-TTTS- CS
                    Ribosomal_S27e  2 rskFldvkCpdCen 15
                                      + kF+ v C +C+ 
  gi|336253235|ref|YP_004596342.1| 36 NRKFMVVSCTNCGY 49
                                      56899999999975 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   0.00036       0.3      24      69 ..       8      65 ..       3      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00036
                              Elf1 24 CpfCnheksvevkldkkek............iaevsCkvCgesfetkvnalsepvDvY 69
                                      Cp C+h+++   ++ ++ +              +vsC++Cg s  ++ ++  + vD +
  gi|336253235|ref|YP_004596342.1|  8 CPKCGHTETEMDEIATTGSglskmfdiqnrkFMVVSCTNCGYSELYRGQSSGNMVDLF 65
                                      999999965444455444478888888888899********99888888888888876 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 ?    3.5   0.5     0.072        59      20      25 ..       8      13 ..       3      14 .. 0.90
   2 ?    9.1   0.1    0.0013         1      17      29 ..      41      53 ..      32      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.072
                                      -SSS-- CS
                    DNA_RNApol_7kD 20 CkeCGh 25
                                      C +CGh
  gi|336253235|ref|YP_004596342.1|  8 CPKCGH 13
                                      99***9 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                                      ----SSS-----B CS
                    DNA_RNApol_7kD 17 piRCkeCGhRilY 29
                                      ++ C++CG+  lY
  gi|336253235|ref|YP_004596342.1| 41 VVSCTNCGYSELY 53
                                      689*****98777 PP

>> GcpE  GcpE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.015        12     267     282 ..       8      23 ..       4      26 .. 0.88
   2 ?    7.7   0.0     0.002       1.7     239     274 ..      15      51 ..      14      63 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.015
                                       ----TTS-CHHHHHHH CS
                              GcpE 267 CPsCgRtlfdlqelve 282
                                       CP+Cg t++++ e+++
  gi|336253235|ref|YP_004596342.1|   8 CPKCGHTETEMDEIAT 23 
                                       *********9999875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.002
                                       S-CCHHHHH.HHHHHHHTTS--SS-EEEE----TTS- CS
                              GcpE 239 edpeeEvkv.akeiLqalrlrksktelisCPsCgRtl 274
                                       e+ ++E+ + ++ + +  +++++k  ++sC  Cg  +
  gi|336253235|ref|YP_004596342.1|  15 ETEMDEIATtGSGLSKMFDIQNRKFMVVSCTNCGYSE 51 
                                       5556676541566667889***************765 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 ?    8.0   0.2    0.0035       2.8      57      69 ..       5      17 ..       2      25 .. 0.87
   2 ?    4.1   0.1     0.056        46      37      49 ..      39      51 ..      25      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0035
                       Zn_Tnp_IS91 57 srhCpsCqkkate 69
                                      +r Cp+C++ +te
  gi|336253235|ref|YP_004596342.1|  5 ERGCPKCGHTETE 17
                                      699******9987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.056
                       Zn_Tnp_IS91 37 faryeCeeCghek 49
                                      f+++ C++Cg ++
  gi|336253235|ref|YP_004596342.1| 39 FMVVSCTNCGYSE 51
                                      7889999999765 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 ?    7.5   2.4    0.0046       3.7      31      54 ..       8      49 ..       6      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0046
                    OrfB_Zn_ribbon 31 CseCgsknke..................alsgrtfkCpnCgf 54
                                      C++Cg++ +e                  +++  ++ C+nCg+
  gi|336253235|ref|YP_004596342.1|  8 CPKCGHTETEmdeiattgsglskmfdiqNRKFMVVSCTNCGY 49
                                      9*****999988888888888888865555555667888887 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.0     0.018        15      28      34 ..       8      14 ..       7      14 .. 0.89
   2 ?    6.6   0.3    0.0088       7.2       1      32 [.      40      48 ..      30      50 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.018
                     zinc_ribbon_4 28 CskCghv 34
                                      C+kCgh+
  gi|336253235|ref|YP_004596342.1|  8 CPKCGHT 14
                                      99**996 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0088
                     zinc_ribbon_4  1 MkitCpsCkakyeiddeklpakgvkvrCskCg 32
                                      M ++                       C++Cg
  gi|336253235|ref|YP_004596342.1| 40 MVVS-----------------------CTNCG 48
                                      4455.......................55555 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.2     0.014        12      17      22 ..       8      13 ..       5      14 .. 0.80
   2 ?    5.7   0.2      0.02        16      15      23 ..      42      50 ..      41      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.014
                           UPF0547 17 CphCGy 22
                                      Cp CG+
  gi|336253235|ref|YP_004596342.1|  8 CPKCGH 13
                                      999998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                           UPF0547 15 qfCphCGyv 23
                                      ++C  CGy+
  gi|336253235|ref|YP_004596342.1| 42 VSCTNCGYS 50
                                      68******7 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.6      0.46   3.8e+02      24      28 ..       8      12 ..       7      14 .. 0.87
   2 ?    9.2   0.8    0.0012         1       9      28 ..      31      48 ..      28      49 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.46
                                      -TTTS CS
                           zf-HYPF 24 CtnCG 28
                                      C++CG
  gi|336253235|ref|YP_004596342.1|  8 CPKCG 12
                                      99999 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0012
                                      HC-TTSTTTT-TT---TTTS CS
                           zf-HYPF  9 ykdpldRRfhaqfisCtnCG 28
                                      ++d ++R f    +sCtnCG
  gi|336253235|ref|YP_004596342.1| 31 MFDIQNRKFM--VVSCTNCG 48
                                      6677777765..59*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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):              22  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 482.61
//
Query:       gi|336253236|ref|YP_004596343.1|  [L=249]
Description: V-type ATP synthase subunit D [Halopiger xanaduensis SH-6]
Scores for 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-53  180.0   8.8    4.5e-53  180.0   8.8    1.5  2  ATP-synt_D  ATP synthase subunit D
  ------ inclusion threshold ------
        2.4    8.0  18.3        4.2    7.2  15.3    2.3  2  DUF1168     Protein of unknown function (DUF1168)
        4.5    7.7  14.2    1.3e+02    3.0  14.2    2.7  1  RICH        RICH domain


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 !  180.0   8.8   7.5e-57   4.5e-53       1     196 []      11     204 ..      11     204 .. 0.96
   2 ?   -2.7   0.9      0.75   4.5e+03      39      59 ..     209     229 ..     205     246 .. 0.58

  Alignments for each domain:
  == domain 1  score: 180.0 bits;  conditional E-value: 7.5e-57
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-. CS
                        ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvkl 77 
                                       +L+++++r++l +rgh +L+kKrd Li+ef++il+++++ r +l++ +++a++++ +a+a++g+ +++ a+++ ++ 
  gi|336253236|ref|YP_004596343.1|  11 NLMEIEDRIELSERGHGTLEKKRDGLIMEFMDILDKAQDVRGDLADDYEAAQKKINMARAMEGDVAVRGAAAALQE- 86 
                                       68999****************************************************************9996666. PP

                                       .TSS-SEEEEEEBTTSEEEEEEE-...S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  78 akvvkvelktenvaGVkvpvfeleee.ksdstelygllrtgaqldeavealrellellvelasletslelLdeeikk 153
                                         + +++++++n++GV vp++e ++  ks +++ yg+++++a++dea+ea+++lle ++ +a++et+++++ +ei++
  gi|336253236|ref|YP_004596343.1|  87 --HPEITTESKNIMGVVVPQIESSRVsKSLDERGYGIMGSSARIDEAAEAYEDLLESIILAAEVETAMKKMLREIET 161
                                       ..699****************9877687778889******************************************* PP

                                       HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 154 tnrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                                       t+rRvNaLe +++P+l +   yI+++L+Eqeree+frlkk+k+
  gi|336253236|ref|YP_004596343.1| 162 TKRRVNALEFKLLPELYDSQEYIEQKLEEQEREETFRLKKIKE 204
                                       *****************************************96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.75
                                       HHHHHHHHHHHHHHTTSTSTT CS
                        ATP-synt_D  39 elreeleeelkeayfslaeaf 59 
                                       e +ee +++ +ea  + aea+
  gi|336253236|ref|YP_004596343.1| 209 EEKEEQRKAAEEADAAEAEAK 229
                                       445666666666666666653 PP

>> DUF1168  Protein of unknown function (DUF1168)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.045   2.7e+02      55      96 ..     122     163 ..     109     172 .. 0.82
   2 ?    7.2  15.3   0.00071       4.2      50     113 ..     179     242 ..     176     249 .] 0.76

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.045
                           DUF1168  55 ieekskkeeedeefqqkleenkeeaeektaKkrakRekkkqk 96 
                                       + + ++ +e+ e++++ le+   +ae  ta k+  Re + +k
  gi|336253236|ref|YP_004596343.1| 122 MGSSARIDEAAEAYEDLLESIILAAEVETAMKKMLREIETTK 163
                                       666778889999999999999999999999999999877644 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00071
                           DUF1168  50 eRlklieekskkeeedeefqqkleenkeeaeektaKkrakRekkkqkakkkkkakkkkkkekek 113
                                       + +++ie+k +++e +e+f+ k+ ++k+eaeek ++++a  e   ++a++k+++ ++ + ++++
  gi|336253236|ref|YP_004596343.1| 179 DSQEYIEQKLEEQEREETFRLKKIKEKKEAEEKEEQRKAAEEADAAEAEAKQDELEDVQPDTAA 242
                                       5689999999999999999999999999999999999888887776666666665555555444 PP

>> RICH  RICH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0  14.2     0.022   1.3e+02       8      78 ..     145     225 ..     140     230 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.022
                              RICH   8 kdeVkeylekiLseikkqldKrkhtqnvaLikkLseIkteyLyelkvlkeksk............aeleelvsktka 72 
                                       ++eV++ ++k+L+ei +  ++r +   ++L+ +L +  +ey+ ++ + +e+++            ae++e   k+ +
  gi|336253236|ref|YP_004596343.1| 145 AAEVETAMKKMLREI-ETTKRRVNALEFKLLPELYDS-QEYIEQKLEEQEREEtfrlkkikekkeAEEKEEQRKAAE 219
                                       679************.667777788889999888884.456655444333321233333433334444444555556 PP

                              RICH  73 eldaaf 78 
                                       e daa 
  gi|336253236|ref|YP_004596343.1| 220 EADAAE 225
                                       666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2868  (0.159964); expected 358.6 (0.02)
Passed bias filter:                      854  (0.0476323); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); 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: 0.62u 0.23s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 1758.34
//
Query:       gi|336253237|ref|YP_004596344.1|  [L=143]
Description: hypothetical protein Halxa_1837 [Halopiger xanaduensis SH-6]
Scores for 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   11.4   2.5       0.56   10.3   2.5    1.6  1  DZR          Double zinc ribbon
       0.27   10.6   1.3        9.3    5.7   0.1    2.3  2  zf-TFIIB     Transcription factor zinc-finger
       0.42   10.8   2.4         15    5.8   0.2    2.4  2  Zn-ribbon_8  Zinc ribbon 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 ?   10.3   2.5   9.4e-05      0.56       9      36 ..       3      44 ..       1      51 [. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.4e-05
                               DZR  9 ppdarfCseCgtk...lkavaa............edrCpsCge 36
                                      +p+++ C++C t+   + +v++              +Cp+C +
  gi|336253237|ref|YP_004596344.1|  3 RPQSQSCPACSTSmllV-SVPDeyrehtpdeapaVAFCPQCLA 44
                                      68999********7742.33336888999999999******65 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0016       9.3       2      10 ..       9      17 ..       8      26 .. 0.84
   2 ?    3.7   0.1    0.0067        40       2      20 ..      39      59 ..      38      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0016
                          zf-TFIIB  2 CPkCqdele 10
                                      CP+C++++ 
  gi|336253237|ref|YP_004596344.1|  9 CPACSTSML 17
                                      ******996 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0067
                          zf-TFIIB  2 CPkCqd..eleeserggveid 20
                                      CP C +  +le++ + + +id
  gi|336253237|ref|YP_004596344.1| 39 CPQCLAleSLEPASVADTPID 59
                                      999976547999999999998 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2    0.0057        34      25      34 ..       4      14 ..       1      17 [. 0.71
   2 ?    5.8   0.2    0.0025        15      22      32 ..      31      42 ..      24      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0057
                       Zn-ribbon_8 25 plta.CPeCgs 34
                                      p+ + CP+C  
  gi|336253237|ref|YP_004596344.1|  4 PQSQsCPACST 14
                                      56677****65 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0025
                       Zn-ribbon_8 22 sdaplta.CPeC 32
                                      ++ap +a CP+C
  gi|336253237|ref|YP_004596344.1| 31 DEAPAVAfCPQC 42
                                      5899999***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1073.57
//
Query:       gi|336253238|ref|YP_004596345.1|  [L=132]
Description: hypothetical protein Halxa_1838 [Halopiger xanaduensis SH-6]
Scores for 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:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 994.24
//
Query:       gi|336253239|ref|YP_004596346.1|  [L=161]
Description: Pyruvoyl-dependent arginine decarboxylase [Halopiger xanaduensis SH-6]
Scores for complete 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-38  132.4   0.1    1.4e-38  132.2   0.1    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 !  132.2   0.1     8e-43   1.4e-38       3     161 ..       4     154 ..       2     155 .. 0.93

  Alignments for each domain:
  == domain 1  score: 132.2 bits;  conditional E-value: 8e-43
                          PvlArgDC   3 kkvfltkGvgeskeelasFdlALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepgrl 79 
                                       +++++++G++++++++as+d+AL++Ag+en+NLv+vSS++P+++++ +v +++++ p+G++++vv ara+s+ pgr 
  gi|336253239|ref|YP_004596346.1|   4 STIRVVWGAASAPTAMASYDAALAEAGVENYNLVSVSSVIPADVDVEAVGTAPDLGPAGERLTVVEARATSAGPGR- 79 
                                       6789***********************************************************************7. PP

                          PvlArgDC  80 iaaavgvaipkdekkgGyiaEysgfgeseeeaeeeaeelaaemlattrgllee.kiietkeievaaveakvekygtv 155
                                       ++aa+++  + d + +G+++E  g     e+++e++e++++e+la+ ++l+++ ++    ++ v++ +a++++y+t+
  gi|336253239|ref|YP_004596346.1|  80 VSAALAWSQSVD-DGPGLFYETAG-----ETDREDVERRVREGLAAGQELRDWeFTDP--RVAVESSQAESGTYTTA 148
                                       ********9888.9**********.....88*******************88866666..5555566688******* PP

                          PvlArgDC 156 laaavf 161
                                       l++av+
  gi|336253239|ref|YP_004596346.1| 149 LVLAVY 154
                                       ****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1168.71
//
Query:       gi|336253240|ref|YP_004596347.1|  [L=410]
Description: proteasome-activating nucleotidase [Halopiger xanaduensis SH-6]
Scores for 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-45  153.1   1.1    1.1e-44  152.1   0.1    2.0  2  AAA              ATPase family associated with various cellul
      8e-16   57.6   0.3    2.9e-15   55.8   0.3    2.0  1  AAA_lid_3        AAA+ lid domain
    1.7e-08   34.8   0.0    4.8e-08   33.3   0.0    1.8  1  AAA_2            AAA domain (Cdc48 subfamily)
    9.4e-07   28.7   0.0    4.3e-06   26.6   0.0    2.1  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.1e-06   27.8   2.1    5.1e-06   26.5   0.2    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
    8.3e-06   26.3   1.8    0.00016   22.1   0.1    3.1  2  AAA_16           AAA ATPase domain
    2.6e-05   24.5   2.6     0.0011   19.3   0.5    3.1  2  AAA_22           AAA domain
      5e-05   23.8   0.4     0.0043   17.6   0.0    2.6  2  AAA_18           AAA domain
      6e-05   22.9   2.8    6.2e-05   22.9   1.1    2.0  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    0.00019   20.7   0.1    0.00049   19.3   0.0    1.8  2  DUF815           Protein of unknown function (DUF815)
    0.00076   18.3   0.4      0.058   12.0   0.6    2.2  2  AAA_13           AAA domain
    0.00096   19.4   1.2     0.0037   17.5   0.0    2.5  2  AAA_28           AAA domain
     0.0013   18.7   0.0     0.0036   17.3   0.0    1.7  1  AAA_14           AAA domain
     0.0015   17.9   0.0      0.003   16.8   0.0    1.5  1  TIP49            TIP49 P-loop domain
     0.0015   18.2   0.9     0.0036   16.9   0.9    1.6  1  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
     0.0017   17.8   0.0     0.0039   16.6   0.0    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0039   16.9   0.2      0.013   15.2   0.2    2.0  1  AAA_24           AAA domain
      0.004   16.9   0.1      0.014   15.1   0.0    1.9  1  IstB_IS21        IstB-like ATP binding protein
     0.0043   16.8   0.1      0.071   12.8   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
     0.0044   17.2   0.0      0.011   15.9   0.1    1.8  1  AAA_33           AAA domain
      0.005   17.3   0.3      0.005   17.3   0.3    2.6  2  AAA_17           AAA domain
      0.008   15.4   0.0      0.044   13.0   0.0    2.1  1  NB-ARC           NB-ARC domain
     0.0094   16.3   0.0      0.019   15.3   0.0    1.5  1  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.011   15.7   1.0      0.099   12.6   0.1    2.6  2  NACHT            NACHT domain
      0.013   15.0   0.0      0.036   13.6   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
      0.015   15.1   0.6      0.059   13.1   0.8    1.9  1  DUF3287          Protein of unknown function (DUF3287)
      0.017   15.0   0.6       0.22   11.2   0.0    2.4  2  AAA_11           AAA domain
      0.018   15.6   2.5       0.06   13.9   2.5    1.8  1  APG6_N           Apg6 coiled-coil region
      0.027   13.6   0.2      0.064   12.3   0.0    1.6  2  Parvo_NS1        Parvovirus non-structural protein NS1
      0.039   13.8   0.0      0.076   12.9   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
       0.04   13.8   1.1       0.19   11.6   0.1    2.4  1  ATPase_2         ATPase domain predominantly from Archaea
      0.042   13.9   0.0      0.078   13.0   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.044   14.3   0.2       0.37   11.3   0.0    2.4  2  ABC_tran         ABC transporter
      0.047   13.0   3.2      0.088   12.2   3.2    1.4  1  GAS              Growth-arrest specific micro-tubule binding
      0.055   12.9   0.0        1.7    8.0   0.0    2.4  2  TniB             Bacterial TniB protein
      0.087   12.2   6.1       0.18   11.2   0.5    3.0  2  ATPase           KaiC
       0.15   12.5   8.1      0.041   14.3   4.0    2.2  1  ZapB             Cell division protein ZapB
       0.21   11.1   0.1       0.21   11.1   0.1    3.3  3  AAA_25           AAA domain
       0.23   11.5   2.4        2.9    8.0   1.6    2.6  2  Med28            Mediator complex subunit 28
       0.56   10.4   9.5        4.1    7.6   9.5    2.2  1  CENP-Q           CENP-Q, a CENPA-CAD centromere complex subun
       0.57   10.1   0.1       0.57   10.1   0.1    2.9  4  NTPase_1         NTPase
       0.86   10.1   3.1         41    4.6   0.0    2.7  2  AAA_23           AAA domain
        1.4    8.8   9.0          1    9.2   0.4    2.5  2  GvpL_GvpF        Gas vesicle synthesis protein GvpL/GvpF


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 ?   -1.4   0.1       7.2     3e+03      79      99 ..      46      66 ..      31     101 .. 0.65
   2 !  152.1   0.1   2.6e-47   1.1e-44       1     131 [.     189     321 ..     189     322 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 7.2
                                      CHHHHHHHHHHHHHHHHTTTS CS
                               AAA 79 seeeervvnqLlteldgvkkk 99
                                       +e+e+  +qL +++d+v+++
  gi|336253240|ref|YP_004596347.1| 46 LDEAEQRREQLREKVDRVERE 66
                                      344445555666666666554 PP

  == domain 2  score: 152.1 bits;  conditional E-value: 2.6e-47
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       vllyGppGtGKT+lakava++++++f+++ gsel+ k++ge+++ +r+lf+ a+e + p i+fiDEida+a++r   
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAVANKTDATFIKMAGSELVRKFIGEGSRLVRDLFEMARERE-PAIIFIDEIDAIATTRses 264
                                       79******************************************************8.****************986 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       ++s + e +r++ qLl+e+dg++ + +++ +i+atnr d+ld+a+lr gRfdr ie++
  gi|336253240|ref|YP_004596347.1| 265 KTSGDAEVQRTMMQLLSEMDGFEAR-GEIRIIAATNRFDMLDRAILRpGRFDRLIEVP 321
                                       666788899***************7.66***************************987 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.3     7e-18   2.9e-15       2      44 ..     345     387 ..     344     388 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 7e-18
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                       vd++++A +TeGySGAD+++l  eA++ A+r  + e+t +df 
  gi|336253240|ref|YP_004596347.1| 345 VDFDAIADETEGYSGADIESLATEAGMFAIRNERNEVTHKDFV 387
                                       9****************************************96 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   1.2e-10   4.8e-08       5     104 ..     188     281 ..     184     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.2e-10
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG-- CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKih 81 
                                        +ll gp g+Gkt+laka+a+  ++    ++i +  sel    +     srl+     + +  e  i+++DEid i+
  gi|336253240|ref|YP_004596347.1| 188 GVLLYGPPGTGKTMLAKAVANKTDA----TFIKMAGSELVR--KFIGEGSRLVRDLFEMAREREPAIIFIDEIDAIA 258
                                       57999******************96....999999999999..33334456666666677788889*********** PP

                                       -----------HHHHHHHHHHHH CS
                             AAA_2  82 pkessgadvSregVqrdLLqile 104
                                        ++s+++     +Vqr ++q+l 
  gi|336253240|ref|YP_004596347.1| 259 TTRSESKTSGDAEVQRTMMQLLS 281
                                       *87777777788*********95 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 !   26.6   0.0     1e-08   4.3e-06      35     100 ..     188     261 ..     181     273 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1e-08
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvleka.....gdlaalltnl...eekdvlfideihrlsrav 100
                                        vllyGpPG Gkt lak +a++ ++++   +g  l ++     + l+  l ++   +e  ++fidei  ++++ 
  gi|336253240|ref|YP_004596347.1| 188 GVLLYGPPGTGKTMLAKAVANKTDATFIKMAGSELVRKfigegSRLVRDLFEMareREPAIIFIDEIDAIATTR 261
                                       69**********************9987777776655434222344444444422134469******9887765 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 ?   -1.6   0.1         6   2.5e+03      78     124 ..      39      84 ..      32     107 .. 0.56
   2 !   26.5   0.2   1.2e-08   5.1e-06       1      79 [.     188     259 ..     188     311 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6
                                       -HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                             AAA_5  78 esevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                       + + ++ L    e+rr +l e   +v  +n++l +    iat ++++
  gi|336253240|ref|YP_004596347.1|  39 HEQLTDQL-DEAEQRREQLREKVDRVERENETLKSSSLYIATVEDVM 84 
                                       55555555.23344555555555555555444444455556555555 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 1.2e-08
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK++la+ +a  + +++  +++++  ++    g+r         +d  l + ar  e++i+++DE++
  gi|336253240|ref|YP_004596347.1| 188 GVLLYGPPGTGKTMLAKAVANKTDATFIKMAGSELVRKFIGEGSRL-------VRD--LFEMARerEPAIIFIDEID 255
                                       59**********************9999888887444433333444.......344..44444455**********9 PP

                                       G--H CS
                             AAA_5  76 raes 79 
                                        + +
  gi|336253240|ref|YP_004596347.1| 256 AIAT 259
                                       7764 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1         3   1.3e+03      90     104 ..      45      59 ..      13     120 .. 0.60
   2 !   22.1   0.1   3.8e-07   0.00016      23      93 ..     185     245 ..     158     283 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3
                            AAA_16  90 esaeleawrekleea 104
                                       + +e+e+ re+l+e 
  gi|336253240|ref|YP_004596347.1|  45 QLDEAEQRREQLREK 59 
                                       122223333333332 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 3.8e-07
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesae 93 
                                        p+ vll+G++G+GK+ l++++++   k+++ f++    +l      +  ++     ++l+r+l ++a+++e
  gi|336253240|ref|YP_004596347.1| 185 PPSGVLLYGPPGTGKTMLAKAVAN---KTDATFIKMAGSEL------VRkFIGE--GSRLVRDLFEMARERE 245
                                       3499*******************7...44466877777777......1112222..2356677766644433 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       1.6   6.6e+02      24      64 ..      41      83 ..      18     111 .. 0.64
   2 !   19.3   0.5   2.6e-06    0.0011       8      34 ..     189     214 ..     184     297 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.6
                            AAA_22 24 rlleqldeeakaee.erpevvfvtlpsst.sskdllrellral 64
                                      +l++qlde+++ +e  r +v +v+  ++t +s++l+ + ++++
  gi|336253240|ref|YP_004596347.1| 41 QLTDQLDEAEQRREqLREKVDRVERENETlKSSSLYIATVEDV 83
                                      4556666555555533333336666666666666665555555 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.6e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeak 34 
                                       ++++G++GtGKT+l++ ++++ d+  +
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAVANKTDA-TF 214
                                       689*****************9853.22 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4      0.22        91      25      87 ..      29      99 ..      22     142 .. 0.75
   2 !   17.6   0.0     1e-05    0.0043       1      44 [.     189     253 ..     189     308 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.22
                            AAA_18 25 gvnlrdvakenglllevdpealdeskrldedkldklldaleenss.........aleegknlvidghlaele 87
                                       ++  d++  ++ l+++ +e  ++ ++  ++k+d++ +++e   s         + +  + +v+ +h ++ e
  gi|336253240|ref|YP_004596347.1| 29 RDHFEDIVDVHEQLTDQLDE-AEQRREQLREKVDRVERENETLKSsslyiatveDVMADDEVVVKQHGNNQE 99
                                      67778888888888888888.456666666666666666666666666888888777777778888877655 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpe 44 
                                       +ll G+pG+GKt lak++++++ +                     ++ l ++a+e+++ + + +e
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAVANKTdATfikmagselvrkfigegsrlVRDLFEMAREREPAIIFIDE 253
                                       799***************99974336777776666666777666666666666666666655555 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 !   22.9   1.1   1.5e-07   6.2e-05       1      47 [.      77     122 ..      77     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-07
                                       EEEEEEE-TTSSEEEEE-TT.S-EEEEEE-GGGSSST--TTEEEEEET CS
                    Prot_ATP_ID_OB   1 VatVsEvlddteraiVktss.deevvvslagavpremLrpgDlVavdk 47 
                                       +atV +v+ d + ++Vk+++  +ev+  ++  v+ +++ pgD+Vav+ 
  gi|336253240|ref|YP_004596347.1|  77 IATVEDVMAD-DEVVVKQHGnNQEVLTEVSPRVA-DRVEPGDRVAVND 122
                                       89********.*******9967899999*****9.66*********95 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       6.8   2.8e+03      15      46 ..      31      62 ..      26      69 .. 0.71
   2 !   19.3   0.0   1.2e-06   0.00049      18     116 ..     142     254 ..     127     308 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.8
                            DUF815 15 alepveevdevklddLvgidkqkealventeq 46
                                      ++e + +v+e   d+L + ++++e+l e + +
  gi|336253240|ref|YP_004596347.1| 31 HFEDIVDVHEQLTDQLDEAEQRREQLREKVDR 62
                                      56667777777778888888888888776655 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.2e-06
                            DUF815  18 pveevdevklddLvgidkqkealventeqfleg.........lpannvLLwGarGtGKSslvkallneyaeegLrli 85 
                                        ++   ev  +d+ gid+q +++ e +eq l+          +p + vLL+G  GtGK  l ka+ n++ ++ +++ 
  gi|336253240|ref|YP_004596347.1| 142 EITAKPEVGYEDIGGIDEQVREVREAVEQPLSEpevfdevgiEPPSGVLLYGPPGTGKTMLAKAVANKTDATFIKMA 218
                                       56666678888889999998888888888665422222222357789*************************99886 PP

                            DUF815  86 ..evekedlkelpklvellr...erperfilfvDDL 116
                                         e+ ++ + e ++lv+ l    +++e  i+f+D +
  gi|336253240|ref|YP_004596347.1| 219 gsELVRKFIGEGSRLVRDLFemaREREPAIIFIDEI 254
                                       559999999999999988762224556789999975 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.6   0.00014     0.058     267     355 ..      22     112 ..      18     177 .. 0.68
   2 ?    3.8   0.0     0.042        17      20      40 ..     190     210 ..     189     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                            AAA_13 267 aerkaaLeahFddefeekqerLekliekveskkselleklkavsdeasensafeed...keelkaeaealeeqLkgl 340
                                       +er +aL +hF+d ++   e+L + +++ e+++++l ek++ v  e++  + +      +e++ a  e++ +q  ++
  gi|336253240|ref|YP_004596347.1|  22 DERLEALRDHFEDIVDV-HEQLTDQLDEAEQRREQLREKVDRVERENETLKSSSLYiatVEDVMADDEVVVKQHGNN 97 
                                       67888888888886666.77888888888888888888887777765444444433233566666667777777777 PP

                            AAA_13 341 qraleaKrkepfksv 355
                                       q++l++   +++ +v
  gi|336253240|ref|YP_004596347.1|  98 QEVLTEVSPRVADRV 112
                                       777766555555444 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.042
                            AAA_13  20 liYGwNGaGKTtLSrllrsle 40 
                                       l+YG  G+GKT L+++ ++ +
  gi|336253240|ref|YP_004596347.1| 190 LLYGPPGTGKTMLAKAVANKT 210
                                       68*************999853 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2       2.7   1.1e+03      42      60 ..      42      61 ..      16      78 .. 0.49
   2 !   17.5   0.0     9e-06    0.0037       2      48 ..     189     240 ..     188     322 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.7
                            AAA_28 42 gedalpwv.edllafaervl 60
                                       +d+l+++ +++ +++e+v 
  gi|336253240|ref|YP_004596347.1| 42 LTDQLDEAeQRREQLREKVD 61
                                      22223333333333333333 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 9e-06
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileeklakgedalpw 48 
                                       + + G+++tGKT l++a a++     +++   E +r+++ e+++  +d  ++
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAVANKtdatFIKMAgSELVRKFIGEGSRLVRDLFEM 240
                                       6799***************665555777778999999998888555543333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   8.7e-06    0.0036       5      81 ..     189     262 ..     187     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.7e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewek 81 
                                       +++ G+  +GKT+l+k ++++       ++ ++  +   k + + ++l + ++e+++e++  ++f+DEi  + + ++
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAVANKTD---ATFIKMAGSELVRKFIGEGSRLVRDLFEMAREREPAIIFIDEIDAIATTRS 262
                                       6799**************98877...777777777755554555557888888886666899*******99977665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.1e-06     0.003      52      93 ..     188     227 ..     185     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.1e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslev 93 
                                       +vLl Gp+gtGkt la a++++   d  f++++gse+ +  +
  gi|336253240|ref|YP_004596347.1| 188 GVLLYGPPGTGKTMLAKAVANKT--DATFIKMAGSELVRKFI 227
                                       79******************975..689********977655 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 !   16.9   0.9   8.7e-06    0.0036       3      59 ..      78     134 ..      76     136 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.7e-06
                     Prot_ATP_OB_N   3 GtflavnsqdgtadVlv..ggrrmrVavsPlvdaeeLrpGqeVlLnEalvvVealgyer 59 
                                       +t+  v + d+++ V +  +++++   vsP+v  ++ +pG++V +n+++++  +l+ e+
  gi|336253240|ref|YP_004596347.1|  78 ATVEDVMA-DDEVVVKQhgNNQEVLTEVSPRVA-DRVEPGDRVAVNDSFAIQTVLDAET 134
                                       66777774.444444441134566678*****9.*****************99988876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.3e-06    0.0039      25      43 ..     189     207 ..     180     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.3e-06
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKtmlak+++
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAVA 207
                                       89*************9875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   3.1e-05     0.013       5      29 ..     189     215 ..     186     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfi 29 
                                       +l+yGp+g+GKT+lak    + ++ fi
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAVanKTDATFI 215
                                       79**************99665555555 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   3.4e-05     0.014      48      70 ..     187     209 ..     176     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                        +++l Gp+G+GK+ la a++ +
  gi|336253240|ref|YP_004596347.1| 187 SGVLLYGPPGTGKTMLAKAVANK 209
                                       6799***************9986 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00017     0.071      22      55 ..     186     216 ..     163     229 .. 0.81
   2 ?    1.2   0.1      0.62   2.6e+02     117     143 ..     272     300 ..     235     320 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                                       SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEE CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfva 55 
                                       ++ vl+ G  GtGK++la+a+ ++++   + f++
  gi|336253240|ref|YP_004596347.1| 186 PSGVLLYGPPGTGKTMLAKAVANKTD---ATFIK 216
                                       5789****************987654...45555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.62
                                       HHHSEEESBTSSS..EEE--EEEEEEESS CS
                   Sigma54_activat 117 lqegevervGssk..eikvdvriiaatne 143
                                       +q+  ++ + + +  e + ++riiaatn+
  gi|336253240|ref|YP_004596347.1| 272 VQRTMMQLLSEMDgfEARGEIRIIAATNR 300
                                       34444444444332245567888888886 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.7e-05     0.011       2      28 ..     189     215 ..     189     320 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavll 28 
                                       vll G+pG+GK+ la+ +++k++a+++
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAVANKTDATFI 215
                                       7899***************99997766 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3       3.1   1.3e+03      36      80 ..      53      95 ..      26     140 .. 0.52
   2 !   17.3   0.3   1.2e-05     0.005       1      66 [.     192     258 ..     192     344 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.1
                                      TTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-S CS
                            AAA_17 36 rgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghp 80
                                      r++l ++ d+++++  +e+ +   + ++++++  ++++v+v+ h 
  gi|336253240|ref|YP_004596347.1| 53 REQLREKVDRVERE--NETLKSSSLYIATVEDVMADDEVVVKQHG 95
                                      33332222222211..11222222333333333344445555554 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.2e-05
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH..HHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa..Gdllreeakrgglakardemrklpleekkelqkeaaekia 66 
                                       +G+PG GK+ +++ ++ k + t++ +  ++l+r+ + +g+    rd ++ + ++e   +    +++ia
  gi|336253240|ref|YP_004596347.1| 192 YGPPGTGKTMLAKAVANKTDATFIKMagSELVRKFIGEGS-RLVRDLFEMAREREPAIIFIDEIDAIA 258
                                       7*******************99998875667777776654.344555554444444433333333343 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0    0.0001     0.044      23      76 ..     189     280 ..     184     353 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                                       EEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE......................................EEES CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksdevegrFdsvawv......................................vvsk 61 
                                       v l+G +G GKt lak + nk d +  +  +   v                                      + sk
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAVANKTDATFIKMAGSELVrkfigegsrlvrdlfemarerepaiifideidaiattrSESK 265
                                       679******************77655455444444666677777777777777777777777777776666666666 PP

                                       XXHHHHHHHXXHHHH CS
                            NB-ARC  62 tdkseeiletilkeL 76 
                                       t+   e+++t+++ L
  gi|336253240|ref|YP_004596347.1| 266 TSGDAEVQRTMMQLL 280
                                       666666666666666 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.6e-05     0.019       1      65 [.     189     244 ..     189     277 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.6e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdee 65 
                                       ++lyGp+g+GK++lak +          +k+d ++++ + ++ + ++ g+   ++ D+ ++  e 
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAV---------ANKTDATFIKMAGSELVRKFIGEGSRLVRDLFEMARER 244
                                       689**************3.........45556666777777777777777777777776666554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00024     0.099       3      23 ..     189     209 ..     187     216 .. 0.90
   2 ?    0.7   0.0         1   4.3e+02      76     114 ..     240     281 ..     220     287 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00024
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G GKT+L++ +a +
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAVANK 209
                                       799*************99976 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1
                                       HCCSCCCEEEEEE-STT-SS-TCH............HHHHHC CS
                             NACHT  76 llelperlLlilDglDelvtdlgq...kekqpvrtlLselir 114
                                       +++ +e + + +D +D ++t  ++   ++ ++v++ + +l++
  gi|336253240|ref|YP_004596347.1| 240 MAREREPAIIFIDEIDAIATTRSEsktSGDAEVQRTMMQLLS 281
                                       445555666778999999998888777777777777777776 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 ?   13.6   0.0   8.5e-05     0.036      35      61 ..     188     213 ..     180     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.5e-05
                             AAA_7  35 pvllvGptGtGKtviikdllkkldkek 61 
                                        vll+Gp GtGKt+++k + +k d  +
  gi|336253240|ref|YP_004596347.1| 188 GVLLYGPPGTGKTMLAKAVANKTD-AT 213
                                       69*****************99998.44 PP

>> DUF3287  Protein of unknown function (DUF3287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.8   0.00014     0.059      52      98 ..      27      73 ..      13      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                           DUF3287 52 ealdfidkvvekHrrlcderqklgkkrqtleaRiarveRklrelese 98
                                         d+++ +v+ H +l+d+  +  ++r++l  ++ rveR+  +l+s 
  gi|336253240|ref|YP_004596347.1| 27 ALRDHFEDIVDVHEQLTDQLDEAEQRREQLREKVDRVERENETLKSS 73
                                      34599**************************************9986 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.3      0.56   2.3e+02     153     186 ..      39      72 ..      13     105 .. 0.58
   2 ?   11.2   0.0   0.00054      0.22       7      39 ..     165     208 ..     159     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.56
                            AAA_11 153 kkskekskskleqerrklkkerkelskeleeaee 186
                                       +++ +++ +++eq+r++l+++++++++e e+ ++
  gi|336253240|ref|YP_004596347.1|  39 HEQLTDQLDEAEQRREQLREKVDRVERENETLKS 72 
                                       3333444444444444444444444444333333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00054
                            AAA_11   7 reaiksalsese...........itliqGPPGtgKTktivells 39 
                                       rea++++lse+e            +l+ GPPGtgKT    ++ +
  gi|336253240|ref|YP_004596347.1| 165 REAVEQPLSEPEvfdevgieppsGVLLYGPPGTGKTMLAKAVAN 208
                                       56677777777777777777777789**********76655555 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.5   0.00014      0.06      45      96 ..      21      72 ..       6      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00014
                            APG6_N 45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealee 96
                                      +de le+l++ +e++ +  e+l  +L+e+e+ re+l++++   e+e e l+ 
  gi|336253240|ref|YP_004596347.1| 21 DDERLEALRDHFEDIVDVHEQLTDQLDEAEQRREQLREKVDRVERENETLKS 72
                                      578999999**************************************99986 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 ?   -2.8   0.0       6.5   2.7e+03      38      75 ..      46      83 ..      31     110 .. 0.65
   2 ?   12.3   0.0   0.00015     0.064     117     138 ..     189     210 ..     184     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.5
                         Parvo_NS1 38 lsrsragrrqienaleqakirmfstkaaldilakkevt 75
                                      l  ++++r+q+++  + +++++ + k+ + ++a+ e +
  gi|336253240|ref|YP_004596347.1| 46 LDEAEQRREQLREKVDRVERENETLKSSSLYIATVEDV 83
                                      45556666666666666666666666666666555555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00015
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                       v++yGp+ tGkt+la+a a+ +
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAVANKT 210
                                       89****************9976 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 ?   12.9   0.0   0.00018     0.076       2      30 ..     189     217 ..     188     301 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG++kt+l+ka+a++ d++f ++
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAVANKTDATFIKM 217
                                       7999*******************999664 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   0.1   0.00046      0.19      20      52 ..     186     217 ..     180     283 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00046
                          ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdkyvi 52 
                                        + +++YGp g GKt L k ++++  d  + ++
  gi|336253240|ref|YP_004596347.1| 186 PSGVLLYGPPGTGKTMLAKAVANKT-DATFIKM 217
                                       556899************9999887.4455555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00019     0.078      21      59 ..     181     226 ..     158     263 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00019
                                       E.......EEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEE CS
                              TsaE  21 v.......ilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeY 59 
                                       v       +lL+G+ G+GKT+l++++a++ + + +k     lv+++
  gi|336253240|ref|YP_004596347.1| 181 VgieppsgVLLYGPPGTGKTMLAKAVANKTDATFIKMAGSELVRKF 226
                                       144445559******************9998776666555666665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1         2   8.5e+02      79     104 ..      41      72 ..      18     142 .. 0.71
   2 ?   11.3   0.0   0.00088      0.37       7      37 ..     182     212 ..     179     296 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2
                                       H......HHHTCHHHHHHHSTTGGTTCBGEST CS
                                       x......xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n......esdeeiekalsklglkelkdtvvks 104
                                       +      e++++ e++++k++ +e +++++ks
  gi|336253240|ref|YP_004596347.1|  41 QltdqldEAEQRREQLREKVDRVERENETLKS 72 
                                       23333444455555555555555555444433 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00088
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkp 37 
                                        +++ + v + G+ G+GK+ L+k++a++++ 
  gi|336253240|ref|YP_004596347.1| 182 GIEPPSGVLLYGPPGTGKTMLAKAVANKTDA 212
                                       567777899****************999876 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 ?   12.2   3.2   0.00021     0.088      42     102 ..      25      85 ..      22     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                               GAS  42 eernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelk 102
                                        e+ + ++++i    ++l+++L +ae+ +e+Lr+++ + e++ + lk++   + ++e+ + 
  gi|336253240|ref|YP_004596347.1|  25 LEALRDHFEDIVDVHEQLTDQLDEAEQRREQLREKVDRVERENETLKSSSLYIATVEDVMA 85 
                                       56677788899999999*****************************999988888887665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0     0.004       1.7      36      61 ..     187     212 ..     175     225 .. 0.83
   2 ?    2.2   0.0      0.25     1e+02     108     139 ..     234     265 ..     223     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.004
                              TniB  36 pnlllvGdsnnGKtmivekFarlhpp 61 
                                       + +ll+G++ +GKtm+++  a++  +
  gi|336253240|ref|YP_004596347.1| 187 SGVLLYGPPGTGKTMLAKAVANKTDA 212
                                       679**************998877655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.25
                              TniB 108 eqqvlrllrelkvrvLiiDEihnllagsarkq 139
                                        ++  ++ re ++ ++ iDEi+ + + +++++
  gi|336253240|ref|YP_004596347.1| 234 VRDLFEMAREREPAIIFIDEIDAIATTRSESK 265
                                       56667888999999*********998877665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.9       1.4   5.8e+02      57     114 ..      50     108 ..      35     145 .. 0.57
   2 ?   11.2   0.5   0.00042      0.18      14      38 ..     181     205 ..     154     283 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.4
                            ATPase  57 eepaedlrenakslGwdlekleeegklaiidasesaeesaee..kdkedleelieelaea 114
                                       e++ e+lre++ ++  + e l+++ +l+i  +   +++++    ++ ++ e l+e   ++
  gi|336253240|ref|YP_004596347.1|  50 EQRREQLREKVDRVERENETLKSS-SLYIATVEDVMADDEVVvkQHGNNQEVLTEVSPRV 108
                                       556688888888888888888887.44443333333332222324444444444444444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00042
                            ATPase  14 gGipegrvvlitGepGtGKtifalq 38 
                                        Gi   + vl++G pGtGKt++a+ 
  gi|336253240|ref|YP_004596347.1| 181 VGIEPPSGVLLYGPPGTGKTMLAKA 205
                                       48888999**************985 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   4.0   9.7e-05     0.041       4      53 ..      23      72 ..      21     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.7e-05
                              ZapB  4 elLeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlke 53
                                      e Le L    +  +d  ++L  +++e +++ e+l e+ +++e+ene lk 
  gi|336253240|ref|YP_004596347.1| 23 ERLEALRDHFEDIVDVHEQLTDQLDEAEQRREQLREKVDRVERENETLKS 72
                                      6799999999**************************************93 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.5       0.5   2.1e+02      78     138 ..      48     113 ..      26     140 .. 0.80
   2 ?   11.1   0.1   0.00051      0.21      36      53 ..     189     206 ..     182     210 .. 0.87
   3 ?    0.8   0.1      0.76   3.2e+02     130     164 ..     234     267 ..     209     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.5
                            AAA_25  78 saEdsedelrrRlravgeal..rddarllvldlagv.eslpLfakdrggtl..ltadvdaleaaie 138
                                        aE+++++lr+++ +v +++     + l++ ++++v  +  ++ k++g+++  lt++  ++++++e
  gi|336253240|ref|YP_004596347.1|  48 EAEQRREQLREKVDRVERENetLKSSSLYIATVEDVmADDEVVVKQHGNNQevLTEVSPRVADRVE 113
                                       58999999**99999998886544788999999999888888877777666656776666666655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00051
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll+G+pgtGKt+la  +
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAV 206
                                       69************9665 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.76
                            AAA_25 130 vdaleaaieevegvrlvviDplsralggdensnsd 164
                                       v++l + ++e  +++ + iD ++++    ++s++ 
  gi|336253240|ref|YP_004596347.1| 234 VRDLFEMARE-REPAIIFIDEIDAIATTRSESKTS 267
                                       6778888899.56*********9977774444443 PP

>> Med28  Mediator complex subunit 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.6     0.007       2.9      69     127 ..      48     109 ..      28     114 .. 0.74
   2 ?    0.7   0.0       1.2   5.1e+02      47      81 ..     211     245 ..     201     286 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.007
                             Med28  69 qlatqlkalrekgqnvfgdgtkidstidyleklkqvlsdaedvykv...rdevlnearqrla 127
                                       +   + + lrek + v  ++  + s+  y+ + + v+ d e v k+   ++evl e+  r+a
  gi|336253240|ref|YP_004596347.1|  48 EAEQRREQLREKVDRVERENETLKSSSLYIATVEDVMADDEVVVKQhgnNQEVLTEVSPRVA 109
                                       22334568*******************************99776642227999999988887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.2
                             Med28  47 kaekykvapeellmkHlqktseqlatqlkalrekg 81 
                                       +a   k+a  el++k + + s  +   ++  re+ 
  gi|336253240|ref|YP_004596347.1| 211 DATFIKMAGSELVRKFIGEGSRLVRDLFEMARERE 245
                                       35567999*********997766655556667665 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 ?    7.6   9.5    0.0098       4.1      26     106 ..      31     114 ..      19     289 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0098
                            CENP-Q  26 dfeklldekaaleaqLspelhslelLeaeie...keeralerdyeaLreLeknakaearerkeklkkehvllqesds 99 
                                       +fe ++d + +l +qL+ +++  e+L++ ++   +e ++l++   ++++ e  + + +   k+   +++vl++ s +
  gi|336253240|ref|YP_004596347.1|  31 HFEDIVDVHEQLTDQLDEAEQRREQLREKVDrveRENETLKSSSLYIATVEDVMADDEVVVKQHGNNQEVLTEVSPR 107
                                       69**************************9872224556788888899999999999999988877777788875544 PP

                            CENP-Q 100 eelslle 106
                                        +++ + 
  gi|336253240|ref|YP_004596347.1| 108 VADRVEP 114
                                       4333333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2       5.3   2.2e+03     120     136 ..      68      84 ..      32     111 .. 0.53
   2 ?   -1.6   0.1       5.5   2.3e+03     103     124 ..     153     174 ..     141     178 .. 0.85
   3 ?   10.1   0.1    0.0014      0.57       2      55 ..     189     243 ..     188     252 .. 0.77
   4 ?   -0.8   0.0         3   1.2e+03      91     104 ..     240     254 ..     225     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5.3
                                       HHHTTTSEEEEE--SS- CS
                          NTPase_1 120 evLksekpvlavihrrk 136
                                       e+Lks+   +a++    
  gi|336253240|ref|YP_004596347.1|  68 ETLKSSSLYIATVEDVM 84 
                                       23333333333333333 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.5
                                       --STTGGG-HHHHHHHHHHHTT CS
                          NTPase_1 103 EiGkmElkskkfkeaveevLks 124
                                        iG +  ++++++eave+ L++
  gi|336253240|ref|YP_004596347.1| 153 DIGGIDEQVREVREAVEQPLSE 174
                                       5899999999999999999884 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0014
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEE.EEEEE-------EEEEEET.T- CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf.yteevreggrrigFkivdlasg 55 
                                       v++ GppG+GKt l k v+++ +   +k++G  ++++   +g+r   ++ ++a +
  gi|336253240|ref|YP_004596347.1| 189 VLLYGPPGTGKTMLAKAVANKTDATFIKMAGSeLVRKFIGEGSRLVRDLFEMARE 243
                                       6788*****************9999999999624555557777777777666555 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3
                                       HHH.HHH-EEEE--- CS
                          NTPase_1  91 kal.seadviviDEi 104
                                        a  +e+ +i iDEi
  gi|336253240|ref|YP_004596347.1| 240 MAReREPAIIFIDEI 254
                                       44446778******9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.0       0.1        42     153     196 ..      23      64 ..      12      76 .. 0.59
   2 ?    4.6   0.0     0.097        41      21      39 ..     189     206 ..     178     292 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.1
                            AAA_23 153 erleelekeleeledekkllekleqekekekeleeleeeleeil 196
                                       erle+l++ +e++ d+ ++l +++   e e++ e+l+e+   ++
  gi|336253240|ref|YP_004596347.1|  23 ERLEALRDHFEDIVDVHEQLTDQL--DEAEQRREQLREKVDRVE 64 
                                       466777777777777666666653..233344444444433333 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.097
                            AAA_23  21 ltlItGpNGaGKTTildAi 39 
                                       + l++Gp G+GKT +  A+
  gi|336253240|ref|YP_004596347.1| 189 V-LLYGPPGTGKTMLAKAV 206
                                       3.99*********999886 PP

>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   3.1      0.28   1.2e+02     103     149 ..      23      69 ..      22      85 .. 0.88
   2 ?    9.2   0.4    0.0025         1      85     172 ..      85     170 ..      81     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.28
                         GvpL_GvpF 103 eaLerlagkvEygvkvlwdeealleelleedpelrelreeieaases 149
                                       e+Le+l+++ E  v v+++  + l+e++++ ++lre  +++e+++e+
  gi|336253240|ref|YP_004596347.1|  23 ERLEALRDHFEDIVDVHEQLTDQLDEAEQRREQLREKVDRVERENET 69 
                                       689*****************99****************999999985 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0025
                         GvpL_GvpF  85 kdeeavrelLeeeadelreaLerlagkvEygvkvlwdeealleelleedpelrelreeieaasesgtayllrkrlgq 161
                                        d+e v +   ++++ l e   r+a++vE g +v ++++ + +++l+ + ++r++  ei+a++e    y++   +++
  gi|336253240|ref|YP_004596347.1|  85 ADDEVVVKQHGNNQEVLTEVSPRVADRVEPGDRVAVNDSFAIQTVLDAETDARAQSMEITAKPEV--GYEDIGGIDE 159
                                       5666667777888999999999******************************************5..5999999999 PP

                         GvpL_GvpF 162 rleealeerre 172
                                       +++e +e+ ++
  gi|336253240|ref|YP_004596347.1| 160 QVREVREAVEQ 170
                                       99999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1606  (0.0895755); expected 358.6 (0.02)
Passed bias filter:                     1116  (0.0622455); expected 358.6 (0.02)
Passed Vit filter:                       256  (0.0142785); 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):              43  [number of targets reported over threshold]
# CPU time: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.43
# Mc/sec: 2852.43
//
Query:       gi|336253241|ref|YP_004596348.1|  [L=597]
Description: oligoendopeptidase F [Halopiger xanaduensis SH-6]
Scores for 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-67  229.4   4.1      1e-67  229.4   4.1    2.2  2  Peptidase_M3    Peptidase family M3
    7.5e-22   77.4   0.5    7.5e-22   77.4   0.5    3.3  3  Peptidase_M3_N  Oligopeptidase F
  ------ inclusion threshold ------
      0.038   14.4   3.0       0.81   10.1   0.7    3.1  2  DASH_Dad2       DASH complex subunit Dad2
        4.1    6.5   8.1        1.2    8.2   0.1    3.1  3  RmuC            RmuC family


Domain annotation for each model (and alignments):
>> Peptidase_M3  Peptidase family M3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   2.0    0.0023        10      13     123 ..      30     149 ..      23     178 .. 0.65
   2 !  229.4   4.1   2.2e-71     1e-67       2     457 ..     204     583 ..     203     584 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0023
                                       HHHHHHCTTTCCSS......THHHHHHHHHHHHHHHH.HHHTT-SSHHHHHHTT.STT-SHHHHHHHHHHHHHHHHH CS
                      Peptidase_M3  13 eayeashskaaeqrnt....lensklleellklrael.Akllgyesyaelaled.kmaknpetvldfleelvkklrp 83 
                                       +ayea  ++++e +       en+++l ++l+lr+e   ++     ya ++ ++ + +++ +++    ++l + + +
  gi|336253241|ref|YP_004596348.1|  30 AAYEAVAERVEELQTYegqvTENAETLLSVLQLRDEImREVSTVAAYARMRRDEdTTDQQYQALTARAQSLAADAQS 106
                                       6777777777765543444689************9986556666666666655403344444444444555555555 PP

                                       HHHHHHHHHHHHHHHC....CT-S.SS--CCCHHHHHHHHHCCCC CS
                      Peptidase_M3  84 llekelkllkelkkke....lgle.gelqpwDvaYYsekqreeky 123
                                       +++    +++el ++e      +e ++l+ +D+ Y++   r + +
  gi|336253241|ref|YP_004596348.1| 107 AASFIDPEIQELTREEfdemV-DEePDLETYDH-YVDDVLRMKPH 149
                                       555555677888888887643.3368*******.77766654444 PP

  == domain 2  score: 229.4 bits;  conditional E-value: 2.2e-71
                                       HHC-S-HHHHHHHHHHHCTTTCCSS..THHHHHHHHHHHHHHHHHHHTT-SSHHHHHHTTSTT-SHHHHHHHHHHHH CS
                      Peptidase_M3   2 lkespdrelRkeayeashskaaeqrntlensklleellklraelAkllgyesyaelaledkmaknpetvldfleelv 78 
                                       l++ pdr+ R+e+ye + ++ ++ rnt+  +  +++ +k   + A++++y++++e+al+    + p +v+d+l ++v
  gi|336253241|ref|YP_004596348.1| 204 LLKRPDRDFRREVYEGYFDEWESVRNTV--ASAYKNSVKADVKTARARNYDTAREAALDG--PNVPVEVYDTLVDTV 276
                                       67889***********************..***********999****************..*************** PP

                                       HHHHHHHHHHHHHHHHHHHHCCT-SSS--CCCHHHHHHHHHCCCCS--CCCCGGG-BHHHHHHCHHHHHHHHHTEEE CS
                      Peptidase_M3  79 kklrpllekelkllkelkkkelglegelqpwDvaYYsekqreekydldqeelkeyfpletvleGllelfeeLfGikf 155
                                       + +  +l+   +l++e     l +e elq+wD+           y +   +  + +++++++e             +
  gi|336253241|ref|YP_004596348.1| 277 HDNLDKLHHHAELKRE----ALDVE-ELQMWDL-----------YMPLTGDEGPDLEYDQATE------------YV 325
                                       **********999999....99889.*******...........7755556899999999999............34 PP

                                       EEETTS..--SSTT-EEEEEEET.TT-EEEEEEEEEEC--TTS-SS-EEEEEE--BTTS-B--EEEEEEEEE---BT CS
                      Peptidase_M3 156 veekdakgevwhedVrkleVvdeilsegligeiylDlyerkgKrggAasfglvksredgtrqlpviylllNftkpss 232
                                       v+  +  ge++ +          ++ egl  ++++D+ye++gK++gA+s g ++         + +++l+N+++   
  gi|336253241|ref|YP_004596348.1| 326 VDSLEPLGEEYQS----------RVAEGL-DSRWVDVYENEGKQSGAYSGGTYD---------TQPFILMNYQD--- 379
                                       4444444******..........99****.************************.........79*********... PP

                                       TS--B--HHHHHHHHHHHHHHHHHHC--BSSGGGSTT-S-CCCCCHHHHHHHHGGGSHHHHHCC-B-TTT--B--HH CS
                      Peptidase_M3 233 kkPsLLtldevetLfHEfGHsmHsllsrteysnvsgtnvpidfvElpSqlmEnlltepevlkslskhyetgeaipee 309
                                             +++++ tL+HE+GHsmHs l+++e++   +  ++i+++E++S+++E llt++++ +    + e ++ +++e
  gi|336253241|ref|YP_004596348.1| 380 ------DISSMYTLAHELGHSMHSELTKEEQPF-VYSGYEIFVAEVASTVNEALLTKHLLETVE--DPEFKKHVLNE 447
                                       ......************************877.99***********************99999..9********** PP

                                       HHHHHHCCCCTTHHHHHHHHHHHHHHHHHCTT-TCCGHH.....HHHHHHHHHHCTTSCTTBTTSSGGGC-CCCHTS CS
                      Peptidase_M3 310 lleklikaknvnaalellrqlvfaafdqelHeeaeeeqilk.kdlletyaelrkkflglpvapdeasqasFghlfah 385
                                        le+++        ++l+rq+ fa+f++e H+ +ee+++l+ + l+e y+el+ ++++ p+a d+++    + +  h
  gi|336253241|ref|YP_004596348.1| 448 FLERVR--------STLYRQTLFAEFEHEAHRLEEEGEALTaDRLDELYRELKAQYYE-PAAIDDRIAREWMRIP-H 514
                                       ******........***************************99***************.5666666666666774.* PP

                                       S-TTTTCHHHHHHHH..HHHHHHCCHHCCTT-CCHHHHHHHHTTTTTTSS-HHHHHHCCCSS---SHHHHHHCT CS
                      Peptidase_M3 386 gYaanYYsylyaevl..aldifekffeedplnretGeryrkeiLsrGgskdplellkkflgrepsadallkalg 457
                                       +Y   +Y+y+ya+++  al+i  ++f e+   +    + + e+L+ G+ ++plell+ +++++ s++++++al+
  gi|336253241|ref|YP_004596348.1| 515 FYR-AFYVYQYATGIsaALAITDRIFDEGTAAA----EDYLEFLRQGSREYPLELLRIAGVDMSSSEPIERALE 583
                                       ***.9***********999********995555....*********************************9986 PP

>> Peptidase_M3_N  Oligopeptidase F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.79   3.6e+03      40      61 ..      37      58 ..      23      64 .. 0.55
   2 !   77.4   0.5   1.7e-25   7.5e-22       1      70 []     114     183 ..     114     183 .. 0.99
   3 ?    2.4   2.3     0.043   1.9e+02       8      48 ..     443     482 ..     439     488 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.79
                    Peptidase_M3_N 40 eeeEklLaelsevggaawnifs 61
                                      e++E+l +  ++v+++a++ +s
  gi|336253241|ref|YP_004596348.1| 37 ERVEELQTYEGQVTENAETLLS 58
                                      3445555555555555555555 PP

  == domain 2  score: 77.4 bits;  conditional E-value: 1.7e-25
                    Peptidase_M3_N   1 EllaldeekleellkeepelaeyrfyleeilrqkphtLseeeEklLaelsevggaawnifsdltnadlkF 70 
                                       E+ +l  e+++e+++eep+l+ y +y +++lr+kpht s+e+E++Laelsev+ga  +++++l+nad++F
  gi|336253241|ref|YP_004596348.1| 114 EIQELTREEFDEMVDEEPDLETYDHYVDDVLRMKPHTRSAEVEEVLAELSEVTGATGEVYNMLSNADMEF 183
                                       89*******************************************************************9 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.043
                    Peptidase_M3_N   8 ekleellkeepelaeyrfyleeilrqkphtLseeeEklLae 48 
                                        +l+e+l++  +   yr  l   ++  +h+L ee E+l a+
  gi|336253241|ref|YP_004596348.1| 443 HVLNEFLER-VRSTLYRQTLFAEFEHEAHRLEEEGEALTAD 482
                                       578888887.8899999999999*************99875 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.7   0.00018      0.81      23      80 ..      34      91 ..      28     120 .. 0.78
   2 ?    2.7   0.1     0.037   1.6e+02      11      57 ..     159     206 ..     150     274 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00018
                         DASH_Dad2 23 slakqleeLeeklstladgteavasVlanWqnvlraismaslkllqkaeeeaeeeeed 80
                                      ++a+++eeL++  +++++++e+  sVl+  ++++r +s   +    +++e++++++ +
  gi|336253241|ref|YP_004596348.1| 34 AVAERVEELQTYEGQVTENAETLLSVLQLRDEIMREVSTVAAYARMRRDEDTTDQQYQ 91
                                      78999********************************987666543444444444333 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.037
                         DASH_Dad2  11 LeaLkqlrdlsdslakqleeLeeklstlad.gteavasVlanWqnvlr 57 
                                       L++L +++  ++++ + l++ + ++ t++d  +eav+   +n+ n l+
  gi|336253241|ref|YP_004596348.1| 159 LAELSEVTGATGEVYNMLSNADMEFPTVEDpEGEAVEITQSNFTNLLK 206
                                       788999999999999999999999999988457899888888888874 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00027       1.2       9      61 ..       9      61 ..       6      67 .. 0.89
   2 ?   -2.4   0.6      0.45     2e+03     125     155 ..      74     105 ..      72     109 .. 0.77
   3 ?    2.2   0.2     0.018        81     125     166 ..     215     255 ..     209     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00027
                              RmuC  9 plkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLtkaLk 61
                                      +++e+ +  +e+v +++++ + ++e++ e ++elq+ + q++++ae+L ++L+
  gi|336253241|ref|YP_004596348.1|  9 EVDEEYTWDLESVYATDEDWEAAYEAVAERVEELQTYEGQVTENAETLLSVLQ 61
                                      6777777788999999999******************************9997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.45
                              RmuC 125 eaYerlveaedde.ereealkahaksvkkhik 155
                                        aY r+   ed++ ++ +al a a+s+ + ++
  gi|336253241|ref|YP_004596348.1|  74 AAYARMRRDEDTTdQQYQALTARAQSLAADAQ 105
                                       68899998888666888889888888877765 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.018
                              RmuC 125 eaYerlveaeddeereealkahaksvkkhikeLseKdYeele 166
                                       e Ye ++++ + + r++ + a+++svk+ +k+ ++++Y ++ 
  gi|336253241|ref|YP_004596348.1| 215 EVYEGYFDEWE-SVRNTVASAYKNSVKADVKTARARNYDTAR 255
                                       66888888655.78999999******************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 4165.06
//
Query:       gi|336253242|ref|YP_004596349.1|  [L=488]
Description: peptidase M28 [Halopiger xanaduensis SH-6]
Scores for 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  115.1   0.0    4.6e-33  114.6   0.0    1.2  1  Peptidase_M28  Peptidase family M28
    3.3e-10   39.8   0.5    6.3e-10   39.0   0.5    1.5  1  PA             PA domain
    4.5e-05   23.2   0.5    0.00044   20.0   0.5    2.2  1  Peptidase_M20  Peptidase family M20/M25/M40
  ------ inclusion threshold ------
      0.014   14.4   0.3      0.024   13.7   0.3    1.3  1  Peptidase_M42  M42 glutamyl aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6   0.0     1e-36   4.6e-33       1     197 [.     259     447 ..     259     448 .. 0.92

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 1e-36
                                       EEEEEESTTCESEEEEEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHH CS
                     Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllG 77 
                                       Nv ++l +++ de +++ AHyD + +  ++   GA Dn++g+a++   + +la+ +++++r+vr++ +++EE gllG
  gi|336253242|ref|YP_004596349.1| 259 NVHGRLGPET-DEEVVVVAHYDAHDI--TE---GALDNGCGIATVAAASGILADVEEDLERTVRIVGVGCEEIGLLG 329
                                       9*****9999.**************9..99...*********************9999******************* PP

                                       HHHHHHHHCCCTTEEEEEEECS-SSSS--EEEHHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHH CS
                     Peptidase_M28  78 SkafakakpelkkiaavlnlDmvgsggkellfesgdkssselekelkalakpvgraaaedpfdersgrgrsDhspfl 154
                                       S+a+a ++ +l+ ++av+n+D +g+ ++         +s+ l + +++ a+++g+ ++ +p ++ +    sDh+pfl
  gi|336253242|ref|YP_004596349.1| 330 SEALA-DQLDLESVRAVVNVDGAGRFRNLRAL---AHGSEPLAELAEEIASEAGQPVSREPDPHPF----SDHWPFL 398
                                       *****.999****************9999997...6667777777777777777777668888877....******* PP

                                       TTT--EEEE.....CTSSS-TTT.TSTTSSGGGB-HHHHHHHHHHHHHH CS
                     Peptidase_M28 155 kagvpvldl.....aetgfpevy.HtprDtldnidkdtlariaelvlel 197
                                       +agvp l+l     +  + ++ + Ht++Dt d+ d+++l+++a l + l
  gi|336253242|ref|YP_004596349.1| 399 RAGVPSLQLhseppEGRERGRGWgHTTADTRDKADPRNLREHAMLTALL 447
                                       *********9999888999**********************99988765 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.5   1.4e-13   6.3e-10       1      89 []     142     234 ..     142     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.4e-13
                                PA   1 vtgplVyscfagygisadfegvdvkGkivLvqr.........tfaeKarnAqaaGAagviiv..ndgelgaatgasg 66 
                                       v+gplV   ++g+g++++ +  d++G +++ +           + eK+ +A +aGA++++++  ++g+  ++tga +
  gi|336253242|ref|YP_004596349.1| 142 VEGPLV---DVGSGTPEEIADADLRGAVAVASTttpegqrfvHRMEKFGHAVDAGAEAFVFAnhVPGQ-LPPTGALK 214
                                       78****...*****999999***********5333434324444******************643333.23332222 PP

                                PA  67 negepdgitiPavgvsredgeal 89 
                                        +  + +  +P +gvs e+g+ l
  gi|336253242|ref|YP_004596349.1| 215 -F--NAEAAVPGIGVSAETGDWL 234
                                       .2..34589***********976 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.5   9.9e-08   0.00044      34      95 ..     286     346 ..     279     416 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.9e-08
                                       TTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHH.TTTCESEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                     Peptidase_M20  34 GaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegle.erekvdavf 95 
                                       Ga d+ +g++++++a   l+d   ++++t++++ ++ EE+g  G++al+++l  e   v+av+
  gi|336253242|ref|YP_004596349.1| 286 GALDNGCGIATVAAASGILADVEEDLERTVRIVGVGCEEIGLLGSEALADQLDlE--SVRAVV 346
                                       899************************************999********66633..555544 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   5.4e-06     0.024     126     188 ..     281     345 ..     257     352 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-06
                                       ECEEETTHHHHHHHHHHHHHHHHHCT..SS-SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEE CS
                     Peptidase_M42 126 gkivskalDdragvavllellkelke..eeleatvylvatvqEEvGlrGaktsaekikpdiaiav 188
                                       + i+  alD+  g+a ++++   l++  e+le tv +v+   EE+Gl G++++a +++++ + av
  gi|336253242|ref|YP_004596349.1| 281 HDITEGALDNGCGIATVAAASGILADveEDLERTVRIVGVGCEEIGLLGSEALADQLDLESVRAV 345
                                       4588889******99999988877761145669***********************998876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); 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:                         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: 00:00:00.41
# Mc/sec: 3557.22
//
Query:       gi|336253243|ref|YP_004596350.1|  [L=269]
Description: hypothetical protein Halxa_1843 [Halopiger xanaduensis SH-6]
Scores for 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:                       425  (0.0237046); 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:                         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 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1989.17
//
Query:       gi|336253244|ref|YP_004596351.1|  [L=309]
Description: Nucleotidyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-27   95.8   0.0    4.1e-27   95.4   0.0    1.2  1  RlaP            RNA repair pathway DNA polymerase beta family
    0.00041   20.4   0.0    0.00094   19.2   0.0    1.6  1  Polbeta         Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
       0.04   14.2   0.0      0.066   13.5   0.0    1.4  1  NTP_transf_2    Nucleotidyltransferase domain
      0.049   13.7   0.8        0.2   11.7   0.1    2.1  2  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
      0.089   13.4   0.4       0.54   10.9   0.0    2.3  2  Hemerythrin     Hemerythrin HHE cation binding domain


Domain annotation for each model (and alignments):
>> RlaP  RNA repair pathway DNA polymerase beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   0.0   1.1e-30   4.1e-27       2     242 ..       9     300 ..       8     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 1.1e-30
                              RlaP   2 reriqeeLeeieeeeevkilyacesGSrawGfpspdsDyDvrfiyiep.aewylglertrdvielpiddelDlvgwe 77 
                                       +e+i+++L+++e++++v + +a+  GS+awG +sp+sDyDv f+y++   ++y  le   ++i  +  ++++  g  
  gi|336253244|ref|YP_004596351.1|   9 HETIDDRLAALEQRHDVTVAFAVARGSHAWGAASPESDYDVGFVYVPDdLRTYAHLEGASETIT-DSGGDVEFQGLN 84 
                                       899*******************************************8637999***88888887.8999******** PP

                              RlaP  78 lrKalrLllksNptvlewlsspivyledtseleellrlaekvflsrrvahhYlgmakkqlrrylkgeevr....... 147
                                       +rK+++Ll+ sN   + +l+sp+ y+   ++ + l +  ++++++ +++h ++ +a++++r+yl+++ vr       
  gi|336253244|ref|YP_004596351.1|  85 VRKFAGLLADSNEGAIDLLRSPVRYRVLYDP-DDLMEYITRAYNPIECYHDWRAIAANNYRKYLSDHLVRsddaifp 160
                                       ************************7777776.777777888888********************************* PP

                              RlaP 148 ......................................lKkylyvlRpllagrwllekget.....pPmefesllaa 181
                                                                             +K+ l v+R+++ +r+l e+ge      p ++fe+ la+
  gi|336253244|ref|YP_004596351.1| 161 ilertengyvveaadsdtgtmtiaadderfeetrtrptVKRNLTVFRAAMYARYLKETGERgdhnlPAIDFEKFLAE 237
                                       *******************************************************9987532334255899998876 PP

                              RlaP 182 ...lv.dasleaeieeLlaikkggeekeagkrvpeldafiereLesaeeesklpedpdlaelnal 242
                                           v da+  +++++Ll++k++ge   ++   +++  ++    +++  +++ ++ pd ++lna+
  gi|336253244|ref|YP_004596351.1| 238 qapAVfDADRIDRAQTLLERKRRGEGGVRV--GDRVGREFAHPPKRIDPAVHVRDGPDCERLNAF 300
                                       222357999************988766553..333433333333444444444444777777776 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.6e-07   0.00094      12      70 ..      26      84 ..      15      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.6e-07
                                      HHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH..SSSEEEEEETT CS
                           Polbeta 12 eielaylFGSrakgkareeSDiDlavllkekldleeelelaaeledi.klgkkvDlvdln 70
                                       +++a+  GS a g a +eSD+D+++++  + dl +++ l+ + e i  +g +v+++ ln
  gi|336253244|ref|YP_004596351.1| 26 TVAFAVARGSHAWGAASPESDYDVGFVYVPD-DLRTYAHLEGASETItDSGGDVEFQGLN 84
                                      7899999******************999999.8888888888888886667777777666 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.8e-05     0.066       7      47 ..      18      60 ..      12     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                                      HHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH CS
                      NTP_transf_2  7 elkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsre 47
                                      +l++++   va +v+ GS a G a ++SD D+  v+  +  r 
  gi|336253244|ref|YP_004596351.1| 18 ALEQRHDvtVAFAVARGSHAWGAASPESDYDVGFVYVPDDLRT 60
                                      566666677999999*****************77776665543 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   5.5e-05       0.2      33      63 ..     116     146 ..     108     154 .. 0.92
   2 ?   -0.8   0.1      0.44   1.6e+03      30      46 ..     198     214 ..     180     218 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.5e-05
                    Sulfolobus_pRN  33 eellvyltrlykrGlisrkWrkiaGkkvrey 63 
                                       ++l+ y+tr y+    +  Wr ia   +r y
  gi|336253244|ref|YP_004596351.1| 116 DDLMEYITRAYNPIECYHDWRAIAANNYRKY 146
                                       78999************************99 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.44
                    Sulfolobus_pRN  30 iekeellvyltrlykrG 46 
                                         k +l v+ + +y r 
  gi|336253244|ref|YP_004596351.1| 198 TVKRNLTVFRAAMYARY 214
                                       346779999999*9996 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.43   1.5e+03      79      92 ..       8      21 ..       2      41 .. 0.62
   2 ?   10.9   0.0   0.00015      0.54      34      75 ..     133     173 ..     112     218 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.43
                                      HHHHHHHHHHHHHH CS
                       Hemerythrin 79 eHdeirelleelre 92
                                      +H+ i+++l +l++
  gi|336253244|ref|YP_004596351.1|  8 VHETIDDRLAALEQ 21
                                      45555555555542 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00015
                                       HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH.......CCC.HHHHHH CS
                       Hemerythrin  34 lrklaelldelvdeleaHhaaEEellfPlle......drpggravldv 75 
                                        ++ a +++ ++++l +H+ + ++ +fP+le              +++
  gi|336253244|ref|YP_004596351.1| 133 HDWRAIAANNYRKYLSDHLVRSDDAIFPILErtengyV-------VEA 173
                                       55666678899********************5444441.......333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); 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:                         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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2446.57
//
Query:       gi|336253245|ref|YP_004596352.1|  [L=78]
Description: glutaredoxin [Halopiger xanaduensis SH-6]
Scores for 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-15   55.9   0.1    4.8e-15   55.5   0.1    1.2  1  Glutaredoxin  Glutaredoxin
    2.7e-14   53.3   0.0    2.9e-14   53.2   0.0    1.0  1  GST_N_3       Glutathione S-transferase, N-terminal domain
    7.2e-10   39.0   0.0    8.1e-10   38.9   0.0    1.0  1  GST_N_2       Glutathione S-transferase, N-terminal domain
    3.1e-05   24.2   0.0    3.3e-05   24.1   0.0    1.0  1  GST_N         Glutathione S-transferase, N-terminal domain
      0.001   19.4   0.1     0.0013   19.1   0.1    1.3  1  DUF836        Glutaredoxin-like domain (DUF836)
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.015   15.6   0.0    1.0  1  NTP_transf_3  MobA-like NTP transferase domain
       0.16   12.1   0.1        0.3   11.2   0.1    1.4  1  Trans_coact   Phage late-transcription coactivator


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.1   1.9e-18   4.8e-15       1      54 [.       2      55 ..       2      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.9e-18
                                      EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEE CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvf 54
                                      v+l++  +CpyC ++ + L+el +++e + vd+ +++r+e+k++sg+r+vP+++
  gi|336253245|ref|YP_004596352.1|  2 VTLYQLDGCPYCEAVADRLEELDIDYESVWVDAPHSERDEVKRVSGQRQVPVIV 55
                                      89**************************************************98 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   1.1e-17   2.9e-14       1      71 [.       4      77 ..       4      78 .] 0.94

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1.1e-17
                                      EES-TTSHHHHHHHHHHHHHT--EEEE---.TTTTHHHHHHH-TT--SSEEETT..S-EEESHHHHHHHHHHHH CS
                           GST_N_3  1 LygfpaSpyarrvrlaLnekglpvevvevt.pgehdeellaknplgkvPvLedd..gealtdSlaIidyLeely 71
                                      Ly   ++py+  v+  L+e+++++e v+v+ p + ++e+++++++++vPv++d   g  + +S+ I+d+Le+ y
  gi|336253245|ref|YP_004596352.1|  4 LYQLDGCPYCEAVADRLEELDIDYESVWVDaPHSERDEVKRVSGQRQVPVIVDEeyGVTMAESERILDFLETSY 77
                                      99***************************846666*****************988999*************987 PP

>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   3.2e-13   8.1e-10       2      69 ..      10      75 ..       9      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 3.2e-13
                                      -HHHHHHHHHHHHCT--EEEEEEH...-TTSHHHHHHHHCTTTSSSEEE-C.TTEEEESHHHHHHHHHH CS
                           GST_N_2  2 CPwahRvlialalkglediisvvvlepkgfekseefprlnprgtVPvLwdk.dgqvineSseIlrylet 69
                                      CP++  v   l+++ ++++  +v+    +++  +e++r++++ +VPv++d+  g   +eS +Il++let
  gi|336253245|ref|YP_004596352.1| 10 CPYCEAVADRLEELDIDYESVWVD---APHSERDEVKRVSGQRQVPVIVDEeYGVTMAESERILDFLET 75
                                      *******************99994...47777789***************94455666*********98 PP

>> GST_N  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.3e-08   3.3e-05       3      74 ..       2      73 ..       1      75 [. 0.93

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.3e-08
                                      EEEESSSTSHTHHHHHHHHHHTT-EEEEEEECSTTTCGGC.HHHHHHCTTS-SSEEEET..TEEEESHHHHHHHH CS
                             GST_N  3 ltlysirgsprahrirlllaakgveyevvpldfeageeks.pellklnplgkvPaLedn..gkkltESraIleYi 74
                                      +tly+  g+p+ +++   l++++++ye v +d    ++ + +e +++    +vP+ +d+  g + +ES  Il ++
  gi|336253245|ref|YP_004596352.1|  2 VTLYQLDGCPYCEAVADRLEELDIDYESVWVDA---PHSErDEVKRVSGQRQVPVIVDEeyGVTMAESERILDFL 73
                                      799*****************************7...88877999999999*********************9887 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   5.2e-07    0.0013       2      58 ..       2      59 ..       1      76 [. 0.65

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.2e-07
                                      EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETT...T-CCCHCCCCTTTTEEEECTT CS
                            DUF836  2 ltLyskpgChlCeqakekLkelkleegleleviDIa...kdeeleakYgleipvlalegv 58
                                      +tLy  +gC+ Ce + ++L+el    ++e + +D     +de+ +   + ++pv++ e+ 
  gi|336253245|ref|YP_004596352.1|  2 VTLYQLDGCPYCEAVADRLEELD--IDYESVWVDAPhseRDEVKRVSGQRQVPVIVDEEY 59
                                      89******************654..44445555544543333344456666777766665 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 ?   15.6   0.0     6e-06     0.015      18      75 ..       4      66 ..       3      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6e-06
                                      HHCCCCCCHHHHHHHHHCTT.-..CEEEEECSH...CHHHHHHTTCTS-EEE-TTSS-SHHHH CS
                      NTP_transf_3 18 llplggkpllervldalraagv..devvvvggd...eevlaalarlgvrvvededpgkgplas 75
                                      l++l+g p  e v+d+l+++ +  + v+v +++   +ev++   +++v+v++de++g  +++s
  gi|336253245|ref|YP_004596352.1|  4 LYQLDGCPYCEAVADRLEELDIdyESVWVDAPHserDEVKRVSGQRQVPVIVDEEYGVTMAES 66
                                      899*****************873258888888855557777778889*******999888776 PP

>> Trans_coact  Phage late-transcription coactivator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00012       0.3      14      37 ..       7      30 ..       3      31 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                       Trans_coact 14 eeglsYlEAvlewceendieeeqv 37
                                       +g+ Y EAv++ +ee di++e+v
  gi|336253245|ref|YP_004596352.1|  7 LDGCPYCEAVADRLEELDIDYESV 30
                                      57899****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 653.97
//
Query:       gi|336253246|ref|YP_004596353.1|  [L=179]
Description: histidine triad (HIT) protein [Halopiger xanaduensis SH-6]
Scores for complete 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   47.9   0.0    2.9e-12   47.2   0.0    1.3  1  HIT       HIT domain
    1.7e-05   24.7   0.0    3.1e-05   23.8   0.0    1.4  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1
    7.3e-05   23.2   0.0    0.00013   22.4   0.0    1.4  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   4.8e-16   2.9e-12       8      95 ..      41     129 ..      35     132 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 4.8e-16
                                       EEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-S CS
                               HIT   8 vvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqs 84 
                                       +v + ++++++l++ p  pgh+ vip++h+ ++ +l++e l ++ ++ ++ + al++ ++ +g++   n g  ag s
  gi|336253246|ref|YP_004596353.1|  41 LVARSEHAFVMLNNYPYNPGHVMVIPRAHTGDYGELEDEQLLDHARLKQRTFDALEDALEPDGFNAGLNLGDGAGGS 117
                                       678899******************************************************************99999 PP

                                       S.SS-EEEEEEC CS
                               HIT  85 v.ahlHiHvipr 95 
                                       +  hlH+Hv+pr
  gi|336253246|ref|YP_004596353.1| 118 IdDHLHTHVVPR 129
                                       945********8 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   5.1e-09   3.1e-05       5      66 ..      16      79 ..      13      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.1e-09
                                      HHHHHHHHH-S--.-.-SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HH CS
                          CwfJ_C_1  5 krikasldsClfC.l.snpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldee 66
                                       +++a +++C fC + ++ +  ++l+v+ +++++++l + p + gHv++ip +H+    +l++e
  gi|336253246|ref|YP_004596353.1| 16 DEKNADVEDCVFCeFpEQHDDRENLLVARSEHAFVMLNNYPYNPGHVMVIPRAHTGDYGELEDE 79
                                      56678899*****533555667889*****************************9988777665 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.2e-08   0.00013       2     100 ..      25     127 ..      24     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.2e-08
                                       -HHHHHHTTSS.-B-E.EEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T CS
                            DcpS_C   2 wvfnilakgke.perv.vyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne 76 
                                       +vf+++ ++ + +e++ v ++e++ v+   +p ++ h++vip+++  +  +L++e+l   +++++   +++e+    
  gi|336253246|ref|YP_004596353.1|  25 CVFCEFPEQHDdRENLlVARSEHAFVMLNNYPYNPGHVMVIPRAHTGDYGELEDEQLLDHARLKQRTFDALEDA--- 98 
                                       999999877775777735588*******************************9665444444455555555554... PP

                                       -EEEEE--SCCCT-....-S.-S--EEEE CS
                            DcpS_C  77 vdaeelrvgvhyqP....sv.yhlHlHvi 100
                                       ++++ +++g+++      s+ +hlH Hv+
  gi|336253246|ref|YP_004596353.1|  99 LEPDGFNAGLNLGDgaggSIdDHLHTHVV 127
                                       4677777777777666666636*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); 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:                         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 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1358.66
//
Query:       gi|336253247|ref|YP_004596354.1|  [L=66]
Description: hypothetical protein Halxa_1847 [Halopiger xanaduensis SH-6]
Scores for 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   18.1   1.6        0.3   11.3   0.1    2.1  2  NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
  ------ inclusion threshold ------
       0.49   10.8   1.2          8    7.0   0.1    2.0  2  DUF983        Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> 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 !   11.3   0.1   3.3e-05       0.3      22      44 ..      11      33 ..       2      51 .. 0.79
   2 !    6.7   0.3   0.00089         8      26      38 ..      52      64 ..      48      66 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.3e-05
                      NOB1_Zn_bind 22 tkkFCpkCGnktLkrvavsvden 44
                                        + C+ C  +tL+ v+v+++ +
  gi|336253247|ref|YP_004596354.1| 11 MTEHCDDCDLDTLHEVSVQIRTE 33
                                      5678***************9887 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00089
                      NOB1_Zn_bind 26 CpkCGnktLkrva 38
                                      C++CGn+t +r++
  gi|336253247|ref|YP_004596354.1| 52 CQRCGNRTSQRMN 64
                                      ********99975 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1   0.00089         8       4      20 ..       8      24 ..       6      29 .. 0.82
   2 ?    3.2   0.1     0.013   1.2e+02       9      20 ..      50      61 ..      47      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00089
                            DUF983  4 fLkvadaCeaCgldlsh 20
                                      f  ++++C+ C+ld  h
  gi|336253247|ref|YP_004596354.1|  8 FNGMTEHCDDCDLDTLH 24
                                      66799********9766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.013
                            DUF983  9 daCeaCgldlsh 20
                                      ++C++Cg + s+
  gi|336253247|ref|YP_004596354.1| 50 SECQRCGNRTSQ 61
                                      68*****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 539.39
//
Query:       gi|336253248|ref|YP_004596355.1|  [L=304]
Description: methionine aminopeptidase, type II [Halopiger xanaduensis SH-6]
Scores for 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-43  146.7   0.8    9.5e-43  146.3   0.8    1.1  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 !  146.3   0.8   5.3e-47   9.5e-43       1     209 []      16     292 ..      16     292 .. 0.86

  Alignments for each domain:
  == domain 1  score: 146.3 bits;  conditional E-value: 5.3e-47
                                       HHHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC..SSSB--TTE CS
                     Peptidase_M24   1 elirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp..ndrvlkegd 75 
                                       e++r+a+ri ++++e+++++++ g ++ e+a+ +e++  +r+ ++++afp+++++ e+aa  h+tp  +d++   ++
  gi|336253248|ref|YP_004596355.1|  16 EKHREAGRILAQVREEAADRVEVGASHLEVAEYAEDR--IRELGGEPAFPVNISIDEEAA--HATPsiDDDTTFGEE 88 
                                       579********************************99..778889*****6666666666..89886655555566* PP

                                       EEEEEEEEEETTEEEEEEEEE.ECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSS CS
                     Peptidase_M24  76 lvlidagaeydgyasDitrTv.lvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffph 151
                                       +v++d+g+++dg+ +D++ Tv l G  +p   el ea ++a+eaa++ v+pGv+++ei+a +++v+  +g+  ++ +
  gi|336253248|ref|YP_004596355.1|  89 MVNLDIGVHVDGWLADTAITVdLSG--NP---ELAEASEQALEAALEVVEPGVETGEIGAEIEDVIDGYGY-NPVVN 159
                                       *********************9999..88...699************************************.999** PP

                                       CSEEEESS.SSSEEEEEESS.STTCSSB--TTBEEEEEE......EEEEETTT........................ CS
                     Peptidase_M24 152 glGHgvGl.evhdegpsvsr.esndgrkleeGmvftiEp......giyfapge........................ 196
                                       ++GHg+G+ e h + p++++ + ++g +le G+v++iEp      g      +                        
  gi|336253248|ref|YP_004596355.1| 160 LTGHGLGHwEQHTS-PNIPNrAVSQGATLEVGDVVAIEPfatdggG------Kvtegaseeifalehegtvrnrqar 229
                                       *******99***98.**96535559**************7666652......1222234456666666777778888 PP

                                       .................................................E.EEEEBEEEEEES CS
                     Peptidase_M24 197 .................................................g.gvriedtvlvte 209
                                                                                        + + + e+tv+vte
  gi|336253248|ref|YP_004596355.1| 230 aaldqiteefrtlpfatrwletdrpemalrrlkrndivhgypvlkeddgYlVSQKEHTVIVTE 292
                                       888888889999999999999999999999999999999999999999977999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2505.01
//
Query:       gi|336253249|ref|YP_004596356.1|  [L=306]
Description: beta-aspartyl-peptidase [Halopiger xanaduensis SH-6]
Scores for 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-62  210.7   8.8    2.7e-62  210.5   8.8    1.0  1  Asparaginase_2  Asparaginase


Domain annotation for each model (and alignments):
>> Asparaginase_2  Asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.5   8.8   1.5e-66   2.7e-62       3     295 ..       3     304 ..       1     306 [] 0.88

  Alignments for each domain:
  == domain 1  score: 210.5 bits;  conditional E-value: 1.5e-66
                                       EEEEEEEESE-G-HHHHHHHHHCHHHHHHHHHHHHHTT--HHHHHHHHHHHHHCTCCCSSSTTSS-BTTS---EEEE CS
                    Asparaginase_2   3 lvihGGAgsilktkereeavrkalkealeagykvLkeggsaldaVeaavrllEddplfnaGkGsvltedgeveldAs 79 
                                       l++hGGAgs ++   + + + + l++a+e+g+    e  + +daVeaav++lE +p+fnaG Gs++++dge++ dA 
  gi|336253249|ref|YP_004596356.1|   3 LLVHGGAGSEPD---EPAPRAAVLERAAETGA----ERSTPVDAVEAAVNVLESSPRFNAGVGSAVQSDGEIRTDAG 72 
                                       89******9999...55666677788888775....6899************************************* PP

                                       EEETTTTEEEEEEEESSBS-HHHHHHHHHHHCS-SEEEHHHHHHHHHHTT-----CGGG--HHHHHHHHHHHHCCCH CS
                    Asparaginase_2  80 imdgktlraGaVagvkrvknpislArlvmeksehvlLvgegAeefareqglelvdeesllteerlkelekakkekae 156
                                       im  ++  +Ga +++  v+ +is+Ar+vm +++h + +ge A  +a++ ++e     +l ++++++++ + +  +  
  gi|336253249|ref|YP_004596356.1|  73 IMTDDRS-VGAACSMPGVERAISVARVVMAETPHGFVSGEHAVSLAEAFDIE--TGVDLWADRTRERWADLEPPTGG 146
                                       **98766.******************************************95..56677777777777777766665 PP

                                       S..B-S-BS-TTT......................TT---EEEEEE-TTS-EEEEEEE--STTB-TTEE-STTSTTT CS
                    Asparaginase_2 157 kkeaknvsekelk......................aklgTvGaValDsegnlAaaTSTgGltnklvGRvGDspiiGa 211
                                       ++++ +  +++                        +++ TvGaVa+D +  lAaaTSTgG    l+GRvGD p +Ga
  gi|336253249|ref|YP_004596356.1| 147 TTAELEWVRERYGrsesdpdgrdhddgrdrasndpQDHDTVGAVAVDGD-ALAAATSTGGRWLALAGRVGDVPQVGA 222
                                       554444333322256688999999988888777777777********86.7************************** PP

                                       SEEEETTTEEEEEEE-HHHHCCTTHHHHHHHHHHTTT--HHHHHHHHHHCHHHHTTT-EEEEEEETTS-EEEEECSC CS
                    Asparaginase_2 212 GtYAdnkvgAvsaTGkGeeiirellaadivalmeykglsleeAaekvieeklkrvkgsgGviavdkkGevaaefnse 288
                                       G Y+ + ++A+saTG Ge+i r++l++++++++e+ gl++++Aae++iee  + ++ s+Gviavd++G+++ + ns+
  gi|336253249|ref|YP_004596356.1| 223 GFYC-SPAAAASATGAGEDIARVTLSRRVASHVER-GLDAQAAAETAIEEFGELTGSSAGVIAVDAEGRLGSAYNSA 297
                                       ****.999***************************.***************999999******************** PP

                                       CCEEEEE CS
                    Asparaginase_2 289 gmlraya 295
                                        m +a a
  gi|336253249|ref|YP_004596356.1| 298 AMQTARA 304
                                       **98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2369.59
//
Query:       gi|336253250|ref|YP_004596357.1|  [L=101]
Description: hypothetical protein Halxa_1850 [Halopiger xanaduensis SH-6]
Scores for 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   11.0   8.5       0.23   10.4   8.5    1.3  1  AbrB      Transition state regulatory protein AbrB
       0.73    9.4   5.3       0.89    9.2   5.3    1.1  1  PRA1      PRA1 family protein
        3.3    7.9  13.7        3.5    7.8   3.0    2.8  3  DUF2613   Protein of unknown function (DUF2613)


Domain annotation for each model (and alignments):
>> AbrB  Transition state regulatory protein AbrB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   8.5   3.9e-05      0.23     186     257 ..      12      84 ..       1      86 [. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.9e-05
                              AbrB 186 llsaalqlagllt.ialPalllalaqlliGasiGlrftreslrellralpaallstlllialcallalllall 257
                                       +++ a+ l  +l  ++ +++ + +aq+++G+++G+ +   s+++ l  + ++++ +l+l a+c+++  ++ ++
  gi|336253250|ref|YP_004596357.1|  12 AVMSAVALGRVLRaASRDPVDVGAAQVVVGITLGTVLWVGSVESWLTGVTRIVVGILALAAICLGVTTIVRYW 84 
                                       33344444444443445888899******************************************99988766 PP

>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   5.3   0.00015      0.89      58     125 ..       3      69 ..       1      85 [. 0.64

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00015
                              PRA1  58 plslivllllvlawlflyf.lr...seplvlfgrelsdrvvlivllvvsvlllfltgavlvllwalliglll 125
                                       p++l+v++++v++++ l   lr   ++p+      +   +v++++ + +vl +  ++++l+ +  +++g+l+
  gi|336253250|ref|YP_004596357.1|   3 PVALLVAFCAVMSAVALGRvLRaasRDPV-----DVGAAQVVVGITLGTVLWVGSVESWLTGVTRIVVGILA 69 
                                       77776666666665555554667778888.....55555666666666666666666666666666666654 PP

>> DUF2613  Protein of unknown function (DUF2613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.4      0.35   2.1e+03       6      12 ..      12      18 ..       6      27 .. 0.67
   2 ?    7.8   3.0   0.00058       3.5       6      23 ..      34      51 ..      33      59 .. 0.87
   3 ?    7.5   0.2   0.00074       4.5       7      37 ..      60      90 ..      55      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.35
                           DUF2613  6 aaaSaVa 12
                                      a+ SaVa
  gi|336253250|ref|YP_004596357.1| 12 AVMSAVA 18
                                      5566664 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00058
                           DUF2613  6 aaaSaVaGivlGvvavfg 23
                                      +aa +V+Gi+lG+v+ +g
  gi|336253250|ref|YP_004596357.1| 34 GAAQVVVGITLGTVLWVG 51
                                      6889**********9887 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.00074
                           DUF2613  7 aaSaVaGivlGvvavfgvtavvqqdsrPstd 37
                                      +  +V+Gi+  ++  +gvt++v   + P  +
  gi|336253250|ref|YP_004596357.1| 60 VTRIVVGILALAAICLGVTTIVRYWDDPGRE 90
                                      5668****9999999*****99877666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 732.88
//
Query:       gi|336253251|ref|YP_004596358.1|  [L=425]
Description: isocitrate dehydrogenase, NADP-dependent [Halopiger xanaduensis SH-6]
Scores for 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-104  348.1   0.0   7.3e-104  347.6   0.0    1.1  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 !  347.6   0.0  4.1e-108  7.3e-104       2     348 .]      33     417 ..      32     417 .. 0.97

  Alignments for each domain:
  == domain 1  score: 347.6 bits;  conditional E-value: 4.1e-108
                                       EEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHS..SSS-HHHHHHHHHSSEEEEEE---CSS CS
                            Iso_dh   2 iallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetg..eplpeetleaikeadvvllgavgtpke 76 
                                       i++l gdgiG++v +aa +vl+aa+e+ g+e++++ v++G++a++++g    lp+et+eaike +v+++g+++tp++
  gi|336253251|ref|YP_004596358.1|  33 IPILHGDGIGKDVGPAAQEVLEAAAEATGREINWMRVYAGESAREKYGedVNLPDETVEAIKEHRVAIKGPLTTPVG 109
                                       899********************************************955689************************ PP

                                       SSSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET.......... CS
                            Iso_dh  77 kevrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg.......... 143
                                       ++ r+ n  +aLr++ldl+an+rp  ++   +v+sp+ +  +e++d+v +Re+t+++Y+g+e e+ +          
  gi|336253251|ref|YP_004596358.1| 110 AGFRSLN--VALRQTLDLYANVRPTYYL--DGVPSPMSE--PEQMDMVTFRENTEDVYAGIEWEEGTeeveqvrdfi 180
                                       *******..*******************..89******8..9********************9999999******** PP

                                       ........TG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCC..... CS
                            Iso_dh 144 ........sifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaee..... 206
                                               +i ++ v++++k+++e++++r++r a+++Al+++++kvtlv+K+n++k++e ++ ++  eva+e     
  gi|336253251|ref|YP_004596358.1| 181 enemgfdsTIHDGPVGIGIKPITEKGSKRLVREAIDYALEHDRDKVTLVHKGNIMKFTEgQFSEWGMEVADEeypdd 257
                                       ******9644899**********************************************************9***** PP

                                       ..................TTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEE CS
                            Iso_dh 207 ..................eypdielehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslg 265
                                                           + + +e++l+D++++ +  + ++fdV++++Nl+GD+lSD+a a++G+lG++p+ + g
  gi|336253251|ref|YP_004596358.1| 258 evfaapdslweeqddidiPEGAVMVEERLADAMLQWMQLRTDEFDVLAMPNLNGDYLSDAAGAQIGGLGIAPGGNFG 334
                                       ****************776678*************9999999*********************************** PP

                                       TSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHTSCCHHHCTTS..TCCCH CS
                            Iso_dh 266 ekkvaifEavHGsapdiagkdkaNpiavilSaalmLryslgleeaAdkiekAvekvleagivTkDlagea..akevs 340
                                        k+ +++E+vHGsap+ ag+d+aNp+a+ilS  lm  y lg+++aAd i +Ave+++ +g+vT+Dl+++   a+++ 
  gi|336253251|ref|YP_004596358.1| 335 -KGRMLAEPVHGSAPKRAGQDMANPTAMILSGRLMFDY-LGWDDAADLIRDAVEETISSGKVTYDLERQLedAEKLA 409
                                       .789**********************************.*****************************998889999 PP

                                       HHHHHHHH CS
                            Iso_dh 341 tsefgdav 348
                                       ts+++ +v
  gi|336253251|ref|YP_004596358.1| 410 TSDYTAEV 417
                                       99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3079.72
//
Query:       gi|336253252|ref|YP_004596359.1|  [L=150]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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   0.2    1.5e-23   83.2   0.2    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    6.1e-12   45.8   0.2    7.4e-12   45.5   0.2    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.2e-11   44.9   0.2    1.9e-11   44.2   0.2    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.4e-07   30.0   0.3    5.5e-07   29.7   0.3    1.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0038   17.9   2.0     0.0068   17.1   1.1    2.0  2  Acetyltransf_5   Acetyltransferase (GNAT) domain
     0.0076   16.4   0.2      0.013   15.6   0.2    1.5  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
       0.04   13.9   0.1      0.079   12.9   0.1    1.5  1  FR47             FR47-like protein
       0.15   12.1   0.0       0.25   11.4   0.0    1.3  1  Acetyltransf_13  ESCO1/2 acetyl-transferase


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 !   83.2   0.2   6.5e-27   1.5e-23      12     127 .]      23     149 ..       7     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 6.5e-27
                   Acetyltransf_10  12 tf.kefispealrerie...egealllvaeeggkivGvielrdgs........hisllfVdpeyrgqGigkaLleav 76 
                                       +f +e+  +e l+   +   + +a+++va+ gg++vG+++lr+ +        ++++++V +++r  G+g++L++a 
  gi|336253252|ref|YP_004596359.1|  23 VFvEEQGVDEDLEYDEHdepDADAVHFVAYAGGQPVGAARLREYEtddgdvvgKVERVAVLESHREAGVGRELMDAT 99 
                                       56666666655554442356899****************9988888999**************************** PP

                   Acetyltransf_10  77 eeeaekdgikleltvnaspyavpfYeklGFkavgeeqeenGirfvpMekel 127
                                       e++a+++g + +++++a+   ++fY++lG++  gee+ee+Gi +v+M+k+l
  gi|336253252|ref|YP_004596359.1| 100 EAAARERGFG-AIKLHAQMRVEGFYRSLGYESRGEEFEEAGIPHVEMRKSL 149
                                       *******999.*************************************986 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.2   3.3e-15   7.4e-12      14     117 .]      29     128 ..      11     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.3e-15
                                       HHHHHHHHHHHHHHHHSTTC.EEEEEEETTEEEEEEEEEEEET.TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHH CS
                    Acetyltransf_1  14 ppnedaseeefeesfsleae.gllvaeedgeliGfisllkipd.ekggvayieslaVspeyrgkGlGsaLlealeer 88 
                                        ++ed +++e+ e    +a+  ++va+ +g+++G ++l+ +       v+ +e++aV +++r  G+G++L++a e  
  gi|336253252|ref|YP_004596359.1|  29 GVDEDLEYDEHDEP---DADaVHFVAYAGGQPVGAARLREYETdDGDVVGKVERVAVLESHREAGVGRELMDATEAA 102
                                       34455555554444...55568999****************99888899**************************** PP

                                       HHHTTESEEEEEEETTEHHHHHHHHH.TTE CS
                    Acetyltransf_1  89 areegikkivlaveedndaairlYek.lGF 117
                                       are+g+ +i l     + +  ++Y + lG+
  gi|336253252|ref|YP_004596359.1| 103 ARERGFGAIKL---HAQMRVEGFY-RsLGY 128
                                       ******99***...558888****.55*98 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.2   8.6e-15   1.9e-11       3      75 ..      46     129 ..      44     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 8.6e-15
                                       EEEEEEEETTEEEEEEEEEEES.......TCTEEEEE-GGGTTSSHHHHHHHH...TT....SE.EEEE.EEEETHH CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld.......aeitrlaVdpeyrgkGiGraLlea...ae....kg.iile.qlelnae 63 
                                       + +fVa+ +g++vG ++l +++       +  +r+aV++++r  G+Gr+L++a   a+     g i+l+ q      
  gi|336253252|ref|YP_004596359.1|  46 AVHFVAYAGGQPVGAARLREYEtddgdvvGKVERVAVLESHREAGVGRELMDAteaAArergFGaIKLHaQM----- 117
                                       56899************99999999877777777******************86551155344433333333..... PP

                                       HHHHHHHHTTEE CS
                    Acetyltransf_7  64 kaikfYeklGFe 75 
                                       + ++fY++lG+e
  gi|336253252|ref|YP_004596359.1| 118 RVEGFYRSLGYE 129
                                       4488*******8 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.3   2.5e-10   5.5e-07      10     126 ..      13     129 ..       3     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.5e-10
                                       HHHHHHHHHHHTT----H..HHHHHHHHHHTT.SEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCG CS
                    Acetyltransf_9  10 ldevlellkyaFqdeespleeireyfrkllee.srvlgaedngelvgqlallplelnvpGktlkaagvtgVavapeh 85 
                                         +++++ +++F +e+   e++++  ++  +  + +++a+ +g+ vg ++l  +e   ++    ++ v  Vav   h
  gi|336253252|ref|YP_004596359.1|  13 RADAFAVRQTVFVEEQGVDEDLEYDEHDEPDAdAVHFVAYAGGQPVGAARLREYETDDGDV---VGKVERVAVLESH 86 
                                       56788899999999998853555555555554157889999**************999997...578899******* PP

                                       TTS-HHHHHHHHHHHHHHHTT--EEEE--..SSHHHHHTTT-E CS
                    Acetyltransf_9  86 rgrgvlskLlaraleemreegqplsllfP..ssipiYrrfGye 126
                                       r  gv ++L++++ + +re+g   + l++  + +++Yr++Gye
  gi|336253252|ref|YP_004596359.1|  87 REAGVGRELMDATEAAARERGFGAIKLHAqmRVEGFYRSLGYE 129
                                       *****************************65447********8 PP

>> Acetyltransf_5  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.1     3e-06    0.0068       1      55 [.      19      70 ..      19     106 .. 0.82
   2 ?   -0.1   0.1      0.69   1.5e+03      63      63 ..     111     111 ..      69     148 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3e-06
                    Acetyltransf_5  1 LRyevFreemgaegeaaapeldiDefDavcdhllvideaeevVGtyRllrpdeae 55
                                      +R  vF+ee g  ++   +  + De Da ++h++ ++  +  VG+ Rl + + + 
  gi|336253252|ref|YP_004596359.1| 19 VRQTVFVEEQGVDEDL--EYDEHDEPDADAVHFVAYAGGQ-PVGAARLREYETDD 70
                                      5899*****9999877..446688888********99999.*******9988876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.69
                    Acetyltransf_5  63 e 63 
                                        
  gi|336253252|ref|YP_004596359.1| 111 I 111
                                       1 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 !   15.6   0.2   5.7e-06     0.013      15      58 ..      63     108 ..      34     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.7e-06
                   Acetyltransf_CG  15 l.eYevrkeg.vldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                       l eYe+++++ v +++ + V e++r  G++++L++a    are+g+
  gi|336253252|ref|YP_004596359.1|  63 LrEYETDDGDvVGKVERVAVLESHREAGVGRELMDATEAAARERGF 108
                                       24787555553559*****************************997 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.5e-05     0.079      22      80 ..      75     131 ..      67     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.5e-05
                                       SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                       g +  + vl++hr  G g+ l  a  ++ +erg  ++     +  + + +y +lG+e +
  gi|336253252|ref|YP_004596359.1|  75 GKVERVAVLESHREAGVGRELMDATEAAARERGFGAI--KLHAQMRVEGFYRSLGYESR 131
                                       788899*****************99888888886554..4456778999*******987 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.25       7      30 ..      77     100 ..      72     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                   Acetyltransf_13   7 isriWvssshRrkgiAtkLldaar 30 
                                       ++r+ v +shR  g+ ++L+da  
  gi|336253252|ref|YP_004596359.1|  77 VERVAVLESHREAGVGRELMDATE 100
                                       89999****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); 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:                         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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1171.02
//
Query:       gi|336253253|ref|YP_004596360.1|  [L=459]
Description: natural resistance-associated macrophage protein [Halopiger xanaduensis SH-6]
Scores for complete 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-61  208.1  29.0    1.9e-61  208.1  29.0    1.6  2  Nramp     Natural resistance-associated macrophage protein


Domain annotation for each model (and alignments):
>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.1  29.0     1e-65   1.9e-61       2     351 ..      39     390 ..      38     397 .. 0.88
   2 ?   -1.5   0.2     0.054   9.6e+02     273     309 ..     412     445 ..     409     455 .. 0.48

  Alignments for each domain:
  == domain 1  score: 208.1 bits;  conditional E-value: 1e-65
                             Nramp   2 atdlqaGaqfGykLlwvlllstllaillqelsarLGlvTgkglaelirerlpkkvsillwilaelaiiatdlaeviG 78 
                                       a+ + aGa++Gy+Llwv+lls +l++  q+l++rLGl T+kg++++++e+l+  ++++l+i+a+la+ +++la ++ 
  gi|336253253|ref|YP_004596360.1|  39 ASLVVAGASYGYALLWVVLLSAVLGATGQYLAMRLGLLTEKGIVAVVEEHLGSFWAWVLVIDAVLAAGLAQLAIMLT 115
                                       7899************************************************************************* PP

                             Nramp  79 aAialnllfg....ipl......lvgvlitavlvllllflekggyrklEaliialvlvialsFiaelflvkpdwgev 145
                                        A +  +++g      +        +++ +av+ +l l+   ggyr  E   ++lv++++l+F+a+++++++d +++
  gi|336253253|ref|YP_004596360.1| 116 LADVSATIVGsvgiG-IaaladpRFWGVGWAVILALGLA--GGGYRIAELGAKVLVSLVVLAFVASALVAPIDPAAA 189
                                       ***999999654540.24455556677777777777777..9*********************************** PP

                             Nramp 146 lkglvvPslpg..keslllavgilGatvmphnlflhsslvqerkitidrsekeealkyeriDtiial.ivaflinla 219
                                       ++glv P++pg   + + +a+gilG  v+++ l ++s+++  r++t     ++     +++D++ ++ +++++ +la
  gi|336253253|ref|YP_004596360.1| 190 ATGLV-PEIPGsgLGGAAVAAGILGGAVHITLLTMQSYTMGARGWTE----RD--RDIATFDVVSSMlVAFGVFSLA 259
                                       ***99.*****9999*****************************887....66..89**********5556688*** PP

                             Nramp 220 ilivaAavly.sggk.dvesledaaeaLepllGskaasvlFaigLlaaGlsStitgtlagqyvmegflglrislwlr 294
                                       +++vaA++l  +g    + +  +aa+aLep++G ++a+++F +gL++a++s++  +t+   y++++ lg++ s++  
  gi|336253253|ref|YP_004596360.1| 260 VFLVAASILPeAGVDpGTVDEIQAAQALEPVAG-EYAMWIFLLGLWGAAVSTLGGNTIVPPYLLADKLGWERSVDDP 335
                                       **********65555655666799*********.7***************************************666 PP

                             Nramp 295 rlitralafvpalivilligaele.....lvkllvlsqvllslllPfaliplllltsskklM 351
                                       r       +++al++++l++a++      ++++lvl+ ++  +++Pfal+++l+l+++ ++ 
  gi|336253253|ref|YP_004596360.1| 336 R-------YRGALVAVALASAAGAflqgaFLQVLVLVLAFGLVGTPFALAVILYLLNDPDVV 390
                                       6.......44444444444444444445567***************************9875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.054
                             Nramp 273 gtlagqyvmegflglrislwlrrlitralafvpaliv 309
                                       ++lag++v+e++     +  + ++i   +a  +al++
  gi|336253253|ref|YP_004596360.1| 412 AALAGEFVLEELQTATEPA-SAFVIV--FAAAMALAI 445
                                       5667777777766555555.222222..222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); 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: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3376.75
//
Query:       gi|336253254|ref|YP_004596361.1|  [L=113]
Description: Cupin 2 barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   63.3   1.1    1.6e-17   63.0   1.1    1.1  1  Cupin_2          Cupin domain
    4.5e-05   23.4   0.7    6.1e-05   22.9   0.7    1.1  1  AraC_binding     AraC-like ligand binding domain
  ------ inclusion threshold ------
      0.028   14.0   0.0      0.037   13.6   0.0    1.2  1  Cupin_1          Cupin
        0.1   12.5   0.0       0.13   12.1   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
       0.11   12.8   0.0       0.14   12.4   0.0    1.2  1  CENP-C_C         Mif2/CENP-C like


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 !   63.0   1.1   4.4e-21   1.6e-17       2      71 .]      33     101 ..      32     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 4.4e-21
                                       EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEEE CS
                           Cupin_2   2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvvy 71 
                                       ++e++ G++ ++h+Hp+e +++++ eGe+++  ++ e++ ++Gds+ +p  +pH+ +N+gdep+r ++++
  gi|336253254|ref|YP_004596361.1|  33 HFEIEAGATVEEHSHPHE-QTGFIYEGELTFLTEDDEITCGPGDSYAIPGDQPHAAENRGDEPVRGVDIF 101
                                       689***************.*************99999****************************99986 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 !   22.9   0.7   1.7e-08   6.1e-05      14      69 ..      40      95 ..      31      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.7e-08
                                      -SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEE CS
                      AraC_binding 14 hsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgw 69
                                        +++h h++ + + + eG+ ++  ++ +  +gpGd   +p ++pH  e  ++++ 
  gi|336253254|ref|YP_004596361.1| 40 ATVEEHSHPHEQTGFIYEGELTFLTEDDEITCGPGDSYAIPGDQPHAAENRGDEPV 95
                                      45689******************************************999888765 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     1e-05     0.037      33     107 ..      29      95 ..      13     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                                       EEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSE CS
                           Cupin_1  33 isaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepa 107
                                       + +  + +e+g+ ++ h h   ++  ++ +Ge++  f+++++     + +  +Gd  ++P   +h++ n gdep+
  gi|336253254|ref|YP_004596361.1|  29 MNVQHFEIEAGATVEEHSH-PHEQTGFIYEGELT--FLTEDD-----EITCGPGDSYAIPGDQPHAAENRGDEPV 95 
                                       6677888999*********.788999*******9..888886.....5569********************9997 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.7e-05      0.13      57     135 ..      23     100 ..      17     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                   MannoseP_isomer  57 ldegeryqvkritvkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkipleli 133
                                       +  +e+ +v++ +++ g+++  + h h    ++  +G     ++d++++    +s  ip ++ h+ en G  p++ +
  gi|336253254|ref|YP_004596361.1|  23 MAGSESMNVQHFEIEAGATVEEHSHPHEQTGFI-YEGELTFLTEDDEITCGPGDSYAIPGDQPHAAENRGDEPVRGV 98 
                                       556788999********9999999998887776.6899999999999999*********************999877 PP

                   MannoseP_isomer 134 ev 135
                                       ++
  gi|336253254|ref|YP_004596361.1|  99 DI 100
                                       76 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.9e-05      0.14      28      79 ..      44      95 ..      25      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                                      EE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE-SSS-E CS
                          CENP-C_C 28 knskkatlvFyViqGrvevtvsktsfvigkgsvFqvPagneysieNklnkea 79
                                      ++s+ +  + ++++G++    ++ + ++g+g+++ +P     + eN++++ +
  gi|336253254|ref|YP_004596361.1| 44 EHSHPHEQTGFIYEGELTFLTEDDEITCGPGDSYAIPGDQPHAAENRGDEPV 95
                                      56777777889***********************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); 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 0.20s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 921.52
//
Query:       gi|336253255|ref|YP_004596362.1|  [L=174]
Description: hypothetical protein Halxa_1855 [Halopiger xanaduensis SH-6]
Scores for 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   13.4   0.2       0.18   12.1   0.2    1.6  1  PaaX            PaaX-like protein
      0.078   13.1   0.3       0.12   12.5   0.3    1.3  1  TerY_C          TerY-C metal binding domain
       0.12   12.4   0.7       0.25   11.4   0.7    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.13   12.4   0.7       0.19   11.8   0.7    1.3  1  Zn_Tnp_IS91     Transposase zinc-binding domain
       0.14   12.2   0.5       0.24   11.5   0.3    1.8  1  CpXC            CpXC protein
       0.16   11.9   1.0       0.33   10.9   1.0    1.5  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.21   11.3   2.3          4    7.2   0.4    2.6  2  zf-CSL          CSL zinc finger
       0.22   11.4   2.8       0.93    9.4   0.5    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.25   11.3   1.5         23    5.0   0.3    2.5  2  zinc_ribbon_4   zinc-ribbon domain
       0.47   10.6   2.5        1.2    9.3   2.5    1.7  1  Zn-ribbon_8     Zinc ribbon domain


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 ?   12.1   0.2   9.8e-05      0.18      30      64 ..     141     171 ..     133     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.8e-05
                              PaaX  30 laelGiseslvRaalsRlakaGwlvrekegrrsfY 64 
                                         e G+s+  vR++l  l+++G++ +++      Y
  gi|336253255|ref|YP_004596362.1| 141 AGERGVSADDVRTGLEKLTRRGDVSESRGR----Y 171
                                       55679*******************998865....5 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 ?   12.5   0.3   6.6e-05      0.12      85     117 ..       3      37 ..       1      46 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.6e-05
                            TerY_C  85 afavC.eCgkllCidg.eeeatCpwCgkevkfgea 117
                                       a++ C eC++l  i+g +e+++Cp+Cg + ++++ 
  gi|336253255|ref|YP_004596362.1|   3 AVVGCsECSNLWIIEGrSETTQCPRCGARKAYEKR 37 
                                       5666637********9567789******9999854 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   0.7   0.00014      0.25      69      96 ..       3      32 ..       1      41 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                      -EEEETTTS-EEECHHH..HHS-TTTSSS- CS
                              HypA 69 vkvrCreCgkefeleek..alrCpkCgsad 96
                                      ++v C+eC++ + +e +  +++Cp+Cg+++
  gi|336253255|ref|YP_004596362.1|  3 AVVGCSECSNLWIIEGRseTTQCPRCGARK 32
                                      5688********9887446789*****986 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 ?   11.8   0.7   0.00011      0.19      37      70 ..       2      35 ..       1      43 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                       Zn_Tnp_IS91 37 faryeCeeCghekivyfsCksrhCpsCqkkatee 70
                                      +a++ C+eC++  i+  + +   Cp+C+++++ e
  gi|336253255|ref|YP_004596362.1|  2 YAVVGCSECSNLWIIEGRSETTQCPRCGARKAYE 35
                                      56789***********************998755 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00013      0.24      30      52 ..      15      37 ..      12     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                              CpXC 30 lldgslfeatCpkCgatakleap 52
                                      +++g+  +++Cp+Cga+ ++e  
  gi|336253255|ref|YP_004596362.1| 15 IIEGRSETTQCPRCGARKAYEKR 37
                                      7899************9988765 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 ?   10.9   1.0   0.00018      0.33       4      30 ..       7      31 ..       7      36 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                                      ESTTTSBEEEEECSCCCEEEESSSS-E CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCgYe 30
                                      C++C Nl ++ +  e++   C  Cg+ 
  gi|336253255|ref|YP_004596362.1|  7 CSECSNLWIIEGRSETTQ--CPRCGAR 31
                                      ****************96..****986 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.4    0.0022         4      43      54 ..       3      15 ..       1      16 [. 0.82
   2 ?    3.2   0.1      0.04        72      19      29 ..      23      36 ..      18      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0022
                                      -EEEETTSS.EEE CS
                            zf-CSL 43 vvvqCssCS.Lwi 54
                                       vv+Cs+CS Lwi
  gi|336253255|ref|YP_004596362.1|  3 AVVGCSECSnLWI 15
                                      69*******7776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.04
                                      EEE.TTSSE..EEE CS
                            zf-CSL 19 ypC.RCgde..Fel 29
                                       +C RCg +  +e 
  gi|336253255|ref|YP_004596362.1| 23 TQCpRCGARkaYEK 36
                                      57999999877765 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 ?    2.0   0.1      0.11     2e+02      29      38 ..       5      14 ..       1      15 [. 0.79
   2 ?    9.4   0.5   0.00052      0.93       1      12 [.      23      34 ..      23      37 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                           TFIIS_C 29 ykCtkCghrW 38
                                      + C +C + W
  gi|336253255|ref|YP_004596362.1|  5 VGCSECSNLW 14
                                      6799999988 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00052
                           TFIIS_C  1 akCpkCgsreay 12
                                      ++Cp+Cg r+ay
  gi|336253255|ref|YP_004596362.1| 23 TQCPRCGARKAY 34
                                      59********98 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.016        28      26      35 ..       5      14 ..       2      15 .. 0.85
   2 ?    5.0   0.3     0.013        23       4      10 ..      24      30 ..      22      34 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.016
                     zinc_ribbon_4 26 vrCskCghvF 35
                                      v Cs C++++
  gi|336253255|ref|YP_004596362.1|  5 VGCSECSNLW 14
                                      77*******9 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.013
                     zinc_ribbon_4  4 tCpsCka 10
                                      +Cp+C+a
  gi|336253255|ref|YP_004596362.1| 24 QCPRCGA 30
                                      7888877 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.5   0.00066       1.2       8      35 ..       7      32 ..       2      37 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00066
                       Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgs.e 35
                                      C eC     ++   s   +t+ CP+Cg+ +
  gi|336253255|ref|YP_004596362.1|  7 CSECS-NLWIIEGRS---ETTqCPRCGArK 32
                                      66666.333344333...5555*****964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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):              10  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1306.91
//
Query:       gi|336253256|ref|YP_004596363.1|  [L=416]
Description: 3-hydroxy-3-methylglutaryl Coenzyme A reductase [Halopiger xanaduensis SH-6]
Scores for complete 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-131  439.2   4.3   1.3e-131  439.0   4.3    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase


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 !  439.0   4.3  7.1e-136  1.3e-131       2     367 .]      38     416 .]      37     416 .] 0.98

  Alignments for each domain:
  == domain 1  score: 439.0 bits;  conditional E-value: 7.1e-136
                                       HHHHHHHHHHS-HHHHHHHTT----HHHHHHHSSS---------EEEEEEEETTE....EEEEEE---STTHHHHHH CS
                       HMG-CoA_red   2 veeRrklleelteeeleelkeesldeevadkmiEnviGyvqlPlGvagpllingk....eylvPmAteEgslvAsas 74 
                                       +e+Rr l+e++t+++le+++++++d+e+ad +iEn+iG++q+P+Gv+gp+ i+g     e+++P+At+Eg+l As++
  gi|336253256|ref|YP_004596363.1|  38 AEARRLLVERETDADLEAVGDYTFDAEQADPNIENMIGAAQVPMGVVGPVPIDGGaadgEHYLPLATTEGALLASVN 114
                                       689**************************************************9999******************** PP

                                       HHHHHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHHHTHHHHHHHHHHCSHHCCT-EEEEEEEEE-SSEEE CS
                       HMG-CoA_red  75 rgakainesgGvkttvlkdgmtraqvvllesvedaaelkkwiekkeeleelanaaestsrggglkdievvlagrlvv 151
                                       rg ++i+++gG++++v+k+gmtra+v++++ v++aae+ +w+  +++ ++l++aaest+++g+l d+e++++g++v+
  gi|336253256|ref|YP_004596363.1| 115 RGLSVIRSAGGADARVTKNGMTRAPVFRVDGVAEAAEVVEWV--DDNTDALREAAESTTSHGELIDVEPYVVGDSVY 189
                                       ******************************************..********************************* PP

                                       EEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHHHH CS
                       HMG-CoA_red 152 lrlkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevvekil 228
                                       lr+ +dt+DAmG+Nm ++at +a+e++e+e++ ++l+++++Nlc+dkk++a+na+egrg+sv+a+++i+ e+ve+ l
  gi|336253256|ref|YP_004596363.1| 190 LRFAYDTKDAMGMNMATIATGEACEVVENETP-ADLVALSGNLCSDKKPAAVNAVEGRGRSVTADVVIPGELVEERL 265
                                       ********************************.9******************************************* PP

                                       HHHHHHHH-HHHH....HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTTSEEE..TTTE...EEEEEE CS
                       HMG-CoA_red 229 kasaealvdlnra.n.igtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaaleev..edgd...lygsvt 298
                                       +++aea+v++n++ n +g+a++G++gfnahaaN++aA flAtGqD a+v+e+++ai+++++   edg+   ly+sv+
  gi|336253256|ref|YP_004596363.1| 266 HTTAEAIVEANTRkNlTGSAKAGSLGFNAHAANVVAAAFLATGQDEAQVVEGANAITTMDTRgsEDGGpadLYASVS 342
                                       **************************************************************886665788****** PP

                                       EE.----SBSHHHHH-HHHHHHHHTT---HH........HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                       HMG-CoA_red 299 lPsleVGtvGGgtklppqaellkllgvkgak.....nakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                       l+sleVGtvGGgtklp+qae+l++lg++g +     na++Laeiia  +LA+els+l+AL++++l+++H+ l+r
  gi|336253256|ref|YP_004596363.1| 343 LASLEVGTVGGGTKLPTQAEALDILGLRGGGdppgsNADALAEIIAVGALAGELSLLAALSSRHLASAHEDLGR 416
                                       ***********************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2982.90
//
Query:       gi|336253257|ref|YP_004596364.1|  [L=139]
Description: hypothetical protein Halxa_1857 [Halopiger xanaduensis SH-6]
Scores for 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  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1060.20
//
Query:       gi|336253258|ref|YP_004596365.1|  [L=528]
Description: Amidohydrolase 3 [Halopiger xanaduensis SH-6]
Scores for 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-99  332.5  17.4    7.9e-99  332.2  17.4    1.0  1  Amidohydro_3  Amidohydrolase family
      3e-19   69.5   0.4    6.5e-14   52.0   0.1    2.8  2  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
        1.5    9.3   8.3        1.1    9.7   1.2    3.0  2  DinB_2        DinB superfamily


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.2  17.4  1.3e-102   7.9e-99       1     473 []      52     523 ..      52     523 .. 0.97

  Alignments for each domain:
  == domain 1  score: 332.2 bits;  conditional E-value: 1.3e-102
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagtt.......pkgrwivgeGwdeaq 70 
                                       eviD+ Gr+vlPGF+D+HtH+   g+ l +++l++  ++s++++l+ ++++a++t         ++wi+g+G+de+ 
  gi|336253258|ref|YP_004596365.1|  52 EVIDCGGRVVLPGFIDAHTHMEQLGQHLVHADLSQ--ADSADECLELLAAEAERTaadadgdASDDWILGFGYDESE 126
                                       79*********************************..**************************************** PP

                      Amidohydro_3  71 faeerfpyalaeldevledapvllaaldtHaavrnsaaldl.agiteatpdpaggeilrdangegatgllregafhl 146
                                       +++++ + ++a+ld+v+ed+p+ + ++d H+  +nsaal++ a++ ++++          ++ge +tg+  e+a+++
  gi|336253258|ref|YP_004596365.1| 127 WTDRSSRLTRADLDAVSEDRPIAALRVDLHTVSLNSAALERlADDLPESDLH-------YEDGE-PTGVAVEDAAEA 195
                                       *****************************************99999999985.......99***.************ PP

                      Amidohydro_3 147 vldlaplareaeaaavaaalaalasyGitsveagggnvsslddleplfeltaeeklplrvi...ikelldaaerlgl 220
                                       v+  + ++rea+++ ++aa +++   G+t+v   ++ v +++++ +++el+a + lplrv     ++ l++   +gl
  gi|336253258|ref|YP_004596365.1| 196 VRREVTADREAMREVLEAATERAVELGVTGV---HDKVRNSKAPRVYRELAADGDLPLRVRidyWSDHLESLVDVGL 269
                                       *******************************...***************************9997888999999999 PP

                      Amidohydro_3 221 plspgseeltigavklfadgvlgsrtalltepyf...........tgwpdfedealaelvaaadergldvaihaigd 286
                                       +++ g + ++ ga+k f dg+lgs+ta l epy+           +g+  ++ ++la+lv++ad+ g+++ +haigd
  gi|336253258|ref|YP_004596365.1| 270 TTNAGGDLVRTGAIKSFSDGSLGSQTAKLREPYAdaaddgededaRGQWVVDPDDLAALVERADDDGYQLTVHAIGD 346
                                       999************************************************************************** PP

                      Amidohydro_3 287 aavddvldafeaaaekngnqdrrrlehaegvtesqiervaalqvaagvqpvfnf...edelldsrlgperargstpv 360
                                       +a++++l+ +e +a+  g +   r+ehae  t++q er+a+ ++ a++qp f     e +l+d+rlg+er++ ++++
  gi|336253258|ref|YP_004596365.1| 347 EAIEETLTRLEDTADPAGSRH--RIEHAELATDDQFERMAEAGIVASMQPNFHRwadEGGLYDQRLGEERRKRTNRF 421
                                       *************88888885..9*************************7776699*99****************** PP

                      Amidohydro_3 361 kellnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevG 437
                                       ++ l+ag ++a+gsD  + p+dp+ ++++av+         +++ ++ls++eal++yT+g+A+a + edr GtLevG
  gi|336253258|ref|YP_004596365.1| 422 RRALEAGAPLAFGSD--CMPLDPLLGVHHAVN--------APTEPQRLSVTEALRAYTSGAAYAGFDEDRLGTLEVG 488
                                       ***************..**************5........5679********************************* PP

                      Amidohydro_3 438 adADlvvldadpldvdppelaearvrltvvdGrvvy 473
                                       ++ADlvvl+  p ++ + ++ e+ v +tvvdG++v+
  gi|336253258|ref|YP_004596365.1| 489 KRADLVVLEESPWERAD-RIDEIDVAMTVVDGEPVF 523
                                       **************995.8***************97 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.3e-06     0.014       1      23 [.      60      75 ..      60     108 .. 0.65
   2 !   52.0   0.1   1.1e-17   6.5e-14     123     342 ..     314     520 ..     177     522 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-06
                                      EEEE-EEEEEEECETTECSSSGH CS
                      Amidohydro_1  1 ivlPGlIDaHvHleqsllrgatl 23
                                      +vlPG+IDaH+H eq       l
  gi|336253258|ref|YP_004596365.1| 60 VVLPGFIDAHTHMEQ-------L 75
                                      69**********983.......2 PP

  == domain 2  score: 52.0 bits;  conditional E-value: 1.1e-17
                                       ECGTCCSHHHHHHHHHHHHHHHTTEEEEEE..TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCE CS
                      Amidohydro_1 123 pheapafsdeelkealkeakkrdlpvaiHa..letkgevedaeaafgetiehgthlevaeslglldeiklilahgvh 197
                                        ++++ + ++ l+++++ a++ + ++++Ha   e  +e   ++++ ++ + + +  e ae  +  d    +++ g+ 
  gi|336253258|ref|YP_004596365.1| 314 ARGQWVVDPDDLAALVERADDDGYQLTVHAigDEAIEETLTRLEDTADPAGSRHRIEHAEL-ATDDQFERMAEAGIV 389
                                       578999999*********************8744444444444444444444445555443.444777999999999 PP

                                       EE..HHHHHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCC CS
                      Amidohydro_1 198 lt..pteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgll 272
                                        +  p+     ++ ++e g+ + +  +++ r+ ++++r+al++G+  ++g+D    +  l+ l ++ +a+      +
  gi|336253258|ref|YP_004596365.1| 390 ASmqPN----FHRWADEGGLYDQRLGEER-RKRTNRFRRALEAGAPLAFGSD----CMPLDPLLGVHHAV------N 451
                                       996666....7888999999987777775.677889****************....44455557788888......3 PP

                                       TTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT...CGGGTTTCTSEEEEEEEETTE CS
                      Amidohydro_1 273 yedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldi...laafvglkkdgnvkkvivkGk 342
                                       +  e + ls+ ealr++T ++A a   +d++G++evGk+ADlvv++  +      + ++     v++++v+G+
  gi|336253258|ref|YP_004596365.1| 452 APTEPQRLSVTEALRAYTSGAAYAGFDEDRLGTLEVGKRADLVVLEESPwerADRIDEI----DVAMTVVDGE 520
                                       3334555************9998877789****************66443333333333....3566666665 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.2   0.00019       1.1      37     101 ..     155     226 ..     123     261 .. 0.77
   2 ?    2.8   0.4     0.027   1.6e+02      57     101 ..     300     344 ..     254     361 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00019
                            DinB_2  37 aHlgnveelllerlr.geeaprpgldpltp......psaaealaylaevrarllallealtdadldrpltap 101
                                        H+++ +  +lerl  + ++ + ++++++p       +a+ ++++  + r++++++lea+t+ + +  +t  
  gi|336253258|ref|YP_004596365.1| 155 LHTVSLNSAALERLAdDLPESDLHYEDGEPtgvaveDAAEAVRREVTADREAMREVLEAATERAVELGVTGV 226
                                       699999999**99995445557888888887777755888999******************98888777765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.027
                            DinB_2  57 rpgldpltppsaaealaylaevrarllallealtdadldrpltap 101
                                       +p  d + +++ ++a+ ++    + l al+e+++d+ ++ +++a 
  gi|336253258|ref|YP_004596365.1| 300 EPYADAADDGEDEDARGQWVVDPDDLAALVERADDDGYQLTVHAI 344
                                       23444445589999**********************9**999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3526.45
//
Query:       gi|336253259|ref|YP_004596366.1|  [L=219]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-19   68.6   0.5    1.5e-18   66.3   0.1    2.0  2  HTH_10         HTH DNA binding domain
    4.2e-11   43.0   1.0    6.2e-11   42.4   1.0    1.3  1  BAT            GAF and HTH_10 associated domain
    2.5e-06   27.3   0.2    1.1e-05   25.2   0.2    2.1  1  MarR_2         MarR family
    2.1e-05   23.9   0.1      6e-05   22.5   0.0    1.8  2  Sigma70_r4     Sigma-70, region 4
    9.1e-05   21.9   0.0    0.00017   21.1   0.0    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
    0.00095   18.8   0.2     0.0019   17.8   0.2    1.5  1  Sigma70_r4_2   Sigma-70, region 4
      0.001   18.9   0.9     0.0027   17.5   0.9    1.7  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
       0.03   14.4   0.0       0.06   13.5   0.0    1.5  1  HTH_AraC       Bacterial regulatory helix-turn-helix proteins


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 ?    0.1   0.0      0.31     7e+02       1      16 [.      87     102 ..      87     103 .. 0.93
   2 !   66.3   0.1   6.8e-22   1.5e-18       1      52 [.     162     213 ..     162     214 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.31
                            HTH_10   1 LTdkqlevlklAyemG 16 
                                       LT +++ vl  A e+G
  gi|336253259|ref|YP_004596366.1|  87 LTSAERLVLPRAAELG 102
                                       89********999998 PP

  == domain 2  score: 66.3 bits;  conditional E-value: 6.8e-22
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT  q+e+l++Ay++GYF++PR++++++LA++lGIs s++s +Lr+a++ l+
  gi|336253259|ref|YP_004596366.1| 162 LTAVQRETLAAAYDAGYFNEPRDASVADLADRLGISSSAASSRLRRAMRALV 213
                                       8***********************************************9886 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   1.0   2.8e-14   6.2e-11       7     136 ..       9     139 ..       4     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 2.8e-14
                               BAT   7 eleirdeddvlv.alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtllel 82 
                                       el++  +++vl+ ++ a  +   ele  +  + ge+ +ff+v g+d  ++  a +d ++v++ +++ +++d  ++++
  gi|336253259|ref|YP_004596366.1|   9 ELTLAHPELVLApTIEAVPEVSAELEYQTIAGPGEYYLFFEVYGGDFGRFDRAIADDPTVSEPSIIIDGGDFRVYRM 85 
                                       4555555666666777888888888877778899*************************************999999 PP

                               BAT  83 tvs.gpslas.tlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdv 136
                                       +++  + l+  + ae G +v +ae  +g++  ++evP+  d+R++ e ++++   v
  gi|336253259|ref|YP_004596366.1|  86 RLTsAERLVLpRAAELGMRVLRAESAPGGWAATLEVPDLDDLRAFREHCRDKD--V 139
                                       96623344445**************************************9975..3 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.2   4.8e-09   1.1e-05       2      47 ..     161     210 ..     160     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4.8e-09
                                       T--HHHHHHHHHHHCTTTS.....EEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2   2 gltpaqarvLaaLgrrpgr.....dltvgelarrlglsksavsrilkrLva 47 
                                       glt  q+  Laa ++++ +     d +v++la+rlg+s sa+s +l+r+ +
  gi|336253259|ref|YP_004596366.1| 161 GLTAVQRETLAAAYDAG-YfneprDASVADLADRLGISSSAASSRLRRAMR 210
                                       77777777777777775.55666699**********************876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         3   6.8e+03       4      13 ..      86      95 ..      86      96 .. 0.84
   2 !   22.5   0.0   2.7e-08     6e-05       5      48 ..     162     212 ..     161     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3
                                      HS-HHHHHHH CS
                        Sigma70_r4  4 sLpererevl 13
                                      +L+  er vl
  gi|336253259|ref|YP_004596366.1| 86 RLTSAERLVL 95
                                      5899999997 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.7e-08
                                       S-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   5 Lpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       L++ +re l   +        ++ + +++++rlgiS ++++++++rA+r L
  gi|336253259|ref|YP_004596366.1| 162 LTAVQRETLAAAYdagyfnePRDASVADLADRLGISSSAASSRLRRAMRAL 212
                                       667778888888888877777899*************************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 !   21.1   0.0   7.4e-08   0.00017      16      42 ..     182     209 ..     179     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.4e-08
                            HTH_24  16 pr.isqreLAerlglSpstvnrrlkrLe 42 
                                       pr  s ++LA+rlg+S+s+ + rl+r +
  gi|336253259|ref|YP_004596366.1| 182 PRdASVADLADRLGISSSAASSRLRRAM 209
                                       66689********************976 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 !   17.8   0.2   8.7e-07    0.0019      28      54 .]     186     212 ..     184     212 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.7e-07
                                       -HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsRArkkL 54 
                                       s ++ A +lgis+++  srl+RA+++L
  gi|336253259|ref|YP_004596366.1| 186 SVADLADRLGISSSAASSRLRRAMRAL 212
                                       889*********************987 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 !   17.5   0.9   1.2e-06    0.0027      18      40 ..     185     207 ..     183     209 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.2e-06
                     HTH_AsnC-type  18 isyaeLAervGlSestvlrRvrr 40 
                                       +s+a+LA+r+G+S s++  R+rr
  gi|336253259|ref|YP_004596366.1| 185 ASVADLADRLGISSSAASSRLRR 207
                                       89********************9 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 ?   13.5   0.0   2.7e-05      0.06       7      33 ..     183     209 ..     180     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                                       CT--HHHHHHHTTSSHHHHHHHHHHHS CS
                          HTH_AraC   7 tnltiediAdelgfSrsyFsrlFkket 33 
                                       ++ +++d+Ad lg+S+s  s ++++++
  gi|336253259|ref|YP_004596366.1| 183 RDASVADLADRLGISSSAASSRLRRAM 209
                                       5679*******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1669.92
//
Query:       gi|336253260|ref|YP_004596367.1|  [L=132]
Description: hypothetical protein Halxa_1860 [Halopiger xanaduensis SH-6]
Scores for complete 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-13   50.5   4.6    3.3e-13   49.7   4.6    1.4  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   4.6   1.8e-17   3.3e-13       3      75 .]      24      94 ..      22      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.8e-17
                            HalOD1  3 espstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75
                                      ++++ a+v+ava+v++++p  ++pL ++ D dAL+aL+a+  ++++ + +  +  +eg +V+V sdg+i V++
  gi|336253260|ref|YP_004596367.1| 24 DQLVDAIVTAVATVADREPASIPPLAETTDIDALEALIAH--ARTTGSAIDTTAVVEGLDVRVVSDGRILVYD 94
                                      78999***********************************..6677788899999****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 996.44
//
Query:       gi|336253261|ref|YP_004596368.1|  [L=155]
Description: hypothetical protein Halxa_1861 [Halopiger xanaduensis SH-6]
Scores for complete 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  121.8   0.5    2.3e-35  121.5   0.5    1.1  1  DUF2267   Uncharacterized conserved protein (DUF2267)


Domain annotation for each model (and alignments):
>> DUF2267  Uncharacterized conserved protein (DUF2267)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.5   0.5   1.3e-39   2.3e-35       1     122 []       7     139 ..       7     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 1.3e-39
                                       HHHHHHHHHHHHT---HHHHHHHHHHHHHHHHTTS-HHHHHHHHTTS-HHHHHHHHTT--TTS-----SHHHHHHHH CS
                           DUF2267   1 ydefleevqerlgledreeAeratravLrtLrdrlteeeaadlaaqLPeelrgllrdgwppvepgkrfdreeflerv 77 
                                       y +f++evq+r++ + ++eA r+travL+tL++r++e++a+d+a+ LP+e++++l +++    +g++fd +ef++rv
  gi|336253261|ref|YP_004596368.1|   7 YTDFVGEVQHRIEAGRQAEAVRTTRAVLETLGERVEEGAATDVASPLPMEIDRYLLAAD----HGQQFDFDEFVTRV 79 
                                       679*******************************************************9....999*********** PP

                                       HHTS....................EHHHHHHHHHHHHHHHS-HHHHHHHHHTS-HHHHTT CS
                           DUF2267  78 aeelg...............vdpedaeqaaraVfaalkealsegeiedvaaqLPkdlrel 122
                                       +e+l+               +d++da+ +a+aV+a+l+e++++gei +++aqLP+++ el
  gi|336253261|ref|YP_004596368.1|  80 RERLNyedldletgygrpsgIDESDAVFRAKAVVALLAERVPGGEIGNIEAQLPDEYGEL 139
                                       *****99999999999999999999*******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1204.80
//
Query:       gi|336253262|ref|YP_004596369.1|  [L=176]
Description: hypothetical protein Halxa_1862 [Halopiger xanaduensis SH-6]
Scores for 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-06   27.5   0.0      4e-06   27.2   0.0    1.1  1  LTD         Lamin Tail Domain
  ------ inclusion threshold ------
       0.15   12.0   0.6       0.15   12.0   0.6    2.4  3  TAT_signal  TAT (twin-arginine translocation) pathway signal 


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 !   27.2   0.0   4.5e-10     4e-06       7     110 ..      36     152 ..      30     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.5e-10
                               LTD   7 dvvIsevmedgagnnan....efvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsgtt.... 74 
                                       ++ I  v+++  +++ +     +v l+N  +++ + sg+ +e+ +++ y++++   tl+ag+++ v++ +g +    
  gi|336253262|ref|YP_004596369.1|  36 SLRIVGVYAAD-ADR-DfidgPYVALENGADEPRNVSGYVVEHPADRrYRITDL--TLEAGAQLAVVHENGDDstll 108
                                       56677777655.333.247889***********************99****999..5******99999988888899 PP

                               LTD  75 ..........sasngskasssavwnnggdavaLydasgevvdsvgy 110
                                                 +a+n+  a s+ +  +++ +v+ +d++g vv++  y
  gi|336253262|ref|YP_004596369.1| 109 ssppvylrytGADND--AGSAESGLETNGTVRVRDPAGAVVAEARY 152
                                       888888775422222..22333333367799*********999877 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   1.6e-05      0.15       2      25 ..       1      22 [.       1      23 [. 0.78
   2 ?   -4.1   1.1       1.9   1.7e+04      11      14 ..     144     147 ..     143     148 .. 0.32
   3 ?   -3.4   1.7       1.2   1.1e+04      10      17 ..     159     166 ..     159     167 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      ++RR +L   A +  Aa+lggc+a
  gi|336253262|ref|YP_004596369.1|  1 MNRRELLA--ASVVTAAGLGGCLA 22
                                      89******..66666788888876 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 1.9
                        TAT_signal  11 sAAa 14 
                                       +A++
  gi|336253262|ref|YP_004596369.1| 144 GAVV 147
                                       3333 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.2
                        TAT_signal  10 gsAAaaAA 17 
                                       g+ ++ AA
  gi|336253262|ref|YP_004596369.1| 159 GGTVTSAA 166
                                       55666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1415.27
//
Query:       gi|336253263|ref|YP_004596370.1|  [L=356]
Description: glucose-fructose oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-24   87.6   0.0    1.6e-24   87.0   0.0    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    6.7e-08   32.5   0.0    1.9e-07   31.1   0.0    1.7  2  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 


Domain annotation for each model (and alignments):
>> 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 !   87.0   0.0   1.8e-28   1.6e-24       2     120 .]      25     146 ..      24     146 .. 0.94

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 1.8e-28
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE...EESSHHHHHTCTTESEEEE-S-GGGH CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve...aysdleelladpeidavivatpngth 75 
                                       r a++G+G ++++ + p  ++ r  e +al+  ++ ra+++a +f+ve    y+ +++    +  dav+vatpn+th
  gi|336253263|ref|YP_004596370.1|  25 RLAVVGIGGFARNRALPGIAAGRYCETTALVTGSPDRARTIAGEFDVEhviGYDAFRAGNHAETYDAVYVATPNSTH 101
                                       89*******************9999***********************7777777777777779************* PP

                                       HHHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  76 eelakaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                        e+a+aa+e+gkhvl+EKPl ttv+ a+e+v+++  +g++++ +y
  gi|336253263|ref|YP_004596370.1| 102 GEYAIAAAEHGKHVLCEKPLETTVDRAEEIVDACSDNGVTLMTAY 146
                                       ***************************************998765 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.55   4.9e+03      67     101 ..      76     109 ..      60     113 .. 0.56
   2 !   31.1   0.0   2.1e-11   1.9e-07       1     105 [.     158     259 ..     158     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.55
                                       EEE.SEEESCTCCSCSEEEEEEEEEEETTEEEEEE CS
                    GFO_IDH_MocA_C  67 algrmrqnaeaaededaavmsvlnlekgsgevitl 101
                                        +++   ++++ae +da+  + +n+ +g+++++ +
  gi|336253263|ref|YP_004596370.1|  76 GYDA-FRAGNHAETYDAVYVATPNSTHGEYAIAAA 109
                                       4433.556666777776666666666666666555 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 2.1e-11
                                       HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSH.HCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESC CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrk.kksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnae 76 
                                       +e +++g++Gevv+v++ +         +  w+ ++   +gG+l+dlg++ ++ +++ +  +p+ v+a++r  +n++
  gi|336253263|ref|YP_004596370.1| 158 REFVRDGVIGEVVQVHGGFAHPLLDHAGPDTWRLDPdLAGGGALVDLGVYPLNTTRYVLDCDPTAVYATTR--SNGG 232
                                       68899***********9776655555555556666678*******************************95..5555 PP

                                       TCCSCSEEEEEEEEEEETTEEEEEEEECC CS
                    GFO_IDH_MocA_C  77 aaededaavmsvlnlekgsgevitlesgv 105
                                         +d d  v    +le+ +g+++++++++
  gi|336253263|ref|YP_004596370.1| 233 PFADVDEHV--AFQLEFPTGATASCTASF 259
                                       555555554..388888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2700.62
//
Query:       gi|336253264|ref|YP_004596371.1|  [L=377]
Description: Quinolinate synthase A [Halopiger xanaduensis SH-6]
Scores for 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-104  348.5   0.1   3.3e-104  348.3   0.1    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 !  348.3   0.1  1.8e-108  3.3e-104       2     299 .]      39     376 ..      38     376 .. 0.95

  Alignments for each domain:
  == domain 1  score: 348.3 bits;  conditional E-value: 1.8e-108
                                       HHHHHHHH..HTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHS.TTSEEE-SST CS
                              NadA   2 eikelkke..knavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLs.pekkvllpdl 75 
                                       +i+++ +e  +++vil+HnYq++ei+e+adfvGDS++L+++aae++ae+++f GV+FMae+a+i++ ++++v+lp++
  gi|336253264|ref|YP_004596371.1|  39 RIEAALEElgDDVVILGHNYQRREIVEHADFVGDSYQLSKEAAEADAEYVIFGGVTFMAESADIITdDDQTVILPSM 115
                                       78888888899*******************************************************99********* PP

                                       T---HHHCT--HHHHHHHHHH....STTS-E..EEESSS-HHHHTT-....SEEE-TTTHHHHH.HHSS.-SEEEEE CS
                              NadA  76 eagCsladmitaeeveelkee....lpdaav..vtYvNssaevKals....divcTSsnavkvv.ealk.ekkilfl 140
                                       ea+C++a m++a +v+++++e     pda +  +tY+Ns a++Ka++    ++vcTSsna+k +  a++ ++k+lfl
  gi|336253264|ref|YP_004596371.1| 116 EASCPMAGMAEALQVDSAWAEitaaAPDADIvpITYMNSYADLKAFCasqgGLVCTSSNAHKAFeYAFDkGDKVLFL 192
                                       *********************9999777766347******************************667755******* PP

                                       S-HHHHHHHHHHH.......................SEEEEESSSS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS- CS
                              NadA 141 PDqnLgryvakklg......................ekkiilwkgaCsvHeefkaeeveelkeehpdakvlvHPEck 195
                                       PD++Lg+++a++l+                      e++iilw+g+C+vHe+f+++++e+++e+hp+a+v+vHPEc+
  gi|336253264|ref|YP_004596371.1| 193 PDKHLGENTAHRLDmeseiaewdpwdpegkdaaevaERDIILWDGYCQVHERFREDHIEQIREDHPEANVVVHPECR 269
                                       ************************************899************************************** PP

                                       HHHHHCSSEE--HHHHCCCCGT.TSSSCEEEES-THHHHHHHHH-TTSEEE.....ECSSSSSTTGGG--HHHHHHH CS
                              NadA 196 eevveaadvvgSTsqiikavke.seakefiigTelglverlkkeapekefialsaeaaeeavCetMkkitlekllea 271
                                       +evveaadvvgSTs+i+++v++ +++++++igTe++l+++l++ +pe e++ l+ e    + C+ M++i+++ l+++
  gi|336253264|ref|YP_004596371.1| 270 REVVEAADVVGSTSTICETVANaDPGETWAIGTEIHLTNHLQRWHPEVEVLPLCGE--ACMDCNAMRQIDPNYLTWV 344
                                       ********************9989***************************99754..2456*************** PP

                                       HHHT-S....B.----HHHHHHHHHHHHHHHH CS
                              NadA 272 Leelee...ee.ikvdeevaekAkkalermle 299
                                       Leel e   ++ i+v +e +e A++al+rmle
  gi|336253264|ref|YP_004596371.1| 345 LEELVEgreRNvIEVAPEEKELAEVALDRMLE 376
                                       ***988887446******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2941.84
//
Query:       gi|336253265|ref|YP_004596372.1|  [L=515]
Description: L-aspartate oxidase [Halopiger xanaduensis SH-6]
Scores for 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-74  250.7   3.4    3.3e-74  250.4   3.4    1.1  1  FAD_binding_2   FAD binding domain
    4.5e-12   45.8   1.6    4.7e-06   26.0   1.0    3.0  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.5e-09   37.4   0.2    7.7e-07   28.5   0.3    2.2  2  GIDA            Glucose inhibited division protein A
    1.4e-08   34.5   6.2    8.8e-08   31.9   2.5    2.4  2  FAD_oxidored    FAD dependent oxidoreductase
    1.9e-08   34.3   4.4    9.5e-08   32.0   0.8    2.6  3  DAO             FAD dependent oxidoreductase
    5.7e-05   23.3   0.4    0.00018   21.7   0.4    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00015   21.7   0.0    0.00044   20.3   0.0    1.7  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    0.00026   19.8   0.2      0.017   13.8   0.6    2.1  2  HI0933_like     HI0933-like protein
    0.00065   19.1   0.2     0.0011   18.3   0.2    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0014   17.9   0.1     0.0027   17.0   0.1    1.4  1  FAD_binding_3   FAD binding domain
  ------ inclusion threshold ------
      0.013   16.0   0.0      0.036   14.6   0.0    1.7  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.045   13.0   0.1      0.094   12.0   0.1    1.4  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.085   11.9   0.7       0.15   11.1   0.7    1.4  1  Lycopene_cycl   Lycopene cyclase protein
       0.15   12.5   0.1       0.32   11.5   0.1    1.5  1  NAD_binding_7   Putative NAD(P)-binding
       0.17   11.5   0.0       0.35   10.5   0.0    1.6  1  ApbA            Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.4   3.4   2.8e-77   3.3e-74       1     417 []      14     380 ..      14     380 .. 0.93

  Alignments for each domain:
  == domain 1  score: 250.4 bits;  conditional E-value: 2.8e-77
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS.GGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT- CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg.atawsqGgidavlspeqkkagikdspelhrtdtlkaldel 76 
                                       Dv+V+GsG+AG+aAAl+aa++G++v++v+k+++    +t w+qGgi   +         +d pe+  +d ++a+d+ 
  gi|336253265|ref|YP_004596372.1|  14 DVLVVGSGIAGCAAALAAAREGADVLLVTKAERPDDaSTDWAQGGISTTR---------GD-PESLKEDIIAASDGT 80 
                                       9*****************************99876669************.........68.*************** PP

                                       S-HHHHHHHHHTHHHHHHHHHHT..T----B...CCTS..SB-EEE-TT-SSTEEEE-.STT-......HHHHHHHH CS
                     FAD_binding_2  77 adqplveafveaapeavdeLeel..gvpfsr...tedg..pvdvrelGglsatartlhdaadarretlvtghallar 146
                                       ad+++v+++ve+a +av+       g+ f++   ++dg  ++d ++  ++s++ r+lh + +       tg ++l +
  gi|336253265|ref|YP_004596372.1|  81 ADPEAVDVLVENADDAVEDVLIDtlGIEFDEagrSDDGdaAFDYAREAAHSEE-RILH-VDAS------TGSHILRP 149
                                       *****************98655448999999665444489*************.****.6665......******** PP

                                       HHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSG CS
                     FAD_binding_2 147 lvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettna 222
                                       +++++++++ ++++  t+a+eLi+++grv+G+v    e+++ + i a a++latgG+g+           +  +tn+
  gi|336253265|ref|YP_004596372.1| 150 FLHYVDDRErIEVRQDTAALELITHEGRVHGIVSD--EEPEGHPIYAGATILATGGIGA----------LYGRSTNP 214
                                       ********************************999..99999****************9..........******** PP

                                       TT-S-HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH......GGGS-HH CS
                     FAD_binding_2 223 pavtGdglalalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm......nelasrd 293
                                         +tGdg+a+a+ aga+++d  +e vqfhPt+    +d    L++ealrgeG++l++ + +rFm      +elasrd
  gi|336253265|ref|YP_004596372.1| 215 DDATGDGIAMAALAGADVAD--LEYVQFHPTAYA--GDDPF-LLSEALRGEGAVLRNGEDERFMpdyhpdAELASRD 286
                                       ********************..************..44444.678******************************** PP

                                       HHHHHHH.HHHHTTTSCCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEE CS
                     FAD_binding_2 294 vvsrailekeiaeggseanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqh 370
                                       vv+ra+  +e++ +g+   v+ld+s       +e+++++  +++++  +        + d+ ip       v p  h
  gi|336253265|ref|YP_004596372.1| 287 VVARAVA-TEREATGE---VVLDVSP----LEFETDFPDLAQKCRE-RG-------LEGDE-IP-------VAPCEH 339
                                       *******.77777776...8999988....679******9999988.55.......66777.8*.......****** PP

                                       EES-EEEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHHH CS
                     FAD_binding_2 371 ytmgGvetdengrvldadgqpipGLYAaGevaaggvhganrlgGnsl 417
                                       +++gG+ +d++gr+       ++ LYA+Ge+a +gvhganrl+++sl
  gi|336253265|ref|YP_004596372.1| 340 FCCGGIDVDDRGRT------SLDQLYAVGECARSGVHGANRLASTSL 380
                                       **************......*************************98 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 !   26.0   1.0     4e-09   4.7e-06       2     108 ..      14     202 ..      13     231 .. 0.62
   2 !   16.4   0.0   3.3e-06     0.004     256     279 ..     343     368 ..     332     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 4e-09
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE.......TTHCHHHCSHHHHCHHHHHHHHHHHHH.............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve.......legtclnggcllskallgvaedaeias.............. 57 
                                       dv+v+G+G+AG+aaal +a+ ga+v+lv        + + +  gg++ +    ++ ++  ia+              
  gi|336253265|ref|YP_004596372.1|  14 DVLVVGSGIAGCAAALAAAREGADVLLVTkaerpddASTDWAQGGISTTRGDPESLKEDIIAAsdgtadpeavdvlv 90 
                                       89**************************5444443333333333333333333333332222255555555566666 PP

                                       .................................................................HHHHCHHHHCCC CS
                                       .................................................................xxxxxxxxxxxx RF
                       Pyr_redox_2  58 .................................................................evvkklnqgiel 69 
                                                                                                        +     ++ ie+
  gi|336253265|ref|YP_004596372.1|  91 enaddavedvlidtlgiefdeagrsddgdaafdyareaahseerilhvdastgshilrpflhyvdD-----RERIEV 162
                                       666666666666666666666666666666666666666666666666666666666666543321.....234566 PP

                                       CHCCTCEEEEESCEEEEETEEEC.TCEEEEEESEEEE--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  70 llgeevvkidpgkkkvklekkke.gdeekiaydklvlAtG 108
                                       + ++ ++++++ +++v+   ++e  +++ i +++ +lAtG
  gi|336253265|ref|YP_004596372.1| 163 RQDTAALELITHEGRVHGIVSDEePEGHPIYAGATILATG 202
                                       6665566666666666554333335666666666666666 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.3e-06
                                       TEEE--TTSBESSTTEEE-GGGC..T CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..x RF
                       Pyr_redox_2 256 ggivvdeflrtnvpgiyaiGDva..g 279
                                       ggi vd+++rt+ +++ya+G +a  g
  gi|336253265|ref|YP_004596372.1| 343 GGIDVDDRGRTSLDQLYAVGECArsG 368
                                       99*********************541 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.3   6.4e-10   7.7e-07       1      30 [.      14      43 ..      14      54 .. 0.92
   2 !    6.7   0.0    0.0028       3.4     103     150 ..     152     203 ..     142     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 6.4e-10
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLith 30
                                      dv V+G G AGc+AAlaaar Ga+vlL+t+
  gi|336253265|ref|YP_004596372.1| 14 DVLVVGSGIAGCAAALAAAREGADVLLVTK 43
                                      79**************************75 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0028
                                       HHHHTSTTEEEEES-EE.EEEECTTEEEEEEETT...S-EEEECEEEE--TT CS
                              GIDA 103 eklenepnleiieeeve.eliveekkvkgvvted...getikakavviatGt 150
                                       +++++ + +e+++++++ eli++e++v+g+v ++   g+ i a a+++atG 
  gi|336253265|ref|YP_004596372.1| 152 HYVDDRERIEVRQDTAAlELITHEGRVHGIVSDEepeGHPIYAGATILATGG 203
                                       6889999*****99865389999******998752226789999*******7 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   2.5   7.4e-11   8.8e-08       1      31 [.      14      44 ..      14      51 .. 0.95
   2 ?    3.8   0.1     0.025        30      82     144 ..     133     202 ..      88     297 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 7.4e-11
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      Dv+VvG+g+aG+aAA+aAar+Ga vlLv + 
  gi|336253265|ref|YP_004596372.1| 14 DVLVVGSGIAGCAAALAAAREGADVLLVTKA 44
                                      9***************************875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.025
                      FAD_oxidored  82 n...tfepevakavleeml....aeagvtvllntrlvevekegkriesvtveske.grktirAkvfiDATg 144
                                       +   +++ ++   +l  +l    ++++++v  +t + e ++ ++r+++++   +e +++ i A  +i ATg
  gi|336253265|ref|YP_004596372.1| 133 ErilHVDASTGSHILRPFLhyvdDRERIEVRQDTAALELITHEGRVHGIVSD-EEpEGHPIYAGATILATG 202
                                       13557888999999999998888778**********999998889****995.565899999999999986 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.8   7.9e-11   9.5e-08       1      52 [.      14      67 ..      14     146 .. 0.77
   2 ?    2.9   0.1     0.054        65     161     203 ..     160     204 ..     150     297 .. 0.74
   3 ?   -3.3   0.0       4.4   5.3e+03      78     111 ..     336     369 ..     307     401 .. 0.64

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 7.9e-11
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHH CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylp 52
                                      dv+++G+Gi+G+++A+++ar+g  V+l+ k++++  +++  ++g ++    +++
  gi|336253265|ref|YP_004596372.1| 14 DVLVVGSGIAGCAAALAAAREGadVLLVTKAERPDDASTDWAQGGISTTRGDPE 67
                                      8********************9*************9999999999998665444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.054
                                       -EEEESECEEEEEEEETCEEEEE.EECT.EEEEEEEEEEE--GGG CS
                               DAO 161 veilegtevtgleeedgkvwgve.rttp.gendaadavVnaaGaw 203
                                       +e+++ t + +l  ++g+v+g+  +++p g+   a a ++a+G  
  gi|336253265|ref|YP_004596372.1| 160 IEVRQDTAALELITHEGRVHGIVsDEEPeGHPIYAGATILATGGI 204
                                       68999999999888899*****98777767654457799999953 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.4
                                       TTSEEEEEEEEEESSHHHHHHHHHHHHHH..HHTTT CS
                               DAO  78 didyrrtGllslaadeeelealdkllall..leagl 111
                                       ++++  +G + +   ++ +  ld+l+a +  ++ g+
  gi|336253265|ref|YP_004596372.1| 336 PCEHFCCGGIDVD--DRGRTSLDQLYAVGecARSGV 369
                                       4778888888884..335777777777655533444 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 !   21.7   0.4   1.5e-07   0.00018       1      31 [.      17      47 ..      17      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.5e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31
                                      +vG+G++G++aA ++a++g+dvll+ k++r+
  gi|336253265|ref|YP_004596372.1| 17 VVGSGIAGCAAALAAAREGADVLLVTKAERP 47
                                      8***********************9988875 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.6e-07   0.00044       3      85 ..     427     502 ..     426     512 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.6e-07
                                       HHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-BT CS
                    Succ_DH_flav_C   3 eLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESrG 79 
                                       +L+++m+++ g +R+ +++++a + l++l+ +++    t +s        + +el+n   +A +ia++A +  ES G
  gi|336253265|ref|YP_004596372.1| 427 RLKQTMDEYLGLERDPDEIARASAVLRRLKGEVDAYIRTRTS-------RDLYELRNASVVALLIARAASENPESKG 496
                                       799*****************************9844333333.......47799*********************** PP

                                       TBEBTT CS
                    Succ_DH_flav_C  80 aHared 85 
                                       +H+  d
  gi|336253265|ref|YP_004596372.1| 497 CHYVVD 502
                                       **9877 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.6   1.5e-05     0.017       2      34 ..      14      46 ..      13      49 .. 0.93
   2 ?    3.5   0.0      0.02        24     105     191 ..     140     236 ..     126     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                      dv+v+G G AG  aA++aa++g++Vll+ ka++
  gi|336253265|ref|YP_004596372.1| 14 DVLVVGSGIAGCAAALAAAREGADVLLVTKAER 46
                                      89**************************99876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.02
                                       T.-CHHHHHHHHHHHHH.HT-EEE-S--EEEEECETTE.EEEEE....TTEEEEESEEEE----......SS-GGGT CS
                       HI0933_like 105 sdkaedivdallkelke.agvklrletevksvekeedgkfrvktk...seeeleadklvlAtGG......lSiPklG 171
                                       + + ++i++ +l+ +++ +++++r +t+  ++ ++e++++ +  +   +++ + a +++lAtGG       S     
  gi|336253265|ref|YP_004596372.1| 140 ASTGSHILRPFLHYVDDrERIEVRQDTAALELITHEGRVHGIVSDeepEGHPIYAGATILATGGigalygRSTNPDD 216
                                       4566788888888887636899***9999999999999888877434567789**********73222224666667 PP

                                       --SHHHHHHHHTT--EEEEE CS
                       HI0933_like 172 stgkgyklaeqfghtivplr 191
                                       +tg+g+ +a+ +g ++++l+
  gi|336253265|ref|YP_004596372.1| 217 ATGDGIAMAALAGADVADLE 236
                                       88888888888888877765 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 !   18.3   0.2   9.5e-07    0.0011      28      87 ..      12      71 ..       6     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.5e-07
                                      --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHH CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellae 87
                                       a vlv+G G+aG +A+ +a++ ga+V ++ + ++      ++ +  +++ + + e+l+e
  gi|336253265|ref|YP_004596372.1| 12 TADVLVVGSGIAGCAAALAAAREGADVLLVTKAERPDDASTDWAQGGISTTRGDPESLKE 71
                                      799************************988776666555555444446665555555555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.3e-06    0.0027       2      36 ..      13      47 ..      12      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.3e-06
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                      +dVl+VG+G aG  +al  ++ G +v+lv+k ++ 
  gi|336253265|ref|YP_004596372.1| 13 ADVLVVGSGIAGCAAALAAAREGADVLLVTKAERP 47
                                      69****************************98865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     3e-05     0.036       2      34 ..      15      47 ..      14      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkl 34
                                      v+vvG+G  g+ +A a+a+ g++V +v  ++++
  gi|336253265|ref|YP_004596372.1| 15 VLVVGSGIAGCAAALAAAREGADVLLVTKAERP 47
                                      89*************************999886 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   0.1   7.9e-05     0.094     161     205 ..       9      53 ..       2      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.9e-05
                       Pyr_redox_3 161 kyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesd 205
                                        y + +v+V+G +  ++ aAl  +r+ga+V +vt+ +  ++ ++d
  gi|336253265|ref|YP_004596372.1|   9 AYDTADVLVVGSGIAGCAAALAAAREGADVLLVTKAERPDDASTD 53 
                                       68899*****************************99876666555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7   0.00013      0.15       1      34 [.      14      45 ..      14      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasp 34
                                      Dv+v+G+G Ag++ A     a+ g  v+l+  ++
  gi|336253265|ref|YP_004596372.1| 14 DVLVVGSGIAGCAAALAA--AREGADVLLVTKAE 45
                                      9***********988777..99999999995554 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 ?   11.5   0.1   0.00027      0.32       7      55 ..      12      59 ..       9     102 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                     NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeel 55
                                      +  vlvvG G  +   +   +++ga+v +v+++ ++  +   ++a+  +
  gi|336253265|ref|YP_004596372.1| 12 TADVLVVGSGIAGCAAALAAAREGADVLLVTKA-ERPDDASTDWAQGGI 59
                                      578*****************************9.455556666766554 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00029      0.35       1      47 [.      15      65 ..      15     102 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00029
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH....HHHHHHHHCEEEEETT CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr....rlealkknGlrltseg 47
                                      ++++G+G  G+  a   a+ gadv l+++ +       ++ + G++ t+ +
  gi|336253265|ref|YP_004596372.1| 15 VLVVGSGIAGCAAALAAAREGADVLLVTKAErpddASTDWAQGGISTTRGD 65
                                      68*********************9999876520133444677777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 3654.53
//
Query:       gi|336253266|ref|YP_004596373.1|  [L=271]
Description: nicotinate-nucleotide pyrophosphorylase [Halopiger xanaduensis SH-6]
Scores for 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-56  188.3   2.1    1.1e-55  188.0   2.1    1.1  1  QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal
    3.3e-19   68.7   0.2    6.9e-19   67.7   0.2    1.6  1  QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal


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 !  188.0   2.1   1.2e-59   1.1e-55       1     168 [.     100     267 ..     100     268 .. 0.97

  Alignments for each domain:
  == domain 1  score: 188.0 bits;  conditional E-value: 1.2e-59
                                       HHHHHHHHHHHHHCT..SSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksa..kvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvre 75 
                                       iAt t+r+v++a+ +   vri++TRkttPglr lek+Av +GGgd+hrl+Ls mv++kdnh+a +g +++a+ +++e
  gi|336253266|ref|YP_004596373.1| 100 IATRTRRVVDEARVEsdDVRIAATRKTTPGLRGLEKRAVVAGGGDTHRLDLSHMVMVKDNHVAEMG-LEDAIAHFQE 175
                                       9*********9998878************************************************9.********** PP

                                       HHTTTSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEE CS
                         QRPTase_C  76 avdkevkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvi 152
                                        ++++ k+ veve+++++ +++ a+adi++LDn+++ e+++av+ l   +  vl e+SGg+tle+v++ya +gvdvi
  gi|336253266|ref|YP_004596373.1| 176 RTSFATKLDVEVETVADAPRAADAGADIVLLDNMTPAETREAVDALADYE-GVLAEASGGITLETVADYAATGVDVI 251
                                       ********************************************885555.5************************* PP

                                       EECHHCHTB----EEE CS
                         QRPTase_C 153 svgalthsvkalDisl 168
                                       s+g+lths+++lD+s 
  gi|336253266|ref|YP_004596373.1| 252 SMGSLTHSAPSLDLSF 267
                                       **************96 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 !   67.7   0.2   7.7e-23   6.9e-19       2      89 .]      16      98 ..      15      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 7.7e-23
                                      TT--HHHHHHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHH CS
                         QRPTase_N  2 grgDlttealipeekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERv 80
                                      g+ D+t+   +p+  + +++++ake+gv aGle+a+ vfe+l g+ v    +DG+++e+gd ll++eG ar++l++ERv
  gi|336253266|ref|YP_004596373.1| 16 GHHDVTN--EVPG--ETTGRLVAKESGVAAGLEAAASVFEYL-GVDVVDRLEDGTTLEEGDGLLQVEGAARDVLRGERV 89
                                      6677777..4444..45678**********************.************************************ PP

                                      HHHHHHHHH CS
                         QRPTase_N 81 aLnllqrlS 89
                                      a nl  ++S
  gi|336253266|ref|YP_004596373.1| 90 AVNLAGHAS 98
                                      *****9998 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:                      229  (0.0127726); 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 0.21s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2002.99
//
Query:       gi|336253267|ref|YP_004596374.1|  [L=221]
Description: RNA 2'-phosphotransferase [Halopiger xanaduensis SH-6]
Scores for 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  107.4   0.0      1e-30  107.1   0.0    1.0  1  PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family


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 !  107.1   0.0   5.7e-35     1e-30       2     175 ..      37     203 ..      36     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 5.7e-35
                         PTS_2-RNA   2 revqlskaLsyiLRhgaekegLkiredGyvkvedlLelpklkslkvtleeikevVesndKqRFelvel.....eell 73 
                                       r+ +lsk +s  LRh ++++g+ ++e G+++ edl++  + k   ++++++ ev+++++K RFe         e+  
  gi|336253267|ref|YP_004596374.1|  37 RRHRLSKFMSGALRHFPSDAGIDLDERGWAAYEDLVAAVERKYDWADERHVAEVIATDPKGRFER--TsgndgERNR 111
                                       6789*********************************6666665599*****************4..245676449* PP

                         PTS_2-RNA  74 iranqghsikkvesselllepiesaeelpevvvHgTylkawesilasggLkrmsrnhihlatglpgekevisgmrks 150
                                       +ra  ghs+   ++    lep   a+++p+ ++HgT+ +++e i+ ++gLk+msr+++hl+++   e++  +g r+ 
  gi|336253267|ref|YP_004596374.1| 112 VRAAYGHSV---DV---DLEPT--AAPVPDELYHGTAPENLEPIR-EEGLKPMSRQQVHLSESR--EAARQVGQRHA 177
                                       ********5...22...38994..56789****************.99**************85..567899****7 PP

                         PTS_2-RNA 151 ae.vliyidvekaladgikfyvseng 175
                                       a+ v++++d++++ladg ++ +  ++
  gi|336253267|ref|YP_004596374.1| 178 ADpVVLVVDAAAMLADGHRITKRGEE 203
                                       655**************998776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1651.87
//
Query:       gi|336253268|ref|YP_004596375.1|  [L=222]
Description: TrkA-N domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   95.4   2.5    4.9e-27   94.5   2.5    1.4  1  TrkA_N           TrkA-N domain
    2.9e-13   49.5   0.2    2.8e-12   46.3   0.0    2.3  2  TrkA_C           TrkA-C domain
    8.1e-07   29.5   0.2    1.6e-06   28.6   0.2    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    1.5e-06   28.5   0.4    2.5e-06   27.8   0.4    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    3.6e-06   27.3   2.1    2.5e-05   24.6   0.3    2.4  2  NAD_binding_7    Putative NAD(P)-binding
    3.5e-05   23.8   1.4    0.00017   21.5   1.6    2.0  2  NAD_binding_10   NAD(P)H-binding
    7.7e-05   22.7   0.2    0.00012   22.0   0.2    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00015   21.1   1.2    0.00024   20.5   1.2    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    0.00031   20.4   0.5    0.00069   19.2   0.5    1.5  1  NmrA             NmrA-like family
     0.0029   17.7   0.2     0.0043   17.1   0.2    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0036   16.8   0.2     0.0057   16.2   0.2    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0089   16.5   0.1      0.019   15.5   0.1    1.6  1  XdhC_C           XdhC Rossmann domain
  ------ inclusion threshold ------
       0.01   16.0   0.1      0.023   14.8   0.0    1.7  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.024   15.5   1.6      0.045   14.6   1.6    1.6  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
       0.04   13.4   0.5       0.15   11.5   0.5    1.9  1  adh_short        short chain dehydrogenase
      0.041   13.5   0.0      0.067   12.8   0.0    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.065   13.6   0.4       0.13   12.6   0.2    1.6  2  Peripla_BP_3     Periplasmic binding protein-like domain
       0.08   12.9   0.0       0.12   12.3   0.0    1.3  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge


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 !   94.5   2.5     5e-30   4.9e-27       1     115 [.       3     117 ..       3     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 5e-30
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddean 76 
                                       i+iiG+G +G++l++   ++g+dvvvi++deer++e+++e  + v+++dat+  +L++a+i++adavi +t+ d++n
  gi|336253268|ref|YP_004596375.1|   3 IVIIGAGSIGSNLIDLAVDDGNDVVVIESDEERANEVSAEYdCLVLNADATNHGTLQDAEIDRADAVISTTDVDAVN 79 
                                       89*****************7669***************999999********************************* PP

                                       HHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEE CS
                            TrkA_N  77 ilavllakelnpkkkiiaraqdpehaellkklgadvvis 115
                                       i+++lla+e ++ ++ ++ ++dp++  +++k+g++ + +
  gi|336253268|ref|YP_004596375.1|  80 IMVMLLAQE-HDVPNLVSVVHDPDNLPVFEKIGVTLIEN 117
                                       *******97.7779********************98765 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.48   4.8e+02       4      30 ..       4      29 ..       1      43 [. 0.67
   2 !   46.3   0.0   2.8e-15   2.8e-12       1      68 [.     147     217 ..     147     219 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.48
                                      EEEE--GGGTTSBHHHHTHHHH.S-EEE CS
                            TrkA_C  4 vtvpagsplvGktlkelnlrar.gvlvv 30
                                      v ++ags  +G  l +l + +  +v v+
  gi|336253268|ref|YP_004596375.1|  4 VIIGAGS--IGSNLIDLAVDDGnDVVVI 29
                                      5566666..7888888888886666554 PP

  == domain 2  score: 46.3 bits;  conditional E-value: 2.8e-15
                                       CEEEEEE--GGGTTSBHHHHT....HHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkeln....lrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                       lve+tv++++p+ G+ l+ ++    l++ g+lvva+ R+ge+  p g t++++GD+++v++++++l+++ + 
  gi|336253268|ref|YP_004596375.1| 147 LVELTVTEDAPMNGQVLSTAQekgrLPE-GCLVVALERDGEVQAPKGGTTIRAGDTVTVFTDDATLSDAVAA 217
                                       69*****************888888888.************************************9997665 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 !   28.6   0.2   1.6e-09   1.6e-06       2      58 ..       3      57 ..       2     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.6e-09
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.......-EEECECHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.......vkvtavdneea 58
                                      i iiGaG++g+ l+  ++  g   +++vv+ ++++e+a+e  +e+        +     +n  +
  gi|336253268|ref|YP_004596375.1|  3 IVIIGAGSIGSNLIDLAVDDG---NDVVVI-ESDEERANEVSAEYDclvlnadA-----TNHGT 57
                                      88*******************...****99.**************977644331.....22222 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 !   27.8   0.4   2.5e-09   2.5e-06       1      94 [.       3      91 ..       3     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.5e-09
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S.S CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls.p 78
                                      ++iiGaGs+G+ +++l ++ ++    ++v++ ++e+++++    ++ ++     da n+  + +a +  +d+v++ + +
  gi|336253268|ref|YP_004596375.1|  3 IVIIGAGSIGSNLIDLAVDDGND---VVVIESDEERANEVS---AEYDCLVLNADATNHGTLQDAEIDRADAVISTTdV 75
                                      89******************985...**********99888...67999***********955555********98634 PP

                                      GGGHHHHHHHHHHHT- CS
                   Sacchrp_dh_NADP 79 pissldvlkaCietgv 94
                                      +  +  v+ ++ e+ v
  gi|336253268|ref|YP_004596375.1| 76 DAVNIMVMLLAQEHDV 91
                                      5567777777777665 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 !   24.6   0.3   2.5e-08   2.5e-05      10      96 ..       3     102 ..       1     107 [. 0.73
   2 ?    2.0   0.1      0.27   2.7e+02      16      78 ..     185     215 ..     130     221 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.5e-08
                     NAD_binding_7  10 vlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee...........l..ekdlegadlviaatddre 73 
                                       ++++G+G+++ + +   ++ g +v+v+  +   e  + v+++ ++              ++++++ad vi +td ++
  gi|336253268|ref|YP_004596375.1|   3 IVIIGAGSIGSNLIDLAVDDGNDVVVIESDE--ERANEVSAEYDClvlnadatnhgTlqDAEIDRADAVISTTDVDA 77 
                                       69*************************9994..33333333332222111122222234577*************** PP

                     NAD_binding_7  74 lneriaeaakarri..lvnvadkpe 96 
                                       +n  ++ +a++  +  lv v+ +p+
  gi|336253268|ref|YP_004596375.1|  78 VNIMVMLLAQEHDVpnLVSVVHDPD 102
                                       ********99888755788887776 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.27
                     NAD_binding_7  16 GevAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatddrelneri 78 
                                       Gev a k  + ++a                                 d+v + tdd+ l++++
  gi|336253268|ref|YP_004596375.1| 185 GEVQAPKGGTTIRA--------------------------------GDTVTVFTDDATLSDAV 215
                                       33333333333333................................45555555555555555 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 !   21.5   1.6   1.7e-07   0.00017       3      71 ..       8      76 ..       7     100 .. 0.84
   2 ?   -0.4   0.0      0.89   8.8e+02      13      44 ..      83     115 ..      77     117 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.7e-07
                                      TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHH.HTT-SEEEES---T CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaea.lkgadaVvsalggg 71
                                       G++G+ l++ ++++g  +v+++  ++e+++e++ae  + v+ +d+t++ +l++a ++ adaV+s++  +
  gi|336253268|ref|YP_004596375.1|  8 AGSIGSNLIDLAVDDG-NDVVVIESDEERANEVSAEYDCLVLNADATNHGTLQDAeIDRADAVISTTDVD 76
                                      79*************6.8****************999***************9886899******98543 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.89
                                       HHHHC-T-EE...EEEETTHHHCHHHHCTTTCEEE CS
                    NAD_binding_10  13 ellargghev...talvRnpeklaeleaeeglevv 44 
                                        lla++ h+v   + +v +p+ l+ +e + g++++
  gi|336253268|ref|YP_004596375.1|  83 MLLAQE-HDVpnlVSVVHDPDNLPVFE-KIGVTLI 115
                                       567774.66533377899999999876.6888887 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 !   22.0   0.2   1.2e-07   0.00012       2      73 ..       3      75 ..       2      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.2e-07
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH..HHHCCTTTTSS-HHHHCCCHHCEEEES-H CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiek..sleklvekgklkeeeveaalarisfttdl 73
                                      + +iGaG +G+ +  +++  g +Vv+++ +ee+++++ ++       + + ++g l+++e+++a a is+t d+
  gi|336253268|ref|YP_004596375.1|  3 IVIIGAGSIGSNLIDLAVDDGNDVVVIESDEERANEVSAEYDClvLNADATNHGTLQDAEIDRADAVISTT-DV 75
                                      679**********************************9999985444566788999999998887777754.44 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 !   20.5   1.2   2.4e-07   0.00024      31     102 ..       3      76 ..       2      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.4e-07
                                       EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCHHHHHHH.HHHHH-SEEEE---BT CS
                       AlaDh_PNT_C  31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlksqeella.eavkeadvvigtvlip 102
                                       +++iG+G  G + i  a+  g +V+v++ +++r++++++ +   ++++ + ++ +l+  ++ +ad vi+t  + 
  gi|336253268|ref|YP_004596375.1|   3 IVIIGAGSIGSNLIDLAVDDGNDVVVIESDEERANEVSAeYDCLVLNADATNHGTLQdAEIDRADAVISTTDVD 76 
                                       79************************************9888888888888887776157**********8876 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.5   6.9e-07   0.00069       1      75 [.       3      76 ..       3      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.9e-07
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEE.ES-TT-HHHHHHH.HTT-SEEEE---GG CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelv.kgdlddkeslvea.lkgvdvvfsvtgfy 75
                                      I++i ++G++G+ +++ ++++g++v ++  ++++e+a++++++   lv ++d+ ++  l+ a ++ +d+v+s+t + 
  gi|336253268|ref|YP_004596375.1|  3 IVII-GAGSIGSNLIDLAVDDGNDVVVI--ESDEERANEVSAEYDCLVlNADATNHGTLQDAeIDRADAVISTTDVD 76
                                      4555.56*****************9655..89999********999999***********9889*********9854 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   4.3e-06    0.0043      15      85 ..       3      75 ..       1      90 [. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.3e-06
                                      EEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E..T-EEEEGCGHH.HHHHT-SEEEE-SSS CS
                      Shikimate_DH 15 vlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkge..eiealkleelk.ellaeadvvisatas 85
                                      +++iGaG +++ ++   ++ g + vvv+  + era+e+  e++    ++ a++   l+ + +++ad vis t  
  gi|336253268|ref|YP_004596375.1|  3 IVIIGAGSIGSNLIDLAVDDGND-VVVIESDEERANEVSAEYDCLvlNADATNHGTLQdAEIDRADAVISTTDV 75
                                      79************988877766.****************9954411344444445541459*******99965 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   5.7e-06    0.0057       1      71 [.       3      72 ..       3      95 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.7e-06
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.EEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.elveldltdrsalerlfkeeqpdavihl 71
                                      i+++Ga G iGs+l++   + g +v+++ +++++ n+ + e    + ++d t++  l+++  + ++davi  
  gi|336253268|ref|YP_004596375.1|  3 IVIIGA-GSIGSNLIDLAVDDGNDVVVIESDEERANEVSAEYDcLVLNADATNHGTLQDAEID-RADAVIST 72
                                      567777.************************87777766665585555555555555554332.55555543 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.9e-05     0.019       2      45 ..       4      78 ..       3     112 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                                      EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG.................-GGG-TT-SE................... CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefa.................tkerfpeade................... 44
                                      vi+Gag ++  l++la   g +v+v++++ee a                 +        +                   
  gi|336253268|ref|YP_004596375.1|  4 VIIGAGSIGSNLIDLAVDDGNDVVVIESDEERAnevsaeydclvlnadatN--------Hgtlqdaeidradavisttd 74
                                      8*****************************977566666655555555541........03334444455533444444 PP

                                      ...- CS
                            XdhC_C 45 ...t 45
                                          
  gi|336253268|ref|YP_004596375.1| 75 vdaV 78
                                      4332 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 ?   14.8   0.0   2.4e-05     0.023       2      43 ..       3      58 ..       2     103 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                                      EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..............E CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..............a 43
                                      i +iG G +Gsn++   ++ g +v+v++ ++e+++e+ ae               +
  gi|336253268|ref|YP_004596375.1|  3 IVIIGAGSIGSNLIDLAVDDGNDVVVIESDEERANEVSAEYdclvlnadatnhgtL 58
                                      678*********************************99987777766663333330 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 ?   14.6   1.6   4.5e-05     0.045       3      69 ..       3      81 ..       1     103 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.5e-05
                                      EEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS...............HHHHHTCTTESEE CS
                      GFO_IDH_MocA  3 vaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd...............leelladpeidav 66
                                      ++iiGaG igs+ +  l    ++ +vv ++++d+era +v++++++ + +                 +++ + +++dav
  gi|336253268|ref|YP_004596375.1|  3 IVIIGAGSIGSNLI-DLAVD-DGNDVV-VIESDEERANEVSAEYDCLVLNAdatnhgtlqdaeidrADAVISTTDVDAV 78
                                      89************.66666.677777.9***********888877733333455566666776667777777777777 PP

                                      EE- CS
                      GFO_IDH_MocA 67 iva 69
                                       ++
  gi|336253268|ref|YP_004596375.1| 79 NIM 81
                                      665 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   0.00015      0.15       3      61 ..       3      55 ..       1      83 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdr 61
                                      ++++Ga+  IG ++ +  + +G +vvv+++ ee+++ev +e        l++++D t++
  gi|336253268|ref|YP_004596375.1|  3 IVIIGAG-SIGSNLIDLAVDDGNDVVVIESDEERANEVSAEYD-----CLVLNADATNH 55
                                      7888887.7****************************999977.....45555555544 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.7e-05     0.067       1      47 [.       3      50 ..       3      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.7e-05
                                      EEEES-SHHHHHHHHHHHH.HTHCEEEE-SCH.HHHHHHHHCEEEEETT CS
                              ApbA  1 iailGaGaiGsllaakLak.agadvtlilrsr.rlealkknGlrltseg 47
                                      i+i+GaG+iGs l   La   g+dv++i  ++ r+++++ +  +l  + 
  gi|336253268|ref|YP_004596375.1|  3 IVIIGAGSIGSNLI-DLAVdDGNDVVVIESDEeRANEVSAEYDCLVLNA 50
                                      89*********986.56655************99999776655555444 PP

>> Peripla_BP_3  Periplasmic binding protein-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00013      0.13      57     108 ..      36      99 ..      19     128 .. 0.65
   2 ?   -2.5   0.0       5.5   5.5e+03      88     110 ..     161     182 ..     151     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                       HHHHH..........HHH......HHCC...-SEEEEESSCCHHHHHHHHHCCTT--TTTTEEEEB CS
                      Peripla_BP_3  57 aaaaraal..ll...qal......klaa...lPtAviaasDelAlgvlqalreaglrvPedlsvig 108
                                       a+++ a    l+   +a       +  a   +++Avi ++D+ A+ ++  l +++  vP+ +sv+ 
  gi|336253268|ref|YP_004596375.1|  36 ANEVSAEYdcLVlnaDATnhgtlqD--AeidRADAVISTTDVDAVNIMVMLLAQEHDVPNLVSVVH 99 
                                       3333333333222321112221232..0346889******************************95 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.5
                                       HHHHHHCCTT--TTTTEEEEBSS CS
                      Peripla_BP_3  88 gvlqalreaglrvPedlsvigfd 110
                                       +vl+ ++e+g   Pe   v++++
  gi|336253268|ref|YP_004596375.1| 161 QVLSTAQEKGR-LPEGCLVVALE 182
                                       67888888877.68888888876 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 ?   12.3   0.0   0.00013      0.12       2      64 ..       3      76 ..       2      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S-H.........HHHHHHHHHSSBTTTBTT----..TTEEEES-HH CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvree.........elieeineehenvkyLpgiklp..enlvattdla 64
                                      i ++GaGs G+ l  +  + g++v+++  +e           + ++n++ +n   L++ +++  +++  ttd++
  gi|336253268|ref|YP_004596375.1|  3 IVIIGAGSIGSNLIDLAVDDGNDVVVIESDEeranevsaeYDCLVLNADATNHGTLQDAEIDraDAVISTTDVD 76
                                      88***************************996676666555566677777788777776665224566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 1733.41
//
Query:       gi|336253269|ref|YP_004596376.1|  [L=515]
Description: cation transporter [Halopiger xanaduensis SH-6]
Scores for 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-71  240.1  14.6      3e-70  237.1  14.6    2.0  1  TrkH             Cation transport protein
  ------ inclusion threshold ------
      0.022   15.0   0.3       0.45   10.8   0.1    2.9  2  DUF2871          Protein of unknown function (DUF2871)
       0.75    9.7   0.0       0.75    9.7   0.0    3.7  4  Flp_Fap          Flp/Fap pilin component


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 !  237.1  14.6     5e-74     3e-70      64     491 ..     122     505 ..     105     509 .. 0.90

  Alignments for each domain:
  == domain 1  score: 237.1 bits;  conditional E-value: 5e-74
                              TrkH  64 ldalfeavsgltttglsvivveeslprsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkel 140
                                       l+ +fe+ sg+t tgl+++ +ee+lp   l++r+++++iGg+gv+vl++++l+++g+gs  ly+sea    ++ k +
  gi|336253269|ref|YP_004596376.1| 122 LNGIFESLSGFTSTGLTMARTEEQLPATLLWWRSFTEWIGGVGVIVLTVAILARPGSGSLTLYESEA----RSTKIH 194
                                       7789***************************************************************....****** PP

                              TrkH 141 rslselikilvvyyvgleilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnkni 217
                                       +s+ ++++ ++++yv+l++ +++ll         + +++      plw a++h+m+++ ++Gfs++++S++ +++ +
  gi|336253269|ref|YP_004596376.1| 195 PSIVSTVREIWKIYVILTVGGIALL---------FVAGM------PLWGAINHAMTGIATGGFSIHADSIGHYDS-A 255
                                       *************************.........899**......******************************.9 PP

                              TrkH 218 villvaiifiilGnigFpillrviiaikkkilrdlkqikeslsflldlprrcftLllasgfvwllllelavlnvtdn 294
                                        i+ ++i+++++G i+Fp+++ ++       l          +f++dl++r+ ++ + +g + l+ +  +       
  gi|336253269|ref|YP_004596376.1| 256 AIEYAVIPIMVAGSIAFPVHYLLFK----GELE---------NFYKDLQTRWVFIWFTVGSLALTGTL-Y------- 311
                                       9*******************98873....3334.........599********887777777665543.3....... PP

                              TrkH 295 ilfilldegslvvksipkgsrvlkalFqsvstrta.GFsvvdlsn.....lhpaikvllvlmmyigglpgStaggIr 365
                                                    + ++  ++++++lFq vs  +  GF +  ++n     + +   +++   m  g+++gSt+ggI+
  gi|336253269|ref|YP_004596376.1| 312 --------LRGTYDTLE--ESFRHGLFQFVSGTSNaGFGTTAIGNgaeqiWTADATLIVCAGMLTGAAAGSTVGGIK 378
                                       ........245556666..99**********76655*******9944444445556788888*************** PP

                              TrkH 366 rtnvyeefslgkyeieqekepk.avskksidgkhlerqllvdlws....lflvlliilileglklsdvqepdfsffd 437
                                        +++ ++++  +++i + +ep+ av++ +i+ + l +    +       +f+++l++l + + +l    ++d    +
  gi|336253269|ref|YP_004596376.1| 379 LIRAITLVRGARWRIAGVFEPSsAVRRLRIGDRSLSETQASKELEeaaiVFVLWLLFLAVGVAVLLATLPTDVRAEY 455
                                       ***********************************8755444444466699999999999***************** PP

                              TrkH 438 iLfevvSaygtvGLSlGaknaslsaqlttisklvlialmirGrlrglpvlldra 491
                                       +Lfev+Sa+ tvGLS G    ++ ++++t++klv++++m++Grl+++pvl++++
  gi|336253269|ref|YP_004596376.1| 456 VLFEVMSAQSTVGLSAG----ITGPEMPTAAKLVFLLNMWVGRLEIIPVLVLFR 505
                                       *****************....******************************997 PP

>> DUF2871  Protein of unknown function (DUF2871)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.14   8.6e+02     108     125 ..     156     173 ..     142     175 .. 0.85
   2 ?   10.8   0.1   7.6e-05      0.45      45     116 ..     265     340 ..     254     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.14
                           DUF2871 108 aisgiaGigHilltvglv 125
                                         ++i G+g i+ltv+++
  gi|336253269|ref|YP_004596376.1| 156 FTEWIGGVGVIVLTVAIL 173
                                       567899********9986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 7.6e-05
                           DUF2871  45 lvLGfvvfLlvlllekl..fklseekkfkkffivYniglvltvvmmlvrGilqvlgaelskaasaaisgi..aGig 116
                                       +v G + f + +ll k    ++ ++ ++++ fi +++g + +++++ +rG+++ l++++ +   + +sg+  aG+g
  gi|336253269|ref|YP_004596376.1| 265 MVAGSIAFPVHYLLFKGelENFYKDLQTRWVFIWFTVGSLALTGTLYLRGTYDTLEESFRHGLFQFVSGTsnAGFG 340
                                       66777777776666553227889999******************************99999999999987334554 PP

>> Flp_Fap  Flp/Fap pilin component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.8   0.7         3   1.8e+04      14      22 ..     164     172 ..     164     175 .. 0.72
   2 ?    0.0   0.3      0.13   7.6e+02      18      44 ..     214     239 ..     210     240 .. 0.71
   3 ?    9.7   0.0   0.00012      0.75       9      29 ..     255     275 ..     254     294 .. 0.70
   4 ?   -0.3   0.1      0.16   9.6e+02      16      31 ..     436     451 ..     435     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.8 bits;  conditional E-value: 3
                           Flp_Fap  14 gLIaaliAv 22 
                                       g+I+  +A+
  gi|336253269|ref|YP_004596376.1| 164 GVIVLTVAI 172
                                       678877776 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.13
                           Flp_Fap  18 aliAvviiayvttlgtaLktkFtkigt 44 
                                       + iA++ +a++  l +a++ ++t i+t
  gi|336253269|ref|YP_004596376.1| 214 GGIALLFVAGM-PLWGAINHAMTGIAT 239
                                       56666665554.566899999999987 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00012
                           Flp_Fap   9 TAIEYgLIaaliAvviiayvt 29 
                                       +AIEY++I +++A  i + v 
  gi|336253269|ref|YP_004596376.1| 255 AAIEYAVIPIMVAGSIAFPVH 275
                                       7***********988876554 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.16
                           Flp_Fap  16 IaaliAvviiayvttl 31 
                                       +a+ +Av++ +  t++
  gi|336253269|ref|YP_004596376.1| 436 LAVGVAVLLATLPTDV 451
                                       799*****99988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.21s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 4017.65
//
Query:       gi|336253270|ref|YP_004596377.1|  [L=116]
Description: hypothetical protein Halxa_1870 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00037   21.2   3.1    0.00057   20.6   1.0    2.3  3  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.15   2.7e+03      45      63 ..       3      21 ..       2      21 .. 0.82
   2 !   20.6   1.0   3.2e-08   0.00057       1      62 [.      31      85 ..      31      93 .. 0.87
   3 ?   -1.4   0.1      0.24   4.2e+03      27      46 ..      88     104 ..      84     109 .. 0.45

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.15
                           Fer4_15 45 pddeeeaaqeAaraCPvdA 63
                                      +dd e  +q+A ++ P dA
  gi|336253270|ref|YP_004596377.1|  3 DDDSESGIQRASDVGPSDA 21
                                      6889999999999888776 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.2e-08
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvd 62
                                      +v++ ++C g g C++++++       g+a+         e +++d++ e+  +Aa++CP++
  gi|336253270|ref|YP_004596377.1| 31 IVFEANKCFGAGKCAEVSDNWEMSIASGIAQPN-------EYFIDDEDLEHNVRAAAVCPAK 85
                                      78999************9877777778999555.......68******************85 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.24
                           Fer4_15  27 dglasvllddgeiaegevpd 46 
                                       dg   v+ d++   ++e+++
  gi|336253270|ref|YP_004596377.1|  88 DGCIHVV-DRR--TDEEIAP 104
                                       4444233.322..2444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.33u 0.19s 00:00:00.52 Elapsed: 00:00:00.32
# Mc/sec: 1075.20
//
Query:       gi|336253271|ref|YP_004596378.1|  [L=330]
Description: short-chain dehydrogenase/reductase SDR [Halopiger xanaduensis SH-6]
Scores for complete 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   80.3   0.0    6.8e-22   77.9   0.0    1.9  1  adh_short       short chain dehydrogenase
    3.7e-12   46.3   0.9    2.8e-11   43.4   0.9    2.0  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    2.9e-07   30.6   0.1    4.9e-07   29.8   0.1    1.3  1  KR              KR domain
     0.0004   19.9   0.0    0.00063   19.3   0.0    1.3  1  Epimerase       NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.026   13.6   0.1      0.038   13.1   0.1    1.2  1  RmlD_sub_bind   RmlD substrate binding domain
       0.09   12.7   0.9       0.14   12.0   0.9    1.6  1  NAD_binding_10  NAD(P)H-binding
       0.15   10.6   0.3       0.22   10.1   0.3    1.2  1  MutL            MutL protein


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 !   77.9   0.0   2.7e-25   6.8e-22       2     189 ..      15     223 ..      14     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 2.7e-25
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklg 76 
                                       + ++tGa sGIG++  +ela++G  vv++ rs e+ e +a+ ++e+   a++++ ++D++d e+v+a+ ++ +++  
  gi|336253271|ref|YP_004596378.1|  15 TFVITGANSGIGLEATRELARNGGAVVMACRSVERGEDAADDVREDvpDADLHVEELDLADLESVRAFADRLQDD-A 90 
                                       569*******************************************99999********************9666.7 PP

                                       SESEEEE---SS--SSGGGCSHHH.HHHHHHHHTHHHHHHHHHHHHHHH........HCTTEEEEEEEEGG...... CS
                         adh_short  77 kldvLvnNAGitgsgpfselseee.wervievNltgvflltravlpaml........kqssGrIvnvsSva...... 138
                                       ++d+L+nNAG+    ++ + + ++ +e  + vN  g f lt ++l+ +         +   +r+v+vsS +      
  gi|336253271|ref|YP_004596378.1|  91 TIDALINNAGV---MAIPRSETADgFETQFGVNHLGHFALTGLLLDRLAtdpgeagdDDGDARVVTVSSGVhergei 164
                                       9**********...45555666666**********************999999999999999*******75222222 PP

                                       ......GTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEE..EEEEESSBSSHHHHH CS
                         adh_short 139 ......gkvpvagvaaYsAsKaavagltrslakelaptgirv..navaPGlvdTdmake 189
                                             ++  + ++ aY+ sK a + ++ +l + + +  +    +av+PG+ +T+++++
  gi|336253271|ref|YP_004596378.1| 165 dfedlqSERTYDEWDAYAQSKLANVLFAYELERRFLTGDVAAksTAVHPGYANTQLQTR 223
                                       22222256678899********************99999765227899*******9876 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 !   43.4   0.9   1.1e-14   2.8e-11       1     134 [.      20     162 ..      20     261 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.1e-14
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE...EEE--TTSHHHHHHHHHHHHHHHSSEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae...vlecDVtdeeqvealveevvekfgklDil 73 
                                       Ga sgIG ++ ++la++G  vv++ ++ e+ +++++++ e+++ +   v e+D +d e+v+a++++++++  ++D l
  gi|336253271|ref|YP_004596378.1|  20 GANSGIGLEATRELARNGGAVVMACRSVERgEDAADDVREDVPDAdlhVEELDLADLESVRAFADRLQDDA-TIDAL 95 
                                       899************************9999999******9995556569*****************9995.9**** PP

                                       EE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.........CEEEEEEEGGGTSB CS
                      adh_short_C2  74 vnnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.........gsivnlssvgaerv 134
                                       +nnag++     p  + + ++f++ + vn  + f+l+  +l  l+++          +++v++ss   er+
  gi|336253271|ref|YP_004596378.1|  96 INNAGVMAI---P-RSETADGFETQFGVNHLGHFALTGLLLDrLATDPgeagdddgdARVVTVSSGVHERG 162
                                       *******98...3.456799*****************9999953333245666666667788877655544 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   1.9e-10   4.9e-07       2      93 ..      15     103 ..      14     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.9e-10
                                       EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                                KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78 
                                       t++itG+  g+Gle +r la++g + +v+  Rs +  ed+++ ++e    +a+ +v ++D++d ++v+a  ++++ +
  gi|336253271|ref|YP_004596378.1|  15 TFVITGANSGIGLEATRELARNGGA-VVMACRSVERGEDAADDVRE-DVPDADLHVEELDLADLESVRAFADRLQ-D 88 
                                       689********************75.66777887888888877775.33499******************99998.5 PP

                                       SS---EEEE------ CS
                                KR  79 eppikGvihaAgvlr 93 
                                       +++i   i+ Agv++
  gi|336253271|ref|YP_004596378.1|  89 DATIDALINNAGVMA 103
                                       56**********986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.4e-07   0.00063       2     149 ..      17     188 ..      16     204 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.4e-07
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHHH....T-S CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerlfkee....qpd 66 
                                       ++tGa+  iG   +++l+++g  v+   r  ++++ a+++          ++ eldl d ++++++ ++      +d
  gi|336253271|ref|YP_004596378.1|  17 VITGANSGIGLEATRELARNGGAVVMACRSVERGEDAADDVRedvpdadlHVEELDLADLESVRAFADRLqddaTID 93 
                                       69*******************8888777776666665555558999***************9998876541112688 PP

                                       EEEE--S---HHHHHHSH..HHHHHHHTHHHHHHHHHHH............HHTCTEEEEEEEGGGGTSCSSSSBST CS
                         Epimerase  67 avihlAavggvaassedp..adfieknlqgtlnlleaar............kagvkrllflsSsevYGkdaeqpkee 129
                                       a i+ A+v  +++s +    +  +  n  g   l   +             + g  r++ +sS  v  +++   + e
  gi|336253271|ref|YP_004596378.1|  94 ALINNAGVMAIPRSETADgfETQFGVNHLGHFALTGLLLdrlatdpgeagdDDGDARVVTVSS-GVHERGEI--DFE 167
                                       888888888888877654223445566666666666666555555554443222226666666.33333333..444 PP

                                       CSTTS--.--SSHHHHHHHHH CS
                         Epimerase 130 ttltgpl.kpnspYaaaKlag 149
                                       +++++ +     +Ya +Kla 
  gi|336253271|ref|YP_004596378.1| 168 DLQSERTyDEWDAYAQSKLAN 188
                                       444444435555666666665 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 ?   13.1   0.1   1.5e-05     0.038       3      80 ..      16     122 ..      14     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.......................T--TTSHHHHHHHH....HHH-- CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre.......................eldltdaeavaell....keakp 52 
                                        ++tGan  +G e +++la++g +v+   r+                       eldl+d e+v+++     ++a  
  gi|336253271|ref|YP_004596378.1|  16 FVITGANSGIGLEATRELARNGGAVVMACRSvergedaaddvredvpdadlhveELDLADLESVRAFAdrlqDDATI 92 
                                       689***************9987666555466689******************************9988444466777 PP

                                       SEEEE------HHHHHHS..HHHHHHHHTH CS
                     RmlD_sub_bind  53 dvvvnaAAytavDkaEse..eeaayavnae 80 
                                       d+++n A   a+ + E+    e ++ vn  
  gi|336253271|ref|YP_004596378.1|  93 DALINNAGVMAIPRSETAdgFETQFGVNHL 122
                                       789999988888888876334556666655 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 ?   12.0   0.9   5.6e-05      0.14       1      49 [.      20      67 ..      20     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.6e-05
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvt 49
                                      GA+ ++G ++++el+++g  +v++  R+ e+ ++ +++ + +v ++d++
  gi|336253271|ref|YP_004596378.1| 20 GANSGIGLEATRELARNG-GAVVMACRSVERGEDAADDVREDVPDADLH 67
                                      9****************6.799999999888886666665555555554 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   8.6e-05      0.22      75     134 ..      16      75 ..      12     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.6e-05
                              MutL  75 mvviGlvedltaeaarraAlgAgakvlkvlageltredleelrelrpdiiLLaGGtDgGn 134
                                        v++G  + + +ea r+ A++ ga+v++  ++e  ++  +++re  pd  L +   D  +
  gi|336253271|ref|YP_004596378.1|  16 FVITGANSGIGLEATRELARNGGAVVMACRSVERGEDAADDVREDVPDADLHVEELDLAD 75 
                                       58899999************************************9999866555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.46u 0.19s 00:00:00.65 Elapsed: 00:00:00.34
# Mc/sec: 2945.26
//
Query:       gi|336253272|ref|YP_004596379.1|  [L=1417]
Description: multi-sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for complete 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-79  263.7  38.3      7e-13   48.8   0.1    9.0  8  PAS_4        PAS fold
    2.9e-58  194.6   0.0    6.9e-11   42.3   0.0    8.6  8  PAS_9        PAS domain
    2.8e-52  174.9   1.7      4e-17   62.3   0.0    9.0  9  PAS_3        PAS fold
    6.4e-44  148.6   2.9      4e-13   49.3   0.0    9.5  9  PAS          PAS fold
    6.4e-29  100.7   0.0    8.3e-28   97.1   0.0    2.4  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    4.2e-22   77.7   6.9    5.9e-10   38.9   0.1    7.7  7  PAS_8        PAS domain
    4.2e-11   43.0   4.3      0.019   15.1   0.0    8.0  7  PAS_7        PAS fold
    1.6e-10   41.4   0.6    7.5e-10   39.2   0.2    2.4  2  GAF_3        GAF domain
    1.3e-09   38.0   0.1    1.3e-09   38.0   0.1    3.3  3  HisKA        His Kinase A (phospho-acceptor) domain
    1.7e-09   38.1   3.9    1.7e-09   38.1   3.9    4.4  5  GAF_2        GAF domain
    1.9e-09   38.3   0.0    1.8e-08   35.1   0.4    2.6  2  GAF          GAF domain
    4.1e-05   24.1   0.1        2.8    8.6   0.0    4.8  4  PAS_10       PAS domain
     0.0018   18.6   0.1       0.93    9.9   0.0    3.5  3  sCache_3_3   Single cache domain 3
      0.003   17.4   0.0     0.0062   16.4   0.0    1.5  1  HATPase_c_5  GHKL domain
     0.0081   16.1   0.0      0.034   14.1   0.0    2.1  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.013   15.4   0.0        1.1    9.1   0.0    3.5  3  PAS_6        YheO-like PAS domain
      0.093   12.4   0.0        3.4    7.2   0.0    2.7  2  dCache_3     Double sensory domain of two-component sensor ki


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.5   2.7e-14   2.9e-11       7     109 ..     194     300 ..     188     301 .. 0.93
   2 !   20.0   0.7     6e-07   0.00064      17     110 .]     328     428 ..     310     428 .. 0.82
   3 !   48.8   0.1   6.7e-16     7e-13       2     109 ..     445     548 ..     444     549 .. 0.92
   4 !   25.5   0.6   1.2e-08   1.2e-05      41     110 .]     606     679 ..     582     679 .. 0.81
   5 !   36.5   0.4   4.5e-12   4.7e-09       1     110 []     695     812 ..     695     812 .. 0.82
   6 !   43.1   0.1   3.8e-14     4e-11       1     109 [.     835     942 ..     835     943 .. 0.96
   7 !   33.8   0.4     3e-11   3.2e-08       2     109 ..     956    1063 ..     955    1064 .. 0.91
   8 !   35.7   0.1   7.8e-12   8.3e-09       2     110 .]    1081    1185 ..    1080    1185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.7e-14
                             PAS_4   7 alavldpdgrvlyaNaaaaelfgappeellGktlae..llpee..daarleralrrvlegeepiefleelllpgeer 79 
                                       ++  l pdg+v+++N +a+e+++a+ ++++G++++e  ++ e+   ++++++  +r+++ge + ++++ + + ge+ 
  gi|336253272|ref|YP_004596379.1| 194 LVGLLEPDGTVIDINGTAMEYVAADLADVTGEPFWEtpWWGEGdeIRDDVREWTERAAAGEYVTFEADLTQPTGERY 270
                                       577889*****************************76699888999***************99999999999***** PP

                             PAS_4  80 hyelrllPlrdesGevigvlvisrDiTerr 109
                                       ++e  ++P+ d++G+v  ++v  rD+T+r+
  gi|336253272|ref|YP_004596379.1| 271 TIEGAFRPVTDDDGDVTSIVVSDRDVTARE 300
                                       ****************************97 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 6e-07
                             PAS_4  17 vlyaNaaaaelfgappeel.lGktla..ellpeedaarleralrr..vlegeepiefleelll..pgeerhyelrll 86 
                                       +++++ a a+l+g++p++l +G+  +  +++ + d++ l + ++r  +++g ++ ++++++ +  +ge+r++    +
  gi|336253272|ref|YP_004596379.1| 328 MEFVSDACADLAGYDPDALeRGEVSWgeDVMVQADREKLWETVQRetAADGADRTFSETYRIDtaDGERRWVRDYGR 404
                                       578888999999999999945777778889999999988776655449999999999999999*999999999999* PP

                             PAS_4  87 PlrdesGevigvlvisrDiTerrr 110
                                        l+de+Ge +++ +i+ DiTer++
  gi|336253272|ref|YP_004596379.1| 405 GLFDEDGELVAIEGIIADITERKQ 428
                                       **********************85 PP

  == domain 3  score: 48.8 bits;  conditional E-value: 6.7e-16
                             PAS_4   2 dslpdalavl.dpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       d+ p ++++l d+d++++ +   +++ + ap+ee+ G+++ e++++e+aa+l + ++++lege + ++++       
  gi|336253272|ref|YP_004596379.1| 445 DHFPNGVVALvDEDLTYRTVGGDSQYTADAPAEEIEGRSVSEVVSAELAAELVPRYEAALEGESSGFEAT-----IN 516
                                       67788887777***************************************************97777766.....46 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +r++++r++P+rd++Gev ++l++s+ iTer+
  gi|336253272|ref|YP_004596379.1| 517 GRTFDFRIVPIRDDDGEVFAALGMSQNITERY 548
                                       69*****************************8 PP

  == domain 4  score: 25.5 bits;  conditional E-value: 1.2e-08
                             PAS_4  41 aellpee...daarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       + +l +    d++r+e+ ++++le +  +e +  ++  +ge r++  r +  +d++Ge++ + + ++DiTer+r
  gi|336253272|ref|YP_004596379.1| 606 ERFLAAIhedDRDRVEAKIAAALEAGGEYEAEYRVRNaDGELRWVVSRGRVECDADGEPQKFTGAVTDITERKR 679
                                       3333333344***************9888888888889**********************************97 PP

  == domain 5  score: 36.5 bits;  conditional E-value: 4.5e-12
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaae.lfgappeellGktla..e.llpee..daarleralrrvlegeepieflee 71 
                                       +d lp++++v ++dg ++ +N +a++ + ga  ++     ++    ++ ++    a+ e  l+rvl+gee+ e   +
  gi|336253272|ref|YP_004596379.1| 695 FDVLPVGVIVAGADGEIRQTNDTARDiWDGAVLDAGSVAEYEkyPiWWADSgePVAPEELTLARVLDGEEVTEPDVF 771
                                       789********************99977777666666666554433454446677788889*******988876655 PP

                             PAS_4  72 lll..pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                            +ge+r++  + +P+r+e+Gev+  +++++DiTer++
  gi|336253272|ref|YP_004596379.1| 772 EIEtgDGERRIVRAEGMPIRNERGEVVRGVATITDITERKE 812
                                       555789*********************************85 PP

  == domain 6  score: 43.1 bits;  conditional E-value: 3.8e-14
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       l+++ d+++v+++dg  +++N++ a++ g++ ee+  +++ +++ +++aa+ ++a+r  le++ +  +le+ + +ge
  gi|336253272|ref|YP_004596379.1| 835 LNAIDDVFYVVSEDGDLQRWNRSLAAVTGYTNEEVEAMSPTDFFADDQAAAAAAAIRTGLETGSVNAELEVSTKDGE 911
                                       68999**********************************************************99999999999*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       + ++e+++++l+d+ G    + +++rDiT+r+
  gi|336253272|ref|YP_004596379.1| 912 RIPFEFNASRLEDPWGN-TVLAGMGRDITDRV 942
                                       *****************.77899*******97 PP

  == domain 7  score: 33.8 bits;  conditional E-value: 3e-11
                             PAS_4    2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.p 75  
                                        + + d+++v+d+dg ++ +N+++ae++g++p++l+G+++  l+ +e  +r+++  + + +g+e  +++  l++ +
  gi|336253272|ref|YP_004596379.1|  956 EVVDDGVYVVDEDGYFTMVNETYAEMLGYEPDDLVGEHVSLLVDDEILERVAELEATATSGDEWPTMEADLRTaD 1030
                                        6789************************************999999*****************9999999999** PP

                             PAS_4   76 geerhyelrllPlrdesGe.vigvlvisrDiTerr 109 
                                        g+++++e ++  l +   + + + ++++rDi++r+
  gi|336253272|ref|YP_004596379.1| 1031 GGTVPVEANFAMLPE--NDsAWHRVGVARDISDRK 1063
                                        **********77743..333678899999999997 PP

  == domain 8  score: 35.7 bits;  conditional E-value: 7.8e-12
                             PAS_4    2 dslpdalavl.dpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllp 75  
                                        ++ pd+ + l d+++ ++ a  +  + +g+pp++ +G++ +el+pee+ +++e++  ++lege   +++e++ + 
  gi|336253272|ref|YP_004596379.1| 1081 ENFPDGAVGLfDENLEYTVAGGQLLDEVGVPPADRVGSSIYELYPEELVEEVEPYFHAALEGEPNSFEVEFYGR- 1154
                                        66677655555***********************************************************9888. PP

                             PAS_4   76 geerhyelrllPlrdesGevigvlvisrDiTerrr 110 
                                            h+    lP+r++ G++ + +++++D+Terr+
  gi|336253272|ref|YP_004596379.1| 1155 ----HLHGYTLPVRNAAGDIYAGMIVVQDVTERRE 1185
                                        ....999999***********************96 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   3.1e-08   3.3e-05       6     103 ..     197     297 ..     191     298 .. 0.84
   2 !   22.0   0.0   1.4e-07   0.00015       8     104 .]     322     425 ..     315     425 .. 0.88
   3 !   15.6   0.0   1.4e-05     0.015      28     104 .]     476     546 ..     466     546 .. 0.88
   4 !   15.8   0.0   1.2e-05     0.012      40     104 .]     609     676 ..     582     676 .. 0.84
   5 !   15.7   0.0   1.3e-05     0.014       3     104 .]     701     809 ..     699     809 .. 0.68
   6 !   42.3   0.0   6.6e-14   6.9e-11       2     104 .]     840     940 ..     839     940 .. 0.86
   7 !   41.0   0.0   1.7e-13   1.8e-10       1     104 []     959    1061 ..     959    1061 .. 0.90
   8 ?    6.4   0.0      0.01        11       8     104 .]    1092    1182 ..    1084    1182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.1e-08
                             PAS_9   6 idnpdgrilyaNeaalrllGyspeevlgksitdlf.....vtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       +  pdg+++++N +a++    + ++v g +++++      ++  ++ ++  +   +g+    ++e +l+ ++ge++ 
  gi|336253272|ref|YP_004596379.1| 197 LLEPDGTVIDINGTAMEYVAADLADVTGEPFWETPwwgegDEIRDDVREWTERAAAGE--YVTFEADLTQPTGERYT 271
                                       367********************************76555444455555555555555..9**************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDit 103
                                       ++  ++pv dddg +++i+v  rD+t
  gi|336253272|ref|YP_004596379.1| 272 IEGAFRPVTDDDGDVTSIVVSDRDVT 297
                                       *****************999999999 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.4e-07
                             PAS_9   8 npdg.rilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrk.....kerevevvlirkngetfw 77 
                                       n+ g +++++++a ++l Gy+p+++    +++   v  + ++e+l++ +++ +        +++++ + + +ge+ w
  gi|336253272|ref|YP_004596379.1| 322 NERGwPMEFVSDACADLAGYDPDALERGEVSWGEdVMVQADREKLWETVQRETAadgadRTFSETYRIDTADGERRW 398
                                       67785566*******************99888886677777777777777777799***9***************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       v+   + ++d+dgelv+i +i+ Dite
  gi|336253272|ref|YP_004596379.1| 399 VRDYGRGLFDEDGELVAIEGIIADITE 425
                                       ****************999*******8 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.4e-05
                             PAS_9  28 peevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                       +ee+ g+s+++++  ++e + +l   +e+    e e    + + ng+tf   ++++p++dddge++++++ +++ite
  gi|336253272|ref|YP_004596379.1| 476 AEEIEGRSVSEVV--SAELAAELVPRYEAAL--EGESSGFEATINGRTFD--FRIVPIRDDDGEVFAALGMSQNITE 546
                                       799**********..8888888888888888..89999999999999999..999*********************8 PP

  == domain 4  score: 15.8 bits;  conditional E-value: 1.2e-05
                             PAS_9  40 f.....vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                       +     ++ ++ + +++aale+g   e+e e+  ++ +ge  wv  + +   d+dge + + + ++Dite
  gi|336253272|ref|YP_004596379.1| 609 LaaiheDDRDRVEAKIAAALEAGG--EYEAEYRVRNADGELRWVVSRGRVECDADGEPQKFTGAVTDITE 676
                                       345566777888999*********..*****************98888888999***************8 PP

  == domain 5  score: 15.7 bits;  conditional E-value: 1.3e-05
                             PAS_9   3 gilidnpdgrilyaNeaalrl.....lG.yspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirk 71 
                                       g+++   dg+i   N++a+++     l   s +e    +i++    ++ + ++ +l+++l+  +   + +  ++ + 
  gi|336253272|ref|YP_004596379.1| 701 GVIVAGADGEIRQTNDTARDIwdgavLDaGSVAEYEKYPIWWADsgEPVAPEELTLARVLDGEE-VTEPDVFEIETG 776
                                       6666666666666666666663333322223444444444444455555666667777777777.667777788899 PP

                             PAS_9  72 ngetfwvlltaspvkdddgelvgiivilrDite 104
                                       +ge+  v++   p++++ ge+v+ +++++Dite
  gi|336253272|ref|YP_004596379.1| 777 DGERRIVRAEGMPIRNERGEVVRGVATITDITE 809
                                       99******************************8 PP

  == domain 6  score: 42.3 bits;  conditional E-value: 6.6e-14
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfw 77 
                                       d + ++ +dg + ++N++++ ++Gy+ eev   s td+f  +++ +   +aa+++g +    + e++  +k+ge+++
  gi|336253272|ref|YP_004596379.1| 840 DVFYVVSEDGDLQRWNRSLAAVTGYTNEEVEAMSPTDFF--ADDQAAAAAAAIRTGLEtGSVNAELEVSTKDGERIP 914
                                       5566778***9****************************..55555566666665555577**************** PP

                             PAS_9  78 vlltaspvkdd.dgelvgiivilrDite 104
                                       ++++as++ d  ++++ +  +  rDit+
  gi|336253272|ref|YP_004596379.1| 915 FEFNASRLEDPwGNTVLA--GMGRDITD 940
                                       ***********8877777..******96 PP

  == domain 7  score: 41.0 bits;  conditional E-value: 1.7e-13
                             PAS_9    1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkng 73  
                                        +dg+ ++++dg  + +Ne+ +++lGy p++++g +++ l+  d+e  er++++  + ++  +  + e +l++ +g
  gi|336253272|ref|YP_004596379.1|  959 DDGVYVVDEDGYFTMVNETYAEMLGYEPDDLVGEHVSLLV--DDEILERVAELEATATSgdEWPTMEADLRTADG 1031
                                        58999999********************************..777777777777777778789999********* PP

                             PAS_9   74 etfwvlltaspvkdddgelvgiivilrDite 104 
                                        +t++v+++++ + ++ +  ++ +++ rDi++
  gi|336253272|ref|YP_004596379.1| 1032 GTVPVEANFAMLPEN-DSAWHRVGVARDISD 1061
                                        ************865.68999********96 PP

  == domain 8  score: 6.4 bits;  conditional E-value: 0.01
                             PAS_9    8 npdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvllt 81  
                                        +++ + + a  ++l+  G  p++ +g si +l+  ++e  e+++ ++ +  + ++ ++ev+++ +     + +  
  gi|336253272|ref|YP_004596379.1| 1092 DENLEYTVAGGQLLDEVGVPPADRVGSSIYELY--PEELVEEVEPYFHAALEgEPNSFEVEFYGR-----HLHGY 1159
                                        477777788889999999***************..777777777777776666899*********.....77766 PP

                             PAS_9   82 aspvkdddgelvgiivilrDite 104 
                                          pv+++ g + +  ++++D+te
  gi|336253272|ref|YP_004596379.1| 1160 TLPVRNAAGDIYAGMIVVQDVTE 1182
                                        6799***99999999******98 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.17   1.8e+02      43      86 ..     247     290 ..     236     292 .. 0.81
   2 !   45.4   0.1   7.2e-15   7.6e-12       3      89 .]     330     420 ..     328     420 .. 0.91
   3 ?   -2.4   0.0       5.9   6.3e+03      68      85 ..     520     537 ..     516     540 .. 0.77
   4 !   62.3   0.0   3.8e-20     4e-17       6      88 ..     586     670 ..     581     671 .. 0.94
   5 !    8.7   0.0    0.0019         2      55      88 ..     769     803 ..     750     804 .. 0.80
   6 !   12.9   0.0   9.4e-05     0.099       4      80 ..     854     927 ..     852     932 .. 0.90
   7 !   26.7   0.0   4.9e-09   5.2e-06       3      88 ..     973    1055 ..     971    1056 .. 0.86
   8 ?    1.4   0.0      0.38     4e+02      12      64 ..    1108    1159 ..    1100    1167 .. 0.82
   9 ?    2.9   0.0      0.13   1.4e+02      32      70 ..    1356    1400 ..    1352    1401 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.17
                             PAS_3  43 qealkkgepyegeyRirrkdGeyrwveararvirdengkpvrvi 86 
                                        e ++ ge +++e  + ++ Ge + +e   r++ d++g ++ ++
  gi|336253272|ref|YP_004596379.1| 247 TERAAAGEYVTFEADLTQPTGERYTIEGAFRPVTDDDGDVTSIV 290
                                       34446778779****************************99886 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 7.2e-15
                             PAS_3   3 yvserveeilGyspeellgk.veswldlvhpeDrervrealq.ealkkge..pyegeyRirrkdGeyrwveararvi 75 
                                       +vs+++ ++ Gy+p+ l+   v+   d++   Dre+++e++q e +++g+   +++ yRi ++dGe rwv++++r +
  gi|336253272|ref|YP_004596379.1| 330 FVSDACADLAGYDPDALERGeVSWGEDVMVQADREKLWETVQrETAADGAdrTFSETYRIDTADGERRWVRDYGRGL 406
                                       89******************888889****************755555556788999******************** PP

                             PAS_3  76 rdengkpvrvigva 89 
                                       +de+g+ v + g++
  gi|336253272|ref|YP_004596379.1| 407 FDEDGELVAIEGII 420
                                       **********9985 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.9
                             PAS_3  68 veararvirdengkpvrv 85 
                                       ++ r+++ird++g++   
  gi|336253272|ref|YP_004596379.1| 520 FDFRIVPIRDDDGEVFAA 537
                                       5668899******98765 PP

  == domain 4  score: 62.3 bits;  conditional E-value: 3.8e-20
                             PAS_3   6 erveeilGyspeellgk..veswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdeng 80 
                                       +++ e+++++pe  ++    e++l ++h +Dr+rv++++++al+ g++ye eyR+r++dGe rwv +r+rv  d +g
  gi|336253272|ref|YP_004596379.1| 586 ATFAETFDVDPEAAREGvsSERFLAAIHEDDRDRVEAKIAAALEAGGEYEAEYRVRNADGELRWVVSRGRVECDADG 662
                                       678999999999999988899******************************************************** PP

                             PAS_3  81 kpvrvigv 88 
                                       +p+++ g 
  gi|336253272|ref|YP_004596379.1| 663 EPQKFTGA 670
                                       *****996 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0019
                             PAS_3  55 e.yRirrkdGeyrwveararvirdengkpvrvigv 88 
                                       + + i + dGe r v+a + +ir+e g++vr +++
  gi|336253272|ref|YP_004596379.1| 769 DvFEIETGDGERRIVRAEGMPIRNERGEVVRGVAT 803
                                       35888899**********************98877 PP

  == domain 6  score: 12.9 bits;  conditional E-value: 9.4e-05
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdeng 80 
                                       ++++   ++Gy+ ee+++   s  d+   +  + + +a+ + l++g+ ++ e  + +kdGe + +e  a+ + d  g
  gi|336253272|ref|YP_004596379.1| 854 WNRSLAAVTGYTNEEVEAM--SPTDFFADDQAAAAAAAIRTGLETGS-VNAELEVSTKDGERIPFEFNASRLEDPWG 927
                                       99*****************..*************************9.89***********9988877766666555 PP

  == domain 7  score: 26.7 bits;  conditional E-value: 4.9e-09
                             PAS_3    3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepy.egeyRirrkdGeyrwveararvir 76  
                                         v+e++ e+lGy+p++l g    + +l+  +++ +  ++l++ +++g ++ + e  +r++dG+++ vea    + 
  gi|336253272|ref|YP_004596379.1|  973 MVNETYAEMLGYEPDDLVGE---HVSLLVDDEILERVAELEATATSGDEWpTMEADLRTADGGTVPVEANFAML- 1043
                                        689*****************...9999999997777777777777888899*******************9998. PP

                             PAS_3   77 dengkpvrvigv 88  
                                         en   ++ +gv
  gi|336253272|ref|YP_004596379.1| 1044 PENDSAWHRVGV 1055
                                        888877777777 PP

  == domain 8  score: 1.4 bits;  conditional E-value: 0.38
                             PAS_3   12 lGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGe 64  
                                        +G+ p++  g+  s+++l   e  e+v+  +++al++   ++e+e+  r+ +G 
  gi|336253272|ref|YP_004596379.1| 1108 VGVPPADRVGS--SIYELYPEELVEEVEPYFHAALEGEPnSFEVEFYGRHLHGY 1159
                                        69999999999..******9999************6666788888877777665 PP

  == domain 9  score: 2.9 bits;  conditional E-value: 0.13
                             PAS_3   32 peDrervrealqealkkgepyege.......yRirrkdGeyrwvea 70  
                                        p+D+erv++ ++++  ++++yeg         Ri+ ++G+ +wv++
  gi|336253272|ref|YP_004596379.1| 1356 PDDQERVFTIFDRLH-SRADYEGTgiglalcERIVERHGGEIWVDS 1400
                                        9**********9776.555576666666676899999999999986 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.024        25      16     112 ..     197     295 ..     182     296 .. 0.78
   2 ?    1.4   0.0      0.29   3.1e+02      68     113 .]     376     423 ..     328     423 .. 0.67
   3 !    7.5   0.0    0.0038         4       2     109 ..     439     540 ..     438     544 .. 0.71
   4 !   16.1   0.0   7.8e-06    0.0083      37     113 .]     599     674 ..     560     674 .. 0.90
   5 !    6.7   0.0    0.0066       6.9       2      32 ..     690     720 ..     689     722 .. 0.91
   6 ?    2.0   0.1      0.19     2e+02      82     113 .]     776     807 ..     754     807 .. 0.81
   7 !   42.0   0.0     7e-14   7.4e-11       4     113 .]     832     938 ..     829     938 .. 0.92
   8 !   49.3   0.0   3.8e-16     4e-13       1     113 []     949    1059 ..     949    1059 .. 0.93
   9 !    7.6   0.0    0.0036       3.7       2     108 ..    1075    1175 ..    1074    1180 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.024
                                       EEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGG.BSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEE CS
                               PAS  16 vvDedgrilyvNaaaeellGlsreevlgkslldl.iheedda.elaelleqlleqgeesrageisfklrdgrpihle 90 
                                       ++  dg ++ +N +a e    +  +v g+++ +  ++ e d+  +  + ++ ++++ e  ++e +++ + g+ + +e
  gi|336253272|ref|YP_004596379.1| 197 LLEPDGTVIDINGTAMEYVAADLADVTGEPFWETpWWGEGDEiRDDVREWTERAAAGEYVTFEADLTQPTGERYTIE 273
                                       56678899999999999999999999999988863444444457777788888889999999999999********* PP

                                       EEEEEEEETTEEEEEEEEEEEE CS
                               PAS  91 vraspvrdaggeilgflgvlrd 112
                                          +pv+d +g ++ +++  rd
  gi|336253272|ref|YP_004596379.1| 274 GAFRPVTDDDGDVTSIVVSDRD 295
                                       *************999987666 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.29
                                       HTT-ECCCCEEEEC..TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  68 qgeesrageisfkl..rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +    r++  + +    dg+ ++++   + ++d++ge+  + g++ di
  gi|336253272|ref|YP_004596379.1| 376 ADGADRTFSETYRIdtADGERRWVRDYGRGLFDEDGELVAIEGIIADI 423
                                       22333333333333669*******************998887777776 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0038
                                       HHHHHHHHSSSEEEE.EETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   2 dlraileslpdpifv.vDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       ++ra++++ p+++++ vDed     v    +     ++ee+ g+s++++++ e  ael+ ++e +le    s+++e 
  gi|336253272|ref|YP_004596379.1| 439 RYRALIDHFPNGVVAlVDEDLTYRTVGGDSQYTADAPAEEIEGRSVSEVVSAELAAELVPRYEAALEGE--SSGFEA 513
                                       78888888888887624677777777777777777888************9995556666666555554..445555 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEE CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgv 109
                                       +++      + ++ r +p+rd +ge+  +lg+
  gi|336253272|ref|YP_004596379.1| 514 TING-----RTFDFRIVPIRDDDGEVFAALGM 540
                                       5555.....77888889999999998777766 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 7.8e-06
                                       THHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  37 sreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +re v+++ +l  ihe+d++ + +++  +le+g e +a+ + ++  dg+ ++++ r +   da+ge+  f g + di
  gi|336253272|ref|YP_004596379.1| 599 AREGVSSERFLAAIHEDDRDRVEAKIAAALEAGGEYEAEYRVRNA-DGELRWVVSRGRVECDADGEPQKFTGAVTDI 674
                                       56889999999**********************************.*********************9999999987 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.0066
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHH CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaee 32 
                                       +l+++++ lp++++v  +dg+i  +N++a++
  gi|336253272|ref|YP_004596379.1| 690 QLETLFDVLPVGVIVAGADGEIRQTNDTARD 720
                                       78889999********************987 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.19
                                       TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  82 rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        dg+ + ++ +  p+r++ ge+   + ++ di
  gi|336253272|ref|YP_004596379.1| 776 GDGERRIVRAEGMPIRNERGEVVRGVATITDI 807
                                       59*******************98777777776 PP

  == domain 7  score: 42.0 bits;  conditional E-value: 7e-14
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       +ail++++d   vv edg+   +N++ +  +G++ eev   s  d++  ++ a  a+++++ le+g+ +   e+s k
  gi|336253272|ref|YP_004596379.1| 832 DAILNAIDDVFYVVSEDGDLQRWNRSLAAVTGYTNEEVEAMSPTDFFADDQAAAAAAAIRTGLETGSVNAELEVSTK 908
                                       79*******************************************99988777999999999999999888888776 PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                          g+ i++e +as + d++g+   + g++rdi
  gi|336253272|ref|YP_004596379.1| 909 D--GERIPFEFNASRLEDPWGNT-VLAGMGRDI 938
                                       5..*******************7.999**9998 PP

  == domain 8  score: 49.3 bits;  conditional E-value: 3.8e-16
                                        HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECC CS
                               PAS    1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesra 74  
                                        e++++i+e  +d++ vvDedg ++ vN++++e+lG+++++++g++++ l+   d+  e++++le  + +g e+ +
  gi|336253272|ref|YP_004596379.1|  949 ERYETIVEVVDDGVYVVDEDGYFTMVNETYAEMLGYEPDDLVGEHVSLLVD--DEIlERVAELEATATSGDEWPT 1021
                                        689********************************************8883..33469***************** PP

                                        CCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS   75 geisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113 
                                        +e ++++ dg+++++e + + + + ++ + + +gv+rdi
  gi|336253272|ref|YP_004596379.1| 1022 MEADLRTADGGTVPVEANFAMLPENDSAW-HRVGVARDI 1059
                                        ******************99999999998.888888887 PP

  == domain 9  score: 7.6 bits;  conditional E-value: 0.0036
                                        HHHHHHHHSSSEEEEE.ETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-..EC CS
                               PAS    2 dlraileslpdpifvv.DedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgee..sr 73  
                                        ++r+++e+ pd+ +++ De+ + + +     +  G ++ + +g+s+++l++ee    l+e++e + +++ e  ++
  gi|336253272|ref|YP_004596379.1| 1075 RYRTLVENFPDGAVGLfDENLEYTVAGGQLLDEVGVPPADRVGSSIYELYPEE----LVEEVEPYFHAALEgePN 1145
                                        7999999999999987469999999999999999*****************98....555555555544330033 PP

                                        CCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEE CS
                               PAS   74 ageisfklrdgrpihlevraspvrdaggeilgflg 108 
                                        ++e+ f       +hl+  + pvr+a g i   + 
  gi|336253272|ref|YP_004596379.1| 1146 SFEVEFYG-----RHLHGYTLPVRNAAGDIYAGMI 1175
                                        44665555.....8888888888888888754444 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 ?    0.5   0.0      0.81   8.5e+02      35      56 ..    1279    1302 ..    1246    1304 .. 0.77
   2 !   97.1   0.0   7.9e-31   8.3e-28       2     110 ..    1306    1414 ..    1305    1416 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.81
                                        E..TEEEEEEEESSSSSTTHHHTG CS
                         HATPase_c   35 e..ddlvisveDnGiGipkedlkk 56  
                                        e   dl++++e +G  i +edl++
  gi|336253272|ref|YP_004596379.1| 1279 EvlADLQFRIEESGAEIAVEDLPE 1302
                                        355799***************985 PP

  == domain 2  score: 97.1 bits;  conditional E-value: 7.9e-31
                                        HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSS CS
                         HATPase_c    2 dekrLrqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggt 74  
                                        d ++Lrq+++nl++Na+ + + ++  +v+i a+   d+ vi veD GiGi+++d++++f+ f++  +++ +++gt
  gi|336253272|ref|YP_004596379.1| 1306 DDSQLRQVFQNLLSNAITY-SGDEPPRVRIGADRrgDEWVIAVEDRGIGIDPDDQERVFTIFDR-LHSRADYEGT 1378
                                        6789***************.54555555555533459***************************.889999**** PP

                                        SHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c   75 GlGlsivkklvelmgGeiwvesepgrGttftftlpl 110 
                                        G+Gl++++++ve++gGeiwv+sepg+G+tf ftlp 
  gi|336253272|ref|YP_004596379.1| 1379 GIGLALCERIVERHGGEIWVDSEPGEGSTFSFTLPA 1414
                                        **********************************97 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.092        97       2      63 ..     183     247 ..     182     252 .. 0.74
   2 ?    0.6   0.0      0.58   6.2e+02       2      40 ..     305     346 ..     304     372 .. 0.71
   3 !    7.4   0.0    0.0043       4.5       1      20 [.     438     458 ..     438     464 .. 0.79
   4 !   14.2   0.0   3.2e-05     0.034       1      34 [.     689     722 ..     689     749 .. 0.84
   5 !    6.9   0.1    0.0062       6.5       4      43 ..     832     872 ..     825     888 .. 0.83
   6 !   38.9   0.1   5.6e-13   5.9e-10       1      57 [.     949    1006 ..     949    1020 .. 0.80
   7 ?    1.6   0.0      0.28     3e+02       1      15 [.    1074    1088 ..    1074    1106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.092
                             PAS_8   2 rlralfe..sspdgiavvd.lgdrivdvNqaalellGys.adlkgellg..qllpvlrplledaeqll 63 
                                       r++a+fe  ++ +g++    +g+ ++d+N +a e    + ad+ ge+++  +++ + ++ ++d +++ 
  gi|336253272|ref|YP_004596379.1| 183 RFEAIFEdpNILVGLL--EpDGT-VIDINGTAMEYVAADlADVTGEPFWetPWWGEGDEIRDDVREWT 247
                                       8889999777777777..74555.************98899999999987655555555555777765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.58
                             PAS_8   2 rlralfesspdgiavvd..lgdrivdvNqaalellGys.adl 40 
                                       rl +l++++p  +  +   +g+   +v +a ++l Gy+ + l
  gi|336253272|ref|YP_004596379.1| 305 RLSTLMDNVPGMVYRCEneRGWPMEFVSDACADLAGYDpDAL 346
                                       889999999999997763344415669999999999994333 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0043
                             PAS_8   1 erlralfesspdgiav.vdlg 20 
                                       +r+ral+++ p+g++  vd++
  gi|336253272|ref|YP_004596379.1| 438 QRYRALIDHFPNGVVAlVDED 458
                                       7*************9735643 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 3.2e-05
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalell 34 
                                       e+l++lf+ +p+g++v+ +++ i++ N++a +++
  gi|336253272|ref|YP_004596379.1| 689 EQLETLFDVLPVGVIVAGADGEIRQTNDTARDIW 722
                                       689************8653366*********998 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0062
                             PAS_8   4 ralfesspdgiavvd.lgdrivdvNqaalellGys.adlkge 43 
                                        a++++++d   vv  +gd +  +N++ +  +Gy+ +++ ++
  gi|336253272|ref|YP_004596379.1| 832 DAILNAIDDVFYVVSeDGD-LQRWNRSLAAVTGYTnEEVEAM 872
                                       459*********9988999.***************7776664 PP

  == domain 6  score: 38.9 bits;  conditional E-value: 5.6e-13
                             PAS_8    1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrplle 57  
                                        er+++++e ++dg+ vvd +g  +++vN++++e+lGy+ +dl ge +  l+++   +++
  gi|336253272|ref|YP_004596379.1|  949 ERYETIVEVVDDGVYVVDeDGY-FTMVNETYAEMLGYEpDDLVGEHVSLLVDDEILERV 1006
                                        7*****************6666.******************999999866665555544 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.28
                             PAS_8    1 erlralfesspdgia 15  
                                        +r+r+l+e+ pdg +
  gi|336253272|ref|YP_004596379.1| 1074 RRYRTLVENFPDGAV 1088
                                        59**********966 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.23   2.4e+02      49      96 ..     168     213 ..     151     223 .. 0.75
   2 ?   -1.3   0.2       2.2   2.3e+03      59     114 ..     239     303 ..     233     304 .. 0.53
   3 ?    2.3   0.1      0.17   1.8e+02      24     114 ..     588     681 ..     582     682 .. 0.54
   4 !    9.9   0.0   0.00075      0.79       5     114 ..     699     814 ..     695     815 .. 0.74
   5 ?    3.5   0.0     0.073        77       1      42 [.     835     876 ..     835     916 .. 0.83
   6 !   15.1   0.0   1.8e-05     0.019       2      42 ..     956     995 ..     955    1028 .. 0.82
   7 ?    2.1   0.0       0.2   2.1e+02      59     114 ..    1128    1187 ..    1115    1188 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.23
                             PAS_7  49 aergefgagdveaeverrlaaaragkphsfererpdgrvievrgnplp 96 
                                       +e+ +++ +d  +  err++a+ ++ +  +   +pdg+vi+++g++++
  gi|336253272|ref|YP_004596379.1| 168 VENADVR-RD-LERTERRFEAIFEDPNILVGLLEPDGTVIDINGTAME 213
                                       4444444.33.34457888888888888888999***********997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                             PAS_7  59 veaeverrlaaaragkphsfer..erpdgrvievrgn..pl.....pdgGfVttytDiTerrrae 114
                                       +++ v++++++a+ag+  +fe   ++p+g+   ++g   p+     +   +V++  D+T+r + e
  gi|336253272|ref|YP_004596379.1| 239 IRDDVREWTERAAAGEYVTFEAdlTQPTGERYTIEGAfrPVtdddgDVTSIVVSDRDVTAREERE 303
                                       55666666666666666666541134555544444431133221113346777788999988776 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.17
                             PAS_7  24 ylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfererpdgrvievrgnpl..... 95 
                                       + e +d+ +e ++ gv+ e +l+ ++e      ++vea++++ l+a  + ++++  r  +dg+   v ++       
  gi|336253272|ref|YP_004596379.1| 588 FAETFDVDPEAAREGVSSERFLAAIHEDDR---DRVEAKIAAALEAGGEYEAEYRVR-NADGELRWVVSRGRvecda 660
                                       677788888888888888877777655444...457777777776555544444333.3344322222211112322 PP

                             PAS_7  96 ..pdgGfVttytDiTerrrae 114
                                         +   f    tDiTer+ra+
  gi|336253272|ref|YP_004596379.1| 661 dgEPQKFTGAVTDITERKRAQ 681
                                       221122444557888888876 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00075
                             PAS_7   5 sqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfere 81 
                                       + G++v  ad++++  N+  +++ d     +   +++e+   + a+ ge   + +e +++r+l+  +  +p+ fe e
  gi|336253272|ref|YP_004596379.1| 699 PVGVIVAGADGEIRQTNDTARDIWDGAVLDAGSVAEYEKYPIWWADSGEPV-APEELTLARVLDGEEVTEPDVFEIE 774
                                       568888888888888888888888887777777777888888888888888.5567778888888888999999999 PP

                             PAS_7  82 rpdg..rvievrgnpl.pdgGf....VttytDiTerrrae 114
                                       + dg  r+++ +g p+  ++G     V+t tDiTer++ e
  gi|336253272|ref|YP_004596379.1| 775 TGDGerRIVRAEGMPIrNERGEvvrgVATITDITERKERE 814
                                       9998335666666666535664222268*********988 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.073
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvple 42 
                                       l+ +++ + v+++d+ L  wNr    + ++++e v++  p +
  gi|336253272|ref|YP_004596379.1| 835 LNAIDDVFYVVSEDGDLQRWNRSLAAVTGYTNEEVEAMSPTD 876
                                       567788899*********************999998776655 PP

  == domain 6  score: 15.1 bits;  conditional E-value: 1.8e-05
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvple 42 
                                       e +++G+ v+D+d+  +++N+ y e+l++ ++ + vg +++
  gi|336253272|ref|YP_004596379.1| 956 EVVDDGVYVVDEDGYFTMVNETYAEMLGYEPDDL-VGEHVS 995
                                       67899************************76665.555554 PP

  == domain 7  score: 2.1 bits;  conditional E-value: 0.2
                             PAS_7   59 veaeverrlaaaragkphsfererp....dgrvievrgnplpdgGfVttytDiTerrrae 114 
                                          +eve  ++aa +g+p+sfe+e       g ++ vr+ + +    +++ +D+Terr+ e
  gi|336253272|ref|YP_004596379.1| 1128 LVEEVEPYFHAALEGEPNSFEVEFYgrhlHGYTLPVRNAAGDIYAGMIVVQDVTERREYE 1187
                                        55556666666666666666665431111677888888888888889999*******988 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.2   7.1e-13   7.5e-10       2     129 .]      35     170 ..      34     170 .. 0.76
   2 ?   -1.9   0.0       3.9   4.1e+03      22      65 ..     610     655 ..     609     665 .. 0.71

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 7.1e-13
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesldedsalar..ralssgevvsepsfaeed 76 
                                       +d+ll+++  +++ +l++e++a++++++dg  ++ +a ++ +   + + + ++ la+  r+l  +e+v+  ++++ +
  gi|336253272|ref|YP_004596379.1|  35 IDQLLDDATAAVAAALDLEYCAIVERRADGTGAVSRAESGLETGRVGATVPADRLAQfeRVLRADEPVVD-EWPADE 110
                                       699****************************9988888855554455555555555556********966.443322 PP

                             GAF_3  77 g.......lpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                       g       +      av +  ++ + Gvl+++ t+ raf+++dl++le +A+++a+a+e+
  gi|336253272|ref|YP_004596379.1| 111 GapapltdHGVVDSAAVRIGPRDDPWGVLCAYATDRRAFTEDDLAFLERVAAVLASAVEN 170
                                       21223222334555665555555************************************8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.9
                             GAF_3  22 galllldedgnklqvaagwdgkpalse..sldedsalarralssge 65 
                                       +a+++ d+d+ ++++aa+ +++   +    +++++   r+++s+g 
  gi|336253272|ref|YP_004596379.1| 610 AAIHEDDRDRVEAKIAAALEAGGEYEAeyRVRNADGELRWVVSRGR 655
                                       799999*******999999444433333455677777777777665 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.5   5.8e+03      35      57 ..     168     190 ..     155     191 .. 0.72
   2 ?   -3.2   0.2       8.4   8.9e+03      42      57 ..    1067    1082 ..    1057    1083 .. 0.78
   3 !   38.0   0.1   1.2e-12   1.3e-09       2      66 ..    1197    1263 ..    1196    1264 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.5
                                       SSCHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  35 eelkeyletiesearrldhlved 57 
                                        e ++  +++e+ +rr +++ ed
  gi|336253272|ref|YP_004596379.1| 168 VENADVRRDLERTERRFEAIFED 190
                                       56667777888888899998887 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.4
                                        HHHHHHHHHHHHHHHH CS
                             HisKA   42 etiesearrldhlved 57  
                                        +++e+++rr + lve+
  gi|336253272|ref|YP_004596379.1| 1067 RQLEESERRYRTLVEN 1082
                                        6788999999999997 PP

  == domain 3  score: 38.0 bits;  conditional E-value: 1.2e-12
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA    2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66  
                                        l+rf+   +H+L  PL  +  ++ +L+++  ++ +e+ +e+le ++++a+r++++++ lL++sr e+
  gi|336253272|ref|YP_004596379.1| 1197 LERFAYAASHDLQEPLRMVTSYLTLLENRyaDAFDEDGREFLEFAVDGAERMRDMIDGLLEYSRVET 1263
                                        789***********************7777*999******************************986 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   3.9   1.6e-12   1.7e-09       2     138 .]      33     169 ..      32     169 .. 0.83
   2 ?    6.2   0.1     0.011        12      19     118 ..     445     548 ..     438     557 .. 0.57
   3 ?   -1.5   0.1       2.7   2.9e+03      13      64 ..     597     652 ..     586     668 .. 0.56
   4 ?   -3.1   0.0       8.5   8.9e+03      25      43 ..     962     987 ..     952    1012 .. 0.62
   5 ?   -2.6   0.0       5.8   6.2e+03      20     110 ..    1083    1177 ..    1077    1200 .. 0.57

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.6e-12
                                       HHHHHHHHHHHHHHHH.SS..EEEEEEE-TTS-EEEE..EEEES-TTSTT-S-B--.-TTHHHHHHHHTS-EEES-G CS
                             GAF_2   2 adleelldlvldelve.lgaalgyillvdddgglrla..awgeaeeefgaaldrpl.geglvgealrtgrpvilndl 74 
                                       a +++lld ++ +++  l+ +++ i++  +dg   ++   +g +++++ga +  p  + + ++++lr  +pv+ + +
  gi|336253272|ref|YP_004596379.1|  33 AAIDQLLDDATAAVAAaLDLEYCAIVERRADGTGAVSraESGLETGRVGATV--PAdRLAQFERVLRADEPVVDEWP 107
                                       6799**********8879*****99997777763333447777777777777..442445699**********7778 PP

                                       GG-S-HHHHHHHHHTT--EEEEEE.-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  75 eedpdkkglpaghaglrsflavPl.isegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       ++     ++p+ ++g+  ++av +  + + + Gvl+ ya++++af+e+dl++Le +a+ +a a+e
  gi|336253272|ref|YP_004596379.1| 108 AD--EGAPAPLTDHGVVDSAAVRIgPR-DDPWGVLCAYATDRRAFTEDDLAFLERVAAVLASAVE 169
                                       88..6678889*************544.56*********************************97 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.011
                                       S...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B--.-TTHHHHHHHHTS-EEES-GGG-S-HHHHH.HHHHTT-- CS
                             GAF_2  19 g.aalgyillvdddgglrlaawgeaeeefgaaldrpl.geglvgealrtgrpvilndleedpdkkglp.aghaglrs 92 
                                       + +  g+++lvd  ++l++++ g++     +a+   + g+++ + + ++  + ++  +e+     ++  ++  + r+
  gi|336253272|ref|YP_004596379.1| 445 DhFPNGVVALVD--EDLTYRTVGGDSQYTADAPAEEIeGRSVSEVVSAELAAELVPRYEAALEGESSGfEATINGRT 519
                                       557788999988..555566444444444444433332333333333333555555555533334444245555555 PP

                                       E..EEEEE-T.TS---EEEEES......- CS
                             GAF_2  93 f..lavPlis.egrvvGvlnlyankppaf 118
                                       f   +vP+++ +g+v+++l+++ n  +++
  gi|336253272|ref|YP_004596379.1| 520 FdfRIVPIRDdDGEVFAALGMSQNITERY 548
                                       5899******99********965544445 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.7
                                       HHHHH.SS....EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B---TT.HHHHHHH CS
                             GAF_2  13 delve.lgaa..lgyillvdddgg.lrlaawgeaeeefgaaldrplgeg.lvgealr 64 
                                       ++++e + ++  l+ i+++d d+   ++aa+ ea++e  a+ + + ++g l  +++ 
  gi|336253272|ref|YP_004596379.1| 597 EAAREgVSSErfLAAIHEDDRDRVeAKIAAALEAGGEYEAEYRVRNADGeL-RWVVS 652
                                       677774445577888999775554433333334444444444334466633.44444 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 8.5
                                       EEEE-TTS-EEEE.......EEEES- CS
                             GAF_2  25 illvdddgglrla.......awgeae 43 
                                       +++vd+dg+++++         +e++
  gi|336253272|ref|YP_004596379.1| 962 VYVVDEDGYFTMVnetyaemLGYEPD 987
                                       35677889988875544443333333 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 5.8
                                        ..EEEEEEE-TTS-EEEE.EEEES-TTSTT-S-B---TTHHH....HHHHHTS-EEES-GGG-S-HHHHHHHHHT CS
                             GAF_2   20 aalgyillvdddgglrla.awgeaeeefgaaldrplgeglvg....ealrtgrpvilndleedpdkkglpaghag 89  
                                        +  g ++l d  ++l++  a g+  +e+g  + +++g+++ +    e +++ +p +++ le +p++   +  + +
  gi|336253272|ref|YP_004596379.1| 1083 FPDGAVGLFD--ENLEYTvAGGQLLDEVGVPPADRVGSSIYElypeELVEEVEPYFHAALEGEPNSFEVE-FYGR 1154
                                        5556666666..4433333666666666666666663333222232677777777777777777666665.5555 PP

                                        T--EEEEEE-T.TS---E.EEEE CS
                             GAF_2   90 lrsflavPlis.egrvvG.vlnl 110 
                                          ++  +P++   g +++ ++++
  gi|336253272|ref|YP_004596379.1| 1155 HLHGYTLPVRNaAGDIYAgMIVV 1177
                                        55566777766666666634444 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.4   1.7e-11   1.8e-08       2     133 .]      35     168 ..      34     168 .. 0.73
   2 ?   -2.1   0.0       5.3   5.6e+03      92     109 ..     524     542 ..     519     556 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.7e-11
                                       HHHHHHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECCEEEET.TSHHHH.........HHHHHSSSEEESTGG CS
                               GAF   2 leelldtvveelrellgadrvalylpdydGlhydipqasrwlfmkn.grgicg.........qvlatgqplvipdst 68 
                                       +++lld +++ ++ +l+++++a+   ++dG  + ++ a + l++   g +            +vl+ ++p+v + + 
  gi|336253272|ref|YP_004596379.1|  35 IDQLLDDATAAVAAALDLEYCAIVERRADGTGA-VSRAESGLETGRvGAT--VpadrlaqfeRVLRADEPVVDE-WP 107
                                       689********************9978899534.3333333222221222..0223444566788878888877.43 PP

                                       TSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHHH CS
                               GAF  69 pdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvaval 133
                                       +d+          l+ +g++ s++v +  +++ wG+l+++ +++  ft+++l++l+ +a+ +a a+
  gi|336253272|ref|YP_004596379.1| 108 ADEGAP-----APLTDHGVVDSAAVRIGPRDDPWGVLCAYATDRrAFTEDDLAFLERVAAVLASAV 168
                                       444433.....47889*************************65568*************9999875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.3
                                       EEEEEE.TTEEEEEEEEEE CS
                               GAF  92 vvPlvn.dgelwGllvlhn 109
                                        vP+++ dge++++l   +
  gi|336253272|ref|YP_004596379.1| 524 IVPIRDdDGEVFAALGMSQ 542
                                       59***77******998887 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0052       5.5      40      95 ..     481     534 ..     450     545 .. 0.80
   2 ?   -0.5   0.0       1.7   1.8e+03      70     106 .]     771     808 ..     754     808 .. 0.74
   3 ?    0.5   0.0      0.89   9.4e+02      12      64 ..     962    1015 ..     933    1029 .. 0.83
   4 !    8.6   0.0    0.0027       2.8      36     106 .]    1113    1181 ..    1103    1181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0052
                            PAS_10  40 Grpladihpkkavknveeviealrtgekdevevvvpkngkwvlvrylpyrdedgei 95 
                                       Gr+++++++ +   ++    ea  +ge+   e   + ng+++  r+ p+rd+dge+
  gi|336253272|ref|YP_004596379.1| 481 GRSVSEVVSAELAAELVPRYEAALEGESSGFE--ATINGRTFDFRIVPIRDDDGEV 534
                                       89999998887777777777777778776655..7899****************97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                            PAS_10  70 vevvvp.kngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                        e++    + ++v  + +p+r e ge+   v t++Dit
  gi|336253272|ref|YP_004596379.1| 771 FEIETGdGERRIVRAEGMPIRNERGEVVRGVATITDIT 808
                                       44444236789999999********9877788999996 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.89
                            PAS_10   12 ltflDdnlqirrFtpaakklfklipad.vGrpladihpkkavknveeviealrt 64  
                                        +  +D++  ++  ++++++++ + p+d vG++++ ++ ++++++v e+  +  +
  gi|336253272|ref|YP_004596379.1|  962 VYVVDEDGYFTMVNETYAEMLGYEPDDlVGEHVSLLVDDEILERVAELEATATS 1015
                                        567899999999999888777777777579999999999999999887766655 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0027
                            PAS_10   36 padvGrpladihpkkavknveeviealrtgekdevevvvpkngkwvlvrylpyrdedgeiaGvvetfvDit 106 
                                        ++ vG ++ ++ p++ v++ve  ++a  +ge +  e  v+  g++   ++lp+r   g+i   +++++D+t
  gi|336253272|ref|YP_004596379.1| 1113 ADRVGSSIYELYPEELVEEVEPYFHAALEGEPNSFE--VEFYGRHLHGYTLPVRNAAGDIYAGMIVVQDVT 1181
                                        5689***************************99777..5567****************9888889999986 PP

>> sCache_3_3  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.5   1.5e+03      75      91 ..     274     290 ..     253     299 .. 0.82
   2 !    9.9   0.0   0.00088      0.93      42      98 ..     487     545 ..     475     552 .. 0.83
   3 ?    3.6   0.0     0.082        87      52      93 ..    1135    1177 ..    1126    1187 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
                        sCache_3_3  75 taYePlkdadgkviGml 91 
                                       +a++P++d+dg+v  ++
  gi|336253272|ref|YP_004596379.1| 274 GAFRPVTDDDGDVTSIV 290
                                       699*********98776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00088
                        sCache_3_3  42 avGtklsee..vaeavlkkGetysgraeilgkkyltaYePlkdadgkviGmlfvGlpee 98 
                                       +v  +l++e  + +++  +Ge+   +a+i+g+ +    +P++d+dg+v  +l ++++++
  gi|336253272|ref|YP_004596379.1| 487 VVSAELAAElvPRYEAALEGESSGFEATINGRTFDFRIVPIRDDDGEVFAALGMSQNIT 545
                                       556666666777888889****999***********************99998877665 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.082
                        sCache_3_3   52 aeavlkkGetysgraeilgkkyltaYePlkdadgk.viGmlfv 93  
                                        +  +  +Ge+ s ++e  g++  ++  P+++a+g+   Gm++v
  gi|336253272|ref|YP_004596379.1| 1135 YFHAALEGEPNSFEVEFYGRHLHGYTLPVRNAAGDiYAGMIVV 1177
                                        5556679999999*********************966788876 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.9e-06    0.0062       3      91 ..    1307    1402 ..    1305    1411 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.9e-06
                       HATPase_c_5    3 dldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ek......kklesskskkee 66  
                                        d  l  ++ nlL NAi  + + +   + +r+ + ++ +  +i +e    g     ++      ++l+s   + e 
  gi|336253272|ref|YP_004596379.1| 1307 DSQLRQVFQNLLSNAITYSGDEP---PRVRIGADRRGDEWVIAVEDRGIGidpddQErvftifDRLHS-RADYEG 1377
                                        677899**********9888755...99******************9766666652234444555655.668999 PP

                       HATPase_c_5   67 hGiGlksireivkkykgnlsieaed 91  
                                         GiGl   ++iv++++g+++++ e 
  gi|336253272|ref|YP_004596379.1| 1378 TGIGLALCERIVERHGGEIWVDSEP 1402
                                        ********************99876 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.2e-05     0.034      31     111 ..    1309    1391 ..    1277    1409 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                       HATPase_c_2   31 eirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep......keslkegG 99  
                                        ++r + + +++Na+++  +e p  +v++ +++++++ ++ v+D+G g dp ++++             ++ +  G
  gi|336253272|ref|YP_004596379.1| 1309 QLRQVFQNLLSNAITYSGDEPP--RVRIGADRRGDEWVIAVEDRGIGIDPDDQERVFT--IfdrlhsRADYEGTG 1379
                                        56667777899******99877..***********************99987654332..25577778999999* PP

                       HATPase_c_2  100 rGlalikglvDe 111 
                                        +Glal +++v+ 
  gi|336253272|ref|YP_004596379.1| 1380 IGLALCERIVER 1391
                                        *****9999875 PP

>> PAS_6  YheO-like PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0     0.001       1.1      52     108 ..     491     546 ..     444     552 .. 0.72
   2 ?    1.2   0.0      0.31   3.3e+02      52     108 ..     753     809 ..     745     815 .. 0.75
   3 ?   -1.6   0.0       2.3   2.4e+03      78     109 ..    1152    1183 ..    1136    1188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.001
                             PAS_6  52 dlvlellkeeeeeeedvlvnyktktkdgkilksstifirdekgkliglLCiNldlsk 108
                                       +l+ el+ + e+  e    + ++ t +g+++    + ird++g+++++L++  ++++
  gi|336253272|ref|YP_004596379.1| 491 ELAAELVPRYEAALEGES-SGFEATINGRTFDFRIVPIRDDDGEVFAALGMSQNITE 546
                                       444555555555544444.34455899***************************997 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.31
                             PAS_6  52 dlvlellkeeeeeeedvlvnyktktkdgkilksstifirdekgkliglLCiNldlsk 108
                                       +l+l ++ + ee +e ++ + +t   + +i++   + ir+e+g+++      +d+++
  gi|336253272|ref|YP_004596379.1| 753 ELTLARVLDGEEVTEPDVFEIETGDGERRIVRAEGMPIRNERGEVVRGVATITDITE 809
                                       5555555555555555666899999999****************9987777777765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.3
                             PAS_6   78 dgkilksstifirdekgkliglLCiNldlskl 109 
                                         g+ l+  t+ +r++ g++ + + +  d+++ 
  gi|336253272|ref|YP_004596379.1| 1152 YGRHLHGYTLPVRNAAGDIYAGMIVVQDVTER 1183
                                        5899**************99888888888875 PP

>> dCache_3  Double sensory domain of two-component sensor kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0032       3.4     188     237 ..     500     546 ..     473     548 .. 0.83
   2 ?    1.8   0.0      0.14   1.5e+02      34      78 ..     603     649 ..     597     668 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0032
                          dCache_3 188 lkelkeqqtlgklfreleidgrsylvvllpLkdysgeligvlvigldvta 237
                                       +++ +e++   +++ e +i+gr + +  +p++d +ge  + l++ +++t+
  gi|336253272|ref|YP_004596379.1| 500 YEAALEGE---SSGFEATINGRTFDFRIVPIRDDDGEVFAALGMSQNITE 546
                                       44555555...5899********************************997 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.14
                          dCache_3  34 asspgvaeaisegdreqlerlldsiwndlg..leqivlldadgtvil 78 
                                       +ss+++ +ai e+dr+++e +++ + +  g  +++  + +adg++++
  gi|336253272|ref|YP_004596379.1| 603 VSSERFLAAIHEDDRDRVEAKIAAALEAGGeyEAEYRVRNADGELRW 649
                                       789999****************9988666677666677777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.84u 0.25s 00:00:01.08 Elapsed: 00:00:00.38
# Mc/sec: 11275.53
//
Query:       gi|336253273|ref|YP_004596380.1|  [L=210]
Description: peptidylprolyl isomerase [Halopiger xanaduensis SH-6]
Scores for 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-50  169.1   0.0    1.1e-49  168.8   0.0    1.1  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


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 !  168.8   0.0   6.1e-54   1.1e-49       2     158 .]      44     207 ..      43     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: 168.8 bits;  conditional E-value: 6.1e-54
                     Pro_isomerase   2 vdietsskGrivieLfadkaPktvenFlklvkeg.................fYdgttFhRvikgfmvqgGdptgkts 61 
                                       ++++ts  G+i +eL++++aP tv+nF+ l++ g                  Yd + FhRvi+gfm+q+Gdptg+++
  gi|336253273|ref|YP_004596380.1|  44 ATLHTS-TGDIDVELYGERAPRTVANFVGLAT-GeqpwtdpetgeelegepLYDDVLFHRVIEGFMIQTGDPTGTGR 118
                                       578996.************************6.446666777777777777***********************965 PP

                     Pro_isomerase  62 ageqekkggesiraipdEitsklkh.krGalamartgkepnsagsqFfItlkeaphldgkytvFGkVveGmdvveki 137
                                              gg   ++++dE++++l+h ++G+l+ma++g  p+++gsqFfItl+++phldg++tvFG+V++G+d+v++i
  gi|336253273|ref|YP_004596380.1| 119 -------GG-PGYRFDDEFHEELRHdDAGVLSMANSG--PDTNGSQFFITLAPQPHLDGRHTVFGTVISGLDIVREI 185
                                       .......33.24689*****99999899********8..8************************************* PP

                     Pro_isomerase 138 ekvetde.erpkknvkivsaev 158
                                        +vetd+ +rp+++v+++s++v
  gi|336253273|ref|YP_004596380.1| 186 GSVETDGnDRPVEDVRLESVTV 207
                                       *****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1640.96
//
Query:       gi|336253274|ref|YP_004596381.1|  [L=172]
Description: peptidylprolyl isomerase [Halopiger xanaduensis SH-6]
Scores for complete 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-49  168.2   0.0    1.8e-49  168.1   0.0    1.0  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


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 !  168.1   0.0   9.9e-54   1.8e-49       2     157 ..       6     168 ..       5     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 168.1 bits;  conditional E-value: 9.9e-54
                     Pro_isomerase   2 vdietsskGrivieLfadkaPktvenFlklvkeg.................fYdgttFhRvikgfmvqgGdptgkts 61 
                                       ++++ts kG+i +eL++++aP tvenF+ l++ g                  Yd + FhR+i+gfm+q+Gdptg+++
  gi|336253274|ref|YP_004596381.1|   6 ATLHTS-KGDIDVELYDERAPRTVENFVGLAT-GertwtdpetgeevdgepLYDDVLFHRIIEGFMIQTGDPTGTGR 80 
                                       578996.************************6.446677777777777777***********************966 PP

                     Pro_isomerase  62 ageqekkggesiraipdEitsklkh.krGalamartgkepnsagsqFfItlkeaphldgkytvFGkVveGmdvveki 137
                                              gg   ++++dE++++l+h ++G+l+ma++g  pn++gsqFfItl+++phld++++vFG+V++Gmdvv++i
  gi|336253274|ref|YP_004596381.1|  81 -------GG-PGYQFDDEFHDELRHdDAGVLSMANSG--PNTNGSQFFITLDAQPHLDDRHAVFGTVTDGMDVVREI 147
                                       .......33.23689*****99999899********8..8************************************* PP

                     Pro_isomerase 138 ekvetde.erpkknvkivsae 157
                                        +v+td+ +rp+++v ++s++
  gi|336253274|ref|YP_004596381.1| 148 GSVSTDAnDRPQEEVLLESVT 168
                                       **************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       168  (0.00937029); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); 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: 0.39u 0.19s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1415.00
//
Query:       gi|336253275|ref|YP_004596382.1|  [L=329]
Description: succinylglutamate desuccinylase/aspartoacylase [Halopiger xanaduensis SH-6]
Scores for 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-34  117.2   0.0    8.3e-34  117.0   0.0    1.0  1  AstE_AspA      Succinylglutamate desuccinylase / Aspartoacyla
  ------ inclusion threshold ------
       0.18   11.5   0.0       0.48   10.2   0.0    1.6  1  Peptidase_M14  Zinc carboxypeptidase


Domain annotation for each model (and alignments):
>> AstE_AspA  Succinylglutamate desuccinylase / Aspartoacylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   0.0   9.2e-38   8.3e-34       2     289 ..      39     324 ..      38     326 .. 0.88

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 9.2e-38
                                       S-EEEEEE-SSTT-HHHHHHHHHHHHHHHCCCESCCEEEEEESSHHHHHCTSSSSS....TT-S-CTTTTTCCCCCS CS
                         AstE_AspA   2 gpkvlisAGvHGnElaGvellrqllkqleeadilgeitlvplaNppAiaagsRyip....idredLNRaFpgrslgr 74 
                                        p+++++A+ HG E++G+e+lr++  ++  ++++g++++vp+aNp+ + + s + p      + ++NR++pg+++g 
  gi|336253275|ref|YP_004596382.1|  39 EPTLYVQAAQHGREINGTEVLRRFHDRIPLESLSGTVVAVPVANPLTFDRVSYTTPeildSVNPNMNRVWPGDADG- 114
                                       599*************************************************888887665568************. PP

                                       STCHHHHHHHHHHHHHHHCHCTCCCGCEEEEEEEESSTBCCSSEEEE---SSHHHHHHHHHHTTTSEEEEEESS--S CS
                         AstE_AspA  75 sldealrateaerladalfaaalpeadivlDLHtgtrglkhllfaeadiaeaqlqslallkalglpavllldekesa 151
                                               t  +r+a +l++ a  +ad ++DLHtg   +  +++++ +  +++    +l++a+g +++l+ + +e+a
  gi|336253275|ref|YP_004596382.1| 115 --------TLHQRMAARLWEYA-GRADAIVDLHTGSPDM--YPHVVFREGDERS--RRLAEAFGSDLLLGEQADEDA 178
                                       ........***********888.7***********9999..6666666666655..899**********66666666 PP

                                       ..........SHHHHHHHHCTSEEEEEEEES.TTTTCCHHCCHHHHHHHHHHHHCTCHTT-SCC.CEEEEEEEEEEG CS
                         AstE_AspA 152 ..........gfletaaeelgalaftlElGgagrlgaedisrtakgvlnvlahigvvagqeavepaklyrvlrelde 218
                                                 g+l+ aa + g++++t+El+    +  + +++ ++g+l vl+++ ++ g++       ++++   ++
  gi|336253275|ref|YP_004596382.1| 179 ddewhrrnfkGKLRVAASNEGIPSITPELAHNKQILDDVVENGVEGLLDVLRYLDLLPGDV--P-DREREQTLARNH 252
                                       ************************************************************2..2.345555566667 PP

                                       GSCCCSSCSEEECCC..CSTTTTETCTEEEETTEEEEECTSTEEEEESSSSEEEESCCTSCCTTTTEEEEEEE CS
                         AstE_AspA 219 prdiraeeaGlvefk..vklgddveagellakalvldslggekvelrapqdgvivfineaalvekgaalvkva 289
                                         +++a ++Gl+ ++  +++gd+v ag+ l +++  +++ +  +  +a++dg++ +  ++a v  g+ l+ va
  gi|336253275|ref|YP_004596382.1| 253 LGQVNAADSGLFRPQpsLEVGDRVTAGTPLGTVYHPTTY-EPLQDAVADRDGILYALTREATVVAGDQLASVA 324
                                       777888888***87644899**********888888888.55559999********************99886 PP

>> Peptidase_M14  Zinc carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   5.3e-05      0.48      41      69 ..      34      62 ..       7      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.3e-05
                                      STTST-CEEEEEE-SSTT-HHHHHHHHHH CS
                     Peptidase_M14 41 eaeegkpvvlidggiHarEwigsalllyl 69
                                      +a+e +p+  +++ +H+rE+ g+++l ++
  gi|336253275|ref|YP_004596382.1| 34 SANESEPTLYVQAAQHGREINGTEVLRRF 62
                                      7999********************99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2438.02
//
Query:       gi|336253276|ref|YP_004596383.1|  [L=136]
Description: hypothetical protein Halxa_1876 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.001   19.3   5.1     0.0015   18.7   5.1    1.3  1  DUF3006   Protein of unknown function (DUF3006)
  ------ inclusion threshold ------
      0.045   12.8   0.5      0.057   12.5   0.5    1.1  1  S-layer   S-layer protein


Domain annotation for each model (and alignments):
>> DUF3006  Protein of unknown function (DUF3006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   5.1   1.7e-07    0.0015       1      44 [.      72     121 ..      72     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-07
                           DUF3006   1 aviDRfEg.dlAVleled.getid...iprsdLpegakeGdvLeie.dd.e 44 
                                       av+DR+ + +++Vl+le+ +e +d   ++++++ + + eGd L ++ +d e
  gi|336253276|ref|YP_004596383.1|  72 AVVDRIVDgEHVVLLLEKdDEPVDqlvVSVDEFDA-IAEGDLLLVDvEDgE 121
                                       79******89********777799999******99.*********976634 PP

>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   6.3e-06     0.057     135     160 ..      78     103 ..      66     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.3e-06
                           S-layer 135 vdgdkvwleLtkdgeevdskvisssk 160
                                       vdg++v+l L+kd+e vd+ v+s+++
  gi|336253276|ref|YP_004596383.1|  78 VDGEHVVLLLEKDDEPVDQLVVSVDE 103
                                       8**********************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1097.19
//
Query:       gi|336253277|ref|YP_004596384.1|  [L=662]
Description: Kinetochore-Ndc80 complex subunit Spc25 [Halopiger xanaduensis SH-6]
Scores for 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-09   37.4  26.3    3.7e-09   37.4  26.3    5.6  2  AAA_23           AAA domain
    9.4e-06   24.7  81.0     0.0022   17.0  23.2    4.3  4  Spc7             Spc7 kinetochore protein
    0.00049   19.5  64.8      0.026   13.9  22.3    3.8  3  GAS              Growth-arrest specific micro-tubule binding
     0.0028   18.1  27.1        2.1    8.9   1.2    6.3  5  NPV_P10          Nucleopolyhedrovirus P10 protein
  ------ inclusion threshold ------
      0.013   13.0  60.4      0.054   11.0  29.4    2.1  2  DUF3584          Protein of unknown function (DUF3584)
      0.015   15.6  56.1        4.1    7.7  11.0    6.2  4  DUF5082          Domain of unknown function (DUF5082)
      0.018   15.1  12.8      0.018   15.1  12.8    5.8  3  DHR10            Designed helical repeat protein 10 domain
      0.022   13.9  58.8      0.027   13.6  15.8    3.9  3  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.055   12.8  56.4       0.38   10.1   4.7    3.9  4  DUF4407          Domain of unknown function (DUF4407)
       0.15   12.3  21.8        2.9    8.2   0.0    7.1  6  WXG100           Proteins of 100 residues with WXG
       0.17   12.3   0.2       0.17   12.3   0.2    4.2  3  MitMem_reg       Maintenance of mitochondrial structure and f
       0.18   11.9  20.9        3.4    7.7   0.9    5.0  4  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.32   10.2  50.8       0.22   10.8  18.6    2.5  2  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
       0.42   10.6  36.9      0.042   13.9   7.9    5.0  4  Laminin_II       Laminin Domain II
       0.79    9.7  54.1       0.23   11.5   3.2    5.4  5  FlxA             FlxA-like protein
       0.98    9.4  92.6        4.5    7.3  16.6    5.1  4  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
        1.3    8.3  43.5      0.022   14.0   7.8    4.2  4  HemX             HemX, putative uroporphyrinogen-III C-methyl
        1.3    9.0  43.6        1.8    8.6   7.8    5.1  5  DUF1664          Protein of unknown function (DUF1664)
        2.1    8.9  61.7        2.8    8.5   4.3    6.1  6  Spectrin         Spectrin repeat
        2.8    7.7  57.6        4.3    7.0  17.2    3.8  3  DUF4201          Domain of unknown function (DUF4201)
        2.9    8.6  74.8        1.1   10.0  19.3    6.4  6  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
          3    6.1  64.1        2.3    6.5  22.1    2.4  2  MAD              Mitotic checkpoint protein
          3    8.0  29.0      0.041   14.0   2.8    4.4  4  COG5             Golgi transport complex subunit 5
        3.5    7.7  80.7        3.8    7.6  20.3    5.4  5  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        3.7    7.5  61.3        0.2   11.6   3.7    9.2 11  Prefoldin        Prefoldin subunit
          5    6.4  29.9       0.72    9.1   7.2    3.3  3  YPEB             YpeB sporulation
        5.7    7.2  66.8       0.32   11.2   7.2    5.7  4  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        8.3    6.6  51.8        1.8    8.7   5.7    5.8  6  Med9             RNA polymerase II transcription mediator com


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 !   37.4  26.3   5.8e-12   3.7e-09       5     194 ..      16     228 ..      13     284 .. 0.59
   2 ?    0.2   0.1       1.5   9.4e+02      58     139 ..     515     599 ..     509     640 .. 0.59

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 5.8e-12
                            AAA_23   5 enfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkay.veltfe 80 
                                       +n++ ++++++++++g+t++ G+N +  T++l+A+  aL+ge++ l+     ++e+++ve+e +g++ +  +++   
  gi|336253277|ref|YP_004596384.1|  16 RNIGGINETTVELESGVTVLAGQNATNRTSLLQAFMAALGGESASLKA----DAEEGEVELELDGETYTRqLRRA-- 86 
                                       69***************************************9988877....57799999999877654445555.. PP

                            AAA_23  81 nkdgry............................trsiererelskk..kgkttkkaklelleideleqfisellgs 127
                                         +++                                ++ +  l++       t++ + e+++ ++ +++is++l++
  gi|336253277|ref|YP_004596384.1|  87 --GNTVvtegdpylddpelaelfafllesnparrA--VTTQDDLREIilRPIDTDEIEAEITRLTAEKDEISDELDR 159
                                       ..232234445668888888888777755555331..2222222222002222233344455555555555555554 PP

                            AAA_23 128 kki...ilnlilflgqer.....feefelkdkkerleelekeleeledekkllekleqekekekeleeleeelee 194
                                        ++    l+ +  +  +      +++ el++ ke++e++e+e +++++e ++le++       +el e ++ele+
  gi|336253277|ref|YP_004596384.1| 160 LESlksDLPELERQRTDIetqieEKRAELEEVKEAIEAAEDESDDQQAESDELEEK------LEELRERRSELED 228
                                       44433322222222222222222333333444443333333333333333333333......3333333333322 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.5
                            AAA_23  58 feksdveiesegkvkayvelt.fenkdgrytrsiererelskkkgkttkka..klellei....deleqfisellgs 127
                                       +e++ ve ++e + ++++e+  +en+d+++   ier  ++ ++  +++ ++  +l +++     ++ e++i++l +s
  gi|336253277|ref|YP_004596384.1| 515 IEREAVESFNE-HMDTVLEILeYENIDRIW---IERVGQTVREGRRKVEQTafDLHIVRSteegSTYEDTINHLSES 587
                                       55566665554.777886665699999988...55545544444444444422222333344468888888888777 PP

                            AAA_23 128 kkiilnlilflg 139
                                       + +   li+ l+
  gi|336253277|ref|YP_004596384.1| 588 EREVTGLIFALA 599
                                       777666665554 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0  18.8   2.8e-05     0.018     163     247 ..     137     227 ..     134     229 .. 0.81
   2 !    6.9  13.8    0.0038       2.4     174     261 ..     207     300 ..     203     313 .. 0.46
   3 !   17.0  23.2   3.4e-06    0.0022     154     251 ..     345     441 ..     340     446 .. 0.93
   4 !    7.7   9.3    0.0022       1.4     215     296 ..     453     533 ..     445     545 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                              Spc7 163 eeldellpeleeekaeleeeleklqeaaeeles.....id.keeLeelreelaelkaeieekkkelaelqeqleele 233
                                       +e+++   +l++ek+e+++el++l++ + +l +      d ++++ee r el+e+k+ ie+ ++e ++ q++ +ele
  gi|336253277|ref|YP_004596384.1| 137 DEIEAEITRLTAEKDEISDELDRLESLKSDLPElerqrTDiETQIEEKRAELEEVKEAIEAAEDESDDQQAESDELE 213
                                       45666677888888888888888888666666555555677899999999999999999999999999999999999 PP

                              Spc7 234 ekieelkeqksele 247
                                       ek+eel+e++sele
  gi|336253277|ref|YP_004596384.1| 214 EKLEELRERRSELE 227
                                       99999999999986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0038
                              Spc7 174 eekaeleeeleklqeaaeeles......idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqks 244
                                       +e +elee+le+l+e++ ele+       ++e+L++lree ++++ae +e+ +  a+ qe ++e  ++++  +++++
  gi|336253277|ref|YP_004596384.1| 207 AESDELEEKLEELRERRSELEDvrfdleTERESLAALREEREDIEAERDELPEADATDQESIDEEIDRLQRQSQSID 283
                                       44555555555555555555554444333344444444444444444444444444444444444444444444444 PP

                              Spc7 245 eleeeiaeaervleeck 261
                                        + +++++  ++ ee  
  gi|336253277|ref|YP_004596384.1| 284 GVVSQLQSIVQFNEEML 300
                                       44444444444444444 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 3.4e-06
                              Spc7 154 dkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqle 230
                                       +++++e+  e l +l +e  +e++e+ee++e+l+++++e+e+ ++++ e lre+l+++ +eie+++++l+el+eq e
  gi|336253277|ref|YP_004596384.1| 345 QRSEIEETIERLRSLQEEKLSERDEIEERIESLRAERREIEQTERKR-ERLRERLTDVRNEIERREDRLEELTEQQE 420
                                       5678999**********************************977655.9**************************** PP

                              Spc7 231 eleekieelkeqkseleeeia 251
                                       +le++i++l+++ +ele+e +
  gi|336253277|ref|YP_004596384.1| 421 NLESEIDDLEDEAAELEAEAE 441
                                       ****************99865 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0022
                              Spc7 215 ieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivslsg 291
                                       + e++++ +el+  l +le ++e+++e+++e+e++++ +e+ le++++  ++e++ l+++ +++e++   ++ +  +
  gi|336253277|ref|YP_004596384.1| 453 LLELNRRANELEFSLGRLERELETTTEEIEEIESALEDQEE-LEQRREEIRDELEDLRTRIDRIEREAVESFNEHMD 528
                                       44556666677777777777777777777777777764443.44556666667777777777777766666666666 PP

                              Spc7 292 stlel 296
                                       ++le+
  gi|336253277|ref|YP_004596384.1| 529 TVLEI 533
                                       66555 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 !   13.9  22.3     4e-05     0.026      21     133 ..     153     265 ..     150     318 .. 0.87
   2 !   10.0  19.8   0.00062       0.4      37     128 ..     348     439 ..     343     443 .. 0.92
   3 !    7.1   6.2    0.0047         3      51     128 ..     462     525 ..     449     561 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
                               GAS  21 trnNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkel 97 
                                       +++ L+  +slK+++ el+++ +  e +++e  +e ++ ke +++ae e +  +++  + e++ ++l++ +++l+++
  gi|336253277|ref|YP_004596384.1| 153 ISDELDRLESLKSDLPELERQRTDIETQIEEKRAELEEVKEAIEAAEDESDDQQAESDELEEKLEELRERRSELEDV 229
                                       678899999*******************************************9999999999999999999999999 PP

                               GAS  98 ekelkdlkwehevleqrfekvekerdelykkfeaai 133
                                          l++ +++   l+++ e +e+erdel +   +  
  gi|336253277|ref|YP_004596384.1| 230 RFDLETERESLAALREEREDIEAERDELPEADATDQ 265
                                       99999999999999************9988765554 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00062
                               GAS  37 elkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleq 113
                                       e+++  er + + +e  +e  +++e ++ +++e+ e ++  ++ e+ +++l+ +++++++ e+ l++l++++e+le 
  gi|336253277|ref|YP_004596384.1| 348 EIEETIERLRSLQEEKLSERDEIEERIESLRAERREIEQTERKRERLRERLTDVRNEIERREDRLEELTEQQENLES 424
                                       667777888888899999*********************************************************** PP

                               GAS 114 rfekvekerdelykk 128
                                       +++ +e+e  el+++
  gi|336253277|ref|YP_004596384.1| 425 EIDDLEDEAAELEAE 439
                                       ***********9986 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0047
                               GAS  51 eisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelyk 127
                                       e++    rl+ +L++ +ee+ee + +l+++e+  q+ ++++ +l++l   + +++ e                e  +
  gi|336253277|ref|YP_004596384.1| 462 ELEFSLGRLERELETTTEEIEEIESALEDQEELEQRREEIRDELEDLRTRIDRIERE--------------AVESFN 524
                                       444444455556666666666666666666666666666666666665555555554..............444333 PP

                               GAS 128 k 128
                                       +
  gi|336253277|ref|YP_004596384.1| 525 E 525
                                       3 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   4.5      0.18   1.1e+02      18      60 ..     141     183 ..     129     219 .. 0.61
   2 ?    3.9   0.4      0.11        74      12      47 ..     194     229 ..     185     259 .. 0.49
   3 ?    5.4   0.5     0.038        25      34      66 ..     262     294 ..     255     309 .. 0.69
   4 !    8.9   1.2    0.0032       2.1      10      63 ..     381     431 ..     346     443 .. 0.85
   5 !    8.6   0.5    0.0041       2.6      23      62 ..     477     516 ..     467     522 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.18
                           NPV_P10  18 dkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                         ++ l ++ d+++++l  ++ l++ L ++  q +++et++e+
  gi|336253277|ref|YP_004596384.1| 141 AEITRLTAEKDEISDELDRLESLKSDLPELERQRTDIETQIEE 183
                                       4555555555555555555555555555555555555555443 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.11
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaq 47 
                                       +i+a +d  d  q++ d+++e+l+++ e  ++L++ 
  gi|336253277|ref|YP_004596384.1| 194 AIEAAEDESDDQQAESDELEEKLEELRERRSELEDV 229
                                       444444444444444444444444433333333333 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.038
                           NPV_P10  34 lpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                         d + + e++d+++ q ++++  v++ q+i  
  gi|336253277|ref|YP_004596384.1| 262 ATDQESIDEEIDRLQRQSQSIDGVVSQLQSIVQ 294
                                       556667888888888888888888888888865 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0032
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       r +i++++ k + l ++++dv+++++     +++L+++++q ++le+++++ +d
  gi|336253277|ref|YP_004596384.1| 381 RREIEQTERKRERLRERLTDVRNEIER---REDRLEELTEQQENLESEIDDLED 431
                                       678888888999999999999987776...569999999999999998888776 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0041
                           NPV_P10  23 lqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                         ++++++++ l+d +el+++ +++ ++L++l t ++ I+
  gi|336253277|ref|YP_004596384.1| 477 TTEEIEEIESALEDQEELEQRREEIRDELEDLRTRIDRIE 516
                                       567899*******************************997 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  23.0   0.00073      0.47     361     520 ..     137     301 ..     120     318 .. 0.62
   2 ?   11.0  29.4   8.4e-05     0.054     249     435 ..     348     530 ..     326     566 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00073
                           DUF3584 361 eeleeeldaltekhqdvqekydrrkqkike..eleeeleklkerleaireekdrlkaaieealealesql..rkqle 433
                                        e+e+e+ +lt +  ++  ++dr+++  ++  ele++  +++ + e+ r e +++k+aie+a ++   q+   ++le
  gi|336253277|ref|YP_004596384.1| 137 DEIEAEITRLTAEKDEISDELDRLESLKSDlpELERQRTDIETQIEEKRAELEEVKEAIEAAEDESDDQQaeSDELE 213
                                       56777788888888888888887777655423344444444444444444444445555544444333331134567 PP

                           DUF3584 434 aqkeelneeekelesrlselklrldsatateEeleqieeadealekaqee.lekaeaevealqaeeeqlrkkrdead 509
                                       ++ eel+e++ ele     l++ ++s  a  Ee e+ie++ ++l +a+++ +e+  +e  +lq++ + ++    + +
  gi|336253277|ref|YP_004596384.1| 214 EKLEELRERRSELEDVRFDLETERESLAALREEREDIEAERDELPEADATdQESIDEEIDRLQRQSQSIDGVVSQLQ 290
                                       77777777777777777777777777778888888888777777777765244445556677777777776666666 PP

                           DUF3584 510 ealqkaerrle 520
                                        + q  e+ le
  gi|336253277|ref|YP_004596384.1| 291 SIVQFNEEMLE 301
                                       55555555555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.4e-05
                           DUF3584 249 klqeefeqleslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeaidelnqelsaakaklaake 325
                                       +++e +e l sl ++  +   e+++ +e l+ ++ e+++  ++++++lr+   ++ ++i++++ +l+++ ++ ++ e
  gi|336253277|ref|YP_004596384.1| 348 EIEETIERLRSLQEEKLSERDEIEERIESLRAERREIEQ-TERKRERLRERLTDVRNEIERREDRLEELTEQQENLE 423
                                       344444444444444444444444444444444444432.2333344444444444444444444444444444444 PP

                           DUF3584 326 selealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkike..eleeeleklk 400
                                       se++ le+++      ++e  ++  d ++  +++l el+++ + l+ +   +++++++   +i+e  +  e++e+l+
  gi|336253277|ref|YP_004596384.1| 424 SEIDDLEDEAA-----ELEAEAEPDDDEDGDEESLLELNRRANELEFSLGRLERELETTTEEIEEieSALEDQEELE 495
                                       44444444432.....3333333444445555666667777777777777777777776666664224556666677 PP

                           DUF3584 401 erleaireekdrlkaaieealealesqlrkqleaq 435
                                       +r+e+ir+e + l+++i+    +  +++++ ++  
  gi|336253277|ref|YP_004596384.1| 496 QRREEIRDELEDLRTRIDRIEREAVESFNEHMDTV 530
                                       77777777777777776666655555555555443 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   2.9     0.038        24      21      50 ..     138     167 ..     132     190 .. 0.61
   2 ?    7.7  11.0    0.0064       4.1       2     116 ..     192     291 ..     191     296 .. 0.69
   3 ?    3.5   3.9      0.13        83       4      39 ..     352     387 ..     349     389 .. 0.90
   4 ?    6.6  14.1     0.014       9.3       3     121 ..     389     515 ..     387     517 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.038
                           DUF5082  21 aleekIerLkeaktklsdekeslkqkkkkl 50 
                                        +e  I+rL + k+++sde  +l++ k++l
  gi|336253277|ref|YP_004596384.1| 138 EIEAEITRLTAEKDEISDELDRLESLKSDL 167
                                       445555555555555555555555555554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0064
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnless 78 
                                       k+ i++++ + ++ ++e + leek+e+L+e +++l+d+   l++++++l+    + e          + +r +l  +
  gi|336253277|ref|YP_004596384.1| 192 KEAIEAAEDESDDQQAESDELEEKLEELRERRSELEDVRFDLETERESLAALREERED--------IEAERDELP-E 259
                                       56799999*****************************999999999988877655532........222222222.2 PP

                           DUF5082  79 yqtyvdkldelidaieeEIerLenqiseaqgvldtlqs 116
                                        ++     d  + +i+eEI rL+ q ++  gv+++lqs
  gi|336253277|ref|YP_004596384.1| 260 ADAT----D--QESIDEEIDRLQRQSQSIDGVVSQLQS 291
                                       2222....2..245666666666666666666666665 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.13
                           DUF5082   4 kisklqaqiaelrseiaaleekIerLkeaktklsde 39 
                                        i++l++ ++e+ se++ +ee Ie L++ +++++++
  gi|336253277|ref|YP_004596384.1| 352 TIERLRSLQEEKLSERDEIEERIESLRAERREIEQT 387
                                       6999***********************999998865 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.014
                           DUF5082   3 tkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnsse.......sWkGk.eennydgi 71 
                                       +k+++l+++  + r+ei+  e+ +e+L e  + l++e   l+++  +le  +  ++       s+    +++n+ ++
  gi|336253277|ref|YP_004596384.1| 389 RKRERLRERLTDVRNEIERREDRLEELTEQQENLESEIDDLEDEAAELEAEAEPDDdedgdeeSLLELnRRANELEF 465
                                       799*********************************************98888777566777766555466666666 PP

                           DUF5082  72 rs.nlessyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnsl 121
                                           le + +t  ++++e+++a+e+  e+Le+ ++e    l+ l + ++ +
  gi|336253277|ref|YP_004596384.1| 466 SLgRLERELETTTEEIEEIESALEDQ-EELEQRREEIRDELEDLRTRIDRI 515
                                       668********************976.889999999998888888888765 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 ?   15.1  12.8   2.8e-05     0.018      43     109 ..     137     203 ..     136     207 .. 0.95
   2 ?    0.2  29.8       1.1   7.2e+02       7     102 ..     345     441 ..     342     447 .. 0.92
   3 ?    9.6  13.3    0.0014       0.9       7      78 ..     449     517 ..     443     520 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.8e-05
                             DHR10  43 eeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaak 109
                                       +eieae+ +l  +k+++++  d+le+++ +l eler+++ ++ q+e ++ +le ++e  e+ +++++
  gi|336253277|ref|YP_004596384.1| 137 DEIEAEITRLTAEKDEISDELDRLESLKSDLPELERQRTDIETQIEEKRAELEEVKEAIEAAEDESD 203
                                       79********************************************************999888775 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                             DHR10   7 ekeelaelErkarelqa.kidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeer 82 
                                       +++e++e+ ++ r lq+ k+   +++e+ ++s+ +   eie+  +k e  +++l++ r+++e +e +l+el+ ++e 
  gi|336253277|ref|YP_004596384.1| 345 QRSEIEETIERLRSLQEeKLSERDEIEERIESLRAERREIEQTERKRERLRERLTDVRNEIERREDRLEELTEQQEN 421
                                       57899999999999995489999****************************************************** PP

                             DHR10  83 lqrqlenaeeklerlreqae 102
                                       l+  ++  e++ + l+ +ae
  gi|336253277|ref|YP_004596384.1| 422 LESEIDDLEDEAAELEAEAE 441
                                       ***********999999887 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0014
                             DHR10   7 ekeelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielreler 78 
                                       + e+l el r+a+el+ +   l+++e++l+ +++ +eeie+ l+ +ee +++ +e rd+le+++++   +er
  gi|336253277|ref|YP_004596384.1| 449 DEESLLELNRRANELEFS---LGRLERELETTTEEIEEIESALEDQEELEQRREEIRDELEDLRTRIDRIER 517
                                       678888999999999885...7999*************************************9998887776 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 ?    6.0  20.9    0.0087       5.6      22     150 ..     151     282 ..     134     291 .. 0.66
   2 ?   13.6  15.8   4.2e-05     0.027      13     103 ..     337     432 ..     332     441 .. 0.72
   3 ?    3.3   6.6     0.058        37      23      82 ..     459     518 ..     449     587 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0087
                             Atg14  22 erlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdk...lsqlkk 95 
                                       + + ++  rl +lks+  +l+++ ++++++ e   +++++++  k+++e    ++ d++++  el++k   l+++++
  gi|336253277|ref|YP_004596384.1| 151 DEISDELDRLESLKSDLPELERQRTDIETQIE---EKRAELEEVKEAIEAAEDESDDQQAESDELEEKleeLRERRS 224
                                       45667777777888888888877777777777...444444444444444444444444444444444000444556 PP

                             Atg14  96 eieekkkklaklsdklk...kRrsdleslqneleerrkkqiaklqdaikrieqklssl 150
                                       e+e+ +  l++ +++l+   + r+d+e+ ++el e+ ++  +++ ++i r +++ +s+
  gi|336253277|ref|YP_004596384.1| 225 ELEDVRFDLETERESLAalrEEREDIEAERDELPEADATDQESIDEEIDRLQRQSQSI 282
                                       6777788888888888877777888999999999988888888888888888877766 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.2e-05
                             Atg14  13 CesC...lrngperlyelrerlaklksekeslkkkiekalegke....eaeqledkiknkkakleelksliadlrer 82 
                                       C +C   +++  + ++e  erl++l++ek s + +ie+ +e+ +    e eq+e+k ++++++l + +++i++ ++r
  gi|336253277|ref|YP_004596384.1| 337 CWTCgseVQR--SEIEETIERLRSLQEEKLSERDEIEERIESLRaerrEIEQTERKRERLRERLTDVRNEIERREDR 411
                                       5566433444..56777777777777666666666666666655555599999999999999999999999999999 PP

                             Atg14  83 lqelkdklsqlkkeieekkkk 103
                                       l+el +++++l +ei++   +
  gi|336253277|ref|YP_004596384.1| 412 LEELTEQQENLESEIDDLEDE 432
                                       999999999999999876555 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.058
                             Atg14  23 rlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrer 82 
                                       r +el + l +l  e e+  ++ie++++  e++e+le++ +  ++ le+l+++i +++++
  gi|336253277|ref|YP_004596384.1| 459 RANELEFSLGRLERELETTTEEIEEIESALEDQEELEQRREEIRDELEDLRTRIDRIERE 518
                                       445555555555555555555555555555555555555555555555555555554444 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   1.5      0.17   1.1e+02     130     232 ..      39     156 ..      15     161 .. 0.62
   2 ?    7.0  19.7    0.0052       3.4     106     233 ..     137     261 ..     134     269 .. 0.77
   3 ?   10.1   4.7   0.00059      0.38     128     236 ..     265     391 ..     256     399 .. 0.71
   4 ?    7.6  16.3    0.0033       2.1     118     231 ..     392     517 ..     387     530 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.17
                           DUF4407 130 altaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaake.................kk 189
                                       ++t++++ l+a  aal +e ++++a++  ++ e++ eldg++ t+  ++aG+  +++                    
  gi|336253277|ref|YP_004596384.1|  39 NATNRTSLLQAFMAALGGESASLKADA--EEGEVELELDGETYTRQLRRAGNTVVTEGdpylddpelaelfafllES 113
                                       378888888888888888888887655..555566669998866666778887777778888778888888887544 PP

                           DUF4407 190 aqldaaqaelaelkakldatarlaalraelaeleaerakeraa 232
                                       + + +a ++ ++l++ + +  ++++ +ae+++l+ae++++ ++
  gi|336253277|ref|YP_004596384.1| 114 NPARRAVTTQDDLREIILRPIDTDEIEAEITRLTAEKDEISDE 156
                                       4444444444444444444455555555555555555544443 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0052
                           DUF4407 106 keIdaelaeeqqeeakelkeqlaaa..ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaG 180
                                       +eI+ae+ +  +e+ +e++++l+    l+++l ele+q+++++++i++++a+l++ +++ ++  d   ++     + 
  gi|336253277|ref|YP_004596384.1| 137 DEIEAEITRLTAEK-DEISDELDRLesLKSDLPELERQRTDIETQIEEKRAELEEVKEAIEAAEDE--SDD---QQA 207
                                       67888877777666.666677665567889999999999999999999999888887777766665..333...456 PP

                           DUF4407 181 kgpaakekkaqldaaqaelaelkakld.atarlaalraelaeleaerakeraas 233
                                       + ++ +ek ++l +++ el++++ +l+ +++ laalr+e++++eaer++  +a 
  gi|336253277|ref|YP_004596384.1| 208 ESDELEEKLEELRERRSELEDVRFDLEtERESLAALREEREDIEAERDELPEAD 261
                                       788999999999999999999999988999****************99865554 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00059
                           DUF4407 128 aaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..........gtgttgvaGkgpaake....... 187
                                       +++ ++e+++l++q +++++ ++++++ ++ +++ +                   +g     G+g+++++       
  gi|336253277|ref|YP_004596384.1| 265 QESIDEEIDRLQRQSQSIDGVVSQLQSIVQFNEEML-------EgshpeirellAAGDDDASGDGTVTDAlleddet 334
                                       233444444444444444444444444443333333.......2334555667777888999*************** PP

                           DUF4407 188 ..........kkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaa 236
                                                  ++++++  ++l +l+++  + +++++ ++++++l+aer++++++ +++
  gi|336253277|ref|YP_004596384.1| 335 vrcwtcgsevQRSEIEETIERLRSLQEE--KLSERDEIEERIESLRAERREIEQTERKR 391
                                       *******999999999999999999999..99999999999999999999999888775 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0033
                           DUF4407 118 eeakelkeqlaaa...ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaake.... 187
                                       e+ +e  + ++++    +++l+el++q+++l++eid +e+++++l+aea+   d + g+++        +a e    
  gi|336253277|ref|YP_004596384.1| 392 ERLRERLTDVRNEierREDRLEELTEQQENLESEIDDLEDEAAELEAEAEPDDDED-GDEE-SLLELNRRANElefs 466
                                       333444444444455589999************************99998554433.2222.234444444442223 PP

                           DUF4407 188 ...kkaqldaaqaelaelkakld....atarlaalraelaeleaerakera 231
                                           +++l++ ++e++e+++ l+     ++r+++ r+el++l+++++++++
  gi|336253277|ref|YP_004596384.1| 467 lgrLERELETTTEEIEEIESALEdqeeLEQRREEIRDELEDLRTRIDRIER 517
                                       333555555555555555555554444555555555555555555555444 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 ?    8.2   0.0    0.0045       2.9       4      37 ..     134     167 ..     133     170 .. 0.92
   2 ?    1.7   0.7      0.49   3.1e+02       5      38 ..     187     220 ..     175     229 .. 0.74
   3 ?    4.9   0.4     0.048        31       5      35 ..     264     294 ..     262     303 .. 0.88
   4 ?    1.4   0.2      0.61   3.9e+02      22      35 ..     414     427 ..     390     440 .. 0.53
   5 ?    4.9   0.2     0.049        32      54      86 .]     461     493 ..     455     493 .. 0.90
   6 ?   -0.2   0.0       1.8   1.2e+03      18      37 ..     496     515 ..     493     519 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0045
                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                            WXG100   4 vdpeelrqaaarfqkqaeeledelqrlkaevdal 37 
                                       +d++e+++ ++r+ ++++e++del+rl++  ++l
  gi|336253277|ref|YP_004596384.1| 134 IDTDEIEAEITRLTAEKDEISDELDRLESLKSDL 167
                                       799*************************988776 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.49
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCG CS
                            WXG100   5 dpeelrqaaarfqkqaeeledelqrlkaevdalq 38 
                                       + ee+ +a+ ++ +++++ ++e ++l+ ++++l+
  gi|336253277|ref|YP_004596384.1| 187 ELEEVKEAIEAAEDESDDQQAESDELEEKLEELR 220
                                       5567777777777777777777777777777764 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.048
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   5 dpeelrqaaarfqkqaeeledelqrlkaevd 35 
                                       d e +++ + r+q+q++++ +++++l++ v+
  gi|336253277|ref|YP_004596384.1| 264 DQESIDEEIDRLQRQSQSIDGVVSQLQSIVQ 294
                                       6688999999****************99876 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.61
                                       HHHHHHHHHHHHHH CS
                            WXG100  22 eledelqrlkaevd 35 
                                       el++++++l++e+d
  gi|336253277|ref|YP_004596384.1| 414 ELTEQQENLESEID 427
                                       33333333333333 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.049
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                            WXG100  54 eewkqaaqklvdaLeeisealkqaanafedaDe 86 
                                       +e+  ++ +l ++Le+++e+++++ +a+ed++e
  gi|336253277|ref|YP_004596384.1| 461 NELEFSLGRLERELETTTEEIEEIESALEDQEE 493
                                       577888999*********************996 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHHHC CS
                            WXG100  18 kqaeeledelqrlkaevdal 37 
                                       + +ee++del++l+  +d +
  gi|336253277|ref|YP_004596384.1| 496 QRREEIRDELEDLRTRIDRI 515
                                       66788999999999888876 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       3.1     2e+03      27      27 ..     182     182 ..     130     253 .. 0.59
   2 ?   12.3   0.2   0.00026      0.17      17      62 ..     264     307 ..     234     316 .. 0.81
   3 ?   -1.2   4.5       4.2   2.7e+03      21      76 ..     462     516 ..     372     534 .. 0.48

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.1
                        MitMem_reg  27 n 27 
                                       +
  gi|336253277|ref|YP_004596384.1| 182 E 182
                                       1 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00026
                        MitMem_reg  17 das..stlstglnrqyyslkilqerldlikdYlkkveegelpvnheil 62 
                                       d++   + + +l+rq +s+ ++ + l++i +++++  eg       ++
  gi|336253277|ref|YP_004596384.1| 264 DQEsiDEEIDRLQRQSQSIDGVVSQLQSIVQFNEEMLEGSH----PEI 307
                                       3334568999***************************9884....333 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.2
                        MitMem_reg  21 tlstglnrqyyslkilqerldlikdYlkkveegelpvnhe.ilrnlqkllnllPhle 76 
                                       +l   l+r +  l+   e +++i++ l++ e  el++  e i  +l +l +++  +e
  gi|336253277|ref|YP_004596384.1| 462 ELEFSLGRLERELETTTEEIEEIESALEDQE--ELEQRREeIRDELEDLRTRIDRIE 516
                                       2222223333333333333333333333333..333332225555555555555554 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.6    0.0083       5.3      17      89 ..     152     235 ..     146     252 .. 0.69
   2 ?    2.3   0.4      0.24   1.5e+02      22      94 ..     240     293 ..     211     313 .. 0.50
   3 ?    7.7   0.9    0.0054       3.4      17      82 ..     369     432 ..     365     441 .. 0.78
   4 ?    5.5   6.2     0.025        16      19     139 ..     399     535 ..     398     540 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0083
                      Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnalq......d 81 
                                       ++++ L+ + ++++ +  +l+++ ++ietq+++  ++l+++ +++++      + ++ +++L+++l +l       +
  gi|336253277|ref|YP_004596384.1| 152 EISDELDRLESLKSDL-PELERQRTDIETQIEEKRAELEEVKEAIEAaedesdDQQAESDELEEKLEELRerrselE 227
                                       7788888888888888.888888888888888888888877777776667777666677777777777773333333 PP

                      Baculo_PEP_C  82 tlrneLtn 89 
                                       ++r +L++
  gi|336253277|ref|YP_004596384.1| 228 DVRFDLET 235
                                       44444444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.24
                      Baculo_PEP_C  22 LnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsil 94 
                                       L+a+r     i a+                        el ++ +t  + +++ + +lq   ++++     l+si+
  gi|336253277|ref|YP_004596384.1| 240 LAALREEREDIEAERD----------------------ELPEADATDQESIDEEIDRLQrqsQSIDGVVSQLQSIV 293
                                       3333333333333333......................33334444444444444444443333333333333333 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0054
                      Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdt 82 
                                       ++ + ++++r+   +i  q ++  + + ++L+++ +++++  ++  ++l+++ +nL++ +  l+d+
  gi|336253277|ref|YP_004596384.1| 369 EIEERIESLRAERREI-EQTERKRERLRERLTDVRNEIER-REDRLEELTEQQENLESEIDDLEDE 432
                                       5666778888888888.89999999999999999999999.4555567888888888888888865 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.025
                      Baculo_PEP_C  19 tnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt............rldtlltnLtdalnalq... 80 
                                       t+v n i   +  +  +l+++ +++e+++++l+++  +l ae +             +l+  +++L+ +l +l+   
  gi|336253277|ref|YP_004596384.1| 399 TDVRNEIERREDRL-EELTEQQENLESEIDDLEDEAAELEAEAEPdddedgdeesllELNRRANELEFSLGRLErel 474
                                       55556665555555.88999999999999999999999999888789999999999999999999999999999999 PP

                      Baculo_PEP_C  81 dtlrneLtnlnsiltn...LlssvtNinstLnnllqalnnldlgalsqeledaldtveeile 139
                                       +t ++e++ ++s l +   L      i   L+ l + ++ ++ +a+++  e  +dtv eile
  gi|336253277|ref|YP_004596384.1| 475 ETTTEEIEEIESALEDqeeLEQRREEIRDELEDLRTRIDRIEREAVESFNE-HMDTVLEILE 535
                                       999999999999996433377777888888888888888887777766655.7777777775 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 ?   10.8  18.6   0.00035      0.22     115     276 ..     135     301 ..     116     304 .. 0.78
   2 ?    4.7  24.2     0.024        15      15     169 ..     345     511 ..     324     563 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                    ALIX_LYPXL_bnd 115 peeeleaalpssssaaasesveeqirklrsllekldelkaereqllkdlke.kaendDitpklltekkr.diaanef 189
                                       + +e+ea +   + +  +++ ++++ +l+sl ++l el+++r++++ +++e  ae + +++++ +++ + d + +e 
  gi|336253277|ref|YP_004596384.1| 135 DTDEIEAEITRLTAE--KDEISDELDRLESLKSDLPELERQRTDIETQIEEkRAELEEVKEAIEAAEDEsDDQQAE- 208
                                       667888888865544..56******************************993455667777775544443333333. PP

                    ALIX_LYPXL_bnd 190 ealfeeelekydplqeqleqsl...akqeellkeiqeaneefeqskksdseq...sqrqreevlqkleaaydkykel 260
                                       ++ +ee+le +++ +++le+     + + e l++++e  e++e+++ + +e+    q++ +e + +l++  + +  +
  gi|336253277|ref|YP_004596384.1| 209 SDELEEKLEELRERRSELEDVRfdlETERESLAALREEREDIEAERDELPEAdatDQESIDEEIDRLQRQSQSIDGV 285
                                       555666666666666666664344499***********************99754499999**************** PP

                    ALIX_LYPXL_bnd 261 ksnleeglkFYndlte 276
                                       +s l++ ++F +++ e
  gi|336253277|ref|YP_004596384.1| 286 VSQLQSIVQFNEEMLE 301
                                       **********999876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                    ALIX_LYPXL_bnd  15 sqgglqrlekllqdlqelkerneeiLdeieklLdeEesedeklrakygtrWtrqpSseltaelraelqkyreileeA 91 
                                       ++  +++  + l +lqe k + ++ ++e  + L++E++e e+  +k +    r    e  +  r+e+++ +  lee 
  gi|336253277|ref|YP_004596384.1| 345 QRSEIEETIERLRSLQEEKLSERDEIEERIESLRAERREIEQTERKRER--LR----ERLTDVRNEIERREDRLEEL 415
                                       3556677777778888888888888888888889999888888777766..33....33588999999999999999 PP

                    ALIX_LYPXL_bnd  92 sesDkivrqklqenkedlelLsg......peeeleaalpssssa............aasesveeqirklrsllekld 150
                                       +e  + +++++++ +++ ++L++      +e+ +e++l + +++            +  e+++e+i++++s+le+ +
  gi|336253277|ref|YP_004596384.1| 416 TEQQENLESEIDDLEDEAAELEAeaepddDEDGDEESLLELNRRanelefslgrleRELETTTEEIEEIESALEDQE 492
                                       99999999999999999999977577665444444445533333345666665554227899999999999999999 PP

                    ALIX_LYPXL_bnd 151 elkaereqllkdlkekaen 169
                                       el+++re++ ++l++  ++
  gi|336253277|ref|YP_004596384.1| 493 ELEQRREEIRDELEDLRTR 511
                                       9999999999999764333 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   7.9   6.6e-05     0.042      15      92 ..     156     233 ..     145     251 .. 0.86
   2 ?    0.1   0.1       1.2   7.5e+02      20      48 ..     266     294 ..     250     313 .. 0.69
   3 ?    3.1   6.7      0.14        91      37      81 ..     381     425 ..     345     442 .. 0.41
   4 ?    5.8   1.1      0.02        13      11      55 ..     483     528 ..     475     535 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHH CS
                        Laminin_II  15 vleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdn 91 
                                        l+ l+ l+ +l++++ +   i++++ee  +++++ ++ai+ A++++ + + + ++L++kl+el++++++ + +  +
  gi|336253277|ref|YP_004596384.1| 156 ELDRLESLKSDLPELERQRTDIETQIEEKRAELEEVKEAIEAAEDESDDQQAESDELEEKLEELRERRSELEDVRFD 232
                                       5788999*************************************************************997766555 PP

                                       H CS
                        Laminin_II  92 i 92 
                                       +
  gi|336253277|ref|YP_004596384.1| 233 L 233
                                       5 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.2
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  20 aplsqnlentkeklseinrsveetnekvk 48 
                                       + +++++++++ + ++i++ v + +  v+
  gi|336253277|ref|YP_004596384.1| 266 ESIDEEIDRLQRQSQSIDGVVSQLQSIVQ 294
                                       56667777777777777666666655555 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.14
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II  37 nrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       +r++e+t+ k + + + + d+r+++   e  +++L ++ ++l+  
  gi|336253277|ref|YP_004596384.1| 381 RREIEQTERKRERLRERLTDVRNEIERREDRLEELTEQQENLESE 425
                                       333333333333333333333333333333333333333333222 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.02
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                        Laminin_II  11 takevleqlaplsqnlentkeklseinrsveetne.kvkdankair 55 
                                        +++ le+ ++l+q+ e+++++l+ +++ +++++   v+++n+ ++
  gi|336253277|ref|YP_004596384.1| 483 EIESALEDQEELEQRREEIRDELEDLRTRIDRIEReAVESFNEHMD 528
                                       3344556666666666666666666666666665414556666554 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  10.4     0.045        29      14      91 ..     138     215 ..     135     225 .. 0.72
   2 ?    4.0   3.4     0.077        49      18      70 ..     239     291 ..     234     303 .. 0.79
   3 ?    3.9   3.1     0.082        52      44      74 ..     360     390 ..     343     395 .. 0.75
   4 ?    7.9   7.2    0.0045       2.9      18      82 ..     383     450 ..     380     462 .. 0.85
   5 ?   11.5   3.2   0.00036      0.23      20      73 ..     468     520 ..     457     528 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.045
                              FlxA  14 gsasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqq..qqaekaqekqqsekeeks 88 
                                       +++++i +L+ + ++++++L+ l +  + +  e + q+  i++QI+  +a+++ +++  ++ae++++ qq +++++ 
  gi|336253277|ref|YP_004596384.1| 138 EIEAEITRLTAEKDEISDELDRLESL-KSDLPELERQRTDIETQIEEKRAELEEVKEaiEAAEDESDDQQ-AESDEL 212
                                       6789999****************999.66666799*****************998751134444333333.333444 PP

                              FlxA  89 ksk 91 
                                       ++k
  gi|336253277|ref|YP_004596384.1| 213 EEK 215
                                       444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.077
                              FlxA  18 qiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqq 70 
                                        +a+L+++ ++++ + +el e d++++e   + ++ +q Q q++   + qlq+
  gi|336253277|ref|YP_004596384.1| 239 SLAALREEREDIEAERDELPEADATDQESIDEEIDRLQRQSQSIDGVVSQLQS 291
                                       56788888888888888999987777777778888888888888877777775 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.082
                              FlxA  44 keekkkqqqliqaQIqqlqaQIaqlqqqqae 74 
                                       +eek   +++i++ I++l+a+ + ++q +++
  gi|336253277|ref|YP_004596384.1| 360 QEEKLSERDEIEERIESLRAERREIEQTERK 390
                                       678889**************97777666555 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0045
                              FlxA  18 qiasLqkQiknlqkqLkelses...deltkeekkkqqqliqaQIqqlqaQIaqlqqqqaekaqekqqs 82 
                                       +i++ ++  ++l + L ++ ++    e   ee  +qq+ ++++I++l+ + a l+++++ + +e  ++
  gi|336253277|ref|YP_004596384.1| 383 EIEQTERKRERLRERLTDVRNEierREDRLEELTEQQENLESEIDDLEDEAAELEAEAEPDDDEDGDE 450
                                       6788888889999999999999988888899999*********************9998887776655 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00036
                              FlxA  20 asLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqqa 73 
                                        +L++++++ +++++e+ +   +++ee ++++++i  ++++l+  I ++++++ 
  gi|336253277|ref|YP_004596384.1| 468 GRLERELETTTEEIEEIESA-LEDQEELEQRREEIRDELEDLRTRIDRIEREAV 520
                                       589***************99.88888999********************99975 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 ?    6.8  13.3    0.0098       6.3      23      68 ..     157     202 ..     135     213 .. 0.68
   2 ?    4.7  18.1     0.044        28      16     112 ..     206     302 ..     199     311 .. 0.84
   3 ?    3.9  25.2      0.08        51      14      90 ..     362     441 ..     346     447 .. 0.84
   4 ?    7.3  16.6     0.007       4.5       9      82 ..     450     519 ..     443     541 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0098
                    CENP-F_leu_zip  23 kdkvenLerelemseenqekvileaEtskaevetlkeeieelaeel 68 
                                        d+ e+L+++l ++e+++++++++ E+++ae+e++ke ie  + e 
  gi|336253277|ref|YP_004596384.1| 157 LDRLESLKSDLPELERQRTDIETQIEEKRAELEEVKEAIEAAEDES 202
                                       2677888889999999999999999999999999999888766555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.044
                    CENP-F_leu_zip  16 erkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelrel....eldLvalrsekeeLeke 88 
                                       + ++d L++k e    el +  +++e+v  + Et+++ + +l+ee e +++e+ el     +d +++ +e + L+++
  gi|336253277|ref|YP_004596384.1| 206 QAESDELEEKLE----ELRERRSELEDVRFDLETERESLAALREEREDIEAERDELpeadATDQESIDEEIDRLQRQ 278
                                       667777777776....456677899******************************9643346788899********* PP

                    CENP-F_leu_zip  89 lqkkqervseLeslnsslenllee 112
                                        q     vs+L+s+    e++le 
  gi|336253277|ref|YP_004596384.1| 279 SQSIDGVVSQLQSIVQFNEEMLEG 302
                                       ************999888888875 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.08
                    CENP-F_leu_zip  14 eserkadsLkdkvenLe...relemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLek 87 
                                       e  ++ d +++++e+L    re+e+ e+++e++     + ++e+e  ++ +eel+e+ ++le+++++l  e  eLe 
  gi|336253277|ref|YP_004596384.1| 362 EKLSERDEIEERIESLRaerREIEQTERKRERLRERLTDVRNEIERREDRLEELTEQQENLESEIDDLEDEAAELEA 438
                                       333688**********644478999999***********************************************98 PP

                    CENP-F_leu_zip  88 elq 90 
                                       e +
  gi|336253277|ref|YP_004596384.1| 439 EAE 441
                                       876 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.007
                    CENP-F_leu_zip   9 lekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsek 82 
                                       +e L e +r+a+ L+    +Lerele+  e+ e    e E++ +  e+l++  ee++ el++l++ ++ + +e 
  gi|336253277|ref|YP_004596384.1| 450 EESLLELNRRANELEFSLGRLERELETTTEEIE----EIESALEDQEELEQRREEIRDELEDLRTRIDRIEREA 519
                                       68899999********************99955....66777778899*******************9987764 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 ?    6.9   7.9    0.0051       3.3      34     102 ..     147     222 ..     139     230 .. 0.66
   2 ?   -1.3   8.6       1.6     1e+03      34     101 ..     206     284 ..     204     310 .. 0.53
   3 ?   14.0   7.8   3.5e-05     0.022      26     102 ..     357     432 ..     349     443 .. 0.88
   4 ?    3.9   2.1     0.041        26      39     101 ..     455     517 ..     445     529 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0051
                              HemX  34 taevaelqqqlaaleqqlaq.......veaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga 102
                                       tae++e++++l  le+ ++         +  ++q +e  ++l++ +e++ea+e e++++q++ +el+++l+++  +
  gi|336253277|ref|YP_004596384.1| 147 TAEKDEISDELDRLESLKSDlpelerqRTDIETQIEEKRAELEEVKEAIEAAEDESDDQQAESDELEEKLEELRER 222
                                       4555555555555555555533333222224555666667777889999999999999999999999999998766 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.6
                              HemX  34 taevaelqqqlaaleqqlaq.......veaekeqkqeleerlqqlaeklealek....eleqlqkqleelqqqlskv 99 
                                       +ae++el+++l++l +  ++       +e+e+e+ + l e+ ++ + + ++l +     +e+ ++++++lq+q + +
  gi|336253277|ref|YP_004596384.1| 206 QAESDELEEKLEELRERRSEledvrfdLETERESLAALREEREDIEAERDELPEadatDQESIDEEIDRLQRQSQSI 282
                                       34444444444444444444444333366666666666655555544333333300003444455555555555555 PP

                              HemX 100 sg 101
                                       +g
  gi|336253277|ref|YP_004596384.1| 283 DG 284
                                       44 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3.5e-05
                              HemX  26 gqqqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga 102
                                       + +q  e+ +e +e+++++++l ++  ++e+ +++ ++l erl +  +++e++e +le+l++q+e+l++++ +++ +
  gi|336253277|ref|YP_004596384.1| 357 RSLQE-EKLSERDEIEERIESLRAERREIEQTERKRERLRERLTDVRNEIERREDRLEELTEQQENLESEIDDLEDE 432
                                       55663.667788**********************************************************9998765 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.041
                              HemX  39 elqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsg 101
                                       el+ + ++le +l+++e e e+ +e +e+++ + e+ e+le++ e+   +le l++++ +++ 
  gi|336253277|ref|YP_004596384.1| 455 ELNRRANELEFSLGRLERELETTTEEIEEIESALEDQEELEQRREEIRDELEDLRTRIDRIER 517
                                       666777777777777777777777777777777777888888888888888888888877765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   7.0     0.062        39      47     121 ..     154     220 ..     136     229 .. 0.48
   2 ?    5.0   6.3     0.037        24      39     121 ..     170     251 ..     162     254 .. 0.70
   3 ?    5.2   2.1     0.032        21      48     112 ..     231     295 ..     223     302 .. 0.67
   4 ?    8.6   7.8    0.0028       1.8      48     122 ..     354     431 ..     345     433 .. 0.86
   5 ?    7.8   3.0    0.0051       3.2      53     117 ..     470     531 ..     454     538 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.062
                           DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       s +l+++        + L+s++ +++++  + +  ++e ++e++ev+e +++ +++++  ++   +le+kle++ 
  gi|336253277|ref|YP_004596384.1| 154 SDELDRL--------ESLKSDLPELERQRTDIETQIEEKRAELEEVKEAIEAAEDESDDQQAESDELEEKLEELR 220
                                       3333332........334444444444444444444444445555555555555555555555555555555443 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.037
                           DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       l+   +++ +q+e+  ++l+++k+ +++  d+ d+++ e+ e+ +++ ee+ e r++l++++ d+e+ +e    l +
  gi|336253277|ref|YP_004596384.1| 170 LERQRTDIETQIEEKRAELEEVKEAIEAAEDESDDQQAESDELEEKL-EELRERRSELEDVRFDLETERESLAALRE 245
                                       45556677777777778888777777777777777777777776665.46777777888888888877777777766 PP

                           DUF1664 116 klerie 121
                                       + e+ie
  gi|336253277|ref|YP_004596384.1| 246 EREDIE 251
                                       666655 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.032
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkei.skeikeevtevredlseigedvesvkeaveg 112
                                        +le+  eslaa +++  ++i+   ++l e  ++ +++i+ee+++++++ ++i+  v++++++v+ 
  gi|336253277|ref|YP_004596384.1| 231 FDLETERESLAALREE-REDIEAERDELPEADATdQESIDEEIDRLQRQSQSIDGVVSQLQSIVQF 295
                                       4555556666655555.4566666666655544426789999999999999999999999999975 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0028
                           DUF1664  48 kqleqvseslaatkrhLssridrvd...kkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       ++l +++e+  + ++++++ri+++    ++++++++  + ++e +t+vr+++++ ++ +e++ e  e+les+++++e
  gi|336253277|ref|YP_004596384.1| 354 ERLRSLQEEKLSERDEIEERIESLRaerREIEQTERKRERLRERLTDVRNEIERREDRLEELTEQQENLESEIDDLE 430
                                       56777888888999*********97222467888888899***********************************99 PP

                           DUF1664 122 e 122
                                       +
  gi|336253277|ref|YP_004596384.1| 431 D 431
                                       7 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0051
                           DUF1664  53 vseslaatkrhLssridrvdkkldeqkei...skeikeevtevredlseigedvesvkeavegleskl 117
                                       +  +l++t    +++i+++++ l++q+e+    +ei++e++++r  +++i+++  +v++  e++++ l
  gi|336253277|ref|YP_004596384.1| 470 LERELETT----TEEIEEIESALEDQEELeqrREEIRDELEDLRTRIDRIERE--AVESFNEHMDTVL 531
                                       33333333....34444444444444443111567777777777777777654..3444445555555 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  12.7     0.015       9.8      31      94 ..     158     228 ..     134     232 .. 0.58
   2 ?    3.7  10.0      0.13        85      22      97 ..     205     280 ..     204     294 .. 0.90
   3 ?    1.8   0.9      0.53   3.4e+02      30      74 ..     262     306 ..     248     312 .. 0.70
   4 ?    4.9   4.7     0.056        36      53     102 ..     345     393 ..     341     396 .. 0.76
   5 ?    8.5   4.3    0.0044       2.8      37      73 ..     392     428 ..     390     439 .. 0.81
   6 ?    6.7  10.9     0.015       9.7       9      98 ..     425     514 ..     423     521 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.015
                                       SSHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHTT......HTTHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  31 kdleevqallkkhkaleaelaa.qqervkalnelaeklldeg......hsaseeieerleelnerWeeLke 94 
                                         le++++ l ++++ + ++++  +e+  +l+e++e++++++      + +s+e+ee+leel+er  eL++
  gi|336253277|ref|YP_004596384.1| 158 DRLESLKSDLPELERQRTDIETqIEEKRAELEEVKEAIEAAEdesddqQAESDELEEKLEELRERRSELED 228
                                       23344444444555555555555555555555555555222223344377779************999986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.13
                                       HHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  22 ellssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaa 97 
                                       ++++s++l+++lee+++   ++++++ +l++++e + al e  e++++e ++ +e+  + +e ++e  + L+++ +
  gi|336253277|ref|YP_004596384.1| 205 QQAESDELEEKLEELRERRSELEDVRFDLETERESLAALREEREDIEAERDELPEADATDQESIDEEIDRLQRQSQ 280
                                       57889999************99999999999999999999999999999999999999999999999999988765 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.53
                                       SSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTT CS
                          Spectrin  30 gkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsa 74 
                                       + d e++ + ++++++  + ++    +++++ ++ e++l+ +h++
  gi|336253277|ref|YP_004596384.1| 262 ATDQESIDEEIDRLQRQSQSIDGVVSQLQSIVQFNEEMLEGSHPE 306
                                       467777777777888888888888888888888888888887665 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  53 qqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaerkqk 102
                                       q+ ++++  e  ++l++e+ s+ +eieer+e l+   +e++++  +r+ +
  gi|336253277|ref|YP_004596384.1| 345 QRSEIEETIERLRSLQEEKLSERDEIEERIESLRAERREIEQTERKRE-R 393
                                       45555555566677788889999*****************98766665.3 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0044
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHT CS
                          Spectrin  37 qallkkhkaleaelaaqqervkalnelaeklldeghs 73 
                                       ++l ++++++++e++ +++r+++l+e++e+l++e ++
  gi|336253277|ref|YP_004596384.1| 392 ERLRERLTDVRNEIERREDRLEELTEQQENLESEIDD 428
                                       5788999************************877543 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHCCSSC.SSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHH CS
                          Spectrin   9 dadeleeWieekeellssedl.gkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerlee 84 
                                       ++d+le+   e e++++ +d    d e++ +l ++  +le  l   ++++++ +e  e+++++  +++ee+e+r ee
  gi|336253277|ref|YP_004596384.1| 425 EIDDLEDEAAELEAEAEPDDDeDGDEESLLELNRRANELEFSLGRLERELETTTEEIEEIESA-LEDQEELEQRREE 500
                                       778899999999999977777799******************************999999555.6999999999999 PP

                                       HHHHHHHHHHHHHH CS
                          Spectrin  85 lnerWeeLkelaae 98 
                                       +++  e+L++++++
  gi|336253277|ref|YP_004596384.1| 501 IRDELEDLRTRIDR 514
                                       99999999999876 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  19.5      0.01       6.4      17     155 ..     135     280 ..     121     301 .. 0.67
   2 ?    7.0  17.2    0.0068       4.3      44     127 ..     356     439 ..     345     442 .. 0.88
   3 ?    5.2   5.0     0.024        16      87     152 ..     461     528 ..     450     539 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.01
                           DUF4201  17 slkhqlakiqeklekkeelgegLt.....lidFeqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhm 88 
                                        + +  a+i++   +k+e++++L       +d   l+++ +  +++Iee+ +eL++ k+ +     +  + +   ++
  gi|336253277|ref|YP_004596384.1| 135 DTDEIEAEITRLTAEKDEISDELDrleslKSDLPELERQRTDIETQIEEKRAELEEVKEAIEAAEDESDDQQAESDE 211
                                       55555566777777888888888622222478888999999999999999999999999988776666666666666 PP

                           DUF4201  89 leselselk...kelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekve 155
                                       le++l+el+   +el++   +l+  r++l  +++er+ +++++++l +  +  + +++ ++ d+ + + +
  gi|336253277|ref|YP_004596384.1| 212 LEEKLEELRerrSELEDVRFDLETERESLAALREEREDIEAERDELPEADAT-DQESIDEEIDRLQRQSQ 280
                                       6666555550005555555566667889999999999999999999776655.55555555555555555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0068
                           DUF4201  44 FeqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvkle 120
                                         +lq e  + +++Ieer + L + ++ + +t  + + l+e+l+ +++e ++++++l+e++e+++ l+ e+  ++ e
  gi|336253277|ref|YP_004596384.1| 356 LRSLQEEKLSERDEIEERIESLRAERREIEQTERKRERLRERLTDVRNEIERREDRLEELTEQQENLESEIDDLEDE 432
                                       56788888888999999999999999999999999999999999999999999999999999999999999999999 PP

                           DUF4201 121 rdklrkq 127
                                        + l+++
  gi|336253277|ref|YP_004596384.1| 433 AAELEAE 439
                                       9988876 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.024
                           DUF4201  87 hmleselselkkelkekeerlaklrkel...ykvklerdklrkqneklkqqggllrvPaLlkDYdktke 152
                                       ++le  l +l+ el++ +e++++++  l   ++++++r+ +r++ e+l+++   ++++a+   + + ++
  gi|336253277|ref|YP_004596384.1| 461 NELEFSLGRLERELETTTEEIEEIESALedqEELEQRREEIRDELEDLRTRIDRIEREAVES-FNEHMD 528
                                       44444555555555555555555554441114566777777777777777777777777665.665555 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 ?    3.6  12.5      0.16     1e+02      25      93 ..     146     213 ..     136     217 .. 0.78
   2 ?    4.4  19.6     0.091        58      18      99 .]     177     257 ..     169     257 .. 0.67
   3 ?    1.9   2.9      0.53   3.4e+02      26      83 ..     244     301 ..     242     313 .. 0.77
   4 ?   10.0  19.3    0.0016       1.1      16      99 .]     354     436 ..     345     436 .. 0.89
   5 ?    8.3   7.1    0.0054       3.5      43      91 ..     456     504 ..     449     513 .. 0.78
   6 ?    4.0   3.1      0.12        77      21      50 ..     490     519 ..     489     565 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.16
                    HIP1_clath_bdg  25 verekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLq 93 
                                       + +ek+e+++el+rl++ ++  l e + +   +++++e+krael+++k+++e  e ++++ +++ ++L+
  gi|336253277|ref|YP_004596384.1| 146 LTAEKDEISDELDRLESLKSD-LPELERQRTDIETQIEEKRAELEEVKEAIEAAEDESDDQQAESDELE 213
                                       678999999999999876655.4444444555779999*************999999998888888776 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.091
                    HIP1_clath_bdg  18 arqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqa 94 
                                          + ee  +e +e++e +e++++e++ + +e  e  ekL +el ++r el+ ++  Le++ +s + l ++ ++++a
  gi|336253277|ref|YP_004596384.1| 177 IETQIEEKRAELEEVKEAIEAAEDESDDQQAESDELEEKL-EELRERRSELEDVRFDLETERESLAALREEREDIEA 252
                                       3333344444444555555555555555544444444444.588999****************************** PP

                    HIP1_clath_bdg  95 EkesL 99 
                                       E+++L
  gi|336253277|ref|YP_004596384.1| 253 ERDEL 257
                                       **997 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.53
                    HIP1_clath_bdg  26 erekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsge 83 
                                         e++++e e ++l e      e   ee+++L+r+ ++    +++l+s ++ +e+  e
  gi|336253277|ref|YP_004596384.1| 244 REEREDIEAERDELPEADATDQESIDEEIDRLQRQSQSIDGVVSQLQSIVQFNEEMLE 301
                                       4567778888888888888888888899999999999999999999999988777655 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0016
                    HIP1_clath_bdg  16 svarqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaL 92 
                                          r  qee   e++e+ee++e+l++e+ r++e+ + + e+L++ l++ r+e++r +  Le+ ++++e+l+s++++L
  gi|336253277|ref|YP_004596384.1| 354 ERLRSLQEEKLSERDEIEERIESLRAER-REIEQTERKRERLRERLTDVRNEIERREDRLEELTEQQENLESEIDDL 429
                                       566889******************9886.5677778899************************************** PP

                    HIP1_clath_bdg  93 qaEkesL 99 
                                       + E ++L
  gi|336253277|ref|YP_004596384.1| 430 EDEAAEL 436
                                       ***8876 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0054
                    HIP1_clath_bdg  43 aerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaa 91 
                                        +r+ +e ++ l +L+rele++ +e+++++s+Le++e+ +++ ++  ++
  gi|336253277|ref|YP_004596384.1| 456 LNRRANELEFSLGRLERELETTTEEIEEIESALEDQEELEQRREEIRDE 504
                                       567788999999**********************998877655443333 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.12
                    HIP1_clath_bdg  21 aqeeverekkeleeelerlkeeaerkleeq 50 
                                        qee+e+ ++e+ +ele+l+   +r ++e 
  gi|336253277|ref|YP_004596384.1| 490 DQEELEQRREEIRDELEDLRTRIDRIEREA 519
                                       599999999999999999998877766554 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  22.1    0.0036       2.3      38     197 ..     148     280 ..     116     312 .. 0.55
   2 ?    5.1  34.0    0.0096       6.2      82     242 ..     339     517 ..     324     538 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0036
                               MAD  38 alkrqleeesdrnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekesklaearevisalknela 114
                                       a k+++  e                                   +  le+l++ + e e + ++++  i++++ el+
  gi|336253277|ref|YP_004596384.1| 148 AEKDEISDE-----------------------------------LDRLESLKSDLPELERQRTDIETQIEEKRAELE 189
                                       223333333...................................334555556666666666666666666666666 PP

                               MAD 115 elkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqs........qe 183
                                       e k+ ie +e e   ++ e  el+e+l++l+++ sele+ + +le++ ++la+  +   ++e e  +        qe
  gi|336253277|ref|YP_004596384.1| 190 EVKEAIEAAEDESDDQQAESDELEEKLEELRERRSELEDVRFDLETERESLAALREEREDIEAERDElpeadatdQE 266
                                       66666666666666666666666666666666666666666666666666666665555655555444333333333 PP

                               MAD 184 ddslivknsksela 197
                                       +  +++   + + +
  gi|336253277|ref|YP_004596384.1| 267 SIDEEIDRLQRQSQ 280
                                       33333333333333 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0096
                               MAD  82 kknlealnkkekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqliqql 158
                                       +   e + ++ +e  ++l +++e + + ++e++e+ ++++ +  e++++e + e+l+erl   +++++  e++ ++l
  gi|336253277|ref|YP_004596384.1| 339 TCGSEVQRSEIEETIERLRSLQEEKLSERDEIEERIESLRAERREIEQTERKRERLRERLTDVRNEIERREDRLEEL 415
                                       44555666667777788888888888888888888888888888888888888888888888888888888877777 PP

                               MAD 159 ekkqkelaeaeqrikeLefeiqs..........qeddslivknsksel.aripelekelerlreenkklnelkenke 224
                                        ++q++l+ + + + +   e++            e++ l++    +el  ++ +le+ele   ee++++++  e++e
  gi|336253277|ref|YP_004596384.1| 416 TEQQENLESEIDDLEDEAAELEAeaepdddedgDEESLLELNRRANELeFSLGRLERELETTTEEIEEIESALEDQE 492
                                       77776665544433333333333555588888877788888888888889999999999999999999999888887 PP

                               MAD 225 lLk.......EevedlkkkLereEk 242
                                        L+        e+edl+++++r E+
  gi|336253277|ref|YP_004596384.1| 493 ELEqrreeirDELEDLRTRIDRIER 517
                                       7652222111467778888888775 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.6     0.029        18      51     110 ..     137     196 ..     121     203 .. 0.89
   2 ?   -0.5   0.1       2.1   1.3e+03      26      57 ..     263     297 ..     254     304 .. 0.58
   3 ?    3.3   3.2      0.14        88      42     114 ..     353     424 ..     330     437 .. 0.80
   4 ?   14.0   2.8   6.5e-05     0.041      25     101 ..     450     525 ..     444     535 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.029
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHH CS
                              COG5  51 qlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeaeklqsalk 110
                                       ++i ++ + L+++ ++++ + + l++lks l +L+     +++++ e+ +e+e++++a++
  gi|336253277|ref|YP_004596384.1| 137 DEIEAEITRLTAEKDEISDELDRLESLKSDLPELERQRTDIETQIEEKRAELEEVKEAIE 196
                                       57888899999999999999999*******************************999986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.1
                                       XXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXX CS
                              COG5  26 dteldlstplkrln...ydiqeldkrlrqlitsnh 57 
                                       +++++++ ++ rl+   + i+ + ++l+++++ n+
  gi|336253277|ref|YP_004596384.1| 263 TDQESIDEEIDRLQrqsQSIDGVVSQLQSIVQFNE 297
                                       44555555555554111556666677777766655 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.14
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHH CS
                              COG5  42 iqeldkrlrqlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeaeklqsalkrlhq 114
                                       i+ l+  l+++  s+ +e+ e++++ + ++   ++ + + e+L + +  +++++ ++ +++e+l++++++l +
  gi|336253277|ref|YP_004596384.1| 353 IERLR-SLQEEKLSERDEIEERIESLRAERREIEQTERKRERLRERLTDVRNEIERREDRLEELTEQQENLES 424
                                       44443.4666667778888888888888888889999999999999999999999999999999999999876 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 6.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHH CS
                              COG5  25 ddteldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepyee 101
                                       +++ l l+ +++ l++ +  l+++l++ +t++ +e+ + l+++++l++  +e++ +le+L   ++r++++ +e ++e
  gi|336253277|ref|YP_004596384.1| 450 EESLLELNRRANELEFSLGRLERELET-TTEEIEEIESALEDQEELEQRREEIRDELEDLRTRIDRIEREAVESFNE 525
                                       555678899999*************97.678999************************************9999886 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1         3   1.9e+03      69     105 ..      47      83 ..      35      89 .. 0.58
   2 ?    6.4  17.7     0.014       8.9      46     115 ..     154     226 ..     136     229 .. 0.50
   3 ?    3.0  11.2      0.15        97      54     114 ..     221     281 ..     212     292 .. 0.84
   4 ?    7.6  20.3    0.0059       3.8      28     117 ..     346     438 ..     340     440 .. 0.87
   5 ?    6.9   9.9    0.0093         6      66     113 ..     467     513 ..     449     518 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3
                        TPR_MLP1_2  69 lkaeiaelkaeaesakaeleeseesweeqkeelekel 105
                                       l+a +a l  e  s+ka+ ee e ++e   e++ ++l
  gi|336253277|ref|YP_004596384.1|  47 LQAFMAALGGESASLKADAEEGEVELELDGETYTRQL 83 
                                       4444555555555556666666655555555555555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                        TPR_MLP1_2  46 erelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqk...eelekelselekriedl 115
                                       + el   ++   +l +l  +  +++++i+e +ae+e++k+++e++e + + q+   +ele++l+el++r+ +l
  gi|336253277|ref|YP_004596384.1| 154 SDELDRLESLKSDLPELERQRTDIETQIEEKRAELEEVKEAIEAAEDESDDQQaesDELEEKLEELRERRSEL 226
                                       4444444444455555555555555555555555555555555555555444411134555666666665555 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.15
                        TPR_MLP1_2  54 edvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekried 114
                                       e   el+++r +l++ ++ +a l++e+e+ +ae +e  e+ ++ +e++++e++ l+++ + 
  gi|336253277|ref|YP_004596384.1| 221 ERRSELEDVRFDLETERESLAALREEREDIEAERDELPEADATDQESIDEEIDRLQRQSQS 281
                                       5667899999999999999999999999999999999999999999999999999988765 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0059
                        TPR_MLP1_2  28 qedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseeswe...eqkeel 101
                                       ++++e+  e+++  q+   +e  + +e +++l+a r e+++++ +++ l++++ ++++e+e+ e  +e   eq+e+l
  gi|336253277|ref|YP_004596384.1| 346 RSEIEETIERLRSLQEEKLSERDEIEERIESLRAERREIEQTERKRERLRERLTDVRNEIERREDRLEeltEQQENL 422
                                       678888888888888888888889999**********************************99976542227***** PP

                        TPR_MLP1_2 102 ekelselekriedlne 117
                                       e+e+++le    +l++
  gi|336253277|ref|YP_004596384.1| 423 ESEIDDLEDEAAELEA 438
                                       *********9999986 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0093
                        TPR_MLP1_2  66 lnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekrie 113
                                       l +l+ e+++ ++e e+ +++le +e ++e+++ee+++el++l++ri+
  gi|336253277|ref|YP_004596384.1| 467 LGRLERELETTTEEIEEIESALEDQE-ELEQRREEIRDELEDLRTRID 513
                                       33455555555555555555555433.456666666666666666665 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.9     0.017        11       2      43 ..     140     181 ..     136     185 .. 0.80
   2 ?    3.5   4.4     0.099        63      83     115 ..     164     196 ..     160     208 .. 0.55
   3 ?    3.8   5.3     0.079        50      74     112 ..     190     228 ..     186     230 .. 0.92
   4 ?    1.4   3.4      0.44   2.8e+02       4      31 ..     208     235 ..     205     250 .. 0.77
   5 ?    0.1   0.1       1.1     7e+02       3      34 ..     231     262 ..     229     268 .. 0.74
   6 ?    2.7   0.1      0.18   1.1e+02      80     113 ..     266     299 ..     261     304 .. 0.70
   7 ?    1.1   0.3      0.54   3.5e+02      18      37 ..     345     364 ..     342     371 .. 0.79
   8 ?    4.2   1.7     0.061        39       2      35 ..     371     404 ..     370     409 .. 0.84
   9 ?   11.6   3.7   0.00031       0.2      80     114 ..     406     440 ..     400     442 .. 0.91
  10 ?    3.8   0.4      0.08        51      82     114 ..     456     488 ..     450     491 .. 0.67
  11 ?    7.7   0.6    0.0051       3.3      87     114 ..     492     519 ..     489     525 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEE CS
                         Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkkedegkevlv 43 
                                       ++e+++l+ae +++++++++le++++ l +l+ +  ++e+++
  gi|336253277|ref|YP_004596384.1| 140 EAEITRLTAEKDEISDELDRLESLKSDLPELERQRTDIETQI 181
                                       678888888888888888888888888888888777777776 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.099
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  83 kkkleelekqlekleeeleklkdqittleanla 115
                                       k  l ele+q++++e ++e+++++++++ ++++
  gi|336253277|ref|YP_004596384.1| 164 KSDLPELERQRTDIETQIEEKRAELEEVKEAIE 196
                                       555555555555555555555555555544443 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.079
                                       EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  74 sleeAiellkkkleelekqlekleeeleklkdqittlea 112
                                       +++eAie  +++ ++ ++ +++lee+le+l+++  +le+
  gi|336253277|ref|YP_004596384.1| 190 EVKEAIEAAEDESDDQQAESDELEEKLEELRERRSELED 228
                                       5789****************************9999886 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin   4 eleslqaelaqlkeaieelektletlkt 31 
                                       e ++l+++l++l+e+ +ele+++  l+t
  gi|336253277|ref|YP_004596384.1| 208 ESDELEEKLEELRERRSELEDVRFDLET 235
                                       5678888888888888888888888876 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                         Prefoldin   3 eeleslqaelaqlkeaieelektletlktlkk 34 
                                       + le+ +++la+l+e+ e++e+ ++ l + ++
  gi|336253277|ref|YP_004596384.1| 231 FDLETERESLAALREEREDIEAERDELPEADA 262
                                       67888889999999999999887777666655 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  80 ellkkkleelekqlekleeeleklkdqittlean 113
                                       e ++++++ l++q++++   + +l++ +++ e++
  gi|336253277|ref|YP_004596384.1| 266 ESIDEEIDRLQRQSQSIDGVVSQLQSIVQFNEEM 299
                                       5677777777777777777777777777666655 PP

  == domain 7  score: 1.1 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHHHHHHTT.-T CS
                         Prefoldin  18 aieelektletlktlkkede 37 
                                       + +e+e+t+e+l++l++e+ 
  gi|336253277|ref|YP_004596384.1| 345 QRSEIEETIERLRSLQEEKL 364
                                       57899999999999999544 PP

  == domain 8  score: 4.2 bits;  conditional E-value: 0.061
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT. CS
                         Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkke 35 
                                       +e +esl+ae+++++++ ++ e+++e+l ++++e
  gi|336253277|ref|YP_004596384.1| 371 EERIESLRAERREIEQTERKRERLRERLTDVRNE 404
                                       7889999999999999999999999999999884 PP

  == domain 9  score: 11.6 bits;  conditional E-value: 0.00031
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  80 ellkkkleelekqlekleeeleklkdqittleanl 114
                                       e  +++leel++q+e+le e+++l d++ +lea++
  gi|336253277|ref|YP_004596384.1| 406 ERREDRLEELTEQQENLESEIDDLEDEAAELEAEA 440
                                       56689***************************987 PP

  == domain 10  score: 3.8 bits;  conditional E-value: 0.08
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanl 114
                                       l+++ +ele +l  le ele  +++i+++e +l
  gi|336253277|ref|YP_004596384.1| 456 LNRRANELEFSLGRLERELETTTEEIEEIESAL 488
                                       566667777777777777777777777766655 PP

  == domain 11  score: 7.7 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  87 eelekqlekleeeleklkdqittleanl 114
                                       eele+ +e++ +ele+l+++i+ +e+++
  gi|336253277|ref|YP_004596384.1| 492 EELEQRREEIRDELEDLRTRIDRIEREA 519
                                       899*********************9987 PP

>> YPEB  YpeB sporulation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.2    0.0011      0.72     110     190 ..     151     235 ..     141     297 .. 0.76
   2 ?   -0.4   5.2      0.86   5.5e+02     114     159 ..     378     423 ..     361     441 .. 0.77
   3 ?    8.4   2.8    0.0019       1.2     114     194 ..     447     527 ..     426     583 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                              YPEB 110 epLteeeyktLeeLyeqakelekeLrkvqekvaegglrwgelekalas.....eqekadntiidgnfktvekeveky 181
                                       ++++ +e + Le+L++   ele++  +++++++e++ +++e+++a+++     ++++a+++ ++++++++ ++ +++
  gi|336253277|ref|YP_004596384.1| 151 DEIS-DELDRLESLKSDLPELERQRTDIETQIEEKRAELEEVKEAIEAaedesDDQQAESDELEEKLEELRERRSEL 226
                                       4454.689************************************995533444666777888888899998888888 PP

                              YPEB 182 peliydGpf 190
                                        ++ +d ++
  gi|336253277|ref|YP_004596384.1| 227 EDVRFDLET 235
                                       888888666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.86
                              YPEB 114 eeeyktLeeLyeqakelekeLrkvqekvaegglrwgelekalaseq 159
                                        +e+ ++e+  ++ ++l+++L +v++++++++ r++el ++ ++ +
  gi|336253277|ref|YP_004596384.1| 378 RAERREIEQTERKRERLRERLTDVRNEIERREDRLEELTEQQENLE 423
                                       4789999999********************9999999888854422 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0019
                              YPEB 114 eeeyktLeeLyeqakelekeLrkvqekvaegglrwgelekalas.eqekadntiidgnfktvekevekypeliydGp 189
                                       + + ++L eL + a+ele +L  +++++++ + +++e+e al++ e+ +++ + i ++++++ ++++++        
  gi|336253277|ref|YP_004596384.1| 447 DGDEESLLELNRRANELEFSLGRLERELETTTEEIEEIESALEDqEELEQRREEIRDELEDLRTRIDRIEREAV-ES 522
                                       557899************************************7764445555556666****999999886666.55 PP

                              YPEB 190 fsdhl 194
                                       f++h+
  gi|336253277|ref|YP_004596384.1| 523 FNEHM 527
                                       66776 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 ?    9.4   7.8    0.0019       1.2      26      99 ..     124     197 ..     113     201 .. 0.87
   2 ?    6.1  14.8      0.02        13      11      95 ..     150     228 ..     142     233 .. 0.80
   3 ?    4.4  17.4     0.069        44      15      97 ..     361     440 ..     353     446 .. 0.91
   4 ?   11.2   7.2    0.0005      0.32      29      96 ..     451     518 ..     443     522 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  26 advdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelek 99 
                                        d+ e++       e+++e+  l ae+ e+s e  ++   k d  el  +  ++ ++++++ ael+e+++++e+
  gi|336253277|ref|YP_004596384.1| 124 DDLREIILRPIDTDEIEAEITRLTAEKDEISDELDRLESLKSDLPELERQRTDIETQIEEKRAELEEVKEAIEA 197
                                       5666777777777899999**************************************************99876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.02
                                       HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHH CS
                      Seryl_tRNA_N  11 peavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkale 87 
                                        +++ + l  R   +++  +l el+++r  +++++ee +ae  e+ ++I+ a ++    ++  ae++el e+l++l 
  gi|336253277|ref|YP_004596384.1| 150 KDEISDELD-R--LESLKSDLPELERQRTDIETQIEEKRAELEEVKEAIEAAEDES---DDQQAESDELEEKLEELR 220
                                       555555553.3..4667778889999999999999999999999999999999875...667799999999999999 PP

                                       HHHHHHHH CS
                      Seryl_tRNA_N  88 aelkelea 95 
                                       ++ +ele+
  gi|336253277|ref|YP_004596384.1| 221 ERRSELED 228
                                       99999886 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.069
                                       HHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  15 keklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelk 91 
                                       +ekl +R e ++ +++l +  ++ ++++ + e l+++   + +eI++  ++    eel ++ ++l  e+++le+e +
  gi|336253277|ref|YP_004596384.1| 361 EEKLSERDEIEERIESLRAERREIEQTERKRERLRERLTDVRNEIERREDR---LEELTEQQENLESEIDDLEDEAA 434
                                       689999*999999999999999999999*****************999976...68999999999*******99999 PP

                                       HHHHHH CS
                      Seryl_tRNA_N  92 eleael 97 
                                       eleae 
  gi|336253277|ref|YP_004596384.1| 435 ELEAEA 440
                                       999985 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.0005
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleae 96 
                                       ++llel+++  el++ l  l +e  + ++eI+++  + ed eel ++ +e+ +el++l ++ + +e e
  gi|336253277|ref|YP_004596384.1| 451 ESLLELNRRANELEFSLGRLERELETTTEEIEEIESALEDQEELEQRREEIRDELEDLRTRIDRIERE 518
                                       67888888888888888888888888888888888888888888888888888888888888888765 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         6   3.8e+03      43      73 ..      16      46 ..      14      49 .. 0.83
   2 ?    4.3   4.9     0.069        44      10      73 ..     131     195 ..     128     199 .. 0.82
   3 ?    8.7   5.7    0.0028       1.8      13      67 ..     195     248 ..     190     259 .. 0.89
   4 ?   -1.4   0.1       3.9   2.5e+03      52      77 ..     265     290 ..     252     293 .. 0.65
   5 ?    4.8  11.0     0.048        31      10      67 ..     374     434 ..     349     439 .. 0.72
   6 ?    7.0   4.7    0.0096       6.1      18      77 ..     457     516 ..     438     519 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6
                              Med9 43 relpgidrsveeqeaeieeleeqlakKrelL 73
                                      r++ gi++++ e e  +  l  q+a+ r  L
  gi|336253277|ref|YP_004596384.1| 16 RNIGGINETTVELESGVTVLAGQNATNRTSL 46
                                      78999*****999999999999988887766 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.069
                              Med9  10 lksiekdp.nlsskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKrelL 73 
                                       l+ i+ d+ + +++ l ++ +e+ + L++  +l + lp+++r   + e +iee++ +l+  +e +
  gi|336253277|ref|YP_004596384.1| 131 LRPIDTDEiEAEITRLTAEKDEISDELDRLESLKSDLPELERQRTDIETQIEEKRAELEEVKEAI 195
                                       66666666677888899999999999999999999999999999999999999999998877665 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0028
                              Med9  13 iekdpnlsskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqla 67 
                                       ie ++  +s d +++ +el  kL++ re  +el+++    e+  + +++l+e+ +
  gi|336253277|ref|YP_004596384.1| 195 IEAAE-DESDDQQAESDELEEKLEELRERRSELEDVRFDLETERESLAALREERE 248
                                       55566.78999999*************************************9876 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 3.9
                              Med9  52 veeqeaeieeleeqlakKrelLkkyk 77 
                                       +e+ ++ei+ l+ q +    + ++++
  gi|336253277|ref|YP_004596384.1| 265 QESIDEEIDRLQRQSQSIDGVVSQLQ 290
                                       45556777777777777666666665 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.048
                              Med9  10 lksiekdpnlsskdletktgelrhkLkkarelirelpg....idrsveeqeaeieeleeqla 67 
                                       ++s++ +  ++++++e k   lr +L  +r+ i+  ++    + + +e+ e ei++le++ a
  gi|336253277|ref|YP_004596384.1| 374 IESLRAER-REIEQTERKRERLRERLTDVRNEIERREDrleeLTEQQENLESEIDDLEDEAA 434
                                       55556666.78888888888888888888888887777766666666666777777777665 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.0096
                              Med9  18 nlsskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKrelLkkyk 77 
                                       n+ +++le ++g l   L++  e i+e++   + +ee e++ ee +++l+  r  + ++ 
  gi|336253277|ref|YP_004596384.1| 457 NRRANELEFSLGRLERELETTTEEIEEIESALEDQEELEQRREEIRDELEDLRTRIDRIE 516
                                       8999**************************999999999999999999999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3059  (0.170617); expected 358.6 (0.02)
Passed bias filter:                     1133  (0.0631937); expected 358.6 (0.02)
Passed Vit filter:                       368  (0.0205254); expected 17.9 (0.001)
Passed Fwd filter:                       229  (0.0127726); 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: 3.13u 0.33s 00:00:03.46 Elapsed: 00:00:00.66
# Mc/sec: 3020.40
//
Query:       gi|336253278|ref|YP_004596385.1|  [L=390]
Description: glutaryl-CoA dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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  116.6   1.3    1.8e-33  115.8   1.3    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    2.5e-25   89.3   0.1    1.8e-24   86.6   0.1    2.3  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    4.3e-24   84.5   0.0    8.4e-24   83.6   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    9.9e-10   38.8   0.6    1.6e-09   38.2   0.6    1.3  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
     0.0057   16.4   0.0      0.022   14.4   0.0    1.9  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   1.3   5.2e-37   1.8e-33       3     149 ..     237     383 ..     236     384 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 5.2e-37
                                       HHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--- CS
                     Acyl-CoA_dh_1   3 GfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaeald 79 
                                       G++  ++ l++ R ++a++a+g+ar ++e+a+eya +r++fg+p++ +ql +eklaema++++ a+ll+yr+a + +
  gi|336253278|ref|YP_004596385.1| 237 GMKGPLSCLTQARYGIAWGAVGAARDCFEQAREYALEREQFGGPIGRFQLQQEKLAEMATQITLAQLLAYRLADLKE 313
                                       8888999********************************************************************** PP

                                       -----HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  80 agkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       +g+ +++ +smaK    ++a+e  + a ++lGg+G++++y+  r++ ++ +   +eGt +i+ +i+++ l
  gi|336253278|ref|YP_004596385.1| 314 RGDLRPQHVSMAKRNNVRTAREQSKVAREMLGGNGITTDYSPMRHMANMETVYTYEGTHDIHTLILGEEL 383
                                       *****************************************************************99875 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.1     5e-28   1.8e-24       2     113 .]      13     123 ..      12     123 .. 0.98
   2 ?   -0.2   0.0      0.43   1.5e+03      40      55 ..     216     231 ..     187     264 .. 0.69

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 5e-28
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                       ee++ +rdt+ref++e+++p + ++ eeg+fp +l+ +++elG+++ ++ e yg  +++ +++ ++++el+++d+gl
  gi|336253278|ref|YP_004596385.1|  13 EEERLIRDTAREFVAEQVKPDIGDHFEEGTFPTDLIPEMGELGFYAPNL-EGYGSPNVSETAYGLLMQELEAGDSGL 88 
                                       89*********************************************99.9************************** PP

                                       HHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  79 alllgvhsslvapailrfGteeqkrryLpklasge 113
                                       +++ +v+ +lv+++i ++G+e+qk+++Lp l +ge
  gi|336253278|ref|YP_004596385.1|  89 RSMASVQGALVMYPIRAYGSEAQKEEWLPVLGEGE 123
                                       *****************************998887 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.43
                                       HHHTTCTSTTS-GGGT CS
                     Acyl-CoA_dh_N  40 laelGllgitvpeeyg 55 
                                        +e Gl  ++vpee  
  gi|336253278|ref|YP_004596385.1| 216 TGEIGLHDVHVPEENV 231
                                       4899********9965 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.0   2.3e-27   8.4e-24       1      97 []     127     224 ..     127     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 2.3e-27
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE...TS---.----EEEEEEE..GGGE CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar...tekpd.rarglslflvprdapgv 73 
                                       +f+lTEp++Gs+ a+++t  aerdg +yvlnG+K+witna+ia+la+v+ar   +e    +++ ++ flv++d+ gv
  gi|336253278|ref|YP_004596385.1| 127 CFGLTEPEHGSNPAGMET-YAERDGSGYVLNGSKTWITNAPIADLAVVWARdrsSE--GeGDDPVRGFLVETDRDGV 200
                                       9*****************.99999999************************75333..2469*************** PP

                                       EE-----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  74 svrrieeklGlrglptgelvfedv 97 
                                       + ++i+ kl +r   tge+ ++dv
  gi|336253278|ref|YP_004596385.1| 201 TTNEIDGKLSMRASITGEIGLHDV 224
                                       ******************998886 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.6   4.3e-13   1.6e-09       2     131 ..     251     370 ..     250     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 4.3e-13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       gia  a+GaAr +++++ e+a er +  +g ++  ++  q +lae+a+++  A++l +r a+      ++g+   ++
  gi|336253278|ref|YP_004596385.1| 251 GIAWGAVGAARDCFEQAREYALEREQ--FGGPIGRFQLQQEKLAEMATQITLAQLLAYRLADL----KERGDL-RPQ 320
                                       688889********************..***********************************....666666.688 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGG CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaa 131
                                       ++  a+r+ ++++++  +++++   + Gg+++++++   R++ +++++ ++++
  gi|336253278|ref|YP_004596385.1| 321 HVSMAKRNNVRTAREQSKVARE---MLGGNGITTDYSPMRHMANMETVYTYEG 370
                                       8888888888877777777765...5799999999888888888888877776 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   6.2e-06     0.022     173     228 ..     147     202 ..     131     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.2e-06
                                       EE-SSEEEEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEEE CS
                            HpaB_N 173 eetddGivVrGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlkl 228
                                       e++  G v +G k  +T+a++ad  +v    +  + e +d    f v++d +G++ 
  gi|336253278|ref|YP_004596385.1| 147 ERDGSGYVLNGSKTWITNAPIADLAVVWARDRSSEGEGDDPVRGFLVETDRDGVTT 202
                                       67778*************************6665667788899**********984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 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:                        22  (0.00122706); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.57
# Mc/sec: 2044.34
//
Query:       gi|336253279|ref|YP_004596386.1|  [L=1024]
Description: D-lactate dehydrogenase (cytochrome) [Halopiger xanaduensis SH-6]
Scores for complete 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-63  215.3   0.0    2.2e-63  214.2   0.0    1.6  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    5.5e-42  142.8   0.0    1.3e-41  141.6   0.0    1.7  1  FAD_binding_4  FAD binding domain
    4.5e-09   36.6   4.4      1e-08   35.5   4.4    1.6  1  Fer4_8         4Fe-4S dicluster domain
    1.5e-08   35.1   3.8    2.9e-08   34.1   3.8    1.5  1  Fer4_17        4Fe-4S dicluster domain
      4e-08   33.3   0.0    0.00014   22.0   0.1    2.7  2  CCG            Cysteine-rich domain
    4.1e-05   23.1   0.2    6.3e-05   22.5   0.2    1.2  1  Cytokin-bind   Cytokinin dehydrogenase 1, FAD and cytokinin b
     0.0035   17.4   4.7      0.022   14.9   5.3    2.0  2  Fer4_10        4Fe-4S dicluster domain
     0.0035   17.5   1.5       0.22   11.7   0.3    2.5  2  Fer4_9         4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.045   13.9   1.9       0.51   10.5   0.3    2.5  2  Fer4_21        4Fe-4S dicluster domain
          2    9.1   8.1         13    6.4   8.1    2.3  2  Fer4_7         4Fe-4S dicluster 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 !  214.2   0.0   1.3e-66   2.2e-63       2     250 .]     303     569 ..     302     569 .. 0.97

  Alignments for each domain:
  == domain 1  score: 214.2 bits;  conditional E-value: 1.3e-66
                                       -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SS...TTS-TTT-EEEEEEEEE-HHHH CS
                     FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgak...kglpdeeealllvefegddeee 75 
                                       pe +av l+ + ++ +a++ v +i ++  +paa+e++d++ +dl+++t ++    + lpd+++a+llvef++ d ++
  gi|336253279|ref|YP_004596386.1| 303 PETKAVSLLCYRDLHEAMEDVTAILEH--DPAAVEVLDDVLIDLARGTAEFGpvtEILPDGTNAVLLVEFYAEDTDH 377
                                       899************************..**********************99999********************* PP

                                       HHHHHHH.HHHHTTT-EEEEE..........................ETGGGGGGGGHHHHHHHHHCTTEEEEEEEE CS
                     FAD-oxidase_C  76 aeeelea.lveaileatgaad................vlvaqdeaeaealwkaRkaalpylrdallkagvavlseDt 135
                                        +e+++  l++++ +at+ ++                +l a+deae+++lwk+Rk+ lp+l +++ +++++ ++eDt
  gi|336253279|ref|YP_004596386.1| 378 GREQVAGlLADRCPDATAEGEpaddaprtdaetlaidALEAYDEAERAKLWKLRKSGLPILLSRTTDEKHISFIEDT 454
                                       *******77777777777777************99877*************************************** PP

                                       EEEHHHHHHHHHHHHHHHHHHHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT--------- CS
                     FAD-oxidase_C 136 svPvsrladlvrdikalldkyglevvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGv 212
                                       ++P+++l+++v+ ++++l+++++ ++ ++Hag+g+lh+++l++ + +   e+++ ++d+v+dl+velgGs+sgEHG 
  gi|336253279|ref|YP_004596386.1| 455 AIPPAKLPEFVEGFEEILEDHDTYASFYAHAGPGVLHVRPLVNTKTDVGLEQLYGIADDVTDLVVELGGSVSGEHGD 531
                                       ***************************************************************************** PP

                                       --------------THHHHHHHHHHHH-TT--BSTT-- CS
                     FAD-oxidase_C 213 GldkkaylerekgeeglalmrriKaalDPkgiLNPgkv 250
                                       G+++ ++ ++ +ge+++++++ +K a+DP++iLNPg+v
  gi|336253279|ref|YP_004596386.1| 532 GRARTQWNRKLYGEQLWETFQDLKTAFDPDWILNPGQV 569
                                       ************************************86 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6   0.0     7e-45   1.3e-41       1     138 [.      62     199 ..      62     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 7e-45
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETT.S--EEEEETTTTEEEEETTSBHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsr.lnrileideeegtatveaGvtlgd 76 
                                       p av++pes+++va +l++++e+++pvl+rGgG+sl+gq v +++vvld++r +n ileid+e++tatv++G++lg 
  gi|336253279|ref|YP_004596386.1|  62 PIAVAFPESTADVAGILEYCAERRIPVLPRGGGTSLAGQTV-NRAVVLDFTRhMNEILEIDPEDRTATVQPGTILGT 137
                                       679*************************************9.********999************************ PP

                                       HHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                     FAD_binding_4  77 lvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                       l+eal+++   + ++p+ g+ + +GGai +n+ G++s kyG++  +++++evvladG+v ++
  gi|336253279|ref|YP_004596386.1| 138 LNEALSPHDVKFAPDPAWGDKSAIGGAIGNNSTGSHSLKYGKTDAYIESAEVVLADGTVTEF 199
                                       ***********************************************************986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   4.4   5.7e-12     1e-08       3      64 ..     612     691 ..     610     692 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 5.7e-12
                            Fer4_8   3 ekCieCgaCq........saCpvlrrtkkhlldargeaaedvqeeqvlee..........eealwsCttcgaCtevC 61 
                                       e C++Cg C+         +Cp++r++++++  +rg++++  q   ++ e          ee ++ C +c+ C+  C
  gi|336253279|ref|YP_004596386.1| 612 ELCHGCGGCRgqqsttggVMCPTYRASREEITATRGRVNALRQAMSGNLEpeeafsdefvEEVMGLCIGCKGCSIDC 688
                                       67*********999999999********************333333333366778888999**************** PP

                            Fer4_8  62 pvg 64 
                                       p +
  gi|336253279|ref|YP_004596386.1| 689 PSE 691
                                       *87 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   3.8   1.6e-11   2.9e-08       2      61 .]     614     693 ..     613     693 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.6e-11
                           Fer4_17   2 CiqCgyClp........eCpsyeaydnepkkllraakl......glleeaeke......ekaslCieCgeCerkCPq 58 
                                       C++Cg C+         +Cp+y+a ++e   ++ ++++      g le +e+       e+++lCi+C++C+ +CP+
  gi|336253279|ref|YP_004596386.1| 614 CHGCGGCRGqqsttggvMCPTYRASREEITATRGRVNAlrqamsGNLEPEEAFsdefveEVMGLCIGCKGCSIDCPS 690
                                       ************************998866555555554443435444433324568878***************** PP

                           Fer4_17  59 gld 61 
                                       ++d
  gi|336253279|ref|YP_004596386.1| 691 EVD 693
                                       997 PP

>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0014       2.5      10      67 ..     797     856 ..     791     870 .. 0.85
   2 !   22.0   0.1     8e-08   0.00014       2      84 ..     921    1002 ..     920    1003 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0014
                               CCG  10 lraaypevrkalkkllealgveleel.ekesC.CGagggrsgkeelaealakrnvetaee 67 
                                        +++ype +ka  ++lea+gv++  + + + C  G +++ +g+ e+a++ a +nve++  
  gi|336253279|ref|YP_004596386.1| 797 TNYSYPEAGKAAVRVLEAAGVHVALPdDPDLCdTGRPAFSKGFLEQARETAVENVEALAP 856
                                       5788**********************9999996699999999988999999999998865 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 8e-08
                               CCG    2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkee...laealakrnvetaeetgadai 73  
                                        +y+  Ch   +++ + ++    +l+++g  +++l ++ CCG +g +  + e    + a+a+  +e++ e + d +
  gi|336253279|ref|YP_004596386.1|  921 TYHGHCH---QKSTAKDHHAVGVLRRAGYAVDPL-DSGCCGMAGSFGYEAEhasMSDAIADILYEQVTESNGDRV 991 
                                        6777774...44444455556788999*****99.***********99988777777****************** PP

                               CCG   74 vtacpgCllql 84  
                                        v++ ++C +ql
  gi|336253279|ref|YP_004596386.1|  992 VAPGASCRTQL 1002
                                        *********98 PP

>> Cytokin-bind  Cytokinin dehydrogenase 1, FAD and cytokinin binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.2   3.5e-08   6.3e-05     246     281 .]     534     571 ..     530     571 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.5e-08
                                       SHHHH.HHHHGHH.HHHHHHHHHHH-TT--B-GGG-SS CS
                      Cytokin-bind 246 sqeeW.kkhfGak.WerfverKakyDPkaiLspGqriF 281
                                       ++++W +k +G++ We+f++ K+++DP  iL pGq +F
  gi|336253279|ref|YP_004596386.1| 534 ARTQWnRKLYGEQlWETFQDLKTAFDPDWILNPGQVVF 571
                                       5789*66779*666*********************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 !   14.9   5.3   1.2e-05     0.022       7      56 .]     612     689 ..     607     689 .. 0.95
   2 !   11.2   1.1   0.00017       0.3       8      27 ..     677     696 ..     669     711 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                           Fer4_10   7 dtCirCgkCvk........aCPadl....................tsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       + C +Cg C+         +CP++                     +++   +ea  +e v+++++ C+gc  C   C
  gi|336253279|ref|YP_004596386.1| 612 ELCHGCGGCRGqqsttggvMCPTYRasreeitatrgrvnalrqamSGNLEPEEAFSDEFVEEVMGLCIGCKGCSIDC 688
                                       68********99******99***99******************999999999999********************** PP

                           Fer4_10  56 P 56 
                                       P
  gi|336253279|ref|YP_004596386.1| 689 P 689
                                       9 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00017
                           Fer4_10   8 tCirCgkCvkaCPadltsvg 27 
                                        Ci+C+ C   CP+ +++ +
  gi|336253279|ref|YP_004596386.1| 677 LCIGCKGCSIDCPSEVDMAK 696
                                       6*************553333 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.028        50      33      43 ..     604     621 ..     576     623 .. 0.75
   2 !   11.7   0.3   0.00012      0.22       2      16 ..     678     692 ..     631     709 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.028
                            Fer4_9  33 e.......eaCigCgaCv 43 
                                       +       e C+gCg C 
  gi|336253279|ref|YP_004596386.1| 604 DngmqgmvELCHGCGGCR 621
                                       1334445678*******6 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00012
                            Fer4_9   2 CtgCgaCveaCpagv 16 
                                       C+gC+ C   Cp++v
  gi|336253279|ref|YP_004596386.1| 678 CIGCKGCSIDCPSEV 692
                                       555555555555555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.16   2.8e+02      25      47 ..     598     620 ..     593     626 .. 0.85
   2 ?   10.5   0.3   0.00028      0.51      38      53 ..     675     690 ..     655     703 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.16
                           Fer4_21  25 aieidaktvlkvvedeCvGCnlC 47 
                                       a+e d+++ ++ + + C GC  C
  gi|336253279|ref|YP_004596386.1| 598 ALEWDNDNGMQGMVELCHGCGGC 620
                                       6677888888889999****999 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00028
                           Fer4_21  38 edeCvGCnlCssvCPv 53 
                                          C+GC+ Cs+ CP 
  gi|336253279|ref|YP_004596386.1| 675 MGLCIGCKGCSIDCPS 690
                                       5579999999999984 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   2.2       1.7   3.1e+03      34      44 ..     610     620 ..     593     635 .. 0.72
   2 ?    6.4   8.1    0.0074        13       2      51 ..     614     691 ..     613     692 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.7
                            Fer4_7  34 dpekClgCgaC 44 
                                         e C gCg C
  gi|336253279|ref|YP_004596386.1| 610 MVELCHGCGGC 620
                                       56677777777 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0074
                            Fer4_7   2 CigCgaCv........aaCpvkaieldeeenekgt.....ekv................eidpekClgCgaCvavCP 49 
                                       C gCg C         ++Cp++  + +e +  +g+     + +                e ++  C+gC+ C   CP
  gi|336253279|ref|YP_004596386.1| 614 CHGCGGCRgqqsttggVMCPTYRASREEITATRGRvnalrQ-AmsgnlepeeafsdefvEEVMGLCIGCKGCSIDCP 689
                                       77777775555555557899888887775555533222220.02333333333444443888999************ PP

                            Fer4_7  50 tg 51 
                                       ++
  gi|336253279|ref|YP_004596386.1| 690 SE 691
                                       97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1024 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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):              10  [number of targets reported over threshold]
# CPU time: 0.71u 0.24s 00:00:00.95 Elapsed: 00:00:00.41
# Mc/sec: 7585.67
//
Query:       gi|336253280|ref|YP_004596387.1|  [L=130]
Description: hypothetical protein Halxa_1881 [Halopiger xanaduensis SH-6]
Scores for 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:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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 0.19s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1103.62
//
Query:       gi|336253281|ref|YP_004596388.1|  [L=355]
Description: Anthranilate phosphoribosyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-35  121.2   0.0    8.6e-35  120.5   0.0    1.3  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    6.4e-09   35.5   0.1    5.9e-08   32.4   0.0    2.6  2  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 !  120.5   0.0   9.6e-39   8.6e-35      22     252 ..     109     345 ..      94     346 .. 0.91

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 9.6e-39
                                       HHHHHHHHHTT-BEEEEE-STCTTCS-HH..HHHCTST--ST--HHHHHHHHHHHSEEEEEHHSSSSHHHHHHHHHH CS
                   Glycos_transf_3  22 taaaivvAaaGvkvakhgnrsvssksGsa..DvLealgvnleltpeeveklleevgvgflfapeyhkamkhvapvrr 96 
                                         a++v+AaaG++++ h++  v  +  +a   vLe+lgv+ el+p e + +++e+g+gf  +p +++a++  +  r 
  gi|336253281|ref|YP_004596388.1| 109 VGAGVVAAAAGTPIVVHSGDRVPTQKETAykHVLEELGVRTELEPAESADMVDETGFGFYYQPAFNPAVHDLLDRRD 185
                                       5688999********998866655554442379******************************************** PP

                                       HHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEE...EEEESTTSSCCS.TSHHHHHHHHHHHHHHHH.T CS
                   Glycos_transf_3  97 elgirTvfnlLGPLinparvkkqllgvyskelaeklaevlk...elgveralvvhg.dGldevsllakttvaelk.d 168
                                       ++g+rT  n +    npa+++ +l + y+  +a+kl  +++   el+ +ra++++g +G+d++++ + t vae +  
  gi|336253281|ref|YP_004596388.1| 186 QMGVRTFINTIETVANPANADVHLGSFYHLAFAKKLTDLIResdELEYSRAIFFQGmEGYDDIRP-GYTKVAEWNeG 261
                                       *************************************999733369*****************98.89*******55 PP

                                       TEEEEEEEEEGSSTSSSEEESHHHHSSH.HHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHHHHHHHHH CS
                   Glycos_transf_3 169 geiteytlepedfglkraelealeggep.kenaeilkavlegkksaakrdlvllnagaalvlagkadslkegvakae 244
                                       ++++ y++e ++ g++  e e+le+++   e+a+i ++vl+g++++  +d+++ln++  +++ +++d+l++g+++a+
  gi|336253281|ref|YP_004596388.1| 262 EDLEDYEIETAEYGMEM-ENEDLEVENVaAESAAITEEVLAGEREDDFADAIALNGALRMYARQDVDTLEDGLERAR 337
                                       69************975.6789999875489999999********999***************************** PP

                                       HHHHTSHH CS
                   Glycos_transf_3 245 evidsGkA 252
                                       evi +G+A
  gi|336253281|ref|YP_004596388.1| 338 EVIADGSA 345
                                       ******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 !   32.4   0.0   6.6e-12   5.9e-08      11      62 ..      29      80 ..      20      81 .. 0.95
   2 ?   -1.0   0.0      0.18   1.6e+03       2      23 ..     140     161 ..     139     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 6.6e-12
                                      .---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHH CS
                   Glycos_trans_3N 11 eeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmres 62
                                      e+ t+e++r+a++ i+ ge  +  ++Af  A r k+ ++eE+aa a++mre 
  gi|336253281|ref|YP_004596388.1| 29 EDMTREQAREALQRIFAGEPDETTLGAFWLANRWKRNNPEELAAYADVMREE 80
                                      699***********************************************86 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.18
                                       HHHHHHHTT.---HHHHHHHHH CS
                   Glycos_trans_3N   2 diikklrdgeeLtaeeirfaih 23 
                                       ++++ l  + eL ++e +++++
  gi|336253281|ref|YP_004596388.1| 140 HVLEELGVRTELEPAESADMVD 161
                                       6789999999******999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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 0.19s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 3001.94
//
Query:       gi|336253282|ref|YP_004596389.1|  [L=127]
Description: hypothetical protein Halxa_1883 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        1.4    7.0   4.6        1.6    6.9   4.6    1.1  1  YfhO         Bacterial membrane protein YfhO
        1.4    7.2   5.8        1.6    7.0   5.8    1.1  1  Mem_trans    Membrane transport protein


Domain annotation for each model (and alignments):
>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.6   0.00018       1.6     364     437 ..      44     112 ..      18     124 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00018
                              YfhO 364 lkklkllaailllvlllliilllknkksynfltssqlllgllllllalllllllllkkkkkklvllllllvlvl 437
                                       +    l aa+l   l+++++l l  +  + ++t ++ l+g ++ll+++ll++l + +     +v+ l++lv v+
  gi|336253282|ref|YP_004596389.1|  44 V----LGAALLATGLVVIGSL-LILAGREGIVTAENKLIGTFVLLAMVLLVGLSTFTDVAFEVVFGLVVLVGVV 112
                                       2....2222222222222222.2233344667777777777777777777777776777777777777777554 PP

>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   5.8   0.00018       1.6     261     329 ..      31      91 ..      18     120 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00018
                         Mem_trans 261 vsfkwnvimpkiiqksisilgdaglpmalfslGlfLalqpkkiacgnsvatfalavRlilgPlvmlvav 329
                                       ++f        ++++s ++lg a l+  l+++G+ L+l  ++  ++++ +   l++ ++l+ +v+lv +
  gi|336253282|ref|YP_004596389.1|  31 IGFA-----YGLVAESTTVLGAALLATGLVVIGSLLILAGREGIVTAENK---LIGTFVLLAMVLLVGL 91 
                                       3333.....3699*************************998877776666...7777777777766543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 985.10
//
Query:       gi|336253283|ref|YP_004596390.1|  [L=216]
Description: FxsA cytoplasmic membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-28   97.2  10.8    7.6e-28   96.8  10.8    1.1  1  FxsA           FxsA cytoplasmic membrane protein
  ------ inclusion threshold ------
       0.28   11.3   1.1       0.45   10.7   1.1    1.2  1  DNA_ligase_IV  DNA ligase IV


Domain annotation for each model (and alignments):
>> FxsA  FxsA cytoplasmic membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8  10.8   8.5e-32   7.6e-28       2     108 ..       7     116 ..       5     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 8.5e-32
                              FxsA   2 lllllpvlEilllvlvasaiGvla...tllllvltallGallvrrqgrralrrlqeklaqgelpaeelldglllllg 75 
                                       +lll+p+l+ +ll  +++++G+++   ++ll+vlt+l+G+llvr++grr++ ++q++laqg++p++elldg ll+++
  gi|336253283|ref|YP_004596390.1|   7 ALLLIPFLDAVLLGFLVTQFGGFTwvgMVLLVVLTGLVGMLLVRAEGRRTIGKMQRSLAQGKPPTNELLDGGLLIAA 83 
                                       678**********988888876652336899********************************************** PP

                              FxsA  76 gvLLllPGfvtdvlGlllllPptRkllrrllkr 108
                                       g++Ll+PG+vtd++G+ll +P tR  +r+llkr
  gi|336253283|ref|YP_004596390.1|  84 GAFLLTPGLVTDLIGFLLAVPLTRVPIRALLKR 116
                                       *****************************9998 PP

>> DNA_ligase_IV  DNA ligase IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   5.1e-05      0.45      14      23 ..     181     190 ..     176     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.1e-05
                     DNA_ligase_IV  14 DSYtvDtdee 23 
                                       DSYtvDtde+
  gi|336253283|ref|YP_004596390.1| 181 DSYTVDTDEP 190
                                       ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1731.32
//
Query:       gi|336253284|ref|YP_004596391.1|  [L=559]
Description: hypothetical protein Halxa_1885 [Halopiger xanaduensis SH-6]
Scores for complete 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-24   87.0   0.0    2.6e-24   86.0   0.0    1.4  1  Thioredox_DsbH  Protein of unknown function, DUF255
    1.4e-11   44.4   0.0    3.1e-11   43.3   0.0    1.6  1  Thioredoxin_7   Thioredoxin-like
    1.9e-08   34.2   0.0    3.3e-08   33.4   0.0    1.3  1  Thioredoxin     Thioredoxin
      6e-06   26.7   0.0      1e-05   25.9   0.0    1.4  1  Thioredoxin_2   Thioredoxin-like domain
     0.0037   16.6   1.2        1.9    7.6   0.1    2.2  2  GlcNAc_2-epim   N-acylglucosamine 2-epimerase (GlcNAc 2-epime
     0.0068   16.6   0.0      0.028   14.6   0.0    2.0  2  RTP1_C1         Required for nuclear transport of RNA pol II 
     0.0079   15.3   0.1        2.6    7.0   0.0    2.6  2  Glyco_hydro_88  Glycosyl Hydrolase Family 88
  ------ inclusion threshold ------
      0.023   14.2   0.1        5.9    6.3   0.0    2.2  2  Glyco_hydro_76  Glycosyl hydrolase family 76
       0.16   11.4   0.1        1.8    8.1   0.0    2.2  2  C5-epim_C       D-glucuronyl C5-epimerase C-terminus


Domain annotation for each model (and alignments):
>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.0   1.3e-27   2.6e-24      17     148 ..       5     122 ..       2     132 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 1.3e-27
                    Thioredox_DsbH  17 knpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkvDreerPdldkiymea 93 
                                       ++ v+W +wg++a+++a + + p+lls+  ++c  Ch m+ e+++++++aa +n+sfv+++vD +  P + + y   
  gi|336253284|ref|YP_004596391.1|   5 TTRVEWREWGQDAFDEAAAAEAPVLLSLTATWCDHCHEMDAETYAEPRIAANINDSFVPIRVDVDRYPRVRDRYN-- 79 
                                       578*******************************************************************99994.. PP

                    Thioredox_DsbH  94 vqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeer 148
                                              gg+P +vfl pd++ + g+ Y+         g+++vl++++++w+++ 
  gi|336253284|ref|YP_004596391.1|  80 ------MGGFPSTVFLAPDGNVLTGAGYLGA------DGMRQVLDSVRTMWQTKG 122
                                       ......6*********************976......6899**********9875 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   1.5e-14   3.1e-11       1      83 []       9      91 ..       9      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.5e-14
                                      ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG..-TT---SSEE CS
                     Thioredoxin_7  1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdani.leldeqgvPvv 78
                                      ew  +  +a+++aa+ + pvl+ ++a+wc +C+ ++ ++  +++++a +++ fv  rvdv++  + +  ++ + g+P  
  gi|336253284|ref|YP_004596391.1|  9 EWREWGQDAFDEAAAAEAPVLLSLTATWCDHCHEMDAETYAEPRIAANINDSFVPIRVDVDRYPR-VrDRYNMGGFPST 86
                                      68888999****************************************************87666.312233478**** PP

                                      EEE-T CS
                     Thioredoxin_7 79 afldp 83
                                      +fl p
  gi|336253284|ref|YP_004596391.1| 87 VFLAP 91
                                      **988 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   1.7e-11   3.3e-08       7      92 ..      15     102 ..      10     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.7e-11
                                       HHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHH.HHH..HHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEE CS
                       Thioredoxin   7 kenFeeevakekklvlveFyApwCghCkalaPe.lek..laeelkdkvklakvdvdenedlakkyevegiPtlklfk 80 
                                       +++F+e+ a+ + +vl+  +A+wC hC ++  e +++  +a +++d ++ ++vdvd  + + ++y+  g+P  +++ 
  gi|336253284|ref|YP_004596391.1|  15 QDAFDEAAAA-EAPVLLSLTATWCDHCHEMDAEtYAEprIAANINDSFVPIRVDVDRYPRVRDRYNMGGFPSTVFLA 90 
                                       6789999999.9******************8762443448999999*************************887776 PP

                                       TTEEEEEEESS- CS
                       Thioredoxin  81 ngkevkkyegar 92 
                                        + +v +  g  
  gi|336253284|ref|YP_004596391.1|  91 PDGNVLTGAGYL 102
                                       655555555544 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   5.1e-09     1e-05       2     109 .]      22     111 ..      21     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5.1e-09
                     Thioredoxin_2   2 kgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygv 78 
                                       ++ + pvl+  t+++C  C+ + +e+   +++        +++sf+p+ v++++ + +              ++y++
  gi|336253284|ref|YP_004596391.1|  22 AAAEAPVLLSLTATWCDHCHEMDAETYAEPRIAAN-----INDSFVPIRVDVDRYPRVR-------------DRYNM 80 
                                       56789******************************.....****************997.............89*** PP

                     Thioredoxin_2  79 rgtPtivfldgkeivarlpGyvpaeeleall 109
                                        g+P++vfl ++  v++  Gy+ a+ ++++l
  gi|336253284|ref|YP_004596391.1|  81 GGFPSTVFLAPDGNVLTGAGYLGADGMRQVL 111
                                       *****99998885556779999999999987 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1   0.00096       1.9      47     129 ..     190     275 ..     177     286 .. 0.76
   2 !    7.5   0.1     0.001       2.1      95     182 ..     319     405 ..     313     407 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00096
                                       HHHHHTTTTTB-TTTSSB-SEEETTEE.EE--EEHHHHHHHHH.HHHH.HHTTT-TTHHHHHHHHHHHHHHHTEETT CS
                     GlcNAc_2-epim  47 hGlkflekvlrdaehggyfsalrdggv.ldaskdaYdhaFvll.alas.alaageeeakdlldetlavlekhlweek 120
                                          ++ + +l d+  gg+++ ++d++    +++++ d   +l  a+a+  l +g++e+++ ++ t+++l + lw+ +
  gi|336253284|ref|YP_004596391.1| 190 RSFDAVSANLLDEYDGGFYRFATDRDWgGVQREKLLDSNGALVrAFANaYLLTGKDEYREPAERTIDFLTTTLWNGD 266
                                       555556666668888999998877764367777777777665548888457899********************999 PP

                                       TTEE--EE- CS
                     GlcNAc_2-epim 121 aglvkeesd 129
                                         ++++++ 
  gi|336253284|ref|YP_004596391.1| 267 VDAFANSQA 275
                                       999888765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.001
                                       TTT-TTHHHHHHHHHHHHHHHTEETTTTEE--EE-TTSS-BEEHHHHHHHHHHHHHHHHTT-BTHHHHHHHHHHHHH CS
                     GlcNAc_2-epim  95 aageeeakdlldetlavlekhlweekaglvkeesdkefsklrgsnpnMhlleAmLalaeatgdkeyleraeeiaelv 171
                                       ++ +e+a++ ++ +la+l ++l  e   + + ++d++ ++++    + ++leA+   a+   d e+l+ a ++a+++
  gi|336253284|ref|YP_004596391.1| 319 YTDDERARRYAERALATLREDLLAEGVVAHRYTADGNDAPTPLLTNQARALEAL-TTAASVLDAEFLADARRVADAT 394
                                       56788999999*******9999999998889999998888866677789***75.5557778*************** PP

                                       TTTTGGGGTT- CS
                     GlcNAc_2-epim 172 isefadaesgl 182
                                       i+++ d+ s++
  gi|336253284|ref|YP_004596391.1| 395 IERLHDEDSFV 405
                                       *****999886 PP

>> RTP1_C1  Required for nuclear transport of RNA pol II C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.9   3.8e+03       4      17 ..      53      66 ..      52      67 .. 0.85
   2 !   14.6   0.0   1.4e-05     0.028      11      56 ..     360     405 ..     354     406 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.9
                           RTP1_C1  4 alkdlqdpllpvra 17
                                      + ++++d+ +p+r+
  gi|336253284|ref|YP_004596391.1| 53 IAANINDSFVPIRV 66
                                      5689********96 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.4e-05
                           RTP1_C1  11 pllpvrahglvlLrkliekkskeavldiekilkllleaLkdedsYv 56 
                                       pll  +a++l  L++ ++  ++e ++d++++++  +e L+deds+v
  gi|336253284|ref|YP_004596391.1| 360 PLLTNQARALEALTTAASVLDAEFLADARRVADATIERLHDEDSFV 405
                                       78999****************************************8 PP

>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0     0.004       7.9      30      62 ..     227     259 ..     199     288 .. 0.82
   2 !    7.0   0.0    0.0013       2.6      31      65 ..     306     340 ..     302     402 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.004
                                       HHHHHHHHHHHHHHHH--HHHHHHHHHHHHHCC CS
                    Glyco_hydro_88  30 tnGvflsglleayeatgdkeyldyakawadsli 62 
                                        nG++++++++ay  tg++ey++ a+++ d l 
  gi|336253284|ref|YP_004596391.1| 227 SNGALVRAFANAYLLTGKDEYREPAERTIDFLT 259
                                       5899*******************9999887654 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHH--HHHHHHHHHHHHHCCCTT CS
                    Glyco_hydro_88  31 nGvflsglleayeatgdkeyldyakawadslideg 65 
                                       n+++++gll +y +t d++ + ya++   +l ++ 
  gi|336253284|ref|YP_004596391.1| 306 NALAIEGLLTYYAYTDDERARRYAERALATLREDL 340
                                       8999********************99776666554 PP

>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0041       8.1     155     192 ..     227     263 ..     194     294 .. 0.84
   2 ?    6.3   0.0     0.003       5.9      38     131 ..     306     402 ..     296     407 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0041
                                       HHHHHHHHHHHHHHHH--CHHHHHHHHHHHHHHHHSCS CS
                    Glyco_hydro_76 155 sngplfqlaarLarytgnetYlewAekvwdWvedvgli 192
                                       sng+l  + a  +  tg+++Y e Ae++ d+++++ l 
  gi|336253284|ref|YP_004596391.1| 227 SNGALVRAFANAYLLTGKDEYREPAERTIDFLTTT-LW 263
                                       89999999999999999999999999999999885.33 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHHHHCTTCCCHHHHHHHHHCCCTCE.E-SSSTTCTCSSEHHHHHHHHHHHHHHHHH......H--HH CS
                    Glyco_hydro_76  38 agalfgalidywrltgdstyndlitqallaqagen.ydympanqsrtegnDDqafwglaamtaaernfpep.tdeps 112
                                       ++ +++ l+ y+ +t+d++ ++  ++al   +++   + + a+  + +gnD      + + +a e+  ++    + +
  gi|336253284|ref|YP_004596391.1| 306 NALAIEGLLTYYAYTDDERARRYAERALATLREDLlAEGVVAHRYTADGNDAPTPLLTNQARALEALTTAAsVLDAE 382
                                       5678899***********************999887676666666669***99999999999999988888788999 PP

                                       HHHHHHHHHHHHHHC.B-SC CS
                    Glyco_hydro_76 113 wLalAqavfntqasr.wdee 131
                                       +La A+ v +  ++r +de+
  gi|336253284|ref|YP_004596391.1| 383 FLADARRVADATIERlHDED 402
                                       **************977776 PP

>> C5-epim_C  D-glucuronyl C5-epimerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00088       1.8      31      68 ..     228     265 ..     227     275 .. 0.86
   2 ?    0.6   0.0      0.17   3.5e+02      99     130 ..     309     340 ..     306     351 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00088
                         C5-epim_C  31 qgqaisvllrAYeltgdekYlkaakkalksfkipvekG 68 
                                       +g ++ +++ AY ltg+++Y + a++ +++++++  +G
  gi|336253284|ref|YP_004596391.1| 228 NGALVRAFANAYLLTGKDEYREPAERTIDFLTTTLWNG 265
                                       6788999***********************99987666 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.17
                         C5-epim_C  99 sligLydlstakkseeakelfkkglkslkall 130
                                       ++ gL  ++ ++ +e+a+++ ++ l +l++ l
  gi|336253284|ref|YP_004596391.1| 309 AIEGLLTYYAYTDDERARRYAERALATLREDL 340
                                       45677777777777777777777777776644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 4105.26
//
Query:       gi|336253285|ref|YP_004596392.1|  [L=267]
Description: transcriptional regulator TrmB [Halopiger xanaduensis SH-6]
Scores for 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   72.5   0.2    3.5e-20   71.6   0.2    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.032   13.4   0.0      0.052   12.7   0.0    1.3  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
       0.12   12.3   0.0       0.26   11.3   0.0    1.5  1  PadR            Transcriptional regulator PadR-like family
       0.17   11.8   0.0       0.34   10.8   0.0    1.5  1  PLDc_2          PLD-like domain


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 !   71.6   0.2   7.8e-24   3.5e-20       1      67 [.       4      71 ..       4      72 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 7.8e-24
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravdp 67
                                      L++lGLseyEa++Y aLl+ gp ta+e++++++vp  ++Y+vL+s e+  lV+ +  +rpk+Y+av+p
  gi|336253285|ref|YP_004596392.1|  4 LRDLGLSEYEARAYRALLNTGPTTAKELSRASDVPMGRIYDVLNSIEQYSLVRSQTaSRPKKYVAVEP 71
                                      789****************************************************9566*******99 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.2e-05     0.052      37     134 ..     158     264 ..     149     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHTT-EEEEEESS..........----GGGSSSSEEEEEE-S---S..EEEEETTTEEEEE-SSS-EE CS
                    Regulator_TrmB  37 elreeliaaaergvtVllliyp..........dedleeldleevatevrvrrsga.pllvivDrkrgvvaprevlrd 102
                                       ++  +l++a +rgv+V +l++            e  +e   ++   +vr+++  + ++ +i D + ++ +  ++l++
  gi|336253285|ref|YP_004596392.1| 158 DVTAQLEDALDRGVSVDVLMTRqmvpalservGERYRETLQARDDFDVRTNEDVTgTFNLIDDVEVCIQV-PNPLSS 233
                                       56789****************99*9999887644445555566778999999999555556555555555.558999 PP

                                       EE--HHHHHHHHHHHHHH........HHH-EE CS
                    Regulator_TrmB 103 keeeyaiifkekelihvlshyFlttlWktsev 134
                                        e +  i  k++e++  ++  F  + W+++e 
  gi|336253285|ref|YP_004596392.1| 234 GEAFGMIDLKDPEFAASVHDEFVPR-WQEAEP 264
                                       999**********************.**9986 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.8e-05      0.26      26      62 ..      34      66 ..      23      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.8e-05
                                      -CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEE CS
                              PadR 26 llelseGslYpaLkrLekeglveseweesgegpprky 62
                                      + ++ +G++Y++L++ e+  lv s+ +     +p+ky
  gi|336253285|ref|YP_004596392.1| 34 ASDVPMGRIYDVLNSIEQYSLVRSQTAS----RPKKY 66
                                      35899******************99775....56666 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.5e-05      0.34      20      68 ..     154     201 ..     128     219 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.5e-05
                            PLDc_2  20 vsdreildallkaakrgvkvrilldskkddagavdeaslkelke.lllea 68 
                                         ++++ ++l +a +rgv v +l+ ++   +++  e+   +++e l ++ 
  gi|336253285|ref|YP_004596392.1| 154 ALSEDVTAQLEDALDRGVSVDVLMTRQ-MVPALS-ERVGERYREtLQARD 201
                                       456677999****************94.444444.455555544044444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      761  (0.0424452); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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 0.22s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 2156.21
//
Query:       gi|336253286|ref|YP_004596393.1|  [L=311]
Description: hypothetical protein Halxa_1887 [Halopiger xanaduensis SH-6]
Scores for 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-76  256.3   3.0    3.5e-76  256.1   3.0    1.0  1  GCHY-1    Type I GTP cyclohydrolase folE2
  ------ inclusion threshold ------
      0.042   14.3   0.6        1.2    9.6   0.0    2.7  3  RecX      RecX family
      0.072   13.0   0.0       0.21   11.4   0.0    1.8  1  PASTA     PASTA domain


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 !  256.1   3.0   5.9e-80   3.5e-76       1     259 []       5     293 ..       5     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 256.1 bits;  conditional E-value: 5.9e-80
                                       .XXXXXXXXXX----SEEEEEEEEEEEEE--TTTS-EEEEEEEEEEEES-SS--GGGGGHHHHHHHHS-SSEEG... CS
                            GCHY-1   1 lpDvqsekderkipldrVGvkgvklpvkvkdkekkaqtlvaevdlfvdLpaekkGihmSRlvevleeaeeelee... 74 
                                       lpDvq++++++++ l++VGv+gv+++vk+++++k+++ l+ae+++fvdLpa +kG++mSR++ev++e  e+ +    
  gi|336253286|ref|YP_004596393.1|   5 LPDVQATSPDVTVGLSQVGVTGVEKLVKIAREDKRPIVLTAEFEVFVDLPAWRKGADMSRNMEVIDEILEDATReea 81 
                                       79****************************************************************44444443456 PP

                                       GGHHH....HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE..TTEEEEEEEEEEEEEEE- CS
                            GCHY-1  75 kslee....ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaelerkeevkltvgvevpvttlC 147
                                       +++ee     +e+llek++y+++a+v++++e++ ++++p+s++e+++++++++ a+++++  ++ ++g+ev+++t+C
  gi|336253286|ref|YP_004596393.1|  82 YRVEEvcgdAAERLLEKHDYTSKAQVSMEAEFMRREQTPASDRETQHTVDIIAAATATEE-GTREEIGAEVTGMTVC 157
                                       5555577779***********************************************773.6*************** PP

                                       HHHHHHS.........................SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE--S-- CS
                            GCHY-1 148 PCskeisrell.....................eagaHnQRsvvtvkvelaeeekeveiedlielvessassevyell 203
                                       PCs+ +s + +                     +++ H+QR+++t++ve a+ + ev+++d+i+++++s+s+++y+l 
  gi|336253286|ref|YP_004596393.1| 158 PCSQGMSAARAkqtledlgvdeetitefldevPQPGHSQRGHATLTVE-ANGDPEVDLNDIIDVARDSMSARIYNLA 233
                                       *******77779************************************.66999*********************** PP

                                       -HHHHHHHHHHHHTS---HHHHHHHHHHHHHS-TTEEEE.........EEEEEEE-TTTSSEEEE CS
                            GCHY-1 204 KReDEkavtekayenpkFvEDvvRevaaaleeeerveef.........sveveneESiHnHnavA 259
                                       KR+DE+++t +a++ +kFvED+vR++a+ +     veef         +++++n ESiH+Hna A
  gi|336253286|ref|YP_004596393.1| 234 KRPDEDHMTYAAHADAKFVEDCVRSMAEGV-----VEEFdhleddavvTMKQSNDESIHQHNAHA 293
                                       *****************************9.....6666666888999***************98 PP

>> RecX  RecX family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2     0.053   3.2e+02      61      83 ..      68     100 ..      64     121 .. 0.55
   2 ?    9.6   0.0    0.0002       1.2      41      72 ..     161     192 ..     158     216 .. 0.87
   3 ?   -1.8   0.0       0.7   4.2e+03      26      39 ..     248     261 ..     247     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.053
                                       HHHHHHTTS-HHHH..........HHHHHHHHH CS
                              RecX  61 lieqaleeldeeeq..........arelaekkl 83 
                                       +i++ le+ ++ee+          a++l+ek+ 
  gi|336253286|ref|YP_004596393.1|  68 VIDEILEDATREEAyrveevcgdaAERLLEKHD 100
                                       555555544444444544575555555555543 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0002
                                       ----HHHHHHHHHTTT--HHHHHHHHTTS-HH CS
                              RecX  41 rgyGprrikqeLkqkGiseelieqaleeldee 72 
                                       +g+++ r kq L   G++ee+i + l+e+ + 
  gi|336253286|ref|YP_004596393.1| 161 QGMSAARAKQTLEDLGVDEETITEFLDEVPQP 192
                                       788999********************987665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.7
                                       HHHHHHHHHHHHHH CS
                              RecX  26 DerfAesfvrsrlr 39 
                                       D++f+e +vrs+++
  gi|336253286|ref|YP_004596393.1| 248 DAKFVEDCVRSMAE 261
                                       77888888888764 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.6e-05      0.21       8      36 ..     162     190 ..     161     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                                       TSBHHHHHHHHHHTT--CCCEEEECTCCG CS
                             PASTA   8 GmsvdeAkatLkalGlkiktveetsddvp 36 
                                       Gms + Ak+tL++lG+   t++e+ d+vp
  gi|336253286|ref|YP_004596393.1| 162 GMSAARAKQTLEDLGVDEETITEFLDEVP 190
                                       9***************9999999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2433.95
//
Query:       gi|336253287|ref|YP_004596394.1|  [L=257]
Description: hypothetical protein Halxa_1888 [Halopiger xanaduensis SH-6]
Scores for 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   16.7   0.0      0.019   14.8   0.0    1.9  2  LppX_LprAFG  LppX_LprAFG lipoprotein
  ------ inclusion threshold ------
       0.01   16.0   0.2       0.46   10.7   0.0    2.3  2  Adeno_PIX    Adenovirus hexon-associated protein (IX)
      0.025   14.8   0.3       0.06   13.6   0.3    1.6  1  TetR_C_6     BetI-type transcriptional repressor, C-terminal


Domain annotation for each model (and alignments):
>> LppX_LprAFG  LppX_LprAFG lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.44   2.6e+03     144     144 ..      69      69 ..      36      96 .. 0.49
   2 !   14.8   0.0   3.2e-06     0.019     113     189 ..     147     236 ..     142     239 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.44
                                       C CS
                       LppX_LprAFG 144 p 144
                                       +
  gi|336253287|ref|YP_004596394.1|  69 G 69 
                                       2 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.2e-06
                                       EEEEEEEEEETTEEEEEEEEEE-HHHHHH..H-CC...G-SS..S.EEEEEEEESS.....TT--EEEEEE.EECTC CS
                       LppX_LprAFG 113 dakaegreeidGtatvkitGtvdadvvsa..ivps...lked..gtvpitlWiaed.....gelrlvrvvv.dkesg 176
                                       d++ +g+e+ dG++++++tG  +ad+ +   i +s   +++   +   +tlW++ +     +++   +v+  d++ +
  gi|336253287|ref|YP_004596394.1| 147 DLHWNGTETYDGREAIRLTGSPPADAFDDgrIGGSrfdFGGPnlEDASTTLWLDAEtgrplETSVEFEVSGnDETAT 223
                                       67889*********************9853366656554443345689*****998555444444445555445555 PP

                                       EEEEEEEESTT-- CS
                       LppX_LprAFG 177 esveltlskwgkp 189
                                       +s+++  s +++p
  gi|336253287|ref|YP_004596394.1| 224 ASITMRYSAYDEP 236
                                       5599999999998 PP

>> Adeno_PIX  Adenovirus hexon-associated protein (IX)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.018   1.1e+02      32      53 ..      74      95 ..      59     101 .. 0.78
   2 ?   10.7   0.0   7.8e-05      0.46      23      71 ..     178     227 ..     162     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.018
                         Adeno_PIX 32 pvlpansttltyetvsgtplet 53
                                       v  an t  t  t+ gt le+
  gi|336253287|ref|YP_004596394.1| 74 AVDLANETMYTNATIDGTTLES 95
                                      46679***************96 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.8e-05
                         Adeno_PIX  23 vmgssid.grpvlpansttltyetvsgtpletaasaaasaaaatargivt 71 
                                       + gs  d g p l   sttl  ++ +g plet+     s    ta   +t
  gi|336253287|ref|YP_004596394.1| 178 IGGSRFDfGGPNLEDASTTLWLDAETGRPLETSVEFEVSGNDETATASIT 227
                                       5567777789***********************99998888777765554 PP

>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3     1e-05      0.06      42     101 ..      47     105 ..      33     108 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHHHHHHHHHHHHTTSCTTSTHHHHHHHHHHHHHHHHHHHHHTCTTCHHHH CS
                          TetR_C_6  42 lqrenyarlrsnlrallaelaegglradadaeaaAerlaAlidGLwlraalapeeldaer 101
                                          ++y+   ++ +a+  +  +g ++ ++d++ ++   +A idG +l++ l+ +++++e+
  gi|336253287|ref|YP_004596394.1|  47 DETATYRYEGELSVAADHQHIDGSVFGAVDLANETMYTNATIDGTTLESYLE-GDTRREQ 105
                                       33333333333333333344559****************************9.5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1993.68
//
Query:       gi|336253288|ref|YP_004596395.1|  [L=417]
Description: MiaB-like tRNA modifying protein [Halopiger xanaduensis SH-6]
Scores for 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-24   85.7   0.4    8.6e-24   84.8   0.2    1.6  2  Radical_SAM  Radical SAM superfamily
    7.9e-19   67.5   0.1      2e-18   66.3   0.1    1.7  1  UPF0004      Uncharacterized protein family UPF0004
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.24   11.4   0.0    1.5  1  TRAM         TRAM 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 ?   -3.8   0.0       2.5   1.5e+04      33      51 ..      56      72 ..      47     102 .. 0.58
   2 !   84.8   0.2   1.4e-27   8.6e-24       2     166 ..     128     300 ..     127     301 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.5
                                      HHHHHHHHHHHHTTSEEEE CS
                                      xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 33 eileevkelkaekgvkevi 51
                                      + l+ ++el a+  +  ++
  gi|336253288|ref|YP_004596395.1| 56 NMLRRAEEL-ADE-TADLF 72
                                      334444444.233.33333 PP

  == domain 2  score: 84.8 bits;  conditional E-value: 1.4e-27
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS......TTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly......pdfvellerlak 72 
                                       ++ rgC  +Cs+C+++e    +g+  s +vee +e++++l  + g+ke+ ++g++  +y      ++++eller+++
  gi|336253288|ref|YP_004596395.1| 128 PIARGCMSNCSYCITKE---ATGKIDSPPVEENVEKARAL-IHAGAKEIRITGQDTGVYgwdtgeRKLHELLERICE 200
                                       689*************9...8*******************.899*********************9*********** PP

                                       TCCCTEEEEEEECSSCHG....HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  73 lavpgiritvetngtlpd....eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreagik 143
                                       ++  ++r++v    ++      ee +e ++e     d ++ ++++++d+ vl  m+r+h +ee++e++e++ ++ ++
  gi|336253288|ref|YP_004596395.1| 201 IE-GDFRVRVGMANPKGVhgirEELAEVFAEHDelYDFLHAPVQSGSDD-VLGDMRRQHQVEEYVEVVETFDDR-LD 274
                                       *8.555555544444433569988888888888999*************.999999******************.99 PP

                                       T...EEEEEEEBTTTSHHHHHHHHHH CS
                                       x...xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 144 r...vvdrivglpGendeeleellel 166
                                           ++d+ivg+p e+++++e+ + l
  gi|336253288|ref|YP_004596395.1| 275 YwtlSTDFIVGFPTETEHDHEQSMAL 300
                                       9*******************998876 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.1   3.3e-22     2e-18       1      89 [.       3      88 ..       3      95 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 3.3e-22
                                      XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHH CS
                           UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCma 79
                                      +++iet+GC+ N+ +s e+ ++L+++g+ +v+ +e Adv ++nTC+v+ek+e++++++ +el+++    + ++++GCma
  gi|336253288|ref|YP_004596395.1|  3 RYHIETYGCTSNRGESREIERRLRDAGHYRVDGPEVADVAILNTCTVVEKTERNMLRRAEELADET---ADLFITGCMA 78
                                      789*************************************************99888877777766...99******** PP

                                      HS-HHHHHHH CS
                           UPF0004 80 qrekeellke 89
                                       +++ee+ ++
  gi|336253288|ref|YP_004596395.1| 79 LAQGEEFRAA 88
                                      ****998765 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     4e-05      0.24      30      62 .]     382     417 .]     366     417 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4e-05
                                       EEEEETT-.....-T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM  30 kvvfvpgd.....lpgIGdfVeVkItkvkrqyLrGell 62 
                                       + ++v+++     +p  GdfV+ ++t  +  y++G+++
  gi|336253288|ref|YP_004596395.1| 382 RQIIVQNAsdhglEP--GDFVDLEVTAHETMYAFGDPV 417
                                       5567777777777**..******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); 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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.34
# Mc/sec: 3624.71
//
Query:       gi|336253289|ref|YP_004596396.1|  [L=366]
Description: peptidase M48 Ste24p [Halopiger xanaduensis SH-6]
Scores for complete 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   97.0   0.0    1.6e-27   96.5   0.0    1.2  1  Peptidase_M48  Peptidase family M48
    0.00084   18.6   3.9     0.0026   17.0   0.0    2.6  3  Peptidase_M56  BlaR1 peptidase M56
     0.0036   17.2   0.0     0.0062   16.4   0.0    1.4  1  SprT-like      SprT-like family
  ------ inclusion threshold ------
      0.043   13.4   0.0      0.068   12.7   0.0    1.2  1  DUF2268        Predicted Zn-dependent protease (DUF2268)


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 !   96.5   0.0   3.7e-31   1.6e-27       5     195 ..      93     356 ..      90     357 .. 0.88

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 3.7e-31
                                       SHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   5 aelkevveelakeaglpkpltkvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsv 81 
                                        ++ ++v++la  a++  p++ v v+++++   +++g+    +iv+t+gL+ ++l+ +el+aVl+HE++H+++r+++
  gi|336253289|ref|YP_004596396.1|  93 HDVARTVRRLAMTADV--PEPSVRVIDDDEPSCYTVGRLTDATIVVTTGLV-DTLDADELEAVLAHEIAHVVNRDVT 166
                                       67999***********..*********************888*********.************************* PP

                                       HHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHH.HHHHHHHTT.....................HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.....................xxxxxx RF
                     Peptidase_M48  82 vslivsllasillllglallisraeedaagafldalavli.glliillfl.....................alSRkr 136
                                        ++i +l  +i+ +  + + ++r  +++  +  ++  v++ ++l+++  l                      lS +r
  gi|336253289|ref|YP_004596396.1| 167 LMTITTLFVEIADQAYHWARLARRALFDPRQLSTRGRVAVqWFLPLV-ALtyvfvapllwvfptiadwatrTLSHAR 242
                                       ***********998888777666666665555555555440444444.44589999********************* PP

                                       HHHHHHHHHHTTT.HHHHHHHHHHHHHHTT--S---HHHH..................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                     Peptidase_M48 137 EyqADeagvellkrakdlvraliklakdlerqdvsaslrs..................................... 176
                                       E+ AD a+++++ ++ +l++al++la+  e+ + +  + +                                     
  gi|336253289|ref|YP_004596396.1| 243 EFAADDAAARITGKPLALATALVTLAEATETPETDLRTAKtralcivptelvtgravgsasdvadgastttpaerre 319
                                       ******************************97777776667788888888888888888888888888899999999 PP

                                       ..................HHS-SS--HHHHHHHHHH- CS
                                       ..................xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 177 ..................ellstHPplleRiqalkel 195
                                                         + + tHPp  +R+++l+++
  gi|336253289|ref|YP_004596396.1| 320 tvsawlegatpatattapTGTGTHPPVNRRLERLQTI 356
                                       99999999**************************986 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.7      0.45     2e+03     102     126 ..      20      42 ..      12      48 .. 0.71
   2 !   17.0   0.0   5.8e-07    0.0026     179     221 ..     132     174 ..     118     178 .. 0.89
   3 ?    2.0   0.0     0.021        95     215     253 ..     214     253 ..     208     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.45
                     Peptidase_M56 102 lkillliWivgalilllyliaallv 126
                                       l +l+l+W+ g+l+    ++a+  v
  gi|336253289|ref|YP_004596396.1|  20 LFVLVLLWAYGVLL--PGVVAGTIV 42 
                                       56789999999998..555555555 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5.8e-07
                     Peptidase_M56 179 prIvlPadflkklsdeeleyillHElaHlkrkDllvnllvavl 221
                                         Iv+ + ++ +l+++ele +l+HE aH+ ++D+    + +++
  gi|336253289|ref|YP_004596396.1| 132 ATIVVTTGLVDTLDADELEAVLAHEIAHVVNRDVTLMTITTLF 174
                                       6799******************************999888876 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.021
                     Peptidase_M56 215 nllvavlqclfwfNPlvh.laarkirlDqElaCDaaVLar 253
                                        l ++++  l w  P +   a r++ +++E a+D a+ ++
  gi|336253289|ref|YP_004596396.1| 214 ALTYVFVAPLLWVFPTIAdWATRTLSHAREFAADDAAARI 253
                                       5567788888999998874688999*********987655 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.4e-06    0.0062      45      77 ..     130     162 ..      85     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-06
                         SprT-like  45 hhasIeLseklldsrsedrllntLaHElcHlal 77 
                                       ++a+I   + l+d+ ++d+l+ +LaHE++H+++
  gi|336253289|ref|YP_004596396.1| 130 TDATIVVTTGLVDTLDADELEAVLAHEIAHVVN 162
                                       568999************************998 PP

>> DUF2268  Predicted Zn-dependent protease (DUF2268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.5e-05     0.068      42      79 ..     126     163 ..     107     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                           DUF2268  42 kgglaipdkiflfl.leneyskerlaallaHEyhHvvrl 79 
                                       +g+l  +  i+++  l ++ ++++l+a+laHE+ Hvv  
  gi|336253289|ref|YP_004596396.1| 126 VGRLT-DATIVVTTgLVDTLDADELEAVLAHEIAHVVNR 163
                                       44444.445555555999******************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 00:00:00.35
# Mc/sec: 3110.46
//
Query:       gi|336253290|ref|YP_004596397.1|  [L=585]
Description: hypothetical protein Halxa_1891 [Halopiger xanaduensis SH-6]
Scores for 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-06   28.9   9.3      1e-06   28.9   9.3    2.2  2  DUF4129          Domain of unknown function (DUF4129)
    0.00027   21.4   1.1       0.11   12.9   0.0    2.4  2  DUF4198          Domain of unknown function (DUF4198)
     0.0034   17.6   6.7      0.018   15.3   0.8    3.7  5  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.093   12.8  12.6       0.66   10.0   0.2    4.0  4  Big_1            Bacterial Ig-like domain (group 1)
       0.12   12.3   0.6         10    6.2   0.1    2.5  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
        2.3    8.6   6.4        1.9    8.8   1.6    2.8  3  AglB_L1          Archaeal glycosylation protein B long periph


Domain annotation for each model (and alignments):
>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.95   2.9e+03      33      46 ..     369     382 ..     335     383 .. 0.71
   2 !   28.9   9.3   3.4e-10     1e-06       1      69 []     497     562 ..     494     562 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.95
                           DUF4129  33 pspaaalaalaelf 46 
                                         +a+a+ +la lf
  gi|336253290|ref|YP_004596397.1| 369 DGAARAVSRLAGLF 382
                                       33677888888877 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 3.4e-10
                           DUF4129   1 ayrallraLaergldrrpgeTprEyarrvriapspaaalaalaelfeearYGgrpasaeeyrrlvealr 69 
                                       a+ a+l++L    + rr++ Tp+++arr+ +++ pa+ +a+l+++++++ YG+r++s+e + +++ea r
  gi|336253290|ref|YP_004596397.1| 497 AWHAFLDRL---EVTRRETLTPGQVARRALQSGFPATLVARLVAIVRDVEYGRREPSPERVLEAREAAR 562
                                       355555555...59***************88899********************************976 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.3    0.0026       7.7     160     201 ..     164     210 ..     143     213 .. 0.74
   2 !   12.9   0.0   3.6e-05      0.11     147     179 ..     244     276 ..     225     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0026
                           DUF4198 160 dGk.Plagaeveveyggt....ryrdapdeikv......ktdadGvvtftlpk 201
                                       dG  P+ + ev+++ g+t      +       v      +td+dG++t+tlp 
  gi|336253290|ref|YP_004596397.1| 164 DGAvPAGDMEVSAVVGSTpvpdATVF------VdgvsaaETDEDGRATVTLPD 210
                                       55558888999999988744433333......2334445***********985 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.6e-05
                           DUF4198 147 lkageelevqvlldGkPlagaeveveyggtryr 179
                                       l+ g +++vqv  dG P ++a+v++e ggt   
  gi|336253290|ref|YP_004596397.1| 244 LFPGSPAPVQVSADGTPIPNATVSLESGGTATT 276
                                       689*************************98433 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.1   1.2e+04      52      70 ..      99     117 ..      93     122 .. 0.54
   2 ?   -2.2   0.6       1.7   5.2e+03      16      36 ..     138     158 ..     129     163 .. 0.70
   3 !   14.0   0.7   1.6e-05     0.047      11      73 ..     180     236 ..     172     243 .. 0.82
   4 !   15.3   0.8   6.2e-06     0.018       7      55 ..     254     297 ..     252     314 .. 0.78
   5 ?   -3.3   0.1       3.7   1.1e+04       2      43 ..     346     385 ..     345     387 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.1
                   CarboxypepD_reg  52 vtvsapGyatatreevtlt 70 
                                       vt+s +   t++ ++v+++
  gi|336253290|ref|YP_004596397.1|  99 VTISIDSASTFNEQTVEVN 117
                                       4555555555555545444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                   CarboxypepD_reg  16 gatVtvtnadtgtvastttda 36 
                                       ++tV+v+ ++ + +  + t+a
  gi|336253290|ref|YP_004596397.1| 138 EMTVRVAETNASRTVDVETNA 158
                                       567777766666666666765 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 1.6e-05
                   CarboxypepD_reg  11 gapiagatVtvtnadtgtvastttdadGafrlrglpp..gtysvtvsapGyatatreevtltagq 73 
                                        +p++ atV v       v+ + td+dG+ +++ lp   g+ +++v+++     +  +v++t+ q
  gi|336253290|ref|YP_004596397.1| 180 STPVPDATVFVD-----GVSAAETDEDGRATVT-LPDeaGPTDLRVEREPVTGER--AVEVTEPQ 236
                                       47**********.....899************9.77669*******988766655..47777666 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 6.2e-06
                   CarboxypepD_reg   7 tdasgapiagatVtvtnadtgtvastttdadGafrlrglpp.gtysvtvs 55 
                                       ++a+g+pi++atV+++     +  ++tt++dG+ rl  lp  ++ +vt s
  gi|336253290|ref|YP_004596397.1| 254 VSADGTPIPNATVSLE-----SGGTATTGDDGRTRLW-LPIaDEATVTTS 297
                                       4689************.....79999******99986.666577777663 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 3.7
                   CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlr 43 
                                       +sG V+   g +++g++ +++  + +  a++++   G f+++
  gi|336253290|ref|YP_004596397.1| 346 LSGFVVG-LGDVLSGVAAALSG-AIDGAARAVSRLAGLFTVQ 385
                                       6777775.56677777777772.3344566777777777765 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 ?    1.0   0.1      0.14   4.2e+02      20      39 ..      93     112 ..      89     123 .. 0.75
   2 ?    8.2   0.2   0.00083       2.5      36      52 ..     189     208 ..     173     217 .. 0.74
   3 ?   10.0   0.2   0.00022      0.66      16      42 ..     256     282 ..     252     286 .. 0.81
   4 ?   -3.5   0.4       3.7   1.1e+04      26      32 ..     294     300 ..     289     308 .. 0.41

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.14
                             Big_1  20 pvagatVtfsvsggalsass 39 
                                         +g +Vt+s++++++++ +
  gi|336253290|ref|YP_004596397.1|  93 LEPGNEVTISIDSASTFNEQ 112
                                       56899********8887333 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00083
                             Big_1  36 s...assgtTdanGkatvtl 52 
                                       +    s + Td++G+atvtl
  gi|336253290|ref|YP_004596397.1| 189 FvdgVSAAETDEDGRATVTL 208
                                       234456789**********9 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00022
                             Big_1  16 angnpvagatVtfsvsggalsassgtT 42 
                                       a+g+p+++atV++++ g+a++   g+T
  gi|336253290|ref|YP_004596397.1| 256 ADGTPIPNATVSLESGGTATTGDDGRT 282
                                       89************9997766555554 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 3.7
                             Big_1  26 Vtfsvsg 32 
                                       Vt sv +
  gi|336253290|ref|YP_004596397.1| 294 VTTSVGD 300
                                       3333322 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.018        54      10      39 ..     179     207 ..     173     236 .. 0.78
   2 ?    6.2   0.1    0.0034        10       9      49 ..     256     295 ..     252     308 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.018
                   CarbopepD_reg_2  10 tkeplpgatVyvkgtkkgtvTdenGnFelk 39 
                                       + +p+p atV+v g +  + Tde+G+ +++
  gi|336253290|ref|YP_004596397.1| 179 GSTPVPDATVFVDGVS-AAETDEDGRATVT 207
                                       4579********9876.5789****97776 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0034
                   CarbopepD_reg_2   9 etkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLv 49 
                                        +++p+p atV++++ ++ t T ++G+ +l  + a++ t++
  gi|336253290|ref|YP_004596397.1| 256 ADGTPIPNATVSLESGGTAT-TGDDGRTRLWLPIADEATVT 295
                                       3467*********9988766.56677766655445555544 PP

>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.6   0.00063       1.9       3      86 ..      88     188 ..      87     194 .. 0.73
   2 ?    0.9   0.0      0.19   5.7e+02      33      47 ..     195     209 ..     193     239 .. 0.76
   3 ?   -2.5   0.0       2.2   6.6e+03      34      54 ..     274     294 ..     272     307 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00063
                                       EEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BT..TEEEEEE---SS.........-SSSSEESS-EEEEETT CS
                           AglB_L1   3 titGsaeagatvtasveletnqgrtftYrqeaeaded..GefeltvPYstegee...dgetnssveaagpYevtagn 74 
                                       +i G  e+g++vt+s++  ++ + +    +  +++e   G+   tvPY+ e +    + +++ +v  +++ ++++ +
  gi|336253290|ref|YP_004596397.1|  88 EIDGALEPGNEVTISIDSASTFNEQTVEVNGDDVGETgwGSVDATVPYAEEMTVrvaETNASRTVDVETNATIRTHD 164
                                       68999999******999998887777777777778773368999*******65588766666777777777887755 PP

                                       ............EEEEE---HHHH CS
                           AglB_L1  75 ............vtaeveVpEeaV 86 
                                                   v+ ++ Vp+++V
  gi|336253290|ref|YP_004596397.1| 165 gavpagdmevsaVVGSTPVPDATV 188
                                       555555566666777777777776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.19
                                       EEE.-BTTEEEEEE- CS
                           AglB_L1  33 eaeadedGefeltvP 47 
                                        ae+dedG+ ++t+P
  gi|336253290|ref|YP_004596397.1| 195 AAETDEDGRATVTLP 209
                                       578999999999998 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.2
                                       EE.-BTTEEEEEE---SS... CS
                           AglB_L1  34 aeadedGefeltvPYstegee 54 
                                       a+++ dG+ +l +P + e++ 
  gi|336253290|ref|YP_004596397.1| 274 ATTGDDGRTRLWLPIADEATV 294
                                       677888888888888877533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 4393.52
//
Query:       gi|336253291|ref|YP_004596398.1|  [L=264]
Description: hypothetical protein Halxa_1892 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        2.6    8.1   7.1        5.4    7.1   7.1    1.5  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> 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 ?    7.1   7.1    0.0003       5.4      37      90 ..      26      82 ..      21      94 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0003
                   Phage_holin_3_6 37 agllgaagvlallalllllval.alala.a.lwlaalivaavllvlagvlalvglkk 90
                                      a++++++g ++++a ++l  ++   +la + + la l+ a+ ++v+ g++ +++++ 
  gi|336253291|ref|YP_004596398.1| 26 AVAVIVGGTVLAFASVVLGGFApYGLLAdVfYPLAVLLPAIGVVVAFGACWWATVAG 82
                                      556666666666666666666657777777999999999888888888888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2164.28
//
Query:       gi|336253292|ref|YP_004596399.1|  [L=465]
Description: hypothetical protein Halxa_1893 [Halopiger xanaduensis SH-6]
Scores for 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-15   55.9   1.0    8.5e-15   54.8   1.0    1.6  1  DUF58           Protein of unknown function DUF58
      9e-09   35.5   2.6    2.3e-08   34.2   1.9    2.1  1  DUF11           Domain of unknown function DUF11
    1.4e-06   28.4   0.9    1.4e-06   28.4   0.9    2.6  3  NPCBM_assoc     NPCBM-associated, NEW3 domain of alpha-galact
  ------ inclusion threshold ------
      0.023   14.8   0.4      0.023   14.8   0.4    2.7  3  Acetyltransf_6  Acetyltransferase (GNAT) domain
      0.063   11.6   0.0      0.089   11.1   0.0    1.1  1  ACD             Actin cross-linking domain
       0.14   11.5   0.1       0.23   10.9   0.1    1.2  1  TRAP_beta       Translocon-associated protein beta (TRAPB)
        2.6    8.0   5.6        4.2    7.4   0.1    3.3  4  Glyco_transf_4  Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   1.0   3.3e-18   8.5e-15       1      86 []     227     314 ..     227     314 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 3.3e-18
                             DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstg..dekletavsaaaslar 75 
                                       g++f+++R+Y+ gDp+  IdW+ +A t+el + e+ aera++v+ v+d++++  +++t+    +++ +++aa    +
  gi|336253292|ref|YP_004596399.1| 227 GVEFYSVRDYELGDPVGAIDWRRYAATRELSTVEYRAERATRVVCVVDARRSQLRAATTaeIPAVDLSADAAERTFD 303
                                       689*************************************************9988887778899************ PP

                             DUF58  76 qlldegdrvgl 86 
                                        l+deg+++g+
  gi|336253292|ref|YP_004596399.1| 304 ALVDEGHPTGV 314
                                       *******9986 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   1.9   9.1e-12   2.3e-08       7      80 ..      99     164 ..      91     170 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 9.1e-12
                             DUF11   7 ksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtr 80 
                                       +++++pGdtvt+    +N g  + ++++v D +P+gl+ vs+s +        +  +Le+ e+atl+++v v+r
  gi|336253292|ref|YP_004596399.1|  99 TVTADPGDTVTVRTAIQNDGSETITDLRVVDAVPEGLSVVSGSPR-------AC-VTLEPLETATLEYEVVVRR 164
                                       45899****************************************.......33.49*************9987 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.9   5.5e-10   1.4e-06       2      74 ..     103     176 ..     102     181 .. 0.85
   2 ?   -3.2   0.0       4.2   1.1e+04      34      57 ..     247     269 ..     246     274 .. 0.78
   3 ?   -2.4   0.1       2.3   5.9e+03      36      52 ..     314     330 ..     312     338 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.5e-10
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveat..vkVtppagaaaGdyevta 74 
                                       +pG+tvt+++++ ndg++++t++++   +PeG +vv+ sp+   +l+p et++ +  v V+ ++ a+ Gd +v++
  gi|336253292|ref|YP_004596399.1| 103 DPGDTVTVRTAIQNDGSETITDLRVVDAVPEGLSVVSGSPRACVTLEPLETATLEyeVVVRRGEHAF-GDATVRT 176
                                       79**********************************************8887766115555567777.7877776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.2
                       NPCBM_assoc  34 WtvvevspasaaslapGetveatv 57 
                                       W+ + +++++++++++ ++  + v
  gi|336253292|ref|YP_004596399.1| 247 WR-RYAATRELSTVEYRAERATRV 269
                                       88.888999999999888776665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.3
                       NPCBM_assoc  36 vvevspasaaslapGet 52 
                                       vv ++ +++++++pG  
  gi|336253292|ref|YP_004596399.1| 314 VVGIAEERIEAVEPGTD 330
                                       56677788888888865 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2       1.3   3.4e+03      62     100 ..       8      48 ..       5      73 .. 0.74
   2 ?   -1.8   0.4       1.3   3.2e+03      39      46 ..     277     286 ..     247     313 .. 0.44
   3 ?   14.8   0.4     9e-06     0.023      25      94 ..     331     399 ..     317     447 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.3
                    Acetyltransf_6  62 laalaargalrlyvlrld..grpvAvalglrsgdrlyywlg 100
                                       +++ +++++++ ++l l   g +v++++++++ ++  ++ +
  gi|336253292|ref|YP_004596399.1|   8 VERVDRGEWGVAVALALAgiGLVVGSQVLVVAATVPLWYAA 48 
                                       56677777777777777635678888888888887777765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                    Acetyltransf_6  39 raqwarr..p 46 
                                       r+q ++    
  gi|336253292|ref|YP_004596399.1| 277 RSQLRAAttA 286
                                       2222222131 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 9e-06
                    Acetyltransf_6  25 atdpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrl..dgrpvAvalglrsgdr 94 
                                        +++e+++++l+ ++++  +   + + p   ++ ++l+ +l  +g +++y  +   d++pv  ++glr ++ 
  gi|336253292|ref|YP_004596399.1| 331 PATREEVSRVLDEVWDLEHGS-QYVQQPSGDDLAAELATTL--PGEAQVYLFSSfvDDEPVDLVAGLRTRGY 399
                                       368899***********9999.9999***************..8887777777555************9985 PP

>> ACD  Actin cross-linking 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     0.089     102     189 ..      44     132 ..      35     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHHHHHSTTB-----B-TTSSEEEEES--..S-EEEETTS-SSS------EEEEEEEEEEEEEEGGGTTT CS
                               ACD 102 lwlakeftdhidqsnhqsladlvsedgrftlvisna..khviaagngisadaqgktigmtpsgqqatvavsakefgt 176
                                       lw a       +q    +l    + dg  ++v+ +     +  +gng+s   +g+t++  p g+  tv  + ++ g+
  gi|336253292|ref|YP_004596399.1|  44 LWYAAAAVFGTHQPTMVRLQRELAADGDDAVVVGDGgrTGLEVTGNGTSSGDEGRTVTADP-GDTVTVRTAIQNDGS 119
                                       66666655555677777888878888888888876521457789**************998.899************ PP

                                       --SHHHHHHHT-T CS
                               ACD 177 ssspevrllesap 189
                                        +  ++r++++ p
  gi|336253292|ref|YP_004596399.1| 120 ETITDLRVVDAVP 132
                                       ********99988 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   8.9e-05      0.23      34     113 ..     105     180 ..      99     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.9e-05
                         TRAP_beta  34 gedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvvepkksgsfngtaavvtYr 110
                                       g  +tv+  i N Gs++ +d+++vD    +e  +vvsgs  a + +l+p e+ +  ++v+ +  g   + +a+v  r
  gi|336253292|ref|YP_004596399.1| 105 GDTVTVRTAIQNDGSETITDLRVVDA--VPEGLSVVSGSPRACV-TLEPLETATLEYEVVVR-RGEHAFGDATVRTR 177
                                       5679********************97..57889******99976.89999999888888765.56777777777665 PP

                         TRAP_beta 111 ese 113
                                       +++
  gi|336253292|ref|YP_004596399.1| 178 NAT 180
                                       554 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.21   5.4e+02       8      33 ..      59      84 ..      56     113 .. 0.79
   2 ?   -0.4   0.2       0.4     1e+03     118     150 ..     251     282 ..     239     288 .. 0.72
   3 ?   -2.0   0.0       1.2     3e+03     153     168 ..     316     331 ..     313     333 .. 0.89
   4 ?    7.4   0.1    0.0016       4.2      10      38 ..     389     421 ..     388     456 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.21
                    Glyco_transf_4  8 vleLaraLarrGheVtvvtpgddgpl 33
                                      +++L r+La++G + +vv +g++  l
  gi|336253292|ref|YP_004596399.1| 59 MVRLQRELAADGDDAVVVGDGGRTGL 84
                                      67899************987766544 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.4
                    Glyco_transf_4 118 plsrllralerrllrradrviavSeatadelre 150
                                        ++r l  +e+r+  ra rv++v +a + +lr+
  gi|336253292|ref|YP_004596399.1| 251 AATRELSTVEYRA-ERATRVVCVVDARRSQLRA 282
                                       4444455556665.99******99888888876 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.2
                    Glyco_transf_4 153 gvppekitVipnGvDl 168
                                       g+++e+i+ + +G D+
  gi|336253292|ref|YP_004596399.1| 316 GIAEERIEAVEPGTDP 331
                                       899***********98 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0016
                    Glyco_transf_4  10 eLaraLarrGheVtvvtpgddgpleeev....e 38 
                                       +L+ +L+ rG+ V+vv+p++   ++ +      
  gi|336253292|ref|YP_004596399.1| 389 DLVAGLRTRGYSVRVVSPDVTASADGAAddtaT 421
                                       899*************88777766666443331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.52u 0.19s 00:00:00.71 Elapsed: 00:00:00.36
# Mc/sec: 3833.36
//
Query:       gi|336253293|ref|YP_004596400.1|  [L=477]
Description: hypothetical protein Halxa_1894 [Halopiger xanaduensis SH-6]
Scores for 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  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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):               0  [number of targets reported over threshold]
# CPU time: 0.73u 0.24s 00:00:00.97 Elapsed: 00:00:00.41
# Mc/sec: 3502.68
//
Query:       gi|336253294|ref|YP_004596401.1|  [L=325]
Description: ATPase [Halopiger xanaduensis SH-6]
Scores for 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-65  217.8   0.1    5.1e-65  217.2   0.1    1.3  1  AAA_3            ATPase family associated with various cellul
    1.3e-16   60.2   2.9      3e-16   59.0   2.9    1.6  1  AAA_lid_2        AAA lid domain
    1.8e-15   57.2   0.0    3.5e-15   56.2   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
    6.2e-06   26.7   0.0      2e-05   25.1   0.0    1.9  2  AAA              ATPase family associated with various cellul
    6.1e-05   22.8   0.0      0.001   18.8   0.0    2.1  1  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.027   13.6   0.0      0.036   13.2   0.0    1.3  1  MCM              MCM P-loop domain
      0.073   12.8   0.0        2.7    7.7   0.0    2.3  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.11   11.8   0.1        3.5    7.0   0.0    2.1  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.13   11.5   0.0       0.21   10.9   0.0    1.2  1  ATPase           KaiC


Domain annotation for each model (and alignments):
>> 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 !  217.2   0.1   2.6e-68   5.1e-65       1     131 []      40     170 ..      40     170 .. 1.00

  Alignments for each domain:
  == domain 1  score: 217.2 bits;  conditional E-value: 2.6e-68
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       hvlle+vPG++ktl+++++a+al+l+f+riqftpdl+Psd++G+ vfee + ef+f++Gpvfan++ladeinrappk
  gi|336253294|ref|YP_004596401.1|  40 HVLLEDVPGTGKTLTARSFATALGLDFSRIQFTPDLMPSDVTGSYVFEEGTGEFHFTEGPVFANVVLADEINRAPPK 116
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                       tqsalleam+e qvtv+geth+lp+pf+v+atqnP+eqeGt++lpeaq drf++
  gi|336253294|ref|YP_004596401.1| 117 TQSALLEAMAEDQVTVDGETHELPDPFIVIATQNPVEQEGTFELPEAQRDRFMI 170
                                       ****************************************************96 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   2.9   1.5e-19     3e-16       2      71 ..     234     304 ..     233     306 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.5e-19
                         AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeive 71 
                                       atr + ++ +gvs+r + + l +++rA+A legr+yV+p+Dvk++ap + aHRl+  +e++ eg + +++ve
  gi|336253294|ref|YP_004596401.1| 234 ATRRDGRVDVGVSPR-GVQRLFEVSRARAVLEGREYVVPDDVKHIAPAAIAHRLVltPEASVEGASRRAVVE 304
                                       8999999********.***************************************99999999999888887 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 !   56.2   0.0   1.7e-18   3.5e-15       1     138 []      40     168 ..      40     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.7e-18
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       +vlL   pGtgK+  a+++a al+  +  +q+t d+ ++d++g++ ++   g+  ++++p+      + +++ DE++
  gi|336253294|ref|YP_004596401.1|  40 HVLLEDVPGTGKTLTARSFATALGLDFSRIQFTPDLMPSDVTGSYVFEegTGEFHFTEGPVF-----ANVVLADEIN 111
                                       6888889*****************************************888889999*****.....9********* PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra+++++++Ll  + e+++   +g + +  ++      f viat np++  +  el +a r+Rf
  gi|336253294|ref|YP_004596401.1| 112 RAPPKTQSALLEAMAEDQVT-VDGETHELPDP------FIVIATQNPVEqEGTFELPEAQRDRF 168
                                       *******************9.55555555666......***********9999**********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 !   25.1   0.0   9.8e-09     2e-05       2     127 ..      42     171 ..      41     176 .. 0.74
   2 ?   -3.4   0.0       6.1   1.2e+04      39      58 ..     243     265 ..     235     290 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 9.8e-09
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SS.....STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHH CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisg.sell.sk.....yvgesekkirelfkeakekakpsilfiDEidala 71 
                                       ll   pGtGKTl+a++ a+ lg +f +i+  ++l+ s+     +++e+  +++  f+e    a   +++ DEi +  
  gi|336253294|ref|YP_004596401.1|  42 LLEDVPGTGKTLTARSFATALGLDFSRIQFtPDLMpSDvtgsyVFEEGTGEFH--FTEGPVFA--NVVLADEINRAP 114
                                       67778*****************9999999625666333666544444444444..44444444..8**********9 PP

                                       HHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEE CS
                               AAA  72 ksrsgseseeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrk 127
                                       ++            +++Ll+++ + +           +++ivi++ n        +l++a + +Rf +k
  gi|336253294|ref|YP_004596401.1| 115 PKT-----------QSALLEAMAEDQVTvdgethelPDPFIVIATQNPveqegTFELPEAQR-DRFMIK 171
                                       999...........999999999999999999999977799999999755545556777777.777666 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.1
                                       TTHHHHHHHHHHHHHHHTS...T CS
                               AAA  39 vgesekkirelfkeakeka...k 58 
                                       vg s++ ++ lf+  ++ a   +
  gi|336253294|ref|YP_004596401.1| 243 VGVSPRGVQRLFEVSRARAvleG 265
                                       57777777777777666555433 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   5.2e-07     0.001      11     147 ..      27     154 ..      19     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.2e-07
                                       HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEH CS
                   Sigma54_activat  11 lleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkG 87 
                                       +le+i++    + +vl++   GtGK+l ar+  +a    + + +++    +p+++  s +F    G F  +    +G
  gi|336253294|ref|YP_004596401.1|  27 VLEEITAGLLARGHVLLEDVPGTGKTLTARSFATALG-LDFSRIQFTPDLMPSDVTGSYVFEEGTGEFHFT----EG 98 
                                       6677777777788888888899999999888766554.333345555556666666666666555555433....34 PP

                                       HHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-HHH CS
                   Sigma54_activat  88 lfekadgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedlee 147
                                        +      +++ Dei++ p+++Q+ Ll+++ e +v+  G+++e +    i+ at++ +e+
  gi|336253294|ref|YP_004596401.1|  99 PVF---ANVVLADEINRAPPKTQSALLEAMAEDQVTVDGETHELPDP-FIVIATQNPVEQ 154
                                       332...246788************************99999999855.566677776665 PP

>> MCM  MCM P-loop 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     0.036      95     178 ..      78     158 ..      11     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                                       SHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE CS
                               MCM  95 agLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAa 171
                                       ++ t + v +e tgef +  G +      v++ De+++   +++sal+Eam ++++++   G +  L+    v+a  
  gi|336253294|ref|YP_004596401.1|  78 SDVTGSYVFEEGTGEFHFTEGPVFA---NVVLADEINRAPPKTQSALLEAMAEDQVTVD--GETHELPDPFIVIATQ 149
                                       5566666777777777777777654...399*************************997..5568899999999999 PP

                                       --S..SSSC CS
                               MCM 172 npk..agry 178
                                       np+  +g +
  gi|336253294|ref|YP_004596401.1| 150 NPVeqEGTF 158
                                       997444555 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 ?    7.7   0.0    0.0014       2.7      33      61 ..      38      66 ..      16      84 .. 0.87
   2 ?    2.7   0.0     0.049        97      86     113 ..     103     130 ..      94     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0014
                            RuvB_N 33 ldhvllyGpPGlGkttlakiiakelgvkl 61
                                        hvll   PG Gkt  a+  a+ lg ++
  gi|336253294|ref|YP_004596401.1| 38 RGHVLLEDVPGTGKTLTARSFATALGLDF 66
                                      57****************99999998776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.049
                            RuvB_N  86 dvlfideihrlsraveevlysamedfrl 113
                                       +v++ dei r  ++++  l  am + ++
  gi|336253294|ref|YP_004596401.1| 103 NVVLADEINRAPPKTQSALLEAMAEDQV 130
                                       78999*****************976555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0017       3.5      21      46 ..      37      62 ..      18      67 .. 0.77
   2 ?    2.6   0.0     0.039        77     109     160 ..     104     153 ..      98     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0017
                      Mg_chelatase 21 GgHnlllvGppGsGKtmlakrlpsll 46
                                       + ++ll   pG+GKt+ a+ +++ l
  gi|336253294|ref|YP_004596401.1| 37 ARGHVLLEDVPGTGKTLTARSFATAL 62
                                      456899*************9987755 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.039
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcp 160
                                       v++ DE+     k+  +L e + + +vt+   ++  e p  f ++a+ Np  
  gi|336253294|ref|YP_004596401.1| 104 VVLADEINRAPPKTQSALLEAMAEDQVTVDGETH--ELPDPFIVIATQNPVE 153
                                       6778*************************87665..56889********975 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.21       8      41 ..      28      60 ..      13      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                            ATPase  8 lDeilkgGipegrvvlitGepGtGKtifalqFli 41
                                      l+ei+  G+  +  vl+  +pGtGKt+ a  F+ 
  gi|336253294|ref|YP_004596401.1| 28 LEEIT-AGLLARGHVLLEDVPGTGKTLTARSFAT 60
                                      45554.899999999****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2634.70
//
Query:       gi|336253295|ref|YP_004596402.1|  [L=391]
Description: FO synthase subunit 1 [Halopiger xanaduensis SH-6]
Scores for 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-10   42.3   0.1    1.8e-10   41.5   0.1    1.4  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 !   41.5   0.1   9.8e-15   1.8e-10       2     164 ..      45     213 ..      44     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 9.8e-15
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS.............TTHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.............xxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggeplly.............pdfv 64 
                                       + t +C++ C++C+      + g +  ls+ee+ e+ +e+ a  g ++ ++ +g++p+++             + ++
  gi|336253295|ref|YP_004596402.1|  45 PLTTACRYTCTYCTYFD---PPGQASLLSLEEVREICREG-AAAGcTEALFTFGDDPDDRyteihaqleewghDSIH 117
                                       6799************9...9*******************.79999*************998888888888887777 PP

                                       HHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  65 ellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklrea 140
                                        +l+++++ a  +  +   +n++  ++e++++ ++ +   + + le++ +  v+ + + r +++ ++l++++++ e+
  gi|336253295|ref|YP_004596402.1| 118 TYLREACQVA-LEEGLLPHANPGDQTREQMAAVADVN-ASMGVMLETTAE--VRAHGGpRSKEPGQRLRTIRNAGEL 190
                                       7788888776.899999999999999*********99.************..999999******************* PP

                                       TSETEEEEEEEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 141 gikrvvdrivglpGendeeleell 164
                                       ++   +++i+++ Ge ++++ e l
  gi|336253295|ref|YP_004596402.1| 191 DVA-FTTGILVGVGEDWRDRAESL 213
                                       ***.***************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 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:                        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 0.20s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 3069.88
//
Query:       gi|336253296|ref|YP_004596403.1|  [L=52]
Description: hypothetical protein Halxa_1897 [Halopiger xanaduensis SH-6]
Scores for 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:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 403.67
//
Query:       gi|336253297|ref|YP_004596404.1|  [L=226]
Description: 2-phospho-L-lactate guanylyltransferase CofC [Halopiger xanaduensis SH-6]
Scores for complete 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-40  139.0   0.0    1.5e-40  138.7   0.0    1.1  1  CofC          Guanylyl transferase CofC like
  ------ inclusion threshold ------
      0.024   15.0   5.6      0.038   14.4   5.4    1.4  1  NTP_transf_3  MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.7   0.0   1.7e-44   1.5e-40       1     207 [.       1     217 [.       1     224 [. 0.82

  Alignments for each domain:
  == domain 1  score: 138.7 bits;  conditional E-value: 1.7e-44
                              CofC   1 mkviiPvsainsaktrlseilseeerkellkamlldvidalkr..ld..vlvvsed..eev..leyaldelgvevvk 69 
                                       m+v++P+    s+ktrls++l+e er+ l++aml dv +a+     +  vl  + +  e+   l    d+l + ++ 
  gi|336253297|ref|YP_004596404.1|   1 MRVVVPFAVE-SPKTRLSPVLAERERRSLARAMLADVLGAIVAagHEptVLATAPIdlEDDfdLALSDDVLAATTIA 76 
                                       89*****765.5**************************997553344434444332113331144556899999999 PP

                              CofC  70 ekekdlntavekafeeieek......eviiipsdiPlikkedvkdllelekradvviaPargGGtnllllrksalev 140
                                        +++ l +av+  + + + +       v+++++d+ l + + +++l+  +   dv iaP+rgGGtn l +r+  ++v
  gi|336253297|ref|YP_004596404.1|  77 VDDRPLTEAVNARLPAEDADgdsvpeAVAVVMADLALTTPDALERLFAGDA--DVAIAPGRGGGTNALAVRHPDFRV 151
                                       999********98554443222222269******************97665..************************ PP

                              CofC 141 kyedfsflkhleearkrglkvkiydsfylsvdinteedlgeillhGegtkakeylrklgfsvepees 207
                                        y+++s+l+h e a + gl v+  dsf l+ di++++dl e+l+hG + +a   lr++gf++e +++
  gi|336253297|ref|YP_004596404.1| 152 DYHGASYLDHREIAADSGLAVEAVDSFRLATDIDEPNDLVEVLIHGTE-HAPARLRSFGFELEEQDG 217
                                       **********************************************86.77888******9987654 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 ?   14.4   5.4   4.2e-06     0.038      24     132 ..      30     143 ..      19     171 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.2e-06
                                       CCHHHHHHHHHCTT.-CEEEEECSHCHHHH....HHTTCTS-EEE-TTSS-SHHHHHHHHHHHH......SSSCEEE CS
                      NTP_transf_3  24 kpllervldalraagvdevvvvggdeevla....alarlgvrvvededpgkgplaslaaalraaa.....dadavlv 91 
                                       + +l+ vl a+ aag ++ v+++ + ++++    al +  +  ++ +  ++   +++ a l a         +av+v
  gi|336253297|ref|YP_004596404.1|  30 RAMLADVLGAIVAAGHEPTVLATAPIDLEDdfdlALSDDVLAATTIAVDDRPLTEAVNARLPAEDadgdsVPEAVAV 106
                                       57888888888888888888888885555533323333333333333334555667777776521223445678*** PP

                                       EETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCE CS
                      NTP_transf_3  92 lacDmPlltpelverllaaaaasgadvvvptyegerghpll 132
                                       +++D++l tp+++erl+a     +adv+++  +g+  + l+
  gi|336253297|ref|YP_004596404.1| 107 VMADLALTTPDALERLFAG----DADVAIAPGRGGGTNALA 143
                                       ******************7....667766666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1688.26
//
Query:       gi|336253298|ref|YP_004596405.1|  [L=392]
Description: Tubulin/FtsZ GTPase [Halopiger xanaduensis SH-6]
Scores for 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-28   97.7   0.0    1.8e-27   96.9   0.0    1.5  1  Tubulin       Tubulin/FtsZ family, GTPase domain
  ------ inclusion threshold ------
      0.036   13.3   0.1      0.055   12.6   0.1    1.4  1  Tubulin_2     Tubulin like
       0.13   12.6   1.1       0.28   11.6   0.0    2.0  2  Endotoxin_C2  Delta endotoxin


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 !   96.9   0.0   2.9e-31   1.8e-27       3     194 ..       4     174 ..       2     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 2.9e-31
                                       EEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE-- CS
                           Tubulin   3 ivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllg 79 
                                        +ig+Gq+G++i++++ +    +               +sg   ++  ++a++  + +l  +++     ++n++l+g
  gi|336253298|ref|YP_004596405.1|   4 AMIGFGQAGGKIVDRFLD---YDDRT------------NSG---IVRAAIAVNSAKADLIGLDNI---PQENRVLIG 59 
                                       68****************...33222............345...444569***977766555555...556****** PP

                                       CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE...SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEE CS
                           Tubulin  80 kegagnngaggypevgkeaaeeileeirkevekcds..lqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvv 154
                                       +   +++g+g+++e+g+e+aee  +e+++++++  +  +++f+++a++gGGTGSG +pv+++ lk+ y  ++v++  
  gi|336253298|ref|YP_004596405.1|  60 QARVKGHGVGADNELGAEVAEEDIDEVQNAIDSIPTheVDAFLVVAGMGGGTGSGGAPVLAKHLKRIY-TIPVYGLG 135
                                       ********************************86554499***************************9.9******* PP

                                       EE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHC CS
                           Tubulin 155 vlPsefsevvvepynailalkelieesdavividNdaLlk 194
                                       +lP ++ e+ ++  na+ + +++++e+d ++v+dNd++ +
  gi|336253298|ref|YP_004596405.1| 136 ILPGTD-EGGIYTLNAARSFQTFVREVDNLLVFDNDSWRQ 174
                                       ***876.******************************987 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   9.2e-06     0.055     139     221 ..      86     154 ..      60     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.2e-06
                         Tubulin_2 139 lrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllrkilkeekqkvkiiglvllPdvfplnkeggervka 215
                                       +++ai+ + +    +e+  + Vv ++ GGTGSG +  +a  l+ i+        ++gl +lP       ++g  + +
  gi|336253298|ref|YP_004596405.1|  86 VQNAIDSIPT----HEVDAFLVVAGMGGGTGSGGAPVLAKHLKRIYTIP-----VYGLGILPGT-----DEGGIYTL 148
                                       4444444444....4556788************9988888888777654.....4677777776.....34667777 PP

                         Tubulin_2 216 NayaaL 221
                                       Na++++
  gi|336253298|ref|YP_004596405.1| 149 NAARSF 154
                                       777665 PP

>> Endotoxin_C2  Delta endotoxin
   #    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      21      49 ..      73     101 ..      69     103 .. 0.86
   2 ?   -2.0   0.2      0.79   4.7e+03      34      44 ..     362     372 ..     353     381 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.6e-05
                      Endotoxin_C2  21 kikdtttqaaIdaAqalVdkvtdstkKae 49 
                                       ++ +++ +++Id++q+ +d+++++++ a 
  gi|336253298|ref|YP_004596405.1|  73 ELGAEVAEEDIDEVQNAIDSIPTHEVDAF 101
                                       488999****************9998765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.79
                      Endotoxin_C2  34 AqalVdkvtds 44 
                                       Aq+ +d ++++
  gi|336253298|ref|YP_004596405.1| 362 AQDNIDDIQQE 372
                                       56666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 00:00:00.38
# Mc/sec: 3058.23
//
Query:       gi|336253299|ref|YP_004596406.1|  [L=297]
Description: NAD-dependent epimerase/dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-28   97.6   0.0    1.6e-27   96.6   0.0    1.5  1  NAD_binding_10   NAD(P)H-binding
    4.4e-19   68.9   0.0    9.2e-18   64.6   0.0    2.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.2e-12   45.5   0.0    1.9e-07   30.5   0.0    2.3  2  RmlD_sub_bind    RmlD substrate binding domain
    1.2e-10   40.9   0.0    2.5e-09   36.6   0.0    2.1  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.5e-09   37.8   0.0    2.1e-09   37.3   0.0    1.4  1  NmrA             NmrA-like family
    1.3e-08   34.6   0.0    2.4e-08   33.8   0.0    1.4  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
     0.0012   18.1   0.0       0.57    9.3   0.0    2.3  2  NAD_binding_4    Male sterility protein
     0.0019   17.4   0.1      0.031   13.4   0.1    2.3  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0082   15.6   0.0      0.012   15.1   0.0    1.3  1  adh_short        short chain dehydrogenase
       0.01   16.3   0.7      0.051   14.0   0.1    2.3  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.021   14.8   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
      0.013   15.7   0.0      0.026   14.7   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.021   15.4   0.0      0.081   13.5   0.0    1.9  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.022   14.7   0.0      0.045   13.7   0.0    1.5  1  KR               KR domain
      0.047   13.3   0.0      0.091   12.3   0.0    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.077   13.6   0.0       0.36   11.4   0.0    2.1  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas


Domain annotation for each model (and alignments):
>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.0   1.4e-30   1.6e-27       1     147 [.       7     150 ..       7     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 1.4e-30
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-......... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal......... 68 
                                       G+tG +G  l++el++r ghevtal Rnp++   l+  + +++  gdv+  ++++ a++g+daVv  +         
  gi|336253299|ref|YP_004596406.1|   7 GGTGFIGTNLCTELAER-GHEVTALSRNPDRNG-LP--DDVDLEMGDVSAYDSIEGAVAGHDAVVNLValsplyqas 79 
                                       9****************.5************98.87..6899999******************98777668877653 PP

                                       ..--TCCHHHH....HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHHHSSSEEE CS
                    NAD_binding_10  69 ..ggggkdeeg....aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellrasgldwT 139
                                         g    +e++    ++n+v+aa+ +gv R++ +sa+g++ +  ++          + ++ak +ae+++ +s+l+wT
  gi|336253299|ref|YP_004596406.1|  80 dpG---AQERVhlggTENLVRAAEDHGVDRYLQISALGADPD--SDI---------DHIRAKGKAEKVVTDSDLEWT 142
                                       222...233337778************************942..222.........3479***************** PP

                                       EEEE-CEE CS
                    NAD_binding_10 140 ivrpggLt 147
                                       ivrp+   
  gi|336253299|ref|YP_004596406.1| 143 IVRPSIVF 150
                                       ****9765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.0   8.2e-21   9.2e-18       1     228 [.       3     197 ..       3     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 8.2e-21
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.--- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.vgg 76 
                                       +lV+G+tGfiG++l+ +l+e+g+ev++l+r+   +++++ +d++l  +d+   +++e +++  + dav++l a    
  gi|336253299|ref|YP_004596406.1|   3 VLVAGGTGFIGTNLCTELAERGHEVTALSRN--PDRNGLPDDVDLEMGDVSAYDSIEGAVA--GHDAVVNLVAlSPL 75 
                                       79*****************************..5566778888******************..89******994555 PP

                                       HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHH CS
                         Epimerase  77 vaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklv 153
                                       ++  ++dp +  + +l gt nl+ aa ++gv+r+l++s     G+d+++ +                +aK  +ek+v
  gi|336253299|ref|YP_004596406.1|  76 YQ--ASDPGAQERVHLGGTENLVRAAEDHGVDRYLQISA---LGADPDS-DI------------DHIRAKGKAEKVV 134
                                       55..57888889**************************8...5555542.22............2336666666666 PP

                                       HHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHH CS
                         Epimerase 154 eayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvleh 228
                                       ++     +l+ +i+r++ ++G +   ge       + +++ +      l g g+ + + ++v D++ ++  ++e 
  gi|336253299|ref|YP_004596406.1| 135 TDS----DLEWTIVRPSIVFGDG---GEFVD----FTKQLTTPY-VTGLPGGGETRFQPIWVGDLVPMLADAIED 197
                                       654....4445666666666666...22222....222222222.233456666666666666666666666665 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 !   30.5   0.0   1.7e-10   1.9e-07       1      94 [.       1     104 [.       1     112 [. 0.87
   2 !   12.7   0.0   4.4e-05     0.049     127     241 ..     125     235 ..     123     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.7e-10
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.............T--TTSHHHHHHHHHHH--SEEEE------H CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre.............eldltdaeavaellkeakpdvvvnaAAytav 64 
                                       mk+lv G++G +G++L  +lae+g+ev+al+r+               d++  ++++ +++    d+vvn+ A    
  gi|336253299|ref|YP_004596406.1|   1 MKVLVAGGTGFIGTNLCTELAERGHEVTALSRNpdrnglpddvdleMGDVSAYDSIEGAVAG--HDAVVNLVALSPL 75 
                                       89******************************9********885555556666666666655..789********** PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHCT- CS
                     RmlD_sub_bind  65 DkaEseeeaayavnaeavealAeaaaavga 94 
                                        +a s++ a+++v   ++e+l +aa+ +g+
  gi|336253299|ref|YP_004596406.1|  76 YQA-SDPGAQERVHLGGTENLVRAAEDHGV 104
                                       **9.789999*****************998 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHHHHHH-SSEEEEEE-SEESSSSS-HHHHHHHHH.HH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH CS
                     RmlD_sub_bind 127 rtKlaGEqavlaagkkalivRtswvygekgknfvktmlrla.kereelkvvaDqlgsPTsardlAevllqllekaae 202
                                       r+K + E++v ++  +++ivR s v+g+ g +fv    +l       l        +P ++ dl  +l++++e  a+
  gi|336253299|ref|YP_004596406.1| 125 RAKGKAEKVVTDSDLEWTIVRPSIVFGD-GGEFVDFTKQLTtPYVTGLPGGGETRFQPIWVGDLVPMLADAIEDDAH 200
                                       678899*********************9.667888877777345567888888999999999999999999999887 PP

                                       .GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEEE CS
                     RmlD_sub_bind 203 ekelagvyHlanegetswlefArailkeagadseevkpi 241
                                          + ++y l++ ++++ ++  + + ++ g+d   + p+
  gi|336253299|ref|YP_004596406.1| 201 ---AGEIYELGGPQVVTLADATELVYAAEGKDV-TIVPV 235
                                       ...788999999999998888888877766655.45555 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 !   36.6   0.0   2.2e-12   2.5e-09       1     117 [.       4     113 ..       4     132 .. 0.86
   2 ?    2.4   0.0     0.058        65     170     197 ..     138     164 ..     123     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 2.2e-12
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +v Gg+GF+G +l+ eL ++++  ev +l  + + +       v+      gDv   d++e a+ g d+v+ l +l+
  gi|336253299|ref|YP_004596406.1|   4 LVAGGTGFIGTNLCTELAERGH--EVTALSRNPDRNG--LPDDVDL---EMGDVSAYDSIEGAVAGHDAVVNLVALS 73 
                                       699*****************95..7777655444444..4444444...499************************* PP

                         3Beta_HSD  78 dvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsa 117
                                       ++ +    +   +v + GT+n++ a+ ++gv + +  S++
  gi|336253299|ref|YP_004596406.1|  74 PLYQASDPGAQERVHLGGTENLVRAAEDHGVDRYLQISAL 113
                                       *******************************998777765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.058
                         3Beta_HSD 170 rlyTcaLRpagiyGegdkllvpllkqla 197
                                       +l    +Rp++++G+g ++ v + kql+
  gi|336253299|ref|YP_004596406.1| 138 DLEWTIVRPSIVFGDGGEF-VDFTKQLT 164
                                       5555679********9865.45555554 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   1.9e-12   2.1e-09       1     200 [.       3     201 ..       3     250 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.9e-12
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG.. CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy.. 75 
                                       +lv G+TG +G  +   l+++gh+v al R+++++ +       v l  gd+  ++s++ a+ g d+v   +++   
  gi|336253299|ref|YP_004596406.1|   3 VLVAGGTGFIGTNLCTELAERGHEVTALSRNPDRNGLP----DDVDLEMGDVSAYDSIEGAVAGHDAVVNLVALSpl 75 
                                       79******************************999875....4688889*******************999998788 PP

                                       ..........S-HHHHHHHHHHHHHHHS-SEEEE.EE---GG.GT.SSS---TTTHHHHHHHHHHHHCTS-EEEEEE CS
                              NmrA  76 ..........skeiedgkklvdAakeaGvkhfiy.SslgddndrsnaeepavphfdsKaeieeyvralgipytfvya 141
                                                 + ++    +lv+Aa   Gv +++  S lg+d   s     +++h  +K + e++v  + +  t+v++
  gi|336253299|ref|YP_004596406.1|  76 yqasdpgaqeRVHLGGTENLVRAAEDHGVDRYLQiSALGADP-DS-----DIDHIRAKGKAEKVVTDSDLEWTIVRP 146
                                       99****9955555666689*************9625566666.55.....699***********************9 PP

                                       -EEGGG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHH CS
                              NmrA 142 gffmenflsllaqlkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprkl 200
                                        +  +    ++    ++++ +p     l+g g++   ++  + D  ++ + +++d + +
  gi|336253299|ref|YP_004596406.1| 147 SIVFGDGGEFVDF--TKQLTTPY-VTGLPGGGETRFQPI-WVGDLVPMLADAIEDDAHA 201
                                       9866655553322..33344443.455566666555555.6777777777777766655 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 !   33.8   0.0   2.1e-11   2.4e-08       1     128 [.       4     111 ..       4     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.1e-11
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+ G++GfiG +l+  L e+g+ev+ + r+ +       + l         +++ l  gD++  +s+e ++a +  d
  gi|336253299|ref|YP_004596406.1|   4 LVAGGTGFIGTNLCTELAERGHEVTALSRNPDR------NGLP--------DDVDLEMGDVSAYDSIEGAVAGH--D 64 
                                       8***********************999777665......2343........3467899***************9..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEE CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaS 128
                                       +v+nL A s   +  ++P +  +v + Gt +L+ a+ ++g++   r++q+S
  gi|336253299|ref|YP_004596406.1|  65 AVVNLVALSPLYQ-ASDPGAQERVHLGGTENLVRAAEDHGVD---RYLQIS 111
                                       *********9866.677***********************97...788887 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00051      0.57       2      33 ..       6      35 ..       5      57 .. 0.88
   2 !    6.5   0.0    0.0035         4     180     209 ..     127     152 ..     121     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00051
                                      E-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSS CS
                     NAD_binding_4  2 TGaTGFLGkvLlekLLrttpevkiyllvRaks 33
                                       G+TGF+G+ L  +L ++    ++++l R+ +
  gi|336253299|ref|YP_004596406.1|  6 AGGTGFIGTNLCTELAERGH--EVTALSRNPD 35
                                      7***************9998..7999988766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHHH---EEEEEE-EEE-- CS
                     NAD_binding_4 180 KalaEklvrearrrsglpvvivRpsiitge 209
                                       K  aEk+v +      l ++ivRpsi+ g+
  gi|336253299|ref|YP_004596406.1| 127 KGKAEKVVTDSD----LEWTIVRPSIVFGD 152
                                       777888887765....899********994 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   2.8e-05     0.031       1     128 [.       3     112 ..       3     137 .. 0.79
   2 ?   -3.8   0.0       4.9   5.5e+03     204     216 ..     213     225 ..     190     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vlv+G++G iG +l+++++++   ++  l+r+  +           l  +++++e    +gdv   +++e a+   +
  gi|336253299|ref|YP_004596406.1|   3 VLVAGGTGFIGTNLCTELAERGH-EVTALSRNPDR-NG--------LP-DDVDLE----MGDVSAYDSIEGAVA--G 62 
                                       89***************998765.55555554322.11........22.234456....999999999999999..9 PP

                                       -SEEEE------HHHHHH.SHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlvee.npleaiktNvlgtenvieaaieagvkkvvliSt 128
                                        d+v++  Al   Pl +   p    +    gten+++aa ++gv++ + iS+
  gi|336253299|ref|YP_004596406.1|  63 HDAVVNLVALS--PLYQAsDPGAQERVHLGGTENLVRAAEDHGVDRYLQISA 112
                                       99999999996..666542566667788899999999999999999999995 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.9
                                       E-HHHHHHHHHHH CS
                   Polysacc_synt_2 204 mtieeavqLvlqa 216
                                       +t+++a++Lv  a
  gi|336253299|ref|YP_004596406.1| 213 VTLADATELVYAA 225
                                       5777777777665 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     1e-05     0.012       3      36 ..       3      36 ..       1      71 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseek 36
                                      vlv G+++ IG +++ ela++G +v++++r++++
  gi|336253299|ref|YP_004596406.1|  3 VLVAGGTGFIGTNLCTELAERGHEVTALSRNPDR 36
                                      9*****************************9886 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 !   14.0   0.1   4.6e-05     0.051       1      35 [.       7      41 ..       7     105 .. 0.76
   2 ?   -0.2   0.1       1.1   1.2e+03      22      47 ..     211     237 ..     207     269 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-05
                   Glyco_trans_4_4  1 gGigryvaelaraLaarGheVtvltpapapgapel 35
                                      gG g    +l+ +La+rGheVt l ++p+++  + 
  gi|336253299|ref|YP_004596406.1|  7 GGTGFIGTNLCTELAERGHEVTALSRNPDRNGLPD 41
                                      6777888899****************999995542 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                   Glyco_trans_4_4  22 tvltpapapg.apeleedgvrvhrlpv 47 
                                       +v+t a+a++  +++e+  v+++++p+
  gi|336253299|ref|YP_004596406.1| 211 QVVTLADATElVYAAEGKDVTIVPVPM 237
                                       355544444424445555666655553 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.9e-05     0.021       2      32 ..       7      37 ..       6      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                    Glyco_transf_4  2 GGverhvleLaraLarrGheVtvvtpgddgp 32
                                      GG +    +L+ +La+rGheVt +++++d+ 
  gi|336253299|ref|YP_004596406.1|  7 GGTGFIGTNLCTELAERGHEVTALSRNPDRN 37
                                      88888889****************9998865 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 ?   14.7   0.0   2.3e-05     0.026       6      64 ..       8      71 ..       5      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                                      --SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT......EEE-SSHHHHHHHCSEEEE-SS CS
                     NAD_binding_2  6 GlGvMGsnmalnllkagykvavynrtkekveelvaeg......akaaesieelvasldvvitmvk 64
                                      G+G +G+n++++l+++g++v++  r++++   l ++       ++a++sie +va+ d+v+ +v 
  gi|336253299|ref|YP_004596406.1|  8 GTGFIGTNLCTELAERGHEVTALSRNPDRN-GLPDDVdlemgdVSAYDSIEGAVAGHDAVVNLVA 71
                                      99************************8764.3333323446679999999999999999988875 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 ?   13.5   0.0   7.2e-05     0.081       6      38 ..       8      36 ..       3      77 .. 0.84
   2 ?   -1.9   0.0       4.6   5.2e+03      55      71 ..     221     237 ..     200     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.2e-05
                                      TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCC CS
                     F420_oxidored  6 GaGnmgealasgllaagaqpheivvansrnpek 38
                                      G+G +g  l   l+++g   he++ a srnp++
  gi|336253299|ref|YP_004596406.1|  8 GTGFIGTNLCTELAERG---HEVT-ALSRNPDR 36
                                      9****************...****.99****97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.6
                                       HHHHHHH-SEEEE-S-H CS
                     F420_oxidored  55 neeaaeeadvvvlavkp 71 
                                          aae  dv ++ v++
  gi|336253299|ref|YP_004596406.1| 221 LVYAAEGKDVTIVPVPM 237
                                       55688888888888876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     4e-05     0.045       3      37 ..       3      35 ..       2      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-05
                                      EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..- CS
                                KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaa 37
                                      +l++GG+G +G+ l++ lae+g  ++  lsR++  
  gi|336253299|ref|YP_004596406.1|  3 VLVAGGTGFIGTNLCTELAERGH-EVTALSRNP-D 35
                                      69********************7.578889994.2 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 ?   12.3   0.0   8.1e-05     0.091       4      31 ..       4      32 ..       1      36 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.1e-05
                                      EEE.--STTHHHHHHHHHHCTSEEEEE-S CS
                    UDPG_MGDP_dh_N  4 svi.GlGYvGlvtaavlaeighevigvDi 31
                                       v  G+G++G   ++ lae+ghev+ +  
  gi|336253299|ref|YP_004596406.1|  4 LVAgGTGFIGTNLCTELAERGHEVTALSR 32
                                      55427*******************98755 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00032      0.36       2      32 ..       3      34 ..       2      49 .. 0.82
   2 ?   -2.3   0.0         6   6.8e+03      18      28 ..     223     233 ..     217     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                                      EEEECS.SHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  2 vvvvGg.GyiglElAgalaelgkkVtvversd 32
                                      v+v Gg G+ig  l ++lae g++Vt + r++
  gi|336253299|ref|YP_004596406.1|  3 VLVAGGtGFIGTNLCTELAERGHEVTALSRNP 34
                                      5566554********************99987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6
                                       HHHTTSEEEEE CS
                         Pyr_redox  18 laelgkkVtvv 28 
                                       +a+ gk+Vt+v
  gi|336253299|ref|YP_004596406.1| 223 YAAEGKDVTIV 233
                                       4778999*998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2292.62
//
Query:       gi|336253300|ref|YP_004596407.1|  [L=200]
Description: Thymidylate kinase [Halopiger xanaduensis SH-6]
Scores for 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-36  124.6   0.0    6.4e-36  123.8   0.0    1.4  1  Thymidylate_kin  Thymidylate kinase
    2.4e-06   27.6   0.0    9.8e-06   25.6   0.0    1.8  1  dNK              Deoxynucleoside kinase
      3e-06   27.5   0.0    1.4e-05   25.3   0.0    2.0  1  AAA_33           AAA domain
    7.2e-06   26.6   0.0      4e-05   24.2   0.0    2.1  1  AAA_18           AAA domain
     0.0029   17.9   0.2     0.0037   17.5   0.2    1.4  1  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.012   16.1   0.0        1.7    9.1   0.0    2.5  2  AAA_17           AAA domain
      0.032   13.6   0.1      0.037   13.4   0.1    1.2  1  DUF3179          Protein of unknown function (DUF3179)
      0.038   14.4   0.0      0.064   13.6   0.0    1.4  1  AAA_16           AAA ATPase domain
      0.054   13.5   0.0      0.087   12.8   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
       0.14   12.4   0.0       0.48   10.7   0.0    1.9  2  AAA_22           AAA 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 !  123.8   0.0   3.6e-39   6.4e-36       1     184 [.       5     189 ..       5     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 3.6e-39
                                       EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSS.TTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHH CS
                   Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrep.ggteiGekirelllkeeeleeqteallfaadriehleekikpa 76 
                                       +EGlDG+GKtt+ e+l er++++     +trep +++ +Ge + ++++   + ++++e++l++ad++ hl+++i pa
  gi|336253300|ref|YP_004596407.1|   5 LEGLDGSGKTTVWEALQERYPDAV----FTREPtDDSWYGEAVYRSIE-DDDADSLAELFLYTADHAAHLARVIDPA 76 
                                       6********************998....5666616789**********.99999*********************** PP

                                       HHTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTS..........E-SEEEEEESSHHHHHTSCCTTSSTTT CS
                   Thymidylate_kin  77 lkqgktvivdRylfSslaYqgakegvdldlvlslnedvll..........kPdltflldvdpevalkRlakrdelde 143
                                       l++g++vi+dRy +S  aYqga+   d +  + l++ +            +Pdlt++ld+dpe+a++R++++++   
  gi|336253300|ref|YP_004596407.1|  77 LERGDLVISDRYSDSRFAYQGATL-ADSERDYGLEDPLEYvvdvhdpfsiTPDLTIYLDLDPETAAERAGATNK--- 149
                                       *********************965.3544444443322111123456677************************... PP

                                       SHHHHHHHHHHHHHHHHHHHH.TTSTEEEEETTS-HHHHHHH CS
                   Thymidylate_kin 144 eeeeqldflrkvrerylelak.ederiliidasksieevhee 184
                                         +e  d+l  v+++y +l++ +++r++ +da+++ ++v e+
  gi|336253300|ref|YP_004596407.1| 150 --FEHADYLADVQANYERLIErDPDRFVRVDATQPQDAVLER 189
                                       ..*********************************9999775 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   5.5e-09   9.8e-06       2     169 ..       4     169 ..       3     197 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 5.5e-09
                                       EEEESTTSSHHHHHHHHHCCST.CEEEE-HHHH.CCSSSSHHHHHHHHSHHHHHHHH..HHHHHHHHHHHHHCHHSS CS
                               dNK   2 vveGnIgaGKstlvklLskklg.vkvfeEpvdk.wtnvqknlLekfYkdpsrwsfal..qtyvllsrlkqqlealat 74 
                                       ++eG  g+GK+t+ + L+++++  ++ +Ep d+ w   ++ + +   +d+  ++  +       ++  +++  al++
  gi|336253300|ref|YP_004596407.1|   4 TLEGLDGSGKTTVWEALQERYPdAVFTREPTDDsW-YGEAVYRSIEDDDADSLAELFlyTADHAAHLARVIDPALER 79 
                                       689******************98888899987625.222222222223333444333112233445556666666** PP

                                       S-EEEEES-HHHHHHTHHHHHHHTTSS-HHHHH.HHHHHHHHHH...HHCCH....-SEEEEEE--HHHHHHHHHHC CS
                               dNK  75 kqvvvleRsiysdryiFakalaekgtlseeelk.iykelldnll...eelak....pdlliYLkasletclerikkR 143
                                       ++ v+ +R  ysd   Fa    +  tl ++e +  +++ l+ ++   +        pdl iYL++++et  er    
  gi|336253300|ref|YP_004596407.1|  80 GDLVISDR--YSDS-RFAY---QGATLADSERDyGLEDPLEYVVdvhD---PfsitPDLTIYLDLDPETAAERAGAT 147
                                       *******9..7777.4554...33333333332145555555553221...13335****************98887 PP

                                       TTCCCTTS-HHHHHHHHHHHHHHHTS CS
                               dNK 144 greeekkieldYlekLhekyeewlkk 169
                                       ++ e    + dYl  ++ +ye  ++ 
  gi|336253300|ref|YP_004596407.1| 148 NKFE----HADYLADVQANYERLIER 169
                                       7777....789*****9999998876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   7.8e-09   1.4e-05       1     119 [.       2     148 ..       2     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 7.8e-09
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg.avllssdt........lrrrlfgtdqqsktdytrvldrlyqilnelarkals 68 
                                       lv l Gl GsGK+t+ e l ++ + av+ +++t        ++r ++ +d +s+ ++   + +  ++l+++++ al+
  gi|336253300|ref|YP_004596407.1|   2 LVTLEGLDGSGKTTVWEALQERYPdAVFTREPTddswygeaVYRSIEDDDADSLAELFLYTADHAAHLARVIDPALE 78 
                                       7899***************999999***********999999999999***************************** PP

                            AAA_33  69 agrnvildat..........nlsrrer........arflklarrlgvp.....vrivvvetdeetlkeRlakRa 119
                                       +g  vi d             l  +er        + ++ +      p     ++ ++++ d+et++eR  + +
  gi|336253300|ref|YP_004596407.1|  79 RGDLVISDRYsdsrfayqgaTLADSERdygledplEYVVDVHD----PfsitpDLTIYLDLDPETAAERAGATN 148
                                       ******9654332322222222223333444433333333333....033334777888888888888876655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.2e-08     4e-05       1     114 [.       3     148 ..       3     168 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.2e-08
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss........ 69 
                                       + l G  G+GKtt+ ++L++r      + d ++ +++ ++ +      ++ +++d  d+l +++   ++        
  gi|336253300|ref|YP_004596407.1|   3 VTLEGLDGSGKTTVWEALQER------YPDAVFTREPTDDSWYG-EAVYRSIEDDDADSLAELFLYTADhaahlarv 72 
                                       6799****************9......56666666665555555.45555555566666666666665566666666 PP

                            AAA_18  70 ...................................aleegknlvidghlaeleseaakdikkvvLtaspeelleRle 111
                                                                           le++  +v+d h    + ++++    ++L+++pe+ +eR  
  gi|336253300|ref|YP_004596407.1|  73 idpalergdlvisdrysdsrfayqgatladserdyGLEDPLEYVVDVHDPFSITPDLT----IYLDLDPETAAERAG 145
                                       6674444444444444444444444444444443334444444555555555555555....*************76 PP

                            AAA_18 112 kRg 114
                                       + +
  gi|336253300|ref|YP_004596407.1| 146 ATN 148
                                       655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2     2e-06    0.0037       3      95 ..       4     102 ..       2     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-06
                            AAA_28   3 vitGgestGKTtlleaLaargypvv..pEaareileeklakgedalpwvedllafaervleeqleeeaaa....... 70 
                                        + G  ++GKTt+ eaL++r    v  +E+  + +  ++  +   +++ +d+  +ae++l  + ++++ a       
  gi|336253300|ref|YP_004596407.1|   4 TLEGLDGSGKTTVWEALQERYPDAVftREPTDDSWYGEAVYRS--IED-DDADSLAELFLYTADHAAHLArvidpal 77 
                                       577889**************55444359999999988875544..456.5889999999998888888888888888 PP

                            AAA_28  71 aankvlfcDrglldtlaYaraygge 95 
                                       + ++++++Dr +   +aY  a   +
  gi|336253300|ref|YP_004596407.1|  78 ERGDLVISDRYSDSRFAYQGATLAD 102
                                       899*******998888888666555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00094       1.7       2      20 ..       7      25 ..       6      32 .. 0.87
   2 ?    4.4   0.0     0.027        48      99     119 ..     124     144 ..     105     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00094
                                      E-TTSSHHHHHHHHHHHHT CS
                            AAA_17  2 GgPGsGKgtqceklvekyg 20
                                      G+ GsGK+t+ e l+e+y 
  gi|336253300|ref|YP_004596407.1|  7 GLDGSGKTTVWEALQERYP 25
                                      899*************996 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.027
                                       HH..SEEEEEE--HHHHHHHH CS
                            AAA_17  99 elkpdaiilleadpeeilerr 119
                                       ++ pd+ i+l+ dpe+  er 
  gi|336253300|ref|YP_004596407.1| 124 SITPDLTIYLDLDPETAAERA 144
                                       5789***********988874 PP

>> DUF3179  Protein of unknown function (DUF3179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.1e-05     0.037     131     209 ..      14     103 ..      11     170 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                           DUF3179 131 tttwekwkeahpdtkVlseetgssrdYgrdPygsye.p...........asdrplfpvekrddrlppkerVvgvevg 195
                                       tt we+ +e++pd+   +e+t+ s  Yg+  y+s+e             + d   +  +  d  l++   V+  + +
  gi|336253300|ref|YP_004596407.1|  14 TTVWEALQERYPDAVFTREPTDDS-WYGEAVYRSIEdDdadslaelflyTADHAAHLARVIDPALERGDLVISDRYS 89 
                                       689**********96665666555.5**********55777666666665555556666778888888888888888 PP

                           DUF3179 196 ddavaypkaelkee 209
                                       d + ay+ a+l+++
  gi|336253300|ref|YP_004596407.1|  90 DSRFAYQGATLADS 103
                                       88888888888554 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   3.6e-05     0.064      27      88 ..       3      50 ..       1     130 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88
                                      v l G  G+GK+++ ++l++++ ++  +f+r+ +d++               e ++r ++d+
  gi|336253300|ref|YP_004596407.1|  3 VTLEGLDGSGKTTVWEALQERYPDA--VFTREPTDDS-----------WY-GEAVYRSIEDD 50
                                      77899**************999866..8888888888...........11.22333333333 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 ?   12.8   0.0   4.9e-05     0.087       2      56 ..       3      57 ..       2      74 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.9e-05
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--......... CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvd 56
                                      v L G  G+gK++++e l +++ + v++   t+d  + + ++r   +++  sl +
  gi|336253300|ref|YP_004596407.1|  3 VTLEGLDGSGKTTVWEALQERYPDAVFTREPTDDSWYGEAVYRSIEDDDADSLAE 57
                                      5699******************999998777776666555554443455555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00027      0.48       8      47 ..       3      32 ..       1      83 [. 0.71
   2 ?   -1.1   0.0       1.2   2.1e+03      37      52 ..     165     185 ..     146     199 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtl 47
                                      +++ G  G+GKTt+ + l+e+++            vf   
  gi|336253300|ref|YP_004596407.1|  3 VTLEGLDGSGKTTVWEALQERYPD----------AVFTRE 32
                                      567899***************853..........333333 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                            AAA_22  37 e....erpevvfvtlpsst.s 52 
                                       +     ++++v+v+++++   
  gi|336253300|ref|YP_004596407.1| 165 RlierDPDRFVRVDATQPQdA 185
                                       123335788888888887733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1486.39
//
Query:       gi|336253301|ref|YP_004596408.1|  [L=76]
Description: transcription regulator, AsnC-type [Halopiger xanaduensis SH-6]
Scores for 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   45.3   0.1    6.8e-12   45.2   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.064   13.3   1.3       0.11   12.6   1.3    1.3  1  NapD            NapD protein


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 !   45.2   0.1   7.6e-16   6.8e-12       1      73 [.       6      75 ..       6      76 .] 0.97

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 7.6e-16
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                      v+++ + g+    +++++ + +++ V++++ v+Gd d+++k  v+  +a  ++  ++++ ++gv++t+t+i++
  gi|336253301|ref|YP_004596408.1|  6 VMIKANTGE---ADRLRDDILAIEGVESAHIVAGDVDIIAKSQVETPAAVKDIAATQIQGIEGVEDTQTYIAM 75
                                      788999899...9**********************************************************99 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.3   1.2e-05      0.11       7      67 ..       7      69 ..       4      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
                              NapD  7 vVqarperlaavkaalaalpgvEv.hasdeegklVvviEaesedeladtiea.iealpgVlsa 67
                                       ++a+ ++ +++++++ a++gvE  h + ++  ++   + e+  ++ d+ ++ i+ ++gV ++
  gi|336253301|ref|YP_004596408.1|  7 MIKANTGEADRLRDDILAIEGVESaHIVAGDVDIIAKSQVETPAAVKDIAATqIQGIEGVEDT 69
                                      69999******************6256666699999999999999999876559999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 606.66
//
Query:       gi|336253302|ref|YP_004596409.1|  [L=243]
Description: TrkA-N domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-27   93.7   0.3    1.3e-26   93.1   0.3    1.3  1  TrkA_N           TrkA-N domain
    1.5e-13   50.4   0.4    3.4e-13   49.2   0.4    1.6  1  TrkA_C           TrkA-C domain
    7.5e-07   28.9   0.0    1.3e-06   28.1   0.0    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    3.5e-06   27.0   0.1    6.7e-06   26.1   0.1    1.5  1  NAD_binding_10   NAD(P)H-binding
    3.8e-06   27.3   0.1    6.7e-06   26.5   0.1    1.4  1  NAD_binding_7    Putative NAD(P)-binding
    6.6e-06   25.8   0.0    1.1e-05   25.1   0.0    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA
    7.4e-06   25.4   0.0    8.8e-06   25.2   0.0    1.2  1  FAD_binding_3    FAD binding domain
    2.4e-05   24.8   0.1    4.7e-05   23.9   0.1    1.5  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    4.6e-05   23.2   0.0      7e-05   22.6   0.0    1.3  1  DAO              FAD dependent oxidoreductase
    0.00022   20.5   0.0    0.00033   20.0   0.0    1.7  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    0.00022   21.4   0.0    0.00043   20.5   0.0    1.5  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    0.00046   20.1   0.0    0.00067   19.6   0.0    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0005   19.6   0.1      0.001   18.6   0.1    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0016   17.6   0.0      0.025   13.7   0.0    2.0  2  FAD_binding_2    FAD binding domain
     0.0019   18.4   0.0      0.022   14.9   0.0    2.1  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0025   18.1   0.1     0.0043   17.3   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0039   16.6   0.0      0.021   14.2   0.0    1.9  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0044   16.6   0.0     0.0084   15.7   0.0    1.5  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
     0.0058   17.2   0.0      0.046   14.3   0.0    2.1  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.017   15.6   0.0      0.033   14.7   0.0    1.5  1  XdhC_C           XdhC Rossmann domain
      0.022   14.0   0.1      0.032   13.5   0.1    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.024   13.4   0.0      0.033   12.9   0.0    1.2  1  HI0933_like      HI0933-like protein
      0.072   13.2   0.0       0.12   12.4   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.086   12.8   0.4       0.15   12.0   0.2    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
      0.089   12.8   0.0       0.17   11.9   0.0    1.5  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
        0.1   13.1   0.4       0.23   11.9   0.4    1.6  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
       0.11   11.8   0.0       0.16   11.2   0.0    1.2  1  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
       0.17   11.9   0.0       0.33   10.9   0.0    1.4  1  Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion


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 !   93.1   0.3   2.1e-29   1.3e-26       1     116 []       3     118 ..       3     118 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 2.1e-29
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       ++iiG+GrvG + a+ L+e+g+dv++i++de +v+++r+e ++vv gd+++e+vLeeag+ +adav a+tgd  +n 
  gi|336253302|ref|YP_004596409.1|   3 FVIIGAGRVGLRTARVLREEGHDVTLIERDEPKVRRARNEDFRVVEGDGSREDVLEEAGVTDADAVGALTGDLNVNF 79 
                                       79*****************6558****************************************************** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHH..HTTSEEEEH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkk..lgadvvisp 116
                                        a+++a +   ++++i r++++ ++ +++k    +d+vi+p
  gi|336253302|ref|YP_004596409.1|  80 TACMIADH--YGCRTIMRIDEAYREGIYRKyaEAVDEVIYP 118
                                       ******84..669***************9974446***998 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.4   5.3e-16   3.4e-13       1      69 [.     147     215 ..     147     216 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 5.3e-16
                                       CEEEEEE--GGGTTSBHHHHTHHHHS-EEEEE.E-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrargvlvvai.rRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                       +ve+ ++ ++p+ G t++el l+a +++++a  +R+gel ip++d  LeeGD+l+v+++ + l+e+r ll
  gi|336253302|ref|YP_004596409.1| 147 VVELMITDDAPVNGYTISELELPA-DARLLAFgKRDGELAIPDEDESLEEGDRLVVLADFDVLSEVRQLL 215
                                       79**********************.*******99*******************************99876 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 !   28.1   0.0   2.1e-09   1.3e-06       1      50 [.       1      50 [.       1      68 [. 0.92

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.1e-09
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TT CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepg 50
                                      m+ ++iG+G vGl ta vl e gh+v+++  de kv+  +++++ ++e +
  gi|336253302|ref|YP_004596409.1|  1 MRFVIIGAGRVGLRTARVLREEGHDVTLIERDEPKVRRARNEDFRVVEGD 50
                                      7889******************************************9965 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 !   26.1   0.1     1e-08   6.7e-06       3      71 ..       8      75 ..       7     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1e-08
                                      TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHH.HTT-SEEEES---T CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaea.lkgadaVvsalggg 71
                                       G+vG + ++ l ++ gh+vt++ R++ k+ + + +e  +vvegd + ++ l+ea +++adaV + +g  
  gi|336253302|ref|YP_004596409.1|  8 AGRVGLRTARVLREE-GHDVTLIERDEPKVRRAR-NEDFRVVEGDGSREDVLEEAgVTDADAVGALTGDL 75
                                      7**************.5**************875.8****************999679****97777654 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 !   26.5   0.1   1.1e-08   6.7e-06       9      82 ..       2      85 ..       1      99 [. 0.76

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.1e-08
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeel...ekd...........legadlviaatddre 73
                                      + +++G+G+v++r +r l e+g +vt++  +   e ++  ++++e++   e+d           +++ad v a t d +
  gi|336253302|ref|YP_004596409.1|  2 RFVIIGAGRVGLRTARVLREEGHDVTLIERD---E-PKVRRARNEDFrvvEGDgsredvleeagVTDADAVGALTGDLN 76
                                      679**************************99...3.4555566666544433344445666566999**********99 PP

                     NAD_binding_7 74 lneriaeaa 82
                                      +n   +  a
  gi|336253302|ref|YP_004596409.1| 77 VNFTACMIA 85
                                      997776666 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.7e-08   1.1e-05       2      53 ..       4      58 ..       3      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.7e-08
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT..CEEEEE CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg..geeilr 53
                                      +i+GaG +G   a  L + g+dvtli r++ ++ + +++++r+ + +  +e +l+
  gi|336253302|ref|YP_004596409.1|  4 VIIGAGRVGLRTARVLREEGHDVTLIERDEpKVRRARNEDFRVVEGDgsREDVLE 58
                                      7**********************************99999999998854444444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.4e-08   8.8e-06       5      42 ..       4      41 ..       1     113 [. 0.80

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.4e-08
                                      EEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS- CS
                     FAD_binding_3  5 lIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpra 42
                                      +I+GaG +Gl +a++L+e G +v+l+e+ + +v+  r 
  gi|336253302|ref|YP_004596409.1|  4 VIIGAGRVGLRTARVLREEGHDVTLIERDEPKVRRARN 41
                                      7******************************9998875 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   7.4e-08   4.7e-05       1      40 [.       2      42 ..       2      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 7.4e-08
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSS.SSSTTSSH CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversd.kllrllDe 40
                                      + v++G+G +gl  A +l+e g++Vt++er + k++r+ +e
  gi|336253302|ref|YP_004596409.1|  2 RFVIIGAGRVGLRTARVLREEGHDVTLIERDEpKVRRARNE 42
                                      579**************************964144455555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.1e-07     7e-05       2      32 ..       3      34 ..       2      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.1e-07
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSSST CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdia 32
                                       viiG+G +Gl tA+ L ++g  Vtl+e++ ++
  gi|336253302|ref|YP_004596409.1|  3 FVIIGAGRVGLRTARVLREEGhdVTLIERD-EP 34
                                      79***************88899*******9.55 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 !   20.0   0.0   5.1e-07   0.00033       2      33 ..       2      33 ..       1     204 [. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.1e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                      + v+iG+G  Gl++a+ l++ g++vtl+e+++
  gi|336253302|ref|YP_004596409.1|  2 RFVIIGAGRVGLRTARVLREEGHDVTLIERDE 33
                                      56888888888888888888888888886332 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 !   20.5   0.0   6.7e-07   0.00043       1      28 [.       5      32 ..       5      44 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.7e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      I+GaG  Gl +A+ L+++g+dv+l+e+ 
  gi|336253302|ref|YP_004596409.1|  5 IIGAGRVGLRTARVLREEGHDVTLIERD 32
                                      9*************************85 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 !   19.6   0.0   1.1e-06   0.00067       4      42 ..       5      43 ..       2      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                                      EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                           3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdiseealekaleki 42
                                      +iGaG +G   a v+ ++g++V+l++++e ++++a+++ 
  gi|336253302|ref|YP_004596409.1|  5 IIGAGRVGLRTARVLREEGHDVTLIERDEPKVRRARNED 43
                                      9*********************************99875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.6e-06     0.001       5      69 ..       7      69 ..       3      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-06
                                      TTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEE CS
                         Epimerase  5 GatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavi 69
                                      G +G +G  +++ l e+g++v+ + r++ + ++ar+ed ++ve+d   ++ le++  + ++dav 
  gi|336253302|ref|YP_004596409.1|  7 G-AGRVGLRTARVLREEGHDVTLIERDEPKVRRARNEDFRVVEGDGSREDVLEEAGVT-DADAVG 69
                                      5.5*******************************************999999998774.777775 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   3.8e-05     0.025       3      33 ..       4      34 ..       2      39 .. 0.93
   2 ?    2.1   0.0      0.13        81     131     186 ..     117     170 ..      48     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                                      EEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  3 iViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      ++iG+G  GL+ A  ++e+G++v+++e  ++
  gi|336253302|ref|YP_004596409.1|  4 VIIGAGRVGLRTARVLREEGHDVTLIERDEP 34
                                      9**************************9886 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.13
                                       T-.......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT.EEEEEEEEETTTTC CS
                     FAD_binding_2 131 darr.etlvtghallarlvesarkagvdfqerteadeLivedg.rvtGavvenpesgr 186
                                        ++r  +++  +all   ++++     d+ ++++++eL+++d+  v+G +++++e + 
  gi|336253302|ref|YP_004596409.1| 117 YPERlGAIGAKNALLGGTIRAI----ADIAPHLQVVELMITDDaPVNGYTISELELPA 170
                                       5566688899999999999999....9***********99766699999998774333 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 !   14.9   0.0   3.5e-05     0.022       3      54 ..       4      58 ..       2      78 .. 0.82
   2 ?    1.3   0.0      0.55   3.5e+02      47      71 ..     136     160 ..     105     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.5e-05
                                      EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...EEE-SSHHHHHH CS
                     NAD_binding_2  3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...akaaesieelva 54
                                       +iG G  G   a+ l ++g++v++++r++ kv+++ +e    +++  s e++++
  gi|336253302|ref|YP_004596409.1|  4 VIIGAGRVGLRTARVLREEGHDVTLIERDEPKVRRARNEDfrvVEGDGSREDVLE 58
                                      58**********************************9998444444445555555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.55
                                       SSHHHHHHHCSEEEE-SSSHHHHHH CS
                     NAD_binding_2  47 esieelvasldvvitmvkagkavde 71 
                                         i++++ +l+vv +m++++++v+ 
  gi|336253302|ref|YP_004596409.1| 136 RAIADIAPHLQVVELMITDDAPVNG 160
                                       5677888888999999999998875 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 !   17.3   0.1   6.7e-06    0.0043       2      73 ..       4      68 ..       3      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.7e-06
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEE CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlv 73
                                      +iiGaG+vG  +a++l ++++    +t+++r++ k++++    ++++f  ++ d + ++  L+++ ++++d+v
  gi|336253302|ref|YP_004596409.1|  4 VIIGAGRVGLRTARVLREEGHD---VTLIERDEPKVRRA----RNEDFRVVEGDGSREDV-LEEAgVTDADAV 68
                                      8*****************9985...**********8888....67777777777776665.666556666665 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 !   14.2   0.0   3.3e-05     0.021      38      84 ..       2      48 ..       1      62 [. 0.83
   2 ?   -0.1   0.0      0.79     5e+02       8      44 ..      90     126 ..      86     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.3e-05
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECS CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvs 84
                                      +  iiG+Gr+G ++a++l++ g +v+ ++r + k ++++++ +++v+
  gi|336253302|ref|YP_004596409.1|  2 RFVIIGAGRVGLRTARVLREEGHDVTLIERDEPKVRRARNEDFRVVE 48
                                      568***************************99888777776666654 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.79
                                       HTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES- CS
                      2-Hacid_dh_C   8 lrrlaeadeevregewksekallgkelsgktvGiiGl 44 
                                       +r + ++de++reg +++ ++   + ++ +++G iG+
  gi|336253302|ref|YP_004596409.1|  90 CRTIMRIDEAYREGIYRKYAEAVDEVIYPERLGAIGA 126
                                       6899999999999999888888888899999999985 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 !   15.7   0.0   1.3e-05    0.0084       7      54 ..       3      49 ..       1      76 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                                      EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEH CS
                              IlvN  7 iaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltv 54
                                       ++iG G  G   a+ lr+ g dv++  r++  +v++A++e f+v++ 
  gi|336253302|ref|YP_004596409.1|  3 FVIIGAGRVGLRTARVLREEGHDVTLIERDEP-KVRRARNEDFRVVEG 49
                                      589**********************9877766.99*********9874 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 !   14.3   0.0   7.2e-05     0.046       2      46 ..       3      43 ..       2      64 .. 0.74
   2 ?    0.2   0.0       1.8   1.1e+03      43      81 ..     178     215 ..     159     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.2e-05
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeel 46
                                      + iiGaG++g   a+ l ++g   h+++++ +r++ k++ +++e 
  gi|336253302|ref|YP_004596409.1|  3 FVIIGAGRVGLRTARVLREEG---HDVTLI-ERDEPKVRRARNED 43
                                      679******************...****99.88888888777543 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.8
                                       HHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
                     F420_oxidored  43 aeelgvkvtavdneeaaeeadvvvlavkpedveevlsel 81 
                                        ++ g  +++ d  e +ee d +v+   + +++ev + l
  gi|336253302|ref|YP_004596409.1| 178 GKRDGELAIP-DEDESLEEGDRLVVLADFDVLSEVRQLL 215
                                       4556666777.8899999999999999999999987766 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.2e-05     0.033       2      61 ..       4      82 ..       3     103 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.2e-05
                                      EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE.....................-EEEE--S-HHHHHH CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade.....................tavvvlthdhklDae 59
                                      vi+Gag v+   ar++++ g +vt+++ +e   +++r ++                        +av +lt d +  + 
  gi|336253302|ref|YP_004596409.1|  4 VIIGAGRVGLRTARVLREEGHDVTLIERDEPKVRRARNED--FrvvegdgsredvleeagvtdaDAVGALTGDLNVNFT 80
                                      89*************************9995343333332..1224445555555666666666555555555555555 PP

                                      HH CS
                            XdhC_C 60 al 61
                                      a+
  gi|336253302|ref|YP_004596409.1| 81 AC 82
                                      55 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 ?   13.5   0.1     5e-05     0.032      30      86 ..       2      58 ..       1      72 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeella 86
                                      + ++iG+G +Gl  +++ ++ g +Vt+++ ++ + ++ ++   ++ve   s e+ l+
  gi|336253302|ref|YP_004596409.1|  2 RFVIIGAGRVGLRTARVLREEGHDVTLIERDEPKVRRARNEDFRVVEGDGSREDVLE 58
                                      579***************************999988887766666666555555555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.2e-05     0.033       3      33 ..       3      33 ..       1      39 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                                      EEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekak 33
                                       ++iG+G  Gl +A  ++++g++V+l+e+ +
  gi|336253302|ref|YP_004596409.1|  3 FVIIGAGRVGLRTARVLREEGHDVTLIERDE 33
                                      69**************************865 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00019      0.12      14      52 ..       2      39 ..       1      68 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHH CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakel 52
                                      + ++iGaG+++ ++a+ L ++g + v+ + R+  ++++ 
  gi|336253302|ref|YP_004596409.1|  2 RFVIIGAGRVGLRTARVLREEGHD-VTLIERDEPKVRRA 39
                                      579****************99998.*******9998765 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00024      0.15       3      36 ..       7      40 ..       5      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                    Glyco_transf_4  3 GverhvleLaraLarrGheVtvvtpgddgpleee 36
                                      G++r+ l+ ar L++ Gh+Vt++ ++ ++  + +
  gi|336253302|ref|YP_004596409.1|  7 GAGRVGLRTARVLREEGHDVTLIERDEPKVRRAR 40
                                      999********************87777665555 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 ?   11.9   0.0   0.00026      0.17       3      37 ..       4      38 ..       2      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                                      EEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHH CS
                    NAD_Gly3P_dh_N  3 avlGaGswGtalAkvlaenghevrlwvreeeliee 37
                                       ++GaG  G   A+vl e+gh+v+l+ r+e  +++
  gi|336253302|ref|YP_004596409.1|  4 VIIGAGRVGLRTARVLREEGHDVTLIERDEPKVRR 38
                                      59**************************9966654 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 ?   11.9   0.4   0.00036      0.23       2      43 ..       7      47 ..       7      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00036
                   Glyco_trans_4_4  2 GigryvaelaraLaarGheVtvltpapapgapeleedgvrvh 43
                                      G+gr+  ++ar L+++Gh+Vt++ ++++ +++ ++ +  rv+
  gi|336253302|ref|YP_004596409.1|  7 GAGRVGLRTARVLREEGHDVTLIERDEPKVRR-ARNEDFRVV 47
                                      89999*****************9987777766.444455554 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   0.00025      0.16       1      31 [.       4      33 ..       4      40 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      +IiGaG  Gl +a  l++ g  d++ +E+++
  gi|336253302|ref|YP_004596409.1|  4 VIIGAGRVGLRTARVLREEGH-DVTLIERDE 33
                                      7*******************9.899***975 PP

>> Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00051      0.33      66      91 ..     182     206 ..     172     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00051
                   Castor_Poll_mid  66 gkiylnPeddevlqegdkllviaedd 91 
                                       g++++ P++de l+egd+l+v+a+ d
  gi|336253302|ref|YP_004596409.1| 182 GELAI-PDEDESLEEGDRLVVLADFD 206
                                       66655.9****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 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:                        64  (0.00356964); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 1910.71
//
Query:       gi|336253303|ref|YP_004596410.1|  [L=76]
Description: transcription regulator, AsnC-type [Halopiger xanaduensis SH-6]
Scores for complete 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   37.7   0.1    1.7e-09   37.5   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain


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 !   37.5   0.1   9.2e-14   1.7e-09       1      73 [.       6      75 ..       6      76 .] 0.96

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 9.2e-14
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                      ++v++  g+    e +  ++++++ V  ++ v+G yd++++v ++ +  + + ++  ++ l+gv++t+t+i++
  gi|336253303|ref|YP_004596410.1|  6 IMVKTAAGK---SEGLLSRIRDFERVSAAHIVAGNYDIIAEVDAEEVYNILETVSSDMQGLDGVTETKTYIAM 75
                                      789999999...************************************999999999**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 608.37
//
Query:       gi|336253304|ref|YP_004596411.1|  [L=185]
Description: hypothetical protein Halxa_1905 [Halopiger xanaduensis SH-6]
Scores for 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:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1441.79
//
Query:       gi|336253305|ref|YP_004596412.1|  [L=74]
Description: hypothetical protein Halxa_1906 [Halopiger xanaduensis SH-6]
Scores for 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  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      142  (0.00792013); 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: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 604.62
//
Query:       gi|336253306|ref|YP_004596413.1|  [L=128]
Description: hypothetical protein Halxa_1907 [Halopiger xanaduensis SH-6]
Scores for 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  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1000.28
//
Query:       gi|336253307|ref|YP_004596414.1|  [L=428]
Description: O-acetylhomoserine/O-acetylserine sulfhydrylase [Halopiger xanaduensis SH-6]
Scores for complete 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-137  458.4   0.0   1.5e-137  458.2   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    5.8e-08   32.3   0.0    8.1e-08   31.8   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    1.6e-05   24.4   0.7    4.4e-05   22.9   0.4    1.7  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
       0.01   14.5   0.0      0.016   13.9   0.0    1.2  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
      0.014   14.4   0.0      0.027   13.4   0.0    1.5  1  Aminotran_5      Aminotransferase class-V
      0.037   13.3   0.0      0.064   12.5   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase


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 !  458.2   0.0    5e-141  1.5e-137       2     381 ..      12     425 ..      11     426 .. 0.98

  Alignments for each domain:
  == domain 1  score: 458.2 bits;  conditional E-value: 5e-141
                                       HHHHHTTTTCHTTTTBSS--B---SBBBESSHHHH...CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESS CS
                   Cys_Met_Meta_PP   2 Tllvhagqekdeqtgavavpiyltstykfkdvdea...fageekgyeYsRsgnptrsvleeriaaLeggeaalavss 75 
                                       T  vhagqe+d++tga+a+p+y+t++y+f+d+++a   f+ ee+g++YsR++npt+ +leeria+Legg  ala+ss
  gi|336253307|ref|YP_004596414.1|  12 TDSVHAGQEPDPTTGARAPPLYQTTSYEFEDTEHAaalFGLEETGNIYSRIMNPTNAMLEERIATLEGGVGALATSS 88 
                                       889*******************************99***************************************** PP

                                       HHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT- CS
                   Cys_Met_Meta_PP  76 GmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllk 152
                                       GmaA ++a + l+  Gd+iv+s++lYggt+ +l++++ k gie+kfvdt d e+ ++ai++ t  v+lEt++np l 
  gi|336253307|ref|YP_004596414.1|  89 GMAAFDLATFILADVGDNIVSSSSLYGGTYTYLTHTVAKRGIETKFVDTLDYEAYAEAIDDDTAFVHLETIGNPALV 165
                                       ***************************************************************************** PP

                                       ---HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHH.. CS
                   Cys_Met_Meta_PP 153 vvDiekiaklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflq.. 227
                                       ++Die+ia++a++++v+++vDntfa+p+l+rpl++gaD+v +S+TK++ G + +v+G++v+ g++ + +  +     
  gi|336253307|ref|YP_004596414.1| 166 TPDIERIADIAHDHDVPLFVDNTFATPYLCRPLEHGADLVWNSTTKWIHGAGSTVGGILVDGGSFPWPEGDYPEIte 242
                                       *******************************************************************9975543378 PP

                                       ............................HHHT-B--HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEEE CS
                   Cys_Met_Meta_PP 228 ............................nalGavlspfdawlllrGlkTLslRlerhqenAlkvAefLekhpkvekv 276
                                                                   ++lG+  spfdaw++l+ l+ L lR+e+h enA++vAe+Le hp v +v
  gi|336253307|ref|YP_004596414.1| 243 pnpayhgvnfyetfgdmafsvvartrglRDLGNQQSPFDAWVTLQKLESLPLRMEKHCENAMAVAEYLEDHPDVAWV 319
                                       9**************************************************************************** PP

                                       E-TTSTTSTTHHHHHHHSSSG-S.EEEEEESSHHHHHHHHHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCHHHHH CS
                   Cys_Met_Meta_PP 277 yYpglpshpqhelakkqlkgagg.vlsFelkseeekakkfvdnlklfslaeslGgveslielpasmthasipkeere 352
                                       +Ypgl+sh+ he a ++l+g+ g +++F l+++  +a+++++++ l+sl++++G++++li++pas+th+++++ee+ 
  gi|336253307|ref|YP_004596414.1| 320 NYPGLESHETHEEASEYLEGGYGgMITFGLEGGYDAAETVCNEVDLASLLANVGDAKTLIIHPASTTHQQLTEEEKL 396
                                       ******************987555***************************************************** PP

                                       HTTS-TTEEEEE--SS-HHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 353 aagvtddliRlsvGiEdvdDliaDlkqal 381
                                       a+gvtddl+RlsvGiEdvdD+iaDl+qa+
  gi|336253307|ref|YP_004596414.1| 397 ASGVTDDLVRLSVGIEDVDDVIADLEQAI 425
                                       ***************************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 !   31.8   0.0   2.7e-11   8.1e-08      19     194 ..      39     193 ..      30     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.7e-11
                                       HHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT- CS
                     Aminotran_1_2  19 tlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgd 94 
                                       +++++ +a++  g++++g++ +   +   + lee++a + g          +a+ ++sG  a + a + l+  + gd
  gi|336253307|ref|YP_004596414.1|  39 EFEDTEHAAALfGLEETGNIYSRIMNPTNAMLEERIATLEG--------GVGALATSSGMAAFDLATFILA--DVGD 105
                                       55666666666544444444444444558999999999999........8889999999998877666666..5*** PP

                                       EEEEEESS-TH....HHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--H CS
                     Aminotran_1_2  95 eilvpdptyas....yknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatl 167
                                       +i++++  y+      ++ +  +g+e   +        +ld ea+ ea+++       t ++ +e++ NP  + ++ 
  gi|336253307|ref|YP_004596414.1| 106 NIVSSSSLYGGtytyLTHTVAKRGIETKFVD-------TLDYEAYAEAIDD------DTAFVHLETIGNPALVTPDI 169
                                       *****98666500005555666788888888.......*************......899**********8777777 PP

                                       HHHHHHHHHHHHTTEEEEEEETTTTCB CS
                     Aminotran_1_2 168 eeleklldlakkynlllfvDeaYagfv 194
                                       e + ++   a+ + + lfvD ++a+ +
  gi|336253307|ref|YP_004596414.1| 170 ERIADI---AHDHDVPLFVDNTFATPY 193
                                       777777...*************99755 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 !   22.9   0.4   1.5e-08   4.4e-05      21     145 ..      61     187 ..      41     194 .. 0.81
   2 ?   -1.4   0.0      0.36   1.1e+03     225     271 ..     280     326 ..     275     336 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-08
                                       S..SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHH.TTTTTT-EEEEESSS-THH....HHHHHHTT-EEEEE CS
                   DegT_DnrJ_EryC1  21 s..gpeveeFEkafaaylgvkhaiavssGtaAlhlaLra.lgvgpgdeVIvpsltFvat....anavlelgakpvfv 90 
                                       +  +p+++ +E+++a+  g   a+a+ssG aA  la     +vg  d ++  s  + +t     ++v++ g ++ fv
  gi|336253307|ref|YP_004596414.1|  61 RimNPTNAMLEERIATLEGGVGALATSSGMAAFDLATFIlADVG--DNIVSSSSLYGGTytylTHTVAKRGIETKFV 135
                                       2559*******************************988756666..9999999877777222256788889999999 PP

                                       -B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB--....-HHHHHHHHHHCT-EEEEE- CS
                   DegT_DnrJ_EryC1  91 DvdpdtynidpaaieaaitertkaIlpVhlyGqva....dmdalkaiaakhglkvieDa 145
                                       D       +d +a ++ai   t+ +   ++ G++a    d++++ +ia++h+++++ D 
  gi|336253307|ref|YP_004596414.1| 136 DT------LDYEAYAEAIDDDTAFV-HLETIGNPAlvtpDIERIADIAHDHDVPLFVDN 187
                                       95......6************9765.6688999877889****************9996 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSS CS
                   DegT_DnrJ_EryC1 225 iqAAiglaqLerldelvarRreiaelykeeLaelegtaelttpketk 271
                                       + A + l++Le l   +++  e+a    e L++ + +a ++ p  ++
  gi|336253307|ref|YP_004596414.1| 280 FDAWVTLQKLESLPLRMEKHCENAMAVAEYLEDHPDVAWVNYPGLES 326
                                       5688999999*999999999999999999999999877766666555 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 ?   13.9   0.0   5.4e-06     0.016     145     196 ..     141     191 ..     121     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.4e-06
                                       HHHHHCCTCCCEEEEEECSSTTTTB----HHHHHHHHHCCT--EEEEGCCCC CS
                           SepSecS 145 eeiiekkreevilavlstlsffaprspDdvkeiakiCaeydvPhlvNgAYai 196
                                       e+  e + ++ ++ v+  + +++  +  d+++ia i +++dvP+ v + +a 
  gi|336253307|ref|YP_004596414.1| 141 EAYAEAIDDD-TAFVHLETIGNPALVTPDIERIADIAHDHDVPLFVDNTFAT 191
                                       4444555555.566666667777766555*******************9985 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.1e-06     0.027     126     202 ..     137     213 ..      83     220 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.1e-06
                                       CBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT. CS
                       Aminotran_5 126 eldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK. 201
                                       +ld ++++++++++t+ v++  + n   +  ++e+i+++a+++++ ++vD + a +     + + g+D++  s+ K 
  gi|336253307|ref|YP_004596414.1| 137 TLDYEAYAEAIDDDTAFVHLETIGNPALVTPDIERIADIAHDHDVPLFVDNTFATPYLCRPL-EHGADLVWNSTTKw 212
                                       589999********************************************877766544433.45677777776664 PP

                                       T CS
                       Aminotran_5 202 l 202
                                       +
  gi|336253307|ref|YP_004596414.1| 213 I 213
                                       4 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.1e-05     0.064      31     168 ..      64     187 ..      46     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                                       -HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTT CS
                   Beta_elim_lyase  31 dktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaG 107
                                       ++t   Le+++a l g  +al + +G aA  ++  il+  g++++ ++   + +++   + + +      +++k   
  gi|336253307|ref|YP_004596414.1|  64 NPTNAMLEERIATLEGGVGALATSSGMAAFDLATFILADVGDNIVSSSSLYGGTYTYLTHTVAKRG----IETKFVD 136
                                       6778889*************************************9999988888888888776444....5666667 PP

                                       BE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
                   Beta_elim_lyase 108 kmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                                       ++d e+ ++ai++      +++++ l++  n     ++    ++++a+ia+++++pl++D 
  gi|336253307|ref|YP_004596414.1| 137 TLDYEAYAEAIDD------DTAFVHLETIGN----PALVTPDIERIADIAHDHDVPLFVDN 187
                                       899*********9......488***998777....4888889****************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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 0.23s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 3463.39
//
Query:       gi|336253308|ref|YP_004596415.1|  [L=260]
Description: hypothetical protein Halxa_1909 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.21   11.8   1.4       0.76   10.0   0.1    2.4  2  DUF4115   Domain of unknown function (DUF4115)


Domain annotation for each model (and alignments):
>> DUF4115  Domain of unknown function (DUF4115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   4.3e-05      0.76      29      68 ..      35      73 ..      26      78 .. 0.79
   2 ?   -0.2   0.1     0.066   1.2e+03      44      44 ..     146     146 ..     116     186 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 4.3e-05
                           DUF4115 29 Getkevsgk.ppltltiGnagavevsvnGkpvdllgyargn 68
                                      G++ +  ++ +p t+t+ +ag  ++ vn+++vd+ g   ++
  gi|336253308|ref|YP_004596415.1| 35 GDESDAHAApAP-TVTASAAGEPTLVVNDATVDPDGT-ATQ 73
                                      667777566355.***********************4.444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.066
                           DUF4115  44 i 44 
                                       +
  gi|336253308|ref|YP_004596415.1| 146 T 146
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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 0.20s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 2284.47
//
Query:       gi|336253309|ref|YP_004596416.1|  [L=883]
Description: hypothetical protein Halxa_1910 [Halopiger xanaduensis SH-6]
Scores for 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-22   78.8   2.9    9.6e-20   71.2   1.4    3.6  3  DUF839        Bacterial protein of unknown function (DUF839)
    0.00012   22.2   1.5    0.00012   22.2   1.5    2.1  2  Dockerin_1    Dockerin type I domain
  ------ inclusion threshold ------
       0.14   12.7   6.8       0.37   11.3   2.7    3.3  2  EF-hand_7     EF-hand domain pair
       0.15   11.7   9.3        1.3    8.8   0.1    4.2  4  EF-hand_1     EF hand
       0.31   11.1   5.0        2.4    8.3   0.1    3.7  3  EF-hand_6     EF-hand domain


Domain annotation for each model (and alignments):
>> DUF839  Bacterial protein of unknown function (DUF839)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.017        60     489     523 ..      44      77 ..      11      78 .. 0.85
   2 ?   -0.6   0.0      0.15   5.5e+02      21      82 ..     127     199 ..     113     216 .. 0.70
   3 !   71.2   1.4   2.7e-23   9.6e-20     147     460 ..     219     662 ..     213     708 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.017
                            DUF839 489 rgevkrfltepegsEvtGvtfsPdgktlfvnvqhP 523
                                       +g +kr+ t + g+EvtG+ +  d   l+ ++qhP
  gi|336253309|ref|YP_004596416.1|  44 KGDIKRLSTTAFGAEVTGPFVF-DTGELLYSLQHP 77 
                                       6889999************999.8888999****9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.15
                            DUF839  21 eakvlvrwGdklfagapefd...........qsaeaqekqvgynhDgmaffplsrsadeglLvvNhEytseei 82 
                                       e++ lv++Gd++  g++ f            + +e   +  g + D   f+p + ++ eg+L  N+E    +i
  gi|336253309|ref|YP_004596416.1| 127 EYRLLVQTGDEINGGTERFGypqtpdgrslaEITEPWYEGPGDQPDMNFFVPDEDEEIEGYLFTNNETRPGAI 199
                                       6889999999999999999777666664332222222233456666656666666777999999999876555 PP

  == domain 3  score: 71.2 bits;  conditional E-value: 2.7e-23
                            DUF839 147 llktsadaegvkilGTanNCagGtTpWGtyLtcEEnfng.yfggeea...vkadqkryGitgttgy........... 208
                                        +++++++ +++i GT +NC g  +pWGt ++ EE   +   gg  +   + +++  +G++g++++           
  gi|336253309|ref|YP_004596416.1| 219 AMELENTEPFREIGGTKVNCYGDLSPWGTPMSSEEEYGHpRVGGLATvgdIVEEGSGVGLRGSSEFwnrpkilaveq 295
                                       5677788999**************************99985565544455899999********************* PP

                            DUF839 209 .......................................................erFdvanepkkfGyvvEv.dpv 229
                                                                                              e F ++    ++G +vE+ +p 
  gi|336253309|ref|YP_004596416.1| 296 sleeifgedswypmglhnnrnvekmayhlgaepidqagldedgveiddlarpiddEEFPNR---YRYGKIVEItEPT 369
                                       **************************99999999998888877766666544444444444...67888****5577 PP

                            DUF839 230 dprstpvkrtalGrfkHEaaavvveddkrvvvYlgdDerkeylYkFvsndrvgtgnskansaLldeGtLyvakfned 306
                                           tpvk+  +Gr + E  ++ ++d++   vYl  D + + +YkFv+++++ +       ++   GtLy+ k +e 
  gi|336253309|ref|YP_004596416.1| 370 ADVPTPVKHHVMGRSAWECPEF-LSDER--TVYLASDGSAKGIYKFVAEKPIPEY----DDRMDVRGTLYAIKAAEV 439
                                       7799******************.55554..47*******************8755....699*************99 PP

                            DUF839 307 .........gtveWvplveg......................................................... 317
                                                  veW++l ++                                                         
  gi|336253309|ref|YP_004596416.1| 440 gdgpvaktdLDVEWLELGTAsnaeveswiaeyddvtqvdylethadtdweedleaalreadeevakngnqdyitdee 516
                                       99****99999******999*******************************************************99 PP

                            DUF839 318 ....qgglta...engfadqaevl.vktrlaadkvGat.kmdrpEdievnPttg...evyvvltnnkkrdeskidsa 382
                                            +++++   +   ++   v  ++tr+aa+++Gat ++++ E+i    ++     vy+ +++ +++  +  d++
  gi|336253309|ref|YP_004596416.1| 517 lvewAKQYEErgpDEVDEELRRVPfLETRAAAKEIGATiEFNKAEGIDSYDEAEpgdYVYFGISSLSGN--MSDDEG 591
                                       99996677765555556666666526888888*****8569******9666666888999999988744..555666 PP

                            DUF839 383 npr.aknkyGqivrlieesrdvaatkftwdlfllaGdpedakaasaessegndlespDnlafdpaGrlwiatDgsgs 458
                                       + +  + + G ++r   +++    +  t++ +++  ++ da     e+  ++ l ++Dnl++ +  r+++++D+ + 
  gi|336253309|ref|YP_004596416.1| 592 ELQfDTVATGVVYRGELDRN---YNVSTLEPVVVGPNEGDA-----EELMNASLINVDNLMVLDDRRVILCEDKGNF 660
                                       65514557788888765555...88999**99999886666.....667889999******************9875 PP

                            DUF839 459 kd 460
                                         
  gi|336253309|ref|YP_004596416.1| 661 AR 662
                                       44 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       2.1   7.7e+03      34      51 ..     747     764 ..     739     767 .. 0.73
   2 !   22.2   1.5   3.3e-08   0.00012       2      54 ..     831     880 ..     830     883 .] 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.1
                                       HGGGSTT-SSCESHHHHH CS
                        Dockerin_1  34 gkaaDvNgDGrvnalDal 51 
                                        ++aD+ +    +alD++
  gi|336253309|ref|YP_004596416.1| 747 FRFADLENEIDADALDVT 764
                                       577888888888888865 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 3.3e-08
                                       TETTSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHH CS
                        Dockerin_1   2 gDVNgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallvi 54 
                                       +DVNg+g+ +  D+ ++  +l+   ++s + n++a+D N++Gr++  D+  + 
  gi|336253309|ref|YP_004596416.1| 831 EDVNGNGRFDYDDIVVLFEHLE---DDSVQLNEAAYDFNENGRIDYDDVVELY 880
                                       7*********************...********************99988775 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 ?    1.0   0.1      0.16   5.8e+02      16      48 ..     509     538 ..     490     540 .. 0.78
   2 ?   11.3   2.7    0.0001      0.37      12      70 ..     832     880 ..     823     881 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.16
                         EF-hand_7  16 dgyldkeellrllrkifqgagegsklsdeelel 48 
                                         y++ eel +  ++     ++g +  deel++
  gi|336253309|ref|YP_004596416.1| 509 QDYITDEELVEWAKQYE---ERGPDEVDEELRR 538
                                       57999999888888765...7777777777765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0001
                         EF-hand_7  12 DtdgdgyldkeellrllrkifqgagegsklsdeelellfkefDtdkdGvisfdEFlkly 70 
                                       D++g+g+ d++++  l+++          l d++++l     D + +G+i++d+ ++ly
  gi|336253309|ref|YP_004596416.1| 832 DVNGNGRFDYDDIVVLFEH----------LEDDSVQLNEAAYDFNENGRIDYDDVVELY 880
                                       99**********8867774..........34444555556779999********99998 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.8   2.9e+03      16      27 ..     511     522 ..     510     523 .. 0.86
   2 ?   -0.2   0.3      0.25     9e+02      10      16 ..     823     829 ..     822     831 .. 0.90
   3 ?    5.8   0.1     0.003        11      10      28 ..     832     850 ..     829     851 .. 0.91
   4 ?    8.8   0.1   0.00036       1.3       8      27 ..     862     881 ..     861     883 .] 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.8
                                       EEEHHHHHHHHH CS
                         EF-hand_1  16 kIdfeEfkellk 27 
                                       +I+ eE++e+ k
  gi|336253309|ref|YP_004596416.1| 511 YITDEELVEWAK 522
                                       89******9865 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.25
                                       TTTSSSE CS
                         EF-hand_1  10 DkDgdGk 16 
                                       D DgdGk
  gi|336253309|ref|YP_004596416.1| 823 DPDGDGK 829
                                       9*****8 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.003
                                       TTTSSSEEEHHHHHHHHHH CS
                         EF-hand_1  10 DkDgdGkIdfeEfkellkk 28 
                                       D++g+G+ d+++ + l+++
  gi|336253309|ref|YP_004596416.1| 832 DVNGNGRFDYDDIVVLFEH 850
                                       9************999876 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.00036
                                       HHTTTSSSEEEHHHHHHHHH CS
                         EF-hand_1   8 efDkDgdGkIdfeEfkellk 27 
                                        +D + +G+Id+++ +el +
  gi|336253309|ref|YP_004596416.1| 862 AYDFNENGRIDYDDVVELYE 881
                                       59************999865 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.1   3.9e+03      11      27 ..     505     522 ..     501     528 .. 0.80
   2 ?    1.9   1.0     0.077   2.7e+02      10      26 ..     832     848 ..     823     854 .. 0.85
   3 ?    8.3   0.1   0.00068       2.4       8      27 ..     862     881 ..     861     883 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                         EF-hand_6  11 kdgdG.kidaeElrkalr 27 
                                       k+g+  +i+ eEl+ + +
  gi|336253309|ref|YP_004596416.1| 505 KNGNQdYITDEELVEWAK 522
                                       5666679******98766 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.077
                         EF-hand_6  10 DkdgdGkidaeElrkal 26 
                                       D++g+G  d+++++ ++
  gi|336253309|ref|YP_004596416.1| 832 DVNGNGRFDYDDIVVLF 848
                                       99*********997655 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00068
                         EF-hand_6   8 lfDkdgdGkidaeElrkalr 27 
                                       ++D++ +G id+++++ ++ 
  gi|336253309|ref|YP_004596416.1| 862 AYDFNENGRIDYDDVVELYE 881
                                       79************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (883 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 6013.71
//
Query:       gi|336253310|ref|YP_004596417.1|  [L=137]
Description: hypothetical protein Halxa_1911 [Halopiger xanaduensis SH-6]
Scores for 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:                       330  (0.0184059); 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:                         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 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1080.28
//
Query:       gi|336253311|ref|YP_004596418.1|  [L=509]
Description: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [Halopiger xanaduensis SH-6]
Scores for 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-79  265.0   0.7    5.7e-79  264.5   0.7    1.2  1  iPGM_N         BPG-independent PGAM N-terminus (iPGM_N)
    1.3e-72  244.1   0.2    1.5e-72  243.9   0.2    1.0  1  Metalloenzyme  Metalloenzyme superfamily
    9.7e-09   35.3   0.2      1e-07   31.9   0.2    2.3  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
    3.5e-05   23.4   0.4    0.00016   21.2   0.1    2.3  2  Sulfatase      Sulfatase
    0.00059   20.0   0.1     0.0016   18.6   0.1    1.7  1  PglZ           PglZ domain
  ------ inclusion threshold ------
       0.22   12.2   1.4         10    6.8   0.2    3.0  3  PGM_PMM_II     Phosphoglucomutase/phosphomannomutase, alpha/b


Domain annotation for each model (and alignments):
>> iPGM_N  BPG-independent PGAM N-terminus (iPGM_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.5   0.7   1.9e-82   5.7e-79       1     215 []      81     295 ..      81     295 .. 0.96

  Alignments for each domain:
  == domain 1  score: 264.5 bits;  conditional E-value: 1.9e-82
                                       HHHHHHCTGGGG-HHHHHHHHHHHHCTSEEEEEEE-SS--SS--CHHHHHHHHHHHHTT-SEEEEEEEE-SSSSTTT CS
                            iPGM_N   1 inkaiedgslfenealkeaiekakkngkalHllGLlSdGgVHShidhllallelakeegvkkvvvhaflDGRDtapk 77 
                                       i+++i+dg++ en+a+++a+++a +n++++H++GL+SdGgVHS+ +hl+al+ela +++v ++v+ha++DGRDt+p+
  gi|336253311|ref|YP_004596418.1|  81 ISDSIADGTFRENDAINAAFDEALENDGTIHFVGLVSDGGVHSDHEHLHALIELAGDRDV-EAVTHAITDGRDTSPT 156
                                       789*********************************************************.899************* PP

                                       -HHHHHHHHHHHHHHCT--EEEEEEEHHHHT--SS-HHHHHHHHHHHCCSSSEEECTTHHHHHHHHHHTT--GGG-- CS
                            iPGM_N  78 saleyleeleeklkelgvgkiasvsGRyyaMDRdkrwervekaydalvkgegeskaesaveaieesyakgetDefve 154
                                        + +yl++le+ ++e+g+g++a+vsGRyyaMDRd++wer+++ayda+v++e+e +aesav+a+e+sy++++tDefve
  gi|336253311|ref|YP_004596418.1| 157 GGRDYLSTLEDVIDEHGTGHVATVSGRYYAMDRDQNWERTKRAYDAIVEREAEYSAESAVAAVEDSYDRDVTDEFVE 233
                                       **************************************************9999999******************** PP

                                       -EEE...TCCGGS--TT-EEEE----CCCCHHHHHHHH....STTHHCC..--TT-EEEESS-S-T CS
                            iPGM_N 155 ptviaeegkkegtikdgDaviffNFRaDRareltralt....dkefkefe.kakklklvtmteYde 215
                                       ptvi    +   +++dgD+v++fNFR+DRar+ltr+l+    ++  +efe ++ + ++v+mt+Yd+
  gi|336253311|ref|YP_004596418.1| 234 PTVI----EGRPALEDGDSVVWFNFRSDRARQLTRMLAgirpEDWADEFEtHPPDSEVVMMTQYDK 295
                                       ****....56789*************************8854344888887888999*******96 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.9   0.2   5.1e-76   1.5e-72       3     247 ..       3     497 ..       1     498 [. 0.98

  Alignments for each domain:
  == domain 1  score: 243.9 bits;  conditional E-value: 5.1e-76
                                       EEEEEETTBB----..GGGTTHHHS--HHHHHHHHH........SEEEEEESSSTT----HHHHHHHH......... CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                     Metalloenzyme   3 vvlvvlDGlGeapa..delnaihvAktPtldkLkkeaPerw.likahgtavglpeddmgnsevgHlel......... 67 
                                       ++l+vlDG+G + +  +  +a+  A+tPt+d+L+++   ++ +++  g  vglp+++mgnsevgHl++         
  gi|336253311|ref|YP_004596418.1|   3 AALIVLDGWGLGDDdeSTRDAVAAADTPTFDRLAET--GAYgTLEVAGRRVGLPDGQMGNSEVGHLNIgagrvvyqe 77 
                                       689******999882244578***************..8999*********************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|336253311|ref|YP_004596418.1|  78 ytrisdsiadgtfrendainaafdealendgtihfvglvsdggvhsdhehlhalielagdrdveavthaitdgrdts 154
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|336253311|ref|YP_004596418.1| 155 ptggrdylstledvidehgtghvatvsgryyamdrdqnwertkraydaivereaeysaesavaavedsydrdvtdef 231
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|336253311|ref|YP_004596418.1| 232 veptviegrpaledgdsvvwfnfrsdrarqltrmlagirpedwadefethppdsevvmmtqydktfdlpvayppnqp 308
                                       ***************************************************************************** PP

                                       ...............HHHHTT-----EEEEEEEE-S---SSHHHHHT--EEEE--SHHSTT--HHHHHHHHHHHH.C CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  68 ...............lrisetvkfahvtffwnggrsgyfnpleereeipsdtvitfdlqpemkavevaekaldails 129
                                                      lri+e +k+ahvt+f nggr+ +f++ e r  ++s+ v t+d qpem+a ev++ a+d i+s
  gi|336253311|ref|YP_004596418.1| 309 eqvlgevladagksqLRIAESEKYAHVTYFLNGGREVEFDG-EIRQIVESPDVPTYDEQPEMSAPEVTDTAIDVIES 384
                                       *****************************************.*********************************** PP

                                       C.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS........----- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 130 gkfdlvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlep 206
                                       ++ d++v+n++n+DmvGHtgd+ea+i+a+ea+De+++++  ++e+ +  +++tADHgna+dm + +++p+T+Ht + 
  gi|336253311|ref|YP_004596418.1| 385 DDPDVLVLNYANPDMVGHTGDYEAAIEAVEAVDEQLGRLAATLEEYGAHVLITADHGNADDMGT-EDDPHTAHTYNL 460
                                       ****************************************************************.889********* PP

                                       EEEEEESTT----S--SSHHHHTT-TTEEEEGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 207 VPilivgkglapdkvkegakfrekggLanvaatllnllgle 247
                                       VP+++v ++ +     +g ++re g+La++a+tll+l+g++
  gi|336253311|ref|YP_004596418.1| 461 VPLVYVADDGT----DGGRTVREGGTLADIAPTLLELIGVD 497
                                       ****9999655....47999******************987 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.11   3.4e+02       3      35 ..       5      43 ..       3      46 .. 0.69
   2 !   31.9   0.2   3.3e-11     1e-07     170     236 ..     381     444 ..     248     473 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                                      EEEETT-B........TTHHHHHGSTSHHHHHHHHHSEEES CS
                      Phosphodiest  3 vislDGlr........adlldrlaellpnlaaLakegvsap 35
                                      +i+lDG           d + +   ++p +++La++g +++
  gi|336253311|ref|YP_004596418.1|  5 LIVLDGWGlgdddestRDAVAA--ADTPTFDRLAETGAYGT 43
                                      6677777665655333333334..7************9987 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 3.3e-11
                                       T...SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EE CS
                      Phosphodiest 170 l...ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGmad 236
                                           ++pd+l++++ ++D vgH  G d ++  +a++ vD+ +g+L + l+e        +++++DHG ad
  gi|336253311|ref|YP_004596418.1| 381 ViesDDPDVLVLNYANPDMVGH-TG-DYEAAIEAVEAVDEQLGRLAATLEEY----GAHVLITADHGNAD 444
                                       02349*****************.55.88899*********************....99*********665 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.83   2.5e+03       6      36 ..       6      39 ..       5      43 .. 0.61
   2 !   21.2   0.1   5.5e-08   0.00016     149     309 .]     366     496 ..     280     496 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.83
                                      EEESSE-TT..GSGGGTTTSCS..SHHHHHHHHTS CS
                         Sulfatase  6 iladdlgag..dlglyggktat..tpnldrlaeeg 36
                                      i++d +g g  d ++  + +a+  tp++drlae g
  gi|336253311|ref|YP_004596418.1|  6 IVLDGWGLGddD-ESTRDAVAAadTPTFDRLAETG 39
                                      666666666533.33333333346********987 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 5.5e-08
                                       TTCSHHHHHHHHHHHHHHCCCTSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCHHHHHHHHHHHHHHHHHH CS
                         Sulfatase 149 eggysddrlldealefllarndkpfflylatlapHappeapdeyakkyatffddgseaarqlleaylnsveyvDdli 225
                                       ++++s  +++d a++++  + d+p +l+l + +p          ++ +              +ea   +ve vD+++
  gi|336253311|ref|YP_004596418.1| 366 QPEMSAPEVTDTAIDVI--ESDDPDVLVLNYANPDM--------VGHT------------GDYEAAIEAVEAVDEQL 420
                                       34555555555555553..33555555555544443........2222............6788999********** PP

                                       HHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHC.EEECSEEEGGGHHH CS
                         Sulfatase 226 grvlaaLeenglldntlvvftSDhgasleesngplrggkganayeggtrvPllvwwpgekap.rvseelvshiDlfp 301
                                       gr+ a+L    +   + v++t+Dhg + +       + ++  + +    vPl+    ++    r++ e  ++ D++p
  gi|336253311|ref|YP_004596418.1| 421 GRLAATL----EEYGAHVLITADHGNADDM---GTEDDPH--TAHTYNLVPLVYVADDGTDGgRTVREGGTLADIAP 488
                                       *******....777789*********6644...3333333..222334699998888888889************** PP

                                       HHHHHTTE CS
                         Sulfatase 302 tildlagi 309
                                       t+l+l+g+
  gi|336253311|ref|YP_004596418.1| 489 TLLELIGV 496
                                       *****996 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   5.2e-07    0.0016     111     169 ..     386     442 ..     355     444 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.2e-07
                              PglZ 111 dkevvyivhnkvDalgdkasteqksfeaveeslkelkelvkslleengykvlltaDHGf 169
                                       d +v+++   + D++g+ +   ++  eave   ++l +l   l e+ g +vl+taDHG+
  gi|336253311|ref|YP_004596418.1| 386 DPDVLVLNYANPDMVGH-TGDYEAAIEAVEAVDEQLGRLAATLEEY-GAHVLITADHGN 442
                                       55677777777799999.3344455556655555666777778899.***********7 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 ?    6.8   0.2    0.0034        10      54      95 ..     356     399 ..     343     407 .. 0.87
   2 ?    3.2   0.1     0.046   1.4e+02      64      97 ..     414     447 ..     400     452 .. 0.66
   3 ?   -3.9   0.0         6   1.8e+04      30      46 ..     481     497 ..     480     502 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0034
                                       --TT-TT..SS----TT-TTTTHHHHGGGGG-SEEEEE-TTS-B CS
                        PGM_PMM_II  54 pdpdfpt..kapnpeekealkllielvkkegadlglafDgDaDR 95 
                                        +pd pt  + p++ ++e+ + +i+++++++ d+ + ++ + D 
  gi|336253311|ref|YP_004596418.1| 356 ESPDVPTydEQPEMSAPEVTDTAIDVIESDDPDVLVLNYANPDM 399
                                       57888888899*************************99988775 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.046
                                       ---TT-TTTTHHHHGGGGG-SEEEEE-.TTS-BEE CS
                        PGM_PMM_II  64 npeekealkllielvkkegadlglafD.gDaDRlg 97 
                                       +  + e+l +l+++ +++ga++ +  D g+aD +g
  gi|336253311|ref|YP_004596418.1| 414 EAVD-EQLGRLAATLEEYGAHVLITADhGNADDMG 447
                                       4444.677777777777777666666545666555 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 6
                                       -TTHHHHHHHHHHTT-E CS
                        PGM_PMM_II  30 Gaggeilkellkelgvd 46 
                                       G+ ++i+++ll+ +gvd
  gi|336253311|ref|YP_004596418.1| 481 GTLADIAPTLLELIGVD 497
                                       8889999***9999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3852.52
//
Query:       gi|336253312|ref|YP_004596419.1|  [L=559]
Description: HTTM domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-15   56.9   0.0    2.4e-15   56.3   0.0    1.4  1  VKG_Carbox  Vitamin K-dependent gamma-carboxylase
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.029   14.4   0.1    1.7  1  DEC1        Deleted in esophageal cancer 1 family
       0.11   12.6   0.1       0.54   10.4   0.1    2.2  1  DUF2613     Protein of unknown function (DUF2613)


Domain annotation for each model (and alignments):
>> VKG_Carbox  Vitamin K-dependent gamma-carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   4.1e-19   2.4e-15      41     253 ..      82     331 ..      38     405 .. 0.77

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 4.1e-19
                        VKG_Carbox  41 wvkplsl.ew.myllylvmllaalgialGlkYrlsillfvllytyielldktsynNHyYllgllallllflpanryf 115
                                        ++++s+ +w   ll++v +++al + lG++ rl++++  ll   +   +  + n    ll +l ++ +flp  r +
  gi|336253312|ref|YP_004596419.1|  82 SLHAISGaAWvQALLFAVAGAFALALLLGYRTRLATIVSWLLLLSLHARNPMVLNSGDTLLRMLLFWGMFLPLGREW 158
                                       444444313335689************************************************************** PP

                        VKG_Carbox 116 slDalknkkikkk................................svprwnllilkfqlfivYfyAglaKlnsd.Wl 159
                                       s+Da++ ++++                                   +    ++ + +q+ ++Y+  ++ K  sd W+
  gi|336253312|ref|YP_004596419.1| 159 SIDARRLETTRGGedgtvdetrepvtdesgpsagdsddesgmsvpGIVSVPTMAILLQVQLMYLTNAVHKTRSDkWM 235
                                       ****99888777689999************************666333345677889999***********9988** PP

                        VKG_Carbox 160 egaaplklwlfskfklllige.lleeeidalivswfgllfDllivflLllkktRilal.llvvvFhllnsilFqIGm 234
                                        g a+++++  ++  + l+g+ l +++  + +++++ ++  ll + lLll  +   a+  +v+  hl  ++ +qIG+
  gi|336253312|ref|YP_004596419.1| 236 GGDAVVHIFQADHLTI-LLGDvLADQHALLELFTYAWIAVILLSPLLLLLTGVWRAAFaSVVIGMHLGMATTLQIGL 311
                                       ********55555555.59993455555666788888888888888877776655555167889************* PP

                        VKG_Carbox 235 FPyvmlatlllFfsae.wpr 253
                                       FP +++  lllF+ +  w+ 
  gi|336253312|ref|YP_004596419.1| 312 FPLISVGALLLFYPPVvWET 331
                                       *************9873433 PP

>> DEC1  Deleted in esophageal cancer 1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.8e-06     0.029      14      46 ..     205     237 ..     201     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-06
                              DEC1  14 ivPapveGllvvlymmvvtdalhrersvkwqaG 46 
                                       iv  p+  +l  + +m +t+a+h+ rs kw  G
  gi|336253312|ref|YP_004596419.1| 205 IVSVPTMAILLQVQLMYLTNAVHKTRSDKWMGG 237
                                       7888888999999*****************877 PP

>> DUF2613  Protein of unknown function (DUF2613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   9.1e-05      0.54       5      27 ..     290     312 ..     288     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.1e-05
                           DUF2613   5 PaaaSaVaGivlGvvavfgvtav 27 
                                       +a aS+V+G  lG+++++ ++++
  gi|336253312|ref|YP_004596419.1| 290 AAFASVVIGMHLGMATTLQIGLF 312
                                       688***************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); 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:                         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 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 4040.47
//
Query:       gi|336253313|ref|YP_004596420.1|  [L=138]
Description: thiol-disulfide oxidoreductase DCC [Halopiger xanaduensis SH-6]
Scores for 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-34  117.1   0.0    1.1e-33  116.9   0.0    1.1  1  DUF393    Protein of unknown function, DUF393


Domain annotation for each model (and alignments):
>> DUF393  Protein of unknown function, DUF393
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.9   0.0   6.2e-38   1.1e-33       1     113 []      12     121 ..      12     121 .. 0.99

  Alignments for each domain:
  == domain 1  score: 116.9 bits;  conditional E-value: 6.2e-38
                            DUF393   1 vlyDgeCplCnravqflerrdrkgrirfadlqsasgkallkelgidaeqldslllvieagrvysgsdAaleiaralp 77 
                                       vl+Dg+C+lCn++vqfl  rd+++++ fa+lqs+ +++ll+e+++++++l+s++l ie + +y++s+A+l+ia++l+
  gi|336253313|ref|YP_004596420.1|  12 VLFDGVCNLCNGFVQFLVPRDTDEQFYFASLQSDVATELLAEHDLPTDDLESIVL-IEGDDCYVKSAAVLRIAQLLG 87 
                                       89*****************************************************.89999**************** PP

                            DUF393  78 glwrllalllvlprlkklrdalYrliarnRyrlfgr 113
                                       g + ll+ +++lpr+  +rd +Y+l+a nRyrlfg+
  gi|336253313|ref|YP_004596420.1|  88 GVYALLGPFRYLPRP--IRDLAYELVAANRYRLFGK 121
                                       ***************..*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1037.84
//
Query:       gi|336253314|ref|YP_004596421.1|  [L=431]
Description: NurA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-17   63.9   0.0    2.3e-17   63.5   0.0    1.1  1  NurA      NurA domain


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.0   1.3e-21   2.3e-17       5     242 .]      79     392 ..      76     392 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 1.3e-21
                                       EEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEE........................... CS
                              NurA   5 AvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdel........................... 54 
                                       + D + + +++  ++l+i +a a+++ +  +l+ + +  +v +++++de+                           
  gi|336253314|ref|YP_004596421.1|  79 GLDAGTINPTTFKNGLVIDIAQAAMSATPSDLNLHRARTVVATVHSNDETmnvdetwgkfdegysrsravkipplpr 155
                                       67999999******************************************************************998 PP

                                       ..HHHHHHHHHHHHHHHHHHHCGGCCSCEEEEECSHHCCCH.........HHHHHHHHHHHHHHHHHHHHHTT-... CS
                              NurA  55 ..errirllmetlElklgallleekgedllllDGsligslv.........efdelheeleyeeylyslsrllea... 117
                                         e  + +l   l   ++a+    +  dll+lDG+l++  +          +d l e +   ++l  + rl+e+   
  gi|336253314|ref|YP_004596421.1| 156 faEGVVHALALYLAESTHARDHADEVDDLLVLDGPLYPRGLlrwadqhpdLADFLLEDPRPTTVLENYVRLVEEfve 232
                                       88555555555555557889******************************888888888888888888888888888 PP

                                       .TTCEEEEESS-SCTCCHCCC.........S--HHHHCCHHCCHCH---STTS-HHHHTT................. CS
                              NurA 118 .glnlvgvaKsfrskellnll...letlligesisDiallgallrkpgytspllkilrek................. 173
                                         ++l+g +K+  ++ ++++l    +     ++  D al+ +ll+++ y++ + ++ r                   
  gi|336253314|ref|YP_004596421.1| 233 rDVPLIGFVKNPATRVITRTLkgkRDAEISVPWADDSALFTRLLERGEYVDDI-EGKRWErdtsaltytnwfrsrgg 308
                                       8**********************989999999************776665544.444333689************** PP

                                       .............-HCCHHHHHH-EEEEEEESSTTTTEEEEEHHHHHHCCHHHHHHHHHH......TTB-SSSBCCH CS
                              NurA 174 .............pllrealidkeiyfaYvrlegggsilrleipaevstakdedvlslla....sqrlsisGYprpL 233
                                                      +   l+d+e++f+ v   +++ i+r+e p+    ++d+++ ++l+     + + + G p++ 
  gi|336253314|ref|YP_004596421.1| 309 vdqalsangdalgVERHRSLEDYEVTFFVVYDPRDDLIYRIEAPYA--FTRDPETREALTmqvlQDVAVAHGPPTIV 383
                                       *************9999999**********************9977..59999999999999999999********* PP

                                       HHHHHHHCC CS
                              NurA 234 alAhelaki 242
                                       ++A+ela+i
  gi|336253314|ref|YP_004596421.1| 384 EKADELARI 392
                                       *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3145.52
//
Query:       gi|336253315|ref|YP_004596422.1|  [L=750]
Description: 5'-Nucleotidase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-26   92.0   0.0    8.3e-26   91.1   0.0    1.4  1  5_nucleotid_C  5'-nucleotidase, C-terminal domain
  ------ inclusion threshold ------
       0.18   11.2   2.5       0.42   10.0   2.5    1.6  1  UCR_Fe-S_N     Ubiquitinol-cytochrome C reductase Fe-S subuni


Domain annotation for each model (and alignments):
>> 5_nucleotid_C  5'-nucleotidase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.0   9.3e-30   8.3e-26       9     147 ..     357     500 ..     349     508 .. 0.83

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 9.3e-30
                                       ....---HHTS--HHHHHHHHHH.....TGSTT--EEEEEGGG----B..TTTEEEHHHHHHHS-S--EEEEEEEEH CS
                     5_nucleotid_C   9 ldgrdlalrtgetnlgnliadal.....raaagadialangggiradl..paGditvkdlltvlpfgntlvvveltG 78 
                                       ld++ + + + etn gnl++da+        +++dia+ n+ggir+d    +G+it  d++++lpf n++ vve tG
  gi|336253315|ref|YP_004596422.1| 357 LDATYNNY-AIETNWGNLMTDAMravgeIGDVEVDIAANNAGGIRSDStyGPGEITGTDVMDILPFPNEILVVEATG 432
                                       44432233.78************66666566667************6656889************************ PP

                                       HHHHHHHHH...HTTTTTS--TT-EEEESEEEEE-TTS-TT--EEEESSS-BEEE--TTSEEEEEEEHHHH CS
                     5_nucleotid_C  79 aqlkeaLen..esvsaskaasgrflqvsGlrytydlskpagervtslsvtvngkpldddktYkvatnsyla 147
                                       +q+ ++Le+  + + a++ + +   qvsG++y++  + + +  v ++  +v ++p+d+++tY+ a n+y  
  gi|336253315|ref|YP_004596422.1| 433 QQVIDYLEEalRPHPAPDFGAQPAIQVSGVSYEWTGH-EDDAGVENV--FVGDDPIDPEATYTFAHNDYSI 500
                                       ********86655566666666666*********988.5799*****..89******************65 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.5   4.7e-05      0.42       3      24 ..      13      34 ..      12      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 4.7e-05
                        UCR_Fe-S_N  3 eaesdeptRRDFLyiATgavga 24
                                      ++++++ +RR+FL +A+ga +a
  gi|336253315|ref|YP_004596422.1| 13 TNDDVDRSRRRFLGAAAGASAA 34
                                      57899*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (750 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 5550.81
//
Query:       gi|336253316|ref|YP_004596423.1|  [L=297]
Description: hypothetical protein Halxa_1917 [Halopiger xanaduensis SH-6]
Scores for complete 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-05   25.5   0.0    3.4e-05   24.1   0.0    1.6  1  Cohesin   Cohesin domain


Domain annotation for each model (and alignments):
>> Cohesin  Cohesin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.9e-09   3.4e-05       7     118 ..      69     184 ..      66     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.9e-09
                                       EEEE-TTSEEEEEEEEESECTT....EEEEEEEEEE.TTTEEEEEEEE-TTS...SSGGHCEEEEEECGTTEEEEEE CS
                           Cohesin   7 kvsakvGdtvtvpvtvsnvskk....vaaaqftikYDpavlevvsvkaGsiv...knssvnfgsnlleepgkikflf 76 
                                       +v+a +G+t+ v v++++  +     vaa++f  +Y p  le+ +++ G  +    + +v  +++l   +    +l 
  gi|336253316|ref|YP_004596423.1|  69 TVEAGPGETFAVEVELQSDGGHggvgVAAVDFVAQYHPDYLEITDLERGPWLeqgNETTVRPERTLA-HDDGTAIL- 143
                                       78999***************9999**************************99985555556666655.55555666. PP

                                       E.TTSSSTTCBEESSEEEEEEEEEESTTS-TCEEEEEEEEEE CS
                           Cohesin  77 ldlaslgssgiaekdgvlatitfkvkskaaegttaikisdtl 118
                                       ++     ++g++ +++ lat t +v+++a+  tt i +s+t+
  gi|336253316|ref|YP_004596423.1| 144 EQRRDPPAGGAT-GNARLATMTVRVADDAPPSTTTINVSETG 184
                                       344424455555.****************9998888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2368.80
//
Query:       gi|336253317|ref|YP_004596424.1|  [L=113]
Description: hypothetical protein Halxa_1918 [Halopiger xanaduensis SH-6]
Scores for 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:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 891.25
//
Query:       gi|336253318|ref|YP_004596425.1|  [L=223]
Description: hypothetical protein Halxa_1919 [Halopiger xanaduensis SH-6]
Scores for 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  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1722.09
//
Query:       gi|336253319|ref|YP_004596426.1|  [L=275]
Description: cellulosome anchoring protein cohesin region [Halopiger xanaduensis SH-6]
Scores for complete 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   25.4   0.3    5.4e-05   23.5   0.3    1.9  1  Cohesin   Cohesin domain


Domain annotation for each model (and alignments):
>> Cohesin  Cohesin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.3     3e-09   5.4e-05       6     117 ..      46     165 ..      41     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3e-09
                                       SEEEE-TTSEEEEEEEEESECTT...EEEEEEEEEE.TTTEEEEEEEE-TTS.......SSGGHCEEEEEEC..... CS
                           Cohesin   6 dkvsakvGdtvtvpvtvsnvskk...vaaaqftikYDpavlevvsvkaGsiv.......knssvnfgsnlle..... 67 
                                       ++v a++G+tv++ v +++  +    v a+ +  +Y p  l vv+v+ G  +       + + +       +     
  gi|336253319|ref|YP_004596426.1|  46 ETVAAEPGETVELEVVLQSGGSHdagVEAVTLVAQYHPDYLSVVDVERGPWLagggsgnDGDGDVR-----Taetia 117
                                       57888*************9999999*********************99998888665443333333.....233444 PP

                                       .GTTEEEEEEE.TTSSSTTCBEESSEEEEEEEEEESTTS-TCEEEEEEEEE CS
                           Cohesin  68 .epgkikflfldlaslgssgiaekdgvlatitfkvkskaaegttaikisdt 117
                                        e+g+  +l ++    +++g++ + g++at+t  v+++a++ tt+i +++t
  gi|336253319|ref|YP_004596426.1| 118 dENGT-AIL-EQRRDPAAGGVS-GVGTVATVTVEVAEDAPAATTDIAFDAT 165
                                       35555.555.444446788889.*****************99999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2142.97
//
Query:       gi|336253320|ref|YP_004596427.1|  [L=639]
Description: ATPase-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-08   34.7   0.0    3.5e-08   33.8   0.0    1.4  1  DUF87          Helicase HerA, central domain
      3e-07   29.4   0.3    0.00066   18.4   0.1    2.6  2  DUF853         Bacterial protein of unknown function (DUF853)
    8.8e-05   22.6   0.0    0.00035   20.7   0.0    2.0  1  HAS-barrel     HAS barrel domain
     0.0011   18.0   0.0      0.088   11.7   0.0    2.1  2  AAA_10         AAA-like domain
     0.0082   15.1   0.0      0.014   14.3   0.0    1.3  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
  ------ inclusion threshold ------
      0.023   13.8   0.0      0.042   12.9   0.0    1.3  1  T2SSE          Type II/IV secretion system protein
      0.029   14.6   0.0       0.18   12.1   0.0    2.1  2  AAA_22         AAA domain
      0.041   14.3   0.2        1.2    9.5   0.1    2.3  2  AAA            ATPase family associated with various cellular
      0.064   12.6   0.0       0.16   11.3   0.0    1.6  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
      0.067   13.2   0.0        9.7    6.2   0.0    2.2  2  ResIII         Type III restriction enzyme, res subunit
      0.099   13.0   0.0       0.39   11.1   0.0    2.2  1  AAA_16         AAA ATPase domain


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   2.1e-11   3.5e-08      20     206 ..     260     479 ..     256     531 .. 0.63

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.1e-11
                             DUF87  20 klvtrHlAilgsTGsGKSntvavLleelle...........kkga..tililDpHGEYgkal............... 68 
                                        lv rH++i g TGsGK++ ++ +l++ l+           +  +   ++ +Dp+ EY+++                
  gi|336253320|ref|YP_004596427.1| 260 PLVFRHTLIAGGTGSGKTHGAKNILRQYLAdertypmedgrS--VqpAVVQFDPQDEYAQMHddnpdldgefarrle 334
                                       6999**************************999999976433..2669999***********999999999997777 PP

                             DUF87  69 .........ekllsekvkvitpspsa..................kdkelkinpwsldpeelldlleeddkpaaav.q 117
                                                e++             +                  ++ e++i+++ +  +  l    + +++++ +  
  gi|336253320|ref|YP_004596427.1| 335 regvayggiEDT-------------TafvpkvgsasysaghhraEQVEFTIPFSMVHENPWLVAGSGLNDNQYGAlV 398
                                       777664444222.............1233333334555677888999999999888777666555555555555523 PP

                             DUF87 118 rsvleealdqakakeekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdlialll 194
                                         +l ++ +q+ a+  +e++++   ++ l+eel  e+  ++++  +a +r    +++++       ++++++i++l+
  gi|336253320|ref|YP_004596427.1| 399 SVLLPRFRKQYGADATYEEFTTFLDDPALREELD-ESGRVHEATFDAVRRRVLGFDHVF-------DQDARPITDLV 467
                                       3334444444444555555555555666666666.333333333333333322222222.......22223333333 PP

                             DUF87 195 eklekegkitii 206
                                        +  ++g ++++
  gi|336253320|ref|YP_004596427.1| 468 HDFVRPGGLSVV 479
                                       333455555544 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00046      0.75      20      43 ..     262     285 ..     254     292 .. 0.83
   2 !   18.4   0.1   4.1e-07   0.00066     169     316 ..     433     581 ..     418     587 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00046
                            DUF853  20 anrhGliaGatGtGktvtLqvlae 43 
                                       + rh liaG tG Gkt   + +  
  gi|336253320|ref|YP_004596427.1| 262 VFRHTLIAGGTGSGKTHGAKNILR 285
                                       56**************98776654 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 4.1e-07
                            DUF853 169 qygnvskasvgaiqreLltLeqqGaekffGePaLdledllrtd..adGrGvislLaadkllqsPklyatfLlWllse 243
                                       + g v +a+ +a++r++l     G +++f + a  ++dl++    + G  v+   +     +  +   t +l l s 
  gi|336253320|ref|YP_004596427.1| 433 ESGRVHEATFDAVRRRVL-----GFDHVFDQDARPITDLVHDFvrPGGLSVVPTYHI----NDTRAAETVVLALSSL 500
                                       556666666666666666.....4456666666666666654411223333333333....3333333333333333 PP

                            DUF853 244 L....feeLPevGdldkPklvfffdeahLLfndapka....llekveqvvrLirskGvGvyfvtqnPldlPdtvLaq 312
                                       L      + P    +    lv+ +deah +++da  +    ++ k     +  r    G++++tq+P+d+ d+v+ q
  gi|336253320|ref|YP_004596427.1| 501 LidqkLSNDPTYDRIKETPLVLGMDEAHNFLTDADSVqagkVITKFTEAAKQGRKERLGLFLITQDPQDIDDAVFKQ 577
                                       30000333455555556679**************987222245566778899999*********************9 PP

                            DUF853 313 LGnr 316
                                       + + 
  gi|336253320|ref|YP_004596427.1| 578 INTT 581
                                       8765 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.1e-07   0.00035       9      61 ..     105     157 ..      99     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.1e-07
                        HAS-barrel   9 ts.sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvl 61 
                                       ts + +i+r ++s  +++G+y+++++pdge +++++t ++   +++s+d ++++
  gi|336253320|ref|YP_004596427.1| 105 TSlRAYITRGNRS-SIRIGSYLVAPYPDGETLFCRITGLEYAQQYHSDDATEIH 157
                                       5557778888886.***************************8866666666553 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.012        19      23      60 ..     265     314 ..     261     336 .. 0.73
   2 !   11.7   0.0   5.4e-05     0.088     241     293 ..     519     577 ..     479     611 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.012
                            AAA_10  23 asliiGdlGnGKSvlakllvlyisllg............gkaliiDpkke 60 
                                       ++li G++G GK   ak +  + ++ +              ++  Dp+ e
  gi|336253320|ref|YP_004596427.1| 265 HTLIAGGTGSGKTHGAKNILRQYLADErtypmedgrsvqPAVVQFDPQDE 314
                                       89***************999887666556666665555444455566665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.4e-05
                            AAA_10 241 fkvvifDEawift....ssaeGkkllk..elvRiGRsynaavylvtqsadDvlkeelkn 293
                                         v  +DEa  f     s++ Gk + k  e  ++GR+    ++l+tq+++D+++   k+
  gi|336253320|ref|YP_004596427.1| 519 PLVLGMDEAHNFLtdadSVQAGKVITKftEAAKQGRKERLGLFLITQDPQDIDDAVFKQ 577
                                       45667899999963332578899997544889********************9977554 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 !   14.3   0.0   8.5e-06     0.014      16      41 ..     264     289 ..     260     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.5e-06
                     TrwB_AAD_bind  16 qhilivGttGsGKtqalekllraira 41 
                                       +h+li+G+tGsGKt  ++++lr+  a
  gi|336253320|ref|YP_004596427.1| 264 RHTLIAGGTGSGKTHGAKNILRQYLA 289
                                       8*********************9765 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 ?   12.9   0.0   2.6e-05     0.042     132     172 ..     266     305 ..     262     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                             T2SSE 132 ilvsGgTgsGKttllyallkeinksderivtvEDpvEiqle 172
                                        l++GgTgsGKt  +  +l +  ++ er   +ED + +q++
  gi|336253320|ref|YP_004596427.1| 266 TLIAGGTGSGKTHGAKNILRQYLAD-ERTYPMEDGRSVQPA 305
                                       599************8888888888.899999*99988875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.18       7      35 ..     265     293 ..     264     345 .. 0.74
   2 ?   -0.8   0.0         1   1.7e+03      92     104 ..     519     532 ..     499     565 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeaka 35 
                                       ++++ G +G+GKT+ ++++l+q+ +++  
  gi|336253320|ref|YP_004596427.1| 265 HTLIAGGTGSGKTHGAKNILRQYLADERT 293
                                       789*******************9755433 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1
                            AAA_22  92 ielliiDEaqh.lr 104
                                       + +l  DEa++ l+
  gi|336253320|ref|YP_004596427.1| 519 PLVLGMDEAHNfLT 532
                                       458999****9553 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 ?    2.5   0.0      0.11   1.8e+02       2      21 ..     267     286 ..     266     309 .. 0.86
   2 ?    9.5   0.1   0.00076       1.2      53     122 ..     515     576 ..     494     586 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.11
                                       EEESSTTSSHHHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavake 21 
                                       l+ G  G GKT  ak + ++
  gi|336253320|ref|YP_004596427.1| 267 LIAGGTGSGKTHGAKNILRQ 286
                                       7899***********99887 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00076
                                       HHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHST CS
                               AAA  53 akekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrg 122
                                       +ke  +p +l +DE++++ ++    +s ++ +v+ ++ ++ ++ +k  +++ + ++t++p+++d+a+  +
  gi|336253320|ref|YP_004596427.1| 515 IKE--TPLVLGMDEAHNFLTDA---DSVQAGKVITKFTEAAKQGRK--ERLGLFLITQDPQDIDDAVF-K 576
                                       443..489***********999...99999***********99999..589**************997.4 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.9e-05      0.16      40      59 ..     264     283 ..     236     290 .. 0.78
   2 ?   -3.1   0.0       2.5   4.1e+03     215     242 ..     541     568 ..     518     569 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.9e-05
                                       .SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE  40 shllvaGatgsGKStalntL 59 
                                        h+l+aG+tgsGK+ + +++
  gi|336253320|ref|YP_004596427.1| 264 RHTLIAGGTGSGKTHGAKNI 283
                                       6*************887665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
                                       .HHHHHHHHHHHCGGGTEEEEEEES--- CS
                      FtsK_SpoIIIE 215 lvedaivRlarkgraaglHlllatqrls 242
                                        v++ +++ a++gr+++l l l+tq ++
  gi|336253320|ref|YP_004596427.1| 541 KVITKFTEAAKQGRKERLGLFLITQDPQ 568
                                       4556666777779999999999998876 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 ?    6.2   0.0     0.006       9.7      25      50 ..     264     289 ..     242     304 .. 0.88
   2 ?    4.8   0.0     0.016        25     101     158 ..     487     547 ..     416     560 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.006
                                       SEEEEEESTTSTHHHHHHHHHHHH-S CS
                            ResIII  25 krglikmaTGtGKTlvaaklierllk 50 
                                       ++ li+  TG+GKT  a ++ +++l 
  gi|336253320|ref|YP_004596427.1| 264 RHTLIAGGTGSGKTHGAKNILRQYLA 289
                                       6899***********99999999876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.016
                                       ...-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHHHHHT-- CS
                            ResIII 101 stnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swreilekfk 158
                                       +  ++ +v   +sl  d++  +  + +  +++ +v+ +DEaH++  ++   +  +++ kf 
  gi|336253320|ref|YP_004596427.1| 487 TRAAETVVLALSSLLIDQKLSNDPTYDRIKETPLVLGMDEAHNFLTDAdsvQAGKVITKFT 547
                                       4556677777778888886767777778888888999******998733333333455544 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   0.00024      0.39      20      98 ..     256     330 ..     249     563 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                            AAA_16  20 rsgrp...elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesae 93 
                                        sg+p   + +l+ G  G+GK+  ++ +lr++ +d+    r+   +   +++ ++ + +++  + ++q++d+  + +
  gi|336253320|ref|YP_004596427.1| 256 DSGDPlvfRHTLIAGGTGSGKTHGAKNILRQYLADE----RTYPMED--GRSVQPAVVQFDPQDEYAQMHDDNPD-L 325
                                       5788888899********************999993....3333333..33334566666665666666666333.3 PP

                            AAA_16  94 leawr 98 
                                        ++++
  gi|336253320|ref|YP_004596427.1| 326 DGEFA 330
                                       33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.41
# Mc/sec: 4681.98
//
Query:       gi|336253321|ref|YP_004596428.1|  [L=47]
Description: hypothetical protein Halxa_1922 [Halopiger xanaduensis SH-6]
Scores for 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:                       129  (0.00719505); expected 358.6 (0.02)
Passed bias filter:                      110  (0.00613531); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 374.74
//
Query:       gi|336253322|ref|YP_004596429.1|  [L=299]
Description: FRG domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   79.1   0.0    5.8e-22   78.5   0.0    1.3  1  FRG       FRG domain


Domain annotation for each model (and alignments):
>> FRG  FRG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   3.2e-26   5.8e-22       2      93 ..      36     123 ..      35     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 3.2e-26
                               FRG   2 klvyRGqrdadwrlipsleRekkkklsklesekrlleefkklarealeeeaesewdlellalaqHyglpTrLlDwTk 78 
                                        +v+RG  d+++ l++s++R  ++  + ++ e+ ll++f ++a + +e e+es w+  ll++a HyglpTrLlDw+ 
  gi|336253322|ref|YP_004596429.1|  36 PYVFRGVPDRNHALETSIKRFVGDSGE-WKLESLLLRNFLQYALNEIE-EPESVWH--LLSIAEHYGLPTRLLDWSF 108
                                       69*******************988755.****************8776.78899*9..******************* PP

                               FRG  79 splvAlfFaleeakk 93 
                                       splvA +Fa+++ ++
  gi|336253322|ref|YP_004596429.1| 109 SPLVATYFAVRDGDA 123
                                       **********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2375.89
//
Query:       gi|336253323|ref|YP_004596430.1|  [L=252]
Description: 3-oxoacyl-(acyl-carrier-protein) reductase [Halopiger xanaduensis SH-6]
Scores for complete 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  240.9   1.6    1.4e-71  240.7   1.6    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    1.7e-55  187.5   2.3      2e-55  187.3   2.3    1.0  1  adh_short     short chain dehydrogenase
    4.9e-11   42.9   0.5    6.9e-11   42.4   0.5    1.2  1  KR            KR domain
    1.9e-08   34.1   0.4    2.4e-08   33.8   0.4    1.1  1  Epimerase     NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
       0.16   12.6   1.9       0.42   11.3   1.9    1.8  1  Cadherin_4    Bacterial cadherin-like domain
       0.61    9.9   4.0        1.2    9.0   4.1    1.5  1  3HCDH_N       3-hydroxyacyl-CoA dehydrogenase, NAD binding do


Domain annotation for each model (and alignments):
>> 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 !  240.7   1.6   4.8e-75   1.4e-71       1     233 [.      13     249 ..      13     250 .. 0.97

  Alignments for each domain:
  == domain 1  score: 240.7 bits;  conditional E-value: 4.8e-75
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvn 75 
                                       Ga sgIGr++Ak++ae+Ga vv++d++ ++ +++ve++a ++g++ ++e+DV+d+e+ ea++e++v+++g+lD+l n
  gi|336253323|ref|YP_004596430.1|  13 GAGSGIGRQTAKTFAENGAAVVVADVDVDGgRATVESIAGAGGEAtFVEADVSDPEDAEAMIETAVDEYGGLDVLYN 89 
                                       889***************************9**********998857****************************** PP

                                       -----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHH CS
                      adh_short_C2  76 nagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalea 150
                                       na+i  +  +++ e + + f+++++vnl+++++ +k+ ++ ++++g gsiv  ss+g+e++vp+y+ ygaaKaa+ +
  gi|336253323|ref|YP_004596430.1|  90 NAAIEGP-VARLDEYENDAFEQIIEVNLKGVWYGMKYGIRaMLEDGgGSIVSASSIGGEVAVPQYSGYGAAKAAVSH 165
                                       *******.999*****************************6666669****************************** PP

                                       HHHHHHHHHGGGTEEEEEEEE--BHCTG.GGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEE CS
                      adh_short_C2 151 ltrylAvelgpkgiRvNavspgpikTla.asgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqt 226
                                       lt+y+A e++++giR Nav+pg+++T++  ++i++ +e++e++ +  p+  l++pee+a+a+lfL sd++s +tG t
  gi|336253323|ref|YP_004596430.1| 166 LTKYAAIEYAEDGIRANAVAPGIVRTEMiERSIEEHPEMEEQFLNTEPMPGLADPEEIANAVLFLGSDLSSRVTGVT 242
                                       ****************************8899********************************************* PP

                                       EEESTTG CS
                      adh_short_C2 227 lvvDgGl 233
                                       l v gG+
  gi|336253323|ref|YP_004596430.1| 243 LPVEGGY 249
                                       ******8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.3   2.3   6.7e-59     2e-55       1     191 [.       7     198 ..       7     202 .. 0.95

  Alignments for each domain:
  == domain 1  score: 187.3 bits;  conditional E-value: 6.7e-59
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       +v+++tGa+sGIGr++ak++a++Ga vvv+d   +  +++++++  +g +a+++++Dv+d e++ea++e+av+++g+
  gi|336253323|ref|YP_004596430.1|   7 QVAVITGAGSGIGRQTAKTFAENGAAVVVADVDVDGGRATVESIAGAGGEATFVEADVSDPEDAEAMIETAVDEYGG 83 
                                       69*************************************************************************** PP

                                       ESEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                         adh_short  78 ldvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                       ldvL+nNA+i   ++   e++++++e++ievNl+gv   ++  ++aml+  +G+Iv  sS+ g+v+v++++ Y+A+K
  gi|336253323|ref|YP_004596430.1|  84 LDVLYNNAAIeGPVARLDEYENDAFEQIIEVNLKGVWYGMKYGIRAMLEDGGGSIVSASSIGGEVAVPQYSGYGAAK 160
                                       **********55556667777777***************************************************** PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmakelr 191
                                       aav +lt+ +a e+a++gir navaPG+v+T+m +++ 
  gi|336253323|ref|YP_004596430.1| 161 AAVSHLTKYAAIEYAEDGIRANAVAPGIVRTEMIERSI 198
                                       *********************************88765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.5   2.3e-14   6.9e-11       4     163 ..      10     170 ..       8     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 2.3e-14
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       +itG+  g+G+++a++ ae+ga+ +v         +  +a++++++  g e ++v+aDvsd+++ ea++e++ +e +
  gi|336253323|ref|YP_004596430.1|  10 VITGAGSGIGRQTAKTFAENGAAVVVADVDV----DGGRATVESIAGAGGEATFVEADVSDPEDAEAMIETAVDEYG 82 
                                       8*********************977754433....556679************************************ PP

                                       ---EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  81 pikGvihaAgvlr.dklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaa 152
                                        +   ++ A +    + l+e +++++eq+++  +kG+w   ++  +    +    +v  SSi+g +  ++ + Y aa
  gi|336253323|ref|YP_004596430.1|  83 GLDVLYNNAAIEGpVARLDEYENDAFEQIIEVNLKGVWYGMKYGIRamleDGGGSIVSASSIGGEVAVPQYSGYGAA 159
                                       ******99998874789*********************97665444122256679********************** PP

                                       HHHHHHHHHHH CS
                                KR 153 NaflDalaeyr 163
                                        a +  l +y 
  gi|336253323|ref|YP_004596430.1| 160 KAAVSHLTKYA 170
                                       *9999888775 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.4     8e-12   2.4e-08       2     160 ..      10     174 ..       9     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 8e-12
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HH....HHHHHHHHH.T-SE CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrs....alerlfkee.qpda 67 
                                       ++tGa   iG++++k ++e+g  v++ d + ++++   +  +      ++ve+d+ d++     +e +++e+ + d+
  gi|336253323|ref|YP_004596430.1|  10 VITGAGSGIGRQTAKTFAENGAAVVVADVDVDGGRATVESIAgaggeaTFVEADVSDPEdaeaMIETAVDEYgGLDV 86 
                                       79****************************88888776665599*************99666456667788899*** PP

                                       EEE--S.---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHH CS
                         Epimerase  68 vihlAa.vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYa 143
                                        ++ Aa +g va+  e+ +d +e+ ++++l+ + +  k+g++ +l  +  ++  ++      e++    +++ s Y+
  gi|336253323|ref|YP_004596430.1|  87 LYNNAAiEGPVARLDEYENDAFEQIIEVNLKGVWYGMKYGIRAMLEDGGGSIVSASSI--GGEVA----VPQYSGYG 157
                                       ******99****************9999999999999*****************8888..77777....8999**** PP

                                       HHHHHHHHHHHHHHHHH CS
                         Epimerase 144 aaKlageklveayaaqy 160
                                       aaK+a+ +l++++a +y
  gi|336253323|ref|YP_004596430.1| 158 AAKAAVSHLTKYAAIEY 174
                                       ***********999888 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.9   0.00014      0.42      33      64 ..      30      59 ..       8      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                        Cadherin_4 33 agnvlandtDvdgddltvtavtvagtyGtltl 64
                                       + v   d+Dvdg+  tv +++  g++G+ t+
  gi|336253323|ref|YP_004596430.1| 30 GAAVVVADVDVDGGRATVESIA--GAGGEATF 59
                                      2567789************998..55565554 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 ?    9.0   4.1   0.00041       1.2       2      44 ..       8      52 ..       7      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00041
                                      EEEE.--SC.CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N  2 vavi.GaGt.mGagiaavfasagleVvlvdiseealekalekiek 44
                                      vavi GaG  +G++ a+ fa++g  Vv+ d++ +  ++  e+i+ 
  gi|336253323|ref|YP_004596430.1|  8 VAVItGAGSgIGRQTAKTFAENGAAVVVADVDVDGGRATVESIAG 52
                                      66665999769********************98887777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1919.46
//
Query:       gi|336253324|ref|YP_004596431.1|  [L=129]
Description: hypothetical protein Halxa_1925 [Halopiger xanaduensis SH-6]
Scores for 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-08   34.9   0.0    2.9e-08   34.6   0.0    1.1  1  SpoIIAA-like  SpoIIAA-like


Domain annotation for each model (and alignments):
>> SpoIIAA-like  SpoIIAA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   1.6e-12   2.9e-08       4      96 .]      22     127 ..      19     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.6e-12
                                       EEEEEEE-HHHHHH.HHHHHHHHCCSSSEEEEEEE........HHHHHHHCC.......CGGECEEEEE-SSCC.CC CS
                      SpoIIAA-like   4 veisgkitaedykevliellekalahgkirllvdl........ediklglah.......lsrfrrvAvvtdkkw.ik 64 
                                       + +++  t e y+e l++ l+ a+++g  ++l+dl        +d ++++ +        s ++ +A+v+++++ + 
  gi|336253324|ref|YP_004596431.1|  22 MNWHDFATGETYREGLNAGLDLAIEKGAANWLADLrdlgtlseDDQQWTQ-EewhprafESSLSNMAIVQPESVvAN 97 
                                       66888899************999999*********444444432223444.0455666799***********99899 PP

                                       CC.CCHHCCH.-CCEEEEE..SSHHHHHHHHH CS
                      SpoIIAA-like  65 alvallasalflslevkvFkleeeeeAlaWLr 96 
                                         v+ l + +  +++ ++F  +++++A+ WLr
  gi|336253324|ref|YP_004596431.1|  98 LSVEDLVQEVGSNTTSRIF--DDRDDARGWLR 127
                                       99999999999999*****..*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1043.19
//
Query:       gi|336253325|ref|YP_004596432.1|  [L=207]
Description: hydrolase of the alpha/beta superfamily-like protein [Halopiger xanaduensis SH-6]
Scores for 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   32.7   0.0    6.1e-08   32.5   0.0    1.1  1  DLH            Dienelactone hydrolase family
    5.1e-05   23.0   0.1    5.7e-05   22.8   0.1    1.2  1  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
     0.0011   19.0   0.0     0.0025   17.8   0.0    1.6  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
  ------ inclusion threshold ------
       0.01   15.9   0.2       0.78    9.8   0.3    2.1  2  Thioesterase   Thioesterase domain
      0.014   16.0   7.0      0.045   14.3   6.8    1.9  1  Abhydrolase_6  Alpha/beta hydrolase family
      0.018   14.7   0.0      0.051   13.2   0.0    1.7  1  FSH1           Serine hydrolase (FSH1)


Domain annotation for each model (and alignments):
>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0     2e-11   6.1e-08      81     170 ..      77     167 ..      49     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 2e-11
                               DLH  81 dlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYG....lspekeleeaakikapilalfge 153
                                       d++ av++++ +     ++vg+ G+ +G++lall aae ++vda+ a  +          +++ + i++p+++ +ge
  gi|336253325|ref|YP_004596432.1|  77 DVRNAVRWAADRH----DRVGLFGYSFGATLALLGAAECEAVDAVSALAPtarlADDLDAVAALESISCPVQVCYGE 149
                                       5566777777777....9***************************999998554344455667789*********** PP

                               DLH 154 eDefipade.vekleeal 170
                                       +D+ ++ +  ve+l+e+ 
  gi|336253325|ref|YP_004596432.1| 150 RDTTVEWEPiVERLRETA 167
                                       *****9887677787766 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   1.9e-08   5.7e-05      73     141 ..      66     129 ..      52     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.9e-08
                                       S---TTTTTHHHHHHHHHHHHHHCTTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCCC CS
                     Peptidase_S15  73 GeftvgdsdeaedgadvidWlakqpwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlydd 141
                                       G+++  ++ e +d+ ++++W+a      ++Vg +G S+++t++ll aa + +a++a+ ++a+++ l+dd
  gi|336253325|ref|YP_004596432.1|  66 GDWDE-GYGERADVRNAVRWAADR---HDRVGLFGYSFGATLALLGAA-ECEAVDAVSALAPTARLADD 129
                                       88888.99*************985...78***************9998.55555555555555555443 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   8.4e-07    0.0025      20      64 ..      88     132 ..      79     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.4e-07
                                       --SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEE CS
                            BAAT_C  20 kkdkigllGiSkGgelalllasflkkisavvlingsavvvegklv 64 
                                        +d++gl G S+G++lall a+  ++++av +++++a    + ++
  gi|336253325|ref|YP_004596432.1|  88 RHDRVGLFGYSFGATLALLGAAECEAVDAVSALAPTARLADDLDA 132
                                       489***************************999998877666555 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   0.00026      0.78      67      82 ..      91     106 ..      77     114 .. 0.75
   2 ?    4.4   0.0     0.011        34     152     226 ..     115     198 ..     108     203 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00026
                                       SEEEEEETHHHHHHHH CS
                      Thioesterase  67 PyalfGhSlGgllAfe 82 
                                        + lfG+S+G++lA  
  gi|336253325|ref|YP_004596432.1|  91 RVGLFGYSFGATLALL 106
                                       5679**********75 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.011
                                       HHHHHHHTCCS....-TTSCSE........HHCEEEEEEGSS-CTCCCCCCCHCHCHCTCESCEEEEEES..SHCCH CS
                      Thioesterase 152 radyraleqys....lrpeaaq........klratlfngsddklkdldtlelaerweqktsgevsvhvle..gdhfy 214
                                        a+  + ++++    l     +        ++++++ +g++d+   ++   + er++++  g  ++  ++  gdhf+
  gi|336253325|ref|YP_004596432.1| 115 DAVSALAPTARladdL-----DavaalesiSCPVQVCYGERDTTVEWE--PIVERLRETAAGTGDRALVPrsGDHFF 184
                                       4555455555433331.....133444555899999999999999999..67777999999999977664339**** PP

                                       HHS..HHHHHHHHH CS
                      Thioesterase 215 lle..drleavlei 226
                                         +  +  e v+ +
  gi|336253325|ref|YP_004596432.1| 185 VGQqaSIAEDVAAF 198
                                       *9932224444444 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   6.8   1.5e-05     0.045      49     105 ..      67     130 ..      11     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                                       HC.......HHHHHHHCCTT..TTSEEEEEETCHHHHHHHHHHCC.......EEEEES-..----TTT.S CS
                     Abhydrolase_6  49 dl.......adlaalldelaagggpvvlvGHSlGGalalaaapla.....lvvgvlldppptalpagl.l 105
                                       d        ad++++++  a+++++v l+G+S+G++lal+   +a     +++  +l+p   ++++++ l
  gi|336253325|ref|YP_004596432.1|  67 DWdegygerADVRNAVRWAADRHDRVGLFGYSFGATLALL---GAaeceaVDAVSALAP---TARLADdL 130
                                       31222344478888888888889999**************...4444475666699998...33333322 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.7e-05     0.051      97     202 ..      85     184 ..      48     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                              FSH1  97 ikengpfdGiiGFSqGaalaallaslleellkeashpslkfailvsGfkleepkyeeyyeedkiqtptLhvlGelDt 173
                                         +++  +G+ G+S Ga+la l a++ e  +         ++ l+   +l +   ++    ++i++p+   +Ge+Dt
  gi|336253325|ref|YP_004596432.1|  85 AADRHDRVGLFGYSFGATLALLGAAECEAVDA--------VSALAPTARLADD-LDAVAALESISCPVQVCYGERDT 152
                                       45566689********************9775........3333333343333.444446899************** PP

                              FSH1 174 vvdee.rseaLaeafkns..skvlkHpggHfv 202
                                        v+ e   e+L e+ + +  + ++  +g+Hf+
  gi|336253325|ref|YP_004596432.1| 153 TVEWEpIVERLRETAAGTgdRALVPRSGDHFF 184
                                       **966356778887777788999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1616.41
//
Query:       gi|336253326|ref|YP_004596433.1|  [L=285]
Description: alpha/beta hydrolase fold protein [Halopiger xanaduensis SH-6]
Scores for 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-23   81.3   0.0    6.6e-19   68.5   0.0    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    9.1e-22   78.7  10.7    1.1e-21   78.4  10.7    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    4.5e-19   68.7   0.0    7.6e-19   67.9   0.0    1.3  1  Hydrolase_4    Serine aminopeptidase, S33
    5.4e-06   26.5   0.0    2.9e-05   24.1   0.0    2.0  2  Abhydrolase_4  TAP-like protein
     0.0024   17.4   0.2      0.014   14.9   0.0    2.2  2  Peptidase_S9   Prolyl oligopeptidase family
     0.0041   16.8   0.3      0.011   15.3   0.3    1.6  1  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
  ------ inclusion threshold ------
      0.023   15.1   0.7      0.099   13.1   0.4    2.2  2  NTS_2          N-terminal segments of P. falciparum erythrocy
      0.039   14.1   0.6       0.32   11.1   0.6    2.0  1  Thioesterase   Thioesterase domain
       0.17   11.6   0.0        1.3    8.8   0.0    2.1  1  Abhydrolase_5  Alpha/beta hydrolase 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 !   68.5   0.0   3.3e-22   6.6e-19       2     106 ..      33     131 ..      32     152 .. 0.94
   2 !   11.0   0.0   0.00012      0.24     189     253 ..     210     267 ..     168     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 3.3e-22
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       ++v+ hG+++ + + +   l++ La++g+dv+++D rG+g+S+++     d y+ a+ a+dl  ++dal ++ ++l 
  gi|336253326|ref|YP_004596433.1|  33 PFVVAHGITADGRSRIP--LVEPLADAGYDVVTYDARGHGRSDAPA----DGYEYADQAADLVGLVDALELEDPVLY 103
                                       799**************..***************************....6799999******************** PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESE CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllga 106
                                       GhSmGG++++ +aa  pe  +a+vl ++
  gi|336253326|ref|YP_004596433.1| 104 GHSMGGTTVAVAAATEPELPHAVVLEDP 131
                                       ******************9999999887 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00012
                                       HHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHH CS
                     Abhydrolase_1 189 ieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlaf 253
                                       + +++  d a+++ +++       ptl++ ++ Dp   +++ e   +l  + rlv++++agH+++
  gi|336253326|ref|YP_004596433.1| 210 VLEADRVDPAAVFPDIEA------PTLILKADADPGSRERHREAASHLSDG-RLVHVDGAGHCVL 267
                                       445555556666666555......*************98888887766555.**********986 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4  10.7   5.7e-25   1.1e-21       1     219 [.      34     276 ..      34     277 .. 0.66

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 5.7e-25
                                       EEEE--GC.....GCHHHH.HHHHCCTCEEEEE--TTSTS-GGCS--HHH...CHHHHHHHCCTT..TTSEEEEEET CS
                     Abhydrolase_6   1 vlllHGagssassWlvapL.aallaagvhvlapDlpGhGrsdpppldled...ladlaalldelaagggpvvlvGHS 73 
                                       ++++HG  ++++s    pL  +l+ ag+ v+++D++GhGrsd p++++e    +adl+ l+d+l     ++vl GHS
  gi|336253326|ref|YP_004596433.1|  34 FVVAHGITADGRSRI--PLvEPLADAGYDVVTYDARGHGRSDAPADGYEYadqAADLVGLVDALE--LEDPVLYGHS 106
                                       588999887755543..44366677778889********99999977755224566666777775..999******* PP

                                       CHHH.HHHHHHHCC...EEEEES-...........----TTT............S----TTHHHHHHTT-CCCCHCC CS
                     Abhydrolase_6  74 lGGa.lalaaapla.lvvgvlldppp.........talpagl............laaalelllallallrllawlsr 127
                                       +GG+ +a aaa  + l ++v+l+ p+                            l ++ e +++ +a+ r  a l +
  gi|336253326|ref|YP_004596433.1| 107 MGGTtVAVAAATEPeLPHAVVLEDPElllglgadeS-----AsddvdgegegefLERITERIRGQPAPTRE-AVLET 177
                                       **9877777444447445566666553444333331.....034444333333322222222222222221.22211 PP

                                       H............S-HSCCCCHHHCCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCC CS
                     Abhydrolase_6 128 e............plprlfladedadaawrarlarlaallaglgllpaaawadlpvpllvl.ggeDplvprllerll 191
                                       +             l+ ++la      ++   + ++ + l ++   paa ++d+ +p+l+l +++Dp  ++  ++++
  gi|336253326|ref|YP_004596433.1| 178 DaglqtlvdegreRLA-TLLA-----DTYLNVDPAVEQVLEADRVDPAAVFPDIEAPTLILkADADPGSRERHREAA 248
                                       1223333332222222.6666.....999999999999999999**************99999****9999999999 PP

                                       H.STTEEETCE...SSS-HHHHSHHHHHH CS
                     Abhydrolase_6 192 a.qagarlpvvlpgaGHlphleepdevae 219
                                         + + rl v + gaGH+++ ++ ++v++
  gi|336253326|ref|YP_004596433.1| 249 ShLSDGRL-VHVDGAGHCVLRDRHERVVD 276
                                       999*****.************888**998 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.0   3.8e-22   7.6e-19       8     238 ..      35     270 ..      32     271 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 3.8e-22
                       Hydrolase_4   8 vlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelplfllGh 83 
                                       v++HG++   +    l+e La++G++v+++D+rGhGrs+ ++ g   ++ d  +Dl  +v++++ e p    +l+Gh
  gi|336253326|ref|YP_004596433.1|  35 VVAHGITADGRSRIPLVEPLADAGYDVVTYDARGHGRSDaPADG--YEYADQAADLVGLVDALELEDP----VLYGH 105
                                       889999999999999***********************655555..79999999*****999996654....88*** PP

                       Hydrolase_4  84 SmGGliallyllrypdkvaglilsaPalkikakl............kappllklllkllgkllpklqv...snnlka 145
                                       SmGG++++ +++++p+  ++++l  P l +                +   l +++ ++ g+ +p+ +    ++  + 
  gi|336253326|ref|YP_004596433.1| 106 SMGGTTVAVAAATEPELPHAVVLEDPELLLGLGAdesasddvdgegEGEFLERITERIRGQPAPTREAvleTDAGLQ 182
                                       ****************999*********9998889999999998854777778888888888888888888888888 PP

                       Hydrolase_4 146 dslsrdpevvaayeadplvhgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdk 222
                                       + + + +e++a + ad ++  ++ v+ +le+ ++  +++   ++i++P+l+l ++aD+    e +re++ +l+  d 
  gi|336253326|ref|YP_004596433.1| 183 TLVDEGRERLATLLADTYLNVDPAVEQVLEADRVDPAAV--FPDIEAPTLILKADADPGSR-ERHREAASHLS--DG 254
                                       889999999999999999999999999999877655554..67899***********9655.78888888888..9* PP

                       Hydrolase_4 223 tlklypglyHellnEp 238
                                       +l   +g+ H +l+++
  gi|336253326|ref|YP_004596433.1| 255 RLVHVDGAGHCVLRDR 270
                                       ************9986 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         1   2.1e+03      64      77 ..      60      73 ..      51      79 .. 0.80
   2 !   24.1   0.0   1.4e-08   2.9e-05      34      92 ..     226     283 ..     203     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1
                     Abhydrolase_4 64 vlvtvegeGHgala 77
                                       +vt++  GHg + 
  gi|336253326|ref|YP_004596433.1| 60 DVVTYDARGHGRSD 73
                                      689*******9876 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.4e-08
                     Abhydrolase_4  34 aapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLl 92 
                                       +ap+L+l++  Dp    e ++++a+ l +++lv v+g+GH++l++ ++ v + + ++L+
  gi|336253326|ref|YP_004596433.1| 226 EAPTLILKADADPGSR-ERHREAASHLSDGRLVHVDGAGHCVLRDRHERVVDEIHSFLA 283
                                       69***********965.789999999******************888889999999986 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.1e-06     0.014      10      97 ..      54     131 ..      50     135 .. 0.73
   2 ?   -1.9   0.0      0.96   1.9e+03     142     155 ..     225     238 ..     202     283 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.1e-06
                                       HHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-G CS
                      Peptidase_S9  10 ladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrp 86 
                                       lad+Gy vv  + rG g +++a +d   +     +++D++  ++al      + e  +++G+S GG+++++a++ +p
  gi|336253326|ref|YP_004596433.1|  54 LADAGYDVVTYDARGHG-RSDAPAD---GYEYADQAADLVGLVDAL------ELEDPVLYGHSMGGTTVAVAAATEP 120
                                       67788888888888776.5555555...222233445555555555......5677789****************** PP

                                       GG-SEEEEESE CS
                      Peptidase_S9  87 dlFkaavaevp 97 
                                       +l +a+v e+p
  gi|336253326|ref|YP_004596433.1| 121 ELPHAVVLEDP 131
                                       *****999987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.96
                                       ---EEEEEEETT-S CS
                      Peptidase_S9 142 aypplLlihGlaDd 155
                                       +++p+L++ ++aD 
  gi|336253326|ref|YP_004596433.1| 225 IEAPTLILKADADP 238
                                       55555555555553 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   5.8e-06     0.011      51     131 ..      52     128 ..      10     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.8e-06
                                       HHHHHTT-EEEEEE-TTSTTS-S---TT.TTTHHHHHHHHHHHHHHCTTEEEEEEEEEECHHHHHHHHHCTT--TTE CS
                     Peptidase_S15  51 kvfvarGYavVvqdvrGtggSeGeftvg.dsdeaedgadvidWlakqpwsnGkVgmtGiSYlGttqllaaatgvpal 126
                                       +++++ GY vV +d+rG+g S+   +     d+a+d +  +d l  +    + V  +G S +Gtt  +aaat+++  
  gi|336253326|ref|YP_004596433.1|  52 EPLADAGYDVVTYDARGHGRSDAPADGYeYADQAADLVGLVDALELE----DPV-LYGHSMGGTTVAVAAATEPELP 123
                                       3499******************8888755666677777777666555....344.89**************999988 PP

                                       EEEEE CS
                     Peptidase_S15 127 kaivp 131
                                        a+v 
  gi|336253326|ref|YP_004596433.1| 124 HAVVL 128
                                       88775 PP

>> NTS_2  N-terminal segments of P. falciparum erythrocyte membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4     5e-05     0.099      25      44 ..      12      31 ..       8      34 .. 0.88
   2 ?   -2.1   0.0       2.8   5.5e+03      22      31 ..     205     214 ..     200     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5e-05
                             NTS_2 25 eqsLKADPSevqYYrsGGDG 44
                                      e+ L  D + + YYrsGGDG
  gi|336253326|ref|YP_004596433.1| 12 EDDLEVDDASLHYYRSGGDG 31
                                      5678899999*********9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                             NTS_2  22 SkieqsLKAD 31 
                                         +eq L AD
  gi|336253326|ref|YP_004596433.1| 205 PAVEQVLEAD 214
                                       5689999998 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6   0.00016      0.32      28     230 ..      59     281 ..      33     282 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                                       EEEEEECSTTSTSHHHCTTCHH..HHHHHHHHHHHHH-SSSSEEEEEETHHHH.HHHHHHHHHHHC....T-SEEEE CS
                      Thioesterase  28 vevlavqlpgrerdepplesie..elaaeyaealrqiqpegPyalfGhSlGgl.lAfevArqLesq....Glavksl 97 
                                        +v+++ ++g++r+++p+++ e  + aa ++  + +   e+P +l GhS+Gg+ +A ++A++ e       + +  l
  gi|336253326|ref|YP_004596433.1|  59 YDVVTYDARGHGRSDAPADGYEyaDQAADLVGLVDALELEDP-VLYGHSMGGTtVAVAAATEPELPhavvLEDPELL 134
                                       577788888888777777654322567777777777777866.69******95477777775443344788888888 PP

                                       EEESCCCCCCHHCHHCCCHTTHHTHHHHHCCTTHHHCCTTTHCCHHHHHHHHHHHHHHHHHTCCS........-TTS CS
                      Thioesterase  98 flidssapseteaqeasrraedeefveeltdlggtepeelledeellsellpalradyraleqys........lrpe 166
                                          ++  + +   ++  + + +e ++e ++ +     e++le +  l++l++  r++  +l                
  gi|336253326|ref|YP_004596433.1| 135 LGLGADESASDDVDGEGEGEFLERITERIRGQPAPTREAVLETDAGLQTLVDEGRERLATLLADTylnvdpavE--- 208
                                       88887777777777777777777777777777755889999999999999988888776666555567555440... PP

                                       CSE................HHCEEEEEEGSS-CTCCCCCCCHCHCHCTCESCEEEEEESSHCCHHHSHHHHHHHHHH CS
                      Thioesterase 167 aaq................klratlfngsddklkdldtlelaerweqktsgevsvhvlegdhfylledrleavleii 227
                                         q                ++++ ++  + d+ ++ +     e  +++ s    vhv+ ++h  l  dr e+v+++i
  gi|336253326|ref|YP_004596433.1| 209 --QvleadrvdpaavfpdiEAPTLILKADADP-GSRER--HRE-AASHLSDGRLVHVDGAGHCVLR-DRHERVVDEI 278
                                       ..233344445555555543333333333333.33331..222.4567777778999999999999.6999999999 PP

                                       HHH CS
                      Thioesterase 228 ekk 230
                                       +++
  gi|336253326|ref|YP_004596433.1| 279 HSF 281
                                       975 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00063       1.3      51      83 ..      92     124 ..      34     130 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00063
                     Abhydrolase_5  51 keapklekfvvgGhslGGvvasrfaaeeekieg 83 
                                        +a +le+ v+ Ghs+GG  ++  aa e ++  
  gi|336253326|ref|YP_004596433.1|  92 VDALELEDPVLYGHSMGGTTVAVAAATEPELPH 124
                                       345568899*********999988887766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 2406.94
//
Query:       gi|336253327|ref|YP_004596434.1|  [L=294]
Description: phage shock protein PspA [Halopiger xanaduensis SH-6]
Scores for 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-35  120.6  32.2      7e-35  120.6  32.2    2.1  2  PspA_IM30       PspA/IM30 family
      0.004   16.1  26.1      0.004   16.1  26.1    2.9  3  Spc7            Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.012   16.2  27.2       0.22   12.2   7.1    3.6  3  YabA            Initiation control protein YabA
      0.016   15.3  17.5      0.016   15.3  17.5    3.6  3  DHR10           Designed helical repeat protein 10 domain
      0.016   15.2   7.4      0.016   15.2   7.4    3.0  3  DUF1664         Protein of unknown function (DUF1664)
      0.037   13.3  10.7      0.077   12.2  10.7    1.5  1  DUF3535         Domain of unknown function (DUF3535)
       0.12   10.3  13.5       0.16    9.9  13.5    1.1  1  Prominin        Prominin
       0.25   11.7  24.2       0.79   10.1   0.4    3.8  4  BLOC1_2         Biogenesis of lysosome-related organelles com
       0.53   10.3  11.3        3.4    7.7   7.3    3.1  3  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
       0.63    7.5  48.0       0.17    9.4  32.9    2.0  2  DUF3584         Protein of unknown function (DUF3584)
       0.98   10.1  10.5       0.99   10.1   0.2    2.8  2  FOXP-CC         FOXP coiled-coil domain
        1.9    7.1  19.6        8.9    4.9  16.7    2.3  2  Dor1            Dor1-like family
        2.6    6.6  33.5       0.28    9.8  26.5    2.0  2  AAA_13          AAA domain
        3.1    7.5  29.6         20    4.8  28.9    2.6  2  SHE3            SWI5-dependent HO expression protein 3
        3.4    5.8  22.0      0.035   12.3   1.2    2.8  3  COG6            Conserved oligomeric complex COG6
        3.6    7.4  26.0         42    3.9   0.5    3.2  2  FTA4            Kinetochore complex Fta4 of Sim4 subunit, or 
        3.8    7.2   5.1        2.4    7.8   2.9    1.7  2  Endotoxin_N     delta endotoxin, N-terminal domain
        4.2    7.1  16.2         17    5.2  16.2    2.0  1  Sec5            Exocyst complex component Sec5
        5.5    7.3  14.1          2    8.8   2.6    3.8  3  DUF948          Bacterial protein of unknown function (DUF948
        6.9    6.7  42.3        4.7    7.2  18.0    3.7  4  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
        7.4    6.9  27.6        2.3    8.5  12.3    3.7  3  DUF5082         Domain of unknown function (DUF5082)


Domain annotation for each model (and alignments):
>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6  32.2   8.2e-38     7e-35       1     219 [.       2     230 ..       2     232 .. 0.97
   2 ?   -3.4   8.2       6.7   5.7e+03     177     219 ..     251     292 ..     235     294 .] 0.68

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 8.2e-38
                         PspA_IM30   1 gifkrllrllraniselldkaeDPekileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaA 77 
                                       gi++r + ++r++i++ll  aeDP   l+   + m+++l+++++ +a++ +++k+le++ ++ +e ++k  ++A+ A
  gi|336253327|ref|YP_004596434.1|   2 GILSRTSYVIRSKINSLLNRAEDPTETLDYSYEQMRDQLQEVKRGIADLTTQKKRLEMQKRRLEENVEKHNEQARTA 78 
                                       69*************************************************************************** PP

                         PspA_IM30  78 LtkgeeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaakaqeavqks 154
                                        ++++e+LAr al+++k+  +q+e+le q + ++s+ +ql +q ++l  +iee+++kke++kar +aaka  +v+++
  gi|336253327|ref|YP_004596434.1|  79 VQQNREDLARRALEKKKTKMNQIEDLERQISDLQSQQDQLIEQKNELQSRIEEFRTKKETMKARHEAAKASSQVSEA 155
                                       ****************************************************************************9 PP

                         PspA_IM30 155 lgkls..tesatdslerieeKieerearadaaaelae.........saqd.ldakleaagiqkevseqvlarlkaeq 219
                                       + +     e+  ++ er ee  e++eara a+ el e         ++ d  d +le++  +  v e++l+ lk+e 
  gi|336253327|ref|YP_004596434.1| 156 ITATGdeFEDVGRAIERAEEQTEDMEARAAAMDELHEsgafedvmsDK-DdIDRELEQLSTDSGV-EAELETLKSEV 230
                                       99888899****************************999999888444.35**************.********975 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.7
                         PspA_IM30 177 rearadaaaelaesaqdldakleaagiqkevs.eqvlarlkaeq 219
                                         a ada ae +      da+l ++++++++  e++la+l+ e+
  gi|336253327|ref|YP_004596434.1| 251 ADADADADAETE--PEVDDAELTELEEGDQADvEAELAELQDEE 292
                                       334444444444..222688888888888885599999999865 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1  26.1   4.7e-06     0.004     137     260 ..      15     139 ..       9     148 .. 0.89
   2 ?    1.7   1.6      0.11        95     203     239 ..     151     187 ..     133     197 .. 0.41
   3 ?   -1.4   6.7      0.96   8.2e+02     158     233 ..     199     274 ..     193     293 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.7e-06
                              Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelk. 212
                                       +++L +++e+  e+l+  +e++ +q +e+++   +l+++k++le + ++l+e +e++++  ++ +++ re+la+   
  gi|336253327|ref|YP_004596434.1|  15 INSLLNRAEDPTETLDYSYEQMRDQLQEVKRGIADLTTQKKRLEMQKRRLEENVEKHNEQARTAVQQNREDLARRAl 91 
                                       5789999999**********************************************99999***********97661 PP

                              Spc7 213 aeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleec 260
                                       ++ + k++++++l++q+ +l+++ ++l eqk+el+++i+e +  +e  
  gi|336253327|ref|YP_004596434.1|  92 EKKKTKMNQIEDLERQISDLQSQQDQLIEQKNELQSRIEEFRTKKETM 139
                                       45567889*******************************876655554 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                              Spc7 203 elreelaelkaeieekkkelaelqeqleeleekieel 239
                                       ++ e++++   e e   + +++ +eq e+ e++ +++
  gi|336253327|ref|YP_004596434.1| 151 QVSEAITATGDEFEDVGRAIERAEEQTEDMEARAAAM 187
                                       2233333333333333333333333333333333333 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.96
                              Spc7 158 LekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelael.qeqleele 233
                                       ++++++ +d+ l++l++  + +e+ele+l++++ e e+ +++e +++  e a+++a+ ++  +   e+  ++l+ele
  gi|336253327|ref|YP_004596434.1| 199 VMSDKDDIDRELEQLST-DSGVEAELETLKSEVGEGEAATETEAQAADAETADADADADADAETEPEVdDAELTELE 274
                                       56666666666666654.45688888888888888888888888888888888888777544333332133444443 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   7.1   0.00025      0.22      11      74 ..      27      87 ..      20      97 .. 0.80
   2 ?    8.5   9.5    0.0035         3      14      67 ..      98     150 ..      87     194 .. 0.78
   3 ?    2.1   0.4      0.34   2.9e+02      33      51 ..     198     216 ..     150     255 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA 11 eeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLa 74
                                      e+l+ + e++ ++l+e+k+ +a+l+ + ++Le+++++l e++e++++   + ++++++ +e La
  gi|336253327|ref|YP_004596434.1| 27 ETLDYSYEQMRDQLQEVKRGIADLTTQKKRLEMQKRRLEENVEKHNE---QARTAVQQNREDLA 87
                                      67888999**********************************54444...44444455555554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXX CS
                              YabA  14 eeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkels 67 
                                        +q+e+l +++++l+++  +l+e+ +eL+   e++r++ e+ ++++++ k+ +s
  gi|336253327|ref|YP_004596434.1|  98 MNQIEDLERQISDLQSQQDQLIEQKNELQSRIEEFRTKKETMKARHEAAKA-SS 150
                                       468999999999999999999999999999999999988433333333222.22 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHHHHHHH CS
                              YabA  33 elleenaeLeleneklrer 51 
                                       +++ + +++  e e+l + 
  gi|336253327|ref|YP_004596434.1| 198 DVMSDKDDIDRELEQLSTD 216
                                       3333333333333333333 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 ?    4.7  14.9     0.036        31      52     103 ..      33      84 ..      14      99 .. 0.69
   2 ?   15.3  17.5   1.8e-05     0.016       8     102 ..      98     192 ..      91     195 .. 0.95
   3 ?   -1.3   1.4       2.5   2.1e+03      46      79 ..     238     271 ..     233     278 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.036
                             DHR10  52 leeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaee 103
                                       +e+ +++l+e +  +++++++++ le++++rl+  +e+++e+   + +q +e
  gi|336253327|ref|YP_004596434.1|  33 YEQMRDQLQEVKRGIADLTTQKKRLEMQKRRLEENVEKHNEQARTAVQQNRE 84 
                                       5666777777777777777777777777777777777777765555554443 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.8e-05
                             DHR10   8 keelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlq 84 
                                        +++++lEr++ +lq + d l + +++l+s i+   + ++ +++  ea k  ++ ++a++  + e +++ r +er +
  gi|336253327|ref|YP_004596434.1|  98 MNQIEDLERQISDLQSQQDQLIEQKNELQSRIEEFRTKKETMKARHEAAKASSQVSEAITATGDEFEDVGRAIERAE 174
                                       5799************************************************************************* PP

                             DHR10  85 rqlenaeeklerlreqae 102
                                        q e +e + + + e +e
  gi|336253327|ref|YP_004596434.1| 175 EQTEDMEARAAAMDELHE 192
                                       ********9998877665 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.5
                             DHR10  46 eaelakleeakkklkelrdaleekeielrelerk 79 
                                       e+e ++ + + +++++  da +e e e+ + e +
  gi|336253327|ref|YP_004596434.1| 238 ETEAQAADAETADADADADADAETEPEVDDAELT 271
                                       5556666666666666666666666666655554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   9.6     0.031        26      42     124 .]      32     115 ..      26     115 .. 0.70
   2 ?   15.2   7.4   1.9e-05     0.016      48     122 ..     109     182 ..      96     184 .. 0.84
   3 ?   -1.3   0.1       2.5   2.2e+03      83      89 ..     217     223 ..     194     269 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.031
                           DUF1664  42 avesvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk.eavegle 114
                                         e++  ql++v+   ++l+++k++L+ +  r+++++++ +e   + +  v++ redl++   + ++ k + +e+le
  gi|336253327|ref|YP_004596434.1|  32 SYEQMRDQLQEVKrgiADLTTQKKRLEMQKRRLEENVEKHNE---QARTAVQQNREDLARRALEKKKTKmNQIEDLE 105
                                       567889999999944455666777777777777777766654...56778888888887766555544326789999 PP

                           DUF1664 115 sklerieekQ 124
                                        ++++++++Q
  gi|336253327|ref|YP_004596434.1| 106 RQISDLQSQQ 115
                                       9999999988 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.9e-05
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       ++l++ +++l ++k++L+sri++  +k + +k+  ++ ++  ++v+e ++++g+++e v +a+e  e++ e++e+
  gi|336253327|ref|YP_004596434.1| 109 SDLQSQQDQLIEQKNELQSRIEEFRTKKETMKARHEA-AKASSQVSEAITATGDEFEDVGRAIERAEEQTEDMEA 182
                                       357777899****************999888877665.556699************************9999986 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.5
                           DUF1664  83 keikeev 89 
                                       + +++e+
  gi|336253327|ref|YP_004596434.1| 217 SGVEAEL 223
                                       2222222 PP

>> DUF3535  Domain of unknown function (DUF3535)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  10.7     9e-05     0.077     168     302 ..      23     153 ..       7     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9e-05
                           DUF3535 168 kevstlpetlqeklleiLeeeepvyYdElalsltrlrqecqdllatlesvgklpklavvvqgeaekaftleqaeklv 244
                                       ++ +   +  +e+++++L+e +    ++l+++ +rl  + + l + +e+++++ + av+++ e      le+ +k  
  gi|336253327|ref|YP_004596434.1|  23 EDPTETLDYSYEQMRDQLQEVKR-GIADLTTQKKRLEMQKRRLEENVEKHNEQARTAVQQNREDLARRALEK-KKTK 97 
                                       45556677778888888885533.468999*****************9988888888777666635555555.6666 PP

                           DUF3535 245 ttdyekllkslslkqkllaekqLeerrrrlqaaieeakeeqealhvrvqaalAgAlva 302
                                        +++e+l +++s  q +++  qL e++++lq+ iee+++++e+++ r  aa A+  v+
  gi|336253327|ref|YP_004596434.1|  98 MNQIEDLERQISDLQSQQD--QLIEQKNELQSRIEEFRTKKETMKARHEAAKASSQVS 153
                                       777*********9999999..******************************9998775 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  13.5   0.00019      0.16     240     390 ..      32     176 ..       7     217 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00019
                          Prominin 240 elerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcl.d 315
                                       + e++ ++l+e+k+ +  +   +k+L +++++L+++++++ ++ ++a++++ +      +l++++ +k+++ ++l +
  gi|336253327|ref|YP_004596434.1|  32 SYEQMRDQLQEVKRGIADLTTQKKRLEMQKRRLEENVEKHNEQARTAVQQNRE-DLARRALEKKK-TKMNQIEDLeR 106
                                       67899999999999999999999999999999999999999999999999555.33444444443.36777777777 PP

                          Prominin 316 qlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprealdav 390
                                       q+++++++ ++l e  +++l+s ++e  +  ++   k++++ a+  +++ +a++ ++++++++ ++i  e++++ 
  gi|336253327|ref|YP_004596434.1| 107 QISDLQSQQDQLIEQ-KNELQSRIEEFRT--KKETMKARHEAAKASSQVSEAITATGDEFEDVGRAI--ERAEEQ 176
                                       888888887777665.5666666644333..333345566677777777888888888888777777..333333 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 ?    7.1   1.3     0.008       6.8      33      68 ..      30      65 ..      13      70 .. 0.60
   2 ?    4.0   8.8     0.071        60      28      88 ..      71     129 ..      66     137 .. 0.55
   3 ?   10.1   0.4   0.00092      0.79      40      87 ..     143     190 ..     131     193 .. 0.76
   4 ?   -2.7   0.0         9   7.6e+03      72      77 ..     208     213 ..     195     231 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.008
                           BLOC1_2 33 sekykklkdvaaslekkleklnekyeelqpylqqid 68
                                       + y++++d+++++++ + +l  +++ l+ ++++++
  gi|336253327|ref|YP_004596434.1| 30 DYSYEQMRDQLQEVKRGIADLTTQKKRLEMQKRRLE 65
                                      455666666666666666666666666666665554 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.071
                           BLOC1_2  28 lNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                        Ne+a + +++ ++ +a  ++ lek + k ++++ + +qi +++ q ++L e  +eL + +
  gi|336253327|ref|YP_004596434.1|  71 HNEQARTAVQQNREDLA--RRALEKKKTKMNQIEDLERQISDLQSQQDQLIEQKNELQSRI 129
                                       45555554444444443..455666666666666666666666666666665555555544 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00092
                           BLOC1_2  40 kdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDey 87 
                                        ++a+  ++ +e++ ++ +e++   + i++ e+q++++e+ ++++De 
  gi|336253327|ref|YP_004596434.1| 143 HEAAKASSQVSEAITATGDEFEDVGRAIERAEEQTEDMEARAAAMDEL 190
                                       3444445555667788888***************************96 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 9
                           BLOC1_2  72 kqvteL 77 
                                       +++++L
  gi|336253327|ref|YP_004596434.1| 208 RELEQL 213
                                       333333 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.7     0.014        12      39      89 ..      32      81 ..      15      88 .. 0.73
   2 ?    7.7   7.3     0.004       3.4      29     121 ..      44     135 ..      33     154 .. 0.82
   3 ?    2.7   0.1      0.14   1.2e+02      33      91 ..     149     227 ..     139     237 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                      Baculo_PEP_C 39 lldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtn 89
                                        +++  qL++++  + +l + +++rl+ +  +L++ + + +++ r++ + 
  gi|336253327|ref|YP_004596434.1| 32 SYEQMRDQLQEVKRGIADL-TTQKKRLEMQKRRLEENVEKHNEQARTAVQQ 81
                                      5566777777777777774.4467789999999999999888888877654 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.004
                      Baculo_PEP_C  29 nvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNin 105
                                       +  i a+l+t+++ +e q   l+e++++  ++ +t+++++ + L +   + ++t  n+++ l+ ++++L+s+   ++
  gi|336253327|ref|YP_004596434.1|  44 KRGI-ADLTTQKKRLEMQKRRLEENVEKHNEQARTAVQQNREDLARRALEKKKTKMNQIEDLERQISDLQSQQDQLI 119
                                       4456.9**************************************99988888999****************988888 PP

                      Baculo_PEP_C 106 stLnnllqalnnldlg 121
                                       +  n l + ++ + + 
  gi|336253327|ref|YP_004596434.1| 120 EQKNELQSRIEEFRTK 135
                                       8877777777777554 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.14
                      Baculo_PEP_C  33 laqlatlldaietqLnalsedlksllaeldt...................rldtlltnLtdalnalq..dtlrneLt 88 
                                       ++q++++++a   +++++  +++++ +e+++                   ++ +  + +++ l +l+    ++ eL+
  gi|336253327|ref|YP_004596434.1| 149 SSQVSEAITATGDEFEDVGRAIERA-EEQTEdmearaaamdelhesgafeDVMSDKDDIDRELEQLStdSGVEAELE 224
                                       5667777777777777777777773.334441333333333333333333333333344444444443333444444 PP

                      Baculo_PEP_C  89 nln 91 
                                       +l+
  gi|336253327|ref|YP_004596434.1| 225 TLK 227
                                       444 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  32.9   0.00019      0.17     354     503 ..      34     189 ..      20     193 .. 0.72
   2 ?    3.9   8.2    0.0087       7.4     231     328 ..     190     288 ..     188     294 .] 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00019
                           DUF3584 354 psirseleeleeeldaltekhqdvqekydrrkqkikeeleee...leklkerleaireekdrlkaaieealealesq 427
                                       +++r++l+e+++ ++ lt++ + ++ +  r++ ++++++e++   +++++e+l+    ek++ k ++ e+le + s 
  gi|336253327|ref|YP_004596434.1|  34 EQMRDQLQEVKRGIADLTTQKKRLEMQKRRLEENVEKHNEQArtaVQQNREDLARRALEKKKTKMNQIEDLERQISD 110
                                       57888888888888888888888887777777777665554410044444443333334444455555666666666 PP

                           DUF3584 428 lrkqlea...qkeelneeekelesrlselklrldsatateEeleqieeadealekaqeelekaeaevealqaeeeql 501
                                       l++q+++   qk+el+ + +e++ + +  k r ++a+a++  +e+i++  +++e   +++e+ae++ e+ +a  +++
  gi|336253327|ref|YP_004596434.1| 111 LQSQQDQlieQKNELQSRIEEFRTKKETMKARHEAAKASSQVSEAITATGDEFEDVGRAIERAEEQTEDMEARAAAM 187
                                       6665554222777788888888889999999999*********************************9999998888 PP

                           DUF3584 502 rk 503
                                       ++
  gi|336253327|ref|YP_004596434.1| 188 DE 189
                                       76 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0087
                           DUF3584 231 iediqalaaiekvrpeieklqeefeqleslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeai 307
                                       ++++ a +++++ +++i++  e+ ++  ++e++L +lk e+ + e + +++ ++ +++ a+  + ++++ +   e  
  gi|336253327|ref|YP_004596434.1| 190 LHESGAFEDVMSDKDDIDRELEQLSTDSGVEAELETLKSEVGEGEAATETEAQAADAETADADADADADAETEPEVD 266
                                       678889999****************************************************9999999998888888 PP

                           DUF3584 308 delnqelsaak.aklaakesel 328
                                       d+   el++ + a+++a  +el
  gi|336253327|ref|YP_004596434.1| 267 DAELTELEEGDqADVEAELAEL 288
                                       8888888765414455544444 PP

>> FOXP-CC  FOXP coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2    0.0012      0.99      18      63 ..      14      59 ..       9      65 .. 0.89
   2 ?    2.0   5.4      0.39   3.3e+02      17      63 ..      81     127 ..      70     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                           FOXP-CC 18 dveeflkhlnseHalddkstaqlrvqmqvvqqlekqlvkEkerLqa 63
                                      +++++l+++++  ++ d s +q+r q q v+     l+  k+rL+ 
  gi|336253327|ref|YP_004596434.1| 14 KINSLLNRAEDPTETLDYSYEQMRDQLQEVKRGIADLTTQKKRLEM 59
                                      6788999999999999***************************974 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.39
                           FOXP-CC  17 edveeflkhlnseHalddkstaqlrvqmqvvqqlekqlvkEkerLqa 63 
                                       ++ e++ +++ ++ +++ + +++l+ q++ +q+ ++ql++ k+ Lq+
  gi|336253327|ref|YP_004596434.1|  81 QNREDLARRALEKKKTKMNQIEDLERQISDLQSQQDQLIEQKNELQS 127
                                       66788889999999999999***********************9996 PP

>> Dor1  Dor1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   3.6     0.011       9.5      26     103 ..       3      82 ..       1      88 [. 0.69
   2 ?    4.9  16.7      0.01       8.9      13     103 ..      58     156 ..      51     215 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.011
                              Dor1  26 ilaqiqdLarknyktlidaaea.leairqelediraqledLvlklpkLteectrfskkaeeisek.rkenkllldkh 100
                                       il  ++ + r+  + l++ ae  +e++  + e++r+ql+++   + +Lt + +r   +  ++ e+  k n+ +   +
  gi|336253327|ref|YP_004596434.1|   3 ILSRTSYVIRSKINSLLNRAEDpTETLDYSYEQMRDQLQEVKRGIADLTTQKKRLEMQKRRLEENvEKHNEQARTAV 79 
                                       55666667777777777777643788888999999999999999999999999998888777777733333333333 PP

                              Dor1 101 eql 103
                                       +q 
  gi|336253327|ref|YP_004596434.1|  80 QQN 82 
                                       333 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.01
                              Dor1  13 ekepelLaeeaee........ilaqiqdLarknyktlidaaealeairqelediraqledLvlklpkLteectrfsk 81 
                                       e ++ +L e+ e+        +++++ dLar       ++ +++e++ ++++d++ q ++L+++ ++L++ +++f++
  gi|336253327|ref|YP_004596434.1|  58 EMQKRRLEENVEKhneqartaVQQNREDLARRALEKKKTKMNQIEDLERQISDLQSQQDQLIEQKNELQSRIEEFRT 134
                                       44555555544440000000145555566666666666666777777888888888888888888999999999998 PP

                              Dor1  82 kaeeisekrkenkllldkheql 103
                                       k e +    + +k+ ++++e +
  gi|336253327|ref|YP_004596434.1| 135 KKETMKARHEAAKASSQVSEAI 156
                                       8888888888888888887776 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  26.5   0.00033      0.28     271     449 ..      13     187 ..       6     213 .. 0.77
   2 ?    0.7   1.2      0.18   1.6e+02     417     461 ..     202     245 ..     190     287 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00033
                            AAA_13 271 aaLeahFddefeekqerLekliekveskkselleklkavsde.asensafeedkeelkaeaealeeqLkglqralea 346
                                        ++++  ++  e+ +e+L+   e++  + +e++  +++++++ ++++ + ++  e+++++ e+ +++ +++++ l +
  gi|336253327|ref|YP_004596434.1|  13 SKINSLLNR-AEDPTETLDYSYEQMRDQLQEVKRGIADLTTQkKRLEMQKRRLEENVEKHNEQARTAVQQNREDLAR 88 
                                       566666666.5677999999999999999999999999998624555556666899999999999999999999998 PP

                            AAA_13 347 KrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklek 423
                                       +  e  k+ +++++++   +i++l+++  +li++ Ne  +++ee +++ ++   +h+++++ s+++   +++ ++ +
  gi|336253327|ref|YP_004596434.1|  89 RALEK-KKTKMNQIEDLERQISDLQSQQDQLIEQKNELQSRIEEFRTKKETMKARHEAAKASSQVS---EAITATGD 161
                                       88554.4588999999999999***************99999998888888888889888888876...55566666 PP

                            AAA_13 424 aieklekelkeeeaelkkleeeikeL 449
                                       + e++ ++++ +e++++ +e++++++
  gi|336253327|ref|YP_004596434.1| 162 EFEDVGRAIERAEEQTEDMEARAAAM 187
                                       66666666666666666655555444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.18
                            AAA_13 417 kykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaae 461
                                       +++++++++e+l    +  eael++l+ e+ e e+ +++e +aa+
  gi|336253327|ref|YP_004596434.1| 202 DKDDIDRELEQLS-TDSGVEAELETLKSEVGEGEAATETEAQAAD 245
                                       5555555555555.3344555555555555555555555555554 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   6.2      0.23   1.9e+02      58     114 ..      16      72 ..      13      87 .. 0.62
   2 ?    4.8  28.9     0.023        20       6     176 ..      34     215 ..      32     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH CS
                              SHE3  58 sslLkRKerrlkdlekelselkesveelklekkqlkkrlenssaseteleeelerlk 114
                                       +slL+R e     l+  +++++++ +e+k     l ++ ++++ ++ +lee++e+ +
  gi|336253327|ref|YP_004596434.1|  16 NSLLNRAEDPTETLDYSYEQMRDQLQEVKRGIADLTTQKKRLEMQKRRLEENVEKHN 72 
                                       667777777777777666666666666666666666666666666666666555433 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHH..HHHHHHHH..HHHHHHHHHHH CS
                              SHE3   6 esLHeqiDaLtktnlqLtqqsqeLleklelaqkkeskflenlaslkhEN.dnLs..slLkRKer..rlkdlekelse 77 
                                       e + +q+ +  + +++Lt+q++ L  +    ++  +k+ e+  ++ + N + L   +l k+K++  ++ dle+++s+
  gi|336253327|ref|YP_004596434.1|  34 EQMRDQLQEVKRGIADLTTQKKRLEMQKRRLEENVEKHNEQARTAVQQNrEDLArrALEKKKTKmnQIEDLERQISD 110
                                       56778888999999**********999999999999999998877665545564224555555444699******** PP

                                       HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                              SHE3  78 lkesveelklekkqlkkrlenssaseteleeelerlkvqY...dalvdsqkeYkehYqqeieeLkesleklklenek 151
                                       l+++ ++l ++k++l+ r+e+   ++++++++ e  k++    +a+ ++  e+ +   + ie+ +e+ e+++     
  gi|336253327|ref|YP_004596434.1| 111 LQSQQDQLIEQKNELQSRIEEFRTKKETMKARHEAAKASSqvsEAITATGDEFED-VGRAIERAEEQTEDMEARAAA 186
                                       **********************999999999999988874222577777777765.456788888777777765543 PP

                                       SSXX....XXXXXXXXX.XXXXXXXXXXX CS
                              SHE3 152 qlee....lqerissndkdidtkldsynn 176
                                       + e       e++ s++ did +l++++ 
  gi|336253327|ref|YP_004596434.1| 187 MDELhesgAFEDVMSDKDDIDRELEQLST 215
                                       22220011346788888888888888765 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.2   4.1e-05     0.035      41      93 ..      14      66 ..      12      72 .. 0.94
   2 ?   -0.4  11.4       0.3   2.6e+02      25     100 ..      65     141 ..      62     145 .. 0.71
   3 ?   -0.5   0.1      0.31   2.6e+02      37      68 ..     161     192 ..     150     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.1e-05
                              COG6 41 pvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklel 93
                                      +++  L+r e+  e l+ ++++m+++l++ k+  +dl+++ ++L+ +k++le+
  gi|336253327|ref|YP_004596434.1| 14 KINSLLNRAEDPTETLDYSYEQMRDQLQEVKRGIADLTTQKKRLEMQKRRLEE 66
                                      68889********************************************9997 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.3
                              COG6  25 ekellkineefleefqpvaeqLkr..iesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqkllk 99 
                                       e+++ k ne+   + q+ +e L r  +e++ +k+n++ +++++++s  ++++++l+e+ +eL+++ ++ ++k++  k
  gi|336253327|ref|YP_004596434.1|  65 EENVEKHNEQARTAVQQNREDLARraLEKKKTKMNQI-EDLERQISDLQSQQDQLIEQKNELQSRIEEFRTKKETMK 140
                                       4444455555555666666666432277777788774.778999999999999999999999999999999999877 PP

                              COG6 100 a 100
                                       a
  gi|336253327|ref|YP_004596434.1| 141 A 141
                                       5 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.31
                              COG6  37 eefqpvaeqLkriesdveklnelcdemkkkls 68 
                                       +ef+ v ++++r e++ e++++    m +  +
  gi|336253327|ref|YP_004596434.1| 161 DEFEDVGRAIERAEEQTEDMEARAAAMDELHE 192
                                       68888889999999999998888888766444 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3  20.1      0.65   5.5e+02     117     193 ..      21     134 ..      12     142 .. 0.71
   2 ?    3.9   0.5     0.049        42     115     192 ..     149     227 ..     135     231 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.65
                              FTA4 117 aeeepleallerYaelrarLielserrqqlqarlarlrklkallepflgs........................... 166
                                         e+p+e+l  +Y+++r +L+e+++    l+ + +rl+  k+ le+  +                            
  gi|336253327|ref|YP_004596434.1|  21 RAEDPTETLDYSYEQMRDQLQEVKRGIADLTTQKKRLEMQKRRLEENVEKhneqartavqqnredlarralekkktk 97 
                                       44566677777777777777777777777777777777777777666555666677777777777777777777777 PP

                              FTA4 167 ..........edpqesvqenlvtrdgeleaElermRv 193
                                                  ++ +s q++l+ +++el++ +e +R+
  gi|336253327|ref|YP_004596434.1|  98 mnqiedlerqISDLQSQQDQLIEQKNELQSRIEEFRT 134
                                       7777776666556689999**************9997 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.049
                              FTA4 115 keaeeepleallerYaelrarLielserrqqlqarlarlrklkal..lepflgsedpqesvqenlvtrdgeleaEle 189
                                       +++ +e ++a+ ++++++   +   +e+ + ++ar a + +l++    e++++ +d+ ++  e+l t++g +eaEle
  gi|336253327|ref|YP_004596434.1| 149 SSQVSEAITATGDEFEDVGRAIERAEEQTEDMEARAAAMDELHESgaFEDVMSDKDDIDRELEQLSTDSG-VEAELE 224
                                       4445556688889999999***********************9861144443335555555555665555.999998 PP

                              FTA4 190 rmR 192
                                        ++
  gi|336253327|ref|YP_004596434.1| 225 TLK 227
                                       765 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 ?    7.8   2.9    0.0028       2.4      54     118 ..      29      98 ..       5     107 .. 0.75
   2 ?   -1.7   0.1       2.2   1.9e+03      60      84 ..     117     141 ..      96     155 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0028
                       Endotoxin_N  54 tqyddnklkallkglslslkdfrkevknlkadPk..naalks...avnvlylnlendietkylkdlrkeg 118
                                         y + +++++l+ ++  ++d+++++k l  + +  ++++ +   + +++ ++ ++d++ + l+  + + 
  gi|336253327|ref|YP_004596434.1|  29 LDYSYEQMRDQLQEVKRGIADLTTQKKRLEMQKRrlEENVEKhneQARTAVQQNREDLARRALEKKKTKM 98 
                                       46999******************9999875554322677776788999**********999999854444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                       Endotoxin_N  60 klkallkglslslkdfrkevknlka 84 
                                       +l ++ + l++ +++fr++++ +ka
  gi|336253327|ref|YP_004596434.1| 117 QLIEQKNELQSRIEEFRTKKETMKA 141
                                       2333334445555555555555555 PP

>> Sec5  Exocyst complex component Sec5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  16.2      0.02        17      20     146 ..      55     208 ..      12     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.02
                              Sec5  20 dtldqiykefseskteaqed........................slveeLeeslneairkttllfkpvlenkekadk 72 
                                       ++l+  +++++e+ ++++e+                          +e+Le ++++++++ ++l+++  e ++++++
  gi|336253327|ref|YP_004596434.1|  55 KRLEMQKRRLEENVEKHNEQartavqqnredlarralekkktkmNQIEDLERQISDLQSQQDQLIEQKNELQSRIEE 131
                                       55554455554444443222455555556666666666666677788****************************** PP

                              Sec5  73 lraaleviernkflFnLPksLkesiak..gdydklindYkkakslfestrqslv.eedkkqvkvfkkvwsevekiie 146
                                       +r+ +e ++   +  + +++++e+i++  ++++ + +  ++a ++ e+  ++++ +++ +++ +f++v+s+ ++i  
  gi|336253327|ref|YP_004596434.1| 132 FRTKKETMKARHEAAKASSQVSEAITAtgDEFEDVGRAIERAEEQTEDMEARAAaMDELHESGAFEDVMSDKDDIDR 208
                                       ************************99877899************9999977777899999*********99777655 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 ?    3.3   0.8      0.12     1e+02      29      55 ..      34      60 ..       4      86 .. 0.54
   2 ?    8.8   2.6    0.0023         2      33      83 ..      99     152 ..      87     158 .. 0.80
   3 ?    3.5   0.6       0.1        86      30      72 ..     144     189 ..     132     230 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                            DUF948 29 deaaatieelekqvdpilkevedllak 55
                                      ++++++++e+++ +  ++++ ++l  +
  gi|336253327|ref|YP_004596434.1| 34 EQMRDQLQEVKRGIADLTTQKKRLEMQ 60
                                      333444444444444444444444444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0023
                            DUF948  33 atieelekqvdpilkevedllakvnelledvne...klekvdplteavadlges 83 
                                       ++ie+le+q+  +  + ++l+++ nel++ ++e   k e++++  ea++  ++ 
  gi|336253327|ref|YP_004596434.1|  99 NQIEDLERQISDLQSQQDQLIEQKNELQSRIEEfrtKKETMKARHEAAKASSQV 152
                                       68999**********************999998876777777766666555544 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.1
                            DUF948  30 eaaatieelekqvdpilkeved...llakvnelledvneklekvdp 72 
                                       eaa++  ++ + ++++ +e ed   +++ ++e +ed++ + +++d+
  gi|336253327|ref|YP_004596434.1| 144 EAAKASSQVSEAITATGDEFEDvgrAIERAEEQTEDMEARAAAMDE 189
                                       3333333333333333333332000344444444444444444444 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 ?    5.3   7.3     0.022        19      83     136 ..      27      80 ..      12      88 .. 0.48
   2 ?    7.2  18.0    0.0055       4.7      16     106 ..      91     187 ..      80     190 .. 0.76
   3 ?    2.9   6.4      0.12        99      38     114 ..     161     238 ..     147     253 .. 0.67
   4 ?   -0.8   1.1       1.7   1.5e+03      42      52 ..     234     244 ..     217     292 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.022
                    CENP-F_leu_zip  83 eeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeLqtqlk 136
                                       e+L+ + ++++++ +e ++   +l+ + +++E++k++++e+ ++  e+ +t ++
  gi|336253327|ref|YP_004596434.1|  27 ETLDYSYEQMRDQLQEVKRGIADLTTQKKRLEMQKRRLEENVEKHNEQARTAVQ 80 
                                       444444444444444444444444444444444444444444444444333333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0055
                    CENP-F_leu_zip  16 erkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeel......releldLvalrsekeeLe 86 
                                        +k+    +++e Ler++ +++++q+++i ++ + +  +e++++++e+++++       ++ +  ++a+  e e++ 
  gi|336253327|ref|YP_004596434.1|  91 LEKKKTKMNQIEDLERQISDLQSQQDQLIEQKNELQSRIEEFRTKKETMKARHeaakasSQVSEAITATGDEFEDVG 167
                                       4445555689***************************************8654111111566666777778999999 PP

                    CENP-F_leu_zip  87 kelqkkqervseLeslnssl 106
                                       + ++   e+ +++e++   +
  gi|336253327|ref|YP_004596434.1| 168 RAIERAEEQTEDMEARAAAM 187
                                       99999999999988877655 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.12
                    CENP-F_leu_zip  38 enqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqer..vs.eLeslnsslenlle 111
                                        + e+v +  E + ++ e +++    + e  +e +  ++++ s+k+++++el++      v+ eLe+l+s++ +   
  gi|336253327|ref|YP_004596434.1| 161 DEFEDVGRAIERAEEQTEDMEARAAAMDEL-HE-SGAFEDVMSDKDDIDRELEQLSTDsgVEaELETLKSEVGEGEA 235
                                       556777777888888888888888877653.33.4568899999999999998754321143377777776655544 PP

                    CENP-F_leu_zip 112 ekE 114
                                         E
  gi|336253327|ref|YP_004596434.1| 236 ATE 238
                                       444 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.7
                    CENP-F_leu_zip  42 kvileaEtska 52 
                                       ++ +e E + a
  gi|336253327|ref|YP_004596434.1| 234 EAATETEAQAA 244
                                       23333333333 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   7.0      0.36     3e+02       8      54 ..      29      75 ..      22     103 .. 0.74
   2 ?    8.2  13.0    0.0034       2.9       2      52 ..     105     155 ..      81     186 .. 0.63
   3 ?    8.5  12.3    0.0028       2.3       2      55 ..     105     158 ..     104     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.36
                           DUF5082  8 lqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekpl 54
                                      l + ++++r +++ +   I+ L + k++l+ +k +l+++ +k ++++
  gi|336253327|ref|YP_004596434.1| 29 LDYSYEQMRDQLQEVKRGIADLTTQKKRLEMQKRRLEENVEKHNEQA 75
                                      56677788888888888888888888888888888887777766665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0034
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklek 52 
                                        ++is+lq+q+++l ++ + l++ Ie+ ++ k+++++  e++k++ + +e 
  gi|336253327|ref|YP_004596434.1| 105 ERQISDLQSQQDQLIEQKNELQSRIEEFRTKKETMKARHEAAKASSQVSEA 155
                                       455666666666666666666666666666666666666555555444433 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0028
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekpln 55 
                                        ++is+lq+q+++l ++ + l++ Ie+ ++ k+++++  e++k++ + +e + +
  gi|336253327|ref|YP_004596434.1| 105 ERQISDLQSQQDQLIEQKNELQSRIEEFRTKKETMKARHEAAKASSQVSEAITA 158
                                       689***********************************9999998877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3572  (0.19923); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                       191  (0.0106531); expected 17.9 (0.001)
Passed Fwd filter:                       107  (0.00596798); 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: 1.55u 0.33s 00:00:01.88 Elapsed: 00:00:00.52
# Mc/sec: 1705.17
//
Query:       gi|336253328|ref|YP_004596435.1|  [L=172]
Description: hypothetical protein Halxa_1929 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0073   16.5   0.0      0.017   15.3   0.0    1.6  1  DUF3426     Protein of unknown function (DUF3426)
  ------ inclusion threshold ------
      0.043   13.2   2.6      0.076   12.4   2.6    1.4  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> DUF3426  Protein of unknown function (DUF3426)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.9e-06     0.017      49     145 ..      81     166 ..      52     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-06
                           DUF3426  49 ielisiessslrekageanlvlegtlrNradkpqalpaleltLtDaqgqvvarrvlspaeyllanqaantglapgse 125
                                       +e++s+  +++  + g ++  ++gt++N+     +l++++  +++ +g+++ r       y     a+   l  g+ 
  gi|336253328|ref|YP_004596435.1|  81 LESLSLIDHEFVVESGYLGSTIQGTVQNTGGDRIQLVEVRTRIYNGSGNMLGR-------YF----ASTGDLDGGEA 146
                                       55566656666667777779********************************9.......53....344569***** PP

                           DUF3426 126 ipfalvlevpgkrvagyrve 145
                                       ++f++v+  p+++va+y + 
  gi|336253328|ref|YP_004596435.1| 147 WEFQVVVLLPPANVADYDIT 166
                                       *****************986 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.6   8.5e-06     0.076       1      28 [.       1      29 [.       1      31 [. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.5e-06
                        UCR_Fe-S_N  1 mseaesdeptRRDFLy.iATgavgaVGaa 28
                                      m+ +es + +RR++L  +++g+v+a Ga+
  gi|336253328|ref|YP_004596435.1|  1 MTRSESTSRSRRRVLAsLGAGVVAAAGAG 29
                                      67789999*******32555666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1327.81
//
Query:       gi|336253329|ref|YP_004596436.1|  [L=352]
Description: hypothetical protein Halxa_1930 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.43   10.6   3.2        1.7    8.7   1.1    2.6  2  OppC_N    N-terminal TM domain of oligopeptide transport perm


Domain annotation for each model (and alignments):
>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.1   9.5e-05       1.7      13      32 ..      38      57 ..      33      72 .. 0.86
   2 ?    0.5   0.0     0.035   6.2e+02      17      36 ..     298     317 ..     296     345 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 9.5e-05
                            OppC_N 13 NklAvvglvilllllliaif 32
                                      N+lAv+glv l++++l++++
  gi|336253329|ref|YP_004596436.1| 38 NRLAVAGLVSLVIFALVVAL 57
                                      9***************9765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.035
                            OppC_N  17 vvglvilllllliaifaPli 36 
                                       vv+  i+++l  +a++  +i
  gi|336253329|ref|YP_004596436.1| 298 VVSVLIVVVLSPLALLVSYI 317
                                       67777777777777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2675.05
//
Query:       gi|336253330|ref|YP_004596437.1|  [L=348]
Description: hypothetical protein Halxa_1931 [Halopiger xanaduensis SH-6]
Scores for 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  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2675.35
//
Query:       gi|336253331|ref|YP_004596438.1|  [L=340]
Description: hypothetical protein Halxa_1932 [Halopiger xanaduensis SH-6]
Scores for 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  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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 0.22s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2779.73
//
Query:       gi|336253332|ref|YP_004596439.1|  [L=342]
Description: hypothetical protein Halxa_1933 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0021   18.6   0.1       0.02   15.4   0.0    2.4  2  YtxH      YtxH-like protein
     0.0069   15.2   0.8        1.3    7.7   0.0    2.1  2  DUF2207   Predicted membrane protein (DUF2207)
  ------ inclusion threshold ------
      0.077   11.5   0.1        0.5    8.8   0.0    2.0  2  Aldedh    Aldehyde dehydrogenase family
       0.12   12.4   0.0        0.2   11.6   0.0    1.3  1  DUF327    Protein of unknown function (DUF327)
        2.5    8.1   6.5        3.4    7.7   0.3    2.5  2  MRAP      Melanocortin-2 receptor accessory protein family


Domain annotation for each model (and alignments):
>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.2   7.1e+02      44      63 ..     132     151 ..     103     154 .. 0.58
   2 !   15.4   0.0   5.5e-06      0.02      19      72 ..     152     231 ..     151     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.2
                              YtxH  44 lleeakekakekaedlkekv 63 
                                       +l+e+ + ++e+a+dl e+v
  gi|336253332|ref|YP_004596439.1| 132 FLYELVDGVEEEANDLEETV 151
                                       44444444466666666666 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 5.5e-06
                              YtxH  19 APksGketRkdlkekaddlkekakelleeakeka..........................kekaedlkekvkekade 69 
                                       A + G e + ++++++dd+ e+a+ +++++++                            ++ ++dl+e+++++ +e
  gi|336253332|ref|YP_004596439.1| 152 ARDHGDEIQSKVADYVDDAVENAQVVKDDLEDAQfgtfdviwnalnfnysrkiydarkirADHGDDLSEDAEDELNE 228
                                       6789**********************99998888*************************9999********999999 PP

                              YtxH  70 lke 72 
                                       + e
  gi|336253332|ref|YP_004596439.1| 229 MIE 231
                                       877 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.4    0.0011       3.8     385     470 ..      26     130 ..      18     137 .. 0.61
   2 !    7.7   0.0   0.00036       1.3     350     438 ..     219     324 ..     141     327 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0011
                           DUF2207 385 alglgliilglilillallllvll.................lvfllilllillliaiivlllfsrllgrr..teeGa 442
                                        l+ +l+ +++++i++++l+ +++                 ++f ++++ i+   +i+v++    l + +    + +
  gi|336253332|ref|YP_004596439.1|  26 RLNRWLFTAAVLAIVFVVLVGASWlgltplriivarhngtfWIFSAFIGAIITGTSIVVTINQLVLSQELgaIGDQR 102
                                       44444555555555554444444455667799*****9999666666666666666555554433333332256667 PP

                           DUF2207 443 ellakwkgFkkyLeDfsefkerppedle 470
                                       + +  ++ F++ LeD +e ++  p+++ 
  gi|336253332|ref|YP_004596439.1| 103 DRMQNAMDFRQDLEDSLEKEDVTPPEPA 130
                                       7777777777777777777777776665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00036
                           DUF2207 350 akkfkkalkkwksavkk...kergyfdkkgkkklkklsalglgliilglilillallllvll............... 408
                                        +   ++l+++ + +k    +++++     k+ ++ + +++l  ++l++ +  la+++l ++               
  gi|336253332|ref|YP_004596439.1| 219 SEDAEDELNEMIELLKFfgpAREHF-----KTLYFQWELINLSRALLYVSVPALAVMALLMMyidgqalpgttlgad 290
                                       3333333333333333344433333.....44444444444444444444444333344344566779999****** PP

                           DUF2207 409 ....lvfllilllillliaiivlllfsrllgrrt 438
                                           ++ +++++ i +++++iv++l  +++ +rt
  gi|336253332|ref|YP_004596439.1| 291 nlvwVTSAGFVVGIAPFVVFIVYILRIATVAKRT 324
                                       *999888888888888888888888888888887 PP

>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00014       0.5      46     109 ..     122     186 ..     101     203 .. 0.85
   2 ?    0.0   0.0     0.064   2.3e+02      97     136 ..     267     307 ..     253     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00014
                                       TTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHH.HHHHHHHHHHHHHHHHHHHSE CS
                            Aldedh  46 aklpaeeRaeiLrkaadlleerkeelaeletletGkplaeara.eveeaidvlryyaelaekleg 109
                                       ++++++e a+ L+++ d +ee++++l e+ +++ G  +++  a  v++a++ ++ + + +e+ + 
  gi|336253332|ref|YP_004596439.1| 122 EDVTPPEPAAFLYELVDGVEEEANDLEETVARDHGDEIQSKVAdYVDDAVENAQVVKDDLEDAQF 186
                                       67899999********************************9998899999999988887777655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.064
                                       HHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-SEEEEEE-S CS
                            Aldedh  97 lryyaelaeklegevlps.segklalvrrePlGvvgaItPW 136
                                       l  +a l+  ++g++lp  + g+++lv     G+v+ I+P+
  gi|336253332|ref|YP_004596439.1| 267 LAVMALLMMYIDGQALPGtTLGADNLVWVTSAGFVVGIAPF 307
                                       566777788899*****9779*******************9 PP

>> DUF327  Protein of unknown function (DUF327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.7e-05       0.2      20      88 ..     105     179 ..      88     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.7e-05
                                       XXXXX-HHHHHHHHHHH......HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                            DUF327  20 ekkkksFsetlekeeee......eseeelkelleeidkqgerLaesrtiedlkkYkklvkeflkevvknslklkk 88 
                                        ++  +F + le++ e+      e  + l el++ +++++++L+e++  +   + + +v ++++++v+n+  +k+
  gi|336253332|ref|YP_004596439.1| 105 MQNAMDFRQDLEDSLEKedvtppEPAAFLYELVDGVEEEANDLEETVARDHGDEIQSKVADYVDDAVENAQVVKD 179
                                       3577889999988887755556666666****************************************9988876 PP

>> MRAP  Melanocortin-2 receptor accessory protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.2     0.033   1.2e+02      43      80 ..      30      67 ..      24      73 .. 0.83
   2 ?    7.7   0.3   0.00096       3.4      40      60 ..     298     318 ..     266     324 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.033
                              MRAP 43 WvsLavfvvllflvLlylsksGspqqrnsekrhracsw 80
                                      W+  a+   ++f+vL+  s+ G +  r    rh+ + w
  gi|336253332|ref|YP_004596439.1| 30 WLFTAAVLAIVFVVLVGASWLGLTPLRIIVARHNGTFW 67
                                      999999999*************9988887777776666 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00096
                              MRAP  40 iafWvsLavfvvllflvLlyl 60 
                                        +f v++a fvv++ ++L + 
  gi|336253332|ref|YP_004596439.1| 298 AGFVVGIAPFVVFIVYILRIA 318
                                       4799*************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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: 00:00:00.40
# Mc/sec: 2555.94
//
Query:       gi|336253333|ref|YP_004596440.1|  [L=345]
Description: hypothetical protein Halxa_1934 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        9.8    6.4   7.5        2.3    8.5   0.8    2.4  2  RskA             Anti-sigma-K factor rskA


Domain annotation for each model (and alignments):
>> RskA  Anti-sigma-K factor rskA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.8   0.00013       2.3      26      57 ..      15      78 ..       2     151 .. 0.61
   2 ?    1.3   1.0     0.021   3.8e+02      42      55 ..     287     306 ..     256     334 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00013
                                      ...........................XXXXXXXXXXXXXX................................. CS
                              RskA 26 aaaapppaaapaararr..........laaaaAaalllvlg................................q 57
                                      ++ +p+          +          ++++aA+al +++g                                 
  gi|336253333|ref|YP_004596440.1| 15 RSTSPT----------AkhwlllnanrWLVTAALALFVFVGllavarfspvslqalvgardpietvfqalvtaL 78
                                      112222..........1233556677799999999999999666555555554444444444444444444440 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.021
                                       .......XXXXXXXXXXXXX CS
                              RskA  42 r......laaaaAaalllvl 55 
                                       +      ++ +aAaa ++v+
  gi|336253333|ref|YP_004596440.1| 287 AlgidafVWIVAAAATVAVV 306
                                       24566664444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 2764.04
//
Query:       gi|336253334|ref|YP_004596441.1|  [L=235]
Description: iron-sulfur cluster repair di-iron protein [Halopiger xanaduensis SH-6]
Scores for 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-21   75.9  16.2    4.4e-21   75.9  16.2    2.0  2  Hemerythrin  Hemerythrin HHE cation binding domain
    1.7e-18   66.0   0.1    3.5e-18   65.0   0.1    1.6  1  ScdA_N       Domain of Unknown function (DUF542)
  ------ inclusion threshold ------
       0.11   13.0   2.1       0.19   12.2   0.3    2.2  2  Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
       0.26    9.9   0.1       0.36    9.4   0.1    1.2  1  FapA         Flagellar Assembly Protein A
        0.8   10.1   4.7       0.71   10.2   1.9    2.3  2  CCDC-167     Coiled-coil domain-containing protein 167
       0.82   10.2   5.5        3.4    8.2   2.8    2.4  2  APG6_N       Apg6 coiled-coil region


Domain annotation for each model (and alignments):
>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.15   4.4e+02      76     107 ..      41      72 ..      36      83 .. 0.71
   2 !   75.9  16.2   1.5e-24   4.4e-21       5     131 .]      82     228 ..      78     228 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHHCHTCGGSTCHHHHH CS
                       Hemerythrin  76 lereHdeirelleelrellkgleepsaaafae 107
                                       l+   +e++  le+++e l+g+++ ++++ ++
  gi|336253334|ref|YP_004596441.1|  41 LATACEEADLALERVAERLDGADGAPDREHEW 72 
                                       55666889999999999999999666665555 PP

  == domain 2  score: 75.9 bits;  conditional E-value: 1.5e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCCC....HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH............C CS
                       Hemerythrin   5 aldeeHralrallerlraladaaaevhga....lrklaelldelvdeleaHhaaEEellfPlle...........dr 66 
                                       +++++Hr lr+ l +l+al++++a+vhg+    l++++  ++ lvd++ +H  +EE+  fP+++           +r
  gi|336253334|ref|YP_004596441.1|  82 IVWDHHRPLRRNLPDLEALVEKVADVHGDshpeLQEVESEFQDLVDDMFHHIDDEEQNAFPVIKkldtgadltadER 158
                                       6789************************************************************************* PP

                                       CC.HHHHHHHHHHHHHHHHHHHHHHHHCHTCGGSTCHHHHH.....HHHHHHHHHHHHHHHHHHTHHHHH CS
                       Hemerythrin  67 pggravldvlereHdeirelleelrellkgleepsaaafae.....lleeladllreHiakEesilfpll 131
                                       +++++++d+le+eH e +++le+++ l++g++ p++a++ +     +le+l+++ + H+++E+++lfp++
  gi|336253334|ref|YP_004596441.1| 159 ARIEDEIDHLEAEHSETADRLERINDLTDGYAVPEDACASYrrmleRLENLERDTHMHVHRENNVLFPKA 228
                                       ********************************************************************86 PP

>> ScdA_N  Domain of Unknown function (DUF542)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.1   1.2e-21   3.5e-18       2      54 ..       9      61 ..       8      63 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 1.2e-21
                            ScdA_N  2 dqtvGeivaelpraakvFrkygIDFCCgGkvsLaeAckekgidleevlaeLea 54
                                      d ++G++va++p+ a+vF++++ID+CCgG  sLa+Ac+e+++ le v+++L+ 
  gi|336253334|ref|YP_004596441.1|  9 DARLGDLVASNPEYARVFESLDIDYCCGGATSLATACEEADLALERVAERLDG 61
                                      5789**********************************************975 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 ?   -0.6   0.1      0.64   1.9e+03      30      42 ..     114     126 ..      90     137 .. 0.61
   2 ?   12.2   0.3   6.4e-05      0.19      20      45 ..     161     186 ..     159     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.64
                       Cep57_MT_bd  30 elqelaaqynald 42 
                                       elqe+++++++l 
  gi|336253334|ref|YP_004596441.1| 114 ELQEVESEFQDLV 126
                                       3444444444333 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.4e-05
                       Cep57_MT_bd  20 LedEfehlklelqelaaqynaldpsl 45 
                                       +edE++hl +e++e a++++  ++ +
  gi|336253334|ref|YP_004596441.1| 161 IEDEIDHLEAEHSETADRLERINDLT 186
                                       79****************99888544 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00012      0.36     331     399 ..     152     218 ..     143     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00012
                              FapA 331 depelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleelee 399
                                       d ++++e+ +++e+e+  le+e  +  ++++++++l   ++++++   ++ ++le +e+l+++ + + +
  gi|336253334|ref|YP_004596441.1| 152 D-LTADER-ARIEDEIDHLEAEHSETADRLERINDLTDGYAVPEDACASYRRMLERLENLERDTHMHVH 218
                                       5.455555.99************************************************9998777655 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 ?   -1.8   0.0       1.4   4.2e+03      20      36 ..      52      68 ..      43     120 .. 0.60
   2 ?   10.2   1.9   0.00024      0.71       3      41 ..     162     204 ..     160     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                          CCDC-167 20 Leaverrlrkeelseee 36
                                      Le+v  rl ++   +++
  gi|336253334|ref|YP_004596441.1| 52 LERVAERLDGADGAPDR 68
                                      66666666665555554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00024
                          CCDC-167   3 aseIdkleeklascrerLeaverrlrkeelseee....Resle 41 
                                         eId+le + +++ +rLe+++    +  ++e++    R+ le
  gi|336253334|ref|YP_004596441.1| 162 EDEIDHLEAEHSETADRLERINDLTDGYAVPEDAcasyRRMLE 204
                                       67********************999999999988666655555 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.8    0.0012       3.4      47     101 ..     113     175 ..      45     187 .. 0.74
   2 ?    2.1   0.0     0.088   2.6e+02      20      42 ..     191     213 ..     182     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                            APG6_N  47 eeleeleee........leklekeeeelleeLkelekereeleaelaaleeelealeeeeerf 101
                                        el+e e e        +  +++ee++++  +k+l++  +  ++e+a +e e ++le+e  + 
  gi|336253334|ref|YP_004596441.1| 113 PELQEVESEfqdlvddmFHHIDDEEQNAFPVIKKLDTGADLTADERARIEDEIDHLEAEHSET 175
                                       455555555333333345558888888888888888877777777777777777777776554 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.088
                            APG6_N  20 qaekerdaYeeflkklkkekkee 42 
                                         e+ + +Y++ l++l++ ++++
  gi|336253334|ref|YP_004596441.1| 191 VPEDACASYRRMLERLENLERDT 213
                                       55788999999999999875543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 1880.50
//
Query:       gi|336253335|ref|YP_004596442.1|  [L=114]
Description: Cupin 2 barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-11   44.4   0.1    1.3e-11   44.1   0.1    1.1  1  Cupin_2       Cupin domain
    0.00097   18.8   0.1     0.0028   17.3   0.1    1.8  1  Cupin_3       Protein of unknown function (DUF861)
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.015   15.7   0.0    1.2  1  Ppnp          Pyrimidine/purine nucleoside phosphorylase
      0.063   13.6   0.0       0.08   13.3   0.0    1.1  1  Pirin_C       Pirin C-terminal cupin domain
      0.089   12.9   0.0       0.13   12.3   0.0    1.3  1  cNMP_binding  Cyclic nucleotide-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 !   44.1   0.1   3.5e-15   1.3e-11       3      70 ..      39     110 ..      37     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 3.5e-15
                                       EEEETTE.EEE.EECSSSEEEEEEEEESEEEEE.EC.TEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   3 velppGe.sap.shrHpgedeffyVleGegelt.vd.geeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                        el+pG+   +  ++ +g++e++yV++G++e+   d +e+v+lea++++ +++ +  ++ N gde a+l+ v
  gi|336253335|ref|YP_004596442.1|  39 LELEPGAdGMEhDESETGQEEIYYVVSGTVEVAlTDaDETVTLEADELIRIDPEESRQLSNVGDERAKLVLV 110
                                       6899***5444344489999***********99877899*****************************9876 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 !   17.3   0.1   7.8e-07    0.0028       9      58 ..      36      91 ..      26     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.8e-07
                                      EEEEEEECEEEEECESSEEEE.....EEEECEEEEEET.TTEEEEEETTEEEEE-T CS
                           Cupin_3  9 wgiwectpGkfrltyeedEfc.....yileGevkvtpe.ggetvelraGDlvvlpk 58
                                       +i+e +pG   ++ +e+E+      y+++G v+v+     etv+l+a  l+++ +
  gi|336253335|ref|YP_004596442.1| 36 ISILELEPGADGMEHDESETGqeeiyYVVSGTVEVALTdADETVTLEADELIRIDP 91
                                      56667777766666555555555555*********86548999*****99988766 PP

>> Ppnp  Pyrimidine/purine nucleoside phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.0   4.1e-06     0.015      37      78 ..      54      95 ..      47     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.1e-06
                                      EESS-EEEEEEESEEEEEETT-SS-EEEETT-EEEE-TTEEE CS
                              Ppnp 37 gtsakEvmevvsGelevklpgeeewktykagesFevpanssF 78
                                      +t+++E+  vvsG++ev l++++e+ t++a+e  +++ ++s 
  gi|336253335|ref|YP_004596442.1| 54 ETGQEEIYYVVSGTVEVALTDADETVTLEADELIRIDPEESR 95
                                      799*****************************9999877765 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 ?   13.3   0.0   2.2e-05      0.08      16      73 ..      53     114 .]      38     114 .] 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                                       --TT-EEEEEEEES-EEESSTT....EEE-TTEEEEE-SSSEEEEE--SS-EEEEEEEE--- CS
                           Pirin_C  16 lpegleaavyvleGelevgger....seieeeqlavlgdgdslvvkaeekgarvlLlaGePl 73 
                                        + g e + yv++G++ev  ++     ++e+++l+ +++++s +++   ++   l+l G+Pl
  gi|336253335|ref|YP_004596442.1|  53 SETGQEEIYYVVSGTVEVALTDadetVTLEADELIRIDPEESRQLSNVGDERAKLVLVGAPL 114
                                       467889999********99887788899**********888888777666666677778886 PP

>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.8e-05      0.13      17      41 ..      57      80 ..      50      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.8e-05
                                      -SEEEEEEES-EEEEEEETTS.EEE CS
                      cNMP_binding 17 adslyivlsGevrvyrlsedgkevv 41
                                       +++y+v+sG+v+v  l++ +++v+
  gi|336253335|ref|YP_004596442.1| 57 QEEIYYVVSGTVEVA-LTDADETVT 80
                                      459***********6.444443444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 966.25
//
Query:       gi|336253336|ref|YP_004596443.1|  [L=97]
Description: hypothetical protein Halxa_1937 [Halopiger xanaduensis SH-6]
Scores for 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:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 823.18
//
Query:       gi|336253337|ref|YP_004596444.1|  [L=89]
Description: Iron sulfur domain-containing, CDGSH-type [Halopiger xanaduensis SH-6]
Scores for complete 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-11   44.0   0.9      3e-11   43.3   0.2    1.7  2  zf-CDGSH  Iron-binding zinc finger CDGSH type


Domain annotation for each model (and alignments):
>> zf-CDGSH  Iron-binding zinc finger CDGSH type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.2   1.7e-15     3e-11      22      48 .]      20      46 ..       4      46 .. 0.70
   2 ?   -2.0   0.0      0.25   4.5e+03      15      20 ..      60      65 ..      51      74 .. 0.53

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.7e-15
                          zf-CDGSH 22 lregrevvaLCrCgrSknkPfCDgsHk 48
                                      +++++  va+C+Cg+S+++PfCDgsH+
  gi|336253337|ref|YP_004596444.1| 20 IDDEKGDVAVCQCGLSDSFPFCDGSHR 46
                                      2233333*******************6 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.25
                          zf-CDGSH 15 adgesv 20
                                      +dge+ 
  gi|336253337|ref|YP_004596444.1| 60 EDGERR 65
                                      344443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 713.93
//
Query:       gi|336253338|ref|YP_004596445.1|  [L=827]
Description: heavy metal translocating P-type ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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  155.1   1.4    2.7e-45  154.1   1.4    1.5  1  E1-E2_ATPase   E1-E2 ATPase
    6.6e-31  108.2   7.1    1.7e-30  106.9   7.1    1.8  1  Hydrolase      haloacid dehalogenase-like hydrolase
    9.7e-08   32.3   0.0    3.2e-07   30.7   0.0    2.0  1  HMA            Heavy-metal-associated domain
    3.2e-05   23.8   1.3    7.5e-05   22.6   1.3    1.5  1  Hydrolase_3    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.067   13.9   0.4      0.067   13.9   0.4    1.7  2  ATPase-cat_bd  Putative metal-binding domain of cation transp


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 !  154.1   1.4   7.6e-49   2.7e-45      10     181 .]     309     479 ..     300     479 .. 0.94

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 7.6e-49
                                       E-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEEEEE CS
                      E1-E2_ATPase  10 irdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeakavVt 86 
                                        r ++ e+++ + ++pGD +l+++g+rvp+Dg++veg+a vdes++TGEslpv+k+ gd++ +Gtvv++ ++ +v++
  gi|336253338|ref|YP_004596445.1| 309 ARLESGETVPLEAVEPGDRLLVRPGERVPLDGEVVEGTAAVDESLVTGESLPVRKTPGDELRGGTVVTDAPL-VVAV 384
                                       45566789***************************************************************9.5566 PP

                                       E-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTH CS
                      E1-E2_ATPase  87 atgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaL 163
                                           +++l+++++l+ + +s+++ +q+ +dkl+ v+vp+v+++a+ +++++l +g s+ +all +l+++++++PcaL
  gi|336253338|ref|YP_004596445.1| 385 GDEAESTLDRLVSLLWSIQSARPGVQRLADKLATVFVPLVVALAVGTAAVLLATGSSPSTALLVGLTVVIVSCPCAL 461
                                       7778899********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 164 plavplalalgarrlakk 181
                                       +la+pla+a+g++++ak+
  gi|336253338|ref|YP_004596445.1| 462 GLATPLAIAAGVQAAAKR 479
                                       ****************96 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   7.1   4.8e-34   1.7e-30       1     210 []     495     734 ..     495     734 .. 0.86

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 4.8e-34
                                       SSEEEEESBTTTBCHHHHHHHHHHHH......CHHHHHHHHHHHHCHHHHHHHHHHHHH...HHHHHHHHHETTTE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx. RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa......alalaaaletgsehpigkalvaaakar...sgaltgfatfigrg. 67 
                                       +++vv+Dk+GTLttg++ vedv           l +a a e  sehpi++a+++aa      +    + ++ +g+  
  gi|336253338|ref|YP_004596445.1| 495 VDVVVLDKTGTLTTGRMAVEDVHTVDgtdgdeLLRRAGAVESLSEHPIAAAVAEAAPVAaadG---GDLEAETGEDd 568
                                       689******************9888856665555555555555*********88888885662...33333333334 PP

                                       .................................HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHH CS
                                       .................................xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                         Hydrolase  68 .................................ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qara 107
                                                                        ++ +g p++ ++    +p+ l+a i++a ++gr  + +  ++r 
  gi|336253338|ref|YP_004596445.1| 569 gdletgangsaaaaavdsferadrgvsgvvdgdRVVVGHPDYCRERglSVPDALEAPIDDARAAGRVPVAVgwDGRT 645
                                       4556677778888888888888899**************************************************** PP

                                       HHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 108 lavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaair 184
                                       ++v+++ d+   ++e+  a+++L   g evv+ltgd+  taer     G           +e++a++ pe+k ++++
  gi|336253338|ref|YP_004596445.1| 646 HGVIAVGDS--EREELDAALETLS-SGREVVVLTGDEGPTAERFRAVDG----------VDEVFAGVPPEAKAETVD 709
                                       *********..***********99.899**************9888888..........5666************** PP

                                       HHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 185 eLqgkpeevamVGDgvnDaaalaaAg 210
                                       +L++++  +amVGDg nDa+alaaA+
  gi|336253338|ref|YP_004596445.1| 710 RLRARG-TIAMVGDGSNDAPALAAAD 734
                                       **8776.89****************8 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0     9e-11   3.2e-07       2      62 .]      89     149 ..      88     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 9e-11
                               HMA   2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62 
                                       ++v+gmhC  C+a  e+v ++  gV  +  ++at+t  +++d++ +   ++ e ++  gy+
  gi|336253338|ref|YP_004596445.1|  89 LAVEGMHCSTCEAFLESVAEREAGVLGAAASYATDTIRIVYDPDRLAADDLPEIVSGYGYT 149
                                       579******************************************88899******99995 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   1.3   2.1e-08   7.5e-05     206     252 ..     717     763 ..     711     765 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.1e-08
                                       EEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHH CS
                       Hydrolase_3 206 viafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVa 252
                                       ++ +GDg ND + L aa++g+Amg ++e + +aAd v+   + ++Va
  gi|336253338|ref|YP_004596445.1| 717 IAMVGDGSNDAPALAAADVGIAMGGGTELATEAADAVIVGDDLEAVA 763
                                       6779*********************************9877777776 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 ?   13.9   0.4   1.9e-05     0.067       2      41 ..      18      54 ..      17      58 .. 0.78
   2 ?   -3.2   0.1       4.2   1.5e+04      26      40 ..      94     108 ..      92     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                     ATPase-cat_bd  2 CyHCglpveesaklkaeiegeerefCCkGCqavaqlivea 41
                                      C  C l ++ +     + ++ + +fCC+GC  va+++ ++
  gi|336253338|ref|YP_004596445.1| 18 CDLCDLRTPPE---PITASDVDGTFCCRGCLEVARALEQH 54
                                      77777777776...4556677789***********99876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.2
                     ATPase-cat_bd  26 fCCkGCqavaqlive 40 
                                       + C+ C+a  + + e
  gi|336253338|ref|YP_004596445.1|  94 MHCSTCEAFLESVAE 108
                                       569999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (827 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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: 0.66u 0.23s 00:00:00.89 Elapsed: 00:00:00.40
# Mc/sec: 6272.04
//
Query:       gi|336253339|ref|YP_004596446.1|  [L=73]
Description: hypothetical protein Halxa_1940 [Halopiger xanaduensis SH-6]
Scores for 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:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 617.90
//
Query:       gi|336253340|ref|YP_004596447.1|  [L=78]
Description: hypothetical protein Halxa_1941 [Halopiger xanaduensis SH-6]
Scores for 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   13.5   0.1      0.052   13.3   0.1    1.1  1  SPC25     Microsomal signal peptidase 25 kDa subunit (SPC25)
       0.18   12.1   0.0       0.21   11.9   0.0    1.2  1  Orf78     Orf78 (ac78)


Domain annotation for each model (and alignments):
>> SPC25  Microsomal signal peptidase 25 kDa subunit (SPC25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.8e-06     0.052      59      81 ..      37      59 ..      25      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.8e-06
                             SPC25 59 laiavvlYfilsgiltlystfve 81
                                      ++i++++Yf++ ++l+l+++fve
  gi|336253340|ref|YP_004596447.1| 37 TLILIAIYFAILVLLWLFMYFVE 59
                                      7899******************9 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.3e-05      0.21      67      87 ..      38      58 ..       2      64 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                             Orf78 67 lisllavvcvlvllyviyYfv 87
                                      li +   +++lvll++ +Yfv
  gi|336253340|ref|YP_004596447.1| 38 LILIAIYFAILVLLWLFMYFV 58
                                      45556689************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 612.47
//
Query:       gi|336253341|ref|YP_004596448.1|  [L=273]
Description: cytochrome c oxidase subunit II [Halopiger xanaduensis SH-6]
Scores for complete 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   41.4   0.0    1.8e-10   40.7   0.0    1.3  1  COX2            Cytochrome C oxidase subunit II, periplasmic 
    3.3e-09   36.8   0.2    1.4e-08   34.8   0.0    2.0  3  Cupredoxin_1    Cupredoxin-like domain
      0.002   18.3   1.1      0.023   14.9   0.4    2.3  2  Big_3_5         Bacterial Ig-like domain (group 3)
  ------ inclusion threshold ------
      0.096   12.5   0.6       0.16   11.8   0.6    1.3  1  COX2-transmemb  Cytochrome C oxidase subunit II, transmembran


Domain annotation for each model (and alignments):
>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0     4e-14   1.8e-10      48     114 ..      84     150 ..      78     156 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 4e-14
                              COX2  48 vvlpvetkirllvtaedvlhsfavpslgvkvdavpGrlnqvsllidreGvfyGqcselcGvnhssmp 114
                                       + +p ++++ + vt+ dv hsf+v    + + ++pG ++q+++  d +G +   c e cG+ h  m 
  gi|336253341|ref|YP_004596448.1|  84 IDVPANSEVTFYVTSRDVTHSFSVVGTNINTMVIPGEVSQMTVEFDEPGEYGILCNEYCGAGHHDME 150
                                       669************************************************99**********9986 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0     3e-12   1.4e-08      20     102 ..      67     153 ..      60     155 .. 0.85
   2 ?   -1.6   0.0      0.64   2.9e+03      58      79 ..     160     183 ..     157     191 .. 0.63
   3 ?   -2.0   0.0      0.85   3.8e+03      53      53 ..     188     188 ..     170     228 .. 0.57

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 3e-12
                      Cupredoxin_1  20 ektveitvkdggfePskievkagekvklkiknkdktpeefesedlgeekvlapgktttitiaplkpGeYeftcd... 93 
                                       e +v+++++  ++ P++i+v+a+ +v++ ++ +d t ++f++   ++++ + pg+ +++t++ ++pGeY + c    
  gi|336253341|ref|YP_004596448.1|  67 EYEVAVVAQAWSYFPEEIDVPANSEVTFYVTSRDVT-HSFSVVGTNINTMVIPGEVSQMTVEFDEPGEYGILCNeyc 142
                                       56789999999********************99976.99*********************************98633 PP

                      Cupredoxin_1  94 ..mhmdakGkl 102
                                          h d++Gkl
  gi|336253341|ref|YP_004596448.1| 143 gaGHHDMEGKL 153
                                       32233466665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.64
                      Cupredoxin_1  58 efesedlgee..kvlapgktttit 79 
                                       ef +++l++e   +++ g++tti+
  gi|336253341|ref|YP_004596448.1| 160 EFDMTELDVEapDEVEAGNETTIN 183
                                       566666665544677777777765 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.85
                      Cupredoxin_1  53 d 53 
                                       d
  gi|336253341|ref|YP_004596448.1| 188 D 188
                                       2 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.073   3.3e+02      25      45 ..      89     109 ..      80     143 .. 0.56
   2 !   14.9   0.4   5.2e-06     0.023       3      64 ..     173     238 ..     171     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.073
                                       --EEEEEETTEE-SS-EE--T CS
                           Big_3_5  25 tGtVtftdggttlgtavllsa 45 
                                       +  Vtf++++  +     + +
  gi|336253341|ref|YP_004596448.1|  89 NSEVTFYVTSRDVTHSFSVVG 109
                                       556888887755543333332 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 5.2e-06
                                       -EETTSEEEEEEE--CCCCTTS--EEEEEETTEE-SS-EE--TTS....EEEEEEE-SS-EEEEEE CS
                           Big_3_5   3 svtagqtvtltatVtaasggtptGtVtftdggttlgtavllsanG....tAtltvsalaaGthsit 64 
                                       +v+ag+++t++atV+++ +++   t  + +g++++ ++v+++++G      +++++ l  G h+ t
  gi|336253341|ref|YP_004596448.1| 173 EVEAGNETTINATVSDGMQTDLETTAALEIGDQQYEEPVAIEGAGsesvEFAVDTAELGDGDHDWT 238
                                       7899*************99***********************988553333333455778888765 PP

>> COX2-transmemb  Cytochrome C oxidase subunit II, transmembrane
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6   3.6e-05      0.16       9      33 ..       3      27 ..       2      30 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHH CS
                    COX2-transmemb  9 iLAYEKGWLAFsLAmLFvFiALiAY 33
                                      i  YEK WL  ++ ++  FiA i Y
  gi|336253341|ref|YP_004596448.1|  3 IHTYEKIWLVAAMVLIVGFIATITY 27
                                      678**********9999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2231.07
//
Query:       gi|336253342|ref|YP_004596449.1|  [L=585]
Description: cytochrome c oxidase subunit I [Halopiger xanaduensis SH-6]
Scores for 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-89  300.2  68.6      9e-89  298.3  63.6    2.0  2  COX1      Cytochrome C and Quinol oxidase polypeptide I


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.3  63.6     5e-93     9e-89       2     411 ..      15     458 ..      14     473 .. 0.91
   2 !    4.9   0.2   0.00056        10     118     175 ..     476     550 ..     463     559 .. 0.76

  Alignments for each domain:
  == domain 1  score: 298.3 bits;  conditional E-value: 5e-93
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCTCT....-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS-S CS
                              COX1   2 igllylilalvlllvggllgllirlqlafp....dletynqlrtlHgnlmiflfatpfilgfgnylvplllgardla 74 
                                       ++++ ++ ++++l++ggllgl+++l+++      ++  y++++t+Hg+l+++ f+++f++g++ ++v   l +r ++
  gi|336253342|ref|YP_004596449.1|  15 VIKAAFWSSFLALAIGGLLGLVQALHRTDVlrfiESADYYTVLTAHGVLLAITFTIFFLVGVFTWAVTTSL-ERGVV 90 
                                       67899**********************83233447899*******************************98.9**** PP

                                       -HHHHHHHHHHHHHHHHHHHHHHH.CS.............S-STTTTTTTC.SHHHHHHHHHHHHHHHHHHHHHHHH CS
                              COX1  75 fprlnalsfwlvvlgvvllllsll.ga.............attgwteYaplsevdlwllglllvvvssllgainfiv 137
                                       ++r  +  ++++v+g+vl+ ++++ g              a++++t+Y pl++++l++lgl+l+vv+s+l+++  ++
  gi|336253342|ref|YP_004596449.1|  91 DTRFTWSWYAMMVVGTVLVGVTIFaGFleeppsilgselyADVLFTFYSPLQAHPLFYLGLVLFVVGSWLAGVDWFR 167
                                       ******************9999997335567888888999************************************* PP

                                       HHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT-SSSCE-HHHHHHHHHHHHTHHHHHHH CS
                              COX1 138 tilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrslgkffspgdplldqhlfWffgHpeVyili 214
                                       t++ +ra+++  +++pl +++vl+t++ + + ++++al++l+ ll++slg +++ ++pll ++lfW+fgH +Vy+++
  gi|336253342|ref|YP_004596449.1| 168 TWWAWRAENP-DERIPLPTFMVLTTTLFWYICTFGVALSILVFLLPWSLG-VVDSVNPLLTRTLFWYFGHAVVYFWL 242
                                       ********99.889***********************************7.8999********************** PP

                                       HHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTS.SS-HHHHHHHHHHHHHTHHHHHH...... CS
                              COX1 215 lpalgivyyilpkfagrplfsyklsvlafililflsflvwaHHlftt.glpewlkalgsvfslliavPsgl...... 284
                                       +pa++++y +lpk++g +lfs+ l+++ f+l+l+ls++ ++HH++ + g+ e  k+++++ ++++ +Ps+l      
  gi|336253342|ref|YP_004596449.1| 243 MPAYMMWYIMLPKLSGGKLFSDPLARVVFVLFLLLSTPLGIHHQYLDpGIAEGYKFIAMTNTMFLLLPSLLtaftvv 319
                                       ***********************************************************************888888 PP

                                       .............CCCHHHHCC.TTS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHH CS
                              COX1 285 .............kvfnwlatl.wrgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvl 347
                                                    + f+wl  l wr ++ f+ ++l    ++++f ++G++G+++a  ++ny+vhnt wvv+HfHl++
  gi|336253342|ref|YP_004596449.1| 320 asmehgarqrggeGYFGWLRALpWR-DPVFTGMAL----AGLMFAAAGFSGMINAGMNINYLVHNTWWVVGHFHLTV 391
                                       8888888888888888888888333.333444444....66777********************************* PP

                                       TTHHHHHHHHHHHHHHHHHHSB.--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHBSSSST..--S CS
                              COX1 348 lgavvfllfaaiyyllpkltgr.mlserlaklhfwllfiGlvlmflpmhilGllgmprraad..yks 411
                                        +av+++++aa y+ +p++tg+ ++++ +a  ++ l+fiG+++m+ +mh +Gl+gmprr+a+  y++
  gi|336253342|ref|YP_004596449.1| 392 GTAVALTFMAAAYWFIPQVTGKaLWNRSVALGQVLLWFIGMTFMSNAMHRSGLFGMPRRTAEpqYEN 458
                                       ********************653779999********************************522533 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.00056
                                       HHHHHHHHHHHHHHHHHHHHHHHH....................HHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHH CS
                              COX1 118 llglllvvvssllgainfivtilk....................rrapgmtvaklplfvwavlatailillalpvla 174
                                        lg +++ vs  l+++n+i+t ++                      ap +     +l +w+++a +++i+ +++ la
  gi|336253342|ref|YP_004596449.1| 476 ALGAAILTVSLALFLLNMIMTSFNgdgtsaaipdntyagtlsgpEDAPAI---LDNLKLWTAIAIVLVIFAYTLPLA 549
                                       6889999999999***********99988877776666665554444444...335668888888888888877776 PP

                                       H CS
                              COX1 175 l 175
                                        
  gi|336253342|ref|YP_004596449.1| 550 S 550
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.39
# Mc/sec: 4449.53
//
Query:       gi|336253343|ref|YP_004596450.1|  [L=71]
Description: hypothetical protein Halxa_1944 [Halopiger xanaduensis SH-6]
Scores for 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:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 595.65
//
Query:       gi|336253344|ref|YP_004596451.1|  [L=113]
Description: hypothetical protein Halxa_1945 [Halopiger xanaduensis SH-6]
Scores for 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   19.2   2.1      0.002   18.7   2.1    1.4  1  DUF883    Bacterial protein of unknown function (DUF883)


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 !   18.7   2.1   1.1e-07     0.002      13      52 ..      15      54 ..       9      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-07
                            DUF883 13 dleellkeaadeageeaeelRerleerlerarerlrdaee 52
                                       le +l+++ +eage++e+lRe  + +le+are+ + a++
  gi|336253344|ref|YP_004596451.1| 15 RLERFLRSKLREAGEQYEQLRESTDGQLEEAREAYEVAKN 54
                                      699******************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); 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: 0.39u 0.19s 00:00:00.58 Elapsed: 00:00:00.34
# Mc/sec: 983.91
//
Query:       gi|336253345|ref|YP_004596452.1|  [L=209]
Description: hypothetical protein Halxa_1946 [Halopiger xanaduensis SH-6]
Scores for 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   15.0   0.4      0.019   14.5   0.4    1.1  1  LRS4        Monopolin complex subunit LRS4
        0.1   12.2   0.9        0.2   11.3   0.9    1.5  1  Nup54_57_C  NUP57/Nup54 C-terminal domain


Domain annotation for each model (and alignments):
>> LRS4  Monopolin complex subunit LRS4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.4   2.2e-06     0.019       7     100 ..      92     196 ..      89     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.2e-06
                                       HHHHHHHHHHHHHHH...........HHHHHHHXXXXXXXXXXXX..............XXXXXXXXXXXXXXXXXX CS
                              LRS4   7 yydskldneriYlekaLnlah.llrsdslqksfldalktnatdse............lqnekltdEklllqeQinqL 70 
                                       y  +k++  ++Y++ ++   +  l  d+l++ f   +  n + ++             +n  l++E+l  + Qi++L
  gi|336253345|ref|YP_004596452.1|  92 YEATKINDPNLYISLSFQCSKfSLIYDKLEYIFEYEEAANRNPHDsrimleeeshiiAENPDLVEEEL--KSQIKHL 166
                                       66677777777877766655424667888887766666555555556888888888777888899975..789**** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              LRS4  71 nsdlqiqkseneklrklnKdqkalleSkls 100
                                        s+l     e e  r  n+  ka+l+ +++
  gi|336253345|ref|YP_004596452.1| 167 KSELETVILELEEYRMKNRYRKAILDTHVE 196
                                       ****************************98 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 ?   11.3   0.9   2.2e-05       0.2      14      25 ..     162     173 ..     160     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.2e-05
                        Nup54_57_C  14 QLqHLkKElEsi 25 
                                       Q++HLk ElE++
  gi|336253345|ref|YP_004596452.1| 162 QIKHLKSELETV 173
                                       **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1278  (0.0712812); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.23s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 1736.82
//
Query:       gi|336253346|ref|YP_004596453.1|  [L=347]
Description: hypothetical protein Halxa_1947 [Halopiger xanaduensis SH-6]
Scores for 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  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2892.64
//
Query:       gi|336253347|ref|YP_004596454.1|  [L=88]
Description: hypothetical protein Halxa_1948 [Halopiger xanaduensis SH-6]
Scores for complete 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   89.5   0.1    1.5e-25   89.3   0.1    1.1  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   0.1   8.3e-30   1.5e-25       2      75 .]       4      76 ..       3      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 8.3e-30
                            HalOD1  2 eespstaVveavaavegvdptel.epLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75
                                      e+s+s  V+eavaa+egv+p++l +pL++aiDpdALdaLf+s  ++ +++ +sv+Fty+gy++ V++   i+V++
  gi|336253347|ref|YP_004596454.1|  4 EQSISLHVIEAVAAYEGVEPEALrSPLHSAIDPDALDALFRS--ADGEQGAVSVEFTYKGYRIQVDGPDAITVSE 76
                                      789********************999****************..6667999**********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 699.90
//
Query:       gi|336253348|ref|YP_004596455.1|  [L=855]
Description: heavy metal translocating P-type ATPase [Halopiger xanaduensis SH-6]
Scores for 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-42  144.4   0.3    2.6e-42  144.4   0.3    2.7  3  E1-E2_ATPase   E1-E2 ATPase
    7.4e-28   98.3   4.3      1e-27   97.8   2.8    2.1  2  Hydrolase      haloacid dehalogenase-like hydrolase
      4e-07   30.4   0.0    4.7e-05   23.8   0.0    3.3  3  HMA            Heavy-metal-associated domain
    6.5e-05   22.8   0.2    0.00012   21.9   0.2    1.3  1  Hydrolase_3    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.077   13.7   0.2       0.16   12.7   0.2    1.5  1  ATPase-cat_bd  Putative metal-binding domain of cation transp
      0.087   12.8   2.5       0.45   10.5   2.5    2.2  1  RseC_MucC      Positive regulator of sigma(E), RseC/MucC


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 ?   -2.6   1.8       1.1   3.4e+03     121     137 ..     246     262 ..     206     289 .. 0.51
   2 !  144.4   0.3   8.9e-46   2.6e-42       5     180 ..     309     483 ..     305     484 .. 0.96
   3 ?   -1.5   0.3      0.51   1.5e+03     151     176 ..     778     803 ..     759     807 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHS- CS
                      E1-E2_ATPase 121 vlvpvvlliallvflia 137
                                       vlv v++l+a +  ++a
  gi|336253348|ref|YP_004596455.1| 246 VLVSVAVLAAYAYSIAA 262
                                       23333333333333333 PP

  == domain 2  score: 144.4 bits;  conditional E-value: 8.9e-46
                                       -EEEEE.-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-E CS
                      E1-E2_ATPase   5 ptakvi.rdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsge 80 
                                       +t++++ +dg++ee+  +  +pGD vl+ agdr+p Dg ++egs +vdes++TGEs p     gd+v +G+v ++g+
  gi|336253348|ref|YP_004596455.1| 309 TTVRLVvEDGSLEEVSREACEPGDQVLVSAGDRIPFDGTVLEGSGTVDESFVTGESIPRAAFVGDRVVGGAVLTDGT 385
                                       5555556*********************************************************************9 PP

                                       EEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHH CS
                      E1-E2_ATPase  81 akavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallva 157
                                       +   V + g +++l+++++l+ e +s+++  q+ ++ ++  +vp+v+l+a +++ ++ll g+++  all +l++lv+
  gi|336253348|ref|YP_004596455.1| 386 L--TVETDGDSSTLDRLVELLWEVQSAESGAQRLVNAFAVAFVPLVVLLAGAAAGFWLLAGEPAGSALLIGLSVLVV 460
                                       9..6889********************************************************************** PP

                                       HS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 158 aiPcaLplavplalalgarrlak 180
                                       ++Pc L++a+plala+g  r+a+
  gi|336253348|ref|YP_004596455.1| 461 SCPCSLGIATPLALAAGSERAAE 483
                                       ********************997 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.51
                                       HHHHHHHHS-TTHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 151 alallvaaiPcaLplavplalalgar 176
                                       a +  ++aiP a++ a+   +a++++
  gi|336253348|ref|YP_004596455.1| 778 AAGYNLVAIPLAMAGAINPLIAAAMM 803
                                       56666899********9999999886 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.97   2.9e+03       9     109 ..     383     495 ..     382     502 .. 0.50
   2 !   97.8   2.8   3.4e-31     1e-27       3     210 .]     502     729 ..     500     729 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.97
                                       BTTTB...CHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH........HHHHHHHHHETTTE...HHHH CS
                                       xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxx...xxxx RF
                         Hydrolase   9 dGTLt...tgepsvedvivsaalalaaaletgsehpigkalvaaakar........sgaltgfatfigrg...ayai 71 
                                       dGTLt   +g +s  d +v++        e+ s    +++lv+a+            ga +gf  ++g+    a++i
  gi|336253348|ref|YP_004596455.1| 383 DGTLTvetDGDSSTLDRLVEL------LWEVQSAESGAQRLVNAFAVAfvplvvllAGAAAGFWLLAGEPagsALLI 453
                                       899986555555555555555......23333444444444444444434434544555555555555556666666 PP

                                       THHHHHHHH....HCHHHHHHHHHHHHHHCHHHHHHTTHHHH CS
                                       xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  72 gkpewltal....dippdlgaaigsaqsqgrtvallqarala 109
                                       g   ++ +      i + l  a gs+ ++   +a+l+a++l+
  gi|336253348|ref|YP_004596455.1| 454 GLSVLVVSCpcslGIATPLALAAGSERAAENGAAVLSANVLE 495
                                       665555555555555555555555555555555555555555 PP

  == domain 2  score: 97.8 bits;  conditional E-value: 3.4e-31
                                       EEEEESBTTTBCHHHHHHHHHHHH...CHHHHHHHHHHHHCHHHHHHHHHHHHH.....HHHHHHHHHETTTE.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx.... RF
                         Hydrolase   3 tvvfDkdGTLttgepsvedvivsa...alalaaaletgsehpigkalvaaakar.....sgaltgfatfigrg.... 67 
                                        vvfDk+GTLttge+ ve+v++      l+ aaa e  s+hpi++a+v+aa             ++a  i+r     
  gi|336253348|ref|YP_004596455.1| 502 IVVFDKTGTLTTGEMTVETVVADDserVLEYAAAVESRSNHPIAAAIVEAAPSGgvqegD---REIAD-IEREarav 574
                                       69*******************99988888999999999*************999554442...44444.33333556 PP

                                       .........................HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTH CS
                                       .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                         Hydrolase  68 .........................ayaigkpewltaldippdlgaaigsaqsqgrtvall..qaralavftiadpl 117
                                                                + a g + w+        l +a++sa + g   + +  ++ +++v+++ d+ 
  gi|336253348|ref|YP_004596455.1| 575 sgtvdgqrirvghpasfrgssepadESAGGARAWTVTD----RLAEAVESAREGGCRPIAVgwDGAVRGVIAVRDQ- 646
                                       77778885666666444444444444444444444444....78888888888887777779*************9. PP

                                       HBHTTHHHHHHHHHHT.TE.EEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGG CS
                                       xxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 118 kvkpeaaeavasLkaa.gi.evvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpee 192
                                        +++  + +v +  +a    ++v+ltgd+++    + ++ +           ++++a++ pe k+a++r+L++++  
  gi|336253348|ref|YP_004596455.1| 647 -PRENWERVVSEVASAdDArRIVVLTGDDERATGWLQEHPD----------VDDVFAGVRPESKEAIVRRLREDG-T 711
                                       .99999999999888878878********999888888899..........5666****************8777.8 PP

                                       EEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxx RF
                         Hydrolase 193 vamVGDgvnDaaalaaAg 210
                                       + ++GDg nDa+ala+A+
  gi|336253348|ref|YP_004596455.1| 712 TTVIGDGTNDAPALARAD 729
                                       ****************98 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.6e-08   4.7e-05       4      61 ..      90     147 ..      87     148 .. 0.95
   2 ?    2.6   0.0     0.065   1.9e+02      34      57 ..     382     402 ..     379     405 .. 0.79
   3 ?   -2.9   0.1       3.3   9.9e+03      33      47 ..     511     525 ..     510     533 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.6e-08
                               HMA   4 vsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61 
                                        +gmhC+ C++  e+     +gV+ +  ++at     ++d+++++ +++ +ai+  gy
  gi|336253348|ref|YP_004596455.1|  90 LEGMHCTTCERFLERIATDTEGVRGAQASYATEMIRLRYDPDAIDREELPAAISGFGY 147
                                       68*****************************************77799*******999 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.065
                               HMA  34 atktvtVegdaestklrkiieaie 57 
                                         +t+tVe+d +s   +++++ +e
  gi|336253348|ref|YP_004596455.1| 382 TDGTLTVETDGDS---STLDRLVE 402
                                       569**********...77777766 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.3
                               HMA  33 latktvtVegdaest 47 
                                       l t+++tVe++++++
  gi|336253348|ref|YP_004596455.1| 511 LTTGEMTVETVVADD 525
                                       678999999966653 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.2   4.1e-08   0.00012     206     247 ..     712     753 ..     702     760 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.1e-08
                                       EEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GG CS
                       Hydrolase_3 206 viafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnn 247
                                       + ++GDg ND + L +a++g+A++++++ +  aAd v+ + +
  gi|336253348|ref|YP_004596455.1| 712 TTVIGDGTNDAPALARADMGIALESGTDIAMDAADIVVRDDD 753
                                       789*********************************998766 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 ?   12.7   0.2   5.3e-05      0.16       2      44 ..       4      43 ..       3      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.3e-05
                     ATPase-cat_bd  2 CyHCglpveesaklkaeiegeerefCCkGCqavaqliveagle 44
                                      C+ Cglp  +     ++ +  e +fCC+GC  v +++  a+ e
  gi|336253348|ref|YP_004596455.1|  4 CTLCGLPAGDR---PVRDDAVEGTFCCRGCLEVHRAVEGAEAE 43
                                      88888888765...5667778889**********999877766 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.5   0.00015      0.45      65     107 ..     418     461 ..     407     468 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                         RseC_MucC  65 kaallvYllPllllilgallgsall.gssellaalgallglvlg 107
                                         a+ v  +Pl++l++ga++g +ll g+  + a+l++l +lv++
  gi|336253348|ref|YP_004596455.1| 418 VNAFAVAFVPLVVLLAGAAAGFWLLaGEPAGSALLIGLSVLVVS 461
                                       456667779***************98888888999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (855 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.26s 00:00:00.94 Elapsed: 00:00:00.39
# Mc/sec: 6573.76
//
Query:       gi|336253349|ref|YP_004596456.1|  [L=293]
Description: cytochrome c oxidase subunit III [Halopiger xanaduensis SH-6]
Scores for 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-31  109.2  16.5    4.4e-31  108.7  16.5    1.3  1  COX3      Cytochrome c oxidase subunit III


Domain annotation for each model (and alignments):
>> COX3  Cytochrome c oxidase subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7  16.5   2.5e-35   4.4e-31      74     255 ..     113     289 ..      36     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 2.5e-35
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--GGGTSSSS-TT-----TTSHHHHHHHHHHHHHHHHHHHHHHHHT CS
                              COX3  74 kGlklGlilfiisevllflalfwaffhsalsPtvelGatwpPvGikavnPlevPllntiillssGvtvtyahhslie 150
                                         l++G++lf+ ++v+ f a f+ +f             wpP  +  +    + l+nt+il++s vt+  ah  + e
  gi|336253349|ref|YP_004596456.1| 113 IDLRWGMVLFLATDVMTFSAGFVYYFFVR-------TGEWPPGELPHLL-SSLVLVNTAILIASSVTLHVAHEGIRE 181
                                       349****************9999999543.......357***9996654.46789********************** PP

                                       TBHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS...-TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-- CS
                              COX3 151 gnrkkalkgllltillavlftllqaveyleasf...tisdgvyGsvfylatGlhglhviigtillavallrllkyhl 224
                                       g+r++ l  l  t+ll+++f++ q +ey+e      t    v+Gs+f++ tGlhglhv +g ++la+ + r ++  +
  gi|336253349|ref|YP_004596456.1| 182 GHRRRFLGLLGATVLLGLVFVGGQLFEYYELLVvegTGVTDVFGSAFFALTGLHGLHVALGVVILAIVFVRAMAGQF 258
                                       ****************************98654111555669*********************************** PP

                                       BSSB-HHHHHHHHHHHHHHHHHHHHHHHTTT CS
                              COX3 225 tknhhlGfeaailywhfvdvvwlflyvsvyw 255
                                        ++ h+   +a +ywhfvd+vw+ l v++y 
  gi|336253349|ref|YP_004596456.1| 259 DSDRHIAVSTASMYWHFVDLVWVILVVILYV 289
                                       ***************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2260.36
//
Query:       gi|336253350|ref|YP_004596457.1|  [L=149]
Description: cox cluster protein [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.67    9.3  13.1       0.93    8.8  13.1    1.1  1  ThrE         Putative threonine/serine exporter
        1.2    9.0  11.5      0.085   12.7   2.7    2.1  2  DUF2976      Protein of unknown function (DUF2976)


Domain annotation for each model (and alignments):
>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  13.1    0.0001      0.93     103     200 ..      19     132 ..      16     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0001
                              ThrE 103 kpryprwlvvlaaglaaaafallfggdwidflvaflagllggllrlllakrglnsfvleavaaflasllallavsl. 178
                                       ++r + w  v+a g++aa  ++lfg  +i+++ ++++g+ +  + + +    ++   l +++a++a + a++++++ 
  gi|336253350|ref|YP_004596457.1|  19 PSRSSAWPLVAALGIVAAEAGVLFGLVVIAVAGVLAVGASVAGMLHETGYAATPWRPLRLIGAVVAIASAAVWIAVa 95 
                                       778899*********************************************************99999998888865 PP

                              ThrE 179 ...............glglnpdaiiigsillLvPGlp 200
                                                      g+++ ++ ++ ++ ll+++G++
  gi|336253350|ref|YP_004596457.1|  96 paatpaaladaaatdGVAVRAAVVLGAAALLILAGFA 132
                                       5666666666655554455578888888888899986 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.7   9.5e-06     0.085       6      81 ..      18      92 ..      14     100 .. 0.79
   2 ?    1.7   1.6     0.026   2.3e+02      25      45 ..     109     130 ..      98     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.5e-06
                           DUF2976  6 aPssgekggdllelikgylkdgvillgLvlaav.aflaVakaalkkfneisegkaewgkfgltlvvGvvllvvviwL 81
                                      +Ps+++ +  l++ + ++++++ +l gLv+ av ++laV  ++ +  +e       w+ + l+ +v ++   +++w+
  gi|336253350|ref|YP_004596457.1| 18 DPSRSS-AWPLVAALGIVAAEAGVLFGLVVIAVaGVLAVGASVAGMLHETGYAATPWRPLRLIGAVVAIA-SAAVWI 92
                                      567766.6778889999999999999*987665169************************9998875543.344444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.026
                           DUF2976  25 kdgvil.lgLvlaavaflaVak 45 
                                        dgv++ +++vl+a+a+l  a 
  gi|336253350|ref|YP_004596457.1| 109 TDGVAVrAAVVLGAAALLILAG 130
                                       5666652678999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1141.02
//
Query:       gi|336253351|ref|YP_004596458.1|  [L=180]
Description: hypothetical protein Halxa_1952 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        2.4    7.2   8.0        2.9    6.9   8.0    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> 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 ?    6.9   8.0   0.00016       2.9     216     289 ..      49     142 ..      36     175 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00016
                   ABC2_membrane_3 216 vyllqlllilll...afgl..............gipfg.nlglllllfllfglayialgyllssl...fknsetaqi 271
                                       ++l+ ++ il++   +f+l               +  + nl+l +l+f  +g ++++l +++  +    + ++ a +
  gi|336253351|ref|YP_004596458.1|  49 LGLVAMVPILFVppaFFDLfeadalvdvaelgrVLGLEpNLLLGILVFAAGGAVALPLLFVVAGAflpPREPRYARA 125
                                       344444444443443566677799999999999888888*******************9999666234456688888 PP

                   ABC2_membrane_3 272 lifivilllsgffgglfp 289
                                       ++f++i+   gf+++++p
  gi|336253351|ref|YP_004596458.1| 126 ITFATIM-WTGFIIAFWP 142
                                       8888888.7788888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1448.62
//
Query:       gi|336253352|ref|YP_004596459.1|  [L=303]
Description: hypothetical protein Halxa_1953 [Halopiger xanaduensis SH-6]
Scores for 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   14.5   0.1      0.012   14.5   0.1    1.6  2  DUF2207       Predicted membrane protein (DUF2207)
      0.096   12.4   0.2      0.096   12.4   0.2    2.2  2  MNHE          Na+/H+ ion antiporter subunit


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 ?   -3.0   1.3      0.26   2.3e+03     387     409 ..      20      53 ..      14      77 .. 0.46
   2 ?   14.5   0.1   1.3e-06     0.012     349     429 ..     191     286 ..     170     299 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.26
                           DUF2207 387 glgliilglilillallllvll...........l 409
                                         +l+ +++++++ ++ ++ +            l
  gi|336253352|ref|YP_004596459.1|  20 TGILVTMAVVVLIPLFSQFDVRnltpliyiasaL 53 
                                       3444444444444444444433544444333321 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.3e-06
                           DUF2207 349 kakkfkkalkkwksavkk..kergyfdkkg.kkklkklsalglgliilglilillallllvll............lv 410
                                       +++++ ++l+++  ++k+   +r+yf+++  k++l+kls  +l +++l++ l +++l++l+++            ++
  gi|336253352|ref|YP_004596459.1| 191 EHEQLLSTLDALSADLKNldIARQYFTTAFmKEELAKLSRSLLYIGVLAISLPVALLIQLATFptavapmptvlvFT 267
                                       7899999999**********99*****99878888889999999988888888888888888899999988865533 PP

                           DUF2207 411 fllilllillliaiivlll 429
                                       +l +++ +++l+++i+++l
  gi|336253352|ref|YP_004596459.1| 268 LLTVVVGLVPLALLIAFIL 286
                                       3333333333333333333 PP

>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.1e-05     0.096       7      70 ..       7      66 ..       5      97 .. 0.62
   2 ?   -1.5   4.7      0.22     2e+03      15      56 ..     235     274 ..     226     300 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                              MNHE  7 vWllltgslgelllGlllallvalllrrll.....lplrrvllrllayllvflweivkanldVakrvlr 70
                                       Wlll+g+ + +++G+l+ ++v++l+ +l+     ++l+++        ++++  ++  n+  + +v+ 
  gi|336253352|ref|YP_004596459.1|  7 RWLLLSGDRFRVATGILVTMAVVVLI-PLFsqfdvRNLTPL--------IYIASALIGGNITLITLVVA 66
                                      5*******999999999999999999.44445333222222........23333444444444444433 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.22
                              MNHE  15 lgelllGlllallvalllrrlllplrrvllrllayllvflwe 56 
                                       +g l++ l +all+ l++  ++  + +++  l+  ll +++ 
  gi|336253352|ref|YP_004596459.1| 235 IGVLAISLPVALLIQLAT--FPTAVAPMPTVLVFTLLTVVVG 274
                                       566777788888888888..3422233333222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 2505.90
//
Query:       gi|336253353|ref|YP_004596460.1|  [L=601]
Description: cytochrome c oxidase subunit I [Halopiger xanaduensis SH-6]
Scores for 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-140  466.4  56.8   1.3e-139  465.8  56.8    1.3  1  COX1      Cytochrome C and Quinol oxidase polypeptide I


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.8  56.8  7.2e-144  1.3e-139       1     432 []      65     525 ..      65     541 .. 0.96

  Alignments for each domain:
  == domain 1  score: 465.8 bits;  conditional E-value: 7.2e-144
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCTCT.....-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS CS
                              COX1   1 kigllylilalvlllvggllgllirlqlafp.....dletynqlrtlHgnlmiflfatpfilgfgnylvplllgard 72 
                                       +iglly+++++++ l+g + +++ir++l +p     + etyn+++t Hg +m+f+f+tp+++g++ny++plllga+d
  gi|336253353|ref|YP_004596460.1|  65 DIGLLYILFGTAAALWGATDAMMIRTELLVPesavwNVETYNAVFTTHGLTMLFFFVTPVFTGIANYVLPLLLGADD 141
                                       599*************************9996666666*************************************** PP

                                       -S-HHHHHHHHHHHHHHHHHHHHHHH....CS.................S-STTTTTTTC.......SHHHHHHHHH CS
                              COX1  73 lafprlnalsfwlvvlgvvllllsll....ga.................attgwteYapls......evdlwllgll 122
                                       lafpr+na++fwl++ +++++  +l+    g                  +++gwt+Y+pls      ++ ++llgl+
  gi|336253353|ref|YP_004596460.1| 142 LAFPRINAIAFWLLPPSLLMVRGGLItdiiGMvvgvlpvdvtlfealepVAMGWTMYTPLSvemanpQISVALLGLH 218
                                       ************7777777777777654442255567777788888888**************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT.-SSSC..E-HH CS
                              COX1 123 lvvvssllgainfivtilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrslg.kffsp..gdpl 196
                                       l++v+++++ainfivti++ r p++ + kl +f w++l+t++lilla+p l  +l++llldr++g +ff +  g p+
  gi|336253353|ref|YP_004596460.1| 219 LSGVATTMAAINFIVTIFTERPPELGWDKLDIFSWNILVTSALILLAFPLLGSTLIMLLLDRNFGtTFFAIegGGPM 295
                                       *********************************************************************7788**** PP

                                       HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHH CS
                              COX1 197 ldqhlfWffgHpeVyililpalgivyyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsv 273
                                       l+qhlfWffgHpeVyil+lpa+g+v+ ilpkf+gr+lf+ +++v+++i+i++lsf vwaHH+f tg+++ l+a +++
  gi|336253353|ref|YP_004596460.1| 296 LWQHLFWFFGHPEVYILVLPAFGLVSLILPKFCGRRLFGFRFIVYSTIAIGILSFGVWAHHMFATGMDPRLRASFMA 372
                                       ***************************************************************************** PP

                                       HHHHTHHHHHHCCCHHHHCCTTS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTH CS
                              COX1 274 fslliavPsglkvfnwlatlwrgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllga 350
                                       +sl+ia+Ps++k fnw+at+w+g++r+++p+++++g++ +f++gG+tGv+la+++v++v+h+t++vv+HfHl+++g+
  gi|336253353|ref|YP_004596460.1| 373 VSLAIAIPSAIKEFNWIATMWNGRLRLDAPLICIIGAMSTFVVGGITGVFLASVPVDLVLHDTHYVVGHFHLIVVGV 449
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHH CS
                              COX1 351 vvfllfaaiyyllpkltgrmlserlaklhfwllfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrt 427
                                       + ++++aa yy++p +tgrm+++rla+++ +ll+iG++++f+p++ilG++gmprr+  y        e+ +ln++++
  gi|336253353|ref|YP_004596460.1| 450 IPLAMIAASYYWFPLITGRMYNQRLARAQTVLLIIGTFVTFIPLLILGYMGMPRRYGIY------PVEFITLNQVAS 520
                                       *********************************************************99......3599******** PP

                                       HHHHH CS
                              COX1 428 iggvl 432
                                       +g++l
  gi|336253353|ref|YP_004596460.1| 521 LGAFL 525
                                       **986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 4890.98
//
Query:       gi|336253354|ref|YP_004596461.1|  [L=138]
Description: hypothetical protein Halxa_1955 [Halopiger xanaduensis SH-6]
Scores for 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:                       405  (0.0225891); 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:                         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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1082.24
//
Query:       gi|336253355|ref|YP_004596462.1|  [L=264]
Description: cytochrome c oxidase subunit II [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.5   0.3    1.3e-14   54.1   0.0    2.3  3  COX2           Cytochrome C oxidase subunit II, periplasmic d
    6.9e-11   42.1   0.2    1.1e-10   41.5   0.2    1.3  1  COX2_TM        Cytochrome C oxidase subunit II, transmembrane
     0.0081   16.3   0.8      0.013   15.6   0.5    1.5  1  CwsA           Cell wall synthesis protein CwsA
  ------ inclusion threshold ------
      0.012   14.8   0.1       0.02   14.1   0.1    1.4  1  DUF3413        Domain of unknown function (DUF3413)
      0.064   12.1   0.7       0.13   11.0   0.7    1.5  1  AA_permease_2  Amino acid permease
        0.1   12.7   0.0       0.23   11.6   0.0    1.5  1  Cupredoxin_1   Cupredoxin-like domain
       0.26   11.5   5.7       0.65   10.2   5.1    1.8  2  TrbC           TrbC/VIRB2 family
       0.96    8.6   7.7        6.9    5.8   8.6    1.6  2  CitMHS         Citrate transporter


Domain annotation for each model (and alignments):
>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.7     6e+03      67      87 ..      18      41 ..       6      47 .. 0.54
   2 !    6.0   0.1    0.0045        10       6      32 ..     134     160 ..     129     162 .. 0.88
   3 !   54.1   0.0   5.9e-18   1.3e-14      44     118 ..     151     225 ..     147     227 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.7
                              COX2 67 hsfavpslgvk...vdavpGrlnq 87
                                         avp+++v    +d v  rln+
  gi|336253355|ref|YP_004596462.1| 18 AVAAVPTVAVAgsvTDQVIRRLNR 41
                                      445666665532225556666665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0045
                              COX2   6 iGhqwywsyeytdfedlefdsylvpee 32 
                                       + +qw +++ey++ +  + +s+++pe+
  gi|336253355|ref|YP_004596462.1| 134 VTEQWNYTFEYPEENVTTSESLVLPEN 160
                                       578***********99999***99986 PP

  == domain 3  score: 54.1 bits;  conditional E-value: 5.9e-18
                              COX2  44 vdnrvvlpvetkirllvtaedvlhsfavpslgvkvdavpGrlnqvsllidreGvfyGqcselcGvnhssmpivve 118
                                       + +++vlp +++  l +t+edv+hs  vp lg+k+da pG+ n + +  + +G +   c+elcG  h  m   v+
  gi|336253355|ref|YP_004596462.1| 151 TSESLVLPENRTAYLYITSEDVIHSVHVPELGLKQDALPGQYNLLRTEPTEQGEYRLYCAELCGRGHPEMLSTVR 225
                                       67899**************************************************************99976665 PP

>> COX2_TM  Cytochrome C oxidase subunit II, transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.2   4.9e-14   1.1e-10      11      88 ..      27     101 ..      17     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 4.9e-14
                           COX2_TM  11 daasplmeeleelhdyilliltlililVlyilvlilvefrrrknkitakylvhgqeiEiiWTiiPalililialpSl 87 
                                       +a s + + +  l+ ++l++++ i +lV+ il + +++fr + ++ ++k   ++ ++Ei WTi  al+l++++  S+
  gi|336253355|ref|YP_004596462.1|  27 VAGSVTDQVIRRLNRQLLYLAVPIAVLVEAILAYTVWRFRDNDEPEPTK---ENRQLEITWTIATALVLLFVGTASF 100
                                       67788888899****************************8888887755...************************9 PP

                           COX2_TM  88 k 88 
                                        
  gi|336253355|ref|YP_004596462.1| 101 Y 101
                                       6 PP

>> CwsA  Cell wall synthesis protein CwsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.5   5.9e-06     0.013      67     122 ..      15      76 ..       3      86 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.9e-06
                              CwsA  67 aqevvaglPqaleda....rkkrrrkrplllagvavavlaGGavafsivrrs..srPePssl 122
                                       a+ +va++P +        +  rr  r+ll  +v +avl+    a+++ r +   +PeP+  
  gi|336253355|ref|YP_004596462.1|  15 AALAVAAVPTVAVAGsvtdQVIRRLNRQLLYLAVPIAVLVEAILAYTVWRFRdnDEPEPTKE 76 
                                       445678888764433466667899************************99773356666655 PP

>> DUF3413  Domain of unknown function (DUF3413)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   8.8e-06      0.02     129     190 ..      37     108 ..       8     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.8e-06
                           DUF3413 129 ss..wllllilvlvilllelllanlvwkkl........rklkrkklgkpvalvlllaflashlihiwadAnl 190
                                       +    +ll+++v++ +l+e +la+ vw+          ++ ++ ++  ++a +l+l f+ + + +++a+ + 
  gi|336253355|ref|YP_004596462.1|  37 RRlnRQLLYLAVPIAVLVEAILAYTVWRFRdndepeptKENRQLEITWTIATALVLLFVGTASFYVLAQPTV 108
                                       33356899*******************977788887745555888999******************998665 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7   5.9e-05      0.13     362     412 ..      50     109 ..       6     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.9e-05
                     AA_permease_2 362 ylll...iigalilrkkrphlkrpgk......ilvaiigalfllfllvalffppkgpatq 412
                                       +++l   i+++ ++r++ +++++p k      i+++i  al+llf+  a f+++++p+++
  gi|336253355|ref|YP_004596462.1|  50 IAVLveaILAYTVWRFRDNDEPEPTKenrqleITWTIATALVLLFVGTASFYVLAQPTVS 109
                                       333322377888999999999887777788889********************9999876 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.23      34      93 ..     152     210 ..     135     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                      Cupredoxin_1  34 PskievkagekvklkiknkdktpeefesedlgeekvlapgktttitiaplkpGeYeftcd 93 
                                        +++ +++++ + l i+ +d   +++ +++lg +++  pg+ + +  +p ++GeY+++c 
  gi|336253355|ref|YP_004596462.1| 152 SESLVLPENRTAYLYITSED-VIHSVHVPELGLKQDALPGQYNLLRTEPTEQGEYRLYCA 210
                                       57788999998888888776.469**********************************95 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   5.1   0.00029      0.65       9      74 ..       5      67 ..       1     103 [. 0.70
   2 ?    0.2   0.1      0.39   8.8e+02      12      29 ..      84     101 ..      71     117 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00029
                              TrbC  9 rrlllalalalvllllaspalAqaaggdpvetvlqnivdfltgplakviatiaiivaGimlafgrl 74
                                      rr+++ +a +++l+++a p  A a g + +++v+  +  +l   la +ia+++ ++++++++  r+
  gi|336253355|ref|YP_004596462.1|  5 RRTVVIVAFLAALAVAAVPTVAVA-G-SVTDQVIRRLNRQLLY-LAVPIAVLVEAILAYTVWRFRD 67
                                      445555555555555555555544.3.99**************.***************9986554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.39
                              TrbC  12 llalalalvllllaspal 29 
                                       ++ + ++++l++ + +++
  gi|336253355|ref|YP_004596462.1|  84 WTIATALVLLFVGTASFY 101
                                       333333333333333333 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   8.6    0.0031       6.9      77     168 ..       6     104 ..       1     112 [. 0.75
   2 ?    1.0   0.5      0.09     2e+02     255     283 ..      85     113 ..      77     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0031
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xx RF
                            CitMHS  77 llvlltallsafvsn.dgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraa.........ar 143
                                       ++v+++a+l+a++   +++v++ ++++  + +rl++  ++l++p+a+   +  a t +                 ++
  gi|336253355|ref|YP_004596462.1|   6 RTVVIVAFLAALAVAaVPTVAVAGSVTDQVIRRLNRQLLYLAVPIAVLVEAILAYTVWRFRD---NdepeptkenRQ 79 
                                       4677777777777666999**************8888888********99999999987762...244477777666 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 144 pglslpnllllalllvgllplvllf 168
                                       +  +++   +l+ll+vg + +++l+
  gi|336253355|ref|YP_004596462.1|  80 LEITWTIATALVLLFVGTASFYVLA 104
                                       6666666666777777766666665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.09
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 255 lgliallsafisnvavaalmapialgmap 283
                                       ++++al+ +f++++++++l  p + +++ 
  gi|336253355|ref|YP_004596462.1|  85 TIATALVLLFVGTASFYVLAQPTVSTVLD 113
                                       67788899999999999998888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      718  (0.0400469); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.37
# Mc/sec: 2129.23
//
Query:       gi|336253356|ref|YP_004596463.1|  [L=75]
Description: hypothetical protein Halxa_1957 [Halopiger xanaduensis SH-6]
Scores for 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   12.2   0.7       0.14   12.1   0.7    1.1  1  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   8.1e-06      0.14      72     119 ..      17      73 ..      10      75 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-06
                         RseC_MucC  72 llPllllilgallgsall.........gssellaalgallglvlgflivrllskrlk 119
                                       ++Pl++l  +a+l++a++         + + +l+++  +l+l+++++++r++++ ++
  gi|336253356|ref|YP_004596463.1|  17 AVPLVILAYFAVLFEAASpwsfdplpvVLTHTLTLFPLVLLLIATYVVARVIERDAA 73 
                                       69************************99999999999999999*******9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 606.03
//
Query:       gi|336253357|ref|YP_004596464.1|  [L=41]
Description: hypothetical protein Halxa_1958 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.091   12.4   0.3      0.094   12.4   0.3    1.2  1  Phage_holin_2_2  Phage holin T7 family, holin superfamily II


Domain annotation for each model (and alignments):
>> Phage_holin_2_2  Phage holin T7 family, holin superfamily II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   5.2e-06     0.094      30      47 ..      23      40 ..       3      41 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-06
                   Phage_holin_2_2 30 vlvatllYtVlQIGakvv 47
                                       lva+++Y+V+  Ga ++
  gi|336253357|ref|YP_004596464.1| 23 ALVAAIVYLVVFTGATIP 40
                                      58************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); 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: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 320.40
//
Query:       gi|336253358|ref|YP_004596465.1|  [L=326]
Description: formate/nitrite transporter [Halopiger xanaduensis SH-6]
Scores for 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-43  146.5  20.1    8.9e-43  146.3  20.1    1.0  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 !  146.3  20.1   4.9e-47   8.9e-43       1     236 []      53     289 ..      53     289 .. 0.91

  Alignments for each domain:
  == domain 1  score: 146.3 bits;  conditional E-value: 4.9e-47
                                       HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCTTCHHHHHHHHHCCCHHHHHHHHHT---C CS
                    Form_Nir_trans   1 eivekvvaagvkkaklsldklfllgilAGafigfgvllalvvaaalaesnpglakllgglvFpvGlilvvllgaeLf 77 
                                       ei++++vaa+ +++++ +++lf+++++AG+ i++ ++l++ ++ a      g a ++g+l++p+G+ +++++  +Lf
  gi|336253358|ref|YP_004596465.1|  53 EIFHRIVAAADDEITTGTRELFFSALAAGFAITLTFMLYASTTEA-----SGGAPIAGALLYPLGFAYIIIGDYQLF 124
                                       68899************************************9997.....58899********************** PP

                                       CCCCCHHHHHHCTTSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTGG....HHHHHHHHHCCCSS-HHHHHHHH CS
                    Form_Nir_trans  78 TgntllltlavlkkkvslkkllknwlvvllgNliGsllvalllvvlsgll....aekllsiaeaklslsfleaflrG 150
                                       T+ntl  ++ vl++ +s+ +ll +w+vvl+gN++G++l a++l+ ++g++     e ++ i+++ l++ ++ +f++G
  gi|336253358|ref|YP_004596465.1| 125 TENTLPPVALVLERLASVPALLTVWTVVLIGNFAGGALGAFFLA-STGVFsqdvMEVAVGISNSGLETAWWPTFFKG 200
                                       *****8888888***************************96555.777763444667777777777999******** PP

                                       HHHHHHHHHHHHHHCC-SSHHHHHHHHHHHHHHHHHCT---HHHHHHHHHHHHHH...SHHHHHHHCHHHHHHHHHH CS
                    Form_Nir_trans 151 ilCNwlVclavwlalaakdvigkilaiflpifafvasgfeHsvanmfliplglll...tvadfilknlipvtlGNiv 224
                                       i+++++V+  vwl +a++++i++++++++ ++a+ ++++ H+v+  + +++ ++     +a+  +  ++pv+lGN++
  gi|336253358|ref|YP_004596465.1| 201 IFAGLIVAGVVWLDYASQETIARLVLVYVAFLAIPLGNLYHVVVSATEVMFLVFRgevALATGAVEFVLPVLLGNTI 277
                                       ***********************************************999999656555677788899********* PP

                                       HHHCCHHHHHHH CS
                    Form_Nir_trans 225 GGallvgllyly 236
                                       GG++lv+++ ++
  gi|336253358|ref|YP_004596465.1| 278 GGVILVTVVNYF 289
                                       ********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2560.82
//
Query:       gi|336253359|ref|YP_004596466.1|  [L=150]
Description: OsmC family protein [Halopiger xanaduensis SH-6]
Scores for 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-23   82.0   0.1    2.1e-22   79.5   0.0    1.8  2  OsmC      OsmC-like protein


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.05   8.9e+02      40      66 ..      10      36 ..       4      39 .. 0.63
   2 !   79.5   0.0   1.1e-26   2.1e-22       1      98 [.      41     144 ..      41     146 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.05
                                      EEEEEEEECCECTCEEEEEEEEEEE-S CS
                              OsmC 40 veveaerdpegakgiteirlkvevkip 66
                                      vevea+r++ +   +t+  +++ ++ p
  gi|336253359|ref|YP_004596466.1| 10 VEVEADRETPTKSTVTARSFELVIDEP 36
                                      788888876644456666666666544 PP

  == domain 2  score: 79.5 bits;  conditional E-value: 1.1e-26
                                       TTXSSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECT........CEEEEEEEEEEE-SS-H CS
                              OsmC   1 gdgsgpsPeelllaalasCfaitlravakkkgikledleveveaerdpegak........giteirlkvevkipgad 69 
                                       g+++gp+P e+lla+ a+C+++t++ vak++ + ledle+e+++e+d e+++        g+ +i+++ +++++  d
  gi|336253359|ref|YP_004596466.1|  41 GQDDGPNPLEYLLAGQAGCLNVTASQVAKDMDLALEDLEIEISGEFDVETFQteqpddhtGVRNIEVRMDIEADA-D 116
                                       7899*******************************************99998*******************8665.5 PP

                                       ..HHHHHHHHHHHHHSHHHHHHCT-SSSE CS
                              OsmC  70 seeklkkllekaekrCpvsntlkngvkve 98 
                                        +e+l+++ e++ekrCpvsn +++++++ 
  gi|336253359|ref|YP_004596466.1| 117 -QETLEEFGERVEKRCPVSNNIAEATDIG 144
                                       .4*********************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1294.63
//
Query:       gi|336253360|ref|YP_004596467.1|  [L=484]
Description: dihydrolipoyl dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-50  169.6   0.3    1.3e-49  169.1   0.3    1.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    5.6e-23   81.3   0.2    9.5e-23   80.6   0.2    1.4  1  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
    3.6e-19   69.1   0.3      1e-14   54.8   0.0    2.7  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00013   21.3   0.0    0.00072   18.8   0.0    2.1  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
     0.0074   16.3   0.1      0.018   15.0   0.1    1.6  2  Gcw_chp        Bacterial protein of unknown function (Gcw_chp
  ------ inclusion threshold ------
      0.013   14.6   4.8      0.014   14.5   0.9    2.4  2  FAD_binding_2  FAD binding domain
      0.035   14.0   0.2        2.7    7.8   0.0    2.7  3  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.16   11.6   0.0       0.25   10.9   0.0    1.2  1  Bac_transf     Bacterial sugar transferase


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 !  169.1   0.3   5.6e-53   1.3e-49       2     283 ..       5     318 ..       4     331 .. 0.88

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 5.6e-53
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias.................. 57 
                                       d +viG+G  Gl++a  +a+ g  v++ve   l+gtcln+gc++sk ll  ae +e+++                  
  gi|336253360|ref|YP_004596467.1|   5 DFLVIGSGS-GLEVANVAANRGQSVAVVEkgrLGGTCLNRGCIPSKMLLYRAEVRETIErseafgidasvddvafad 80 
                                       789*****7.8*****************999*********************************************9 PP

                                       ......HHHHCHHHHCCCCHCCT.CEEEEESCEEEEETEEEC.....TCEEEEEESEEEE---EEE-BCTCTTC.TT CS
                                       ......xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ......evvkklnqgielllgee.vvkidpgkkkvklekkke.....gdeekiaydklvlAtGssprdlgipGvaen 122
                                             e v + + +i++ l+++   +++++++++++  + e      d+e++a++++++A G +p  ++++G+ e+
  gi|336253360|ref|YP_004596467.1|  81 ivrevnEDVAESSDSIRRGLESSsQHDLYRAEGRFVDDRTIElsggdRDGERLAAETVLVAAGTRPGVPPVEGL-EG 156
                                       99999955666666666666655578999999999997777799999999************************.55 PP

                                       BEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 123 vgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGve 199
                                       +    ++l+s eal+l+  p+++v+vGgGyi+ El  ++  +g++v ++ +r++ll+  d+e++++ +e++ ++  +
  gi|336253360|ref|YP_004596467.1| 157 A----DYLTSREALRLEAPPDHLVIVGGGYIAAELGHFFGTFGSDVSIIGRRPHLLPDADEEVAREFTERMAER-YD 228
                                       5....89*****************************************************************97.77 PP

                                       EEESCEEEEEEETTE..EEE....EEETTSCE..EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBES CS
                                       xxxxxxxxxxxxxxx..xxx....xxxxxxxx..xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 200 vklgtsvkeidgnge..kle....vvledgee..idadlvvvavGvrpstelle.eklglelderggivvdeflrtn 267
                                       v++g +++++ +      +e      +ed ++  ++ d ++va+G+ p+t++l+  ++g+e+d++g++++de+lrt+
  gi|336253360|ref|YP_004596467.1| 229 VYTGYEATAVSESAGkvTVEarpfPDDEDADRisVAGDELLVAAGRVPNTDTLNvSAAGIETDDQGFVETDEYLRTT 305
                                       7888888888877775533355544444444488999**************************************** PP

                                       STTEEE-GGGCTECCS CS
                                       xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 268 vpgiyaiGDvaggkgg 283
                                        +g++a+GD++   g 
  gi|336253360|ref|YP_004596467.1| 306 ADGVWALGDIV---GE 318
                                       **********9...33 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 !   80.6   0.2   4.2e-26   9.5e-23       2     109 ..     350     456 ..     349     457 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 4.2e-26
                                       EEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHH CS
                     Pyr_redox_dim   2 ptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqe 78 
                                       p +vf++peva vG te+e++aa  e+ + + ++++++r  a++ ++g+vK ++   +g++lG+hivGp+a+ li+e
  gi|336253360|ref|YP_004596467.1| 350 PFAVFSSPEVAGVGATEAELRAADREYATRTQRYEDTARGSAMK-AEGVVKPLVSL-EGEILGCHIVGPDASTLIEE 424
                                       789***************************************97.899***98888.8******************* PP

                                       HHHHHHTTS.BHHHHHTSBSSSSSTGGGGHCH CS
                     Pyr_redox_dim  79 lavaikagl.tvedladtihihPtlsealkea 109
                                       + va+kag  tv+d+ + ihihP lse+++ a
  gi|336253360|ref|YP_004596467.1| 425 VVVAMKAGSgTVRDIRESIHIHPALSEVVQRA 456
                                       *******976999**************99976 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.5   0.00018      0.41       3      30 ..       7      33 ..       5      37 .. 0.91
   2 !   54.8   0.0   4.7e-18     1e-14       1      77 [.     174     248 ..     174     256 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                      EEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvver 30
                                      +v+G+G +glE+A+++a+ g++V vve 
  gi|336253360|ref|YP_004596467.1|  7 LVIGSG-SGLEVANVAANRGQSVAVVEK 33
                                      799998.8******************97 PP

  == domain 2  score: 54.8 bits;  conditional E-value: 4.7e-18
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       ++v+vGgGyi+ El+ ++  +g++V+++ r+++ll+  Dee++++++e++ ++  +v+++ +++++ +s+ +v+ v+
  gi|336253360|ref|YP_004596467.1| 174 HLVIVGGGYIAAELGHFFGTFGSDVSIIGRRPHLLPDADEEVAREFTERMAER-YDVYTGYEATAVSESAGKVT-VE 248
                                       79**************************************************9.*************9999844.44 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 ?   -1.5   0.1      0.49   1.1e+03     192     217 ..       4      28 ..       1      32 [. 0.78
   2 !   18.8   0.0   3.2e-07   0.00072     141     241 ..     127     220 ..     110     235 .. 0.82
   3 ?   -2.5   0.0      0.94   2.1e+03     210     260 ..     320     373 ..     316     383 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.49
                       K_oxygenase 192 kriaVvGsGqSaaeifedllrrqkkv 217
                                        +++V+GsG S+ e+++ +++r ++v
  gi|336253360|ref|YP_004596467.1|   4 YDFLVIGSG-SGLEVANVAANRGQSV 28 
                                       67899***9.9999999998886654 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 3.2e-07
                       K_oxygenase 141 egeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkv 217
                                       + + e+l a++++++ Gt+p +P+v e leg ++ + s e+l+ +   + ++++++vG+G  aae+ +    ++  +
  gi|336253360|ref|YP_004596467.1| 127 DRDGERLAAETVLVAAGTRPGVPPV-EGLEG-ADYLTSREALRLE---APPDHLVIVGGGYIAAELGHFFG-TFG-S 196
                                       34567899***************96.67895.9999999999887...899**************976554.444.5 PP

                       K_oxygenase 218 elklvtrsealeplddspfvneif 241
                                       +++++ r+++l p  d +++ e++
  gi|336253360|ref|YP_004596467.1| 197 DVSIIGRRPHLLPDADEEVAREFT 220
                                       899999999999998888888766 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.94
                       K_oxygenase 210 llrrqkkvelklvtrs...ealeplddspfvneifsPeyvdyfyslpeekreal 260
                                       ll+++++ e + v+r+   + lep+d++ +   +fs+  v  + + ++e r a 
  gi|336253360|ref|YP_004596467.1| 320 LLKHSANHEAQAVARNlfgDDLEPVDYTAMPFAVFSSPEVAGVGATEAELRAAD 373
                                       666666677777777522267999999999999999888888877777777665 PP

>> Gcw_chp  Bacterial protein of unknown function (Gcw_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   8.2e-06     0.018      31     148 ..     174     306 ..     168     316 .. 0.79
   2 ?   -2.6   0.0         2   4.5e+03     125     177 ..     328     376 ..     310     378 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.2e-06
                           Gcw_chp  31 kpAiqggldvahesGfYaGvWassls............etaagyg........svElDvYgGykkevaigevtlDvG 87 
                                       ++ i gg  +a e G + G+++s +s            +                  DvY+Gy++  a++e +  v 
  gi|336253360|ref|YP_004596467.1| 174 HLVIVGGGYIAAELGHFFGTFGSDVSiigrrphllpdaD---EEVareftermAERYDVYTGYEA-TAVSESAGKVT 246
                                       566788888999**************9999999885441...333455666655668*******9.789999***** PP

                           Gcw_chp  88 vlqyiyPggenngapedynedttelyaglgykevtlkyaya.ptkdslGfdskdslYidldl 148
                                       v    +P+ e++++ +    d + ++ag  +++ tl+++ a ++ d  Gf ++d  Y+ +++
  gi|336253360|ref|YP_004596467.1| 247 VEARPFPDDEDADRIS-VAGDELLVAAGRVPNTDTLNVSAAgIETDDQGFVETD-EYLRTTA 306
                                       *************766.6667778888888888888887764677899987666.4777666 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                           Gcw_chp 125 yayaptkdslGfdskdslYidldldielpntgltllahvGyqdvknglseysy 177
                                        a a+ ++++G   +d   +d + +++++      +a+vG ++ ++   + +y
  gi|336253360|ref|YP_004596467.1| 328 EAQAVARNLFG---DDLEPVDYT-AMPFAVFSSPEVAGVGATEAELRAADREY 376
                                       56777788888...344444443.46777777788899999998888777777 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.9   6.4e-06     0.014       1      33 [.       5      36 ..       5      44 .. 0.91
   2 ?    0.8   0.0     0.088     2e+02     370     402 ..     282     316 ..     209     321 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.4e-06
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      D +ViGsG  GL  A  aa++G++vavvek+  
  gi|336253360|ref|YP_004596467.1|  5 DFLVIGSGS-GLEVANVAANRGQSVAVVEKGRL 36
                                      88******8.********************974 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.088
                                       EEES-EEEBETTSBE..STTEEESSBTEEE-STCE CS
                     FAD_binding_2 370 hytmgGvetdengrv..ldadgqpipGLYAaGeva 402
                                         +++G+etd++g v  ++   ++ +G +A G   
  gi|336253360|ref|YP_004596467.1| 282 NVSAAGIETDDQGFVetDEYLRTTADGVWALGDIV 316
                                       56789999999998855555678899999998765 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 ?    3.4   0.1     0.027        61       4      30 ..       8      33 ..       6      94 .. 0.84
   2 ?    7.8   0.0    0.0012       2.7       3      51 ..     176     224 ..     174     250 .. 0.83
   3 ?   -3.1   0.0       2.7     6e+03     131     161 ..     407     437 ..     363     443 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.027
                                      EE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdi 30
                                      viG+G  G ++a+v+a++g +V +v+ 
  gi|336253360|ref|YP_004596467.1|  8 VIGSGS-GLEVANVAANRGQSVAVVEK 33
                                      899998.****************9986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0012
                                       EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTT CS
                           3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklve 51 
                                        ++G G + a++ + f   g +V ++ ++++ l +a e++++++ + ++
  gi|336253360|ref|YP_004596467.1| 176 VIVGGGYIAAELGHFFGTFGSDVSIIGRRPHLLPDADEEVAREFTERMA 224
                                       69**********************************9999996655433 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.7
                                       GEEEEEE-SSTTT--EEEEEE-TT--HHHHH CS
                           3HCDH_N 131 rviglHFfnPpplmkLvEvvrgekTseetva 161
                                       +++g H + P     + Evv + k  + tv 
  gi|336253360|ref|YP_004596467.1| 407 EILGCHIVGPDASTLIEEVVVAMKAGSGTVR 437
                                       4556666666555555556666555555555 PP

>> Bac_transf  Bacterial sugar transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.25      92     160 ..     186     255 ..     184     272 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                        Bac_transf  92 ELPqlinVLkGdMslVGpRPelpeeve.eeieeyeee.eerlkvkPGltGlaqvnsgrselsleeklelDl 160
                                       EL  ++  + +d s++G RP+l+   + e ++e++e+ +er++v  G    a   ++ ++ ++e +   D 
  gi|336253360|ref|YP_004596467.1| 186 ELGHFFGTFGSDVSIIGRRPHLLPDADeEVAREFTERmAERYDVYTGYEATAVS-ESAGKVTVEARPFPDD 255
                                       8888999999***********988555355556666645889999998887766.4444466666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); 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:                         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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3523.31
//
Query:       gi|336253361|ref|YP_004596468.1|  [L=118]
Description: hypothetical protein Halxa_1963 [Halopiger xanaduensis SH-6]
Scores for 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-07   30.1   0.1    5.6e-07   29.9   0.1    1.0  1  DrsE            DsrE/DsrF-like family
  ------ inclusion threshold ------
      0.049   13.6   0.0      0.074   13.0   0.0    1.3  1  Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   6.2e-11   5.6e-07       8     117 .]      12     118 .]       4     118 .] 0.84

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 6.2e-11
                                       -S-TTTBSHHHHHHHHHHHHHTTT.-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHHHHHH CS
                              DrsE   8 tggpygseaarealelalaaaalg.hevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgqaaka 83 
                                       t++ +++ +   +le+a+  aa++  +++ +f g+G++++ +     + ++ ++++l++ ++++     vC  +a a
  gi|336253361|ref|YP_004596468.1|  12 TESHADTGRMVNGLEAAREFAANEeDDLEFIFDGAGTQWIAE----LEDEDHDYHDLYRSVQDE---ASVCDYCASA 81 
                                       44455666777778888888777789999*************....777899***********8...59******** PP

                                       TT--GGGE-.T-..-EEEE-HHHHHHHHHH-SEEEE- CS
                              DrsE  84 rgldededl.gv..gvevsglgelaelqnegdrvitf 117
                                       + +d++ +  g+    e  g +++  l+++ + +itf
  gi|336253361|ref|YP_004596468.1|  82 FDVDDAVEDqGIvrIDENEGHPSIRSLVSDDYEIITF 118
                                       ****88866545579999******************9 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.3e-06     0.074       6      37 ..      73     104 ..      69     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.3e-06
                                       EE-SSBTT--EEEEEEETTEEEEEEE-TTSTT CS
                    Molybdop_Fe4S4   6 taCpyCgvgCglevhvkdgkivkvegdpdhpv 37 
                                       ++C yC +   ++  v+d+ iv+++ ++ hp+
  gi|336253361|ref|YP_004596468.1|  73 SVCDYCASAFDVDDAVEDQGIVRIDENEGHPS 104
                                       9*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 874.98
//
Query:       gi|336253362|ref|YP_004596469.1|  [L=628]
Description: glycoside hydrolase 15-like protein [Halopiger xanaduensis SH-6]
Scores for 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  168.5   0.0    1.2e-44  152.9   0.0    2.0  2  Glyco_hydro_15  Glycosyl hydrolases family 15
  ------ inclusion threshold ------
      0.075   13.0   0.1       0.21   11.6   0.1    1.7  1  PepSY_2         Peptidase propeptide and YPEB domain
       0.64   10.8   8.0       0.31   11.8   0.2    3.7  3  TPR_4           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.9   0.0     2e-48   1.2e-44       6     350 ..     237     543 ..     232     552 .. 0.94
   2 !   13.9   0.0   2.9e-06     0.017     400     446 ..     552     598 ..     548     600 .. 0.89

  Alignments for each domain:
  == domain 1  score: 152.9 bits;  conditional E-value: 2e-48
                                       HHHHCBCSTTSSBTTS-TT-B-S-S-BSSS.........B--SEEHHHHHHHHHHHH.......HHHHHTTT-HCCH CS
                    Glyco_hydro_15   6 lylrnvktlilleqnpvtGlliASpstsdp.........DYrytWvRDsvyvilavwglgyrdedrakayeleqslv 73 
                                       +++r+   l+ll+    +G++ A+p+ts+p         DYr+ W+RD+ ++++a+++lg  de+  +  ++   ++
  gi|336253362|ref|YP_004596469.1| 237 AIVRSELVLKLLTHAE-SGGIAAAPTTSLPediggvrnwDYRFNWLRDAGFTVQALMNLGTADEATDYFDWFMDLCQ 312
                                       5555556666666665.9*********************************************************** PP

                                       HHHHHHHHHHHHHCTS-BTTB-TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHHHCTTHCHCCCCH CS
                    Glyco_hydro_15  74 klmrglleamvrqagkvekfketqstkgLhakyftktgstvvGddewghlQlDatslyllalaqmtasglqiistld 150
                                             ++  +  +g+  +++e++++   h +++ ++ ++++G+ + ++ Q D+ ++ lla+ +m   g ++  + +
  gi|336253362|ref|YP_004596469.1| 313 VDDPASIQPLYGLHGD-SDLEERELD---HFEGYRGSSPVRIGNGAADQRQHDTFGELLLAVDEMRRHGRELDADEW 385
                                       99999**********9.88999****...*********************************************999 PP

                                       HHHTHHHHHHHHHHHTTS-EE-TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHST CS
                    Glyco_hydro_15 151 evafvqnlvdYieaayktpdfglWEenqgeselnassvgmakAlleaideadlfgakgdaqlvektkdeilnklqgk 227
                                           ++ +vdY+ + ++ pd g+WE+++g + ++ s+++ ++Al++++++a++ + ++ a+ ++ t++ i  +    
  gi|336253362|ref|YP_004596469.1| 386 DR--IRAIVDYVSEIWTDPDAGIWEVRGGDRRFVFSKAMCWAALDRGLAIATDGDHDAPAEAWQATRERIRADA--- 457
                                       99..*******************************************************************999... PP

                                       TT..GGGEETTCCECECSCH.....HHHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHH CS
                    Glyco_hydro_15 228 ygckrgfwplfntylildgsfaedkeqvqeyrealdasllllpelyfvpaddvdeeyqnpqsprllaqslyildsll 304
                                          + g++ + + +++ +gs             alda  lllp+++f p++d          +r+ +++ +i+d+l 
  gi|336253362|ref|YP_004596469.1| 458 --LENGYDADLGAFVQSYGS------------TALDATALLLPIVGFLPFED----------DRVQGTIEAIDDRLV 510
                                       ..99****************............********************..........*************** PP

                                       HHSGGGTT-STTS--SBTT--CGSSSBSCT--BHHHHHHHHHHHHH CS
                    Glyco_hydro_15 305 segflavgeldplvrRysedvkpdklglsGrpyylctlwtvetlld 350
                                       ++g    g     v Ry  d   d+l ++++++ lc++w    l d
  gi|336253362|ref|YP_004596469.1| 511 DDGD---GI---FVQRYDGD---DGLPGEEGAFVLCSCW----LID 543
                                       **98...54...489**999...689*************....333 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.9e-06
                                       HHHHHHHHHHHHHS-TTS---SEE-TTT--EESSTT-HHHHHHHHHH CS
                    Glyco_hydro_15 400 eeladliveaveednslgvLteevdvylgeliraqpllfsealllri 446
                                       ee +  + +     n lg+++ee+d ++g  ++++p++fs++ +++ 
  gi|336253362|ref|YP_004596469.1| 552 EEARARFETLLSYLNPLGLIAEELDSESGAHLGNFPQAFSHVGIVNS 598
                                       6777888888888999**************************99875 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.4e-05      0.21       8      46 ..     422     464 ..     416     467 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.4e-05
                           PepSY_2   8 lalla...aaAlAgrrdtdspkadwl.preklvakleaqGykv 46 
                                       ++ +a   ++A+A + d d+p + w+ +re ++a + ++Gy+ 
  gi|336253362|ref|YP_004596469.1| 422 MCWAAldrGLAIATDGDHDAPAEAWQaTRERIRADALENGYDA 464
                                       4555555699****************99*************86 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   1.5      0.23   1.4e+03       2      19 ..     424     441 ..     424     447 .. 0.92
   2 ?   11.8   0.2   5.1e-05      0.31       6      25 ..     540     559 ..     536     560 .. 0.90
   3 ?   -2.4   0.0       1.9   1.1e+04      12      20 ..     581     589 ..     581     589 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.23
                             TPR_4   2 rallaLArallalGdlde 19 
                                       +a+l+++ a +  Gd+d+
  gi|336253362|ref|YP_004596469.1| 424 WAALDRGLAIATDGDHDA 441
                                       899*************96 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.1e-05
                             TPR_4   6 aLArallalGdldeAralle 25 
                                       +L  al++ G+l+eAra +e
  gi|336253362|ref|YP_004596469.1| 540 WLIDALALSGRLEEARARFE 559
                                       7889*************987 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.9
                             TPR_4  12 lalGdldeA 20 
                                       ++lG++++A
  gi|336253362|ref|YP_004596469.1| 581 AHLGNFPQA 589
                                       689****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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 0.24s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 4821.71
//
Query:       gi|336253363|ref|YP_004596470.1|  [L=286]
Description: alpha/beta hydrolase fold protein [Halopiger xanaduensis SH-6]
Scores for complete 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   90.2   0.2    1.4e-20   74.0   0.1    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
      1e-19   72.0   1.2    1.3e-19   71.7   1.2    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    5.3e-12   45.5   0.1    5.6e-11   42.2   0.1    2.0  1  Hydrolase_4    Serine aminopeptidase, S33
    9.7e-05   21.2   0.0    0.00015   20.6   0.0    1.2  1  Ndr            Ndr family
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.26   11.4   0.0    1.6  1  Abhydrolase_4  TAP-like protein


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 !   74.0   0.1   3.9e-24   1.4e-20       2     107 ..      42     151 ..      41     192 .. 0.84
   2 !   14.8   0.0   4.7e-06     0.017     207     256 ..     223     272 ..     164     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 3.9e-24
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       ++v++hG+p ss +w+    ap L + + +vi++D+ G+g S  +      d ++ + ++++d++l+ lg++ ++ v
  gi|336253363|ref|YP_004596470.1|  42 PVVFCHGIPTSSFLWRH--AAPELTD-DRRVIAPDMVGYGNSAMHDG---FDRSIRAQEAMIDALLAELGLETVAFV 112
                                       8****************..******9.***************77777...8889999******************** PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESE..........C CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllga..........i 107
                                       Gh++GG ++l yaa  pe V++lvl +a          i
  gi|336253363|ref|YP_004596470.1| 113 GHDLGGGVGLRYAAHEPEAVSKLVLSNAvcydswpvesI 151
                                       ****************************88755554441 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.7e-06
                                       THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                     Abhydrolase_1 207 lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafleg 256
                                         +++a tl+++g++D   p+++ e+l+++++ +++v ++ a H++  ++
  gi|336253363|ref|YP_004596470.1| 223 SAEITAETLLLWGAEDEFQPIEYAERLEEDISTAEVVGLEEANHWVPEDR 272
                                       478999***************************************98776 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   1.2   3.6e-23   1.3e-19       1     220 []      43     279 ..      43     279 .. 0.66

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 3.6e-23
                                       EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH.CHHHHHHHCCTT....TTSEEEEEETC CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldled.ladlaalldelaa..gggpvvlvGHSl 74 
                                       v+++HG ++s+  W+  + a+ l+++ +v+apD  G+G ++ +++++++ +++++a++d+l a  g   v  vGH+l
  gi|336253363|ref|YP_004596470.1|  43 VVFCHGIPTSSFLWR--HAAPELTDDRRVIAPDMVGYG-NSAMHDGFDRsIRAQEAMIDALLAelGLETVAFVGHDL 116
                                       8********999996..666666999888*********.99***99999656668888888777789999******* PP

                                       HHHHHHHHHHCC....EE.EEES-..----TTT..............S----TTHHHHHHTT-CCCCH.CCH...S- CS
                     Abhydrolase_6  75 GGalalaaapla..lvvg.vlldppptalpagl..............laaalelllallallrllawl.sre...pl 130
                                       GG ++l++a++    v++ vl ++   ++ +++              +++ +  l+  l+      ++ +     ++
  gi|336253363|ref|YP_004596470.1| 117 GGGVGLRYAAHEpeAVSKlVLSNA---VCYDSWpvesilelglpdvvADMSVDDLQDMLR----KLYRnT-LygdDP 185
                                       *******55555774444777777...666666544232211111112222222221111....222211.012233 PP

                                       HSCCCCHHHCCCCHCHCCCGHHHHCCHHCHTT....CCHHTT-TTGCEEEC.TT-CHHH.HCHHCCCH..STTEEET CS
                     Abhydrolase_6 131 prlfladedadaawrarlarlaallaglgllp....aaawadlpvpllvlg.geDplvp.rllerlla..qagarlp 199
                                       +++f++++   a+w    a  + ++++ g+++      + a +++ +l+l+ +eD+  p + ++++l   +  a++ 
  gi|336253363|ref|YP_004596470.1| 186 DEEFVDGMI--APWDSQEAKISLSRNAIGTNTshtaEIDSAEITAETLLLWgAEDEFQPiE-YAERLEedISTAEV- 258
                                       336666555..88888888888888877766433223455555555577764778866633.44444458899999. PP

                                       CE...SSS-HHHHSHHHHHHH CS
                     Abhydrolase_6 200 vvlpgaGHlphleepdevaea 220
                                       v l+ a H++ +++p+++ae+
  gi|336253363|ref|YP_004596470.1| 259 VGLEEANHWVPEDRPEAYAER 279
                                       ******************985 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.1   1.6e-14   5.6e-11       7     218 ..      43     254 ..      38     272 .. 0.71

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.6e-14
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGh 83 
                                       vv++HG+  +s    + a +L++ +  v+a D  G+G+s+ + g    fd+ ++  +a+++++ +e + + +  +Gh
  gi|336253363|ref|YP_004596470.1|  43 VVFCHGIPTSSFLWRHAAPELTD-DRRVIAPDMVGYGNSAMHDG----FDRSIRAQEAMIDALLAELGLETVAFVGH 114
                                       9********************86.799************66666....***************************** PP

                       Hydrolase_4  84 SmGGliallyllrypdkvaglilsaPalkikaklkappllklllkllgkllpklqv...........snnlkadsls 149
                                        +GG + l+y++++p+ v++l+ls++++   +++   ++l+l    l  ++ +++v            n        
  gi|336253363|ref|YP_004596470.1| 115 DLGGGVGLRYAAHEPEAVSKLVLSNAVCYDSWPV--ESILEL---GLPDVVADMSVddlqdmlrklyRN--TLYGDD 184
                                       ****************************988774..444444...333333333332222233221111..111112 PP

                       Hydrolase_4 150 rdpevvaayeadplv.hgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlg 218
                                        d+e+v+ + a       ki+++  +  +++  ++e + a+it+ +lll G++D+  + e +++l e ++
  gi|336253363|ref|YP_004596470.1| 185 PDEEFVDGMIAPWDSqEAKISLSRNAIGTNTSHTAEIDSAEITAETLLLWGAEDEFQPIEYAERLEEDIS 254
                                       3455566555555555555555555556666666666667777777777777777766666666666555 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   4.1e-08   0.00015      87     276 ..      95     284 ..      71     285 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.1e-08
                                       TTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---S---HHHHHHH....HHH.......TTTS CS
                               Ndr  87 dqllavldhfklksviglGvgaGAyilarfalkhperveglvLinitskaagwvewake....Klsskllkkvgltd 159
                                        ++ a+l  + l++v  +G   G  + +r+a++ pe v+ lvL n+ +  +  ve++ e     ++   +  + l d
  gi|336253363|ref|YP_004596470.1|  95 AMIDALLAELGLETVAFVGHDLGGGVGLRYAAHEPEAVSKLVLSNAVCYDSWPVESILElglpDVV-ADMSVDDLQD 170
                                       68999******************************************9875445555440000444.2444444444 PP

                                       -HHHHHHHHHS-HHHHHHT-HHHHHHHHHHHT-TTHHHHHHHHHHHHT-------TTSSSS-EEEEEETTSTTHHHH CS
                               Ndr 160 llkdlllahkFgkeeksensdlvreyrkllkerlnsknlelyleaynkRrdleierkklevkvllvvGdkspfvdev 236
                                       +l  l  + ++g +    +++ v       +++  + +l++     n  +  ei+  + + ++ll+ G++  f+   
  gi|336253363|ref|YP_004596470.1| 171 MLRKLYRNTLYGDDP---DEEFVDGMIAPWDSQEAKISLSRNAIGTNTSHTAEIDSAEITAETLLLWGAEDEFQPIE 244
                                       444444444555444...45688888899999999999999888888888888888888899******999997644 PP

                                       HHHHHHS-TTTEEEEEETT-TT-HHHH-HHHHHHHHHHHH CS
                               Ndr 237 vevnskldkkkttllkvadsgglvleeqPdklaeslklfl 276
                                       +  + + d ++++++ ++++   v e++P++ ae l  fl
  gi|336253363|ref|YP_004596470.1| 245 YAERLEEDISTAEVVGLEEANHWVPEDRPEAYAERLAAFL 284
                                       44444444556778999999999*********99999997 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.2e-05      0.26      23      92 ..     218     285 ..     200     286 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.2e-05
                     Abhydrolase_4  23 qrprdestakgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLl 92 
                                       ++++d+++   +a++Lll +  D   P e a++l + +  a++v  e++ H + ++  ++  + ++a+L+
  gi|336253363|ref|YP_004596470.1| 218 TAEIDSAE--ITAETLLLWGAEDEFQPIEYAERLEEDISTAEVVGLEEANHWVPEDRPEAYAERLAAFLA 285
                                       33333333..3799*************************************9988888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2259.94
//
Query:       gi|336253364|ref|YP_004596471.1|  [L=88]
Description: PaaX domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-07   30.6   0.0    2.8e-07   30.0   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    4.8e-07   29.6   0.3      7e-07   29.1   0.3    1.2  1  MarR_2          MarR family
    1.3e-06   28.2   0.0    1.6e-06   27.9   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
    3.6e-05   23.7   0.2    6.7e-05   22.9   0.1    1.5  1  HTH_20          Helix-turn-helix domain
    4.1e-05   23.7   0.1    5.2e-05   23.4   0.1    1.2  1  PaaX            PaaX-like protein
    4.3e-05   23.3   0.0    5.1e-05   23.1   0.0    1.1  1  TFIIE_alpha     TFIIE alpha subunit
     0.0001   21.9   0.2    0.00013   21.5   0.2    1.2  1  GntR            Bacterial regulatory proteins, gntR family
    0.00012   22.4   0.0    0.00015   22.2   0.0    1.1  1  HTH_27          Winged helix DNA-binding domain
    0.00026   20.9   0.0     0.0003   20.7   0.0    1.2  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00044   20.1   0.0    0.00096   19.1   0.0    1.5  2  PadR            Transcriptional regulator PadR-like family
    0.00045   20.5   0.0    0.00066   20.0   0.0    1.2  1  Rrf2            Transcriptional regulator
    0.00065   19.8   0.0     0.0007   19.7   0.0    1.0  1  Replic_Relax    Replication-relaxation
    0.00089   19.3   0.0     0.0018   18.3   0.0    1.5  1  HTH_28          Helix-turn-helix domain
     0.0018   18.1   0.0     0.0025   17.6   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0019   18.0   0.2     0.0029   17.4   0.2    1.4  1  HTH_IclR        IclR helix-turn-helix domain
     0.0028   17.5   0.0     0.0041   17.0   0.0    1.2  1  HTH_11          HTH domain
     0.0035   17.1   0.0      0.005   16.6   0.0    1.3  1  HTH_23          Homeodomain-like domain
     0.0037   17.1   0.3     0.0095   15.7   0.1    1.8  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
     0.0038   16.7   0.0     0.0066   15.9   0.0    1.5  1  Sigma70_r4      Sigma-70, region 4
      0.005   16.8   0.0     0.0057   16.6   0.0    1.2  1  HTH_43          Winged helix-turn helix
     0.0055   16.3   0.0      0.007   16.0   0.0    1.3  1  Sigma70_r4_2    Sigma-70, region 4
     0.0099   15.4   0.0      0.013   15.0   0.0    1.1  1  HTH_CodY        CodY helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.013   15.5   0.0    1.3  1  HTH_29          Winged helix-turn helix
      0.013   15.5   0.0      0.017   15.2   0.0    1.1  1  HTH_Mga         M protein trans-acting positive regulator (MG
      0.015   15.1   0.0      0.017   14.9   0.0    1.1  1  HxlR            HxlR-like helix-turn-helix
      0.022   14.7   0.0      0.026   14.4   0.0    1.2  1  MarR            MarR family
      0.028   14.0   0.0      0.037   13.6   0.0    1.2  1  HTH_47          winged helix-turn-helix
      0.034   14.2   0.0      0.057   13.5   0.0    1.4  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
      0.045   13.7   0.0      0.057   13.4   0.0    1.1  1  Cdc6_C          CDC6, C terminal winged helix domain
      0.067   13.3   0.0      0.077   13.1   0.0    1.1  1  HTH_54          ParA helix turn helix domain
      0.076   13.1   0.0       0.16   12.1   0.0    1.6  2  DUF2250         Uncharacterized protein conserved in archaea 
      0.084   12.8   0.0        0.3   11.1   0.0    1.9  1  HTH_36          Helix-turn-helix domain
       0.14   12.3   0.0       0.32   11.2   0.0    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
        0.2   10.0   0.0        0.2   10.0   0.0    1.1  1  DUF505          Protein of unknown function (DUF505)


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 !   30.0   0.0   5.2e-10   2.8e-07      10      48 .]      19      57 ..      15      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5.2e-10
                            HTH_24 10 elLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++L+ +++++q+e+Ae++ l++ tv+  l rL ++Gl++
  gi|336253364|ref|YP_004596471.1| 19 KALEYDGSLTQAEIAEETLLPRRTVRDALSRLNDAGLVE 57
                                      68999********************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.3   1.3e-09     7e-07      14      61 ..      21      66 ..       6      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.3e-09
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      L   +   lt++e+a+++ l++ +v  +l rL +aGLve r + +D+R
  gi|336253364|ref|YP_004596471.1| 21 LEYDGS--LTQAEIAEETLLPRRTVRDALSRLNDAGLVEGRVSFRDAR 66
                                      444444..*******************************998888888 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   3.1e-09   1.6e-06      13      55 ..      17      59 ..      14      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.1e-09
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      v++aL   g++t  eiaee+ +pr +v ++L++L d+GlVe +
  gi|336253364|ref|YP_004596471.1| 17 VFKALEYDGSLTQAEIAEETLLPRRTVRDALSRLNDAGLVEGR 59
                                      78899999********************************965 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   1.3e-07   6.7e-05      15      60 ..      17      62 ..       8      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.3e-07
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      +++aL  ++ lt +e+ae+  l++ t+++ L  L +agLve++ ++
  gi|336253364|ref|YP_004596471.1| 17 VFKALEYDGSLTQAEIAEETLLPRRTVRDALSRLNDAGLVEGRVSF 62
                                      79999**************99*********************9776 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   9.9e-08   5.2e-05      37      70 .]      40      76 ..      25      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 9.9e-08
                              PaaX 37 eslvRaalsRlakaGwlvre...kegrrsfYrLsdkg 70
                                       ++vR alsRl+ aG++ +    +++r+s+Y+L+d g
  gi|336253364|ref|YP_004596471.1| 40 RRTVRDALSRLNDAGLVEGRvsfRDARQSVYSLTDDG 76
                                      589**************75433499*********976 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   9.7e-08   5.1e-05      14      70 ..      13      70 ..       7      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 9.7e-08
                                      HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE.EETTTEEE CS
                       TFIIE_alpha 14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrr.rdeekswy 70
                                      +a+lv ++L  +g +t  ++a+e+ + +  +r +L rL +a+lv+ + + rd  +s+y
  gi|336253364|ref|YP_004596471.1| 13 SAKLVFKALEYDGSLTQAEIAEETLLPRRTVRDALSRLNDAGLVEGRVSfRDARQSVY 70
                                      6899****************************************98754366666666 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   2.5e-07   0.00013      17      55 ..      20      57 ..      13      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.5e-07
                                      SS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR 17 elrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                       l+    L ++ e+a+e    r tvR AL+rL  +glve
  gi|336253364|ref|YP_004596471.1| 20 ALEYDGSL-TQAEIAEETLLPRRTVRDALSRLNDAGLVE 57
                                      56667789.9****************************8 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 !   22.2   0.0   2.8e-07   0.00015      14      68 .]      22      76 ..      10      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.8e-07
                            HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      + ++  ++a++++ + +   ++  +l++L  +GLve   + +d r++ ++lTd G
  gi|336253364|ref|YP_004596471.1| 22 EYDGSLTQAEIAEETLLPRRTVRDALSRLNDAGLVEGRVSFRDARQSVYSLTDDG 76
                                      57888999***************************999999************98 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 !   20.7   0.0   5.8e-07    0.0003      21      59 ..      26      62 ..       6      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.8e-07
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrriri 59
                                      +ltq+e+A+   l r tv  +ls+L ++gl++ +  +  
  gi|336253364|ref|YP_004596471.1| 26 SLTQAEIAEETLLPRRTVRDALSRLNDAGLVEGR--VSF 62
                                      79*****************************943..444 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.9   2.6e+03      38      57 ..      18      37 ..      17      44 .. 0.64
   2 !   19.1   0.0   1.8e-06   0.00096      36      72 ..      45      79 ..      31      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.9
                                      HHHHHHTTSEEEEEE-STSS CS
                              PadR 38 LkrLekeglveseweesgeg 57
                                      +k Le +g +++ +  +++ 
  gi|336253364|ref|YP_004596471.1| 18 FKALEYDGSLTQAEIAEETL 37
                                      56788888888776555444 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.8e-06
                                      HHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                              PadR 36 paLkrLekeglveseweesgegpprkyYrlTdaGrre 72
                                      +aL+rL + glve++ +   ++ +  +Y lTd+G+r+
  gi|336253364|ref|YP_004596471.1| 45 DALSRLNDAGLVEGRVSF--RDARQSVYSLTDDGERA 79
                                      79*************886..689999********986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.3e-06   0.00066      18      57 ..      20      58 ..      14      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.3e-06
                                      HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      a+e++++ ++ +eiae++ ++++ ++  l++L+ aglv+ 
  gi|336253364|ref|YP_004596471.1| 20 ALEYDGS-LTQAEIAEETLLPRRTVRDALSRLNDAGLVEG 58
                                      5566655.******************************85 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.3e-06    0.0007       2      74 ..      19      85 ..      18      88 .] 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-06
                      Replic_Relax  2 rlLaehrvlTtrqiarllfashratarrrLarLrelgllsr.lrkrvggarggsepyvYaLtpkGarllaaqra 74
                                      + L++ + lT + ia+ +   +r+ +r++L rL++ gl++  +  r +      ++ vY Lt  G+r+ ++ ++
  gi|336253364|ref|YP_004596471.1| 19 KALEYDGSLTQAEIAEETLLPRRT-VRDALSRLNDAGLVEGrVSFR-DA-----RQSVYSLTDDGERATPTAAD 85
                                      667888899********9999999.***************956666.22.....356**********9977654 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.4e-06    0.0018      11      41 ..      24      55 ..      15      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.4e-06
                            HTH_28 11 aGh.svreaArelgisrrtvyrWikryeegGi 41
                                      +G  +++e+A+e  + rrtv++ ++r++  G+
  gi|336253364|ref|YP_004596471.1| 24 DGSlTQAEIAEETLLPRRTVRDALSRLNDAGL 55
                                      56679***********************9885 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 !   17.6   0.0   4.7e-06    0.0025      10      46 ..      20      57 ..      12      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.7e-06
                                      HHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 10 lLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +L+  g+l+  e+aee+ l++ tv+  L++L +aGLVe
  gi|336253364|ref|YP_004596471.1| 20 ALEYdGSLTQAEIAEETLLPRRTVRDALSRLNDAGLVE 57
                                      55556999*****************************7 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 !   17.4   0.2   5.4e-06    0.0029      15      49 ..      23      57 ..       5      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.4e-06
                                      TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                       ++ lt +e+A++t lp+ tv+  L+ L   G+ve
  gi|336253364|ref|YP_004596471.1| 23 YDGSLTQAEIAEETLLPRRTVRDALSRLNDAGLVE 57
                                      45669*****************************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   7.8e-06    0.0041       9      45 ..      21      55 ..      14      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.8e-06
                            HTH_11  9 LleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                      L e +g ++ +e+Aee+ + rrtvr  + +L+++g  
  gi|336253364|ref|YP_004596471.1| 21 L-EYDGSLTQAEIAEETLLPRRTVRDALSRLNDAG-L 55
                                      4.88999**************************99.3 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.6e-06     0.005      17      46 ..      26      55 ..      14      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.6e-06
                            HTH_23 17 GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                       l+++eIA+e   +rrTv+  l+r +  Gl
  gi|336253364|ref|YP_004596471.1| 26 SLTQAEIAEETLLPRRTVRDALSRLNDAGL 55
                                      5799********************998884 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 !   15.7   0.1   1.8e-05    0.0095      11      41 ..      20      50 ..      18      51 .. 0.94
   2 ?   -2.2   0.0       7.1   3.7e+03      14      18 ..      63      67 ..      57      70 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                     HTH_AsnC-type 11 aLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      aL+ d++++ ae+Ae++ l + tv+  + rL
  gi|336253364|ref|YP_004596471.1| 20 ALEYDGSLTQAEIAEETLLPRRTVRDALSRL 50
                                      89***********************999998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.1
                     HTH_AsnC-type 14 edaRi 18
                                      +daR 
  gi|336253364|ref|YP_004596471.1| 63 RDARQ 67
                                      45555 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.3e-05    0.0066      17      42 ..      23      48 ..       6      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                                      HTTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4 17 fgeglTleEIgerlgiSrerVrqiek 42
                                      ++  lT++EI+e+  ++r +Vr  ++
  gi|336253364|ref|YP_004596471.1| 23 YDGSLTQAEIAEETLLPRRTVRDALS 48
                                      6899******************7665 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0057      23      50 ..      29      56 ..      15      80 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHH---HHHHHHHHHGGGGGT-E CS
                            HTH_43 23 vpklieltgmPRRtlqDtlkalaeldie 50
                                        ++ e t +PRRt+ D+l+ l++ ++ 
  gi|336253364|ref|YP_004596471.1| 29 QAEIAEETLLPRRTVRDALSRLNDAGLV 56
                                      568999*****************98863 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 !   16.0   0.0   1.3e-05     0.007      25      49 ..      25      49 ..       5      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                                      S---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 25 eglsykEIAellgisegtVksrlsR 49
                                        l+++EIAe++ ++ +tV+ +lsR
  gi|336253364|ref|YP_004596471.1| 25 GSLTQAEIAEETLLPRRTVRDALSR 49
                                      458*****************99998 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 !   15.0   0.0   2.6e-05     0.013       2      37 ..      24      59 ..      23      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-05
                          HTH_CodY  2 eGrLtaskiaDriGitrsvivnaLrkLesaGiiesr 37
                                      +G Lt ++ia++  + r  + +aL +L+ aG++e r
  gi|336253364|ref|YP_004596471.1| 24 DGSLTQAEIAEETLLPRRTVRDALSRLNDAGLVEGR 59
                                      699*******************************98 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   2.5e-05     0.013       9      41 ..      23      55 ..      20      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-05
                            HTH_29  9 aeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      ++G  t ++iA+ + l rrtv+++l r +  Gl
  gi|336253364|ref|YP_004596471.1| 23 YDGSLTQAEIAEETLLPRRTVRDALSRLNDAGL 55
                                      567779***********************9995 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 ?   15.2   0.0   3.1e-05     0.017      15      47 ..      21      53 ..      14      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-05
                           HTH_Mga 15 teneksltldelakeLglseltlqsdiseLnel 47
                                      +e+++slt  e+a+e+ l ++t+++ +s Ln++
  gi|336253364|ref|YP_004596471.1| 21 LEYDGSLTQAEIAEETLLPRRTVRDALSRLNDA 53
                                      7899***************************87 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.3e-05     0.017      17      74 ..      25      81 ..      14      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-05
                                      S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHH CS
                              HxlR 17 gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslep 74
                                      g+    e++++   +++++    L +L+  gl+e +v  +   +  Yslt+ G+  +p
  gi|336253364|ref|YP_004596471.1| 25 GSLTQAEIAEET-LLPRRTVRDALSRLNDAGLVEGRVSFRDARQSVYSLTDDGERATP 81
                                      666666777666.789999**********************************98776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.9e-05     0.026      12      58 ..      21      67 ..      10      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.9e-05
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                      l++ g+l+++e+a+   + + tv  +l rL ++Gl+e + s +D R+
  gi|336253364|ref|YP_004596471.1| 21 LEYDGSLTQAEIAEETLLPRRTVRDALSRLNDAGLVEGRVSFRDARQ 67
                                      778899******************************98888888775 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     7e-05     0.037      37      77 ..      18      57 ..       6      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-05
                                      HHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 37 lwvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                      ++ L + DG+ +  +iAe++ lp ++v +++ +L++agl++
  gi|336253364|ref|YP_004596471.1| 18 FKALEY-DGSLTQAEIAEETLLPRRTVRDALSRLNDAGLVE 57
                                      555665.9*******************************96 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00011     0.057      18      53 ..      17      52 ..      13      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                                      HHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHH CS
                             HTH_9 18 VvetLlrkgrltlrelvkktkLsldqVkksLvvLiq 53
                                      V + L   g lt  e++++t L+++ V+++L+ L  
  gi|336253364|ref|YP_004596471.1| 17 VFKALEYDGSLTQAEIAEETLLPRRTVRDALSRLND 52
                                      566677789**********************98865 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 ?   13.4   0.0   0.00011     0.057      37      77 ..      38      75 ..      28      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                                      --HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C 37 ltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77
                                      l +r+v+d ls+L++ g++e ++s    r  r++ +sL+ d
  gi|336253364|ref|YP_004596471.1| 38 LPRRTVRDALSRLNDAGLVEGRVS---FRDARQSVYSLTDD 75
                                      5689*******************9...67899999999766 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00015     0.077      19      67 ..      18      66 ..       6      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                            HTH_54 19 lkedeyyqtyskaalaklpklsrrkvdkavsemeaeGyefekkeagste 67
                                      +k+ ey  + ++a++a+++ l rr+v +a+s ++++G +  + +   ++
  gi|336253364|ref|YP_004596471.1| 18 FKALEYDGSLTQAEIAEETLLPRRTVRDALSRLNDAGLVEGRVSFRDAR 66
                                      6777888899***************************987766555554 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 ?   12.1   0.0   0.00031      0.16      27      53 ..      31      57 ..      10      69 .. 0.88
   2 ?   -1.5   0.0       5.3   2.8e+03      80      88 ..      70      78 ..      65      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00031
                           DUF2250 27 siakeleipleevrellkkLeelGLle 53
                                       ia+e+ +p+  vr++l +L+++GL+e
  gi|336253364|ref|YP_004596471.1| 31 EIAEETLLPRRTVRDALSRLNDAGLVE 57
                                      58999*********************9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.3
                           DUF2250 80 YrltreGel 88
                                      Y+lt++Ge 
  gi|336253364|ref|YP_004596471.1| 70 YSLTDDGER 78
                                      99**99996 PP

>> HTH_36  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   0.00056       0.3      27      55 .]      28      56 ..      11      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00056
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      +q+ +a+ + l ++Tv+ a+  L ++G++
  gi|336253364|ref|YP_004596471.1| 28 TQAEIAEETLLPRRTVRDALSRLNDAGLV 56
                                      699***********************985 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 ?   11.2   0.0    0.0006      0.32      13      53 ..      17      57 ..      10      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0006
                                      HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      ++++ e  +  +++++ae+      +V   l++L+++G+ve
  gi|336253364|ref|YP_004596471.1| 17 VFKALEYDGSLTQAEIAEETLLPRRTVRDALSRLNDAGLVE 57
                                      78888888889999*************************97 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00038       0.2     365     401 ..      42      80 ..      24      88 .] 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00038
                            DUF505 365 dlreaLysLesfeLiesev..eekgkevyvlTeyGekvl 401
                                       ++r aL +L+  +L+e +v   +  + vy+lT+ Ge+  
  gi|336253364|ref|YP_004596471.1|  42 TVRDALSRLNDAGLVEGRVsfRDARQSVYSLTDDGERAT 80 
                                       7899***************77667799*********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 708.27
//
Query:       gi|336253365|ref|YP_004596472.1|  [L=254]
Description: hypothetical protein Halxa_1968 [Halopiger xanaduensis SH-6]
Scores for 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  226.4   0.2      3e-67  226.1   0.2    1.0  1  DUF1028   Family of unknown function (DUF1028)


Domain annotation for each model (and alignments):
>> DUF1028  Family of unknown function (DUF1028)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.1   0.2   1.7e-71     3e-67       1     193 []       2     222 ..       2     222 .. 0.97

  Alignments for each domain:
  == domain 1  score: 226.1 bits;  conditional E-value: 1.7e-71
                                       EEEEEEE-T.......TT--EEEEEEESSS-HHHHHEEEETTTEEEEEESS--HHHHHHHHHHHHTT--HHHHHHHH CS
                           DUF1028   1 TfSivardp.......etgelGvAvaskslaVgalvpfaragvGavatQaltnpelgekglelleagasaeealeal 70 
                                       TfSi+++++       e++++GvAv++++++Vg+l+pfa+++ GavatQ+l+n++lg++g++++++g+++++aleal
  gi|336253365|ref|YP_004596472.1|   2 TFSICVHETyetpdgtEHERFGVAVTTRLPGVGTLCPFASEN-GAVATQSLVNVDLGRRGIQYIDDGLAVADALEAL 77 
                                       9*****99889999999*************************.********************************** PP

                                       HHT-TTGGG-EEEEEETTS-EEEEE-TTS-S-EEEE.ETTEEEEEES-S-TCHHHHHHHHH................ CS
                           DUF1028  71 laadegrelRQlavvdakgetaaftGeeclewaghrtgenyavaGNlLageevleamaeafea.............. 133
                                       l+ad+g+ +RQl+ vd  g+ +af+Geec++w ghr+g++++vaGN+L+ge+v++a+aea+ea              
  gi|336253365|ref|YP_004596472.1|  78 LNADDGAPQRQLHGVDSAGT-FAFSGEECVDWFGHREGDHFTVAGNMLTGEAVIDAVAEAYEAnavhettdpatgpa 153
                                       *******************9.****************************************99************** PP

                                       ........S-HHHHHHHHHHHHHHT-------...-EEEEEEEE.....TTEEEEEEEE--SS-HHHHH CS
                           DUF1028 134 .....tegepLaerLlaALeaGeaaGGDkrgr...qSAallVvr.esedeskpyvdLrvddhedpiaeL 193
                                            t+++pLaerL++AL+aG+ +GGDkr++   qSAa++V + es+d   py dLrvd++e+pia+L
  gi|336253365|ref|YP_004596472.1| 154 gvtedTDTDPLAERLIDALAAGHVEGGDKREElpiQSAAVVVEStESHDVVPPYNDLRVDATETPIADL 222
                                       **9765559*********************99999*********999999*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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 0.20s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2103.56
//
Query:       gi|336253366|ref|YP_004596473.1|  [L=120]
Description: hypothetical protein Halxa_1969 [Halopiger xanaduensis SH-6]
Scores for 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-16   59.3   2.3    3.3e-16   59.3   2.3    1.6  2  SepF      Cell division protein SepF
  ------ inclusion threshold ------
      0.034   13.3   0.3      0.041   13.0   0.3    1.2  1  Lar_N     Lactate racemase N-terminal domain
       0.07   13.4   1.4       0.15   12.3   1.2    1.7  1  Rx_N      Rx N-terminal domain


Domain annotation for each model (and alignments):
>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.46   2.8e+03      24      39 ..      19      34 ..      14      37 .. 0.76
   2 !   59.3   2.3   5.6e-20   3.3e-16       1      72 []      38     111 ..      38     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.46
                                      EEEEE-CCCTCHHHHH CS
                              SepF 24 iVilnledldkeeakr 39
                                       V lnl+d+  e+a  
  gi|336253366|ref|YP_004596473.1| 19 YVELNLDDVAAESADA 34
                                      6778999999988865 PP

  == domain 2  score: 59.3 bits;  conditional E-value: 5.6e-20
                                       EEEEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTC..HHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-TT-EE CS
                              SepF   1 vvvveprsfedaqeiadalkegkiVilnledldk..eeakrivdflsgvvyaldGdiqkvgkkvflitPknvdi 72 
                                       v ++e+ +  da +i+da+++g+iVi ++++l +  ++ ++ivd+l++v+ ++dGdi++ g++ ++itP++v++
  gi|336253366|ref|YP_004596473.1|  38 VHIAEVANQTDAIDIKDAVYDGDIVIADITRLRTedSTVEHIVDELRQVAREVDGDIVRKGDDQMIITPTGVRV 111
                                       67999***************************9988999*********************************87 PP

>> Lar_N  Lactate racemase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   6.9e-06     0.041      59      87 ..      61      88 ..      15      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-06
                             Lar_N 59 ivvsDiTRptpskiilpllleelkeagvk 87
                                      iv+ DiTR   ++ +++++++el++ +++
  gi|336253366|ref|YP_004596473.1| 61 IVIADITRLRTEDSTVEHIVDELRQ-VAR 88
                                      999*********************9.444 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.2   2.6e-05      0.15      25      69 ..      47      91 ..      23      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                              Rx_N 25 eeleklkdeLesiqavLedaeerqikdeavkeWlkelrdlaydae 69
                                       +   +kd     + v++d  + +++d++v++ ++elr++a +++
  gi|336253366|ref|YP_004596473.1| 47 TDAIDIKDAVYDGDIVIADITRLRTEDSTVEHIVDELRQVAREVD 91
                                      56667777777777899************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 883.35
//
Query:       gi|336253367|ref|YP_004596474.1|  [L=330]
Description: hypothetical protein Halxa_1970 [Halopiger xanaduensis SH-6]
Scores for 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   12.2   1.7       0.14   12.0   0.1    1.8  2  DUF2826   Protein of unknown function (DUF2826)
       0.19   11.2   2.1       0.36   10.3   2.1    1.4  1  MdcE      Malonate decarboxylase gamma subunit (MdcE)
        1.2    7.9   4.9       0.49    9.2   1.6    1.9  2  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> DUF2826  Protein of unknown function (DUF2826)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.4e-05      0.14     112     134 ..      73      95 ..      48     102 .. 0.89
   2 ?   -1.7   0.1      0.38   2.3e+03      98     131 ..     129     162 ..     118     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                           DUF2826 112 aplrwdmqgcglpltvlgtavwm 134
                                        +lrw +  c lp   lg+avw+
  gi|336253367|ref|YP_004596474.1|  73 GSLRWPIAVCCLPAVALGAAVWL 95 
                                       589*******************8 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.38
                           DUF2826  98 aqdsrvvlrladsqaplrwdmqgcglpltvlgta 131
                                       a+ds v   + d  a+  w++ g    l   g a
  gi|336253367|ref|YP_004596474.1| 129 ARDSDVDSVVGDPVASWTWELSGPDYTLLGWGLA 162
                                       7889999999999999999999987777666655 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.1   6.1e-05      0.36      94     123 ..      16      45 ..      12      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.1e-05
                                       HHHHHHHHHHHT--EEEEEEEEEEHHHHHH CS
                              MdcE  94 lakalarArlaGhpvigllvGkavsGafla 123
                                       +++a++ A l G   ++l+vG+a sGa+l+
  gi|336253367|ref|YP_004596474.1|  16 AVGAYIGALLTGVVALALVVGDASSGALLS 45 
                                       899*************************98 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.6   8.2e-05      0.49     136     191 ..      40      96 ..      15      98 .. 0.89
   2 ?   -0.8   0.1      0.09   5.4e+02       4      59 ..     113     168 ..     111     188 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 8.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHGGGS CS
                          Sugar_tr 136 RgalvslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllilllfl 191
                                        gal sl  +  t+G l++ai+ +   ++       r++++++++pa++l +++++l
  gi|336253367|ref|YP_004596474.1|  40 SGALLSLLPSVFTAGLLIGAIVAWSHpETAVRLGSLRWPIAVCCLPAVALGAAVWLL 96 
                                       799***********************666666889*************998887765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.09
                                       HHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHH CS
                          Sugar_tr   4 vaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGa 59 
                                       +aa+g +l g+ +g i+  + + +++ +  +s + +      +l+g+ +++f+vGa
  gi|336253367|ref|YP_004596474.1| 113 LAAVGATLAGWLLGAIARDSDVDSVVGDPVASWTWELSGPDYTLLGWGLACFVVGA 168
                                       56677777777777777666666666555544433333334456666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2550.62
//
Query:       gi|336253368|ref|YP_004596475.1|  [L=803]
Description: nitrite and sulfite reductase 4Fe-4S region [Halopiger xanaduensis SH-6]
Scores for 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-43  145.9   0.0    4.3e-36  123.8   0.0    2.4  2  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    1.6e-36  125.1   0.0    7.8e-17   61.7   0.0    2.5  2  Rhodanese     Rhodanese-like domain
    3.1e-32  110.2   4.7      1e-14   54.1   0.3    4.4  4  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
  ------ inclusion threshold ------
       0.21   11.7   0.6        2.7    8.1   0.0    2.5  2  DGC           DGC domain


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.0   9.6e-40   4.3e-36       2     155 ..     391     541 ..     390     545 .. 0.97
   2 !   19.7   0.0     1e-07   0.00047       5     151 ..     642     787 ..     639     793 .. 0.78

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 9.6e-40
                                       SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdeke 78 
                                       g+++rnv++cp++g+++++++D++++++++ +++ ++ ++ +lPrKfK++v+gc +nc++++++D+gl +  kd+ e
  gi|336253368|ref|YP_004596475.1| 391 GNSVRNVVGCPASGIDPDETVDVQPVVERVSQRFLGDHHYANLPRKFKVSVTGCHENCARAQIQDLGLTPARKDGRE 467
                                       899**********************************************************************9999 PP

                                       EEEEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  79 igfnilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekveeel 155
                                        gf   vGGgl+  ++ ++ +    fv++e+v ++v a+ ++++dhg   + +  Rl+ lve+lG e Fre++e++ 
  gi|336253368|ref|YP_004596475.1| 468 -GFVAQVGGGLSDGPRIASDID--LFVDPEDVDDLVAAMADLFMDHGSYLDTAVNRLRFLVEELGPETFREELETYA 541
                                       .**************9999999..7************************************************9986 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1e-07
                                       CCCCCCSTCCCTBSS-SS-T....HHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEE.EEETT CS
                                       xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                           NIR_SIR   5 lrnvtlcpgaglceeallDt....telakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvg.vkkde 76 
                                       +r +++c+g ++c   +++t     ++a++++ e  +e g  +     ++ +sgc   c++ +  D+gl g v++d+
  gi|336253368|ref|YP_004596475.1| 642 TRGIVTCTGREFCNYGIIETknraVKWARQLD-EWAEEVGIADDHDAIRVHMSGCAASCAQPQLGDFGLRGeVYRDD 717
                                       78999***************555556666666.77777888888888***********************9445555 PP

                                       CEE..EEEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHH CS
                                       xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  77 kei..gfnilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekv 151
                                        e    + + +GG lg ++     + + g +p e+v +v+ea v+ y+     + +  e ++++ +r+  + +re +
  gi|336253368|ref|YP_004596475.1| 718 FESgrAADMGLGGDLGDDQFI--DWLV-GKIPIEDVPSVIEATVQAYE----DDREPDESFAEWTNRTSNADLREII 787
                                       555667889999999987654..4554.89******************....6666667777777777666666655 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   3.3e-20   1.5e-16       1     106 [.       9     121 ..       9     122 .. 0.84
   2 !   61.7   0.0   1.7e-20   7.8e-17       9     106 ..     158     254 ..     151     255 .. 0.90

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 3.3e-20
                         Rhodanese   1 sakelkellekgkvallDvRppeeYek.ghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvy 72 
                                       s+++l+ ++++++v+++DvR++ +Y++ gh+pgAvnv+ + +++++ + a  l   +++++l    gi++++ vv +
  gi|336253368|ref|YP_004596475.1|   9 SPDWLETHRDDDGVVVVDVREARDYAElGHVPGAVNVPTEVFRDPSSVAAGKLPAADDFAALmreaGIREGDAVVAV 85 
                                       699**********9***********************7777777777777777777777777777************ PP

                         Rhodanese  73 cdgggraaaaaallkk..lGykn.vsvldGGfkawke 106
                                       +d +g  +aa  ll++  +G+   +++ldGG++aw e
  gi|336253368|ref|YP_004596475.1|  86 DDANGV-NAARFLLTAivYGHDGpLYLLDGGLEAWLE 121
                                       *99999.444334443449*8889***********87 PP

  == domain 2  score: 61.7 bits;  conditional E-value: 1.7e-20
                         Rhodanese   9 lekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaal 85 
                                        e ++ +++D+R+++eY+++hIpgAv + ++ l +++ + +p +el e l+++gi++++++v+yc+++ r + +   
  gi|336253368|ref|YP_004596475.1| 158 VEGDA-VVVDTRTAAEYDQSHIPGAVQLGWEDLLEESGRLKPEAELEELLADRGITRDERIVLYCNTARRLSHTFVV 233
                                       44444.49**************************************************************7777889 PP

                         Rhodanese  86 lkklGyknvsvldGGfkawke 106
                                       l+ lGy+nv +++G++++w +
  gi|336253368|ref|YP_004596475.1| 234 LRDLGYENVEFYEGSLTDWVR 254
                                       999**999***********86 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.3   2.3e-18     1e-14       3      66 ..     301     379 ..     299     382 .. 0.91
   2 ?   -2.0   0.1      0.75   3.4e+03      54      68 ..     491     505 ..     489     506 .. 0.86
   3 !   52.7   0.0   6.3e-18   2.8e-14       1      65 [.     566     628 ..     566     630 .. 0.94
   4 ?   -2.4   0.0         1   4.5e+03      25      38 ..     668     681 ..     656     684 .. 0.79

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.3e-18
                      NIR_SIR_ferr   3 qkdgkgyymvrlrvpnGritaeqlraladia................ekygsgeirlTtrQnlqlhgvpeedleeil 63 
                                       qk+  gy+m+r r p+G++taeq+r + ++a                  +g+g ++ TtrQ +q h+++ ed++ei+
  gi|336253368|ref|YP_004596475.1| 301 QKQ-RGYFMLRTRAPGGILTAEQARTIGEVAdefarapdeyggadqnPVFGDGFLDATTRQDIQMHWIEIEDVAEIW 376
                                       778.5777******************************99999976559**************************** PP

                      NIR_SIR_ferr  64 eeL 66 
                                       ++ 
  gi|336253368|ref|YP_004596475.1| 377 DRY 379
                                       985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.75
                      NIR_SIR_ferr  54 vpeedleeileeLae 68 
                                       v++ed++++ +++a+
  gi|336253368|ref|YP_004596475.1| 491 VDPEDVDDLVAAMAD 505
                                       899*******99975 PP

  == domain 3  score: 52.7 bits;  conditional E-value: 6.3e-18
                      NIR_SIR_ferr   1 hkqkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeilee 65 
                                       h+q dg    +v+l+vp Gr+  + l +la++a++ g ge+rlT++Qn++++++ ++dle  le+
  gi|336253368|ref|YP_004596475.1| 566 HEQADGR--SYVGLNVPTGRMGGDDLAELAALADELGGGELRLTPNQNVLVPHLGDDDLERFLEH 628
                                       7788887..88************************************************998875 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1
                      NIR_SIR_ferr  25 qlraladiaekygs 38 
                                        +r+l ++ae+ g+
  gi|336253368|ref|YP_004596475.1| 668 WARQLDEWAEEVGI 681
                                       579999***99885 PP

>> DGC  DGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0006       2.7      54      77 ..     439     462 ..     427     463 .. 0.89
   2 ?    0.7   0.2      0.12   5.5e+02      54      70 ..     690     706 ..     645     713 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0006
                               DGC  54 iaidGCpleCakkilekagvkpde 77 
                                       + + GC+ +Ca+  +++ g++p++
  gi|336253368|ref|YP_004596475.1| 439 VSVTGCHENCARAQIQDLGLTPAR 462
                                       7899**************999876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.12
                               DGC  54 iaidGCpleCakkilek 70 
                                       +   GC+ +Ca+  l +
  gi|336253368|ref|YP_004596475.1| 690 VHMSGCAASCAQPQLGD 706
                                       66789999999876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (803 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.39
# Mc/sec: 6203.26
//
Query:       gi|336253369|ref|YP_004596476.1|  [L=418]
Description: coenzyme F420 hydrogenase/dehydrogenase subunit beta domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-30  105.0   0.0    3.1e-30  105.0   0.0    1.9  1  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    2.5e-20   72.4   0.2    5.2e-20   71.4   0.2    1.5  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    9.4e-10   38.5   8.6    9.4e-10   38.5   8.6    1.6  1  Fer4_21      4Fe-4S dicluster domain
    1.8e-07   31.2  14.2    3.1e-07   30.4  12.5    2.3  2  Fer4_10      4Fe-4S dicluster domain
    3.8e-07   30.2   9.6    3.8e-07   30.2   9.6    2.0  2  Fer4_9       4Fe-4S dicluster domain
    3.9e-07   30.9   7.1      0.023   15.6   2.1    3.4  3  Fer4_16      4Fe-4S double cluster binding domain
    7.4e-07   29.6   2.4     0.0054   17.2   0.3    2.7  2  Fer4_17      4Fe-4S dicluster domain
    9.5e-07   29.3  22.5    4.5e-05   24.0  11.9    2.7  4  Fer4_7       4Fe-4S dicluster domain
    2.5e-06   27.0  18.2    0.00011   21.8   3.9    3.1  3  Fer4         4Fe-4S binding domain
    1.6e-05   25.0  17.6    0.00084   19.7   4.4    3.3  3  Fer4_4       4Fe-4S binding domain
    0.00055   20.1   2.0     0.0013   18.9   2.0    1.6  1  Fer4_18      4Fe-4S dicluster domain
    0.00059   19.8   4.7    0.00059   19.8   4.7    3.1  3  Fer4_6       4Fe-4S binding domain
     0.0008   19.4   3.8     0.0008   19.4   3.8    2.9  2  Fer4_2       4Fe-4S binding domain
     0.0023   18.4  12.2       0.58   10.7   5.8    3.1  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
     0.0043   16.8   0.6     0.0043   16.8   0.6    1.8  1  Fer4_20      Dihydroprymidine dehydrogenase domain II, 4Fe-4S
  ------ inclusion threshold ------
      0.011   16.5   9.4       0.28   12.0   0.9    3.7  3  Fer4_15      4Fe-4S single cluster domain
      0.025   15.0  14.2       0.49   10.9   4.0    2.7  3  Fer4_8       4Fe-4S dicluster domain
        3.4    8.8  20.9       0.22   12.6   4.4    2.9  2  Fer4_3       4Fe-4S binding domain
        7.6    7.5  17.6       0.77   10.6   2.7    2.7  3  Fer4_22      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.0   3.3e-33   3.1e-30       4     153 ..     211     355 ..     209     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 3.3e-33
                       FrhB_FdhB_C   4 vavvGtPCqiaalrklqk..kklkekilltiglfCggnfspealrklleelgvdpedvkklefrgkgkfrvelkd.. 76 
                                       +a+vGtPC i++  +l +  ++ ++ i+lt+ l+C+ +f++e l + +e+++vdpe v+kl++r  g + +   d  
  gi|336253369|ref|YP_004596476.1| 211 LALVGTPCVIQGATALDRygHEPADPIALTVALMCTRTFEHERLLSQIESYDVDPEAVEKLDIR-DGTLAAFDDDge 286
                                       799*****************99*****************************************8.666666444455 PP

                       FrhB_FdhB_C  77 .ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveageleleel 152
                                          e++++e++ +  ++C+ C d+++  ADis G+v      g +++g+stv+vrte+g++++++a++   le++e+
  gi|336253369|ref|YP_004596476.1| 287 iLLETDVEEFDAAGLRGCDECADFVGGAADISAGNV------G-SEDGYSTVVVRTENGRDVWREAADG--LETTEI 354
                                       544556679999************************......8.********************99666..676666 PP

                       FrhB_FdhB_C 153 d 153
                                       d
  gi|336253369|ref|YP_004596476.1| 355 D 355
                                       5 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 !   71.4   0.2   5.5e-23   5.2e-20       2      73 ..     121     192 ..     120     196 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 5.5e-23
                       FrhB_FdhB_N   2 vaArstdkeirkkaqsGGivtallkylLeegiidgvivvaps.kdpwrpkpviattkeellaaaGskYtlspn 73 
                                       +aAr+td      +q+GG+vtall++lL  g+idg++v+++s ++p+r ++++at+ ++ll+a Gs+Yt+++ 
  gi|336253369|ref|YP_004596476.1| 121 YAARATDA-AADAGQDGGAVTALLAELLAAGEIDGAVVARESeDEPLRGEAFLATSHADLLEAGGSIYTQTMG 192
                                       99*****8.89*******************************99*************************8765 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   8.6     1e-12   9.4e-10       1      52 [.      48      96 ..      48     100 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1e-12
                           Fer4_21  1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52
                                      A+i+ d+Ci+C +C+ aC+    + i ida+++ +++ + C+GC  C + CP
  gi|336253369|ref|YP_004596476.1| 48 AVIEADRCIQCASCVAACP---SDSIGIDAEEKRPTLVKMCTGCSRCWDFCP 96
                                      89*****************...699*************************** 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  12.5   3.3e-10   3.1e-07       2      56 .]      48      96 ..      47      96 .. 0.91
   2 ?   -1.2   0.0       2.5   2.3e+03      36      48 ..     295     307 ..     284     313 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.3e-10
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +vi++d+Ci+C+ Cv+aCP+       +  ++ ee+  + v+ Ctgc  C + CP
  gi|336253369|ref|YP_004596476.1| 48 AVIEADRCIQCASCVAACPS------DSIGIDAEEKRPTLVKMCTGCSRCWDFCP 96
                                      689*****************......67777778888889**************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.5
                           Fer4_10  36 eavrkkvekCtgc 48 
                                       e +  ++  C++c
  gi|336253369|ref|YP_004596476.1| 295 EFDAAGLRGCDEC 307
                                       5555566667777 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   9.6     4e-10   3.8e-07       1      49 [.      54      98 ..      54     100 .. 0.92
   2 ?   -2.0   0.0       4.5   4.2e+03      35      39 ..     303     307 ..     287     309 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                      +C++C +Cv+aCp++ +  da e+   l +     C+gC +C + Cp+ 
  gi|336253369|ref|YP_004596476.1| 54 RCIQCASCVAACPSDSIGIDAEEKRPTLVK----MCTGCSRCWDFCPRS 98
                                      6********************999999977....4************94 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.5
                            Fer4_9  35 aCigC 39 
                                        C +C
  gi|336253369|ref|YP_004596476.1| 303 GCDEC 307
                                       34444 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 !   15.6   2.1   2.5e-05     0.023       1      22 [.      54      75 ..      54      82 .. 0.84
   2 !   14.6   0.1   5.1e-05     0.048       2      24 ..      85     107 ..      84     136 .. 0.70
   3 ?    1.3   0.0      0.72   6.8e+02      51      62 ..     298     309 ..     264     310 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekke 22
                                      rC++C  C+ +CP++ i  ++e
  gi|336253369|ref|YP_004596476.1| 54 RCIQCASCVAACPSDSIGIDAE 75
                                      6***************987744 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.1e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekkeke 24 
                                       C++C +C + CP + ++ +++ e
  gi|336253369|ref|YP_004596476.1|  85 CTGCSRCWDFCPRSGLRYERALE 107
                                       *************9999883333 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.72
                           Fer4_16  51 qeaitgCdiCqd 62 
                                       +  + gCd C+d
  gi|336253369|ref|YP_004596476.1| 298 AAGLRGCDECAD 309
                                       455689****87 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   5.8e-06    0.0054      41      59 ..      50      68 ..      26      70 .. 0.82
   2 !   11.5   0.1   0.00037      0.35       2      14 ..      85      97 ..      71     136 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.8e-06
                           Fer4_17 41 ekaslCieCgeCerkCPqg 59
                                       +a++Ci+C  C+++CP++
  gi|336253369|ref|YP_004596476.1| 50 IEADRCIQCASCVAACPSD 68
                                      5799*************86 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00037
                           Fer4_17  2 CiqCgyClpeCps 14
                                      C++C+ C + Cp+
  gi|336253369|ref|YP_004596476.1| 85 CTGCSRCWDFCPR 97
                                      6666666666665 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   2.8   1.7e-06    0.0016      29      51 ..      46      68 ..      24      69 .. 0.72
   2 !   24.0  11.9   4.8e-08   4.5e-05       1      50 [.      54      97 ..      54      98 .. 0.86
   3 !   12.0   1.2   0.00025      0.24       2      20 ..      85     103 ..      84     129 .. 0.80
   4 ?   -1.8   0.0       5.1   4.9e+03       4       9 ..     303     308 ..     288     310 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-06
                            Fer4_7 29 ekveidpekClgCgaCvavCPtg 51
                                      ++++i++++C++C +Cva+CP++
  gi|336253369|ref|YP_004596476.1| 46 DEAVIEADRCIQCASCVAACPSD 68
                                      6679999*************986 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 4.8e-08
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50
                                      rCi+C  CvaaCp++ i +d ee+      +     +C+gC +C + CP 
  gi|336253369|ref|YP_004596476.1| 54 RCIQCASCVAACPSDSIGIDAEEKR-----P-TLVKMCTGCSRCWDFCPR 97
                                      8******************997332.....3.35689************5 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00025
                            Fer4_7   2 CigCgaCvaaCpvkaield 20 
                                       C+gC +C + Cp + ++++
  gi|336253369|ref|YP_004596476.1|  85 CTGCSRCWDFCPRSGLRYE 103
                                       ************8887765 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 5.1
                            Fer4_7   4 gCgaCv 9  
                                       gC  C+
  gi|336253369|ref|YP_004596476.1| 303 GCDECA 308
                                       444454 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   3.9   1.2e-07   0.00011       2      23 ..      49      70 ..      48      71 .. 0.92
   2 !   14.0   1.6   3.6e-05     0.034       7      20 ..      84      97 ..      82     100 .. 0.92
   3 ?   -0.6   0.2       1.4   1.3e+03      10      16 ..     303     309 ..     302     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.2e-07
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      vi  ++Ci C  Cv +CP + I
  gi|336253369|ref|YP_004596476.1| 49 VIEADRCIQCASCVAACPSDSI 70
                                      7999**************9976 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.6e-05
                                      TSSS-THHHHHSTT CS
                              Fer4  7 kCigCGaCvevCPv 20
                                      +C+gC +C + CP 
  gi|336253369|ref|YP_004596476.1| 84 MCTGCSRCWDFCPR 97
                                      7************5 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.4
                                       S-THHHH CS
                              Fer4  10 gCGaCve 16 
                                       gC +C++
  gi|336253369|ref|YP_004596476.1| 303 GCDECAD 309
                                       8****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 !   19.7   4.4   8.9e-07   0.00084       2      16 ..      53      67 ..      52      68 .. 0.92
   2 !   12.4   0.7   0.00018      0.17       3      15 ..      84      96 ..      82     111 .. 0.90
   3 ?    0.9   0.3      0.95     9e+02       6      13 ..     303     310 ..     302     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.9e-07
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      +rCi+C sCvaaCP+
  gi|336253369|ref|YP_004596476.1| 53 DRCIQCASCVAACPS 67
                                      9*************7 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00018
                            Fer4_4  3 rCigCgsCvaaCP 15
                                       C+gC +C ++CP
  gi|336253369|ref|YP_004596476.1| 84 MCTGCSRCWDFCP 96
                                      7************ PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.95
                            Fer4_4   6 gCgsCvaa 13 
                                       gC+ C ++
  gi|336253369|ref|YP_004596476.1| 303 GCDECADF 310
                                       8****986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   2.0   1.4e-06    0.0013      56      96 ..      50      96 ..      23     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.4e-06
                           Fer4_18 56 kgagdcidcescvkvcP...tgidi...rkGlqleciscllcidacd 96
                                       +a  ci+c scv+ cP   +gid    r  l   c  c++c d c 
  gi|336253369|ref|YP_004596476.1| 50 IEADRCIQCASCVAACPsdsIGIDAeekRPTLVKMCTGCSRCWDFCP 96
                                      45667************544478864446789999**********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 !   19.8   4.7   6.3e-07   0.00059       2      22 ..      48      68 ..      47      70 .. 0.89
   2 !    6.6   0.8    0.0095       8.9       8      20 ..      84      96 ..      83     106 .. 0.86
   3 ?   -1.5   0.9       3.4   3.2e+03      11      16 ..     303     308 ..     302     309 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.3e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPeg 22
                                      ++i +d+Ci+C  Cv++CP +
  gi|336253369|ref|YP_004596476.1| 48 AVIEADRCIQCASCVAACPSD 68
                                      7899***************76 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0095
                            Fer4_6  8 kCigCgdCvrvCP 20
                                       C+gC +C + CP
  gi|336253369|ref|YP_004596476.1| 84 MCTGCSRCWDFCP 96
                                      5*******99999 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.4
                            Fer4_6  11 gCgdCv 16 
                                       gC++C+
  gi|336253369|ref|YP_004596476.1| 303 GCDECA 308
                                       799996 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   3.8   8.5e-07    0.0008       3      21 ..      48      66 ..      46      67 .. 0.91
   2 !    9.2   1.7    0.0014       1.3       9      21 ..      84      96 ..      73      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.5e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      +v+++drCi+C +Cv aCP
  gi|336253369|ref|YP_004596476.1| 48 AVIEADRCIQCASCVAACP 66
                                      57999************** PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0014
                            Fer4_2  9 rCigCgaCvsaCP 21
                                      +C+gC+ C + CP
  gi|336253369|ref|YP_004596476.1| 84 MCTGCSRCWDFCP 96
                                      8*******999*9 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 !   10.7   5.8   0.00061      0.58       1      18 [.      50      67 ..      50      68 .. 0.92
   2 !   10.2   0.4   0.00088      0.83       6      19 ..      85      98 ..      83     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00061
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      ++ d+Ci c++Cv+++P 
  gi|336253369|ref|YP_004596476.1| 50 IEADRCIQCASCVAACPS 67
                                      6789*************5 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00088
                           Fer4_13  6 CiacgaCvelaPdv 19
                                      C++c  C++++P  
  gi|336253369|ref|YP_004596476.1| 85 CTGCSRCWDFCPRS 98
                                      ************75 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 !   16.8   0.6   4.6e-06    0.0043      15      38 ..      46      67 ..      41      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.6e-06
                                      HHHHHHHTT----TT-HHHHCSTT CS
                           Fer4_20 15 eealeeAsRClqCkkapcvkgCPv 38
                                      +ea+ eA+RC+qC  a cv++CP 
  gi|336253369|ref|YP_004596476.1| 46 DEAVIEADRCIQC--ASCVAACPS 67
                                      58999********..99******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 ?   12.0   0.9    0.0003      0.28       2      19 ..      49      66 ..      49      81 .. 0.87
   2 ?    7.4   0.3     0.008       7.6       8      21 ..      85      98 ..      82     133 .. 0.68
   3 ?   -0.0   0.1       1.6   1.5e+03      24      40 ..     323     338 ..     302     371 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0003
                           Fer4_15  2 vvDrdaCigcglCvaeap 19
                                      v++ d+Ci c+ Cva++p
  gi|336253369|ref|YP_004596476.1| 49 VIEADRCIQCASCVAACP 66
                                      6899*************7 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.008
                           Fer4_15  8 CigcglCvaeapev 21
                                      C+gc +C++ +p+ 
  gi|336253369|ref|YP_004596476.1| 85 CTGCSRCWDFCPRS 98
                                      ***********964 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.6
                           Fer4_15  24 ldedglasvllddgeia 40 
                                         edg+++v++ +++ +
  gi|336253369|ref|YP_004596476.1| 323 GSEDGYSTVVVRTEN-G 338
                                       456788877764332.2 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.0   0.00052      0.49       2      17 ..      52      67 ..      24      70 .. 0.81
   2 ?    6.8  14.1    0.0099       9.4       2      63 ..      52      97 ..      51     100 .. 0.73
   3 ?    8.7   1.8    0.0024       2.3       3      63 ..      83      97 ..      80     138 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00052
                            Fer4_8  2 lekCieCgaCqsaCpv 17
                                      +++Ci+C  C +aCp+
  gi|336253369|ref|YP_004596476.1| 52 ADRCIQCASCVAACPS 67
                                      5677777777777775 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0099
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      +++Ci+C  C +aCp+ +       da++++               ++ Ct+c +C + Cp 
  gi|336253369|ref|YP_004596476.1| 52 ADRCIQCASCVAACPSDS----IGIDAEEKRPT------L------VKMCTGCSRCWDFCPR 97
                                      789***********9322....32333333333......3......699***********97 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0024
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      + C++C++C + Cp                                               
  gi|336253369|ref|YP_004596476.1| 83 KMCTGCSRCWDFCP----------------------------------------------R 97
                                      45666666666665..............................................3 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   4.4   0.00023      0.22       1      14 [.      55      68 ..      55      69 .. 0.93
   2 ?    6.7   2.6     0.017        16       1      13 [.      85      97 ..      85      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C++C  Cv +CP++
  gi|336253369|ref|YP_004596476.1| 55 CIQCASCVAACPSD 68
                                      ************86 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.017
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      CtgC++C + CP 
  gi|336253369|ref|YP_004596476.1| 85 CTGCSRCWDFCPR 97
                                      ***********95 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   4.6       0.1        96       1      14 [.      54      67 ..      54      80 .. 0.89
   2 ?   10.6   2.7   0.00081      0.77      79      94 ..      82      97 ..      73      98 .. 0.86
   3 ?   -2.4   0.0       9.6   9.1e+03      74      90 ..     293     309 ..     289     311 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.1
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      rC++C++C ++Cp+
  gi|336253369|ref|YP_004596476.1| 54 RCIQCASCVAACPS 67
                                      7***********96 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00081
                           Fer4_22 79 esgCvGCgRCieacpv 94
                                       ++C+GC RC + cp 
  gi|336253369|ref|YP_004596476.1| 82 VKMCTGCSRCWDFCPR 97
                                      689***********96 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 9.6
                           Fer4_22  74 kekfgesgCvGCgRCie 90 
                                       +e+f++ g  GC  C +
  gi|336253369|ref|YP_004596476.1| 293 VEEFDAAGLRGCDECAD 309
                                       56788888889999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 3356.86
//
Query:       gi|336253370|ref|YP_004596477.1|  [L=221]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-21   73.6   0.1    1.4e-20   72.8   0.1    1.4  1  HTH_10      HTH DNA binding domain
     0.0076   16.1   0.0       0.33   10.9   0.0    2.3  2  HTH_5       Bacterial regulatory protein, arsR family
     0.0083   15.7   0.1      0.072   12.6   0.1    2.1  1  GerE        Bacterial regulatory proteins, luxR family
  ------ inclusion threshold ------
      0.024   14.1   0.3       0.13   11.8   0.0    2.4  3  Sigma70_r4  Sigma-70, region 4
      0.025   14.4   0.0        2.5    8.0   0.0    2.5  2  HTH_IclR    IclR helix-turn-helix domain
      0.034   14.6   0.1       0.24   11.9   0.0    2.2  2  HTH_40      Helix-turn-helix domain
       0.11   12.3   0.0       0.44   10.4   0.0    2.0  3  HTH_23      Homeodomain-like domain


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 !   72.8   0.1   5.5e-24   1.4e-20       1      52 [.     164     215 ..     164     216 .. 0.99

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 5.5e-24
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT +q+e+l +A+emGYF+yP+ +++ ++A elG+++st+sehL +a+ kl+
  gi|336253370|ref|YP_004596477.1| 164 LTARQREILETAHEMGYFEYPKGANATDVAAELGVARSTFSEHLAAAQTKLM 215
                                       9**************************************************9 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 ?    2.7   0.0     0.045   1.1e+02      16      32 ..      91     107 ..      85     110 .. 0.81
   2 !   10.9   0.0   0.00013      0.33      18      37 ..     189     208 ..     186     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.045
                                       EEHHHHHHHHTS-HHHH CS
                             HTH_5  16 lcvcelaeelglsqstv 32 
                                        c+ce++e +g + s v
  gi|336253370|ref|YP_004596477.1|  91 DCACEIVEGTGTPLSSV 107
                                       69******999877776 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                                       HHHHHHHHTS-HHHHHHHHH CS
                             HTH_5  18 vcelaeelglsqstvShHLk 37 
                                       +++ a+elg+ +st S+HL+
  gi|336253370|ref|YP_004596477.1| 189 ATDVAAELGVARSTFSEHLA 208
                                       6799***************8 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   2.8e-05     0.072       2      45 ..     163     214 ..     162     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                                       SS-HHHHHHHHHHC........TTS-HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE   2 sLskRErevLrlla........eGksnkeIAeelniSekTVkvhksnimkKL 45 
                                       +L+ R+re+L+           +G   +++A+el+++  T + h++ +++KL
  gi|336253370|ref|YP_004596477.1| 163 VLTARQREILETAHemgyfeypKGANATDVAAELGVARSTFSEHLAAAQTKL 214
                                       79999999999765222333337****************************8 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         3   7.7e+03      19      34 ..      38      53 ..      33      54 .. 0.69
   2 ?   -1.7   0.0      0.87   2.2e+03      21      31 ..     121     131 ..     116     136 .. 0.72
   3 ?   11.8   0.0   5.1e-05      0.13       4      48 ..     163     214 ..     162     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3
                                      TT--HHHHHHHHTS-H CS
                        Sigma70_r4 19 eglTleEIgerlgiSr 34
                                       g T e + e++g++ 
  gi|336253370|ref|YP_004596477.1| 38 TGATGETVVEEFGVPA 53
                                      5666677778889885 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.87
                                       --HHHHHHHHT CS
                        Sigma70_r4  21 lTleEIgerlg 31 
                                         leE++++ +
  gi|336253370|ref|YP_004596477.1| 121 FELEEVAAIVD 131
                                       56999999876 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 5.1e-05
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       +L++r+re+le           +g +  +++++lg+ r++ + +++ A  kL
  gi|336253370|ref|YP_004596477.1| 163 VLTARQREILETAHemgyfeyPKGANATDVAAELGVARSTFSEHLAAAQTKL 214
                                       79************99999988899**************9888888777666 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 ?    3.8   0.0      0.02        50      23      36 ..      95     108 ..      93     109 .. 0.93
   2 ?    8.0   0.0   0.00098       2.5      16      39 ..     184     207 ..     174     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.02
                                       HHHHHHTS-HHHHH CS
                          HTH_IclR  23 elArrtglpkStvh 36 
                                       e+ + tg p S+v+
  gi|336253370|ref|YP_004596477.1|  95 EIVEGTGTPLSSVR 108
                                       89**********97 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00098
                                       BSS-BHHHHHHHHTS-HHHHHHHH CS
                          HTH_IclR  16 pqeltlselArrtglpkStvhRlL 39 
                                       p + + +++A+++g+++St + +L
  gi|336253370|ref|YP_004596477.1| 184 PKGANATDVAAELGVARSTFSEHL 207
                                       566789*************87776 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.49   1.2e+03      16      64 ..     124     178 ..     117     184 .. 0.63
   2 ?   11.9   0.0   9.4e-05      0.24       9      38 ..     183     212 ..     175     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.49
                            HTH_40  16 eeIAke....rglkesTIegHLaelieeg..eeidlerlvseeeekeIeeaiekv 64 
                                       ee+A++    r+   +  ++ La+  e+g  +++ ++r v + +++eI e+  ++
  gi|336253370|ref|YP_004596477.1| 124 EEVAAIvdelRERFDGVLVEDLAQDHEDGstDPVIVDREVLTARQREILETAHEM 178
                                       5555554445555566666666666666633355557778888888887776665 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.4e-05
                            HTH_40   9 leeglsieeIAkerglkesTIegHLaelie 38 
                                       + +g +  ++A+e g+++sT  +HLa +  
  gi|336253370|ref|YP_004596477.1| 183 YPKGANATDVAAELGVARSTFSEHLAAAQT 212
                                       56899999******************9765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.1   1.1e+04      17      29 ..      39      51 ..      34      52 .. 0.78
   2 ?   -3.0   0.0       2.8   7.2e+03       8      22 ..     127     144 ..     123     148 .. 0.57
   3 ?   10.4   0.0   0.00017      0.44      17      35 ..     186     204 ..     167     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.1
                            HTH_23 17 GlsvreIAreLgv 29
                                      G++ +++ +e+gv
  gi|336253370|ref|YP_004596477.1| 39 GATGETVVEEFGV 51
                                      7777888899998 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.8
                            HTH_23   8 lrillllae...Glsvre 22 
                                       + i+  l+e   G  v++
  gi|336253370|ref|YP_004596477.1| 127 AAIVDELRErfdGVLVED 144
                                       556666665555555555 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00017
                            HTH_23  17 GlsvreIAreLgvsrrTvy 35 
                                       G++ +++A+eLgv r+T +
  gi|336253370|ref|YP_004596477.1| 186 GANATDVAAELGVARSTFS 204
                                       89999************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1733.85
//
Query:       gi|336253371|ref|YP_004596478.1|  [L=382]
Description: 2-methylcitrate synthase/citrate synthase II [Halopiger xanaduensis SH-6]
Scores for 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-130  433.1   0.0   8.9e-130  432.9   0.0    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain
  ------ inclusion threshold ------
       0.13   11.8   0.4         13    5.3   0.0    2.1  2  DUF1974       Domain of unknown function (DUF1974)


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.9   0.0  9.9e-134  8.9e-130       1     361 []       8     365 ..       8     365 .. 0.97

  Alignments for each domain:
  == domain 1  score: 432.9 bits;  conditional E-value: 9.9e-134
                                       GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHH CS
                      Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlea 77 
                                       gl+gv ++e+e+s++dg++g+l+YRGy+ie+La + +s+eev ylL++g+lP ++el++f++ l+e+r++ ++vl +
  gi|336253371|ref|YP_004596478.1|   8 GLEGVLVAESELSSIDGDEGRLIYRGYTIEDLA-RGASYEEVLYLLWHGHLPAEDELESFAAALTEERAVSDDVLAT 83 
                                       899******************************.8****************************************** PP

                                       HHCSS.TTS-HHHHHHHHHHHHHHHSTTCTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.-----TTSSHHH CS
                      Citrate_synt  78 lealp.kdahpmavlraavsalsaddeeseakeeseeaalrdalkliAklptiaaaiyrarlgreplepddklsyae 153
                                       +e+l  +d +pma+lr+avs++sa ++es+a+++  ea lr+ +++ Ak+pt++aa+ r+rlg+ep++pd++l +a+
  gi|336253371|ref|YP_004596478.1|  84 MERLAdADEQPMAALRTAVSMFSATEPESDAEADDLEASLRKGRRITAKIPTALAAFERYRLGEEPIDPDPDLGLAA 160
                                       **9999999*******************99999999**********************************99***** PP

                                       HHHHHHHSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHH CS
                      Citrate_synt 154 nflymlrgkkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaagigalkGplhgganeavlkmlee 230
                                       nflyml+g++pd+ +a+ +d+al+lhaDH+lnaSTf+  v++St+ad+ysa+++g++al+Gplhggan+ v+++l e
  gi|336253371|ref|YP_004596478.1| 161 NFLYMLTGEQPDDVAAETFDQALILHADHGLNASTFTSMVIGSTMADIYSAVTGGVSALSGPLHGGANQDVMEVLME 237
                                       ***************************************************************************** PP

                                       HSSGG.GHHHHHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTCHTHHHHHHHHHHHHHHHHHHHHCHHG CS
                      Citrate_synt 231 igsaeveveeylekvlakekerlpGfGHrvykksDpRakilkelaeelaeekgkdpllklaeeleevapevlkekee 307
                                       i++++++  e++e++ ++ ++r+pGfGHrvy ++DpRa+il+e  +ela+e g+++++++ +++ee   e    +e 
  gi|336253371|ref|YP_004596478.1| 238 IDESNKDPLEWVEEATDE-GRRIPGFGHRVYNVKDPRARILQERSKELAAE-GNSKWYDITTTIEEYLTEEKGLVE- 311
                                       *88877***********7.5****************************996.8888**************777677. PP

                                       CT-EB-THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHHHT------E CS
                      Citrate_synt 308 knlypNvDfysgvlyralgipeelftvlfaisRvaGwlAhileqladnkiiRPr 361
                                       k++ pNvDfysg +y++lgip +++t++fa+sR+ Gw+Ah+le+++dn++iRPr
  gi|336253371|ref|YP_004596478.1| 312 KGIAPNVDFYSGSVYYQLGIPIDMYTPIFAMSRAGGWIAHVLEYQEDNRLIRPR 365
                                       *******************************************99********8 PP

>> DUF1974  Domain of unknown function (DUF1974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1    0.0023        20     172     240 ..      54     122 ..      44     140 .. 0.70
   2 ?    5.3   0.0    0.0014        13      15      54 ..     169     208 ..     163     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0023
                           DUF1974 172 rrakkpsDklkhevaelllepseardrLtagvylpedeedplgrlekafkavlaaeplekklkkaikkg 240
                                       + + +++D+l++  a+l  e     d L +   l + +e+p+++l  a ++  a+ep  ++  +  ++ 
  gi|336253371|ref|YP_004596478.1|  54 HGHLPAEDELESFAAALTEERAVSDDVLATMERLADADEQPMAALRTAVSMFSATEPESDAEADDLEAS 122
                                       555677899977777776666667777777888888889*************99999776655555544 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0014
                           DUF1974  15 qsedkekalkaFdkalfghigfvvsn.alrslvlgltggrl 54 
                                       +++d + a+++Fd+al+ h+ + ++  ++ s+v g t + +
  gi|336253371|ref|YP_004596478.1| 169 EQPD-DVAAETFDQALILHADHGLNAsTFTSMVIGSTMADI 208
                                       5566.789**************9875267888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 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:                        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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2964.62
//
Query:       gi|336253372|ref|YP_004596479.1|  [L=116]
Description: hypothetical protein Halxa_1975 [Halopiger xanaduensis SH-6]
Scores for 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:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 956.00
//
Query:       gi|336253373|ref|YP_004596480.1|  [L=359]
Description: hypothetical protein Halxa_1976 [Halopiger xanaduensis SH-6]
Scores for 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   15.5   0.8        1.6    9.5   0.1    2.3  2  Glyco_hydro_2  Glycosyl hydrolases family 2
       0.14   12.5   4.4        0.3   11.3   0.2    2.6  2  NPCBM_assoc    NPCBM-associated, NEW3 domain of alpha-galacto
       0.44   10.9   2.9        9.3    6.6   0.1    2.3  2  Calycin_like   Calycin-like beta-barrel domain
        1.1    9.5   5.0        1.8    8.8   1.7    2.1  2  DUF4330        Domain of unknown function (DUF4330)


Domain annotation for each model (and alignments):
>> Glyco_hydro_2  Glycosyl hydrolases family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00035       1.6      11      59 ..      54     102 ..      44     121 .. 0.77
   2 ?    4.3   0.0     0.014        62      13      68 ..     181     239 ..     174     263 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00035
                                       EEETCSEEEEEEEEEEEEECSSSSCEEEEEEEEETTSTEEEEEEEEEEE CS
                     Glyco_hydro_2  11 dlsddksakvevevelendsdksvevtleteikdaegkkvkeessvlsl 59 
                                       d  + +++++ev++ le+++d  ++vt+  +++d+++  v++++++   
  gi|336253373|ref|YP_004596480.1|  54 DEVSGETVTLEVDTFLEHRGDPVENVTVVHRVTDTDTGLVTATAEQPIG 102
                                       4333399********************************9997776554 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.014
                                       ETC..SEEEEEEEEEEEEECS.SSSCEEEEEEEEETTSTEEEEEEEEEEEESTT-EEEE CS
                     Glyco_hydro_2  13 sdd..ksakvevevelendsd.ksvevtleteikdaegkkvkeessvlslgngetksik 68 
                                       +++  ++a++ev+  l+n++d ++ ++++e +  +a+ + v+++++v + +++  ++ +
  gi|336253373|ref|YP_004596480.1| 181 KSTngETATLEVTSYLTNAGDgETDSLEVELKARQAGSNIVADAERVSVSNVDPGETAT 239
                                       44446899999999777765526778888888888888888887777777666555544 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.6     0.066   2.9e+02       4      62 ..      58     119 ..      56     128 .. 0.71
   2 ?   11.3   0.2   6.8e-05       0.3       6      64 ..     189     249 ..     182     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.066
                       NPCBM_assoc   4 Getvtltl.tvtndgtaaatnvslslslPeGWt..vvevspasaaslapGetveatvkVtpp 62 
                                       Getvtl++ t+  + +++++nv +  ++ +  t  v++++ + + +la   ++ + +++ +p
  gi|336253373|ref|YP_004596480.1|  58 GETVTLEVdTFLEHRGDPVENVTVVHRVTDTDTglVTATAEQPIGRLAGENETAVPATIGVP 119
                                       899999985677888*******9988776666666666666666666666666666666555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.8e-05
                       NPCBM_assoc   6 tvtltltvtndgtaaatnvslslsl.PeGWt.vvevspasaaslapGetveatvkVtppag 64 
                                       t ++t ++tn g+  + +++++l++  +G + v  ++  s++ ++pGet++ t+++ +p++
  gi|336253373|ref|YP_004596480.1| 189 TLEVTSYLTNAGDGETDSLEVELKArQAGSNiVADAERVSVSNVDPGETATPTAELEVPDE 249
                                       44567789****999999999999955555589999999999****************985 PP

>> Calycin_like  Calycin-like beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0021       9.3      23      90 ..      44     115 ..      26     135 .. 0.79
   2 ?    4.4   0.3    0.0095        43      60     104 ..     180     224 ..     172     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0021
                                       S..-EEEEEE-S..SS-EEEEEE-GG..G------EEEEEEEEE-SSSSSBEEEEEEEEE-TT--E...EEEE CS
                      Calycin_like  23 d..akvtitkne..dgtvnlsLknfs.fgelplGditvdnvkvtkeggsyttfsgsqkltlagggdaeeatvs 90 
                                       +  ++vti ++e   +tv+l+++ f    + p+ ++tv    vt+ +++ +t + +q +   +g++++ ++++
  gi|336253373|ref|YP_004596480.1|  44 AslQEVTIAADEvsGETVTLEVDTFLeHRGDPVENVTVV-HRVTDTDTGLVTATAEQPIGRLAGENETAVPAT 115
                                       1558899988874369*********954499******99.679999999999999999988888887765544 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0095
                                       EE-SSSSSBEEEEEEEEE-TT--E...EEEEEEEEEETTEEEEEE CS
                      Calycin_like  60 vtkeggsyttfsgsqkltlagggdaeeatvslsGtisgkklnlti 104
                                       v++ +g++ t++ +  lt ag+g+++ ++v+l++  +g+++ +++
  gi|336253373|ref|YP_004596480.1| 180 VKSTNGETATLEVTSYLTNAGDGETDSLEVELKARQAGSNIVADA 224
                                       555668899999999999999999999******999888887766 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.7    0.0004       1.8      19     102 ..       7      93 ..       7     116 .. 0.71
   2 ?    1.7   0.1     0.061   2.7e+02      84     135 ..     222     270 ..     171     279 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0004
                           DUF4330  19 llailvilavivgiflkpgtsgsvaqaeaaatkpve......vdvvvrglevpeelakvkegektniiirnqPagdv 89 
                                       l++++v++av++   l ++    +a+ e+++ ++ve       +v++   ev+ e++    +  t+   r  P  +v
  gi|336253373|ref|YP_004596480.1|   7 LGVAAVVVAVAALTTLALSGA--IAAPETETGASVErghaslQEVTIAADEVSGETVT--LEVDTFLEHRGDPVENV 79 
                                       578888888888887777666..5555555556666677888999*******999999..78888999999****** PP

                           DUF4330  90 eik.dvkvlprkvv 102
                                       +++ +v+ ++  +v
  gi|336253373|ref|YP_004596480.1|  80 TVVhRVTDTDTGLV 93 
                                       66645555444433 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.061
                           DUF4330  84 qPagdveikdvkvlprkvvvpqpdGkvkalede.pylkdllvtlegkakite.d 135
                                        +a +v++ +v  +p ++++p+++ +   ++de  y+ d+++ l+g+ ++t+ +
  gi|336253373|ref|YP_004596480.1| 222 ADAERVSVSNV--DPGETATPTAELE---VPDEyRYNLDAILWLDGTIVATDrA 270
                                       23344455544..5577777777774...3555579999999999998888744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2840.30
//
Query:       gi|336253374|ref|YP_004596481.1|  [L=179]
Description: AIG2 family protein [Halopiger xanaduensis SH-6]
Scores for 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-17   61.9   0.0    1.1e-16   61.6   0.0    1.1  1  GGACT     Gamma-glutamyl cyclotransferase, AIG2-like
    3.1e-05   24.3   0.0      5e-05   23.6   0.0    1.3  1  AIG2_2    AIG2-like family


Domain annotation for each model (and alignments):
>> GGACT  Gamma-glutamyl cyclotransferase, AIG2-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   1.2e-20   1.1e-16       1     105 [.      39     143 ..      39     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 1.2e-20
                                       EEESSTTSTTSCCCHHHHCS....ECEEEEEEEECCTBEEEE.ETTTEEEETTSSE.EEEEEEEE-HHHHHHHHHCT CS
                             GGACT   1 vFvYGtLkrgepnhqrlllg....arflesgpatlkgyrlydlggkypalvpgdgekVkGelyevddeelarLDelE 73 
                                       vFvYGtL   +p+  +++l+     ++   g+atl+g r++d  g+yp l p  g++V G+l+ vd+ +l+rLD++E
  gi|336253374|ref|YP_004596481.1|  39 VFVYGTLT--DPERVEIVLDgrppTEYAFDGSATLEGLRRVD--GEYPTLAP--GGTVDGQLLSVDETALERLDRYE 109
                                       8*******..999999999944433477899*********98..79*****8..888******************** PP

                                       .TTTTSEEEEEEEEEC...TTS-EEEEEEEEETT CS
                             GGACT  74 peepseYereevkvev..ledgeqveawvYvyag 105
                                       +  +++Y r++v+++   ++d++   a vYv ++
  gi|336253374|ref|YP_004596481.1| 110 GVDRGLYVRVSVPIDGhnNSDNSDDGAAVYVGDP 143
                                       8899******666665776677777999999855 PP

>> AIG2_2  AIG2-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   5.5e-09     5e-05       2      49 ..      90     140 ..      89     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.5e-09
                            AIG2_2   2 VfGvlweidlenlkdLDkqEgvedgiyrpievrVst...atgeevlaraYv 49 
                                       V G l  +d+ +l++LD++Egv+ g+y++++v+++    +++++  a +Yv
  gi|336253374|ref|YP_004596481.1|  90 VDGQLLSVDETALERLDRYEGVDRGLYVRVSVPIDGhnnSDNSDDGAAVYV 140
                                       6689999***************************66323444445566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       185  (0.0103185); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1431.44
//
Query:       gi|336253375|ref|YP_004596482.1|  [L=403]
Description: threonine dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-84  283.3   7.3    2.8e-84  283.0   7.3    1.1  1  PALP             Pyridoxal-phosphate dependent enzyme
     0.0022   17.7   0.0      0.008   15.9   0.0    2.0  1  ACT              ACT domain
     0.0054   17.3   0.0      0.038   14.6   0.0    2.3  2  ACT_4            ACT domain
  ------ inclusion threshold ------
      0.064   12.8   0.0       0.11   12.0   0.0    1.3  1  YhfZ_C           YhfZ C-terminal domain
      0.082   13.3   0.3       0.18   12.2   0.3    1.6  1  FtsA             Cell division protein FtsA
      0.096   12.3   1.4        1.8    8.1   0.1    2.5  2  Pep_deformylase  Polypeptide deformylase


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 !  283.0   7.3   9.2e-88   2.8e-84       6     294 .]      19     304 ..      14     304 .. 0.99

  Alignments for each domain:
  == domain 1  score: 283.0 bits;  conditional E-value: 9.2e-88
                                       SS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEE CS
                              PALP   6 gpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvt 82 
                                       + TPl  ++  s  +g+++ lKlE ++ tg+fK+Rga++++a+l e+++  +vv+as+GNh++++A+aa + G+++ 
  gi|336253375|ref|YP_004596482.1|  19 RHTPLEYSHTYSSMTGADVHLKLETFQRTGAFKIRGATNRIATLSEEQKDAGVVTASAGNHAQGVALAATRVGVDSK 95 
                                       78******************************************9999***************************** PP

                                       EEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEE CS
                              PALP  83 ivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpd 159
                                       iv+p++a+ +kv++++++Gaevv+ g dy ea+++a+el++e eg+++v+ fd+++v++g+gtiglEi+e+  ++++
  gi|336253375|ref|YP_004596482.1|  96 IVMPEHAPISKVKATESYGAEVVLHGADYAEAAEHAHELERE-EGRIYVHAFDDELVMAGQGTIGLEIVEDR-PEVE 170
                                       ******************************************.*****************************.6*** PP

                                       EEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEE CS
                              PALP 160 avvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelldrl 236
                                       +vvvp+GgGgli+Giaa++k ++pd rvigv++eg+++ a+slr+g+rv+++  dtiadg+a++s++e+ fe+++++
  gi|336253375|ref|YP_004596482.1| 171 TVVVPIGGGGLISGIAAAVKGEKPDARVIGVQAEGASSAATSLRKGERVSIEGVDTIADGIATRSVGERPFEHIREY 247
                                       ***************************************************************************** PP

                                       EEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 237 vdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       vde+vtvsd e++ ++  l +r + +ve ++a+ laa+ l e+ ++++++++v +l+g
  gi|336253375|ref|YP_004596482.1| 248 VDEVVTVSDPEIAVTITYLLERSKTLVEGAGAVPLAAV-LFEKFDYADDETIVPVLSG 304
                                       **************************************.****************998 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.7e-06     0.008       3      48 ..     329     370 ..     328     379 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-06
                                       EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEE CS
                               ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvi 48 
                                       +r+ + D+PG+L +++ +++ +  Ni  i++ ++ +    +v + +
  gi|336253375|ref|YP_004596482.1| 329 IRTVLTDQPGALEELLDIFTAHRANIYAIHHDRTSR----EVEMSD 370
                                       677789************************999976....444433 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.1   3.3e+03      17      56 ..      53      92 ..      36      95 .. 0.73
   2 !   14.6   0.0   1.3e-05     0.038       8      71 ..     328     394 ..     325     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                             ACT_4 17 kglLaditqvisee.kanivsvnaktrkkdglaeikitveV 56
                                      +g+ ++i+++ +e+ +a +v  +a ++  +g+a    +v V
  gi|336253375|ref|YP_004596482.1| 53 RGATNRIATLSEEQkDAGVVTASAGNHA-QGVALAATRVGV 92
                                      4677888888888888888888888864.667766666655 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.3e-05
                             ACT_4   8 rleveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkdvehLsrviakLra 71 
                                       +++ + +d++g+L ++++++++++ani +++ + +++    + +e++i++e +  +h++  +  Lr+
  gi|336253375|ref|YP_004596482.1| 328 KIRTVLTDQPGALEELLDIFTAHRANIYAIHHDRTSReveMSDTEVEIELEMRGPDHVDAFLSDLRE 394
                                       688899*************************999887777677999999999999999998888876 PP

>> YhfZ_C  YhfZ C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.7e-05      0.11      19      78 ..      22      81 ..      10      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                            YhfZ_C 19 PlpyskkyeGLatg.lkaafeklgiplnlay.mrGadkRlealkegrydfavvSrlaAeqal 78
                                      Pl ys++y++++ + ++ ++e   ++ + a+ +rGa +R++ l+e++ d+ vv + a ++a+
  gi|336253375|ref|YP_004596482.1| 22 PLEYSHTYSSMTGAdVHLKLET--FQRTGAFkIRGATNRIATLSEEQKDAGVVTASAGNHAQ 81
                                      999*****99965434444554..887888857********************999988865 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3     6e-05      0.18       6     100 ..     154     261 ..     150     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6e-05
                                       -SSSEEEEEEETTEEEEEEEES--HHHHHHHHHHHHT--HHHHHHHHHH.H--S--......EEEEEHHHHH..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx......xxxxxxxxxx..... RF
                              FtsA   6 GagktdvavaedgalvhlrvigvggngitkdiakalrtaveeAerikik.yGsala......ekeigrkels..... 70 
                                       G g++ + ++ed   v + v+++gg g+ ++ia a++    +A  i ++  G+ +a       ++++   ++     
  gi|336253375|ref|YP_004596482.1| 154 GQGTIGLEIVEDRPEVETVVVPIGGGGLISGIAAAVKGEKPDARVIGVQaEGASSAatslrkGERVS---IEgvdti 227
                                       999*********99999**************************999965233333366544422222...3255577 PP

                                       .........GGGGSTTHHHHHHHHHT-..HHHT-GGGHH CS
                                       .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              FtsA  71 .........ggsalpnleelaeralspkleevsdpeyas 100
                                                g+   + ++e++ +++ +    vsdpe+a+
  gi|336253375|ref|YP_004596482.1| 228 adgiatrsvGERPFEHIREYVDEVV-T----VSDPEIAV 261
                                       7888888888888888888888885.3....56777765 PP

>> Pep_deformylase  Polypeptide deformylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1   0.00061       1.8      39      61 ..      78     100 ..      55     111 .. 0.86
   2 ?    2.7   0.2     0.028        83     114     155 ..     106     148 ..     104     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00061
                                       HHCT-SEEEGGGGT--BSEEEEE CS
                   Pep_deformylase  39 keakgvgLAApQigvnkrlfvie 61 
                                       ++a+gv+LAA+++gv+ ++++ e
  gi|336253375|ref|YP_004596482.1|  78 NHAQGVALAATRVGVDSKIVMPE 100
                                       4779**************99755 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.028
                                       EEEEE-TTS-EEEEEEEHH.HHHHHHHHHHHCTT--GGGGC-T CS
                   Pep_deformylase 114 kvkyldltgkeveleaegl.lArvlqHEiDhlnGklfidridk 155
                                       kvk+++  g ev l+  ++ +A+   HE+   +G ++++ +d+
  gi|336253375|ref|YP_004596482.1| 106 KVKATESYGAEVVLHGADYaEAAEHAHELEREEGRIYVHAFDD 148
                                       578888899999998666559999*************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3200.07
//
Query:       gi|336253376|ref|YP_004596483.1|  [L=126]
Description: endoribonuclease L-PSP [Halopiger xanaduensis SH-6]
Scores for complete 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  132.0   0.0    1.2e-38  131.8   0.0    1.0  1  Ribonuc_L-PSP    Endoribonuclease L-PSP
  ------ inclusion threshold ------
      0.054   13.6   0.1      0.087   13.0   0.1    1.5  1  YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endori


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 !  131.8   0.0   1.4e-42   1.2e-38       2     120 ..       8     124 ..       7     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 131.8 bits;  conditional E-value: 1.4e-42
                                       TTSTTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB..-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGG CS
                     Ribonuc_L-PSP   2 eaapaaaapYsqavkagnlvyvsGqlpldpetgelv.egdveeqtrqalenlkavLaaagaslsdvVkvtvFladie 77 
                                       ++apaa+++Ysqa  +g l++++Gq+pl++ +g+l  ++ +++qt+qal nl+a+L++ag+s +d++kvtv+l di+
  gi|336253376|ref|YP_004596483.1|   8 DDAPAAVGAYSQATSNGSLLFTAGQIPLTA-DGDLLdDEPIAAQTEQALYNLDAILDEAGVSSEDILKVTVYLDDID 83 
                                       689*************************95.888887999************************************* PP

                                       GHHHHHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEEE CS
                     Ribonuc_L-PSP  78 dfaevnevyaeafdelkeaParsaveVaaLpkgakvEIeaiav 120
                                       df ++ne+ya++fd++   ParsaveV aLpkg+ vEIea+a 
  gi|336253376|ref|YP_004596483.1|  84 DFDDMNEAYADYFDDEP--PARSAVEVDALPKGVGVEIEAVAS 124
                                       ****************5..*********************995 PP

>> YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endoribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   9.7e-06     0.087      13      42 ..       9      38 ..       3      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.7e-06
                                      -----SSSS-SEEEETTEEEE--B--EETT CS
                   YjgF_endoribonc 13 kvaaalGayepyaivasflttsfqlpylqe 42
                                      +++aa+Gay   +  +s l t++q+p   +
  gi|336253376|ref|YP_004596483.1|  9 DAPAAVGAYSQATSNGSLLFTAGQIPLTAD 38
                                      689***********************8653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 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:                        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 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 966.87
//
Query:       gi|336253377|ref|YP_004596484.1|  [L=95]
Description: hypothetical protein Halxa_1980 [Halopiger xanaduensis SH-6]
Scores for 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   13.3   2.0       0.12   12.6   2.0    1.5  1  DUF5493   Family of unknown function (DUF5493)
       0.17   11.8   3.8       0.24   11.3   3.8    1.1  1  DUF2721   Protein of unknown function (DUF2721)
        1.3    9.3   4.8       0.55   10.4   1.9    1.8  2  DUF2749   Protein of unknown function (DUF2749)


Domain annotation for each model (and alignments):
>> DUF5493  Family of unknown function (DUF5493)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.0   2.1e-05      0.12      29      56 ..      19      46 ..       5      68 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                           DUF5493 29 lmafiigtvaflvfvqgytdiafssstf 56
                                      l+   +g++aflv+vqgy+ +a    t+
  gi|336253377|ref|YP_004596484.1| 19 LLWGAVGALAFLVLVQGYALVAAPLVTI 46
                                      4555799***********9998766554 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.8   4.1e-05      0.24      65     127 ..      17      76 ..      14      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.1e-05
                           DUF2721  65 railllvlsallvvlvvlllflsallsldlsllaailfvlalllllvslllflrEirlslral 127
                                        a+l ++++al+++++v  ++l   +++ l +++++++++a++ +++ +   ++E r+++ra 
  gi|336253377|ref|YP_004596484.1|  17 SALLWGAVGALAFLVLVQGYAL---VAAPLVTIVQAFAIAAVVGIVATVGTYVLEPRIATRAA 76 
                                       4556666666666666665555...6789********************************96 PP

>> DUF2749  Protein of unknown function (DUF2749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.28   1.7e+03      14      27 ..      22      35 ..      16      42 .. 0.73
   2 ?   10.4   1.9   9.2e-05      0.55       5      41 ..      46      83 ..      40      94 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.28
                           DUF2749 14 aagagtilwlvvqp 27
                                      +a+++ ++ ++vq 
  gi|336253377|ref|YP_004596484.1| 22 GAVGALAFLVLVQG 35
                                      67888888888876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9.2e-05
                           DUF2749  5 ilIvlvia..vaagagtilwlvvqpragtsgsgeaqReh 41
                                      i+ + +ia  v+++a+  +++ ++pr +t +++   R+ 
  gi|336253377|ref|YP_004596484.1| 46 IVQAFAIAavVGIVATVGTYV-LEPRIATRAANGSARDT 83
                                      344566667788888888888.9***7777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 759.01
//
Query:       gi|336253378|ref|YP_004596485.1|  [L=262]
Description: 3-oxoacyl-(acyl-carrier-protein) reductase [Halopiger xanaduensis SH-6]
Scores for complete 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-45  155.3   0.0    2.8e-45  154.7   0.0    1.2  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    2.3e-36  125.1   0.0    2.9e-36  124.8   0.0    1.1  1  adh_short       short chain dehydrogenase
    2.2e-10   40.7   0.1      3e-10   40.3   0.1    1.2  1  KR              KR domain
     0.0074   16.2   0.1       0.01   15.7   0.1    1.2  1  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.093   12.1   0.0       0.14   11.5   0.0    1.3  1  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase
       0.13   11.5   0.0        3.8    6.8   0.0    2.2  2  THF_DHG_CYH_C   Tetrahydrofolate dehydrogenase/cyclohydrolase
       0.19   11.3   0.0        0.3   10.7   0.0    1.3  1  ApbA            Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> 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 !  154.7   0.0   1.1e-48   2.8e-45       4     233 ..      17     259 ..      12     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 154.7 bits;  conditional E-value: 1.1e-48
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.E..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.v..lecDVtdeeqvealveevvekfgklDilvnn 76 
                                       sg+G a A+al e+Ga+v ++ ++ ++ +++ +++ae   a  v  +++D+td++++ +lv+++ve+fg+lD lv +
  gi|336253378|ref|YP_004596485.1|  17 SGLGLASARALLEAGANVTICGRDADRlERARDDFAETNTAGdViaVQADITDPDDISRLVSQTVEEFGGLDHLVTS 93 
                                       9**************************6666666666554335557******************************* PP

                                       ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH..HCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHH CS
                      adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalp..lmkeggsivnlssvgaervvpnynaygaaKaaleal 151
                                       ag  p+  + flet+++++ +a d  + s++ ++++a +  l  e+g i +++s   + v ++    + ++ ++++l
  gi|336253378|ref|YP_004596485.1|  94 AGGPPS--TTFLETDEQDWYQAYDLLVMSVVWTVEEAHEhlLESEQGTITCITSRTVREVADGLLLSNSVRRSVIGL 168
                                       ******..*******************************7444456******************************* PP

                                       HHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT..........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGG CS
                      adh_short_C2 152 trylAvelgpkgiRvNavspgpikTlaasgikg..........fdelleelearaplgrlgtpeevaeaalfLasde 218
                                       ++++ +e++p +iR Nav pg i+T+  +++ +            e lee+++++p+ r+g+p+e +e+++fL s++
  gi|336253378|ref|YP_004596485.1| 169 MKTISREFAP-EIRANAVLPGTIETPRIEELIEagidrgtydnYGEGLEEFASEIPMDRIGEPHELGEVVAFLSSPR 244
                                       **********.9*************98554322233225544467899***************************** PP

                                       GTT--SEEEEESTTG CS
                      adh_short_C2 219 asyitGqtlvvDgGl 233
                                       as+++G+++ +DgGl
  gi|336253378|ref|YP_004596485.1| 245 ASFVNGAEIPIDGGL 259
                                       **************7 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.8   0.0   1.1e-39   2.9e-36       2     189 ..       9     197 ..       8     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 124.8 bits;  conditional E-value: 1.1e-39
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklg 76 
                                       ++lvt  ssG+G+a a++l+++Ga+v++++r +++le++ + + e+  + +++a+q+D+td +++++lv++ v+++g
  gi|336253378|ref|YP_004596485.1|   9 AALVTASSSGLGLASARALLEAGANVTICGRDADRLERARDDFAETntAGDVIAVQADITDPDDISRLVSQTVEEFG 85 
                                       69*****************************************99988999************************** PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                       +ld Lv+ AG   s++f e++e++w + +++ +++v+++++++ +++l++++G+I  ++S + ++   g+    +  
  gi|336253378|ref|YP_004596485.1|  86 GLDHLVTSAGGPPSTTFLETDEQDWYQAYDLLVMSVVWTVEEAHEHLLESEQGTITCITSRTVREVADGLLLSNSVR 162
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmake 189
                                         v+gl++++++e+ap+ ir nav PG ++T+  +e
  gi|336253378|ref|YP_004596485.1| 163 RSVIGLMKTISREFAPE-IRANAVLPGTIETPRIEE 197
                                       ****************8.*************97665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.1   1.2e-13     3e-10       3     110 ..      10     115 ..       8     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.2e-13
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        l+t    gLGl+ ar l+e ga ++ +++R+a   e++++ +ae +  g +v +v+aD++d+d++++l+++  +e+
  gi|336253378|ref|YP_004596485.1|  10 ALVTASSSGLGLASARALLEAGA-NVTICGRDADRLERARDDFAETNTAG-DVIAVQADITDPDDISRLVSQTVEEF 84 
                                       58999999**************8.6999****999999999999988877.6888999******************* PP

                                       S---EEEE---------TTT--HHHHHHHHT CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvla 110
                                       + +   + +Ag    +++ e++++d+ q++ 
  gi|336253378|ref|YP_004596485.1|  85 GGLDHLVTSAGGPPSTTFLETDEQDWYQAYD 115
                                       **************************99875 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 !   15.7   0.1   4.1e-06      0.01       6      72 ..      19      98 ..      15     133 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.1e-06
                                      HHHHHHHHHHHC-T-EEEEEETTHHHCH.......HHHCTTTCEEEE--TT-CCHHHHHHT.......T-SEEEES--- CS
                    NAD_binding_10  6 vGrllvkellargghevtalvRnpekla.......eleaeeglevvegdvtdvedlaealk.......gadaVvsalgg 70
                                       G + ++ ll++g  +vt+  R++++l+       e   +  + +v++d+td++d+ + ++       g d  v+++gg
  gi|336253378|ref|YP_004596485.1| 19 LGLASARALLEAG-ANVTICGRDADRLErarddfaETNTAGDVIAVQADITDPDDISRLVSqtveefgGLDHLVTSAGG 96
                                      6888999*****5.***********99855553322334467789**************99777777777854444444 PP

                                      TC CS
                    NAD_binding_10 71 gg 72
                                        
  gi|336253378|ref|YP_004596485.1| 97 PP 98
                                      33 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 ?   11.5   0.0   5.5e-05      0.14      10      95 ..      20      97 ..      11     105 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.5e-05
                                      HHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                     GDP_Man_Dehyd 10 GsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshV 88
                                      G   a+ Lle g +v++  r+++ ++ +r +  a+   +++ +++  +++D+tD + + rl++++    v  +++  h 
  gi|336253378|ref|YP_004596485.1| 20 GLASARALLEAGANVTICGRDADRLERARDD-FAE---TNTAGDVIAVQADITDPDDISRLVSQT----VEEFGGLDHL 90
                                      6667899********9877777776655544.333...345689******************997....5566666666 PP

                                      HHHTTSH CS
                     GDP_Man_Dehyd 89 dvsfekP 95
                                       +s   P
  gi|336253378|ref|YP_004596485.1| 91 VTSAGGP 97
                                      6665555 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 ?    6.8   0.0    0.0015       3.8      32      75 ..       3      46 ..       1      65 [. 0.89
   2 ?    2.7   0.0     0.028        72      39      72 ..     116     150 ..      94     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0015
                                      ---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHH CS
                     THF_DHG_CYH_C 32 ielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlae 75
                                       el++  ++v   s+ +g + a  Lle++a Vt+c + ++ l++
  gi|336253378|ref|YP_004596485.1|  3 LELDDSAALVTASSSGLGLASARALLEAGANVTICGRDADRLER 46
                                      678899999**************************999887765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.028
                                       EEEE---TTTHHHHHHHHHCTT-EEEEE-TTS.CC CS
                     THF_DHG_CYH_C  39 vvvvGrsnivgkplallLleknatVtvchskt.kd 72 
                                        +v+    +v+++ + lL++++ t+t++ s+t ++
  gi|336253378|ref|YP_004596485.1| 116 LLVMSVVWTVEEAHEHLLESEQGTITCITSRTvRE 150
                                       566666778999999***************99444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00012       0.3       9      55 ..      19      66 ..      16      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                                      HHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEEC CS
                              ApbA  9 iGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrpp 55
                                      +G   a  L +aga+vt+++r++ rle+ +++  + ++ g    ++ +
  gi|336253378|ref|YP_004596485.1| 19 LGLASARALLEAGANVTICGRDAdRLERARDDFAETNTAGDVIAVQAD 66
                                      78888999*******************999998888877744444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2112.44
//
Query:       gi|336253379|ref|YP_004596486.1|  [L=279]
Description: UBA/THIF-type NAD/FAD binding protein [Halopiger xanaduensis SH-6]
Scores for 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-67  226.8   0.0    3.3e-67  226.4   0.0    1.0  1  ThiF             ThiF family
     0.0059   16.9   1.0      0.022   15.0   1.0    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.035   14.2   0.1       0.24   11.5   0.0    2.0  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.19   12.4   0.1       0.39   11.4   0.1    1.6  1  PglD_N           PglD N-terminal 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 !  226.4   0.0   7.3e-71   3.3e-67       1     242 [.      14     253 ..      14     259 .. 0.95

  Alignments for each domain:
  == domain 1  score: 226.4 bits;  conditional E-value: 7.3e-71
                                       THHHHHH..HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHH CS
                                       xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   1 ysrqlal..lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKae 75 
                                       ysr++ +  +g++gq++L + +vl+vGaGglGs+++++La++G+g+l +vD+D +e sNl+Rq+ +++ d+G+pK+e
  gi|336253379|ref|YP_004596486.1|  14 YSRHVIMdeIGPEGQQRLLEGSVLVVGAGGLGSPAIQYLAAAGIGRLGIVDDDAVERSNLQRQIVHGDGDVGRPKVE 90 
                                       7788666889******************************************************************* PP

                                       HHHHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  76 vaaealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvvi 152
                                       +aa+ ++++npdv+v +++ r+t+++ +++l+ ++D+V+da+Dn+++r+l+n+ cv  ++pl +++  +fegqv+++
  gi|336253379|ref|YP_004596486.1|  91 SAADYVAALNPDVDVDTYETRLTADN-VDDLVAEYDVVLDASDNFATRYLLNDHCVLTETPLSHGAIYRFEGQVTTF 166
                                       ************************98.69************************************************ PP

                                       EE......CCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECC CS
                                       xx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 153 ip......gktgcyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvd 223
                                        +      ++ +cy+Cl+p   e p++ +vp c ++ g   +++ +++ v++++a+e++k+l gk +l + +l  +d
  gi|336253379|ref|YP_004596486.1| 167 TNerggeaEDPPCYRCLFP---EAPEPGTVPDC-ATTG---VLGVLPGTVGCIQATEVVKYLLGKGELLEGRLLMYD 236
                                       5447888899*********...***********.****...*********************999999999999*** PP

                                       TTTTEEEEECCEEEEEEC- CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              ThiF 224 llesrfenvelerakkskc 242
                                       + +++fe+ve+++++   c
  gi|336253379|ref|YP_004596486.1| 237 AMDMSFETVEMRSNPS--C 253
                                       ***********99884..4 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 !   15.0   1.0   4.8e-06     0.022       1      83 [.      36     137 ..      36     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.8e-06
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.........................TTTCEEEE CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.........................lgvrfeai 52 
                                       vl++GaG+ G++++++la+ +    ++ ++d +  +  +l  ++                           v+   +
  gi|336253379|ref|YP_004596486.1|  36 VLVVGAGGLGSPAIQYLAAAGIG--RLGIVDDDAVERSNLQRQIvhgdgdvgrpkvesaadyvaalnpdVDVDTYET 110
                                       89*****************9855..********99999999988****************98888664444444455 PP

                                       E--TTTHHHHHHHHHTTSSEEEE-SSGGGHH CS
                   Sacchrp_dh_NADP  53 aldaenyeavLaallkegdlvvnlsppissl 83 
                                        l+a+n+++    l++e+d+v+++s ++ ++
  gi|336253379|ref|YP_004596486.1| 111 RLTADNVDD----LVAEYDVVLDASDNFATR 137
                                       566666666....8889********999654 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    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      10      44 ..      31      65 ..      24      85 .. 0.82
   2 ?    0.2   0.0      0.16   7.1e+02      64      83 ..     112     131 ..      90     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.3e-05
                                      .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEES CS
                      Shikimate_DH 10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNR 44
                                      l e  vl++GaG +++ ++++L+a+g+ ++ ++  
  gi|336253379|ref|YP_004596486.1| 31 LLEGSVLVVGAGGLGSPAIQYLAAAGIGRLGIVDD 65
                                      55678**********************99988865 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.16
                                       EEGCGHHHHHHT-SEEEE-S CS
                      Shikimate_DH  64 lkleelkellaeadvvisat 83 
                                       l+ +++++l+ae+dvv+ a 
  gi|336253379|ref|YP_004596486.1| 112 LTADNVDDLVAEYDVVLDAS 131
                                       45678899999999998775 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   8.7e-05      0.39       2      36 ..      36      69 ..      35     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.7e-05
                            PglD_N  2 ivIiGaGGhgkvvadiieangeyeiigflDdnkkt 36
                                      ++++GaGG g   ++ + a g    +g++Dd+  +
  gi|336253379|ref|YP_004596486.1| 36 VLVVGAGGLGSPAIQYLAAAG-IGRLGIVDDDAVE 69
                                      789******************.9999***998632 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2163.83
//
Query:       gi|336253380|ref|YP_004596487.1|  [L=61]
Description: hypothetical protein Halxa_1983 [Halopiger xanaduensis SH-6]
Scores for 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   17.4   0.5     0.0032   17.4   0.5    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.013   14.9   5.8      0.026   13.9   5.5    1.7  2  zf-ribbon_3     zinc-ribbon domain
      0.019   15.7   0.4      0.021   15.6   0.4    1.1  1  zinc_ribbon_15  zinc-ribbon family
      0.027   14.0   0.8       0.04   13.5   0.8    1.2  1  RecR            RecR protein
       0.14   12.2   3.3        3.7    7.6   0.5    2.9  3  DUF1610         Domain of unknown function (DUF1610)
       0.26   11.2   3.1        1.3    9.0   3.1    1.9  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        0.4   10.8   5.7        2.4    8.3   5.7    2.0  1  UPF0547         Uncharacterised protein family UPF0547
       0.67   10.1   4.2       0.41   10.8   0.5    2.1  2  Zn-ribbon_8     Zinc ribbon domain
        3.8    7.4   5.9        7.5    6.5   1.2    2.2  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO


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 !   17.4   0.5   1.6e-06    0.0032       1      19 [.      38      56 ..      14      61 .] 0.67

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                               DZR  1 CpqCgeelppdarfCseCg 19
                                      Cp+Cg  ++ +a  Cs Cg
  gi|336253380|ref|YP_004596487.1| 38 CPECGGLHDTSADNCSVCG 56
                                      5555555555555555555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   5.5   1.3e-05     0.026       2      23 ..      35      56 ..      34      58 .. 0.93
   2 ?    7.5   0.6    0.0014       2.7       3      11 ..      50      59 ..      48      61 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                       zf-ribbon_3  2 tvrCPnCGa.plssddnvCpyCG 23
                                      +++CP+CG  + ++++ +C  CG
  gi|336253380|ref|YP_004596487.1| 35 KKQCPECGGlH-DTSADNCSVCG 56
                                      689******88.**********9 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0014
                       zf-ribbon_3  3 vrCPnCGa.p 11
                                       +C+ CG+ p
  gi|336253380|ref|YP_004596487.1| 50 DNCSVCGWeP 59
                                      58******88 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.4   1.1e-05     0.021      53      86 .]      23      56 ..      11      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                    zinc_ribbon_15 53 lgkeiekkessekkeCknCgkeveeefkyCpkCg 86
                                      + +e+  +++ +kk+C++Cg   + + + C+ Cg
  gi|336253380|ref|YP_004596487.1| 23 SVDEVGWEQEYNKKQCPECGGLHDTSADNCSVCG 56
                                      455555566777*********************9 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.8     2e-05      0.04      17      34 ..      36      55 ..      33      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                                      EE-TTT--E..ESSSS-CCC CS
                              RecR 17 rhCsrCgnl..teedlCaIC 34
                                      ++C++Cg l  t  d C++C
  gi|336253380|ref|YP_004596487.1| 36 KQCPECGGLhdTSADNCSVC 55
                                      79*******6666689**** PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.58   1.2e+03       8      15 ..      17      24 ..      16      25 .. 0.87
   2 ?    7.6   0.5    0.0018       3.7      18      23 ..      37      42 ..      30      43 .. 0.81
   3 ?    3.2   0.5     0.045        89       1       7 [.      52      58 ..      52      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.58
                           DUF1610  8 laprErav 15
                                      l++r+++v
  gi|336253380|ref|YP_004596487.1| 17 LTDRGHSV 24
                                      899**998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0018
                           DUF1610 18 pCPNCG 23
                                       CP+CG
  gi|336253380|ref|YP_004596487.1| 37 QCPECG 42
                                      5****9 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.045
                           DUF1610  1 CtSCGae 7 
                                      C+ CG+e
  gi|336253380|ref|YP_004596487.1| 52 CSVCGWE 58
                                      999***7 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 ?    9.0   3.1   0.00066       1.3      16      53 ..      21      56 ..      13      60 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00066
                    OrfB_Zn_ribbon 16 Gikveev..npayTSktCseCgsknkealsgrtfkCpnCg 53
                                      G +v ev  +++y  k+C+eCg  +++       +C+ Cg
  gi|336253380|ref|YP_004596487.1| 21 GHSVDEVgwEQEYNKKQCPECGGLHDT----SADNCSVCG 56
                                      555655533577899********9999....444566666 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.7    0.0012       2.4       1      22 [.      36      57 ..      36      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                           UPF0547  1 KvCPeCeakvPvaaqfCphCGy 22
                                      K+CPeC     ++a  C+ CG 
  gi|336253380|ref|YP_004596487.1| 36 KQCPECGGLHDTSADNCSVCGW 57
                                      9******999999999999996 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5    0.0002      0.41      23      34 ..      32      43 ..      18      48 .. 0.69
   2 ?    1.4   0.2      0.18   3.5e+02      26      33 ..      49      56 ..      43      60 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                       Zn-ribbon_8 23 dapltaCPeCgs 34
                                      + ++++CPeCg+
  gi|336253380|ref|YP_004596487.1| 32 EYNKKQCPECGG 43
                                      444667*****8 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.18
                       Zn-ribbon_8 26 ltaCPeCg 33
                                         C  Cg
  gi|336253380|ref|YP_004596487.1| 49 ADNCSVCG 56
                                      34488888 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.2    0.0038       7.5      10      20 ..      32      42 ..      30      45 .. 0.84
   2 ?    3.6   0.3     0.031        61      13      20 ..      49      56 ..      43      58 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0038
                         zf-C2H2_3 10 sfgasqCkeCg 20
                                      +++++qC+eCg
  gi|336253380|ref|YP_004596487.1| 32 EYNKKQCPECG 42
                                      567899****8 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.031
                         zf-C2H2_3 13 asqCkeCg 20
                                      a  C++Cg
  gi|336253380|ref|YP_004596487.1| 49 ADNCSVCG 56
                                      345****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 493.96
//
Query:       gi|336253381|ref|YP_004596488.1|  [L=52]
Description: hypothetical protein Halxa_1984 [Halopiger xanaduensis SH-6]
Scores for 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   17.9   0.4     0.0032   17.4   0.4    1.2  1  DZR            Double zinc ribbon
  ------ inclusion threshold ------
      0.012   15.7   1.8      0.022   14.9   1.8    1.5  1  Zn-ribbon_8    Zinc ribbon domain
      0.013   14.9   0.7        3.1    7.3   0.0    2.2  2  zf-ribbon_3    zinc-ribbon domain
      0.051   13.4   1.9       0.67    9.8   0.1    2.2  2  zf-HYPF        HypF finger
       0.06   13.1   3.8       0.92    9.3   0.1    2.2  2  zinc_ribbon_2  zinc-ribbon domain
       0.06   13.6   0.5      0.072   13.3   0.5    1.2  1  DCR            Dppa2/4 conserved region
      0.099   12.6   0.1       0.21   11.5   0.0    1.6  2  DUF4428        Domain of unknown function (DUF4428)
       0.41   10.4   3.8        4.7    7.1   0.1    2.1  2  A2L_zn_ribbon  A2L zinc ribbon domain
       0.62   10.2   4.5          4    7.6   0.0    2.1  2  XPA_N          XPA protein N-terminal
        1.6    8.4   6.0        4.7    6.9   6.0    1.7  1  RecR           RecR 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 !   17.4   0.4   1.8e-06    0.0032      15      41 ..       4      40 ..       2      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                               DZR 15 CseCgtklkavaa..........edrCpsCgekvdpe 41
                                      C++Cg+ +  + a          +++Cp C+ k+  +
  gi|336253381|ref|YP_004596488.1|  4 CQNCGSFVTDAYArvftppgvddPRVCPDCQDKIRDG 40
                                      ********988889*****************998766 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.8   1.2e-05     0.022       7      36 ..       3      37 ..       2      39 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                       Zn-ribbon_8  7 rCeeCghefe......vlqsisdap...lta.CPeCgsev 36
                                      +C++Cg  f       v+ +    p   ++  CP+C+ + 
  gi|336253381|ref|YP_004596488.1|  3 ECQNCG-SFVtdayarVFTP----PgvdDPRvCPDCQDKI 37
                                      6*****.5554866555555....44445555****8765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0017       3.1       4      13 ..       3      12 ..       1      17 [. 0.72
   2 ?    6.4   0.1    0.0033       5.9      17      25 ..      28      36 ..      25      42 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0017
                       zf-ribbon_3  4 rCPnCGapls 13
                                      +C nCG+ ++
  gi|336253381|ref|YP_004596488.1|  3 ECQNCGSFVT 12
                                      6888988444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0033
                       zf-ribbon_3 17 nvCpyCGtk 25
                                      +vCp C+ k
  gi|336253381|ref|YP_004596488.1| 28 RVCPDCQDK 36
                                      789999755 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.039        69      24      28 ..       4       8 ..       3      12 .. 0.84
   2 ?    9.8   0.1   0.00037      0.67       1      13 [.      29      41 ..      29      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.039
                                      -TTTS CS
                           zf-HYPF 24 CtnCG 28
                                      C nCG
  gi|336253381|ref|YP_004596488.1|  4 CQNCG 8 
                                      99**9 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00037
                                      --HHHHHHHC-TT CS
                           zf-HYPF  1 lCedClrEykdpl 13
                                      +C+dC+ +++d +
  gi|336253381|ref|YP_004596488.1| 29 VCPDCQDKIRDGA 41
                                      6********9976 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   0.7     0.012        21       2       6 ..       4       8 ..       2      10 .. 0.68
   2 ?    9.3   0.1   0.00051      0.92       2      13 ..      30      41 ..      29      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.012
                     zinc_ribbon_2 2 CpnCG 6
                                     C nCG
  gi|336253381|ref|YP_004596488.1| 4 CQNCG 8
                                     66666 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00051
                     zinc_ribbon_2  2 CpnCGaelqdna 13
                                      Cp C  ++ d+a
  gi|336253381|ref|YP_004596488.1| 30 CPDCQDKIRDGA 41
                                      **********98 PP

>> DCR  Dppa2/4 conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5     4e-05     0.072      46      64 ..      16      34 ..       2      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
                               DCR 46 acifpppgleDNlLCpecv 64
                                      a +f+ppg++D  +Cp+c 
  gi|336253381|ref|YP_004596488.1| 16 ARVFTPPGVDDPRVCPDCQ 34
                                      578***************6 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2       1.4   2.5e+03      23      27 ..       4       8 ..       4      14 .. 0.80
   2 ?   11.5   0.0   0.00012      0.21      18      33 ..      25      40 ..      17      48 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                           DUF4428 23 CkdCl 27
                                      C++C 
  gi|336253381|ref|YP_004596488.1|  4 CQNCG 8 
                                      88885 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00012
                           DUF4428 18 eDgyvCkdClkKlsef 33
                                      +D  vC+dC  K+ ++
  gi|336253381|ref|YP_004596488.1| 25 DDPRVCPDCQDKIRDG 40
                                      6778********9666 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 ?    4.6   0.6     0.015        27      24      29 ..       4       9 ..       3      12 .. 0.77
   2 ?    7.1   0.1    0.0026       4.7      19      28 ..      25      34 ..      24      34 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.015
                     A2L_zn_ribbon 24 CieCga 29
                                      C++Cg+
  gi|336253381|ref|YP_004596488.1|  4 CQNCGS 9 
                                      888886 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0026
                     A2L_zn_ribbon 19 qgylvCieCg 28
                                      ++ +vC++C+
  gi|336253381|ref|YP_004596488.1| 25 DDPRVCPDCQ 34
                                      6779*****7 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0022         4       2      15 ..       2      15 ..       1      17 [. 0.88
   2 ?    3.6   1.9      0.04        72      23      31 ..      28      36 ..      26      39 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0022
                             XPA_N  2 pkCdeCgkefldSy 15
                                      p+C+ Cg+   d y
  gi|336253381|ref|YP_004596488.1|  2 PECQNCGSFVTDAY 15
                                      89*****9888877 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.04
                             XPA_N 23 sVCDkCRDk 31
                                      +VC  C Dk
  gi|336253381|ref|YP_004596488.1| 28 RVCPDCQDK 36
                                      566666665 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.0    0.0026       4.7      18      40 .]       3      39 ..       1      39 [. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0026
                                      E-TTT--EESSS..............S-CCCCSTTSE CS
                              RecR 18 hCsrCgnlteed..............lCaICsdprRD 40
                                       C++Cg + ++               +C+ C+d+ RD
  gi|336253381|ref|YP_004596488.1|  3 ECQNCGSFVTDAyarvftppgvddprVCPDCQDKIRD 39
                                      69*****95555599999999999999*******999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 424.39
//
Query:       gi|336253382|ref|YP_004596489.1|  [L=632]
Description: UvrD/REP helicase [Halopiger xanaduensis SH-6]
Scores for 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-25   89.3   0.2    2.2e-11   43.8   0.0    2.4  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
      2e-24   86.6   0.0    1.1e-23   84.2   0.0    2.2  2  AAA_19           AAA domain
      5e-14   52.4   0.1    1.5e-08   34.4   0.0    2.3  2  UvrD_C           UvrD-like helicase C-terminal domain
    1.6e-09   37.8   0.3    2.5e-05   24.1   0.0    3.0  3  AAA_30           AAA domain
    2.2e-09   37.0   0.3     0.0034   17.2   0.0    2.8  3  UvrD_C_2         UvrD-like helicase C-terminal domain
    2.8e-05   24.0   0.2        4.2    7.0   0.0    4.2  4  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0011   18.8   0.0     0.0028   17.5   0.0    1.7  1  AAA_11           AAA domain
     0.0018   16.4   0.0     0.0028   15.8   0.0    1.2  1  Herpes_ori_bp    Origin of replication binding protein
     0.0024   17.7   0.1        1.1    9.0   0.0    2.7  3  DEAD             DEAD/DEAH box helicase
     0.0039   17.4   0.1        2.1    8.6   0.0    3.2  3  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.015   14.5   0.0        1.5    8.0   0.0    3.0  3  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.12   12.0   1.0       0.41   10.2   0.0    2.4  3  AAA_25           AAA domain
       0.26   11.7   1.7        1.9    8.9   0.2    2.8  2  AAA_17           AAA domain
        1.2    9.5   4.2        1.3    9.4   0.6    2.9  3  AAA_16           AAA ATPase domain


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 !   43.8   0.0   1.7e-14   2.2e-11      18     105 ..      11      84 ..       2     124 .. 0.88
   2 !   43.0   0.1     3e-14   3.9e-11     256     310 ..     221     275 ..     164     280 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.7e-14
                                       EEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-HHHHHHHHHCTTSEE CS
                     UvrD-helicase  18 veAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdderlrlalqnlseani 94 
                                       +  ++GsGKT+ l + + + +++ +++ ++ilvv +T++Aa+E +eR++e+l ++ +              + + n+
  gi|336253382|ref|YP_004596489.1|  11 LFGGPGSGKTTALLDHVEEILDQDGVTFRDILVVSYTRAAAQEVRERLAERLDESPR--------------ALQGNV 73 
                                       6789************************************************99863..............445678 PP

                                       EEHHHHHHHHH CS
                     UvrD-helicase  95 sTlHsfcqkil 105
                                       +T+H+ ++ +l
  gi|336253382|ref|YP_004596489.1|  74 CTMHAKAYDLL 84 
                                       88887777766 PP

  == domain 2  score: 43.0 bits;  conditional E-value: 3e-14
                                       HSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG--GGGGTB-THHHHHH CS
                     UvrD-helicase 256 rykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQsIYgFRgAdielflkk 310
                                        ++++ iDE+QD    Qy++ +    + +++++ GD++Q +Y+++gAd+ l+l++
  gi|336253382|ref|YP_004596489.1| 221 SVDYLVIDEFQDITTLQYDVYEEWKPHMKQVLIAGDDDQVVYSWQGADPALLLEE 275
                                       67999***********************9**********************9987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0   8.3e-27   1.1e-23       8     144 ..       4     263 ..       1     265 [. 0.92
   2 ?   -1.9   0.0       2.9   3.8e+03     107     126 ..     393     413 ..     367     418 .. 0.71

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 8.3e-27
                            AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae........atTiHrla 76 
                                       ++ kv  + +GpG+GKT+ l   v++++++ gv  ++il+v++t+ Aa+e+rerla+ + e         +T+H+ a
  gi|336253382|ref|YP_004596489.1|   4 TETKVTRLFGGPGSGKTTALLDHVEEILDQDGVTFRDILVVSYTRAAAQEVRERLAERLDEspralqgnVCTMHAKA 80 
                                       6789999************************************************66555589999999*****999 PP

                            AAA_19  77 l............................................................................ 77 
                                                                                                                    
  gi|336253382|ref|YP_004596489.1|  81 Ydlldlsrsdvigesekeefceeyglefedeysgagrrtarsttignkiiatsqwlqrtsrdvsdwydvpfqwdeee 157
                                       9**************************************************************************** PP

                            AAA_19  78 ........................................ldfddlltealelleeaeeekklqeeellivDEfqdv 114
                                                                                  ++ +   + +le+ ++++ l + ++l++DEfqd+
  gi|336253382|ref|YP_004596489.1| 158 vrlppeidpnaqegnkytptwpsdddridvpeairawrsyK-GEQGKIGFADMLERVKQRSLLPSVDYLVIDEFQDI 233
                                       *******************************9999998853.3344445667778878888887777********** PP

                            AAA_19 115 delqyrLlkallgekkklllvGDpdQliyv 144
                                       + lqy + ++++++ k++l+ GD+dQ +y+
  gi|336253382|ref|YP_004596489.1| 234 TTLQYDVYEEWKPHMKQVLIAGDDDQVVYS 263
                                       ************88899**********997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.9
                            AAA_19 107 ivDEfqdvd.elqyrLlkall 126
                                        +DE  dv+  ++ rL + l 
  gi|336253382|ref|YP_004596489.1| 393 AIDEGEDVTgLQARRLADMLQ 413
                                       699999999555555555544 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 !   15.7   0.0   5.7e-06    0.0073       2     107 ..     282     379 ..     281     391 .. 0.86
   2 !   34.4   0.0   1.2e-11   1.5e-08     284     344 ..     493     573 ..     479     576 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.7e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C   2 vLekNyRStksLlkaankflenilnrralekek..ktvekgekivvleaeteeeEaekiaatikalleknekledia 76 
                                        L   yR ++++l+a+n+ +++i +r    ++k  k++++g  ++ + +++  +  +++ +t+ + +       ++ 
  gi|336253382|ref|YP_004596489.1| 282 ILPNSYRLPSNVLNAVNQEIRHIEKR----QDKdlKPRKEGGAVEARANASMLDVVRNVRRTLVETD------GSVM 348
                                       56677***************999999....33346*******9**9999999999888888777776......**** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  77 vLvRsnkdadkiskaLkkegipfnvvdeekf 107
                                       vL+R  ++  ++ +++ +egipf+ + ++++
  gi|336253382|ref|YP_004596489.1| 349 VLFRARYQMFQFIDEFITEGIPFTSLTDQRM 379
                                       ***********************98877665 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 1.2e-11
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...................xxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 284 kekipiiTiHqAKGlEFdvVfl.agleegtfPsyrskk...................ekrleEEkRlfYVaiTRAkk 340
                                        +++ + TiH+AKG E d V++  +l+e+ + ++ ++                        + E+R+fYV+++RA++
  gi|336253382|ref|YP_004596489.1| 493 TDRVRVGTIHSAKGREADHVIVgTDLTEKVVEQMVATVddpedvpgveeftkstspvPVLTDNERRVFYVGMSRARE 569
                                       389*******************55777777774444446666777777777777888555799************** PP

                                       xxxx RF
                            UvrD_C 341 rLfi 344
                                       rL++
  gi|336253382|ref|YP_004596489.1| 570 RLVL 573
                                       **86 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.9e-08   2.5e-05      14      67 ..       2      59 ..       1      92 [. 0.83
   2 !    9.8   0.0   0.00048      0.62      76     175 ..     209     307 ..     191     326 .. 0.78
   3 ?   -0.2   0.0      0.55     7e+02     131     159 ..     365     392 ..     363     431 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.9e-08
                            AAA_30 14 ltsgdrvavltGpAGtGKttal.kalreaweaag...grviglAptgkaAkvLaeelg 67
                                      +t++ +v+ l G++G+GKttal  +++e+++++g   +++++++ t +aA++++e l 
  gi|336253382|ref|YP_004596489.1|  2 ATTETKVTRLFGGPGSGKTTALlDHVEEILDQDGvtfRDILVVSYTRAAAQEVRERLA 59
                                      56777899***********98527889999999999999***************9876 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00048
                            AAA_30  76 llkrlkgrarlepg.tllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaGgvlrdlveaagigtaeL 151
                                       +l+r k+r +l p+ + l++DE   + t q  ++ ++ + +  +v+++GD++Q     +G+  ++l+e+a  + + L
  gi|336253382|ref|YP_004596489.1| 209 MLERVKQR-SLLPSvDYLVIDEFQDITTLQY-DVYEEWKPHMKQVLIAGDDDQVVYSWQGADPALLLEEAVDEDIIL 283
                                       55555554.4445559**********99997.5899999999***********999999999999998888899999 PP

                            AAA_30 152 tevvRqkeseeraaalalregdae 175
                                        + +R  ++   a+ +++r+ + +
  gi|336253382|ref|YP_004596489.1| 284 PNSYRLPSNVLNAVNQEIRHIEKR 307
                                       999999888888888888865554 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.55
                            AAA_30 131 VeaGgvlrdlveaagigtaeLtevvRqke 159
                                       +++G ++++l+ ++++ t +Lt+ vR  e
  gi|336253382|ref|YP_004596489.1| 365 ITEGIPFTSLT-DQRMWTDRLTQYVRAVE 392
                                       66788888886.58889999999988744 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 ?   -2.5   0.0       3.7   4.8e+03      34      47 ..      38      51 ..      29      53 .. 0.76
   2 !   16.8   0.0   3.6e-06    0.0046       3      25 ..     497     518 ..     495     525 .. 0.82
   3 !   17.2   0.0   2.7e-06    0.0034      33      51 ..     555     573 ..     546     574 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.7
                          UvrD_C_2 34 rrrlLYtavTRAre 47
                                      +r +L +  TRA++
  gi|336253382|ref|YP_004596489.1| 38 FRDILVVSYTRAAA 51
                                      78888889999986 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.6e-06
                          UvrD_C_2   3 yaltihkaQGsefpaVivfdpdl 25 
                                        + tih a+G e+++Viv   dl
  gi|336253382|ref|YP_004596489.1| 497 RVGTIHSAKGREADHVIV-GTDL 518
                                       688**************9.4444 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 2.7e-06
                          UvrD_C_2  33 lrrrlLYtavTRAreklil 51 
                                         rr +Y++++RAre+l+l
  gi|336253382|ref|YP_004596489.1| 555 NERRVFYVGMSRARERLVL 573
                                       35***************98 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 !    7.0   0.0    0.0033       4.2       5      25 ..      13      31 ..      11      74 .. 0.77
   2 ?    4.8   0.0     0.015        20      61     141 ..     220     300 ..     186     338 .. 0.70
   3 ?   -3.7   0.0       6.4   8.2e+03      25      65 ..     384     423 ..     377     429 .. 0.60
   4 !    6.0   0.1     0.007         9     213     233 ..     551     574 ..     486     575 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0033
                   Viral_helicase1  5 GvpGcGKStlirkllrtslil 25
                                      G pG+GK+t++ + +++  il
  gi|336253382|ref|YP_004596489.1| 13 GGPGSGKTTALLDHVEE--IL 31
                                      89*********998877..43 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.015
                   Viral_helicase1  61 tkgkililDEylllhaGyill.laalskaklvilfGDplQipfhsrnasfllahlpsslshrvgrrttyllpsdvae 136
                                        + ++l++DE++  ++ + ++    +++ k+v++ GD  Q  ++ + a+     l+  +++       y+lps v +
  gi|336253382|ref|YP_004596489.1| 220 PSVDYLVIDEFQDITTLQYDVyEEWKPHMKQVLIAGDDDQVVYSWQGADPA-LLLEEAVDEDIILPNSYRLPSNVLN 295
                                       34799******99997555554456899*************9997655433.3344445566666667888888888 PP

                   Viral_helicase1 137 ilsak 141
                                       + ++ 
  gi|336253382|ref|YP_004596489.1| 296 AVNQE 300
                                       88776 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 6.4
                   Viral_helicase1  25 ltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgki 65 
                                       lt++++++e++ eg + ++ +  r++ ++l+    +tk + 
  gi|336253382|ref|YP_004596489.1| 384 LTQYVRAVEAIDEGEDVTGLQ-ARRLADMLQESAFGTKERD 423
                                       677888899999997555554.4444444444444444555 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.007
                   Viral_helicase1 213 s...esrenllvAlTRhrkslvil 233
                                           ++r +++v+++R+r++lv+l
  gi|336253382|ref|YP_004596489.1| 551 VltdNERRVFYVGMSRARERLVLL 574
                                       033456999**********99875 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.2e-06    0.0028      14      89 ..       3      72 ..       1     141 [. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.2e-06
                            AAA_11 14 lseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrglldsegekykpk 89
                                       +e+++t + G PG+gKT++++  ++++      ++++ + + iLv + + aA  e+ erl++  ld++ +  + +
  gi|336253382|ref|YP_004596489.1|  3 TTETKVTRLFGGPGSGKTTALLDHVEEI-----LDQDGVTFRDILVVSYTRAAAQEVRERLAE-RLDESPRALQGN 72
                                      566778999999****************.....46789************************9.555555554444 PP

>> Herpes_ori_bp  Origin of replication binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.2e-06    0.0028      59     100 ..      16      60 ..       2      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.2e-06
                     Herpes_ori_bp  59 GsGkttALiewLkevldsedls...vlvvsCRrsFtntlserfnr 100
                                       GsGkttAL+++++e+ld++ +    +lvvs  r+ ++++ er+++
  gi|336253382|ref|YP_004596489.1|  16 GSGKTTALLDHVEEILDQDGVTfrdILVVSYTRAAAQEVRERLAE 60 
                                       9***************9988644449**************99976 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00085       1.1      24      73 ..      16      64 ..       7      93 .. 0.79
   2 ?    5.5   0.1      0.01        13     110     152 ..     208     251 ..     200     263 .. 0.68
   3 ?   -3.1   0.0       4.5   5.7e+03      68     112 ..     305     351 ..     288     361 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00085
                                      TSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 24 GsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky 73
                                      GsGKT+a l  v +i+ +++g t   +l+v+ tr+ a+++ ++l +++++
  gi|336253382|ref|YP_004596489.1| 16 GSGKTTALLDHVEEIL-DQDGVTFRDILVVSYTRAAAQEVRERLAERLDE 64
                                      9******666666555.779***********************9999885 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.01
                                       HHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHH CS
                                       xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 110 dllstgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpqi 152
                                       d+l++ k +  l +v +lV+DE + +    + d +++   +++q 
  gi|336253382|ref|YP_004596489.1| 208 DMLERVKQRslLPSVDYLVIDEFQDITTL-QYDVYEEWKPHMKQV 251
                                       4553333223399***********99998.666666666666555 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4.5
                                       HHHTTTSTSEEEEEETTSSHHHHHHHHH...TTCSEEEEEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
                              DEAD  68 kkfkkyidlrvlliiggvaardqlskld...ngvdivvgtpgrlddll 112
                                       +k+ ++ dl+     g v+ar + s ld   n  + +v t g ++ l+
  gi|336253382|ref|YP_004596489.1| 305 EKRQDK-DLKPRKEGGAVEARANASMLDvvrNVRRTLVETDGSVMVLF 351
                                       333332.35555555666666666666443144777888887777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0016       2.1       7      70 ..       8      68 ..       3      94 .. 0.64
   2 ?    4.6   0.0     0.028        36      74     109 ..     201     241 ..     168     260 .. 0.71
   3 ?   -0.6   0.0       1.2   1.5e+03      74     108 ..     375     404 ..     302     448 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka 70
                                      ++ ++G +G+GKTt l   +e+   +   + ++  vv++t ++     +++++l++ l+++  a
  gi|336253382|ref|YP_004596489.1|  8 VTRLFGGPGSGKTTALLDHVEEILDQDGVTFRDILVVSYTRAAAQ---EVRERLAERLDESPRA 68
                                      66799********98877766664333333355555555555544...7777777777777666 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.028
                            AAA_22  74 sseellealeqalrarav...ielliiDEaqhlr..seeal 109
                                       + +  ++ + + +++r+    +  l+iDE+q ++  + +++
  gi|336253382|ref|YP_004596489.1| 201 QGKIGFADMLERVKQRSLlpsVDYLVIDEFQDITtlQYDVY 241
                                       5555556666666666666777*********9954434444 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.2
                            AAA_22  74 sseell.ealeqalraravielliiDEaqhlrseea 108
                                       + ++++ ++l+q++ra  +     iDE + + +  +
  gi|336253382|ref|YP_004596489.1| 375 TDQRMWtDRLTQYVRAVEA-----IDEGEDV-TGLQ 404
                                       4444444444444444443.....6666655.3222 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0012       1.5       8      55 ..      13      62 ..       7      81 .. 0.73
   2 ?    1.7   0.0     0.096   1.2e+02      96     155 ..     189     252 ..     181     320 .. 0.66
   3 ?    0.3   0.0      0.24   3.1e+02     280     324 ..     497     541 ..     494     574 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0012
                           DUF2075  8 GvaGtGKtvvllnllaeleddeeertavylsvN..hplvlvlrealakke 55
                                      G++G+GKt  ll  + e+ d++    + +l+v+  ++  + +re+la++ 
  gi|336253382|ref|YP_004596489.1| 13 GGPGSGKTTALLDHVEEILDQDGVTFRDILVVSytRAAAQEVRERLAERL 62
                                      9*****************55554444444444311666677788777766 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.096
                           DUF2075  96 EAhrlltksdqaekqse.enqlkelmkrak...vvvalvDegQelntgeigteeelkklakkle 155
                                       EA r++ + + ++ + +  ++l+++ +r+    v  +++De Q ++t ++   ee k  +k++ 
  gi|336253382|ref|YP_004596489.1| 189 EAIRAWRSYKGEQGKIGfADMLERVKQRSLlpsVDYLVIDEFQDITTLQYDVYEEWKPHMKQVL 252
                                       8889999655555555546677777666557778889999999999998877777555555544 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.24
                           DUF2075 280 evgseytiQGleldyvgviiGpdlvyr..keedrikfrgkksedkea 324
                                       +vg+++++ G e+d v+v  G dl+ +  ++   ++ +++ +  +e 
  gi|336253382|ref|YP_004596489.1| 497 RVGTIHSAKGREADHVIV--GTDLTEKvvEQMVATVDDPEDVPGVEE 541
                                       59************8765..777776632333333333333333344 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00032      0.41      33      78 ..       6      45 ..       3      93 .. 0.70
   2 ?   -2.0   0.0       1.8   2.3e+03     132     155 ..     208     234 ..     178     254 .. 0.70
   3 ?   -3.3   0.1       4.3   5.5e+03     101     137 ..     398     429 ..     376     438 .. 0.42

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00032
                            AAA_25 33 gelallaGapgtGKttlaldlalava..tGkpwlgpvapeqgkVlyvs 78
                                       +++ l+G pg+GKtt++ld + +++   G  + +         l+vs
  gi|336253382|ref|YP_004596489.1|  6 TKVTRLFGGPGSGKTTALLDHVEEILdqDGVTFRD--------ILVVS 45
                                      67999***************999999554554433........33333 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                            AAA_25 132 aleaaieeveg...vrlvviDplsral 155
                                       ++ ++++++     v+ +viD ++ ++
  gi|336253382|ref|YP_004596489.1| 208 DMLERVKQRSLlpsVDYLVIDEFQDIT 234
                                       334444443223449999999998765 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.3
                            AAA_25 101 arllvldlagveslpLfakdrggtlltadvdaleaai 137
                                       ++++ l+      ++L+++ ++++  t + d+l ++i
  gi|336253382|ref|YP_004596489.1| 398 EDVTGLQ-----ARRLADMLQESAFGTKERDDLFDTI 429
                                       2222222.....2333333333333333344444444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2    0.0015       1.9       1      18 [.      12      29 ..      12      45 .. 0.83
   2 ?    0.3   0.0      0.69   8.8e+02     103     128 ..      42      68 ..      25      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0015
                                      EE-TTSSHHHHHHHHHHH CS
                            AAA_17  1 lGgPGsGKgtqceklvek 18
                                      +GgPGsGK+t++   ve+
  gi|336253382|ref|YP_004596489.1| 12 FGGPGSGKTTALLDHVEE 29
                                      6*********98666665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.69
                                       SEEEEEE--HHHHHHHHHHH.TTST-T CS
                            AAA_17 103 daiilleadpeeilerrlkd.rtrgrd 128
                                        ++ +  a ++e++er++++ +++ r+
  gi|336253382|ref|YP_004596489.1|  42 LVVSYTRAAAQEVRERLAERlDESPRA 68 
                                       46677889999******9998888886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.6     0.001       1.3      28      91 ..      10      64 ..       2     279 .. 0.81
   2 ?   -0.5   0.2       1.1   1.4e+03      91     142 ..     374     430 ..     331     445 .. 0.57
   3 ?   -3.3   0.0       8.2   1.1e+04      78     127 ..     519     568 ..     500     578 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.001
                            AAA_16 28 llsGesGvGKsslv.rellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaes 91
                                       l G +G+GK++ + +++ + l +d g+++r   + +        +++a+a+ e+ + l++++++
  gi|336253382|ref|YP_004596489.1| 10 RLFGGPGSGKTTALlDHVEEILDQD-GVTFRDILVVS--------YTRAAAQ-EVRERLAERLDE 64
                                      57899*****987768888777777.45544444444........3444422.333333333222 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                            AAA_16  91 saeleawrekleeala......avpelagaeasrllellkrllallsrderplvlvlD 142
                                        ++++ w ++l++ ++      ++ +++g +a+rl++ l++ +  ++++++ l  ++D
  gi|336253382|ref|YP_004596489.1| 374 LTDQRMWTDRLTQYVRaveaidEGEDVTGLQARRLADMLQESAFGTKERDD-LFDTID 430
                                       334555666666666644444455556666668888877777755554444.555555 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8.2
                            AAA_16  78 reellrqlldeaesaeleawrekleealaavpelagaeasrllellkrll 127
                                       +e++++q+ +  ++ e  +  e++++++++vp l++ e++ ++  ++r+ 
  gi|336253382|ref|YP_004596489.1| 519 TEKVVEQMVATVDDPEDVPGVEEFTKSTSPVPVLTDNERRVFYVGMSRAR 568
                                       45677777777777777777777777777888888888866666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 4344.40
//
Query:       gi|336253383|ref|YP_004596490.1|  [L=431]
Description: hypothetical protein Halxa_1986 [Halopiger xanaduensis SH-6]
Scores for 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   18.2   0.1     0.0037   17.0   0.0    1.7  2  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 ?   -2.8   0.0      0.23   4.1e+03      88     121 ..      83     124 ..      80     138 .. 0.63
   2 !   17.0   0.0   2.1e-07    0.0037      65     166 ..     252     353 ..     191     396 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.23
                                       EEEEEEEEE.ECS.......SGSHHHHHHHHHHHHHHHHHHH CS
                     Peptidase_M24  88 yasDitrTv.lvG.......kftpeqrelyeavleaqeaaik 121
                                       +++  +rTv ++G         + ++ e++ av+ a++ a +
  gi|336253383|ref|YP_004596490.1|  83 WHGTAARTVvAIGydgidwlCRSSAASEVHPAVELATDLAER 124
                                       677788888667744333332222477777777777777665 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.1e-07
                                       BCSSSB--TTEEEEEEEEEEET.TEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSB.HHHHHHHHHHH CS
                     Peptidase_M24  65 tpndrvlkegdlvlidagaeyd.gyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvt.lseidaaarev 139
                                       ++++  l++g+++ + a+++   gy++  +rT++v+ +  ++r+++ av +a +   +++ +G++ ++++ a  ++ 
  gi|336253383|ref|YP_004596490.1| 252 DDSEAALRPGEPIGLSAAPRGPdGYHGRLARTLVVDGDGGRERRAHVAVTQAFRSSRAMLTAGTEsVTAVEADLEAE 328
                                       334666**************988**********99756668999***************999976555555555555 PP

                                       HHHT....TBCCGBSSCSEEEESSSSSEEEE CS
                     Peptidase_M24 140 lesa....glakffphglGHgvGlevhdegp 166
                                       +++     g+     +    g+Gle ++  p
  gi|336253383|ref|YP_004596490.1| 329 IRAFgedgGI-----ETRVAGIGLEPRER-P 353
                                       5553111155.....22345666666655.5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 3680.02
//
Query:       gi|336253384|ref|YP_004596491.1|  [L=88]
Description: hypothetical protein Halxa_1987 [Halopiger xanaduensis SH-6]
Scores for 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   16.5   0.1     0.0061   16.2   0.1    1.1  1  DUF4131   Domain of unknown function (DUF4131)
  ------ inclusion threshold ------
       0.11   12.5   0.6       0.27   11.2   0.6    1.7  1  Melittin  Melittin


Domain annotation for each model (and alignments):
>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   6.8e-07    0.0061       8      83 ..      13      80 ..       7      83 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.8e-07
                           DUF4131  8 vllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqllesgqeviveGvvaslpeltg 83
                                       l++++ ++l+ l +ll   +  +++++ ll+l+++l+ +++++p+p+  +   + +        G+v+++pe ++
  gi|336253384|ref|YP_004596491.1| 13 TLVLAIPAALAGLEFLL--VRGETTAGAMLLVLAAGLVALQHWVPTPGDVPELLAKR------ALGTVVKEPESDP 80
                                      44444444444444444..7899************************9976555443......5677777777665 PP

>> Melittin  Melittin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   3.1e-05      0.27       3      20 ..      37      54 ..      35      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                                      HHHHHHHHTHHHHHHHHH CS
                          Melittin  3 GAvLKvLttGLPALisWi 20
                                      GA+L vL  GL AL  W+
  gi|336253384|ref|YP_004596491.1| 37 GAMLLVLAAGLVALQHWV 54
                                      9***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); 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):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 691.43
//
Query:       gi|336253385|ref|YP_004596492.1|  [L=201]
Description: riboflavin synthase subunit alpha [Halopiger xanaduensis SH-6]
Scores for 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-45  151.6   0.1    5.2e-22   77.6   0.0    2.0  2  Lum_binding  Lumazine binding domain
  ------ inclusion threshold ------
       0.15   12.1   0.0       0.24   11.4   0.0    1.3  1  DUF5072      Domain of unknown function (DUF5072)


Domain annotation for each model (and alignments):
>> Lum_binding  Lumazine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.1   2.6e-24   2.3e-20       1      87 []       3      87 ..       3      87 .. 0.87
   2 !   77.6   0.0   5.8e-26   5.2e-22       1      87 []     100     186 ..     100     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 2.6e-24
                                      -S--SEEEEEEEEE.ECGCTTEETEESGGGGG..TTT-EEEETTEEEEEEEEEE.SSEEEEEEEHHHHHHSSGGG--TT CS
                       Lum_binding  1 tGiVeevgtvesiekeekledltielpelakylvekGdsiavnGvcLTVvteeveeeeftvdvipeTlerttlgelkvg 79
                                      tGiVee+g +++ e++ +  +l+i ++    + +e+G+si+v G+cLTV  +  + e+f+v ++ eT+ert lg+l++g
  gi|336253385|ref|YP_004596492.1|  3 TGIVEETGAIVARERTADGLRLRIGAD-AVATDLEHGQSISVSGACLTVE-DYADGEWFEVFLASETVERTYLGDLETG 79
                                      8************87766666666555.55555699*************5.66789*********************** PP

                                      SEEEEEEE CS
                       Lum_binding 80 dkVNlEra 87
                                      d VNlEra
  gi|336253385|ref|YP_004596492.1| 80 DAVNLERA 87
                                      ******96 PP

  == domain 2  score: 77.6 bits;  conditional E-value: 5.8e-26
                                       -S--SEEEEEEEEE.ECGCTTEETEES.GGGGG..TTT-EEEETTEEEEEEEEEE.SSEEEEEEEHHHHHHSSGGG- CS
                       Lum_binding   1 tGiVeevgtvesiekeekledltielp.elakylvekGdsiavnGvcLTVvteeveeeeftvdvipeTlerttlgel 76 
                                       +G+V++v+tv+++e+ e+ + ++++lp  +++y+vekG si+++G++LTV++ + +++++tv++ip+T+e ttl+e+
  gi|336253385|ref|YP_004596492.1| 100 QGHVDAVATVTNVESVEEDWFFEFDLPeGYERYVVEKG-SITLDGISLTVAEFDPDAGRVTVAIIPTTYELTTLSEK 175
                                       8************8888899999999999*********.***********96555699******************* PP

                                       -TTSEEEEEEE CS
                       Lum_binding  77 kvgdkVNlEra 87 
                                       ++gd V lE++
  gi|336253385|ref|YP_004596492.1| 176 APGDPVHLEVD 186
                                       *********97 PP

>> DUF5072  Domain of unknown function (DUF5072)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05      0.24      42      88 ..      93     138 ..      79     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                           DUF5072  42 rvavhiisppgssvtdlanvekvdellteyirlPeGykliavvesGk 88 
                                       r+  h++     +v+ + nve v+e     + lPeGy+ +  ve G 
  gi|336253385|ref|YP_004596492.1|  93 RFDGHVVQGHVDAVATVTNVESVEEDWFFEFDLPEGYERYV-VEKGS 138
                                       66667777777889999*********************874.55565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1546.28
//
Query:       gi|336253386|ref|YP_004596493.1|  [L=705]
Description: AAA ATPase [Halopiger xanaduensis SH-6]
Scores for 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   11.2   0.2       0.42   10.1   0.2    1.5  1  ProQ_C    ProQ C-terminal domain


Domain annotation for each model (and alignments):
>> ProQ_C  ProQ C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   2.3e-05      0.42      16      41 ..      16      41 ..      12      47 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 2.3e-05
                                      SSS---EEEEEE-SSSEEEEETTS-B CS
                            ProQ_C 16 GkspmpAtileiaKddVrVqLasGlv 41
                                       +  + +t+++++ + +rV+  sG+v
  gi|336253386|ref|YP_004596493.1| 16 ANGEVIGTVTDVDGEAARVKPRSGMV 41
                                      5677889******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (705 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1146  (0.0639188); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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):               1  [number of targets reported over threshold]
# CPU time: 0.75u 0.27s 00:00:01.02 Elapsed: 00:00:00.41
# Mc/sec: 5161.18
//
Query:       gi|336253387|ref|YP_004596494.1|  [L=335]
Description: hypothetical protein Halxa_1990 [Halopiger xanaduensis SH-6]
Scores for complete 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  148.6  16.9    1.5e-43  148.6  16.9    2.4  3  PrsW-protease  PrsW family intramembrane metalloprotease
  ------ inclusion threshold ------
        9.8    6.6  13.3        1.5    9.3   0.6    3.6  3  Cyd_oper_YbgE  Cyd operon protein YbgE (Cyd_oper_YbgE)


Domain annotation for each model (and alignments):
>> PrsW-protease  PrsW family intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.022     2e+02     115     135 ..      21      41 ..       8      53 .. 0.83
   2 ?   -1.4   0.2      0.15   1.4e+03      13      39 ..      52      77 ..      40      92 .. 0.41
   3 !  148.6  16.9   1.7e-47   1.5e-43       1     190 [.     101     290 ..     101     296 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.022
                     PrsW-protease 115 lqllilRillsvagHalftal 135
                                       ++++ +R+ +  ++H ++t++
  gi|336253387|ref|YP_004596494.1|  21 VSTWEPRSAVDRFAHSIYTGV 41 
                                       678999*************96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.15
                     PrsW-protease 13 galvavllalllntvlqall.raelgkf 39
                                       al+ ++ all++ +  a l + +lg f
  gi|336253387|ref|YP_004596494.1| 52 VALLITI-ALLVQPAQLA-LeTPWLGAF 77
                                      2333333.4444433222.222233332 PP

  == domain 3  score: 148.6 bits;  conditional E-value: 1.7e-47
                     PrsW-protease   1 eplwlllaaflwgalvavllalllntvlqallraelgkfiaeflaaflvaglvEEllKalgvllllllrrrefdepl 77 
                                       epl ll+a+f++ +l+a++ a+++n+++   l  +  ++++++l+++l++g+vEE++K+l+v  +++ r++ fd ++
  gi|336253387|ref|YP_004596494.1| 101 EPLGLLVATFVLAVLFATF-AAVVNSLIGPRL--QAIPVVGSLLFFYLIVGPVEETVKLLAVRTFAY-RSNSFDAVI 173
                                       79*****************.******999766..78889999************************6.********* PP

                     PrsW-protease  78 dGivygaavglGFavlEnllYyvqalpsaanegqlgglqllilRillsvagHalftallGiglglaksrrraarrvq 154
                                       dG vyga++glGFa++En++Y++ ++ +a     +++++++ +R+l++ +gH++++a++G++lglak+++r  ++ +
  gi|336253387|ref|YP_004596494.1| 174 DGAVYGAVAGLGFAAIENAIYITGTVAEADVGLLTAATGITTVRALVG-PGHVIYSAIAGYYLGLAKFNPR--HAGP 247
                                       **********************99999988889999999*********.******************9998..**** PP

                     PrsW-protease 155 illlglllavllHalwNllasl.aelllav......vgvllyv 190
                                       ++++gll+a+++Ha++N+++++ ++l + +      ++++ yv
  gi|336253387|ref|YP_004596494.1| 248 LVVKGLLVAAFIHATYNVTVGIvPNLIASMypigfgLAFIGYV 290
                                       **********************555544446755443344444 PP

>> Cyd_oper_YbgE  Cyd operon protein YbgE (Cyd_oper_YbgE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.6   0.00016       1.5       1      27 [.      45      71 ..      45      79 .. 0.91
   2 ?    2.0   2.6      0.03   2.7e+02       4      47 ..      80     123 ..      77     128 .. 0.88
   3 ?    0.3   0.1       0.1   9.1e+02      38      53 ..     172     187 ..     134     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00016
                     Cyd_oper_YbgE  1 lRaLslllAlalaavvlwdpelfaaat 27
                                      lR +++l+Al++++++l++p ++a +t
  gi|336253387|ref|YP_004596494.1| 45 LRGIVFLVALLITIALLVQPAQLALET 71
                                      799********************9876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.03
                     Cyd_oper_YbgE   4 LslllAlalaavvlwdpelfaaatsglshgllllllwavcagvv 47 
                                       Ls++ A +la++++    + +++++ l + ++l++l+a+ a+vv
  gi|336253387|ref|YP_004596494.1|  80 LSIVPAALLAGFIWYTDITSSEPLGLLVATFVLAVLFATFAAVV 123
                                       8999999999998888888889999999999*******999998 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.1
                     Cyd_oper_YbgE  38 llwavcagvvhGvGFr 53 
                                       ++ +   g v G+GF 
  gi|336253387|ref|YP_004596494.1| 172 VIDGAVYGAVAGLGFA 187
                                       5567778999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.20s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2671.39
//
Query:       gi|336253388|ref|YP_004596495.1|  [L=127]
Description: hypothetical protein Halxa_1991 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00065   19.9   0.1    0.00069   19.8   0.1    1.1  1  DUF1906   Domain of unknown function (DUF1906)


Domain annotation for each model (and alignments):
>> DUF1906  Domain of unknown function (DUF1906)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   3.8e-08   0.00069      61     131 ..      22      96 ..       5     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.8e-08
                           DUF1906  61 aaaaqGvadAkdAvaaasalGfpagttIYfaVDldaydsei..kaavlpYfkgwkealnakg....ykvGvYgsrnv 131
                                       +aa+++ a+A dA aaa ++ f+++ t+Y   D+d  +s +  +++ ++Y+   ++a + +g       GvY+  + 
  gi|336253388|ref|YP_004596495.1|  22 QAASEAIAEAVDADAAALEAFFERHETVYS--DMDMAHSSAdyPEHAVEYLDLTTHADELRGwlrfETWGVYVEDGR 96 
                                       4558999***********************..77776666666*******976665544444334488899988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1051.56
//
Query:       gi|336253389|ref|YP_004596496.1|  [L=484]
Description: RNA-binding protein AU-1 [Halopiger xanaduensis SH-6]
Scores for 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-17   61.6   2.4    1.5e-16   60.3   2.4    1.8  1  DUF402    Protein of unknown function (DUF402)


Domain annotation for each model (and alignments):
>> DUF402  Protein of unknown function (DUF402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   2.4   8.5e-21   1.5e-16       2      68 .]     389     454 ..     388     454 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 8.5e-21
                                       -EEEEE-TT-SEEEEEEEETTTEEEEEEEEEES--EE..E.EEE-EEEEEEESEEE......-HHHH CS
                            DUF402   2 lelwllplglwynvfhfldgdgrlqglYvDiatppevgegawktiDlyLDlvvspdgevevlDedEL 68 
                                       ++++ +++g+w+  + + d+dg+ +g Yv+i+tp e+ ++a++++Dly+D+++  dgeve++DedEL
  gi|336253389|ref|YP_004596496.1| 389 VAVTKFREGRWWYPTTYKDADGAAKGTYVNICTPVELFPDAVRYVDLYIDVIR-VDGEVEIVDEDEL 454
                                       5788899******************************99*************7.799*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3714.90
//
Query:       gi|336253390|ref|YP_004596497.1|  [L=342]
Description: formate/nitrite transporter [Halopiger xanaduensis SH-6]
Scores for 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-42  144.3  14.9    4.2e-42  144.1  14.9    1.0  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 !  144.1  14.9   2.4e-46   4.2e-42       1     235 [.      41     276 ..      41     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 144.1 bits;  conditional E-value: 2.4e-46
                                       HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCTTCHHHHHHHHHCCCHHHHHHHHHT---C CS
                    Form_Nir_trans   1 eivekvvaagvkkaklsldklfllgilAGafigfgvllalvvaaalaesnpglakllgglvFpvGlilvvllgaeLf 77 
                                       ei+e+v a++ ++++ s ++lf++g++AG+ i + +l + + a+ ++e      ++l+++++p+G+i+++l++ +L+
  gi|336253390|ref|YP_004596497.1|  41 EIFERVLASADEEIAISKQRLFFSGLAAGFAIVLTFLGHSIGATMFPE-----NSFLSAILYPIGFIYIILGQYQLY 112
                                       68999***************************************9843.....469********************* PP

                                       CCCCCHHHHHHCTTSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTGG....HHHHHHHHHCCCSS-HHHHHHHH CS
                    Form_Nir_trans  78 TgntllltlavlkkkvslkkllknwlvvllgNliGsllvalllvvlsgll....aekllsiaeaklslsfleaflrG 150
                                       T++tl  ++ vl++ +sl  ll++w+vv++gN++G++l a+l++  +g+l    +   +++a   l++ ++++f r+
  gi|336253390|ref|YP_004596497.1| 113 TEETLPPVALVLARIASLPLLLRVWIVVIIGNVVGAALGAYLIA-NGGVLdpeaTRVGAEFARIGLEHGWWAVFNRA 188
                                       *****8888888***************************96666.666654554666777888888*********** PP

                                       HHHHHHHHHHHHHHCC-SSHHHHHHHHHHHHHHHHHCT---HHHHHHHHHHHHHH...SHHHHHHHCHHHHHHHHHH CS
                    Form_Nir_trans 151 ilCNwlVclavwlalaakdvigkilaiflpifafvasgfeHsvanmfliplglll...tvadfilknlipvtlGNiv 224
                                        +++wlV+  vwl +a++d+i+++l+i++++++++a+++ H++   + +++ l++       +++  ++pv+lGN+v
  gi|336253390|ref|YP_004596497.1| 189 LFAGWLVAGVVWLDHASRDTISRLLLIYVIFYMIAAAELFHVITAACEVFYYLFVvdgASLAVVHEFWLPVFLGNTV 265
                                       *****************************************************988875567777889********* PP

                                       HHHCCHHHHHH CS
                    Form_Nir_trans 225 GGallvgllyl 235
                                       GG++lv+l+ +
  gi|336253390|ref|YP_004596497.1| 266 GGVFLVALVNY 276
                                       ********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 2841.93
//
Query:       gi|336253391|ref|YP_004596498.1|  [L=152]
Description: NUDIX hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-12   46.1   0.6    5.4e-12   45.9   0.6    1.1  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 !   45.9   0.6     3e-16   5.4e-12       5     110 ..       9     119 ..       5     129 .. 0.65

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 3e-16
                                       EEEEEEEETTSEEEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHSEEE.EEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   5 avgvvllnekgevLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtGlea.ellellgrlhylapydgpygd 80 
                                        ++++++++ ge+L+ +     ++g ++P+G++e gEtp+eA+ RE+ EE Gl+  +  + l+        ++++++
  gi|336253391|ref|YP_004596498.1|   9 KACAYITRGTGELLVFEGP--GHDGLQIPKGTLESGETPREALFREVMEESGLTTlNGAQHLS--------TDVWTR 75 
                                       67889***********977..77779**************************95534444444........334444 PP

                                       .....EEEEEEEEE.......EEECSGCSST..STTT....EEEEEEE CS
                             NUDIX  81 .....eheilyvfl.......eevegelepn..dene....vsevrwv 110
                                            ++++ ++f        +++++    +  d +e      e+rwv
  gi|336253391|ref|YP_004596498.1|  76 resppKRYVRHFFHanvheprDRWTH----TvtDGGEehgaEFEFRWV 119
                                       44574444445555544333333333....255444411123444577 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); 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: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.33
# Mc/sec: 1366.77
//
Query:       gi|336253392|ref|YP_004596499.1|  [L=329]
Description: Bile acid:sodium symporter [Halopiger xanaduensis SH-6]
Scores for 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-37  127.1  16.2    1.1e-36  126.3  16.2    1.4  1  SBF           Sodium Bile acid symporter family
    6.6e-13   48.7  20.6      8e-13   48.4  20.6    1.1  1  SBF_like      SBF-like CPA transporter family (DUF4137)
  ------ inclusion threshold ------
      0.067   11.6   8.3       0.13   10.7   8.3    1.5  1  Mem_trans     Membrane transport protein
        1.2    9.4   4.0        8.1    6.7   0.1    3.0  3  DUF3925       Protein of unknown function (DUF3925)


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 !  126.3  16.2   2.5e-40   1.1e-36       1     193 [.      44     226 ..      44     228 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 2.5e-40
                               SBF   1 ailLilmmfpmglkveveklkellkrpkalllglvlqwvikPllmfilakillrdlklepelavGlilvglapggam 77 
                                       ++lL+++m++mgl+++  +++++l+rp+ +++g + qw+++Pl +++l      +l l+ e+ vGlilvg+apgg++
  gi|336253392|ref|YP_004596499.1|  44 TPLLGIIMLGMGLTLTPADFRRILERPRDVFIGAMSQWLLMPLFAYLLVA----VLGLPWEIGVGLILVGAAPGGTA 116
                                       579***********************************************....8999******************* PP

                               SBF  78 snvwtylakGdlelsvvlvalstllailltPlllyllaksleqttlkvpieeivksvlivviiPliaGillryillk 154
                                       snv+tyl kGd++lsv++++++t++a+l++P ++  la++     + v++ ++ +++++vv++P++ G++lry+l +
  gi|336253392|ref|YP_004596499.1| 117 SNVMTYLGKGDVALSVTITTVTTIAAPLVMPAWVVALAGES----ISVTFGQLSETIVQVVLLPVVGGLVLRYLLDR 189
                                       *****************************************....*******************************9 PP

                               SBF 155 hkGrewfeskllpavspisligllltivvifalkgeliv 193
                                             + +  l ++++is+++++ ++++++ l++e i+
  gi|336253392|ref|YP_004596499.1| 190 Y--APLVAEIGLSIFPAISVVAIVAIVAAVVGLNVETIL 226
                                       4..66677788999*********************9986 PP

>> SBF_like  SBF-like CPA transporter family (DUF4137)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4  20.6   1.8e-16     8e-13       2     293 ..      17     293 ..      16     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.8e-16
                          SBF_like   2 wfllllilvillAslvPvfakaggtikaeyvikygValiFllsGlslsteellanlrnwrlhllvllisflltpliv 78 
                                       +f+l ++++  lA + P++     +i+a   i+ +  +i l  Gl+l   ++ + l++ r  ++  ++  ll+pl +
  gi|336253392|ref|YP_004596499.1|  17 YFVLWVVIAAPLALYTPETFT---PIAA--YITPLLGIIMLGMGLTLTPADFRRILERPRDVFIGAMSQWLLMPLFA 88 
                                       799999999999999998766...7865..68999999*************************************** PP

                          SBF_like  79 lalvsllkaaldpelliGllllaalPtTvssnvvmtsqAgGnealalceavignllGvfltPalvqlllsgssvsvd 155
                                       + lv +l    + e+ +Gl+l+ a+P   +snv mt   +G++al++  +++  ++++++ Pa+v +l  g+s+sv+
  gi|336253392|ref|YP_004596499.1|  89 YLLVAVLGL--PWEIGVGLILVGAAPGGTASNV-MTYLGKGDVALSVTITTVTTIAAPLVMPAWVVALA-GESISVT 161
                                       *******75..666******************6.9********************************98.89***** PP

                          SBF_like 156 yaevlkklllsvllPlvvGqvlqkifpklvkrlkkl.lkkvdslvlllivytsfstafaqgaftsvsh.iillvifn 230
                                       ++++   ++  vllP+v G vl++++ +++  + ++ l+ +  ++++ iv   +  a++     +v++  +  ++++
  gi|336253392|ref|YP_004596499.1| 162 FGQLSETIVQVVLLPVVGGLVLRYLLDRYAPLVAEIgLSIFPAISVVAIVA--IVAAVVG---LNVETiLGAGALVF 233
                                       **************************9997777666566667776666663..3444444...44444445556666 PP

                          SBF_like 231 vallLll.vvlvillllarllklskedeiavlfcgsaKslalgvplisvlfgsnpqlgllllPl 293
                                       +a++L+  ++l   +++  + ++ + ++ a+ f        l+v l++  f +    + +l+P+
  gi|336253392|ref|YP_004596499.1| 234 LAVVLHNgLGLGSGYAVGHATGMAEDRARACAFEVGLQNSGLAVALATAHFSA----SAALIPA 293
                                       6777775256777899*****99999999999988888889999999999965....4555665 PP

>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   8.3   2.8e-05      0.13     284     386 ..      46     149 ..      19     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.8e-05
                         Mem_trans 284 glpmalfslGlfLalqpkkiacgnsvatfa.lavRlilgPlvmlvavlavgLrgslllvaivqaAlPqgivlfviAk 359
                                        l+++++ +Gl+L   + +  ++     f+ ++   +l+Pl+ +++v+++gL+ +   ++i++ A P g+ + v++ 
  gi|336253392|ref|YP_004596499.1|  46 LLGIIMLGMGLTLTPADFRRILERPRDVFIgAMSQWLLMPLFAYLLVAVLGLPWEIGVGLILVGAAPGGTASNVMTY 122
                                       589**********998877666666665656999******************************************* PP

                         Mem_trans 360 eynvherelstllifgmlialpitlvy 386
                                       +   + ++  t+ +++++ a ++++ +
  gi|336253392|ref|YP_004596499.1| 123 LGKGDVALSVTITTVTTIAAPLVMPAW 149
                                       *99999999999999999999999988 PP

>> DUF3925  Protein of unknown function (DUF3925)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.026   1.2e+02      34      51 ..      11      28 ..       3      30 .. 0.86
   2 ?    6.7   0.1    0.0018       8.1      27      57 ..     148     183 ..     142     189 .. 0.72
   3 ?   -2.9   0.3       1.8   8.1e+03      45      59 ..     207     221 ..     194     225 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.026
                           DUF3925 34 GlflskyftlagmimlPl 51
                                      G f skyf l   i  Pl
  gi|336253392|ref|YP_004596499.1| 11 GEFTSKYFVLWVVIAAPL 28
                                      889*******99999886 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0018
                           DUF3925  27 GWvldvnGlflskyf.....tlagmimlPlvGGivG 57 
                                        Wv+ + G  +s  f     t+ + ++lP+vGG+v 
  gi|336253392|ref|YP_004596499.1| 148 AWVVALAGESISVTFgqlseTIVQVVLLPVVGGLVL 183
                                       688888888777777533335667789*******95 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.8
                           DUF3925  45 gmimlPlvGGivGlf 59 
                                          ++ +v  +vGl 
  gi|336253392|ref|YP_004596499.1| 207 VVAIVAIVAAVVGLN 221
                                       445567788888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.56
# Mc/sec: 1756.64
//
Query:       gi|336253393|ref|YP_004596500.1|  [L=89]
Description: hypothetical protein Halxa_1996 [Halopiger xanaduensis SH-6]
Scores for 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:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 713.26
//
Query:       gi|336253394|ref|YP_004596501.1|  [L=77]
Description: hypothetical protein Halxa_1997 [Halopiger xanaduensis SH-6]
Scores for 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   15.9   6.9      0.013   15.7   6.9    1.1  1  DUF3325        Protein of unknown function (DUF3325)
      0.021   14.2   0.5      0.024   14.0   0.5    1.0  1  Polysacc_synt  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> DUF3325  Protein of unknown function (DUF3325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   6.9   1.4e-06     0.013      28      84 ..       6      64 ..       3      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-06
                           DUF3325 28 relsaarrrllrlaGwlll..llslalavaawgwavGlvlwlgllslaAlllvllLayr 84
                                      r++++ar+ l+ ++++++l  ++++ l v+  +++vG+++++gll ++A++l +lL  r
  gi|336253394|ref|YP_004596501.1|  6 RSPAPARVLLVVVLAVAVLlpVAATTLEVSPYRVTVGTAVVTGLLLIGAVALPALLLAR 64
                                      678888888887766665511577777888888****************9998877544 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   2.7e-06     0.024      84     137 ..      14      67 ..      10      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-06
                     Polysacc_synt  84 vllvlvllfllllliaaflglpelavlylilalmllllvgvasfrrglfqgler 137
                                       +l+v++++++ll++ a++l  + ++v + ++ +++lll+g +++++ l+ +++ 
  gi|336253394|ref|YP_004596501.1|  14 LLVVVLAVAVLLPVAATTLEVSPYRVTVGTAVVTGLLLIGAVALPALLLARWQA 67 
                                       56677778888888888********************************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 680.54
//
Query:       gi|336253395|ref|YP_004596502.1|  [L=299]
Description: transferase hexapeptide repeat containing protein [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00033   20.3   5.5        1.1    9.1   0.2    3.6  3  Hexapep    Bacterial transferase hexapeptide (six repeats)
  ------ inclusion threshold ------
       0.47   10.2   8.3        2.1    8.2   0.2    3.0  3  Hexapep_2  Hexapeptide repeat of succinyl-transferase


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 !    9.1   0.2   0.00012       1.1      17      31 ..     146     160 ..     145     164 .. 0.77
   2 !    5.0   0.1    0.0024        22       3      17 ..     170     184 ..     167     186 .. 0.58
   3 !    6.9   0.2    0.0006       5.4      13      30 ..     212     229 ..     200     235 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00012
                                       ETTEEE-TTEEEETT CS
                           Hexapep  17 ggnVkIGdnvkIgag 31 
                                       g+n+++Gdn++I+  
  gi|336253395|ref|YP_004596502.1| 146 GHNITVGDNTVIHDD 160
                                       688999999998765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0024
                                       EEETTEEE-TTEEEE CS
                           Hexapep   3 vIGsnvlIgpfavig 17 
                                       +IG+ v I  +++++
  gi|336253395|ref|YP_004596502.1| 170 TIGDRVSISDGVHVY 184
                                       555555555555554 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0006
                                       TEEEETTEEE-TTEEEET CS
                           Hexapep  13 faviggnVkIGdnvkIga 30 
                                        ++++++ k+G+n+++ga
  gi|336253395|ref|YP_004596502.1| 212 DSMVRAGNKVGENAIVGA 229
                                       555556666677777666 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 ?   -3.2   0.1      0.83   7.4e+03       5       9 ..     132     136 ..     132     137 .. 0.61
   2 ?    8.2   0.2   0.00023       2.1       1      33 [.     148     184 ..     148     185 .. 0.88
   3 ?    5.8   0.3    0.0013        12       3      15 ..     220     232 ..     218     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.83
                                       -TT-E CS
                         Hexapep_2   5 GdnCl 9  
                                       Gd+C 
  gi|336253395|ref|YP_004596502.1| 132 GDDCR 136
                                       66775 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00023
                                       .EEE-TT-EE-TT-EE...S.EEE-TT-EE-TT-EE- CS
                         Hexapep_2   1 pviIGdnCliGanagi...G.vslGdncvvgaGvvit 33 
                                       ++++Gdn++i+ +      G  ++Gd++ ++ Gv ++
  gi|336253395|ref|YP_004596502.1| 148 NITVGDNTVIHDDVHLddrGkLTIGDRVSISDGVHVY 184
                                       589************8777799*****9999999887 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0013
                                       EE-TT-EE-TT-E CS
                         Hexapep_2   3 iIGdnCliGanag 15 
                                       ++G+n ++Ga+ +
  gi|336253395|ref|YP_004596502.1| 220 KVGENAIVGARGV 232
                                       7899999999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2240.32
//
Query:       gi|336253396|ref|YP_004596503.1|  [L=106]
Description: hypothetical protein Halxa_1999 [Halopiger xanaduensis SH-6]
Scores for 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   15.2   3.6      0.033   13.9   3.6    1.7  1  zinc_ribbon_2   zinc-ribbon domain
      0.013   14.9   5.6      0.015   14.7   2.4    2.1  2  zf-ribbon_3     zinc-ribbon domain
      0.019   15.0   0.2      0.024   14.7   0.2    1.3  1  DZR             Double zinc ribbon
      0.037   13.7   0.1      0.074   12.7   0.1    1.5  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.069   13.2   0.2      0.087   12.9   0.2    1.2  1  CpXC            CpXC protein


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 ?   13.9   3.6   9.2e-06     0.033       1      16 [.      80      97 ..      80     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.2e-06
                     zinc_ribbon_2  1 fCpnCGaelqdnakF..C 16
                                      +Cp+CGa++  +++F  C
  gi|336253396|ref|YP_004596503.1| 80 RCPHCGATNAADSTFtyC 97
                                      6********999999666 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.4   4.2e-06     0.015       1      16 [.      77      92 ..      77      97 .. 0.81
   2 ?    0.9   0.7     0.093   3.3e+02       3       8 ..      95     100 ..      93     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.2e-06
                       zf-ribbon_3  1 stvrCPnCGa.plssdd 16
                                      +t+rCP+CGa + ++d 
  gi|336253396|ref|YP_004596503.1| 77 ETIRCPHCGAtN-AADS 92
                                      69********99.5554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.093
                       zf-ribbon_3   3 vrCPnC 8  
                                       ++C++C
  gi|336253396|ref|YP_004596503.1|  95 TYCWRC 100
                                       79**** PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   6.6e-06     0.024       1      18 [.      81     100 ..      50     106 .] 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.6e-06
                               DZR   1 CpqCgeelppdar..fCseC 18 
                                       Cp+Cg+ + +d+   +C +C
  gi|336253396|ref|YP_004596503.1|  81 CPHCGATNAADSTftYCWRC 100
                                       55555554444433345555 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 ?   12.7   0.1   2.1e-05     0.074      14      25 ..      75      86 ..      68      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                                      SSS----SSS-- CS
                    DNA_RNApol_7kD 14 kgdpiRCkeCGh 25
                                      +g+ iRC +CG 
  gi|336253396|ref|YP_004596503.1| 75 EGETIRCPHCGA 86
                                      799********5 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   2.4e-05     0.087      37      57 ..      78      98 ..      63     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                              CpXC 37 eatCpkCgatakleapllyhd 57
                                      +++Cp+Cgat++++  + y +
  gi|336253396|ref|YP_004596503.1| 78 TIRCPHCGATNAADSTFTYCW 98
                                      799**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); 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 0.21s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 874.35
//
Query:       gi|336253397|ref|YP_004596504.1|  [L=105]
Description: hypothetical protein Halxa_2000 [Halopiger xanaduensis SH-6]
Scores for 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-27   94.1   0.1    6.2e-27   93.7   0.1    1.2  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.1   3.4e-31   6.2e-27       4      75 .]      28     100 ..      25     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 3.4e-31
                            HalOD1   4 spstaVveavaavegvdptelep.LydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75 
                                       +++t+V++a+a+++gvdpt+    Lyd++DpdALd+Lf++r+dg+ r++g++sF +++++VtV++dgei +ep
  gi|336253397|ref|YP_004596504.1|  28 TLTTTVIHALADCMGVDPTDGRIsLYDSVDPDALDRLFRPRHDGTPRSSGQLSFVVDDHRVTVHADGEILIEP 100
                                       799******************777**********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 887.69
//
Query:       gi|336253398|ref|YP_004596505.1|  [L=255]
Description: hypothetical protein Halxa_2001 [Halopiger xanaduensis SH-6]
Scores for 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   14.0   0.0        9.8    6.0   0.0    2.1  2  TraB          TraB family
       0.17   12.1   0.0       0.28   11.4   0.0    1.4  1  HTH_Tnp_Mu_1  Mu DNA-binding domain


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 ?    5.9   0.0    0.0012        11      11      48 ..      30      65 ..      21      83 .. 0.84
   2 ?    6.0   0.0    0.0011       9.8     216     244 ..     217     247 ..     206     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0012
                              TraB 11 tsyLfGTiHvskksvyplspeveealeksdtvvvEldl 48
                                      +++L+G +H  + sv  + +++e+    ++tv++El  
  gi|336253398|ref|YP_004596505.1| 30 DLHLLGVVHDHPASVGRVQRVLEA--VDPETVALELPA 65
                                      479*************99999999..5********976 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0011
                              TraB 216 eRnrrwaekieallkep..gsvfvaVGagHl 244
                                        R r +++++e+l +++  g v+++VG+ Hl
  gi|336253398|ref|YP_004596505.1| 217 TRERCMIDRLETLRADEatGDVVAVVGIDHL 247
                                       58899******87755557***********8 PP

>> HTH_Tnp_Mu_1  Mu DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.1e-05      0.28      43     130 ..     140     221 ..     135     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                                       GGGS-HHHHHHHHHHHCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      HTH_Tnp_Mu_1  43 vnslPketraalllrlGllgaslgekevaselvetkderliallsklepdeqrkaaellskaGlkallpvvvaedkl 119
                                       v+sl   tr+al      + a l +   a+++  + d   ++  s+ +p e ++  e  ++aG++all+ v + d +
  gi|336253398|ref|YP_004596505.1| 140 VSSLGGATREAL---TCRVAATLTH---ATSMTIACDDPVEYECSHEDPPERQAEHERSHVAGVQALLGSVETDDSA 210
                                       788889999999...5556677766...7777778899999*******888888888899***************** PP

                                       XXXXXXXXXXX CS
                      HTH_Tnp_Mu_1 120 lealgiskksi 130
                                       l+    ++++ 
  gi|336253398|ref|YP_004596505.1| 211 LAYRDETRERC 221
                                       *9988888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 2245.62
//
Query:       gi|336253399|ref|YP_004596506.1|  [L=83]
Description: hypothetical protein Halxa_2002 [Halopiger xanaduensis SH-6]
Scores for 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:                       154  (0.00858944); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 647.27
//
Query:       gi|336253400|ref|YP_004596507.1|  [L=421]
Description: peptide chain release factor subunit 1 [Halopiger xanaduensis SH-6]
Scores for 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-43  146.6   0.0      1e-42  145.6   0.0    1.6  1  eRF1_2           eRF1 domain 2
    1.4e-29  102.9   0.3    5.3e-29  101.0   0.1    2.2  2  eRF1_3           eRF1 domain 3
    9.3e-18   64.8   0.5    2.5e-17   63.4   0.1    1.9  2  acVLRF1          Actinobacteria/chloroflexi VLRF1 release fac
    9.3e-16   58.3   0.2      1e-14   55.0   0.0    2.5  3  baeRF_family10   Bacterial archaeo-eukaryotic release factor 
    1.8e-11   44.2   0.0    2.7e-11   43.6   0.0    1.3  1  eRF1_1           eRF1 domain 1
    0.00043   19.7   2.1     0.0014   18.1   2.1    2.0  1  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
      0.021   14.7   0.3      0.081   12.8   0.1    2.0  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
      0.047   13.6   1.5       0.11   12.5   1.5    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.065   13.4   3.5      0.063   13.4   1.4    2.1  2  Zn-ribbon_8      Zinc ribbon domain
        0.2   12.1   4.5          4    7.9   0.2    3.0  3  zf-IS66          zinc-finger binding domain of transposase IS
       0.21   12.0   0.8       0.45   10.9   0.8    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.58   10.0   3.0         19    5.2   0.1    2.6  3  zinc_ribbon_2    zinc-ribbon domain
       0.62   10.2   3.6         17    5.6   0.1    2.7  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.86    9.6   4.8        2.6    8.1   0.1    2.9  3  YhfH             YhfH-like protein


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 !  145.6   0.0   7.9e-46     1e-42       2     133 .]     150     280 ..     149     280 .. 0.99

  Alignments for each domain:
  == domain 1  score: 145.6 bits;  conditional E-value: 7.9e-46
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTES CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklk 78 
                                       +glivld++eA++g+l+g+r+e +k+ ++ vP+K+++Ggqsa+rf+Rlr e++++f+++va +an+ f+ +++++l+
  gi|336253400|ref|YP_004596507.1| 150 YGLIVLDRREANVGWLRGKRVEPVKSASSLVPGKQRKGGQSAQRFARLRLEAIDNFYQEVAGMANDLFV-AKRHELD 225
                                       8********************************************************************.69***** PP

                                       EEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHCC CS
                            eRF1_2  79 giilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlkd 133
                                       gi+++gp+++k+efld+d+l++e +++vi  +dv+y++esgl +++++a+++l+d
  gi|336253400|ref|YP_004596507.1| 226 GILVGGPSPTKDEFLDGDYLHHEIQDNVIGKFDVAYTDESGLYDLVDNAEDALAD 280
                                       ****************************************************987 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       3.4   4.4e+03      70      84 ..      46      60 ..       8      86 .. 0.53
   2 !  101.0   0.1   4.1e-32   5.3e-29       1     112 [.     283     418 ..     283     419 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.4
                                      HHHHHHHHHHHTT-E CS
                            eRF1_3 70 lieelvenveesgak 84
                                       i ++v++v +   +
  gi|336253400|ref|YP_004596507.1| 46 QISDVVQHVTQEHSE 60
                                      233333333333333 PP

  == domain 2  score: 101.0 bits;  conditional E-value: 4.1e-32
                                       HHHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS................... CS
                            eRF1_3   1 liqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekv................... 58 
                                       ++++k+ +eef+eel+ + ++a+YG+e++++ l mgAv++LL+se+l+++ +t+ +++                   
  gi|336253400|ref|YP_004596507.1| 283 VMKDKQQMEEFFEELNAG-DLATYGFEQTRQNLVMGAVDRLLISEDLRKDVVTYDCPEcgntdrevidrrkstpdht 358
                                       5899************98.9******************************999766667****************** PP

                                       .-HHH-HHHHHH.....HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                            eRF1_3  59 .ketgeelelve.....lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                        +++g+++e+ e     +i++l+e +e+ g++ ++is+++e+Geql++afgG+a+iLRy+
  gi|336253400|ref|YP_004596507.1| 359 cTDCGTDVEAGEedredAIDHLIEIAEQRGTETKFISTDFEKGEQLYNAFGGFAGILRYS 418
                                       *8999888888888899******************************************7 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         5   6.4e+03      67      67 ..      59      59 ..      32      87 .. 0.54
   2 !   63.4   0.1     2e-20   2.5e-17       4     121 ..     152     282 ..     150     291 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5
                           acVLRF1 67 a 67
                                       
  gi|336253400|ref|YP_004596507.1| 59 S 59
                                      1 PP

  == domain 2  score: 63.4 bits;  conditional E-value: 2e-20
                           acVLRF1   4 gvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae...v 77 
                                       +++l+rr +  vg ++g++++ +k  ++ v g+ ++GG+S qRfaR r + +d+ +++va+ a++l+ ++++e   +
  gi|336253400|ref|YP_004596507.1| 152 LIVLDRREA-NVGWLRGKRVEPVKSASSLVPGKQRKGGQSAQRFARLRLEAIDNFYQEVAGMANDLFVAKRHEldgI 227
                                       589******.*********************************************************888888899* PP

                           acVLRF1  78 vlgGdrslvaevledarlap...........latlareelldvpdprravLedav 121
                                       ++gG+  + +e+l+   l++           +a   +  l+d+ d  +++L+da 
  gi|336253400|ref|YP_004596507.1| 228 LVGGPSPTKDEFLDGDYLHHeiqdnvigkfdVAYTDESGLYDLVDNAEDALADAE 282
                                       ***************8887778889988887777777789999999999999885 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 ?   -0.1   0.0      0.76   9.7e+02      22      62 ..      30      71 ..      29      80 .. 0.66
   2 !   55.0   0.0   7.8e-18     1e-14       4     126 ..     138     263 ..     136     282 .. 0.90
   3 ?   -2.4   0.0       3.9     5e+03      81     104 ..     291     314 ..     271     351 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.76
                    baeRF_family10 22 dreraRlfevylgeleeveevegevpgrtktggwk.sqdrfq 62
                                      d ++  l ++y+ e ++ ++v ++v + + +++   s++ ++
  gi|336253400|ref|YP_004596507.1| 30 DGSGTQLVTIYVPEDRQISDVVQHVTQEHSEAANIkSKQTRT 71
                                      566778899999999998888888887555443322555444 PP

  == domain 2  score: 55.0 bits;  conditional E-value: 7.8e-18
                    baeRF_family10   4 apLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAell 80 
                                       +pL e l +   yg++++dr++a +   ++ ++e v+ +++ vpg++++gg+ s +rf+r + e ++ +++evA ++
  gi|336253400|ref|YP_004596507.1| 138 EPLEEMLADKGLYGLIVLDRREANVGWLRGKRVEPVKSASSLVPGKQRKGGQ-SAQRFARLRLEAIDNFYQEVAGMA 213
                                       79**************************************************.************************ PP

                    baeRF_family10  81 akll..eergverlvlgGdeeetaalld..rlpkalrarvvgtlplpvda 126
                                       ++l+  ++++++ +++gG+   ++++ld   l+ ++++ v+g++++  ++
  gi|336253400|ref|YP_004596507.1| 214 NDLFvaKRHELDGILVGGPSPTKDEFLDgdYLHHEIQDNVIGKFDVAYTD 263
                                       **87325556*********999999986337***********99887744 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.9
                    baeRF_family10  81 aklleergverlvlgGdeeetaal 104
                                       ++++ee ++  l + G e+ +++l
  gi|336253400|ref|YP_004596507.1| 291 EEFFEELNAGDLATYGFEQTRQNL 314
                                       555555555555555555444443 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   2.1e-14   2.7e-11       2     128 ..      21     143 ..      20     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.1e-14
                                       EEEEE..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECT CS
                            eRF1_1   2 kllkr..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdk 76 
                                       k+l+   +++++g+++vt+++++d +++++ + +++++s +a++++k +r         + v+ +Lt+   +++++ 
  gi|336253400|ref|YP_004596507.1|  21 KVLEDlkNFDGSGTQLVTIYVPEDRQISDVVQHVTQEHSEAANIKSKQTR---------TAVQDALTSIKDRLRYYD 88 
                                       5555555999*************************************999.........8***************99 PP

                                       T....SSEEEEEEEEEEGGGG--TTSEEEEEE-.TTSEEEEEECE.ESHHHHHHHHHH CS
                            eRF1_1  77 d....agvlrisGkvieenehvklgafhtldle.lkrpftiikee.wdsfalerLkea 128
                                       +    +g++ +sG v ++ +    ++++t  le +++p++ ++++ +++f +e+L+e+
  gi|336253400|ref|YP_004596507.1|  89 TyppeNGMVLFSGAVDSGGG---RTEMVTKVLEsPPQPVESFRYHcDSEFLTEPLEEM 143
                                       989999**************...8999*****9789*******99999********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 !   18.1   2.1   1.1e-06    0.0014       2      30 ..     336     367 ..     335     383 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                                       EETTTTCEE.CHEE..TSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon   2 kCPnCgstn.lveD..pergelvCtdCGlVle 30 
                                        CP+Cg+t+  v D   ++ +++CtdCG+ +e
  gi|336253400|ref|YP_004596507.1| 336 DCPECGNTDrEVIDrrKSTPDHTCTDCGTDVE 367
                                       6******9955777779999********8665 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 ?   -0.9   0.0       1.1   1.4e+03      40      71 ..      45      77 ..      34      88 .. 0.72
   2 ?   12.8   0.1   6.3e-05     0.081      59     116 ..     307     364 ..     270     365 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.1
                                      TSHHHHHHHHHHHHTSEEEES.ETTEEEESSSS CS
                      eIF-5_eIF-2B 40 rdpehvlkyllkelgtqgsid.engrlilngkf 71
                                      r+ + v++++++e + +++i+ ++ r+ ++ + 
  gi|336253400|ref|YP_004596507.1| 45 RQISDVVQHVTQEHSEAANIKsKQTRTAVQDAL 77
                                      677788888888888888887666666666554 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.3e-05
                                       ESETTEEEESSSSSCCHHHHHHHHHHHHHTSTSSSTSTCEEECC.SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  59 idengrlilngkfeakkleklldkyieeyVlCkeCkspetelek.eerllvlkCkaCga 116
                                       ++++++ ++ g++++  +++ l+k + +y  C+eC++ + e++  ++++   +C+ Cg 
  gi|336253400|ref|YP_004596507.1| 307 FEQTRQNLVMGAVDRLLISEDLRKDVVTY-DCPECGNTDREVIDrRKSTPDHTCTDCGT 364
                                       4577788999999999************9.8**********99866777779*****96 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 ?   12.5   1.5   8.4e-05      0.11      30      56 ..     336     366 ..     334     369 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-05
                    OrfB_Zn_ribbon  30 tCseCgsknke....alsgrtfkCpnCgfea 56 
                                       +C+eCg +++e    ++s+  ++C++Cg+  
  gi|336253400|ref|YP_004596507.1| 336 DCPECGNTDREvidrRKSTPDHTCTDCGTDV 366
                                       6*************9999**********876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.5     7e+03       5      10 ..     128     133 ..     127     145 .. 0.71
   2 ?   13.4   1.4   4.9e-05     0.063       6      37 ..     335     367 ..     330     368 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.5
                       Zn-ribbon_8   5 eYrCee 10 
                                        Y+C++
  gi|336253400|ref|YP_004596507.1| 128 RYHCDS 133
                                       688876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.9e-05
                       Zn-ribbon_8   6 YrCeeCghefe.vlqsisdapltaCPeCgsevr 37 
                                       Y C eCg++   v+ + +  p+ +C +Cg +v+
  gi|336253400|ref|YP_004596507.1| 335 YDCPECGNTDReVIDRRKSTPDHTCTDCGTDVE 367
                                       99*****65444777766889999*****9886 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 ?   -1.5   0.1       2.7   3.5e+03      19      36 ..     113     130 ..     109     132 .. 0.76
   2 ?    4.6   0.1     0.033        42       4      17 ..     337     350 ..     334     354 .. 0.70
   3 ?    7.9   0.2    0.0031         4       2      21 ..     357     374 ..     356     381 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.7
                           zf-IS66  19 vreeldipPakfrViehi 36 
                                       v+ +l+ pP+ ++  +++
  gi|336253400|ref|YP_004596507.1| 113 VTKVLESPPQPVESFRYH 130
                                       788999999988876665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.033
                           zf-IS66   4 CpcCGgllkpiged 17 
                                       Cp+CG + +++ ++
  gi|336253400|ref|YP_004596507.1| 337 CPECGNTDREVIDR 350
                                       99999965665554 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0031
                           zf-IS66   2 rtCpcCGgllkpigedrvre 21 
                                        tC +CG++ +++ge++ re
  gi|336253400|ref|YP_004596507.1| 357 HTCTDCGTD-VEAGEED-RE 374
                                       68*****97.8*****5.44 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 ?   10.9   0.8   0.00035      0.45       4      55 ..     335     377 ..     333     386 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                   Lar_restr_allev   4 kpCPfCgg..ravlersqrvvaeigqcvyCadCgastpwfkiaedeaeaekeai 55 
                                       ++CP Cg+  r+v+ r+++++       +C+dCg         e+ +e++++ai
  gi|336253400|ref|YP_004596507.1| 335 YDCPECGNtdREVIDRRKSTPD-----HTCTDCGT------DVEAGEEDREDAI 377
                                       79*****833456666666665.....7*******......3344444444443 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   0.0         6   7.6e+03       7      13 ..     247     253 ..     246     253 .. 0.82
   2 ?    5.2   0.1     0.015        19      16      20 ..     337     341 ..     328     343 .. 0.62
   3 ?    4.6   0.2     0.021        27       2      12 ..     359     369 ..     357     371 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6
                     zinc_ribbon_2   7 aelqdna 13 
                                       +e+qdn+
  gi|336253400|ref|YP_004596507.1| 247 HEIQDNV 253
                                       79***95 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
                     zinc_ribbon_2  16 CpyCG 20 
                                       Cp+CG
  gi|336253400|ref|YP_004596507.1| 337 CPECG 341
                                       55555 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.021
                     zinc_ribbon_2   2 CpnCGaelqdn 12 
                                       C+ CG+ ++ +
  gi|336253400|ref|YP_004596507.1| 359 CTDCGTDVEAG 369
                                       99999988765 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 ?    5.6   0.1     0.013        17      12      23 ..     330     341 ..     307     344 .. 0.84
   2 ?    4.6   0.4     0.027        35      12      35 ..     352     375 ..     342     386 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.013
                          zf-Mss51  12 pkhvdfeCpdCG 23 
                                       +  v+++Cp+CG
  gi|336253400|ref|YP_004596507.1| 330 KDVVTYDCPECG 341
                                       56799******9 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.027
                          zf-Mss51  12 pkhvdfeCpdCGiptycseehwed 35 
                                       ++  d++C dCG  +   ee  ed
  gi|336253400|ref|YP_004596507.1| 352 KSTPDHTCTDCGTDVEAGEEDRED 375
                                       566789******999888876554 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       3.2   4.1e+03       3      11 ..     289     297 ..     288     299 .. 0.76
   2 ?    2.6   0.1      0.11   1.4e+02      16      21 ..     337     342 ..     334     349 .. 0.85
   3 ?    8.1   0.1     0.002       2.6      10      24 ..     353     367 ..     351     371 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.2
                              YhfH   3 kiveFfrnL 11 
                                       ++ eFf+ L
  gi|336253400|ref|YP_004596507.1| 289 QMEEFFEEL 297
                                       677999998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                              YhfH  16 CteCGk 21 
                                       C+eCG+
  gi|336253400|ref|YP_004596507.1| 337 CPECGN 342
                                       *****8 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.002
                              YhfH  10 nLPkKkCteCGkeie 24 
                                        +P+ +Ct+CG + e
  gi|336253400|ref|YP_004596507.1| 353 STPDHTCTDCGTDVE 367
                                       68999******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1198  (0.0668191); expected 358.6 (0.02)
Passed bias filter:                      947  (0.0528195); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); 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: 0.60u 0.23s 00:00:00.83 Elapsed: 00:00:00.38
# Mc/sec: 3281.94
//
Query:       gi|336253401|ref|YP_004596508.1|  [L=308]
Description: cell division ATPase MinD [Halopiger xanaduensis SH-6]
Scores for 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-22   78.9   0.1    4.8e-22   78.4   0.1    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    3.3e-22   79.2   1.5    1.5e-11   44.3   1.0    2.8  2  ParA         NUBPL iron-transfer P-loop NTPase
    8.8e-21   74.6   0.0    1.4e-20   74.0   0.0    1.2  1  AAA_31       AAA domain
    9.7e-14   51.4   0.0    1.9e-13   50.5   0.0    1.4  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    1.4e-12   47.7   0.1    5.4e-12   45.7   0.1    1.7  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    5.2e-09   35.8   0.9    1.4e-08   34.4   0.1    2.0  2  MipZ         ATPase MipZ
    6.9e-07   28.7   0.8    1.9e-05   24.0   2.0    2.0  2  ArsA_ATPase  Anion-transporting ATPase
    3.4e-05   23.8   1.0    0.00082   19.3   0.0    2.4  2  AAA_26       AAA domain
    0.00017   20.7   2.9    0.00056   19.0   2.9    1.7  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0007   19.0   0.4     0.0012   18.2   0.4    1.3  1  VirC1        VirC1 protein
     0.0025   17.7   0.1     0.0041   17.0   0.1    1.3  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
  ------ inclusion threshold ------
      0.011   15.5   0.3      0.019   14.7   0.3    1.5  1  AAA_30       AAA domain
      0.036   13.8   0.0      0.058   13.1   0.0    1.3  1  AAA_24       AAA domain
      0.081   11.1   1.3       0.12   10.5   1.3    1.1  1  FTHFS        Formate--tetrahydrofolate ligase
       0.25   11.0   1.5       0.49   10.0   1.5    1.4  1  SRP54        SRP54-type protein, GTPase domain


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 !   78.4   0.1     4e-25   4.8e-22       2     127 ..       8     212 ..       7     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 4e-25
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       aias+kGGvGKTt+++n+++ala++g+rV++vD+D  + nla  + + n   +                        
  gi|336253401|ref|YP_004596508.1|   8 AIASGKGGVGKTTTTVNIGTALAQAGKRVAVVDVDLGMANLA-GFVSLNPDSTtlhdvlagdaeiedatyrladniv 83 
                                       8****************************************9.55555555557999******************** PP

                                       ...................................................................CCHCCCHHHH CS
                                       ...................................................................xxxxxxxxxx RF
                              CbiA  55 ...................................................................dlkrllelle 64 
                                                                                                          d k+ +el +
  gi|336253401|ref|YP_004596508.1|  84 avpsgtgldeyaeaspeglgdvvaelraaydyvfldvgagishetvlplgladsvlvvstpepaavqDSKKTIELTA 160
                                       ***************************************************************************** PP

                                       HHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  65 algkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                       + g++      +ag+v++r  +   +   +e ++ ++   ++p+lg ip+d+a  e++  g p
  gi|336253401|ref|YP_004596508.1| 161 RAGGE------VAGLVVTRTHPH--SDISYEEIASRL---EIPLLGTIPEDSAARESVYAGTP 212
                                       ***98......9*******8876..554555555544...9************9999887766 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 !   44.3   1.0   1.2e-14   1.5e-11       4      47 ..       5      48 ..       2      67 .. 0.86
   2 !   31.9   0.0   7.3e-11   8.8e-08     113     245 ..     114     233 ..     108     234 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.2e-14
                              ParA  4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsi 47
                                      +v+a++SgKGGVGK+t++vn+ +aLa+ g++v+++D+D+   ++
  gi|336253401|ref|YP_004596508.1|  5 TVYAIASGKGGVGKTTTTVNIGTALAQAGKRVAVVDVDLGMANL 48
                                      689***********************************965555 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 7.3e-11
                              ParA 113 DyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteif 189
                                       Dy+++D+  G + e  tv+     + +++V+tp+ +a++d kk+ie++ ++  +v G+v             +t+  
  gi|336253401|ref|YP_004596508.1| 114 DYVFLDVGAGISHE--TVLPLGLADSVLVVSTPEPAAVQDSKKTIELTARAGGEVAGLVVT-----------RTHPH 177
                                       77778875555544..55555556899*******************************953...........33344 PP

                              ParA 190 gkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                                       ++ + e++a++l++pllg+ip d++ re++ +g+plv+ epe +aa a++++a+++
  gi|336253401|ref|YP_004596508.1| 178 SDISYEEIASRLEIPLLGTIPEDSAARESVYAGTPLVVYEPEGPAAIAYRTLAADL 233
                                       5567899******************************************9999875 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0   1.2e-23   1.4e-20       3     161 ..       6     156 ..       4     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 1.2e-23
                            AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQ.anattglgiekneiektlyevlieeknikeaiiktkv 78 
                                       v aia  KGGvGKTTt+vn++ ala++gk+v +vD+D   an++  +++  n  ++tl++vl+ +++i++a + +  
  gi|336253401|ref|YP_004596508.1|   6 VYAIASGKGGVGKTTTTVNIGTALAQAGKRVAVVDVDLGmANLAGFVSL--NPDSTTLHDVLAGDAEIEDATY-RLA 79 
                                       66999********************************861555555554..55568*****************.446 PP

                            AAA_31  79 enldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayale 155
                                       +n+  +ps + L e+       e + e l +++ +++  YDy+++D+   ++  t+  L  +dsv+++  +e+ a++
  gi|336253401|ref|YP_004596508.1|  80 DNIVAVPSGTGLDEYA------EASPEGLGDVVAELRAAYDYVFLDVGAGISHETVLPLGLADSVLVVSTPEPAAVQ 150
                                       99999******99875......45677899*******************************************9998 PP

                            AAA_31 156 Gleqll 161
                                         ++ +
  gi|336253401|ref|YP_004596508.1| 151 DSKKTI 156
                                       766655 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   1.6e-16   1.9e-13      10     231 ..      13     231 ..       5     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.6e-16
                          CBP_BcsQ  10 RGGvGttsllaaLawalhelgesvlviD..lspdnlLrlhFnvdieqregwaraeldgapwrqaaleyapgldllPf 84 
                                       +GGvG+t+ ++ +++al + g++v v+D  l  +nl  +       +++++   ++ +a++++a++++a+++  +P 
  gi|336253401|ref|YP_004596508.1|  13 KGGVGKTTTTVNIGTALAQAGKRVAVVDvdLGMANLAGFVSLN--PDSTTLHDVLAGDAEIEDATYRLADNIVAVPS 87 
                                       7**********************99986115677877665444..478999999999******************** PP

                          CBP_BcsQ  85 GelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdanc......hvrL 155
                                       G+  +e +e      +++e l + ++el++ y++++lD+ ag s+ t   l lad+vl v +p+ ++       + L
  gi|336253401|ref|YP_004596508.1|  88 GTGLDEYAE------ASPEGLGDVVAELRAAYDYVFLDVGAGISHETVLPLGLADSVLVVSTPEPAAvqdskkTIEL 158
                                       *87665555......67899999***************************************987763333335889 PP

                          CBP_BcsQ 156 hqqalpaaellLiNqfeaasqlqqDllqlWlqslrrllPl..vihrDealaEalaakqPlgeyrpdslaaeevktLa 230
                                         +a  + + l + + ++ s +  + +       r  +Pl  +i +D a  E++ a  Pl  y p+  aa + +tLa
  gi|336253401|ref|YP_004596508.1| 159 TARAGGEVAGLVVTRTHPHSDISYEEIA-----SRLEIPLlgTIPEDSAARESVYAGTPLVVYEPEGPAAIAYRTLA 230
                                       9999999999999999998877644222.....23336766689*******************************99 PP

                          CBP_BcsQ 231 n 231
                                       +
  gi|336253401|ref|YP_004596508.1| 231 A 231
                                       5 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 !   45.7   0.1   4.5e-15   5.4e-12       6     245 ..      11     234 ..       6     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 4.5e-15
                         Fer4_NifH   6 yGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkGyggvk 82 
                                        GkGG+Gk+tt+ n+ +ala+ gk+v +v  D         ++    +t l+ +       d ++ed  ++   ++ 
  gi|336253401|ref|YP_004596508.1|  11 SGKGGVGKTTTTVNIGTALAQAGKRVAVVDVDLGMANLAGFVSLNPDSTTLHDVLA----GDAEIEDATYRLADNIV 83 
                                       59*****************************9876665555555555555544433....455899*********** PP

                         Fer4_NifH  83 cvesG.GPepGvGCaGrgvitaielleelgayddlDfvlyDvLGDvvCGGfalPiredkaqevyivtsgelmalyaa 158
                                       +v sG G +  +  +  g+++ +  l        +D+v++Dv G  +     lP+    a++v++v++ e  a+   
  gi|336253401|ref|YP_004596508.1|  84 AVPSGtGLDEYAEASPEGLGDVVAELR-----AAYDYVFLDV-GAGISHETVLPLG--LADSVLVVSTPEPAAVQD- 151
                                       **9996667778888889988776543.....2479*****8.7778888999*98..*************98765. PP

                         Fer4_NifH 159 nniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqak 235
                                           k+ie  a+ gg +++Gl++  r   + +   e++a++l++++l ++P d   r++  +   ++ y+pe + a 
  gi|336253401|ref|YP_004596508.1| 152 --SKKTIELTARAGG-EVAGLVVT-RTHPHSDISYEEIASRLEIPLLGTIPEDSAARESVYAGTPLVVYEPEGPAAI 224
                                       ..4578888888877.89*****9.756666666899**************************************** PP

                         Fer4_NifH 236 eyrelarkil 245
                                        yr la +++
  gi|336253401|ref|YP_004596508.1| 225 AYRTLAADLA 234
                                       ******8765 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.1   1.2e-11   1.4e-08       5     125 ..       9     138 ..       5     146 .. 0.70
   2 ?   -1.8   0.0       1.2   1.5e+03      51     106 ..     227     281 ..     224     301 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.2e-11
                                       E--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT-.....-----EEE-SSS-... CS
                              MipZ   5 lgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkgl.....sLplpealalsea... 73 
                                       ++  kGG Gk+tt+v + +aL+++G+rva++d+dl  + la ++    ++++ +++     +++ +++  l+++   
  gi|336253401|ref|YP_004596508.1|   9 IASGKGGVGKTTTTVNIGTALAQAGKRVAVVDVDLGMANLAGFVSLNPDSTTLHDVlagdaEIEDATY-RLADNiva 84 
                                       6889***************************************9855444433332111113333333.33332111 PP

                                       ..HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEE CS
                              MipZ  74 ..eeaeveeeeeaevaeleelvadleaeldfividtPGsdsalsrlahsladtl 125
                                         + + ++e +ea+ + l ++va+l a +d++ +d+    s+ + l   lad++
  gi|336253401|ref|YP_004596508.1|  85 vpSGTGLDEYAEASPEGLGDVVAELRAAYDYVFLDVGAGISHETVLPLGLADSV 138
                                       112234555666666799999999999999999999887777777778888875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                                       HHHHHHHHT------EEE-SSS-HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE CS
                              MipZ  51 raataerkglsLplpealalseaeeaeveeeeeaevaeleelvadleaeldfivid 106
                                       r+  a+  g++L  p+  a +++ eae + ++++ +a+  ++ +++++ +d +  d
  gi|336253401|ref|YP_004596508.1| 227 RTLAADLAGIELSAPSSDAAPDKTEAEST-PDSKATAATGAAETEASSATDAVSSD 281
                                       55667778999999999888886665544.44444466667777777777776655 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   2.0   1.5e-08   1.9e-05       5      38 ..       9      42 ..       5      52 .. 0.92
   2 ?    1.2   0.0      0.14   1.7e+02     208     258 ..     137     186 ..     133     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.5e-08
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      + +GKGGVGKtt    +++ l++ gk+v ++ +D
  gi|336253401|ref|YP_004596508.1|  9 IASGKGGVGKTTTTVNIGTALAQAGKRVAVVDVD 42
                                      679***************************9888 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                                       EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE-TTCSSSTSHHHH CS
                       ArsA_ATPase 208 sfrlVvipEklslkEteRaikeLkkygikvdavivNkllpeeeqenCefle 258
                                       s+ +V++pE  +++++++ i+  ++ g +v  ++v +  p ++ +  e ++
  gi|336253401|ref|YP_004596508.1| 137 SVLVVSTPEPAAVQDSKKTIELTARAGGEVAGLVVTRTHPHSDIS-YEEIA 186
                                       7899******************************99999988875.45555 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.9      0.15   1.8e+02       5      34 ..       9      38 ..       5      40 .. 0.86
   2 !   19.3   0.0   6.8e-07   0.00082     130     194 ..     137     203 ..     133     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.15
                            AAA_26  5 vtgtdtgvGKTvvslgLvralkrkgvkvgy 34
                                      +++   gvGKT+++  +  al + g +v++
  gi|336253401|ref|YP_004596508.1|  9 IASGKGGVGKTTTTVNIGTALAQAGKRVAV 38
                                      6777789**************999999986 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 6.8e-07
                            AAA_26 130 pvilVargglgtinqllltiealrqknvrvlGvilNkvrnpe..nvetlekksgipvlGvvPylpdl 194
                                        v++V +++  ++++   tie+  + + +v+G+++ ++ ++    +e++ +  +ip+lG++P ++  
  gi|336253401|ref|YP_004596508.1| 137 SVLVVSTPEPAAVQDSKKTIELTARAGGEVAGLVVTRTHPHSdiSYEEIASRLEIPLLGTIPEDSAA 203
                                       47788888899**************************64443579*****************99765 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 !   19.0   2.9   4.7e-07   0.00056      35     153 ..      11     145 ..       5     162 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.7e-07
                                       EE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---------..---------HCCC............TSTTEEEEEE CS
                              MeaB  35 tGvPGaGkstlvealglelrrrGkrvavlavDPsspftGG..silGDklRleela............vdegvfiRsl 97 
                                        G  G+Gk t++ ++g+ l+++Gkrvav+ vD +     G  s+  D + l+++                +  i ++
  gi|336253401|ref|YP_004596508.1|  11 SGKGGVGKTTTTVNIGTALAQAGKRVAVVDVDLGMANLAGfvSLNPDSTTLHDVLagdaeiedatyrL--ADNIVAV 85 
                                       5889****************************987766664456667777776554555544433221..2224455 PP

                                       -----HHHHHHHH....HHHHHHHHHTT-SEEEEEEESSTTHHHHHH..TT-SEEEEEEESS CS
                              MeaB  98 psrGalGGlaakt....revvllleaaGfDvvlietvGvGqsevdva..evvdtfvvlllpe 153
                                       ps+  l   a+++    ++vv+ l a  +D v ++ vG+G s   v    ++d ++v+ +pe
  gi|336253401|ref|YP_004596508.1|  86 PSGTGLDEYAEASpeglGDVVAELRA-AYDYVFLD-VGAGISHETVLplGLADSVLVVSTPE 145
                                       55555555554441111334444443.47777765.67777665554224566666666665 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.4     1e-06    0.0012       5      39 ..       8      42 ..       5      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1e-06
                             VirC1  5 tfcslkGGaGkttalmglcsalasdgkrvalfead 39
                                      +++s kGG Gktt+ + + +ala+ gkrva+ + d
  gi|336253401|ref|YP_004596508.1|  8 AIASGKGGVGKTTTTVNIGTALAQAGKRVAVVDVD 42
                                      57999**************************9987 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 !   17.0   0.1   3.4e-06    0.0041       1      47 [.      12      56 ..      12      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-06
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislal 47
                                      G+  +GK+T + ++   ++++g+++++vD+D+G  +  + g++sl +
  gi|336253401|ref|YP_004596508.1| 12 GKGGVGKTTTTVNIGTALAQAGKRVAVVDVDLGMAN--LAGFVSLNP 56
                                      66789*****************************99..557777765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3   1.6e-05     0.019      16      81 ..       3      69 ..       1     118 [. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLae.elgieastiakllkrlk 81
                                      ++  +a++ G  G GKtt+   +  a+++ag+rv+++     +A+  +  +l+ ++ t++ +l   +
  gi|336253401|ref|YP_004596508.1|  3 QETVYAIASGKGGVGKTTTTVNIGTALAQAGKRVAVVDVDLGMANLAGFvSLNPDSTTLHDVLAGDA 69
                                      56678999***************************99888888776664356667777777775554 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   4.9e-05     0.058       9      44 ..      12      54 ..       6     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-05
                            AAA_24  9 GpsgiGKTtlakel.......gpkplfidtekGlksldadkfp 44
                                      G+ g+GKTt+  ++       g++++++d++ G+++l +    
  gi|336253401|ref|YP_004596508.1| 12 GKGGVGKTTTTVNIgtalaqaGKRVAVVDVDLGMANLAGFVSL 54
                                      99********************************999876544 PP

>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.3    0.0001      0.12      59      91 ..       6      38 ..       4      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                      EEESS--TT--SHHHHHHHHHHHHHHTT--EEE CS
                             FTHFS 59 vtaitPtplGeGKttttigLaqalnklgkkava 91
                                      v ai+  + G GKtttt+ +  al+++gk++++
  gi|336253401|ref|YP_004596508.1|  6 VYAIASGKGGVGKTTTTVNIGTALAQAGKRVAV 38
                                      7799999*********************99875 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   1.5   0.00041      0.49       7      38 ..      11      42 ..       5      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00041
                                      EESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  7 vGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                       G  G+GKTtt+  +   l + gk+v++v +D
  gi|336253401|ref|YP_004596508.1| 11 SGKGGVGKTTTTVNIGTALAQAGKRVAVVDVD 42
                                      5889************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 2367.50
//
Query:       gi|336253402|ref|YP_004596509.1|  [L=185]
Description: hypothetical protein Halxa_2005 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.28   10.9  10.4       0.35   10.5  10.4    1.1  1  BSP_II       Bone sialoprotein II (BSP-II)
        3.9    5.6   8.5        4.3    5.4   8.5    1.0  1  Nop14        Nop14-like family


Domain annotation for each model (and alignments):
>> BSP_II  Bone sialoprotein II (BSP-II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  10.4   3.9e-05      0.35     138     217 ..      24     104 ..      16     130 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.9e-05
                            BSP_II 138 eeeeeeeeeeneeeeaevdeneqgvngt...stnsteaengngssggdngeeeeeesvteaeaegteveeeeeagsa 211
                                       + e  eee en++ee   d+ +++ ng    s n +++++g+gs+g +++  + e+++ e  a++t + +  e+++ 
  gi|336253402|ref|YP_004596509.1|  24 S-ETGEEEPENDSEESFGDDGDDTGNGSdadSDNDSDTDSGDGSDGEHDDVPGVENDQIEV-ADDTVTITSIEKDGD 98 
                                       3.33334466666666666666666655111666677888888888544333333333332.223333333333444 PP

                            BSP_II 212 etttsp 217
                                       +  ++ 
  gi|336253402|ref|YP_004596509.1|  99 KLDIVA 104
                                       444444 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   8.5   0.00048       4.3     342     397 ..      23      82 ..       2     129 .. 0.48

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.00048
                             Nop14 342 a..taeee.eeededdfeedddlveseseeee.eeeeedeeeeedeeeeeeeeededdls 397
                                       +  t eee e++ e++f +d d+  ++s++++ ++++ d+ + +d e ++    ++d+ +
  gi|336253402|ref|YP_004596509.1|  23 SseTGEEEpENDSEESFGDDGDDTGNGSDADSdNDSDTDSGDGSDGEHDDVPGVENDQIE 82 
                                       133555555666666666666666666665552222222222222222221111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 1503.50
//
Query:       gi|336253403|ref|YP_004596510.1|  [L=595]
Description: Arginyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for complete 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   0.5    1.8e-37  129.1   0.5    1.1  1  tRNA-synt_1d     tRNA synthetases class I (R)
    9.8e-32  109.6   0.1    6.4e-31  107.0   0.0    2.3  2  DALR_1           DALR anticodon binding domain
    1.2e-09   38.6   0.0    3.9e-09   37.0   0.0    1.9  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
     0.0099   14.8   0.0      0.094   11.6   0.0    2.1  2  tRNA-synt_1f     tRNA synthetases class I (K)
  ------ inclusion threshold ------
        0.1   11.3   0.0        1.4    7.6   0.0    2.6  3  tRNA-synt_1g     tRNA synthetases class I (M)
       0.13   11.5   0.0       0.25   10.7   0.0    1.5  1  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai


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 !  129.1   0.5   5.9e-41   1.8e-37      14     349 .]     108     454 ..      98     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 5.9e-41
                                       ---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTTS CS
                      tRNA-synt_1d  14 kksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekllq 90 
                                            ++ vvv+++s n   ++hvG  r  iiGdav++ll+++Gydv r  +v D G+q+ ++   +e   ++ l  
  gi|336253403|ref|YP_004596510.1| 108 ALEDREESVVVEHTSANPTGPVHVGRARNPIIGDAVANLLDYAGYDVERHYYVNDAGRQMAVFTWAYETFDEDDLED 184
                                       45566789******************************************************999998888888776 PP

                                       ---...--.SCCCHHHHHHHHCC...CSHC..CCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHCT--- CS
                      tRNA-synt_1d  91 eqe...lq.dLeafykeakkdyd...eeei..faerarnyvvkLqsgdedirklwkllvditrtelqklydrldvtl 158
                                       ++e   ++ dL  +y+  +  ++   e+e+   + +  ++++ L++gd+++ +  + +vd +   ++   +rl    
  gi|336253403|ref|YP_004596510.1| 185 DPErdrIEyDLVRYYRAGNAFLEngpEDEVeeAEAEIESIMQGLEEGDDETYERVSEVVDQVLSGMKACLARLPAEF 261
                                       6652224348999***9998876222344433566678999*******99888888888877777777777776666 PP

                                       EC.--CC..CCCCCHHHHHHHHHCTT-EEECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--S CS
                      tRNA-synt_1d 159 ie.rGes..lykeslneivkelkkkglvkesdGalvvfldefgkrlgvvvqksDGgylytttDiaaakerkeelkad 232
                                        e   e+  + +   +++v+ lk+ + ++ ++ a  + lde+g    +v  +sD + ly t+D+a    +    + d
  gi|336253403|ref|YP_004596510.1| 262 DEfVKETrfMRNGDTDDLVARLKELDEAVYEEDAWQLELDEHGIDKNLVFLRSDDTSLYATRDLAHHEWKF--DNYD 336
                                       55534444488999**************************************************9766555..568* PP

                                       EEEEEEECCCHHHHHHHHHHHHCTTSSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCC CS
                      tRNA-synt_1d 233 kvlyvidsrqslhlqqiflilkkigyvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeralqlikek 309
                                       +++ v+ +  +l  +q+   l  ++   ++ +le   +  v    + k++tr+G  v L+dlLdea++ra+q ++++
  gi|336253403|ref|YP_004596510.1| 337 RAVTVLGEDHKLQARQLTTTLELLDN--DTDQLEQVLYSYV-NLPEGKMSTRRGTGVDLDDLLDEAIDRARQEVEDR 410
                                       ******99999999999888888876..8899999999999.556678*************************9999 PP

                                       CCCTS....-CCCCHCHHHHHHHHHHHHCCCCTS-TTS-EE--H CS
                      tRNA-synt_1d 310 nkdkv....lqadelekvaeavgvgaikyaDlsknrindyifdw 349
                                         d++    l  d+ e++a+ vg+ga++y  +sk+ ++   f+w
  gi|336253403|ref|YP_004596510.1| 411 LDDRIrdddLDEDDIERIAHQVGIGAVRYDIVSKQPTKAITFEW 454
                                       888884333567899*********************99999999 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.56   1.7e+03      63      95 ..     252     284 ..     215     291 .. 0.73
   2 !  107.0   0.0   2.2e-34   6.4e-31       1     119 []     468     595 .]     468     595 .] 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.56
                                       HHHHHHHHHHHHHHHHCTSTTSCTHHH.HHHHH CS
                            DALR_1  63 eylyeLaatfhkfYnkervlkeeeeelaaaRLa 95 
                                         l  L a+f +f +++r++ + + +   aRL+
  gi|336253403|ref|YP_004596510.1| 252 ACLARLPAEFDEFVKETRFMRNGDTDDLVARLK 284
                                       456777778888888888887766666677775 PP

  == domain 2  score: 107.0 bits;  conditional E-value: 2.2e-34
                                       HHHHHHHHHHHHHHTTCTTCCCCHCCHCC.........S-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHH CS
                            DALR_1   1 vqyahaRiksilrkaeeegekleeealal.........leeeeekeLlkalaqfpevleeaaeelephklaeylyeL 68 
                                       vqy haR++ il++a+ + e++ +++ +l         le+e+e++Ll ++a+fp v+ eaa++leph++a+y  e 
  gi|336253403|ref|YP_004596510.1| 468 VQYVHARTCGILEEAGLDPEADIADQ-DLdlesldadlLETEAERDLLETIARFPAVVDEAADDLEPHRIATYTREF 543
                                       8************9997776655544.4448999***99999*********************************** PP

                                       HHHHHHHHHHCTSTTSC.THHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                            DALR_1  69 aatfhkfYnkervlkee.eeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                       a+ f++fY++++vl ++ +++ ++aRLaLv a ++++an L++LG+eap  m
  gi|336253403|ref|YP_004596510.1| 544 ADRFNAFYRECPVLADDvDPAVRDARLALVAASKHTIANSLEILGVEAPRSM 595
                                       **************977255569**************************998 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 !   37.0   0.0   1.3e-12   3.9e-09       2      83 ..       8      87 ..       4      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.3e-12
                                      HHHHHHHHHHHHHHSS-HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT..EEEEEEETT CS
                   Arg_tRNA_synt_N  2 elkeaiaealkkaagadleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei..iekvevagp 78
                                      e+++a++ al+++   ++  +++ +e+p++     +a+ va++la +++++P ++A++ia++++  +   +++v+ +gp
  gi|336253403|ref|YP_004596510.1|  8 EVEDALEGALSAL---EFPTDDLGLEEPPEDVESVLASSVAFRLAGEAGQAPPQVAARIADEIDVGDLtyVAAVQTQGP 83
                                      4556666666666...5667789*******************************************9889********* PP

                                      .EEEE CS
                   Arg_tRNA_synt_N 79 GFiNf 83
                                       ++Nf
  gi|336253403|ref|YP_004596510.1| 84 -YLNF 87
                                      .***9 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 !   11.6   0.0   3.1e-05     0.094      17      70 ..     107     162 ..      93     170 .. 0.77
   2 ?    0.3   0.0     0.088   2.6e+02     267     297 ..     368     397 ..     339     401 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.1e-05
                      tRNA-synt_1f  17 kkka.ekdevvve.sGispSGliHiGnlrevltadlvaralrkrgeevrlilisDd 70 
                                        + + ++++vvve + + p G++H+G++r+ + +d+va+ l   g +v+  ++++d
  gi|336253403|ref|YP_004596510.1| 107 GALEdREESVVVEhTSANPTGPVHVGRARNPIIGDAVANLLDYAGYDVERHYYVND 162
                                       444444555666438999***********************999999766655555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.088
                      tRNA-synt_1f 267 ekvvYelillkggekmssSkGnvltledwle 297
                                       e+v Y ++ l +g kms  +G+++ l+d+l+
  gi|336253403|ref|YP_004596510.1| 368 EQVLYSYVNLPEG-KMSTRRGTGVDLDDLLD 397
                                       7899******999.************99985 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 ?   -0.7   0.1      0.16   4.7e+02      11      39 ..     126     154 ..     117     161 .. 0.87
   2 ?   -1.3   0.0      0.23     7e+02      63     111 ..     239     287 ..     233     298 .. 0.82
   3 ?    7.6   0.0   0.00046       1.4     277     344 ..     331     398 ..     317     406 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.16
                                       SS---HHHHHHHHHHHHHHHHHHHTT-EE CS
                      tRNA-synt_1g  11 ngklHlGhllevisaDifaRykrlrgeev 39 
                                       +g++H+G +++ i++D++a      g++v
  gi|336253403|ref|YP_004596510.1| 126 TGPVHVGRARNPIIGDAVANLLDYAGYDV 154
                                       799***************99998888886 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT CS
                      tRNA-synt_1g  63 peelvekvheeikelfkklnisfdkygrttseehkelvqeifkklkekg 111
                                       ++e+v++v + +k+ +++l  +fd++ + t    +  + +++ +lke +
  gi|336253403|ref|YP_004596510.1| 239 VSEVVDQVLSGMKACLARLPAEFDEFVKETRFMRNGDTDDLVARLKELD 287
                                       67899999999***************99998888888888888888754 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00046
                                       -S......EEEEEGGG.HHHHHTHHHHHHHHTT----S-EEEE--EEE--------------HHHHHHH CS
                      tRNA-synt_1g 277 akdkevelvhfigkdi.ikFHtifwPaillgaelklpkkvvaheyltvegkKlSkSrgvvvkakealer 344
                                       + d+  ++v ++g d  ++   +  +  ll+++  ++++v   +y+++ ++K+S+ rg++v+ +++l++
  gi|336253403|ref|YP_004596510.1| 331 KFDNYDRAVTVLGEDHkLQARQLTTTLELLDNDTDQLEQVL-YSYVNLPEGKMSTRRGTGVDLDDLLDE 398
                                       45566667777777742455556666677778888888887.57*********************9987 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 ?   10.7   0.0   8.3e-05      0.25      23      54 ..     129     160 ..     111     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.3e-05
                                       -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEB CS
                      tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvqfvqnv 54 
                                       +h+G+aR+ ++ D ++++l ++gYdv+    v
  gi|336253403|ref|YP_004596510.1| 129 VHVGRARNPIIGDAVANLLDYAGYDVERHYYV 160
                                       7*************************754444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.38
# Mc/sec: 4659.42
//
Query:       gi|336253404|ref|YP_004596511.1|  [L=241]
Description: uridine kinase [Halopiger xanaduensis SH-6]
Scores for complete 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-48  165.6   0.1    1.4e-48  165.3   0.1    1.1  1  PRK              Phosphoribulokinase / Uridine kinase family
      2e-06   27.8   0.1      9e-06   25.7   0.1    1.8  1  dNK              Deoxynucleoside kinase
    0.00034   20.3   0.1     0.0094   15.6   0.0    2.1  2  CoaE             Dephospho-CoA kinase
    0.00053   19.3   0.0     0.0011   18.3   0.0    1.5  1  Zeta_toxin       Zeta toxin
     0.0007   20.2   0.1     0.0014   19.2   0.1    1.6  1  AAA_18           AAA domain
     0.0017   18.3   0.0     0.0044   16.9   0.0    2.0  2  CPT              Chloramphenicol phosphotransferase-like prot
     0.0039   17.4   0.0     0.0074   16.6   0.0    1.4  1  AAA_28           AAA domain
     0.0052   15.9   0.1      0.066   12.3   0.0    2.1  2  T2SSE            Type II/IV secretion system protein
     0.0052   17.2   0.9        1.7    9.1   0.0    2.3  2  AAA_17           AAA domain
  ------ inclusion threshold ------
      0.018   15.2   0.0      0.031   14.5   0.0    1.4  1  AAA_33           AAA domain
      0.023   15.2   0.0      0.031   14.8   0.0    1.3  1  ABC_tran         ABC transporter
      0.026   14.3   2.2       0.81    9.4   0.1    2.1  2  Cytidylate_kin   Cytidylate kinase
      0.028   14.4   0.1      0.044   13.8   0.1    1.2  1  T3SS_needle_reg  YopR, type III needle-polymerisation regulat
      0.052   13.8   0.1      0.082   13.2   0.1    1.5  1  AAA_22           AAA domain
      0.091   11.9   0.4       0.27   10.4   0.3    1.7  2  NB-ARC           NB-ARC domain
      0.099   13.2   2.0        0.2   12.3   2.0    1.4  1  Ribosomal_60s    60s Acidic ribosomal protein
       0.14   12.6   0.0       0.29   11.6   0.0    1.5  1  AAA              ATPase family associated with various cellul
       0.73    9.6   5.4       0.19   11.5   1.7    1.8  2  DUF348           G5-linked-Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.3   0.1   1.4e-51   1.4e-48       1     193 [.       7     188 ..       7     191 .. 0.96

  Alignments for each domain:
  == domain 1  score: 165.3 bits;  conditional E-value: 1.4e-51
                               PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllyev 77 
                                       vIg+ag  GaGkttvar++ + +g e+v          + ld+ ++dl+  e +++k  ev+++ p+a++++ll e 
  gi|336253404|ref|YP_004596511.1|   7 VIGIAGGTGAGKTTVARTVADTVG-EAV--------TRIPLDNYYEDLSHLEFEERK--EVNYDHPDAFEWELLQEH 72 
                                       8**********************9.444........5899************99999..889999************ PP

                               PRK  78 lkelkegkkvdkpiYsheteeaapdkeeliegadvlviEGlhalydervaelldlkiyvdisidlelarklqRDiae 154
                                       l +l  g+ v+ p Y++e ++++  ++ ++e++dv+v+EG+++lyde++ e+ldl++yv ++ d+++ r+++RD+ +
  gi|336253404|ref|YP_004596511.1|  73 LNQLLMGQPVEMPQYDFEIHNRKD-ERVTVEPTDVIVLEGIFSLYDEEILEMLDLRVYVMTDADVRILRRIERDVVD 148
                                       **********************98.9*************************************************** PP

                               PRK 155 RGrsleavldsil.rrkpdyvnyikpqfseadliiqrvpt 193
                                       RGr+le+v++++l  +kp  +++++p++++ad+ii+ + +
  gi|336253404|ref|YP_004596511.1| 149 RGRDLEGVMEQYLeTVKPMHEQFVEPTKKNADVIIPEGAN 188
                                       *************9*********************98765 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1     9e-09     9e-06       1     177 [.       8     183 ..       8     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 9e-09
                                       EEEEESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSSHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHCHHSSS-E CS
                               dNK   1 ivveGnIgaGKstlvklLskklgvkvfeEpvdkwtnvqknlLekfYkdpsrwsfalqtyvllsrlkqqlealatkqv 77 
                                       i + G  gaGK+t++ + ++++g  v + p d++ +    l ++ +++ ++  +   + +  + l+++l+ l  +q+
  gi|336253404|ref|YP_004596511.1|   8 IGIAGGTGAGKTTVARTVADTVGEAVTRIPLDNYYE---DLSHLEFEERKEVNYDHPDAFEWELLQEHLNQLLMGQP 81 
                                       6799*******************9999999999944...44455677777777777777777777777777666666 PP

                                       EEEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH.-SEEEEEE--HHH.HHHHHHH....CTTCCC CS
                               dNK  78 vvleRsiysdryiFakalaekgtlseeelkiykelldnlleelak.pdlliYLkaslet.clerikk....Rgreee 148
                                       v +   ++ d++i      e+ t++++++ +++ +++ + ee+ + +dl +Y+ ++ ++ +l+ri++    Rgr  e
  gi|336253404|ref|YP_004596511.1|  82 VEM---PQYDFEIHNR-KDERVTVEPTDVIVLEGIFSLYDEEILEmLDLRVYVMTDADVrILRRIERdvvdRGRDLE 154
                                       533...5556656544.6788999****************888777***********96499***985555777664 PP

                                       TTS-HHHHHHHHHHHHHHHTSGGCS-.EEE CS
                               dNK 149 kkieldYlekLhekyeewlkklnevp.vlv 177
                                        ++ ++Yle+++  +e++++ +++   v++
  gi|336253404|ref|YP_004596511.1| 155 -GVMEQYLETVKPMHEQFVEPTKKNAdVII 183
                                       .8999*************999877652444 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.4e-06    0.0094       2      24 ..       7      30 ..       6      80 .. 0.85
   2 ?    2.9   0.1     0.076        76     105     149 ..     107     151 ..      86     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.4e-06
                                      EEEEEESTTSSHHHHHHHHHH.TT CS
                              CoaE  2 ivgltGgiasGKstvanlfad.lg 24
                                      ++g++Gg ++GK+tva++ ad +g
  gi|336253404|ref|YP_004596511.1|  7 VIGIAGGTGAGKTTVARTVADtVG 30
                                      8*****************999433 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.076
                                       EEEEE-TTTTTTTGGGGSSEEEEEE--HHHHHHHHHHCCTSTHHH CS
                              CoaE 105 yvlldvPLLvEkqlekliervlvvdvelelqveRlvardgvseee 149
                                       +vl  +  L ++++ ++++  + v  + + ++ R ++rd v++  
  gi|336253404|ref|YP_004596511.1| 107 IVLEGIFSLYDEEILEMLDLRVYVMTDADVRILRRIERDVVDRGR 151
                                       55555666788888889999999****************998865 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.1e-06    0.0011      19      60 ..       8      47 ..       4      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-06
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                      i ++G++GAGK+++a+ ++d +  ++ v r+  D++ e   +
  gi|336253404|ref|YP_004596511.1|  8 IGIAGGTGAGKTTVARTVADTV--GEAVTRIPLDNYYEDLSH 47
                                      569******************9..999999999999776544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.4e-06    0.0014       1     114 [.       8     145 ..       8     162 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss........ 69 
                                       I+++G  G+GKtt+a+ +++    g+ ++ +  +n++++    e ++e k+++ d  d+   +l +           
  gi|336253404|ref|YP_004596511.1|   8 IGIAGGTGAGKTTVARTVADTV--GEAVTRIPLDNYYEDLSHLE-FEERKEVNYDHPDAFEWELLQEHLnqllmgqp 81 
                                       89******************97..77777776666655555555.78888887777666555555533334445555 PP

                            AAA_18  70 ..................aleegknlvidghlaeleseaakdikk.......vvLtaspeelleRlekRg 114
                                                         + e  +++v++g+ + + +e              v++ ++ ++++ R  +R+
  gi|336253404|ref|YP_004596511.1|  82 vempqydfeihnrkdervTVEPTDVIVLEGIFSLYDEE------IlemldlrVYVMTDADVRILRRIERD 145
                                       66666666666666666666666666666665433222......02222245777777777776666665 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.4e-06    0.0044       4      58 ..       8      60 ..       5     170 .. 0.89
   2 ?   -2.0   0.0       2.8   2.8e+03      31      47 ..     189     205 ..     181     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.4e-06
                                      EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS-GGGGTSTTSEEEETTS CS
                               CPT  4 ilLnGgsssGKsslaralqevldepwlhlgvDafvealppkrqdeadglefetel 58
                                      i + Gg+ +GK+++ar + +++ e+   +++D++ e l     +e ++++++  +
  gi|336253404|ref|YP_004596511.1|  8 IGIAGGTGAGKTTVARTVADTVGEAVTRIPLDNYYEDLSHLEFEERKEVNYD--H 60
                                      66789*********************************99999988888886..3 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                                       EEEHHHHHHHS-GGGGT CS
                               CPT  31 hlgvDafvealppkrqd 47 
                                       +++vD ++e++ ++r+d
  gi|336253404|ref|YP_004596511.1| 189 QMAVDLLIEKIEAERTD 205
                                       68899999999888877 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   7.4e-06    0.0074       2      66 ..       8      75 ..       7      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.4e-06
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv..edllafaervleeqlee 66
                                      i i Gg ++GKTt+++  a++ g  v + +   ++e+++  ++++ ++v  + + af+ ++l+e l +
  gi|336253404|ref|YP_004596511.1|  8 IGIAGGTGAGKTTVARTVADTvGEAVTRIPLDNYYEDLSHLEFEERKEVnyDHPDAFEWELLQEHLNQ 75
                                      5589***************9988888888888888888866666555555468889998888887765 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   6.7e-05     0.066     132     160 ..       8      36 ..       3      63 .. 0.82
   2 ?    1.5   0.1      0.12   1.2e+02      16      63 ..      90     137 ..      83     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                             T2SSE 132 ilvsGgTgsGKttllyallkeinksderi 160
                                       i ++GgTg GKtt++ ++  ++ +   ri
  gi|336253404|ref|YP_004596511.1|   8 IGIAGGTGAGKTTVARTVADTVGEAVTRI 36 
                                       6699************9999998886666 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.12
                             T2SSE  16 dihvekpervkvrervdgielreveel.ekaalerlisriaalakldis 63 
                                       +ih  k+erv v e +d i+l+ + +l +++ le+l  r+ +++ +d+ 
  gi|336253404|ref|YP_004596511.1|  90 EIHNRKDERVTV-EPTDVIVLEGIFSLyDEEILEMLDLRVYVMTDADVR 137
                                       899999999***.999**9999998872455677888899999999886 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0017       1.7       2      20 ..      12      30 ..      11      49 .. 0.90
   2 ?    6.4   0.4     0.011        11      86     130 ..     110     154 ..      88     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0017
                                      E-TTSSHHHHHHHHHHHHT CS
                            AAA_17  2 GgPGsGKgtqceklvekyg 20
                                      Gg G+GK+t+++++++ +g
  gi|336253404|ref|YP_004596511.1| 12 GGTGAGKTTVARTVADTVG 30
                                      99**********9998776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                                       TEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH..TTST-TS- CS
                            AAA_17  86 agfldglpkevleelkpdaiilleadpeeilerrlkd..rtrgrddd 130
                                       +g+++ +++e+le l  d+ +++ +d+++ + rr+++    rgrd +
  gi|336253404|ref|YP_004596511.1| 110 EGIFSLYDEEILEML--DLRVYVMTDADVRILRRIERdvVDRGRDLE 154
                                       466677788888888..888899999998888888884557999976 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   3.1e-05     0.031       4      45 ..      10      56 ..       7      82 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-05
                            AAA_33  4 lvGlpGsGKstlaerllkklg..avllssdtlrrrlfg...tdqqsk 45
                                      + G  G+GK+t+a+ ++   g  ++++  d++++ l     ++++  
  gi|336253404|ref|YP_004596511.1| 10 IAGGTGAGKTTVARTVADTVGeaVTRIPLDNYYEDLSHlefEERKEV 56
                                      67889************9999*9999*****9999988655333322 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.1e-05     0.031      13      45 ..       7      39 ..       4     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-05
                                      EEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilld 45
                                      +++i G +GaGK+t+++++a  +  +  +i ld
  gi|336253404|ref|YP_004596511.1|  7 VIGIAGGTGAGKTTVARTVADTVGEAVTRIPLD 39
                                      689***************999888777777666 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00082      0.81       1      23 [.       8      30 ..       8      41 .. 0.90
   2 ?    4.8   0.3      0.02        20     126     205 ..     120     199 ..      92     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00082
                                      EEEE-STTSSHHHHHHHHHHHHT CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklg 23
                                      i i G +g+GK +var++a+++g
  gi|336253404|ref|YP_004596511.1|  8 IGIAGGTGAGKTTVARTVADTVG 30
                                      67999**************9987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.02
                                       ISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHHCTSSS-S---TT-EEEET.TTS-HHHH CS
                    Cytidylate_kin 126 vfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeikeRDklDkerevgpLklaedaliidt.skltieev 201
                                       ++   +l++++   +++R+ RR++         +le ++++  e  k  +e+ v+p k+ +d++i +  ++++++ +
  gi|336253404|ref|YP_004596511.1| 120 ILEMLDLRVYVMTDADVRILRRIERDVVD-RGRDLEGVMEQYLETVKPMHEQFVEPTKKNADVIIPEGaNQMAVDLL 195
                                       55566899**************9874433.34678888888888888888888888888888887654144566666 PP

                                       HHHH CS
                    Cytidylate_kin 202 veki 205
                                       +eki
  gi|336253404|ref|YP_004596511.1| 196 IEKI 199
                                       6665 PP

>> T3SS_needle_reg  YopR, type III needle-polymerisation regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.4e-05     0.044      41     131 ..     101     190 ..      92     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-05
                                       -SS--HHHHHHHHHHHHHHHHHHHTT--S---HHHHHHHHHHHHHHHS-SSHHHHHHHHHHHHT----H...HHHHH CS
                   T3SS_needle_reg  41 kkpsddavlevLlapvkeeLladfgglqgsvkPplDlpeLrkvlrqfaplGkqkeavLlevleeikplPeneylsdL 117
                                        +p+d  vle + +   ee+l     l+  v    D+  Lr++ r+    G+  e v+ + le +kp+   e  ++ 
  gi|336253404|ref|YP_004596511.1| 101 VEPTDVIVLEGIFSLYDEEILEMLD-LRVYVMTDADVRILRRIERDVVDRGRDLEGVMEQYLETVKPMH--EQFVEP 174
                                       5799999999999999999997765.59999999********************************998..788999 PP

                                       HHHHHHHH-XX..XXX CS
                   T3SS_needle_reg 118 irkeLkilipk..nam 131
                                        +k+  ++ip+  n m
  gi|336253404|ref|YP_004596511.1| 175 TKKNADVIIPEgaNQM 190
                                       9999999998633555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   8.3e-05     0.082      10      66 ..      10      79 ..       7     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.3e-05
                            AAA_22 10 vtGesGtGKTtllrrlleqldeeakaee.............erpevvfvtlpsstsskdllrellralgl 66
                                      + G +G+GKTt++r+++++  e+                  e+++ v ++ p   +++ l ++l + l  
  gi|336253404|ref|YP_004596511.1| 10 IAGGTGAGKTTVARTVADTVGEAVTRIPldnyyedlshlefEERKEVNYDHPDAFEWELLQEHLNQLLMG 79
                                      7799**************9865444444777777777776655555666666666777776666666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   0.00027      0.27      19      42 ..       4      27 ..       1      35 [. 0.86
   2 ?   -1.8   0.0       1.4   1.4e+03     158     193 ..     114     149 ..      96     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                                      CSEEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 19 qslvvalvGmgGvGKttlakqiln 42
                                       s+v+++ G  G GKtt+a+ +  
  gi|336253404|ref|YP_004596511.1|  4 PSFVIGIAGGTGAGKTTVARTVAD 27
                                      579****************99875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                                       S--HHHHHHHHHHCCTS-GGCHH..CHHHHHHHHHH CS
                            NB-ARC 158 lLekdeawellenkvfekkleekesleevakeivek 193
                                       +L ++e +e+l   v+ +++ + + l+++ + +v +
  gi|336253404|ref|YP_004596511.1| 114 SLYDEEILEMLDLRVYVMTDADVRILRRIERDVVDR 149
                                       677788888888888888888777788777777765 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.0    0.0002       0.2      30      72 ..     174     230 ..     165     237 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                                       XXXXXXXXXXXXXXXXXX...............XXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Ribosomal_60s  30 legkdieellangaakla...............aaaaaaaaaaaaaaaaaaaeekkke 72 
                                        ++k+ + ++ +ga+++a               + +a +a +aa a +a+++ e++ e
  gi|336253404|ref|YP_004596511.1| 174 PTKKNADVIIPEGANQMAvdlliekieaertdaP-GAGGAGGAAGATEAEPDPEADRE 230
                                       4678888888888888888888888887665531.22222222222222222222222 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   0.0   0.00029      0.29       3      29 ..      10      36 ..       8      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                                      EESSTTSSHHHHHHHHHHHHTHEEEEE CS
                               AAA  3 lyGppGtGKTllakavakelgveflei 29
                                      + G  G GKT++a+ va ++g  + +i
  gi|336253404|ref|YP_004596511.1| 10 IAGGTGAGKTTVARTVADTVGEAVTRI 36
                                      57999*************998777666 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   1.7   0.00019      0.19       7      22 ..      17      32 ..      15      36 .. 0.93
   2 ?   -2.4   0.1       4.2   4.2e+03      26      36 ..      97     107 ..      95     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                      TEEEEE----SSHHHH CS
                            DUF348  7 GktvtvrTaadTVgdl 22
                                      Gkt++ rT adTVg++
  gi|336253404|ref|YP_004596511.1| 17 GKTTVARTVADTVGEA 32
                                      9**************8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.2
                                       TT----TT-EE CS
                            DUF348  26 agitlgeqDkV 36 
                                         +t++++D++
  gi|336253404|ref|YP_004596511.1|  97 ERVTVEPTDVI 107
                                       56888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 1842.61
//
Query:       gi|336253405|ref|YP_004596512.1|  [L=162]
Description: NUDIX hydrolase [Halopiger xanaduensis SH-6]
Scores for 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   63.3   0.3    2.7e-17   63.1   0.3    1.1  1  NUDIX          NUDIX domain
    8.4e-05   22.4   1.3    0.00018   21.3   1.3    1.6  1  Nudix_N_2      Nudix N-terminal
    0.00092   18.5   1.3     0.0019   17.5   1.3    1.5  1  zf-TFIIB       Transcription factor zinc-finger
     0.0049   16.9   0.8     0.0078   16.2   0.8    1.3  1  DZR            Double zinc ribbon
  ------ inclusion threshold ------
      0.053   13.0   3.7        3.3    7.3   0.4    2.3  2  zf-ribbon_3    zinc-ribbon domain
      0.082   12.9   0.6        3.5    7.7   0.1    2.2  2  YhfH           YhfH-like protein
      0.097   12.6   6.3        2.3    8.2   0.9    2.7  2  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.11   12.1   2.3       0.33   10.5   2.3    1.9  1  TF_Zn_Ribbon   TFIIB zinc-binding
       0.24   11.2   4.8        1.7    8.5   0.7    2.4  2  zinc_ribbon_2  zinc-ribbon domain
       0.36   11.0   2.8        1.1    9.4   2.2    2.0  2  Zn-ribbon_8    Zinc ribbon domain
       0.45   10.5   2.7       0.37   10.8   1.3    1.7  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
        6.6    6.9   7.5        3.4    7.8   0.8    2.4  2  UPF0547        Uncharacterised protein family UPF0547


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 !   63.1   0.3   1.8e-20   2.7e-17       6     115 ..      44     155 ..      40     162 .] 0.76

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 1.8e-20
                                       EEEEEEETTSE...EEEEEESSSSTTT...EESSEEECBTTSHHHHHHHHHHHHHHS..EEEEEEEEEEEEEEEEEE CS
                             NUDIX   6 vgvvllnekge...vLlvrrskkpfpg...WelPgGkvepgEtpeeAArREleEEtG..leaellellgrlhylapy 74 
                                       +gv + ++ g    vL v+r    +pg   W++PgG+ve gE+p   A+REleEEtG  +++++l++++     a  
  gi|336253405|ref|YP_004596512.1|  44 AGVAVVDRTGPepaVLCVERG--VPPGvgeWTIPGGHVETGEEPHVGAARELEEETGisVDPDTLTVFD-----AAA 113
                                       45555555555566*******..555557****************************444777778888.....344 PP

                                       EEEEEEEEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHH CS
                             NUDIX  75 dgpygdeheilyvfl.eevegelepndenevsevrwvpleel 115
                                         p  d+h ++ +++ +++e + ep++  + +++r++++ e+
  gi|336253405|ref|YP_004596512.1| 114 LPPRADKHVVMTYYVvDRAETTGEPRAGSDAADARFWTPSEF 155
                                       44444478888777779999999999999999***9999988 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.3   1.2e-07   0.00018       2      31 ..       8      35 ..       7      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
                                      B-TTT--B-EEE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCgti 31
                                      +C+ CG  +e+     D reR +Cp Cg +
  gi|336253405|ref|YP_004596512.1|  8 YCPYCGDGLETIAL--DGRERKRCPGCGEV 35
                                      9*******997665..99**********87 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.3   1.3e-06    0.0019       1      26 [.       8      33 ..       8      33 .. 0.98

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-06
                          zf-TFIIB  1 kCPkCqdeleeserggveidyCpqCr 26
                                      +CP C+d le++ ++g e ++Cp C+
  gi|336253405|ref|YP_004596512.1|  8 YCPYCGDGLETIALDGRERKRCPGCG 33
                                      7************************7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.8   5.2e-06    0.0078      13      38 ..       7      36 ..       2      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.2e-06
                               DZR 13 rfCseCgtklkavaa....edrCpsCgekv 38
                                       +C++Cg  l+  a      +rCp Cge +
  gi|336253405|ref|YP_004596512.1|  7 AYCPYCGDGLETIALdgreRKRCPGCGEVI 36
                                      79********8555599*9********975 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4    0.0022       3.3       4       9 ..       8      13 ..       7      17 .. 0.67
   2 ?    6.5   0.2    0.0038       5.7       3      11 ..      27      35 ..      25      36 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0022
                       zf-ribbon_3  4 rCPnCG 9 
                                      +CP+CG
  gi|336253405|ref|YP_004596512.1|  8 YCPYCG 13
                                      566666 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0038
                       zf-ribbon_3  3 vrCPnCGap 11
                                      +rCP CG++
  gi|336253405|ref|YP_004596512.1| 27 KRCPGCGEV 35
                                      799999985 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.051        76      12      24 ..       5      17 ..       4      20 .. 0.79
   2 ?    7.7   0.1    0.0023       3.5      13      23 ..      26      36 ..      25      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.051
                              YhfH 12 PkKkCteCGkeie 24
                                      P+  C+ CG+ +e
  gi|336253405|ref|YP_004596512.1|  5 PPAYCPYCGDGLE 17
                                      5668*****9876 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
                              YhfH 13 kKkCteCGkei 23
                                       K C+ CG++i
  gi|336253405|ref|YP_004596512.1| 26 RKRCPGCGEVI 36
                                      69*******98 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 ?    6.4   0.4    0.0056       8.4      24      33 ..       5      14 ..       4      17 .. 0.81
   2 ?    8.2   0.9    0.0015       2.3      13      23 ..      28      38 ..      27      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0056
                           DUF35_N 24 PravCphCgs 33
                                      P a+Cp+Cg 
  gi|336253405|ref|YP_004596512.1|  5 PPAYCPYCGD 14
                                      7799****85 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0015
                           DUF35_N 13 rCpdCGtvqfP 23
                                      rCp CG v++ 
  gi|336253405|ref|YP_004596512.1| 28 RCPGCGEVIWH 38
                                      9*******996 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.3   0.00022      0.33       2      29 ..       8      36 ..       7      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                                      EETTTTC..EECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon  2 kCPnCgs..tnlveDpergelvCtdCGlVl 29
                                       CP+Cg   +++ +D  r   +C+ CG+V+
  gi|336253405|ref|YP_004596512.1|  8 YCPYCGDglETIALD-GRERKRCPGCGEVI 36
                                      6*****975557888.88888********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 ?    8.5   0.7    0.0011       1.7      15      21 ..       8      14 ..       7      16 .. 0.79
   2 ?    4.3   0.2     0.024        36      15      21 ..      28      34 ..      25      36 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0011
                     zinc_ribbon_2 15 FCpyCGt 21
                                      +CpyCG 
  gi|336253405|ref|YP_004596512.1|  8 YCPYCGD 14
                                      8****95 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.024
                     zinc_ribbon_2 15 FCpyCGt 21
                                       Cp CG+
  gi|336253405|ref|YP_004596512.1| 28 RCPGCGE 34
                                      5888886 PP

>> 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     0.025        37      25      34 ..       5      14 ..       1      19 [. 0.69
   2 ?    9.4   2.2   0.00075       1.1       8      34 ..       9      34 ..       8      36 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.025
                       Zn-ribbon_8 25 pltaCPeCgs 34
                                      p+  CP Cg 
  gi|336253405|ref|YP_004596512.1|  5 PPAYCPYCGD 14
                                      4445****96 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00075
                       Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgs 34
                                      C  Cg   e ++   d  + + CP Cg+
  gi|336253405|ref|YP_004596512.1|  9 CPYCGDGLETIAL--DGRERKrCPGCGE 34
                                      999**99998874..5556666****96 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 ?   10.8   1.3   0.00025      0.37      20      44 ..       8      33 ..       3      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                     Zn_Tnp_IS1595 20 vCPhCgsr.kayriktrglfqCkeCr 44
                                       CP+Cg   + + + +r++ +C  C+
  gi|336253405|ref|YP_004596512.1|  8 YCPYCGDGlETIALDGRERKRCPGCG 33
                                      4*****99*****************8 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.9      0.11   1.6e+02      17      21 ..       9      13 ..       7      13 .. 0.90
   2 ?    7.8   0.8    0.0022       3.4       1      13 [.      27      39 ..      27      45 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.11
                           UPF0547 17 CphCG 21
                                      Cp+CG
  gi|336253405|ref|YP_004596512.1|  9 CPYCG 13
                                      9***9 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0022
                           UPF0547  1 KvCPeCeakvPva 13
                                      K+CP+C + + ++
  gi|336253405|ref|YP_004596512.1| 27 KRCPGCGEVIWHN 39
                                      99****9977655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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):              12  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1247.93
//
Query:       gi|336253406|ref|YP_004596513.1|  [L=391]
Description: Threonine synthase [Halopiger xanaduensis SH-6]
Scores for 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-56  189.5   1.0      1e-55  189.3   1.0    1.0  1  PALP        Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.039   13.2   0.0      0.057   12.7   0.0    1.1  1  Capsid_VP7  Outer capsid protein VP7
       0.21   11.6   0.9       0.45   10.5   0.9    1.5  1  ADK_lid     Adenylate kinase, active site lid


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 !  189.3   1.0   1.7e-59     1e-55       2     294 .]      68     385 ..      67     385 .. 0.90

  Alignments for each domain:
  == domain 1  score: 189.3 bits;  conditional E-value: 1.7e-59
                                       GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT CS
                              PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallG 78 
                                       t ++g TPlv++p  +   +    +KlE+  ptgSfKdRga+  l+r+ e  g + v+e ssGN+g+a+A +aa++G
  gi|336253406|ref|YP_004596513.1|  68 TFHEGFTPLVDAPESE--WN--AQFKLEYVFPTGSFKDRGATTTLSRAVEL-GVEKVIEDSSGNAGAAIATYAARAG 139
                                       7899*********965..33..56***************************.************************* PP

                                       -EEEEEEETTS-HHHHHHHHHTT-EEEEECCH....HHHHHHHHHHHHHH........STTCEE--TTTSHHHHHHH CS
                              PALP  79 lkvtivvpadaspekvallrllGaevvevggd....ydeavaaaaelaae........gegaylvsqfdnptviegy 143
                                       l++ i+vpad++++k+  +++  a+ v+++g+    +d++ +a++  +a+        g+g+y  + + np+  +g 
  gi|336253406|ref|YP_004596513.1| 140 LEADIYVPADVKQSKLMTIQRADARPVRIEGTrqdvTDACIEAVEGDTADvagaphqsGRGWYASHAW-NPAFYAGT 215
                                       *****************************888555666666666655555888899989999998888.9******* PP

                                       HTHHHHHHHHTT.TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT....-EEEEEEECTTCGGTTCC........S CS
                              PALP 144 gtiglEileqlg.gkpdavvvpvGgGgliaGiaaglke....rrpd....vrvigvepegsdalarsl........r 203
                                        ti++Ei++q + ++pda+v+p+G G l+ G ++g+      +       +r++g++++g  ++ ++l         
  gi|336253406|ref|YP_004596513.1| 216 MTIAFEIAAQRDwTVPDALVLPIGHGTLFLGAYRGFSLlqdaG--ItdemPRLLGAQATGYTPIVDALadegigleT 290
                                       ********88889*************************77642..14589******************544333331 PP

                                       ..S.SS..B............SSS.CCSTCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHH CS
                              PALP 204 agrrvtvpvs...........dtiadglavg..spselafelldrlvdeivtvsdeealeamrllarregivvepss 267
                                                            + iadg+++   +  ++ +e+++++ ++++++  + + +++ +l+ r+g  vep+s
  gi|336253406|ref|YP_004596513.1| 291 ---------DgddtasdgepgSAIADGIQIAdpARQDEILEAIRETDGDAIALGADPIEATLDRLH-RNGFYVEPTS 357
                                       .........344666777788**********999999*****************************.********** PP

                                       HHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 268 aaalaal.klreagelkegdrvvviltg 294
                                       aaa aal + reag l+ +d vvv ltg
  gi|336253406|ref|YP_004596513.1| 358 AAAPAALeQYREAGVLESDDEVVVPLTG 385
                                       *************************998 PP

>> Capsid_VP7  Outer capsid protein VP7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.6e-06     0.057     163     259 ..      86     189 ..      74     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.6e-06
                        Capsid_VP7 163 gdrklPyelPtkaldidhPedkvltrsrkdGll.llfdttaravevlasaaarailmydllklanvddth....... 231
                                       +++kl y +Pt ++ +      +l+r+ + G+  ++ d   +a + +a+ aara l  d+   a+v++++       
  gi|336253406|ref|YP_004596513.1|  86 AQFKLEYVFPTGSFKD-RGATTTLSRAVELGVEkVIEDSSGNAGAAIATYAARAGLEADIYVPADVKQSKlmtiqra 161
                                       579999*****99975.5678899********725567888899**********************98643332222 PP

                        Capsid_VP7 232 karsimyGPsasdlvaactkacaadtar 259
                                        ar +    + +d++ ac +a   dta 
  gi|336253406|ref|YP_004596513.1| 162 DARPVRIEGTRQDVTDACIEAVEGDTAD 189
                                       5678888889999999999998888875 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 ?   10.5   0.9   7.5e-05      0.45       3      25 ..       6      25 ..       5      31 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.5e-05
                                      E-TTT--EEETTTB--SSTTB-T CS
                           ADK_lid  3 vCpkCGrsYhvvfnpPkveglCD 25
                                       Cp+CGr+Y    + P ++  C 
  gi|336253406|ref|YP_004596513.1|  6 SCPDCGRTYE---AGPDEPWRCA 25
                                      7********9...6688888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2868.57
//
Query:       gi|336253407|ref|YP_004596514.1|  [L=319]
Description: succinylglutamate desuccinylase/aspartoacylase [Halopiger xanaduensis SH-6]
Scores for complete 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-57  194.7   0.0    2.1e-57  194.5   0.0    1.0  1  AstE_AspA  Succinylglutamate desuccinylase / Aspartoacylase f


Domain annotation for each model (and alignments):
>> AstE_AspA  Succinylglutamate desuccinylase / Aspartoacylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.5   0.0   1.1e-61   2.1e-57       1     290 [.      43     314 ..      43     315 .. 0.94

  Alignments for each domain:
  == domain 1  score: 194.5 bits;  conditional E-value: 1.1e-61
                                       SS-EEEEEE-SSTT-HHHHHHHHHHHHHHHCCCESCCEEEEEESSHHHHHCTSSSSSTT-S-CTTTTTCCCCCSSTC CS
                         AstE_AspA   1 sgpkvlisAGvHGnElaGvellrqllkqleeadilgeitlvplaNppAiaagsRyipidredLNRaFpgrslgrsld 77 
                                       +g++++++A  +G+El+G+ ++++++ +l++a+i+g+i++v ++N+ A++ ++++ pid++ +NRa+pg+++g    
  gi|336253407|ref|YP_004596514.1|  43 PGKTLYMQAVSDGDELNGIGVIQRVVPRLDPAEISGTILIVGIVNYHAFQVAEHRNPIDDTKMNRAYPGNENG---- 115
                                       69***********************************************************************.... PP

                                       HHHHHHHHHHHHHHHCHCTCCCGCEEEEEEEESSTBCCSSEEEE---SSHHHH...HHHHHHTTTSEEEEEESS--S CS
                         AstE_AspA  78 ealrateaerladalfaaalpeadivlDLHtgtrglkhllfaeadiaeaqlqs...lallkalglpavllldekesa 151
                                            t+ er+a a f+ a  +adi+lDLH+g +++ ++  +++++ + +      l+l+ka+g ++vl  d+k+++
  gi|336253407|ref|YP_004596514.1| 116 -----TSSERIAAATFDVA-TRADIILDLHQGSTSR-MIDEVRVRCGKRHRLYedcLELAKAFGCGYVL--DQKGPD 183
                                       .....***********999.6***********9999.666666666544332269**************..****** PP

                                       SHHHHHHHHCTSEEEEEEEES.TTTTCCHHCCHHHHHHHHHHHHCTCHTT-SCC.CEEEEEEEEEEGGSCCCSSCSE CS
                         AstE_AspA 152 gfletaaeelgalaftlElGgagrlgaedisrtakgvlnvlahigvvagqeavepaklyrvlreldeprdiraeeaG 228
                                       g+l++aa   g++++ +ElGg+  +++++i++ ++gv+nvl+++ ++a++       l r++r ++  +++ a+ +G
  gi|336253407|ref|YP_004596514.1| 184 GQLARAAPDEGIPTIDPELGGTVGWDETSIRKGVEGVFNVLRYYDFLAES-----HDLERQTR-ANGFEQYGAPNGG 254
                                       **************************************************.....55666655.6777889****** PP

                                       EECCCCSTTTTETCTEEEETTEEEEECTSTEEEEESSSSEEEESCCTSCCTTTTEEEEEEEE CS
                         AstE_AspA 229 lvefkvklgddveagellakalvldslggekvelrapqdgvivfineaalvekgaalvkvak 290
                                       lv+f+ +lgd+v+ ge+l  + v++ +g+ k++++a++dg+++  ++ ++v++g+ ++ v++
  gi|336253407|ref|YP_004596514.1| 255 LVDFEKDLGDRVARGETL--FEVTTAFGETKATVTADSDGILWRTRRLPQVASGEYVCSVGT 314
                                       ******************..**************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2506.11
//
Query:       gi|336253408|ref|YP_004596515.1|  [L=414]
Description: hypothetical protein Halxa_2011 [Halopiger xanaduensis SH-6]
Scores for 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-29  102.4   9.4    2.3e-29  102.4   9.4    3.4  3  SpoIIM    Stage II sporulation protein M
  ------ inclusion threshold ------
       0.89    9.0   0.0       0.89    9.0   0.0    4.4  5  DUF4349   Domain of unknown function (DUF4349)


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -14.6  19.8         2   1.8e+04      35      82 ..      57     101 ..       4     128 .. 0.42
   2 ?   -3.6   3.7       1.1   9.8e+03      76     101 ..     151     173 ..     117     197 .. 0.62
   3 !  102.4   9.4   2.6e-33   2.3e-29       5     156 .]     251     407 ..     245     407 .. 0.87

  Alignments for each domain:
  == domain 1  score: -14.6 bits;  conditional E-value: 2
                            SpoIIM  35 slflaifanNlrvalllfllGllllgiptilvl.linGfvlGavaalva 82 
                                         fl +f+  + + ++l+++G    gi+++++   + ++ +Ga++ lv+
  gi|336253408|ref|YP_004596515.1|  57 LRFLGLFVLEFLLWAVLLVGG----GIAIAIAAgGLSAAGVGAFGILVS 101
                                       333333333333322222222....222222222222222333322222 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.1
                            SpoIIM  76 avaalvaefgglllflllilPhgile 101
                                       a+a++v + g    fl++ +  g++ 
  gi|336253408|ref|YP_004596515.1| 151 AFAYYVLSLG---VFLGFSALSGVFA 173
                                       4444444433...3333333333322 PP

  == domain 3  score: 102.4 bits;  conditional E-value: 2.6e-33
                            SpoIIM   5 flvgillgallaa..snfa...eqisseskensalslflaifanNlrvalllfllGllllgiptilvllinGfvlGa 76 
                                        l ++++g+++a          ++i  + + + +++++l++f nN+ val+++ +G+ ++ +p i+++l+nG+ lG+
  gi|336253408|ref|YP_004596515.1| 251 GLGSFAAGWYAADpyV--GaveTSIAARLEGHVPPAAALEFFGNNWLVALTTVYGGV-AFVLPAIVAVLFNGLALGV 324
                                       3555666777666430..133344449999999***********************7.******************* PP

                            SpoIIM  77 vaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal......rsrrkalkeakrellklllllvpllliA 147
                                       +a l +     l++l++++Phgile+pai+iaga+g+ +g++       r rr +++++ ++++++l+++ +ll++A
  gi|336253408|ref|YP_004596515.1| 325 TARLEVAP---LELLAFVVPHGILEIPAIFIAGALGVSVGVDGwrtlqgRMRRATFADRVERAFWVLVGIGILLAVA 398
                                       *9999995...9***************************77777889*988999*********************** PP

                            SpoIIM 148 aliEafvtp 156
                                       + iE+fv+p
  gi|336253408|ref|YP_004596515.1| 399 GAIEGFVSP 407
                                       *******98 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   5.9         1     9e+03     190     209 ..       6      24 ..       2      28 .. 0.69
   2 ?   -0.4   0.6     0.073   6.5e+02     169     207 ..      46      84 ..      31      90 .. 0.61
   3 ?   -5.3   7.0         2   1.8e+04     181     207 ..      89     115 ..      82     128 .. 0.48
   4 ?    9.0   0.0   9.9e-05      0.89     159     190 ..     208     240 ..     199     261 .. 0.67
   5 ?   -2.5   1.1      0.32   2.9e+03     176     205 ..     290     316 ..     270     326 .. 0.52

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1
                           DUF4349 190 llvvlgallPwllvlalvla 209
                                       +++vl+a+l +llv+a v++
  gi|336253408|ref|YP_004596515.1|   6 IAIVLVAILLVLLVAA-VAW 24 
                                       6777888888888877.555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.073
                           DUF4349 169 gegflealsggwnalveflagllvvlgallPwllvlalv 207
                                       ++gf+ a +  ++ l+ f+ ++l+++++l+   + +a++
  gi|336253408|ref|YP_004596515.1|  46 DAGFAGARRHWLRFLGLFVLEFLLWAVLLVGGGIAIAIA 84 
                                       556666666666666777777777666666666666643 PP

  == domain 3  score: -5.3 bits;  conditional E-value: 2
                           DUF4349 181 nalveflagllvvlgallPwllvlalv 207
                                       +a + ++ g+lv l+++l +++ la+v
  gi|336253408|ref|YP_004596515.1|  89 SAAGVGAFGILVSLLVALLLIVALAAV 115
                                       444444444444444433333333322 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 9.9e-05
                           DUF4349 159 eaeteaeeee.gegflealsggwnalveflagl 190
                                       ++++++++ + +++f ++l++gw+++v+f+++ 
  gi|336253408|ref|YP_004596515.1| 208 VRPPTSPDRPlQAQFVDGLRRGWTEMVAFVRAT 240
                                       33343333346899****************987 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 0.32
                           DUF4349 176 lsggwnalveflagllvvlgallPwllvla 205
                                       + ++w   ++++ g +     +lP ++ ++
  gi|336253408|ref|YP_004596515.1| 290 FGNNWLVALTTVYGGVA---FVLPAIVAVL 316
                                       44444443333333333...3444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 3294.22
//
Query:       gi|336253409|ref|YP_004596516.1|  [L=409]
Description: Rhodanese-like protein [Halopiger xanaduensis SH-6]
Scores for 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   53.4   0.0    5.8e-14   52.5   0.0    1.4  1  Rhodanese      Rhodanese-like domain
    2.7e-11   43.9   3.6    2.7e-11   43.9   3.6    1.9  2  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.043   13.3   0.6       0.14   11.7   0.5    1.9  2  Lactamase_B_2  Beta-lactamase superfamily domain
       0.08   13.7   0.0       0.38   11.5   0.0    2.2  2  PTS_IIB        PTS system, Lactose/Cellobiose specific IIB su


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   1.3e-17   5.8e-14       2     105 ..       7     116 ..       6     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 1.3e-17
                         Rhodanese   2 akelkellekgkva..llDvRppeeYekghIpgAvnv....skdtlsrakkseapllelpeellelgidnkktvvvy 72 
                                       a+ l+el+++g+ +  l+D+Rp++ Y+ +h+pgAv++    + +  + ++++ + + ++  e+ ++ + + ++v+++
  gi|336253409|ref|YP_004596516.1|   7 ADRLAELQDEGA-DfvLVDTRPADSYDSWHVPGAVHFpfgpEEELEGAEDRDGDVDEDDRLEDFQETVGDAERVITI 82 
                                       677888886665.347*********************888633333333333333333333333336778******* PP

                         Rhodanese  73 cdgggraaaaaallkk.lGyknvsvldGGfkawk 105
                                       c++g ++ ++a++l++    ++v+ +dGG+k+w+
  gi|336253409|ref|YP_004596516.1|  83 CAKGISSGNLATQLESaTDEYDVHTVDGGMKGWS 116
                                       ******8888888886344478***********7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.79   3.5e+03      73     106 ..      34      63 ..      28      82 .. 0.47
   2 !   43.9   3.6     6e-15   2.7e-11       9     163 ..     146     283 ..     138     326 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.79
                                       TCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCE CS
                       Lactamase_B  73 gavaeeapalfmeeaddaasrkglllagvsadkp 106
                                       ++v+ + + +f++e++ +   +      +++d +
  gi|336253409|ref|YP_004596516.1|  34 WHVPGAVHFPFGPEEELEGAEDR----DGDVDED 63 
                                       55555555555555544333221....1222222 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 6e-15
                                       EEEE..ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                       Lactamase_B   9 ylie..gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                       y++     g+++++D+  + ++   a     ++  ++ +  vi TH H+DHi+g ++l++  dvp +  a +++ + 
  gi|336253409|ref|YP_004596516.1| 146 YVVGcaETGEAVVVDPTDDVDEFEVA-----AEEAGLTIVGVIDTHVHADHISGGRDLADSLDVPYYLGARADERGV 217
                                       677776779***************98.....8********************************************* PP

                                       CHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCC CS
                       Lactamase_B  84 meeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgri 160
                                       + e                     +++e  ++ a g+r+l++   pgh++  + +  + +  ++t D+l++++tgr+
  gi|336253409|ref|YP_004596516.1| 218 EYEY--------------------TPLERNEVLAVGDRELKALFAPGHTSEMVALLVD-DAAVLTADTLHVASTGRT 273
                                       ****....................**************************99998765.55788************* PP

                                       CC........ CS
                       Lactamase_B 161 dl.......t 163
                                       +l        
  gi|336253409|ref|YP_004596516.1| 274 ELefsegseA 283
                                       *955544441 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 ?   -1.7   0.0      0.39   1.8e+03      95     131 ..     123     149 ..      74     160 .. 0.67
   2 ?   11.7   0.5   3.1e-05      0.14      30      61 ..     178     207 ..     155     252 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.39
                                       EEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE CS
                     Lactamase_B_2  95 sfelgdggleitatparhksgrrldrnagdtlGlrie 131
                                       ++++gd+g  +t+++++  +        + +lG++++
  gi|336253409|ref|YP_004596516.1| 123 EVDVGDPG--LTVVQVQRRA--------TGCLGYVVG 149
                                       44445555..4444444444........448888887 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.1e-05
                                       SEEEEE-SS--HHHHGGGGCCCCC--EEEEEE CS
                     Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklply 61 
                                        i +V+ th H+DH+ g  +l+   +  +p y
  gi|336253409|ref|YP_004596516.1| 178 TIVGVIDTHVHADHISGGRDLADSLD--VPYY 207
                                       5889*************999999332..5666 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.4e-05      0.38       1      32 [.      78     108 ..      78     139 .. 0.84
   2 ?   -2.1   0.0       1.5   6.6e+03      21      37 ..     169     185 ..     155     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.4e-05
                                       EEEEEESSSHHHHHHHHHHHHHHHHHCTEEEE CS
                           PTS_IIB   1 killaCgaGmatSlmaaeklekaakelgieae 32 
                                       +++++C+ G+++  +a ++le+a +e ++ ++
  gi|336253409|ref|YP_004596516.1|  78 RVITICAKGISSGNLA-TQLESATDEYDVHTV 108
                                       589*************.*********997763 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                                       HHHHHHCTEEEEETTEE CS
                           PTS_IIB  21 ekaakelgieaegeagv 37 
                                       e aa+e+g+ ++g+  +
  gi|336253409|ref|YP_004596516.1| 169 EVAAEEAGLTIVGVIDT 185
                                       55778888555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 3328.44
//
Query:       gi|336253410|ref|YP_004596517.1|  [L=496]
Description: aldehyde dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-155  515.7   1.4     1e-154  515.5   1.4    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
        0.2   12.1   0.1       0.47   11.0   0.1    1.6  1  DUF3456   TLR4 regulator and MIR-interacting MSAP


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 !  515.5   1.4  1.1e-158    1e-154       1     462 []      20     485 ..      20     485 .. 0.99

  Alignments for each domain:
  == domain 1  score: 515.5 bits;  conditional E-value: 1.1e-158
                                       EET-SS.SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHH CS
                            Aldedh   1 wveses.etievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaelet 76 
                                       w++ses e+i+v +P+t+e++a+vpaat+ dv+aa +aA++a+k+w++ p+ eR+++ +++a+ll e ++e+++l++
  gi|336253410|ref|YP_004596517.1|  20 WTPSESdEEIAVEDPSTREEVARVPAATEGDVEAAYEAAADAQKEWQEAPPIEREQVAQQFAQLLGEYEDEITDLLA 96 
                                       889999677******************************************************************** PP

                                       HHH---HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHH CS
                            Aldedh  77 letGkplaearaeveeaidvlryyaelaeklegevlps.segklalvrrePlGvvgaItPWNfPlllaawklapala 152
                                        e+G      ++ v+ a d +  +a+  ++++ge ++s  +gk+++vrreP Gv+++I+PWNfPl+l+ +++apala
  gi|336253410|ref|YP_004596517.1|  97 HEAGGGPIMGETSVSIASDQAAEAATFPRRMKGEQISSnVPGKENFVRREPQGVITVISPWNFPLNLSGRAIAPALA 173
                                       *********************************9999955************************************* PP

                                       TT-EEEEEE-TTSHHHH.HHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCT CS
                            Aldedh 153 aGNtvvlKPaeetplsa.lllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaakn 228
                                       +GN+vvlKPa++tp++  ll+a+l+eeaglP+g+lnvvtg+gse+g+a+v h e d+v+ftGst+vgr +a++a++n
  gi|336253410|ref|YP_004596517.1| 174 TGNAVVLKPASNTPITGgLLMAKLYEEAGLPDGLLNVVTGHGSEIGDAVVGHAESDLVAFTGSTPVGRGVASTAGEN 250
                                       *****************9*********************************************************** PP

                                       TSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT CS
                            Aldedh 229 lkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdplded 305
                                       l +++lElGG+n++iv++daDl++av+++v+g+f+++GQvCi+++r lv+e++yde+v++l+e+a++l  g++ +ed
  gi|336253410|ref|YP_004596517.1| 251 LSELALELGGNNAHIVTADADLEAAVDSAVFGSFVHQGQVCISINRHLVHEDVYDEYVDRLTERAESLPTGSAHEED 327
                                       ***************************************************************************** PP

                                       -SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEES CS
                            Aldedh 306 tdvGPliseaqlekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfk 381
                                       t v P+i+e+q++++ +yvee++++ga+l +Gge    +g e+  +v+Ptv+++ t+dm+ a++E FGP+++vi+f+
  gi|336253410|ref|YP_004596517.1| 328 TVVAPIIDESQRDEMLEYVEETIDQGATLETGGEtVPMDGVEDSLLVAPTVISDATNDMAAACNEHFGPIAPVIPFS 404
                                       **********************************977999999********************************** PP

                                       SHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEE CS
                            Aldedh 382 deeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeyte 458
                                       d++eaie+  +t+yGL+++v++ d+ + +++aer+++Gnv++Nd+  +++ ++ f G k+Sg+G  ++ + ++e+te
  gi|336253410|ref|YP_004596517.1| 405 DIDEAIEMHDATQYGLSGSVHAGDIGTGMQIAERMDTGNVHVNDQPINDEAHVTFSGTKASGVGTYNSTDIMDEVTE 481
                                       ***************************************************************************** PP

                                       EEEE CS
                            Aldedh 459 vktv 462
                                        k++
  gi|336253410|ref|YP_004596517.1| 482 KKWI 485
                                       9986 PP

>> DUF3456  TLR4 regulator and MIR-interacting MSAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   5.2e-05      0.47      96     139 ..      54      98 ..      24     103 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.2e-05
                           DUF3456  96 evkvdlgipselkde.p.aevkelkkaCeelveeyEdeleelfkee 139
                                         +  +++++e ++e p  e++++ ++ ++l+ eyEde+++l+ +e
  gi|336253410|ref|YP_004596517.1|  54 AYEAAADAQKE-WQEaPpIEREQVAQQFAQLLGEYEDEITDLLAHE 98 
                                       22322333334.444578***********************99984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 3901.14
//
Query:       gi|336253411|ref|YP_004596518.1|  [L=129]
Description: hypothetical protein Halxa_2014 [Halopiger xanaduensis SH-6]
Scores for 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-18   64.9   6.4    9.8e-18   64.7   6.4    1.1  1  SnoaL_2        SnoaL-like domain
    8.1e-09   35.9   1.0    1.1e-08   35.5   1.0    1.1  1  DUF4440        Domain of unknown function (DUF4440)
      3e-07   30.3   1.3    7.3e-07   29.0   1.3    1.6  1  SnoaL          SnoaL-like polyketide cyclase
    1.6e-05   25.1   0.8    1.8e-05   24.9   0.8    1.1  1  SnoaL_4        SnoaL-like domain
     0.0017   18.6   0.1     0.0025   18.1   0.1    1.3  1  SnoaL_3        SnoaL-like domain
  ------ inclusion threshold ------
      0.016   15.9   0.1      0.021   15.5   0.1    1.3  1  Lumazine_bd_2  Putative lumazine-binding
      0.021   14.9   0.9      0.039   14.1   0.9    1.4  1  LEH            Limonene-1,2-epoxide hydrolase catalytic domai
      0.022   15.3   0.0      0.024   15.2   0.0    1.3  1  NTF2           Nuclear transport factor 2 (NTF2) domain
       0.17   12.7   0.0       0.22   12.3   0.0    1.2  1  DUF4829        Domain of unknown function (DUF4829)


Domain annotation for each model (and alignments):
>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   6.4   4.9e-21   9.8e-18       1     101 [.      23     123 ..      23     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 4.9e-21
                                       HHHHHHHHHTTCHHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEE. CS
                           SnoaL_2   1 vraflaalnagdldalaalfapdvvwedpggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgt. 76 
                                       vr++++al+++d+dal+a++apd+v++ p  +++ r+ + +f+r+ +   p  ++e+ d+vad+ +va++++v    
  gi|336253411|ref|YP_004596518.1|  23 VRRYYDALDDHDYDALEAVLAPDFVQRRPDRTFDDRASFVEFMREGRP-NPNTTHEVIDIVADEGTVAARGRVLEAa 98 
                                       8*********************************************85.9********************9986447 PP

                                       EETTSSEEEEEEEEEEEEETTEEEE CS
                           SnoaL_2  77 ipatgrgvtvrgvdvfrvrdGkive 101
                                       + a +++v ++++d+f ++d++iv+
  gi|336253411|ref|YP_004596518.1|  99 TDAGDDRVLFEFADFFAIADDRIVA 123
                                       8999999999*************96 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   1.0   5.3e-12   1.1e-08       3      84 ..      21     101 ..      20     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 5.3e-12
                                       HHHHHHHHHHHCT-HHHHHHCEEEEEEEE-TTS-EEEHHHHHHHHHCCHCEEEEEEEEEEEEEEETTEEEEEEEEEE CS
                           DUF4440   3 aleealeeafvagdaealaallapdavlvgpsgtvldkeellealeagfaagrslelteeevrvlgdlAvvtgrytf 79 
                                       al++++++a+  +d++al+a+lapd+v   p+ t+ d+++++e +++g  + ++ + + +++   +++++++gr+  
  gi|336253411|ref|YP_004596518.1|  21 ALVRRYYDALDDHDYDALEAVLAPDFVQRRPDRTFDDRASFVEFMREG-RPNPNTTHEVIDIVADEGTVAARGRVLE 96 
                                       899******************************************987.5667777777888888888888888554 PP

                                       EECCT CS
                           DUF4440  80 egrgd 84 
                                       +++ +
  gi|336253411|ref|YP_004596518.1|  97 AATDA 101
                                       44444 PP

>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   1.3   3.6e-10   7.3e-07       3     111 ..      22     122 ..      20     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 3.6e-10
                                       HHHHHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHH..HCTTCEEEEEEEEEETTEEEEEEEE CS
                             SnoaL   3 vlrfyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfk..afPDlkvevedlvaegdkvaarltf 77 
                                       ++r+y ++++ +d dal+ ++a+d+v++    +p r  ++ + fve +++    P+ ++ev d+va++ +vaar ++
  gi|336253411|ref|YP_004596518.1|  22 LVRRYYDALDDHDYDALEAVLAPDFVQR----RPDRTFDDRASFVEFMREgrPNPNTTHEVIDIVADEGTVAARGRV 94 
                                       789999999*******************....666777777777777776224567777*************99765 PP

                                       EEEESSEBTTBE-TT-EEEEEEEEEEEEETTEEE CS
                             SnoaL  78 tGthtgeflGipptGkkvkfeeitllrvedGkIv 111
                                            +++  + +   +v fe  +++ ++d++Iv
  gi|336253411|ref|YP_004596518.1|  95 ----LEAA--TDAGDDRVLFEFADFFAIADDRIV 122
                                       ....4444..567788899999999999999987 PP

>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.8     9e-09   1.8e-05       5      99 ..      15     103 ..      11     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 9e-09
                                       HHHHHHHHHHHHHHHHHTT-HHHHHTTEEEEEEEEETTS..--EESHHHHHHHHHSHHHHHH-EEEEE---EEEEET CS
                           SnoaL_4   5 dreaIrdlvarygyylDtkdweeladlFtedavvdytgvgegvlegrdairaalrealdgfaltqHllsnplieldg 81 
                                       + ++ + lv ry  +lD++d+++l+++ ++d v + +     ++  r+++++++re  ++ + t+H + + +   d+
  gi|336253411|ref|YP_004596518.1|  15 AATNASALVRRYYDALDDHDYDALEAVLAPDFVQRRPD---RTFDDRASFVEFMREG-RPNPNTTHEVIDIVA--DE 85 
                                       6677789**************************99996...69*************8.577788887544333..55 PP

                                       TEEEEEEEEEEEEEETTE CS
                           SnoaL_4  82 dtAtgrayllatlvrdgd 99 
                                        t  +r+++l   + +gd
  gi|336253411|ref|YP_004596518.1|  86 GTVAARGRVLEAATDAGD 103
                                       555555555554433333 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   1.2e-06    0.0025       3      60 ..      21      76 ..      19     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-06
                           SnoaL_3  3 alldafyeaaaegdfdalfalwaddivfigtgadelltgreevrrslkqifakgegis 60
                                      al++++y+a+ ++d+dal a++a+d+v   ++    + +r+ +++++++   + ++++
  gi|336253411|ref|YP_004596518.1| 21 ALVRRYYDALDDHDYDALEAVLAPDFVQRRPDR--TFDDRASFVEFMREGRPNPNTTH 76
                                      6889*********************99988666..7889********99987764433 PP

>> Lumazine_bd_2  Putative lumazine-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   1.1e-05     0.021       5      83 ..      18      90 ..      14     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHHHHHHHHHT-HHHHHHHEEEEEEEEEECTCEEEEEECHHHHHHHHHHH..-TT-EE-.EEEEEEEEETTEEE CS
                     Lumazine_bd_2  5 aieavledYfdglaegdaaklrkafhpdaalvgvtkgelremsleellalvaerespakegdprekeIesidvagdvAm 83
                                      + +a++++Y d+l   d ++l+++++pd++    +  + +  ++ +++++++e+++++++++   + I+++  +g+vA+
  gi|336253411|ref|YP_004596518.1| 18 NASALVRRYYDALDDHDYDALEAVLAPDFVQ---RRPDRTFDDRASFVEFMREGRPNPNTTH---EVIDIVADEGTVAA 90
                                      56799************************99...7888899999999999999987544444...46999988888664 PP

>> LEH  Limonene-1,2-epoxide hydrolase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.9   1.9e-05     0.039       5     111 ..      21     125 ..      17     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHHHHT-HHHHHHHEEEEE.EEEETTTEEEE-HHHHHHHHHTT.TTT-EEEEEEEEEEEETTEEE.EEEE CS
                               LEH   5 rvVeaFlaalqeddydaavrrlatdlevyeneglstihGraeaiallerlsadilavevkilriaadgsaVl.tERl 80 
                                         V+ + +al+++dyda ++ la+d    +  +  t   ra  + ++++   +  +   +++ i ad + V    R+
  gi|336253411|ref|YP_004596518.1|  21 ALVRRYYDALDDHDYDALEAVLAPDF--VQRRPDRTFDDRASFVEFMREG-RPNPNTTHEVIDIVADEGTVAaRGRV 94 
                                       57999**************9999988..7888889999999999999998.55555555677777776666515799 PP

                                       EEEEE..TTEEEEEEEEEEEEEETTEEEEEE CS
                               LEH  81 DrliladGplivqltvmGvfeVedgrivlWR 111
                                              G  +v +     f + d+riv+  
  gi|336253411|ref|YP_004596518.1|  95 LEAATDAGDDRVLFEFADFFAIADDRIVALE 125
                                       8888889********************9865 PP

>> NTF2  Nuclear transport factor 2 (NTF2) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.2e-05     0.024       2      57 ..      19      72 ..      18     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHHHHHHHGGGGGGGGEEEEEEEEEETTEEEEESHHHHHHHHHHSSCSC CS
                              NTF2  2 akafvqqYYaaldagdregllalyaadaslltpegsspvkgreaIteffrslpftr 57
                                      a+a+v++YY+ald +d ++l a   a + +  ++++ ++  r++ +ef+r+   + 
  gi|336253411|ref|YP_004596518.1| 19 ASALVRRYYDALDDHDYDALEAVL-APDFVQRRPDR-TFDDRASFVEFMREGRPNP 72
                                      6899*****************998.88888888888.8888888888887755554 PP

>> DUF4829  Domain of unknown function (DUF4829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011      0.22       3      27 ..      22      46 ..      20      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                           DUF4829  3 vieeYFkalnkkdaeaakallskes 27
                                       ++ Y+ al+++d++a++a+l+++ 
  gi|336253411|ref|YP_004596518.1| 22 LVRRYYDALDDHDYDALEAVLAPDF 46
                                      699******************9953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                         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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 972.52
//
Query:       gi|336253412|ref|YP_004596519.1|  [L=625]
Description: Rieske (2Fe-2S) iron-sulfur domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-12   47.7   0.0    2.2e-12   46.7   0.0    1.5  1  Rieske    Rieske [2Fe-2S] domain
    1.9e-12   47.0   0.0    3.8e-12   46.0   0.0    1.5  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   2.5e-16   2.2e-12       8      88 ..      18      96 ..      12      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 2.5e-16
                                      GGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE-TTHHHE CS
                            Rieske  8 esdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvikgPaprpl 85
                                       +d++e      ++ g+p++v+ + +gev+A++++C+H+g pl eg++ ++g l+C +H ++++   G+  + P  +++
  gi|336253412|ref|YP_004596519.1| 18 LEDLEESGRELASLDGTPVAVFHH-EGEVRAVNNRCPHMGFPLVEGTV-DDGILTCHWHHARFElSCGDTFD-PWADDV 93
                                      5667755556667899*******6.***********************.677************65565544.666666 PP

                                      EEE CS
                            Rieske 86 aty 88
                                      +ty
  gi|336253412|ref|YP_004596519.1| 94 PTY 96
                                      666 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   4.3e-16   3.8e-12       2     103 ..      12     107 ..      11     108 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 4.3e-16
                                       EEEEEECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT CS
                          Rieske_2   2 wvpvckledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLkt 78 
                                       + +v++ledl ++ +  a +dg+ va+f+  ++ev A++n++p     +l +G v+d     ++++  +  +f+L+ 
  gi|336253412|ref|YP_004596519.1|  12 FREVVALEDLEESGRELASLDGTPVAVFHH-EGEVRAVNNRCPH-MGFPLVEGTVDDG----ILTCHWHHARFELSC 82 
                                       6799*************************9.9************.5889999998887....99************* PP

                                       -BBSS-TTSB-BEE-EEESTSEEEE CS
                          Rieske_2  79 Gecledeevslkvypvrvedgkvev 103
                                       G+ ++  +  +++ypv v+dg+v+v
  gi|336253412|ref|YP_004596519.1|  83 GDTFDPWADDVPTYPVEVRDGTVYV 107
                                       ***********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 4489.82
//
Query:       gi|336253413|ref|YP_004596520.1|  [L=175]
Description: hypothetical protein Halxa_2016 [Halopiger xanaduensis SH-6]
Scores for 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-43  145.0   0.0    1.1e-42  144.7   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
    2.8e-06   27.1   0.1    5.4e-06   26.1   0.1    1.4  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 !  144.7   0.0   1.3e-46   1.1e-42       1     127 []      42     165 ..      42     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 144.7 bits;  conditional E-value: 1.3e-46
                                       EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHH CS
                     Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaal 77 
                                       +vl+p+a+++lspaD+e     +++++dcsW+++e ++f+      +r+LP+LvAaNpvnYg+p++L++vEAla+a 
  gi|336253413|ref|YP_004596520.1|  42 VVLNPHADQALSPADAEE-GLGTLVALDCSWESAEAASFRMN--GVHRALPFLVAANPVNYGRPFRLTTVEALAGAC 115
                                       89*************877.556899********999986654..79******************************* PP

                                       HHTT-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHHH CS
                     Ribo_biogen_C  78 yilglkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkeyl 127
                                       +i+g ++ a +ll+ f+wge+Fleln+e+l++Y +c+ds+evv+vq++yl
  gi|336253413|ref|YP_004596520.1| 116 CIFGDRDCAADLLEPFRWGETFLELNEEPLRRYGECADSSEVVAVQDDYL 165
                                       ***********************************************996 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 !   26.1   0.1     6e-10   5.4e-06       4      31 ..       6      33 ..       4      36 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6e-10
                                      EEES---------TTHHHHHTTSEEEES CS
                               RLI  4 AivdadqCdPKKCtgkkcarfcpvrlvr 31
                                      ++++++ +dP KCt++++++f+ ++l r
  gi|336253413|ref|YP_004596520.1|  6 HVYYEGDDDPAKCTARRLEKFDKATLYR 33
                                      89********************997755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); 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 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1323.40
//
Query:       gi|336253414|ref|YP_004596521.1|  [L=49]
Description: 50S ribosomal protein L40e [Halopiger xanaduensis SH-6]
Scores for 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-09   35.6   5.3    7.4e-09   35.4   5.3    1.1  1  Ribosomal_L40e  Ribosomal L40e family
    0.00034   20.2   1.7    0.00044   19.9   1.7    1.3  1  zinc_ribbon_2   zinc-ribbon domain
     0.0015   18.5   1.2     0.0016   18.4   1.2    1.2  1  DZR             Double zinc ribbon
     0.0017   18.8   0.9     0.0018   18.7   0.9    1.1  1  zf-CHY          CHY zinc finger
  ------ inclusion threshold ------
      0.065   12.9   7.0       0.11   12.1   7.0    1.5  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.096   12.9   4.9       0.13   12.4   4.9    1.3  1  Ribosomal_L37e  Ribosomal protein L37e
       0.14   12.2   1.4       0.15   12.1   1.4    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.33   10.7   3.0          1    9.2   0.4    2.0  2  Rubredoxin_2    Rubredoxin metal binding domain
        0.5   10.5   2.0       0.54   10.4   2.0    1.1  1  DHHC            DHHC palmitoyltransferase


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 !   35.4   5.3   3.7e-12   7.4e-09       9      49 ..       7      44 ..       2      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 3.7e-12
                    Ribosomal_L40e  9 AqKyncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKKk 49
                                      A+K   +KmiC +C Ar p+rA  Cr  kCg  ++lrpK k
  gi|336253414|ref|YP_004596521.1|  7 AEKRTLEKMICMRCNARNPKRADRCR--KCGY-EKLRPKAK 44
                                      89************************..9**7.67999855 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.7   2.2e-07   0.00044       2      22 ..      17      37 ..      16      44 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.2e-07
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      C +C a ++++a  C +CG++
  gi|336253414|ref|YP_004596521.1| 17 CMRCNARNPKRADRCRKCGYE 37
                                      *******************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.2     8e-07    0.0016       1      21 [.      17      37 ..       7      47 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8e-07
                               DZR  1 CpqCgeelppdarfCseCgtk 21
                                      C +C++ +p++a  C +Cg +
  gi|336253414|ref|YP_004596521.1| 17 CMRCNARNPKRADRCRKCGYE 37
                                      777777777777777777754 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.9   9.3e-07    0.0018      34      62 ..       7      36 ..       3      46 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 9.3e-07
                            zf-CHY 34 lerlevkevlcllCeteq.ekavlCkkCkk 62
                                      +e+ + ++++c++C++++ + a  C+kC+ 
  gi|336253414|ref|YP_004596521.1|  7 AEKRTLEKMICMRCNARNpKRADRCRKCGY 36
                                      57788899*********9455678****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 ?   12.1   7.0   5.7e-05      0.11       2      25 ..      16      36 ..      15      39 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.7e-05
                                      B-SSS--B----SSS----SSS-- CS
                    DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCGh 25
                                      iC++C+a++  ++    RC++CG+
  gi|336253414|ref|YP_004596521.1| 16 ICMRCNARNPKRAD---RCRKCGY 36
                                      8********99988...******8 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   4.9   6.6e-05      0.13      15      43 ..      13      40 ..       2      45 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                    Ribosomal_L37e 15 tHilCrrCgkrsyhvqkktCascGypsak 43
                                        ++C rC+ r    +  +C +cGy + +
  gi|336253414|ref|YP_004596521.1| 13 EKMICMRCNARN-PKRADRCRKCGYEKLR 40
                                      5689*****997.57889*******7655 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   1.4   7.7e-05      0.15      70      98 ..      14      40 ..       6      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-05
                                      EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 70 kvrCreCgkefeleekalrCpkCgsadve 98
                                      k+ C +C+++  ++++  rC kCg ++++
  gi|336253414|ref|YP_004596521.1| 14 KMICMRCNARNPKRAD--RCRKCGYEKLR 40
                                      789*****99997755..9*****98876 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   3.9    0.0059        12       3      21 ..      17      35 ..      16      35 .. 0.93
   2 ?    9.2   0.4    0.0005         1       2      11 ..      30      39 ..      30      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0059
                      Rubredoxin_2  3 CsqCGfesakwfGrCpsCg 21
                                      C +C+++ +k   rC+ Cg
  gi|336253414|ref|YP_004596521.1| 17 CMRCNARNPKRADRCRKCG 35
                                      999***************7 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0005
                      Rubredoxin_2  2 vCsqCGfesa 11
                                      +C++CG+e  
  gi|336253414|ref|YP_004596521.1| 30 RCRKCGYEKL 39
                                      8******965 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.0   0.00027      0.54       4      26 ..      13      35 ..      10      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                              DHHC  4 elkfCstcniykpprskHcrvCn 26
                                      e+ +C  cn + p+r+  cr+C+
  gi|336253414|ref|YP_004596521.1| 13 EKMICMRCNARNPKRADRCRKCG 35
                                      6789******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 349.65
//
Query:       gi|336253415|ref|YP_004596522.1|  [L=203]
Description: beta-lactamase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-10   39.3  10.6    1.2e-07   32.0  10.6    2.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00019   21.0   4.8     0.0013   18.2   4.8    2.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.073   13.3   0.1         26    5.2   0.0    2.9  3  ACP            Malonate decarboxylase delta subunit (MdcD)
      0.099   12.8   0.5       0.21   11.8   0.5    1.5  1  DUF3168        Protein of unknown function (DUF3168)
        0.1   12.6   0.0       0.41   10.6   0.0    2.0  1  DUF1967        Domain of unknown function (DUF1967)
       0.24   11.3   1.8        1.3    8.9   1.8    2.0  1  Lactamase_B_3  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 !   32.0  10.6   3.9e-11   1.2e-07       5     186 ..      14     160 ..      10     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 3.9e-11
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                        +n++l   +++  L+D+G +    ++      ++    d+dav+lTH H DH+  l+ +v+a+d  v+a+ ++   
  gi|336253415|ref|YP_004596522.1|  14 TCNAFLA-LGEEITLVDAGAWDGVVDE------IREHTADLDAVVLTHQHGDHVEQLEAVVDAFDPEVYAYDDHPL- 82 
                                       5777776.89999*************9......8********************************9988766543. PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCC CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetg 158
                                        +++++                       e++d+ + g++++ v+++pgh   + +v++ +++ lf+GD++   + +
  gi|336253415|ref|YP_004596522.1|  83 -RDRAL-----------------------EDGDTVRIGDETFNVVYTPGHA--DDHVSFVSESSLFSGDVVVHDDGA 133
                                       .33333.......................4455555555555555555555..55555667778******9955555 PP

                                       CCCC.TTCEEE-SHCHHHHHHHHHHHHH CS
                       Lactamase_B 159 ridltlrgaevrdpsdaekyldsllkla 186
                                        +     g +++ +++ e +++s+++l 
  gi|336253415|ref|YP_004596522.1| 134 FDYG-SFGRTDMAGQSRERLIRSIDDLL 160
                                       5555.56666666666666666666554 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 !   18.2   4.8   4.5e-07    0.0013      25      61 ..      41      75 ..      26     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.5e-07
                                      S--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEE CS
                     Lactamase_B_2 25 rdelppidaVllthaHyDHlaglltlre.lrpkklply 61
                                      r++ +++daV+lth+H DH++ l  +   + p   ++y
  gi|336253415|ref|YP_004596522.1| 41 REHTADLDAVVLTHQHGDHVEQLEAVVDaFDP---EVY 75
                                      666799**************999988885554...244 PP

>> ACP  Malonate decarboxylase delta subunit (MdcD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0086        26      59      73 ..      24      38 ..      12      46 .. 0.83
   2 ?    4.8   0.0     0.011        33      49      70 ..     115     136 ..     112     149 .. 0.81
   3 ?   -1.4   0.0      0.93   2.8e+03      38      54 ..     148     164 ..     141     193 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0086
                               ACP 59 kveinDkGAldcvir 73
                                      ++++ D GA+d+v+ 
  gi|336253415|ref|YP_004596522.1| 24 EITLVDAGAWDGVVD 38
                                      7999*********94 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                               ACP  49 tleelgvkaakveinDkGAldc 70 
                                       ++ e ++ +++v ++D GA d+
  gi|336253415|ref|YP_004596522.1| 115 FVSESSLFSGDVVVHDDGAFDY 136
                                       67788888999*********98 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.93
                               ACP  38 fgeqieavieetleelg 54 
                                        +e+  + i+++le++ 
  gi|336253415|ref|YP_004596522.1| 148 SRERLIRSIDDLLERMP 164
                                       55555555555555553 PP

>> DUF3168  Protein of unknown function (DUF3168)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5     7e-05      0.21      38     114 ..      25     103 ..      18     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7e-05
                           DUF3168  38 vqsrdasalcg...dgaevrvqldvwarepgraeakalaaavraaLddaalalpggrlaslrlesarllrdpdgkly 111
                                       ++ +da+a +g   + +e++++ld++  +  +++  +  +av +a d   +a +++ l + +le+ +++r +d+ ++
  gi|336253415|ref|YP_004596522.1|  25 ITLVDAGAWDGvvdEIREHTADLDAVVLTHQHGDHVEQLEAVVDAFDPEVYAYDDHPLRDRALEDGDTVRIGDE-TF 100
                                       5567777777778899***********8888888889999999999999999*******************999.77 PP

                           DUF3168 112 rav 114
                                        +v
  gi|336253415|ref|YP_004596522.1| 101 NVV 103
                                       665 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00014      0.41      50      68 ..      82     100 ..      79     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                                       HHTTT--TT-EEEETTEEE CS
                           DUF1967  50 LrkaGakeGdtVrIgdveF 68 
                                       Lr++  ++GdtVrIgd +F
  gi|336253415|ref|YP_004596522.1|  82 LRDRALEDGDTVRIGDETF 100
                                       888899**********888 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 ?    8.9   1.8   0.00044       1.3      29      59 ..      39      81 ..      14     183 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00044
                     Lactamase_B_3 29 gyeppaeeaDlvlisqaledHahletlkql..............a 59
                                      + ++ + + D+v++++++ dH +  +l+++               
  gi|336253415|ref|YP_004596522.1| 39 EIREHTADLDAVVLTHQHGDHVE--QLEAVvdafdpevyayddhP 81
                                      455667899*********99964..44554445555555555551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1436.89
//
Query:       gi|336253416|ref|YP_004596523.1|  [L=57]
Description: hypothetical protein Halxa_2019 [Halopiger xanaduensis SH-6]
Scores for 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:                       575  (0.0320709); 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:                         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: 432.23
//
Query:       gi|336253417|ref|YP_004596524.1|  [L=202]
Description: hypothetical protein Halxa_2020 [Halopiger xanaduensis SH-6]
Scores for 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-59  199.7   0.3      3e-59  199.5   0.3    1.0  1  DUF99     Protein of unknown function DUF99


Domain annotation for each model (and alignments):
>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.5   0.3   1.7e-63     3e-59       2     181 ..       5     186 ..       4     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: 199.5 bits;  conditional E-value: 1.7e-63
                                       GSEEEEEEEEE........-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSE CS
                             DUF99   2 eirvlGiddsffe...rkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrleredirvvlldGit 75 
                                       ++r+lGi++s+     +++ +++s+l+++v+radrvvdg+a++ +tv+GtDat a+ +l++++ r+d+r+vll +++
  gi|336253417|ref|YP_004596524.1|   5 GARALGIAESYGGdraDRDGRRRSTLAAAVVRADRVVDGLAYEACTVGGTDATAAVRSLLETAGRPDVRYVLLGAVA 81 
                                       68*********6666645589******************************************************** PP

                                       ETTTEE--HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTH..HHHHHHHHHC.---EEETT....EEEEEESS CS
                             DUF99  76 iagFNvvDlerlheetglPviavtreepdlgklekaLrkhfpde..eeRlelieklgerieevektgeelyvravGi 150
                                       +a++N++Dl+r+he+ ++Pviavt+ee+  g le+ +r++f+d+  +eRle++++l+er+ + ++ ge++yvr vG+
  gi|336253417|ref|YP_004596524.1|  82 PAWYNILDLSRIHEAADRPVIAVTFEESG-G-LEAGIRDAFSDSerDERLERYRSLPERRPVSVD-GETVYVRHVGC 155
                                       *****************************.8.***********9778*********888888888.*********** PP

                                       -HHHHHHHHHHC-SSSSS-HHHHHHHHHHHH CS
                             DUF99 151 eleeaaklvrkltlegriPEPlRvAhliAsa 181
                                       e+ ea+++vr++t+eg++PEP+RvA+l+A+a
  gi|336253417|ref|YP_004596524.1| 156 EVGEAEEVVRAFTPEGGRPEPVRVARLAARA 186
                                       *****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 1473.62
//
Query:       gi|336253418|ref|YP_004596525.1|  [L=200]
Description: phage SPO1 DNA polymerase-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-36  125.5   0.0      2e-36  125.3   0.0    1.0  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 !  125.3   0.0   1.1e-40     2e-36       2     148 ..      30     175 ..      29     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 1.1e-40
                                       HC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCCT CS
                               UDG   2 gegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaeik 78 
                                       g+gp+da+v++vGe Pga+eda+g+pF+gr+g  l++ l ++gl+r     + v itn v+crpp+nr +pt++e++
  gi|336253418|ref|YP_004596525.1|  30 GTGPEDADVLFVGEGPGAQEDAEGEPFVGRSGTVLDDQLRTVGLDR-----ETVRITNCVRCRPPENR-DPTDEELE 100
                                       89********************************************.....*****************.******** PP

                                       CCHHHHHHHHHHHHSSEEEEESHHHHHH........HHHHSCESCCCSCT..SEEEEES-SSTTTTTTTTSHHHHHH CS
                               UDG  79 acaplleeeiellkprlivllGktaakall......geklgklrgklleak.irvlplphPsplnrnffksnpelka 148
                                       +c+ +le ei+l+ p +iv+lGk + ++ll       ++ g+l + +++    r+l + hP++ ++   +s++e  +
  gi|336253418|ref|YP_004596525.1| 101 NCRGYLETEIDLVDPDVIVTLGKVPSEHLLdrsvavTKEAGSLEEVRINGApRRLLICVHPAATLYD--RSQEETFE 175
                                       ****************************998755554445566666666659**************9..33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 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:                        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 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1533.75
//
Query:       gi|336253419|ref|YP_004596526.1|  [L=132]
Description: hypothetical protein Halxa_2022 [Halopiger xanaduensis SH-6]
Scores for 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-20   72.9   3.1    3.3e-20   72.6   3.1    1.1  1  SnoaL_2   SnoaL-like domain
    9.3e-11   41.6   0.4    2.9e-10   40.0   0.4    1.6  1  SnoaL     SnoaL-like polyketide cyclase
    2.5e-08   34.1   0.2      3e-08   33.8   0.2    1.2  1  SnoaL_4   SnoaL-like domain
    2.8e-05   24.7   0.0    3.6e-05   24.3   0.0    1.3  1  NTF2      Nuclear transport factor 2 (NTF2) domain
     0.0054   17.1   0.6     0.0069   16.8   0.6    1.2  1  DUF4440   Domain of unknown function (DUF4440)
     0.0069   16.6   0.0     0.0098   16.2   0.0    1.4  1  SnoaL_3   SnoaL-like domain
  ------ inclusion threshold ------
      0.066   13.3   0.1      0.091   12.9   0.1    1.2  1  LEH       Limonene-1,2-epoxide hydrolase catalytic domain


Domain annotation for each model (and alignments):
>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   3.1   1.3e-23   3.3e-20       1     101 [.      24     122 ..      24     123 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 1.3e-23
                                       HHHHHHHHHTTCHHHHHHTEEEEEEEEET.TSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEE CS
                           SnoaL_2   1 vraflaalnagdldalaalfapdvvwedp.ggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgt 76 
                                       vr++++ ++a ++d+l++lfa+d+++e p  g++ Gre++r+f+   +  +++  +e+hd+v++g +vav++ + g 
  gi|336253419|ref|YP_004596526.1|  24 VRDYYEYVDAERYDDLVDLFAEDIRYERPgQGAIAGREELREFYLDGRP-LEEGSHEVHDMVVEGSTVAVRGSFAG- 98 
                                       89***************************9999**********999975.*************************8. PP

                                       EETTSSEEEEEEEEEEEEETTEEEE CS
                           SnoaL_2  77 ipatgrgvtvrgvdvfrvrdGkive 101
                                           +++v+++++d+++++dGki++
  gi|336253419|ref|YP_004596526.1|  99 -LQGDERVEFDFADFHEFEDGKIAR 122
                                       .99********************97 PP

>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.4   1.1e-13   2.9e-10       2     118 ..      22     128 ..      21     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.1e-13
                                       HHHHHHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEE CS
                             SnoaL   2 lvlrfyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltft 78 
                                       +v+r y e ++  + d+l +l+aed+ ++ p+++   G+e++r+f+ +  + + + ++ev+d+v+eg +va+r +f 
  gi|336253419|ref|YP_004596526.1|  22 TVVRDYYEYVDAERYDDLVDLFAEDIRYERPGQGAIAGREELREFYLDG-RPLEEGSHEVHDMVVEGSTVAVRGSF- 96 
                                       6889999999***********************************9976.5689*******************887. PP

                                       EEESSEBTTBE-TT-EEEEEEEEEEEEETTEEEEEEEEEC CS
                             SnoaL  79 GthtgeflGipptGkkvkfeeitllrvedGkIveewdviD 118
                                               G+++   +v+f   ++ ++edGkI+ +  + D
  gi|336253419|ref|YP_004596526.1|  97 -------AGLQG-DERVEFDFADFHEFEDGKIARRYTFTD 128
                                       .......55555.457*****************9988877 PP

>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.2   1.2e-11     3e-08      12      89 ..      23      95 ..      18     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.2e-11
                                      HHHHHHHHHHTT-HHHHHTTEEEEEEEEETTS..--EESHHHHHHHHHSHHHHHH-EEEEE---EEEEETTEEEEEEE CS
                           SnoaL_4 12 lvarygyylDtkdweeladlFtedavvdytgvgegvlegrdairaalrealdgfaltqHllsnplieldgdtAtgray 89
                                      +v  y  y+D+ ++++l+dlF+ed++++ +g  +g + gr+++r+++ +  ++    +H ++++++e  g t  +r++
  gi|336253419|ref|YP_004596526.1| 23 VVRDYYEYVDAERYDDLVDLFAEDIRYERPG--QGAIAGREELREFYLDG-RPLEEGSHEVHDMVVE--GSTVAVRGS 95
                                      7889**************************8..5*************997.4566899999999887..444444444 PP

>> NTF2  Nuclear transport factor 2 (NTF2) 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   3.6e-05       5      51 ..      23      68 ..      21     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.4e-08
                                      HHHHHHHHHHHHGGGGGGGGEEEEEEEEEETTEEEEESHHHHHHHHH CS
                              NTF2  5 fvqqYYaaldagdregllalyaadaslltpegsspvkgreaIteffr 51
                                      +v+ YY+ +da++ + l++l+a+d +++ p +  ++ gre+ +ef+ 
  gi|336253419|ref|YP_004596526.1| 23 VVRDYYEYVDAERYDDLVDLFAEDIRYERPGQ-GAIAGREELREFYL 68
                                      89*******************66666665555.5***********96 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.6   2.7e-06    0.0069       4      82 ..      23     108 ..      21     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHHCT-HHHHHHCEEEEEEEE-TT.S-EEEHHHHHHHH......HCCHCEEEEEEEEEEEEEEETTEEEE CS
                           DUF4440   4 leealeeafvagdaealaallapdavlvgps.gtvldkeelleal......eagfaagrslelteeevrvlgdlAvv 73 
                                       ++++++e++ a  ++ l +l+a+d+++  p+ g + ++eel e +      e+g  + ++++++  +v+v g +A +
  gi|336253419|ref|YP_004596526.1|  23 VVRDYYEYVDAERYDDLVDLFAEDIRYERPGqGAIAGREELREFYldgrplEEGSHEVHDMVVEGSTVAVRGSFAGL 99 
                                       78999***********************99988888*********66655555778888999999999999999988 PP

                                       EEEEEEEEC CS
                           DUF4440  74 tgrytfegr 82 
                                        g  ++e  
  gi|336253419|ref|YP_004596526.1| 100 QGDERVEFD 108
                                       888888653 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.8e-06    0.0098       3      51 ..      22      69 ..      21     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.8e-06
                           SnoaL_3  3 alldafyeaaaegdfdalfalwaddivfigtgadelltgreevrrslkq 51
                                       +++++ye + +  +d l++l+a+di +  +g++    gree+r+++ +
  gi|336253419|ref|YP_004596526.1| 22 TVVRDYYEYVDAERYDDLVDLFAEDIRYERPGQGAI-AGREELREFYLD 69
                                      6889*****************************666.59******9854 PP

>> LEH  Limonene-1,2-epoxide hydrolase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.6e-05     0.091       4     109 ..      21     122 ..      18     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHHHHHHT-HHHHHHHEEEEE.EEEETTTEEEE-HHHHHHHHHTT.TTT-EEEEEEEEEEEETTEEEEEEE CS
                               LEH   4 irvVeaFlaalqeddydaavrrlatdlevyeneglstihGraeaiallerlsadilavevkilriaadgsaVltERl 80 
                                         vV+ + + ++ + yd  v  +a+d  +ye +g ++i Gr+e + ++     +  +   +++ +  +gs V     
  gi|336253419|ref|YP_004596526.1|  21 ETVVRDYYEYVDAERYDDLVDLFAEDI-RYERPGQGAIAGREELREFYLDG-RPLEEGSHEVHDMVVEGSTVAVRGS 95 
                                       567888888888889998887666666.9*****************98877.78899999999*******9987554 PP

                                       EEEEE..TTEEEEEEEEEEEEEETTEEEE CS
                               LEH  81 DrliladGplivqltvmGvfeVedgrivl 109
                                        +     G ++v++     +e edg+i+ 
  gi|336253419|ref|YP_004596526.1|  96 FAGL--QGDERVEFDFADFHEFEDGKIAR 122
                                       4444..699*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); 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:                         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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1041.23
//
Query:       gi|336253420|ref|YP_004596527.1|  [L=220]
Description: Imidazole glycerol phosphate synthase subunit hisH [Halopiger xanaduensis SH-6]
Scores for complete 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   83.5   0.0      2e-23   83.2   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    9.8e-08   31.8   0.0    1.6e-07   31.2   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
      1e-06   28.7   0.0    2.5e-06   27.5   0.0    1.6  1  SNO            SNO glutamine amidotransferase family
    0.00033   20.5   0.5     0.0055   16.5   0.5    2.4  1  Peptidase_C26  Peptidase C26
     0.0014   18.4   0.0     0.0023   17.8   0.0    1.3  1  DJ-1_PfpI      DJ-1/PfpI family
  ------ inclusion threshold ------
      0.036   13.2   0.0       0.13   11.4   0.0    2.0  2  GATase_5       CobB/CobQ-like glutamine amidotransferase doma


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 !   83.2   0.0   6.6e-27     2e-23       1     187 [.      16     214 ..      16     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 6.6e-27
                                       EEEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHCT...STS CS
                            GATase   1 lliDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg..vegkieaikeare...nki 72 
                                       +++D++ ++ +++++ l ++g++v++      +        ++dg+++ +G+g+    ve++  +  +++e   ++ 
  gi|336253420|ref|YP_004596527.1|  16 VVVDYGLGNLRSVTRGLERAGADVTITDDPDAFA-------EADGVVL-PGVGAFRegVENAAPIRDHLLEvaeRDQ 84 
                                       589***********************99543333.......4699877.567777778****9999999888889** PP

                                       -EEEETHHHHHHHHHTTT..................EEE..EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEE CS
                            GATase  73 PiLGICLGmQllaiefgr..................kvv..kekekehhggtmrlgddetallyglknevierhrHr 129
                                       P++GICLGmQ+l+ ++ +                  +v     ++ +h+g++    ++++ l++g  +  ++++ H+
  gi|336253420|ref|YP_004596527.1|  85 PLFGICLGMQMLLTSSEEgetdgesavegldlvpgtNVRfsDGQKVPHMGWNELDVQRDHPLVEGV-DGQYAYFVHS 160
                                       ***************9999899998777776666664448866669******98888788888888.999******* PP

                                       EEEESGCHHHTTEEEEEEEETTEEEEEEEEETT.TEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 130 yevnpkelepaglevtakseddeelmeiiekkn.pfvgvQFHPEststpegpellfnfl 187
                                       y + p    ++++  +a ++ ++e+  i+ ++  +++g+QFHPE++ ++ g ++l+nf+
  gi|336253420|ref|YP_004596527.1| 161 YYAVP----DDEFATVASTDYECEFPSIVADDAgNVFGTQFHPEKSGET-GLQILRNFV 214
                                       ****9....8889999999999***********66*********87665.599999984 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 !   31.2   0.0   5.2e-11   1.6e-07      28     188 ..      40     198 ..      18     202 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 5.2e-11
                          GATase_3  28 rfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeage 104
                                        + +   +++ ++ad v+lpG    ++   ++++  +++++ e ae++ p++giC G+qmL ++ e+  g+ + ++ 
  gi|336253420|ref|YP_004596527.1|  40 TITD-DPDAF-AEADGVVLPGVGAFRE--GVENAAPIRDHLLEVAERDQPLFGICLGMQMLLTSSEE--GETDGESA 110
                                       3333.33444.56********876655..5667777*************************999765..4445778* PP

                          GATase_3 105 veglglLdie.tefek.ekltgqvegevel.....aaeg.eevkGyEiHsGrtilkekakpllkvkvggnngekdGa 173
                                       vegl+l++ + ++f++ +k+ +    e+++       eg +  ++y +Hs   +   + +++++v  +  + e   +
  gi|336253420|ref|YP_004596527.1| 111 VEGLDLVPGTnVRFSDgQKVPHMGWNELDVqrdhpLVEGvDGQYAYFVHSYYAV---PDDEFATVASTDYECEFPSI 184
                                       *******96516677777888777777777555542222344556666655333...44555555333344477777 PP

                          GATase_3 174 vkksedgnvlGtYlH 188
                                       v +   gnv+Gt +H
  gi|336253420|ref|YP_004596527.1| 185 VAD-DAGNVFGTQFH 198
                                       754.77899999888 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   8.4e-10   2.5e-06       6     186 ..      23     217 ..      21     219 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 8.4e-10
                                       SSHHHHHHHHHHTTSEEEEE-SGGGGCC-SEEEE-SS-HHHHHH.HHHHTT-HHHHHHHHHTT.--EEEETHHHHHH CS
                               SNO   6 GaveehveaikkclaenktvkrkedlaevdaliiPGGestamsk.liertglyedllefvknsekvvlGtCaGlill 81 
                                       G+++  ++ +++++a+     +++ +ae d++++PG    a++  + +   + ++lle +++ +++++G C G+ +l
  gi|336253420|ref|YP_004596527.1|  23 GNLRSVTRGLERAGADVTITDDPDAFAEADGVVLPGVG--AFREgVENAAPIRDHLLEVAER-DQPLFGICLGMQML 96 
                                       6777788999*************************964..5555155556677888886655.5*********9665 PP

                                       .CCEETTB.....SS-SS--CCEEEETTTT-SCCGEEE.EEEEETTTC......SEEEEEESS--EEEEE-.TTTCE CS
                               SNO  82 .skelene.....lvktlellkvkvkrnafGrqvdsfe.keldfknli......ekftavfiraPvieeilddeavk 145
                                        +   e+e      v+ l+l+  +  r + G++v  +  +eld++         +  +a f+ +     + dde  +
  gi|336253420|ref|YP_004596527.1|  97 lTSSEEGEtdgesAVEGLDLVPGTNVRFSDGQKVPHMGwNELDVQRDHplvegvDGQYAYFVHSY--YAVPDDEFAT 171
                                       2332222234557899999999999999*****98764267888654444544455566666554..3566777666 PP

                                       EEEECT...T.EEEEEEETTEEEESS-GGGS.TTHCHHHHHHHHHH CS
                               SNO 146 vlyeld...g.eivvakqkkilatsfhPela.eddirvhdyfveev 186
                                       v++        +iv+   +++++t fhPe + e + ++   fve +
  gi|336253420|ref|YP_004596527.1| 172 VASTDYeceFpSIVADDAGNVFGTQFHPEKSgETGLQILRNFVEIC 217
                                       6643323432488888899**********87477899999999876 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.5   1.8e-06    0.0055     100     216 .]      78     200 ..      46     200 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                     Peptidase_C26 100 aalergvPilgiCrGlqllnva.lGGtlyqdieeqsgltdhrehe.......q...saashavkvekgsllaellg. 164
                                       ++ er+ P++giC+G+q+l      G++  +     +  d +  +       q        +++v+ +  l e +  
  gi|336253420|ref|YP_004596527.1|  78 EVAERDQPLFGICLGMQMLLTSsEEGETDGESA--VEGLDLVPGTnvrfsdgQkvpHMGWNELDVQRDHPLVEGVDg 152
                                       67899************9833202333322211..122222211112122121233333444444444444444432 PP

                     Peptidase_C26 165 seeievnslHhqaikelaeelrveAvaeDgviEaieseeak.afvlgvQwHPE 216
                                       +    v s+        ++e+  +A  +D   E+ ++ +++   v+g Q+HPE
  gi|336253420|ref|YP_004596527.1| 153 QYAYFVHSYY----AVPDDEFATVAS-TDYECEFPSIVADDaGNVFGTQFHPE 200
                                       3333333332....225555555553.35556666655555467777777777 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 !   17.8   0.0   7.6e-07    0.0023      43     109 ..      29      98 ..       6     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.6e-07
                                       TTS.EEEE-SEEGGGCTCC..G-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHH CS
                         DJ-1_PfpI  43 srG.lkvtvdaslddvkaa..eyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaa 109
                                       +rG ++  +d+++ d  +a  e D +vlpG  a  e +++ + +++ + e+ae++++++ IC g q+L+ 
  gi|336253420|ref|YP_004596527.1|  29 TRGlERAGADVTITDDPDAfaEADGVVLPGVGAFREGVENAAPIRDHLLEVAERDQPLFGICLGMQMLLT 98 
                                       55545556777776533223489*******9999*******************************99975 PP

>> 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 ?   11.4   0.0   4.2e-05      0.13      71     107 ..      65     100 ..      14     128 .. 0.80
   2 ?   -1.5   0.0      0.35     1e+03     213     232 ..     186     205 ..     183     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.2e-05
                          GATase_5  71 slllneklrealekflnredtlaLGiCnGfqlLvklg 107
                                        +++++ +r++l +  +r d+  +GiC G+q+L    
  gi|336253420|ref|YP_004596527.1|  65 GVENAAPIRDHLLEVAER-DQPLFGICLGMQMLLTSS 100
                                       456678899999999999.**************8765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.35
                          GATase_5 213 tspdGRvlalmpHpervvea 232
                                        ++ G v+++  Hpe+++e+
  gi|336253420|ref|YP_004596527.1| 186 ADDAGNVFGTQFHPEKSGET 205
                                       6788***********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1521.60
//
Query:       gi|336253421|ref|YP_004596528.1|  [L=399]
Description: cell division control protein 6-like protein [Halopiger xanaduensis SH-6]
Scores for 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-20   71.0   0.2    2.5e-19   69.0   0.0    2.1  2  Cdc6_C           CDC6, C terminal winged helix domain
      1e-13   51.7   0.2    3.6e-13   50.0   0.0    1.9  2  AAA_22           AAA domain
    1.5e-09   38.5   1.9    2.5e-09   37.7   0.0    2.2  2  AAA_16           AAA ATPase domain
    2.6e-07   31.1   0.0    8.8e-07   29.4   0.0    2.0  1  AAA              ATPase family associated with various cellul
    3.1e-05   23.3   0.0    5.4e-05   22.5   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
    9.5e-05   22.5   0.2     0.0031   17.6   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00015   21.5   0.0    0.00031   20.5   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
    0.00016   21.7   0.0    0.00051   20.0   0.0    1.8  2  NACHT            NACHT domain
    0.00022   20.7   0.0    0.00043   19.7   0.0    1.4  1  TniB             Bacterial TniB protein
     0.0023   17.7   1.5      0.093   12.5   1.5    2.3  1  DEAD             DEAD/DEAH box helicase
     0.0039   17.1   0.4     0.0086   16.0   0.1    1.7  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0043   16.0   0.5      0.026   13.4   0.0    2.1  2  AAA_10           AAA-like domain
     0.0084   15.5   0.1      0.019   14.3   0.1    1.6  1  ATPase           KaiC
  ------ inclusion threshold ------
      0.013   15.6   1.4       0.42   10.7   0.1    2.3  2  DUF87            Helicase HerA, central domain
      0.014   14.9   0.0      0.033   13.8   0.0    1.5  1  AAA_25           AAA domain
       0.02   15.0   0.1      0.041   14.0   0.1    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.025   14.3   0.1        0.1   12.3   0.1    2.0  1  IstB_IS21        IstB-like ATP binding protein
      0.027   13.8   0.1       0.26   10.6   0.0    2.2  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.034   14.1   0.8       0.37   10.8   0.8    2.4  1  AAA_5            AAA domain (dynein-related subfamily)
      0.069   12.8   0.0       0.18   11.4   0.0    1.6  1  Zot              Zonular occludens toxin (Zot)
       0.08   13.3   1.7       0.96    9.8   1.6    2.5  1  AAA_assoc_2      AAA C-terminal domain
      0.085   13.3   0.1       0.51   10.7   0.0    2.2  2  RNA_helicase     RNA helicase
      0.092   12.8   0.1       0.34   11.0   0.1    2.0  1  E2F_TDP          E2F/DP family winged-helix DNA-binding domai
       0.11   11.9   0.1         11    5.5   0.0    2.3  2  PhoH             PhoH-like protein
       0.16   11.5   0.1       0.27   10.7   0.1    1.4  1  AAA_7            P-loop containing dynein motor region


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 ?   -1.3   0.0         3   2.1e+03      27      47 ..     204     225 ..     203     228 .. 0.83
   2 !   69.0   0.0   3.5e-22   2.5e-19       3      83 ..     311     393 ..     309     394 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3
                                       HHHHHT.T-----HHHHHHHHH CS
                            Cdc6_C  27 slCese.gvdpltqrevsdlls 47 
                                       slCe+e  ++p + ++++++l+
  gi|336253421|ref|YP_004596528.1| 204 SLCEREyVFSPYDATQIREILR 225
                                       79999955599999**999986 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 3.5e-22
                                       HHHHHHC..HCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   3 alvlllr..ksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       a++ll++  ++++ +vtt evy+ Y++lC++ + d l+ r+v+d+lseLe+l i+e e++  G+++g++++ +L  d
  gi|336253421|ref|YP_004596528.1| 311 AMALLTQqkEGDDAPVTTNEVYDLYQRLCDRDQSDHLKLRRVRDILSELEFLSIIEQERKWAGKGKGNYMENRLIDD 387
                                       556665555999***************************************************************** PP

                                       CHHHHH CS
                            Cdc6_C  78 pddvle 83 
                                       p+ +++
  gi|336253421|ref|YP_004596528.1| 388 PEVIIA 393
                                       **9976 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0     5e-16   3.6e-13       6     123 ..      56     177 ..      51     191 .. 0.90
   2 ?   -1.2   0.0       3.1   2.2e+03      70      75 ..     322     344 ..     260     366 .. 0.50

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 5e-16
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......erlsse 76 
                                       + ++v+G +GtGK+++ + +++q++ +ak ++ + +v++v++ ++++ ++  +   ++l++++++      ++ls+ 
  gi|336253421|ref|YP_004596528.1|  56 NNVLVYGKTGTGKSLCSKFITNQAVDRAKGNDVSIGVAYVDCLQESTETQAVQSAGHQLNDQGETaisiphSGLSTA 132
                                       6789********************99999999999****************************************** PP

                            AAA_22  77 ellealeqalraravielliiDEaqhlrs.eealeeLrsllnlsrkgv 123
                                       e++++l+q +++r++++l+i+DE++++ + +++l +L++ ++  + ++
  gi|336253421|ref|YP_004596528.1| 133 EYYRRLWQIIDTRYDVALIILDEVDKI-EdDDILMQLSRAVE--SGKL 177
                                       ***************************.55999999988877..4444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.1
                            AAA_22  70 a.................erlss 75 
                                       +                  r++s
  gi|336253421|ref|YP_004596528.1| 322 DdapvttnevydlyqrlcDRDQS 344
                                       24233222222222222223444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   3.5e-12   2.5e-09       2     162 ..      32     172 ..      31     185 .. 0.60
   2 ?   -0.7   0.5       2.2   1.6e+03      95      95 ..     284     284 ..     196     359 .. 0.57

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 3.5e-12
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqala 77 
                                        +GRe+el  L++a++++ +g + ++vl++G  G+GKs   + + +++ ++    ++g+ ++   +++   ++++l 
  gi|336253421|ref|YP_004596528.1|  32 IIGREDELTNLANAIKPATRGNTpNNVLVYGKTGTGKSLCSKFITNQAVDR----AKGNDVSI--GVA---YVDCL- 98 
                                       68**************88888888************************999....77777777..433...34444. PP

                            AAA_16  78 reellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslql 154
                                       +e+  +q  +       + ++   ++++a++ + +g    + +e  +rl + + ++ +  +++lD+++++++++   
  gi|336253421|ref|YP_004596528.1|  99 QESTETQAVQS------AGHQLNDQGETAISIPHSG---LSTAEYYRRLWQIIDTRYDVALIILDEVDKIEDDDI-- 164
                                       22332222222......2222222222221112222...233333333333333333347889999998888543.. PP

                            AAA_16 155 laaLlrll 162
                                       l +L r++
  gi|336253421|ref|YP_004596528.1| 165 LMQLSRAV 172
                                       33444433 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.2
                            AAA_16  95 e 95 
                                       +
  gi|336253421|ref|YP_004596528.1| 284 Q 284
                                       1 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 !   29.4   0.0   1.2e-09   8.8e-07       1     128 [.      58     210 ..      58     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.2e-09
                                       EEEESSTTSSHHHHHHHHHHHH...........THE.............EEEEETTTCSSS................ CS
                               AAA   1 vllyGppGtGKTllakavakel...........gve.............fleisgsellsk................ 37 
                                       vl+yG  GtGK+l+ k + +++           g                ++        +                
  gi|336253421|ref|YP_004596528.1|  58 VLVYGKTGTGKSLCSKFITNQAvdrakgndvsiG-VayvdclqestetqAVQ--------Saghqlndqgetaisip 125
                                       79*******************7555554433331.02333333333333444........04444444588888888 PP

                                       ....STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEES CS
                               AAA  38 ....yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatn 110
                                               +++  r l++ + +  +   +++DE+d++  +          +++ qL ++++  k  es+v vig++n
  gi|336253421|ref|YP_004596528.1| 126 hsglS---TAEYYRRLWQIIDTRYDVALIILDEVDKIEDD----------DILMQLSRAVESGKLTESTVGVIGISN 189
                                       74333...4455555555554444458**********554..........5************************** PP

                                       S...GGGSTHHHHSTTSSEEE CS
                               AAA 111 r...pdkldpallrgRfdrki 128
                                       +    d+ld+ + ++ ++r++
  gi|336253421|ref|YP_004596528.1| 190 KvryKDSLDERIKSSLCEREY 210
                                       988899999999877777665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   7.5e-08   5.4e-05      23      79 ..      25      81 ..      10     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.5e-08
                            DUF815 23 devklddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyae 79
                                      +  + d+++g +++ ++l + ++   +g++ nnvL++G+ GtGKS + k+++n++ +
  gi|336253421|ref|YP_004596528.1| 25 HLPDGDRIIGREDELTNLANAIKPATRGNTPNNVLVYGKTGTGKSLCSKFITNQAVD 81
                                      456678999*****************************************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 !   17.6   0.0   4.3e-06    0.0031       2      47 ..      34      81 ..      33     108 .. 0.83
   2 ?    2.3   0.0      0.24   1.7e+02      83     115 ..     288     319 ..     283     352 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.3e-06
                                      ---HHHHHHHHHHHHHHT-SS-..EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  2 gasaaiqelkerLeqaaqsklp..vfltGekGsgkelvArlLhknsgp 47
                                      g+    ++l++ ++ a + ++p  v++ G  G+gk+l+++++ +++  
  gi|336253421|ref|YP_004596528.1| 34 GREDELTNLANAIKPATRGNTPnnVLVYGKTGTGKSLCSKFITNQAVD 81
                                      666778899999999998887666******************998765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHTTTT-EEEEEEEE-TTT.. CS
                   Sigma54_activ_2  83 kaeqkeLlellakaeksslrlVstsskdleqll 115
                                       ++e ++L+el+ k+ +s+++lV   ++ l+q+ 
  gi|336253421|ref|YP_004596528.1| 288 REETSRLAELISKS-PSHAKLVLEAMALLTQQK 319
                                       67889999***999.9******99999888844 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   4.3e-07   0.00031       1      58 [.      32      92 ..      32     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.3e-07
                                      ----SHHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHH.HSTTTTS-EEEEET CS
                   Sigma54_activat  1 ligesealkelleqikkvaktd..lsvlitGesGtGKellaraihe.askrkekpfvavnc 58
                                      +ig++++l++l + ik +++ +   +vl+ G++GtGK+l+++ i + a +r++++ v++ +
  gi|336253421|ref|YP_004596528.1| 32 IIGREDELTNLANAIKPATRGNtpNNVLVYGKTGTGKSLCSKFITNqAVDRAKGNDVSIGV 92
                                      6899999999999999998554449******************987355666666666655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   7.1e-07   0.00051       3     100 ..      58     176 ..      56     233 .. 0.74
   2 ?   -1.3   0.0       2.5   1.8e+03     101     124 ..     286     308 ..     243     323 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.1e-07
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC..-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C...... CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqga..fklvFflslrelsrsgnarsladllfsqlpepaapvse...... 71 
                                       v++ G+ G GK+    k+++  a ++ +++     + ++ +l+e ++ +++ s   +l +q+   ++ +        
  gi|336253421|ref|YP_004596528.1|  58 VLVYGKTGTGKSLC-SKFITNQAVDRAKGNDvsIGVAYVDCLQESTETQAVQSAGHQLNDQGETAISIPHSglstae 133
                                       899********965.555555555554444435889999999999999999**********99999988889999** PP

                                       ....CHHHHCCSCCCEEEEEE-STT-SS-TCH........... CS
                             NACHT  72 ....vwavllelperlLlilDglDelvtdlgq..........k 100
                                            w+++ ++ + +L+ilD +D++++d+            k
  gi|336253421|ref|YP_004596528.1| 134 yyrrLWQIIDTRYDVALIILDEVDKIEDDDILmqlsravesgK 176
                                       ***************************9775544444444440 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.5
                                       ........HHHHHCTTTTT--EEE CS
                             NACHT 101 ekqpvrtlLselirkkllpeasll 124
                                       ++++    L+eli+k +++ a+l+
  gi|336253421|ref|YP_004596528.1| 286 HEREETSRLAELISK-SPSHAKLV 308
                                       234444445555555.44444433 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.1e-07   0.00043      20     132 ..      39     160 ..      30     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.1e-07
                              TniB  20 lerLeeLleypkrkrm.pnlllvGdsnnGKtmivekFarlhppe.kdedaekvpvlvvqappkpdekrlyaaiLeal 94 
                                       l++L++ ++ ++r  + +n+l++G++ +GK+ +++kF  ++  +  + ++ ++ v +v++ ++++e +  ++  ++l
  gi|336253421|ref|YP_004596528.1|  39 LTNLANAIKPATRGNTpNNVLVYGKTGTGKS-LCSKFITNQAVDrAKGNDVSIGVAYVDCLQESTETQAVQSAGHQL 114
                                       44555555555554442789**********8.789999888776256777899**************9999999999 PP

                              TniB  95 gaplkara.......rvskleqqvlrllr.elkvrvLiiDEihnll 132
                                       + + ++         ++++ +++  ++++ +++v ++i+DE+++++
  gi|336253421|ref|YP_004596528.1| 115 NDQGETAIsiphsglSTAEYYRRLWQIIDtRYDVALIILDEVDKIE 160
                                       98865554555556677788888888886258999******99986 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   1.5   0.00013     0.093       7     148 ..      45     174 ..      41     189 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                       HHHHHHTT...CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                       xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   7 aiplilgg...gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                       ai+ + +g   ++vlv ++TG+GK+l+  +   q+v   + k +   + v+    L e t +++ ++  + +   l 
  gi|336253421|ref|YP_004596528.1|  45 AIKPATRGntpNNVLVYGKTGTGKSLCSKFITNQAVD--RAKGNDVSIGVAYVDCLQESTETQAVQSAGH-Q---LN 115
                                       5555554434479**************9999999994..4666667888888888888888888877774.2...22 PP

                                       EETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  81 iiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnq 148
                                         g++a +  +s l      +     rl ++++t++    +v +++lDE+d++ d++   +++r +++
  gi|336253421|ref|YP_004596528.1| 116 DQGETAISIPHSGL-----STAEYYRRLWQIIDTRY----DVALIILDEVDKIEDDDILMQLSRAVES 174
                                       34555555556666.....34444578888888877....9999999999999999777777776655 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 !   16.0   0.1   1.2e-05    0.0086       4     131 ..      35     160 ..      33     211 .. 0.69
   2 ?   -2.7   0.0       6.3   4.6e+03      56      84 ..     273     300 ..     260     322 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                          ATPase_2   4 Rekelkelee....ilerepneiyfiYGpegsGKtaLlkeiienledkdk......yviyyialreesiskldefie 70 
                                       Re el +l +      + ++ + +++YG  g GK+   k i ++  d  k       v y++ l+e+ ++++ ++ +
  gi|336253421|ref|YP_004596528.1|  35 REDELTNLANaikpATRGNTPNNVLVYGKTGTGKSLCSKFITNQAVDRAKgndvsiGVAYVDCLQESTETQAVQSAG 111
                                       777776555510004567888999**********96555444444444445566779***********999999943 PP

                          ATPase_2  71 eeeekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqkli 131
                                        + +++     ++i +p   l            ++  +l + i  +     ii+De+ k+ 
  gi|336253421|ref|YP_004596528.1| 112 HQLNDQ---GETAISIPHSGL---------STAEYYRRLWQIIDTRYDVALIILDEVDKIE 160
                                       333333...344567777777.........3356778888888888888889999999998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.3
                          ATPase_2  56 alreesiskldefieeeeekkklekalgi 84 
                                       +l+++ +s +d+  +e ee ++l++ +++
  gi|336253421|ref|YP_004596528.1| 273 DLERVTESCVDQA-HEREETSRLAELISK 300
                                       5556666666665.566666667666633 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   3.7e-05     0.026      13      56 ..      49      96 ..      39     121 .. 0.72
   2 ?    0.3   0.1      0.35   2.5e+02      95     161 ..     247     313 ..     237     323 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.7e-05
                            AAA_10 13 evkgsktnasasliiGdlGnGKSvlakllvlyisllg......gkaliiD 56
                                      +++g+  n++  l+ G++G GKS+++k++ ++++ +         + ++D
  gi|336253421|ref|YP_004596528.1| 49 ATRGNTPNNV--LVYGKTGTGKSLCSKFITNQAVDRAkgndvsIGVAYVD 96
                                      5666555665..*****************999875544444444455555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.35
                            AAA_10  95 llkeekeaeslaedilelllgvkkkesekkaalseaveavlegkq.rgllavieelrkedekvareia 161
                                       l+++e+  ++ a+dil ++ ++ ++++ ++ + +  v++  e+++   l ++i +  ++ + v + +a
  gi|336253421|ref|YP_004596528.1| 247 LAAREHGDARKAIDILRFAGEIAEENDLER-VTESCVDQAHEREEtSRLAELISKSPSHAKLVLEAMA 313
                                       56677777888999****999999988888.5788899999977746777788776666666655555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   2.6e-05     0.019      20      62 ..      56      96 ..      50     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-05
                            ATPase 20 rvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaed 62
                                      + vl++G++GtGK++ + +F+ ++a++   +g  v++    +d
  gi|336253421|ref|YP_004596528.1| 56 NNVLVYGKTGTGKSL-CSKFITNQAVD-RAKGNDVSIGVAYVD 96
                                      679***********7.679*****998.777777776666644 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00058      0.42      26      49 ..      58      81 ..      56      91 .. 0.84
   2 ?    3.6   0.2     0.087        63     101     152 ..     260     331 ..     255     380 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00058
                             DUF87 26 lAilgsTGsGKSntvavLleelle 49
                                      +++ g+TG+GKS   + + ++++ 
  gi|336253421|ref|YP_004596528.1| 58 VLVYGKTGTGKSLCSKFITNQAVD 81
                                      689*****************9996 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.087
                             DUF87 101 elldlleeddkpaaavqrsvleealdqakakeekeklssdepveklleelk........................k 152
                                       ++l++++e   ++++ +++v e+++dqa   e++e    +e++ k+ ++ k                         
  gi|336253421|ref|YP_004596528.1| 260 DILRFAGE--IAEENDLERVTESCVDQAH--EREETSRLAELISKSPSHAKlvleamalltqqkegddapvttneV 331
                                       55666666..4445559***********9..999999999***999999997777666655555444444444441 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.6e-05     0.033      36     153 ..      58     158 ..      53     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                            AAA_25  36 allaGapgtGKtt...laldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldla 109
                                       +l++G +gtGK+    + ++ a++ a+G           + V yv++ +   +  + ++ +g++l  d+++++++++
  gi|336253421|ref|YP_004596528.1|  58 VLVYGKTGTGKSLcskFITNQAVDRAKGND-------VSIGVAYVDCLQES-TETQAVQSAGHQL-NDQGETAISIP 125
                                       689********9755589**********95.......478******88888.5566677799999.57888888875 PP

                            AAA_25 110 gveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsr 153
                                                    g  +++ +++l + i+ +++v+l+++D +++
  gi|336253421|ref|YP_004596528.1| 126 H-----------SGLSTAEYYRRLWQIIDTRYDVALIILDEVDK 158
                                       4...........35567899********************9876 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.7e-05     0.041       5     111 ..      57     180 ..      54     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.7e-05
                                       -EEEE--TTSSHHH.....HHHHHHHHTT-....-EEEEEG.GG-------THHHHHHHHHTTT-HHHHTTS..... CS
                             AAA_2   5 silllgptgvGkte.....lakalaellfvkkekklirada.selleeeevehlvsrligappgyvgaeegG..... 70 
                                       ++l+ g+tg+Gk++     +++a+ +    + +  ++ +d+ +e +e ++v++   +l  + +  ++   +G     
  gi|336253421|ref|YP_004596528.1|  57 NVLVYGKTGTGKSLcskfiTNQAVDRAKGNDVSIGVAYVDClQESTETQAVQSAGHQLNDQGETAISIPHSGlstae 133
                                       7899999****999544433333333333255556666665234555777777777788888888888888899*** PP

                                       ................EEEEETGGG-------------HHHHHHHHHHHH--EE--- CS
                             AAA_2  71 ................ivllDEidKihpkessgadvSregVqrdLLqileggtltdk 111
                                                        + lDE+dKi            ++++  L + +e g+lt++
  gi|336253421|ref|YP_004596528.1| 134 yyrrlwqiidtrydvaLIILDEVDKIED----------DDILMQLSRAVESGKLTES 180
                                       ****************99**********..........99**********9999976 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 ?   12.3   0.1   0.00014       0.1      47     145 ..      55     153 ..      49     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                         IstB_IS21  47 kenivllGpsGvGKshlaialgveavr..aglsvlf.vrvedLveelkrarrdgklaralkrllkvdllilDdlgll 120
                                        +n+++ G +G+GKs  +  +  +av   +g  v+  v   d ++e    ++ +++ ++l+   ++++  +   gl 
  gi|336253421|ref|YP_004596528.1|  55 PNNVLVYGKTGTGKSLCSKFITNQAVDraKGNDVSIgVAYVDCLQESTETQAVQSAGHQLNDQGETAIS-IPHSGLS 130
                                       579***********************8556666664355566666666677777777777777776654.5677877 PP

                         IstB_IS21 121 pldqaeaellfeviekryerrsiii 145
                                       + +    + l+++i+ ry+ + ii+
  gi|336253421|ref|YP_004596528.1| 131 TAEY--YRRLWQIIDTRYDVALIIL 153
                                       7654..5679999999999877776 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00036      0.26      38      56 ..      54      72 ..      33      91 .. 0.79
   2 ?    0.4   0.0      0.47   3.4e+02      76     183 ..     281     311 ..     251     321 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00036
                                      S-.SEEEE--TTSSHHHHH CS
                      FtsK_SpoIIIE 38 mashllvaGatgsGKStal 56
                                       ++++lv G tg+GKS + 
  gi|336253421|ref|YP_004596528.1| 54 TPNNVLVYGKTGTGKSLCS 72
                                      359*************885 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.47
                                       EE-TTSSSCGGGTT-TTBSS.S-B-SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHTT---B-TT CS
                      FtsK_SpoIIIE  76 liDykgvelsalediphllsvavatdperalraleeLvkemeeryalfreagvrsiaaydgeiaedpldifgdvflv 152
                                       ++D +  e ++ +                                                                
  gi|336253421|ref|YP_004596528.1| 281 CVDQA-HEREETS---------------------------------------------------------------- 292
                                       33333.2333444................................................................ PP

                                       -......................-------- CS
                      FtsK_SpoIIIE 153 lDnyddlaaeneritsLsnqgpsygvhvlvt 183
                                                   r  +L+++ ps    vl +
  gi|336253421|ref|YP_004596528.1| 293 ------------RLAELISKSPSHAKLVLEA 311
                                       ............5555555555555444433 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   0.8   0.00051      0.37       1     103 [.      57     185 ..      57     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00051
                                       EEEEE--SSSSHHHHHHHGGGGB.........S--EEEEE--TT--HHHHH--B--..............------- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.........nreveyvqltrdtteedlkgrreik.....ngttslvdsplvraa 63 
                                       +vl+ G++GtgKs  ++ +                v yv + +  te++ +++   +     +   s   s l   a
  gi|336253421|ref|YP_004596528.1|  57 NVLVYGKTGTGKSLCSKFITNQAvdrakgndvSIGVAYVDCLQESTETQAVQSAGHQlndqgETAISIPHSGLS-TA 132
                                       58889999999998888777665577777555556788888888888888888776666742222223334444.44 PP

                                       -.............G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE..-SSSEE CS
                             AAA_5  64 r.............egeilvlDEverae.sevlnsLlslleerrllleeggelv 103
                                       +               ++++lDEv+++e +++l+ L +  e  +l  e+  +++
  gi|336253421|ref|YP_004596528.1| 133 EyyrrlwqiidtryDVALIILDEVDKIEdDDILMQLSRAVESGKLT-ESTVGVI 185
                                       468889999999999999**********9*********99999988.5555555 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00025      0.18       3      92 ..      58     159 ..      57     161 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                               Zot   3 slvtGapGsgKtsga..vkkdllpalk.egRki.itnidGlrlerieqvlgekvs.....tarliridnpegaetlk 70 
                                       +lv+G+ G+gK++++  + +++++  k ++ +i ++ +d l+     q ++ + +      +  i i +        
  gi|336253421|ref|YP_004596528.1|  58 VLVYGKTGTGKSLCSkfITNQAVDRAKgNDVSIgVAYVDCLQESTETQAVQSAGHqlndqGETAISIPHSGLSTAEY 134
                                       589**********9855666666655534555525599999944444434433332325545577777555555555 PP

                               Zot  71 efakwatid...kgallviDEcqei 92 
                                       + + w++id     al+++DE+ +i
  gi|336253421|ref|YP_004596528.1| 135 YRRLWQIIDtryDVALIILDEVDKI 159
                                       67889999988788*******9875 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 ?    9.8   1.6    0.0013      0.96      13      58 ..     245     289 ..     240     349 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2  13 ealaeladGDaRkaLnlLElaaeaaeakegkieitledleealqrk 58 
                                       +ala+  +GDaRka+ +L +a e ae+ ++ +++t++ +++a +r+
  gi|336253421|ref|YP_004596528.1| 245 AALAAREHGDARKAIDILRFAGEIAEE-NDLERVTESCVDQAHERE 289
                                       67888899***************9997.777778888887777654 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   0.00072      0.51       1      26 [.      58      83 ..      58     108 .. 0.83
   2 ?   -0.8   0.0       2.7   1.9e+03      52      82 ..     150     177 ..     140     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00072
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                      +++yG++g+GKS+++k ++++  ++ 
  gi|336253421|ref|YP_004596528.1| 58 VLVYGKTGTGKSLCSKFITNQAVDRA 83
                                      689*************9999887655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.7
                      RNA_helicase  52 vvvidDfgqvkdeenpsdlaelirlvsstpy 82 
                                        ++ d++ +++d+   ++l++l r+v+s ++
  gi|336253421|ref|YP_004596528.1| 150 LIILDEVDKIEDD---DILMQLSRAVESGKL 177
                                       6789999999988...999999999998776 PP

>> E2F_TDP  E2F/DP family winged-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00047      0.34      21      64 ..     323     370 ..     291     377 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00047
                           E2F_TDP  21 kgtlslneaakeLv....dkkdekvkkRRiYDilNVLealglieKesk 64 
                                       +  ++ ne+ +  +    ++++++ k RR+ Dil  Le l +ie e+k
  gi|336253421|ref|YP_004596528.1| 323 DAPVTTNEVYDLYQrlcdRDQSDHLKLRRVRDILSELEFLSIIEQERK 370
                                       3336666664443355577788899*******************9976 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.015        11      20      46 ..      56      82 ..      32     102 .. 0.77
   2 ?    4.2   0.0     0.035        25     121     148 ..     149     176 ..     145     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                                      SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH 20 divfaiGpaGtGKtylavalavealkk 46
                                      + v + G++GtGK++ +  +  +a+ +
  gi|336253421|ref|YP_004596528.1| 56 NNVLVYGKTGTGKSLCSKFITNQAVDR 82
                                      468899********9987776666655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.035
                                       EEEEE-SGGG--HHHHHHHHTTB-TT-E CS
                              PhoH 121 afvilDEAQnttkeqmkmfltRlGensk 148
                                       a++ilDE   ++   + m l+R  e+ k
  gi|336253421|ref|YP_004596528.1| 149 ALIILDEVDKIEDDDILMQLSRAVESGK 176
                                       89********************877766 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   0.1   0.00038      0.27      34      56 ..      56      78 ..      50     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                             AAA_7 34 kpvllvGptGtGKtviikdllkk 56
                                      ++vl++G+tGtGK+++ k ++++
  gi|336253421|ref|YP_004596528.1| 56 NNVLVYGKTGTGKSLCSKFITNQ 78
                                      68************998875544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2630.38
//
Query:       gi|336253422|ref|YP_004596529.1|  [L=135]
Description: hypothetical protein Halxa_2025 [Halopiger xanaduensis SH-6]
Scores for 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   15.2   1.3      0.013   15.2   1.3    3.5  4  FixS      Cytochrome oxidase maturation protein cbb3-type


Domain annotation for each model (and alignments):
>> FixS  Cytochrome oxidase maturation protein cbb3-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.3     7e-07     0.013       9      27 ..       8      26 ..       7      27 .. 0.95
   2 ?    1.1   1.0     0.018   3.2e+02       8      25 ..      44      61 ..      40      65 .. 0.70
   3 ?   -3.2   0.2      0.39   7.1e+03       8      16 ..      85      93 ..      82      95 .. 0.55
   4 ?    1.7   1.2     0.012   2.1e+02       6      21 ..     102     117 ..     100     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7e-07
                              FixS  9 lSlllgllalaaFlWavks 27
                                      lSl lgll+la F W+++s
  gi|336253422|ref|YP_004596529.1|  8 LSLGLGLLFLATFAWSLRS 26
                                      79***************98 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.018
                              FixS  8 plSlllgllalaaFlWav 25
                                       ++  l l++ aaF+ a 
  gi|336253422|ref|YP_004596529.1| 44 VAAGGLMLVGSAAFVLAG 61
                                      556678888888888775 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.39
                              FixS  8 plSlllgll 16
                                       + l l+l 
  gi|336253422|ref|YP_004596529.1| 85 AIGLYLALS 93
                                      455555554 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.012
                              FixS   6 LiplSlllgllalaaF 21 
                                       L+ + +++g+l++aaF
  gi|336253422|ref|YP_004596529.1| 102 LVNIVMVVGGLGFAAF 117
                                       67788999****9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); 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):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 983.30
//
Query:       gi|336253423|ref|YP_004596530.1|  [L=118]
Description: zinc finger SWIM domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   15.3   4.4       0.18   11.5   4.4    2.1  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.4     1e-05      0.18       6      38 ..      60      98 ..      54     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1e-05
                              SWIM  6 ddervrlnkatCsCpefqk......ngipCkHalAvlla 38
                                      +d+ + +++  C+C++ ++         +C+H++Av++a
  gi|336253423|ref|YP_004596530.1| 60 YDDEYIVEDGGCTCKDSEYnldpdePTELCWHVIAVAIA 98
                                      44449999999********6655444446*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 939.07
//
Query:       gi|336253424|ref|YP_004596531.1|  [L=373]
Description: N(2),N(2)-dimethylguanosine tRNA methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-91  305.1   0.0    8.5e-91  304.9   0.0    1.0  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    1.9e-05   24.2   0.1    2.9e-05   23.6   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    3.6e-05   23.4   0.0    6.7e-05   22.5   0.0    1.4  1  MTS              Methyltransferase small domain
    0.00014   22.5   0.3    0.00036   21.2   0.3    1.7  1  Methyltransf_25  Methyltransferase domain
    0.00027   20.8   0.0    0.00043   20.1   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
     0.0041   16.8   0.0     0.0066   16.1   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.006   16.7   1.7      0.019   15.1   1.7    1.8  1  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.022   14.5   0.0      0.036   13.7   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020
      0.045   14.5   0.1      0.092   13.5   0.1    1.5  1  Methyltransf_12  Methyltransferase domain
       0.08   13.6   0.2       0.22   12.2   0.2    1.8  1  Methyltransf_11  Methyltransferase domain
       0.15   11.8   0.0       0.19   11.5   0.0    1.2  1  Met_10           Met-10+ like-protein
       0.22   11.9   1.9        3.3    8.1   0.1    3.2  3  Lar_restr_allev  Restriction alleviation protein Lar


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 !  304.9   0.0   5.7e-94   8.5e-91      13     371 ..      17     364 ..       6     369 .. 0.93

  Alignments for each domain:
  == domain 1  score: 304.9 bits;  conditional E-value: 5.7e-94
                                       S--TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHH CS
                               TRM  13 tvskkeeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvel 89 
                                       t   +e VFYNP+qe nRDl+++++r +  ++ +     ++lda++asG+R++R a +      v   D+ e+Av+l
  gi|336253424|ref|YP_004596531.1|  17 TEGVEESVFYNPRQELNRDLTIATLRAFREREPR---AETYLDAMTASGVRGVRAAAD---GWDVTCCDVDEEAVAL 87 
                                       4455789*****************8866666666...4689***************99...6788999********* PP

                                       HHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHH CS
                               TRM  90 ikeNvklneveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspek 166
                                        +eNv  n+ +++ ++++ d n+l+  +++ fdviDlDP+G+p+pf d+a +  ++  l++vTaTDta+L+Ga+ ++
  gi|336253424|ref|YP_004596531.1|  88 ARENVARNDCADRATVEHRDVNALM--HDELFDVIDLDPYGTPMPFADAAFANCRD--LVCVTATDTAPLCGAHFNS 160
                                       ************9999999******..899*********************99988..******************* PP

                                       HHHHHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEET CS
                               TRM 167 clrkYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCs 243
                                       ++r Y+av+ ++++  E+++Ril++a+ar+aa+++  v+pll++++ +Yvr +++++++a+ +++ +++lg+++hC 
  gi|336253424|ref|YP_004596531.1| 161 GVRSYSAVPQNTDYHAEMGVRILISALARSAARFDVGVQPLLTHATSHYVRTYLELEHKATSADAAVDELGYLYHCE 237
                                       ***************************************************************************** PP

                                       TT--EEEE--GGG--.SB-TTT-S.BEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS-- CS
                               TRM 244 gClseekvkglakfk.aecehcga.klhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeEllda 318
                                        C+ +e   gl     + c+hcg  +  +aGP+wlgp++d++fv  v +e+ +  +  ++++ +kl +++++E ld+
  gi|336253424|ref|YP_004596531.1| 238 DCTYREADPGLIADPiETCPHCGGdRILAAGPVWLGPVRDRKFVAAVRDEIPD--AFGTAEKGRKLCETLEAE-LDE 311
                                       **9999999987644599****87256779********************999..566689999*********.9** PP

                                       SS-EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHH CS
                               TRM 319 plyydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleav 371
                                       p+ yd ++l++   l ++ ++++ ++l+++g+e+sr+H+ ++++kT+a++ ++
  gi|336253424|ref|YP_004596531.1| 312 PTHYDQHKLCRNWGLPANAMDDFLADLRAAGYEASRAHYGGTTFKTDASVGEI 364
                                       *************************************************9887 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1     2e-08   2.9e-05     151     230 ..      40     120 ..      35     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2e-08
                              PrmA 151 clealeklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleval..seellkee 225
                                        l+a+ +   + e+ lD  t SG+  + aa  g  +v+  D+De Av  a+eN+++N+++++ +v     + l+++e
  gi|336253424|ref|YP_004596531.1|  40 TLRAFREREPRAETYLDAMTASGVRGVRAAADGW-DVTCCDVDEEAVALARENVARNDCADRATVEHrdVNALMHDE 115
                                       566777777788999************9998775.7999**********************9988421134444578 PP

                              PrmA 226 kadvi 230
                                        +dvi
  gi|336253424|ref|YP_004596531.1| 116 LFDVI 120
                                       88887 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   4.5e-08   6.7e-05      31     102 ..      50     121 ..      29     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.5e-08
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdliv 102
                                       ++++ lD  +  Gv g+ +a+   +  vt++dvd +A+++a+en+++n+++  ++v ++dv + ++++ fd+i 
  gi|336253424|ref|YP_004596531.1|  50 RAETYLDAMTASGVRGVRAAADGWD--VTCCDVDEEAVALARENVARNDCAdrATVEHRDVNALMHDELFDVID 121
                                       5566788888888888888886655..9*********************9999******************995 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.3   2.4e-07   0.00036       3      68 ..      56     120 ..      55     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.4e-07
                                       EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEE CS
                   Methyltransf_25   3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlv 68 
                                       d+ + +G    ++a+ +   +vt++D++ee+++ are+++++++  ++++++ d+++l  +d+ fD++
  gi|336253424|ref|YP_004596531.1|  56 DAMTASGVRGVRAAADG--WDVTCCDVDEEAVALARENVARNDCadRATVEHRDVNALM-HDELFDVI 120
                                       66666777777777774..9*********************9999************97.67799998 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.8e-07   0.00043       5      81 ..      52     123 ..      49     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.8e-07
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlils 80 
                                        ++lD+ +++G  + ++a    ++ +v+  D +eea+ lAren +++    ++++e+ d+++l    +de fD+i  
  gi|336253424|ref|YP_004596531.1|  52 ETYLDAMTASGVRGVRAA---ADGWDVTCCDVDEEAVALARENVARNDCAdRATVEHRDVNALM---HDELFDVIDL 122
                                       678999999999999999...45678****************988888777***********76...3799**9855 PP

                   Methyltransf_31  81 n 81 
                                       +
  gi|336253424|ref|YP_004596531.1| 123 D 123
                                       4 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.4e-06    0.0066      42     127 ..      51     135 ..      40     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.4e-06
                                       C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                        +++LD    sG+ g+ A+  g   +++ + d+eav++ +en+++ ++ +  a++ + +++al +     e fd++ 
  gi|336253424|ref|YP_004596531.1|  51 AETYLDAMTASGVRGVRAAADG-WDVTCCDVDEEAVALARENVARNDCAD-RATVEHRDVNALMHD----ELFDVID 121
                                       5678****************99.789**********************98.555555555555444....68***** PP

                                       E--.....SSSTTC CS
                     Cons_hypoth95 119 lDP.....Pyakel 127
                                       lDP     P+a+ +
  gi|336253424|ref|YP_004596531.1| 122 LDPygtpmPFADAA 135
                                       **966666666655 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   1.7   1.3e-05     0.019       4      34 ..     232     261 ..     232     264 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                       Zn-ribbon_8   4 YeYrCeeCghefevlqsisdapltaCPeCgs 34 
                                       Y Y+Ce+C    e+      +p ++CP+Cg+
  gi|336253424|ref|YP_004596531.1| 232 YLYHCEDCT-YREADPGLIADPIETCPHCGG 261
                                       88******9.444333344667788*****8 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.4e-05     0.036      77     133 ..      73     127 ..      39     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-05
                                       --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE------ CS
                           UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGe 133
                                         + + D d+++v+ areN  +   +d+ +++  d+ +L   ++ +dvi  + PYG 
  gi|336253424|ref|YP_004596531.1|  73 WDVTCCDVDEEAVALARENVARNDCADRATVEHRDVNALM-HDELFDVIDLD-PYGT 127
                                       4489************************************.66579888666.7875 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   6.2e-05     0.092      11      70 ..      63     120 ..      55     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.2e-05
                   Methyltransf_12  11 lralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlv 70 
                                       +r ++++  ++++t++D++++a++ a+e  a+++  + + ve ++ ++l +d+   fD++
  gi|336253424|ref|YP_004596531.1|  63 VRGVRAAADGWDVTCCDVDEEAVALARENVARNDCADRATVEHRDVNALMHDE--LFDVI 120
                                       5566667789*************999999999887777777777777776665..78887 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00015      0.22      13      65 ..      68     120 ..      55     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                       HHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEE CS
                   Methyltransf_11  13 alakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlv 65 
                                       a a  g +v+++D+++e+++la+e++ +++   + ++ + d+  l + d+ fD++
  gi|336253424|ref|YP_004596531.1|  68 A-AADGWDVTCCDVDEEAVALARENVARNDCadRATVEHRDVNAL-MHDELFDVI 120
                                       3.34789*********************99999888888888886.789999997 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   0.00013      0.19     102     193 ..      52     141 ..      22     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                       -EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE--TT CS
                            Met_10 102 evVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnlpk 178
                                       e+ +d +   G   + +a   ++  v   d++ e+v + +en+++N+ +++ ++   D++ +++++l+d + ++   
  gi|336253424|ref|YP_004596531.1|  52 ETYLDAMTASGVRGVRAAA--DGWDVTCCDVDEEAVALARENVARNDCADRATVEHRDVNALMHDELFDVIDLDPYG 126
                                       5667777777777787776..88899*************************************99999977777777 PP

                                       TGGGGHHHHHHHEEE CS
                            Met_10 179 saieFldkvlaalkd 193
                                       + + F d+++a  +d
  gi|336253424|ref|YP_004596531.1| 127 TPMPFADAAFANCRD 141
                                       777777777777666 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 ?    0.0   0.1      0.76   1.1e+03      27      37 ..     115     160 ..      95     178 .. 0.56
   2 ?    0.4   0.0      0.58   8.6e+02      25      36 ..     230     241 ..     208     250 .. 0.74
   3 ?    8.1   0.1    0.0022       3.3       4      16 ..     254     266 ..     251     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.76
                   Lar_restr_allev  27 q............................cvyCad....Cga...s 37 
                                       +                            cv+ +d    Cga   s
  gi|336253424|ref|YP_004596531.1| 115 ElfdvidldpygtpmpfadaafancrdlvCVTATDtaplCGAhfnS 160
                                       1455555555555555666665666666677777777888886440 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.58
                   Lar_restr_allev  25 igqcvyCadCga 36 
                                        g+  +C+dC +
  gi|336253424|ref|YP_004596531.1| 230 LGYLYHCEDCTY 241
                                       344779****98 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0022
                   Lar_restr_allev   4 kpCPfCggravle 16 
                                       + CP+Cgg+ +l 
  gi|336253424|ref|YP_004596531.1| 254 ETCPHCGGDRILA 266
                                       68******98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2681.97
//
Query:       gi|336253425|ref|YP_004596532.1|  [L=67]
Description: hypothetical protein Halxa_2028 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00084   19.3   0.4       0.67   10.0   0.0    2.1  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.016   15.3   2.4       0.85    9.8   0.3    2.2  2  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
       0.11   12.3   0.4       0.18   11.7   0.4    1.4  1  CxC4           CxC4 like cysteine cluster associated with KDZ
        0.3   10.5   0.2        0.3   10.5   0.2    2.2  2  zf-TFIIB       Transcription factor zinc-finger
       0.35   10.7   2.7        5.9    6.8   0.1    2.2  2  zf-C2H2_3      zinc-finger of acetyl-transferase ESCO


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 !   10.0   0.0   0.00019      0.67      18      34 ..       3      20 ..       1      33 [. 0.83
   2 !    8.2   0.1   0.00066       2.4      17      30 ..      49      62 ..      36      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                     Zn_Tnp_IS1595 18 gfvCPhCgsr.kayrikt 34
                                       ++CP Cg++ ++  +++
  gi|336253425|ref|YP_004596532.1|  3 QRRCPDCGVTmEPVPVRD 20
                                      578******988877765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00066
                     Zn_Tnp_IS1595 17 ngfvCPhCgsrkay 30
                                      +g++CP C   ++y
  gi|336253425|ref|YP_004596532.1| 49 QGVCCPECRLVRLY 62
                                      679*****976766 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 ?    5.9   0.1    0.0039        14      15      24 ..       3      12 ..       1      22 [. 0.82
   2 ?    9.8   0.3   0.00024      0.85       7      24 ..      42      59 ..      36      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0039
                     Auto_anti-p27 15 aetCpvCgvP 24
                                      +  Cp+Cgv 
  gi|336253425|ref|YP_004596532.1|  3 QRRCPDCGVT 12
                                      568****985 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00024
                     Auto_anti-p27  7 LlkGwtMLaetCpvCgvP 24
                                      L + +++ + +Cp+C  +
  gi|336253425|ref|YP_004596532.1| 42 LKQRAKLQGVCCPECRLV 59
                                      78999**********654 PP

>> CxC4  CxC4 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   4.9e-05      0.18      15      65 ..       4      66 ..       1      67 [] 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.9e-05
                              CxC4 15 arC.rCgtsl...........dpsrptlekectvytltgalevrielqrCpaCahtrrfiGpD 65
                                       rC  Cg ++           + s  t e+e  + +l   ++++++ ++Cp+C+ +r +++ D
  gi|336253425|ref|YP_004596532.1|  4 RRCpDCGVTMepvpvrdgesmRLSIATGEREGLLGKLGLKQRAKLQGVCCPECRLVRLYAEDD 66
                                      57777877767777777665566677777799999999***************6556677665 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   8.3e-05       0.3       2      18 ..       6      22 ..       5      25 .. 0.82
   2 ?    1.8   0.8     0.041   1.5e+02      22      26 ..      53      57 ..      44      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.3e-05
                          zf-TFIIB  2 CPkCqdeleeserggve 18
                                      CP C++++e++ +++ e
  gi|336253425|ref|YP_004596532.1|  6 CPDCGVTMEPVPVRDGE 22
                                      *********99886655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.041
                          zf-TFIIB 22 CpqCr 26
                                      Cp+Cr
  gi|336253425|ref|YP_004596532.1| 53 CPECR 57
                                      66665 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.5    0.0096        34      14      21 ..       4      11 ..       1      14 [. 0.79
   2 ?    6.8   0.1    0.0017       5.9       5      22 ..      41      59 ..      39      67 .] 0.64

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0096
                         zf-C2H2_3 14 sqCkeCgM 21
                                      ++C+ Cg 
  gi|336253425|ref|YP_004596532.1|  4 RRCPDCGV 11
                                      57****97 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0017
                         zf-C2H2_3  5 dlgqksfga.sqCkeCgMv 22
                                       l q+ + + + C+eC +v
  gi|336253425|ref|YP_004596532.1| 41 GLKQRAKLQgVCCPECRLV 59
                                      456666555455****995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 512.40
//
Query:       gi|336253426|ref|YP_004596533.1|  [L=512]
Description: ribonuclease BN [Halopiger xanaduensis SH-6]
Scores for 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-39  135.7  27.5    2.1e-39  135.7  27.5    2.0  2  Virul_fac_BrkB  Virulence factor BrkB
  ------ inclusion threshold ------
      0.016   13.6   1.6      0.022   13.2   1.6    1.1  1  MAD             Mitotic checkpoint protein
      0.045   13.2   0.0      0.045   13.2   0.0    3.0  3  DUF4349         Domain of unknown function (DUF4349)
      0.052   13.4   0.0      0.052   13.4   0.0    3.4  3  VIT1            VIT family
       0.25   11.8   1.8       0.39   11.1   1.8    1.2  1  DUF1690         Protein of Unknown function (DUF1690)
       0.99    8.5   3.4        1.4    8.0   3.4    1.1  1  Tmemb_cc2       Predicted transmembrane and coiled-coil 2 pro
        1.9    7.5   5.0        2.7    7.0   5.0    1.1  1  Atg14           Vacuolar sorting 38 and autophagy-related sub


Domain annotation for each model (and alignments):
>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.7  27.5   8.2e-43   2.1e-39       3     255 ..      50     285 ..      48     288 .. 0.90
   2 ?   -1.5   2.8      0.62   1.6e+03     129     202 ..     459     486 ..     431     500 .. 0.44

  Alignments for each domain:
  == domain 1  score: 135.7 bits;  conditional E-value: 8.2e-43
                    Virul_fac_BrkB   3 ddlsllAaalayytllSlfPlllvllavlgllglddelqeqlldllaevlpegaaevvedil.qrllnqaslgllgl 78 
                                       ++l+llAa++a+y ++Sl+Plll+ l++++ +g +++l+  l+ ++++vl+++a e++ +++ +++  ++s++++g 
  gi|336253426|ref|YP_004596533.1|  50 QQLTLLAAGVAFYGFISLVPLLLLGLGIAASIG-GEALAVRLTVAASDVLTPAARELLAETVlDET-GRQSATVVGA 124
                                       6799*************************8866.6899999********999888*******5555.5666****** PP

                    Virul_fac_BrkB  79 avllwsasggvsalrralnkiygveesrsflrkrllsllllllllvllllslvlsvflqslllasapllglglelse 155
                                        +llw +s+++++l+ra+ ++yg+   +s + ++ ++++++l++ v l+l+ +l v++++     ap++g       
  gi|336253426|ref|YP_004596533.1| 125 FGLLWGSSRVLRGLDRAFSQVYGTVGEKSVVDTIWDATIVFLVISVGLALVGALEVAIRF-----APVIG------- 189
                                       ************************77789***************************9988.....34555....... PP

                    Virul_fac_BrkB 156 llllqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwllvkilfslylsnfasynaiYGslgalii 232
                                          l +++ +++ll lv+ f+ lY v+p++ v +r+alpG+++aa++w++++  fsly +  a+   +YG+lga+ +
  gi|336253426|ref|YP_004596533.1| 190 ---LGYVGPVFVLLGLVASFLPLYVVFPDADVGVREALPGTVIAAVGWFVLSRTFSLYAAV-ATEYVVYGALGAVFL 262
                                       ...44555558999999*****************************************997.555588********* PP

                    Virul_fac_BrkB 233 lllWlylsalilLlGaelnaelq 255
                                       +l+Wlyl a+il +Ga+ na+l+
  gi|336253426|ref|YP_004596533.1| 263 VLVWLYLGAIILVFGAVCNAVLA 285
                                       ********************997 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.62
                    Virul_fac_BrkB 129 slvlsvflqslllasapllglglelsellllqllrwlvallllvlafallYrvlpnvkvrlraalpGallaall 202
                                       +++                           + +++w+                       +  ++  +l + +l
  gi|336253426|ref|YP_004596533.1| 459 AAFY--------------------------FLTGPWA--------------------ILAMFVVWTSTLGVYVL 486
                                       2222..........................2222222....................22222222222222222 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.6   8.6e-06     0.022     498     540 ..     385     425 ..     377     436 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.6e-06
                               MAD 498 akqqkkeqlekLqaEierlkellkkleedkekkvaslpesslt 540
                                         + ++++ e+L++Eierl++++++ e++ e+   +++++sl+
  gi|336253426|ref|YP_004596533.1| 385 RTRDRADDSEALREEIERLRDRVETFEDNVER--RTVEKESLE 425
                                       568899**********************9997..777777776 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   1.2       1.6     4e+03     191     205 ..     187     201 ..     133     207 .. 0.63
   2 ?   -4.5   4.1       4.7   1.2e+04     188     208 ..     254     274 ..     233     280 .. 0.59
   3 ?   13.2   0.0   1.8e-05     0.045     128     213 .]     396     477 ..     370     480 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.6
                           DUF4349 191 lvvlgallPwllvla 205
                                       ++ lg++ P++++l+
  gi|336253426|ref|YP_004596533.1| 187 VIGLGYVGPVFVLLG 201
                                       555666666666666 PP

  == domain 2  score: -4.5 bits;  conditional E-value: 4.7
                           DUF4349 188 agllvvlgallPwllvlalvl 208
                                        g+l ++ ++l+wl + a++l
  gi|336253426|ref|YP_004596533.1| 254 YGALGAVFLVLVWLYLGAIIL 274
                                       334444444555555555333 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 1.8e-05
                           DUF4349 128 vqaeieslegqlryLdnqvaystvtvtlrepeaeteaeeee...gegflealsggwnalveflagllvvlgallPwl 201
                                        ++eie+l+ + ++ +++v+  tv+ +  e e        +     +++++ + gw   + +l g +++++a+  + 
  gi|336253426|ref|YP_004596533.1| 396 LREEIERLRDRVETFEDNVERRTVEKESLEGEL-------KryvRRRVRRGHAHGWGPYLVLLYGTAMAIAAFYFLT 465
                                       456666666666666666666666555544444.......3345678899999999998888888777777655444 PP

                           DUF4349 202 lvlalvlallvr 213
                                        ++a++++++v+
  gi|336253426|ref|YP_004596533.1| 466 GPWAILAMFVVW 477
                                       444444433333 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4       0.2   5.2e+02     141     188 ..      55      99 ..      29     135 .. 0.70
   2 ?   -9.3  11.1         7   1.8e+04     162     207 ..     239     281 ..     160     295 .. 0.72
   3 ?   13.4   0.0     2e-05     0.052      56     182 ..     372     499 ..     369     508 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.2
                              VIT1 141 salsfliGgliPllpylfvesvglalvvsiavtllalllfGavkallt 188
                                        a++ ++ g+i+l+p l++    l++++si+  +la+ l+ a +++lt
  gi|336253426|ref|YP_004596533.1|  55 LAAGVAFYGFISLVPLLLLG---LGIAASIGGEALAVRLTVAASDVLT 99 
                                       56778888999999999865...5566665555555555555555555 PP

  == domain 2  score: -9.3 bits;  conditional E-value: 7
                              VIT1 162 vglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAa 207
                                       ++  l+++   ++   ++ Ga++a+++ + +l+ +   l++Ga++ 
  gi|336253426|ref|YP_004596533.1| 239 RTFSLYAA---VATEYVVYGALGAVFLVLVWLYLGAIILVFGAVCN 281
                                       44444444...44555566666666666666666666666665554 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 2e-05
                              VIT1  56 vkserdlekaerkreeeeleedpe.egeaeelaeilearglseelaqevaaellknpdalle.lmlr..eel..g.. 124
                                       +++e +  +++ +r++++ +++++ ++   e++++  + +  e+ +++ + e  + + +l++ +  r  +++  g  
  gi|336253426|ref|YP_004596533.1| 372 TETETERRDSRSARTRDRADDSEAlRE---EIERLRDRVETFEDNVERRTVEKESLEGELKRyVRRRvrRGHahGwg 445
                                       556666666666666666666664444...44444444444444444444444444444333122221122222233 PP

                              VIT1 125 psaseelasplkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGa 182
                                       p      +  +  A+++a+++++ g   +l++++v + +l+++v +++ ++ l l+G+
  gi|336253426|ref|YP_004596533.1| 446 PYL----VLLYGTAMAIAAFYFLTGPWAILAMFVVWTSTLGVYVLMVLLGAGLSLLGV 499
                                       332....334679**********************99*****************9997 PP

>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.8   0.00015      0.39      56     109 ..     371     423 ..     359     438 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                           DUF1690  56 kfeeklekellkdeadakdelsskalnekieeLrkkleefkkkeeeklpeevee 109
                                       + e+++e+  + + +++++   s+al+e+ie Lr+++e+f++++e+++  e+e+
  gi|336253426|ref|YP_004596533.1| 371 ATETETERRDSRSARTRDRADDSEALREEIERLRDRVETFEDNVERRT-VEKES 423
                                       3333333333333366899999********************999554.44444 PP

>> Tmemb_cc2  Predicted transmembrane and coiled-coil 2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.4   0.00054       1.4     168     265 ..     335     430 ..     304     434 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00054
                         Tmemb_cc2 168 sstallvskskytsddesssssvesssadsnsnseestasasksaesesqeklekileelqeikeeqerleeelerl 244
                                         t + +++   +sd + ss++ ++++a ++++++ ++++++++++ +++++     ++ + ++ee erl++++e++
  gi|336253426|ref|YP_004596533.1| 335 DDTRTRDRNRDLESDRDRSSAD-TGTDARTTGTETGTATETETERRDSRSARTRDRADDSEALREEIERLRDRVETF 410
                                       2222222222233333333333.566666666666666666666666666666777777777777777777777777 PP

                         Tmemb_cc2 245 keqlkkelkllkqaLqeeryr 265
                                       ++++++  ++ k++L+ e  r
  gi|336253426|ref|YP_004596533.1| 411 EDNVERR-TVEKESLEGELKR 430
                                       7776664.5556666666555 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 ?    7.0   5.0     0.001       2.7      69     133 ..     371     436 ..     340     440 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.001
                             Atg14  69 leelksliadlre.rlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqi 133
                                       + e+ ++++d+r+ r++   d+ + l++eie  + ++++  d++ +R+ + esl+ el+ + ++ +
  gi|336253426|ref|YP_004596533.1| 371 ATETETERRDSRSaRTRDRADDSEALREEIERLRDRVETFEDNVERRTVEKESLEGELKRYVRRRV 436
                                       4555556666554167777889999*********************************99877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1599  (0.0891851); expected 358.6 (0.02)
Passed bias filter:                      790  (0.0440627); expected 358.6 (0.02)
Passed Vit filter:                       132  (0.00736237); 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):               7  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.44
# Mc/sec: 3509.96
//
Query:       gi|336253427|ref|YP_004596534.1|  [L=451]
Description: glutamine synthetase, type I [Halopiger xanaduensis SH-6]
Scores for 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-139  463.3   0.1   5.7e-139  462.9   0.1    1.1  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    3.3e-32  110.1   0.1    6.8e-32  109.1   0.1    1.6  1  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
    0.00051   19.8   0.1     0.0039   17.0   0.1    2.2  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.9   0.1  9.5e-143  5.7e-139       2     345 .]     112     447 ..     111     447 .. 0.98

  Alignments for each domain:
  == domain 1  score: 462.9 bits;  conditional E-value: 9.5e-143
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHH CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrrei 78 
                                       +dPR+vlk+al+r++e+G+tv+++pE+EFflf+++e+++            +++++++ggyf+vap+d a+d+rr+i
  gi|336253427|ref|YP_004596534.1| 112 GDPRRVLKNALERAEEMGYTVNAAPEPEFFLFEEDEEGR-----------ATTETNDAGGYFDVAPKDLASDVRRDI 177
                                       79*********************************9987...........5677899******************** PP

                                       HHHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEE CS
                        Gln-synt_C  79 vealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlS 155
                                       +  le++g+e+eashhEva+gQ+Ein+ ++dal++aDnv+tf++vv+++A++h+++atFmpKp++  nGsgmH+hlS
  gi|336253427|ref|YP_004596534.1| 178 IYGLEEMGFEIEASHHEVAEGQHEINFTYDDALATADNVATFRTVVRAIAAQHDYHATFMPKPIPRINGSGMHTHLS 254
                                       ***************************************************************************** PP

                                       EEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-. CS
                        Gln-synt_C 156 lwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa. 231
                                       l+++dg+n+f+dedde +lse a+ f +G+l+ha+a+ta+++ptvnSYkRlvpgyeaPv++aw+ rNRsal+R pa 
  gi|336253427|ref|YP_004596534.1| 255 LFTEDGENAFHDEDDEFNLSEEAHAFTAGILEHAPAITAVANPTVNSYKRLVPGYEAPVYVAWSDRNRSALIRKPAa 331
                                       ****************************************************************************8 PP

                                       TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHC CS
                        Gln-synt_C 232 skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealee 306
                                         + a+r+ElR+pd+s+NPYLa+Aa++ AgldGie+ l++++pv++++ye ++++r   gie+lP++l +A++alee
  gi|336253427|ref|YP_004596534.1| 332 RVPAASRIELRSPDPSCNPYLAFAAMIHAGLDGIEQDLDCPDPVRENIYEFDEQKRdeYGIETLPSNLGQAVDALEE 408
                                       89***************************************************999999****************** PP

                                       SHHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 307 dellkevlgeevieaylalkraEleeleeevsdwelery 345
                                       de + ++lge+v  +++++kr+E+ee+   vs+wel+ry
  gi|336253427|ref|YP_004596534.1| 409 DEAIYNALGEHVAPKFVEAKRQEFEEYLVDVSQWELDRY 447
                                       ************************************998 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.1   0.1   1.1e-35   6.8e-32       1      82 [.      21     103 ..      21     104 .. 0.97

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 1.1e-35
                                       T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-...EEE CS
                        Gln-synt_N   1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek..ktar 75 
                                       +v f++lqFtDi g++k+v++pa++  e+a++eg+ FDGSsiegf++i+eSDm L+Pd++t++i+P+r+++  + ar
  gi|336253427|ref|YP_004596534.1|  21 DVDFLRLQFTDILGTVKNVAVPARQA-EKAFTEGIYFDGSSIEGFVRIQESDMRLVPDPDTFAILPWRNDEdsAAAR 96 
                                       589***********************.******************************************99999*** PP

                                       EEEEEE- CS
                        Gln-synt_N  76 vicdvyd 82 
                                       +icdvyd
  gi|336253427|ref|YP_004596534.1|  97 MICDVYD 103
                                       ******8 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   6.6e-07    0.0039       3     102 ..      10     104 ..       8     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.6e-07
                                       ........------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-GGGGG--TTS---TT-S-SSS--EEEEE- CS
                      Gln-synt_N_2   3 deavveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGltkatlalserdlidevedlgpvGelrLvpd 79 
                                       ++av++++e ++v+++++ ++d  G ++  a+p  + e+ +++Gi +    ++++    i+e+       ++rLvpd
  gi|336253427|ref|YP_004596534.1|  10 EQAVLDEIEAQDVDFLRLQFTDILGTVKNVAVPARQAEKAFTEGIYFD--GSSIEGFVRIQES-------DMRLVPD 77 
                                       68999****************************999999999999875..4677777788886.......89***** PP

                                       GGG-EEE---SS...TTS..EEEEEE-T CS
                      Gln-synt_N_2  80 PasavalpyaPd...aaa..llgdlvev 102
                                       P ++  lp   d   a a  ++ d++++
  gi|336253427|ref|YP_004596534.1|  78 PDTFAILPWRNDedsA-AarMICDVYDT 104
                                       ********87653323.23699999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3245.06
//
Query:       gi|336253428|ref|YP_004596535.1|  [L=153]
Description: AsnC family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-13   49.0   0.0    7.9e-13   48.2   0.0    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    1.7e-10   40.3   0.0    3.1e-10   39.5   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.5e-07   31.2   0.1    3.2e-07   30.1   0.1    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
    6.7e-07   29.0   0.2    1.1e-06   28.3   0.2    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    3.8e-06   26.8   0.0    9.4e-06   25.5   0.0    1.7  1  HTH_11          HTH domain
    8.9e-06   25.7   0.1    1.8e-05   24.7   0.1    1.5  1  HTH_20          Helix-turn-helix domain
    6.2e-05   22.7   0.0    0.00024   20.8   0.0    1.8  2  HTH_DeoR        DeoR-like helix-turn-helix domain
    0.00066   19.7   0.0     0.0011   19.1   0.0    1.3  1  HTH_28          Helix-turn-helix domain
    0.00072   19.4   0.0     0.0013   18.6   0.0    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00079   19.3   0.0     0.0013   18.6   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0017   18.0   0.0     0.0032   17.1   0.0    1.4  1  GntR            Bacterial regulatory proteins, gntR family
     0.0022   17.7   0.0     0.0044   16.8   0.0    1.5  1  HTH_10          HTH DNA binding domain
     0.0088   16.2   0.0      0.018   15.3   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.022   14.7   0.0    1.5  1  MarR            MarR family
       0.01   15.6   0.0      0.017   14.9   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
      0.024   14.5   0.0      0.043   13.7   0.0    1.4  1  MarR_2          MarR family
      0.025   15.0   0.0      0.062   13.8   0.0    1.7  2  HTH_40          Helix-turn-helix domain
      0.039   13.4   0.0      0.086   12.3   0.0    1.6  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.058   14.0   0.0       0.14   12.7   0.0    1.6  1  Mga             Mga helix-turn-helix domain
      0.087   12.5   0.0       0.18   11.5   0.0    1.5  1  HTH_50          Helix-turn-helix domain
      0.095   12.3   0.1       0.17   11.5   0.1    1.4  1  HTH_47          winged helix-turn-helix
      0.099   13.1   0.0       0.23   12.0   0.0    1.6  1  HTH_27          Winged helix DNA-binding domain
        0.1   12.7   0.0       0.16   12.0   0.0    1.3  1  HTH_29          Winged helix-turn helix
        0.1   12.6   0.0       0.17   11.9   0.0    1.3  1  HTH_36          Helix-turn-helix domain
       0.11   12.9   0.0       0.24   11.8   0.0    1.6  1  Rrf2            Transcriptional regulator
       0.12   12.5   0.2       0.25   11.5   0.2    1.5  1  DprA_WH         DprA winged helix domain
       0.14   12.0   0.0       0.22   11.4   0.0    1.3  1  HTH_23          Homeodomain-like domain


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 !   48.2   0.0   1.2e-15   7.9e-13       1      74 [.      69     138 ..      69     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.2e-15
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       +++++e+++   l ++ + l+++ + +++y vtGdyd +++ +++d++++++ +++ l + p++++++ts+vl+
  gi|336253428|ref|YP_004596535.1|  69 IQLQVEGNA---LPDITDTLKDHRQMISVYEVTGDYDVIAIGKFQDTDEMNDNIKQ-LLTDPDIKSSNTSVVLN 138
                                       678999888...********************************************.***************97 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 !   39.5   0.0   4.6e-13   3.1e-10       5      48 .]       7      50 ..       4      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 4.6e-13
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      d k+ ++L  ++r s r LAe l++S++tv+ +l  Lee+G+I+
  gi|336253428|ref|YP_004596535.1|  7 DAKLVNALLGDGRASLRSLAEDLDVSVTTVSNHLSDLEEDGVIE 50
                                      66889**************************************7 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 !   30.1   0.1   4.9e-10   3.2e-07       6      46 ..       9      50 ..       8      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.9e-10
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      k++++L   g ++   lae+l++s  tvS HL+ L+e G++e
  gi|336253428|ref|YP_004596535.1|  9 KLVNALLGdGRASLRSLAEDLDVSVTTVSNHLSDLEEDGVIE 50
                                      67889999899****************************986 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 !   28.3   0.2   1.7e-09   1.1e-06       4      36 ..       6      38 ..       4      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.7e-09
                     HTH_AsnC-type  4 iDrkILeaLqedaRisyaeLAervGlSestvlr 36
                                      +D k+++aL  d+R+s + LAe + +S +tv +
  gi|336253428|ref|YP_004596535.1|  6 LDAKLVNALLGDGRASLRSLAEDLDVSVTTVSN 38
                                      8******************************86 PP

>> HTH_11  HTH 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   9.4e-06      13      44 ..      17      48 ..       8      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.4e-08
                            HTH_11 13 rgpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      +g  s   LAe L+vS +tv +++ +Lee gv
  gi|336253428|ref|YP_004596535.1| 17 DGRASLRSLAEDLDVSVTTVSNHLSDLEEDGV 48
                                      56678999**********************94 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   2.7e-08   1.8e-05      18      59 ..      13      54 ..       7      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.7e-08
                                      HHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 18 aLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      aL +++ +++  lae ld+s +t+s+HL  Lee g +e+ ++
  gi|336253428|ref|YP_004596535.1| 13 ALLGDGRASLRSLAEDLDVSVTTVSNHLSDLEEDGVIEGYTP 54
                                      555899999*****************************9887 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 !   20.8   0.0   3.6e-07   0.00024       3      44 ..       8      49 ..       7      52 .. 0.94
   2 ?   -1.2   0.0       2.6   1.7e+03       5      26 ..      81     103 ..      79     103 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.6e-07
                          HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                      ++++  l  +g  s+  l+e l+vS +T+ + L+ Lee+g++
  gi|336253428|ref|YP_004596535.1|  8 AKLVNALLGDGRASLRSLAEDLDVSVTTVSNHLSDLEEDGVI 49
                                      688999999*******************************98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.6
                          HTH_DeoR   5 ilellkqqgk.lsveelvellgv 26 
                                       i++ lk+++  +sv e++  ++v
  gi|336253428|ref|YP_004596535.1|  81 ITDTLKDHRQmISVYEVTGDYDV 103
                                       67778877642788888877766 PP

>> HTH_28  Helix-turn-helix 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    0.0011       4      47 ..       9      55 ..       8      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-06
                            HTH_28  4 eiiklla.aGh.svreaArelgisrrtvyrWikryeegG.iagLvpr 47
                                      + + +l+ +G+ s r +A+ l +s +tv+  ++ +ee G i+g  pr
  gi|336253428|ref|YP_004596535.1|  9 KLVNALLgDGRaSLRSLAEDLDVSVTTVSNHLSDLEEDGvIEGYTPR 55
                                      668889989*9****************************77999998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.9e-06    0.0013      10      53 ..       7      50 ..       4      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                                      CCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 10 EakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      +ak   aLl  g+a+ + +ae+l+v+ ++v + L+ Le+ G++e
  gi|336253428|ref|YP_004596535.1|  7 DAKLVNALLGDGRASLRSLAEDLDVSVTTVSNHLSDLEEDGVIE 50
                                      7788889**********************************998 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 !   18.6   0.0     2e-06    0.0013      23      53 ..      21      52 ..       9      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2e-06
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglis.r 53
                                      + + lA+ l ++  tvs  ls+L+++g+i+  
  gi|336253428|ref|YP_004596535.1| 21 SLRSLAEDLDVSVTTVSNHLSDLEEDGVIEgY 52
                                      56789************************942 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.8e-06    0.0032       6      55 ..       3      50 ..       1      51 [. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.8e-06
                                      HHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR  6 yerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                      ye L++++++  l  G +  s r+La+ ++Vs ttv   L+ Le++g++e
  gi|336253428|ref|YP_004596535.1|  3 YENLDAKLVNALLGDGRA--SLRSLAEDLDVSVTTVSNHLSDLEEDGVIE 50
                                      555666666655555544..68*************************996 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.6e-06    0.0044      23      48 ..      19      44 ..      17      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.6e-06
                            HTH_10 23 rvtlkeLAkelGIskstlsehLrkae 48
                                      r++l++LA++l++s +t+s+hL+  e
  gi|336253428|ref|YP_004596535.1| 19 RASLRSLAEDLDVSVTTVSNHLSDLE 44
                                      799*******************8765 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 !   15.3   0.0   2.7e-05     0.018      23      52 ..      20      49 ..      13      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-05
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGyv 52
                                      ++   lae L+vs  +Vs  l+ Le+dG +
  gi|336253428|ref|YP_004596535.1| 20 ASLRSLAEDLDVSVTTVSNHLSDLEEDGVI 49
                                      56678**********************976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.3e-05     0.022      16      48 ..      18      50 ..      14      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-05
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlie 48
                                      g +s+  La+ l vs +tv++ l  Le++G ie
  gi|336253428|ref|YP_004596535.1| 18 GRASLRSLAEDLDVSVTTVSNHLSDLEEDGVIE 50
                                      5678899***********************997 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 ?   14.9   0.0   2.5e-05     0.017      11      49 ..      13      50 ..       8      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                                      T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      al   +++ +l+ lA+ ++++ +tv+++L+ L+e G +e
  gi|336253428|ref|YP_004596535.1| 13 ALLGDGRA-SLRSLAEDLDVSVTTVSNHLSDLEEDGVIE 50
                                      55555565.9************************99876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.4e-05     0.043      16      52 ..      16      50 ..       6      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.4e-05
                                      CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 16 rrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                        ++   + + la+ l++s  +vs++l +L++ G +e
  gi|336253428|ref|YP_004596535.1| 16 GDGR--ASLRSLAEDLDVSVTTVSNHLSDLEEDGVIE 50
                                      4443..79999************************98 PP

>> HTH_40  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   9.3e-05     0.062      14      76 ..      21      85 ..      13     102 .. 0.70
   2 ?   -1.8   0.0       6.5   4.3e+03      52      65 ..     114     127 ..      99     149 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.3e-05
                            HTH_40 14 sieeIAkerglkesTIegHLaelieeg......eeidlerlvseeeekeIeeaiekvgseklkpikeal 76
                                      s+   A+   ++++T+ +HL +l e+g       ++d++ l   +    I+ ++e    + l +i + l
  gi|336253428|ref|YP_004596535.1| 21 SLRSLAEDLDVSVTTVSNHLSDLEEDGviegytPRLDYDAL-GYDVTAVIQLQVEG---NALPDITDTL 85
                                      78899*********************866555545666554.33444444444333...4455555555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.5
                            HTH_40  52 eeekeIeeaiekvg 65 
                                       e  ++I++ +++ +
  gi|336253428|ref|YP_004596535.1| 114 EMNDNIKQLLTDPD 127
                                       55556666555533 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 ?   12.3   0.0   0.00013     0.086      23      46 ..      14      38 ..       5      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                      HTH_Tnp_ISL3 23 llles.rsvkavArqlgvSwtTVwr 46
                                      ll ++ +s ++ A++l+vS tTV +
  gi|336253428|ref|YP_004596535.1| 14 LLGDGrASLRSLAEDLDVSVTTVSN 38
                                      6777799****************86 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00021      0.14      15      56 ..       4      45 ..       1      46 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
                                      HSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
                               Mga 15 eslkyqllkflfeeeevsieelaqelyiSestlkrkikelnk 56
                                      e+l+ +l+  l+ + + s+ +la+ l +S +t+ +++ +l++
  gi|336253428|ref|YP_004596535.1|  4 ENLDAKLVNALLGDGRASLRSLAEDLDVSVTTVSNHLSDLEE 45
                                      678889*******************************99976 PP

>> HTH_50  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   0.00027      0.18      24      44 ..      20      40 ..       3      42 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                            HTH_50 24 pStRklAkrLGvShtaiankl 44
                                       S R lA+ L vS t++ n l
  gi|336253428|ref|YP_004596535.1| 20 ASLRSLAEDLDVSVTTVSNHL 40
                                      69***************9976 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00025      0.17      42      77 ..      15      50 ..       2      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                                      H-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 42 laDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                      l DG+ sL  +Ae +++++ +v + +  L+e g+++
  gi|336253428|ref|YP_004596535.1| 15 LGDGRASLRSLAEDLDVSVTTVSNHLSDLEEDGVIE 50
                                      79*******************************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 ?   12.0   0.0   0.00035      0.23       8      49 ..      10      50 ..       4      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00035
                            HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49
                                      +++ +   ++r++l+ l++ l+v+ +++s+ l+ L+e G++e
  gi|336253428|ref|YP_004596535.1| 10 LVNALL-GDGRASLRSLAEDLDVSVTTVSNHLSDLEEDGVIE 50
                                      566666.799*****************************995 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.16       6      41 ..      13      48 ..       9      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                            HTH_29  6 lllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      +ll +G  + + +A+ l++s +tv ++l + ee+G+
  gi|336253428|ref|YP_004596535.1| 13 ALLGDGRASLRSLAEDLDVSVTTVSNHLSDLEEDGV 48
                                      5777888899*************************4 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00025      0.17      26      54 ..      20      48 ..      16      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                            HTH_36 26 psqetlakrlglsknTvsraikeLeqlGy 54
                                      +s + la++l +s+ Tvs+++  Le+ G 
  gi|336253428|ref|YP_004596535.1| 20 ASLRSLAEDLDVSVTTVSNHLSDLEEDGV 48
                                      68899********************9875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00036      0.24      22      56 ..      17      50 ..       8      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00036
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      ++  +s++++ae  ++s + ++  l+ L++ g+++
  gi|336253428|ref|YP_004596535.1| 17 DG-RASLRSLAEDLDVSVTTVSNHLSDLEEDGVIE 50
                                      44.4899**************************98 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00038      0.25      17      56 ..      11      50 ..       4      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00038
                           DprA_WH 17 vLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlve 56
                                      v a+Lg    ++  L++++ +++ +vs +L+ LE +G +e
  gi|336253428|ref|YP_004596535.1| 11 VNALLGDGRASLRSLAEDLDVSVTTVSNHLSDLEEDGVIE 50
                                      55889999999999********************999886 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00033      0.22      17      46 ..      19      49 ..       8      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00033
                            HTH_23 17 GlsvreIAreLgvsrrTvyrwlkryreeG.l 46
                                      ++s r  A+ L+vs  Tv++ l+  +e+G +
  gi|336253428|ref|YP_004596535.1| 19 RASLRSLAEDLDVSVTTVSNHLSDLEEDGvI 49
                                      7899999****************99989955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1139.88
//
Query:       gi|336253429|ref|YP_004596536.1|  [L=639]
Description: xenobiotic-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-42  143.9   2.0    9.1e-42  143.6   2.0    1.1  1  ABC_membrane  ABC transporter transmembrane region
    7.8e-36  123.6   0.0    1.5e-35  122.7   0.0    1.5  1  ABC_tran      ABC transporter
    0.00049   20.4   0.2     0.0046   17.2   0.2    2.2  1  AAA_22        AAA domain
    0.00093   18.7   0.1      0.025   14.0   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0028   16.9   0.0     0.0078   15.5   0.0    1.7  1  Zeta_toxin    Zeta toxin
     0.0035   17.7   0.6     0.0095   16.3   0.6    1.7  1  AAA_16        AAA ATPase domain
     0.0081   16.1   0.0      0.019   14.9   0.0    1.6  1  RsgA_GTPase   RsgA GTPase
     0.0093   15.7   0.0      0.018   14.7   0.0    1.4  1  AAA_24        AAA domain
  ------ inclusion threshold ------
       0.01   15.6   3.5      0.014   15.1   1.3    2.3  2  AAA_30        AAA domain
      0.011   15.6   0.0      0.044   13.6   0.0    1.7  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      0.011   16.3   0.0       0.12   12.9   0.0    2.4  2  AAA_18        AAA domain
      0.017   14.9   0.0      0.042   13.6   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
      0.053   13.9   0.0       0.65   10.4   0.0    2.3  1  AAA           ATPase family associated with various cellular 
      0.065   13.2   0.1          3    7.7   0.0    2.3  2  NTPase_1      NTPase
       0.13   12.4   0.0       0.48   10.6   0.0    1.9  1  AAA_33        AAA domain
       0.15   12.6   0.0        0.3   11.5   0.0    1.5  1  AAA_23        AAA domain
       0.15   12.2   0.0       0.74    9.9   0.0    2.1  2  MMR_HSR1      50S ribosome-binding GTPase
       0.25   11.6   2.2         16    5.7   0.3    2.5  2  AAA_28        AAA domain
       0.27   11.0   0.6        3.5    7.4   0.6    2.1  1  DEAD          DEAD/DEAH box helicase


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 !  143.6   2.0   9.7e-45   9.1e-42       2     268 ..      37     325 ..      36     331 .. 0.96

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 9.7e-45
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHH...............HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   2 iliillailagvlsplfplvlgrildtlldkgdpet...............ealnvysllllllglaqfilallqsy 63 
                                        +++++ +la ++s++ plvlg  +d +++ g   +                +  +   ++++ +la ++l++++  
  gi|336253429|ref|YP_004596536.1|  37 AIGMVANFLARMASLVPPLVLGAAIDAIFV-GAGPFelpvvpnawlpdesiPQFRFAVAAIVASFLATAVLTWIYGV 112
                                       6899**************************.666666999999999999988888888888999999********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHS CS
                      ABC_membrane  64 llnvtgerlskrlrrklfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylg 140
                                       + n  +  +++++r + f+k+ r++msffd++++Ge+++ l+nd+++l+ +l + l+   + ++++ g+ +v+fyl+
  gi|336253429|ref|YP_004596536.1| 113 TANLFAHDVMHTVRVDSFRKMQRLDMSFFDEKQTGEVMAVLNNDTQNLERFLDNALMNSARLIVMVGGIAGVLFYLN 189
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 141 wkltlvllailpliilvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkag 217
                                       w+l++v+l+ +p ++ +++++++ +++   +e +av+++++ +e ++ g+   k    e+y++e+  +++++  +++
  gi|336253429|ref|YP_004596536.1| 190 WQLAVVTLFAVPAMVAFTIWFMRAVEPRYVRERSAVGRLNTRLENAIAGMALTKTSSSEAYERERVRDSSKNLFERT 266
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT........SSTHHHHHHHHHHHH CS
                      ABC_membrane 218 ikkaianglligitqllgllsyalalwfGttlvisg........elsvgdlvvflslfa 268
                                       + +++++ +  + ++ll+ +++a+++++G+++   g        elsvg++v+fl+l  
  gi|336253429|ref|YP_004596536.1| 267 MDVLKLSYFYRPGMELLAGVAFAATFFVGGYWLTIGtapgpftgELSVGEFVIFLTLTQ 325
                                       ********************************998888889999***********9986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.0   1.6e-38   1.5e-35       2     137 .]     407     555 ..     406     555 .. 0.96

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 1.6e-38
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++vs++ k+g +va+vG++GaGKSt lkll++l++ +eG ++ldg+d+++ +l  lr+ +g+++q+++lf+++ +++
  gi|336253429|ref|YP_004596536.1| 407 EDVSFEAKPGDTVALVGPTGAGKSTALKLLLRLYDVQEGAVKLDGHDVRDVRLADLRSAVGYVSQDTFLFDGT-IAD 482
                                       79***********************************************************************.999 PP

                                       H................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       n                ++ +++++++s l++ +  dt+v++++ +LSgGq+qr+alar++l +p++l+lDE+t+
  gi|336253429|ref|YP_004596536.1| 483 NirygqfdasdeavreaAKAAQAHEFISGLEDGY--DTRVGERGVKLSGGQRQRIALARTVLDDPEVLILDEATS 555
                                       99******99999998888888999999999888..*************************************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   0.2   4.8e-06    0.0046       8      38 ..     419     470 ..     413     582 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.8e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.....................e 38 
                                       ++++G++G+GK+t l+ ll+ +d ++ a +                      
  gi|336253429|ref|YP_004596536.1| 419 VALVGPTGAGKSTALKLLLRLYDVQEGAVKldghdvrdvrladlrsavgyvS 470
                                       689*******************998877778776554444444444444440 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 ?    2.2   0.0      0.11     1e+02      26      40 ..     418     432 ..     396     437 .. 0.76
   2 !   14.0   0.0   2.7e-05     0.025     105     211 ..     441     597 ..     432     603 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                                       EEEEEESTTSSHHHH CS
                                       xxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnl 40 
                                         a+vGp G+GKs  
  gi|336253429|ref|YP_004596536.1| 418 TVALVGPTGAGKSTA 432
                                       5689*********75 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.7e-05
                                       TTSEEEEEETTEEE-HHHHHHHHHCTT-STT.............................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................. RF
                             SMC_N 105 rkgeseykingkevtkkevsellesagiske.............................................. 135
                                         +e  +k++g++v+   +++l + +g  ++                                              
  gi|336253429|ref|YP_004596536.1| 441 DVQEGAVKLDGHDVRDVRLADLRSAVGYVSQdtflfdgtiadnirygqfdasdeavreaakaaqahefisgledgyd 517
                                       55556677888888888888887777776667888888888888888888888888888888888888888888888 PP

                                       ........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC CS
                                       ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlek 204
                                                LSgG+++ +ala        +   + +lDe  +a D k    + + +++ +++   + i++r  ++++
  gi|336253429|ref|YP_004596536.1| 518 trvgergvKLSGGQRQRIALART----VLDDPEVLILDEATSAVDTKTELLIQRSIDRLTEDRTTLAIAHRLSTVKD 590
                                       888888889******98888754....556666789***************************************** PP

                                       -SCEEEE CS
                                       xxxxxxx RF
                             SMC_N 205 adklvgv 211
                                       ad+++ +
  gi|336253429|ref|YP_004596536.1| 591 ADTILVM 597
                                       *998755 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.2e-06    0.0078      18      56 ..     418     456 ..     405     465 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.2e-06
                        Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56 
                                        + l+G +GAGKs++++ll +  + q+++v+ld+ d+R 
  gi|336253429|ref|YP_004596536.1| 418 TVALVGPTGAGKSTALKLLLRLYDVQEGAVKLDGHDVRD 456
                                       67899******************************9996 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   0.6     1e-05    0.0095      25     156 ..     417     566 ..     405     582 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqllde............ 88 
                                         v l+G+ G GKs+ ++ llr +  ++g + l g+ ++          +++++ ++ +  + ++            
  gi|336253429|ref|YP_004596536.1| 417 DTVALVGPTGAGKSTALKLLLRLYDVQEGAVkLDGHDVRD---------VRLADLRSAVGYVSQDtflfdgtiadni 484
                                       5799******************999998777799999888.........3333333444444444444444444443 PP

                            AAA_16  89 ............aesaeleawrekleeala.....................avpelagaea..srllellkrllall 130
                                                    e+a             +                      + +l    +  +r + +l+r +   
  gi|336253429|ref|YP_004596536.1| 485 rygqfdasdeavREAA-------------KaaqahefisgledgydtrvgeRGVKL----SggQRQRIALARTV--- 541
                                       3333322211122222.............122223344444456666443333333....23366666666666... PP

                            AAA_16 131 srderplvlvlDdlqwadeaslql.la 156
                                          ++p vl+lD++  a ++  +l ++
  gi|336253429|ref|YP_004596536.1| 542 --LDDPEVLILDEATSAVDTKTELlIQ 566
                                       ..3667899999988777777777455 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     2e-05     0.019      87     131 ..     403     448 ..     370     467 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       ++ +e+++ + k  +t++lvG++G+GKSt ++ ll   +++ g+v+
  gi|336253429|ref|YP_004596536.1| 403 ETVIEDVSFEAKPgDTVALVGPTGAGKSTALKLLLRLYDVQEGAVK 448
                                       456788888888779*****************99987777777665 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   1.9e-05     0.018       5      88 ..     419     567 ..     416     577 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.........swedfldevvel............. 59 
                                       ++++Gp g+GK+t +k l     + d+ +G+ +ld++++ d++                    +             
  gi|336253429|ref|YP_004596536.1| 419 VALVGPTGAGKSTALKLL---LRLYDVQEGAVKLDGHDVRDVRladlrsavgY----------Vsqdtflfdgtiad 482
                                       89****************...8899*****************76644444440..........33335556666666 PP

                            AAA_24  60 ........................................................aaeladyktlviDtideleel 80 
                                                                                               ++ l+d ++l++D ++ +++ 
  gi|336253429|ref|YP_004596536.1| 483 nirygqfdasdeavreaakaaqahefisgledgydtrvgergvklsggqrqrialaRTVLDDPEVLILDEATSAVDT 559
                                       666666667777777778888999999999*************************999****************999 PP

                            AAA_24  81 claevirq 88 
                                       +++ +i++
  gi|336253429|ref|YP_004596536.1| 560 KTELLIQR 567
                                       99988876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.5   4.2e+03     101     121 ..     156     176 ..     112     180 .. 0.73
   2 ?   15.1   1.3   1.5e-05     0.014      19     104 ..     417     560 ..     410     579 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.5
                            AAA_30 101 dtkqlaallkaaekagakvil 121
                                       dt++l+++l+ a  ++a++i+
  gi|336253429|ref|YP_004596536.1| 156 DTQNLERFLDNALMNSARLIV 176
                                       788888888888777777654 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.5e-05
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g.........grviglAptgkaAkvLa...................... 63 
                                        +++l+Gp G+GK+talk l ++++ + g         ++ + lA    a   ++                      
  gi|336253429|ref|YP_004596536.1| 417 DTVALVGPTGAGKSTALKLLLRLYDVQeGavkldghdvRD-VRLADLRSAVGYVSqdtflfdgtiadnirygqfdas 492
                                       47899***************99999994576677655322.233444444444443333333333333334333222 PP

                            AAA_30  64 .e..elgieastiakllkrlk........................grarlepgtllivDEagmvdtkq 104
                                        e     ++a+  +++++ l+                        +r+ l++ ++li DEa  +  ++
  gi|336253429|ref|YP_004596536.1| 493 dEavREAAKAAQAHEFISGLEdgydtrvgergvklsggqrqrialARTVLDDPEVLILDEATSAVDTK 560
                                       21112223444444444444488888888888889999999998866778888999999987663333 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 ?   13.6   0.0   4.6e-05     0.044       3      26 ..     420     444 ..     419     462 .. 0.78
   2 ?   -2.2   0.0       2.9   2.7e+03     221     265 ..     509     552 ..     470     571 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.6e-05
                            AAA_21   3 vliGpNgsGKSnLLdaldllarl.d 26 
                                       +l+Gp g+GKS+ L++l  l ++  
  gi|336253429|ref|YP_004596536.1| 420 ALVGPTGAGKSTALKLLLRLYDVqE 444
                                       79***************99987752 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                            AAA_21 221 vvflengdgqelparel..SdGtkrllalltallralkkgsllliDE 265
                                       +  le+g++  +  r +  S G+++ +al+  +l+++    +l++DE
  gi|336253429|ref|YP_004596536.1| 509 ISGLEDGYDTRVGERGVklSGGQRQRIALARTVLDDP---EVLILDE 552
                                       5555555555555555555888888888888888877...8899998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.1     1e+03      52      99 ..     151     197 ..     125     204 .. 0.72
   2 ?   12.9   0.0   0.00013      0.12       1      67 [.     419     509 ..     419     579 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.1
                            AAA_18  52 ldedkldklldaleenssaleegknlvidghlaeleseaakdikkvvL 99 
                                       ++ +++ ++l+ +  n+  + ++  +v+ g +a  +++ ++++  v L
  gi|336253429|ref|YP_004596536.1| 151 AVLNNDTQNLERFLDNAL-MNSARLIVMVGGIAGVLFYLNWQLAVVTL 197
                                       444555666666666665.88889999999999999999999886666 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00013
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf........................gvnlrdvakenglllevdpe.aldeskrl 52 
                                       ++l G+ G+GK+t  k L ++  +                        g++++d++  +g+  ++  + ++d s+++
  gi|336253429|ref|YP_004596536.1| 419 VALVGPTGAGKSTALKLLLRLYDVqegavkldghdvrdvrladlrsavGYVSQDTFLFDGTIADNIRYgQFDASDEA 495
                                       6899**************66633366666778777777777777777777777777777777777777777777777 PP

                            AAA_18  53 dedkldklldaleen 67 
                                       +++  +k+ +a+e +
  gi|336253429|ref|YP_004596536.1| 496 VREA-AKAAQAHEFI 509
                                       7776.5555555555 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 ?   13.6   0.0   4.5e-05     0.042      14      39 ..     408     433 ..     400     438 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.5e-05
                            AAA_29  14 ghtieidlkgatlltGpsGsGKSTll 39 
                                       + ++e ++ +++ l+Gp+G+GKST l
  gi|336253429|ref|YP_004596536.1| 408 DVSFEAKPGDTVALVGPTGAGKSTAL 433
                                       46778888889*************76 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   0.0   0.00069      0.65       2      74 ..     420     560 ..     419     600 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00069
                                       EEESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSS....................................... CS
                               AAA   2 llyGppGtGKTllakavakelgve..fleisgsellsk....................................... 37 
                                        l+Gp G GK+++ k + +  +v+   ++++g+++++                                        
  gi|336253429|ref|YP_004596536.1| 420 ALVGPTGAGKSTALKLLLRLYDVQegAVKLDGHDVRDVrladlrsavgyvsqdtflfdgtiadnirygqfdasdeav 496
                                       699****************9865544677777777755677777778888888888888888888888777777777 PP

                                       ...........................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH CS
                               AAA  38 ...........................yvgesekkirelfkeakeka.kpsilfiDEidalaksr 74 
                                                                   v+  +   r+ ++ a++   +p +l++DE+ + + ++
  gi|336253429|ref|YP_004596536.1| 497 reaakaaqahefisgledgydtrvgerGVK-LSGGQRQRIALARTVLdDPEVLILDEATSAVDTK 560
                                       777777777777777777777744433111.1222233333344444567777777777776666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0032         3       2      45 ..     419     464 ..     418     474 .. 0.78
   2 ?    2.7   0.1      0.11   1.1e+02      65     144 ..     514     594 ..     497     609 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0032
                                       EEEE--TTSSHHHHHHHHHHH..H...GGGEEEEEEEEE------- CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlel..lkssgvkvgGfyteevreggrri 45 
                                       v++ Gp G GK+T +k +l+l  +++  vk++G  +++vr  + r+
  gi|336253429|ref|YP_004596536.1| 419 VALVGPTGAGKSTALKLLLRLydVQEGAVKLDGHDVRDVRLADLRS 464
                                       7899************999872245557999999999998666555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.11
                                       ---SSEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE---S.TTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHH CS
                          NTPase_1  65 akreprvgkyvvdvesfeelalealrkalseadviviDEiG.kmElkskkfkeaveevLksekpvlavihrrkdlal 140
                                       +    rvg+  v++   ++  ++  r+ l +++v+++DE       k++ +++   + L++++  la+ hr ++ + 
  gi|336253429|ref|YP_004596536.1| 514 DGYDTRVGERGVKLSGGQRQRIALARTVLDDPEVLILDEATsAVDTKTELLIQRSIDRLTEDRTTLAIAHRLSTVKD 590
                                       5667899********99999999999999**********74156777777776666666777777777777665555 PP

                                       HHHH CS
                          NTPase_1 141 veei 144
                                        ++i
  gi|336253429|ref|YP_004596536.1| 591 ADTI 594
                                       5555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00051      0.48       2      37 ..     419     459 ..     419     505 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00051
                            AAA_33   2 vllvGlpGsGKstlaerllkklg....avllssdtlrr.rl 37 
                                       v lvG+ G+GKst ++ ll+  +    av l+  ++r+ rl
  gi|336253429|ref|YP_004596536.1| 419 VALVGPTGAGKSTALKLLLRLYDvqegAVKLDGHDVRDvRL 459
                                       569*************9986444545577777777665444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00032       0.3      20      37 ..     417     434 ..     399     466 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                            AAA_23  20 gltlItGpNGaGKTTild 37 
                                         ++++Gp+GaGK+T l 
  gi|336253429|ref|YP_004596536.1| 417 DTVALVGPTGAGKSTALK 434
                                       47799**********986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00079      0.74       2      21 ..     419     438 ..     418     463 .. 0.86
   2 ?   -1.3   0.0       2.4   2.3e+03      65      86 ..     580     600 ..     535     622 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00079
                                       EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                       va+vG + +GKSt ++ l++
  gi|336253429|ref|YP_004596536.1| 419 VALVGPTGAGKSTALKLLLR 438
                                       9**************99986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHCTSEEEEEEETT CS
                          MMR_HSR1  65 glgkaflaleeadlillvvdas 86 
                                        +++++  +++ad il++ d  
  gi|336253429|ref|YP_004596536.1| 580 AIAHRLSTVKDADTILVMAD-G 600
                                       45556666777999999998.3 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3     0.017        16       2      19 ..     419     436 ..     418     443 .. 0.90
   2 ?    4.8   0.1     0.033        31      62     104 ..     457     503 ..     446     510 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.017
                            AAA_28   2 ivitGgestGKTtlleaL 19 
                                       ++++G+ ++GK+t l+ L
  gi|336253429|ref|YP_004596536.1| 419 VALVGPTGAGKSTALKLL 436
                                       89************9988 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.033
                            AAA_28  62 eqleeeaaa...aankvlfcDrglldtlaYaraygge.aeaeleaaa 104
                                        +l+++++a    +++++++D  + d++ Y +++  + a +e  +aa
  gi|336253429|ref|YP_004596536.1| 457 VRLADLRSAvgyVSQDTFLFDGTIADNIRYGQFDASDeAVREAAKAA 503
                                       566677777776799******************98882223333333 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.6    0.0037       3.5      13     149 ..     415     572 ..     402     587 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0037
                                       TTCEEEEEESTTSSHHHHHHHHHHHHHHHS................TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  13 gggdvlvaaeTGsGKTlaflipvlqivyet................kgktgpkalivePtreLaeqtlnnlkkfkky 73 
                                        g+ v + ++TG+GK++a  + +  ++y+                   + +  + +v+  + L   t+ +  +++++
  gi|336253429|ref|YP_004596536.1| 415 PGDTVALVGPTGAGKSTALKLLL--RLYDVqegavkldghdvrdvrLADLRSAVGYVSQDTFLFDGTIADNIRYGQF 489
                                       56778889999999999854433..3544333455544444444422222255556666777777777777777774 PP

                                       ..STSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH.....CTTEEEEEEETHHHHHHTTTHHHHH CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  74 ..idlrvlliiggvaardqlskldngvdivvgtpgrlddllstgkln.....lsqvrflVlDEadrlldqgfsdfin 143
                                          d  v    +  +a++ +s l+ g+d  vg  g  ++  +++++      l++ ++l+lDEa    d + +  i+
  gi|336253429|ref|YP_004596536.1| 490 daSDEAVREAAKAAQAHEFISGLEDGYDTRVGERGVKLSGGQRQRIAlartvLDDPEVLILDEATSAVDTKTELLIQ 566
                                       32222222334455566666666777888888777766666555544334447777889999998888888888888 PP

                                       HHHHHS CS
                                       xxxxxx RF
                              DEAD 144 rilnql 149
                                       r + +l
  gi|336253429|ref|YP_004596536.1| 567 RSIDRL 572
                                       877777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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):              19  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.44
# Mc/sec: 4338.80
//
Query:       gi|336253430|ref|YP_004596537.1|  [L=387]
Description: sodium/calcium exchanger membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-23   80.8  40.1    1.6e-17   63.9  12.8    2.1  2  Na_Ca_ex  Sodium/calcium exchanger protein
  ------ inclusion threshold ------
      0.038   13.8   1.8      0.081   12.7   1.8    1.6  1  Git3      G protein-coupled glucose receptor regulating Gpa2


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2  19.3     6e-09   5.3e-05       4     148 ..      13     145 ..      10     148 .. 0.83
   2 !   63.9  12.8   1.8e-21   1.6e-17       4     150 ..     247     385 ..     244     386 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6e-09
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnll 80 
                                       ++f+++++l++++ +++++++++ a slgisg +l++ +lA g  l   ++ ++aa+   +dla+g+v+G  +f+l 
  gi|336253430|ref|YP_004596537.1|  13 AAFLVGVVLVIWCVEVFIEAVAQSAVSLGISGFFLAV-ILA-GIDLENAALGVTAAVVALPDLALGTVFGESLFVLA 87 
                                       579**********************************.555.678999*********9******************* PP

                                       THHHHHHHHHHBTTSSCECCHHH.HHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  81 lviGlialigslkvdseslkldl.gllllvallllllvlllllplfvpgrltvleglvllllYalylvl 148
                                       + +Gl++++ +       +++d+ ++ l ++ll+ l +++ +   ++ g+++   g++ll++++  l +
  gi|336253430|ref|YP_004596537.1|  88 VALGLAGVFVP-------FEMDVpRAYLAMLLLVPLPAFA-M---SLGGTIDAAYGAALLAAFVPLLGY 145
                                       *********55.......7788855544445555444444.4...234999999999999999866655 PP

  == domain 2  score: 63.9 bits;  conditional E-value: 1.8e-21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnll 80 
                                       ++ +l+++++ +++++ v sae +   +gisg  +G t+l++  s+ El++++  +++g ++la+gnv+Gs +f ++
  gi|336253430|ref|YP_004596537.1| 247 GVAVLATVGMTLGSFITVGSAERLFVAFGISGLAFGATVLSFIASIEELALTLEPVRQGRPHLAVGNVVGSTVFYMT 323
                                       567899999******************************************************************** PP

                                       THHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  81 lviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                         +Glial+ ++   +  +++++  ++ ++ll+  ++++l      + r+t+  g++ll+lYa y v+++
  gi|336253430|ref|YP_004596537.1| 324 ANVGLIALLHPVDTGGAVMTVHW-PFFGACLLV--ATAMLA-----RSRVTRAGGVLLLALYAGYWVFNY 385
                                       *********99888888888888.545555555..444444.....39*******************987 PP

>> Git3  G protein-coupled glucose receptor regulating Gpa2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.8   9.1e-06     0.081      40     101 ..       6      66 ..       3     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.1e-06
                              Git3  40 LillLilvdllkalvlliypvkvlvenkvyassafcqvvGfflavaiegsdlailllavhta 101
                                       L l+L+ + +l  +vl+i++v v++ + v++s     ++Gfflav   g dl   +l v  a
  gi|336253430|ref|YP_004596537.1|   6 LELALFGAAFLVGVVLVIWCVEVFI-EAVAQSAVSLGISGFFLAVILAGIDLENAALGVTAA 66 
                                       567899999999*************.6788888899*************9997777666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); 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:                         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: 0.52u 0.20s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3001.21
//
Query:       gi|336253431|ref|YP_004596538.1|  [L=47]
Description: hypothetical protein Halxa_2034 [Halopiger xanaduensis SH-6]
Scores for 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   3.0       0.27   11.5   3.0    1.1  1  DUF4064   Protein of unknown function (DUF4064)
       0.24   11.7   7.7       0.81   10.1   7.8    1.7  1  DUF308    Short repeat of unknown function (DUF308)
       0.96    9.4   7.4        1.2    9.1   0.1    2.1  2  DUF3311   Protein of unknown function (DUF3311)


Domain annotation for each model (and alignments):
>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.0   4.5e-05      0.27      62     102 ..       5      44 ..       2      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                           DUF4064  62 ivlgvialiaivlgivgalllkknkkvsGilfiiaailslf 102
                                       ++lg+ +l +++++++  +l   ++  +G+lf++ ++ +l+
  gi|336253431|ref|YP_004596538.1|   5 TTLGWSLLSSGIVTLILKVLPG-DSLWWGVLFLVLGVTLLI 44 
                                       6778888888888888888887.999***********9987 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 ?   10.1   7.8   0.00014      0.81      26      72 ..       5      43 ..       1      45 [. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00014
                            DUF308 26 llfGilllvsGivqiiaafaarkknrggrwlglllGilyliaGllll 72
                                      + +G+ ll sGiv +i  +      + + w     G+l+l++G+ ll
  gi|336253431|ref|YP_004596538.1|  5 TTLGWSLLSSGIVTLILKV----LPGDSLW----WGVLFLVLGVTLL 43
                                      679************9555....6788888....5667777777776 PP

>> DUF3311  Protein of unknown function (DUF3311)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0002       1.2      34      54 ..       6      26 ..       5      29 .. 0.87
   2 ?    3.2   3.1     0.015        88      31      45 ..      29      43 ..      28      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0002
                           DUF3311 34 qllwvllasvvtwlayrlakr 54
                                      +l+w ll+s + +l+ ++ ++
  gi|336253431|ref|YP_004596538.1|  6 TLGWSLLSSGIVTLILKVLPG 26
                                      699***********9998765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.015
                           DUF3311 31 ywwqllwvllasvvt 45
                                      +ww +l ++l+ +++
  gi|336253431|ref|YP_004596538.1| 29 LWWGVLFLVLGVTLL 43
                                      8*********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 396.60
//
Query:       gi|336253432|ref|YP_004596539.1|  [L=129]
Description: transcriptional regulator NikR [Halopiger xanaduensis SH-6]
Scores for 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   72.4   0.6    3.7e-20   71.9   0.2    1.4  2  NikR_C    NikR C terminal nickel binding domain
     0.0026   17.6   0.1     0.0041   17.0   0.1    1.3  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 ?   -3.1   0.0         1     9e+03      51      62 ..      30      41 ..      25      48 .. 0.49
   2 !   71.9   0.2   4.1e-24   3.7e-20       5      76 ..      55     125 ..      53     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1
                                      E-HHHHHHHHHH CS
                            NikR_C 51 Geaeeikelaek 62
                                      G  e ++e +e+
  gi|336253432|ref|YP_004596539.1| 30 GVREAMREYVEA 41
                                      333444444443 PP

  == domain 2  score: 71.9 bits;  conditional E-value: 4.1e-24
                                       EEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEE CS
                            NikR_C   5 tivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltl 76 
                                       ++ +d++++ + e+l+diqhe++d++++++h h + ++cLe+++++G ae+i+++a +lr  + V++vkl l
  gi|336253432|ref|YP_004596539.1|  55 IVAFDYDHESVIEDLHDIQHEFQDVVTTTTHTH-EGEWCLETVFCRGAAERIRTFAYRLRDFDAVRRVKLLL 125
                                       57788888*************************.***********************************976 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 !   17.0   0.1   4.6e-07    0.0041       1      38 [.       2      40 ..       2      41 .. 0.97

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.6e-07
                                      EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                      r+s+ ++++ll r+d +  ++g  SrS  +ReA rey+e
  gi|336253432|ref|YP_004596539.1|  2 RTSLNVPDDLLSRFDDIWQEQGlESRSRGVREAMREYVE 40
                                      899**********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 1094.33
//
Query:       gi|336253433|ref|YP_004596540.1|  [L=147]
Description: transcriptional regulator NikR [Halopiger xanaduensis SH-6]
Scores for complete 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-21   76.0   0.4    2.6e-21   75.6   0.4    1.2  1  NikR_C           NikR C terminal nickel binding domain
    8.3e-07   28.7   0.1    1.5e-06   27.9   0.1    1.5  1  RHH_1            Ribbon-helix-helix protein, copG family
     0.0024   18.0   0.0      0.004   17.3   0.0    1.4  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
       0.13   12.5   0.0       0.26   11.5   0.0    1.6  1  RHH_8            Ribbon-Helix-Helix transcriptional regulator


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 !   75.6   0.4   5.8e-25   2.6e-21       2      76 ..      59     133 ..      58     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 5.8e-25
                                       EEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEE CS
                            NikR_C   2 GvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltl 76 
                                       +++t+vyd+ ++ +++rlt+++he++ l++ ++h h+d+++cLev+vl G+++ i  +++ +r++  V++v++++
  gi|336253433|ref|YP_004596540.1|  59 CTVTVVYDYCETAVQRRLTELRHEHDSLVTGTTHAHVDDRYCLEVFVLVGPVDAIGGFVHTVRSVPAVRRVDYSI 133
                                       69*********************************************************************9986 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 !   27.9   0.1   3.4e-10   1.5e-06       2      39 .]       4      42 ..       3      42 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.4e-10
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyler 39
                                      vs++++e ll+r+d+ a + g + rSe++ReA+r +le+
  gi|336253433|ref|YP_004596540.1|  4 VSVSMPETLLDRIDRFASDHGySGRSEVLREAARGLLEE 42
                                      9***********************************985 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   8.9e-07     0.004      92     123 .]       4      36 ..       1      36 [. 0.90

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.9e-07
                   HicB_lk_antitox  92 iNitlpervlkriDaavkaag.esRSgflakaa 123
                                       + +++pe++l+riD++++++g + RS  l +aa
  gi|336253433|ref|YP_004596540.1|   4 VSVSMPETLLDRIDRFASDHGySGRSEVLREAA 36 
                                       789******************558***999886 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 ?   11.5   0.0   5.9e-05      0.26       7      51 ..       5      49 ..       2      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.9e-05
                             RHH_8  7 tinlgvvDLgqiDlLveeGfYsnRtDlirtairaqLakhddalkq 51
                                      ++ +    L +iD    +  Ys R++++r+a r  L++ d a ++
  gi|336253433|ref|YP_004596540.1|  5 SVSMPETLLDRIDRFASDHGYSGRSEVLREAARGLLEEFDAADRN 49
                                      56666667899**9999999****************988765443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1106.90
//
Query:       gi|336253434|ref|YP_004596541.1|  [L=405]
Description: cobalamin synthesis protein P47K [Halopiger xanaduensis SH-6]
Scores for 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-49  166.1   0.0      7e-49  165.8   0.0    1.1  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
    6.7e-25   86.8   0.1    1.6e-24   85.6   0.1    1.7  1  CobW_C         Cobalamin synthesis protein cobW C-terminal do
      0.001   18.7   0.0       0.37   10.3   0.0    2.1  2  GTP_EFTU       Elongation factor Tu GTP binding domain
     0.0097   15.8   0.1        1.6    8.6   0.0    2.3  2  RsgA_GTPase    RsgA GTPase
  ------ inclusion threshold ------
      0.015   14.4   0.1      0.024   13.7   0.1    1.2  1  T2SSE          Type II/IV secretion system protein
      0.016   14.5   0.0      0.026   13.8   0.0    1.3  1  Zeta_toxin     Zeta toxin
      0.017   14.1   0.0      0.025   13.5   0.0    1.1  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.044   14.2   0.0      0.092   13.1   0.0    1.6  1  AAA_16         AAA ATPase domain
      0.067   13.4   0.0       0.21   11.8   0.0    1.9  2  AAA_28         AAA domain
       0.11   12.2   0.0       0.19   11.4   0.0    1.3  1  AAA_30         AAA domain
       0.14   12.1   0.0       0.27   11.2   0.0    1.4  1  TsaE           Threonylcarbamoyl adenosine biosynthesis prote


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 !  165.8   0.0   4.3e-52     7e-49       1     176 [.       9     212 ..       9     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: 165.8 bits;  conditional E-value: 4.3e-52
                                       EEEEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCCCT.......EEEETTTTECCHCTT-HHH CS
                              cobW   1 pvtvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellretgve......ivelenGciCctlredllk 71 
                                       pvt+l+G+lG+GKTt lnh+l+  ++l+ av+vN++gev++Da+l++++++       i+el+nGciCc lr d+l 
  gi|336253434|ref|YP_004596541.1|   9 PVTILSGSLGAGKTTTLNHVLNADRELNAAVVVNDMGEVNVDADLVERESALsqadedIIELSNGCICCRLRGDMLD 85 
                                       79********************************************777555566777******************* PP

                                       HHHHHHHHHTT-SEEEEEECTTTTHHHH..HTT......SHHHHHCCCECEEEEEEETTTH................ CS
                              cobW  72 elealeereerldviliEttGlaePapv..aft......eeelksdltldavvavvDaknl................ 124
                                       +l +l++r+ ++d++l+E++G++eP pv  +f       + + +  ++ld++v vvDa  +                
  gi|336253434|ref|YP_004596541.1|  86 QLGRLADRR-DFDYLLVEASGISEPIPVaqTFVrgfedaTFDPTGVYELDTMVSVVDAYSFwqgfdsgrtlmddsid 161
                                       *********.9*****************7655589975444556699***********999*************995 PP

                                       .CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHHTTS-EE CS
                              cobW 125 eaeeekieekaedqlaaadllvlnKtDlldeeallekleerlrqlnpeakvl 176
                                        + ++  e  + dq++++d+l+lnK+Dl+++++l e++e+++++l+p+a+++
  gi|336253434|ref|YP_004596541.1| 162 PQGNRVPEAVLLDQIEFCDVLLLNKCDLVPDDRL-EEMEAVISALQPRAEIV 212
                                       445555566789********************76.**************997 PP

>> CobW_C  Cobalamin synthesis protein cobW C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.6   0.1     1e-27   1.6e-24       1      94 []     260     375 ..     260     375 .. 0.99

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 1e-27
                            CobW_C   1 issfvfrarrpfdperleelleeelpegilRaKGivwlagkpd.alvlqgvggrlrlepagawwaa........... 65 
                                       ++sfvf a+rpf+p+r+++ l++ lp+g++RaKG++w ag++d a+ l+ +g+++r +p g+w a+           
  gi|336253434|ref|YP_004596541.1| 260 VTSFVFDADRPFHPARIADSLSD-LPDGVIRAKGFFWSAGREDvAMGLDKAGQSVRAGPSGTWLATlpeeqreqyfa 335
                                       589********************.***************************************************** PP

                            CobW_C  66 ...........ededrrseLVfIGrdldkealeeaLdacl 94 
                                                  e++dr+ eLVfIGr++d++al ++L+ cl
  gi|336253434|ref|YP_004596541.1| 336 arpgieedwdeEWGDRGIELVFIGREFDRDALVDRLEGCL 375
                                       ***************************************7 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 !    6.4   0.0    0.0035       5.7       7      54 ..      12      60 ..       6      69 .. 0.79
   2 !   10.3   0.0   0.00023      0.37      90     153 ..     129     208 ..     126     301 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0035
                                      EEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHH.HSTHCHSHHHHHHTS CS
                          GTP_EFTU  7 giighvDhGKtTLtdrLlyktgaiskkgekaee.ervlDtlkeErergi 54
                                      ++ g + +GKtT++ ++l +  + + +  +++  e  +D    Ere  +
  gi|336253434|ref|YP_004596541.1| 12 ILSGSLGAGKTTTLNHVLNADRELNAAVVVNDMgEVNVDADLVERESAL 60
                                      5678999***********9999999988887443777888888888765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00023
                                       HHHT-SEEEEEEETT..............TBSTHHHHHHHHHHHHTTTE..EEEEEESCGST.HHHHHHHHHHHHHH CS
                          GTP_EFTU  90 glrvlDgavlvvdav..............eGvepqteevlrlalkegvp..iivfiNKmDrl.kaelkeiveevkqk 149
                                       g+  lD +v vvda               + + pq ++v + +l  +++   ++++NK+D + +++l+e+   ++  
  gi|336253434|ref|YP_004596541.1| 129 GVYELDTMVSVVDAYsfwqgfdsgrtlmdDSIDPQGNRVPEAVLLDQIEfcDVLLLNKCDLVpDDRLEEMEAVIS-A 204
                                       67788999999999988866665544444449*******99999999998789*********7555555544444.5 PP

                                       HHHH CS
                          GTP_EFTU 150 lsrk 153
                                       l+ +
  gi|336253434|ref|YP_004596541.1| 205 LQPR 208
                                       5443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0     0.001       1.6     101     123 ..      10      32 ..       4      48 .. 0.79
   2 ?    4.7   0.0     0.016        26      50      83 ..     181     213 ..     171     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                                       EEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpel 123
                                       +++l G+ G+GK+t +n++l+ +
  gi|336253434|ref|YP_004596541.1|  10 VTILSGSLGAGKTTTLNHVLNAD 32 
                                       799**************998753 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.016
                                       EEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE-- CS
                       RsgA_GTPase  50 vivlnKiDlleeeeeleelkeelealgyevllvs 83 
                                       v++lnK+Dl+ +++ lee+++ ++al+ +  +v+
  gi|336253434|ref|YP_004596541.1| 181 VLLLNKCDLVPDDR-LEEMEAVISALQPRAEIVR 213
                                       899**********9.9999998888876666655 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 ?   13.7   0.1   1.5e-05     0.024     133     174 ..      12      52 ..       8      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                             T2SSE 133 lvsGgTgsGKttllyallkeinksderivtvEDpvEiqlega 174
                                       ++sG  g GKtt+l+ +l+   +  +  v+v D  E++++++
  gi|336253434|ref|YP_004596541.1|  12 ILSGSLGAGKTTTLNHVLNADREL-NAAVVVNDMGEVNVDAD 52 
                                       89****************988887.888999**999998765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.6e-05     0.026      18      52 ..      10      43 ..       1      44 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpD 52
                                      + +l+G+ GAGK+++++ + ++  r+ n+ ++  D
  gi|336253434|ref|YP_004596541.1| 10 VTILSGSLGAGKTTTLNHVLNAD-RELNAAVVVND 43
                                      5699***************9995.56666666555 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 ?   13.5   0.0   1.6e-05     0.025      18      51 ..      11      44 ..       7      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                     TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairargdraivlDl 51
                                      +++ G+ G+GKt++l++ l+a r+ +  ++v D+
  gi|336253434|ref|YP_004596541.1| 11 TILSGSLGAGKTTTLNHVLNADRELNAAVVVNDM 44
                                      6899********************9999999996 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   5.7e-05     0.092      19      57 ..       2      42 ..       1     104 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-05
                            AAA_16 19 vrsgrp.elvllsGesGvGKsslvrellralekd.g.giflr 57
                                      v+s++p ++++lsG  G GK++ ++++l+ + ++ + +++++
  gi|336253434|ref|YP_004596541.1|  2 VSSDTPiPVTILSGSLGAGKTTTLNHVLN-ADRElNaAVVVN 42
                                      67788899********************5.555533233333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.21       3      60 ..      12      75 ..      10     100 .. 0.83
   2 ?   -2.7   0.0       3.7   6.1e+03     124     155 ..     327     358 ..     320     361 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                            AAA_28  3 vitGgestGKTtlleaLaar....gyp.vvpEaareileeklakgedalpwv.edllafaervl 60
                                      +++G  ++GKTt+l++  +     +   vv +++   ++  l ++e al ++ ed++++  +++
  gi|336253434|ref|YP_004596541.1| 12 ILSGSLGAGKTTTLNHVLNAdrelNAAvVVNDMGEVNVDADLVERESALSQAdEDIIELSNGCI 75
                                      689************988544677544266***9999999999999999999899999887765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                            AAA_28 124 dgeRredleereaiderlrealrelgipviiv 155
                                        ++R++ +++r  i+e   e + ++gi+++ +
  gi|336253434|ref|YP_004596541.1| 327 EEQREQYFAARPGIEEDWDEEWGDRGIELVFI 358
                                       56677777778888888888888888887776 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   0.00012      0.19      20      50 ..      10      40 ..       5      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvi 50
                                      v++l G  G+GKtt+l+++ +a ++ +  v+
  gi|336253434|ref|YP_004596541.1| 10 VTILSGSLGAGKTTTLNHVLNADRELNAAVV 40
                                      7899***************999998877766 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017      0.27      21      41 ..      10      30 ..       3      40 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                                      EEEEEESTTSSHHHHHHHHHH CS
                              TsaE 21 vilLeGdLGaGKTtlvrglak 41
                                      v +L+G LGaGKTt   ++++
  gi|336253434|ref|YP_004596541.1| 10 VTILSGSLGAGKTTTLNHVLN 30
                                      568***********9888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2856.92
//
Query:       gi|336253435|ref|YP_004596542.1|  [L=368]
Description: metal ion ABC transporter periplasmic protein [Halopiger xanaduensis SH-6]
Scores for complete 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-53  182.1   0.0    1.5e-53  181.8   0.0    1.0  1  ZnuA      Zinc-uptake complex component A periplasmic


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.8   0.0   8.5e-58   1.5e-53       3     255 ..      48     364 ..      47     365 .. 0.84

  Alignments for each domain:
  == domain 1  score: 181.8 bits;  conditional E-value: 8.5e-58
                                       ESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTT.CCCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                              ZnuA   3 attsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssq.atrvevi 78 
                                       a++++ gd++++vaGd ++ ++Lvp g+  H +ep p+   ++ e+dl+v++  ++++w d+l++s+ + ++ v+++
  gi|336253435|ref|YP_004596542.1|  48 ASFFVFGDFAAAVAGDTARAETLVPIGQHGHGWEPGPQIQGTVLESDLFVSVVHGFQPWADDLVTSLRDdDAAVHIV 124
                                       89**************************************************************9996523444666 PP

                                       ETTTTC........................CSEBCSS.....................................EST CS
                                       xxxxxx........................xxxxxxx.....................................xxx RF
                              ZnuA  79 dlsegv........................eeeeeee.....................................DpH 94 
                                        ++  v                        e     e                                     DpH
  gi|336253435|ref|YP_004596542.1| 125 AAGAEVdllesegghdyghddgdghdhgndE-----EhdheeggehnrsedgddhdhehngsddgdhehdrgtaDPH 196
                                       4332112222222223333333333444331.....023355667777777777777889999999999******** PP

                                       GGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSGTEGEEEESSSTTHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA  95 iWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireelaeipeekrklvtthdafgylarayg 171
                                       +Wl+p +a+  v++i+d+++ +d +nad+y+ana+++  +L++ld+ +r++l++++++  +lv  hd+f+yl+++yg
  gi|336253435|ref|YP_004596542.1| 197 FWLDPVRAKRAVDAIEDGFATVDSDNADAYAANADEFRSRLDDLDETFRSTLEDAERD-VVLVAGHDPFAYLENRYG 272
                                       *****************************************************99966.5***************** PP

                                       -EEEEEESSSSS....HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHHHHT.-EEEEE-STSSSTSTT.S.TTS CS
                                       xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.x.xxx RF
                              ZnuA 172 levagiagiste....aaqiaalieeikeagvkaifveplaspklaetlaeeag.vkvatlysldslgdeg.s.aet 241
                                       +e+ ++ g++++    +a+i++ ++ i+e +++++ ++pl+++++ae+l++e+   +v++l ++ + ++e  + +  
  gi|336253435|ref|YP_004596542.1| 273 FEIETLTGLTPDeqptPADIERAQTVIDEYDLEYVCADPLEPQDAAEQLIAETDaNEVLPLTPIAGQTQEWaDeGWG 349
                                       *****************************************************6378******9998777434578* PP

                                       HHHHHHH.HHHHHHH CS
                                       xxxxxxx.xxxxxxx RF
                              ZnuA 242 Yidmmra.nleslke 255
                                       Y+++m++ nl +l++
  gi|336253435|ref|YP_004596542.1| 350 YVEIMEEiNLATLER 364
                                       *****9867877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2574.03
//
Query:       gi|336253436|ref|YP_004596543.1|  [L=80]
Description: hypothetical protein Halxa_2039 [Halopiger xanaduensis SH-6]
Scores for 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:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 636.79
//
Query:       gi|336253437|ref|YP_004596544.1|  [L=258]
Description: phosphonate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-32  111.5   0.0    5.9e-32  111.0   0.0    1.2  1  ABC_tran     ABC transporter
    9.3e-11   42.1   0.0    3.5e-06   27.1   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00016   22.2   0.0    0.00025   21.6   0.0    1.2  1  AAA_23       AAA domain
    0.00024   20.6   0.0      0.021   14.3   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00074   19.3   0.0     0.0011   18.8   0.0    1.2  1  AAA_15       AAA ATPase domain
    0.00082   19.1   0.0     0.0015   18.2   0.0    1.3  1  AAA_29       P-loop containing region of AAA domain
     0.0069   16.6   0.6       0.15   12.3   0.6    2.4  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
     0.0081   16.6   0.2      0.018   15.4   0.2    1.7  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.021   15.0   0.2      0.096   12.9   0.2    2.2  1  AAA_33       AAA domain
      0.035   14.4   0.1       0.16   12.2   0.0    1.9  2  AAA_22       AAA domain
      0.062   13.2   0.0       0.16   11.9   0.0    1.6  2  NTPase_1     NTPase
       0.12   11.9   0.1       0.21   11.2   0.1    1.3  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.15   12.1   0.0       0.23   11.5   0.0    1.3  1  Dynamin_N    Dynamin family
       0.19   11.6   0.0       0.39   10.6   0.0    1.5  1  RsgA_GTPase  RsgA GTPase


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 !  111.0   0.0   4.6e-35   5.9e-32       1     136 [.      32     179 ..      32     180 .. 0.92

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 4.6e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS...--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe...pqlfpel 74 
                                       l++vs+++++g+ +++vG+nG+GKStLl+ll+gl +p+eG+++l g++ +      +  +ig++pq+   +     +
  gi|336253437|ref|YP_004596544.1|  32 LEDVSIDVEPGTFLGLVGPNGSGKSTLLELLLGLRRPDEGTVQLFGEPAHA---FAAGDRIGYVPQDvttAAREMPM 105
                                       689*********************************************999...899**********7442223334 PP

                                       BHHHH................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       tvre                 ++++ +++a+ ++g+++l+ +++      LSgGq+qrv +aral+++++ll lDEp
  gi|336253437|ref|YP_004596544.1| 106 TVREVvamgryphrlvgrfsrTDRRAVDEAMVRVGIDDLASRRI----GRLSGGQRQRVFIARALASEADLLALDEP 178
                                       58888************999777777******************....***************************** PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                       t
  gi|336253437|ref|YP_004596544.1| 179 T 179
                                       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 !   27.1   0.0   2.7e-09   3.5e-06       2      24 ..      45      67 ..      44      94 .. 0.80
   2 !   13.2   0.0   4.5e-05     0.057     220     290 ..     135     202 ..     110     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.7e-09
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                       +l+GpNgsGKS+LL++l +l+r
  gi|336253437|ref|YP_004596544.1| 45 LGLVGPNGSGKSTLLELLLGLRR 67
                                      68******************986 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.5e-05
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrnga 290
                                        +v +  +d   + +  lS G+++  +++ al++ +   +ll++DEp  g + +  + +++ll+el++ g 
  gi|336253437|ref|YP_004596544.1| 135 AMVRVGIDDLASRRIGRLSGGQRQRVFIARALASEA---DLLALDEPTVGVDAESREAFYDLLSELNAAGM 202
                                       677777777777888999****99989999999888...9***********************88877555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0     2e-07   0.00025      11      39 ..      33      62 ..      26      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2e-07
                            AAA_23 11 rdqeidFskgltl.ItGpNGaGKTTildAi 39
                                      +d++id ++g +l ++GpNG+GK+T+l+ +
  gi|336253437|ref|YP_004596544.1| 33 EDVSIDVEPGTFLgLVGPNGSGKSTLLELL 62
                                      7899*****98866*************976 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 !   14.3   0.0   1.6e-05     0.021      25      44 ..      43      62 ..      32      69 .. 0.77
   2 ?    4.4   0.0     0.017        22     136     191 ..     151     202 ..      91     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                       f  +vGpNGSGKs ll+ +
  gi|336253437|ref|YP_004596544.1| 43 TFLGLVGPNGSGKSTLLELL 62
                                      47789**********99855 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.017
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQ 191
                                        LSgG+++ v +a  +A    + a l  lDe     D++ ++++ +ll e +    
  gi|336253437|ref|YP_004596544.1| 151 RLSGGQRQRVFIARALA----SEADLLALDEPTVGVDAESREAFYDLLSELNAAGM 202
                                       79*****9888877766....5678999****************999999886543 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   8.7e-07    0.0011      14      43 ..      32      62 ..      31      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.7e-07
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsileal 43
                                      l+dv+id+++  +  l+G+N+sGKS++le+l
  gi|336253437|ref|YP_004596544.1| 32 LEDVSIDVEPGtFLGLVGPNGSGKSTLLELL 62
                                      68999**999878889*************99 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 !   18.2   0.0   1.2e-06    0.0015      16      39 ..      36      59 ..      31      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                      +i++++  +  l+Gp+GsGKSTll
  gi|336253437|ref|YP_004596544.1| 36 SIDVEPGTFLGLVGPNGSGKSTLL 59
                                      566666667779***********9 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 !   12.3   0.6   0.00012      0.15      26      88 ..     145     194 ..     126     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                        sr++g+lSGG++q ++   +a ala   s+        +l++LDE   ++D+es+++  +ll
  gi|336253437|ref|YP_004596544.1| 145 ASRRIGRLSGGQRQRVF---IARALA---SE-------ADLLALDEPTVGVDAESREAFYDLL 194
                                       68999********6654...333332...33.......3689999999999999999988887 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   0.2   1.4e-05     0.018      25      88 ..      43      95 ..      31     207 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekd.ggif.lrgkcdqlesaipysalaqalareellrqllde 88
                                        + l+G+ G+GKs+l++ ll  l++  +g + l g+  +             +a+ + +  + ++
  gi|336253437|ref|YP_004596544.1| 43 TFLGLVGPNGSGKSTLLELLLG-LRRPdEGTVqLFGEPAHA------------FAAGDRIGYVPQD 95
                                      56679***************95.555523444333333333............3233344444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   7.5e-05     0.096       4      20 ..      47      63 ..      45     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                            AAA_33  4 lvGlpGsGKstlaerll 20
                                      lvG++GsGKstl+e ll
  gi|336253437|ref|YP_004596544.1| 47 LVGPNGSGKSTLLELLL 63
                                      79***********9886 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   0.00013      0.16       5      27 ..      42      64 ..      38     101 .. 0.87
   2 ?   -0.4   0.0         1   1.3e+03      87     128 ..     167     207 ..     139     211 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            AAA_22  5 agilvvtGesGtGKTtllrrlle 27
                                       ++l ++G+ G+GK+tll+ ll 
  gi|336253437|ref|YP_004596544.1| 42 GTFLGLVGPNGSGKSTLLELLLG 64
                                      578889************99875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1
                            AAA_22  87 raravielliiDEaqh.lr..seealeeLrsllnlsrkgvqliLv 128
                                        + a+  ll +DE    ++  s ea+ +L s ln    g++++L+
  gi|336253437|ref|YP_004596544.1| 167 ASEAD--LLALDEPTVgVDaeSREAFYDLLSELN--AAGMTIVLI 207
                                       33333..555555444444545777777766666..777777665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.16       4      91 ..      47     134 ..      45     144 .. 0.80
   2 ?   -2.4   0.0         3   3.8e+03      91     103 ..     164     177 ..     156     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                       EE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-.------EEEEEET.T--EEEEEETT---SSEETTEEE-HH CS
                          NTPase_1   4 iTGppGvGKtTlvkkvlellkssgvkvgGfyteevr.eggrrigFkivdlasgeegiLarveakreprvgkyvvdve 79 
                                       + Gp G+GK+Tl++ +l l + ++ +v+ f  + +    g rig+   d+++  +++   v+  + + +g+y  ++ 
  gi|336253437|ref|YP_004596544.1|  47 LVGPNGSGKSTLLELLLGLRRPDEGTVQLFGEPAHAfAAGDRIGYVPQDVTTAAREMPMTVR--EVVAMGRYPHRLV 121
                                       77**************************9999999989************998888877777..7788888866543 PP

                                       H.HHHHHHHHHHH CS
                          NTPase_1  80 s.feelalealrk 91 
                                         f++   +a+++
  gi|336253437|ref|YP_004596544.1| 122 GrFSRTDRRAVDE 134
                                       3355555555555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3
                                       HHH.HHH-EEEE-- CS
                          NTPase_1  91 kal.seadviviDE 103
                                       +al sead++ +DE
  gi|336253437|ref|YP_004596544.1| 164 RALaSEADLLALDE 177
                                       34448899999998 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 ?   11.2   0.1   0.00016      0.21       3      22 ..      45      66 ..      43      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                                      EEEEESTTCCHHHHHHHHH..C CS
                              cobW  3 tvltGflGsGKTtLlnhll..e 22
                                      ++l+G+ GsGK+tLl+ ll  +
  gi|336253437|ref|YP_004596544.1| 45 LGLVGPNGSGKSTLLELLLglR 66
                                      6799************999632 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00018      0.23       2      21 ..      46      65 ..      45      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                      EEEEBTTTTHHHHHHHHHTS CS
                         Dynamin_N  2 avvGsqSsGKSSvlnaLlge 21
                                       +vG   sGKS++l+ Llg 
  gi|336253437|ref|YP_004596544.1| 46 GLVGPNGSGKSTLLELLLGL 65
                                      689***************96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00031      0.39     100     121 ..      43      64 ..      16      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00031
                                       SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallp 121
                                        +  lvG+ G GKStL++ ll+
  gi|336253437|ref|YP_004596544.1|  43 TFLGLVGPNGSGKSTLLELLLG 64 
                                       55679*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2028.07
//
Query:       gi|336253438|ref|YP_004596545.1|  [L=328]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-58  197.5  38.6    3.1e-58  197.3  38.6    1.0  1  ABC-3     ABC 3 transport family
    6.5e-06   25.4  38.0    6.5e-06   25.4  38.0    1.8  2  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.3  38.6   3.4e-62   3.1e-58       2     255 ..      55     315 ..      54     318 .. 0.98

  Alignments for each domain:
  == domain 1  score: 197.3 bits;  conditional E-value: 3.4e-62
                             ABC-3   2 yeflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvn......lllgailvgliaavale 72 
                                       y+++qra la++ ++++ +l+g+f+v r +s++gd+l+H a++Gva++++l+ +      +ll a++++++ a+ +e
  gi|336253438|ref|YP_004596545.1|  55 YPYMQRAYLAAVCIAVIGPLVGTFLVHREISMIGDTLAHTAFAGVAVGLFLNATlslslsPLLTAFVTAVVTALLVE 131
                                       789*************************************************999999999**************** PP

                             ABC-3  73 llkrktklkedtaigivlsvflalglvlvslikk.skvdldsyLfGniltisqedliliaiieavvllllllfwkel 148
                                       ll ++   ++dt+++ivl+ ++alg vl++ +++ ++v++d+yLfG+++t+s+ d+ l++++ ++v  l+ l +++l
  gi|336253438|ref|YP_004596545.1| 132 LLIEHGGAYSDTSLAIVLTGGFALGSVLITATDGgIAVGIDAYLFGSLATVSRADVALLVAMCLLVGGLVTLAYRPL 208
                                       *********************************99****************************************** PP

                             ABC-3 149 llitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsv 225
                                       l +tfd + A+++ l+v+l+k l+++l+al vv a+q++GviLv+a+l++P a+A +++rs+++ +++Ail++ +++
  gi|336253438|ref|YP_004596545.1| 209 LYVTFDTTGARAARLNVRLYKRLMVVLTALVVVSAMQIMGVILVAAMLVVPVAAAALVARSFKRSILLAILVAEFAA 285
                                       ***************************************************************************** PP

                             ABC-3 226 vaGlllSyyldlatGavivlvatllfllal 255
                                       vaG+++Sy++ +a+G++ivl a++++ ++l
  gi|336253438|ref|YP_004596545.1| 286 VAGVTVSYSYGIAAGGSIVLAAIAIYAAVL 315
                                       **********************99997765 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.19   1.7e+03     229     242 ..      61      74 ..      52      81 .. 0.76
   2 !   25.4  38.0   7.3e-10   6.5e-06      82     284 ..      94     293 ..      85     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.19
                             FecCD 229 alltavavalvGpi 242
                                       a l+av++a++Gp+
  gi|336253438|ref|YP_004596545.1|  61 AYLAAVCIAVIGPL 74 
                                       56777777777776 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 7.3e-10
                             FecCD  82 gaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLa...Giavsallsaltsllllll 155
                                        a +g++++l+l ++ + + + +l af+ a++++llv ll ++++  s ++l ++   G+a++++l  +t       
  gi|336253438|ref|YP_004596545.1|  94 TAFAGVAVGLFLNATLSLSLSPLLTAFVTAVVTALLVELLIEHGGAYSDTSLAIVltgGFALGSVLITATDGG---- 166
                                       57778888888776666677888999***************88888877777654223455555555555555.... PP

                             FecCD 156 neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvallt 232
                                           +  i  +l+Gsl+++s  +v+ll++++ll+  l+ l +r+l  ++++ + A++  +nv+ ++ l+++l+al++
  gi|336253438|ref|YP_004596545.1| 167 ---IAVGIDAYLFGSLATVSRADVALLVAMCLLVGGLVTLAYRPLLYVTFDTTGARAARLNVRLYKRLMVVLTALVV 240
                                       ...5669********************************************************************** PP

                             FecCD 233 avavalvGpigFvG.LivPhiarllvgadhrkllplsallGallllladllar 284
                                        +a+ ++G+i   + L+vP  a +lv +++++ ++l++l++ +  ++  +++ 
  gi|336253438|ref|YP_004596545.1| 241 VSAMQIMGVILVAAmLVVPVAAAALVARSFKRSILLAILVAEFAAVAGVTVSY 293
                                       **********98875789***************99999998776666555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1208  (0.0673769); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2366.37
//
Query:       gi|336253439|ref|YP_004596546.1|  [L=556]
Description: thermosome [Halopiger xanaduensis SH-6]
Scores for 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-167  557.2  12.9   3.3e-167  557.0  12.9    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


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 !  557.0  12.9  1.8e-171  3.3e-167       1     489 [.      37     523 ..      37     525 .. 0.97

  Alignments for each domain:
  == domain 1  score: 557.0 bits;  conditional E-value: 1.8e-171
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++v++tlGPkGmdKmlv+++g+v++TnDG+til+e++i++P+a++++e+ae+q++e+GDGTtt+v +ageLl++a
  gi|336253439|ref|YP_004596546.1|  37 VAEAVRSTLGPKGMDKMLVDSMGSVTITNDGVTILQEMDIDNPTAEMIIEVAETQEDEAGDGTTTAVAIAGELLKNA 113
                                       689************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCH CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.kli 153
                                       e+l+++++hpt+ii+g+++a e+a ++++ ia++++  ++d+e L++va+ts+++k t+ ++e+ls+l++dAv +++
  gi|336253439|ref|YP_004596546.1| 114 EDLLEQDIHPTAIIKGFHMASEQARDEIDDIAQDVD--TDDEELLRSVAETSMTGKGTEVNKEHLSQLIIDAVkQVT 188
                                       *******************************55555..569********************************7666 PP

                                       CCCS...EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSC CS
                        Cpn60_TCP1 154 eene...keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsda 227
                                        e+e   + +dl+  ++++ +g+s  +s l+eG ++dk++++ +mp++ ++a +lll+ ++e e+t+++t+v ++d+
  gi|336253439|ref|YP_004596546.1| 189 VEDEngdNVVDLEFLNIETQTGRSAGESDLLEGGIVDKDPVHDNMPTEATDADILLLNEPIEVEETDVDTEVSVTDP 265
                                       655589999******************************************************************** PP

                                       CHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGG CS
                        Cpn60_TCP1 228 eeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledl 304
                                       ++l+k++++ee+ql+e++++i+++g++vv+cqkgiddla+h+lak+gila+rr+kk+dle l +++Gat+vs+l++ 
  gi|336253439|ref|YP_004596546.1| 266 DQLQKFLDREEEQLREKVDQIAALGADVVFCQKGIDDLAQHYLAKEGILAVRRAKKSDLEFLQEVVGATVVSDLDSA 342
                                       ***************************************************************************** PP

                                       GCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHH CS
                        Cpn60_TCP1 305 tpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatel 381
                                       t+++lG  +     + ++++++++++ ++++ +t+llrg+td+v+de+er ++dAl+vv++++ d++v++GGGa+e+
  gi|336253439|ref|YP_004596546.1| 343 TEDDLGFGDVT---RDEEDELFYVTG-EDAHGVTLLLRGSTDHVVDELERGVNDALDVVAQTVSDGRVLAGGGAIEV 415
                                       *******8777...5568*******9.9************************************************* PP

                                       HHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCT CS
                        Cpn60_TCP1 382 elakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveag 458
                                       ela++l++ya+svsg+eqla+eafa++Le +p++LaeNaGld+i++l +lraah+ g++e+g++v +g+++d  eag
  gi|336253439|ref|YP_004596546.1| 416 ELASRLRDYADSVSGREQLAVEAFADSLELVPRVLAENAGLDSIDTLVDLRAAHEDGDIEAGLNVFTGDVEDTYEAG 492
                                       ***************************************************************************** PP

                                       XEEEHHHHHHHHHHHHHHHHHHHCEEEEEXX CS
                        Cpn60_TCP1 459 vvDplkvkrqalksAteaastiLrideiika 489
                                       vv+p+++k+qa++sA+eaa+++L+id+ii+a
  gi|336253439|ref|YP_004596546.1| 493 VVEPAHAKEQAVTSAAEAANLVLKIDDIISA 523
                                       *****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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 0.26s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3989.87
//
Query:       gi|336253440|ref|YP_004596547.1|  [L=313]
Description: UDP-glucose 4-epimerase [Halopiger xanaduensis SH-6]
Scores for 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-51  173.9   0.0    4.5e-51  173.6   0.0    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.1e-41  142.4   0.0    1.1e-40  140.1   0.0    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    5.4e-16   58.6   0.0    2.9e-15   56.2   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.1e-15   57.1   0.3    3.9e-15   56.2   0.1    1.5  2  NAD_binding_10   NAD(P)H-binding
    6.2e-14   51.8   0.0    7.2e-14   51.5   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    9.8e-14   51.0   0.0    1.2e-13   50.8   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.5e-10   40.7   0.1    3.8e-05   23.0   0.0    2.8  2  NAD_binding_4    Male sterility protein
    5.8e-07   29.2   0.4    2.7e-05   23.7   0.4    2.6  1  adh_short        short chain dehydrogenase
    5.9e-06   26.0   0.1     0.0002   21.0   0.1    2.0  2  NmrA             NmrA-like family
     0.0041   17.5   0.0     0.0087   16.5   0.0    1.5  1  NAD_binding_7    Putative NAD(P)-binding
     0.0048   17.1   0.2      0.011   16.0   0.2    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0053   16.6   0.1       0.01   15.7   0.1    1.5  1  DFP              DNA / pantothenate metabolism flavoprotein
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.054   13.4   0.0    2.2  3  KR               KR domain
      0.018   15.2   0.0      0.095   12.9   0.0    2.1  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.028   14.7   0.1      0.056   13.7   0.1    1.6  1  TrkA_N           TrkA-N domain
      0.039   13.8   0.1      0.065   13.1   0.1    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.051   14.1   0.1       0.12   12.9   0.1    1.8  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.061   13.4   0.0       0.13   12.3   0.0    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.061   14.0   0.2       0.34   11.6   0.1    2.0  2  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
      0.078   13.1   0.1       0.12   12.5   0.1    1.3  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
       0.14   11.7   0.1       0.32   10.6   0.0    1.6  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family


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 !  173.6   0.0   5.3e-54   4.5e-51       1     241 []       8     237 ..       8     237 .. 0.94

  Alignments for each domain:
  == domain 1  score: 173.6 bits;  conditional E-value: 5.3e-54
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HH..HHHHHHHHHT-SEEEE--S-- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrs..alerlfkeeqpdavihlAavg 75 
                                       ilVtG++GfiGs+l+++ll+ g +v+ +d ls++ +    + +e+ve+dlt  +  al++ ++  ++d v+hlAa +
  gi|336253440|ref|YP_004596547.1|   8 ILVTGGAGFIGSHLAERLLADGADVTIVDDLSNGAADRVPDAAEFVEADLTSIAadALADHLE--GVDLVFHLAASK 82 
                                       8******************************999999999999********877446666666..**********99 PP

                                       -HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSS.BSTCSTTS----SSHHHHHHHHHHH CS
                         Epimerase  76 gvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqp.keettltgplkpnspYaaaKlagek 151
                                       +v++  ++p   +e+n+++t+++lea+ +a+v  + + sSs+vYG+ ++ p  e+++   pl+p s+Y+a+Kla e 
  gi|336253440|ref|YP_004596547.1|  83 HVDT--DRPHGQFEDNTRMTRTVLEAMAEADVTDIAYTSSSTVYGEAPR-PtPEDYA---PLEPISAYGASKLADEG 153
                                       9999..9**************************************9998.7467777...***************** PP

                                       HHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHH CS
                         Epimerase 152 lveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvleh 228
                                       l+ a +++++l + ++r  n++Gpr     +  vip +i+k+++  + +t+lg+g++   +l+veD+ +a+l+v+e+
  gi|336253440|ref|YP_004596547.1| 154 LLSARTHSHDLTVWNFRFANVVGPR----LRGAVIPDFIEKLQDDPETLTILGNGRQEKSYLHVEDCLDAMLHVIER 226
                                       *************************....9**************999****************************** PP

                                       HTT-STTEEEEES CS
                         Epimerase 229 vdagdkgeiyniG 241
                                        da    ++yn+G
  gi|336253440|ref|YP_004596547.1| 227 ADAA--VNTYNLG 237
                                       7775..569*998 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 !  140.1   0.0   1.3e-43   1.1e-40       1     276 [.       9     265 ..       9     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 140.1 bits;  conditional E-value: 1.3e-43
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-..HHHHHHHHHHHT CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltD..ssslerllaevq 75 
                                       L+TG+aGfiGs+lae+Ll+ g +v++++++s + +++r+               +++++Dlt   +++l + l+ v 
  gi|336253440|ref|YP_004596547.1|   9 LVTGGAGFIGSHLAERLLADGADVTIVDDLS-NGAADRVPDA-----------AEFVEADLTSiaADALADHLEGV- 72 
                                       9***********************8776555.5566666443...........469*****984455566666555. PP

                                       -SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SH CS
                     GDP_Man_Dehyd  76 pdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsP 152
                                        d v++LAA +hVd+  + P+  +e n   t ++Lea+ ++ +   + +  +S+s+vYG++ +   ++  p++P s 
  gi|336253440|ref|YP_004596547.1|  73 -DLVFHLAASKHVDT--DRPHGQFEDNTRMTRTVLEAMAEADV---TDIAYTSSSTVYGEAPRPTPEDYAPLEPISA 143
                                       .9************8..9********************99876...68999***********9999999******** PP

                                       HHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHH CS
                     GDP_Man_Dehyd 153 YaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDy 229
                                       Y+a+Kl+ + +  +  ++++l + n ++ n  +pr         i++++ + + + ++ ++lGn+++ ++++hv+D 
  gi|336253440|ref|YP_004596547.1| 144 YGASKLADEGLLSARTHSHDLTVWNFRFANVVGPRL----RGAVIPDFIEKLQDDPETLTILGNGRQEKSYLHVEDC 216
                                       ***********************************4....5679********************************* PP

                                       HHHHHHHHHCSS-..--EEE-TT-EEECHHCHHCCHHCCCHHHHHH... CS
                     GDP_Man_Dehyd 230 veamwlmlqqdkp..edyviatgethsvrefvelaflelgktiewegkg 276
                                        +am  ++++  +  ++y+++t +t+sv+ ++ + + e+g + ++e +g
  gi|336253440|ref|YP_004596547.1| 217 LDAMLHVIERADAavNTYNLGTRTTTSVDRIAAIVADEMGLEPDFEYTG 265
                                       ********985432389*********************99988776443 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   3.3e-18   2.9e-15       1     194 [.       8     200 ..       8     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 3.3e-18
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       +lvtG++G iGs+l +++l+  +   i+ + +  + +++ +    e+ +    ++    +++++ ++ l++ le  +
  gi|336253440|ref|YP_004596547.1|   8 ILVTGGAGFIGSHLAERLLADGADVTIVDDLSNGAADRVPDAA--EFVE----AD----LTSIA-ADALADHLE--G 71 
                                       89*******************9999999999999999998876..2322....33....66776.567899999..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE.............GGG.SS--SHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt.............DKA.vnPtnvmGa 140
                                       vd+vfh AA KhV +    p+  ++ N   t++v+ea  ea+v+++ + S+             D A  +P++++Ga
  gi|336253440|ref|YP_004596547.1|  72 VDLVFHLAASKHVDT--DRPHGQFEDNTRMTRTVLEAMAEADVTDIAYTSSstvygeaprptpeDYApLEPISAYGA 146
                                       *************97..7899**************************999733444444444445555689****** PP

                                       HHHHHHHHHHHGGG--SSS--EEEEEEE-EETTG..TTSSHHHHHHHHHTT.SSEEE CS
                   Polysacc_synt_2 141 tKrlaekllqalakeseekktkfvvvRfGNVlgS..rGSviplFkkqikeg.gpvtv 194
                                       +K++ e ll a  +++   + ++   Rf NV+g   rG vip F ++++++ + +t+
  gi|336253440|ref|YP_004596547.1| 147 SKLADEGLLSARTHSH---DLTVWNFRFANVVGPrlRGAVIPDFIEKLQDDpETLTI 200
                                       *******999988877...8999999*******7446***********998666776 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 !   56.2   0.1   4.6e-18   3.9e-15       1     133 [.      12     157 ..      12     171 .. 0.78
   2 ?   -2.6   0.0       5.1   4.4e+03      52      74 ..     218     240 ..     194     255 .. 0.58

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 4.6e-18
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-..CCHHHHHHTT-SEEEES---TCCHH CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtd..vedlaealkgadaVvsalggggkde 75 
                                       G+ G +G++l+++lla+g  +vt++  + +  a+ +  +++e ve+d+t+  +++la++l+g+d V+  +++++ d+
  gi|336253440|ref|YP_004596547.1|  12 GGAGFIGSHLAERLLADG-ADVTIV-DDLSNGAADRVPDAAEFVEADLTSiaADALADHLEGVDLVFHLAASKHVDT 86 
                                       99***************5.999976.55444333334589*********955699***********99997776633 PP

                                       HH...........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHH..HCCHHHHHHHHHHHHHHHH CS
                    NAD_binding_10  76 eg...........aknivdaakeagvkRfvlvsaigvgdevpgefgewnk..ellkaylaakraaeellra 133
                                       +            ++++++a+ ea+v  + + s+  v+ e+p++++e +   e ++ay a k a e ll a
  gi|336253440|ref|YP_004596547.1|  87 DRphgqfedntrmTRTVLEAMAEADVTDIAYTSSSTVYGEAPRPTPEDYAplEPISAYGASKLADEGLLSA 157
                                       3334455555556******************************9988776345778888888888777766 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.1
                                       CHHHHHHTT-SEEEES---TCCH CS
                    NAD_binding_10  52 edlaealkgadaVvsalggggkd 74 
                                       +++ ++++ ada v + + g ++
  gi|336253440|ref|YP_004596547.1| 218 DAMLHVIERADAAVNTYNLGTRT 240
                                       55666666677655555333332 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 !   51.5   0.0   8.5e-17   7.2e-14       2     235 ..       7     259 ..       6     305 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 8.5e-17
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHHHHH--SEEEE------ CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre...............eldltdaeavaellkeakpdvvvnaAAyta 63 
                                       +ilvtG+ G +Gs+La++l ++g++v+ ++                 e+dlt  +a a + +    d+v ++AA + 
  gi|336253440|ref|YP_004596547.1|   7 RILVTGGAGFIGSHLAERLLADGADVTIVDDLsngaadrvpdaaefvEADLTSIAADALADHLEGVDLVFHLAASKH 83 
                                       79*************************996667899********99988988765443333444589********** PP

                                       HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-.B-TTS----SSHHHHHHHHHHHHHHH CS
                     RmlD_sub_bind  64 vDkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrp.YeeddetsPlnvYGrtKlaGEqavla 138
                                       vD   + ++ +++ n + ++++ ea a+++++ + + S+  V+ Ge++rp  e  ++ +P+++YG++Kla E    a
  gi|336253440|ref|YP_004596547.1|  84 VDT--DRPHGQFEDNTRMTRTVLEAMAEADVTdIAYTSSSTVY-GEAPRPtPEDYAPLEPISAYGASKLADEGLLSA 157
                                       **8..89999***************999999747788999998.77788824555788***************9998 PP

                                       ....H-SSEEEEEE-SEESS..SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG- CS
                     RmlD_sub_bind 139 ....agkkalivRtswvyge..kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekela 207
                                           +  +++ +R++ v g   +g      + +l+++ e+l++     q  s  +++d  +++l+++e+a +   + 
  gi|336253440|ref|YP_004596547.1| 158 rthsHDLTVWNFRFANVVGPrlRGAVIPDFIEKLQDDPETLTILGNgrQEKSYLHVEDCLDAMLHVIERADA---AV 231
                                       442222345669*******95556666678999999*******975337778889**************997...89 PP

                                       EEEE---BS-EEHHHHHHHHHHHHCHTT CS
                     RmlD_sub_bind 208 gvyHlanegetswlefArailkeagads 235
                                        +y l+ + +ts   +A  +++e+g ++
  gi|336253440|ref|YP_004596547.1| 232 NTYNLGTRTTTSVDRIAAIVADEMGLEP 259
                                       9*********************998765 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 !   50.8   0.0   1.3e-16   1.2e-13       1     151 [.       9     149 ..       9     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.3e-16
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtd..kdkleealegvdvvihlas 75 
                                       +vtGgaGF+G++l ++L+  +   +v ++D   +    +++   + ++++e+D+t+  +d l + legvd+v+hla+
  gi|336253440|ref|YP_004596547.1|   9 LVTGGAGFIGSHLAERLLADG--ADVTIVDDLSNGAA-DRV--PDAAEFVEADLTSiaADALADHLEGVDLVFHLAA 80 
                                       69*****************99..59999985544444.444..3455689****9744689**************99 PP

                         3Beta_HSD  76 lvdvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKa 151
                                          v     ++   + n + Tr+vlea  +a+v+ + YtSs  v g+     +      e + +  + +ay  sK 
  gi|336253440|ref|YP_004596547.1|  81 SKHVDTDRPHG-QFEDNTRMTRTVLEAMAEADVTDIAYTSSSTVYGE--APRPT----PEDYAPLEPISAYGASKL 149
                                       99999866666.6778****************************998..22222....244555556666666664 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.8e-05     0.015       1      25 [.      10      34 ..      10      36 .. 0.92
   2 !   23.0   0.0   4.4e-08   3.8e-05      76     214 ..      60     182 ..      38     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                      EE-TTSHHHHHHHHHHHHHS-.TEE CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevki 25
                                      +TG+ GF+G++L e+LL + ++v+i
  gi|336253440|ref|YP_004596547.1| 10 VTGGAGFIGSHLAERLLADGADVTI 34
                                      7*****************9999877 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 4.4e-08
                                       --HHHHHHHHHH--EEEE--SS-S.STTSSE.EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  76 LseedlqelaeevdviihsaAtvnfdepyke.llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                       + +++l +  e vd+++h aA+ ++d + +   ++ N++ tr vle  ++   +  + + S+++v+ge  +      
  gi|336253440|ref|YP_004596547.1|  60 IAADALADHLEGVDLVFHLAASKHVDTDRPHgQFEDNTRMTRTVLEAMAEADVT-DIAYTSSSTVYGEAPRP----- 130
                                       66788888889**************996665499************99988888.9************9954..... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST- CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGw 214
                                                  + e     +   +Y  sK + E l+ +  ++++l v  +R  +++g    G+
  gi|336253440|ref|YP_004596547.1| 131 -----------TPEDYAPLEPISAYGASKLADEGLLSARTHSHDLTVWNFRFANVVGPRLRGA 182
                                       ...........4556666777789*************999999***********999665555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.4   3.1e-08   2.7e-05       3     162 ..       8     157 ..       7     179 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.1e-08
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkld 79 
                                       +lvtG+++ IG  +a++l+++Ga+v++vd  ++ +   a+ + ++   a ++++D+t+      + ++ +++l+++d
  gi|336253440|ref|YP_004596547.1|   8 ILVTGGAGFIGSHLAERLLADGADVTIVDDLSNGA---ADRVPDA---AEFVEADLTS-----IAADALADHLEGVD 73 
                                       89*************************99998877...6666654...89******94.....45677778889999 PP

                                       EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEE..GGGTSB-TT......... CS
                         adh_short  80 vLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsS..vagkvpvag......... 145
                                       ++ + A+       ++++ ++    +e N      +tr+vl+am ++   +I  +sS  v g+ p +          
  gi|336253440|ref|YP_004596547.1|  74 LVFHLAAS------KHVDTDRPHGQFEDN----TRMTRTVLEAMAEADVTDIAYTSSstVYGEAPRPTpedyaplep 140
                                       99999998......455555555555555....46899999999999999999998833356665543223333333 PP

                                       BHHHHHHHHHHHHHHHH CS
                         adh_short 146 vaaYsAsKaavagltrs 162
                                        +aY+AsK a +gl ++
  gi|336253440|ref|YP_004596547.1| 141 ISAYGASKLADEGLLSA 157
                                       78888888888887544 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   2.3e-07    0.0002       1      99 [.       8     117 ..       8     128 .. 0.84
   2 ?    2.9   0.0     0.079        67     153     226 ..     184     256 ..     176     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.3e-07
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT..-HHHHHHHHTT-SEEEE---GG CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdld..dkeslvealkgvdvvfsvtgfy 75 
                                       Ilv+G++G +G+++++ ll++g +v + v d+++ +a+ + +a +e+v++dl     + l+  l+gvd+vf   +++
  gi|336253440|ref|YP_004596547.1|   8 ILVTGGAGFIGSHLAERLLADGADVTI-VDDLSNGAADRVPDA-AEFVEADLTsiAADALADHLEGVDLVFHLAASK 82 
                                       9************************85.899999999999886.8******99444789*************99977 PP

                                       ...........S-HHHHHHHHHHHHHHHS-SEEEE CS
                              NmrA  76 ...........skeiedgkklvdAakeaGvkhfiy 99 
                                                  +++++   ++ +A +ea v  + y
  gi|336253440|ref|YP_004596547.1|  83 hvdtdrphgqfEDNTRMTRTVLEAMAEADVTDIAY 117
                                       78888887777777777777777777777776666 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.079
                                       -SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHT CS
                              NmrA 153 aqlkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkig 226
                                        + ++++++ + +++t+lg+g  +  +l ++eD   ++++++++ +++ + +   +  t s++ i+++   ++g
  gi|336253440|ref|YP_004596547.1| 184 IPDFIEKLQDDPETLTILGNGRQEKSYL-HVEDCLDAMLHVIERADAAVNTYNLGTRTTTSVDRIAAIVADEMG 256
                                       5667788888888*********999999.***************999988888899999999999999887776 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 !   16.5   0.0     1e-05    0.0087       5      72 ..       3      82 ..       1      92 [. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-05
                     NAD_binding_7  5 lkgkkvlvvGg.GevAarkvrklleagakvtvvapevkeele...........elvklaeeelekdlegadlviaatdd 71
                                      +++ ++lv Gg G ++ + +++ll+ ga+vt+v+  ++ +++           +l ++a + l ++leg+dlv+     
  gi|336253440|ref|YP_004596547.1|  3 VSDGRILVTGGaGFIGSHLAERLLADGADVTIVDDLSNGAADrvpdaaefveaDLTSIAADALADHLEGVDLVFHLAAS 81
                                      56778888875599******************9998855555555666566577777888889999*******976655 PP

                     NAD_binding_7 72 r 72
                                      +
  gi|336253440|ref|YP_004596547.1| 82 K 82
                                      5 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   0.2   1.2e-05     0.011       3      77 ..      10      79 ..       8      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                                      EE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP  3 iiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77
                                      + G+ G++G+ +ae l++ +    ++t++d   ++++  +      +f  + l+    +a La +l++ dlv +l+
  gi|336253440|ref|YP_004596547.1| 10 VTGGaGFIGSHLAERLLADGA---DVTIVDDLSNGAADRVP--DAAEFVEADLTSIAADA-LADHLEGVDLVFHLA 79
                                      55555*************997...59***998888666654..67899***********9.***********9997 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.2e-05      0.01      23      92 ..       9      81 ..       5     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                                      EEE----HHHHHHHHHHHHTT-EEEEEE-S-SS--...-TT-EEEE--SHHHHHHHHHHHHTT-SEEEE---S CS
                               DFP 23 isNrSSGkmGyalAeaaaarGaeVtlvsgpvslet...pegvevvkvesaeemleaveealkeadivimaAAv 92
                                      +     G  G  lAe+++a Ga+Vt+v   ++ ++   p+++e+v+ + ++  ++a+ ++l+  d+v++ AA 
  gi|336253440|ref|YP_004596547.1|  9 LVTGGAGFIGSHLAERLLADGADVTIVDDLSNGAAdrvPDAAEFVEADLTSIAADALADHLEGVDLVFHLAAS 81
                                      555667999******************877543322338889*****************************95 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.4e-05     0.054       1      29 [.       6      34 ..       6      81 .. 0.84
   2 ?   -2.4   0.0       4.5   3.8e+03      14      35 ..     101     122 ..      97     147 .. 0.64
   3 ?   -2.2   0.0       3.8   3.2e+03     141     176 ..     201     237 ..     198     240 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.4e-05
                                      SEEEEETTTSHHHHHHHHHHHHHHS-EEE CS
                                KR  1 gtylitGGlGgLGlelarwlaekgarhlv 29
                                      g  l+tGG+G +G +la+ l+++ga   +
  gi|336253440|ref|YP_004596547.1|  6 GRILVTGGAGFIGSHLAERLLADGADVTI 34
                                      5689********************87544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.5
                                       HHHHHHHHHHHS-EEEEE-SS. CS
                                KR  14 lelarwlaekgarhlvllsRsa 35 
                                       +++ + +ae   + ++++s s 
  gi|336253440|ref|YP_004596547.1| 101 RTVLEAMAEADVTDIAYTSSST 122
                                       6667777777777777777765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.8
                                       H--TT-.HHHHHHHHHHHHHHHHHHHHHHTEEEEEE- CS
                                KR 141 lgsagq.anYaaaNaflDalaeyrrsqglpavsinwg 176
                                       lg+  q  +Y     +lDa+ +  ++  +++ + n+g
  gi|336253440|ref|YP_004596547.1| 201 LGNGRQeKSYLHVEDCLDAMLHVIERADAAVNTYNLG 237
                                       5665552578999999999999888887777666665 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   0.0   0.00011     0.095       6      70 ..      13      85 ..      10      87 .. 0.78
   2 ?   -1.8   0.0       3.6     3e+03      14      29 ..     220     235 ..     196     254 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                      --SHHHHHHHHHHHHTT-EEEEE-.SSHHHHHHHHHTT........EEE-SSHHHHHHHCSEEEE-SSSHHHHH CS
                     NAD_binding_2  6 GlGvMGsnmalnllkagykvavyn.rtkekveelvaeg........akaaesieelvasldvvitmvkagkavd 70
                                      G G +Gs++a++ll+ g +v++++ +++ +++++ ++           aa+ +++ ++++d+v+  + a+k+vd
  gi|336253440|ref|YP_004596547.1| 13 GAGFIGSHLAERLLADGADVTIVDdLSNGAADRVPDAAefveadltSIAADALADHLEGVDLVFH-LAASKHVD 85
                                      899******************99867888888887776777766766667777777777788875.55666665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.6
                                       HHHHHHHTT-EEEEE- CS
                     NAD_binding_2  14 malnllkagykvavyn 29 
                                       m   +++a+  v  yn
  gi|336253440|ref|YP_004596547.1| 220 MLHVIERADAAVNTYN 235
                                       3334444444555554 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   6.6e-05     0.056       5      53 ..      13      61 ..       8     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.6e-05
                                      S-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHH CS
                            TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdee 53
                                      G+G +G++lae+L ++g dv+++d+  + ++    + +e+v +d t+ +
  gi|336253440|ref|YP_004596547.1| 13 GAGFIGSHLAERLLADGADVTIVDDLSNGAADRVPDAAEFVEADLTSIA 61
                                      89*************7768******998887777788888888888765 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 ?   13.1   0.1   7.6e-05     0.065       6      52 ..      13      63 ..       8     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.6e-05
                                      --SCCHHHHHHHHHHTT-EEEEE-S....-HHHHHHHHHHHHHHHHCCTTT CS
                           3HCDH_N  6 GaGtmGagiaavfasagleVvlvdi....seealekalekieksleklvek 52
                                      GaG +G+ +a+ +++ g +V++vd     +++++ +a+e +e+ l + +++
  gi|336253440|ref|YP_004596547.1| 13 GAGFIGSHLAERLLADGADVTIVDDlsngAADRVPDAAEFVEADLTSIAAD 63
                                      99*********************9864333333333444444444444433 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00014      0.12       3      32 ..      10      39 ..       7      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                                      EEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvversd 32
                                      v  G+G+ig  lA+ l + g++Vt+v+  +
  gi|336253440|ref|YP_004596547.1| 10 VTGGAGFIGSHLAERLLADGADVTIVDDLS 39
                                      45589*********************9876 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.13      13      88 ..       6      84 ..       2     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                      -EEEEE.S-SHHHHHHHHHHHCCT-CEEEEE....ESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSS CS
                      Shikimate_DH 13 kkvlli.GaGemaelvakhLlakgvkkvvva....NRtlerakelaeelkgeeiealkleelkellaeadvvisatase 86
                                       ++l+  GaG +++ +a+ Lla g++ v+++    N   +r+ + ae + +++++ ++ + l ++l+ +d+v+   as+
  gi|336253440|ref|YP_004596547.1|  6 GRILVTgGAGFIGSHLAERLLADGAD-VTIVddlsNGAADRVPDAAEFV-EADLTSIAADALADHLEGVDLVFHLAASK 82
                                      56666637*****************9.7776444477788888877777.5559999****************998888 PP

                                      S- CS
                      Shikimate_DH 87 ep 88
                                      ++
  gi|336253440|ref|YP_004596547.1| 83 HV 84
                                      75 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 ?   11.6   0.1    0.0004      0.34       1      72 [.      13      84 ..      13      86 .. 0.75
   2 ?   -0.6   0.0       2.3     2e+03      48      87 ..     185     224 ..     171     239 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0004
                                      --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TT.HHHHHT--CB---HHHHHHHHS.-EEEEE-S--HHH CS
                     NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrdsllskd.rkallasealtldlddliahld.pdvvVEcasseav 72
                                      G+G iGs ++e+l+++ +  ++++v  + +  + + + +++++++  +    d+l++hl+ +d+v  +a+s+ v
  gi|336253440|ref|YP_004596547.1| 13 GAGFIGSHLAERLLADGA--DVTIVDDLSNGAADRVPdAAEFVEADLTSIAADALADHLEgVDLVFHLAASKHV 84
                                      99***************9..56666555555333333366677777777788999999977****999988766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.3
                                       ---HHHHHHHHS-EEEEE-S--HHHHTTHHHHHHTTEEEE CS
                     NAD_binding_3  48 tldlddliahldpdvvVEcasseavaelvlkaLkagkdvv 87 
                                       ++ +++l ++++   ++ ++ +e    +v+++L a  +v+
  gi|336253440|ref|YP_004596547.1| 185 PDFIEKLQDDPETLTILGNGRQEKSYLHVEDCLDAMLHVI 224
                                       4555555555566666677777777778888888888887 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 ?   12.5   0.1   0.00014      0.12       2     107 ..       7     109 ..       6     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                       EEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-..EEEEESSGGGGTTESEEEE- CS
                           Ldh_1_N   2 kvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvk..vkvsekeeealkdadvvvit 76 
                                       ++ v+G aG+iG++la  l++ +   +++++D  ++   G a  + +++ f++++  +++ +   + l+++d+v   
  gi|336253440|ref|YP_004596547.1|   7 RILVTGGAGFIGSHLAERLLADGA--DVTIVDDLSN---GAADRVPDAAEFVEADltSIAADALADHLEGVDLVFHL 78 
                                       799****************99864..4678877754...55555555555544441045556889999999999999 PP

                                       -S-SS-TTTTHHHHHHHHHHHHHHHHHHHHH CS
                           Ldh_1_N  77 agvprkpGetRddLlkvNakIvkeiveaiak 107
                                       a+ +  +    +  +++N ++++++ ea+a+
  gi|336253440|ref|YP_004596547.1|  79 AASKHVDTDRPHGQFEDNTRMTRTVLEAMAE 109
                                       9988888777778888888888888877776 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 ?   10.6   0.0   0.00037      0.32       7      64 ..      13      69 ..       7      86 .. 0.82
   2 ?   -3.2   0.0       6.2   5.3e+03      62      83 ..      95     116 ..      92     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                                      --STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTE CS
                    UDPG_MGDP_dh_N  7 GlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrl 64
                                      G+G++G   a  l + g +v++vD  ++  +    +  +++e +L ++ ++a++ ++l
  gi|336253440|ref|YP_004596547.1| 13 GAGFIGSHLAERLLADGADVTIVDDLSNGAADRVPDAAEFVEADLTSIAADALA-DHL 69
                                      89*********************998888888889999*******999988874.444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.2
                                       TTEEEES-HHHHHHC-SEEEE- CS
                    UDPG_MGDP_dh_N  62 grlsfttdvekaveeadvifia 83 
                                       ++ + t  v +a++eadv+ ia
  gi|336253440|ref|YP_004596547.1|  95 DNTRMTRTVLEAMAEADVTDIA 116
                                       5677888888999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2169.77
//
Query:       gi|336253441|ref|YP_004596548.1|  [L=393]
Description: hypothetical protein Halxa_2044 [Halopiger xanaduensis SH-6]
Scores for 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  125.9  44.5    2.2e-36  125.9  44.5    1.5  2  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.9  44.5   1.3e-40   2.2e-36       2     299 ..      36     353 ..      35     356 .. 0.90
   2 ?   -1.2   0.1     0.062   1.1e+03     265     284 ..     353     372 ..     350     376 .. 0.76

  Alignments for each domain:
  == domain 1  score: 125.9 bits;  conditional E-value: 1.3e-40
                   LPG_synthase_TM   2 llglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayligl 78 
                                       ++g al++l l+++ r +dl+a+ a  +s+dp++l+la++++++s+ +r+ r++ +l++ g+r + + l++a+++++
  gi|336253441|ref|YP_004596548.1|  36 IAGTALVVLGLVVAARELDLEAVVADAASADPRLLALAIAVYAVSWPIRGRRYGDVLSATGHRAGTGLLTAAVFVSQ 112
                                       678899988888889************************************************************** PP

                   LPG_synthase_TM  79 fvnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaa........... 144
                                        +n ++P+++ G+++ray+++++ +v++++ +a + verl+dl+++++l + a ++l    + g+            
  gi|336253441|ref|YP_004596548.1| 113 TANLAIPARA-GDAARAYVVNERANVPYTAGFAGLAVERLFDLATIAVLAGGATAWLAISGNVGPLeiaaeaggarv 188
                                       *********9.**********************************998887777777776666666799******87 PP

                   LPG_synthase_TM 145 .vllllalallllavlalllllllrrrlarlarvlkrlarllarfarklasakr.....klvlasprrlllafllsl 215
                                        ++++++++ ++++v + ++  ++ ++  r+a++l+ la  ++r+ + l++a r       v+++pr l+ + + sl
  gi|336253441|ref|YP_004596548.1| 189 aFVGAAVVSTATVGVGLAVATTARSGYGPRIAARLRTLADGSPRLEGALEAALRfaadvGVVARRPRVLAAVAGTSL 265
                                       76777777777777777999999***********************99999999*****999999************ PP

                   LPG_synthase_TM 216 liwllealtlylllralgvdvslalll....lillaltlvgalpplPgGlGvrEaalalllall.Gvsaaealaaal 287
                                       l+w+l++lt+ l+l+al+  + l+ ll    l++ + +l+ +lp++ gG+G++Eaa+++l++ l  v+a++alaaa+
  gi|336253441|ref|YP_004596548.1| 266 LVWALDVLTAVLVLAALDSGLALGPLLavgtLAVSVGNLAKVLPLSQGGVGLYEAAFTALVVGLaPVGASTALAAAV 342
                                       *****************999999999997888888888888888888**********66555555************ PP

                   LPG_synthase_TM 288 lyrlitlyllll 299
                                       +++++    ++l
  gi|336253441|ref|YP_004596548.1| 343 VDHALKN-GVTL 353
                                       ****987.4444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.062
                   LPG_synthase_TM 265 EaalalllallGvsaaeala 284
                                        a+ a+++a++Gvs a+a+ 
  gi|336253441|ref|YP_004596548.1| 353 LAGGAAAVAAFGVSFADATN 372
                                       57788999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2905.79
//
Query:       gi|336253442|ref|YP_004596549.1|  [L=390]
Description: alpha-1,4-glucan-protein synthase [Halopiger xanaduensis SH-6]
Scores for 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-18   64.7   0.0      1e-17   64.3   0.0    1.2  1  RGP       Reversibly glycosylated polypeptide


Domain annotation for each model (and alignments):
>> RGP  Reversibly glycosylated polypeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   5.8e-22     1e-17       5     339 ..       4     375 ..       1     378 [. 0.67

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 5.8e-22
                               RGP   5 evdiviaalka..dltsfleewrpl...lsrfhliivkdpdl....keelkiPeGfdldvyt...ksdiervlgael 69 
                                       ++ +v+++++    + s++++ r+    lsr+h+++v ++       e++   eG + +v+    +++  +  g e 
  gi|336253442|ref|YP_004596549.1|   4 DICVVVPTIREyeCMRSYFDNAREHgfdLSRLHVVLVTEDFCetdeMERMLEEEGVSGEVFDgsrREEWYEAHGVEE 80 
                                       56677777764213566777777644346777777776543321113444456777777776211333333444333 PP

                               RGP  70 ..ksisfsgsscryfG..ylvskk..kyivsidddcvpa..kdekGllvdavaqhiknlktPatPfffntlydPyre 138
                                         + +    ++  +fG  y+ ++    y + iddd +p   +d  G+++d +a      +  +   + n ly    e
  gi|336253442|ref|YP_004596549.1|  81 ygHIVPAASHAETSFGllYMWAHDefDYGFFIDDDTLPHpeEDFFGTHMDNLAFEGGIEEVSSDEQWVNVLYQNADE 157
                                       2345556666777888444455542258899****99752267789****9988777777888999*********** PP

                               RGP 139 GadfvrGyPfs.lreGvet..........alslGlwlnladydaptqlvk......aeerntr..yvdavltvPkka 196
                                          + rGyP+s + e vet          + s Glw n++d+da   l+       a++r++r  + d  +   ++ 
  gi|336253442|ref|YP_004596549.1| 158 HGLYPRGYPYSaMGETVETgtteieagevVASQGLWTNVPDLDAVRILMDgdlegqAQTRTSRddFGD-DFVAARGN 233
                                       **********9444555542222222222679************998875222111333444322333.45567899 PP

                               RGP 197 llpvsGinlafdrelvGpalfealkl.agegklryetledlwaGlcvkvicdhlglGvktGlPyvlrkeas.nales 271
                                        l+v+ +nlaf re++  a+++  +  ++    r++   d+w+G+ +k  cd l+  +  G P   +++a  ++++ 
  gi|336253442|ref|YP_004596549.1| 234 YLTVCSMNLAFRREVIP-AFYQLPMDdNEWEVGRFD---DIWSGVFLKRACDVLDKRIYNGAPLCEHNKAPrSTFDD 306
                                       9*************995.555555550455667888...****************************977526799* PP

                               RGP 272 lkkeweGvklmeevvpffqslklsktavtvedcvlelaka.vkeklg..kvdpvfakaadamvewvkawks 339
                                       l++e  G++l e++    + +     a++  d +  +a++ v    +  ++ + f+ +++ m +w++  ++
  gi|336253442|ref|YP_004596549.1| 307 LNNEVPGLELNEHLWRVIDDVGAD--ADSYADVFEAMARElVDGDWSdyNNGAFFNYVGEHMLDWLECLST 375
                                       ***************999998654..444444444444331333444113458999999999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2787.29
//
Query:       gi|336253443|ref|YP_004596550.1|  [L=387]
Description: family 1 extracellular solute-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-16   58.7   0.1    7.2e-16   58.3   0.1    1.1  1  SBP_bac_6   Bacterial extracellular solute-binding protein
    2.2e-07   31.2   7.0    5.4e-07   29.9   7.0    1.6  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    2.4e-07   30.9   2.7    3.3e-07   30.4   2.7    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    2.4e-05   24.2   1.4    3.4e-05   23.7   1.4    1.2  1  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.1   1.6e-19   7.2e-16       4     220 ..     130     348 ..     127     372 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.6e-19
                         SBP_bac_6   4 pdlilsfdkdflekfieeglfqpldpanlpnvnkdfaeeglkdpdgkyypygvgplvlavnkdrlkgrpvPksWaDL 80 
                                       +d+++s d ++l+  ++++ ++pl ++ ++ v +    +++  +d+ +++++  +  + +n+++l + ++P + +D+
  gi|336253443|ref|YP_004596550.1| 130 ADVFWSIDASSLGFVADNDAYEPLSDEAVEAVGN----AQFVGDDNAWAGVAGRARAVPYNTEELSESDIPNTVQDF 202
                                       8********************************5....9999999******************************** PP

                         SBP_bac_6  81 l.dPeykgkvalpgnngsdlfealllalykdfgedgvkkllrnlkanlhpaqmvkaa..gslesgepavsvvpyffa 154
                                          + ++g  +   +   ++f+ ++ a++  ++ed+ +++l ++++ +   +++++a  ++++sg+ a+  + +++a
  gi|336253443|ref|YP_004596550.1| 203 PgTEALQGTMGWAPTY--GAFKSFVTAMRLIQDEDATRQWLVDMREAGTERYGNEYAvsQNVASGSLAAGFANHYYA 277
                                       9889999999988877..7*********************************66666448899999*********** PP

                         SBP_bac_6 155 dilpekkkgknlkvvwPed..Galvspifmlvkkg.kkkelakafidfllspevqailakaggvfPvv..t 220
                                         +++++  +++++   e   Gal+++  +l+++g ++ el++ f+  lls+e+q++++  ++ +P++  +
  gi|336253443|ref|YP_004596550.1| 278 MRVKNQQPDAPIDLAFTEGdaGALINVAGALKVQGtQRGELVDNFVRHLLSAEAQEYFTTVSFAYPMIegV 348
                                       ******999988888888668*********************************************97542 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   7.0   1.2e-10   5.4e-07      13     315 .]      92     333 ..      82     333 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.2e-10
                                       HHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCHHHHHHTTECTTCC CS
                         SBP_bac_1  13 lvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllpldpyvkaylapgvkd 88 
                                       +v + +++ +p+ +V  ++ +s slaq +   + +G+++aDv+++ d + ++  a++++++pl++ +++  ++ +  
  gi|336253443|ref|YP_004596550.1|  92 FV-NMLQEIYPDFEVYPNDDSSASLAQTIVEEVDSGAAQADVFWSiDASSLGFVADNDAYEPLSDEAVEAVGNAQFV 167
                                       44.4457779************************************************************9988877 PP

                                       TEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHHH CS
                         SBP_bac_1  89 aadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggsasgta 165
                                       + d+++  v +              ar++ YN+  + ++++  p t +++       +e+  ++             
  gi|336253443|ref|YP_004596550.1| 168 GDDNAWAGVAGR-------------ARAVPYNTEELSESDI--PNTVQDFP-----GTEALQGT------------- 211
                                       788887777655.............8889998888888777..78888777.....44444444............. PP

                                       HHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHH.HHHTTSCSEEEEE CS
                         SBP_bac_1 166 yyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaala.lfeaGeaamaivg 241
                                             +a  +g           ++  +vta   +++  a++ +  +++ +g+e ++++ a++  +++G  a++++ 
  gi|336253443|ref|YP_004596550.1| 212 ----MGWAPTYG-----------AFKSFVTAMRLIQDEDATRQWLVDMREAGTERYGNEYAVSqNVASGSLAAGFAN 273
                                       ....22233334...........55666778888888889999999999999999999987751577*******999 PP

                                       HHHHHHHHCEEEEECHHCHHHHT.TSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHHHH CS
                         SBP_bac_1 242 lwaalaamkvapkvafaadkekp.keelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspeaqa 315
                                       +++   am v++++++a+++  + +++ g+             +++ g   + g++  e +  F++ lls+eaq+
  gi|336253443|ref|YP_004596550.1| 274 HYY---AMRVKNQQPDAPIDLAFtEGDAGAL------------INVAGALKVQGTQRGELVDNFVRHLLSAEAQE 333
                                       999...4555555544444444403344444............599***************************96 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   2.7   7.3e-11   3.3e-07      20     267 ..     111     347 ..      96     359 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 7.3e-11
                                       -SSSHHHHHHHHHHTT---SEE.EEE-.HHHHHHHHHTTSB--GGGSTTHHH-HHHHHTT..--TS.----EEEEEE CS
                         SBP_bac_8  20 asndleqklkaalaagtapdidvvwan.edalatlaeeglladlsdldnlddltdalaav..gydgklygvPyaset 93 
                                       +s+ l+q++  ++ +g a+ +dv+w   ++ l+  a++++ ++lsd+     ++++ +a+  g d + +gv      
  gi|336253443|ref|YP_004596550.1| 111 SSASLAQTIVEEVDSGAAQ-ADVFWSIdASSLGFVADNDAYEPLSDE----AVEAVGNAQfvGDDNAWAGVAGR--- 179
                                       567899***********96.5888876266688888899999*9983....33333333333667756666644... PP

                                       E-EEEEEHHHHHHS.---BHHHHHHHHHHHHHH-SEGG---G....GGGGGTHHETTEE---H..HHH.HHHHHHHH CS
                         SBP_bac_8  94 pyvliynkdllekaedpktwdellaaakklkgkfglpdpasg....wlqaallakdgksldddggkdglkealellk 166
                                         ++ yn++ l++ + p t++++    ++l+g +g++ p++g    ++ a+ l+ +     d       ++++++l 
  gi|336253443|ref|YP_004596550.1| 180 ARAVPYNTEELSESDIPNTVQDFPG-TEALQGTMGWA-PTYGafksFVTAMRLI-Q-----DE------DATRQWLV 242
                                       46899*******868********77.79*******84.5555222233444444.2.....22......899***** PP

                                       HHHHTT-.EE-S..--SSTTTTTSBSEEEE...-TTHHHHHH-TTT.SEEEE--S--EEEEEEEEEEBTTS-HHHHH CS
                         SBP_bac_8 167 klkdngk.tydtgadavsefanGevaftin...gswdiaaaqkagk.klgaivpkqgsfaggkglavpknaknedla 238
                                       +++++g+  y++  ++ +++a+G+ a++++   +  ++ + q + + +l+++    g++++++g +   ++   +l 
  gi|336253443|ref|YP_004596550.1| 243 DMREAGTeRYGNEYAVSQNVASGSLAAGFAnhyYAMRVKNQQPDAPiDLAFTEGDAGALINVAGALKVQGTQRGEL- 318
                                       ******889999999**************6343666666666433225555433558********99999999999. PP

                                       HHHHHHHHTTSHHHHHHHHHH---BS-S- CS
                         SBP_bac_8 239 AldFlkwltspenqaalaektgyipvnks 267
                                          F+++l+s+e+q+ + + +   p + +
  gi|336253443|ref|YP_004596550.1| 319 VDNFVRHLLSAEAQEYFTTVSFAYPMIEG 347
                                       ***************99887666666665 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   1.4   7.6e-09   3.4e-05      24     225 ..     101     336 ..      80     340 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 7.6e-09
                                       H---EEEEESSHHHHHHHH....HHH...-SEEEESSH.HHHHHHHHGGGGG........GG-EEEEEEEEEEEEST CS
                        SBP_bac_11  24 tgvkvevsaggsgklarqi....adga.rpDvwipassawlellaaaglvqa........esavplassplviavpk 87 
                                       ++ +v     +s+ la++i     +ga ++Dv+++ ++  l  +a++++  +          ++ +++   ++a  +
  gi|336253443|ref|YP_004596550.1| 101 PDFEVYPNDDSSASLAQTIveevDSGAaQADVFWSIDASSLGFVADNDAYEPlsdeaveaVGNAQFVGDDNAWAGVA 177
                                       5556677777888888888777788888****************999888888877777777788888889999999 PP

                                       T-.TT---SHHHHHHS..........S--EEEE--T-TTTTHH.HHHHGGG--.......HHHHHHHHHTEEEEESS CS
                        SBP_bac_11  88 gn.pkkikgwadLlkp..........glklavadPttspsGlaalalleaaga.......qellkalekkvvklges 146
                                       g+  + +++ ++L             g++    +  ++p++ a +++++a          +++l  +++  +   ++
  gi|336253443|ref|YP_004596550.1| 178 GRaRAVPYNTEELSESdipntvqdfpGTEALQGTMGWAPTYGAFKSFVTAMRLiqdedatRQWLVDMREAGTERYGN 254
                                       995234445555554434444444548899999999*9*99999999998855445567788888888888877778 PP

                                       HHHHHHHHHTTT-SEEEEEHHHH...H..HSTTSSEEE.E--TTT--...EEEEEE.EE-TT--HHHHHHHHHTTSH CS
                        SBP_bac_11 147 srqlltaveageadagivyesea...kaaengdkleav.ylpeglnldpldypaav.lkkaakreaAraFlafLrsp 218
                                       +  + + v++g+ +ag+++   a   k +++ +++++  +  +   l  + ++ a+ ++++++ e  + F++ L+s+
  gi|336253443|ref|YP_004596550.1| 255 EYAVSQNVASGSLAAGFANHYYAmrvKNQQPDAPIDLAfTEGDAGAL--INVAGALkVQGTQRGELVDNFVRHLLSA 329
                                       8888888**********988877665767777777776444444444..444444404577777************* PP

                                       HHHHHHH CS
                        SBP_bac_11 219 eaqailr 225
                                       eaq+ ++
  gi|336253443|ref|YP_004596550.1| 330 EAQEYFT 336
                                       ****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); 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:                         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 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2962.50
//
Query:       gi|336253444|ref|YP_004596551.1|  [L=536]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-28   97.2  53.4    5.6e-15   55.5  12.2    3.8  3  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 !   54.3  14.5   7.8e-19   1.4e-14       2     132 ..      82     229 ..      81     267 .. 0.84
   2 !    4.2   6.0    0.0018        32      96     168 ..     295     358 ..     288     365 .. 0.60
   3 !   55.5  12.2   3.1e-19   5.6e-15       2     173 ..     359     527 ..     358     535 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 7.8e-19
                      BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf..............vilsilghlilpviilll 61 
                                       il+G+ +a   ++ + +++++ ++li ++l++Ps++ a+ +v +f              v +    +++ +++++l+
  gi|336253444|ref|YP_004596551.1|  82 ILIGVPLAlltVQGSIPFSRFWTVLIALPLAVPSYLGAFAFVSAFgpegefadllaplgVESVPSIYGFAGAAFVLT 158
                                       67777778777788899*******************99999999999999999999996555555588999****** PP

                      BPD_transp_1  62 lsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflg 132
                                       l++ pyv+l++ra l sl+ +lveaar+l a+rw+ fr+++lP++lp i +g++l++ ++l ++  + ++ 
  gi|336253444|ref|YP_004596551.1| 159 LYTYPYVFLTTRASLLSLDGSLVEAARTLNAGRWEAFRRITLPQILPGITAGALLVALYALADFGTPNIMR 229
                                       *************************************************************9998776655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0018
                      BPD_transp_1  96 qifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlll 168
                                       + +   vlP a+  ++  l++a+         l +++++pG +  +l++ ++y +++++ +++la++++vl+ 
  gi|336253444|ref|YP_004596551.1| 295 R-YAALVLPTAIALLAIALPIAIF-------GLWLVTGGPGYQVGRLTFDWEYGFNSAY-VALLAAIASVLVA 358
                                       4.3334444444444444444444.......4446777999999999999999999888.5555555555443 PP

  == domain 3  score: 55.5 bits;  conditional E-value: 3.1e-19
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.vilsilghlilpviillllsaapyvrlirraalr 77 
                                       ++++i +a  + ++l  l ++  +v++++P +vlai l+ +   +l +++ ++  +++++++ ++p ++  +r    
  gi|336253444|ref|YP_004596551.1| 359 LPIAIGSA-TSDSRLAALADRAPYVGYATPGIVLAIALLSFTlDVLPAIYKTVPLLVFAYVVRFMPQAIGSIRTSTL 434
                                       68888888.89999***********************997778888899999999********************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                       ++++ lveaar+lG sr  +fr v+lP++lp ++tg++l+f   +++  ++++l    +lg  +l + +++   +++
  gi|336253444|ref|YP_004596551.1| 435 QVDRRLVEAARTLGRSRLNTFRSVTLPLILPGVVTGAALVFLTTMKELPATLMLR---PLGFETLVTFIWRVEEAGL 508
                                       ******************************************************9...6777777777777777676 PP

                      BPD_transp_1 155 nggvlalviavlllnlvad 173
                                       +g +++ ++++++++ +++
  gi|336253444|ref|YP_004596551.1| 509 YGQAAVPALVLVVVSGLSM 527
                                       5555555555555544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); 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:                         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: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3876.72
//
Query:       gi|336253445|ref|YP_004596552.1|  [L=697]
Description: hypothetical protein Halxa_2048 [Halopiger xanaduensis SH-6]
Scores for complete 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   51.7  12.5    1.1e-13   51.7  12.5    3.3  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
    0.00075   19.2   6.0    0.00075   19.2   6.0    2.0  2  PMT       Dolichyl-phosphate-mannose-protein mannosyltransfer


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 ?    0.7   0.2     0.061   5.4e+02      26      48 ..      18      40 ..       9      44 .. 0.77
   2 !   51.7  12.5   1.2e-17   1.1e-13      10     154 ..      93     239 ..      85     244 .. 0.89
   3 ?    2.6   0.2     0.016   1.5e+02      32      69 ..     308     345 ..     297     356 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.061
                             PMT_2 26 lvsalagvltilllyllarrlfg 48
                                       + a+++++++++++lla r f+
  gi|336253445|ref|YP_004596552.1| 18 AAVAVVALVGAVAVWLLATRTFQ 40
                                      56678888889999999988886 PP

  == domain 2  score: 51.7 bits;  conditional E-value: 1.2e-17
                             PMT_2  10 lalftklfgfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwalal 86 
                                        a++++l g+  ++ rl+   +++  ++l+ l++r+ f+ r++++aa+ + ++plf+  sa + p+ap +++ ++++
  gi|336253445|ref|YP_004596552.1|  93 PAAIFAL-GELVWSYRLALPAIAAAILALVALVVREAFDGRTGIAAAVAVLCSPLFLLESAVYLPYAPTTMCNLAFA 168
                                       5678888.9999***************************************************************** PP

                             PMT_2  87 ylllraleknklkywllagvlfGlgflsK.ytaallliaallyllis.arr.ilkekkpylalllalllfs 154
                                       y+++ra  ++ +++ + ag+++Gl+f+ + yta+l++ ++++ + ++ +r  + + ++ +++++l+l+ ++
  gi|336253445|ref|YP_004596552.1| 169 YCYFRADRTDDVRWAAGAGAAIGLAFFARpYTAVLFAAPFIVHACWTlWRDpRAALPRQLATATLGLAGVA 239
                                       *****************************555666666688888888777778888888888888888775 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.016
                             PMT_2  32 gvltilllyllarrlfgkraallaalllavvplfvals 69 
                                       ++ +++++ +++rr +++r a+la +  +vv  +v+  
  gi|336253445|ref|YP_004596552.1| 308 AAAAAVGFVATVRRGLSPRQAVLAGVAPSVVVGNVFFW 345
                                       5677889999******************9987655544 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.15   1.3e+03     183     205 ..      17      39 ..      11      58 .. 0.73
   2 !   19.2   6.0   8.3e-08   0.00075      83     204 ..     104     220 ..      98     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.15
                               PMT 183 wvglftvllvgllliwelwqllg 205
                                       + ++ +v+lvg +++w l ++ +
  gi|336253445|ref|YP_004596552.1|  17 YAAVAVVALVGAVAVWLLATRTF 39 
                                       55677788888888887776655 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 8.3e-08
                               PMT  83 vslRlfsallgslivplvyltllelgfskltallaallvllenslitlsryilldspLlfftllsmyclvkferkap 159
                                       +s+Rl      + i++lv  ++++  f+ +t++ aa+ vl +++++ +s   l  +p ++ +l+  yc+ ++     
  gi|336253445|ref|YP_004596552.1| 104 WSYRLALPAIAAAILALVA-LVVREAFDGRTGIAAAVAVLCSPLFLLESAVYLPYAPTTMCNLAFAYCYFRAD---- 175
                                       6777644444444555554.55666899********************************************6.... PP

                               PMT 160 fsrswwlwllltgvalglavsvK.wvglftvllvgllliwelwqll 204
                                        +     w+  +g a+gla  +  + ++++ +++ + ++w lw+  
  gi|336253445|ref|YP_004596552.1| 176 -RTDDVRWAAGAGAAIGLAFFARpYTAVLFAAPFIVHACWTLWRDP 220
                                       .7899**************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 5106.86
//
Query:       gi|336253446|ref|YP_004596553.1|  [L=177]
Description: hypothetical protein Halxa_2049 [Halopiger xanaduensis SH-6]
Scores for 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   34.0   0.0    3.9e-08   33.6   0.0    1.2  1  Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3


Domain annotation for each model (and alignments):
>> Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   2.2e-12   3.9e-08       5     128 ..      41     156 ..      37     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.2e-12
                   Gluconate_2-dh3   5 allaaladrIiPstdtgpgakeagvaafidrqlad..aplppeqeayrkg....laaldayaraeygksFveldgaq 75 
                                       +++ a+a++++Ps+ +       gv +f++ ++ d  a+     ea+  +    +a ld+ya+a y+ sF++l+++ 
  gi|336253446|ref|YP_004596553.1|  41 ETMVAAAEVLYPSAVD-------GVREFVESYVGDraAA----DEAWAGEvadvVAYLDDYADAWYDGSFASLSPEN 106
                                       6788899999999655.......899***9999993333....455555544449999******************* PP

                   Gluconate_2-dh3  76 qdalLealekeaeakgtgealeasaeahfFsllreltlegyftspigggna.lg 128
                                       +da L+ + ++a a+++    ++ + ++    + +  l + ++sp gg+ + l+
  gi|336253446|ref|YP_004596553.1| 107 RDAALRRMGADAAASDP----DGGSVERVRYYVVNELLFALYASPTGGELVgLE 156
                                       ***********876333....444445566669999***********9866555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1510.92
//
Query:       gi|336253447|ref|YP_004596554.1|  [L=348]
Description: Ion transport 2 domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-18   66.5  13.1    8.5e-09   34.9   0.3    3.6  3  Pentapeptide    Pentapeptide repeats (8 copies)
    2.8e-14   52.8   0.2    2.8e-14   52.8   0.2    1.6  2  Ion_trans_2     Ion channel
    1.5e-13   50.7   1.8    2.3e-08   34.0   0.2    2.4  2  Pentapeptide_4  Pentapeptide repeats (9 copies)
    4.4e-10   39.5  10.3    0.00095   19.3   0.7    3.3  2  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
      0.076   12.2   0.0      0.094   11.9   0.0    1.2  1  Ion_trans       Ion transport protein


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 !   10.5   0.2    0.0001      0.37      13      28 ..      60      75 ..      59      77 .. 0.56
   2 !   34.9   0.3   2.4e-12   8.5e-09       8      40 .]      76     108 ..      76     108 .. 0.96
   3 !   26.7   2.5   8.7e-10   3.1e-06       2      39 ..     115     152 ..     114     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                      CEECCCESEEECT-B- CS
                      Pentapeptide 13 LsganlsgAnLtgAnl 28
                                      L+gan+++A+L+++++
  gi|336253447|ref|YP_004596554.1| 60 LDGANFREATLSDTSF 75
                                      5555555555555554 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 2.4e-12
                                       -CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   8 LsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                       L g++L +a++++A+L+gA+ls +dL++a +++
  gi|336253447|ref|YP_004596554.1|  76 LAGCSLVEADFTDAVLDGADLSETDLRRATFRD 108
                                       789****************************97 PP

  == domain 3  score: 26.7 bits;  conditional E-value: 8.7e-10
                                       B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                       +++ AnL+ a +  a+l+gA++++A l++A L++++L+
  gi|336253447|ref|YP_004596554.1| 115 SFRAANLHDAAFVFADLRGADFRDARLYRAALTDVRLN 152
                                       68889999999999999999999999999999988875 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       4.3   1.5e+04      54      63 ..     246     255 ..     241     264 .. 0.52
   2 !   52.8   0.2   7.9e-18   2.8e-14      24      77 ..     293     346 ..     266     348 .] 0.89

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4.3
                                       HHHHHHHHHH CS
                       Ion_trans_2  54 ftivyillGl 63 
                                       +++ ++l+ +
  gi|336253447|ref|YP_004596554.1| 246 VATSLLLIVV 255
                                       4444444333 PP

  == domain 2  score: 52.8 bits;  conditional E-value: 7.9e-18
                                       -HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2  24 sfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkvl 77 
                                        fl++lYfs+vt+ T+GYGdi p++++ r+++ v++llG +l+al++ vl++ +
  gi|336253447|ref|YP_004596554.1| 293 AFLKSLYFSVVTFATLGYGDIQPVGQWARAIASVETLLGSLLMALLVFVLTQSV 346
                                       69**********************9999*******************9998876 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.2   6.6e-12   2.3e-08      13      77 .]      60     126 ..      57     126 .. 0.93
   2 !   23.7   0.1   1.1e-08     4e-05      16      77 .]     104     167 ..     103     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 6.6e-12
                    Pentapeptide_4  13 lsnvnFsearlrdcnF.tecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdidF 77 
                                       l+++nF+ea+l d++F  +c l+++ F++++l+ +d++e+dl+ra+F  ++  ++ f++  l+d+ F
  gi|336253447|ref|YP_004596554.1|  60 LDGANFREATLSDTSFlAGCSLVEADFTDAVLDGADLSETDLRRATFRDVDAHGTSFRAaNLHDAAF 126
                                       7899*********988358**************************************8768999987 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 1.1e-08
                    Pentapeptide_4  16 vnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlk.nvnf.sdklkdidF 77 
                                       ++F+ ++ ++++F++++l+++ F  ++l+ +df++++l ra+++ ++l+ +++f +++ ++++F
  gi|336253447|ref|YP_004596554.1| 104 ATFRDVDAHGTSFRAANLHDAAFVFADLRGADFRDARLYRAALTDVRLNlETEFgDRTVYEDEF 167
                                       7899999999999999999999999999999999999999999999999999996669888877 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   5.8   3.3e-07    0.0012       2      48 .]      61     105 ..      56     119 .. 0.80
   2 !   19.3   0.7   2.7e-07   0.00095       3      44 ..     113     151 ..     111     152 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.3e-07
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsgat 48 
                                       +ganF+ a +++++ F  + s  +adF++a ++ga  + ++d+++at
  gi|336253447|ref|YP_004596554.1|  61 DGANFREA-TLSDTSFLAGCSLVEADFTDAVLDGADLS-ETDLRRAT 105
                                       67888888.88888888888888888888888888887.88888775 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.7e-07
                    Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdF 44 
                                       g++F+ a ++++a F  a + ++adF++a++ +a  t dv++
  gi|336253447|ref|YP_004596554.1| 113 GTSFRAA-NLHDAAFVFA-DLRGADFRDARLYRAALT-DVRL 151
                                       8999999.**********.*****************9.9987 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.6e-05     0.094     173     237 ..     288     346 ..     205     348 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                                       SSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Ion_trans 173 ntnFdnfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsflllNlliaviadnf 237
                                       +  ++ f+++l++++++  t g+gdi ++ + ++        +++  l + ll++ll+ v + ++
  gi|336253447|ref|YP_004596554.1| 288 RVLVRAFLKSLYFSVVTFATLGYGDIQPVGQWAR------AIASVETLLGSLLMALLVFVLTQSV 346
                                       4446779***************************......9999999999999999998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2922.52
//
Query:       gi|336253448|ref|YP_004596555.1|  [L=156]
Description: DoxX family protein [Halopiger xanaduensis SH-6]
Scores for 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-05   23.7   7.4    5.4e-05   23.7   7.4    1.4  2  DoxX           DoxX
  ------ inclusion threshold ------
      0.016   15.4   0.0      0.029   14.6   0.0    1.4  1  HR_lesion      HR-like lesion-inducing
      0.023   14.8   5.5      0.033   14.3   5.5    1.2  1  DoxX_2         DoxX-like family
      0.042   13.7   0.0      0.048   13.5   0.0    1.1  1  FA_desaturase  Fatty acid desaturase


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   7.4   1.2e-08   5.4e-05       4      85 .]      39     118 ..      36     118 .. 0.97
   2 ?   -3.5   0.1       3.6   1.6e+04      40      43 ..     143     146 ..     132     152 .. 0.47

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.2e-08
                              DoxX   4 llRlllgvlfiahGlqkltgfglegtaaslaalglpppellaylaalvElvgglllllGlltRlaAlalavtllvat 80 
                                       l+Rll g+++ a  ++ l+  + e+ a++ aa g+p+p+l+ + a ++ l+ggl+++l + + +aA a a + l++t
  gi|336253448|ref|YP_004596555.1|  39 LGRLLYGGVLAAMAVDGLM--NTEERAEYAAAKGVPMPALANVGAHALLLLGGLGVALWRVPAIAASAAATFFLGVT 113
                                       89*****************..9******************************************************* PP

                              DoxX  81 ltvhr 85 
                                        ++h+
  gi|336253448|ref|YP_004596555.1| 114 PAMHD 118
                                       *9995 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.6
                              DoxX  40 ppel 43 
                                        ++l
  gi|336253448|ref|YP_004596555.1| 143 GTAL 146
                                       2222 PP

>> HR_lesion  HR-like lesion-inducing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   6.5e-06     0.029      98     137 ..     112     150 ..      82     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.5e-06
                         HR_lesion  98 atvvlydfynydldtkeflrlllkfvqnlalvGaLLffvg 137
                                       +t+ ++df+  d d ++ +++ ++f++n+al+G+ L f+g
  gi|336253448|ref|YP_004596555.1| 112 VTPAMHDFWTVD-DPEQRQQQQINFLKNVALLGTALAFLG 150
                                       68999***9987.44555677789************9998 PP

>> DoxX_2  DoxX-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   5.5   7.3e-06     0.033       6     101 ..      47     146 ..      42     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.3e-06
                            DoxX_2   6 lalffllsGvakllraeevvakfaqlgfpssfvrllGvvellgalgLllplvtaprltplAavglallmvgAiathl 82 
                                       + ++++++G++++   ee ++  a  g+p+ ++  +G+  ll   gL ++l ++p+++  Aa+ ++l ++ A++  +
  gi|336253448|ref|YP_004596555.1|  47 VLAAMAVDGLMNT---EERAEYAAAKGVPMPALANVGAHALLLLGGLGVALWRVPAIAASAAATFFLGVTPAMHDFW 120
                                       4556667776666...8888888999************999999999999877************************ PP

                            DoxX_2  83 rrgdpka.......valpavllalal 101
                                       +++dp++        + +++ll  al
  gi|336253448|ref|YP_004596555.1| 121 TVDDPEQrqqqqinFLKNVALLGTAL 146
                                       *****643344444666666666655 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.1e-05     0.048      89     202 ..      32     136 ..       9     153 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                     FA_desaturase  89 feglfryllrlllgllvlgwllalvlglwlrrlarrrapsksrrrkwrllawlllllawlglwlalllllglalllw 165
                                       +++ + +l rll+g ++++        ++  +l  ++++++++++k + + +l+ +    + +l+ll+ lg+a  lw
  gi|336253448|ref|YP_004596555.1|  32 PRRTAVRLGRLLYGGVLAA--------MAVDGLMNTEERAEYAAAKGVPMPALANV---GAHALLLLGGLGVA--LW 95 
                                       4444445677777777777........38888888888888877644444443333...34444444444555..99 PP

                     FA_desaturase 166 lvplllllfllalvl..nyveHyg..gdwgerqvetsasir 202
                                        vp++++ ++ +++l  + + H +  +d++e++ +++ ++ 
  gi|336253448|ref|YP_004596555.1|  96 RVPAIAASAAATFFLgvTPAMHDFwtVDDPEQRQQQQINFL 136
                                       99999999988888888888888888777777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1187.24
//
Query:       gi|336253449|ref|YP_004596556.1|  [L=247]
Description: family 2 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for 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-20   72.3   0.0    5.2e-20   71.9   0.0    1.1  1  Glycos_transf_2  Glycosyl transferase family 2
    6.1e-05   23.0   0.1    7.5e-05   22.7   0.1    1.1  1  Glyco_tranf_2_3  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 !   71.9   0.0   5.8e-24   5.2e-20       1     168 [.      30     184 ..      30     186 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 5.8e-24
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       svv+ tyNee+ + ++l  + +  ++ + e+++vD +S D+t+ei++e+     + +v+ +   +G++ a++a++ +
  gi|336253449|ref|YP_004596556.1|  30 SVVMGTYNEEEAIGKVLSDIEEV-TDGKAEVVCVDGSS-DRTPEIAREH-----GATVVEQR-PQGYGVAVRAAILE 98 
                                       8**********************.**********9999.**********.....99999999.88************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                        +  ++++ D Dd+++ + l++++e +++ g+dvv g r +++ e  +   +    + ++ +  +     +  +++ 
  gi|336253449|ref|YP_004596556.1|  99 PDRPIVVTTDCDDTYPMEQLPEFLELINE-GYDVVSGDRLYHGAEAMPAFNR----FGNHAFAAIASVLMGTRVHDT 170
                                       *****************************.********************98....78******************* PP

                                       STCCCEEEEHHHHH CS
                   Glycos_transf_2 155 igsaallrrealee 168
                                       + +++++rr+++e+
  gi|336253449|ref|YP_004596556.1| 171 TTGMRAYRRDVVES 184
                                       ***********986 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   0.1   8.4e-09   7.5e-05       3     180 ..      28     189 ..      26     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8.4e-09
                   Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksral 79 
                                       dl+v+  t+nee+ +g+vl ++   + +  ev v+vd+s++ t e a+e    +++   + vv +r  g ++++r  
  gi|336253449|ref|YP_004596556.1|  28 DLSVVMGTYNEEEAIGKVLSDIEEVTDGKAEV-VCVDGSSDRTPEIARE----HGA---T-VVEQRPQGYGVAVR-- 93 
                                       599********************988788886.6889999999999998....555...4.45777556666666.. PP

                   Glyco_tranf_2_3  80 nealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarralg 156
                                         a+   ++ +v+  D D+    + l+ +l ++  +++++v ++++ +++  +++a ++ + ++ ++ + ++    +
  gi|336253449|ref|YP_004596556.1|  94 -AAILEPDRPIVVTTDCDDTYPMEQLPEFLELI-NEGYDVVSGDRL-YHGAEAMPAFNR-FGNHAFAAIASVLMGTR 166
                                       .788888899***********9999*******9.********9975.667777777777.33555555555555556 PP

                   Glyco_tranf_2_3 157 vltlnGsgslirrevlkelegldp 180
                                       v   ++ + ++rr+v++ +  +++
  gi|336253449|ref|YP_004596556.1| 167 VHDTTTGMRAYRRDVVESI-AWTE 189
                                       877688899********99.7776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1998.48
//
Query:       gi|336253450|ref|YP_004596557.1|  [L=543]
Description: GMC oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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   83.3   0.2    8.4e-23   81.5   0.2    2.0  1  GMC_oxred_C     GMC oxidoreductase
    1.8e-14   53.9   0.0    2.9e-14   53.1   0.0    1.4  1  GMC_oxred_N     GMC oxidoreductase
    6.4e-09   35.4   0.5     0.0018   17.5   0.2    2.2  2  FAD_binding_2   FAD binding domain
    2.8e-07   30.1   1.6    0.00053   19.3   0.1    2.1  2  FAD_binding_3   FAD binding domain
      1e-06   28.6   5.8    1.4e-05   24.9   3.8    3.0  3  DAO             FAD dependent oxidoreductase
    6.7e-06   25.1   0.4    0.00072   18.4   0.2    2.1  2  HI0933_like     HI0933-like protein
    3.4e-05   23.2   0.0     0.0012   18.1   0.0    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0001   22.5   0.2    0.00047   20.3   0.2    2.2  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00025   20.2   0.3    0.00035   19.7   0.3    1.2  1  Lycopene_cycl   Lycopene cyclase protein
     0.0072   16.0   0.0      0.026   14.2   0.0    1.9  2  ApbA            Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.026   15.1   2.3      0.065   13.8   2.3    1.7  1  Fer4_7          4Fe-4S dicluster domain
      0.033   14.4   0.0       0.42   10.9   0.0    2.4  2  TrkA_N          TrkA-N domain
      0.041   13.8   0.0      0.074   12.9   0.0    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.046   14.3   0.1       0.35   11.5   0.0    2.3  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.051   14.1   0.1       0.71   10.5   0.1    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.058   12.7   0.0       0.12   11.6   0.0    1.4  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.06   13.5   0.1       0.12   12.5   0.1    1.5  1  Fer4_10         4Fe-4S dicluster domain
      0.076   12.9   1.0        0.2   11.6   1.0    1.8  1  Fer4            4Fe-4S binding domain
       0.17   11.1   0.0       0.29   10.3   0.0    1.3  1  Thi4            Thi4 family
       0.19   11.8   0.0       0.49   10.4   0.0    1.6  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
        0.2   11.8   0.6       0.38   10.9   0.6    1.4  1  Fer4_21         4Fe-4S dicluster domain
       0.23   11.0   0.1       0.42   10.2   0.1    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,


Domain annotation for each model (and alignments):
>> GMC_oxred_C  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.2     1e-25   8.4e-23       1     144 []     413     535 ..     413     535 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 1e-25
                                       ----EEEEEST..T-TCCEEEEE--TT-SHHHHHHHHHHHHHHHHHCTSGGGTTEECCEECCCTTTTS.HCHHCHHC CS
                       GMC_oxred_C   1 PesrGrvtlss..sdptgaplidpnylsdprdlaalvealkaarkilaaaaldvleeeltpgaaeetsdaavesdea 75 
                                       P+++++v l++  +d +g+p++d+++ + +r l+++ ++ +   +il++ +   +           + +++v +d+ 
  gi|336253450|ref|YP_004596557.1| 413 PREDSYVGLDRstTDDRGNPVPDVHWNVGDRALRTIERVNEIQERILEELG---A-----------EITWQVGPDN- 474
                                       88999****9999******************99999999999999999992...2...........3445556666. PP

                                       HHCHHHHH-EE-S--B-TT-B-STCGCBSB-TTSBBTT-CSEEE-SGGGSSS--SS-THHHHHHHHHHH CS
                       GMC_oxred_C  76 lekfvkeavltsaHplGtcrMGadpkdsVVDsdlrvhgvdnLrVvDaSvfPsapganptltilalAeka 144
                                               +   +H++Gt+rMG+dp++sVV+++lr+h+++n +++ +SvfP+a+  nptlti+alA ka
  gi|336253450|ref|YP_004596557.1| 475 --------TGPAYHHMGTTRMGDDPAESVVNARLRTHDLENCWIASSSVFPTAGAMNPTLTIAALALKA 535
                                       ........56789*****************************************************997 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.0   3.6e-17   2.9e-14       3     266 ..      27     303 ..      25     327 .. 0.72

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 3.6e-17
                       GMC_oxred_N   3 elveggGsagsvvAaRLsedpstsvlvleaggreknrl..imvlalalklidkklnta..yetepekalngrrlil. 74 
                                         v+g+G ag  vA RL++ + ++v+vleag+r  + +    +  ++ +  d   +++   e+ ++ a+ +    l 
  gi|336253450|ref|YP_004596557.1|  27 VCVIGAGPAGGLVADRLADAG-HEVVVLEAGPRFDSEDrlARQERAIRPAYDRPDVWDgdPERDAHSASGEWYYPLn 102
                                       5689*************9776.6899******977776665555555556666666651144555555554443331 PP

                       GMC_oxred_N  75 .paGktlGGgsvvNwsayiRtpaadldeWeeeagleg...wssdevlpafkkvetaqale.......sdlhgvdgrl 140
                                        ++ k++GG+++   ++ +R +++d+++ +++ g+     +++ +++p++ ++e++  +        +  +    ++
  gi|336253450|ref|YP_004596557.1| 103 hARVKGVGGSTLHWQGMVMRLHEDDFNSESAR-GVGTdwpIDYPDLRPYYAEAERELGVAgasdnpfAPPREEPHPM 178
                                       147789********************996665.66533235899**********66655565544443333334444 PP

                       GMC_oxred_N 141 gvtekgkeesplnkallkaaeelGlp.....vprdlngk....hqcGvcllgvtcrtgarqstarawLrpalerpnl 208
                                       ++     e s   + + +a+ee+G++       r+++         G++  + +c+ ga++++    ++ a e ++ 
  gi|336253450|ref|YP_004596557.1| 179 PA----FEPSYSDSLFAEACEEVGVAmhsvpNARNSEAYddrsACVGYGTCQPVCPAGAKYDATVH-VERA-ESKGT 249
                                       44....344445589***********9997655666666532222244555558*******97654.4445.555** PP

                       GMC_oxred_N 209 eiltgakaekiilegrkkravGVeasdkkgtvkrlvvaakevvvaaGalnsPqlLqrS 266
                                       +++ +a ++++  e+  +r+ +  + + + +  + + +a+  vva+G +++P lL++S
  gi|336253450|ref|YP_004596557.1| 250 TVIDRAPVQRL--EHGADRIEAAVYATPEDE--EQRQEADAFVVACGGVETPRLLLLS 303
                                       ***********..999***988777777777..688899****************998 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   2.2e-06    0.0018       1      36 [.      26      61 ..      26      67 .. 0.93
   2 !   16.0   0.0   6.1e-06     0.005     147     204 ..     240     296 ..     229     313 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.2e-06
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      Dv ViG+G AG   A ++a+aG++v+v+e +++f +
  gi|336253450|ref|YP_004596557.1| 26 DVCVIGAGPAGGLVADRLADAGHEVVVLEAGPRFDS 61
                                      99*****************************99877 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 6.1e-06
                                       HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                        ve+a++ g+++ +r+++++L +  +r+  av + pe++++++ +a+a v+a+gG++ 
  gi|336253450|ref|YP_004596557.1| 240 HVERAESKGTTVIDRAPVQRLEHGADRIEAAVYATPEDEEQRQ-EADAFVVACGGVET 296
                                       578999999**************999********888877665.99*********996 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   6.5e-07   0.00053       2      32 ..      25      55 ..      24      64 .. 0.92
   2 !    9.9   0.3   0.00047      0.38     109     166 ..     238     296 ..     192     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.5e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                      +dV+++GaGpaG + a  L+ aG +vv++e 
  gi|336253450|ref|YP_004596557.1| 25 ADVCVIGAGPAGGLVADRLADAGHEVVVLEA 55
                                      79***************************96 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00047
                                       HHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEE.EEEE--GTT- CS
                     FAD_binding_3 109 riLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrak.YlvGaDGgrS 166
                                        + ve+ae++g++v   + v+ le+  + ++a v+   ++ee++ +a+ ++v++ G+ +
  gi|336253450|ref|YP_004596557.1| 238 TVHVERAESKGTTVIDRAPVQRLEHGADRIEAAVYATPEDEEQRQEADaFVVACGGVET 296
                                       556899*****************************88888888888866*******976 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   3.8   1.7e-08   1.4e-05       1     207 [.      26     300 ..      26     321 .. 0.60
   2 ?   -3.9   0.0       9.4   7.7e+03      60      77 ..     347     364 ..     331     371 .. 0.81
   3 ?   -0.6   0.0      0.92   7.5e+02     123     157 ..     504     536 ..     420     539 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.7e-08
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGGGSSEEEEESSS....STHHSTH............... CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags.gaSgrnsgllhsgl....rylpeas............... 55 
                                       dv++iG+G +G  +A  La +g  V++le+g+++ s     r  + +++++                          
  gi|336253450|ref|YP_004596557.1|  26 DVCVIGAGPAGGLVADRLADAGheVVVLEAGPRFDSeDRLARQERAIRPAYdrpdV-----Wdgdperdahsasgew 97 
                                       9******************9999********9888658888888999998854440.....2445555566666777 PP

                                       ................................................HHHHHHHHHHHHHHHHHHHHSSTTSEEEE CS
                               DAO  56 ................................................elarlslealeelreleeelgididyrrt 84 
                                                                                       +l + ++ea +el                
  gi|336253450|ref|YP_004596557.1|  98 yyplnharvkgvggstlhwqgmvmrlheddfnsesargvgtdwpidypDLRPYYAEAEREL---------------- 158
                                       7777778888887766655544444444444444444444444444443334444444444................ PP

                                       EEEEEESS...............HHHHHHHH............HHHHHHHHTTTTEEEEEHHHHHHHSTTSTTTSEE CS
                               DAO  85 Gllslaad...............eeeleald............kllallleagldaelldaeevrelepalpgllga 134
                                              +               +                     +++++e g+  + +    +r  e   ++  + 
  gi|336253450|ref|YP_004596557.1| 159 -------GvagasdnpfappreeP------HpmpafepsysdsLFAEACEEVGVAMHSVPN--ARNSEA-YDDRSAC 219
                                       .......03333333333333331......0222222322222244445778887654444..333333.2233455 PP

                                       EEETTEEEEEH..HHHHHHHHHH.HHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEE.EEEEE.EEE--GGGH CS
                               DAO 135 lfypdtgqvdp..akltaalara.aealGveilegtevtgleeedgkvwgve.rttp.gen.daada.vVnaaGaws 204
                                       ++y ++  v+p  ak+ a +  + ae++G +++ +++v++le+  +++      t + +e+ ++ada vV + G+ +
  gi|336253450|ref|YP_004596557.1| 220 VGYGTCQPVCPagAKYDATVHVErAESKGTTVIDRAPVQRLEHGADRIEAAVyATPEdEEQrQEADAfVVACGGVET 296
                                       667777666551146666655555*****************885444444446555556555688998888888888 PP

                                       H.HH CS
                               DAO 205 d.ll 207
                                         ll
  gi|336253450|ref|YP_004596557.1| 297 PrLL 300
                                       8543 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 9.4
                                       HHHHHHHHHHHHHHHHSS CS
                               DAO  60 lslealeelreleeelgi 77 
                                       l+ e++++++e ++e+++
  gi|336253450|ref|YP_004596557.1| 347 LTSESHQFYDEADDEYAP 364
                                       678999999999999875 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.92
                                       HHSTTSTTTS.EEEEETTEEEEEHHHHHHHHHHHHH CS
                               DAO 123 elepalpgll.galfypdtgqvdpakltaalaraae 157
                                       +le   +++   + ++p++g ++p   +aala +a+
  gi|336253450|ref|YP_004596557.1| 504 DLE---NCWIaSSSVFPTAGAMNPTLTIAALALKAA 536
                                       344...245535578999999999999999999886 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   8.8e-07   0.00072       2      35 ..      26      59 ..      25      62 .. 0.93
   2 ?    4.7   0.0     0.012        10     117     170 ..     242     299 ..     234     300 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.8e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35
                                      dv viG+G+AG + A ++a++g++V++le+++++
  gi|336253450|ref|YP_004596557.1| 26 DVCVIGAGPAGGLVADRLADAGHEVVVLEAGPRF 59
                                      89***************************99875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.012
                                       HHHHHHT-EEE-S--EEEEECETTE...EEEEE...TTEEEEESEEEE----SS-GGG CS
                       HI0933_like 117 kelkeagvklrletevksvekeedgk..frvkt..kseeeleadklvlAtGGlSiPkl 170
                                       ++++++g ++  +  v+++e+ +d++     +t  ++e++ ead+ v+A+GG   P+l
  gi|336253450|ref|YP_004596557.1| 242 ERAESKGTTVIDRAPVQRLEHGADRIeaAVYATpeDEEQRQEADAFVVACGGVETPRL 299
                                       67778888888888888887766652112233333588899***********999986 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 !   18.1   0.0   1.5e-06    0.0012       2     175 ..      26      57 ..       9      72 .. 0.71
   2 ?    2.7   0.0     0.073        59      66     110 ..     248     296 ..     194     316 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.5e-06
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvki 78 
                                       dv+viG+GpAG  +a +la ag++v+++e++                                              
  gi|336253450|ref|YP_004596557.1|  26 DVCVIGAGPAGGLVADRLADAGHEVVVLEAG---------------------------------------------- 56 
                                       6777777777777777777777777776533.............................................. PP

                                       EESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  79 dpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGv 155
                                                                                                                    
  gi|336253450|ref|YP_004596557.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHHHHHT-EEEEEESSS CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 156 ElAaalaklgkevtlveard 175
                                                          +
  gi|336253450|ref|YP_004596557.1|  57 -------------------P 57 
                                       ...................3 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.073
                                       HCCCCHCCTCEEEEESCEEEEETEEEC..TCEEEEEESEEEE---E..E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx..x RF
                       Pyr_redox_2  66 gielllgeevvkidpgkkkvklekkke..gdeekiaydklvlAtGs..s 110
                                       g +++ +++v ++++g+ +++     +  ++e++ ++d+ v+A G+  +
  gi|336253450|ref|YP_004596557.1| 248 GTTVIDRAPVQRLEHGADRIEAAVYATpeDEEQRQEADAFVVACGGveT 296
                                       3444444445555544444433222113366667777777777775333 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 !   20.3   0.2   5.8e-07   0.00047       1      30 [.      29      58 ..      29      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.8e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdr 30
                                      ++GaG +G + A +La+ag++v++le+++r
  gi|336253450|ref|YP_004596557.1| 29 VIGAGPAGGLVADRLADAGHEVVVLEAGPR 58
                                      8**************************998 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.3   4.4e-07   0.00035       1      35 [.      26      58 ..      26      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.4e-07
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasps 35
                                      Dv viGaGpAg ++A rl  a +g +vv++ea+p 
  gi|336253450|ref|YP_004596557.1| 26 DVCVIGAGPAGGLVADRL--ADAGHEVVVLEAGPR 58
                                      9*****************..999**********97 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   3.1e-05     0.026       1      31 [.      27      57 ..      27      70 .. 0.88
   2 ?   -2.2   0.0       3.6     3e+03     124     149 ..     228     254 ..     224     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                      ++++GaG  G+l+a +La ag++v+++  ++
  gi|336253450|ref|YP_004596557.1| 27 VCVIGAGPAGGLVADRLADAGHEVVVLEAGP 57
                                      69*********************99886665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.6
                                       EEE-EEEEEETTEEEECS.--EEEEEE CS
                              ApbA 124 vtthgatregpgevhhag.kgeikige 149
                                       v++ ga+ +++ +v++a  kg+++i  
  gi|336253450|ref|YP_004596557.1| 228 VCPAGAKYDATVHVERAEsKGTTVIDR 254
                                       89999999******9998688888765 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   2.3   7.9e-05     0.065      10      52 .]     192     233 ..     191     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.9e-05
                            Fer4_7  10 aaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +aC    + ++ + n+ ++ +++ d + C+g g C+ vCP+ga
  gi|336253450|ref|YP_004596557.1| 192 EACEEVGVAMHSVPNA-RNSEAYDDRSACVGYGTCQPVCPAGA 233
                                       5777666777776544.44777888999*************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   0.0   0.00052      0.42       1      31 [.      27      57 ..      27      82 .. 0.84
   2 ?    0.6   0.0      0.77   6.3e+02      25      54 ..     250     280 ..     238     303 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00052
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkde 31
                                      + +iG+G  G  +a++L + g+ +vvv +  +
  gi|336253450|ref|YP_004596557.1| 27 VCVIGAGPAGGLVADRLADaGH-EVVVLEAGP 57
                                      579****************666.6***99866 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.77
                                       EEEESSHHHHHHHHHTTSE.EEES-TTSHHH CS
                            TrkA_N  25 vvidkdeerveelreegle.vvvgdatdeev 54 
                                       +vid+ + +  e+ ++ +e +v++ + dee 
  gi|336253450|ref|YP_004596557.1| 250 TVIDRAPVQRLEHGADRIEaAVYATPEDEEQ 280
                                       5555555333333333333355555555443 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 ?   12.9   0.0     9e-05     0.074       2      43 ..      27      73 ..      26      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S.....-HHHHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi.....seealekalekie 43
                                      v viGaG  G  +a  +a ag+eVv+++      se++l++ +++i+
  gi|336253450|ref|YP_004596557.1| 27 VCVIGAGPAGGLVADRLADAGHEVVVLEAgprfdSEDRLARQERAIR 73
                                      89**************************9777777777777777665 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 ?   11.5   0.0   0.00044      0.35       2      31 ..      27      53 ..      26      72 .. 0.88
   2 ?   -0.4   0.0       2.2   1.8e+03      37      70 ..     258     292 ..     240     307 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00044
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEE CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivva 31
                                      +++iGaG  g  +a +l+ ag   he+vv 
  gi|336253450|ref|YP_004596557.1| 27 VCVIGAGPAGGLVADRLADAG---HEVVVL 53
                                      789******************...***975 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.2
                                       CCHHHHHHHHC..-EEECECHHHHHHH-SEEEE-S- CS
                     F420_oxidored  37 ekaeelaeelg..vkvtavdneeaaeeadvvvlavk 70 
                                       +++e+ a++++  v +t+ + ee  +ead  v+a+ 
  gi|336253450|ref|YP_004596557.1| 258 QRLEHGADRIEaaVYATP-EDEEQRQEADAFVVACG 292
                                       566666666664455677.77778888999999986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00087      0.71       2      37 ..      27      61 ..      26      70 .. 0.88
   2 ?   -0.2   0.0       1.8   1.5e+03      47      72 ..     241     266 ..     235     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00087
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTT CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrl 37
                                      v v+G+G  g  +A  la+ g++V v+e+++++   
  gi|336253450|ref|YP_004596557.1| 27 VCVIGAGPAGGLVADRLADAGHEVVVLEAGPRFD-S 61
                                      78***************************99986.4 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.8
                                       HHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  47 qeklekngievllntkveeiegsedg 72 
                                        e+ e +g +v+  + v+++e+ +d 
  gi|336253450|ref|YP_004596557.1| 241 VERAESKGTTVIDRAPVQRLEHGADR 266
                                       68899999999999999999988876 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 ?   11.6   0.0   0.00015      0.12       2      48 ..      29      74 ..      22      86 .. 0.84
   2 ?   -3.8   0.0       7.3     6e+03     248     267 ..     274     293 ..     242     300 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgnignsiyrypkemtfisp 48
                                      +iGaGPaG  +a  l +ag  ++++lE g   +s  r  ++ + i p
  gi|336253450|ref|YP_004596557.1| 29 VIGAGPAGGLVADRLADAGH-EVVVLEAGPRFDSEDRLARQERAIRP 74
                                      89*****************9.699***99877777777777666665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.3
                       Pyr_redox_3 248 ktedgkkvevkddvvlatGy 267
                                       + ed+++ ++ d +v+a G 
  gi|336253450|ref|YP_004596557.1| 274 TPEDEEQRQEADAFVVACGG 293
                                       33444555556666666554 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00015      0.12       3      24 ..     213     242 ..     211     284 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                           Fer4_10   3 vidddtCirCgkCvkaCPadl........t 24 
                                       + d++ C++ g+C+ +CPa +        +
  gi|336253450|ref|YP_004596557.1| 213 YDDRSACVGYGTCQPVCPAGAkydatvhvE 242
                                       568999*************66555433331 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.0   0.00024       0.2       3      22 ..     214     233 ..     212     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                                       EETTTSSS-THHHHHSTTTE CS
                              Fer4   3 ideekCigCGaCvevCPvgA 22 
                                        d + C+g G+C  vCP gA
  gi|336253450|ref|YP_004596557.1| 214 DDRSACVGYGTCQPVCPAGA 233
                                       689999999**********9 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00036      0.29      17      49 ..      24      55 ..      15      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00036
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer 49
                                      ++Dv ++GaG++G   a  la + + +v++le+
  gi|336253450|ref|YP_004596557.1| 24 DADVCVIGAGPAGGLVADRLADA-GHEVVVLEA 55
                                      68***********99999****9.99****996 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00061      0.49      12      41 ..      24      52 ..      17      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00061
                                      T-EEEEES-SHHHHHHHHHHHCCT-CEEEE CS
                      Shikimate_DH 12 ekkvlliGaGemaelvakhLlakgvkkvvv 41
                                      ++ v++iGaG  + lva  L+++g + vvv
  gi|336253450|ref|YP_004596557.1| 24 DADVCVIGAGPAGGLVADRLADAGHE-VVV 52
                                      789*******************9998.555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.6   0.00047      0.38      17      53 ..     193     231 ..     189     234 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00047
                           Fer4_21  17 aCedtshqaieidaktvlkvv..edeCvGCnlCssvCPv 53 
                                       aCe+ ++   ++ +++  +     + CvG   C  vCP 
  gi|336253450|ref|YP_004596557.1| 193 ACEEVGVAMHSVPNARNSEAYddRSACVGYGTCQPVCPA 231
                                       78887776666655555555422679************5 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 ?   10.2   0.1   0.00051      0.42       2      29 ..      26      53 ..      25      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00051
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigv 29
                                       ++viG+G  G+  a  la +ghev+++
  gi|336253450|ref|YP_004596557.1| 26 DVCVIGAGPAGGLVADRLADAGHEVVVL 53
                                      59***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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):              22  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3792.61
//
Query:       gi|336253451|ref|YP_004596558.1|  [L=240]
Description: hypothetical protein Halxa_2054 [Halopiger xanaduensis SH-6]
Scores for complete 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-67  227.1   0.0      2e-67  226.9   0.0    1.0  1  SRAP      SOS response associated peptidase (SRAP)


Domain annotation for each model (and alignments):
>> SRAP  SOS response associated peptidase (SRAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.9   0.0   1.1e-71     2e-67       1     218 [.       1     225 [.       1     226 [. 0.92

  Alignments for each domain:
  == domain 1  score: 226.9 bits;  conditional E-value: 1.1e-71
                              SRAP   1 MCgRyaltlapeelaeeleae..eedkelrpsynvaptqkvpvvvaeeeeeeeeeeerklqamkwGlvPswakdpkk 75 
                                       MCgRy+ltl++++ +++++a+  ++  e++p+yn ap+q+ pv++++++e        ++++++wGlvPswa+d+  
  gi|336253451|ref|YP_004596558.1|   1 MCGRYTLTLERDAFEDRFGATvdDSVGEFEPRYNAAPGQELPVITDDAPE--------TVRQLEWGLVPSWADDD-- 67 
                                       *******************7654333349****************88888........89************887.. PP

                              SRAP  76 lglktiNaRsetlaekplfrsalkkkRcvvpadGFYEWkkkgkekqPyfikrkdgkllalAGLydvwe......... 143
                                           +iNaR+et+ ekp+fr+a++++Rc+vpadGFYEW ++++ kqPy +  +d++++a+AGL+++we         
  gi|336253451|ref|YP_004596558.1|  68 -CGGMINARAETVDEKPSFRDAYERRRCLVPADGFYEWVETERGKQPYRVALEDDRPFAMAGLWERWEpddettqag 143
                                       .468**********************************889999***********************9888888888 PP

                              SRAP 144 ..........eegeeeklytytiiTteankqlaelHdRmPviLeeeelraWLdprkedskelqellkpaeeeelevy 210
                                                 e+++++ l t+t++T+e+n+ +a+lH+Rm+viLe+++ r+WL     d+ +++ ll+p++++e+++y
  gi|336253451|ref|YP_004596558.1| 144 ldafgggledEDDDDTALETFTVLTAEPNDLVADLHHRMAVILEPDREREWLTA---DDPKAEGLLEPYPADEMRAY 217
                                       88888888764557899***********************************99...6667789************* PP

                              SRAP 211 pVskeVnk 218
                                       pVs++Vn+
  gi|336253451|ref|YP_004596558.1| 218 PVSTAVND 225
                                       ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1860.71
//
Query:       gi|336253452|ref|YP_004596559.1|  [L=159]
Description: universal PUA-domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   60.4   1.3    1.9e-16   59.8   1.3    1.3  1  PUA            PUA domain
  ------ inclusion threshold ------
      0.016   15.4   0.0      0.024   14.9   0.0    1.2  1  UPF0113        UPF0113 PUA domain
      0.086   12.8   0.0       0.13   12.2   0.0    1.3  1  Inhibitor_I24  PinA peptidase inhibitor


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 !   59.8   1.3   3.1e-20   1.9e-16       3      73 ..      79     150 ..      77     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 3.1e-20
                                       EEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA   3 vvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveierv 73 
                                       v+vd+gAv +++ ga+++ pG++e+ +d+e++d V i  e  g+++a+G+a++ +e++   +g++++ +++v
  gi|336253452|ref|YP_004596559.1|  79 VTVDAGAVSFVSDGADVMRPGITEATDDIEPDDLVIIAEEShGKVLAIGRARVPGEDMVGDEGKVVDSLHHV 150
                                       99**************************************88************************999997 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   4.1e-06     0.024      15      71 ..      92     151 ..      78     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.1e-06
                           UPF0113  15 GrdvlkesilkitesvkenqvvvV.lnengeplGiGkirkdt.k.aspgkivvknlaDiG 71 
                                       G dv++ +i + t++++  + v++     g++l+iG++r  + +   ++++vv+ l  +G
  gi|336253452|ref|YP_004596559.1|  92 GADVMRPGITEATDDIEPDDLVIIaEESHGKVLAIGRARVPGeDmVGDEGKVVDSLHHVG 151
                                       89***************9999999345579********9977766778888887776655 PP

>> Inhibitor_I24  PinA peptidase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.2e-05      0.13      31      60 ..      97     126 ..      75     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                     Inhibitor_I24  31 relvkeceddiepdtgiieielsdgkiini 60 
                                       r  + e+ ddiepd  +i  e s gk++ i
  gi|336253452|ref|YP_004596559.1|  97 RPGITEATDDIEPDDLVIIAEESHGKVLAI 126
                                       667899*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1190.62
//
Query:       gi|336253453|ref|YP_004596560.1|  [L=106]
Description: hypothetical protein Halxa_2056 [Halopiger xanaduensis SH-6]
Scores for 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   15.1   0.3       0.67    9.9   0.1    2.1  2  ADD_ATRX         Cysteine Rich ADD domain
      0.041   14.7   4.1        2.4    9.0   0.6    2.2  2  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
      0.053   13.5   0.0      0.084   12.9   0.0    1.3  1  DUF1930          Domain of unknown function (DUF1930)
      0.091   13.1   0.4       0.12   12.7   0.4    1.2  1  DUF3268          zinc-finger-containing domain
       0.17   12.0   3.8         10    6.3   0.1    2.3  2  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> ADD_ATRX  Cysteine Rich ADD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00019      0.67       6      24 ..       7      25 ..       4      31 .. 0.81
   2 ?    3.4   0.0     0.019        69      13      29 ..      47      63 ..      37      65 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00019
                          ADD_ATRX  6 keleeivsCtaCgqqvnhf 24
                                      ++++ +v+C aCg +v + 
  gi|336253453|ref|YP_004596560.1|  7 RNRTTTVTCLACGDEVTRS 25
                                      567789********99865 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.019
                          ADD_ATRX 13 sCtaCgqqvnhfqkdsl 29
                                       C +C +++ h  ++ l
  gi|336253453|ref|YP_004596560.1| 47 LCKSCDRELCHHPRNEL 63
                                      68888888888877765 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2    0.0031        11      10      23 ..       7      19 ..       4      24 .. 0.79
   2 ?    9.0   0.6   0.00067       2.4      16      29 ..      45      58 ..      38      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0031
                   Tnp_zf-ribbon_2 10 kikkeTriiCqeCd 23
                                      ++++ T+ +C +C+
  gi|336253453|ref|YP_004596560.1|  7 RNRT-TTVTCLACG 19
                                      4566.********6 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00067
                   Tnp_zf-ribbon_2 16 riiCqeCdvplCrn 29
                                       + C++Cd  lC  
  gi|336253453|ref|YP_004596560.1| 45 EYLCKSCDRELCHH 58
                                      589*********86 PP

>> DUF1930  Domain of unknown function (DUF1930)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.3e-05     0.084      26      63 ..      52      89 ..      46      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                                      TTEEESS--HHHHHHHTT-BTT-EEEEEETTS-EEEEE CS
                           DUF1930 26 DGavverPDaElksAlvHlHiGEkAqvfFksrRvvviE 63
                                      D  ++++P +El++ lv l +GE+ q  F +r  + +E
  gi|336253453|ref|YP_004596560.1| 52 DRELCHHPRNELEDLLVDLEAGERDQTAFLARYLAAVE 89
                                      7789*************************999888777 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   3.4e-05      0.12       2      46 ..      12      61 ..      11      69 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                           DUF3268  2 ttrCpyCGekvilvsasei..Ykers...kgkllylCpkCdayvgvhkgt 46
                                      t++C  CG++v+   a+e   Y +r     ++  ylC++Cd     h+++
  gi|336253453|ref|YP_004596560.1| 12 TVTCLACGDEVTRSMAREYdkYGNRWdreDKEFEYLCKSCDRELCHHPRN 61
                                      67899****9987766653227654343378899*******999998876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0029        10      25      38 ..      10      24 ..       3      26 .. 0.69
   2 ?    6.2   1.1    0.0031        11       4      14 ..      44      54 ..      43      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0029
                       Zn-ribbon_8 25 plta.CPeCgsevrr 38
                                        t+ C +Cg ev+r
  gi|336253453|ref|YP_004596560.1| 10 TTTVtCLACGDEVTR 24
                                      34555****999998 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0031
                       Zn-ribbon_8  4 YeYrCeeCghe 14
                                      +eY C++C++e
  gi|336253453|ref|YP_004596560.1| 44 FEYLCKSCDRE 54
                                      79******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 836.35
//
Query:       gi|336253454|ref|YP_004596561.1|  [L=265]
Description: hypothetical protein Halxa_2057 [Halopiger xanaduensis SH-6]
Scores for 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-38  130.8  13.5      8e-37  127.1  13.5    1.9  1  ABC2_membrane_2  ABC-2 family transporter protein
    1.9e-09   37.1   4.2    2.6e-09   36.6   4.2    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
    9.9e-07   28.4   5.0    1.4e-06   27.9   5.0    1.2  1  ABC2_membrane    ABC-2 type transporter
    2.1e-06   27.4   1.6    2.1e-06   27.4   1.6    1.6  2  ABC2_membrane_5  ABC-2 family transporter protein
    0.00035   20.6   4.1    0.00051   20.0   4.1    1.2  1  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.13   11.9   5.5       0.26   10.9   5.5    1.5  1  Kinocilin        Kinocilin protein
       0.92    9.0   6.0        2.6    7.5   3.1    2.1  2  DUF1129          Protein of unknown function (DUF1129)
        1.8    8.0   9.3        2.1    7.8   6.8    2.1  2  MTABC_N          Mitochondrial ABC-transporter N-terminal fiv


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 !  127.1  13.5   3.6e-40     8e-37       3     288 .]       8     265 .]       6     265 .] 0.91

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 3.6e-40
                   ABC2_membrane_2   3 iakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvst 79 
                                       ia+kE+ d++r+r ++ +++l++l+ +al +++  ++    +  a+ e+++ l                      s+
  gi|336253454|ref|YP_004596561.1|   8 IARKEVGDAIRNRQLYTNAALFALV-FALIAYLHVDQARAGY--AEPENLVGLL---------------------SG 60 
                                       9************************.6666666544333332..2333344432.....................34 PP

                   ABC2_membrane_2  80 imavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivl 156
                                         +vl+p +a+++++ ai++ +e+g l+llL +P+ R+++++g  +g+ a+   +a +l+++vl+a +++la++++l
  gi|336253454|ref|YP_004596561.1|  61 VSIVLVPAVALMLSYAAIVKRREDGQLALLLGLPHDRRDVVVGTYLGRYAV---LAASLVVGVLAAAVVTLAFSVEL 134
                                       778************************************************...*********************** PP

                   ABC2_membrane_2 157 aledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp...qein 230
                                       a+ +l   +va+ +l+l  +++a+++ lS+++r+++ a   a+++f+++++++  v  +   l +g ++p   + ++
  gi|336253454|ref|YP_004596561.1| 135 AAVELGGYLVAAAVLGL--AYVAIATCLSTLTRDQTWASIGAFVVFMLFVFAWRFVPDAAVFLVNGLEMPsqrPWWH 209
                                       *****************..89**************************************9999999999888899** PP

                   ABC2_membrane_2 231 dflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkrkDl 288
                                       + +  lsp +ay+ +l+ +l gs+ +  ++ a+ +l+ll++++   + gyv+Fk+ Dl
  gi|336253454|ref|YP_004596561.1| 210 PYVGALSPSVAYERALDLVLGGSGDR--TLSAFGALVLLGWAVLAPAAGYVRFKTSDL 265
                                       ***********************877..9**************************997 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 !   36.6   4.2   1.2e-12   2.6e-09     156     340 ..      51     251 ..      17     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.2e-12
                   ABC2_membrane_3 156 lsnvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill..... 226
                                        +n +  l g  i+++++   +++ a +iv+ +e + + l+l  + ++   +++ +lg ++v + +l++ +l     
  gi|336253454|ref|YP_004596561.1|  51 PENLVGLLSGvSIVLVPAVALMLSYA-AIVKRREDGQLALLLGLPHDRRDVVVGTYLGRYAVLAASLVVGVLaaavv 126
                                       45566666664444444444444444.79*****************************9999988887654434443 PP

                   ABC2_membrane_3 227 .lafglgipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffggl.....fp...ledlp 294
                                        laf++++   +lg  l+   + glay+a+++ ls+l+++++ a+i +f+v++l+ +++ ++     f+   le ++
  gi|336253454|ref|YP_004596561.1| 127 tLAFSVELAAVELGGYLVAAAVLGLAYVAIATCLSTLTRDQTWASIGAFVVFMLFVFAWRFVpdaavFLvngLEMPS 203
                                       33777566666*************************************99999666664433333323333444333 PP

                   ABC2_membrane_3 295 ...salkwifsiiPffapglgllrlitgdplweillsliilalfavvyl 340
                                           +  +++ + P++a+  +l +l+ g ++ ++l ++++l+l++ ++l
  gi|336253454|ref|YP_004596561.1| 204 qrpWWHPYVGALSPSVAYERAL-DLVLGGSGDRTLSAFGALVLLGWAVL 251
                                       7778888999999999999999.77777778899999999999988776 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   5.0   6.3e-10   1.4e-06       3     174 ..       5     183 ..       3     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 6.3e-10
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg....nsedglnr....pgllffsvlflafsaltsv 71 
                                       ++++ ++e+  ++r+++l+     ++ l++al+  +   ++     + e+         g+ + +v  +a ++l+ +
  gi|336253454|ref|YP_004596561.1|   5 WRLIARKEVGDAIRNRQLY-TNAALFALVFALIAYLHVDQARagyaEPEN---LvgllSGVSIVLVPAVA-LMLSYA 76 
                                       6778899999999***988.999999999999999988875533433444...14445999999999999.999999 PP

                     ABC2_membrane  72 apvferergvlerelvsplyslsayvlakvlve.lpvsllqalifllivyflvgldls....rfflflllllltala 143
                                       a+v  re g l+ +l  p   + ++v++ +l+  +++++ +++ +l+ +++++ + ++      + +l+++ +++la
  gi|336253454|ref|YP_004596561.1|  77 AIVKRREDGQLALLLGLPH-DRRDVVVGTYLGRyAVLAASLVVGVLAAAVVTLAFSVElaavELGGYLVAAAVLGLA 152
                                       99999**************.99999999999995555555555555555555555555656555999********** PP

                     ABC2_membrane 144 asslgllisalapsfedasqlaslvllplll 174
                                        ++++ ++s+l++++  as+ a++v++++++
  gi|336253454|ref|YP_004596561.1| 153 YVAIATCLSTLTRDQTWASIGAFVVFMLFVF 183
                                       *************************999998 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 ?    1.4   0.4      0.09     2e+02     152     199 ..      26      76 ..      19      81 .. 0.53
   2 !   27.4   1.6   9.5e-10   2.1e-06      40     163 ..      62     186 ..      50     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.09
                   ABC2_membrane_5 152 iiifgiifllvaifslsklelslidlsny...illiillviillliivSyf 199
                                       ++ f+++f l+a +++ +  +   + +n+   ++ + ++++ ++ +++Sy 
  gi|336253454|ref|YP_004596561.1|  26 AALFALVFALIAYLHVDQARAGYAEPENLvglLSGVSIVLVPAVALMLSYA 76 
                                       567777787777777766644444444432212222222333456777775 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 9.5e-10
                   ABC2_membrane_5  40 fsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavl.ikgnvtise 115
                                        ++l+++++ +l   ++ + + ++  ++ll LP +r+++V   Yl+ + + ++++++++l++++++l ++ ++   e
  gi|336253454|ref|YP_004596561.1|  62 SIVLVPAVALMLSYAAIVKRREDGQLALLLGLPHDRRDVVVGTYLGRYAVLAASLVVGVLAAAVVTLaFSVELAAVE 138
                                       45667777777777888888899999**********************************99987772555699999 PP

                   ABC2_membrane_5 116 vllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllva 163
                                       +   ++++ v++l+++ai   l  ++  ++   +  +++f+++++   
  gi|336253454|ref|YP_004596561.1| 139 LGGYLVAAAVLGLAYVAIATCLSTLTRDQTWASIGAFVVFMLFVFAWR 186
                                       ***************************999999888888888776544 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 !   20.0   4.1   2.3e-07   0.00051      19     177 ..      27     180 ..      17     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.3e-07
                   ABC2_membrane_4  19 vlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtkll 95 
                                        l al+++l+a l + ++++ +++p++++ l  ++   ++l+p++  +++   i + ++++ l  Ll +P  r+ ++
  gi|336253454|ref|YP_004596561.1|  27 ALFALVFALIAYLHVDQARAGYAEPENLVGL--LSGVSIVLVPAVALMLSYAAIVKRREDGQLALLLGLPHDRRDVV 101
                                       4566777778888888888888999888875..33344668899988888888888889999*************** PP

                   ABC2_membrane_4  96 laKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpi.ialvllkk.syvlpli 170
                                       ++ ++    + ++ ++v     vl+a +++  +fsv+l +  l  +l+ ++++ +a ++i  +l++l++ + +++++
  gi|336253454|ref|YP_004596561.1| 102 VGTYLGRYAVLAASLVV----GVLAAAVVT-LAFSVELAAVELGGYLVAAAVLGLAYVAIaTCLSTLTRdQTWASIG 173
                                       99877765554444444....444444444.3466777777777777777777777777646898777736799999 PP

                   ABC2_membrane_4 171 ltlvyti 177
                                         +v+++
  gi|336253454|ref|YP_004596561.1| 174 AFVVFML 180
                                       8888765 PP

>> Kinocilin  Kinocilin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.5   0.00012      0.26      16      76 ..     114     175 ..      99     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                         Kinocilin  16 acvalsllags.iiigvsvskaaaavggifigaaglgllllaypflkarfnldrilpaignl 76 
                                       a   +++la + + ++ sv  aa  +gg ++ aa lgl  +a     + +  d+  ++ig++
  gi|336253454|ref|YP_004596561.1| 114 ASLVVGVLAAAvVTLAFSVELAAVELGGYLVAAAVLGLAYVAIATCLSTLTRDQTWASIGAF 175
                                       33445666555155789**********************99999999999999999999976 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.048   1.1e+02      89     135 ..      26      79 ..      18      92 .. 0.75
   2 ?    7.5   3.1    0.0012       2.6      99     166 ..     127     188 ..     101     221 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.048
                           DUF1129  89 lalfallfgilalfskkkqtas.......iGlitlllvalvgGlamvlvyrllt 135
                                        alfal+f+++a+++ +++ a        +Gl++ +++ lv  +a++l y  + 
  gi|336253454|ref|YP_004596561.1|  26 AALFALVFALIAYLHVDQARAGyaepenlVGLLSGVSIVLVPAVALMLSYAAIV 79 
                                       579999999999999988877667787888888888777777776666665554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0012
                           DUF1129  99 lalfskkkqtasiGlitlllvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftl 166
                                       + +fs + +     l  +l+ a+v Gla+v ++++l+       r ++w ++ + ++++++ +++ ++
  gi|336253454|ref|YP_004596561.1| 127 TLAFSVELAAV--ELGGYLVAAAVLGLAYVAIATCLST----LTRDQTWASIGAFVVFMLFVFAWRFV 188
                                       34455444444..4778999****************75....77888888887777777776666554 PP

>> MTABC_N  Mitochondrial ABC-transporter N-terminal five TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2    0.0095        21     168     197 ..      98     127 ..      91     134 .. 0.85
   2 ?    7.8   6.8   0.00092       2.1      71     161 ..     117     208 ..     105     211 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0095
                           MTABC_N 168 dqvefglfvvryvvtlllfvlGlkaPglpk 197
                                         v  g+++ ry+v++  +v+G++a+++++
  gi|336253454|ref|YP_004596561.1|  98 RDVVVGTYLGRYAVLAASLVVGVLAAAVVT 127
                                       567889*******************99875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00092
                           MTABC_N  71 allllllalarlilraallksgevygylilalvlsllawlfsllllllerrkllpslptrgHglvlLlfwtlafvae 147
                                        + +l+ a+++l++++  l   e+ gyl+ a+vl l++ +++ +l +l r ++++s+   +  + +L+ ++  fv  
  gi|336253454|ref|YP_004596561.1| 117 VVGVLAAAVVTLAFSVE-LAAVELGGYLVAAAVLGLAYVAIATCLSTLTRDQTWASIG--AFVVFMLFVFAWRFVPD 190
                                       22222222333333333.5678899*****************************9994..55666666677778877 PP

                           MTABC_N 148 nlafv....swnsedwWf 161
                                       +  f+     + s++ W+
  gi|336253454|ref|YP_004596561.1| 191 AAVFLvnglEMPSQRPWW 208
                                       666531211355666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 1841.75
//
Query:       gi|336253455|ref|YP_004596562.1|  [L=302]
Description: sulfate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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-28   99.7   0.0    6.7e-28   97.9   0.0    1.8  2  ABC_tran     ABC transporter
    1.4e-12   48.0   0.1    2.8e-08   34.0   0.0    2.4  3  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.9e-06   27.9   0.0    1.1e-05   26.0   0.0    1.9  2  DUF4162      Domain of unknown function (DUF4162)
     0.0011   18.7   0.2     0.0044   16.8   0.0    1.9  2  AAA_30       AAA domain
     0.0084   15.6   0.0        3.6    7.0   0.0    2.3  2  SMC_N        RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.016   15.7   0.0      0.025   15.1   0.0    1.2  1  AAA_23       AAA domain
      0.024   14.3   0.0      0.047   13.4   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.031   14.2   0.0       0.05   13.5   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
       0.08   13.3   0.4       0.17   12.3   0.4    1.8  1  AAA_16       AAA ATPase domain
       0.13   12.0   0.0         12    5.6   0.0    2.2  2  IstB_IS21    IstB-like 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 !   97.9   0.0   3.7e-31   6.7e-28       1     136 [.      19     157 ..      19     158 .. 0.96
   2 ?   -1.0   0.0       1.3   2.4e+03     119     134 ..     257     272 ..     244     275 .. 0.87

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 3.7e-31
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ ++l++++ge+ +++G+nGaGKSt +++l++  +p +G++++ g+d++  +   +r+++g+lp+    f+++t r
  gi|336253455|ref|YP_004596562.1|  19 LRGIDLEIERGEVFGFLGPNGAGKSTTINVLLHYAHPSAGTVEVLGRDVTA-DPVAVRQRVGILPEGFAPFETMTGR 94 
                                       57899**********************************************.88899*****************999 PP

                                       HH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++         +d++++++l+++gl+++ d+ +    s +S+G+ qr+ala+al+ +p+ll+lDEp+
  gi|336253455|ref|YP_004596562.1|  95 QHleyaieanGADDDPDALLERVGLEGVGDRLA----SDYSKGMAQRLALAMALVGEPDLLILDEPS 157
                                       99***9999989999************999999....*****************************7 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.3
                                       HHHHHHHTSSEEEEES CS
                                       xxxxxxxxxxxxxxxx RF
                          ABC_tran 119 larallkkpkllllDE 134
                                       l+ a ++++kl +lDE
  gi|336253455|ref|YP_004596562.1| 257 LVVACARDAKLTVLDE 272
                                       7788999********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 !   12.2   0.0   6.5e-05      0.12       2      24 ..      32      54 ..      31     115 .. 0.69
   2 !   34.0   0.0   1.5e-11   2.8e-08     227     297 ..     120     187 ..      86     190 .. 0.85
   3 ?   -3.7   0.0       4.6   8.3e+03     247     266 ..     257     273 ..     256     273 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.5e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                       ++ GpNg+GKS+ +  l + a 
  gi|336253455|ref|YP_004596562.1| 32 FGFLGPNGAGKSTTINVLLHYAH 54
                                      5789***********99988763 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 1.5e-11
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       ++ +++ a++ S G+ + lal+ al   +   +ll++DEp +gL+P+ +rr  e++ +++++ga v++++H
  gi|336253455|ref|YP_004596562.1| 120 EGVGDRLASDYSKGMAQRLALAMALVGEP---DLLILDEPSTGLDPHGVRRMREIVAAERDRGAAVFFSSH 187
                                       46677888999****9999*******999...9************************************** PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.6
                            AAA_21 247 lltallralkkgsllliDEp 266
                                       l++a++r++   +l+++DE+
  gi|336253455|ref|YP_004596562.1| 257 LVVACARDA---KLTVLDEI 273
                                       788999999...89****97 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.7   3.1e+03      36      60 ..      94     121 ..      58     123 .. 0.66
   2 !   26.0   0.0   6.3e-09   1.1e-05      17      81 .]     228     298 ..     212     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.7
                                       TT.S-EEEEE--.-----------.--- CS
                           DUF4162  36 eg.gelelkled.eeaanellkal.tsg 60 
                                       ++  e+ ++ ++ ++++ +ll+++  +g
  gi|336253455|ref|YP_004596562.1|  94 RQhLEYAIEANGaDDDPDALLERVgLEG 121
                                       3334567777777889999998884455 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 6.3e-09
                                       EE.....--.-----..---EEEE-TTS-EEEEE-------------.----EEEEEEEE---HHHHHHHHH CS
                           DUF4162  17 ve.....ad.aeelleepgveeveeeggelelkledeeaanellkal.tsgveirsFeeeePsLndIFiekv 81 
                                       ve     +  a +l +++gv++v  ++g+l++ +   +a+ ++l+++ ++g++ir F+  e+sL+d F+ ++
  gi|336253455|ref|YP_004596562.1| 228 VElaydpGAvAPALDDLEGVSSVVARDGNLVVACAR-DAKLTVLDEIrAAGGTIRDFTTGEASLEDLFVSYT 298
                                       5555433113667778899****999999****998.5999******77*******************9875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.4e-06    0.0044      20     121 ..      31     184 ..      25     204 .. 0.82
   2 ?   -1.2   0.1      0.76   1.4e+03      81      97 ..     245     273 ..     186     282 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.4e-06
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Laeelgi........eastiakllkrlk...... 81 
                                       v    Gp G+GK+t++++l + ++ + g+v +l    +a  v +++ +gi        e++t  + l   +      
  gi|336253455|ref|YP_004596562.1|  31 VFGFLGPNGAGKSTTINVLLHYAHPSAGTVEVLGRDVTADPVaVRQRVGIlpegfapfETMTGRQHL---Eyaiean 104
                                       55678**************888888888999999999988777899999755555555666666666...1346899 PP

                            AAA_30  82 ....................................grarlepgtllivDEagmv....dtkqlaallkaaekagak 118
                                                                           ++a + + +lli DE +      + + ++++++a +++ga 
  gi|336253455|ref|YP_004596562.1| 105 gadddpdallervglegvgdrlasdyskgmaqrlalAMALVGEPDLLILDEPSTGldphGVRRMREIVAAERDRGAA 181
                                       99999999999999*****************9999976777888*******99877777999999999999999999 PP

                            AAA_30 119 vil 121
                                       v +
  gi|336253455|ref|YP_004596562.1| 182 VFF 184
                                       876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.76
                            AAA_30  81 k............grarlepg.tllivDEa 97 
                                       +              ++++++ +l + DE+
  gi|336253455|ref|YP_004596562.1| 245 EgvssvvardgnlV-VACARDaKLTVLDEI 273
                                       23333333333432.223333366677765 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 !    6.2   0.0    0.0033         6      29      46 ..      34      51 ..      20      57 .. 0.82
   2 !    7.0   0.0     0.002       3.6     147     212 ..     136     202 ..     111     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0033
                                      EEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 29 ivGpNGSGKsnlldAilF 46
                                       +GpNG+GKs  ++ +l+
  gi|336253455|ref|YP_004596562.1| 34 FLGPNGAGKSTTINVLLH 51
                                      57********99887765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.002
                                       HHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 147 laLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvt 212
                                         L +A+  v    l +lDe    LD + v+++ e++ +++++ a ++  s+  e++e +   vg+ 
  gi|336253455|ref|YP_004596562.1| 136 QRLALAMALVGEPDLLILDEPSTGLDPHGVRRMREIVAAERDRgAAVFFSSHILEQVEAVADRVGIL 202
                                       56778888888889***********************977766599999999999999888877775 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.4e-05     0.025      19      38 ..      29      48 ..      15      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                            AAA_23 19 kgltlItGpNGaGKTTildA 38
                                        ++ + GpNGaGK+T ++ 
  gi|336253455|ref|YP_004596562.1| 29 GEVFGFLGPNGAGKSTTINV 48
                                      36999***********9985 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   2.6e-05     0.047      16      39 ..      23      46 ..      18      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                      ++ei++ +++ + Gp+G+GKST +
  gi|336253455|ref|YP_004596562.1| 23 DLEIERGEVFGFLGPNGAGKSTTI 46
                                      56777666999***********88 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.8e-05      0.05      99     126 ..      29      56 ..      11      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-05
                                       TSEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelk 126
                                       +++  ++G+ G+GKSt in+ll  ++ +
  gi|336253455|ref|YP_004596562.1|  29 GEVFGFLGPNGAGKSTTINVLLHYAHPS 56 
                                       47888****************9865544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   9.5e-05      0.17      26      63 ..      31      69 ..      16     275 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.5e-05
                            AAA_16 26 lvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                      +  + G+ G GKs+ ++ ll+++  + g + + g+ +  
  gi|336253455|ref|YP_004596562.1| 31 VFGFLGPNGAGKSTTINVLLHYAHPSAGTVeVLGRDVTA 69
                                      55678***************9999994443444443333 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 ?    4.2   0.0     0.018        32      36      62 ..      17      44 ..       6      56 .. 0.81
   2 ?    5.6   0.0    0.0068        12      58     151 ..      92     189 ..      89     199 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.018
                         IstB_IS21 36 keLatlsf.iekkenivllGpsGvGKsh 62
                                      ++L++ +  ie+ e + +lGp G+GKs 
  gi|336253455|ref|YP_004596562.1| 17 AALRGIDLeIERGEVFGFLGPNGAGKST 44
                                      566666655899999***********95 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0068
                         IstB_IS21  58 vGKshlaialgveavraglsvlfvrv..edLveelkrarrdgklar...alkrllkvdllilDdlgllpldqaeael 129
                                       +G+ hl  a+  +++ ++   l  rv  e +  +l+ + ++g ++r   a++ + ++dllilD+ ++  ld +  + 
  gi|336253455|ref|YP_004596562.1|  92 TGRQHLEYAIEANGADDDPDALLERVglEGVGDRLASDYSKGMAQRlalAMALVGEPDLLILDEPST-GLDPHGVRR 167
                                       566666666666666666555554432256666676666666555511156667788*******865.689999999 PP

                         IstB_IS21 130 lfeviekryerrsiiitsnlpf 151
                                       + e++++  +r + +  s   +
  gi|336253455|ref|YP_004596562.1| 168 MREIVAAERDRGAAVFFSSHIL 189
                                       9999999988888877666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2142.57
//
Query:       gi|336253456|ref|YP_004596563.1|  [L=432]
Description: Exoribonuclease II [Halopiger xanaduensis SH-6]
Scores for 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-83  278.3   0.0    1.7e-81  274.1   0.0    2.1  1  RNB       RNB domain


Domain annotation for each model (and alignments):
>> RNB  RNB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.1   0.0   9.7e-86   1.7e-81       1     321 [.      71     372 ..      71     374 .. 0.93

  Alignments for each domain:
  == domain 1  score: 274.1 bits;  conditional E-value: 9.7e-86
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RNB   1 RkdlrdllvitIdpedakdlDdAisieklpngnyelgVhIADvshyvkegspldkearkratsvyLpekvvpMLPqe 77 
                                       Rkdlrdl+++t dp da+d+DdA+sie+ ++ +y l+VhIADv+hyv++++++++ea +r+++vyLp+ +++MLP+ 
  gi|336253456|ref|YP_004596563.1|  71 RKDLRDLTTWTTDPIDAQDFDDALSIEERDD-EYVLWVHIADVTHYVNPDTAMWDEAVERGNTVYLPGYTIHMLPPV 146
                                       9*************************96666.5******************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RNB  78 lsedlcSLnpgedrlalsvlidvdek.gevlsveiylsvIkskarltydevqdlleqkdekeekktaedLellyela 153
                                       l+e +cSL p+edrla +v++++d++    +  eiy+svI+s++rlty+++++ le++d+    + +e+ +l+ye+a
  gi|336253456|ref|YP_004596563.1| 147 LAETVCSLVPNEDRLAHTVEMHLDKEnLGYETIEIYKSVIRSDERLTYSQAENRLEDPDA----DLHEENKLVYEVA 219
                                       ************************886666999**********************87775....79*********** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                               RNB 154 kalrkkRlkkgalefdspeikllldedkgnrielkveeetkahslveelmllANelvArfl.seleipailriheep 229
                                       ++++++R+++g+l +         ++            ++ ah+++ee+ml AN++v++ l   ++++a++r+h++p
  gi|336253456|ref|YP_004596563.1| 220 NRMHEQRKEDGSLVL---------NP-----------SRDRAHTIIEECMLKANKAVTHELmWSRGVEAMYRVHPQP 276
                                       **********99888.........44...........3456*******************99*************** PP

                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                               RNB 230 snekledliklakklglk....lednsskknlqeslekleeeeaeqllselllrllkeakyssep.vgHfgLaleeY 301
                                       s++++ + ++  ++l+       + ++ +k+++  le+   ++  + ++  +++++++aky+ +p  gH +L++e+Y
  gi|336253456|ref|YP_004596563.1| 277 SPDEWSEALQEIQDLDGVsipgSTWDDPRKAVNATLEEAPGRQ-LDKIQWAVMKVMPRAKYMNDPfGGHHALNFEIY 352
                                       *999999999999554447878888888899999999999988.8899**************999889********* PP

                                       xxxxxxxxxxxxxxxxxxxx RF
                               RNB 302 thfTSPirRYpDlvvhrllk 321
                                        hfTSPirR +Dl++h++++
  gi|336253456|ref|YP_004596563.1| 353 GHFTSPIRRLSDLINHWIVY 372
                                       *****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3282.18
//
Query:       gi|336253457|ref|YP_004596564.1|  [L=193]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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   42.8   0.0    6.6e-11   42.5   0.0    1.4  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.3e-08   34.8   0.0    1.9e-08   34.3   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.3e-06   27.9   0.0      3e-06   27.6   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.027   14.5   0.0      0.043   13.8   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 !   42.5   0.0   1.5e-14   6.6e-11      38     117 .]      93     170 ..      15     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.5e-14
                                       EEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHH CS
                    Acetyltransf_1  38 aeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYek 114
                                       a    e+ Gf+ +   pd ++  ay+ +l+V+p  +g G G+aLle +e   +e  ++++ l+v +dn+  + +Ye 
  gi|336253457|ref|YP_004596564.1|  93 AGVSAEIEGFAHAGLHPD-DPTAAYLVRLYVRPGTWGEGTGTALLERIEA-TFEPTCDRLRLTVLADNEIGVSFYES 167
                                       333366779999999999.88****************************9.88899*******************99 PP

                                       TTE CS
                    Acetyltransf_1 115 lGF 117
                                        GF
  gi|336253457|ref|YP_004596564.1| 168 AGF 170
                                       **9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   4.3e-12   1.9e-08      42     115 ..      99     179 ..      93     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 4.3e-12
                   Acetyltransf_10  42 ivGvi..el.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnasp.yavpfYeklGFkavge 111
                                       i G++  +l  d+    ++ +l+V+p   g G g+aLle++e+ +e    +l+ltv a++   v+fYe+ GF++v+ 
  gi|336253457|ref|YP_004596564.1|  99 IEGFAhaGLhPDDPtaaYLVRLYVRPGTWGEGTGTALLERIEATFEPTCDRLRLTVLADNeIGVSFYESAGFERVQT 175
                                       55555334433333667999*************************8887777********999************77 PP

                   Acetyltransf_10 112 eqee 115
                                        q +
  gi|336253457|ref|YP_004596564.1| 176 RQSD 179
                                       7654 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   6.7e-10     3e-06      15      76 .]     100     172 ..      62     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 6.7e-10
                                       EEEEEEEEES.....TCTEEEEE-GGGTTSSHHHHHHH.HTT....SEEE.EEEEEE.THHHHHHHHHHTTEEE CS
                    Acetyltransf_7  15 vGfialslld.....aeitrlaVdpeyrgkGiGraLle.aae....kgii.leqlel.naekaikfYeklGFee 76 
                                        Gf+ + l+      a++ rl+V+p   g G G+aLle + e      +  l  + l ++e  ++fYe+ GFe+
  gi|336253457|ref|YP_004596564.1| 100 EGFAHAGLHPddptaAYLVRLYVRPGTWGEGTGTALLErI-EatfePTCDrLRLTVLaDNEIGVSFYESAGFER 172
                                       46666666667788899999*****************943.224432233222223334446778*******95 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.5e-06     0.043      22      82 ..     115     175 ..     101     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.5e-06
                                       SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEEE CS
                              FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekiee 82 
                                        +l  l+v+p   ++G g+ l + + +      + + l v a+N+   ++ye+ Gfe  ++
  gi|336253457|ref|YP_004596564.1| 115 AYLVRLYVRPGTWGEGTGTALLERIEATFEPTCDRLRLTVLADNEIGVSFYESAGFERVQT 175
                                       68999***************************************************98754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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: 0.40u 0.19s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 1676.13
//
Query:       gi|336253458|ref|YP_004596565.1|  [L=174]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-13   48.7   0.0    9.4e-13   48.4   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.5e-06   26.6   0.0    6.3e-06   26.1   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    5.9e-05   23.4   0.0    9.3e-05   22.8   0.0    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0025   18.5   0.0     0.0031   18.2   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.028   14.4   0.0    1.6  2  FR47             FR47-like protein
      0.058   13.1   0.0       0.13   11.9   0.0    1.4  1  NAT              NAT, N-acetyltransferase, of N-acetylglutama


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 !   48.4   0.0   3.2e-16   9.4e-13      30     117 .]      60     151 ..      17     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 3.2e-16
                                       STTCEEEEEEET......TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEE CS
                    Acetyltransf_1  30 leaegllvaeed......geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivla 100
                                       +e+ ++lv+e d      +e  Gf+ + + p+ ++ vay+ +++Vsp+++g G+G++Lle le  ++   ++++ la
  gi|336253458|ref|YP_004596565.1|  60 REDAEFLVVEPDdsgggpEECRGFAHAVPWPE-DPAVAYVARFYVSPDAWGEGVGTTLLERLEA-LLADSFDRVRLA 134
                                       23445555444459999999************.99****************************9.666669****** PP

                                       EETTEHHHHHHHHHTTE CS
                    Acetyltransf_1 101 veedndaairlYeklGF 117
                                       v +dnd  i + e  GF
  gi|336253458|ref|YP_004596565.1| 135 VLADNDVGISFAESSGF 151
                                       ************99998 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   2.1e-09   6.3e-06      53     113 ..      97     158 ..      81     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.1e-09
                   Acetyltransf_10  53 hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnasp.yavpfYeklGFkavgeeq 113
                                       ++++++V+p++ g G+g+ Lle++e+ + +   +++l v a++   ++f e+ GF++v   +
  gi|336253458|ref|YP_004596565.1|  97 YVARFYVSPDAWGEGVGTTLLERLEALLADSFDRVRLAVLADNdVGISFAESSGFERVAVRE 158
                                       799************************97887777********99***********994433 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   3.1e-08   9.3e-05       2      75 ..      62     152 ..      39     153 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.1e-08
                                       TEEEEEEEET......TEEEEEEEEEEES.....TCTEEEEE-GGGTTSSHHHHHHH.HTT......SEEEEEEEEE CS
                    Acetyltransf_7   2 kgevfVaedd......gkivGfialslld.....aeitrlaVdpeyrgkGiGraLle.aae......kgiileqlel 60 
                                       ++e++V+e d      ++  Gf+ +++       a+  r++V+p++ g G+G+ Lle +++        ++l    l
  gi|336253458|ref|YP_004596565.1|  62 DAEFLVVEPDdsgggpEECRGFAHAVPWPedpavAYVARFYVSPDAWGEGVGTTLLErLEAlladsfDRVRLA--VL 136
                                       567888877777766544447777777668899899999*****************95322333222112222..33 PP

                                       .THHHHHHHHHHTTEE CS
                    Acetyltransf_7  61 .naekaikfYeklGFe 75 
                                        +++  i+f e+ GFe
  gi|336253458|ref|YP_004596565.1| 137 aDNDVGISFAESSGFE 152
                                       3333678888888887 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     1e-06    0.0031       5     138 .]       6     152 ..       4     152 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1e-06
                    Acetyltransf_3   5 rplteeDlealfe.lrsdpevmry..lpepltleea.eewlera......waeeseeegygwaivlkdtg.....v. 65 
                                       r++t +D+ a++e  r+ ++   y  +  p t++e  +ew++         a+   +e+  +++v++d++     + 
  gi|336253458|ref|YP_004596565.1|   6 RRATTDDAWAIHEtARASWHAA-YddILGPGTVDEVvDEWYA-LgdlessIADVIGREDAEFLVVEPDDSgggpeEc 80 
                                       7888888888887233333322.4552225555555466666.2233444444444567789998855533455533 PP

                    Acetyltransf_3  66 iGsvglrdleeedee.aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                        G++   + +e++       +++ p++wg G++t  ++ l  ++ +    +r++  + ++N   i  +e+ Gfe
  gi|336253458|ref|YP_004596565.1|  81 RGFAHAVPWPEDPAVaYVARFYVSPDAWGEGVGTTLLERLEALLADSF--DRVRLAVLADNDVGISFAESSGFE 152
                                       666655544444443444558899****************99996555..99********************96 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.5   7.3e+03      48      65 ..      55      72 ..      51      73 .. 0.74
   2 ?   14.4   0.0   9.3e-06     0.028      12      80 ..      86     154 ..      80     160 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.5
                                      HHHHHS-S-EEEEEETT- CS
                              FR47 48 keiaergktvllvvvasN 65
                                      ++++ r++  +lvv +++
  gi|336253458|ref|YP_004596565.1| 55 ADVIGREDAEFLVVEPDD 72
                                      567778888899888876 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 9.3e-06
                                       EEEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  12 laawilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                       ++ w   + + ++   +v p++ ++G g+ l + l + +a   + v l v a+N+  i++ e+ Gfe  
  gi|336253458|ref|YP_004596565.1|  86 AVPWPEDPAVAYVARFYVSPDAWGEGVGTTLLERLEALLADSFDRVRLAVLADNDVGISFAESSGFERV 154
                                       6778888889999999**************************************************976 PP

>> NAT  NAT, N-acetyltransferase, of N-acetylglutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.3e-05      0.13      57     113 ..      49     120 ..      39     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.3e-05
                                       HHHTSXEEEEEETTXSEEEEE.....EXSS...................SSXEEEEEEEXHHHHHTTHHHHHHHHH CS
                               NAT  57 rlkgkiakiyiaedyeglAivtwedpkeek...................evayLdkFavlkssqgsgvsdvvfkal 113
                                        l+++ia ++  ed e l++     p++++                    vay+ +F v+++++g+gv   + ++l
  gi|336253458|ref|YP_004596565.1|  49 DLESSIADVIGREDAEFLVVE----PDDSGggpeecrgfahavpwpedpAVAYVARFYVSPDAWGEGVGTTLLERL 120
                                       677888888888888877554....444445778889999999999999*******************99998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 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:                        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: 0.38u 0.19s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1512.78
//
Query:       gi|336253459|ref|YP_004596566.1|  [L=495]
Description: dihydrolipoyl dehydrogenase [Halopiger xanaduensis SH-6]
Scores for complete 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  119.8   0.1    1.8e-34  119.3   0.1    1.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.1e-08   35.5   0.9    2.1e-07   31.4   0.0    2.7  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    8.5e-08   32.4   0.0    4.1e-07   30.2   0.0    1.9  2  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
    0.00017   21.6   3.1      0.069   13.1   0.1    2.7  3  NAD_binding_9  FAD-NAD(P)-binding
  ------ inclusion threshold ------
       0.11   11.5   0.0        1.7    7.6   0.0    2.1  2  GIDA           Glucose inhibited division protein A


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 !  119.3   0.1     5e-38   1.8e-34       2     293 ..       3     336 ..       2     337 .. 0.88

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 5e-38
                                       SEEEE--.SHHHHHHHHHHHH...........HTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH..... CS
                                       xxxxxxx.xxxxxxxxxxxxx...........xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                       Pyr_redox_2   2 dvvviGg.GpAGlaaaltlaq...........agakvtlve....legtclnggcllskallgvaedaeias..... 57 
                                       +v+++G+ G AG+a+a +l +            g++ tl++     +g c ++gc++sk +l++++++ +a+     
  gi|336253459|ref|YP_004596566.1|   3 HVAIVGAyGSAGVAVADELLEradelesedatDGLELTLIDdgepGGGLCILRGCMPSKDVLSAGQHRYQARhddrl 79 
                                       69****99***********99999***999888*******88889999********************9999***** PP

                                       .......................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC..TCEEEEEESEEEE---E CS
                                       .......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .......................evvkklnqgielllgeevvkidpgkkkvklekkke..gdeekiaydklvlAtGs 109
                                                                    +++++ l+++e+v++ ++ +++++e   e  + +++i+ d++v+AtGs
  gi|336253459|ref|YP_004596566.1|  80 qgvpevdpeavvarkdehvssfaA---HRRSHVHDLAEREGVEFVHDTARFVDERVLEleERGRRIEPDYVVIATGS 153
                                       ****************55543321...2345577777799*************7766688999************** PP

                                       EE-BC.TCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHH.T-EEEEEESSSSSSTTS-HH CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 110 sprdl.gipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalakl.gkevtlveardrllraldke 184
                                         + +  +pG  ++v    +  +sa+ l   + p++++v G Gy+++El  +l+++ g++ t++e+  r+l+ ++++
  gi|336253459|ref|YP_004596566.1| 154 VVNVPaELPGI-DDV----SFQTSADVLDATEFPDSAIVMGHGYVSLELGPYLSEVgGVDLTVIEHDRRPLEDVPDA 225
                                       *****9*****.555....5679*********************************9999***************** PP

                                       HHHHHHHHHHHT.TEEEEESCEEEEEEETTE.....EEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEE CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                       Pyr_redox_2 185 lsaaleealeke.Gvevklgtsvkeidgnge.....klevvledgeeidadlvvvavGvrpstelle.eklglelde 254
                                        ++al e  +++ ++ev ++t  k++++ ++      +e ++++ ++++ad +   +G+rp+ e+l+ e+  le   
  gi|336253459|ref|YP_004596566.1| 226 YGDALLELYRDHfDIEVLTETDEKRVEPTDDggvrmVVEQQDGEPRTVEADELYCFTGRRPNLEGLGlEHTRLEP-- 300
                                       ********************************776555577777778****************999887777776.. PP

                                       TTEEE--TTSBES.STTEEE-GGGCTECCSS--HHHHHHH CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 255 rggivvdeflrtn.vpgiyaiGDvaggkggpelaqaAvqq 293
                                        g   v ++++   ++ ++++GD     g+    ++A +q
  gi|336253459|ref|YP_004596566.1| 301 -GEGWVTSTMQAAdDERVFVVGDAN---GREPILHVAKEQ 336
                                       .8888999998876*********88...555556666555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       1.5   5.5e+03       1      22 [.       3      25 ..       3      29 .. 0.79
   2 ?    1.3   0.0      0.15   5.3e+02      27      61 ..      90     124 ..      89     126 .. 0.89
   3 !   31.4   0.0   5.7e-11   2.1e-07       2      76 ..     185     262 ..     184     268 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                                      EEEEECS.SHHHHHHHHHHHHTT CS
                         Pyr_redox  1 kvvvvGg.GyiglElAgalaelg 22
                                      +v++vG+ G  g+ +A +l e +
  gi|336253459|ref|YP_004596566.1|  3 HVAIVGAyGSAGVAVADELLERA 25
                                      78999987888999998887766 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                                       EEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSE CS
                         Pyr_redox  27 vversdkllrllDeeaskilqeklekngievllnt 61 
                                       vv r+d+  + + +  ++ +++  e++g+e++++t
  gi|336253459|ref|YP_004596566.1|  90 VVARKDEHVSSFAAHRRSHVHDLAEREGVEFVHDT 124
                                       7889999999999999999************9876 PP

  == domain 3  score: 31.4 bits;  conditional E-value: 5.7e-11
                                       EEEECSSHHHHHHHHHHHHTT.SEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTS.EEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelg.kkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedg.ves 75 
                                       ++v+G Gy+ lEl+ +l+e g  + tv+e   ++l   +++ +++l e  +++  ievl++t  +++e ++dg v+ 
  gi|336253459|ref|YP_004596566.1| 185 AIVMGHGYVSLELGPYLSEVGgVDLTVIEHDRRPLEDVPDAYGDALLELYRDHfDIEVLTETDEKRVEPTDDGgVRM 261
                                       68*****************8768**********************************************99997875 PP

                                       E CS
                         Pyr_redox  76 v 76 
                                       v
  gi|336253459|ref|YP_004596566.1| 262 V 262
                                       5 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 ?   -1.0   0.0      0.57   2.1e+03      37      60 ..     245     268 ..     233     269 .. 0.84
   2 !   30.2   0.0   1.2e-10   4.1e-07      12     105 ..     374     466 ..     366     470 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.57
                                       CGHHHCHTTHTEEEEEEEEETTTT CS
                     Pyr_redox_dim  37 angralayaetkgfvKlvadaktg 60 
                                       +++  ++++ ++g v++v+++++g
  gi|336253459|ref|YP_004596566.1| 245 ETDEKRVEPTDDGGVRMVVEQQDG 268
                                       66777888999*********9987 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 1.2e-10
                                       EEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHHHHHTTSB CS
                     Pyr_redox_dim  12 asvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelavaikaglt 88 
                                         +G t + A + g++  v++ + ++ g  + +++ +g + lv+ a+tg vlG + +  + + + + ++va+++gl 
  gi|336253459|ref|YP_004596566.1| 374 VRIGHTPATAADSGMDAFVVTREASSDGVFKSKNHPEGRATLVVSAETGAVLGYQGLHLHGDVMAKTMQVAVEMGLD 450
                                       579***********999999999999999999999****************************************** PP

                                       HHHHHTSBSSSSSTGGG CS
                     Pyr_redox_dim  89 vedladtihihPtlsea 105
                                       v+dl +  ++hPt  e 
  gi|336253459|ref|YP_004596566.1| 451 VRDLPKR-AYHPTTPEI 466
                                       **99765.799999876 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 !   13.1   0.1   1.9e-05     0.069       1      39 [.       5      50 ..       5      59 .. 0.88
   2 !    8.1   0.4   0.00069       2.5      81     155 ..      78     153 ..      65     154 .. 0.74
   3 ?   -2.2   0.0         1   3.6e+03     111     148 ..     234     277 ..     225     284 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                     NAD_binding_9  1 aivGa.GprGlavlerLlara......kkkspleitlfdpsepgag 39
                                      aivGa G +G+av+++Ll+ra      + ++ le+tl+d+ epg g
  gi|336253459|ref|YP_004596566.1|  5 AIVGAyGSAGVAVADELLERAdeleseDATDGLELTLIDDGEPGGG 50
                                      89**88***************99988666778********999834 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00069
                     NAD_binding_9  81 e...aeeldpddfvpRa..lyGrYlrdlfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLA 152
                                       +   ++e+dp+++v R+  +++ + +++ +++ + + e+  ve++++++  ++er  +   l+++g++++ d+Vv+A
  gi|336253459|ref|YP_004596566.1|  78 RlqgVPEVDPEAVVARKdeHVSSFAAHRRSHVHDLA-EREGVEFVHDTARFVDERVLE---LEERGRRIEPDYVVIA 150
                                       133478899999999964368889999988887666.455899999998888766444...5799************ PP

                     NAD_binding_9 153 lGh 155
                                       +G 
  gi|336253459|ref|YP_004596566.1| 151 TGS 153
                                       *95 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1
                     NAD_binding_9 111 lpegvtvevhra.evvdleeradg...qavlladg..aslaada 148
                                       +++++++ev+++ +  ++e+++dg   + v ++dg  ++++ad+
  gi|336253459|ref|YP_004596566.1| 234 YRDHFDIEVLTEtDEKRVEPTDDGgvrMVVEQQDGepRTVEADE 277
                                       46667777764425556888887743224555666444567766 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.032   1.2e+02     133     151 ..     136     154 ..      83     177 .. 0.84
   2 ?    7.6   0.0   0.00048       1.7     346     392 .]     305     352 ..     289     352 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.032
                                       ETTS-EEEECEEEE--TT- CS
                              GIDA 133 tedgetikakavviatGtf 151
                                        e+g+ i+ + vviatG+ 
  gi|336253459|ref|YP_004596566.1| 136 EERGRRIEPDYVVIATGSV 154
                                       578999***********94 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00048
                                       B-TTSBBSSSBTEEE-CGGGTB-SHHHHHH..HHHHHHHHHHHHHCTS- CS
                              GIDA 346 llntLetkkvkgLflAGqinGteGYeEaaa..qGllAGinaarkakgke 392
                                       +++t++  + +++f+ G+ nG e  +  +a  qG+ AG n++++a+g+e
  gi|336253459|ref|YP_004596566.1| 305 VTSTMQAADDERVFVVGDANGREPILH-VAkeQGFAAGENIVHHARGEE 352
                                       4569******************96554.4447*************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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 0.22s 00:00:00.73 Elapsed: 00:00:00.36
# Mc/sec: 4095.75
//
Query:       gi|336253460|ref|YP_004596567.1|  [L=442]
Description: hypothetical protein Halxa_2063 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.33   10.9   3.2       0.41   10.5   1.8    2.0  2  Peptidase_M43  Pregnancy-associated plasma protein-A


Domain annotation for each model (and alignments):
>> Peptidase_M43  Pregnancy-associated plasma protein-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.25   4.5e+03      19      38 ..     233     250 ..     176     264 .. 0.70
   2 ?   10.5   1.8   2.3e-05      0.41      55     114 ..     322     381 ..     291     407 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.25
                     Peptidase_M43  19 nvyiqndladGltknsGvaw 38 
                                        v++ +  +dG t  s va+
  gi|336253460|ref|YP_004596567.1| 233 EVHVED--RDGETATSAVAY 250
                                       455555..566666666664 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 2.3e-05
                     Peptidase_M43  55 nGaylaadststnksstLthelGhfLgLihtfeggCerGegDkvsDtpsedgkevsavnk 114
                                         +y++a++ + n  +t+   + hf +   t +g  + G++D++sD +s+d +  ++ ++
  gi|336253460|ref|YP_004596567.1| 322 SSKYMVAQQAEANGEATVYIAFNHFSERTATIDGSDDGGSTDGSSDGDSTDDGSNTTDET 381
                                       359*******************************99899999999999987665554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); 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:                        10  (0.000557756); expected 0.2 (1e-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 0.25s 00:00:00.85 Elapsed: 00:00:00.38
# Mc/sec: 3467.36
//
Query:       gi|336253461|ref|YP_004596568.1|  [L=317]
Description: PfkB domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-50  170.3   0.0    7.2e-50  170.0   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 !  170.0   0.0     4e-54   7.2e-50       1     294 [.       1     294 [.       1     301 [. 0.95

  Alignments for each domain:
  == domain 1  score: 170.0 bits;  conditional E-value: 4e-54
                                       EEEEEEEEEEEEEEEEECSSHTTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTE CS
                              PfkB   1 mtkvvviGealidliavseklegelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegv 77 
                                       m ++v++Ge++  l++ +++    l    ++e + GGa  NvA a++rlg ++++++++   ++G+++  +l++ g+
  gi|336253461|ref|YP_004596568.1|   1 MSDLVSFGETMLRLSPPDNE---RLEDTDEFEVHVGGAESNVAIAAQRLGTSATWLSKLPENPLGRQVVGKLRQYGI 74 
                                       6789**************99...999*************************************************** PP

                                       EETTEEEESSSEEEEEEEEETTT.SEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEES...EECTTSHHHHHHH CS
                              PfkB  78 dtdyvkidedtrtglalivvded.gertivfnrgaaadltkeeleededlleeadllyisg...llsselpeavlee 150
                                       +td v ++++ r g+++ +  ++   ++++++r +aa  t +  e d++ +  a+++   g   +ls+ l+++++ +
  gi|336253461|ref|YP_004596568.1|  75 ETD-VAWSPQGRVGTYYMEQAGEpRGTNVIYDRQNAAVTTAKTREFDLEPIRDAKVFFTTGitpALSPTLRDTTMSL 150
                                       **6.666****************9889999999999999999999******************************** PP

                                       HHHHHHHTTE..EEEEECESSSHH..HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTS.SE CS
                              PfkB 151 laeaaknggt..fdpnlldplgaq..fkeallellaladllkpneeElealtgekledieealaalhklkakga.kt 222
                                       l++a++ g+t  fd n++++l++   +ke+l +l++++d+l   +++++ ++g ++ d+ +++++l     ++  +t
  gi|336253461|ref|YP_004596568.1| 151 LKAAKEGGTTtaFDFNYRAKLWSPdeAKEVLTQLFPGIDVLVIAARDAQNVLGLEG-DPRQIAHQLGS---QYDfET 223
                                       *****99999************99*******************************6.77666666655...8999** PP

                                       EEEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSS CS
                              PfkB 223 vvvtlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkg 294
                                       v+vt+G+eGa+   +d++++ + v++++ v+++G+GD+f+g f+a  l+g ++ +al++  a+Aal  + +g
  gi|336253461|ref|YP_004596568.1| 224 VIVTRGAEGAIGW-HDNVVHEQDVYETDTVSPIGTGDAFTGTFVARRLDGDDVPTALEYSAAAAALKRTIPG 294
                                       *************.9**************************************************9987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2421.75
//
Query:       gi|336253462|ref|YP_004596569.1|  [L=386]
Description: RNA 3'-phosphate cyclase [Halopiger xanaduensis SH-6]
Scores for complete 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-64  217.6   0.0    1.4e-64  217.3   0.0    1.1  1  RTC         RNA 3'-terminal phosphate cyclase
    2.3e-10   40.9   0.3    3.4e-09   37.2   0.3    2.3  2  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 !  217.3   0.0   1.6e-68   1.4e-64       4     215 ..      15     351 ..      13     357 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.3 bits;  conditional E-value: 1.6e-68
                                       TSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE--......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                               RTC   4 gGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPg......... 71 
                                        Ggq+LRtal L++l +++vr+en+R  R++PGLr+qhl++++ + +i++a+v+gae+g +++ F Pg         
  gi|336253462|ref|YP_004596569.1|  15 AGGQFLRTALGLAVLENEAVRLENVRGDRSTPGLRHQHLAVLETMVEICDANVSGAELGAETVAFDPGlsmddgads 91 
                                       6**************************************************************************** PP

                                       ......----SEEEEEEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEE CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC  72 ......eikageyevdigtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlele 142
                                             ++++gey vdigtAGs+tll++ llpl+ + ++p+++t +GgT+v+++p++dy+++v lpll+r+g l++ 
  gi|336253462|ref|YP_004596569.1|  92 gpnghpKLEGGEYAVDIGTAGSVTLLFESLLPLATILESPLRITATGGTDVKWSPPLDYFRYVKLPLLRRYG-LTAA 167
                                       ****98899***************************************************************.6*** PP

                                       EEEEE--BTTTB-EEEEEEEE-.-S---EB............................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
                               RTC 143 lelkkrGfypkGgGevelevepskklkpie............................................... 172
                                       +e+ +rGfyp GgG+ +l++ ps +l+pie                                               
  gi|336253462|ref|YP_004596569.1| 168 CEVDRRGFYPDGGGRATLHLGPS-ELEPIElaergpleavriystesesladrdvafrqvegalerlavddlerggs 243
                                       ********************995.8**************************************************** PP

                                       ...................................................................BSS-HHHHHH CS
                                       ...................................................................xxxxxxxxxx RF
                               RTC 173 ...................................................................acvDehlqdq 182
                                                                                                          a+vD+h++dq
  gi|336253462|ref|YP_004596569.1| 244 dsgsrepaerrettaaspspgsalvvridhgtgiagftalgergkpaervgedaadaanrflereatAPVDRHMADQ 320
                                       ***************************************************************************** PP

                                       HHHHHHHHT.-EEEEESS--HHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC 183 lilfmaLakgksrirvaeltlhtetairvieqf 215
                                       l++f+a+a g  r+rv e+t+h+    +++e f
  gi|336253462|ref|YP_004596569.1| 321 LLVFLAIAGG--RVRVPEVTDHVAASRELLEAF 351
                                       ********98..8**********9998888877 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 !   37.2   0.3   3.8e-13   3.4e-09       2     100 ..     199     303 ..     198     306 .. 0.80
   2 ?    1.1   0.0     0.064   5.7e+02      27      67 ..     341     377 ..     331     383 .. 0.71

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 3.8e-13
                                       S----SEEEEEEEEES..S-THHHHHHHHHHHHHHTTTSS.........EEEEEEE..EE-CGGC-SS-EEEEEEEE CS
                        RTC_insert   2 drGrvkrirGvafaar..vspsvanrmveaargvLnkllp.........dvyiytdv.vkegkesgkspGfgisLva 66 
                                       +rG ++ +r+++  ++    ++va r+ve+a ++L  ++                 + ++e+ +++ spG+++++ +
  gi|336253462|ref|YP_004596569.1| 199 ERGPLEAVRIYSTESEslADRDVAFRQVEGALERL--AVDdlerggsdsG--SREPAeRRETTAASPSPGSALVVRI 271
                                       7999*********9999999**************9..4443456666431..22223255666699999******** PP

                                       E-T.TS-EEEEEEEE-TT--HHHHHHHHHHHHHH CS
                        RTC_insert  67 etttegvllgaealgekgvppedvGeeaaeeLle 100
                                        +    ++ g++alge+g+p+e+vGe+aa++  +
  gi|336253462|ref|YP_004596569.1| 272 DHG--TGIAGFTALGERGKPAERVGEDAADAANR 303
                                       **5..59**********************98655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.064
                                       HHHHHHHHTTTSSEEEEEEE.EE-CGGC-SS-EEEEEEEEE CS
                        RTC_insert  27 veaargvLnkllpdvyiytdvvkegkesgkspGfgisLvae 67 
                                       v+a r++L+++   v i ++  + g++ + s G   +++ae
  gi|336253462|ref|YP_004596569.1| 341 VAASRELLEAF--GVSIDLE--EGGDNGSDSGGGPATVTAE 377
                                       78899999999..6664466..5566666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2836.50
//
Query:       gi|336253463|ref|YP_004596570.1|  [L=310]
Description: hypothetical protein Halxa_2066 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.042   13.9   0.0      0.095   12.7   0.0    1.6  1  SRP_TPR_like  Putative TPR-like repeat
       0.13   11.9   0.0        0.2   11.3   0.0    1.3  1  CBM_17_28     Carbohydrate binding domain (family 17/28)


Domain annotation for each model (and alignments):
>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.1e-05     0.095      74     114 ..      62     103 ..      37     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                      SRP_TPR_like  74 eekvkvlksqvlYrlgsyekAYklL.skekkedelvvNllAv 114
                                        +  + ++  v+ + + +e+AY+l+ ++ ++ +e+ vN++A+
  gi|336253463|ref|YP_004596570.1|  62 ASTERFVLEDVYDYDEAFEQAYDLItAELDRGNEVWVNIAAM 103
                                       44557788899999*********998999************9 PP

>> CBM_17_28  Carbohydrate binding domain (family 17/28)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.3e-05       0.2     114     157 ..      92     135 ..      40     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.3e-05
                                       XXXXXXXXXXXXXXXXXX.XXXXXXXXXX.........XXXXXX CS
                         CBM_17_28 114 vkepltvsiaavPqssnhgWanperavavtpddfelqeDgtyka 157
                                         +++ v+iaa+P++++  +a ++++++v  +d ++q    y a
  gi|336253463|ref|YP_004596570.1|  92 RGNEVWVNIAAMPRTVSFAFATAANSLMVEREDDREQIHTYYTA 135
                                       457899***************************99999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2260.62
//
Query:       gi|336253464|ref|YP_004596571.1|  [L=892]
Description: Valyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-124  415.9   0.1   4.7e-123  411.5   0.1    2.0  1  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
      8e-35  120.0   0.9    1.2e-34  119.5   0.2    1.7  2  Anticodon_1     Anticodon-binding domain of tRNA
    7.6e-21   74.3   0.5    1.1e-09   37.5   0.0    3.4  3  tRNA-synt_1g    tRNA synthetases class I (M)
      7e-07   28.9   0.0    1.6e-06   27.7   0.0    1.5  1  tRNA-synt_1_2   Leucyl-tRNA synthetase, Domain 2
    4.6e-05   22.9   0.0      0.004   16.5   0.0    2.4  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
    0.00076   18.5   0.0     0.0025   16.8   0.0    1.9  2  tRNA-synt_1f    tRNA synthetases class I (K)
     0.0034   17.5   3.1      0.044   13.9   0.8    2.7  2  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.096   11.0   0.0       0.15   10.3   0.0    1.2  1  SpecificRecomb  Site-specific recombinase
        7.6    6.7   8.3          2    8.6   0.4    3.0  3  UPF0547         Uncharacterised protein family UPF0547


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 !  411.5   0.1  2.4e-126  4.7e-123       2     598 ..      31     593 ..      30     597 .. 0.93

  Alignments for each domain:
  == domain 1  score: 411.5 bits;  conditional E-value: 2.4e-126
                       tRNA-synt_1   2 lyekWeeedvfkkelekeke.kkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77 
                                       ++++W +e+v+  e + e++ +  + +  +PP v GslH+Gh + +tl+d+  r++rm+  +vl+ +G+D  G+a e
  gi|336253464|ref|YP_004596571.1|  31 WQQRWVDEEVYAYESDPERDpNTLYAIDTPPPTVSGSLHMGHLYGSTLQDFAARFQRMNDGDVLFPFGYDDNGIASE 107
                                       899********9998888886888***************************************************** PP

                       tRNA-synt_1  78 akvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkg 154
                                          e++l ++++    ++ r ef+e +re  +ey +e ++q++ lG+s+D+   y+T+++ ++   +  f  l++kg
  gi|336253464|ref|YP_004596571.1| 108 RLTERELDIRHQ----DYERREFQELCREVCQEYEAEFTDQMQSLGTSIDWTSTYKTIEPRVQRISQLSFLDLYEKG 180
                                       *******88885....************************************************************* PP

                       tRNA-synt_1 155 liyrgkklvnwstklktalselEveykdkkdalihvafpladkee..vklviaTTtPeTllgdtavavnpeldyvit 229
                                         yr k +  w+++++ta+s++E+e  +  + + ++af+l ++++   ++vi TT+Pe +++ ++v v+p+      
  gi|336253464|ref|YP_004596571.1| 181 REYRKKAPAIWCPDCETAISQVEMEDDERGSHFNDIAFELVGDDAprDEFVISTTRPELIPACVSVFVHPD------ 251
                                       ****************************************555544489**********************...... PP

                       tRNA-synt_1 230 keklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevg 306
                                                                d + ++L+g +++ p+ + ++piiadd vd+e+G+G+V +    d+ D e  
  gi|336253464|ref|YP_004596571.1| 252 -------------------------DDENQDLVGETARIPIFGHEVPIIADDRVDMEKGSGIVMCCTFGDQKDIEWY 303
                                       .........................9999************************************************ PP

                       tRNA-synt_1 307 kkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvr 383
                                       + ++l++ +++de++t+t+ a+++eg++ ++ar+++ve+l+++g l    +i+h+v + er ++p+++r+++qW+v+
  gi|336253464|ref|YP_004596571.1| 304 QAHDLPLRVAIDESATMTDLAGDYEGMSTEEAREAIVEDLDDEGYLRDRWDISHTVQVHERCETPVEFRVSKQWYVE 380
                                       ***************************************************************************** PP

                       tRNA-synt_1 384 vkeladaalkavekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeee 459
                                       + + +++ l+a +++ ++p++  +ry++w+e  + dW iSRqr  G + p+++ ++ + +++        +++  + 
  gi|336253464|ref|YP_004596571.1| 381 ILDHKEEYLEAGREMDWYPEKMFTRYKHWIEGLEwDWLISRQRDSGIPFPVWYCADCDHEIM-----AAREDLPVDP 452
                                       *******************************9866*********************887777.....2222222222 PP

                       tRNA-synt_1 460 aekkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypee.dteelk....kffpadmlleGlDiirgWv 531
                                        +++     +++  +++++++  ++dv+D+W  S+++p    g+    ++ee++    + +p+d+  +G Dii +W+
  gi|336253464|ref|YP_004596571.1| 453 LSDE---PPVEECPECGHDDFVPEDDVFDTWATSSLTPLINAGWDWDaEAEEFTmdkpELYPFDLRPQGHDIISFWL 526
                                       2222...22333337899********************9888886543566665222268***************** PP

                       tRNA-synt_1 532 arlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgrd 598
                                          ++   + tg++Pf   +++g v+de+  KmSKs+gNv+dp+dv+  y +da+R++ +++ vg d
  gi|336253464|ref|YP_004596571.1| 527 FHTVVKCYEHTGEVPFDATMINGHVLDENREKMSKSKGNVVDPDDVLADYPVDAVRFWAASAAVGDD 593
                                       ************************************************************9999887 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 ?   -3.5   0.0       4.6   9.2e+03      17      42 ..     119     144 ..     118     156 .. 0.73
   2 !  119.5   0.2     6e-38   1.2e-34       1     149 [.     636     778 ..     636     782 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.6
                       Anticodon_1  17 eayeeyrfnkaasalyeffwndlcdw 42 
                                       ++ye+ +f++ ++++ +    ++ d 
  gi|336253464|ref|YP_004596571.1| 119 QDYERREFQELCREVCQEYEAEFTDQ 144
                                       67888888888888877777777665 PP

  == domain 2  score: 119.5 bits;  conditional E-value: 6e-38
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       drw+l+el+++++e t+ +eey+f+ka ++l +ffwn++cd yle++k r ++    ++  +q++l+++ +t+l l 
  gi|336253464|ref|YP_004596571.1| 636 DRWLLAELDDAIEELTAQLEEYEFAKARDRLRTFFWNTFCDDYLEIAKGREDN----PS--TQYALRTAHRTFLELW 706
                                       9************************************************9754....33..79************** PP

                       Anticodon_1  78 aPfmPfitEelwqr......eeeelgkkesimlaewpekaeelekeleeeevellkeivkairklrselkikpssel 148
                                       aPf+P+ tEe+wq       e     + +si++++wp +++  +++l  e+ e + e+++a+r+++se++++ +++l
  gi|336253464|ref|YP_004596571.1| 707 APFLPHATEEIWQAvysddpE---NLETNSIHVRDWP-APQGYDADL--EAGETAMEVISALRRYKSEQQLPLNADL 777
                                       ************999987642...245699*******.665665555..688899999**************99986 PP

                       Anticodon_1 149 k 149
                                       +
  gi|336253464|ref|YP_004596571.1| 778 E 778
                                       5 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 !   37.5   0.0   5.8e-13   1.1e-09       3     132 ..      57     201 ..      55     214 .. 0.77
   2 !    5.6   0.2    0.0027       5.4     172     238 ..     365     430 ..     357     442 .. 0.79
   3 !   27.1   0.0   8.5e-10   1.7e-06     289     371 ..     518     601 ..     516     615 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 5.8e-13
                                       EEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT......TS-.......HHHH CS
                      tRNA-synt_1g   3 vttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke......gvt.......peel 66 
                                       + t+ p ++g+lH+Ghl+     D  aR++r+++ +vlf  g D  G++ e   e+e      + +        +e+
  gi|336253464|ref|YP_004596571.1|  57 IDTPPPTVSGSLHMGHLYGSTLQDFAARFQRMNDGDVLFPFGYDDNGIASERLTEREldirhqDYErrefqelCREV 133
                                       77888999**********77778************************998765443221111122211111123456 PP

                                       HHHHHHHHHHHHHHTT..---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-G CS
                      tRNA-synt_1g  67 vekvheeikelfkkln..isfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpd 132
                                       ++++++e+++++++l+  i +++ ++t + + ++++q  f  l+ekg  y+k+   ++cp++e+ +++
  gi|336253464|ref|YP_004596571.1| 134 CQEYEAEFTDQMQSLGtsIDWTSTYKTIEPRVQRISQLSFLDLYEKGREYRKKAPAIWCPDCETAISQ 201
                                       7778888888888876115555778999**********************************987765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0027
                                       .....EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 172 sgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                       +++  e++ +++++ ++ ++++++ e   +e    +e++ +  k+w++    d+ isr+ d Gip+P
  gi|336253464|ref|YP_004596571.1| 365 CETPVEFRVSKQWYVEILDHKEEYLEAG-REMDWYPEKMFTRYKHWIEGLEWDWLISRQRDSGIPFP 430
                                       6666789999999999988887766665.333347889999999***87555*************99 PP

  == domain 3  score: 27.1 bits;  conditional E-value: 8.5e-10
                                       EGGGHH...HHHTHHHHHHHHTT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS CS
                      tRNA-synt_1g 289 gkdiik...FHtifwPaillgaelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekk 362
                                       g dii    FHt++  +  +  e+ +  +++    l  + +K+SkS+g+vv+++++l  +++d++R++ a++a   +
  gi|336253464|ref|YP_004596571.1| 518 GHDIISfwlFHTVV-KCYEHTGEVPFDATMINGHVLDENREKMSKSKGNVVDPDDVLADYPVDAVRFWAASAA-VGD 592
                                       56666522267776.56667777777777777777888899**************************977655.567 PP

                                       -EEE-HHHH CS
                      tRNA-synt_1g 363 Dldfswedf 371
                                       D+ ++++d+
  gi|336253464|ref|YP_004596571.1| 593 DFPYQEKDL 601
                                       787777776 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 !   27.7   0.0   8.2e-10   1.6e-06      86     149 ..     260     323 ..     254     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 8.2e-10
                     tRNA-synt_1_2  86 glkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedeekkl 149
                                       g +a  Pi g+++pi   + v me g+g vm++   dq+D e+ + ++lp++  i ++ + ++l
  gi|336253464|ref|YP_004596571.1| 260 GETARIPIFGHEVPIIADDRVDMEKGSGIVMCCTFGDQKDIEWYQAHDLPLRVAIDESATMTDL 323
                                       678999*************************************************976654444 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 ?    3.8   0.0     0.016        31      17      93 ..      62     151 ..      52     195 .. 0.71
   2 !   16.5   0.0     2e-06     0.004     242     298 ..     546     603 ..     527     606 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                                       EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-................HHHHHH CS
                      tRNA-synt_1e  17 ptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeks................vkelae 77 
                                       ptv    h+Gh       D  +r+ ++ + dv f       dD  i+  r  e++                ++e+++
  gi|336253464|ref|YP_004596571.1|  62 PTVSGSLHMGHLYGSTLQDFAARFQRMNDGDVLFPFGY---DDNGIASERLTEREldirhqdyerrefqelCREVCQ 135
                                       78999999999999999999999988888888886443...444443333333333566677778888888999999 PP

                                       HHHHHHHHHHHHTT-- CS
                      tRNA-synt_1e  78 kfieefkkdleaLnvl 93 
                                       ++++ef++++++L+  
  gi|336253464|ref|YP_004596571.1| 136 EYEAEFTDQMQSLGTS 151
                                       9999999999999754 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2e-06
                                       EEE--E.EETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHH CS
                      tRNA-synt_1e 242 lhnghl.kiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeellee 298
                                       + ngh+   ++ekmsks +n++   dvl  +   ++R+  +sa   + + ++e++l++
  gi|336253464|ref|YP_004596571.1| 546 MINGHVlDENREKMSKSKGNVVDPDDVLADYPVDAVRFWAASAAVGDDFPYQEKDLRA 603
                                       556776145679*******************************999999999999875 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 ?   -3.2   0.0       1.5     3e+03     108     133 ..     134     159 ..     118     179 .. 0.74
   2 !   16.8   0.0   1.3e-06    0.0025     273     312 ..     550     589 ..     516     635 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.5
                      tRNA-synt_1f 108 aehfnaelvesLdelgievefisate 133
                                        + ++ae+ +++++lg  +++ s+ +
  gi|336253464|ref|YP_004596571.1| 134 CQEYEAEFTDQMQSLGTSIDWTSTYK 159
                                       45677788888888888888877665 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.3e-06
                      tRNA-synt_1f 273 lillkggekmssSkGnvltledwlevaepevlrflilrrk 312
                                        +l++++ekms+SkGnv+ ++d+l  ++ + +rf  +++ 
  gi|336253464|ref|YP_004596571.1| 550 HVLDENREKMSKSKGNVVDPDDVLADYPVDAVRFWAASAA 589
                                       58999*****************************988753 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.074   1.5e+02      23      36 ..     186     199 ..     177     202 .. 0.70
   2 !   13.9   0.8   2.2e-05     0.044       8      34 ..     434     467 ..     431     471 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.074
                       Zn-ribbon_8  23 dapltaCPeCgsev 36 
                                       +ap + CP+C  + 
  gi|336253464|ref|YP_004596571.1| 186 KAPAIWCPDCETAI 199
                                       456666****8765 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.2e-05
                       Zn-ribbon_8   8 CeeCghefe......vlqsisdaplta.CPeCgs 34 
                                       C +C+he        ++ + sd+p+++ CPeCg+
  gi|336253464|ref|YP_004596571.1| 434 CADCDHEIMaaredlPVDPLSDEPPVEeCPECGH 467
                                       ******9999999**9999996666666*****8 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   7.6e-05      0.15     200     259 ..     115     175 ..     103     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.6e-05
                    SpecificRecomb 200 deeeaeedlkhlrvll.dqcreavdrvrkhleenGvsvslvfllerlrqrleRleeLldll 259
                                       d ++++++ ++++ l  + c+e+ +++++++++ G+s++ +   ++++ r++R+++L  l 
  gi|336253464|ref|YP_004596571.1| 115 DIRHQDYERREFQELCrEVCQEYEAEFTDQMQSLGTSIDWTSTYKTIEPRVQRISQLSFLD 175
                                       4556666667776665267************************************995443 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3      0.11   2.2e+02       3      11 ..     192     200 ..     191     201 .. 0.88
   2 ?   -2.6   0.1       3.1   6.1e+03       3      10 ..     434     441 ..     433     444 .. 0.57
   3 ?    8.6   0.4     0.001         2      15      23 ..     460     468 ..     459     470 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.11
                           UPF0547   3 CPeCeakvP 11 
                                       CP Ce+ ++
  gi|336253464|ref|YP_004596571.1| 192 CPDCETAIS 200
                                       *****9886 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.1
                           UPF0547   3 CPeCeakv 10 
                                       C  C++++
  gi|336253464|ref|YP_004596571.1| 434 CADCDHEI 441
                                       33466555 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.001
                           UPF0547  15 qfCphCGyv 23 
                                       ++Cp+CG++
  gi|336253464|ref|YP_004596571.1| 460 EECPECGHD 468
                                       79******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (892 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 5711.25
//
Query:       gi|336253465|ref|YP_004596572.1|  [L=90]
Description: hypothetical protein Halxa_2068 [Halopiger xanaduensis SH-6]
Scores for 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-17   61.2   0.0    9.7e-17   61.0   0.0    1.1  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   5.4e-21   9.7e-17       2      69 ..      19      80 ..      18      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 5.4e-21
                            HalOD1  2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdg 69
                                      +es+s a v+av+++++++p el+pLy +iDp+ Ld+L++s      ++dg v+F y g+++tV++  
  gi|336253465|ref|YP_004596572.1| 19 DESVSMAAVHAVSSLKECEPWELSPLYRTIDPEMLDDLCES------QRDGIVKFVYSGFHITVEEGE 80
                                      89***************************************......7789*************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 670.74
//
Query:       gi|336253466|ref|YP_004596573.1|  [L=242]
Description: ribonuclease H [Halopiger xanaduensis SH-6]
Scores for 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-10   39.0   0.0    7.9e-10   38.6   0.0    1.2  1  RVT_3     Reverse transcriptase-like
      1e-08   35.5   0.0    1.8e-08   34.7   0.0    1.3  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 !   38.6   0.0   8.8e-14   7.9e-10       2     122 ..     110     231 ..     109     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 8.8e-14
                             RVT_3   2 fdgafkkksgaggagvvirdsnGevllagaeklqgkasveeAElqALlrGLq.lalklgirrlvvegDsktvvqlln 77 
                                       +dg+ + + g +gag+vi d+  + l+   ++++ ++ + +AE+ AL  GL  l ++++ rrl+v +Ds+tv+q + 
  gi|336253466|ref|YP_004596573.1| 110 VDGSSRGNPGPAGAGAVIMDAAEDELARLGRPVGARTGNNTAEYVALQLGLSeLLARYEPRRLEVRIDSMTVIQDVW 186
                                       799999***************888888888899******************72556778999*************** PP

                             RVT_3  78 grekvksselanlldeirkllksfesvsvehipReqNrvAdalAk 122
                                       g  +++++ ++++ + + + l+s    + +h       +AdalA+
  gi|336253466|ref|YP_004596573.1| 187 GGDDPTEPGVEAYSEAVAAALSSVPDHRYTHLADGDPNPADALAT 231
                                       *******************************************97 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0     2e-12   1.8e-08       3      75 ..     105     183 ..     103     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2e-12
                                       SEEEEEEEEEECTTTCEEEEEEECTT...E..EEEEEECCCCHHHHHHHHHHHHHHHTT....SCSEEEEEES-HHH CS
                           RNase_H   3 avvvYtDGsclgnpgeggagavlykeg.ar..nisapleeaqtnnraELsAvieaLkal...ksdekvniytDSkYv 73 
                                       a v+Y+DGs++gnpg++gagav+     ++   + +p+ +++ nn+aE  A+   L++l   +++ +++++ DS  v
  gi|336253466|ref|YP_004596573.1| 105 AFVLYVDGSSRGNPGPAGAGAVIMDAAeDElaRLGRPVGARTGNNTAEYVALQLGLSELlarYEPRRLEVRIDSMTV 181
                                       679******************6643332335567788889*****************875666779999*****888 PP

                                       HH CS
                           RNase_H  74 vk 75 
                                       ++
  gi|336253466|ref|YP_004596573.1| 182 IQ 183
                                       77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1945.55
//
Query:       gi|336253467|ref|YP_004596574.1|  [L=718]
Description: PAS/PAC sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for 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-31  107.4   7.3    3.6e-14   52.9   0.3    3.9  3  PAS_4        PAS fold
    9.8e-29  100.1   0.0    4.8e-28   97.9   0.0    2.1  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    3.8e-18   65.6   0.0    2.2e-06   27.8   0.0    4.2  4  PAS_9        PAS domain
    2.8e-13   49.9   1.6    8.7e-05   22.5   0.0    5.4  5  PAS          PAS fold
    8.4e-11   42.0   1.5    0.00021   21.5   0.0    5.4  6  PAS_3        PAS fold
      1e-10   41.4   0.5    0.00012   22.0   0.0    4.2  3  PAS_8        PAS domain
    3.5e-10   39.8   1.4    8.5e-10   38.5   0.1    2.4  2  HisKA        His Kinase A (phospho-acceptor) domain
     0.0037   17.2   1.8     0.0044   17.0   0.1    2.1  2  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0046   17.1   0.1         19    5.4   0.0    4.5  4  PAS_7        PAS fold
  ------ inclusion threshold ------
      0.029   14.3   0.0       0.07   13.0   0.0    1.6  1  HATPase_c_5  GHKL domain
      0.038   13.9   0.0       0.12   12.3   0.0    1.8  1  HTH_11       HTH domain
        0.2   11.5   1.3         11    5.9   0.2    2.6  2  Phage_GP20   Phage minor structural protein GP20


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2     9e-08   0.00013       1     109 [.     113     226 ..     113     227 .. 0.86
   2 !   34.5   0.1   1.3e-11   1.9e-08       1     109 [.     243     359 ..     243     360 .. 0.90
   3 !   52.9   0.3   2.4e-17   3.6e-14       3     110 .]     382     481 ..     380     481 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9e-08
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla..ellpee..daarleralrrvlegeepiefleell 73 
                                       l+ +p ++ v+ +dg+v++ N++  + + +p  ++    +    l+ ++    ++ er+++rv + +ep+++ e+ +
  gi|336253467|ref|YP_004596574.1| 113 LETVPIGIGVVAADGTVVRGNERLFDRLPCPNGDCESDGVDawTLYDADgePIPNDERPWARVFDAGEPVTDYECQV 189
                                       6789999****************8888999999998666662244444345556669******************** PP

                             PAS_4  74 l..pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                          +ge+r+ ++++ P+  ++G+  +vl+ + D+ +r+
  gi|336253467|ref|YP_004596574.1| 190 EfaDGERRWRSITAAPIAGDDGD-EFVLLSIDDVADRK 226
                                       ***********************.**********9998 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 1.3e-11
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla....ellpee..daarleralrrvlegeepieflee 71 
                                       l+  p a+av ++d   ++aN++a+e fg++ +e+++ ++      ++ e+  + +  e+   rvl+++ep+ ++e 
  gi|336253467|ref|YP_004596574.1| 243 LETAPIAIAVQNADRETIRANQRAQEAFGLSEQEFRDNPVDtgewRIYDEDgeLLDSSETTSGRVLATGEPVLDEEL 319
                                       5778999**********************************995558888888888888999999999999877775 PP

                             PAS_4  72 lll..pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +    +ge+ ++ ++  P++ ++Ge+  ++  + D+Te++
  gi|336253467|ref|YP_004596574.1| 320 VFEppNGERLYFRVNSAPIFGPDGEIERIVTAAKDVTELK 359
                                       54479*********************************87 PP

  == domain 3  score: 52.9 bits;  conditional E-value: 2.4e-17
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeer 79 
                                       +++da+++ld++ r++++N++aa+++ +++eellG++++e  p+ +   ++++++r++e++ep++f++e  +   + 
  gi|336253467|ref|YP_004596574.1| 382 RVSDAFYALDEEWRYTHLNEQAAAILDRSREELLGRPVWETIPDAVESFFREQYQRAMETQEPVSFEIEAAT--FDA 456
                                       5799****************************************************************9999..9** PP

                             PAS_4  80 hyelrllPlrdesGevigvlvisrDiTerrr 110
                                       ++e+ ++P +       g+ v++rDiTer+r
  gi|336253467|ref|YP_004596574.1| 457 WLEFAVYPSES------GLSVYFRDITERKR 481
                                       ********976......99**********97 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 ?   -1.2   0.0       1.9   2.9e+03      32      55 ..     570     597 ..     541     599 .. 0.56
   2 !   97.9   0.0   3.2e-31   4.8e-28       1     109 [.     601     709 ..     601     711 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                                       EE.....EETEEEEEEEESSSSSTTHHHT CS
                         HATPase_c  32 ka.....seddlvisveDnGiGipkedlk 55 
                                       +a     + +dl++++e +   i +edl+
  gi|336253467|ref|YP_004596574.1| 570 NAvladvR-EDLRVRIEESDADIAVEDLP 597
                                       33332223.48888888888888888876 PP

  == domain 2  score: 97.9 bits;  conditional E-value: 3.2e-31
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSS CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtG 75 
                                       gd ++Lrq+++nl++Nav++ + +g  +v+++a+   d   +sv+D G Gi+++d++++fe f++  + + ++ gtG
  gi|336253467|ref|YP_004596574.1| 601 GDASQLRQVFQNLLTNAVQY-SGDGPPQVRVSAERagDMWDVSVRDEGVGIDPDDQDRIFEVFQR-LHGREEHPGTG 675
                                       7899****************.66666677777533569***************************.8889999**** PP

                                       HHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  76 lGlsivkklvelmgGeiwvesepgrGttftftlp 109
                                       +Gls+++++ve++gG+i+v+sepg+Gttf ftlp
  gi|336253467|ref|YP_004596574.1| 676 IGLSLCRRIVERHGGDIRVDSEPGEGTTFSFTLP 709
                                       ********************************99 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.9   8.8e+03      61      78 ..      53      70 ..      37      85 .. 0.74
   2 !   11.2   0.0   0.00023      0.34      43     100 ..     165     220 ..     148     224 .. 0.80
   3 !   27.8   0.0   1.5e-09   2.2e-06       3     104 .]     249     357 ..     247     357 .. 0.81
   4 !   21.5   0.0   1.4e-07   0.00021       8     104 .]     391     478 ..     384     478 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.9
                             PAS_9 61 erevevvlirkngetfwv 78
                                       ++ e+   r +g+++w 
  gi|336253467|ref|YP_004596574.1| 53 IERNELRTKRIDGTRVWW 70
                                      466788889999999995 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00023
                             PAS_9  43 dpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdd.dgelvgiivilr 100
                                        p++++  ++++++g+ ++ ++e +    +ge+ w  +ta+p+  d ++e+v+  + + 
  gi|336253467|ref|YP_004596574.1| 165 IPNDERPWARVFDAGE-PVTDYECQVEFADGERRWRSITAAPIAGDdGDEFVL--LSID 220
                                       5788899999999**9.**************************7774666666..5555 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 1.5e-09
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgks....itdlf....vtdpeanerlraaleqgrkkerevevvlirk 71 
                                       +i++ n d + ++aN+ a + +G s++e+   +     + ++    +  ++++ +  ++l +g+ ++ ++e+v+  +
  gi|336253467|ref|YP_004596574.1| 249 AIAVQNADRETIRANQRAQEAFGLSEQEFRDNPvdtgEWRIYdedgELLDSSETTSGRVLATGE-PVLDEELVFEPP 324
                                       6778899999***************999888774443555555554444555555566666666.************ PP

                             PAS_9  72 ngetfwvlltaspvkdddgelvgiivilrDite 104
                                       nge+++++++ +p++  dge+ +i+   +D+te
  gi|336253467|ref|YP_004596574.1| 325 NGERLYFRVNSAPIFGPDGEIERIVTAAKDVTE 357
                                       ***************99***************8 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 1.4e-07
                             PAS_9   8 npdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkngetfwvllta 82 
                                       +++ r ++ Ne+a+ +l  s+ee+lg+++++++  ++  ++++r+++++  +  ++ ++e++  + +    w ++ +
  gi|336253467|ref|YP_004596574.1| 391 DEEWRYTHLNEQAAAILDRSREELLGRPVWETI--PDAVESFFREQYQRAMEtqEPVSFEIEAATFDA---WLEFAV 462
                                       466677899************************..777777777777666655668889988888888...988888 PP

                             PAS_9  83 spvkdddgelvgiivilrDite 104
                                       +p  ++      + v +rDite
  gi|336253467|ref|YP_004596574.1| 463 YPSESG------LSVYFRDITE 478
                                       888433......3378899887 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.54   8.1e+02      74     102 ..      56      83 ..      40      85 .. 0.80
   2 ?    0.7   0.0      0.34     5e+02       4      24 ..     110     130 ..     108     136 .. 0.89
   3 ?   -0.9   0.0       1.1   1.6e+03      66     107 ..     176     216 ..     167     222 .. 0.79
   4 !   22.5   0.0   5.8e-08   8.7e-05       4     113 .]     240     355 ..     237     355 .. 0.88
   5 !   18.5   0.1     1e-06    0.0015       4      72 ..     377     445 ..     370     451 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.54
                                       CCCEEEECTTSSEEEEEEEEEEEEETTEE CS
                               PAS  74 ageisfklrdgrpihlevraspvrdagge 102
                                       ++ ++ +  dg+ ++++  + pv ++g++
  gi|336253467|ref|YP_004596574.1|  56 NELRTKRI-DGTRVWWRPATQPVDERGDR 83 
                                       44455555.*************9999876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.34
                                       HHHHHHSSSEEEEEETTSBEE CS
                               PAS   4 raileslpdpifvvDedgril 24 
                                       ++ile+ p +i vv +dg ++
  gi|336253467|ref|YP_004596574.1| 110 ERILETVPIGIGVVAADGTVV 130
                                       79****************998 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.1
                                       HHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEE CS
                               PAS  66 leqgeesrageisfklrdgrpihlevraspvrdaggeilgfl 107
                                         +ge+ +++e  +++ dg+ ++  ++a+p+   +g    +l
  gi|336253467|ref|YP_004596574.1| 176 FDAGEPVTDYECQVEFADGERRWRSITAAPIAGDDGDE-FVL 216
                                       56788888999999999*************99888874.444 PP

  == domain 4  score: 22.5 bits;  conditional E-value: 5.8e-08
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBG.GGGBSTTHHH.....HHHHHHHHHHHHTT-ECC CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgksl.ldliheedda.....elaelleqlleqgeesra 74 
                                       + +le++p +i v ++d + + +N+ a+e +Gls++e    ++  +++   d++            ++l++ge+  +
  gi|336253467|ref|YP_004596574.1| 240 EKLLETAPIAIAVQNADRETIRANQRAQEAFGLSEQEFRDNPVdTGEWRIYDEDgelldSSETTSGRVLATGEPVLD 316
                                       789***********************************999995567887777795554455555568********* PP

                                       CCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  75 geisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +e  f+ ++g+  +++v+ +p++ ++gei  ++  ++d+
  gi|336253467|ref|YP_004596574.1| 317 EELVFEPPNGERLYFRVNSAPIFGPDGEIERIVTAAKDV 355
                                       *****************************9998877775 PP

  == domain 5  score: 18.5 bits;  conditional E-value: 1e-06
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-E CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgees 72 
                                       ++il    d+  ++De  r ++ N+ a+ +l  sree+lg+++ + i+   ++ ++e++++++e++e+ 
  gi|336253467|ref|YP_004596574.1| 377 SEILGRVSDAFYALDEEWRYTHLNEQAAAILDRSREELLGRPVWETIPDAVESFFREQYQRAMETQEPV 445
                                       556666789999************************************998889999999999999876 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       0.4     6e+02      54      81 ..      56      82 ..      43      86 .. 0.84
   2 ?    4.2   0.0     0.035        52      42      82 ..     172     213 ..     163     219 .. 0.83
   3 !   21.5   0.0   1.4e-07   0.00021       2      87 ..     260     350 ..     259     352 .. 0.89
   4 !    8.3   0.0    0.0019       2.8       2      56 ..     397     449 ..     396     453 .. 0.92
   5 ?   -2.4   0.0       4.1   6.1e+03      34      54 ..     602     622 ..     600     623 .. 0.85
   6 ?   -0.4   0.0      0.99   1.5e+03      32      45 ..     652     665 ..     650     675 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.4
                             PAS_3 54 geyRirrkdGeyrwveararvirdengk 81
                                       e R +r dG+ +w++  ++++ de g 
  gi|336253467|ref|YP_004596574.1| 56 NELRTKRIDGTRVWWRPATQPV-DERGD 82
                                      57888999*************9.88875 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.035
                             PAS_3  42 lqealkkgepy.egeyRirrkdGeyrwveararvirdengkp 82 
                                       ++++++ gep+ + e ++  +dGe rw + +a +i  ++g +
  gi|336253467|ref|YP_004596574.1| 172 WARVFDAGEPVtDYECQVEFADGERRWRSITAAPIAGDDGDE 213
                                       56777888955588999999***************9999976 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 1.4e-07
                             PAS_3   2 iyvserveeilGyspeellgk.veswldlvhpeDrervrealq...ealkkge.pyegeyRirrkdGeyrwvearar 73 
                                       i +++r +e +G+s++e++++ v++   +++ eD e + ++     ++l++ge ++++e  +  ++Ge  +++    
  gi|336253467|ref|YP_004596574.1| 260 IRANQRAQEAFGLSEQEFRDNpVDTGEWRIYDEDGELLDSSETtsgRVLATGEpVLDEELVFEPPNGERLYFRVNSA 336
                                       789******************99***********66655555544599*****666********************* PP

                             PAS_3  74 virdengkpvrvig 87 
                                       +i+  +g++ r++ 
  gi|336253467|ref|YP_004596574.1| 337 PIFGPDGEIERIVT 350
                                       ***********986 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0019
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegey 56 
                                       ++++e+   il+ s+eellg+   + + +     + +re++q+a++++ep+++e+
  gi|336253467|ref|YP_004596574.1| 397 THLNEQAAAILDRSREELLGR--PVWETIPDAVESFFREQYQRAMETQEPVSFEI 449
                                       5789*****************..99**999999****************999886 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 4.1
                             PAS_3  34 Drervrealqealkkgepyeg 54 
                                       D +++r+ +q++l++  +y+g
  gi|336253467|ref|YP_004596574.1| 602 DASQLRQVFQNLLTNAVQYSG 622
                                       8899*********98888876 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 0.99
                             PAS_3  32 peDrervrealqea 45 
                                       p+D++r++e +q++
  gi|336253467|ref|YP_004596574.1| 652 PDDQDRIFEVFQRL 665
                                       9**********986 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.18   2.7e+02       3      34 ..     109     140 ..     107     180 .. 0.72
   2 !   22.0   0.0   8.3e-08   0.00012       4      47 ..     240     287 ..     237     304 .. 0.74
   3 !   12.3   0.0   8.7e-05      0.13      10      57 ..     383     428 ..     376     443 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.18
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalell 34 
                                        + ++e++p gi vv +++++v  N++  + l
  gi|336253467|ref|YP_004596574.1| 109 AERILETVPIGIGVVAADGTVVRGNERLFDRL 140
                                       6789********99884455999999876666 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 8.3e-08
                             PAS_8   4 ralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg...q 47 
                                       + l+e++p +iav ++++  + +Nq+a+e +G+s +++++ +++   +
  gi|336253467|ref|YP_004596574.1| 240 EKLLETAPIAIAVQNADRETIRANQRAQEAFGLSeQEFRDNPVDtgeW 287
                                       679**********998788*************6666665555533232 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 8.7e-05
                             PAS_8  10 spdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrplle 57 
                                       ++d+   +d+ +r ++ N++a+ +l  s ++l+g ++++ +p+     e
  gi|336253467|ref|YP_004596574.1| 383 VSDAFYALDEEWRYTHLNEQAAAILDRSrEELLGRPVWETIPDA---VE 428
                                       678888899777*************8666666666666333333...33 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.1   5.7e-13   8.5e-10       2      66 ..     493     559 ..     492     560 .. 0.94
   2 ?   -1.9   0.1       2.4   3.6e+03      39      59 ..     594     614 ..     571     616 .. 0.75

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 5.7e-13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l++f+   +H+L  PL  +  ++++L+++  ++l+++ +e++e ++++a+r++++++ lL++sr e+
  gi|336253467|ref|YP_004596574.1| 493 LEQFAYAASHDLQEPLRMVTSYLQLLENRygDELDDDAEEFIEFAVDGAERMREMIDGLLEYSRVET 559
                                       789***********************7777999*******************************987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  39 eyletiesearrldhlvedlL 59 
                                       e l t+e  a +l+++ ++lL
  gi|336253467|ref|YP_004596574.1| 594 EDLPTVEGDASQLRQVFQNLL 614
                                       467788888889999999987 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.3       8.6   1.3e+04       6      42 ..     346     382 ..     344     386 .. 0.64
   2 !   17.0   0.1     3e-06    0.0044      28     111 ..     602     687 ..     569     707 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 8.6
                       HATPase_c_2   6 ehvrtvrevaeavlrraglseelldeirlaveEactN 42 
                                       e++ t+++ ++++ +r +  e++ +e++  ++E++ +
  gi|336253467|ref|YP_004596574.1| 346 ERIVTAAKDVTELKARERQLEQRKAELETELSEILGR 382
                                       5667777778888555555555555777777777655 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3e-06
                       HATPase_c_2  28 lldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep....keslkegGr 100
                                       ++ ++r + + ++tNav++  ++ p  +v+v++e++++   v+v+D+G g dp ++++  e  +     e+ +  G+
  gi|336253467|ref|YP_004596574.1| 602 DASQLRQVFQNLLTNAVQYSGDGPP--QVRVSAERAGDMWDVSVRDEGVGIDPDDQDRIFEVFQrlhgREEHPGTGI 676
                                       4557888888899********9888..8999999****************999876665544337777777888888 PP

                       HATPase_c_2 101 GlalikglvDe 111
                                       Gl l +++v+ 
  gi|336253467|ref|YP_004596574.1| 677 GLSLCRRIVER 687
                                       88888888765 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.6   8.3e+03      39      76 ..      10      51 ..       8      62 .. 0.61
   2 ?    1.5   0.0      0.22   3.3e+02       1      33 [.     113     145 ..     113     160 .. 0.89
   3 ?    4.0   0.0     0.035        52       2      68 ..     244     309 ..     243     363 .. 0.60
   4 ?    5.4   0.0     0.013        19      61     115 .]     429     484 ..     380     484 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.6
                             PAS_7 39 vpleellrynaergefgagdveaeverrl....aaaragkph 76
                                      v+le++ r+ ae ++ ga  ++ ev++rl    +aar++ ++
  gi|336253467|ref|YP_004596574.1| 10 VTLEDVRRVVAESEHPGAPVAAGEVAERLgcstRAARTKLSE 51
                                      567888888888888886666666666663222444444444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.22
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpee 33 
                                       le ++ Gi v+ ad+ +v  N+r  + l  p++
  gi|336253467|ref|YP_004596574.1| 113 LETVPIGIGVVAADGTVVRGNERLFDRLPCPNG 145
                                       789999*****************9988877765 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.035
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrla 68 
                                       e  + +i+v +ad + +  N+r +e ++l+e+ ++     +   r+  e ge+  +++e +  r+la
  gi|336253467|ref|YP_004596574.1| 244 ETAPIAIAVQNADRETIRANQRAQEAFGLSEQEFRDNPVDTGEWRIYDEDGELL-DSSETTSGRVLA 309
                                       66677899*********************9988765544444445555555555.444444445554 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.013
                             PAS_7  61 aeverrl.aaaragkphsfererpd.grvievrgnplpdgGfVttytDiTerrraee 115
                                       +++++   +a+++++p sfe e ++   ++e+   p  + G+ + + DiTer+r e+
  gi|336253467|ref|YP_004596574.1| 429 SFFREQYqRAMETQEPVSFEIEAATfDAWLEFAVYPS-ESGLSVYFRDITERKRYEQ 484
                                       4444333144555677777776655256777776664.5678889********9986 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.7e-05      0.07       5      92 ..     605     699 ..     602     708 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-05
                       HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg..........ek.kklesskskkeehGiG 70 
                                        l  ++ nlL NA++ + + +   + +r+++++  ++  +s+  +  g          e  ++l+   +++   GiG
  gi|336253467|ref|YP_004596574.1| 605 QLRQVFQNLLTNAVQYSGDGP---PQVRVSAERAGDMWDVSVRDEGVGidpddqdrifEVfQRLHG-REEHPGTGIG 677
                                       57789*********9998877...89***********99999999666666654433322344444.5567789*** PP

                       HATPase_c_5  71 lksireivkkykgnlsieaedg 92 
                                       l+  r+iv++++g+++++ e g
  gi|336253467|ref|YP_004596574.1| 678 LSLCRRIVERHGGDIRVDSEPG 699
                                       ****************998765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     8e-05      0.12      15      48 ..      27      65 ..      22      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8e-05
                            HTH_11 15 p.isgeeLAeeLnvSrrtvrrdIkaLeelg....vpIes 48
                                        + + e Ae+L++S+r+ r  + +L e       +I++
  gi|336253467|ref|YP_004596574.1| 27 ApVAAGEVAERLGCSTRAARTKLSELIERNelrtKRIDG 65
                                      44889999*****************97765555555555 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 ?    3.6   0.0     0.035        53      38      72 ..     342     376 ..     340     390 .. 0.82
   2 ?    5.9   0.2     0.007        11      25      78 ..     477     528 ..     474     579 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.035
                        Phage_GP20  38 dkqLedLkkkakdneeLqkqieelqaknkkakaey 72 
                                       d+++e + ++akd++eL++   +l++  ++ ++e 
  gi|336253467|ref|YP_004596574.1| 342 DGEIERIVTAAKDVTELKARERQLEQRKAELETEL 376
                                       77899999999999999999888888877776665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.007
                        Phage_GP20  25 eerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiad 78 
                                       +er+ +++ql++ ++ Le++  +   + +Lq+ +  ++  ++  ++ y  ++ d
  gi|336253467|ref|YP_004596574.1| 477 TERKRYEQQLEASNERLEQFAYA--ASHDLQEPLRMVTSYLQLLENRYGDELDD 528
                                       79******************766..88888888777777766666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (718 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); 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:                        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: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.40
# Mc/sec: 5349.35
//
Query:       gi|336253468|ref|YP_004596575.1|  [L=236]
Description: hypothetical protein Halxa_2071 [Halopiger xanaduensis SH-6]
Scores for 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-49  167.1  16.7      4e-49  166.6  16.7    1.2  1  DUF1405   Protein of unknown function (DUF1405)


Domain annotation for each model (and alignments):
>> DUF1405  Protein of unknown function (DUF1405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.6  16.7   2.2e-53     4e-49       1     157 []      42     214 ..      42     214 .. 0.94

  Alignments for each domain:
  == domain 1  score: 166.6 bits;  conditional E-value: 2.2e-53
                           DUF1405   1 gtvyGyiyYgkqlaetplllwpfvpDSPtAtlffalallllllgrelellealAfvtlikyGlWtvvvlllvllkgg 77 
                                       gt++G++yY+ q+a+tp+++wp+vpDSP+Atl++ala+++++lgre+++l+alAf+++i +GlWt+++ll+++  + 
  gi|336253468|ref|YP_004596575.1|  42 GTAFGFWYYSGQFATTPTAMWPWVPDSPMATLLIALAIACWKLGREQPWLTALAFFGNIILGLWTPYTLLAFADAYS 118
                                       89**********************************************************************95555 PP

                           DUF1405  78 ....leelm...LilsHlamavealllarilrfsvkalavalawlllndvvDYvlgvlpelhetl............ 135
                                           l   m   L++sHlam+v+al+l+ri++f+v+++aval+w++ n vvDY+++vl+++h+t+            
  gi|336253468|ref|YP_004596575.1| 119 yihpL---MyqfLFWSHLAMVVQALVLHRITDFPVWSVAVALVWYGSNLVVDYFVPVLGDPHHTFipvardtpmflg 192
                                       63333...3667****************************************************************7 PP

                           DUF1405 136 eeeleliaafavvltvlsllla 157
                                       +++l +iaa+ v++t+l+l+la
  gi|336253468|ref|YP_004596575.1| 193 ADALGVIAAGEVTFTLLALFLA 214
                                       777***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); 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):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1794.62
//
Query:       gi|336253469|ref|YP_004596576.1|  [L=288]
Description: acetoacetate decarboxylase [Halopiger xanaduensis SH-6]
Scores for complete 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   0.1    2.6e-15   56.6   0.1    1.3  1  ADC       Acetoacetate decarboxylase (ADC)


Domain annotation for each model (and alignments):
>> ADC  Acetoacetate decarboxylase (ADC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.1   1.5e-19   2.6e-15      30     120 ..      69     179 ..      54     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.5e-19
                                       HHHHHTTSBTTEEECS....TSEEEEEEEEEEEECTTTC....EEEEEEEEEEEEET............TEEEEEEE CS
                               ADC  30 peaaaallPepLelae....rplvavyfaeypdssfggg....qYneagivvpvryg............gkegayil 86 
                                       +  ++++lP  Le+ +     + va++ ++y+ +  +gg    +Y e+++ vp+  g            g+ g y++
  gi|336253469|ref|YP_004596576.1|  69 RRVLESVLPSKLEPLAiapgIGCVALVGIRYRQVGRDGGtglePYDEFAVIVPAVRGsrtrlplaqlfgGELGGYVH 145
                                       566899***********94445555555666666655559**************999889999999995556***** PP

                                       EEEESSHHHHHHHHHHTT--EEE-EEEEEEETTE CS
                               ADC  87 vlwvdkeaalaaGRElwGfPKklAditltregdt 120
                                        l+v+++a++a GRE+wG+PK+ +  t++ + + 
  gi|336253469|ref|YP_004596576.1| 146 RLPVTSDASVALGREIWGYPKERGALTVADTPRG 179
                                       ************************9999875544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       148  (0.00825478); expected 358.6 (0.02)
Passed bias filter:                      133  (0.00741815); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2142.73
//
Query:       gi|336253470|ref|YP_004596577.1|  [L=315]
Description: Pyridoxal biosynthesis lyase pdxS [Halopiger xanaduensis SH-6]
Scores for 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-102  340.5   9.2   4.4e-102  340.2   9.2    1.1  1  SOR_SNZ       SOR/SNZ family
    1.6e-10   40.7   6.6    3.8e-07   29.7   1.0    2.2  2  ThiG          Thiazole biosynthesis protein ThiG
    4.6e-05   22.7   1.3      0.015   14.4   0.1    2.4  2  Dus           Dihydrouridine synthase (Dus)
    0.00083   19.0   0.2       0.79    9.3   0.0    2.4  2  OMPdecase     Orotidine 5'-phosphate decarboxylase / HUMPS fa
     0.0055   15.9   0.1       0.15   11.2   0.0    2.4  2  IGPS          Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
      0.014   14.5   1.6       0.36   10.0   0.1    2.8  3  NanE          Putative N-acetylmannosamine-6-phosphate epimer
      0.015   14.3   0.6       0.13   11.2   0.0    2.2  2  FMN_dh        FMN-dependent dehydrogenase
      0.055   12.9   0.4       0.59    9.6   0.0    2.6  2  His_biosynth  Histidine biosynthesis protein
      0.064   12.6   1.2       0.36   10.1   0.1    2.2  2  TMP-TENI      Thiamine monophosphate synthase
       0.17   11.3   2.5        1.4    8.3   0.1    2.7  3  MttA_Hcf106   mttA/Hcf106 family


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 !  340.2   9.2  2.5e-105  4.4e-102       3     207 .]      29     233 ..      27     233 .. 0.99

  Alignments for each domain:
  == domain 1  score: 340.2 bits;  conditional E-value: 2.5e-105
                                       HHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEET CS
                           SOR_SNZ   3 kvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvri 79 
                                        vk+g+a+m+kgGvimdvvn+eqa+iae+aGavavmale vpadirk+ggvarm+dp+ ++ei+e vsipvm k+ri
  gi|336253470|ref|YP_004596577.1|  29 LVKRGFARMQKGGVIMDVVNPEQARIAEDAGAVAVMALEAVPADIRKRGGVARMADPADVEEIVEEVSIPVMGKSRI 105
                                       69*************************************************************************** PP

                                       T-HHHHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHH CS
                           SOR_SNZ  80 GhfveaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveav 156
                                       Gh+ eaqilea+gvd+iDesevltpad+++hidk++f++pfvcGarnlgealrri+eGaamirtkGeagtGdv +av
  gi|336253470|ref|YP_004596577.1| 106 GHTKEAQILEAVGVDMIDESEVLTPADDAYHIDKREFTAPFVCGARNLGEALRRIDEGAAMIRTKGEAGTGDVNQAV 182
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHTTS-HHHHHHHHHHHHGGGHHHHHHHHHTTS-S---T. CS
                           SOR_SNZ 157 rhvrkikeeirklkslseeelvalakelkaplelvkevaelgrlpvvnfaa 207
                                       +h r+ik+ irk++ +++ee  a+a+e++ap elv+e+ae+grlpvvnfaa
  gi|336253470|ref|YP_004596577.1| 183 HHQRNIKSAIRKIEGMTHEEREAFAREIEAPAELVHETAEMGRLPVVNFAA 233
                                       *************************************************98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.4   1.3e-05     0.023     117     211 ..      27     132 ..      16     146 .. 0.72
   2 !   29.7   1.0   2.1e-10   3.8e-07     174     225 ..     223     277 ..     207     290 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                                       HHHHHTT-EEEEE..E-S-HH...HHHHHHHTT-SEBEEBSS...STTS---...-S-HHHHHHHHHH-SS-BEEES CS
                              ThiG 117 eiLvkeGFevlpY..vsdDlv...larrleevGcaavmPlaa...piGsglG...llnkealkiiieeakvPvivDA 182
                                         Lvk GF+ +    v  D+v    ar  e++G+ avm l a    i    G   +++++ ++ i+ee+++Pv+   
  gi|336253470|ref|YP_004596577.1|  27 TDLVKRGFARMQKggVIMDVVnpeQARIAEDAGAVAVMALEAvpaDIRKRGGvarMADPADVEEIVEEVSIPVMGKS 103
                                       557777777775322445554222688899********98652225655555111567899**************** PP

                                       ---SHHHHHHHHHTT-SEEEESHHHHTSS CS
                              ThiG 183 GigspsdaaqamelGadavllntavaeak 211
                                        ig++++a     +G+d +     ++ a+
  gi|336253470|ref|YP_004596577.1| 104 RIGHTKEAQILEAVGVDMIDESEVLTPAD 132
                                       *******9998889999775555555555 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 2.1e-10
                                       -.SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                              ThiG 174 a.kvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklave 225
                                       + ++Pv+  A  Gi +p daa  m  G+d++++ + +  a++p amA+a+ +a++
  gi|336253470|ref|YP_004596577.1| 223 MgRLPVVNFAagGIATPADAALMMHHGCDGIFVGSGIFGAENPPAMAEAIVAATN 277
                                       3378888544449*************************************99976 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0016       2.8      96     138 ..      74     112 ..      48     131 .. 0.65
   2 !   14.4   0.1   8.4e-06     0.015     182     233 ..     226     279 ..     200     297 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0016
                                       TEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC CS
                               Dus  96 rggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeee 138
                                       r+ +G a +++p+ v++iv+     v+iPv  k rig  +e +
  gi|336253470|ref|YP_004596577.1|  74 RKRGGVARMADPADVEEIVE----EVSIPVMGKSRIGHTKEAQ 112
                                       55556666666665555544....4677777777777664333 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 8.4e-06
                                       -SS-EEEESS--SHHHHHHHHHHH--SEEEESCH...HCCSTTHHHHHHHHHHSC CS
                               Dus 182 vsipviaNGdIkdaedaqaileetGadgvmigrg...algnPwlfaestavktge 233
                                       ++++ +a G+I ++ da  ++++ G+dg+ +g g   a++ P++ ++  a+ ++ 
  gi|336253470|ref|YP_004596577.1| 226 LPVVNFAAGGIATPADAALMMHH-GCDGIFVGSGifgAENPPAMAEAIVAATNNW 279
                                       56777899***********9999.********98222444455544343444333 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 !    7.7   0.4    0.0013       2.4      80     155 ..     157     231 ..     151     242 .. 0.86
   2 !    9.3   0.0   0.00044      0.79     190     225 .]     237     272 ..     227     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0013
                                       CHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHH.SHHHHHHHHHHHHHHHTTESEE CS
                         OMPdecase  80 sarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqek.gytqacveaarehkaedfvmGf 155
                                         ri+e+a ++   + aG++ v ++++  +  +   +  ++ m++++ ++++++ ++  ++v++ +e+ +   v+ f
  gi|336253470|ref|YP_004596577.1| 157 LRRIDEGAAMIRTKGEAGTGDVNQAVHHQRNIK-SAIRKIEGMTHEEREAFAREiEAPAELVHETAEMGRL-PVVNF 231
                                       469*************************99997.9******************779*********999954.44444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00044
                                       CGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHHH CS
                         OMPdecase 190 qyntpekligiagadiiivGRgIlkagdpveeaery 225
                                             +l+   g+d i vG gI++a++p + ae++
  gi|336253470|ref|YP_004596577.1| 237 ATPADAALMMHHGCDGIFVGSGIFGAENPPAMAEAI 272
                                       555566778889*******************99986 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.04        71      61      88 ..      39      66 ..      35     122 .. 0.74
   2 !   11.2   0.0   8.3e-05      0.15     208     249 ..     226     267 ..     177     272 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.04
                                      TEESBSS--HHHHHHHHTTT.-SEEEEE CS
                              IGPS 61 kgliredfdpaeiAkkyeeagAsaiSVL 88
                                      kg + +d++ +e+A+  e+agA a+  L
  gi|336253470|ref|YP_004596577.1| 39 KGGVIMDVVNPEQARIAEDAGAVAVMAL 66
                                      7888899999999999999999988655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.3e-05
                                       TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHH CS
                              IGPS 208 kdvllvaeSGiktredveklkeegvnafLvGeslmrqedvek 249
                                         v+  a  Gi+t++d+  + ++g +++ vG+ +  +e+  +
  gi|336253470|ref|YP_004596577.1| 226 LPVVNFAAGGIATPADAALMMHHGCDGIFVGSGIFGAENPPA 267
                                       447778999***********************9999888655 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 ?    0.2   0.0       0.2   3.5e+02     154     172 ..      47      65 ..      12      73 .. 0.71
   2 ?    2.3   0.2     0.047        83      82     124 ..      67     108 ..      42     124 .. 0.57
   3 ?   10.0   0.1    0.0002      0.36     147     176 ..     230     259 ..     186     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.2
                                       -SHHHHHHHHTT--SEEEE CS
                              NanE 154 ntPekakkaieiGvdavvv 172
                                         Pe+a+ a + G++av+ 
  gi|336253470|ref|YP_004596577.1|  47 VNPEQARIAEDAGAVAVMA 65 
                                       4699999999999988865 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.047
                                       HHHHHHHHHH-.-EEEEE-SSHHHHHHHHHTT-SEEE-TTTTSS CS
                              NanE  82 eelikkikeky.qllmaDistleeglvakklGvdivGttlsGyt 124
                                       e++ ++i++++ +  maD + +ee +  +++ + ++G    G+t
  gi|336253470|ref|YP_004596577.1|  67 EAVPADIRKRGgVARMADPADVEEIV--EEVSIPVMGKSRIGHT 108
                                       44444555554344455555555532..3444444554444444 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0002
                                       EEEES---SHHHHHHHHTT--SEEEE-HHH CS
                              NanE 147 viaeGrintPekakkaieiGvdavvvGsai 176
                                         a G i tP+ a+ ++++G d + vGs i
  gi|336253470|ref|YP_004596577.1| 230 NFAAGGIATPADAALMMHHGCDGIFVGSGI 259
                                       4689************************98 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3     0.095   1.7e+02     201     241 ..      81     122 ..      24     126 .. 0.74
   2 ?   11.2   0.0   7.4e-05      0.13     193     243 ..     205     255 ..     137     258 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.095
                                       TC--HHHHHHHHHHHSSEEEEEE.E-SHHHHHHHHHTTESEE CS
                            FMN_dh 201 psltwddikwlreqtklplvvKG.vltaedakraveaGvdgi 241
                                       +  + +d++++ e++++p++ K  + + ++a+ + ++Gvd i
  gi|336253470|ref|YP_004596577.1|  81 RMADPADVEEIVEEVSIPVMGKSrIGHTKEAQILEAVGVDMI 122
                                       344677899999999999999965888999999999999888 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 7.4e-05
                                       HHCCCHB-TC--HHHHHHHHHHHSSEEEEEEE-SHHHHHHHHHTTESEEEE CS
                            FMN_dh 193 efvgkqldpsltwddikwlreqtklplvvKGvltaedakraveaGvdgivv 243
                                       +f++++  p+   ++ +++ +   +++   G+ t++da +++++G+dgi v
  gi|336253470|ref|YP_004596577.1| 205 AFAREIEAPAELVHETAEMGRLPVVNFAAGGIATPADAALMMHHGCDGIFV 255
                                       444444444444445555555556667788*******************99 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.24   4.4e+02      63      96 ..      86     119 ..      62     125 .. 0.73
   2 ?    9.6   0.0   0.00033      0.59      63     223 ..     215     259 ..     204     295 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.24
                                       HHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT- CS
                      His_biosynth  63 dlveeiaeevfipvqvGGGIrsledveelleaga 96 
                                       + veei+eev+ipv+  + I + ++++ l   g+
  gi|336253470|ref|YP_004596577.1|  86 ADVEEIVEEVSIPVMGKSRIGHTKEAQILEAVGV 119
                                       5688899999988876666666666665555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00033
                                       HHHHHHHHH-SSEE..EEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEE CS
                      His_biosynth  63 dlveeiaeevfipv..qvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykva 137
                                       +lv+e+ae  ++pv     GGI +  d++ +++ g+d + +g+                                  
  gi|336253470|ref|YP_004596577.1| 215 ELVHETAEMGRLPVvnFAAGGIATPADAALMMHHGCDGIFVGSG--------------------------------- 258
                                       45555555555554222455555555555555555555555554................................. PP

                                       ETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTC CS
                      His_biosynth 138 ikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegv 214
                                                                                                                    
  gi|336253470|ref|YP_004596577.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       SEEEESHHH CS
                      His_biosynth 215 davivgsal 223
                                               +
  gi|336253470|ref|YP_004596577.1| 259 --------I 259
                                       ........3 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.13   2.3e+02     106     168 ..      49     114 ..      44     123 .. 0.63
   2 ?   10.1   0.1    0.0002      0.36     140     181 .]     215     259 ..     204     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.13
                          TMP-TENI 106 leeaeeaealgadYigvGpifpTdtKkda...eplgleglkelaealeiPvvaiGGitlenvaevl 168
                                       +e+a+ ae++ga  +++    p d +k     ++++ + ++e++e+++iPv+    i + + a++l
  gi|336253470|ref|YP_004596577.1|  49 PEQARIAEDAGAVAVMALEAVPADIRKRGgvaRMADPADVEEIVEEVSIPVMGKSRIGHTKEAQIL 114
                                       566777777777444444444555554432446778889999999999999986666655555555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0002
                          TMP-TENI 140 eglkelaealeiPvv..aiGGi.tlenvaevleagadgvavvsai 181
                                       e++ e+ae+ ++Pvv  a GGi t++++a ++++g+dg+ v s+i
  gi|336253470|ref|YP_004596577.1| 215 ELVHETAEMGRLPVVnfAAGGIaTPADAALMMHHGCDGIFVGSGI 259
                                       6778899999988854499**967899**************9987 PP

>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.073   1.3e+02      26      34 ..     150     158 ..     149     161 .. 0.92
   2 ?   -3.0   0.0       2.7   4.9e+03      16      27 ..     259     270 ..     259     272 .. 0.79
   3 ?    8.3   0.1   0.00079       1.4      19      34 ..     282     297 ..     282     308 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.073
                                       HHHHHHHHH CS
                       MttA_Hcf106  26 araLGktLr 34 
                                       ar+LG++Lr
  gi|336253470|ref|YP_004596577.1| 150 ARNLGEALR 158
                                       8*******9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.7
                                       HS-TTTHHHHHH CS
                       MttA_Hcf106  16 lFGpkkLPEvar 27 
                                       +FG++  P +a 
  gi|336253470|ref|YP_004596577.1| 259 IFGAENPPAMAE 270
                                       8***98888776 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00079
                                       TTTHHHHHHHHHHHHH CS
                       MttA_Hcf106  19 pkkLPEvaraLGktLr 34 
                                       p+ L+E+ ++LGk+++
  gi|336253470|ref|YP_004596577.1| 282 PEALAEISKNLGKGMK 297
                                       678***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2348.20
//
Query:       gi|336253471|ref|YP_004596578.1|  [L=47]
Description: hypothetical protein Halxa_2074 [Halopiger xanaduensis SH-6]
Scores for 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   20.8   0.5    0.00027   20.8   0.5    1.1  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type
    0.00028   20.8   0.9    0.00033   20.6   0.9    1.1  1  DZR             Double zinc ribbon
    0.00034   20.1   0.7      0.086   12.4   0.1    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
    0.00066   19.3   1.7      0.025   14.3   0.4    2.1  2  zinc_ribbon_2   zinc-ribbon domain
    0.00093   18.5   1.6       0.24   10.9   0.4    2.1  2  zf-ribbon_3     zinc-ribbon domain
     0.0045   17.1   2.5     0.0085   16.2   2.5    1.5  1  Zn-ribbon_8     Zinc ribbon domain
     0.0088   16.1   0.8       0.01   15.9   0.8    1.1  1  DUF1272         Protein of unknown function (DUF1272)
  ------ inclusion threshold ------
      0.014   15.3   1.8       0.88    9.6   0.2    2.1  2  YhfH            YhfH-like protein
      0.016   15.0   2.0      0.036   13.8   2.0    1.6  1  Rubredoxin_2    Rubredoxin metal binding domain
      0.017   15.1   0.3      0.021   14.8   0.3    1.1  1  zinc-ribbons_6  zinc-ribbons
       0.03   14.3   0.8      0.032   14.2   0.8    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.052   13.8   1.4       0.11   12.7   1.3    1.6  2  zinc_ribbon_9   zinc-ribbon
       0.06   13.2   0.2       0.06   13.2   0.2    1.0  1  MCM_OB          MCM OB domain
       0.11   12.5   0.9       0.13   12.2   0.9    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.13   12.0   4.1        5.1    6.9   0.2    2.2  2  zf-CCHC_5       GAG-polyprotein viral zinc-finger
       0.29   11.1   2.7        1.7    8.6   2.7    1.9  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.74   10.0   3.7        3.7    7.7   0.1    2.1  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
        1.1    9.0   3.5        1.3    8.8   0.4    2.1  2  zf-C2H2_11      zinc-finger C2H2-type


Domain annotation for each model (and alignments):
>> 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 !   20.8   0.5   2.7e-07   0.00027      17      47 ..      13      42 ..       6      47 .] 0.86

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.7e-07
                          zf-C2HC5 17 apnClnCGkiiCakeglskpCsfCgspllss 47
                                      +  Cl CGk i a  ++ + C+ Cg+ + ++
  gi|336253471|ref|YP_004596578.1| 13 TYECLRCGKLITASTHP-GACPECGAGIQNR 42
                                      568**************.*******987655 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.9   3.3e-07   0.00033      13      43 ..      14      44 ..       7      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.3e-07
                               DZR 13 rfCseCgtklkavaaedrCpsCgekvdpear 43
                                        C +Cg+ + a +++ +Cp+Cg+ ++++a+
  gi|336253471|ref|YP_004596578.1| 14 YECLRCGKLITASTHPGACPECGAGIQNRAN 44
                                      56**********************9999876 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   8.6e-05     0.086       1      15 [.      12      26 ..      12      29 .. 0.85
   2 !    6.6   0.1    0.0058       5.7       5      12 ..      32      39 ..      30      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.6e-05
                            zf_UBZ  1 dtylCerCgkeipes 15
                                      +ty C rCgk i  s
  gi|336253471|ref|YP_004596578.1| 12 STYECLRCGKLITAS 26
                                      59********99765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0058
                            zf_UBZ  5 CerCgkei 12
                                      C++Cg+ i
  gi|336253471|ref|YP_004596578.1| 32 CPECGAGI 39
                                      *****987 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.026        26       2       7 ..      16      21 ..       9      27 .. 0.74
   2 !   14.3   0.4   2.5e-05     0.025       2      14 ..      32      44 ..      31      45 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.026
                     zinc_ribbon_2  2 CpnCGa 7 
                                      C +CG+
  gi|336253471|ref|YP_004596578.1| 16 CLRCGK 21
                                      666666 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.5e-05
                     zinc_ribbon_2  2 CpnCGaelqdnak 14
                                      Cp+CGa +q++a+
  gi|336253471|ref|YP_004596578.1| 32 CPECGAGIQNRAN 44
                                      **********997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0036       3.6       1      14 [.      12      25 ..      12      27 .. 0.80
   2 !   10.9   0.4   0.00024      0.24       5      17 ..      32      44 ..      31      45 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0036
                       zf-ribbon_3  1 stvrCPnCGaplss 14
                                      st++C +CG+++++
  gi|336253471|ref|YP_004596578.1| 12 STYECLRCGKLITA 25
                                      6899******6664 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00024
                       zf-ribbon_3  5 CPnCGa.plssddn 17
                                      CP+CGa + + ++n
  gi|336253471|ref|YP_004596578.1| 32 CPECGAgI-QNRAN 44
                                      99999966.76665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.5   8.5e-06    0.0085       6      34 ..      14      37 ..      13      42 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.5e-06
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs 34
                                      Y+C +Cg+  +    +s   + aCPeCg+
  gi|336253471|ref|YP_004596578.1| 14 YECLRCGKLIT----ASTH-PGACPECGA 37
                                      *******6555....3422.356*****8 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.8     1e-05      0.01      25      54 ..      12      42 ..       3      44 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                           DUF1272 25 csyEctFCaeCaeevl.envCPncgGelvkR 54
                                       +yEc  C +  ++    + CP+cg ++++R
  gi|336253471|ref|YP_004596578.1| 12 STYECLRCGKLITASThPGACPECGAGIQNR 42
                                      58******99776655279********9998 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.015        15      15      23 ..      15      23 ..      13      29 .. 0.88
   2 ?    9.6   0.2   0.00089      0.88      15      29 ..      31      45 ..      26      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
                              YhfH 15 kCteCGkei 23
                                      +C  CGk i
  gi|336253471|ref|YP_004596578.1| 15 ECLRCGKLI 23
                                      7*****987 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00089
                              YhfH 15 kCteCGkeieEqaec 29
                                       C+eCG  i+  a +
  gi|336253471|ref|YP_004596578.1| 31 ACPECGAGIQNRANS 45
                                      5*******9988765 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.0   3.6e-05     0.036       1      22 [.      14      37 ..      14      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-05
                      Rubredoxin_2  1 YvCsqCGf..esakwfGrCpsCgs 22
                                      Y+C +CG   +++++ G Cp+Cg+
  gi|336253471|ref|YP_004596578.1| 14 YECLRCGKliTASTHPGACPECGA 37
                                      99*****64489**********96 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   2.1e-05     0.021      12      40 ..       9      40 ..       4      44 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                                      E-SSEEE-TTT--...EEEEEEE-SSS-S--- CS
                    zinc-ribbons_6 12 krgeqyhCeaCqe...dlkkealCpeCeqele 40
                                      +++++y+C  C +     +    CpeC+  ++
  gi|336253471|ref|YP_004596578.1|  9 ETESTYECLRCGKlitASTHPGACPECGAGIQ 40
                                      567899******97656666789****99887 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   0.8   3.2e-05     0.032      66      94 ..       9      37 ..       5      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-05
                                      EE--EEEETTTS-EEECHHHHHS-TTTSS CS
                              HypA 66 evpvkvrCreCgkefeleekalrCpkCgs 94
                                      e++ +++C +Cgk ++ +++   Cp+Cg+
  gi|336253471|ref|YP_004596578.1|  9 ETESTYECLRCGKLITASTHPGACPECGA 37
                                      567889******99997765568****97 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.19   1.9e+02      19      28 ..      11      20 ..       5      23 .. 0.62
   2 ?   12.7   1.3   0.00011      0.11       3      30 ..      14      38 ..      12      39 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.19
                     zinc_ribbon_9 19 dsdvlCPhCg 28
                                      +s   C +Cg
  gi|336253471|ref|YP_004596578.1| 11 ESTYECLRCG 20
                                      3333499998 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00011
                     zinc_ribbon_9  3 yWChqCdrfVsvspdedsdvlCPhCggg 30
                                      y C +C + +++s+  ++ + CP+Cg g
  gi|336253471|ref|YP_004596578.1| 14 YECLRCGKLITAST--HPGA-CPECGAG 38
                                      55999999999965..4666.****988 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2     6e-05      0.06      31      61 ..      10      37 ..       3      47 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6e-05
                                      EEEEEEETTT-.-EEES----SB-..TTT-H CS
                            MCM_OB 31 kkavfeckkcgktveveleePrkCeekeCes 61
                                      +++++ec +cgk ++ + ++P  C  +eC++
  gi|336253471|ref|YP_004596578.1| 10 TESTYECLRCGKLIT-ASTHPGAC--PECGA 37
                                      6899*******9666.7899****..99*94 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 ?   12.2   0.9   0.00013      0.13      23      56 ..       8      39 ..       3      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                    OrfB_Zn_ribbon 23 npayTSktCseCgsknkealsgrtfkCpnCgfea 56
                                      ++  +  +C +Cg+  +   s+    Cp+Cg+ +
  gi|336253471|ref|YP_004596578.1|  8 SETESTYECLRCGKLITA--STHPGACPECGAGI 39
                                      56678889**********..***********874 PP

>> zf-CCHC_5  GAG-polyprotein viral zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.6    0.0069       6.9       5      10 ..      16      21 ..      14      22 .. 0.93
   2 ?    6.9   0.2    0.0051       5.1       2      11 ..      29      38 ..      28      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0069
                                      -TTT-S CS
                         zf-CCHC_5  5 CpRCkk 10
                                      C+RC+k
  gi|336253471|ref|YP_004596578.1| 16 CLRCGK 21
                                      *****9 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0051
                                      --B-TTT-SS CS
                         zf-CCHC_5  2 pglCpRCkkg 11
                                      pg Cp C+ g
  gi|336253471|ref|YP_004596578.1| 29 PGACPECGAG 38
                                      89*****976 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 ?    8.6   2.7    0.0017       1.7       3      31 ..      12      36 ..      10      40 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                    Zn_ribbon_SprT  3 yvYrCtgCgreythhlsi.rrhnYrCrrCk 31
                                       +Y C +Cg   + +  +  + +  C+ C+
  gi|336253471|ref|YP_004596578.1| 12 STYECLRCG---KLITAStHPGA--CPECG 36
                                      58*******...88888888888..99887 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 ?    7.7   0.1    0.0037       3.7      11      25 ..       8      22 ..       2      29 .. 0.77
   2 ?    4.0   0.7     0.053        53      18      24 ..      31      37 ..      24      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0037
                          zf-Mss51 11 apkhvdfeCpdCGip 25
                                      ++ + ++eC +CG  
  gi|336253471|ref|YP_004596578.1|  8 SETESTYECLRCGKL 22
                                      567899*******65 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.053
                          zf-Mss51 18 eCpdCGi 24
                                       Cp+CG 
  gi|336253471|ref|YP_004596578.1| 31 ACPECGA 37
                                      6*****7 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 ?    8.8   0.4    0.0013       1.3       2      11 ..      11      20 ..      10      27 .. 0.90
   2 ?    1.6   0.2      0.25   2.4e+02       7      12 ..      32      37 ..      24      38 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                        zf-C2H2_11  2 estcqCleCG 11
                                      est+ Cl CG
  gi|336253471|ref|YP_004596578.1| 11 ESTYECLRCG 20
                                      79*******9 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.25
                        zf-C2H2_11  7 CleCGl 12
                                      C eCG 
  gi|336253471|ref|YP_004596578.1| 32 CPECGA 37
                                      99**95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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: 0.32u 0.20s 00:00:00.52 Elapsed: 00:00:00.34
# Mc/sec: 418.33
//
Query:       gi|336253472|ref|YP_004596579.1|  [L=438]
Description: glutamate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-72  243.0   0.1    5.1e-72  242.5   0.1    1.2  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    2.9e-56  188.9   0.0    4.8e-56  188.2   0.0    1.4  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
     0.0008   18.8   0.0     0.0014   18.0   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.025   12.1   0.1      0.083   10.4   0.0    1.7  2  Bac_GDH          Bacterial NAD-glutamate dehydrogenase
        0.1   12.9   0.0        0.7   10.3   0.0    2.3  2  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA


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 !  242.5   0.1   1.4e-75   5.1e-72       1     243 []     200     435 ..     200     435 .. 0.98

  Alignments for each domain:
  == domain 1  score: 242.5 bits;  conditional E-value: 1.4e-75
                                       T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HH CS
                     ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldie 77 
                                       GGs++r+ea g++v+++++e+++++++  le+++va++G+G vg +aa+ll e+ga+vva+sD +G+ ydp+G+ ++
  gi|336253472|ref|YP_004596579.1| 200 GGSEGREEAPGRSVAIVTREACDYYDQP-LEETTVAVQGFGSVGANAARLLDEWGATVVAISDVNGAAYDPDGIPVQ 275
                                       9***********************7777.************************************************ PP

                                       HHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHH CS
                     ELFV_dehydrog  78 ellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeA 154
                                       e+ ++ ee ++v+ey++ +++  + i+ne +ll+l+vd+l+P+A+ n+i+e+na+  ++  ++lvvEgAN+ptt++A
  gi|336253472|ref|YP_004596579.1| 276 EIPSHDEEPEAVTEYANAHAD--QIITNE-KLLQLDVDVLIPAAIGNVITEANAD-DVR--ASLVVEGANGPTTSAA 346
                                       ****************87765..799996.*************************.999..**************** PP

                                       HHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHHH CS
                     ELFV_dehydrog 155 keileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqelvkganiag 231
                                       + il+e+g+ v+pd++aNaGGVtvS++E+lq+++r sw+ e+v+++l+++m+++++av +e+++++++++++ +i++
  gi|336253472|ref|YP_004596579.1| 347 DAILTERGIPVIPDILANAGGVTVSYFEWLQDINRRSWSLERVNSELEAEMEAAWNAVQREVDDRGVTWRDATYIVA 423
                                       ***************************************************************************** PP

                                       HHHHHHHHHHCT CS
                     ELFV_dehydrog 232 fekvaeamkaqG 243
                                       ++++ +a++a+G
  gi|336253472|ref|YP_004596579.1| 424 LDRIGRAHEARG 435
                                       **********99 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 !  188.2   0.0   1.3e-59   4.8e-56       1     130 []      54     182 ..      54     182 .. 0.99

  Alignments for each domain:
  == domain 1  score: 188.2 bits;  conditional E-value: 1.3e-59
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       p +v +v+vp++rd+G+lev++gyr+qh+s++gP+kGG+R+hp+v+ +e+  L+++mt+K+a++d+pfGGakgg+++
  gi|336253472|ref|YP_004596579.1|  54 PAHVHEVNVPIERDDGSLEVYTGYRVQHDSVRGPFKGGLRYHPEVTREECIGLSMWMTWKCAVMDIPFGGAKGGIIV 130
                                       789************************************************************************** PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeykk 130
                                       dpk+lse+e er+trrf++e++ + iGp++D+pApD+gt++++m+wl+d y++
  gi|336253472|ref|YP_004596579.1| 131 DPKDLSEAETERLTRRFTEEIR-DAIGPNKDIPAPDMGTDPQTMSWLMDAYSM 182
                                       **********************.****************************97 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 !   18.0   0.0     4e-07    0.0014      29      69 ..     223     263 ..     211     326 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4e-07
                                       GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
                      2-Hacid_dh_C  29 llgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrsk 69 
                                       +  + l++ tv++ G+G++G ++a++l ++g+ v+a++  +
  gi|336253472|ref|YP_004596579.1| 223 YYDQPLEETTVAVQGFGSVGANAARLLDEWGATVVAISDVN 263
                                       5567899****************************998764 PP

>> Bac_GDH  Bacterial NAD-glutamate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.09   3.2e+02     738     783 ..      89     134 ..      85     149 .. 0.79
   2 ?   10.4   0.0   2.3e-05     0.083    1050    1099 ..     325     374 ..     319     376 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.09
                           Bac_GDH 738 RGGlRWSDRreDfRtEvLGLvKaQqvKNavI.VPv.GaKGGFvvkrlp 783
                                       +GGlR+    e  R E +GL    + K av+ +P  GaKGG +v  + 
  gi|336253472|ref|YP_004596579.1|  89 KGGLRYH--PEVTREECIGLSMWMTWKCAVMdIPFgGAKGGIIVDPKD 134
                                       5999995..78899******999999***988998469***9986544 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 2.3e-05
                           Bac_GDH 1050 ngkelrakvvgEGgNLGltQlgRiEyalkggrintDaiDNsaGVdcSDhE 1099
                                        n+ ++ra  v EG+N   t  +    +++g+ +  D + N++GV +S  E
  gi|336253472|ref|YP_004596579.1|  325 NADDVRASLVVEGANGPTTSAADAILTERGIPVIPDILANAGGVTVSYFE 374 
                                        99*******************************************99665 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 ?   -0.7   0.0       0.5   1.8e+03      39      57 ..      75      93 ..      51     101 .. 0.80
   2 ?   10.3   0.0    0.0002       0.7       2      37 ..     232     266 ..     231     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.5
                                      HHHHHHEETTTEC-SS-EE CS
                           Gp_dh_N 39 layllkyDsvhgrfkgeve 57
                                        y +++Dsv g fkg ++
  gi|336253472|ref|YP_004596579.1| 75 TGYRVQHDSVRGPFKGGLR 93
                                      5578999******998765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0002
                                       EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-HH CS
                           Gp_dh_N   2 kvainGfGRIGrlvlralleekelevvaindltdle 37 
                                        va+ GfG +G +++r l e+   +vvai d+  ++
  gi|336253472|ref|YP_004596579.1| 232 TVAVQGFGSVGANAARLLDEW-GATVVAISDVNGAA 266
                                       69**************98766.88999999976654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3056.43
//
Query:       gi|336253473|ref|YP_004596580.1|  [L=117]
Description: hypothetical protein Halxa_2076 [Halopiger xanaduensis SH-6]
Scores for 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   14.6   2.6      0.032   14.6   2.6    2.0  2  ATP-synt_I  ATP synthase I chain
      0.081   11.2   2.5      0.092   11.0   2.5    1.0  1  DUF2070     Predicted membrane protein (DUF2070)
        0.9    9.8   0.0        0.9    9.8   0.0    2.5  2  VirB3       Type IV secretory pathway, VirB3-like protein


Domain annotation for each model (and alignments):
>> ATP-synt_I  ATP synthase I chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   2.0      0.13     8e+02      10      33 ..      13      36 ..       7      49 .. 0.47
   2 ?   14.6   2.6   5.4e-06     0.032       1      51 [.      61     111 ..      61     117 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.13
                        ATP-synt_I 10 lavlalgwlltgsasvalsallGg 33
                                      ++++++++++  +a+v++ a++ g
  gi|336253473|ref|YP_004596580.1| 13 VLAATIAAFVRVGAPVSWPAAVLG 36
                                      333444444444444444333333 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.4e-06
                        ATP-synt_I   1 rivliqlvllavlalgwlltgsasvalsallGglisvlpfalfalrvfrfs 51 
                                       riv + +v+lav++++ +    +   lsa++G+l+  l f++ ++ ++ ++
  gi|336253473|ref|YP_004596580.1|  61 RIVQVAAVILAVVVIIVGARVAPAPVLSAIAGALVTYLGFLVIVTVAVGTR 111
                                       68889999*****99999999999*******************99984333 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.5   1.5e-05     0.092      48     126 ..      33     112 ..       5     115 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.5e-05
                           DUF2070  48 alvaflltlpvlrilggrltykrslflalltelivviisllaillsall.qalvllalvlslalvfalrllvlvavs 123
                                       a++ ++ tl +  ++ + +++ r ++   + ++ +vi+ ++ i++ a + +a vl a++ +l+ ++++ ++v+vav+
  gi|336253473|ref|YP_004596580.1|  33 AVLGGAGTLAFELVAARDPELVREYWEQRIVQVAAVILAVVVIIVGARVaPAPVLSAIAGALVTYLGFLVIVTVAVG 109
                                       3444444444444444445555555555555555555444444444444577899********************99 PP

                           DUF2070 124 des 126
                                        ++
  gi|336253473|ref|YP_004596580.1| 110 TRH 112
                                       876 PP

>> VirB3  Type IV secretory pathway, VirB3-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00015       0.9      25      68 ..      12      58 ..       5      66 .. 0.76
   2 ?   -0.8   6.4      0.32   1.9e+03      25      42 ..      66      92 ..      60     116 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00015
                             VirB3 25 lnllvsvilfl...vglslwillllvplhlvlrliakrDpqmfrvll 68
                                      l+l++++ +f+   + +s+ +++l  +  l++ l+a+rDp ++r ++
  gi|336253473|ref|YP_004596580.1| 12 LVLAATIAAFVrvgAPVSWPAAVLGGAGTLAFELVAARDPELVREYW 58
                                      444555555557677777777777889***************99884 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.32
                             VirB3 25 lnllvsvilfl..............vglslwi 42
                                      ++++++v++++              +      
  gi|336253473|ref|YP_004596580.1| 66 AAVILAVVVIIvgarvapapvlsaiA-----G 92
                                      44455555555233444444333321.....2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 868.72
//
Query:       gi|336253474|ref|YP_004596581.1|  [L=293]
Description: Homoserine kinase [Halopiger xanaduensis SH-6]
Scores for 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-15   55.8   3.8    7.4e-15   54.9   1.6    2.4  2  GHMP_kinases_N  GHMP kinases N terminal domain
    1.3e-07   31.9   0.0    2.9e-07   30.7   0.0    1.6  1  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 ?   -0.1   0.0      0.12   1.1e+03      52      65 ..      12      25 ..       2      26 .. 0.78
   2 !   54.9   1.6   8.3e-19   7.4e-15       1      66 []      72     139 ..      72     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.12
                                      HHHHSHHHHHHHHS CS
                    GHMP_kinases_N 52 gngsggDvaasvyG 65
                                        gsg+Dv+ +++G
  gi|336253474|ref|YP_004596581.1| 12 NLGSGFDVFGVALG 25
                                      349*****988877 PP

  == domain 2  score: 54.9 bits;  conditional E-value: 8.3e-19
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                       +i+i++ + +++GLGSSAA a+a+++Al++l++     ee + +a+e+e l+  g+ + ++va+s++Gg
  gi|336253474|ref|YP_004596581.1|  72 RIHIDKGVRPSSGLGSSAASAAAAAVALNDLYDRGYtrEElVPIAAEGEALVS-GEAHADNVAPSLLGG 139
                                       69******************************877445447***********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 !   30.7   0.0   3.3e-11   2.9e-07       7      84 ..     200     271 ..     188     272 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 3.3e-11
                    GHMP_kinases_C   7 rgdlellgellnlsqrs...elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralr 80 
                                       r+d +l+g+++     +   ++   + +l +  e++  a++++Ga g+ +sGa  Gp v a++ ++ ++ +va+a+ 
  gi|336253474|ref|YP_004596581.1| 200 RNDPDLVGRGME----DaivTP--KRTSLIDGYEQVRTAALDAGATGVTVSGA--GPGVLAVC-HQHDQRAVASAML 267
                                       79999*******....556689..*****************************..********.************9 PP

                    GHMP_kinases_C  81 eefe 84 
                                       e+fe
  gi|336253474|ref|YP_004596581.1| 268 EAFE 271
                                       9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2316.12
//
Query:       gi|336253475|ref|YP_004596582.1|  [L=421]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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  64.3    1.1e-29  103.5  37.9    2.0  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.074   13.3   0.7      0.074   13.3   0.7    3.4  4  LHC       Antenna complex alpha/beta subunit


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 !  103.5  37.9   1.2e-33   1.1e-29       5     344 ..      16     359 ..      12     369 .. 0.80
   2 !   16.0  18.5   4.8e-07    0.0043      41     172 ..     269     402 ..     265     419 .. 0.84

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 1.2e-33
                             MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                       ++l+++  + + ++l     +++ + ++ +gl+++l ++ +++++lp+G l+dr+G++r++l++l ++++++lll++
  gi|336253475|ref|YP_004596582.1|  16 HALVHWFETSIPIFLV-VWLNEFDVGVALFGLIVALGYAPFGAGALPGGILADRYGPKRLILCCLGGMSVAFLLLSV 91 
                                       5666666666666666.5569**************************************************666665 PP

                             MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyila 158
                                       ++s+++++v+ +l G++a+++ pag++li+  ++  erg ++++ +++ ++G++lgp +++ l+  l Wr+v  +la
  gi|336253475|ref|YP_004596582.1|  92 GTSIYAVAVGLILWGVAASVYHPAGLSLISTGVA--ERGTVFAWHGIAGNVGIALGPFVAATLLIVLEWRLVVALLA 166
                                       58888*************************9777..6**************************************** PP

                             MFS_1 159 ivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg........ll 227
                                       i +lla++  + l  e +p+ + + ++e     g  ++++ +++ll++     l+++++   f++ +        +l
  gi|336253475|ref|YP_004596582.1| 167 IPGLLAVL--YGLTAEFDPTAAVDGDVEA----GADEALS-LSELLTNSRT--LFASAFALIFVIVAfeglyyrgML 234
                                       ******66..4666666666666666777....7788888.9999999988..444444443344444556667799 PP

                             MFS_1 228 tllplylqevlgls..............glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalg 290
                                       t+lp +l++   +                ++++g  l +++++g   +  +g+l dr+ +   + la l++++++l+
  gi|336253475|ref|YP_004596582.1| 235 TYLPEILHSAPAIEalplpadlegiepsRYIYVG--LLVVGMAG---QYAGGKLTDRVDP--ERGLAALFAVFVVLA 304
                                       9999998888888899999****87777667777..77777777...999*******999..555555555555555 PP

                             MFS_1 291 lallavtssavllll.vlvliGfglgfvfpsllalasdlappeeagtasglfnta 344
                                       la+++v +  +  ++ ++ ++Gf+l+ ++p ++ +++ ++p++ +g  +g++ + 
  gi|336253475|ref|YP_004596582.1| 305 LAFVPVVEMGLGPIVaLCGVFGFFLFAIQPFYQDAVAVYTPADTRGLSYGYTYLG 359
                                       5555555444444443566689988888*******************99998755 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 4.8e-07
                             MFS_1  41 yalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa.sslwlllvlrvlqGlgagalfpagaaliadwfp 115
                                         ++ +++++ +G l+dr+ + r l + +++f++ +l+++ ++  +l ++++l  + G++  a+ p  + ++a ++p
  gi|336253475|ref|YP_004596582.1| 269 LLVVGMAGQYAGGKLTDRVDPERGLAALFAVFVVLALAFVpVVeMGLGPIVALCGVFGFFLFAIQPFYQDAVAVYTP 345
                                       5677899****************777777777777344443336777789999999********************* PP

                             MFS_1 116 keergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                        + rg+ +g+ ++g         ++gg+++++++ ++ f+ +a+++l + vl + ll
  gi|336253475|ref|YP_004596582.1| 346 ADTRGLSYGYTYLGEFGIGSASIAVGGFVLEAFSTTGFFLTIAGFALAGTVLSAGLL 402
                                       *************97777778889*************************99755554 PP

>> LHC  Antenna complex alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   1.0       1.4   1.3e+04      14      26 ..     161     173 ..     159     174 .. 0.59
   2 ?   -3.6   0.9       1.5   1.4e+04      13      21 ..     215     223 ..     209     225 .. 0.47
   3 ?   13.3   0.7   8.3e-06     0.074       8      27 ..     287     306 ..     286     307 .. 0.95
   4 ?   -3.3   0.3       1.3   1.1e+04      18      25 ..     381     388 ..     379     391 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHH CS
                               LHC  14 lvallgffavlAl 26 
                                       +vall + ++lA+
  gi|336253475|ref|YP_004596582.1| 161 VVALLAIPGLLAV 173
                                       5666666666666 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.5
                                       HHHHHHHHH CS
                               LHC  13 glvallgff 21 
                                        + ++++++
  gi|336253475|ref|YP_004596582.1| 215 AFALIFVIV 223
                                       334444444 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 8.3e-06
                                       ...HHHHHHHHHHHHHHHHH CS
                               LHC   8 vdPhrglvallgffavlAll 27 
                                       vdP rgl al+ +f+vlAl+
  gi|336253475|ref|YP_004596582.1| 287 VDPERGLAALFAVFVVLALA 306
                                       8*****************96 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 1.3
                                       HHHHHHHH CS
                               LHC  18 lgffavlA 25 
                                       +gff+++A
  gi|336253475|ref|YP_004596582.1| 381 TGFFLTIA 388
                                       78999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3309.98
//
Query:       gi|336253476|ref|YP_004596583.1|  [L=204]
Description: hypothetical protein Halxa_2079 [Halopiger xanaduensis SH-6]
Scores for 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  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1702.25
//
Query:       gi|336253477|ref|YP_004596584.1|  [L=412]
Description: Ferredoxin--NAD(+) reductase [Halopiger xanaduensis SH-6]
Scores for complete 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-47  162.1   0.3    2.2e-47  161.7   0.3    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    5.2e-13   48.9   0.0    6.3e-10   38.8   0.0    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    2.3e-11   44.1   0.3    1.5e-05   25.4   0.0    3.4  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    4.3e-09   36.2   0.0    1.4e-07   31.3   0.0    2.6  2  Rubredoxin_C   Rubredoxin NAD+ reductase C-terminal domain
    0.00069   19.8   0.2       0.22   11.8   0.0    3.3  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00089   18.1   0.1       0.06   12.0   0.0    3.0  4  HI0933_like    HI0933-like protein
     0.0087   15.3   0.1      0.099   11.9   0.0    2.3  2  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.058   12.5   0.0       0.97    8.5   0.0    2.1  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
       0.12   13.0   0.0       0.39   11.3   0.0    1.9  1  Reductase_C    Reductase C-terminal
       0.22   11.0   4.9        1.7    8.1   0.0    3.1  4  DAO            FAD dependent oxidoreductase
       0.34   10.9   4.0        3.7    7.5   0.0    2.8  3  NAD_binding_9  FAD-NAD(P)-binding


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 !  161.7   0.3   1.4e-50   2.2e-47       2     283 ..       3     290 ..       2     307 .. 0.90

  Alignments for each domain:
  == domain 1  score: 161.7 bits;  conditional E-value: 1.4e-50
                                       SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.......HHHHCHHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias.......evvkklnqgiel 69 
                                       ++v+iG G+ G +aa+tl++    ak+t++ +eg+ l++++l+++ + g   +a i         e       +i+l
  gi|336253477|ref|YP_004596584.1|   3 EYVIIGDGISGSSAAETLREedPDAKITVITDEGEALYNRILIKEHAKGKLPEAPISIhdedwydE------RDIDL 73 
                                       68******************766********************99999998888877777656532......36*** PP

                                       CHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC..TTBEECCSECHHHHHHCCSS-T.SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Pyr_redox_2  70 llgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv.aenvgklvrtldsaealklkllp.kr 144
                                        l+++v+++d++ k+v+       ++e i ydkl++AtG++p  l+++   ae+v+++  t+++a++++++  + ++
  gi|336253477|ref|YP_004596584.1|  74 SLNTHVTSVDTDDKTVHT-----HEGEAIGYDKLLIATGGTPTQLPVENSdAEGVHHF-WTFQDARRIRKAAENsED 144
                                       ******************.....6788*********************7735555555.*********9999888** PP

                                       EEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.EEE.E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.x RF
                       Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgnge.kle.v 218
                                       +v+vG+G+ G+++Aa+    g e  ++ ++dr    al  + ++++++ ++++Gve ++ + v +++ +++ ++e  
  gi|336253477|ref|YP_004596584.1| 145 AVIVGAGLLGIDFAAVCGAQGIEGKYLMRGDRWWrYALSGDGAEIMHDGMREKGVEPVFDSGVDRFEVDDDgHVEaA 221
                                       **********************************8889999***********************999999987889* PP

                                       EETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.......TECCS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxx RF
                       Pyr_redox_2 219 vledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.......ggkgg 283
                                       ++ +g+++++d   va+G++ +te+l + +g+e   ++givvde+++tn +++ya+GD +       g++ +
  gi|336253477|ref|YP_004596584.1| 222 IDPNGDRFECDWAGVAIGLTFNTEFL-RGSGIEQ--DNGIVVDEYMQTNLEDVYAAGDLTrfydvllGEQAQ 290
                                       **************************.*****99..**********************99775555544444 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 !   15.9   0.1   3.6e-06    0.0059     165     274 ..       2     115 ..       1     119 [. 0.78
   2 !   38.8   0.0   3.9e-13   6.3e-10      91     305 .]      66     275 ..      49     275 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.6e-06
                       Pyr_redox_3 165 qkvvViGgknSavDaAlelvrk..gaeVtvvtrgseiekeesdpsyslkpdienrleelvke.........ekikvl 230
                                       +++v+iG + S+  aA  l ++  +a++tv+t++ e   ++    + +k + + +l e+  +         + i++ 
  gi|336253477|ref|YP_004596584.1|   2 TEYVIIGDGISGSSAAETLREEdpDAKITVITDEGEALYNR----ILIKEHAKGKLPEAPISihdedwydeRDIDLS 74 
                                       689*************99998877899****9998877765....4555555555555544444557777667**** PP

                       Pyr_redox_3 231 fnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsfl 274
                                        n++v+++++++++  v+t++g+    +d+ ++atG +p+  ++
  gi|336253477|ref|YP_004596584.1|  75 LNTHVTSVDTDDKT--VHTHEGEA-IGYDKLLIATGGTPTQLPV 115
                                       *********99886..78888766.5689*********987665 PP

  == domain 2  score: 38.8 bits;  conditional E-value: 3.9e-13
                       Pyr_redox_3  91 aksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtGefdkPnklnipGeek.lvkhyskvkefhkya.. 163
                                        ++ +++  l+++V+sv+ +d+  +v+t ++  +  +k++iAtG    P +l ++ ++   v h+ ++++++ ++  
  gi|336253477|ref|YP_004596584.1|  66 YDERDIDLSLNTHVTSVDTDDK--TVHTHEGeAIGYDKLLIATGG--TPTQLPVENSDAeGVHHFWTFQDARRIRka 138
                                       577889999********99875..78998865999*********8..********9997245566677777665422 PP

                       Pyr_redox_3 164 ...gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevke 237
                                           ++ v++G++  ++D A  + ++g e + ++rg+ +        y l+ d  + ++++++e+ ++ +f++ v++
  gi|336253477|ref|YP_004596584.1| 139 aenSEDAVIVGAGLLGIDFAAVCGAQGIEGKYLMRGDRWW------RYALSGDGAEIMHDGMREKGVEPVFDSGVDR 209
                                       233689******************************9665......589***************88**********9 PP

                       Pyr_redox_3 238 ikekeeey.kvk.tedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                        + ++  + +    ++g+++e  d   +a+G + +++fl+ s++e+ ++g   + +e ++tn+++++ aG
  gi|336253477|ref|YP_004596584.1| 210 FEVDDDGHvEAAiDPNGDRFEC-DWAGVAIGLTFNTEFLRGSGIEQ-DNG--IVVDEYMQTNLEDVYAAG 275
                                       9976554313334889999887.677889***********888877.444..345789**********99 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00056      0.91       3      35 ..       5      39 ..       3      54 .. 0.83
   2 ?    4.7   0.0     0.027        44      52      78 ..      68      91 ..      59      94 .. 0.84
   3 !   25.4   0.0   9.2e-09   1.5e-05       2      74 ..     145     219 ..     144     223 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00056
                                      EEECSSHHHHHHHHHHHHTT..SEEEEEESSSSSS CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelg..kkVtvversdkll 35
                                      v++G G +g  +A++l+e    +k+tv+  + + l
  gi|336253477|ref|YP_004596584.1|  5 VIIGDGISGSSAAETLREEDpdAKITVITDEGEAL 39
                                      9***************9977669*****9999888 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.027
                                      HTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox 52 kngievllntkveeiegsedgvesvkl 78
                                      ++ i++ lnt v+++++++++   v++
  gi|336253477|ref|YP_004596584.1| 68 ERDIDLSLNTHVTSVDTDDKT---VHT 91
                                      67899************9997...554 PP

  == domain 3  score: 25.4 bits;  conditional E-value: 9.2e-09
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedg.ve 74 
                                       +v+vG+G++g+++A++  + g + + + r+d+    +l  + ++i+++ ++++g+e ++++ v ++e ++dg ve
  gi|336253477|ref|YP_004596584.1| 145 AVIVGAGLLGIDFAAVCGAQGIEGKYLMRGDRWWrYALSGDGAEIMHDGMREKGVEPVFDSGVDRFEVDDDGhVE 219
                                       69**********************9999**9999899**********************************9776 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 ?    1.8   0.0      0.14   2.3e+02      21      44 ..      24      47 ..      10      49 .. 0.81
   2 !   31.3   0.0   8.8e-11   1.4e-07       9      69 ..     329     386 ..     323     387 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.14
                                      ---SEEEEEE-SS-..EEEEEEET CS
                      Rubredoxin_C 21 eekaeelveedkekgkYkklfikn 44
                                      + +a++ v  d+ +  Y +++ik+
  gi|336253477|ref|YP_004596584.1| 24 DPDAKITVITDEGEALYNRILIKE 47
                                      3338889999999999******97 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 8.8e-11
                                       TEEEEEES--TT---SEEEEEE-SS-..EEEEEEETTEEEEEEEES-HHHHHHHHHHHHTT CS
                      Rubredoxin_C   9 gidlfSvGdieeeekaeelveedkekgkYkklfikngklvGAiliGDtkesaklkkliekk 69 
                                       ++   S+G     +   + ++++   ++ +++ +k+gk+vG +liGD +  +k+k+l++++
  gi|336253477|ref|YP_004596584.1| 329 DFPFLSFGHPTLGD-EHAERKYS--DTEWRRIAFKDGKIVGGVLIGDLSPQSKFKQLMREQ 386
                                       56667888888777.33333333..3448*****************************986 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 !   11.8   0.0   0.00013      0.22       1      25 [.       6      32 ..       6      36 .. 0.90
   2 ?   -0.9   0.0       1.2     2e+03      48      63 ..     122     137 ..     119     141 .. 0.84
   3 ?    4.0   0.1     0.036        59       1      20 [.     147     166 ..     147     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                      EE--SHHHHHHHHHHHCC..TEEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlll 25
                                      I+G G+sG++aA +L+++  +++++++
  gi|336253477|ref|YP_004596584.1|  6 IIGDGISGSSAAETLREEdpDAKITVI 32
                                      89**************98778888886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.2
                                       S---EEETTHHHHCHH CS
                     NAD_binding_8  48 gahifhgsgyypnvrr 63 
                                       g+h f+++++ +++r+
  gi|336253477|ref|YP_004596584.1| 122 GVHHFWTFQDARRIRK 137
                                       89******99998876 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.036
                                       EE--SHHHHHHHHHHHCCTE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagf 20 
                                       IvGaGl G  +A+ +  +g+
  gi|336253477|ref|YP_004596584.1| 147 IVGAGLLGIDFAAVCGAQGI 166
                                       9********99998877755 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.049        80       3      39 ..       4      43 ..       2      47 .. 0.72
   2 !   12.0   0.0   3.7e-05      0.06     119     165 ..      66     109 ..      62     124 .. 0.86
   3 ?   -2.4   0.3      0.88   1.4e+03       2      23 ..     144     165 ..     143     187 .. 0.78
   4 ?   -0.7   0.0      0.28   4.6e+02     113     163 ..     188     239 ..     156     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.049
                                      EEEE--SHHHHHHHHHH..HHTT--EEEE.-SSSSS-HHH CS
                       HI0933_like  3 viviGgGaAGlmaAisa..akrgkrVlll.ekakklgrKi 39
                                       ++iG G +G  aA+++  ++ +++++++ +++++l ++i
  gi|336253477|ref|YP_004596584.1|  4 YVIIGDGISGSSAAETLreEDPDAKITVItDEGEALYNRI 43
                                      69**************955556677776635555555555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.7e-05
                                       HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 119 lkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                        +e++++l l+t+v+sv+++++   +v+t+++e++  dkl++AtGG+
  gi|336253477|ref|YP_004596584.1|  66 YDERDIDLSLNTHVTSVDTDDK---TVHTHEGEAIGYDKLLIATGGT 109
                                       578999***********65444...699999***************7 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.88
                                       SEEEE--SHHHHHHHHHHHHTT CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrg 23 
                                       d +++G+G  G+  A+ ++++g
  gi|336253477|ref|YP_004596584.1| 144 DAVIVGAGLLGIDFAAVCGAQG 165
                                       7899999999987777776665 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE--- CS
                       HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtG 163
                                       +++   ++e+gv+   ++ v ++e ++dg+++ ++  +++++e+d   +A+G
  gi|336253477|ref|YP_004596584.1| 188 EIMHDGMREKGVEPVFDSGVDRFEVDDDGHVEAAIdPNGDRFECDWAGVAIG 239
                                       5666778899999999999999999999988888855888888887666655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   6.1e-05     0.099      19      88 ..       3      64 ..       1      80 [. 0.81
   2 ?    0.6   0.1      0.17   2.7e+02      18      37 ..     143     162 ..     132     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.1e-05
                                      EEEEE--SHHHHHHHHHHHHC.TTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHTT---EEES CS
                              Thi4 19 DvvivGaGssGLtaayylakk.pdlkvailersvspGGGawlGGqlfsaivvrkpakelLdelgikyedeg 88
                                      + vi+G G sG +aa +l ++ pd k++++  +         G  l+++i++++ ak  L e  i  +de+
  gi|336253477|ref|YP_004596584.1|  3 EYVIIGDGISGSSAAETLREEdPDAKITVITDE---------GEALYNRILIKEHAKGKLPEAPISIHDED 64
                                      569*****************99*******9754.........66677777777777777777777666665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.17
                                       EEEEEE--SHHHHHHHHHHH CS
                              Thi4  18 sDvvivGaGssGLtaayyla 37 
                                        D vivGaG  G+  a + +
  gi|336253477|ref|YP_004596584.1| 143 EDAVIVGAGLLGIDFAAVCG 162
                                       699*******9998877665 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 ?    1.6   0.0     0.077   1.3e+02     195     225 ..       5      35 ..       2      40 .. 0.89
   2 ?    8.5   0.0    0.0006      0.97     116     201 ..      76     152 ..      66     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.077
                       K_oxygenase 195 aVvGsGqSaaeifedllrrqkkvelklvtrs 225
                                       +++G G S++  +e l ++ ++++++++t +
  gi|336253477|ref|YP_004596584.1|   5 VIIGDGISGSSAAETLREEDPDAKITVITDE 35 
                                       79************************99865 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0006
                       K_oxygenase 116 geeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtep.kiPevleklegkervvHsseylerkeellak 191
                                       +++v++v+ d++      tv++     e e +   +l++++G++p ++P    + eg ++++  +++ + +++ +++
  gi|336253477|ref|YP_004596584.1|  76 NTHVTSVDTDDK------TVHT----HEGEAIGYDKLLIATGGTPtQLPVENSDAEGVHHFWTFQDARRIRKAAENS 142
                                       555666666554......3554....3556777789******776479*9999999988888888888888889999 PP

                       K_oxygenase 192 kriaVvGsGq 201
                                       ++ ++vG+G 
  gi|336253477|ref|YP_004596584.1| 143 EDAVIVGAGL 152
                                       *********7 PP

>> Reductase_C  Reductase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00024      0.39      14      84 ..     335     406 ..     327     407 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                                       EE--TT--EEEEEEETTTTEEEEEEEETTEEEEEEEES-HHHHHHHHHHTTTT---..-HHHHH-TTS-HHH. CS
                       Reductase_C  14 aGlatgadevvvRgdpeerafsvfylrdgrlvaveavnrprdlmaarrliaagasv..dpaalaDpavdLkkl 84 
                                        G++t  de   R+  +  ++  + ++dg++v+ + +++ +     ++l+ ++++v  +++ l +++vdL +l
  gi|336253477|ref|YP_004596584.1| 335 FGHPTLGDEHAERKYSD-TEWRRIAFKDGKIVGGVLIGDLSPQSKFKQLMREQREVadQKEVLLEKQVDLDEL 406
                                       69999999***999988.79*******************9999999***988876511567788999999887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0011       1.7       2      27 ..       4      33 ..       3      38 .. 0.82
   2 ?    3.3   0.0      0.03        49     160     203 ..      70     109 ..      65     137 .. 0.75
   3 ?   -2.9   2.5       2.3   3.8e+03       1      12 [.     144     155 ..     144     166 .. 0.89
   4 ?   -3.5   0.0       3.7     6e+03     154     183 ..     192     219 ..     179     244 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                                      EEEECTSHHHHHHHHHHHHTT....EEEEE CS
                               DAO  2 vviiGGGiiGlstAyeLarrg....Vtlle 27
                                       viiG Gi G+s+A  L ++     +t++ 
  gi|336253477|ref|YP_004596584.1|  4 YVIIGDGISGSSAAETLREEDpdakITVIT 33
                                      69***************7653489999986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.03
                                       T-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGG CS
                               DAO 160 Gveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaw 203
                                        +++ ++t vt+++ +d   ++v  +t+ ge   +d++ +a+G  
  gi|336253477|ref|YP_004596584.1|  70 DIDLSLNTHVTSVDTDD---KTV--HTHeGEAIGYDKLLIATGGT 109
                                       578899*******7654...567..44446655569999999954 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.3
                                       EEEEECTSHHHH CS
                               DAO   1 dvviiGGGiiGl 12 
                                       d vi+G+G  G+
  gi|336253477|ref|YP_004596584.1| 144 DAVIVGAGLLGI 155
                                       78******9996 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 3.7
                                       HHHHHTT-EEEESECEEEEEEEE.TCEEEEE CS
                               DAO 154 raaealGveilegtevtgleeed.gkvwgve 183
                                       + ++++Gve ++ + v ++e +d g    ve
  gi|336253477|ref|YP_004596584.1| 192 DGMREKGVEPVFDSGVDRFEVDDdGH---VE 219
                                       55788888888888888887655233...32 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 ?    7.5   0.0    0.0023       3.7       1      32 [.       5      33 ..       5      56 .. 0.82
   2 ?    4.1   0.1     0.026        42     121     155 ..      76     108 ..      67     109 .. 0.81
   3 ?   -2.8   0.5       3.5   5.7e+03       1      11 [.     146     156 ..     146     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0023
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfd 32
                                      +i+G G++G +++e L ++   + + +it++ 
  gi|336253477|ref|YP_004596584.1|  5 VIIGDGISGSSAAETLREE---DPDAKITVIT 33
                                      7***************999...5778888873 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.026
                     NAD_binding_9 121 raevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       +++v++++++++  +v++++g+ + +d++ +A+G 
  gi|336253477|ref|YP_004596584.1|  76 NTHVTSVDTDDK--TVHTHEGEAIGYDKLLIATGG 108
                                       556677665544..69*****************95 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.5
                     NAD_binding_9   1 aivGaGprGla 11 
                                       +ivGaG  G+ 
  gi|336253477|ref|YP_004596584.1| 146 VIVGAGLLGID 156
                                       79****99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 3216.32
//
Query:       gi|336253478|ref|YP_004596585.1|  [L=446]
Description: polysulfide reductase NrfD [Halopiger xanaduensis SH-6]
Scores for complete 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   73.8  21.2    1.9e-20   73.8  21.2    1.8  2  NrfD      Polysulphide reductase, NrfD
  ------ inclusion threshold ------
       0.18   12.1   0.2       0.18   12.1   0.2    3.9  5  DUF996    Protein of unknown function (DUF996)
        3.1    8.3   7.2        1.7    9.1   3.8    2.4  2  DUF2583   Protein of unknown function (DUF2583)


Domain annotation for each model (and alignments):
>> NrfD  Polysulphide reductase, NrfD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.26   1.6e+03     255     283 ..      21      48 ..      13      51 .. 0.73
   2 !   73.8  21.2   3.1e-24   1.9e-20       6     309 ..      59     379 ..      56     382 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.26
                              NrfD 255 vlFwlgvvllglaiplllslavprlrenv 283
                                       ++++l v+++gla+ ++l  + ++l++  
  gi|336253478|ref|YP_004596585.1|  21 KYYAL-VAVAGLALGVFLIGWAYQLQQGL 48 
                                       56655.88888888888888888877765 PP

  == domain 2  score: 73.8 bits;  conditional E-value: 3.1e-24
                              NrfD   6 snsvvWglliavylFligisAgalilaillklfkkkegkslkliirtgallaalavlagllilvldlgrperflkll 82 
                                          v Wg++i  +++ +gi+ g +il+++++l+  +++ +++++   + +l ++ + a+   +++++grp+r++  +
  gi|336253478|ref|YP_004596585.1|  59 GGGVTWGVYIGAFIWWVGIAHGGIILSAAVRLLGMERYMPVARL---AEMLTLAGLSAAGFYILVHMGRPDRMVTSV 132
                                       57899******************************999885555...66665666666666777********99999 PP

                              NrfD  83 l.yynfs...Simswgvlllslyivvlvlyllvifekdlaakg..lpalg.ilaklisla.........ervakila 143
                                       + +y ++   S+++w+v++ ++y+v+ + yl + ++ d+  +   lp++   +++++ l          +r++ +la
  gi|336253478|ref|YP_004596585.1| 133 IgHYHITvnnSPLVWDVTVITAYFVLTATYLSLTLRYDVHRLRdqLPDYFdPIYAVMTLGyseredeivQRMVWWLA 209
                                       7777774445**************************99998888878755466666666555666666699999*** PP

                              NrfD 144 iialilavll..gsytgfllsavlsrplwnspllpvlFlasaiasGlavlllasllaarfek.esedagllkklell 217
                                       ++ +i+a ll  g++  +l++++  +p w++++ ++ Fl  a++s+++ ++++s+ + r  + e +  + +  + +l
  gi|336253478|ref|YP_004596585.1| 210 LAIIIMAPLLlhGGVIPWLFAVLPTYPRWFGGVQGPQFLTIALTSAISGVIILSYSFRRAYDwEHIITDDI--FRGL 284
                                       ***9999665447899*************************************999999766444444433..4555 PP

                              NrfD 218 vilteagllvilfvglal.........eggekiealeaalsggfltvlFwlgvvllglaiplllslavpr.lrenva 284
                                        ++   + l+ l++ l+          +      ++ea l +      ++l ++l+gl+++ + +  ++  l ++++
  gi|336253478|ref|YP_004596585.1| 285 TLWLGFFCLLFLWLQLQQvttgtfsppT--GLGHTWEATLEQ----PAYILSMTLVGLVLAYIFAQTIRPaLFSKTR 355
                                       5555556666665554443333333211..113344444566....99*********99998887777777999999 PP

                              NrfD 285 vvviasilalvgvlllrfllliagq 309
                                       ++ i + ++l  +ll+++l +i g 
  gi|336253478|ref|YP_004596585.1| 356 AL-ICAFAVLTATLLEKILFVIEGF 379
                                       98.778888888999*999999886 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.0      0.11   6.3e+02      36      99 ..      27      92 ..      17     119 .. 0.58
   2 ?   -2.1   0.4       0.7   4.2e+03      78      90 ..     144     156 ..      82     167 .. 0.52
   3 ?   12.1   0.2     3e-05      0.18      15     108 ..     190     282 ..     185     298 .. 0.78
   4 ?    0.4   1.5      0.12   7.2e+02      69      83 ..     328     342 ..     284     382 .. 0.69
   5 ?   -3.0   3.8       1.4   8.5e+03      37      61 ..     358     382 ..     331     431 .. 0.40

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                            DUF996 36 siialvvailalllvlgalatalelpgleeaas..lilllllvliiayvlliis.avflkksyellg 99
                                      ++++l++  + l++++++l  +l  +gl+ +    ++++ + +  +++ + i+  ++ l+ +++llg
  gi|336253478|ref|YP_004596585.1| 27 AVAGLAL-GVFLIGWAYQLQQGLAVTGLSDWGTggGVTWGVYIGAFIWWVGIAHgGIILSAAVRLLG 92
                                      3333333.23344555566666666666666666666666666666665555541455555566555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.7
                            DUF996  78 iiayvlliisavf 90 
                                        +++ +++i+a+f
  gi|336253478|ref|YP_004596585.1| 144 PLVWDVTVITAYF 156
                                       2223333333333 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 3e-05
                            DUF996  15 eiskavndekifsnaliafilsiialvvailalllvlgalatalelpgleeaaslilllllvliiayvlliisavfl 91 
                                       ++    ++++i +++++++ l+ii ++ + l  +++   +a+  ++p    + ++ ++l ++l  a+  +ii ++ +
  gi|336253478|ref|YP_004596585.1| 190 TLGYSEREDEIVQRMVWWLALAIIIMAPLLLHGGVIPWLFAVLPTYPRWFGGVQGPQFLTIALTSAISGVIILSYSF 266
                                       555566899********************999999999999999999998888877766666666666677888999 PP

                            DUF996  92 kksyellgkrtgvklFe 108
                                       +++y+  + ++  ++F+
  gi|336253478|ref|YP_004596585.1| 267 RRAYDW-EHIITDDIFR 282
                                       999986.5555566665 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.12
                            DUF996  69 lilllllvliiayvl 83 
                                       +++++l+ l++ay++
  gi|336253478|ref|YP_004596585.1| 328 ILSMTLVGLVLAYIF 342
                                       566666666666655 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 1.4
                            DUF996  37 iialvvailalllvlgalatalelp 61 
                                       i a++v++++ll ++ +++ +  +p
  gi|336253478|ref|YP_004596585.1| 358 ICAFAVLTATLLEKILFVIEGFFHP 382
                                       2233333333333333333333333 PP

>> DUF2583  Protein of unknown function (DUF2583)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.8   0.00029       1.7      15      65 ..      30      81 ..      20      89 .. 0.86
   2 ?   -3.5   0.1       2.4   1.5e+04      49      58 ..     279     288 ..     269     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00029
                           DUF2583 15 glGlllmvaslaysvlnqlpelelpellaeaal.lgifiGallWlaGarvgG 65
                                      gl l +++++ ay++ + l   +l+++ + + +  g++iGa++W +G   gG
  gi|336253478|ref|YP_004596585.1| 30 GLALGVFLIGWAYQLQQGLAVTGLSDWGTGGGVtWGVYIGAFIWWVGIAHGG 81
                                      5666678999*****************99887736************98777 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.4
                           DUF2583  49 gifiGallWl 58 
                                        if G  lWl
  gi|336253478|ref|YP_004596585.1| 279 DIFRGLTLWL 288
                                       6999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3069.88
//
Query:       gi|336253479|ref|YP_004596586.1|  [L=49]
Description: hypothetical protein Halxa_2082 [Halopiger xanaduensis SH-6]
Scores for 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   15.2   0.3      0.028   14.4   0.3    1.4  1  RHH_1       Ribbon-helix-helix protein, copG family
       0.18   11.4   0.1       0.34   10.6   0.0    1.5  2  Vac_Fusion  Chordopoxvirus multifunctional envelope protein A


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 ?   14.4   0.3   3.1e-06     0.028       3      37 ..       4      37 ..       4      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-06
                                      EEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                             RHH_1  3 sirldeellerLdelarrrgrSrSelIReAlreyl 37
                                      ++ ++++l++rL+ ++++ g+S  el++e++ +y 
  gi|336253479|ref|YP_004596586.1|  4 TLEISDDLMDRLESHCEA-GQSPEELVEELVSMYE 37
                                      6789***********987.788899*999999996 PP

>> Vac_Fusion  Chordopoxvirus multifunctional envelope protein A27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   3.8e-05      0.34      21      38 ..       3      20 ..       1      21 [. 0.85
   2 ?   -2.3   0.0       0.4   3.6e+03      16      22 ..      29      35 ..      26      43 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.8e-05
                                      HHHHHHHHHHHHHH-XXX CS
                        Vac_Fusion 21 kcckrvnealkRlEnHle 38
                                      +   ++++ ++RlE H e
  gi|336253479|ref|YP_004596586.1|  3 QTLEISDDLMDRLESHCE 20
                                      5667899*********98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.4
                                      HHHHHHH CS
                        Vac_Fusion 16 fqlvikc 22
                                      ++++++ 
  gi|336253479|ref|YP_004596586.1| 29 VEELVSM 35
                                      3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 373.62
//
Query:       gi|336253480|ref|YP_004596587.1|  [L=79]
Description: hypothetical protein Halxa_2083 [Halopiger xanaduensis SH-6]
Scores for 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   15.2   0.0      0.015   15.1   0.0    1.1  1  YihI      Der GTPase activator (YihI)


Domain annotation for each model (and alignments):
>> YihI  Der GTPase activator (YihI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   8.2e-07     0.015     119     154 ..      31      67 ..      18      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.2e-07
                              YihI 119 dqkyvdekLdrideLmeeLGie.ddeeeeekdddllq 154
                                        ++yvd + +  ++ m++LG+e ddee+   ++d+l+
  gi|336253480|ref|YP_004596587.1|  31 SRAYVDPNPSLTEQFMASLGWEgDDEEDYIVTEDMLE 67 
                                       689*******************766777778999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 643.24
//
Query:       gi|336253481|ref|YP_004596588.1|  [L=179]
Description: CheD [Halopiger xanaduensis SH-6]
Scores for complete 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-28   99.0   0.0    2.1e-28   98.6   0.0    1.2  1  CheD      CheD chemotactic sensory transduction


Domain annotation for each model (and alignments):
>> CheD  CheD chemotactic sensory transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.0   1.2e-32   2.1e-28       1     109 []      68     171 ..      68     171 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 1.2e-32
                                       -BS--....SS-TTSCCCBHHHHHHHHHHHHHTTT--GGG-EEEEEE----S.....---SS-HHHHHHHHHHHHHH CS
                              CheD   1 mLPdskeskeksasnpakyadtaielLinellklgakkerleaklaGGAqmfafessksdvlniGerNveavkelLk 77 
                                       mLP+s  +++++ + +ak+adt++e++++e++++g+ ++r  akl+GGA+m++f+    +  +iG++Nv+a+k+lL+
  gi|336253481|ref|YP_004596588.1|  68 MLPES--DSRTRPEPDAKFADTGLEAMLDEFEREGGVPDRSWAKLVGGATMIEFSG---AGGSIGDQNVAAAKALLE 139
                                       9****..444444799*************************************955...4678************** PP

                                       HTT--EEEEEE-SSS-EEEEEETTTTEEEEE- CS
                              CheD  78 eegipivaedvggnygRtvlfdpatgkvlvkk 109
                                       ++gip+ a +vgg+ gR+++fdp++g+v++++
  gi|336253481|ref|YP_004596588.1| 140 AYGIPVRAVEVGGSAGRSITFDPSSGDVVIRT 171
                                       *****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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: 0.38u 0.19s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1565.28
//
Query:       gi|336253482|ref|YP_004596589.1|  [L=372]
Description: cysteine desulfurase [Halopiger xanaduensis SH-6]
Scores for 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-54  183.0   0.0    1.4e-53  182.2   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
        0.2   10.2   0.0       0.28    9.7   0.0    1.2  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 !  182.2   0.0   1.6e-57   1.4e-53       6     369 ..      22     364 ..      17     366 .. 0.90

  Alignments for each domain:
  == domain 1  score: 182.2 bits;  conditional E-value: 1.6e-57
                                       TTS----HHHHHHHHHHHHCT.CCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHC CS
                       Aminotran_5   6 aAttqkpqeVldalqeyytdy.nanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalsl 81 
                                        A+ + p++V++a++  ++++ +a++  +   +   a +a++ear+ va+l++a+  +ei  t +tt++in +a ++
  gi|336253482|ref|YP_004596589.1|  22 GASGPSPRRVVEAAESALEHHeYAAP--GDEGMYPAALDAYDEARAAVADLLGATP-DEIALTESTTDGINRIAGAV 95 
                                       688899********999987624555..7777888899*****************7.******************** PP

                                       CCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--H CS
                       Aminotran_5  82 arslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpv 158
                                         +++++d +v t++eh a ++pwq+l++++g++v+v++  e+g+ldl++++++ + +++l +++    ++Gt  pv
  gi|336253482|ref|YP_004596589.1|  96 SLEWDEDDAVVRTDLEHAAGVLPWQRLERQRGIDVRVLET-ERGRLDLEDVKAA-AADASLFCVSSLTWTHGTRLPV 170
                                       999************************************8.9*********666.5899****************** PP

                                       HHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEE CS
                       Aminotran_5 159 eeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemveev 234
                                        ei+++a+++galvlvDa+qa g+ p+dv ++++Df++  ghK ll+P G G+ yv +++   l p  +g   v+++
  gi|336253482|ref|YP_004596589.1| 171 SEIVDIAHDAGALVLVDAVQAPGQGPVDVTEWDADFVVGAGHKwLLAPFGSGFCYVDEDVAADLVPPAIGYRSVKDP 247
                                       ***************************************************************************** PP

                                       ETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSE CS
                       Aminotran_5 235 sleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasi 311
                                       +  e+++a   ++fe  T   +   gl +a++ leeigle+++ + ++l+++l++++++   +     ++ e ++++
  gi|336253482|ref|YP_004596589.1| 248 DATEYQYAAGARRFEVATASPVPHAGLVEAIDCLEEIGLETVRDRIERLTDRLKAGISDERLL-----SPREFESGL 319
                                       ********************************************************9865443.....346888899 PP

                                       EEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHH CS
                       Aminotran_5 312 vsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevd 369
                                       v++ +++  +e  +  L+ ++I +rs              + ++R+S + +nt ++vd
  gi|336253482|ref|YP_004596589.1| 320 VTIDVDD--PEATVERLAAHDITIRSL-----------PYPDAIRISVHAVNTPADVD 364
                                       9988884..667777888888888862...........23456777777777777776 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 ?    9.7   0.0   3.1e-05      0.28     126     200 ..     141     215 ..     100     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 3.1e-05
                                       SHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTTTT CS
                   Cys_Met_Meta_PP 126 dleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp.llqrplklgaDivvhSaTKyl 200
                                       dle++++a     +l+ + ++t      + + +i+++a++ag+lv+vD++ a +   +   +++aD vv ++ K+l
  gi|336253482|ref|YP_004596589.1| 141 DLEDVKAAAA-DASLFCVSSLTWTHGTRLPVSEIVDIAHDAGALVLVDAVQAPGqGPVDVTEWDADFVVGAGHKWL 215
                                       5555555544.456777777777777778899*****************999886678888999**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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 0.21s 00:00:00.66 Elapsed: 00:00:00.35
# Mc/sec: 3205.79
//
Query:       gi|336253483|ref|YP_004596590.1|  [L=54]
Description: hypothetical protein Halxa_2086 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.02   15.2   0.3      0.024   15.0   0.3    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar


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 ?   15.0   0.3   1.4e-06     0.024       9      37 ..       8      39 ..       7      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-06
                   Lar_restr_allev  9 Cggravlersqrvvaeigq...cvyCadCgas 37
                                      C + a+le++q+ v+e+g    +  C+dCg  
  gi|336253483|ref|YP_004596590.1|  8 CLCGATLEFRQDIVKEGGGvypTWKCKDCGTE 39
                                      9999***********99999**********92 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 0.34u 0.20s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 465.50
//
Query:       gi|336253484|ref|YP_004596591.1|  [L=176]
Description: hypothetical protein Halxa_2087 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.002   18.3   3.3      0.002   18.3   3.3    2.2  2  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding
     0.0074   16.2   0.1      0.077   13.0   0.0    2.1  2  Med10           Transcription factor subunit Med10 of Mediato
  ------ inclusion threshold ------
      0.046   12.6   5.9      0.072   12.0   5.7    1.4  2  Spc7            Spc7 kinetochore protein
      0.059   13.6   1.8       0.34   11.2   0.0    2.3  2  DUF948          Bacterial protein of unknown function (DUF948
      0.092   11.5   0.2        0.2   10.4   0.0    1.5  2  HlyD_2          HlyD family secretion protein
       0.67   10.3   5.2        4.4    7.7   0.1    2.6  2  CLZ             C-terminal leucine zipper domain of cyclic nu
        1.6    9.1   5.8          3    8.2   1.6    2.2  2  Mobilization_B  Mobilization protein B
        2.2    8.1  10.0        7.8    6.4   3.5    2.3  2  ARGLU           Arginine and glutamate-rich 1
        2.9    8.7   5.4        1.3    9.8   2.2    2.2  2  DUF3073         Protein of unknown function (DUF3073)
        3.2    8.5   5.7         11    6.8   5.7    1.9  1  DUF2203         Uncharacterized conserved protein (DUF2203)
        4.8    7.5   8.2          9    6.6   0.9    2.6  2  Osmo_CC         Osmosensory transporter coiled coil
        6.3    7.3  10.7       0.53   10.8   5.2    1.9  2  DUF3391         Domain of unknown function (DUF3391)
        7.9    7.4   7.6      2e+02    2.9   7.3    2.3  1  Histone_HNS     H-NS histone family


Domain annotation for each model (and alignments):
>> 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 ?    2.7   0.3       0.1   1.4e+02      88     111 ..      34      57 ..      21      60 .. 0.68
   2 !   18.3   3.3   1.5e-06     0.002      55     112 ..      80     137 ..      78     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                       TMF_TATA_bd  88 GeksEeveELraDvaDlKemykeq 111
                                       +e +E  +E ++ vaD++  ++eq
  gi|336253484|ref|YP_004596591.1|  34 KEADELLDEIEETVADIRSRLEEQ 57 
                                       455666777777777777666555 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.5e-06
                       TMF_TATA_bd  55 eneelkelkkeleelekeleelqeryetlLellGeksEeveELraDvaDlKemykeqv 112
                                       ++e+++e++++lee ++ +e+ q r ++  el    +E  eEL+ D +D ++ + + v
  gi|336253484|ref|YP_004596591.1|  80 DVEDVEEMAADLEEKQTIVEAKQARMQAFQELAADYTELAEELQSDAEDGRAAMTRVV 137
                                       5799*********************************************999988777 PP

>> Med10  Transcription factor subunit Med10 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   5.6e-05     0.077      70     119 ..       5      54 ..       2      56 .. 0.91
   2 ?    1.0   0.1      0.28   3.9e+02      17      42 ..      97     122 ..      81     136 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.6e-05
                                       B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-GGGHHHH CS
                             Med10  70 rNPdiYtrefvelvrrkNqlmkGkmeafkkfrdvLaeelekalPelredv 119
                                         Pd+   efve +r +  l+ G++e++ k  d L +e+e+++ ++r+++
  gi|336253484|ref|YP_004596591.1|   5 TEPDLSVGEFVEYCRTQAGLLSGQVETMGKEADELLDEIEETVADIRSRL 54 
                                       57999999*********************************999988765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.28
                                       HHHS--TT.S-TTHHHHHHHHHHHHH CS
                             Med10  17 qvsdydenessqevlaqklktlvesL 42 
                                       +v++ ++  +  ++la + ++l e+L
  gi|336253484|ref|YP_004596591.1|  97 IVEAKQARMQAFQELAADYTELAEEL 122
                                       33333333333333333333333333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   5.7   5.2e-05     0.072     152     245 ..      34     128 ..      22     144 .. 0.73
   2 ?    2.3   0.1     0.047        65      63      98 ..     115     151 ..     105     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.2e-05
                              Spc7 152 eedkelLekqeeeldellpeleeeka.eleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqe 227
                                       +e +elL++ ee + ++  +lee++  + + +++   +a    +++d e++ee+  +l+e ++ +e+k+++++  qe
  gi|336253484|ref|YP_004596591.1|  34 KEADELLDEIEETVADIRSRLEEQQGaNTKGTATPTSTADPGADDVDVEDVEEMAADLEEKQTIVEAKQARMQAFQE 110
                                       34456677777777777777777665356666666666666777799999999999999999999999999999988 PP

                              Spc7 228 qleeleekieelkeqkse 245
                                         ++ +e  eel++  ++
  gi|336253484|ref|YP_004596591.1| 111 LAADYTELAEELQSDAED 128
                                       888888888888776655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.047
                              Spc7  63 YqhscreLkkyisegrkiire.ieeetleenPpLfre 98 
                                       Y+ + +eL+++ ++gr  ++  +e e   + P+ f e
  gi|336253484|ref|YP_004596591.1| 115 YTELAEELQSDAEDGRAAMTRvVEFELDRDAPAYFDE 151
                                       7778899999999999866541577888888888876 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 ?   11.2   0.0   0.00025      0.34      30      68 ..      17      55 ..       9      72 .. 0.66
   2 ?    1.4   0.4      0.27   3.8e+02      48      86 ..      83     121 ..      76     138 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                            DUF948 30 eaaatieelekqvdpilkevedllakvnelledvnekle 68
                                        +++   l  qv+ + ke+++ll++++e+++d++++le
  gi|336253484|ref|YP_004596591.1| 17 YCRTQAGLLSGQVETMGKEADELLDEIEETVADIRSRLE 55
                                      445555556666666666666666666666666666665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.27
                            DUF948  48 evedllakvnelledvneklekvdplteavadlgesvse 86 
                                       +ve++ a  +e +  v+ k ++++++ e +ad +e  +e
  gi|336253484|ref|YP_004596591.1|  83 DVEEMAADLEEKQTIVEAKQARMQAFQELAADYTELAEE 121
                                       555555555555555566666666666555555555444 PP

>> HlyD_2  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.86   1.2e+03     125     150 ..      31      56 ..      26      62 .. 0.69
   2 ?   10.4   0.0   0.00014       0.2     156     219 ..      81     143 ..      76     156 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.86
                            HlyD_2 125 niekdiekldreInvlekdikesikn 150
                                        + k+ ++l  eI++ ++di+ ++++
  gi|336253484|ref|YP_004596591.1|  31 TMGKEADELLDEIEETVADIRSRLEE 56 
                                       44567777777788888887777665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00014
                            HlyD_2 156 ieelKeelnalldkKkllygskslsgkdleqlkkkkkeienklesskevikakesGvlsysiDg 219
                                       +e++ ee++a l++K+++ ++k+   +  ++l +   e+ ++l+s  e  +a+   v+ ++ D 
  gi|336253484|ref|YP_004596591.1|  81 VEDV-EEMAADLEEKQTIVEAKQARMQAFQELAADYTELAEELQSDAEDGRAAMTRVVEFELDR 143
                                       5566.89******************************************999999999999985 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 ?    7.7   0.1    0.0032       4.4      35      66 ..      24      55 ..      13      58 .. 0.87
   2 ?    3.0   2.0     0.093   1.3e+02      20      61 ..      82     122 ..      73     128 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0032
                               CLZ 35 rLessLeaLqtrlarLlaeyessqrkLkqRit 66
                                       L +++e++ +    Ll+e e++ + +++R++
  gi|336253484|ref|YP_004596591.1| 24 LLSGQVETMGKEADELLDEIEETVADIRSRLE 55
                                      58899999999999*******99999999997 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.093
                               CLZ  20 akagaeqkeleekverLessLeaLqtrlarLlaeyessqrkL 61 
                                       ++ ++ + +leek + +e++   +q  ++ L a+y++ +++L
  gi|336253484|ref|YP_004596591.1|  82 EDVEEMAADLEEKQTIVEAKQARMQA-FQELAADYTELAEEL 122
                                       33334444444444444444444443.455555555555555 PP

>> Mobilization_B  Mobilization protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.081   1.1e+02      16      56 ..      25      65 ..      13      91 .. 0.76
   2 ?    8.2   1.6    0.0022         3      47      88 ..      92     133 ..      69     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.081
                    Mobilization_B 16 laeeieplaqsmatladearqviaevqqaseeqaaewlkaq 56
                                      l+ ++e + +    l de  +++a+++   eeq    +k  
  gi|336253484|ref|YP_004596591.1| 25 LSGQVETMGKEADELLDEIEETVADIRSRLEEQQGANTKGT 65
                                      67789999999999999999999999998888876666544 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0022
                    Mobilization_B  47 eqaaewlkaqrqagaawvelakelrevaaelakaaqsarsaa 88 
                                       e+    ++a++  + a++ela +  e a el + a+  r+a 
  gi|336253484|ref|YP_004596591.1|  92 EEKQTIVEAKQARMQAFQELAADYTELAEELQSDAEDGRAAM 133
                                       33445677888889*******************999999875 PP

>> ARGLU  Arginine and glutamate-rich 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   6.2      0.19   2.7e+02      32     123 ..      36     105 ..      28     113 .. 0.51
   2 ?    6.4   3.5    0.0057       7.8      23      84 ..     106     167 ..      88     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.19
                             ARGLU  32 keeiekeverrveearkkmekqveeelerereaeleeekrkeeeerkkreelerileenkrkveeaqrkla...... 102
                                        +e+                                             +e e+++++ + ++ee+q          
  gi|336253484|ref|YP_004596591.1|  36 ADEL--------------------------------------------LDEIEETVADIRSRLEEQQGANTkgtatp 68 
                                       3344............................................44555555555555555554444555666 PP

                             ARGLU 103 ................Eerlaeleekrrlkeerqrlk 123
                                                       Ee  a leek+ + e++q + 
  gi|336253484|ref|YP_004596591.1|  69 tstadpgaddvdvedvEEMAADLEEKQTIVEAKQARM 105
                                       6666666665555555555555555555544444443 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0057
                             ARGLU  23 rVeeelekrkeeiekeverrveearkkmekqveeelerereaeleeekrkeeeerkkreele 84 
                                       +  +el+    e+ +e++   e +r +m + ve el+r + a   e+++  e + +  e  +
  gi|336253484|ref|YP_004596591.1| 106 QAFQELAADYTELAEELQSDAEDGRAAMTRVVEFELDRDAPAYFDERQTLAEAAADATESDD 167
                                       445688888899*********************************99999988877776655 PP

>> DUF3073  Protein of unknown function (DUF3073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       2.4   3.4e+03      45      45 ..      75      75 ..      37      95 .. 0.56
   2 ?    9.8   2.2   0.00092       1.3      10      42 ..     100     132 ..      93     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.4
                           DUF3073 45 e 45
                                       
  gi|336253484|ref|YP_004596591.1| 75 G 75
                                      1 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00092
                           DUF3073  10 tKvAReLKYlspetDydaLerELsgkseesdsa 42 
                                        K AR   ++    Dy++L++EL++ +e+ + a
  gi|336253484|ref|YP_004596591.1| 100 AKQARMQAFQELAADYTELAEELQSDAEDGRAA 132
                                       5899999999*************8877665444 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.7    0.0079        11       6      87 ..      34     116 ..      28     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0079
                           DUF2203   6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekse.aaeleaeleeleaeieelveeieelGvevkdlea 81 
                                       +eA +lL +++e+++++r+  +e + + ++ +++ ++++  +    + +++ee++a +ee  + +e+  + ++ +++
  gi|336253484|ref|YP_004596591.1|  34 KEADELLDEIEETVADIRSRLEEQQGANTKGTATPTSTADPGaDDVDVEDVEEMAADLEEKQTIVEAKQARMQAFQE 110
                                       68999999999999999966666666555444444333333355555666777777777777777777777777777 PP

                           DUF2203  82 glvDFp 87 
                                       +  D+ 
  gi|336253484|ref|YP_004596591.1| 111 LAADYT 116
                                       766664 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.9    0.0066         9       5      30 ..      35      56 ..      33      61 .. 0.79
   2 ?    4.2   1.0     0.037        52      21      35 ..      81      95 ..      78     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0066
                                      XXXXXXXXXXTHHHHHHHHHHHHHHH CS
                           Osmo_CC  5 EAkelLqehYdnIEqkvedideeIaa 30
                                      EA elL    d+IE++v di   +++
  gi|336253484|ref|YP_004596591.1| 35 EADELL----DEIEETVADIRSRLEE 56
                                      777777....78********877665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.037
                                      HHHHHHHHHHHHHHH CS
                           Osmo_CC 21 vedideeIaaLeekR 35
                                      ved++e  a+Leek+
  gi|336253484|ref|YP_004596591.1| 81 VEDVEEMAADLEEKQ 95
                                      9************86 PP

>> DUF3391  Domain of unknown function (DUF3391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   5.2   0.00038      0.53      36     131 ..      32     132 ..       7     137 .. 0.57
   2 ?   -0.4   0.3       1.1   1.5e+03      55      81 ..     141     167 ..     132     176 .] 0.39

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                           DUF3391  36 seadierLrasgiqeVwidtdksdeeelagldvpaaeaaeeakaaeesaeleeekqerperleaere.......ele 105
                                         ++ + L +  i+e + d +  + ee++g +++  + +++++   ++    e+ +e +++le++++       +++
  gi|336253484|ref|YP_004596591.1|  32 MGKEADELLDE-IEETVADIRS-RLEEQQGANTKGTATPTSTADPGADDVDVEDVEEMAADLEEKQTiveakqaRMQ 106
                                       45566666666.7777777755.666666664444433333333333332333333333333333335555555*** PP

                           DUF3391 106 raeklyeeakqlvrslfsdvrlgkai 131
                                         ++l +++++l+++l sd+++g+a 
  gi|336253484|ref|YP_004596591.1| 107 AFQELAADYTELAEELQSDAEDGRAA 132
                                       ***********************985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                           DUF3391  55 tdksdeeelagldvpaaeaaeeakaae 81 
                                       +d+ +++   ++++ a++aa++++ ++
  gi|336253484|ref|YP_004596591.1| 141 LDRDAPAYFDERQTLAEAAADATESDD 167
                                       445333333333333332222222211 PP

>> Histone_HNS  H-NS histone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   7.3      0.14     2e+02      12      59 ..      92     144 ..      24     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.14
                                       XXXXXXXXXXXXXXXXXXXXXXXXX----SSS-----EEEEE..........- CS
                       Histone_HNS  12 qeealeaeerkealaeirelaaeyGltleelaaeakkakkkkakakk.....v 59 
                                       +e++   e++++ +++ +elaa+y   +eel+++a+ ++++ +++ +      
  gi|336253484|ref|YP_004596591.1|  92 EEKQTIVEAKQARMQAFQELAADYTELAEELQSDAEDGRAAMTRVVEfeldrD 144
                                       34445566667777777777777777777777776666666555444555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1605  (0.0895198); expected 358.6 (0.02)
Passed bias filter:                      736  (0.0410508); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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):              13  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 1315.26
//
Query:       gi|336253485|ref|YP_004596592.1|  [L=988]
Description: UvrABC system protein A [Halopiger xanaduensis SH-6]
Scores for complete 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  112.0   0.9    5.6e-32  110.1   0.0    2.5  2  UvrA_inter       UvrA interaction domain
    2.1e-30  105.3   0.6    5.4e-28   97.5   0.1    3.6  4  UvrA_DNA-bind    UvrA DNA-binding domain
    5.5e-22   78.7   0.0    1.2e-11   45.3   0.0    4.2  3  ABC_tran         ABC transporter
    1.1e-12   47.9   0.1     0.0094   15.4   0.1    4.1  3  SMC_N            RecF/RecN/SMC N terminal domain
      1e-08   34.8   0.0     0.0024   17.5   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
    1.4e-07   32.0   0.1      0.025   15.0   0.0    3.2  2  AAA_16           AAA ATPase domain
    5.6e-06   26.7   0.1       0.12   12.7   0.0    3.3  2  AAA_22           AAA domain
    4.8e-05   23.3   8.0       0.29   10.9   0.0    4.4  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    7.5e-05   22.6   0.1       0.39   10.4   0.0    4.1  4  AAA_15           AAA ATPase domain
    0.00016   21.7   0.1       0.19   11.7   0.0    3.5  3  AAA_14           AAA domain
    0.00018   20.9   0.1       0.11   11.8   0.0    2.8  3  ATPase           KaiC
    0.00018   21.4   0.0       0.53   10.2   0.0    2.4  2  RsgA_GTPase      RsgA GTPase
    0.00024   21.4   9.9      0.013   15.8   0.8    3.8  3  DnaJ_CXXCXGXG    DnaJ central domain
    0.00025   21.6   0.4       0.79   10.3   0.0    3.6  3  AAA_18           AAA domain
    0.00027   20.6   0.1      0.046   13.3   0.0    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00087   18.9   0.0        1.4    8.4   0.0    3.2  2  AAA_25           AAA domain
    0.00092   19.8   0.1       0.53   10.8   0.0    2.9  2  AAA_23           AAA domain
      0.001   19.0   0.1        1.1    9.2   0.0    2.7  2  APS_kinase       Adenylylsulphate kinase
     0.0013   18.9   0.1        1.5    9.0   0.0    3.4  3  AAA_33           AAA domain
      0.008   15.9   0.0       0.45   10.2   0.0    2.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
  ------ inclusion threshold ------
      0.014   15.3   0.0       0.79    9.6   0.0    2.4  2  NACHT            NACHT domain
      0.022   14.0   0.1        5.8    6.1   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.026   14.4   0.0        8.1    6.3   0.0    2.5  2  ATPase_2         ATPase domain predominantly from Archaea
      0.033   14.2   1.9        1.9    8.6   0.0    3.2  3  Zn_Tnp_IS91      Transposase zinc-binding domain
      0.046   12.9   0.0       0.81    8.8   0.0    2.5  2  NB-ARC           NB-ARC domain
      0.061   13.0   0.4        3.3    7.4   0.0    2.9  2  AAA_30           AAA domain
      0.082   13.0  15.0        5.6    7.2   1.1    4.6  4  Zn-ribbon_8      Zinc ribbon domain
      0.095   12.4   1.3          4    7.1   0.0    3.2  3  AAA_24           AAA domain
        0.1   13.0   0.1        3.7    8.0   0.0    2.3  2  RNA_helicase     RNA helicase
       0.17   10.7   0.0       0.27   10.1   0.0    1.2  1  NMDAR2_C         N-methyl D-aspartate receptor 2B3 C-terminus
       0.18   10.8   0.1        5.9    5.8   0.0    3.0  4  DUF3987          Protein of unknown function (DUF3987)
       0.21   11.5   0.6        1.6    8.6   0.0    2.5  2  NTPase_1         NTPase
       0.53   10.3   8.3        4.8    7.3   0.4    3.9  4  DZR              Double zinc ribbon
       0.79    9.7   9.8         10    6.2   0.0    4.2  4  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
          1    9.4   0.0          1    9.4   0.0    3.0  3  DUF87            Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.0   1.1e-34   5.6e-32       1     105 [.     132     237 ..     132     241 .. 0.97
   2 ?   -1.2   0.0       4.1   2.1e+03      80     107 ..     546     573 ..     519     575 .. 0.74

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 1.1e-34
                        UvrA_inter   1 QsveqIvdqilkleegtkllilaPvvrerkgefkkllenlkkkGfvrvriDgeiydld.edieldknkkhsievvvD 76 
                                       Qs++++v++il+l+egtk+ + aPvvr++kg f++l+e+l ++G+ rv iDge +dl+ +d++ld+n  h+i+v+vD
  gi|336253485|ref|YP_004596592.1| 132 QSAQNMVERILELPEGTKAKLAAPVVRDQKGAFEDLFEELVSEGYARVEIDGEEHDLTlDDPDLDENFDHTIDVIVD 208
                                       9*******************************************************9846***************** PP

                        UvrA_inter  77 rlvvkkeersrlaesvetAlklgeglviv 105
                                       r++v+ e+r r+ +svetAl  +eg++ v
  gi|336253485|ref|YP_004596592.1| 209 RVKVSAEDRPRIIDSVETALAEAEGVLKV 237
                                       *************************9987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.1
                        UvrA_inter  80 vkkeersrlaesvetAlklgeglvivse 107
                                       +++++++rl + +e+  +lg+ l++v++
  gi|336253485|ref|YP_004596592.1| 546 LHQRDNDRLLDTLEELRDLGNTLLVVEH 573
                                       4455668888888888888888888876 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 ?    3.1   0.0      0.24   1.2e+02      78     108 ..      37      67 ..      25      69 .. 0.85
   2 !   97.5   0.1   1.1e-30   5.4e-28       1     109 [.     318     423 ..     318     424 .. 0.94
   3 ?   -0.8   0.0       3.7   1.9e+03      26      70 ..     480     524 ..     471     531 .. 0.85
   4 ?   -1.4   0.0         6     3e+03      74     105 ..     716     749 ..     701     751 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.24
                                       .......---HHHHHHHHHH-------HHHH CS
                     UvrA_DNA-bind  78 krsyektfeGvipnlerryreteSeavreel 108
                                       + + +  fe +  + +rry e+ S ++r+ l
  gi|336253485|ref|YP_004596592.1|  37 SGKSSLAFETIYAEGQRRYIESLSAYARNFL 67 
                                       5677889********************9865 PP

  == domain 2  score: 97.5 bits;  conditional E-value: 1.1e-30
                                       -S----.-----------GGG..TT-HHHHHHHHHHHTTTS------------S-THHHHH----............ CS
                     UvrA_DNA-bind   1 DpdlvvpdpslslaegAiapwsskkssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgeekikveyksggr 77 
                                       D+dlvv+dps+ l+   +++w s ++syy++ l+avaeh++++l+tpf+eL+e+++  +LyG++ee + ++++ +++
  gi|336253485|ref|YP_004596592.1| 318 DEDLVVQDPSKPLK-HVFEAW-SYNRSYYQTRLDAVAEHFDVSLSTPFEELDEDIRRQFLYGTDEE-VLFKRHTKNG 391
                                       9************9.899***.88899*************************************85.6677778889 PP

                                       .......---HHHHHHHHHH-------HHHHH CS
                     UvrA_DNA-bind  78 krsyektfeGvipnlerryreteSeavreele 109
                                       +r+++k+feGvipnlerry et+S+++re++e
  gi|336253485|ref|YP_004596592.1| 392 TRRKRKRFEGVIPNLERRYLETDSDSTREHIE 423
                                       99999*************************98 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3.7
                                       -HHHHHHHHHHHTTTS------------S-THHHHH----..... CS
                     UvrA_DNA-bind  26 ssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgeekikv 70 
                                       + + +++l+++ +++g+++++ ++ L+ +     L G ++++i+ 
  gi|336253485|ref|YP_004596592.1| 480 KVIAEEILKEIRARLGFMVEVGLEYLTLDREASTLSGGESQRIRL 524
                                       55678999*******************999999999999988876 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 6
                                       .............---HHHHHHHHHH-------H CS
                     UvrA_DNA-bind  74 s..ggrkrsyektfeGvipnlerryreteSeavr 105
                                       s  g++ rs  +t+ Gv  ++++ + +t+  ++r
  gi|336253485|ref|YP_004596592.1| 716 SpiGRTPRSNPATYTGVFDHIRELFASTKLSKQR 749
                                       3567778888999***********9999977766 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00015     0.078       1      28 [.      16      43 ..      16     103 .. 0.93
   2 !   14.9   0.0   5.6e-05     0.029      43     135 ..     447     542 ..     360     544 .. 0.74
   3 !   45.3   0.0   2.4e-14   1.2e-11       1     136 [.     648     885 ..     648     886 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00015
                                      EEEEEEEEETTSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  1 lknvslklkegekvaivGenGaGKStLl 28
                                      lk++++++ + e ++++G +G+GKS+L+
  gi|336253485|ref|YP_004596592.1| 16 LKDLDVEIPREEFTVVTGLSGSGKSSLA 43
                                      799***********************95 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 5.6e-05
                                       EETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH.HHHTCHHHHHHHSTTGG...TTCBGESTTSGGS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
                          ABC_tran  43 lldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren.esdeeiekalsklglke...lkdtvvksspssLSgGqk 114
                                       l+dg++++e    +   +ig   ++ ++l  +lt re+  ++e +++++++lg      l+  ++++++s+LSgG+ 
  gi|336253485|ref|YP_004596592.1| 447 LVDGTSITE----INGMSIGDALEHfESLEADLTEREKvIAEEILKEIRARLGFMVevgLEYLTLDREASTLSGGES 519
                                       455555544....33333333333335555555555554333445555555554434557778888889******** PP

                                       HHHHHHHHHHHT..SSEEEEEST CS
                                       xxxxxxxxxxxx..xxxxxxxxx RF
                          ABC_tran 115 qrvalarallkk..pkllllDEp 135
                                       qr+ la  + +     l++lDEp
  gi|336253485|ref|YP_004596592.1| 520 QRIRLATQIGSGlvGVLYVLDEP 542
                                       ******99877622468888988 PP

  == domain 3  score: 45.3 bits;  conditional E-value: 2.4e-14
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHH.HHTTSS--SEEEE.....................EETTCEGGGB-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx.....................xxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlk.llagllkpteGei.....................lldgkdlkeqele 55 
                                       lk++++++  g  +ai+G +G+GKStL+  +l++ l  ++ +                      l+d+ ++ +++++
  gi|336253485|ref|YP_004596592.1| 648 LKELDVDIPLGCFTAITGVSGSGKSTLMHeVLYKGLARQMNDNtsvipgdyddlegleeietvrLIDQSPIGRTPRS 724
                                       68999*********************9853666555553333335579999*9999999999999999999999999 PP

                                       HCCHCEEEE-SS--S-TTSBHHHH..................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..................................................... RF
                          ABC_tran  56 slrkeigvlpqepqlfpeltvren..................................................... 79 
                                             gv+ +  +lf  +++ ++                                                     
  gi|336253485|ref|YP_004596592.1| 725 NPATYTGVFDHIRELFASTKLSKQrgyekgrfsfnvkggrceecggqgtvkiemnflsdvyvpceecdgaryndatl 801
                                       9999999999999999999977778**************************************************** PP

                                       ........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHT...SSE CS
                                       ........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx RF
                          ABC_tran  80 ........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkk...pkl 129
                                                               es+++i + l+ l++++l+  ++++  ++LSgG+ qr++la+ l kk    +l
  gi|336253485|ref|YP_004596592.1| 802 dvtykgktiadvlemsveeayeffESSSQIRRRLKLLKDVGLDYMKLGQPSTTLSGGEAQRIKLAEELGKKdsgETL 878
                                       ***********************************************9999*****************99833358* PP

                                       EEEESTT CS
                                       xxxxxxx RF
                          ABC_tran 130 lllDEpt 136
                                       +llDEpt
  gi|336253485|ref|YP_004596592.1| 879 YLLDEPT 885
                                       ******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 !   15.4   0.1   1.8e-05    0.0094      23     211 ..      25     587 ..       7     592 .. 0.81
   2 !    9.4   0.0    0.0013      0.65      25      46 ..     659     680 ..     643     690 .. 0.81
   3 !   12.4   0.0   0.00016      0.08     135     211 ..     795     929 ..     728     935 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                                       TSSEEEEEESTTSSHHHH.HHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEE....... CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx....... RF
                             SMC_N  23 sksftaivGpNGSGKsnl.ldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkk....... 89 
                                        ++ft+++G  GSGKs+l ++ i +  G+r + +  s+ +++ + +  + + + v+  + +i +d+++++       
  gi|336253485|ref|YP_004596592.1|  25 REEFTVVTGLSGSGKSSLaFETI-YAEGQRRYIESLSAYARNFLGQmdKPQVETVEGLSPAISIDQKNAAnnprstv 100
                                       35599999999999999834555.99998776444444555555542322222222223333333333332233322 PP

                                       SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                             SMC_N  90 lkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske............................... 135
                                        ++++ + +++    r g+ +    g+ev ++  ++++e+    +e                               
  gi|336253485|ref|YP_004596592.1| 101 GTVTELHDYLRLLYARVGTPHCPECGREVGEQSAQNMVERILELPEgtkaklaapvvrdqkgafedlfeelvsegya 177
                                       22222223333333344444444455555555555555555544448888999999999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|336253485|ref|YP_004596592.1| 178 rveidgeehdltlddpdldenfdhtidvivdrvkvsaedrpriidsvetalaeaegvlkvilpdppeeaaedlgeea 254
                                       99999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|336253485|ref|YP_004596592.1| 255 rrtgalgdegdddddrfvvefskdlacthcgidvpeietrsfsfnsphgacpeceglgetkevdedlvvqdpskplk 331
                                       99999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|336253485|ref|YP_004596592.1| 332 hvfeawsynrsyyqtrldavaehfdvslstpfeeldedirrqflygtdeevlfkrhtkngtrrkrkrfegvipnler 408
                                       99999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|336253485|ref|YP_004596592.1| 409 ryletdsdstrehiedymsvtecpacdgtrlkpasravlvdgtsiteingmsigdalehfesleadlterekviaee 485
                                       9999999999999999999999999999999999999999999999999999999999999999999999999**** PP

                                       ...........................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH CS
                                       ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ...........................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellke 185
                                                                  +LSgGe + + la    i +     ly+lDe    L ++   ++ + l+e
  gi|336253485|ref|YP_004596592.1| 486 ilkeirarlgfmvevgleyltldreasTLSGGESQRIRLATQ--IGSGLVGVLYVLDEPSIGLHQRDNDRLLDTLEE 560
                                       **************************9******998777776..55666678************************9 PP

                                       HCTT.SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 186 kskn.aQfivislreemlekadklvgv 211
                                        ++    ++v+ ++ee++++ad++v +
  gi|336253485|ref|YP_004596592.1| 561 LRDLgNTLLVVEHDEETMRRADQVVDM 587
                                       998767899*************99865 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                                       SEEEEEESTTSSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilF 46 
                                        ftai+G  GSGKs l+  +l+
  gi|336253485|ref|YP_004596592.1| 659 CFTAITGVSGSGKSTLMHEVLY 680
                                       59**************988866 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00016
                                       T..........................................................CS-HHHHHHHHHHHHHHH CS
                                       x..........................................................xxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e..........................................................lLSgGektLvalaLlfAi 153
                                                                                                  +LSgGe + + la  +  
  gi|336253485|ref|YP_004596592.1| 795 RyndatldvtykgktiadvlemsveeayeffesssqirrrlkllkdvgldymklgqpstTLSGGEAQRIKLAEELG- 870
                                       055555555555555555555555555555555555555555555555555577777779******9999999887. PP

                                       HCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 154 qkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgv 211
                                       +k + + lyllDe    L  +  +k+ ++l++ ++n   ++vi ++ +++++ad+++ +
  gi|336253485|ref|YP_004596592.1| 871 KKDSGETLYLLDEPTTGLHSEDERKLIDVLHRLTDNgNTVVVIEHELDLVKNADHIIDL 929
                                       5567789*************************99997789999***********99865 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 !   14.5   0.0   4.2e-05     0.021      10      38 ..      14      42 ..       7      49 .. 0.86
   2 !   17.5   0.0   4.8e-06    0.0024      17      39 ..     653     675 ..     645     690 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
                            AAA_29 10 gtfdghtieidlkgatlltGpsGsGKSTl 38
                                      + +++ ++ei ++++t++tG sGsGKS+l
  gi|336253485|ref|YP_004596592.1| 14 HNLKDLDVEIPREEFTVVTGLSGSGKSSL 42
                                      56667789999899*************98 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.8e-06
                            AAA_29  17 ieidlkg.atlltGpsGsGKSTll 39 
                                       ++i l g +t +tG sGsGKSTl+
  gi|336253485|ref|YP_004596592.1| 653 VDIPL-GcFTAITGVSGSGKSTLM 675
                                       45543.459**************8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   4.9e-05     0.025      18      75 ..      20      80 ..       9     221 .. 0.76
   2 !   13.3   0.0   0.00016     0.083      25      63 ..     659     701 ..     645     736 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.9e-05
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslv.rellralekdggif..lrgkcdql..esaipysalaqa 75
                                      +v  +r+e ++++G sG+GKssl+ ++++   e+++ +   l++ ++ +  +++ p +  ++ 
  gi|336253485|ref|YP_004596592.1| 20 DVEIPREEFTVVTGLSGSGKSSLAfETIYA--EGQRRYIesLSAYARNFlgQMDKPQVETVEG 80
                                      57778899****************555554..4443344445555555555666665444444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00016
                            AAA_16  25 elvllsGesGvGKsslvrell.ralekd...ggiflrgkcdql 63 
                                       + + ++G sG+GKs+l+ e+l + l ++   +  ++ g++d+l
  gi|336253485|ref|YP_004596592.1| 659 CFTAITGVSGSGKSTLMHEVLyKGLARQmndNTSVIPGDYDDL 701
                                       56789************88872455555665577788888877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0015      0.75       5      38 ..      26      63 ..      23     121 .. 0.74
   2 !   12.7   0.0   0.00023      0.12       7      30 ..     660     683 ..     658     746 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0015
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee....e 38
                                      + ++vvtG sG+GK+ l+ +  +   ++ ++e     +
  gi|336253485|ref|YP_004596592.1| 26 EEFTVVTGLSGSGKSSLAFETIYAEGQRRYIESlsayA 63
                                      5799*************988888888877777777652 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00023
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqld 30 
                                       ++++tG sG+GK+tl+ ++l++  
  gi|336253485|ref|YP_004596592.1| 660 FTAITGVSGSGKSTLMHEVLYKGL 683
                                       689***************998864 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 ?    2.6   0.8      0.19     1e+02       1      15 [.      28      42 ..      28      43 .. 0.95
   2 ?    6.0   0.1     0.017       8.9     229     294 ..     506     570 ..     350     579 .. 0.81
   3 ?    5.4   0.0     0.026        13       1      16 [.     660     675 ..     660     678 .. 0.95
   4 !   10.9   0.0   0.00057      0.29     258     294 ..     873     912 ..     821     943 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.19
                            AAA_21  1 lnvliGpNgsGKSnL 15
                                      ++v++G  gsGKS+L
  gi|336253485|ref|YP_004596592.1| 28 FTVVTGLSGSGKSSL 42
                                      89***********98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.017
                            AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                       + ++ a+ lS G  + ++l+t + + l    l+++DEp  gLH +   rll+ l+el++ g  +++
  gi|336253485|ref|YP_004596592.1| 506 TLDREASTLSGGESQRIRLATQIGSGLVG-VLYVLDEPSIGLHQRDNDRLLDTLEELRDLGNTLLV 570
                                       34455666799999999*******99999.9************99888888888888887777666 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.026
                            AAA_21   1 lnvliGpNgsGKSnLL 16 
                                       +++++G  gsGKS+L+
  gi|336253485|ref|YP_004596592.1| 660 FTAITGVSGSGKSTLM 675
                                       89************96 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00057
                            AAA_21 258 g...sllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                       +   +l+l+DEp +gLH +  r+l+++l +l++ng  v++
  gi|336253485|ref|YP_004596592.1| 873 DsgeTLYLLDEPTTGLHSEDERKLIDVLHRLTDNGNTVVV 912
                                       14459***********************888886666665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.18        90      15      39 ..      20      42 ..      14      47 .. 0.78
   2 ?    0.9   0.0      0.59     3e+02     325     355 ..     535     565 ..     365     584 .. 0.86
   3 ?    2.7   0.0      0.17        87      12      41 ..     649     676 ..     644     714 .. 0.85
   4 !   10.4   0.0   0.00075      0.39     318     360 ..     870     912 ..     850     917 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.18
                            AAA_15 15 kdveidlseeltvliGkNnsGKSsi 39
                                      + vei+ +e +tv+ G  +sGKSs+
  gi|336253485|ref|YP_004596592.1| 20 D-VEIPREE-FTVVTGLSGSGKSSL 42
                                      3.6777556.**************8 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.59
                            AAA_15 325 villiEEPEahLHpqaqkvlikllkelandn 355
                                       v+++++EP + LH      l ++l el + +
  gi|336253485|ref|YP_004596592.1| 535 VLYVLDEPSIGLHQRDNDRLLDTLEELRDLG 565
                                       79999********999999999999886665 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.17
                            AAA_15  12 RslkdveidlseeltvliGkNnsGKSsile 41 
                                       + l+ v+i+l   +t + G  +sGKS++++
  gi|336253485|ref|YP_004596592.1| 649 KELD-VDIPLGC-FTAITGVSGSGKSTLMH 676
                                       4454.7899999.**************985 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00075
                            AAA_15 318 dekeeknvilliEEPEahLHpqaqkvlikllkelandnktQvi 360
                                        +k++   ++l++EP + LH +  + li+ l +l ++++t v+
  gi|336253485|ref|YP_004596592.1| 870 GKKDSGETLYLLDEPTTGLHSEDERKLIDVLHRLTDNGNTVVV 912
                                       567777899****************************996554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.039        20       3      27 ..      27      51 ..      25      81 .. 0.81
   2 !   11.7   0.0   0.00038      0.19       6      58 ..     662     715 ..     659     755 .. 0.75
   3 ?   -0.9   0.0         3   1.6e+03      63      92 ..     874     908 ..     845     961 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.039
                            AAA_14  3 kilvitGaRrvGKTtllkqlikell 27
                                      +  v+tG+  +GK+ l+++ i+ + 
  gi|336253485|ref|YP_004596592.1| 27 EFTVVTGLSGSGKSSLAFETIYAEG 51
                                      5689***************998776 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00038
                            AAA_14   6 vitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelile 58 
                                       +itG+  +GK+tl+++++++ l    ++++  i  d ++++ l++ e   +li +
  gi|336253485|ref|YP_004596592.1| 662 AITGVSGSGKSTLMHEVLYKGLarQMNDNTSVIPGDYDDLEGLEEIE-TVRLIDQ 715
                                       79****************99999977788888888887777666553.3444444 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3
                            AAA_14  63 ekktylflDEiqev......pewekalkslvdegkn 92 
                                       +++t+ +lDE          +++ ++l +l d+g n
  gi|336253485|ref|YP_004596592.1| 874 SGETLYLLDEPTTGlhsedeRKLIDVLHRLTDNG-N 908
                                       4556666666544444444444555555555555.3 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.015       7.9      16      41 ..      23      48 ..      16      56 .. 0.86
   2 ?   -2.7   0.0       5.9     3e+03     102     137 ..     197     232 ..     162     239 .. 0.58
   3 !   11.8   0.0   0.00022      0.11      16      46 ..     655     685 ..     648     695 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.015
                            ATPase 16 ipegrvvlitGepGtGKtifalqFli 41
                                      ip+++ + +tG +G+GK+ +a + ++
  gi|336253485|ref|YP_004596592.1| 23 IPREEFTVVTGLSGSGKSSLAFETIY 48
                                      89****************99987666 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.9
                            ATPase 102 edleelieelaeaikeika.krvviDsitglayeeke 137
                                       e+ ++ i+ + + +k   + +  +iDs+++    e e
  gi|336253485|ref|YP_004596592.1| 197 ENFDHTIDVIVDRVKVSAEdRPRIIDSVETA-LAEAE 232
                                       4444444444444443333466799999988.44444 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00022
                            ATPase  16 ipegrvvlitGepGtGKtifalqFlikgaek 46 
                                       ip g  + itG++G+GK+++  + l+kg+++
  gi|336253485|ref|YP_004596592.1| 655 IPLGCFTAITGVSGSGKSTLMHEVLYKGLAR 685
                                       7888899*********************876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0     0.001      0.53      82     116 ..       8      43 ..       2      60 .. 0.83
   2 !    8.6   0.0    0.0031       1.6      87     120 ..     645     679 ..     629     694 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                                       --TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHH CS
                       RsgA_GTPase  82 vsaktkegleelkellkd.ktsvlvGqSGvGKStLi 116
                                       v+  ++++l++l  ++   +++v+ G SG GKS+L 
  gi|336253485|ref|YP_004596592.1|   8 VRGAEEHNLKDLDVEIPReEFTVVTGLSGSGKSSLA 43 
                                       55667889999998887769**************95 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0031
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       +++l+el   +    ++++ G SG GKStL+ ++l
  gi|336253485|ref|YP_004596592.1| 645 QHNLKELDVDIPLgCFTAITGVSGSGKSTLMHEVL 679
                                       556666666665547899************98754 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.025        13      38      54 ..     299     315 ..     273     325 .. 0.56
   2 ?    3.0   0.0      0.26   1.4e+02      14      23 ..     428     437 ..     415     451 .. 0.66
   3 !   15.8   0.8   2.6e-05     0.013      15      50 ..     763     794 ..     750     799 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.025
                     DnaJ_CXXCXGXG  38 qqsqstCpeCeGtGkvi 54 
                                       ++ +  CpeCeG G++ 
  gi|336253485|ref|YP_004596592.1| 299 NSPHGACPECEGLGETK 315
                                       33445666666666643 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.26
                     DnaJ_CXXCXGXG  14 kktCktCkGs 23 
                                       +++C++C+G+
  gi|336253485|ref|YP_004596592.1| 428 VTECPACDGT 437
                                       3445555554 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 2.6e-05
                     DnaJ_CXXCXGXG  15 ktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGt 50 
                                        +C++C+G+G+v+ e+    +f + +  +C+eC+G 
  gi|336253485|ref|YP_004596592.1| 763 GRCEECGGQGTVKIEM----NFLSDVYVPCEECDGA 794
                                       47********766665....36677889******97 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.028        14       2      17 ..      30      45 ..      30      66 .. 0.91
   2 ?    0.0   0.2       2.3   1.2e+03     100     121 ..     377     398 ..     346     412 .. 0.70
   3 !   10.3   0.0    0.0016      0.79       3      18 ..     663     678 ..     662     715 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.028
                            AAA_18  2 lltGtpGvGKttlake 17
                                      ++tG +G+GK++la e
  gi|336253485|ref|YP_004596592.1| 30 VVTGLSGSGKSSLAFE 45
                                      59***********965 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.3
                            AAA_18 100 taspeelleRlekRgyeeakik 121
                                        +++e+l++R  k g++ ++++
  gi|336253485|ref|YP_004596592.1| 377 GTDEEVLFKRHTKNGTRRKRKR 398
                                       35669*********98888765 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0016
                            AAA_18   3 ltGtpGvGKttlakeL 18 
                                       +tG++G+GK+tl +e+
  gi|336253485|ref|YP_004596592.1| 663 ITGVSGSGKSTLMHEV 678
                                       9***********9998 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 ?    4.8   0.0     0.037        19       3      24 ..      29      50 ..      27      57 .. 0.79
   2 !   13.3   0.0   8.9e-05     0.046       3      38 ..     661     700 ..     659     710 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.037
                                      EEEEESTTCCHHHHHHHHHCT- CS
                              cobW  3 tvltGflGsGKTtLlnhllenr 24
                                      tv+tG  GsGK++L  +++  +
  gi|336253485|ref|YP_004596592.1| 29 TVVTGLSGSGKSSLAFETIYAE 50
                                      89************88887443 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.9e-05
                                       EEEEESTTCCHHHHHHHHH....CT--SS-EEEEESS-SS CS
                              cobW   3 tvltGflGsGKTtLlnhll....enraglklavivNefge 38 
                                       t +tG  GsGK+tL+ ++l    +++ + ++ vi +++ +
  gi|336253485|ref|YP_004596592.1| 661 TAITGVSGSGKSTLMHEVLykglARQMNDNTSVIPGDYDD 700
                                       78*****************999888888999999999875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0028       1.4      30      52 ..      23      45 ..      10      50 .. 0.87
   2 !    6.6   0.0    0.0099       5.1      30      52 ..     655     677 ..     630     713 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0028
                            AAA_25 30 lpagelallaGapgtGKttlald 52
                                      +p++e+++++G +g+GK+ la +
  gi|336253485|ref|YP_004596592.1| 23 IPREEFTVVTGLSGSGKSSLAFE 45
                                      69******************976 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0099
                            AAA_25  30 lpagelallaGapgtGKttlald 52 
                                       +p+g +++++G +g+GK+tl  +
  gi|336253485|ref|YP_004596592.1| 655 IPLGCFTAITGVSGSGKSTLMHE 677
                                       599****************9765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.041        21      17      35 ..      23      42 ..       7      45 .. 0.81
   2 !   10.8   0.0     0.001      0.53       6      36 ..     642     675 ..     637     691 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.041
                            AAA_23 17 F.skgltlItGpNGaGKTTi 35
                                           +t++tG  G+GK+++
  gi|336253485|ref|YP_004596592.1| 23 IpREEFTVVTGLSGSGKSSL 42
                                      455679************98 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.001
                            AAA_23   6 nfrsf..rdqeidF.skgltlItGpNGaGKTTil 36 
                                       + r++  ++ ++d     +t+ItG  G+GK+T++
  gi|336253485|ref|YP_004596592.1| 642 GARQHnlKELDVDIpLGCFTAITGVSGSGKSTLM 675
                                       55666333333333322489*************8 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.011       5.7       7      21 ..      31      45 ..      26      58 .. 0.84
   2 !    9.2   0.0    0.0021       1.1       2      38 ..     658     696 ..     657     699 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                                      EESSTTSSHHHHHHH CS
                        APS_kinase  7 ltGlsgsGKstiana 21
                                      +tGlsgsGKs++a++
  gi|336253485|ref|YP_004596592.1| 31 VTGLSGSGKSSLAFE 45
                                      7***********986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0021
                                       -EEEEEESSTTSSHHHHHHH.HHHHHHHTT.--EEEEEH CS
                        APS_kinase   2 gvvvwltGlsgsGKstiana.lekkLvekg.isvylLdG 38 
                                       g+   +tG+sgsGKst+ ++ l k L ++   ++ ++ G
  gi|336253485|ref|YP_004596592.1| 658 GCFTAITGVSGSGKSTLMHEvLYKGLARQMnDNTSVIPG 696
                                       566779**********98862566676654355555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.027        14       3      18 ..      30      45 ..      28      94 .. 0.86
   2 ?   -1.8   0.1       6.2   3.2e+03     127     127 ..     400     400 ..     344     432 .. 0.55
   3 !    9.0   0.0     0.003       1.5       5      20 ..     664     679 ..     661     742 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.027
                            AAA_33  3 llvGlpGsGKstlaer 18
                                      ++ Gl+GsGKs la +
  gi|336253485|ref|YP_004596592.1| 30 VVTGLSGSGKSSLAFE 45
                                      688*********9865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.2
                            AAA_33 127 e 127
                                       e
  gi|336253485|ref|YP_004596592.1| 400 E 400
                                       1 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.003
                            AAA_33   5 vGlpGsGKstlaerll 20 
                                        G++GsGKstl +++l
  gi|336253485|ref|YP_004596592.1| 664 TGVSGSGKSTLMHEVL 679
                                       7***********9987 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 ?    3.1   0.0      0.13        66       1      21 [.      29      49 ..      29      91 .. 0.67
   2 !   10.2   0.0   0.00089      0.45       2      42 ..     662     702 ..     661     721 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
                   Viral_helicase1  1 ivvhGvpGcGKStlirkllrt 21
                                      +vv G  G+GKS+l  + +  
  gi|336253485|ref|YP_004596592.1| 29 TVVTGLSGSGKSSLAFETIYA 49
                                      69**********987666555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00089
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegkpkl 42 
                                        + Gv G+GKStl  ++l + l  ++n +t ++  +  + +
  gi|336253485|ref|YP_004596592.1| 662 AITGVSGSGKSTLMHEVLYKGLARQMNDNTSVIPGDYDDLE 702
                                       589**************998766666666666555555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.16        80       3      19 ..      29      45 ..      27      98 .. 0.87
   2 ?    9.6   0.0    0.0015      0.79       4      23 ..     662     681 ..     660     694 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.16
                                      EEEEC-TTTCHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqk 19
                                       +++G +GsGK+ L+ +
  gi|336253485|ref|YP_004596592.1| 29 TVVTGLSGSGKSSLAFE 45
                                      6899**********855 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                                       EEEC-TTTCHHHHHHHHHHH CS
                             NACHT   4 ilqGeaGsGKTtLlqklala 23 
                                       +++G +GsGK+tL++++  +
  gi|336253485|ref|YP_004596592.1| 662 AITGVSGSGKSTLMHEVLYK 681
                                       799************98765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.017       8.5       4      25 ..      29      50 ..      26     108 .. 0.77
   2 ?    6.1   0.0     0.011       5.8       5      25 ..     662     682 ..     659     696 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.017
                           DUF2075  4 vlVtGvaGtGKtvvllnllael 25
                                       +VtG +G+GK+ ++++ +++ 
  gi|336253485|ref|YP_004596592.1| 29 TVVTGLSGSGKSSLAFETIYAE 50
                                      79**************999886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
                           DUF2075   5 lVtGvaGtGKtvvllnllael 25 
                                        +tGv+G+GK+ ++ ++l++ 
  gi|336253485|ref|YP_004596592.1| 662 AITGVSGSGKSTLMHEVLYKG 682
                                       59**************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 ?    6.3   0.0     0.016       8.1      20      48 ..      26      54 ..      13     119 .. 0.69
   2 ?    5.3   0.0     0.031        16      24      43 ..     662     681 ..     647     719 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkd 48
                                      +e+ +++G  gsGK++L  e i    +  
  gi|336253485|ref|YP_004596592.1| 26 EEFTVVTGLSGSGKSSLAFETIYAEGQRR 54
                                      6899*************999997774433 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.031
                          ATPase_2  24 fiYGpegsGKtaLlkeiien 43 
                                        i+G  gsGK++L+ e++ +
  gi|336253485|ref|YP_004596592.1| 662 AITGVSGSGKSTLMHEVLYK 681
                                       699************99765 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 ?    8.6   0.0    0.0037       1.9      50      82 ..     112     144 ..     105     146 .. 0.87
   2 ?    3.3   0.1      0.16        84      40      67 ..     279     312 ..     275     322 .. 0.75
   3 ?   -2.2   0.2       8.8   4.5e+03      41      50 ..     764     773 ..     755     798 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0037
                       Zn_Tnp_IS91  50 ivyfsCksrhCpsCqkkateewlekqqeellpv 82 
                                       ++y + +  hCp+C+++  e+ ++++ e++l++
  gi|336253485|ref|YP_004596592.1| 112 LLYARVGTPHCPECGREVGEQSAQNMVERILEL 144
                                       667777889********************9986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.16
                       Zn_Tnp_IS91  40 yeCeeCg....hekivyfsCksrh..CpsCqkka 67 
                                       ++C++Cg    + ++  fs +s h  Cp+C+   
  gi|336253485|ref|YP_004596592.1| 279 LACTHCGidvpEIETRSFSFNSPHgaCPECEGLG 312
                                       68****88887667777777777777****9765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 8.8
                       Zn_Tnp_IS91  41 eCeeCgheki 50 
                                       +CeeCg + +
  gi|336253485|ref|YP_004596592.1| 764 RCEECGGQGT 773
                                       5666654433 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.53   2.7e+02      22      39 ..      28      45 ..      15      55 .. 0.78
   2 ?    8.8   0.0    0.0016      0.81      21      43 ..     659     681 ..     646     693 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.53
                                      EEEEEESTTSSHHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlakq 39
                                      +  + G  G+GK+ la +
  gi|336253485|ref|YP_004596592.1| 28 FTVVTGLSGSGKSSLAFE 45
                                      66799*********9865 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0016
                                       EEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  21 lvvalvGmgGvGKttlakqilnk 43 
                                        + a+ G  G+GK+tl++++l k
  gi|336253485|ref|YP_004596592.1| 659 CFTAITGVSGSGKSTLMHEVLYK 681
                                       5779***************9876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.24   1.2e+02      19      34 ..      27      42 ..      23      69 .. 0.86
   2 ?    7.4   0.0    0.0065       3.3      21      38 ..     661     678 ..     658     694 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.24
                            AAA_30 19 rvavltGpAGtGKtta 34
                                       ++v+tG  G+GK+ +
  gi|336253485|ref|YP_004596592.1| 27 EFTVVTGLSGSGKSSL 42
                                      589**********986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0065
                            AAA_30  21 avltGpAGtGKttalkal 38 
                                       +++tG+ G+GK+t++ ++
  gi|336253485|ref|YP_004596592.1| 661 TAITGVSGSGKSTLMHEV 678
                                       789************987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1      0.06        31      27      36 ..     120     129 ..     112     132 .. 0.79
   2 ?    7.2   1.1     0.011       5.6       7      34 ..     280     310 ..     274     317 .. 0.79
   3 ?    2.6   0.1       0.3   1.5e+02      26      35 ..     428     438 ..     416     440 .. 0.74
   4 ?    5.4   0.6      0.04        21       7      34 ..     764     793 ..     764     797 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.06
                       Zn-ribbon_8  27 taCPeCgsev 36 
                                       ++CPeCg ev
  gi|336253485|ref|YP_004596592.1| 120 PHCPECGREV 129
                                       45****9876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.011
                       Zn-ribbon_8   7 rCeeCghefe..vlqsis.dapltaCPeCgs 34 
                                        C+ Cg +    + +s+s  +p  aCPeC +
  gi|336253485|ref|YP_004596592.1| 280 ACTHCGIDVPeiETRSFSfNSPHGACPECEG 310
                                       6999*97666777778888999999****87 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.3
                       Zn-ribbon_8  26 ltaCPeCgs.e 35 
                                        t+CP+C + +
  gi|336253485|ref|YP_004596592.1| 428 VTECPACDGtR 438
                                       456****8855 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.04
                       Zn-ribbon_8   7 rCeeCghefevlqsis.daplta.CPeCgs 34 
                                       rCeeCg + +v  +++  ++  + C eC +
  gi|336253485|ref|YP_004596592.1| 764 RCEECGGQGTVKIEMNfLSDVYVpCEECDG 793
                                       8*********88888876666667****87 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.29   1.5e+02       6      22 ..      30      46 ..      27      55 .. 0.88
   2 ?   -1.9   0.0       4.4   2.3e+03     112     137 ..     552     579 ..     545     588 .. 0.74
   3 ?    7.1   0.0    0.0078         4       6      31 ..     662     687 ..     660     758 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.29
                            AAA_24  6 liyGpsgiGKTtlakel 22
                                      +++G sg+GK++la e 
  gi|336253485|ref|YP_004596592.1| 30 VVTGLSGSGKSSLAFET 46
                                      799**********9875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.4
                            AAA_24 112 rrllkklqelrk..nvifiahektrkde 137
                                        rll++l+elr+  n  ++ + +++++ 
  gi|336253485|ref|YP_004596592.1| 552 DRLLDTLEELRDlgNTLLVVEHDEETMR 579
                                       5788999999999977777777777665 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0078
                            AAA_24   6 liyGpsgiGKTtlakelgpkplfidt 31 
                                       +i+G sg+GK+tl+ e  +k l  ++
  gi|336253485|ref|YP_004596592.1| 662 AITGVSGSGKSTLMHEVLYKGLARQM 687
                                       79************999554444433 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      0.36   1.9e+02       2      17 ..      30      45 ..      29      69 .. 0.75
   2 ?    8.0   0.0    0.0073       3.7       3      29 ..     663     690 ..     661     700 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.36
                      RNA_helicase  2 wlyGpsgeGKStlake 17
                                      +++G sg GKS+la e
  gi|336253485|ref|YP_004596592.1| 30 VVTGLSGSGKSSLAFE 45
                                      6899*********988 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0073
                      RNA_helicase   3 lyGpsgeGKStlake.Lakallkklklk 29 
                                       ++G sg GKStl++e L k l+++++++
  gi|336253485|ref|YP_004596592.1| 663 ITGVSGSGKSTLMHEvLYKGLARQMNDN 690
                                       7899**********97888888888544 PP

>> NMDAR2_C  N-methyl D-aspartate receptor 2B3 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00053      0.27     382     446 ..     276     340 ..     245     392 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00053
                                       XXXXXXXXXXXXXXXX.XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX........X CS
                          NMDAR2_C 382 eksthCRsClsklsaygagsssvrspykrCdaCkklgnLYdisEDnllqeaiasaeslasgkgas 446
                                       +k   C  C  +++   + s+s  sp   C  C  lg+  +++ED ++q+  ++ +++ ++ + +
  gi|336253485|ref|YP_004596592.1| 276 SKDLACTHCGIDVPEIETRSFSFNSPHGACPECEGLGETKEVDEDLVVQDPSKPLKHVFEAWSYN 340
                                       45677*********************************************999998554433333 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.77   3.9e+02      38      53 ..      28      43 ..      17      61 .. 0.88
   2 ?   -3.6   0.0       8.1   4.1e+03     248     282 ..     159     192 ..     149     193 .. 0.68
   3 ?    5.8   0.0     0.012       5.9      32      57 ..     654     679 ..     637     688 .. 0.81
   4 ?   -0.5   0.0      0.95   4.8e+02     135     158 ..     900     923 ..     898     931 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.77
                           DUF3987 38 ytlvvapsGerKSpvd 53
                                      +t+v++ sG++KS+++
  gi|336253485|ref|YP_004596592.1| 28 FTVVTGLSGSGKSSLA 43
                                      89***********986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.1
                           DUF3987 248 avleayearfrellae.pelellegelepitlrlsd 282
                                       + + a+e++f+el+ e +++   +g  e + l+l+d
  gi|336253485|ref|YP_004596592.1| 159 DQKGAFEDLFEELVSEgYARVEIDG--EEHDLTLDD 192
                                       344699999***9999554444444..777777776 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.012
                           DUF3987  32 teplnLytlvvapsGerKSpvdklvl 57 
                                         pl  +t++++ sG++KS+++  vl
  gi|336253485|ref|YP_004596592.1| 654 DIPLGCFTAITGVSGSGKSTLMHEVL 679
                                       569999***************98775 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.95
                           DUF3987 135 lelLaengggililsdEggiflaa 158
                                       l++L +ng+++ +++ E++ +++a
  gi|336253485|ref|YP_004596592.1| 900 LHRLTDNGNTVVVIEHELDLVKNA 923
                                       6899****************9987 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.9     1e+03       3      17 ..      30      44 ..      29      51 .. 0.84
   2 ?    8.6   0.0    0.0031       1.6       3      20 ..     662     679 ..     661     688 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.9
                                      EEE--TTSSHHHHHH CS
                          NTPase_1  3 fiTGppGvGKtTlvk 17
                                      ++TG +G+GK+ l  
  gi|336253485|ref|YP_004596592.1| 30 VVTGLSGSGKSSLAF 44
                                      69*********9875 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0031
                                       EEE--TTSSHHHHHHHHH CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvl 20 
                                       +iTG +G+GK+Tl++ vl
  gi|336253485|ref|YP_004596592.1| 662 AITGVSGSGKSTLMHEVL 679
                                       69*************997 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.23   1.2e+02      30      38 ..     121     129 ..     102     138 .. 0.71
   2 ?    7.3   0.4    0.0093       4.8      14      35 ..     280     309 ..     275     316 .. 0.89
   3 ?   -0.6   0.0       2.6   1.4e+03      28      35 ..     428     435 ..     416     445 .. 0.65
   4 ?    1.7   0.2      0.52   2.7e+02      29      48 ..     763     791 ..     742     795 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.23
                               DZR  30 rCpsCgekv 38 
                                       +Cp+Cg++v
  gi|336253485|ref|YP_004596592.1| 121 HCPECGREV 129
                                       455555544 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0093
                               DZR  14 fCseCgtklkavaa........edrCpsCg 35 
                                        C +Cg ++++ ++        + +Cp+C+
  gi|336253485|ref|YP_004596592.1| 280 ACTHCGIDVPEIETrsfsfnspHGACPECE 309
                                       7********988889**************7 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.6
                               DZR  28 edrCpsCg 35 
                                        + Cp+C+
  gi|336253485|ref|YP_004596592.1| 428 VTECPACD 435
                                       56777775 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.52
                               DZR  29 drCpsCgek..vdpearf.......CpeC 48 
                                        rC +Cg +  v+ e +f       C eC
  gi|336253485|ref|YP_004596592.1| 763 GRCEECGGQgtVKIEMNFlsdvyvpCEEC 791
                                       56777776655555666666666666666 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 ?   -1.7   0.2       5.9     3e+03      32      37 ..     121     126 ..     116     133 .. 0.79
   2 ?    2.8   0.3      0.23   1.2e+02      12      21 ..     304     313 ..     280     323 .. 0.76
   3 ?    6.2   0.0      0.02        10      24      43 ..     422     441 ..     403     446 .. 0.78
   4 ?    4.0   0.3     0.097        50      12      40 ..     764     795 ..     762     812 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.9
                                       E-TTTT CS
                         Anti-TRAP  32 eCPkCs 37 
                                        CP+C+
  gi|336253485|ref|YP_004596592.1| 121 HCPECG 126
                                       699996 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.23
                                       E-TTTTTTSE CS
                         Anti-TRAP  12 kCdaCngsGk 21 
                                       +C++C+g G+
  gi|336253485|ref|YP_004596592.1| 304 ACPECEGLGE 313
                                       4555555555 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.02
                                       TE......E-TTTTTSSEEE CS
                         Anti-TRAP  24 peeprasleCPkCsGkglip 43 
                                        e+  +  eCP+C G  l p
  gi|336253485|ref|YP_004596592.1| 422 IEDYMSVTECPACDGTRLKP 441
                                       456777889******99877 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.097
                                       E-TTTTTTSEETTE.........E-TTTTTSS CS
                         Anti-TRAP  12 kCdaCngsGkiepe...eprasleCPkCsGkg 40 
                                        C++C g G ++ e        ++C +C G  
  gi|336253485|ref|YP_004596592.1| 764 RCEECGGQGTVKIEmnfLSDVYVPCEECDGAR 795
                                       59999999988888645456678999999965 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       7.9   4.1e+03     120     170 ..     343     394 ..     331     428 .. 0.56
   2 ?    9.4   0.0     0.002         1      26      55 ..     661     693 ..     651     734 .. 0.79
   3 ?   -1.8   0.0       5.4   2.8e+03      94     176 ..     813     904 ..     790     930 .. 0.49

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.9
                             DUF87 120 vleealdqakakeekeklssdepveklleelk...............kekeelrklknqaiarlld 170
                                       +++  ld +    e  ++s  +p+e+l e+++                           ++++  +
  gi|336253485|ref|YP_004596592.1| 343 YYQTRLDAV---AEHFDVSLSTPFEELDEDIRrqflygtdeevlfkrH-----------TKNGTRR 394
                                       444444433...577788889999999999988888666544444331...........2222222 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.002
                             DUF87  26 lAilgsTGsGKSntv.avLleelle..kkgati 55 
                                       +Ai g +GsGKS+++  vL + l++   +++++
  gi|336253485|ref|YP_004596592.1| 661 TAITGVSGSGKSTLMhEVLYKGLARqmNDNTSV 693
                                       69************9458888888865444444 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 5.4
                             DUF87  94 pwsldpeelldlleeddkpaaavqrsvleealdqaka..keekeklssdepveklleelk.........kekeelrk 159
                                       + ++++ee  +++e    ++  +  ++l+++   + +  + + +   +++   kl+eel            +e+   
  gi|336253485|ref|YP_004596592.1| 813 VLEMSVEEAYEFFES--SSQIRRRLKLLKDVGLDYMKlgQPSTTLSGGEAQRIKLAEELGkkdsgetlyLLDEPTTG 887
                                       556666666666666..444444333333333333222422222222222223333333333333333333333334 PP

                             DUF87 160 lknqaiarlldkledll 176
                                       l ++ +++l+d l +l 
  gi|336253485|ref|YP_004596592.1| 888 LHSEDERKLIDVLHRLT 904
                                       44444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (988 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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):              35  [number of targets reported over threshold]
# CPU time: 0.89u 0.27s 00:00:01.16 Elapsed: 00:00:00.45
# Mc/sec: 6630.61
//
Query:       gi|336253486|ref|YP_004596593.1|  [L=260]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-23   83.4   0.1    2.4e-23   82.6   0.1    1.4  1  Methyltransf_11  Methyltransferase domain
    1.3e-21   77.1   0.1    2.4e-21   76.2   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
    1.3e-21   76.9   0.0    1.7e-21   76.6   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.1e-17   64.4   0.0    1.4e-17   64.0   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      2e-15   57.3   0.0    3.5e-15   56.5   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    6.8e-10   38.7   0.0    9.4e-10   38.2   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.8e-07   31.0   0.0    2.5e-07   30.5   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    1.1e-06   28.2   0.0      1e-05   25.0   0.0    1.9  2  CMAS             Mycolic acid cyclopropane synthetase
      2e-06   27.0   0.0    2.7e-06   26.5   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
      1e-05   25.3   0.0    1.6e-05   24.7   0.0    1.3  1  TPMT             Thiopurine S-methyltransferase (TPMT)
    6.3e-05   23.0   0.1    0.00011   22.2   0.0    1.5  1  Methyltransf_32  Methyltransferase domain
    0.00023   20.4   0.0    0.00031   19.9   0.0    1.2  1  DREV             DREV methyltransferase
    0.00068   19.3   0.0    0.00094   18.8   0.0    1.1  1  NodS             Nodulation protein S (NodS)
     0.0017   17.8   0.0       0.45   10.0   0.0    2.2  2  Methyltransf_4   Putative methyltransferase
     0.0027   16.3   0.0     0.0044   15.6   0.0    1.3  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
     0.0046   16.5   0.0     0.0072   15.9   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0092   15.5   0.0       0.56    9.6   0.0    2.4  2  CheR             CheR methyltransferase, SAM binding domain
  ------ inclusion threshold ------
      0.014   16.4   0.1      0.039   15.0   0.1    1.8  1  Methyltransf_24  Methyltransferase domain
      0.038   13.8   0.0      0.094   12.5   0.0    1.6  1  Methyltransf_8   Hypothetical methyltransferase
      0.049   13.1   0.0      0.066   12.6   0.0    1.2  1  TehB             Tellurite resistance protein TehB
      0.067   12.9   0.0       0.12   12.2   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.19   11.1   0.0       0.28   10.5   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


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 !   82.6   0.1   2.9e-26   2.4e-23       1      95 [.      49     142 ..      49     143 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 2.9e-26
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC.TS.S-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaek.lp.fednsfDlvvssevlhhve 75 
                                       Ld+GcG G +a+ la+rga+v+g+D s+em+++a+e+  ++   v+f++a++ + l  +ed+sfDlv++++v+ h++
  gi|336253486|ref|YP_004596593.1|  49 LDAGCGDGHYAARLADRGADVLGIDASQEMIRTAEERHGDR---VDFRRARVDEpLEfLEDDSFDLVCCQHVFSHLP 122
                                       8*********************************9999988...8********97744899**************** PP

                                       CHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllv 95 
                                        +e  ++e+aRvL+pgG +v
  gi|336253486|ref|YP_004596593.1| 123 SLETPVEEFARVLRPGGSVV 142
                                       *****************987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.1   2.9e-24   2.4e-21       1      97 []      48     139 ..      48     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.9e-24
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG.BSS.STTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaed.lpf.edgsfDlvvssgalh 75 
                                       vLd+GcG G+++++la+r+  a+v+g+D s+em+++a+er+   g +v+f+++ +++ l+f ed+sfDlv+++++++
  gi|336253486|ref|YP_004596593.1|  48 VLDAGCGDGHYAARLADRG--ADVLGIDASQEMIRTAEERH---GDRVDFRRARVDEpLEFlEDDSFDLVCCQHVFS 119
                                       9*****************5..********************...569********6659977999*******877** PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       hl+   le+ ++e+arvL+pgG
  gi|336253486|ref|YP_004596593.1| 120 HLP--SLETPVEEFARVLRPGG 139
                                       *98..78899***********9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   2.1e-24   1.7e-21       3     114 ..      44     156 ..      42     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 2.1e-24
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDli 78 
                                       +glrvlD+GCG G+++ +la++   +a+v GiD s+e+i+ A+e+   +  d+v F+++ + e le  led++fDl+
  gi|336253486|ref|YP_004596593.1|  44 DGLRVLDAGCGDGHYAARLADR---GADVLGIDASQEMIRTAEER---H-GDRVDFRRARVDEpLEF-LEDDSFDLV 112
                                       689*****************87...799****************7...3.479**********8886.799****** PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedpr........l 114
                                       +++ v+ +l++++   ee  rvl+pgg +++++++         
  gi|336253486|ref|YP_004596593.1| 113 CCQHVFSHLPSLETPVEEFARVLRPGGSVVLSTHHpfhdfqvvR 156
                                       *********************************99555555432 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   1.7e-20   1.4e-17      22     162 ..      44     223 ..      13     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 1.7e-20
                   Methyltransf_23  22 aggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..........kakkaqkdqfdeqeaaepqgkfdlIvl 88 
                                        g rvLd GcG+G+ +  l+++g++v g+D+s e++  ae           a+  ++  f       ++++fdl+++
  gi|336253486|ref|YP_004596593.1|  44 DGLRVLDAGCGDGHYAARLADRGADVLGIDASQEMIRTAEerhgdrvdfrRARVDEPLEF------LEDDSFDLVCC 114
                                       4559*********************************99877765444333333333333......5888******* PP

                   Methyltransf_23  89 revlehvpdppellrqiatllkpgGylllseplasl.................................kedrlll. 131
                                        +v+ h+p+++  +  +a+ l+pgG ++ls++   +                                 +e+++++ 
  gi|336253486|ref|YP_004596593.1| 115 QHVFSHLPSLETPVEEFARVLRPGGSVVLSTHHPFHdfqvvrdeaypdayaaledlnpvvepssprtnyHETERFKi 191
                                       *******************************9877799999999999999999999999999999999878888653 PP

                   Methyltransf_23 132 dwlylvpag.rhisffsarslkelleeaGlev 162
                                       +w+ +   + ++ +  s ++l + l e G+++
  gi|336253486|ref|YP_004596593.1| 192 HWTGEESSNpGVYYRRSLTELLRPLLETGFDL 223
                                       68888777756667778888888888888876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   4.4e-18   3.5e-15       1      98 [.      49     140 ..      49     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 4.4e-18
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L+ GcG+G+++++l+++  +++++g+D s+++i  a+e++ +r + + ++v+   + l+d    +sfDlv + +v++
  gi|336253486|ref|YP_004596593.1|  49 LDAGCGDGHYAARLADR--GADVLGIDASQEMIRTAEERHGDRVDFRRARVDEPLEFLED----DSFDLVCCQHVFS 119
                                       89***************..**************888888888886555555544444433....4************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                       hl+ ++  +++++++L+pgG 
  gi|336253486|ref|YP_004596593.1| 120 HLPSLETPVEEFARVLRPGGS 140
                                       ********************6 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   1.1e-12   9.4e-10      14     154 ..       6     145 ..       4     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.1e-12
                                       X-HHHHHHHHHHHHH......TTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHH CS
                   Ubie_methyltran  14 esvaskyDlmndvls......lgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenm 84 
                                       +s+ ++yD + d+ +       + h lW   +  l  +  g +vlD  +G g +a++l+d      +v ++D +++m
  gi|336253486|ref|YP_004596593.1|   6 DSIEHHYDAVADIWAeftqqpTKKHLLWP-TIRSLLPPVDGLRVLDAGCGDGHYAARLADR---GADVLGIDASQEM 78 
                                       68889999999997542222235677786.5788899999****************99875...5689********* PP

                                       HHHHHHHHHHHTSSTEEEEE--T.TT-TT.S-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE CS
                   Ubie_methyltran  85 Lkvgekklkeegkinieflqana.eeLpf.eddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlef 154
                                       ++++e++  +    +++f  a   e L+f eddsfD+v   + +  ++  ++ ++e  rvl+pGG +v l +
  gi|336253486|ref|YP_004596593.1|  79 IRTAEERHGD----RVDFRRARVdEPLEFlEDDSFDLVCCQHVFSHLPSLETPVEEFARVLRPGGSVV-LST 145
                                       ****999766....688888875256998567*********************************985.444 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0     3e-10   2.5e-07      13      90 ..      44     123 ..      33     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3e-10
                              MetW  13 pgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvak.G..lsviqgdldkdlenfedksfdyvvlsqtlq 86 
                                       +g rvld GcGdG+    l++ ++ d  G++ ++e +  + ++ G  +   +  +d+ le+ ed+sfd+v  +  + 
  gi|336253486|ref|YP_004596593.1|  44 DGLRVLDAGCGDGHYAARLAD-RGADVLGIDASQEMIRTAEERhGdrVDFRRARVDEPLEFLEDDSFDLVCCQHVFS 119
                                       477****************88.9**************99988744346668899****************9877655 PP

                              MetW  87 atrn 90 
                                        +  
  gi|336253486|ref|YP_004596593.1| 120 HLPS 123
                                       4444 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.29   2.4e+02       8      25 ..       6      23 ..       2      31 .. 0.60
   2 !   25.0   0.0   1.2e-08     1e-05      62     171 ..      44     150 ..      37     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.29
                                      HHHHHHHTS-HHHHCTTS CS
                              CMAS  8 enikahYDlsndffalfl 25
                                      + i++hYD   d++a f 
  gi|336253486|ref|YP_004596593.1|  6 DSIEHHYDAVADIWAEFT 23
                                      456666666666665553 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.2e-08
                                       TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEE.ES-GGG-----SEEEEES-G CS
                              CMAS  62 pGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevk.lldyedldekvdrvvsvgaf 137
                                       +G ++Ld GcG G+ + r ++r +++v+g+  S+e  ++a++r  ++   r+++v+  l++ + d+ +d v    +f
  gi|336253486|ref|YP_004596593.1|  44 DGLRVLDAGCGDGHYAARLADR-GADVLGIDASQEMIRTAEERHGDRVDFRRARVDePLEFLE-DDSFDLVCCQHVF 118
                                       5999******************.*****************99975544445555541455544.559********** PP

                                       GGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE-- CS
                              CMAS 138 ehvgkenydtffkklkkllkedGllllhtitslh 171
                                        h+   +++t ++++ ++l+++G ++l t    h
  gi|336253486|ref|YP_004596593.1| 119 SHLP--SLETPVEEFARVLRPGGSVVLSTHHPFH 150
                                       **96..688889*************998866555 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 !   26.5   0.0   3.3e-09   2.7e-06     103     220 ..      32     146 ..      24     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.3e-09
                                       HHHHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T CS
                    Methyltransf_9 103 kWdrvlphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe 179
                                        W  ++  l+++ g ++ld Gcg+G++  r++ +ga+ v+Gid s+  + + e  r+    d r   +   +e l+ 
  gi|336253486|ref|YP_004596593.1|  32 LWPTIRSLLPPVDGLRVLDAGCGDGHYAARLADRGAD-VLGIDASQEMIRTAEE-RHGDRVDFRRARVDEPLEFLE- 105
                                       58999999**********************9999986.89*****998776654.333445666666666677665. PP

                                       ---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEEEEEE CS
                    Methyltransf_9 180 leafdtvfsmGvlyhrrsPldhllqlkdqlvkgGelvletl 220
                                        ++fd v    v+ h  s    + ++   l+ gG +vl t 
  gi|336253486|ref|YP_004596593.1| 106 DDSFDLVCCQHVFSHLPSLETPVEEFARVLRPGGSVVLSTH 146
                                       589************9887777788888999******9985 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.9e-08   1.6e-05      33     109 ..      40     111 ..      17     123 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.9e-08
                                       .T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE--...........-TTT- CS
                              TPMT  33 lkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepkvkelsgvkeysageiellcgdvFtl 109
                                       l    glrvl  +CG ++ ++ lA++g +v+G++ s+  ++ + e ++   +v+   +++    + +e l  d F+l
  gi|336253486|ref|YP_004596593.1|  40 LPPVDGLRVLDAGCGDGHYAARLADRGADVLGIDASQEMIRTAEERHGD--RVD---FRRARVDEPLEFLEDDSFDL 111
                                       5567899***********************************6444443..222...22221234455555555543 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.3e-07   0.00011      25      71 ..      44      86 ..      22     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.3e-07
                   Methyltransf_32 25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekra 71
                                      + l+v+D+G+G g+ + +la+     +  v+gida++e++++ae+r 
  gi|336253486|ref|YP_004596593.1| 44 DGLRVLDAGCGDGHYAARLAD----RGADVLGIDASQEMIRTAEERH 86
                                      6679*****************....499***************9986 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.9e-07   0.00031      95     195 ..      45     152 ..      28     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.9e-07
                              DREV  95 dkklldlGaGdGeitkrvaptfeevyatelsetmr........drlkkkkynvlsalelqetdvkldlilclnlldr 163
                                         ++ld G GdG+ + r+a+   +v   ++s++m+        dr++ ++ +v   le+   d  +dl+ c  ++  
  gi|336253486|ref|YP_004596593.1|  45 GLRVLDAGCGDGHYAARLADRGADVLGIDASQEMIrtaeerhgDRVDFRRARVDEPLEFL-EDDSFDLVCCQHVFSH 120
                                       569*******************************83333333345556666777778877.4668************ PP

                              DREV 164 cfdplklledirsalepngrvivalvlPvshy 195
                                         +  + +e+   +l+p g v+++   P++ +
  gi|336253486|ref|YP_004596593.1| 121 LPSLETPVEEFARVLRPGGSVVLSTHHPFHDF 152
                                       99999************************987 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.2e-06   0.00094      47     145 ..      48     144 ..      22     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                              NodS  47 alevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdv.qqfstdekfdlivvaevlyyiedv 122
                                       +l+ Gc  G ++ rla     +  +d  +e i  a er  +  +      d   +f  d+ fdl+ +  v+ ++   
  gi|336253486|ref|YP_004596593.1|  48 VLDAGCGDGHYAARLADRGADVLGIDASQEMIRTAEERHGDRVDFRRARVDEpLEFLEDDSFDLVCCQHVFSHL--- 121
                                       899**************************************9999887766427899************98766... PP

                              NodS 123 aelraavrnlvsllapdgqlvfG 145
                                         l + v+++ ++l+p+g +v+ 
  gi|336253486|ref|YP_004596593.1| 122 PSLETPVEEFARVLRPGGSVVLS 144
                                       57889*************99975 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00056      0.45       5      46 ..      48      87 ..      44     107 .. 0.88
   2 ?    5.8   0.0     0.011       8.6      99     123 ..     127     151 ..     124     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00056
                                      EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHH CS
                    Methyltransf_4  5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkie 46
                                      vl+ GcG G+   +lA + +d  +lGi+ ++++++++ ++ +
  gi|336253486|ref|YP_004596593.1| 48 VLDAGCGDGHYAARLADRGAD--VLGIDASQEMIRTAEERHG 87
                                      899**************9987..69**********9988765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.011
                                       HHHHHHHHEEEEEEEEEEESHHHHH CS
                    Methyltransf_4  99 llkelarvLkkgGvlelaTDveeya 123
                                        ++e+arvL++gG+++l T ++   
  gi|336253486|ref|YP_004596593.1| 127 PVEEFARVLRPGGSVVLSTHHPFHD 151
                                       589***************9765433 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 !   15.6   0.0   5.4e-06    0.0044     121     220 ..      48     146 ..      41     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.4e-06
                   Methyltransf_29 121 vlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaLeRgvpai..lavlgtkrlpy.PsrsfdlihCsrCridw 194
                                       vlD GCg   ++a l +r+   l +   D  ++ +  a eR    +    +   + l +    sfdl+ C     + 
  gi|336253486|ref|YP_004596593.1|  48 VLDAGCGDGHYAARLADRGADVLGI---DASQEMIRTAEERHGDRVdfRRARVDEPLEFlEDDSFDLVCCQHVFSHL 121
                                       8*****************9998887...89999********7544311344455667772468*****998877666 PP

                   Methyltransf_29 195 teedgilllevdRvlRpgGyfvlsap 220
                                        +   + + e  RvlRpgG  vls++
  gi|336253486|ref|YP_004596593.1| 122 PSL-ETPVEEFARVLRPGGSVVLSTH 146
                                       655.57899**************986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.9e-06    0.0072      32     105 ..      45     116 ..      31     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.9e-06
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE-- CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsNP 105
                                         +vlD GcG G  +a la++  +  v  +d++ + ++ a+e   +   +  +++  + le +e+++fdl+ +  
  gi|336253486|ref|YP_004596593.1|  45 GLRVLDAGCGDGHYAARLADRGAD--VLGIDASQEMIRTAEERHGDRV-DfRRARVDEPLEFLEDDSFDLVCCQH 116
                                       557*****************9988..9************998776654.54888888899999999***999864 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.032        26      31      81 ..      44      83 ..      19      88 .. 0.68
   2 !    9.6   0.0   0.00069      0.56     115     173 ..      85     143 ..      73     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.032
                                      SSEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHHHH CS
                              CheR 31 krvriwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlekAk 81
                                        +r++ agc++G+ +      l++   +      ++l++D +++++ +A+
  gi|336253486|ref|YP_004596593.1| 44 DGLRVLDAGCGDGHYA----ARLAD---RG----ADVLGIDASQEMIRTAE 83
                                      5589999999999843....33333...22....35888888888888886 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00069
                                       HHHTTEEEEE--TTT..-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
                              CheR 115 eikelvkFeklnlle..kksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLll 173
                                          ++v+F++  + e  +    +++D++ c+ v++ +  ++ e+ +e+fa+ l+pgg ++l
  gi|336253486|ref|YP_004596593.1|  85 RHGDRVDFRRARVDEplEFLEDDSFDLVCCQHVFSHL--PSLETPVEEFARVLRPGGSVVL 143
                                       555788888888888656666789*********9998..5667889***********9987 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   4.8e-05     0.039      15     103 ..      60     143 ..      49     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.8e-05
                   Methyltransf_24  15 lralrrngagrlvavdhdpgaeeaaalareaglddrvrlikadseealaslaagsiDllfiDgghaa.eavledlea 90 
                                       +r+  ++ga  ++ +d  +   e  + a+ +   drv++++a+ +e l+ l+++s+Dl+ +    ++  +    +e 
  gi|336253486|ref|YP_004596593.1|  60 ARL-ADRGA-DVLGIDASQ---EMIRTAE-ERHGDRVDFRRARVDEPLEFLEDDSFDLVCCQHVFSHlPSLETPVEE 130
                                       333.34444.699999999...6444454.599****************************95444333445559** PP

                   Methyltransf_24  91 llprlapggvvlf 103
                                       + ++l+pgg v++
  gi|336253486|ref|YP_004596593.1| 131 FARVLRPGGSVVL 143
                                       *********9986 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012     0.094      72     155 ..      44     142 ..      22     156 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                       TTS-EEEES-TT-HHHHH--.S-..EEEEES......S-SSTTEEES-T..TS-..S...--TT-EEEEEEES---S CS
                    Methyltransf_8  72 dnlvvadlGcGeakiaeavr.ekekvrsfdl......vavnervvacdl..akv..P...ledesvdvavfclslmg 134
                                       d l v d GcG+ + a +   +  +v  +d       +a + +    d+  a+v  P   led+s d+ v+c  + +
  gi|336253486|ref|YP_004596593.1|  44 DGLRVLDAGCGDGHYAARLAdRGADVLGIDAsqemirTAEERHGDRVDFrrARVdePlefLEDDSFDL-VCCQHVFS 119
                                       56679999999988775544144567666641111213455666778884344444433468*****8.67877776 PP

                                       S..-HHHHHHHHHHHEEEEEEEE CS
                    Methyltransf_8 135 t..nladflkeanrvlkvGGllk 155
                                           l+++++e  rvl++GG + 
  gi|336253486|ref|YP_004596593.1| 120 HlpSLETPVEEFARVLRPGGSVV 142
                                       53489***************875 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.1e-05     0.066      31      72 ..      45      86 ..      33     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.1e-05
                                      S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHH CS
                              TehB 31 pgkvldlgcgqgrnslylsllgydvtawdknensiafleeik 72
                                        +vld gcg+g  +  l+  g dv  +d  ++ i   ee +
  gi|336253486|ref|YP_004596593.1| 45 GLRVLDAGCGDGHYAARLADRGADVLGIDASQEMIRTAEERH 86
                                      5689***************************99998877643 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 ?   12.2   0.0   0.00014      0.12      72     117 ..      43      85 ..      13      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                       -TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHH CS
                              PCMT  72 kkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrn 117
                                        +g rvL+ G+G G  +a la    + + v++i+ ++e++++a+++
  gi|336253486|ref|YP_004596593.1|  43 VDGLRVLDAGCGDGHYAARLA---DRGADVLGIDASQEMIRTAEER 85 
                                       5789************98666...5777899*********999876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00035      0.28     164     259 ..      47     144 ..      40     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                              PrmA 164 evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellkeekadvivaNILaevl 239
                                       +vlD G+G G  a   a  ga +v+++D  +  ++ a+e  +  +v+  + +v  + e l++ ++d++ +  + + l
  gi|336253486|ref|YP_004596593.1|  47 RVLDAGCGDGHYAARLADRGA-DVLGIDASQEMIRTAEER-HGDRVDFrRARVDEPLEFLEDDSFDLVCCQHVFSHL 121
                                       79********99987777776.69***********99875.556666658889999999999********9999888 PP

                              PrmA 240 iel...aedikklvkeggllilS 259
                                        +l   +e++++++++gg+++lS
  gi|336253486|ref|YP_004596593.1| 122 PSLetpVEEFARVLRPGGSVVLS 144
                                       8885557899999******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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):              22  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 2195.25
//
Query:       gi|336253487|ref|YP_004596594.1|  [L=345]
Description: hypothetical protein Halxa_2090 [Halopiger xanaduensis SH-6]
Scores for 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   53.3   0.0    4.8e-06   25.6   0.0    3.9  3  Sortilin-Vps10  Sortilin, neurotensin receptor 3,
    1.1e-10   39.8   7.5       0.56   10.4   0.1    6.1  5  BNR             BNR/Asp-box repeat
    0.00012   21.5   0.8      0.097   11.9   0.0    3.3  4  PSII_BNR        Photosynthesis system II assembly factor YCF4


Domain annotation for each model (and alignments):
>> Sortilin-Vps10  Sortilin, neurotensin receptor 3,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   8.1e-10   4.8e-06       3      67 ..      58     126 ..      56     141 .. 0.83
   2 !    8.4   0.0   0.00014      0.82      28      83 ..     141     194 ..     131     203 .. 0.85
   3 !   13.0   0.0   5.5e-06     0.033       6      57 ..     205     257 ..     202     324 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 8.1e-10
                                       EEEESSTTSS-EE-GGGGTTEEBE-EEE-STTS--EEEEEES-EEEEESSTTSSEEE....EE-SS-BS CS
                    Sortilin-Vps10   3 vyiSeDeGktwkkvkeklkgeaiqeivvhpfdkkkaylltdskklyvttDrGktwkk....fklpfkps 67 
                                       +++S+D G+t+  +++++ ++a++++ ++p+d + +y+ t+ +++y++ + G++w+     ++lp++p+
  gi|336253487|ref|YP_004596594.1|  58 LHRSSDGGETFAPLETDFVSQAVTSLAISPHDPDVVYAGTEPSRVYRSANGGDSWTLleglTDLPSEPE 126
                                       689****************************************************97333345666665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00014
                                       EEE-STTS--EEEEEES-EEEEESSTTSSEEEEE-SS-BS...S--EEESSETTEE CS
                    Sortilin-Vps10  28 ivvhpfdkkkaylltdskklyvttDrGktwkkfklpfkpslsaeplsfhakdkdwl 83 
                                       + v+pfd ++ y+  + + + ++ D G+tw++    ++++  + +l++h++++ ++
  gi|336253487|ref|YP_004596594.1| 141 LEVDPFDPERLYVGIEAGAFVYSPDGGETWHERPDGSRRD--NHSLATHPDREGRI 194
                                       56899********999***************998888887..79999999988765 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 5.5e-06
                                       ESSTTSS-EE-GGGGTTEEBE-EEE-STTS--EEEEEE.S-EEEEESSTTSSE CS
                    Sortilin-Vps10   6 SeDeGktwkkvkeklkgeaiqeivvhpfdkkkaylltd.skklyvttDrGktw 57 
                                       S+D G++w + ++ l+++   ++v+hp d +++++ ++ + +   t  r++++
  gi|336253487|ref|YP_004596594.1| 205 SDDGGESWRRPQDGLEHTYCWSVVPHPADPDRVLVSSAsGASAAHTAERAESY 257
                                       99*****************99*************9998755555566666555 PP

>> BNR  BNR/Asp-box repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0022        13       2      11 ..      60      69 ..      59      70 .. 0.86
   2 !    7.6   0.2    0.0008       4.8       1      11 [.     103     113 ..     103     114 .. 0.90
   3 !   10.2   0.0   0.00011      0.68       2      11 ..     162     171 ..     161     172 .. 0.88
   4 !   10.4   0.1   9.3e-05      0.56       3      11 ..     205     213 ..     203     214 .. 0.89
   5 !    4.8   0.0    0.0067        40       1      11 [.     312     322 ..     312     323 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0022
                                      EESSTTSS-E CS
                               BNR  2 yStDgGktWs 11
                                       S DgG+t+ 
  gi|336253487|ref|YP_004596594.1| 60 RSSDGGETFA 69
                                      69******95 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0008
                                       EEESSTTSS-E CS
                               BNR   1 yyStDgGktWs 11 
                                       y S +gG +W+
  gi|336253487|ref|YP_004596594.1| 103 YRSANGGDSWT 113
                                       78********8 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00011
                                       EESSTTSS-E CS
                               BNR   2 yStDgGktWs 11 
                                       yS DgG+tW+
  gi|336253487|ref|YP_004596594.1| 162 YSPDGGETWH 171
                                       888******9 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 9.3e-05
                                       ESSTTSS-E CS
                               BNR   3 StDgGktWs 11 
                                       S+DgG++W 
  gi|336253487|ref|YP_004596594.1| 205 SDDGGESWR 213
                                       9*******7 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.0067
                                       EEESSTTSS-E CS
                               BNR   1 yyStDgGktWs 11 
                                       +++t++G  W 
  gi|336253487|ref|YP_004596594.1| 312 FVTTNFGDRWR 322
                                       79********7 PP

>> PSII_BNR  Photosynthesis system II assembly factor YCF48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   1.6e-05     0.097      32     108 ..      49     126 ..      21     130 .. 0.80
   2 !    4.5   0.0    0.0029        17     242     269 ..     146     173 ..     127     182 .. 0.70
   3 ?    0.8   0.1      0.04   2.4e+02      41      52 ..     203     214 ..     189     228 .. 0.70
   4 ?   -2.8   0.0      0.49     3e+03      31      58 ..     301     329 ..     287     334 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                                       EEEET.TTEEEEESSTTSS-EE-----S--.--EEEEEEEETTEEEEEE.ETTEEEEESSTTSS-EE----TT-SS- CS
                          PSII_BNR  32 flvGt.katlletlDGGktWeersldleeevnyrlesvsfkgdegwivG.kPslllhttdgGksWerikLsekLPGe 106
                                        +vGt +  l  ++DGG+t+ + + d+ ++  +   ++s ++ +   +G +Ps +  + +gG+sW+ ++  + LP e
  gi|336253487|ref|YP_004596594.1|  49 VFVGTfEDGLHRSSDGGETFAPLETDFVSQ-AVTSLAISPHDPDVVYAGtEPSRVYRSANGGDSWTLLEGLTDLPSE 124
                                       4566536678999**************999.55556778777776666648******************999***99 PP

                                       EE CS
                          PSII_BNR 107 Pl 108
                                       P 
  gi|336253487|ref|YP_004596594.1| 125 PE 126
                                       95 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0029
                                       SSSS-EEEEESTT-EEEESSTTSS-EE- CS
                          PSII_BNR 242 rdekeiwvaGGsgtllvskDgGktwkkd 269
                                        d++ ++v+  +g++++s DgG+tw++ 
  gi|336253487|ref|YP_004596594.1| 146 FDPERLYVGIEAGAFVYSPDGGETWHER 173
                                       4556677777777777777777777665 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.04
                                       EEESSTTSS-EE CS
                          PSII_BNR  41 letlDGGktWee 52 
                                        e+ DGG++W++
  gi|336253487|ref|YP_004596594.1| 203 AESDDGGESWRR 214
                                       567777777765 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 0.49
                                       EEEEET.TTEEEEESSTTSS-EE-----S CS
                          PSII_BNR  31 GflvGt.katlletlDGGktWeersldle 58 
                                       G + G  ++ l+ t++ G++W++  +d +
  gi|336253487|ref|YP_004596594.1| 301 GVVYGVnNQGLFVTTNFGDRWRPVGIDWD 329
                                       55555413456666667777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); 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):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2840.82
//
Query:       gi|336253488|ref|YP_004596595.1|  [L=177]
Description: hypothetical protein Halxa_2091 [Halopiger xanaduensis SH-6]
Scores for 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:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); 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):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.19s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1511.61
//
Query:       gi|336253489|ref|YP_004596596.1|  [L=102]
Description: hypothetical protein Halxa_2092 [Halopiger xanaduensis SH-6]
Scores for 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   13.7   3.5      0.047   13.3   2.5    1.6  2  MatE      MatE
        8.5    6.2  11.5       0.37   10.6   0.6    2.3  2  DUF2157   Predicted membrane protein (DUF2157)


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 ?    2.1   1.4     0.015   1.4e+02      46      82 ..      12      47 ..       5      52 .. 0.76
   2 ?   13.3   2.5   5.3e-06     0.047      32      91 ..      31      91 ..      19     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.015
                              MatE 46 lglstalttlvgqalGaknfkrakealrqglilllll 82
                                      lg++++l ++vg alG+ n   + + +  ++++++++
  gi|336253489|ref|YP_004596596.1| 12 LGIGIGL-VVVGSALGQPNLGLMTRLAALATLFGIGF 47
                                      5666666.57899999999988888888888888776 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.3e-06
                              MatE 32 sialsilsllfvfllg.lstalttlvgqalGaknfkrakealrqglilllllsliiallvl 91
                                      ++ ++++ l ++f++g l++a ++  ++alGa ++++++ + +++++++l++ +i+  +++
  gi|336253489|ref|YP_004596596.1| 31 GLMTRLAALATLFGIGfLGAAFEPPLTNALGASRWDELGGVKQTAVLFVLAVVAIVLWFAV 91
                                      567788888888888746999***********************99999888777666555 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   3.0      0.04   3.6e+02      37      56 ..      32      51 ..      22      52 .. 0.82
   2 ?   10.6   0.6   4.1e-05      0.37      53      83 ..      60      90 ..      57      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.04
                           DUF2157 37 allvlGalllglGlilfvAa 56
                                      ++  l+al+ ++G+ ++ Aa
  gi|336253489|ref|YP_004596596.1| 32 LMTRLAALATLFGIGFLGAA 51
                                      566799**********9997 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 4.1e-05
                           DUF2157 53 fvAanWqglsrlvkfllllvllllslllgav 83
                                      + A+ W++l+ + ++++l+vl++++++l + 
  gi|336253489|ref|YP_004596596.1| 60 LGASRWDELGGVKQTAVLFVLAVVAIVLWFA 90
                                      789*********************9998743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 784.33
//
Query:       gi|336253490|ref|YP_004596597.1|  [L=104]
Description: 30S ribosomal protein S24e [Halopiger xanaduensis SH-6]
Scores for 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-25   87.3   0.2    5.9e-25   87.0   0.2    1.1  1  Ribosomal_S24e  Ribosomal protein S24e


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 !   87.0   0.2   3.3e-29   5.9e-25       2      78 ..      21      96 ..      20      97 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 3.3e-29
                                      EEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS---S CS
                    Ribosomal_S24e  2 vdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekkk 78
                                      ++++H+  atp + ++r++la++++ d+d+vv+++++t+fG++kt G+ak+Y+s++ a+++E++h+l+Rn++  +++
  gi|336253490|ref|YP_004596597.1| 21 FELTHED-ATPERLQVRDSLAAKLNKDADEVVIRNLNTKFGMRKTVGEAKVYESADFAREVEQDHMLERNKIGVEEE 96
                                      899****.****************************************************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 773.74
//
Query:       gi|336253491|ref|YP_004596598.1|  [L=44]
Description: 30S ribosomal protein S27a [Halopiger xanaduensis SH-6]
Scores for 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   38.4   5.8    1.1e-09   38.3   5.5    1.3  1  Ribosomal_S27   Ribosomal protein S27a
      0.009   15.9   1.3      0.014   15.3   1.3    1.3  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
  ------ inclusion threshold ------
      0.063   13.2   5.0        1.8    8.5   0.2    2.1  2  Nudix_N_2       Nudix N-terminal


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 !   38.3   5.5   1.8e-13   1.1e-09      14      45 .]      12      41 ..       3      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.8e-13
                                      EESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
                     Ribosomal_S27 14 erlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                                      +  r++Cpr CG   f+A+h dRk+CGkC +T
  gi|336253491|ref|YP_004596598.1| 12 STDREQCPR-CG-DSFLADHGDRKHCGKCSYT 41
                                      56799****.*6.69****************9 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 !   15.3   1.3   2.3e-06     0.014       4      31 ..      18      42 ..      16      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-06
                                      ESTTTSBEEEEECSCCCEEEESSSS-EE CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCgYee 31
                                      Cp Cg+  l + ++ +    C +C+Y e
  gi|336253491|ref|YP_004596598.1| 18 CPRCGDSFLADHGDRKH---CGKCSYTE 42
                                      ***********999997...******75 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.8   0.00087       5.2      16      29 ..       9      22 ..       3      23 .. 0.84
   2 ?    8.5   0.2    0.0003       1.8      18      32 ..      28      42 ..      26      44 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00087
                                      TT-SS-EEEETTTT CS
                         Nudix_N_2 16 dgDnreRlvCpaCg 29
                                      d+++  R  Cp+Cg
  gi|336253491|ref|YP_004596598.1|  9 DDGSTDREQCPRCG 22
                                      677889999****8 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0003
                                      -SS-EEEETTTTEEE CS
                         Nudix_N_2 18 DnreRlvCpaCgtih 32
                                      D+  R  C +C+++ 
  gi|336253491|ref|YP_004596598.1| 28 DHGDRKHCGKCSYTE 42
                                      7888*******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 352.74
//
Query:       gi|336253492|ref|YP_004596599.1|  [L=548]
Description: O-sialoglycoprotein endopeptidase [Halopiger xanaduensis SH-6]
Scores for 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-76  257.2   0.0    2.8e-76  256.8   0.0    1.1  1  Peptidase_M22  Glycoprotease family
     0.0014   18.1   0.1     0.0026   17.2   0.1    1.4  1  Kdo            Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0029   17.6  10.0      0.013   15.4  10.0    2.1  1  APH            Phosphotransferase enzyme family
  ------ inclusion threshold ------
       0.15   11.4   0.0       0.22   10.8   0.0    1.2  1  Pkinase        Protein kinase 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 !  256.8   0.0   6.2e-80   2.8e-76       7     270 ..      30     301 ..      25     302 .. 0.94

  Alignments for each domain:
  == domain 1  score: 256.8 bits;  conditional E-value: 6.2e-80
                                       EEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGG......GEEEEEEEEESS-HHHHHHHHHHHHHHH CS
                     Peptidase_M22   7 vasqkelhakyGGvvPelasraHserllplieealaeaglsle......dldaIavtkgPGlftgLrvGvsfAkgla 77 
                                       ++++++++++ GG++P++a+++  e++++++e+al+ a  + +       +da+a+++gPGl+++Lr + ++A++l+
  gi|336253492|ref|YP_004596599.1|  30 FIESDAYQPDSGGIHPREAAEHMHEAIPQVVERALEHARETSDgpadepPVDAVAFSRGPGLGPCLRTVGTAARALS 106
                                       5556679999****************************555444444448*************************** PP

                                       HHCT--EEEEEHHHHHHHCCHCTSEC.SSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SS CS
                     Peptidase_M22  78 lalnkPlvgVnhleahalaarleeke.efPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpyp 153
                                        +l++PlvgVnh+ ah++ +r + ++ + Pv+l  sG + +++++++gry++lget+d  +g+a+dk++r +g+++p
  gi|336253492|ref|YP_004596599.1| 107 QSLEVPLVGVNHMVAHLEIGRHT-ADfDSPVCLNASGANAHLLAYRNGRYRVLGETMDTGVGNAIDKFTRHVGWSHP 182
                                       *********************55.56799****************99****************************** PP

                                       CCHHHHHHHCTCS.......EETTEEE.CHHHHHHHHHHSTT..HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEE CS
                     Peptidase_M22 154 ggpkieklakegkkiefprplkgldfsfsGlktavlkeleke..vedlaasfqeavvdhlvekteralklpkakelv 228
                                       ggpk+e++akeg+++++p+++kg+dfsfsG+ +a+ +   +   ved+++s+qe+v+ +l+e++eral+l++++elv
  gi|336253492|ref|YP_004596599.1| 183 GGPKVEEAAKEGEYVDLPYVVKGMDFSFSGIMSAAKQRYDDGvpVEDICYSLQENVFGMLTEVAERALSLTGSDELV 259
                                       ************99*****************9999999955368********************************* PP

                                       EESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHH CS
                     Peptidase_M22 229 ilGGvaankrLrealeeeaeelglkliiPplkyctdnaamia 270
                                       ++GGv++n+rLre+l e+++++g+++++P++++++dna mia
  gi|336253492|ref|YP_004596599.1| 260 LGGGVGQNARLREMLVEMCDQRGAEFHAPEPRFLRDNAGMIA 301
                                       *****************************************8 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   5.8e-07    0.0026     115     170 ..     432     482 ..     422     495 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.8e-07
                               Kdo 115 laeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkar 170
                                       l e+l+++ +++vgr  a+lh+ag  H+d   +n+         ++ +liD+  ++
  gi|336253492|ref|YP_004596599.1| 432 LRESLTAERVRDVGRHLARLHNAGFVHGDPTTRNVRTSD-----RRTSLIDFGLGY 482
                                       6789999***************************85444.....579****97665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4  10.0   2.9e-06     0.013      97     234 ..     390     528 ..     260     534 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-06
                                       HHHHHHCCHHCH..-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCCHHHHHHHH..............HHHHHHH CS
                               APH  97 algeflaalhqvd.paalpladflaqdlellrqlesatarllaselldlleeleeq..............vlaalaa 158
                                       +   + a+l +++  +  p +  +++d++++r++                     +                + + +
  gi|336253492|ref|YP_004596599.1| 390 ERTTLEARLTSLArREGVPTPVLSDVDPREARLEL--------------------EyvgecdlresltaeRVRDVGR 446
                                       22222223333333333333333334444444444....................0444444333333332333333 PP

                                       H--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCH......HHCSCHCCCHCHHHHHHHHC CS
                               APH 159 llpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavll......rswtseldpeflaallraye 229
                                       +l++   ++++HgD+ ++N+     d r t +iDf++  + + + D a+ +         t +  + +++a l++y 
  gi|336253492|ref|YP_004596599.1| 447 HLARLHNAGFVHGDPTTRNVRTS--DRR-TSLIDFGLGYHTDHVEDYAMDVhvfdqsLVGTADDPEPLREAVLEGYR 520
                                       3333557**************99..666.579****************99955554322344444666667777776 PP

                                       ...S-HHH CS
                               APH 230 ...qeagl 234
                                          +e++l
  gi|336253492|ref|YP_004596599.1| 521 evgDERVL 528
                                       44444555 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.9e-05      0.22      95     153 ..     432     489 ..     418     506 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.9e-05
                                       --HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS CS
                           Pkinase  95 lseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk 153
                                       l e+ + + ++ + + l+ lH++g++H D  + N+  + ++   ++DFGl  + ++ ++
  gi|336253492|ref|YP_004596599.1| 432 LRESLTAERVRDVGRHLARLHNAGFVHGDPTTRNVRTS-DRRTSLIDFGLGYHTDHVED 489
                                       6666777788999999*******************999.999********988776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 4471.24
//
Query:       gi|336253493|ref|YP_004596600.1|  [L=236]
Description: hypothetical protein Halxa_2096 [Halopiger xanaduensis SH-6]
Scores for complete 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-71  240.2   0.2    1.9e-71  240.0   0.2    1.0  1  DUF2071   Uncharacterized conserved protein (COG2071)
     0.0049   16.4   0.1     0.0067   16.0   0.1    1.3  1  ADC       Acetoacetate decarboxylase (ADC)


Domain annotation for each model (and alignments):
>> DUF2071  Uncharacterized conserved protein (COG2071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.0   0.2   2.2e-75   1.9e-71       2     212 .]       7     224 ..       6     224 .. 0.97

  Alignments for each domain:
  == domain 1  score: 240.0 bits;  conditional E-value: 2.2e-75
                           DUF2071   2 qeWrdllflhwpvdpealapllPaglelDtfdGkayvslvpFrmedvrvrglpavpglstfpelNvRtYvrdk..eg 76 
                                       + Wr+llf +wpvd+eal+p+lP++l++Dt+dG+ ++s++pF+ + vr+rg+pa  g++ +pe+NvRtYv+++  +g
  gi|336253493|ref|YP_004596600.1|   7 MGWRHLLFENWPVDAEALEPHLPDELAVDTHDGSGWLSVIPFTNVAVRPRGVPARAGIR-LPEINVRTYVTRDgsDG 82 
                                       78***************************************************999999.**********999999* PP

                           DUF2071  77 rrGVvFlsldadrllivlvarllfglpYvtarmrveeee.geveyksrr.....sparfaatyrptaeveeaepgsl 147
                                       +++V+F+sldad  ++vl+ar++++lpY++ar+++e+++ g ++++srr     +p +++atyr+t+++++a++++l
  gi|336253493|ref|YP_004596600.1|  83 EPAVYFFSLDADGIASVLGARWFHHLPYYYARISLERSDdGGIRFESRRrhpgsRPGAYEATYRATGDPFAAPEDPL 159
                                       ************************************888899***99966****9*****************99*** PP

                           DUF2071 148 eeflteryrlYtrrrg.rlleyeveHepwplqeaellelentlleaaglplkpsseplvlyspgvd 212
                                       +efl+eryr+Yt++ + +l++++v+H+pw+l++a+++  +ntll+a+ +++ ps+ep+ +yspg+d
  gi|336253493|ref|YP_004596600.1| 160 AEFLVERYRFYTEAPDgSLRYTDVDHPPWTLYPATATVERNTLLAANAFER-PSTEPVRYYSPGLD 224
                                       *************9999*********************************8.966********985 PP

>> ADC  Acetoacetate decarboxylase (ADC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   7.4e-07    0.0067      24     127 ..      15     131 ..       3     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.4e-07
                                       EEEEE-HHHHHTTSBTTEEECS.TSEEEEEEEEEEEECTTTC........EEEEEEEEEEEEET...TEEEEEEEEE CS
                               ADC  24 vsyrtdpeaaaallPepLelae.rplvavyfaeypdssfggg........qYneagivvpvryg...gkegayilvl 88 
                                         +++d+ea++  lP+ L ++   + +++ ++ ++++++ +            e+ +   v+ +   g+++ y+++l
  gi|336253493|ref|YP_004596600.1|  15 ENWPVDAEALEPHLPDELAVDThDGSGWLSVIPFTNVAVRPRgvparagiRLPEINVRTYVTRDgsdGEPAVYFFSL 91 
                                       579*******************999*************98779999999988888888888855355668******* PP

                                       EESSHHHHHHHHHHTT--EEE-EEEEEE.ETTEEEEEEEE CS
                               ADC  89 wvdkeaalaaGRElwGfPKklAditltr.egdtlggtver 127
                                         d  a++++ R + ++P  +A+i+l+r +++ ++++ +r
  gi|336253493|ref|YP_004596600.1|  92 DADGIASVLGARWFHHLPYYYARISLERsDDGGIRFESRR 131
                                       ****************************866666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1772.51
//
Query:       gi|336253494|ref|YP_004596601.1|  [L=92]
Description: hypothetical protein Halxa_2097 [Halopiger xanaduensis SH-6]
Scores for 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  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 740.21
//
Query:       gi|336253495|ref|YP_004596602.1|  [L=360]
Description: oxidoreductase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   87.4   0.2    2.4e-24   86.5   0.2    1.5  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    1.5e-07   31.5   0.0    2.5e-07   30.7   0.0    1.4  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
    2.1e-05   24.8   0.4    9.3e-05   22.6   0.2    2.2  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      0.001   18.7   0.3     0.0021   17.7   0.0    1.6  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.001   19.6   0.1     0.0027   18.2   0.1    1.7  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0041   16.5   0.1     0.0091   15.4   0.1    1.5  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
      0.078   12.9   0.1       0.13   12.1   0.1    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.12   11.9   0.2       0.45   10.1   0.1    2.0  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,


Domain annotation for each model (and alignments):
>> 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 !   86.5   0.2   1.1e-27   2.4e-24       2     120 .]       8     124 ..       7     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 1.1e-27
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheel 78 
                                       r +++G+G++g+ h+   n+++ +++vva  d  ae  e++a+++g+  y+++e++ + ++ dav v tpn  he  
  gi|336253495|ref|YP_004596602.1|   8 RLGVVGLGFMGQTHA--TNAEEFGHDVVAGADVVAETREEFAQAYGATTYEEFEAMYEAEDLDAVAVSTPNAFHEPA 82 
                                       89************9..55555599**************************************************** PP

                                       HHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  79 akaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       + aale+g +vl+EKPla ++e a++++ +a++++  ++v++
  gi|336253495|ref|YP_004596602.1|  83 VVAALERGYDVLCEKPLANDLESAERIASAAAESDGFCTVNF 124
                                       **********************************99999875 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.1e-10   2.5e-07       6      85 ..     141     220 ..     136     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.1e-10
                                       TTTTSSEEEEEEEEECBEEECHHHHCCGGSH.HCSTSHHHHTCHHHHHHHHHHHTSEEEEEE.EEE.SEEESCTCCS CS
                    GFO_IDH_MocA_C   6 ngklGevvsvdvwtldtragaeakkrwkrrk.kksgGvlgdlgiHdiDllqwLfGqppsvva.algrmrqnaeaaed 80 
                                       +g +Ge+++vd   +  r+g +   +w  +    +gG+++d+g+H iD++ +L+  p+++++ a +r  + ++++++
  gi|336253495|ref|YP_004596602.1| 141 EGHFGEITHVD-ANYVRRRGIPGVGSWFTNEeLSGGGAVVDIGVHAIDFALYLMEYPSVEEVfAVTR-TEFGDRDDY 215
                                       789*******9.77777888888888888888**********************9988765547776.455556666 PP

                                       CSEEE CS
                    GFO_IDH_MocA_C  81 edaav 85 
                                        d  +
  gi|336253495|ref|YP_004596602.1| 216 VDPGD 220
                                       66654 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 !   22.6   0.2   4.2e-08   9.3e-05       2      72 ..       9      83 ..       8     107 .. 0.78
   2 ?   -1.5   0.0       1.1   2.5e+03      57      84 ..     326     353 ..     282     356 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.2e-08
                                      EEEE--SHHHHHHHHHHHHTT-EEE.EE-SSHHHHHHHHHT.TEEE-SSHHHHHHHC..SEEEE-SSSHHHHHHH CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkagykva.vynrtkekveelvae.gakaaesieelvasl..dvvitmvkagkavdev 72
                                      +g++GlG MG+  a+n ++ g++v+ + ++ +e  ee++++ ga+++e+ e++ ++   d+v +  ++  +  +v
  gi|336253495|ref|YP_004596602.1|  9 LGVVGLGFMGQTHATNAEEFGHDVVaGADVVAETREEFAQAyGATTYEEFEAMYEAEdlDAVAVSTPNAFHEPAV 83
                                      79********************98626889999999999884588888877665544447777776666555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                                       SEEEE-SSSHHHHHHHHHSHCCC--TT- CS
                     NAD_binding_2  57 dvvitmvkagkavdeviegllealkkgd 84 
                                          i  v +   v+ vi+ + ++++kg+
  gi|336253495|ref|YP_004596602.1| 326 APAINTVDQALMVQRVIDAIYRSAEKGT 353
                                       3444455555566666666666666665 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 !   17.7   0.0   9.3e-07    0.0021       7      74 ..       9      80 ..       6      92 .. 0.84
   2 ?   -3.9   0.1       3.9   8.7e+03      41      61 ..     111     131 ..     105     135 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.3e-07
                                      EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-H.HHHHHHHTT-EEEEHHHHHHT-...SEEEE-S-HHHHH CS
                              IlvN  7 iaviGyGsqGhaqalnlrdsgldvvvglregsk.svkkAkeegfevltvaeavkka...dvvmiliPDelqk 74
                                      + v+G G  G+++a+n  + g dvv g    ++   + A++ g ++++  ea+ +a   d v++ +P+ +++
  gi|336253495|ref|YP_004596602.1|  9 LGVVGLGFMGQTHATNAEEFGHDVVAGADVVAEtREEFAQAYGATTYEEFEAMYEAedlDAVAVSTPNAFHE 80
                                      679************************99877636778***********9*998885557888888888775 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.9
                                       HHHHHHTT-EEEEHHHHHHT- CS
                              IlvN  41 vkkAkeegfevltvaeavkka 61 
                                        + A+++gf +++ ++ v++a
  gi|336253495|ref|YP_004596602.1| 111 SAAAESDGFCTVNFHNRVSTA 131
                                       467888999888887777665 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 !   18.2   0.1   1.2e-06    0.0027       1      70 [.       8      75 ..       8      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-06
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH..H-SEEEE-S- CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae..eadvvvlavk 70
                                      ++g++G G mg++ a ++ + g   h++v +++   e++ee+a+++g+++ + + e + e  + d v ++ +
  gi|336253495|ref|YP_004596602.1|  8 RLGVVGLGFMGQTHATNAEEFG---HDVVAGADVVAETREEFAQAYGATTYE-EFEAMYEaeDLDAVAVSTP 75
                                      689*******************...*********************955555.4444433114455555555 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 !   15.4   0.1   4.1e-06    0.0091      38      93 ..       8      66 ..       5      79 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.1e-06
                                      EEEEES-SHHHHHHHHHHHHTT-EEEE.ESSSHHHHH.CHHHHTC.EECSHHHHHHH-S CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkvia.ydrskkkee.eeeelgv.elvsleellaesD 93
                                      ++G++GlG +Gq+ a  +++fg +v+a  d+  +++e  ++++g+ +++++e++++  D
  gi|336253495|ref|YP_004596602.1|  8 RLGVVGLGFMGQTHATNAEEFGHDVVAgADVVAETREeFAQAYGAtTYEEFEAMYEAED 66
                                      79*********************887615555444444456666667788888887654 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 ?   12.1   0.1     6e-05      0.13       2      44 ..       9      52 ..       8      96 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEE.E-S-HHHHHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvl.vdiseealekalekiek 44
                                      ++v+G G mG+  a+ + + g++Vv   d+ +e+ e+ +++  +
  gi|336253495|ref|YP_004596602.1|  9 LGVVGLGFMGQTHATNAEEFGHDVVAgADVVAETREEFAQAYGA 52
                                      69*********************986345544444444444333 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 ?   10.1   0.1    0.0002      0.45       2      28 ..       8      34 ..       7      66 .. 0.85
   2 ?   -0.7   0.0      0.39   8.7e+02      66      90 ..      54      78 ..      36      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
                                      EEEEE--STTHHHHHHHHHHCTSEEEE CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevig 28
                                      ++ v+GlG++G ++a+   e gh+v+ 
  gi|336253495|ref|YP_004596602.1|  8 RLGVVGLGFMGQTHATNAEEFGHDVVA 34
                                      689*********************983 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.39
                                      EES-HHHHHHC-SEEEE-----B-T CS
                    UDPG_MGDP_dh_N 66 fttdvekaveeadvifiaVgTPskk 90
                                         ++e   e+ d+  +aV TP+  
  gi|336253495|ref|YP_004596602.1| 54 TYEEFEAMYEAEDLDAVAVSTPNAF 78
                                      45567777888899999****9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2474.74
//
Query:       gi|336253496|ref|YP_004596603.1|  [L=182]
Description: RdgB/HAM1 family non-canonical purine NTP pyrophosphatase [Halopiger xanaduensis SH-6]
Scores for 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-56  190.4   0.0    3.2e-56  190.2   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 !  190.2   0.0   1.8e-60   3.2e-56       2     187 .]       4     177 ..       3     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 190.2 bits;  conditional E-value: 1.8e-60
                                       EEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHHH...TS-EEEEEEEEEEGGGT CS
                        Ham1p_like   2 vfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaaea...glpvladDsgLevdaLn 74 
                                        f+TgN+gK+re++e+l++ +++v+++    + +++E+q +++ e+a+  ar+a+e+   + pv++dD+gL+vdaL+
  gi|336253496|ref|YP_004596603.1|   4 RFVTGNEGKAREAREYLEG-ITAVNQV----EYDYTEVQsDSLSEIAARGAREAYEElggTEPVVVDDTGLFVDALE 75 
                                       59***************64.4444444....44677***9***************84466566************** PP

                                       TTBGGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTG CS
                        Ham1p_like  75 glPGvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyD 151
                                       g+PG+ysa+++     d+ ++++l++ ++ eee+r+A+f++v+a+ad+  e++++feG+v+G+iv  prgeggfGyD
  gi|336253496|ref|YP_004596603.1|  76 GFPGPYSAYVE-----DTVGVERLWNLVS-EEENRRAQFRTVVAFADG--ERTETFEGSVRGTIVA-PRGEGGFGYD 143
                                       **********4.....566899****997.5579***********995..7779***********6.********** PP

                                       GGEEETT-SSBTTTS.CHHHHHHSHHHHHHHHHHHH CS
                        Ham1p_like 152 piFvpeegektfaelskeeknaiShRgkAlekllef 187
                                       piF++ + ++tfae+s+eeknaiShRg+Ale++ ++
  gi|336253496|ref|YP_004596603.1| 144 PIFEY-D-GRTFAEMSAEEKNAISHRGRALEAFSAW 177
                                       *****.5.79**********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1348.34
//
Query:       gi|336253497|ref|YP_004596604.1|  [L=215]
Description: hypothetical protein Halxa_2100 [Halopiger xanaduensis SH-6]
Scores for 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   15.0   0.6      0.019   14.5   0.6    1.2  1  EBV-NA3   Epstein-Barr virus nuclear antigen 3 (EBNA-3)


Domain annotation for each model (and alignments):
>> EBV-NA3  Epstein-Barr virus nuclear antigen 3 (EBNA-3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.6   1.1e-06     0.019     185     236 ..       2      55 ..       1      69 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-06
                                       XXXXXXXXXXXXXXSXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           EBV-NA3 185 teeaidaafargqaqgiellrt..egepvedatsetseesedveaesddeelPq 236
                                       t+  +d  f rg  +g++l r+   +++++++++et  +  ++e e  d++ P 
  gi|336253497|ref|YP_004596604.1|   2 TATSWDDLFDRGASYGVDLERIraVDDNLDESVAETGADGTETEIEEADDNRPD 55 
                                       7889************9987651179**********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1666.97
//
Query:       gi|336253498|ref|YP_004596605.1|  [L=424]
Description: family 1 extracellular solute-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-22   80.2   0.3    2.9e-22   79.8   0.3    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    2.4e-13   50.7   6.0    3.3e-13   50.3   6.0    1.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    0.00012   21.7   4.1    0.00027   20.7   4.1    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
     0.0004   21.0   1.7      0.033   14.8   0.1    3.2  3  SnoaL_2     SnoaL-like domain


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.3   6.5e-26   2.9e-22       2     272 ..      57     362 ..      56     370 .. 0.76

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 6.5e-26
                                       HHHHHHHH-.TEEEEEEE-...-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB-.-GGGS.TTHHH-H CS
                         SBP_bac_8   2 lakefekkt.gvkvnvvta...asndleqklkaalaagtapdidvvwanedalatlaeeglla.dlsdl.dnlddlt 72 
                                       l++ fe+ + ++++ v+ +   a + le+ ++  l +g+ p+  ++w+ ++ l+  ++ g ++ d+ d   + ++l+
  gi|336253498|ref|YP_004596605.1|  57 LVEGFEENYpDIDFGVEDVqggARDNLETVVSRRLRDGDPPSTWQEWPGANLLQFGDNLGDIEgDVWDDdMKENYLE 133
                                       678888988887755555422467899**************977888876666655554433334433312333344 PP

                                       HHHHTT--TS.----EEEEEEE-EEEEEHHHHHHS.....---BHHHHHHHHHHHHHH-.......SEGG---G... CS
                         SBP_bac_8  73 dalaavgydgklygvPyasetpyvliynkdlleka....edpktwdellaaakklkgkf.......glpdpasg... 135
                                          +a+  dg++ +vP+++ +   l+yn +++e+a    e++++ ++l++a++++++++       g     +g   
  gi|336253498|ref|YP_004596605.1| 134 GPQEAARPDGTYVAVPLNIHRINNLFYNVSVVEEAgvdpESIDGPEALVDAFQTVEENTdatpfvnG-----TGelf 205
                                       44455589*************99***********999999999999999998888666643333331.....22233 PP

                                       .....GGGGGTHHETTEE---H.....HHH.HHHHHHHHHHHHTT-EE.....-S...--SSTTTTTSBSEEEE-TT CS
                         SBP_bac_8 136 .....wlqaallakdgksldddg...gkdglkealellkklkdngkty.....dtg.adavsefanGevaftingsw 198
                                            w  ++l + +g++  dd    + d+++++++ l+ l +++ ++     +t+ ++a++ + +G++af+ +g+w
  gi|336253498|ref|YP_004596605.1| 206 tvfqlWETIFLAQ-AGADAYDDLingEFDDVDAVRDSLALLAEYVEFFpddhfSTSfTEANERVIDGDAAFIHQGDW 281
                                       3434344344444.77776555449999999**************9776777654449******************* PP

                                       HHHHHH.....-TTTSEEEE.--.S--.EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S- CS
                         SBP_bac_8 199 diaaaq.....kagkklgai.vp.kqg.sfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnks 267
                                       ++ +++     + g+++  + +p  +g ++++++++  p++++ ++  ++ Fl+++ s ++q+ +    g ip++ +
  gi|336253498|ref|YP_004596605.1| 282 AAGTYRnrdgfDYGDDWDHVpFPgTEGlYALNMDSFTYPADNPTPED-TKTFLSYVGSTDAQERFNPLKGSIPPRVD 357
                                       ******77777777888888667656689*****************7.***************999999****9999 PP

                                       TTTHH CS
                         SBP_bac_8 268 aalsp 272
                                        ++s 
  gi|336253498|ref|YP_004596605.1| 358 IDESQ 362
                                       88754 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   6.0   7.4e-17   3.3e-13       3     315 .]      49     343 ..      46     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 7.4e-17
                                       SHHHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHH...HHHHHHHTTSSSCSEEEECGGHHHHHHHT..TSBECC CS
                         SBP_bac_1   3 sltegaalqalvakafekehpgikVeiesvgsgslaq...kltlaiaaGdgpaDviavdndwiarlaka..glllpl 74 
                                       + +e  a+qalv + fe+ +p+i++ +e+v++g+  +    ++ ++  Gd+p  +  + ++ + ++ ++  +   ++
  gi|336253498|ref|YP_004596605.1|  49 DGQE--AIQALV-EGFEENYPDIDFGVEDVQGGARDNletVVSRRLRDGDPPSTWQEWPGANLLQFGDNlgDIEGDV 122
                                       4566..9*****.*****************7777777777************9999997777778888875444444 PP

                                       .HHHHHHTTECTTCCTEEEEHHHHTHHHHCEEE.ES.EEEE.E.EEEEEEETTTHHCTTGGG..SHBHHHHHHHHHH CS
                         SBP_bac_1  75 .dpyvkaylapgvkdaadklsssvlpkildskv.ly.vPly.a.argliYNkdlfekagldp..pwtWdelveaakk 144
                                        d+++k++  +g+++aa ++            + ++ vPl+ +  + l+YN +++e+ag+dp      + lv+a + 
  gi|336253498|ref|YP_004596605.1| 123 wDDDMKENYLEGPQEAARPD------------GtYVaVPLNiHrINNLFYNVSVVEEAGVDPesIDGPEALVDAFQT 187
                                       13333333344444444442............24566************************99844445999999** PP

                                       HHHHCTCTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT.HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEEC CS
                         SBP_bac_1 145 lkekgkkpiggarggsasgtayyfalalakslggkvfdkdgg.gldnpegvtaatylvklyavanltkelkgkgaen 220
                                       + e++ +++ + ++g   +  +++ + +++++g++ +d+  +  +d+  +v +  +l + y       e ++++  +
  gi|336253498|ref|YP_004596605.1| 188 VEENTDATPFVNGTGELFTVFQLWETIFLAQAGADAYDDLINgEFDDVDAVRDSLALLAEY------VEFFPDDHFS 258
                                       ********999**********************9999987776666666666666666666......6888999999 PP

                                       SSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE..EEEEEEEEBTTC CS
                         SBP_bac_1 221 kdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi..lgayglaipkgs 295
                                       ++ ++a   +  G+aa++  g waa        +   + d  +++++++  p+P++     g+  l+ + ++ p+++
  gi|336253498|ref|YP_004596605.1| 259 TSFTEANERVIDGDAAFIHQGDWAA--------GTYRNRDGFDYGDDWDHVPFPGT----EGLyaLNMDSFTYPADN 323
                                       9999999999999999988888885........33347788888899999999954....44467899999****** PP

                                       STHHHHHHHHHHHTSHHHHH CS
                         SBP_bac_1 296 knpeaAkkFldfllspeaqa 315
                                       + pe  k Fl ++ s +aq+
  gi|336253498|ref|YP_004596605.1| 324 PTPEDTKTFLSYVGSTDAQE 343
                                       *****************996 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   4.1     6e-08   0.00027       4      23 ..      11      29 ..      10      31 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6e-08
                        TAT_signal  4 RRdFLKgsAAaaAAaalggc 23
                                      RR+FLK+++Aa+ Aa++g c
  gi|336253498|ref|YP_004596605.1| 11 RRSFLKAAGAAGVAATAG-C 29
                                      9*****999999777655.3 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   7.4e-06     0.033      30      94 ..      45     111 ..      12     118 .. 0.66
   2 ?    1.0   0.0      0.15   6.5e+02      32      49 ..     172     191 ..     153     200 .. 0.76
   3 ?    2.2   0.2     0.064   2.9e+02      30      75 ..     229     283 ..     215     308 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.4e-06
                                       TSEEESHHHHHHHHHHHHHHEEEEEEEEEEE...EEETTEEEEEEEEEEEEETTSSEEEEEEEEEEEE CS
                           SnoaL_2  30 ggelrGreairaffralfaafpdlrfeihdv...vadgdrvavewtvtgtipatgrgvtvrgvdvfrv 94 
                                        +e +G eai+a ++++ +++pd++f ++dv   + d+ + +v+ +++    +  +  +++g+ ++++
  gi|336253498|ref|YP_004596605.1|  45 WAEGDGQEAIQALVEGFEENYPDIDFGVEDVqggARDNLETVVSRRLRD-GDPPSTWQEWPGANLLQF 111
                                       56789**************************875555444444444443.244444445677766666 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                                       E..EESHHHHHHHHHHHHHH CS
                           SnoaL_2  32 e..lrGreairaffralfaa 49 
                                       +  ++G+ea+ ++f+++ ++
  gi|336253498|ref|YP_004596605.1| 172 PesIDGPEALVDAFQTVEEN 191
                                       24699**********99874 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.064
                                       TSEEESHHHHHH...HHHHHHHHEEEEEEEEEEE.....EEETTEEEEE.EEEEE CS
                           SnoaL_2  30 ggelrGreaira...ffralfaafpdlrfeihdv.....vadgdrvave.wtvtg 75 
                                        ge++  +a+r+    ++++ + fpd +f+         v dgd ++++ +++ +
  gi|336253498|ref|YP_004596605.1| 229 NGEFDDVDAVRDslaLLAEYVEFFPDDHFSTSFTeanerVIDGDAAFIHqGDWAA 283
                                       5666777777775556666666777777777776667778888888886555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 0.49u 0.18s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 3624.51
//
Query:       gi|336253499|ref|YP_004596606.1|  [L=892]
Description: DNA mismatch repair protein mutS [Halopiger xanaduensis SH-6]
Scores for 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  288.6   0.1    7.3e-86  287.0   0.0    1.9  2  MutS_V    MutS domain V
    3.4e-36  125.3   5.6    5.9e-36  124.5   5.6    1.4  1  MutS_III  MutS domain III
    4.5e-28   97.7   0.0    1.5e-27   96.1   0.0    1.9  2  MutS_I    MutS domain I
    6.1e-26   90.6   1.9    1.4e-25   89.5   1.9    1.6  1  MutS_IV   MutS family domain IV
    2.8e-20   73.0   0.0    1.7e-19   70.5   0.0    2.4  3  MutS_II   MutS domain II
     0.0042   17.6   0.4        1.4    9.3   0.0    2.9  3  AAA_23    AAA domain
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.47   10.5   0.0    2.2  1  AAA_14    AAA domain
       0.13   12.0   0.0       0.28   10.9   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
       0.91   10.1  12.0      0.062   13.8   6.0    2.1  2  APG6_N    Apg6 coiled-coil region


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       5.9   1.2e+04      82      97 ..     549     564 ..     542     572 .. 0.73
   2 !  287.0   0.0   3.7e-89   7.3e-86       1     187 [.     616     802 ..     616     803 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 5.9
                                       EEESTS-SS-HHHHHH CS
                            MutS_V  82 ilDElGRGtstydGla 97 
                                       +l ++GR  +t+d la
  gi|336253499|ref|YP_004596606.1| 549 LLQDVGRALATVDALA 564
                                       5778889888888765 PP

  == domain 2  score: 287.0 bits;  conditional E-value: 3.7e-89
                                       EEEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--T CS
                            MutS_V   1 llitGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknate 77 
                                       l++tGpnm+Gksty+rqva ivllaqiGsfvpa+ aei++vd iftRvga D+la+g+stFmvEm+E+++il++ate
  gi|336253499|ref|YP_004596606.1| 616 LVVTGPNMSGKSTYMRQVACIVLLAQIGSFVPAKDAEIGLVDGIFTRVGALDELAQGRSTFMVEMSELSNILHTATE 692
                                       58*************************************************************************** PP

                                       TSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEEEEEEE CS
                            MutS_V  78 kslvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavkeeeedivflykvk 154
                                       +slvilDE+GRGt+tydG++ia+a +eyl+++++aktlfatHyhelt lae+l++v+n+h+a++e++ d++fl++v+
  gi|336253499|ref|YP_004596606.1| 693 DSLVILDEVGRGTATYDGISIAWAATEYLHNEVQAKTLFATHYHELTGLAEELPRVANVHVAADESDGDVTFLRTVR 769
                                       ***************************************************************************** PP

                                       ES--SS--HHHHHHHTT--HHHHHHHHHHHHHT CS
                            MutS_V 155 egaaeksyGikvaklaglPesvverArevlkel 187
                                       +g +++syGi+va lag+P+ vv+r r+vl++l
  gi|336253499|ref|YP_004596606.1| 770 DGPTDRSYGIHVAGLAGVPDPVVDRSRTVLERL 802
                                       ****************************99987 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.5   5.6   2.9e-39   5.9e-36       1     191 []     272     567 ..     272     567 .. 0.91

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 2.9e-39
                                       HHHHHTTSSS-TTS.SSSS-HHHHH---SSHHHHHHHHHHHH--BS-HHHHHHHHHHHHH.T..TT.HHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                          MutS_III   1 aTlrnLeilenlrggskegsLlgvldrTvTamGaRlLrewllqPltdleeInaRldaVee.leneelreelrellrr 76 
                                       +T+rnLe++e+++g ++egsL+ ++d+T T+ G RlL+ewl +P ++le++++R++ V+   + +  r+elr++l +
  gi|336253499|ref|YP_004596606.1| 272 TTQRNLELTETMQG-EREGSLFRTIDHTETSAGGRLLKEWLQRPRRSLETLEQRQESVAAlSTAALARDELRDELGE 347
                                       599*******9997.779*****************************************9555666699999***** PP

                                       ---HHHHHHHHHTT---HHHHHHHHHHHHHHHTTTTT---SSTHHHHH..............HHHHHHHHHHB-SS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxx RF
                          MutS_III  77 lpDleRllsrislgkakardlkallealkaleelvallekeklaesee..............eslaelleeaideep 139
                                        +Dl Rl s+ ++g+a+ardl++++++l  l+ l+++ +++     e+              ++l+e l ea+ e+p
  gi|336253499|ref|YP_004596606.1| 348 AYDLARLASKATHGSADARDLLSVRDTLAVLPTLAEIIQSNPD-LAESplaeivdrpdreaaADLRETLAEALAEDP 423
                                       *****************************99999999854433.333367777777777655456677777788888 PP

                                       -SSGGGS--B-T................................................................. CS
                                       xxxxxxxxxxxx................................................................. RF
                          MutS_III 140 lalekegedlra................................................................. 151
                                       ++   +g+ l+                                                                  
  gi|336253499|ref|YP_004596606.1| 424 PSTVTQGGLLTRgydpeldevierheevrewldtlaerekrqynlshvtvdrnktdgyyiqvgksaadgvpdhyeei 500
                                       888888887777***************************************************************** PP

                                       ...........................HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH CS
                                       ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III 152 ...........................iealeqelfqelleeveealerlrrlaealaeLDvllSlA 191
                                                                  + +le+elf+el+eev+e++e l+++ +ala++D+l+SlA
  gi|336253499|ref|YP_004596606.1| 501 ktlknskrfttdeleekereilrleeqRGDLEYELFEELREEVAERAELLQDVGRALATVDALASLA 567
                                       ***********************999888899***********9999*******************9 PP

>> MutS_I  MutS domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   0.0   7.6e-31   1.5e-27       2     111 ..       6     110 ..       5     112 .. 0.91
   2 ?   -2.3   0.0       2.6   5.2e+03      27      82 ..     533     588 ..     514     599 .. 0.70

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 7.6e-31
                                       HHHHHHHCCCHH-TTCEEEEEETTEEEEECHHHHHHHHHCSSSSTT.ESSSSC.EEEEEEEHHHHHHHHHHHHHTT- CS
                            MutS_I   2 plmkqylelkkkykdavlffrvGdfYelfgeDAviaareleitltkrkkssekeipmagvPehalekylrkLvekgy 78 
                                       ++   +l+lk++ +  +l +++GdfYe+f eDA+i+a el+++++k++ s+++++pmagvP   l  yl+ Lve+gy
  gi|336253499|ref|YP_004596606.1|   6 GIVGEFLSLKENTDAELLAMQCGDFYEFFDEDAEIVADELDLKVSKKS-SHGSSYPMAGVPVDDLTPYLKALVERGY 81 
                                       566689***************************************665.56666*********************** PP

                                       EEEEEEE-S-HHHHS.S--EEEEEEEBTTC-TT CS
                            MutS_I  79 kVavveqtetpaekkgvvkrevvrviTpGtltd 111
                                       +Vav++q et +     + re+vrv+TpGtl++
  gi|336253499|ref|YP_004596606.1|  82 RVAVADQYETDS----GHAREIVRVVTPGTLLE 110
                                       ********9954....567***********987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.6
                                       EEEECHHHHHHHHHCSSSSTT.ESSSSC..EEEEEEEHHHHH.HHHHHHHHTT-EEEE CS
                            MutS_I  27 YelfgeDAviaareleitltkrkksseke.ipmagvPehale.kylrkLvekgykVav 82 
                                       Yelf+e  + +a+  e+   + +    ++  + a++ +ha+e ++++  +++g + a+
  gi|336253499|ref|YP_004596606.1| 533 YELFEELREEVAERAELLQDVGRA--LATvDALASLATHAAEnRWVQPNLHRGDRLAI 588
                                       888888888888888875554442..22224777887777752688888888887776 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   1.9   6.9e-29   1.4e-25       1      91 [.     436     526 ..     436     527 .. 0.99

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 6.9e-29
                                       TTSHHHHHHHHHHHHHHHHHHHHHCCCCCCCT-TTBEECCCSSSEEEEEE-TCCCTTT--SEEEEEECTCEEEEECC CS
                           MutS_IV   1 gfdeeLdelrdrleelekeleeleekereklgikslkveynkvlGyylevtrseakkvpkefirlqtlknserytta 77 
                                       g+d+eLde  +r+ee++++l++l+e+e+++++++++ v++nk++Gyy++v +s a+ vp+++++++tlkns+r+tt+
  gi|336253499|ref|YP_004596606.1| 436 GYDPELDEVIERHEEVREWLDTLAEREKRQYNLSHVTVDRNKTDGYYIQVGKSAADGVPDHYEEIKTLKNSKRFTTD 512
                                       8**************************************************************************** PP

                                       CHHHHHHHHHHHHH CS
                           MutS_IV  78 elkkleaelleaee 91 
                                       el+++e+e+l++ee
  gi|336253499|ref|YP_004596606.1| 513 ELEEKEREILRLEE 526
                                       ***********997 PP

>> MutS_II  MutS domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   8.5e-23   1.7e-19       2     129 ..     118     249 ..     117     256 .. 0.84
   2 ?   -2.5   0.0       2.8   5.5e+03      62      91 ..     435     464 ..     413     468 .. 0.77
   3 ?   -4.1   0.0         9   1.8e+04      21      34 ..     824     837 ..     822     837 .. 0.83

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 8.5e-23
                                       EEEEEEEE.......TTTSE.EEEEEEETTTTEEEEEEEEE-HHHHHHHHHH-ESEEEEESS-SCCCHHHHHHCHCT CS
                           MutS_II   2 ylaAisek.......regrr.vGlafiDlstgefvvsefedfeeleaeLsrlsPkElllpedlsestaeeessklre 70 
                                       ylaA+++          +++ +Glaf+D++tg+f v+e  d ++ ++eL+r+ P+E+l ++d+     +++++ l  
  gi|336253499|ref|YP_004596606.1| 118 YLAAVVDGsrsgagsSGADAdYGLAFADVTTGRFLVAEADDSDDALTELYRFDPVEVLPGPDA-----RTDDDLLNA 189
                                       788866556778887677888*****************************************8.....556778888 PP

                                       TT-EEEEE....SCCCCSHCCHHHHCHHHB--STTTTTTTGGG-HHHHHHHHHHHHHCCCCCS CS
                           MutS_II  71 lrsrvgvr....etvefesekaserleedfsvedldgfglekekklalaAlgalisYleetqk 129
                                       +r+r+g++    et+ f+ + a + + e+f++e+++ + +    ++ +aA+ga+++Y+eet  
  gi|336253499|ref|YP_004596606.1| 190 VRERIGATltlhETEAFAPKRADHAVREQFGTETVERLSV---GEPTVAAAGAILDYVEETGA 249
                                       8888888833335577888889***************977...6899999**********965 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.8
                                       HHHHHCHCTTT-EEEEESCCCCSHCCHHHH CS
                           MutS_II  62 eeessklrelrsrvgvretvefesekaser 91 
                                       + ++++l e+++r + ++++++ ++++++r
  gi|336253499|ref|YP_004596606.1| 435 RGYDPELDEVIERHEEVREWLDTLAEREKR 464
                                       788999999999999999999988887765 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 9
                                       ETTTTEEEEEEEEE CS
                           MutS_II  21 Dlstgefvvsefed 34 
                                       Dls+g+f+ s ++d
  gi|336253499|ref|YP_004596606.1| 824 DLSSGQFRGSASAD 837
                                       9******9887776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.3   2.5e+03      94     164 ..     273     347 ..     235     390 .. 0.56
   2 ?    3.6   1.4     0.042        84     121     192 ..     455     543 ..     425     557 .. 0.42
   3 !    9.3   0.0   0.00073       1.4      17      36 ..     602     630 ..     593     650 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                            AAA_23  94 relskkkgkttkka....klellei...deleqfisellgskkiilnlilflgqerfeefelkdkkerleelekele 163
                                        +++ + ++t +++     ++ +++   ++  ++++e l++  ++l+ +   +++ +   +l++   + +el++el 
  gi|336253499|ref|YP_004596606.1| 273 TQRNLELTETMQGEregsLFRTIDHtetSAGGRLLKEWLQRPRRSLETLEQRQESVA---ALSTAALARDELRDELG 346
                                       333333333333332111222222233355555666666666666666654444443...23333334444444444 PP

                            AAA_23 164 e 164
                                       e
  gi|336253499|ref|YP_004596606.1| 347 E 347
                                       4 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.042
                            AAA_23 121 isellgskkiilnlilflgqer..................feefelkdkkerleelekeleeledekkllekl.... 175
                                       +++l +++k++ nl+    + +                   +++e k+ k+  +  ++elee+e e+  le++    
  gi|336253499|ref|YP_004596606.1| 455 LDTLAEREKRQYNLSHVTVDRNktdgyyiqvgksaadgvpDHYEEIKTLKNSKRFTTDELEEKEREILRLEEQrgdl 531
                                       44444444443333322222223333333333333444442233333333333333333333333333333332322 PP

                            AAA_23 176 .....eqekekekeleeleeel 192
                                            e          el+ee 
  gi|336253499|ref|YP_004596606.1| 532 eyelfE----------ELREEV 543
                                       221322..........333333 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00073
                            AAA_23  17 F.........skgltlItGpNGaGKTTil 36 
                                       F         ++g+ ++tGpN +GK+T +
  gi|336253499|ref|YP_004596606.1| 602 FvpndvemdeDRGFLVVTGPNMSGKSTYM 630
                                       444444555599***************77 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   0.00024      0.47       3      74 ..     614     702 ..     612     722 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell.........vkkesilyinldderd...kkladpe....kllelileklke. 62 
                                         lv+tG+  +GK+t+++q++   l         +k+ +i  ++    r    ++l   +    +++ ++ e+ ++ 
  gi|336253499|ref|YP_004596606.1| 614 GFLVVTGPNMSGKSTYMRQVACIVLlaqigsfvpAKDAEIGLVDGIFTRVgalDEL---AqgrsTFMVEMSEL-SNi 686
                                       579*****************876665555555443333333333333333333111...11222233333332.112 PP

                            AAA_14  63 ....ekktylflDEiq 74 
                                            ++++++lDE+ 
  gi|336253499|ref|YP_004596606.1| 687 lhtaTEDSLVILDEVG 702
                                       3345677888888875 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 ?   10.9   0.0   0.00014      0.28      17      39 ..     607     630 ..     600     643 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                            AAA_29  17 ieidlkg.atlltGpsGsGKSTll 39 
                                       +e+d++  + ++tGp+ sGKST +
  gi|336253499|ref|YP_004596606.1| 607 VEMDEDRgFLVVTGPNMSGKSTYM 630
                                       56665555999***********76 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       2.8   5.6e+03      70      82 ..     318     330 ..     279     350 .. 0.57
   2 ?   13.8   6.0   3.1e-05     0.062       9      92 ..     432     543 ..     431     570 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.8
                            APG6_N  70 Lkelekereelea 82 
                                       L+ le+ +e+++a
  gi|336253499|ref|YP_004596606.1| 318 LETLEQRQESVAA 330
                                       2333332222222 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.1e-05
                            APG6_N   9 lLleeldkqleqaekerdaYeeflkklkkekkeeek............................qdeeleeleeele 57 
                                       lL  ++d +l+++ + +++ +e l++l +++k + +                            + ee++ l+++ +
  gi|336253499|ref|YP_004596606.1| 432 LLTRGYDPELDEVIERHEEVREWLDTLAEREKRQYNlshvtvdrnktdgyyiqvgksaadgvpdHYEEIKTLKNSKR 508
                                       67889999*******************999776544999******************77777777777777777777 PP

                            APG6_N  58 klekeeeelleeLkelekereeleaelaaleeele 92 
                                        + +e ee+++e+ +le++r +le el +  +e+ 
  gi|336253499|ref|YP_004596606.1| 509 FTTDELEEKEREILRLEEQRGDLEYELFEELREEV 543
                                       77777777777777777777777766633333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (892 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.44
# Mc/sec: 6138.99
//
Query:       gi|336253500|ref|YP_004596607.1|  [L=499]
Description: methyl-accepting chemotaxis sensory transducer [Halopiger xanaduensis SH-6]
Scores for complete 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-46  158.7  48.4    5.6e-44  150.0  24.7    3.4  3  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
    4.4e-09   36.4   0.1    1.6e-08   34.6   0.0    2.1  1  Protoglobin     Protoglobin
    4.4e-07   30.1  35.0      0.013   15.7   3.4    5.1  4  DUF948          Bacterial protein of unknown function (DUF948
    6.2e-06   26.3  29.3     0.0064   16.5   1.9    4.4  4  DUF1664         Protein of unknown function (DUF1664)
    5.5e-05   23.2  35.0      0.061   13.3   4.3    4.9  5  Laminin_II      Laminin Domain II
    0.00021   21.6  21.2       0.63   10.5   4.0    5.2  5  DASH_Dad2       DASH complex subunit Dad2
     0.0042   16.1   3.9     0.0042   16.1   3.9    3.2  2  IFT57           Intra-flagellar transport protein 57
     0.0065   16.7   7.0         14    6.0   0.1    5.0  5  KxDL            Uncharacterized conserved protein
     0.0071   15.3  31.5      0.015   14.2   6.0    3.1  3  Spc7            Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.011   16.0  29.0       0.35   11.2   0.1    5.5  5  BLOC1_2         Biogenesis of lysosome-related organelles com
      0.015   15.7   9.0          4    7.9   0.2    4.6  5  Syntaxin_2      Syntaxin-like protein
      0.015   15.2   6.5        1.8    8.5   0.2    3.4  3  STAT_alpha      STAT protein, all-alpha domain
      0.016   14.5  17.3       0.13   11.6   3.1    3.3  3  CorA            CorA-like Mg2+ transporter protein
      0.028   14.1  26.7      0.091   12.5   4.9    3.4  3  DUF745          Protein of unknown function (DUF745)
      0.031   13.4  17.9        3.5    6.7   0.1    4.5  4  RmuC            RmuC family
      0.032   14.3   0.1      0.032   14.3   0.1    4.7  4  Mod_r           Modifier of rudimentary (Mod(r)) protein
      0.049   13.7  26.1          1    9.4   2.2    5.5  5  COG2            COG (conserved oligomeric Golgi) complex comp
      0.055   14.2   8.8       0.72   10.6   0.1    4.7  4  RecG_N          RecG N-terminal helical domain
      0.078   12.8   6.5        0.2   11.5   0.2    2.9  3  Yuri_gagarin    Yuri gagarin
      0.091   12.5   0.6       0.31   10.8   0.6    1.9  1  SHOCT           Short C-terminal domain
       0.11   12.9  18.8      0.079   13.4   0.9    4.3  3  DUF4200         Domain of unknown function (DUF4200)
       0.14   12.0   7.8         70    3.3   0.0    6.0  6  DASH_Dam1       DASH complex subunit Dam1
       0.26   11.9  27.9       0.52   10.9   1.6    5.0  4  Syntaxin-6_N    Syntaxin 6, N-terminal
       0.26   10.5  27.1        1.5    8.0   8.4    2.9  3  ISG65-75        Invariant surface glycoprotein
       0.29   10.4  11.3       0.78    8.9   1.1    2.8  2  TMPIT           TMPIT-like protein
        0.3   10.9   5.4        1.4    8.7   3.3    2.8  1  Sec5            Exocyst complex component Sec5
       0.31   11.0   4.9        5.1    7.1   1.9    3.0  2  DUF489          Protein of unknown function (DUF489)
       0.46   10.7  27.9       0.54   10.5   8.6    3.6  3  ATG16           Autophagy protein 16 (ATG16)
       0.48   10.2  17.6        3.6    7.4   0.6    4.9  5  Bacillus_HBL    Bacillus haemolytic enterotoxin (HBL)
       0.75   10.0  12.8       0.89    9.7   0.2    3.8  3  CREPT           Cell-cycle alteration and expression-elevated
       0.76    9.7   5.0        1.5    8.7   0.1    3.0  3  Lipoprotein_20  YfhG lipoprotein
       0.77    9.9  17.4        2.1    8.5   0.5    4.1  5  Fib_alpha       Fibrinogen alpha/beta chain family
       0.81    9.7   6.4         14    5.6   0.2    4.0  4  ApoO            Apolipoprotein O
       0.83    9.5  26.0         12    5.7  12.7    3.9  3  CheZ            Chemotaxis phosphatase, CheZ
       0.86    8.4  17.7          1    8.2   2.1    3.7  4  Fmp27_WPPW      RNA pol II promoter Fmp27 protein domain
        0.9    9.4  15.5         20    5.0   0.8    5.0  5  Sec34           Sec34-like family
       0.93    9.6  15.2        3.4    7.8   0.3    5.7  4  HisKA           His Kinase A (phospho-acceptor) domain
       0.94   10.0  20.2        3.8    8.0   3.2    3.6  4  FlgN            FlgN protein
       0.97    8.9  11.6       0.54    9.7   1.1    3.3  3  Allexi_40kDa    Allexivirus 40kDa protein
        1.7    7.6   5.8        2.6    7.0   0.9    2.3  2  Atg14           Vacuolar sorting 38 and autophagy-related sub
          2    7.4  28.4       0.27   10.3   4.3    3.0  2  APG17           Autophagy protein Apg17
        3.4    7.0  21.3        3.7    6.9   5.1    2.4  2  HMMR_N          Hyaluronan mediated motility receptor N-termi
        3.8    5.3  13.7        1.6    6.6   1.1    2.5  3  Prominin        Prominin
        4.9    7.2  31.7        3.5    7.7  13.7    3.8  2  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
        5.9    6.5  24.4        2.5    7.8   2.5    4.3  5  LXG             LXG domain of WXG superfamily
        5.9    7.2  26.9        5.9    7.2   3.3    6.0  7  WXG100          Proteins of 100 residues with WXG
        6.4    4.5  17.1        1.2    6.9   3.7    2.4  3  Nup88           Nuclear pore component
        7.8    7.2  21.3       0.16   12.6   2.3    4.2  4  Cytochrom_B562  Cytochrome b562
        8.4    4.9  24.9        1.6    7.3   7.2    2.3  2  AAA_13          AAA domain
        8.7    6.1   9.0       0.94    9.2   0.5    2.8  2  Dna2            DNA replication factor Dna2
        8.8    6.0  12.9       0.37   10.5   1.2    3.0  4  SHE3            SWI5-dependent HO expression protein 3


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   7.1     2e-05    0.0069      97     170 ..     212     282 ..     191     284 .. 0.77
   2 !  150.0  24.7   1.6e-46   5.6e-44       2     168 ..     289     455 ..     281     459 .. 0.90
   3 ?    2.9   2.0      0.24        85      73      99 ..     462     487 ..     459     496 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2e-05
                                       .............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  97 eiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveevak 170
                                        + ++ +d+ve le+  +r+  g+e++++ ++   e ++++ae+a+++++++a++ee+++  eev+ + e+ ++
  gi|336253500|ref|YP_004596607.1| 212 SVRADLEDTVEELEDYAERIGDGTETIDDVAT---EQSSSTAEIASEMSNLSATVEEIASNTEEVSATAERAEE 282
                                       46677788888888888888888877776554...456789999999999999999999999999999888776 PP

  == domain 2  score: 150.0 bits;  conditional E-value: 1.6e-46
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHH CS
                         MCPsignal   2 dlaeeaseeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVr 78 
                                       d+ae a ++ e  +    +v +++e++++ ++ i +i++Vi++iadQTNlLALNA+iEAA AGe+G+GFaVVAdEV+
  gi|336253500|ref|YP_004596607.1| 289 DTAERAIDKMEGVQDAAGEVTEDVEDLREGVQRIDEIVDVINDIADQTNLLALNASIEAATAGEAGDGFAVVADEVK 365
                                       344444444444455566677778888888*********************************************** PP

                                       HHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  79 kLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqs 155
                                       +LAe+s++ a  ie+++ +iq++++++vesle+++ +++ g+elve+t e+l ei +av+e a+ v+e+a+a+++q+
  gi|336253500|ref|YP_004596607.1| 366 NLAEESQEEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDEVATATDDQA 442
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHH CS
                         MCPsignal 156 asieevnqaveev 168
                                       as ee++   +ev
  gi|336253500|ref|YP_004596607.1| 443 ASTEEIAGMADEV 455
                                       ******9877665 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHHHHHHH.... CS
                         MCPsignal  73 VAdEVrkLAersaqaakeiealiieiq 99 
                                       VA EV +LAe s +  ++++ +  e++
  gi|336253500|ref|YP_004596607.1| 462 VAAEVESLAEVSEDVERQVQVVT-EMV 487
                                       77788888888888777776655.333 PP

>> Protoglobin  Protoglobin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   4.5e-11   1.6e-08       3     149 ..      22     192 ..      20     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 4.5e-11
                                       HHHHHHHHHTT-SHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSHHHHHHHCHHC.HHHHHHHHHHHHHHHCCCSS CS
                       Protoglobin   3 arlayllsflglteedlaaLralapliealipavvdafYekllsfpetarifetss.qierlkdflksyllklfsgp 78 
                                       a+++++++f+g+  ed+++L + a l e   +++ d+ Ye+++s  ++ ++f  s+ + ++ k+  ++yl+ + +g+
  gi|336253500|ref|YP_004596607.1|  22 ASVDRVKEFVGFGPEDERRLESQAHLFERVSDDLADEYYENVRSRRKLDEAFAASAlSEAEFKREHRQYLEAFGEGD 98 
                                       68999************************************************966145689*************** PP

                                       CCHHHHHHHHHHHHHHCHCT--HHHHHHCHHHHHHHHHHHHCCCS........................-SHHHHHH CS
                       Protoglobin  79 fdsayveyldkvGkmhtrlgleprwyiaalglvqevllealleke.......................klsaaekta 132
                                       + +a++e++ + + +   +   +  y++ + ++ e+lle ++++                        +   +e  +
  gi|336253500|ref|YP_004596607.1|  99 YGPAFFERRAEFSPADLFVEPGLNEYVGSYMVYYEQLLEEIADEVtaeyapdpgaeatgdepdaaaavEDAVDETVE 175
                                       ***********976544333334689999999999999999999988889999999999999999988888888888 PP

                                       HHHHHHHHHHHHHHHHC CS
                       Protoglobin 133 lvkalnKliwldndlal 149
                                          +  +l++ld+++++
  gi|336253500|ref|YP_004596607.1| 176 RTLSTLRLAVLDQQFVI 192
                                       88888899999998887 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 !    8.7   0.9    0.0059       2.1      27      75 ..     195     243 ..     173     268 .. 0.58
   2 !    9.4   5.5    0.0036       1.3      28      87 ..     256     315 ..     244     342 .. 0.60
   3 !   15.7   3.4   3.7e-05     0.013      20      86 ..     360     426 ..     356     429 .. 0.83
   4 !   10.7   5.1    0.0014       0.5      29      83 ..     439     496 ..     431     498 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0059
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvdplte 75 
                                        +d + +++++++++ +++  ++ed++++ ++ +e + + +e++d + +
  gi|336253500|ref|YP_004596607.1| 195 KVDDFMEQLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDVAT 243
                                       4566666666666666666666666666666655555554444444433 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0036
                            DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       +++++at+ee+ +++++++  +e++ + + e+++  ++ ++k++ + +a+++++e v++l
  gi|336253500|ref|YP_004596607.1| 256 MSNLSATVEEIASNTEEVSATAERAEEIAGETTDTAERAIDKMEGVQDAAGEVTEDVEDL 315
                                       555666666666555555555555555555555555555555555555555555555555 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 3.7e-05
                            DUF948  20 vllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       v  ++k++++e ++  +++e+ v++i ++++++++  ++  +++ + +e v+  +e+++++ ++vse
  gi|336253500|ref|YP_004596607.1| 360 VADEVKNLAEESQEEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSE 426
                                       555677778888888888888888888888888888888888***********************98 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.0014
                            DUF948  29 deaaatieelekqvdpilkevedllakvne...lledvneklekvdplteavadlges 83 
                                       d  aa+ ee+   +d+++++++++ a+v+    + edv+++++ v ++++ +ad+ e+
  gi|336253500|ref|YP_004596607.1| 439 DDQAASTEEIAGMADEVMENADQVAAEVESlaeVSEDVERQVQVVTEMVDRLADVQEN 496
                                       555566666666667777777777666666444889******************9887 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.9   1.8e-05    0.0064      26     112 ..     194     279 ..     180     288 .. 0.88
   2 !    8.1   0.8    0.0076       2.7      70     110 ..     293     333 ..     278     340 .. 0.82
   3 ?    7.5   2.9     0.012       4.1      62     114 ..     365     418 ..     355     426 .. 0.74
   4 !    9.7   2.7    0.0023      0.82      58     111 ..     435     488 ..     418     495 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-05
                           DUF1664  26 wklsdlmfvTkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseiged 102
                                        k+ d+m     s+++  esv  +le+  e+l++  +++ +  +++d+   eq+  ++ei++e+++++  ++ei ++
  gi|336253500|ref|YP_004596607.1| 194 SKVDDFME-QLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATVEEIASN 269
                                       56666664.346999999**********************************************************9 PP

                           DUF1664 103 vesvkeaveg 112
                                        e+v+++ e 
  gi|336253500|ref|YP_004596607.1| 270 TEEVSATAER 279
                                       9999988765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0076
                           DUF1664  70 rvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                       r  +k++ +++++ e++e+v+++re++++i+e v+ ++++ 
  gi|336253500|ref|YP_004596607.1| 293 RAIDKMEGVQDAAGEVTEDVEDLREGVQRIDEIVDVINDIA 333
                                       45568888889999999999999999999999999998775 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.012
                           DUF1664  62 rhLssridrvdkkldeq.keiskeikeevtevredlseigedvesvkeavegle 114
                                       ++L+++ ++  ++++ + ++i+++++e v+++++  +ei++ ve v+++ve+l+
  gi|336253500|ref|YP_004596607.1| 365 KNLAEESQEEAATIERMvNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLG 418
                                       555555555566666652467888999999999999999999999999999986 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0023
                           DUF1664  58 aatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       a++ ++ ++  +++    de++e + ++++ev+++ e  ++++++v+ v e+v 
  gi|336253500|ref|YP_004596607.1| 435 ATATDDQAASTEEIAGMADEVMENADQVAAEVESLAEVSEDVERQVQVVTEMVD 488
                                       222233333333444444555555555555555555555555555555555555 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.15        53      14      57 ..     198     241 ..     184     247 .. 0.57
   2 !    9.8   6.1    0.0022      0.76       6      72 ..     250     316 ..     235     334 .. 0.54
   3 !    8.5   0.4    0.0053       1.9       4      56 ..     290     342 ..     287     353 .. 0.83
   4 !   13.3   4.3   0.00017     0.061       1      62 [.     364     425 ..     364     426 .. 0.94
   5 !    8.9   5.2     0.004       1.4       4      73 ..     423     492 ..     420     496 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.15
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  14 evleqlaplsqnlentkeklseinrsveetnekvkdankairdA 57 
                                          eqla + q+ e ++++l+   +++e   e + d +++i+d+
  gi|336253500|ref|YP_004596607.1| 198 DFMEQLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDV 241
                                       33445555555555555555555555555555555555555555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0022
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXX--TTTTTG CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvk...dankairdArrsvkkLeklapqLl 72 
                                       ae+ + +++  + +++++ n+e++++ ++++++ + et++ ++   d++++++dA  +   +++ +++L 
  gi|336253500|ref|YP_004596607.1| 250 AEIASEMSNLSATVEEIASNTEEVSATAERAEEIAGETTDTAEraiDKMEGVQDAAGE---VTEDVEDLR 316
                                       4555555666666666666666666666555555555555555222444444444443...334444443 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0053
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankaird 56 
                                       +a+ a ++++ v++   ++ +++e ++e +++i++ v+ +n+ +++ n     
  gi|336253500|ref|YP_004596607.1| 290 TAERAIDKMEGVQDAAGEVTEDVEDLREGVQRIDEIVDVINDIADQTNLLALN 342
                                       68888899999999999999999999999999999999999988887765554 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00017
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   1 skelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvk 62 
                                       +k+la+e +e a+ +++ ++++++++++t e+l+ +n++++   e+v+d  + + + +++v+
  gi|336253500|ref|YP_004596607.1| 364 VKNLAEESQEEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVS 425
                                       599********************************************999999988888876 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.004
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGG CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLld 73 
                                        ++ea + + ev   + + ++ +e++   + e+ ++++++ ++v+++ ++ +d++r+v+ +++ +++L d
  gi|336253500|ref|YP_004596607.1| 423 AVSEAASGVDEVATATDDQAASTEEIAGMADEVMENADQVAAEVESLAEVSEDVERQVQVVTEMVDRLAD 492
                                       57899999999999999*9**********************************************99976 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.013       4.7      20      49 ..     213     242 ..     194     247 .. 0.82
   2 !    8.5   0.7    0.0078       2.7      19      50 ..     247     278 ..     243     303 .. 0.84
   3 ?    3.1   0.4      0.36   1.3e+02      29      73 ..     306     360 ..     289     382 .. 0.57
   4 !   10.5   4.0    0.0018      0.63      16      79 ..     381     444 ..     366     458 .. 0.76
   5 ?    0.8   0.1       1.9   6.5e+02      14      40 ..     466     492 ..     461     496 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.013
                         DASH_Dad2  20 lsdslakqleeLeeklstladgteavasVl 49 
                                       + ++l++ +eeLe+  + + dgte++ +V 
  gi|336253500|ref|YP_004596607.1| 213 VRADLEDTVEELEDYAERIGDGTETIDDVA 242
                                       55789*********************9996 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0078
                         DASH_Dad2  19 dlsdslakqleeLeeklstladgteavasVla 50 
                                       + ++++a+++++L+  ++++a++te v++  +
  gi|336253500|ref|YP_004596607.1| 247 SSTAEIASEMSNLSATVEEIASNTEEVSATAE 278
                                       5799***********************97655 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.36
                         DASH_Dad2  29 eeLeeklstladgteavasVlanWqnvlraismaslkllqkaee..........e 73 
                                        e+ e ++ l++g + + ++++  + +    ++  l+   +a++           
  gi|336253500|ref|YP_004596607.1| 306 GEVTEDVEDLREGVQRIDEIVDVINDIADQTNLLALNASIEAATageagdgfavV 360
                                       4566777888888888888888877777666665544332222234445555551 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.0018
                         DASH_Dad2  16 qlrdlsdslakqleeLeeklstladgteavasVlanWqnvlraismaslkllqkaeeeaeeeee 79 
                                        ++++ ++ ++ +e+Le+  ++++dg e v++ ++n  ++  a+s a +++ + a++++++ ++
  gi|336253500|ref|YP_004596607.1| 381 MVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDEVATATDDQAAS 444
                                       467788889999**************************************97444433322222 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 1.9
                         DASH_Dad2  14 LkqlrdlsdslakqleeLeeklstlad 40 
                                        + l ++s+++++q++ + e ++ lad
  gi|336253500|ref|YP_004596607.1| 466 VESLAEVSEDVERQVQVVTEMVDRLAD 492
                                       567889999999999999999998887 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   3.9   1.2e-05    0.0042     204     322 ..     174     299 ..     168     332 .. 0.66
   2 ?    1.1   9.3      0.43   1.5e+02     224     313 ..     380     468 ..     360     496 .. 0.39

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
                             IFT57 204 leRvlpqLkv.......tikadakdWrahleqmkkhkksieeslpetksqlkklhedisktlekiesr...Ekylns 270
                                       +eR l++L+         i ++  d+ ++l +m + ++s++++l++t ++l++  e i    e i      ++  + 
  gi|336253500|ref|YP_004596607.1| 174 VERTLSTLRLavldqqfVIGSKVDDFMEQLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDVateQSSSTA 250
                                       677777777766666655566677********************************997666666555000555555 PP

                             IFT57 271 qleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqeme 322
                                       ++ +++++++++ ee+++ +e+++   e+ +e      e+++  e++  +me
  gi|336253500|ref|YP_004596607.1| 251 EIASEMSNLSATVEEIASNTEEVSATAERAEEIAG---ETTDTAERAIDKME 299
                                       55555555555555555555555555555555544...55555555555554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.43
                             IFT57 224 ahleqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegv 300
                                       + ++q+++  ++  esl++++ ++++  e ++ t+e++ + E+ + +   + ++e  +a +  ++ +e++  + ++v
  gi|336253500|ref|YP_004596607.1| 380 RMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEA-ASGVDEVATATDDQAASTEEIAGMADEV 455
                                       223333333333334444444444444444444444444444444322.2223333333333333333333333333 PP

                             IFT57 301 seltrelaeisee 313
                                       +e  ++ a   e 
  gi|336253500|ref|YP_004596607.1| 456 MENADQVAAEVES 468
                                       3333333333333 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0       0.6   2.1e+02      42      71 ..     195     224 ..     182     233 .. 0.73
   2 ?    2.7   0.2      0.43   1.5e+02       9      61 ..     236     288 ..     234     305 .. 0.86
   3 ?   -0.3   0.1       3.8   1.3e+03      37      75 ..     285     323 ..     255     336 .. 0.66
   4 ?    6.0   0.1     0.041        14      26      71 ..     379     424 ..     361     429 .. 0.70
   5 ?    5.1   0.0     0.081        28      41      69 ..     467     495 ..     432     497 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.6
                              KxDL  42 rlaklrarfkqgtkllkevkkdLesifkki 71 
                                       ++ ++ +++++ t+   +v++dLe + + +
  gi|336253500|ref|YP_004596607.1| 195 KVDDFMEQLASMTQRRESVRADLEDTVEEL 224
                                       566677788888888888888888776655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.43
                              KxDL   9 edldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevk 61 
                                       e++d +   Q+   +++ ++   L++  ++  +  ++++a  ++  + + e+ 
  gi|336253500|ref|YP_004596607.1| 236 ETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTEEVSATAERAEEIAGETT 288
                                       678999999************************99999999999888877765 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 3.8
                              KxDL  37 alsqerlaklrarfkqgtkllkevkkdLesifkkirslk 75 
                                        ++    +++ ++++  + ++ ev +d e +++ ++++ 
  gi|336253500|ref|YP_004596607.1| 285 GETTDTAERAIDKMEGVQDAAGEVTEDVEDLREGVQRID 323
                                       444455555566666666667777777777766666654 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.041
                              KxDL  26 nkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkki 71 
                                       +   ++++e  +++ e l++++a++ +g++l+ ++ ++L  i   +
  gi|336253500|ref|YP_004596607.1| 379 ERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAV 424
                                       4444455555666667788888888888888888888888877666 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.081
                              KxDL  41 erlaklrarfkqgtkllkevkkdLesifk 69 
                                       e la+++++++++++++ e+ + L  +++
  gi|336253500|ref|YP_004596607.1| 467 ESLAEVSEDVERQVQVVTEMVDRLADVQE 495
                                       57899999999999999999999988875 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3       1.7     6e+02     153     189 ..      36      73 ..      35      94 .. 0.70
   2 !   14.2   6.0   4.2e-05     0.015     134     282 ..     207     326 ..     176     348 .. 0.54
   3 !   11.0  11.6   0.00041      0.14     135     248 ..     380     495 ..     362     497 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.7
                              Spc7 153 edkelLekqeeeldellpeleeekaeleeeleklqe.a 189
                                       ed+++Le+q ++++++ ++l  e+ e  +  +kl e +
  gi|336253500|ref|YP_004596607.1|  36 EDERRLESQAHLFERVSDDLADEYYENVRSRRKLDEaF 73 
                                       79999999999999999999888776666666666632 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.2e-05
                              Spc7 134 mqllegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelae 210
                                       +q  e+++  le+++e+le+ +e++ +  e +d++  e ++  ae                             +a+
  gi|336253500|ref|YP_004596607.1| 207 TQRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAE-----------------------------IAS 254
                                       233334444444444444444444444444444444444444444.............................444 PP

                              Spc7 211 lkaeieekkkelaelqeqleeleekieelkeqkse.leeeiaeaervleeckgwsesevsrlkeevkaleelt 282
                                        ++++++  +e+a+ +e++ + +e+ ee++ + ++ +e +i + e v+++  +++ ++v+ l+e v++++e+ 
  gi|336253500|ref|YP_004596607.1| 255 EMSNLSATVEEIASNTEEVSATAERAEEIAGETTDtAERAIDKMEGVQDAAGEVT-EDVEDLREGVQRIDEIV 326
                                       4444444444555555555555555555544433303344555555444444433.45555555555555544 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00041
                              Spc7 135 qllegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles..idkeeLeelreela 209
                                       +++++++e  +e++e+le+ ++++++  e++++ +++l e +++++e +    e a+  ++     ee++ + +e+ 
  gi|336253500|ref|YP_004596607.1| 380 RMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDEVATATDDqaASTEEIAGMADEVM 456
                                       57999*********************************************99998877776335599********** PP

                              Spc7 210 elkaeieekkkelaelqeqleeleekieelkeqkselee 248
                                       e+  ++++  + lae+ e++e++ + ++e+ ++ ++++e
  gi|336253500|ref|YP_004596607.1| 457 ENADQVAAEVESLAEVSEDVERQVQVVTEMVDRLADVQE 495
                                       *************************99999999998887 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 ?    4.3   0.2      0.15        51      61      91 ..     200     231 ..     191     235 .. 0.67
   2 ?    4.0   0.4      0.17        60      28      71 ..     241     284 ..     233     290 .. 0.67
   3 ?   11.2   0.1     0.001      0.35      30      79 ..     292     341 ..     288     345 .. 0.90
   4 ?    5.6   4.0     0.056        20      42      93 ..     360     412 ..     352     415 .. 0.84
   5 ?    5.4   1.7     0.065        23      38      84 ..     444     490 ..     414     496 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.15
                           BLOC1_2  61 qpylqqidqiekqv.teLeeavseLDeyskeL 91 
                                        ++l ++ q  ++v ++Le++v+eL+ y  ++
  gi|336253500|ref|YP_004596607.1| 200 MEQLASMTQRRESVrADLEDTVEELEDYAERI 231
                                       55555555556666247888888888887765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.17
                           BLOC1_2  28 lNeaasekykklkdvaaslekkleklnekyeelqpylqqidqie 71 
                                       + +++s+  +++++++++l++++e++ +  ee++   ++ ++i 
  gi|336253500|ref|YP_004596607.1| 241 VATEQSSSTAEIASEMSNLSATVEEIASNTEEVSATAERAEEIA 284
                                       55666777777777777777777777777777777666666665 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.001
                           BLOC1_2  30 eaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                       e+a+ k + ++d+a ++++++e+l+e  + +++ ++ i++i +q++ L  
  gi|336253500|ref|YP_004596607.1| 292 ERAIDKMEGVQDAAGEVTEDVEDLREGVQRIDEIVDVINDIADQTNLLAL 341
                                       678899999**********************************9987765 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.056
                           BLOC1_2  42 vaaslekkleklnekyeelqpylqqid.qiekqvteLeeavseLDeyskeLEa 93 
                                       va+++++ +e+ +e+ ++++ +++qi+ + +++v++Le+a +e+D  +   E+
  gi|336253500|ref|YP_004596607.1| 360 VADEVKNLAEESQEEAATIERMVNQIQeDTQETVESLEDANAEIDDGVELVED 412
                                       67788888999999999*********7369999*******9999988777776 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.065
                           BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseL 84 
                                       + +++a  + + +e+ ++  +e++++ +  +++e+qv+  +e+v++L
  gi|336253500|ref|YP_004596607.1| 444 STEEIAGMADEVMENADQVAAEVESLAEVSEDVERQVQVVTEMVDRL 490
                                       33444444444444444444455555555555555555555555555 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.088        31      14      70 ..     195     252 ..     188     280 .. 0.70
   2 ?    2.7   0.6      0.45   1.6e+02      26      44 ..     310     331 ..     246     351 .. 0.52
   3 ?    3.6   1.4      0.24        85       9      60 ..     316     389 ..     308     407 .. 0.45
   4 ?    7.9   0.2     0.011         4      12      61 ..     375     422 ..     364     430 .. 0.77
   5 ?    5.6   0.0     0.057        20       3      68 ..     415     481 ..     413     496 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.088
                        Syntaxin_2  14 tleklvkqLgtkk.dteelreklhelieeinelikktnellkklsqldnsssdsqqkl 70 
                                       + + +++qL + +   e +r  l++++ee+ + ++++ +  + ++ ++  +s+s+  +
  gi|336253500|ref|YP_004596607.1| 195 KVDDFMEQLASMTqRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEI 252
                                       4555666666664147889999999999999999999999999998888776653333 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.45
                        Syntaxin_2  26 kdteelr...eklhelieeine 44 
                                        d e+lr   ++++e+++ in+
  gi|336253500|ref|YP_004596607.1| 310 EDVEDLRegvQRIDEIVDVIND 331
                                       2344444333444455555555 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.24
                        Syntaxin_2   9 nsnvstleklvkqLgtkkdteelr......................eklhelieeinelikktnellkklsqld 60 
                                        + v+ +++ v+ +++  d+++l                       +++++l ee +e + ++++ ++++++++
  gi|336253500|ref|YP_004596607.1| 316 REGVQRIDEIVDVINDIADQTNLLalnasieaatageagdgfavvaDEVKNLAEESQEEAATIERMVNQIQEDT 389
                                       44444444444444444444444444444444444444444444443333333333333333333333333333 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.011
                        Syntaxin_2  12 vstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldn 61 
                                         t+e++v+q++   dt+e+ e+l++   ei + ++ +++ +++l +++ 
  gi|336253500|ref|YP_004596607.1| 375 AATIERMVNQIQE--DTQETVESLEDANAEIDDGVELVEDTVENLGEIET 422
                                       689********98..68888888888888888888887777777777765 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.057
                        Syntaxin_2   3 snlqkinsnvstleklvkqLgtkkd.teelreklhelieeinelikktnellkklsqldnsssdsqq 68 
                                       +nl +i + vs+  + v+ + t++d +    e++  + +e+ e + ++ + +++l+++++  + + q
  gi|336253500|ref|YP_004596607.1| 415 ENLGEIETAVSEAASGVDEVATATDdQAASTEEIAGMADEVMENADQVAAEVESLAEVSEDVERQVQ 481
                                       789999*****************86444445555555555555555555555555555554443333 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.5      0.09        32       4      83 ..     196     274 ..     193     303 .. 0.59
   2 ?    8.5   0.2     0.005       1.8       3      87 ..     307     404 ..     305     422 .. 0.72
   3 ?    4.0   0.0      0.11        40     113     149 ..     454     490 ..     445     498 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.09
                        STAT_alpha   4 ieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkl.......eqeraesekkelkkqkellqqmlnaLdqkRk 73 
                                       +++ +e+l s++q+ e+   +Led+ ee++ +y e            +++++s+++e++ ++ +l +++++      
  gi|336253500|ref|YP_004596607.1| 196 VDDFMEQLASMTQRRESVRADLEDTVEELE-DYAERIGDgtetiddVATEQSSSTAEIASEMSNLSATVEE------ 265
                                       667789999999999999999999998888.6666555534445552333333334455555555555555...... PP

                        STAT_alpha  74 elvdklkell 83 
                                        ++++++e+ 
  gi|336253500|ref|YP_004596607.1| 266 -IASNTEEVS 274
                                       .333333332 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.005
                        STAT_alpha   3 eieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkl.............eqeraesekkelkkqkellqqmln 66 
                                       e+++ +e+lr+ vq++++ +  ++d  ++ ++   + + +              ++++++  +e +++ +++++m+n
  gi|336253500|ref|YP_004596607.1| 307 EVTEDVEDLREGVQRIDEIVDVINDIADQTNLLALNASIEaatageagdgfavVADEVKNLAEESQEEAATIERMVN 383
                                       67788999999999988888877776654444444433334456777777777555566666667899999999999 PP

                        STAT_alpha  67 aLdqkRkelvdklkellnlle 87 
                                       ++++  +e+v+ l++   +++
  gi|336253500|ref|YP_004596607.1| 384 QIQEDTQETVESLEDANAEID 404
                                       999999999998887666655 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.11
                        STAT_alpha 113 pfnesLDqlqkwfealaeliwqlrqqlkkleelrqkl 149
                                         +e+ Dq    +e+lae+   + +q++ + e+  +l
  gi|336253500|ref|YP_004596607.1| 454 EVMENADQVAAEVESLAEVSEDVERQVQVVTEMVDRL 490
                                       456799999999****************999999998 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       1.2   4.3e+02     100     128 ..      36      64 ..      17      88 .. 0.81
   2 ?   11.6   3.1   0.00036      0.13     116     223 ..     217     327 ..     195     341 .. 0.76
   3 ?    9.0   3.4    0.0023       0.8      94     223 ..     360     491 ..     352     497 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.2
                              CorA 100 deggkpkspgellyrlldeivdrlfelle 128
                                       +++++ +s ++l++r+ d ++d++ e ++
  gi|336253500|ref|YP_004596607.1|  36 EDERRLESQAHLFERVSDDLADEYYENVR 64 
                                       45688999999999999999999999887 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00036
                              CorA 116 ldeivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrlla.kaddklldde 189
                                       l+  v++l+++ e + + ++ ++d    ++s+++ei++e+++l  ++ ++ +   +  ++ +r  +  +++    + 
  gi|336253500|ref|YP_004596607.1| 217 LEDTVEELEDYAERIGDGTETIDDVAteQSSSTAEIASEMSNLSATVEEIASNTEEVSATAERAEEiAGETTDTAER 293
                                       56778889999999999999999999999999999999999999998888777777777774444453333333333 PP

                              CorA 190 dkeylrdlldelerllemlealrerleslqdtys 223
                                       + + ++ ++d +  + e++e lre ++++ ++  
  gi|336253500|ref|YP_004596607.1| 294 AIDKMEGVQDAAGEVTEDVEDLREGVQRIDEIVD 327
                                       3344888888888899999999999999888764 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0023
                              CorA  94 vikrlkdeggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapn 170
                                       v++++k+  ++ +  +  ++r +++i ++  e++e le+   e++d +  +  ++ ++ l ++++ + +  + + + 
  gi|336253500|ref|YP_004596607.1| 360 VADEVKNLAEESQEEAATIERMVNQIQEDTQETVESLEDANAEIDDGV--ELVEDTVENLGEIETAVSEAASGVDEV 434
                                       66777778899999999*******************************..555556666666666666665555555 PP

                              CorA 171 revlkrlla.kaddkllddedkeylrdlldeler...llemlealrerleslqdtys 223
                                        ++ ++  a +++   + de +e+ +++  e+e+   ++e++e + ++++ + d ++
  gi|336253500|ref|YP_004596607.1| 435 ATATDDQAAsTEEIAGMADEVMENADQVAAEVESlaeVSEDVERQVQVVTEMVDRLA 491
                                       555553333355666666666666666777777733333333333333333333333 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   4.9   0.00026     0.091      66     169 ..     216     319 ..     208     324 .. 0.93
   2 ?   12.1   4.8   0.00033      0.12      92     170 ..     361     439 ..     351     449 .. 0.90
   3 ?    0.3   3.1       1.4     5e+02     101     146 ..     444     488 ..     432     497 .. 0.39

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00026
                            DUF745  66 qleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlle 142
                                        le+ ++e e+  +++ + +++    a+  +++ +++ ++++ l+a+++++ +n e++ ++a+ a++ + e t+  e
  gi|336253500|ref|YP_004596607.1| 216 DLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTEEVSATAERAEEIAGETTDTAE 292
                                       68999999999999999999999999999999********************************************* PP

                            DUF745 143 aAkkRveeLkkqlkearkdlektkkaA 169
                                        A  ++e ++    e+ +d e+ ++  
  gi|336253500|ref|YP_004596607.1| 293 RAIDKMEGVQDAAGEVTEDVEDLREGV 319
                                       ********************9998865 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00033
                            DUF745  92 akaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektkka 168
                                       a+ +++ a++ q++++++++++++++e  +++ +  + a++e+++  +l+e+  + + e+++ ++ea +  +++  a
  gi|336253500|ref|YP_004596607.1| 361 ADEVKNLAEESQEEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDEVATA 437
                                       56678999***********************************************************9999988777 PP

                            DUF745 169 Ay 170
                                       + 
  gi|336253500|ref|YP_004596607.1| 438 TD 439
                                       65 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.4
                            DUF745 101 qaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkk 146
                                       + ++ + +  +++++a + ++++e++a+ ++++++ + q +++   
  gi|336253500|ref|YP_004596607.1| 444 STEEIAGMADEVMENADQVAAEVESLAE-VSEDVERQVQVVTEMVD 488
                                       3333333333333333333333333332.23333334443333333 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1      0.01       3.5      12      59 ..     194     241 ..     190     248 .. 0.88
   2 ?    3.9   0.8      0.07        25     231     275 ..     252     295 ..     241     335 .. 0.49
   3 ?    6.3   1.3     0.013       4.6       2      47 ..     377     422 ..     331     441 .. 0.53
   4 ?    6.2   0.4     0.013       4.7     219     268 ..     443     492 ..     434     498 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
                              RmuC  12 eklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLtka 59 
                                       +k+++f e++ ++++++++ ++ l+  ++el++ +e++gd +e++ ++
  gi|336253500|ref|YP_004596607.1| 194 SKVDDFMEQLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDV 241
                                       6889999*********************************99988765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.07
                              RmuC 231 iaellgelydkfekfgedleklgkklekaqksydkavkklegnil 275
                                       ia+++++l   +e+++ + e++    e+a++   ++ ++ e + +
  gi|336253500|ref|YP_004596607.1| 252 IASEMSNLSATVEEIASNTEEVSATAERAEEIAGETTDTAE-RAI 295
                                       44444444444444444444444444444444333222222.122 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.013
                              RmuC   2 qleellkplkeklekfeekveeeskeeaeeleslkeqlkelqelne 47 
                                        +e+++++++e  +++ e++e+ + e  +  e ++  +++l e ++
  gi|336253500|ref|YP_004596607.1| 377 TIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIET 422
                                       2333333333333333333333333333333333333333333333 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.013
                              RmuC 219 wrqeaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavk 268
                                         +e+++  a+e++e + ++  ++e+++e  e+++++++ + + +d++++
  gi|336253500|ref|YP_004596607.1| 443 ASTEEIAGMADEVMENADQVAAEVESLAEVSEDVERQVQVVTEMVDRLAD 492
                                       56788888889999999999999999999999999999888888887654 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 ?   -0.6   0.4       3.6   1.3e+03      98     121 ..      39      65 ..      38      92 .. 0.75
   2 ?    2.6   0.4      0.38   1.3e+02      26      71 ..     201     257 ..     177     265 .. 0.53
   3 ?   14.3   0.1   9.1e-05     0.032      11     104 ..     256     349 ..     245     354 .. 0.88
   4 ?   -1.9   7.3         9   3.2e+03      31      95 ..     378     442 ..     355     496 .. 0.44

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.6
                             Mod_r  98 arLqtavaeaeeeSealaeefle...g 121
                                       +rL+ +++  e  S++la+e +e   +
  gi|336253500|ref|YP_004596607.1|  39 RRLESQAHLFERVSDDLADEYYEnvrS 65 
                                       588889999999999999999874542 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.38
                             Mod_r  26 pevkqlkeekeellaeneslaeknlslep...........eleelrselqekleelk 71 
                                       +++ ++++++e+++a  e++ e+  +  +             +e++s+++e  +e+ 
  gi|336253500|ref|YP_004596607.1| 201 EQLASMTQRRESVRADLEDTVEELEDYAErigdgtetiddVATEQSSSTAEIASEMS 257
                                       555566666666666666666654444442333333333333444444444444444 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 9.1e-05
                             Mod_r  11 lledeeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldel 87 
                                       + +    +e+++++++ev +  e+ ee+  e+ ++ae+ +++ + +++   e++e  e l+e  ++ +e     +++
  gi|336253500|ref|YP_004596607.1| 256 MSNLSATVEEIASNTEEVSATAERAEEIAGETTDTAERAIDKMEGVQDAAGEVTEDVEDLREGVQRIDEIVDVINDI 332
                                       444456788899999************************************************************** PP

                             Mod_r  88 lqkfspdallarLqtav 104
                                        +++++ al a  ++a+
  gi|336253500|ref|YP_004596607.1| 333 ADQTNLLALNASIEAAT 349
                                       *****999999888876 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 9
                             Mod_r  31 lkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspda 95 
                                       ++    ++ + ++++ e+  + + e+++  + ++++ e+l e+e+++ e  +  de+   ++++a
  gi|336253500|ref|YP_004596607.1| 378 IERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDEVATATDDQA 442
                                       33333333333333333333333344444444444444444444444444444444443333333 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 ?    9.4   2.2    0.0029         1      62     118 ..     201     259 ..     184     274 .. 0.69
   2 ?    5.9   1.8     0.037        13      72     113 ..     239     280 ..     234     315 .. 0.59
   3 ?    1.9   0.1      0.64   2.3e+02      66     107 ..     300     330 ..     292     350 .. 0.48
   4 ?    8.2   1.0    0.0073       2.6      68     112 ..     379     423 ..     373     438 .. 0.90
   5 ?    3.5   2.4      0.19        68      65     104 ..     449     488 ..     429     497 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0029
                              COG2  62 ghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr..ellkl 118
                                       ++L ++ ++ e v+ +l+ +++++e+  e + +  e++++   e+++ +++   e+ +l
  gi|336253500|ref|YP_004596607.1| 201 EQLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIasEMSNL 259
                                       47888888888888888888888888888888888888888888776655543333333 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.037
                              COG2  72 eevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                       + v ++ ++ + ++ s +++ls++ ee+ s+ ee ++ +e  
  gi|336253500|ref|YP_004596607.1| 239 DDVATEQSSSTAEIASEMSNLSATVEEIASNTEEVSATAERA 280
                                       556666666666666666666666666666666655544433 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.64
                              COG2  66 glqeeleevesplaaarkkvesvreklsereeeveskleeak 107
                                       g+q++  ev+ +++ +r+ v           +++++ ++  +
  gi|336253500|ref|YP_004596607.1| 300 GVQDAAGEVTEDVEDLREGV-----------QRIDEIVDVIN 330
                                       33344444444444443333...........33333333333 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0073
                              COG2  68 qeeleevesplaaarkkvesvreklsereeeveskleeakeleek 112
                                       ++ +++++ + +++++ +e++++++++  e ve+ +e+  e+e +
  gi|336253500|ref|YP_004596607.1| 379 ERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETA 423
                                       67899*********************************9999875 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.19
                              COG2  65 vglqeeleevesplaaarkkvesvreklsereeeveskle 104
                                        g+ +e+ e   ++aa ++ + +v e ++++ + v++ ++
  gi|336253500|ref|YP_004596607.1| 449 AGMADEVMENADQVAAEVESLAEVSEDVERQVQVVTEMVD 488
                                       3444444444444444444444444444444444444444 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1     0.002      0.72       2      66 ..     196     260 ..     195     266 .. 0.93
   2 ?    0.5   0.0       2.9     1e+03      10      64 ..     281     334 ..     277     338 .. 0.71
   3 ?    1.9   0.8       1.1   3.8e+02       9      37 ..     382     403 ..     359     422 .. 0.45
   4 ?    2.5   0.0      0.72   2.5e+02       1      84 [.     409     490 ..     409     494 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHTS---TTT........HHHHHHH---GGGG-HHHH.HHHHHHHHHHTTSSSS- CS
                            RecG_N   2 iEeFLeelekllkkvlsgkleteelieeikkkleliddplleneevlkeklskfldYikpiasLp 66 
                                       + +F+e+l  + +  +s + + e+ +ee+++ +e i d      +v+ e+ s+  + ++++ +L+
  gi|336253500|ref|YP_004596607.1| 196 VDDFMEQLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLS 260
                                       78**************************************9999999999999999999999887 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.9
                                       HHHHTS---TTT........HHHHHHH---GGGG-HHHH.HHHHHHHHHHTTSSS CS
                            RecG_N  10 ekllkkvlsgkleteelieeikkkleliddplleneevlkeklskfldYikpias 64 
                                       e+++ +  ++     + +e +++ + ++ +++ +  e+  +++++++d i+ ia+
  gi|336253500|ref|YP_004596607.1| 281 EEIAGETTDTAERAIDKMEGVQDAAGEVTEDVEDLREGV-QRIDEIVDVINDIAD 334
                                       555555666666666677778888888888888888888.888888888887775 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 1.1
                                       HHHHHTS---TTT........HHHHHHH- CS
                            RecG_N   9 lekllkkvlsgkleteelieeikkkleli 37 
                                       ++++ ++ +       e +e +++   +i
  gi|336253500|ref|YP_004596607.1| 382 VNQIQEDTQ-------ETVESLEDANAEI 403
                                       122222222.......3333333333333 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.72
                                       SHHHHHHHHHHHHTS---TTT........HHHHHHH---GGGG-HHHH.HHHHHHHHHHTTSSSS-HHHHHHHHHHH CS
                            RecG_N   1 liEeFLeelekllkkvlsgkleteelieeikkkleliddplleneevlkeklskfldYikpiasLpeeRkikRlkng 77 
                                       l+E+  e+l ++  +v +    ++e+     +++   ++    + ev  e  ++    ++++a+ +e+  +  ++ +
  gi|336253500|ref|YP_004596607.1| 409 LVEDTVENLGEIETAVSEAASGVDEVATATDDQAASTEEIAGMADEVM-ENADQVAAEVESLAEVSEDV-ERQVQVV 483
                                       577777777777777777777777777777777766666666666777.77777777777777777663.4457888 PP

                                       HHHHHHH CS
                            RecG_N  78 lemiekl 84 
                                        em+++l
  gi|336253500|ref|YP_004596607.1| 484 TEMVDRL 490
                                       8888887 PP

>> Yuri_gagarin  Yuri gagarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.2      0.27        93      36     143 ..     166     277 ..     149     326 .. 0.54
   2 ?    1.4   0.7      0.66   2.3e+02      68     151 ..     309     393 ..     258     422 .. 0.66
   3 ?   11.5   0.2   0.00057       0.2      34      95 ..     376     497 ..     356     499 .] 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.27
                      Yuri_gagarin  36 vmdifeekseqeqkekeflvanerla..ceidalketl....kdrdeqikqlqsmitsysdlsennrlkeeiydlkq 106
                                       v d  +e  e++       v +++++   ++d++ e+l    + r+    +l++ +++ +d  e  r+ + +  +  
  gi|336253500|ref|YP_004596607.1| 166 VEDAVDETVERTLSTLRLAVLDQQFVigSKVDDFMEQLasmtQRRESVRADLEDTVEELEDYAE--RIGDGTETIDD 240
                                       5555555555555555555555554411344444444411112344444456666666666655..55555555566 PP

                      Yuri_gagarin 107 knceqarkvrelaeelkgeeeqrvelvdkyekllasf 143
                                         +eq+    e+a+e+ +      e+++  e+++a+ 
  gi|336253500|ref|YP_004596607.1| 241 VATEQSSSTAEIASEMSNLSATVEEIASNTEEVSATA 277
                                       6666666666666666666555555555555555544 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.66
                      Yuri_gagarin  68 ketlkdrdeqikqlqsmitsysdlsennrlkeeiydlkqknceqar.kvrelaeelkgeeeqrvelvdkyekllasf 143
                                        e ++d  e +++++++++  +d+ + + l   +  +    + +a      +a e+k+  e++ e +   e+++   
  gi|336253500|ref|YP_004596607.1| 309 TEDVEDLREGVQRIDEIVDVINDIADQTNLLALNASIEAATAGEAGdGFAVVADEVKNLAEESQEEAATIERMVNQI 385
                                       45566666667777777777777777777766666666655544431445566777777777777777777777777 PP

                      Yuri_gagarin 144 eeqckelk 151
                                       +e  +e  
  gi|336253500|ref|YP_004596607.1| 386 QEDTQETV 393
                                       66666633 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00057
                      Yuri_gagarin  34 aavmdifeekseqeqkekef......................................................... 53 
                                       a++  + ++ +e +q+ +e+                                                         
  gi|336253500|ref|YP_004596607.1| 376 ATIERMVNQIQEDTQETVESledanaeiddgvelvedtvenlgeietavseaasgvdevatatddqaasteeiagma 452
                                       56666777777777777777777888888888888888888888888888888888888888888888888888888 PP

                      Yuri_gagarin  54 ...lvanerlaceidalketlkdrdeqikqlqsmitsysdlsenn 95 
                                          + + +++a e+++l e  +d ++q++ + +m++  +d++en 
  gi|336253500|ref|YP_004596607.1| 453 devMENADQVAAEVESLAEVSEDVERQVQVVTEMVDRLADVQENG 497
                                       875566689**********************************95 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.6   0.00088      0.31       4      25 ..      67      88 ..      65      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00088
                             SHOCT  4 ekLkeLyarGeIteEEFeakKa 25
                                      +kL+e +a+ +++e+EF +  +
  gi|336253500|ref|YP_004596607.1| 67 RKLDEAFAASALSEAEFKREHR 88
                                      89***************99766 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.55   1.9e+02      82     110 ..     200     228 ..     188     231 .. 0.68
   2 ?   13.4   0.9   0.00023     0.079       8      93 ..     238     323 ..     233     337 .. 0.92
   3 ?    2.1   6.7      0.72   2.5e+02      21      89 ..     363     431 ..     357     494 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.55
                           DUF4200  82 ikklkaeietlkseiekleekleeykkYe 110
                                       +++l + +++ +s ++ le+++ee++ Y 
  gi|336253500|ref|YP_004596607.1| 200 MEQLASMTQRRESVRADLEDTVEELEDYA 228
                                       35555556666677777888888888775 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00023
                           DUF4200   8 mfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikk 84 
                                       +++v  +++   +ei+  + +l+   ee+  + +e   ++++ ++   e  +  +ra+ k+e  +++  e ++++++
  gi|336253500|ref|YP_004596607.1| 238 IDDVATEQSSSTAEIASEMSNLSATVEEIASNTEEVSATAERAEEIAGETTDTAERAIDKMEGVQDAAGEVTEDVED 314
                                       6678888899999**************************************************************** PP

                           DUF4200  85 lkaeietlk 93 
                                       l++ ++++ 
  gi|336253500|ref|YP_004596607.1| 315 LREGVQRID 323
                                       *99888876 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.72
                           DUF4200  21 eiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaei 89 
                                       e ++l e+ +++ + +e+  ++++ed ++  + l++ +a+  +  + +e+  ++  e e  + ++ + +
  gi|336253500|ref|YP_004596607.1| 363 EVKNLAEESQEEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGV 431
                                       556666666666666666666666666666666666666666666666655555555555544444433 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.24        85       6      32 ..     215     241 ..     211     248 .. 0.85
   2 ?    2.2   0.1      0.45   1.6e+02       6      30 ..     250     274 ..     245     279 .. 0.73
   3 ?    1.4   0.0      0.77   2.7e+02       7      31 ..     307     331 ..     301     343 .. 0.78
   4 ?   -1.4   0.0       5.9   2.1e+03       5      18 ..     357     370 ..     354     387 .. 0.78
   5 ?    3.3   0.0       0.2        70       2      31 ..     397     426 ..     396     430 .. 0.87
   6 ?   -1.1   0.1       4.7   1.6e+03       6      30 ..     467     491 ..     447     496 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.24
                         DASH_Dam1   6 aeLaDsletLdknledLqqihesLsdf 32 
                                       a+L+D +e+L++  e++ + +e+++d+
  gi|336253500|ref|YP_004596607.1| 215 ADLEDTVEELEDYAERIGDGTETIDDV 241
                                       6899********999999998888875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.45
                         DASH_Dam1   6 aeLaDsletLdknledLqqihesLs 30 
                                       ae+a ++++L++ +e++ + +e++s
  gi|336253500|ref|YP_004596607.1| 250 AEIASEMSNLSATVEEIASNTEEVS 274
                                       6788888888888888877766665 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.77
                         DASH_Dam1   7 eLaDsletLdknledLqqihesLsd 31 
                                       e ++ +e+L++ ++++++i + ++d
  gi|336253500|ref|YP_004596607.1| 307 EVTEDVEDLREGVQRIDEIVDVIND 331
                                       6778888888888888888877776 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 5.9
                         DASH_Dam1   5 faeLaDsletLdkn 18 
                                       fa  aD++++L + 
  gi|336253500|ref|YP_004596607.1| 357 FAVVADEVKNLAEE 370
                                       88899999998765 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.2
                         DASH_Dam1   2 epafaeLaDsletLdknledLqqihesLsd 31 
                                       e+a ae+ D +e +++ +e+L +i+ ++s+
  gi|336253500|ref|YP_004596607.1| 397 EDANAEIDDGVELVEDTVENLGEIETAVSE 426
                                       566689******************999875 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 4.7
                         DASH_Dam1   6 aeLaDsletLdknledLqqihesLs 30 
                                       ++La+  e+++++++   ++ ++L+
  gi|336253500|ref|YP_004596607.1| 467 ESLAEVSEDVERQVQVVTEMVDRLA 491
                                       4444444555555555555555444 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 ?    2.5   8.1      0.59   2.1e+02       6      78 ..     213     277 ..     161     299 .. 0.61
   2 ?    6.2   1.4     0.042        15       8      67 ..     264     322 ..     259     344 .. 0.66
   3 ?   10.9   1.6    0.0015      0.52       1      62 [.     355     419 ..     355     431 .. 0.70
   4 ?    5.8   1.4     0.056        20       9      69 ..     419     485 ..     418     496 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.59
                      Syntaxin-6_N   6 vkeeVqkslnkaeslyrrwerlledtsss.tseeldetrteLrkalrsiewdledLeetvriveknpskfkide 78 
                                       v+++ +++++++e   +r             +e +d+  te  ++  +i  ++++L  tv+ + +n ++++ ++
  gi|336253500|ref|YP_004596607.1| 213 VRADLEDTVEELEDYAERI---------GdGTETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTEEVSATA 277
                                       3333333333333333333.........0345555555555555555555555555555555555554444333 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.042
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriv 67 
                                       ee+ ++ +++ ++ +r e++  +t++ t e   + ++ ++ a +++ +d+edL+e v+ +
  gi|336253500|ref|YP_004596607.1| 264 EEIASNTEEVSATAERAEEIAGETTD-TAERAIDKMEGVQDAAGEVTEDVEDLREGVQRI 322
                                       56666666666666666665544443.466666667778888888888888888777533 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.0015
                      Syntaxin-6_N   1 DPFfevkeeVqkslnkaeslyrrw....erlledtssstseeldetrteLrkalrsiewdledLee 62 
                                       D F +v++eV++ +++ ++  ++     ++++edt++ t e+l++++ e+   ++ +e ++e+L e
  gi|336253500|ref|YP_004596607.1| 355 DGFAVVADEVKNLAEESQEEAATIermvNQIQEDTQE-TVESLEDANAEIDDGVELVEDTVENLGE 419
                                       8899******999999888877772223455555544.4777888888888888888877777765 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.056
                      Syntaxin-6_N   9 eVqkslnkaeslyrrwerlledtsss......tseeldetrteLrkalrsiewdledLeetvrivek 69 
                                       e++ ++++a+s +++     +d+ +s        +e+ e  +++ ++++s+ +  ed e+ v++v +
  gi|336253500|ref|YP_004596607.1| 419 EIETAVSEAASGVDEVATATDDQAASteeiagMADEVMENADQVAAEVESLAEVSEDVERQVQVVTE 485
                                       5566666666666666443444333234566689999999999999999999999999999999976 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   8.4    0.0041       1.5      51     147 ..     209     305 ..     199     322 .. 0.83
   2 ?    2.1   0.7      0.27        96      56     130 ..     305     382 ..     294     385 .. 0.68
   3 ?    7.8  10.0    0.0049       1.7      50     136 ..     380     466 ..     339     480 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0041
                          ISG65-75  51 tadyllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekae 127
                                       + + + ++ +d+++ +e++ e++   +e + ++ +e+   +   +s++ +l  ++ee    +++ +++a+ a e+a 
  gi|336253500|ref|YP_004596607.1| 209 RRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTEEVSATAERAEEIAG 285
                                       45566678899999999999999999999999999999999999999999999999999999999999999999999 PP

                          ISG65-75 128 kaskkakeaakkAlGeelee 147
                                       ++ ++a +a  k  G +   
  gi|336253500|ref|YP_004596607.1| 286 ETTDTAERAIDKMEGVQDAA 305
                                       99999999998888875544 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.27
                          ISG65-75  56 lketkdklayienakekvdyyvekleslleeake...kgtltesdaeklkkaceeAkaknkkarekakkalekaeka 129
                                         e+ ++++ + + ++++d+ v+ ++++ ++ +    ++++++++a ++   ++ + +++k+  e+++++++++e+ 
  gi|336253500|ref|YP_004596607.1| 305 AGEVTEDVEDLREGVQRIDEIVDVINDIADQTNLlalNASIEAATAGEAGDGFAVVADEVKNLAEESQEEAATIERM 381
                                       44566777777777777777777777777776655557777777777777777777777777777777777777766 PP

                          ISG65-75 130 s 130
                                       +
  gi|336253500|ref|YP_004596607.1| 382 V 382
                                       5 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0049
                          ISG65-75  50 etadyllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkaleka 126
                                          +++ ++t+++++++e+a +++d  ve +e+ +e+  e +t+ +++a  +++ ++++ +++++ +e a  a e++
  gi|336253500|ref|YP_004596607.1| 380 RMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDEVATATDDQAASTEEIAGMADEVM 456
                                       33466677777777777777777777777777777777776666777777777777777777777777766666666 PP

                          ISG65-75 127 ekaskkakea 136
                                       e+a + a+e 
  gi|336253500|ref|YP_004596607.1| 457 ENADQVAAEV 466
                                       6666655544 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.1    0.0022      0.78       6      87 ..     216     300 ..     210     342 .. 0.59
   2 ?    5.7   3.0     0.021       7.3       2      86 ..     373     467 ..     357     496 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0022
                             TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelk.erk 79 
                                       +le+ ++ele+ a+++   +e++    ++ s+++++   ++++l+++++++ ++++  + ++e++ee++ e+  +++
  gi|336253500|ref|YP_004596607.1| 216 DLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTEevSATAERAEEIAGETTdTAE 292
                                       56666666666666665555555555555555555555555555555555555433334455555555544330344 PP

                             TMPIT  80 kvlkeves 87 
                                       + ++++e 
  gi|336253500|ref|YP_004596607.1| 293 RAIDKMEG 300
                                       44555554 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.021
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.........eeeeeeve 69 
                                       ee++++e+ +++++e  +e  ++le+ ++ +++ ++ ++   ++l e+++++++  + v+         + + ee++
  gi|336253500|ref|YP_004596607.1| 373 EEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDevatatddqAASTEEIA 449
                                       45566666666666666666666666666666666666666666666666666666665555555545533333333 PP

                             TMPIT  70 elkeelkerkkvlk.eve 86 
                                        +++e++e   +++ eve
  gi|336253500|ref|YP_004596607.1| 450 GMADEVMENADQVAaEVE 467
                                       444333333333322444 PP

>> Sec5  Exocyst complex component Sec5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.3     0.004       1.4      40     178 ..     293     422 ..     186     429 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.004
                              Sec5  40 slveeLeeslneairkttllfkpvlenkekadklraaleviernkflFnLPksLkesiakgdydklindYkkakslf 116
                                         ++++e  +++a+ + t+ ++++ e  +++d++ ++++ i     l+ L  s++ + a +  d +    +++k+l 
  gi|336253500|ref|YP_004596607.1| 293 RAIDKMEG-VQDAAGEVTEDVEDLREGVQRIDEIVDVINDIADQTNLLALNASIEAATAGEAGDGFAVVADEVKNLA 368
                                       44455543.566666677777888888899999999999999999*************9999999999999****** PP

                              Sec5 117 estrqslveedkkqvkvfkkvwsevekiieeyrkklwekLleldesqeeflkliskLleLev 178
                                       e++        +++  +++++ +++++ ++e  ++l +   e+d+ +e +++++++L e+e+
  gi|336253500|ref|YP_004596607.1| 369 EES--------QEEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIET 422
                                       *99........7799*********************99999999***********9998865 PP

>> DUF489  Protein of unknown function (DUF489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.16        57      51     113 ..     226     288 ..     195     334 .. 0.79
   2 ?    7.1   1.9     0.015       5.1      12      71 ..     360     419 ..     355     493 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.16
                                       S.GGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHTTHHHHT CS
                            DUF489  51 g.lanlklGletlleqlekekkkkdaeltryalsllalerkLsknkealaklgerieqierqle 113
                                       +  +++  G et+ ++ +++++ ++ae+++ + +l a  +++++n+e +++ +er e+i+ +++
  gi|336253500|ref|YP_004596607.1| 226 DyAERIGDGTETIDDVATEQSS-STAEIASEMSNLSATVEEIASNTEEVSATAERAEEIAGETT 288
                                       3367888899999998888887.68888888888888888888888888888888888876654 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHS---HHHHHHHHHHHH--S-SSHHHHTTSGGGGHHHHHHHHHHHHT--S CS
                            DUF489  12 aaklvqqlArtGqadeealetllkslletdpestedvygglanlklGletlleqlekekk 71 
                                        a+ v++lA++ q +++++e +++ + e ++e++e++ + +a++  G+e +++++e+  +
  gi|336253500|ref|YP_004596607.1| 360 VADEVKNLAEESQEEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGE 419
                                       6889**********************99999999999999***********999988766 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1         7   2.5e+03      71     123 ..      36      88 ..      11      93 .. 0.71
   2 ?    7.6   7.2     0.012       4.2      67     156 ..     177     283 ..     123     299 .. 0.73
   3 ?   10.5   8.6    0.0015      0.54      17     177 ..     322     476 ..     312     496 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 7
                             ATG16  71 kqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedee 123
                                       +++ +++s++ +  ++ ++la+ y ++  +  +l e+ ++ +  e++ k++ +
  gi|336253500|ref|YP_004596607.1|  36 EDERRLESQAHLFERVSDDLADEYYENVRSRRKLDEAFAASALSEAEFKREHR 88 
                                       55566677777777777777777777777777777777777666666666655 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
                             ATG16  67 q.................snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerla 126
                                       +                 +  +  ++++s++q++ ++r++l+++  + ++ a+r+ + +e++++  ++ ++ ++++a
  gi|336253500|ref|YP_004596607.1| 177 TlstlrlavldqqfvigsKVDDFMEQLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIA 253
                                       14456666666677777667777899*************************************************** PP

                             ATG16 127 eleaeraaletklkdreeelrekeklvqdl 156
                                       +  ++ +a  +++++++ee+   ++  +++
  gi|336253500|ref|YP_004596607.1| 254 SEMSNLSATVEEIASNTEEVSATAERAEEI 283
                                       *99999999999999999999888777665 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0015
                             ATG16  17 faeliqaynrLldrtsaleaenaklekaaasaks.sksskksakekeasasqsnskqsakiqsleqklaqlreelae 92 
                                         e+++  n+++d+t++l+  na++e+a+a +     +  +++ +++a++sq      ++ ++ e  + q++e+ +e
  gi|336253500|ref|YP_004596607.1| 322 IDEIVDVINDIADQTNLLA-LNASIEAATAGEAGdGFAVVADEVKNLAEESQ------EEAATIERMVNQIQEDTQE 391
                                       5699************996.56777555555444666667788888998888......8888999999999999999 PP

                             ATG16  93 lyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnq 169
                                       +  s ++ +  + +  e +++  e+l e e+++ e+ + + ++ t+ +d+++  +e + + +++ +  ++   ++++
  gi|336253500|ref|YP_004596607.1| 392 TVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDEVATATDDQAASTEEIAGMADEVMENADQVAAEVES 468
                                       99999999999999999999999999999999999999999999999999999999888888777777776666666 PP

                             ATG16 170 aEeklrkl 177
                                       + e ++++
  gi|336253500|ref|YP_004596607.1| 469 LAEVSEDV 476
                                       55555554 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.87   3.1e+02      77      98 ..     121     142 ..     115     156 .. 0.83
   2 ?    7.4   0.6      0.01       3.6      99     175 ..     195     274 ..     179     276 .. 0.80
   3 ?    3.7   0.3      0.14        48      91     154 ..     263     327 ..     253     350 .. 0.78
   4 ?    4.5   1.1     0.077        27     107     140 ..     375     408 ..     339     429 .. 0.51
   5 ?    4.0   0.9      0.11        39      95     152 ..     435     493 ..     410     498 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.87
                      Bacillus_HBL  77 iigYstkFqsyyktlveavdkk 98 
                                       +++Y   +  yy++l e +  +
  gi|336253500|ref|YP_004596607.1| 121 LNEYVGSYMVYYEQLLEEIADE 142
                                       689**************99444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.01
                      Bacillus_HBL  99 dkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdv...deltsilagdsgvisqlqneiedlqg 172
                                       + ++++e+l  + +   +  +  +++++eL+++++++   +++ +  +   +  t+ +a++  ++s+  +ei++  +
  gi|336253500|ref|YP_004596607.1| 195 KVDDFMEQLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDVAteqSSSTAEIASEMSNLSATVEEIASNTE 271
                                       557999*******************************9988776644433377788888888888888888877777 PP

                      Bacillus_HBL 173 kik 175
                                       +++
  gi|336253500|ref|YP_004596607.1| 272 EVS 274
                                       665 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.14
                      Bacillus_HBL  91 lveav.dkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsila 154
                                       ++e + ++++     e+ e++  e +   + + ++++ +++ + ++++d++++ + v+ +++i+ 
  gi|336253500|ref|YP_004596607.1| 263 VEEIAsNTEEVSATAERAEEIAGETTDTAERAIDKMEGVQDAAGEVTEDVEDLREGVQRIDEIVD 327
                                       33333777888888888999999999999999999999999999999999999999999988865 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.077
                      Bacillus_HBL 107 lekLqeeiqqnqkevkqlikeLkklklklakdsk 140
                                          ++++++q+q+ ++++++ L++ + +++  ++
  gi|336253500|ref|YP_004596607.1| 375 AATIERMVNQIQEDTQETVESLEDANAEIDDGVE 408
                                       3334444445555555555555444444444333 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.11
                      Bacillus_HBL  95 v.dkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsi 152
                                       +  + d+a  +e +  + +e+++n  +v + ++ L +  ++++  ++  ++ vd l  +
  gi|336253500|ref|YP_004596607.1| 435 AtATDDQAASTEEIAGMADEVMENADQVAAEVESLAEVSEDVERQVQVVTEMVDRLADV 493
                                       34577889999***************************999999999999998888766 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2    0.0025      0.89      59     123 ..     195     259 ..     184     274 .. 0.91
   2 ?    3.8   0.8      0.17        61      56     114 ..     356     415 ..     323     423 .. 0.68
   3 ?    1.9   0.6      0.64   2.2e+02      11      69 ..     435     492 ..     425     496 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0025
                             CREPT  59 llaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelkshiqsL 123
                                        +++++++L++ ++ R+++   led +e + + +++     e + + + + +s  +e+ s +++L
  gi|336253500|ref|YP_004596607.1| 195 KVDDFMEQLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNL 259
                                       58999***************************999999999999999999999999999999999 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.17
                             CREPT  56 alellaeYnkrLeaele.eRkklakmledfleaqkellakaeekleelkeklekvksvrk 114
                                       + +++a+ +k L++e + e  ++++m+++++e  +e+++  e   +e+ + +e v+   +
  gi|336253500|ref|YP_004596607.1| 356 GFAVVADEVKNLAEESQeEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVE 415
                                       456778888888888651456788888888888888888888888888777777766555 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.64
                             CREPT  11 ensassdaavReriaklPpevsdvsllekik.dkeeaekllkqveealellaeYnkrLea 69 
                                        ++    aa  e+ia + +ev +   ++++  + e+  + ++ ve  +++++e + rL++
  gi|336253500|ref|YP_004596607.1| 435 ATATDDQAASTEEIAGMADEVME--NADQVAaEVESLAEVSEDVERQVQVVTEMVDRLAD 492
                                       55555566677778888888765..45566446677888888888888888888888875 PP

>> Lipoprotein_20  YfhG lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.98   3.4e+02     128     155 ..     200     227 ..     175     231 .. 0.82
   2 ?    8.7   0.1    0.0042       1.5     120     167 ..     382     429 ..     365     437 .. 0.85
   3 ?   -0.3   0.1       2.5   8.7e+02     128     158 ..     463     493 ..     446     496 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.98
                    Lipoprotein_20 128 dskldslreqqaaLeaeLeettrKLenL 155
                                        ++l s+ ++++ ++a+Le+t   Le+ 
  gi|336253500|ref|YP_004596607.1| 200 MEQLASMTQRRESVRADLEDTVEELEDY 227
                                       47899999*************9999975 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0042
                    Lipoprotein_20 120 yqrlqeesdskldslreqqaaLeaeLeettrKLenLtdiERqLssRkq 167
                                        +++qe++++ ++sl +++a+++  +e ++  +enL +iE  +s   +
  gi|336253500|ref|YP_004596607.1| 382 VNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAAS 429
                                       46799***********************************99887655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.5
                    Lipoprotein_20 128 dskldslreqqaaLeaeLeettrKLenLtdi 158
                                        ++++sl e  + +e +++ +t  +++L+d+
  gi|336253500|ref|YP_004596607.1| 463 AAEVESLAEVSEDVERQVQVVTEMVDRLADV 493
                                       4688899999999999999999999999887 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 ?    2.4   0.1      0.46   1.6e+02      52      99 ..     194     240 ..     168     252 .. 0.56
   2 ?    7.6   0.9     0.012       4.2      38     107 ..     215     283 ..     193     300 .. 0.74
   3 ?    8.5   0.5     0.006       2.1      29     105 ..     255     330 ..     249     345 .. 0.78
   4 ?    4.1   1.4      0.13        47      40      99 ..     364     426 ..     357     443 .. 0.56
   5 ?    4.1   4.2      0.14        49      30     123 ..     386     485 ..     377     496 .. 0.40

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHC CS
                         Fib_alpha  52 keaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketida 99 
                                       +++++ ++++ ++++++++  +d + +++++++  e +i +  etid+
  gi|336253500|ref|YP_004596607.1| 194 SKVDDFMEQLASMTQRRESVRADLEDTVEELEDYAE-RIGDGTETIDD 240
                                       555666666666666666666666666666655555.55555555544 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
                                       CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                         Fib_alpha  38 ekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvL 107
                                       ++le+++ee+++  + + + +++i+d+ +e+ +s+++  + ++++s ++e ei+   e+++a+ ++ +++
  gi|336253500|ref|YP_004596607.1| 215 ADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATVE-EIASNTEEVSATAERAEEI 283
                                       57888888888888899999999999999999999988999999999999.9998888888887666555 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.006
                                       CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHH CS
                         Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnir 105
                                         ++++ ++e++ ++ ee+s + + aee+  e++d+ +++  + ++ + +  ++++++e +  +  ++id+ +  i+
  gi|336253500|ref|YP_004596607.1| 255 EMSNLSATVEEIASNTEEVSATAERAEEIAGETTDTAERAIDKMEGVQDAAGEVTEDVE-DLREGVQRIDEIVDVIN 330
                                       55678889999999999999999999999999999999999999988999999998888.66666666666555554 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.13
                                       CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHCCCHHHHHHHC CS
                         Fib_alpha  40 leneleeisnstkeaeelvkeikdslrekqkskkdn....dnvikksskeleeeilrlketida 99 
                                       ++n  ee +++  ++e++v++i++ ++e+ +s +d     d  ++ +++++e +  +++  +++
  gi|336253500|ref|YP_004596607.1| 364 VKNLAEESQEEAATIERMVNQIQEDTQETVESLEDAnaeiDDGVELVEDTVE-NLGEIETAVSE 426
                                       4455555666666666666666666666665555532334444455555555.55555555554 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.14
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHHHHHHHCCH.. CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrlketidaqe.. 101
                                       ++d+++++e+le+  +ei +  + +e++v+++ ++ ++  + +++     +++ + + + e ei+ + +++ ++   
  gi|336253500|ref|YP_004596607.1| 386 QEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVdevATATDDQAASTE-EIAGMADEVMENAdq 461
                                       5555555555555555555555444444444444433333333332111222333333333.444444444433310 PP

                                       ..HHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 102 ..snirvLqnvlesneqkiqkLeq 123
                                          +++ L +v e+ e+++q   +
  gi|336253500|ref|YP_004596607.1| 462 vaAEVESLAEVSEDVERQVQVVTE 485
                                       012233344444444444443333 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0       0.3   1.1e+02      14      64 ..     172     222 ..     159     232 .. 0.79
   2 ?    0.6   0.2       1.5   5.2e+02      23      54 ..     213     244 ..     204     322 .. 0.60
   3 ?    5.6   0.2      0.04        14      26      63 ..     363     400 ..     346     424 .. 0.64
   4 ?    1.3   0.1      0.89   3.1e+02      42      70 ..     452     480 ..     415     496 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.3
                              ApoO  14 drLeegvrslRkslepytsavqdelnkvkskvetaeqsvtdtiasLkeppe 64 
                                       +++e+  ++lR+++ ++   + ++++++++++ +  q  ++  a L +  e
  gi|336253500|ref|YP_004596607.1| 172 ETVERTLSTLRLAVLDQQFVIGSKVDDFMEQLASMTQRRESVRADLEDTVE 222
                                       578999999999999999999999988888888888887777777776544 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.5
                              ApoO  23 lRkslepytsavqdelnkvkskvetaeqsvtd 54 
                                       +R  le+++++++d+ +++ ++ et     t+
  gi|336253500|ref|YP_004596607.1| 213 VRADLEDTVEELEDYAERIGDGTETIDDVATE 244
                                       55555555555555554444443333322222 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.04
                              ApoO  26 slepytsavqdelnkvkskvetaeqsvtdtiasLkepp 63 
                                       ++++ +++ q+e  +++  v++ ++ +++t++sL +++
  gi|336253500|ref|YP_004596607.1| 363 EVKNLAEESQEEAATIERMVNQIQEDTQETVESLEDAN 400
                                       55555566666666666666666666666666666654 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.89
                              ApoO  42 kskvetaeqsvtdtiasLkeppedllPrl 70 
                                        + v++   +v  +++sL+e +ed+  ++
  gi|336253500|ref|YP_004596607.1| 452 ADEVMENADQVAAEVESLAEVSEDVERQV 480
                                       34444444444444444444444433332 PP

>> CheZ  Chemotaxis phosphatase, CheZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3       0.5   1.8e+02      53     116 ..     174     239 ..     152     252 .. 0.63
   2 ?    5.7  12.7     0.035        12      11     112 ..     249     375 ..     239     441 .. 0.78
   3 ?    5.6   3.4     0.037        13      27     111 ..     416     496 ..     403     498 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.5
                                       XXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CheZ  53 Aertldavekalp.ladklkeeakeleeewerllere.lekeefrelvkeveaflkeveektealk 116
                                        ertl++   a    +  + +++++  e+++++++r+     ++++ v+e+e++ +++ + te+++
  gi|336253500|ref|YP_004596607.1| 174 VERTLSTLRLAVLdQQFVIGSKVDDFMEQLASMTQRReSVRADLEDTVEELEDYAERIGDGTETID 239
                                       455555544333202334556666666666666665524567778888888888888777777665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.035
                                       XXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CheZ  11 tReLhdalrelgldekllekaaeeipdardrLeyvielTeqAAertldavekalpladklkeeakeleeewerller 87 
                                       t e+   +++l+   +++++ +ee++ + +r e ++  T + Aer++d +e  +  a +++e++++l+e  +r+ e 
  gi|336253500|ref|YP_004596607.1| 249 TAEIASEMSNLSATVEEIASNTEEVSATAERAEEIAGETTDTAERAIDKMEGVQDAAGEVTEDVEDLREGVQRIDEI 325
                                       6677788999**9999******************************************************9999875 PP

                                       XXXXXX.........................XXXXXXXXXXXXXXXXXXX CS
                              CheZ  88 elekee.........................frelvkeveaflkeveekt 112
                                           ++                         f  +++ev+++ +e++e++
  gi|336253500|ref|YP_004596607.1| 326 VDVINDiadqtnllalnasieaatageagdgFAVVADEVKNLAEESQEEA 375
                                       53322224446677777777777777777773333333333333333333 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.037
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CheZ  27 llekaaeeipdardrLeyvielTeqAAertldavekalpladklkeeakeleeewerllerelekeefrelvkevea 103
                                       +l + ++++++a +  + v++ T++ A      +e+++ +ad++ e+a+++++e e+l+e + ++e+  ++v+e+ +
  gi|336253500|ref|YP_004596607.1| 416 NLGEIETAVSEAASGVDEVATATDDQAAS----TEEIAGMADEVMENADQVAAEVESLAEVSEDVERQVQVVTEMVD 488
                                       55677788888888889999988876654....58999999999999999999999999999888888888888888 PP

                                       XXXXXXXX CS
                              CheZ 104 flkeveek 111
                                        l++v+e+
  gi|336253500|ref|YP_004596607.1| 489 RLADVQEN 496
                                       88888765 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.1    0.0028         1     163     256 ..     193     286 ..     157     306 .. 0.67
   2 ?    4.4   0.2     0.039        14     176     239 ..     276     339 ..     268     356 .. 0.84
   3 ?    4.9   3.1     0.027       9.5     182     245 ..     363     435 ..     357     458 .. 0.62
   4 ?    2.2   0.2      0.18        63     189     241 ..     443     495 ..     436     498 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0028
                        Fmp27_WPPW 163 gkendpervqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkes 239
                                       g++ d    q   + +R e++++++e++ e+le++ ++    +e++++   e ++ ++e+ ++++ l++++e++ ++
  gi|336253500|ref|YP_004596607.1| 193 GSKVDDFMEQLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATVEEIASN 269
                                       44445555566677788888888888888888888888877777777777777777777777777777777777777 PP

                        Fmp27_WPPW 240 eesseeeeskskelsaa 256
                                       +e+ + + ++ +e   +
  gi|336253500|ref|YP_004596607.1| 270 TEEVSATAERAEEIAGE 286
                                       66544333333333333 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.039
                        Fmp27_WPPW 176 leeRleeleeqie.kleekleelelksekedeelkeeieelekeikelkeklefletlledlkes 239
                                         eR+ee+  +   + e++++++e  +     e++e++e+l++ +++++e +++++++ ++++  
  gi|336253500|ref|YP_004596607.1| 276 TAERAEEIAGETTdTAERAIDKMEGVQDA-AGEVTEDVEDLREGVQRIDEIVDVINDIADQTNLL 339
                                       67999999876552789999999999999.79**************************9998765 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.027
                        Fmp27_WPPW 182 eleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesse.........e 245
                                       e+++  e+ +e+  ++e   ++ +e+++e +e+le+  +e+++ +e++e+++e+l e e++ +          
  gi|336253500|ref|YP_004596607.1| 363 EVKNLAEESQEEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSeaasgvdevA 435
                                       4444455555555555555555556999***************************998875443333322210 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.18
                        Fmp27_WPPW 189 kleekleelelksekedeelkeeieelekeikelkeklefletlledlkesee 241
                                         +e++  + ++ +++ +++++e+e+l + +++++++++++++++++l   +e
  gi|336253500|ref|YP_004596607.1| 443 ASTEEIAGMADEVMENADQVAAEVESLAEVSEDVERQVQVVTEMVDRLADVQE 495
                                       4566777777777777999***************************9987765 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.59   2.1e+02      17      53 ..     194     230 ..     184     244 .. 0.67
   2 ?    5.0   0.8     0.057        20       5      63 ..     221     279 ..     217     286 .. 0.78
   3 ?    1.3   0.0      0.81   2.8e+02      23      65 ..     288     330 ..     273     340 .. 0.63
   4 ?    4.1   0.7      0.11        38       6      66 ..     372     433 ..     364     438 .. 0.84
   5 ?    4.5   0.2     0.084        29      12      55 ..     452     495 ..     441     498 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.59
                             Sec34  17 eqtdealeqLeeleekfksvsektsslheaceqllee 53 
                                       +++d+ +eqL++++++ +sv ++ ++  e+ e+  e 
  gi|336253500|ref|YP_004596607.1| 194 SKVDDFMEQLASMTQRRESVRADLEDTVEELEDYAER 230
                                       6788888888888888888887766665555555444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.057
                             Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaee 63 
                                       +e+ e+  +++ + t+++ +  +e +++  ++++++s+l+++ e++ +++++++ +ae 
  gi|336253500|ref|YP_004596607.1| 221 VEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTEEVSATAER 279
                                       55666777777788888888888888899999999999999999999888888888775 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.81
                             Sec34  23 leqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                        ++ e   +k++ v++   ++ e+ e+l e  +r++e+++ i+
  gi|336253500|ref|YP_004596607.1| 288 TDTAERAIDKMEGVQDAAGEVTEDVEDLREGVQRIDEIVDVIN 330
                                       4444555566666666666666666666666666666666665 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.11
                             Sec34   6 eskeeecdelleqtd.ealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                       +++ ++++++++q++ +++e++e+le+   ++++  + ++++ e+l e ++ ++e a  ++e
  gi|336253500|ref|YP_004596607.1| 372 QEEAATIERMVNQIQeDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDE 433
                                       56677888899888625899999999999999999999999999999999999999888765 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.084
                             Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqk 55 
                                        de++e++d++  ++e+l e  ++v+ + + + e+ ++l + q+
  gi|336253500|ref|YP_004596607.1| 452 ADEVMENADQVAAEVESLAEVSEDVERQVQVVTEMVDRLADVQE 495
                                       57888888888888999999999999888888888888887775 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2      0.48   1.7e+02      33      61 ..     213     241 ..     199     247 .. 0.53
   2 ?    7.8   0.3    0.0096       3.4      33      62 ..     304     333 ..     249     337 .. 0.88
   3 ?    2.9   0.8      0.33   1.2e+02      35      58 ..     362     385 ..     340     423 .. 0.76
   4 ?    2.3   0.2      0.49   1.7e+02      34      60 ..     466     492 ..     441     497 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.48
                                       -HSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  33 lteelkeyletiesearrldhlvedlLdl 61 
                                        + +l++ +e +e+ a+r+ +  e++ d 
  gi|336253500|ref|YP_004596607.1| 213 VRADLEDTVEELEDYAERIGDGTETIDDV 241
                                       34455555555555555665555555555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0096
                                       -HSSCHHHHHHHHHHHHHHHHHHHHHHHHC CS
                             HisKA  33 lteelkeyletiesearrldhlvedlLdls 62 
                                       +  e+ e +e+++++++r+d++v+ + d++
  gi|336253500|ref|YP_004596607.1| 304 AAGEVTEDVEDLREGVQRIDEIVDVINDIA 333
                                       56788999***************9888877 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.33
                                       SSCHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  35 eelkeyletiesearrldhlvedl 58 
                                       +e+k + e  ++ea  ++++v+++
  gi|336253500|ref|YP_004596607.1| 362 DEVKNLAEESQEEAATIERMVNQI 385
                                       566777777777777777777776 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.49
                                       HSSCHHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  34 teelkeyletiesearrldhlvedlLd 60 
                                        e+l+e  e++e++++ ++++v++l d
  gi|336253500|ref|YP_004596607.1| 466 VESLAEVSEDVERQVQVVTEMVDRLAD 492
                                       377888888888888888888888755 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.2     0.011       3.8      37     119 ..     200     282 ..     177     306 .. 0.66
   2 ?    7.7   1.9     0.014       4.8      34     113 ..     253     339 ..     249     354 .. 0.76
   3 ?    8.0   2.5     0.011         4      51     132 ..     312     400 ..     293     407 .. 0.71
   4 ?    3.2   7.6      0.33   1.2e+02       4     103 ..     364     476 ..     362     495 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCT..TCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FlgN  37 ieaLeelleekqellekleqleqkrakllaelglsaeeatlsellak..eedeelkelwqelkelleelkelnelNg 111
                                       +e+L + +++ +++ ++le + ++++   +++g +  ++t+++++ +  ++ +e+++ ++ l++++ee+    e   
  gi|336253500|ref|YP_004596607.1| 200 MEQLASMTQRRESVRADLEDTVEELEDYAERIGDG--TETIDDVATEqsSSTAEIASEMSNLSATVEEIASNTEEVS 274
                                       77888888888888888888888888888888888..7777777777776666666666666666666665555544 PP

                                       HHHHHCCH CS
                              FlgN 112 rlieqsle 119
                                        + e++ e
  gi|336253500|ref|YP_004596607.1| 275 ATAERAEE 282
                                       44444433 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.014
                                       TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--.....SCHHHHHHHHCT..TCCHHHHHHHHHHHHHHHHH CS
                              FlgN  34 agdieaLeelleekqellekleqleqkrakllaelgls.....aeeatlsellak..eedeelkelwqelkelleel 103
                                       a++++ L +++ee+++  e++++++++ +++  e   +     ++ +++++++ +  e+ e l+e +q+++e+++ +
  gi|336253500|ref|YP_004596607.1| 253 ASEMSNLSATVEEIASNTEEVSATAERAEEIAGETTDTaeraiDKMEGVQDAAGEvtEDVEDLREGVQRIDEIVDVI 329
                                       66788888888888888888888888888777777777666677777777777778999999999999999999999 PP

                                       HHHHHHHHHH CS
                              FlgN 104 kelnelNgrl 113
                                        +++++ + l
  gi|336253500|ref|YP_004596607.1| 330 NDIADQTNLL 339
                                       8887764444 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHTT--.......SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                              FlgN  51 lekleqleqkrakllaelgls.......aeeatlsellakeedeelkelwqelkelleelkelnelNgrlieqslef 120
                                       +e+l++  q+++++++ ++         a +a+++++ a e+ +  + + +e+k+l+ee +e + + +r+++q +e 
  gi|336253500|ref|YP_004596607.1| 312 VEDLREGVQRIDEIVDVINDIadqtnllALNASIEAATAGEAGDGFAVVADEVKNLAEESQEEAATIERMVNQIQED 388
                                       4444444444444444444442222333666677777766************************************* PP

                                       HHHHHHHCCHXX CS
                              FlgN 121 nqrllnllqgaa 132
                                       +q++++ l  a+
  gi|336253500|ref|YP_004596607.1| 389 TQETVESLEDAN 400
                                       ***999988766 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.33
                                       HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--...... CS
                              FlgN   4 leeLielleeelelleeLlelleeEteaLkag...dieaLeelleekqellekleqleqkrakllaelgls...... 71 
                                       +++L+e  +ee++++e++   ++e t+  +++     +++++ +e  ++++e+l ++e + +++ + + ++      
  gi|336253500|ref|YP_004596607.1| 364 VKNLAEESQEEAATIERMVNQIQEDTQETVESledANAEIDDGVELVEDTVENLGEIETAVSEAASGVDEVatatdd 440
                                       68999999*********9999999999999998854799********************************655554 PP

                                       ..SCHHHHHHHHCT..TCCHHHHHHHHHHHHHHHHH CS
                              FlgN  72 ..aeeatlsellak..eedeelkelwqelkelleel 103
                                         a+++++  ++ +  e ++++++ +++l e+ e++
  gi|336253500|ref|YP_004596607.1| 441 qaASTEEIAGMADEvmENADQVAAEVESLAEVSEDV 476
                                       433333333333334444444444444444443333 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.1    0.0015      0.54      56     152 ..     191     288 ..     176     303 .. 0.76
   2 ?    1.2   0.0       0.6   2.1e+02      62     106 ..     292     338 ..     288     353 .. 0.72
   3 ?    3.1   1.0      0.16        57      83     142 ..     371     429 ..     355     461 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                      Allexi_40kDa  56 hishdvdsiinklnpvsllsqttlLselrdalrtltklldklksvekklelsaet..asdskllkklesietsleel 130
                                        i++ vd  +++l ++ +  ++++ ++l d++++l++  +++ + ++++ + a++   s  +++ +++ +  ++ee+
  gi|336253500|ref|YP_004596607.1| 191 VIGSKVDDFMEQLASM-TQRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEqsSSTAEIASEMSNLSATVEEI 266
                                       5889999999999999.55667788999**************99888877655440044557889999999999999 PP

                      Allexi_40kDa 131 hakldelsssetsesegPsssp 152
                                         + +e+s+++++++e    ++
  gi|336253500|ref|YP_004596607.1| 267 ASNTEEVSATAERAEEIAGETT 288
                                       9999999998888776644443 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.6
                      Allexi_40kDa  62 dsiinklnpvslls..qttlLselrdalrtltklldklksvekklel 106
                                       ++ i+k++ v+  +   t  + +lr+ ++++++++d ++++ ++++l
  gi|336253500|ref|YP_004596607.1| 292 ERAIDKMEGVQDAAgeVTEDVEDLREGVQRIDEIVDVINDIADQTNL 338
                                       56677777776555445667888999999999999999888877765 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.16
                      Allexi_40kDa  83 lrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelssset 142
                                        +++  t+++++++++++++++ +s e+a + ++ + +e +e ++e+l++    +s++++
  gi|336253500|ref|YP_004596607.1| 371 SQEEAATIERMVNQIQEDTQETVESLEDA-NAEIDDGVELVEDTVENLGEIETAVSEAAS 429
                                       44555666666666666666665555443.333444455555444444432222222222 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 ?    7.0   0.9    0.0075       2.6      28     140 ..     200     305 ..     192     338 .. 0.74
   2 ?    2.8   0.3      0.15        51      72     179 ..     364     479 ..     341     494 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0075
                             Atg14  28 rerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkkl 104
                                        e+la++  ++es++  +e+ +e+ e   + +++i   ++ +++  ++++++ ++++  +  ls   +ei+   +++
  gi|336253500|ref|YP_004596607.1| 200 MEQLASMTQRRESVRADLEDTVEELE---DYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTEEV 273
                                       57899999999999999999999999...778888888888888888877777777777777777777777666666 PP

                             Atg14 105 aklsdklkkRrsdleslqneleerrkkqiaklqdai 140
                                       ++     ++R ++++  ++  +er  ++++++qda 
  gi|336253500|ref|YP_004596607.1| 274 SAT----AERAEEIAGETTDTAERAIDKMEGVQDAA 305
                                       543....45566777777777777777777777665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.15
                             Atg14  72 lksliadlrerlqelkdklsqlkkeieekkkklaklsdklk.......kRrsdleslqneleerr..kkqiaklqda 139
                                        k+l ++++e+ ++++  + q ++ ++e+ + l+  ++++        +  + l  +++ ++e+    +++a+ +d+
  gi|336253500|ref|YP_004596607.1| 364 VKNLAEESQEEAATIERMVNQIQEDTQETVESLEDANAEIDdgvelveDTVENLGEIETAVSEAAsgVDEVATATDD 440
                                       44444444444444444444444444444444433333333333222244444444444444332114555555555 PP

                             Atg14 140 ikrieqklsslssktlesrsslcselaklyglrrtsyerg 179
                                          +++ ++ + ++ +e   + + e+ +l+++++ ++er+
  gi|336253500|ref|YP_004596607.1| 441 QAASTEEIAGMADEVMENADQVAAEVESLAEVSE-DVERQ 479
                                       5566666666666666666666666666666665.55554 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   4.3   0.00075      0.27     238     321 ..     215     302 ..     195     310 .. 0.85
   2 ?    2.7  14.8      0.16        55     202     325 ..     365     488 ..     362     492 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00075
                                       HHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HH CS
                             APG17 238 aeledVvkelqerleem....ekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeek 310
                                       a+led v+el++ +e +    e++ +   e+ +++ ++ s+++++ +++ee+ ++ +e+ a+ +++ee+  +++++ 
  gi|336253500|ref|YP_004596607.1| 215 ADLEDTVEELEDYAERIgdgtETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTEEVSATAERAEEIAGETTDTA 291
                                       68999999999999999999999999999999999999999999999999999999999998888888888877777 PP

                                       HHHHHHHHHHH CS
                             APG17 311 ekieekleele 321
                                       e+  +k+e ++
  gi|336253500|ref|YP_004596607.1| 292 ERAIDKMEGVQ 302
                                       77777766665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.16
                                       HHH.................S-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 202 vkAvkltegggal.rraaaelseeereelleVlekDaaeledVvkelqerleemekakkllsekkeeiekllsalkk 277
                                       +++ +++++++a  + + ++  +e+ +e +e le  +ae++d v+ +++++e++ ++  ++se ++ ++++ +a+ +
  gi|336253500|ref|YP_004596607.1| 365 KNLAEESQEEAATiE-RMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDEVATATDD 440
                                       555555555555534.4444467888999999999999****************9999******************* PP

                                       HHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHH CS
                             APG17 278 aleeleevgkklpeylaifkaeeeflerweeekekieekleeleeLre 325
                                       + +  ee+    +e++++  + ++ +e  +e  e++e++++ ++e+++
  gi|336253500|ref|YP_004596607.1| 441 QAASTEEIAGMADEVMENADQVAAEVESLAEVSEDVERQVQVVTEMVD 488
                                       ******999999999998888888888889999999999999998875 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.1     0.011       3.7     225     324 ..     206     297 ..     169     318 .. 0.47
   2 ?    5.9   7.7     0.022       7.6     210     325 ..     362     477 ..     352     493 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                            HMMR_N 225 eteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekckllekekeelvr 301
                                        t++ +   + l+ + e+le y ++i    e+++  + e +s   ++  +  +ls++v++  ++ +++         
  gi|336253500|ref|YP_004596607.1| 206 MTQRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTEEVS-------- 274
                                       223333333444444444444444444444444444444444444444444444444444444444444........ PP

                            HMMR_N 302 eeeekeqtlsaEleelkeklklk 324
                                          e+++++  E  ++ e+   k
  gi|336253500|ref|YP_004596607.1| 275 ATAERAEEIAGETTDTAERAIDK 297
                                       34444444444444444433333 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.022
                            HMMR_N 210 eklvslekekieekseteklleyiee.lsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdl 285
                                       +  ++l +e +ee + +e+++++i+e  +++ e+le  + +i+   el++   +++ ++ ++++e +  +++ +   
  gi|336253500|ref|YP_004596607.1| 362 DEVKNLAEESQEEAATIERMVNQIQEdTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDEVATAT 438
                                       55556666666666666777766665345555666777777777777777777777777777766666666666666 PP

                            HMMR_N 286 nekckllekekeelvreeeekeqtlsaEleelkeklklke 325
                                       + +    e+    +  e  e+++++ aE+e+l e  +  e
  gi|336253500|ref|YP_004596607.1| 439 DDQAASTEEIAG-MADEVMENADQVAAEVESLAEVSEDVE 477
                                       666555554443.555555666666666666555433333 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.2     0.017       6.1     617     689 ..     208     279 ..     167     315 .. 0.49
   2 ?    6.6   1.1    0.0045       1.6     606     697 ..     320     417 ..     298     435 .. 0.69
   3 ?    2.9   4.9     0.058        20     239     365 ..     362     487 ..     357     496 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.017
                          Prominin 617 lckkltkvnletlaekleelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensd 689
                                        +++ +  +le + e+le+ a+++  g++++    +++ +++ +i +e + +l+++v+++ +++++++++++ 
  gi|336253500|ref|YP_004596607.1| 208 QRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASE-MSNLSATVEEIASNTEEVSATAER 279
                                       222333444444444444444444444433333333333333333332.233444444444444444432222 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0045
                          Prominin 606 skihsslyleqlckkltkvnletlaekleelanelsngk.........knlkqslkneaqdlraiqqelvlplessv 673
                                       ++i  +++++ +++   ++nl +l +++e+                  knl ++ ++ea +++++ +++ +  +++v
  gi|336253500|ref|YP_004596607.1| 320 QRI--DEIVDVINDIADQTNLLALNASIEAATAGEAG-DgfavvadevKNLAEESQEEAATIERMVNQIQEDTQETV 393
                                       444..35566666666678888887777765544433.246777888888888888888888888888888888888 PP

                          Prominin 674 kklkksvkkldeensdlqesikkl 697
                                       ++l+    ++d+  +  ++++++l
  gi|336253500|ref|YP_004596607.1| 394 ESLEDANAEIDDGVELVEDTVENL 417
                                       888888888888666666666654 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.058
                          Prominin 239 aelerllenlkeakeqLeq.vnklekeLrksgsqLrdglrgvkrdlnqalsnlCqs.eeCskilssleiekldtskc 313
                                       +e+++l+e+ +e  + +e  vn+ +++ +++ + L+d+  ++ + ++ +++++ ++  e +++ s++     ++ + 
  gi|336253500|ref|YP_004596607.1| 362 DEVKNLAEESQEEAATIERmVNQIQEDTQETVESLEDANAEIDDGVE-LVEDTVENlGEIETAVSEAASGVDEVATA 437
                                       56677777766666665541466666677777777666665555443.23332332234444444444433333333 PP

                          Prominin 314 l.dqlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlk 365
                                         dq  + +e++ ++ + + +n ++++  ++++l e++e v++q++ v++ + 
  gi|336253500|ref|YP_004596607.1| 438 TdDQAAS-TEEIAGMADEVMENADQVA-AEVESLAEVSEDVERQVQVVTE-MV 487
                                       3344444.4444444444455555444.6677777777777777754443.33 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5  10.0      0.41   1.4e+02      13     101 ..     210     298 ..     194     339 .. 0.47
   2 ?    7.7  13.7    0.0099       3.5       6     118 ..     364     479 ..     361     495 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.41
                        TPR_MLP1_2  13 lkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaelee 89 
                                        ++  +++e+++++l++  e   + +++  +   ++    ae + e+++l + ++e+ +  +e+ a ae+a++   e
  gi|336253500|ref|YP_004596607.1| 210 RESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTEEVSATAERAEEIAGE 286
                                       22223333333333333333333333333333334444444444444444444444444444444444444444433 PP

                        TPR_MLP1_2  90 seesweeqkeel 101
                                        +   e+  +++
  gi|336253500|ref|YP_004596607.1| 287 TTDTAERAIDKM 298
                                       333333333333 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0099
                        TPR_MLP1_2   6 leeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaes 82 
                                       +++ +++ +ee++  e+ ++++qed ++  e++++a+      + + +++v++l ++ + ++e+ + + e+ ++ ++
  gi|336253500|ref|YP_004596607.1| 364 VKNLAEESQEEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDEVATATDD 440
                                       5666788999*************************************************999999877777666666 PP

                        TPR_MLP1_2  83 aka...eleeseesweeqkeelekelselekriedlneq 118
                                         a   e++    +  e  ++   e+++l +  ed++ q
  gi|336253500|ref|YP_004596607.1| 441 QAAsteEIAGMADEVMENADQVAAEVESLAEVSEDVERQ 479
                                       555000555566777778888888999998888888888 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.5     0.007       2.5     134     195 ..     211     272 ..     166     279 .. 0.86
   2 ?    3.5   4.8      0.14        50     145     195 ..     222     272 ..     217     337 .. 0.70
   3 ?    0.8   3.3      0.98   3.4e+02      92     193 ..     292     389 ..     273     390 .. 0.71
   4 ?    5.9   6.1     0.027       9.5      90     197 ..     340     442 ..     320     447 .. 0.68
   5 ?    1.7   0.4      0.51   1.8e+02       6      43 ..     453     490 ..     451     493 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.007
                               LXG 134 slpelddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLeemtsk 195
                                       + ++ d+++ +++l++  + + + +e ++d  +eq+s++a++ s+++ l+++v+e+ + t++
  gi|336253500|ref|YP_004596607.1| 211 ESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTEE 272
                                       5567788999999999999999**********************************999986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                               LXG 145 dslqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLeemtsk 195
                                       ++l++  + + + +e ++d  +eq+s++a++ s+++ l+++v+e+ + t++
  gi|336253500|ref|YP_004596607.1| 222 EELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTEE 272
                                       455555555666667777777777777777777777777777777766654 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.98
                               LXG  92 ngfidedfLeqelenglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeq 168
                                       +  id     q+++ ++++  e+++e  ++i++i++ ++di   ++ ++ ++++s++ a     e  +++     e 
  gi|336253500|ref|YP_004596607.1| 292 ERAIDKMEGVQDAAGEVTEDVEDLREGVQRIDEIVDVINDI--ADQTNLLALNASIEAATAG--EAGDGFAVVADEV 364
                                       44455544455777888888888888888888888888888..7777888888888887766..7777777777888 PP

                               LXG 169 ksalanlesdlkalktyvseLeemt 193
                                       k++ ++++++ ++++++v++++e t
  gi|336253500|ref|YP_004596607.1| 365 KNLAEESQEEAATIERMVNQIQEDT 389
                                       8888888888888888888877755 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.027
                               LXG  90 ssngfidedfLeqelenglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdq 166
                                       + n+ i+ +    e+ +g+  +  ++++l++e ++  a++  +v+  + d++e ++sl++a+ ++++ +e +ed   
  gi|336253500|ref|YP_004596607.1| 340 ALNASIEAATAG-EAGDGFAVVADEVKNLAEESQEEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVED--- 412
                                       556666666666.7777777777778888888888888888888888888888888888888888877776655... PP

                               LXG 167 eqksalanlesdlkalktyvseLeemtskgk 197
                                        + + l ++e  +++++++v+e+ ++t  + 
  gi|336253500|ref|YP_004596607.1| 413 -TVENLGEIETAVSEAASGVDEVATATDDQA 442
                                       .455566667777777777777777766665 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.51
                               LXG   6 aelieaieqlkseleelkeqleqlkkaiqklveledsl 43 
                                       +e+ e ++q+  e e+l e  e++++++q ++e+ d+l
  gi|336253500|ref|YP_004596607.1| 453 DEVMENADQVAAEVESLAEVSEDVERQVQVVTEMVDRL 490
                                       68899999*********************999998876 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 ?    1.1   0.1       1.4   4.8e+02      43      76 ..     193     226 ..     159     233 .. 0.62
   2 ?    4.3   3.3      0.13        46       7      85 ..     201     281 ..     192     282 .. 0.77
   3 ?    7.2   3.3     0.017       5.9       7      83 ..     236     314 ..     234     317 .. 0.87
   4 ?    3.9   0.0      0.18        64       7      37 ..     299     329 ..     295     332 .. 0.88
   5 ?    5.7   2.6     0.048        17      35      80 ..     343     388 ..     311     401 .. 0.53
   6 ?    5.1   2.3     0.076        27      15      84 ..     363     399 ..     353     436 .. 0.63
   7 ?    3.0   0.7      0.34   1.2e+02       5      37 ..     444     476 ..     440     481 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.4
                                       HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  43 GaaadafqaefeewkqaaqklvdaLeeisealkq 76 
                                       G+  d f ++++ ++q  + + + Le++ e+l+ 
  gi|336253500|ref|YP_004596607.1| 193 GSKVDDFMEQLASMTQRRESVRADLEDTVEELED 226
                                       5555555555555555555555555555555554 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCT..HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdalqsgWs..GaaadafqaefeewkqaaqklvdaLeeisealkqaanaf 81 
                                       e+l+++ +r  + +++led +++l+   + +++g +   + a++  +  +e+  ++ +l +  eei++++++++++ 
  gi|336253500|ref|YP_004596607.1| 201 EQLASMTQRRESVRADLEDTVEELEDYAERIGDGTEtiDDVATEQSSSTAEIASEMSNLSATVEEIASNTEEVSATA 277
                                       67777777888888888888888888888886666667888888888888888888888888888888888888777 PP

                                       HHHH CS
                            WXG100  82 edaD 85 
                                       e a+
  gi|336253500|ref|YP_004596607.1| 278 ERAE 281
                                       7776 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCT..HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdalqsgWs..GaaadafqaefeewkqaaqklvdaLeeisealkqaanaf 81 
                                       e ++++a++ +++ +e+ +e ++l a+v++++s+ +   a+a++ ++   e + +a++ +d++e++++a  ++++ +
  gi|336253500|ref|YP_004596607.1| 236 ETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTEevSATAERAEEIAGETTDTAERAIDKMEGVQDAAGEVTEDV 312
                                       7899***************************7766646777777888888*****************9999888877 PP

                                       HH CS
                            WXG100  82 ed 83 
                                       ed
  gi|336253500|ref|YP_004596607.1| 313 ED 314
                                       76 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdal 37 
                                       e +++aa ++ +  e+l++ +qr++  vd +
  gi|336253500|ref|YP_004596607.1| 299 EGVQDAAGEVTEDVEDLREGVQRIDEIVDVI 329
                                       7899*******************99998876 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.048
                                       HHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  35 dalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaana 80 
                                       ++++++  G+a+d f+ + +e+k+ a++ +++ ++i++ ++q+ + 
  gi|336253500|ref|YP_004596607.1| 343 ASIEAATAGEAGDGFAVVADEVKNLAEESQEEAATIERMVNQIQED 388
                                       5555555666666666666666666666666655555555555443 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.076
                                       HHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  15 rfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafeda 84 
                                       +                                  ++  ee +++a+++ ++ ++i+e ++++ +++eda
  gi|336253500|ref|YP_004596607.1| 363 E---------------------------------VKNLAEESQEEAATIERMVNQIQEDTQETVESLEDA 399
                                       3.................................334444555555555555555555555555555554 PP

  == domain 7  score: 3.0 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                            WXG100   5 dpeelrqaaarfqkqaeeledelqrlkaevdal 37 
                                       ++ee++ +a ++ ++a+++ +e+++l+   +++
  gi|336253500|ref|YP_004596607.1| 444 STEEIAGMADEVMENADQVAAEVESLAEVSEDV 476
                                       678888888888888888888888887766655 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.7    0.0034       1.2     573     709 ..     195     326 ..     166     337 .. 0.64
   2 ?    6.6   5.4    0.0041       1.4     573     704 ..     255     387 ..     247     393 .. 0.84
   3 ?    2.5   5.9      0.07        25     579     705 ..     362     486 ..     355     491 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0034
                             Nup88 573 elqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelekikeklkslknalk 649
                                        + +  e+  s+++r e++  ++e+  ++ e++++r+ +  +++ + +   s++  e+++e+++++ ++++++ + +
  gi|336253500|ref|YP_004596607.1| 195 KVDDFMEQLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATVEEIASNTE 271
                                       45566667777888888888888999999999999999999999999999999999999999999999999999999 PP

                             Nup88 650 qvkkkldkqrkqiakskeeekksslelsekqkktikeiLkeegeeieelikqvkdikkiv 709
                                       +v  + +  ++   ++++++++ ++    ++ + +++   e +e++e+l + v++i +iv
  gi|336253500|ref|YP_004596607.1| 272 EVSATAERAEEIAGETTDTAER-AI----DKMEGVQDAAGEVTEDVEDLREGVQRIDEIV 326
                                       9999976655544444333222.22....2333333344444444444444444443333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0041
                             Nup88 573 elqsleeerksl...seraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelekikeklkslkn 646
                                       e+++l  + +++   +e++   Ae+ eei  +  + ++r+ + ++ +++++  ++e   ++++ +++i+e +++++ 
  gi|336253500|ref|YP_004596607.1| 255 EMSNLSATVEEIasnTEEVSATAERAEEIAGETTDTAERAIDKMEGVQDAAGEVTEDVEDLREGVQRIDEIVDVIND 331
                                       5555555555551115677778***************************************************9999 PP

                             Nup88 647 alkqvkkkldkqrkqiakskeeekksslelsekqkktikeiLkeegeeieelikqvkd 704
                                         +q +      +  i++++  e+ + +++ ++  k++ e  +ee+ +ie++++q+++
  gi|336253500|ref|YP_004596607.1| 332 IADQTNLL--ALNASIEAATAGEAGDGFAVVADEVKNLAEESQEEAATIERMVNQIQE 387
                                       88888765..56677777777778999****************************975 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.07
                             Nup88 579 eerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelekikeklkslknalkqvkkkl 655
                                       +e k+l e+ ++ A   e + ++ ++ ++   + l+++n++  + +e   +  ++l +i++++++ +  +++v + +
  gi|336253500|ref|YP_004596607.1| 362 DEVKNLAEESQEEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDEVATAT 438
                                       45566666666666666665554444444455567888888888888888889999999999999999999999999 PP

                             Nup88 656 dkqrkqiakskeeekksslelsekqkktikeiLkeegeeieelikqvkdi 705
                                       d q+  +++ + +   +++  +++q     e L e +e++e++++ v ++
  gi|336253500|ref|YP_004596607.1| 439 DDQAASTEEIAGM--ADEVMENADQVAAEVESLAEVSEDVERQVQVVTEM 486
                                       9999998876666..56666677777777788999999999999988765 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1       1.8   6.2e+02      28      72 ..     202     242 ..     188     248 .. 0.67
   2 ?   12.6   2.3   0.00045      0.16       2      87 ..     252     345 ..     251     350 .. 0.92
   3 ?    3.9   1.5      0.24        85      19      77 ..     368     426 ..     358     440 .. 0.78
   4 ?    0.4   0.7       2.9     1e+03      21      70 ..     440     489 ..     431     499 .] 0.43

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.8
                    Cytochrom_B562  28 alkelraaaedakeatpsklekdseeqkdYqeGldklidqldkae 72 
                                       +l+++++      e+  ++le+  ee +dY e + + ++++d++ 
  gi|336253500|ref|YP_004596607.1| 202 QLASMTQRR----ESVRADLEDTVEELEDYAERIGDGTETIDDVA 242
                                       333333333....33334677888999999999888888888775 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00045
                    Cytochrom_B562   2 lkeeMkqmkkalkqva.kaddaeelkkalkelraaaedakeatpsklek.......dseeqkdYqeGldklidqldk 70 
                                       + +eM+++++ ++++a +++++ + ++ ++e+    +d  e  ++k+e+         e+++d +eG + + + +d 
  gi|336253500|ref|YP_004596607.1| 252 IASEMSNLSATVEEIAsNTEEVSATAERAEEIAGETTDTAERAIDKMEGvqdaageVTEDVEDLREGVQRIDEIVDV 328
                                       6789********9999789999999**************************9999999******************* PP

                    Cytochrom_B562  71 aealakagkleeakaal 87 
                                       ++  a++ +l +  a++
  gi|336253500|ref|YP_004596607.1| 329 INDIADQTNLLALNASI 345
                                       *******9998887766 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.24
                    Cytochrom_B562  19 addaeelkkalkelraaaedakeatpsklekdseeqkdYqeGldklidqldkaealaka 77 
                                       a++++e +++++++ ++ ++  ++t+++le+ ++e +d  e  ++ +++l ++e+++ +
  gi|336253500|ref|YP_004596607.1| 368 AEESQEEAATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSE 426
                                       55667777888999988888899999999999999999888888888888888888764 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 2.9
                    Cytochrom_B562  21 daeelkkalkelraaaedakeatpsklekdseeqkdYqeGldklidqldk 70 
                                       d ++ +++++ +   + +   + ++++e  +e  +d +   + +++ +d+
  gi|336253500|ref|YP_004596607.1| 440 DQAASTEEIAGMADEVMENADQVAAEVESLAEVSEDVERQVQVVTEMVDR 489
                                       44444444444444443333333334444333333333333333333333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   7.2    0.0046       1.6     338     465 ..     204     331 ..     135     347 .. 0.52
   2 ?    2.8  10.0       0.1        35     357     467 ..     375     487 ..     357     495 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0046
                            AAA_13 338 kglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlv.........e 405
                                        ++ ++              esv a++e   +++++  e i +  e+++++++e+++ + ++   +          +
  gi|336253500|ref|YP_004596607.1| 204 ASMTQRR-------------ESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSnlsatveeiA 267
                                       2222222.............344444444445555555555555555555555555555555443322233332222 PP

                            AAA_13 406 eleseldeyk....kkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeink 465
                                       + ++e+++      +   ++++++e + ++++  ++++ ++ e++++L++ ++ + +++++in+
  gi|336253500|ref|YP_004596607.1| 268 SNTEEVSATAeraeEIAGETTDTAERAIDKMEGVQDAAGEVTEDVEDLREGVQRIDEIVDVIND 331
                                       2222222222111022222333333333444445555555556677777777777777777776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.1
                            AAA_13 357 lesvkakiesikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkykklekaiekleke 431
                                          ++  +++i+++ +e  e+ ++ N+ +++  e +e+  ++l   +  v+e+ s +de  ++ ++ +++ e+    
  gi|336253500|ref|YP_004596607.1| 375 AATIERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIEtaVSEAASGVDEVATATDDQAASTEEIAGM 451
                                       33344445677777777777777777777777777777777776554335666677776666666666666666666 PP

                            AAA_13 432 lkeeeaelkkleeeikeLekqlrdekpaaeeinkeL 467
                                       ++e  +++ ++++e++ L +  +d+++ ++++++ +
  gi|336253500|ref|YP_004596607.1| 452 ADEVMENADQVAAEVESLAEVSEDVERQVQVVTEMV 487
                                       666666666666666666666666666666665544 PP

>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.5    0.0027      0.94     111     187 ..     189     267 ..     161     314 .. 0.80
   2 ?   -0.1   2.6       1.9   6.8e+02     108     149 ..     379     420 ..     332     496 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0027
                              Dna2 111 eelldklleknleelyalglteeeakeeikekleeiekwakkyvkksnkakakvekkkekke..klsiskvldiEEn 185
                                       +  + + +++ +e+l ++ + +e+++ ++++++ee+e++a+++   +++ + + +++++++     + s++ ++ E+
  gi|336253500|ref|YP_004596607.1| 189 QFVIGSKVDDFMEQLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAeiASEMSNLSATVEE 265
                                       55566778899********************************9999988888777777666563344444444444 PP

                              Dna2 186 iw 187
                                       i 
  gi|336253500|ref|YP_004596607.1| 266 IA 267
                                       44 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.9
                              Dna2 108 ekleelldklleknleelyalglteeeakeeikekleeiekw 149
                                       e++ +++++ +++++e+l  ++ ++++  e +++++e++ ++
  gi|336253500|ref|YP_004596607.1| 379 ERMVNQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEI 420
                                       222222222223444444444444444444444444444433 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.2    0.0011      0.37      55     117 ..     201     263 ..     194     339 .. 0.90
   2 ?    0.9   1.1       0.9   3.2e+02      48     103 ..     365     421 ..     315     434 .. 0.56
   3 ?   -0.8   4.1         3   1.1e+03      34     116 ..     383     465 ..     358     480 .. 0.52
   4 ?    0.1   0.2       1.5   5.4e+02      77     124 ..     447     494 ..     437     496 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH CS
                              SHE3  55 dnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenssaseteleeelerlkvqY 117
                                       ++L s+ +R+e    dle+ ++el++  e +   ++++++ + ++s+s +e   e+++l +  
  gi|336253500|ref|YP_004596607.1| 201 EQLASMTQRRESVRADLEDTVEELEDYAERIGDGTETIDDVATEQSSSTAEIASEMSNLSATV 263
                                       789*********99*******************************************998765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.9
                                       HHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH CS
                              SHE3  48 aslkhENdnLsslLkRKerrlk.dlekelselkesveelklekkqlkkrlenssase 103
                                        +l +E +   + ++R   +++ d+++ +++l++ + e+    + +++ +en+ + e
  gi|336253500|ref|YP_004596607.1| 365 KNLAEESQEEAATIERMVNQIQeDTQETVESLEDANAEIDDGVELVEDTVENLGEIE 421
                                       333333333334444443333312333333344444444444444444444444444 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH CS
                              SHE3  34 elaqkkeskflenlaslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenssaseteleeel 110
                                       ++ q+  ++ +e+l  +  E d  + l++     l ++e+ +se  + v+e+++ ++     +e+      e++e+ 
  gi|336253500|ref|YP_004596607.1| 383 NQIQEDTQETVESLEDANAEIDDGVELVEDTVENLGEIETAVSEAASGVDEVATATDDQAASTEEIAGMADEVMENA 459
                                       22333334445555555555555555555555555555555555555555555555555555555555555555555 PP

                                       HHHHHH CS
                              SHE3 111 erlkvq 116
                                       +++ ++
  gi|336253500|ref|YP_004596607.1| 460 DQVAAE 465
                                       555555 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  77 elkesveelklekkqlkkrlenssaseteleeelerlkvqYdalvdsq 124
                                       e     +e+ ++ +q+  ++e++ + ++++e +++ +    d l d q
  gi|336253500|ref|YP_004596607.1| 447 EIAGMADEVMENADQVAAEVESLAEVSEDVERQVQVVTEMVDRLADVQ 494
                                       555567788888888888888888888888888888877777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2283  (0.127336); expected 358.6 (0.02)
Passed bias filter:                      896  (0.0499749); expected 358.6 (0.02)
Passed Vit filter:                       164  (0.00914719); expected 17.9 (0.001)
Passed Fwd filter:                       103  (0.00574488); 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: 1.73u 0.41s 00:00:02.14 Elapsed: 00:00:00.59
# Mc/sec: 2536.28
//
Query:       gi|336253501|ref|YP_004596608.1|  [L=108]
Description: t-RNA-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-14   52.3   0.0    5.8e-14   52.0   0.0    1.0  1  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 !   52.0   0.0   3.2e-18   5.8e-14       1      94 [.      10     104 ..      10     105 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 3.2e-18
                                       EEEEEEEEEEEETTSST..EEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEE CS
                         tRNA_bind   1 lrvGkvleaeehpnadk..LlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsae 75 
                                       +rvG+vleae +++a+k  +++l +d+Ge+   q  +++  +y peel +++v +  nl+  ++ G++Se++ +++ 
  gi|336253501|ref|YP_004596608.1|  10 IRVGEVLEAESFEEANKpkMTKLWIDLGEHGEVQSAAQLDHHYDPEELEGRQVLCATNLGSVRIAGFKSEALTVGVP 86 
                                       79**************999********************************************************** PP

                                       CCESSCEEEEEESST--TT CS
                         tRNA_bind  76 eldekevgilelpadveaG 94 
                                       + +e+   ++e+++dv++G
  gi|336253501|ref|YP_004596608.1|  87 D-EEEFPVLVEPEQDVPLG 104
                                       5.888899********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 833.58
//
Query:       gi|336253502|ref|YP_004596609.1|  [L=327]
Description: luciferase-like protein [Halopiger xanaduensis SH-6]
Scores for 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-61  206.8   4.4    9.8e-61  205.9   4.4    1.4  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
      0.058   12.9   0.1       0.13   11.6   0.0    1.6  2  PEP_mutase      Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.9   4.4   1.1e-64   9.8e-61      20     313 ..      19     300 ..       6     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: 205.9 bits;  conditional E-value: 1.1e-64
                    Bac_luciferase  20 aslrylvelaraaEelGfdavwvaehhggpgga.....ldaftllaalaaaTerirlgtavtplytrhPavlAqqaa 91 
                                        +++ ++e +r+aE+lG+ +vw+ +h + + g+     ++++t+l+a+a+ T+ irlgt vt+   rhPavlA++aa
  gi|336253502|ref|YP_004596609.1|  19 TDVATVRETVREAERLGYRSVWLEDHFQSWIGDqrratHECWTTLSAVAETTDEIRLGTLVTCQSYRHPAVLAKMAA 95 
                                       48999************************************************************************ PP

                    Bac_luciferase  92 tLdhlsgGRfglglgtggpaveerrfGv....dhderyarlrEfvevlrrlwrgeevdfeGeffsv..kgalllprp 162
                                       t+d++s+GR+++glg+g++a e++rfG     + +er  rl E++e+l++lw+ ++ ++eGe++ v  ++a+  p+p
  gi|336253502|ref|YP_004596609.1|  96 TVDRISEGRLEVGLGAGWYADEYDRFGYefrePPAERIHRLGETIEILQGLWTNDTYSHEGEYLDVdlEEAFCEPQP 172
                                       ****************************************************66666******99999********* PP

                    Bac_luciferase 163 gqgpiP.vyvaaas.paglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeA 237
                                       +q+p+P +++++++ + +l +aa+ adg+     +pe  + ++e lr+  a   r  ++i+  + l+  v++t +eA
  gi|336253502|ref|YP_004596609.1| 173 VQEPHPpIWIGGGGeDVTLPYAAELADGWNYGTLEPEGFEGKLEVLREHCASDER-YDEIAKSAELFAFVGETTDEA 248
                                       ****666*******9*********************************9999999.679****************** PP

                    Bac_luciferase 238 raearaliagldfyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvd 313
                                       +++++++                     ++++   + + ++ + a    ++ +ta  Gtp+ v+e laaya+ag++
  gi|336253502|ref|YP_004596609.1| 249 EKKREQFR--------------------TEFLLDEPAEPREFFLA----GYLETAPTGTPAAVRESLAAYADAGIE 300
                                       ****9999....................67789999999999988....69999********************97 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.5e-05      0.13      80     129 ..      17      66 ..      15     100 .. 0.74
   2 ?   -2.9   0.0      0.41   3.7e+03     162     176 ..     291     305 ..     276     322 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.5e-05
                        PEP_mutase  80 ygespeevaetvrrliaaGvvgvniEDk.....kkndaerqlldieefaekiaaa 129
                                       yg ++++v+etvr+++++G   v +ED+            q    +e    ++a+
  gi|336253502|ref|YP_004596609.1|  17 YGTDVATVRETVREAERLGYRSVWLEDHfqswiG-----DQRRATHECWTTLSAV 66 
                                       8999************************543331.....2222333333333333 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.41
                        PEP_mutase 162 araYaeAGAdgvfvp 176
                                       + aYa+AG + v+ +
  gi|336253502|ref|YP_004596609.1| 291 LAAYADAGIEEVMLV 305
                                       457888887766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2452.01
//
Query:       gi|336253503|ref|YP_004596610.1|  [L=463]
Description: phosphomethylpyrimidine kinase [Halopiger xanaduensis SH-6]
Scores for 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-88  293.8   2.8    8.9e-88  293.8   2.8    1.7  2  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    4.3e-56  189.1   1.2    8.7e-56  188.1   1.2    1.5  1  ThiP_synth    Thiamine-phosphate synthase
    1.2e-10   41.2   1.7    2.3e-10   40.3   1.7    1.4  1  PfkB          pfkB family carbohydrate kinase
    0.00092   18.8   3.4     0.0016   18.0   3.4    1.3  1  Carb_kinase   Carbohydrate kinase
  ------ inclusion threshold ------
      0.078   12.4   2.3        1.2    8.5   2.3    2.3  1  HK            Hydroxyethylthiazole kinase family


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 !  293.8   2.8   2.5e-91   8.9e-88       1     246 []      19     261 ..      19     261 .. 0.98
   2 ?   -1.9   0.1       0.5   1.8e+03      36      64 ..     275     303 ..     270     305 .. 0.83

  Alignments for each domain:
  == domain 1  score: 293.8 bits;  conditional E-value: 2.5e-91
                                       ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHH CS
                      Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiiev 77 
                                       Ds+GGAGiqADl t++a+gv+g+s+ita+taq t+gv++ h lp e +eaq++av+ d++v+a+K+Gmla++ei+e+
  gi|336253503|ref|YP_004596610.1|  19 DSGGGAGIQADLATMAAHGVFGTSAITAVTAQHTRGVESSHVLPLEEIEAQIDAVTGDFDVAAAKTGMLATTEIVEL 95 
                                       9**************************************************************************** PP

                                       HHHHHHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHT CS
                      Phos_pyr_kin  78 vaeklkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllkl 154
                                       vaek +++++p+V+DPVmva+sg++lle+ea +a+++ Ll  atv tPN +Eae+L+g ++ +ee+++ea++++lk+
  gi|336253503|ref|YP_004596610.1|  96 VAEKASEFDFPLVVDPVMVATSGDRLLEPEAERAYED-LLSAATVATPNADEAEVLTGVEVVDEESAREAGREILKT 171
                                       ***********************************98.*************************************** PP

                                       T-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHH CS
                      Phos_pyr_kin 155 gakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvtea 231
                                       g++aVl+kGgh++g  ++v+dvl++ +ev+ +e++ri t+ thG+GC+l++aia++la+g++l +Av  A++++ +a
  gi|336253503|ref|YP_004596610.1| 172 GVDAVLVKGGHVPG--ERVQDVLVTADEVRAFEHPRIGTDATHGSGCALAAAIASRLANGQPLSDAVGGATDFLARA 246
                                       ***********966..5566********************************************************* PP

                                       HHCG-BSTSSS-B-- CS
                      Phos_pyr_kin 232 ikealelgkgagpvn 246
                                       +++ +++g+g+g vn
  gi|336253503|ref|YP_004596610.1| 247 VRYYYDVGEGHGAVN 261
                                       ************986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.5
                                       CEEEEEE--HHHHHHHHHHHHHTS--SEE CS
                      Phos_pyr_kin  36 gvkevhplpaelveaqleavledvkvdav 64 
                                         +ev+++ +e+vea + a++ +v++++v
  gi|336253503|ref|YP_004596610.1| 275 TAEEVEAVVEEFVEADVAALVPEVGMNVV 303
                                       56789999999999999999999888775 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.1   1.2   2.4e-59   8.7e-56       1     163 [.     278     444 ..     278     446 .. 0.97

  Alignments for each domain:
  == domain 1  score: 188.1 bits;  conditional E-value: 2.4e-59
                                       HHHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC CS
                        ThiP_synth   1 eleralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkf 77 
                                       e+e ++e+++e++ +a+l+Pevg+N++ a+p+A+ ++++aav+GRI+r+ ++v+++++++fgasshva +llaa++f
  gi|336253503|ref|YP_004596610.1| 278 EVEAVVEEFVEAD-VAALVPEVGMNVVGATPYAEAVDETAAVEGRITRTLSGVHPNRGVRFGASSHVAWFLLAAREF 353
                                       68999********.9************************************************************** PP

                                       -TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCC....T-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EE CS
                        ThiP_synth  78 dpevraainirydekilealeelglkvvefdreeepeev....gstmewgvaeaieel.evpdviydeGgvGkEpmi 149
                                       +p +r+a+n+r+de++++ale+l++ v+e+dr+eep+e+    g+tm+wg+++a+e++ e+   ++d+G+vGkE+m+
  gi|336253503|ref|YP_004596610.1| 354 FPGLRFAVNCRFDEDVEAALEDLEWAVAEYDRSEEPTEIagieGRTMQWGAQRAFEDRdEPTAGVIDRGAVGKEAMV 430
                                       **************************************999*****************777788************* PP

                                       EEEESSHHHHHHHH CS
                        ThiP_synth 150 yvlgkdaeevvekv 163
                                        ++++d +++ve+ 
  gi|336253503|ref|YP_004596610.1| 431 TLVAADLRTLVERT 444
                                       ***********986 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   1.7   6.4e-14   2.3e-10     160     279 ..     105     236 ..      78     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 6.4e-14
                                       E...EEEEECESSSHH.....HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEG CS
                              PfkB 160 t...fdpnlldplgaq.....fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlG 228
                                       +   +dp++++++g+      +  a+++ll+ a++++pn++E+e ltg + +d+e+a +a+ +++++g++ v+v+ G
  gi|336253503|ref|YP_004596610.1| 105 FplvVDPVMVATSGDRllepeAERAYEDLLSAATVATPNADEAEVLTGVEVVDEESAREAGREILKTGVDAVLVKGG 181
                                       35667899999999889999999****************************************************** PP

                                       GGEEEEEE.......TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHH CS
                              PfkB 229 keGalvve.......kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleeal 279
                                         +   v+       ++  +++   p +    t G G + ++++++ l++g++l +a+
  gi|336253503|ref|YP_004596610.1| 182 HVPGERVQdvlvtadEVRAFEH---PRIGTDATHGSGCALAAAIASRLANGQPLSDAV 236
                                       6443333335443234444444...545566699**********************98 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   3.4   4.3e-07    0.0016       2     211 ..      13     236 ..      12     249 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-07
                                       EEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT..HTTTS...--SSS-SEEEE-TT CS
                       Carb_kinase   2 lvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll..edeqakileklerldavviGpG 76 
                                       l i+Gs+   GA++ a la++++  g   v+  s   av  +++  v  +++l  e+ +a+i +     d+ +   G
  gi|336253503|ref|YP_004596610.1|  13 LTIAGSDSGGGAGIQADLATMAAH-G---VFGTSAITAVTAQHTRGVESSHVLplEEIEAQIDAVTGDFDVAAAKTG 85 
                                       5699**********9999998763.2...222233333333334444333333322223367788899999999999 PP

                                       -SSSHCHHH.HCHHHCCCCS-EEEE.......GGGGGSGGGG......TTTTSSEEEE--HHHHHHHCTTTCHHCCS CS
                       Carb_kinase  77 Lgrdekikk.lleevlekdeplviD.......AdgLnllaqkne...lserkaeviLTPhkkEfkrLlkaivkkedd 142
                                       + ++ +i + + e++ e d plv+D       +d L  l+ + e       +a+++ TP++ E + L+++ v  e++
  gi|336253503|ref|YP_004596610.1|  86 MLATTEIVElVAEKASEFDFPLVVDpvmvatsGDRL--LEPEAErayEDLLSAATVATPNADEAEVLTGVEVVDEES 160
                                       66666655527788889999*999944444333333..33333355778889*******************999*** PP

                                       HHHHHHHHHHHHTTEEEEESTT.......SEEEECTTEEEEE----.GGG-STTHHHHHHHHHHHHHHCTSSHHHHH CS
                       Carb_kinase 143 rlelarelaqklnavvllkgek.......dvivspegevlinstgs.salakGGsGDvLaGligalLaqneasyeaa 211
                                         e++re+ +     vl+kg +       dv+v+ ++ev + +    +  a+ GsG  La +i++ La  ++  +a+
  gi|336253503|ref|YP_004596610.1| 161 AREAGREILKTGVDAVLVKGGHvpgervqDVLVT-ADEVRAFEHPRiGTDATHGSGCALAAAIASRLANGQPLSDAV 236
                                       *******************974333333377777.777777766542667899999999999999999888777766 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.3   0.00033       1.2      57     202 ..      84     230 ..      44     259 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00033
                                       -TT--HHHHHHHHHHHHHHHHTT--EEEE-TTBTTBHHH......HHHHHHHHHHS--SEEEEEHHHHHHHHTSSCC CS
                                HK  57 iGtleekaiealkaAvksakevnrPvvlDPVgvgAtelR......relalellkevklavikGNasEilslaglelk 127
                                       +G l++  +e++   +++a e + P+v+DPV v+ +  R      ++  ++ll+ + +a     ++E+  l+g+e+ 
  gi|336253503|ref|YP_004596610.1|  84 TGMLAT--TEIVELVAEKASEFDFPLVVDPVMVATSGDRllepeaERAYEDLLSAATVATPNADEAEV--LTGVEV- 155
                                       677877..888999999999**********99988877733222235566777666555544444444..444433. PP

                                       SCSSSSSS-SHHHHHHHHHHHHHHTSEEEEESSS......EEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHH CS
                                HK 128 vkGvDskeaataavaavqkvAqklrvvvvvtGev......DvvsdgkkvyklknGtellgkitasGCllgsvvaafl 198
                                          vD ++a++a     +++ + +++v v  G+v      Dv+  + +v   +          +sGC+l++++a+ l
  gi|336253503|ref|YP_004596610.1| 156 ---VDEESAREA---GREILKTGVDAVLVKGGHVpgervqDVLVTADEVRAFEHPRIGTDATHGSGCALAAAIASRL 226
                                       ...565555553...34444455666666666543322335555555555555544444456699999999999998 PP

                                       TTBS CS
                                HK 199 avkk 202
                                       a  +
  gi|336253503|ref|YP_004596610.1| 227 ANGQ 230
                                       8544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 3765.30
//
Query:       gi|336253504|ref|YP_004596611.1|  [L=336]
Description: AIR synthase-like protein domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-24   87.0   1.6    1.9e-24   86.5   1.6    1.2  1  AIRS_C    AIR synthase related protein, C-terminal domain
    1.5e-08   35.2   1.3    6.7e-08   33.1   0.1    2.2  2  AIRS      AIR synthase related protein, N-terminal domain
  ------ inclusion threshold ------
       0.16   11.8   0.0       0.28   11.0   0.0    1.4  1  YL1_C     YL1 nuclear protein C-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 !   86.5   1.6   3.2e-28   1.9e-24       1     150 [.     157     309 ..     157     313 .. 0.80

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 3.2e-28
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgal 76 
                                       ++Gd+l+lt +  + ++g+++    ++ + + d         l e  +++ ++ +aa+ g+v+a+hDvT+GGL+gal
  gi|336253504|ref|YP_004596611.1| 157 RVGDRLLLTTGPAVEAVGLLSTHFPDAID-VSDGaLADAQARLEEVHCVRDALTAAAA-GPVRAMHDVTEGGLAGAL 231
                                       68*********888888855544444443.3333333344555566777777777777.****************** PP

                                       HHHHHTTTEEEEEECG......THHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEE CS
                            AIRS_C  77 aemapasgvgaeidld......kvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevta 147
                                       +ema++++  +++d +       v+ ++e+ ++++++ + ++G ll+av+p+  d v+ +le+++   +a+IG+v+ 
  gi|336253504|ref|YP_004596611.1| 232 NEMADGADARFVVDRAavpmrpGVREVCEA-LEIDPWATTSCGSLLIAVDPDGVDDVRTALEDRDT-VVAEIGRVES 306
                                       ****************77655555555555.**********************************8.7********9 PP

                                       SSS CS
                            AIRS_C 148 kee 150
                                       +++
  gi|336253504|ref|YP_004596611.1| 307 GNG 309
                                       975 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 !   33.1   0.1   1.1e-11   6.7e-08       6      90 ..      48     141 ..      25     146 .. 0.77
   2 ?    0.7   0.2      0.14   8.5e+02      24      58 ..     222     258 ..     185     268 .. 0.61

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.1e-11
                                       EEEEEEEE.EECCTCCCC...HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EE CS
                              AIRS   6 vvttdshnrpvlvepvhf...iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvpl 73 
                                       v +td    p+ + p  +   +++ a+  +l D+a+ G  P  l+ +++lp      +++ v + ++e ++ lgv++
  gi|336253504|ref|YP_004596611.1|  48 VTATD----PISILPPLGlerAARFALDLILADVAVSGVPPSHLSICFTLPeemtdeEFATVWETIHEECADLGVSV 120
                                       44555....444433333688999***************************************************** PP

                                       EEEEEEEESS....EEEEEEE CS
                              AIRS  74 vgGdtsfsne....ptisvta 90 
                                       v+G+t+++++     + ++ta
  gi|336253504|ref|YP_004596611.1| 121 VTGHTARYSDpsypWIGAATA 141
                                       *******98756632333444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC...HHHHH CS
                              AIRS  24 iGakavavnlsDlaamGArPlalllslalp...wleev 58 
                                       +++ ++a++l+  +a GA+ +++++  a+p    ++ev
  gi|336253504|ref|YP_004596611.1| 222 VTEGGLAGALNE-MADGADARFVVDRAAVPmrpGVREV 258
                                       444555555555.3567777766776666655544444 PP

>> YL1_C  YL1 nuclear protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.6e-05      0.28       2      15 ..     119     132 ..     118     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.6e-05
                             YL1_C   2 CdITGlpAkYrDPk 15 
                                       +++TG+ A+Y DP+
  gi|336253504|ref|YP_004596611.1| 119 SVVTGHTARYSDPS 132
                                       79***********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); 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:                         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 0.19s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 2910.55
//
Query:       gi|336253505|ref|YP_004596612.1|  [L=366]
Description: sulfate transporter [Halopiger xanaduensis SH-6]
Scores for complete 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-41  141.5  32.0    3.4e-24   85.4  12.5    3.6  4  MFS_MOT1  Molybdate transporter of MFS superfamily
  ------ inclusion threshold ------
        1.3    8.3   9.6       0.88    8.8   4.2    2.9  2  PorA      Porin PorA


Domain annotation for each model (and alignments):
>> MFS_MOT1  Molybdate transporter of MFS superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8  11.5   2.7e-23   2.4e-19       1     111 []      18     132 ..      18     132 .. 0.97
   2 ?    2.0   2.1      0.03   2.7e+02      17      53 ..     152     188 ..     138     204 .. 0.67
   3 !   85.4  12.5   3.8e-28   3.4e-24       2     111 .]     206     320 ..     205     320 .. 0.97
   4 ?   -2.9   1.0         1   9.1e+03      26      44 ..     339     357 ..     331     363 .. 0.47

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 2.7e-23
                          MFS_MOT1   1 aelsgalgdlglTllnlvialaalaslsltalllsvGlmnlltglfggvPmc.....hgAgglaaqyrfgartgaag 72 
                                       +el+galgd   T+l+l++alaa++s+sl ++l+ +G++++++gl++g+P++     +  g ++    + ++++aag
  gi|336253505|ref|YP_004596612.1|  18 GELTGALGDSI-TVLPLLVALAATTSVSLPHVLVGFGVFQIVWGLYYGMPLSvepmkALVGLAIVGSLSYPELAAAG 93 
                                       589********.*********************************************999999999778******** PP

                          MFS_MOT1  73 illGlvllllgltgllerllrliPksvlgglllgaGleL 111
                                       +l G vll++g +gl+ r++r++ ++v++g++++++l L
  gi|336253505|ref|YP_004596612.1|  94 LLAGGVLLTVGQFGLVGRVQRVVGEPVIRGVQFAVALLL 132
                                       ************************************987 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.03
                          MFS_MOT1  17 lvialaalaslsltalllsvGlmnlltglfggvPmch 53 
                                       +v++l ala+   +++l+++Gl   +++ + g P ++
  gi|336253505|ref|YP_004596612.1| 152 AVVGLLALAGYRQSSVLVVLGLGGAAAVAAAGAPTPT 188
                                       4666666666666777777777666666666666664 PP

  == domain 3  score: 85.4 bits;  conditional E-value: 3.8e-28
                          MFS_MOT1   2 elsgalgdlglTllnlvialaala......slsltalllsvGlmnlltglfggvPmchgAgglaaqyrfgartgaag 72 
                                       +l+g++++lg+T+ n++ia+a+l+      ++s++ l++s+G+  l+++++gg+Pmchg+ggla++y+fgartg+a+
  gi|336253505|ref|YP_004596612.1| 206 ALEGTVAQLGMTVGNAAIATALLCgdlydrDISADDLSTSMGVTCLAAVPLGGIPMCHGSGGLAGKYAFGARTGGAN 282
                                       6899**************************999******************************************** PP

                          MFS_MOT1  73 illGlvllllgltgllerllrliPksvlgglllgaGleL 111
                                       +llG+ +++l+++    +ll+++P+++lg+ll++++leL
  gi|336253505|ref|YP_004596612.1| 283 VLLGIGYVALAMVA-TGALLAAFPTALLGVLLAVVALEL 320
                                       ***********996.899*******************98 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 1
                          MFS_MOT1  26 slsltalllsvGlmnlltg 44 
                                       ++ +  l++ vG++ +l++
  gi|336253505|ref|YP_004596612.1| 339 GVGVVGLAVNVGVAFVLGA 357
                                       3334444444444444444 PP

>> PorA  Porin PorA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2     0.023   2.1e+02       2      18 ..      46      62 ..      45      86 .. 0.84
   2 ?    8.8   4.2   9.8e-05      0.88       3      40 ..     168     205 ..     166     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.023
                              PorA  2 sllllalGvallvlAil 18
                                      +++l+++Gv+ +v+++ 
  gi|336253505|ref|YP_004596612.1| 46 PHVLVGFGVFQIVWGLY 62
                                      789***********985 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 9.8e-05
                              PorA   3 llllalGvallvlAillptyvvpklkklPldldattvt 40 
                                       l++l+lG a+ v+A+ +pt +vp+l++ P+ + + t +
  gi|336253505|ref|YP_004596612.1| 168 LVVLGLGGAAAVAAAGAPTPTVPELAVFPAGTPSLTAA 205
                                       689**************************998776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.19s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 3113.64
//
Query:       gi|336253506|ref|YP_004596613.1|  [L=295]
Description: dihydrodipicolinate synthase [Halopiger xanaduensis SH-6]
Scores for 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-66  222.7   0.0    4.9e-66  222.4   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
       0.19   12.2   1.9        4.3    7.8   0.0    2.7  3  PRA-PH    Phosphoribosyl-ATP pyrophosphohydrolase


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 !  222.4   0.0   5.4e-70   4.9e-66       2     286 ..       7     289 ..       6     291 .. 0.96

  Alignments for each domain:
  == domain 1  score: 222.4 bits;  conditional E-value: 5.4e-70
                                       -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE-- CS
                             DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvG 78 
                                       ++gi  ++vtpfd + ++d+ al+++ + l+  g+d+++  GttGE+a+ls +e+  ++e +ve ++g +pv+ag+G
  gi|336253506|ref|YP_004596613.1|   7 LAGITCPVVTPFDDANQIDEDALETVLDDLVSGGIDAVFPNGTTGEFASLSPDERRRVLEFTVEQVGGDVPVVAGAG 83 
                                       68999************************************************************************ PP

                                       -SSHHHHHHHHHCCCCCT-SEEEEE---SS--.-HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTS CS
                             DHDPS  79 snstseaiklakkaeeaGadgvlavtPYYnkp.sqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLael 154
                                       + s++e ++  ++a++ Gad++++v+PY+    +++g + +f++++ +  lp++lYn+p+ tg ++++etv++ ae 
  gi|336253506|ref|YP_004596613.1|  84 ATSVAETLEYLEEAADLGADAAVVVPPYFHAAnAPAGNERFFETVADESPLPLLLYNIPACTGGEIAVETVEAVAEH 160
                                       ****************************98752689**********8888*************************** PP

                                       TTEEEEEE-SS-CTHHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHH CS
                             DHDPS 155 enivgvKeavgdleevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaae 231
                                       +n+vg+K+ +gdle+    ++ + ++++++ G+d+lll+ l +GadG + + sn ++e + +l++ ++    +  a+
  gi|336253506|ref|YP_004596613.1| 161 DNVVGLKDSSGDLEYFLAAMRATPDEFLLLQGYDALLLPSLRMGADGGVNALSNAVPEAYSELYETAET---ERGAT 234
                                       ****************************************************************99887...999** PP

                                       HHHHHHHHHHHCCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHH CS
                             DHDPS 232 lnekllplikilfaepnvilvktalellGlvveatlrkPltpleeeekeeleall 286
                                       l+  + +l+++  a ++    k+ale  ++  ++ +r+Pl+++ ++   ++e+++
  gi|336253506|ref|YP_004596613.1| 235 LQDAIADLFEACGAYGFAPATKAALEHRDVIPTDAVRPPLVTVPDDGCAAIEDAV 289
                                       *******************************************999887777765 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.73   6.6e+03      46      57 ..      89     100 ..      55     106 .. 0.76
   2 ?    7.8   0.0   0.00048       4.3      32      64 ..     147     180 ..     126     184 .. 0.84
   3 ?    2.9   0.1     0.017   1.5e+02      29      58 ..     214     243 ..     204     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.73
                                       HHHHHHHHHHHH CS
                            PRA-PH  46 dlaeladelaDl 57 
                                       +  e+ +e+aDl
  gi|336253506|ref|YP_004596613.1|  89 ETLEYLEEAADL 100
                                       556777778776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00048
                                       HHHHHHHHHHT-SC.HHHHHHHHHHHHHHHHHHH CS
                            PRA-PH  32 gEEavElleaaseg.dlaeladelaDllYvtygl 64 
                                       gE avE++ea++e+ + ++l d   Dl Y++ ++
  gi|336253506|ref|YP_004596613.1| 147 GEIAVETVEAVAEHdNVVGLKDSSGDLEYFLAAM 180
                                       6778*******97736789***********9876 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHT-SCHHHHHHHHHHHHH CS
                            PRA-PH  29 aligEEavElleaasegdlaeladelaDll 58 
                                       +++ E   El e+a+ ++ a l d++aDl+
  gi|336253506|ref|YP_004596613.1| 214 NAVPEAYSELYETAETERGATLQDAIADLF 243
                                       56778889********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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 0.20s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2492.08
//
Query:       gi|336253507|ref|YP_004596614.1|  [L=737]
Description: DNA mismatch repair protein mutL [Halopiger xanaduensis SH-6]
Scores for complete 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  122.5   0.0    1.8e-35  121.9   0.0    1.3  1  MutL_C          MutL C terminal dimerisation domain
      5e-33  113.3   0.0    9.2e-33  112.4   0.0    1.4  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai
      5e-13   49.0   0.0    1.1e-12   48.0   0.0    1.6  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    1.8e-05   25.2   0.0    3.5e-05   24.3   0.0    1.5  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
  ------ inclusion threshold ------
        2.5    6.5   5.0        3.7    6.0   5.0    1.2  1  Macoilin        Macoilin family


Domain annotation for each model (and alignments):
>> MutL_C  MutL C terminal dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.9   0.0   4.9e-39   1.8e-35       3     147 .]     541     688 ..     539     688 .. 0.96

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 4.9e-39
                                       -EEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHCCHSSB-EEEEEEEEEEE--HHHHHHHHHCHHHHHHC CS
                            MutL_C   3 GkalgqvhgtyilaenedglvlvDqhaAherilyeklkeqlkeeelksQpLliPlvlelspeeaalleehkeeLakl 79 
                                       +++lgq+++ty+++e++dgl lvDqhaA+er++ye+l+ +++ +  ++Q+L  P++lel++ ea+++  + ++L++l
  gi|336253507|ref|YP_004596614.1| 541 LRVLGQFDDTYLVCETPDGLALVDQHAADERVNYERLRDAFADDP-AAQALASPVELELTAAEAEAFAGYEDALERL 616
                                       799***************************************975.******************************* PP

                                       T-EEEE-STTEEEEEEEECCCTTTSHHHHHHHHHHHHCCCSS....-H-HCCHHHHHHHHCTTSSSSSS--- CS
                            MutL_C  80 GfeleefgpnslivravPallrqqnleelirelleelaekgk....esleekleellatmachssvkagrrl 147
                                       Gf   ++++++++v++vPa+l+++ ++e +r++l+++ e ++    e++++  +e l  +ac  s   +++l
  gi|336253507|ref|YP_004596614.1| 617 GFYADRVDDRTIAVTTVPAVLEETLEPENLRDVLTSFIEGDReagaETVDALADEFLGDLACYPSLTGNTSL 688
                                       ***************************************9999997669**************999888765 PP

>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4   0.0   2.6e-36   9.2e-33       3     118 ..     216     337 ..     214     338 .. 0.97

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 2.6e-36
                                       HHHHHHHHCCEEEEEEEETT......EEEEEEEE-CCG-BTTGGEEEEEETTEEE--HHHHHHHHHHHHCCSSSSSB CS
                    DNA_mis_repair   3 avlgkevaenlleiekeeeq......lkieGfiskpelsrskrdkqflfvNgRlvkskelkkaireaYkellpkgry 73 
                                       +v+g+eva++++++e++e++        ++G++s+pe++rs+r++  ++vNgR+v+   +++ i+ aY ++l  +ry
  gi|336253507|ref|YP_004596614.1| 216 SVYGREVASSMIRVEADEDElppgpvDAVSGLVSHPETNRSSREYLATYVNGRAVTADAIREGIMGAYGTQLGGDRY 292
                                       79*************8888879999889************************************************* PP

                                       -EEEEEEEESSGGEE-TSSTT----EETTHHCHHHHHHHHHHHHH CS
                    DNA_mis_repair  74 pvvvLnleidpeevDvNvhPtKreVrfqdeeevieaieealkeal 118
                                       p+vvL+le++ ++vDvNvhP+KreVrf d+++v+++i++a+++al
  gi|336253507|ref|YP_004596614.1| 293 PFVVLFLEVPGDAVDVNVHPRKREVRFDDDDAVRRQIDAAVESAL 337
                                       ******************************************998 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 !   48.0   0.0     3e-16   1.1e-12       4      67 ..      28      89 ..      24     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 3e-16
                       HATPase_c_3  4 ekAlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrks 67
                                       +A+ elv+NsldAda++v+++v++    t+ i++ DdG Gm+e++l+ a r +t+sk +  + 
  gi|336253507|ref|YP_004596614.1| 28 ASAVKELVENSLDADANRVDVTVEEG--GTELIRVADDGRGMNEADLRAAVREHTTSKIEGLED 89
                                      78**********************95..689********************9999998754333 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 !   24.3   0.0   9.7e-09   3.5e-05       6      58 ..      27      76 ..      22     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 9.7e-09
                                      HHHHHHHHHHHHHHHHSTTTEEEEEEEEEE.TEEEEEEEESSSSSTTHHHTGTC CS
                         HATPase_c  6 LrqiisnlvdNavkfatkageieveikase.ddlvisveDnGiGipkedlkklf 58
                                         ++++lv+N++++  +a++++v+++  e ++  i+v D+G+G++++dl    
  gi|336253507|ref|YP_004596614.1| 27 PASAVKELVENSLDA--DANRVDVTVE--EgGTELIRVADDGRGMNEADLRAAV 76
                                      56789*********6..899*******..44799***************99333 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.0     0.001       3.7     256     367 ..     397     513 ..     341     571 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.001
                          Macoilin 256 rekkksakssrsdskkkhehn....esvdsklqekeymenkskskrlsksessgsesellveesvkskssssssssn 328
                                         + +++ +s+ d++++ ++     ++v s ++e e ++n s +    ++e++ +e   + ++s++ + +  +  ++
  gi|336253507|ref|YP_004596614.1| 397 DASGTESDDSSRDTAESSSDDgstaSAVASAASESEPTANASAASSTGRTETERTERAATDSDSASPSRTDRTDGTA 473
                                       22211111111111111111111112333333333333333333333222222222222222222222222222222 PP

                          Macoilin 329 knskkasagsagssnssskkhsessksvt.sssssknskk 367
                                       ++++  s++sags+ s s+++ +  +  +  + s++ ++k
  gi|336253507|ref|YP_004596614.1| 474 PSTEFVSSSSAGSAGSGSRSKPDDGSTAAdRTDSDRTDRK 513
                                       4444444444444444333332222222102223334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (737 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.39
# Mc/sec: 5601.72
//
Query:       gi|336253508|ref|YP_004596615.1|  [L=218]
Description: hypothetical protein Halxa_2111 [Halopiger xanaduensis SH-6]
Scores for 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  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1645.38
//
Query:       gi|336253509|ref|YP_004596616.1|  [L=519]
Description: Na+/solute symporter [Halopiger xanaduensis SH-6]
Scores for complete 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-42  146.1  24.2    1.9e-42  145.5  24.2    1.2  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 !  145.5  24.2   1.1e-46   1.9e-42       1     403 [.      35     429 ..      35     431 .. 0.86

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 1.1e-46
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvll.elgalllvlllllllaerlr....nagalTlp 72 
                                       ++la+r l+ +vl  +++a+ +sa  f  ++ +++a G ++vl+  l   +++ +l+++++ +      + g +Tl 
  gi|336253509|ref|YP_004596616.1|  35 FYLASRTLGTVVLLFTTFATLLSAFTFFAGPNVAYAQGPEWVLVmGLMDGIIFAILWYVIGYKQWllgrQRGYVTLG 111
                                       8***************************************987514555567777888887654457889******* PP

                               SSF  73 dylskRfkgkrilvylsalslllvitlklsvdlvggaklielal..GlnyetavlllaaltalYtviGGllAvvytd 147
                                       ++l  Rf +kr l+ l a ++ll ++ +++ + vg++  +e +    + y ++  l+ a ++lY+v+ G++ + +td
  gi|336253509|ref|YP_004596616.1| 112 EMLGDRFASKR-LRGLVAGVSLLWLFPYVMLQQVGAGTALEALTdgAVPYAAGAGLITAFMILYVVVAGMRGIAWTD 187
                                       ***********.6777777777777778888888887777766533589**************************** PP

                               SSF 148 tiqavlmlvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvR 224
                                       t+q+  mlv + + l+  l evGg  +++  l++ +  ++ +l  +s  ++     +ls  + +++Gva+ p + +R
  gi|336253509|ref|YP_004596616.1| 188 TLQGAFMLVTTWVALLWLLAEVGGPGAATAALASSEE-TAGFLSLGS--DYYTRRWMLSTAITIGFGVAMFPQVNQR 261
                                       ***********************99999998888877.445555444..34556678888899************** PP

                               SSF 225 flaakdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavm 301
                                       f+aa +   + +++  l ++l ++l+        +  + ga  +  g +v +   ++p    +  p ++a+l++a +
  gi|336253509|ref|YP_004596616.1| 262 FFAAGSRTVLKRSF-ALWPILCVLLFV-------PSFMLGAWARGLGVAVPEGGNVLPAVLAEYTPVWFAALVIAGA 330
                                       ****9876666665.555555544444.......677777888888999999999********************** PP

                               SSF 302 lAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafagla 378
                                       +Aa+ms+ +s+lls+ss ft+DlY  ++ +   +e+++  ++r+ v+v +  a+++ + ++   ++++  +af+g+a
  gi|336253509|ref|YP_004596616.1| 331 MAAMMSSSDSMLLSGSSYFTRDLYRPFVDRT-LSERREDLLARVGVVVFATGAFVASLLSPAP-LFDIGDAAFSGFA 405
                                       ****************************999.99999999*******************9999.************9 PP

                               SSF 379 savlavillalfwkrvneqGAlagl 403
                                          l+v l al+w   ++ G  +g+
  gi|336253509|ref|YP_004596616.1| 406 QLALPV-LVALYWRGTTRTGITVGI 429
                                       988887.56********99987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); 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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 3601.36
//
Query:       gi|336253510|ref|YP_004596617.1|  [L=88]
Description: hypothetical protein Halxa_2113 [Halopiger xanaduensis SH-6]
Scores for 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-15   54.5  13.6    9.3e-15   54.3  13.6    1.1  1  DUF3311     Protein of unknown function (DUF3311)
  ------ inclusion threshold ------
      0.075   12.6   0.3      0.093   12.3   0.3    1.1  1  TRAP-gamma  Translocon-associated protein, gamma subunit (TRA


Domain annotation for each model (and alignments):
>> DUF3311  Protein of unknown function (DUF3311)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3  13.6     1e-18   9.3e-15       1      59 [.       9      67 ..       9      69 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1e-18
                           DUF3311  1 vlllvpvlvalllvpfynrvdpvllGlPffywwqllwvllasvvtwlayrlakredaee 59
                                      ++++  vl al +++f++++d ++ G+P+++ww+++w+ las+v+  ++++a++ ++e 
  gi|336253510|ref|YP_004596617.1|  9 WIAVGVVLCALSIPWFLWGNDATVAGVPLWLWWHVGWMGLASLVFRYFAQRAWGLGIEP 67
                                      7889999***********************************************99986 PP

>> TRAP-gamma  Translocon-associated protein, gamma subunit (TRAP-gamma)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3     1e-05     0.093      20      51 ..      24      55 ..      19      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1e-05
                        TRAP-gamma 20 lfyvnalivsaipiwlfwrihqmelleslilf 51
                                      ++++n + v+ +p+wl+w +  m l++ ++ +
  gi|336253510|ref|YP_004596617.1| 24 FLWGNDATVAGVPLWLWWHVGWMGLASLVFRY 55
                                      579********************998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); 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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 665.28
//
Query:       gi|336253511|ref|YP_004596618.1|  [L=306]
Description: ArsR family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-15   56.4   0.3      5e-15   55.3   0.0    1.7  2  HTH_20    Helix-turn-helix domain
      2e-05   24.1   0.0    3.6e-05   23.2   0.0    1.5  1  HTH_24    Winged helix-turn-helix DNA-binding
    0.00014   21.6   0.0    0.00029   20.6   0.0    1.5  1  MarR_2    MarR family
     0.0006   19.6   0.0    0.00099   18.9   0.0    1.3  1  HTH_5     Bacterial regulatory protein, arsR family
     0.0014   19.0   0.0     0.0026   18.1   0.0    1.3  1  FaeA      FaeA-like protein
     0.0048   16.8   0.1      0.014   15.2   0.0    1.8  2  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.052   13.8   0.0      0.083   13.2   0.0    1.3  1  DUF2513   Hypothetical protein (DUF2513)
       0.11   12.5   0.0        0.2   11.6   0.0    1.4  1  HTH_12    Ribonuclease R winged-helix domain
        0.2   11.2   0.0        0.3   10.7   0.0    1.2  1  ArsR      ArsR 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 !   55.3   0.0   2.5e-18     5e-15       1      58 [.      29      85 ..      29      86 .. 0.97
   2 ?   -3.7   0.0       6.4   1.3e+04      24      34 ..     111     121 ..     109     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 2.5e-18
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      d +++AL++ + rri++ L ++e+ t+s++a+++d s ++++yHL+ LeeagLvevv+
  gi|336253511|ref|YP_004596618.1| 29 DAVFSALSSTTARRIYARL-DEEPGTPSDVADAVDSSIQNVRYHLENLEEAGLVEVVD 85
                                      679****************.************************************96 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.4
                                       TB-HHHHHHHH CS
                            HTH_20  24 gltaselaerl 34 
                                       + tas+l+ +l
  gi|336253511|ref|YP_004596618.1| 111 ESTASQLKTAL 121
                                       56899999887 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   1.8e-08   3.6e-05       4      48 .]      39      82 ..      36      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.8e-08
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      t r+I+  L ++p+ + +++A++++ S+++v+++l++Lee+Gl++
  gi|336253511|ref|YP_004596618.1| 39 TARRIYARLDEEPG-TPSDVADAVDSSIQNVRYHLENLEEAGLVE 82
                                      67889999999999.679*************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.5e-07   0.00029       6      54 ..      39      84 ..      33      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.5e-07
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      + +r+ a L  +pg   t++++a++ + s ++v ++l+ L++aGLve +
  gi|336253511|ref|YP_004596618.1| 39 TARRIYARLDEEPG---TPSDVADAVDSSIQNVRYHLENLEEAGLVEVV 84
                                      44455555899999...*****************************987 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 !   18.9   0.0     5e-07   0.00099      11      46 ..      47      82 ..      39      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5e-07
                                      HTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 11 LaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      L e++ + ++ a++++ s  +v++HL  L+eaGLVe
  gi|336253511|ref|YP_004596618.1| 47 LDEEPGTPSDVADAVDSSIQNVRYHLENLEEAGLVE 82
                                      56788899***************************8 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.3e-06    0.0026      14      47 ..      50      83 ..      39      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.3e-06
                                      ----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEE CS
                              FaeA 14 apckTreiAdalglsaYQaRyYLeqLekegkikr 47
                                       p++ +++Ada+  s+  +Ry Le+Le +g ++ 
  gi|336253511|ref|YP_004596618.1| 50 EPGTPSDVADAVDSSIQNVRYHLENLEEAGLVEV 83
                                      79999*************************9985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.1e-06     0.014      18      56 ..      47      85 ..      39     102 .. 0.90
   2 ?   -1.9   0.0       1.6   3.2e+03      10      31 ..      94     120 ..      90     123 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.1e-06
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      l ++p t +++a +++ + ++v   L++Le++GlVe+++
  gi|336253511|ref|YP_004596618.1| 47 LDEEPGTPSDVADAVDSSIQNVRYHLENLEEAGLVEVVD 85
                                      468999******************************975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                                       CCCHCHH.....HHHHCCCHHCHHCCC CS
                              TrmB  10 EakvYla.....Llklgpatadeiaee 31 
                                       E++vY++     +++++++ta+++  +
  gi|336253511|ref|YP_004596618.1|  94 EMSVYATtdgplIVTSDESTASQLKTA 120
                                       666666433333568888888887766 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.2e-05     0.083      36      65 ..      62      91 ..      36     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                           DUF2513 36 gyskeeiiyhlkllaeagLieaekkkakss 65
                                      + s +++ yhl+ l+eagL+e+++++++s+
  gi|336253511|ref|YP_004596618.1| 62 DSSIQNVRYHLENLEEAGLVEVVDTWYSSR 91
                                      3455689******************99988 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 ?   11.6   0.0    0.0001       0.2      33      49 ..      66      82 ..      56      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                            HTH_12 33 ravRyrLrkleergltr 49
                                      + vRy+L  lee gl++
  gi|336253511|ref|YP_004596618.1| 66 QNVRYHLENLEEAGLVE 82
                                      78*************97 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00015       0.3      10      59 ..      31      83 ..      27     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                              ArsR 10 llqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEs 59
                                      ++ +++s+t +++y +l +e  t +++++ ++++   v+  l+ L++++l+E 
  gi|336253511|ref|YP_004596618.1| 31 VFSALSSTTARRIYARLDEEPGTPSDVADAVDSSiqnVRYHLENLEEAGLVEV 83
                                      78999**************************9875568889**********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2333.17
//
Query:       gi|336253512|ref|YP_004596619.1|  [L=522]
Description: hypothetical protein Halxa_2115 [Halopiger xanaduensis SH-6]
Scores for 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-12   46.3   0.4      2e-11   44.2   0.3    2.2  2  Toprim_4  Toprim domain
    2.3e-06   28.0   0.0    7.3e-06   26.3   0.0    2.0  1  Toprim_2  Toprim-like
  ------ inclusion threshold ------
       0.03   14.5   0.2       0.16   12.2   0.2    2.2  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 !   44.2   0.3   3.3e-15     2e-11       2      70 ..     168     245 ..     167     266 .. 0.86
   2 ?   -3.0   0.0       1.7     1e+04      49      65 ..     267     283 ..     255     301 .. 0.68

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 3.3e-15
                          Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklkt.enlve....aekkvkevilaldgDa.....eGe 68 
                                       +ii+VEg+aDvl l k+g+kn++av g+++ p + +++++ +t +++++    ++ +++e+ +++d D+     +Ge
  gi|336253512|ref|YP_004596619.1| 168 AIIVVEGRADVLTLLKYGVKNAIAVEGTNV-PDAVAELTRHRTvTAFLDgdrgGDLILEELSQVGDIDYvafapAGE 243
                                       79****************************.******9999999999999999999999999999999955555555 PP

                          Toprim_4  69 at 70 
                                        +
  gi|336253512|ref|YP_004596619.1| 244 SV 245
                                       44 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                          Toprim_4  49 eaekkvkevilaldgDa 65 
                                        ++++ +e + a+dg+ 
  gi|336253512|ref|YP_004596619.1| 267 SGLNEPREAVAATDGST 283
                                       35666689999999876 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.2e-09   7.3e-06       1      66 [.     170     229 ..     170     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.2e-09
                          Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlae 66 
                                       +v+Eg  D+l l+++g k   n++a+ Gt + + a+ +l r+  ++v   lD D+ G+   ++l++
  gi|336253512|ref|YP_004596619.1| 170 IVVEGRADVLTLLKYGVK---NAIAVEGT-NVPDAVAELTRH--RTVTAFLDGDRGGDLILEELSQ 229
                                       69***************9...********.888888889999..899999********99998876 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   2.7e-05      0.16       2      86 ..     169     230 ..     168     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                                       EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHH CS
                            Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGea 78 
                                       +++vEg +d+ t+ k+   g ++++a+ G+ +  +                      ++ r   +   +D+Dr G  
  gi|336253512|ref|YP_004596619.1| 169 IIVVEGRADVLTLLKY---GVKNAIAVEGTNVPDAV--------------------AELTRHRTVTAFLDGDRGGDL 222
                                       89**************...9*********9887776....................455588888888999999999 PP

                                       HHHHHHHH CS
                            Toprim  79 iawellev 86 
                                       i  el +v
  gi|336253512|ref|YP_004596619.1| 223 ILEELSQV 230
                                       98888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3401.59
//
Query:       gi|336253513|ref|YP_004596620.1|  [L=97]
Description: hypothetical protein Halxa_2116 [Halopiger xanaduensis SH-6]
Scores for 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   12.1   6.1       0.22   11.5   6.1    1.3  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)


Domain annotation for each model (and alignments):
>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   6.1   1.3e-05      0.22      63     109 ..      37      87 ..      22      94 .. 0.42

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.3e-05
                       Trypan_PARP  63 pepepepepepepepep.......etepeeepepepepepepepepepepepep 109
                                           pepe epe+ep          +   +  + + +   +p ++p+ e+e  p
  gi|336253513|ref|YP_004596620.1|  37 AVSVPEPELEPESEPATvesdgaaRA-DADRYDSNDGATSNPVSDPNQESE--P 87 
                                       33445555555555544322221111.111222222333344444443333..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 770.12
//
Query:       gi|336253514|ref|YP_004596621.1|  [L=352]
Description: hypothetical protein Halxa_2117 [Halopiger xanaduensis SH-6]
Scores for 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  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2926.84
//
Query:       gi|336253515|ref|YP_004596622.1|  [L=447]
Description: hypothetical protein Halxa_2118 [Halopiger xanaduensis SH-6]
Scores for 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-50  170.9  16.6    2.8e-50  170.9  16.6    3.1  2  DUF92     Integral membrane protein DUF92


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 ?   -4.6   6.5      0.65   1.2e+04     171     193 ..      89     142 ..       8     146 .. 0.70
   2 !  170.9  16.6   1.6e-54   2.8e-50       2     233 ..     210     430 ..     209     433 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 0.65
                             DUF92 171 l...............................lillltlaGllGsllDSlLGat 193
                                       +                               +++++t+a+++G+++   +G+t
  gi|336253515|ref|YP_004596622.1|  89 VfvgtavlvgygnlgeqlarlrtdhdvarvtvFAAVATVAAVVGQVATAAIGGT 142
                                       133333333444555666666666677776666677777788888877777776 PP

  == domain 2  score: 170.9 bits;  conditional E-value: 1.6e-54
                             DUF92   2 ltlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKa..kleeekegaRdav 76 
                                       +t+ ++++a+  ++ +++G+l++vl+++l+++  +g+ +f++l+ Ff +g l tk+++++K+  +++e+++gaR+  
  gi|336253515|ref|YP_004596622.1| 210 VTVGFGYLAYALETASVAGMLTGVLLCLLTIVL-GGYGWFVVLVSFFAIGGLSTKFRYDRKEqlGVAEDNDGARGSG 285
                                       688999**********************99999.5668************************88889999******* PP

                             DUF92  77 qVlanslvalllally...........lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnG 142
                                       +Vl+n++va++++l y           l+ +++l+++++s+A++++DTl+SE+G++++  +prlittl++v+pGt+G
  gi|336253515|ref|YP_004596622.1| 286 NVLGNAAVAIAAVLGYaassatllpgeLEPSVFLFAFAGSVATAMSDTLSSEIGSVFE--TPRLITTLEPVEPGTDG 360
                                       *****************99999988774478999********************9995..6**************** PP

                             DUF92 143 gVsllGllasllGalliallavlllllel..lillltlaGllGsllDSlLGatlqasvvdkrtgkvvegeggekvvs 217
                                       gV++ G la+l+Ga+++a +++ll++      ++++++aG++G+++DSlLGatl+ s                    
  gi|336253515|ref|YP_004596622.1| 361 GVTWQGELAGLAGAAVVAGISYLLFPEVGvaGAAIIVAAGFVGMTVDSLLGATLEGS-------------------- 417
                                       ******************88655544333688899999*****************99.................... PP

                             DUF92 218 GldlLdNnaVNllsal 233
                                          +L N++VN+l++l
  gi|336253515|ref|YP_004596622.1| 418 ---FLGNQGVNFLATL 430
                                       ...6666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); 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:                         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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.37
# Mc/sec: 3624.85
//
Query:       gi|336253516|ref|YP_004596623.1|  [L=210]
Description: undecaprenyl diphosphate synthase [Halopiger xanaduensis SH-6]
Scores for 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-24   84.2   0.0    2.5e-23   82.8   0.0    1.6  2  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 ?   -1.7   0.0     0.092   1.7e+03     179     194 ..      39      56 ..      27      64 .. 0.70
   2 !   82.8   0.0   1.4e-27   2.5e-23     117     224 .]     105     209 ..      92     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.092
                                       -S-TTSSTTTTTT-E..E CS
                      Prenyltransf 179 eRlSnFllwqlayse..l 194
                                       e l +F+ w  ay++   
  gi|336253516|ref|YP_004596623.1|  39 ETLTDFFEWAFAYASrvT 56 
                                       567888888888877431 PP

  == domain 2  score: 82.8 bits;  conditional E-value: 1.4e-27
                                       EEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT- CS
                      Prenyltransf 117 lvlniavnYgsrdeiveavrelvkekseekkk.eeideetlekhlytakalpdpDlliRtsGeeRlSnFllwqlays 192
                                       + ++i +  g+++e ++avr+l++++ + + + ++id+e +e+hl       +pDl+i+t+  eRlS+F++wq++ys
  gi|336253516|ref|YP_004596623.1| 105 APIQIGIGLGGKHEFTSAVRTLAESVDNGDLEpAAIDDERVEEHLVF--P-SEPDLVIKTG-AERLSDFMIWQSVYS 177
                                       567888999*************9888766666466799********8..4.78******97.579************ PP

                                       EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                      Prenyltransf 193 elyfldvlWPdfskedllealleyqkrerrfg 224
                                       elyf+d  W df+++d+l+a++e+ +r+rrfg
  gi|336253516|ref|YP_004596623.1| 178 ELYFTDINWRDFRERDFLRAVREFCNRSRRFG 209
                                       ******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1603.07
//
Query:       gi|336253517|ref|YP_004596624.1|  [L=104]
Description: hypothetical protein Halxa_2120 [Halopiger xanaduensis SH-6]
Scores for 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:                       359  (0.0200234); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 832.18
//
Query:       gi|336253518|ref|YP_004596625.1|  [L=313]
Description: Undecaprenyl pyrophosphate synthase [Halopiger xanaduensis SH-6]
Scores for 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-65  218.8   0.0    8.1e-65  218.5   0.0    1.1  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 !  218.5   0.0   4.5e-69   8.1e-65       1     221 [.      31     252 ..      31     255 .. 0.91

  Alignments for each domain:
  == domain 1  score: 218.5 bits;  conditional E-value: 4.5e-69
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHH...HHHHHH CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellk...eellke 74 
                                       i DGNrR+A+++g e++e Gh+aGae+ +++le+c+e+gv+ +t+Y+fSteNf R++e+ +al++ll    +e+++ 
  gi|336253518|ref|YP_004596625.1|  31 IQDGNRRYARQNGDEPHE-GHRAGAETTEQVLEWCQEIGVEELTLYTFSTENFDRPAEQKEALFDLLCeklREFAD- 105
                                       78***********66666.************************************************733333443. PP

                                       HHHHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GG CS
                      Prenyltransf  75 elkellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.ee 150
                                        ++++++++v++r+iG++e+lpe+v++a++ ae++t++ + ++vlnia++Yg+r+ ++ea+r +++++ + + + +e
  gi|336253518|ref|YP_004596625.1| 106 -ADRVHENEVSIRAIGEIEMLPERVQDAVDYAERRTRDYD-RFVLNIALAYGGRSRLLEAARGVARDVDAGELEpNE 180
                                       .4699999*****************************555.5**********************9998766655577 PP

                                       HSHHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-E..EEEESSSGGG--HHHHHHHHHHHHHCHH CS
                      Prenyltransf 151 ideetlekhlytakalpdpDlliRtsGeeRlSnFllwqlayse..lyfldvlWPdfskedllealleyqkrer 221
                                       id et+e++ly  + + d+Dl+iR +GeeR SnFl w++  +e  ++f++ +WP+fsk+d+l+ +++y++r++
  gi|336253518|ref|YP_004596625.1| 181 IDVETIERRLYD-RPVRDVDLIIRPAGEERTSNFLPWHANGNEaaVFFCTPYWPEFSKADFLRGIRTYEHRKE 252
                                       899********6.558**********************988889999**********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2359.24
//
Query:       gi|336253519|ref|YP_004596626.1|  [L=135]
Description: hypothetical protein Halxa_2122 [Halopiger xanaduensis SH-6]
Scores for 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   13.0   0.1       0.26   11.6   0.1    1.7  1  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 ?   11.6   0.1   1.4e-05      0.26      25      48 .]     110     133 ..     108     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                             Nif11  25 acsdheevvalAkeaGyefteeel 48 
                                       a +dhe++++ ++e+Gy++t  e+
  gi|336253519|ref|YP_004596626.1| 110 ASADHEAILEDVRELGYDVTGVEG 133
                                       667*****************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1112.97
//
Query:       gi|336253520|ref|YP_004596627.1|  [L=332]
Description: transcription initiation factor IIB [Halopiger xanaduensis SH-6]
Scores for 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-32  111.1   0.9    2.7e-15   56.2   0.0    2.5  3  TFIIB           Transcription factor TFIIB repeat
      2e-13   49.6   0.3    3.4e-13   48.9   0.3    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
    0.00031   20.8   0.0     0.0063   16.6   0.0    2.2  2  Cyclin_C        Cyclin, C-terminal domain
     0.0029   17.5   1.6     0.0076   16.1   0.8    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.034   13.9   0.0        0.1   12.3   0.0    1.8  2  Cyclin_N        Cyclin, N-terminal domain
      0.066   13.2   0.0       0.16   12.0   0.0    1.6  1  HTH_11          HTH domain
       0.14   12.2   0.7         15    5.7   0.1    2.5  2  TFIIB_C_1       Transcription factor IIB C-terminal module 1
       0.21   11.9   0.3       0.21   11.9   0.3    2.0  2  zinc_ribbon_9   zinc-ribbon
        3.1    7.5   5.0        8.1    6.1   1.3    2.7  3  zf_UBZ          Ubiquitin-Binding Zinc Finger


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 ?   -3.9   0.0       7.6   1.5e+04      32      40 ..      10      18 ..       8      19 .. 0.80
   2 !   56.2   0.0   1.4e-18   2.7e-15       2      67 ..     152     217 ..     151     221 .. 0.97
   3 !   53.2   0.2   1.1e-17   2.2e-14       3      71 .]     247     315 ..     245     315 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7.6
                                      TSGCTTHHH CS
                             TFIIB 32 kGrspagia 40
                                       Gr+p+ +a
  gi|336253520|ref|YP_004596627.1| 10 DGRQPQEVA 18
                                      799999988 PP

  == domain 2  score: 56.2 bits;  conditional E-value: 1.4e-18
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS-- CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVs 67 
                                       +r+a+al+Lpe  ++ A  l+++a++e++l Grs +++a Acly A+r+ ++ rt + + sv++V+
  gi|336253520|ref|YP_004596627.1| 152 ERMASALDLPEPCRETAAVLYRRAVDEELLPGRSIEAMATACLYAAARQHGTPRTWATFESVSRVE 217
                                       79**************************************************************96 PP

  == domain 3  score: 53.2 bits;  conditional E-value: 1.1e-17
                                       HHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   3 rfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       +fa+al ++++ +  A e++++a+e++++ G+spag+aA+++y A+r+ +++ tqk i + + Vse ti
  gi|336253520|ref|YP_004596627.1| 247 QFASALSISDEAEHVAREILETAKEKGIHVGKSPAGLAASAIYAAARLTNERVTQKTIDEQTGVSEFTI 315
                                       79****************************************************************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 !   48.9   0.3   1.7e-16   3.4e-13       2      42 ..      36      75 ..      35      76 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.7e-16
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewre 42
                                      +CP+C+++ +v D+e+ge+ C +CGlVl+ +  d+gpewr+
  gi|336253520|ref|YP_004596627.1| 36 TCPECSGR-IVHDAEHGEHACAECGLVLDADELDYGPEWRA 75
                                      7******8.9******************************7 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.14   2.8e+02      47      83 ..     189     225 ..     185     232 .. 0.80
   2 !   16.6   0.0   3.2e-06    0.0063       3      90 ..     241     326 ..     240     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.14
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcv 83 
                                       +A+a+l++a ++ ++p    t+e++++++  +++  +
  gi|336253520|ref|YP_004596627.1| 189 MATACLYAAARQHGTPRTWATFESVSRVEIGRVQRAY 225
                                       8**********99888877888888888877776665 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.2e-06
                                       HHHHHHHHHCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHH CS
                          Cyclin_C   3 plsFlrrflkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgyskedl 79 
                                       pl++l  f  a  + +d e +++a+ +le++      ++ +p  +Aa+a+++a +  n+   ++t+ + tg+s+  +
  gi|336253520|ref|YP_004596627.1| 241 PLQYLGQFASAL-SISD-EAEHVAREILETAKEKGIHVGKSPAGLAASAIYAAARLTNERVTQKTIDEQTGVSEFTI 315
                                       677777775552.3346.99999***9999988888999************************************** PP

                                       HHHHHHHHHHH CS
                          Cyclin_C  80 kpcvelilell 90 
                                       ++ ++ +l+++
  gi|336253520|ref|YP_004596627.1| 316 RNRYQELLDAY 326
                                       ****9999876 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 !   16.1   0.8   3.8e-06    0.0076      30      59 ..      36      65 ..      24      67 .. 0.95
   2 ?   -1.5   0.0       1.2   2.4e+03       6      19 ..     263     276 ..     259     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.8e-06
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfeadrD 59
                                      tC+eC  +  ++ ++ ++ C +Cg+++d+D
  gi|336253520|ref|YP_004596627.1| 36 TCPECSGRIVHDAEHGEHACAECGLVLDAD 65
                                      8****9999999*****************9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                    OrfB_Zn_ribbon   6 eqleykakeyGikv 19 
                                       + + + ake+Gi+v
  gi|336253520|ref|YP_004596627.1| 263 REILETAKEKGIHV 276
                                       567789******98 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.2e-05       0.1      38      99 ..     151     211 ..     117     255 .. 0.84
   2 ?   -1.4   0.0      0.89   1.8e+03      43      91 ..     250     298 ..     239     320 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.2e-05
                                       HHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHH CS
                          Cyclin_N  38 lvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlv 99 
                                       l ++a+ ++l + +  +a++++ R + ++ +p + ++ ++++cL+ Aa+ + + p ++  + 
  gi|336253520|ref|YP_004596627.1| 151 LERMASALDLPEPCRETAAVLYRRAVDEELLPGRSIEAMATACLYAAARQHGT-PRTWATFE 211
                                       78899999****************************************98766.66665555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.89
                                       HHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS CS
                          Cyclin_N  43 ekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeis 91 
                                       + ++++ e  ++a ++l+   +k ++  +    ++a++++ Aa++ + +
  gi|336253520|ref|YP_004596627.1| 250 SALSISDEAEHVAREILETAKEKGIHVGKSPAGLAASAIYAAARLTNER 298
                                       5555555555555555555555555555556667777777777775544 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.8e-05      0.16      10      39 ..     293     322 ..     285     327 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.8e-05
                            HTH_11  10 leargpisgeeLAeeLnvSrrtvrrdIkaL 39 
                                       + +++ ++ +++ e+++vS+ t+r++ ++L
  gi|336253520|ref|YP_004596627.1| 293 RLTNERVTQKTIDEQTGVSEFTIRNRYQEL 322
                                       556777*******************87776 PP

>> TFIIB_C_1  Transcription factor IIB C-terminal module 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.019        38      16      65 ..     158     204 ..     145     222 .. 0.74
   2 ?    5.7   0.1    0.0075        15      21      63 ..     253     295 ..     243     300 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.019
                         TFIIB_C_1  16 srrdeavleealelakrfvGkrrergervekqeevaaaclmlaaerlrqP 65 
                                          +e+ +e a  l +r v +    g+ +e    +a acl  aa ++++P
  gi|336253520|ref|YP_004596627.1| 158 LDLPEPCRETAAVLYRRAVDEELLPGRSIEA---MATACLYAAARQHGTP 204
                                       5556666666666666666666666666654...589**********999 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0075
                         TFIIB_C_1  21 avleealelakrfvGkrrergervekqeevaaaclmlaaerlr 63 
                                       ++ +ea ++a++   + +e+g +v k     aa+ + aa+rl 
  gi|336253520|ref|YP_004596627.1| 253 SISDEAEHVAREILETAKEKGIHVGKSPAGLAASAIYAAARLT 295
                                       57899999*****************************999875 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00011      0.21      12      33 ..      21      46 ..      18      49 .. 0.79
   2 ?   -1.0   0.1       1.1   2.3e+03      19      28 ..      50      59 ..      43      59 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                     zinc_ribbon_9 12 Vsvspdedsd....vlCPhCgggFVE 33
                                      Vs++++e+++    ++CP+C g  V+
  gi|336253520|ref|YP_004596627.1| 21 VSAEETESAErsirATCPECSGRIVH 46
                                      7777777777776659*******998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                     zinc_ribbon_9 19 dsdvlCPhCg 28
                                      + + +C +Cg
  gi|336253520|ref|YP_004596627.1| 50 HGEHACAECG 59
                                      33456***97 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.3    0.0041       8.1       4      20 ..      36      53 ..      34      54 .. 0.93
   2 ?    2.7   0.1     0.047        94       4      17 ..      54      67 ..      53      68 .. 0.83
   3 ?   -3.2   0.0       3.3   6.6e+03      24      28 ..     260     264 ..     253     265 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0041
                            zf_UBZ  4 lCerCgkeipes.elqEH 20
                                      +C++C  +i ++ e  EH
  gi|336253520|ref|YP_004596627.1| 36 TCPECSGRIVHDaEHGEH 53
                                      8*********999****9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.047
                            zf_UBZ  4 lCerCgkeipesel 17
                                       C++Cg  +  +el
  gi|336253520|ref|YP_004596627.1| 54 ACAECGLVLDADEL 67
                                      6*****99988886 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.3
                            zf_UBZ  24 HfAkd 28 
                                       H+A++
  gi|336253520|ref|YP_004596627.1| 260 HVARE 264
                                       66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2483.72
//
Query:       gi|336253521|ref|YP_004596628.1|  [L=219]
Description: siroheme synthase [Halopiger xanaduensis SH-6]
Scores for 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   84.1   0.0    1.5e-23   83.2   0.0    1.5  1  NAD_binding_7   Putative NAD(P)-binding
    8.6e-07   28.3   0.0    2.1e-06   27.1   0.0    1.7  1  Sirohm_synth_M  Sirohaem biosynthesis protein central
  ------ inclusion threshold ------
      0.028   14.1   0.6       0.16   11.7   0.0    2.3  2  CysG_dimeriser  Sirohaem synthase dimerisation region
       0.12   12.0   0.1       0.16   11.5   0.1    1.3  1  Peripla_BP_4    Periplasmic binding protein domain


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 !   83.2   0.0   3.3e-27   1.5e-23       1     104 []       4     116 ..       4     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 3.3e-27
                     NAD_binding_7   1 lfldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele......elvkla..eeelekdlegad..lvia 67 
                                       l++d+++++vlvvGgG+v+ark+r+++++ a v+vv+p+   +++      el+++a  ++e+ ++le++d  l++a
  gi|336253521|ref|YP_004596628.1|   4 LLHDFTDETVLVVGGGPVGARKARRFARE-AAVVVVSPD---FADrefggaELIRAApdPDEIGGWLERVDpaLAVA 76 
                                       689**************************.*********...5555688899999975578899******999**** PP

                     NAD_binding_7  68 atddrelneriaeaakarrilvnvad...kpelcdfifpa 104
                                       atdd+++n+++ +aa++r+ilvn+ad   +++ +++++pa
  gi|336253521|ref|YP_004596628.1|  77 ATDDEAVNDALEAAARDRGILVNRADragERDAGSVVVPA 116
                                       **************************44444556677775 PP

>> Sirohm_synth_M  Sirohaem biosynthesis protein central
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   4.7e-10   2.1e-06       6      27 ..     125     146 ..     121     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.7e-10
                    Sirohm_synth_M   6 IaiSTnGksPrLAaliRreier 27 
                                       + iST+G +P+L++ +R+e+e+
  gi|336253521|ref|YP_004596628.1| 125 VSISTGGTAPALSKYLRQELEE 146
                                       78*******************8 PP

>> CysG_dimeriser  Sirohaem synthase dimerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.4      0.24   1.1e+03      39      57 ..      72      90 ..      68      90 .. 0.86
   2 ?   11.7   0.0   3.7e-05      0.16       3      45 ..     152     195 ..     150     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.24
                                      HHHHHTT-HHHHHHHHHHH CS
                    CysG_dimeriser 39 aelvlaGdeeeAealleqa 57
                                      a +v+a d+e+++ +le+a
  gi|336253521|ref|YP_004596628.1| 72 ALAVAATDDEAVNDALEAA 90
                                      6789999****99999976 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.7e-05
                                       HHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHT.-HHHHHHHHTT CS
                    CysG_dimeriser   3 GrLAelagrlRdrVkarlpdvaaRRrFWerff.dgpvaelvlaG 45 
                                       G++Ael+ +lR++ k+r   +++RR    +++ + +v  ++++G
  gi|336253521|ref|YP_004596628.1| 152 GDMAELCNELRSELKSRDVAPTRRREIVTDVVnSPDVWTALRSG 195
                                       99***********************9888888444455555555 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.6e-05      0.16      57      89 ..      70     104 ..      66     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                                       S.EEEE--SSHHHHHHHHHH.HHHTT-EEEEESTT CS
                      Peripla_BP_4  57 d.giivapvdstalapalkk.akaaGIpVvafdsd 89 
                                       d +++va++d +a+++al++ a+++GI V   d++
  gi|336253521|ref|YP_004596628.1|  70 DpALAVAATDDEAVNDALEAaARDRGILVNRADRA 104
                                       5599***************9899****99888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1679.48
//
Query:       gi|336253522|ref|YP_004596629.1|  [L=448]
Description: glutamyl-tRNA reductase [Halopiger xanaduensis SH-6]
Scores for 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  118.0   0.0    6.2e-34  116.9   0.0    1.5  1  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
      3e-34  118.1   0.9      5e-34  117.3   0.2    1.7  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    7.3e-22   77.6   1.6    1.6e-21   76.6   1.6    1.6  1  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
    1.3e-06   28.9   0.2    5.8e-06   26.8   0.2    2.2  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    3.9e-05   23.9   0.4    0.00016   21.8   0.1    2.0  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00014   21.9   0.2    0.00032   20.8   0.2    1.5  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
    0.00023   20.2   0.6    0.00039   19.4   0.6    1.3  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    0.00026   21.2   1.5     0.0023   18.2   0.2    2.8  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0003   21.2   2.0    0.00065   20.1   0.3    2.3  2  NAD_binding_7    Putative NAD(P)-binding
    0.00034   20.2   1.0    0.00034   20.2   1.0    2.8  4  Glu_dehyd_C      Glucose dehydrogenase C-terminus
      0.001   18.5   0.1      0.002   17.5   0.1    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.016   14.5   0.6      0.036   13.4   0.6    1.5  1  ThiF             ThiF family
      0.078   13.3   0.2       0.13   12.5   0.2    1.3  1  zf-C4H2          Zinc finger-containing protein
      0.093   12.4   0.0       0.18   11.5   0.0    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
       0.16   12.2   2.8       0.19   12.0   0.7    2.3  2  TrkA_N           TrkA-N domain
        0.3   11.2   1.3        1.3    9.1   1.6    2.0  1  SAM_Exu          Exuperantia SAM-like domain


Domain annotation for each model (and alignments):
>> 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 !  116.9   0.0   5.5e-37   6.2e-34       4     146 .]      13     151 ..      11     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 116.9 bits;  conditional E-value: 5.5e-37
                           GlutR_N   4 nhktapvelreklafseeelkellkel.ee.kvkeaviLsTCNRtEiylsaeeeeeaseellellaevsleelkekl 78 
                                       +h++ +v+ +   a s +++++++++l +  +v+ea +LsTCNR+E y+++ +++  +++l e++a +     ++++
  gi|336253522|ref|YP_004596629.1|  13 THESGTVDQLA--AASPDSQRSAVSQLlSIpDVEEAYVLSTCNRVEAYVVSPDAAVGRAALEEFFAPA----DDDAV 83 
                                       55555555555..445566778888876667899**************99999888888888888433....34678 PP

                           GlutR_N  79 yvlegeeavrHlfrVasGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                                          +++e++rHl+rVa+GL+S+vlGEdqI+gQv+ aye a+eag +g++Le  + kai+v+ r+rtet
  gi|336253522|ref|YP_004596629.1|  84 VHTDHDESLRHLLRVAAGLESVVLGEDQIIGQVRAAYEDAREAGGIGSMLEPAVTKAIHVGERARTET 151
                                       88999**************************************************************8 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.3   0.2   4.5e-37     5e-34       2     138 .]     167     306 ..     166     306 .. 0.92
   2 ?   -2.8   0.0       5.3     6e+03      75      99 ..     340     364 ..     317     371 .. 0.68

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 4.5e-37
                                       HHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT-S CS
                      Shikimate_DH   2 lakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel.kgeeiealkleelkellaead 77 
                                       la  +++ l+++++l++GaGem++l+a+ L+++gv+++vvaNRt++ra++la el  ++++ea++le l+++  ead
  gi|336253522|ref|YP_004596629.1| 167 LAAAEIG-LEGATALVVGAGEMGQLAARSLADAGVDDLVVANRTVSRADHLAAELdVDADLEAVPLEALETVAPEAD 242
                                       5666665.999********************************************657789**************** PP

                                       EEEE-SSSSS-SB-HHHHHCCHHH.S.....EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHHH CS
                      Shikimate_DH  78 vvisataseepilekeeveealkkrk...kplllvDiavPRdvepevaeledvrlytvDdLkev 138
                                       vv++at+seep+le +++e+  +  +   + +++vD+++PRdv+p+  +l  v +y++DdL++v
  gi|336253522|ref|YP_004596629.1| 243 VVVAATGSEEPVLEPHHLEAETDGGTataTDRVVVDLGQPRDVDPAADDLAAVAVYDLDDLESV 306
                                       ******************98877655555778*****************************987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.3
                                       T-SEEEE-SSSSS-SB-HHHHHCCH CS
                      Shikimate_DH  75 eadvvisataseepilekeeveeal 99 
                                       +ad vi+a   +   ++++e+e al
  gi|336253522|ref|YP_004596629.1| 340 RADEVIAAMYESAERMKERELETAL 364
                                       4566666666666666666666655 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 !   76.6   1.6   1.4e-24   1.6e-21       1      96 [.     320     418 ..     320     419 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 1.4e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S....--------TTHHHHHHHHHHHHHHH CS
                       GlutR_dimer   1 kAeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkkla..ldgedreelekltrslvnkllhepta 75 
                                       k+ea+I++e e +++++k+ +++++I+a++e+ae+++e+ele al++l+  l+  +re++e+++++lv +ll +pt+
  gi|336253522|ref|YP_004596629.1| 320 KVEAMIDREYELLCDQYKRARADEVIAAMYESAERMKERELETALSRLDddLSAAQREVVESMADALVSQLLAPPTK 396
                                       79*************************************************************************** PP

                                       HHHSS-TTTT.HHHHHHHHH.. CS
                       GlutR_dimer  76 rLkeaedeee.ellealrrlFn 96 
                                       +L++a++e++ ++++++ +lF+
  gi|336253522|ref|YP_004596629.1| 397 SLRQAAAEDDwSTINTALQLFD 418
                                       *****666668**********7 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 !   26.8   0.2   5.1e-09   5.8e-06       4      69 ..     181     248 ..     178     280 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.1e-09
                                       EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....-EEECECHHHHHH.H-SEEEE-S CS
                     F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....vkvtavdneeaae.eadvvvlav 69 
                                       ++GaG+mg+  a+ l+ ag    ++vva +r+ ++a++la+el      ++ + ++ e+++ eadvvv a 
  gi|336253522|ref|YP_004596629.1| 181 VVGAGEMGQLAARSLADAG--VDDLVVA-NRTVSRADHLAAELDvdadLEAVPLEALETVApEADVVVAAT 248
                                       57*****************..9999988.***************887766677777777777******986 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 !   21.8   0.1   1.5e-07   0.00016       4      69 ..     181     254 ..     178     259 .. 0.90
   2 ?   -1.4   0.0       2.1   2.3e+03      33      54 ..     305     326 ..     286     365 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.5e-07
                                       EE--SHHHHHHHHHHHHTT-.EEEEE-SSHHHHHHHHHTT.......EEE-SSHHHHHHHCSEEEE-SSSHHHH CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagy.kvavynrtkekveelvaeg.......akaaesieelvasldvvitmvkagkav 69 
                                       ++G G+MG+  a+ l++ag  +++v nrt +++++l+ae        a+++e +e ++ ++dvv+    ++++v
  gi|336253522|ref|YP_004596629.1| 181 VVGAGEMGQLAARSLADAGVdDLVVANRTVSRADHLAAELdvdadleAVPLEALETVAPEADVVVAATGSEEPV 254
                                       79****************973699*************997788999999***************9988777776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                                       HHHHHHHHTTEEE-SSHHHHHH CS
                     NAD_binding_2  33 ekveelvaegakaaesieelva 54 
                                       + ++e  +++a+aa ++e++++
  gi|336253522|ref|YP_004596629.1| 305 SVTQETREQRADAARKVEAMID 326
                                       5555555555555555554443 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 !   20.8   0.2   2.8e-07   0.00032      16      97 ..     169     260 ..     163     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.8e-07
                                       HH-S--TTSEEEEE--SHHHHHHHHHHHHCT......-EEEEE-S-HHHH...HHHHCTT-EE--HHHCTTT-SEEE CS
                     AdoHcyase_NAD  16 atdvllaGkvavvaGyGdvGkGcaaslkglG......arvivtevdPica...lqaameGfevvtleevvkkadivv 83 
                                       a+++ l G +a+v+G G++G+ +a+sl  +G      a  +v+  d ++a   + a +e   +  le+v+ +ad+vv
  gi|336253522|ref|YP_004596629.1| 169 AAEIGLEGATALVVGAGEMGQLAARSLADAGvddlvvANRTVSRADHLAAeldVDADLEAVPLEALETVAPEADVVV 245
                                       5677789**********************9943333334467788999886667899******************** PP

                                       E-SSSSS.SB-HHHH CS
                     AdoHcyase_NAD  84 tttGnkd.iitlehl 97 
                                       ++tG+++ +++ +hl
  gi|336253522|ref|YP_004596629.1| 246 AATGSEEpVLEPHHL 260
                                       ****98724444555 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 !   19.4   0.6   3.5e-07   0.00039     131     214 ..     178     261 ..     162     272 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.5e-07
                                       EEEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHHHHHHHCCS..CTT-EEECSCHHHHTTSSEEEE----SS- CS
                   OCD_Mu_crystall 131 vlaiiGaGvqaetqlealkavldikevriydrdeeaaekfaenlqe.fefevsackseeeavegadivvtvTaakap 206
                                       ++ ++GaG + ++ ++ l a ++++ + + +r+ + a+ +a +l   +++e +  +  e+++ +ad+vv++T +++p
  gi|336253522|ref|YP_004596629.1| 178 TALVVGAGEMGQLAARSL-ADAGVDDLVVANRTVSRADHLAAELDVdADLEAVPLEALETVAPEADVVVAATGSEEP 253
                                       5669********999998.5689**********************9789999999999******************* PP

                                       SB-GGGS- CS
                   OCD_Mu_crystall 207 ilkaewvk 214
                                       +l    ++
  gi|336253522|ref|YP_004596629.1| 254 VLEPHHLE 261
                                       **877766 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 ?   -3.1   0.0         8     9e+03       9      37 ..      66      92 ..      46     103 .. 0.55
   2 !   18.2   0.2     2e-06    0.0023       2      75 ..     180     246 ..     179     253 .. 0.77
   3 ?    0.7   0.0      0.52   5.8e+02      45     101 ..     358     414 ..     317     439 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8
                                      HHHHHHHHHHCTCCT-GEEEEEESSHHHH CS
                   Sacchrp_dh_NADP  9 vGqavaellarhfdvdaeitvadrskekl 37
                                      vG+a++e+  +  d   + +v + ++e+l
  gi|336253522|ref|YP_004596629.1| 66 VGRAALEEFFAPADD--DAVVHTDHDESL 92
                                      444444444444444..344444444444 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2e-06
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvn 75 
                                       l++GaG +Gq +a+ la+ +    +++va r+ +++++laa+ l v+++ +a+  e   a L+ +  e+d+vv 
  gi|336253522|ref|YP_004596629.1| 180 LVVGAGEMGQLAARSLADAGVD--DLVVANRTVSRADHLAAE-LDVDADLEAVPLE---A-LETVAPEADVVVA 246
                                       89*****************987..9**************987.4555555555443...3.4445556677665 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.52
                                       TTTCEEEEE--TTTHHHHHHHHHTTS.SEEEE-SSGGGHHHHHHHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  45 lgvrfeaialdaenyeavLaallkeg.dlvvnlsppissldvlkaCietgvhyvdtsi 101
                                       ++ +     ld +  +a   +++++  d++v+ +    + ++ +a++e   + ++t+ 
  gi|336253522|ref|YP_004596629.1| 358 RELETALSRLDDDLSAA-QREVVESMaDALVSQLLAPPTKSLRQAAAEDDWSTINTAL 414
                                       44444444444444444.4444555579999999999999999999999999999987 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 !   20.1   0.3   5.8e-07   0.00065       5      73 ..     174     252 ..     172     256 .. 0.70
   2 ?   -1.4   0.1       2.8   3.2e+03      55      55 ..     329     329 ..     288     400 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.8e-07
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele..........elvklaeeelekdlegadlviaatdd 71 
                                       l+g + lvvG+Ge+++  +r+l++ag +  vva+++ + ++          +l  +  e le    +ad+v+aat  
  gi|336253522|ref|YP_004596629.1| 174 LEGATALVVGAGEMGQLAARSLADAGVDDLVVANRTVSRADhlaaeldvdaDLEAVPLEALETVAPEADVVVAATGS 250
                                       7899************************99*9999644444333333222211112223335556679*******87 PP

                     NAD_binding_7  72 re 73 
                                       +e
  gi|336253522|ref|YP_004596629.1| 251 EE 252
                                       65 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.8
                     NAD_binding_7  55 l 55 
                                       +
  gi|336253522|ref|YP_004596629.1| 329 Y 329
                                       1 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.57   6.4e+02     159     200 ..       6      48 ..       4      57 .. 0.78
   2 ?   -3.9   0.0       6.9   7.7e+03     149     165 ..     105     121 ..     101     126 .. 0.59
   3 !   20.2   1.0     3e-07   0.00034      27     116 ..     172     256 ..     156     285 .. 0.82
   4 ?   -2.0   0.0       1.8     2e+03     178     212 .]     379     416 ..     368     416 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.57
                       Glu_dehyd_C 159 svNanr.rhfeaavdtLaalpeslldelvtkvvdldeleeAfe 200
                                        v a r +h   +vd+Laa++ +  ++ v++ + + ++eeA+ 
  gi|336253522|ref|YP_004596629.1|   6 VVAAARvTHESGTVDQLAAASPDSQRSAVSQLLSIPDVEEAYV 48 
                                       5555540455556899999999999999999999999999995 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.9
                       Glu_dehyd_C 149 lvleNkalvGsvNanrr 165
                                       +vl  + ++G v a ++
  gi|336253522|ref|YP_004596629.1| 105 VVLGEDQIIGQVRAAYE 121
                                       56666666776666544 PP

  == domain 3  score: 20.2 bits;  conditional E-value: 3e-07
                       Glu_dehyd_C  27 fewepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipeaseemdl 103
                                          e ++alv+GaG +G La+  l+  + g++++ v +r+   +++ +l +el+    d +  p++ +  +  e d+
  gi|336253522|ref|YP_004596629.1| 172 IGLEGATALVVGAGEMGQLAARSLA--DAGVDDLVVANRT--VSRADHLAAELDVD-ADLEAVPLEALETVAPEADV 243
                                       5567899*************99998..589**99766654..35666788888865.67788999***99******* PP

                       Glu_dehyd_C 104 vvEaTGsakhafe 116
                                       vv aTGs + ++e
  gi|336253522|ref|YP_004596629.1| 244 VVAATGSEEPVLE 256
                                       ******9988877 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.8
                       Glu_dehyd_C 178 peslldelvtkvv..dldeleeAf.edddetiKtvvel 212
                                        es+ d+lv++ +  ++++l++A  edd  ti t+++l
  gi|336253522|ref|YP_004596629.1| 379 VESMADALVSQLLapPTKSLRQAAaEDDWSTINTALQL 416
                                       34557778887653245666666515555999999986 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 !   17.5   0.1   1.8e-06     0.002      27      98 ..     167     247 ..     142     253 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH........CHHHHTCEECSHHHHHHH-SE CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkee........eeeelgvelvsleellaesDi 94 
                                        a     l+g t  ++G+G++Gq +a+ l+  g+ ++++ +r+ ++ +        +++ + v l+ le++  e+D+
  gi|336253522|ref|YP_004596629.1| 167 LAAAEIGLEGATALVVGAGEMGQLAARSLADAGVdDLVVANRTVSRADhlaaeldvDADLEAVPLEALETVAPEADV 243
                                       455566899*************************7788888888866666665554444445577789999999999 PP

                                       EEE- CS
                      2-Hacid_dh_C  95 vslh 98 
                                       v+ +
  gi|336253522|ref|YP_004596629.1| 244 VVAA 247
                                       9865 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   3.2e-05     0.036      16      48 ..     174     206 ..     160     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                                       HHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  16 LrdskvllvGaGglGsellknLalsGvgkltlv 48 
                                       L+ ++ l+vGaG  G+ +++ La +Gv  l ++
  gi|336253522|ref|YP_004596629.1| 174 LEGATALVVGAGEMGQLAARSLADAGVDDLVVA 206
                                       677899*********************999875 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00012      0.13      60     137 ..     299     377 ..     291     431 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                           zf-C4H2  60 DinalEsvikeaeeekekslekakkly.eeykklkeevnelrselglekledleeeeeellkeeifekqklkaaave 135
                                       D+++lEsv++e++e++  + +k++ ++ +ey+ l ++  + r +  +  + + +e  +e   e+ +++   + +a++
  gi|336253522|ref|YP_004596629.1| 299 DLDDLESVTQETREQRADAARKVEAMIdREYELLCDQYKRARADEVIAAMYESAERMKERELETALSRLDDDLSAAQ 375
                                       99*****************99999887589**************888888877666555555555555444433222 PP

                           zf-C4H2 136 lk 137
                                        +
  gi|336253522|ref|YP_004596629.1| 376 RE 377
                                       22 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016      0.18       2      35 ..     180     215 ..     179     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                                       EEES-SHHHHHHHHHHHHHTHC.EEEE-SCH.HHHH CS
                              ApbA   2 ailGaGaiGsllaakLakagad.vtlilrsr.rlea 35 
                                       +++GaG +G+l a +La ag d  ++ +r+  r+++
  gi|336253522|ref|YP_004596629.1| 180 LVVGAGEMGQLAARSLADAGVDdLVVANRTVsRADH 215
                                       69****************999955555555555554 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.7   0.00017      0.19       2      74 ..     180     252 ..     179     256 .. 0.78
   2 ?   -2.1   0.1       4.1   4.6e+03      61      68 ..     339     346 ..     293     356 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgdde 74 
                                       +++G+G++G+  a+ L + g +d vv  +  +r+++l++e       +a   e+Le   + +ad+v+aatg+ e
  gi|336253522|ref|YP_004596629.1| 180 LVVGAGEMGQLAARSLADaGVDDLVVANRTVSRADHLAAELDVDADLEAVPLEALETV-APEADVVVAATGSEE 252
                                       79****************5558899999999999999999854455566666666655.567888888888765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                                       GGESEEEE CS
                            TrkA_N  61 ekadavia 68 
                                       ++ad via
  gi|336253522|ref|YP_004596629.1| 339 ARADEVIA 346
                                       34444444 PP

>> SAM_Exu  Exuperantia SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.6    0.0012       1.3      15      66 ..     312     363 ..     303     369 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                           SAM_Exu  15 RvravklRrlLAEngidyesLkeiweekkkeGlekllkekitslkeedkeeL 66 
                                        +ra   R++ A  + +ye L + ++  + + + +++ e+ +++ke ++e  
  gi|336253522|ref|YP_004596629.1| 312 EQRADAARKVEAMIDREYELLCDQYKRARADEVIAAMYESAERMKERELETA 363
                                       3789999***************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3202.17
//
Query:       gi|336253523|ref|YP_004596630.1|  [L=94]
Description: transcriptional coactivator/pterin dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-24   83.5   0.0      1e-23   83.3   0.0    1.0  1  Pterin_4a  Pterin 4 alpha carbinolamine dehydratase


Domain annotation for each model (and alignments):
>> Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   0.0   5.8e-28     1e-23       3      89 ..       5      88 ..       3      89 .. 0.95

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 5.8e-28
                         Pterin_4a  3 lseeeiqkllaelpgWrleeaeelerefkfkdfeeaiafvnrvaalaeeenHhpdilvsynkvtvrltThdaggltenD 81
                                      ls++ei++ l + ++W++ e++e+ r+++f+++  +++f++ v+++ae++ Hhp+i ++y++v+vrlt+h+ gg+te D
  gi|336253523|ref|YP_004596630.1|  5 LSDDEIEAGL-P-DNWTR-EGDEIVRTYEFDEYLRGVNFAQMVGEIAESQFHHPEIVIRYEEVEVRLTSHEEGGITEDD 80
                                      899*******.3.69**9.7889******************************************************** PP

                         Pterin_4a 82 fklAakid 89
                                      +++A+ i+
  gi|336253523|ref|YP_004596630.1| 81 LEMAELIE 88
                                      *****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 745.96
//
Query:       gi|336253524|ref|YP_004596631.1|  [L=127]
Description: hypothetical protein Halxa_2127 [Halopiger xanaduensis SH-6]
Scores for 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:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1120.14
//
Query:       gi|336253525|ref|YP_004596632.1|  [L=209]
Description: Haloacid dehalogenase domain-containing protein hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-10   40.0   0.0      1e-09   38.7   0.0    1.6  1  HAD_2      Haloacid dehalogenase-like hydrolase
    5.9e-08   33.3   0.1    1.1e-06   29.2   0.1    2.0  1  Hydrolase  haloacid dehalogenase-like hydrolase
    2.9e-05   24.6   0.7    4.4e-05   24.0   0.7    1.4  1  HAD        haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.024   14.5   0.0    1.2  1  DUF86      Protein of unknown function DUF86


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 !   38.7   0.0   2.3e-13     1e-09       2     178 .]       9     184 ..       8     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.3e-13
                             HAD_2   2 iFDlDgTlldt.eeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkk.. 75 
                                       + DlDgTl+d    +  ++f ++ ++ g  e+s+ e + l +  +    r+l e      + e +++ +++e++   
  gi|336253525|ref|YP_004596632.1|   9 LLDLDGTLVDVdWSYTRDVFDRVGDRLGR-EFSDREAEILWNGLTGSRNRQLREWGI---DPEAFWEVFHDEEDPmv 81 
                                       67999999996257778899999999866.566555555544333233334333222...55566666666555544 PP

                             HAD_2  76 .kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklk 151
                                         e + + +  e++ +L   +  +g+vT  ++  +e  l+++gi + Fd  ++ ++ ++ KPdpe+++++++ l++ 
  gi|336253525|ref|YP_004596632.1|  82 rAEQTYLHEDAEFVGDL---EAPVGLVTHCQEFLAEPVLDNVGIRDWFDARLCCTEETGWKPDPEPVQQVMRDLGVA 155
                                       44555555556888999...679***************************************************998 PP

                             HAD_2 152 ke..eviyvGDsptDieaakkagikviav 178
                                       ++  + +  GD   D+ aa +ag+++i v
  gi|336253525|ref|YP_004596632.1| 156 NNghRGVLAGDGDCDVGAAWNAGLDAIHV 184
                                       752267899****************9976 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1   2.3e-10   1.1e-06       5     210 .]       9     178 ..       5     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.3e-10
                                       EEESBTTTBCHH.HHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH..HHHHHETTTEHHHHTHHHHHH CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   5 vfDkdGTLttge.psvedvivsaalalaaaletgsehpigkalvaaakarsgal..tgfatfigrgayaigkpewlt 78 
                                       ++D+dGTL++   +  +dv++++                g +l +++ +r+ ++   g +         +  +ew  
  gi|336253525|ref|YP_004596632.1|   9 LLDLDGTLVDVDwSYTRDVFDRV----------------GDRLGREFSDREAEIlwNGLTG-----SRNRQLREWGI 64 
                                       57888888888888888888888................7777777777744444467777.....77777777777 PP

                                       HHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  79 aldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanql 155
                                       +                ++  ++++ ++++ ++ ++++     e ae+v  L a    v+l+t  ++  ae +++++
  gi|336253525|ref|YP_004596632.1|  65 DP---------------EAFWEVFH-DEEDPMVRAEQT--YLHEDAEFVGDLEAP---VGLVTHCQEFLAEPVLDNV 120
                                       77...............44444444.377777777777..777778999999955...******************* PP

                                       T.GGGESEEEEHHCESSTTTSHHHHHHHHHHHT..STGGGEEEEESSHHHHHHHHHTT CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 156 G.ddyfdaviasdietvakpspegkvaaireLq..gkpeevamVGDgvnDaaalaaAg 210
                                       G +d fda ++ ++et  kp+pe +++++r L+   ++++ +  GDg  D+ a+ +Ag
  gi|336253525|ref|YP_004596632.1| 121 GiRDWFDARLCCTEETGWKPDPEPVQQVMRDLGvaNNGHRGVLAGDGDCDVGAAWNAG 178
                                       *********************************8788*************99998886 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.7   9.9e-09   4.4e-05       2     184 ..       9     171 ..       8     175 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 9.9e-09
                               HAD   2 lfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfva 78 
                                       l+D+DgTL+d d  + ++r +  r + rl+r+   +  ++l + +l+ +r+   + +    +++ e +++e + +v+
  gi|336253525|ref|YP_004596632.1|   9 LLDLDGTLVDVD--WSYTRDVFDRVGDRLGREFSDREAEIL-WNGLTGSRNRQLREWGIDPEAFWEVFHDEEDPMVR 82 
                                       68*********6..444454555555566777777777777.55555556666666666677777888888888885 PP

                               HAD  79 evirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkv 155
                                       ++++   +  +  e++    +   +v +v+ + ++l+ep+l+++g    +         ++++l   +   ++  ++
  gi|336253525|ref|YP_004596632.1|  83 AEQT---YLHEDAEFVG---DLEAPVGLVTHCQEFLAEPVLDNVG----IRD------WFDARLCCTEETGWK-PDP 142
                                       5554...5567779999...8889*********************....666......444443333333332.233 PP

                               HAD 156 aalrewlaaegegidleevvayGDspsDl 184
                                         +++ + + g +   ++ v  GD+  D+
  gi|336253525|ref|YP_004596632.1| 143 EPVQQVMRDLGVANNGHRGVLAGDGDCDV 171
                                       33333333344444444445566666555 PP

>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.3e-06     0.024      69     110 ..      38      78 ..      28      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.3e-06
                                       TSS-HHHHHHHHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCH CS
                             DUF86  69 gviaeepeepwrkmiglRNrLvHgYlgidpeivwsiikenlp 110
                                       ++ ++e e+ w+ ++g RNr   ++  idpe  w++ +++ +
  gi|336253525|ref|YP_004596632.1|  38 EFSDREAEILWNGLTGSRNRQLREWG-IDPEAFWEVFHDEED 78 
                                       5778999******************9.*********999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); 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:                         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 0.18s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 1841.63
//
Query:       gi|336253526|ref|YP_004596633.1|  [L=224]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   64.8   0.1    7.3e-18   64.1   0.1    1.4  1  HTH_10         HTH DNA binding domain
    8.4e-07   29.0   4.2    1.3e-06   28.3   4.2    1.3  1  BAT            GAF and HTH_10 associated domain
     0.0005   19.6   0.0     0.0016   17.9   0.0    1.9  2  HTH_24         Winged helix-turn-helix DNA-binding
    0.00096   19.0   0.1     0.0028   17.5   0.1    1.9  1  MarR_2         MarR family
    0.00098   18.8   0.2     0.0028   17.4   0.2    1.8  1  HTH_psq        helix-turn-helix, Psq domain
     0.0011   18.8   0.3     0.0063   16.3   0.2    2.2  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0018   18.3   0.0      0.016   15.3   0.0    2.4  3  HTH_AraC       Bacterial regulatory helix-turn-helix proteins
     0.0035   17.4   1.4     0.0042   17.2   1.4    1.3  1  GPP34          Golgi phosphoprotein 3 (GPP34)
     0.0098   15.4   0.5      0.023   14.2   0.5    1.6  1  Sigma70_r4     Sigma-70, region 4
  ------ inclusion threshold ------
       0.02   15.0   0.0      0.081   13.0   0.0    1.9  2  Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix do
       0.02   14.9   0.0      0.046   13.8   0.0    1.5  1  HTH_3          Helix-turn-helix
      0.032   14.3   0.4      0.099   12.7   0.4    1.8  1  Malate_DH      Malate dehydrogenase enzyme
       0.04   14.2   0.0      0.064   13.5   0.0    1.3  1  UPF0122        Putative helix-turn-helix protein, YlxM / p13 
       0.04   13.7   0.1       0.11   12.3   0.1    1.9  1  TetR_N         Bacterial regulatory proteins, tetR family
      0.055   13.1   0.4       0.65    9.7   0.4    2.2  1  Sigma70_r4_2   Sigma-70, region 4
       0.13   12.0   0.0        1.2    8.8   0.1    2.2  2  GntR           Bacterial regulatory proteins, gntR family
       0.14   12.3   0.0       0.28   11.3   0.0    1.5  1  HTH_22         HTH domain


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 !   64.1   0.1   6.9e-21   7.3e-18       1      52 [.     157     208 ..     157     209 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 6.9e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT++q+e+l +A+e+GYF+ PR ++++eLA+elGIs ++lse+ r+a ++l+
  gi|336253526|ref|YP_004596633.1| 157 LTPQQREALEAALEYGYFEIPRAISMAELADELGISHQALSERFRRAYETLV 208
                                       9**********************************************99987 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   4.2   1.3e-09   1.3e-06       8     145 ..       7     145 ..       3     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.3e-09
                               BAT   8 leirdeddvlv.alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtllelt 83 
                                       l++  +d +l  a  ++ d+++ele++v+++       ++v+g+   ++++a+++ + ve ++ + e+  + l+ + 
  gi|336253526|ref|YP_004596633.1|   7 LRLPASDTLLEaAFERAPDAAFELESAVSQTPP----SIWVAGVGRSRAETAFDADPEVETYEPLVETSARHLFDVD 79 
                                       444444444443889999***********7665....569999999******************************* PP

                               BAT  84 .vsgpslas...tlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrere 145
                                        v+g  + +   +l + Gg++ +a+ +dg ++ +v++P++  +   +++l +r  +++L++   ++
  gi|336253526|ref|YP_004596633.1|  80 fVAGAGPERlwdALLADGGSLLEARGTDGWWQARVRFPDRGTLCDAYDRLVDRGVNADLRRLTDVT 145
                                       888766666666***********************************************9877766 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   1.5e-06    0.0016      17      40 ..     178     202 ..     177     205 .. 0.91
   2 ?   -2.5   0.0       3.6   3.8e+03      10      20 ..     210     220 ..     210     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                            HTH_24  17 r.isqreLAerlglSpstvnrrlkr 40 
                                       r is++eLA++lg+S +++++r +r
  gi|336253526|ref|YP_004596633.1| 178 RaISMAELADELGISHQALSERFRR 202
                                       559*******************998 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.6
                            HTH_24  10 elLqknprisq 20 
                                       e+Lq n+  s 
  gi|336253526|ref|YP_004596633.1| 210 EELQSNGEASL 220
                                       689***99885 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.7e-06    0.0028       3      45 ..     157     203 ..     155     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.7e-06
                                       --HHHHHHHHHHHCTTTS.....EEEHHHHHHHHTSSHHHHHHHHHHH CS
                            MarR_2   3 ltpaqarvLaaLgrrpgr.....dltvgelarrlglsksavsrilkrL 45 
                                       ltp+q+ +L a    + +      ++++ela++lg+s++a+s + +r+
  gi|336253526|ref|YP_004596633.1| 157 LTPQQREALEAALEYG-YfeiprAISMAELADELGISHQALSERFRRA 203
                                       7788888888877775.55677677*****************998886 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 !   17.4   0.2   2.6e-06    0.0028       2      43 ..     162     206 ..     161     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.6e-06
                           HTH_psq   2 pealaaAleavv...nGkmSirkAArkYgiPrsTLwrrkrgkysl 43 
                                       +eal+aAle+       ++S++++A++ gi++  L++r+r+ y++
  gi|336253526|ref|YP_004596633.1| 162 REALEAALEYGYfeiPRAISMAELADELGISHQALSERFRRAYET 206
                                       799999999977788667************************997 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 !   16.3   0.2     6e-06    0.0063      18      40 ..     180     202 ..     178     203 .. 0.96
   2 ?   -0.5   0.0       1.1   1.2e+03      10      21 ..     210     221 ..     210     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6e-06
                     HTH_AsnC-type  18 isyaeLAervGlSestvlrRvrr 40 
                                       is+aeLA+++G+S ++  +R rr
  gi|336253526|ref|YP_004596633.1| 180 ISMAELADELGISHQALSERFRR 202
                                       8*******************998 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                     HTH_AsnC-type  10 eaLqedaRisya 21 
                                       e+Lq ++ +s  
  gi|336253526|ref|YP_004596633.1| 210 EELQSNGEASLV 221
                                       58*****99975 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 ?   -1.3   0.0       2.4   2.5e+03      18      33 ..     114     130 ..     112     135 .. 0.82
   2 ?   -1.8   0.0       3.4   3.6e+03      11      18 ..     144     151 ..     142     156 .. 0.78
   3 !   15.3   0.0   1.5e-05     0.016       9      33 ..     180     204 ..     176     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.4
                                       TTS.SHHHHHHHHHHHS CS
                          HTH_AraC  18 lgf.SrsyFsrlFkket 33 
                                       + f +r +++ ++ + +
  gi|336253526|ref|YP_004596633.1| 114 VRFpDRGTLCDAYDRLV 130
                                       78999*****9998865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.4
                                       HHHHHHHT CS
                          HTH_AraC  11 iediAdel 18 
                                       ++d+A++ 
  gi|336253526|ref|YP_004596633.1| 144 VTDVAQHT 151
                                       89***996 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.5e-05
                                       --HHHHHHHTTSSHHHHHHHHHHHS CS
                          HTH_AraC   9 ltiediAdelgfSrsyFsrlFkket 33 
                                       ++++++Adelg+S + +s +F++++
  gi|336253526|ref|YP_004596633.1| 180 ISMAELADELGISHQALSERFRRAY 204
                                       699********************98 PP

>> GPP34  Golgi phosphoprotein 3 (GPP34)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.4   3.9e-06    0.0042      81     182 ..     111     211 ..      10     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.9e-06
                             GPP34  81 ktwvdlls...ksvrervakgLvdkGilrtekrrflglfdmtthpvadtaakeavrrrvraaltsgepadprtaaLv 154
                                       +   ++ +   ++++   +++Lvd+G+     rr+  ++d ++h+ a ++   + r++++aal  g  + pr+  ++
  gi|336253526|ref|YP_004596633.1| 111 Q---ARVRfpdRGTLCDAYDRLVDRGVNAD-LRRLTDVTDVAQHTKASSRLTPQQREALEAALEYGYFEIPRAISMA 183
                                       2...22224446666669********9765.588889**************************88888899****** PP

                             GPP34 155 allaaagllenllpdleareaaarakel 182
                                        l+ ++g+ +++l+++ +r+ ++ ++e 
  gi|336253526|ref|YP_004596633.1| 184 ELADELGISHQALSERFRRAYETLVDEE 211
                                       **************98777666666665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.5   2.2e-05     0.023       4      48 ..     156     207 ..     155     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       +L++++re le           +  +++E++++lgiS  + + + +rA + L
  gi|336253526|ref|YP_004596633.1| 156 RLTPQQREALEAALeygyfeiPRAISMAELADELGISHQALSERFRRAYETL 207
                                       7***********9999999988999**************9999999998765 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 ?   -1.7   0.0       3.1   3.3e+03      16      28 ..     139     151 ..     125     154 .. 0.70
   2 ?   13.0   0.0   7.7e-05     0.081      14      36 ..     182     203 ..     179     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.1
                                       HHHHCCTT--HHH CS
                     Phage_CI_repr  16 keLAdlLgiakss 28 
                                       + L d  ++a+++
  gi|336253526|ref|YP_004596633.1| 139 RRLTDVTDVAQHT 151
                                       5678888888887 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.7e-05
                                       SCHHHHCCTT--HHHHHHHHHSS CS
                     Phage_CI_repr  14 mqkeLAdlLgiakssvstwvrRd 36 
                                       m  eLAd+Lgi+++ +s + rR 
  gi|336253526|ref|YP_004596633.1| 182 MA-ELADELGISHQALSERFRRA 203
                                       44.9***************9995 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.3e-05     0.046      10      31 ..     180     201 ..     175     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-05
                                       HHHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3  10 lsqeeLAeklGvsrstisriEn 31 
                                       +s++eLA++lG+s +++s  ++
  gi|336253526|ref|YP_004596633.1| 180 ISMAELADELGISHQALSERFR 201
                                       89****************8665 PP

>> Malate_DH  Malate dehydrogenase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   9.4e-05     0.099       5      28 ..     149     171 ..     146     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.4e-05
                         Malate_DH   5 QpaaskedlKeqqraaLRkAALeY 28 
                                       Q +++   l  qqr+aL +AALeY
  gi|336253526|ref|YP_004596633.1| 149 QHTKASSRLTPQQREAL-EAALEY 171
                                       66777888889******.9***** PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     6e-05     0.064      32      63 ..     178     209 ..     154     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-05
                           UPF0122  32 dDlSlsEiAeefnvsrqavydnikrtekllek 63 
                                         +S++E+A+e  +s+qa+++  +r+ + l +
  gi|336253526|ref|YP_004596633.1| 178 RAISMAELADELGISHQALSERFRRAYETLVD 209
                                       568**********************9988866 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 ?   12.3   0.1   0.00011      0.11      15      38 ..     178     201 ..     164     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                       TT--HHHHHHHHTSSHHHHHHHTS CS
                            TetR_N  15 dattvreIAkrAGvskgalYryFp 38 
                                       +a +++e+A+++G+s  al  +F+
  gi|336253526|ref|YP_004596633.1| 178 RAISMAELADELGISHQALSERFR 201
                                       688******************997 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 ?    9.7   0.4   0.00061      0.65       9      53 ..     155     206 ..     151     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00061
                                       TTS-HHHHHHHHHHHTS--.......-HHHHHHHHT--HHHHHHHHHHHHHH CS
                      Sigma70_r4_2   9 aeLperqreifllrylegl.......sykEIAellgisegtVksrlsRArkk 53 
                                       ++L+++qre+++   + g+       s +E A +lgis ++   r +RA + 
  gi|336253526|ref|YP_004596633.1| 155 SRLTPQQREALEAALEYGYfeipraiSMAELADELGISHQALSERFRRAYET 206
                                       789**********999998888888899999999999999988888888765 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.71   7.5e+02      38      52 ..     119     133 ..     118     134 .. 0.86
   2 ?    8.8   0.1    0.0012       1.2       7      51 ..     163     210 ..     159     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.71
                                       HHHHHHHHHHHHHTT CS
                              GntR  38 rttvReALrrLeaeg 52 
                                       r t+  A++rL+ +g
  gi|336253526|ref|YP_004596633.1| 119 RGTLCDAYDRLVDRG 133
                                       789999*****9988 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                                       HHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHH....HHHHHHHHHT CS
                              GntR   7 erLredIlsgelrpGdkLPsereLaaefgVsrttv....ReALrrLeae 51 
                                       e+L++ +  g ++   ++ s  eLa+e+g+s++ +    R+A+ +L+ e
  gi|336253526|ref|YP_004596633.1| 163 EALEAALEYGYFEIPRAI-SMAELADELGISHQALserfRRAYETLVDE 210
                                       688999999999999999.*************99855556677666666 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00027      0.28      11      56 ..     148     194 ..     140     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                            HTH_22  11 adlgkpverltkeekieivraLdekGiFllkgave..kvAekLgiSra 56 
                                       a++ k+ +rlt +++ ++ +aL e G F++ +a++  ++A++LgiS +
  gi|336253526|ref|YP_004596633.1| 148 AQHTKASSRLTPQQREALEAAL-EYGYFEIPRAISmaELADELGISHQ 194
                                       4566777999999988777777.79*******9862269*******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1635.54
//
Query:       gi|336253527|ref|YP_004596634.1|  [L=622]
Description: molybdenum cofactor synthesis domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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  132.3   5.0    2.4e-38  131.4   5.0    1.5  1  MoeA_N          MoeA N-terminal region (domain I and II)
    6.8e-24   84.1   0.3    5.3e-23   81.1   0.0    2.4  2  PBP_like        PBP superfamily domain
    9.8e-24   83.7   0.0    1.7e-23   82.9   0.0    1.4  1  MoCF_biosynth   Probable molybdopterin binding domain
    1.9e-16   60.0   0.0    7.7e-16   58.0   0.0    2.1  1  MoeA_C          MoeA C-terminal region (domain IV)
  ------ inclusion threshold ------
      0.071   12.8   0.0       0.15   11.8   0.0    1.5  1  SBP_bac_11      Bacterial extracellular solute-binding protei
      0.083   12.5   0.0       0.17   11.4   0.0    1.5  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.4   5.0   7.9e-42   2.4e-38       2     157 .]      11     176 ..      10     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 7.9e-42
                                       -HHHHHHHHHHH-HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--.............. CS
                            MoeA_N   2 sveealaiilaaleleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........s 69 
                                       s +ea+++i ++  +   e vpl +ea grvl++ + A+ dvP+fd++  DGYA+ra+++ ga+e +p        +
  gi|336253527|ref|YP_004596634.1|  11 SPAEAREAIDSLSLTAGVErVPL-EEARGRVLVARLDAELDVPGFDRASLDGYALRARDTFGADEADParlevvgeV 86 
                                       56899999988885556666***.99**************************************************8 PP

                                       .....-S---TT-.EEEE-TTSB--TT--EEEEGGGE..E....EETTE...S--STTTTEE-TTSSB-TTSEEE-T CS
                            MoeA_N  70 aageeperllpgg.avrimTGaplPegadaVvpvEdte.eeeaketvev...kavkpgenvrraGedikaGevllra 141
                                       +ageep+ +l++g a++i TGa++P+gada vpvE+t+ + +  e   v   ++v+pg+nv  aG d++aGe +l  
  gi|336253527|ref|YP_004596634.1|  87 HAGEEPDVELEEGqAAEISTGAVMPDGADAMVPVERTDtAADGGE---VlvrTSVAPGDNVMFAGADVAAGERALGP 160
                                       88888888888888**********************964222233...23469************************ PP

                                       TBB--CCCHHHHHHCT CS
                            MoeA_N 142 gtrltpaeigllasvG 157
                                       gtr+tp++igll ++G
  gi|336253527|ref|YP_004596634.1| 161 GTRITPRDIGLLSALG 176
                                       *************998 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.58   1.7e+03     137     152 ..     148     163 ..      45     171 .. 0.56
   2 !   81.1   0.0   1.8e-26   5.3e-23      60     191 ..     474     612 ..     439     614 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.58
                                       HCCHCCETTCCECCCG CS
                          PBP_like 137 aaaVaagradvgvgie 152
                                        a Vaag+ + g+g++
  gi|336253527|ref|YP_004596634.1| 148 GADVAAGERALGPGTR 163
                                       4556666666666665 PP

  == domain 2  score: 81.1 bits;  conditional E-value: 1.8e-26
                                       EEEEE-CC-HCHCCCCHCCHHHS--BGGGC-S-B-EEEEE-TTSHHHHHHHHHHC-CEECT........E-SSTTSE CS
                          PBP_like  60 evvlvnlarreqglvvakgnpkkitnwkdladaplrlvnRetGSGtrdlfdellkkegisk........ssikgyaq 128
                                       ++v++  ++re gl+ ++gnpk+i++++dl d++lr+vnR t+SG r  +  ++++  +++        ++i g + 
  gi|336253527|ref|YP_004596634.1| 474 DAVELGRWEREWGLIARAGNPKEIEGLEDLIDRDLRFVNRTTDSGLRTSLGAAVADLAAERgvdrrdlvDAIDGFDL 550
                                       45778889**********************************************99988888889************ PP

                                       EESSHHHHHCCHCCETTCCECCCGG-HCCCCCCECTTCE-EEEEEEEECTCCCSHHHHHHHHH CS
                          PBP_like 129 earshlavaaaVaagradvgvgieavaeelkgldfvplaeerydlvvrkealddpevqaflef 191
                                         r h + a+ V ag+ad+g+g++ +ae+l +ldfvp+ +++  +v + ++ d+  v+++ ++
  gi|336253527|ref|YP_004596634.1| 551 GLRAHESPARKVIAGDADAGLGLRETAERL-DLDFVPVGTQPVRVVANPDRTDKAGVRDLERV 612
                                       ****************************98.**************************998665 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.0   5.7e-27   1.7e-23       1     143 [.     189     327 ..     189     328 .. 0.96

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 5.7e-27
                                       EEEEE-HHHH.........TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SS CS
                     MoCF_biosynth   1 avitvGdell.........sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGp 68 
                                       +++++Gdel+         +g+i+D n++++a+ ++++g e+  y + +D+ +e+++ l++a+ee d+++++G t++
  gi|336253527|ref|YP_004596634.1| 189 GIVSTGDELVrpgedvdsdRGEIYDVNSYTIAAGVEDAGGEAVLYPHAGDEQDEMERILREAAEECDLVLSSGSTSA 265
                                       69*********************************************************9999999*********** PP

                                       STT--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  69 tpdDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                       ++ Dv ++++++ +e        ++++v+ kpgkp++v+++a  +    +  +gLPG+p+++++++++++ pa++
  gi|336253527|ref|YP_004596634.1| 266 SAVDVIYRVIEEQGE-------LLLHGVAVKPGKPMLVGRLA--D----SAYVGLPGYPVSAMMVFRTFVAPAIR 327
                                       ***************.......8******************4..2....359******************99987 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   2.6e-19   7.7e-16       4      72 .]     344     412 ..     341     412 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 2.6e-19
                                       ESS-EE--SSS-EEEEEEEE.S-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                            MoeA_C   4 laedlksdpgrreflRvilt.eedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                       +a++ +  +gr+++++v l  + +g+  ++p+  +gSg+++slaeA+g +++p++t++le+Ge+V+v+l+
  gi|336253527|ref|YP_004596634.1| 344 MAREERYSEGRMRLMPVGLVeDGEGDTLVYPV-DKGSGATTSLAEADGVVEVPPETDYLEEGESVDVQLF 412
                                       5666677899**********7777********.**********************************987 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     5e-05      0.15      81     181 ..     485     585 ..     443     614 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5e-05
                                       EEEEESTT-TT---SHHHHHHSS--EE..EE--T-TTTTHH.HHHHGGG--....HHHHHHHHHTEEEEESSHHHHH CS
                        SBP_bac_11  81 lviavpkgnpkkikgwadLlkpglkla..vadPttspsGlaalalleaaga....qellkalekkvvklgessrqll 151
                                         +++++gnpk i g++dL++ +l+++  ++d    +s  aa+a l+a ++    ++l++a+ +   +l+   ++ +
  gi|336253527|ref|YP_004596634.1| 485 WGLIARAGNPKEIEGLEDLIDRDLRFVnrTTDSGLRTSLGAAVADLAA-ERgvdrRDLVDAIDGFDLGLRA-HESPA 559
                                       6799******************99875335555444444466655555.4457888899998877665554.45556 PP

                                       HHHHTTT-SEEEEEHHHHH..HSTTSSEEE CS
                        SBP_bac_11 152 taveageadagivyeseakaaengdkleav 181
                                         v ag+adag++ +  a     + +l++v
  gi|336253527|ref|YP_004596634.1| 560 RKVIAGDADAGLGLRETAE----RLDLDFV 585
                                       6788899999999999996....4444444 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 ?   11.4   0.0   5.8e-05      0.17      89     171 ..     487     580 ..     465     612 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.8e-05
                                       EEEETTSS..--SHHHHGG-EEEE--TT-TTTTHHHH....HHTCCCCT--HHHHSSEE..E...E--HHHHHHHHH CS
                    Phosphonate-bd  89 iivradsd..iqsledLkgktiafvspsStsGylvpa....alLvkeagldpeddfsev..f...sgshdaavlavl 154
                                       +i+ra+++  i+ ledL ++ + fv ++  sG    +    a L +e+g+d  d+ ++   f      h++ ++ v+
  gi|336253527|ref|YP_004596634.1| 487 LIARAGNPkeIEGLEDLIDRDLRFVNRTTDSGLRTSLgaavADLAAERGVDRRDLVDAIdgFdlgLRAHESPARKVI 563
                                       6888888556*******999999999999999887652222568899999999765444223333579********* PP

                                       TTSSSEEEEEHHHHHHH CS
                    Phosphonate-bd 155 sgdadaaavsadaledl 171
                                       +gdada+    +++e+l
  gi|336253527|ref|YP_004596634.1| 564 AGDADAGLGLRETAERL 580
                                       *******9777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4375.67
//
Query:       gi|336253528|ref|YP_004596635.1|  [L=494]
Description: MATE efflux family protein [Halopiger xanaduensis SH-6]
Scores for 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  167.2  20.3      2e-25   89.3   5.3    2.7  2  MatE             MatE
    3.1e-09   37.0   9.6    3.1e-09   37.0   9.6    4.4  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    1.3e-08   33.9   2.4    1.3e-08   33.9   2.4    2.1  2  MurJ             Lipid II flippase MurJ


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 !   89.3   5.3   3.3e-29     2e-25       1     160 [.      45     205 ..      45     206 .. 0.97
   2 !   87.3   2.6   1.4e-28   8.3e-25       1     159 [.     273     432 ..     273     434 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 3.3e-29
                              MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl 76 
                                       P +++ ++ ++ s++d+ +vg   g+ a+++v++a++ + + f+f+ g++ a+  lv+q++Ga+  +++++a+ ++ 
  gi|336253528|ref|YP_004596635.1|  45 PRIVTGIARMSKSAADVAMVGIAlGPAAIGGVGLATPYWGIGFAFGGGIAGATIGLVSQRYGAGAEEDLSRAVTTSA 121
                                       5678888888999********999***************************************************** PP

                              MatE  77 illlllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisll 153
                                       +++++l++++a+l  + +e ++ l+++d++ ++++++ylr +++g+p+ al+l+ s++l ga ++ +p+++ + +++
  gi|336253528|ref|YP_004596635.1| 122 LIVAALAIPLAVLFGAVPERLIALVGDDPNSIAYGADYLRTVAVGLPFAALNLIGSRTLVGADDAWTPMVLRAGGAV 198
                                       ***************************************************************************** PP

                              MatE 154 lniplny 160
                                       +ni +n 
  gi|336253528|ref|YP_004596635.1| 199 VNIAINA 205
                                       ****996 PP

  == domain 2  score: 87.3 bits;  conditional E-value: 1.4e-28
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+a++n++    ++ +  lv+++g++ lAa+ +a ++  l+ ++++g+s a ++lvgq+lG ++  +a ++ r  l+
  gi|336253528|ref|YP_004596635.1| 273 PLAFTNIARRAAQFPMLALVAMFGPNVLAAYIVARRVRGLMNTPGWGFSLASSSLVGQELGTGDESDADTYGREVLW 349
                                       99*************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.l 153
                                       ++++++++  ++vl+f+eq  ++f +d+ +l+l+  ++ ++++++++l+++  ++g lr+ g+t +p+y  +++  +
  gi|336253528|ref|YP_004596635.1| 350 FGTAVYVVSGAIVLVFAEQVGRIFVDDPSILPLVTSFIAVACVSVVFLGISSGATGPLRASGDTNWPFYGQVLGRyV 426
                                       *********************************************************************99999889 PP

                              MatE 154 lnipln 159
                                       + ip++
  gi|336253528|ref|YP_004596635.1| 427 FAIPVT 432
                                       999987 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 ?   -3.9   5.3       2.2   1.3e+04      50     136 ..      80     100 ..      18     138 .. 0.55
   2 !   37.0   9.6   5.2e-13   3.1e-09       1      72 [.     159     232 ..     159     238 .. 0.92
   3 ?   -1.5   0.1      0.39   2.3e+03      93     112 ..     286     305 ..     269     329 .. 0.57
   4 !    4.2   1.9    0.0067        40       2      76 ..     387     472 ..     386     488 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.2
                   Polysacc_synt_C  50 iplfgivGaaiatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllgllllaalallla 126
                                       +p++g +G                                                                 ++++
  gi|336253528|ref|YP_004596635.1|  80 TPYWG-IG-----------------------------------------------------------------FAFG 90 
                                       33333.22.................................................................2222 PP

                   Polysacc_synt_C 127 vlvgalvYll 136
                                       ++++++  +l
  gi|336253528|ref|YP_004596635.1|  91 GGIAGATIGL 100
                                       2222222222 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 5.2e-13
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgi..vGaaiatvlallvvavl 72 
                                       +L+ +a++++f++l+ ++s  L g + ++++++  + ga+v++++n +li  fg+  vGaai+t++a ++v++ 
  gi|336253528|ref|YP_004596635.1| 159 YLRTVAVGLPFAALNLIGSRTLVGADDAWTPMVLRAGGAVVNIAINAVLIFAFGMgvVGAAIGTAVANVLVLAA 232
                                       58899*********************************************9886444***********999875 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.39
                   Polysacc_synt_C  93 kpllaalvmgivvyllllll 112
                                        p+la ++m++  +l ++++
  gi|336253528|ref|YP_004596635.1| 286 FPMLALVAMFGPNVLAAYIV 305
                                       57777777777733233322 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.0067
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigal.vklilnllli.....plfgi.....vGaaiatvlall 67 
                                       +a+ ++s++fl++s+  ++ L + g + ++++  v+g   + + ++ l +     p++ +     +Ga++a ++ ++
  gi|336253528|ref|YP_004596635.1| 387 IAVACVSVVFLGISSGATGPLRASGDTNWPFYGQVLGRYvFAIPVTALGVyavplPHLEAvtplgIGALYAALILET 463
                                       578999**************************999985414455555544333344444477777888888888777 PP

                   Polysacc_synt_C  68 vvavlnlya 76 
                                       +v ++  y+
  gi|336253528|ref|YP_004596635.1| 464 LVPAVVTYY 472
                                       776666655 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   2.4   2.1e-12   1.3e-08     262     400 ..     101     237 ..      84     261 .. 0.84
   2 ?    0.1   0.4      0.04   2.4e+02      48     136 ..     336     422 ..     291     481 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.1e-12
                              MurJ 262 lSrsakekdedevrdllsqairltllllipvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalv 338
                                       +S+ + ++ e+++ + + ++  ++++l+ip+++++ ++ ++++ l+      +++++++ a  L+  a+gL++ al+
  gi|336253528|ref|YP_004596635.1| 101 VSQRYGAGAEEDLSRAVTTSALIVAALAIPLAVLFGAVPERLIALVG----DDPNSIAYGADYLRTVAVGLPFAALN 173
                                       56666667777777777777778888888888888888888887775....79************************ PP

                              MurJ 339 klllrvfYAredtktPvkislislvlnills..llllpplgvvglalatslsaliglvllyvll 400
                                        + +r++    d++tP+ +    +v+ni+++  l++++ +gvvg a++t++++++ l+ ++v l
  gi|336253528|ref|YP_004596635.1| 174 LIGSRTLVGADDAWTPMVLRAGGAVVNIAINavLIFAFGMGVVGAAIGTAVANVLVLAAFTVGL 237
                                       *******************************8888889999************99998887766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.04
                              MurJ  48 deekaaefvrkvltllilvlllvtligilaapllirllatgfdeetlelavsllrillpylllvslsavfgavLnar 124
                                       de+ a    r+vl + ++v ++  +i +++a+++ r++  +     l l +s+++    +++++++s+ + + L a+
  gi|336253528|ref|YP_004596635.1| 336 DESDADTYGREVLWFGTAVYVVSGAIVLVFAEQVGRIFVDDP--SILPLVTSFIAVACVSVVFLGISSGATGPLRAS 410
                                       566666677777766666666666666789999988888755..788888889999999999998888888877777 PP

                              MurJ 125 kkFfapafsPvl 136
                                       +    p + +vl
  gi|336253528|ref|YP_004596635.1| 411 GDTNWPFYGQVL 422
                                       765555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); 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:                         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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3483.36
//
Query:       gi|336253529|ref|YP_004596636.1|  [L=109]
Description: hypothetical protein Halxa_2132 [Halopiger xanaduensis SH-6]
Scores for 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   12.4   0.0       0.25   12.0   0.0    1.2  1  Lumazine_bd_2  Putative lumazine-binding


Domain annotation for each model (and alignments):
>> Lumazine_bd_2  Putative lumazine-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.4e-05      0.25      66      95 ..      55      84 ..      35      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                                      EE-.EEEEEEEEETTEEEEEEEEEETTEEE CS
                     Lumazine_bd_2 66 dprekeIesidvagdvAmvkvelelpdenf 95
                                      + r++++++ +v++++A+v+v+++++ e+f
  gi|336253529|ref|YP_004596636.1| 55 TGRAWSVSIFRVTENTAVVRVRTPVGREKF 84
                                      446689*******************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       189  (0.0105416); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 870.87
//
Query:       gi|336253530|ref|YP_004596637.1|  [L=553]
Description: TrkA-N domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-34  117.6   9.4      1e-16   61.2   2.3    2.4  2  TrkA_N       TrkA-N domain
      3e-15   55.8   7.1    2.3e-07   30.5   0.6    3.8  4  TrkA_C       TrkA-C domain
  ------ inclusion threshold ------
       0.01   15.8   3.4      0.018   15.0   3.4    1.4  1  Ion_trans_2  Ion channel


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 !   60.4   0.8     3e-20   1.8e-16       8     116 .]     133     239 ..     126     239 .. 0.91
   2 !   61.2   2.3   1.7e-20     1e-16       1     115 [.     351     458 ..     351     459 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 3e-20
                                       HHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHHHH CS
                            TrkA_N   8 rvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilavlla 83 
                                       r +  l++eL+e +  d+v+i++dee +++l+++g+++++gd+ d++ L++a ie+a+++i+ ++d +a+il+  +a
  gi|336253530|ref|YP_004596637.1| 133 RDTGVLLDELEElDA-DYVLIESDEEEAKRLSDDGYQAINGDPEDRADLDRAMIEDASLLITDAEDRTASILL--TA 206
                                       55678999****777.7***********************************************999999988..56 PP

                                       HHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  84 kelnpkkkiiaraqdpehaellkklgadvvisp 116
                                        e np++++i+ +++  h  +l ++g+d+++ p
  gi|336253530|ref|YP_004596637.1| 207 LEANPDLRTISFTESTRHDAALTEIGVDRAVAP 239
                                       6789*************************9976 PP

  == domain 2  score: 61.2 bits;  conditional E-value: 1.7e-20
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       i+++G+G+ G + ++ L ++ + v v+d++ ++v e        +vgd t++ +L++ag+e+a+a+i++++dd++ +
  gi|336253530|ref|YP_004596637.1| 351 ILVAGAGEGGAAAVDALPDDVS-VAVVDQSADAVIEPD------IVGDITEPGTLRAAGLEEASALIVTVDDDASAL 420
                                       79*****************995.*************66......********************************* PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEE CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkklgadvvis 115
                                       l++++a++l ++ +i ar+ d  ++  + k+gad+v+s
  gi|336253530|ref|YP_004596637.1| 421 LTIATARSLSDDVEILARVTDTRKVTPAFKAGADYVLS 458
                                       ************************************87 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.42   2.5e+03      25      49 ..     122     153 ..     112     156 .. 0.65
   2 ?   -2.7   0.0      0.89   5.3e+03       8      19 ..     238     249 ..     235     251 .. 0.80
   3 !   26.8   0.1   5.7e-10   3.4e-06       1      68 [.     267     336 ..     267     338 .. 0.88
   4 !   30.5   0.6   3.9e-11   2.3e-07       5      67 ..     486     548 ..     482     550 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.42
                                       H..S-EEEEEE-T.....-EEES--TT-B--T CS
                            TrkA_C  25 r..gvlvvairRg.....geliipsgdtvLee 49 
                                       +   v v+ +rR+     +el+  + d+vL e
  gi|336253530|ref|YP_004596637.1| 122 KddHVVVAEYRRDtgvllDELEELDADYVLIE 153
                                       34578888889988566555556666666655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.89
                                       --GGGTTSBHHH CS
                            TrkA_C   8 agsplvGktlke 19 
                                       a + l+G++l+e
  gi|336253530|ref|YP_004596637.1| 238 APHALIGRRLAE 249
                                       56779*****99 PP

  == domain 3  score: 26.8 bits;  conditional E-value: 5.7e-10
                                       CEEEEEE--GGGTTSBHHHHTHHHH..S-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar..gvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                       ++e+ v+ +spl G +l+e+ + ++    lv +   g   ++p++dt+L+++ vl+v+g+   ++++ ++
  gi|336253530|ref|YP_004596637.1| 267 VREILVRRESPLHGVRLGESPVADHpeLTLVGGWFDGVLRLSPPSDTRLTPNTVLVVAGPAGVIDDVSSE 336
                                       689***********************6666666688877788888********************99876 PP

  == domain 4  score: 30.5 bits;  conditional E-value: 3.9e-11
                                       EEE--GGGTTSBHHHHTHHHH...S-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   5 tvpagsplvGktlkelnlrar...gvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       + +  +p+vG +l +  +r+    g +vv+i+R+   i+ +++ ++e++D ++v+gs+++++e+++
  gi|336253530|ref|YP_004596637.1| 486 VRTDAAPFVGDSLID--FRRDterGWTVVGIVRD-GTILTDEHATIESDDDVIVAGSDETIREFER 548
                                       5556789********..999999***********.8***************************987 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   3.4     3e-06     0.018       3      75 ..      29     105 ..      26     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-06
                                       HHHTCHHHHHHHHT.........T---HHHHHHHHHHHHTTS----SSTT.-----HHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2   3 lllvlifgaviysl.....eegwekwsfldalYfsfvtltTiGYGdivpe.tdagrlftivyillGlalfalflavl 73 
                                       +++v++f +viy l     e+    +s++ +l  ++ t+tT G+G  +p  t++  l+++++ ++G+++ +++l vl
  gi|336253530|ref|YP_004596637.1|  29 VVAVVLFYTVIYNLgmrylEHR--PHSIFRSLQTVTETMTTTGFGADSPWaTPVMNLLMVAIQVTGILIGFVALRVL 103
                                       5667777777777775443333..68*******************************************99999998 PP

                                       HH CS
                       Ion_trans_2  74 gk 75 
                                       ++
  gi|336253530|ref|YP_004596637.1| 104 VI 105
                                       86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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 0.23s 00:00:00.79 Elapsed: 00:00:00.38
# Mc/sec: 4332.40
//
Query:       gi|336253531|ref|YP_004596638.1|  [L=433]
Description: molybdenum cofactor synthesis domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-41  139.3   5.5    1.4e-40  138.6   5.5    1.4  1  MoeA_N         MoeA N-terminal region (domain I and II)
    1.8e-24   86.1   0.1    2.9e-24   85.4   0.1    1.4  1  MoCF_biosynth  Probable molybdopterin binding domain
      8e-18   64.4   3.1    6.3e-17   61.5   0.0    3.5  3  MoeA_C         MoeA C-terminal region (domain IV)


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.6   5.5   2.4e-44   1.4e-40       2     157 .]      18     190 ..      17     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 138.6 bits;  conditional E-value: 2.4e-44
                                       -HHHHHHHHHHH-.HH........-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--..... CS
                            MoeA_N   2 sveealaiilaal.el........eeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep 68 
                                       +v+ea++i+++a+           + +e v++ ++a gr+la+++ ++++vP+++++amDGYAvrae++ gas ++p
  gi|336253531|ref|YP_004596638.1|  18 PVDEARRILREAIeGQqsddepcaTGTEtVDV-ERADGRTLAAPLESARNVPHYRRAAMDGYAVRAEDTFGASDRSP 93 
                                       799****9999995449999999966666***.9999**************************************** PP

                                       ..........-S---TT-.EEEE-TTSB--TT--EEEEGGGE...E.....EETTE.S--STTTTEE-TTSSB-TTS CS
                            MoeA_N  69 ....saageeperllpgg.avrimTGaplPegadaVvpvEdte..eee.aketvev.kavkpgenvrraGedikaGe 136
                                           +a+g  ++++++++ a+r++TG++lPegadaVv++E++e  e + ++e  ev +av++genv ++Ged+++G+
  gi|336253531|ref|YP_004596638.1|  94 evlgIAEGIGADATVEPEtAARVHTGSALPEGADAVVMIEEVEelESTgVPE-LEVgDAVAEGENVAPIGEDVAEGQ 169
                                       ****777777777777777***********************6543333333.33379******************* PP

                                       EEE-TTBB--CCCHHHHHHCT CS
                            MoeA_N 137 vllragtrltpaeigllasvG 157
                                        l +ag+rl+p+++gl+ s+G
  gi|336253531|ref|YP_004596638.1| 170 HLYEAGHRLRPSDLGLIRSAG 190
                                       ******************998 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.1   4.9e-28   2.9e-24       1     143 [.     203     336 ..     203     337 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 4.9e-28
                                       EEEEE-HHHH.....TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT- CS
                     MoCF_biosynth   1 avitvGdell.....sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdD 72 
                                       +vi +G el+     +g+++ tng ++++l ++ g+++  + vv Dd+e ++ a+ + l + dv++ttGG +++++D
  gi|336253531|ref|YP_004596638.1| 203 GVIPTGEELVegdpgPGEVVETNGLTVSRLAERWGARATYRDVVTDDPESLRVAIQRDLTK-DVVVTTGGSSVGERD 278
                                       6999***************************************************888677.*************** PP

                                       -HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  73 vtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                       + pe++ +l+e       +++++v+lkpg+pv+++ +   +++   ++++LPG+p+a+ + +  +l+p+l+
  gi|336253531|ref|YP_004596638.1| 279 LLPEVIDDLGE-------VLVHGVGLKPGHPVCLGIV---EDT---PVLALPGYPVACIVNAVQFLRPTLR 336
                                       ***********.......8**************9999...765...7*******************99986 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.067     4e+02       3      23 ..      56      76 ..      55      89 .. 0.82
   2 ?   -1.8   0.2       0.6   3.6e+03      48      59 ..     126     137 ..     125     159 .. 0.56
   3 !   61.5   0.0   1.1e-20   6.3e-17       2      71 ..     351     428 ..     350     429 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.067
                                      EESS-EE--SSS-EEEEEEEE CS
                            MoeA_C  3 rlaedlksdpgrreflRvilt 23
                                      +la++l s+++ +++ R+ ++
  gi|336253531|ref|YP_004596638.1| 56 TLAAPLESARNVPHYRRAAMD 76
                                      58999*************998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.6
                                       --EEEEE-TT-- CS
                            MoeA_C  48 Anglivipegte 59 
                                       A++ ++i+e +e
  gi|336253531|ref|YP_004596638.1| 126 ADAVVMIEEVEE 137
                                       667777766555 PP

  == domain 3  score: 61.5 bits;  conditional E-value: 1.1e-20
                                       EEESS-EE--SSS-EEEEEEEE..S-S......-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEE CS
                            MoeA_C   2 arlaedlksdpgrreflRvilt..eed......geyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevi 70 
                                       a+l ++++s+pg r+f Rv+l+  ++d      +++ a+pt+ +gSg+Lss a A+g++v++ ++eg+ aGe+V+v+
  gi|336253531|ref|YP_004596638.1| 351 AVLERKIPSEPGTRTFARVQLEerDPDeigdgePRFAATPTRASGSGVLSSVALADGWVVVDDDREGIPAGETVSVE 427
                                       8999******************76333677777******************************************98 PP

                                       E CS
                            MoeA_C  71 l 71 
                                        
  gi|336253531|ref|YP_004596638.1| 428 D 428
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 3478.17
//
Query:       gi|336253532|ref|YP_004596639.1|  [L=272]
Description: hypothetical protein Halxa_2135 [Halopiger xanaduensis SH-6]
Scores for 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-11   42.5   0.0    2.4e-08   33.6   0.0    3.0  2  GIDE      E3 Ubiquitin ligase
  ------ inclusion threshold ------
       0.13   12.2   5.2        2.7    8.0   0.1    2.3  2  IncE      Inclusion membrane protein E


Domain annotation for each model (and alignments):
>> GIDE  E3 Ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   2.6e-12   2.4e-08       6     106 ..      84     198 ..      79     205 .. 0.85
   2 ?    2.0   0.0     0.014   1.2e+02     119     137 ..     232     250 ..     219     271 .. 0.68

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.6e-12
                              GIDE   6 kreskkstetrrrsetvasnersvpFvlrDd................t.grVlV.dpegaeielttvldefepaeas 64 
                                       ++e +   +  r++ t+as  + vpF l+D+                t +r++V   ++ + ++    d++e ++++
  gi|336253532|ref|YP_004596639.1|  84 EEERD--SKNGRHWATIASGDEYVPFRLDDGsgsvlieppgadfrlaTdDRIEVdGGTEPPAPIARFIDRTEAVDSE 158
                                       33333..579*********************9999999999999999559999955566678999999999999999 PP

                              GIDE  65 rvtlllgffsldlektlGyryeEkvLpvgkrvtvvGeaqsde 106
                                        +++ l  f+l+    ++ r +E+ L +g +v v+G+a+ d 
  gi|336253532|ref|YP_004596639.1| 159 NTSIDLHVFELRT--GRDRRFVERRLEPGETVHVLGTARYDP 198
                                       9999999999999..***********************7765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.014
                              GIDE 119 gqpffisekseeeLiesla 137
                                       g pf+is+ se+ L  +++
  gi|336253532|ref|YP_004596639.1| 232 GHPFVISDSSERWLGVRAG 250
                                       579*******999988776 PP

>> IncE  Inclusion membrane protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0003       2.7      50     109 ..       8      63 ..       2      71 .. 0.81
   2 ?    5.1   1.9    0.0024        21      51      70 ..     251     270 ..     244     272 .] 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0003
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              IncE  50 lalgiaaaavgvscsgfaiglgviaillgivlfaisaldvledhglvgcpfklpcksspa 109
                                       +alg+ a av vs   +a+g g+  + l +++f      vle  g  g p++l   + pa
  gi|336253532|ref|YP_004596639.1|   8 FALGLLALAVAVS--MVALGYGIAELRLAVLVFRSQPDSVLETPG--GGPVELRGTAEPA 63 
                                       5889888888776..5799**************999999999887..6677666666665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0024
                                       XXXXXXXXXXXXXXXXXXXX CS
                              IncE  51 algiaaaavgvscsgfaigl 70 
                                       a+g+aa+ vgv++ gfai +
  gi|336253532|ref|YP_004596639.1| 251 AVGLAATLVGVAALGFAIAV 270
                                       89****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1962.38
//
Query:       gi|336253533|ref|YP_004596640.1|  [L=159]
Description: heat shock protein Hsp20 [Halopiger xanaduensis SH-6]
Scores for 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-13   48.4   0.0    1.1e-12   48.0   0.0    1.2  1  HSP20        Hsp20/alpha crystallin family
     0.0002   20.8   0.2    0.00036   20.0   0.2    1.5  1  ArsA_HSP20   HSP20-like domain found in ArsA
  ------ inclusion threshold ------
      0.065   13.3   0.6      0.065   13.3   0.6    2.3  2  GvpH         GvpH
       0.79    9.7   8.3        1.1    9.3   8.3    1.2  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)


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 !   48.0   0.0   2.4e-16   1.1e-12       2      98 ..      19     112 ..      18     116 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 2.4e-16
                                       --SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEET CS
                             HSP20   2 ikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkd 78 
                                         e+ +++ + ldvpg+ ++ +++ +ed+r+++ +++++   d+  + +e +s  F+ ++ LP+++ + + +a+++ 
  gi|336253533|ref|YP_004596640.1|  19 LLESTDRYLLVLDVPGVTADSIDLAIEDGRLSIDAQRQKDLPDDYRYLEENRSLFFDVELPLPDDAVEADLDAAVDR 95 
                                       578899********************************9999*********************************** PP

                                       TEEEEEEEBSS--..----- CS
                             HSP20  79 GvLtvtvpkkepekkkkerk 98 
                                       GvL++++pk++ +    e +
  gi|336253533|ref|YP_004596640.1|  96 GVLELSIPKRTGD---GETT 112
                                       *********9887...4444 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 !   20.0   0.2     8e-08   0.00036       2      59 ..      24      98 ..      23     102 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8e-08
                        ArsA_HSP20  2 deyvlkldLPfvdkeeidlsrsgdeLtIkig..................nfrRqitLPsvlarkevtsAkfedgvL 59
                                      d+y l+ld+P+v+ ++idl++++  L+I ++                   f  + +LP+   + +  +A +  gvL
  gi|336253533|ref|YP_004596640.1| 24 DRYLLVLDVPGVTADSIDLAIEDGRLSIDAQrqkdlpddyryleenrslFFDVELPLPDDAVEADL-DAAVDRGVL 98
                                      79****************************966666666666644444444444666665555555.555555555 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   1.4e-05     0.065      98     128 ..      21      49 ..      10      59 .. 0.85
   2 ?   -1.4   8.0      0.46   2.1e+03      78     124 ..     104     153 ..      73     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                              GvpH  98 ddsdelvvvadlpGvtdedvdvaletdeqal 128
                                       +++d  ++v d+pGvt +++d a+e  ++ l
  gi|336253533|ref|YP_004596640.1|  21 ESTDRYLLVLDVPGVTADSIDLAIE--DGRL 49 
                                       57899999****************9..4444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.46
                              GvpH  78 qrsgqqrttedsihvetrasddsdel...vvvadlpGvtdedvdvaletd 124
                                       +r+g+  tt d +    r ++d+de     v ad p  td d d   e+d
  gi|336253533|ref|YP_004596640.1| 104 KRTGDGETTIDVVEGTVRDGEDGDENedgDVDADEPAGTDPDADPEPESD 153
                                       68999999999999999*99999975222699********9999766655 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   8.3   0.00024       1.1      38      73 ..     122     158 ..     103     159 .] 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00024
                       Trypan_PARP  38 kggkgk.ekgtkvsdddtngtdpepepepepepepep 73 
                                        g  g  ++   v++d+  gtdp+ +pepe + +pep
  gi|336253533|ref|YP_004596640.1| 122 DGEDGDeNEDGDVDADEPAGTDPDADPEPESDADPEP 158
                                       4555654456678888888888887777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1141.43
//
Query:       gi|336253534|ref|YP_004596641.1|  [L=565]
Description: ABC-1 domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-27   94.0   0.0    1.8e-17   63.6   0.0    3.0  3  ABC1      ABC1 family
    0.00015   21.8   0.1     0.0019   18.2   0.0    2.5  2  APH       Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.019   14.4   0.0       0.03   13.7   0.0    1.3  1  Pkinase   Protein kinase domain


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0     1e-09   6.2e-06       4      33 ..      89     117 ..      86     122 .. 0.89
   2 !   63.6   0.0     3e-21   1.8e-17      34     118 ..     146     231 ..     141     232 .. 0.97
   3 ?   -0.8   0.0      0.27   1.6e+03      74      98 ..     402     426 ..     386     437 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1e-09
                              ABC1   4 gkkleeiFaefdeePiAaASiaqVhrAklk 33 
                                       g ++ee F efd ePi  AS++qV+rA++ 
  gi|336253534|ref|YP_004596641.1|  89 G-PVEERFLEFDTEPISGASLGQVYRARID 117
                                       4.89***********************986 PP

  == domain 2  score: 63.6 bits;  conditional E-value: 3e-21
                              ABC1  34 sgeeVavKvqrpgvkkriksDlellkllakllkkflkelr.ldleelvdefskslleEldferEAknaekfrenfak 109
                                        g+eVavK++rp+++  +++Dl+++++ + l+  f+ e r  +le+l+defs++++eE+++erEA+   ++r+nfa 
  gi|336253534|ref|YP_004596641.1| 146 PGQEVAVKIRRPDIEPLVEADLRVIRWSLPLVMFFVDESRsFSLENLADEFSRTIREEMNYEREAEMLTEIRSNFAG 222
                                       599************************************999*********************************** PP

                              ABC1 110 lkevkvPkv 118
                                       ++++++P v
  gi|336253534|ref|YP_004596641.1| 223 DDRFRIPAV 231
                                       *******98 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.27
                              ABC1  74 ldleelvdefskslleEldferEAk 98 
                                       l++ ++v+ +  +l +E df   A 
  gi|336253534|ref|YP_004596641.1| 402 LRVATVVEGVCVTLDQEFDFISTAT 426
                                       5688999999999******987665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.1e-07    0.0019     139     201 ..     256     315 ..     225     317 .. 0.75
   2 ?   -0.6   0.0      0.17     1e+03      62     140 ..     414     491 ..     396     498 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-07
                                       CCTCC..HHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEEC CS
                               APH 139 selld..lleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpp 201
                                       ++ ++  ++ +++e++ +a ++      + ++ H D+hpgNl v+ d+gr+  + Df+++g  +p
  gi|336253534|ref|YP_004596641.1| 256 ELERKgiDRTRVAENLERAYLQMIM---DDGVFHADPHPGNLAVT-DEGRI-VFYDFGMSGRVDP 315
                                       3333345566666667777777777...89***************.77887.699***9987766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.17
                                       S-EEETTEEEEEEE----EE-SS...HHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHCHTCCHHHHHHCHHHC CS
                               APH  62 tddeeigllfalieyvpgrsllr...klsaaqlpellealgeflaalhqvdpaalpladflaqdlellrqlesatar 135
                                       t d+e  + + + ey+  + +++   + + +++ e++++ ge l ++  +++a+  l++  ++dl++ + +e++  +
  gi|336253534|ref|YP_004596641.1| 414 TLDQEFDFISTATEYLTEQGYREesiRRYVRESAEQIRESGESLTRI--APKAEGALDRLDRDDLYVRIGVEDS--D 486
                                       55555555677777777666666666777888888888888888877..4457777777777778777777776..5 PP

                                       CCGCC CS
                               APH 136 llase 140
                                       ++ ++
  gi|336253534|ref|YP_004596641.1| 487 DVFAK 491
                                       55555 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     5e-06      0.03      72     149 ..     238     314 ..     193     327 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5e-06
                                       EEEEEEE--TTEBHHHHHH.HHSS--HHHHHHHHHHHHHH.HHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSE CS
                           Pkinase  72 elylvleyveggeladlle.rkgslseeeakkiakqileg.leylHskgiiHrDlKpeNiLidekgelKitDFGlak 146
                                        ++l +ey++g++++dl e +++ ++ +++ + +++   + l+ + + g++H D  p N+ + ++g +   DFG++ 
  gi|336253534|ref|YP_004596641.1| 238 PRVLTMEYIRGTKINDLEElERKGIDRTRVAENLER---AyLQMIMDDGVFHADPHPGNLAVTDEGRIVFYDFGMSG 311
                                       56899***********99965555666655554444...3388999*****************************98 PP

                                       ESS CS
                           Pkinase 147 ele 149
                                       +++
  gi|336253534|ref|YP_004596641.1| 312 RVD 314
                                       876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4133.77
//
Query:       gi|336253535|ref|YP_004596642.1|  [L=245]
Description: hypothetical protein Halxa_2138 [Halopiger xanaduensis SH-6]
Scores for 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  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1819.18
//
Query:       gi|336253536|ref|YP_004596643.1|  [L=367]
Description: hypothetical protein Halxa_2139 [Halopiger xanaduensis SH-6]
Scores for 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   17.0   0.0     0.0075   15.9   0.0    1.6  1  MR_MLE_C  Enolase C-terminal domain-like


Domain annotation for each model (and alignments):
>> 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 !   15.9   0.0   4.2e-07    0.0075      19     173 ..     176     327 ..     160     353 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.2e-07
                                       EEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTS.........BHHHHHHHHHHHGGGTESEEESSSSTTTH CS
                          MR_MLE_C  19 KlkvggddvaedvervravreavgpgddvdlmvDanqaw.........dlatAirvareleeldllwlEEPvppedd 86 
                                       Kl+   +++++d++ v+ + ++vg+  d+  ++D  + +         d+     v+++   +  + +E+P    d+
  gi|336253536|ref|YP_004596643.1| 176 KLD---PTPEWDAALVEDIVDTVGQ--DAVRILDLKGHYqgtevdtppDPGLYELVLEA---FPEAVIEDPALT-DE 243
                                       333...3699*************55..66999******988888643333333333333...56699*****99.55 PP

                                       HHHHHHHHH..HHSSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSC.SSH CS
                          MR_MLE_C  87 leglaelra..rasipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsg.sgg 160
                                        e l e ++  +   ++ ++  ++++ad+++l  +   d++++++sr g +  ++++++ ++++g+++  +++ ++g
  gi|336253536|ref|YP_004596643.1| 244 TEPLFEDSDirK---RVSWDAPIHGLADVEALPWEP--DWLNVKPSRFGSLESLLETIDFCRERGIRMYGGGQfELG 315
                                       776644443325...9****************7666..*****************************9999973468 PP

                                       HHHHHHHHHHHTT CS
                          MR_MLE_C 161 lglaaslhlaaai 173
                                       +g+   l+l+aa+
  gi|336253536|ref|YP_004596643.1| 316 VGR-GQLQLLAAL 327
                                       887.468887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2639.15
//
Query:       gi|336253537|ref|YP_004596644.1|  [L=124]
Description: translation initiation factor 5A [Halopiger xanaduensis SH-6]
Scores for 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   0.0      0.011   15.7   0.0    2.2  2  EFP_N     Elongation factor P (EF-P) KOW-like domain
  ------ inclusion threshold ------
      0.028   14.4   0.4      0.051   13.6   0.4    1.5  1  EFP       Elongation factor P (EF-P) OB 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 !   15.7   0.0   1.2e-06     0.011       3      47 ..       9      54 ..       7      58 .. 0.86
   2 !    4.6   0.0    0.0038        34       6      24 ..      73      91 ..      69      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-06
                                      GG--TT-EEEETTEEEEEEEEEEEEETT.S--EEEEEEEETTTS-E CS
                             EFP_N  3 selkkGlvieidgklyvVlefehvkpGk.GqafvrvklknlrtGak 47
                                       +l  G  ++id+  +++ ++   kpGk G+a  rv+   + +G+k
  gi|336253537|ref|YP_004596644.1|  9 RDLQEGSYVMIDDAACKINSYSTAKPGKhGSAKARVEAEGVFDGKK 54
                                      6999***********************6378888888877777776 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0038
                                      -TT-EEEETTEEEEEEEEE CS
                             EFP_N  6 kkGlvieidgklyvVlefe 24
                                      k G+v+ +dg  ++V++ e
  gi|336253537|ref|YP_004596644.1| 73 KQGQVVSVDGSDMQVMDLE 91
                                      89*************9976 PP

>> EFP  Elongation factor P (EF-P) OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   5.6e-06     0.051       9      26 ..      81      98 ..      74     124 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.6e-06
                                      ETTEEEEEETTT--EEEE CS
                               EFP  9 dgdeyvFMdnetYeqiel 26
                                      dg+++ +Md etYe i++
  gi|336253537|ref|YP_004596644.1| 81 DGSDMQVMDLETYETITM 98
                                      999************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1018.07
//
Query:       gi|336253538|ref|YP_004596645.1|  [L=287]
Description: Agmatinase [Halopiger xanaduensis SH-6]
Scores for complete 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  185.2   0.1      2e-54  185.0   0.1    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 !  185.0   0.1   1.1e-58     2e-54       2     277 ..      24     278 ..      23     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 185.0 bits;  conditional E-value: 1.1e-58
                                       EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHH CS
                          Arginase   2 dvallGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeava 77 
                                       +++++G+P+da+++++pG+rfGPr ir+  + ++    y+ ++++ ++el +vd gdv     d ee le ++++++
  gi|336253538|ref|YP_004596645.1|  24 NFVVVGAPLDATTTFQPGTRFGPRRIRSFAEPFDD---YDRRTDQhFSELGVVDRGDVRAWD-DLEEYLEYLTSTLR 96 
                                       689**************************777776...77777778************9985.8888********** PP

                                       HHHHTTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEE CS
                          Arginase  78 eilkagklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvq 154
                                       e++ ++++p++lGG+H+++l+  ra+  +       + +DAH+D+ +++ +g+ +sh+ + rr++ e++ + ++ v+
  gi|336253538|ref|YP_004596645.1|  97 EAVWNDAVPLLLGGEHTVSLAGARAVNPE-----VFVCLDAHLDCYDAY-DGNPLSHAAVTRRIL-EDVDSVEEAVI 166
                                       ********************999988854.....5789***********.9**************.888999***** PP

                                       EEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-H CS
                          Arginase 155 iGirsvdneeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltl 231
                                       +G r+ ++ e+e a+   ++v+  +++ +       e++++rv+  +   ylS+DiD+ Dp +aPGtGt+ep Gl++
  gi|336253538|ref|YP_004596645.1| 167 LGARTGSEAEWERADADDVTVVPPEDVVQFTC----EHLEDRVT--DCEAYLSVDIDAADPGYAPGTGTTEPFGLEP 237
                                       **************889**********88775....99999996..5699*************************** PP

                                       HHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
                          Arginase 232 rellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                                       rel++++r++a   +  g+DvvEvn+  d    q a+la +lvre+
  gi|336253538|ref|YP_004596645.1| 238 RELRDVVRTVAP--HAGGFDVVEVNDRDDG---QAASLAGKLVREF 278
                                       **********77..67**********9443...89********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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 0.21s 00:00:00.63 Elapsed: 00:00:00.45
# Mc/sec: 1907.41
//
Query:       gi|336253539|ref|YP_004596646.1|  [L=133]
Description: hypothetical protein Halxa_2142 [Halopiger xanaduensis SH-6]
Scores for 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  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 993.55
//
Query:       gi|336253540|ref|YP_004596647.1|  [L=315]
Description: acetamidase/formamidase [Halopiger xanaduensis SH-6]
Scores for 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-35  121.1   1.3    1.3e-16   60.5   0.6    2.8  2  FmdA_AmdA  Acetamidase/Formamidase family


Domain annotation for each model (and alignments):
>> FmdA_AmdA  Acetamidase/Formamidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   1.2e-20   2.2e-16      15     157 ..      12     157 ..       1     161 [. 0.86
   2 !   60.5   0.6   7.2e-21   1.3e-16     197     367 ..     155     307 ..     155     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.2e-20
                         FmdA_AmdA  15 lhNRwHpdipavaevkpgetvkvecldwtdgqiknndsaddvrtvdlkkvHeltgPvevegAepGDllvveildiev 91 
                                           + pd++a+++v+pge++ +e++d  dg +++    +dv++   ++v   tgP++vegAepGD+l vei+d++ 
  gi|336253540|ref|YP_004596647.1|  12 AIYEFTPDLEAITTVEPGEELTIETRDSLDGAVQT---ESDVIESVPDEVNAATGPIAVEGAEPGDVLRVEIEDVRL 85 
                                       555688**************************986...579999999****************************** PP

                         FmdA_AmdA  92 leeaewGytgifdkenggGfl..kdafpeaakaiwdlegiyassrq.........ipgvrfrglphpGllGtapske 157
                                        e++  G  +   + +g+G+l  ++ ++ +   i  +++  a  +            ++++++ p +G++G+ap++e
  gi|336253540|ref|YP_004596647.1|  86 AEDR--GRII---TIDGFGLLdgDEEIEAPRTRITPVSQADADGEAdgdgeptitFDDLEVPVEPVIGTIGVAPAAE 157
                                       *987..4443...35699999888889999999998888888888788999998899*****************987 PP

  == domain 2  score: 60.5 bits;  conditional E-value: 7.2e-21
                         FmdA_AmdA 197 aaegartvpprengGnmDiknlsrGskvylPVkveGaklsvGDlHfsqGDGEisfcg.aiemsgvvtlkvevikggm 272
                                       aae+  t+ p ++gGn+D  +++ G +vy+PV+  Ga l +GD  ++  DGE+  cg   e++  ++++v+v+    
  gi|336253540|ref|YP_004596647.1| 155 AAESYATLVPHDHGGNLDTTDVTGGNTVYFPVFQAGAMLAMGDCKAAMADGEM--CGtGAEIATEIDVTVDVLDADE 229
                                       678899***********************************************..**99****************99 PP

                         FmdA_AmdA 273 eklgiknpiflpeev.epryseylsfeGisvdesgkqhyldltvAyrnallraieyLk.kfGytkeqaylllsvapv 347
                                       + ++++ p+++ +++ +p       +       s +    +l+ A + a + a+++L  + G++++ ayl+ s++  
  gi|336253540|ref|YP_004596647.1| 230 TAVDLERPLVETDDAwKP-------I-A-----SAE----TLEAACELANRDAVDLLAaEHGFDDTDAYLFSSLT-G 288
                                       999*****9988665145.......2.1.....233....6888899999999999987899******9999988.5 PP

                         FmdA_AmdA 348 egrisgivdiPnvvatlalP 367
                                          is++vd P v +  a+P
  gi|336253540|ref|YP_004596647.1| 289 GLEISQVVD-PLVTVRNAIP 307
                                       566888887.5555555565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2238.79
//
Query:       gi|336253541|ref|YP_004596648.1|  [L=257]
Description: NGG1p interacting factor 3 protein, NIF3 [Halopiger xanaduensis SH-6]
Scores for 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  176.9   0.0    5.9e-52  176.7   0.0    1.0  1  NIF3          NIF3 (NGG1p interacting factor 3)
  ------ inclusion threshold ------
      0.073   13.9   2.1      0.092   13.5   0.3    1.9  2  Glyoxalase_6  Glyoxalase-like domain
       0.12   12.6   1.0       0.55   10.5   0.1    2.2  3  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge


Domain annotation for each model (and alignments):
>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.7   0.0   9.8e-56   5.9e-52      14     240 ..      21     243 ..       7     248 .. 0.93

  Alignments for each domain:
  == domain 1  score: 176.7 bits;  conditional E-value: 9.8e-56
                              NIF3  14 lae.swDnvGlqvgdpekevkkvllaldlteevleeAiekgadliithHPlifkplkrlteddykkrllkkliknni 89 
                                       +a+ +   +Glqvg  e+e+++v++a+d  +e++e+Ai++gad++++hH++ +++++r+t++   + +++ li++++
  gi|336253541|ref|YP_004596648.1|  21 YADlDASANGLQVGPDEAEIEHVAFAVDGVQETFERAIDAGADALVVHHGISWGGFDRVTGR--TYDRIAPLIEHDC 95 
                                       445566788*****9999********************************************..99*********** PP

                              NIF3  90 slysaHtnlDaapg.Gvndwlakalglekieplepskeekkeeeeglgrigeleepvsleelakklkkkl..glekv 163
                                       +ly  H++lD +++ G+++ +a++l+le+  p+++         e +g  g+ +e+  +++l ++l+++l  g ++v
  gi|336253541|ref|YP_004596648.1|  96 ALYVSHLPLDGHQElGNAAGVADVLELEDRAPFGELG------PEYIGQRGTASESYGAADLRERLENELvtGEHSV 166
                                       **********************************987......678************************544455* PP

                              NIF3 164 rvagdldkkvkkvaicaGsGaslieeakakgaDlliTGelkhhealdakekgiavidvgHyatErvflealaelLke 240
                                       rv    + +++ vai++GsG+++++ea ++gaD+liTGe k + +++a+e+g++v ++gHyatE++++++l++l++ 
  gi|336253541|ref|YP_004596648.1| 167 RVLDFGPDELEDVAIVTGSGTDWLDEAVDAGADALITGEGKQKVYHEAQEAGVTVALAGHYATETFGVRSLQDLVEG 243
                                       ************************************************************************99875 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   1.5e-05     0.092      59      89 ..      40      70 ..       6      82 .. 0.72
   2 ?   -0.6   0.1      0.39   2.4e+03      63      84 ..     170     201 ..     130     222 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                      Glyoxalase_6 59 rvHldlavedldaevarlvalGArvlreprd 89
                                        H+ +av+ ++++ +r++++GA  l  +++
  gi|336253541|ref|YP_004596648.1| 40 IEHVAFAVDGVQETFERAIDAGADALVVHHG 70
                                      35*********************98766655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.39
                      Glyoxalase_6  63 dlavedld..........aevarlvalGArvl 84 
                                       d+  ++l+             +++v++GA  l
  gi|336253541|ref|YP_004596648.1| 170 DFGPDELEdvaivtgsgtDWLDEAVDAGADAL 201
                                       55554443333444444456667777777665 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   9.2e-05      0.55      66      94 ..      37      65 ..       8      78 .. 0.83
   2 ?   -2.2   0.0      0.82   4.9e+03      60      93 ..     167     200 ..     131     211 .. 0.61
   3 ?   -0.5   0.0      0.25   1.5e+03      83     101 ..     211     229 ..     200     235 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.2e-05
                                      S-EEEEEEEEES-HHHHHHHHCTTTEEEE CS
                      Glyoxalase_4 66 geglhhlaywvddldaavarleeqGfevv 94
                                      ++++ h+a++vd ++++ +r+ ++G+  +
  gi|336253541|ref|YP_004596648.1| 37 EAEIEHVAFAVDGVQETFERAIDAGADAL 65
                                      6799*********************9855 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.82
                                       -THHHTS-EEEEEEEEES-HHHHHHHHCTTTEEE CS
                      Glyoxalase_4  60 eflaehgeglhhlaywvddldaavarleeqGfev 93 
                                         l+ +  +l  +a+ + +    ++++ ++G+  
  gi|336253541|ref|YP_004596648.1| 167 RVLDFGPDELEDVAIVTGSGTDWLDEAVDAGADA 200
                                       4444455556666666655555555555555554 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.25
                                       HHHHCTTTEEEEEEEE-GG CS
                      Glyoxalase_4  83 varleeqGfevvqkgvrag 101
                                         +++e+G++v+ +g +a+
  gi|336253541|ref|YP_004596648.1| 211 YHEAQEAGVTVALAGHYAT 229
                                       4678888888888876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2023.41
//
Query:       gi|336253542|ref|YP_004596649.1|  [L=394]
Description: hypothetical protein Halxa_2145 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.46    8.7   5.8       0.56    8.4   5.8    1.1  1  CDC45        CDC45-like protein
       0.46    9.3   5.5       0.62    8.9   5.5    1.1  1  NARP1        NMDA receptor-regulated protein 1
        1.2    8.3   3.6        1.6    7.9   3.6    1.2  1  Zip          ZIP Zinc transporter


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 ?    8.4   5.8   9.3e-05      0.56     106     181 ..     140     212 ..      97     273 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 9.3e-05
                             CDC45 106 vfDDgd..ieeeleeereayealeeeeesdeedeeeeeeddddeeeeeeeeedeedeeedeeeskkkrksksdeeee 180
                                       v  Dg+  ++++  e+ ++ e+ e+ +++     +++++ ++  +++e+++e+++ +e++++++k k+++k d +++
  gi|336253542|ref|YP_004596649.1| 140 VTYDGEtvVNQNCGEQSDDGENGEDGKDDG----KDHKKGEK--AKKEKKKEKGHYDETEKTHEKGKKHDKGDGTDD 210
                                       333333222333333333222222222221....11111111..111111112222222222222222233333333 PP

                             CDC45 181 .s 181
                                        +
  gi|336253542|ref|YP_004596649.1| 211 gD 212
                                       22 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.5    0.0001      0.62     398     458 ..     160     215 ..     120     232 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0001
                                       HHHHHT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--.......-------------S CS
                             NARP1 398 eeaksaelseaerkklrkkakkaekkaekeeaekaekekekkaaekkakkedeeakkeded 458
                                       e+++ ++ + +++kk  +kakk++kk++ + +e+++++++ k    k++k d++ + +d+d
  gi|336253542|ref|YP_004596649.1| 160 ENGEDGKDDGKDHKKG-EKAKKEKKKEKGHYDETEKTHEKGK----KHDKGDGTDDGDDDD 215
                                       2222333333333333.3666666666655555444443322....222223333322222 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.6   0.00026       1.6     109     178 ..     150     217 ..     116     254 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00026
                               Zip 109 ktpkkasssssesaakksvsndkveeseekedhvaeadtdadskeelrngkqeksesekeqaseeedkek 178
                                       ++++++s++ ++ +++k   +d  ++++ k+++++e+++ +++++++ +gk++ +++++    +++d+ +
  gi|336253542|ref|YP_004596649.1| 150 QNCGEQSDDGENGEDGKDDGKDHKKGEKAKKEKKKEKGHYDETEKTHEKGKKHDKGDGTDD--GDDDDDD 217
                                       2333334444444444444444444444444555566666665555555555555555554..3344443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1156  (0.0644765); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.40
# Mc/sec: 2926.80
//
Query:       gi|336253543|ref|YP_004596650.1|  [L=359]
Description: deoxyhypusine synthase [Halopiger xanaduensis SH-6]
Scores for 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-99  332.4   0.0    2.6e-99  332.1   0.0    1.1  1  DS        Deoxyhypusine synthase
  ------ inclusion threshold ------
       0.14   10.8   0.0          7    5.3   0.0    2.1  2  DHDPS     Dihydrodipicolinate synthetase family


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 !  332.1   0.0  2.9e-103   2.6e-99       1     287 [.      52     351 ..      52     352 .. 0.94

  Alignments for each domain:
  == domain 1  score: 332.1 bits;  conditional E-value: 2.9e-103
                                DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlika 77 
                                       el ++y+++g  a++l+ea+di+++m  d+++t+f+gl+++++++G+r+i+adl++++++dv+vtT++++++D+i+a
  gi|336253543|ref|YP_004596650.1|  52 ELADEYGSAGVGAANLHEAVDITESM-FDDDVTVFFGLAGAMVPTGMRRIVADLIRDGHIDVLVTTGANLTHDAIEA 127
                                       6899**********************.6899********************************************** PP

                                DS  78 lgkktylg.......dfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelG...k 144
                                       +g k+++g       +++ +de+Lr+++++Ri+n+++p+e + +fe+++re +  ++ee+ + s+++l++elG   +
  gi|336253543|ref|YP_004596650.1| 128 IGGKHHHGqvhaegkTEREHDETLRDEEVDRIYNVYLPQEFFADFESHLREEVFPVLEEEGIVSIQRLTEELGranA 204
                                       *******87777776778899******************************888888888899**********7774 PP

                                DS 145 ein......deeSilywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiil 215
                                       ein      +  +i+++Ay+nd+p++cpa++D++lG+q+++++   ++++++ld+++D++ l+dia++a+++ga+++
  gi|336253543|ref|YP_004596650.1| 205 EINerddvdEGPGIAAAAYENDVPIYCPAVQDSVLGLQAWMYS---QTSDFSLDALADMTPLTDIAFEADEAGAFVV 278
                                       55566666477********************************...7899*************************** PP

                                DS 216 GGGvpKhhilnanlm.rngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                                       GGGvpK+++l+++l+  + +dyav++t++ +++G+lsgatldEa+Swgk++++a++v+vyaDaTi+lPL+vaa
  gi|336253543|ref|YP_004596650.1| 279 GGGVPKNFTLQTMLVsPDAYDYAVQLTMDPKQTGGLSGATLDEARSWGKLEKDAENVSVYADATITLPLVVAA 351
                                       *************874579****************************************************97 PP

>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0    0.0032        29      75      93 ..      60      78 ..      59      86 .. 0.89
   2 ?    5.3   0.0   0.00078         7      67      88 ..     106     127 ..      96     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0032
                                      EE---SSHHHHHHHHHCCC CS
                             DHDPS 75 agvGsnstseaiklakkae 93
                                      agvG+ +++ea+++++++ 
  gi|336253543|ref|YP_004596650.1| 60 AGVGAANLHEAVDITESMF 78
                                      89*************9876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.00078
                                       HTTSSEEEEE---SSHHHHHHH CS
                             DHDPS  67 akgripviagvGsnstseaikl 88 
                                        +g+i v+  +G+n t++ai++
  gi|336253543|ref|YP_004596650.1| 106 RDGHIDVLVTTGANLTHDAIEA 127
                                       589*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2692.88
//
Query:       gi|336253544|ref|YP_004596651.1|  [L=113]
Description: hypothetical protein Halxa_2147 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.055   13.9   1.9       0.49   10.9   0.7    2.1  2  PP2C_C    Protein serine/threonine phosphatase 2C, C-terminal
      0.082   12.0   0.0      0.097   11.7   0.0    1.1  1  DUF4049   Domain of unknown function (DUF4049)
       0.16   12.4   3.4       0.17   12.3   2.6    1.6  1  PRA-PH    Phosphoribosyl-ATP pyrophosphohydrolase


Domain annotation for each model (and alignments):
>> PP2C_C  Protein serine/threonine phosphatase 2C, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.029   1.7e+02      22      42 ..       3      23 ..       1      30 [. 0.79
   2 ?   10.9   0.7   8.2e-05      0.49      16      55 ..      31      70 ..      23      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.029
                            PP2C_C 22 keldekleervkeiiekeekk 42
                                      +e d+ ++ r+ eiie++ ++
  gi|336253544|ref|YP_004596651.1|  3 REYDKLVRDRIPEIIERNGET 23
                                      588999**********65554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.2e-05
                            PP2C_C 16 eavkkEkeldekleervkeiiekeekkeeldlekvlkvLa 55
                                      +  + E+ l ekl+e+v+e +e+++ +e  d+ +v ++++
  gi|336253544|ref|YP_004596651.1| 31 DDAEYEAYLLEKLQEEVDEYVESRDPEELADVLEVAHEIR 70
                                      5677899999************99999999*****99986 PP

>> DUF4049  Domain of unknown function (DUF4049)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.6e-05     0.097     187     223 ..      32      68 ..      26      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
                           DUF4049 187 deekkryilGalqvsidemknaldpeelaaiinkkhk 223
                                       d e   y+l  lq  +de  ++ dpeela++++  h+
  gi|336253544|ref|YP_004596651.1|  32 DAEYEAYLLEKLQEEVDEYVESRDPEELADVLEVAHE 68 
                                       678899**************************98886 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.6   2.9e-05      0.17      13      50 ..      21      62 ..       4      82 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
                                      -SS-...---.-HHHHHHHHHHHHHHHHHHHHHT-SCHHHHH CS
                            PRA-PH 13 petP...eas.taelaslraaligEEavElleaasegdlael 50
                                       etP   +as +ae ++ ++++++EE++E++e+  +++la++
  gi|336253544|ref|YP_004596651.1| 21 GETPvvrTASdDAEYEAYLLEKLQEEVDEYVESRDPEELADV 62
                                      455511155656666666**************9977755544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 906.64
//
Query:       gi|336253545|ref|YP_004596652.1|  [L=93]
Description: hypothetical protein Halxa_2148 [Halopiger xanaduensis SH-6]
Scores for 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  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 807.26
//
Query:       gi|336253546|ref|YP_004596653.1|  [L=293]
Description: hypothetical protein Halxa_2149 [Halopiger xanaduensis SH-6]
Scores for 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   0.2    4.2e-18   65.6   0.2    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
      3e-11   43.5   0.0    1.2e-10   41.5   0.0    2.0  2  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0012   18.9   7.8     0.0013   18.8   3.2    2.6  2  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 !   65.6   0.2     7e-22   4.2e-18      16     201 .]      64     249 ..      41     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 7e-22
                                       TCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE CS
                     Lactamase_B_2  16 lral.qPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvlavleanfvylaleeepavnvhel 90 
                                       +r++  P+   delppid++ll+h H DH+   + ++e   +k+lp++ +++ +a+le+++         + ++ +l
  gi|336253546|ref|YP_004596653.1|  64 SRRRtDPAIDIDELPPIDFILLSHYHGDHF---DRVAEaKLDKDLPIVTTPHAAAELEEKG---------FRQTYPL 128
                                       3444478889********************...56666534556****************4.........6678899 PP

                                       -TTSEEEE..CSTTEEEEEEEE-EE--C...TCCE-TTTSEEEEEECTTEE......EEEESS-S---..HHHHHHH CS
                     Lactamase_B_2  91 dwgesfel..gdggleitatparhksgr...rldrnagdtlGlriegggkr......vyyigDtgyip..eeigerl 154
                                       +++e+ ++  gd+ l+ita+p rh+ +    +l + +g +l +r ++++        +y +gDt  ++  eei er+
  gi|336253546|ref|YP_004596653.1| 129 ETWEECRIrkGDARLSITAMPGRHGPPVlskGLPPVMGSMLEFRPDDADPDeppllrLYISGDTLVYDalEEIPERY 205
                                       ********999999*************965555555555555555533333667777***********99******* PP

                                       CT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 155 ggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                        ++dl+ll  + ++         +++  + vea++ ++a ++++iH+
  gi|336253546|ref|YP_004596653.1| 206 PDIDLALLHLGGTRILG---VLLTMDAAQGVEAVDLIDADTAIPIHY 249
                                       **************988...789***********************7 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 !   41.5   0.0     2e-14   1.2e-10       2     163 .]      26     248 ..      25     248 .. 0.80
   2 ?   -2.2   0.0      0.56   3.3e+03      57      75 ..     270     288 ..     264     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2e-14
                     Lactamase_B_3   2 ltwlghnsflletagarilvDPf......kanlgyeppa.............eeaDlvlisqaledHahletlkql. 58 
                                       + ++g ++++le ag +il+DP       + +lgy+++              + +D +l+s+ + dH++  + ++l 
  gi|336253546|ref|YP_004596653.1|  26 IFFVGTATIVLEYAGFTILTDPNflhsgdHVHLGYGIKSrrrtdpaididelPPIDFILLSHYHGDHFDRVAEAKLd 102
                                       6699*******************99887633666666667888889999999************************6 PP

                     Lactamase_B_3  59 ...................aenvkvleegeslev....ggleiravatshdav...ggsergenngflleqd..... 104
                                                          ++++  le++e+ ++    + l+i+a+++ h +    +g ++  +++  ++ d     
  gi|336253546|ref|YP_004596653.1| 103 kdlpivttphaaaeleekgFRQTYPLETWEECRIrkgdARLSITAMPGRHGPPvlsKGLPPVMGSMLEFRPDdadpd 179
                                       66677777777777766666666666669998885543378999999999555222566777788888887545677 PP

                     Lactamase_B_3 105 ...gltiyhlGhlahelsseel.kelgrvDvvltPvgg......pltlgqeealelakrLkpklvlPmh 163
                                           l++y  G++      ee+ +   ++D+ l+  gg       lt+++++ +e++ +++++  +P+h
  gi|336253546|ref|YP_004596653.1| 180 eppLLRLYISGDTLVYDALEEIpERYPDIDLALLHLGGtrilgvLLTMDAAQGVEAVDLIDADTAIPIH 248
                                       78789*******8776666665477889**************999**********************99 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.56
                     Lactamase_B_3  57 qlaenvkvleegeslevgg 75 
                                       +l+++v++le+ge++e+++
  gi|336253546|ref|YP_004596653.1| 270 GLEDQVEYLEHGETFEFES 288
                                       4566999999999999875 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   3.2   2.2e-07    0.0013      38      98 ..      73     136 ..      26     184 .. 0.78
   2 ?    1.5   0.1     0.042   2.5e+02      14      51 ..     189     226 ..     183     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.2e-07
                                       HTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH...T CS
                       Lactamase_B  38 lglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgll...l 98 
                                          ++ ++d ++l+H+H DH+  +++ +   d p++  +++a++l++ +  + ++ + ++   +
  gi|336253546|ref|YP_004596653.1|  73 DIDELPPIDFILLSHYHGDHFDRVAEAKLDKDLPIVTTPHAAAELEEKGFRQTYPLETWEecrI 136
                                       566789***************************************9999988877766555551 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.042
                                       TTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-S CS
                       Lactamase_B  14 dggviLiDtGtsteaaraalelaalglkpkdvdavilT 51 
                                        g+++++D++ + ++     +la+l+l++ ++  v+lT
  gi|336253546|ref|YP_004596653.1| 189 SGDTLVYDALEEIPERYPDIDLALLHLGGTRILGVLLT 226
                                       57899999999999999999999999999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2439.29
//
Query:       gi|336253547|ref|YP_004596654.1|  [L=375]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-28   98.6   0.2    4.8e-28   98.2   0.2    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.4e-12   47.5   0.0    6.4e-08   32.2   0.0    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    9.2e-06   25.8   0.2    2.4e-05   24.5   0.2    1.8  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    3.4e-05   23.6   6.4    0.00037   20.2   6.4    2.5  1  DAO            FAD dependent oxidoreductase
    3.6e-05   23.0   5.0    4.3e-05   22.8   0.3    2.5  2  FAD_binding_2  FAD binding domain
    0.00011   21.5   0.2    0.00018   20.7   0.2    1.4  1  GIDA           Glucose inhibited division protein A
    0.00014   20.7   0.0    0.00047   19.0   0.1    1.7  2  HI0933_like    HI0933-like protein
    0.00016   21.2   0.5    0.00026   20.5   0.5    1.3  1  FAD_oxidored   FAD dependent oxidoreductase
    0.00035   19.9   0.3    0.00071   18.9   0.1    1.6  2  FAD_binding_3  FAD binding domain
     0.0037   16.6   0.0     0.0062   15.9   0.0    1.3  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
     0.0044   16.3   0.0     0.0084   15.4   0.0    1.4  1  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.015   15.9   0.3      0.051   14.1   0.2    1.9  2  Pyr_redox      Pyridine nucleotide-disulphide 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 !   98.2   0.2   3.2e-31   4.8e-28       1     290 [.       8     301 ..       8     306 .. 0.79

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 3.2e-31
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE.TTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve.legtclnggcllskallgvaedaeias......evvkklnqgiell 70 
                                       ++v+v+GgGpAGl+aal+  + g++++++e ++g +  +  +    llgv+e+ + ++      ++++ ++ ++   
  gi|336253547|ref|YP_004596654.1|   8 YEVAVVGGGPAGLTAALYTTRLGHRTAVFEkDGGRHASVNHVH--NLLGVSENVSGEQlathavDQFEHYGGDFYPD 82 
                                       579**************************96444444444444..66677777766667787774444455442222 PP

                                       HCCTCEEEEESCEEEEETEEEC.....TCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T CS
                                       xxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  71 lgeevvkidpgkkkvklekkke.....gdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp 142
                                       + e+v+++d g+++ ++ +k         + +++++++v AtG++ r +++p ++  +g++++++ +++a++l   p
  gi|336253547|ref|YP_004596654.1|  83 AVESVTRLDGGEENDEDGDK-PrfrleAAHATVDAERVVFATGFRDRSPDVPELERFTGRGLHYCLHCDAYSLGDGP 158
                                       22356666655533333222.1456667889********************************************** PP

                                       SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                       Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge..... 214
                                         + v G    +  +A+++ ++ ++v l+ ++ ++      e++++ e +l ++ ve   +t v+ + ++++     
  gi|336253547|ref|YP_004596654.1| 159 --VFVLGHTESAAHVAMTMLNFTADVDLLLDGREP------EWGDETETQLCAHPVERI-ETAVVSAYEDETlgede 226
                                       ..************************999997776......6***************99.55555666566668555 PP

                                       ..EEE..EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--H CS
                                       ..xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 215 ..kle..vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpela 287
                                              +  +dg+e d+   +   G + +  l+  +lg+el e+g+i vde+ +t+v+g ya+GDv+   +g +++
  gi|336253547|ref|YP_004596654.1| 227 ppW-LggLSFGDGTERDYLGGFAMYGSSYNAGLA-ADLGCELGENGAIDVDERRETSVDGAYAVGDVT---HGQNQT 298
                                       543.158***********************9999.*********************************...444444 PP

                                       HHH CS
                                       xxx RF
                       Pyr_redox_2 288 qaA 290
                                       + A
  gi|336253547|ref|YP_004596654.1| 299 TIA 301
                                       444 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 !   13.3   0.0   2.5e-05     0.037       2      31 ..      12      40 ..      11      76 .. 0.78
   2 !   32.2   0.0   4.3e-11   6.4e-08     112     305 .]     103     289 ..      97     289 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgn 31
                                      ++G+GPaGl+aa+   ++g  +  + Ek+ 
  gi|336253547|ref|YP_004596654.1| 12 VVGGGPAGLTAALYTTRLGH-RTAVFEKDG 40
                                      8******************9.678999975 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 4.3e-11
                       Pyr_redox_3 112 egfevetsketyeAkkviiAtGefdk.PnklnipGeeklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkg 187
                                         f++e+ ++t+ A++v+ AtG+ d+ P++++ +  +    hy    ++  + +  v V G  +Sa+ +A+ + + +
  gi|336253547|ref|YP_004596654.1| 103 PRFRLEAAHATVDAERVVFATGFRDRsPDVPELERFTGRGLHYCLHCDAYSLGDGPVFVLGHTESAAHVAMTMLNFT 179
                                       5799******************9764344444444443457887777887888************************ PP

                       Pyr_redox_3 188 aeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvla 264
                                       a+V ++ +g e  ++ ++ + +l ++  +r+e++v    + +++++++ e + +     +++ dg++ + +   +++
  gi|336253547|ref|YP_004596654.1| 180 ADVDLLLDGRE-PEWGDETETQLCAHPVERIETAV----VSAYEDETLGEDEPP-WLGGLSFGDGTE-RDYLGGFAM 249
                                       ******98875.44556789999********9986....578899888887765.444788999877.667777888 PP

                       Pyr_redox_3 265 tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                        G + ++ + ++ + el e+g + ++e   et v+g + +G
  gi|336253547|ref|YP_004596654.1| 250 YGSSYNAGLAADLGCELGENGAIDVDER-RETSVDGAYAVG 289
                                       9999999999999999999999999875.577899999887 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 !   24.5   0.2   1.6e-08   2.4e-05       1      40 [.      12      48 ..      12      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.6e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev 40
                                      +vG+G +Gl+aA + ++ g++  ++ek    GGr as+++
  gi|336253547|ref|YP_004596654.1| 12 VVGGGPAGLTAALYTTRLGHRTAVFEKD---GGRHASVNH 48
                                      8**************************9...999988876 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   6.4   2.5e-07   0.00037       2     136 ..      10     144 ..       9     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.5e-07
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelg 76 
                                       v+++GGG +Gl++A++ +r g  ++++ek+   g++aS +    l + +++  ++ e  +l+ +a++ ++++ ++  
  gi|336253547|ref|YP_004596654.1|  10 VAVVGGGPAGLTAALYTTRLGhrTAVFEKD--GGRHASVNHVHNLLG-VSENVSG-E--QLATHAVDQFEHYGGDFY 80 
                                       9****************99999********..444555554444433.2323333.3..899999999999999876 PP

                                       STTSEEEEEEEEEESSHHHHHHHHHHHHHH.HHTTTTE.EEEEHHHHHHHSTTST...TTS.EEEE CS
                               DAO  77 ididyrrtGllslaadeeelealdkllall.leaglda.elldaeevrelepalp...gll.galf 136
                                       +d  ++  + l  ++ e+++++ + +++l  + a +da +++ a   r+++p +p   +++  +l+
  gi|336253547|ref|YP_004596654.1|  81 PDA-VESVTRLDGGE-ENDEDGDKPRFRLEaAHATVDAeRVVFATGFRDRSPDVPeleRFTgRGLH 144
                                       653.45556666653.33333322222222222445553466666678888873334456523343 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.3   2.9e-08   4.3e-05       2      33 ..      10      41 ..       9      50 .. 0.91
   2 ?    1.6   0.3      0.08   1.2e+02     377     404 ..     273     294 ..     256     303 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.9e-08
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      v V+G+G AGL+AAl  ++ G+++av ek + 
  gi|336253547|ref|YP_004596654.1| 10 VAVVGGGPAGLTAALYTTRLGHRTAVFEKDGG 41
                                      89***************************875 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.08
                                       EBETTSBESTTEEESSBTEEE-STCEES CS
                     FAD_binding_2 377 etdengrvldadgqpipGLYAaGevaag 404
                                        +      +++ ++ ++G YA+G v++g
  gi|336253547|ref|YP_004596654.1| 273 DV------DERRETSVDGAYAVGDVTHG 294
                                       33......556666***********944 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2   1.2e-07   0.00018       2      38 ..      10      46 ..       9      79 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.2e-07
                                      EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT-- CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkldtiael 38
                                      v V+GgG AG+ AAl + rlG++++ + ++ ++ a++
  gi|336253547|ref|YP_004596654.1| 10 VAVVGGGPAGLTAALYTTRLGHRTAVFEKDGGRHASV 46
                                      89*************************5554444443 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   3.1e-07   0.00047       2      32 ..       9      39 ..       8      43 .. 0.94
   2 ?   -1.6   0.0      0.55   8.3e+02     140     163 ..     102     124 ..      92     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.1e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                      +v+v+GgG+AGl aA+   + g+r++++ek 
  gi|336253547|ref|YP_004596654.1|  9 EVAVVGGGPAGLTAALYTTRLGHRTAVFEKD 39
                                      79***************************96 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.55
                                       TE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 140 dgkfrvktkseeeleadklvlAtG 163
                                       + +fr+++  + ++ a+++v+AtG
  gi|336253547|ref|YP_004596654.1| 102 KPRFRLEA-AHATVDAERVVFATG 124
                                       45688888.999***********9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.5   1.7e-07   0.00026       1      31 [.       9      39 ..       9      69 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.7e-07
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      +v VvGGgpaG++AA+   r G ++++ e++
  gi|336253547|ref|YP_004596654.1|  9 EVAVVGGGPAGLTAALYTTRLGHRTAVFEKD 39
                                      599************************9986 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   4.7e-07   0.00071       1      35 [.       7      41 ..       7      47 .. 0.90
   2 ?   -3.1   0.0       2.4   3.6e+03     132     165 ..      95     126 ..      87     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.7e-07
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      e++V++VG+GpaGl++al  ++ G r+ + ek   
  gi|336253547|ref|YP_004596654.1|  7 EYEVAVVGGGPAGLTAALYTTRLGHRTAVFEKDGG 41
                                      579**************************999765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                                       EECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT CS
                     FAD_binding_3 132 eqdeegvtaevrdketgeeetvrakYlvGaDGgr 165
                                       e+de+g ++++r ++  ++ tv+a+ +v a G+r
  gi|336253547|ref|YP_004596654.1|  95 ENDEDGDKPRFRLEA--AHATVDAERVVFATGFR 126
                                       567888888887776..66789999999888887 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 !   15.9   0.0   4.1e-06    0.0062      30      73 ..       9      52 ..       4      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.1e-06
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTC CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgak 73
                                      +v v+GgG aGl A+   ++lg ++ v++++  r   ++++++ 
  gi|336253547|ref|YP_004596654.1|  9 EVAVVGGGPAGLTAALYTTRLGHRTAVFEKDGGRHASVNHVHNL 52
                                      799***************************99999998886654 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.6e-06    0.0084      17      49 ..       7      38 ..       3      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.6e-06
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer 49
                                      e +v++vG+G++GLtaa y ++  + ++a++e+
  gi|336253547|ref|YP_004596654.1|  7 EYEVAVVGGGPAGLTAALYTTRL-GHRTAVFEK 38
                                      6789***************9999.999999997 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   3.4e-05     0.051       2      30 ..      10      38 ..       9      41 .. 0.93
   2 ?   -2.4   0.0       5.1   7.6e+03       3      29 ..     160     186 ..     159     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.4e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                      v+vvGgG  gl +A + ++lg+++ v+e 
  gi|336253547|ref|YP_004596654.1| 10 VAVVGGGPAGLTAALYTTRLGHRTAVFEK 38
                                      89**********************99985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.1
                                       EEECSSHHHHHHHHHHHHTTSEEEEEE CS
                         Pyr_redox   3 vvvGgGyiglElAgalaelgkkVtvve 29 
                                        v+G   ++  +A ++ ++ ++V ++ 
  gi|336253547|ref|YP_004596654.1| 160 FVLGHTESAAHVAMTMLNFTADVDLLL 186
                                       577777788889999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2750.49
//
Query:       gi|336253548|ref|YP_004596655.1|  [L=201]
Description: HAD-superfamily hydrolase [Halopiger xanaduensis SH-6]
Scores for complete 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-19   70.5   0.0    2.4e-19   70.1   0.0    1.1  1  HAD_2            Haloacid dehalogenase-like hydrolase
    4.9e-13   49.8   0.6    6.6e-12   46.2   0.6    2.0  1  Hydrolase        haloacid dehalogenase-like hydrolase
    4.2e-09   37.1   1.8      5e-09   36.8   1.8    1.1  1  HAD              haloacid dehalogenase-like hydrolase
    2.4e-07   30.7   0.2    5.5e-07   29.6   0.2    1.6  1  Hydrolase_like   HAD-hyrolase-like
  ------ inclusion threshold ------
      0.041   14.0   0.0       0.24   11.5   0.0    2.0  2  Hydrolase_6      Haloacid dehalogenase-like hydrolase
      0.045   13.2   0.1      0.059   12.8   0.1    1.2  1  DUF222           Domain of unknown function (DUF222)
       0.09   12.4   0.0       0.43   10.1   0.0    1.9  2  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph


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 !   70.1   0.0   9.3e-23   2.4e-19       1     173 [.       4     180 ..       4     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 9.3e-23
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleey.......glselseeelrkliglslrellrklgeseeeeekieellrkyn 70 
                                       i+FD+DgTll +   +  +++ ++e         +l+ ++e  +++++ ++ + + r +g+ +++  + e +     
  gi|336253548|ref|YP_004596655.1|   4 IVFDVDGTLLRSDCPYRGIVADAIETVrgdapeaWLDAYEEAFFESFFAFEPDPVERAFGQIDDCA-DPEPYAAALL 79 
                                       89**********99999999999988899999999999**************77777777776655.8999999999 PP

                             HAD_2  71 eekkkkevkpydgvkelLeeL.keagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekale 146
                                       e + +  ++p dgv++ Le L +e ++ lg+ T++ r+ +  kl++ ++ +yFd +v s +v+ +KP++e+++++ e
  gi|336253548|ref|YP_004596655.1|  80 EAEIE-ALSPPDGVHDDLERLaAETDVDLGVLTNGVRDWQLGKLRAADLAEYFDAVVASYEVGAHKPATEPYRALEE 155
                                       99998.9**************77889**********************************************99888 PP

                             HAD_2 147 klklkkeeviyvGDsptDieaakkagi 173
                                       +l   +++ ++vGDs  D+ +a +ag 
  gi|336253548|ref|YP_004596655.1| 156 RL--PADRYVMVGDSDDDVDGAAQAGW 180
                                       76..56789****************95 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.6   2.6e-15   6.6e-12       1     210 []       1     179 [.       1     179 [. 0.76

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 2.6e-15
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH.HHHHHETTTEHHHHTHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgal.tgfatfigrgayaigkpew 76 
                                       ++++vfD+dGTL+++    + +++ a               i      a +a   a+ + f +      +   +p+ 
  gi|336253548|ref|YP_004596655.1|   1 MTAIVFDVDGTLLRSDCPYRGIVADA---------------IETVRGDAPEAWLDAYeEAFFE-----SFFAFEPDP 57 
                                       689*************6667777777...............2222344444444444577777.....788889998 PP

                                       HHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHT.TEEEEEEESSEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  77 ltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaa.gievvlltgdnpetaeraa 152
                                       +++         +i+++ +    +a l   + ++ +++ p+ v ++++ + a       +++++lt++ +  +   +
  gi|336253548|ref|YP_004596655.1|  58 VERA------FGQIDDCADPEPYAAAL--LEAEIEALSPPDGVHDDLERLAA----EtDVDLGVLTNGVRDWQLGKL 122
                                       8888......45555555555555555..45666666666556666655544....4379*************9999 PP

                                       HHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 153 nqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       + ++ ++yfdav+as++++  kp  e ++a+ ++L ++    +mVGD+  D+ ++a+Ag
  gi|336253548|ref|YP_004596655.1| 123 RAADlAEYFDAVVASYEVGAHKPATEPYRALEERLPADR--YVMVGDSDDDVDGAAQAG 179
                                       9999999****************************6665..*****************8 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   1.8     2e-12     5e-09       1     185 [.       4     173 ..       4     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2e-12
                               HAD   1 alfDfDgTLldgdsle.lllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaeler 75 
                                       ++fD+DgTLl++d  +  ++   +++ + ++ +a + ++++a+f++++ ++ + +++++  +  + + e+ aa l +
  gi|336253548|ref|YP_004596655.1|   4 IVFDVDGTLLRSDCPYrGIVADAIETVRGDAPEAWLDAYEEAFFESFFAFEPDPVERAFGQIDDCADpEPYAAALLE 80 
                                       79**********88888555558888888999999999*****************************9888888888 PP

                               HAD  76 fvaevirpklldp.galellaahr.aaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvr 150
                                       +  e+  p    p g+ + l++ + +  + + v+++g r +   +l++ +    la+      ++++ +  ++   +
  gi|336253548|ref|YP_004596655.1|  81 AEIEALSP----PdGVHDDLERLAaETDVDLGVLTNGVRDWQLGKLRAAD----LAE------YFDAVVASYEVGAH 143
                                       88555554....35777777744416666*********************....***......*****888887777 PP

                               HAD 151 gegkvaalrewlaaegegidleevvayGDspsDlp 185
                                       +     a +  + a +e ++ ++ v +GDs  D+ 
  gi|336253548|ref|YP_004596655.1| 144 K----PATEP-YRALEERLPADRYVMVGDSDDDVD 173
                                       7....44444.4444556666678999******86 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.2   2.2e-10   5.5e-07       3      45 ..     143     182 ..     141     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.2e-10
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EE CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwks 45 
                                        KP+ e y++  e+l  + ++ +m+GD+ ++D+ gA +aGw+ 
  gi|336253548|ref|YP_004596655.1| 143 HKPATEPYRALEERL--PADRYVMVGDS-DDDVDGAAQAGWTP 182
                                       69***********97..779********.************85 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.3e-05      0.24       1      27 [.       4      31 ..       4      50 .. 0.89
   2 ?    0.3   0.0       0.3   7.8e+02      18      66 ..      91     137 ..      83     180 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.3e-05
                                      EEEESTTTSEETTEE-TT.HHHHHHHHH CS
                       Hydrolase_6  1 flfDidGvLwrgdkaipg.aaealnalr 27
                                      ++fD+dG+L+r d ++ g +a+a++++r
  gi|336253548|ref|YP_004596655.1|  4 IVFDVDGTLLRSDCPYRGiVADAIETVR 31
                                      69**************996778888877 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.3
                                       THHHHHHHHHHT.T-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEH CS
                       Hydrolase_6  18 gaaealnalraa.gkpvvllTNnsskseeeyakkleklgvditeeqvvts 66 
                                       g+++ l++l a+  +++ +lTN+ +      + kl++ ++    + vv s
  gi|336253548|ref|YP_004596655.1|  91 GVHDDLERLAAEtDVDLGVLTNGVRD---WQLGKLRAADLAEYFDAVVAS 137
                                       66666777766635777888886533...244455555555544555554 PP

>> DUF222  Domain of unknown function (DUF222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.3e-05     0.059     102     189 ..      36     144 ..      21     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                            DUF222 102 latvdkaeaallrraakldpaeLaklvdrlvarld..................pDgvrrdeeaar.rreltltkded 159
                                        a +d+ e a  ++   ++p++++++  ++ +++d                  pDgv+ d e+ + +  ++l+  ++
  gi|336253548|ref|YP_004596655.1|  36 EAWLDAYEEAFFESFFAFEPDPVERAFGQIDDCADpepyaaalleaeiealspPDGVHDDLERLAaETDVDLGVLTN 112
                                       56678888888899999*****************************************88877544999******** PP

                            DUF222 160 Gmsris.geldaea.aaaldavLdslaapvca 189
                                       G+  ++ g+l a++ a+++dav +s     ++
  gi|336253548|ref|YP_004596655.1| 113 GVRDWQlGKLRAADlAEYFDAVVASYEVGAHK 144
                                       ***99878998765388999999887655555 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 ?   10.1   0.0   0.00017      0.43      74      92 ..       2      21 ..       1      44 [. 0.86
   2 ?   -0.0   0.0      0.22   5.5e+02     197     211 ..     163     177 ..     133     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                                      EEEEE--BTTTE.EHHHHHH CS
                   Acid_phosphat_B 74 davvfDiDeTvL.snspYqk 92
                                       a+vfD+D T+L s+ pY +
  gi|336253548|ref|YP_004596655.1|  2 TAIVFDVDGTLLrSDCPYRG 21
                                      69***************964 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.22
                                       EEEESSGGGCHCCHH CS
                   Acid_phosphat_B 197 lniGDnlsDlngake 211
                                       +++GD+++D  ga +
  gi|336253548|ref|YP_004596655.1| 163 VMVGDSDDDVDGAAQ 177
                                       579******998544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); 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 0.20s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1586.06
//
Query:       gi|336253549|ref|YP_004596656.1|  [L=127]
Description: pyridoxamine 5'-phosphate oxidase-like FMN-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-16   58.6   0.0    7.1e-16   58.2   0.0    1.2  1  Putative_PNPOx   Pyridoxamine 5'-phosphate oxidase
    2.3e-14   53.6   0.2    2.7e-14   53.4   0.2    1.0  1  Pyridox_ox_2     Pyridoxamine 5'-phosphate oxidase
      0.003   17.1   0.0     0.0037   16.9   0.0    1.2  1  Pyrid_ox_like    Pyridoxamine 5'-phosphate oxidase like
  ------ inclusion threshold ------
       0.03   14.4   0.4      0.063   13.4   0.4    1.7  1  F420H2_quin_red  F420H(2)-dependent quinone reductase


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 !   58.2   0.0   1.6e-19   7.1e-16       3      87 ..       5      88 ..       3      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 1.6e-19
                                      HHHHHHHHHS.SEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT...GSEEEEE CS
                    Putative_PNPOx  3 eelreflaes.kavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde...lgrgvri 77
                                      +e++ +l+++  +++l+T+  dGrP+v pv++ ++dg+    + + +  rkl+n++enprv+l++  d+   +++ v++
  gi|336253549|ref|YP_004596656.1|  5 DEAERLLESEpLMAHLGTC-VDGRPHVAPVWYRYDDGE----VEIVTTGRKLANIRENPRVSLSVQKDDagkTRWMVTL 78
                                      788888886615568****.******************....44446689***************************** PP

                                      EEEEEEESCH CS
                    Putative_PNPOx 78 eGtaelvsdg 87
                                       Gta++v+d+
  gi|336253549|ref|YP_004596656.1| 79 LGTATIVEDE 88
                                      ********98 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.2     6e-18   2.7e-14       3     138 ..       5     123 ..       4     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 6e-18
                                       HHHHHHHHC-S.EEEEEEEETTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGEE CS
                      Pyridox_ox_2   3 eeilalLdege.vgrlafvddgepvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfnsl 77 
                                       +e+++lL++++ +++l++ +dg+p++ Pv y +d++++ + ++   r++a +r++p v+ +v++ d+   a +   +
  gi|336253549|ref|YP_004596656.1|   5 DEAERLLESEPlMAHLGTCVDGRPHVAPVWYRYDDGEVEIVTTG--RKLANIRENPrVSLSVQK-DD---AGK---T 72 
                                       7999***9665279************************998876..88888887778*******.44...333...2 PP

                                       EEEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTTGGCSB---CCCCCTEEEEEEEEEEEE CS
                      Pyridox_ox_2  78 nyrSVvvrGraeevtdeeekaealellvekivpgrwenlrpptrkelkatsvlrlkieevs 138
                                        +  V++ G+a+ v+de+e a a++++ ek+          +++++ ++++++r+++ + +
  gi|336253549|ref|YP_004596656.1|  73 RW-MVTLLGTATIVEDEAETADARRRINEKYD---------AEPDAYAENTLVRIDVGSTT 123
                                       4*.**************************992.........33445566777888776665 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 !   16.9   0.0   8.2e-07    0.0037      51     122 ..      48     122 ..      26     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.2e-07
                     Pyrid_ox_like  51 sdkvkeirkdsqvnlafsdes..kkky.vsvsGtaevvedrakieelWspvvkawfpegkddpnltlikvtpeea 122
                                        +k ++ir++++v+l +++ +  k+ + v++ Gta++ved+a   +    + +++ +e    ++ tl+++++ ++
  gi|336253549|ref|YP_004596656.1|  48 GRKLANIRENPRVSLSVQKDDagKTRWmVTLLGTATIVEDEAETADARRRINEKYDAEPDAYAENTLVRIDVGST 122
                                       67899***********997652266774689************99998888888877776666777777766555 PP

>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   1.4e-05     0.063      34      89 ..      24      72 ..       6     121 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                                      TT-SEEEEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEEETTEEEEEE CS
                   F420H2_quin_red 34 ktgkprktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevqvgakkldvt 89
                                      + g+p   p+ ++ d++++ +v   g        + N++ nPrv + v+++    t
  gi|336253549|ref|YP_004596656.1| 24 VDGRPHVAPVWYRYDDGEVEIVTT-G------RKLANIRENPRVSLSVQKDDAGKT 72
                                      56999****************975.4......3589************98765433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 909.66
//
Query:       gi|336253550|ref|YP_004596657.1|  [L=234]
Description: family 2 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for complete 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   96.2   0.0    4.2e-27   95.0   0.0    1.6  2  Glycos_transf_2  Glycosyl transferase family 2
    1.4e-12   48.0   0.0    1.2e-11   44.9   0.0    1.9  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.3e-07   30.5   0.0    3.6e-07   29.8   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
    3.4e-06   26.7   0.0    2.1e-05   24.2   0.0    1.9  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
    1.1e-05   25.9   0.4    0.00013   22.4   0.1    2.8  3  Glyco_tranf_2_4  Glycosyl transferase family 2
    1.3e-05   25.2   0.0    0.00011   22.2   0.0    2.0  1  Glyco_trans_2_3  Glycosyl transferase family group 2
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.055   13.4   0.0    1.6  2  SgrT             Inhibitor of glucose uptake transporter SgrT


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 !   95.0   0.0   1.6e-30   4.2e-27       1     129 [.      15     137 ..      15     167 .. 0.83
   2 ?   -1.9   0.0         1   2.6e+03      55      73 ..     213     232 ..     205     234 .] 0.81

  Alignments for each domain:
  == domain 1  score: 95.0 bits;  conditional E-value: 1.6e-30
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       svv+p+ Ne+++l+ tl+sl+  d+++++e++vvD  S+D t++i++e+     + +v+  + ++  a+++n g+r+
  gi|336253550|ref|YP_004596657.1|  15 SVVVPARNEADYLRGTLASLAGLDTDYEYEVLVVDGDSSDATPAIAREY-----GATVLEGP-GTSIAAGRNYGARR 85 
                                       8************************************************.....9*******.66************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiern 129
                                       a+gd+++f+DaD+ +  d+l +l++++e++g +++    +  +  + +i  +
  gi|336253550|ref|YP_004596657.1|  86 ASGDWLAFVDADTRVRADYLTELLGYAEATGLAAASSRCRIAGPRRAKIMEA 137
                                       *****************************99855554444444444444444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1
                                       TEEEEEESSS-.HHHHHHHH CS
                   Glycos_transf_2  55 rvrvirreenv.Gkagalna 73 
                                        v+++r+++ +   ++a++ 
  gi|336253550|ref|YP_004596657.1| 213 LVHYLRLDRERlRASRARRG 232
                                       599****9999888888875 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 !   44.9   0.0   4.7e-15   1.2e-11       3     127 ..      13     125 ..      11     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 4.7e-15
                   Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqey.prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksra 78 
                                       d++v+Vp+ ne+d+l+ +l+sl+  +   ++ev vv+  s+++t + a+e    +++   +v+   + +g t+ + +
  gi|336253550|ref|YP_004596657.1|  13 DVSVVVPARNEADYLRGTLASLAGLDTdYEYEVLVVDGDSSDATPAIARE----YGA---TVL---EGPG-TSIAAG 78 
                                       79*********************8875488*******9999**9**9998....776...566...4478.699999 PP

                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfll 127
                                        n + r++++d++++vD+Dt+v  d+l  ll ++++   g + ++ +++
  gi|336253550|ref|YP_004596657.1|  79 RNYGARRASGDWLAFVDADTRVRADYLTELLGYAEAT--GLAAASSRCR 125
                                       *******************************999333..3333333333 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 !   29.8   0.0   1.4e-10   3.6e-07      25     158 ..      82     206 ..      79     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.4e-10
                   Glyco_transf_21  25 aleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlqaklsglgfa 101
                                       + ++a  d+l + D+d+rv++dyL+ell++ e   +gl  + +++  a    a++  a +n +  +l +      + 
  gi|336253550|ref|YP_004596657.1|  82 GARRASGDWLAFVDADTRVRADYLTELLGYAEA--TGLAAASSRCRIAGPRRAKIMEATINYVFPRLER-----PIL 151
                                       5678999*************************7..6666666666666556666666666555555555.....899 PP

                   Glyco_transf_21 102 vGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvpr..r 158
                                        G  ++++r+a+e++GGf        eD+a++++l ++ + +  +p+++++ s++r  +
  gi|336253550|ref|YP_004596657.1| 152 PGFNLLVHRSAFEDAGGFPD---VPNEDTAFSRRLGRR-YPTGYCPEVLVESSGRRieA 206
                                       9*****************98...556899999999776.44444455566666666544 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 !   24.2   0.0     8e-09   2.1e-05       1     105 [.      15     111 ..      15     122 .. 0.75
   2 ?   -0.0   0.0      0.19   4.9e+02     167     204 ..     155     188 ..     133     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 8e-09
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyy.deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrG 76 
                                       svv+p r+  e  y++ ++   a    d e e++vvd+ Ss+ +     +i    +   l+       s aa rN G
  gi|336253550|ref|YP_004596657.1|  15 SVVVPARN--EADYLRGTLASLAGLDtDYEYEVLVVDGDSSDATP----AIAREYGATVLEGP---GTSIAAGRNYG 82 
                                       57777665..4567999995555443388*************944....44444444443333...559******** PP

                   Glyco_tranf_2_2  77 askaesdlvlFlDaDcfissDkfekilkl 105
                                       a +a +d + F+DaD  +  D +  +l  
  gi|336253550|ref|YP_004596657.1|  83 ARRASGDWLAFVDADTRVRADYLTELLGY 111
                                       ********************999988765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.19
                   Glyco_tranf_2_2 167 silinrraflevGGyDErfrGhgaEDfdlllRlakaik 204
                                       ++l++r af   GG+ +       ED  +  Rl+++++
  gi|336253550|ref|YP_004596657.1| 155 NLLVHRSAFEDAGGFPDVP----NEDTAFSRRLGRRYP 188
                                       78999*********98755....788888888888876 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 !   22.4   0.1   5.2e-08   0.00013       1      81 [.      21      97 ..      21     104 .. 0.78
   2 ?   -1.8   0.0       1.8   4.6e+03       4      19 ..     102     117 ..      99     120 .. 0.82
   3 ?   -1.8   0.0       1.9   4.8e+03       3      22 ..     205     224 ..     203     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.2e-08
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdr...ilvydndstDgtrailkelpevkllhvdk.syederrqvellkallaryaeadwv 75
                                      rnead+L  +la +  l+ d+   +lv+d ds+D t ai +e+  +++l+ ++ s+       ++ ++  ar a +dw+
  gi|336253550|ref|YP_004596657.1| 21 RNEADYLRGTLASLAGLDTDYeyeVLVVDGDSSDATPAIAREYG-ATVLEGPGtSI-------AAGRNYGARRASGDWL 91
                                      8*************9999875557*****************964.44444444144.......3444444455789*** PP

                   Glyco_tranf_2_4 76 lvvDaD 81
                                      ++vDaD
  gi|336253550|ref|YP_004596657.1| 92 AFVDAD 97
                                      *****9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                   Glyco_tranf_2_4   4 adiLpeflahhlalgf 19 
                                       ad+L e l++++a g 
  gi|336253550|ref|YP_004596657.1| 102 ADYLTELLGYAEATGL 117
                                       899******9998875 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.9
                   Glyco_tranf_2_4   3 eadiLpeflahhlalgfdri 22 
                                       ea+ L  +l h+l+l+++r+
  gi|336253550|ref|YP_004596657.1| 205 EAQGLTGTLVHYLRLDRERL 224
                                       6777888999*****99875 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 !   22.2   0.0   4.4e-08   0.00011       1     126 [.      90     201 ..      90     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.4e-08
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvm..nvanwleelaalffaedhgkdilvrealgrvvpsvGs 75 
                                       + +++DaDt++ +d+l e++   +    a+++  + ++  ++a+++e ++ + f            +l r+  ++G 
  gi|336253550|ref|YP_004596657.1|  90 WLAFVDADTRVRADYLTELLGYAEATGLAAASSRCRIAgpRRAKIMEATINYVF-----------PRLERP-ILPGF 154
                                       7789***************99888655555554444434477888888777766...........345555.688** PP

                   Glyco_trans_2_3  76 gaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkeks 126
                                       + +++rsa++++gg++   +   ED+ ++ rl r+ y + ++pe+lv  ++
  gi|336253550|ref|YP_004596657.1| 155 NLLVHRSAFEDAGGFP---DVPNEDTAFSRRLGRR-YPTGYCPEVLVESSG 201
                                       ***************9...9*************99.999999999655443 PP

>> SgrT  Inhibitor of glucose uptake transporter SgrT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.4   1.1e+04      17      24 ..      20      27 ..      19      28 .. 0.87
   2 ?   13.4   0.0   2.1e-05     0.055      14      34 ..      81     101 ..      76     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.4
                              SgrT 17 aklsadWL 24
                                      a++ ad+L
  gi|336253550|ref|YP_004596657.1| 20 ARNEADYL 27
                                      8999*998 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.1e-05
                              SgrT  14 qGaaklsadWLarvnvkyrqd 34 
                                        Ga + s+dWLa v+  +r +
  gi|336253550|ref|YP_004596657.1|  81 YGARRASGDWLAFVDADTRVR 101
                                       4999**********9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); 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:                         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: 00:00:00.42
# Mc/sec: 1660.38
//
Query:       gi|336253551|ref|YP_004596658.1|  [L=81]
Description: hypothetical protein Halxa_2154 [Halopiger xanaduensis SH-6]
Scores for 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  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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 0.26s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 635.63
//
Query:       gi|336253552|ref|YP_004596659.1|  [L=223]
Description: HhH-GPD family protein [Halopiger xanaduensis SH-6]
Scores for 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-14   53.6   0.0    3.3e-14   53.2   0.0    1.1  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
      6e-07   29.0   0.0    1.1e-06   28.1   0.0    1.5  1  HHH            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.031   14.9   0.0       0.34   11.6   0.0    2.1  2  HHH_5          Helix-hairpin-helix domain
       0.22   11.9   3.9       0.33   11.3   3.9    1.2  1  Opy2           Opy2 protein
        1.9    8.9   5.1        3.4    8.1   5.1    1.5  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III


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 !   53.2   0.0   9.3e-18   3.3e-14       1      98 [.      42     166 ..      42     173 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 9.3e-18
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       v++++ qqts   +  ++  ++e+   ptpe++++ + e L++ i++lG+  ++ +y  e++++lv           
  gi|336253552|ref|YP_004596659.1|  42 VAELMLQQTSARQVLNVYDAFVET--YPTPESILETPRERLADDIEPLGLR-KRTRYFYEASEQLVaehdgavpndr 115
                                       7899********************..59*********************99.************************* PP

                                       ....................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHH CS
                                       ....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ....................gkpdvlivvDvhvrrilkrlrsikekktkkkv 98 
                                                           g+ + + +vD++v+r+l+r++++++  t+ ++
  gi|336253552|ref|YP_004596659.1| 116 sellelrgvgeytaasvlahGFEKDVAAVDTNVARVLSRVFGLDRE-TEPEA 166
                                       ********************887889*****************996.44333 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   3.2e-10   1.1e-06       1      30 []     106     135 ..     106     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.2e-10
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                                       +++g +p++r eLl+l GVG++tA ++l++
  gi|336253552|ref|YP_004596659.1| 106 EHDGAVPNDRSELLELRGVGEYTAASVLAH 135
                                       589************************985 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.22   7.8e+02      18      39 ..      62      82 ..      55      87 .. 0.87
   2 ?   11.6   0.0   9.4e-05      0.34       3      45 ..     117     160 ..     115     163 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.22
                                      HHTTT--SHHHHHHS-HHHHHT CS
                             HHH_5 18 llsaGiesvedlaaadveeLak 39
                                       +++ + ++e +++  +e+La+
  gi|336253552|ref|YP_004596659.1| 62 FVET-YPTPESILETPRERLAD 82
                                      5778.899********999986 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 9.4e-05
                                       HHHTSTT--HHHHHHHHTTT--.SHHHHHHS-HHHHHTSTTS-H CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGie.svedlaaadveeLakipGiGk 45 
                                       eLl++ G+G+ tA ++l +G+e  v+++    +  L+++ G+  
  gi|336253552|ref|YP_004596659.1| 117 ELLELRGVGEYTAASVLAHGFEkDVAAVDTNVARVLSRVFGLDR 160
                                       89*****************8883355533333334777766665 PP

>> Opy2  Opy2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.9   9.2e-05      0.33       3      23 ..     196     216 ..     195     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.2e-05
                              Opy2   3 sCpdsapsCPsCpsgeeCvlt 23 
                                       +C  + p C sCp+g +C ++
  gi|336253552|ref|YP_004596659.1| 196 VCTATDPNCESCPAGPVCEFR 216
                                       6999**************875 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.1   0.00095       3.4       1      12 [.     197     208 ..     197     208 .. 0.99

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00095
                     EndIII_4Fe-2S   1 CTARkPkCeaCP 12 
                                       CTA  P Ce CP
  gi|336253552|ref|YP_004596659.1| 197 CTATDPNCESCP 208
                                       ***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1795.70
//
Query:       gi|336253553|ref|YP_004596660.1|  [L=312]
Description: Pectinesterase [Halopiger xanaduensis SH-6]
Scores for complete 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-75  253.5   0.0    2.2e-75  253.1   0.0    1.0  1  Pectinesterase  Pectinesterase
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.033   14.0   0.0    1.3  1  Beta_helix      Right handed beta helix region


Domain annotation for each model (and alignments):
>> Pectinesterase  Pectinesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.1   0.0   2.5e-79   2.2e-75       1     294 [.      10     294 ..      10     298 .. 0.92

  Alignments for each domain:
  == domain 1  score: 253.1 bits;  conditional E-value: 2.5e-79
                                       SEEE-TTS-SSBSSHHHHHHHS-SS-SS-EEEEE-SEEEE--EEE-TTS-SEEEEES-TTTEEEEE---TT..T.T- CS
                    Pectinesterase   1 dvvvakdgsgkfktiseavaavpeksekrfviyvkaGvYeenvevekkktnvvlvGdGkektvitgsknvv..d.gk 74 
                                       d vv  dgsg+++ i++a++ +++  ++r+ i++k+GvYee+v+v++ + ++ l+G+  + tvi+ + ++   d g 
  gi|336253553|ref|YP_004596660.1|  10 DCVVDPDGSGDYERIQAAIDDAKSFPRERIAIFLKEGVYEEKVTVHSWNPKIDLIGESADGTVIAHDDHFEriDrGR 86 
                                       57999************************************************************965543113244 PP

                                       .-SGGG-SEEE-STT-EEES-EEEE---GGG----SEEE--TTEEEES-EEE-STT-EEE-..SSEEEEES-EEEES CS
                    Pectinesterase  75 .ttfktatvavvgegfiarditfentaGpekhqavalrvdsDlsvfyrcslegyqDtlyvh..skRqfyreceitGt 148
                                        +tf t t+ v g+ f ar++t++n aGpek qaval v++D++vf +c++ g+qDt+y+    +Rq++ +c + Gt
  gi|336253553|ref|YP_004596660.1|  87 nSTFFTYTLKVCGNDFRARNLTVRNDAGPEKGQAVALHVEADRAVFENCRFVGNQDTVYAAgeGSRQYFDDCYLEGT 163
                                       69*********************************************************972257************ PP

                                       SS-EEE--EEEEES-EEEE---STT--EEEEEE----TTS--EEEEES-EEEE-TTTGGGTTTS-EEEE--SSTT-E CS
                    Pectinesterase 149 vDfifGnaaavlqnceivarkplkgqkntvtaqgrkdpnqntGiviqnckitaeedllavkkkvktyLGRPWkeysr 225
                                        Df+fG a+av+ nce++++       ++vta +   +++  G+v+  c++tae+++       + yLGRPW+++++
  gi|336253553|ref|YP_004596660.1| 164 TDFVFGGATAVFDNCEVHSKA-----DSYVTAAST-PRTEPFGFVFDGCTLTAEPNVS------EVYLGRPWRDHAH 228
                                       *****************9875.....458999875.567889**********998866......89*********** PP

                                       EEEES-EE-TTB-TT-S--SSTTTTTTT-EEEEES-BSTT---TTS---TTEEEE--HHHHGGGSHHHH CS
                    Pectinesterase 226 tvimeskiedvidpeGwleWngdfalktlyYgeyknsGpgaetskRvkWkgykvilskeeaekftvakf 294
                                       + +++s+++d+i p+Gw++W+    ++ + Y+ey+n+Gpg++t +Rv W+    +ls +eae++++++ 
  gi|336253553|ref|YP_004596660.1| 229 VTFLRSHMDDHILPAGWHDWSRPDVVDDVTYAEYENRGPGSRTDDRVPWSE---TLSPAEAERYAAENV 294
                                       *************************************************98...579999999999876 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.7e-06     0.033      12      93 ..     103     186 ..      94     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-06
                                       EEESEEEES-......SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT.-S-EEES-EEE---SEEE-TT--S--E CS
                        Beta_helix  12 tiknntisns......ggyGiylrgssnvvienneiannsgsGiyilgs.snntisnntisdnngggialfgasnnl 81 
                                         +n t++n       ++ +++++ ++  v+en+++ + +++ +y  g  s+  +++++ ++ +     +fg+   +
  gi|336253553|ref|YP_004596660.1| 103 RARNLTVRNDagpekgQAVALHVEADRA-VFENCRFVG-NQDTVYAAGEgSRQYFDDCYLEGTT---DFVFGGATAV 174
                                       5678888888888877777788888887.*********.66666666555***********766...778899999* PP

                                       EES-EEES-SS- CS
                        Beta_helix  82 ienneitdnggs 93 
                                       ++n+e++  ++s
  gi|336253553|ref|YP_004596660.1| 175 FDNCEVHSKADS 186
                                       *****9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.44u 0.17s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 2726.38
//
Query:       gi|336253554|ref|YP_004596661.1|  [L=144]
Description: hypothetical protein Halxa_2157 [Halopiger xanaduensis SH-6]
Scores for 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-12   46.9   0.3    5.6e-12   46.0   0.3    1.4  1  DUF2085   Predicted membrane protein (DUF2085)
     0.0024   18.0   7.1      0.036   14.2   5.2    2.0  1  FUSC_2    Fusaric acid resistance protein-like
  ------ inclusion threshold ------
        1.9    7.8   7.0        2.5    7.4   7.0    1.1  1  ThrE      Putative threonine/serine exporter
        6.5    6.8   9.1       0.91    9.6   0.3    2.7  3  DUF543    Domain of unknown function (DUF543)


Domain annotation for each model (and alignments):
>> DUF2085  Predicted membrane protein (DUF2085)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.3   1.2e-15   5.6e-12       9      88 ..      34     111 ..      29     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.2e-15
                           DUF2085   9 fflkgyqfpvCaRctgiylGlllgllllllkaklsklsllllvllllpmaiDgltqllglyestnllRlitGllaGl 85 
                                         ++g ++ +CaRc g+y G+++g+l++l+       s+ ++++l lp + D+ + ++     +n +R+ tG+l G 
  gi|336253554|ref|YP_004596661.1|  34 PRIGGRPVHICARCLGVYPGIAAGFLAALF--LPNDPSVAIVAFLPLPALFDWALTTFRPARGSNVVRTATGALLGC 108
                                       5689***********************988..34566777799999******************************9 PP

                           DUF2085  86 ala 88 
                                       +++
  gi|336253554|ref|YP_004596661.1| 109 GYG 111
                                       986 PP

>> FUSC_2  Fusaric acid resistance protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   5.2     8e-06     0.036      24     125 ..      31     134 ..      28     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8e-06
                            FUSC_2  24 vlsptlgasltravqRilGtvlGavlallllyllpgn.lalallvfllvfli..afflkrnyalafiflt.llalll 96 
                                       ++sp +g++   +++R lG+  G+++++l+  +lp++  +++++++ l  l+  a++  r+  + +++ t   all 
  gi|336253554|ref|YP_004596661.1|  31 CYSPRIGGRPVHICARCLGVYPGIAAGFLAALFLPNDpSVAIVAFLPLPALFdwALTTFRPARGSNVVRTaTGALLG 107
                                       67999**************************9999976666666666666662244445778888888775677777 PP

                            FUSC_2  97 yslaagsgnpieialhRlld.vliGilial 125
                                         +   + + + ++l+R l+ v+iG++ a+
  gi|336253554|ref|YP_004596661.1| 108 CGY---GLGVSLLLLERELAvVAIGAVYAV 134
                                       777...344555777886551567877776 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   7.0   0.00055       2.5     116     201 ..      53     140 ..      42     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00055
                              ThrE 116 glaaaafallf.ggdwidflvafl.agllggllrlllakrglnsfvleavaaflasllallavslglglnpdaiiig 190
                                       g+aa+++a lf   d+ +++vafl + +l +++   ++  +  ++v +a++a+l +  +l +  l l+ +++ ++ig
  gi|336253554|ref|YP_004596661.1|  53 GIAAGFLAALFlPNDPSVAIVAFLpLPALFDWALTTFRPARGSNVVRTATGALLGCGYGLGVSLLLLERELAVVAIG 129
                                       899999999997889**9**99985677777777777777777777778887777777766666666889******* PP

                              ThrE 191 sillLvPGlpl 201
                                       ++  +v+G+ l
  gi|336253554|ref|YP_004596661.1| 130 AVYAVVAGFLL 140
                                       *********87 PP

>> DUF543  Domain of unknown function (DUF543)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.63   2.8e+03      35      46 ..      53      64 ..      46      75 .. 0.67
   2 ?    1.7   1.0     0.057   2.6e+02      52      64 ..     102     114 ..      86     116 .. 0.72
   3 ?    9.6   0.3    0.0002      0.91      25      50 ..     119     144 .]     117     144 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.63
                            DUF543 35 gllvGvvasvll 46
                                      g+++G +a+++l
  gi|336253554|ref|YP_004596661.1| 53 GIAAGFLAALFL 64
                                      566677777666 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.057
                            DUF543  52 apvalGaGvGiGa 64 
                                         + lG G+G+G 
  gi|336253554|ref|YP_004596661.1| 102 TGALLGCGYGLGV 114
                                       4467888888886 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0002
                            DUF543  25 lsnllvkvglgllvGvvasvllfrrR 50 
                                       l++ l  v++g++++vva++ll+r+R
  gi|336253554|ref|YP_004596661.1| 119 LERELAVVAIGAVYAVVAGFLLARAR 144
                                       67778889****************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.19s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1162.35
//
Query:       gi|336253555|ref|YP_004596662.1|  [L=143]
Description: hypothetical protein Halxa_2158 [Halopiger xanaduensis SH-6]
Scores for 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-16   58.7   3.8    7.8e-16   58.1   3.8    1.2  1  TM2              TM2 domain
    2.7e-12   45.6  11.6    4.1e-06   26.0   2.0    2.2  2  zf-ribbon_3      zinc-ribbon domain
    3.3e-09   36.6   7.5    5.6e-09   35.9   7.4    1.4  1  DZR              Double zinc ribbon
    6.8e-07   28.8  11.4     0.0032   17.1   2.2    2.7  2  zinc_ribbon_2    zinc-ribbon domain
    3.1e-05   24.6  11.3     0.0048   17.6   1.4    2.2  2  zinc_ribbon_15   zinc-ribbon family
    0.00015   21.7  19.6      0.011   15.7   3.0    4.0  4  YhfH             YhfH-like protein
    0.00034   20.5   7.2       0.13   12.2   3.4    2.4  2  DUF2116          Uncharacterized protein containing a Zn-ribb
    0.00098   19.1  13.4      0.076   13.1   1.9    2.3  2  UPF0547          Uncharacterised protein family UPF0547
      0.009   15.9   5.9       0.92    9.4   0.3    2.8  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.071   13.1  12.1       0.89    9.6   3.1    2.2  2  HypA             Hydrogenase/urease nickel incorporation, met
      0.074   13.0   8.0        1.3    9.1   1.5    2.2  2  zf-C2HC5         Putative zinc finger motif, C2HC5-type
      0.097   13.0   8.0        1.6    9.0   0.2    2.1  2  zf-C4H2          Zinc finger-containing protein
       0.33   10.5  12.3          1    9.0   3.9    3.3  3  TF_Zn_Ribbon     TFIIB zinc-binding
       0.39   10.7   8.7          3    7.9   1.4    2.9  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.49   10.3   9.7        2.1    8.3   0.5    2.3  2  C1_1             Phorbol esters/diacylglycerol binding domain
       0.72    9.5  10.6        0.6    9.7   1.0    2.3  2  RecR             RecR protein
        2.2    8.2  16.5         37    4.4   5.1    4.0  2  Nudix_N_2        Nudix N-terminal
        2.3    8.5   9.7        8.2    6.7   1.0    2.1  2  PHF5             PHF5-like protein
        2.8    7.6   9.0        2.7    7.7   0.5    2.2  2  Zn_ribbon_17     Zinc-ribbon, C4HC2 type
        2.8    8.7   7.2        2.5    8.8   1.4    2.2  2  zinc-ribbon_6    zinc-ribbon domain
        4.5    7.2  10.0        8.8    6.3   2.0    2.2  2  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
        7.5    6.9   5.7        6.4    7.1   1.1    2.3  2  Ribosomal_L32p   Ribosomal L32p protein family


Domain annotation for each model (and alignments):
>> TM2  TM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   3.8   9.6e-19   7.8e-16       3      51 .]      72     121 ..      70     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 9.6e-19
                               TM2   3 ksklvaylLwffLGglGvHRFYlGktgsGvlqlltfv.Gglgiwwlidli 51 
                                        +k++a++L+++LGglG+H+FY G+++ Gvl+l++f+ G++ + +l+++i
  gi|336253555|ref|YP_004596662.1|  72 SDKVAAGVLALLLGGLGAHKFYQGNVKLGVLYLCFFWtGIPALLGLVEGI 121
                                       5799*******************************************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 !   25.0   2.4     1e-08   8.3e-06       2      24 ..       1      23 [.       1      25 [. 0.93
   2 !   26.0   2.0     5e-09   4.1e-06       2      25 ..      40      63 ..      39      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1e-08
                       zf-ribbon_3  2 tvrCPnCGaplssddnvCpyCGt 24
                                      +++C nCG+++++++ vC++CG 
  gi|336253555|ref|YP_004596662.1|  1 MKHCINCGEQITAQAEVCTHCGV 23
                                      89*******99***********6 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 5e-09
                       zf-ribbon_3  2 tvrCPnCGaplssddnvCpyCGtk 25
                                      +++C +CG+++ +++ +Cp CG +
  gi|336253555|ref|YP_004596662.1| 40 EKYCVECGTLINEQAEICPDCGVQ 63
                                      79*******99***********76 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   7.4   6.8e-12   5.6e-09       1      49 []       4      61 ..       4      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 6.8e-12
                               DZR  1 CpqCgeelppdarfCseCgtklkavaa.........edrCpsCgekvdpearfCpeCG 49
                                      C +Cge+++++a++C +Cg +     +         e+ C++Cg+ ++++a++Cp CG
  gi|336253555|ref|YP_004596662.1|  4 CINCGEQITAQAEVCTHCGVNQTTSLEgsyeergenEKYCVECGTLINEQAEICPDCG 61
                                      *******************997655558899**************************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 !   17.1   2.2   3.9e-06    0.0032       2      20 ..       4      22 ..       3      24 .. 0.96
   2 !   16.3   1.9   7.2e-06    0.0059       1      20 [.      42      61 ..      42      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.9e-06
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCG 20
                                      C nCG+++   a  C++CG
  gi|336253555|ref|YP_004596662.1|  4 CINCGEQITAQAEVCTHCG 22
                                      99****************9 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 7.2e-06
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCG 20
                                      +C +CG+ + + a  Cp CG
  gi|336253555|ref|YP_004596662.1| 42 YCVECGTLINEQAEICPDCG 61
                                      8******************9 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   2.9   0.00028      0.23      66      86 .]       2      22 ..       1      22 [. 0.96
   2 !   17.6   1.4   5.9e-06    0.0048      59      86 .]      34      61 ..      23      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00028
                    zinc_ribbon_15 66 keCknCgkeveeefkyCpkCg 86
                                      k+C nCg++++++ + C++Cg
  gi|336253555|ref|YP_004596662.1|  2 KHCINCGEQITAQAEVCTHCG 22
                                      79******************9 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 5.9e-06
                    zinc_ribbon_15 59 kkessekkeCknCgkeveeefkyCpkCg 86
                                      +++ +++k+C +Cg+ ++e+ + Cp Cg
  gi|336253555|ref|YP_004596662.1| 34 EERGENEKYCVECGTLINEQAEICPDCG 61
                                      33445599*******************9 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   7.1    0.0056       4.5      13      28 ..       1      16 [.       1      21 [. 0.85
   2 ?    2.4   1.1       0.2   1.6e+02      15      21 ..      17      23 ..      16      35 .. 0.85
   3 !   15.7   3.0   1.3e-05     0.011      13      28 ..      40      55 ..      38      60 .. 0.89
   4 ?    1.0   0.3      0.54   4.4e+02      16      20 ..      57      61 ..      56      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0056
                              YhfH 13 kKkCteCGkeieEqae 28
                                      +K C +CG++i  qae
  gi|336253555|ref|YP_004596662.1|  1 MKHCINCGEQITAQAE 16
                                      69************98 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.2
                              YhfH 15 kCteCGk 21
                                      +Ct+CG 
  gi|336253555|ref|YP_004596662.1| 17 VCTHCGV 23
                                      5*****5 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.3e-05
                              YhfH 13 kKkCteCGkeieEqae 28
                                      +K C+eCG  i+Eqae
  gi|336253555|ref|YP_004596662.1| 40 EKYCVECGTLINEQAE 55
                                      69*************8 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.54
                              YhfH 16 CteCG 20
                                      C++CG
  gi|336253555|ref|YP_004596662.1| 57 CPDCG 61
                                      ****9 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 !   12.2   3.4   0.00016      0.13       4      21 ..       2      19 ..       1      26 [. 0.91
   2 !    9.9   0.1   0.00086       0.7       4      24 ..      41      60 ..      38      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                           DUF2116  4 kHCivCGkaIpldesfCs 21
                                      kHCi+CG+ I  +  +C 
  gi|336253555|ref|YP_004596662.1|  2 KHCINCGEQITAQAEVCT 19
                                      8****************6 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00086
                           DUF2116  4 kHCivCGkaIpldesfCsekC 24
                                      k C+ CG+ I+++  +C + C
  gi|336253555|ref|YP_004596662.1| 41 KYCVECGTLINEQAEICPD-C 60
                                      89***************54.5 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   4.1   0.00031      0.26       1      21 [.       2      22 ..       2      23 .. 0.97
   2 !   13.1   1.9   9.3e-05     0.076       1      21 [.      41      61 ..      41      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                           UPF0547  1 KvCPeCeakvPvaaqfCphCG 21
                                      K+C  C +++ + a++C hCG
  gi|336253555|ref|YP_004596662.1|  2 KHCINCGEQITAQAEVCTHCG 22
                                      89999***************9 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.3e-05
                           UPF0547  1 KvCPeCeakvPvaaqfCphCG 21
                                      K C eC + + + a++Cp+CG
  gi|336253555|ref|YP_004596662.1| 41 KYCVECGTLINEQAEICPDCG 61
                                      6799****************9 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 !    8.3   0.9    0.0026       2.1      13      34 ..       3      24 ..       1      27 [. 0.83
   2 !    9.4   0.3    0.0011      0.92      13      34 ..      42      63 ..      41      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0026
                           DUF35_N 13 rCpdCGtvqfPPr.avCphCgsd 34
                                      +C +CG  +  ++  vC+hCg+ 
  gi|336253555|ref|YP_004596662.1|  3 HCINCGEQI-TAQaEVCTHCGVN 24
                                      799999998.6777******986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                           DUF35_N 13 rCpdCGtvqfPPravCphCgsd 34
                                      +C  CGt++     +Cp Cg+ 
  gi|336253555|ref|YP_004596662.1| 42 YCVECGTLINEQAEICPDCGVQ 63
                                      899******9999******986 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 ?    9.6   3.1    0.0011      0.89      72     103 ..       3      32 ..       1      35 [. 0.86
   2 ?    9.1   1.8    0.0016       1.3      70      96 ..      40      64 ..      33      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                                       EETTTS-EEECHHHHHS-TTTSSS-EEEEESS CS
                              HypA  72 rCreCgkefeleekalrCpkCgsadveivsGe 103
                                       +C +Cg++++ +  a+ C +Cg ++++ ++G+
  gi|336253555|ref|YP_004596662.1|   3 HCINCGEQITAQ--AEVCTHCGVNQTTSLEGS 32 
                                       6*******9977..458*******99999885 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0016
                                      EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA 70 kvrCreCgkefeleekalrCpkCgsad 96
                                      + +C eCg+ ++++  a+ Cp+Cg ++
  gi|336253555|ref|YP_004596662.1| 40 EKYCVECGTLINEQ--AEICPDCGVQQ 64
                                      668*****999977..457****9875 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 ?    9.1   1.5    0.0015       1.3      19      43 ..       3      24 ..       1      33 [. 0.82
   2 ?    7.8   0.6    0.0039       3.2      19      41 ..      42      61 ..      38      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                          zf-C2HC5 19 nClnCGkiiCakeglskpCsfCgsp 43
                                       C+nCG  i a+ ++   C++Cg +
  gi|336253555|ref|YP_004596662.1|  3 HCINCGEQITAQAEV---CTHCGVN 24
                                      6******99999888...****954 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0039
                          zf-C2HC5 19 nClnCGkiiCakeglskpCsfCg 41
                                       C++CG  i ++ ++   C+ Cg
  gi|336253555|ref|YP_004596662.1| 42 YCVECGTLINEQAEI---CPDCG 61
                                      6********999888...99998 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.2    0.0093       7.6     178     198 ..       1      21 [.       1      27 [. 0.95
   2 ?    9.0   0.2    0.0019       1.6     179     198 ..      41      60 ..      24      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0093
                           zf-C4H2 178 MKsClsChqqIHRNAPiCPlC 198
                                       MK C +C  qI   A +C  C
  gi|336253555|ref|YP_004596662.1|   1 MKHCINCGEQITAQAEVCTHC 21 
                                       9*****************999 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0019
                           zf-C4H2 179 KsClsChqqIHRNAPiCPlC 198
                                       K C  C   I   A iCP C
  gi|336253555|ref|YP_004596662.1|  41 KYCVECGTLINEQAEICPDC 60 
                                       99****************** PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.36   2.9e+02      22      29 ..       4      11 ..       3      14 .. 0.79
   2 ?    9.0   3.9    0.0012         1       2      31 ..      17      52 ..      16      54 .. 0.83
   3 ?    4.4   0.2     0.033        26      21      26 ..      56      61 ..      55      64 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.36
                                      ESSSSBEE CS
                      TF_Zn_Ribbon 22 CtdCGlVl 29
                                      C +CG+ +
  gi|336253555|ref|YP_004596662.1|  4 CINCGEQI 11
                                      88999866 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0012
                                      EETTTTCEEC......HEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnl......veDpergelvCtdCGlVled 31
                                      +C  Cg  ++      +e+  ++e +C +CG+++ +
  gi|336253555|ref|YP_004596662.1| 17 VCTHCGVNQTtslegsYEERGENEKYCVECGTLINE 52
                                      79****9884588888788888888*******9987 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.033
                                      EESSSS CS
                      TF_Zn_Ribbon 21 vCtdCG 26
                                      +C+dCG
  gi|336253555|ref|YP_004596662.1| 56 ICPDCG 61
                                      466665 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 ?   -0.9   0.2         2   1.7e+03      20      27 ..       3      10 ..       2      15 .. 0.70
   2 ?    7.9   1.4    0.0036         3      19      44 ..      16      47 ..       9      49 .. 0.79
   3 ?    6.7   0.0    0.0088       7.2      20      30 ..      56      66 ..      51      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2
                     Zn_Tnp_IS1595 20 vCPhCgsr 27
                                      +C +Cg +
  gi|336253555|ref|YP_004596662.1|  3 HCINCGEQ 10
                                      48888865 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0036
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayrikt......rglfqCkeCr 44
                                       vC hCg+ + +++++           C eC+
  gi|336253555|ref|YP_004596662.1| 16 EVCTHCGVNQTTSLEGsyeergENEKYCVECG 47
                                      68********9999998888664555577776 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0088
                     Zn_Tnp_IS1595 20 vCPhCgsrkay 30
                                      +CP Cg++++ 
  gi|336253555|ref|YP_004596662.1| 56 ICPDCGVQQPA 66
                                      6******9654 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 ?    5.9   3.3     0.014        12      12      36 ..       2      23 ..       1      25 [. 0.87
   2 ?    8.3   0.5    0.0026       2.1       9      35 ..      38      61 ..      32      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                                      -B-TTT-SB--SSSS-EEEETTT-- CS
                              C1_1 12 tfCkhCgeflwgkekqglkCswCkl 36
                                      ++C  Cge++     q+  C+ C++
  gi|336253555|ref|YP_004596662.1|  2 KHCINCGEQI---TAQAEVCTHCGV 23
                                      68********...999999999986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0026
                                      SS--B-TTT-SB--SSSS-EEEETTT- CS
                              C1_1  9 kqptfCkhCgeflwgkekqglkCswCk 35
                                      +++++C +Cg ++   + q+  C +C+
  gi|336253555|ref|YP_004596662.1| 38 ENEKYCVECGTLI---NEQAEICPDCG 61
                                      6899*********...99999999997 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   2.9     0.037        30      17      34 ..       2      21 ..       1      24 [. 0.79
   2 ?    9.7   1.0   0.00074       0.6      15      34 ..      39      60 ..      29      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.037
                                      EE-TTT--E..ESSSS-CCC CS
                              RecR 17 rhCsrCgnl..teedlCaIC 34
                                      +hC +Cg    +  ++C+ C
  gi|336253555|ref|YP_004596662.1|  2 KHCINCGEQitAQAEVCTHC 21
                                      8*****97554555999999 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00074
                                      H-EE-TTT--E.ESS.SS-CCC CS
                              RecR 15 kvrhCsrCgnl.tee.dlCaIC 34
                                      + ++C +Cg+l  e+ ++C+ C
  gi|336253555|ref|YP_004596662.1| 39 NEKYCVECGTLiNEQaEICPDC 60
                                      569********8444489*988 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   5.1     0.045        37       1      29 [.       2      22 ..       2      25 .. 0.87
   2 ?    3.7   3.5     0.071        58       1      14 [.      41      54 ..      41      62 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.045
                                      -B-TTT--B-EEE--TT-SS-EEEETTTT CS
                         Nudix_N_2  1 kFCsqCGtpvelripdgDnreRlvCpaCg 29
                                      k+C +CG++++ + +        vC++Cg
  gi|336253555|ref|YP_004596662.1|  2 KHCINCGEQITAQAE--------VCTHCG 22
                                      89******9999984........999998 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.071
                                      -B-TTT--B-EEE- CS
                         Nudix_N_2  1 kFCsqCGtpvelri 14
                                      k+C +CGt ++ + 
  gi|336253555|ref|YP_004596662.1| 41 KYCVECGTLINEQA 54
                                      89****99766554 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.1     0.012       9.5      56      78 ..       2      24 ..       1      34 [. 0.84
   2 ?    6.7   1.0      0.01       8.2      52      78 ..      37      63 ..      32      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.012
                              PHF5 56 ekciicgskgvsdayyclecvrl 78
                                      ++ci cg++ + +a  c++c   
  gi|336253555|ref|YP_004596662.1|  2 KHCINCGEQITAQAEVCTHCGVN 24
                                      68*****************9654 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.01
                              PHF5 52 gkleekciicgskgvsdayyclecvrl 78
                                      g++e+ c+ cg+  +++a  c +c  +
  gi|336253555|ref|YP_004596662.1| 37 GENEKYCVECGTLINEQAEICPDCGVQ 63
                                      678889999999999999999999665 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.4     0.051        42       5      25 ..       2      22 ..       1      25 [. 0.93
   2 ?    7.7   0.5    0.0033       2.7       3      25 ..      39      61 ..      37      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.051
                      Zn_ribbon_17  5 ksCayCelavkgrvvlcgvCe 25
                                      k+C  C  +++ +  +c+ C+
  gi|336253555|ref|YP_004596662.1|  2 KHCINCGEQITAQAEVCTHCG 22
                                      78******************6 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0033
                      Zn_ribbon_17  3 llksCayCelavkgrvvlcgvCe 25
                                      + k+C+ C + ++ +  +c+ C+
  gi|336253555|ref|YP_004596662.1| 39 NEKYCVECGTLINEQAEICPDCG 61
                                      6899******************6 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.4    0.0031       2.5       3      24 ..       3      24 ..       1      31 [. 0.91
   2 ?    3.1   0.4      0.19   1.5e+02       4      24 ..      43      63 ..      40      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0031
                     zinc-ribbon_6  3 eCeqCgqllffenssClkCgaa 24
                                      +C +Cg+++  + + C++Cg +
  gi|336253555|ref|YP_004596662.1|  3 HCINCGEQITAQAEVCTHCGVN 24
                                      8******************975 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.19
                     zinc-ribbon_6  4 CeqCgqllffenssClkCgaa 24
                                      C +Cg l+  + + C +Cg +
  gi|336253555|ref|YP_004596662.1| 43 CVECGTLINEQAEICPDCGVQ 63
                                      999999999999999999865 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 ?    6.3   2.0     0.011       8.8      26      44 ..       4      22 ..       1      27 [. 0.88
   2 ?    5.6   1.2     0.017        14      25      44 ..      42      61 ..      40      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                                      -HHHHHHHHHTT-B-TTT- CS
                        zf-C3HC4_3 26 CeeCaekllkrkkkCpiCr 44
                                      C +C e++ ++ + C  C 
  gi|336253555|ref|YP_004596662.1|  4 CINCGEQITAQAEVCTHCG 22
                                      99******99********6 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.017
                                      E-HHHHHHHHHTT-B-TTT- CS
                        zf-C3HC4_3 25 lCeeCaekllkrkkkCpiCr 44
                                      +C eC + + ++ + Cp C 
  gi|336253555|ref|YP_004596662.1| 42 YCVECGTLINEQAEICPDCG 61
                                      6********99******996 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.1    0.0078       6.4      28      48 ..       3      24 ..       1      31 [. 0.79
   2 ?    1.8   0.2      0.37     3e+02      40      47 ..      55      62 ..      39      66 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0078
                                      EETTTC.CEECTTC-BTTTTBS CS
                    Ribosomal_L32p 28 ecpncg.elklpHrvcpscGyY 48
                                       c ncg + + +  vc++cG+ 
  gi|336253555|ref|YP_004596662.1|  3 HCINCGeQITAQAEVCTHCGVN 24
                                      69****66777778*****975 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.37
                                      C-BTTTTB CS
                    Ribosomal_L32p 40 rvcpscGy 47
                                       +cp+cG+
  gi|336253555|ref|YP_004596662.1| 55 EICPDCGV 62
                                      47888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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):              22  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1016.96
//
Query:       gi|336253556|ref|YP_004596663.1|  [L=446]
Description: Malate dehydrogenase (acceptor) [Halopiger xanaduensis SH-6]
Scores for complete 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-26   94.2   0.2    1.9e-26   93.5   0.2    1.3  1  DAO            FAD dependent oxidoreductase
    1.4e-24   86.6   0.0      3e-23   82.1   0.0    2.0  1  Mqo            Malate:quinone oxidoreductase (Mqo)
    6.8e-08   32.1   0.1    0.00043   19.6   0.0    2.2  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00012   21.4   0.3     0.0013   18.0   0.1    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    0.00033   20.7   0.1       0.14   12.2   0.0    2.3  2  NAD_binding_9  FAD-NAD(P)-binding
     0.0043   16.4   0.0     0.0077   15.6   0.0    1.5  2  Amino_oxidase  Flavin containing amine oxidoreductase
     0.0045   16.1   0.0     0.0059   15.7   0.0    1.1  1  FAD_binding_2  FAD binding domain
      0.006   15.3   0.1       0.04   12.6   0.0    1.9  2  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
      0.012   16.2   0.2        7.6    7.2   0.0    2.7  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.024   14.9   0.2       0.11   12.8   0.0    2.2  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   0.2   1.1e-29   1.9e-26       1     315 [.       6     378 ..       6     408 .. 0.78

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 1.1e-29
                                       EEEEECTSHHHHHHHHHHHHTT....EEEEESSSSTT..SSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg....Vtllekgdiag..sgaSgrnsgllhsglrylpeaselarlslealeelrel 71 
                                       d+vi+GGGi G+s  y  a+      ++l+ek+++++       +ns  lh g  ++ +  e+a+ ++e+ e+l+ +
  gi|336253556|ref|YP_004596663.1|   6 DLVIVGGGISGASLLYTTAKFStidsIALIEKEPEIAaiNSHHTNNSQTLHFGDIETNYTLEKAEEVKEGAELLAGY 82 
                                       89****************99766789*******9999443445567788999884455555777************* PP

                                       HHHHSSTTS.EEEEEEEEEESSHHHHHHHHHHHHHH..HHTTTTEEEEEHHHHHHHSTT.ST.....TTSEEEEETT CS
                               DAO  72 eeelgidid.yrrtGllslaadeeelealdkllall..leagldaelldaeevrelepa.lp.....gllgalfypd 139
                                        e++++d + ++++ +++l+ + ee ++l+++ ++   +++ ++ + + +ee++e ep  ++     + + al +pd
  gi|336253556|ref|YP_004596663.1|  83 LENHDPDREmHDKRSKMVLGVGKEEVAKLERRHEEEgfGDLFPKLQAIGREEIAEYEPKvVEgrdpdKEMLALQTPD 159
                                       *******887999999999998889****88888876654445669************873356676545689**** PP

                                       EEEEEHHHHHHHHHHHH.HHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.HHHTTCTT. CS
                               DAO 140 tgqvdpakltaalaraa.ealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd.llgllkel. 213
                                       + +vd+ + t+++ ++a e+  v++++gt v+++  +  +++++ +tt+g+ da da V+aaG +s  ++   kel 
  gi|336253556|ref|YP_004596663.1| 160 GYVVDYGETTKSFVDEArEESNVDVYTGTAVKDI-TPTLDGYTI-ETTNGRFDA-DATVVAAGSHSLqFA---KELg 230
                                       9999************944556************.555557888.666687565.99********97444...5555 PP

                                       ...TSEEEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSE..EEEEESSE............... CS
                               DAO 214 ...dlpispvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgr..vlvGgtad............... 270
                                          d+ + pv g+ +  + l      + +++++ ++  ++  v+  ++  ++  +++G+ta                
  gi|336253556|ref|YP_004596663.1| 231 ygqDKVLLPVAGSFFLADDL-----LNGKVYTLQMKKLPFAAVHGDADVHDSsiTRFGPTAKlvptlergristvgd 302
                                       5556788*********9543.....4457888888999999999999865554467999999999998888888888 PP

                                       ..........................EETTCSSTSCSHHHHHHHHHHHHHHSGG..GCGEEE..EEEEEEEE.TTS CS
                               DAO 271 ..........................eesgdddpevdeedidellealrklfPq..lgdvlr..kwaGlrpl.pdg 315
                                                                 +  +  + + +e   +++l++++k++P+  l+d++r   + G+rp+ +d+
  gi|336253556|ref|YP_004596663.1| 303 fldvfglnaaaflsyaniladrvllpYVLRNLVYDLPEVGPRQFLPHVQKVVPSveLEDIERakGYGGVRPQiVDT 378
                                       8888888888888888777777777755555555666668899***********7779999777999****54665 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.0   1.7e-26     3e-23       2     437 ..       4     412 ..       3     421 .. 0.81

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 1.7e-26
                               Mqo   2 kvdvvliGaGimsatlgvllkelepelsievlerldkvaeessnawnnaGtGHsalcElnYtpekedgsidiskAvk 78 
                                       k+d+v++G+Gi  a+l     +++   si+++e+  ++a+ +s++ nn+ t H + +E nYt ek         A +
  gi|336253556|ref|YP_004596663.1|   4 KYDLVIVGGGISGASLLYTTAKFSTIDSIALIEKEPEIAAINSHHTNNSQTLHFGDIETNYTLEK---------AEE 71 
                                       689***********************************************************765.........777 PP

                               Mqo  79 ineqfevsrqfwaylvekgllkdpkefinkvpHlsfvageenveflkkRyealkksplfegmeysedkeelkewlPl 155
                                       ++e  e+   +      +      +e   k + + +  g+e+v+ l++R+e+     lf +++    +ee++e+ P 
  gi|336253556|ref|YP_004596663.1|  72 VKEGAELLAGYLENHDPD------REMHDKRSKMVLGVGKEEVAKLERRHEEEGFGDLFPKLQAI-GREEIAEYEPK 141
                                       777666544444433333......34445677999***************************977.5789******* PP

                               Mqo 156 vmegRdakekvaatrieeGtdvnfgaltrqllkalekkkgvelklkhevkdlkreedgkWkvkvkdlktgekkkvka 232
                                       v+egRd+++++ a ++  G  v++g+ t++++++++++++v++ +++ vkd++ + dg +++++++       +++a
  gi|336253556|ref|YP_004596663.1| 142 VVEGRDPDKEMLALQTPDGYVVDYGETTKSFVDEAREESNVDVYTGTAVKDITPTLDG-YTIETTN------GRFDA 211
                                       *******************************************************996.7777764......45677 PP

                               Mqo 233 kfvfiGaGGgalklLqksgipeakgyggfPvsGqflvcknpevveqheakvYgkaavgaPPmsvpHlDtRvidgkks 309
                                       +   + aG ++l++ ++ g  + k    +Pv+G+f+ +++       + kvY+     + P +  H D+ v d  + 
  gi|336253556|ref|YP_004596663.1| 212 DATVVAAGSHSLQFAKELGYGQDK--VLLPVAGSFFLADD-----LLNGKVYTLQM-KKLPFAAVHGDADVHD-SSI 279
                                       778899********9988776666..569*******9975.....3589***9765.56678888***99766.567 PP

                               Mqo 310 llfGPfagfstkflke.....gslldllksvklsnllpllavglknldLvkYlieqvlks.....kedrlealrefl 376
                                         fGP a   + + +      g++ld++  +++  +l++ ++ + +  L  Y++++++ +      ++ l ++++ +
  gi|336253556|ref|YP_004596663.1| 280 TRFGPTAKLVPTLERGristvGDFLDVF-GLNAAAFLSYANILA-DRVLLPYVLRNLVYDlpevgPRQFLPHVQKVV 354
                                       89*******9987663111114444443.355555666655555.555777877777654222225677899***** PP

                               Mqo 377 peakkedWelvv..aGqRvqvikkdeekggvlefGtevvasadgslaalLGasPGAstavsim 437
                                       p+ + ed e ++   G R q++ +   k+ +l++G   +  +d      +  sPGAst+ + +
  gi|336253556|ref|YP_004596663.1| 355 PSVELEDIERAKgyGGVRPQIVDT---KKKSLDMGEAKIVGEDII--FNITPSPGASTCLKNA 412
                                       *******998763379******98...4568****9999998854..45789******98754 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 !   10.5   0.0   0.00014      0.26       1      58 [.       5      91 ..       5     138 .. 0.64
   2 !   19.6   0.0   2.4e-07   0.00043     181     238 ..     165     221 ..     150     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                                      CSEEEE--SHHHHHHHHHHHH..HTS-EEEEE..............TTHCHHHCSHHHHCHHHHHHHHHHHHH...... CS
                                      xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaq..agakvtlve..............legtclnggcllskallgvaedaeias...... 57
                                      +d+v++GgG+ G ++  t a+      ++l+e                +t+++g++   ++l++++e +e a+      
  gi|336253556|ref|YP_004596663.1|  5 YDLVIVGGGISGASLLYTTAKfsTIDSIALIEkepeiaainshhtnNSQTLHFGDIETNYTLEKAEEVKEGAEllagyl 83
                                      689******************7635667777544444443355555666666666666666666666666666666555 PP

                                      .......H CS
                                      .......x RF
                       Pyr_redox_2 58 .......e 58
                                             e
  gi|336253556|ref|YP_004596663.1| 84 enhdpdrE 91
                                      54444331 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.4e-07
                                       S-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 181 ldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvr 238
                                       +++  + ++ ea+e+++v+v++gt vk+i++  + ++ ++++g+ +dad  vva+G  
  gi|336253556|ref|YP_004596663.1| 165 YGETTKSFVDEAREESNVDVYTGTAVKDITPTLDGYTIETTNGR-FDADATVVAAGSH 221
                                       67888899**********************99997776666666.9*********965 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 ?    1.1   0.0       0.1   1.8e+02       1      46 [.       8      55 ..       8     107 .. 0.70
   2 !   18.0   0.1   7.4e-07    0.0013      82     135 ..     168     221 ..     162     232 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.1
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkk.agledylilEkg.nignsiyrypkemtfi 46
                                      +I+G+G  G +  ++  k + ++++  +Ek+ +i +  ++  ++ +++
  gi|336253556|ref|YP_004596663.1|  8 VIVGGGISGASLLYTTAKfSTIDSIALIEKEpEIAAINSHHTNNSQTL 55
                                      799999999988766555156789999999966665555555555554 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 7.4e-07
                       Pyr_redox_3  82 ealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGef 135
                                       +  ++++e  ++ ++++ + + V++++++ +g+++et+++ + A+  ++A+G  
  gi|336253556|ref|YP_004596663.1| 168 TTKSFVDEAREESNVDVYTGTAVKDITPTLDGYTIETTNGRFDADATVVAAGSH 221
                                       566788899999****************************************85 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 !    6.3   0.0    0.0048       8.6       1      43 [.       8      48 ..       8      97 .. 0.78
   2 !   12.2   0.0   7.6e-05      0.14     103     154 ..     168     219 ..     164     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0048
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvwr 43
                                      +ivG+G++G+++l   ++    ++  +i l+++++   a   ++
  gi|336253556|ref|YP_004596663.1|  8 VIVGGGISGASLLYTTAKF---STIDSIALIEKEPEiAAINSHH 48
                                      7***********9988887...4777888888866524444444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.6e-05
                     NAD_binding_9 103 lfeellarlpegvtvevhra.evvdleeradgqavlladgaslaadaVvLAlG 154
                                       + ++++++++e+ +v+v+++  v d++++ dg+++ +++g +++ada v+A G
  gi|336253556|ref|YP_004596663.1| 168 TTKSFVDEAREESNVDVYTGtAVKDITPTLDGYTIETTNG-RFDADATVVAAG 219
                                       567899999999*****98735669********9966655.699999999998 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.3e-06    0.0077     215     266 ..     171     224 ..      52     236 .. 0.80
   2 ?   -4.1   0.0         4   7.2e+03     126     154 ..     403     431 ..     376     437 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.3e-06
                                       HHHH...TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHH CS
                     Amino_oxidase 215 alae...elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlk 266
                                       ++ +   e++++d+ ++t Vk+i+   dg+t+++++g+  +aDa vv++    l+
  gi|336253556|ref|YP_004596663.1| 171 SFVDearEESNVDVYTGTAVKDITPTLDGYTIETTNGRF-DADATVVAAGSHSLQ 224
                                       4444445699****************************5.*********999998 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 4
                                       HHHCCCCHHHHHHHHHCHHHHHHHHHHHH CS
                     Amino_oxidase 126 qktldeldldskslaesleelgrrepgdv 154
                                        +++++l++++ ++++ le+lg++ + d 
  gi|336253556|ref|YP_004596663.1| 403 PGASTCLKNAMRDTHQLLEFLGDDYEFDE 431
                                       46677888888888888888888887774 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.3e-06    0.0059       1     203 [.       6     222 ..       6     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.3e-06
                                       SEEEE--SHHHHHHHHHHHH.TTT.-EEEEESSSGGGS....GGGG--S-EE-....TT..SSGGSTC.CHHHHHHH CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaae.aGl.kvavvekeqefgg....atawsqGgida....vlspeqkkagikdspelhrt 67 
                                       D++++G+G++G +  ++ a+     ++a++eke+e       +t  sq   +        +  k+ ++k+  el + 
  gi|336253556|ref|YP_004596663.1|   6 DLVIVGGGISGASLLYTTAKfSTIdSIALIEKEPEIAAinshHTNNSQTLHFGdietNY-TLEKAEEVKEGAELLAG 81 
                                       89***************99965558*********9877777999999866555111044.44567778888889999 PP

                                       HHHHHTTT-S.-HHHHHHHHHTHHHHHHHHHHT......T----B....CCTS.....SB-EEE-TT-SSTEEEE-. CS
                     FAD_binding_2  68 dtlkaldela.dqplveafveaapeavdeLeel......gvpfsr....tedg.....pvdvrelGglsatartlhd 128
                                       ++ +  ++++ + +++++++  ++e+v+ Le+       g ++++       g     ++  + + g  ++ + +  
  gi|336253556|ref|YP_004596663.1|  82 YLENHDPDREmHDKRSKMVLGVGKEEVAKLERRheeegfG-DLFPklqaI--GreeiaEYEPKVVEGRDPD-KEML- 153
                                       99888899999**********************9888743.333334330..1444667777777777777.4555. PP

                                       STT-......HHHHHHHHHHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----G CS
                     FAD_binding_2 129 aadarretlvtghallarlvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfg 203
                                       a++ ++  +v+  +  + +v++ar+   vd+++ t+++++   +    G ++e  ++ +  r+ a+a+v+a+g  +
  gi|336253556|ref|YP_004596663.1| 154 ALQTPDGYVVDYGETTKSFVDEAREESnVDVYTGTAVKDI---TPTLDGYTIE--TTNG--RFDADATVVAAGSHS 222
                                       5666568999*************99989************...5588898888..5555..567999999998766 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.12   2.2e+02       2      35 ..       6      41 ..       5      43 .. 0.66
   2 !   12.6   0.0   2.2e-05      0.04     119     167 ..     177     223 ..     167     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.12
                                      SEEEE--SHHH...HHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like  2 dviviGgGaAG...lmaAisaakrgkrVlllekakkl 35
                                      d++++GgG +G   l+++++  ++  +++l+ek++++
  gi|336253556|ref|YP_004596663.1|  6 DLVIVGGGISGaslLYTTAK-FSTIDSIALIEKEPEI 41
                                      899****9999442333333.3556788888888766 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.2e-05
                                       HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS- CS
                       HI0933_like 119 lkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSi 167
                                        +e++v++++ t+vk+++ + dg ++++t +++++ ad++v+A G+ S+
  gi|336253556|ref|YP_004596663.1| 177 REESNVDVYTGTAVKDITPTLDG-YTIET-TNGRFDADATVVAAGSHSL 223
                                       4679***************9999.*****.9**************9996 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0085        15       2      35 ..       7      42 ..       6      78 .. 0.78
   2 ?    7.2   0.0    0.0042       7.6      40      77 ..     167     203 ..     162     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0085
                                      EEEECSSHHHHHHHHHHHHTT..SEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg..kkVtvversdkll 35
                                      +v+vGgG +g  l  + a++   +++ ++e ++++ 
  gi|336253556|ref|YP_004596663.1|  7 LVIVGGGISGASLLYTTAKFStiDSIALIEKEPEIA 42
                                      79**********999999998667999999999887 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0042
                                       HHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox  40 eeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       e++ + + e  e+ +++v+++t v+ i+ + dg ++++
  gi|336253556|ref|YP_004596663.1| 167 ETTKSFVDEAREESNVDVYTGTAVKDITPTLDG-YTIE 203
                                       55566666666777**************99887.3355 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 ?   12.8   0.0     6e-05      0.11       1      31 [.       9      41 ..       9      59 .. 0.84
   2 ?   -2.4   0.1       3.3   5.9e+03       7      18 ..     307     318 ..     306     327 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-05
                                      EE--SHHHHHHHHHHHCC.TE.EEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka.gf.dvlllekrdrl 31
                                      IvG+G+sG+++ y+ ak   + ++ l+ek + +
  gi|336253556|ref|YP_004596663.1|  9 IVGGGISGASLLYTTAKFsTIdSIALIEKEPEI 41
                                      9****************536657******9987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHCC CS
                     NAD_binding_8   7 sGlvaAylLaka 18 
                                       +Gl aA++L+ a
  gi|336253556|ref|YP_004596663.1| 307 FGLNAAAFLSYA 318
                                       79999*999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); 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:                        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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3197.76
//
Query:       gi|336253557|ref|YP_004596664.1|  [L=444]
Description: sodium/calcium exchanger membrane protein [Halopiger xanaduensis SH-6]
Scores for 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   66.7  29.0    7.5e-11   42.2   7.3    2.5  3  Na_Ca_ex  Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   7.3   4.2e-15   7.5e-11       6     149 ..      37     201 ..      33     203 .. 0.76
   2 !   33.5  10.2     2e-12   3.6e-08       3     148 ..     232     376 ..     230     379 .. 0.85
   3 ?   -3.8   0.1      0.61   1.1e+04      81      88 ..     403     410 ..     390     419 .. 0.51

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 4.2e-15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHT......TT.....HHHHHHHH CS
                          Na_Ca_ex   6 filslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaalt......ge.....vdlaignv 71 
                                        ++ + l +++++fl  +a+e+a+  ++++  +++ +lA    +pE++++   a++      +e     ++la++n+
  gi|336253557|ref|YP_004596664.1|  37 TVIVTGLAVLGSSFLLAWAAETAE-KDVPQ-AFAIAVLAVLAVAPEYAVDALYAWNagvhagTErgieaGNLAVANM 111
                                       344444555566666666666663.47777.67788*******************76666652244567******** PP

                                       HHHHHHHHHTHHHHHHHHHH.........BTTSSCE..........CCHHHHHHHHHHHHHHHHHHHTCHHHHHHTE CS
                          Na_Ca_ex  72 lGsnifnlllviGlialigs.........lkvdses..........lkldlgllllvallllllvlllllplfvpgr 129
                                       +G+n + ++++++ +al++          +                +kld ++ l +++lll+++ ++l+pl   g 
  gi|336253557|ref|YP_004596664.1| 112 TGANRILIGIGWAGVALFTIfragaatdpA-----VddrpgvlsdvVKLDREIGLEIVFLLLATMWAFLVPLN--GG 181
                                       ******************776666444441.....25555677777788888888888888899999999986..** PP

                                       EHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex 130 ltvleglvllllYalylvls 149
                                       +++l+ lvl+++Y++y+++ 
  gi|336253557|ref|YP_004596664.1| 182 IDILDMLVLVGIYVCYIAVI 201
                                       *****************986 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 2e-12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       +vlf++s ++i ++ + +   +e +++s+gi+  ++  ++ +l++ +pEli+ ++ + +   + + +++++s +  +
  gi|336253557|ref|YP_004596664.1| 232 LVLFAFSGAMIFTAVEPFAHGLEDLGESVGIPSFFMIQWIAPLASEAPELIVVVYLVNKARSTAGFNALISSKLNQW 308
                                       799************************************************************************** PP

                                       HTHHHHHHHHHH...BTTSSCECCHHH..HHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigs...lkvdseslkldl..gllllvallllllvlllllplfvpgrltvleglvllllYalylvl 148
                                       +l iG+ +++ s     +  + ++++   +++l++a  ++++ ll+        +++v e+++ll+l++  +++
  gi|336253557|ref|YP_004596664.1| 309 TLLIGTLVVVHSlalGRYGVLAFDFKQaaEIWLTAAQSFFAIGLLIR------FEISVKEAVTLLSLFLSQVFI 376
                                       **********9964323333334443333566666666666666655......9**************988877 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 0.61
                                       THHHHHHH CS
                          Na_Ca_ex  81 lviGlial 88 
                                       +v+Gl+++
  gi|336253557|ref|YP_004596664.1| 403 IVLGLALF 410
                                       22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); 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):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3438.32
//
Query:       gi|336253558|ref|YP_004596665.1|  [L=277]
Description: hypothetical protein Halxa_2161 [Halopiger xanaduensis SH-6]
Scores for 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-06   25.1   0.0    2.1e-05   23.9   0.0    1.5  1  Zip       ZIP Zinc transporter


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 !   23.9   0.0   1.2e-09   2.1e-05      42     118 ..      56     137 ..      52     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.2e-09
                               Zip  42 afavGvllgtaflhLlPealealeesqleeehth......plagllvllGflllllveklltmivekksshkektpk 112
                                         a+Gv ++  f+hLlP ++ea  + +  e  +           l++llGf++++ +e+l++    + +s++  +++
  gi|336253558|ref|YP_004596665.1|  56 SAAGGVSVAYVFVHLLPGVHEAATTLDAYEL-PTptafadHHGYLIALLGFVTFYGLEQLARRSRRSRRSESASSSE 131
                                       5799**********************98773.3355889999********************877773333333333 PP

                               Zip 113 kassss 118
                                       ++s+ +
  gi|336253558|ref|YP_004596665.1| 132 PESTRT 137
                                       333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2107.01
//
Query:       gi|336253559|ref|YP_004596666.1|  [L=161]
Description: hypothetical protein Halxa_2162 [Halopiger xanaduensis SH-6]
Scores for complete 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-06   28.1   1.1    2.2e-06   27.2   1.2    1.4  1  DUF2391   Putative integral membrane protein (DUF2391)
      0.006   15.3   0.0      0.011   14.4   0.0    1.4  1  2HCT      2-hydroxycarboxylate transporter family


Domain annotation for each model (and alignments):
>> DUF2391  Putative integral membrane protein (DUF2391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   1.2   2.4e-10   2.2e-06     142     229 ..      14     102 ..       4     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.4e-10
                           DUF2391 142 ladlgltliGAlllafniAPTeEvvllaaavspvqllalillsLlisylivfeagftgqekreeq.rgifqrflset 217
                                       lad +  ++G  lla +   TeEv  la +++ +q+l ++++   i y+ +++a+ t++ + e++  gi  rf+s  
  gi|336253559|ref|YP_004596666.1|  14 LADSAQQIVGGFLLAGPFVVTEEVWTLAGSMNGWQTLGIVIVVFGIGYGALYAADTTRDVEEEQEvAGIPLRFISLM 90 
                                       567778899*********************************************99877665554267888888888 PP

                           DUF2391 218 vvsYlvsLlvsl 229
                                       vvs+  + l +l
  gi|336253559|ref|YP_004596666.1|  91 VVSFGSVTLLAL 102
                                       888753333333 PP

>> 2HCT  2-hydroxycarboxylate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.2e-06     0.011     181     223 ..     115     157 ..     108     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-06
                              2HCT 181 kdaeellsqlipavllgnivaivvagllkklgkkkpsltGnGk 223
                                       +++ +++ + ++av++g+++++v a++ ++l++k  + +GnG 
  gi|336253559|ref|YP_004596666.1| 115 ESTRTVVETTFTAVSIGSVFSVVGAATADSLFSKPDTNNGNGD 157
                                       6778899999*******************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1186.48
//
Query:       gi|336253560|ref|YP_004596667.1|  [L=275]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-17   61.3   0.1    2.1e-16   60.2   0.0    1.6  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.1e-12   47.1   0.1    7.6e-12   45.3   0.0    1.9  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.4e-09   38.2   0.4    9.3e-09   35.6   0.0    2.2  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.8e-06   26.8   0.0    7.3e-06   25.9   0.0    1.4  1  FR47             FR47-like protein
      4e-06   27.5   0.2    9.8e-06   26.3   0.0    1.7  2  Acetyltransf_3   Acetyltransferase (GNAT) domain
    5.2e-05   23.4   0.0    0.00019   21.6   0.0    1.8  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00011   22.2   0.0    0.00025   21.1   0.0    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
     0.0084   16.2   0.0      0.018   15.1   0.0    1.8  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.019   14.4   0.1      0.029   13.8   0.1    1.2  1  Mcm10            Mcm10 replication factor
       0.02   14.6   0.0      0.046   13.4   0.0    1.6  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
       0.25   11.1   1.6        8.6    6.2   0.4    2.3  2  A2L_zn_ribbon    A2L zinc ribbon domain
       0.26   11.0   0.6       0.47   10.2   0.6    1.5  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit


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 !   60.2   0.0   1.4e-19   2.1e-16      15     116 ..      37     141 ..      14     142 .. 0.78
   2 ?   -2.4   0.0       3.6   5.4e+03      34      35 ..     204     205 ..     170     234 .. 0.56

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 1.4e-19
                                       HHHHHHHHHHHHHHHSTTC.EEEEEEET.....TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHH CS
                    Acetyltransf_1  15 pnedaseeefeesfsleae.gllvaeed.....geliGfisllkipdekggvayieslaVspeyrgkGlGsaLleal 85 
                                       ++e+ s e++++   +++e  llvae +     + ++Gf+ ++  +d  g+ ++i+ l+V+pe+rg+G+G+aL+ea+
  gi|336253560|ref|YP_004596667.1|  37 TDEQLSDEAVADKI-DDDEtVLLVAETGediegEAIAGFVEGRLSDD--GEWGEINWLFVDPEHRGHGIGTALYEAA 110
                                       45555555544442.34443566655555556455************..9*************************** PP

                                       HHHHHHTTESEEEE.EEETTEHHHHHHHHHTT CS
                    Acetyltransf_1  86 eerareegikkivl.aveedndaairlYeklG 116
                                       ++ +r++g++ + + +v e n+  + + e++G
  gi|336253560|ref|YP_004596667.1| 111 ADALRDRGVDHV-CvTVLEANTEGHQFVEQFG 141
                                       *********995.5489999********9999 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.6
                                       EE CS
                    Acetyltransf_1  34 gl 35 
                                       + 
  gi|336253560|ref|YP_004596667.1| 204 TV 205
                                       22 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   5.1e-15   7.6e-12       9     113 ..      32     150 ..      24     163 .. 0.79
   2 ?   -1.0   0.1       1.1   1.6e+03       8      40 ..     180     212 ..     173     225 .. 0.61

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 5.1e-15
                   Acetyltransf_10   9 gietf.kefispealrerieegealllvaeeg.....gkivGvi..elrdgs...hisllfVdpeyrgqGigkaLle 74 
                                       +i+++ +e++s+ea++++i++ e++llvae g     + i+G++  +l+d++   +i  lfVdpe+rg Gig+aL e
  gi|336253560|ref|YP_004596667.1|  32 QIDAItDEQLSDEAVADKIDDDETVLLVAETGediegEAIAGFVegRLSDDGewgEINWLFVDPEHRGHGIGTALYE 108
                                       67788899**********************99333334455777888855556************************ PP

                   Acetyltransf_10  75 aveeeaekdgikl.eltvnasp.yavpfYeklGFkav.geeq 113
                                       a+ ++++++g  +  +tv +++ +  +f e++G +   ++  
  gi|336253560|ref|YP_004596667.1| 109 AAADALRDRGVDHvCVTVLEANtEGHQFVEQFGLEHEaDRRV 150
                                       ******999999996666555549999999999877755554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                   Acetyltransf_10   8 egietf.kefispealrerieegealllvaeegg 40 
                                        ++e+f ++  s+ +l++   +g  +++va +++
  gi|336253560|ref|YP_004596667.1| 180 AEAEEFpETERSDGQLTATT-DGGETVYVARDEE 212
                                       33367766666666677666.5555666666554 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   6.2e-12   9.3e-09       5      71 ..      57     139 ..      52     143 .. 0.63
   2 ?    0.0   0.1      0.79   1.2e+03       4      19 ..     204     218 ..     201     244 .. 0.55

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 6.2e-12
                                       EEEEEET.....TEEEEEEEEEEES....TCTEEEEE-GGGTTSSHHHHHHHHTT.....SEEEEE.EEEE.THHHH CS
                    Acetyltransf_7   5 vfVaedd.....gkivGfialslld....aeitrlaVdpeyrgkGiGraLleaae.....kgiile.qlel.naeka 65 
                                       ++Vae +     + i Gf+   l+d    +ei++l+Vdpe+rg+GiG+aL eaa+     +g+  + ++ l ++++ 
  gi|336253560|ref|YP_004596667.1|  57 LLVAETGediegEAIAGFVEGRLSDdgewGEINWLFVDPEHRGHGIGTALYEAAAdalrdRGVDHVcVTVLeANTEG 133
                                       4566665555544445887777777999999999******************7333455566432233333222244 PP

                                       HHHHHH CS
                    Acetyltransf_7  66 ikfYek 71 
                                       ++f e+
  gi|336253560|ref|YP_004596667.1| 134 HQFVEQ 139
                                       555555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.79
                                       EEEEEEETTEEEEEEE CS
                    Acetyltransf_7   4 evfVaeddgkivGfia 19 
                                       +v+Va+d+++  G++a
  gi|336253560|ref|YP_004596667.1| 204 TVYVARDEEES-GTAA 218
                                       56666655333.3332 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.9e-09   7.3e-06      16      80 ..      78     145 ..      66     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.9e-09
                                       EEE-TT..SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  16 ilrkdg..gelgalqvlpehrrrGlgsrlvkalakeiaerg.ktvllvvvasNtpsirlyeklGfeki 80 
                                       +l  dg  ge+  l v+pehr+ G g+ l +a a +++ rg ++v + v ++Nt+  ++ e+ G e  
  gi|336253560|ref|YP_004596667.1|  78 RLSDDGewGEINWLFVDPEHRGHGIGTALYEAAADALRDRGvDHVCVTVLEANTEGHQFVEQFGLEHE 145
                                       555565569******************************995678889999********999998765 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   6.6e-09   9.8e-06       3     136 ..       2     141 ..       1     143 [. 0.69
   2 ?   -1.4   0.0       2.3   3.5e+03      19      40 ..     162     185 ..     148     239 .. 0.53

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.6e-09
                    Acetyltransf_3   3 lLrplteeDlealfelrsdpevmry..lpepltleeaeewlera.waeeseeegygwaivlkdtg....v.iGsvgl 71 
                                        +r ++++++e++ e++    ++ +   p  + ++ ++e l++   a++ ++++  +++ + +++    +  G+v  
  gi|336253560|ref|YP_004596667.1|   2 EIRDPEPDEAERIQEVVDSSMTTSFrlSPG-QIDAITDEQLSDEaVADKIDDDETVLLVAETGEDiegeAiAGFVEG 77 
                                       6899999999**999655555666764433.3333344444433355444445555666553332334444999988 PP

                    Acetyltransf_3  72 rdleeedeeaelgymla.psfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklG 136
                                       r  ++  e++e+ +++  p+++g+G++t   +a+ +++ ++ g++++++++ + N+   +  e  G
  gi|336253560|ref|YP_004596667.1|  78 RLSDDG-EWGEINWLFVdPEHRGHGIGTALYEAAADAL-RDRGVDHVCVTVLEANTEGHQFVEQFG 141
                                       866655.78******99677******************.7888************98766666666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.3
                    Acetyltransf_3  19 rsdpevmry.lpe..pltleeaeew 40 
                                       +sdp+     lp+  +++++eaee+
  gi|336253560|ref|YP_004596667.1| 162 YSDPDAD-LdLPTdeTEEDAEAEEF 185
                                       5555533.22333122333333333 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.2e-07   0.00019       1     139 [.       3     147 ..       3     154 .. 0.76
   2 ?   -1.0   0.0       1.2   1.8e+03      81     103 ..     204     225 ..     188     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-07
                    Acetyltransf_4   1 iraateeDakeilaiyaeyvvntait....feyevssveefekflealdsekeyvflvae.sdrivGyaylgqfkkr 72 
                                       ir+++++ a++i++++    + t +     ++ ++   +  +   ++ + + e v+lvae  ++i G a +g ++ r
  gi|336253560|ref|YP_004596667.1|   3 IRDPEPDEAERIQEVVDS-SMTTSFRlspgQIDAITDEQLSDEAVADKIDDDETVLLVAEtGEDIEGEAIAGFVEGR 78 
                                       677777777777777764.34444443333333333333333555555577899******999************** PP

                    Acetyltransf_4  73 .akdwkaelsvyla.erdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgi 139
                                          d+++   ++l+ +   +  g+g +l++a  + l+  ++   +  +  +n++  qf +++G e +++
  gi|336253560|ref|YP_004596667.1|  79 lSDDGEWGEINWLFvDPEHRGHGIGTALYEAAADALRDRGVDHVCVTVLEANTEGHQFVEQFGLEHEAD 147
                                       999988855555554999999******************************************887665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                    Acetyltransf_4  81 svylaerdnnkeglgrelidale 103
                                       +vy+a rd ++ g++  +++a e
  gi|336253560|ref|YP_004596667.1| 204 TVYVA-RDEEESGTAAPFYAAYE 225
                                       57887.78888888877777755 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 !   21.1   0.0   1.7e-07   0.00025      26      58 ..      87     119 ..      60     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.7e-07
                   Acetyltransf_CG  26 dfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                       +++  +V++e+rG+Gi+ +L +aa d  r++g 
  gi|336253560|ref|YP_004596667.1|  87 EINWLFVDPEHRGHGIGTALYEAAADALRDRGV 119
                                       78889************************9996 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05     0.018      74     114 ..      86     126 ..       2     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                                       EEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE-- CS
                    Acetyltransf_9  74 agvtgVavapehrgrgvlskLlaraleemreegqplsllfP 114
                                       + + +  v+pehrg+g+ ++L ++a + +r++g+  ++ + 
  gi|336253560|ref|YP_004596667.1|  86 GEINWLFVDPEHRGHGIGTALYEAAADALRDRGVDHVCVTV 126
                                       5677889*************************998776654 PP

>> Mcm10  Mcm10 replication factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.9e-05     0.029     293     325 ..     235     267 ..     226     269 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                             Mcm10 293 FkCakCgkRtvsldrlPskhCsnCgeskwerdg 325
                                       F Ca+Cg   +sld++   +C  Cg+s+ +r g
  gi|336253560|ref|YP_004596667.1| 235 FYCANCGSLDISLDNMDRLECGDCGNSHASRSG 267
                                       89************************9988876 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.1e-05     0.046      85     141 ..      91     146 ..      80     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
                                       EESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                    Acetyltransf_8  85 ligeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                                       l  ++e+rg+g++tal +a ++ l +d+++++v+v     N++ ++++e+ G e+e 
  gi|336253560|ref|YP_004596667.1|  91 LFVDPEHRGHGIGTALYEAAADAL-RDRGVDHVCVTVLEANTEGHQFVEQFGLEHEA 146
                                       555899*************99876.666************************99875 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 ?    6.2   0.4    0.0058       8.6      14      29 ..     228     242 ..     225     243 .. 0.88
   2 ?    3.7   0.0     0.035        52      22      32 ..     253     263 ..     247     264 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0058
                     A2L_zn_ribbon  14 ilnseqgylvCieCga 29 
                                       ++ seq++ +C +Cg+
  gi|336253560|ref|YP_004596667.1| 228 DF-SEQFGFYCANCGS 242
                                       68.9***********7 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.035
                     A2L_zn_ribbon  22 lvCieCgasfp 32 
                                       l C +Cg+s++
  gi|336253560|ref|YP_004596667.1| 253 LECGDCGNSHA 263
                                       6699****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 ?   10.2   0.6   0.00032      0.47       2      24 ..     236     259 ..     235     262 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00032
                                       B-SSS--.B----SSS----SSS- CS
                    DNA_RNApol_7kD   2 iCgeCga.evslkkgdpiRCkeCG 24 
                                        C++Cg+ + sl++ d + C +CG
  gi|336253560|ref|YP_004596667.1| 236 YCANCGSlDISLDNMDRLECGDCG 259
                                       5****987899************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 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:                        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):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2027.15
//
Query:       gi|336253561|ref|YP_004596668.1|  [L=76]
Description: hypothetical protein Halxa_2164 [Halopiger xanaduensis SH-6]
Scores for 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:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 567.56
//
Query:       gi|336253562|ref|YP_004596669.1|  [L=153]
Description: AsnC family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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   49.3   0.0    6.3e-13   48.5   0.0    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    2.8e-11   42.8   0.3    6.8e-11   41.6   0.0    1.7  2  HTH_24          Winged helix-turn-helix DNA-binding
    6.2e-08   32.4   0.3    3.5e-07   30.0   0.1    2.1  2  HTH_5           Bacterial regulatory protein, arsR family
    2.6e-07   30.5   0.0      1e-06   28.6   0.0    2.0  2  HTH_11          HTH domain
    6.6e-06   25.9   0.1    9.7e-06   25.3   0.1    1.3  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.2e-05   25.3   0.6    2.7e-05   24.1   0.1    1.9  1  HTH_20          Helix-turn-helix domain
    2.9e-05   23.6   0.1    7.8e-05   22.2   0.1    1.7  1  GntR            Bacterial regulatory proteins, gntR family
      4e-05   23.3   0.1    0.00026   20.7   0.0    2.1  2  HTH_DeoR        DeoR-like helix-turn-helix domain
    9.4e-05   22.5   0.0    0.00052   20.1   0.0    1.9  2  HTH_28          Helix-turn-helix domain
    0.00019   21.4   0.0    0.00033   20.6   0.0    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00039   20.3   0.0    0.00073   19.4   0.0    1.3  1  MarR_2          MarR family
    0.00067   19.5   0.0     0.0012   18.6   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00086   19.1   0.1      0.002   17.9   0.1    1.6  1  HTH_10          HTH DNA binding domain
     0.0011   18.9   0.0     0.0039   17.1   0.0    1.9  2  MarR            MarR family
     0.0017   18.1   0.1     0.0038   17.0   0.1    1.6  1  HTH_IclR        IclR helix-turn-helix domain
     0.0027   17.8   0.0     0.0061   16.7   0.0    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0029   18.0   0.1      0.006   17.0   0.1    1.8  1  HTH_40          Helix-turn-helix domain
     0.0039   16.8   0.1     0.0066   16.1   0.1    1.6  1  E3_UFM1_ligase  E3 UFM1-protein ligase 1
     0.0067   16.2   0.0       0.13   12.0   0.0    2.2  2  HTH_38          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.034   14.2   0.0    1.8  1  HTH_7           Helix-turn-helix domain of resolvase
      0.011   15.5   0.0      0.025   14.4   0.0    1.6  1  HTH_23          Homeodomain-like domain
      0.015   14.8   0.1       0.22   11.1   0.0    2.2  2  GerE            Bacterial regulatory proteins, luxR family
      0.031   14.9   0.1       0.13   12.9   0.0    1.9  2  Mga             Mga helix-turn-helix domain
      0.034   13.7   0.0      0.064   12.9   0.0    1.5  1  HTH_50          Helix-turn-helix domain
      0.035   13.5   0.0      0.067   12.6   0.0    1.5  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.036   14.6   0.1       0.13   12.8   0.1    1.9  1  HTH_27          Winged helix DNA-binding domain
      0.038   14.3   0.1       0.14   12.5   0.0    2.0  1  Rrf2            Transcriptional regulator
      0.074   12.9   0.1       0.26   11.1   0.0    1.8  2  DUF742          Protein of unknown function (DUF742)
      0.081   12.9   0.0       0.13   12.3   0.0    1.3  1  HTH_36          Helix-turn-helix domain
      0.087   12.8   0.3        0.2   11.6   0.3    1.6  1  GYD             GYD domain
      0.093   12.4   0.1       0.53   10.0   0.0    2.0  2  HTH_41          Helix-turn-helix domain
       0.11   12.5   0.0       0.28   11.2   0.0    1.7  1  HTH_1           Bacterial regulatory helix-turn-helix protein
       0.12   12.4   0.0        0.2   11.7   0.0    1.4  1  HTH_29          Winged helix-turn helix
       0.16   11.7   0.0       0.32   10.7   0.0    1.5  1  Sigma70_r4_2    Sigma-70, region 4


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 !   48.5   0.0   1.2e-15   6.3e-13       3      75 .]      71     139 ..      69     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1.2e-15
                                       EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg   3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                       ++ e+++   l e+ e l+e+++ +++y vtGdyd ++  +++d++++++ +++ l + p++ +++ts+vl++
  gi|336253562|ref|YP_004596669.1|  71 LKAEGNA---LPEITETLREHEQMISVYEVTGDYDVIAVGKFKDTDDMNDQIKQ-LLTDPDINQSNTSVVLNQ 139
                                       5667666...9*******************************************.****************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 !   41.6   0.0   1.3e-13   6.8e-11       7      48 .]       9      50 ..       4      50 .. 0.93
   2 ?   -1.8   0.0       4.6   2.4e+03      11      21 ..     121     131 ..     119     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.3e-13
                            HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++ ++L  n+r s r LAe+l++S++tv+ +l  LeeeG+I+
  gi|336253562|ref|YP_004596669.1|  9 DLVNELLGNGRASLRSLAEELDVSVTTVSNHLSDLEEEGVIE 50
                                      6789*************************************7 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.6
                            HTH_24  11 lLqknprisqr 21 
                                        L  +p+i+q+
  gi|336253562|ref|YP_004596669.1| 121 QLLTDPDINQS 131
                                       67779999997 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 !   30.0   0.1   6.6e-10   3.5e-07      11      46 ..      14      50 ..       8      50 .. 0.86
   2 ?   -0.5   0.0       2.1   1.1e+03      21      36 ..     122     137 ..     118     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 6.6e-10
                                      HTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 11 Lae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      L   g ++   laeel++s  tvS HL+ L+e+G++e
  gi|336253562|ref|YP_004596669.1| 14 LLGnGRASLRSLAEELDVSVTTVSNHLSDLEEEGVIE 50
                                      44448889999***********************996 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.1
                                       HHHHHTS-HHHHHHHH CS
                             HTH_5  21 laeelglsqstvShHL 36 
                                       l  + +++qs++S  L
  gi|336253562|ref|YP_004596669.1| 122 LLTDPDINQSNTSVVL 137
                                       5555579999999655 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.9e-09     1e-06      13      44 ..      17      48 ..       8      63 .. 0.82
   2 ?   -2.0   0.0       6.6   3.5e+03       5      19 ..      81      95 ..      80      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.9e-09
                            HTH_11 13 rgpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      +g  s   LAeeL+vS +tv +++ +Lee gv
  gi|336253562|ref|YP_004596669.1| 17 NGRASLRSLAEELDVSVTTVSNHLSDLEEEGV 48
                                      44579999***********************3 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.6
                            HTH_11  5 ilelLleargpisge 19
                                      i e L+e+++ is  
  gi|336253562|ref|YP_004596669.1| 81 ITETLREHEQMISVY 95
                                      567798888889976 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 !   25.3   0.1   1.8e-08   9.7e-06       3      36 ..       5      38 ..       4      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.8e-08
                     HTH_AsnC-type  3 eiDrkILeaLqedaRisyaeLAervGlSestvlr 36
                                      ++D  ++++L  ++R+s + LAe++ +S +tv +
  gi|336253562|ref|YP_004596669.1|  5 HLDADLVNELLGNGRASLRSLAEELDVSVTTVSN 38
                                      589*****************************86 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   5.2e-08   2.7e-05      19      58 ..      14      53 ..       5      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.2e-08
                                      HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      L +++ +++  lae+ld+s +t+s+HL  Lee g +e+ +
  gi|336253562|ref|YP_004596669.1| 14 LLGNGRASLRSLAEELDVSVTTVSNHLSDLEEEGVIEGYT 53
                                      5588889999***************************876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   1.5e-07   7.8e-05       6      55 ..       3      50 ..       1      51 [. 0.87

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.5e-07
                                      HHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR  6 yerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                      ye+L++d+++  l  G +  s r+La+e++Vs ttv   L+ Le+eg++e
  gi|336253562|ref|YP_004596669.1|  3 YEHLDADLVNELLGNGRA--SLRSLAEELDVSVTTVSNHLSDLEEEGVIE 50
                                      899999999966666655..79*************************996 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 !   20.7   0.0   4.9e-07   0.00026       4      44 ..       9      49 ..       7      51 .. 0.93
   2 ?   -0.2   0.0       1.6   8.4e+02       4      26 ..      80     103 ..      78     104 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.9e-07
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                       ++  l   g  s+  l+e+l+vS +T+ + L+ Lee+g++
  gi|336253562|ref|YP_004596669.1|  9 DLVNELLGNGRASLRSLAEELDVSVTTVSNHLSDLEEEGVI 49
                                      578889999******************************98 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
                          HTH_DeoR   4 qilellkqqg.klsveelvellgv 26 
                                       +i+e l+++   +sv e++  ++v
  gi|336253562|ref|YP_004596669.1|  80 EITETLREHEqMISVYEVTGDYDV 103
                                       688888887515788888877776 PP

>> HTH_28  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   9.8e-07   0.00052       6      46 ..      11      54 ..       8      55 .. 0.89
   2 ?   -0.1   0.0         2   1.1e+03       5      20 ..      68      83 ..      66      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 9.8e-07
                            HTH_28  6 iklla.aGh.svreaArelgisrrtvyrWikryeegG.iagLvp 46
                                      + +l+ +G+ s r +A+el +s +tv+  ++ +ee+G i+g  p
  gi|336253562|ref|YP_004596669.1| 11 VNELLgNGRaSLRSLAEELDVSVTTVSNHLSDLEEEGvIEGYTP 54
                                      778888999****************************6688766 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2
                            HTH_28  5 iikllaaGhsvreaAr 20
                                      i++l a+G++ +e+ +
  gi|336253562|ref|YP_004596669.1| 68 IMQLKAEGNALPEITE 83
                                      7788889998888755 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 !   20.6   0.0   6.2e-07   0.00033      23      53 ..      21      51 ..       8      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.2e-07
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisr 53
                                      + + lA+ l ++  tvs  ls+L++eg+i+ 
  gi|336253562|ref|YP_004596669.1| 21 SLRSLAEELDVSVTTVSNHLSDLEEEGVIEG 51
                                      5678*************************94 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.4e-06   0.00073       7      52 ..       7      50 ..       3      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.4e-06
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +a++ ++L  +++   + + la++l++s  +vs++l +L++ G +e
  gi|336253562|ref|YP_004596669.1|  7 DADLVNELLGNGR--ASLRSLAEELDVSVTTVSNHLSDLEEEGVIE 50
                                      5789999999998..9***************************998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.4e-06    0.0012      16      53 ..      13      50 ..       4      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-06
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                       Ll +g+a+ + +aeel+v+ ++v + L+ Le+ G++e
  gi|336253562|ref|YP_004596669.1| 13 ELLGNGRASLRSLAEELDVSVTTVSNHLSDLEEEGVIE 50
                                      6999*******************************998 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   3.8e-06     0.002      23      48 ..      19      44 ..      18      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.8e-06
                            HTH_10 23 rvtlkeLAkelGIskstlsehLrkae 48
                                      r++l++LA+el++s +t+s+hL+  e
  gi|336253562|ref|YP_004596669.1| 19 RASLRSLAEELDVSVTTVSNHLSDLE 44
                                      799*******************9766 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.4e-06    0.0039      15      48 ..      17      50 ..       9      54 .. 0.91
   2 ?   -1.6   0.0       5.1   2.7e+03      28      40 ..     127     139 ..     118     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.4e-06
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      +g +s+  La+ l vs +tv++ l  Le++G ie
  gi|336253562|ref|YP_004596669.1| 17 NGRASLRSLAEELDVSVTTVSNHLSDLEEEGVIE 50
                                      5788999************************997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.1
                                       TS-HHHHHHHHHH CS
                              MarR  28 gvskstvtrvldr 40 
                                        +++s+++ vl +
  gi|336253562|ref|YP_004596669.1| 127 DINQSNTSVVLNQ 139
                                       6889999988876 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 !   17.0   0.1   7.2e-06    0.0038      17      49 ..      18      50 ..      13      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.2e-06
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      ++ +l+ lA++++++ +tv+++L+ L+e+G +e
  gi|336253562|ref|YP_004596669.1| 18 GRASLRSLAEELDVSVTTVSNHLSDLEEEGVIE 50
                                      4568**************************886 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 !   16.7   0.0   1.1e-05    0.0061      23      52 ..      20      49 ..      12      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGyv 52
                                      ++   lae+L+vs  +Vs  l+ Le++G +
  gi|336253562|ref|YP_004596669.1| 20 ASLRSLAEELDVSVTTVSNHLSDLEEEGVI 49
                                      67789**********************966 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.1e-05     0.006      13      78 ..      20      87 ..      12     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-05
                            HTH_40 13 lsieeIAkerglkesTIegHLaelieegeeidlerlvseeeekeIeeaiekvgsek..lkpikealpe 78
                                       s+   A+e  ++++T+ +HL +l eeg    ++ +v+ +      +ai +++ e   l +i e l e
  gi|336253562|ref|YP_004596669.1| 20 ASLRSLAEELDVSVTTVSNHLSDLEEEGVIEGYTPIVDYDAVGYDVTAIMQLKAEGnaLPEITETLRE 87
                                      689999*********************95333444444433333333333433322337777777654 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 !   16.1   0.1   1.3e-05    0.0066      51      97 ..       1      46 [.       1     106 [. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                    E3_UFM1_ligase 51 lTpeqLekeikdelekagGRvnlvdLakilnvdlshiekkaeeivke 97
                                      +T e+L+ ++ +el  + GR +l  La+ l+v ++ ++++++++ +e
  gi|336253562|ref|YP_004596669.1|  1 MTYEHLDADLVNELLGN-GRASLRSLAEELDVSVTTVSNHLSDLEEE 46
                                      79**************9.9**********************999544 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00025      0.13      20      41 ..      18      40 ..      12      41 .. 0.87
   2 ?    1.9   0.0      0.37     2e+02      10      33 ..      65      88 ..      63      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                            HTH_38 20 G.lslreIArrLgrspsTIsREl 41
                                      G  slr  A +L++s +T+s++l
  gi|336253562|ref|YP_004596669.1| 18 GrASLRSLAEELDVSVTTVSNHL 40
                                      5579****************987 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.37
                            HTH_38 10 ReeIerllaeGlslreIArrLgrs 33
                                         I +l aeG  l eI   L  +
  gi|336253562|ref|YP_004596669.1| 65 VTAIMQLKAEGNALPEITETLREH 88
                                      56899*********9998777655 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 ?   14.2   0.0   6.5e-05     0.034       9      38 ..       5      36 ..       2      37 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.5e-05
                                      H.HHGGGGSSTTTT.--STTTSSSS---SSSS CS
                             HTH_7  9 n.dinrvvkLleeG.isiskIAkevnisRsTv 38
                                      + d + v +Ll +G  s + +A+e+++s++Tv
  gi|336253562|ref|YP_004596669.1|  5 HlDADLVNELLGNGrASLRSLAEELDVSVTTV 36
                                      55899**************************8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.7e-05     0.025      17      46 ..      19      49 ..       9      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.7e-05
                            HTH_23 17 GlsvreIAreLgvsrrTvyrwlkryreeG.l 46
                                      ++s r  A+eL+vs  Tv++ l+  +eeG +
  gi|336253562|ref|YP_004596669.1| 19 RASLRSLAEELDVSVTTVSNHLSDLEEEGvI 49
                                      6789999******************99*955 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00043      0.22      22      40 ..      24      42 ..      17      45 .. 0.88
   2 ?    1.5   0.0       0.4   2.1e+02      10      36 ..      68      94 ..      66      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00043
                                      HHHHHHTS-HHHHHHHHHH CS
                              GerE 22 eIAeelniSekTVkvhksn 40
                                        Aeel++S +TV++h+s 
  gi|336253562|ref|YP_004596669.1| 24 SLAEELDVSVTTVSNHLSD 42
                                      569*************986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.4
                                      HHHHHCTTS-HHHHHHHHTS-HHHHHH CS
                              GerE 10 vLrllaeGksnkeIAeelniSekTVkv 36
                                      +++l aeG+   eI e l   e+ ++v
  gi|336253562|ref|YP_004596669.1| 68 IMQLKAEGNALPEITETLREHEQMISV 94
                                      89***********99988766665555 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   0.0   0.00024      0.13      18      56 ..       7      45 ..       2      46 .. 0.89
   2 ?   -1.5   0.0       7.3   3.8e+03      14      23 ..     129     138 ..     114     150 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00024
                                      HHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
                               Mga 18 kyqllkflfeeeevsieelaqelyiSestlkrkikelnk 56
                                      +  l+  l+ + + s+ +la+el +S +t+ +++ +l++
  gi|336253562|ref|YP_004596669.1|  7 DADLVNELLGNGRASLRSLAEELDVSVTTVSNHLSDLEE 45
                                      56789999**************************99986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 7.3
                                       HHSHHHHHHH CS
                               Mga  14 keslkyqllk 23 
                                       ++s++  +l 
  gi|336253562|ref|YP_004596669.1| 129 NQSNTSVVLN 138
                                       3344444444 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.064      10      44 ..       5      40 ..       2      42 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            HTH_50 10 efErelikkayek.YpStRklAkrLGvShtaiankl 44
                                      + +++l+++++ +   S R lA+ L vS t++ n l
  gi|336253562|ref|YP_004596669.1|  5 HLDADLVNELLGNgRASLRSLAEELDVSVTTVSNHL 40
                                      56666777776552469***************9976 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 ?   12.6   0.0   0.00013     0.067      22      46 ..      13      38 ..       8      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                      HTH_Tnp_ISL3 22 ellles.rsvkavArqlgvSwtTVwr 46
                                      ell ++ +s ++ A++l+vS tTV +
  gi|336253562|ref|YP_004596669.1| 13 ELLGNGrASLRSLAEELDVSVTTVSN 38
                                      6899999*****************86 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 ?   12.8   0.1   0.00024      0.13      15      49 ..      16      50 ..       6      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00024
                            HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLve 49
                                       ++r++l+ l++ l+v+ +++s+ l+ L+e G++e
  gi|336253562|ref|YP_004596669.1| 16 GNGRASLRSLAEELDVSVTTVSNHLSDLEEEGVIE 50
                                      47999***************************995 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00027      0.14      24      56 ..      18      50 ..      10      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00027
                                      C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvk 56
                                      + +s++++ae+ ++s + ++  l+ L+++g+++
  gi|336253562|ref|YP_004596669.1| 18 GRASLRSLAEELDVSVTTVSNHLSDLEEEGVIE 50
                                      45899**************************98 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00049      0.26      55      96 ..      19      60 ..       7      75 .. 0.80
   2 ?   -0.6   0.0       2.1   1.1e+03      39      62 ..      75      98 ..      64     103 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00049
                            DUF742 55 plsVaelaAelklPvgvvrvLlsdLldaglltvrapvtdraa 96
                                      + s   la el++ v++v   lsdL + g ++ ++p++d  a
  gi|336253562|ref|YP_004596669.1| 19 RASLRSLAEELDVSVTTVSNHLSDLEEEGVIEGYTPIVDYDA 60
                                      677788999***************************999433 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.1
                            DUF742 39 arlqpehrailrLcreplsVaela 62
                                       ++ pe ++ lr  +++ sV e+ 
  gi|336253562|ref|YP_004596669.1| 75 GNALPEITETLREHEQMISVYEVT 98
                                      445666666666666666666665 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00024      0.13      26      54 ..      20      48 ..      16      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00024
                            HTH_36 26 psqetlakrlglsknTvsraikeLeqlGy 54
                                      +s + la+ l +s+ Tvs+++  Le+ G 
  gi|336253562|ref|YP_004596669.1| 20 ASLRSLAEELDVSVTTVSNHLSDLEEEGV 48
                                      78999********************9886 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00038       0.2      13      61 ..      69     115 ..      60     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00038
                               GYD  13 kglkdsperreeakealveslGgkleslyatlGeyDvvvivEapDdeta 61 
                                        +lk  ++   e+ e+l ++   ++ s+y ++G+yDv+++  + D + +
  gi|336253562|ref|YP_004596669.1|  69 MQLKAEGNALPEITETL-RE-HEQMISVYEVTGDYDVIAVGKFKDTDDM 115
                                       55666666666666666.33.35799***************99998876 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0     0.001      0.53       8      36 ..      21      49 ..      15      51 .. 0.90
   2 ?   -0.3   0.0       1.7     9e+02       2      17 ..      74      89 ..      73      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                            HTH_41  8 tIeelakeleLSvGlvQkALklLeddkai 36
                                      +  +la+el++Sv +v   L  Le++++i
  gi|336253562|ref|YP_004596669.1| 21 SLRSLAEELDVSVTTVSNHLSDLEEEGVI 49
                                      5679************************9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.7
                            HTH_41  2 vGdRlktIeelakele 17
                                      +G+ l+ I+e   e e
  gi|336253562|ref|YP_004596669.1| 74 EGNALPEITETLREHE 89
                                      6999999999877655 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 ?   11.2   0.0   0.00053      0.28      20      40 ..      26      46 ..      18      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00053
                                      HHHHTS-HHHHHHHHHHHHHH CS
                             HTH_1 20 AeeLglsqpavsrqikrLEee 40
                                      AeeL +s  +vs ++++LEee
  gi|336253562|ref|YP_004596669.1| 26 AEELDVSVTTVSNHLSDLEEE 46
                                      9******************96 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00038       0.2      13      41 ..      20      48 ..      10      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00038
                            HTH_29 13 stvsqiAkllglsrrtvyrwlkrfeegGl 41
                                       + + +A+ l++s +tv ++l + ee+G+
  gi|336253562|ref|YP_004596669.1| 20 ASLRSLAEELDVSVTTVSNHLSDLEEEGV 48
                                      36899***********************4 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 ?   10.7   0.0    0.0006      0.32      32      48 ..      25      41 ..      20      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0006
                                      HHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 32 IAellgisegtVksrls 48
                                       Ae+l++s++tV ++ls
  gi|336253562|ref|YP_004596669.1| 25 LAEELDVSVTTVSNHLS 41
                                      6**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1161.26
//
Query:       gi|336253563|ref|YP_004596670.1|  [L=184]
Description: phosphoribosyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-19   67.5   1.7    1.1e-18   67.2   1.7    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00014   21.4   0.1    0.00022   20.8   0.1    1.2  1  UPRTase       Uracil phosphoribosyltransferase
     0.0066   16.0   0.3      0.011   15.2   0.3    1.4  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 !   67.2   1.7   1.9e-22   1.1e-18      17     135 ..      40     161 ..      34     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.9e-22
                                       ETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE............EE----TTSE CS
                      Pribosyltran  17 rlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes....rlledpagkk 89 
                                       +   e  ++ +   d +v+++  G+ +a++l+ + ++pl+++rk+ y  +g  + ++     s        + +g +
  gi|336253563|ref|YP_004596670.1|  40 EVVVEVMRTVDLDVDKIVAPEAMGIHLATALSLQTDIPLVVIRKREYGLEGEVSLHQETGY-SesemYINDIEDGDR 115
                                       556666777778899********************************99998888764433.24778889999**** PP

                                       EEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHH CS
                      Pribosyltran  90 VliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdk 135
                                       V+iVDD+l+tGgTl a++ +L e g+e+v i+v+++k      +d 
  gi|336253563|ref|YP_004596670.1| 116 VVIVDDMLSTGGTLAAICGALDEIGAEIVDIVVVMRKVGESALDDT 161
                                       ***********************************66554444433 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   3.6e-08   0.00022     110     172 ..     105     164 ..      88     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.6e-08
                           UPRTase 110 eyynkLPkki.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaee 172
                                       +y+n    +i + ++v+++D +++TGg++aa++  L e g++  +I+v+   + e++++   +e
  gi|336253563|ref|YP_004596670.1| 105 MYIN----DIeDGDRVVIVDDMLSTGGTLAAICGALDEIGAEIVDIVVVMRKVGESALDDTEYE 164
                                       3443....4445689***********************99998888888766666666655555 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   1.9e-06     0.011     118     155 ..     110     148 ..      99     178 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-06
                          PRTase_2 118 laaakelvLvDDEistGktalnliralqeklpr.kryvv 155
                                       +++ +++v+vDD +stG t+++++ al e   +   +vv
  gi|336253563|ref|YP_004596670.1| 110 IEDGDRVVIVDDMLSTGGTLAAICGALDEIGAEiVDIVV 148
                                       566789*******************99988766434333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1399.26
//
Query:       gi|336253564|ref|YP_004596671.1|  [L=470]
Description: uracil-xanthine permease [Halopiger xanaduensis SH-6]
Scores for 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-86  290.2  43.2    2.8e-86  289.7  43.2    1.2  1  Xan_ur_permease  Permease family
  ------ inclusion threshold ------
       0.15   11.8   0.2       0.27   11.0   0.2    1.4  1  Per1             Per1-like family


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 !  289.7  43.2   3.1e-90   2.8e-86       2     388 ..      23     407 ..      22     408 .. 0.95

  Alignments for each domain:
  == domain 1  score: 289.7 bits;  conditional E-value: 3.1e-90
                                       HHHHHHHHHHHHHHHHHHHHHHTTTS-..........H.HHHHHHHHHHHHHHHH...HTTT-----EEE-GGGHHH CS
                   Xan_ur_permease   2 qllllglQhllamfaalvvvPllvgdalgl.aeelrqlisatllasGiatllqll...ifgirlpillgssfafvta 74 
                                       + +llglQh+++m++ +  v+++v+  +gl  +++++++++ ll+sG+at++q+    ++g rlpi++gssf+fv+ 
  gi|336253564|ref|YP_004596671.1|  23 KSILLGLQHVAVMIVPATAVAYVVAGGVGLsPADTAYIVQMVLLFSGLATMIQAYtvgPVGARLPIVMGSSFTFVG- 98 
                                       689************************999888899*******************99*******************. PP

                                       HHGGG-....HHHHHHHHHHHHHHHHHHH.HHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHTTSS-..B CS
                   Xan_ur_permease  75 lmialGsaedieialagllgallvagvlf.ilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkvgggwaav 150
                                        +i +G     ++++a+++ga+lv g+++  li+  +   r+ +++pP+vtg vv++iGl l+++a++ ++gg+   
  gi|336253564|ref|YP_004596671.1|  99 ASISIG----ADYGMAAVFGAILVTGFVVeGLIGWQFK--RIKPFFPPLVTGLVVVIIGLYLIPVAMDYAAGGA--- 166
                                       999999....5**************9876156666555..9********************************6... PP

                                       TT.B---HHHHHHHHHHHHHHHHHHHSSSTTTTTHHHHHHHHHHHHHHHHHH......HTTSSHHHHS-SS------ CS
                   Xan_ur_permease 151 egltvvslkllllavvvllvilllsvflkglfsqlpiLigiiagwllalfmg......ivnlspevseapwfqlpsp 221
                                       ++  +++l +++la  vl++++ l+++++g+ ++l++L++i++g+++a++++       v++sp v ea+w+ lp+p
  gi|336253564|ref|YP_004596671.1| 167 DAADFGALHNIGLAALVLAIAVGLNMLTRGVTRLLSVLVAIAVGYAVAVALTfatgleLVDFSP-VGEAAWVALPKP 242
                                       66789******************************************99988777788899999.************ PP

                                       -----HH..H.HHHHTHHH.HHHHHHHHHHHHHHHHHHTS-TIIIIIHHHHHHHHHHHHHHHHHHT---EEE-HHHH CS
                   Xan_ur_permease 222 lkfgtplfnlgliltvlavalvavvesvGdiravakvvgrslkpkpdlrralladGlatllsgllGalpvttyaeni 298
                                       ++fg   f++ +i+t+ +++lv+ +e+vGd+ +v    gr+++ + + r +l+ dGl + +++++Ga+p t++++n+
  gi|336253564|ref|YP_004596671.1| 243 THFGFE-FEPIAIATFAVLFLVSAMETVGDMSGVTAAEGRNPT-NEEFRGGLFNDGLLSSVGAVFGAFPITSFSQNV 317
                                       *****9.9*******************************9999.9******************************** PP

                                       HHHHHHTB--HHHHHHHHHHHHHHT--HHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHH.TTS-SHHHHHHHH CS
                   Xan_ur_permease 299 GvvaltkvasrrvmvtagvilillglipklaallssIPepvlgGvllvvfgmiaasgvsnlqt.vdldsarnlliva 374
                                       G+v  t+v sr v+ ++gv+l +lgl+pk++a +++IP++v gG+ l++ gm+aasg++ + t +dld +rn+++va
  gi|336253564|ref|YP_004596671.1| 318 GIVNFTGVMSRHVVGIGGVFLAVLGLSPKVGAAVTTIPSAVFGGAVLLMAGMVAASGFRLIVThADLD-RRNTVVVA 393
                                       ***********************************************************776526788.******** PP

                                       HHHHHHHH-----S CS
                   Xan_ur_permease 375 vslvlGlgvatvpe 388
                                       vsl+lGlg+at pe
  gi|336253564|ref|YP_004596671.1| 394 VSLGLGLGIATTPE 407
                                       **********9986 PP

>> Per1  Per1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2     3e-05      0.27     153     227 ..     144     232 ..      91     237 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3e-05
                              Per1 153 lalyllHvlyLllvrfdYtYnmaanvvvgllqnllwlllsl......ktl........akklvsl.....klillvl 210
                                        +++++  lyL  v +dY+   a    +g l+n+ +++l+l      + +         +    +     + +++++
  gi|336253564|ref|YP_004596671.1| 144 GLVVVIIGLYLIPVAMDYAAGGADAADFGALHNIGLAALVLaiavglN-MltrgvtrlLS----VlvaiaVGYAVAV 215
                                       344444556777778899988888888999999888888774454441.04444332222....1222336667888 PP

                              Per1 211 llllamllEllDFppll 227
                                       +l++a+ lEl+DF p+ 
  gi|336253564|ref|YP_004596671.1| 216 ALTFATGLELVDFSPVG 232
                                       999************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3431.27
//
Query:       gi|336253565|ref|YP_004596672.1|  [L=275]
Description: 3-oxoacyl-(acyl-carrier-protein) reductase [Halopiger xanaduensis SH-6]
Scores for 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-60  204.0   1.7    7.3e-59  199.2   1.7    2.0  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    1.3e-51  174.9   0.4    1.5e-51  174.6   0.4    1.0  1  adh_short       short chain dehydrogenase
    7.8e-14   52.0   0.2      1e-13   51.6   0.2    1.1  1  KR              KR domain
    3.9e-07   29.8   0.3    8.2e-07   28.7   0.2    1.5  2  Epimerase       NAD dependent epimerase/dehydratase family
    0.00071   18.7   0.1    0.00099   18.2   0.1    1.2  1  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase
  ------ inclusion threshold ------
      0.011   14.8   0.5      0.015   14.4   0.5    1.2  1  RmlD_sub_bind   RmlD substrate binding domain
      0.033   13.6   0.0       0.05   13.0   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.038   13.9   1.2      0.054   13.4   1.2    1.4  1  NAD_binding_10  NAD(P)H-binding
      0.065   12.6   0.0      0.077   12.4   0.0    1.2  1  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase
      0.073   12.2   0.0      0.095   11.9   0.0    1.2  1  NAD_binding_4   Male sterility protein


Domain annotation for each model (and alignments):
>> 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 !  199.2   1.7   4.1e-62   7.3e-59       1     234 []      17     273 ..      17     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 199.2 bits;  conditional E-value: 4.1e-62
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH..HH....HHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea..kk....rveelaeelgae.vlecDVtdeeqvealveevvekfgkl 70 
                                       G asgIGr++A ++ e+Ga+v+++d++ee   +     + e++++++g++ ++e+DVtd+++v+a+ve++ ++fg++
  gi|336253565|ref|YP_004596672.1|  17 GGASGIGREVATRFGEAGATVIVADVREEPkrEGestpTHERIEDAGGRAtFVETDVTDPDDVAAVVEAA-REFGGV 92 
                                       669************************9984333111133455555554446**************9986.57**** PP

                                       EEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC..CEEEEEEEGGGTSBSTTTTHHHHH CS
                      adh_short_C2  71 Dilvnnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg..gsivnlssvgaervvpnynaygaa 144
                                       D++vnna+i ++  g++let+ e fdr l++n++++++ ++aa++ ++++   g +vn++s+++e +  ++++y  +
  gi|336253565|ref|YP_004596672.1|  93 DVMVNNAAIYRH--GSVLETDLETFDRLLEINVQGVLAGTRAAARdMLARDepGTVVNTASISSEYAQLGHSMYDSS 167
                                       ************..*******************************97776679************************ PP

                                       HHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT..........HHH.......HHHHHHHHSTTSS-B-H CS
                      adh_short_C2 145 KaalealtrylAvelgpkgiRvNavspgpikTlaasgikg..........fde.......lleelearaplgrlgtp 204
                                       K+a+  ltr +A el+p+ +RvNav+pg++kT   ++ ++            +        + e+   +p+gr+++ 
  gi|336253565|ref|YP_004596672.1| 168 KGAVMMLTRVAALELAPYDVRVNAVAPGIVKTAFGAEGPDrsrdeglileD-AdvpdpleREGEIGTDIPMGRMAES 243
                                       ********************************9955544434333333321.0333333355678899********* PP

                                       HHHHHHHHHHCSGGGTT--SEEEEESTTGG CS
                      adh_short_C2 205 eevaeaalfLasdeasyitGqtlvvDgGlt 234
                                       e++a  +lfLasd+a+y+tG+ l+vDgG++
  gi|336253565|ref|YP_004596672.1| 244 EDIAGPYLFLASDDAEYMTGHLLYVDGGYS 273
                                       ****************************96 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.6   0.4   8.6e-55   1.5e-51       2     188 ..      12     203 ..      11     209 .. 0.93

  Alignments for each domain:
  == domain 1  score: 174.6 bits;  conditional E-value: 8.6e-55
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHH.....HHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHH CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseeklee.....vakelkeegakalaiqvDvtdreevealvekavk 73 
                                       +++vtG++sGIGr++a ++ ++Ga+v+v+d +ee+ +e     +++ ++++g +a+++++Dvtd ++v a+ve+a  
  gi|336253565|ref|YP_004596672.1|  12 TAIVTGGASGIGREVATRFGEAGATVIVADVREEPKREgestpTHERIEDAGGRATFVETDVTDPDDVAAVVEAA-R 87 
                                       79****************************99998776222224556666699*******************999.8 PP

                                       HHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBHHH CS
                         adh_short  74 klgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagvaaY 149
                                       ++g++dv+vnNA+i + g++ e++ e+++r++e+N++gv+  tra+++ ml + + G++vn++S+ ++++  g ++Y
  gi|336253565|ref|YP_004596672.1|  88 EFGGVDVMVNNAAIYRHGSVLETDLETFDRLLEINVQGVLAGTRAAARDMLaRDEPGTVVNTASISSEYAQLGHSMY 164
                                       9**************************************************88999********************* PP

                                       HHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHH CS
                         adh_short 150 sAsKaavagltrslakelaptgirvnavaPGlvdTdmak 188
                                        +sK+av +ltr +a elap+ +rvnavaPG+v+T++ +
  gi|336253565|ref|YP_004596672.1| 165 DSSKGAVMMLTRVAALELAPYDVRVNAVAPGIVKTAFGA 203
                                       ***********************************9765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.2   5.7e-17     1e-13       3     151 ..      13     166 ..      11     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 5.7e-17
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHH.HHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedska.liaelealgaevevvaaDvsdkdavealleeikae 78 
                                        ++tGG+ g+G+e+a+   e ga+ +v   R+++++e +++ + +++e+ g + ++v+ Dv+d+d+v+a++e+++ e
  gi|336253565|ref|YP_004596672.1|  13 AIVTGGASGIGREVATRFGEAGATVIVADVREEPKREGESTpTHERIEDAGGRATFVETDVTDPDDVAAVVEAAR-E 88 
                                       69******************************76665554427789**************************997.8 PP

                                       SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT.....S--SEEEEEEEHHHHH--TT-HHHH CS
                                KR  79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled.....esldffvlfSSiagllgsagqanYa 150
                                       ++ +   ++ A + r + + e++ e+++++l+  v+G+    ++ ++     ++   +v ++Si++ + + g++ Y 
  gi|336253565|ref|YP_004596672.1|  89 FGGVDVMVNNAAIYRHGSVLETDLETFDRLLEINVQGVLAGTRAAARdmlarDEPGTVVNTASISSEYAQLGHSMYD 165
                                       99***********************************9887766655455557778899999999999988888887 PP

                                       H CS
                                KR 151 a 151
                                       +
  gi|336253565|ref|YP_004596672.1| 166 S 166
                                       6 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.2   4.6e-10   8.2e-07       2      94 ..      14     121 ..      13     162 .. 0.78
   2 ?   -1.5   0.0      0.76   1.4e+03      54      76 ..     132     154 ..     128     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 4.6e-10
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...........EEEE--TT-HH...HHHHHHHHH. CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl...........elveldltdrs...alerlfkee. 63 
                                       +VtG++  iG+ ++ ++ e+g +vi+ d +++ +++++   +           ++ve d+td++   a+ ++ +e+ 
  gi|336253565|ref|YP_004596672.1|  14 IVTGGASGIGREVATRFGEAGATVIVADVREEPKREGESTPTheriedaggraTFVETDVTDPDdvaAVVEAAREFg 90 
                                       8*****************************88888887777799********************5555555566678 PP

                                       T-SEEEE--S.---HHHHHHSHHHHHHHHTHH CS
                         Epimerase  64 qpdavihlAa.vggvaassedpadfieknlqg 94 
                                       ++d+ ++ Aa + + +   e+  +++++ l++
  gi|336253565|ref|YP_004596672.1|  91 GVDVMVNNAAiYRH-GSVLETDLETFDRLLEI 121
                                       89********5555.44455555555443333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.76
                                       HHHHHHHHHHT-SEEEE--S--- CS
                         Epimerase  54 salerlfkeeqpdavihlAavgg 76 
                                       +a ++++++ +p +v++ A +++
  gi|336253565|ref|YP_004596672.1| 132 AAARDMLARDEPGTVVNTASISS 154
                                       66778888889999999988543 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 !   18.2   0.1   5.5e-07   0.00099       1      95 [.      14     125 ..      14     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.5e-07
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleels.kvnvkk.......viegDvtdkdkleeale.... 65 
                                       +vtGga  +Gr++  ++ +++   +v v+D+re+p+   e++ + ++++       ++e+Dvtd d++ +++e    
  gi|336253565|ref|YP_004596672.1|  14 IVTGGASGIGREVATRFGEAG--ATVIVADVREEPKREGESTpTHERIEdaggratFVETDVTDPDDVAAVVEaare 88 
                                       69***************9999..59*****99998875443313333335666668***********9988764444 PP

                         3Beta_HSD  66 ..gvdvvihlaslvdvag.....kltedeimkvnvkG 95 
                                         gvdv++  a++    +       t+d++ ++nv+G
  gi|336253565|ref|YP_004596672.1|  89 fgGVDVMVNNAAIYRHGSvletdLETFDRLLEINVQG 125
                                       5578999888888766551111145788999999998 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   0.5   8.6e-06     0.015       4      90 ..      14     134 ..      11     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.6e-06
                                       EEESTTSHHHHHHHHHCTTTSEEEEEE-TT..........................T--TTSHHHHHHHHHHH--.. CS
                     RmlD_sub_bind   4 lvtGanGqlGseLakqlaeeglevlaltre..........................eldltdaeavaellkeakp.. 52 
                                       +vtG+   +G+e+a ++ e+g+ v+  + +                          e+d+td++ va+++++a+   
  gi|336253565|ref|YP_004596672.1|  14 IVTGGASGIGREVATRFGEAGATVIVADVReepkregestptheriedaggratfvETDVTDPDDVAAVVEAAREfg 90 
                                       79*********************999987779**************************************9998533 PP

                                       ..SEEE.E------HHHHHHS...HHHHHHHHTHHHHHHHHHHH CS
                     RmlD_sub_bind  53 ..dvvv.naAAytavDkaEse...eeaayavnaeavealAeaaa 90 
                                         dv v naA y+     E++    ++  ++n+++v a  +aaa
  gi|336253565|ref|YP_004596672.1|  91 gvDVMVnNAAIYRHGSVLETDletFDRLLEINVQGVLAGTRAAA 134
                                       33565515677998888888743345677899999877666666 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   0.0   2.8e-05      0.05      42      95 ..      17      69 ..       4      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                                      ES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEE CS
                      2-Hacid_dh_C 42 iGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDiv 95
                                       G+  IG++va r+ + g+ vi+ d+++++++ e e   +++ +e++  ++ +v
  gi|336253565|ref|YP_004596672.1| 17 GGASGIGREVATRFGEAGATVIVADVREEPKR-EGESTPTHERIEDAGGRATFV 69
                                      47889**********************99888.444455667777776666666 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 ?   13.4   1.2     3e-05     0.054       1      68 [.      17      99 ..      17     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH........HHHCT.TTCEEEE--TT-CCHHHHHHT......T-SEE CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpekla........eleae.eglevvegdvtdvedlaealk......gadaV 64
                                      G+  ++Gr+++++  ++g + ++a vR++ k +        ++e++  +++ ve dvtd++d+a++++      g+d+ 
  gi|336253565|ref|YP_004596672.1| 17 GGASGIGREVATRFGEAGATVIVADVREEPKREgestptheRIEDAgGRATFVETDVTDPDDVAAVVEaarefgGVDVM 95
                                      6667799999999999987677888999666655555555556544489******************966666667766 PP

                                      EES- CS
                    NAD_binding_10 65 vsal 68
                                      v ++
  gi|336253565|ref|YP_004596672.1| 96 VNNA 99
                                      5554 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 ?   12.4   0.0   4.3e-05     0.077       1      74 [.      14      86 ..      14     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                                      EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH CS
                     GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev 74
                                      ++TG+a  iG  +a ++ e g +v++ + r++  + g+     ++  e++ ++ ++++ D+tD + +  +++ +
  gi|336253565|ref|YP_004596672.1| 14 IVTGGASGIGREVATRFGEAGATVIVADVREEPKREGESTPTHERI-EDAGGRATFVETDVTDPDDVAAVVEAA 86
                                      59************************99999998888777766554.45678****************999876 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.3e-05     0.095      43     152 ..      48     164 ..      39     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-05
                                       HHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--SS-S.ST.......TSSEEHHHHH CS
                     NAD_binding_4  43 eelekkelfsallkelaerikvveGDlseprlGLseedlqelaeevdviihsaAtvnfde.......pykellrvNv 112
                                       +e e+++  +++ +++  r ++ve+D+++p+      ++ +    vdv++++aA +++ +       + ++ll++Nv
  gi|336253565|ref|YP_004596672.1|  48 REGESTPTHERI-EDAGGRATFVETDVTDPDDVAAVVEAAREFGGVDVMVNNAAIYRHGSvletdleTFDRLLEINV 123
                                       566666677777.5888999*********996666666667779*************97644443446777****** PP

                                       HHHHHHHHHHT..SSS--.-EEEEEEGGGTTS-TTT--SSS- CS
                     NAD_binding_4 113 eGtrevlelak..klkklkvllhvSTayvngeregeveekvy 152
                                       +G+    + a+   l++ ++   v Ta ++ e   ++   +y
  gi|336253565|ref|YP_004596672.1| 124 QGVLAGTRAAArdMLARDEPGTVVNTASISSEYA-QLGHSMY 164
                                       ***9999988843244446777777766666666.3344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2109.12
//
Query:       gi|336253566|ref|YP_004596673.1|  [L=496]
Description: aldehyde dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-159  532.0   1.9   1.2e-159  531.8   1.9    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
          3    7.9   4.9       0.67   10.0   0.9    2.0  2  OmdA      Bacteriocin-protection, YdeI or OmpD-Associated


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 !  531.8   1.9  1.3e-163  1.2e-159       1     462 []      20     485 ..      20     485 .. 0.99

  Alignments for each domain:
  == domain 1  score: 531.8 bits;  conditional E-value: 1.3e-163
                                       EET-SS.SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHH CS
                            Aldedh   1 wveses.etievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaelet 76 
                                       w+++es eti+v +P+t+e++a+vpa+ ++dvdaa +aA++a+++w++ p+++Rae++r++++++ee+ ee+++l++
  gi|336253566|ref|YP_004596673.1|  20 WTAGESeETIAVEDPSTREPVAEVPAGVEADVDAAYEAAAAAQEEWKDQPPARRAEVIRQFHEAVEEHSEEIVDLLA 96 
                                       888899667******************************************************************** PP

                                       HHH---HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEEC.TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHH CS
                            Aldedh  77 letGkplaearaeveeaidvlryyaelaeklegevlpss.egklalvrrePlGvvgaItPWNfPlllaawklapala 152
                                        e+G +    ++ ++ a d++  + +l ++++ge+++s+ +gk+++v+re+ Gvv++I+PWNfPl+l+++++apa+a
  gi|336253566|ref|YP_004596673.1|  97 HEVGGSRIMGETSIHIAGDHATEAETLPRRMKGEHAASNiPGKENIVQREAKGVVTVISPWNFPLNLSMRAVAPAIA 173
                                       **********************************999955************************************* PP

                                       TT-EEEEEE-TTSHHHH.HHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCT CS
                            Aldedh 153 aGNtvvlKPaeetplsa.lllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaakn 228
                                       aGN+vvlKP++++p++  ll+a+lfee +lP+gvlnvvtg+gse+g+ +++hpe d+v+ftGstevg+++a+ a++n
  gi|336253566|ref|YP_004596673.1| 174 AGNSVVLKPSTNSPITGgLLFAKLFEETDLPDGVLNVVTGRGSEIGDRVASHPESDVVAFTGSTEVGQHVASLAGEN 250
                                       *****************9*********************************************************** PP

                                       TSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT CS
                            Aldedh 229 lkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdplded 305
                                       l   ++ElGG+n+++v++daDl++a++++ +g+f+++GQvCi+++r +v+e+iyde+ve+l+e+a++l vg++ d d
  gi|336253566|ref|YP_004596673.1| 251 LAVPAMELGGNNAFVVTDDADLERALDGATFGSFVHQGQVCISINRHIVHEDIYDEYVERLTERAEELPVGSAHDAD 327
                                       ***************************************************************************** PP

                                       -SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEES CS
                            Aldedh 306 tdvGPliseaqlekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfk 381
                                       t vGP+i+e+q++++ +yvee++++ga+l +Gg+    +g ++  +v+Ptvl++vt+dm+ a++E FGP+++vi+f+
  gi|336253566|ref|YP_004596673.1| 328 TIVGPIIDESQRDEMLEYVEETVDQGATLETGGKtIPVEGVDDSLVVAPTVLSDVTNDMAAACNEHFGPIAPVIPFS 404
                                       **********************************9778999************************************ PP

                                       SHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEE CS
                            Aldedh 382 deeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeyte 458
                                       d++ea+eiaN+te+GL+++v++ dle a+ +a+r+e+Gnv+iNd+  +++ ++pf G+++Sg+G  ++ + l+e+te
  gi|336253566|ref|YP_004596673.1| 405 DIDEAVEIANATEFGLSGAVHAGDLEVAKDIADRMETGNVHINDQPINDEAHVPFSGIGASGMGTYNSDAFLREITE 481
                                       ***************************************************************************** PP

                                       EEEE CS
                            Aldedh 459 vktv 462
                                       +k++
  gi|336253566|ref|YP_004596673.1| 482 TKWI 485
                                       **96 PP

>> OmdA  Bacteriocin-protection, YdeI or OmpD-Associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.9   7.4e-05      0.67       4      40 ..      47      83 ..      44      87 .. 0.91
   2 ?   -3.6   0.2       1.3   1.2e+04       6      13 ..     270     277 ..     269     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.4e-05
                              OmdA  4 vPedlaaaLdadpaakaaFealtpsyrreylrwiesa 40
                                      v +d+ aa +a  aa++ ++  +p +r e++r++ +a
  gi|336253566|ref|YP_004596673.1| 47 VEADVDAAYEAAAAAQEEWKDQPPARRAEVIRQFHEA 83
                                      678999**************************99877 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.3
                              OmdA   6 edlaaaLd 13 
                                       +dl++aLd
  gi|336253566|ref|YP_004596673.1| 270 ADLERALD 277
                                       89*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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 0.22s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3739.89
//
Query:       gi|336253567|ref|YP_004596674.1|  [L=270]
Description: transcriptional regulator-like protein [Halopiger xanaduensis SH-6]
Scores for 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   26.9   0.0    7.1e-06   26.1   0.0    1.5  1  DUF1724        Domain of unknown function (DUF1724)
    6.2e-05   22.8   0.1    0.00081   19.2   0.0    2.3  2  HTH_5          Bacterial regulatory protein, arsR family
     0.0001   22.2   0.1    0.00026   20.9   0.1    1.7  1  HTH_Crp_2      Crp-like helix-turn-helix domain
    0.00051   19.8   0.4      0.002   17.9   0.0    2.1  2  HTH_IclR       IclR helix-turn-helix domain
    0.00075   19.3   1.6    0.00096   19.0   0.2    1.9  2  MarR_2         MarR family
     0.0042   17.2   0.1       0.04   14.0   0.0    2.2  2  Trp_repressor  Trp repressor protein
     0.0096   15.7   0.1       0.03   14.1   0.1    1.8  1  HTH_23         Homeodomain-like domain
  ------ inclusion threshold ------
      0.026   14.5   0.0      0.044   13.8   0.0    1.3  1  HTH_45         Winged helix-turn-helix
      0.028   14.3   0.0      0.064   13.2   0.0    1.6  1  MarR           MarR family
       0.03   14.7   0.0      0.087   13.3   0.0    1.8  1  HTH_26         Cro/C1-type HTH DNA-binding domain
      0.049   13.7   0.0       0.14   12.3   0.0    1.8  2  HTH_7          Helix-turn-helix domain of resolvase
      0.059   12.9   0.0       0.16   11.6   0.0    1.8  1  HTH_24         Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   4.7e-09   7.1e-06       3      61 ..     205     261 ..     203     262 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.7e-09
                           DUF1724   3 lyvydeeikplsltvtDkflslslfdkdgkydhkdlisfdesAlkWGeeLFeyYlkrSe 61 
                                       +++yd+ei pl+ ++ D++++l + d++g   +  + s+d++   W++e Fe Y++++e
  gi|336253567|ref|YP_004596674.1| 205 VRIYDDEI-PLAAMIIDDVVYLLVRDDQGIL-RASIDSDDDEIRAWARETFESYWESAE 261
                                       89******.********************77.456**********************97 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 !   19.2   0.0   5.4e-07   0.00081       3      33 ..      22      52 ..      20      55 .. 0.94
   2 ?    0.8   0.0       0.3   4.5e+02      29      41 ..     187     199 ..     185     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.4e-07
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHH CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvS 33
                                      +R+++L+lL+e  ++ +ela+e+g sq+t+ 
  gi|336253567|ref|YP_004596674.1| 22 NRVDVLRLLSEDRYTRTELARETGASQATLG 52
                                      7****************************86 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHH CS
                             HTH_5  29 qstvShHLkkLre 41 
                                        s+++ +L++L e
  gi|336253567|ref|YP_004596674.1| 187 DSALRTQLRALLE 199
                                       699********87 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 !   20.9   0.1   1.8e-07   0.00026      21      54 ..      34      67 ..      14      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.8e-07
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrg 54
                                      + t++elA+  G+++ t+ ril+++ ++ +i+r 
  gi|336253567|ref|YP_004596674.1| 34 RYTRTELARETGASQATLGRILGDFADRSWIERD 67
                                      79*****************************963 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 !   17.9   0.0   1.3e-06     0.002       7      52 .]      25      68 ..      22      68 .. 0.93
   2 ?   -2.0   0.0       2.2   3.4e+03       7      16 ..     135     144 ..     133     151 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                      ++L++l+e +     +elAr+tg + +t  R+L  +  + ++e+dg
  gi|336253567|ref|YP_004596674.1| 25 DVLRLLSEDRYT--RTELARETGASQATLGRILGDFADRSWIERDG 68
                                      899999999985..9*****************************97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                                       HHHCT-CTTB CS
                          HTH_IclR   7 aiLdalaeap 16 
                                       ++Ld+l+ a+
  gi|336253567|ref|YP_004596674.1| 135 RLLDLLENAT 144
                                       4566666655 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   6.5e-07   0.00096       2      54 ..      18      67 ..      17      73 .. 0.86
   2 ?   -2.6   0.1       3.5   5.2e+03       6      16 ..     192     202 ..     188     206 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.5e-07
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +l+    +vL  L        t +elar++g s++++ ril ++ ++ ++er 
  gi|336253567|ref|YP_004596674.1| 18 ALSANRVDVLRLLSEDR---YTRTELARETGASQATLGRILGDFADRSWIERD 67
                                      57777888999887665...6*****************************986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHC CS
                            MarR_2   6 aqarvLaaLgr 16 
                                       +q+r+L++  r
  gi|336253567|ref|YP_004596674.1| 192 TQLRALLETDR 202
                                       66666666555 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   2.7e-05      0.04      36      69 ..      21      54 ..      10      58 .. 0.82
   2 ?    0.3   0.0      0.53   7.9e+02       3      33 ..     133     165 ..     126     170 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-05
                     Trp_repressor 36 aqRlqvvkeLLkeelsqreIaeelgvSiAtItRv 69
                                      a+R+ v++ L ++ ++ +e+a e+g+S At +R 
  gi|336253567|ref|YP_004596674.1| 21 ANRVDVLRLLSEDRYTRTELARETGASQATLGRI 54
                                      58******5556778****************995 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.53
                     Trp_repressor   3 ldallelilkleneeeleell..elllTpdEre 33 
                                       l+ ll+l+ ++ +   +++ +  + l T++Er 
  gi|336253567|ref|YP_004596674.1| 133 LQRLLDLLENATEVRAVSHAFneQNLTTVQERA 165
                                       566666666666666666666333566666665 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1     2e-05      0.03       7      41 ..      23      58 ..      20      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                            HTH_23  7 Rlrillllae.GlsvreIAreLgvsrrTvyrwlkry 41
                                      R  +l+ll e +++++e Are g s+ T+ r+l  +
  gi|336253567|ref|YP_004596674.1| 23 RVDVLRLLSEdRYTRTELARETGASQATLGRILGDF 58
                                      67799999999*********************9777 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.9e-05     0.044       9      75 ..      24      90 ..      23      92 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                            HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkeleel 75
                                      +d+L+ +se++ + T++  +   s  +l + L    ++  i+ ++++Y  T+ G+ + + + +++++
  gi|336253567|ref|YP_004596674.1| 24 VDVLRLLSEDRYTRTELARETGASQATLGRILGDFADRSWIERDGSEYAATATGQLVASGFTDMQDI 90
                                      699****************************************************999888888775 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-05     0.064       1      49 [.      19      66 ..      19      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      l+++++++Lr+l+e +  + +eLa+  g s++t+ r+l    ++ +ieR
  gi|336253567|ref|YP_004596674.1| 19 LSANRVDVLRLLSE-DRYTRTELARETGASQATLGRILGDFADRSWIER 66
                                      67888899998876.567889***************************9 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 ?   13.3   0.0   5.8e-05     0.087       5      33 ..      29      57 ..      26      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.8e-05
                            HTH_26  5 lmadrgitkseLargtgisaatlsrlvkg 33
                                      l+ + ++t++eLar tg s+atl r++ +
  gi|336253567|ref|YP_004596674.1| 29 LLSEDRYTRTELARETGASQATLGRILGD 57
                                      788999*****************999865 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 ?   12.3   0.0   9.1e-05      0.14      14      42 ..      26      55 ..      17      57 .. 0.85
   2 ?   -3.1   0.0         6     9e+03      12      31 ..     134     153 ..     127     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.1e-05
                                      GGSSTTTT.--STTTSSSS---SSSS--SS CS
                             HTH_7 14 vvkLleeG.isiskIAkevnisRsTvYRyl 42
                                      v++Ll+e  ++++++A+e++ s +T+ R+l
  gi|336253567|ref|YP_004596674.1| 26 VLRLLSEDrYTRTELARETGASQATLGRIL 55
                                      678888888*****************9998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6
                                       GGGGSSTTTT--STTTSSSS CS
                             HTH_7  12 nrvvkLleeGisiskIAkev 31 
                                       +r++ Lle+ + ++++  ++
  gi|336253567|ref|YP_004596674.1| 134 QRLLDLLENATEVRAVSHAF 153
                                       68888999888887776555 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 ?   11.6   0.0   0.00011      0.16       5      47 ..      23      64 ..      19      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      + ++L+lL +  r + +eLA+++g S++t+ r l  + +  +I
  gi|336253567|ref|YP_004596674.1| 23 RVDVLRLLSE-DRYTRTELARETGASQATLGRILGDFADRSWI 64
                                      5567777777.9*****************99998877766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2161.37
//
Query:       gi|336253568|ref|YP_004596675.1|  [L=332]
Description: hypothetical protein Halxa_2171 [Halopiger xanaduensis SH-6]
Scores for 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-33  114.8  38.3    2.6e-19   69.7  13.1    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
       0.16   12.0   4.1        1.1    9.4   1.0    2.4  2  TMEM234   Putative transmembrane family 234
        0.4   10.2  11.0        1.9    8.1   0.1    3.5  3  PGPGW     Putative transmembrane protein (PGPGW)


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 !   69.7  13.1   4.4e-23   2.6e-19       5     136 ..       9     143 ..       5     144 .. 0.93
   2 !   51.4  17.1     2e-17   1.2e-13       5     135 ..     159     291 ..     155     293 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 4.4e-23
                              EamA   5 llallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl..aklslkdwllllllgllgtvlaf 79 
                                        +++l++lf++ +fv++k++l++++pl ++++rf +a++++  + +l+ ++      ++ d l ++ +g++ + l +
  gi|336253568|ref|YP_004596675.1|   9 AFFVLSSLFFGGTFVAAKAGLEFFPPLLFVALRFDVAAVIMAGYVALTVSREdlLPTTRGDALGIVATGVFVIGLSN 85 
                                       6789*************************************88877777777656777788**************** PP

                              EamA  80 llffyalkktsasnaslitslePvftlilsvlll.gekltlkqllgivlillGvllil 136
                                        l+f ++++ ++++ ++++sl P++t ++++lll +e+l+ +  +g++l+llGv+l++
  gi|336253568|ref|YP_004596675.1|  86 ALLFVGQQYATSAVGAIVFSLNPILTPVFAALLLsNERLSARGAIGMMLGLLGVALVV 143
                                       ********************************************************97 PP

  == domain 2  score: 51.4 bits;  conditional E-value: 2e-17
                              EamA   5 llallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl..aklslkdwllllllgllgtvlaf 79 
                                        +++++a++ a+++vl++++ ++vs+    ++ + +a++l   +++l +++     +++ ++++l++++++++vla+
  gi|336253568|ref|YP_004596675.1| 159 AILFAGAVSAALGAVLIRRADATVSSTVRIAWGLPLAAALSHGFSALAGESAasIAWTPGAIAALAYVSVFAGVLAY 235
                                       567999***********************************999999999998999999****************** PP

                              EamA  80 llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       +++f +l +t+a +a li++++P+++++ +++ll e++  +  lg++ i++G +++
  gi|336253568|ref|YP_004596675.1| 236 IAYFALLDSTGAIRANLIFYVVPAVSTLGGWALLDERIAPSAALGFLTIFAGFAVL 291
                                       ****************************************************9986 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.0   0.00018       1.1      68     116 .]      94     143 ..      74     143 .. 0.80
   2 ?    3.5   0.1     0.011        68      53     114 ..     230     290 ..     185     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00018
                           TMEM234  68 adlslavpiaNslafvfTvlte.lllgekvlkkktvlgmllvvvgialcv 116
                                          s + +i+ sl+ ++T + + lll ++ l+++  +gm+l ++g+al+v
  gi|336253568|ref|YP_004596675.1|  94 YATSAVGAIVFSLNPILTPVFAaLLLSNERLSARGAIGMMLGLLGVALVV 143
                                       44566778999***999977665999*********************986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.011
                           TMEM234  53 lNqsgSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgial 114
                                         +++ + +f+ll ++    a  i   +  v T l +++l ++ +  ++ lg l +++g a+
  gi|336253568|ref|YP_004596675.1| 230 AGVLAYIAYFALLDSTGAIRANLIFYVVPAVST-LGGWALLDERIAPSAALGFLTIFAGFAV 290
                                       467788899999999988888888877777766.6889999999999999****99999887 PP

>> PGPGW  Putative transmembrane protein (PGPGW)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.6       1.6   9.6e+03       9      13 ..      76      80 ..      70      84 .. 0.39
   2 ?    8.0   0.7   0.00034         2       5      27 ..     128     150 ..     125     152 .. 0.90
   3 ?    8.1   0.1   0.00032       1.9      25      39 ..     280     294 ..     277     300 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.6
                             PGPGW  9 wvvvv 13
                                      + v v
  gi|336253568|ref|YP_004596675.1| 76 TGVFV 80
                                      22222 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00034
                             PGPGW   5 lvlGwvvvvvGiiliplPGPGwl 27 
                                       + +G+++ ++G++l++ P P+ l
  gi|336253568|ref|YP_004596675.1| 128 GAIGMMLGLLGVALVVSPDPANL 150
                                       679*****************976 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00032
                             PGPGW  25 GwlvvflGLaiLsle 39 
                                       G+l++f+G+a+L++e
  gi|336253568|ref|YP_004596675.1| 280 GFLTIFAGFAVLGSE 294
                                       99**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2640.32
//
Query:       gi|336253569|ref|YP_004596676.1|  [L=357]
Description: eRF1 domain 2 protein [Halopiger xanaduensis SH-6]
Scores for 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-23   82.3   0.0    5.9e-23   81.7   0.0    1.3  1  eRF1_2          eRF1 domain 2
    9.4e-18   64.8   6.6    9.4e-18   64.8   6.6    2.2  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    1.9e-16   60.6   0.0    1.3e-15   57.8   0.0    2.2  1  eRF1_3          eRF1 domain 3
      3e-15   56.7   0.7      3e-15   56.7   0.7    1.9  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    0.00022   21.6   2.3    0.00039   20.7   2.3    1.6  1  baeRF_family3   Bacterial archaeo-eukaryotic release factor f
    0.00038   20.5   7.5    0.00087   19.4   7.5    1.5  1  baeRF_family2   Bacterial archaeo-eukaryotic release factor f
      0.002   18.7   0.3       0.03   14.9   0.1    2.4  2  baeRF_family12  Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
        8.4    6.6  12.5       0.18   12.0   4.9    2.1  3  Metal_resist    Heavy-metal resistance


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 !   81.7   0.0   2.6e-26   5.9e-23       3     130 ..     132     257 ..     130     260 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 2.6e-26
                                       EEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESE CS
                            eRF1_2   3 glivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkg 79 
                                       gl+v+++g+A +g l ++ ++ +++++++vP+K  +Ggqsa+rfeR re++ +ef+++vae a  +fl  + d ++g
  gi|336253569|ref|YP_004596676.1| 132 GLLVVERGGAALGRLDETGVKPIDTFDSDVPGKSSAGGQSAERFERDRERQKREFFDEVAERAALEFL--ESDPVDG 206
                                       89****************************************************************99..69***** PP

                                       EEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHH CS
                            eRF1_2  80 iilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaev 130
                                       ++l+g   + e+f ++  ld++l+++ +  + v y  e+gl+++ ek  ++
  gi|336253569|ref|YP_004596676.1| 207 VLLGGTTGTVEDFREEADLDHRLEDRLVGEFAVEYASEQGLRQLAEKGRSA 257
                                       ********************************************9996665 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       2.3   5.3e+03      97     120 ..      47      67 ..       8      75 .. 0.57
   2 !   64.8   6.6   4.2e-21   9.4e-18       3     127 ..     131     257 ..     129     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.3
                           acVLRF1  97 platlareelldvpdprravLeda 120
                                       ++++l ++    +p+p  ++Le++
  gi|336253569|ref|YP_004596676.1|  47 EASQLDEQ---SFPKPLTDALETV 67 
                                       22333333...4555555555544 PP

  == domain 2  score: 64.8 bits;  conditional E-value: 4.2e-21
                           acVLRF1   3 lgvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae..v 77 
                                        g+l+v rgg a+g+++++ +    ++ +dv g+++aGG+S +Rf+R re q ++ +++vae+aa  + e ++   v
  gi|336253569|ref|YP_004596676.1| 131 SGLLVVERGGAALGRLDETGVKPIDTFDSDVPGKSSAGGQSAERFERDRERQKREFFDEVAERAALEFLESDPVdgV 207
                                       5899*************************************************************88888888789* PP

                           acVLRF1  78 vlgGdrslvaevledarlap.latlareelldvpdprravLedavrrarav 127
                                       +lgG   +v++++e+a+l++ l+++ + e+ +v+ ++++ L++ ++++r++
  gi|336253569|ref|YP_004596676.1| 208 LLGGTTGTVEDFREEADLDHrLEDRLVGEF-AVEYASEQGLRQLAEKGRSA 257
                                       ***************995553555555544.78888888888888888765 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.0     6e-19   1.3e-15       5     113 .]     267     356 ..     264     356 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 6e-19
                                       HHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHHT CS
                            eRF1_3   5 kklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenvees 81 
                                       +++le+f+e ++ d++ ++YG +ev +ale+ Av+tLL+s  le ++                   ++ + + + e+
  gi|336253569|ref|YP_004596676.1| 267 REALEDFFEAVRDDDRAVAYGTDEVDDALEYDAVDTLLLSAALEGQQ-------------------LRTFGDRATEQ 324
                                       689******************************************97...................78899****** PP

                                       T-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  82 gakveiisseseeGeqlvkafgGiaaiLRykv 113
                                       g++ ++++++++ G+++ +af G++a+LR+ +
  gi|336253569|ref|YP_004596676.1| 325 GGDTVVVPDDFPDGNRFAEAFDGVGALLRFAI 356
                                       ******************************75 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 !   56.7   0.7   1.3e-18     3e-15       3     127 ..     118     243 ..     117     257 .. 0.89
   2 ?   -0.6   0.1      0.64   1.4e+03      69     105 ..     259     296 ..     248     304 .. 0.70

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 1.3e-18
                    baeRF_family10   3 lapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAel 79 
                                       l+pL ++++ +   g+++v+r++a+l +     ++  +++ ++vpg+  +gg+ s +rf+r +e q +++++evAe 
  gi|336253569|ref|YP_004596676.1| 118 LSPLEDVAEPDSTSGLLVVERGGAALGRLDETGVKPIDTFDSDVPGKSSAGGQ-SAERFERDRERQKREFFDEVAER 193
                                       79***************************************************.*********************98 PP

                    baeRF_family10  80 la.klleergverlvlgGdeeetaalld..rlpkalrarvvgtlplpvdas 127
                                       +a ++le ++v+ ++lgG++   + +++   l  +l++r+vg++ ++  as
  gi|336253569|ref|YP_004596676.1| 194 AAlEFLESDPVDGVLLGGTTGTVEDFREeaDLDHRLEDRLVGEFAVEY-AS 243
                                       8835666666*********99999997522799**********99987.33 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.64
                    baeRF_family10  69 aerhlkevAellaklleerg.verlvlgGdeeetaall 105
                                        er  +++ e+l++++e  +  +r v  G++e+++al+
  gi|336253569|ref|YP_004596676.1| 259 DERDRRDAREALEDFFEAVRdDDRAVAYGTDEVDDALE 296
                                       45556666677777777655467888888888888775 PP

>> baeRF_family3  Bacterial archaeo-eukaryotic release factor family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   2.3   1.7e-07   0.00039      25     150 ..     154     279 ..      42     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.7e-07
                     baeRF_family3  25 ve..adgfPltleealgeedperqe...ghgdkkseyrdedtrrFlreVd.kalqevlsesplp.lvlaGveenlsl 94 
                                       ++  ++++P             +++   ++ ++ + +r+ + r+F+ eV  +a  e+l  +p   ++l G++  +  
  gi|336253569|ref|YP_004596676.1| 154 IDtfDSDVP------------GKSSaggQSAERFERDRERQKREFFDEVAeRAALEFLESDPVDgVLLGGTTGTVED 218
                                       333333333............222232212223344578899******9725789****99986267778999**** PP

                     baeRF_family3  95 frevsknpsliegglegnp.....aelsaeeLreaawplveayaeeeraealeeldeargr 150
                                       fre ++ ++ +e+ l g++     +e+  ++L+e+ +++v+++ ++++ eale++ ea+  
  gi|336253569|ref|YP_004596676.1| 219 FREEADLDHRLEDRLVGEFaveyaSEQGLRQLAEKGRSAVDERDRRDAREALEDFFEAVRD 279
                                       ********999999988886655667788889999999*****************999864 PP

>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   7.5   3.9e-07   0.00087       6     145 ..     135     275 ..     132     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.9e-07
                     baeRF_family2   6 evDrtGadltlvdaggeeeeetveGghdpv.hkvraggwshrryqrraeeswerNaeavAeevd.rlvresgaelVv 80 
                                       +v r Ga l   d++     + ++  + +v  k++agg s +r++r  e + ++  ++vAe+ + +  ++  ++ V+
  gi|336253569|ref|YP_004596676.1| 135 VVERGGAALGRLDET---GVKPIDTFDSDVpGKSSAGGQSAERFERDRERQKREFFDEVAERAAlEFLESDPVDGVL 208
                                       677778887777755...44444444444437999***************************993455556679*** PP

                     baeRF_family2  81 laGDvrarsllrde..Lpervrelvvevegggraagadrealaeevaealaerrarrreevlerfra 145
                                       l G +  +++ r+e  L +r+++++v   + + a++   ++lae+ ++a++er +r+ +e+le f +
  gi|336253569|ref|YP_004596676.1| 209 LGGTTGTVEDFREEadLDHRLEDRLVGEFAVEYASEQGLRQLAEKGRSAVDERDRRDAREALEDFFE 275
                                       ***********98655899*******9999999999***************************9966 PP

>> baeRF_family12  Bacterial archaeo-eukaryotic release factor family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.22     5e+02      55      87 ..      35      69 ..      12      77 .. 0.71
   2 !   14.9   0.1   1.3e-05      0.03      45     129 ..     159     244 ..     148     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.22
                    baeRF_family12 55 gagrsame..etdfkeqeeerFakeladeLkkrak 87
                                      g++r+ +e    +  +++e+ F k l d+L+  + 
  gi|336253569|ref|YP_004596676.1| 35 GQARQPVEtdYAEASQLDEQSFPKPLTDALETVRS 69
                                      45555553324455556*************99554 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.3e-05
                    baeRF_family12  45 sdrpGrsssggagrsameetdfkeq.eeerFakeladeLkk.rakegkferlvlvappetlgelrkh..lhkevkkr 117
                                       sd pG+ss gg++   +e+++   + ++ +F+ e+a++     ++ + ++ + l +   t++++r++  l+ ++++r
  gi|336253569|ref|YP_004596676.1| 159 SDVPGKSSAGGQS---AERFERDRErQKREFFDEVAERAALeFLESDPVDGVLLGGTTGTVEDFREEadLDHRLEDR 232
                                       6778886666665...45555544436888*******9887255556688899999********985559******* PP

                    baeRF_family12 118 lvgeiaknltkh 129
                                       lvge+a +++ +
  gi|336253569|ref|YP_004596676.1| 233 LVGEFAVEYASE 244
                                       *****9988765 PP

>> Metal_resist  Heavy-metal resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.7     6e+03      33      69 ..      38      74 ..      27     100 .. 0.63
   2 ?   -2.8   0.4       3.2   7.1e+03      98     112 ..     181     195 ..     170     205 .. 0.49
   3 ?   12.0   4.9   8.1e-05      0.18      33      95 ..     248     310 ..     232     324 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.7
                                      .HHHHHHHS-TTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Metal_resist 33 raellraalgLpaeqraelraalrdharelralrrel 69
                                      r++ ++ +++ ++ +++ + + l d+ +++r + ++ 
  gi|336253569|ref|YP_004596676.1| 38 RQPVETDYAEASQLDEQSFPKPLTDALETVRSELNDY 74
                                      4555666666666666666666666666666555554 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHHHHH CS
                      Metal_resist  98 raaqaalraqieeal 112
                                       r+ ++ +++  e+a+
  gi|336253569|ref|YP_004596676.1| 181 RQKREFFDEVAERAA 195
                                       333333333333333 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 8.1e-05
                                       .HHHHHHHS-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSSSHHHHHHHHH CS
                      Metal_resist  33 raellraalgLpaeqraelraalrdharelralrrelraarrelaallaaepfDaaaieaala 95 
                                       r+  + ++++ ++++r+ +r+al d+++++r+  r+     +e++++l  + +D+  + aal+
  gi|336253569|ref|YP_004596676.1| 248 RQLAEKGRSAVDERDRRDAREALEDFFEAVRDDDRAVAYGTDEVDDALEYDAVDTLLLSAALE 310
                                       688899999*********************************************999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); 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:                         9  (0.00050198); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2759.87
//
Query:       gi|336253570|ref|YP_004596677.1|  [L=212]
Description: hypothetical protein Halxa_2173 [Halopiger xanaduensis SH-6]
Scores for 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   15.7   0.1      0.023   14.6   0.1    1.6  1  zinc_ribbon_4  zinc-ribbon domain
       0.13   12.7   0.0       0.31   11.5   0.0    1.6  1  HTH_40         Helix-turn-helix domain


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 ?   14.6   0.1   2.6e-06     0.023       3      16 ..     185     198 ..     184     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-06
                     zinc_ribbon_4   3 itCpsCkakyeidd 16 
                                       +tC++Ck++y+++d
  gi|336253570|ref|YP_004596677.1| 185 VTCEECKTQYTVQD 198
                                       89**********98 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.4e-05      0.31      25      59 ..     116     153 ..     106     181 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.4e-05
                            HTH_40  25 kesTIegHLaelieegeeidl..erlv.seeeekeIee 59 
                                       + +T+++HL++++e+  e +   erl  s+++  ++++
  gi|336253570|ref|YP_004596677.1| 116 SHQTVYNHLTDCLEASLETPSdeERLErSRDKLGALRN 153
                                       789************75555411444223344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1692.20
//
Query:       gi|336253571|ref|YP_004596678.1|  [L=452]
Description: hydroxypyruvate reductase [Halopiger xanaduensis SH-6]
Scores for complete 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  267.1   2.6    1.1e-79  267.1   2.6    2.2  3  DUF4147   Domain of unknown function (DUF4147)
    1.2e-30  105.9   4.8    1.5e-30  105.6   3.2    2.1  2  MOFRL     MOFRL family
  ------ inclusion threshold ------
      0.016   15.2   0.5      0.052   13.5   0.0    2.2  2  CbiG_N    Cobalamin synthesis G N-terminal


Domain annotation for each model (and alignments):
>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.1   2.6   1.9e-83   1.1e-79       2     229 .]      21     259 ..      20     259 .. 0.94
   2 ?   -0.2   0.0       0.1   6.1e+02      36      56 ..     280     301 ..     268     350 .. 0.72
   3 ?   -2.6   0.1      0.53   3.2e+03     186     205 ..     394     413 ..     375     431 .. 0.65

  Alignments for each domain:
  == domain 1  score: 267.1 bits;  conditional E-value: 1.9e-83
                                       HHHHHHHHHHTTSHHHHHHTTHHH..........H--..........-SEEEEEESTTHHHHHHHHH....HHHGEE CS
                           DUF4147   2 lraifeaaveavdpeklvkralsl..........kee...eldlskkkrvvvvgaGKAaaamaaalee...ealksg 62 
                                       + ++++a++ea++p++ v++++++          +     e+ l+++++v+++g G+Aa + a+ale+   ++l++g
  gi|336253571|ref|YP_004596678.1|  21 ALECVRAGIEAAHPAARVEETIAVrdgtlavtavD-GtttEYALDEYEDVFLIGGGNAAGHFARALEDelaDRLTDG 96 
                                       57899*****************9966666666551.05569**************************98888899** PP

                                       EEEEETT-----TT-EEEEE-SSS--HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHH CS
                           DUF4147  63 vvvvkkghaeekerievleaahplPdeesveaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqalt 139
                                        vv+    ++e+ +++vl ++hp+P+e++ve ar+ile+ae ++e+dlv++ i+GGgSAllaaPae+++l+d+qa+t
  gi|336253571|ref|YP_004596678.1|  97 AVVTDD--STETATVDVLAGDHPVPSERGVEHARRILEIAECAGEGDLVIATITGGGSALLAAPAEPLSLSDLQATT 171
                                       ****74..467889*************************************************************** PP

                                       HHHHHCT--HHHHHHHHHTTBSSTTTHHHHHHTTSEEEEEEE--STT--TTTGGG-TTS-----HHHHHHHHHHTT- CS
                           DUF4147 140 kaLlasGasIqelNtVRkhlsaikGGrLaraaaparvvsLilSDVvgddldvIASGPtvpdsstfadalailekykl 216
                                       ++Lla+Ga+I+e+N+VRkh+saikGGrLaraaapa+v +++lSDVvgdd++vIASGPtvpd+st+adal++le+y+l
  gi|336253571|ref|YP_004596678.1| 172 EELLACGATIDEINAVRKHCSAIKGGRLARAAAPATVATVALSDVVGDDVSVIASGPTVPDPSTYADALTVLERYDL 248
                                       ***************************************************************************** PP

                                       --..-HHHHHHH. CS
                           DUF4147 217 eeklpesvrelLe 229
                                       +  +p++vre+Le
  gi|336253571|ref|YP_004596678.1| 249 D--VPTAVREHLE 259
                                       9..9*******96 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.1
                                       -SEEEEEESTTHHHHH.HHHH. CS
                           DUF4147  36 krvvvvgaGKAaaama.aalee 56 
                                       ++ +v+g G+ a++ a  a++e
  gi|336253571|ref|YP_004596678.1| 280 TSAHVLGSGRTALEAArDAARE 301
                                       6789999999999999544443 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.53
                                       T--TTTGGG-TTS-----HH CS
                           DUF4147 186 gddldvIASGPtvpdsstfa 205
                                        d   +IA   tvpd+   +
  gi|336253571|ref|YP_004596678.1| 394 TDAAGAIANATTVPDAAGRN 413
                                       45666777777777754433 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.2     7e+03      17      32 ..     194     209 ..     174     227 .. 0.65
   2 !  105.6   3.2   2.6e-34   1.5e-30       2     109 .]     343     442 ..     342     442 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                                       ----HHHHHHHHHHH. CS
                             MOFRL  17 GkGGrnqelalalale 32 
                                        kGGr    a  + ++
  gi|336253571|ref|YP_004596678.1| 194 IKGGRLARAAAPATVA 209
                                       6788877777666554 PP

  == domain 2  score: 105.6 bits;  conditional E-value: 2.6e-34
                                       EEEEEE--B----S-.----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS--EEEEETTHHHHHHHTT-- CS
                             MOFRL   2 vllsgGEttvtvkgk.GkGGrnqelalalalelkelegaeevvllsagtDGiDGptdaaGaivdaetleraeaagld 77 
                                       vllsgGEttvt+  + G+GG+nqe++l+ alel++    +++v++s++tDGiDG+tdaaGai++a+t+ +a+     
  gi|336253571|ref|YP_004596678.1| 343 VLLSGGETTVTLCDTpGRGGPNQEFVLSGALELEA----DGIVVASVDTDGIDGATDAAGAIANATTVPDAAG---- 411
                                       89**********5435***************6664....69***************************99887.... PP

                                       HHHHHHTT-HHHHHHHTT-EE-----S----E CS
                             MOFRL  78 akeaLanndsyeffeklgallktgpTgtNVnD 109
                                        ++aL++nd+ +++++++all+tgpTgtNVnD
  gi|336253571|ref|YP_004596678.1| 412 -RNALERNDALPVLDDADALLRTGPTGTNVND 442
                                       .89****************************9 PP

>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.8e-06     0.052      18      56 ..      77     115 ..      57     148 .. 0.79
   2 ?   -2.4   0.1      0.86   5.1e+03      56      71 ..     389     404 ..     375     407 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.8e-06
                                       -HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT CS
                            CbiG_N  18 aaGivvRliapllkdKktDpaVvvvdeagrfvisllsGh 56 
                                       aaG   R++ + l+d+ tD aVv  d++ ++ + +l+G 
  gi|336253571|ref|YP_004596678.1|  77 AAGHFARALEDELADRLTDGAVVTDDSTETATVDVLAGD 115
                                       99**********************************996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.86
                                       T.TTHHHHHHHHHHHT CS
                            CbiG_N  56 hlggAnelAeeiaall 71 
                                        + gA + A  ia+++
  gi|336253571|ref|YP_004596678.1| 389 GIDGATDAAGAIANAT 404
                                       4678888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3653.68
//
Query:       gi|336253572|ref|YP_004596679.1|  [L=392]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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-47  160.3  54.6    3.5e-35  121.6  22.4    2.0  2  MFS_1       Major Facilitator Superfamily
  ------ inclusion threshold ------
        0.3   10.3  35.7       0.47    9.7  35.7    1.2  1  MFS_4       Uncharacterised MFS-type transporter YbfB
       0.37    9.6  19.9        2.9    6.6  13.9    3.2  2  MFS_1_like  MFS_1 like family
        2.8    7.5   5.9       0.25   10.9   1.0    1.7  2  DUF4225     Protein of unknown function (DUF4225)


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 !  121.6  22.4   7.9e-39   3.5e-35       2     247 ..      16     250 ..      14     252 .. 0.87
   2 !   47.6  26.0   2.4e-16   1.1e-12      28     167 ..     243     382 ..     240     390 .. 0.88

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 7.9e-39
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                        la+f ++ +r +++p++p  ++ ++g++ + +g++lt+  l++a+a++p G l+dr+G r v+l+++ ++++++ll
  gi|336253572|ref|YP_004596679.1|  16 TLAFFATMVGRLAFSPVVP-EITGEFGVTNTHVGIALTGMWLAYALAQYPSGILADRYGERLVILASVGGTGATCLL 91 
                                       589999999999*******.9*****************************************************777 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                        +fa++ + +++++ +l G++ag+ ++++ al+++++ +   g a+g+ +ag+ ++ +++p++ +++a  +gWr + 
  gi|336253572|ref|YP_004596679.1|  92 VVFAPH-FaVFVLGAILLGAAAGLHYSVATALLTRIYDD--LGTAVGIHNAGAPVAGLMTPVAVSWIAVRYGWRPAV 165
                                       779555.55****************************85..************************************ PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllp 231
                                        i a+v++ a++lf++ ++ ++p+r+  + +++       +  p ++ l ++p ++   +++++f f ++gl ++lp
  gi|336253572|ref|YP_004596679.1| 166 AITAAVAAPAALLFAWRVRPTEPRRPDHPLRDR------LSPGPMLEVLSRPPIVY-TGVIAIIFDFTWQGLASFLP 235
                                       ************766666555555555544444......44444334556666555.7777778888********** PP

                             MFS_1 232 lylqevlglsglllag 247
                                       +++++ +g++   +ag
  gi|336253572|ref|YP_004596679.1| 236 TFFVQFHGYA-TTTAG 250
                                       *********9.56655 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 2.4e-16
                             MFS_1  28 gispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.sslwlllvlrvlqGlgagalf 103
                                       g++ +++g ++++y+++++v+++ +Gr++drfGr   +l+++++ ++g l+ll+a +sl +l ++ vl G g+g+++
  gi|336253572|ref|YP_004596679.1| 243 GYATTTAGSMFAAYFIVQGVLQIAVGRVADRFGRDIGILCCAATAIAG-LALLVAgASLVALSAGIVLVGTGMGWGA 318
                                       678899******************************999999999999.45553547777***************** PP

                             MFS_1 104 pagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla.fvl 167
                                       ++   ++ +++   e++ ++gl+ + + + a  g ++ g++a+ +gW ++f +la+++ +  ++l
  gi|336253572|ref|YP_004596679.1| 319 AVFPRFMDHLSEA-EQSAGFGLVRTVYMIVASTGSIAVGFVADRAGWAVSFGLLAALLSIIlCLL 382
                                       **99999998888.************************************988877666650433 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 ?    9.7  35.7   0.00011      0.47       7     358 ..      24     379 ..      19     384 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                             MFS_4   7 iGRFsytpiLPallaegqlslsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaa 83 
                                       +GR ++ p++P++  e +++ +++g+  ++ +l Y +      + + +  eRl++la++  t +  l ++++ +fa+
  gi|336253572|ref|YP_004596679.1|  24 VGRLAFSPVVPEITGEFGVTNTHVGIALTGMWLAYALAQYPSGILADRYGERLVILASVGGTGATCLLVVFAPHFAV 100
                                       8*****************************99999888888878889999*************************** PP

                             MFS_4  84 flliRflaGvasAvvlvfgsslvlahaaaarrervgallfaG.vGlGiavsgllvllllqlglsasslWlalavlsa 159
                                       f+l  +l+G a+++   ++++l  +   + +  +  +++ aG + +G + +  + ++++++g+  + + + +av + 
  gi|336253572|ref|YP_004596679.1| 101 FVLGAILLGAAAGLHYSVATALLTRIYDDLG--TAVGIHNAGaPVAGLMTPVAVSWIAVRYGWRPA-VAITAAVAAP 174
                                       **********999999888888777755544..445788888467899999999999999999988.5578888888 PP

                             MFS_4 160 vllllvalllp......raalreasaaaeaakaeqksl.pllalllaYglaGfGYiitatFlvaiardgaggallea 229
                                       ++ll  + ++p       ++lr+  ++ ++   e  s+ p++ + +   ++ f +   a Fl+ +  + ++g + + 
  gi|336253572|ref|YP_004596679.1| 175 AALLFAWRVRPteprrpDHPLRDRLSPGPM--LEVLSRpPIVYTGVIAIIFDFTWQGLASFLPTFFVQ-FHGYATTT 248
                                       888999999884433222333444444444..233333144455556667888888889999988888.77777776 PP

                             MFS_4 230 llWllvGlaaivgv..lvwlrvakrsglrralaaallieavgvllsllspsplglivssvllGltflaitalvlql. 303
                                       +  + +   ++ gv   +  rva+r g    +    ++  +g++l +++ s+++l  + vl+G   ++  a v ++ 
  gi|336253572|ref|YP_004596679.1| 249 AGSMFAAYFIVQGVlqIAVGRVADRFGRDIGILCCAATAIAGLALLVAGASLVALSAGIVLVGT-GMGWGAAVFPRf 324
                                       6666666666777732345567777666655555555666677788888888888888888886.566666666650 PP

                             MFS_4 304 arelappatrrllglmTasfgigQilGpllasllaeatgslalallvaaaalvla 358
                                       + +l+  ++ + +gl+ +++ i    G ++++ +a+++g   +  l+aa + ++ 
  gi|336253572|ref|YP_004596679.1| 325 MDHLSEAEQSAGFGLVRTVYMIVASTGSIAVGFVADRAGWAVSFGLLAALLSIIL 379
                                       555666666889***************************8888777777655443 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 ?    3.8   1.2    0.0049        22     256     338 ..      41     123 ..       8     137 .. 0.66
   2 ?    6.6  13.9   0.00065       2.9     214     383 ..     200     368 ..      96     370 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0049
                        MFS_1_like 256 gasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwa 332
                                       g +nt +G++++   +a     + +  l +++G + ++++++  + ++ ll+ +   + + ++  +L g++ gl ++
  gi|336253572|ref|YP_004596679.1|  41 GVTNTHVGIALTGMWLAYALAQYPSGILADRYGERLVILASVGGTGATCLLVVFAPHFAVFVLGAILLGAAAGLHYS 117
                                       55555555555555555555556666666666666666666666666666666666666666666666666666666 PP

                        MFS_1_like 333 aaveyv 338
                                       +a+   
  gi|336253572|ref|YP_004596679.1| 118 VATALL 123
                                       666555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00065
                        MFS_1_like 214 slqvllnilknpeviifllvalilgmswgiienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGh 289
                                       s+  +l++l++p +++  ++a+i  ++w  + +Fl  ++ + +g+ +t++Gs+ a   + + +l +   ++ +++G 
  gi|336253572|ref|YP_004596679.1| 200 SPGPMLEVLSRPPIVYTGVIAIIFDFTWQGLASFLPTFFvQFHGYATTTAGSMFAAYFIVQGVLQIAVGRVADRFGR 276
                                       34889******************************99998999*********************************9 PP

                        MFS_1_like 290 vklliiallayilrfllyaiienawlvlpievLhgisfgllwaaav..eyvskiapksleatgqgllsglyfglGra 364
                                          ++ +  + i+ + l+ +  +++ +    vL g  +g  w+aav  +++  + ++  ++ g gl+ ++y+ +   
  gi|336253572|ref|YP_004596679.1| 277 DIGILCCAATAIAGLALLVAGASLVALSAGIVLVGTGMG--WGAAVfpRFMD-HLSEAEQSAGFGLVRTVYMIVA-S 349
                                       998999999999999999888888888887888887666..66655226888.567778899********98765.6 PP

                        MFS_1_like 365 lGsliGGllwdlksaiflF 383
                                        Gs++ G++ d  + ++ F
  gi|336253572|ref|YP_004596679.1| 350 TGSIAVGFVADRAGWAVSF 368
                                       7*******99887777666 PP

>> DUF4225  Protein of unknown function (DUF4225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.3       1.6   7.1e+03      42      56 ..     254     268 ..     246     270 .. 0.74
   2 ?   10.9   1.0   5.6e-05      0.25      43     110 ..     277     349 ..     274     373 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.6
                           DUF4225  42 kgigvVagglqivaG 56 
                                       ++  +V g+lqi+ G
  gi|336253572|ref|YP_004596679.1| 254 AAYFIVQGVLQIAVG 268
                                       566688888888877 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 5.6e-05
                           DUF4225  43 gigvVagglqivaGvalvskasetvvgavaGalLilhGan....nvvenisyllgreekt..GlvrdvYreaae 110
                                        ig+   ++  +aG+al+ +a  + v  +aG++L+  G++     +   + +l + e++   Glvr vY+ +a 
  gi|336253572|ref|YP_004596679.1| 277 DIGILCCAATAIAGLALL-VAGASLVALSAGIVLVGTGMGwgaaVFPRFMDHLSEAEQSAgfGLVRTVYMIVAS 349
                                       589999999999****99.9999999999*****999876222144556778887777765688*****99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 2894.62
//
Query:       gi|336253573|ref|YP_004596680.1|  [L=751]
Description: malic protein NAD-binding protein [Halopiger xanaduensis SH-6]
Scores for 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  318.9   0.0    5.3e-95  318.4   0.0    1.2  1  PTA_PTB   Phosphate acetyl/butaryl transferase
    1.2e-28  100.1   0.0    2.4e-26   92.7   0.0    2.5  1  malic     Malic enzyme, N-terminal domain
    2.7e-21   76.0   1.9    6.1e-21   74.9   1.9    1.6  1  Malic_M   Malic enzyme, NAD binding domain


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 !  318.4   0.0   8.9e-99   5.3e-95       3     318 ..     430     743 ..     428     744 .. 0.97

  Alignments for each domain:
  == domain 1  score: 318.4 bits;  conditional E-value: 8.9e-99
                                       HHHHHHHHCTS--EEEES-TTSHHHHHHHHHHHHTTSSEEEEES-HHHHHHHHHHCTB--TT-EEE-TTT-CCHHHH CS
                           PTA_PTB   3 lerivekakkekkrivlpegedervlkAakelleegiadviLigdeaeikakaleldldlsgieivdpetsekleey 79 
                                       ++ +++ka++++kr +l+eg++e++++Aa +l e+gia+++Lig++ ei++ a+ l+l+ +  e+vdpet + +eey
  gi|336253573|ref|YP_004596680.1| 430 MRVVLNKAQSDPKRLALAEGHNEKIIRAAYQLREQGIAEPVLIGNRDEIERTAADLGLEFD-PEVVDPETGD-YEEY 504
                                       678999**************************************99999997777777766.69*****998.**** PP

                                       HHHHHHHCCCC.S-HCCHHHHTTSHHHHHHHHHHTTSSSEEEE-TTS-HHHHHHHHHHCT-B-TT----EEEEEEEE CS
                           PTA_PTB  80 adelyelrkrkgvtieearevvrdatyfaamlvklgeaDglvsGavnttadtlrpalqiiktkpgvklvSsvfimll 156
                                       +d ly++rkrkg+t +ea e+++d +yfa  +v +g+aD++++G+++ +  +lrp lq+i+t++ v  +++v ++  
  gi|336253573|ref|YP_004596680.1| 505 VDALYQRRKRKGITRTEAAEFIEDSNYFASVMVDQGDADAMLTGLTHHYPSALRPLLQVIGTAEDVDYAAGVYMLTF 581
                                       ***************************************************************************** PP

                                       TTEEEEEESSSS-SS--HHHHHHHHHHHHHHHHHCCSS--EEEEE-SSSTTSS-SHHHHHHHHHHHHHHHH.-TTSE CS
                           PTA_PTB 157 edrlllfaDcavnvnPtaeelaeialesaktakalgeeeprvAlLSyStkgsakgesvekvrealkivkek.apdlv 232
                                       ++r++++aD+ vn++P+ae lae+++ +a+ a+++   epr+AlLSyS++gs + e + k r a+++++   a+d+ 
  gi|336253573|ref|YP_004596680.1| 582 KNRVVFLADATVNQDPDAETLAEVTQHAAEIARRFD-VEPRAALLSYSDFGSVDNEGTRKPRRAAEMLRDDpAVDFP 657
                                       ************************************.******************************9865389*** PP

                                       EEEEE-HHHHH-HHHHHHH-TTSTTTT--SEEE-SSHHHHHHHHHHHHHCCTEEEEEEEEESBSS-EEE--TT--HH CS
                           PTA_PTB 233 vdGelqlDaAlseevaekkapesevaGkAnvlvfPdLeagnigykivqrlakaeaiGPilqGlakPvndlSrgasve 309
                                       vdGe+q+D A++ee+ +  +   ++   Anvlv+P+Leagni+yk++qrl++aea+GP+l G+a+Pv++l r ++v+
  gi|336253573|ref|YP_004596680.1| 658 VDGEMQADTAVVEETLQGTYEFADLDDPANVLVLPNLEAGNITYKLLQRLGGAEAVGPMLAGMAEPVHVLQRDDEVK 734
                                       ***************************************************************************** PP

                                       HHHHHHHHH CS
                           PTA_PTB 310 divnvaait 318
                                       divn+aa++
  gi|336253573|ref|YP_004596680.1| 735 DIVNLAAVA 743
                                       *******97 PP

>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   0.0     4e-30   2.4e-26       2     182 .]      17     149 ..      16     149 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 4e-30
                                       TTECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSB CS
                             malic   2 eknetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeri 78 
                                       +k+e+ ++k+++++  + l+++Y+P+v+ +c+++ +++++a+  y+ +++                 v vv++g+++
  gi|336253573|ref|YP_004596680.1|  17 GKLEIRTTKPTNTQ--RELSLAYSPGVAGPCRAIDKDPDEAY-RYTVKGNL----------------VGVVSNGSAV 74 
                                       57888899999999..**************************.********................9********* PP

                                       TTTBS-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHH CS
                             malic  79 LGlGdlG.vagvgimvGKlaLytalagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveav 154
                                       LGlGd+G  a++++m+GK +L++++a+id   v++v+ld+                            + d+fv+ v
  gi|336253573|ref|YP_004596680.1|  75 LGLGDIGpQASKPVMEGKGVLFKRFADID---VFDVELDHD---------------------------DPDDFVDSV 121
                                       *****************************...********9...........................99******* PP

                                       HHHHGCTSEEEE-S--CCHHHHHHHHHC CS
                             malic 155 kelfppkaliqfEDfkaknafeileryr 182
                                       + ++p++++i++ED+ka+++f i+er+r
  gi|336253573|ref|YP_004596680.1| 122 AGMEPTFGGINLEDIKAPECFVIEERLR 149
                                       **************************97 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 !   74.9   1.9     1e-24   6.1e-21       3     230 ..     163     360 ..     161     365 .. 0.86

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1e-24
                                       HHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S-.. CS
                           Malic_M   3 gTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrek.. 77 
                                       gTa+++ a+ll+a++i+gk l++ ++ ++GaG+a++  a+  ++     G+++    ++i +vD +G+lt++r++  
  gi|336253573|ref|YP_004596680.1| 163 GTAIISGAALLNATEIAGKDLEDLEVTFAGAGAAAVATAKFYAS----LGVQK----ENITMVDIDGILTTERAEag 231
                                       9**********************************988776554....56554....5799***********97622 PP

                                       .--TTTGGGSBS--SS--S....SHHHHHHHH--SEEEE-SSSSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS- CS
                           Malic_M  78 .leeekkpfakkkeelkeakdkltLeevvkkvkptvliGlsgvagafteeivremaksterPiilplSNPtskaEat 153
                                        l+ ++++fa +  e         Le++++   ++v +Gl++ + + ++++vr+ma   + Pii+++ NPt   E  
  gi|336253573|ref|YP_004596680.1| 232 dLNAYNREFAADVPEG-------GLEQAIDG--ADVFVGLAA-GDIVSQDMVRSMA---DDPIIFAMANPTP--EIG 293
                                       2566666666555555.......6*****97..69*****76.7899*******98...57**********8..677 PP

                                       HHHHHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHHH CS
                           Malic_M 154 aedvlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseeel 230
                                        e++ +  d+++++a+G          +  +++Q NN++ fP +  g++ +ra++i++ m +aaaeala+l++e+ +
  gi|336253573|ref|YP_004596680.1| 294 YEEAKAARDDTVIMATG----------RSDYPNQVNNVLGFPFIFRGALDVRATEINEAMKVAAAEALADLAKEDVP 360
                                       89999999********8..........56789***************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (751 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.62u 0.22s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 5686.63
//
Query:       gi|336253574|ref|YP_004596681.1|  [L=166]
Description: hypothetical protein Halxa_2177 [Halopiger xanaduensis SH-6]
Scores for 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   1.6       0.11   12.8   1.6    2.0  1  DUF2171   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2171  Uncharacterized protein conserved in bacteria (DUF2171)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.6   6.2e-06      0.11       4      58 ..      10      76 ..       8      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.2e-06
                           DUF2171  4 hmeVvgsdGehvGtVDhvegdrikLtkddseeg............gqhhyiplswVasvdddkVhLs 58
                                      + +V  ++G +vGt + vegd   +  +  +              ++ + +  + Va v+dd+V+L+
  gi|336253574|ref|YP_004596681.1| 10 GKPVENANGDRVGTIETVEGDVAHVRPNADAVDsikssigwesraDETLPLTRDRVADVTDDAVRLE 76
                                      568999**************98888776665556888999999777778888899*********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1274.47
//
Query:       gi|336253575|ref|YP_004596682.1|  [L=475]
Description: peptidase M14 carboxypeptidase A [Halopiger xanaduensis SH-6]
Scores for 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-09   37.0   0.0    7.9e-09   35.7   0.0    1.5  1  Peptidase_M14  Zinc carboxypeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M14  Zinc carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   4.4e-13   7.9e-09      12     114 ..      50     136 ..      43     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 4.4e-13
                                       STTTEEEEEEEE-TTS-EEEEEEE-SSTTSTTST-CEEEEEE-SSTT-HHHHHHHHHHHHHHHHHTTTSHHHHHHHH CS
                     Peptidase_M14  12 ypdlvrlvsiGkSvegRplkvlkisssateaeegkpvvlidggiHarEwigsalllylleqLlsaYgedeeikelld 88 
                                       + + v++ ++G+S+ g+p+++++++++        ++ l+ g  H++E igs ++  ll++L++    ++e++  l 
  gi|336253575|ref|YP_004596682.1|  50 EHEHVTYEELGESADGNPIWAATVGEG-------SRTALMLGAPHPNEPIGSMTVDFLLHELAT----NDELRASL- 114
                                       3455799******************75.......8999*************************6....57786666. PP

                                       HEEEEEES-STHHHHHHHHHT-TTTT CS
                     Peptidase_M14  89 dtdiyilpvlNPDGyeysstedrlwr 114
                                       d++++ +pv+ PDG+ +       w 
  gi|336253575|ref|YP_004596682.1| 115 DYEFVCVPVADPDGVRRNE----GWF 136
                                       689***********99877....454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 3326.01
//
Query:       gi|336253576|ref|YP_004596683.1|  [L=388]
Description: Butyryl-CoA dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-52  176.3   4.1    6.6e-52  175.7   4.1    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    4.1e-33  114.4   0.1    1.1e-32  113.0   0.1    1.7  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
      4e-25   87.9   0.0      1e-24   86.5   0.0    1.8  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    9.6e-25   87.4   8.0    1.9e-24   86.4   8.0    1.5  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
      0.022   14.8   0.5      0.039   14.0   0.5    1.3  1  DUF743         Protein of unknown function (DUF743)
        1.3    9.3   4.1        5.5    7.3   0.1    3.2  3  PDZ_5          PDZ domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.7   4.1   2.2e-55   6.6e-52       1     149 [.     238     386 ..     238     387 .. 0.97

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 2.2e-55
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       gkG+++a + l+ +R+a+a +a+gla++al+ aleya +r++fgk ++dhq+v++kla+m+++++aarll+++aa++
  gi|336253576|ref|YP_004596683.1| 238 GKGLKAAFSILTGGRIAIASQAVGLAQAALDDALEYATEREQFGKSIADHQAVAHKLADMRTQVQAARLLARDAARK 314
                                       79*************************************************************************97 PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                          ++ d+++as aK+fase+a+eva++a+q++Gg+Gy+++  ver+yrda+v++i+eGtseiq++iia++l
  gi|336253576|ref|YP_004596683.1| 315 NGGDDVDPMAASTAKYFASEAAVEVANEAVQIHGGYGYTTDFDVERYYRDAKVTTIYEGTSEIQKEIIAQHL 386
                                       7777777**************************************************************975 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.1   3.7e-36   1.1e-32       1     112 [.       4     114 ..       4     115 .. 0.97

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 3.7e-36
                                       THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HH CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradag 77 
                                       ++eqe +rd+vref+e+e++p+aae+d++gefp+++w++lael+l+g+tvpeeygG ++d+l+a +v+eela++ ++
  gi|336253576|ref|YP_004596683.1|   4 SPEQELVRDSVREFVEREVEPVAAEADANGEFPEDVWDALAELDLTGLTVPEEYGGFDADPLTASVVYEELAYGHLS 80 
                                       68*************************************************************************** PP

                                       HHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                     Acyl-CoA_dh_N  78 lalllgvhsslvapailrfGteeqkrryLpklasg 112
                                       la++l+vhs      i +fG e++ +++Lp++++g
  gi|336253576|ref|YP_004596683.1|  81 LATALSVHSLAT-ACIREFGAEAHMDEWLPEMVDG 114
                                       *******98555.69******************98 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   3.5e-28     1e-24       1      96 [.     119     225 ..     119     226 .. 0.92

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 3.5e-28
                                       EEE---SS-SS-GGG---EE.EEETT.EEEEEEEEEEEETTTT-SEEEEEEE........TS---.....----EEE CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvktta.aerdggeyvlnGeKiwitnaaiatlalvlar........tekpd.....rarglsl 63 
                                       afal+Ep+aGs+ a+++tta  ++d geyvlnG+K+witn++ + +++++a+        +   d      a++++ 
  gi|336253576|ref|YP_004596683.1| 119 AFALSEPDAGSNPAEMSTTArLDEDAGEYVLNGTKQWITNGERSGVVILFAKvagesdgdS---DadsspDADTITQ 192
                                       79***************************************************99876652...13456779***** PP

                                       EEEE..GGGEEE-----BSS-TTS-EEEEEEE. CS
                     Acyl-CoA_dh_M  64 flvprdapgvsvrrieeklGlrglptgelvfed 96 
                                       flvp+d+ g++v+++e+klGlr  +t+ lvf+d
  gi|336253576|ref|YP_004596683.1| 193 FLVPKDTAGLEVGKKEDKLGLRASDTTTLVFDD 225
                                       *******************************98 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4   8.0   6.4e-28   1.9e-24       2     133 ..     254     375 ..     253     376 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 6.4e-28
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                        ia +a+G+A+aal++++e+a+er +  +g+++ad++a+ ++la+++++++AAr+l ++aa++     ++g+ v   
  gi|336253576|ref|YP_004596683.1| 254 AIASQAVGLAQAALDDALEYATEREQ--FGKSIADHQAVAHKLADMRTQVQAARLLARDAARK-----NGGDDV--- 320
                                       699***********************..**************************988888777.....899998... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                       d   a++a+ +a+e a+++++++++++Gg++++++  ++R++RDa++++++++++
  gi|336253576|ref|YP_004596683.1| 321 DPMAASTAKYFASEAAVEVANEAVQIHGGYGYTTDFDVERYYRDAKVTTIYEGTS 375
                                       778999*********************************************9987 PP

>> DUF743  Protein of unknown function (DUF743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   1.3e-05     0.039      13      95 ..     246     331 ..     241     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                            DUF743  13 aiveGkkldlaarqleldkaaldterelalaklalerqalnnqvekfdkilelrvqGdlqrvrllraa....Glrvd 85 
                                       +i+ G ++ +a++ + l +aald   e+a ++ ++ +   + q    +k  ++r q ++ r+ +  aa    G  vd
  gi|336253576|ref|YP_004596683.1| 246 SILTGGRIAIASQAVGLAQAALDDALEYATEREQFGKSIADHQ-AVAHKLADMRTQVQAARLLARDAArkngGDDVD 321
                                       6778999*****************************9955555.566899999*99999998665554333356677 PP

                            DUF743  86 Pysytrqniy 95 
                                       P + +  +++
  gi|336253576|ref|YP_004596683.1| 322 PMAASTAKYF 331
                                       7766655555 PP

>> PDZ_5  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2       0.3   9.1e+02      57      66 ..      21      30 ..      13      34 .. 0.81
   2 ?    0.4   0.0      0.27   8.1e+02      57      68 ..      61      72 ..      59      74 .. 0.91
   3 ?    7.3   0.1    0.0018       5.5      53      65 ..     313     327 ..     307     332 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.3
                             PDZ_5 57 dvDPvaAsAE 66
                                      +v+PvaA A+
  gi|336253576|ref|YP_004596683.1| 21 EVEPVAAEAD 30
                                      8******996 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.27
                             PDZ_5 57 dvDPvaAsAEYE 68
                                      d DP++As  YE
  gi|336253576|ref|YP_004596683.1| 61 DADPLTASVVYE 72
                                      78*******998 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0018
                             PDZ_5  53 RRn..edvDPvaAsA 65 
                                       R+n  +dvDP+aAs 
  gi|336253576|ref|YP_004596683.1| 313 RKNggDDVDPMAAST 327
                                       666558*******94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2657.24
//
Query:       gi|336253577|ref|YP_004596684.1|  [L=568]
Description: methylmalonyl-CoA mutase, large subunit [Halopiger xanaduensis SH-6]
Scores for 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-215  714.4   0.3     8e-215  714.2   0.3    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase
     0.0039   15.7   0.1     0.0075   14.8   0.1    1.4  1  Met_asp_mut_E  Methylaspartate mutase E chain (MutE)
  ------ inclusion threshold ------
       0.41   10.2   6.8       0.25   10.9   4.6    1.7  2  PrkA           PrkA serine protein kinase C-terminal domain


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.2   0.3  1.3e-218    8e-215       2     513 .]      38     559 ..      37     559 .. 0.97

  Alignments for each domain:
  == domain 1  score: 714.2 bits;  conditional E-value: 1.3e-218
                     MM_CoA_mutase   2 TaegievkplYtaedl...eekklgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtgl 75 
                                       T ++ ev++lYt+ed+   +  +    +PGe P+tRG+++tmyrgr+Wt+rq+agf+taeetner+++l+++Gqtgl
  gi|336253577|ref|YP_004596684.1|  38 TVSNHEVDRLYTPEDIadlDY-EEDLGFPGEPPYTRGPYPTMYRGRTWTMRQFAGFGTAEETNERFHYLIDEGQTGL 113
                                       88999***********85522.34446************************************************** PP

                     MM_CoA_mutase  76 svafdlptlrgyDsdhpraegevGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdle 152
                                       s+afd+p+l+g+Dsdhp++egevGk+Gva+d+l+dme+l+dgid+ +vs+s+tin +a+ ++amy+a+a++qgv+++
  gi|336253577|ref|YP_004596684.1| 114 STAFDMPSLMGIDSDHPMSEGEVGKEGVAVDTLRDMEILFDGIDVGEVSTSFTINPSAPVIYAMYVALADRQGVPRD 190
                                       ***************************************************************************** PP

                     MM_CoA_mutase 153 klsgtiqnDiLkellargtyiyppepslrliadiieyaakevpkfntisvsgyhireaGatavqElAftladGveYv 229
                                       +++gt+qnD+Lke++a++++++ppepsl++++d+ie+a +e+pkf++is+sgyhireaG+ta+qE AftladG++Yv
  gi|336253577|ref|YP_004596684.1| 191 EIRGTLQNDMLKEFIAQKEWVIPPEPSLEVVTDTIEFAVEETPKFHPISISGYHIREAGSTAAQEAAFTLADGFAYV 267
                                       ***************************************************************************** PP

                     MM_CoA_mutase 230 ralleaGldvdefaprlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklrvhaqTsgvsltaqdpyv 306
                                       + +le+Gldvdefap lsFff+ ++ +feeiAk+RAaRr++ar+++++++a++ +s ++++h+qT+g sltaq+p +
  gi|336253577|ref|YP_004596684.1| 268 EDCLERGLDVDEFAPLLSFFFNSHNSIFEEIAKFRAARRVYARTMEDRYDAAKAESKRMKFHTQTAGQSLTAQQPLN 344
                                       ***************************************************************************** PP

                     MM_CoA_mutase 307 NilRttlealaAvlggtqslhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaeka 383
                                       Ni+R+t++ala+vlggtqslhtnsfDealalP+e+++r+A++tq+i+aeEsg a++vDP+gGS+ +E+LT+e++e++
  gi|336253577|ref|YP_004596684.1| 345 NIVRVTIQALAGVLGGTQSLHTNSFDEALALPSEEAVRVALRTQQIIAEESGAADIVDPMGGSFAIEKLTNEMEEEI 421
                                       ***************************************************************************** PP

                     MM_CoA_mutase 384 wklfqeieeaG......GmlkaiesGlvqeeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkideeveer 454
                                       +++++eiee+G      G+l+ i+ G++q+ei+++++++q+++e+++ev+vGvN+++  ee++  ++l+ide+++er
  gi|336253577|ref|YP_004596684.1| 422 TAYLAEIEELGdgslrdGVLEGISGGYFQREIQDASYEYQQRVERGEEVVVGVNAYT-IEEDTSPDILQIDETTRER 497
                                       ********************************************************5.555789************* PP

                     MM_CoA_mutase 455 qaerlealraerdeaavkaaLaalgeaarse...nllaraveaaralatlGeisdaleevfg 513
                                       q erle+++aerd++av+aaL+al +a+ ++   n+++++v+a++a+ t+Gei++++e+ +g
  gi|336253577|ref|YP_004596684.1| 498 QLERLESVKAERDDEAVEAALEALADAIAEDkneNVMPYIVDAVKAYTTMGEIMRVFEDRYG 559
                                       **************************66645699***********************99886 PP

>> Met_asp_mut_E  Methylaspartate mutase E chain (MutE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.3e-06    0.0075     267     362 ..     349     448 ..     298     462 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-06
                     Met_asp_mut_E 267 islgaavaalakatkvivKtphEalgvptkeanaaglratkqvlnlledqklee....teeleeekelikketrail 339
                                       +++ a + +l++++ + + + +Eal  p++ea   +lr+ + + +     ++ +    + ++e+ ++ +++e++a l
  gi|336253577|ref|YP_004596684.1| 349 VTIQALAGVLGGTQSLHTNSFDEALALPSEEAVRVALRTQQIIAEESGAADIVDpmggSFAIEKLTNEMEEEITAYL 425
                                       5567888999****************************988888777666665312225578888889999****** PP

                     Met_asp_mut_E 340 dkvlelgdGDvavgavrafeaGv 362
                                        ++ elgdG ++ g++++++ G 
  gi|336253577|ref|YP_004596684.1| 426 AEIEELGDGSLRDGVLEGISGGY 448
                                       ******************99986 PP

>> PrkA  PrkA serine protein kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.3   7.9e+03      30      40 ..     106     116 ..      91     119 .. 0.67
   2 ?   10.9   4.6   4.2e-05      0.25      17     136 ..     426     547 ..     408     563 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.3
                              PrkA  30 ereGmsGispR 40 
                                        +eG++G+s+ 
  gi|336253577|ref|YP_004596684.1| 106 IDEGQTGLSTA 116
                                       37999999985 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.2e-05
                              PrkA  17 eeedvkeLreeaeereG.msGispRyvikilsealss...seakeekcinpldvlealeeglkeheviseeerekyl 89 
                                       +e  ++eL + +  r+G  +Gis+ y ++ +++a  +   + ++ e+++  ++     e+   +  +i+e++re+ l
  gi|336253577|ref|YP_004596684.1| 426 AE--IEELGDGS-LRDGvLEGISGGYFQREIQDASYEyqqRVERGEEVVVGVNAYTIEEDTSPDILQIDETTRERQL 499
                                       22..44443333.3788459************99665443455778888889998889999999999********** PP

                              PrkA  90 eflevvreeydervkkevqeAllyseeeqieelvenYl.dhveayikk 136
                                       e+le+v+ e d+ + +   eAl+ +  e  +e v+ Y+ d+v+ay++ 
  gi|336253577|ref|YP_004596684.1| 500 ERLESVKAERDDEAVEAALEALADAIAEDKNENVMPYIvDAVKAYTTM 547
                                       *************************************54999*99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 4118.59
//
Query:       gi|336253578|ref|YP_004596685.1|  [L=265]
Description: alpha/beta hydrolase fold protein [Halopiger xanaduensis SH-6]
Scores for 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   89.7   3.5    4.9e-25   89.4   3.5    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.3e-19   70.9   0.0    1.5e-18   67.4   0.0    2.0  1  Abhydrolase_1  alpha/beta hydrolase fold
    1.6e-15   57.0   0.1    6.2e-15   55.1   0.1    1.8  1  Hydrolase_4    Serine aminopeptidase, S33
    4.9e-05   23.4   0.0    0.00014   21.8   0.0    1.7  2  UPF0227        Uncharacterised protein family (UPF0227)
    0.00098   17.9   0.0      0.002   16.9   0.0    1.4  2  Ndr            Ndr family
  ------ inclusion threshold ------
      0.021   14.5   0.0      0.028   14.0   0.0    1.4  1  Esterase       Putative esterase
      0.025   14.4   0.0       0.03   14.2   0.0    1.1  1  Palm_thioest   Palmitoyl protein thioesterase
      0.058   13.2   0.0       0.22   11.3   0.0    1.9  3  Abhydrolase_5  Alpha/beta hydrolase family
      0.072   12.2   0.0      0.087   12.0   0.0    1.1  1  DUF2920        Protein of unknown function (DUF2920)
      0.073   12.8   0.1          2    8.1   0.1    2.1  2  PGAP1          PGAP1-like protein
        0.1   12.5   0.0        3.8    7.3   0.0    2.1  2  Ser_hydrolase  Serine hydrolase
       0.16   12.1   0.0       0.24   11.5   0.0    1.3  1  Thioesterase   Thioesterase domain
       0.28    9.9   0.0        0.4    9.4   0.0    1.1  1  Peptidase_S28  Serine carboxypeptidase S28


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   3.5   3.6e-28   4.9e-25       1     215 [.      24     247 ..      24     252 .. 0.68

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 3.6e-28
                                       EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH.CHHHHHHHCCTT..TTSEEEEEETCHH CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldled.ladlaalldelaagggpvvlvGHSlGG 76 
                                       ++++HGa +++ +Wl  p ++ la+ ++v+apDlpGhG++ +  +  ++ + +l+++++     +g ++lvG SlGG
  gi|336253578|ref|YP_004596685.1|  24 IVFVHGAAMTRKMWL--PQRRDLAGEFRVVAPDLPGHGSRAREQFRMDPaISQLHDVVRTHT--DGSAILVGLSLGG 96 
                                       8*************8..777777999************554444444443344455555554..5668********* PP

                                       HHHHHHHHCC.........EEEEES-..----TTTS----TTHHHHHH........TT-C...CCCHCCHS-HSCCC CS
                     Abhydrolase_6  77 alalaaapla.......lvvgvlldppptalpagllaaalelllalla........llrl...lawlsreplprlfl 135
                                       ++a+++a+         +++g  ++p   + ++g l +a   l +ll+                +w++r+    ++ 
  gi|336253578|ref|YP_004596685.1|  97 YVATEYAHRYpsnvdglVLSGSSVNP---VRGMGVLTRATGGLTRLLTkpdagkraG--ErfaTRWVRRR----DLP 164
                                       *****776669977776556677777...6666663333333333333222322222..02345999655....444 PP

                                       CHHH....CCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH.STTEEETCE...SS CS
                     Abhydrolase_6 136 aded....adaawrarlarlaallaglgllpaaawadlpvpllvl.ggeDplvprllerlla.qagarlpvvlpgaG 206
                                        d++    +   +   + ++a+  ag+++++  a+ ++p p+lvl g++D+l++r  +++++ ++  r+ +vl++aG
  gi|336253578|ref|YP_004596685.1| 165 QDVEreiiEAGFYPKQFGDAAPDIAGRDFRS--ALSTYPGPTLVLnGENDKLMRRGEQAHARaAQNGRI-EVLADAG 238
                                       4444322236788888888888888888777..*********99999****99966555555669****.******* PP

                                       S-HHHHSHH CS
                     Abhydrolase_6 207 Hlphleepd 215
                                       H  +l +p+
  gi|336253578|ref|YP_004596685.1| 239 HICNLHRPR 247
                                       *55554775 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0   1.1e-21   1.5e-18       2     254 ..      23     243 ..      22     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 1.1e-21
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       ++v++hG +++  +w      ++La  +f+v+++Dl+G+g+   a +    +++++     l+ ++  + d++ +lv
  gi|336253578|ref|YP_004596685.1|  23 AIVFVHGAAMTRKMWLP--QRRDLAG-EFRVVAPDLPGHGSR--ARE----QFRMDPAISQLHDVVRTHTDGSAILV 90 
                                       79***************..******9.***********9964..553....49************99999******* PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHH CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrh 155
                                       G S+GG +a++ya +yp++V++lvl g+       +    + +  + ++  g     +++ ag  ++ + a+ ++r 
  gi|336253578|ref|YP_004596685.1|  91 GLSLGGYVATEYAHRYPSNVDGLVLSGS-------SVNPVRGMGVLTRATGGLTRLLTKPDAGKRAGERFATRWVRR 160
                                       ****************************.......888888888888889999999999999999999999999995 PP

                                       HHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHH CS
                     Abhydrolase_1 156 rlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaled 232
                                               +d  ++ +++ +    +++++++ + + +  +d+++ l  + +      ptlv+ g++D+l+  +++  
  gi|336253578|ref|YP_004596685.1| 161 --------RDLPQDVEREIIEAGFYPKQFGDAAPDIA-GRDFRSALSTYPG------PTLVLNGENDKLMRRGEQAH 222
                                       ........79999999999999999999996666655.5555556667777......******************** PP

                                       HHHCHTSEEEEEEETCSSSHHH CS
                     Abhydrolase_1 233 laqllpkkrlvvisdagHlafl 254
                                        +++ ++ r +v++dagH+ +l
  gi|336253578|ref|YP_004596685.1| 223 ARAAQNG-RIEVLADAGHICNL 243
                                       *******.**********9776 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.1   4.5e-18   6.2e-15       5     231 ..      22     238 ..      18     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 4.5e-18
                       Hydrolase_4   5 avvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfll 81 
                                       +++v+vHG a + +      ++La  +f v+a D  GhG  + ++ ++++    +  l+     v+++h +   +l+
  gi|336253578|ref|YP_004596685.1|  22 QAIVFVHGAAMTRKMWLPQRRDLAG-EFRVVAPDLPGHGSRAREQFRMDPA---ISQLHD----VVRTHTDGSAILV 90 
                                       689*******************987.6**************8777744443...444433....3567778889*** PP

                       Hydrolase_4  82 GhSmGGliallyllrypdkvaglilsaPalkikaklk.appllklllkllgkllpklqvsnnlkadslsrdpevvaa 157
                                       G S+GG++a++y++ryp++v+gl+ls++ +++   +  ++++   l +ll k     +  ++  ++++ r    ++ 
  gi|336253578|ref|YP_004596685.1|  91 GLSLGGYVATEYAHRYPSNVDGLVLSGSSVNPVRGMGvLTRATGGLTRLLTKPDAGKRAGERFATRWVRRRDLPQD- 166
                                       *********************************9987788888888888888888888877777777777666555. PP

                       Hydrolase_4 158 yeadplv.hgkitvrlllelld.amkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypgly 231
                                         + +++  g    +++  + d a+ + ++  + +  P+l+l Ge+Dk++ ++++++  +r+++ + ++++ + + 
  gi|336253578|ref|YP_004596685.1| 167 -VEREIIeAGFYPKQFGDAAPDiAGRDFRSALSTYPGPTLVLNGENDKLMRRGEQAH--ARAAQ-NGRIEVLADAG 238
                                       .6778884555555555555553567777777888899***********99666533..33332.45565555555 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     1e-07   0.00014      41      80 ..      67     106 ..      59     126 .. 0.88
   2 ?   -1.6   0.0       1.6   2.3e+03     131     150 ..     198     217 ..     184     254 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1e-07
                           UPF0227  41 dpqqalkeleklvaelgddnillvGssLGGyyatrlgerf 80 
                                        +  a+ +l+ +v  ++d + +lvG sLGGy+at  ++r+
  gi|336253578|ref|YP_004596685.1|  67 RMDPAISQLHDVVRTHTDGSAILVGLSLGGYVATEYAHRY 106
                                       57789*****************************999988 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                           UPF0227 131 lkrperilvllskqDevldy 150
                                        + p ++lvl + +D  +  
  gi|336253578|ref|YP_004596685.1| 198 STYPGPTLVLNGENDKLMRR 217
                                       56688889999988887755 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.4e-06     0.002      55     129 ..      47     115 ..      33     128 .. 0.78
   2 ?   -3.8   0.0       2.9     4e+03     199     216 ..     151     168 ..     143     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.4e-06
                                       TSEEEEEE-TT-STT-----TT-----HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEE CS
                               Ndr  55 kfvilhvdaPGqeegaaslpedyqfpslddladqllavldhfklksviglGvgaGAyilarfalkhperveglvL 129
                                       +f ++  d PG+ + a + ++    p++     ql  v+   +  s+i +G   G y+ + +a ++p+ v glvL
  gi|336253578|ref|YP_004596685.1|  47 EFRVVAPDLPGHGSRAREQFRM--DPAIS----QLHDVVRTHTDGSAILVGLSLGGYVATEYAHRYPSNVDGLVL 115
                                       5566666777777777543332..25554....566688888889*****************************9 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.9
                                       HHHHHHHHT-------TT CS
                               Ndr 199 elyleaynkRrdleierk 216
                                       e++ + + +Rrdl ++ +
  gi|336253578|ref|YP_004596685.1| 151 ERFATRWVRRRDLPQDVE 168
                                       578888999999998766 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.1e-05     0.028     110     153 ..      79     123 ..      54     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                                       CSEECCC.EEEEEETHHHHHHHHHHHCSTTTC.CEEEEES--S-CC CS
                          Esterase 110 frtapdg.ravaGqSmGGlgALilalkhpdrF.gsvssfSpivnps 153
                                        rt++dg   ++G S+GG++A  +a ++p    g v+s S  vnp+
  gi|336253578|ref|YP_004596685.1|  79 VRTHTDGsAILVGLSLGGYVATEYAHRYPSNVdGLVLSGS-SVNPV 123
                                       56777776779******************98845677766.67877 PP

>> Palm_thioest  Palmitoyl protein thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.2e-05      0.03       2     109 ..      24     126 ..      23     182 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                      Palm_thioest   2 vviwhGldsaesn.mqklaeliekligtyvknveigeseaedrkasffgnlndqveavckklelangfhaiGfSQGg 77 
                                       +v++hG     +  + + ++l+ +     v+  ++  + ++ r++  + ++  q+ +v++  +++   +++G+S Gg
  gi|336253578|ref|YP_004596685.1|  24 IVFVHGAAMTRKMwLPQRRDLAGE---FRVVAPDLPGHGSRAREQFRMDPAISQLHDVVRT-HTDGSAILVGLSLGG 96 
                                       788888833333355555555555...444444555556677888999999*******999.678999********* PP

                      Palm_thioest  78 lflRaliercddkknvrnlislggpqaGvfgl 109
                                        ++  ++ r++  + v+ l+  g+  + v g+
  gi|336253578|ref|YP_004596685.1|  97 YVATEYAHRYP-SN-VDGLVLSGSSVNPVRGM 126
                                       **********4.44.9****999998888774 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    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      46      89 ..      75     118 ..      69     134 .. 0.84
   2 ?   -3.5   0.0       5.6   7.7e+03     144     156 ..     175     187 ..     160     195 .. 0.67
   3 ?   -2.0   0.0       1.9   2.6e+03      96     119 ..     197     220 ..     189     233 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                     Abhydrolase_5  46 aeeiikeapklekfvvgGhslGGvvasrfaaee.ekiegvvflas 89 
                                        +++++ + +    ++ G slGG va+++a++  ++++g+v+ +s
  gi|336253578|ref|YP_004596685.1|  75 LHDVVRTHTDG-SAILVGLSLGGYVATEYAHRYpSNVDGLVLSGS 118
                                       56788888874.478889*************98579****99776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.6
                     Abhydrolase_5 144 GsYGeqkGDkkat 156
                                       G Y +q GD +  
  gi|336253578|ref|YP_004596685.1| 175 GFYPKQFGDAAPD 187
                                       5577777776655 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.9
                     Abhydrolase_5  96 lselskkvlsivgteDgvlnvksl 119
                                       ls+   ++l + g++D ++   + 
  gi|336253578|ref|YP_004596685.1| 197 LSTYPGPTLVLNGENDKLMRRGEQ 220
                                       566677899999999999876554 PP

>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.3e-05     0.087     169     217 ..      74     122 ..      69     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-05
                           DUF2920 169 dlvkrfpkeadlpviliGgsyGGYlalLiaKiaPwyvdgvlDnssvakp 217
                                       +l     +++d   il+G s GGY+a   a   P  vdg++   s+ +p
  gi|336253578|ref|YP_004596685.1|  74 QLHDVVRTHTDGSAILVGLSLGGYVATEYAHRYPSNVDGLVLSGSSVNP 122
                                       55555567788999*************************8765555554 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.062        86       5      27 ..      22      48 ..      19      69 .. 0.81
   2 ?    8.1   0.1    0.0014         2      66     124 ..      63     115 ..      56     123 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.062
                             PGAP1  5 ipVlFvpGnagsykqv....rslAsea 27
                                        ++Fv+G a++ k +    r lA+e 
  gi|336253578|ref|YP_004596685.1| 22 QAIVFVHGAAMTRKMWlpqrRDLAGEF 48
                                      579********9997766668888876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0014
                             PGAP1  66 ldqaeylndaIkyIlslysssekeptsviliGHSmGGivaraaltlknyikqsvntilt 124
                                       ++q ++ + aI ++ ++   +++   s il+G S+GG va   + +++  +++v+ ++ 
  gi|336253578|ref|YP_004596685.1|  63 REQFRM-DPAISQLHDVV--RTHTDGSAILVGLSLGGYVA---TEYAHRYPSNVDGLVL 115
                                       555555.67777777777..56667899************...4455555666666665 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.056        77      47      86 ..      76     115 ..      53     132 .. 0.81
   2 ?    7.3   0.0    0.0027       3.8      75     153 ..     161     240 ..     150     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.056
                                       HHHHHC.-STTEEEEEETCHHHHHHHHHHHTTSSSEEEEEE CS
                     Ser_hydrolase  47 eaavea.aeekvvlvAHSlgclavlhaaelqlakkvagalL 86 
                                       +  v++ + + ++lv  Slg  ++ ++a  + +++v+g +L
  gi|336253578|ref|YP_004596685.1|  76 HDVVRThTDGSAILVGLSLGGYVATEYA-HRYPSNVDGLVL 115
                                       444443145679****************.9999***99988 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0027
                                       HTTSSSEEEEEEET--SGGS..TT.GGGCGCTTS.-SSHHCCHCEEEEETTBTTC-HHHHHHHHHHCT-EEEEETT- CS
                     Ser_hydrolase  75 lqlakkvagalLVapadveeeaaklaelaefapl.preklpfpslvvaSenDpyvsfeeaeelaeawgaelvdlgea 150
                                       + l++ v++ ++ a++ +++   +++ +a ++     ++ p p+lv+  enD++++  e ++  +a + ++ +l  a
  gi|336253578|ref|YP_004596685.1| 161 RDLPQDVEREIIEAGFYPKQFGDAAPDIAGRDFRsALSTYPGPTLVLNGENDKLMRRGEQAHARAAQNGRIEVLADA 237
                                       55566666666666666665555555555554330345678899***********987766666666779999**** PP

                                       TTS CS
                     Ser_hydrolase 151 GHi 153
                                       GHi
  gi|336253578|ref|YP_004596685.1| 238 GHI 240
                                       **9 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00018      0.24      34      97 ..      54     113 ..      23     124 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                       CSTTSTSHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHHHHHHHHCT-SEEEE CS
                      Thioesterase  34 qlpgrerdepplesieelaaeyaealrqiqpegPyalfGhSlGgllAfevArqLesqGlavksl 97 
                                        lpg+++  ++   ++  ++++ + +r ++ +g   l+G SlGg++A e A+++ s+   v +l
  gi|336253578|ref|YP_004596685.1|  54 DLPGHGSRAREQFRMDPAISQLHDVVR-THTDGSAILVGLSLGGYVATEYAHRYPSN---VDGL 113
                                       555555555555555555555555555.5677899*****************98765...4444 PP

>> Peptidase_S28  Serine carboxypeptidase S28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00029       0.4     100     148 ..      72     120 ..      68     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00029
                     Peptidase_S28 100 ikalkqkfklsssskwitfGgSYsgsLaawarkkyPelvvgavaSSaPl 148
                                       i +l+  ++++++   i++G S +g  a++  + yP  v+g v S + +
  gi|336253578|ref|YP_004596685.1|  72 ISQLHDVVRTHTDGSAILVGLSLGGYVATEYAHRYPSNVDGLVLSGSSV 120
                                       7777778888999999*************************99887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2088.30
//
Query:       gi|336253579|ref|YP_004596686.1|  [L=262]
Description: 3-oxoacyl-(acyl-carrier-protein) reductase [Halopiger xanaduensis SH-6]
Scores for 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-48  162.7   0.0    1.4e-47  162.3   0.0    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    2.9e-38  131.3   0.0    3.4e-38  131.1   0.0    1.1  1  adh_short     short chain dehydrogenase
    3.1e-08   33.7   0.0    5.1e-08   33.0   0.0    1.3  1  KR            KR domain
  ------ inclusion threshold ------
      0.016   15.1   0.1      0.031   14.2   0.1    1.4  1  3HCDH_N       3-hydroxyacyl-CoA dehydrogenase, NAD binding do


Domain annotation for each model (and alignments):
>> 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 !  162.3   0.0   3.1e-51   1.4e-47       4     234 .]      17     258 ..      12     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 162.3 bits;  conditional E-value: 3.1e-51
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.E.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.v.lecDVtdeeqvealveevvekfgklDilvnna 77 
                                       sg+G+a A ala+eG +vv+  ++e++ +++ ++++e    e v  + D t+e+++e+lve++v++fg+lD lv +a
  gi|336253579|ref|YP_004596686.1|  17 SGLGKASATALAREGVNVVINGRDEDRlADAKADIEEVATGEvVaQPGDLTEEDDIEQLVETTVDEFGGLDHLVTSA 93 
                                       9**************************5555555555444443479******************************* PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealt 152
                                       g  p+  gpflet++e++ +a +  + s+++la++a+p++keg  g ivn++s + + ++++    + ++ ++++l 
  gi|336253579|ref|YP_004596686.1|  94 GGPPS--GPFLETDDEDWYEAYELLVMSVVRLAREAEPHLKEGegGTIVNITSRSVKEAIDSLVLSNSVRMSVIGLE 168
                                       *****..*********************************99999******************************** PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT.......HHHHHHHHH..HHSTTSS-B-HHHHHHHHHHHCSGGGT CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgikg.......fdelleele..araplgrlgtpeevaeaalfLasdeas 220
                                       ++l  e++p  +R Nav pgp +T   +++ +        d+ +e le  a  pl+r+g+p e +++++fL s+++ 
  gi|336253579|ref|YP_004596686.1| 169 KTLSQEFAP-DVRANAVLPGPHETSRIEDLVEqavergeYDSYEEGLEnwADNPLERVGDPMELGNTVAFLSSPQSG 244
                                       *********.9*************88665544333334444455555422567************************ PP

                                       T--SEEEEESTTGG CS
                      adh_short_C2 221 yitGqtlvvDgGlt 234
                                       +i+Gq +v+DgG t
  gi|336253579|ref|YP_004596686.1| 245 FINGQSIVIDGGTT 258
                                       ************87 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.1   0.0   7.6e-42   3.4e-38       2     191 ..       9     198 ..       8     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 131.1 bits;  conditional E-value: 7.6e-42
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgk 77 
                                       ++lvt  ssG+G+a a +la+eG++vv+ +r e++l+ +++ ++e    +++a ++D+t+++++e+lve+ v+++g+
  gi|336253579|ref|YP_004596686.1|   9 AALVTASSSGLGKASATALAREGVNVVINGRDEDRLADAKADIEEVaTGEVVAQPGDLTEEDDIEQLVETTVDEFGG 85 
                                       79********************************************999**************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       ld Lv+ AG   sgpf e+++e+w + +e+ +++v+ l+r++ p+++++++G+Ivn++S   k++  +++   +   
  gi|336253579|ref|YP_004596686.1|  86 LDHLVTSAGGPPSGPFLETDDEDWYEAYELLVMSVVRLAREAEPHLKEGEGGTIVNITSRSVKEAIDSLVLSNSVRM 162
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakelr 191
                                        v+gl ++l++e+ap+ +r nav PG+ +T   ++l 
  gi|336253579|ref|YP_004596686.1| 163 SVIGLEKTLSQEFAPD-VRANAVLPGPHETSRIEDLV 198
                                       ***************8.************98766655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   1.1e-11   5.1e-08       4     110 ..      11     114 ..       9     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.1e-11
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       l+t    gLG++ a+ la++g  ++v+ +R++   +d+ka i+e++    ev + + D++++d++e+l+e+  +e++
  gi|336253579|ref|YP_004596686.1|  11 LVTASSSGLGKASATALAREGV-NVVINGRDEDRLADAKADIEEVAT--GEVVAQPGDLTEEDDIEQLVETTVDEFG 84 
                                       7888999**************7.7999****9999999999998876..68999*********************** PP

                                       ---EEEE---------TTT--HHHHHHHHT CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvla 110
                                        +   + +Ag    +++ e+++ed+ ++++
  gi|336253579|ref|YP_004596686.1|  85 GLDHLVTSAGGPPSGPFLETDDEDWYEAYE 114
                                       *************************99876 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 ?   14.2   0.1   6.8e-06     0.031      10      59 ..      19      70 ..      16      84 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.8e-06
                                      CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH..HHHCCTTTTSS-HHH CS
                           3HCDH_N 10 mGagiaavfasagleVvlvdiseealekalekiek..sleklvekgklkeee 59
                                      +G+  a+++a++g++Vv+  ++e++l++a++ ie+  + e +++ g l+ee+
  gi|336253579|ref|YP_004596686.1| 19 LGKASATALAREGVNVVINGRDEDRLADAKADIEEvaTGEVVAQPGDLTEED 70
                                      69999*****************************954445566777777444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.34
# Mc/sec: 2280.78
//
Query:       gi|336253580|ref|YP_004596687.1|  [L=130]
Description: Cupin 2 barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-16   58.5   0.4    5.4e-16   58.1   0.4    1.2  1  Cupin_2          Cupin domain
     0.0002   20.7   0.0       0.01   15.1   0.0    2.1  1  CDO_I            Cysteine dioxygenase type I
    0.00049   19.7   0.1    0.00068   19.3   0.1    1.3  1  Cupin_3          Protein of unknown function (DUF861)
     0.0013   18.8   0.0     0.0016   18.5   0.0    1.2  1  HutD             HutD
     0.0013   18.6   0.0     0.0015   18.4   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
     0.0016   18.4   0.0     0.0021   18.0   0.0    1.2  1  AraC_binding     AraC-like ligand binding domain
  ------ inclusion threshold ------
      0.024   14.1   0.0      0.052   13.0   0.0    1.5  2  PCO_ADO          PCO_ADO
       0.17   11.5   0.2       0.39   10.4   0.2    1.7  1  Auxin_BP         Auxin binding protein


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 !   58.1   0.4   2.4e-19   5.4e-16       4      71 .]      35     101 ..      32     101 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 2.4e-19
                                       EEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEEE CS
                           Cupin_2   4 elppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvvy 71 
                                       e ppG+s+p+h H++e ++ ++leGe+++  ++ ev+le+ dsv  +a++ Hr++Ntgde a+ l+v+
  gi|336253580|ref|YP_004596687.1|  35 EKPPGHSSPMHDHENE-QVCVCLEGELTVVTENDEVTLERYDSVWLDAWESHRVENTGDERAVGLDVF 101
                                       569*************.*************99999****************************99996 PP

>> CDO_I  Cysteine dioxygenase type I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.7e-06      0.01      63     158 ..      23     103 ..       2     107 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.7e-06
                                       E-GGGT-EEEEEEE-TT-B--EE--TT-EEEEEEEES-EEEEEE----SS-----EEEEEE--TT-EEEE-TTT-EE CS
                             CDO_I  63 vagngksellllcWgpGtassvHDHtdsvgalkllaGeLkEtkfAwalkrleesdivdekrllsngtayvndelglH 139
                                       +ag+ ++       +pG++s +HDH + + + + l+GeL+              +  ++++ l+  ++   d  + H
  gi|336253580|ref|YP_004596687.1|  23 LAGSDRFSFEWFEKPPGHSSPMHDHENEQ-VCVCLEGELTV-------------VTENDEVTLERYDSVWLDAWESH 85 
                                       566666666666679**********9876.456899*9973.............33333344445567777788888 PP

                                       EEEES-SSS-EEEEEEEES CS
                             CDO_I 140 rveNlSsdegAVSlHlYaP 158
                                       rveN+  de AV l ++aP
  gi|336253580|ref|YP_004596687.1|  86 RVENTG-DERAVGLDVFAP 103
                                       888888.888888888887 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 !   19.3   0.1     3e-07   0.00068       4      61 ..      26      84 ..      23      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3e-07
                                      CTCCEEEEEEEECEEE.EECESS.EEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEE CS
                           Cupin_3  4 lgvfswgiwectpGkf.rltyee.dEfcyileGevkvtpeggetvelraGDlvvlpkgls 61
                                      +++fs   +e  pG   +++  e ++ c  leGe +v+  +  +v+l+ +D+v l ++ s
  gi|336253580|ref|YP_004596687.1| 26 SDRFSFEWFEKPPGHSsPMHDHEnEQVCVCLEGELTVVT-ENDEVTLERYDSVWLDAWES 84
                                      5667777788888875246666658889***********.9999***********99985 PP

>> HutD  HutD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     7e-07    0.0016     125     178 ..      41      92 ..      18      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7e-07
                                       EEEEE.--SEEEEEESSS-EEEEETTE..EEEE-TT-EEEEES--EEEEEEEEE CS
                              HutD 125 aaasasgastvllfllkgqlevtlsveaadetlaagdalllegeaalelelege 178
                                       ++ ++++++  ++++l+g+l+v +  e++++tl+++d+++l++ +++++e +g+
  gi|336253580|ref|YP_004596687.1|  41 SSPMHDHENEQVCVCLEGELTVVT--ENDEVTLERYDSVWLDAWESHRVENTGD 92 
                                       333444788889******998854..5789************999666666655 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   6.8e-07    0.0015      60     127 ..      26      92 ..       8     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.8e-07
                   MannoseP_isomer  60 geryqvkritvkPgeklslqkhhhraeh.WvvvkGtakvtvddevlllkenestyiplgaihrlenpGk 127
                                       ++r+     +  Pg+  s  +h h  e   v+++G   v +++++++l+  +s+++ + + hr+en G 
  gi|336253580|ref|YP_004596687.1|  26 SDRFSFEWFEKPPGH--SSPMHDHENEQvCVCLEGELTVVTENDEVTLERYDSVWLDAWESHRVENTGD 92 
                                       566666666655554..5678999998735889**********************************96 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 !   18.0   0.0   9.3e-07    0.0021      11      67 ..      37      93 ..      31     112 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.3e-07
                                      STT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTS CS
                      AraC_binding 11 ypdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsed 67
                                       p+hs p h h++ ++++++eG+ ++  ++ ++ l+  d ++l   e H+ e  +++
  gi|336253580|ref|YP_004596687.1| 37 PPGHSSPMHDHENEQVCVCLEGELTVVTENDEVTLERYDSVWLDAWESHRVENTGDE 93
                                      699**********************************************99988765 PP

>> PCO_ADO  PCO_ADO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.3e-05     0.052      38      67 ..      23      52 ..       8      77 .. 0.84
   2 ?   -2.2   0.0         1   2.3e+03     126     143 ..      85     103 ..      83     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                           PCO_ADO 38 lyetdsfslgvFvlppgaviPLHdHPgMtv 67
                                      l  +d+fs  +F  ppg++ P+HdH + +v
  gi|336253580|ref|YP_004596687.1| 23 LAGSDRFSFEWFEKPPGHSSPMHDHENEQV 52
                                      66789********************77665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                           PCO_ADO 126 Heitait.gpaaflDilsP 143
                                       H++++   + a+ lD+ +P
  gi|336253580|ref|YP_004596687.1|  85 HRVENTGdERAVGLDVFAP 103
                                       8888888788888999999 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00017      0.39      52      80 ..      37      65 ..      31     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                                      -TT-B--EEEESS-EEEEEEE--EEEEE- CS
                          Auxin_BP 52 apgsrtpihrhsceevfvvlkgkgtlyla 80
                                       pg+ +p+h h  e+v v l g+ t++  
  gi|336253580|ref|YP_004596687.1| 37 PPGHSSPMHDHENEQVCVCLEGELTVVTE 65
                                      59********************9998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1129.49
//
Query:       gi|336253581|ref|YP_004596688.1|  [L=277]
Description: fumarylacetoacetate (FAA) hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-48  163.0   0.0    9.8e-48  162.7   0.0    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.7   0.0   5.5e-52   9.8e-48       2     218 .]      75     276 ..      74     276 .. 0.91

  Alignments for each domain:
  == domain 1  score: 162.7 bits;  conditional E-value: 5.5e-52
                                       EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE........EEEEEEEESS-B--T- CS
                     FAA_hydrolase   2 ivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPag..sekldyEvELavvigkplrevl 76 
                                        +++glnyaeh+ ++    e+ p+     ep+ f+k++s+l+gpg pir+P    se++  E+ELavv g+++r v 
  gi|336253581|ref|YP_004596688.1|  75 LWGIGLNYAEHAGDLD---EQRPE-----EPASFMKPSSALTGPGGPIRLPPLerSERVTAEAELAVVAGRQCRSV- 142
                                       689***********96...66666.....888********************989999******************. PP

                                       -HHHHHTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT--...-SS-EEEEEETTEEEEE CS
                     FAA_hydrolase  77 sveeAedaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeled...pedlelrlrvngeevqd 150
                                       + + ++daiaGy+ + D++a d+ +++      +++ksfd+f ++Gp +  + e +d    e+l++r+ vn+ +  +
  gi|336253581|ref|YP_004596688.1| 143 DEDGVDDAIAGYLPVIDMTAEDVLQRNPR--FLTRAKSFDSFLVVGPTV-AVPEPDDalaLEELTVRTVVNDRVAAE 216
                                       99*********************999983..4567************96.444444444589*************** PP

                                       EEGGGTTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE. CS
                     FAA_hydrolase 151 sntkdmifspaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrVa 218
                                        ++++m+f+p e++a  s ++tLe Gdl++tGTp g  a     + +++gD v++e+eg+G++ ++V+
  gi|336253581|ref|YP_004596688.1| 217 NEIRNMLFPPREIVAFHSDVMTLESGDLFSTGTP-G--A-----EPIEPGDDVRAEVEGIGTVSAPVV 276
                                       **********************************.5..3.....46*****************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       182  (0.0101512); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); 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: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 2408.07
//
Query:       gi|336253582|ref|YP_004596689.1|  [L=402]
Description: threonine synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-70  238.0   4.7    1.8e-70  237.7   4.7    1.0  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 !  237.7   4.7     1e-74   1.8e-70       5     294 .]      71     370 ..      68     370 .. 0.94

  Alignments for each domain:
  == domain 1  score: 237.7 bits;  conditional E-value: 1e-74
                                       SSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                              PALP   5 igpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllar.lkegtgaktvveassGNhgralAaaaallGlk 80 
                                        g TPlvr+++l +  g++l lK E+ nptgSfKdRg +  +++ l+ g   + + + s GN++++++a+aa++Gl+
  gi|336253582|ref|YP_004596689.1|  71 PGTTPLVRAEGLDEYAGCRLSLKPEGQNPTGSFKDRGTAVGVEYgLRDG--HDWIGTVSHGNMALSTSAYAAAAGLE 145
                                       589*****************************************55555..************************** PP

                                       EEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT.T CS
                              PALP  81 vtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlg.g 156
                                       + ++vpad++ e+++l+ ++Ga++ +v+gdy +  a    l+ae  g+++ s++  p++++g++t+++Eileq++  
  gi|336253582|ref|YP_004596689.1| 146 AAVFVPADTPLERLELIARHGARIFRVEGDYGRLYAETLGLEAE-VGRFVNSDT--PLRVAGQKTVAYEILEQFQpS 219
                                       *************************************9999999.999999988..*******************99 PP

                                       TEEEEEEE-SSSHHHHHHHHHHHH........HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B...SSS.CCST CS
                              PALP 157 kpdavvvpvGgGgliaGiaaglke........rrpd..vrvigvepegsdalarslragrrvtvpvs..dtiadgla 221
                                       +pda+v+pv++Gg ++G++++l+e        +  d  +r++ v+++ +d++a++ r+gr++    +  +tia ++a
  gi|336253582|ref|YP_004596689.1| 220 APDAIVLPVSSGGQASGVWKALREleaaglldA--DdvPRLYLVQAAACDPIATASREGRESVSAIEpgETIAVSIA 294
                                       ************************887776422..268******************9999876555555******** PP

                                       CS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 222 vg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                       +    ++++a+ +++++++ +v+v+de++ eam +la+++gi vepssa+ala++ +l ++gel++++ vv+iltg
  gi|336253582|ref|YP_004596689.1| 295 NAdpPSGTRALTAARETGGAVVSVPDEATREAMDRLATAAGISVEPSSAVALAGVrELSRRGELDADEEVVTILTG 370
                                       **99999********************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2766.69
//
Query:       gi|336253583|ref|YP_004596690.1|  [L=217]
Description: metallophosphoesterase [Halopiger xanaduensis SH-6]
Scores for complete 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   31.7   0.6    8.5e-07   29.3   0.5    2.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    6.5e-07   30.1   0.3    1.6e-05   25.6   0.3    2.2  1  Metallophos    Calcineurin-like phosphoesterase
    6.9e-06   25.6   0.0    1.3e-05   24.7   0.0    1.3  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 !   29.3   0.5   1.4e-10   8.5e-07       4     142 ..       2     185 ..       1     201 [. 0.62

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.4e-10
                     Metallophos_2   4 aiiSDlH.snldaleavlealkevgvdaiihaGDleeeepevleellelapvlaVrGNnD................. 62 
                                       +++ D H +  ++ e++le  ++v++d+++ +GDl        ++l +  p   + GNn+                 
  gi|336253583|ref|YP_004596690.1|   2 LVLGDAHaADPARRETLLELYRRVDPDRVLQVGDL------EYYDLPA--PTWFIAGNNEdfdviesmranerpfge 70 
                                       7899***55566778899****************6......3344444..555555555555555555554444444 PP

                     Metallophos_2  63 ..............................eev.veedvlreaaelgtdlpeeaelelagekvlliHgdpl...... 102
                                                                     ++   + +  r+ ++ ++d++ +++l  ++++v+l+H+ p       
  gi|336253583|ref|YP_004596690.1|  71 snvhllastaatvdgvrvaglsgnyaptkyDQPrSKLAGERRRHFTREDVERARDL--ENVDVFLTHEAPTgllsyg 145
                                       44444444444444444444444444554322233333334444444444444444..5888*******88*99885 PP

                     Metallophos_2 103 ..gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvn 142
                                          + +++++ll++   + +++++GH H+++ ++ g+++vv 
  gi|336253583|ref|YP_004596690.1| 146 ydPGCEHVDDLLEA--IDPELCLVGHHHEHRETELGETRVVS 185
                                       55444444444444..4444*****************99995 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.3   2.6e-09   1.6e-05       4     203 ..       2     172 ..       1     173 [. 0.63

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.6e-09
                                       EEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS....C CS
                       Metallophos   4 lvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe....g 76 
                                       lv+gD H a  +++ ++ll+l++++    +pd vl +GD          l+++   l   p p ++++GN e     
  gi|336253583|ref|YP_004596690.1|   2 LVLGDAH-AADPARRETLLELYRRV----DPDRVLQVGD----------LEYY--DL---PAPTWFIAGNNEdfdvI 58 
                                       5666666.55555555555555555....6666666666..........3333..33...4489********55320 PP

                                       HHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHH CS
                       Metallophos  77 fee.ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepgdewlk 152
                                         e    n +++ + + ++  s a +++++ +a+l ++  +  + +   p+   +l   ++            ++ +
  gi|336253583|ref|YP_004596690.1|  59 --EsMRANERPFGESNVHLLASTAATVDGVRVAGLSGN--YAPTKYDQ-PRS--KLAGERR-----------RHFTR 117
                                       ..212233333333337777777888888888886666..33333333.222..2222222...........34444 PP

                                       H..HHHHTTCSEEEEEESSESS..CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 153 d..lekrekadwvivlgHsply..rgsgylfgdealedllkkygvdlvisGHtHv 203
                                       +   ++r+   ++++l+H  ++   ++gy  g e+++dll+  ++ l++ GH H+
  gi|336253583|ref|YP_004596690.1| 118 EdvERARDLENVDVFLTHEAPTglLSYGYDPGCEHVDDLLEAIDPELCLVGHHHE 172
                                       4455667777799*********9*9*****************************7 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.1e-09   1.3e-05     114     233 ..      67     185 ..      37     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.1e-09
                                       TTT-TTEEE-SSEEEEETTTEEEEEE-SEEESS--BS.SSS-EEEHHHHHHHGGGGGGS---EE..EEEESS--S-S CS
                     Metallophos_3 114 evvfpnlkvvhesfaekeGevliaGmGGeivdgekee.efrLkYPaweveyrLkvlkelkdrrk..vlllatpPige 187
                                           +n++ +  + a  +G v +aG+ G+    + ++   +L+   +   ++   ++ ++d     v+l +  P+g 
  gi|336253583|ref|YP_004596690.1|  67 PFGESNVHLLASTAATVDG-VRVAGLSGNYAPTKYDQpRSKLA-GERRRHFTREDVERARDLENvdVFLTHEAPTGL 141
                                       5567999************.*********98888877444454.4555677777777777766522788899****9 PP

                                       STBTTBS---S-HHHHHHHHHH--SEEEE-SS--EE.EEETTEEEEE CS
                     Metallophos_3 188 lvadkglkekgsevvaelvktlnPevvvvghavkeh.eelgktlvvn 233
                                       l    +    g e v +l+  ++Pe+ +vgh + ++  elg+t vv+
  gi|336253583|ref|YP_004596690.1| 142 LSYGYD---PGCEHVDDLLEAIDPELCLVGHHHEHReTELGETRVVS 185
                                       987766...7999******************98888558****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1683.34
//
Query:       gi|336253584|ref|YP_004596691.1|  [L=45]
Description: hypothetical protein Halxa_2187 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00012   22.0   0.7    0.00014   21.8   0.7    1.1  1  zinc-ribbons_6  zinc-ribbons
    0.00061   19.9   3.8    0.00094   19.3   3.8    1.4  1  Zn-ribbon_8     Zinc ribbon domain
     0.0017   18.4   1.2     0.0021   18.0   1.2    1.2  1  DZR             Double zinc ribbon
     0.0029   17.6   1.1     0.0029   17.6   1.1    1.0  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.01   15.9   4.6      0.023   14.8   4.6    1.6  1  DUF1272         Protein of unknown function (DUF1272)
  ------ inclusion threshold ------
       0.02   14.6   0.6       0.02   14.5   0.6    1.0  1  TackOD1         Thaumarchaeal output domain 1
      0.021   14.5   0.4      0.026   14.2   0.4    1.1  1  zf-P11          P-11 zinc finger
      0.051   13.6   1.4      0.059   13.4   1.4    1.1  1  Zn_Tnp_IS91     Transposase zinc-binding domain
      0.069   12.7   2.4       0.81    9.3   0.2    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.074   13.0   2.3       0.15   11.9   2.3    1.6  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.11   12.6   4.7       0.97    9.6   4.7    2.0  1  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.11   12.2   0.9        2.3    8.0   0.1    2.1  2  zinc_ribbon_5   zinc-ribbon domain
       0.17   11.7   5.5          1    9.2   0.5    2.1  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
       0.18   11.5   4.1       0.37   10.5   4.1    1.5  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.36   11.2   0.3       0.36   11.2   0.3    2.0  2  DUF983          Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.7   1.2e-07   0.00014      11      40 ..       2      34 ..       1      38 [. 0.80

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.2e-07
                                      EE-SSEEE-TTT--...EEEEEEE-SSS-S--- CS
                    zinc-ribbons_6 11 ekrgeqyhCeaCqe...dlkkealCpeCeqele 40
                                      ++ +++y+Ce+C++    ++  a Cp+C+ +l 
  gi|336253584|ref|YP_004596691.1|  2 KRYENHYECEECESevhPVSYRARCPDCGGPLR 34
                                      56779*********4444567899*****9986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   3.8   7.8e-07   0.00094       6      37 ..       8      34 ..       1      35 [. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.8e-07
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgsevr 37
                                      Y+CeeC +e  ++          CP+Cg+++r
  gi|336253584|ref|YP_004596691.1|  8 YECEECESEVHPVSY-----RARCPDCGGPLR 34
                                      9******99888863.....345******987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.2   1.8e-06    0.0021      13      39 ..       8      34 ..       2      39 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.8e-06
                               DZR 13 rfCseCgtklkavaaedrCpsCgekvd 39
                                        C+eC +++ +v+   rCp Cg ++ 
  gi|336253584|ref|YP_004596691.1|  8 YECEECESEVHPVSYRARCPDCGGPLR 34
                                      5699*****9999999******98865 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 !   17.6   1.1   2.4e-06    0.0029      67      94 ..       4      31 ..       1      38 [. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-06
                                      E--EEEETTTS-EEECHHHHHS-TTTSS CS
                              HypA 67 vpvkvrCreCgkefeleekalrCpkCgs 94
                                       + +++C+eC++e++  ++++rCp+Cg+
  gi|336253584|ref|YP_004596691.1|  4 YENHYECEECESEVHPVSYRARCPDCGG 31
                                      567899*********7766789****97 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   4.6   1.9e-05     0.023      27      55 ..       8      37 ..       3      39 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                           DUF1272 27 yEctFCaeCaeev.lenvCPncgGelvkRP 55
                                      yEc  C++ ++ v ++ +CP+cgG l + P
  gi|336253584|ref|YP_004596691.1|  8 YECEECESEVHPVsYRARCPDCGGPLRASP 37
                                      777777665554425899*******99887 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.6   1.7e-05      0.02     142     169 ..       3      30 ..       1      37 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                           TackOD1 142 rplevykCnsCkslfsepevkarClsCe 169
                                       r +++y+C++C+s +   + +arC +C+
  gi|336253584|ref|YP_004596691.1|   3 RYENHYECEECESEVHPVSYRARCPDCG 30 
                                       5566777777777777777777777775 PP

>> zf-P11  P-11 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   2.2e-05     0.026      19      46 ..       5      34 ..       2      37 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                                      SSSEEEHHHHHHHHHHS..SBETTTSSB-- CS
                            zf-P11 19 sdHYLClrClqllLsvs..erCpiCkkPLP 46
                                      ++HY C +C   +  vs   rCp C  PL 
  gi|336253584|ref|YP_004596691.1|  5 ENHYECEECESEVHPVSyrARCPDCGGPLR 34
                                      79********99988873368****99995 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 ?   13.4   1.4     5e-05     0.059      38      65 ..       6      31 ..       3      37 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5e-05
                       Zn_Tnp_IS91 38 aryeCeeCghekivyfsCksrhCpsCqk 65
                                      ++yeCeeC+ +++++ s + r Cp C+ 
  gi|336253584|ref|YP_004596691.1|  6 NHYECEECE-SEVHPVSYRAR-CPDCGG 31
                                      589*****8.5999***9988.****96 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2   0.00068      0.81       1      13 [.       6      18 ..       6      22 .. 0.85
   2 ?    3.9   0.1     0.035        41       5       9 ..      26      30 ..      23      36 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00068
                            zf_UBZ  1 dtylCerCgkeip 13
                                      ++y Ce+C +e+ 
  gi|336253584|ref|YP_004596691.1|  6 NHYECEECESEVH 18
                                      58******99986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.035
                            zf_UBZ  5 CerCg 9 
                                      C++Cg
  gi|336253584|ref|YP_004596691.1| 26 CPDCG 30
                                      ****9 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 ?   11.9   2.3   0.00013      0.15       5      35 ..       8      34 ..       4      36 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                    Zn_ribbon_SprT  5 YrCtgCgreythhlsirrhnYrCrrCkgtLr 35
                                      Y C  C   +++h  + r++  C+ C+g Lr
  gi|336253584|ref|YP_004596691.1|  8 YECEECE--SEVHPVSYRAR--CPDCGGPLR 34
                                      7777777..67888888866..888888776 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 ?    9.6   4.7   0.00081      0.97       2      29 ..      10      36 ..       2      39 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00081
                          zf-Mss51  2 CPvpkhkqtapkhvdfeCpdCGiptycs 29
                                      C  ++++  +p + +  CpdCG p   s
  gi|336253584|ref|YP_004596691.1| 10 CEECESEV-HPVSYRARCPDCGGPLRAS 36
                                      77775555.68889999******98776 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.057        68       4      10 ..       9      15 ..       8      20 .. 0.86
   2 ?    8.0   0.1     0.002       2.3       2      10 ..      23      31 ..      22      38 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.057
                     zinc_ribbon_5  4 rCpdCdt 10
                                       C++C++
  gi|336253584|ref|YP_004596691.1|  9 ECEECES 15
                                      6****98 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.002
                     zinc_ribbon_5  2 iirCpdCdt 10
                                      + rCpdC+ 
  gi|336253584|ref|YP_004596691.1| 23 RARCPDCGG 31
                                      679****95 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 ?    5.7   0.5     0.011        13       3      12 ..       9      18 ..       7      24 .. 0.85
   2 ?    9.2   0.5   0.00085         1       3      12 ..      25      34 ..      23      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                                      E-SSS--EEE CS
                    zf-C4_Topoisom  3 kCPkCggdLv 12
                                      +C++C ++++
  gi|336253584|ref|YP_004596691.1|  9 ECEECESEVH 18
                                      8*****9986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00085
                                      E-SSS--EEE CS
                    zf-C4_Topoisom  3 kCPkCggdLv 12
                                       CP Cgg+L 
  gi|336253584|ref|YP_004596691.1| 25 RCPDCGGPLR 34
                                      6******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 ?   10.5   4.1   0.00031      0.37       1      24 [.       8      30 ..       8      31 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                                      -B-SSS--B--.--SSS----SSS- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevs.lkkgdpiRCkeCG 24
                                      Y C eC++ev  ++ +   RC +CG
  gi|336253584|ref|YP_004596691.1|  8 YECEECESEVHpVSYR--ARCPDCG 30
                                      9*********977777..8*****9 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.6      0.13   1.5e+02       9      20 ..       8      19 ..       4      24 .. 0.82
   2 ?   11.2   0.3   0.00031      0.36       6      28 ..      21      43 ..      18      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.13
                            DUF983  9 daCeaCgldlsh 20
                                       +Ce+C+ + + 
  gi|336253584|ref|YP_004596691.1|  8 YECEECESEVHP 19
                                      58*****99875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00031
                            DUF983  6 kvadaCeaCgldlsharaddgPa 28
                                      + + +C+ Cg  l++ ++ dg+a
  gi|336253584|ref|YP_004596691.1| 21 SYRARCPDCGGPLRASPSYDGAA 43
                                      5689*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 348.90
//
Query:       gi|336253585|ref|YP_004596692.1|  [L=169]
Description: hypothetical protein Halxa_2188 [Halopiger xanaduensis SH-6]
Scores for 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:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1249.39
//
Query:       gi|336253586|ref|YP_004596693.1|  [L=246]
Description: xylose isomerase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   68.2   3.2      1e-18   67.6   3.2    1.3  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.094   11.5   0.0       0.16   10.7   0.0    1.3  1  UxuA          D-mannonate dehydratase (UxuA)


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 !   67.6   3.2   1.1e-22     1e-18       2     209 ..      23     203 ..      22     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 1.1e-22
                                       HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraiel 78 
                                       +++ e+ fdgvE+++r  +  +     +l+++  al++++l++a+ +   ++          +      +++   el
  gi|336253586|ref|YP_004596693.1|  23 DLVGETSFDGVEFATRIRDEET-----DLEAVIDALERNDLEVAAAHVGLDDLE--------N------DYEAVTEL 80 
                                       5666888**************8.....58*************999999988888........3......57899*** PP

                                       HHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC.HHHHHHHHHHTTT CS
                      AP_endonuc_2  79 aaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd.eelarlldavdsp 154
                                         +LG+++lv++   +  +++   e+ ++ +ae+l ++ad +++ g  l +++++ ++v+lg    l++ll + +  
  gi|336253586|ref|YP_004596693.1|  81 YGRLGCRTLVVP---WLEPERFASEDSIADAAERLSAVADDLAADGFDLQYHNHDQEFVSLGTkTGLDELLGRAE-- 152
                                       ************...5599999999**********************************9999999********9.. PP

                                       TEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSS CS
                      AP_endonuc_2 155 nvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeGe 209
                                       nvg+ +D g++ + ++d+ ++++++adri+h H++Da+g         v++geG+
  gi|336253586|ref|YP_004596693.1| 153 NVGFEIDLGWARAGGADPVAVVDRYADRISHAHFADADG----ETMTCVELGEGD 203
                                       5*************************************9....555555555554 PP

>> UxuA  D-mannonate dehydratase (UxuA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   1.8e-05      0.16     254     311 ..     169     222 ..     159     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.8e-05
                                       -HHHHHHHHGGGEEEEE--EEEE-SSTT-EEEE-TTSSSS-HHHHHHHHHHHHHHH-E CS
                              UxuA 254 dlvemikefadriyFahlRnikreedeksFveaahleGsvdlaevvkalleeeyrryl 311
                                       d v+++ ++adri  ah+ +   e    + +  +  eG++d+ + ++a+   + ++y+
  gi|336253586|ref|YP_004596693.1| 169 DPVAVVDRYADRISHAHFADADGE----TMTCVELGEGDLDVERALEAVRRADVEWYI 222
                                       56899*************998877....566777899*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1748.44
//
Query:       gi|336253587|ref|YP_004596694.1|  [L=71]
Description: hypothetical protein Halxa_2190 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0012   18.6   1.8      0.036   13.8   0.2    2.4  2  Rubredoxin_2     Rubredoxin metal binding domain
     0.0088   16.4   0.5      0.011   16.1   0.5    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
       0.12   12.3   5.2       0.28   11.1   1.1    2.4  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.22   11.6   3.7       0.33   11.0   0.4    2.1  2  Rubredoxin       Rubredoxin
        1.1    9.4   3.9       0.67   10.0   1.7    1.9  2  Ogr_Delta        Ogr/Delta-like zinc finger
        5.9    6.7   7.0        7.8    6.3   1.4    2.2  2  zf-MIZ           MIZ/SP-RING zinc finger


Domain annotation for each model (and alignments):
>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.2   1.2e-05     0.036      12      22 ..      10      20 ..       7      25 .. 0.87
   2 ?    3.9   0.1     0.015        46      11      19 ..      31      39 ..      29      44 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                      Rubredoxin_2 12 kwfGrCpsCgs 22
                                      +w +rCp C +
  gi|336253587|ref|YP_004596694.1| 10 RWGWRCPRCDA 20
                                      8********86 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.015
                      Rubredoxin_2 11 akwfGrCps 19
                                       ++++ Cp+
  gi|336253587|ref|YP_004596694.1| 31 ETFLWECPE 39
                                      6799****6 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 !   16.1   0.5   3.7e-06     0.011       6      59 ..      15      67 ..      13      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.7e-06
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCad..CgastpwfkiaedeaeaekeaieaWN 59
                                      CP C  +a++ +++r+        +C +  C a +  f+ + +   a  e  e +N
  gi|336253587|ref|YP_004596694.1| 15 CPRCDADATVTKDPRTETF---LWECPEesCSAIGFGFSSRRKARIALREYRERYN 67
                                      *****************97...999*7778***99999999999999999999888 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 ?   11.1   1.1   9.2e-05      0.28       2      23 ..      10      31 ..       9      38 .. 0.76
   2 ?    3.7   0.5     0.019        57       2      25 ..      32      62 ..      31      71 .] 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.2e-05
                    Zn_ribbon_SprT  2 kyvYrCtgCgreythhlsirrh 23
                                      ++ +rC++C+   t++   r++
  gi|336253587|ref|YP_004596694.1| 10 RWGWRCPRCDADATVTKDPRTE 31
                                      799*******877776666665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.019
                    Zn_ribbon_SprT  2 kyvYrCt..gCgreythhlsirrhn......Y 25
                                      ++ + C+  +C   +++ +s+rr +      Y
  gi|336253587|ref|YP_004596694.1| 32 TFLWECPeeSCS-AIGFGFSSRRKArialreY 62
                                      789999866677.5788888888776666665 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00011      0.33      33      43 ..      11      21 ..       6      25 .. 0.79
   2 ?    1.5   0.2       0.1     3e+02      35      39 ..      35      39 ..      33      47 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                      TT-BBTTTB-B CS
                        Rubredoxin 33 ddWvCPdCgve 43
                                        W+CP C+++
  gi|336253587|ref|YP_004596694.1| 11 WGWRCPRCDAD 21
                                      57******997 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.1
                                      -BBTT CS
                        Rubredoxin 35 WvCPd 39
                                      W+CP+
  gi|336253587|ref|YP_004596694.1| 35 WECPE 39
                                      9***6 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 ?   10.0   1.7   0.00022      0.67       1      23 [.      14      36 ..      14      57 .. 0.86
   2 ?   -0.7   1.1      0.47   1.4e+03      14      14 ..      51      51 ..      36      68 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
                         Ogr_Delta  1 rCPhCgapaaartsrnlskdvre 23
                                      rCP C a a++++  ++ + ++e
  gi|336253587|ref|YP_004596694.1| 14 RCPRCDADATVTKDPRTETFLWE 36
                                      7**************99999987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.47
                         Ogr_Delta 14 s 14
                                      s
  gi|336253587|ref|YP_004596694.1| 51 S 51
                                      1 PP

>> zf-MIZ  MIZ/SP-RING zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.4    0.0026       7.8      42      49 ..      13      20 ..       5      21 .. 0.85
   2 ?    4.5   0.2    0.0098        29      37      46 ..      28      39 ..      19      44 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0026
                                      -B-TTT-- CS
                            zf-MIZ 42 WnCPvCsk 49
                                      W+CP C++
  gi|336253587|ref|YP_004596694.1| 13 WRCPRCDA 20
                                      ******97 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0098
                                      HHS--..-B-TT CS
                            zf-MIZ 37 ertet..WnCPv 46
                                       rtet  W+CP 
  gi|336253587|ref|YP_004596694.1| 28 PRTETflWECPE 39
                                      4555566****5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 519.14
//
Query:       gi|336253588|ref|YP_004596695.1|  [L=569]
Description: Spermine synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-09   37.8   0.0    1.9e-09   37.2   0.0    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
  ------ inclusion threshold ------
      0.043   13.4   0.0      0.072   12.6   0.0    1.3  1  MTS              Methyltransferase small domain
      0.063   13.2   0.0       0.12   12.3   0.0    1.3  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
       0.16   11.7   0.0       0.28   10.9   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
        0.2   12.4   8.0        3.2    8.5   0.8    3.4  3  PrgI             PrgI family protein


Domain annotation for each model (and alignments):
>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   5.4e-13   1.9e-09      10     131 ..     283     401 ..     276     452 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 5.4e-13
                                       HHHHCCSS...ST-EEEEESSTT..SHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEEEST CS
                    Spermine_synth  10 hvplmlhk...npkevLiiGGgD..GgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklvlgd 81 
                                       h+p++      +  +vL iGGg   G +  e  ++n   ++++v+iD  v d  k++++  +++      ++++ gd
  gi|336253588|ref|YP_004596695.1| 283 HLPMLMADdpdEIDRVLFIGGGGytGPQDFE-ERYN--ATVDVVEIDPTVTDAAKEYFGLEENE-----NLTVHTGD 351
                                       7777665545667789***999766777777.6899..9*******************976666.....9******* PP

                                       CHHHHCTCSS-EEEEEEECCSTTCSSCGCSSHHHHHHHHHTEEEEEEEEE CS
                    Spermine_synth  82 gfkflkayekkfdvvivdsldpvgpaenlFskeffdllkkvlkedGviil 131
                                       g ++l+++++++d ++ d  +      +l ++ef++   + l++dG++ +
  gi|336253588|ref|YP_004596695.1| 352 GRQYLERTNETYDLIVLDAYQKDQVPFHLTTEEFMEVASERLTDDGMLYA 401
                                       *********************555555689****************9765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     2e-05     0.072      39     136 ..     302     400 ..     284     426 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                                       T-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST..TS-EEEEEE---STTTCH CS
                               MTS  39 GcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve..ekkfdlivsNPPfhagka 112
                                       G G G+ g +  +e  +a+v++v++d    ++ake +  ++ e ++v++ d+ + +e  ++ +dliv    +++++ 
  gi|336253588|ref|YP_004596695.1| 302 G-GGGYTGPQDFEERYNATVDVVEIDPTVTDAAKEYFGLEENEnLTVHTGDGRQYLErtNETYDLIVLDA-YQKDQV 376
                                       4.5588888888889999*****************98877777799999998776665489*******96.566666 PP

                                       CHHHHHHHHHHHHHHHEEEEEEEE CS
                               MTS 113 telavaeeliaeAkeaLkegGeLl 136
                                         + ++ee+++ A e+L+++G L+
  gi|336253588|ref|YP_004596695.1| 377 PFHLTTEEFMEVASERLTDDGMLY 400
                                       688899***************997 PP

>> Methyltransf_30  S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.2e-05      0.12      28      86 ..     340     399 ..     326     407 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.2e-05
                                       TTTEEEEEEES-HHHHHHHC-T-EEEEEE-SS-TTTSG.GGCSHHHHHHHHHHEEEEEEE CS
                   Methyltransf_30  28 aeevtlklligdarealkeldekadawFlDgFsPaknP.elwseellkelarllkkkgtl 86 
                                       +e+ +l+++ gd r+ l++ +e +d + lD++   + P  l +ee+++  +++l + g l
  gi|336253588|ref|YP_004596695.1| 340 EENENLTVHTGDGRQYLERTNETYDLIVLDAYQKDQVPfHLTTEEFMEVASERLTDDGML 399
                                       37889*****************************99996788999999999999888876 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 ?   10.9   0.0   7.9e-05      0.28      74     160 ..     295     381 ..     283     384 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.9e-05
                                       T-EEEEES-TTSHHH.HHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGG.G-SEEEEEE CS
                              PCMT  74 garvLevGsGsGylt.avlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyee.kaPYdaihv 148
                                        +rvL +G+G Gy     + +  +++  vv  e  + ++++ak+    ++ en++v++gDGr+  e  +  Yd i++
  gi|336253588|ref|YP_004596695.1| 295 IDRVLFIGGG-GYTGpQDFEERYNATVDVV--EIDPTVTDAAKEYFGLEENENLTVHTGDGRQYLERtNETYDLIVL 368
                                       5678888866.6654134555555555555..5558899999*********************99862568****99 PP

                                       SSBB.SS--HHHH CS
                              PCMT 149 gaaa.peiPeali 160
                                        a   +++P  l+
  gi|336253588|ref|YP_004596695.1| 369 DAYQkDQVPFHLT 381
                                       9965156887775 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.8    0.0009       3.2      17      63 ..      74     123 ..      69     143 .. 0.81
   2 ?    4.2   1.3      0.02        70      15      61 ..     173     221 ..     166     243 .. 0.69
   3 ?    0.9   0.0      0.22   7.8e+02      47      83 ..     397     434 ..     376     440 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0009
                              PrgI  17 LtlRQliflvlallvaiglylllrafl...eelasvlvillavPvaalgf 63 
                                        t R++ ++ la +v +g++++ +++l   +++ ++ + ++a+P +++ f
  gi|336253588|ref|YP_004596695.1|  74 ATTREMTWIMLATAVYMGVVIYANELLvvqTSTLALPARYAALPSVIVLF 123
                                       599************************88888888888888999554433 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.02
                              PrgI  15 fg.LtlRQliflvlallvaiglylllrafl.eelasvlvillavPvaal 61 
                                       ++ Lt+ Q++ l++ +lva +l++  +++  +++a+ +v+++ + vaa 
  gi|336253588|ref|YP_004596695.1| 173 IPlLTIGQIALLFGLMLVATALAIEAPSLPrKPTAASVVVAVLLVVAAG 221
                                       4449999999999999977777777666669555555555555544443 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.22
                              PrgI  47 asvlvillavPvaal.gfykkdglplekylkaiikfkl 83 
                                       +++ + ++++P     +fy+ +  ++++++  ++ f++
  gi|336253588|ref|YP_004596695.1| 397 GMLYANVISAPTGSAgAFYRAQYRTMDEVFPEVYSFRT 434
                                       5566667888977662555555559****999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.20s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 4247.68
//
Query:       gi|336253589|ref|YP_004596696.1|  [L=75]
Description: hypothetical protein Halxa_2192 [Halopiger xanaduensis SH-6]
Scores for 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:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 612.02
//
Query:       gi|336253590|ref|YP_004596697.1|  [L=137]
Description: polyketide cyclase/dehydrase [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00043   20.6   1.1    0.00084   19.6   1.1    1.6  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.1   4.7e-08   0.00084       1     141 [.       1     135 [.       1     137 [] 0.72

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.7e-08
                                       EEEEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCS..SEEEEEEEEEETTTTEE CS
                   Polyketide_cyc2   1 mvkvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggr..gtvreelvevdpegrll 75 
                                       m++vt+s+ ++a pe+  a++  ++ + +  ++ +++  + + ++      tv v+g    +v  ++++++  g  +
  gi|336253590|ref|YP_004596697.1|   1 MREVTASRGVDAAPEELSARLEPPTIVEAEGSFTVES--VHERDD-----ATVVVAGGpgLQVPLRFEAREN-GLYY 69 
                                       6899999999999999999999999999544444433..331233.....3333333112346666666665.8888 PP

                                       EEEEE.SSS-TSEEEEEEEEECCET..EEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHH CS
                   Polyketide_cyc2  76 syrivkpvpvanyvatwtvtpdggg..trvtwtgefdagplggpfekpaaakavkgdleagLerLkar 141
                                       + ++    p+++ ++ ++++p+++g  trv  + ++   +++ pf +  aa    g+le++Ler+ a+
  gi|336253590|ref|YP_004596697.1|  70 TQEGD-GGPFSHLETWLEFEPVDAGskTRVLMRSTVSL-AVPLPFADRIAAWKRSGELERALERIDAE 135
                                       88884.899**99**********996766666666665.678999999999999999*****999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1047.62
//
Query:       gi|336253591|ref|YP_004596698.1|  [L=684]
Description: hypothetical protein Halxa_2194 [Halopiger xanaduensis SH-6]
Scores for 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       0.51   10.8   0.1    3.1  2  CBM60     Ca-dependent carbohydrate-binding module xylan-bind


Domain annotation for each model (and alignments):
>> CBM60  Ca-dependent carbohydrate-binding module xylan-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   2.8e-05      0.51      16      61 ..     365     411 ..     357     420 .. 0.83
   2 ?    0.7   0.0      0.04   7.2e+02      40      63 ..     654     677 ..     616     684 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.8e-05
                             CBM60  16 pefrl.lvdGqkvgeadvasteaktytftadltagahklqirylNDl 61 
                                       p++ + l+ + ++g+ + ++t  + ++f+ d++++a++l+++y++D+
  gi|336253591|ref|YP_004596698.1| 365 PNLSVtLTHDHELGSSSSTTTVLNHFRFEYDYDVNAETLTVEYADDY 411
                                       56666567788888888899999***********************6 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.04
                             CBM60  40 ytftadltagahklqirylNDlyv 63 
                                        +f++d++a+ h++  ry+   +v
  gi|336253591|ref|YP_004596698.1| 654 DSFDLDVDAELHTVHLRYDGEHHV 677
                                       57999*************977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (684 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 4885.12
//
Query:       gi|336253592|ref|YP_004596699.1|  [L=99]
Description: hypothetical protein Halxa_2195 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.16   11.8   0.1       0.27   11.0   0.1    1.4  1  Cytochrom_B559a  Lumenal portion of Cytochrome b559, alpha (g


Domain annotation for each model (and alignments):
>> Cytochrom_B559a  Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   1.5e-05      0.27       4      18 ..      53      67 ..      52      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.5e-05
                                      HHHT---TTSSS-SS CS
                   Cytochrom_B559a  4 DvFGTPRPneYftqe 18
                                      D+FG P P +Y+t+e
  gi|336253592|ref|YP_004596699.1| 53 DAFGIPSPVSYYTAE 67
                                      9************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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: 00:00:00.42
# Mc/sec: 703.65
//
Query:       gi|336253593|ref|YP_004596700.1|  [L=337]
Description: arsenite-activated ATPase ArsA [Halopiger xanaduensis SH-6]
Scores for 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-69  233.7   0.0      3e-69  233.5   0.0    1.0  1  ArsA_ATPase     Anion-transporting ATPase
    1.2e-09   38.3   0.0    3.4e-09   36.8   0.0    1.8  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    1.9e-09   37.7   0.0    3.4e-09   36.9   0.0    1.3  1  AAA_31          AAA domain
    2.1e-05   24.1   0.0     0.0013   18.2   0.0    2.2  2  ParA            NUBPL iron-transfer P-loop NTPase
     0.0034   17.2   0.0       0.12   12.2   0.0    2.2  2  AAA_26          AAA domain
  ------ inclusion threshold ------
       0.01   15.2   0.1      0.018   14.4   0.1    1.4  1  ATPase          KaiC
      0.012   15.1   0.1      0.025   14.0   0.0    1.5  2  PhoH            PhoH-like protein
      0.014   15.8   0.3      0.051   14.0   0.3    2.0  1  AAA_16          AAA ATPase domain
      0.021   14.3   0.1      0.051   13.0   0.0    1.6  2  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
      0.021   14.4   3.4      0.052   13.1   1.8    2.3  3  AAA_25          AAA domain
      0.052   13.5   2.7       0.11   12.5   0.5    2.0  2  CHAD            CHAD domain
      0.061   13.2   0.1      0.097   12.5   0.1    1.3  1  Tir_receptor_N  Translocated intimin receptor (Tir) N-terminu
      0.073   13.2   0.4       0.38   10.9   0.0    2.4  3  AAA_33          AAA domain
      0.094   12.2   0.0       0.14   11.6   0.0    1.2  1  CBP_BcsQ        Cellulose biosynthesis protein BcsQ
        0.1   11.8   0.1       0.21   10.7   0.1    1.4  1  NB-ARC          NB-ARC domain
       0.11   11.8   0.3       0.24   10.6   0.0    1.7  2  Zeta_toxin      Zeta toxin
       0.16   11.7   0.1        1.4    8.6   0.1    2.4  2  AAA_24          AAA domain
       0.18   11.4   0.1       0.47   10.1   0.0    1.6  2  SRP54           SRP54-type protein, GTPase domain
       0.36   10.1   2.2         21    4.3   0.2    2.9  4  DUF1611         Domain of unknown function (DUF1611_C) P-loop
       0.72   10.4   4.3          1    9.9   0.5    2.7  3  AAA_18          AAA domain


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 !  233.5   0.0   3.3e-72     3e-69       2     303 ..      23     332 ..      22     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: 233.5 bits;  conditional E-value: 3.3e-72
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEET..SSEEEEE--HHHHHHHH CS
                       ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvk..eNLsavEidpeveleea 76 
                                       ++++vgGKGGVGKttvs+a a+++++ g ++l++stDPAhs +D+f+q++  +p+ v+  + Lsa+Eidp++e+ee 
  gi|336253593|ref|YP_004596700.1|  23 EFVFVGGKGGVGKTTVSSAYALECADAGLETLIVSTDPAHSTADVFEQEFDDDPQPVEgyDGLSAMEIDPDQEVEEH 99 
                                       79*************************************************************************** PP

                                       HCCHHGGGSCCH...HHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHH.CSSSSEEEEESBSCCHTCGGGGHHHHHH CS
                       ArsA_ATPase  77 kqevqkeeeall...gleeledvlaeelaslPGideilsfeellkyvk.eeeydvvvlDtaPTGhtlrllslpevle 149
                                         + +++ +++l   +++e++ +l+++ ++ PG  e++ f+++++ ++ ++ yd vv+Dt+PTG tlrll lp+ le
  gi|336253593|ref|YP_004596700.1| 100 LMDLKRQLNDQLsagMVNEVDAQLEMAHQT-PGAYEAALFDRFIEVMRnADPYDRVVFDTSPTGATLRLLALPDLLE 175
                                       ******999999554556666678888888.****************95667************************* PP

                                       HHHHHHHHHHHHHHHHHHHHCCCSHCHHHHHH..HHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHH CS
                       ArsA_ATPase 150 klleklvklkeklsplakqlvkllglggvsie..ealeeleetkeeikkveeiltdpertsfrlVvipEklslkEte 224
                                        ++++l+  +e+  +l ++     ++    ++    l++l+++ke+++ + e+l  +  +sf lV++p++ls++Et+
  gi|336253593|ref|YP_004596700.1| 176 GWIDRLMAKREHSIDLYEKAAIGNQAPRRVMDgdPILSRLQARKERFEFAGEVLRGQ--SSFYLVLNPDELSIRETQ 250
                                       *******99998888877664444444444445589******************875..57**************** PP

                                       HHHHHHHHTT-EEEEEEEEEE-TTCSSS....TSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHHH CS
                       ArsA_ATPase 225 RaikeLkkygikvdavivNkllpeeeqe....nCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekle 297
                                       R++++L   ++ v+ ++vN+l pe e +      ++l++r ++++++l++ie +f+  +v+++    eEv+G   le
  gi|336253593|ref|YP_004596700.1| 251 RSLAQLRDADLPVEGLVVNRLTPEPEPHeegrGATYLRQRVETERERLERIEREFDVPVVATIETRVEEVRGS-LLE 326
                                       **********************9987655577789*************************************5.677 PP

                                       HHHHHH CS
                       ArsA_ATPase 298 klsell 303
                                       ++++ l
  gi|336253593|ref|YP_004596700.1| 327 EVAAEL 332
                                       777665 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 !   36.8   0.0   3.8e-12   3.4e-09       2     112 ..      25     301 ..      24     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 3.8e-12
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       +++++kGGvGKTt++ + a   a++gl++l v +Dp  + +  ++  e d +p                        
  gi|336253593|ref|YP_004596700.1|  25 VFVGGKGGVGKTTVSSAYALECADAGLETLIVSTDPAHSTAD-VFEQEFDDDPqpvegydglsameidpdqeveehl 100
                                       689**********************************77777.666666666689********************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|336253593|ref|YP_004596700.1| 101 mdlkrqlndqlsagmvnevdaqlemahqtpgayeaalfdrfievmrnadpydrvvfdtsptgatlrllalpdllegw 177
                                       ***************************************************************************** PP

                                       ...................................................................CCHCCCHHHH CS
                                       ...................................................................xxxxxxxxxx RF
                              CbiA  55 ...................................................................dlkrllelle 64 
                                                                                                          ++    ++l+
  gi|336253593|ref|YP_004596700.1| 178 idrlmakrehsidlyekaaignqaprrvmdgdpilsrlqarkerfefagevlrgqssfylvlnpdelSIRETQRSLA 254
                                       ****************************************************************7777777777777 PP

                                       HHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC..TS-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                              CbiA  65 algkkkalllkiagvvlnrvdgeneetllkealeelkqry..gvpvlgvi 112
                                       +l+      l + g+v+nr  +e e +++  + + l qr   +++ l  i
  gi|336253593|ref|YP_004596700.1| 255 QLRDA---DLPVEGLVVNRLTPEPEPHEEGRGATYLRQRVetERERLERI 301
                                       77755...49***********99888777777777777666655555555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   3.8e-12   3.4e-09       6     130 ..      26     163 ..      23     171 .. 0.74

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 3.8e-12
                            AAA_31   6 ianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne......iektlyevli.eeknikeaiik 75 
                                       ++  KGGvGKTT s + a   a +g  +L+v  Dp  +++  ++ e ++          l  + i  +++++e ++ 
  gi|336253593|ref|YP_004596700.1|  26 FVGGKGGVGKTTVSSAYALECADAGLETLIVSTDPAHSTADVFEQEFDDdpqpveGYDGLSAMEIdPDQEVEEHLMD 102
                                       5667*********************************9999887654444555443335666667688999999997 PP

                            AAA_31  76 tk.venldlipssidLaeaeielvelekk..eeil.kellekvkde..YDyiiiDcpPsLg 130
                                        k + n +l  + ++ ++a+ e+++ +    e +l ++++e +++   YD +++D++P+  
  gi|336253593|ref|YP_004596700.1| 103 LKrQLNDQLSAGMVNEVDAQLEMAHQTPGayEAALfDRFIEVMRNAdpYDRVVFDTSPTGA 163
                                       772445577777777777777777666556644443999988887677**********855 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 !   18.2   0.0   1.5e-06    0.0013       8      41 ..      26      59 ..      21      91 .. 0.88
   2 ?    3.7   0.0     0.039        35     141     175 ..     237     271 ..     227     333 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                              ParA  8 vlSgKGGVGKStvavnlAlaLakkglkvgllDaD 41
                                       + gKGGVGK+tv++  Al+ a+ gl++ ++ +D
  gi|336253593|ref|YP_004596700.1| 26 FVGGKGGVGKTTVSSAYALECADAGLETLIVSTD 59
                                      568***********************99988777 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.039
                              ParA 141 iVttpqevaladvkkaiemfkkvkvkvlGvveNms 175
                                       +V  p e+++ +++++++ +++++++v G+v N  
  gi|336253593|ref|YP_004596700.1| 237 LVLNPDELSIRETQRSLAQLRDADLPVEGLVVNRL 271
                                       6889**************************99843 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.11     1e+02      94     135 ..      17      57 ..       3      69 .. 0.73
   2 !   12.2   0.0   0.00013      0.12     133     189 ..     237     314 ..     233     318 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                            AAA_26  94 elekdadivvVEGagglgvpiteellnadiaknlgapvilVa 135
                                       +   ++++v+V G gg+g+ +++ +   + a   g+++++V 
  gi|336253593|ref|YP_004596700.1|  17 DAGSETEFVFVGGKGGVGKTTVSSAYALECAD-AGLETLIVS 57 
                                       45667889999999999998888888887765.477777776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                            AAA_26 133 lVargglgtinqllltiealrqknvrvlGvilNkvrnp.....e................nvetlekksgipvlGvv 188
                                       lV+++++ +i  +  +++ lr+ +++v G+++N+++++     e                ++e +e  + +pv++++
  gi|336253593|ref|YP_004596700.1| 237 LVLNPDELSIRETQRSLAQLRDADLPVEGLVVNRLTPEpepheEgrgatylrqrvetereRLERIEREFDVPVVATI 313
                                       899999999*************************85555666515566666666667777999************99 PP

                            AAA_26 189 P 189
                                       +
  gi|336253593|ref|YP_004596700.1| 314 E 314
                                       7 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1     2e-05     0.018      19      93 ..      22      95 ..      18     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                            ATPase 19 grvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesae 93
                                       + v + G+ G GKt+++  ++++ a   g ++++v+++   +      ++++ d + +e  + l  +++  ++e
  gi|336253593|ref|YP_004596700.1| 22 TEFVFVGGKGGVGKTTVSSAYALECADA-GLETLIVSTDPAHSTADVFEQEFDDDPQPVEGYDGLSAMEIDPDQE 95
                                      5678999******************999.*********9877555555556777777777666666555555544 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.8e-05     0.025      10      59 ..      13      62 ..       5      73 .. 0.83
   2 ?   -3.7   0.0       7.6   6.8e+03      65      96 ..      85     116 ..      77     123 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                                      HHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S- CS
                              PhoH 10 keylealkkndivfaiGpaGtGKtylavalavealkkkkvkriiltrpav 59
                                      +++++a ++ ++vf+ G+ G GKt ++ a+a+e   ++  + i+ t pa 
  gi|336253593|ref|YP_004596700.1| 13 ATAVDAGSETEFVFVGGKGGVGKTTVSSAYALECADAGLETLIVSTDPAH 62
                                      56677777999**********************99998888888877765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.6
                                       --SS---------TTTHHHHHHHTTTS-TTCH CS
                              PhoH  65 lGflpgdleekvdpylrplydaLkdllgaekv 96 
                                       l +++ d ++ v+  l  l  +L+d l+a  v
  gi|336253593|ref|YP_004596700.1|  85 LSAMEIDPDQEVEEHLMDLKRQLNDQLSAGMV 116
                                       55566666666676666666666666665555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   5.6e-05     0.051      19     106 ..      16     128 ..      11     187 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.6e-05
                            AAA_16  19 vrsgrp.elvllsGesGvGKsslvrellralekd..............ggiflrgkcdqlesa.......ipy.... 69 
                                       v +g++ e v++ G  GvGK+++  + + +  ++               + ++++++d+ ++               
  gi|336253593|ref|YP_004596700.1|  16 VDAGSEtEFVFVGGKGGVGKTTVSSAYALECADAgletlivstdpahsTADVFEQEFDDDPQPvegydglS-Ameid 91 
                                       4556666****************988886666666655555554443322234444444422222222321.02333 PP

                            AAA_16  70 .sa.laqalareellrqlldeaesaeleawrekleeala 106
                                        ++ + + l   +l rql+d++++  +++ +++le a +
  gi|336253593|ref|YP_004596700.1|  92 pDQeVEEHL-M-DLKRQLNDQLSAGMVNEVDAQLEMAHQ 128
                                       333233333.3.555555555555566666666555555 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 ?   13.0   0.0   5.6e-05     0.051       5      43 ..      27      65 ..      23      74 .. 0.88
   2 ?   -3.0   0.1       4.4     4e+03     185     214 ..     290     320 ..     285     333 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.6e-05
                         Fer4_NifH  5 iyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDst 43
                                      + GkGG+Gk+t s+  +   a+ g   liv  DP + ++
  gi|336253593|ref|YP_004596700.1| 27 VGGKGGVGKTTVSSAYALECADAGLETLIVSTDPAHSTA 65
                                      67********************************88655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.4
                         Fer4_NifH 185 kvddereliekfaeelgtkvlevvPr.deiv 214
                                       +v++ere +e++ +e +++v++++ +  e+v
  gi|336253593|ref|YP_004596700.1| 290 RVETERERLERIEREFDVPVVATIETrVEEV 320
                                       5889999999999999999998885403444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.8   5.8e-05     0.052      32      65 ..      21      55 ..      16     161 .. 0.73
   2 ?   -1.3   0.0       1.5   1.4e+03      88     117 ..     139     168 ..     134     189 .. 0.55
   3 ?   -3.6   0.0       7.5   6.7e+03     170     186 ..     296     312 ..     289     319 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.8e-05
                            AAA_25 32 agelallaGapgtGKttlaldlalava.tGkpwlg 65
                                      + e++ + G +g+GKtt+ +  al++a  G + l 
  gi|336253593|ref|YP_004596700.1| 21 ETEFVFVGGKGGVGKTTVSSAYALECAdAGLETLI 55
                                      568999*********************88877665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                            AAA_25  88 rRlravgealrddarllvldlagveslpLf 117
                                        R+ +v++++++ +r+ + + ++   l+L+
  gi|336253593|ref|YP_004596700.1| 139 DRFIEVMRNADPYDRVVFDTSPTGATLRLL 168
                                       466666666666666666665555444444 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 7.5
                            AAA_25 170 ealeriarrtgaavllv 186
                                       e+leri+r++++ v+++
  gi|336253593|ref|YP_004596700.1| 296 ERLERIEREFDVPVVAT 312
                                       45777777777777765 PP

>> CHAD  CHAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.39   3.5e+02      71     139 ..      65     148 ..      51     222 .. 0.62
   2 ?   12.5   0.5   0.00012      0.11      57     109 ..     245     299 ..     236     332 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.39
                                       HHHHHHTHHHHH.HTS-TTTCGGGHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHT--S--......... CS
                              CHAD  71 ldVllerllsrleerlpaaeqealerllkrlekerkrararvlaaLdsaryqalldaldallaaerle......... 138
                                       +dV+++++ +     +p++  ++l +++ + ++e +++  ++ + L+++   ++++++da l+ + ++         
  gi|336253593|ref|YP_004596700.1|  65 ADVFEQEFDDD---PQPVEGYDGLSAMEIDPDQEVEEHLMDLKRQLNDQLSAGMVNEVDAQLEMAHQTpgayeaalf 138
                                       57777777764...566666677777777777777777777777777777777777777777544444333333333 PP

                                       .........T CS
                              CHAD 139 .........a 139
                                                a
  gi|336253593|ref|YP_004596700.1| 139 drfievmrnA 148
                                       3333333330 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHHHHHH.HHHTHHHHH..HTS-TTTCGGGHHHHHHHHHHHHHHH CS
                              CHAD  57 elrwlaraLGeaRDldV.llerllsrle.erlpaaeqealerllkrlekerkrar 109
                                        +r+  r+L+++RD+d  ++  + +rl  e +p +e+ +   l++r+e+er+r  
  gi|336253593|ref|YP_004596700.1| 245 SIRETQRSLAQLRDADLpVEGLVVNRLTpEPEPHEEGRGATYLRQRVETERERLE 299
                                       6899*************74444455555578899999999999999999999744 PP

>> Tir_receptor_N  Translocated intimin receptor (Tir) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00011     0.097     143     176 ..      14      47 ..       4      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                    Tir_receptor_N 143 qaidpegkdkfvftggrggaghamvtvasdiaea 176
                                        a+d+  +  fvf gg+gg g++ v+ a  +  a
  gi|336253593|ref|YP_004596700.1|  14 TAVDAGSETEFVFVGGKGGVGKTTVSSAYALECA 47 
                                       5899999****************99988765444 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   0.00043      0.38       2      47 ..      25      92 ..      24     168 .. 0.58
   2 ?   -1.7   0.0       3.3     3e+03      83     103 ..     216     236 ..     192     274 .. 0.56
   3 ?   -1.5   0.1       2.9   2.6e+03      82      99 ..     292     309 ..     279     321 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00043
                            AAA_33  2 vllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfg......tdqqskt...............d 47
                                      v++ G  G+GK+t++  ++ + +     + ++s+d ++++  +      +    +                 
  gi|336253593|ref|YP_004596700.1| 25 VFVGGKGGVGKTTVSSAYALECAdagleTLIVSTDPAHSTADVfeqefdD----DPqpvegydglsameidP 92
                                      688899************87777778989999999988865553233211....112334555555555542 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.3
                            AAA_33  83 rerarflklarrlgvpvrivv 103
                                       ++r++ +++a +     +  +
  gi|336253593|ref|YP_004596700.1| 216 QARKERFEFAGEVLRGQSSFY 236
                                       333333333333333333334 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.9
                            AAA_33  82 rrerarflklarrlgvpv 99 
                                       + er+r+ ++ r+++vpv
  gi|336253593|ref|YP_004596700.1| 292 ETERERLERIEREFDVPV 309
                                       456667777777777665 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.14       5     123 ..      25     158 ..      22     171 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                          CBP_BcsQ   5 alqGvRGGvGttsllaaLawalhelgesvlviDlspd....nlLrlhFnvd...ieqregwaraeld.gapwrqaal 73 
                                       ++ G +GGvG+t++++a a      g + l++ + p+    ++ +  F+ d   +e  +g+ + e+d +++ ++  +
  gi|336253593|ref|YP_004596700.1|  25 VFVGGKGGVGKTTVSSAYALECADAGLETLIVSTDPAhstaDVFEQEFDDDpqpVEGYDGLSAMEIDpDQEVEEHLM 101
                                       567889**************************876661111555555543311133345566666653677888888 PP

                          CBP_BcsQ  74 eyapgl.dllPfGelnveekenlqqlaek....aeallaalkelk...eqyrwillDl 123
                                       +++ +l d l  G +n+ +++ l+  +++    + al +++ e+      y+ +++D 
  gi|336253593|ref|YP_004596700.1| 102 DLKRQLnDQLSAGMVNEVDAQ-LEMAHQTpgayEAALFDRFIEVMrnaDPYDRVVFDT 158
                                       888887457888887766554.333222200112233333332223555666666665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00023      0.21      19      38 ..      21      40 ..      13      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                                      CSEEEEEEESTTSSHHHHHH CS
                            NB-ARC 19 qslvvalvGmgGvGKttlak 38
                                      ++ +v++ G+gGvGKtt+++
  gi|336253593|ref|YP_004596700.1| 21 ETEFVFVGGKGGVGKTTVSS 40
                                      4459*************976 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00027      0.24      14      52 ..      20      59 ..       7      85 .. 0.76
   2 ?   -2.6   0.1       3.1   2.8e+03     165     189 ..     293     318 ..     285     321 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                        Zeta_toxin 14 erPklillgGqpGAGKselaellkdele.rqgnvvrldpD 52
                                      ++   +++gG  G GK++++++ + e + ++ + + +++D
  gi|336253593|ref|YP_004596700.1| 20 SETEFVFVGGKGGVGKTTVSSAYALECAdAGLETLIVSTD 59
                                      566789***************9998887455555555555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.1
                        Zeta_toxin 165 glresvealeeekqldrvk.ikdrdg 189
                                         re +e++e+e+++  v  i +r +
  gi|336253593|ref|YP_004596700.1| 293 TERERLERIEREFDVPVVAtIETRVE 318
                                       55788999999999998887887766 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0016       1.4       6      59 ..      26      75 ..      24     160 .. 0.53
   2 ?   -0.7   0.0       1.1   9.6e+02     141     176 ..     282     317 ..     273     332 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                            AAA_24  6 liyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel 59
                                      ++ G+ g+GKTt+ + +       g ++l++ t+           p  ++ + f +e++ +
  gi|336253593|ref|YP_004596700.1| 26 FVGGKGGVGKTTVSSAYalecadaGLETLIVSTD-----------PAHSTADVFEQEFDDD 75
                                      5679***********9955555555555555444...........4444444444444444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                            AAA_24 141 geakytrlepklgkktanelkeevDlvlranlkred 176
                                       ++a+y r + + +    + ++ e+D+ + a++++ +
  gi|336253593|ref|YP_004596700.1| 282 RGATYLRQRVETERERLERIEREFDVPVVATIETRV 317
                                       335888888888888899999999999999988654 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00052      0.47       5      39 ..      25      60 ..      22      70 .. 0.83
   2 ?   -2.4   0.0       3.5   3.2e+03      58      92 ..     124     159 ..     109     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00052
                                      EEE.ESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  5 llv.GlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      ++v G  G+GKTt  +  a  + + g ++l+v++D 
  gi|336253593|ref|YP_004596700.1| 25 VFVgGKGGVGKTTVSSAYALECADAGLETLIVSTDP 60
                                      45515567**************************96 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.5
                                       EEEESSTTSCHHHHHHHHHHHHHHTT.SSEEEEEE- CS
                             SRP54  58 pvikkkeeadpaavakeavekakeek.idvvlvDTa 92 
                                       ++ +++ +a +aa+  + +e +++ + +d v+ DT+
  gi|336253593|ref|YP_004596700.1| 124 EMAHQTPGAYEAALFDRFIEVMRNADpYDRVVFDTS 159
                                       455566666677777777776665545999999997 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 ?    4.3   0.2     0.024        21      10      52 ..      20      61 ..      11      66 .. 0.82
   2 ?   -2.7   0.0       3.2   2.9e+03     133     176 ..      84     129 ..      80     146 .. 0.66
   3 ?   -2.3   0.0       2.4   2.2e+03     159     182 ..     235     258 ..     212     270 .. 0.71
   4 ?    4.1   0.1     0.027        25     173     198 ..     294     319 ..     283     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.024
                           DUF1611 10 vkakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqt 52
                                       +++ v+v+G +  vGK t + + + ++ ++Gl++ +v+T+++
  gi|336253593|ref|YP_004596700.1| 20 SETEFVFVGGKG-GVGKTTVSSAYALECADAGLETLIVSTDPA 61
                                      566667776665.79*************************975 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.2
                           DUF1611 133 glpeialppleeeieliealaakk..kvvgislNtknlseeeakea 176
                                       gl+ +++ p +e+ e +  l+++   ++ + ++N+ +++ e a++ 
  gi|336253593|ref|YP_004596700.1|  84 GLSAMEIDPDQEVEEHLMDLKRQLndQLSAGMVNEVDAQLEMAHQT 129
                                       5666667666666666666665555677788888777776655555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.4
                           DUF1611 159 vgislNtknlseeeakealeelee 182
                                       + + lN  +ls +e++++l++l++
  gi|336253593|ref|YP_004596700.1| 235 FYLVLNPDELSIRETQRSLAQLRD 258
                                       456688888888888888888765 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.027
                           DUF1611 173 akealeeleeelglpvvdpvregaek 198
                                        +e+le++e+e+++pvv  +++ +e+
  gi|336253593|ref|YP_004596700.1| 294 ERERLERIEREFDVPVVATIETRVEE 319
                                       57899************999987766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.5    0.0011         1       1      25 [.      25      58 ..      25     168 .. 0.60
   2 ?   -1.7   0.0       4.3   3.9e+03      96     110 ..     223     248 ..     170     255 .. 0.63
   3 ?    0.6   0.1      0.86   7.7e+02      71     112 ..     260     300 ..     240     306 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf...........g 25
                                      +++ G+ GvGKtt++ + + +  +            
  gi|336253593|ref|YP_004596700.1| 25 VFVGGKGGVGKTTVSSAYALE--CadagletlivsT 58
                                      799***********9986444..2233555555552 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.3
                            AAA_18  96 k...........vvLtaspeelleRl 110
                                                   ++L ++p+el  R 
  gi|336253593|ref|YP_004596700.1| 223 EfagevlrgqssFYLVLNPDELSIRE 248
                                       12222344446677777777777665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.86
                            AAA_18  71 leegknlvidghlaeleseaakdikkvvLtaspeelleRlek 112
                                           + lv+  +  e+e+++  ++   +L+ + e+ +eRle+
  gi|336253593|ref|YP_004596700.1| 260 DLPVEGLVVNRLTPEPEPHEEGRGA-TYLRQRVETERERLER 300
                                       4466788999999999999998888.8998888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2294.06
//
Query:       gi|336253594|ref|YP_004596701.1|  [L=610]
Description: carbon starvation protein CstA [Halopiger xanaduensis SH-6]
Scores for complete 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-105  353.4  20.6   1.3e-105  353.4  20.6    1.5  2  CstA      Carbon starvation protein CstA
    3.5e-31  108.0   3.7    3.5e-31  108.0   3.7    4.4  5  CstA_5TM  5TM C-terminal transporter carbon starvation CstA


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 !  353.4  20.6  1.5e-109  1.3e-105       4     350 ..       5     384 ..       1     390 [. 0.92
   2 ?   -3.9   0.0      0.56     5e+03     340     358 ..     525     543 ..     516     557 .. 0.65

  Alignments for each domain:
  == domain 1  score: 353.4 bits;  conditional E-value: 1.5e-109
                              CstA   4 vllvvvavvvfviayrfYgkfiakkvlklddkraTPaerledgkdyvptnklvlfghhFasiagagPlvGpvlAa.q 79 
                                       +++v++ +v+f +ay+ Yg+++++  + ldd+r+TPa++++dg++yvp++k vl+ghh++siag++P+vGp++Aa  
  gi|336253594|ref|YP_004596701.1|   5 IWIVALVLVLFSVAYVGYGRYLSQF-VDLDDSRETPAHKYQDGQEYVPAKKPVLLGHHYSSIAGGAPIVGPITAAlV 80 
                                       799999****************998.9*********************************************98758 PP

                              CstA  80 fGylPgllWilvGavfagavhDfvvlvasvrrkgkslgelakkelgkvakllallaillililvlavlalvvvkala 156
                                       +G++P+llW+ +G+ ++gavhDfv+l  s r++gks+g ++ +++g+++k ++l +++l++ilv+av+alv+   + 
  gi|336253594|ref|YP_004596701.1|  81 WGWVPALLWVAIGNPLIGAVHDFVSLSSSLRHEGKSIGYIIGEYVGERGKNMLLWFAFLLTILVVAVFALVIGIVFD 157
                                       ***************************************************************************** PP

                              CstA 157 espaavfsviltipialllGvllrklrkgvleasvigvvllllavvvgseveea.laell................. 215
                                       + p a+++++l++ +a+++G+ l++l+    + +++ v+ ++++v+vg +   a +++ +                 
  gi|336253594|ref|YP_004596701.1| 158 AYPQAATASLLYVGLAFVFGFWLYQLNLPFSIGTIVFVTGIFATVWVGIQYPIAlFGAEFpnatdtivlfgetapwf 234
                                       **************************************************944447777799*************** PP

                              CstA 216 ......tlsketlaivlivYvfvAsvlPvwlllaPrdYlstflligtivllalgilv.......vap.elklpavte 278
                                               +  ++++v++vY+ +AsvlPvw+ll+PrdYls+fll+ ++ +++l+++v       ++p e++++a   
  gi|336253594|ref|YP_004596701.1| 235 iptlgqGANVGAWVLVMLVYGGLASVLPVWMLLQPRDYLSSFLLYSGVGGALLAVIVgtfvtttSQPlEFQIDAWYG 311
                                       **9998888899*********************************99999988888743333332223456666666 PP

                              CstA 279 f.vdgegpvfagslfPllfitiACGaiSGFHslvssgttskllekesdarlvgygamllEslvailalvaaav 350
                                       +  + ++     +lfPllfitiACG+iSGFHslvssgtt+k+l+ke+darl+gyg+ml E+l+a +al +++v
  gi|336253594|ref|YP_004596701.1| 312 LlGSDNAAYDLMPLFPLLFITIACGTISGFHSLVSSGTTAKQLDKETDARLIGYGGMLGEGLLAAVALCTIGV 384
                                       6333344555689*******************************************************98765 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.56
                              CstA 340 vailalvaaavlepaayfa 358
                                       +a++a ++++ l   a+++
  gi|336253594|ref|YP_004596701.1| 525 LALMAFITVCGLLWVAFYQ 543
                                       5677777776664444433 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 ?   -2.0   2.6       0.5   4.5e+03      67      91 ..     132     156 ..     114     215 .. 0.61
   2 ?   -2.4   0.1      0.69   6.2e+03      11      19 ..     290     298 ..     281     335 .. 0.53
   3 ?   -1.8   0.1      0.44     4e+03      79      90 ..     373     384 ..     372     398 .. 0.85
   4 !  108.0   3.7   3.9e-35   3.5e-31       2     115 ..     416     534 ..     415     535 .. 0.92
   5 ?    0.9   1.8     0.065   5.8e+02      66      96 ..     553     583 ..     536     590 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.5
                          CstA_5TM  67 ntlWplFGaaNQlLAalaLlvvtvw 91 
                                       + lW +F  +  ++A +aL+++ v+
  gi|336253594|ref|YP_004596701.1| 132 MLLWFAFLLTILVVAVFALVIGIVF 156
                                       3344444444444444444444443 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.69
                          CstA_5TM  11 fvalfalTt 19 
                                       +v +f+ Tt
  gi|336253594|ref|YP_004596701.1| 290 IVGTFVTTT 298
                                       444444443 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.44
                          CstA_5TM  79 lLAalaLlvvtv 90 
                                       lLAa+aL+++ v
  gi|336253594|ref|YP_004596701.1| 373 LLAAVALCTIGV 384
                                       89*****99866 PP

  == domain 4  score: 108.0 bits;  conditional E-value: 3.9e-35
                          CstA_5TM   2 avaytfailfvalfalTtlDtatRlaRyilqellgelk...kkaltnkyvatliavalavllllwggintlWplFGa 75 
                                       ++++ f++l++a+f+lT++Dta+Rl+Ry+++e++g+ +   +   +n+yv+t+++va+a++ll +g+++ lW lFG 
  gi|336253594|ref|YP_004596701.1| 416 TYGAPFMALVLASFLLTSMDTAVRLSRYMVEEIVGTPEtaiEGYGANRYVNTTFVVAFAFVLLGTGSWEDLWLLFGG 492
                                       57899******************************988665444789***************99999********** PP

                          CstA_5TM  76 aNQlLAalaLlvvtvwllktgr..kalvtliPmvfmlvvtlt 115
                                       aNQlLAalaLl++tvwl++++r  +++ t +P+++m+++t++
  gi|336253594|ref|YP_004596701.1| 493 ANQLLAALALLTGTVWLANWDRskQLYSTGAPLALMAFITVC 534
                                       ******************988887999999*********985 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.065
                          CstA_5TM  66 intlWplFGaaNQlLAalaLlvvtvwllktg 96 
                                         t+W   +   Q+L  l+Ll++++ ll+ g
  gi|336253594|ref|YP_004596701.1| 553 DPTVWTWIAGGGQILINLTLLALALALLRIG 583
                                       4789*********************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 4009.39
//
Query:       gi|336253595|ref|YP_004596702.1|  [L=218]
Description: hypothetical protein Halxa_2198 [Halopiger xanaduensis SH-6]
Scores for 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  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1725.61
//
Query:       gi|336253596|ref|YP_004596703.1|  [L=78]
Description: hypothetical protein Halxa_2199 [Halopiger xanaduensis SH-6]
Scores for 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:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 581.34
//
Query:       gi|336253597|ref|YP_004596704.1|  [L=399]
Description: GTPase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-32  111.2   0.0    7.2e-32  110.3   0.0    1.4  1  MMR_HSR1_C     GTPase of unknown function C-terminal
      1e-19   70.7   0.0    1.4e-18   67.0   0.0    2.8  2  MMR_HSR1       50S ribosome-binding GTPase
    6.6e-08   32.5   0.0    1.5e-07   31.3   0.0    1.6  1  TGS            TGS domain
    2.2e-06   27.3   0.0    0.00039   20.0   0.0    2.6  3  FeoB_N         Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.034   13.7   0.0      0.074   12.6   0.0    1.6  1  GTP_EFTU       Elongation factor Tu GTP binding domain
      0.038   14.0   0.1       0.53   10.3   0.0    2.7  3  Dynamin_N      Dynamin family
       0.05   13.8   0.0        3.8    7.8   0.0    2.6  2  YchF-GTPase_C  Protein of unknown function (DUF933)
      0.088   13.5   0.1        6.8    7.4   0.0    2.9  3  VWA_2          von Willebrand factor type A domain
       0.14   12.4   0.0        2.2    8.5   0.0    2.6  3  Roc            Ras of Complex, Roc, domain of DAPkinase
       0.16   11.8   0.2        8.8    6.2   0.0    2.3  2  RsgA_GTPase    RsgA GTPase
       0.19   11.6   1.1       0.48   10.3   0.6    1.8  2  Phage_Mu_Gam   Bacteriophage Mu Gam like protein


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 !  110.3   0.0   4.4e-35   7.2e-32       1     109 [.     224     328 ..     224     329 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 4.4e-35
                        MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdk.kvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLek 76 
                                       a+NK+Dlp+a+en+e+++++ ++d+ ++vp+sA+aE aL++a+k+g+++Y+pgd+dfei++d    ++ +q++ Le+
  gi|336253597|ref|YP_004596704.1| 224 AANKMDLPEAQENYEEITDDPDYDHlTFVPCSAHAEKALKSADKAGVVDYRPGDADFEITGD----ISGEQEQGLEQ 296
                                       89******************9988889***********************************....*********** PP

                        MMR_HSR1_C  77 irdlvlkrygsTGVqealnaavfelldlivVYP 109
                                       ird +l++yg TGVq+al++a+f++l++++V+P
  gi|336253597|ref|YP_004596704.1| 297 IRD-FLSEYGATGVQAALETALFDVLGVVPVFP 328
                                       ***.****************************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 !   67.0   0.0   8.7e-22   1.4e-18       1      87 [.       6     126 ..       6     227 .. 0.83
   2 ?   -0.5   0.0      0.77   1.3e+03      70      86 ..     359     376 ..     234     397 .. 0.60

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 8.7e-22
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.........................EEEEE CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.........................ielvD 52 
                                       ++++vG+p vGKS+++na t + +  +++p+tT+d+  g+  ++  +                          +lvD
  gi|336253597|ref|YP_004596704.1|   6 RIGLVGKPSVGKSSFFNAATMNDVPEGAYPFTTIDPSVGEAYVRV-DcaapefdeectpnvgycdhgtrfvpTKLVD 81 
                                       699************************************988441.123344555566666666666666669**** PP

                                       CGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT.........T CS
                          MMR_HSR1  53 tpGliegaseekglgkaflalee.adlillvvdas.........e 87 
                                       ++Gli ga+e+ glg++fl   + +d++++vvd s         +
  gi|336253597|ref|YP_004596704.1|  82 VAGLIPGAHEGAGLGNQFLTDLNeTDVLVHVVDFSgqtdlegepT 126
                                       *******************966659********887666554441 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.77
                                       HHHHHCT.SEEEEEEETT CS
                          MMR_HSR1  70 flaleea.dlillvvdas 86 
                                       +  + +  d +l+ +d++
  gi|336253597|ref|YP_004596704.1| 359 YSLHSDIgDGFLHAIDCR 376
                                       222333226666666665 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   9.4e-11   1.5e-07      12      60 .]     344     397 ..     337     397 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 9.4e-11
                                       E...EETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEEE CS
                               TGS  12 d...lprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIvt 60 
                                       d   +p ++t+eDfAy++h+++++ f++A+     ++ g d+++e  dv+e++t
  gi|336253597|ref|YP_004596704.1| 344 DcylIPPNSTAEDFAYSLHSDIGDGFLHAIDCRtnRQLGKDYEVEPRDVIEVIT 397
                                       35557999*************************999****************97 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 !   20.0   0.0   2.4e-07   0.00039       2      42 ..       6      46 ..       5      53 .. 0.91
   2 ?   -3.2   0.0       3.3   5.4e+03      77      87 ..     104     114 ..      96     120 .. 0.72
   3 ?    4.4   0.0     0.015        25      94     122 ..     207     235 ..     199     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.4e-07
                                      EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEE CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegkl 42
                                      ++ lvG+p vGk+++fna t  +   g +p +t++ + g+ 
  gi|336253597|ref|YP_004596704.1|  6 RIGLVGKPSVGKSSFFNAATMNDVPEGAYPFTTIDPSVGEA 46
                                      689*******************************9988875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.3
                                       TSSSEEEEEEE CS
                            FeoB_N  77 eepdvvvnvvd 87 
                                       +e+dv+v+vvd
  gi|336253597|ref|YP_004596704.1| 104 NETDVLVHVVD 114
                                       56788888888 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHTTSSEEEEEETHHHHHHTT CS
                            FeoB_N  94 nLyLtlqllelgvpvvlalnmideaekkg 122
                                       +L L  ++   ++p+v+a n++d  e+++
  gi|336253597|ref|YP_004596704.1| 207 KLRLAREIRKETKPMVVAANKMDLPEAQE 235
                                       78999999999************766554 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 ?   12.6   0.0   4.5e-05     0.074     114     147 ..     210     245 ..     205     331 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.5e-05
                                       HHHHHHHTTTEEEEEEESCGST..HHHHHHHHHHHH CS
                          GTP_EFTU 114 vlrlalkegvpiivfiNKmDrl..kaelkeiveevk 147
                                       ++r ++ke  p++v+ NKmD +  +++++ei ++  
  gi|336253597|ref|YP_004596704.1| 210 LAREIRKETKPMVVAANKMDLPeaQENYEEITDDPD 245
                                       56778899999**********988888888877654 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00032      0.53       1      32 [.       7      37 ..       7      40 .. 0.86
   2 ?   -1.5   0.0       1.4   2.3e+03     103     139 ..      77     116 ..      65     123 .. 0.77
   3 ?   -0.6   0.0      0.73   1.2e+03     141     167 ..     201     227 ..     198     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00032
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS-- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptT 32
                                      i +vG+ S GKSS+ na +  d  p g+ p T
  gi|336253597|ref|YP_004596704.1|  7 IGLVGKPSVGKSSFFNAATMND-VPEGAYPFT 37
                                      789**************99888.587777776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                                       EEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETT CS
                         Dynamin_N 103 ltlvDlPGldsvnkrdq...elvkeyikkadiilavtsan 139
                                        +lvD+ Gl+  +++     +   + +++ d++++v++++
  gi|336253597|ref|YP_004596704.1|  77 TKLVDVAGLIPGAHEGAglgNQFLTDLNETDVLVHVVDFS 116
                                       5789999988888777766677777778889999888765 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.73
                                       -CCC-CHHHHHHHHSTTBTTEEEEEE- CS
                         Dynamin_N 141 dlsnsealflarevdpkgkrtivvltk 167
                                       ++ + e+l+lare++++ k ++v  +k
  gi|336253597|ref|YP_004596704.1| 201 AWEDDEKLRLAREIRKETKPMVVAANK 227
                                       577899***********9999987776 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 ?    7.8   0.0    0.0024       3.8      16      41 ..     347     372 ..     339     380 .. 0.88
   2 ?    3.4   0.0     0.054        88      65      81 ..     379     395 ..     373     397 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0024
                     YchF-GTPase_C  16 tikkgttapqaAgviHsDfekgFira 41 
                                        i  ++ta++ A   HsD+  gF++a
  gi|336253597|ref|YP_004596704.1| 347 LIPPNSTAEDFAYSLHSDIGDGFLHA 372
                                       678899*****************998 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.054
                     YchF-GTPase_C  65 rlegkdyvvqdgDiilf 81 
                                       r+ gkdy v+  D+i++
  gi|336253597|ref|YP_004596704.1| 379 RQLGKDYEVEPRDVIEV 395
                                       789***********975 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 ?    1.7   0.0      0.24   3.9e+02      29      60 ..      97     130 ..      89     146 .. 0.79
   2 ?   -0.7   0.0       1.4   2.2e+03      49      72 ..     173     196 ..     169     224 .. 0.72
   3 ?    7.4   0.0    0.0042       6.8      37      85 ..     265     316 ..     252     323 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.24
                             VWA_2  29 eallkslp.gd.rvglvtfsdgpevlipltkdka 60 
                                       +++l +l+ +d  v +v fs++  ++  +t+d++
  gi|336253597|ref|YP_004596704.1|  97 NQFLTDLNeTDvLVHVVDFSGQTDLEGEPTEDHD 130
                                       56777775344699************99998875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                             VWA_2  49 pevlipltkdkakilnalrnleak 72 
                                       +e  + ++++ ++i++ +r+++  
  gi|336253597|ref|YP_004596704.1| 173 AEQMSAFKTNEDEIKRLIRRTDVG 196
                                       566778999999999999998865 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0042
                             VWA_2  37 gdrvglvtfsd.gpevli..pltkdkakilnalrnleakgggtnlaaaLqla 85 
                                        d+ g+v ++  ++  +i  + +  +++ l+ +r+   + g+t ++aaL++a
  gi|336253597|ref|YP_004596704.1| 265 ADKAGVVDYRPgDADFEItgDISGEQEQGLEQIRDFLSEYGATGVQAALETA 316
                                       7899*****9975655551156788999999999999999**********98 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0014       2.2       2      26 ..       7      31 ..       6      50 .. 0.81
   2 ?   -1.5   0.0       1.7   2.8e+03      53      68 ..     105     120 ..      96     123 .. 0.77
   3 ?    0.0   0.0      0.57   9.3e+02     106     120 .]     216     230 ..     202     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
                                      EEEESSTTSSHHHHHHCHCT-CCC- CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfse 26
                                      + lvG+ +vGK+s+++  + +++ e
  gi|336253597|ref|YP_004596704.1|  7 IGLVGKPSVGKSSFFNAATMNDVPE 31
                                      779************9998887765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.7
                                       TTCEEEEEEEE-SGGC CS
                               Roc  53 vkkvklniWDtaGqer 68 
                                        ++v +++ D++Gq++
  gi|336253597|ref|YP_004596704.1| 105 ETDVLVHVVDFSGQTD 120
                                       35688999******86 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.57
                                       CSSS-EEEEEE-TTT CS
                               Roc 106 agkspvilvgnkiDl 120
                                        +++p+++ +nk+Dl
  gi|336253597|ref|YP_004596704.1| 216 KETKPMVVAANKMDL 230
                                       356799999****95 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.05        81     104     120 ..       9      25 ..       3      32 .. 0.85
   2 ?    6.2   0.0    0.0054       8.8      45      91 ..     217     263 ..     206     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.05
                                       EECSTTSSHHHHHHHHC CS
                       RsgA_GTPase 104 lvGqSGvGKStLinall 120
                                       lvG+  vGKS++ na +
  gi|336253597|ref|YP_004596704.1|   9 LVGKPSVGKSSFFNAAT 25 
                                       89999*********865 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0054
                                       TT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHH CS
                       RsgA_GTPase  45 kgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegle 91 
                                       +  ++v++ nK+Dl e +e++ee+ ++     ++++ +sa+ +++l+
  gi|336253597|ref|YP_004596704.1| 217 ETKPMVVAANKMDLPEAQENYEEITDDPDYDHLTFVPCSAHAEKALK 263
                                       444667889**********9999999887777788888888776665 PP

>> Phage_Mu_Gam  Bacteriophage Mu Gam like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.74   1.2e+03      45      59 ..     133     147 ..     126     152 .. 0.87
   2 ?   10.3   0.6    0.0003      0.48      12      55 ..     148     191 ..     146     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.74
                                       HHHHHHHHHHHHHHH CS
                      Phage_Mu_Gam  45 keieylesllkqYae 59 
                                       k+i++le++l q++ 
  gi|336253597|ref|YP_004596704.1| 133 KDIDFLEEELDQWYL 147
                                       89***********85 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0003
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHH CS
                      Phage_Mu_Gam  12 aelkreleeieaeaneeiaaikekleaeleplkkeieylesllk 55 
                                       + l++ +e++e+ + +e +ai+e+l++++++ k++ +++++l++
  gi|336253597|ref|YP_004596704.1| 148 GVLEKGIERYESGYTTEDDAIEEELAEQMSAFKTNEDEIKRLIR 191
                                       668999********************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2760.10
//
Query:       gi|336253598|ref|YP_004596705.1|  [L=92]
Description: hypothetical protein Halxa_2201 [Halopiger xanaduensis SH-6]
Scores for 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   19.3   0.6    0.00092   19.0   0.6    1.1  1  DUF2976          Protein of unknown function (DUF2976)
     0.0033   17.1   1.3     0.0035   17.1   1.3    1.1  1  Cation_ATPase_C  Cation transporting ATPase, C-terminus
     0.0097   16.0   0.2      0.013   15.6   0.2    1.3  1  Ferric_reduct    Ferric reductase like transmembrane componen
  ------ inclusion threshold ------
        0.1   12.0   0.6       0.13   11.7   0.1    1.4  1  DUF2417          Region of unknown function (DUF2417)
        0.2   11.7  12.1       0.27   11.3  11.6    1.4  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.6   2.6e-07   0.00092      15      70 ..      24      78 ..       8      85 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.6e-07
                           DUF2976 15 dllelikgylk.dgvillgLvlaavaflaVakaalkkfnei.segkaewgkfgltlvv 70
                                      ++  +i++++  ++v + gL+l ava+++ a+ ++ +f  + +++ ++wg f++++++
  gi|336253598|ref|YP_004596705.1| 24 QW--MIRNWIGvAVVSIFGLLLLAVAMMQ-ATGVMDVFGSVaETQTQQWGAFAVLALI 78
                                      33..5788865277889*********998.78899****9989999*******99987 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.3   9.9e-07    0.0035     122     175 ..      26      82 ..      13      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.9e-07
                   Cation_ATPase_C 122 lfsnkl..lllaillslllqvlivyvpglnavfgta.plsleewlialllalvvllv 175
                                       + +n++  ++++i++ lll+v++++  g+ +vfg + +   ++w   ++lal+ l++
  gi|336253598|ref|YP_004596705.1|  26 MIRNWIgvAVVSIFGLLLLAVAMMQATGVMDVFGSVaETQTQQWGAFAVLALIWLAL 82 
                                       44675566899999999999999999*******766488999998888888888776 PP

>> Ferric_reduct  Ferric reductase like transmembrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   3.7e-06     0.013      32      97 ..      23      84 ..       9      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.7e-06
                     Ferric_reduct 32 klllfHkwlgvlafl.lallHvilyllnflrfsaldeerlldsllkkpynllGvlalllliilaitS 97
                                      + ++++ w+gv+++  + ll  ++ +++++        +++ s  ++  +++G +a+l+li+la+  
  gi|336253598|ref|YP_004596705.1| 23 DQWMIRNWIGVAVVSiFGLLLLAVAMMQATG-----VMDVFGSVAETQTQQWGAFAVLALIWLALAG 84
                                      56889******99983444444444444443.....689************************9986 PP

>> DUF2417  Region of unknown function (DUF2417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.6e-05      0.13     163     212 ..      10      58 ..       6      75 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                           DUF2417 163 kkeeeerltgreetrhtlkewlsilvrniikllllvvlilltltllLral 212
                                       kk  + + + +ee+++ ++ w+ ++v +i+ llll+v +++ +t ++ ++
  gi|336253598|ref|YP_004596705.1|  10 KKPTNTKQEAKEEDQWMIRNWIGVAVVSIFGLLLLAV-AMMQATGVMDVF 58 
                                       55566667788899************99998877765.556666666555 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 ?   -0.4   0.0      0.32   1.2e+03      96     112 ..      10      26 ..       6      27 .. 0.79
   2 ?   11.3  11.6   7.6e-05      0.27      23      82 ..      16      85 ..      14      90 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.32
                   Phage_holin_3_6  96 plpertieelkedvaal 112
                                       ++p+ t +e+ke  +++
  gi|336253598|ref|YP_004596705.1|  10 KKPTNTKQEAKEEDQWM 26 
                                       47999*9**99998886 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.6e-05
                   Phage_holin_3_6 23 kaElkeeakragsgagllgaagvlallalllllvala.....lalaa......lwlaalivaavllvlagv 82
                                      k+E+kee + +++  + +++  +++ll l+++++ +      ++  +      +w a+ ++a+++l+lag 
  gi|336253598|ref|YP_004596705.1| 16 KQEAKEEDQWMIRNWIGVAVVSIFGLLLLAVAMMQATgvmdvFGS-VaetqtqQWGAFAVLALIWLALAGW 85
                                      667777777777777777666666666665555555323443322.1345779****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 704.79
//
Query:       gi|336253599|ref|YP_004596706.1|  [L=372]
Description: Alanine--glyoxylate transaminase [Halopiger xanaduensis SH-6]
Scores for 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-21   74.5   0.0    9.4e-21   74.2   0.0    1.0  1  Aminotran_5  Aminotransferase class-V


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 !   74.2   0.0   5.3e-25   9.4e-21       5     341 ..       9     340 ..       6     362 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 5.3e-25
                                       TTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHH.HHHHHHHH CS
                       Aminotran_5   5 saAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtte.ainlvals 80 
                                        +++t++p++V ++++e     n  v ++  +    +t+ +e + +   +   a+++ +++++ G +  ++++++ s
  gi|336253599|ref|YP_004596706.1|   9 TPGPTEVPAAVRQRMAEP--MPNPDVESEFFETYRSLTANLERIYAAGGDADDASTDRDVVVLGGEGIlGLEAAIAS 83 
                                       689999999999999999..55889999999999999999999999999999***************99******** PP

                                       CCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-......-TTEEEEEEESBETT CS
                       Aminotran_5  81 larslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekll......nektklvaithvsnv 151
                                       l   +++gd+++  +++  +    +  + ++ g + +  ++ ++g+l+ d++++ l       e  +l ++ h ++ 
  gi|336253599|ref|YP_004596706.1|  84 L---VEDGDRVLCLSNGLYGDG-FADFV-EDYGGEAVTCEFPWRGTLEADTVREELeraadaGEPFDLATMVHCETP 155
                                       *...*****************9.55555.577888889******************88877668889********** PP

                                       TTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.S CS
                       Aminotran_5 152 tGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllg 227
                                       tGt+ ++e + +++ ++g+l +vDa++a+g  p+ +++++v      ++K l +P+G++   ++++++e++e +++ 
  gi|336253599|ref|YP_004596706.1| 156 TGTLSDLEPVLDALEDHGVLSVVDAVSALGGTPVPTDRIDV--CLGASQKcLSAPPGLTTCAISERAWERIEAVETR 230
                                       **************************************999..8889999999***********************9 PP

                                       TTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B CS
                       Aminotran_5 228 gemveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdk 304
                                       + + +     ++  ++  + f   T   a++ gl++a ++l e gle++ ++++ +a +++er ++l+  +   pd+
  gi|336253599|ref|YP_004596706.1| 231 SLYTNLEPWRNAADEDVEW-FPY-THLSANVAGLETATDLLLEEGLENVFERHADAARRCRERAAELGLETY--PDE 303
                                       9988888887777688888.665.*******************************************99999..899 PP

                                       -CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TT CS
                       Aminotran_5 305 aerrasivsfnfkgvhaedvatlLdeegIavrsGhhc 341
                                         ++++++++ + g  +e  +++ +e++I + +G   
  gi|336253599|ref|YP_004596706.1| 304 GAASPTVTALEVGGRATELQERMREEHDIVLATGLGD 340
                                       ************999998888888888*****99655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2845.29
//
Query:       gi|336253600|ref|YP_004596707.1|  [L=229]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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   77.6   0.0    1.3e-21   77.1   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.3e-16   61.0   0.0    2.1e-16   60.4   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    5.3e-16   58.9   0.0    7.1e-16   58.5   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    7.2e-13   48.6   0.0    8.7e-13   48.3   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    6.7e-12   46.0   0.0    1.1e-11   45.3   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    6.2e-08   32.3   0.0    8.1e-08   31.9   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00011   21.8   0.0    0.00017   21.3   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
       0.16   10.5   0.0       0.21   10.1   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m


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 !   77.1   0.0   5.7e-25   1.3e-21       1      93 [.      49     144 ..      49     147 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 5.7e-25
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       L++G G+G+++ ++a+ +    ++ +++++++m+++a + a+e+gl+v+++ a+ae+lp++d+sfD+vvs  v+++v
  gi|336253600|ref|YP_004596707.1|  49 LEIGPGSGAMFPYVADGAaadLEYHAIEPDPNMRTRAAKTAREAGLTVDLRDARAESLPYPDDSFDAVVSALVFCTV 125
                                       89*************4446689******************************************************* PP

                                       CCHHHHHHHHHHHEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGl 93 
                                       +dp++al+ei RvL+p+  
  gi|336253600|ref|YP_004596707.1| 126 QDPDAALSEITRVLRPDSE 144
                                       ****************976 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   9.4e-20   2.1e-16       1      96 [.      48     142 ..      48     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 9.4e-20
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       vL++G G+G +  ++a+    + ++++++++++m  +a++ a+e+gl v+++ + ae+lp++d+sfD+vvs+ +++ 
  gi|336253600|ref|YP_004596707.1|  48 VLEIGPGSGAMFPYVADGAaADLEYHAIEPDPNMRTRAAKTAREAGLTVDLRDARAESLPYPDDSFDAVVSALVFCT 124
                                       9***************998559*************************************************755655 PP

                                       SSHHHHHHHHHHHHHHEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpg 96 
                                       ++  d ++al+ei rvL+p+
  gi|336253600|ref|YP_004596707.1| 125 VQ--DPDAALSEITRVLRPD 142
                                       55..6669**********96 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.0   3.2e-19   7.1e-16      12     155 ..      36     186 ..      27     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 3.2e-19
                   Methyltransf_23  12 klerllpklraggrvLdiGcGtGillevlrengf...svtgvDlspeaveiae.....kakkaqkdqfdeqeaaepq 80 
                                        +e l+  ++ +grvL+iG+G+G + ++ ++  +   ++ +++++p++  +a+        +     +++++ ++p+
  gi|336253600|ref|YP_004596707.1|  36 HREYLA--RDLSGRVLEIGPGSGAMFPYVADGAAadlEYHAIEPDPNMRTRAAktareAGLTVDLRDARAESLPYPD 110
                                       456666..8999*****************66544456999***********98655552222222223333556699 PP

                   Methyltransf_23  81 gkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllld..wlylvpagrhisffsarslkell 155
                                       ++fd +v+  v+++v+dp ++l+ i + l+p+  + ++e+  ++ ++r  ++  ++++  a++ +++ + +++ + +
  gi|336253600|ref|YP_004596707.1| 111 DSFDAVVSALVFCTVQDPDAALSEITRVLRPDSEFRFLEHVGNDGWRRTGQNllNPLWKRASGGCHLTR-DTISRFV 186
                                       9***************************************99999999998866789999966665555.8887765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   3.9e-16   8.7e-13       6     113 ..      47     151 ..      43     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 3.9e-16
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       rvl++G G+G+     a+ +  + e++ i+ ++++ ++A + a++ gl+ v ++ + +e+l+  + d++fD ++s  
  gi|336253600|ref|YP_004596707.1|  47 RVLEIGPGSGAMFPYVADGAAADLEYHAIEPDPNMRTRAAKTAREAGLT-VDLRDARAESLP--YPDDSFDAVVSAL 120
                                       79***************9999999************************8.************..************* PP

                   Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr 113
                                       v++++ dpd++l ei+rvl+p++++   ++ 
  gi|336253600|ref|YP_004596707.1| 121 VFCTVQDPDAALSEITRVLRPDSEFRFLEHV 151
                                       *************************999988 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0     5e-15   1.1e-11       1      96 [.      49     142 ..      49     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 5e-15
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       LeiG G+G++  ++++    d+ey++++++p++   +++k+a++ ++ ++  + +a++l   d  +sfD+vv++ v+
  gi|336253600|ref|YP_004596707.1|  49 LEIGPGSGAMFPYVADGAaADLEYHAIEPDPNMR-TRAAKTAREAGLTVDLRDARAESLPYPD--DSFDAVVSALVF 122
                                       8**************9999***************.5555556666667777777777766555..5*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpg 96 
                                       + ++d++++l++i ++L+p+
  gi|336253600|ref|YP_004596707.1| 123 CTVQDPDAALSEITRVLRPD 142
                                       *******************8 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   3.6e-11   8.1e-08      50     153 ..      47     149 ..      18     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3.6e-11
                                       EEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-G CS
                   Ubie_methyltran  50 kvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGl 126
                                       +vl++  G+g +   ++d + +  + + ++ ++nm   + k ++e g   +++  a ae Lp+ ddsfD v  +  +
  gi|336253600|ref|YP_004596707.1|  47 RVLEIGPGSGAMFPYVADGAAADLEYHAIEPDPNMRTRAAKTAREAGL-TVDLRDARAESLPYPDDSFDAVVSALVF 122
                                       689999999999999999999999***********9999988888775.7*************************** PP

                                       GG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran 127 rnvtDklkaLkeayrvlkpGGrlvvle 153
                                         v D + aL e+ rvl+p  ++  le
  gi|336253600|ref|YP_004596707.1| 123 CTVQDPDAALSEITRVLRPDSEFRFLE 149
                                       ********************9999998 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   7.5e-08   0.00017      15     102 ..      46     139 ..      38     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7.5e-08
                              MetW  15 srvldlGcGdGellellke..ekqvdgrGleldee....gvaecvakGlsviqgdldkdlenfedksfdyvvlsqtl 85 
                                        rvl++G G G ++ ++++    +++ + +e d +    + + + + Gl+v   d+  +   ++d+sfd vv +  +
  gi|336253600|ref|YP_004596707.1|  46 GRVLEIGPGSGAMFPYVADgaAADLEYHAIEPDPNmrtrAAKTAREAGLTVDLRDARAESLPYPDDSFDAVVSALVF 122
                                       59***************983346788999*98865111134445567****************************** PP

                              MetW  86 qatrnpkevldellrig 102
                                        ++++p+  l+e+ r+ 
  gi|336253600|ref|YP_004596707.1| 123 CTVQDPDAALSEITRVL 139
                                       *************9985 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 ?   10.1   0.0   9.3e-05      0.21     170     213 ..     101     143 ..      69     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.3e-05
                   Methyltransf_29 170 lgtkrlpyPsrsfdlihCsrCridwteedgilllevdRvlRpgG 213
                                         ++ lpyP  sfd +  +      ++ d + l e+ RvlRp+ 
  gi|336253600|ref|YP_004596707.1| 101 ARAESLPYPDDSFDAVVSALVFCTVQDPD-AALSEITRVLRPDS 143
                                       55688*********998887666665555.579*********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1696.76
//
Query:       gi|336253601|ref|YP_004596708.1|  [L=75]
Description: hypothetical protein Halxa_2204 [Halopiger xanaduensis SH-6]
Scores for 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:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); 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: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 597.27
//
Query:       gi|336253602|ref|YP_004596709.1|  [L=968]
Description: GAF sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for complete 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  180.6   1.3    6.3e-53  178.9   1.3    2.0  1  MEDS         MEDS: MEthanogen/methylotroph, DcmR Sensory doma
    1.7e-30  105.8   0.0    9.9e-30  103.3   0.0    2.2  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.4e-10   41.6   5.3     0.0019   18.5   0.0    5.0  6  GAF_2        GAF domain
      4e-10   40.4   0.0    0.00013   22.6   0.0    3.4  4  GAF          GAF domain
    1.6e-09   38.2   0.0     0.0059   17.0   0.0    4.1  3  GAF_3        GAF domain
    3.5e-09   36.6   0.1    3.5e-09   36.6   0.1    3.6  5  HisKA        His Kinase A (phospho-acceptor) domain
    0.00011   22.0   0.0    0.00026   20.9   0.0    1.6  1  HATPase_c_5  GHKL domain
      0.002   17.5   0.0     0.0039   16.6   0.0    1.5  1  ATPase       KaiC
  ------ inclusion threshold ------
      0.035   14.1   0.0      0.085   12.8   0.0    1.6  1  HATPase_c_2  Histidine kinase-like ATPase domain
       0.17   11.7   0.0       0.38   10.6   0.0    1.5  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
       0.23   11.4   4.5        0.3   11.0   0.4    3.0  3  UPF0158      Uncharacterised protein family (UPF0158)


Domain annotation for each model (and alignments):
>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.9   1.3   3.9e-56   6.3e-53       1     161 []      44     205 ..      44     205 .. 0.99

  Alignments for each domain:
  == domain 1  score: 178.9 bits;  conditional E-value: 3.9e-56
                              MEDS   1 dHvclfyedeeellealvpfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrggg 77 
                                       dH++l+yed+++++e +vpfi++gl+rge+++yva+++t+de++ea+r +g++v++a+esg+l +++aeety r g+
  gi|336253602|ref|YP_004596709.1|  44 DHFALIYEDRRQQFETVVPFIEEGLERGERCIYVADDNTVDEVLEAMRIRGIPVERARESGALVVHTAEETYRRTGE 120
                                       8**************************************************************************** PP

                              MEDS  78 fdpermlealrralakaladgyaglrvigemtwalrspa.ereelleyEallneliadepvtalClYdrrrfsaevl 153
                                       fd e+mle+++ ala+a+ad+++glr+++emtwal++++ e+++l eyE+lln l+++e+ ++lC+Y+r+rf+ae+l
  gi|336253602|ref|YP_004596709.1| 121 FDREAMLEFWEGALADATADEFTGLRAAAEMTWALDDDEtELDDLCEYEELLNPLYDGEDYAVLCQYNRNRFPAEIL 197
                                       *********************************9999966************************************* PP

                              MEDS 154 advlrtHp 161
                                       +dvl+tHp
  gi|336253602|ref|YP_004596709.1| 198 HDVLKTHP 205
                                       *******8 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 ?    0.5   0.0      0.53   8.7e+02      35      60 ..     829     856 ..     796     859 .. 0.70
   2 !  103.3   0.0   6.1e-33   9.9e-30       1     110 [.     855     964 ..     855     966 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.53
                                       E..TEEEEEEEESSSSSTTHHHTGTCST CS
                         HATPase_c  35 e..ddlvisveDnGiGipkedlkklfek 60 
                                          +dl+i++  +   i+ +dl+++ + 
  gi|336253602|ref|YP_004596709.1| 829 AvrEDLQIQIDETDAEITADDLPRVSGD 856
                                       14469******************98775 PP

  == domain 2  score: 103.3 bits;  conditional E-value: 6.1e-33
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSS CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtG 75 
                                       gd ++Lrq+++nl++Na+++ + ++  +++ +a+    + visveD+GiGi+++d++++f+ f++  +++ +++gtG
  gi|336253602|ref|YP_004596709.1| 855 GDASQLRQVFQNLLENAIRY-SGDDPPRIRTDATRrgREWVISVEDDGIGIDPDDQDRVFTVFDR-LHSREEYEGTG 929
                                       7899****************.667777888887334589**************************.889999***** PP

                                       HHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  76 lGlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       +Gl++++++ve++gG+iwv+sepg+G+tf ftlp 
  gi|336253602|ref|YP_004596709.1| 930 IGLALCQRIVERHGGDIWVDSEPGEGSTFSFTLPA 964
                                       *********************************96 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.5   1.1e+04      48      71 ..      88     109 ..      45     127 .. 0.54
   2 ?    0.8   0.0      0.35   5.7e+02      94     121 ..     171     195 ..     131     215 .. 0.69
   3 !   17.1   0.0   3.1e-06     0.005       2     130 ..     272     403 ..     271     407 .. 0.85
   4 !   18.5   0.0   1.1e-06    0.0019       2     131 ..     431     565 ..     430     571 .. 0.83
   5 ?    2.9   0.0     0.074   1.2e+02       8     131 ..     598     725 ..     591     728 .. 0.74
   6 ?   -3.1   0.1       5.3   8.6e+03       5      27 ..     785     808 ..     777     847 .. 0.59

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.5
                                       T-S-B---TT.HHHHHHHHTS-EEE CS
                             GAF_2  48 aaldrplgeg.lvgealrtgrpvil 71 
                                       +a   +  +g +v++a ++g  v++
  gi|336253602|ref|YP_004596709.1|  88 EAM--R-IRGiPVERARESGALVVH 109
                                       222..2.255456666666555554 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.35
                                       EEEEE-TTS---EEEEES......--HH CS
                             GAF_2  94 lavPlisegrvvGvlnlyankppafdee 121
                                       l  Pl++ g+ ++vl+    ++++f +e
  gi|336253602|ref|YP_004596709.1| 171 LLNPLYD-GEDYAVLCQ--YNRNRFPAE 195
                                       4557766.578888883..455566544 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 3.1e-06
                                       HHHHHHHHHHHHHHHH.SS..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-.GGG CS
                             GAF_2   2 adleelldlvldelve.lgaalgyillvdddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvilnd.lee 76 
                                       a+l e  +++l+  ++ lg ++gy+ +  d++ ++++ + ++ e+ +  + ++l +  +++ l++   + + d  e 
  gi|336253602|ref|YP_004596709.1| 272 ASLGEKIENLLELGRQrLGLEIGYFTETRDENAFEIVEAVGDHEQIRPGVTDSLCDTYCEKLLASPGTIAVRDaAEV 348
                                       567777889999998879*********9999999999999999999999988998889*******99******6666 PP

                                       -S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES........--HHHHHHHHHHH CS
                             GAF_2  77 dpdkkglpaghaglrsflavPlisegrvvGvlnlyankppa..fdeedlelLeela 130
                                        +  +++  ++ gl +  +  +  +g+ +G l+++a+ p++  ++++++++L++++
  gi|336253602|ref|YP_004596709.1| 349 GWTDDPAY-ERFGLDAYFGTTVHVGGEEYGTLCFAAETPRErsYTDAERTFLDLMG 403
                                       66666666.99999999*****999*********555555556*********9987 PP

  == domain 4  score: 18.5 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHHHHHHH.SS..EE.EEEEE-TTS-EEEEEEEES-TTSTT-S-B---TT.HHHHHHHHTS-EEES-GG CS
                             GAF_2   2 adleelldlvldelve.lgaalg.yillvdddgglrlaawgeaeeefgaaldrplgeg.lvgealrtgrpvilndle 75 
                                       ++++e l+++l+  +e +g ++g   +l+  +g++rl+   + +   +++l + +g g  + + ++  +p+  +d++
  gi|336253602|ref|YP_004596709.1| 431 RNFDEKLEELLELGREwFGLEMGgLNHLPAWGGEFRLERGVGLGVDPDEELWSNPGYGcFCRQTIEADEPIAMADVR 507
                                       5677888888888888668884437777777777999988888888899999999***99***************77 PP

                                       G-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES........--HHHHHHHHHHHH CS
                             GAF_2  76 edpdkkglpaghaglrsflavPlisegrvvGvlnlyankppa..fdeedlelLeelae 131
                                            +   +++ gl s l+  ++ +  ++G +++++++p++  f+e++++++e++++
  gi|336253602|ref|YP_004596709.1| 508 GTNWEDDVIHREFGLTSYLGTRVMNGSTPYGTFWFGSTEPRDrpFSETERTFIELMGQ 565
                                       7444444446***************999*******988888899**********9986 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.074
                                       HHHHHHHHHH.SS..EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EE.ES-GGG-S-HH CS
                             GAF_2   8 ldlvldelve.lgaalgyillvdddgg.lrlaawgeaeeefgaaldrplgeglvgealrtgrpvi.lndleedpdkk 81 
                                       ld +++  +e ++ ++g i+ +d++++ +++ a +++ +++   ++ pl+e  +   + + +p+  ++d+e+    +
  gi|336253602|ref|YP_004596709.1| 598 LDDLFELGCErFDLEMGGIAKIDPATDsFTVQATNGDHDQLQPGAEAPLSETYCRATVDD-EPIAnVTDPERAGFGN 673
                                       455555555546777887888886666588899999999999999889999988888888.9999899999988888 PP

                                       HHHHHHHTT--EEEEEE.-T.T.S---EEEEES......--HHHHHHHHHHHH CS
                             GAF_2  82 glpaghaglrsflavPl.is.e.grvvGvlnlyankppafdeedlelLeelae 131
                                        l+ ++ g+ + ++  + ++ e +r++ +++   ++++af++++l++ +++a+
  gi|336253602|ref|YP_004596709.1| 674 TLAYDEFGVETYIGTRIeLEnEpDRTFFFVST-ESRDRAFTDAELTFHQLMAQ 725
                                       99999999999999999777444455555553.56666699999999888875 PP

  == domain 6  score: -3.1 bits;  conditional E-value: 5.3
                                       HHHHHHHHHHHHHS.S..EEEEEE CS
                             GAF_2   5 eelldlvldelvel.gaalgyill 27 
                                       ee+l++++d ++++  +  g +++
  gi|336253602|ref|YP_004596709.1| 785 EEFLEFAVDGAERMrEMIDGLLAY 808
                                       566666666666663333343333 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       7.5   1.2e+04      92     117 ..      94     124 ..      53     136 .. 0.59
   2 !   13.8   0.0   4.1e-05     0.067       7     127 ..     279     404 ..     273     410 .. 0.69
   3 !   22.6   0.0   8.1e-08   0.00013       3     132 ..     434     570 ..     432     571 .. 0.72
   4 ?   -2.3   0.0         4   6.5e+03     112     130 ..     709     728 ..     675     731 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.5
                                       EEEEEETTEEEEEEEEEE.....SSS..CSHHH CS
                               GAF  92 vvPlvndgelwGllvlhn.....psp..pftre 117
                                       ++P+   +e  G+lv+h      + +  +f+re
  gi|336253602|ref|YP_004596709.1|  94 GIPVERARE-SGALVVHTaeetyR-RtgEFDRE 124
                                       444443333.46666666544431.13556444 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.1e-05
                                       HHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECC...EEEETTSHHHH....HHHHHSSSEEESTGG.....TST CS
                               GAF   7 dtvveelrellgadrvalylpdydGlhydipqasrw...lfmkngrgicg....qvlatgqplvipdst.....pdp 71 
                                       ++++e  r+ lg++ + +   ++d + ++i +a      +++ + +++c+    + la++ ++ + d++     +dp
  gi|336253602|ref|YP_004596709.1| 279 ENLLELGRQRLGLEIGYFTE-TRDENAFEIVEAVGDheqIRPGVTDSLCDtyceKLLASPGTIAVRDAAevgwtDDP 354
                                       56666677777777777754.23333222555444443333333556677777688999999999984434444777 PP

                                       THHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS...CSHHHHHHHHHHHHH CS
                               GAF  72 rfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp...pftreelellqvlad 127
                                        + +         +g  ++ +  ++++ge +G+l++  ++p   ++t++e+ +l  +++
  gi|336253602|ref|YP_004596709.1| 355 AYER---------FGLDAYFGTTVHVGGEEYGTLCFAAETPrerSYTDAERTFLDLMGQ 404
                                       7777.........*************************77777899******9987766 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 8.1e-08
                                       HHHHHHHHHHHHHHHTESEEEE.EEEEETTEEE.........CEEEEECCEEEETTSH.HHHHHHHHSSSEEESTGG CS
                               GAF   3 eelldtvveelrellgadrval.ylpdydGlhy.........dipqasrwlfmkngrg.icgqvlatgqplvipdst 68 
                                       +e l++++e  re +g++ + l +lp + G ++           p++  w+ +  g g +c q+++ ++p+  +d++
  gi|336253602|ref|YP_004596709.1| 434 DEKLEELLELGREWFGLEMGGLnHLPAWGG-EFrlergvglgVDPDEELWSNP--GYGcFCRQTIEADEPIAMADVR 507
                                       566788888888888888888877765555.4433444444333334444333..3334699************976 PP

                                       ....TSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS...CSHHHHHHHHHHHHHHHHHH CS
                               GAF  69 ....pdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp...pftreelellqvladqvava 132
                                           +     +     + +++g  s+l+  ++n+   +G++ + ++ p   pf++ e+ +++ +++ v+ +
  gi|336253602|ref|YP_004596709.1| 508 gtnwE----DD----VIHREFGLTSYLGTRVMNGSTPYGTFWFGSTEPrdrPFSETERTFIELMGQWVSYE 570
                                       33332....22....44567*************************666779************99999876 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4
                                       S.CSHHHHHHHHHHHHHHHH CS
                               GAF 112 p.pftreelellqvladqva 130
                                       +  ft++el + q +a+ + 
  gi|336253602|ref|YP_004596709.1| 709 DrAFTDAELTFHQLMAQWIQ 728
                                       2469*******999999876 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00048      0.79       1     121 [.     273     404 ..     273     412 .. 0.73
   2 !   17.0   0.0   3.6e-06    0.0059       2     129 .]     433     573 ..     432     573 .. 0.80
   3 !    6.2   0.0    0.0078        13       3     129 .]     595     733 ..     593     733 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00048
                             GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesld..edsalarralssgevvsepsfae. 74 
                                       sl e +e ll+l+ + lg+e+g + + + d+n + ++ + + ++++   ++   ++  +  +l+s + ++++++ae 
  gi|336253602|ref|YP_004596709.1| 273 SLGEKIENLLELGRQRLGLEIGYFTETR-DENAFEIVEAVGDHEQIRPGVTdsLCDTYCEKLLASPGTIAVRDAAEv 348
                                       5789999****************98877.889999998886666676655448777777788888888989886552 PP

                             GAF_3  75 .......edglpdraalavPLvagrqviGvlal..astkprafdaedlelleslAr 121
                                               ++  + a+    + +g + +G+l++  +++++r+++++++ +l+ +++
  gi|336253602|ref|YP_004596709.1| 349 gwtddpaYERFGLDAYFGTTVHVGGEEYGTLCFaaETPRERSYTDAERTFLDLMGQ 404
                                       2222222344555666666667777*******9433556777***********998 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.6e-06
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse...sldedsalarralssgevvsepsfaee 75 
                                        de le+ll+l+ + +g+e g l+ l + g +++  +g + + ++ e   s +   + +r +++ +e+++ ++++++
  gi|336253602|ref|YP_004596709.1| 433 FDEKLEELLELGREWFGLEMGGLNHLPAWGGEFRLERGVGLGVDPDEelwSNPGYGCFCRQTIEADEPIAMADVRGT 509
                                       68899999999999999999999987777777766666655555555334667889999**********99999995 PP

                             GAF_3  76 dglpd.........raalavPLvagrqviGvlalastkpra..fdaedlelleslArqiataier 129
                                        +++d         +++l   ++ g++++G+  ++st+pr+  f+++++ ++e ++++++ ++er
  gi|336253602|ref|YP_004596709.1| 510 -NWEDdvihrefglTSYLGTRVMNGSTPYGTFWFGSTEPRDrpFSETERTFIELMGQWVSYELER 573
                                       .4443355555555999988889999***********999888******************9997 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0078
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse..sldedsalarralssgevvsepsfaeedg 77 
                                       +  l++l +l+++ +++e g +   d+  +++ v a  + +++l+   + +  +  +r++++ + ++ +++ +e+ g
  gi|336253602|ref|YP_004596709.1| 595 EAKLDDLFELGCERFDLEMGGIAKIDPATDSFTVQATNGDHDQLQPgaEAPLSETYCRATVDDEPIANVTD-PERAG 670
                                       67789999999999999999999999999999888777666666555555677777788877555544444.44322 PP

                             GAF_3  78 .........lpdraalavPLvagrqviGvlalastkpra..fdaedlelleslArqiataier 129
                                                   + ++   + +++++  + ++ st+ r+  f++++l + + +A++i  ++er
  gi|336253602|ref|YP_004596709.1| 671 fgntlaydeFGVETYIGTRIELENEPDRTFFFVSTESRDraFTDAELTFHQLMAQWIQYELER 733
                                       122222221444555555566655777777777665443349999999999999999777765 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.18   2.9e+02      37      64 ..     260     287 ..     240     290 .. 0.79
   2 ?   -3.5   0.4       6.8   1.1e+04      37      63 ..     419     445 ..     410     446 .. 0.70
   3 ?   -3.9   0.0       9.1   1.5e+04      27      45 ..     571     587 ..     558     592 .. 0.61
   4 !   36.6   0.1   2.1e-12   3.5e-09       2      66 ..     747     813 ..     746     814 .. 0.94
   5 ?   -2.7   0.2       3.8   6.3e+03      35      60 ..     844     869 ..     828     871 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.18
                                       CHHHHHHHHHHHHHHHHHHHHHHHHCCH CS
                             HisKA  37 lkeyletiesearrldhlvedlLdlsri 64 
                                       ++e+ eti + +  l + +e+lL+l+r 
  gi|336253602|ref|YP_004596709.1| 260 QRELYETIADPTASLGEKIENLLELGRQ 287
                                       5669999******************996 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.8
                                       CHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                             HisKA  37 lkeyletiesearrldhlvedlLdlsr 63 
                                       l+e  ++  + +r  d+ +e+lL+l+r
  gi|336253602|ref|YP_004596709.1| 419 LRESYRITADTTRNFDEKLEELLELGR 445
                                       455666677777788888888888877 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 9.1
                                       HHC..T-HSSCHHHHHHHH CS
                             HisKA  27 Lkregklteelkeyletie 45 
                                       L+r  + +e  ++ l +i 
  gi|336253602|ref|YP_004596709.1| 571 LER--EQREHHQQTLSRIA 587
                                       233..46688888887775 PP

  == domain 4  score: 36.6 bits;  conditional E-value: 2.1e-12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l++f+   +H+L  PL  +  ++++L+++  ++ +e+ +e+le ++++a+r++++++ lL +sr e+
  gi|336253602|ref|YP_004596709.1| 747 LEQFAYAASHDLQEPLRMVTSYLQLLENRyaDAFDEDGEEFLEFAVDGAERMREMIDGLLAYSRVET 813
                                       789***********************7777*999******************************986 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 3.8
                                       SSCHHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  35 eelkeyletiesearrldhlvedlLd 60 
                                       e  ++ l ++   a +l+++ ++lL+
  gi|336253602|ref|YP_004596709.1| 844 EITADDLPRVSGDASQLRQVFQNLLE 869
                                       55666777888888999999999986 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.6e-07   0.00026       5      92 ..     859     953 ..     856     962 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.6e-07
                       HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ek......kklesskskkeehGiG 70 
                                        l  ++ nlL+NAi  + + +   + Ir  ++++ +  +is+e    g     +       ++l+s  ++ e  GiG
  gi|336253602|ref|YP_004596709.1| 859 QLRQVFQNLLENAIRYSGDDP---PRIRTDATRRGREWVISVEDDGIGidpddQDrvftvfDRLHS-REEYEGTGIG 931
                                       57789*********9888755...9*******************9766666652234444466666.5568899*** PP

                       HATPase_c_5  71 lksireivkkykgnlsieaedg 92 
                                       l   ++iv++++g+++++ e g
  gi|336253602|ref|YP_004596709.1| 932 LALCQRIVERHGGDIWVDSEPG 953
                                       ****************998765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.4e-06    0.0039      39     109 ..      63     128 ..      59     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.4e-06
                            ATPase  39 FlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaeesaeekdkedleelie 109
                                       F+ +g+e+ ge++++v+ + +  ++ e ++  G+ +e+ +e+g l++  a e+ ++    ++++d e+++e
  gi|336253602|ref|YP_004596709.1|  63 FIEEGLER-GERCIYVADDNTVDEVLEAMRIRGIPVERARESGALVVHTAEETYRR----TGEFDREAMLE 128
                                       9999*999.************************************99998888765....34455544444 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.2e-05     0.085      32     110 ..     860     940 ..     835     955 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.2e-05
                       HATPase_c_2  32 irlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep.....keslkegGrGla 103
                                       +r + + ++ Na+++  ++ p  +++  +++++++ +++v+D+G g dp ++++            e+ +  G+Gla
  gi|336253602|ref|YP_004596709.1| 860 LRQVFQNLLENAIRYSGDDPP--RIRTDATRRGREWVISVEDDGIGIDPDDQDRVFTV-FdrlhsREEYEGTGIGLA 933
                                       55556667789***9998766..99999******************999876554333.2577878899999***** PP

                       HATPase_c_2 104 likglvD 110
                                       l +++v+
  gi|336253602|ref|YP_004596709.1| 934 LCQRIVE 940
                                       *999986 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 ?   10.6   0.0   0.00023      0.38      29      62 ..     888     921 ..     865     938 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                       HATPase_c_3  29 nrgktgeivieDdGkGmseeelknalrlatsske 62 
                                       +rg +  i++eDdG G+++++ ++++++    ++
  gi|336253602|ref|YP_004596709.1| 888 RRGREWVISVEDDGIGIDPDDQDRVFTVFDRLHS 921
                                       4567788**************9998876554444 PP

>> UPF0158  Uncharacterised protein family (UPF0158)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.8   6.2e+03     100     119 ..     429     448 ..     425     451 .. 0.85
   2 ?    0.1   0.1      0.45   7.3e+02     103     126 ..     551     574 ..     542     592 .. 0.78
   3 ?   11.0   0.4   0.00019       0.3     102     150 ..     710     761 ..     685     767 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.8
                           UPF0158 100 alenFlefiydfeaelekWq 119
                                       + +nF+e++++  ++  +W 
  gi|336253602|ref|YP_004596709.1| 429 TTRNFDEKLEELLELGREWF 448
                                       5789*******999999996 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.45
                           UPF0158 103 nFlefiydfeaelekWqqfeqerl 126
                                        F e    f ++  +W  +e er 
  gi|336253602|ref|YP_004596709.1| 551 PFSETERTFIELMGQWVSYELERE 574
                                       588888899999999999999985 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00019
                           UPF0158 102 enFlefiydfeaelekWqqfeqerl.RirileWLre..nelefvfeedldlp 150
                                       ++F +    f+++  +W q+e er  R+r+le  +e  +++ +++ +dl+ p
  gi|336253602|ref|YP_004596709.1| 710 RAFTDAELTFHQLMAQWIQYELERTqRERALEESNErlEQFAYAASHDLQEP 761
                                       678888899**************9559****987651146666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (968 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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 0.24s 00:00:00.97 Elapsed: 00:00:00.41
# Mc/sec: 7118.54
//
Query:       gi|336253603|ref|YP_004596710.1|  [L=258]
Description: YjeF-like protein [Halopiger xanaduensis SH-6]
Scores for 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-34  118.0   1.8      6e-34  117.6   1.8    1.2  1  Carb_kinase  Carbohydrate kinase
    1.2e-05   24.8   0.9     0.0023   17.4   0.1    2.2  2  HK           Hydroxyethylthiazole kinase family


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 !  117.6   1.8   6.7e-38     6e-34       2     243 ..      23     254 ..      22     255 .. 0.93

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 6.7e-38
                                       EEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT.....HTTTS....--SSS-SEEE CS
                       Carb_kinase   2 lvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll.....edeqa.kileklerldavv 72 
                                        v+gGs dy+  + +a+ aalr g++ v+ ++ ++    + +++p+++++++      e + + + l+   ++da+v
  gi|336253603|ref|YP_004596710.1|  23 AVVGGSIDYPNQPAIAGMAALRTGSDHVRALVAENIYEIVATHSPNLLASYYAgerfsE-DAVeQALDVCGWADALV 98 
                                       69***************************************************999854.444589*********** PP

                                       E-TT-SSSHCHHHHCHHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHH CS
                       Carb_kinase  73 iGpGLgrdekikklleevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelare 149
                                       iGpGL   e+ +++ e +   d+p+v+DA ++    +     +  +  iLTP   E   + +a +          ++
  gi|336253603|ref|YP_004596710.1|  99 IGPGLVDAET-EAVCETIDGVDVPVVVDALAIEPALD-----ADLSSAILTPSSSEDDPIREAYG--------SLET 161
                                       *****99999.99****************98876655.....467889********999988888........6778 PP

                                       HHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHC CS
                       Carb_kinase 150 laqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaa 226
                                       + ++ +av+ l g +d iv+ +ge l+n+tg+sal+++G+GD+LaG+ ++lL q  +   aa  +aw+ g+++++a+
  gi|336253603|ref|YP_004596710.1| 162 FTEETGAVITLTGDVDEIVA-GGERLHNETGTSALTVAGTGDTLAGITASLLGQGMDRTAAAELGAWILGKSGELAT 237
                                       9*******************.******************************************************** PP

                                       CCT-TS-HCHHHHHHHC CS
                       Carb_kinase 227 ekkgvgmlatelskiip 243
                                       +++g g+lat++++ +p
  gi|336253603|ref|YP_004596710.1| 238 AEYGPGVLATDVIDRVP 254
                                       ***********998775 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1   0.00066       5.9      16      89 ..      59     129 ..      47     141 .. 0.79
   2 !   17.4   0.1   2.6e-07    0.0023     145     239 ..     160     252 ..     145     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00066
                                       -TTTHHHHHHHHHHHT-EEEE--STTT.HHHHHHTSSEEEEE-TT--HHHHHHHHHHHHHHHHTT--EEEE-TTB CS
                                HK  16 NkVaqnfsANvllAlgaSPimseaeeE.vselakianaLllNiGtleekaiealkaAvksakevnrPvvlDPVgv 89 
                                        +++++ s N l   +a    se+  E + ++   a+aL++  G +++ ++ea+ +   +   v++Pvv+D  ++
  gi|336253603|ref|YP_004596710.1|  59 YEIVATHSPNLLASYYAGERFSEDAVEqALDVCGWADALVIGPGLVDA-ETEAVCE---TIDGVDVPVVVDALAI 129
                                       5677888999999999999999877662679*************9999.6676655...5567899999998775 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.6e-07
                                       HHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHH.HHHHHHHHHHH. CS
                                HK 145 qkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaa.veavllykvAgk 220
                                       ++  +++++v+ +tG+vD +  g + ++ + Gt+ l+ + ++G +l+ + a+ l+   d+  aa + a +l    g 
  gi|336253603|ref|YP_004596710.1| 160 ETFTEETGAVITLTGDVDEIVAGGERLHNETGTSALT-VAGTGDTLAGITASLLGQGMDRTAAAeLGAWIL-GKSG- 233
                                       56778999************99999**********97.9****************9999988885666555.4455. PP

                                       HHHHHHHTTHHHHHHHHHH CS
                                HK 221 eaaarsegsgsFqvellda 239
                                       e a+ + g+g   + ++d+
  gi|336253603|ref|YP_004596710.1| 234 ELATAEYGPGVLATDVIDR 252
                                       5666777888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1932.09
//
Query:       gi|336253604|ref|YP_004596711.1|  [L=212]
Description: phosphoribosyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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   0.5    5.8e-26   90.9   0.5    2.0  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0079   15.7   0.0      0.011   15.2   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
       0.18   11.3   0.0       0.44   10.0   0.0    1.6  2  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 !   90.9   0.5   9.7e-30   5.8e-26      13     157 ..       7     192 ..       2     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 9.7e-30
                                       EEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE.................. CS
                      Pribosyltran  13 davarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.......... 79 
                                       +a +rlaae+    + + dvv+gi+rg++p+a  +ad+Le+ l++v ++k  +++++e a g++++           
  gi|336253604|ref|YP_004596711.1|   7 EAGDRLAAELEGR-GVEADVVLGIPRGALPVARPVADALEADLDVVVARKLGAPNNPELALGAVASDgsvwyndali 82 
                                       5678999999999.999**********************************************9999********** PP

                                       ...............................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE CS
                      Pribosyltran  80 ...............................rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvd 125
                                                                        l+d++g++Vl+VDD+++tG T +a l+ ++++++  v++av+v 
  gi|336253604|ref|YP_004596711.1|  83 drldvsddyleeiraeeaqnarekadryrdsPGLPDLEGERVLVVDDGVATGATATACLRQVRAADADYVGLAVPVG 159
                                       ******************************99********************************************* PP

                                       -HHHHHHHHHH-TTS......EEEEEEE-SEE- CS
                      Pribosyltran 126 kpateeevdknakrvfsls.pdnfvavvgfeld 157
                                        p+++ + +++a++v+ l+ p+nf av +f+  
  gi|336253604|ref|YP_004596711.1| 160 SPQSVADLEAEADEVIALEtPENFRAVGQFYRE 192
                                       ******************************865 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-06     0.011     118     176 ..     118     174 ..      92     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                           UPRTase 118 kiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpkv 176
                                       +++ ++vl++D  +aTG++a a++++++   ++ + + ++  + s++ v+ l +e  +v
  gi|336253604|ref|YP_004596711.1| 118 DLEGERVLVVDDGVATGATATACLRQVRA--ADADYVGLAVPVGSPQSVADLEAEADEV 174
                                       347889***********************..5567899999999999999998887765 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       0.4   2.4e+03      33      78 ..       6      47 ..       3      55 .. 0.72
   2 ?   10.0   0.0   7.4e-05      0.44     122     147 ..     122     147 ..     113     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.4
                          PRTase_2 33 reagaaLaellaeakkeelpepvlvigfAEtAtaLghgvadaleee 78
                                       eag++La++l+     +  e  +v+g+   A  +++ vadale++
  gi|336253604|ref|YP_004596711.1|  6 SEAGDRLAAELE----GRGVEADVVLGIPRGALPVARPVADALEAD 47
                                      567778888887....455667788888888888888888888654 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 7.4e-05
                          PRTase_2 122 kelvLvDDEistGktalnliralqek 147
                                       +++++vDD ++tG ta++ +r+++++
  gi|336253604|ref|YP_004596711.1| 122 ERVLVVDDGVATGATATACLRQVRAA 147
                                       56889**************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1535.20
//
Query:       gi|336253605|ref|YP_004596712.1|  [L=74]
Description: hypothetical protein Halxa_2208 [Halopiger xanaduensis SH-6]
Scores for 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   1.7       0.41   10.5   1.7    1.5  1  DUF412    Protein of unknown function, DUF412


Domain annotation for each model (and alignments):
>> DUF412  Protein of unknown function, DUF412
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.7   2.3e-05      0.41      43      88 ..      13      63 ..       2      70 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.3e-05
                            DUF412 43 alavltlvlqlylagse.alpqailtalfllsLPlQG....lywlGkrakt 88
                                       l+ + ++  +yl +    l+ a ++al +ls+Pl G    l++l +r++ 
  gi|336253605|ref|YP_004596712.1| 13 LLIQFPIAALVYLDARRlDLERATMYALGILSVPLAGwvvvLWYLSQRSEL 63
                                      3333444444444443389****************9977777899999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 549.27
//
Query:       gi|336253606|ref|YP_004596713.1|  [L=223]
Description: helix-hairpin-helix motif protein [Halopiger xanaduensis SH-6]
Scores for complete 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-11   44.8   0.0    3.7e-11   43.5   0.0    1.6  1  HHH_5     Helix-hairpin-helix domain
    3.1e-11   43.2   0.0    8.9e-11   41.7   0.0    1.7  2  HHH_2     Helix-hairpin-helix motif
    1.3e-09   38.4   0.0    1.7e-09   38.1   0.0    1.1  1  ERCC4     ERCC4 domain
    2.2e-06   27.3   0.2    0.00011   21.9   0.1    2.5  2  HHH       Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   8.2e-15   3.7e-11       7      56 ..     168     216 ..     167     217 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 8.2e-15
                                       STT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   7 vsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                       ++GiGp++A +l++  + +ve l+aad e+L++i GiG+ +Ae i  + +
  gi|336253606|ref|YP_004596713.1| 168 IDGIGPELATTLYER-YPTVESLLAADLEDLTRIDGIGETRAETIYAAFR 216
                                       79*************.*****************************98766 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.6   7.2e+03      21      32 ..      87      98 ..      84     102 .. 0.76
   2 !   41.7   0.0     2e-14   8.9e-11       8      59 ..     168     219 ..     165     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
                             HHH_2 21 krFksldaLkka 32
                                        F +l+ L++a
  gi|336253606|ref|YP_004596713.1| 87 GDFLDLESLRTA 98
                                      679999999988 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 2e-14
                             HHH_2   8 IrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFenek 59 
                                       I  +G + A +L +r+ +++ L +a+le+L+ +d+iGe+ A+ i+  F+n+ 
  gi|336253606|ref|YP_004596713.1| 168 IDGIGPELATTLYERYPTVESLLAADLEDLTRIDGIGETRAETIYAAFRNDG 219
                                       6789*********************************************985 PP

>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   3.8e-13   1.7e-09       1     152 [.       9     131 ..       9     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 3.8e-13
                                       EEGGGCTSHHHH..HHTTTS.EEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCC..S CS
                             ERCC4   1 iDsrelksgieeylleelgv.evvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikd..g 74 
                                       +D+re  sg+ e + e  +v evv+ +lp gd+  +    ++               +  erk+ +d v++ +   g
  gi|336253606|ref|YP_004596713.1|   9 VDDRE-PSGLVEAVREHPDVtEVVVDRLPSGDI-AI----DS---------------IGFERKTPRDYVSTAMGrsG 64 
                                       68888.667777756777788************.77....88...............***************88543 PP

                                       .HHHHHHHHHHH.H-SEEEEEEES..-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHH CS
                             ERCC4  75 .rleeqvsrlkrngykkpillveg..ldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesane 148
                                        +leeqv+r+++ +y++ ++l+eg  ld  + +               +++++i +++++++  ++v+++ + +++ 
  gi|336253606|ref|YP_004596713.1|  65 pDLEEQVARMAE-SYDHSYVLLEGdfLDLESLRTA-------------VSPESIRGSMASITARHEVPVVPCTDRSR 127
                                       7***********.***********88555555432.............***************************99 PP

                                       HHHH CS
                             ERCC4 149 taew 152
                                        +++
  gi|336253606|ref|YP_004596713.1| 128 LVDF 131
                                       9987 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.025   1.1e+02      16      26 ..     168     178 ..     168     181 .. 0.80
   2 !   21.9   0.1   2.4e-08   0.00011       2      29 ..     186     213 ..     185     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.025
                                       STT-SHHHHHH CS
                               HHH  16 lPGVGpktAea 26 
                                       + G+Gp+ A  
  gi|336253606|ref|YP_004596713.1| 168 IDGIGPELATT 178
                                       67*****9965 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.4e-08
                                       HHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   2 leglipasreeLlalPGVGpktAeaIls 29 
                                       +e+l +a++e+L+ + G+G+ +Ae I++
  gi|336253606|ref|YP_004596713.1| 186 VESLLAADLEDLTRIDGIGETRAETIYA 213
                                       68999*********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 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:                        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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1748.58
//
Query:       gi|336253607|ref|YP_004596714.1|  [L=364]
Description: aminoglycoside phosphotransferase [Halopiger xanaduensis SH-6]
Scores for 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-38  130.8   4.1    1.2e-37  130.1   4.1    1.3  1  APH       Phosphotransferase enzyme family
    0.00046   19.2   0.0    0.00061   18.8   0.0    1.1  1  DUF1679   Protein of unknown function (DUF1679)
     0.0021   17.5   0.0      0.003   16.9   0.0    1.2  1  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 !  130.1   4.1     2e-41   1.2e-37      16     229 ..      41     265 ..      28     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 2e-41
                                       EEETT.-.-EEEEEE-TT...S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS... CS
                               APH  16 vttpa.g.ryvlrrnppa...raaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr... 84 
                                       + t++ +  yvlr + +     a +++rre+++l+lL+++   +Pe++ +++dd   g +f+l +y++g++++    
  gi|336253607|ref|YP_004596714.1|  41 ISTAEaKnAYVLRKPDKLrdtGAFNSLRREFDVLQLLEETTGAAPEPVLLCEDDSIVGAPFLLTTYLEGEPVRLgsy 117
                                       4455532599999965555567****************99999********************************** PP

                                       ....HHHHHHHHHHHHHHHHHHCCHHCH..-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCCHHHHHHHHHHHHH CS
                               APH  85 ....klsaaqlpellealgeflaalhqvd.paalpladflaqdlellrqlesatarllaselldlleeleeqvlaal 156
                                             +++ ++ + ++l+e+la+lh++d  ++  ++ ++++++ l+  +++     + se++ +   l++ v+++l
  gi|336253607|ref|YP_004596714.1| 118 lperFRNPDARRTVSGRLIETLAELHSADaEPFEEVCERRRPQAQLAHGVDRL--EAVTSETDLEPRGLWD-VADWL 191
                                       ***9999*********************9999999999999999999999999..88888888878899**.***** PP

                                       HHH--SSS-EEEE-SS-SGGGEEEC...TTEEEEE---TT-EEEECCHHHHCCHHHCSCHCCCHCHHHHHHHHC CS
                               APH 157 aallpgelptvllHgDlhpgNllvd.pddgrvtGviDfedaglgpplyDlavllrswtseldpeflaallraye 229
                                       ++++p+ ++++l+HgD++p N+l+  +d+++++Gv+D+e+a lg+p+ +l++ll +w+++ dp +  + ++a +
  gi|336253607|ref|YP_004596714.1| 192 ERNVPTGSRATLVHGDYRPSNVLFAgDDHPELSGVLDWETAFLGDPVTELGYLLLRWRDDGDPTPSLGDIEARH 265
                                       **************************9***************************99******999888888877 PP

>> DUF1679  Protein of unknown function (DUF1679)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     1e-07   0.00061     263     315 ..     196     246 ..     142     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1e-07
                           DUF1679 263 vlGikkvlvhgDlwsaNiLfseeeegklklkkviDyQlvslgnpaeDlvrlll 315
                                         G +  lvhgD   +N+Lf+ +++   +l+ v+D+ ++ lg p + l+ lll
  gi|336253607|ref|YP_004596714.1| 196 PTGSRATLVHGDYRPSNVLFAGDDH--PELSGVLDWETAFLGDPVTELGYLLL 246
                                       5688999**************9665..899******************99885 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     5e-07     0.003     164     262 ..     140     246 ..     118     249 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-07
                          EcKinase 164 eelleellkaalealreelpelekea..ekleklkenlferllelve........ekeeefnvlnHGDlwvnNimfk 230
                                       +el ++  + + e+ +++ p+ +     ++le+++++   + + l++         +++  ++l+HGD+  +N++f 
  gi|336253607|ref|YP_004596714.1| 140 AELHSADAEPFEEVCERRRPQAQLAHgvDRLEAVTSETDLEPRGLWDvadwlernVPTGSRATLVHGDYRPSNVLFA 216
                                       55555555555555555555555444555555555555555555555555665666778889**************9 PP

                          EcKinase 231 ydeegepedvilvDFQlsrygSpalDLlyfly 262
                                        d+   pe    +D+ ++++g p+  L y+l+
  gi|336253607|ref|YP_004596714.1| 217 GDDH--PELSGVLDWETAFLGDPVTELGYLLL 246
                                       9866..7777789**************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); 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:                         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 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2701.97
//
Query:       gi|336253608|ref|YP_004596715.1|  [L=290]
Description: ribonuclease BN [Halopiger xanaduensis SH-6]
Scores for 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-33  116.0  29.2    2.6e-33  115.7  29.2    1.0  1  Virul_fac_BrkB  Virulence factor BrkB
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.022   14.7   0.1    1.5  1  DUF1077         Protein of unknown function (DUF1077)


Domain annotation for each model (and alignments):
>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7  29.2   2.9e-37   2.6e-33       2     255 ..      23     266 ..      22     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 2.9e-37
                    Virul_fac_BrkB   2 eddlsllAaalayytllSlfPlllvllavlgllglddelqeqlldllaevlpegaaevvedilqrllnqa..slgll 76 
                                       e+++s+ Aa+lay+++ +l+Pl++++l  ++ l+   +  e ll  la+ +   + + + +  +++  +a  ++++l
  gi|336253608|ref|YP_004596715.1|  23 ERQISVKAAGLAYHAFNTLVPLVILALVGAA-LV---DSLEPLLGELASAAGL-GGTGLDGAAAAADGSArtRAAVL 94 
                                       57899*****************666555554.44...4566777777777554.5577777776666555569**** PP

                    Virul_fac_BrkB  77 glavllwsasggvsalrralnkiygveesrsflrkrllsllllllllvllllslvlsvflqslllasapllglglel 153
                                       +l++llwsa+++++a+ +a++ +yg ++  s++   +  +l++ l +vl+ ++l++ v+l s++  s+  lg gl  
  gi|336253608|ref|YP_004596715.1|  95 ALSILLWSAVRLFQAINSAFTDVYGSRKDVSYVDEATTVTLVTALYVVLVTVTLAVGVALVSAVGLSLSALGGGL-- 169
                                       **************************9989********************************8887754444332.. PP

                    Virul_fac_BrkB 154 sellllqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwllvkilfslylsnfasynaiYGslgal 230
                                            l l++ +++++ll+ +f+ +Y+++p+  v++ ++lpG+++aal+w+++  +f ly++  +  +a++G +ga+
  gi|336253608|ref|YP_004596715.1| 170 ----PLALGGSVLLAALLTGVFLPMYYLFPQSDVSVGEVLPGTAFAALSWTALAGGFRLYVAT-SESVALFGVAGAV 241
                                       ....255666668999999*******************************************8.7899********* PP

                    Virul_fac_BrkB 231 iilllWlylsalilLlGaelnaelq 255
                                       +++l W+yl +l+lLlGa+lna+l+
  gi|336253608|ref|YP_004596715.1| 242 LLILTWVYLGGLCLLLGAVLNAVLA 266
                                       **********************997 PP

>> DUF1077  Protein of unknown function (DUF1077)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.5e-06     0.022      45     104 ..      94     160 ..      85     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-06
                           DUF1077  45 mmvlmllvnpikallsvnkaFkkleseks.......ksklllqklvyvllqllllalglyklnsmGL 104
                                       + + +ll+++++ + ++n+aF+++ ++++        ++++l  ++yv+l  ++la+g+  ++++GL
  gi|336253608|ref|YP_004596715.1|  94 LALSILLWSAVRLFQAINSAFTDVYGSRKdvsyvdeATTVTLVTALYVVLVTVTLAVGVALVSAVGL 160
                                       566789*******************97664444333448999**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2143.85
//
Query:       gi|336253609|ref|YP_004596716.1|  [L=68]
Description: hypothetical protein Halxa_2212 [Halopiger xanaduensis SH-6]
Scores for 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   62.2   1.7    3.6e-17   62.1   1.7    1.0  1  DUF2196     Uncharacterized conserved protein (DUF2196)
  ------ inclusion threshold ------
      0.055   13.2   0.2       0.12   12.2   0.2    1.5  1  SNN_linker  Stannin unstructured linker


Domain annotation for each model (and alignments):
>> DUF2196  Uncharacterized conserved protein (DUF2196)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   1.7     4e-21   3.6e-17       3      61 .]       6      64 ..       4      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 4e-21
                           DUF2196  3 ktrkdikpGleVeivlkkdqrtGklteGiVkdilTnssthphGIKVrLedGeVGRVqei 61
                                      +t++++++G +Veiv++++++++++ e+iV +i T + ++p+G+ V+L++G VG+Vq++
  gi|336253609|ref|YP_004596716.1|  6 PTAEELRQGITVEIVQGDQDVQSEDREPIVGEIGTVYGDDPKGPEVELKSGVVGHVQSV 64
                                      7899*****************************************************85 PP

>> SNN_linker  Stannin unstructured linker
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   1.3e-05      0.12      10      20 ..      27      37 ..      26      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.3e-05
                        SNN_linker 10 QsEDEESIVGd 20
                                      QsED E IVG+
  gi|336253609|ref|YP_004596716.1| 27 QSEDREPIVGE 37
                                      9*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      156  (0.00870099); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 546.77
//
Query:       gi|336253610|ref|YP_004596717.1|  [L=244]
Description: beta-lactamase [Halopiger xanaduensis SH-6]
Scores for 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-14   52.4   0.1    6.2e-14   52.0   0.1    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    8.9e-13   48.4   0.1    1.1e-12   48.1   0.1    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    4.2e-07   30.2   3.0    3.8e-06   27.1   1.6    2.2  2  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 !   52.0   0.1     1e-17   6.2e-14       3     200 ..      26     212 ..      24     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1e-17
                                       EEES--TT...........HHHH..HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHH CS
                     Lactamase_B_2   3 iLiDagpd...........lrqq..alralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgv 66 
                                       +L+D+++               +  ++++  P + +d+  + daV++th H DH+ +     el++ ++pl+++++ 
  gi|336253610|ref|YP_004596717.1|  26 FLVDPMFAspgenppvpnsP--NdrENPLV-PMPDVDR--SHDAVVVTHRHTDHF-DEAAKDELEA-DVPLFCQPEE 95 
                                       67777777666776654331..12245665.6666666..99*************.5444455544.69*****999 PP

                                       HHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS- CS
                     Lactamase_B_2  67 lavleanfvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDt 143
                                       +++ ++++         +++v+++d  ++++++  g++++ tp +h+ g+ l++++g++ G+++e g++++y +gDt
  gi|336253610|ref|YP_004596717.1|  96 ADEFAEEG---------FTDVRPVD--DEVSFD--GVTVRRTPGQHGYGQ-LAEEMGPVSGFVFE-GDETLYLAGDT 157
                                       99999994.........66777777..777776..689***********9.9*************.999******** PP

                                       S---..HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 144 gyip..eeigerlggadllllditayeddemir.hmgHltpeeaveaaadlgakrlvliH 200
                                         ++  ee  e+++ +++++l+++     ++++ +++++ +e+ +++ ++++a++  ++H
  gi|336253610|ref|YP_004596717.1| 158 IWYEpvEETLEEYD-PEVVVLNGGEA---QFEQgEPITMGVEDVAAVREATDATV-AVVH 212
                                       *9996666666665.88999999933...333349******99666555555554.4455 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 !   48.1   0.1   1.9e-16   1.1e-12       5     158 ..      12     208 ..       8     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.9e-16
                     Lactamase_B_3   5 lghnsflletagarilvDPfkanlgyeppa..................eeaDlvlisqaledHahletlkqlaenvk 63 
                                       + h+++l+++++++ lvDP++a+ g +pp                   ++ D+v+++++++dH++ ++  +l+ +v+
  gi|336253610|ref|YP_004596717.1|  12 VRHATVLVTIGDTTFLVDPMFASPGENPPVpnspndrenplvpmpdvdRSHDAVVVTHRHTDHFDEAAKDELEADVP 88 
                                       67******************8766666555777888888899999999************************77777 PP

                     Lactamase_B_3  64 vlee..................geslevggleiravatshdavg.gsergenngflleqdgltiyhlGhlahelsse 121
                                       +  +                  ++++ ++g+ +r ++++h  ++  +e g+ +gf++e ++ t+y  G++      e
  gi|336253610|ref|YP_004596717.1|  89 LFCQpeeadefaeegftdvrpvDDEVSFDGVTVRRTPGQHGYGQlAEEMGPVSGFVFE-GDETLYLAGDTIWYEPVE 164
                                       76663444444444454444455669**************666426688********6.5889******98666666 PP

                     Lactamase_B_3 122 elkelgrvDvvltPvgg.......pltlgqeealelakrLkpkl 158
                                       e  e  +++vv+++ g+       p+t+g e+++ + ++ ++ +
  gi|336253610|ref|YP_004596717.1| 165 ETLEEYDPEVVVLNGGEaqfeqgePITMGVEDVAAVREATDATV 208
                                       6666669*****99988******99*******999988777665 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.025   1.5e+02       7      24 ..      15      32 ..      10      39 .. 0.83
   2 !   27.1   1.6   6.3e-10   3.8e-06      46     163 ..      63     176 ..      59     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.025
                                      EEEEEEETTCEEEES--S CS
                       Lactamase_B  7 nsyliegdggviLiDtGt 24
                                       ++l++ +++++L+D+ +
  gi|336253610|ref|YP_004596717.1| 15 ATVLVTIGDTTFLVDPMF 32
                                      578999*********966 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 6.3e-10
                                       EEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEE CS
                       Lactamase_B  46 davilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrra 122
                                       dav++TH H+DH+  +++   ++dvp ++ +eea ++ +e+  d           v++ +++v  ++ ++ + +++ 
  gi|336253610|ref|YP_004596717.1|  63 DAVVVTHRHTDHFDEAAKDELEADVPLFCQPEEADEFAEEGFTD-----------VRPVDDEVSFDGVTVRRTPGQH 128
                                       8*****************************************55...........6666777888888888888888 PP

                                       EEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC........ CS
                       Lactamase_B 123 lyvtggpghghghgvveygggkvlftGDallagetgridl.......t 163
                                       +y       g+++g v+ g++++ ++GD++  ++ +++ +        
  gi|336253610|ref|YP_004596717.1| 129 GYGQLAEEMGPVSGFVFEGDETLYLAGDTIWYEPVEETLEeydpevvV 176
                                       888888889**********************99998887755555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1795.15
//
Query:       gi|336253611|ref|YP_004596718.1|  [L=140]
Description: peptide methionine sulfoxide reductase msrB [Halopiger xanaduensis SH-6]
Scores for 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-55  184.5   0.2    7.2e-55  184.3   0.2    1.0  1  SelR            SelR domain
  ------ inclusion threshold ------
       0.02   13.8   0.0        1.7    7.4   0.0    2.0  2  HECT_2          HECT-like Ubiquitin-conjugating enzyme (E2)-b
       0.02   14.6   0.3        1.1    9.1   0.0    2.3  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.025   14.1   5.1        1.9    8.0   0.2    3.2  3  TF_Zn_Ribbon    TFIIB zinc-binding
      0.028   14.6   0.3      0.075   13.2   0.3    1.7  1  Yippee-Mis18    Yippee zinc-binding/DNA-binding /Mis18, centr
      0.031   14.1   0.2        3.8    7.5   0.0    2.2  2  ADD_ATRX        Cysteine Rich ADD domain
      0.062   13.3   0.3      0.062   13.3   0.3    2.4  3  DUF1610         Domain of unknown function (DUF1610)
       0.12   11.8   2.1         12    5.5   0.0    2.9  3  zf-ribbon_3     zinc-ribbon domain
       0.16   12.2   1.7       0.47   10.7   1.6    1.8  2  DUF2072         Zn-ribbon containing protein
       0.22   11.6   3.8        2.4    8.3   3.8    2.3  1  DZR             Double zinc ribbon
       0.24   11.6   2.4         19    5.5   0.0    2.5  2  Zn-ribbon_8     Zinc ribbon domain
       0.26   11.1   3.4        2.3    8.1   0.5    2.6  2  zinc_ribbon_2   zinc-ribbon domain
       0.31   10.8   5.4          4    7.2   0.1    3.3  3  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
        0.6   10.3   3.4        3.6    7.8   0.3    2.2  2  Ribosomal_L37e  Ribosomal protein L37e


Domain annotation for each model (and alignments):
>> SelR  SelR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.3   0.2   5.6e-58   7.2e-55       1     120 [.      18     135 ..      18     136 .. 0.98

  Alignments for each domain:
  == domain 1  score: 184.3 bits;  conditional E-value: 5.6e-58
                                       HHHCTSHCCHHHHHHHTT-SSTTSSSTSS--SSCEEEETTTS-EEEECCCCE-STTSSSEESS-STTTTEEEEEEEC CS
                              SelR   1 elkkkLtpeqyevlrekgterpftgeyekekekGvyecavcgepLfssetkfdsgcGwpsFaeaikeeavkekkdts 77 
                                       e++++L++e+y++lre+gte+pf+gey ++k +G y+c++cg++Lf+setkf+sgcGwpsF+++ ++ +v+++ dts
  gi|336253611|ref|YP_004596718.1|  18 EWRERLSDEEYRILREAGTEAPFSGEYVDHKADGSYACTACGAELFDSETKFESGCGWPSFYDVDDD-KVETRVDTS 93 
                                       7*************************************************************98887.********* PP

                                       TTSEEEEEEETTCECEEEEEECTSSSSS.SEEEEE-CCCEEEE CS
                              SelR  78 lgmertevvcakcdahlGhvFedgpkpttgkrycinsvslkfk 120
                                       +gm+rtevvca+c++hlGhvFedgp+pt gkrycinsv+l+f+
  gi|336253611|ref|YP_004596718.1|  94 HGMRRTEVVCAECGGHLGHVFEDGPEPT-GKRYCINSVALEFE 135
                                       **************************95.*************7 PP

>> HECT_2  HECT-like Ubiquitin-conjugating enzyme (E2)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.007       8.9      98     130 ..      28      69 ..       2      78 .. 0.65
   2 ?    7.4   0.0    0.0013       1.7     203     244 ..      91     135 ..      74     140 .] 0.73

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.007
                            HECT_2  98 s......ekevpWsakdlsa..etslrCrsCknvllks.rki 130
                                       +       +e+p s + +    + s  C++C+++l++s +k+
  gi|336253611|ref|YP_004596718.1|  28 YrilreaGTEAPFSGEYVDHkaDGSYACTACGAELFDSeTKF 69 
                                       12233334467888877777546999***********95555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0013
                            HECT_2 203 eetkpkkeeslsCkrCkatlGeeds...aaegvkLfkwnvslqps 244
                                       +++  ++++++ C++C+ +lG++ +   +  g +    +v+l+ +
  gi|336253611|ref|YP_004596718.1|  91 DTSHGMRRTEVVCAECGGHLGHVFEdgpEPTGKRYCINSVALEFE 135
                                       5678899**************987766655666666666666655 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 ?    3.6   0.1     0.044        56      37      52 ..      45      60 ..      40      62 .. 0.78
   2 ?    9.1   0.0   0.00084       1.1      16      47 ..      94     126 ..      88     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.044
                    zinc_ribbon_10 37 keeleevkyrCpkCga 52
                                      ++ +++ +y C  Cga
  gi|336253611|ref|YP_004596718.1| 45 VDHKADGSYACTACGA 60
                                      56677789******97 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00084
                    zinc_ribbon_10  16 saknryalICskChshnGlapkeeleev.kyrC 47 
                                       + + r  ++C +C  h G + ++ +e++ k +C
  gi|336253611|ref|YP_004596718.1|  94 HGMRRTEVVCAECGGHLGHVFEDGPEPTgKRYC 126
                                       5578999***********998888877765555 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.8   2.3e+03      31      42 ..      10      21 ..       9      22 .. 0.78
   2 ?    7.1   0.1     0.003       3.9      16      29 ..      49      62 ..      40      68 .. 0.81
   3 ?    8.0   0.2    0.0015       1.9      17      26 ..      98     107 ..      96     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.8
                                      ECCCCCCCHHHH CS
                      TF_Zn_Ribbon 31 dnsidegpewre 42
                                      d+  ++  ewre
  gi|336253611|ref|YP_004596718.1| 10 DDLPESDAEWRE 21
                                      677788899*98 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.003
                                      STTCEEESSSSBEE CS
                      TF_Zn_Ribbon 16 ergelvCtdCGlVl 29
                                      + g + Ct+CG+ l
  gi|336253611|ref|YP_004596718.1| 49 ADGSYACTACGAEL 62
                                      679999*****866 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0015
                                       TTCEEESSSS CS
                      TF_Zn_Ribbon  17 rgelvCtdCG 26 
                                       r+e+vC +CG
  gi|336253611|ref|YP_004596718.1|  98 RTEVVCAECG 107
                                       89*******7 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   5.9e-05     0.075       5      85 ..      55     132 ..      51     136 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.9e-05
                                       ETTTS-EEEECCCEEEEECCCEEEES---CCCEEEECEEEETTSTTEEEEEEEETTT--EEEEEEEECSCC..CCCC CS
                      Yippee-Mis18   5 CkkCktilgdslqlvsegralnivvlkkvtrnvvvgkelvtdeegkctystlsCkgCnsvlGwkYksteee..lkyk 79 
                                       C  C ++l ds   +++g  +  + ++   ++v ++  +++        +++ C+ C+ +lG ++++ +e    +y+
  gi|336253611|ref|YP_004596718.1|  55 CTACGAELFDSETKFESGCGWPSF-YDVDDDKVETRVDTSH----GMRRTEVVCAECGGHLGHVFEDGPEPtgKRYC 126
                                       666666666666555555442222.2222233333322222....366679***************99887455566 PP

                                       CTCEEE CS
                      Yippee-Mis18  80 rglfil 85 
                                       ++   l
  gi|336253611|ref|YP_004596718.1| 127 INSVAL 132
                                       555555 PP

>> ADD_ATRX  Cysteine Rich ADD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0029       3.8      10      23 ..      51      64 ..      44      69 .. 0.75
   2 ?    4.6   0.0     0.024        30       9      24 ..      98     113 ..      91     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0029
                          ADD_ATRX 10 eivsCtaCgqqvnh 23
                                          CtaCg +++ 
  gi|336253611|ref|YP_004596718.1| 51 GSYACTACGAELFD 64
                                      4568*****99875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.024
                          ADD_ATRX   9 eeivsCtaCgqqvnhf 24 
                                          v C+ Cg ++ h+
  gi|336253611|ref|YP_004596718.1|  98 RTEVVCAECGGHLGHV 113
                                       34699*******9997 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   4.9e-05     0.062       1      17 [.      55      69 ..      55      70 .. 0.93
   2 ?   -2.1   0.2       3.1     4e+03       4       7 ..      73      76 ..      71      76 .. 0.75
   3 ?   -2.9   0.8       5.8   7.4e+03      19      23 ..     103     107 ..     102     108 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.9e-05
                           DUF1610  1 CtSCGaelaprEravvF 17
                                      Ct+CGael + E  ++F
  gi|336253611|ref|YP_004596718.1| 55 CTACGAELFDSE--TKF 69
                                      ***********9..887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                           DUF1610  4 CGae 7 
                                      CG++
  gi|336253611|ref|YP_004596718.1| 73 CGWP 76
                                      9996 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.8
                           DUF1610  19 CPNCG 23 
                                       C +CG
  gi|336253611|ref|YP_004596718.1| 103 CAECG 107
                                       66787 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.015        19      16      26 .]      52      62 ..      47      62 .. 0.76
   2 ?   -1.5   0.0       1.5   1.9e+03       8      11 ..      73      76 ..      71      80 .. 0.81
   3 ?    5.5   0.0     0.009        12      16      24 ..     100     108 ..      96     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                       zf-ribbon_3 16 dnvCpyCGtkl 26
                                        +C+ CG++l
  gi|336253611|ref|YP_004596718.1| 52 SYACTACGAEL 62
                                      55899999876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                       zf-ribbon_3  8 CGap 11
                                      CG+p
  gi|336253611|ref|YP_004596718.1| 73 CGWP 76
                                      9997 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.009
                       zf-ribbon_3  16 dnvCpyCGt 24 
                                        +vC+ CG+
  gi|336253611|ref|YP_004596718.1| 100 EVVCAECGG 108
                                       679*****7 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.6   0.00037      0.47       3      44 ..      54      92 ..      52     113 .. 0.81
   2 ?   -0.6   0.1       1.2   1.5e+03      22      28 ..     103     109 ..      91     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00037
                           DUF2072  3 kCtkCekvfedgskeilkGCpsCGgkkFlyvkeeekkedvse 44
                                       Ct C+ ++ d++++  +GC   G+  F  v +++ ++ v +
  gi|336253611|ref|YP_004596718.1| 54 ACTACGAELFDSETKFESGC---GWPSFYDVDDDKVETRVDT 92
                                      6*****************95...9999999988877665544 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                           DUF2072  22 CpsCGgk 28 
                                       C++CGg+
  gi|336253611|ref|YP_004596718.1| 103 CAECGGH 109
                                       7777764 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.8    0.0018       2.4      10      35 ..      50     107 ..      21     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                               DZR  10 pdarfCseCgtklkavaa................................edrCpsCg 35 
                                       +++  C +Cg++l   ++                                e +C +Cg
  gi|336253611|ref|YP_004596718.1|  50 DGSYACTACGAELFDSETkfesgcgwpsfydvdddkvetrvdtshgmrrtEVVCAECG 107
                                       5667788888887655557888888888888888888888888888888888888887 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.7     0.017        21       6      14 ..      53      61 ..      52      73 .. 0.83
   2 ?    5.5   0.0     0.015        19      22      36 ..      97     110 ..      85     116 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                       Zn-ribbon_8  6 YrCeeCghe 14
                                      Y C++Cg e
  gi|336253611|ref|YP_004596718.1| 53 YACTACGAE 61
                                      99****976 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
                       Zn-ribbon_8  22 sdapltaCPeCgsev 36 
                                         + +++C eCg+++
  gi|336253611|ref|YP_004596718.1|  97 R-RTEVVCAECGGHL 110
                                       3.4467799999865 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   0.5    0.0018       2.3       2       9 ..      55      62 ..      49      74 .. 0.64
   2 ?    2.9   0.1     0.075        95      14      21 ..     101     108 ..      99     110 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0018
                     zinc_ribbon_2  2 CpnCGael 9 
                                      C+ CGael
  gi|336253611|ref|YP_004596718.1| 55 CTACGAEL 62
                                      56666665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.075
                     zinc_ribbon_2  14 kFCpyCGt 21 
                                       + C +CG 
  gi|336253611|ref|YP_004596718.1| 101 VVCAECGG 108
                                       67999985 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 ?    7.2   0.1    0.0031         4       6      17 ..      54      65 ..      49      67 .. 0.84
   2 ?    4.4   0.1     0.024        31       3      12 ..      99     108 ..      97     116 .. 0.81
   3 ?   -0.5   0.1      0.79     1e+03      20      24 ..     122     126 ..     121     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0031
                           zf-RRN7  6 pCgvCgcrsftl 17
                                      +C +Cg+ +f++
  gi|336253611|ref|YP_004596718.1| 54 ACTACGAELFDS 65
                                      599999999987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.024
                           zf-RRN7   3 kgppCgvCgc 12 
                                       ++ +C++Cg+
  gi|336253611|ref|YP_004596718.1|  99 TEVVCAECGG 108
                                       6779999997 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.79
                           zf-RRN7  20 GfyyC 24 
                                       G++yC
  gi|336253611|ref|YP_004596718.1| 122 GKRYC 126
                                       99*** PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0028       3.6      18      41 ..      54      77 ..      46      78 .. 0.91
   2 ?    3.1   0.3     0.084   1.1e+02       6      25 ..      93     109 ..      89     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0028
                    Ribosomal_L37e 18 lCrrCgkrsyhvqkktCascGyps 41
                                       C  Cg + +  ++k  + cG+ps
  gi|336253611|ref|YP_004596718.1| 54 ACTACGAELFDSETKFESGCGWPS 77
                                      7*********************96 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.084
                    Ribosomal_L37e   6 sfGkrqkkktHilCrrCgkr 25 
                                       s G r   +t ++C  Cg +
  gi|336253611|ref|YP_004596718.1|  93 SHGMR---RTEVVCAECGGH 109
                                       66666...467889999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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):              14  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1037.72
//
Query:       gi|336253612|ref|YP_004596719.1|  [L=52]
Description: hypothetical protein Halxa_2215 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0039   16.7   2.5      0.077   12.5   0.3    2.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0044   16.7   3.4       0.19   11.5   0.3    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
     0.0062   16.5   0.2     0.0063   16.5   0.2    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.011   15.4   0.3       0.21   11.4   0.0    2.0  2  PADR1           PADR1 (NUC008) domain
      0.014   15.3   1.6       0.42   10.6   0.1    2.1  2  zinc_ribbon_4   zinc-ribbon domain
      0.017   14.0   0.3      0.018   13.8   0.3    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
      0.037   14.7   5.0        5.2    7.8   0.2    3.0  3  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
      0.044   13.7   2.7          4    7.4   0.3    2.2  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.053   13.2   0.9       0.36   10.5   0.1    2.1  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.055   13.3   0.3        6.5    6.7   0.0    2.1  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO
      0.065   12.7   2.8        1.3    8.5   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain
      0.071   13.0   1.6        2.6    8.0   0.1    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)
      0.076   13.2   2.5       0.32   11.2   3.0    1.7  2  zf-RING_7       C4-type zinc ribbon domain
      0.088   12.9   4.3       0.28   11.3   4.3    1.7  1  Zn-ribbon_8     Zinc ribbon domain
      0.097   12.4   0.2      0.097   12.4   0.2    2.2  2  Zn_Tnp_IS1      InsA N-terminal domain
      0.099   12.9   0.2        8.3    6.8   0.1    2.1  2  Ribosomal_L32p  Ribosomal L32p protein family
       0.18   11.9   4.1        2.3    8.4   0.0    2.1  2  UPF0547         Uncharacterised protein family UPF0547


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 ?    4.8   0.1     0.019        20      14      26 ..       4      16 ..       1      18 [. 0.77
   2 !   12.5   0.3   7.3e-05     0.077       2      12 ..      39      50 ..      38      52 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.019
                                      ETSTTCEEESSSS CS
                      TF_Zn_Ribbon 14 DpergelvCtdCG 26
                                      D++++  +C +CG
  gi|336253612|ref|YP_004596719.1|  4 DTATALSRCRNCG 16
                                      7777777888888 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.3e-05
                                      EETTTTCEE.CH CS
                      TF_Zn_Ribbon  2 kCPnCgstn.lv 12
                                      +CPnC st+ ++
  gi|336253612|ref|YP_004596719.1| 39 QCPNCESTDvIT 50
                                      8*******9555 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.3   0.00018      0.19       2      11 ..      11      20 ..      11      21 .. 0.91
   2 !    6.2   0.2    0.0081       8.6      16      22 ..      39      45 ..      37      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                      Rubredoxin_2  2 vCsqCGfesa 11
                                      +C++CGfe++
  gi|336253612|ref|YP_004596719.1| 11 RCRNCGFEAP 20
                                      8******986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0081
                      Rubredoxin_2 16 rCpsCgs 22
                                      +Cp+C s
  gi|336253612|ref|YP_004596719.1| 39 QCPNCES 45
                                      8****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 !   16.5   0.2     6e-06    0.0063      65      97 ..       4      48 ..       1      52 [] 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6e-06
                                      EEE--EEEETTTS-EEECHHHHH.............S-TTTSSS-E CS
                              HypA 65 eevpvkvrCreCgkefeleekal.............rCpkCgsadv 97
                                      ++  +  rCr+Cg e    ++ +             +Cp+C+s+dv
  gi|336253612|ref|YP_004596719.1|  4 DTATALSRCRNCGFEAPGGDE-AwlrlevpklgrmtQCPNCESTDV 48
                                      5667889******88884432.23466899*************987 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.11   1.2e+02      12      20 ..       8      16 ..       5      20 .. 0.86
   2 ?   11.4   0.0    0.0002      0.21      10      24 ..      34      48 ..      30      52 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                             PADR1 12 alekCpeCk 20
                                      al +C +C+
  gi|336253612|ref|YP_004596719.1|  8 ALSRCRNCG 16
                                      6899****7 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0002
                             PADR1 10 fGalekCpeCkegql 24
                                      +G++ +Cp+C++  +
  gi|336253612|ref|YP_004596719.1| 34 LGRMTQCPNCESTDV 48
                                      7*********97665 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.034        36      27      32 ..      11      16 ..       5      18 .. 0.78
   2 ?   10.6   0.1    0.0004      0.42      19      32 ..      31      44 ..      28      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.034
                     zinc_ribbon_4 27 rCskCg 32
                                      rC +Cg
  gi|336253612|ref|YP_004596719.1| 11 RCRNCG 16
                                      788887 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0004
                     zinc_ribbon_4 19 lpakgvkvrCskCg 32
                                      +p+ g++ +C++C 
  gi|336253612|ref|YP_004596719.1| 31 VPKLGRMTQCPNCE 44
                                      89999999999996 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   1.7e-05     0.018     505     536 ..       7      51 ..       3      52 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                                       --EEEETT.--...EESS..............SB-TTT--BE.EEEEEE CS
                              NRDD 505 pkidvCnecgy...kgei..............ekCpkCgseeevevirR 536
                                       + +++C++cg+    g                ++Cp+C+  + ++vi+R
  gi|336253612|ref|YP_004596719.1|   7 TALSRCRNCGFeapGG-DeawlrlevpklgrmTQCPNCE--S-TDVITR 51 
                                       789********76433.2589***********99*****..4.667777 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 ?    4.1   0.8      0.07        74       3       9 ..      10      16 ..       8      21 .. 0.83
   2 ?    4.1   0.0     0.071        74      29      41 ..      21      33 ..      17      34 .. 0.88
   3 ?    7.8   0.2    0.0049       5.2       3      12 ..      38      47 ..      36      52 .] 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.07
                           zf-ISL3  3 hrCPnCg 9 
                                       rC+nCg
  gi|336253612|ref|YP_004596719.1| 10 SRCRNCG 16
                                      5899999 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.071
                           zf-ISL3 29 ggkrvyLrlrkrR 41
                                      gg +++Lrl++++
  gi|336253612|ref|YP_004596719.1| 21 GGDEAWLRLEVPK 33
                                      6899*******98 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0049
                           zf-ISL3  3 hrCPnCgskt 12
                                      ++CPnC s+ 
  gi|336253612|ref|YP_004596719.1| 38 TQCPNCESTD 47
                                      68*****994 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 ?    7.4   0.3    0.0038         4      11      18 ..       9      16 ..       7      17 .. 0.86
   2 ?    6.5   0.1    0.0076         8      28      35 ..      40      47 ..      36      48 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0038
                           DUF35_N 11 gqrCpdCG 18
                                      ++rC++CG
  gi|336253612|ref|YP_004596719.1|  9 LSRCRNCG 16
                                      68*****9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0076
                           DUF35_N 28 CphCgsdd 35
                                      Cp+C s+d
  gi|336253612|ref|YP_004596719.1| 40 CPNCESTD 47
                                      78887776 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 ?   10.5   0.1   0.00035      0.36      19      25 ..      11      17 ..       3      18 .. 0.84
   2 ?    1.5   0.1      0.22   2.4e+02      19      23 ..      39      43 ..      33      51 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                                      --SSS-- CS
                    DNA_RNApol_7kD 19 RCkeCGh 25
                                      RC++CG+
  gi|336253612|ref|YP_004596719.1| 11 RCRNCGF 17
                                      9*****8 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.22
                                      --SSS CS
                    DNA_RNApol_7kD 19 RCkeC 23
                                      +C +C
  gi|336253612|ref|YP_004596719.1| 39 QCPNC 43
                                      56666 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.018        19      13      21 ..       8      17 ..       2      18 .. 0.74
   2 ?    6.7   0.0    0.0061       6.5       4      20 ..      27      44 ..      26      46 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.018
                         zf-C2H2_3 13 a.sqCkeCgM 21
                                      a s+C +Cg 
  gi|336253612|ref|YP_004596719.1|  8 AlSRCRNCGF 17
                                      4478****97 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0061
                         zf-C2H2_3  4 Ldlgqksfga.sqCkeCg 20
                                      L+l   + g  +qC++C+
  gi|336253612|ref|YP_004596719.1| 27 LRLEVPKLGRmTQCPNCE 44
                                      5566667788789****7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2      0.02        21      19      24 ..      12      17 ..      10      18 .. 0.83
   2 ?    8.5   0.2    0.0012       1.3       2       8 ..      37      43 ..      36      48 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.02
                       zf-ribbon_3 19 CpyCGt 24
                                      C +CG 
  gi|336253612|ref|YP_004596719.1| 12 CRNCGF 17
                                      999996 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0012
                       zf-ribbon_3  2 tvrCPnC 8 
                                      +++CPnC
  gi|336253612|ref|YP_004596719.1| 37 MTQCPNC 43
                                      7889999 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 ?    4.6   0.1     0.027        28      26      36 ..       7      17 ..       2      18 .. 0.75
   2 ?    8.0   0.1    0.0025       2.6       1      12 [.      38      49 ..      38      52 .] 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.027
                           TFIIS_C 26 tvfykCtkCgh 36
                                      t   +C +Cg+
  gi|336253612|ref|YP_004596719.1|  7 TALSRCRNCGF 17
                                      66678999986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0025
                           TFIIS_C  1 akCpkCgsreay 12
                                      ++Cp+C s++++
  gi|336253612|ref|YP_004596719.1| 38 TQCPNCESTDVI 49
                                      59*****99876 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 ?    4.6   0.3     0.036        38      23      30 ..       9      16 ..       3      16 .. 0.83
   2 ?   11.2   3.0    0.0003      0.32       1      29 [.      11      43 ..      11      45 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.036
                                      -EE-TTT- CS
                         zf-RING_7 23 vvtCpeCG 30
                                      + +C +CG
  gi|336253612|ref|YP_004596719.1|  9 LSRCRNCG 16
                                      78*****9 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0003
                                      EETTT--B--CCHHHHHCCS....TB-EE-TTT CS
                         zf-RING_7  1 tCgGChmelppqvlselrag....devvtCpeC 29
                                      +C  C+ e p ++++ lr      + + +Cp+C
  gi|336253612|ref|YP_004596719.1| 11 RCRNCGFEAPGGDEAWLRLEvpklGRMTQCPNC 43
                                      7****************999999999******* PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.3   0.00026      0.28       7      36 ..      11      48 ..      10      51 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                       Zn-ribbon_8  7 rCeeCghefe.........vlqsisdap...ltaCPeCgs.ev 36
                                      rC++Cg  fe         +l     ++   +t+CP+C s +v
  gi|336253612|ref|YP_004596719.1| 11 RCRNCG--FEapggdeawlRLE---VPKlgrMTQCPNCEStDV 48
                                      8*****..99778888665222...222443888****99665 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 ?    0.8   1.3      0.41   4.3e+02      30      34 ..      11      15 ..      10      16 .. 0.90
   2 ?   12.4   0.2   9.2e-05     0.097       7      17 ..      39      49 ..      37      52 .] 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.41
                        Zn_Tnp_IS1 30 rCrdC 34
                                      rCr+C
  gi|336253612|ref|YP_004596719.1| 11 RCRNC 15
                                      8***9 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9.2e-05
                        Zn_Tnp_IS1  7 hCPrCsstdVy 17
                                       CP C+stdV+
  gi|336253612|ref|YP_004596719.1| 39 QCPNCESTDVI 49
                                      6********75 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0078       8.3      22      33 ..       5      16 ..       2      19 .. 0.85
   2 ?    4.7   0.0     0.036        38      21      34 ..      29      45 ..      24      49 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0078
                                      ----EEEETTTC CS
                    Ribosomal_L32p 22 kapnlvecpncg 33
                                      +a +l++c ncg
  gi|336253612|ref|YP_004596719.1|  5 TATALSRCRNCG 16
                                      5679*******9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.036
                                      -----E...EEETTTCC CS
                    Ribosomal_L32p 21 lkapnl...vecpncge 34
                                      l++p+l   ++cpnc +
  gi|336253612|ref|YP_004596719.1| 29 LEVPKLgrmTQCPNCES 45
                                      55555544489***976 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0022       2.3      11      23 ..       6      18 ..       2      18 .. 0.85
   2 ?    4.2   1.6     0.044        46       2       8 ..      39      45 ..      39      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                           UPF0547 11 PvaaqfCphCGyv 23
                                      ++a  +C+ CG++
  gi|336253612|ref|YP_004596719.1|  6 ATALSRCRNCGFE 18
                                      578889*****97 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.044
                           UPF0547  2 vCPeCea 8 
                                      +CP Ce+
  gi|336253612|ref|YP_004596719.1| 39 QCPNCES 45
                                      6****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 400.06
//
Query:       gi|336253613|ref|YP_004596720.1|  [L=409]
Description: hypothetical protein Halxa_2216 [Halopiger xanaduensis SH-6]
Scores for 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  120.7   0.0    6.1e-35  119.6   0.0    1.6  1  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
     0.0019   17.9   0.1     0.0071   16.1   0.0    2.0  2  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.027   13.7   0.0       0.21   10.8   0.0    2.0  2  DS              Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> 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 !  119.6   0.0     1e-38   6.1e-35       2     100 .]       5     103 ..       4     103 .. 0.99

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 1e-38
                                       EEEEEEEXXTTSSHHHHHHHHHHHTTXEEEEEEEEXXSSTTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSCCCCE CS
                    Saccharop_dh_N   2 reveleGhliDsgilnkvldlileaggsfevlefevGkkkkdtSyaelevsaedeevLeeileeltelgaelveeed 78 
                                       r+veleGh+iDsg++ +++ +++++gg+fev+efevG++k++++y++++v+a++ee L++il+el+++ga++++++d
  gi|336253613|ref|YP_004596720.1|   5 RTVELEGHIIDSGTMGHCMGVVMDMGGEFEVEEFEVGRHKHAETYCRMTVMADTEEDLRAILHELNQQGATVADPRD 81 
                                       79*************************************************************************** PP

                                       EEECESSCTTB--TTB----SS CS
                    Saccharop_dh_N  79 vklekaekdgvlpedFYsttnh 100
                                       ++l++a++dgv+p dFYsttnh
  gi|336253613|ref|YP_004596720.1|  82 ATLHEAPEDGVVPVDFYSTTNH 103
                                       *********************8 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 ?   -1.6   0.0      0.33     2e+03      13      37 ..     206     230 ..     191     259 .. 0.78
   2 !   16.1   0.0   1.2e-06    0.0071      68     135 ..     333     401 ..     313     403 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.33
                                       SEEEEE-CHHCHTTGHHHHHHHHHH CS
                      TPP_enzyme_M  13 rpvilvGggvarsgaseelrelaek 37 
                                       +++ ++G  +  +g +++l++l+ +
  gi|336253613|ref|YP_004596720.1| 206 NVLAVCGPAIVHAGGRDALADLVGA 230
                                       5677999999999999999999865 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.2e-06
                                       CHHHHHHHHH-SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC....--SEEEECTHHHHHH CS
                      TPP_enzyme_M  68 skaanealeeaDlvlalGarfddirttgsepefapeakiihididpaeigkny....qvdlaivgdvketle 135
                                       ++a +e ++eaDlvl+l + ++ + +++     ++ +k + +di+pa++ +        ++++v d+++++ 
  gi|336253613|ref|YP_004596720.1| 333 QNAIREQAHEADLVLMLSTLLHSVAVGNCL---PSTTKTVCVDINPATVTQLLdrgsAQAIGMVTDIGTFIP 401
                                       56788999*************997776532...334499*******99988774332356888888888775 PP

>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.4e-05      0.21      20      80 ..     194     253 ..     185     275 .. 0.75
   2 ?    0.4   0.0     0.051     3e+02     134     166 ..     276     313 ..     258     347 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.4e-05
                                DS  20 idilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgk 80 
                                       +++++++ ++++  ++  +  +++ +G r+ +adlv  ++vd+i +  g   +Dl + l  
  gi|336253613|ref|YP_004596720.1| 194 AEEMREV-RENDGNVLAVCGPAIVHAGGRDALADLVGAGYVDAISAGNGFAVHDLERDLYG 253
                                       3333343.45565666666778999*******************99988889998776655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.051
                                DS 134 spselikelG..kein...deeSilywAykndipvfcp 166
                                       ++se+ +  G  ++++    +e+++y +  nd+p    
  gi|336253613|ref|YP_004596720.1| 276 TISEIARLGGieEAVEkgvVDEGVMYECVANDVPFVLA 313
                                       66665554445444444445699**********96554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2977.28
//
Query:       gi|336253614|ref|YP_004596721.1|  [L=544]
Description: PAS/PAC sensor protein [Halopiger xanaduensis SH-6]
Scores for 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-44  150.9  10.8    2.5e-44  150.9  10.8    2.8  3  BAT           GAF and HTH_10 associated domain
      3e-20   71.7   0.0    6.8e-20   70.6   0.0    1.6  1  HTH_10        HTH DNA binding domain
    5.9e-18   65.5   0.8    5.9e-18   65.5   0.8    2.9  4  GAF_2         GAF domain
      8e-08   32.7   0.1    5.2e-07   30.1   0.0    2.4  2  GAF_3         GAF domain
      1e-07   32.2   0.7      1e-07   32.2   0.7    3.4  3  PAS_4         PAS fold
      1e-07   32.6   0.1    9.5e-07   29.5   0.0    2.5  2  GAF           GAF domain
    3.8e-05   23.1   0.0    0.00019   20.9   0.0    2.4  1  Sigma70_r4    Sigma-70, region 4
    0.00059   19.7   0.0     0.0015   18.4   0.0    1.7  1  HTH_11        HTH domain
     0.0042   17.1   0.2      0.017   15.1   0.0    2.2  2  PAS           PAS fold
     0.0089   16.3   0.0      0.024   14.9   0.0    1.7  1  UPF0122       Putative helix-turn-helix protein, YlxM / p13 l
  ------ inclusion threshold ------
       0.02   15.4   0.0      0.059   13.9   0.0    1.8  1  DUF134        Protein of unknown function  DUF134
      0.025   14.1   0.0       0.25   10.9   0.0    2.4  2  GerE          Bacterial regulatory proteins, luxR family
      0.046   13.4   0.1       0.24   11.1   0.1    2.4  1  Sigma70_r4_2  Sigma-70, region 4
      0.089   12.4   0.0       0.36   10.4   0.0    2.1  2  HTH_24        Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.4       1.1   1.4e+03      21      65 ..      31      76 ..      16      81 .. 0.66
   2 ?   -1.6   1.0       1.8   2.2e+03      66     105 ..     160     203 ..     113     219 .. 0.61
   3 !  150.9  10.8   1.9e-47   2.5e-44       1     155 [.     321     474 ..     321     475 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                               BAT 21 aaeldcrveleglvprsdge.vlvfftvdgadpeevrdaaedldav 65
                                      + ++ +++e +++++++ g  +++ + +d +d e +  a+e l++v
  gi|336253614|ref|YP_004596721.1| 31 TNRAWREFEADETTADHVGHnYVATAAMDADDDEHAKRAVEGLESV 76
                                      5566667777777777766624445555555556677777777776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.8
                               BAT  66 edvrvvseeddg....tlleltvsgpslastlaehGgtvrsaea 105
                                       +d+ v + + d+       +l+ ++p +++++ + ++t+r+++ 
  gi|336253614|ref|YP_004596721.1| 160 TDAAVGAGSRDEierrVCRRLADTDPYVLAWIGRVDVTTRRISP 203
                                       33333333333233333334444577777777777777777766 PP

  == domain 3  score: 150.9 bits;  conditional E-value: 1.9e-47
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       ++vveLe +i+d+++++++la++l  +v ++gl+ +++g++l+ff+v+ adp++++daa+dl+ave ++v++e++d+
  gi|336253614|ref|YP_004596721.1| 321 ETVVELEATIEDPSLFVAELADALSSTVIYRGLTYDEGGTPLAFFRVETADPDRAVDAAADLEAVEAASVLTEYEDS 397
                                       69*************************************************************************** PP

                               BAT  78 tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrref 154
                                        +lel++ g  ++++la+hG++++++ a+d   +l +e+P+g+++Rs ++ l+ery++veL++++e+++p+rt+r++
  gi|336253614|ref|YP_004596721.1| 398 VVLELAL-GNGIVTALADHGAVIQRLDADDRVLDLALELPNGQAARSAYDLLDERYDRVELRSYHETDQPTRTPRDL 473
                                       *******.*******************************************************************99 PP

                               BAT 155 r 155
                                       +
  gi|336253614|ref|YP_004596721.1| 474 Q 474
                                       7 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.0   5.3e-23   6.8e-20       1      53 []     481     533 ..     481     533 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 5.3e-23
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LTd+q ++l++Ay + YFd+PR v+ +eLA+ +++s+st+++hLr+a++kl+e
  gi|336253614|ref|YP_004596721.1| 481 LTDRQQAALRKAYYADYFDWPRGVSGEELAESMNVSRSTFHQHLRAAQRKLLE 533
                                       9**************************************************85 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.1     9e+03      25      57 ..      19      51 ..       7      71 .. 0.58
   2 !   65.5   0.8   4.6e-21   5.9e-18       3     137 ..     168     309 ..     166     310 .. 0.84
   3 ?    0.0   0.3      0.75   9.6e+02       9      65 ..     426     443 ..     372     476 .. 0.52
   4 ?   -0.3   0.1      0.92   1.2e+03       9      44 ..     426     463 ..     417     510 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.1
                                      EEEE-TTS-EEEEEEEES-TTSTT-S-B---TT CS
                             GAF_2 25 illvdddgglrlaawgeaeeefgaaldrplgeg 57
                                      ++++d+dg++ l  ++ +e e ++ + + +g+ 
  gi|336253614|ref|YP_004596721.1| 19 VAVLDGDGEILLTNRAWREFEADETTADHVGHN 51
                                      455677777444433333444444443344555 PP

  == domain 2  score: 65.5 bits;  conditional E-value: 4.6e-21
                                       HHHHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B..---TT.HHHHHHHHTS-EEES-G CS
                             GAF_2   3 dleelldlvldelvelg.aalgyillvdddgg.lrlaawgeaeeefgaaldr..plgeg.lvgealrtgrpvilndl 74 
                                       + +e+ ++v+++l++++   l++i+ vd  ++ +  + w+++++   +  d   + +e  ++ +al+ g+p +++dl
  gi|336253614|ref|YP_004596721.1| 168 SRDEIERRVCRRLADTDpYVLAWIGRVDVTTRrISPREWAGRDDVPLEDDDLvlDSDEThPAVRALEAGEPYVIQDL 244
                                       679*************8799********76662444466666666655554433449999****************9 PP

                                       GG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  75 eedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       ++ +d +++    ++ ++rs +a+Pl++++ ++Gvl+l+a++p+ fde++l +Le+lae++++a+
  gi|336253614|ref|YP_004596721.1| 245 AAFEDADRWWptGADDHYRSVAAIPLTYGDVTYGVLALFAADPDVFDERELPILESLAETVSTAL 309
                                       996666666656899999999*******99*********************************98 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.75
                                       HHHHHHHHHSS..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHH CS
                             GAF_2   9 dlvldelvelgaalgyillvdddgglrlaawgeaeeefgaaldrplgeglvgealrt 65 
                                       d+vld ++el                                       + g+a+r+
  gi|336253614|ref|YP_004596721.1| 426 DRVLDLALEL---------------------------------------PNGQAARS 443
                                       3344444444.......................................34444433 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.92
                                       HHHHHHHHHS..S...EEEEEEE-TT.S-EEEEEEEES-T CS
                             GAF_2   9 dlvldelvel..g.aalgyillvddd.gglrlaawgeaee 44 
                                       d+vld ++el  g aa + + l+d++ ++  ++ +++ e 
  gi|336253614|ref|YP_004596721.1| 426 DRVLDLALELpnGqAARSAYDLLDERyDR--VELRSYHET 463
                                       78999999999767776666666633133..333333333 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.9   4.9e+03      23      40 ..      18      35 ..       5      64 .. 0.72
   2 !   30.1   0.0     4e-10   5.2e-07      53     127 ..     225     309 ..     205     311 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.9
                             GAF_3 23 alllldedgnklqvaagw 40
                                       + +ld+dg+ l ++++w
  gi|336253614|ref|YP_004596721.1| 18 TVAVLDGDGEILLTNRAW 35
                                      455678899988888888 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 4e-10
                             GAF_3  53 dsalarralssgevvsepsfae...edg.......lpdraalavPLvagrqviGvlalastkprafdaedlellesl 119
                                       ++  a ral+ ge+++ ++ a+   +d+        + r++ a+PL+ g+ ++Gvlal   +p  fd+++l  lesl
  gi|336253614|ref|YP_004596721.1| 225 ETHPAVRALEAGEPYVIQDLAAfedADRwwptgadDHYRSVAAIPLTYGDVTYGVLALFAADPDVFDERELPILESL 301
                                       4555668999999988855544211444544443345588999********************************** PP

                             GAF_3 120 Arqiatai 127
                                       A  ++ta+
  gi|336253614|ref|YP_004596721.1| 302 AETVSTAL 309
                                       *******8 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.7   8.1e-11     1e-07       1     109 [.      12     125 ..      12     126 .. 0.89
   2 ?    3.4   1.6      0.07        89      35     108 ..     121     200 ..     120     202 .. 0.74
   3 ?    0.8   0.1      0.45   5.7e+02      49      81 ..     222     254 ..     199     258 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 8.1e-11
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaae.lfgappeellGktla.....ellpee...daarleralrrvlegeepief 68 
                                       l+ lp  +avld dg +l +N+a++e  +  + ++++G+ +      +   ++   +a r  + l+ vleg++ +++
  gi|336253614|ref|YP_004596721.1|  12 LETLPITVAVLDGDGEILLTNRAWREfEADETTADHVGHNYVataamD---ADddeHAKRAVEGLESVLEGDRDAFS 85 
                                       688999********************6667788999999999653332...33677********************* PP

                             PAS_4  69 leelll.pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +e++ + p+e r++ +r+ ++   +G  + v vi  DiT+r+
  gi|336253614|ref|YP_004596721.1|  86 MEYPCHsPDEKRWFMMRAGRF-TVDGA-VRVTVIHLDITDRK 125
                                       ***999**************9.79999.99**********97 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.07
                             PAS_4  35 llGktlaellpee...daarleralrrvlegeepiefleelll..pgeerhyelrl.lPlrdesGevigvlvisrDi 105
                                       +++++lae++ ee   + ++ +ral++vle  + + ++ +      g++  +e r+ ++l d++  v+++++ +  +
  gi|336253614|ref|YP_004596721.1| 121 ITDRKLAEIAAEEsaeQVREEHRALEHVLERVDGLVREVTDAAvgAGSRDEIERRVcRRLADTDPYVLAWIGRVDVT 197
                                       6789999*999998888999999999**9998887777755558855555555555488888887788888876555 PP

                             PAS_4 106 Ter 108
                                       T+r
  gi|336253614|ref|YP_004596721.1| 198 TRR 200
                                       554 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.45
                             PAS_4  49 aarleralrrvlegeepiefleelllpgeerhy 81 
                                         +  ++  r+le +ep+  ++   +++++r++
  gi|336253614|ref|YP_004596721.1| 222 DSDETHPAVRALEAGEPYVIQDLAAFEDADRWW 254
                                       456667778999999*******9999*****99 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.2   1.6e+03       6      53 ..      66     109 ..      62     151 .. 0.69
   2 !   29.5   0.0   7.4e-10   9.5e-07      14     133 .]     178     309 ..     168     309 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECCEEEETTSHHHH CS
                               GAF   6 ldtvveelrellgadrvalylpdydGlhydipqasrwlfmkngrgicg 53 
                                       ++++ve l+++l+ dr a+ + +y     + p++ rw +m+ gr  ++
  gi|336253614|ref|YP_004596721.1|  66 AKRAVEGLESVLEGDRDAFSM-EYPC---HSPDEKRWFMMRAGRFTVD 109
                                       678899999999999999988.3444...4899999977777665444 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 7.4e-10
                                       HHHHTESEEEE.EE............EEETTEEECEEEEECC..EEEETTSHHHHHHHHHSSSEEESTGGTSTTHHT CS
                               GAF  14 rellgadrval.yl............pdydGlhydipqasrw..lfmkngrgicgqvlatgqplvipdstpdprfaq 75 
                                       r+l + d  +l ++             ++ G + d+p +++   l   + ++ + ++l+ g+p vi+d+++ ++  +
  gi|336253614|ref|YP_004596721.1| 178 RRLADTDPYVLaWIgrvdvttrrispREWAGRD-DVPLEDDDlvLDSDETHP-AVRALEAGEPYVIQDLAAFEDADR 252
                                       555555553443665555555555543333422.455555554233333444.5699**********9765555444 PP

                                       THHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHHH CS
                               GAF  76 ynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvaval 133
                                         +  + +  ++rs++++Pl+ ++ ++G+l+l   +p  f++ el +l++la+ v+ al
  gi|336253614|ref|YP_004596721.1| 253 --WWPTGADDHYRSVAAIPLTYGDVTYGVLALFAADPdVFDERELPILESLAETVSTAL 309
                                       ..44467789************************77778****************9987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.5e-07   0.00019       4      48 ..     480     531 ..     479     533 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.5e-07
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       +L++r++  l+  +        +g + eE++e +++Sr++ +q+++ A rkL
  gi|336253614|ref|YP_004596721.1| 480 KLTDRQQAALRKAYyadyfdwPRGVSGEELAESMNVSRSTFHQHLRAAQRKL 531
                                       7*************9**9999999************************9998 PP

>> HTH_11  HTH 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    0.0015      16      41 ..     504     529 ..     501     537 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                            HTH_11  16 isgeeLAeeLnvSrrtvrrdIkaLee 41 
                                       +sgeeLAe +nvSr+t +++++a + 
  gi|336253614|ref|YP_004596721.1| 504 VSGEELAESMNVSRSTFHQHLRAAQR 529
                                       9******************9988655 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.3e-05     0.017       5      51 ..      10      57 ..       7     121 .. 0.78
   2 ?   -2.0   0.1       2.8   3.6e+03      64      99 ..     134     169 ..     123     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                                      HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTH.HHCTTSBGGGGBS CS
                               PAS  5 aileslpdpifvvDedgrilyvNaaaeellGlsr.eevlgkslldlih 51
                                      a le+lp  + v+D dg+il++N+a++e+   +   + +g +++    
  gi|336253614|ref|YP_004596721.1| 10 AALETLPITVAVLDGDGEILLTNRAWREFEADETtADHVGHNYVATAA 57
                                      789***********************9976655555666665555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                                       HHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEET CS
                               PAS  64 qlleqgeesrageisfklrdgrpihlevraspvrda 99 
                                        +++++ee ra e+ ++++dg ++++   a+  +++
  gi|336253614|ref|YP_004596721.1| 134 SAEQVREEHRALEHVLERVDGLVREVTDAAVGAGSR 169
                                       466777777777777777888877777666655555 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    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      13      61 ..     476     531 ..     467     535 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                           UPF0122  13 iYqsLLTekqanylelyyadDl.......SlsEiAeefnvsrqavydnikrtekll 61 
                                       + ++ LT++q+  l+  y  D+       S +E+Ae +nvsr++ +++++ +++ l
  gi|336253614|ref|YP_004596721.1| 476 TIETKLTDRQQAALRKAYYADYfdwprgvSGEELAESMNVSRSTFHQHLRAAQRKL 531
                                       556779***99999875555544556666889*****************9887544 PP

>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.6e-05     0.059      51      86 ..     504     539 ..     456     541 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                            DUF134  51 lkqeeaaklmGiskatlwrlltearkkiakalveGr 86 
                                       ++ ee a+ m +s++t+++ l +a++k+ + l+ G 
  gi|336253614|ref|YP_004596721.1| 504 VSGEELAESMNVSRSTFHQHLRAAQRKLLEELFAGD 539
                                       477999***********************9999885 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.66   8.5e+02       2      16 ..     289     303 ..     288     308 .. 0.85
   2 ?   10.9   0.0   0.00019      0.25      17      45 ..     503     531 ..     498     532 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.66
                                       SS-HHHHHHHHHHCT CS
                              GerE   2 sLskRErevLrllae 16 
                                       ++++RE+ +L+ lae
  gi|336253614|ref|YP_004596721.1| 289 VFDERELPILESLAE 303
                                       7899*******9997 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00019
                                       TS-HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE  17 GksnkeIAeelniSekTVkvhksnimkKL 45 
                                       G s +e Ae++n+S  T + h++ +++KL
  gi|336253614|ref|YP_004596721.1| 503 GVSGEELAESMNVSRSTFHQHLRAAQRKL 531
                                       78889***********************8 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 ?   11.1   0.1   0.00019      0.24      26      54 .]     503     531 ..     479     531 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                                       ---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  26 glsykEIAellgisegtVksrlsRArkkL 54 
                                       g s +E Ae +++s +t  ++l+ A +kL
  gi|336253614|ref|YP_004596721.1| 503 GVSGEELAESMNVSRSTFHQHLRAAQRKL 531
                                       7799******************9997776 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 ?   -2.8   0.0       3.9     5e+03      10      27 ..     327     344 ..     326     345 .. 0.79
   2 ?   10.4   0.0   0.00028      0.36      19      41 ..     505     527 ..     501     530 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.9
                            HTH_24  10 elLqknprisqreLAerl 27 
                                       e+  ++p++  +eLA++l
  gi|336253614|ref|YP_004596721.1| 327 EATIEDPSLFVAELADAL 344
                                       566788999899***987 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00028
                            HTH_24  19 sqreLAerlglSpstvnrrlkrL 41 
                                       s  eLAe  ++S+st +++l+  
  gi|336253614|ref|YP_004596721.1| 505 SGEELAESMNVSRSTFHQHLRAA 527
                                       5679****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); 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:                        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: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 3960.24
//
Query:       gi|336253615|ref|YP_004596722.1|  [L=332]
Description: Phytoene synthase [Halopiger xanaduensis SH-6]
Scores for 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-67  227.3   9.0    2.8e-67  227.0   9.0    1.0  1  SQS_PSY          Squalene/phytoene synthase
  ------ inclusion threshold ------
      0.093   11.8   0.0       0.41    9.7   0.0    1.9  2  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> SQS_PSY  Squalene/phytoene synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.0   9.0   3.1e-71   2.8e-67       2     261 ..      14     269 ..      13     271 .. 0.95

  Alignments for each domain:
  == domain 1  score: 227.0 bits;  conditional E-value: 3.1e-71
                                       XHH-HHHHHHHTTS-HHHHHHHHHHHHHHHHHT-.-----..........------------..---------THHH CS
                           SQS_PSY   2 raasksfylaslllppelRdalgalYafcreaddlvDdvs..eplqararldwwrdavdavyaedklkpprepvlra 76 
                                       r+ +k+fyla+++lp+++R+a ++lYaf r ad++vDd++  +p+++ra+l+ +r++  +        +p++pvl+a
  gi|336253615|ref|YP_004596722.1|  14 RRTGKTFYLATKFLPERVRHATHVLYAFFRIADEVVDDAEgvSPARQRAELESLRAQALGEA------EPEDPVLEA 84 
                                       7899************************************9999***********9988666......689****** PP

                                       HHHHHHHHT--HHHHHHHHHHTS--SS-..--SHHHHHHHHHHHHHHHHHHHHHHH-S..S-HHHHHHHHHHHHHHH CS
                           SQS_PSY  77 laqlirtyklpkellleliegmeadleftryetlddLeeYcyrvagvVgelclrllgar.rsdralaeaarrlGkal 152
                                       +++l ++y+++ e ++e++++m++d+++tryet++dLe Y++ +a++Vg ++++++ ++ +++++++++ar+lG a+
  gi|336253615|ref|YP_004596722.1|  85 FRELREEYDIDDETVDEFVDAMATDIDTTRYETYADLESYMRGSAAAVGVMMTAIMDLEpEVEETALPHARKLGEAF 161
                                       ********************************************************9954555889*********** PP

                                       HHHHHHT---SH.HHHTT..S-HHHHHHHT--HHHHHHT-.-SHHHHHHHHHHHHHHHHHHHHHHHTGGGS.-HHHH CS
                           SQS_PSY 153 QltnilRdvpeD.aergrvyLPadvlkefgvseedllrkgvrsaelrallrrlaerArelldearellkqlpdrrar 228
                                       Qltn+lRdv+eD +er+r+yLP++ l+++gvs +++ r +  s+++ a++r++++rA+ l++e+ ++++ l +++++
  gi|336253615|ref|YP_004596722.1| 162 QLTNFLRDVREDvLERDRIYLPQETLRRHGVSNDEIERLE-YSESFAAAMREELRRAESLYREGVAGIRYL-PEDCQ 236
                                       ************************************8887.7878**************************.999** PP

                                       HHHHHHHHHHHHHHHHHHHTTT-TTT------H CS
                           SQS_PSY 229 palllavalyrailerieaadydvlsrrvklsl 261
                                       +++lla++ly++    i+ ++ydvls  ++ls+
  gi|336253615|ref|YP_004596722.1| 237 LPVLLAAVLYAEHHALIRSQGYDVLSAEPSLST 269
                                       ***********************9998888886 PP

>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0     0.074   6.7e+02      42      65 ..      29      52 ..       7      53 .. 0.69
   2 ?    9.7   0.0   4.6e-05      0.41     133     198 ..     108     172 ..      69     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.074
                                      HHHHHHHHHHHHHHHHHHHHHTT- CS
                   polyprenyl_synt 42 avlawivellhaasLvhDDimDds 65
                                       ++  ++ +l a++ ++D ++Dd+
  gi|336253615|ref|YP_004596722.1| 29 ERVRHATHVLYAFFRIADEVVDDA 52
                                      456667778888888888888887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 4.6e-05
                                       TTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                   polyprenyl_synt 133 ddlskfsleeyleivkyKTaylfalpvalaallagasdeelealkdiglelGlaFQiqDDylDlfg 198
                                       +d++    e+y +   y  ++  a+ v + a++   ++e+ e++   +++lG+aFQ+   + D+ +
  gi|336253615|ref|YP_004596722.1| 108 TDIDTTRYETYADLESYMRGSAAAVGVMMTAIMDL-EPEVEETALPHARKLGEAFQLTNFLRDVRE 172
                                       34444467777777777777777777776666665.57889****************988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2794.65
//
Query:       gi|336253616|ref|YP_004596723.1|  [L=53]
Description: hypothetical protein Halxa_2219 [Halopiger xanaduensis SH-6]
Scores for 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  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 465.88
//
Query:       gi|336253617|ref|YP_004596724.1|  [L=302]
Description: carotene biosynthesis associated membrane protein [Halopiger xanaduensis SH-6]
Scores for complete 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-62  211.1  14.3    2.2e-62  210.7  14.3    1.2  1  Caroten_synth  Carotenoid biosynthesis protein
  ------ inclusion threshold ------
      0.063   13.5   0.9      0.063   13.5   0.9    2.3  2  TMEM238        TMEM238 protein family


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 !  210.7  14.3   2.4e-66   2.2e-62       1     208 [.      70     283 ..      70     284 .. 0.96

  Alignments for each domain:
  == domain 1  score: 210.7 bits;  conditional E-value: 2.4e-66
                     Caroten_synth   1 ggvvlillgtaalalyav....rllglrralaflllavllslaiEllGvstGfpfGeYsYlsglgpkllglVPltiP 73 
                                       ++++li +gta+++++++    ++++ rral++l l++++++aiE++Gv+tG+p+G+++Y+ +lgp+l g++Pl++P
  gi|336253617|ref|YP_004596724.1|  70 FNPLLIFVGTAVMRSPLIvgllPRID-RRALGCLGLLTAYTYAIETVGVRTGWPYGAFEYGIELGPMLGGEIPLALP 145
                                       6899**************9*******.************************************************** PP

                     Caroten_synth  74 lswfplvlaayllarlllesr....akrslvrlllaalllvawDlvLDPamvalgfWvweepGafygvPlqNflGWl 146
                                       l+++plvl+a+ll+ l+le+      +r+ +rl++a++++va+DlvLDP++va+gfW + e+G +ygvPl+N+ GWl
  gi|336253617|ref|YP_004596724.1| 146 LFFIPLVLNAFLLTLLVLERWwpsgLERTSIRLPVAVAAVVAVDLVLDPGAVAIGFWSY-ETGGYYGVPLSNYRGWL 221
                                       *****************997666556777777***************************.6678************* PP

                     Caroten_synth 147 ltglvlvlvlellwrkkaleerreqlelplavllsnfllaavlnllagllipallglllgvl 208
                                       l+g+v+v++++l+++++al er +++e++l++l+s++ll++++nll+g++i+a+++ l++++
  gi|336253617|ref|YP_004596724.1| 222 LSGAVAVALVDLAFDRSALLERVRTCEFVLDDLVSFVLLWGAINLLYGNWIAAAVAGLFCAG 283
                                       *********************************************************99875 PP

>> TMEM238  TMEM238 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.9     7e-06     0.063       7      44 ..      42      83 ..      39      91 .. 0.82
   2 ?   -2.6   0.2      0.74   6.7e+03      36      41 ..     259     264 ..     247     280 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7e-06
                           TMEM238  7 lalavvfdvvGlvlLlvGifael....lfgDllvytGaliif 44
                                      +++avvf vvG+++L++ +   l     f  ll+++G+ ++ 
  gi|336253617|ref|YP_004596724.1| 42 FTIAVVFPVVGAIMLVASVEDLLpaslAFNPLLIFVGTAVMR 83
                                      89***********99998754446666**********98875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.74
                           TMEM238  36 vytGal 41 
                                       ++ Ga+
  gi|336253617|ref|YP_004596724.1| 259 LLWGAI 264
                                       222332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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 0.21s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2279.22
//
Query:       gi|336253618|ref|YP_004596725.1|  [L=305]
Description: UbiA prenyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-27   96.8  17.6    1.8e-27   96.3  17.6    1.3  1  UbiA      UbiA prenyltransferase family


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 !   96.3  17.6     1e-31   1.8e-27       4     229 ..      50     270 ..      47     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 1e-31
                              UbiA   4 palvglalaaggspdlllllllllgtl...laaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivll 77 
                                       p+lvg+a+aa +  dl + + ++l+++    a+++ +++Nd++DreiDa ++ + +   ++ r   + + +++ v++
  gi|336253618|ref|YP_004596725.1|  50 PVLVGVAYAAESRADLVTPASIVLFAYfllPANVFLYGINDIYDREIDAANPKKEEK-EARYRG-QRYVPLAVGVCA 124
                                       99*************955444444444455********************9998877.333332.467778888888 PP

                              UbiA  78 ilgllllalllnpltallgllalllyvvYt.g.lrlKrrtllgtvvggiafglppllgwaavtgslsllalllalav 152
                                       +l ll++  ll p+++ ++++ lll+  Y+ + +r+K +++l+ v  g+  ++p  +++aav+g  ++++++l++  
  gi|336253618|ref|YP_004596725.1| 125 ALPLLFA-PLLEPVVWPWLVAFLLLGAGYSaPpVRFKTTPILDSVSNGLY-VTPGAAAYAAVAGAQPPAIAVLGA-- 197
                                       8889999.***********************99***************95.577777999999995555555555.. PP

                              UbiA 153 flltwaialandlrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaalall 228
                                       +l++++++++ +++d+e Dr+ gi+t+++vlG+++++ +  a++l  +     l+++a  + l ++++++ a+++ +
  gi|336253618|ref|YP_004596725.1| 198 WLWAMGMHTFSAIPDIEPDRETGIRTTATVLGERRTYAYcGACWLGSA-----LAFAAVDGRLGAVMLVYPALVGAI 269
                                       5************************************96422222222.....233333333333333333333333 PP

                              UbiA 229 r 229
                                       +
  gi|336253618|ref|YP_004596725.1| 270 V 270
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2465.64
//
Query:       gi|336253619|ref|YP_004596726.1|  [L=495]
Description: phytoene desaturase [Halopiger xanaduensis SH-6]
Scores for 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-30  105.8   0.0    4.1e-30  105.5   0.0    1.1  1  Amino_oxidase   Flavin containing amine oxidoreductase
    1.1e-16   60.8   0.1    2.7e-16   59.5   0.1    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.2e-12   46.0   9.1    2.2e-10   40.6   9.1    2.5  1  DAO             FAD dependent oxidoreductase
    2.7e-06   26.7   2.5    4.4e-06   26.0   2.1    1.5  2  FAD_binding_2   FAD binding domain
    3.4e-06   26.5   0.4    2.2e-05   23.8   0.5    2.1  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.2e-06   26.1   0.0      1e-05   25.1   0.0    1.5  2  FAD_oxidored    FAD dependent oxidoreductase
      1e-05   26.0   1.6    0.00014   22.4   0.5    2.9  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0001   21.7   0.5    0.00018   20.9   0.5    1.3  1  FAD_binding_3   FAD binding domain
    0.00012   20.9   0.1    0.00045   19.0   1.0    1.4  2  HI0933_like     HI0933-like protein
    0.00066   19.0   0.7     0.0011   18.3   0.7    1.3  1  Thi4            Thi4 family
     0.0021   17.4   0.5     0.0031   16.8   0.5    1.2  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0026   17.1   0.0      0.011   15.0   0.1    1.9  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.016   14.3   1.7      0.025   13.7   1.7    1.2  1  GIDA            Glucose inhibited division protein A
       0.03   13.9   0.1      0.049   13.2   0.1    1.3  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.039   12.8   0.0       0.05   12.4   0.0    1.1  1  MCRA            MCRA family
       0.05   13.5   0.3      0.084   12.7   0.3    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.054   13.9   0.0      0.089   13.2   0.0    1.4  1  NAD_binding_7   Putative NAD(P)-binding
      0.062   13.0   0.0        0.1   12.3   0.0    1.3  1  ApbA            Ketopantoate reductase PanE/ApbA
       0.41   10.2   0.7       0.73    9.4   0.7    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5   0.0   4.3e-33   4.1e-30       2     452 .]      17     489 ..      16     489 .. 0.80

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 4.3e-33
                                       HHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEETTTHHHHHHHHHTTCCCCEE..EESCCGCE CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftgagnpllellkelgledsls..lpdpgapk 76 
                                        GLa+A +L++aG dV v+E ++++GGR++  ++dG+ +++G++w+ +  + + +++ +++   s+   l + ++ +
  gi|336253619|ref|YP_004596726.1|  17 GGLATACYLADAGADVRVIEKNEQLGGRASHLERDGFRFDMGPSWYLM-PDVFERFFADFDRTPSDYyeLTHLDPHY 92 
                                       6***********************************************.88888999996665555567888889** PP

                                       EEEETTEECC............TTEECHH.HHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH....HHHCCCCHHHH CS
                     Amino_oxidase  77 rvlskggref............pgdlspv.paewealleqgalsaellsleeklrlgleall....qktldeldlds 136
                                       r+ +k+g ++             +++++   +++e++le         + +e  + g+e +        +d+ldld 
  gi|336253619|ref|YP_004596726.1|  93 RIFFKDGDQVdvtpdlertkevFEEYEDGaGEALERYLE---------KSKENYEVGMEHFVyedrTRLRDYLDLDV 160
                                       ********9999999999866666666663333666666.........23333333333333655577778888888 PP

                                       HHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETTHTHHHH CS
                     Amino_oxidase 137 kslaesleelgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllprgGlsqlp 213
                                        + a  l+ lg  +       +++++p+l + +++ + +++g p     + al+ l+   +f  ++++p+gG ++ +
  gi|336253619|ref|YP_004596726.1| 161 ARQARGLSLLGSMQGHV---EGYFDHPKLQQIMQYTLVFLGGSP---KNTPALYNLMSHVDFNLGVWYPDGGVAAAV 231
                                       88888777777776655...899999***************888...****************************** PP

                                       HHHHH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEES...CCSH..HHHHHHH CS
                     Amino_oxidase 214 ealae..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsP...plpd..ekaeair 283
                                       +a+a+  +++g++  +n++ + ik  ++   v++  g+  + D Vv+ ++ ++    l+ P   +     + +e+  
  gi|336253619|ref|YP_004596726.1| 232 DAIADlgRELGVEYDTNRPATAIKGREGAFLVETPEGQL-RPDLVVSNADYAHTEQDLLPPerrG--YdaDYWES-- 303
                                       ************************988889999988886.9**************7777775322..22355555.. PP

                                       HSEEEEEEEEEEEESSGGSGCSTS.......E.CE....CECCCEEETTTEEEEECC...ECCCSTTTEEEEEEEEE CS
                     Amino_oxidase 284 nlgfgsvnkvilefdrkfwednal.......g.qg....vlvseltttlgeafissd...fpsrappgkglvllvyv 345
                                       +  ++s++ ++l +++++ +++a+       + ++       +  +++ +  +++ +    ++ ap+g++  l+v+v
  gi|336253619|ref|YP_004596726.1| 304 RTYAPSAFLLYLGVEGEV-DELAHhtlvlptDwDEhfdqIFDDPQWPDDPAYYVCVPsetDDDVAPDGHSA-LFVLV 378
                                       668999999********9.77664444544433336777667777777777788888999999999*9999.***** PP

                                       C.HHHHHHHTTS-HHHHHHHHHHHHHHHHT....GTSSTCSEEEEEECCT..ETTTSSSEEE.BTTHHHHHHHHHHC CS
                     Amino_oxidase 346 g.gdaaneleslsdeelvqavlrdLrklfg....eevpepkatlvtrWht..dplargsysyvsvgpghedydplak 415
                                       + +   ++ +   +++  +++l+d++   g    + +  +++++v ++    +++ +++  + ++  ++  ++p+++
  gi|336253619|ref|YP_004596726.1| 379 PiAPGLED-TPEIRQQYRDKILEDIADYTGtalrDRIVVEERFCVEDFANryNSYDGTALGLAHTLRQTALFRPPHR 454
                                       95555444.3336788888899999999997666666666668888888666666677777777777********** PP

                                       HHCSTTEEE.SGGGCTTTTTS.HHHHHHHHHHHHHHHH CS
                     Amino_oxidase 416 pegdprlffAGehtsreypgt.vegAilSGlraAaril 452
                                       ++g ++l+f G  t+   pg  v+ ++ SG  +A+ +l
  gi|336253619|ref|YP_004596726.1| 455 SKGADGLYFVGGDTT---PGIgVPMCLISGELTAEKVL 489
                                       ***************...****************9986 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 !   59.5   0.1   2.9e-19   2.7e-16       1      66 [.      11      76 ..      11      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 2.9e-19
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHHC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrllr 66
                                      ++GaG++Gl++A++La+ag+dv ++ek+++lGGra+  e++g+r+d g++++  ++ ++++++ ++
  gi|336253619|ref|YP_004596726.1| 11 VIGAGVGGLATACYLADAGADVRVIEKNEQLGGRASHLERDGFRFDMGPSWYLMPDVFERFFADFD 76
                                      8***************************************************99887777776655 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   9.1   2.4e-13   2.2e-10       2     351 ..       9     486 ..       8     487 .. 0.60

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.4e-13
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTH..................... CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeas..................... 55 
                                       vv+iG+G+ Gl+tA +La +g  V ++ek++++g    gr+s l + g+r +  +                      
  gi|336253619|ref|YP_004596726.1|   9 VVVIGAGVGGLATACYLADAGadVRVIEKNEQLG----GRASHLERDGFR-FDMGPswylmpdvferffadfdrtps 80 
                                       9*****************9999************....777777777775.33332244445556666666666666 PP

                                       ...........................................................HHHHHHHHHHHHHHHHHH CS
                               DAO  56 ...........................................................elarlslealeelrelee 73 
                                                                                                   +  +++e + +l     
  gi|336253619|ref|YP_004596726.1|  81 dyyelthldphyriffkdgdqvdvtpdlertkevfeeyedgagealerylekskenyevGMEHFVYEDRTRL----- 152
                                       666666666666666666666666666666664444444444433333333333333332222222222222..... PP

                                       HHSSTTSEEEEEEEEEESSHHHHHHHH..................................HHHHHHHHTTTTEEEE CS
                               DAO  74 elgididyrrtGllslaadeeeleald..................................kllallleagldaell 116
                                                                 +                                  + ++      l   +l
  gi|336253619|ref|YP_004596726.1| 153 --------------------------RdyldldvarqarglsllgsmqghvegyfdhpklqQIMQYT----LV--FL 197
                                       ..........................13333333333333333333333333333332111444433....22..34 PP

                                       EH..HHHHHHSTT.ST.TTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.E CS
                               DAO 117 da..eevrelepa.lp.gllgalfypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.g 188
                                        +  +++ +l+   ++ ++  +++ypd+g+   a+++ a+a+  ++lGve  +++++t+++ ++ ++    ++tp g
  gi|336253619|ref|YP_004596726.1| 198 GGspKNTPALYNLmSHvDFNLGVWYPDGGV---AAAVDAIADLGRELGVEYDTNRPATAIKGRE-GAFL--VETPeG 268
                                       3322556666654323699999*******9...999************************5543.2344..599988 PP

                                       EEEEEEEEEE--...............GGGHH..HHHTTCTT.............TSEEEEEEEEEEEEEECCTHST CS
                               DAO 189 endaadavVnaa...............Gawsd..llgllkel.............dlpispvrgqvlvlkplseklv 235
                                       + +  d vV  a               G  +d  ++                   +  +  + ++ lvl p++  ++
  gi|336253619|ref|YP_004596726.1| 269 QLRP-DLVVSNAdyahteqdllpperrGYDADywES-----RtyapsafllylgvEGEVDELAHHTLVL-PTDWDEH 338
                                       7555.6655555555555555555555444442222.....0112112334444334555599999999.8777665 PP

                                       GSGCSEEEEEEEETTTTEEEEEE.......TTSEEEEEESSE.........EETTCSSTSCSHHHHHHHHHHHHHHS CS
                               DAO 236 spaailpvpetdddgrgvyvtpr.......kdgrvlvGgtad.........eesgdddpevdeedidellealrklf 296
                                       +  +i+ +p++ dd  ++ ++p+       +dg        +          ++ +d+pe+ ++ +d++le ++++ 
  gi|336253619|ref|YP_004596726.1| 339 FD-QIFDDPQWPDDPAYYVCVPSetdddvaPDG--------HsalfvlvpiAPGLEDTPEIRQQYRDKILEDIADYT 406
                                       55.999999977777888888875433333333........223455555435556668****************** PP

                                       GG.GCG..EEEEEEEEEE.....E.TTSSEEEEEEE...................TEEEEEEEEEC..TTTHHHHHH CS
                               DAO 297 Pq.lgd..vlrkwaGlrp.....l.pdglpligetp...................gvkglylatGh..sghGltlap 343
                                        + l+d  v++++ ++ +     +  dg                           g +gly++ G    g G+ +++
  gi|336253619|ref|YP_004596726.1| 407 GTaLRDriVVEERFCVEDfanryNsYDGTA-----LglahtlrqtalfrpphrskGADGLYFVGGDttPGIGVPMCL 478
                                       886555555578999999543221224422.....13333567778888889999999********55555566899 PP

                                       HHHHHHHH CS
                               DAO 344 atGkllae 351
                                        +G+l+ae
  gi|336253619|ref|YP_004596726.1| 479 ISGELTAE 486
                                       99999987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   2.1   4.6e-09   4.4e-06       2      38 ..       9      46 ..       8      49 .. 0.93
   2 ?   -3.7   0.0       4.8   4.6e+03      86     132 ..     227     281 ..     224     292 .. 0.65

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 4.6e-09
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS.GG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg.at 38
                                      v+ViG+G++GLa A  +a+aG++v v+ek ++ gg a+
  gi|336253619|ref|YP_004596726.1|  9 VVVIGAGVGGLATACYLADAGADVRVIEKNEQLGGrAS 46
                                      9********************************99655 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.8
                                       HHTHHHHHHHHHHT.T----B........CCTS.SB-EEE-TT-SSTEEEE-.STT- CS
                     FAD_binding_2  86 veaapeavdeLeel.gvpfsr........tedg.pvdvrelGglsatartlhdaada 132
                                       v+aa +a++ L +  gv +++         ++g  +  ++ G+l+++ +++  +ad+
  gi|336253619|ref|YP_004596726.1| 227 VAAAVDAIADLGRElGVEYDTnrpataikGREGaFLVETPEGQLRPD-LVVS-NADY 281
                                       67788888888887888888865655554233346666777777777.4444.6655 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 !   23.8   0.5   2.4e-08   2.2e-05       2      35 ..       8      40 ..       7      50 .. 0.82
   2 ?   -0.6   0.0      0.67   6.3e+02     190     232 ..     235     276 ..     228     279 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.4e-08
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtc 35
                                      +vvviG+G++Gla+a +la aga+v ++e +++ 
  gi|336253619|ref|YP_004596726.1|  8 SVVVIGAGVGGLATACYLADAGADVRVIE-KNEQ 40
                                      79**************************5.4433 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.67
                                       HHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 190 eealekeGvevklgtsvkeidgngeklevvledgeeidadlvv 232
                                       ++  ++ Gve  ++  +++i+g++    v++ +g+ +  dlvv
  gi|336253619|ref|YP_004596726.1| 235 ADLGRELGVEYDTNRPATAIKGREGAFLVETPEGQ-LRPDLVV 276
                                       5556788***************9994445555554.6666665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.1e-08     1e-05       2      40 ..       9      47 ..       8     140 .. 0.70
   2 ?   -3.2   0.0       4.2     4e+03      11     159 ..     226     238 ..     224     303 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.1e-08
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40
                                      vvV+G+g++G+a A   a aGa v ++e+++ lGG ++ 
  gi|336253619|ref|YP_004596726.1|  9 VVVIGAGVGGLATACYLADAGADVRVIEKNEQLGGRASH 47
                                      9**********************************9986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.2
                      FAD_oxidored  11 GvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrggarlkkrskwntfepe 87 
                                       GvaAA+ A                                                                     
  gi|336253619|ref|YP_004596726.1| 226 GVAAAVDA--------------------------------------------------------------------- 233
                                       44444444..................................................................... PP

                      FAD_oxidored  88 vakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATgdGdlaalaGvpyrvG 159
                                                                                                             +G
  gi|336253619|ref|YP_004596726.1| 234 -------------------------------------------------------------------IADLG 238
                                       ...................................................................33333 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.5   1.4e-07   0.00014       1      35 [.       8      42 ..       8      50 .. 0.93
   2 ?   -0.3   0.0       1.7   1.6e+03      29      53 ..     109     133 ..     100     160 .. 0.86
   3 ?   -0.2   0.0       1.6   1.5e+03      45      72 ..     233     260 ..     228     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.4e-07
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      +vvv+G+G+ gl  A++la+ g++V v+e +++l 
  gi|336253619|ref|YP_004596726.1|  8 SVVVIGAGVGGLATACYLADAGADVRVIEKNEQLG 42
                                      69******************************998 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.7
                                       ESSSSSSTTSSHHHHHHHHHHHHHT CS
                         Pyr_redox  29 ersdkllrllDeeaskilqeklekn 53 
                                       er +++   +++ a+++l+++lek 
  gi|336253619|ref|YP_004596726.1| 109 ERTKEVFEEYEDGAGEALERYLEKS 133
                                       78888888999999999**999986 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.6
                                       HHHHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  45 ilqeklekngievllntkveeiegsedg 72 
                                       ++++  +++g+e  +n+ +++i+g e  
  gi|336253619|ref|YP_004596726.1| 233 AIADLGRELGVEYDTNRPATAIKGREGA 260
                                       566777999**************98865 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.5   1.9e-07   0.00018       3      35 ..       8      40 ..       7      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.9e-07
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      +V+++GaG  Gl +a  L+ aG +v+++ek ++
  gi|336253619|ref|YP_004596726.1|  8 SVVVIGAGVGGLATACYLADAGADVRVIEKNEQ 40
                                      69****************************875 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.0   4.8e-07   0.00045       2      36 ..       8      42 ..       7      46 .. 0.95
   2 ?   -3.5   0.0       3.2   3.1e+03     112     156 ..     231     273 ..     222     276 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.8e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      +v+viG+G  Gl +A  +a++g++V ++ek+++lg
  gi|336253619|ref|YP_004596726.1|  8 SVVVIGAGVGGLATACYLADAGADVRVIEKNEQLG 42
                                      69*******************************98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEES CS
                       HI0933_like 112 vdallkelkeagvklrletevksvekeedgkfrvktkseeelead 156
                                       vda+    +e gv++ +++  ++++  ++g+f v+t  e++l+ d
  gi|336253619|ref|YP_004596726.1| 231 VDAIADLGRELGVEYDTNRPATAIK-GREGAFLVET-PEGQLRPD 273
                                       5666666789999999999999995.5666699999.66666655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.7   1.1e-06    0.0011      14      56 ..       3      44 ..       1      49 [. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-06
                                      HHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4 14 kyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                      ++a s vv++GaG  GL++a yla + +  v ++e++  +GG 
  gi|336253619|ref|YP_004596726.1|  3 SLAGSSVVVIGAGVGGLATACYLADA-GADVRVIEKNEQLGGR 44
                                      567899********************.99999****9999985 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 !   16.8   0.5   3.3e-06    0.0031      28      62 ..       6      40 ..       1      54 [. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.3e-06
                                      --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                       + v+viG+Gv Gl+ +   +  ga+V+v++++++
  gi|336253619|ref|YP_004596726.1|  6 GSSVVVIGAGVGGLATACYLADAGADVRVIEKNEQ 40
                                      578****************************9987 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 !   15.0   0.1   1.1e-05     0.011       1      31 [.      10      40 ..       3      56 .. 0.80
   2 ?   -3.1   0.0       3.9   3.7e+03     100     128 ..     247     275 ..     238     279 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.n 31
                                      ++iGaG  Gla+a+ l +ag  d+ ++Ek+ +
  gi|336253619|ref|YP_004596726.1| 10 VVIGAGVGGLATACYLADAGA-DVRVIEKNeQ 40
                                      688888888888888888888.7888888744 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.9
                       Pyr_redox_3 100 lfeeVesvkkedegfevetsketyeAkkv 128
                                       ++   +++k  ++ f vet +++++ + v
  gi|336253619|ref|YP_004596726.1| 247 TNRPATAIKGREGAFLVETPEGQLRPDLV 275
                                       56667888888888999988888776555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.7   2.7e-05     0.025       2      33 ..       9      39 ..       8      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-05
                                      EEEE-SSHHHHHHHHHHHHTT--EEEEES-GG CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkld 33
                                      v+ViG+G  G++ A  +a +Ga+v  i ++ +
  gi|336253619|ref|YP_004596726.1|  9 VVVIGAGVGGLATACYLADAGADVRVIEKN-E 39
                                      9************************99444.3 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 ?   13.2   0.1   5.2e-05     0.049       2      38 ..       4      40 ..       3      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-05
                                      HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT- CS
                              IlvN  2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregs 38
                                      l g  ++viG G  G a a  l d+g dv v  ++++
  gi|336253619|ref|YP_004596726.1|  4 LAGSSVVVIGAGVGGLATACYLADAGADVRVIEKNEQ 40
                                      67889************************99877766 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.3e-05      0.05       4      58 ..       9      57 ..       6      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.3e-05
                                      EEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS-----------------CCC- CS
                              MCRA  4 aylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldgagdpekGyvlrg 58
                                      + ++G+G+++La+A+yL       g ++ ++e+++ +gg   + ++  +G+ +  
  gi|336253619|ref|YP_004596726.1|  9 VVVIGAGVGGLATACYLAD----AGADVRVIEKNEQLGGRASHLER--DGFRFDM 57
                                      678**************76....4789********99999887654..4555444 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 ?   12.7   0.3   8.9e-05     0.084       2      34 ..       9      41 ..       8      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.9e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      v viGaG+ G   a  +a ag +V++++ +e+ 
  gi|336253619|ref|YP_004596726.1|  9 VVVIGAGVGGLATACYLADAGADVRVIEKNEQL 41
                                      89**************************99875 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 ?   13.2   0.0   9.5e-05     0.089       5      45 ..       4      42 ..       1     103 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.5e-05
                     NAD_binding_7  5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele 45
                                      l g +v+v+G+G  ++  +  l++aga+v v+ ++  e+l 
  gi|336253619|ref|YP_004596726.1|  4 LAGSSVVVIGAGVGGLATACYLADAGADVRVIEKN--EQLG 42
                                      77899***************************999..4444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011       0.1       1      32 [.       9      40 ..       9      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrr 32
                                      ++++GaG  G   a++La agadv +i ++++
  gi|336253619|ref|YP_004596726.1|  9 VVVIGAGVGGLATACYLADAGADVRVIEKNEQ 40
                                      689**********************9988764 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 ?    9.4   0.7   0.00078      0.73       3      34 ..       9      40 ..       7      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00078
                                      EEEE--STTHHHHHHHHHHCTSEEEEE-S-HH CS
                    UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvDidee 34
                                      ++viG+G  Gl ta  la +g +v ++ ++e+
  gi|336253619|ref|YP_004596726.1|  9 VVVIGAGVGGLATACYLADAGADVRVIEKNEQ 40
                                      89*************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.38
# Mc/sec: 3954.92
//
Query:       gi|336253620|ref|YP_004596727.1|  [L=631]
Description: formate/nitrite transporter [Halopiger xanaduensis SH-6]
Scores for 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-45  154.0  14.6    4.9e-45  153.7  14.6    1.1  1  Form_Nir_trans  Formate/nitrite transporter
    6.9e-15   55.8  14.6    9.7e-10   39.1   0.3    4.0  3  Usp             Universal stress protein family


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 !  153.7  14.6   5.5e-49   4.9e-45       1     236 []      68     304 ..      68     304 .. 0.92

  Alignments for each domain:
  == domain 1  score: 153.7 bits;  conditional E-value: 5.5e-49
                                       HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCTTCHHHHHHHHHCCCHHHHHHHHHT---C CS
                    Form_Nir_trans   1 eivekvvaagvkkaklsldklfllgilAGafigfgvllalvvaaalaesnpglakllgglvFpvGlilvvllgaeLf 77 
                                       e+++++vaa+ ++++   ++lf++g++AG+ i++ +ll++ + +a+         +l+ l++p+G+i+++++g +L+
  gi|336253620|ref|YP_004596727.1|  68 EVFQRIVAAADEEVTSGNRELFFSGLAAGFAITITFLLYASLYGAT-----DGDPILSTLLYPLGFIYIIIGGYQLY 139
                                       6899****************************************85.....3456999******************* PP

                                       CCCCCHHHHHHCTTSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTGG....HHHHHHHHHCCCSS-HHHHHHHH CS
                    Form_Nir_trans  78 TgntllltlavlkkkvslkkllknwlvvllgNliGsllvalllvvlsgll....aekllsiaeaklslsfleaflrG 150
                                       T+ntl  ++ +l++ +sl  ll++wl+vl+gN+ G++l a++l++ +g++    a++++sia++ +++s++++f+++
  gi|336253620|ref|YP_004596727.1| 140 TENTLPPVALTLERLASLPMLLRHWLIVLAGNFTGGALGAVALTW-GGVFdpdaADAAMSIAHHGIETSWWQLFFKA 215
                                       *****8888888****************************77775.55555666*********************** PP

                                       HHHHHHHHHHHHHHCC-SSHHHHHHHHHHHHHHHHHCT---HHHHHHHHHHHHHH...SHHHHHHHCHHHHHHHHHH CS
                    Form_Nir_trans 151 ilCNwlVclavwlalaakdvigkilaiflpifafvasgfeHsvanmfliplglll...tvadfilknlipvtlGNiv 224
                                        +++++V+  vw+++a++d+i+++++++l ++a+ ++++ H+v+ ++ + + +++   ++   ++  ++pv+lGN++
  gi|336253620|ref|YP_004596727.1| 216 AFAGLIVAGVVWVTFASRDTISRLVVVYLAFLAIPLGNLFHVVVSFTEMLYLVFAgeaQLFVGVTEFVLPVLLGNTI 292
                                       ***********************************************999999888775555556778********* PP

                                       HHHCCHHHHHHH CS
                    Form_Nir_trans 225 GGallvgllyly 236
                                       GG+llv+++ +y
  gi|336253620|ref|YP_004596727.1| 293 GGILLVTVVNYY 304
                                       ********9997 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.5      0.19   1.7e+03      47      81 ..      15      55 ..       3      80 .. 0.46
   2 !   39.1   0.3   1.1e-13   9.7e-10       4     139 ..     357     489 ..     355     491 .. 0.89
   3 !   20.1   2.2   7.7e-08   0.00069       4     139 ..     499     615 ..     497     616 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.19
                                      CCCCHHHHHHHHHHHHHHHHHHHH......HHHHHHCTTCE CS
                               Usp 47 vsdadeeaeeeeleleeaeleada......akaaaeaggvk 81
                                       +dade++  ++++ + a ++a++      a ++ + g ++
  gi|336253620|ref|YP_004596727.1| 15 QGDADETESGQQAQTAPADSVAEQgtavrdAVERSRHGAPA 55
                                      33333333333333333333333233333333333333333 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 1.1e-13
                                       EEEEEE-SSHHHHHHHHHHHHHHHH.CTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   4 rIlVavDgseeskkAlewAlelaka.rgaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                       rI+V++ +  +   ++e+A++la +  +a++++ h++ ++ s+a++d  ++    e+e  +a le       ++ ++
  gi|336253620|ref|YP_004596727.1| 357 RIVVPIANPRTEAPLVEFAARLASDhEHATVHVEHIVQTPGSSATADRQRDRIVTESERLLADLEGI----VTDHEV 429
                                       8*****8888888*************************************************99976....7***** PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                          + +v+ +   eei ++a++e+adl+++G+   +  s +      + +  + pc+ l+
  gi|336253620|ref|YP_004596727.1| 430 DCQTSTVVTHRSFEEIFDTADREHADLVLMGWDENTLWSAARAERPLSELTTRLPCDYLI 489
                                       ********************************9977777666666666666666666666 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 7.7e-08
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       r l+++ g ++s+  +  A  la ++g+e+ llhv+d+++   +++ + ++     +l  a                
  gi|336253620|ref|YP_004596727.1| 499 RLLLPTAGGPDSELSAAVARTLADTDGSEVSLLHVVDSPDERDEGEQFLKEWAVDNDLPDA---------------- 559
                                       7899999******99999999****************999988888888888877777776................ PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                        + +v  +gd+ ++i+++a++    ++++G++ r+ lsrl+  S    v+++++ +V++
  gi|336253620|ref|YP_004596727.1| 560 -EIIVDDSGDVEDAICRAADD--HTMVLIGATERGLLSRLVTSSLHLDVVNEVDTSVVL 615
                                       .568899************98..89*******************999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 4702.41
//
Query:       gi|336253621|ref|YP_004596728.1|  [L=39]
Description: hypothetical protein Halxa_2224 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0092   16.7   0.2       0.01   16.6   0.2    1.1  1  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   5.6e-07      0.01       3      35 ..       5      35 ..       4      39 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.6e-07
                      VAPB_antitox  3 IsIsdevYekLkklKregeSFsdvIerLlekkk 35
                                      +++s+  YekL++     eS  dv+ +L+ +++
  gi|336253621|ref|YP_004596728.1|  5 VTVSERLYEKLEEQTD--ESVEDVLWELMYQSE 35
                                      89*********99765..**********85443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 308.24
//
Query:       gi|336253622|ref|YP_004596729.1|  [L=83]
Description: S1 IF1 family protein [Halopiger xanaduensis SH-6]
Scores for 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-19   68.5   0.1    3.8e-19   68.3   0.1    1.1  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 !   68.3   0.1   2.1e-23   3.8e-19       1      64 []       5      67 ..       5      67 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 2.1e-23
                                      EEEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                            eIF-1a  1 gevigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                      +ev ++V+e lg+n+++ +++ +g+e+l++ipg+++ + wi ++d+V+ e+++ +++k+ I +r
  gi|336253622|ref|YP_004596729.1|  5 DEVFAVVTEHLGGNHVQLRCE-DGEERLGRIPGRMKYRTWIEQDDIVVAEPWDWQDEKATIEWR 67
                                      589*****************7.6**************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 653.92
//
Query:       gi|336253623|ref|YP_004596730.1|  [L=171]
Description: hypothetical protein Halxa_2226 [Halopiger xanaduensis SH-6]
Scores for 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   24.7   2.6      5e-05   23.9   2.6    1.5  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 !   23.9   2.6   2.8e-09     5e-05       1      71 [.      29     116 ..      29     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.8e-09
                          CxxCxxCC   1 eCke.CgaCCkelkvklteedlerlkaaevaeeeeeskkiak...............adgrCvfldeetklCkiYee 61 
                                       eC + C  CC+ ++v l ++dl +l++     e+++  + +k                + +C fl+e+ +lC+++ e
  gi|336253623|ref|YP_004596730.1|  29 ECVDdCTWCCH-HGVLLYDRDLLELAQRANLAETTTDFRGEKfvtreekgredhvaeDGCACAFLRED-GLCSLHLE 103
                                       58777******.9***********9998888888888888778889*********988899*****99.6*****95 PP

                          CxxCxxCC  62 R...pkicrlfpa 71 
                                           p+ c +fp 
  gi|336253623|ref|YP_004596730.1| 104 EdwkPTRCSVFPL 116
                                       4444*****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1341.35
//
Query:       gi|336253624|ref|YP_004596731.1|  [L=243]
Description: fumarylacetoacetate (FAA) hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-49  167.5   0.0    3.9e-49  167.3   0.0    1.0  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
  ------ inclusion threshold ------
      0.068   14.1   0.1       0.22   12.5   0.1    1.9  1  DUF2437        Domain of unknown function (DUF2437)


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.3   0.0   4.3e-53   3.9e-49       2     218 .]      46     236 ..      45     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 167.3 bits;  conditional E-value: 4.3e-53
                                       EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--H CS
                     FAA_hydrolase   2 ivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsv 78 
                                        +c+g+nyae +++++    e p+     ep ff+k+++sl +++dpi++P+++++l y +ELa+vi  ++r+v s 
  gi|336253624|ref|YP_004596731.1|  46 LYCVGRNYAETLEQME---YERPE-----EPDFFIKPPASLLAHEDPIEYPEFTNELTYAGELAAVIDERCRDV-SE 113
                                       59************96...34444.....556******************************************.9* PP

                                       HHHHTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGG CS
                     FAA_hydrolase  79 eeAedaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkd 155
                                       +eA d+++Gyt++nDv a d q +        + k+fd++ p+Gpw+ t  +l dp+ +++ + v ge++q++nt+ 
  gi|336253624|ref|YP_004596731.1| 114 DEAPDVVRGYTVMNDVDALDQQGRT-------ARKAFDGSGPLGPWLET--DL-DPRGIDMHTDVAGERRQEANTEL 180
                                       ******************9988555.......59*************44..66.568******************** PP

                                       TTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE. CS
                     FAA_hydrolase 156 mifspaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrVa 218
                                       m+f+p+e+i++ls+ +t++pGd+i+ G+p+++        ++++gD ve++ eg+G+lrn+V+
  gi|336253624|ref|YP_004596731.1| 181 MLFDPYEVISYLSRRFTFRPGDVIAFGSPANP-------GLVEPGDAVEITYEGVGTLRNTVV 236
                                       *****************************775.......59********************96 PP

>> DUF2437  Domain of unknown function (DUF2437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.4e-05      0.22       1      50 []       1      40 [.       1      40 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                                      -EEEEEEETTEEEEEEEE.EEEEEESS-TTSS-EEEEEEEEG.GGSEEE-S CS
                           DUF2437  1 MriaRFshgggpryGvlegdtvvvlagdpfgavqpTGervpL.adVrLLAP 50
                                      Mr+aR ++++gp  G  e+++v++ +g           ++++ +d +LL+P
  gi|336253624|ref|YP_004596731.1|  1 MRLARLETPDGPVRGRYEDGVVHADDG-----------TYAVgEDGELLPP 40
                                      ************************999...........6666666677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1971.46
//
Query:       gi|336253625|ref|YP_004596732.1|  [L=66]
Description: hypothetical protein Halxa_2228 [Halopiger xanaduensis SH-6]
Scores for 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:                       185  (0.0103185); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); 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: 0.34u 0.20s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 555.36
//
Query:       gi|336253626|ref|YP_004596733.1|  [L=69]
Description: hypothetical protein Halxa_2229 [Halopiger xanaduensis SH-6]
Scores for 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   18.2   0.4     0.0021   17.7   0.4    1.2  1  HTH_39    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.037   13.5   0.1      0.038   13.5   0.1    1.0  1  TRM13     Methyltransferase TRM13


Domain annotation for each model (and alignments):
>> HTH_39  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.4   2.4e-07    0.0021      11      55 ..      17      59 ..      17      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.4e-07
                            HTH_39 11 rqhgsittleamrelditr.laaRIkeLrekGyeIktervteater 55
                                      r++g++tt e +r+ d+t+ + aRI e  ++  +++ter    +++
  gi|336253626|ref|YP_004596733.1| 17 RREGTVTTAERRRRIDVTDlPTARIEEFVRA--NVSTER-VSLEHC 59
                                      689****************999*****9986..777777.444455 PP

>> TRM13  Methyltransferase TRM13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   4.3e-06     0.038      51     115 ..       3      67 ..       1      69 [] 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-06
                             TRM13  51 vLidrasnrlkaDrklrkdeselaikRlkidIkdLnlsaleele.kkkkvvavsKHLCGaATDLtL 115
                                       +++d a  r  +D++ +    ++a +R +id+ dL   ++ee    + ++  vs   CGa T L L
  gi|336253626|ref|YP_004596733.1|   3 LIVDAADDRSEVDSRREGTV-TTAERRRRIDVTDLPTARIEEFVrANVSTERVSLEHCGARTYLVL 67 
                                       5799999******9988777.5888999************99776777788899999**9998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 577.06
//
Query:       gi|336253627|ref|YP_004596734.1|  [L=150]
Description: hypothetical protein Halxa_2230 [Halopiger xanaduensis SH-6]
Scores for 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       0.24   11.3   0.0    1.7  1  Flg_hook  Flagellar hook-length control protein FliK


Domain annotation for each model (and alignments):
>> Flg_hook  Flagellar hook-length control protein FliK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.3e-05      0.24      10      49 ..      33      75 ..      26      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.3e-05
                                      CTTSEEEEEECCCCCEEEEEEE...EEETTEEEEEEEE-SCHH CS
                          Flg_hook 10 ngsqeatlrLdppeLGkvevkl...tlrggqlsvqltaenpet 49
                                      ++  ea lr +pp +G++ +++   ++++ q++  +++  +++
  gi|336253627|ref|YP_004596734.1| 33 ENPGEAVLRVTPPFHGRMRARIhvyRVDDTQVTGAVHVPPEDV 75
                                      67789*****************877788888888887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1247.20
//
Query:       gi|336253628|ref|YP_004596735.1|  [L=276]
Description: adenosylcobinamide hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-39  134.2   1.4    9.1e-39  133.6   1.4    1.3  1  CbiZ      Adenosylcobinamide amidohydrolase
  ------ inclusion threshold ------
      0.048   14.6   2.3       0.98   10.4   0.1    2.5  2  LytR_C    LytR cell envelope-related transcriptional attenuat


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 !  133.6   1.4     1e-42   9.1e-39       8     192 .]      34     230 ..      29     230 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 1e-42
                              CbiZ   8 vlssavlngGlrelravlnhqvpegyeredpeeyleeyleel.............glppektvgllTaadmenaaia 71 
                                        + s+ + gG r++++++n++vp+g++r+d  +y++e+le++             +  +++ ++llT++d+e+a+ a
  gi|336253628|ref|YP_004596735.1|  34 EWLSTGWSGGRRTADCAYNVSVPDGWDRTDLGAYVDERLERAgfadgggdsgdnrDA-SGQPPVLLTGVDLEDARGA 109
                                       46667799**********************************999999998887544.7999*************** PP

                              CbiZ  72 eeefedlevtavvTaGvesnavragd.............edeeaekpGTINiivlinaaLtdaalvralitatEAKt 135
                                       + +     vt+++TaG+ sn++++ +              d e+ + GT+N++v +++aL+++al++++++a+EAK+
  gi|336253628|ref|YP_004596735.1| 110 QYG----PVTVYATAGI-SNPAALPMepgvegtaetgtePDAEPDPTGTVNLVVGTTRALEPGALANVIAVAAEAKA 181
                                       ***....**********.********************977899********************************* PP

                              CbiZ 136 aalqdlgvrsrysegatGTgTDaiavaadkegeeeltyaGkhtklGeliaraVyeAv 192
                                       a+l++ +        ++GT+TDai+  +d++g++  +++G+ t +G++++++V+e+v
  gi|336253628|ref|YP_004596735.1| 182 ATLLAETG-------FPGTTTDAIVAGHDPSGRS-TSFSGSGTAVGAATRACVRESV 230
                                       *****999.......9*****************6.********************98 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00011      0.98       3      83 ..      52     160 ..      50     161 .. 0.64
   2 ?    3.8   0.3     0.013   1.2e+02      17      46 ..     179     211 ..     175     264 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                            LytR_C   3 kVeVlNgtgvsGlAarvadaLeerGftvgevgnagnadee.......ttivyreaaaaaak....alaaalglge.. 66 
                                        V V +g +++ l a v + Le++Gf+ g  ++ +n+d++       t +   e+a+  a+    ++ a+ g+++  
  gi|336253628|ref|YP_004596735.1|  52 NVSVPDGWDRTDLGAYVDERLERAGFADGGGDSGDNRDASgqppvllTGVDL-EDAR-GAQygpvTVYATAGISNpa 126
                                       688999999*****************88875555555444888777755554.4444.3334555666666655555 PP

                            LytR_C  67 ...............lqedsvkdas..vtvvlGk 83 
                                                      ++ d+++d++  v +v+G+
  gi|336253628|ref|YP_004596735.1| 127 alpmepgvegtaetgTEPDAEPDPTgtVNLVVGT 160
                                       5555555555544444445555555888888886 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.013
                            LytR_C  17 arvadaLeerGftvgevgn..agnadee.ttiv 46 
                                       a++a++L+e Gf  +++++  ag++++  +t +
  gi|336253628|ref|YP_004596735.1| 179 AKAATLLAETGFPGTTTDAivAGHDPSGrSTSF 211
                                       6899********665555433555544363333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); 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 0.19s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 2357.81
//
Query:       gi|336253629|ref|YP_004596736.1|  [L=349]
Description: L-threonine-O-3-phosphate decarboxylase [Halopiger xanaduensis SH-6]
Scores for 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-41  140.5   0.0    9.5e-41  140.2   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0088   14.6   0.0      0.012   14.2   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.037   13.3   0.0      0.061   12.6   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.067   12.5   0.0       0.23   10.7   0.0    1.9  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 !  140.2   0.0   2.1e-44   9.5e-41      15     363 .]      27     342 ..      21     342 .. 0.90

  Alignments for each domain:
  == domain 1  score: 140.2 bits;  conditional E-value: 2.1e-44
                                       TSS.HHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHH CS
                     Aminotran_1_2  15 sgk.ptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllkl 90 
                                       +++ p +p+ ++a    a a +++ +y++ + + +++ a a+f+g       +++  v+ ++G  a+i ++   + l
  gi|336253629|ref|YP_004596736.1|  27 ANTnPRIPDGVEAVY--ADALEDARRYPDDE-YIDFRAAAARFVG------CEPD-DVIPTPGGLAAIRLAVEST-L 92 
                                       444577788888885..69999*********.*************......9999.8887777777777777777.7 PP

                                       TTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--H CS
                     Aminotran_1_2  91 npgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatl 167
                                       +pgde lvp p++++y + +rl g+  + ++++       dl +le+   e         + +v++p+NPtG +a++
  gi|336253629|ref|YP_004596736.1|  93 EPGDEALVPYPSFGEYAREVRLQGARPRFVRYD-------DLFDLEDEGLE------SAALAIVCTPNNPTGEAADP 156
                                       8******************************99.......77777774443......234889************** PP

                                       HHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHH CS
                     Aminotran_1_2 168 eeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlr 244
                                       +el + ++ +++    l+vDea+ gf    ++a a+ra   +  n+++++sl K fGl+G+R G+++++ + +++l+
  gi|336253629|ref|YP_004596736.1| 157 DELAAFAARCERADTTLLVDEAFLGFTDL-PSA-ALRARDRDLENVIVARSLTKLFGLPGLRAGFAVATGERRDALE 231
                                       *************************9998.444.45999999999******************************** PP

                                       HHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHH CS
                     Aminotran_1_2 245 klsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakels 321
                                        + r++   ++++++ a  l+ ++    ++ e+r+r++++r++lrd+L +  ++v +s++ ++l  ++++   + + 
  gi|336253629|ref|YP_004596736.1| 232 TARRAWSLGTPAARVGAYCLRQDE----FVRETRERVASERERLRDAL-SERFDVHPSDAPYLLCNVGDRD-VDRVI 302
                                       *****999**************99....89******************.77******************99.88888 PP

                                       HHHHHTCTEEEEEGGGGTS.TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 322 kkLleevgvyvtpgtsftv.pgrlRitvAglteeeleelveal 363
                                       ++ +e+ gv+++  t f+  ++++R+ v   ++e +++l+ al
  gi|336253629|ref|YP_004596736.1| 303 ESARER-GVAIRDATTFRGlESHVRVAV--EDREANDRLLAAL 342
                                       889999.*********9999********..9999999999876 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   2.7e-06     0.012      72     178 ..      76     181 ..      69     253 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-06
                                       EESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-T CS
                   Cys_Met_Meta_PP  72 avssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptn 148
                                        ++ G+aAi +a+ + l+ Gde +v    +g   r +    +  g + +fv  +dl +le    e   l  + tp n
  gi|336253629|ref|YP_004596736.1|  76 PTPGGLAAIRLAVESTLEPGDEALVPYPSFGEYAREV----RLQGARPRFVRYDDLFDLEDEGLESAALAIVCTPNN 148
                                       5788**********************99999876654....4467889***************************** PP

                                       TTT----HHHHHHHHHHTT...-EEEEEGTTTH CS
                   Cys_Met_Meta_PP 149 pllkvvDiekiaklakkag...vlvvvDntfas 178
                                       p+ + +D  ++a++a   +   ++++vD +f+ 
  gi|336253629|ref|YP_004596736.1| 149 PTGEAADPDELAAFAARCEradTTLLVDEAFLG 181
                                       *******999988765544467********974 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 ?   12.6   0.0   1.4e-05     0.061      23     101 ..      54     132 ..      38     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHHHHT..-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTS CS
                   DegT_DnrJ_EryC1  23 peveeFEkafaaylg..vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdty 97 
                                       +e  +F +a a+++g   + +i++  G aA+ la +   ++pgde +vp  +F   a  v+  ga+p fv  d d +
  gi|336253629|ref|YP_004596736.1|  54 DEYIDFRAAAARFVGcePDDVIPTPGGLAAIRLAVES-TLEPGDEALVPYPSFGEYAREVRLQGARPRFVRYD-DLF 128
                                       55567999999999965679**************997.5789****************************887.555 PP

                                       SB-G CS
                   DegT_DnrJ_EryC1  98 nidp 101
                                        ++ 
  gi|336253629|ref|YP_004596736.1| 129 DLED 132
                                       5555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.2e-05      0.23      24     169 ..      46     178 ..      33     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.2e-05
                                       --CCCT--HHHHHHHHHHHHHTT-S..EEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EE CS
                   Beta_elim_lyase  24 GdesYgedktvnrLedavaelfgke..aalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvkl 98 
                                       +d+    d ++ ++ +a+a+ +g e   ++++p G aA +++++  l++g+e +v  p+   f e    + l+g+++
  gi|336253629|ref|YP_004596736.1|  46 EDARRYPDDEYIDFRAAAARFVGCEpdDVIPTPGGLAAIRLAVESTLEPGDEALVPYPS---FGEYAREVRLQGARP 119
                                       455444455677788888888777654899****************************9...66777788899**** PP

                                       EEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase  99 rdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                       r ++ ++  +++ e le+a             + +  T n   G++  ++el++ aa +++ + +l++D A
  gi|336253629|ref|YP_004596736.1| 120 RFVRYDDLFDLEDEGLESAA------------LAIVCTPNNPTGEAADPDELAAFAARCERADTTLLVDEA 178
                                       *9999994333333333332............23333444456***********************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 2955.39
//
Query:       gi|336253630|ref|YP_004596737.1|  [L=344]
Description: hypothetical protein Halxa_2233 [Halopiger xanaduensis SH-6]
Scores for 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:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2687.73
//
Query:       gi|336253631|ref|YP_004596738.1|  [L=196]
Description: GTP:adenosylcobinamide-phosphateguanylyl transferase-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-18   68.1   2.3    2.1e-18   67.2   2.3    1.5  1  NTP_transf_3     MobA-like NTP transferase domain
    1.7e-05   24.7   0.0    2.7e-05   24.0   0.0    1.5  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    0.00024   20.8   0.0    0.00028   20.6   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
     0.0016   18.4   0.0      0.011   15.7   0.0    1.9  1  CTP_transf_3     Cytidylyltransferase
  ------ inclusion threshold ------
      0.036   14.8   1.7       0.99   10.2   0.7    2.4  2  PSK_trans_fac    Rv0623-like transcription factor


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 !   67.2   2.3   5.8e-22   2.1e-18       5     127 ..       2     135 ..       1     182 [. 0.79

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 5.8e-22
                                       EESS-TTTTT..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC...TS-EEE-TTSS-SHHH CS
                      NTP_transf_3   5 AGGrSsRmgg..dKallplggkpllervldalraagvdevvvvggd..eevlaalarl...gvrvvededpgkgpla 74 
                                       +GG+++R+ +  +K+l p+gg+p+++rv++al+++ v+ ++ ++ +  +e +a+l+r    + ++++ e pg+g +a
  gi|336253631|ref|YP_004596738.1|   2 CGGKGTRLESprEKPLHPIGGTPMVDRVVAALADSRVETIYAAVSPnaPETRARLERAagdREDLTAVETPGEGYVA 78 
                                       8********877****************************99986644666666654433344445555569***** PP

                                       HHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCH....HHHTSSEEEEESSSEE CS
                      NTP_transf_3  75 slaaalraaadadavlvlacDmPlltpelverllaaa....aasgadvvvptyeger 127
                                        l a l++   +++vl +a+D+Pll++ +v+r+l+++    + ++  v+vp++ ++r
  gi|336253631|ref|YP_004596738.1|  79 DLMAILERDDISTPVLTVAADLPLLEAPVVDRVLERHvqgeRGRSRTVCVPVALKRR 135
                                       ********989*************************954433334566777766665 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 !   24.0   0.0   7.6e-09   2.7e-05       8     136 ..       3     134 ..       1     151 [. 0.83

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7.6e-09
                                       TTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG....CCEEEEE--SSHHHH CS
                              IspD   8 AGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld....ksiqlvaGGdeRaes 80 
                                        G+G+R+++ ++K +  + g +++ + v+al++ ++v++i  +vs++  e+ + l  +    +   l a  +  +  
  gi|336253631|ref|YP_004596738.1|   3 GGKGTRLESPREKPLHPIGGTPMVDRVVAALAD-SRVETIYAAVSPNAPETRARLERAagdrE--DLTAVETPGEGY 76 
                                       59***************************9999.78**********99777777776676443..444444444555 PP

                                       HHHHHHTTSSTT..SEEEE--TT-TT--HHHHHHHHHHHHTTCSEEEEEEE-SSEEEE CS
                              IspD  81 Vlnglkalegea..kfVLvHDaARpllkaadiaellaaaeqstqgailalpvkDtikr 136
                                       V   + +le ++  + VL   a  pll+a++++++l+   q+  g    + v  ++kr
  gi|336253631|ref|YP_004596738.1|  77 VADLMAILERDDisTPVLTVAADLPLLEAPVVDRVLERHVQGERGRSRTVCVPVALKR 134
                                       6666666666668789*************************99999998888888887 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   7.8e-08   0.00028       5     143 ..       1     131 [.       1     145 [. 0.67

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.8e-08
                                       E--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
                   NTP_transferase   5 LaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                       ++GG+GtRL    + + k+l p++g+ ++++ ++ +la+s++e+i+  + + ++++ +  l++++    e l a+e+
  gi|336253631|ref|YP_004596738.1|   1 MCGGKGTRLE---SPREKPLHPIGGT-PMVDRVVAALADSRVETIYAAV-SPNAPETRARLERAAGD-REDLTAVET 71 
                                       89******96...799**********.*****************55555.55555555555555432.358889999 PP

                                       S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST..THHHHHHHHHTHSSTTSEEEEEEESS CS
                   NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikd..ayeeavkkaiekaakgtvtfgivpve 143
                                       +g+g          +le+++  + vl +++D    +   + ++++++++ ++ g   ++ vpv+
  gi|336253631|ref|YP_004596738.1|  72 PGEGYVAD---LMAILERDDISTPVLTVAADLPLLEapVVDRVLERHVQGER-GRSRTVCVPVA 131
                                       99987443...33344444444567777777644443566667777766666.44444445555 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     3e-06     0.011      15      59 ..      14      59 ..       7     137 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3e-06
                                      TGGGSEETTEEHHHHHHHHHHHTTTTSE.EEEEES-HHHHHHHHHT CS
                      CTP_transf_3 15 gKnlldlggkpliayvleaalkskafek.vivaTDseeiknvakef 59
                                      +K+l ++gg p++++v+ a+ +s + +    v+    e++  ++ +
  gi|336253631|ref|YP_004596738.1| 14 EKPLHPIGGTPMVDRVVAALADSRVETIyAAVSPNAPETRARLERA 59
                                      8*********************998432344555555555555444 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.7   0.00028      0.99       8      54 ..      24      68 ..      23      98 .. 0.82
   2 ?    3.3   0.0     0.041   1.5e+02      14      37 ..     113     136 ..     105     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00028
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHHHH CS
                     PSK_trans_fac  8 peverlareLarltgeskteAvrrAleerlerlrreraepllerlla 54
                                      p v+r +  La+ + e++ +Av     e+ +rl+r  a+  +e+l a
  gi|336253631|ref|YP_004596738.1| 24 PMVDRVVAALADSRVETIYAAVSPNAPETRARLER--AAGDREDLTA 68
                                      679******************************95..4444555544 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.041
                                       XXXXXXXXXXXXXXXXXXXXXXXX CS
                     PSK_trans_fac  14 areLarltgeskteAvrrAleerl 37 
                                        r+++  +g s t  v  Al++rl
  gi|336253631|ref|YP_004596738.1| 113 ERHVQGERGRSRTVCVPVALKRRL 136
                                       57888999**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1524.98
//
Query:       gi|336253632|ref|YP_004596739.1|  [L=255]
Description: Cobalamin synthase [Halopiger xanaduensis SH-6]
Scores for 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-41  140.6  15.8    8.4e-41  140.4  15.8    1.0  1  CobS      Cobalamin-5-phosphate synthase


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 !  140.4  15.8   4.7e-45   8.4e-41       1     202 [.      15     244 ..      15     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 140.4 bits;  conditional E-value: 4.7e-45
                              CobS   1 alsflTrlPvp.......elaralaffPlvGlllGlll.llallllllllllaallavaalvlltgglHlDGlaDta 69 
                                       a++flTrlPvp       ++++  a+fPlvGl+ G l+ +++l++ +l ++  al +++a++++tg++HlDG+aD++
  gi|336253632|ref|YP_004596739.1|  15 AVGFLTRLPVPlregdwnAFRSRPAAFPLVGLVSGSLAaVPLLAADALPASTVALGYLLAVYAVTGIHHLDGIADLG 91 
                                       689*******988886555577999************86666666554333333333555567************** PP

                              CobS  70 DglgsgrdrerrleImkDsrvGafGvlalvlvlllkvaa...laala.......lllapvlsRlaallaiallpyae 136
                                       D+l+ ++d err e++kD+++G+++vla++++++  ++a   la l+       +++a++ ++l++++++++++   
  gi|336253632|ref|YP_004596739.1|  92 DALVVHGDAERRREVLKDTTTGVGAVLAVAITVAGLALAglgLAGLPprtavavAIAAEIGAKLGMAAMACFGTAGF 168
                                       ***8889**************************9999997554333366666677799************9999445 PP

                              CobS 137 eglgalfaeaqkk...lv...llal..........avllllla..lllaallvalllrrlarrklggvtGDvlGavi 195
                                       eg+g++f+ea++    +v   +  l                 a  +l  al+   l +++a+r+lgg++GDv+Ga++
  gi|336253632|ref|YP_004596739.1| 169 EGMGQQFTEASTPgrfVVpagI--LagatafiwphP------AavALWSALAGIGLPWYWANRNLGGINGDVFGAAN 237
                                       9*******96555665224331..133322222220......21122333334445678****************** PP

                              CobS 196 eltellv 202
                                       e++++++
  gi|336253632|ref|YP_004596739.1| 238 EIGRVVA 244
                                       ****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); 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):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2036.77
//
Query:       gi|336253633|ref|YP_004596740.1|  [L=333]
Description: Cobalamin biosynthesis protein cbiB [Halopiger xanaduensis SH-6]
Scores for 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-79  266.6  11.9    2.1e-79  266.6  11.9    1.3  1  CobD_Cbib  CobD/Cbib protein


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 !  266.6  11.9   1.2e-83   2.1e-79       2     265 ..       3     287 ..       2     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 266.6 bits;  conditional E-value: 1.2e-83
                         CobD_Cbib   2 llAlllDlllgdprrllhPvvligklisalekrlrk..........akkerlaGvllalllvllallvalllllla. 67 
                                        lA+ lDll+g+p+++ hPv+++g+l++al+                +++r+aG+++al+++ll +++a++l+ +a 
  gi|336253633|ref|YP_004596740.1|   3 GLAFSLDLLIGEPPNAAHPVAWFGRLVDALDCDR-GattdtrtenaDRRQRRAGFAIALFAPLLPAVAAAVLVIAAt 78 
                                       58****************************8744.12356678888778889************9999999988775 PP

                         CobD_Cbib  68 .laallglvlealllkltlalrsLleevrkvakal.kgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsD 142
                                        la+l+g v++al+l+l+++lrsLle + +v +a  + dle+aRe+v+ +VgR+ts+l+++e+++AavEs+aENl+D
  gi|336253633|ref|YP_004596740.1|  79 aLAPLAGAVAAALVLFLSMSLRSLLELTDSVVAATaAADLETARERVRGLVGRETSTLSAAELRSAAVESAAENLAD 155
                                       444455889*********************99999559*************************************** PP

                         CobD_Cbib 143 gvvaPlfyflll.......glpgalaykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllalaaa.. 210
                                       g+va+l+ f+ll       ++++a+++k vnTlDsm+GY +   + +G+a+ArlDDl++++PARl+a+ +a+aa+  
  gi|336253633|ref|YP_004596740.1| 156 GLVATLVPFALLapispaaAAAAAAWVKGVNTLDSMLGYPD---KPIGTASARLDDLVMWLPARLSAVAIAVAAVdp 229
                                       ***********988877766678999**************5...99**************************84455 PP

                         CobD_Cbib 211 ..lriarrdarkhpSpNsgwpeaalAgalgvrLggpnvY.lgkleekptlgdkkrple 265
                                         l +arr+ar+ pSpNsgwp+a+lA+al+vrL++p+vY l+  ++ ptl d++r+++
  gi|336253633|ref|YP_004596740.1| 230 laLGRARRWARAPPSPNSGWPMATLACALDVRLRKPGVYdLNPERDLPTLADGERAVR 287
                                       55*************************************7776777777766555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2391.98
//
Query:       gi|336253634|ref|YP_004596741.1|  [L=224]
Description: Haloacid dehalogenase domain-containing protein hydrolase [Halopiger xanaduensis SH-6]
Scores for complete 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-09   38.7   0.3    4.7e-09   36.8   0.3    1.8  1  Hydrolase       haloacid dehalogenase-like hydrolase
    1.9e-06   28.1   0.0    2.7e-06   27.6   0.0    1.2  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.4e-05   25.1   0.1    2.9e-05   24.0   0.1    1.6  1  Hydrolase_like  HAD-hyrolase-like


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.3   7.8e-13   4.7e-09       4     200 ..       3     175 ..       1     179 [. 0.72

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 7.8e-13
                                       EEEESBTTTBCHH.HHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH.HHHHHETTTEHHHHTHHHHHH CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   4 vvfDkdGTLttge.psvedvivsaalalaaaletgsehpigkalvaaakarsgal.tgfatfigrgayaigkpewlt 78 
                                       v fD+ GTL+t e ps     v                        +  +r+ a+ +++++     aya+  ++  +
  gi|336253634|ref|YP_004596741.1|   3 VSFDLFGTLVTAEtPSDPAGAVA----------------------TELAERGVAVpDDWQA-----AYAEPHVDAPE 52 
                                       56888888888884333333333......................3556666666677777.....77777777766 PP

                                       HH..HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTH.HBHTTHHHHHHHHHHTTEEEEEEESSEH.HHHHHH CS
                                       xx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                         Hydrolase  79 al..dippdlgaaigsaqsqgrtvallqaralavftiadpl.kvkpeaaeavasLkaagievvlltgdnp.etaera 151
                                           +    l a +  a +   + + ++a  +av+++ dp+ + +++a eav + ++ g  v+++++ +  e + r+
  gi|336253634|ref|YP_004596741.1|  53 GAevP----LPAHVARALASRGIDYEHNAVRRAVVAAFDPDvTTRDGAIEAVGAARELGP-VAICSNCSVpELVART 124
                                       66333....3333444444444444445666777777777625678888*****999998.*****86651555599 PP

                                       HHHTT..GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSH CS
                                       xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 152 anqlG..ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgv 200
                                       + +++  +d+fd v++s   +  kp pe+++ +++eL+++p++ ++VGD +
  gi|336253634|ref|YP_004596741.1| 125 LIRADleRDAFDTVVTSVGCGWRKPAPEIFELTADELGVDPSDLVHVGDDP 175
                                       99999999999**************************************86 PP

>> HAD_2  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   4.5e-10   2.7e-06      77     164 ..      89     178 ..      54     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.5e-10
                             HAD_2  77 evkpydgvkelLeeLkeagyklgivTsk.sreaveekleqlgie.syFdvivtsedvekkKPdpeviekaleklklk 151
                                        v+  dg++e++    ++   ++i ++    e v + l + ++e + Fd++vts  ++ +KP+pe++e + ++l+++
  gi|336253634|ref|YP_004596741.1|  89 DVTTRDGAIEAVGAA-RELGPVAICSNCsVPELVARTLIRADLErDAFDTVVTSVGCGWRKPAPEIFELTADELGVD 164
                                       666667777777666.4444677777763456677778888887689****************************** PP

                             HAD_2 152 keeviyvGDsp.tD 164
                                       +++ + vGD p tD
  gi|336253634|ref|YP_004596741.1| 165 PSDLVHVGDDPdTD 178
                                       *********99666 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   4.9e-09   2.9e-05       2      34 ..     146     178 ..     145     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.9e-09
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTH CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatD 34 
                                       ++KP+pe+++  + +lg+dp++ + +GD+++tD
  gi|336253634|ref|YP_004596741.1| 146 WRKPAPEIFELTADELGVDPSDLVHVGDDPDTD 178
                                       69******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1748.86
//
Query:       gi|336253635|ref|YP_004596742.1|  [L=203]
Description: translation initiation factor 2 subunit beta [Halopiger xanaduensis SH-6]
Scores for 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  111.1   0.0    4.1e-32  110.5   0.0    1.3  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
      1e-08   35.0   0.9    1.8e-08   34.2   0.9    1.4  1  TRAM             TRAM domain
  ------ inclusion threshold ------
      0.047   14.0   0.1      0.084   13.1   0.1    1.5  1  CBM_4_9          Carbohydrate binding domain
      0.052   13.9   0.5       0.63   10.5   0.5    2.2  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.14   12.3   0.7        0.3   11.2   0.7    1.6  1  Zn-ribbon_8      Zinc ribbon domain
       0.15   12.0   3.8       0.11   12.4   1.6    1.9  2  Nudix_N_2        Nudix N-terminal
       0.16   11.4   0.4        5.6    6.5   0.0    2.3  2  zf-ribbon_3      zinc-ribbon domain


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 !  110.5   0.0   1.6e-35   4.1e-32       7     116 ..      20     127 ..      15     128 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 1.6e-35
                                       SSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHH CS
                      eIF-5_eIF-2B   7 kkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldky 83 
                                       +++r+++p+++++++g+  t ++N+ eia+ L+r++eh+++++++e+gt+g++ e+gr  +ng f++++++ ++d+y
  gi|336253635|ref|YP_004596742.1|  20 DEQRLQIPDAETQKDGA-FTRFRNLGEIADVLSREDEHLHRFIQREMGTSGKL-EDGRGRYNGTFSEQDFDMAVDAY 94 
                                       578**************.***********************************.999******************** PP

                                       HHHHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  84 ieeyVlCkeCkspetelekeerllvlkCkaCga 116
                                       ++eyVlC+eC+ p+t+l++e+r+ +l+C+aCga
  gi|336253635|ref|YP_004596742.1|  95 VDEYVLCSECGLPDTRLVREDRTPMLRCDACGA 127
                                       ********************************7 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.9   7.1e-12   1.8e-08       3      61 ..     148     202 ..     146     203 .] 0.96

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 7.1e-12
                                       XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61 
                                       ++G+t++V+++g + ++g+g++     +++fvpg+++  Gd+Ve+ I+    + ++++l
  gi|336253635|ref|YP_004596742.1| 148 EEGKTYTVEITGTG-RKGDGVAEKG-EYTIFVPGAEE--GDVVEIYIKNISGNLAFAKL 202
                                       79************.**********.***********..**************999986 PP

>> CBM_4_9  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.3e-05     0.084      41      76 ..     131     164 ..     126     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.3e-05
                                       EESCSSTTCEEEEEEECCS-TT-EEEEEEEEEESST CS
                           CBM_4_9  41 vsgrgetwdgqaiditirlekgktYtvsfwvkassg 76 
                                       v++r++  + q++++  ++e+gktYtv+++  + +g
  gi|336253635|ref|YP_004596742.1| 131 VTKRSA--SSQQQQQQEAVEEGKTYTVEITGTGRKG 164
                                       677766..778888889**********998776655 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 ?    4.7   0.0     0.015        38      27      36 ..      90     106 ..      63     117 .. 0.69
   2 ?   10.5   0.5   0.00025      0.63       6      55 ..     101     147 ..      97     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.015
                   Lar_restr_allev  27 q.......cvyCadCga 36 
                                               +v C +Cg 
  gi|336253635|ref|YP_004596742.1|  90 AvdayvdeYVLCSECGL 106
                                       04445555********9 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00025
                   Lar_restr_allev   6 CPfCggravlersqrvvaeigqcvyCadCga.stpwfkiaedeaeaekeai 55 
                                       C  Cg +++   +++++     +  C+ Cga    + + a+ +++ ++ea+
  gi|336253635|ref|YP_004596742.1| 101 CSECGLPDTRLVREDRTP----MLRCDACGAfRPVTKRSASSQQQQQQEAV 147
                                       777888888888888888....*********95555556666666666666 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   0.7   0.00012       0.3       5      38 ..      97     133 ..      89     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                       Zn-ribbon_8   5 eYr.CeeCghefevlqsisdapltaCPeCgs..evrr 38 
                                       eY  C eCg   ++l++ ++ p+  C +Cg+  +v++
  gi|336253635|ref|YP_004596742.1|  97 EYVlCSECGLPDTRLVREDRTPMLRCDACGAfrPVTK 133
                                       5666*****9999***988999999*****9766665 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.4   3.5e+03       9      19 ..      21      31 ..      19      33 .. 0.72
   2 ?   12.4   1.6   4.5e-05      0.11       3      30 ..     101     127 ..     100     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
                                      B-EEE--TT-S CS
                         Nudix_N_2  9 pvelripdgDn 19
                                      + +l+ipd ++
  gi|336253635|ref|YP_004596742.1| 21 EQRLQIPDAET 31
                                      55789999887 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.5e-05
                                       -TTT--B-EEE--TT-SS-EEEETTTTE CS
                         Nudix_N_2   3 CsqCGtpvelripdgDnreRlvCpaCgt 30 
                                       Cs+CG p  +r+  +D  + l+C+aCg+
  gi|336253635|ref|YP_004596742.1| 101 CSECGLP-DTRLVREDRTPMLRCDACGA 127
                                       *******.6666689***********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 ?    2.8   0.1     0.031        80       5       9 ..     101     105 ..      97     110 .. 0.64
   2 ?    6.5   0.0    0.0022       5.6       2      11 ..     119     128 ..     118     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.031
                       zf-ribbon_3   5 CPnCG 9  
                                       C++CG
  gi|336253635|ref|YP_004596742.1| 101 CSECG 105
                                       56665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0022
                       zf-ribbon_3   2 tvrCPnCGap 11 
                                       + rC +CGa 
  gi|336253635|ref|YP_004596742.1| 119 MLRCDACGAF 128
                                       789*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      715  (0.0398795); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1506.74
//
Query:       gi|336253636|ref|YP_004596743.1|  [L=170]
Description: hypothetical protein Halxa_2239 [Halopiger xanaduensis SH-6]
Scores for 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   13.9   0.3          1    9.6   0.3    2.4  1  DUF2795   Protein of unknown function (DUF2795)


Domain annotation for each model (and alignments):
>> DUF2795  Protein of unknown function (DUF2795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3   5.7e-05         1       1      44 []      79     127 ..      79     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 5.7e-05
                           DUF2795   1 LkgadyPatKdeLv.eyArrngA....pdevleaLeaLPdreYespaeV 44 
                                       L+++ yP+t +eL+ ey  ++       + + + +++L  ++Y++p+eV
  gi|336253636|ref|YP_004596743.1|  79 LGDLEYPVTSEELAtEYGDEAIDmpneTESLGSVFDRLAGEQYDDPEEV 127
                                       7889999999999743444333243347777889999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1321.38
//
Query:       gi|336253637|ref|YP_004596744.1|  [L=342]
Description: G6PDH family F420-dependent oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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   0.1    2.6e-53  181.5   0.1    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.5   0.1   1.4e-57   2.6e-53       2     314 .]       3     310 ..       1     310 [. 0.93

  Alignments for each domain:
  == domain 1  score: 181.5 bits;  conditional E-value: 1.4e-57
                    Bac_luciferase   2 efgvflptrqggalgaasaslrylvelaraaEelGfdavwvaehhggpgga.........ldaftllaalaaaTeri 69 
                                       +fg+f++ +         +++++ ++++++aEe+Gfd++wv++h +++  +          +a+++l a++++T+ +
  gi|336253637|ref|YP_004596744.1|   3 RFGWFASLEE--------FTPDECLQQVELAEEAGFDTAWVSDHFHPWLDHkqdgssgnaGNAWSWLPAALERTDDL 71 
                                       7999999999........8*****************************999************************** PP

                    Bac_luciferase  70 rlgtavtply.trhPavlAqqaatLdhlsgGRfglglgtggpaveerrfGv...dhderyarlrEfvevlrrlwrge 142
                                        +gt+vt +  ++hP ++A   atL ++++ R+ lglg+g++ +e    G+   ++ e  +r++E+v+ +r+l++ge
  gi|336253637|ref|YP_004596744.1|  72 VMGTGVTAVIhRYHPGNVAHRLATLAEMYPDRIFLGLGSGEALNE-SPLGLpmpEFGECAKRTAEAVRMMRALFEGE 147
                                       *******9999**********************************.7779999*********************888 PP

                    Bac_luciferase 143 evdfeGeffsvkgalllprpgqgpiPvyvaaaspaglelaarhadglllag.eppeeaaelierlragaaeagrdpa 218
                                        v+++G+++s ++a l   p++  +Pvy+a+ +p  +++a+  +dg++++  +p+ + +el++++r+g ++ +r ++
  gi|336253637|ref|YP_004596744.1| 148 FVSYDGQYWSFDEANLYTGPDEM-PPVYIASNGPTLARMAGDLGDGYVTVFeSPERAQEELFPSVRKGVKKSDRNDS 223
                                       88*********999999999888.99*************************99999999***************999 PP

                    Bac_luciferase 219 ..dirvgisltvivadteeeAraea.raliagldfyaldsegagreaeaaeiqeeedanlwagaadavpdelvaata 292
                                         +++  i l+v++++++eeA  e  + +              g + +  ++ +  d++  + ++d v++e++++ +
  gi|336253637|ref|YP_004596744.1| 224 leEMDRSIHLHVSYDPDSEEAALEPcLPW-------------RGTMLDIFFEANIADPRTVQYHGDKVDPEVLKEEM 287
                                       99*************77776654431444.............59999999******************888888777 PP

                    Bac_luciferase 293 l.vGtpeqvaerlaayaeagvde 314
                                       +   +p+++++  + y++ag+++
  gi|336253637|ref|YP_004596744.1| 288 TiTTDPQDIVDVTEKYVDAGFNH 310
                                       73669***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2867.70
//
Query:       gi|336253638|ref|YP_004596745.1|  [L=236]
Description: CopG family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-11   42.0  31.4    1.8e-07   31.0   8.9    2.2  3  DZR             Double zinc ribbon
    1.2e-07   31.2  13.2     0.0007   19.2   5.1    2.7  2  zinc_ribbon_2   zinc-ribbon domain
    7.3e-07   28.4  11.2     0.0049   16.2   5.1    2.8  2  zf-ribbon_3     zinc-ribbon domain
    3.9e-06   27.5   8.3    0.00034   21.3   1.5    2.3  2  zinc_ribbon_15  zinc-ribbon family
    6.6e-05   22.7   3.4    6.6e-05   22.7   3.4    3.3  3  RHH_1           Ribbon-helix-helix protein, copG family
    0.00069   19.2  11.3       0.45   10.2   0.1    4.2  4  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0047   16.9   8.2      0.013   15.4   4.1    2.3  2  zinc-ribbons_6  zinc-ribbons
  ------ inclusion threshold ------
      0.034   14.1  12.8       0.26   11.3   1.3    3.9  3  Nudix_N_2       Nudix N-terminal
      0.034   13.7   3.3        4.4    7.0   0.1    3.3  3  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.038   14.0   2.0        4.1    7.5   0.1    3.1  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.22   11.4   5.0       0.52   10.2   0.5    2.2  2  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.24   11.2   4.1        5.1    7.0   0.3    2.3  2  Cys_rich_KTR    Cysteine-rich KTR
       0.31   11.2  10.9        5.9    7.1   5.0    2.6  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
       0.33   11.0   8.8        2.1    8.4   2.2    2.4  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.35   10.8   6.6        0.2   11.6   2.9    2.4  2  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
       0.52   10.5  12.5        1.2    9.3   3.5    3.3  3  Zn-ribbon_8     Zinc ribbon domain
       0.62   10.2   4.6        2.7    8.2   0.2    2.4  2  Lsr2            Lsr2
        1.1    9.2   3.9        7.6    6.5   0.2    2.7  2  DUF3797         Domain of unknown function (DUF3797)
          2    8.4   5.6         23    5.0   0.3    2.6  2  zf-C2HC_2       zinc-finger of a C2HC-type
        2.2    8.3  10.9        1.2    9.1   4.6    2.9  3  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        2.3    7.9   5.9        6.8    6.4   0.3    2.7  3  Sgf11           Sgf11 (transcriptional regulation protein)
        3.3    8.0  13.3        2.8    8.2   0.6    3.3  2  zf-RING_7       C4-type zinc ribbon domain
        3.7    7.6   9.0        8.3    6.5   0.7    3.3  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        4.9    7.1  16.9        1.1    9.2   5.6    2.9  2  HscB_4_cys      Co-chaperone HscB tetracysteine metal binding
        5.5    7.0  13.3         15    5.6   0.4    3.7  3  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        7.3    6.4  11.1       0.45   10.2   3.0    2.5  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
        8.5    7.1  12.8         14    6.4   0.7    3.7  3  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
        9.6    4.8   8.0        7.7    5.2   5.5    1.8  2  NRDD            Anaerobic ribonucleoside-triphosphate reducta


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 !   23.3   6.0   7.6e-08   4.9e-05       6      46 ..     167     204 ..     163     206 .. 0.87
   2 !   31.0   8.9   2.9e-10   1.8e-07       1      49 []     176     220 ..     176     220 .. 0.95
   3 !   13.0   1.3   0.00013     0.082       4      19 ..     205     220 ..     203     227 .. 0.58

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 7.6e-08
                               DZR   6 eelppdarfCseCgtklkavaaedrCpsCgekvdpearfCp 46 
                                       + +p+++r+C++Cg++++   ++ +Cp+Cgekv+ +  fC+
  gi|336253638|ref|YP_004596745.1| 167 SRTPSRQRTCGQCGEDVD--GEHVFCPNCGEKVSRR-LFCD 204
                                       568999***********9..789**********987.7886 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 2.9e-10
                               DZR   1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49 
                                       C qCge+++ +  fC++Cg+k+++     +C+ Cg ++ ++++fCp+CG
  gi|336253638|ref|YP_004596745.1| 176 CGQCGEDVDGEHVFCPNCGEKVSR---RLFCD-CGDELRSDWAFCPSCG 220
                                       99********************94...88885.***************9 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00013
                               DZR   4 CgeelppdarfCseCg 19 
                                       Cg el++d  fC+ Cg
  gi|336253638|ref|YP_004596745.1| 205 CGDELRSDWAFCPSCG 220
                                       5555555555555555 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   5.1   1.1e-06    0.0007       2      22 ..     176     196 ..     175     197 .. 0.94
   2 !   16.1   1.1     1e-05    0.0065       4      21 ..     204     221 ..     202     222 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.1e-06
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtp 22 
                                       C +CG+ ++ + +FCp+CG++
  gi|336253638|ref|YP_004596745.1| 176 CGQCGEDVDGEHVFCPNCGEK 196
                                       99*****************98 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1e-05
                     zinc_ribbon_2   4 nCGaelqdnakFCpyCGt 21 
                                        CG el  +  FCp CG 
  gi|336253638|ref|YP_004596745.1| 204 DCGDELRSDWAFCPSCGR 221
                                       5****************5 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   5.1   7.6e-06    0.0049       3      25 ..     174     196 ..     172     197 .. 0.91
   2 !   14.9   0.4     2e-05     0.013       8      23 ..     205     220 ..     204     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.6e-06
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyCGtk 25 
                                       ++C +CG+ + + + ++Cp+CG+k
  gi|336253638|ref|YP_004596745.1| 174 RTCGQCGEdV-DGEHVFCPNCGEK 196
                                       5799****88.***********86 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2e-05
                       zf-ribbon_3   8 CGa.plssddnvCpyCG 23 
                                       CG  + +sd+ +Cp+CG
  gi|336253638|ref|YP_004596745.1| 205 CGDeL-RSDWAFCPSCG 220
                                       99966.*********** PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.5   5.4e-07   0.00034      52      86 .]     160     194 ..     136     194 .. 0.76
   2 !   10.2   0.7    0.0015      0.96      67      86 .]     202     220 ..     195     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 5.4e-07
                    zinc_ribbon_15  52 elgkeiekkessekkeCknCgkeveeefkyCpkCg 86 
                                       e +++ ++++ s++++C +Cg+ v+ e  +Cp+Cg
  gi|336253638|ref|YP_004596745.1| 160 EPQSQSQSRTPSRQRTCGQCGEDVDGEHVFCPNCG 194
                                       2334444444555*********************9 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0015
                    zinc_ribbon_15  67 eCknCgkeveeefkyCpkCg 86 
                                        C +Cg e+ ++ ++Cp+Cg
  gi|336253638|ref|YP_004596745.1| 202 FC-DCGDELRSDWAFCPSCG 220
                                       56.8***************9 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 !   22.7   3.4     1e-07   6.6e-05       2      39 .]       4      37 ..       3      37 .. 0.92
   2 ?   -1.6   0.3       4.5   2.9e+03       5      15 ..      73      83 ..      66      85 .. 0.60
   3 ?   -1.3   0.0       3.7   2.3e+03       2      16 ..     108     122 ..     107     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1e-07
                                      EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyler 39
                                      +++r d++l+e+L++    ++ S+Se++ReAlr+yle+
  gi|336253638|ref|YP_004596745.1|  4 ITFRADDDLVEELEA----LETSKSEAMREALRAYLEE 37
                                      799**********86....59***************95 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.5
                                      EEEHHHHHHHH CS
                             RHH_1  5 rldeellerLd 15
                                      r+de l erL 
  gi|336253638|ref|YP_004596745.1| 73 RVDELLTERLA 83
                                      45555555555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.7
                                       EEEEEEHHHHHHHHH CS
                             RHH_1   2 vsirldeellerLde 16 
                                       v+i l++  ++r+de
  gi|336253638|ref|YP_004596745.1| 108 VTIALEDGRARRVDE 122
                                       899999988899987 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 ?   -0.8   0.0         2   1.3e+03      13      23 ..     109     119 ..     108     119 .. 0.86
   2 ?    3.8   0.5      0.07        45       3      10 ..     173     180 ..     171     183 .. 0.70
   3 !   10.2   0.1    0.0007      0.45       3      14 ..     187     198 ..     186     200 .. 0.85
   4 !    9.8   0.4   0.00094       0.6       5      16 ..     215     226 ..     213     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2
                     zf-NADH-PPase  13 tepaeggwarv 23 
                                       t+  e+g+ar+
  gi|336253638|ref|YP_004596745.1| 109 TIALEDGRARR 119
                                       77889****97 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.07
                     zf-NADH-PPase   3 hrFCgrCG 10 
                                       +r Cg+CG
  gi|336253638|ref|YP_004596745.1| 173 QRTCGQCG 180
                                       56688888 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0007
                     zf-NADH-PPase   3 hrFCgrCGapte 14 
                                       h FC+ CG ++ 
  gi|336253638|ref|YP_004596745.1| 187 HVFCPNCGEKVS 198
                                       99******9875 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00094
                     zf-NADH-PPase   5 FCgrCGaptepa 16 
                                       FC+ CG +t+ a
  gi|336253638|ref|YP_004596745.1| 215 FCPSCGRRTASA 226
                                       *********876 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   4.1   2.1e-05     0.013       7      52 ..     164     203 ..     158     213 .. 0.67
   2 ?    4.6   0.6     0.049        31      17      38 ..     201     222 ..     198     228 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-05
                                       -S--EE-SSEEE-TTT--EEE.EEEE-SSS-S---EEEETTEEEE-- CS
                    zinc-ribbons_6   7 qqelekrgeqyhCeaCqedlk.kealCpeCeqelevlkaCgavdyfC 52 
                                       q++ ++ ++q +C +C ed++ ++ +Cp+C++++++         fC
  gi|336253638|ref|YP_004596745.1| 164 QSQSRTPSRQRTCGQCGEDVDgEHVFCPNCGEKVSRRL-------FC 203
                                       44444555889999999999834578999999987543.......33 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.049
                                       EE-TTT--EEEEEEE-SSS-S- CS
                    zinc-ribbons_6  17 yhCeaCqedlkkealCpeCeqe 38 
                                       ++C++ +e  +  a+Cp C+ +
  gi|336253638|ref|YP_004596745.1| 201 LFCDCGDELRSDWAFCPSCGRR 222
                                       5677666666678999999875 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.36   2.3e+02       3      10 ..     176     183 ..     172     186 .. 0.78
   2 ?   11.3   1.3    0.0004      0.26       2      14 ..     189     201 ..     189     211 .. 0.88
   3 ?    7.2   0.1    0.0074       4.7       2      11 ..     215     224 ..     214     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.36
                                       -TTT--B- CS
                         Nudix_N_2   3 CsqCGtpv 10 
                                       C qCG+ v
  gi|336253638|ref|YP_004596745.1| 176 CGQCGEDV 183
                                       88888765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0004
                                       B-TTT--B-EEE- CS
                         Nudix_N_2   2 FCsqCGtpvelri 14 
                                       FC++CG++v++r+
  gi|336253638|ref|YP_004596745.1| 189 FCPNCGEKVSRRL 201
                                       9*********986 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0074
                                       B-TTT--B-E CS
                         Nudix_N_2   2 FCsqCGtpve 11 
                                       FC++CG +++
  gi|336253638|ref|YP_004596745.1| 215 FCPSCGRRTA 224
                                       9*****9875 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.32   2.1e+02       3      11 ..     174     182 ..     172     185 .. 0.81
   2 ?    7.0   0.1    0.0069       4.4       1      13 [.     186     198 ..     186     201 .. 0.87
   3 ?    4.2   0.0     0.053        34       4      19 ..     215     230 ..     212     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.32
                            zf_UBZ   3 ylCerCgke 11 
                                        +C +Cg+ 
  gi|336253638|ref|YP_004596745.1| 174 RTCGQCGED 182
                                       58*****86 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0069
                            zf_UBZ   1 dtylCerCgkeip 13 
                                       ++++C+ Cg++++
  gi|336253638|ref|YP_004596745.1| 186 EHVFCPNCGEKVS 198
                                       579*******987 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.053
                            zf_UBZ   4 lCerCgkeipeselqE 19 
                                       +C+ Cg++  ++++ E
  gi|336253638|ref|YP_004596745.1| 215 FCPSCGRRTASADVLE 230
                                       8******999888776 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 ?    7.5   0.1    0.0064       4.1       2      11 ..     190     199 ..     189     201 .. 0.89
   2 ?    4.7   0.2     0.048        31       2       7 ..     216     221 ..     215     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0064
                    DNA_ligase_ZBD   2 CPvCGsavvR 11 
                                       CP CG +v R
  gi|336253638|ref|YP_004596745.1| 190 CPNCGEKVSR 199
                                       *******987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.048
                    DNA_ligase_ZBD   2 CPvCGs 7  
                                       CP+CG 
  gi|336253638|ref|YP_004596745.1| 216 CPSCGR 221
                                       *****5 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 ?   10.2   0.5   0.00081      0.52      25      49 ..     175     199 ..     168     200 .. 0.88
   2 ?    3.2   0.4      0.13        83      28      46 ..     204     222 ..     199     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00081
                                       E-HHHHHHHHHTT-B-TTT--B--E CS
                        zf-C3HC4_3  25 lCeeCaekllkrkkkCpiCrrpiek 49 
                                       +C +C e++  ++  Cp C +++++
  gi|336253638|ref|YP_004596745.1| 175 TCGQCGEDVDGEHVFCPNCGEKVSR 199
                                       8********88*********99976 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                                       HHHHHHHHTT-B-TTT--B CS
                        zf-C3HC4_3  28 eCaekllkrkkkCpiCrrp 46 
                                       +C ++l++  + Cp C r 
  gi|336253638|ref|YP_004596745.1| 204 DCGDELRSDWAFCPSCGRR 222
                                       6999998899999999875 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.3    0.0083       5.3       3      35 ..     187     221 ..     185     223 .. 0.81
   2 ?    7.0   0.3     0.008       5.1       2      13 ..     212     223 ..     211     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0083
                      Cys_rich_KTR   3 WvlcPvCgnkTRlkiredT..vLknfpLfCPKCkq 35 
                                        v+cP Cg k   ++  d   +L+    fCP C +
  gi|336253638|ref|YP_004596745.1| 187 HVFCPNCGEKVSRRLFCDCgdELRSDWAFCPSCGR 221
                                       589******99999888854489999999999966 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.008
                      Cys_rich_KTR   2 eWvlcPvCgnkT 13 
                                       +W +cP Cg +T
  gi|336253638|ref|YP_004596745.1| 212 DWAFCPSCGRRT 223
                                       7********998 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 ?    7.1   5.0    0.0092       5.9      11      39 ..     176     203 ..     171     210 .. 0.73
   2 ?    6.3   0.8     0.016        10      24      33 ..     214     223 ..     205     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0092
                      NOB1_Zn_bind  11 ChaCfkvtkdmtkkFCpkCGnktLkrvav 39 
                                       C  C +   d + +FCp+CG+k  +r  +
  gi|336253638|ref|YP_004596745.1| 176 CGQCGED-VDGEHVFCPNCGEKVSRRLFC 203
                                       5555543.35789********98777665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.016
                      NOB1_Zn_bind  24 kFCpkCGnkt 33 
                                        FCp+CG +t
  gi|336253638|ref|YP_004596745.1| 214 AFCPSCGRRT 223
                                       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 ?    8.4   2.2    0.0033       2.1      70      95 ..     173     196 ..     162     200 .. 0.79
   2 ?    7.0   0.7    0.0087       5.6      66      96 ..     196     223 ..     195     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0033
                                       EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  70 kvrCreCgkefeleekalrCpkCgsa 95 
                                       + +C +Cg++++ e  ++ Cp+Cg++
  gi|336253638|ref|YP_004596745.1| 173 QRTCGQCGEDVDGE--HVFCPNCGEK 196
                                       568*****999977..457****985 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0087
                                       EE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  66 evpvkvrCreCgkefeleekalrCpkCgsad 96 
                                       +v+ ++ C +Cg e +++  a+ Cp+Cg++ 
  gi|336253638|ref|YP_004596745.1| 196 KVSRRLFC-DCGDELRSD-WAF-CPSCGRRT 223
                                       67778899.6**999987.445.*****875 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.9   0.00032       0.2      22      40 ..      21      39 ..       3      44 .. 0.79
   2 ?   -1.8   0.1       4.7     3e+03      31      39 ..      65      73 ..      63      83 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                                      XXXXXXXXXXXXX------ CS
                    VapB_antitoxin 22 ktKrEaVnlALreLiqrrk 40
                                      + K+Ea+++ALr+++++++
  gi|336253638|ref|YP_004596745.1| 21 TSKSEAMREALRAYLEEEE 39
                                      67**************986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.7
                                      XXXX----- CS
                    VapB_antitoxin 31 ALreLiqrr 39
                                      A+ +L+++r
  gi|336253638|ref|YP_004596745.1| 65 AIDDLVRER 73
                                      667777765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.5      0.16     1e+02      24      36 ..     170     183 ..     155     185 .. 0.67
   2 ?    9.3   3.5    0.0019       1.2       8      39 ..     176     200 ..     173     202 .. 0.74
   3 ?    4.4   1.1     0.065        42      28      35 ..     214     223 ..     203     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.16
                       Zn-ribbon_8  24 aplta.CPeCgsev 36 
                                       ++ +  C +Cg++v
  gi|336253638|ref|YP_004596745.1| 170 PSRQRtCGQCGEDV 183
                                       34444499999876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0019
                       Zn-ribbon_8   8 CeeCghefevlqsisdaplta.CPeCgsevrrv 39 
                                       C +Cg++ +         + + CP+Cg++v r+
  gi|336253638|ref|YP_004596745.1| 176 CGQCGEDVDG--------EHVfCPNCGEKVSRR 200
                                       8888877662........4455******88875 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.065
                       Zn-ribbon_8  28 a.CPeCgs.e 35 
                                       a CP+Cg  +
  gi|336253638|ref|YP_004596745.1| 214 AfCPSCGRrT 223
                                       55****9844 PP

>> Lsr2  Lsr2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0042       2.7      35      82 ..      19      66 ..       3      82 .. 0.82
   2 ?    3.4   0.7      0.13        80      28      77 ..     105     154 ..      98     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0042
                              Lsr2 35 LseenaeklrdaLapyieaarrvggrkkkrrarrkaaaaasreqaaai 82
                                      L+++  e++r+aL+ y+e   +v+g++ + ++  +++++a+r++++ai
  gi|336253638|ref|YP_004596745.1| 19 LETSKSEAMREALRAYLEEEEEVSGTSVQDGSDGAENESAARANETAI 66
                                      67788999****************998877777777777777777776 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.13
                              Lsr2  28 gveYeiDLseenaeklrdaLapyieaarrvggrkkkrrarrkaaaaasre 77 
                                       +v+ +i L++  a+++ +a  +  ++ar  +++++ +ra r++++ ++r+
  gi|336253638|ref|YP_004596745.1| 105 DVNVTIALEDGRARRVDEAQGSASSHARPHTQARSDSRAGRESEHGRDRS 154
                                       56677888888888888888888888888776665444433333333333 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.012       7.6      10      21 ..     184     195 ..     181     200 .. 0.84
   2 ?    3.4   0.0      0.11        69       9      20 ..     209     220 ..     207     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.012
                           DUF3797  10 dekYvqCPeCgN 21 
                                       d+  v CP+Cg 
  gi|336253638|ref|YP_004596745.1| 184 DGEHVFCPNCGE 195
                                       78899*****96 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.11
                           DUF3797   9 LdekYvqCPeCg 20 
                                       L   ++ CP Cg
  gi|336253638|ref|YP_004596745.1| 209 LRSDWAFCPSCG 220
                                       6667899****9 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 ?    5.0   0.3     0.036        23       3      11 ..     188     196 ..     187     197 .. 0.85
   2 ?    4.9   0.9     0.039        25       5      10 ..     216     221 ..     214     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.036
                         zf-C2HC_2   3 vpCpkCgRs 11 
                                       v Cp+Cg +
  gi|336253638|ref|YP_004596745.1| 188 VFCPNCGEK 196
                                       67*****86 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.039
                         zf-C2HC_2   5 CpkCgR 10 
                                       Cp CgR
  gi|336253638|ref|YP_004596745.1| 216 CPSCGR 221
                                       ****** 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   0.3      0.48   3.1e+02      42      57 ..     169     184 ..     159     189 .. 0.70
   2 ?    8.1   2.3     0.004       2.5      30      58 ..     175     199 ..     170     201 .. 0.76
   3 ?    9.1   4.6     0.002       1.2      31      60 ..     190     228 ..     188     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.48
                    OrfB_Zn_ribbon  42 lsgrtfkCpnCgfead 57 
                                         +r+ +C +Cg   d
  gi|336253638|ref|YP_004596745.1| 169 TPSRQRTCGQCGEDVD 184
                                       5677778888887655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.004
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfeadr 58 
                                       t   Cg+ +++ ++g+ + CpnCg +  r
  gi|336253638|ref|YP_004596745.1| 175 T---CGQCGED-VDGEHVFCPNCGEKVSR 199
                                       4...5555555.6669********99766 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.002
                    OrfB_Zn_ribbon  31 CseCgsknke........alsgrtfkCpnCgfe.adrDv 60 
                                       C++Cg+k+++        +l +++  Cp+Cg + a +Dv
  gi|336253638|ref|YP_004596745.1| 190 CPNCGEKVSRrlfcdcgdELRSDWAFCPSCGRRtASADV 228
                                       **********9****9999999999*****988788887 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       5.5   3.5e+03       6      14 ..     175     183 ..     173     186 .. 0.78
   2 ?    6.4   0.3     0.011       6.8       3      15 ..     186     198 ..     184     203 .. 0.84
   3 ?    4.1   0.1     0.054        35       6      13 ..     215     222 ..     210     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.5
                                       E-TTTSSEE CS
                             Sgf11   6 tCpnCgRqi 14 
                                       tC  Cg ++
  gi|336253638|ref|YP_004596745.1| 175 TCGQCGEDV 183
                                       799998766 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                                       -EEE-TTTSSEEE CS
                             Sgf11   3 eyvtCpnCgRqia 15 
                                       e+v CpnCg +++
  gi|336253638|ref|YP_004596745.1| 186 EHVFCPNCGEKVS 198
                                       6788*****8886 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.054
                                       E-TTTSSE CS
                             Sgf11   6 tCpnCgRq 13 
                                        Cp CgR 
  gi|336253638|ref|YP_004596745.1| 215 FCPSCGRR 222
                                       5******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 ?    2.4   6.3      0.29   1.8e+02      21      30 ..     185     194 ..     160     194 .. 0.77
   2 ?    8.2   0.6    0.0044       2.8      24      31 ..     214     221 ..     205     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.29
                                       TB-EE-TTT- CS
                         zf-RING_7  21 devvtCpeCG 30 
                                       +e v+Cp+CG
  gi|336253638|ref|YP_004596745.1| 185 GEHVFCPNCG 194
                                       4469*****9 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0044
                                       EE-TTT-- CS
                         zf-RING_7  24 vtCpeCGR 31 
                                       ++Cp+CGR
  gi|336253638|ref|YP_004596745.1| 214 AFCPSCGR 221
                                       79*****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 ?    0.5   0.6      0.95   6.1e+02      18      26 ..     172     181 ..     164     189 .. 0.65
   2 ?    6.5   0.7     0.013       8.3      18      30 ..     187     199 ..     184     203 .. 0.71
   3 ?    4.1   0.0     0.071        45      21      29 ..     216     224 ..     209     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.95
                     Zn_Tnp_IS1595  18 g.fvCPhCgs 26 
                                       + ++C  Cg 
  gi|336253638|ref|YP_004596745.1| 172 RqRTCGQCGE 181
                                       4345666664 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                     Zn_Tnp_IS1595  18 gfvCPhCgsrkay 30 
                                       ++ CP+Cg + ++
  gi|336253638|ref|YP_004596745.1| 187 HVFCPNCGEKVSR 199
                                       455*****88554 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.071
                     Zn_Tnp_IS1595  21 CPhCgsrka 29 
                                       CP Cg r+a
  gi|336253638|ref|YP_004596745.1| 216 CPSCGRRTA 224
                                       *****8754 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   5.6    0.0017       1.1       6      23 ..     176     193 ..     175     194 .. 0.97
   2 ?    2.5   3.6       0.2   1.3e+02      12      23 ..     208     219 ..     202     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0017
                                       S--B--SS-S---B-TTT CS
                        HscB_4_cys   6 CGgpgapgrgdefFCpqC 23 
                                       CG+ g+  +g+  FCp C
  gi|336253638|ref|YP_004596745.1| 176 CGQCGEDVDGEHVFCPNC 193
                                       ****************** PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.2
                                       SS-S---B-TTT CS
                        HscB_4_cys  12 pgrgdefFCpqC 23 
                                        +r d  FCp C
  gi|336253638|ref|YP_004596745.1| 208 ELRSDWAFCPSC 219
                                       5788999***** 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 ?    1.5   0.3      0.45   2.9e+02      27      31 ..     176     180 ..     164     185 .. 0.64
   2 ?    5.6   0.4     0.024        15       7      18 ..     190     201 ..     189     204 .. 0.91
   3 ?    4.8   2.9      0.04        26      18      31 ..     209     220 ..     202     224 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.45
                    Zn_ribbon_SprT  27 CrrCk 31 
                                       C++C+
  gi|336253638|ref|YP_004596745.1| 176 CGQCG 180
                                       66665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.024
                    Zn_ribbon_SprT   7 CtgCgreythhl 18 
                                       C++Cg+++ ++l
  gi|336253638|ref|YP_004596745.1| 190 CPNCGEKVSRRL 201
                                       *******99987 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.04
                    Zn_ribbon_SprT  18 lsirrhnYrCrrCk 31 
                                       l+++++   C+ C+
  gi|336253638|ref|YP_004596745.1| 209 LRSDWAF--CPSCG 220
                                       5666655..66654 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   3.0    0.0007      0.45       2      27 ..     175     197 ..     175     198 .. 0.89
   2 ?    0.1   1.1         1   6.4e+02      20      26 ..     216     222 ..     203     223 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0007
                                       B-SSS--B----SSS----SSS---- CS
                    DNA_RNApol_7kD   2 iCgeCgaevslkkgdpiRCkeCGhRi 27 
                                       +Cg+Cg++v    g+ + C +CG ++
  gi|336253638|ref|YP_004596745.1| 175 TCGQCGEDV---DGEHVFCPNCGEKV 197
                                       5******99...5999*******876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                                       -SSS--- CS
                    DNA_RNApol_7kD  20 CkeCGhR 26 
                                       C  CG R
  gi|336253638|ref|YP_004596745.1| 216 CPSCGRR 222
                                       9999987 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 ?    2.6   0.4      0.36   2.3e+02       2      11 ..     173     182 ..     172     189 .. 0.80
   2 ?    6.4   0.7     0.022        14       4      12 ..     189     197 ..     186     202 .. 0.81
   3 ?    5.4   0.0     0.045        29       4      13 ..     215     224 ..     213     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.36
                           zf-ISL3   2 phrCPnCgsk 11 
                                       +++C +Cg+ 
  gi|336253638|ref|YP_004596745.1| 173 QRTCGQCGED 182
                                       689*****87 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.022
                           zf-ISL3   4 rCPnCgskt 12 
                                        CPnCg+k+
  gi|336253638|ref|YP_004596745.1| 189 FCPNCGEKV 197
                                       7*****995 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.045
                           zf-ISL3   4 rCPnCgsktv 13 
                                        CP Cg++t+
  gi|336253638|ref|YP_004596745.1| 215 FCPSCGRRTA 224
                                       7******975 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   5.5     0.012       7.7     508     530 ..     174     196 ..     168     205 .. 0.83
   2 ?   -0.5   0.2      0.61   3.9e+02     513     530 ..     205     224 ..     201     230 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.012
                                       EEETT.--..EESSSB-TTT--BE. CS
                              NRDD 508 dvCnecgy..kgeiekCpkCgseee 530
                                        +C +cg   +ge+  Cp+Cg  e+
  gi|336253638|ref|YP_004596745.1| 174 RTCGQCGEdvDGEHVFCPNCG--EK 196
                                       58************99*****..42 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.61
                                       .--..EESSSB-TTT--BE. CS
                              NRDD 513 cgy..kgeiekCpkCgseee 530
                                       cg   +     Cp+Cg++  
  gi|336253638|ref|YP_004596745.1| 205 CGDelRSDWAFCPSCGRRTA 224
                                       56533333367*****7754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1398  (0.0779742); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); 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: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 1651.06
//
Query:       gi|336253639|ref|YP_004596746.1|  [L=59]
Description: CopG-like DNA-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-08   32.8   0.1      6e-08   32.3   0.1    1.3  1  RHH_1          Ribbon-helix-helix protein, copG family
    2.7e-05   24.3   0.0    2.7e-05   24.3   0.0    1.0  1  RHH_8          Ribbon-Helix-Helix transcriptional regulator f
  ------ inclusion threshold ------
      0.022   14.7   0.8      0.024   14.5   0.8    1.1  1  CHASE3         CHASE3 domain
      0.053   14.3   0.3      0.084   13.6   0.3    1.4  1  PSK_trans_fac  Rv0623-like transcription factor


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 !   32.3   0.1   1.3e-11     6e-08       1      35 [.       3      38 ..       3      44 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.3e-11
                                      EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlre 35
                                      rv++r++++ +e++++l++ ++ ++rSe+IR A+re
  gi|336253639|ref|YP_004596746.1|  3 RVTLRIPKQQIEEVEQLVDSGEfPNRSEAIRSAVRE 38
                                      9**********************************8 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 !   24.3   0.0   6.1e-09   2.7e-05       4      57 ..       2      55 ..       1      59 [] 0.83

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.1e-09
                             RHH_8  4 ekvtinlgvvDLgqiDlLveeGfYsnRtDlirtairaqLakhddalkqavkrks 57
                                      e+vt+ +    + +++ Lv+ G + nR++ ir+a+r+ ++++ d  ++  ++++
  gi|336253639|ref|YP_004596746.1|  2 ERVTLRIPKQQIEEVEQLVDSGEFPNRSEAIRSAVREMINEEYDGQTEQSRQRN 55
                                      89************************************9876665554444444 PP

>> CHASE3  CHASE3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.8   5.4e-06     0.024      95     136 ..      11      51 ..       2      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.4e-06
                            CHASE3  95 eggleaalalvrsdegkelmdeiraliaemrdeerrllaqre 136
                                       + + e+ ++lv s+e  ++ ++ir++++em++ee +   +++
  gi|336253639|ref|YP_004596746.1|  11 Q-QIEEVEQLVDSGEFPNRSEAIRSAVREMINEEYDGQTEQS 51 
                                       3.78899***************************87666555 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   1.9e-05     0.084      24      53 ..      27      56 ..      10      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                                      XXXXXXXXXXXXXXXXXXXXXX--HHHHHH CS
                     PSK_trans_fac 24 skteAvrrAleerlerlrreraepllerll 53
                                      +  eA+r A++e ++++   ++e++++r +
  gi|336253639|ref|YP_004596746.1| 27 NRSEAIRSAVREMINEEYDGQTEQSRQRNW 56
                                      678************986559999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 445.36
//
Query:       gi|336253640|ref|YP_004596747.1|  [L=399]
Description: cell division protein FtsZ [Halopiger xanaduensis SH-6]
Scores for 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-38  130.5   3.0    8.4e-38  130.5   3.0    2.2  2  Tubulin   Tubulin/FtsZ family, GTPase domain
      2e-35  121.0   0.7      2e-35  121.0   0.7    3.0  3  FtsZ_C    FtsZ family, C-terminal domain
  ------ inclusion threshold ------
      0.045   13.9   0.0       0.12   12.5   0.0    1.7  1  ZT_dimer  Dimerisation domain of Zinc Transporter
      0.085   12.2   0.0       0.17   11.2   0.0    1.5  1  ThiF      ThiF family
       0.13   12.1   0.0       0.48   10.3   0.0    1.9  1  Csm1_B    Csm1 subunit domain B


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 !  130.5   3.0   2.4e-41   8.4e-38       1     195 [.      32     190 ..      32     192 .. 0.96
   2 ?   -2.3   0.2       1.2   4.3e+03     119     133 ..     366     380 ..     328     389 .. 0.62

  Alignments for each domain:
  == domain 1  score: 130.5 bits;  conditional E-value: 2.4e-41
                                       EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE CS
                           Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnkll 77 
                                       +i+++g+G++Gn+++n+l++      g+             +g ++++    ai+td+q+l+ i+a+      +k+l
  gi|336253640|ref|YP_004596747.1|  32 RIVIVGCGGAGNNTVNRLYN-----IGV-------------DG-ADTV----AINTDKQHLKMIEAD------TKIL 79 
                                       59******************.....488.............66.7777....***************......**** PP

                                       --CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEE CS
                           Tubulin  78 lgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvv 154
                                       +gk+ ++++gagg+p++g++a+e  +  i++ + ++d+   +f+ta++gGGTG+G++pv+ e++ke+  +a+vv++v
  gi|336253640|ref|YP_004596747.1|  80 VGKSLTQGLGAGGDPSMGERATEMAQGTIKEVLGDADL---VFVTAGMGGGTGTGAAPVVSEIAKEQ--GAIVVGMV 151
                                       **************************************...**************************..******** PP

                                       EE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCC CS
                           Tubulin 155 vlPsefsevvvepynailalkelieesdavividNdaLlki 195
                                        +P++   +  +  +a+++l++l+e++d++iv+dN++Ll+ 
  gi|336253640|ref|YP_004596747.1| 152 STPFNV--ERARTVKAEEGLEKLREQADSIIVLDNNRLLDY 190
                                       ****98..899***************************986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                                       EEEEEETTSSHHHHH CS
                           Tubulin 119 ffitaslgGGTGSGl 133
                                        + tas + GTG G+
  gi|336253640|ref|YP_004596747.1| 366 NVETASSSTGTGYGA 380
                                       444556666666555 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       0.7   2.5e+03      30      56 ..      51      76 ..      43     111 .. 0.66
   2 ?    0.3   0.1      0.25   8.9e+02      13      33 ..      97     117 ..      84     162 .. 0.69
   3 !  121.0   0.7   5.6e-39     2e-35       1      95 []     239     333 ..     239     333 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.7
                                      T--GGG-SEEEEEEEE-TT--HHHHHH CS
                            FtsZ_C 30 dvdlsgAkgvlvnitggsdltlkEvee 56
                                      ++ ++gA +v +n t  + l++ E+++
  gi|336253640|ref|YP_004596747.1| 51 NIGVDGADTVAIN-TDKQHLKMIEADT 76
                                      5566666666666.4455555555554 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.25
                                       TTHHHHHHHHHHTSGGGT--G CS
                            FtsZ_C  13 edraeeaaeaaisspLLdvdl 33 
                                        +ra+e a+ +i++ L d+dl
  gi|336253640|ref|YP_004596747.1|  97 GERATEMAQGTIKEVLGDADL 117
                                       567777777777777766664 PP

  == domain 3  score: 121.0 bits;  conditional E-value: 5.6e-39
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       GvA+m vGe++++++++e++++a+++pLLdvd++gA+g lv+itgg+dltlkE+e +a++i+e+++ +anvi+Ga+i
  gi|336253640|ref|YP_004596747.1| 239 GVAVMLVGETQDKNKTDEVVKDAMNHPLLDVDYRGASGGLVHITGGPDLTLKEAEGIADNITERLEASANVIWGARI 315
                                       99*************************************************************************** PP

                                       -TT--SEEEEEEEEES-X CS
                            FtsZ_C  78 deeledeirvtvvatglk 95 
                                       +e++++++rv++++tg++
  gi|336253640|ref|YP_004596747.1| 316 QENYKGKVRVMAIMTGVQ 333
                                       ****************96 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 ?   12.5   0.0   3.3e-05      0.12      38      65 ..     279     306 ..     278     311 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                                       EEEEE-TTS-HHHHHHHHHHHHHHHHHH CS
                          ZT_dimer  38 lhievdgdlsvkeaHeiadevekrikee 65 
                                       +hi+  +dl++kea  iad++ +r++++
  gi|336253640|ref|YP_004596747.1| 279 VHITGGPDLTLKEAEGIADNITERLEAS 306
                                       799999*******************976 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.8e-05      0.17      13      43 ..      25      55 ..      14      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.8e-05
                                      HHHHHTSEEEEE--SHHHHHHHHHHHHHTTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 13 qekLrdskvllvGaGglGsellknLalsGvg 43
                                      +++  d ++++vG+Gg G++ +  L  +Gv 
  gi|336253640|ref|YP_004596747.1| 25 DDEFGDPRIVIVGCGGAGNNTVNRLYNIGVD 55
                                      56667789*********************96 PP

>> Csm1_B  Csm1 subunit domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00013      0.48      20      73 ..     214     267 ..     210     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHTT--CCCEEEEETTEEEEEEE--HHHHHHHHHHHHHHHHHCC CS
                            Csm1_B  20 lleeivdelleklelsranllYagGGhfylLlpntekvkekleeiekelnewll 73 
                                       ++e i +  l +l+  +++ +++ GG +++L+ +t++ +++ e +++++n+ ll
  gi|336253640|ref|YP_004596747.1| 214 ISETITQPSLINLDYADMSTIMNQGGVAVMLVGETQDKNKTDEVVKDAMNHPLL 267
                                       67899999999*************************888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); 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: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2927.19
//
Query:       gi|336253641|ref|YP_004596748.1|  [L=132]
Description: hypothetical protein Halxa_2244 [Halopiger xanaduensis SH-6]
Scores for 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   38.8  13.4    0.00064   19.0   3.6    3.3  3  zf-ribbon_3      zinc-ribbon domain
    3.1e-09   36.7   7.3    5.1e-07   29.6   2.7    2.3  2  DZR              Double zinc ribbon
    9.6e-08   31.5  13.1      0.049   13.4   5.1    3.3  3  zinc_ribbon_2    zinc-ribbon domain
    1.8e-06   27.5   7.5      0.064   12.9   0.2    3.7  3  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
    3.2e-06   26.9  10.4      0.098   12.6   0.0    4.3  3  Nudix_N_2        Nudix N-terminal
      7e-05   22.6  10.4       0.24   11.3   1.8    3.3  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.019   15.7  11.1        1.8    9.3   8.3    2.6  2  zinc_ribbon_15   zinc-ribbon family
      0.035   14.1   8.0       0.47   10.5   0.3    3.1  3  zinc-ribbons_6   zinc-ribbons
       0.07   13.5   9.1        4.3    7.8   0.3    3.1  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.073   13.2  11.5        5.4    7.3   0.1    3.4  3  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.11   12.1  10.2        3.9    7.1   0.0    3.3  3  RecR             RecR protein
       0.21   11.2   8.3        1.3    8.7   0.1    3.3  3  zf_C2H2_13       Zinc finger domain
       0.34   10.6  10.7        4.9    6.8   0.1    3.2  3  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
        0.4   10.8  17.2        1.9    8.7   0.7    4.0  5  Zn-ribbon_8      Zinc ribbon domain
       0.52    9.7  13.4       0.21   10.9   2.8    3.3  3  zf-RanBP         Zn-finger in Ran binding protein and others
       0.55   10.3   4.8         32    4.6   0.0    3.2  3  DUF2116          Uncharacterized protein containing a Zn-ribb
        0.6   10.4   7.5        3.5    8.0   0.2    2.9  3  Ribosomal_L32p   Ribosomal L32p protein family
       0.63   10.0   9.0         21    5.2   0.2    4.0  4  zf-dskA_traR     Prokaryotic dksA/traR C4-type zinc finger
       0.89    9.2   6.1       0.61    9.7   0.5    2.4  3  DUF2321          Uncharacterized protein conserved in bacteri
       0.95    9.4  11.9          4    7.4   3.2    3.1  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
        1.1    9.6   7.1         20    5.6   3.6    2.9  2  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain
        2.4    8.6  11.2        9.7    6.7   0.0    4.1  4  zf-IS66          zinc-finger binding domain of transposase IS
        3.4    7.4   7.1        3.4    7.5   0.1    2.9  3  DUF3090          Protein of unknown function (DUF3090)
        4.4    7.3   9.6         20    5.2   0.7    2.4  2  HypA             Hydrogenase/urease nickel incorporation, met
        5.1    7.1  14.7        0.8    9.7   1.7    3.1  3  DUF1610          Domain of unknown function (DUF1610)
        5.2    7.7   8.6         37    4.9   0.2    3.5  3  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
        9.7    6.5  11.0        8.7    6.6   0.5    3.8  4  zf-RING_7        C4-type zinc ribbon domain


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 !   15.3   0.3   1.5e-05    0.0097       3      14 ..      38      49 ..      36      50 .. 0.86
   2 !   10.3   0.1   0.00055      0.37       3      13 ..      69      79 ..      67      80 .. 0.85
   3 !   19.0   3.6   9.6e-07   0.00064       3      25 ..     109     131 ..     108     132 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                       zf-ribbon_3  3 vrCPnCGaplss 14
                                      ++CPnCG+p++s
  gi|336253641|ref|YP_004596748.1| 38 NYCPNCGSPVDS 49
                                      69******9997 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00055
                       zf-ribbon_3  3 vrCPnCGapls 13
                                      ++C+ CGapl+
  gi|336253641|ref|YP_004596748.1| 69 RYCSTCGAPLE 79
                                      79******987 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 9.6e-07
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyCGtk 25 
                                       ++C+ CGa + ++d ++C++C ++
  gi|336253641|ref|YP_004596748.1| 109 TNCSDCGApN-DPDRTTCKHCDAE 131
                                       58******88.**********765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.2    0.0016       1.1      29      40 ..      38      49 ..      23      52 .. 0.68
   2 !   29.6   2.7   7.6e-10   5.1e-07      12      48 ..      68     128 ..      61     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0016
                               DZR 29 drCpsCgekvdp 40
                                      + Cp+Cg++vd+
  gi|336253641|ref|YP_004596748.1| 38 NYCPNCGSPVDS 49
                                      456666666554 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 7.6e-10
                               DZR  12 arfCseCgtklkavaa........................edrCpsCgekvdpearfCpeC 48 
                                        r+Cs+Cg++l++  +                         ++C+ Cg+++dp+ ++C++C
  gi|336253641|ref|YP_004596748.1|  68 VRYCSTCGAPLESFLSlrsrgsdtssvderfetgtdrsgtVTNCSDCGAPNDPDRTTCKHC 128
                                       68*********9877799******************************************* 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   0.3   0.00012     0.082      15      22 ..      39      46 ..      38      50 .. 0.57
   2 !    9.5   0.0    0.0012      0.79      13      23 .]      68      78 ..      65      79 .. 0.83
   3 !   13.4   5.1   7.3e-05     0.049       2      19 ..     111     128 ..     110     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                     zinc_ribbon_2 15 FCpyCGtp 22
                                      +Cp+CG+p
  gi|336253641|ref|YP_004596748.1| 39 YCPNCGSP 46
                                      55555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                     zinc_ribbon_2 13 akFCpyCGtpl 23
                                      +++C+ CG+pl
  gi|336253641|ref|YP_004596748.1| 68 VRYCSTCGAPL 78
                                      68999999987 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 7.3e-05
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyC 19 
                                       C+ CGa+++++ + C +C
  gi|336253641|ref|YP_004596748.1| 111 CSDCGAPNDPDRTTCKHC 128
                                       ****************** 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 !    9.3   0.0    0.0013      0.86       5      13 ..      39      47 ..      38      50 .. 0.86
   2 !   12.9   0.2   9.7e-05     0.064       4      14 ..      69      79 ..      67      80 .. 0.89
   3 !    7.2   1.1    0.0061         4       6      25 ..     111     129 ..     111     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0013
                     zf-NADH-PPase  5 FCgrCGapt 13
                                      +C+ CG+p+
  gi|336253641|ref|YP_004596748.1| 39 YCPNCGSPV 47
                                      9******97 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.7e-05
                     zf-NADH-PPase  4 rFCgrCGapte 14
                                      r+C++CGap e
  gi|336253641|ref|YP_004596748.1| 69 RYCSTCGAPLE 79
                                      9********76 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0061
                     zf-NADH-PPase   6 CgrCGaptepaeggwarvCp 25 
                                       C+ CGap+ p +  ++++C+
  gi|336253641|ref|YP_004596748.1| 111 CSDCGAPNDPDRT-TCKHCD 129
                                       ********99988.777775 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00015     0.098       1      11 [.      38      48 ..      38      57 .. 0.89
   2 !   12.3   0.1   0.00018      0.12       1      11 [.      69      79 ..      69      87 .. 0.90
   3 ?    1.2   4.6      0.54   3.6e+02       3      29 ..     111     129 ..     110     130 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                                      -B-TTT--B-E CS
                         Nudix_N_2  1 kFCsqCGtpve 11
                                      ++C++CG+pv 
  gi|336253641|ref|YP_004596748.1| 38 NYCPNCGSPVD 48
                                      7********96 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00018
                                      -B-TTT--B-E CS
                         Nudix_N_2  1 kFCsqCGtpve 11
                                      ++Cs CG+p+e
  gi|336253641|ref|YP_004596748.1| 69 RYCSTCGAPLE 79
                                      8********98 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.54
                                       -TTT--B-EEE--TT-SS-EEEETTTT CS
                         Nudix_N_2   3 CsqCGtpvelripdgDnreRlvCpaCg 29 
                                       Cs CG+p         +  R +C++C+
  gi|336253641|ref|YP_004596748.1| 111 CSDCGAP--------NDPDRTTCKHCD 129
                                       7777776........345577777775 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 !    7.2   0.2    0.0069       4.6      26      34 ..      38      46 ..      35      49 .. 0.80
   2 !    8.9   0.1    0.0021       1.4       2      19 ..      59      76 ..      58      78 .. 0.86
   3 !   11.3   1.8   0.00035      0.24      14      32 ..     111     129 ..     104     132 .] 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0069
                           DUF35_N 26 avCphCgsd 34
                                      ++Cp+Cgs 
  gi|336253641|ref|YP_004596748.1| 38 NYCPNCGSP 46
                                      579999985 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0021
                           DUF35_N  2 daaaegrLvgqrCpdCGt 19
                                      +a  +g  ++++C+ CG+
  gi|336253641|ref|YP_004596748.1| 59 EADEDGDWRVRYCSTCGA 76
                                      57788999*********8 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00035
                           DUF35_N  14 CpdCGtvqfPPravCphCg 32 
                                       C+dCG+   P r  C hC 
  gi|336253641|ref|YP_004596748.1| 111 CSDCGAPNDPDRTTCKHCD 129
                                       ******************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 ?    6.1   0.7     0.028        19      65      75 ..      37      47 ..      16      53 .. 0.61
   2 ?    9.3   8.3    0.0028       1.8      38      85 ..      69     128 ..      35     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.028
                    zinc_ribbon_15 65 kkeCknCgkev 75
                                       ++C+nCg+ v
  gi|336253641|ref|YP_004596748.1| 37 LNYCPNCGSPV 47
                                      55666666655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0028
                    zinc_ribbon_15  38 lacskCkslleaskelgkeiekkesse............kkeCknCgkeveeefkyCpkC 85 
                                        +cs+C++ le+  +l ++ ++++s++            ++ C++Cg+  +++ + C +C
  gi|336253641|ref|YP_004596748.1|  69 RYCSTCGAPLESFLSLRSRGSDTSSVDerfetgtdrsgtVTNCSDCGAPNDPDRTTCKHC 128
                                       5799999999999988888888888889999***************************** PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3    0.0078       5.2      23      40 ..      31      48 ..      19      50 .. 0.80
   2 ?   10.5   0.3   0.00071      0.47       2      41 ..      39      80 ..      38      84 .. 0.75
   3 ?    5.8   0.8      0.02        14       2      25 ..     110     131 ..      99     132 .] 0.59

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0078
                                      --EEEEEEE-SSS-S--- CS
                    zinc-ribbons_6 23 qedlkkealCpeCeqele 40
                                      ++++   ++Cp+C+++++
  gi|336253641|ref|YP_004596748.1| 31 ERECAALNYCPNCGSPVD 48
                                      567788999****99985 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00071
                                      --SSS-S--EE-S.SEEE-TTT--EEE.EEEE-SSS-S---E CS
                    zinc-ribbons_6  2 kCpeCqqelekrg.eqyhCeaCqedlk.kealCpeCeqelev 41
                                      +Cp+C ++++++g + +  ++ +ed + ++ +C +C+ +le 
  gi|336253641|ref|YP_004596748.1| 39 YCPNCGSPVDSEGfDAIDDSEADEDGDwRVRYCSTCGAPLES 80
                                      8*********66646666666666655367899999999986 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.02
                                       --SSS-S--EE-SSEEE-TTT--E CS
                    zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqed 25 
                                       +C +C ++ + +  +++C++C+++
  gi|336253641|ref|YP_004596748.1| 110 NCSDCGAPNDPD--RTTCKHCDAE 131
                                       355555554433..3566666654 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 ?    7.8   0.3    0.0065       4.3      28      52 ..      37      63 ..      17      68 .. 0.64
   2 ?    5.2   6.9     0.042        28       3      38 ..      37     118 ..      35     131 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0065
                   Lar_restr_allev 28 cvyCadCga..stpwfkiaedeaeaek 52
                                        yC +Cg    +  f  ++d +++e+
  gi|336253641|ref|YP_004596748.1| 37 LNYCPNCGSpvDSEGFDAIDDSEADED 63
                                      678999999885666666666666654 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.042
                   Lar_restr_allev   3 LkpCPfCggravlersqrvvaeigq..............................................cvyCad 33 
                                       L+ CP Cg++   e     + + +                                               + +C d
  gi|336253641|ref|YP_004596748.1|  37 LNYCPNCGSPVDSEGFDAIDDSEADedgdwrvrycstcgaplesflslrsrgsdtssvderfetgtdrsgtVTNCSD 113
                                       56677777776655544444433335677774444444444444444444444455666666666666666666777 PP

                   Lar_restr_allev  34 Cgast 38 
                                       Cga +
  gi|336253641|ref|YP_004596748.1| 114 CGAPN 118
                                       77744 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 ?    7.3   0.1    0.0081       5.4      17      25 ..      39      47 ..      37      51 .. 0.84
   2 ?    5.1   0.1     0.038        25      17      25 ..      70      78 ..      69      81 .. 0.91
   3 ?    4.8   3.3     0.046        31      16      40 .]     109     129 ..     107     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0081
                     Auto_anti-p27 17 tCpvCgvPL 25
                                      +Cp+Cg+P 
  gi|336253641|ref|YP_004596748.1| 39 YCPNCGSPV 47
                                      7*****996 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.038
                     Auto_anti-p27 17 tCpvCgvPL 25
                                      +C++Cg+PL
  gi|336253641|ref|YP_004596748.1| 70 YCSTCGAPL 78
                                      8*******8 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.046
                     Auto_anti-p27  16 etCpvCgvPLmrdrkggkvyCvaCd 40 
                                       ++C++Cg+P   dr    + C  Cd
  gi|336253641|ref|YP_004596748.1| 109 TNCSDCGAPNDPDR----TTCKHCD 129
                                       68*******99976....4788886 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.063        42      15      24 ..      36      45 ..      32      50 .. 0.77
   2 ?    7.1   0.0    0.0059       3.9      15      23 ..      67      75 ..      65      80 .. 0.88
   3 ?    4.8   2.5     0.031        21      15      35 ..     107     129 ..     105     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.063
                                      H-EE-TTT-- CS
                              RecR 15 kvrhCsrCgn 24
                                       + +C++Cg 
  gi|336253641|ref|YP_004596748.1| 36 ALNYCPNCGS 45
                                      5789****96 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0059
                                      H-EE-TTT- CS
                              RecR 15 kvrhCsrCg 23
                                      +vr+Cs Cg
  gi|336253641|ref|YP_004596748.1| 67 RVRYCSTCG 75
                                      69******9 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.031
                                       H-EE-TTT--EESSS..S-CCCC CS
                              RecR  15 kvrhCsrCgnlteed..lCaICs 35 
                                       +v+ Cs Cg   + d   C  C 
  gi|336253641|ref|YP_004596748.1| 107 TVTNCSDCGAPNDPDrtTCKHCD 129
                                       5899******9777644799996 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.6      0.04        27      20      30 ..      40      50 ..      33      55 .. 0.85
   2 ?    8.7   0.1    0.0019       1.3      17      28 ..      68      79 ..      53      82 .. 0.73
   3 ?    1.3   0.3       0.4   2.7e+02      20      26 ..     111     117 ..     109     119 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.04
                        zf_C2H2_13 20 CnkCGkPisle 30
                                      C +CG P+ +e
  gi|336253641|ref|YP_004596748.1| 40 CPNCGSPVDSE 50
                                      9******9876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0019
                        zf_C2H2_13 17 YRvCnkCGkPis 28
                                       R C  CG P+ 
  gi|336253641|ref|YP_004596748.1| 68 VRYCSTCGAPLE 79
                                      466*******96 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.4
                        zf_C2H2_13  20 CnkCGkP 26 
                                       C  CG P
  gi|336253641|ref|YP_004596748.1| 111 CSDCGAP 117
                                       99***99 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 ?    3.6   0.2     0.076        50      12      17 ..      39      44 ..      36      46 .. 0.84
   2 ?    6.8   0.1    0.0074       4.9       9      18 ..      67      76 ..      65      77 .. 0.92
   3 ?    4.6   2.0     0.037        24      11      28 ..     109     126 ..     106     131 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.076
                           zf-tcix 12 kCpkCG 17
                                       Cp+CG
  gi|336253641|ref|YP_004596748.1| 39 YCPNCG 44
                                      5***** PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0074
                           zf-tcix  9 GvrkCpkCGt 18
                                      +vr C++CG+
  gi|336253641|ref|YP_004596748.1| 67 RVRYCSTCGA 76
                                      79*******7 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.037
                           zf-tcix  11 rkCpkCGtyNGtRglsCk 28 
                                         C+ CG+ N      Ck
  gi|336253641|ref|YP_004596748.1| 109 TNCSDCGAPNDPDRTTCK 126
                                       57******9965555565 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.7    0.0029       1.9      25      36 ..      36      47 ..      21      50 .. 0.73
   2 ?    4.0   0.1     0.085        57      28      37 ..      69      79 ..      48      82 .. 0.67
   3 ?    3.8   0.1     0.093        62       8      17 ..      71      80 ..      65      92 .. 0.68
   4 ?    3.8   0.3     0.099        65      26      34 ..     107     116 ..      93     119 .. 0.63
   5 ?    1.9   6.1      0.38   2.5e+02       8      34 ..     111     130 ..     110     132 .] 0.68

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0029
                       Zn-ribbon_8 25 pltaCPeCgsev 36
                                      +l  CP+Cgs+v
  gi|336253641|ref|YP_004596748.1| 36 ALNYCPNCGSPV 47
                                      3455*****987 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.085
                       Zn-ribbon_8 28 a.CPeCgsevr 37
                                        C +Cg++++
  gi|336253641|ref|YP_004596748.1| 69 RyCSTCGAPLE 79
                                      44888887664 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.093
                       Zn-ribbon_8  8 CeeCghefev 17
                                      C  Cg   e 
  gi|336253641|ref|YP_004596748.1| 71 CSTCGAPLES 80
                                      6666666664 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.099
                       Zn-ribbon_8  26 lta.CPeCgs 34 
                                        ++ C +Cg+
  gi|336253641|ref|YP_004596748.1| 107 TVTnCSDCGA 116
                                       3445999997 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.38
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgs 34 
                                       C +Cg          d++ t+C++C +
  gi|336253641|ref|YP_004596748.1| 111 CSDCGAPN-------DPDRTTCKHCDA 130
                                       77777333.......566788****87 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 ?    1.9   0.7      0.22   1.5e+02      16      27 ..      35      46 ..      34      47 .. 0.84
   2 ?    2.9   0.1       0.1        70      20      27 ..      70      77 ..      64      80 .. 0.75
   3 ?   10.9   2.8   0.00032      0.21       6      26 ..     110     130 ..     110     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.22
                                      SSSSB-TTT--B CS
                          zf-RanBP 16 awstkCvaCqap 27
                                      a  ++C +C++p
  gi|336253641|ref|YP_004596748.1| 35 AALNYCPNCGSP 46
                                      67899*9**998 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.1
                                      B-TTT--B CS
                          zf-RanBP 20 kCvaCqap 27
                                      +C  C+ap
  gi|336253641|ref|YP_004596748.1| 70 YCSTCGAP 77
                                      57777776 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00032
                                       E-SSS--EEESSSSB-TTT-- CS
                          zf-RanBP   6 dCskClvqNfawstkCvaCqa 26 
                                       +Cs C++ N + +t+C  C+a
  gi|336253641|ref|YP_004596748.1| 110 NCSDCGAPNDPDRTTCKHCDA 130
                                       5******************98 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 ?    4.6   0.0     0.049        32       5      16 ..      39      50 ..      36      52 .. 0.87
   2 ?    2.0   0.0      0.31   2.1e+02       4      14 ..      69      79 ..      68      84 .. 0.86
   3 ?    3.2   1.2      0.13        86       6      24 ..     111     128 ..     109     132 .] 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.049
                           DUF2116  5 HCivCGkaIpld 16
                                       C++CG +++++
  gi|336253641|ref|YP_004596748.1| 39 YCPNCGSPVDSE 50
                                      6*******9876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.31
                           DUF2116  4 kHCivCGkaIp 14
                                      + C  CG++ +
  gi|336253641|ref|YP_004596748.1| 69 RYCSTCGAPLE 79
                                      68******987 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.13
                           DUF2116   6 CivCGkaIpldesfCsekC 24 
                                       C  CG++ ++d  +C  +C
  gi|336253641|ref|YP_004596748.1| 111 CSDCGAPNDPDRTTCK-HC 128
                                       999************6.45 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0052       3.5      15      35 ..      24      46 ..      18      48 .. 0.66
   2 ?   -0.1   0.1       1.7   1.1e+03      28      35 ..      70      77 ..      67      79 .. 0.79
   3 ?    5.0   0.6     0.044        29      25      45 ..     107     128 ..     102     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0052
                                      HGGGT..------EEEETTTCCE CS
                    Ribosomal_L32p 15 Rrahw..klkapnlvecpncgel 35
                                      Rr      ++ ++l+ cpncg++
  gi|336253641|ref|YP_004596748.1| 24 RREWSeaERECAALNYCPNCGSP 46
                                      33333334555699*******87 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.7
                                      EETTTCCE CS
                    Ribosomal_L32p 28 ecpncgel 35
                                       c++cg++
  gi|336253641|ref|YP_004596748.1| 70 YCSTCGAP 77
                                      59999986 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.044
                                       -EEEETTTCCEECT.TC-BTTT CS
                    Ribosomal_L32p  25 nlvecpncgelklp.Hrvcpsc 45 
                                       ++++c+ cg++  p ++ c++c
  gi|336253641|ref|YP_004596748.1| 107 TVTNCSDCGAPNDPdRTTCKHC 128
                                       6789*******98845578888 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 ?    3.2   0.1      0.13        84       4      13 ..      38      47 ..      36      50 .. 0.83
   2 ?    4.4   0.1     0.055        36       4      12 ..      69      77 ..      67      79 .. 0.82
   3 ?    5.2   0.2     0.031        21       2      12 ..     107     117 ..     104     117 .. 0.72
   4 ?    0.1   0.1       1.2     8e+02      22      30 ..     120     128 ..     118     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.13
                      zf-dskA_traR  4 gsCeeCGEpI 13
                                       +C  CG p+
  gi|336253641|ref|YP_004596748.1| 38 NYCPNCGSPV 47
                                      57*****887 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.055
                      zf-dskA_traR  4 gsCeeCGEp 12
                                      ++C++CG p
  gi|336253641|ref|YP_004596748.1| 69 RYCSTCGAP 77
                                      78*****76 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.031
                      zf-dskA_traR   2 iygsCeeCGEp 12 
                                       +   C++CG p
  gi|336253641|ref|YP_004596748.1| 107 TVTNCSDCGAP 117
                                       4445*****76 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.2
                      zf-dskA_traR  22 PgarlCveC 30 
                                       P+++ C+ C
  gi|336253641|ref|YP_004596748.1| 120 PDRTTCKHC 128
                                       778888888 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 ?    9.7   0.5   0.00092      0.61      35      75 ..      35      77 ..      19      80 .. 0.75
   2 ?    6.0   0.2     0.013       8.7      17      74 ..      59     116 ..      47     118 .. 0.64
   3 ?    1.5   0.9       0.3     2e+02      27      45 ..     109     130 ..      91     132 .] 0.67

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00092
                           DUF2321 35 ktitkcpkCstei..rGkyyvegvislgkeyevpsyCkkCgkp 75
                                      + ++ cp+C++++  +G + ++++    +     +yC++Cg p
  gi|336253641|ref|YP_004596748.1| 35 AALNYCPNCGSPVdsEGFDAIDDSEADEDGDWRVRYCSTCGAP 77
                                      457889***99985569999999866555444558*****987 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.013
                           DUF2321  17 svnkkeelveeyCekcGektitkcpkCsteirGkyyvegvislgk.eyevpsyCkkCgk 74 
                                        ++++ + +  yC+ cG+ + +++ + +++   +  v++    g+ +  + + C+ Cg 
  gi|336253641|ref|YP_004596748.1|  59 EADEDGDWRVRYCSTCGAPL-ESFLSLRSRGSDTSSVDERFETGTdRSGTVTNCSDCGA 116
                                       45556666778999999874.55555566555566677766666545555666777776 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.3
                           DUF2321  27 eyCekcGekt...itkcpkCst 45 
                                         C++cG+      t+c++C++
  gi|336253641|ref|YP_004596748.1| 109 TNCSDCGAPNdpdRTTCKHCDA 130
                                       4588888764222567777765 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 ?    4.6   2.2     0.046        31      30      54 ..      39      76 ..      17      79 .. 0.74
   2 ?    2.7   0.1      0.18   1.2e+02      30      42 ..      70      84 ..      68      99 .. 0.77
   3 ?    7.4   3.2     0.006         4      23      55 ..     103     131 ..      85     132 .] 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.046
                    OrfB_Zn_ribbon 30 tCseCgsknke.............alsgrtfkCpnCgf 54
                                       C++Cgs ++              + ++r+ +C+ Cg+
  gi|336253641|ref|YP_004596748.1| 39 YCPNCGSPVDSegfdaiddseadeDGDWRVRYCSTCGA 76
                                      69999998887788888777776666777777888875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.18
                    OrfB_Zn_ribbon 30 tCseCgsknke..al 42
                                       Cs Cg+ ++   +l
  gi|336253641|ref|YP_004596748.1| 70 YCSTCGAPLESflSL 84
                                      69****998885544 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.006
                    OrfB_Zn_ribbon  23 npayTSktCseCgsknkealsgrtfkCpnCgfe 55 
                                       +++ T ++Cs Cg+ n++    ++ +C++C +e
  gi|336253641|ref|YP_004596748.1| 103 DRSGTVTNCSDCGAPNDP----DRTTCKHCDAE 131
                                       45668899******9999....88899999865 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 ?   -0.2   0.1       1.9   1.2e+03      46      53 ..      38      45 ..      19      49 .. 0.81
   2 ?    5.6   3.6      0.03        20      42      90 .]      65     115 ..      54     128 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.9
                                      TB-TTT-- CS
                              Rpr2 46 tvCkkCgs 53
                                       +C +Cgs
  gi|336253641|ref|YP_004596748.1| 38 NYCPNCGS 45
                                      57888887 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.03
                                       TCCCTB-TTT--B--CTTTEEEEEE-SSS-E.............EEEEETTTT CS
                              Rpr2  42 svkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkka....dvlvvtClaCg 90 
                                       +++ ++C++Cg+ l + ++ + r   +s+ +++ +  +    +  v++C  Cg
  gi|336253641|ref|YP_004596748.1|  65 DWRVRYCSTCGAPLESFLSLRSRGSDTSSVDERFETGTdrsgT--VTNCSDCG 115
                                       567789*******999999999997766655444433355441..45666664 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 ?    6.7   0.0     0.015       9.7       3      17 ..      39      53 ..      38      59 .. 0.82
   2 ?    3.0   0.0      0.21   1.4e+02       3      11 ..      70      78 ..      69      98 .. 0.81
   3 ?    2.7   0.6      0.27   1.8e+02       2       9 ..     109     116 ..     109     124 .. 0.80
   4 ?   -0.0   0.9       1.8   1.2e+03      41      45 ..     124     128 ..     121     129 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.015
                           zf-IS66  3 tCpcCGgllkpiged 17
                                       Cp+CG++++  g d
  gi|336253641|ref|YP_004596748.1| 39 YCPNCGSPVDSEGFD 53
                                      5*****987888777 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.21
                           zf-IS66  3 tCpcCGgll 11
                                       C+ CG++l
  gi|336253641|ref|YP_004596748.1| 70 YCSTCGAPL 78
                                      7999*9943 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.27
                           zf-IS66   2 rtCpcCGg 9  
                                       ++C++CG+
  gi|336253641|ref|YP_004596748.1| 109 TNCSDCGA 116
                                       58*****8 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 1.8
                           zf-IS66  41 aCpcC 45 
                                       +C++C
  gi|336253641|ref|YP_004596748.1| 124 TCKHC 128
                                       68888 PP

>> DUF3090  Protein of unknown function (DUF3090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0051       3.4     155     168 ..      38      51 ..      22      53 .. 0.88
   2 ?    0.1   0.1       0.9   5.9e+02     156     165 ..      70      79 ..      67      81 .. 0.87
   3 ?    2.2   0.6      0.22   1.4e+02     156     171 .]     110     125 ..     104     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0051
                           DUF3090 155 psCplCgqPldpeg 168
                                       + Cp+Cg+P+d eg
  gi|336253641|ref|YP_004596748.1|  38 NYCPNCGSPVDSEG 51 
                                       68*********998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.9
                           DUF3090 156 sCplCgqPld 165
                                        C++Cg+Pl+
  gi|336253641|ref|YP_004596748.1|  70 YCSTCGAPLE 79 
                                       7*******97 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.22
                           DUF3090 156 sCplCgqPldpegHlC 171
                                       +C+ Cg+P dp+  +C
  gi|336253641|ref|YP_004596748.1| 110 NCSDCGAPNDPDRTTC 125
                                       7**********98777 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   0.7      0.03        20      70      94 ..      37      76 ..      19      84 .. 0.68
   2 ?    3.1   6.0      0.14        91      68      94 ..     106     130 ..      68     132 .] 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.03
                                      EEEETTTS-EEECHH.HHH..............S-TTTSS CS
                              HypA 70 kvrCreCgkefelee.kal..............rCpkCgs 94
                                        +C +Cg+ +++e  +a+               C +Cg+
  gi|336253641|ref|YP_004596748.1| 37 LNYCPNCGSPVDSEGfDAIddseadedgdwrvrYCSTCGA 76
                                      4467777777776653222556677777777777777776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.14
                                       --EEEETTTS-EEECHHHHHS-TTTSS CS
                              HypA  68 pvkvrCreCgkefeleekalrCpkCgs 94 
                                         ++ C++Cg+  + +  +++C++C++
  gi|336253641|ref|YP_004596748.1| 106 GTVTNCSDCGAPNDPD--RTTCKHCDA 130
                                       56789*****888776..458****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   1.7    0.0012       0.8      15      23 ..      36      44 ..      30      45 .. 0.71
   2 ?    6.1   0.4     0.016        11       1       8 [.      71      78 ..      71      79 .. 0.94
   3 ?   -1.3   0.7       3.3   2.2e+03       1       7 [.     111     117 ..     111     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                           DUF1610 15 vvFpCPNCG 23
                                         +CPNCG
  gi|336253641|ref|YP_004596748.1| 36 ALNYCPNCG 44
                                      5559****9 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
                           DUF1610  1 CtSCGael 8 
                                      C++CGa+l
  gi|336253641|ref|YP_004596748.1| 71 CSTCGAPL 78
                                      ******98 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.3
                           DUF1610   1 CtSCGae 7  
                                       C+ CGa+
  gi|336253641|ref|YP_004596748.1| 111 CSDCGAP 117
                                       8889985 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 ?    4.5   0.0     0.077        51       7      14 ..      39      46 ..      35      50 .. 0.87
   2 ?    4.9   0.2     0.056        37       7      18 ..      70      85 ..      68     112 .. 0.64
   3 ?   -0.2   3.1       2.3   1.5e+03       8      14 ..     111     117 ..     105     132 .] 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.077
                   Zn_ribbon_recom  7 rCgeCGsp 14
                                      +C +CGsp
  gi|336253641|ref|YP_004596748.1| 39 YCPNCGSP 46
                                      9******8 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.056
                   Zn_ribbon_recom  7 rCgeCGspmtr....r 18
                                      +C  CG+p+      r
  gi|336253641|ref|YP_004596748.1| 70 YCSTCGAPLESflslR 85
                                      8*******86544434 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.3
                   Zn_ribbon_recom   8 CgeCGsp 14 
                                       C +CG+p
  gi|336253641|ref|YP_004596748.1| 111 CSDCGAP 117
                                       9999987 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 ?    6.6   0.5     0.013       8.7      23      30 ..      37      44 ..      24      45 .. 0.77
   2 ?    1.7   0.0      0.46     3e+02      23      31 ..      68      76 ..      47      76 .. 0.70
   3 ?    2.9   0.1      0.19   1.3e+02      20      31 ..     105     116 ..      94     116 .. 0.85
   4 ?   -0.2   0.2       1.8   1.2e+03      25      30 ..     124     129 ..     122     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
                                      -EE-TTT- CS
                         zf-RING_7 23 vvtCpeCG 30
                                      + +Cp+CG
  gi|336253641|ref|YP_004596748.1| 37 LNYCPNCG 44
                                      569****9 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.46
                                      -EE-TTT-- CS
                         zf-RING_7 23 vvtCpeCGR 31
                                      v +C  CG+
  gi|336253641|ref|YP_004596748.1| 68 VRYCSTCGA 76
                                      779999*95 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.19
                                       STB-EE-TTT-- CS
                         zf-RING_7  20 gdevvtCpeCGR 31 
                                        + v  C  CG+
  gi|336253641|ref|YP_004596748.1| 105 SGTVTNCSDCGA 116
                                       46799*****96 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.8
                                       E-TTT- CS
                         zf-RING_7  25 tCpeCG 30 
                                       tC +C 
  gi|336253641|ref|YP_004596748.1| 124 TCKHCD 129
                                       9****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 894.84
//
Query:       gi|336253642|ref|YP_004596749.1|  [L=321]
Description: hypothetical protein Halxa_2245 [Halopiger xanaduensis SH-6]
Scores for complete 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-12   47.4   0.0    2.6e-12   46.8   0.0    1.3  1  ATP_bind_3     PP-loop family
    3.5e-05   23.9   0.0    5.9e-05   23.2   0.0    1.3  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
    8.9e-05   21.9   3.3    8.9e-05   21.9   3.3    3.0  4  zn-ribbon_14   Zinc-ribbon
     0.0015   17.7   0.0     0.0026   16.9   0.0    1.4  1  NAD_synthase   NAD synthase
  ------ inclusion threshold ------
      0.037   13.6   2.1      0.037   13.6   2.1    3.2  4  RecR           RecR protein
      0.055   12.3   0.0       0.08   11.7   0.0    1.3  1  tRNA_Me_trans  tRNA methyl transferase
        0.2   11.2   0.0       0.37   10.4   0.0    1.4  1  ThiI           Thiamine biosynthesis protein (ThiI)
        1.6    8.3   5.5         15    5.1   0.2    3.0  2  zf-ribbon_3    zinc-ribbon domain


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 !   46.8   0.0   1.2e-15   2.6e-12       2     123 ..      56     189 ..      55     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.2e-15
                                       EEEE--SCHHHHHHHHHHHHHCTTTTT.EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H......... CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgi.klvaihvdhglreeskeeaelvkelckklnikleiekvdv......... 68 
                                       +++++SgG DS++L+++l++   +    +lv ++++ g+    ++  +++ el + l+i++e  +            
  gi|336253642|ref|YP_004596749.1|  56 WVIGLSGGKDSVVLTQILHDTFAEDPRiELVGLTIHEGIEGYRDKSVDACVELTDDLEIRHELVSYAEefgvrmddv 132
                                       689***************9987766555*********************************9998888888899877 PP

                                       ..HHCTTSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--C CS
                        ATP_bind_3  69 ..akkkgknleeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsgl 123
                                         +  ++    +    +R ++l++++ ++g+++ll++h+ dD a t+l+++  g   
  gi|336253642|ref|YP_004596749.1| 133 veDDPENMAACAYCGVFRRDILERYADEYGADLLLTGHNLDDEAQTALMNFLEGDVA 189
                                       54333344444455689*********************************9998766 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.6e-08   5.9e-05       3     156 ..      57     238 ..      55     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.6e-08
                                       EEE--SSCTCHHHHHHHHHHCTTH.......EEEEEE-STB-HHHHHHHHHHHHHTT-E..EEEEE-SCHHHHHHHH CS
                       PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpv.......pvvfvdtghefpetiefvdeleeryglr..lkvyepeeevaekina 70 
                                       v+  sgGkds+Vl +++  +f +         +++   +   ++ ++   el++ +++r  l  y +e +v+   + 
  gi|336253642|ref|YP_004596749.1|  57 VIGLSGGKDSVVLTQILHDTFAEDprielvgLTIHEGIEGYRDKSVDACVELTDDLEIRheLVSYAEEFGVRMDDVV 133
                                       6678******************9755677666777777777777777777888888777556667777777888888 PP

                                       HH-S-THHHCHHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S.................. CS
                       PAPS_reduct  71 ekhgsslyeeaaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek.................. 129
                                       e+ +++    a++ + + + l++  +++++d+lltG   d++++ a ++++e d ++ +                  
  gi|336253642|ref|YP_004596749.1| 134 EDDPENMAACAYCGVFRRDILERYADEYGADLLLTGHNLDDEAQTALMNFLEGDVAQIAkhfdaslgplseredqdd 210
                                       8888888888*******************************************999777899*************** PP

                                       .CEEE-CCCT--HHHHHHHHHHCT--B- CS
                       PAPS_reduct 130 .slrvfPllnWteedvwqyilrenipyn 156
                                          r  Pl +  e++v  y+  +++p +
  gi|336253642|ref|YP_004596749.1| 211 fIPRAKPLRDVPEKEVALYAHLNDLPAH 238
                                       777999****************999965 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.4      0.68   1.5e+03       2       7 ..       2       7 ..       1       7 [. 0.81
   2 ?   -3.7   0.4       3.9   8.8e+03       3       7 ..     143     147 ..     142     148 .. 0.79
   3 ?   -0.4   0.0      0.37   8.2e+02      20      30 ..     256     266 ..     255     268 .. 0.87
   4 !   21.9   3.3     4e-08   8.9e-05       1      24 [.     297     320 ..     297     321 .] 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.68
                      zn-ribbon_14 2 kCerCG 7
                                      C+rC+
  gi|336253642|ref|YP_004596749.1| 2 DCNRCD 7
                                     6****5 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.9
                      zn-ribbon_14   3 CerCG 7  
                                       C  CG
  gi|336253642|ref|YP_004596749.1| 143 CAYCG 147
                                       99998 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.37
                      zn-ribbon_14  20 LLegLnkgrpk 30 
                                       LL +L+ ++p 
  gi|336253642|ref|YP_004596749.1| 256 LLYDLEENHPG 266
                                       999******96 PP

  == domain 4  score: 21.9 bits;  conditional E-value: 4e-08
                      zn-ribbon_14   1 gkCerCGylSSqkiCkACvLLegL 24 
                                       + Ce+CG ++   +C+ C LLe+L
  gi|336253642|ref|YP_004596749.1| 297 QECEQCGSMTTRNVCRKCSLLETL 320
                                       68********************98 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.2e-06    0.0026      19     130 ..      54     171 ..      39     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                                       SEEEEEE-SSHHHHHHHHHHHHHH...TCGEEEEEE--..SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHH CS
                      NAD_synthase  19 kgvvlGlSGGvDSslvaalavkal...gkenvlalllP..ssvsseedvedalalaenlgievktidikpivrafeq 90 
                                       +  v+GlSGG DS +  ++  + +    + + ++l +    +   +++v + ++l ++l+i+ + ++ ++   +  +
  gi|336253642|ref|YP_004596749.1|  54 ETWVIGLSGGKDSVVLTQILHDTFaedPRIELVGLTIHegIEGYRDKSVDACVELTDDLEIRHELVSYAEEFGVRMD 130
                                       5689********************43333456788887422334678889999*************99888776555 PP

                                       .HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BH CS
                      NAD_synthase  91 .elkeakedlakgNlkaRiRmailyaianklnllvlgTgnk 130
                                         ++++ e++a+   +   R  il  +a++++  +l Tg++
  gi|336253642|ref|YP_004596749.1| 131 dVVEDDPENMAACAYCGVFRRDILERYADEYGADLLLTGHN 171
                                       2777778*****************99999998877777775 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.9       4.3   9.6e+03      31      36 ..       3       8 ..       2       9 .. 0.58
   2 ?   -0.4   0.1      0.38   8.6e+02      17      38 ..     141     150 ..     134     152 .. 0.55
   3 ?   -1.4   0.0       0.8   1.8e+03       6      20 ..     229     243 ..     227     244 .. 0.81
   4 ?   13.6   2.1   1.7e-05     0.037      16      35 ..     296     315 ..     294     316 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.3
                                      -CCCCS CS
                              RecR 31 CaICsd 36
                                      C+ C d
  gi|336253642|ref|YP_004596749.1|  3 CNRCDD 8 
                                      555655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.38
                                       EE-TTT--EESSSS-CCCCSTT CS
                              RecR  17 rhCsrCgnlteedlCaICsdpr 38 
                                         C  Cg              r
  gi|336253642|ref|YP_004596749.1| 141 AACAYCG------------VFR 150
                                       4455555............444 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.8
                                       HHHHHHHHHH-EE-T CS
                              RecR   6 aeaLqeakekvrhCs 20 
                                          L+++  +++ C+
  gi|336253642|ref|YP_004596749.1| 229 YAHLNDLPAHITECP 243
                                       567899999*****7 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 1.7e-05
                                       -EE-TTT--EESSSS-CCCC CS
                              RecR  16 vrhCsrCgnlteedlCaICs 35 
                                       ++ C++Cg +t++++C+ Cs
  gi|336253642|ref|YP_004596749.1| 296 LQECEQCGSMTTRNVCRKCS 315
                                       689****************7 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.6e-05      0.08       4     124 ..      57     170 ..      54     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                     tRNA_Me_trans   4 vvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfe 80 
                                       v++lSgG DS v   +l++ + e  ++ l   + ++  g e   ++ +    +  + l+i++e v++++e+  ++ +
  gi|336253642|ref|YP_004596749.1|  57 VIGLSGGKDSVVLTQILHDTFAEDPRIELVGLTIHE--GIEGYRDKSVDACVELTDDLEIRHELVSYAEEFGVRM-D 130
                                       789******************999999887776633..334677888999999******************7664.4 PP

                     tRNA_Me_trans  81 efleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGH 124
                                       +++e+  e      ++ C    + + l ++a+e  gad l tGH
  gi|336253642|ref|YP_004596749.1| 131 DVVEDDPE--NMAACAYCGV-FRRDILERYADE-YGADLLLTGH 170
                                       44443222..2234555543.233444444444.7777777777 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00016      0.37      10     129 ..      60     183 ..      53     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                              ThiI  10 lSgGiDSpVaayll...lkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekv 83 
                                       lSgG DS V + +l   +    r++lv l+ + g +    + v   +el  + +  +e+  ++ +f   +++++e  
  gi|336253642|ref|YP_004596749.1|  60 LSGGKDSVVLTQILhdtFAEDPRIELVGLTIHEGIEGYRDKSVDACVELTDDLEIRHELVSYAEEFGVRMDDVVEDD 136
                                       7888888888776522234555788888877777777788888899999999998888888888999999******9 PP

                              ThiI  84 kekltivllkrkmlr.iAekvaeeegakalvtGesLgqVaSqtleNl 129
                                       +e++    +   + r i e++a+e+ga+ l+tG +L   a   l N 
  gi|336253642|ref|YP_004596749.1| 137 PENMAACAYCGVFRRdILERYADEYGADLLLTGHNLDDEAQTALMNF 183
                                       999976665555554499******************99888888775 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2    0.0068        15      17      24 ..     141     148 ..     138     149 .. 0.81
   2 ?    3.7   1.3     0.019        43       3      22 ..     297     314 ..     296     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0068
                       zf-ribbon_3  17 nvCpyCGt 24 
                                        +C+yCG 
  gi|336253642|ref|YP_004596749.1| 141 AACAYCGV 148
                                       68*****5 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.019
                       zf-ribbon_3   3 vrCPnCGaplssddnvCpyC 22 
                                       ++C +CG+   +  nvC +C
  gi|336253642|ref|YP_004596749.1| 297 QECEQCGSM--TTRNVCRKC 314
                                       5899****8..678999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2388.88
//
Query:       gi|336253643|ref|YP_004596750.1|  [L=247]
Description: hypothetical protein Halxa_2246 [Halopiger xanaduensis SH-6]
Scores for 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  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); 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:                         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: 00:00:00.41
# Mc/sec: 1787.71
//
Query:       gi|336253644|ref|YP_004596751.1|  [L=244]
Description: hypothetical protein Halxa_2247 [Halopiger xanaduensis SH-6]
Scores for complete 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   26.2   5.0    1.4e-05   25.8   5.0    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family
     0.0007   19.4   0.0    0.00084   19.1   0.0    1.2  1  Abhydrolase_5  Alpha/beta hydrolase family


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   5.0   1.6e-09   1.4e-05       3     173 ..      16     173 ..      14     235 .. 0.50

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.6e-09
                                       EE--GC.....G.C..HHHH.HHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT..TTSEEEEEETCH CS
                     Abhydrolase_6   3 llHGagssassW.l..vapL.aallaagvhvlapDlpGhGrsdpppldledladlaalldelaagggpvvlvGHSlG 75 
                                       ++ G g     W +  v+ L  +l  ag++v+a+ lp +   d+   d+  l+ +a+++ +l        l+GHS G
  gi|336253644|ref|YP_004596751.1|  16 FVMGWGN---RWtHenVSWLiGKLTDAGYRVHAFELPTN--IDDFKADW--LEPIAEYVLDL----EGYQLLGHSAG 81 
                                       5555331...244244555535556666999******99..57777888..77776666666....34567****** PP

                                       HHHHHHHHHCC...EEEEES-....................----TTT....S----TTHHHHHHTT-CCCCHCCHS CS
                     Abhydrolase_6  76 Galalaaapla.lvvgvlldp..................pptalpagl....laaalelllallallrllawlsrep 129
                                       +++a+a   l   +  v+l+p                   pt++p++      + al   ++  +l++l++w+s   
  gi|336253644|ref|YP_004596751.1|  82 ALVAQA---LDgADNHVYLSPwwgysnaypdlalegvsqVPTTFPFLPvgemDRSALGEKATDHQLATLPRWVS--- 152
                                       ******...7754455*****66655554444433333211222222222223333333333333444466665... PP

                                       -HSCCCCHHH.CCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGC CS
                     Abhydrolase_6 130 lprlfladed.adaawrarlarlaallaglgllpaaawadlpvpl 173
                                         + f++++  a++                      ++ ++    
  gi|336253644|ref|YP_004596751.1| 153 --PAFVRETRhAQE----------------------ELLAIDHDA 173
                                       ..344444442122......................222222222 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.4e-08   0.00084      11      79 ..      25      93 ..      15     163 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.4e-08
                     Abhydrolase_5 11 eaesYaelaeklaksGyevvlvklPlnlavlgknkaeeiikeapklekfvvgGhslGGvvasrfaaeee 79
                                        e  + l  kl+++Gy v   +lP n+  +  +  e i +   +le + + Ghs G  va  +   ++
  gi|336253644|ref|YP_004596751.1| 25 THENVSWLIGKLTDAGYRVHAFELPTNIDDFKADWLEPIAEYVLDLEGYQLLGHSAGALVAQALDGADN 93
                                      5667788999***********************************************999877654433 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:                      355  (0.0198003); 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 0.20s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1889.34
//
Query:       gi|336253645|ref|YP_004596752.1|  [L=231]
Description: hypothetical protein Halxa_2248 [Halopiger xanaduensis SH-6]
Scores for 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  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1935.63
//
Query:       gi|336253646|ref|YP_004596753.1|  [L=132]
Description: hypothetical protein Halxa_2249 [Halopiger xanaduensis SH-6]
Scores for 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   21.1   3.0    0.00043   20.3   0.6    2.4  2  HTH_20         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.028   13.9   0.0      0.031   13.8   0.0    1.1  1  Exo_endo_phos  Endonuclease/Exonuclease/phosphatase 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 !   20.3   0.6   4.8e-08   0.00043       4      60 ..      18      96 ..      15      97 .. 0.75
   2 ?   -3.0   0.1      0.91   8.2e+03       5      13 ..     107     115 ..     103     120 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.8e-08
                                      HHHHS-HHHHHHHHHH..STCTTB-HHHHHHHH.T..............S-HHHH.....HHHHHHHHHCTTEEEECTE CS
                            HTH_20  4 aeALahPvRrrilraL..araegltaselaerl.d..............lskntl.....syHLrvLeeagLvevvreg 60
                                      ++AL++P Rr+++r+   ++a+ + ++el + l d              +s++tl     ++HL +L+eag ve  r++
  gi|336253646|ref|YP_004596753.1| 18 FDALSDPYRRALCRYVlrTDADIVAFEELVDYLaDeataaigtegeeedCSRQTLetdlhHRHLPALAEAGVVEYDRHS 96
                                      89**************9966666666666666651333444444444459999997777779************99975 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.91
                                       HHHS-HHHH CS
                            HTH_20   5 eALahPvRr 13 
                                        AL+++v++
  gi|336253646|ref|YP_004596753.1| 107 AALLERVQA 115
                                       455555554 PP

>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.5e-06     0.031      10      84 ..      18     106 ..       5     129 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-06
                                       HHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHH........TTCEEEEECCH.......ECSSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxx.......xxxxxxx RF
                     Exo_endo_phos  10 spalgssrrsdrladlltaydaDvlgLQEvdddelsriplllal........ggflgasstsp.......tgggggg 71 
                                       ++al++++r + l   + ++daD++++ E+ d+ +++  ++           +++l ++ + +        g + + 
  gi|336253646|ref|YP_004596753.1|  18 FDALSDPYRRA-LCRYVLRTDADIVAFEELVDYLADEATAAIGTegeeedcsRQTLETDLHHRhlpalaeAGVVEYD 93 
                                       56777777777.8888889**************99998888865655555552222222222255556665556666 PP

                                       SSEEEEEECSTEE CS
                                       xxxxxxxxxxxxx RF
                     Exo_endo_phos  72 gnggavlsrfplt 84 
                                       ++ gav+  +  t
  gi|336253646|ref|YP_004596753.1|  94 RHSGAVYLDRAAT 106
                                       6666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1014.06
//
Query:       gi|336253647|ref|YP_004596754.1|  [L=230]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-14   53.3   0.0    2.8e-14   52.6   0.0    1.3  1  HTH_10    HTH DNA binding domain
    2.9e-09   37.0   2.4    4.3e-09   36.4   2.4    1.2  1  BAT       GAF and HTH_10 associated domain


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 !   52.6   0.0   3.1e-18   2.8e-14       1      53 []     168     220 ..     168     220 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 3.1e-18
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LT  q+e+l +A+++GY d PR ++l+eLA++++Is +++se+ r+  ++lie
  gi|336253647|ref|YP_004596754.1| 168 LTASQRETLVAAVDAGYLDIPRACSLAELADRFDISSNAASERFRRGVRTLIE 220
                                       9*********************************************9999985 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   2.4   4.8e-13   4.3e-09      19     145 ..      16     148 ..      11     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 4.8e-13
                               BAT  19 alaaeldcrveleglvprsdgevlvfftvdgad..peevrdaaedldavedvrvvseeddgtlleltvs....gpsl 89 
                                       +l+++ d+ v+ e++  ++dg  +++++vdg+d   +++ da+e+ ++v++   v + d++ l+ l+++     +s+
  gi|336253647|ref|YP_004596754.1|  16 TLSHAPDAIVTWEQSDLTGDGAHRMLVWVDGDDdaIAAFDDALEADPTVAEPLRVVDFDERRLYHLELTceghRESV 92 
                                       5899***************************6633778***********9988888888888888887766778999 PP

                               BAT  90 astlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrere 145
                                          ++e Gg++++++a+ +++ ++v +P+ +   ++ e + er  dve+++   ++
  gi|336253647|ref|YP_004596754.1|  93 YPIVVEGGGVLQDVTATAEGWFFRVAFPSAETFGRFHEFFVERDLDVEVRQLYDVS 148
                                       99**********************************************99866665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1834.38
//
Query:       gi|336253648|ref|YP_004596755.1|  [L=264]
Description: hypothetical protein Halxa_2251 [Halopiger xanaduensis SH-6]
Scores for 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-14   52.2  16.8      1e-13   51.2  16.8    1.5  1  ABC2_membrane_2  ABC-2 family transporter protein
    1.1e-06   28.1   6.7    1.1e-06   28.1   6.7    1.6  1  ABC2_membrane_3  ABC-2 family transporter protein
    3.4e-05   23.5   4.9    3.4e-05   23.5   4.9    1.9  2  ABC2_membrane_5  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.054   12.9  12.5      0.009   15.5   8.5    1.7  1  ABC2_membrane    ABC-2 type transporter
        2.3    8.2  11.0          1    9.3   8.0    2.0  2  ABC2_membrane_4  ABC-2 family transporter protein


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 !   51.2  16.8   2.8e-17     1e-13      77     288 .]      77     263 ..       4     263 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 2.8e-17
                   ABC2_membrane_2  77 vstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalg 153
                                       +    +++++++ a ++a  iag+ e g + +lLs PvsR+  ++ Kf + ++    i+v   ++ ++  +  + + 
  gi|336253648|ref|YP_004596755.1|  77 YIFGWTIMLGLYLAYLAAGTIAGDVEHGRMDILLSMPVSRARTVAEKFASLAVP---IVVVNAVVPVVVYVAAALVD 150
                                       6666789999*******************************************9...55555555556666788888 PP

                   ABC2_membrane_2 154 ivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqein 230
                                        +++++dll l +++v +l+  + +++gl+ S+v+  +++a  lalg+ + l++l ++++ g ++ +a         
  gi|336253648|ref|YP_004596755.1| 151 ESVSAADLLALHAFAVPYLF--ACAGIGLVASVVVDRTSVAQRLALGVTFGLFMLESLLA-G-TDYEA--------- 214
                                       89999***************..55***********************9999955555555.4.34444......... PP

                   ABC2_membrane_2 231 dflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkrkDl 288
                                         +  + p ++++   n+il  s      ++   +++l+++++vll+ + + F+r+D+
  gi|336253648|ref|YP_004596755.1| 215 --VGAIAPMRYFD--PNAILLES-----SYDLVDAGVLVAMTLVLLAASQWWFRRRDI 263
                                       ..34457777777..57777777.....58999***********************96 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 !   28.1   6.7     3e-10   1.1e-06     147     282 ..      62     203 ..      54     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3e-10
                   ABC2_membrane_3 147 vestqleeelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdfl.....vyl 218
                                       +++++  e    ++ +++g  +++ +++ ++ +a  i+ + e++ + ++l+++vs++  +  k+ ++++     +++
  gi|336253648|ref|YP_004596755.1|  62 IRTMAVLEGFLAFELYIFGWTIMLGLYLAYL-AAGTIAGDVEHGRMDILLSMPVSRARTVAEKFASLAVpivvvNAV 137
                                       5556666666677778888888888888877.6668***************************99766511111555 PP

                   ABC2_membrane_3 219 lqlllilll.afglgipfgnlglllllfllfglayialgyllsslfknsetaqilifivil.llsg 282
                                       ++++++++  +++ +++  +l++l  + +++++a++ +g++ s+++++++ aq l++ v++ l+++
  gi|336253648|ref|YP_004596755.1| 138 VPVVVYVAAaLVDESVSAADLLALHAFAVPYLFACAGIGLVASVVVDRTSVAQRLALGVTFgLFML 203
                                       5555555543445499999**********************************9887777744444 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 ?   -0.8   0.1      0.25   9.1e+02     180     195 ..      19      34 ..      10      43 .. 0.48
   2 !   23.5   4.9   9.4e-09   3.4e-05      31     159 ..      74     202 ..      54     258 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.25
                   ABC2_membrane_5 180 yilliillviilllii 195
                                       + +++ ll++++++i+
  gi|336253648|ref|YP_004596755.1|  19 LSVAMSLLAVVVIWIY 34 
                                       2333333333333333 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 9.4e-09
                   ABC2_membrane_5  31 flndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavli 107
                                       f  + +++  +i+  + +++l+  t++ D  ++ + +ll++Pv+r   V++K+ ++++ i+++  ++ +++++a  +
  gi|336253648|ref|YP_004596755.1|  74 F--ELYIFGWTIMLGLYLAYLAAGTIAGDVEHGRMDILLSMPVSRARTVAEKFASLAVPIVVVNAVVPVVVYVAAAL 148
                                       3..45566677888888899999*****************************************9999999986655 PP

                   ABC2_membrane_5 108 kgn.vtisevllsiliglvialiflaivlPlyfkfgvekgri.vliiiifgiif 159
                                        ++ v   ++l   ++++ + +++  i l+         +   +++ + fg+++
  gi|336253648|ref|YP_004596755.1| 149 VDEsVSAADLLALHAFAVPYLFACAGIGLVASVVVDRTSVAQrLALGVTFGLFM 202
                                       555499899988888888888888877777777666444332355555555544 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   8.5   2.5e-06     0.009      24     177 ..      57     205 ..      41     235 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-06
                     ABC2_membrane  24 wrliqplllalvfgtvfgnlgnsedglnrpgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlak 100
                                        +++ +  +a++ g++ +       +l + g  +++ l+la ++++++ +  ++e+g ++ +l++p+ s++  v+ k
  gi|336253648|ref|YP_004596755.1|  57 IQMFDIRTMAVLEGFLAF-------ELYIFGWTIMLGLYLA-YLAAGT-IAGDVEHGRMDILLSMPV-SRARTVAEK 123
                                       456666677777788877.......33469999********.555555.699999999999999999.666666666 PP

                     ABC2_membrane 101 vlvelpvsllqalifllivyf...lvgldls..rfflflllllltalaasslgllisalapsfedasqlaslvllpl 172
                                       +++ ++ ++++ +++ ++vy+   lv+  +s    + + ++++ +++a+ ++gl+ s+++    +a+ la  v++ l
  gi|336253648|ref|YP_004596755.1| 124 FASLAVPIVVVNAVVPVVVYVaaaLVDESVSaaDLLALHAFAVPYLFACAGIGLVASVVVDRTSVAQRLALGVTFGL 200
                                       655544444444444444444111335555555559999***********************************999 PP

                     ABC2_membrane 173 lllsG 177
                                       ++l  
  gi|336253648|ref|YP_004596755.1| 201 FMLES 205
                                       99865 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 ?    9.3   8.0   0.00028         1      45     173 ..      70     200 ..      15     204 .. 0.65
   2 ?   -3.3   0.0       2.1   7.6e+03     148     151 ..     244     246 ..     215     258 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00028
                   ABC2_membrane_4  45 efyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlf. 120
                                       +f  ++ + f+ +++l l l+ +a+  i    + + +  Ll +Pvsr++ ++ K++ l++ +v++  v  +++ ++ 
  gi|336253648|ref|YP_004596755.1|  70 GFLAFELYIFGWTIMLGLYLAYLAAGTIAGDVEHGRMDILLSMPVSRARTVAEKFASLAVPIVVVNAVVPVVVYVAa 146
                                       44445555566677888888899999999999999999********************9988877666554444440 PP

                   ABC2_membrane_4 121 allsgfvgfsvklvle.llkkclelgllvffavlpiialvllkksyvlpliltl 173
                                       al+  +v+    l l+ + + +l  ++++ ++ ++++  +++ +  +l++++ l
  gi|336253648|ref|YP_004596755.1| 147 ALVDESVSAADLLALHaFAVPYLFACAGIGLVASVVVDRTSVAQRLALGVTFGL 200
                                       444444443333333313345666666666555555555666666666666555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                   ABC2_membrane_4 148 vffa 151
                                       v+ +
  gi|336253648|ref|YP_004596755.1| 244 VA-M 246
                                       11.1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1960.83
//
Query:       gi|336253649|ref|YP_004596756.1|  [L=340]
Description: ABC transporter-like protein [Halopiger xanaduensis SH-6]
Scores for 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   79.4   0.0    4.9e-22   78.9   0.0    1.2  1  ABC_tran     ABC transporter
    1.6e-13   51.2   1.6    7.7e-10   39.1   0.1    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
  ------ inclusion threshold ------
      0.074   12.9   0.0       0.12   12.2   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
       0.24   11.9   0.1       0.45   11.0   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 !   78.9   0.0   1.1e-25   4.9e-22       2     136 ..      20     156 ..      19     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 1.1e-25
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       ++v++++++ge+ + +G+nGaGK+t +++l+g  +pt+G+ +l g+d+++  el ++++++g+lp +p +++  t r
  gi|336253649|ref|YP_004596756.1|  20 DDVTFEVEAGEIFGYLGPNGAGKTTTIRTLLGFISPTAGTARLLGRDVTDeSELLEAKRNLGYLPDNPAFDESATGR 96 
                                       689**********************************************98889999*****************999 PP

                                       HH.......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       e        + de+ +++l+ ++ +   d+ v    +++S+G  +++ l+ +++ +p+l++lDEpt
  gi|336253649|ref|YP_004596756.1|  97 EIldlhasiKGDERSDELLELFDPPL--DREV----REYSHGNVRKLGLVTTFMHDPDLVVLDEPT 156
                                       99988777666666777777776444..6666....9****************************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 !   11.7   0.2   3.6e-05      0.16       6      23 ..      36      53 ..      35      75 .. 0.75
   2 !   39.1   0.1   1.7e-13   7.7e-10     168     297 ..      73     186 ..      53     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                            AAA_21  6 GpNgsGKSnLLdaldlla 23
                                      GpNg+GK++ +++l ++ 
  gi|336253649|ref|YP_004596756.1| 36 GPNGAGKTTTIRTLLGFI 53
                                      **************7764 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 1.7e-13
                            AAA_21 168 llnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrl 244
                                       ll++ +++ + ++++ + +  +++  l+     + +e++++  + ++++++             + +re S G  r 
  gi|336253649|ref|YP_004596756.1|  73 LLEAKRNLGYLPDNPAFDESATGREILDLHASIKGDERSDELLELFDPPLD-------------REVREYSHGNVRK 136
                                       555556666677777777777777777777777777777778888888777.............788888******* PP

                            AAA_21 245 lalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       l+l+t +  ++   +l+++DEp  gL+P ++ r++e+l++++++g+ v++++H
  gi|336253649|ref|YP_004596756.1| 137 LGLVTTFMHDP---DLVVLDEPTGGLDPLMQQRFAEFLRAERDRGVTVFFSSH 186
                                       *********99...9************************************** PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.8e-05      0.12     100     163 ..      30      91 ..       5      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                                       SEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTT.EEEESS-SSSS CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaeg.glliDtPGfre 163
                                       ++   +G+ G+GK+t i +ll+  +   g  +     G+  T ++elle +++ g+l D P f e
  gi|336253649|ref|YP_004596756.1|  30 EIFGYLGPNGAGKTTTIRTLLGFISPTAGTARL---LGRDVTDESELLEAKRNlGYLPDNPAFDE 91 
                                       667779****************97666665554...8************998559******9987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1    0.0001      0.45      22      37 ..      32      47 ..      15      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                            AAA_23 22 tlItGpNGaGKTTild 37
                                      +   GpNGaGKTT ++
  gi|336253649|ref|YP_004596756.1| 32 FGYLGPNGAGKTTTIR 47
                                      5557*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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 0.24s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2392.34
//
Query:       gi|336253650|ref|YP_004596757.1|  [L=273]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-17   62.3   0.5    4.1e-16   59.5   0.1    2.4  3  Methyltransf_25  Methyltransferase domain
    1.2e-16   61.2   0.1    3.1e-16   59.8   0.1    1.7  1  Methyltransf_11  Methyltransferase domain
    1.2e-15   57.6   0.0    1.8e-15   57.1   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    4.7e-11   42.8   0.0    9.1e-11   41.9   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
    3.6e-10   40.5   0.1    1.6e-09   38.4   0.0    2.0  2  Methyltransf_12  Methyltransferase domain
    1.4e-07   31.1   0.0    2.6e-07   30.2   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.1e-06   28.3   0.0    2.3e-06   27.4   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
    3.3e-05   23.5   0.0    6.9e-05   22.5   0.0    1.5  1  MTS              Methyltransferase small domain
    5.3e-05   23.1   0.0    9.9e-05   22.2   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00046   20.2   0.0    0.00087   19.3   0.0    1.4  1  Methyltransf_32  Methyltransferase domain
     0.0027   17.9   0.0     0.0038   17.3   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
     0.0028   17.1   0.1     0.0041   16.5   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.031   13.6   0.0      0.049   12.9   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
       0.17   10.4   0.1       0.23   10.0   0.1    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
       0.27   10.3   0.0       0.89    8.6   0.0    1.7  2  RrnaAD           Ribosomal RNA adenine dimethylase


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 !   59.5   0.1   3.5e-19   4.1e-16       1      92 [.      35     118 ..      35     121 .. 0.90
   2 ?   -0.0   0.0       1.3   1.5e+03      16      46 ..     146     176 ..     142     196 .. 0.76
   3 ?   -2.1   0.0       5.6   6.6e+03      35      46 ..     200     211 ..     173     239 .. 0.58

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 3.5e-19
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       +Ld+GcGtG+l++ la++ + +++v+g+D ++++le a e++        +v gda +lpf+d+ fDlvv++  l  
  gi|336253650|ref|YP_004596757.1|  35 ILDVGCGTGELSRVLAAESPaDCEVVGCDADPALLELAGEHV-------PVVAGDALRLPFADDAFDLVVCQALLIN 104
                                       8*****************8569****************9998.......79********************644655 PP

                                       SSHHHHHHHHHHHHHH CS
                   Methyltransf_25  77 lsdedlekalkeiarv 92 
                                       l+  d ++a++e+arv
  gi|336253650|ref|YP_004596757.1| 105 LP--DPAAAVSEFARV 118
                                       65..6779******98 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.3
                                       HCTSTSSEEEEEESSHHHHHHHHHHHHHTTT CS
                   Methyltransf_25  16 akrlgkakvtgvDiseemleaareraeeegl 46 
                                        +r  +a + gvD + ++ + ar  +e++gl
  gi|336253650|ref|YP_004596757.1| 146 ERRARRAYLDGVDTDVALGADARDAFEDAGL 176
                                       4554468899999999999999999988876 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.6
                                       HHHHHHHHHTTT CS
                   Methyltransf_25  35 eaareraeeegl 46 
                                        +ar++a  +gl
  gi|336253650|ref|YP_004596757.1| 200 LEARRKATGAGL 211
                                       444554444333 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.1   2.6e-19   3.1e-16       1      87 [.      36     118 ..      36     121 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 2.6e-19
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       LdvGcGtG l++ la      ++vvg+D ++++l+la      e+  v +v +da +lpf+d+ fDlvv++  l ++
  gi|336253650|ref|YP_004596757.1|  36 LDVGCGTGELSRVLAAESpadCEVVGCDADPALLELAG-----EH--VPVVAGDALRLPFADDAFDLVVCQALLINL 105
                                       8**************555679*************8883.....33..5679************************** PP

                                       CCHHHHHHHHHHH CS
                   Methyltransf_11  75 edpekalkeiaRv 87 
                                       +dp++a++e+aRv
  gi|336253650|ref|YP_004596757.1| 106 PDPAAAVSEFARV 118
                                       ************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   1.5e-18   1.8e-15       4     101 ..      32     119 ..      29     157 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.5e-18
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                         r+lD+GCGtGel+ +la e   ++evvG D ++  +elA e+        v + +gd+  l+  ++d+ fDl+++
  gi|336253650|ref|YP_004596757.1|  32 RERILDVGCGTGELSRVLAAESPADCEVVGCDADPALLELAGEH--------VPVVAGDALRLP--FADDAFDLVVC 98 
                                       679*****************9999*******************6........99**********..*********** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervl 101
                                       +++l  l+dp+++  e  rv 
  gi|336253650|ref|YP_004596757.1|  99 QALLINLPDPAAAVSEFARVS 119
                                       **************9999985 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   7.6e-14   9.1e-11       5     110 ..      13     120 ..       8     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 7.6e-14
                   Methyltransf_23   5 reeelsdklerllpk.lraggrvLdiGcGtGillevlreng...fsvtgvDlspeaveiae.....kakkaqkdqfd 72 
                                       r+  ++d +e l p  l ++ r+Ld+GcGtG+l++vl+++    ++v+g D++p++ e+a                d
  gi|336253650|ref|YP_004596757.1|  13 RRGMWDDSREALEPLdLASRERILDVGCGTGELSRVLAAESpadCEVVGCDADPALLELAGehvpvV-----AG--D 82 
                                       445688899999887579999****************66642226**********999984222211.....11..2 PP

                   Methyltransf_23  73 eqeaaepqgkfdlIvlrevlehvpdppellrqiatllk 110
                                       +   ++ ++ fdl+v+  +l ++pdp+++++ +a+  +
  gi|336253650|ref|YP_004596757.1|  83 ALRLPFADDAFDLVVCQALLINLPDPAAAVSEFARVSS 120
                                       235556888**********************9999554 PP

>> Methyltransf_12  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   1.6e-09       1      92 [.      36     118 ..      36     125 .. 0.86
   2 ?   -0.9   0.0       2.4   2.8e+03      26      52 ..     133     160 ..     120     188 .. 0.59

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.3e-12
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       L++GcGtG+l+r+l+++   d+e++g+D +p+ +        +  ++++ +v  +al l   d+  +fDlvv+  +l
  gi|336253650|ref|YP_004596757.1|  36 LDVGCGTGELSRVLAAESpADCEVVGCDADPALL--------ELAGEHVPVVAGDALRLPFADD--AFDLVVCQALL 102
                                       8*****************9***************........4444456677777777766655..9********** PP

                   Methyltransf_12  77 hhlkdirevldnirkl 92 
                                        +l+d+++++++++++
  gi|336253650|ref|YP_004596757.1| 103 INLPDPAAAVSEFARV 118
                                       *********9999876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.4
                   Methyltransf_12  26 vDispsai.edakeklakrennnnnnve 52 
                                       vD+++s+  eda e+ a+r  ++    +
  gi|336253650|ref|YP_004596757.1| 133 VDVDSSVDrEDALERRARRAYLDGVDTD 160
                                       5555555555666666555554444433 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   2.1e-10   2.6e-07      49     142 ..      33     118 ..      13     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.1e-10
                                       TEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES- CS
                   Ubie_methyltran  49 akvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfG 125
                                       +++lDv +Gtg+l+  l+ +  +  +vv++D ++ +L+ + +        ++  + ++a +Lpf dd+fD+v     
  gi|336253650|ref|YP_004596757.1|  33 ERILDVGCGTGELSRVLAAESPADCEVVGCDADPALLELAGE--------HVPVVAGDALRLPFADDAFDLVVCQAL 101
                                       589**********************************99876........57899********************** PP

                                       GGG-S-HHHHHHHHHHH CS
                   Ubie_methyltran 126 lrnvtDklkaLkeayrv 142
                                       l n++D   a+ e  rv
  gi|336253650|ref|YP_004596757.1| 102 LINLPDPAAAVSEFARV 118
                                       *************9998 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.9e-09   2.3e-06      13     107 ..      31     124 ..      21     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.9e-09
                              MetW  13 pgsrvldlGcGdGellellkeekqvdgrGleldee.gvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqat 88 
                                       ++ r+ld+GcG Gel ++l+ e   d + +  d++ ++ e     + v+ gd+ +    f+d++fd+vv +  l ++
  gi|336253650|ref|YP_004596757.1|  31 SRERILDVGCGTGELSRVLAAESPADCEVVGCDADpALLELAGEHVPVVAGDALR--LPFADDAFDLVVCQALLINL 105
                                       5789*****************999998888887763678888899******9854..469**********999**** PP

                              MetW  89 rnpkevldellrigrraiv 107
                                        +p+  ++e  r++   + 
  gi|336253650|ref|YP_004596757.1| 106 PDPAAAVSEFARVSSDLVA 124
                                       *************987665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.8e-08   6.9e-05      24      73 ..      24      74 ..      18      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.8e-08
                                      HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHH CS
                               MTS 24 letlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesake 73
                                      le l+ + ++++lD+GcG+G l+ +la+esp    v+ +d+d + le+a e
  gi|336253650|ref|YP_004596757.1| 24 LEPLDLASRERILDVGCGTGELSRVLAAESPADCeVVGCDADPALLELAGE 74
                                      55667777889******************9975449*****9999888866 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 !   22.2   0.0   8.2e-08   9.9e-05      65     126 ..      23      84 ..      20      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.2e-08
                                       HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSE CS
                              PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenv 126
                                       ale l+l   +r+L+vG+G+G l+ vla    +++ vv+ +  + l e a +++   + + +
  gi|336253650|ref|YP_004596757.1|  23 ALEPLDLASRERILDVGCGTGELSRVLAAESPADCEVVGCDADPALLELAGEHVPVVAGDAL 84 
                                       678899*****************************************999988866655555 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   7.2e-07   0.00087      25      65 ..      31      70 ..      21      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.2e-07
                   Methyltransf_32 25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelve 65
                                      ++++++DvG+G g Ls+vla  e+   ++vvg da  +l e
  gi|336253650|ref|YP_004596757.1| 31 SRERILDVGCGTGELSRVLAA-ESPADCEVVGCDADPALLE 70
                                      5689*****************.66689********998876 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.2e-06    0.0038      21      77 ..      31      90 ..      16     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.2e-06
                                      TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS..HHH.TTEEEECS-CCCSSHHH CS
                              FtsJ 21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm..apl.pgvttiqgditdpetie 77
                                        ++++D+g+++G  s vl+ +  a++ vv++D  p   ++  ++v ++ gd ++   ++
  gi|336253650|ref|YP_004596757.1| 31 SRERILDVGCGTGELSRVLAAESPADCEVVGCDADPAllELAgEHVPVVAGDALRLPFAD 90
                                      55689*****************9889*********9965555899999999997776666 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   3.4e-06    0.0041     154     203 ..      23      75 ..      20     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.4e-06
                              PrmA 154 aleklvk.egeevlDvGtGSGiLa..iaaakLgakkvvavDiDevAvkvakeN 203
                                       ale l   ++e++lDvG+G+G L+  +aa   +  +vv+ D D+  ++ a e 
  gi|336253650|ref|YP_004596757.1|  23 ALEPLDLaSRERILDVGCGTGELSrvLAAESPADCEVVGCDADPALLELAGEH 75 
                                       667665404579***********987899999999*********988888765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.1e-05     0.049      52      83 ..      21      52 ..      17      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.1e-05
                                      HHHHTTTT--TT-EEEEES-TTSHHHHHHHHH CS
                              CMAS 52 dlileklelkpGmtlLdiGcGWGslvrraver 83
                                      + +le l+l   +++Ld+GcG G+l r  +++
  gi|336253650|ref|YP_004596757.1| 21 REALEPLDLASRERILDVGCGTGELSRVLAAE 52
                                      568999*******************9987765 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 ?   10.0   0.1   0.00019      0.23     119     194 ..      33     105 ..      22     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                   Methyltransf_29 119 rtvlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaLeRgvpailavlgtkrlpyPsrsfdlihCsrCridw 194
                                       + +lDvGCg   ++ +l  +      +   D   a + +a e  vp + +   + rlp+   +fdl+ C   +i+ 
  gi|336253650|ref|YP_004596757.1|  33 ERILDVGCGTGELSRVLAAESPADCEVVGCDADPALLELAGEH-VPVVAG--DALRLPFADDAFDLVVCQALLINL 105
                                       569*************************************995.898877..578**************9999986 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00075      0.89      21      72 ..      22      76 ..      20     102 .. 0.84
   2 ?   -1.0   0.0      0.61   7.3e+02     165     195 ..     118     206 ..     110     212 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00075
                                      HHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHT CS
                            RrnaAD 21 eIldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkl 72
                                      e+l+ l+l     +l++g G+G l++ La  +    +vv    d++L++l  +++
  gi|336253650|ref|YP_004596757.1| 22 EALEPLDLASRERILDVGCGTGELSRVLAAESpadCEVVGCDADPALLELAGEHV 76
                                      678899999*******************776667778999999999998877755 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.61
                                       EEEEEEEEC-GG..........................................................CECS--S CS
                            RrnaAD 165 tdvklvakveks..........................................................ifsPppk 183
                                       +++ lva+ve++                                                           + +pp 
  gi|336253650|ref|YP_004596757.1| 118 VSSDLVAAVEPNnaavdvdssvdredalerrarrayldgvdtdvalgadardafedaglellatrrydhvRTVEPPY 194
                                       56778888888866666666666666666666666666666666666666666666666666666666665566667 PP

                                       SSEEEEEEEE-S CS
                            RrnaAD 184 vdsalvelerkd 195
                                        ++al+e +rk+
  gi|336253650|ref|YP_004596757.1| 195 DEGALLEARRKA 206
                                       777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1992.64
//
Query:       gi|336253651|ref|YP_004596758.1|  [L=291]
Description: endonuclease 4 [Halopiger xanaduensis SH-6]
Scores for 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-27   93.9   1.6    2.3e-26   92.5   0.6    2.0  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 !   92.5   0.6   1.3e-30   2.3e-26       7     210 .]      38     247 ..      18     247 .. 0.87
   2 ?    0.1   0.0     0.025   4.6e+02     112     148 ..     251     289 ..     249     291 .] 0.80

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.3e-30
                                       CT-SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS...HHHHHHHHHHHHHH CS
                      AP_endonuc_2   7 aGfdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederear...reesvdalkraiel 78 
                                        G ++ ++f+ +++ +++   sde+++ ++   +e     ++++  +  +        ++   r++s++ ++ ++++
  gi|336253651|ref|YP_004596758.1|  38 FGGNCGQIFTTSPQVWAQPeiSDEAAEGFQDETEEQLEGPWVIHSAYLVNLCT-----PKddlRRKSKESMQAELDA 109
                                       56666677777777777777777777777777777666666655555544432.....234689999********** PP

                                       HHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTT CS
                      AP_endonuc_2  79 aaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavds 153
                                       aa+LG+p++++h G   a+ + + e  ++++a+ ++el ++  + +v++++E  agsg+ lg+  e+la ++d+++ 
  gi|336253651|ref|YP_004596758.1| 110 AAQLGIPYVNVHLG---AHTGAGVEGGLDNAASLIDEL-EV--PDDVQILIESDAGSGTKLGGefEHLAGIIDRTET 180
                                       **************...********************9.66..78******************************96 PP

                                       TTEEEEEEHHHHHHH......TTTHHHHHHHHHGG.....EEEEEE.EESSTTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 154 pnvgvclDtgHllia......eedvddalraladr.....ikhvHikDakgdlgagrdrhvpigeGei 210
                                       + +g+c+Dt+H+l a       e vd+++++++d      + ++H++D+k d g ++d+h+ igeG i
  gi|336253651|ref|YP_004596758.1| 181 D-IGICIDTAHTLVAgndlttPEAVDETVQRFDDEvgleyLEYIHLNDSKHDVGTHKDEHAHIGEGYI 247
                                       5.****************************************************************76 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHH CS
                      AP_endonuc_2 112 slneladyaekegvklalEtlagsgvelgd..eelarll 148
                                       ++++++ + + ++  +alEt +++g  + +  +++++l 
  gi|336253651|ref|YP_004596758.1| 251 GMKAIVNHPDLRDLPFALETPTEDGRGFEWniQKVKELR 289
                                       5777777777788999*********99999997777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2294.36
//
Query:       gi|336253652|ref|YP_004596759.1|  [L=306]
Description: biotin/lipoate A/B protein ligase [Halopiger xanaduensis SH-6]
Scores for complete 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   25.1   0.0    4.9e-05   23.2   0.0    2.0  2  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.7e-09   4.9e-05      22     128 ..      77     214 ..      62     217 .. 0.80
   2 ?   -3.0   0.0      0.36   6.4e+03      24      36 ..     236     248 ..     227     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.7e-09
                                       -TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHH..HHHHHHHHHHHH..............HHT CS
                     BPL_LplA_LipB  22 esgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlely..vsllvlavlealg......yrd..skpgi 88 
                                       + +g++v+rrqtgG  ++h+   +++y+++  ++   ++ + + +y   ++ +l ++e lg      + +  ++ ++
  gi|336253652|ref|YP_004596759.1|  77 DREGIDVTRRQTGGGGIYHDRRVDISYTIVAPADE--VPGDLMDCYalFCEPILEAFERLGvdadfaS-SeqDAIYQ 150
                                       56899***************666999999999876..88889999998*************9877431.23455555 PP

                                       T-TTEEEE.TTTEEEE.......................TTEEEEEEEEEEEETTS-EEEEEEE CS
                     BPL_LplA_LipB  89 egipvfik.wpnDlyv.......................ngrKlaGiavtstrgktlhhivigv 128
                                       ++ + ++     D+++                         +K++G a+ ++r + ++h++i  
  gi|336253652|ref|YP_004596759.1| 151 PSCYLRDIhPAHDIVApassaatddgdergdssgddgnpAPKKISGNAQYRQRDVVIQHGSISF 214
                                       55555555345677778888888888899999999888899*******************9965 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.36
                                       T-EEEEEEESS-B CS
                     BPL_LplA_LipB  24 gglvvvrrqtgGr 36 
                                       +++  +r+qtgG 
  gi|336253652|ref|YP_004596759.1| 236 DRVTSIREQTGGE 248
                                       5666789999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2486.40
//
Query:       gi|336253653|ref|YP_004596760.1|  [L=44]
Description: hypothetical protein Halxa_2256 [Halopiger xanaduensis SH-6]
Scores for 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  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); 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):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 330.16
//
Query:       gi|336253654|ref|YP_004596761.1|  [L=352]
Description: NAD-dependent epimerase/dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-21   76.4   0.1    2.8e-19   69.5   0.1    2.4  1  Epimerase        NAD dependent epimerase/dehydratase family
    6.4e-11   41.9   0.8    0.00016   20.9   0.0    3.0  2  RmlD_sub_bind    RmlD substrate binding domain
    7.6e-09   35.7   0.1    5.9e-08   32.8   0.1    2.2  1  NAD_binding_10   NAD(P)H-binding
    2.9e-08   33.5   0.1     0.0023   17.4   0.1    2.9  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    4.2e-06   26.0   0.0    0.00016   20.8   0.0    2.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    0.00015   21.4   0.0     0.0006   19.4   0.0    2.0  3  NmrA             NmrA-like family
      0.003   17.6   0.6      0.038   14.0   0.1    2.6  3  Glyco_transf_4   Glycosyltransferase Family 4
     0.0079   16.7   2.0      0.051   14.0   0.6    2.6  3  Glyco_trans_4_4  Glycosyl transferase 4-like 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 !   69.5   0.1   1.3e-22   2.8e-19       2     228 ..       4     225 ..       3     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.3e-22
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggva 78 
                                       l +G+tG i + ++++l ++g+ev++++r +++ +    + +e+v++d  dr+aler+ +e +pd+v+ +  v+  +
  gi|336253654|ref|YP_004596761.1|   4 LCIGGTGVISTGITRQLVDAGHEVVCFTRGETDAPV--PDAVEFVTGDRNDRAALERAAREADPDCVVDM--VCFTP 76 
                                       779***************************776664..4555****************************..99999 PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSS.S.BSTCSTTS--...--SSHHHHHHHHHH CS
                         Epimerase  79 assedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeq.p.keettltgpl...kpnspYaaaKlage 150
                                       ++++++ d               a+   +++++f+s++ vY ++ e  p +e+   ++ l   +p s Y+a K+a+e
  gi|336253654|ref|YP_004596761.1|  77 EQASEAVD---------------AFGGAIEQYVFCSTVDVYHRPLERnPaTEDAPRESDLegvEPVSEYGADKAAAE 138
                                       99999888...............44566789***********999954854444444444778************** PP

                                       HHHHHHHHHHT..........-EEEEEEESEEESTT..S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEH CS
                         Epimerase 151 klveayaaqyg..........lnaiilrlfnlyGpr..ngegevsrvipalirkilegkqevtllgdgtalRdflyv 215
                                        +  a+++  +          + ++i+r+ + yG++   ++++ s+   +++ +i +gk ++++ gdgt+l+  ++ 
  gi|336253654|ref|YP_004596761.1| 139 DVFLAAHDGPEsvtgtdsdgeFATTIVRPWSTYGEGgsVFHTFGSGT--YYLDRIRKGK-PIVVHGDGTSLWGSCHR 212
                                       *****9998877899999999***************88888888876..679*******.***************** PP

                                       HHHHHHHHHHHHH CS
                         Epimerase 216 eDvaeaillvleh 228
                                       +Dva+a++ ++ +
  gi|336253654|ref|YP_004596761.1| 213 DDVARAFVGAVGN 225
                                       ********99887 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 !   20.9   0.0     7e-08   0.00016       1      69 [.       1      82 [.       1      95 [. 0.92
   2 !   17.8   0.2   6.2e-07    0.0014     185     251 ..     211     274 ..     110     318 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 7e-08
                                      EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.............T--TTSHHHHHHHHHHH--SEEEE------HHH CS
                     RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlaltre.............eldltdaeavaellkeakpdvvvnaAAytavDk 66
                                      m++l +G++G + + +++ql  +g+ev+ +tr              + d +d++a++++ +ea+pd+vv++  +t   +
  gi|336253654|ref|YP_004596761.1|  1 MRVLCIGGTGVISTGITRQLVDAGHEVVCFTRGetdapvpdavefvTGDRNDRAALERAAREADPDCVVDMVCFTPEQA 79
                                      89******************************9999999999999999999999999999**********999997776 PP

                                      HHH CS
                     RmlD_sub_bind 67 aEs 69
                                       E 
  gi|336253654|ref|YP_004596761.1| 80 SEA 82
                                      665 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 6.2e-07
                                       EHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS- CS
                     RmlD_sub_bind 185 sardlAevllqllekaaeekelagvyHlanegetswlefArailkeagadseevkpistaeyptpAk 251
                                       + +d+A++ + ++ ++++   + + yH+++e++++w ++ + ++++++a   e+  i+t++  ++A+
  gi|336253654|ref|YP_004596761.1| 211 HRDDVARAFVGAVGNETA---YGEAYHVTSEEVITWNQYHQRVANAMDAPDPELVHIPTEQLREAAP 274
                                       456788888887777775...899***********************************99988884 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 !   32.8   0.1   2.6e-11   5.9e-08       1     145 [.       7     169 ..       7     226 .. 0.63

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.6e-11
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-S..EEEES---TCCHH CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgad..aVvsalggggkde 75 
                                       G+tG +   ++++l+++ ghev+ ++R + +++ ++  +++e v+gd +d ++l++a + ad   Vv  +  +    
  gi|336253654|ref|YP_004596761.1|   7 GGTGVISTGITRQLVDA-GHEVVCFTRGETDAP-VP--DAVEFVTGDRNDRAALERAAREADpdCVVDMVCFTP--- 76 
                                       9****************.5**************.76..79******************9998766666665443... PP

                                       HHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHH...........CCHHHHHHHHHHHHH.HHH....... CS
                    NAD_binding_10  76 egaknivdaakeagvkRfvlvsaigvgdevpgefgewnke...........llkaylaakraaeel.lra....... 133
                                       e+a  +vda     ++++v++s+++v+++ p e ++ +++            +++y a+k+aae++ l a       
  gi|336253654|ref|YP_004596761.1|  77 EQASEAVDAFGG-AIEQYVFCSTVDVYHR-PLERNPATEDapresdlegvePVSEYGADKAAAEDVfLAAhdgpesv 151
                                       468888888865.4999*********974.33333322221111222222266777899999999834336666666 PP

                                       ......SSSEEEEEEE-C CS
                    NAD_binding_10 134 ......sgldwTivrpgg 145
                                              ++  Tivrp  
  gi|336253654|ref|YP_004596761.1| 152 tgtdsdGEFATTIVRPWS 169
                                       665533356678888766 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 !   12.8   0.0   2.6e-05     0.058       3      82 ..       6      71 ..       4      80 .. 0.84
   2 !   17.4   0.1     1e-06    0.0023     147     332 .]     124     314 ..      81     314 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                                      ETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                     GDP_Man_Dehyd  3 TGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81
                                       G++G i   ++++L++ g+ev+ ++r ++                 + + ++++ gD +D+++ler+ +e++pd v+ 
  gi|336253654|ref|YP_004596761.1|  6 IGGTGVISTGITRQLVDAGHEVVCFTRGETDAP--------------VPDAVEFVTGDRNDRAALERAAREADPDCVVD 70
                                      699*******************99877655422..............234578************************97 PP

                                      - CS
                     GDP_Man_Dehyd 82 L 82
                                      +
  gi|336253654|ref|YP_004596761.1| 71 M 71
                                      6 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1e-06
                                       ----SHHHHHHHHHHHHHHHHHHH.........H--.-EEEEEE-EEESTTS-TTSCCC.HHHHHHHHHHTTS-C-E CS
                     GDP_Man_Dehyd 147 fyPrsPYaaaKlyadwivvnyrea.........ygl.favngilfnhesprrgetfvtr.kitravarialgkqevl 212
                                       ++P s Y+a K++a+ +  + ++           g   +++ +   +++   g  f t    t ++ ri +gk +++
  gi|336253654|ref|YP_004596761.1| 124 VEPVSEYGADKAAAEDVFLAAHDGpesvtgtdsDGEfATTIVRPWSTYGEG-GSVFHTFgSGTYYLDRIRKGK-PIV 198
                                       446666777777766666666654222222222222234445556666665.343443325566778888887.778 PP

                                       ECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEEC..HHCHHCCHHCCCHHHHHH............TT CS
                     GDP_Man_Dehyd 213 ylGnldakRdwghvkDyveamwlmlqqdkpedyviatgethsv..refvelaflelgktiewegkgeeevgrakesg 287
                                       + G++ +     h +D+++a++ ++ +++      a ge + v  +e+++++  +      ++  + e v+  +e+ 
  gi|336253654|ref|YP_004596761.1| 199 VHGDGTSLWGSCHRDDVARAFVGAVGNET------AYGEAYHVtsEEVITWNQYHQRVANAMDAPDPELVHIPTEQL 269
                                       88999888777888999999999888877......445555442233333333333333333444455566667777 PP

                                       GGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 288 kvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvrem 332
                                       ++  + +    +   +  ++ d++ka+++Lg++ +++fee++r++
  gi|336253654|ref|YP_004596761.1| 270 REAAPDRTDMLKAHFQYSTVFDNAKARRDLGFEYTIDFEEGMRRT 314
                                       766666555555555566799*********************986 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 !   20.8   0.0     7e-08   0.00016     104     273 ..      86     259 ..       4     266 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7e-08
                         3Beta_HSD 104 vkagvrvlvYtSsaevvgpnslgeeilngdEeleyesl.....hqdaypesKalaEklvlkaNgrt..l..kngg.r 170
                                       +   ++  v++S+++v     + ++ +   E+ ++es      +++ y   Ka aE++ l+a + +  +   +   +
  gi|336253654|ref|YP_004596761.1|  86 FGGAIEQYVFCSTVDVYHRPLERNPAT---EDAPRESDlegvePVSEYGADKAAAEDVFLAAHDGPesVtgTDSDgE 159
                                       44568999********99877666655...333333322233599*****************985311211333349 PP

                         3Beta_HSD 171 lyTcaLRpagiyGegdkllvpl.....lkqlaklglalfkigdeevlsdrvYvgNvawahilAaralqdpkkkssva 242
                                       + T  +Rp   yGeg +++ ++     +   +++g+ ++  gd  +l      + va a + A+ +       +++ 
  gi|336253654|ref|YP_004596761.1| 160 FATTIVRPWSTYGEGGSVFHTFgsgtyYLDRIRKGKPIVVHGDGTSLWGSCHRDDVARAFVGAVGN-------ETAY 229
                                       ***************999987633322455567777888889999999999999999999988753.......4556 PP

                         3Beta_HSD 243 gqayfisddsPvesyddfnltllkelglelk 273
                                       g+ay+++ ++  + ++++   + ++++ +++
  gi|336253654|ref|YP_004596761.1| 230 GEAYHVTSEEVIT-WNQYHQRVANAMDAPDP 259
                                       7777777666655.66666666666666555 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.7e-07    0.0006       1      67 [.       3      65 ..       3     112 .. 0.79
   2 ?   -2.0   0.0      0.97   2.2e+03     168     216 ..     198     245 ..     178     253 .. 0.73
   3 ?   -3.7   0.0       3.2   7.1e+03     215     227 ..     333     345 ..     327     346 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.7e-07
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SE CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdv 67
                                      +l iG+TG +   ++r l++agh+v   +R ++   +       ve+v gd +d++ l++a +++d 
  gi|336253654|ref|YP_004596761.1|  3 VLCIGGTGVISTGITRQLVDAGHEVVCFTRGETDAPVP----DAVEFVTGDRNDRAALERAAREADP 65
                                      688***************************88776664....579******************9973 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.97
                                       EEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHH CS
                              NmrA 168 tllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgne 216
                                       +++g+g +      + +D++++ + ++ +++++   +   ++++++ n+
  gi|336253654|ref|YP_004596761.1| 198 VVHGDGTSLWGS-CHRDDVARAFVGAVGNETAYGEAYHVTSEEVITWNQ 245
                                       555555533333.377888888888888888887777777888888776 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHTS CS
                              NmrA 215 neivelfekkigk 227
                                       +ei+e++  +igk
  gi|336253654|ref|YP_004596761.1| 333 DEIIEAWDTAIGK 345
                                       6999***999998 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.7e-05     0.038       1      37 [.       6      42 ..       6      76 .. 0.78
   2 ?    0.6   0.0      0.21   4.8e+02      56      86 ..     179     209 ..     139     218 .. 0.70
   3 ?   -2.9   0.0       2.6   5.7e+03      60      80 ..     246     266 ..     233     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                    Glyco_transf_4  1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev 37
                                      +GG ++    ++r+L ++GheV+ +t+g  +++    
  gi|336253654|ref|YP_004596761.1|  6 IGGTGVISTGITRQLVDAGHEVVCFTRGETDAPVPDA 42
                                      69999999*******************9888776663 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.21
                    Glyco_transf_4  56 rslaflrrlrrllkrekpDvvHahspaalga 86 
                                       +++ +  +   +++++kp vvH  +   +g 
  gi|336253654|ref|YP_004596761.1| 179 HTFGSGTYYLDRIRKGKPIVVHGDGTSLWGS 209
                                       4555556677788888888888887666655 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.6
                    Glyco_transf_4  60 flrrlrrllkrekpDvvHahs 80 
                                       +++r+++++++ +p +vH+ +
  gi|336253654|ref|YP_004596761.1| 246 YHQRVANAMDAPDPELVHIPT 266
                                       567788888888999999865 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 !   14.0   0.6   2.3e-05     0.051       1      32 [.       7      38 ..       7      62 .. 0.74
   2 ?    1.1   0.0      0.21   4.8e+02      85     129 ..      54      97 ..      37     103 .. 0.72
   3 ?   -1.3   0.1       1.2   2.6e+03     113     113 ..     237     237 ..     176     277 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                   Glyco_trans_4_4  1 gGigryvaelaraLaarGheVtvltpapapga 32
                                      gG g+    + r+L+++GheV+++t++++ ++
  gi|336253654|ref|YP_004596761.1|  7 GGTGVISTGITRQLVDAGHEVVCFTRGETDAP 38
                                      899999*******************7665442 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.21
                   Glyco_trans_4_4  85 glaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrr 129
                                       +++ r+ar  +++ +vv++   ++++ s av ++  a+e++++++
  gi|336253654|ref|YP_004596761.1|  54 AALERAAR-EADPDCVVDMVCFTPEQASEAVDAFGGAIEQYVFCS 97 
                                       45566667.888889998888888888888888888887777665 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.2
                   Glyco_trans_4_4 113 g 113
                                       +
  gi|336253654|ref|YP_004596761.1| 237 S 237
                                       0 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2536.99
//
Query:       gi|336253655|ref|YP_004596762.1|  [L=258]
Description: xylose isomerase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-18   66.7   1.7    3.6e-18   65.8   1.5    1.6  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
    0.00024   20.1   0.0    0.00036   19.5   0.0    1.2  1  UxuA          D-mannonate dehydratase (UxuA)
  ------ inclusion threshold ------
      0.027   14.9   0.7         12    6.5   0.0    3.0  3  AvrPtoB_bdg   Avirulence AvrPtoB, BAK1-binding domain


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 !   65.8   1.5   6.1e-22   3.6e-18      69     194 ..      79     200 ..      34     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 6.1e-22
                                       HHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC.... CS
                      AP_endonuc_2  69 vdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd.... 141
                                         ++++ + +a++LGa++++++           ++ +++ + e l +la+ +e   + +a+++  + ++ ++     
  gi|336253655|ref|YP_004596762.1|  79 TGEAREYVAFASRLGADYVTVN-----------YPPDRDDITEELLALAAAFE---IDVAIHNYSSVHHDDLSqvfs 141
                                       4577888999************...........6799**************99...************99999**** PP

                                       ..HHHHHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESS....T CS
                      AP_endonuc_2 142 ..eelarlldavdspnvgvclDtgHlliaeedvddalraladrikhvHikDakg....d 194
                                         ++++++l++ d+p++gvc DtgH+l a  d+++++r+++dri +vH+kD+ +    d
  gi|336253655|ref|YP_004596762.1| 142 siDDVRAVLERHDDPRLGVCVDTGHFLVASVDPAAVVREFGDRIVAVHLKDTSDaeveD 200
                                       ***************************************************99855550 PP

>> UxuA  D-mannonate dehydratase (UxuA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0     6e-08   0.00036     190     278 ..     111     197 ..     108     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6e-08
                                       HHHHHHHHHT-EEEE---SSSS-BTTB--SSSSHHHHHHHHHH--STTEEEEEEHHHHTTSTT--HHHHHHHHGGGE CS
                              UxuA 190 eiiPvaeevgvklaihPDDPPlpifGlpRivstkedlqrlldlvdspangitlCtGslgaradndlvemikefadri 266
                                       e++  a + ++ +aih     +    l  + s+++d++ +l+ +d p  g+ + tG + + +  d  ++++ef+dri
  gi|336253655|ref|YP_004596762.1| 111 ELLALAAAFEIDVAIHNYS-SVHHDDLSQVFSSIDDVRAVLERHDDPRLGVCVDTGHFLVAS-VDPAAVVREFGDRI 185
                                       5666777778888888644.45567899******************************9988.7889********** PP

                                       EEEE--EEEE-S CS
                              UxuA 267 yFahlRnikree 278
                                         +hl++++  e
  gi|336253655|ref|YP_004596762.1| 186 VAVHLKDTSDAE 197
                                       *******99875 PP

>> AvrPtoB_bdg  Avirulence AvrPtoB, BAK1-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.42   2.5e+03      14      31 ..      49      68 ..      42      74 .. 0.62
   2 ?    6.5   0.0    0.0019        12      26      57 ..     138     169 ..     127     190 .. 0.82
   3 ?    5.1   0.0    0.0053        31      15      53 ..     192     231 ..     183     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.42
                                      HHHHH.HHH.HHHHCTT--H CS
                       AvrPtoB_bdg 14 ndead.aal.rglvqqgvnl 31
                                      +d ad aal rgl   gv++
  gi|336253655|ref|YP_004596762.1| 49 DDAADrAALqRGLAGAGVDV 68
                                      45555333337777777765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0019
                                       CTT--HHHHHHHHHHHHHH-----HHHHHHHH CS
                       AvrPtoB_bdg  26 qqgvnlehlrtalerhvmqrlpipldigsalq 57 
                                       q    ++ +r+ lerh   rl + +d g  l 
  gi|336253655|ref|YP_004596762.1| 138 QVFSSIDDVRAVLERHDDPRLGVCVDTGHFLV 169
                                       555678999******************98774 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0053
                                       HHHHHHHHHHHCTT.--HHHHHHHHHHHHHH-----HHHH CS
                       AvrPtoB_bdg  15 deadaalrglvqqg.vnlehlrtalerhvmqrlpipldig 53 
                                       d +da +  l   g ++le +   l+ hv + +p+pl i 
  gi|336253655|ref|YP_004596762.1| 192 DTSDAEVEDLPGAGaLELERVVGLLDEHVDREVPLPLIIE 231
                                       777888888877663689*******************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2021.60
//
Query:       gi|336253656|ref|YP_004596763.1|  [L=352]
Description: heat domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-20   72.2  16.3    1.8e-10   41.1   3.2    4.1  4  HEAT_2         HEAT repeats
    1.2e-10   41.6  10.3       0.15   12.6   0.1    5.7  5  HEAT_EZ        HEAT-like repeat
    4.5e-08   32.7   6.6       0.66   10.4   0.1    5.7  5  HEAT           HEAT repeat
    2.1e-07   31.1   0.0    2.5e-05   24.4   0.0    2.6  3  Cnd1           non-SMC mitotic condensation complex subunit 1
    2.5e-05   23.8   3.0    4.8e-05   22.9   3.0    1.5  1  zinc_ribbon_2  zinc-ribbon domain
      0.002   17.8   0.0        1.1    8.7   0.0    2.5  3  CLASP_N        CLASP N terminal
     0.0045   15.6   0.0      0.039   12.5   0.0    2.0  2  Adaptin_N      Adaptin N terminal region
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.037   14.2   0.0    2.0  2  RTP1_C1        Required for nuclear transport of RNA pol II C
      0.012   15.6   0.9      0.024   14.6   0.9    1.5  1  DZR            Double zinc ribbon
       0.21   11.5   1.5        0.4   10.6   1.5    1.4  1  Prok-RING_1    Prokaryotic RING finger family 1
       0.29   10.6   5.7       0.85    9.1   5.7    1.7  1  zf-ribbon_3    zinc-ribbon domain
        3.3    7.9   7.9        9.4    6.5   0.8    2.6  2  Zn-ribbon_8    Zinc ribbon domain
        8.1    6.8   8.7         11    6.4   1.7    2.8  2  zinc_ribbon_9  zinc-ribbon


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   3.2   1.3e-13   1.8e-10       5      88 .]      29     124 ..      25     124 .. 0.82
   2 !   23.0   0.2   5.8e-08     8e-05       1      65 [.      99     174 ..      99     175 .. 0.90
   3 !   31.3   1.0   1.4e-10     2e-07      16      88 .]     159     239 ..     151     239 .. 0.75
   4 !    9.4   2.5     0.001       1.4       7      63 ..     220     291 ..     216     298 .. 0.68

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1.3e-13
                            HEAT_2   5 lqalendpdpevrraairaLgrignpea......lpaLvellededpavRraaaeaLgaig..dpe....alpaLke 69 
                                       l+ l  d+dpevr++a+r L ++ +++       +p+L+++led+ +avR + a+  +a++  +p+    a+paL e
  gi|336253656|ref|YP_004596763.1|  29 LEGL-ADADPEVRKTALRDLRTLVDEQGagvrplVPTLRRFLEDDGRAVRLTTAKLFVAVAanEPDavveAVPALGE 104
                                       5678.8***************7655433366666*********************8888863323334449****** PP

                            HEAT_2  70 llddddd.dvvReaAaeaLa 88 
                                       +l+dd + ++vR++ aeaL+
  gi|336253656|ref|YP_004596763.1| 105 RLADDAEfYYVRARCAEALG 124
                                       *****999**********96 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 5.8e-08
                            HEAT_2   1 ldaLlqalen.dpdpevrraairaLg........rignpealpaLvellededpavRraaaeaLg..aigdpealp 65 
                                       ++aL ++l++  ++++vr++ ++aLg        + ++p++l+ L+  l+ ++++vR   a+aL+  aig+p  l+
  gi|336253656|ref|YP_004596763.1|  99 VPALGERLADdAEFYYVRARCAEALGyvalehpdEVASPDVLADLRIGLSFDETDVRPKLAKALAcvAIGEPTRLD 174
                                       5889999977577889**********9999999889999*************************777999998887 PP

  == domain 3  score: 31.3 bits;  conditional E-value: 1.4e-10
                            HEAT_2  16 vrraairaLg.rignpealpaLvellededpavRraaaeaLgaig......dpealpaLkellddddd.dvvReaAa 84 
                                        ++ a+ a+g   + +  +++L  +l de++ vR++ a+aL+aig      + ea   L +++ d+ + d+vR +Aa
  gi|336253656|ref|YP_004596763.1| 159 AKALACVAIGePTRLDHHVETLAAFLGDEHELVRYHLATALVAIGcerpgaLGEASGGLVARVEDEAEnDYVRGRAA 235
                                       234555555532344467**************************9764443355889999999998755******** PP

                            HEAT_2  85 eaLa 88 
                                       eaL+
  gi|336253656|ref|YP_004596763.1| 236 EALG 239
                                       **96 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.001
                            HEAT_2   7 alen.dpdpevrraairaLgrignp.............ealpaLvellededpavRraaaeaLg.aigdpea 63 
                                       ++e+  ++++vr +a++aLg ++               ++l+a +e+led+d+a  ++ a++++ a+++p++
  gi|336253656|ref|YP_004596763.1| 220 RVEDeAENDYVRGRAAEALGLLARAdgvgaesesdveaSVLQAEFEVLEDADTAFLAERARYAArALAEPDS 291
                                       5544478999**********6655545555566767667799999999999988777766644424555554 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.028        39      36      54 ..      31      49 ..      27      50 .. 0.77
   2 !   12.6   0.1   0.00011      0.15       1      50 [.      37      82 ..      37      85 .. 0.81
   3 !   11.4   0.0   0.00027      0.37      24      54 ..      93     125 ..      85     126 .. 0.85
   4 !   12.3   0.1   0.00014      0.19       4      52 ..     155     199 ..     152     203 .. 0.85
   5 !    6.8   0.2    0.0071       9.7      10      54 ..     201     240 ..     195     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.028
                           HEAT_EZ 36 lLnddsdeVRaaAagaLgn 54
                                      +L d ++eVR++A++ L+ 
  gi|336253656|ref|YP_004596763.1| 31 GLADADPEVRKTALRDLRT 49
                                      5667777*******98875 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00011
                           HEAT_EZ  1 wrvRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAag 50
                                      ++vR  A++ L +l  + +  ++     ++p L ++L+dd  +VR ++a 
  gi|336253656|ref|YP_004596763.1| 37 PEVRKTALRDLRTLVDEQGAGVR----PLVPTLRRFLEDDGRAVRLTTAK 82
                                      67999999999767745555555....8*****************99985 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00027
                           HEAT_EZ  24 plvpeilpaLlalLnddsd..eVRaaAagaLgn 54 
                                       ++v e++paL+ +L dd     VRa +a aLg 
  gi|336253656|ref|YP_004596763.1|  93 DAVVEAVPALGERLADDAEfyYVRARCAEALGY 125
                                       466699********99999*999********95 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00014
                           HEAT_EZ   4 RraAawaLGrlaggepellqplvpeilpaLlalLnddsd.eVRaaAagaL 52 
                                       R   a aL+++a gep  l  +v+ + ++L+     d+  +VR+  a aL
  gi|336253656|ref|YP_004596763.1| 155 RPKLAKALACVAIGEPTRLDHHVETLAAFLG-----DEHeLVRYHLATAL 199
                                       555678*************************.....88868898888777 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.0071
                           HEAT_EZ  10 aLGrlaggepellqplvpeilpaLlalLnd..dsdeVRaaAagaLgn 54 
                                       a+G    ++p +l     e+   L+a+ +d  ++d VR+ Aa aLg 
  gi|336253656|ref|YP_004596763.1| 201 AIG---CERPGALG----EASGGLVARVEDeaENDYVRGRAAEALGL 240
                                       555...56666666....77788999999988899**********96 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00048      0.66       5      22 ..      28      45 ..      26      52 .. 0.88
   2 ?    3.0   0.0      0.11   1.6e+02       1      28 [.      61      88 ..      61      90 .. 0.87
   3 ?    6.2   0.0     0.011        15       3      26 ..     100     125 ..      98     128 .. 0.75
   4 ?    5.5   0.0     0.018        24       4      27 ..     179     202 ..     177     203 .. 0.88
   5 ?    6.3   0.1      0.01        14      11      28 ..     225     242 ..     217     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00048
                                      HHHHHT-SSHHHHHHHHH CS
                              HEAT  5 llkllsDpspeVReaAak 22
                                      +l+ l D +peVR++A++
  gi|336253656|ref|YP_004596763.1| 28 CLEGLADADPEVRKTALR 45
                                      7999************86 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                                      HHHHHHHHHT-SSHHHHHHHHHHHHHHH CS
                              HEAT  1 llPlllkllsDpspeVReaAakaLgala 28
                                      l+P+l + l+D+   VR ++ak ++a+a
  gi|336253656|ref|YP_004596763.1| 61 LVPTLRRFLEDDGRAVRLTTAKLFVAVA 88
                                      689999999999999********99987 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.011
                                       HHHHHHHT-..SSHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsD..pspeVReaAakaLga 26 
                                       P+l + l D  +   VR+ +a+aLg 
  gi|336253656|ref|YP_004596763.1| 100 PALGERLADdaEFYYVRARCAEALGY 125
                                       666556644478899*********96 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.018
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +l   l D++  VR+  a aL+a+
  gi|336253656|ref|YP_004596763.1| 179 TLAAFLGDEHELVRYHLATALVAI 202
                                       677789***************998 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.01
                                       -SSHHHHHHHHHHHHHHH CS
                              HEAT  11 DpspeVReaAakaLgala 28 
                                        ++  VR  Aa+aLg la
  gi|336253656|ref|YP_004596763.1| 225 AENDYVRGRAAEALGLLA 242
                                       48999**********998 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.8e-08   2.5e-05      28     107 ..      30     109 ..      22     129 .. 0.92
   2 ?    3.4   0.0     0.051        71       7      45 ..     159     199 ..     153     210 .. 0.76
   3 ?   -1.5   0.0       1.6   2.2e+03      28      52 ..     219     245 ..     195     285 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.8e-08
                              Cnd1  28 krLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteiseksenaiynllpdiiskl 104
                                       ++L D dp VRkta+  +  L++++   ++ ++ +l++ leD+ + V+  +  ++  ++ ++++a+++ +p +  +l
  gi|336253656|ref|YP_004596763.1|  30 EGLADADPEVRKTALRDLRTLVDEQGAGVRPLVPTLRRFLEDDGRAVRLTTAKLFVAVAANEPDAVVEAVPALGERL 106
                                       5799****************************************************************999998888 PP

                              Cnd1 105 sda 107
                                        d+
  gi|336253656|ref|YP_004596763.1| 107 ADD 109
                                       864 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.051
                              Cnd1   7 irtlg..cirvpnlveylvepLrkrLkDedpyVRktaaivv 45 
                                        ++l+  +i  p+ ++  ve L + L De++ VR + a ++
  gi|336253656|ref|YP_004596763.1| 159 AKALAcvAIGEPTRLDHHVETLAAFLGDEHELVRYHLATAL 199
                                       55666344556788899999999999999999998777665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.6
                              Cnd1  28 krLkD..edpyVRktaaivvakLilnd 52 
                                       +r++D  e+ yVR  aa ++  L ++d
  gi|336253656|ref|YP_004596763.1| 219 ARVEDeaENDYVRGRAAEALGLLARAD 245
                                       555552247899999988877776665 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   3.0   3.5e-08   4.8e-05       2      22 ..     330     351 ..     329     352 .] 0.98

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.5e-08
                     zinc_ribbon_2   2 CpnCGaelqdnakF.CpyCGtp 22 
                                       Cp+CG  l+d+a+  Cp+CG+p
  gi|336253656|ref|YP_004596763.1| 330 CPHCGLALPDGAPPmCPRCGAP 351
                                       ********************98 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0047       6.4     181     196 ..      28      43 ..      12      50 .. 0.81
   2 !    8.7   0.0   0.00082       1.1     169     209 ..      53      93 ..      45     102 .. 0.91
   3 ?   -3.5   0.0       4.4     6e+03     174     193 ..     173     192 ..     168     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0047
                           CLASP_N 181 lkkgleDanptVReta 196
                                         +gl+Da+p+VR+ta
  gi|336253656|ref|YP_004596763.1|  28 CLEGLADADPEVRKTA 43 
                                       4589*********997 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00082
                           CLASP_N 169 easllldliekslkkgleDanptVRetaRstfweffkvwPs 209
                                       e+ ++++ ++++l+++leD   +VR t+ ++f+ ++ + P+
  gi|336253656|ref|YP_004596763.1|  53 EQGAGVRPLVPTLRRFLEDDGRAVRLTTAKLFVAVAANEPD 93 
                                       567899****************************9999887 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.4
                           CLASP_N 174 ldliekslkkgleDanptVR 193
                                       ld ++++l ++l D    VR
  gi|336253656|ref|YP_004596763.1| 173 LDHHVETLAAFLGDEHELVR 192
                                       46677778888888777777 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   2.8e-05     0.039      88     165 ..      32     110 ..      24     148 .. 0.80
   2 ?    1.0   0.0     0.085   1.2e+02     353     409 ..     151     207 ..     132     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                                       CCSSSHHHHHHHHHHHCCC--CCCH..HHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT CS
                         Adaptin_N  88 lkdpnqlirglALrvLssirvpela..edlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikells 162
                                       l d ++ +r  ALr L ++ +++ a  + l+p++++ l+d+   vr + a  ++++  ++pd++ +  v+ + e l+
  gi|336253656|ref|YP_004596763.1|  32 LADADPEVRKTALRDLRTLVDEQGAgvRPLVPTLRRFLEDDGRAVRLTTAKLFVAVAANEPDAVVEA-VPALGERLA 107
                                       7788999999999999999988887779999999999999999999999999999999999999998.999999998 PP

                                       -SS CS
                         Adaptin_N 163 dkd 165
                                       d+ 
  gi|336253656|ref|YP_004596763.1| 108 DDA 110
                                       875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.085
                                       XHHHHHHHHHHHHHHHHHSCCHHHHHHHHHHHHHTTXXHHHHHHHHHHHHHHHHHST CS
                         Adaptin_N 353 dedfksklvkaIgrlaekfatdaewvldvllellslsgesvkdeivevirdliqkvp 409
                                       + d++ kl+ka++ +a+  +t  ++++++l  +l ++ e v++  + ++  +  ++p
  gi|336253656|ref|YP_004596763.1| 151 ETDVRPKLAKALACVAIGEPTRLDHHVETLAAFLGDEHELVRYHLATALVAIGCERP 207
                                       567888888888888888899999999999999998888888888877777765555 PP

>> RTP1_C1  Required for nuclear transport of RNA pol II C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-05     0.037       3     103 ..      27     124 ..      25     166 .. 0.84
   2 ?   -2.0   0.0       2.8   3.9e+03      82     107 ..     220     243 ..     172     248 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                           RTP1_C1   3 ealkdlqdpllpvrahglvlLrkliekkskeavldiekilkllleaLkdedsYvYLnaikgLvaLadvfpeevl... 76 
                                       ++l+ l d  + vr  +l+ Lr+l+ ++     + ++ ++ +l + L+d+   v L   k++va+a   p+ v+   
  gi|336253656|ref|YP_004596763.1|  27 TCLEGLADADPEVRKTALRDLRTLVDEQG----AGVRPLVPTLRRFLEDDGRAVRLTTAKLFVAVAANEPDAVVeav 99 
                                       67899*********************997....8899999999999**********************999987222 PP

                           RTP1_C1  77 klLleeyeeenekeslderlkvGEaLl 103
                                       + L e+   +++ e    r + +EaL 
  gi|336253656|ref|YP_004596763.1| 100 PALGERL--ADDAEFYYVRARCAEALG 124
                                       4455555..444444556777777776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                           RTP1_C1  82 eyeeenekesld.erlkvGEaLlrvir 107
                                       ++   +++++ d  r +++EaL  ++r
  gi|336253656|ref|YP_004596763.1| 220 RV---EDEAENDyVRGRAAEALGLLAR 243
                                       33...3333334256778888876665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.9   1.8e-05     0.024      12      37 ..     327     351 ..     320     352 .] 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                               DZR  12 arfCseCgtklkavaaedrCpsCgek 37 
                                       +  C++Cg +l+   a+ +Cp+Cg++
  gi|336253656|ref|YP_004596763.1| 327 DDECPHCGLALP-DGAPPMCPRCGAP 351
                                       556777777774.5667777777764 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   1.5   0.00029       0.4       4      30 ..     327     352 .]     325     352 .] 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                       Prok-RING_1   4 gkkCpvCgkelkeedDiVvCpeCgtpy 30 
                                       +++Cp Cg +l ++    +Cp Cg+py
  gi|336253656|ref|YP_004596763.1| 327 DDECPHCGLALPDG-APPMCPRCGAPY 352
                                       679********999.5579*******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 ?    9.1   5.7   0.00062      0.85       4      25 ..     329     351 ..     327     351 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00062
                       zf-ribbon_3   4 rCPnCGa.plssddnvCpyCGtk 25 
                                       +CP+CG  +++   ++Cp CG++
  gi|336253656|ref|YP_004596763.1| 329 ECPHCGLaLPDGAPPMCPRCGAP 351
                                       7******88788889******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 ?    6.5   0.8    0.0068       9.4      22      34 ..     322     335 ..     313     339 .. 0.66
   2 ?    4.8   1.2     0.022        30      24      34 ..     340     350 ..     336     352 .] 0.76

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0068
                       Zn-ribbon_8  22 sdaplta.CPeCgs 34 
                                       s ++  + CP+Cg 
  gi|336253656|ref|YP_004596763.1| 322 SSPDADDeCPHCGL 335
                                       43334444****95 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.022
                       Zn-ribbon_8  24 apltaCPeCgs 34 
                                        +++ CP+Cg+
  gi|336253656|ref|YP_004596763.1| 340 GAPPMCPRCGA 350
                                       55677*****8 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   1.7    0.0079        11      13      28 ..     320     334 ..     318     336 .. 0.82
   2 ?    3.8   0.7     0.051        70      22      29 ..     343     350 ..     335     352 .] 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0079
                     zinc_ribbon_9  13 svspdedsdvlCPhCg 28 
                                       +vs+++ +d  CPhCg
  gi|336253656|ref|YP_004596763.1| 320 TVSSPDADDE-CPHCG 334
                                       5677889999.****8 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.051
                     zinc_ribbon_9  22 vlCPhCgg 29 
                                       ++CP+Cg 
  gi|336253656|ref|YP_004596763.1| 343 PMCPRCGA 350
                                       48****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2471.41
//
Query:       gi|336253657|ref|YP_004596764.1|  [L=58]
Description: hypothetical protein Halxa_2260 [Halopiger xanaduensis SH-6]
Scores for 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:                       132  (0.00736237); expected 358.6 (0.02)
Passed bias filter:                      115  (0.00641419); 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: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 471.43
//
Query:       gi|336253658|ref|YP_004596765.1|  [L=390]
Description: hypothetical protein Halxa_2261 [Halopiger xanaduensis SH-6]
Scores for complete 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      2e-16   60.3   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
     0.0019   18.0   1.3     0.0031   17.3   1.3    1.4  1  TAT_signal    TAT (twin-arginine translocation) pathway signa


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 !   60.3   0.0   2.3e-20     2e-16       5     234 ..      83     342 ..      82     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 2.3e-20
                                       SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-H.......HHHHHH--SEEEE-GGG...GG CS
                      Peripla_BP_2   5 spsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidv.......EklaalkPDlvilskglgltde 74 
                                       + +++++ +alG++d ++g++  +++ +  ++++   v+v  d+   +       E+  +l  D+ + ++++     
  gi|336253658|ref|YP_004596765.1|  83 TGDYADMGVALGQADGLTGIGVRARFGTHLYDEL-PGVSVAEDDLTELwqdgtgkERFYELEADVHLIDPNF--MIN 156
                                       678999999*****************99999988.5555555555555666666699999999998888888..455 PP

                                       GHHHHHHHS-EEE----TTS................HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT CS
                      Peripla_BP_2  75 deellksgiptvivessntg................eslkeqiralgellgledeaeklvaeidsklaaaksaidse 135
                                         e ++ +++ ++ + ++++                ++l+e +++++e++++ +++e++ + +d+ l +++s+++ e
  gi|336253658|ref|YP_004596765.1| 157 RLEWDRGDVDEIATQVGPFIgntsftrvydwheyryYGLYEAFETVAEVFQERARYEAFEQLHDGVLSDVQSRLPAE 233
                                       5555555555555555555555556669999********************************************** PP

                                       .-EEEEEEEETTE....EEEE-TTSTTTHHHHTS--EESTTT--....STT-EEE-HHHHHHH--SEEEEEEH.... CS
                      Peripla_BP_2 136 kpkpvlvfggade..ggyvvagsnsyigdlldalgieniaaesk....kseyeeisaEqilasdpdvifvsgr.... 202
                                       +p+ ++++    +   +y +   ++  ++  ++l + +++a+++    + +++ei+ E++l+ dpdv+ ++ +    
  gi|336253658|ref|YP_004596765.1| 234 TPDVAVLYPAEVPpeTFYPYRIGDGIQSKHWRDLEVGDALAAEGvadaQAGGGEIDYETLLEIDPDVLAIRLQgeit 310
                                       666555554443433666666666666777777******888888******************************** PP

                                       HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 203 aeadnktgleflkenpllaelpAvkngrVyal 234
                                       +e + ++++++l ++++++el Av+n r+++ 
  gi|336253658|ref|YP_004596765.1| 311 EEYFESEIASHLRNHEVASELQAVQNDRIIYG 342
                                       *****************************997 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.3   3.4e-07    0.0031       3      25 ..      11      33 ..       9      34 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.4e-07
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                      +RRd +K ++Aa  +++l+gc++
  gi|336253658|ref|YP_004596765.1| 11 TRRDAIKYGGAAIGGGLLAGCTG 33
                                      8********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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 0.21s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3008.58
//
Query:       gi|336253659|ref|YP_004596766.1|  [L=303]
Description: Non-specific serine/threonine protein kinase [Halopiger xanaduensis SH-6]
Scores for complete 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  155.2   0.2      2e-45  154.7   0.2    1.1  1  RIO1      RIO1 family
    3.1e-28   97.8   0.1    6.2e-28   96.9   0.1    1.5  1  Rio2_N    Rio2, N-terminal
    6.6e-05   23.0   1.2      0.011   15.7   1.1    2.9  1  APH       Phosphotransferase enzyme family
     0.0051   16.2   0.1     0.0088   15.4   0.1    1.4  1  Pkinase   Protein kinase domain
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.18   11.4   0.0    1.2  1  WaaY      Lipopolysaccharide core biosynthesis protein (WaaY)


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 !  154.7   0.2   5.6e-49     2e-45       1     182 [.     107     276 ..     107     282 .. 0.95

  Alignments for each domain:
  == domain 1  score: 154.7 bits;  conditional E-value: 5.6e-49
                                       EEEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEE CS
                              RIO1   1 nVyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpie 77 
                                       +Vy+++s   k +a+K ++ ++t+F++++k ++++++    +++ ++ ++++ +ae+Ef++L++l+   v+vP+pi+
  gi|336253659|ref|YP_004596766.1| 107 DVYEVRS--YKPLALKYHREGYTNFREVHKERDYTSD----REHVSWMYTARKAAEREFDILEELYPD-VSVPRPID 176
                                       5888866..889************************9....789***********************9.******** PP

                                       EETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEE CS
                              RIO1  78 lkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQave 154
                                        +rh++vme ++  gv++ + k  +  ++   +++ +l+e++++  e+g+vHaD+SeyNv+v+e +v+i+D++Qav+
  gi|336253659|ref|YP_004596766.1| 177 QNRHAIVMEKMD--GVELSRTKLDD--DQVLGVLDLLLSEIARAH-EHGYVHADMSEYNVFVSEAGVTIFDWPQAVP 248
                                       ************..99999988877..8999********999998.******************************* PP

                                       TTSTTHHHHHHHHHHHHHHHHHTTC--- CS
                              RIO1 155 ldhpnalefLerDveniikfFrrkgvek 182
                                       +dh+na+efL+rD++n i +Frrk+ ++
  gi|336253659|ref|YP_004596766.1| 249 TDHENAAEFLRRDLSNAIGYFRRKYPQH 276
                                       ************************9875 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.1   1.7e-31   6.2e-28       2      82 .]      10      90 ..       9      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 1.7e-31
                            Rio2_N  2 ryLskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyLALktlv 80
                                       +L++edf +L++vE+gmr +e+V +e++ e+++l+eeev++rl+r+lk++li++kt++y+GY L++eGyD+LAL++lv
  gi|336253659|ref|YP_004596766.1| 10 PELEEEDFYILSGVEQGMRFSEWVQREKLPEFANLTEEEVDYRLERCLKRGLIEKKTIQYEGYTLQFEGYDTLALRALV 88
                                      68****************************************************************************9 PP

                            Rio2_N 81 kr 82
                                      +r
  gi|336253659|ref|YP_004596766.1| 89 QR 90
                                      98 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.1   2.9e-06     0.011       4     117 ..      99     243 ..      97     289 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.9e-06
                                       EE--.SSCEEEEEEETT--EEEEEE-TT.S-HHHHHHHHH....................HHHHHHHTT-..B--B- CS
                               APH   4 elsggasnrtylvttpagryvlrrnppa.raaeeirreva....................llrlLakagv..pvPev 57 
                                       +l+ g ++++y+v + + +++l+ ++++  + +e+++e +                    +++ L+++ +  +vP++
  gi|336253659|ref|YP_004596766.1|  99 PLGVGKESDVYEVRSYK-PLALKYHREGyTNFREVHKERDytsdrehvswmytarkaaerEFDILEELYPdvSVPRP 174
                                       56667777777777765.77777777776666666666666666666666665555555544444444334478888 PP

                                       CTTBS-EEETTEEEEEEE----EE-SS.HHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-...............S CS
                               APH  58 lagdtddeeigllfalieyvpgrsllr.klsaaqlpellealgeflaalhqvdpaalpla...............d 117
                                       ++       + +++ ++e ++g  l+r kl+++q   +l+ l + +a+ h++++ ++ ++               +
  gi|336253659|ref|YP_004596766.1| 175 ID-------QNRHAIVMEKMDGVELSRtKLDDDQVLGVLDLLLSEIARAHEHGYVHADMSeynvfvseagvtifdW 243
                                       88.......4445668888888888888888888888888888888888888644333332333333333333330 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.5e-06    0.0088       6     144 ..      99     245 ..      94     259 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-06
                                       EEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTT.B--EEEEEEE............ CS
                           Pkinase   6 klGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpn.ivrlyevfee............ 69 
                                        lG G+ + Vy+++   + k  A+K  ++  ++    ++v +E  +    +h     +  ++ e+            
  gi|336253659|ref|YP_004596766.1|  99 PLGVGKESDVYEVR---SYKPLALKYHREGYTNF---REVHKERDYTSDREHVSwMYTARKAAERefdileelypdv 169
                                       56777777777776...56667776655443332...3355555555555543302222222222566666677777 PP

                                       .......SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE CS
                           Pkinase  70 .......kdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKi 139
                                              +++  +v+e ++g el +       l+++++  ++  +l+ ++  H++g +H D+   N++++ ++ + i
  gi|336253659|ref|YP_004596766.1| 170 svprpidQNRHAIVMEKMDGVELSRTK-----LDDDQVLGVLDLLLSEIARAHEHGYVHADMSEYNVFVS-EAGVTI 240
                                       7777775777789******99887665.....99************************************.777888 PP

                                       -SGTT CS
                           Pkinase 140 tDFGl 144
                                        D+  
  gi|336253659|ref|YP_004596766.1| 241 FDWPQ 245
                                       88855 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     5e-05      0.18     119     190 ..     181     255 ..     171     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5e-05
                              WaaY 119 imiieyiegielvdmpeiddevkakik...qsieklhqlgmvsgdphrgnfivkkdevriidlsgkrasaerkak 190
                                        +++e ++g+el+     dd+v + +    + i + h++g v  d    n  v++ +v i d     ++ +  a 
  gi|336253659|ref|YP_004596766.1| 181 AIVMEKMDGVELSRTKLDDDQVLGVLDlllSEIARAHEHGYVHADMSEYNVFVSEAGVTIFDWPQAVPTDHENAA 255
                                       5789*********99999999988765222678899**************************8877777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2112.09
//
Query:       gi|336253660|ref|YP_004596767.1|  [L=390]
Description: iron-III ABC transporter periplasmic substrate-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-22   79.8   0.0    3.9e-22   79.0   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 !   79.0   0.0   2.2e-26   3.9e-22       2     234 ..      76     341 ..      76     343 .. 0.83

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 2.2e-26
                                       EE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT............TS-BSBESSSB-H..HHHHHH--SEEEE- CS
                      Peripla_BP_2   2 aslspsvteillalGatdkvvgvdtttsdpldadklee..........aivevgadgeidv..EklaalkPDlvils 66 
                                       ++++ +++++ +alG+++ ++g+++++++ +d ++++           + +ev+++ e+      +   +P +++  
  gi|336253660|ref|YP_004596767.1|  76 VAYDGGYADMAVALGQAEGMTGIGGADRYYTDVYDELPdvsvnreaieSYPEVRTREEFYEleNDVHLYDPQMLVNW 152
                                       78999*****************************9997666655544444666666666334445666677777777 PP

                                       GGG.....GGGHHHHHHHS-EEE----TTS.....HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT. CS
                      Peripla_BP_2  67 kgl..gltdedeellksgiptvivessntg.....eslkeqiralgellgledeaeklvaeidsklaaaksaidsek 136
                                        ++  ++++e+ +   + +  +i++ s        + l+e ++ ++e++++++++e+++  +d+ +a+++  ++ ++
  gi|336253660|ref|YP_004596767.1| 153 FDWreEDVAEIADSVGPFVGNLIFRRSDDWheyryYTLYEAFEKVAEVFQEQARYEAFADLHDEFIADIQRQLPPAD 229
                                       7774444444444444444445555555449*********************************************7 PP

                                       -EEEEEEEETTE........EEEE-TTSTTTHHHHTS--EESTTT--.....STT-EEE-HHHHHHH--SEEEEEEH CS
                      Peripla_BP_2 137 pkpvlvfggade......ggyvvagsnsyigdlldalgieniaaesk.....kseyeeisaEqilasdpdvifvsgr 202
                                       ++p +++ +++       ++y ++ +++ +++  d lg+e+++a  +     + ++++++ E +l+ dpdvi+ +g+
  gi|336253660|ref|YP_004596767.1| 230 DRPSVLLTYDETlepesfSPYRLTDRGTSKKQWRD-LGVEDALAGTGidnlsTTDRGKLDYEGLLEIDPDVILLRGH 305
                                       77777777777789999777777777777777655.*********99****************************** PP

                                       ....HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                      Peripla_BP_2 203 ....aeadnktgleflkenpllaelpAvkngrVyal 234
                                           a++++ t+le + e+  +++l+Av+n rVy+ 
  gi|336253660|ref|YP_004596767.1| 306 erksATEFRETVLEYMREHSSASRLTAVQNDRVYRG 341
                                       **********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2991.99
//
Query:       gi|336253661|ref|YP_004596768.1|  [L=196]
Description: 50S ribosomal protein L15e [Halopiger xanaduensis SH-6]
Scores for 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-83  276.6   6.0    1.1e-82  276.4   6.0    1.0  1  Ribosomal_L15e  Ribosomal L15
  ------ inclusion threshold ------
       0.12   12.1   0.3       0.85    9.4   0.3    2.0  1  YjbF            Group 4 capsule polysaccharide lipoprotein gf


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 !  276.4   6.0   1.3e-86   1.1e-82       1     188 [.       4     188 ..       4     190 .. 0.99

  Alignments for each domain:
  == domain 1  score: 276.4 bits;  conditional E-value: 1.3e-86
                                       -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..--- CS
                    Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskg 77 
                                       ++y++++++wk++++  l el+++r +e+r++ a++r+erptrld+Ar+LGYkakqGivv rv+vr+G+++k  +++
  gi|336253661|ref|YP_004596768.1|   4 SFYSHIKDAWKDPDDGKLGELQWQRKQEWRKQGAIERIERPTRLDKARELGYKAKQGIVVTRVSVRKGTARK--QRF 78 
                                       68**********************************************************************..*** PP

                                       SS---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGG CS
                    Ribosomal_L15e  78 ktgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkv 154
                                       k+gr++krqgvn++ ++k++q+i eerv+rk+pnlrvLnSYwvgeDg++k++EvilvDp+h+ai+nd+++nwic++ 
  gi|336253661|ref|YP_004596768.1|  79 KAGRRSKRQGVNRIGRRKNIQRIGEERVSRKYPNLRVLNSYWVGEDGSQKWFEVILVDPEHPAIENDDDLNWICDDA 155
                                       ***************************************************************************** PP

                                       GTTGGGGT-SHHHHHHTT-S-SS.TT-TTTSS-T CS
                    Ribosomal_L15e 155 hkhRelrGltsagkksRGlrkkglkgaekirgsr 188
                                       h++R++rGlt+agk +RGl+++g kgaek+r+s+
  gi|336253661|ref|YP_004596768.1| 156 HQNRAFRGLTNAGKDNRGLNNRG-KGAEKVRPSN 188
                                       ***********************.*******997 PP

>> YjbF  Group 4 capsule polysaccharide lipoprotein gfcB, YjbF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.3   9.4e-05      0.85      88     165 ..      11     124 ..       3     129 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 9.4e-05
                                       -GGGGGGG--.TT-EEEEEEEE....................................EETTEEEEEEEEEEEEEEE CS
                              YjbF  88 dplalallalsragswqrildw....................................qekyrygyladstfrragk 128
                                       d++++++  + +  +wqr+ +w                                    +++   + +++  +r+ ++
  gi|336253661|ref|YP_004596768.1|  11 DAWKDPDDGKLGELQWQRKQEWrkqgaierierptrldkarelgykakqgivvtrvsvRKGTARKQRFKAGRRS-KR 86 
                                       56666665555666666666666666666666666666666666666666666665552222222223333333.33 PP

                                       EEEEETTEEEEEEEE.EEEEEETTTTEEEEEEEEEETT CS
                              YjbF 129 etvtilektvettri.eEsvevpaleaefqNqYwvdsq 165
                                       ++v+  +++ +++ri eE+v+ +  + ++ N+Ywv ++
  gi|336253661|ref|YP_004596768.1|  87 QGVNRIGRRKNIQRIgEERVSRKYPNLRVLNSYWVGED 124
                                       444444666666655378999999***********543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1418.66
//
Query:       gi|336253662|ref|YP_004596769.1|  [L=144]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-34  118.7   0.4      3e-34  118.6   0.4    1.0  1  Usp            Universal stress protein family
  ------ inclusion threshold ------
       0.13   11.8   0.0       0.21   11.1   0.0    1.3  1  AA_permease_N  Amino acid permease N-terminal


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 !  118.6   0.4   3.3e-38     3e-34       3     141 .]       3     144 .]       1     144 [] 0.94

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 3.3e-38
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.....HHHH CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.....akaa 74 
                                        ++lV++D+s++s++Ale+A  +   ++a++++lhv+dp +++a+   +  +     +l+e  +e+++     a+++
  gi|336253662|ref|YP_004596769.1|   3 NHVLVPIDDSSQSTEALEFACSE--YPDATITALHVLDPGDFYAATGVEGGTMANYDQLQEHHEERAEnllegARER 77 
                                       69*******************95..56689***************99999999988888888888888899****** PP

                                       HHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  75 aeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       a+++gv+ e++ ++g ++++i+++a+e+d+d iV+Gs+gr+g sr+llGSv+e v+r++p+pV++Vr
  gi|336253662|ref|YP_004596769.1|  78 AADRGVEIETDHVVGGVSRSIVDYADEHDVDHIVIGSHGRTGASRILLGSVAETVARRSPVPVTIVR 144
                                       ******************************************************************8 PP

>> AA_permease_N  Amino acid permease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.3e-05      0.21      24      59 ..      41      76 ..      36      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.3e-05
                     AA_permease_N 24 dfYrntasvsgaklsRPsLaeLHeelkknsal.avee 59
                                      dfY+ t++ +g  ++   L+e Hee ++n  l  ++e
  gi|336253662|ref|YP_004596769.1| 41 DFYAATGVEGGTMANYDQLQEHHEERAEN-LLeGARE 76
                                      9***************************9.3333444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1047.62
//
Query:       gi|336253663|ref|YP_004596770.1|  [L=239]
Description: phosphoribosyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-11   41.5   0.2    1.5e-10   40.9   0.2    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00075   19.5   0.0     0.0025   17.8   0.0    1.8  2  HTH_3         Helix-turn-helix
  ------ inclusion threshold ------
      0.064   13.1   0.0       0.18   11.6   0.0    1.8  1  HTH_IclR      IclR helix-turn-helix domain
       0.12   11.9   0.0         16    5.0   0.0    2.2  2  DUF4992       Domain of unknown function


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 !   40.9   0.2   3.2e-14   1.5e-10      21     132 ..     104     220 ..      86     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3.2e-14
                                       EEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE................EE----TTSE CS
                      Pribosyltran  21 eileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes........rlledpagkk 89 
                                       e +e    +pdvv++ a+ G+++a  la++ +v++ay  k+k  +      ar +  +s          +++  g++
  gi|336253663|ref|YP_004596770.1| 104 EGFEF--DRPDVVLTAATDGITLAASLASYYGVRCAYAKKSKETAVEEFIEAR-QRLQSgieltyylPESAIDSGES 177
                                       44444..89****************************9887766544433333.333336899****9********* PP

                                       EEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHH CS
                      Pribosyltran  90 VliVDDildtGgTllaalelLkekgpeevriavlvdkpateee 132
                                       Vl+VDD++ +G T +  l+++  +++ + ++ +l++ +++ +e
  gi|336253663|ref|YP_004596770.1| 178 VLVVDDLIRSGETQELLLDIVTTARADVAGVFALIAAGDDGIE 220
                                       ***********************************98887766 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.6e-07    0.0025       7      51 ..      21      65 ..      17      67 .. 0.91
   2 ?   -2.0   0.0      0.85   3.8e+03      40      52 ..     124     136 ..     122     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.6e-07
                                      HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSE CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvs 51
                                      +   +  eLAe +G++   ++r+ nG+  P  +++ ++ + Lg +
  gi|336253663|ref|YP_004596770.1| 21 KETRTYDELAETTGLPAGDLNRYVNGHVLPGTDRAREIVEDLGRD 65
                                      6778999*********************************99975 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.85
                                       HHHHHHHHHTSEH CS
                             HTH_3  40 tlkklakaLgvsl 52 
                                        +  la ++gv  
  gi|336253663|ref|YP_004596770.1| 124 LAASLASYYGVRC 136
                                       5678999**9975 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 ?   11.6   0.0     4e-05      0.18       4      39 ..      12      44 ..      11      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4e-05
                                      HHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHH CS
                          HTH_IclR  4 RalaiLdalaeapqeltlselArrtglpkStvhRlL 39
                                      Ra+++L++l e++      elA+ tglp     R++
  gi|336253663|ref|YP_004596770.1| 12 RAVDVLRMLKETRT---YDELAETTGLPAGDLNRYV 44
                                      9************9...5**********98777765 PP

>> DUF4992  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0036        16     140     179 ..      25      62 ..      19      65 .. 0.89
   2 ?    4.7   0.0    0.0043        19     133     169 ..     139     175 ..     132     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0036
                           DUF4992 140 kfstlvatyatipeGtdlaeyfeenpipdeekeeelayeL 179
                                       +++ l++t + +p+G dl  y++  ++p ++  +e++ +L
  gi|336253663|ref|YP_004596770.1|  25 TYDELAET-TGLPAG-DLNRYVNGHVLPGTDRAREIVEDL 62 
                                       79999999.99****.***************999998877 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0043
                           DUF4992 133 aesatevkfstlvatyatipeGtdlaeyfeenpipde 169
                                       a+++ e++ + ++++++ + +G +l+ y+ e +i+  
  gi|336253663|ref|YP_004596770.1| 139 AKKSKETAVEEFIEARQRLQSGIELTYYLPESAIDSG 175
                                       7888899999*******************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); 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:                         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 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1881.18
//
Query:       gi|336253664|ref|YP_004596771.1|  [L=245]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-15   54.6   0.1    1.1e-14   54.0   0.1    1.3  1  HTH_10    HTH DNA binding domain
  ------ inclusion threshold ------
      0.019   14.9   0.0      0.069   13.1   0.0    1.7  2  VWA_3     von Willebrand factor type A domain


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 !   54.0   0.1   1.2e-18   1.1e-14       1      52 [.     163     214 ..     163     215 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 1.2e-18
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT++qle++++A+e GY+++PR++ ++ +A++lG + st+   L+ka+ +++
  gi|336253664|ref|YP_004596771.1| 163 LTERQLEAVAAAVEVGYYEVPREAGVEVVADRLGCASSTAATLLQKAQARVM 214
                                       9************************************************998 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 ?   13.1   0.0   7.7e-06     0.069      24      70 ..     131     177 ..     127     189 .. 0.91
   2 ?   -1.1   0.0      0.18   1.6e+03     130     151 ..     202     224 ..     184     227 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.7e-06
                             VWA_3  24 LsvalrqLptndkiavllfgtkprplfpgsravsaaelqealqkike 70 
                                       L+++l++Lp++  ++v++ g ++r   p    + +++l++++++++ 
  gi|336253664|ref|YP_004596771.1| 131 LQAMLEGLPDEIDVTVRAIGEYDRHHAPLTGDLTERQLEAVAAAVEV 177
                                       899*******************9*999****************9986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.18
                             VWA_3 130 alglgsslsaamlqaLAe.asgG 151
                                       a +l ++++a+++q+L + +++G
  gi|336253664|ref|YP_004596771.1| 202 AATLLQKAQARVMQRLVQqRGRG 224
                                       55677778888888876514555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2006.76
//
Query:       gi|336253665|ref|YP_004596772.1|  [L=209]
Description: hypothetical protein Halxa_2268 [Halopiger xanaduensis SH-6]
Scores for complete 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-17   63.7   0.2    1.8e-17   63.7   0.2    2.3  3  PEMT        Phospholipid methyltransferase
      5e-05   23.6   0.1     0.0001   22.6   0.1    1.4  1  ICMT        Isoprenylcysteine carboxyl methyltransferase (ICM
    9.2e-05   21.4   0.1    0.00015   20.7   0.1    1.2  1  ERG4_ERG24  Ergosterol biosynthesis ERG4/ERG24 family
     0.0004   20.4   0.0    0.00055   20.0   0.0    1.3  1  Steroid_dh  3-oxo-5-alpha-steroid 4-dehydrogenase
    0.00055   19.5   0.4    0.00069   19.2   0.4    1.3  1  DUF1295     Protein of unknown function (DUF1295)
  ------ inclusion threshold ------
       0.13   11.5   0.1        9.1    5.4   0.0    2.1  2  Zincin_2    Zincin-like metallopeptidase


Domain annotation for each model (and alignments):
>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.9      0.19   5.6e+02      57      87 ..       5      35 ..       3      36 .. 0.85
   2 ?   -3.4   0.1       4.2   1.2e+04      71      85 ..      52      66 ..      47      70 .. 0.57
   3 !   63.7   0.2   5.9e-21   1.8e-17       3     106 .]      77     173 ..      75     173 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.19
                              PEMT 57 vgstlgflGlaLitgsaaglllallvllvyl 87
                                      ++s +   G+ L+  ++ag+++++l l+ y+
  gi|336253665|ref|YP_004596772.1|  5 LMSAVFAAGVGLALANLAGIVASALGLISYW 35
                                      56778889999********999999998886 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.2
                              PEMT 71 gsaaglllallvllv 85
                                      +s+ +++lal+ l +
  gi|336253665|ref|YP_004596772.1| 52 HSLNVVMLALTYLSW 66
                                      455555555555554 PP

  == domain 3  score: 63.7 bits;  conditional E-value: 5.9e-21
                              PEMT   3 lilGlllialglllvlssiealgefgtfygdfFlelmdklvtsGiYrylnnPeyvgstlgflGlaLitgsaagllla 79 
                                       l++G++l++ g+++++++  +lg+ +t        l   l t+G+Yry++nP+yvg +++ +G aL+ +sa  ++++
  gi|336253665|ref|YP_004596772.1|  77 LAAGAVLFVGGYAVAIAAGLDLGVEETK------GLAGDLRTGGWYRYSRNPQYVGYIVATVGFALLANSAS-VAVV 146
                                       678************************9......56789*******************************99.8888 PP

                              PEMT  80 llvllvylialkfvEephlakiYgkre 106
                                       + ++l++++ l f Eep+l+++Yg+++
  gi|336253665|ref|YP_004596772.1| 147 CAIYLCWWLSLPFAEEPWLRERYGAEY 173
                                       8899999*****************875 PP

>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   3.4e-08    0.0001      37      81 ..     112     155 ..     107     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.4e-08
                              ICMT  37 ksglykylrHPnYllfvilelatllLlcnakltalvllalvalll 81 
                                       + g y+y r P Y+++++  ++ +lL+ +a  +a+v+ ++  + l
  gi|336253665|ref|YP_004596772.1| 112 TGGWYRYSRNPQYVGYIVATVGFALLANSA-SVAVVCAIYLCWWL 155
                                       6799***********999888887777777.99999999998877 PP

>> ERG4_ERG24  Ergosterol biosynthesis ERG4/ERG24 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   4.9e-08   0.00015     350     424 ..     109     181 ..     101     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.9e-08
                        ERG4_ERG24 350 kLlvsGWyglarkinYlgDwlqslswsLatgfqsv..lpyfyvlyFlvlLvhRelRDeekCkkkYGedweeYkkkvp 424
                                        L + GWy+++r+++Y+g ++ ++ ++L +  +sv  +   y +++l l     + +e   +++YG+++e+Y  +vp
  gi|336253665|ref|YP_004596772.1| 109 DLRTGGWYRYSRNPQYVGYIVATVGFALLANSASVavVCAIYLCWWLSL----PFAEEPWLRERYGAEYERYAERVP 181
                                       57789***********************998887511444555555554....6788999**************998 PP

>> Steroid_dh  3-oxo-5-alpha-steroid 4-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.8e-07   0.00055      42     123 ..      77     158 ..      47     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-07
                        Steroid_dh  42 lllgivlfvlgmliniksdiiLrelrkegetkykiprgglFelvsapnyfgEilewigyalvtksla.alaFalftv 117
                                       l  g+vlfv g  + i +   L    + +  +  + +gg++ +   p+y+g i+  +g+al++ s   a++ a++ +
  gi|336253665|ref|YP_004596772.1|  77 LAAGAVLFVGGYAVAIAAGLDLG-VEETKGLAGDLRTGGWYRYSRNPQYVGYIVATVGFALLANSASvAVVCAIYLC 152
                                       66789999999999999999998.555555666899***************************98753778888888 PP

                        Steroid_dh 118 lnltvr 123
                                         l++ 
  gi|336253665|ref|YP_004596772.1| 153 WWLSLP 158
                                       877653 PP

>> DUF1295  Protein of unknown function (DUF1295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.4   2.3e-07   0.00069     152     235 .]     107     180 ..      43     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.3e-07
                           DUF1295 152 kgkvldsGLwrysRHPNYfgealiWwglflialealeglealaiagpllltlllvfvsgipllEkkalkkykdkeey 228
                                       +g + + G +rysR P Y g ++  +g+ l+a +a+     +++++ +     l  + + p  E+  l++++  +ey
  gi|336253665|ref|YP_004596772.1| 107 AGDLRTGGWYRYSRNPQYVGYIVATVGFALLANSASV----AVVCA-IY----LCWWLSLPFAEEPWLRERY-GAEY 173
                                       57788899**********************9987732....23333.33....3444468889988888776.699* PP

                           DUF1295 229 reYqkkt 235
                                       ++Y++++
  gi|336253665|ref|YP_004596772.1| 174 ERYAERV 180
                                       ***9986 PP

>> Zincin_2  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1    0.0058        17      94     124 ..       1      31 [.       1      98 [. 0.88
   2 ?    5.4   0.0    0.0031       9.1     170     192 ..     159     181 ..     155     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0058
                                       ------HHHHHHHHHHHHHHHHTT--BTTSS CS
                          Zincin_2  94 llrqvggavfgaqvGqalgeLssevlgqtdv 124
                                       +++++ +avf+a vG al++L++ v ++  +
  gi|336253665|ref|YP_004596772.1|   1 MTDALMSAVFAAGVGLALANLAGIVASALGL 31 
                                       56778999***************99887655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0031
                                       HHTSTHHHHHHHHHHHHHHT--- CS
                          Zincin_2 170 FaavpWLrehllsaveeyargit 192
                                       Fa+ pWLre+  ++ e+ya+ + 
  gi|336253665|ref|YP_004596772.1| 159 FAEEPWLRERYGAEYERYAERVP 181
                                       99*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 1736.57
//
Query:       gi|336253666|ref|YP_004596773.1|  [L=439]
Description: hypothetical protein Halxa_2269 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.083   11.1   0.1       0.63    8.2   0.0    2.4  2  EzrA             Septation ring formation regulator, EzrA
          3    8.2   6.7        7.9    6.9   6.0    2.1  1  Fez1             Fez1


Domain annotation for each model (and alignments):
>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0     7e-05      0.63     118     157 ..      98     137 ..      69     148 .. 0.82
   2 ?   -0.8   0.0     0.035   3.2e+02     345     395 ..     387     435 ..     383     437 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 7e-05
                                       HHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTT CS
                              EzrA 118 kkileelkelteseeknreeieklkekYrelrkkllanrf 157
                                       +++++e++ + e  +  re++ +  +++r+lr++++a++ 
  gi|336253666|ref|YP_004596773.1|  98 EAVRKEIDRIHETARSRREAVAESPDRFRTLRRSIRARES 137
                                       6899*******************************98764 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.035
                                       THHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHH CS
                              EzrA 345 klrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekq 395
                                       +++++++++ +l ++ +++  +le++ +aY  +  +le + + ++ +ee++
  gi|336253666|ref|YP_004596773.1| 387 RIEQIDSQIRDLIDWNRKM--ELESEYAAYVVVGAQLEAIPDAVSVFEERL 435
                                       5555555555555555544..455666666666666666666666666655 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.0   0.00089       7.9      41     147 ..      70     195 ..      65     339 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00089
                              Fez1  41 relrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa... 114
                                       + ++ +l++ ee i+ + + l+  +  +e + +e++r +++a   re v +  + ++ lr+++++ ++  e a+   
  gi|336253666|ref|YP_004596773.1|  70 KAVEDALDRLEELIDAVPAPLSADDVPNEAVRKEIDRIHETARSRREAVAESPDRFRTLRRSIRARESAGEAAVafe 146
                                       6678899999***************************************************9999766555554655 PP

                              Fez1 115 ................lesdeakaqrqeaeeleelkreverlraeLkee 147
                                                       +  ++ +++r++ +++++ ++++  l+ +L+ e
  gi|336253666|ref|YP_004596773.1| 147 avegdrsradveaareEVRTRLEERRAAVDHVGDDRQRTLLLEYRLERE 195
                                       5555544444433332222222222333333333333333333344443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.21s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 3423.19
//
Query:       gi|336253667|ref|YP_004596774.1|  [L=647]
Description: threonyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-32  111.5   0.0    8.4e-32  110.6   0.0    1.5  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
    2.8e-16   59.4   0.6    2.8e-16   59.4   0.6    2.4  3  HGTP_anticodon   Anticodon binding domain
    1.9e-13   50.3   0.0    3.5e-13   49.4   0.0    1.5  1  tRNA_SAD         Threonyl and Alanyl tRNA synthetase second a
    1.2e-12   47.6   0.1    2.5e-12   46.6   0.1    1.6  1  TGS              TGS domain
  ------ inclusion threshold ------
      0.089   12.3   0.9       0.16   11.5   0.9    1.3  1  HGTP_anticodon2  Anticodon binding domain of tRNAs
      0.091   12.0   0.0       0.21   10.8   0.0    1.6  2  tRNA-synt_His    Histidyl-tRNA synthetase


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 !  110.6   0.0   2.8e-35   8.4e-32       7     179 .]     329     534 ..     323     534 .. 0.92

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 2.8e-35
                                       TSEEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevlrskr.LPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeaslddslr 81 
                                        d+e+ LkP+n+++++++++d+   s+r LP+++++ + +yR+E++ +++GL Rv  F+ +dg+ f+ +++++++++
  gi|336253667|ref|YP_004596774.1| 329 GDDEFGLKPMNCPGHAAIFQDQ-SWSYRdLPIRYAENGKVYRKEQRgELSGLSRVWAFTIDDGHLFVRPDQIEQEVE 404
                                       689*******************.777555*****************99***************************** PP

                                       HHHHHHHHHHHHTT.SCEEEEEEGTTSC.................................BTTSEEEEEEEEETTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  82 dlikaisriferlglefraiielmsaks.................................adykdkkefeavsesl 125
                                       +++  i +++e++ le+   +   + ++                                 a+y++k +f   +  +
  gi|336253667|ref|YP_004596774.1| 405 QIMDMITDVLETFDLEYEMALAT-RPEKsvgsdeiweraeeqlesvledhgheyeveegdgAFYGPKIDFAFEDA-I 479
                                       ***************97544444.3333466799999999******************************99999.9 PP

                                       SEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxx RF
                      tRNA-synt_2b 126 tkgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileqn 179
                                       ++ ++  t+q + ++++er++++++ e+n+e++++mi++a  g  eR+  +++e++
  gi|336253667|ref|YP_004596774.1| 480 GRSWDGPTVQLD-FNMPERFDLNYVGEDNEEHRPVMIHRAlYGsYERFFMMLIEHY 534
                                       ***********9.***************************9999********9986 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.1   6.3e+03      10      41 ..      71     102 ..      67     103 .. 0.79
   2 ?   -2.5   0.1       1.9   5.8e+03      78      92 ..     142     156 ..     133     158 .. 0.80
   3 !   59.4   0.6   9.4e-20   2.8e-16       1      92 [.     546     632 ..     546     634 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.1
                                       SHHHHHHHHHHHHHHHHTTTSEEEEESSSSTH CS
                    HGTP_anticodon  10 kaeeleeyakklaeeLraagirvelddsnesi 41 
                                       +++e++e++++ a+  +a+ +++++dd +  i
  gi|336253667|ref|YP_004596774.1|  71 GSDEYLEVMRHSAAHCLAQAVERHYDDVDLAI 102
                                       45678999999999999999999999987666 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                                       EEEEEETTHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklk 92 
                                       e+e+vs++e++e l 
  gi|336253667|ref|YP_004596774.1| 142 EREEVSIEEAKERLA 156
                                       678999999998875 PP

  == domain 3  score: 59.4 bits;  conditional E-value: 9.4e-20
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       qv v+p+++   + + ya ++a+e+   ++rve+dd+++++ +kir a    +p+ ++vG++e e g ++vrdr ++
  gi|336253667|ref|YP_004596774.1| 546 QVRVLPISD---DNLGYAHRVANEFD--DFRVEVDDRDSTLERKIRAAHDDRVPYQIIVGDNEEEAGNISVRDRFED 617
                                       89*******...89***********9..678********************************************** PP

                                       EEEEEETTHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklk 92 
                                       +++ v++de++e l+
  gi|336253667|ref|YP_004596774.1| 618 QEYDVEIDEFKEHLE 632
                                       **********99886 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 !   49.4   0.0   1.2e-16   3.5e-13       1      44 []     175     224 ..     175     224 .. 0.99

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.2e-16
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEE.......CCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkil.......seesiakglrRIy 44 
                                       v+++s+G+ + +lC G+Hv++TgeIg + +l       ++++ +++ +RIy
  gi|336253667|ref|YP_004596774.1| 175 VTFYSQGE-WEDLCAGPHVDSTGEIGVVELLeiagaywRGDEENEMQTRIY 224
                                       89*****8.*****************************************9 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.1   8.4e-16   2.5e-12       1      60 []      10      69 ..      10      69 .. 0.98

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 8.4e-16
                                      EEEEETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECSEEEETTSBB-SSEEEEEEE CS
                               TGS  1 irvytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnGqrvgldhvLedgdvveIvt 60
                                      i v++PdG++ d++ gatveD+Ay I+ +l+ ++++++ +G +v  + ++ dg+ +eIvt
  gi|336253667|ref|YP_004596774.1| 10 IAVVLPDGSELDVDAGATVEDCAYEIGPGLGSDTVAGKLDGDLVAKEEPVYDGAELEIVT 69
                                      5699*******************************************************8 PP

>> HGTP_anticodon2  Anticodon binding domain of tRNAs
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.9   5.2e-05      0.16      43     107 ..     578     639 ..     568     646 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.2e-05
                   HGTP_anticodon2  43 sksleelvskarddgvswiviikqqnkskskekplkvkslekkedvdldldelvswlkqeirere 107
                                        ++le  ++ a+dd+v + +i+  ++   ++   + v+   +++++d+++de+ ++l++e++e++
  gi|336253667|ref|YP_004596774.1| 578 DSTLERKIRAAHDDRVPYQIIVGDNE---EEAGNISVRDRFEDQEYDVEIDEFKEHLEAELEEQR 639
                                       347888899999**********9954...444579***************************997 PP

>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.2e-05      0.21      13     105 ..     280     375 ..     272     382 .. 0.84
   2 ?   -3.7   0.1       1.8   5.4e+03      13      30 ..     439     456 ..     437     457 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.2e-05
                                       HHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH.HS-EEE-TTSSEEEE-SSSHHHHHHHHHHHH.H.TS CS
                     tRNA-synt_His  13 ieelrrrlldlfeswGYelVspPllEyldslltgagedld.qtfklvDqsgrllglRaDiTpqvaRiaahrl.n.re 86 
                                        +el+  + dl  ++GYe+V +P++  +d  ++ ++ ++  + + ++D  ++  gl +   p  a i +    + r+
  gi|336253667|ref|YP_004596774.1| 280 LKELEDFVEDLNTDAGYEYVETPHVFKTDLWHRSGHYENYqDDMFIFDVGDDEFGLKPMNCPGHAAIFQDQSwSyRD 356
                                       578888999999*****************8888876554435666999**************99999998763589* PP

                                       S-EEEEEEEEEEESS-SST CS
                     tRNA-synt_His  87 rplRlcYaGsvlrtrpdgl 105
                                        p R+   G+v+r++++g+
  gi|336253667|ref|YP_004596774.1| 357 LPIRYAENGKVYRKEQRGE 375
                                       *************998874 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHTT-E CS
                     tRNA-synt_His  13 ieelrrrlldlfeswGYe 30 
                                       +e+ +++l +++e++G e
  gi|336253667|ref|YP_004596774.1| 439 WERAEEQLESVLEDHGHE 456
                                       789999*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); 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 0.24s 00:00:00.87 Elapsed: 00:00:00.39
# Mc/sec: 4921.60
//
Query:       gi|336253668|ref|YP_004596775.1|  [L=239]
Description: HAD-superfamily hydrolase [Halopiger xanaduensis SH-6]
Scores for 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   89.9   0.0    3.1e-25   89.3   0.0    1.3  1  HAD_2            Haloacid dehalogenase-like hydrolase
    2.9e-15   57.1   0.1    5.6e-15   56.2   0.1    1.5  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.6e-12   47.3   0.1    6.4e-12   45.4   0.1    1.9  2  Hydrolase_like   HAD-hyrolase-like
     0.0028   17.8   0.0       0.01   15.9   0.0    1.8  2  Hydrolase_6      Haloacid dehalogenase-like hydrolase
     0.0041   17.0   0.0        1.5    8.6   0.0    2.2  2  Acid_PPase       Acid Phosphatase
      0.008   16.6   1.0      0.074   13.4   1.0    2.7  1  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.018   14.6   0.0        1.4    8.5   0.0    2.2  2  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph


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 !   89.3   0.0   1.2e-28   3.1e-25       1     176 [.       5     201 ..       5     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 1.2e-28
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleey.gls.elseeelrkliglslrellrklgeseeeee............... 60 
                                       ++FDlD+Tl+   ++  +  + +le+  +l+ +++ e +++++    re+ r  g +   +e               
  gi|336253668|ref|YP_004596775.1|   5 VLFDLDNTLYPYPPCNQAGKAAALERAqELGyDFDHESFAEFYQAGRREVKRDTGGTAASHErylyfkralelhtgs 81 
                                       79********9988887777777765434556************************999999*************** PP

                             HAD_2  61 .....kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedve 132
                                                l + y +   + e+++++++ke+LeeL+e+g+ ++i T+ ++  +  kle+lg+++y d ++tse+++
  gi|336253668|ref|YP_004596775.1|  82 prpgdA-LALGDAYWSAYLE-EMSLVPDAKETLEELQEQGVDIAITTNLTTTIQLAKLERLGLTDYVDLVLTSEETG 156
                                       ***963.4444444444444.5999**************************************************** PP

                             HAD_2 133 kkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikvi 176
                                       ++KP+  ++   l +l+  ++e+++vGD    Di +a ++g++++
  gi|336253668|ref|YP_004596775.1| 157 QEKPASVMFTLPLARLDSRASEAVMVGDDLeADIAGANAVGLETV 201
                                       ******************************9**********9987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.1   2.2e-18   5.6e-15       2     210 .]       3     197 ..       2     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 2.2e-18
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHH.HHHHHHHHHHHHHHHHETTTEHHHHTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkal.vaaakarsgaltgfatfigrgayaigkpewl 77 
                                       ++v+fD+d+TL+   p + ++ + aal++a+ l +  +h  ++ + +a   +++ ++ g a++ +r  y +   e+ 
  gi|336253668|ref|YP_004596775.1|   3 TAVLFDLDNTLY-PYPPCNQAGKAAALERAQELGYDFDHESFAEFyQAGRREVKRDTGGTAASHERYLYFKRALELH 78 
                                       589*********.8889999999994444444444477777777756666666666666666555666666666666 PP

                                       HHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  78 taldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq 154
                                       t                + g   al   +a++   +++  ++ p+a+e++++L+++g+++++ t+   + + + +++
  gi|336253668|ref|YP_004596775.1|  79 TGS-------------PRPGDALALG--DAYWSAYLEEM-SLVPDAKETLEELQEQGVDIAITTNLTTTIQLAKLER 139
                                       666.............7777777777..55555555544.79**********************99998888***** PP

                                       TT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 155 lG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                       lG  dy+d v++s++++  kp   ++   + +L  + +e +mVGD +  D+a++ a+g
  gi|336253668|ref|YP_004596775.1| 140 LGlTDYVDLVLTSEETGQEKPASVMFTLPLARLDSRASEAVMVGDDLEaDIAGANAVG 197
                                       ******************************************************9987 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.2     3e+03      10      32 ..      71      95 ..      66      96 .. 0.70
   2 !   45.4   0.1   2.5e-15   6.4e-12       4      74 ..     159     233 ..     157     234 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.2
                                      HHHHHHHH..---GGGEEEEES-TT CS
                    Hydrolase_like 10 ydfalevl..gsdpeevlmiGDrla 32
                                      +++ale +  +  p++ l+ GD ++
  gi|336253668|ref|YP_004596775.1| 71 FKRALELHtgSPRPGDALALGDAYW 95
                                      5667776654444889999999865 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 2.5e-15
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSS....S-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGv....trpedleepehkptyvaddlae 74 
                                       KP+ +m+   l++l+s  +e +m+GD+l++DiagAn++G+++vL         t+ +d+++ e ++++ +d+l e
  gi|336253668|ref|YP_004596775.1| 159 KPASVMFTLPLARLDSRASEAVMVGDDLEADIAGANAVGLETVLFDPSEesdaTESADRAATERQADHSIDTLGE 233
                                       9********************************************876622224446666688899999999887 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.88   2.2e+03      46      56 ..      26      36 ..       5      63 .. 0.60
   2 !   15.9   0.0     4e-06      0.01      12      66 ..     101     152 ..      95     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.88
                                      HHHHHHHHTT- CS
                       Hydrolase_6 46 eyakkleklgv 56
                                      + +++ ++lg+
  gi|336253668|ref|YP_004596775.1| 26 AALERAQELGY 36
                                      33344444444 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4e-06
                                       TTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEH CS
                       Hydrolase_6  12 gdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvts 66 
                                       +++++p a+e+l+ l+++g+++++ TN ++      ++kle+lg+    + v+ts
  gi|336253668|ref|YP_004596775.1| 101 EMSLVPDAKETLEELQEQGVDIAITTNLTTTI---QLAKLERLGLTDYVDLVLTS 152
                                       67899**********************88776...67789999988766666666 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0028       7.1       4      32 ..       3      32 ..       1      56 [. 0.67
   2 !    8.6   0.0    0.0006       1.5      42      76 ..     100     135 ..      86     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0028
                                      SEEEE-STTTSSSS.-TTTSS-S-EEE-TT CS
                        Acid_PPase  4 klivFDLDyTLWpf.evdtlvsaplkkesk 32
                                       ++ FDLD TL p+  +++  +a+  ++++
  gi|336253668|ref|YP_004596775.1|  3 TAVLFDLDNTLYPYpPCNQAGKAAALERAQ 32
                                      5799*******9851455555555555544 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0006
                                       -EE---TTHHHHHHHHHHTT--EEEEE-.-S-HHHH CS
                        Acid_PPase  42 eelklypdveeileelkskevklavaSr.tdepdla 76 
                                       ee++l pd++e leel++++v +a+    t + +la
  gi|336253668|ref|YP_004596775.1| 100 EEMSLVPDAKETLEELQEQGVDIAITTNlTTTIQLA 135
                                       799*********************986524444655 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   1.0   2.9e-05     0.074       1     140 [.       5     152 ..       5     187 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-05
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprl.wralreklllal............frellrldraglaelleallag 64 
                                       +lfD+D TL +  +     ++ + ++a +l ++  +e + + +               +++ +++ ++++le l+ g
  gi|336253668|ref|YP_004596775.1|   5 VLFDLDNTLYPYPPCNQAGKAAALERAQELgYDFDHESFAEFYqagrrevkrdtgGTAASHERYLYFKRALE-LHTG 80 
                                       79**********777744443332222222233333333333333333333333311122222333333333.6777 PP

                               HAD  65 ls.eelaaelerfvaevirpk..lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.r 137
                                        + + +a  l++++ +++++   l  p+a+e l++ +++G+ +++ ++    +  ++l++lg    l     ++d +
  gi|336253668|ref|YP_004596775.1|  81 SPrPGDALALGDAYWSAYLEEmsL-VPDAKETLEELQEQGVDIAITTNLTTTIQLAKLERLG----LTD---YVDlV 149
                                       776777777777776667666534.59******************99999999999999999....444...22223 PP

                               HAD 138 ltg 140
                                       lt 
  gi|336253668|ref|YP_004596775.1| 150 LTS 152
                                       333 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 ?    4.1   0.0     0.012        30      74     114 ..       3      51 ..       1      58 [. 0.67
   2 ?    8.5   0.0   0.00053       1.4     116     178 ..     103     162 ..      93     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.012
                                       EEEEE--BTTTEEHHH.HHHHCHH.......HTCHH-TTHHHHHHHTTG CS
                   Acid_phosphat_B  74 davvfDiDeTvLsnsp.Yqkyqgl.......gkkkfdpekfdewvnkge 114
                                        av fD+D+T+   +p +q+ ++         + +fd+e+f e+ ++g+
  gi|336253668|ref|YP_004596775.1|   3 TAVLFDLDNTLYPYPPcNQAGKAAaleraqeLGYDFDHESFAEFYQAGR 51 
                                       699*******985555144333335565555556778888888888775 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00053
                                       CCECCHHHHHHHHHHTTEEEEEEEEEECC.CHHHHHHHHHHCT-TTBSCCEEECCSTTC---HH CS
                   Acid_phosphat_B 116 kaipgalelikkvverGvkiffvsgRsee.qkaaTvenLkkagfssweklilkgkkdkqkksvv 178
                                         +p a+e +++++e+Gv+i   ++ + + q    +++L++ g ++  +l+l +++ +q+k + 
  gi|336253668|ref|YP_004596775.1| 103 SLVPDAKETLEELQEQGVDIAITTNLTTTiQ----LAKLERLGLTDYVDLVLTSEETGQEKPAS 162
                                       67999********************999944....8899999*999999999999998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1909.38
//
Query:       gi|336253669|ref|YP_004596776.1|  [L=219]
Description: L-fuculose-phosphate aldolase [Halopiger xanaduensis SH-6]
Scores for complete 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  145.5   0.2      2e-42  145.2   0.2    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 !  145.2   0.2   1.1e-46     2e-42      14     186 .]      19     190 ..       8     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 145.2 bits;  conditional E-value: 1.1e-46
                                       TSSCTTBCEEEEEE...T....STTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHHHHHHH CS
                       Aldolase_II  14 glvegtgGniSvrv...p....eedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHlaiyka 83 
                                       +l+ g  Gn+Svr    +     +d f itp+gv+++  + ed+ vv  d ge+++g   + +psse+p+H+aiy+ 
  gi|336253669|ref|YP_004596776.1|  19 DLTPGRTGNLSVRGsgdDtdagPGDAFAITPTGVPYDGFDVEDVPVVGTD-GERLDG---EMAPSSEVPMHSAIYR- 90 
                                       6888999******534415664466777********************88.****66...578*************. PP

                                       -TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHH.HS-SEEEETTT CS
                       Aldolase_II  84 rpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealk.edakavllrnH 159
                                       r+d++a+vHtHsp+a+al+ +a +++lpp+++++ + + g++vpv++ya++gt+el+e+++ a+  + + a l++nH
  gi|336253669|ref|YP_004596776.1|  91 REDVGAIVHTHSPWATALA-VA-NQPLPPIHYMIVA-V-GKRVPVAEYAPYGTDELAENIVTAMTeAGSTASLIENH 163
                                       59*****************.65.789*********9.4.789***********************77889******* PP

                                       EEEEEESSHHHHHHHHHHHHHHHHHHH CS
                       Aldolase_II 160 GlltvGetleeAvalaetleeaaeiql 186
                                       Gl++++++le A++++  +e +a+++l
  gi|336253669|ref|YP_004596776.1| 164 GLVVTAPDLETALENTHHVESLARLYL 190
                                       ************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1863.77
//
Query:       gi|336253670|ref|YP_004596777.1|  [L=167]
Description: NUDIX hydrolase [Halopiger xanaduensis SH-6]
Scores for complete 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   64.0   0.2    1.8e-17   63.6   0.2    1.1  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 !   63.6   0.2   9.9e-22   1.8e-17       5     111 ..      37     149 ..      33     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 9.9e-22
                                       EEEEEEEETTSEEEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   5 avgvvllnekgevLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygde 81 
                                       ++++ +++++g++ lv+ +    +gW +PgG ve gE+p++AArRE++EEtGlea   e l  ++ ++ +++ +g e
  gi|336253670|ref|YP_004596777.1|  37 TAAARITDPDGRIALVKNR--WSDGWIVPGGAVESGEAPADAARREVREETGLEATIDEPLLGIDQTYVSETENGGE 111
                                       667779******9999855..3555****************************996667777799999999999987 PP

                                       EEEE...EEEEEEECSGCSST.....STTTEEEEEEEE CS
                             NUDIX  82 heil...yvfleevegelepn.....denevsevrwvp 111
                                       + ++   +vf ++++g ++       + +e++++rw++
  gi|336253670|ref|YP_004596777.1| 112 TRLSaqfLVFDARADGSIPDVerlgvEQGEIRAARWFE 149
                                       7777443444478887766668999***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1258.75
//
Query:       gi|336253671|ref|YP_004596778.1|  [L=177]
Description: Orotate phosphoribosyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-16   58.1   1.3      1e-15   57.6   1.3    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00049   19.6   0.0    0.00061   19.3   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.019   14.5   0.2      0.028   13.9   0.2    1.3  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 !   57.6   1.3   1.7e-19     1e-15       7     132 ..      40     152 ..      37     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.7e-19
                                       T---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE-- CS
                      Pribosyltran   7 enpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlle 83 
                                       + p  l+a+a++ ae++e      d ++g+a g+vp+a +++ + ++p+++ rk++++ ++++ +           +
  gi|336253671|ref|YP_004596778.1|  40 TDPTCLEAIADAFAERIEP----GDKLAGVALGAVPLAAATSVAADAPYVIARKQRKDYGTANLI---------EGR 103
                                       5677788999999999999....9*****************************************.........789 PP

                                       --TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHH CS
                      Pribosyltran  84 dpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateee 132
                                       + +g+ V++ +Di++tG++l  a+e+L+e+g+++ r+ v+vd+ ++ +e
  gi|336253671|ref|YP_004596778.1| 104 LEEGEEVVVLEDIVTTGTSLVDAIEALREAGATVERALVVVDRQEGGRE 152
                                       99*******************************9999999999888765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     1e-07   0.00061     119     157 ..     104     143 ..      72     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1e-07
                           UPRTase 119 i.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvl 157
                                       + + ++v++l+ ++ TG s+++ai+ L+e+g+++e+ lv+
  gi|336253671|ref|YP_004596778.1| 104 LeEGEEVVVLEDIVTTGTSLVDAIEALREAGATVERALVV 143
                                       445678****************************987775 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   4.7e-06     0.028     116     160 ..     102     145 ..      90     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-06
                          PRTase_2 116 ellaaakelvLvDDEistGktalnliralqeklpr.kryvvvslvd 160
                                        +l++ +e+v+  D ++tG+++++ i+al+e+    +r  vv  vd
  gi|336253671|ref|YP_004596778.1| 102 GRLEEGEEVVVLEDIVTTGTSLVDAIEALREAGATvERALVV--VD 145
                                       5788999************************97775555443..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1349.68
//
Query:       gi|336253672|ref|YP_004596779.1|  [L=320]
Description: Triacylglycerol lipase [Halopiger xanaduensis SH-6]
Scores for complete 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-75  253.8   0.3    1.7e-75  253.5   0.3    1.1  1  Abhydrolase_3    alpha/beta hydrolase fold
    1.1e-07   31.2   0.0    3.6e-07   29.4   0.0    1.6  1  COesterase       Carboxylesterase family
     0.0011   19.6  10.0      0.002   18.8  10.0    1.4  1  Abhydrolase_6    Alpha/beta hydrolase family
     0.0017   17.9   0.0      0.028   13.9   0.0    2.1  2  Peptidase_S9     Prolyl oligopeptidase family
  ------ inclusion threshold ------
      0.011   14.7   0.0      0.016   14.1   0.0    1.1  1  Say1_Mug180      Steryl acetyl hydrolase
      0.055   13.0   0.0        1.6    8.2   0.0    2.7  3  DLH              Dienelactone hydrolase family
      0.084   11.5   0.1       0.31    9.7   0.0    1.8  2  AXE1             Acetyl xylan esterase (AXE1)
      0.085   11.7   0.0       0.14   11.0   0.0    1.3  1  Chlorophyllase2  Chlorophyllase enzyme


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 !  253.5   0.3   7.7e-79   1.7e-75       1     210 [.      84     292 ..      84     293 .. 0.95

  Alignments for each domain:
  == domain 1  score: 253.5 bits;  conditional E-value: 7.7e-79
                                       EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTH.H.HHTETTCEEEE CS
                     Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqa.w.elgadpsrivl 75 
                                       ++yfHGGG+v+gs+dthd++cr++a+e+g+ vvsvdY lAPe+pfP  + d++aal+w+ae + + el+adp+r+vl
  gi|336253672|ref|YP_004596779.1|  84 VLYFHGGGWVVGSVDTHDDTCRKFADETGYPVVSVDYGLAPEYPFPEGLLDCYAALEWAAEAEtAaELRADPDRLVL 160
                                       79**********************************************************988425889******** PP

                                       EEETHHHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSS.GGGGG CS
                     Abhydrolase_3  76 aGdSaGGnlaaavalrardegepkvagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylp.eadrd 151
                                       aGdSaGGnlaaa+al ard+g+p va qvl+yPvt   +  ++++   ee+a+g++l++a+  +f r+y + + dr 
  gi|336253672|ref|YP_004596779.1| 161 AGDSAGGNLAAATALLARDRGGPDVAYQVLLYPVTGD-PRPTDAF---EENAEGYFLSAADSSWFERHYFArDVDRG 233
                                       *********************************9966.4435666...7889******************77***** PP

                                       STTTSGGGCS-SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                     Abhydrolase_3 152 dplaspllaedlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgfa 210
                                       + +a p +a+dls+lpp++vv+a+fDplrd+g+ayaerl++agv+v++++ye+m+Hgf+
  gi|336253672|ref|YP_004596779.1| 234 NVYALPRRAHDLSDLPPATVVTAGFDPLRDDGAAYAERLEEAGVPVSYHNYEDMIHGFF 292
                                       ********99************************************************7 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.6e-10   3.6e-07      92     204 ..      71     175 ..      68     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.6e-10
                                       EEEESSSSSTTSSEEEEEEE--STTTS-BGCGS-..THHHHHHHTSEEEEE----HHHHH-B-SSTTSBS-HHHHHH CS
                        COesterase  92 vytPkekkeakkklPVlVwihGggfqtgsaseyd..gsaLaaegnvivVtinYRlGvlGFlstgdeeapGNvGllDq 166
                                       vy P +  +  +++P + ++hGgg ++gs  ++d  ++++a+e +  vV++ Y l +         e p   GllD 
  gi|336253672|ref|YP_004596779.1|  71 VYEPGT--D-GEERPLVLYFHGGGWVVGSVDTHDdtCRKFADETGYPVVSVDYGLAP---------EYPFPEGLLDC 135
                                       899963..3.4555****************997622579**************9986.........777788***** PP

                                       HHHHHHHH..HHGGGGTEEEEEEEEEEETHHHHHHHHHHH CS
                        COesterase 167 vlALrWVk..enIasFGGdpervtlfGesAGaasvsllll 204
                                        +AL+W    e+ a+   dp+r  l+G+sAG+ ++++  l
  gi|336253672|ref|YP_004596779.1| 136 YAALEWAAeaETAAELRADPDRLVLAGDSAGGNLAAATAL 175
                                       ******9722589*******************99887665 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8  10.0   8.8e-07     0.002       2     183 ..      85     268 ..      84     317 .. 0.51

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.8e-07
                                       EEE--GC.....GCHHHH.......HHHHCCT..CEEEEE--TTSTS-GGCS....--HHHCHHH...HHHHCCTT. CS
                     Abhydrolase_6   2 lllHGagssassWlvapL.......aallaag..vhvlapDlpGhGrsdppp....ldledladl...aalldelaa 62 
                                       l  HG+g     W v+++       ++++     + v+++D+ G  +  p p    + +++ +++   a++++el+a
  gi|336253672|ref|YP_004596779.1|  85 LYFHGGG-----WVVGSVdthddtcRKFAD-EtgYPVVSVDY-GLAPEYPFPegllDCYAA-LEWaaeAETAAELRA 153
                                       6679999.....966666665555433333.246788*****.886333333122133333.333344557777777 PP

                                       .TTSEEEEEETCHHHHHHHHHHCC..EE.......EEES-..----TTTS----TTHHHHHHTT-C.CCCHCCHS-H CS
                     Abhydrolase_6  63 gggpvvlvGHSlGGalalaaaplalvvg.......vlldppptalpagllaaalelllallallrl.lawlsreplp 131
                                       ++++ vl G S GG la+a+a la+++g       vll p   +++++ + +a+e  +  + l ++           
  gi|336253672|ref|YP_004596779.1| 154 DPDRLVLAGDSAGGNLAAATALLARDRGgpdvayqVLLYP---VTGDPRPTDAFEENAEGYFLSAAdS--------- 218
                                       99*****************777775555555213444444...3333333333333333333222213......... PP

                                       SCCCCHHHCCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-C......HH CS
                     Abhydrolase_6 132 rlfladedadaawrarlarlaallaglgllpaaawadlpvpllvl.ggeDp......lv 183
                                        ++++     +++ ar+ +     a +   +a+++ dlp+++ v+ +g Dp      ++
  gi|336253672|ref|YP_004596779.1| 219 -SWFE-----RHYFARDVDRGNVYALPR--RAHDLSDLPPAT-VVtAGFDPlrddgaAY 268
                                       .4444.....444444444444444444..344555555555.3223334422212211 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.2e-05     0.028      47      83 ..     134     175 ..     130     180 .. 0.73
   2 ?    1.6   0.0     0.071   1.6e+02     161     188 ..     264     291 ..     240     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHH.....HHTTS--GGGEEEEEETHHHHHHHHHHH CS
                      Peptidase_S9  47 Dfiaaaeal.....akegyvdserlaitGgSyGGyltgaaln 83 
                                       D+ aa+e++     a+e  +d++rl++ G S+GG l++a++ 
  gi|336253672|ref|YP_004596779.1| 134 DCYAALEWAaeaetAAELRADPDRLVLAGDSAGGNLAAATAL 175
                                       55566666533332444489****************999875 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.071
                                       HHHHHHHHHH--S-SEEEEEETTS-SST CS
                      Peptidase_S9 161 ealklvaaLqkkgknvlllifpdegHgv 188
                                        ++ ++++L+++g++v ++ + d  Hg+
  gi|336253672|ref|YP_004596779.1| 264 DGAAYAERLEEAGVPVSYHNYEDMIHGF 291
                                       56889999**************999975 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.9e-06     0.016     119     208 ..      74     169 ..      66     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.9e-06
                       Say1_Mug180 119 PkvD....pvllylHGGgfalklipvtlvfLsnlrklfpdm..ailvsDYtvtaakdqskkYplqvleslavydylv 189
                                       P++D    p++ly+HGGg++++ + +      + rk  ++   +++ +DY +       + +p  +l++ a  ++  
  gi|336253672|ref|YP_004596779.1|  74 PGTDgeerPLVLYFHGGGWVVGSVDTH---DDTCRKFADETgyPVVSVDYGLAP----EYPFPEGLLDCYAALEWAA 143
                                       444444459************998875...34455555544669*******988....899**************** PP

                       Say1_Mug180 190 kskgfkn.......vvvlGdSaGGnl 208
                                       ++++  +       +v+ GdSaGGnl
  gi|336253672|ref|YP_004596779.1| 144 EAETAAElradpdrLVLAGDSAGGNL 169
                                       999987622222336899*******8 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.11   2.5e+02      22      44 ..      93     116 ..      69     120 .. 0.75
   2 ?   -0.5   0.0      0.33   7.4e+02      86     117 ..     145     175 ..     134     217 .. 0.71
   3 ?    8.2   0.0   0.00072       1.6     149     210 ..     253     312 ..     242     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.11
                               DLH  22 ifGvndnikdiserlaee.GYval 44 
                                       ++G  d+++d+++++a+e GY ++
  gi|336253672|ref|YP_004596779.1|  93 VVGSVDTHDDTCRKFADEtGYPVV 116
                                       57888***********86588765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.33
                               DLH  86 vaylksvpevstkkvgvvGfCmGGalalllaa 117
                                        +++++ + ++++++++ G   GG+la + a 
  gi|336253672|ref|YP_004596779.1| 145 AETAAELR-ADPDRLVLAGDSAGGNLAAATAL 175
                                       45556666.7889999999999**99987764 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00072
                               DLH 149 alfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsresyneeaaedawervl 210
                                       ++ ++ D+  + +     +e l++a+v++  + Y++  H+F+   ++  +   a++a++rv 
  gi|336253672|ref|YP_004596779.1| 253 VVTAGFDPLRDDG--AAYAERLEEAGVPVSYHNYEDMIHGFFGMISAPVDVDVAHEAYARVA 312
                                       5566666666555..46789999*******************99999999999999988876 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.23   5.1e+02      73     101 ..      71     101 ..      64     120 .. 0.69
   2 ?    9.7   0.0   0.00014      0.31     170     196 ..     152     178 ..      97     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.23
                                       EEEES.SSSSEEEEEEEE-..TT--GGGHHH CS
                              AXE1  73 lvlPkekeeklPavvefhG..Yegsrgeihd 101
                                       +  P +  e+ P+v+ fhG  +  ++ ++hd
  gi|336253672|ref|YP_004596779.1|  71 VYEPGTDGEERPLVLYFHGggWVVGSVDTHD 101
                                       56788888999*******8224444555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00014
                                       TEEEEEEEEEEETHHHHHHHHHHHH-S CS
                              AXE1 170 evDeeRvavlGasqGGalalavaalek 196
                                         D++R++ +G+s GG la a+a l +
  gi|336253672|ref|YP_004596779.1| 152 RADPDRLVLAGDSAGGNLAAATALLAR 178
                                       479****************99987765 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.4e-05      0.14       8     129 ..      71     196 ..      66     205 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
                   Chlorophyllase2   8 vvaPteag.eYpvllflhGyl...llnslYsqlLkhia.shgfivvapqlykvaeada.keiksaakvlnWlakgLe 78 
                                       v+ P + g e p++l++hG        +   +  ++ a   g+ vv++      e    + +    + l+W a+  +
  gi|336253672|ref|YP_004596779.1|  71 VYEPGTDGeERPLVLYFHGGGwvvGSVDTHDDTCRKFAdETGYPVVSVDYGLAPEYPFpEGLLDCYAALEWAAEAET 147
                                       66665544145777777765432223345556666665245777777775554444445667777777888776544 PP

                   Chlorophyllase2  79 svlpeevepdlsklalsgHSrGgktafalalgkaktsl.kfsaligvdPvag 129
                                          + e+++d ++l+l+g S+Gg+ a+a al  ++    +++  + + Pv+g
  gi|336253672|ref|YP_004596779.1| 148 ---AAELRADPDRLVLAGDSAGGNLAAATALLARDRGGpDVAYQVLLYPVTG 196
                                       ...7899*********************999777633235555666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); 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 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2465.19
//
Query:       gi|336253673|ref|YP_004596780.1|  [L=228]
Description: hypothetical protein Halxa_2276 [Halopiger xanaduensis SH-6]
Scores for 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-47  160.0   0.6    6.7e-47  159.7   0.6    1.0  1  CarS-like        CDP-archaeol synthase
    1.9e-06   27.8   0.7    1.9e-06   27.8   0.7    1.6  1  CTP_transf_1     Cytidylyltransferase family
  ------ inclusion threshold ------
       0.31   10.8   7.8        2.6    7.9   0.7    2.4  2  Gly-zipper_YMGG  YMGG-like Gly-zipper


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 !  159.7   0.6   1.1e-50   6.7e-47       2     175 .]      51     228 .]      50     228 .] 0.92

  Alignments for each domain:
  == domain 1  score: 159.7 bits;  conditional E-value: 1.1e-50
                         CarS-like   2 ldlilksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsilal 78 
                                       l+ ++ + + +lpayv+n+ avl GGG+p+d G+t+ d rr++GdG+t+rGt++G+l+G+  + +  +l      al
  gi|336253673|ref|YP_004596780.1|  51 LETVVVAFWAMLPAYVPNNAAVLAGGGRPIDGGRTWGD-RRVLGDGKTWRGTATGILAGLALAALLTVLAPAVSDAL 126
                                       56678899***************************988.99****************************99999*** PP

                         CarS-like  79 dssgsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllayp......vkllpieliil 149
                                        +  +  e +  al la Ga+lGd+  sf+krr + +rG  ++ ldqldfv+++l l+          +++ ++i++
  gi|336253673|ref|YP_004596780.1| 127 GFDVPAFEPL-AALGLAAGAMLGDILASFLKRRAGRQRGAMFPGLDQLDFVVVSLPLTALlatdwfRDVFTWDVILV 202
                                       ****999876.6899*************************************99977633223333579******** PP

                         CarS-like 150 ivlitlvlhlsaniiayklglkdvwy 175
                                       +v++t++lh+s+n+iayklglk+ ++
  gi|336253673|ref|YP_004596780.1| 203 VVVVTPILHVSTNVIAYKLGLKNEPW 228
                                       **********************9988 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.7   3.2e-10   1.9e-06     155     262 ..      83     186 ..      82     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3.2e-10
                                       HHCH---B-S-TTS---BHHHHHHHHHHHHHHHHHHHHHHHCTS......---TTSHHHHHHHHHHHHHHHHHHHHH CS
                      CTP_transf_1 155 GklfGktkllpkiSPkKTveGfigGlvaavvvglllalvlskal......alsllhllllslllslvavfGDLveSg 225
                                       G+++G +++l +   +KT+ G   G++a ++++ ll+ +++          + +  l++l+  l+  a++GD+++S 
  gi|336253673|ref|YP_004596780.1|  83 GRTWGDRRVLGD---GKTWRGTATGILAGLALAALLTVLAPAVSdalgfdVPAFEPLAALG--LAAGAMLGDILASF 154
                                       666666655444...8********************9999987777775444444444444..455689******** PP

                                       HHHHHT-SSS-S-SSSSS-HHHHHHHHHHHHHHHHHH CS
                      CTP_transf_1 226 lKRafgiKDsGkliPGhGGilDRlDsllfaapvvyll 262
                                       lKR++g    G + PG    lD lD +++++p+++ll
  gi|336253673|ref|YP_004596780.1| 155 LKRRAGR-QRGAMFPG----LDQLDFVVVSLPLTALL 186
                                       ******5.78999**9....89999999999988765 PP

>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.3    0.0013       7.8       2      20 ..      96     114 ..      95     124 .. 0.88
   2 ?    7.9   0.7   0.00043       2.6       7      29 ..     137     165 ..     136     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0013
                                       ...XXXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG   2 gavrGAaiGAaaGAvvGal 20 
                                       ++ rG+a+G  aG ++ al
  gi|336253673|ref|YP_004596780.1|  96 KTWRGTATGILAGLALAAL 114
                                       7889**********99997 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00043
                                       XXXXXXXXXXXXXXXX......XXXXXXX CS
                   Gly-zipper_YMGG   7 AaiGAaaGAvvGaliG......sgggkGA 29 
                                       Aa G aaGA +G++        +g+++GA
  gi|336253673|ref|YP_004596780.1| 137 AALGLAAGAMLGDILAsflkrrAGRQRGA 165
                                       89999999999999877777666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 1929.77
//
Query:       gi|336253674|ref|YP_004596781.1|  [L=280]
Description: Proline dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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   86.6   0.0    3.7e-24   85.8   0.0    1.4  1  Pro_dh    Proline dehydrogenase
  ------ inclusion threshold ------
       0.15   12.4   0.7        1.1    9.6   0.0    2.7  3  PqqD      Coenzyme PQQ synthesis protein D (PqqD)


Domain annotation for each model (and alignments):
>> Pro_dh  Proline dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.0   4.2e-28   3.7e-24       3     293 ..      20     272 ..      18     275 .. 0.87

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 4.2e-28
                                       HHHHHHHHTTEEEEEEES-SS--SHHHHHHHHHHHHHHHHHHHHHHCCS-TTCC-S.EEE-GGGTT-SGGGHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh   3 ktieklkkrgvrlsldllgeavlteedadryleayleaiksiekaskalkvleapg.vsvklsaprletaeeeevme 78 
                                       +++++l+ r+v+ +++llge + ++  +++ +++y+ +  +i+ ++        +g +svk+++  l+  e     +
  gi|336253674|ref|YP_004596781.1|  20 EHVRRLNGRNVKAIVNLLGEHYDERPPVRSDAAEYRALAGDIAGSNL-------DGcISVKPTQLGLDLGE-----D 84 
                                       67888888888999999999999999999999999999998855554.......45599999874333332.....3 PP

                                       HHHHHHHHHHHHHHHTT-EEEE----GGGHHHHHHHHHHHHHSCCTTT---EEEEEETTBTTHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh  79 elverlrtlakeakelgvrlliDaEeaklqeltlelfrklnkepelkdwevvgntyQaYlkdalevlqkllelAere 155
                                        + e+l  ++++a+++gv ++iD+E+++  + tl++f+ l +e e     +vg+ +Qa lk++ +++++l++     
  gi|336253674|ref|YP_004596781.1|  85 VFREELAGVVEAAADHGVFVWIDMEDHTTTDATLDAFEDLAREHEG----GVGVCVQANLKRTRDDVERLAD----- 152
                                       4568999**********************************98888....8*****************9975..... PP

                                       TS-EEEEEE--S-HHHHHHHHHHTT-S-SB-SSHHHHHHHHHHHHHHHH.HTTTTEEEEEE-S-HHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh 156 gfrlgvkLVrGAYldsErkraqelgyespifdtkeeTDanYdavaelll.enrdeiypavAsHNaesvakalalaee 231
                                        ++ +v++V+GAY   E++        +  + + e   + Y+a++e+ + ++ d   +av+sH    +++a+ l ee
  gi|336253674|ref|YP_004596781.1| 153 -VPGKVRFVKGAY--DEPA--------DIAYRDAERVNREYEALLEYAFaHYDDGPTIAVGSHDPAMIERAIDLHEE 218
                                       .6899********..5666........56799*****************5566688999****************** PP

                                       T..T--GGGEEEEEETTSSHHHHHHHHHTTS-EEEEEEECEHHHHHHHHHHHHHHHH-TT-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh 232 lgqekeksevefqqLlGMadnlsfalakagynvrkYlPvGpveevlpYLvRRleENtanssf 293
                                              +++efq+L+G  ++ ++ la a+y+v  Y+P+Gp     +Y  RR+ E t+n+ f
  gi|336253674|ref|YP_004596781.1| 219 Y-----GTDCEFQMLMGVREDAQYDLA-ANYEVWQYVPYGPR--WKSYFYRRAMERTENLRF 272
                                       *.....99******************5.789*********95..679**********99987 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00013       1.1      24      56 ..      23      53 ..      18      56 .. 0.85
   2 ?   -1.3   0.0      0.32   2.9e+03      17      38 ..      99     120 ..      96     129 .. 0.67
   3 ?   -1.4   0.2      0.33     3e+03      42      56 ..     163     177 ..     157     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00013
                                      HH-SSSS-HHHHHHHHHHHCT--HHHHHHHHHH CS
                              PqqD 24 klldgersveeivaalaeeydvdeeeaeadvla 56
                                      ++l+g r+v +iv  l e+yd+   +++ d ++
  gi|336253674|ref|YP_004596781.1| 23 RRLNG-RNVKAIVNLLGEHYDER-PPVRSDAAE 53
                                      7899*.99************765.569998877 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.32
                                       CHHHHHHHH-SSSS-HHHHHHH CS
                              PqqD  17 etgafiWklldgersveeivaa 38 
                                       ++g f+W  ++++++ ++  +a
  gi|336253674|ref|YP_004596781.1|  99 DHGVFVWIDMEDHTTTDATLDA 120
                                       5789999777665555554444 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.33
                                       HCT--HHHHHHHHHH CS
                              PqqD  42 eydvdeeeaeadvla 56 
                                        yd++++ a++d ++
  gi|336253674|ref|YP_004596781.1| 163 AYDEPADIAYRDAER 177
                                       688888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.44u 0.19s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2405.51
//
Query:       gi|336253675|ref|YP_004596782.1|  [L=229]
Description: hypothetical protein Halxa_2278 [Halopiger xanaduensis SH-6]
Scores for 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-19   68.0   0.2    8.7e-19   67.4   0.2    1.3  1  DUF502    Protein of unknown function (DUF502)


Domain annotation for each model (and alignments):
>> DUF502  Protein of unknown function (DUF502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.2   4.9e-23   8.7e-19       2     106 .]      70     165 ..      69     165 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 4.9e-23
                            DUF502   2 vvlllillvGllasnligrkllklgerllkriPlvksiYsalkqvvetfsseekksfrevvlve.yprkglwalgFv 77 
                                       v+ +l++ vG+l+++++g+ + +l++++ +r+P+++ iY+a+k  +et ++ e++s++++v +e +  +gl++++F 
  gi|336253675|ref|YP_004596782.1|  70 VFTILTFSVGYLMRTTVGSLVERLVDNVANRVPVMRVIYNASKMAAETAFG-EQESLQKPVKLEvW--EGLRMTAFK 143
                                       578999********************************************9.9999********87..9******** PP

                            DUF502  78 tgetegelatkgeedlvaVfvPtspnpts 106
                                       tg+      t  ++ +  +f+Ptspn+t+
  gi|336253675|ref|YP_004596782.1| 144 TGKV-----T--DDGREILFLPTSPNITT 165
                                       ***6.....3..67899**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 1992.70
//
Query:       gi|336253676|ref|YP_004596783.1|  [L=166]
Description: DoxX family protein [Halopiger xanaduensis SH-6]
Scores for complete 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   25.6   0.4    2.1e-05   25.0   0.4    1.3  1  DoxX       DoxX
    2.7e-05   24.4   0.0    0.00059   20.0   0.0    2.0  2  HR_lesion  HR-like lesion-inducing


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.4   2.4e-09   2.1e-05       4      85 .]      47     126 ..      44     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.4e-09
                              DoxX   4 llRlllgvlfiahGlqkltgfglegtaaslaalglpppellaylaalvElvgglllllGlltRlaAlalavtllvat 80 
                                       l+R ++g+++  + ++ l+  +le+ +++  a   p+pe  + ++  + l+ggl+++l + +  +A+a+a +l+++t
  gi|336253676|ref|YP_004596783.1|  47 LGRAIFGGILAFTAVDNLR--NLEERVQYADAKDAPAPERSVPAVSSALLAGGLGVALWRRPAAGAAAIAGFLAGTT 121
                                       79*****************..9******************************************************* PP

                              DoxX  81 ltvhr 85 
                                        ++h+
  gi|336253676|ref|YP_004596783.1| 122 PVMHD 126
                                       *9995 PP

>> HR_lesion  HR-like lesion-inducing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.017   1.6e+02       7      53 ..      47      93 ..      43     104 .. 0.79
   2 !   20.0   0.0   6.5e-08   0.00059      94     136 ..     116     157 ..     106     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.017
                         HR_lesion  7 iGrvlfasvfllsawqdyaefgadggpaekalkPkfnllskkvskal 53
                                      +Gr++f  +  ++a ++  ++++    a+ + +P+ + ++  vs+al
  gi|336253676|ref|YP_004596783.1| 47 LGRAIFGGILAFTAVDNLRNLEERVQYADAKDAPAPERSVPAVSSAL 93
                                      7****************999988888777777777777777777665 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 6.5e-08
                         HR_lesion  94 yqaiatvvlydfynydldtkeflrlllkfvqnlalvGaLLffv 136
                                       ++a +t+v++df+n d d +  ++ l++f++n al+Ga L f+
  gi|336253676|ref|YP_004596783.1| 116 FLAGTTPVMHDFWNED-DPETKQQELTHFLKNGALFGAALAFM 157
                                       56678*********87.44555799*************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 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:                        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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1276.21
//
Query:       gi|336253677|ref|YP_004596784.1|  [L=309]
Description: branched-chain amino acid aminotransferase [Halopiger xanaduensis SH-6]
Scores for complete 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  168.6   0.0    2.2e-49  168.4   0.0    1.1  1  Aminotran_4  Amino-transferase class IV


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 !  168.4   0.0   1.2e-53   2.2e-49       1     223 []      37     270 ..      37     270 .. 0.95

  Alignments for each domain:
  == domain 1  score: 168.4 bits;  conditional E-value: 1.2e-53
                       Aminotran_4   1 glfEtmrvy....ngeiffldeHleRLrksaellglelpfdeeelrkileelleannsengrlrllvsrgggglgaa 73 
                                       g+fE+ r y       if+++eHleRL +sa+  +++++f++eel+++++el+++++ e +++r++ + g ++lg +
  gi|336253677|ref|YP_004596784.1|  37 GVFEGARCYdtenGPAIFRWEEHLERLFQSAKPYDMDIDFTKEELTEATKELIQRQELESCYIRPIAFYGYNSLGVS 113
                                       89*****997774555588********************************************************88 PP

                       Aminotran_4  74 tsepsvavyvsalppgpeseke.....lplvtssdvrrdapsplpgaKtln.yldnvlarreakergadevllvded 144
                                        ++    + ++ +p+g++   +     +++++ss++++   +  ++aKt+  y +++la +ea+++g+ e+++++++
  gi|336253677|ref|YP_004596784.1| 114 PKDCPTKTAIAVWPWGAYLGEDalengIEVMISSWRKHASSQIPTNAKTTGlYVNSMLAGEEARRNGFAEAIVLNKE 190
                                       888888888889999999999999**********99999999999******************************** PP

                       Aminotran_4 145 gnvtEgstsNvfivkggelitPplssgiLpGitrrallelakalgleve.ereitlkdleeadeafltntlrgvlpv 220
                                       g+v Eg   N+f+v++ge++tP ls++iL+Gitr++++ela++lg +v+    i+ ++l+ ade+f+t+++++v+p+
  gi|336253677|ref|YP_004596784.1| 191 GHVAEGPGENLFLVRDGEIYTPGLSESILDGITRDTVIELAEDLGYTVHdNVSISRGELHTADELFFTGSAAEVTPI 267
                                       ************************************************999************************** PP

                       Aminotran_4 221 rsi 223
                                       r++
  gi|336253677|ref|YP_004596784.1| 268 RKV 270
                                       986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2442.21
//
Query:       gi|336253678|ref|YP_004596785.1|  [L=177]
Description: ArsR family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for complete 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-11   43.7   0.0    4.5e-06   26.1   0.0    2.2  2  HTH_24           Winged helix-turn-helix DNA-binding
    3.1e-11   43.2   1.0    1.2e-07   31.7   0.2    2.2  2  HTH_20           Helix-turn-helix domain
    3.6e-08   33.2   0.8    1.7e-05   24.6   0.2    2.4  2  MarR_2           MarR family
      4e-07   29.8   0.0    1.9e-05   24.4   0.0    2.3  2  HTH_5            Bacterial regulatory protein, arsR family
    0.00025   20.9   0.0     0.0015   18.4   0.0    1.9  2  TrmB             Sugar-specific transcriptional regulator Trm
    0.00081   19.8   0.1     0.0033   17.9   0.1    2.0  2  HTH_27           Winged helix DNA-binding domain
     0.0025   17.7   0.0      0.016   15.1   0.0    2.1  2  MarR             MarR family
      0.003   17.3   0.0     0.0072   16.1   0.0    1.7  1  HTH_IclR         IclR helix-turn-helix domain
     0.0076   16.8   0.0        1.1    9.9   0.0    2.2  2  RusA             Endodeoxyribonuclease RusA
  ------ inclusion threshold ------
      0.011   15.4   0.0        0.2   11.3   0.0    2.2  2  RP-C             Replication protein C N-terminal domain
      0.012   16.0   0.0        1.2    9.5   0.0    2.2  2  Penicillinase_R  Penicillinase repressor
      0.015   15.1   0.1      0.041   13.7   0.1    1.8  1  HTH_30           PucR C-terminal helix-turn-helix domain
      0.018   14.9   0.0      0.055   13.3   0.0    1.8  2  HTH_10           HTH DNA binding domain
       0.06   13.4   1.0       0.28   11.2   0.2    1.9  2  GPP34            Golgi phosphoprotein 3 (GPP34)
       0.12   12.6   0.0       0.82    9.9   0.0    1.9  2  HTH_34           Winged helix DNA-binding domain
       0.14   12.1   0.0        1.1    9.3   0.0    2.2  2  BLACT_WH         Beta-lactamase associated winged helix domai
       0.17   12.5   0.0       0.64   10.7   0.0    1.8  2  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 !   15.6   0.0   8.2e-06    0.0086       3      44 ..       3      44 ..       1      45 [. 0.89
   2 !   26.1   0.0   4.3e-09   4.5e-06       2      48 .]      76     122 ..      75     122 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.2e-06
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeee 44
                                      +t+r I   +q n++i  +eL +++   p+ + ++++rL +e
  gi|336253678|ref|YP_004596785.1|  3 DTRRTIRAHVQSNAGIHFNELVRESEFAPGQIQYHVRRLLDE 44
                                      5666666789*****************************987 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 4.3e-09
                            HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       +et r+I  +L  +     r +A++l++ +st+ ++l+rL+e G+++
  gi|336253678|ref|YP_004596785.1|  76 RETSRDIVVYLIGDEPAAPRAVADALDIARSTLEYHLDRLVERGIVE 122
                                       6899*****************************************96 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   0.00062      0.65      11      57 ..       4      51 ..       2      55 .. 0.92
   2 !   31.7   0.2   1.1e-10   1.2e-07      10      57 ..      77     124 ..      68     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00062
                                      HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHH.CTTEEEE CS
                            HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLee.agLvevv 57
                                      +Rr i ++  +++g  ++el ++ + ++ ++ yH+r L +  +Lv+ +
  gi|336253678|ref|YP_004596785.1|  4 TRRTIRAHVQSNAGIHFNELVRESEFAPGQIQYHVRRLLDeDDLVREE 51
                                      8999*******************************9999989999875 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 1.1e-10
                                       HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57 
                                       ++ r+i  +L ++e++ + ++a++ld++++tl yHL+ L+e g+ve +
  gi|336253678|ref|YP_004596785.1|  77 ETSRDIVVYLIGDEPAAPRAVADALDIARSTLEYHLDRLVERGIVEKR 124
                                       6899*****************************************976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0053       5.6      13      47 ..      11      43 ..       1      51 [. 0.82
   2 !   24.6   0.2   1.6e-08   1.7e-05      12      56 ..      85     126 ..      71     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0053
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLva 47
                                      ++  + g  +  +el+r+    ++ ++++++rL +
  gi|336253678|ref|YP_004596785.1| 11 HVQSNAG--IHFNELVRESEFAPGQIQYHVRRLLD 43
                                      5666777..8899*******************976 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.6e-08
                                       HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                       + +g++p    +++++a++l++ +s++ ++l+rLv++G ve+r +
  gi|336253678|ref|YP_004596785.1|  85 YLIGDEP---AAPRAVADALDIARSTLEYHLDRLVERGIVEKRYD 126
                                       4455565...7*******************************944 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 ?    3.2   0.0     0.076        80      19      42 ..      21      44 ..      19      49 .. 0.89
   2 !   24.4   0.0   1.8e-08   1.9e-05       5      47 .]      80     123 ..      76     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.076
                                      HHHHHHHTS-HHHHHHHHHHHHHT CS
                             HTH_5 19 celaeelglsqstvShHLkkLrea 42
                                       el++e +  ++ + +H ++L ++
  gi|336253678|ref|YP_004596785.1| 21 NELVRESEFAPGQIQYHVRRLLDE 44
                                      7999999*************9986 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1.8e-08
                                       HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5   5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                       ++I+ +L   +++     a++l++ +st+ +HL +L e G+Vek
  gi|336253678|ref|YP_004596785.1|  80 RDIVVYLIGdEPAAPRAVADALDIARSTLEYHLDRLVERGIVEK 123
                                       678888888788******************************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 ?   -0.1   0.0      0.82   8.6e+02      26      62 ..      21      59 ..      14      62 .. 0.67
   2 !   18.4   0.0   1.4e-06    0.0015      16      58 ..      85     127 ..      78     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.82
                                      CHHCCCTTSSCHCHHHHHHHHHHCTSEEEES..STTTEE CS
                              TrmB 26 deiaeelgvprskvYevLrsLedkGlVerek..grpklY 62
                                      +e+ +e++    +++  +r+L+d +   re+  gr+++Y
  gi|336253678|ref|YP_004596785.1| 21 NELVRESEFAPGQIQYHVRRLLDEDDLVREEfyGRTHYY 59
                                      577788888888898899999887654444433444444 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.4e-06
                                       HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       +L+  +pa  + +a +l++ rs+    L +L+++G+Ve++   
  gi|336253678|ref|YP_004596785.1|  85 YLIGDEPAAPRAVADALDIARSTLEYHLDRLVERGIVEKRYDD 127
                                       4677899*******************************99765 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 ?   -1.1   0.0       2.7   2.9e+03      34      49 ..      33      49 ..      17      55 .. 0.71
   2 !   17.9   0.1   3.1e-06    0.0033       7      57 ..      82     130 ..      77     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.7
                            HTH_27 34 hisyslkkLtek.GLve 49
                                      +i y +++L    +Lv 
  gi|336253678|ref|YP_004596785.1| 33 QIQYHVRRLLDEdDLVR 49
                                      56677777766657774 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.1e-06
                            HTH_27   7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadr 57 
                                       +v+ li+  +++++ ++++++l++  s+  y l++L+e+G ve+  d+++r
  gi|336253678|ref|YP_004596785.1|  82 IVVYLIG--DEPAAPRAVADALDIARSTLEYHLDRLVERGIVEKRYDDRNR 130
                                       5667777..788888***************************877776544 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.2   1.3e+03      19      44 ..      19      44 ..      10      50 .. 0.76
   2 !   15.1   0.0   1.5e-05     0.016      24      56 ..      98     130 ..      89     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                                      EHHHHHHHHTS-HHHHHHHHHHHHHT CS
                              MarR 19 svseLakklgvskstvtrvldrLekk 44
                                         eL + ++  ++ +   ++rL ++
  gi|336253678|ref|YP_004596785.1| 19 HFNELVRESEFAPGQIQYHVRRLLDE 44
                                      44588889999999999999999886 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.5e-05
                                       HHHHTS-HHHHHHHHHHHHHTTSEEEEEETTST CS
                              MarR  24 akklgvskstvtrvldrLekkGlieRskspeDr 56 
                                       a++l + +st+   ldrL+++G +e++ + ++r
  gi|336253678|ref|YP_004596785.1|  98 ADALDIARSTLEYHLDRLVERGIVEKRYDDRNR 130
                                       899***********************9988876 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 !   16.1   0.0   6.8e-06    0.0072      17      50 ..      90     123 ..      71     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.8e-06
                                       SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       ++   + +A+++++++St   +L  Lve+G+ve+
  gi|336253678|ref|YP_004596785.1|  90 EPAAPRAVADALDIARSTLEYHLDRLVERGIVEK 123
                                       4457899*************************97 PP

>> RusA  Endodeoxyribonuclease RusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.033        35      14      40 ..      54      78 ..      31      84 .. 0.81
   2 !    9.9   0.0     0.001       1.1      88     123 ..      96     135 ..      92     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.033
                                      ESSSSEEE-HHHHHHHHHHHHHHHHTT CS
                              RusA 14 kkggrtytpkktkayeeevkaylekqy 40
                                          ++y p+++ ++e+++ a+++++ 
  gi|336253678|ref|YP_004596785.1| 54 G--RTHYYPPEYDEWERAALALFRRET 78
                                      3..356***********9999888876 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.001
                                       HHHHHH....HTTSBS-GGGEEEEEEE--TT-..EEEEEE CS
                              RusA  88 avlDal....ngivwkDDsqvvdlivekvyseeprvevei 123
                                       av Dal    ++  ++ D++v + ivek y++++rv++e+
  gi|336253678|ref|YP_004596785.1|  96 AVADALdiarSTLEYHLDRLVERGIVEKRYDDRNRVTLEL 135
                                       78899999999999**********************9875 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 ?    1.8   0.0      0.16   1.6e+02      75      97 ..      21      43 ..      14      51 .. 0.87
   2 ?   11.3   0.0   0.00019       0.2      77     104 ..      97     124 ..      91     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.16
                              RP-C 75 aqLsralglsestlrrhlaaLve 97
                                      ++L r+  +++ ++++h+++L +
  gi|336253678|ref|YP_004596785.1| 21 NELVRESEFAPGQIQYHVRRLLD 43
                                      579999***************87 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00019
                              RP-C  77 LsralglsestlrrhlaaLveaGliirr 104
                                        + al++++stl++hl +Lve G++  r
  gi|336253678|ref|YP_004596785.1|  97 VADALDIARSTLEYHLDRLVERGIVEKR 124
                                       568999******************9765 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.037        39      25      69 ..      21      66 ..       6      74 .. 0.74
   2 ?    9.5   0.0    0.0011       1.2      28      59 ..      98     129 ..      80     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.037
                                      HT--GGG---HHHHHHHHHHHHHTT.S-EEEEETTEEEEE----XX CS
                   Penicillinase_R 25 eeleeekelaysTVktllrrLvkKg.llsrekegrafiYsplvsee 69
                                      +el +e+e a+  ++  +rrL++ + l+++e  gr++ Y p  +e 
  gi|336253678|ref|YP_004596785.1| 21 NELVRESEFAPGQIQYHVRRLLDEDdLVREEFYGRTHYYPPEYDEW 66
                                      567777788888899999999987615555556******9988875 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                                       -GGG---HHHHHHHHHHHHHTTS-EEEEETTE CS
                   Penicillinase_R  28 eeekelaysTVktllrrLvkKgllsrekegra 59 
                                       ++  + a+sT    l rLv++g+++++ + r 
  gi|336253678|ref|YP_004596785.1|  98 ADALDIARSTLEYHLDRLVERGIVEKRYDDRN 129
                                       5667899******************9988775 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 ?   13.7   0.1   3.9e-05     0.041      16      39 ..      95     118 ..      84     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
                                       HHHHHHHTS-HHHHHHHHHHHHHH CS
                            HTH_30  16 satAkaLhvHrnTlryRLrrieel 39 
                                       +a+A+aL + r Tl y L+r+ e 
  gi|336253678|ref|YP_004596785.1|  95 RAVADALDIARSTLEYHLDRLVER 118
                                       789*****************9885 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.8   6.1e+03      37      46 ..      31      40 ..      18      41 .. 0.70
   2 ?   13.3   0.0   5.2e-05     0.055      27      47 ..      95     115 ..      92     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.8
                            HTH_10 37 kstlsehLrk 46
                                      +  +++h+r+
  gi|336253678|ref|YP_004596785.1| 31 PGQIQYHVRR 40
                                      5567889887 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.2e-05
                            HTH_10  27 keLAkelGIskstlsehLrka 47 
                                       +++A++l+I++stl++hL + 
  gi|336253678|ref|YP_004596785.1|  95 RAVADALDIARSTLEYHLDRL 115
                                       579***************885 PP

>> GPP34  Golgi phosphoprotein 3 (GPP34)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.14   1.5e+02      90     132 ..      33      75 ..       2     101 .. 0.56
   2 ?   11.2   0.2   0.00027      0.28      76     131 ..      93     143 ..      80     172 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.14
                             GPP34  90 svrervakgLvdkGilrtekrrflglfdmtthpvadtaakea.....v 132
                                       + +  v+  L + +++r+e   f g  +++ +p++ +++++a      
  gi|336253678|ref|YP_004596785.1|  33 QIQYHVRRLLDEDDLVREE---FYG--RTHYYPPEYDEWERAalalfR 75 
                                       4444477777788888888...664..456669977777777444431 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00027
                             GPP34  76 rprsvktwvdllsksvrervakgLvdkGilrte..krrflglfdmtthpvadtaakea 131
                                        pr v++ +d  + s++e  +++Lv++Gi++ +   r+++      t+++a ++   +
  gi|336253678|ref|YP_004596785.1|  93 APRAVADALDIAR-STLEYHLDRLVERGIVEKRydDRNRV------TLELAAPDRTGE 143
                                       4678888887776.****************9985333322......233333333333 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 ?    0.2   0.0      0.82   8.7e+02      11      40 ..      14      43 ..       6      55 .. 0.82
   2 ?    9.9   0.0   0.00078      0.82       5      53 ..      82     130 ..      80     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.82
                            HTH_34 11 svdeadfvelkealeatdgnLsvhlkkLek 40
                                      s+  + f+el  + e   g++  h++ L +
  gi|336253678|ref|YP_004596785.1| 14 SNAGIHFNELVRESEFAPGQIQYHVRRLLD 43
                                      577789999999999999999999998865 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00078
                            HTH_34   5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgk 53 
                                       ++ yL+ ++ a ++ + +al +  + L  hl+ L + g +e + + +++
  gi|336253678|ref|YP_004596785.1|  82 IVVYLIGDEPAAPRAVADALDIARSTLEYHLDRLVERGIVEKRYDDRNR 130
                                       789***********************************87655444443 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.1   1.2e+03      21      40 ..      30      49 ..      28      52 .. 0.69
   2 ?    9.3   0.0     0.001       1.1      19      42 ..     102     125 ..      97     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.1
                          BLACT_WH 21 AergvlahLeKLeeeGkVkr 40
                                      A  +++ h ++L +e+  +r
  gi|336253678|ref|YP_004596785.1| 30 APGQIQYHVRRLLDEDDLVR 49
                                      66678889999888765444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.001
                          BLACT_WH  19 paAergvlahLeKLeeeGkVkreg 42 
                                        +A+ ++  hL++L e+G V++  
  gi|336253678|ref|YP_004596785.1| 102 DIARSTLEYHLDRLVERGIVEKRY 125
                                       689*****************9865 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 ?   10.7   0.0   0.00061      0.64      57      94 ..       7      44 ..       5      45 .. 0.92
   2 ?   -1.1   0.0       2.8   2.9e+03      73      97 ..      97     121 ..      93     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00061
                                      HHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHT CS
                             RPA_C 57 likqspeseeGvhvdeiaqklrlsvndvkqavdeLsne 94
                                      +i+ +++s++G+h++e+ ++ ++   +++  v+ L++e
  gi|336253678|ref|YP_004596785.1|  7 TIRAHVQSNAGIHFNELVRESEFAPGQIQYHVRRLLDE 44
                                      6899********************99999999999875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.8
                                       HHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C  73 iaqklrlsvndvkqavdeLsneGii 97 
                                       +a +l +  ++++  +d L++ Gi+
  gi|336253678|ref|YP_004596785.1|  97 VADALDIARSTLEYHLDRLVERGIV 121
                                       677888889999999999**99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1447.77
//
Query:       gi|336253679|ref|YP_004596786.1|  [L=116]
Description: hypothetical protein Halxa_2282 [Halopiger xanaduensis SH-6]
Scores for 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   13.8   4.7      0.048   13.6   4.7    1.1  1  7TMR-DISM_7TM    7TM diverse intracellular signalling
      0.063   13.2   3.1       0.08   12.9   3.1    1.1  1  ABC2_membrane_4  ABC-2 family transporter protein
      0.079   12.7   4.3       0.27   11.0   2.2    2.3  3  DUF3481          C-terminal domain of neuropilin glycoprotein
       0.14   11.8   3.4       0.16   11.5   3.4    1.2  1  SUR7             SUR7/PalI family
       0.17   12.2   5.4       0.25   11.6   5.4    1.3  1  TctB             Tripartite tricarboxylate transporter TctB f
       0.45   10.8   6.6       0.34   11.2   4.1    1.9  2  DUF2530          Protein of unknown function (DUF2530)


Domain annotation for each model (and alignments):
>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   4.7   1.6e-05     0.048     123     196 ..      20      96 ..      11     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                     7TMR-DISM_7TM 123 lslaqllallvillllligikaw.rkgnkparyfliawlllligvlidilsllgllpsn..ffteyllqigvllevl 196
                                       l  +++la+++  +l+++g++a+ r++ +   ++++ + ll++ ++  + +++gl+p +   + e+++ +++++ vl
  gi|336253679|ref|YP_004596786.1|  20 LLAVIVLAVVGTTILFACGVVAYsRRRSRRYLLITVVLGLLVARSITGLGTVFGLVPMTahHLVEHSFDFAIAVLVL 96 
                                       45667999999999********9655555555555666666666666666799988888734555999999988776 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 ?   12.9   3.1   2.7e-05      0.08      98     177 ..      15      99 ..      11     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                   ABC2_membrane_4  98 Klivllllsvllmlvtflitvlfallsgfvgfs.....vklvlellkkclelgllvffavlpiialvllkksyvlpl 169
                                       Kl+ +ll +++l +v ++i +++++++ + + s     ++ vl ll+   ++gl+++f ++p+ a  l+  s+ +++
  gi|336253679|ref|YP_004596786.1|  15 KLAPVLLAVIVLAVVGTTILFACGVVAYSRRRSrryllITVVLGLLVARSITGLGTVFGLVPMTAHHLVEHSFDFAI 91 
                                       8888999999*****999999999999887655344446678899999999************************** PP

                   ABC2_membrane_4 170 iltlvyti 177
                                       ++ ++y++
  gi|336253679|ref|YP_004596786.1|  92 AVLVLYAV 99 
                                       **999986 PP

>> DUF3481  C-terminal domain of neuropilin glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.2     9e-05      0.27      12      40 ..      15      43 ..       6      51 .. 0.89
   2 ?   -1.9   0.0      0.95   2.8e+03      27      35 ..      67      73 ..      44      80 .. 0.54
   3 ?    1.0   0.0      0.11   3.4e+02      32      51 ..      90     109 ..      84     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9e-05
                           DUF3481 12 tldPilitiiamsalGvllGaicGvvlyc 40
                                       l P+l+++i+++ +G  +   cGvv y 
  gi|336253679|ref|YP_004596786.1| 15 KLAPVLLAVIVLAVVGTTILFACGVVAYS 43
                                      589**************9999*****996 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.95
                           DUF3481 27 GvllGaicG 35
                                      G  lG++ G
  gi|336253679|ref|YP_004596786.1| 67 G--LGTVFG 73
                                      2..444444 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.11
                           DUF3481  32 aicGvvlycacsqaslsdrn 51 
                                       ai  +vly     +s +dr+
  gi|336253679|ref|YP_004596786.1|  90 AIAVLVLYAVYRSGSDADRS 109
                                       788999**998888777776 PP

>> SUR7  SUR7/PalI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.4   5.5e-05      0.16     111     161 ..      16      64 ..      14     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.5e-05
                              SUR7 111 ltkalfilhiialvlsfislvvgllaicvspdnsrllsflnlllsvlsfla 161
                                       l  +l+++++ a+v ++i++ +g++a +  +  sr++++++ +l +l++ +
  gi|336253679|ref|YP_004596786.1|  16 LAPVLLAVIVLAVVGTTILFACGVVAYS--RRRSRRYLLITVVLGLLVARS 64 
                                       56789**********************8..777777999998888776543 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   5.4   8.5e-05      0.25      27     123 ..      13     100 ..       3     102 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.5e-05
                              TctB  27 gpgffPlll.gvllallgllllvaadgekeekearedwrkllklvlallaalll..yallleplGfilata.lflll 99 
                                        p++ P ll +++la++g+ +l+   + +    +r++ r+ l l+ ++l +l++     l +++G+++ ta  ++  
  gi|336253679|ref|YP_004596786.1|  13 DPKLAPVLLaVIVLAVVGTTILF---ACGVVAYSRRRSRRYL-LITVVLGLLVArsITGLGTVFGLVPMTAhHLV-- 83 
                                       48999988658889999988888...4444455555566666.56665666666644446666677777774333.. PP

                              TctB 100 llgreerkwlkalilavvlallvy 123
                                                  ++++av++  +vy
  gi|336253679|ref|YP_004596786.1|  84 --E-----HSFDFAIAVLVLYAVY 100
                                       ..2.....4566666666665555 PP

>> DUF2530  Protein of unknown function (DUF2530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.1   0.00011      0.34       4      51 ..      14      61 ..      12      79 .. 0.84
   2 ?   -0.3   0.0      0.43   1.3e+03      21      36 ..      86     101 ..      74     109 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                           DUF2530  4 PeLprrLtdprpvivvgtllWlvalvvllvvgdaleswlpvclaGlvv 51
                                      P+L ++L+ + + +vvgt + ++  vv++  +++   +l + + Gl+v
  gi|336253679|ref|YP_004596786.1| 14 PKLAPVLLAVIVLAVVGTTILFACGVVAYSRRRSRRYLLITVVLGLLV 61
                                      99***************9877777777777878888889999999987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.43
                           DUF2530  21 tllWlvalvvllvvgd 36 
                                       +  +++a++vl++v +
  gi|336253679|ref|YP_004596786.1|  86 SFDFAIAVLVLYAVYR 101
                                       5568899998887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 887.76
//
Query:       gi|336253680|ref|YP_004596787.1|  [L=247]
Description: 3,4-dihydroxy-2-butanone 4-phosphate synthase [Halopiger xanaduensis SH-6]
Scores for complete 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  197.9   0.1    1.3e-58  197.7   0.1    1.1  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 !  197.7   0.1   7.2e-63   1.3e-58       1     191 [.      38     244 ..      38     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 197.7 bits;  conditional E-value: 7.2e-63
                                       HHHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-S..... CS
                     DHBP_synthase   1 eeaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveene..... 72 
                                       +ea+eal+aG++++v+D +dre+e+dLi++A++vtpe+va ++++a+Gl+cval +++a++++Lp+  ee +     
  gi|336253680|ref|YP_004596787.1|  38 DEALEALRAGEPILVHDAADREGETDLIYHADAVTPEAVARLRNDAGGLVCVALGHDVAEAFDLPFYGEEVDhpaae 114
                                       589****************************************************************9644488889 PP

                                       .....STT---BB--EEESST-SSS-SHHHHHHHHHHHH-T......T--GGGEEEEEEEEEEEE-TTGGGTS-SHH CS
                     DHBP_synthase  73 .....dkhktaftvsvdaaegttTGIsaaDRalTirkladp......kakpedfrrPGhvfplrareggvleRrghT 138
                                               +++f+++v+++ +t TGI+++DR++Tir+l ++      +  +++fr PGhv++l+a+++ + +R+ghT
  gi|336253680|ref|YP_004596787.1| 115 ahelgYDDRSSFSLTVNHR-DTYTGITDNDRSTTIRALGEAaaapadTDFADQFRVPGHVHLLKAAPDLLSQREGHT 190
                                       999994457**********.9******************97344443334589************************ PP

                                       HHHHHHHHHTTS-SBEEEEEBB-TT.SCB-BHHHHHHHHHHHT-EEEEHHHHHH CS
                     DHBP_synthase 139 EaavdLarlaglkpaavicellndd.gtmarrdeleefakkhglkiitiedlie 191
                                       E++++La++a+l+pa v+ce+l+d+ g++++ ++++++a++h++ +++++d++e
  gi|336253680|ref|YP_004596787.1| 191 ELGIALANAADLPPAVVVCEMLDDEtGEALSPADARAYANRHDFAYLEGRDVLE 244
                                       ***********************99899*********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1963.88
//
Query:       gi|336253681|ref|YP_004596788.1|  [L=235]
Description: riboflavin kinase [Halopiger xanaduensis SH-6]
Scores for 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-48  162.5   0.0    6.2e-48  161.9   0.0    1.3  1  CTP-dep_RFKase  Domain of unknown function DUF120
    1.4e-07   31.4   1.3    2.4e-07   30.7   1.3    1.4  1  HTH_20          Helix-turn-helix domain
    1.6e-05   24.4   0.2    2.7e-05   23.6   0.2    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    2.9e-05   23.9   0.5      6e-05   22.9   0.5    1.5  1  MarR_2          MarR family
    9.1e-05   22.2   0.7    9.1e-05   22.2   0.7    2.0  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    0.00053   19.9   0.1     0.0011   18.9   0.1    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0011   18.9   0.1     0.0025   17.7   0.1    1.6  1  MarR            MarR family
     0.0016   18.3   0.1     0.0028   17.6   0.1    1.4  1  HTH_11          HTH domain
     0.0025   18.0   0.0     0.0056   16.9   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0031   18.0   0.1     0.0049   17.3   0.1    1.4  1  HTH_27          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.4   0.1       0.02   14.6   0.1    1.4  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.017   15.0   0.1      0.037   14.0   0.1    1.6  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.093   12.6   0.9       0.15   11.9   0.9    1.3  1  HTH_IclR        IclR helix-turn-helix domain
       0.17   11.5   0.4       0.33   10.6   0.4    1.5  1  GntR            Bacterial regulatory proteins, gntR family
       0.21   11.3   0.0        0.3   10.8   0.0    1.2  1  DUF4423         Domain of unknown function (DUF4423)


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 !  161.9   0.0   5.2e-51   6.2e-48       1     121 []     105     231 ..     105     231 .. 0.96

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 5.2e-51
                                       EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEE CS
                    CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypaki 77 
                                       V+sG+geG++y+sl+gy++qfee+lg+ep+pGTLNv+l+e+s+++r+a+++l++++i+g+ed++rt+g +++ypa+i
  gi|336253681|ref|YP_004596788.1| 105 VTSGMGEGRHYISLPGYNRQFEERLGYEPFPGTLNVDLREDSVRRRSAVSSLEPVPIDGWEDDDRTYGPAVCYPATI 181
                                       89*************************************************************************** PP

                                       CCEEEE......EEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEEE CS
                    CTP-dep_RFKase  78 ekikaa......vvvperthyeedvlEiiapekLReklelkdgdevevev 121
                                       ++ +++       ++perth++ed+lE+iap+kLR++l+l+dgd+v+v+v
  gi|336253681|ref|YP_004596788.1| 182 STSDGDtydgahTIAPERTHHDEDQLEVIAPDKLRDELGLEDGDHVTVSV 231
                                       888666667778************************************86 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   1.3     2e-10   2.4e-07      15      60 ..      16      67 ..      13      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2e-10
                                      HHHHH......STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 15 ilraL......araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      +l++L       ++   +++ laerld s +t+s++L+ Le+a+L+e+ +++
  gi|336253681|ref|YP_004596788.1| 16 VLKLLalegglEGDVKISCARLAERLDASNQTASRRLQRLESADLLERDTVS 67
                                      55555666666889999******************************99875 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 !   23.6   0.2   2.3e-08   2.7e-05      15      47 ..      29      61 ..      15      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.3e-08
                            HTH_24 15 nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      + +is + LAerl+ S +t +rrl+rLe++ l+
  gi|336253681|ref|YP_004596788.1| 29 DVKISCARLAERLDASNQTASRRLQRLESADLL 61
                                      6689************************99886 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.5     5e-08     6e-05      13      55 ..      19      65 ..       9      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5e-08
                                      HHHCTTTS....EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 13 aLgrrpgr....dltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                       L+ ++g     +++ + la+rl+ s +++sr+l+rL++a L+er +
  gi|336253681|ref|YP_004596788.1| 19 LLALEGGLegdvKISCARLAERLDASNQTASRRLQRLESADLLERDT 65
                                      555555435545569999**************************976 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 !   22.2   0.7   7.6e-08   9.1e-05      12      42 .]      26      56 ..      25      56 .. 0.94
   2 ?   -1.4   0.1       1.8   2.2e+03      27      37 ..     140     150 ..     139     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7.6e-08
                     HTH_AsnC-type 12 LqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      L+ d +is+a+LAer+  S +t+ rR++rLe
  gi|336253681|ref|YP_004596788.1| 26 LEGDVKISCARLAERLDASNQTASRRLQRLE 56
                                      56699*************************8 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                     HTH_AsnC-type  27 vGlSestvlrR 37 
                                       v l e+ v+rR
  gi|336253681|ref|YP_004596788.1| 140 VDLREDSVRRR 150
                                       7899999***9 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 !   18.9   0.1   9.1e-07    0.0011      17      54 ..      27      64 ..      15      78 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.1e-07
                                      EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 17 eielpltqeelAsmlGltretvsrilseLkreglisrg 54
                                      e +++++ + lA++l ++ +t sr l++L+ + l++r 
  gi|336253681|ref|YP_004596788.1| 27 EGDVKISCARLAERLDASNQTASRRLQRLESADLLERD 64
                                      336899999**************************963 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   2.1e-06    0.0025      20      49 ..      32      63 ..      13      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                                      HH..HHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 20 vs..eLakklgvskstvtrvldrLekkGlieR 49
                                      +s   La++l  s+ t++r l rLe ++l+eR
  gi|336253681|ref|YP_004596788.1| 32 IScaRLAERLDASNQTASRRLQRLESADLLER 63
                                      33448**************************9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.3e-06    0.0028      13      41 ..      29      57 ..      16      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.3e-06
                            HTH_11 13 rgpisgeeLAeeLnvSrrtvrrdIkaLee 41
                                      + +is ++LAe+L+ S +t  r++++Le+
  gi|336253681|ref|YP_004596788.1| 29 DVKISCARLAERLDASNQTASRRLQRLES 57
                                      5569***********************97 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 !   16.9   0.0   4.6e-06    0.0056      18      53 ..      27      62 ..      25      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.6e-06
                                      HHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 18 eekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      e+ ++++ ++laerL+ s  ++s  l++Le++ ++e
  gi|336253681|ref|YP_004596788.1| 27 EGDVKISCARLAERLDASNQTASRRLQRLESADLLE 62
                                      56788999***********************99986 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 !   17.3   0.1   4.1e-06    0.0049      16      54 ..      28      67 ..       9      78 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.1e-06
                            HTH_27 16 rrrkkl.adlcgrlnvedshisyslkkLtekGLvertgde 54
                                      ++ k+  a+l++rl+ + +++s  l +L+ ++L+er +  
  gi|336253681|ref|YP_004596788.1| 28 GDVKIScARLAERLDASNQTASRRLQRLESADLLERDTVS 67
                                      34445579**************************777653 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 ?   14.6   0.1   1.7e-05      0.02      13      46 ..      30      63 ..      21      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
                          HTH_DeoR 13 gklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                       k+s  +l+e+l+ S +T+ R L+ Le ++ll+R
  gi|336253681|ref|YP_004596788.1| 30 VKISCARLAERLDASNQTASRRLQRLESADLLER 63
                                      578999*************************998 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 ?   14.0   0.1   3.1e-05     0.037      20      60 .]      38      79 ..      32      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.1e-05
                                      HHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSE....EEE-HHHH CS
                             HTH_1 20 AeeLglsqpavsrqikrLEeelgvpLfeRtgrg....lrLTeaGe 60
                                      Ae+L  s  ++sr+++rLE+   ++L+eR++ +    +  T+ Ge
  gi|336253681|ref|YP_004596788.1| 38 AERLDASNQTASRRLQRLES---ADLLERDTVSdgqwVAITDDGE 79
                                      9******************8...5899986642335788888886 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 ?   11.9   0.9   0.00013      0.15       7      51 ..      15      64 ..      14      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                      HHHCT-CTTBSS.....-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  7 aiLdalaeapqe.....ltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      a+L++la +++       + + lA+r++ +  t++R Lq L+   ++e+d
  gi|336253681|ref|YP_004596788.1| 15 AVLKLLALEGGLegdvkISCARLAERLDASNQTASRRLQRLESADLLERD 64
                                      677777766666667767899***************************99 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   0.00027      0.33      23      57 ..      31      64 ..      17      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                                      B---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 23 kLPsereLaaefgVsrttvReALrrLeaeglverr 57
                                      k+ s   La++++ s +t  + L+rLe+++l+er 
  gi|336253681|ref|YP_004596788.1| 31 KI-SCARLAERLDASNQTASRRLQRLESADLLERD 64
                                      66.7789*************************995 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00025       0.3      36      77 ..      31      72 ..      14      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                           DUF4423 36 kadpeelakrlrpkisaeevekalefLlklgllkkded..gkyr 77
                                      k + + la+rl   +s++ +++ l++L++++ll++d    g+++
  gi|336253681|ref|YP_004596788.1| 31 KISCARLAERLD--ASNQTASRRLQRLESADLLERDTVsdGQWV 72
                                      677899******..*********************975446666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.42u 0.19s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 2028.16
//
Query:       gi|336253682|ref|YP_004596789.1|  [L=271]
Description: hypothetical protein Halxa_2285 [Halopiger xanaduensis SH-6]
Scores for 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:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 2046.75
//
Query:       gi|336253683|ref|YP_004596790.1|  [L=274]
Description: MarR family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-08   33.0   0.0    9.5e-08   31.9   0.0    1.6  1  MarR             MarR family
    6.1e-07   29.2   0.0    1.1e-06   28.4   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    7.2e-07   29.0   0.4    4.3e-06   26.5   0.2    2.2  2  MarR_2           MarR family
    1.6e-06   27.6   0.0    2.6e-06   26.9   0.0    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    2.1e-06   27.5   0.0    4.5e-06   26.4   0.0    1.6  1  HTH_5            Bacterial regulatory protein, arsR family
    1.4e-05   24.8   0.3    8.3e-05   22.3   0.1    2.1  2  HTH_IclR         IclR helix-turn-helix domain
    2.2e-05   24.0   0.1    4.9e-05   22.9   0.1    1.6  1  GntR             Bacterial regulatory proteins, gntR family
     0.0005   20.2   0.0    0.00081   19.5   0.0    1.4  1  DUF1724          Domain of unknown function (DUF1724)
    0.00085   19.2   0.0     0.0019   18.1   0.0    1.5  1  HTH_11           HTH domain
     0.0013   18.8   0.3     0.0025   17.8   0.3    1.5  1  HTH_20           Helix-turn-helix domain
     0.0019   18.7   0.0     0.0035   17.8   0.0    1.4  1  HTH_27           Winged helix DNA-binding domain
     0.0024   17.8   0.1     0.0046   16.9   0.1    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0035   17.7   0.0      0.006   16.9   0.0    1.4  1  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.021   15.0   0.0    1.4  1  HTH_34           Winged helix DNA-binding domain
      0.031   14.5   0.0      0.069   13.4   0.0    1.6  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
       0.07   12.8   0.0       0.11   12.2   0.0    1.3  1  Ribosomal_S19e   Ribosomal protein S19e
       0.12   12.4   0.0        0.2   11.6   0.0    1.4  1  HTH_36           Helix-turn-helix domain
       0.12   12.1   0.0       0.21   11.4   0.0    1.3  1  HTH_DeoR         DeoR-like helix-turn-helix domain
       0.28   10.6   0.0       0.44    9.9   0.0    1.2  1  RepL             Firmicute plasmid replication protein (RepL)


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 !   31.9   0.0     1e-10   9.5e-08       4      51 ..      19      66 ..      17      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1e-10
                                      HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      ++++iL+ l e+gp+++ eL   l  s+stv r l +Le+ G++eR  
  gi|336253683|ref|YP_004596790.1| 19 ARIDILTRLFESGPATQRELRTELDSSRSTVARSLSALEECGWVERHA 66
                                      6789******************************************76 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   1.2e-09   1.1e-06      12      56 ..      22      66 ..      17      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.2e-09
                                      CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      ++ + L ++gpat +e+  el+ +rs+v ++L+ Le++G+Ver  
  gi|336253683|ref|YP_004596790.1| 22 DILTRLFESGPATQRELRTELDSSRSTVARSLSALEECGWVERHA 66
                                      6778899***********************************975 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.2   4.5e-09   4.3e-06       6      56 ..      19      67 ..      11      70 .. 0.87
   2 ?   -1.1   0.0       1.9   1.8e+03      21      36 ..     162     177 ..     152     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.5e-09
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      a  ++L  L  +++   t++el  +l+ s+s+v r l  L++ G+ver ++
  gi|336253683|ref|YP_004596790.1| 19 ARIDILTRLFESGP--ATQRELRTELDSSRSTVARSLSALEECGWVERHAD 67
                                      55678888888888..9*******************************876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                                       EEEHHHHHHHHTSSHH CS
                            MarR_2  21 dltvgelarrlglsks 36 
                                       ++t g+l+++l +s++
  gi|336253683|ref|YP_004596790.1| 162 RVTNGDLEAELIVSPA 177
                                       378899****999986 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 !   26.9   0.0   2.8e-09   2.6e-06       3      48 .]      18      63 ..      16      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.8e-09
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + +++IL  L + +  +qreL  +l+ S+stv r l  Lee G+++
  gi|336253683|ref|YP_004596790.1| 18 DARIDILTRLFESGPATQRELRTELDSSRSTVARSLSALEECGWVE 63
                                      66789***************************************96 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 !   26.4   0.0   4.8e-09   4.5e-06       2      46 ..      18      63 ..      17      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.8e-09
                                      HHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       +R++IL  L e g+++  el  el+ s+stv + L++L+e+G Ve
  gi|336253683|ref|YP_004596790.1| 18 DARIDILTRLFEsGPATQRELRTELDSSRSTVARSLSALEECGWVE 63
                                      579****************************************886 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 !   22.3   0.1   8.8e-08   8.3e-05      14      51 ..      29      65 ..      21      66 .. 0.83
   2 ?   -0.2   0.0      0.94   8.9e+02      40      49 ..      75      84 ..      69      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 8.8e-08
                                      TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      e ++  t +el  +++ ++Stv R L+ L+e+G+ve++
  gi|336253683|ref|YP_004596790.1| 29 ESGP-ATQRELRTELDSSRSTVARSLSALEECGWVERH 65
                                      4444.4899***************************85 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.94
                                      HHHHHTTSEE CS
                          HTH_IclR 40 qtLvelGyve 49
                                       tLv +G++ 
  gi|336253683|ref|YP_004596790.1| 75 GTLVAEGFLD 84
                                      69******95 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   5.2e-08   4.9e-05      12      57 ..      22      65 ..      15      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.2e-08
                                      HHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 12 dIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverr 57
                                      dIl+  ++ G +  ++reL++e++ sr+tv ++L+ Le+ g+ver+
  gi|336253683|ref|YP_004596790.1| 22 DILTRLFESGPA--TQRELRTELDSSRSTVARSLSALEECGWVERH 65
                                      566666666655..59****************************97 PP

>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   8.6e-07   0.00081       3      61 ..     202     259 ..     200     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.6e-07
                           DUF1724   3 lyvydeeikplsltvtDkflslslfdkdgkydhkdlisfdesAlkWGeeLFeyYlkrSe 61 
                                       ++v de++ p+ l + D++++    ++d  + +  l   ++s+ +W++eL++ Y+++++
  gi|336253683|ref|YP_004596790.1| 202 VFVSDEPL-PFYLGIDDDWTIQLGVEDDEGFPRALLETAEPSVAEWATELYREYRSNAR 259
                                       8999****.*******99888666777777*9999999*******************98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.1e-06    0.0019       3      43 ..      21      60 ..      20      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.1e-06
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                       +il++L+e+ +  +  eL  eL+ Sr+tv r + aLee g
  gi|336253683|ref|YP_004596790.1| 21 IDILTRLFESGP-ATQRELRTELDSSRSTVARSLSALEECG 60
                                      589****88887.9*************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.3   2.7e-06    0.0025       8      57 ..      16      65 ..      10      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.7e-06
                                      S-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  8 ahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                       +  R +il  L + +++t  el  +ld s++t+ + L +Lee g ve+ 
  gi|336253683|ref|YP_004596790.1| 16 RSDARIDILTRLFESGPATQRELRTELDSSRSTVARSLSALEECGWVERH 65
                                      5679***************************************9999976 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 !   17.8   0.0   3.7e-06    0.0035       8      66 ..      23      73 ..      18      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.7e-06
                            HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTd 66
                                      +L  +  + +++++++l+  l+ + s+++ sl++L+e G+ver +d        +rlT+
  gi|336253683|ref|YP_004596790.1| 23 ILTRLF-ESGPATQRELRTELDSSRSTVARSLSALEECGWVERHADG-------HRLTP 73
                                      566777.8899******************************999998.......77777 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 !   16.9   0.1   4.8e-06    0.0046      21      54 ..      32      65 ..      11      76 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.8e-06
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrg 54
                                      p tq+el   l ++r+tv r ls+L++ g+++r+
  gi|336253683|ref|YP_004596790.1| 32 PATQRELRTELDSSRSTVARSLSALEECGWVERH 65
                                      99*****************************963 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.4e-06     0.006       4      59 ..      19      70 ..      16      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.4e-06
                                      S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTE CS
                   Penicillinase_R  4 lEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegra 59
                                      +   ++  l e+g+at +e+++el++     +sTV+  l+ L++ g+++r+ +g +
  gi|336253683|ref|YP_004596790.1| 19 ARIDILTRLFESGPATQRELRTELDSS----RSTVARSLSALEECGWVERHADGHR 70
                                      5567888999999***99999999988....**********************986 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 ?   15.0   0.0   2.3e-05     0.021       2      48 ..      20      66 ..      19      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                            HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdk 48
                                      R+ +l+ L +   a+ +el+++l  + +  +  l++Le+ g++e++ 
  gi|336253683|ref|YP_004596790.1| 20 RIDILTRLFESGPATQRELRTELDSSRSTVARSLSALEECGWVERHA 66
                                      8899***************************************9865 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 ?   13.4   0.0   7.3e-05     0.069      19      59 ..      29      69 ..      22      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.3e-05
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykg 59
                                      e++++++ +l  +L+ s s+V  +l+ Le+ G ve + +++
  gi|336253683|ref|YP_004596790.1| 29 ESGPATQRELRTELDSSRSTVARSLSALEECGWVERHADGH 69
                                      78899999**************************9988766 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.11      87     124 ..      40      76 ..      13      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                       HHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--S CS
                    Ribosomal_S19e  87 hfvkasgsvirkilqqLeklglvkkekkkgrrltkkGq 124
                                          ++s+s + + l +Le++g+v+++++ g+rlt+ G 
  gi|336253683|ref|YP_004596790.1|  40 TELDSSRSTVARSLSALEECGWVERHAD-GHRLTPVGT 76 
                                       5567899999999**********88856.******996 PP

>> HTH_36  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   0.00022       0.2      27      55 .]      34      62 ..      32      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      +q+ l + l  s++Tv r +  Le++G++
  gi|336253683|ref|YP_004596790.1| 34 TQRELRTELDSSRSTVARSLSALEECGWV 62
                                      566777777789****************6 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 ?   11.4   0.0   0.00022      0.21       5      51 ..      23      69 ..      20      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                          HTH_DeoR  5 ilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthGGa 51
                                      il  l ++g  +  el  +l+ S  T+ R L+ Lee g ++R+  G 
  gi|336253683|ref|YP_004596790.1| 23 ILTRLFESGPATQRELRTELDSSRSTVARSLSALEECGWVERHADGH 69
                                      78888999999999****************************97775 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00047      0.44      76     111 ..      33      68 ..      32      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00047
                              RepL  76 atnRelaeetgislktvsetlkileeanilkkkanG 111
                                       at+Rel  e + s  tv + l +lee + + ++a+G
  gi|336253683|ref|YP_004596790.1|  33 ATQRELRTELDSSRSTVARSLSALEECGWVERHADG 68 
                                       69*******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2169.20
//
Query:       gi|336253684|ref|YP_004596791.1|  [L=111]
Description: hypothetical protein Halxa_2287 [Halopiger xanaduensis SH-6]
Scores for 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   14.6   0.7       0.22   11.6   0.7    2.3  1  HTH_20    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 ?   11.6   0.7   1.2e-05      0.22       1      40 [.      10      51 ..      10      87 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHH..TS-HHH CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerl..dlsknt 40
                                      d+++++ a++ Rr+i + +++++++t+ el +++  + ++ t
  gi|336253684|ref|YP_004596791.1| 10 DELHRIAANERRRAIVATIRDRGAVTVDELVATVaeREPQPT 51
                                      6789999************77777777777666644333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 921.29
//
Query:       gi|336253685|ref|YP_004596792.1|  [L=326]
Description: Wyosine base formation domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-20   72.2   0.1    2.3e-19   69.5   0.0    2.3  2  Wyosine_form  Wyosine base formation
      1e-19   71.5   1.3    3.5e-19   69.8   1.3    1.8  1  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.21   1.9e+03      39      61 ..     197     219 ..     185     221 .. 0.69
   2 !   69.5   0.0   2.5e-23   2.3e-19       2      63 .]     241     302 ..     240     302 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.21
                                       HHHTSSS.EEEEEEETTTTEEEE CS
                      Wyosine_form  39 rlegsaedYellaehrhSrvvll 61 
                                       +  + +e  ++l e ++ r+vl 
  gi|336253685|ref|YP_004596792.1| 197 AWDRLLETMDVLREKEETRTVLR 219
                                       444556688999******99996 PP

  == domain 2  score: 69.5 bits;  conditional E-value: 2.5e-23
                                       HT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                      Wyosine_form   2 aepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                       a+pdF+E+Kay++vG+s+ rL+++ +P+he+v+ fa+ ++++  +++ l   ++Srv+lla+
  gi|336253685|ref|YP_004596792.1| 241 ADPDFIELKAYMHVGHSQGRLDRSSMPDHEDVVAFAEDVQEYMPEFDELKGVPPSRVALLAK 302
                                       89**********************************************************96 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   1.3     4e-23   3.5e-19       2     161 ..      57     232 ..      56     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 4e-23
                                       EEESEESS--TTTSCCTT...........................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEE CS
                                       xxxxxxxxxxxxxxxxxx...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet...........................vrregrgrslsveeileevkelkaekgvkevi 51 
                                       +++  Cn rC+fC+r +                              ++  g +  ++e  ee+ e       ++ i
  gi|336253685|ref|YP_004596792.1|  57 TPVVKCNERCVFCWRDHRghayelddvewddpeavadasirlqkkLLSGFGGNDEVPRERFEEAMEP-----RHVAI 128
                                       67789************9**99999999999999999999986664445555555555555555444.....78999 PP

                                       EESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT..CTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                       Radical_SAM  52 lgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn..rght 126
                                       ++ gep+lyp + elle+ + +   +i++++++ngt p     + l+e  +++++++++a+   ++ + ++    + 
  gi|336253685|ref|YP_004596792.1| 129 SLDGEPTLYPYLPELLEAFHDR---DITTFLVSNGTNP-----DVLRECDPTQLYVSVDAPERHTFDQVVKavEDDA 197
                                       99*******************9...*************.....*********************66666666688** PP

                                       HHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 127 feevlealeklreagikrvvdrivglpGendeele 161
                                       ++++le+++ lre+   r+v r+++++Gen+++ +
  gi|336253685|ref|YP_004596792.1| 198 WDRLLETMDVLREKEETRTVLRTTLVEGENMHHPD 232
                                       **************9888*************9966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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 0.22s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 2625.32
//
Query:       gi|336253686|ref|YP_004596793.1|  [L=155]
Description: curlin associated repeat-containing protein [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0041   16.2   0.5        2.3    7.2   0.0    2.6  3  DUF4831         Domain of unknown function (DUF4831)
  ------ inclusion threshold ------
      0.017   14.1   5.7        1.4    7.7   0.1    2.5  2  DUF3370         Protein of unknown function (DUF3370)
        1.2    9.4   8.5         33    4.8   0.4    3.5  3  CXCR4_N         CXCR4 Chemokine receptor N terminal
        1.6    8.6   4.5         30    4.5   0.2    3.0  3  Phycoerythr_ab  Phycoerythrin, alpha/beta chain


Domain annotation for each model (and alignments):
>> DUF4831  Domain of unknown function (DUF4831)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0006       2.7     240     281 ..      26      67 ..       4      71 .. 0.74
   2 !    7.2   0.0   0.00052       2.3     243     282 ..      73     112 ..      65     117 .. 0.78
   3 ?   -0.6   0.0      0.12   5.3e+02     245     280 ..     119     153 ..     109     155 .] 0.60

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0006
                           DUF4831 240 ekleapaekeeekkkkkkkgiaynvPgkakvtlteekkelak 281
                                       + ++ + ++++++ ++++++ +y+ Pg+ +v l++++ + ++
  gi|336253686|ref|YP_004596793.1|  26 AAAHHAPNHQQQDVDQENDATVYTGPGSGDVDLEQNNDNHQH 67 
                                       44555555667777777779***************9988766 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00052
                           DUF4831 243 eapaekeeekkkkkkkgiaynvPgkakvtlteekkelake 282
                                       +ap+++++++ ++++++ +y+ Pg+ +v l++++ + +++
  gi|336253686|ref|YP_004596793.1|  73 HAPSQQQQQDVDQDNDATVYTGPGSGDVDLEQNNDNHQHQ 112
                                       4555667777777777****************99887665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.12
                           DUF4831 245 paekeeekkkkkkkgiaynvPgkakvtlteekkela 280
                                       p++++++  ++++ +i  + Pg+ +v l +++++ +
  gi|336253686|ref|YP_004596793.1| 119 PSQQQQDVDQNNDADI-RTGPGSGDVDLAQSNNNHQ 153
                                       3333333333333344.5679999999999998765 PP

>> DUF3370  Protein of unknown function (DUF3370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00032       1.4      98     126 ..      26      54 ..       6      69 .. 0.84
   2 ?    7.3   1.6   0.00042       1.9      58     125 ..      71     140 ..      69     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00032
                           DUF3370  98 lsqpdApfielpalvenpegkvfaGPGsr 126
                                          ++Ap ++++++ ++++ +v++GPGs 
  gi|336253686|ref|YP_004596793.1|  26 AAAHHAPNHQQQDVDQENDATVYTGPGSG 54 
                                       44578**********************95 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00042
                           DUF3370  58 aHHiaraeeaeklktLylgvlvanptkepvtvkilqgasyls..qpdApfielpalvenpegkvfaGPGs 125
                                       +HH  +++++++  +   + + + p++ +v ++ ++ + + +  +++Ap ++++++ +n++  + +GPGs
  gi|336253686|ref|YP_004596793.1|  71 SHHAPSQQQQQDVDQDNDATVYTGPGSGDVDLEQNNDNHQHQhgSHHAPSQQQQDVDQNNDADIRTGPGS 140
                                       5899888888888888899999999999999988776655543478999999999999999999999998 PP

>> CXCR4_N  CXCR4 Chemokine receptor N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.012        55       9      17 ..      46      57 ..      40      65 .. 0.79
   2 ?    4.8   0.4    0.0074        33       5      17 ..      86     101 ..      85     109 .. 0.83
   3 ?    4.0   0.1     0.013        57       9      17 ..     133     144 ..     126     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.012
                           CXCR4_N  9 d...ElGSGDyd 17
                                      +   ++GSGD d
  gi|336253686|ref|YP_004596793.1| 46 TvytGPGSGDVD 57
                                      44669*****87 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0074
                           CXCR4_N   5 DNntd...ElGSGDyd 17 
                                       DN  +   ++GSGD d
  gi|336253686|ref|YP_004596793.1|  86 DNDATvytGPGSGDVD 101
                                       67666678******87 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.013
                           CXCR4_N   9 d...ElGSGDyd 17 
                                       d   ++GSGD d
  gi|336253686|ref|YP_004596793.1| 133 DirtGPGSGDVD 144
                                       46669*****87 PP

>> Phycoerythr_ab  Phycoerythrin, alpha/beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1    0.0075        33      19      32 ..      47      60 ..      41      62 .. 0.85
   2 ?    4.5   0.2    0.0066        30      19      32 ..      91     104 ..      84     106 .. 0.83
   3 ?   -1.0   0.1      0.35   1.6e+03      21      29 ..     136     144 ..     130     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0075
                                      S--S---SSGGGGE CS
                    Phycoerythr_ab 19 eytGpKaGdqdDem 32
                                       ytGp +Gd d e+
  gi|336253686|ref|YP_004596793.1| 47 VYTGPGSGDVDLEQ 60
                                      5********99775 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0066
                                       S--S---SSGGGGE CS
                    Phycoerythr_ab  19 eytGpKaGdqdDem 32 
                                        ytGp +Gd d e+
  gi|336253686|ref|YP_004596793.1|  91 VYTGPGSGDVDLEQ 104
                                       6********99775 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.35
                                       -S---SSGG CS
                    Phycoerythr_ab  21 tGpKaGdqd 29 
                                       tGp +Gd d
  gi|336253686|ref|YP_004596793.1| 136 TGPGSGDVD 144
                                       9******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1197  (0.0667633); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1181.34
//
Query:       gi|336253687|ref|YP_004596794.1|  [L=268]
Description: hypothetical protein Halxa_2290 [Halopiger xanaduensis SH-6]
Scores for 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-06   28.7   0.1    3.1e-06   27.2   0.1    1.8  1  HTH_20           Helix-turn-helix domain
    3.9e-05   23.5   0.0      8e-05   22.5   0.0    1.4  1  MarR             MarR family
    0.00013   21.8   0.1    0.00025   20.8   0.1    1.5  1  MarR_2           MarR family
     0.0047   16.6   0.5     0.0088   15.8   0.5    1.5  1  HTH_DeoR         DeoR-like helix-turn-helix domain
     0.0054   16.9   0.0     0.0096   16.1   0.0    1.4  1  HTH_34           Winged helix DNA-binding domain
     0.0054   16.4   0.2      0.013   15.1   0.2    1.7  1  GntR             Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.016   15.0   0.2       0.04   13.8   0.2    1.6  1  HxlR             HxlR-like helix-turn-helix
       0.03   14.2   0.1      0.056   13.3   0.1    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
      0.033   14.1   0.3      0.065   13.2   0.3    1.5  1  HTH_11           HTH domain
       0.12   12.9   0.1       0.28   11.7   0.1    1.5  1  HTH_27           Winged helix DNA-binding domain
       0.17   11.5   0.1        1.3    8.7   0.1    2.2  2  HTH_24           Winged helix-turn-helix DNA-binding
        0.2   11.4   2.1         37    4.1   0.0    3.3  3  Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation 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 !   27.2   0.1     2e-09   3.1e-06       8      50 ..      21      63 ..      11      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2e-09
                                      S-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_20  8 ahPvRrrilraLaraegltaselaerldlskntlsyHLrvLee 50
                                       +PvR +il++L++a+ l  sel+er+d+s+ tl ++L++Lee
  gi|336253687|ref|YP_004596794.1| 21 QSPVRVAILKHLSDADRLRKSELKERFDVSQVTLTRNLDALEE 63
                                      46****************************************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.4e-08     8e-05       3      48 ..      23      68 ..      22      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.4e-08
                                      HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  3 ltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      ++++ iL  l++ + l+ seL +++ vs+ t+tr ld+Le++ +i+
  gi|336253687|ref|YP_004596794.1| 23 PVRVAILKHLSDADRLRKSELKERFDVSQVTLTRNLDALEERAWIR 68
                                      66789*************************************9996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.7e-07   0.00025       5      52 ..      23      68 ..      19      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.7e-07
                                      HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      p    +L +L ++++  l+ +el +r+++s+ +++r l+ L+++ +++
  gi|336253687|ref|YP_004596794.1| 23 PVRVAILKHLSDADR--LRKSELKERFDVSQVTLTRNLDALEERAWIR 68
                                      677889********9..*****************************97 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 !   15.8   0.5   5.9e-06    0.0088       4      47 ..      27      69 ..      25      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.9e-06
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRt 47
                                      +il+ l + + l+  el e+++vS+ T  R L+ Lee    +R+
  gi|336253687|ref|YP_004596794.1| 27 AILKHLSDADRLRKSELKERFDVSQVTLTRNLDALEERAW-IRN 69
                                      699*********************************9988.444 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 !   16.1   0.0   6.5e-06    0.0096       1      45 [.      24      68 ..      24      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.5e-06
                            HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                      vR a+l  L+++d+   +elke   +++  L  +l++Le+  +i 
  gi|336253687|ref|YP_004596794.1| 24 VRVAILKHLSDADRLRKSELKERFDVSQVTLTRNLDALEERAWIR 68
                                      89*************************************998875 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2     9e-06     0.013      17      56 ..      31      69 ..      24      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9e-06
                                      SS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR 17 elrpGdkLPsereLaaefgVsrttvReALrrLeaeglver 56
                                      +l+  d+L + +eL ++f+Vs  t+ + L+ Le++ ++  
  gi|336253687|ref|YP_004596794.1| 31 HLSDADRL-RKSELKERFDVSQVTLTRNLDALEERAWIRN 69
                                      6777799*.**************************99975 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.6e-05      0.04       8      81 ..      26      92 ..      23      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                                      HHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHH CS
                              HxlR  8 llilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkk 81
                                      + il +l +  + R selk+++ ++sq +L+++L +Le+   i  +v        eY+l + G+ + ++++++ +
  gi|336253687|ref|YP_004596794.1| 26 VAILKHLSDaDRLRKSELKERF-DVSQVTLTRNLDALEERAWIRNHVR-------EYELLPSGKLVVDAVETMLE 92
                                      5699999997789*********.9**************9999876653.......67777777777777777765 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 ?   13.3   0.1   3.8e-05     0.056       1      41 [.      22      63 ..      22      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                                      SHHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_5  1 dptRlkILklLae.gelcvcelaeelglsqstvShHLkkLre 41
                                      +p R+ ILk L++   l  +el e +++sq t+ + L +L+e
  gi|336253687|ref|YP_004596794.1| 22 SPVRVAILKHLSDaDRLRKSELKERFDVSQVTLTRNLDALEE 63
                                      699**********666***********************997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   4.4e-05     0.065       5      41 ..      28      63 ..      25      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.4e-05
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLee 41
                                      il+ L +a+  +  +eL+e+++vS  t  r ++aLee
  gi|336253687|ref|YP_004596794.1| 28 ILKHLSDADR-LRKSELKERFDVSQVTLTRNLDALEE 63
                                      7888866665.8889********************97 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 ?   11.7   0.1   0.00018      0.28       5      48 ..      25      67 ..      22      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                            HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                       +++L ++    +r ++++l +r +v++ +   +l++L+e+ ++
  gi|336253687|ref|YP_004596794.1| 25 RVAILKHLS-DADRLRKSELKERFDVSQVTLTRNLDALEERAWI 67
                                      578999**9.******************************9888 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 ?    8.7   0.1   0.00084       1.3       7      44 ..      27      64 ..      22      68 .. 0.93
   2 ?   -0.2   0.0       0.5   7.5e+02      33      41 ..     135     143 ..     133     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00084
                            HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeee 44
                                      +IL+ L +  r+  +eL er ++S+ t++r l+ Lee 
  gi|336253687|ref|YP_004596794.1| 27 AILKHLSDADRLRKSELKERFDVSQVTLTRNLDALEER 64
                                      7***********************************96 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.5
                            HTH_24  33 tvnrrlkrL 41 
                                       +vnr+++ +
  gi|336253687|ref|YP_004596794.1| 135 PVNRHIEAM 143
                                       9*****987 PP

>> Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.025        37      22      32 ..      41      51 ..      39      53 .. 0.87
   2 ?    2.2   0.1     0.096   1.4e+02      13      24 ..      89     100 ..      83     102 .. 0.85
   3 ?    2.6   0.1     0.076   1.1e+02      27      39 ..     113     127 ..     110     136 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.025
                                      HHHHHHTTHHH CS
                   Ribosomal_L12_N 22 kalEekFGVsA 32
                                      ++l+e+F+Vs 
  gi|336253687|ref|YP_004596794.1| 41 SELKERFDVSQ 51
                                      79*******95 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.096
                                       BHHHHHHHHHHH CS
                   Ribosomal_L12_N  13 tvLElseLvkal 24 
                                       t+LE++e+v+ +
  gi|336253687|ref|YP_004596794.1|  89 TMLETVEFVESI 100
                                       78*******987 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.076
                                       HTTHHHH..HHHHHH CS
                   Ribosomal_L12_N  27 kFGVsAA..APvava 39 
                                       +F+V+A   A v+va
  gi|336253687|ref|YP_004596794.1| 113 EFDVTALadATVVVA 127
                                       8****9934447666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2022.60
//
Query:       gi|336253688|ref|YP_004596795.1|  [L=96]
Description: hypothetical protein Halxa_2291 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.029   14.7   0.1      0.034   14.5   0.1    1.1  1  DUF1772      Domain of unknown function (DUF1772)
        2.7    8.3   5.4       0.46   10.8   0.5    2.0  2  HIG_1_N      Hypoxia induced protein conserved region


Domain annotation for each model (and alignments):
>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.8e-06     0.034      42      95 ..      10      66 ..       4      91 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-06
                           DUF1772 42 lallsalafa.yla..araasrgarllylaaaallllsivpyTllvmvPtNnkLaal 95
                                      l+ll++++++ y++  a     g++ll++++aa+ +l+ + + l++ vPt  +++++
  gi|336253688|ref|YP_004596795.1| 10 LGLLATVGVFgYVYrdATNVEMGRPLLWATIAAAPVLVGLGLYLFASVPTTGTIMTA 66
                                      44455555554556668888999999**99999966677889999999998887766 PP

>> HIG_1_N  Hypoxia induced protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5   5.1e-05      0.46       1      21 [.       4      24 ..       4      33 .. 0.88
   2 ?   -0.1   0.4      0.13   1.2e+03       9      23 ..      40      54 ..      32      76 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.1e-05
                           HIG_1_N  1 eeplvpiGilatvgalvrglr 21
                                      e+p  ++G+latvg+  + +r
  gi|336253688|ref|YP_004596795.1|  4 ESPIAVLGLLATVGVFGYVYR 24
                                      68999***********99887 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.13
                           HIG_1_N  9 ilatvgalvrglrsm 23
                                      i+a  + + +gl+ +
  gi|336253688|ref|YP_004596795.1| 40 IAAAPVLVGLGLYLF 54
                                      555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 726.03
//
Query:       gi|336253689|ref|YP_004596796.1|  [L=397]
Description: alcohol dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-118  393.2   4.8     1e-117  393.0   4.8    1.0  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    2.8e-16   60.0   2.8    5.5e-12   45.9   0.4    2.1  2  Fe-ADH_2      Iron-containing alcohol dehydrogenase
     0.0025   17.5   0.6     0.0048   16.6   0.6    1.5  1  Peripla_BP_6  Periplasmic binding protein
  ------ inclusion threshold ------
       0.12   10.9   0.0       0.21   10.0   0.0    1.3  1  Borrelia_P83  Borrelia P83/100 protein


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 !  393.0   4.8  2.3e-121    1e-117       1     364 []      17     389 ..      17     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 393.0 bits;  conditional E-value: 2.3e-121
                                       -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaala 77 
                                       P+ i++g ga++el++++ + g+++al+vtd+g+l ++g++d v+++le+ag+ev++++gv+p+p+l+  e+aa+ +
  gi|336253689|ref|YP_004596796.1|  17 PNDIRYGMGAAAELEAYAGEEGIDSALLVTDEGVL-EAGAADPVVDALEAAGVEVATYGGVTPEPKLALAEAAAEEV 92 
                                       899******************************99.9**************************************** PP

                                       -TT.--EEEEEESHHHHHHHHHHHHHTT...................--EEEEESS-S-S-TT-SEEEEE.-TTS.E CS
                            Fe-ADH  78 reegadvviavGGGsviDtAKaialllanpe.vedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeeg.e 152
                                        + +advvi+vGGGs++DtAK++++l++++e v+++lg g++ + ++ p +  PTtaGtGsevt++ v+ d+e+g  
  gi|336253689|ref|YP_004596796.1|  93 AAVDADVVIGVGGGSSMDTAKLASVLVEYDEpVREMLGMGNV-PGPGRPTVLLPTTAGTGSEVTHIGVFADKEDGgN 168
                                       *****************************966*****88876.8999************************999559 PP

                                       EEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHH. CS
                            Fe-ADH 153 klsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadge. 228
                                       k+++++++l++dla+vDpelt +lP++v+aatg+Dal+ha+E+yvs+ ++p++dalal+ai+li +nl++av++ge 
  gi|336253689|ref|YP_004596796.1| 169 KKVVYSEHLFADLALVDPELTRSLPPQVAAATGMDALTHAVESYVSTLRTPYTDALALHAIELIGDNLREAVHQGEh 245
                                       99*************************************************************************88 PP

                                       HHHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHHHHT...... CS
                            Fe-ADH 229 dleareqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaaperlaqlaralgge.. 303
                                       + ear +m la+tlag+af n+glgavHal+++lg  +g+ hglana+llp+v+++n +a+p+r+ ++a  lg    
  gi|336253689|ref|YP_004596796.1| 246 NDEARYAMSLAATLAGQAFVNSGLGAVHALTYPLGTECGLGHGLANAVLLPHVMEYNVPAEPDRFTEIAGLLGVPer 322
                                       ************************************************************************999** PP

                                       ......T--HHHHHHHHHHHHHTT---SHHHHT.-TT-HHHHHHHHHT-T..SGGGGSSS---HHHH CS
                            Fe-ADH 304 ...sdeeaaeeliealrellkelglptsLselg.vdeedldklaeaalkd..rslannpreltaedv 364
                                          s+ e+a+++++a+++l++++g+p++++e+g vde+++d++a+ al+    ++ +npr++++ed+
  gi|336253689|ref|YP_004596796.1| 323 edeSTLERAHRAVDAVKALNDDIGIPNQIREVGdVDESEFDSFADIALEHsqHNIDRNPRRMEKEDI 389
                                       ***999*******************************************9999************97 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 !   45.9   0.4   1.2e-15   5.5e-12       3      97 ..      23     118 ..      21     122 .. 0.95
   2 !   14.2   0.1   5.8e-06     0.026     140     236 ..     183     280 ..     163     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1.2e-15
                          Fe-ADH_2   3 gegaleklgellkelelkkvllvadentkka.agekveeslkeagikvevveeveeeadleeveklvealreketdl 78 
                                       g ga  +l+++  e++++ +llv+de++ +a a++ v ++l+ ag++v+++  v++e++l  +e+ +e++++ ++d+
  gi|336253689|ref|YP_004596796.1|  23 GMGAAAELEAYAGEEGIDSALLVTDEGVLEAgAADPVVDALEAAGVEVATYGGVTPEPKLALAEAAAEEVAAVDADV 99 
                                       67999**********************999879999***************************************** PP

                          Fe-ADH_2  79 vvavGgGtiiDiakyvsak 97 
                                       v++vGgG+ +D+ak++s  
  gi|336253689|ref|YP_004596796.1| 100 VIGVGGGSSMDTAKLASVL 118
                                       ****************976 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.8e-06
                          Fe-ADH_2 140 iaDldvlaeAPrrllasGvGDllgkytaladwklanevseplaklsaamvqeaaeklved.kketealeellealal 215
                                       ++D ++ +  P +  a+   D+l   +  + + l + +++ la+ +++ + ++++++v++ ++++ea  ++  a +l
  gi|336253689|ref|YP_004596796.1| 183 LVDPELTRSLPPQVAAATGMDALTHAVESYVSTLRTPYTDALALHAIELIGDNLREAVHQgEHNDEARYAMSLAATL 259
                                       6899999********99999**************************************97245789989999999** PP

                          Fe-ADH_2 216 sgigisrpaSGsEHliSHald 236
                                       +g ++ +++ G+ H +   l 
  gi|336253689|ref|YP_004596796.1| 260 AGQAFVNSGLGAVHALTYPLG 280
                                       **************9976665 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.6   1.1e-06    0.0048     118     202 ..      22     108 ..      11     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHHHHHHHHHHHHHCCTEEEEEEEEE-TTH..HHHHHHHHHHHTTT-S CS
                      Peripla_BP_6 118 ysaqasalveylakelggkkvalvyadyafgregiaalkaaakaaGgevvgeepvplgt..tdfsaqvlqikaagad 192
                                       y + a+a +e+ a e+g+ ++ lv++     + +++++ +a++aaG+ev  +  v+++   +  +a++ +++a  ad
  gi|336253689|ref|YP_004596796.1|  22 YGMGAAAELEAYAGEEGIDSALLVTDEGVLEAGAADPVVDALEAAGVEVATYGGVTPEPklALAEAAAEEVAAVDAD 98 
                                       5566777778889999********************************66665555544449999999999999*** PP

                                       EEEEESSHHH CS
                      Peripla_BP_6 193 avllagtgad 202
                                       +v+++g+g++
  gi|336253689|ref|YP_004596796.1|  99 VVIGVGGGSS 108
                                       *999999875 PP

>> Borrelia_P83  Borrelia P83/100 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   4.8e-05      0.21      18      54 ..     218     254 ..     204     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 4.8e-05
                      Borrelia_P83  18 GpydsvdsaeqirgiGefLaralkagnagdsarYavi 54 
                                        py++  + ++i  iG++L +a+++g+ +d arYa+ 
  gi|336253689|ref|YP_004596796.1| 218 TPYTDALALHAIELIGDNLREAVHQGEHNDEARYAMS 254
                                       69999999**************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3088.37
//
Query:       gi|336253690|ref|YP_004596797.1|  [L=168]
Description: hypothetical protein Halxa_2293 [Halopiger xanaduensis SH-6]
Scores for 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:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1429.63
//
Query:       gi|336253691|ref|YP_004596798.1|  [L=154]
Description: pyridoxamine 5'-phosphate oxidase-like FMN-binding protein [Halopiger xanaduensis SH-6]
Scores for 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   16.8   0.0     0.0087   16.2   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 !   16.2   0.0   4.9e-07    0.0087       4      73 ..      11      77 ..       8      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.9e-07
                                      HHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSE CS
                    Putative_PNPOx  4 elreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgr 73
                                       l+++l+++ ++ lA +   G P +sp+++ + d+   ++++  +d+  l++  + p  a+ ++d++ ++
  gi|336253691|ref|YP_004596798.1| 11 DLESVLERPLFCYLAQAIDAG-PRLSPLWFLWEDES--LWIIARTDRSYLERADRRPETAVAIVDFDRRT 77
                                      578899999999999995556.**************..****************************9333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1330.62
//
Query:       gi|336253692|ref|YP_004596799.1|  [L=230]
Description: phosphoglycolate phosphatase [Halopiger xanaduensis SH-6]
Scores for 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   84.8   0.0    1.5e-16   60.9   0.1    2.0  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
    4.2e-08   33.7   0.4    4.3e-07   30.4   0.1    2.3  2  Hydrolase    haloacid dehalogenase-like hydrolase
    8.3e-06   25.5   0.0    0.00016   21.3   0.1    2.0  2  S6PP         Sucrose-6F-phosphate phosphohydrolase
    4.9e-05   23.8   4.4      0.036   14.5   0.1    3.2  3  HAD          haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.1e-08   9.2e-05       1      76 [.       7      79 ..       7     107 .. 0.88
   2 !   60.9   0.1   3.4e-20   1.5e-16     178     254 ..     143     219 ..     115     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.1e-08
                                      EEEEIIIIIS-TTS-.--HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEEEE CS
                       Hydrolase_3  1 ialDlDGTLlnsdkk.isektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekgkilyk 76
                                      ++lD+DGTL + ++  i+++  + i+++      vviATG  +     + +  g+   v+a NG+++ ++ + + ++
  gi|336253692|ref|YP_004596799.1|  7 LVLDIDGTLTRPEGWgIDPRVFDPIREWD---APVVIATGKAFPYPVALCHFAGVPELVVAENGGVV-YTGDDVFFT 79
                                      589********88888*******999977...9**********************************.888777765 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 3.4e-20
                                       EEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHHH CS
                       Hydrolase_3 178 yleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVaka 254
                                        + +  ++ +Kg++l+ +a++ +++l+e +a+GD+ ND++ +e+ag+++A++na+e +k aAd v ++ + dG + +
  gi|336253692|ref|YP_004596799.1| 143 AYHVKDADPNKGEGLEVIAEHVGFDLAEAVAVGDSINDVSTFEVAGRSFAVKNADEAAKRAADEVLEDVHADGTLSV 219
                                       556667788**************************************************************997665 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   9.7e-11   4.3e-07       4     210 .]       7     188 ..       7     188 .. 0.82
   2 ?   -3.9   0.0         3   1.4e+04     150     172 ..     202     209 ..     194     226 .. 0.45

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 9.7e-11
                                       EEEESBTTTBCHH.....HHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHH CS
                                       xxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   4 vvfDkdGTLttge.....psvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpe 75 
                                       +v+D+dGTLt+ e     p+v d i++   +  ++++tg   p+  al ++a   +  +++++      ++  g   
  gi|336253692|ref|YP_004596799.1|   7 LVLDIDGTLTRPEgwgidPRVFDPIREW--DAPVVIATGKAFPYPVALCHFAGVPELVVAENGG-----VVYTGDDV 76 
                                       699*******999999999999999999..8889999999999999999999999999999999.....******** PP

                                       HHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  76 wltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraa 152
                                       ++ta                  r++a      +a+   a  + +  + +++v+++++   e+++   +  e+ +++a
  gi|336253692|ref|YP_004596799.1|  77 FFTAD-----------------REAAQA----VAEEYRAAGYDLGWGREDTVNRWRET--EIAVNLEQPVEPLREIA 130
                                       *****.................333333....22222222334678889*******76..77999999********* PP

                                       HHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 153 nqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                         +G + +d  +a+ ++     + eg++ +++  + + +e ++VGD++nD++ ++ Ag
  gi|336253692|ref|YP_004596799.1| 131 ADYGLEVIDTGYAYHVKDADPNKGEGLEVIAEHVGFDLAEAVAVGDSINDVSTFEVAG 188
                                       ****4444555555555555559*****************************999987 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3
                                       HHHHHTTGGGESEEEEHHCESST CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 150 raanqlGddyfdaviasdietva 172
                                       raa++               +  
  gi|336253692|ref|YP_004596799.1| 202 RAADE---------------VLE 209
                                       22222...............222 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.028   1.3e+02       5      76 ..       7      74 ..       5      94 .. 0.72
   2 !   21.3   0.1   3.5e-08   0.00016     164     221 ..     151     204 ..     137     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.028
                                      EEE-TBTTTB.S-HHHHHHHHHHHH.GGGGGEEEEEE-SS-HHHHHHHHHHHT----SEEEETTTTEEEE.. CS
                              S6PP  5 lvsdLDntlvdgdnealarlnelleaeerkdvllvfaTGRsldsakellkeknllkPdvlitsvGteiyyge 76
                                      lv d+D+tl+ ++   ++   ++ +  ++ d  +v+aTG+ +    +l +   +  P++++++ G  +y g 
  gi|336253692|ref|YP_004596799.1|  7 LVLDIDGTLTRPEGWGIDP--RVFDPIREWDAPVVIATGKAFPYPVALCHFAGV--PELVVAENGGVVYTGD 74
                                      7999*****9888777753..333333458899999999998887777777766..5677777777777665 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 3.5e-08
                                       -SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHHHHHHHHH- CS
                              S6PP 164 askgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeellqwllena 221
                                        +kge l+ +a++ +++l + + +Gds nD + ++   ++  V+na+e+    ++ +a
  gi|336253692|ref|YP_004596799.1| 151 PNKGEGLEVIAEHVGFDLAEAVAVGDSINDVSTFEVAGRSFAVKNADEA----AKRAA 204
                                       68*********************************************99....33333 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.036   1.6e+02       2      11 ..       8      17 ..       7      21 .. 0.86
   2 !    7.2   0.0    0.0014       6.3     101     172 ..      35     102 ..      19     107 .. 0.80
   3 !   14.5   0.1   8.1e-06     0.036     115     187 ..     126     184 ..     121     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.036
                               HAD  2 lfDfDgTLld 11
                                      ++D+DgTL++
  gi|336253692|ref|YP_004596799.1|  8 VLDIDGTLTR 17
                                      89******97 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0014
                               HAD 101 GdrvvvvSgglrplvepllaelg.adevlatelevdd..rltgelglegkpvrgegkvaalrewlaaegegidle 172
                                         +vv+ +g   p+  +l+ + g ++ v+a+    ++  ++tg    +  ++++++ ++a++e + a+g+++ + 
  gi|336253692|ref|YP_004596799.1|  35 DAPVVIATGKAFPYPVALCHFAGvPELVVAE----NGgvVYTGD---DVFFTADREAAQAVAEEYRAAGYDLGWG 102
                                       459********************55555666....33589****...999999999999**99999999988775 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 8.1e-06
                               HAD 115 vepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                       +++++a +g  ev++t +++  +       + +p +g      l+    ae+ g dl+e va+GDs++D+  +
  gi|336253692|ref|YP_004596799.1| 126 LREIAADYG-LEVIDTGYAY--H-----VKDADPNKG----EGLEV--IAEHVGFDLAEAVAVGDSINDVSTF 184
                                       789999999.9999995333..2.....256688888....55555..55599****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 1982.82
//
Query:       gi|336253693|ref|YP_004596800.1|  [L=468]
Description: family 1 extracellular solute-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-43  147.1   1.6    1.1e-42  146.8   1.6    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    1.4e-32  114.0   2.8    1.7e-32  113.7   2.8    1.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein
     0.0061   17.1   0.0      0.022   15.3   0.0    2.0  1  LGFP        LGFP repeat
     0.0069   16.1   0.0       0.09   12.5   0.0    2.6  3  SBP_bac_11  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.03   13.7   0.0       0.48    9.8   0.0    2.2  2  SBP_bac_6   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.8   1.6     3e-46   1.1e-42       2     276 ..      79     395 ..      78     401 .. 0.86

  Alignments for each domain:
  == domain 1  score: 146.8 bits;  conditional E-value: 3e-46
                                       HHHHHHHH-TEEEEEEE-.-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGS.TTHHH-HHHHH CS
                         SBP_bac_8   2 lakefekktgvkvnvvta.asndleqklkaalaagtapdidvvwanedalatlaeeglladlsdl.dnlddltdala 76 
                                       l ++f+++tg++v+ v++ +++d+ ++  a ++agt+p++  v++++  +++  + ++++ ++ + ++  +++d+l+
  gi|336253693|ref|YP_004596800.1|  79 LGDQFQEATGIDVEMVYQgSYEDTLNQSFAGIEAGTMPEV--VQIDSLHAKQILDTDAFQSVEGIlPDDYPVDDFLD 153
                                       5689**************9999999999999*******95..6777788999999********66677777888888 PP

                                       TT....--TS.----EEEEEEE-EEEEEHHHHHHS......---BHHHHHHHHHHH..HHH-....SEGG---GGGG CS
                         SBP_bac_8  77 av....gydgklygvPyasetpyvliynkdlleka.....edpktwdellaaakkl..kgkf....glpdpasgwlq 138
                                       +v    ++dg+ly++P++ ++  +l+ynkd++e+a     ++p+t+de++++   +   g++    ++p+  ++  +
  gi|336253693|ref|YP_004596800.1| 154 PVtdffTVDGELYSLPFNNSN-AILYYNKDVFEEAgldpeSPPETLDEVTEYSRSIvdSGAAeygiTWPNHVWFIEH 229
                                       88777899************9.6***********9999999**********988776634445566999****999* PP

                                       GGTHHETTEE---H.....HHH.........HHHHHHHHHHHHTT-EE....-S..--SSTTTTTSBSEEEE-TTHH CS
                         SBP_bac_8 139 aallakdgksldddg...gkdgl........kealellkklkdngkty....dtgadavsefanGevaftingswdi 200
                                       ++ la ++  +d+ +   +++++        ++ + +++++ +   ++    +++ +a+++f  ++v + +++++++
  gi|336253693|ref|YP_004596800.1| 230 WYGLA-GQTLVDNENgwaDDPTTvhtetdvgEQLWSWWRDMAQEDLYTnpgmEAWGEATDLFYGQNVGMLLTSTASV 305
                                       *****.7777765555654444478888999***********9998555666************************* PP

                                       HHHH....-TTTSEEEE.--....S--EEEEEEEEEEBTTS-HHHH.HHHHHHHHHTTSHHHHHHHHHH---BS-S- CS
                         SBP_bac_8 201 aaaq....kagkklgai.vp....kqgsfaggkglavpknaknedl.aAldFlkwltspenqaalaektgyipvnks 267
                                       a a     ++g++lg + +p    ++g+++gg++l+vp + +++++ +  +Fl++++ penq  +++ tgy pv+ +
  gi|336253693|ref|YP_004596800.1| 306 AGAIsqseEQGFELGTGfYPaidgREGVVIGGASLWVPEDMSDQRAeEVGQFLEFMSRPENQITWHKETGYYPVRGD 382
                                       *99988877789*****889888889**************8888888****************************** PP

                                       TTT....HHHHHH CS
                         SBP_bac_8 268 aal....spevkk 276
                                       a +    + ++ +
  gi|336253693|ref|YP_004596800.1| 383 AVDqleeDGWFEE 395
                                       9975544445555 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   2.8   4.7e-36   1.7e-32       7     314 ..      73     367 ..      69     368 .. 0.87

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 4.7e-36
                                       HHHHHHHHHHHHHHHHTTEEEEEEEE.CHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTT CS
                         SBP_bac_1   7 gaalqalvakafekehpgikVeiesv.gsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkayl 82 
                                       g+++++l  ++f++  +gi+Ve +++ ++ +  ++  + i+aG+ p +v+++d+ + ++  + ++++ +  ++ ++ 
  gi|336253693|ref|YP_004596800.1|  73 GETMEELG-DQFQE-ATGIDVEMVYQgSYEDTLNQSFAGIEAGTMP-EVVQIDSLHAKQILDTDAFQSVEGILPDD- 145
                                       56999***.***99.8******888845555555899999******.*****888887777777777777777776. PP

                                       ECTTCCTEEEEHHHHTHHHHCE.EE...ES.EEEE.EEEEEEEETTTHHCTTGGG...SHBHHHHHHHHHHHHHHCT CS
                         SBP_bac_1  83 apgvkdaadklsssvlpkilds.kv...ly.vPly.aargliYNkdlfekagldp...pwtWdelveaakklkekgk 150
                                        + v+d        +l+ + d+ +v   ly +P++ ++  l+YNkd+fe+agldp   p+t de++e+ + ++++g 
  gi|336253693|ref|YP_004596800.1| 146 -YPVDD--------FLDPVTDFfTVdgeLYsLPFNnSNAILYYNKDVFEEAGLDPespPETLDEVTEYSRSIVDSGA 213
                                       .34444........5555555557788********66**************************************** PP

                                       CTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHS..HHHHHHHHHHHHHHHHHHHTTEEECSSHHH CS
                         SBP_bac_1 151 kpiggarggsasgtayyfalalakslggkvfdkdgggldnpegvt..aatylvklyavanltkelkgkgaenkdgaa 225
                                       ++     +g  + +  +f +++++ +g++++d+++g  d+p+ v   ++   + + +++   +e    ++  + + +
  gi|336253693|ref|YP_004596800.1| 214 AE-----YGITWPNHVWFIEHWYGLAGQTLVDNENGWADDPTTVHteTDVGEQLWSWWRDMAQEDLYTNPGMEAWGE 285
                                       **.....*****************************6677777766788888888888888889999********** PP

                                       HHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCST..HHH CS
                         SBP_bac_1 226 alalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgskn..pea 300
                                       a++lf+  +++m++ ++ +          ++++ ++e+ ++elg    Pa++g+ +  +g+  l++p + ++   e+
  gi|336253693|ref|YP_004596800.1| 286 ATDLFYGQNVGMLLTSTAS---------VAGAISQSEEQGFELGTGFYPAIDGREGVVIGGASLWVPEDMSDqrAEE 353
                                       *******************.........9999*******************9999888***********99954555 PP

                                       HHHHHHHHTSHHHH CS
                         SBP_bac_1 301 AkkFldfllspeaq 314
                                       + +Fl+f+  pe+q
  gi|336253693|ref|YP_004596800.1| 354 VGQFLEFMSRPENQ 367
                                       ************99 PP

>> LGFP  LGFP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.1e-06     0.022       6      50 ..     347     392 ..     346     394 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.1e-06
                              LGFP   6 tdetatpdggGryqhFeg...GsiyWspatGahavkgaIrdkWaalGw 50 
                                       +d++a    +G++ +F       i W+++tG ++v+g+  d+ ++ Gw
  gi|336253693|ref|YP_004596800.1| 347 SDQRA--EEVGQFLEFMSrpeNQITWHKETGYYPVRGDAVDQLEEDGW 392
                                       67777..899999999544557*************************9 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   2.5e-05      0.09       5      55 ..      68     123 ..      62     147 .. 0.74
   2 ?   -2.6   0.0         1   3.7e+03     151     169 ..     206     224 ..     181     243 .. 0.74
   3 ?    0.3   0.0      0.14     5e+02     202     226 ..     348     372 ..     264     376 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                                       E-SSTHHHHHHHHHHHHHHH---EEEEESSH.....HHHHHHHHHH..-SEEEESS CS
                        SBP_bac_11   5 aagslaaalrelaaaFeahtgvkvevsaggs.....gklarqiadgarpDvwipas 55 
                                       ++g+  ++++el ++F+++tg++ve+ ++gs     ++  + i++g+ p+v+  +s
  gi|336253693|ref|YP_004596800.1|  68 MGGGNGETMEELGDQFQEATGIDVEMVYQGSyedtlNQSFAGIEAGTMPEVVQIDS 123
                                       56677899***********************6444444444667777777777766 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1
                                       HHHHHTTT-SEEEEEHHHH CS
                        SBP_bac_11 151 ltaveageadagivyesea 169
                                        + v++g a++gi++ + +
  gi|336253693|ref|YP_004596800.1| 206 RSIVDSGAAEYGITWPNHV 224
                                       3449999999999998776 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.14
                                       TT--HHHHHHHHHTTSHHHHHHHHH CS
                        SBP_bac_11 202 aakreaAraFlafLrspeaqailrk 226
                                       ++++e+   Fl+f+  pe q +++k
  gi|336253693|ref|YP_004596800.1| 348 DQRAEEVGQFLEFMSRPENQITWHK 372
                                       4778999999999999999988754 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.051   1.8e+02      46      76 ..     162     193 ..     126     213 .. 0.82
   2 ?    9.8   0.0   0.00013      0.48     173     224 ..     331     386 ..     322     394 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.051
                         SBP_bac_6  46 dpdgkyypygvgplvlavnkdrlkgrpv.Pks 76 
                                       d++ +  p++ + ++l++nkd++++  + P+s
  gi|336253693|ref|YP_004596800.1| 162 DGELYSLPFNNSNAILYYNKDVFEEAGLdPES 193
                                       44455559999************999888654 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00013
                         SBP_bac_6 173 dGalvspifmlvkkg...kkkelakafidfllspevqailakaggvfPvv.tnpav 224
                                       +G ++   ++ v+ +   +++e++ +f++f+  pe q  + k++g +Pv  +++++
  gi|336253693|ref|YP_004596800.1| 331 EGVVIGGASLWVPEDmsdQRAEEVGQFLEFMSRPENQITWHKETGYYPVRgDAVDQ 386
                                       7888888888888888899*****************************95433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.36
# Mc/sec: 3890.10
//
Query:       gi|336253694|ref|YP_004596801.1|  [L=344]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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   62.9  11.8    3.2e-17   62.9  11.8    2.3  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
          1    8.8   8.0      0.065   12.7   1.0    2.7  2  SKG6          Transmembrane alpha-helix domain


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 ?    0.3   3.4     0.057   5.1e+02     149     175 ..     109     143 ..      58     148 .. 0.59
   2 !   62.9  11.8   3.6e-21   3.2e-17      23     183 ..     157     340 ..     145     342 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.057
                      BPD_transp_1 149 dyseis...........nggvlalviavlllnlvadil 175
                                        +   s           ++ ++a+v+ v+ l+lv+ +l
  gi|336253694|ref|YP_004596801.1| 109 LL---SsssyhrsvaitVAFAAAVVVGVMTLSLVVSFL 143
                                       22...122345554445566666666666666666655 PP

  == domain 2  score: 62.9 bits;  conditional E-value: 3.6e-21
                      BPD_transp_1  23 liivllslPsfvlaillvlvf...................vilsilghlilpviillllsaapyvrlirraalrslp 80 
                                         i +++lP+ v +i++++++                    ++s+  +++  v++++++ +++y+++++ aal+++p
  gi|336253694|ref|YP_004596801.1| 157 AAIWPYALPPAVAGIVFLFLIhpsigtltavlegytglevDWFSDGRQAFVVVAVAAIWKQLGYNVIFTVAALNNVP 233
                                       556689******9999998789*****************99999999****************************** PP

                      BPD_transp_1  81 kdlveaaralGasrwqifrkvvlPnalppiitglilafggl.lggavlleflgswpG....lgtllleailgydyse 152
                                       + l+eaa+++G +rw++++++ +P++ p+++ +++++ +++ +g ++++ +++++ G        ++ + l+++  e
  gi|336253694|ref|YP_004596801.1| 234 ETLREAAELDGIGRWTRLVRIYVPLISPTLLFLVVMNTIYAfFGTFAFIDLMTQG-GpggaT--NVMIFDLYRNAFE 307
                                       *****************************************55555555555544.446532..2333333333222 PP

                      BPD_transp_1 153 is..nggvlalviavlllnlvadilqrlldprv 183
                                        +    +++  v++++++++++++  r+ d rv
  gi|336253694|ref|YP_004596801.1| 308 FNnhGLASAQSVVLFAVVSVLMYAQLRFSDERV 340
                                       223679999999999999999999999999887 PP

>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.0   7.3e-06     0.065       9      32 ..     122     145 ..     111     147 .. 0.79
   2 ?   -2.8   1.0      0.47   4.3e+03      12      17 ..     207     212 ..     203     214 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-06
                              SKG6   9 tvaIavaVaVPVaViiivLlaili 32 
                                       tva a+aV+V+V    +v+ ++l+
  gi|336253694|ref|YP_004596801.1| 122 TVAFAAAVVVGVMTLSLVVSFLLY 145
                                       566699***************998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.47
                              SKG6  12 IavaVa 17 
                                       ++vaVa
  gi|336253694|ref|YP_004596801.1| 207 VVVAVA 212
                                       444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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: 0.46u 0.19s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 2912.34
//
Query:       gi|336253695|ref|YP_004596802.1|  [L=300]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-13   49.1  17.7    5.3e-13   49.1  17.7    2.1  2  BPD_transp_1    Binding-protein-dependent transport system in
     0.0066   16.6   0.0      0.013   15.7   0.0    1.5  1  DDE_Tnp_IS66_C  IS66 C-terminal element
  ------ inclusion threshold ------
       0.13   10.4   3.8       0.13   10.3   3.8    1.2  1  UPF0182         Uncharacterised protein family (UPF0182)


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 ?   -1.0   2.4      0.22   1.3e+03      43      55 ..      66      99 ..      39     120 .. 0.35
   2 !   49.1  17.7   8.9e-17   5.3e-13       4     155 ..     114     272 ..     111     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.22
                      BPD_transp_1 43 f.....................vilsilghlilp 55
                                                             +  + g+++l 
  gi|336253695|ref|YP_004596802.1| 66 RatftsfselsletaaqnyrdvLFRYDMGQYMLN 99
                                      1222222222222222222222222222222222 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 8.9e-17
                      BPD_transp_1   4 lGilaa...lnrnkkldkllrpliivllslPsfv.laillvlvfvilsilghlilpviillllsaapyvrlirraal 76 
                                       +++laa   +++++++++++  ++ ++l+lP+ v +++l++    +  +lg+++  +++++ + a ++++++ r+ +
  gi|336253695|ref|YP_004596802.1| 114 VSLLAAlaiVYYRFPFKNAVFAVVLLTLMLPVPVrIVPLFQ----LAADLGWANSFAALTIPYLASATTVFLLRQHF 186
                                       5667777789************************8888888....56****************************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.....lgtllleailgy 148
                                        s+p +lve a+++G+++ + +  v++P+++ +i+   ++ f+++++++++++++  ++      +g +ll+     
  gi|336253695|ref|YP_004596802.1| 187 LSIPASLVESAKLDGVGPLRFLAFVLIPMSKGMIAGVSVIMFIYSWNQYLWPLLIVDDQSmqvaqVGIRLLQGV--- 260
                                       ********************************************************665533222222222222... PP

                      BPD_transp_1 149 dyseis..........n 155
                                                       +
  gi|336253695|ref|YP_004596802.1| 261 -----VesgeiawpllM 272
                                       .....133334322332 PP

>> DDE_Tnp_IS66_C  IS66 C-terminal element
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.2e-06     0.013       1      21 [.     192     212 ..     192     218 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.2e-06
                    DDE_Tnp_IS66_C   1 SLieTAKlNgvdPyaYLkdvL 21 
                                       SL+e+AKl gv P + L+ vL
  gi|336253695|ref|YP_004596802.1| 192 SLVESAKLDGVGPLRFLAFVL 212
                                       9*******************9 PP

>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.8   2.2e-05      0.13      86     167 ..      46     128 ..       9     277 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.2e-05
                           UPF0182  86 lkllllaialvlsllvglvassqwekvllf.lnstsfgvkDpifgkDisFYvFklPflelllslllalvllaliavl 161
                                       l + l+a++lv+++l+++ + ++++++ ++ l+ ++ + +D +f+ D++ Y+++  ++++++ +   +v l++++++
  gi|336253695|ref|YP_004596802.1|  46 LAVSLMALPLVIAALISFGTRATFTSFSELsLETAAQNYRDVLFRYDMGQYMLNSLIMSVIVVIGKLAVSLLAALAI 122
                                       56778999***************9988765267777899**************998888887766655555555555 PP

                           UPF0182 162 lvylls 167
                                       ++y + 
  gi|336253695|ref|YP_004596802.1| 123 VYYRFP 128
                                       554433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2246.05
//
Query:       gi|336253696|ref|YP_004596803.1|  [L=398]
Description: glycerol-3-phosphate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-31  110.3   0.0    1.5e-31  109.8   0.0    1.2  1  ABC_tran         ABC transporter
    2.1e-11   44.4   0.3    2.4e-10   41.1   0.2    2.8  2  OB_MalK          MalK OB fold domain
    2.9e-08   33.7   1.6      2e-07   31.1   0.5    2.8  2  TOBE_2           TOBE domain
    5.7e-07   29.6   0.0     0.0086   15.9   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.4e-06   28.7   3.2    0.00012   22.5   0.1    3.4  3  CysA_C_terminal  CysA C-terminal regulatory domain
    3.2e-05   23.5   0.0    6.3e-05   22.5   0.0    1.4  1  SMC_N            RecF/RecN/SMC N terminal domain
    0.00015   22.2   0.3    0.00039   20.8   0.3    1.7  1  AAA_16           AAA ATPase domain
    0.00029   20.8   0.0    0.00044   20.2   0.0    1.2  1  Rad17            Rad17 P-loop domain
     0.0024   18.2   0.3     0.0045   17.3   0.3    1.6  1  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.028   14.3   0.0      0.052   13.5   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
      0.037   14.5   0.0      0.067   13.7   0.0    1.3  1  AAA_23           AAA domain
      0.053   13.3   0.0       0.11   12.3   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.055   14.0   0.0      0.099   13.2   0.0    1.4  1  CRISPR_Cse2      CRISPR-associated protein Cse2 (CRISPR_cse2)
      0.061   13.4   0.0       0.16   12.1   0.0    1.8  1  MMR_HSR1         50S ribosome-binding GTPase
       0.15   11.6   0.0       0.32   10.6   0.0    1.4  1  AAA_27           AAA domain
       0.17   12.0   0.3       0.42   10.8   0.3    1.8  1  AAA_33           AAA domain
       0.29   10.2   0.0       0.36    9.9   0.0    1.1  1  G-alpha          G-protein alpha subunit


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 !  109.8   0.0   1.4e-34   1.5e-31       2     136 ..      20     162 ..      19     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 1.4e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + ++l+++ ge +++vG++G+GKSt l+++agl++pt G+i++ ++d++    e  ++ i++++q+  l p++t+++
  gi|336253696|ref|YP_004596803.1|  20 DGIDLEVRDGEFLVVVGPSGCGKSTTLRCIAGLESPTDGRIRIGDEDVTA--QEPHERDIAMVFQNYALYPHMTAER 94 
                                       7899*********************************************9..899999*****************99 PP

                                       H..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n              e d+++++a+++l++ +l d++     s LSgG++qrval ra++++p ++l+DEp 
  gi|336253696|ref|YP_004596803.1|  95 NmtfgmqsatdfsseEIDQRVAEAAETLDIADLLDRTP----SALSGGEQQRVALGRAIVRDPAVFLMDEPL 162
                                       9**********999999999************999998....*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.2   2.3e-13   2.4e-10       1      52 [.     236     287 ..     236     288 .. 0.95
   2 ?   -0.7   0.0       2.5   2.7e+03      18      32 ..     356     370 ..     345     384 .. 0.73

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2.3e-13
                           OB_MalK   1 GSPaMNflpatveedg..vlvegggvtlplpeeqklalklyagkevilGiRPEh 52 
                                       G PaMN+l++tve++    +v  + +t+++p++   +l++ +g++ +lG+RPE+
  gi|336253696|ref|YP_004596803.1| 236 GDPAMNMLEVTVEDGPsgPIVRHEAFTIEVPDAP--ELEGLDGDRAVLGFRPED 287
                                       89***********655******************..*****************8 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.5
                           OB_MalK  18 lvegggvtlplpeeq 32 
                                        ++g+gvtl+l++++
  gi|336253696|ref|YP_004596803.1| 356 RAAGDGVTLTLDADR 370
                                       678999999998876 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0         1   1.1e+03      51      66 ..     191     207 ..     175     211 .. 0.67
   2 !   31.1   0.5   1.9e-10     2e-07       1      76 []     281     374 ..     281     374 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1
                            TOBE_2  51 nadr.dsalapGdtVel 66 
                                       ++++  +a++ Gd+V +
  gi|336253696|ref|YP_004596803.1| 191 VTHDqTEAMTLGDRVVV 207
                                       23332359999999987 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 1.9e-10
                            TOBE_2   1 laiRPEklrla..................aagga......n.glsGtVedveylGsstryvvelaggqlvvvrqpna 52 
                                       l+ RPE+ +la                  +   +      +  +++tV+ +e lG++++ +++ ++ ++ +v+++++
  gi|336253696|ref|YP_004596803.1| 281 LGFRPEDASLAdrdaaagggadapdrrqtG---RgdpertTgPIEATVQVTEPLGDTLLCYCRAGEDEF-KVQTAPR 353
                                       578********9999887777666665441...04555654599*******************877766.9****** PP

                            TOBE_2  53 drdsalapGdtVelswdpddavvl 76 
                                       +     a+Gd V+l++d+d+++++
  gi|336253696|ref|YP_004596803.1| 354 T---GRAAGDGVTLTLDADRLHLF 374
                                       9...899***************98 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 !   15.9   0.0   8.1e-06    0.0086       1      49 [.      31      72 ..      31      85 .. 0.75
   2 !   11.6   0.0   0.00016      0.17     230     298 ..     128     194 ..      98     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.1e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsll 49
                                      + v++Gp g+GKS+ L+++ +l       e+ td + ++g++++ + ++
  gi|336253696|ref|YP_004596803.1| 31 FLVVVGPSGCGKSTTLRCIAGL-------ESPTDGRIRIGDEDVTAQEP 72
                                      579****************999.......56666666666666555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00016
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                        +++++ lS G ++  al  a+ r++   +++l DEp ++L+ kl     + l++l++  g+  + +TH+
  gi|336253696|ref|YP_004596803.1| 128 LDRTPSALSGGEQQRVALGRAIVRDP---AVFLMDEPLSNLDAKLRVQMRTELSRLHEeLGTTTVYVTHD 194
                                       45677788999999999999999999...*********************99966655589999*****8 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.031        33       9      27 ..      57      75 ..      56      81 .. 0.81
   2 !   22.5   0.1   1.2e-07   0.00012       1      40 [.     241     287 ..     241     290 .. 0.91
   3 ?   -2.7   0.0         9   9.5e+03      21      33 ..     351     363 ..     341     366 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.031
                   CysA_C_terminal  9 dGklriGglalpvPelaga 27
                                      dG++riG+ ++ + e +++
  gi|336253696|ref|YP_004596803.1| 57 DGRIRIGDEDVTAQEPHER 75
                                      9*********999866554 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.2e-07
                   CysA_C_terminal   1 NlFhGrvedG..k..lriGglalpvP...elagadgqevvayVRPhD 40 
                                       N+++ +vedG  +  +r   ++++vP   el+g dg+++v++ RP+D
  gi|336253696|ref|YP_004596803.1| 241 NMLEVTVEDGpsGpiVRHEAFTIEVPdapELEGLDGDRAVLGFRPED 287
                                       99********6516699999****99999999**************9 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 9
                   CysA_C_terminal  21 vPelagadgqevv 33 
                                       +P+++ a+g+ v+
  gi|336253696|ref|YP_004596803.1| 351 APRTGRAAGDGVT 363
                                       5677777777776 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     6e-08   6.3e-05      25     204 ..      30     198 ..      22     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6e-08
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSC.EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekee.vsis 100
                                       +f ++vGp G+GKs  l  i    G +s +  r +  ++ +++    ++ ++ +++++f+n     ++++e+ ++  
  gi|336253696|ref|YP_004596803.1|  30 EFLVVVGPSGCGKSTTLRCI---AGLESPTDGRIRIGDEDVTA----QEPHERDIAMVFQNYALYPHMTAERnMTFG 99 
                                       6899***************9...67777766677766666665....455666777777777777444444314444 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                        +  + + s+ +i+++ ++ +e  ++    + ++++LSgGe++ val    Ai  v+  +++l+De  ++LD+k + 
  gi|336253696|ref|YP_004596803.1| 100 MQSAT-DFSSEEIDQRVAEAAETLDIADLLDRTPSALSGGEQQRVALG--RAI--VRDPAVFLMDEPLSNLDAKLRV 171
                                       44444.446779*********99999999999**********977664..444..5677789**********99888 PP

                                       HHHHHHHHHCTTSEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 178 kvaellkeksknaQfivislreemlek 204
                                       ++ + l + +++     + ++++++e 
  gi|336253696|ref|YP_004596803.1| 172 QMRTELSRLHEELGTTTVYVTHDQTEA 198
                                       887777766666444443333333333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.3   3.7e-07   0.00039      19     126 ..      26     180 ..       5     210 .. 0.55

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.7e-07
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekd............................ggiflrgkcdql.... 63 
                                       vr+g  e ++++G+sG+GKs+ +r+++  le                              +          +    
  gi|336253696|ref|YP_004596803.1|  26 VRDG--EFLVVVGPSGCGKSTTLRCIAG-LESPtdgririgdedvtaqepherdiamvfqnY--------ALYphmt 91 
                                       4444..89******************95.444445666666666666666665443333321........2222222 PP

                            AAA_16  64 .esaipysa.laqalareellrqlldeaesaeleawrekleeala........................avpelaga 114
                                        e+++++ +  a+ ++ ee+ + ++++ae+ + ++  ++ ++al+                        + ++l+++
  gi|336253696|ref|YP_004596803.1|  92 aERNMTFGMqSATDFSSEEIDQRVAEAAETLDIADLLDRTPSALSggeqqrvalgraivrdpavflmdePLSNLDAK 168
                                       22223333334444433333333333333333333333333333344444444446666666666666666666666 PP

                            AAA_16 115 easrllellkrl 126
                                       ++ +++ +l+rl
  gi|336253696|ref|YP_004596803.1| 169 LRVQMRTELSRL 180
                                       664444444444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.1e-07   0.00044      30      66 ..      15      50 ..       3      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.1e-07
                             Rad17 30 evkewlkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                      +v ++++   Le r  + L++ GPsGCgkst+++ ++
  gi|336253696|ref|YP_004596803.1| 15 DV-TAVDGIDLEVRDGEFLVVVGPSGCGKSTTLRCIA 50
                                      55.56778889999999****************9876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.3   4.3e-06    0.0045       4      26 ..      28      50 ..      25     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.3e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                      +  +lvv+G+sG+GK+t+lr ++
  gi|336253696|ref|YP_004596803.1| 28 DGEFLVVVGPSGCGKSTTLRCIA 50
                                      6789***************9876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.9e-05     0.052      91     122 ..      20      52 ..       3      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.9e-05
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       + +  +++d ++ v+vG+SG GKSt +  +++ 
  gi|336253696|ref|YP_004596803.1|  20 DGIDLEVRDgEFLVVVGPSGCGKSTTLRCIAGL 52 
                                       555556666699*************99998874 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.3e-05     0.067      17      40 ..      24      50 ..      12      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.3e-05
                            AAA_23 17 F...skgltlItGpNGaGKTTildAik 40
                                      +   +  + +++Gp G+GK+T l++i 
  gi|336253696|ref|YP_004596803.1| 24 LevrDGEFLVVVGPSGCGKSTTLRCIA 50
                                      55545556789**************96 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 ?   12.3   0.0    0.0001      0.11      16      39 ..      23      46 ..      17      59 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTll 39
                                      ++e++  g + +++GpsG GKST l
  gi|336253696|ref|YP_004596803.1| 23 DLEVRD-GeFLVVVGPSGCGKSTTL 46
                                      556653.458999**********87 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 ?   13.2   0.0   9.4e-05     0.099      28     104 ..      65     136 ..      43     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.4e-05
                                       TTT.HHHHHHHHHHHHHHHHHCCHCS-SB.-TT-CHHHHHHHHHHHTCTHHHHHHHHHHHCT-SSCCCHHHHHHHHH CS
                       CRISPR_Cse2  28 eseeekepeeraayavaalyaahqqekeh.dsgkslgaalgrlreasessesierRfqalltadtpeelarrLrrlv 103
                                       e+  ++ep+er +  v++ ya++++  ++ +++ ++g + ++     + se i++R++  + + + ++l++r ++++
  gi|336253696|ref|YP_004596803.1|  65 EDVTAQEPHERDIAMVFQNYALYPH--MTaERNMTFGMQSATD---FS-SEEIDQRVAEAAETLDIADLLDRTPSAL 135
                                       456789******************9..67799999****9922...23.477*********9999****99999887 PP

                                       H CS
                       CRISPR_Cse2 104 k 104
                                       +
  gi|336253696|ref|YP_004596803.1| 136 S 136
                                       6 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.16       3      42 ..      33      78 ..      31     193 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                                      EEEESTTSSHHHHHHHHHT.....S.TEEESSSTTSSSSEEEEEEE CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltg.....e.kaivsdkpgtTrdinegrvk 42
                                      ++vG +  GKSt ++ + g     + + +++d+  t +++ e+ ++
  gi|336253696|ref|YP_004596803.1| 33 VVVGPSGCGKSTTLRCIAGlesptDgRIRIGDEDVTAQEPHERDIA 78
                                      79***************9877665258999*******999999887 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0003      0.32      19      48 ..      22      51 ..      11      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisd 48
                                      +d++  + ++ +++Gp   GKst+lr i  
  gi|336253696|ref|YP_004596803.1| 22 IDLEVRDGEFLVVVGPSGCGKSTTLRCIAG 51
                                      678888999*****************9975 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    0.0004      0.42       2      20 ..      32      50 ..      31     205 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0004
                            AAA_33  2 vllvGlpGsGKstlaerll 20
                                      +++vG++G+GKst ++ ++
  gi|336253696|ref|YP_004596803.1| 32 LVVVGPSGCGKSTTLRCIA 50
                                      579**********998764 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00034      0.36      26     102 ..      32     119 ..      24     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00034
                                       EEEEESTTSSHHHHHHHHHHHCS--..........--HHHHHC.CHHHHHHHHHHHHHHHHHHHHHTT.......HH CS
                           G-alpha  26 llllGqseSGKsTilkqlkllykkg..........fseeelat.wraviqlnivrsiktilealesleselsesfel 91 
                                       l+++G s++GKsT+l+ +  l+ ++          ++ +e  +   a++++n     ++  e  ++++ ++  +f++
  gi|336253696|ref|YP_004596803.1|  32 LVVVGPSGCGKSTTLRCIAGLESPTdgririgdedVTAQEPHErDIAMVFQNYALYPHMTAERNMTFGMQSATDFSS 108
                                       6789*****************99999999988888666666444778899998888888888888888888888877 PP

                                       HC-SS-SCCCS CS
                           G-alpha  92 qelkerldplk 102
                                       +e+ +r+++  
  gi|336253696|ref|YP_004596803.1| 109 EEIDQRVAEAA 119
                                       77777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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 0.26s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 2973.43
//
Query:       gi|336253697|ref|YP_004596804.1|  [L=255]
Description: glycerophosphoryl diester phosphodiesterase [Halopiger xanaduensis SH-6]
Scores for complete 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-29  103.6   0.0    6.7e-19   68.6   0.0    2.0  2  GDPD      Glycerophosphoryl diester phosphodiesterase family


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0   3.8e-23   6.7e-19       1     112 [.      39     137 ..      39     142 .. 0.93
   2 !   33.2   0.0   2.5e-12   4.4e-08     150     255 ..     155     249 ..     144     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 3.8e-23
                                       TTTTTTTSSTTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECCTTC CS
                              GDPD   1 HRGasgnlpEnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkiaken 77 
                                       HRG+ +++pEnTle+ + A+ + ad iE+Dv+    g +V++HD++l+r+td+a   +v  l++e l++ + i+++ 
  gi|336253697|ref|YP_004596804.1|  39 HRGFAAERPENTLEAVRYAIPR-ADGIEVDVRRCGSGELVCVHDETLERLTDGAVTDRVGRLDWERLQTVS-IGSS- 112
                                       *******************876.8*******************************99**************.6444. PP

                                       CCCSCCCSSGCCB...BHHHHHHH.HHHCCSEEEEE CS
                              GDPD  78 kaqlsenrvrlefpfptleevlkk.pqnvglnieik 112
                                            + rv      p+l++vl+  p++v lnie k
  gi|336253697|ref|YP_004596804.1| 113 -----DARV------PQLADVLEAvPPDVRLNIELK 137
                                       .....5665......******************987 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 2.5e-12
                                       SCEEEESTHHHHHHHHHTCTCTEEEEEEHHHHHHC-E.EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHHHHTT- CS
                              GDPD 150 kvifssfnpdilkllrekqpklpllflteggteaeadssleraakfakadallgevsavaeglgdpdlVkraksrgl 226
                                       +  +ssf+p++l+ ++ +++    l ++ g ++ +      + a+ + + a++++  ++ e     + V+ra++rg 
  gi|336253697|ref|YP_004596804.1| 155 RALVSSFDPTALWQVQSLTD-GVALAYIFGDDPDRGL----ERAADLECAAVHPSAGLCRET----EIVDRAHDRGF 222
                                       5566****************.6666666677777776....68999**************99....8********** PP

                                       EEEEBSB-THSHHHHHHHHCCC-SEEEES CS
                              GDPD 227 vvhvytvnnedeeemkrlleagvdgvitD 255
                                       +v ++tv+     e +rl  +gvdgv+ D
  gi|336253697|ref|YP_004596804.1| 223 AVNAWTVDSG--LETARLALTGVDGVFSD 249
                                       **********..***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1952.82
//
Query:       gi|336253698|ref|YP_004596805.1|  [L=357]
Description: hypothetical protein Halxa_2301 [Halopiger xanaduensis SH-6]
Scores for 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   0.5       0.01   15.6   0.5    2.3  2  PAP2      PAP2 superfamily
      0.042   13.5   2.0      0.082   12.6   2.0    1.4  1  RTX       N-terminal domain in RTX protein


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.5   1.1e-06      0.01      64     129 ..      91     175 ..      89     180 .. 0.84
   2 ?   -1.7   0.7      0.26   2.3e+03      95      95 ..     308     308 ..     247     348 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-06
                              PAP2  64 afalalllalllrrkrkkig...................lvllalillllavlvalsRlylgvHflsDvlaGlliGi 121
                                       afa+ ++++++ ++k++ +                    + +la+ +++ ++++ ++R+ +gv f++D +a  ++++
  gi|336253698|ref|YP_004596805.1|  91 AFAGGVAATAYAGKKYPEMEpdgwdyhfgkdilyafgtkPDILAVGAIFGVIGMLFTRVMDGVGFPTDNIALSVVAT 167
                                       777778888888888888778888888888888888888999***************************99988888 PP

                              PAP2 122 alaalayr 129
                                       a++a ++ 
  gi|336253698|ref|YP_004596805.1| 168 AFLARIVF 175
                                       88876655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.26
                              PAP2  95 a 95 
                                       a
  gi|336253698|ref|YP_004596805.1| 308 A 308
                                       1 PP

>> RTX  N-terminal domain in RTX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.0   9.1e-06     0.082      89     127 ..     279     318 ..     271     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.1e-06
                               RTX  89 avvsaaaaasgVGa.Pvallvalitglisgileaskqail 127
                                       + ++a+ aas+VG+ Pv llva+  g+is+++  + q ++
  gi|336253698|ref|YP_004596805.1| 279 GSTGAVIAASVVGSdPVILLVAGAFGAISALIGELSQRVF 318
                                       678999*******88*****************99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); 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:                         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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2614.05
//
Query:       gi|336253699|ref|YP_004596806.1|  [L=513]
Description: glycerol kinase [Halopiger xanaduensis SH-6]
Scores for complete 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-80  270.6   0.0    1.6e-80  270.2   0.0    1.1  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 
    9.6e-59  198.4   0.3    2.3e-58  197.2   0.2    1.6  2  FGGY_C       FGGY family of carbohydrate kinases, C-terminal 
    0.00037   20.1   0.1     0.0017   17.9   0.0    1.9  2  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family


Domain annotation for each model (and alignments):
>> 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 !  270.2   0.0   2.7e-84   1.6e-80       1     245 []       6     263 ..       6     263 .. 0.96

  Alignments for each domain:
  == domain 1  score: 270.2 bits;  conditional E-value: 2.7e-84
                                       EEEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE CS
                            FGGY_N   1 lilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisg 77 
                                       ++ ++D+Gtt+t++i++d+ g+vva a++++e+++p++gw+e+dp+eiw+ + ++++++l+qagis++q +aIg+++
  gi|336253699|ref|YP_004596806.1|   6 YVGAIDQGTTGTRFIIFDHRGQVVANAYEKHEQIYPEPGWVEHDPMEIWENTKAVTTQALSQAGISPDQLEAIGVTN 82 
                                       7899************************************************************************* PP

                                       -SS-EEEEETTT.EESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHH.SCCHHCCHC. CS
                            FGGY_N  78 qreglvllDknd.kpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlken.epevfekie. 151
                                       qre++vl+D +  +p+ nai+w+drrt e ve+l+e+g  + +++ktgl  +++f ++k +Wl+e+  p ++e+++ 
  gi|336253699|ref|YP_004596806.1|  83 QRETTVLWDADSgQPVHNAIVWQDRRTTERVEQLEEDGMTETIRSKTGLEPDAYFAATKAEWLLEEgDPIKMERARp 159
                                       ***********99*************************************************998746889999999 PP

                                       ............EEEEHHHHHHHHHCT--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCC..EEE CS
                            FGGY_N 152 ............kflliddyLiwrLtgqfvtdvtnasesmlfnikklewdeellailgipeelLPklvesse..iig 214
                                                   +f++id++Li+ Ltg+++t+vtnas++ml+ni++lewd+ ll+ +gip+e+LP++++ss    +g
  gi|336253699|ref|YP_004596806.1| 160 edvqdraesgdvLFGTIDSWLIYNLTGNHITEVTNASRTMLYNIHDLEWDDDLLEEFGIPREMLPEVRPSSDedTYG 236
                                       9********************************************************************98522789 PP

                                       EEECCCCCCTT.S-EEEEEEEEEHHHHHHHH CS
                            FGGY_N 215 elkpelaaklGlkegvpvvggggDqqaaalG 245
                                       ++ p    ++    +vpv+g++gDqqaa++G
  gi|336253699|ref|YP_004596806.1| 237 TTDPDGFLEA----EVPVAGALGDQQAALFG 263
                                       9988887776....9***************9 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.52   3.1e+03      20      59 ..     116     151 ..     109     197 .. 0.68
   2 !  197.2   0.2   3.8e-62   2.3e-58       1     197 [.     272     461 ..     272     462 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.52
                            FGGY_C  20 isehglltpvagedgkpeyalegsiavagslvawlldnl.g 59 
                                       ++e+g++ +++        +le   ++a    +wll++   
  gi|336253699|ref|YP_004596806.1| 116 LEEDGMTETIR-----SKTGLEPDAYFAATKAEWLLEEGdP 151
                                       57777778887.....6677777777777777888877542 PP

  == domain 2  score: 197.2 bits;  conditional E-value: 3.8e-62
                            FGGY_C   1 akvslGTssflll.vgtkpvisehglltpva..gedgkpeyalegsiavagslvawlldnlglreeirdageveesl 74 
                                       ak+++GT+sf+l+ +g++ v+s hgllt+++   + ++ +yalegsi+v+g++++wl d   l   i+d +++   l
  gi|336253699|ref|YP_004596806.1| 272 AKNTYGTGSFFLMnTGDEAVESDHGLLTTIGfqRSGEPVQYALEGSIFVTGAAIEWLEDV-DL---IDDPAQT-AEL 343
                                       79*****************************886669********************998.55...9999999.888 PP

                            FGGY_C  75 aelaaaeavadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpld 151
                                       a     ++v ++ gv++vpaf+gl ap+wd++argti+g++++t ++h++rA+le++a+q+r++ ea+ +dsg++++
  gi|336253699|ref|YP_004596806.1| 344 A-----RSVDSTDGVYVVPAFTGLGAPHWDQRARGTIVGMTRGTRKEHLVRATLESIAYQTRDVAEAMVADSGIEMT 415
                                       8.....999999***************************************************************** PP

                            FGGY_C 152 rlavdGGgskndllmqllAdilgvpVerpktaeatalGaAilAava 197
                                       +l vdGG++kn++l+ql+ di+g  ++rp  +e+talG A++A++a
  gi|336253699|ref|YP_004596806.1| 416 SLKVDGGAVKNNFLCQLQSDIIGSEIVRPIVDETTALGSAYAAGLA 461
                                       ********************************************98 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 !   17.9   0.0   2.9e-07    0.0017       3      68 ..      10      81 ..       7     103 .. 0.83
   2 ?   -0.6   0.1      0.12   7.4e+02     195     262 ..     392     453 ..     379     458 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.9e-07
                                      EEE-SSEEEEEEEETTTEEEEEEEE--.......TTS-HHH.........HHHHHHHHHHT--GGGECEE..E CS
                       BcrAD_BadFG  3 iDgGsTttkavlmdekgevlgrgitns.......anlesvrfeaaekvleealtealerageeeadieetylv 68
                                      iD G+T t+++++d +g+v+++++ +            +++  + +++ + + t+al++ag +++++e + ++
  gi|336253699|ref|YP_004596806.1| 10 IDQGTTGTRFIIFDHRGQVVANAYEKHeqiypepG-WVEHDPMEIWENTKAVTTQALSQAGISPDQLEAIGVT 81
                                      9************************9934444322.2235556789999******************988544 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHH CS
                       BcrAD_BadFG 195 laglhraialrvialisrsggvtdevtltGGvakneaavkelrklvkenygevkininpdsiytgalG 262
                                       l+ ++ +  + ++a++  sg +   + + GG  kn+ + +      ++++ + +i + p+ + t alG
  gi|336253699|ref|YP_004596806.1| 392 LESIAYQTRDVAEAMVADSGIEMTSLKVDGGAVKNNFLCQL-----QSDIIGSEI-VRPIVDETTALG 453
                                       44555555566778888888888889999999999444433.....455554432.335555555666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3761.04
//
Query:       gi|336253700|ref|YP_004596807.1|  [L=575]
Description: glycerol-3-phosphate dehydrogenase subunit A [Halopiger xanaduensis SH-6]
Scores for 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-54  184.4   1.7    6.2e-54  183.9   1.7    1.2  1  DAO            FAD dependent oxidoreductase
    4.8e-11   42.8   3.6    4.8e-11   42.8   3.6    2.3  1  Fer2_BFD       BFD-like [2Fe-2S] binding domain
      1e-07   31.5   0.2    8.7e-07   28.4   0.2    2.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.9e-07   30.5   3.0    9.1e-07   28.3   2.9    1.9  1  FAD_binding_2  FAD binding domain
    2.6e-07   30.2   6.5    3.1e-06   26.7   6.5    2.1  1  FAD_binding_3  FAD binding domain
    0.00018   22.0   1.4    0.00081   19.9   0.5    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0022   18.2   0.3     0.0078   16.4   0.3    2.0  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0059   15.9   0.3       0.01   15.1   0.0    1.5  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.013   15.4   0.2      0.021   14.7   0.2    1.3  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.014   14.5   0.9      0.039   13.0   0.2    2.0  2  Lycopene_cycl  Lycopene cyclase protein
       0.02   14.5   0.2      0.038   13.6   0.2    1.5  1  ApbA           Ketopantoate reductase PanE/ApbA
      0.035   14.0   0.0      0.071   13.0   0.0    1.6  1  DAO_C          C-terminal domain of alpha-glycerophosphate ox
      0.051   12.9   6.1       0.54    9.5   6.2    2.1  1  FAD_oxidored   FAD dependent oxidoreductase
      0.056   12.5   0.4      0.092   11.8   0.4    1.3  1  GIDA           Glucose inhibited division protein A
      0.062   13.9   0.0       0.16   12.6   0.0    1.6  1  YbjQ_1         Putative heavy-metal-binding
      0.071   13.1   0.0       0.25   11.3   0.0    2.0  1  DUF3606        Protein of unknown function (DUF3606)
      0.072   12.3   0.1       0.16   11.2   0.1    1.5  1  Thi4           Thi4 family
      0.091   11.4   0.5        0.2   10.3   0.2    1.7  2  HI0933_like    HI0933-like protein
       0.15   12.5   0.0       0.29   11.6   0.0    1.6  1  NAD_binding_7  Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9   1.7   6.5e-57   6.2e-54       2     346 ..       7     358 ..       6     370 .. 0.81

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 6.5e-57
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelg 76 
                                       v++iGGG +G+++A++La rg  Vtl+e+g  +  g++gr  gllhsg ry+ + +     + e++ee + l +  g
  gi|336253700|ref|YP_004596807.1|   7 VLVIGGGSTGCGIARDLAMRGleVTLVERG-NLTDGTTGRMHGLLHSGGRYAVSDQ---ASATECIEENEILRDIAG 79 
                                       99****************************.5555**************9888663...555566777766666655 PP

                                       STTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT.STTTSEEEEETTEEEEEHHHHHHHH CS
                               DAO  77 ididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa.lpgllgalfypdtgqvdpakltaal 152
                                        ++ +++tG l++ + e++ ++++++l+ +++ g++a++l+a+e+re+ep   ++++ a+ +pd g vdp++l+ a 
  gi|336253700|ref|YP_004596807.1|  80 -HC-VEETGGLFVQRPEDSDDYFREKLEGCRDCGIPARVLSAREAREIEPYlAKDIKRAIEVPD-GAVDPFRLCVAN 153
                                       .34.899*******98888999*********9**********99******9655**********.999********* PP

                                       HHHHHHTT-EEEESECEEEEEEEETCEEEEE...........EECT.EEEE..EEEEEEE--GGGHHHH.HTTCTTT CS
                               DAO 153 araaealGveilegtevtgleeedgkvwgve...........rttp.gend..aadavVnaaGawsdll.gllkeld 214
                                       a +ae++G+++ +++ev +l +e+++v+gve           + ++ g+++  +a++vVna Gaw++++ ++  +ld
  gi|336253700|ref|YP_004596807.1| 154 AIDAERHGARVETHAEVIDLLREGDDVYGVEvrhdsgpgkrtH-KApGTTEeiTAEYVVNASGAWAGQIgAM-ADLD 228
                                       *******************97888999****998777777742.3335543345577**********88444.5778 PP

                                       SEEEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHH CS
                               DAO 215 lpispvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellea 291
                                       + ++p +g +  ++ ++  +v ++        +  g+  +++p +  + ++G+t++e +++dd + ++ ++d++++ 
  gi|336253700|ref|YP_004596807.1| 229 IEVRPSKGVMTIMNVRQVDTVVNR-------CRPKGDADIIVPHE-TTAILGTTDEEVEDPDDYPEEQWEVDQMIDT 297
                                       8************55444555554.......88999999999986.77999****98888888899999******** PP

                                       HHHHSGGG..CGEEEEEEEEEEE..TTSSEEEEEEETEEEEEEEEEC...TTTHHHHHHHHH CS
                               DAO 292 lrklfPql..gdvlrkwaGlrpl..pdglpligetpgvkglylatGh...sghGltlapatG 346
                                       l++l+P l  ++  r++ G+rpl  p+g    ++t ++++++l+  +   + +G+++  + G
  gi|336253700|ref|YP_004596807.1| 298 LSELVPILeeARTIRSFWGVRPLyePPGTGTQDPTDITRDFFLLDHAdrdEVSGISSIVG-G 358
                                       *******833445589999***55688877777766667777665444445555555555.5 PP

>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   3.6     5e-14   4.8e-11       1      48 [.     437     487 ..     437     488 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 5e-14
                          Fer2_BFD   1 iVCrCegvtegeIrdairraglttveevkrrtkagtg.Cgg...Crpaieei 48 
                                       ++C+Cegvt+ eIrdai ++  +++++v+ rt+a++g C+g   C+++++e+
  gi|336253700|ref|YP_004596807.1| 437 VICQCEGVTRAEIRDAI-EQSGSDLNAVRIRTRASMGnCQGgfcCQNMANEL 487
                                       69***************.7678*********************999999886 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 !   28.4   0.2   9.3e-10   8.7e-07       2     116 ..       6     223 ..       5     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 9.3e-10
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias..................... 57 
                                       +v+viGgG  G+  a++la  g++vtlve +g++  g+    + ll++++++ +                       
  gi|336253700|ref|YP_004596807.1|   6 EVLVIGGGSTGCGIARDLAMRGLEVTLVE-RGNLTDGTTGRMHGLLHSGGRYAVSDqasatecieeneilrdiaghc 81 
                                       69**************************5.44444444444455555555554444555567888999999****** PP

                                       .......................................................................HHHHCH CS
                                       .......................................................................xxxxxx RF
                       Pyr_redox_2  58 .......................................................................evvkkl 63 
                                                                                                              + ++  
  gi|336253700|ref|YP_004596807.1|  82 veetgglfvqrpedsddyfreklegcrdcgiparvlsareareiepylakdikraievpdgavdpfrlcvaNAIDAE 158
                                       ***********************************************************************777777 PP

                                       HHHCCCCHCCTCEEEEESCEEEEETEEEC............TCEEEEEESEEEE---EEE-BCTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  64 nqgielllgeevvkidpgkkkvklekkke............gdeekiaydklvlAtGssprdlgi 116
                                       ++g ++ + +ev+++ ++  +v   + +             g +e+i+++++v A+G+++  +g 
  gi|336253700|ref|YP_004596807.1| 159 RHGARVETHAEVIDLLREGDDVYGVEVRHdsgpgkrthkapGTTEEITAEYVVNASGAWAGQIGA 223
                                       77877777777888887777777765555778888888888*****************9987754 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   2.9   9.6e-10   9.1e-07       2     204 ..       7     219 ..       6     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 9.6e-10
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S- CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldelad 78 
                                       v+ViG+G  G+  A  +a +Gl+v++ve ++ + g+t    G +   + + + +++   ++    ++ l   ++++ 
  gi|336253700|ref|YP_004596807.1|   7 VLVIGGGSTGCGIARDLAMRGLEVTLVERGNLTDGTTGRMHGLLHSGG-RYAVSDQASATECIEENEILRDIAGHCV 82 
                                       9**********************************9988888777777.44433434344555667888889***** PP

                                       HHHHHHHHHTHHHHHHHHHHT.......T----BCCTSSB-EEE-TT-SST..EEEE-.STT-......HHHHHHHH CS
                     FAD_binding_2  79 qplveafveaapeavdeLeel.......gvpfsrtedgpvdvrelGglsat..artlhdaadarretlvtghallar 146
                                       ++   +fv++ ++  d+++e+       g+p      ++  +re     a+  +r    ++d      v+ ++l+++
  gi|336253700|ref|YP_004596807.1|  83 EETGGLFVQRPEDSDDYFREKlegcrdcGIPARV--LSAREAREIEPYLAKdiKRAIE-VPD----GAVDPFRLCVA 152
                                       ******************9998866655555444..2233333333333333322222.333....36677999999 PP

                                       HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET.........TTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenp.........esgrevrirakavvlatgGfgr 204
                                        +  a+++g ++ +++e+ +L++e+++v+G++v+ +         + g++++i+a  vv a+g++ +
  gi|336253700|ref|YP_004596807.1| 153 NAIDAERHGARVETHAEVIDLLREGDDVYGVEVRHDsgpgkrthkAPGTTEEITAEYVVNASGAWAG 219
                                       999999****************************99999999999999999*************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 !   26.7   6.5   3.3e-09   3.1e-06       1     202 [.       4     252 ..       4     314 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.3e-09
                                       EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EE..EHHHHHHHHHTT-HHHHHHHSEECCCCEE CS
                     FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radgl..nqrtmellrqlGledrilaegapnelmge 74 
                                       +t+Vl++G+G +G   a+ L+++G +v+lve+ + t  ++ r +gl  +     + +q+   + i+++   +++ g+
  gi|336253700|ref|YP_004596807.1|   4 DTEVLVIGGGSTGCGIARDLAMRGLEVTLVERGNLTDGTTgRMHGLlhSGGRYAVSDQASATECIEENEILRDIAGH 80 
                                       69******************************997766655877762144567788888888889999999999999 PP

                                       EEEEE...............................CCCCCEEEEEHHCHHCST-CEE--HHHHHHH...HHH..HH CS
                     FAD_binding_3  75 alyne...............................lsdtpkaradlelesspervtvypqteleri...Lve..ha 115
                                        ++++                               ls ++ ++++  l    +r   +p   +++    +++  +a
  gi|336253700|ref|YP_004596807.1|  81 CVEETgglfvqrpedsddyfreklegcrdcgiparvLSAREAREIEPYLAKDIKRAIEVPDGAVDPFrlcVANaiDA 157
                                       9999999999999**99999999888777776666533333333332245666666666666666532112222246 PP

                                       HHHTEEETCSEEEECCEECCCCCCCEEE..........ECCTTEEEEEEEEEEEE--GTT.-HHHHHHTGGEEEEEE CS
                     FAD_binding_3 116 eerglqvrfktevesleqdeegvtaevr..........dketgeeetvrakYlvGaDGgr.Stvrktlgiefegeet 181
                                       e++g++v+ ++ev  l+++++ v  +             k+ g++e+++a+Y+v a G++ +++ + +++++e   +
  gi|336253700|ref|YP_004596807.1| 158 ERHGARVETHAEVIDLLREGDDVYGVEVrhdsgpgkrtHKAPGTTEEITAEYVVNASGAWaGQIGAMADLDIEVRPS 234
                                       899999999999888888887776543336677777768999999**************845777777777777766 PP

                                       EEEEEEEEEEEEC-SCCCTTC CS
                     FAD_binding_3 182 vyeagvldvlfdadlsdivep 202
                                       +   gv+ +++  +++ +v+ 
  gi|336253700|ref|YP_004596807.1| 235 K---GVMTIMNVRQVDTVVNR 252
                                       6...44444444444433333 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.5   8.6e-07   0.00081       2      32 ..       7      37 ..       6      41 .. 0.95
   2 ?   -1.5   0.0       4.2     4e+03      51      79 ..     158     186 ..     156     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.6e-07
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                      v+v+GgG +g+  A  la  g +Vt+ver++
  gi|336253700|ref|YP_004596807.1|  7 VLVIGGGSTGCGIARDLAMRGLEVTLVERGN 37
                                      89**************************975 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.2
                                       HHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                         Pyr_redox  51 ekngievllntkveeiegsedgvesvklk 79 
                                       e++g +v ++++v  +  ++d v++v+++
  gi|336253700|ref|YP_004596807.1| 158 ERHGARVETHAEVIDLLREGDDVYGVEVR 186
                                       67788999999999999999999999987 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 !   16.4   0.3   8.3e-06    0.0078       1      31 [.       9      39 ..       9      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.3e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31
                                      ++G+G +G+ +A+ La +g++v+l+e+++ +
  gi|336253700|ref|YP_004596807.1|  9 VIGGGSTGCGIARDLAMRGLEVTLVERGNLT 39
                                      8**************************9744 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 !   15.1   0.0   1.1e-05      0.01     163     198 ..       3      38 ..       1      50 [. 0.87
   2 ?   -4.2   0.1       8.4     8e+03     120     134 ..     202     216 ..     200     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                       Pyr_redox_3 163 agqkvvViGgknSavDaAlelvrkgaeVtvvtrgse 198
                                       ++++v+ViGg+ +++ +A +l+ +g eVt+v rg+ 
  gi|336253700|ref|YP_004596807.1|   3 RDTEVLVIGGGSTGCGIARDLAMRGLEVTLVERGNL 38 
                                       57899**************************99975 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 8.4
                       Pyr_redox_3 120 ketyeAkkviiAtGe 134
                                       +e+++A++v+ A G 
  gi|336253700|ref|YP_004596807.1| 202 TEEITAEYVVNASGA 216
                                       6899******99996 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 ?   14.7   0.2   2.2e-05     0.021       2      30 ..       7      35 ..       6      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                      v viG G  G gia  +a +gleV+lv++
  gi|336253700|ref|YP_004596807.1|  7 VLVIGGGSTGCGIARDLAMRGLEVTLVER 35
                                      78*************************97 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   4.1e-05     0.039       2      34 ..       7      37 ..       6      43 .. 0.93
   2 ?   -1.3   0.0      0.89   8.4e+02     112     145 ..     185     220 ..     182     248 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieasp 34
                                      v+viG+G  g+ +A  l  a  gl+v+l+e ++
  gi|336253700|ref|YP_004596807.1|  7 VLVIGGGSTGCGIARDL--AMRGLEVTLVERGN 37
                                      89***************..**********9886 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.89
                     Lycopene_cycl 112 veeeea.geslvvleggr.kirarlvvdarglaslk 145
                                       v++++  g+++   +g   +i a  vv a+g+ +++
  gi|336253700|ref|YP_004596807.1| 185 VRHDSGpGKRTHKAPGTTeEITAEYVVNASGAWAGQ 220
                                       66666666777777776669***********87666 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2     4e-05     0.038       1      31 [.       7      37 ..       7      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                      ++++G G+ G+ +a  La  g +vtl+ r++
  gi|336253700|ref|YP_004596807.1|  7 VLVIGGGSTGCGIARDLAMRGLEVTLVERGN 37
                                      68***************************98 PP

>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.6e-05     0.071       1      78 [.     384     453 ..     384     483 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-05
                                       --TTS---TT--.......TT-STTHT--HHHHHHHHHHHGGGHHHHHHHHHHTH...HHHHHTTS-HHHHHHHHHH CS
                             DAO_C   1 crTkklpLvGaenwsknlaaelaqeygldeevaehLaerYGsraeevlelakedekpelaerlspelpyieaevvYa 77 
                                       c T++ pL+G+e+   ++  e ++++gl + va++  +r Gsra+evle + +         +++ + +++ae++ a
  gi|336253700|ref|YP_004596807.1| 384 CATAEEPLPGSED--LSVLEEGMDDFGLRSPVARRSKQRLGSRAKEVLEGDGA------NPVICQCEGVTRAEIRDA 452
                                       99**********5..77889***************************943332......345666666666666665 PP

                                       H CS
                             DAO_C  78 v 78 
                                       +
  gi|336253700|ref|YP_004596807.1| 453 I 453
                                       5 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.2   0.00057      0.54       1     181 [.       6     252 ..       6     319 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00057
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG.......Glltsglvatdignkaee..............qvv 56 
                                       +v+V+GGg+ G+  A   a +G +v Lve+ +          Gll sg++ ++  + +++              + v
  gi|336253700|ref|YP_004596807.1|   6 EVLVIGGGSTGCGIARDLAMRGLEVTLVERGNLTDgttgrmhGLLHSGGRYAVSDQASATecieeneilrdiagHCV 82 
                                       59***************************876655000011144444444444443333367666655555555555 PP

                      FAD_oxidored  57 tgiareflerlrqrgga.rlkkrskwn...........................tfepevakavleeml........ 97 
                                       + + + f++r ++ +++ r       +                           + + + a +v +  +        
  gi|336253700|ref|YP_004596807.1|  83 EETGGLFVQRPEDSDDYfR-------EklegcrdcgiparvlsareareiepylAKDIKRAIEVPDGAVdpfrlcva 152
                                       5555555555555444431.......022223344556667777777777888844444444444444455555557 PP

                      FAD_oxidored  98 .....aeagvtvllntrlvevekegkriesvtves.........ke.g.rktirAkvfiDATg..dGdlaalaGvpy 156
                                            +++g +v +++++++  +eg+++ +v+v++         k+ g +++i+A++++ A+g   G+++a+a+  +
  gi|336253700|ref|YP_004596807.1| 153 naidaERHGARVETHAEVIDLLREGDDVYGVEVRHdsgpgkrthKApGtTEEITAEYVVNASGawAGQIGAMADLDI 229
                                       77777678999999999999999986677777654111111111444566789999999999944599999999999 PP

                      FAD_oxidored 157 rvGresreetgepaagtlmfrlegv 181
                                       +v r s++     ++++++ ++ + 
  gi|336253700|ref|YP_004596807.1| 230 EV-RPSKG-VMTIMNVRQVDTVVNR 252
                                       88.56665.2222344444444444 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   9.7e-05     0.092       2      29 ..       7      36 ..       6      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.7e-05
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE..E CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi..t 29
                                      v ViGgG  Gc  A  +a +G++v+L+   
  gi|336253700|ref|YP_004596807.1|  7 VLVIGGGSTGCGIARDLAMRGLEVTLVerG 36
                                      89************************9541 PP

>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00017      0.16      33      74 ..     346     387 ..     339     389 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                            YbjQ_1  33 kdilaglrslvGGelkayeeeleeareeAlerlkeeAeelGA 74 
                                       +d ++g++s+vGG+ ++y  + ee+ ++++e+l  +A+   A
  gi|336253700|ref|YP_004596807.1| 346 RDEVSGISSIVGGKFTTYRAMAEEISNHVCEKLGVDARCATA 387
                                       77789****************************999987665 PP

>> DUF3606  Protein of unknown function (DUF3606)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00026      0.25      29      50 ..     443     464 ..     439     466 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                           DUF3606  29 gvteeqLraAVraVGnsakkVr 50 
                                       gvt++++r+A+++ G++  +Vr
  gi|336253700|ref|YP_004596807.1| 443 GVTRAEIRDAIEQSGSDLNAVR 464
                                       8********************8 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00016      0.16      18      50 ..       5      36 ..       2      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailers 50
                                      ++v+++G+Gs+G   a+ la + +l+v+++er 
  gi|336253700|ref|YP_004596807.1|  5 TEVLVIGGGSTGCGIARDLAMR-GLEVTLVERG 36
                                      789*******************.********95 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00021       0.2       2      33 ..       6      37 ..       5      66 .. 0.93
   2 ?   -2.6   0.0       1.8   1.7e+03     267     316 ..     486     535 ..     481     546 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      +v+viGgG  G   A  +a rg +V+l+e+++
  gi|336253700|ref|YP_004596807.1|  6 EVLVIGGGSTGCGIARDLAMRGLEVTLVERGN 37
                                      79***************************986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
                                       ECSTTS-...HHHHHHHHHHHTTTSBHHHHHTTTS-HHHHHHHHHC..TT CS
                       HI0933_like 267 dllPdldaeelkaalekekekeskkslknalaellpkrlvevlleealie 316
                                       +l P++d++++++al +  +++ k + +    e l + ++++ l+ ++++
  gi|336253700|ref|YP_004596807.1| 486 ELHPEYDEATVREALDELFQERWKGQRHALWGEQLSQAMLNYALHATTMN 535
                                       78999999999999999999999999999999999999999988887664 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 ?   11.6   0.0    0.0003      0.29       6      39 ..       3      36 ..       1     135 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                     NAD_binding_7  6 kgkkvlvvGgGevAarkvrklleagakvtvvape 39
                                      ++ +vlv+GgG+ +   +r l+  g +vt+v   
  gi|336253700|ref|YP_004596807.1|  3 RDTEVLVIGGGSTGCGIARDLAMRGLEVTLVERG 36
                                      6889**************************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 4011.75
//
Query:       gi|336253701|ref|YP_004596808.1|  [L=440]
Description: glycerol-3-phosphate dehydrogenase subunit B [Halopiger xanaduensis SH-6]
Scores for 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-37  127.8   3.1    6.6e-37  127.6   3.1    1.0  1  FAD_binding_2   FAD binding domain
    8.9e-08   31.6   0.1    8.9e-08   31.6   0.1    2.1  3  GIDA            Glucose inhibited division protein A
    1.7e-06   27.5   0.2     0.0003   20.1   0.0    2.7  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.5e-06   27.1   2.7    4.4e-06   26.3   2.0    1.7  2  FAD_oxidored    FAD dependent oxidoreductase
    1.6e-05   24.7   7.9    0.00011   21.9   7.9    2.1  1  DAO             FAD dependent oxidoreductase
    1.9e-05   24.1   0.6    0.00014   21.2   0.6    2.0  2  FAD_binding_3   FAD binding domain
    2.1e-05   23.4   0.3    2.1e-05   23.4   0.3    2.0  3  HI0933_like     HI0933-like protein
    8.5e-05   23.0   0.2     0.0041   17.6   0.3    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0006   19.2   1.0     0.0011   18.3   1.0    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.013   15.4   0.2      0.022   14.6   0.2    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.077   11.8   0.3      0.077   11.8   0.3    1.4  2  Trp_halogenase  Tryptophan halogenase
       0.11   11.7   0.2       0.24   10.6   0.2    1.4  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.52   10.6   5.4       0.13   12.5   0.8    2.4  3  NAD_binding_8   NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.6   3.1   4.8e-40   6.6e-37       1     417 []       6     421 ..       6     421 .. 0.84

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 4.8e-40
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldela 77 
                                       Dv+ViG+G+AG +AAl aa++G++v +v+ +++   ++  ++G +d++++++      ++ p + ++d+l+ l+e+ 
  gi|336253701|ref|YP_004596808.1|   6 DVLVIGGGIAGSMAALVAADRGARVRLVTHKES---TLRNASGLVDVLGYTPE-----GEGPLAEPFDALEDLPEE- 73 
                                       9*******************************9...*************9999.....689*************65. PP

                                       -HHHHHHHHHTHHHHHHHHHHT.T----B..CCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHH CS
                     FAD_binding_2  78 dqplveafveaapeavdeLeel.gvpfsr..tedgpvdvrelGglsatartlhdaadarretlvtghallarlvesa 151
                                        +p+ +++++a++ea++ + e  g  + +  t+++++  ++ G++++tar+++++a+       + +  l +++e++
  gi|336253701|ref|YP_004596808.1|  74 -HPYERVGIDAVREALSVFDEVtGDAYAGghTDTNALVPTHGGTVKPTARYPASTAAG---LASDDRDALLVGFETL 146
                                       .99******************99777777333444******************99997...8899999********* PP

                                       HTCTEEEEESEEEEEEEECTT...EEEEEEEEET....TTTCEEEEEES.EEEE-----GG................ CS
                     FAD_binding_2 152 rkagvdfqerteadeLivedg...rvtGavvenp....esgrevrirak.avvlatgGfgr.........allkell 211
                                            df + ++a++L    g   +++Ga+v++p    +   + +++   +++++ + ++          al+ ++ 
  gi|336253701|ref|YP_004596808.1| 147 ----PDFDAPLAAQHLEA-AGvpfEARGATVAFPgirrD---DAKVTRYaHLLDHDETVETgagetgareALAATVE 215
                                       ....************66.44799**********86541...22333333455555555445555678988888888 PP

                                       ...GSSSBSSGTT-S-HHHHHHHCTTSS.EES..TT-EEEEEEEET....TTTB...B--THHHHTT-E.EE-.TTS CS
                     FAD_binding_2 212 gaaaeaettnapavtGdglalalragaa.lnddrmeevqfhPtslvpirdgsgi...LitealrgeGgi.lvd.kdG 282
                                         + +++ ++ pa+ Gd +a+++ra +a   +  ++ev+++P+sl+++r++  +   L ++++r  +g+ +vd  +G
  gi|336253701|ref|YP_004596808.1| 216 HLLEDESRVGFPAILGDENAAEVRADLAeRLGVDVFEVPMGPPSLPGLRLEDLLydaLEDRGVRVTSGVpVVDyETG 292
                                       88899999********************99999*******************9977777777777666524556666 PP

                                       SBTH...GGGS-HHHHHHHHH..HHHHTTTSCCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSE CS
                     FAD_binding_2 283 rrFm...nelasrdvvsrail.ekeiaeggseanvyldashgldaegleatleaineeaangldkdfgrgidpadrp 355
                                              + +++ d++ + i+ +++ +++ + a+ y++a++gl  +g+++++e+   e+++++ ++     ++ dr 
  gi|336253701|ref|YP_004596808.1| 293 GEGAgssASVNDGDRIDHVIVdRNGTEIPHR-ADQYVLATGGLVGKGVRSERER-VFEPIFDCYVP-----HADDR- 361
                                       6644788666666777666651566677777.999*******************.67777778856.....89999. PP

                                       EE.......EEEEEEEES-EEEBETTSBESTTEE.ESSBTEEE-STCEESSSSTTS--TTHHH CS
                     FAD_binding_2 356 ipgpfyavkvvpaqhytmgGvetdengrvldadg.qpipGLYAaGevaaggvhganrlgGnsl 417
                                          +++ ++ +  q+y  +G++ d ++r+lda++    ++L AaG+v+ gg++ a + +G ++
  gi|336253701|ref|YP_004596808.1| 362 --YDWFVDDAFGEQPYARFGLAPDRELRPLDANDePEFDNLRAAGAVL-GGYDFAAEKSGAGV 421
                                       ..89*************************776651569**********.********999875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.1   6.4e-11   8.9e-08       1      39 [.       6      44 ..       6      70 .. 0.81
   2 ?   -3.1   0.0       2.2   3.1e+03     130     150 ..     311     333 ..     301     344 .. 0.71
   3 ?   -1.7   0.8      0.84   1.2e+03     372     389 ..     421     438 ..     396     440 .] 0.69

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 6.4e-11
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--S CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaels 39
                                      dv ViGgG AG+ AAl aa +Ga+v L+thk +t+ + s
  gi|336253701|ref|YP_004596808.1|  6 DVLVIGGGIAGSMAALVAADRGARVRLVTHKESTLRNAS 44
                                      79******************************9998876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.2
                                       EEEETTS-EEEEC..EEEE--TT CS
                              GIDA 130 gvvtedgetikak..avviatGt 150
                                       ++v ++g++i  +  + v+atG 
  gi|336253701|ref|YP_004596808.1| 311 VIVDRNGTEIPHRadQYVLATGG 333
                                       46777788876555599****98 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.84
                                       HHHHHHHHHHHHHHHHHC CS
                              GIDA 372 EaaaqGllAGinaarkak 389
                                        + a+G +AG+ aa +++
  gi|336253701|ref|YP_004596808.1| 421 VSLATGYVAGRQAAEEVE 438
                                       46789******9999876 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 !   20.1   0.0   2.2e-07    0.0003       2      34 ..       6      39 ..       5      90 .. 0.85
   2 ?    4.7   0.0     0.011        15     162     235 ..     244     331 ..     167     334 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.2e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEE.TTHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.legt 34
                                      dv+viGgG+AG  aal +a  ga+v lv  +e t
  gi|336253701|ref|YP_004596808.1|  6 DVLVIGGGIAGSMAALVAADRGARVRLVThKEST 39
                                      89**************************743333 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.011
                                       HHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE..............EEEEEETTSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxx RF
                       Pyr_redox_2 162 aklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge..............klevvledge 224
                                        +lg++v  v  ++  l+  + +l++ l +ale++Gv+v  g  v++ +  ge              ++  v+ +g+
  gi|336253701|ref|YP_004596808.1| 244 ERLGVDVFEVPMGPPSLP--GLRLEDLLYDALEDRGVRVTSGVPVVDYETGGEgagssasvndgdriDHVIVDRNGT 318
                                       455555555555555554..457999999999999999999999999998888775544444433222224444444 PP

                                       E..EEESEEEE-S CS
                                       x..xxxxxxxxxx RF
                       Pyr_redox_2 225 e..idadlvvvav 235
                                       e    ad  v+a+
  gi|336253701|ref|YP_004596808.1| 319 EipHRADQYVLAT 331
                                       4444455555555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   2.0   3.2e-09   4.4e-06       1      30 [.       6      35 ..       6      39 .. 0.94
   2 ?   -1.8   0.0       1.1   1.5e+03     111     144 ..     299     332 ..     265     333 .. 0.61

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.2e-09
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      Dv+V+GGg+aG +AA+ Aa +Ga+v Lv  
  gi|336253701|ref|YP_004596808.1|  6 DVLVIGGGIAGSMAALVAADRGARVRLVTH 35
                                      9**************************986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                      FAD_oxidored 111 vevekegkriesvtveskeg.rktirAkvfiDATg 144
                                       ++ + +g+ri++v+v  ++g ++  rA+ ++ ATg
  gi|336253701|ref|YP_004596808.1| 299 SASVNDGDRIDHVIVD-RNGtEIPHRADQYVLATG 332
                                       233334589*****95.554499999999988886 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   7.9   8.2e-08   0.00011       1     205 [.       6     336 ..       6     357 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.2e-08
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeel 75 
                                       dv++iGGGi+G+ +A+ +a rg  V l+  +    + +  ++sgl+   l y+pe+ e  +l++  ++ l++l ee+
  gi|336253701|ref|YP_004596808.1|   6 DVLVIGGGIAGSMAALVAADRGarVRLVTHK----ESTLRNASGLVDV-LGYTPEG-EG-PLAE-PFDALEDLPEEH 74 
                                       8************************999999....3677777888877.5558877.32.5555.578888888883 PP

                                       SSTTSEEEEEEEEEESS............................................................ CS
                               DAO  76 gididyrrtGllslaad............................................................ 92 
                                           +y+r G   +  +                                                            
  gi|336253701|ref|YP_004596808.1|  75 ----PYERVGIDAVR-Ealsvfdevtgdayagghtdtnalvpthggtvkptarypastaaglasddrdallvgfetl 146
                                       ....57777777774.3344555666777777777777777777788888888888888888888888888888777 PP

                                       .............................................................HHHHHHHHHHHHHHHH CS
                               DAO  93 .............................................................eeelealdkllallle 108
                                                                                                    e+  + ++ ll++ ++
  gi|336253701|ref|YP_004596808.1| 147 pdfdaplaaqhleaagvpfeargatvafpgirrddakvtryahlldhdetvetgagetgarEALAATVEHLLEDESR 223
                                       77777777777777777777777777777777777777777777766666666666554432222223344555566 PP

                                       TTTTEEEEEHHHHHHHSTT.STTTSEEEE.ETTE.EEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEE...... CS
                               DAO 109 agldaelldaeevrelepa.lpgllgalf.ypdt.gqvdpakltaalaraaealGveilegtevtgleeed...... 176
                                        g +a +l  e+++e+     ++l   +f +p +   +   +l   l++a+e++Gv++  g +v++ e  +      
  gi|336253701|ref|YP_004596808.1| 224 VGFPA-ILGDENAAEVRADlAERLGVDVFeVPMGpPSLPGLRLEDLLYDALEDRGVRVTSGVPVVDYETGGegagss 299
                                       77765.7777777777765333555444448887666788888888********************97633445444 PP

                                       ......TCEEEEEEECTEEE..EEEEEEEE--GGGHH CS
                               DAO 177 ......gkvwgverttpgen..daadavVnaaGawsd 205
                                             +++ +v ++ +g++  ++ad+ V+a+G  ++
  gi|336253701|ref|YP_004596808.1| 300 asvndgDRIDHVIVDRNGTEipHRADQYVLATGGLVG 336
                                       555444455555433334443457799******7755 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.6     1e-07   0.00014       3      39 ..       6      42 ..       4      47 .. 0.92
   2 ?    0.5   0.0      0.21   2.9e+02      92     137 ..     250     295 ..     192     322 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1e-07
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvl 39
                                      dVl++G+G aG m+al+ + +G rv+lv+  ++t ++
  gi|336253701|ref|YP_004596808.1|  6 DVLVIGGGIAGSMAALVAADRGARVRLVTHKESTLRN 42
                                      8*****************************9999887 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.21
                                       CHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCC CS
                     FAD_binding_3  92 lesspervtvypqteleriLvehaeerglqvrfktevesleqdeeg 137
                                       +   p+ +  +p  +le +L++++e rg++v  +  v+  e  +eg
  gi|336253701|ref|YP_004596808.1| 250 VFEVPMGPPSLPGLRLEDLLYDALEDRGVRVTSGVPVVDYETGGEG 295
                                       4456667777888999999999999999999988877766666555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.3   1.5e-08   2.1e-05       2      37 ..       6      41 ..       5      44 .. 0.94
   2 ?   -2.3   0.0      0.95   1.3e+03     152     164 ..     321     333 ..     242     335 .. 0.62
   3 ?   -3.6   0.7       2.4   3.3e+03     389     408 ..     405     431 ..     404     432 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.5e-08
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37
                                      dv+viGgG AG maA+ aa+rg+rV l+ ++++++r
  gi|336253701|ref|YP_004596808.1|  6 DVLVIGGGIAGSMAALVAADRGARVRLVTHKESTLR 41
                                      89***************************9998776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.95
                                       EEEESEEEE---- CS
                       HI0933_like 152 eleadklvlAtGG 164
                                         +ad+ vlAtGG
  gi|336253701|ref|YP_004596808.1| 321 PHRADQYVLATGG 333
                                       3457777777777 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.4
                                       E-TTTHHHHH.......HHHHHHHHHH CS
                       HI0933_like 389 gvtGGynlqa.......AwasgyaAGk 408
                                       +v+GGy + a       ++a+gy+AG+
  gi|336253701|ref|YP_004596808.1| 405 AVLGGYDFAAeksgagvSLATGYVAGR 431
                                       578888886433333337899999997 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3     3e-06    0.0041       2      35 ..       7      40 ..       6      46 .. 0.91
   2 ?    2.3   0.0      0.19   2.6e+02      18      72 ..     243     295 ..     227     305 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v+v+GgG  g ++A ++a+ g++V +v  ++  l
  gi|336253701|ref|YP_004596808.1|  7 VLVIGGGIAGSMAALVAADRGARVRLVTHKESTL 40
                                      89*************************9998877 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.19
                                       HHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  18 laelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg 72 
                                       + +lg +V  v +++  l+  +  ++++l + le++g++v  +  v+  e+ ++g
  gi|336253701|ref|YP_004596808.1| 243 AERLGVDVFEVPMGPPSLP--GLRLEDLLYDALEDRGVRVTSGVPVVDYETGGEG 295
                                       4568888888888888884..4467799999********9999888888866665 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 !   18.3   1.0     8e-07    0.0011      30      67 ..       6      43 ..       3      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8e-07
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleql 67
                                       vlviGgG+aG  A+ +a+  ga+V+++  ++++l++ 
  gi|336253701|ref|YP_004596808.1|  6 DVLVIGGGIAGSMAALVAADRGARVRLVTHKESTLRNA 43
                                      59************************999999888875 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 ?   14.6   0.2   1.6e-05     0.022       2      39 ..       7      44 ..       6      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekal 39
                                      v viG G+ G+  a v+a +g +V+lv  +e++l++a 
  gi|336253701|ref|YP_004596808.1|  7 VLVIGGGIAGSMAALVAADRGARVRLVTHKESTLRNAS 44
                                      78******************************999886 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   5.6e-05     0.077       1      33 [.       6      35 ..       6      41 .. 0.83
   2 ?   -3.6   0.1       2.7   3.7e+03     157     199 ..     266     309 ..     264     318 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                                      +++++GGG+aG++aA + a  +   ++v lv  
  gi|336253701|ref|YP_004596808.1|  6 DVLVIGGGIAGSMAALVAADRG---ARVRLVTH 35
                                      699************9888777...77777765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHCT-EEEE--.EEEEEE-TTS-EEEEEETTS-EEE CS
                    Trp_halogenase 157 akfLrrvaearGvtrvegk.vvevqldedgrveslrledgreve 199
                                       +++L +  e+rGv++++g  vv+ ++  +g+ +s  ++dg +++
  gi|336253701|ref|YP_004596808.1| 266 EDLLYDALEDRGVRVTSGVpVVDYETGGEGAGSSASVNDGDRID 309
                                       67788888999999999973566677778887777778877765 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 ?   10.6   0.2   0.00017      0.24     165     201 ..       5      41 ..       2      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00017
                       Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgseiek 201
                                       ++v+ViGg+  +  aAl  +++ga+V++vt++++  +
  gi|336253701|ref|YP_004596808.1|   5 DDVLVIGGGIAGSMAALVAADRGARVRLVTHKESTLR 41 
                                       79****************************9987655 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 ?   12.5   0.8   9.2e-05      0.13       1      25 [.       9      33 ..       9      39 .. 0.92
   2 ?   -2.5   0.1       4.7   6.5e+03      31      53 ..     100     129 ..      96     137 .. 0.64
   3 ?   -2.5   0.0       4.6   6.3e+03      27      45 ..     291     308 ..     269     314 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.2e-05
                                      EE--SHHHHHHHHHHHCCTEEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlll 25
                                      ++G+G++G+ aA  +a++g++v l+
  gi|336253701|ref|YP_004596808.1|  9 VIGGGIAGSMAALVAADRGARVRLV 33
                                      8********************9885 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
                                       SSGGG-EECE....TT...CEECTS---EE CS
                     NAD_binding_8  31 lGGraasyev....pg...vrvdygahifh 53 
                                        GG+  ++ +    +g    ++ y+a++ +
  gi|336253701|ref|YP_004596808.1| 100 AGGHTDTNALvpthGGtvkPTARYPASTAA 129
                                       688888887765533355556666666655 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.6
                                       SSSSSSGGG-EECETTCEE CS
                     NAD_binding_8  27 krdrlGGraasyevpgvrv 45 
                                       ++    G +as+++ g r+
  gi|336253701|ref|YP_004596808.1| 291 TGGEGAGSSASVND-GDRI 308
                                       43333344444433.3344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); 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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2984.62
//
Query:       gi|336253702|ref|YP_004596809.1|  [L=446]
Description: glycerol-3-phosphate dehydrogenase subunit C [Halopiger xanaduensis SH-6]
Scores for 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-23   80.7   0.9    3.7e-11   43.1   0.1    2.7  2  CCG              Cysteine-rich domain
    1.8e-08   34.7   8.1    1.8e-08   34.7   8.1    3.0  3  Fer4_8           4Fe-4S dicluster domain
    4.9e-06   27.0   9.0    4.9e-06   27.0   9.0    3.0  3  Fer4_17          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.013   15.7  16.7      0.019   15.1  12.9    3.1  4  Fer4_9           4Fe-4S dicluster domain
      0.016   14.2   0.0      0.029   13.3   0.0    1.3  1  DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
      0.017   15.2  18.1      0.034   14.2  13.1    3.3  4  Fer4_10          4Fe-4S dicluster domain
      0.031   14.9  20.0      0.061   13.9  15.0    3.2  4  Fer4_7           4Fe-4S dicluster domain
      0.049   14.0   0.1      0.088   13.2   0.1    1.4  1  DUF3390          Domain of unknown function (DUF3390)
      0.063   13.0  12.3        0.2   11.4   0.0    4.1  2  zf-CSL           CSL zinc finger
       0.57   11.1  15.6       0.32   12.0  10.6    3.1  4  Fer4_16          4Fe-4S double cluster binding domain
        1.3    9.2   5.0       0.38   10.9   0.3    2.4  2  ETF_QO           Electron transfer flavoprotein-ubiquinone ox
        2.1    8.3  15.2        1.4    8.8   3.3    2.7  2  Fer4             4Fe-4S binding domain
        2.6    8.3  13.2       0.75   10.0   0.8    3.0  3  Fer4_21          4Fe-4S dicluster 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 !   43.1   0.1   2.7e-14   3.7e-11       1      85 []     202     286 ..     202     286 .. 0.89
   2 !   35.6   0.1   5.6e-12   7.8e-09       2      84 ..     334     416 ..     333     417 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 2.7e-14
                               CCG   1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaee...tgadaiv 74 
                                       vayf+gC + +++ pev kal ++ e  g e++++ ++ C G + + +g+ e a++ a+ nv ++     +gad iv
  gi|336253702|ref|YP_004596809.1| 202 VAYFHGC-YSNYNTPEVAKALVHVYEHFGYEIMVP-DQHCSGTPMFANGMLEDARRAAETNVPELAAaidEGAD-IV 275
                                       89*****.9************************99.**************998888888888777764425666.** PP

                               CCG  75 tacpgCllqlk 85 
                                       + c++C+++l+
  gi|336253702|ref|YP_004596809.1| 276 ASCSSCSMSLR 286
                                       ********985 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 5.6e-12
                               CCG   2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkee...laealakrnvetaeetgadaivt 75 
                                       ay+ +Ch+ ++  +  +  l  l  ++g+e ++  ++sC G +g++ +kee   ++++++++++e+++ ++a+  +t
  gi|336253702|ref|YP_004596809.1| 334 AYHAPCHARNQGLDGQTVELLSL--VDGIEAHDV-GDSCSGISGTYGWKEEnyeTSMKIGEEMFEHMDAADAEQGLT 407
                                       8*****97777755555555555..79*****99.**************99999999******************** PP

                               CCG  76 acpgCllql 84 
                                       +cp+C++q+
  gi|336253702|ref|YP_004596809.1| 408 ECPTCSMQM 416
                                       *******98 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   8.1   1.3e-11   1.8e-08       2      65 .]      38     102 ..      37     102 .. 0.84
   2 ?    0.2   0.1      0.77   1.1e+03      44      55 ..     263     282 ..     236     283 .. 0.61
   3 ?    1.0   0.1      0.43   5.9e+02      44      55 ..     395     413 ..     361     414 .. 0.59

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.3e-11
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaae..dvqeeqvlee...eealwsCttcgaCtevCpvgi 65 
                                       +++C +C+ C ++Cpv++  ++++  + ++ ++     ++q+  +   +e++ +C++c++C+ +Cp ++
  gi|336253702|ref|YP_004596809.1|  38 ADNCYKCSTCDTECPVAEVDDEFPGPKFQGPEQwrL--KRQE--DhdiDESVMKCSNCMRCDGACPSEV 102
                                       689***************************999431..2222..23469*****************875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.77
                            Fer4_8  44 e........eealwsCttcg 55 
                                       e        ++++ sC++c 
  gi|336253702|ref|YP_004596809.1| 263 ElaaaidegADIVASCSSCS 282
                                       03334455578999999995 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.43
                            Fer4_8  44 e.......eealwsCttcg 55 
                                       e       e++l +C tc 
  gi|336253702|ref|YP_004596809.1| 395 EhmdaadaEQGLTECPTCS 413
                                       02344556899****9996 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   9.0   3.6e-09   4.9e-06       1      60 [.      40     102 ..      40     103 .. 0.86
   2 ?   -1.0   0.1         2   2.7e+03      42      50 ..     274     282 ..     239     286 .. 0.64
   3 ?   -0.6   0.1       1.5     2e+03      26      50 ..     384     413 ..     366     415 .. 0.56

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3.6e-09
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepk...kllraaklglleeaekeekaslCieCgeCerkCPqgl 60 
                                       +C +C+ C  eCp  e  d+ p    +  ++++l++ e++  +e + +C++C +C+ +CP+++
  gi|336253702|ref|YP_004596809.1|  40 NCYKCSTCDTECPVAEVDDEFPGpkfQGPEQWRLKRQEDHDIDESVMKCSNCMRCDGACPSEV 102
                                       6****************88854443577888888888888889*****************998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2
                           Fer4_17  42 kaslCieCg 50 
                                        + +C++C 
  gi|336253702|ref|YP_004596809.1| 274 IVASCSSCS 282
                                       456666664 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.5
                           Fer4_17  26 lraakl.....glleeaekeekaslCieCg 50 
                                          +k+     + +++a +e+   +C +C 
  gi|336253702|ref|YP_004596809.1| 384 ETSMKIgeemfEHMDAADAEQGLTECPTCS 413
                                       444433332234455555557777777775 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.4    0.0016       2.2      34      48 ..      39      53 ..      19      56 .. 0.69
   2 ?   15.1  12.9   1.4e-05     0.019       1      49 [.      40     101 ..      40     103 .. 0.76
   3 ?   -2.1   0.0       3.3   4.5e+03      35      39 ..     277     281 ..     253     285 .. 0.67
   4 ?   -1.0   0.0       1.4     2e+03      34      39 ..     407     412 ..     382     425 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                            Fer4_9 34 eaCigCgaCveaCpk 48
                                      ++C++C +C   Cp 
  gi|336253702|ref|YP_004596809.1| 39 DNCYKCSTCDTECPV 53
                                      579999999999986 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.4e-05
                            Fer4_9   1 kCtgCgaCveaCpagvvved.aaerkarlraase............eaCigCgaCveaCpkg 49 
                                       +C++C +C + Cp   v ++  ++++   ++++              +C  C++C  aCp++
  gi|336253702|ref|YP_004596809.1|  40 NCYKCSTCDTECPVAEVDDEfPGPKFQGPEQWRLkrqedhdidesvMKCSNCMRCDGACPSE 101
                                       6***********876664440444444444444488888999999999************86 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.3
                            Fer4_9  35 aCigC 39 
                                       +C +C
  gi|336253702|ref|YP_004596809.1| 277 SCSSC 281
                                       44444 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.4
                            Fer4_9  34 eaCigC 39 
                                       ++C +C
  gi|336253702|ref|YP_004596809.1| 407 TECPTC 412
                                       334444 PP

>> DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.1e-05     0.029     148     179 ..     166     197 ..     160     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                   DDE_Tnp_ISAZ013 148 wvsvgtdkdtaefavesirrwWqevgkarypk 179
                                       ++ v+++++  efa e++r+wW ++g a+  +
  gi|336253702|ref|YP_004596809.1| 166 VMGVTSERELPEFATETFREWWAKRGGAKVEN 197
                                       578999*******************9877655 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2  13.1   2.5e-05     0.034       6      56 .]      38      99 ..      35      99 .. 0.89
   2 ?   12.9   2.2   6.3e-05     0.087       8      28 ..      87     111 ..      80     128 .. 0.69
   3 ?   -2.3   0.0       3.7   5.1e+03      37      48 ..     270     281 ..     257     284 .. 0.62
   4 ?   -0.3   0.1      0.84   1.2e+03      37      49 ..     401     413 ..     387     418 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                           Fer4_10  6 ddtCirCgkCvkaCPadl...........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +d C +C +C + CP+                + + ++ e+  +++ v kC +c  C  aCP
  gi|336253702|ref|YP_004596809.1| 38 ADNCYKCSTCDTECPVAEvddefpgpkfqGPEQWRLKRQEDHDIDESVMKCSNCMRCDGACP 99
                                      589*************76********998777888888888888899999999999999999 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 6.3e-05
                           Fer4_10   8 tCirCgkCvkaCPadl....tsvga 28 
                                       +C +C +C  aCP+ +     ++ a
  gi|336253702|ref|YP_004596809.1|  87 KCSNCMRCDGACPSEVplsqMHNTA 111
                                       8*************77776522222 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.7
                           Fer4_10  37 avrkkvekCtgc 48 
                                       +  + v +C  c
  gi|336253702|ref|YP_004596809.1| 270 EGADIVASCSSC 281
                                       445556666666 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.84
                           Fer4_10  37 avrkkvekCtgcg 49 
                                         + ++ +C++c 
  gi|336253702|ref|YP_004596809.1| 401 DAEQGLTECPTCS 413
                                       4455889999996 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.4   0.00029       0.4      29      50 ..      32      53 ..       8      55 .. 0.74
   2 ?   13.9  15.0   4.4e-05     0.061       2      51 ..      41     101 ..      40     102 .. 0.68
   3 ?   -2.8   0.0       7.3     1e+04      37      41 ..     277     281 ..     252     284 .. 0.65
   4 ?   -2.3   0.1       5.1   7.1e+03      45      50 ..     406     411 ..     368     414 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                            Fer4_7 29 ekveidpekClgCgaCvavCPt 50
                                      ++++  +++C+ C  C ++CP+
  gi|336253702|ref|YP_004596809.1| 32 MDLRPGADNCYKCSTCDTECPV 53
                                      34455679*************8 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.4e-05
                            Fer4_7   2 CigCgaCvaaCpvkaield....eeenek.......gtekveidpekClgCgaCvavCPtg 51 
                                       C +C  C   Cpv  ++ +    +++ ++       + ++++ + +kC++C +C  +CP++
  gi|336253702|ref|YP_004596809.1|  41 CYKCSTCDTECPVAEVDDEfpgpKFQGPEqwrlkrqEDHDIDESVMKCSNCMRCDGACPSE 101
                                       ************8888844222222222233333223477788899*************97 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.3
                            Fer4_7  37 kClgC 41 
                                       +C++C
  gi|336253702|ref|YP_004596809.1| 277 SCSSC 281
                                       34444 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 5.1
                            Fer4_7  45 vavCPt 50 
                                        ++CPt
  gi|336253702|ref|YP_004596809.1| 406 LTECPT 411
                                       344443 PP

>> DUF3390  Domain of unknown function (DUF3390)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   6.4e-05     0.088      62      87 ..     166     191 ..     118     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.4e-05
                           DUF3390  62 lkaWtsvRtlPkpakkslrdlakerg 87 
                                       +++ ts R+lP++a +++r+++++rg
  gi|336253702|ref|YP_004596809.1| 166 VMGVTSERELPEFATETFREWWAKRG 191
                                       5555899****************997 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014       0.2      39      55 ..     268     286 ..     247     289 .. 0.76
   2 ?    5.8   0.0    0.0082        11      39      53 ..     399     415 ..     381     417 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                       .....--EEEETTSSEEEE CS
                            zf-CSL  39 e..gaevvvqCssCSLwik 55 
                                       +  ga++v+ CssCS+ ++
  gi|336253702|ref|YP_004596809.1| 268 IdeGADIVASCSSCSMSLR 286
                                       04589**********9876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0082
                                       .....--EEEETTSSEE CS
                            zf-CSL  39 e..gaevvvqCssCSLw 53 
                                       +    + +++C++CS+ 
  gi|336253702|ref|YP_004596809.1| 399 AadAEQGLTECPTCSMQ 415
                                       13355779*******86 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 ?   12.0  10.6   0.00023      0.32       1      65 [.      40      99 ..      40     101 .. 0.86
   2 ?    7.5   2.9    0.0056       7.7       1      20 [.      87     106 ..      87     137 .. 0.68
   3 ?   -1.8   0.0       4.5   6.2e+03      48      61 ..     268     282 ..     244     284 .. 0.60
   4 ?   -1.7   0.1       4.3   5.9e+03      51      61 ..     403     413 ..     378     419 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                           Fer4_16  1 rCgtCgkCaevCPtnaikek.kekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                      +C +C  C   CP++ ++ +   ++++ +e+   + +e++d+ e+  kc        C +C  +CP
  gi|336253702|ref|YP_004596809.1| 40 NCYKCSTCDTECPVAEVDDEfPGPKFQGPEQWRLKRQEDHDIDESVMKCS------NCMRCDGACP 99
                                      6*****************88778899999998888888888888877777......9********9 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0056
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C +C +C  +CP+++  ++
  gi|336253702|ref|YP_004596809.1|  87 KCSNCMRCDGACPSEVPLSQ 106
                                       5************9985555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.5
                           Fer4_16  48 ckkqeai.tgCdiCq 61 
                                        +++ +i + C  C 
  gi|336253702|ref|YP_004596809.1| 268 IDEGADIvASCSSCS 282
                                       333434447888885 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.3
                           Fer4_16  51 qeaitgCdiCq 61 
                                       ++ +t C +C 
  gi|336253702|ref|YP_004596809.1| 403 EQGLTECPTCS 413
                                       34456666664 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00027      0.38      62      95 ..      28      61 ..      14      71 .. 0.80
   2 ?   -1.0   0.7       1.4   1.9e+03      64      79 ..      80      95 ..      68     110 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                                      TTSSEEEEE-CCC--S--HHHHH-TT--EEE--- CS
                            ETF_QO 62 eakekklqinaqnCvhCktCdikdpsqniewvvP 95
                                      ea+++ l+  a nC  C tCd   p  +++ + P
  gi|336253702|ref|YP_004596809.1| 28 EAEDMDLRPGADNCYKCSTCDTECPVAEVDDEFP 61
                                      4678889999************999998876665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                      SSEEEEE-CCC--S-- CS
                            ETF_QO 64 kekklqinaqnCvhCk 79
                                      +  + ++  +nC+ C 
  gi|336253702|ref|YP_004596809.1| 80 DIDESVMKCSNCMRCD 95
                                      3444456667777775 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   4.2     0.028        38       6      20 ..      39      53 ..      37      54 .. 0.92
   2 ?    8.8   3.3     0.001       1.4       7      21 ..      87     101 ..      84     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.028
                                      TTSSS-THHHHHSTT CS
                              Fer4  6 ekCigCGaCvevCPv 20
                                      + C +C +C   CPv
  gi|336253702|ref|YP_004596809.1| 39 DNCYKCSTCDTECPV 53
                                      89************8 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.001
                                       TSSS-THHHHHSTTT CS
                              Fer4   7 kCigCGaCvevCPvg 21 
                                       kC +C++C  +CP +
  gi|336253702|ref|YP_004596809.1|  87 KCSNCMRCDGACPSE 101
                                       9************86 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.8   0.00054      0.75      38      55 ..      38      55 ..      19      57 .. 0.81
   2 ?    6.4   0.6    0.0071       9.8       7      20 ..      87     100 ..      75     119 .. 0.69
   3 ?   -2.5   0.0       4.3     6e+03      10      16 ..     277     283 ..     266     293 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00054
                           Fer4_21 38 edeCvGCnlCssvCPved 55
                                      +d+C  C  C + CPv +
  gi|336253702|ref|YP_004596809.1| 38 ADNCYKCSTCDTECPVAE 55
                                      799************965 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0071
                           Fer4_21   7 kCigCgkCliaCed 20 
                                       kC +C +C  aC+ 
  gi|336253702|ref|YP_004596809.1|  87 KCSNCMRCDGACPS 100
                                       67777777777773 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.3
                           Fer4_21  10 gCgkCli 16 
                                       +C +C +
  gi|336253702|ref|YP_004596809.1| 277 SCSSCSM 283
                                       4555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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):              13  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3138.61
//
Query:       gi|336253703|ref|YP_004596810.1|  [L=393]
Description: Cdc6-like protein AAA superfamily ATPase-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-09   38.4   0.7    6.2e-09   36.5   0.1    2.1  2  AAA_16         AAA ATPase domain
    2.9e-05   24.4   0.0    8.3e-05   22.9   0.0    1.7  2  AAA_22         AAA domain
     0.0016   18.4   0.1     0.0037   17.2   0.1    1.7  1  HTH_Crp_2      Crp-like helix-turn-helix domain
     0.0026   17.5   0.0     0.0084   15.9   0.0    2.0  1  HTH_IclR       IclR helix-turn-helix domain
     0.0066   16.3   0.0      0.013   15.4   0.0    1.5  1  MarR           MarR family
     0.0077   16.3   3.5       0.12   12.6   0.5    3.4  3  DprA_WH        DprA winged helix domain
  ------ inclusion threshold ------
      0.013   15.0   0.0       0.03   13.9   0.0    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
      0.018   15.4   0.0      0.035   14.5   0.0    1.4  1  FaeA           FaeA-like protein
      0.027   14.4   0.0      0.059   13.3   0.0    1.5  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.028   14.3   3.5      0.035   14.0   0.6    2.6  2  MarR_2         MarR family
      0.095   12.4   0.0       0.18   11.5   0.0    1.4  1  Guanylate_kin  Guanylate kinase
       0.15   12.2   2.0        4.4    7.5   0.7    3.0  2  TmoB           Toluene-4-monooxygenase system protein B (TmoB


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.1   4.2e-12   6.2e-09       2     145 ..      35     168 ..      34     197 .. 0.76
   2 ?   -0.1   0.1      0.72   1.1e+03      99     107 ..     274     287 ..     230     347 .. 0.46

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 4.2e-12
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqala 77 
                                        vGR+  le+Ll+++e+v +g+   +v ++G++G G s++v++l++al+++    + + ++  ++  +++  a++ +
  gi|336253703|ref|YP_004596810.1|  35 PVGRGPVLEELLDVFEPVFEGSIpDSVAVVGPAGAGTSAVVTALFDALNDS----VDTGNRPIGTT-TRAGSADLGT 106
                                       79********************99***************************....77777777222.2233555554 PP

                            AAA_16  78 reellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlq 145
                                       r  ++ +  +   +++++ +r+ l e  a+  + +g +  +l++ +++ l   +r++r  v+ +D+ +
  gi|336253703|ref|YP_004596810.1| 107 RFVYVDARRT---ESAFAFYRTVLAEISAEPVPESGVGTDDLRDRVRERL---ERRDRRAVVAIDHHD 168
                                       4444444444...4788889998888888777777777788888888888...555666899999877 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.72
                            AAA_16  99 ekleeala.....a 107
                                       ++  e+++     +
  gi|336253703|ref|YP_004596810.1| 274 DQHVERATeavpeD 287
                                       22222222111121 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       7.9   1.2e+04      78      98 ..       3      22 ..       2      49 .. 0.67
   2 !   22.9   0.0   5.5e-08   8.3e-05       7      98 ..      60     165 ..      58     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.9
                            AAA_22 78 llealeqalraravielliiD 98
                                      l+e++++  +a+++ + l++D
  gi|336253703|ref|YP_004596810.1|  3 LRERIARRRSAHRT-RGLVVD 22
                                      56666666677777.778887 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 5.5e-08
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee.............erpevvfvtlpsstsskdllrellralglelka 70 
                                       +++v+G++G+G + ++  l++ l+   +  +              + ++v+v++   +s   ++r +l ++  e   
  gi|336253703|ref|YP_004596810.1|  60 SVAVVGPAGAGTSAVVTALFDALNDSVDTGNrpigtttragsadLGTRFVYVDARRTESAFAFYRTVLAEISAEPVP 136
                                       579*******************9655444449**********9999********************99999998888 PP

                            AAA_22  71 .erlsseellealeqalraravielliiD 98 
                                        ++  +++l++++++ l++r++++++ iD
  gi|336253703|ref|YP_004596810.1| 137 eSGVGTDDLRDRVRERLERRDRRAVVAID 165
                                       8999******************9999999 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   0.1   2.5e-06    0.0037       1      61 [.     302     358 ..     302     360 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.5e-06
                                       HHHHHHHHHHHCTTTCEEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES- CS
                         HTH_Crp_2   1 qRlArfLlrlaeraggeielpltqeelAsmlGltretvsrilseLkreglisrgrririld 61 
                                       qR+ + L+ ++ r++    ++   ee+A++  lt  tv r l eL ++g+i+r   ++++d
  gi|336253703|ref|YP_004596810.1| 302 QRVLAHLISIDSRDR---PIRDVAEEIAERSSLTAGTVKRFLYELADRGVIERVP-LTVTD 358
                                       677777777766543...3555579***************************765.66666 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 !   15.9   0.0   5.6e-06    0.0084      22      51 ..     323     352 ..     302     353 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.6e-06
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  22 selArrtglpkStvhRlLqtLvelGyveqd 51 
                                        e+A+r+ l+  tv R+L  L  +G +e+ 
  gi|336253703|ref|YP_004596810.1| 323 EEIAERSSLTAGTVKRFLYELADRGVIERV 352
                                       59*************************997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     9e-06     0.013      21      51 ..     323     353 ..     308     356 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9e-06
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  21 seLakklgvskstvtrvldrLekkGlieRsk 51 
                                        e+a++++++ +tv r+l +L ++G ieR +
  gi|336253703|ref|YP_004596810.1| 323 EEIAERSSLTAGTVKRFLYELADRGVIERVP 353
                                       49***************************86 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.12   1.7e+02      15      28 ..     124     137 ..     115     140 .. 0.91
   2 ?   -1.4   0.0       1.7   2.5e+03       9      23 ..     141     155 ..     136     165 .. 0.74
   3 !   12.6   0.5   7.8e-05      0.12      10      59 ..     297     353 ..     278     353 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.12
                           DprA_WH  15 rrvLaaLgpePvhv 28 
                                       r+vLa +++ePv++
  gi|336253703|ref|YP_004596810.1| 124 RTVLAEISAEPVPE 137
                                       89**********86 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
                           DprA_WH   9 plddlerrvLaaLgp 23 
                                       ++ddl++rv ++L+ 
  gi|336253703|ref|YP_004596810.1| 141 GTDDLRDRVRERLER 155
                                       679999999999964 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 7.8e-05
                           DprA_WH  10 lddlerrvLaaL.......gpePvhvDqLvrrtglpaaevsaaLleLELaGlverlp 59 
                                       l+++++rvLa+L        p     +++++r+ l+a++v + L eL   G +er p
  gi|336253703|ref|YP_004596810.1| 297 LAETRQRVLAHLisidsrdRPIRDVAEEIAERSSLTAGTVKRFLYELADRGVIERVP 353
                                       5899********99998666666699*********************8888888876 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 ?   13.9   0.0     2e-05      0.03      22      48 .]     324     350 ..     321     350 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                            HTH_24  22 eLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       e+Aer+ l+ +tv+r l +L + G+I+
  gi|336253703|ref|YP_004596810.1| 324 EIAERSSLTAGTVKRFLYELADRGVIE 350
                                       9*************************7 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.3e-05     0.035       4      50 ..     303     354 ..     300     359 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHH....S----..HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE-- CS
                              FaeA   4 eIleylnsi...kapck..TreiAdalglsaYQaRyYLeqLekegkikrspv 50 
                                        +l +l+si     p +    eiA+  +l+a  ++ +L  L   g i+r+p+
  gi|336253703|ref|YP_004596810.1| 303 RVLAHLISIdsrDRPIRdvAEEIAERSSLTAGTVKRFLYELADRGVIERVPL 354
                                       689999999887677774468******************************8 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     4e-05     0.059      25      56 ..     322     353 ..     319     364 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
                                       HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB  25 adeiaeelgvprskvYevLrsLedkGlVerek 56 
                                       a+eiae++ +   +v + L +L d+G++er++
  gi|336253703|ref|YP_004596810.1| 322 AEEIAERSSLTAGTVKRFLYELADRGVIERVP 353
                                       89***************************986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.1   1.6e+03       3      27 ..     153     181 ..     152     183 .. 0.72
   2 ?   14.0   0.6   2.3e-05     0.035       9      55 ..     303     353 ..     296     364 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                                       --HHHHHHHHHHHCTTTS.....EEEHHHH CS
                            MarR_2   3 ltpaqarvLaaLgrrpgr.....dltvgel 27 
                                       l++ ++r+  a+ +++++     d +++el
  gi|336253703|ref|YP_004596810.1| 153 LERRDRRAVVAIDHHDEPealayD-RATEL 181
                                       567889999999999998655554.55555 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHCTTTS.....EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2   9 rvLaaLgrrpgr.....dltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       rvLa+L   + r     d  + e+a+r  l+ ++v r l +L ++G +er+p
  gi|336253703|ref|YP_004596810.1| 303 RVLAHLISIDSRdrpirD-VAEEIAERSSLTAGTVKRFLYELADRGVIERVP 353
                                       677777777777666744.99*****************************95 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.18       5      53 ..      61     110 ..      58     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                       EEEESTTTSSHHHHHHHHHHHSTTTE..E.E--EEESS---TTS-TTTSEEE CS
                     Guanylate_kin   5 vvlvgpsgaGksslkkaLlselpekf..g.vsvshtTrdprkgevdGkdYyF 53 
                                       v +vgp gaG+s +  aL++ l+++   g  ++  tTr+ ++    G  + +
  gi|336253703|ref|YP_004596810.1|  61 VAVVGPAGAGTSAVVTALFDALNDSVdtGnRPIGTTTRAGSA--DLGTRFVY 110
                                       679******************9998765579*******9887..34555555 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 ?    7.5   0.7    0.0029       4.4      25      52 ..     182     210 ..     160     236 .. 0.81
   2 ?    2.6   0.0     0.098   1.5e+02      14      34 ..     306     327 ..     295     331 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0029
                              TmoB  25 mdqVaekvahhavGrrvrpkp.gaplrVr 52 
                                       ++ Vae va  avG  v+++  g+++rV 
  gi|336253703|ref|YP_004596810.1| 182 LEPVAESVATVAVGQHVPEDWsGRVVRVP 210
                                       678***************77669999985 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.098
                              TmoB  14 vqLvaVdted.tmdqVaekvah 34 
                                       ++L+ +d  d +++ Vae +a 
  gi|336253703|ref|YP_004596810.1| 306 AHLISIDSRDrPIRDVAEEIAE 327
                                       799****86648*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2830.98
//
Query:       gi|336253704|ref|YP_004596811.1|  [L=689]
Description: hypothetical protein Halxa_2307 [Halopiger xanaduensis SH-6]
Scores for 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  (689 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); 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: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 5054.04
//
Query:       gi|336253705|ref|YP_004596812.1|  [L=44]
Description: hypothetical protein Halxa_2308 [Halopiger xanaduensis SH-6]
Scores for 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  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 356.33
//
Query:       gi|336253706|ref|YP_004596813.1|  [L=168]
Description: membrane-bound metal-dependent hydrolase [Halopiger xanaduensis SH-6]
Scores for 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   39.1  10.0    7.9e-10   38.3  10.0    1.4  1  YdjM             LexA-binding, inner membrane-associated puta
  ------ inclusion threshold ------
      0.013   15.3   1.1      0.013   15.3   1.1    2.2  3  Rick_17kDa_Anti  Glycine zipper 2TM domain
      0.044   13.9   0.1      0.044   13.9   0.1    2.9  3  DUF4229          Protein of unknown function (DUF4229)


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3  10.0   1.3e-13   7.9e-10       3     164 ..       4     154 ..       1     162 [. 0.77

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.3e-13
                              YdjM   3 gltHallGaalglalaallgaakeavllavavlgAllPDiD.....hpsstlgrklgllskklaklvgHRgftHSll 74 
                                        l+H+l + a++ ++ ++l   ++ + +ava++gAllPD+      ++ +tl   lg  ++            H+l 
  gi|336253706|ref|YP_004596813.1|   4 LLSHVLAAYAIFTVASWRLEWLTK-RWVAVAMIGALLPDLNriglfVTDATLEAVLGVPFS--------VDGIHTLG 71 
                                       459***********9999987665.****************87777666666666666555........3789**** PP

                              YdjM  75 flallalvlllllrlfgrsalrlgll.lllgvlsHlllDlltk....yGvpllwPfskkkvrlsllfiiidplltll 146
                                       ++++la v++++l + +r+    +++ ll g+lsHll+D +      +   +l+Pf+ ++   ++l i  dp     
  gi|336253706|ref|YP_004596813.1|  72 GALVLAGVGSMVLTSQHRR----AFGtLLGGALSHLLIDGVKAyadgAAGAWLYPFTWYRPPTPSLYISSDP----- 139
                                       *****99999999999999....66735566***********977554559*****9777777777777777..... PP

                              YdjM 147 srrglvalelvllvlylv 164
                                          +lv +++v+++l+l+
  gi|336253706|ref|YP_004596813.1| 140 --ATLV-VTAVAAGLVLL 154
                                       ..3334.66666666555 PP

>> Rick_17kDa_Anti  Glycine zipper 2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3      0.87   5.2e+03       5       7 ..      35      37 ..      31      39 .. 0.42
   2 ?   15.3   1.1   2.2e-06     0.013       3      33 ..      69     100 ..      67     104 .. 0.94
   3 ?   -4.9   1.6         3   1.8e+04      32      34 ..     115     117 ..     114     118 .. 0.27

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.87
                   Rick_17kDa_Anti  5 iGA 7 
                                      iGA
  gi|336253706|ref|YP_004596813.1| 35 IGA 37
                                      222 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.2e-06
                   Rick_17kDa_Anti   3 aliGAaaGgvaGaai.gggggrvlGavvGAaa 33 
                                       +l+GA++ + +G+ +  + + r+ G+++G+a+
  gi|336253706|ref|YP_004596813.1|  69 TLGGALVLAGVGSMVlTSQHRRAFGTLLGGAL 100
                                       89**************999***********97 PP

  == domain 3  score: -4.9 bits;  conditional E-value: 3
                   Rick_17kDa_Anti  32 aaG 34 
                                       aaG
  gi|336253706|ref|YP_004596813.1| 115 AAG 117
                                       333 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   1.3      0.48   2.9e+03      19      39 ..      17      37 ..       5      39 .. 0.45
   2 ?   13.9   0.1   7.3e-06     0.044       7      57 ..      44      92 ..      41     107 .. 0.85
   3 ?    0.1   0.1      0.14   8.6e+02      31      41 ..     142     152 ..     134     162 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.48
                           DUF4229 19 llvarliglpvpllvaallAl 39
                                      ++ +rl +l+ +++ +a++++
  gi|336253706|ref|YP_004596813.1| 17 VASWRLEWLTKRWVAVAMIGA 37
                                      223344444445555554444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.3e-06
                           DUF4229  7 RlaLfvvltavillvarliglp..vpllvaallAlvvalplSmvllkklRdra 57
                                      R++Lfv  + + ++++    +p  v  +  +  Alv+a++ Smvl ++ R+++
  gi|336253706|ref|YP_004596813.1| 44 RIGLFVTDATLEAVLG----VPfsVDGIHTLGGALVLAGVGSMVLTSQHRRAF 92
                                      8888888888777777....444488999999******************987 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.14
                           DUF4229  31 llvaallAlvv 41 
                                       l+v a+ A +v
  gi|336253706|ref|YP_004596813.1| 142 LVVTAVAAGLV 152
                                       44444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1268.96
//
Query:       gi|336253707|ref|YP_004596814.1|  [L=183]
Description: OB-fold tRNA/helicase-type nucleic acid binding protein [Halopiger xanaduensis SH-6]
Scores for 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   12.5   0.1       0.18   11.8   0.1    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding 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 ?   11.8   0.1     1e-05      0.18       1      61 [.      52     107 ..      52     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1e-05
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEEC CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrr 61 
                                       V + G+v+s+   +++++i+i ++D  + + + l     + + + +++G vv+v+G ++++
  gi|336253707|ref|YP_004596814.1|  52 VLLFGEVQSV--DGESNAITIHVTDSADDVAAELEI---RGFEKPVEPGGVVQVYGVLEAD 107
                                       5678******..****************99999999...9999*************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1353.93
//
Query:       gi|336253708|ref|YP_004596815.1|  [L=163]
Description: sugar metabolism cluster protein [Halopiger xanaduensis SH-6]
Scores for 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-06   27.6   0.2    5.3e-06   27.1   0.2    1.3  1  VanZ      VanZ like family
  ------ inclusion threshold ------
       0.15   11.9   2.3       0.54   10.2   0.1    2.6  3  DUF1072   Protein of unknown function (DUF1072)


Domain annotation for each model (and alignments):
>> VanZ  VanZ like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.2   5.9e-10   5.3e-06      64     122 ..      80     143 ..      47     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 5.9e-10
                              VanZ  64 plGfllplllkkk..flk...vlllgfllslsiElhQlfvpgRsfdvdDvilntlGallGilly 122
                                        lG+   l+ +++  ++k   v++l+  + ++ E+ Qlf p R++ v+D  +n lGal++++ y
  gi|336253708|ref|YP_004596815.1|  80 ALGLAYALADRESgiIRKallVIILATTYGVLMEIGQLFRPERTATVTDGTVNALGALTALCWY 143
                                       366666666655585333677999999*******************************988665 PP

>> DUF1072  Protein of unknown function (DUF1072)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1     6e-05      0.54      20      37 ..      18      35 ..      14      37 .. 0.85
   2 ?   -3.5   0.0       1.1     1e+04      11      15 ..     103     107 ..     101     109 .. 0.79
   3 ?    0.4   0.0     0.068   6.1e+02      18      29 ..     132     142 ..     124     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6e-05
                           DUF1072 20 igavagcCvGCisatpns 37
                                      +g+++g+C +++  tp++
  gi|336253708|ref|YP_004596815.1| 18 VGIAVGICYWSLVTTPPT 35
                                      9***********999765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.1
                           DUF1072  11 vLalT 15 
                                       +La+T
  gi|336253708|ref|YP_004596815.1| 103 ILATT 107
                                       89998 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.068
                           DUF1072  18 agigavagcCvG 29 
                                        ++ga   +C +
  gi|336253708|ref|YP_004596815.1| 132 NALGALTALC-W 142
                                       4699999999.6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1230.89
//
Query:       gi|336253709|ref|YP_004596816.1|  [L=425]
Description: polysaccharide deacetylase [Halopiger xanaduensis SH-6]
Scores for complete 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-22   79.9   0.0    2.5e-22   79.1   0.0    1.3  1  Polysacc_deac_1  Polysaccharide deacetylase


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 !   79.1   0.0   1.4e-26   2.5e-22       7     119 ..     216     334 ..     211     337 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 1.4e-26
                                       TEEEEEEEESSCSCHHHHHHHHHHCT--EEEEE-HHHHCH-.....HHHHHHHHHTTEEEEE--SS--EGGGSHHHH CS
                   Polysacc_deac_1   7 ksvalTfDdgprdntteilpvLkkykvkatffvigglvedy.....pdevremaasGveignHtinhsnlkrlseee 78 
                                        +v++ fDdg+ + +te+lp+L++y+ +a  fv+++ ++++      d++ e+ ++G+ ignHt +h +l +l  +e
  gi|336253709|ref|YP_004596816.1| 216 GAVMIQFDDGSATDYTEALPILEDYGYPAATFVNSESIDSGeqwltTDQLYELDDAGWCIGNHTRSHGRLPELNIAE 292
                                       689**********************************9999999999****************************** PP

                                       HHHHHHHHHHHHHHH.HS----EEE-GGGEE-HHHHHHHHHT CS
                   Polysacc_deac_1  79 vrreierakdalrka.lgreprlfryPygsasatvlevarel 119
                                       +++ei + k+ l +  +++ + +f+yPyg+++at+le + e+
  gi|336253709|ref|YP_004596816.1| 293 QAAEIREGKQWLVERgFEDGAEYFAYPYGRYDATTLELVDEH 334
                                       *************995666*****************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2900.38
//
Query:       gi|336253710|ref|YP_004596817.1|  [L=133]
Description: PilT protein domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-08   35.1   2.1    1.9e-08   34.8   2.1    1.0  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 !   34.8   2.1   1.1e-12   1.9e-08       2     118 ..       2     119 ..       1     123 [. 0.82

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.1e-12
                                       EE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEE.BCHH CS
                               PIN   2 vlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilp.idae 76 
                                       ++ T +lial+ ++   ++a  ++lee ++++ts+l++aE+l     r+  +++ ++ ++   ll+ + i+p   ++
  gi|336253710|ref|YP_004596817.1|   2 YVGTDFLIALVkDDYWLQDAEIRALEEHDDIHTSILAYAEVLVLFYDREAAEYEIDAPRAITNLLELVPIVPeEHED 78 
                                       6778899999977777888888899988**************9999956666666666666666********77788 PP

                                       HHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                               PIN  77 iaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrr 118
                                       +++ aa++ ++y+l+p+Dal+a +    + +++ +   d + 
  gi|336253710|ref|YP_004596817.1|  79 AVLAAAAFLDEYDLTPFDALHAGLVTTGKERVL-STEQDYDA 119
                                       88999999***************9999999988.76666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 998.88
//
Query:       gi|336253711|ref|YP_004596818.1|  [L=88]
Description: hypothetical protein Halxa_2314 [Halopiger xanaduensis SH-6]
Scores for 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   13.8   0.1      0.036   13.6   0.1    1.1  1  SQS_PSY   Squalene/phytoene synthase


Domain annotation for each model (and alignments):
>> SQS_PSY  Squalene/phytoene synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     2e-06     0.036     166     221 ..       7      73 ..       3      84 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-06
                                       HHTT..S-HHHHHHHT--HHHHHHT-.........-SHH.HHHHHHHHH..HHHHHHHHHHHHTGGG CS
                           SQS_PSY 166 ergrvyLPadvlkefgvseedllrkg........vrsae.lrallrrla..erArelldearellkq 221
                                       ergr+yLP+dv ++fg++   + + +        +++ + lra++ +    ++A el  +are + q
  gi|336253711|ref|YP_004596818.1|   7 ERGRIYLPKDVRERFGDQYRIVELPShvalfpvdEDPLDgLRAAVGDAFteTEADELKSDAREAISQ 73 
                                       79***************98877665588888777666666777776554113456666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 702.71
//
Query:       gi|336253712|ref|YP_004596819.1|  [L=335]
Description: aryl-alcohol dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-69  232.3   0.0    8.1e-69  232.0   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family


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 !  232.0   0.0   4.5e-73   8.1e-69       1     287 [.      15     317 ..      15     322 .. 0.94

  Alignments for each domain:
  == domain 1  score: 232.0 bits;  conditional E-value: 4.5e-73
                                       .EEEE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE.-- CS
                      Aldo_ket_red   1 elglGtwqlgsk....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv.dl 72 
                                       +l++Gtw++g +     e+ +eea ell+++ e+G nf+DtA+ Yg+g se+++Ge+l++   +re+++ia+K+ + 
  gi|336253712|ref|YP_004596819.1|  15 PLCFGTWRFGKEqdgvVETGREEAHELLDAFAERGGNFIDTANGYGNGDSEQWIGEWLAD--RDREDFVIASKCyWS 89 
                                       69********99*9999999****************************************..************444 PP

                                       SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH CS
                      Aldo_ket_red  73 rdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka 149
                                         +  +++ls++n+r+++e sl+rLgtdy+D+l+lHr d ++p ie +l+++++lv+eGk+ ++G+S  ++++l k 
  gi|336253712|ref|YP_004596819.1|  90 TVSRFQENLSRKNVRAEVEGSLERLGTDYLDILYLHRFDDETP-IETTLRTIDDLVSEGKVHYVGISTCDAWKLTKG 165
                                       56789**************************************.**************************7777766 PP

                                       ....HHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------... CS
                      Aldo_ket_red 150 ....kkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd... 219
                                              ++  +++ q  ++    ++ +++le+c+++++++ +yspl+gG+ltgky++ +d   +  +++ +r    
  gi|336253712|ref|YP_004596819.1| 166 lwkaDVNNYEAFSVTQPLFHAAYYEDVTEYLEVCADQNLAVCPYSPLAGGFLTGKYERVGDGTYDLDAPEGTRAels 242
                                       57767778888***********9***********************************9999999999988888999 PP

                                       ......TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTS.TT-SEEEE--SSHHHHHHHHGGGG----HHHHH CS
                      Aldo_ket_red 220 ......ertsknldaaeelselakehgvslaqlalryalsq.pavgivipgasnieqlednldalelklseeeva 287
                                                ++  + +++++++a e + ++aq+alr+++ q ++  ++i+ga++++ql++nl+a+++ l++e+++
  gi|336253712|ref|YP_004596819.1| 243 drftdfYVSERGWHVLDAVRDVADEVNATPAQVALRWLMDQpDFDCVPIIGARTVDQLDENLGAVDISLTDEQFD 317
                                       999*9988889999***************************778899**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2779.97
//
Query:       gi|336253713|ref|YP_004596820.1|  [L=42]
Description: hypothetical protein Halxa_2316 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0031   17.6   0.5     0.0034   17.5   0.5    1.2  1  Sigma70_r3  Sigma-70 region 3
     0.0076   16.2   0.3     0.0085   16.0   0.3    1.1  1  HTH_15      Helix-turn-helix domain of alkylmercury lyase
  ------ inclusion threshold ------
       0.13   12.7   0.0       0.16   12.4   0.0    1.1  1  HTH_26      Cro/C1-type HTH DNA-binding domain


Domain annotation for each model (and alignments):
>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   5.7e-07    0.0034      18      39 ..       4      25 ..       1      34 [. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.7e-07
                                      SSXXXHHHHHHHHTXXHHHHHH CS
                        Sigma70_r3 18 grePtpeEiAeeLglseekVre 39
                                      +  Pt+eE+Ae++g see++r+
  gi|336253713|ref|YP_004596820.1|  4 DEIPTVEELAEATGQSEEQLRR 25
                                      678*****************97 PP

>> HTH_15  Helix-turn-helix domain of alkylmercury lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   1.4e-06    0.0085      37      65 ..       8      36 ..       4      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                            HTH_15 37 tveeLAaatgrsveevrqaLaalpstEyd 65
                                      tveeLA+atg+s e+ r+  +al+ +  +
  gi|336253713|ref|YP_004596820.1|  8 TVEELAEATGQSEEQLRRDQEALSRVAPE 36
                                      8****************999998877554 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 ?   12.4   0.0   2.7e-05      0.16       6      29 ..       1      25 [.       1      26 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                            HTH_26  6 madrgi.tkseLargtgisaatlsr 29
                                      ma  +i t+ eLa++tg s+ +l r
  gi|336253713|ref|YP_004596820.1|  1 MAMDEIpTVEELAEATGQSEEQLRR 25
                                      7888999***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 331.87
//
Query:       gi|336253714|ref|YP_004596821.1|  [L=40]
Description: hypothetical protein Halxa_2317 [Halopiger xanaduensis SH-6]
Scores for 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:                       160  (0.00892409); expected 358.6 (0.02)
Passed bias filter:                      127  (0.0070835); 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: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 308.90
//
Query:       gi|336253715|ref|YP_004596822.1|  [L=178]
Description: hypothetical protein Halxa_2318 [Halopiger xanaduensis SH-6]
Scores for 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   15.7   0.2      0.019   15.2   0.2    1.3  1  CBM_4_9   Carbohydrate binding domain


Domain annotation for each model (and alignments):
>> CBM_4_9  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.2   1.1e-06     0.019       2      71 ..      81     146 ..      80     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-06
                                       BCCCECTSTTSTTTTSEECSSTCEEEEECGCSSSSEEEEEESCSSTTCEEEEEEECCS-TT-EEEEEEEE CS
                           CBM_4_9   2 nllkngtFedgglegWkargkssgkasvdvsyngtyslkvsgrgetwdgqaiditirlekgktYtvsfwv 71 
                                       n  +  +Fed+ ++gW+  ++   +as+d+   g+ysl+v ++++  + +  +++  ++ g + ++s ++
  gi|336253715|ref|YP_004596822.1|  81 NASYYDDFEDRSVDGWTDHEDI--SASTDSF-YGNYSLQVVNGTA-ETEARWNDGPEFDLGDNFEISGTI 146
                                       556789**************95..9999999.***********99.333333444555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); 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: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1441.15
//
Query:       gi|336253716|ref|YP_004596823.1|  [L=142]
Description: hypothetical protein Halxa_2319 [Halopiger xanaduensis SH-6]
Scores for 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:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1063.93
//
Query:       gi|336253717|ref|YP_004596824.1|  [L=274]
Description: family 2 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for 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-24   84.7   0.2    9.1e-24   84.2   0.2    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    5.3e-18   65.8   0.2    1.1e-17   64.8   0.2    1.4  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.6e-09   37.0   0.0    3.2e-09   36.7   0.0    1.1  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    0.00034   20.6   0.3     0.0016   18.4   0.3    1.9  1  Glyco_trans_2_3  Glycosyl transferase family group 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 !   84.2   0.2     2e-27   9.1e-24       1     160 [.       7     166 ..       7     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 2e-27
                                       EEEEEESS-..TTTHHHHHHHHHHHGGCCEEEEEEEEES-.SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHH CS
                   Glycos_transf_2   1 svviptyNe..ektlletlesllaqdpypdfeiivvDDgS.tDetveileelak.edprvrvirreenvGkagalna 73 
                                       sv i++y +  ++ l+ +l s+++q +   +e+++v Dg  tD+++++++++++ +++ vr +++e n+G+++al +
  gi|336253717|ref|YP_004596824.1|   7 SVLICVYERddSDHLRLALQSVIDQ-TVVPDELVLVADGPlTDSLRSVIDDFRSeYPDIVRMVQLETNQGLGAALQT 82 
                                       89***********************.****************************899999***************** PP

                                       HHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEE.CCCCCCCHC-SSEEEECCHCCCCHCCCCC CS
                   Glycos_transf_2  74 glraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprif.getdeiernkrvgenerlyfkerkrslkg 149
                                       g++++++++++ +DaDd+   d++e+ +e+l  +++  v+g+    f +++ ei++ ++     +l   e + +   
  gi|336253717|ref|YP_004596824.1|  83 GVEECKHNIVARMDADDVAVNDRFERQLEYLSSNPDVDVVGGYIGEFqDDPEEINQVRE----VPLESDEVESFSRF 155
                                       *********************************86655555555555055555555543....44444444555555 PP

                                       CSTTCSTCCCE CS
                   Glycos_transf_2 150 nlsfeigsaal 160
                                         + ++++ + 
  gi|336253717|ref|YP_004596824.1| 156 RCPTNHPTVMF 166
                                       55555555555 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 !   64.8   0.2   2.4e-21   1.1e-17       1     216 [.       4     214 ..       4     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 2.4e-21
                   Glyco_tranf_2_3   1 prdlavlVptfneed..vlgevlesllaqeyprvevvvvvde.sdaetlevaeelaaalpdvrvrvvvnarnlgstg 74 
                                       p  ++vl+++++++d   l+  l s++ q+  ++e+v+v+d+  +++ ++v++ +  ++pd+ vr v+ + n g   
  gi|336253717|ref|YP_004596824.1|   4 PA-FSVLICVYERDDsdHLRLALQSVIDQTVVPDELVLVADGpLTDSLRSVIDDFRSEYPDI-VRMVQLETNQGL-- 76 
                                       56.9**********99888889*******9999999999966599999*************8.****99888775.. PP

                   Glyco_tranf_2_3  75 ksralnealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpv.fllnrstlvsalgalefaerhl.rf 148
                                          al+ +++ +k+ +v+ +D+D+v   d ++r+l ++   p+v++vg+   +++ +   ++++  + ++ +   +f
  gi|336253717|ref|YP_004596824.1|  77 -GAALQTGVEECKHNIVARMDADDVAVNDRFERQLEYLsSNPDVDVVGGYIgEFQDDPEEINQVREVPLESDEVeSF 152
                                       .44678********************************9999******88889999999999998888777777233 PP

                   Glyco_tranf_2_3 149 laarralgvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpss 216
                                       +++r     +t n  ++++rre + e +  +       Dyel++r+ ++g+++  +p+++vr+  +++
  gi|336253717|ref|YP_004596824.1| 153 SRFR----CPT-NHPTVMFRRESVLEAGSYQS-LRSQQDYELWMRMLSQGYKIENLPEVLVRCRAGED 214
                                       3333....333.33469999999999976666.7789*************************987766 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 !   36.7   0.0   7.1e-13   3.2e-09       1     219 [.       7     211 ..       7     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 7.1e-13
                   Glyco_tranf_2_2   1 svviplraseerhyieerv...lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarN 74 
                                       sv+i+++  ++  +++  +     ++    ++  ++v d+  ++ + +++  +      +    + ++  +l+aa  
  gi|336253717|ref|YP_004596824.1|   7 SVLICVYERDDSDHLRLALqsvIDQTVV--PDELVLVADGPLTDSLRSVIDDFRSEYPDIVRMVQLETNQGLGAALQ 81 
                                       7999999999998877665222444444..5555666777789999999999999988886555558899******* PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledll 151
                                        G+++++ ++v  +DaD+    D+fe++l+      l+ n+d  vv  ++   ++d e + +v ++  +s+   + +
  gi|336253717|ref|YP_004596824.1|  82 TGVEECKHNIVARMDADDVAVNDRFERQLE-----YLSSNPDVDVVGGYIGEFQDDPEEINQVREVPLESDEV-ESF 152
                                       ******************************.....9*******************************999988.445 PP

                   Glyco_tranf_2_2 152 aakstlvkffapss.ssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykara 219
                                              +f  p    +++ +r+ +le G y  ++   ++ D++l +R++ +  ++e+ p  l  + ra
  gi|336253717|ref|YP_004596824.1| 153 S------RFRCPTNhPTVMFRRESVLEAGSYQ-SL--RSQQDYELWMRMLSQGYKIENLPEVLV-RCRA 211
                                       5......8999988678888999999999885.78..799**********99999988887776.5555 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 !   18.4   0.3   3.6e-07    0.0016       2     130 ..      92     215 ..      91     258 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.6e-07
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelas.pevaivqgpvl.vmnvanwleelaalff.aedhgkdilvrealgrvvpsvGs 75 
                                       ++ +DaD+v   d +++ ++ l+s p+v++v g ++ ++   + + ++  +   ++ + ++ ++r+      p    
  gi|336253717|ref|YP_004596824.1|  92 VARMDADDVAVNDRFERQLEYLSSnPDVDVVGGYIGeFQDDPEEINQVREVPLeSDEVESFSRFRC------PTNHP 162
                                       667999999999999999999995599999999999444444333333333333444444444443......33333 PP

                   Glyco_trans_2_3  76 gaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltl 130
                                        +++rr+ + e+g ++  +     D+++++r++++Gy++   pe+lv++    +l
  gi|336253717|ref|YP_004596824.1| 163 TVMFRRESVLEAGSYQ--SLRSQQDYELWMRMLSQGYKIENLPEVLVRCRAGEDL 215
                                       5789*********999..778899*********************9998877744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2135.40
//
Query:       gi|336253718|ref|YP_004596825.1|  [L=383]
Description: hypothetical protein Halxa_2322 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0022   17.9   1.0       0.76    9.8   0.1    3.7  4  PD40      WD40-like Beta Propeller Repeat


Domain annotation for each model (and alignments):
>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.35   6.4e+03      16      21 ..     128     133 ..     127     133 .. 0.81
   2 ?   -0.5   0.0     0.073   1.3e+03      25      33 ..     230     237 ..     229     238 .. 0.86
   3 !    3.8   0.0    0.0032        57      11      24 ..     292     305 ..     287     305 .. 0.87
   4 !    9.8   0.1   4.2e-05      0.76      14      29 ..     350     365 ..     347     373 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.35
                                       E-TTSS CS
                              PD40  16 fSPDGk 21 
                                       + PDGk
  gi|336253718|ref|YP_004596825.1| 128 VHPDGK 133
                                       68***8 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.073
                                       EEEECT.TC CS
                              PD40  25 FsSdRgsGk 33 
                                       ++SdR+ G+
  gi|336253718|ref|YP_004596825.1| 230 YVSDRD-GN 237
                                       99***9.97 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.0032
                                       EEEEEE-TTSSEEE CS
                              PD40  11 egaPsfSPDGkrla 24 
                                       +g Ps+SP+ ++++
  gi|336253718|ref|YP_004596825.1| 292 DGHPSLSPNRRYII 305
                                       889********996 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 4.2e-05
                                       EEE-TTSSEEEEEEEC CS
                              PD40  14 PsfSPDGkrlaFsSdR 29 
                                       P++SPDG+ + F S+ 
  gi|336253718|ref|YP_004596825.1| 350 PRWSPDGTAISFDSTH 365
                                       9******988666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2944.66
//
Query:       gi|336253719|ref|YP_004596826.1|  [L=373]
Description: group 1 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for complete 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-17   64.2   0.0    2.9e-17   63.4   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    6.6e-16   58.3   0.0      1e-15   57.7   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    4.1e-15   56.2   0.0    6.4e-15   55.6   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    4.3e-06   27.3   0.0    6.6e-06   26.7   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0079   16.2   0.0      0.016   15.3   0.0    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.096   13.1   0.0       0.19   12.2   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> 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 !   63.4   0.0   9.7e-21   2.9e-17       3     130 ..     199     329 ..     197     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 9.7e-21
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHTT-T.TEEEE---THHHHHHHH-SEEEE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaagleerveftGfvedlaellaaadvfva 78 
                                       +++ +G+l   +k+   +++ +++   +d +l++  dgp + e++e+laag ++r+++ G+v+++ e+l a+d fv 
  gi|336253719|ref|YP_004596826.1| 199 IFVSIGSLI-SRKNPTDVIKGFQRADLEDSTLLMLSDGPlK-EKCERLAAG-DDRIRIEGWVDNVLEYLGASDYFVS 272
                                       678999995.55**********99998889*********55.699977776.699*******99************* PP

                                       --..---SHHHHHHHHTT-EEEE-TGGGTTT--...TTSSEE--TT-HHHHHHHHHH CS
                   Glyco_trans_1_4  79 Ps..egfglkllEamaaglpvVatdvggiaevv...gengllvppgdpealaeailr 130
                                        s  eg++++++Ea+a+glpvV +d++  +e++    + g+ ++ gd+ +l e i +
  gi|336253719|ref|YP_004596826.1| 273 ASssEGLPNTVMEALAVGLPVVLSDIQPHREILqynSNVGMTFDLGDVVSLSESINA 329
                                       **999*********************8679999875467999999999999998876 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   3.4e-19     1e-15       4     157 ..     186     332 ..     183     345 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 3.4e-19
                                       HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEEC CS
                   Glycos_transf_1   4 kkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflge 80 
                                       + r+ l++ e   i++s+g l  +K+++ +ik f++   +l++ + l +   g+ +++ ++la+     d++++ g 
  gi|336253719|ref|YP_004596826.1| 186 QLRRNLNISESATIFVSIGSLISRKNPTDVIKGFQRA--DLEDSTLLMLSD-GPLKEKCERLAA---GDDRIRIEGW 256
                                       678899999**************************75..457777777777.899888888843...4599****** PP

                                       CHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT.SEEEE-TT-HHHHHHHHHHHH CS
                   Glycos_transf_1  81 vsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdge.tGllvkpnnaealaeairkll 156
                                       v+  ++ e+l ++d fv  s sEg++ +++EA+a+glpv+ s++++ +e+++ +   G  ++ +++ +l+e i+ + 
  gi|336253719|ref|YP_004596826.1| 257 VD--NVLEYLGASDYFVSASSSEGLPNTVMEALAVGLPVVLSDIQPHREILQYNSnVGMTFDLGDVVSLSESINAVC 331
                                       *9..***********************************************99987899999999999999998876 PP

                                       H CS
                   Glycos_transf_1 157 e 157
                                       +
  gi|336253719|ref|YP_004596826.1| 332 D 332
                                       5 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   2.1e-18   6.4e-15      10     169 ..      23     174 ..      19     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 2.1e-18
                    Glyco_transf_4  10 eLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalga 86 
                                       +  ++L ++ ++  ++t +++++  e ++  + ++ + +++l r++  l  +++lr+++ +++pD+vH+h+  a  +
  gi|336253719|ref|YP_004596826.1|  23 YTLQHLDDD-FNANILTLSPEPEDTELPRFQKLGIDYETLGLSRWKGLLYGPKQLREIIAKHDPDIVHTHGIRADTL 98 
                                       555666666.66777777777766666456666667778899999999999*********************99988 PP

                    Glyco_transf_4  87 allalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekitVip 163
                                       ++l +   +  p ++t+H+  ++ +  ++   + ++      ++++r d+ ia+Se++ad +++ +g+++   t i 
  gi|336253719|ref|YP_004596826.1|  99 SALFI---SEYPRITTIHNYPYDDYPAKFGTIQGNVMAVEHTQMIQRIDHPIACSETIADMMQS-HGIDA---TPIQ 168
                                       86644...59***********85555555556666666666677********************.****8...999* PP

                    Glyco_transf_4 164 nGvDle 169
                                       nGvD+e
  gi|336253719|ref|YP_004596826.1| 169 NGVDTE 174
                                       *****8 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 !   26.7   0.0   2.2e-09   6.6e-06      23     154 ..      36     167 ..      19     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.2e-09
                   Glyco_trans_4_4  23 vltpapapg...apeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvhahsptaglaarlarrrrg 96 
                                       +lt +p p+    p+ +  g+ +  l ++r  +    l  + +lr+++  ++  pd+vh+h++ a  + +l      
  gi|336253719|ref|YP_004596826.1|  36 ILTLSPEPEdteLPRFQKLGIDYETLGLSRWKG---LLYGPKQLREII--AKHDPDIVHTHGIRADTLSALFI--SE 105
                                       566555444222444778888888888887764...4445788*****..************99876555544..48 PP

                   Glyco_trans_4_4  97 iplvvtlhglllrrg....sgavrrlyralerrllrradavlvvseaeaeelralgvpadrv 154
                                        p + t+h+  ++++    ++ ++++++  +  +++r d+ ++ se +a+ ++ +g++a+ +
  gi|336253719|ref|YP_004596826.1| 106 YPRITTIHNYPYDDYpakfGTIQGNVMAVEHTQMIQRIDHPIACSETIADMMQSHGIDATPI 167
                                       9*******977665555677778888888899**************************8775 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 !   15.3   0.0   5.3e-06     0.016      64     107 ..      74     113 ..      29     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.3e-06
                   Glyco_trans_4_2  64 fklkklikkikPDvvhahyakpygllgslaarlsgvipvvlsvw 107
                                       ++l+++i+k  PD+vh+h +    l + l+  +s   p +++++
  gi|336253719|ref|YP_004596826.1|  74 KQLREIIAKHDPDIVHTHGIRADTLSA-LF--ISE-YPRITTIH 113
                                       699****************98766655.43..455.77778888 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 ?   12.2   0.0   6.2e-05      0.19       5      90 ..     273     359 ..     264     361 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.2e-05
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgk.evilfe..dleelaekiryllanpeerraiaeaarervl 78 
                                        s se++   + Ea+a G +++ +d++ ++e+++ +   +++f+  d+ +l e i+++   ++ ++a++  ar  + 
  gi|336253719|ref|YP_004596826.1| 273 ASSSEGLPNTVMEALAVGLPVVLSDIQPHREILQYNSnVGMTFDlgDVVSLSESINAV--CDGSYSARSDSARSLIT 347
                                       5667889999****************99999877664145677677777777777776..68899999999998888 PP

                   Glyco_trans_1_2  79 aehtydhraeql 90 
                                       ++++ +   +q+
  gi|336253719|ref|YP_004596826.1| 348 ENLSSNEMSNQY 359
                                       888877776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 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:                        29  (0.00161749); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2941.28
//
Query:       gi|336253720|ref|YP_004596827.1|  [L=413]
Description: hypothetical protein Halxa_2324 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        2.5    8.5  16.2       0.15   12.3   5.1    3.4  3  Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD


Domain annotation for each model (and alignments):
>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.1   8.6e-06      0.15       7      84 ..      12     144 ..       8     159 .. 0.79
   2 ?    1.9   0.3     0.015   2.6e+02      11      60 ..     183     251 ..     179     277 .. 0.67
   3 ?   -0.4   0.2     0.077   1.4e+03      24      61 ..     353     390 ..     330     404 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.6e-06
                                       --TT----GGGHHHHHHHHCSS......................................................S CS
                     Cytochrom_B_C   7 tPahIaPeWYflpfYaiLraip......................................................a 29 
                                       t +h  P W f  f+ai+  +p                                                      a
  gi|336253720|ref|YP_004596827.1|  12 TEHHTPPAWLFYLFFAIVLFFPilrvaglpvllpmsfsiiflwkpiniprlylisvtsatiyligvtlftvtrkdaA 88 
                                       778999************9998888899999999******************************************5 PP

                                       HHHHHHHH...HHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHT CS
                     Cytochrom_B_C  30 kllGvvam...gaaivilfllpwldrskvksiryrkplakvllallvvsfvvLgylGv 84 
                                        +++vv +   +  ++i++l   l   + k+++yr  l++++++ l ++f+++ +l  
  gi|336253720|ref|YP_004596827.1|  89 GFADVVYIivpISIVLIIALTASLAGANKKQATYR--LTQFAYLYLYFQFIIVLLLYL 144
                                       5666655511155666666667799999*******..555555555555555544443 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.015
                                       ----GGGHHHHHHHHCSS...................SHHHHHHHHHHHHHGGGCHHHH---SSSSSTT CS
                     Cytochrom_B_C  11 IaPeWYflpfYaiLraip...................akllGvvamgaaivilfllpwldrskvksiry 60 
                                       I P W  +++Y   r++                    +  + +++++   +++fl+ ++++++++si+ 
  gi|336253720|ref|YP_004596827.1| 183 INPTWVGFAVYPFARYLTtytgryryvlialtttllsSGRMAMITIFSTEAMIFLITLIQNRDTQSISR 251
                                       788888888888888864444555555555666655566677777777778888888877777777654 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.077
                                       HHCSSSHHHHHHHHHHHHHGGGCHHHH---SSSSSTT- CS
                     Cytochrom_B_C  24 LraipakllGvvamgaaivilfllpwldrskvksiryr 61 
                                       Lr + +  + ++ mg+ i  +++l  l + + +++ + 
  gi|336253720|ref|YP_004596827.1| 353 LRGVRSGDGRLLKMGIVITSVAILSSLTTTTASNMLFI 390
                                       66666666777777777777777777777766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2880.33
//
Query:       gi|336253721|ref|YP_004596828.1|  [L=358]
Description: group 1 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for 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-37  128.3   0.0    3.5e-37  127.6   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    2.5e-30  105.6   0.0    5.2e-30  104.6   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    3.8e-20   72.6   0.0    6.3e-20   71.8   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    3.2e-08   34.2   0.0    5.3e-08   33.5   0.0    1.4  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.6e-07   31.7   0.0    2.9e-07   30.8   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
     0.0007   19.2   0.1     0.0011   18.6   0.1    1.4  1  Glyco_trans_4_5  Glycosyl-transferase family 4
  ------ inclusion threshold ------
      0.015   14.3   0.0      0.024   13.7   0.0    1.4  1  Type_ISP_C       Type ISP C-terminal specificity domain
      0.029   14.2   0.0      0.094   12.5   0.0    1.9  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 
      0.033   13.8   0.2       0.31   10.6   0.0    2.4  3  DUF3732          Protein of unknown function (DUF3732)
       0.13   12.3   0.3       0.31   11.1   0.0    1.8  2  Glyco_trans_4_2  Glycosyl transferase 4-like
       0.19   11.6   0.1         17    5.3   0.0    2.5  2  YjeF_N           YjeF-related protein N-terminus


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 !  127.6   0.0   2.1e-40   3.5e-37      10     170 ..     182     341 ..     176     343 .. 0.97

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 2.1e-40
                                       TTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSH CS
                   Glycos_transf_1  10 gknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredl 86 
                                       +++ + k+il vgr +++K++++li++fa l k+  ++v+l+i G+ge   e+k+la  l+++++v f g+v+  d 
  gi|336253721|ref|YP_004596828.1| 182 EFKRNSKTILGVGRHTPQKDFKTLIRSFAILSKEYSEDVQLIILGKGECTSEYKSLAGRLNIREDVYFPGFVD--DP 256
                                       5678999******************************************************************..** PP

                                       HHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHH CS
                   Glycos_transf_1  87 eellknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnnaealaeairklledeelr 162
                                        ++++nad+f+l+s+ Eg++ vl+EAma+g+pv++++  +gpaev+k+g+ G lv+ +++ea++ a++  le++ ++
  gi|336253721|ref|YP_004596828.1| 257 FQYMSNADVFCLSSRLEGLANVLIEAMACGTPVVSTDcPSGPAEVLKNGKYGKLVPIEDPEAMKSALITTLENPISA 333
                                       ***************************************************************************** PP

                                       HHHHHHHH CS
                   Glycos_transf_1 163 erlgenar 170
                                       e+l+++a+
  gi|336253721|ref|YP_004596828.1| 334 EKLKKRAQ 341
                                       *****997 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 !  104.6   0.0   3.2e-33   5.2e-30       2     134 .]     188     329 ..     187     329 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 3.2e-33
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..H.EEEEEES---...HHHHHHHT..T-T.TEEEE---THHHHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..d.vrlvivGdgp.rpeeleelaa..gleerveftGfvedlaellaa 72 
                                       ++il vGr   ++k ++ l++ ++ l k+  + v+l+i G+g+  + e+++la   +++e+v f Gfv+d  +++++
  gi|336253721|ref|YP_004596828.1| 188 KTILGVGRH-TPQKDFKTLIRSFAILSKEysEdVQLIILGKGEcTS-EYKSLAGrlNIREDVYFPGFVDDPFQYMSN 262
                                       78999****.567**************886526*********9765.888877458999****************** PP

                                       -SEEEE--..---SHHHHHHHHTT-EEEE-TGG.GTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  73 advfvaPs..egfglkllEamaaglpvVatdvg.giaevv..gengllvppgdpealaeailrLled 134
                                       advf++ s  eg+ ++l+Eama+g+pvV+td++ g+aev+  g+ g lvp +dpea+  a+++ le+
  gi|336253721|ref|YP_004596828.1| 263 ADVFCLSSrlEGLANVLIEAMACGTPVVSTDCPsGPAEVLknGKYGKLVPIEDPEAMKSALITTLEN 329
                                       ********999*********************889***99*99*******************99986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.0   3.9e-23   6.3e-20       1     166 [.      14     167 ..      14     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 3.9e-23
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvH 77 
                                       +GG+er++++La++L ++Gh+V+v++ +++g+l +e      +    +++  +  r+l+++  l+++l++ + Dv+ 
  gi|336253721|ref|YP_004596828.1|  14 IGGAERVTVNLANQLSENGHQVEVLVISQQGKLINE------LSPDVRLSVLPVNRMLWSIIPLAKHLRQSQSDVII 84 
                                       7*******************************9999......44444556678899********************9 PP

                    Glyco_transf_4  78 ahspaalgaallalrr.rlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelreryg 153
                                         ++++ ++  l  +   + + +++t H        +++++ l+ ++ +   +l++ ad v+ vSe + ++++++ +
  gi|336253721|ref|YP_004596828.1|  85 PMMAGPNILTILSRKIsLTSPQVIVTEHINR----TNNYHNELHDIFPK---YLYKYADNVVGVSEGVTEHIKDWAK 154
                                       999999999988777799************9....35555555555554...56778******************** PP

                    Glyco_transf_4 154 vppekitVipnGv 166
                                       ++p+k+t+i+n+v
  gi|336253721|ref|YP_004596828.1| 155 IDPDKVTTIYNPV 167
                                       ***********98 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 !   33.5   0.0   3.2e-11   5.3e-08       1     159 [.      15     165 ..      15     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 3.2e-11
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvv 77 
                                       gG++r++ +la +L + Gh+V+vl+ +++++   +  + vr+  lpv       ++l+++  l+  l  r+ + dv+
  gi|336253721|ref|YP_004596828.1|  15 GGAERVTVNLANQLSENGHQVEVLVISQQGKLINELSPDVRLSVLPVN------RMLWSIIPLAKHL--RQSQSDVI 83 
                                       8************************98888888788999********9......4688999999999..99999999 PP

                   Glyco_trans_4_4  78 h..ahspt.aglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelra.lgvp 150
                                       +    +p  + ++ r ++  +++ ++vt h + ++ +      l + + ++l++ ad v+ vse++ e++ +   ++
  gi|336253721|ref|YP_004596828.1|  84 IpmMAGPNiLTILSRKIS-LTSPQVIVTEHINRTNNY---HNELHDIFPKYLYKYADNVVGVSEGVTEHIKDwAKID 156
                                       955555533777788888.89*********7655555...4556677799**********************555** PP

                   Glyco_trans_4_4 151 adrvvvvpn 159
                                       +d+v+++ n
  gi|336253721|ref|YP_004596828.1| 157 PDKVTTIYN 165
                                       *******98 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 !   30.8   0.0   1.8e-10   2.9e-07       5      76 ..     269     343 ..     261     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.8e-10
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltdda.egleelftpgkevilfe..dleelaekiryllanpeerraiaeaarer 76 
                                        sr e++  +l Ea+acG++++++d  +g++e +++gk + l+   d+e +  ++   l+np  ++++ ++a+ +
  gi|336253721|ref|YP_004596828.1| 269 SSRLEGLANVLIEAMACGTPVVSTDCpSGPAEVLKNGKYGKLVPieDPEAMKSALITTLENPISAEKLKKRAQDF 343
                                       46679999****************999***********66555555*************************9976 PP

>> Glyco_trans_4_5  Glycosyl-transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   6.8e-07    0.0011       3      57 ..       3      58 ..       1     108 [. 0.87

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.8e-07
                   Glyco_trans_4_5  3 krvllishelsltGaPlvlmelatlLrsvgaevvvltlskkggllkela.drgikv 57
                                       +v l    ls++Ga +v ++la  L + g +v vl++s++g l++el+ d +  v
  gi|336253721|ref|YP_004596828.1|  3 SKVTLFIGDLSIGGAERVTVNLANQLSENGHQVEVLVISQQGKLINELSpDVRLSV 58
                                      578888899*************************************9973445555 PP

>> Type_ISP_C  Type ISP C-terminal specificity 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     0.024      99     179 ..      76     149 ..      71     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                        Type_ISP_C  99 rprqlpelfphlskenlvivvsgsgsgkgfsvlvtdlipdlhllskrggqvfPlylyeeeesnlaagerkdnitdel 175
                                       r++q + + p +   n++ ++s++ s ++++v+vt++i   + + ++  ++fP yly+ ++       +  ++++ +
  gi|336253721|ref|YP_004596828.1|  76 RQSQSDVIIPMMAGPNILTILSRKISLTSPQVIVTEHINRTNNYHNELHDIFPKYLYKYAD-------NVVGVSEGV 145
                                       567778899999*****************************99999***********9987.......234444444 PP

                        Type_ISP_C 176 laef 179
                                        +++
  gi|336253721|ref|YP_004596828.1| 146 TEHI 149
                                       4444 PP

>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.8e-05     0.094      28      72 ..     300     343 ..     296     346 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.8e-05
                                       EEEETTEEEEEEEEHHHHHHHHH.HHHHHCSHHHHHHHHHHHHHH CS
                   PhdYeFM_antitox  28 iItrrGkpvaVlvsleeyerlqeltekllslplnaerlaesgaev 72 
                                        + ++Gk    lv++e+ e+++ + +  l +p +ae+l + ++++
  gi|336253721|ref|YP_004596828.1| 300 EVLKNGK-YGKLVPIEDPEAMKSALITTLENPISAEKLKKRAQDF 343
                                       6778888.8****************************99977665 PP

>> DUF3732  Protein of unknown function (DUF3732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019      0.31     143     169 ..      94     118 ..      84     133 .. 0.71
   2 ?    0.1   0.0      0.31     5e+02     129     160 ..     196     224 ..     158     227 .. 0.80
   3 ?   -3.2   0.0       3.2   5.2e+03      26      46 ..     334     354 ..     324     357 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                           DUF3732 143 klLaefieelkeklQiIvleHadelvl 169
                                       ++L+  i+ +  ++Q+Iv+eH++ ++ 
  gi|336253721|ref|YP_004596828.1|  94 TILSRKISLT--SPQVIVTEHINRTNN 118
                                       5555555544..57********97743 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.31
                           DUF3732 129 ekedeDikavrklfklLaefieelkeklQiIv 160
                                       ++ ++D k++ + f +L+++ +e    +Q+I+
  gi|336253721|ref|YP_004596828.1| 196 HTPQKDFKTLIRSFAILSKEYSED---VQLII 224
                                       567899999999999999887664...55665 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.2
                           DUF3732  26 eaiseilkkldleesykdsel 46 
                                       e++++ ++++ +ees k++e+
  gi|336253721|ref|YP_004596828.1| 334 EKLKKRAQDFSIEESTKKYEA 354
                                       456667777777777666655 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 ?   11.1   0.0   0.00019      0.31      10     134 ..      18     137 ..       7     142 .. 0.63
   2 ?   -3.6   0.1       6.2     1e+04      70      84 ..     152     166 ..     149     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                   Glyco_trans_4_2  10 svhtlrlakeLakrgyeVhvitp.kkga.kdeleaegihvhrlkvdrkgpleyl..kafklkklikkikPDvvhahy 82 
                                       + +t++la+ L+++g++V+v+   ++g+  +el ++++++  l+      ++ +  +++ l+k +++ + Dv++ + 
  gi|336253721|ref|YP_004596828.1|  18 ERVTVNLANQLSENGHQVEVLVIsQQGKlINEL-SPDVRLSVLP------VNRMlwSIIPLAKHLRQSQSDVIIPMM 87 
                                       557999*************99883444323333.4444444444......444323688999999*******98888 PP

                   Glyco_trans_4_2  83 akpygllgslaarlsgvipvv.lsvwGldvlkfpkksk.lkklllklalkkatk 134
                                       a p ++l  l  ++s  +p v ++ +   + ++++  + l+ +  k+++k a++
  gi|336253721|ref|YP_004596828.1|  88 AGP-NILTILSRKISLTSPQViVTEH---INRTNNYHNeLHDIFPKYLYKYADN 137
                                       777.5666566555555555515555...6444444444666655555555555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.2
                   Glyco_trans_4_2  70 ikkikPDvvhahyak 84 
                                       ++ki PD v ++y +
  gi|336253721|ref|YP_004596828.1| 152 WAKIDPDKVTTIYNP 166
                                       789999999998843 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 ?    3.7   0.0      0.03        49      28      67 ..       4      46 ..       2      92 .. 0.79
   2 ?    5.3   0.0      0.01        17     126     145 ..     279     298 ..     266     330 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.03
                            YjeF_N 28 kvlvlvGsgnnGgd...glaaArhLaqegakVtvllleeeekl 67
                                      kv++++G+   Gg     + +A +L ++g++V+vl+++++ kl
  gi|336253721|ref|YP_004596828.1|  4 KVTLFIGDLSIGGAervTVNLANQLSENGHQVEVLVISQQGKL 46
                                      566666666666643446779*************999887655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.01
                            YjeF_N 126 iewlnsseapvlavDiPSGl 145
                                       + ++ + ++pv++ D+PSG 
  gi|336253721|ref|YP_004596828.1| 279 LIEAMACGTPVVSTDCPSGP 298
                                       444555589**********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2553.77
//
Query:       gi|336253722|ref|YP_004596829.1|  [L=414]
Description: group 1 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for complete 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   96.0   0.0    3.1e-27   95.2   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.7e-21   77.1   0.0    2.7e-21   76.4   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    9.5e-10   38.7   0.2    0.00045   20.3   0.0    2.5  3  Glyco_transf_4   Glycosyltransferase Family 4
    5.1e-06   27.0   0.0    1.1e-05   25.9   0.0    1.6  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    0.00091   19.6   0.0     0.0017   18.7   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1


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 !   95.2   0.0   8.5e-31   3.1e-27      13     159 ..     237     382 ..     228     394 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 8.5e-31
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleel 89 
                                       +++  il+vg l+++Kg d+li+ +++l ++ + +++l iaG+g+ + +l++++++ +lsdn++++g+v++++l+++
  gi|336253722|ref|YP_004596829.1| 237 TEPFNILFVGTLRHRKGTDRLIDIAQKLHREHECKFNLSIAGDGDLRPTLEREIDKEKLSDNITLHGHVPYNQLPTM 313
                                       567779*************************9********************************************* PP

                                       HHCESEEEEEESS.BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH CS
                   Glycos_transf_1  90 lknadifvlpsis.EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede 159
                                       +++ d+f+++ ++ E+fG v lEAm a +p++++++g + +++ d      v  ++a+++ ++++++l+  
  gi|336253722|ref|YP_004596829.1| 314 YSKHDLFLYTGRWdEPFGRVFLEAMGASTPIFSTDVGSIDKIIGDCG--QTVTYTSADEFTQELTSVLDPA 382
                                       *******************************************9866..5566667899999998888755 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 !   76.4   0.0   7.4e-25   2.7e-21       2     132 ..     240     379 ..     239     381 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 7.4e-25
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H.H..EEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d..vrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaell 70 
                                       ++ilfvG l +++kg d l++ +++l+++ +  ++l i+Gdg+ rp  le++++  +l+++++++G+v  ++l+ ++
  gi|336253722|ref|YP_004596829.1| 240 FNILFVGTL-RHRKGTDRLIDIAQKLHREhEckFNLSIAGDGDlRP-TLEREIDkeKLSDNITLHGHVpyNQLPTMY 314
                                       589******.566**********999966436799********776.9*99996699***********9889***** PP

                                       HH-SEEEE--...---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  71 aaadvfvaPs...egfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeailrLl 132
                                       +++d+f+ +    e fg + lEam a +p+ +tdvg i +++g+ g  v   +++++++++  +l
  gi|336253722|ref|YP_004596829.1| 315 SKHDLFLYTGrwdEPFGRVFLEAMGASTPIFSTDVGSIDKIIGDCGQTVTYTSADEFTQELTSVL 379
                                       **********9999*********************9999999*9**9999999******999887 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.2e-06    0.0078       3      86 ..      17      99 ..      15     116 .. 0.66
   2 !   20.3   0.0   1.2e-07   0.00045     113     168 ..     173     226 ..     126     228 .. 0.84
   3 ?   -3.8   0.0       3.2   1.1e+04      97     108 ..     310     321 ..     300     337 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-06
                    Glyco_transf_4  3 GverhvleLaraLarrGheVtvvtpgddgpleeev.elvvrvprvplpllkrllrslaflrrlrrllkre.....kpDv 75
                                      G+  ++ +++++ a r h+Vtv++ +  + +++++ ++v +++ ++       ++++ f+  l +++ r      k+D+
  gi|336253722|ref|YP_004596829.1| 17 GATHSADQIINHIAGRSHDVTVYCTSEYDYQAQQDlYDVEELGVRR-------GKIYNFAEELNKAITRKeselgKYDI 88
                                      888899999**************76666666666334444444444.......4444444444444444444566**** PP

                    Glyco_transf_4 76 vHahspaalga 86
                                      vH+    ++ a
  gi|336253722|ref|YP_004596829.1| 89 VHSYLMRSIPA 99
                                      **876666544 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.2e-07
                    Glyco_transf_4 113 karlkplsrllralerrllrradrviavSeatadelrerygvppekitVipnGvDl 168
                                        ar+++ +r++r+ ++ l     ++ a S+++++++ + +g+p++ki Vipn  D 
  gi|336253722|ref|YP_004596829.1| 173 FARRMRNYRMIRKGYKNL-PGISHFQALSPHVKERYDA-FGYPADKISVIPNMFDD 226
                                       456666777777777765.999****************.*************8885 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 3.2
                    Glyco_transf_4  97 iplVltvHglye 108
                                       +p+ ++ H+l+ 
  gi|336253722|ref|YP_004596829.1| 310 LPTMYSKHDLFL 321
                                       455666666662 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 !   25.9   0.0   3.1e-09   1.1e-05       1     159 [.      16     222 ..      16     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 3.1e-09
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrll...rqrrerp 74 
                                       +G++  + +++ + a r h+Vtv++++++  +  +++d   v  l v+r+      + ++  l  ++   + +  ++
  gi|336253722|ref|YP_004596829.1|  16 TGATHSADQIINHIAGRSHDVTVYCTSEYDYQ--AQQDLYDVEELGVRRGK----IYNFAEELNKAItrkESELGKY 86 
                                       58888899*****************9665554..589***********994....7889999999988887799*** PP

                   Glyco_trans_4_4  75 dvvhahsptaglaarlarrrrgiplvvtl.................................h...........g.. 105
                                       d+vh+    + +a+ ++   + +  vvtl                                 h           +  
  gi|336253722|ref|YP_004596829.1|  87 DIVHSYLMRSIPAMGHLGTNTQTSPVVTLnafggicprndllymnqapcesngllkcatcsvHesttinwqednSip 163
                                       *****997766666666658888888889788888888888888888888888877777777355544444433132 PP

                   Glyco_trans_4_4 106 ll.lrrgsgavrrly..raler..rllrradavlvvseaeaeelralgvpadrvvvvpn 159
                                       ++ lr+g+ ++rr++  r++ +    l +  ++ ++s+++ e++ a+g pad++ v+pn
  gi|336253722|ref|YP_004596829.1| 164 WDiLRSGNVFARRMRnyRMIRKgyKNLPGISHFQALSPHVKERYDAFGYPADKISVIPN 222
                                       22466775555555552666333367777999**************************9 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 !   18.7   0.0   4.8e-07    0.0017       9      90 ..     328     407 ..     307     409 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.8e-07
                   Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaehtydh 85 
                                       e +  +++Ea+++ +++ ++d  ++++++ +    +++ + +e+ + +  +l +p+  r+ +e+a  + l++++ + 
  gi|336253722|ref|YP_004596829.1| 328 EPFGRVFLEAMGASTPIFSTDVGSIDKIIGDCGQTVTYTSADEFTQELTSVL-DPAILRSYSEQAESQ-LRQYSPEV 402
                                       34677899**********************999****************986.89999999**99999.88888877 PP

                   Glyco_trans_1_2  86 raeql 90 
                                         e++
  gi|336253722|ref|YP_004596829.1| 403 ITEKF 407
                                       77766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3003.28
//
Query:       gi|336253723|ref|YP_004596830.1|  [L=503]
Description: polysaccharide biosynthesis protein [Halopiger xanaduensis SH-6]
Scores for 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-18   64.8  19.3    8.7e-18   64.8  19.3    3.7  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    2.2e-13   50.3  22.1    2.2e-13   50.3  22.1    2.6  2  Polysacc_synt    Polysaccharide biosynthesis protein
    3.4e-13   49.5  13.5    3.4e-13   49.5  13.5    2.1  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    5.5e-05   22.0  17.5    5.5e-05   22.0  17.5    2.9  3  MurJ             Lipid II flippase MurJ


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 ?   -8.3  10.6         4   1.8e+04      85     141 ..      71     129 ..      15     131 .. 0.46
   2 ?    1.1  10.2     0.085   3.8e+02      44      86 ..     163     214 ..     119     255 .. 0.68
   3 !   64.8  19.3   1.9e-21   8.7e-18       2     142 ..     338     473 ..     337     474 .. 0.89

  Alignments for each domain:
  == domain 1  score: -8.3 bits;  conditional E-value: 4
                   Polysacc_synt_C  85 l...ellrrllkpllaalvmgivvylllllllgllllaal.alllavlvgalvYlllllll 141
                                           + +++ +  + + +++g++ + ll+++l +++  +l   l++v +   +Yll +l+l
  gi|336253723|ref|YP_004596830.1|  71 DrdqQNWQDYVFGFYFRVALGLAFLVLLSFVLFAWT--GLpRQLFGVEFVLYFYLLGVLVL 129
                                       245433444433333334444442223333333332..34466666767777777777666 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.085
                   Polysacc_synt_C  44 ilnllli.plfgivGaaiatvlallvvavlnlyalrrllgikl........e 86 
                                       i++l l+   +g+vG++++ ++a +vv+++ l++l ++l ++          
  gi|336253723|ref|YP_004596830.1| 163 IISLSLVyVGYGVVGVLVGQIVATVVVSIIALVILFKRLDLDAvfgrvpsdF 214
                                       55555554479************************99999998666555542 PP

  == domain 3  score: 64.8 bits;  conditional E-value: 1.9e-21
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalr 78 
                                       L il +++i +++s++  +i qg g  + +++a+  +al++l lnlllip++g++Gaaiat +++  +++++ +++ 
  gi|336253723|ref|YP_004596830.1| 338 LLILLPGVIGFAISRPIFAIGQGKGSLRVLIMATGTAALINLFLNLLLIPEYGMTGAAIATSIGYGSMLIFH-VLAA 413
                                       789*******************************************************************99.6777 PP

                   Polysacc_synt_C  79 rllgikl.ellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                       r++g+++ + lr l ++++ ++v +iv   +++ +  + +   l+l++   vg +vY+l+ l++r
  gi|336253723|ref|YP_004596830.1| 414 RQIGFNPlMDLR-LNRIAVTGFVTAIV---IFSSTALIESAI-LSLVVVPPVGFVVYMLIGLKIR 473
                                       779****64344.449***********...778777776644.57777778*********99998 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3  22.1   4.8e-17   2.2e-13       4     246 ..       8     258 ..       5     273 .. 0.78
   2 ?   -6.4   7.8         4   1.8e+04     147     193 ..     364     409 ..     296     455 .. 0.66

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 4.8e-17
                     Polysacc_synt   4 gvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslilln 80 
                                       g++++l s+l + ll+++++++l r+lg + +G +a++++++++ +il++ G+     +++ + r++++   + +  
  gi|336253723|ref|YP_004596830.1|   8 GFLSILGSKLGVVLLGLIITPILVRLLGSTLYGDYAFVMSMLGITMILVNAGIFDGTRKFMVEDRDQQNWQDYVFGF 84 
                                       7899999***********************************************************95555555555 PP

                     Polysacc_synt  81 vllvllvlvllfllllliaaflglpe..lavlylilalmllllvgvasfrrglfqglerm...kyaavsqvveqlsr 152
                                        + v l l+ l+ll+++++a +glp+  + v  +++++ l +lv + ++++    gl      k      +++++ +
  gi|336253723|ref|YP_004596830.1|  85 YFRVALGLAFLVLLSFVLFAWTGLPRqlFGVEFVLYFYLLGVLVLGRQVFSVARGGLISLgleKKSEPLPIIKKVLF 161
                                       566666666666666666676666662255566666666667777766666555555554111445556799***** PP

                     Polysacc_synt 153 vilvliavflfldivaavlgavlaalvggivslavlrkkfr...prfvilslklvrellsfsapltisslaillyty 226
                                        i +l++v+ ++ +v++++g+ +a++v +i++l++l+k++    +   ++s    r+llsf+   ++  l+++ +  
  gi|336253723|ref|YP_004596830.1| 162 GIISLSLVYVGYGVVGVLVGQIVATVVVSIIALVILFKRLDldaVFGRVPSDFPKRRLLSFNKLSVVFILLTTSLYH 238
                                       ****************************************5355333444455579999998655555555555557 PP

                     Polysacc_synt 227 idsillglllgaeavGiYna 246
                                       id +ll+ l+g++a G+Y+a
  gi|336253723|ref|YP_004596830.1| 239 IDILLLQPLAGSQATGYYRA 258
                                       9*****************97 PP

  == domain 2  score: -6.4 bits;  conditional E-value: 4
                     Polysacc_synt 147 veqlsrvilvliavflfld.ivaavlgavlaalvggivslavlrkkfr 193
                                       +++l+ ++ +++++ lfl  +++   g + aa++++i++  +l   f+
  gi|336253723|ref|YP_004596830.1| 364 LRVLIMATGTAALINLFLNlLLIPEYGMTGAAIATSIGYGSMLI--FH 409
                                       45566666666666666664444455566666666666666665..33 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5  13.5   7.6e-17   3.4e-13       1     292 [.      29     335 ..      29     336 .. 0.84
   2 ?    2.1   1.3      0.02        89      98     153 ..     405     457 ..     363     482 .. 0.71

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 7.6e-17
                   Polysacc_synt_3   1 vLARLLspedFGvvaialvvislanlfvdmGl....ssaliqke.dlteedlstvftfnlvlgll....ialvlfll 68 
                                       +L RLL    +G +a+++ +++++ ++v++G+     ++++  + +++ +d+   f+f ++lgl+    +++vlf++
  gi|336253723|ref|YP_004596830.1|  29 ILVRLLGSTLYGDYAFVMSMLGITMILVNAGIfdgtRKFMVEDRdQQNWQDYVFGFYFRVALGLAflvlLSFVLFAW 105
                                       89****************************9955445778887744455699999*****99976111156677888 PP

                   Polysacc_synt_3  69 apliasfynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvig 145
                                         l  ++++ + +     +  lvl  + +s+    l++  l+ kk     ++ +v+ +i+++ l+++g+gv  +++g
  gi|336253723|ref|YP_004596830.1| 106 TGLPRQLFGVEFVLYFYLLGVLVLGRQVFSVARGGLISLGLE-KKSEPLPIIKKVLFGIISLSLVYVGYGVVGVLVG 181
                                       888888999887776666666666666666666667777776.5666789*************************** PP

                   Polysacc_synt_3 146 tllssllslvllwlaskwrprlkfslksl......kelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsv 216
                                       ++++ ++ +++ ++++  r++l   + ++      ++l+sf +  +++ ll +   ++d ll   + +s+a G+Y  
  gi|336253723|ref|YP_004596830.1| 182 QIVATVVVSIIALVILFKRLDLDAVFGRVpsdfpkRRLLSFNKLSVVFILLTTSLYHIDILLLQPLAGSQATGYYRA 258
                                       ************9999999999888777544445589**************************************99 PP

                   Polysacc_synt_3 217 akrlaslpvaeitsviakVlfPalSrl..qddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWlea 291
                                       +  +a+++   + +v ++Vl+ + S+l  +++ +++ el+ +v+r    + + +  gl ++a+ +v++ +G +++e+
  gi|336253723|ref|YP_004596830.1| 259 SLVIAEFL-WLVPNVCQTVLLHSSSELwsKKQTDEITELISRVTRYNIAFLVLVGLGLTALAKDFVPLYFGAEFEES 334
                                       99888876.57899999***999999744667789**********97777777**********************99 PP

                   Polysacc_synt_3 292 v 292
                                       v
  gi|336253723|ref|YP_004596830.1| 335 V 335
                                       7 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.02
                   Polysacc_synt_3  98 ssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllsslls 153
                                       +++   l +r++ F+ l+  +l  ++v+++v+   A+++++  AL+ + +ls ++ 
  gi|336253723|ref|YP_004596830.1| 405 MLIFHVLAARQIGFNPLMDLRLNRIAVTGFVT---AIVIFSSTALIESAILSLVVV 457
                                       44556788999999*99999999999887665...777777788887777776654 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   1.1     0.059   2.6e+02      65     104 ..      14      52 ..       3      57 .. 0.72
   2 ?   -3.7   0.4      0.76   3.4e+03     380     405 ..      91     113 ..      80     138 .. 0.56
   3 !   22.0  17.5   1.2e-08   5.5e-05     142     431 ..     163     441 ..     154     459 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.059
                              MurJ  65 lvlllvtligilaapllirllatgfdeetlelavsllril 104
                                       ++ l+v+l+g++  p+l+rll ++    + ++ +s+l i+
  gi|336253723|ref|YP_004596830.1|  14 GSKLGVVLLGLIITPILVRLLGSTL-YGDYAFVMSMLGIT 52 
                                       467899***************9998.44444444555555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.76
                              MurJ 380 glalatslsaliglvllyvllrkrlk 405
                                       gla+   ls+   +++++  l ++l 
  gi|336253723|ref|YP_004596830.1|  91 GLAFLVLLSF---VLFAWTGLPRQLF 113
                                       3333333333...5556666666654 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 1.2e-08
                              MurJ 142 IltllllanklgeeailaLaiGvliGgvlqllvqlpalkkagll........lkprfafrdeglkkflklllptllg 210
                                       I++l l+++ +g       ++Gvl+G ++ ++v  +    + ++         +  ++f +++l  f kl   ++++
  gi|336253723|ref|YP_004596830.1| 163 IISLSLVYVGYG-------VVGVLVGQIVATVVVSIIALVILFKrldldavfGRVPSDFPKRRLLSFNKL---SVVF 229
                                       445555555555.......456666655554433222222222223323554344445555555555554...4444 PP

                              MurJ 211 vsvsqlnllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltll 287
                                       ++       +d+ l + la + ++ ++ a++++   l l  +   tvlL + S+  ++k++de+ +l+s  +r  ++
  gi|336253723|ref|YP_004596830.1| 230 ILLTTSLYHIDILLLQPLAGSQATGYYRASLVIAEFLWLVPNVCQTVLLHSSSELWSKKQTDEITELISRVTRYNIA 306
                                       444444445566666666667777777777777777889999*********************************** PP

                              MurJ 288 llipvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvl 364
                                        l++v  gl++l+k  v l+f  ++F+e+        L + + g+i +a+     r  +A ++ k  + + ++++ +
  gi|336253723|ref|YP_004596830.1| 307 FLVLVGLGLTALAKDFVPLYF-GAEFEES-----VLPLLILLPGVIGFAIS----RPIFAIGQGKGSLRVLIMATGT 373
                                       *********************.5555543.....33455556677777754....4556777777777777766655 PP

                              MurJ 365 nills....llllpplgvvglalatslsaliglvllyvllrkrlklteargiktflaklvvllalaavvil 431
                                        +l++    lll+p +g+ g a+ats+++  +++++ vl++++ ++ +  ++ + l +++v+ ++ a+vi 
  gi|336253723|ref|YP_004596830.1| 374 AALINlflnLLLIPEYGMTGAAIATSIGY-GSMLIFHVLAARQIGFNP--LMDLRLNRIAVTGFVTAIVIF 441
                                       555555554********************.999999999999966544..444445554444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); 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: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 3613.10
//
Query:       gi|336253724|ref|YP_004596831.1|  [L=279]
Description: FkbM family methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-18   67.9   0.0    8.6e-18   64.9   0.0    1.9  2  Methyltransf_21  Methyltransferase FkbM domain
    0.00089   19.1   0.0     0.0015   18.3   0.0    1.3  1  Met_10           Met-10+ like-protein
     0.0029   18.3   0.0     0.0081   16.9   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.025   14.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      0.047   13.2   0.0      0.092   12.3   0.0    1.5  2  MTS              Methyltransferase small domain
      0.052   12.8   0.0       0.21   10.8   0.0    1.8  2  V_cholerae_RfbT  Vibrio cholerae RfbT protein
      0.097   12.5   0.0       0.49   10.2   0.0    2.0  2  Methyltransf_23  Methyltransferase domain
       0.14   11.3   0.0       0.21   10.7   0.0    1.2  1  Methyltransf_3   O-methyltransferase
       0.21   11.5   0.1       0.37   10.7   0.1    1.4  1  DUF1601          Protein of unknown function (DUF1601)


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.24   4.8e+02     132     168 ..      48      82 ..      42      86 .. 0.76
   2 !   64.9   0.0   4.3e-21   8.6e-18       1     171 [.      91     260 ..      91     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.24
                   Methyltransf_21 132 aqkglkrcqpnlivvEvhkfkefetelfdeirqflre 168
                                       + +++++  p++ +vE ++  e+++++ +e+ +fl e
  gi|336253724|ref|YP_004596831.1|  48 EGWTVRFSAPSVAMVERNH--ERFNSEKEELADFLDE 82 
                                       568999999***9999887..6666777777777754 PP

  == domain 2  score: 64.9 bits;  conditional E-value: 4.3e-21
                   Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavg.ndvglyelivegksg..gkyfpfa 74 
                                       d+Gan+g   + + ++a++c  g+ v+a+EP p    +++ l++ +     + n+++ +e+i  + s+  g+     
  gi|336253724|ref|YP_004596831.1|  91 DIGANTG--LYSL-FAANECPDGN-VIAFEPYPP---NLDLLKQDI-----SrNGFEHIEVIEMALSNsvGTIGFSQ 155
                                       9******..3333.3334555555.88*******...*****9994.....33557777777777766666666666 PP

                   Methyltransf_21  75 vgdtngfstssvlg.gedaryievpvvtldsfleeikksridllkiDvEGaElevLeGaqkglkrcqpnlivvEvhk 150
                                        ++++++ +ss  g g+++++ievp++t d++++++ ++ ++++kiDvEGaE  v+ G +++l+    +++++Evh 
  gi|336253724|ref|YP_004596831.1| 156 PKESDIGYGSSAIGpGDNKDTIEVPTTTGDQLIDDGEIPPPNVVKIDVEGAEPLVIDGLERALSAPSCRVVYCEVHL 232
                                       666666666665668*******************************************999999978888889**** PP

                   Methyltransf_21 151 fkefet.......elfdeirqflrecgy 171
                                        ++++        ++  +ir  ++e+g+
  gi|336253724|ref|YP_004596831.1| 233 PGNERRpsvedfdSSATDIRNRFEEFGF 260
                                       9955556******999**********99 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   7.5e-07    0.0015      88     152 ..      70     137 ..      43     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.5e-07
                                       HHHHHHHHTT...--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTC CS
                            Met_10  88 eaErerlakl...veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekv 152
                                       ++E+e la     ++ ++vV d+ A  G +++ +a  + +  v+a +  P    +lk+ i +N  e++
  gi|336253724|ref|YP_004596831.1|  70 NSEKEELADFldeIRADDVVYDIGANTGLYSLFAANECPDGNVIAFEPYPPNLDLLKQDISRNGFEHI 137
                                       55666666542227789**********************************************99874 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.1e-06    0.0081       1      55 [.      89     144 ..      89     156 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.1e-06
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBC CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgda 55 
                                       v d+G+ tG ++l +a+++++++v+++++ +  l+  ++ ++++g+ ++e++++ +
  gi|336253724|ref|YP_004596831.1|  89 VYDIGANTGLYSLFAANECPDGNVIAFEPYPPNLDLLKQDISRNGFeHIEVIEMAL 144
                                       78*****************99************************99999998766 PP

>> Methyltransf_31  Methyltransferase 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     0.025       3      59 ..      85     140 ..      83     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFe 59 
                                        + +v+D+G++tG +++ +a + +p+++v+ ++  +  + l ++  +++g++ +e+ 
  gi|336253724|ref|YP_004596831.1|  85 ADDVVYDIGANTGLYSLFAA-NECPDGNVIAFEPYPPNLDLLKQDISRNGFEHIEVI 140
                                       5778****************.88****************************988875 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       4.4   8.7e+03     141     156 ..      13      28 ..      11      30 .. 0.75
   2 ?   12.3   0.0   4.6e-05     0.092      23      89 ..      76     144 ..      65     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.4
                                       TTSCHHHHHHHHHS-- CS
                               MTS 141 rklgyeslleelfgnv 156
                                       +++g+++ll+++f++ 
  gi|336253724|ref|YP_004596831.1|  13 QNQGAKTLLKRAFKKA 28 
                                       5678888899998875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.6e-05
                                       HHHHCHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-ST CS
                               MTS  23 Lletlpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdv 89 
                                       L++ l++  +++ v D+G+ +G+ ++ +a+e+p+ +v +++     l++ k+ +++n++e +ev++  +
  gi|336253724|ref|YP_004596831.1|  76 LADFLDEIrADDVVYDIGANTGLYSLFAANECPDGNVIAFEPYPPNLDLLKQDISRNGFEhIEVIEMAL 144
                                       666777764556689********************************************9988877655 PP

>> V_cholerae_RfbT  Vibrio cholerae RfbT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.21      76     112 ..      82     118 ..      62     143 .. 0.88
   2 ?   -0.7   0.0      0.36   7.1e+02     194     206 ..     198     210 ..     188     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                   V_cholerae_RfbT  76 hckhdttyidiganvgtfcgiaarhitqgkiiaiepl 112
                                         + d    digan g +   aa    +g++ia ep 
  gi|336253724|ref|YP_004596831.1|  82 EIRADDVVYDIGANTGLYSLFAANECPDGNVIAFEPY 118
                                       566788889**************************97 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.36
                   V_cholerae_RfbT 194 vikidaegaeiei 206
                                       v+kid egae  +
  gi|336253724|ref|YP_004596831.1| 198 VVKIDVEGAEPLV 210
                                       89*******9655 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00025      0.49       3      61 ..      66     126 ..      63     187 .. 0.79
   2 ?   -0.6   0.0      0.51     1e+03     147     161 ..     247     261 ..     244     264 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00025
                   Methyltransf_23   3 aqreeelsdklerllpklraggrvLdiGcGtGillevlrengf...svtgvDlspeaveiae 61 
                                       ++r++  +++l+ +l++ ra+  v diG++tG l +++++n +   +v++++++p + ++++
  gi|336253724|ref|YP_004596831.1|  66 HERFNSEKEELADFLDEIRADDVVYDIGANTG-LYSLFAANECpdgNVIAFEPYPPNLDLLK 126
                                       6777777788888888899*************.55557777777899*******98877765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.51
                   Methyltransf_23 147 sarslkelleeaGle 161
                                       sa+++++ +ee+G++
  gi|336253724|ref|YP_004596831.1| 247 SATDIRNRFEEFGFT 261
                                       789***********7 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.21      41     104 ..      79     140 ..      59     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                                       HHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEE CS
                    Methyltransf_3  41 lLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieli 104
                                       +L ++     v +iG  tG   L  a + P DG+++a +  + + ++ ++ i + g+++ ie+i
  gi|336253724|ref|YP_004596831.1|  79 FLDEIRADDVVYDIGANTGLYSLFAANECP-DGNVIAFEPYPPNLDLLKQDISRNGFEH-IEVI 140
                                       5556666777889******88888898887.9************************987.4444 PP

>> DUF1601  Protein of unknown function (DUF1601)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00018      0.37      19      31 ..      60      72 ..      51      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                           DUF1601 19 vaIrrnaerFNsQ 31
                                      + + rn+erFNs+
  gi|336253724|ref|YP_004596831.1| 60 AMVERNHERFNSE 72
                                      4678*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2172.35
//
Query:       gi|336253725|ref|YP_004596832.1|  [L=35]
Description: hypothetical protein Halxa_2331 [Halopiger xanaduensis SH-6]
Scores for 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:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 286.92
//
Query:       gi|336253726|ref|YP_004596833.1|  [L=307]
Description: UDP-glucose 4-epimerase [Halopiger xanaduensis SH-6]
Scores for 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-64  216.1   0.1    6.2e-64  215.7   0.1    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.6e-62  211.2   0.0      5e-62  210.2   0.0    1.4  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.6e-27   94.2   0.0    9.1e-27   93.8   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.2e-23   83.6   0.1    1.5e-23   83.3   0.1    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    1.5e-21   76.9   0.3    2.4e-20   72.9   0.3    2.4  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.2e-16   59.8   0.1    2.6e-13   49.7   0.1    2.4  1  NAD_binding_4    Male sterility protein
    1.4e-10   41.3   0.0    2.4e-10   40.6   0.0    1.5  1  NAD_binding_10   NAD(P)H-binding
    0.00017   21.2   0.1    0.00037   20.1   0.0    1.6  2  NmrA             NmrA-like family
     0.0011   18.8   0.0     0.0093   15.8   0.0    2.0  2  Methyltransf_31  Methyltransferase domain
     0.0048   16.4   0.2      0.017   14.6   0.1    2.1  2  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.085   12.8   1.7       0.38   10.6   0.4    2.6  2  KR               KR domain
        0.1   12.9   1.1       0.59   10.4   0.2    2.4  2  TrkA_N           TrkA-N 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 !  215.7   0.1   4.2e-67   6.2e-64       1     241 []      15     243 ..      15     243 .. 0.98

  Alignments for each domain:
  == domain 1  score: 215.7 bits;  conditional E-value: 4.2e-67
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       il+tG++GfiGs++v+al +++ ev +ld+lss+s+++  ++++l+e+d++++++l+r+ +  ++d+++h Aa  +v
  gi|336253726|ref|YP_004596833.1|  15 ILITGGAGFIGSNIVEALVDEN-EVRVLDNLSSGSRSNVPDEATLIEGDIRNDDDLDRATA--DVDVIFHQAALISV 88 
                                       8*******************97.9*************************************..89************ PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                       + s+ +p+ + ++n+  tl+ll+ a++  + r++f+sS++vYG+++++p +e++   p++p+spY+++Kla+e++v+
  gi|336253726|ref|YP_004596833.1|  89 EKSMHHPELTHDINVTATLKLLKRAHDESA-RFVFASSAAVYGQPESVPISEDA---PTNPTSPYGVSKLAAEEYVQ 161
                                       ****************************99.***********************...******************** PP

                                       HHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT CS
                         Epimerase 155 ayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvda 231
                                        y ++++l+a+ilr+fn+yGp++ +++ s vi  +++++ +g  e+t+ gdgt+ Rdf++v+D+++a+ll+l     
  gi|336253726|ref|YP_004596833.1| 162 LYIEEFDLDAVILRYFNVYGPGQLDSDYSAVIGVFVEQATTGN-EITVEGDGTQTRDFVHVQDIVRANLLALHS--- 234
                                       ******************************************9.*****************************9... PP

                                       -STTEEEEES CS
                         Epimerase 232 gdkgeiyniG 241
                                        ++ +++n+G
  gi|336253726|ref|YP_004596833.1| 235 -EATGVFNVG 243
                                       .556799998 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 !  210.2   0.0   3.3e-65     5e-62       1     330 [.      16     304 ..      16     306 .. 0.91

  Alignments for each domain:
  == domain 1  score: 210.2 bits;  conditional E-value: 3.3e-65
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       LiTG+aGfiGs+++e L+++  ev +++++ss  +    +++         ++ +l++gD+++ + l+r+ a+v  d
  gi|336253726|ref|YP_004596833.1|  16 LITGGAGFIGSNIVEALVDE-NEVRVLDNLSSGSR----SNVP--------DEATLIEGDIRNDDDLDRATADV--D 77 
                                       9******************8.78989988887633....3333........3468**************99998..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        +++ AA   V++s+++Pe t ++nv++tl+LL+ + +    +++rf++aS++ vYG++++vp++E+ p++P+sPY+
  gi|336253726|ref|YP_004596833.1|  78 VIFHQAALISVEKSMHHPELTHDINVTATLKLLKRAHD----ESARFVFASSAAVYGQPESVPISEDAPTNPTSPYG 150
                                       **********************************9966....579******************************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                       ++Kl+a+  v+ y e+++l av+ ++fn ++p +  +     i  +v +++ g+ e+++ G++ ++Rd+ hv+D+v+
  gi|336253726|ref|YP_004596833.1| 151 VSKLAAEEYVQLYIEEFDLDAVILRYFNVYGPGQLDSDYSAVIGVFVEQATTGN-EITVEGDGTQTRDFVHVQDIVR 226
                                       ************************************9999************98.67778***************** PP

                                       HHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B CS
                     GDP_Man_Dehyd 232 amwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllg 308
                                       a  l+l+++ +  ++++tge++s+ e++e ++ e+ +                 s+++ v+vd    rp++ ++  +
  gi|336253726|ref|YP_004596833.1| 227 ANLLALHSEATGVFNVGTGESVSILELAE-TIREIAN-----------------SESEIVHVD---ARPSDIEKSRA 282
                                       *********************99998887.3444432.................223455665...89********* PP

                                       -THHHHHHH----SS-HHHHHH CS
                     GDP_Man_Dehyd 309 daskakeeLgWkpkvsfeelvr 330
                                       d+sk+k++ g++p+vs+e++++
  gi|336253726|ref|YP_004596833.1| 283 DISKLKSNFGFSPSVSLEKGLA 304
                                       ******************9986 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 !   93.8   0.0   6.1e-30   9.1e-27       1     229 [.      16     232 ..      16     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 6.1e-30
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       ++tGgaGF+G+++v++Lv+++   evrvlD   s +    ++  + +++iegD+++ d+l++a+ +vdv++h a+l+
  gi|336253726|ref|YP_004596833.1|  16 LITGGAGFIGSNIVEALVDEN---EVRVLDNLSSGSR---SNVPDEATLIEGDIRNDDDLDRATADVDVIFHQAALI 86 
                                       69*****************99...6*****8777666...2333445589*************************** PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                        v + + + +   ++nv  T ++l+ + + +  ++v+ Ssa v g+  ++ +i      +  +++++++y  sK  a
  gi|336253726|ref|YP_004596833.1|  87 SVEKsMHHPELTHDINVTATLKLLKRAHDESA-RFVFASSAAVYGQ-PESVPIS-----EDAPTNPTSPYGVSKLAA 156
                                       **99788889999**************99886.589*******999.5566665.....45677899********** PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyGegd.....kllvpllkqlaklglalfkigdeevlsdrvYvgNvawah 225
                                       E++v    +       +l  + LR   +yG+g+     + +  ++++ a +g+++   gd  ++ d+v v  ++ a 
  gi|336253726|ref|YP_004596833.1| 157 EEYVQLYIE-----EFDLDAVILRYFNVYGPGQldsdySAVIGVFVEQATTGNEITVEGDGTQTRDFVHVQDIVRAN 228
                                       ****88766.....3499*************9733322234455677788899************************ PP

                         3Beta_HSD 226 ilAa 229
                                       +lA 
  gi|336253726|ref|YP_004596833.1| 229 LLAL 232
                                       **97 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 !   83.3   0.1     1e-26   1.5e-23       2     258 ..      14     287 ..      13     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 1e-26
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHHHHH--SEEEE------ CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre...............eldltdaeavaellkeakpdvvvnaAAyta 63 
                                       +il+tG+ G +Gs+++++l  e+ ev  l++                e d+++ + ++++ ++   dv+ + AA   
  gi|336253726|ref|YP_004596833.1|  14 EILITGGAGFIGSNIVEALVDEN-EVRVLDNLssgsrsnvpdeatliEGDIRNDDDLDRATAD--VDVIFHQAALIS 87 
                                       69**************9988766.55555433458999**********************999..899********* PP

                                       HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH- CS
                     RmlD_sub_bind  64 vDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaag 140
                                       v k  +++e+ + +n++a+ +l + a+   a +++ S+  V+   ++ p +ed++t+P + YG +Kla E+ v+ + 
  gi|336253726|ref|YP_004596833.1|  88 VEKSMHHPELTHDINVTATLKLLKRAHDESARFVFASSAAVYGQPESVPISEDAPTNPTSPYGVSKLAAEEYVQLYI 164
                                       ******************************************999****************************9865 PP

                                       S....SEEEEEE-SEESS.....SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG CS
                     RmlD_sub_bind 141 k....kalivRtswvyge.....kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekel 206
                                       +    +a+i+R   vyg           + ++++ a++ +e++v  D  q++   +++d+ ++ l +l+ +a     
  gi|336253726|ref|YP_004596833.1| 165 EefdlDAVILRYFNVYGPgqldsDYSAVIGVFVEQATTGNEITVEGDgtQTRDFVHVQDIVRANLLALHSEA----- 236
                                       5233379*********76544433344566889***********9885566667777777777766666666..... PP

                                       -EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B CS
                     RmlD_sub_bind 207 agvyHlanegetswlefArailkeagadseevkpistaeyptpAkRPanSvL 258
                                        gv+ ++  +++s le+A+ i + a+++s e+  +++     + +R   S+L
  gi|336253726|ref|YP_004596833.1| 237 TGVFNVGTGESVSILELAETIREIANSES-EIVHVDARPSDIEKSRADISKL 287
                                       6********************99999966.6666655544444445444444 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.3   1.6e-23   2.4e-20       1     251 [.      15     265 ..      15     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 1.6e-23
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       +l+tG++G iGs++v+ +++++  ++++l++       +++  ++++ ++ + +e     gd+r+ + l++a    +
  gi|336253726|ref|YP_004596833.1|  15 ILITGGAGFIGSNIVEALVDEN--EVRVLDN-------LSSGSRSNVPDEATLIE-----GDIRNDDDLDRATA--D 75 
                                       89**************998765..5666654.......44444445566444355.....************99..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-S.............EEEEEEEGGGSS--SHHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvk.............kvvliStDKAvnPtnvmGat 141
                                       vdv+fh AAl  V    ++p  + + Nv++t ++++ a++   +             + v iS D   nPt+ +G++
  gi|336253726|ref|YP_004596833.1|  76 VDVIFHQAALISVEKSMHHPELTHDINVTATLKLLKRAHDESARfvfassaavygqpESVPISEDAPTNPTSPYGVS 152
                                       *********************************99988765543111111111111166889*************** PP

                                       HHHHHHHHHHGGG--SSS--EEEEEEE-EETT.....GTTS.SHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHHHHH CS
                   Polysacc_synt_2 142 KrlaekllqalakeseekktkfvvvRfGNVlg.....SrGS.viplFkkqikeggpvtv.TdpemtRyfmtieeavq 211
                                       K++ae ++q + +e    +   v+ R+ NV g     S  S vi +F +q ++g+++tv  d + tR f+ +++ v+
  gi|336253726|ref|YP_004596833.1| 153 KLAAEEYVQLYIEEF---DLDAVILRYFNVYGpgqldSDYSaVIGVFVEQATTGNEITVeGDGTQTRDFVHVQDIVR 226
                                       *********999988...899999******7633333554449****************448899************ PP

                                       HHHHHHHH--SS-EEEE--.-EEEHHHHHHHH........ CS
                   Polysacc_synt_2 212 LvlqalalakggeifvldmGepvkivdlakalielsglee 251
                                         l al+   +  +f +  Ge+v+i++la+++ e+++ e+
  gi|336253726|ref|YP_004596833.1| 227 ANLLALHSEAT-GVFNVGTGESVSILELAETIREIANSES 265
                                       99999876655.5999999*************98887544 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.1   1.7e-16   2.6e-13       1     229 [.      17     199 ..      17     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.7e-16
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TG+ GF+G+ ++e L+++++       vR  ++ s   R        ++++++        + +eGD+ +++    
  gi|336253726|ref|YP_004596833.1|  17 ITGGAGFIGSNIVEALVDENE-------VRVLDNLSSGSRS-------NVPDEA--------TLIEGDIRNDD---- 67 
                                       799999999999999999997.......6666663333343.......455444........69*****9876.... PP

                                       HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                         dl++ ++ vdvi+h aA ++++++++      ++Nv++t ++l+ a+  ++   +++ S+a+v+g+ e+      
  gi|336253726|ref|YP_004596833.1|  68 --DLDRATADVDVIFHQAALISVEKSMHHpelTHDINVTATLKLLKRAHDESA--RFVFASSAAVYGQPESV----- 135
                                       ..999********************9998777789**************6655..5***********99953..... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHHH CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwingsdlgirgllgl 228
                                                    +++  ++ +  Y  sK +aE+ v+ + ++ +l +vi+R  +++g   +G+++++   + g+++ 
  gi|336253726|ref|YP_004596833.1| 136 -----------PISEDAPTNPTSPYGVSKLAAEEYVQLYIEEFDLDAVILRYFNVYG---PGQLDSDYSAVIGVFVE 198
                                       ...........3556667778899*******************************99...67777666555555444 PP

                                       H CS
                     NAD_binding_4 229 i 229
                                        
  gi|336253726|ref|YP_004596833.1| 199 Q 199
                                       3 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 !   40.6   0.0   1.6e-13   2.4e-10       1     143 [.      19     176 ..      19     219 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.6e-13
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-........- CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal........g 69 
                                       G+ G +G+ +v+ l++++  ev++l  n ++ ++    ++++++egd+ + +dl +a +++d+++  +         
  gi|336253726|ref|YP_004596833.1|  19 GGAGFIGSNIVEALVDEN--EVRVL-DNLSSGSRSNVPDEATLIEGDIRNDDDLDRATADVDVIFHQAalisveksM 92 
                                       99***************6..77765.77666665555689************************9998777544431 PP

                                       -TCCHHHH...........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHH...HHHHHCCHHHHHHHHHHHHHH. CS
                    NAD_binding_10  70 gggkdeeg...........aknivdaakeagvkRfvlvsaigvgdevpgefg...ewnkellkaylaakraaeell. 131
                                       +                  + ++++ a  +   Rfv+ s++ v+  +p++++   +  ++  ++y   k aaee++ 
  gi|336253726|ref|YP_004596833.1|  93 H------HpelthdinvtaTLKLLKRAHDE-SARFVFASSAAVYG-QPESVPiseDAPTNPTSPYGVSKLAAEEYVq 161
                                       1......02233344533355555555554.56**********96.4554431113344567888889999999862 PP

                                       ...HHSSSEEEEEEE CS
                    NAD_binding_10 132 ...rasgldwTivrp 143
                                          ++ +ld +i+r 
  gi|336253726|ref|YP_004596833.1| 162 lyiEEFDLDAVILRY 176
                                       222678999999996 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.5e-07   0.00037       1      74 [.      15      85 ..      15      99 .. 0.83
   2 ?   -2.8   0.0       2.6   3.8e+03     161     194 ..     200     232 ..     191     259 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.5e-07
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---G CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgf 74
                                      Il++G++G +G+ +v+al+++ ++vr+l  d  s  ++s     ++l++gd+ +++ l++a  +vdv+f   ++
  gi|336253726|ref|YP_004596833.1| 15 ILITGGAGFIGSNIVEALVDE-NEVRVL--DNLSSGSRSNVPDEATLIEGDIRNDDDLDRATADVDVIFHQAAL 85
                                      89***************9975.689988..555555555555669************************87765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.6
                                       -TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHH CS
                              NmrA 161 appedkvtllgpgnpkavlldaeeDiGafvikil 194
                                       a+ ++ +t+ g+g     ++ +++Di ++ + +l
  gi|336253726|ref|YP_004596833.1| 200 ATTGNEITVEGDGTQTRDFV-HVQDIVRANLLAL 232
                                       44445677777777666666.7777766555444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.25   3.7e+02      54     107 ..      54     120 ..      38     162 .. 0.68
   2 !   15.8   0.0   6.2e-06    0.0093       4      55 ..     236     290 ..     233     301 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.25
                   Methyltransf_31  54 dnveFeqgdieelekl.ledekfDlilsnevl............naladpdkileeiervlkpggil 107
                                       d++++ +gdi + + l  + + +D+i+ +++l             +  +  ++l+ ++r+  +  ++
  gi|336253726|ref|YP_004596833.1|  54 DEATLIEGDIRNDDDLdRATADVDVIFHQAALisveksmhhpelTHDINVTATLKLLKRAHDESARF 120
                                       6778888888885544444488999999988877776655555544444444455555555555555 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 6.2e-06
                   Methyltransf_31   4 glrvlDlGCGtGeltfelae....elgpkaevvGiDiseeaielArenaqklgldn 55 
                                       ++ v  +G+G++  ++elae     +++++e+v +D  +  ie++r+  +kl++ n
  gi|336253726|ref|YP_004596833.1| 236 ATGVFNVGTGESVSILELAEtireIANSESEIVHVDARPSDIEKSRADISKLKS-N 290
                                       5667889*************88755566888****************9999987.3 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.1e-05     0.017       1     119 [.      13     113 ..      13     191 .. 0.75
   2 ?   -3.4   0.0       3.6   5.3e+03      16      44 ..     256     284 ..     252     292 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       k +l+tG+++ IG +i+++l+ e  +v v+d+ ++      +++ +   +a+ i++D+++ ++++++ +++      
  gi|336253726|ref|YP_004596833.1|  13 KEILITGGAGFIGSNIVEALVDE-NEVRVLDNLSSGS---RSNVPD---EATLIEGDIRNDDDLDRATADV------ 76 
                                       569******************99.5777777766655...455554...499*************999887...... PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltrav 119
                                        dv+ + A++       e s    e + ++N+t++++l + +
  gi|336253726|ref|YP_004596833.1|  77 -DVIFHQAALI----SVEKSMHHPELTHDINVTATLKLLKRA 113
                                       .7777777763....222333334555666666666666655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.6
                                       HHHHHHHTT-EEEEEESCHHHHHHHHHHH CS
                         adh_short  16 iakelakeGakvvvvdrseekleevakel 44 
                                       + +e+a++  ++v vd +++++e+  + +
  gi|336253726|ref|YP_004596833.1| 256 TIREIANSESEIVHVDARPSDIEKSRADI 284
                                       44555555555555555555555554444 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   0.00026      0.38       4      29 ..      16      41 ..      14     136 .. 0.72
   2 ?   -1.9   0.0       1.7   2.6e+03      44      66 ..     259     281 ..     246     291 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
                                      EEETTTSHHHHHHHHHHHHHHS-EEE CS
                                KR  4 litGGlGgLGlelarwlaekgarhlv 29
                                      litGG+G +G  +++ l+++ + +++
  gi|336253726|ref|YP_004596833.1| 16 LITGGAGFIGSNIVEALVDENEVRVL 41
                                      9*****************98754443 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                                       HHHHHHHTT-EEEE----TT-HH CS
                                KR  44 liaelealgaevevvaaDvsdkd 66 
                                       +ia+ e+  ++v++++ D+ ++ 
  gi|336253726|ref|YP_004596833.1| 259 EIANSESEIVHVDARPSDIEKSR 281
                                       33444444445555555555433 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00039      0.59       5      60 ..      20      74 ..      15     128 .. 0.88
   2 ?    0.4   0.0      0.51   7.6e+02      14      38 ..     254     281 ..     243     289 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00039
                                      S-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTG CS
                            TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagi 60
                                      G+G +G++++e L ++++ v v d+  +  ++   ++++ + gd  +++ L++a +
  gi|336253726|ref|YP_004596833.1| 20 GAGFIGSNIVEALVDENE-VRVLDNLSSGSRSNVPDEATLIEGDIRNDDDLDRATA 74
                                      79*************995.********99999999999*************99965 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.51
                                       HHHHHH.TT..EEEEEEESSHHHHHHHH CS
                            TrkA_N  14 aeeLse.gg..kdvvvidkdeerveelr 38 
                                       ae+++e ++  +++v +d +++ +e+ r
  gi|336253726|ref|YP_004596833.1| 254 AETIREiANseSEIVHVDARPSDIEKSR 281
                                       5555554444556888888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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 0.24s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 2374.44
//
Query:       gi|336253727|ref|YP_004596834.1|  [L=494]
Description: exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase [Halopiger xanaduensis SH-6]
Scores for 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-59  200.3   0.0    3.2e-59  199.6   0.0    1.3  1  Bac_transf  Bacterial sugar transferase
    3.4e-12   46.6   0.0    7.7e-12   45.5   0.0    1.7  1  DUF1970     Domain of unknown function (DUF1970)


Domain annotation for each model (and alignments):
>> Bac_transf  Bacterial sugar transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.6   0.0   3.6e-63   3.2e-59       1     183 [.     300     484 ..     300     485 .. 0.90

  Alignments for each domain:
  == domain 1  score: 199.6 bits;  conditional E-value: 3.6e-63
                        Bac_transf   1 KrlfDivlsllalillsplllvialliklessggpvffkqkRvGkngkpFkiyKFRsmvkdaekkl....gavvklk 73 
                                       KrlfDi+++++al+ l+p++++i+++ikl+ +gg+v+++q+R+   g+ F +yKFRsmv++ae+k+    +++ + +
  gi|336253727|ref|YP_004596834.1| 300 KRLFDIAFATAALVALAPIIVAISAAIKLD-DGGSVLYQQDRTAVFGESFAVYKFRSMVENAESKTgakiSEEDAGD 375
                                       9******************899******99.789*******************************944444444455 PP

                        Bac_transf  74 ndpritkvGrflRktslDELPqlinVLkGdMslVGpRPelpeeveeeieeyeee.eerlkvkPGltGlaqvnsgrse 149
                                        dpr+t+vGr+lRkt+lDE+Pql+++L GdMs+VGpRPe+pe  ++ei++     e+r  vkPGltGlaq+n+  + 
  gi|336253727|ref|YP_004596834.1| 376 VDPRVTRVGRLLRKTHLDEIPQLWSILVGDMSVVGPRPERPE-LDTEIQRDGIDwEKRWFVKPGLTGLAQINDVTG- 450
                                       689***************************************.556665665665688*************87777. PP

                        Bac_transf 150 lsleeklelDleYvenlslllDlkillktvkavl 183
                                        +  +kl +DleYv+++s+++D+ki+++ +++vl
  gi|336253727|ref|YP_004596834.1| 451 HEPGKKLWYDLEYVRRQSFWFDVKIVVRQIWKVL 484
                                       99*****************************998 PP

>> DUF1970  Domain of unknown function (DUF1970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   8.5e-16   7.7e-12       1     112 []     112     232 ..     112     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 8.5e-16
                                       ---SSHHHHHHHHHHHHHH.HHHHHTT-S-SS-TT----TT-SS---.....S-S---S----------.------- CS
                           DUF1970   1 dkkkllvvvgvllvllliw.lwirrrpavdvasnweGrtvivyddpq.....aGevslpvlGyvspssa.lpnrras 70 
                                       ++++l++++g l ++l++w +wirrrp        +Grt++v+dd       a  v  pvlGy +pss    + +  
  gi|336253727|ref|YP_004596834.1| 112 PRATLVMIIGLLGIVLPAWfVWIRRRPQGA-----DGRTLLVGDDLAqieriAPAVDAPVLGYLCPSSVdYYEFNEG 183
                                       699************************988.....9*********8889999***************9735677888 PP

                                       -------------------......------..TTTTHHHHHHHHHHHHH CS
                           DUF1970  71 vtgetdvsdavadGadlls......kltdsi..tsqlndyasslddvlve 112
                                         ge d     adG+  l       +l +++   s++++  s+l+d lve
  gi|336253727|ref|YP_004596834.1| 184 AIGEDDGMRVTADGGLALQhtggnqELEQALdeLSRIGGL-SRLEDTLVE 232
                                       9999999999999986554112222454444224777787.888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 3674.97
//
Query:       gi|336253728|ref|YP_004596835.1|  [L=374]
Description: hypothetical protein Halxa_2334 [Halopiger xanaduensis SH-6]
Scores for 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-22   79.3  14.4    7.4e-12   45.8   4.4    3.9  3  DUF4330   Domain of unknown function (DUF4330)


Domain annotation for each model (and alignments):
>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   4.4   4.1e-16   7.4e-12       1     166 [.       1     151 [.       1     152 [. 0.71
   2 ?    1.3   0.4      0.02   3.6e+02      46      87 ..     154     193 ..     149     208 .. 0.71
   3 !   33.0   0.2   3.5e-12   6.3e-08      87     154 ..     295     361 ..     248     368 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.1e-16
                           DUF4330   1 MkliDskgrlfgkvnilDllailvilavivgiflkpgts..gsvaqaeaaatkpvevdvvvrglev.peelak.vke 73 
                                       M+liD+kg+lfg vn++D+l++l++lav +++++++g    g   ++ + +  ++e ++    l + +++ a+ +  
  gi|336253728|ref|YP_004596835.1|   1 MELIDEKGNLFGVVNVIDALVVLLVLAVGIAGIAVVGVLgpGDDTTD-GDNGPSIETRYATIDLDTqSSSSAEaIAT 76 
                                       9**********************888885555555554433444444.44555566555444444436666665578 PP

                           DUF4330  74 gektniiirnqPagdveikdvkvlprkvvvpqpdGkvkaledepylkdllvtlegkakite.dglvlggqkvkvGke 149
                                       g++++         +++++dv + p +                  + d++v+ e +++  e  +l ++g+++  G++
  gi|336253728|ref|YP_004596835.1|  77 GDNMTSGVDD---ERLTVTDVYAIPTSSE----------------TADVTVRTEVEGTQYEnGTLAFSGSELASGHN 134
                                       9999988855...9999999999776654................2456666666666666256999********** PP

                           DUF4330 150 velegknyefnGsvidv 166
                                       + +++ +y+++Gs+  v
  gi|336253728|ref|YP_004596835.1| 135 ISIQTDEYDVTGSIKTV 151
                                       *************9887 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.02
                           DUF4330  46 eaaatkpvevdvvvrglevpeelak.vkegektniiirnqPag 87 
                                       ++a+ ++ e +v+++  +v++e+a+ ++ g++ +  ++    g
  gi|336253728|ref|YP_004596835.1| 154 TTAKLQTNETEVLFE-QTVDQETAEaIETGDESQLGNET--IG 193
                                       334566777888888.888******77999999988855..34 PP

  == domain 3  score: 33.0 bits;  conditional E-value: 3.5e-12
                           DUF4330  87 gdveikdvkvlprkvvvpqpdGkvkaledepylkdllvtlegkakitedglvlggqkvkvGkeveleg 154
                                       + +++++v+ +p++v v+++dG++++ ++ p ++d+++t+e + + t+ gl + +q+ + G +++l+ 
  gi|336253728|ref|YP_004596835.1| 295 TWATVTSVDREPASVIVETEDGNLHERQH-PTKYDVTLTVELQTRETDLGLQFKSQSFRNGETIYLDF 361
                                       557**************************.***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2837.23
//
Query:       gi|336253729|ref|YP_004596836.1|  [L=222]
Description: hypothetical protein Halxa_2335 [Halopiger xanaduensis SH-6]
Scores for 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   14.0   0.4        0.1   12.6   0.4    1.8  1  Sugarporin_N  Maltoporin periplasmic N-terminal extension


Domain annotation for each model (and alignments):
>> Sugarporin_N  Maltoporin periplasmic N-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   5.6e-06       0.1      21      40 ..       2      21 ..       1      32 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.6e-06
                      Sugarporin_N 21 aaaasltiEaRLaaLEkrLq 40
                                      +++++++i + L+aLE+rL+
  gi|336253729|ref|YP_004596836.1|  2 SDSNADSIQQTLEALEQRLR 21
                                      78999**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1769.58
//
Query:       gi|336253730|ref|YP_004596837.1|  [L=293]
Description: Undecaprenyl-diphosphatase [Halopiger xanaduensis SH-6]
Scores for 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-51  173.5  13.4      8e-51  173.2  13.4    1.0  1  BacA      Bacitracin resistance protein BacA
  ------ inclusion threshold ------
      0.071   12.9   2.4       0.71    9.7   0.1    3.0  3  DUF3767   Protein of unknown function (DUF3767)


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 !  173.2  13.4     9e-55     8e-51       1     254 [.      26     278 ..      26     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 173.2 bits;  conditional E-value: 9e-55
                              BacA   1 aiilGivqGltefLPvSSsGhlilveellglekedlllfdvvihlGtllAvlvlfrkdilrllkgllkslkkkkkek 77 
                                       a++ GivqG+ e+LPvSS+G l l+ +l+g++ e++l + +++++Gt l+  +++r+di + ++++ +++ +++   
  gi|336253730|ref|YP_004596837.1|  26 AVLAGIVQGIVEWLPVSSQGNLSLFLTLVGTSPEHALQLALFLQVGTTLSSALYYRDDIRESFAAVPEWRPSTAFIG 102
                                       6899*************************9986666779**********************9988888776665444 PP

                              BacA  78 eelrlllliivatipaailglllkdlieellrsp......lvvaialivtglllllaeklrkkkkksledltlkdal 148
                                       +++ +   ++va++ ++++g++l  +  ++++++       +++++l++tg+l l++e+++    ++ ++ tl+da+
  gi|336253730|ref|YP_004596837.1| 103 ANAVT-TFVVVACLATGLVGIPLYVFAADFVNELsgglfiAAIGALLVATGVLQLVSESVA---FEDRNEPTLRDAV 175
                                       44444.459***********9997555444444444457789999*************774...466678******* PP

                              BacA 149 liGlaQalAllPGvSRSGaTivaglllglsreaaaefSFllaiPailgagllkllksaealtasellllvgfvvafv 225
                                       ++G++Q+l++lPG+SRSG+T ++ l++ ++  +a+++SFll+iPa lgag+l ++++++    s  ++++++v+++v
  gi|336253730|ref|YP_004596837.1| 176 IVGAFQGLSILPGISRSGVTTSVLLFRSYQAPSAFRLSFLLSIPAGLGAGVLTVVTEGGVPGVSPSAAALAIVTSAV 252
                                       *****************************************************98777553344444499******* PP

                              BacA 226 vallaikfllkllkkkklkvFaiYrivlG 254
                                       v++++i +l++++++     F+i ++ lG
  gi|336253730|ref|YP_004596837.1| 253 VGYATIGLLMRVVERIP---FWIVCFGLG 278
                                       **************986...888888887 PP

>> DUF3767  Protein of unknown function (DUF3767)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2     0.034     3e+02      45      68 ..      10      33 ..       2      39 .. 0.72
   2 ?   -1.3   0.0      0.21   1.9e+03      21      37 ..     167     183 ..     149     194 .. 0.80
   3 ?    9.7   0.1   7.9e-05      0.71      20      65 ..     204     250 ..     188     258 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.034
                           DUF3767 45 vlkknvakaaNWavgafllgsiva 68
                                      ++  +v+++aNW   + +l+ iv+
  gi|336253730|ref|YP_004596837.1| 10 IVAPPVSTSANWEFLVAVLAGIVQ 33
                                      555689999***777777766654 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.21
                           DUF3767  21 siPCaRdslltGigaga 37 
                                       + P  Rd++++G   g 
  gi|336253730|ref|YP_004596837.1| 167 NEPTLRDAVIVGAFQGL 183
                                       56899999999976655 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 7.9e-05
                           DUF3767  20 vsiP.CaRdslltGigagavvGglrfvlkknvakaaNWavgafllgs 65 
                                       +++P  +R s+l++i ag ++G+l++v ++ v+  +  a +  +++s
  gi|336253730|ref|YP_004596837.1| 204 YQAPsAFRLSFLLSIPAGLGAGVLTVVTEGGVPGVSPSAAALAIVTS 250
                                       5666248*********************9955443333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); 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 0.18s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2478.35
//
Query:       gi|336253731|ref|YP_004596838.1|  [L=48]
Description: hypothetical protein Halxa_2337 [Halopiger xanaduensis SH-6]
Scores for 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  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 421.00
//
Query:       gi|336253732|ref|YP_004596839.1|  [L=805]
Description: hypothetical protein Halxa_2338 [Halopiger xanaduensis SH-6]
Scores for 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   2.0    0.00044   20.5   2.0    2.6  1  AglB_L1          Archaeal glycosylation protein B long periph
    0.00088   19.1   2.7     0.0031   17.4   2.7    1.9  1  Mannosyl_trans4  DolP-mannose mannosyltransferase
  ------ inclusion threshold ------
      0.041   12.8   5.1      0.068   12.1   5.1    1.5  1  STT3             Oligosaccharyl transferase STT3 subunit


Domain annotation for each model (and alignments):
>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   2.0   7.4e-08   0.00044       1      63 [.     731     791 ..     731     801 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.4e-08
                                       -EEEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS......-SSSSE CS
                           AglB_L1   1 GAtitGsaeagatvtasveletnqgrtftYrqeaeadedGefeltvPYstegeedgetnssve 63 
                                       GAt+  s+eag +v ++++++++ + + tY++ +  + dG+ ++tvPY+ e +  g++ ++v+
  gi|336253732|ref|YP_004596839.1| 731 GATLDVSGEAGSSVPLETTVSVS-DESITYERDVAIGDDGQGTVTVPYAGE-YAVGNQTVTVS 791
                                       9*********************9.679**********************99.67777776665 PP

>> Mannosyl_trans4  DolP-mannose mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   2.7   5.2e-07    0.0031      14      99 ..     174     263 ..     166     310 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.2e-07
                   Mannosyl_trans4  14 PlsfeiaavlallsgGdmyvlhtlsvvltilaaialvllvsliaseitGddiaallaGlallvlPelfllavaGvka 90 
                                       P s+++   la l gGd +    +++ l i+a++al +l+  +++ +t d  +++++ l + v P+  + +  G+  
  gi|336253732|ref|YP_004596839.1| 174 PSSHATNWFLAELLGGDQWAADIVAAWLPIVASVALAALIYKLTVLLTRDVRVGIASVLLFAVTPTHVVYTELGFID 250
                                       778888889*****************************************************************965 PP

                   Mannosyl_trans4  91 ....kyyvllfGl 99 
                                           +y+ l + l
  gi|336253732|ref|YP_004596839.1| 251 hqlhQYFWLGVTL 263
                                       1111455332222 PP

>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.1   1.1e-05     0.068     102     202 ..     197     314 ..     177     523 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.1e-05
                                       HHHCCHHHHHHHHCHHHHHHH.HHHS-CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHHHH....HHHHHH CS
                              STT3 102 vclwlpallgsLlaIpiyflv.relksdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllfvl....ffflka 173
                                       v+ wlp + +  la +iy l+   + + + G+++ ll a+ P+ +  t +Gf D+   + ++l ++l    ++ +  
  gi|336253732|ref|YP_004596839.1| 197 VAAWLPIVASVALAALIYKLTvLLTRDVRVGIASVLLFAVTPTHVVYTELGFIDHQLHQYFWLGVTLltlgWLAVDL 273
                                       677999999988999999988677777899***************************99999877762223445555 PP

                                       HHCCS..........TTCHHHHHHHHHHHHHH..TTSCCGG CS
                              STT3 174 iktks..........nkislaviaaliifliv..laWggya 202
                                       +++ +           +  + v++ + i + v   aWgg  
  gi|336253732|ref|YP_004596839.1| 274 QHRLEtggvvsdhlrSPATWVVACTFGISVAVgtHAWGGSP 314
                                       555559********989999998876665555116899964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (805 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); 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:                         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: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 5695.68
//
Query:       gi|336253733|ref|YP_004596840.1|  [L=795]
Description: hypothetical protein Halxa_2339 [Halopiger xanaduensis SH-6]
Scores for 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   26.6   7.9    3.9e-06   26.6   7.9    1.8  2  PGF-CTERM  PGF-CTERM motif
     0.0013   18.9   0.1     0.0013   18.9   0.1    4.3  6  CARDB      CARDB


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   1.1      0.75   6.7e+03       7      17 ..      20      30 ..      19      31 .. 0.81
   2 !   26.6   7.9   4.4e-10   3.9e-06       1      23 []     771     793 ..     771     793 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.75
                         PGF-CTERM  7 vlAlaGLLaaa 17
                                      vl ++++ aa+
  gi|336253733|ref|YP_004596840.1| 20 VLSVVAMSAAF 30
                                      8999**99975 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 4.4e-10
                         PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                       tPGFG+++A+++LLaaa La Rr
  gi|336253733|ref|YP_004596840.1| 771 TPGFGVAVAAIALLAAAMLALRR 793
                                       9****************999998 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2       1.7   1.5e+04      82      93 ..      82      93 ..      74      95 .. 0.85
   2 ?   -1.4   0.1      0.31   2.8e+03      25      59 ..     202     237 ..     182     289 .. 0.61
   3 ?   -0.7   0.1      0.19   1.7e+03      18      60 ..     310     354 ..     304     386 .. 0.71
   4 ?   -1.7   0.3      0.39   3.5e+03      74      94 ..     512     533 ..     472     544 .. 0.69
   5 ?   -1.8   0.3      0.42   3.8e+03      38      69 ..     578     608 ..     560     632 .. 0.61
   6 !   18.9   0.1   1.5e-07    0.0013       1      82 [.     641     718 ..     641     726 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.7
                                      EEESTT-SS--S CS
                             CARDB 82 vvvDpdnevaEs 93
                                      + vD+d++v E+
  gi|336253733|ref|YP_004596840.1| 82 AEVDSDADVVEE 93
                                      679999999997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.31
                                       EEEEE-SSS-.EEEEEEEEEETTEEEEEEEESEE-C CS
                             CARDB  25 vtvkNqGtaa.sgatkvalyldgelvgtvtvpsLaa 59 
                                       +t+kN G+++   a  +++ +d+ + +  t  sLa 
  gi|336253733|ref|YP_004596840.1| 202 LTLKNIGEDQeFSANFTDIDADDYEFDFETTDSLAE 237
                                       567777777633333345555555554444444443 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.19
                                       TSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE..SEE-CT CS
                             CARDB  18 geentitvtvkNqGtaasgatkvalyldgelvgtvtv..psLaag 60 
                                        ++++ ++t +N+G    +a + ++++++++v+ ++   ++Laa 
  gi|336253733|ref|YP_004596840.1| 310 YNTYSHNFTGENHGWSVHEAYEDDVTIEETNVSASPSqgNPLAAH 354
                                       566677778889999999999999999999985443333555554 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.39
                                       S-CEEEEEEEESTT-S.S--SS CS
                             CARDB  74 tegevtltvvvDpdne.vaEsn 94 
                                       t ++++lt++v +dn  v++++
  gi|336253733|ref|YP_004596840.1| 512 TDQSYDLTYTVTEDNPfVSDED 533
                                       5677778877777774143333 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 0.42
                                       EEEEEEETTEEEEEEEESEE-CTEEEEEEEEE CS
                             CARDB  38 tkvalyldgelvgtvtvpsLaagesttvsftw 69 
                                       + +++ ++g+ +++ +v ++a++++ t ++ +
  gi|336253733|ref|YP_004596840.1| 578 VDTSVRASGTFTESEDV-EVASDGTFTATYDF 608
                                       45666667777666666.45555555555444 PP

  == domain 6  score: 18.9 bits;  conditional E-value: 1.5e-07
                                       S--EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CE CS
                             CARDB   1 tpDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteatege 77 
                                       +pD  +  t++p+e++vg++ ++ vtv+N G  a++++++ + + +e v++ +v  L++g++ ++s+ + t+ ++g+
  gi|336253733|ref|YP_004596840.1| 641 QPDINI-DTSAPGEVTVGDDASLDVTVSNDGG-AAEEVEIGVDIADEPVASENV-TLEPGDEWSESYDFDTS-EAGD 713
                                       599999.9**********************95.6789****************9.8**********999998.8888 PP

                                       EEEEE CS
                             CARDB  78 vtltv 82 
                                       v   v
  gi|336253733|ref|YP_004596840.1| 714 VSWGV 718
                                       87555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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):               2  [number of targets reported over threshold]
# CPU time: 0.73u 0.23s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 5448.70
//
Query:       gi|336253734|ref|YP_004596841.1|  [L=969]
Description: Oligosaccharyl transferase STT3 subunit [Halopiger xanaduensis SH-6]
Scores for 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-26   91.5   6.2    8.7e-26   90.0   6.2    1.9  1  AglB_L1       Archaeal glycosylation protein B long periphera
    2.5e-20   72.9  15.4    1.3e-19   70.5  15.4    2.0  1  STT3          Oligosaccharyl transferase STT3 subunit
  ------ inclusion threshold ------
       0.14   12.8   4.2       0.86   10.2   4.2    2.4  1  Transmemb_17  Predicted membrane protein


Domain annotation for each model (and alignments):
>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.0   6.2   1.5e-29   8.7e-26       1      92 []     800     909 ..     800     909 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 1.5e-29
                                       -EEEEEEBSSS.....SEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS.........-SSSSEESS-EE CS
                           AglB_L1   1 GAtitGsaeag.....atvtasveletnqgrtftYrqeaeadedGefeltvPYstegee...dgetnssveaagpYe 69 
                                       GAtitG+++++     atvta+velet+ grtftY+qea ++edG+feltvPY+t++e    dg+tnssvea ++Y 
  gi|336253734|ref|YP_004596841.1| 800 GATITGTVDDQsivenATVTAAVELETDPGRTFTYEQEASVNEDGSFELTVPYATNDELsveDGYTNSSVEALSDYV 876
                                       9********9999999****************************************998999*************** PP

                                       EEETT..........EEEEE---HHHHHHT-EE CS
                           AglB_L1  70 vtagn..........vtaeveVpEeaVlsgetv 92 
                                       v++++          ++ ++eV+E+a+++getv
  gi|336253734|ref|YP_004596841.1| 877 VSVEQpgeqdlgvteYQGQTEVTESAIVDGETV 909
                                       ***888889999999****************98 PP

>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5  15.4   2.2e-23   1.3e-19      14     477 ..      41     589 ..      29     593 .. 0.70

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 2.2e-23
                                       CCHCC.CCCCCCT--S--SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEE.STTCCHCCC.CHHHH CS
                              STT3  14 avasrdlFtdedglsylsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrv.dygplivlLamlasa 89 
                                        + s+d Ft  dg + l   D++Y +R+++ +++n       ++++ ++   + +P G++v ++g+l   L ++++a
  gi|336253734|ref|YP_004596841.1|  41 RTQSFDRFTTGDGTPALAGIDSWYHWRTIQWTAEN-------YPHTMPYEIWTGFPEGNYVgQFGTLFDQL-IVTAA 109
                                       3444556****************************.......9*****************978********.999** PP

                                       HHCCHHC...HHHHHHHHCCHHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CC.CCCTTSTT--STCCCCHHH CS
                              STT3  90 iinhsld...vsirevclwlpallgsLlaIpiyflvrelksdiaGllAAlllaiaPg.YlsrtvaGfyDtdmfeivl 162
                                       +i    d    ++  v l+ ++l++ L+aIp++++ r+l + ++G+++ ++la++ g +lsr+  G  D+++ e+++
  gi|336253734|ref|YP_004596841.1| 110 MIVGLGDpsaQTLYTVSLLSIPLMAALVAIPVFYMGRRLGGTLGGIISIIILALSRGqFLSRSTVGQLDHHVGEALF 186
                                       **999999*99*************************************************************99998 PP

                                       HHHHHHHHHHHHHCCS..................TTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTT CS
                              STT3 163 llfvlffflkaiktks..................nkislaviaaliiflivlaWggyailiyallllfilalLiigr 221
                                       + +++  ++ a+  ++                   +  ++v+a+l++ l++  W    + ++ +  +f+++ L    
  gi|336253734|ref|YP_004596841.1| 187 MAIAVLAMMVALTVGErekpiyeliadkdwqplrTPALYSVLAGLALSLYIWVWPSG-VVLVGIFGAFFAVQLCLDY 262
                                       8777777777777777789**************99*********************9.8889999999999998776 PP

                                       ...S-CCHHHHH.HHHHHHHHHH..CCCCCCCTTCHHHSTTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCC.CH CS
                              STT3 222 ...felklkiav.tfsviiaflviaiivllflgfqvvavseiigalgifgllqlvafgsvvvlvaelkfyqfis.lf 293
                                          ++ +  + v  +s+ + +lv  +i++   gf              ++ll l + ++   + a+l+ +     + 
  gi|336253734|ref|YP_004596841.1| 263 lrgVSPDHIAFVgAVSLGVTTLV-TAILIERPGFGTTN------FSYLQPLLALSVAVGCLFM-AWLAREWNNRsID 331
                                       56666665555536666666666.67777777887533......3333444444444444443.2222222222022 PP

                                       HTT.HHHHTT--GGGHHHHHHHHHHHHC................................................C CS
                              STT3 294 qpgilsevlgligevvtalavlglialw................................................l 322
                                       +  +   v+g+ g    al +l+l+ l+                                                +
  gi|336253734|ref|YP_004596841.1| 332 RRYYPAAVVGI-GAGALALIWLVLPDLYstlvgnltgrllpvgasesaltvqevqppdnyfnhvfsesgsafytmlI 407
                                       22222233333.55555555666666555555666566666677778888889999999999999999998888775 PP

                                       CCCCTS---...--TTHHHHHHHHHS---S.--CCHHHCCSSSTTTTCCCHHHCHHCCHHCTCHHHHHHH....... CS
                              STT3 323 gilyslldl...eyaklkikiiilvsvwlp.vgllaltkglrfliftvPlgiifvgllleflavfvkiys....... 388
                                       g+ +  ++     +   ++ ++i+ s +l+ + ++ + ++ +++++++ + + fv  +++   + +++         
  gi|336253734|ref|YP_004596841.1| 408 GLVFLAIRPlfgRKFRAEHTLVIVWSLFLIsMAAAQVRFSYYLVLAIAVVNAAFVAEVVRLFDLDLTKRLesvrqle 484
                                       55555555577766666667777777666625555566777777777777777777777765555554445666555 PP

                                       HHHHHHCCC-SCHCCCCCHHHHHHHCCCHHHHHHHHCCHH...HHHHHHHHHHHH..............HHHHCT.T CS
                              STT3 389 vsqilfsgvvvillmltllpvlallaavkiskifstykde...keakikvaakav..............aptksngl 448
                                         q+l ++ vv ll + llp +a   a   ++ +  + d+   +ea+ +     +               + +  g+
  gi|336253734|ref|YP_004596841.1| 485 TYQVLTVVIVVLLLFAPLLPPIATATAWGSAESVGPNSDAmtwEEANHWLE---GntpepgdwadanntDELEYYGT 558
                                       555555555555555566666666666665543333333301133333332...13357788888633333333344 PP

                                       TTTHHH.TTHHHCHHH.HHHHHHHHHHHHHH CS
                              STT3 449 keslew.kantnrdsv.vitwwdyghilave 477
                                       +e  e   +  ++ s+ vi+wwdygh++++ 
  gi|336253734|ref|YP_004596841.1| 559 YEYPEDgDYDYPKGSYgVISWWDYGHLITTQ 589
                                       45555556777777766999******99876 PP

>> Transmemb_17  Predicted membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.2   0.00014      0.86      11      85 ..     430     500 ..     423     509 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00014
                      Transmemb_17  11 vlfflaelllliykgkllpypsnyllldvvllvlllllEvlRlylgykgNltekvpelalfllltlpvllplvyl 85 
                                       ++++l+ + +  ++   ++   +yl+l ++++ +++++Ev+Rl+      + e+v +l    +lt++++++l++ 
  gi|336253734|ref|YP_004596841.1| 430 IVWSLFLISMAAAQVR-FS---YYLVLAIAVVNAAFVAEVVRLFDLDLTKRLESVRQLETYQVLTVVIVVLLLFA 500
                                       6788888777766655.66...8*********************************************9999665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (969 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); 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:                         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: 0.76u 0.27s 00:00:01.03 Elapsed: 00:00:00.42
# Mc/sec: 6865.36
//
Query:       gi|336253735|ref|YP_004596842.1|  [L=306]
Description: family 2 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for 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-23   82.3   0.3    4.9e-23   81.8   0.3    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    8.2e-14   52.0   0.4    1.3e-13   51.3   0.4    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    6.2e-07   29.2   2.8    6.6e-07   29.1   0.4    1.9  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
      1e-05   25.6   0.0    1.4e-05   25.1   0.0    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
  ------ inclusion threshold ------
       0.12   12.7   0.8       0.88    9.9   0.1    2.1  2  PDZ_2            PDZ 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 !   81.8   0.3   1.4e-26   4.9e-23       1     166 [.       4     168 ..       4     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 1.4e-26
                                       EEEEEESS-..TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNe..ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnagl 75 
                                       svv +ty    ++   e+ +s+l+q +y+d+e++vv Dg     + +le++   +++v v  +++n G+ +++n+g+
  gi|336253735|ref|YP_004596842.1|   4 SVVLCTYDTdaYDDFCEAATSVLEQ-TYDDVELVVVVDGTDAVHERVLEDF-GDRDDVVVHCNDKNMGLLASRNRGA 78 
                                       89*******99**************.**************44455555555.6799999999*************** PP

                                       HH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCST CS
                   Glycos_transf_2  76 raatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnls 152
                                       + atgd+++f+D+D + d++wle lv+a+e+ +a ++ g+   +   +++   +++ +++  + + ++    +g++ 
  gi|336253735|ref|YP_004596842.1|  79 ELATGDVVAFIDDDAVADEQWLESLVDAYEEKNAIAAGGKMTPRWTADHPDFLPEE-FYWLVGVTHRGFADGPGEVR 154
                                       *******************************7776666666655556666666655.6899999999999999999* PP

                                       TCSTCCCEEEEHHH CS
                   Glycos_transf_2 153 feigsaallrreal 166
                                          gs+  +rr+++
  gi|336253735|ref|YP_004596842.1| 155 NTFGSNISFRRDVF 168
                                       ***********998 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 !   51.3   0.4   3.8e-17   1.3e-13       3     213 ..       2     223 ..       1     241 [. 0.79

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 3.8e-17
                   Glyco_tranf_2_3   3 dlavlVptfneed..vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77 
                                       d++v+ +t++ ++  +  e  +s+l q+y++ve+vvvvd+ da   +v+e + ++ + v v++  n++n g   +sr
  gi|336253735|ref|YP_004596842.1|   2 DVSVVLCTYDTDAydDFCEAATSVLEQTYDDVELVVVVDGTDAVHERVLEDFGDRDDVV-VHC--NDKNMGL-LASR 74 
                                       489*******99999999999**********************9999999876666443.554..7888886.7777 PP

                   Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarra 154
                                         n++ + +++d+v+++DdD+v +   l++l+ +++ +++ a+g+++  +    + ++l   ++      ++ +++ 
  gi|336253735|ref|YP_004596842.1|  75 --NRGAELATGDVVAFIDDDAVADEQWLESLVDAYEEKNAIAAGGKMTPRWTADHPDFLPEEFYWLVGVTHRGFADG 149
                                       ..9********************************666666666666666688999999998888888888888855 PP

                   Glyco_tranf_2_3 155 lg.vltlnGsgslirrevlkelegldp..lflltdDy......elglrlrr.agfrtayvpgaavrev.....f 213
                                        g v    Gs   +rr+v+ +leg+d   ++ ++d +      el+ r+ r +g  + yvp+a+v++      +
  gi|336253735|ref|YP_004596842.1| 150 PGeVRNTFGSNISFRRDVFLNLEGFDTdiGGRKGDKNlqggetELCARMQRkYGRGVWYVPEAEVEHKvfryrT 223
                                       55355445***************88877777777666666644777777668999999******8887544431 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 !   29.1   0.4   1.8e-10   6.6e-07      22     102 ..      26     103 ..       4     114 .. 0.72
   2 ?   -0.1   0.1      0.14   5.1e+02     165     187 ..     158     180 ..     153     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.8e-10
                   Glyco_tranf_2_2  22 kakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaDcfissDk 98 
                                         + yd ++el+vv dg       +++ + d    v   + +dk  +l a+rNrGa+ a +d+v F+D D       
  gi|336253735|ref|YP_004596842.1|  26 LEQTYD-DVELVVVVDGTDAVHERVLEDFGDRDDVVV--HCNDKNMGLLASRNRGAELATGDVVAFIDDDAVADEQW 99 
                                       333345.577777777777776889999999888887..8899***************************9887777 PP

                   Glyco_tranf_2_2  99 feki 102
                                       +e +
  gi|336253735|ref|YP_004596842.1| 100 LESL 103
                                       7765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.14
                   Glyco_tranf_2_2 165 sssilinrraflevGGyDErfrG 187
                                       +s+i  +r  fl++ G+D  + G
  gi|336253735|ref|YP_004596842.1| 158 GSNISFRRDVFLNLEGFDTDIGG 180
                                       799999************98855 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 !   25.1   0.0     4e-09   1.4e-05       1     130 [.      85     223 ..      85     303 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4e-09
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsga 77 
                                       +++++D+D v +++ l+ +++ +++ ++ ++ g+++++  a++   l   f+ +    ++ +++++g+v   +Gs++
  gi|336253735|ref|YP_004596842.1|  85 VVAFIDDDAVADEQWLESLVDAYEEKNAIAAGGKMTPRWTADHPDFLPEEFYWLVGVTHRGFADGPGEVRNTFGSNI 161
                                       5899********************98888888999998334444444444455677789999*************** PP

                   Glyco_trans_2_3  78 flrrsalq.......evggwdgdessvsEDfdmglrlq.rkGyrvrfvpeslv.kekspltl 130
                                       ++rr+++        ++gg +gd    +  ++++ r+q ++G  v +vpe+ v + +++++ 
  gi|336253735|ref|YP_004596842.1| 162 SFRRDVFLnlegfdtDIGGRKGDKNLQGGETELCARMQrKYGRGVWYVPEAEVeHKVFRYRT 223
                                       *******977777777779999999************9456688889999944244455543 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.13   4.6e+02      19      49 ..      36      71 ..      24      77 .. 0.70
   2 ?    9.9   0.1   0.00025      0.88      29      61 ..      77     109 ..      72     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.13
                                      EEE-TTSGGGGT.--T.....T-EEEEETTB--SSH CS
                             PDZ_2 19 vsVkeggPaakaglka.....gDvilkvdgkkvksl 49
                                      v V +g+ a  + +       +Dv+++ ++k +  l
  gi|336253735|ref|YP_004596842.1| 36 VVVVDGTDAVHERVLEdfgdrDDVVVHCNDKNMGLL 71
                                      45667777777775555888899*****99987655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00025
                                       GT.--TT-EEEEETTB--SSHHHHHHHHHTS-T CS
                             PDZ_2  29 kaglkagDvilkvdgkkvksledlislllkkkp 61 
                                       +a l++gDv+  +d+ +v +++ l+sl+ ++++
  gi|336253735|ref|YP_004596842.1|  77 GAELATGDVVAFIDDDAVADEQWLESLVDAYEE 109
                                       688*******************99999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2189.11
//
Query:       gi|336253736|ref|YP_004596843.1|  [L=340]
Description: group 1 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for complete 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   51.4   0.0    3.5e-13   50.2   0.0    1.6  2  Glyco_trans_1_4  Glycosyl transferases group 1
    8.4e-09   35.2   0.0    1.6e-08   34.3   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
     0.0042   17.5   3.4     0.0044   17.5   0.5    2.3  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0052   16.8   0.1       0.38   10.8   0.0    2.8  2  B12-binding      B12 binding domain
      0.008   16.2   0.1       0.06   13.4   0.0    2.0  2  Glyco_transf_4   Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> 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 ?   -3.6   0.0       3.8   1.4e+04      15      28 ..      98     111 ..      91     118 .. 0.68
   2 !   50.2   0.0   9.6e-17   3.5e-13       2     130 ..     172     298 ..     171     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.8
                                       GTHHHHHHHHHHHH CS
                   Glyco_trans_1_4  15 kgvdllleavpllr 28 
                                        + ++l+e v +l 
  gi|336253736|ref|YP_004596843.1|  98 NNPRWLAEIVRRLE 111
                                       57788888888877 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 9.6e-17
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEE CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprpeeleelaagleerveftGfv..edlaellaaadvf 76 
                                       +v ++vG l e++  ++ ll a+ +l ++ ++l++ G g+ +e++e+ aa  +e++++ G v  ed++ +l+aadv 
  gi|336253736|ref|YP_004596843.1| 172 NVAIYVGGL-EPIYHIRDLLAAATQLDES-WTLLVLGTGSLSEQIERAAA-AHENIVYPGTVphEDIPGYLRAADVG 245
                                       5789*****.899**************55.*********95579995554.4689********999*********** PP

                                       EE--.---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE-.-TT-HHHHHHHHHH CS
                   Glyco_trans_1_4  77 vaPs.egfglkllEamaaglpvVatdvggiaevvgengllv.ppgdpealaeailr 130
                                       v+       lk+lE+ aaglp+V  +   ++e    +gl+   +  p+++a+ai+r
  gi|336253736|ref|YP_004596843.1| 246 VCLVdDPHTLKVLEYGAAGLPTVQVRG-RAEE--RFDGLVEfCDPTPDSIARAIER 298
                                       ****889******************98.4477..4555322132269999999987 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   4.4e-12   1.6e-08      15     158 ..     171     302 ..     161     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 4.4e-12
                                       -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHH CS
                   Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellk 91 
                                       ++++++vg le+   +  l+ a+ +l    ++ + l++ G g+  +++++ a+++e+   + + g v++ed++ +l+
  gi|336253736|ref|YP_004596843.1| 171 ENVAIYVGGLEPIYHIRDLLAAATQL----DESWTLLVLGTGSLSEQIERAAAAHEN---IVYPGTVPHEDIPGYLR 240
                                       799*********************98....789***********9999999999988...***************** PP

                                       CESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHS CS
                   Glycos_transf_1  92 nadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklled 158
                                       +ad+ v+    ++  + +lE+ aaglp++ +   g ae   dg    +++p+ ++++a+ai++++e+
  gi|336253736|ref|YP_004596843.1| 241 AADVGVCL-VDDPHTLKVLEYGAAGLPTVQVR--GRAEERFDGLV-EFCDPT-PDSIARAIERAEEE 302
                                       *******9.779999************98654..33333222221.344444.67777777777766 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 !   17.5   0.5   1.2e-06    0.0044      63     148 ..      50     136 ..       8     143 .. 0.77
   2 ?   -0.2   0.1      0.33   1.2e+03      59      94 ..     185     221 ..     140     278 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.2e-06
                   Glyco_trans_4_4  63 lrrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtlhg..lllrrg.sgavrrlyralerrllrradavlvv 136
                                       l++l  +++ ++dvv   +  +++a+ ++++++g+pl+v+  +  + ++    ++++ ++r+le  ++r ad+vl+v
  gi|336253736|ref|YP_004596843.1|  50 LQSL--RDAGQYDVVAGTTRAGAIAGTAIKLATGTPLIVDHIDpiRQFETNnPRWLAEIVRRLENVAFRVADRVLYV 124
                                       3333..4889*********9999*******999*******99865556655689999999****************9 PP

                   Glyco_trans_4_4 137 seaeaeelralg 148
                                        ++e  ++ ++g
  gi|336253736|ref|YP_004596843.1| 125 YDEETPRVGRFG 136
                                       988877766665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.33
                   Glyco_trans_4_4  59 alralrrllrqrrerpdvvhahs.ptaglaarlarrr 94 
                                       ++r+l ++  q +e + ++++ + +++ ++ r+a++ 
  gi|336253736|ref|YP_004596843.1| 185 HIRDLLAAATQLDESWTLLVLGTgSLSEQIERAAAAH 221
                                       3444444434446666655554436666666666633 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00011      0.38      15      60 ..      23      67 ..      16      82 .. 0.88
   2 ?    2.8   0.0     0.032   1.1e+02      75     102 ..     166     193 ..     154     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                       B12-binding 15 lGlavlaaalrdagfeVqllganvenedivaairae.kpdvvglSal 60
                                      +G + +a++l+++g++V+l g +   +++++++r+  ++dvv+ +++
  gi|336253736|ref|YP_004596843.1| 23 VGRRRIADHLEESGVDVTLRGTTP--KTVLQSLRDAgQYDVVAGTTR 67
                                      67788***************9988..9********99*****98765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.032
                       B12-binding  75 lkrirprvkvvvGGahpsldpeetleak 102
                                       + ++ ++v + vGG  p ++ +++l+a+
  gi|336253736|ref|YP_004596843.1| 166 EGTVAENVAIYVGGLEPIYHIRDLLAAA 193
                                       5567789***********9999999765 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.11   3.9e+02       9      25 ..      26      42 ..      21      53 .. 0.82
   2 !   13.4   0.0   1.7e-05      0.06      64     143 ..      50     127 ..      41     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.11
                    Glyco_transf_4  9 leLaraLarrGheVtvv 25
                                      +++a +L + G++Vt+ 
  gi|336253736|ref|YP_004596843.1| 26 RRIADHLEESGVDVTLR 42
                                      5799***********97 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.7e-05
                    Glyco_transf_4  64 lrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviav 140
                                       l+ l +++++Dvv   +  a+  a+ a+++++g pl++  H    + +  ++ ++l  ++r+le+ ++r adrv+ v
  gi|336253736|ref|YP_004596843.1|  50 LQSLRDAGQYDVVAGTTR-AGAIAGTAIKLATGTPLIV-DHIDPIRQFETNNPRWLAEIVRRLENVAFRVADRVLYV 124
                                       55556677*****66665.555777888888*****87.56666699999999*********************998 PP

                    Glyco_transf_4 141 Sea 143
                                        ++
  gi|336253736|ref|YP_004596843.1| 125 YDE 127
                                       655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2463.67
//
Query:       gi|336253737|ref|YP_004596844.1|  [L=452]
Description: sulfatase [Halopiger xanaduensis SH-6]
Scores for 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  148.4   0.7    6.9e-43  147.2   0.3    1.7  2  Sulfatase      Sulfatase
    2.7e-05   24.4   0.5     0.0012   19.1   0.0    2.5  2  DUF4976        Domain of unknown function (DUF4976)
    0.00056   19.8   0.2       0.05   13.5   0.2    2.4  1  DUF4994        Domain of unknown function
     0.0064   17.2   0.0      0.016   15.9   0.0    1.7  1  Sulfatase_C    C-terminal region of aryl-sulfatase
  ------ inclusion threshold ------
      0.086   12.2   0.1       0.38   10.1   0.1    1.9  2  Metalloenzyme  Metalloenzyme superfamily


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.2   0.3   1.9e-46   6.9e-43       2     308 ..       3     332 ..       2     333 .. 0.88
   2 ?   -1.1   0.0      0.27   9.7e+02      96     139 ..     356     402 ..     342     429 .. 0.78

  Alignments for each domain:
  == domain 1  score: 147.2 bits;  conditional E-value: 1.9e-46
                                       EEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHHC CS
                         Sulfatase   2 nvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevggggl 78 
                                       +vvl+++d+l+a+++g  g++++ttpnld+la++  + tn+++ a ++ ps +++lt+ y+  +g +       + +
  gi|336253737|ref|YP_004596844.1|   3 DVVLVTVDSLRADHVGWHGYERETTPNLDALAKRSHTCTNAFAHACSTRPSFPSILTSSYALMYGGY-------ERI 72 
                                       69*************************************************************9977.......999 PP

                                       TTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHCCTTTSEEEETSSSCHHTCCCCCCCCCECTCCC......... CS
                         Sulfatase  79 pqteatLpellkeaGYntaaigkwhlgwssrqsvyknrgfdrflgfptgsaalkdpekseyngevlrv......... 146
                                        ++ + + e++ eaGY+t    ++h +++   ++   rgfd+f+++ t  +a ++   ++   ++l++         
  gi|336253737|ref|YP_004596844.1|  73 SPERTLISEVFDEAGYRT---AGFHSNLYLSADFDYDRGFDEFYDSKTDPSATAR--LRQFVKDQLDSdglvyqtla 144
                                       ******************...55566666555666699*******7777766666..33444444455799****** PP

                                       .............TTTTCSHHHHHHHHHHHHHHCCC.TSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH. CS
                         Sulfatase 147 .............ppeggysddrlldealefllarn.dkpfflylatlapHappeapdeyakkyatffddgseaar. 208
                                                    + + ++s d+++d ale+    + d p fl+++++ +H+p+  p++++ +++  +++ +e+ + 
  gi|336253737|ref|YP_004596844.1| 145 rafetaeetagvnIGSAYVSADEITDHALEWAESVTdDGPRFLWVHYMDVHHPYVPPERHQRAFR--DEPIGERRAi 219
                                       *******************************977777**************97666666666654..4455555445 PP

                                       ...................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTC CS
                         Sulfatase 209 ...................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkga 266
                                                            ++ y++ ++ +D++i+r+++++   + + +++ ++t+Dhg++  +   + + + +a
  gi|336253737|ref|YP_004596844.1| 220 qlrrkmiespedvteseleDIIDLYDAEIRFTDEQISRLIDTV--RERWGDVTALVTADHGEEFLD---HGQFSHYA 291
                                       8889999999999999***************************..*******************55...55555555 PP

                                       SSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHHHTT CS
                         Sulfatase 267 nayeggtrvPllvwwpgekaprvseelvshiDlfptildlag 308
                                       + y++ ++vPll   + +  +   + lv + D++pt+ + ag
  gi|336253737|ref|YP_004596844.1| 292 TFYDEVLHVPLLYDDSSGDGE-EHDDLVGLLDVTPTLVESAG 332
                                       89***********99999999.9***************9998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.27
                                       EEEEEES-SCCSGGGSHHC...CTTTSEEEETSSSCHHTCCCCCCCC CS
                         Sulfatase  96 taaigkwhlgwssrqsvyk...nrgfdrflgfptgsaalkdpeksey 139
                                        ++ig w+++ s +q +     ++ + r  ++ ++++  +dp+ +e 
  gi|336253737|ref|YP_004596844.1| 356 EHIIGDWENTNSGEQRFSYrdrEWKYIRTGDGEELYDLTADPDEREN 402
                                       578999****9999996547888888888888888888888876654 PP

>> DUF4976  Domain of unknown function (DUF4976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.034   1.2e+02      43      75 ..      91     123 ..      83     136 .. 0.81
   2 !   19.1   0.0   3.2e-07    0.0012       2      81 ..     336     407 ..     335     431 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.034
                           DUF4976  43 ygvrteryklihfykdidewelyDlkkDpkelk 75 
                                        g + + y    f +d  + e+yD k+Dp+   
  gi|336253737|ref|YP_004596844.1|  91 AGFHSNLYLSADFDYDRGFDEFYDSKTDPSATA 123
                                       56667777778899999999*********8765 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.2e-07
                           DUF4976   2 padmqGksllpllkgkkkkewrkalyYhyyeyPaehavkrhygvrteryklihfykdidewelyDlkkDpkelknly 78 
                                       p +  G+sl+ l++g  + + r+++  ++    ++++ ++ ++ r+ ++k i+   + d  elyDl +Dp+e +n++
  gi|336253737|ref|YP_004596844.1| 336 PPNFYGESLQSLFDG--DGWSREHIIGDW---ENTNSGEQRFSYRDREWKYIR---TGDGEELYDLTADPDERENVV 404
                                       666778888888884..566676666554...346888899999999999665...77999***************9 PP

                           DUF4976  79 ddp 81 
                                       d++
  gi|336253737|ref|YP_004596844.1| 405 DTE 407
                                       964 PP

>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   1.4e-05      0.05      56      93 ..     378     413 ..     341     418 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                           DUF4994  56 kltkielGnskepqLydlkkdegekenvaekhpekvke 93 
                                       +++ i +G    + Lydl++d+ e+env +++pe++++
  gi|336253737|ref|YP_004596844.1| 378 EWKYIRTGDG--EELYDLTADPDERENVVDTEPEILEH 413
                                       4555666654..679**************999998765 PP

>> Sulfatase_C  C-terminal region of aryl-sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.5e-06     0.016      52     104 ..     386     435 ..     360     445 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.5e-06
                                       CCEEEEETTT-TT--S-TTSTTCCHHHHHHHHHHHHHHHCCC------TCCHH CS
                       Sulfatase_C  52 dpPllFdlerDpsEkyplsaespeykevlkeikkaveehkktlkpvpnqlakg 104
                                       d   l+dl++Dp E+ ++       +e+l+++++++++h+++++++++ +  +
  gi|336253737|ref|YP_004596844.1| 386 DGEELYDLTADPDERENVV---DTEPEILEHARSVIDDHRQEVAATETDIGDV 435
                                       55679**************...567899999***********99998877665 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.2   7.3e+02      22      36 ..      22      36 ..       3      50 .. 0.68
   2 ?   10.1   0.1   0.00011      0.38     156     187 ..     246     279 ..     238     335 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.2
                                      HHHS--HHHHHHHHH CS
                                      xxxxxxxxxxxxxxx RF
                     Metalloenzyme 22 ihvAktPtldkLkke 36
                                       +   tP+ld+L+k 
  gi|336253737|ref|YP_004596844.1| 22 YERETTPNLDALAKR 36
                                      455569******987 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHTTS-TT..TEEEEEE-SSB- CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                     Metalloenzyme 156 aaieaaDeavkeildaieqv..dgilvvtADHgn 187
                                       a i   De++ +++d++++   d + +vtADHg 
  gi|336253737|ref|YP_004596844.1| 246 AEIRFTDEQISRLIDTVRERwgDVTALVTADHGE 279
                                       678889***********997557899*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3419.04
//
Query:       gi|336253738|ref|YP_004596845.1|  [L=315]
Description: family 2 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for complete 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  116.2   0.3    1.9e-33  115.6   0.3    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
      4e-23   82.5   0.2    6.3e-23   81.9   0.1    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    5.7e-13   49.0   0.0    7.3e-13   48.6   0.0    1.1  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
       0.21   11.8   0.0       0.45   10.8   0.0    1.4  1  EGF_CA           Calcium-binding EGF domain
          3    8.9   5.4        1.3   10.1   1.5    2.6  3  TPR_14           Tetratricopeptide repeat


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 !  115.6   0.3   5.4e-37   1.9e-33       1     114 [.       9     122 ..       9     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 5.4e-37
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak.edprvrvirreenvGkagalnaglr 76 
                                       sv++ptyN+++ l ++les+++q +y+++ei+vvDD+S+  + e +e l++  +  + vir++en+G  +a+n+g+r
  gi|336253738|ref|YP_004596845.1|   9 SVIVPTYNRPERLVRSLESIAEQ-TYDELEIVVVDDCSETPASEAIEPLRDeFPYELVVIRHDENRGANAARNTGIR 84 
                                       8**********************.**************99999999*****99************************ PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEE CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvvlg 114
                                       +a+g++++flD+Dde++p ++++ v+a+ + ++dv l+
  gi|336253738|ref|YP_004596845.1|  85 EASGEFLAFLDDDDEWAPSKVRRQVAAFRRAPEDVGLV 122
                                       ******************************99887544 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 !   81.9   0.1   1.8e-26   6.3e-23       4     212 ..       8     209 ..       6     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.8e-26
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       ++v+Vpt+n++++l++ les++ q+y+++e+vvv+d s++ + e +e l +++p  +++v++ ++n   +g+  a n
  gi|336253738|ref|YP_004596845.1|   8 VSVIVPTYNRPERLVRSLESIAEQTYDELEIVVVDDCSETPASEAIEPLRDEFPY-ELVVIRHDEN---RGANAARN 80 
                                       89*****************************************************.6999977775...56677778 PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqff.ltp.kvgavgtpv.fllnrstlvsalgalefaerhlrflaarra 154
                                        ++r +++++++++DdD+ + P  ++r++++f ++p +vg v+t   +++ +   ++ ++a  +  + +r+l+ r+a
  gi|336253738|ref|YP_004596845.1|  81 TGIREASGEFLAFLDDDDEWAPSKVRRQVAAFrRAPeDVGLVYTALqLVDDDGEEIRTTDA-SVSGDVTRTLLCRNA 156
                                       ********************************84446******666388888888888888.999************ PP

                   Glyco_tranf_2_3 155 lgvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrev 212
                                       +g      s++++r + +++ ++ld+ f  + D++   r+ ++++r+   p+++v+  
  gi|336253738|ref|YP_004596845.1| 157 IGSF----SCVMVRNAAVDDAGLLDEEFPSWQDLDWYIRI-SEEWRVEAIPEPLVTNH 209
                                       **87....58*************************66665.679********998765 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 !   48.6   0.0     2e-16   7.3e-13       1     206 [.       9     199 ..       9     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 2e-16
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGa 77 
                                       sv++p ++  er  +   +  +a +  +e+e++vvdd S  +  e ++ + d      +    d+  +  aarN G+
  gi|336253738|ref|YP_004596845.1|   9 SVIVPTYNRPER--LVRSLESIAEQTYDELEIVVVDDCSETPASEAIEPLRDEFPYELVVIRHDENRGANAARNTGI 83 
                                       799999999999..667787777777679*********************9986555444444567899******** PP

                   Glyco_tranf_2_2  78 skaesdlvlFlDaDcfissDkfekilklitikklreni.daavvlpvvdlnkedsevlkdvedltassrvledllaa 153
                                        +a ++++ FlD D+ +++ k+ +++      ++r+ + d  +v++  +l+++d e ++ + d  +s++v + ll  
  gi|336253738|ref|YP_004596845.1|  84 REASGEFLAFLDDDDEWAPSKVRRQVA-----AFRRAPeDVGLVYTALQLVDDDGEEIRTT-DASVSGDVTRTLLC- 153
                                       ************************999.....7777763678***************9876.57889****99999. PP

                   Glyco_tranf_2_2 154 kstlvkffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaiksl 206
                                            +  + s s ++++  a+   G  DE+f  ++  D d ++R+    +  
  gi|336253738|ref|YP_004596845.1| 154 -----RNAIGSFSCVMVRNAAVDDAGLLDEEF--PSWQDLDWYIRISEEWRVE 199
                                       .....44445559999****************..************9876543 PP

>> EGF_CA  Calcium-binding EGF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013      0.45      16      28 ..     151     163 ..     145     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                            EGF_CA  16 tvCvNteGsfeCv 28 
                                         C N +Gsf+Cv
  gi|336253738|ref|YP_004596845.1| 151 LLCRNAIGSFSCV 163
                                       57**********7 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         5   1.8e+04      16      30 ..      17      31 ..      16      38 .. 0.66
   2 ?   -2.6   0.0         4   1.4e+04      23      36 ..     111     120 ..     106     128 .. 0.58
   3 ?   10.1   1.5   0.00035       1.3       9      42 ..     261     294 ..     250     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5
                            TPR_14 16 dpdeAiallrralal 30
                                      +p++ ++ l+ + ++
  gi|336253738|ref|YP_004596845.1| 17 RPERLVRSLESIAEQ 31
                                      577777778777665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4
                            TPR_14  23 llrralalaPddae 36 
                                       ++    ++aP+d  
  gi|336253738|ref|YP_004596845.1| 111 AF----RRAPEDVG 120
                                       33....44577764 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00035
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeawllla 42 
                                       ++ l +G++++A +  rra+al+P ++++ l+ a
  gi|336253738|ref|YP_004596845.1| 261 WYALPAGQYETAQRFVRRAIALYPLEPQFFLYAA 294
                                       444458******************9998766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); 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:                         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 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2297.55
//
Query:       gi|336253739|ref|YP_004596846.1|  [L=359]
Description: cysteine synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-61  208.5   0.2    1.6e-61  208.3   0.2    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.073   13.1   1.5       0.73    9.9   0.0    2.6  3  CbiG_N    Cobalamin synthesis G N-terminal


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 !  208.3   0.2   1.8e-65   1.6e-61       4     293 ..      43     328 ..      40     329 .. 0.90

  Alignments for each domain:
  == domain 1  score: 208.3 bits;  conditional E-value: 1.8e-65
                                       CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaall 77 
                                        ig+TPlv+ p      g++++lKlE  nptgS+KdR a  ++ +l+ +   ++ ++vveassGN++ a+A++ ++l
  gi|336253739|ref|YP_004596846.1|  43 RIGETPLVDYPEP--TEGGDILLKLEADNPTGSMKDRVALGMIRELEAKgqlEADDVVVEASSGNTAGAVALVTNRL 117
                                       589*********5..59999*************************77777999************************ PP

                                       T-EEEEEEETTS-HHHHHHHHHTT-EEEEE....CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHH CS
                              PALP  78 GlkvtivvpadaspekvallrllGaevvev....ggdydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglE 149
                                       G+++++ vp+++s +k+   r++G e+ve+     gd  + +++a+++aae +g ++++q++  ++    y+++g+E
  gi|336253739|ref|YP_004596846.1| 118 GYDSVLTVPEGTSGQKIGYVRAFGSEIVECpdleSGDERHYRSTAERIAAE-RGGVWLDQYSTQLNPTVhYEWTGPE 193
                                       ******************************9887777777777799*****.************************* PP

                                       HHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B..SSS.CCSTCS.C CS
                              PALP 150 ileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvs.dtiadglavg.s 224
                                       +++q  g++++vv+p+G+Gg+++Gia+++ke+ +dv ++gv++e s+   +++     ++ p + dt ++gl+   +
  gi|336253739|ref|YP_004596846.1| 194 LWQQAAGDLTHVVCPMGTGGTLSGIARYVKEQTSDVDIVGVDAEKSNISEAFY-----DRDPGTyDTDVEGLGKErE 265
                                       ********************************************998888888.....222333499********77 PP

                                       GTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE- CS
                              PALP 225 pselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvvilt 293
                                         ++ f+++    de+ +v d  a+e +r+ a ++g++v+ ss+aa+a++  + a + ++  r+ vi +
  gi|336253739|ref|YP_004596846.1| 266 LPTMWFDYI----DEVRSVGDRRAFEEARRAAAEHGVLVGGSSGAAIAVA-REVADDQPNA-RIAVIGC 328
                                       788888666....56666********************************.5555555555.8888766 PP

>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.86   7.7e+03      48      63 ..      97     112 ..      93     124 .. 0.64
   2 ?    9.9   0.0   8.2e-05      0.73       3      47 ..     195     239 ..     193     242 .. 0.89
   3 ?    1.3   0.2     0.038   3.4e+02      52      69 ..     299     316 ..     293     326 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.86
                                       EEEEEE-TT.TTHHHH CS
                            CbiG_N  48 fvisllsGhlggAnel 63 
                                       +v+   sG   gA +l
  gi|336253739|ref|YP_004596846.1|  97 VVVEASSGNTAGAVAL 112
                                       5666677777777655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 8.2e-05
                                       HHHHCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT-- CS
                            CbiG_N   3 lrelfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagr 47 
                                       ++++  +   +v+ + +G +   ia ++k+ ++D  +v vd + +
  gi|336253739|ref|YP_004596846.1| 195 WQQAAGDLTHVVCPMGTGGTLSGIARYVKEQTSDVDIVGVDAEKS 239
                                       5677778899*******************************9876 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.038
                                       EE-TT.TTHHHHHHHHHH CS
                            CbiG_N  52 llsGhlggAnelAeeiaa 69 
                                       l++G +g A ++A+e+a+
  gi|336253739|ref|YP_004596846.1| 299 LVGGSSGAAIAVAREVAD 316
                                       89**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2772.55
//
Query:       gi|336253740|ref|YP_004596847.1|  [L=632]
Description: asparagine synthase [Halopiger xanaduensis SH-6]
Scores for complete 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    2.5e-08   33.9   0.0    1.6  1  GATase_7      Glutamine amidotransferase domain
    1.3e-06   28.4   0.7    1.1e-05   25.3   0.7    2.1  1  Asn_synthase  Asparagine synthase
    0.00032   20.9   0.1     0.0034   17.6   0.0    2.2  2  GATase_6      Glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   4.2e-12   2.5e-08       8     122 ..      47     158 ..      40     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 4.2e-12
                          GATase_7   8 dseagaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllalleaewgeealerlnGmfAfaiw 83 
                                            aQP ++  e+g+  + + G +   ++      ++    ++++D+  ++ lle+ +g ++++ ln +fA +++
  gi|336253740|ref|YP_004596847.1|  47 RETDAAQPATAqMESGEQLCWVWGDVIGAEDSTGYTPRQ---DQSTCDAAYCAGLLEE-QGLSFVDGLNSEFAGLVV 119
                                       555566666665556666666666666666666555444...4899******999997.9***************** PP

                          GATase_7  84 deeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       d+++++ +l  DrlG +P+y++e+ ++++lf++ l+ +l
  gi|336253740|ref|YP_004596847.1| 120 DRDRGEATLFTDRLGARPIYLTEALDGRVLFSTHLNTIL 158
                                       ************************988******999887 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.7   1.8e-09   1.1e-05      21     285 ..     252     516 ..     233     602 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.8e-09
                      Asn_synthase  21 GalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhlee 97 
                                       G+++SGG DS l+ +l       +++ +++    + +deak a +v+e l +e + l+ ++e l+d+l++v  +   
  gi|336253740|ref|YP_004596847.1| 252 GIFISGGSDSRLLLSLFEDR---DVTGYHLND--AMNDEAKTAYKVCEMLDVEFRFLQRDPEYLTDVLERVGDFQIF 323
                                       99**************9984...899999999..*******************999999999999999999885444 PP

                      Asn_synthase  98 .pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaalsrsrefeklp...............larsl 158
                                         f d++ ++   +  ++  +++  v+ G+ aD +  G  +  ++  +    +  +p                    
  gi|336253740|ref|YP_004596847.1| 324 sSFFDQAHFAG--FEDEL-TDEIDAVFAGHTADTVLEGFYMPTRDVDVP-GLEWTIPvpildqiagvdeyaeH---- 392
                                       56788885554..46778.888****************97444444444.33335556677776664443331.... PP

                      Asn_synthase 159 rasllarklrklaellelaeardleelaelyrlkasdsae...........aelegedelhrelyldlktllpgdll 224
                                                  ++  +++ +  ++ ++ ++++l+++ +a             +++g ++ + e+++++  ++p +  
  gi|336253740|ref|YP_004596847.1| 393 -----------ITCDYQYHRGPSVNSQPKCVTLEKDPVAVlrehmsesggaIDHHGVRYPSLESLVHTGGFYPITNN 458
                                       ...........222222222222222222222222211113333333456755666666666666666666666666 PP

                      Asn_synthase 225 rk..DrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLRealegylPeeileRpK 285
                                       ++     s+ + l +++P+lD+r++e+ l++p ++ +r    +++  +a+++   ++++e pK
  gi|336253740|ref|YP_004596847.1| 459 KAylMYYSANQMLPTHYPYLDNRVIEFSLSVPHRHHVR----RSVVNRAVAK-RNRALAEIPK 516
                                       66556679999***********************9999....5555555554.3455555555 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.6e-07    0.0034      29     132 ..      49     151 ..      29     153 .. 0.85
   2 ?    0.6   0.0       0.1   6.2e+02      62      97 ..     249     291 ..     237     299 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.6e-07
                          GATase_6  29 eegaqPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevllalleelGeevlerlrGmfafaiwdk 103
                                       +++aqP   + e+g+ l  + G++  +++     p+    + +s++D++  + llee G   ++ l+  fa  ++d+
  gi|336253740|ref|YP_004596847.1|  49 TDAAQPAtaQMESGEQLCWVWGDVIGAEDSTGYTPR----QDQSTCDAAYCAGLLEEQGLSFVDGLNSEFAGLVVDR 121
                                       466788877788888888888888888766666666....33568***99999************************ PP

                          GATase_6 104 rentlilardrlgvkplyyavd.esglafa 132
                                       ++++ +l +drlg +p y ++  +++++f+
  gi|336253740|ref|YP_004596847.1| 122 DRGEATLFTDRLGARPIYLTEAlDGRVLFS 151
                                       *******************99989888886 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.1
                          GATase_6  62 alkglafrsrsDtevllall...eelG...eevl.erlrGmfa 97 
                                       +++g  + + sD+ +ll l+   + +G    +++ ++++ +++
  gi|336253740|ref|YP_004596847.1| 249 DDDGIFISGGSDSRLLLSLFedrDVTGyhlNDAMnDEAKTAYK 291
                                       5566667889*********955433445555555455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); 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:                         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 0.22s 00:00:00.83 Elapsed: 00:00:00.39
# Mc/sec: 4846.90
//
Query:       gi|336253741|ref|YP_004596848.1|  [L=298]
Description: FkbM family methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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   54.2   0.0    2.7e-14   53.5   0.0    1.3  1  Methyltransf_21  Methyltransferase FkbM domain
    1.5e-05   24.4   0.0    3.9e-05   23.1   0.0    1.5  1  V_cholerae_RfbT  Vibrio cholerae RfbT protein


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0     3e-18   2.7e-14       1     169 [.     113     268 ..     113     272 .. 0.78

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 3e-18
                   Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndvglyelivegksg..gkyfpfav 75 
                                       dvGanig   + +  +   + +g++++a+EP+     + +kl +n     ++ + ++++ +  + s+  g++++   
  gi|336253741|ref|YP_004596848.1| 113 DVGANIG--THALLPA--AAHPGARIIAVEPHHR---NVAKLIRN---KTLNES-DSVTILPIALSDhtGTATLRGA 178
                                       9******..5555444..5689************...*****999...677755.6666666666666555666666 PP

                   Methyltransf_21  76 gdtngfstssvlggedaryievpvvtldsfleeikksridllkiDvEGaElevLeGaqkglkrcqpnlivvEvhkfk 152
                                        d  g ++ s   +++++  +vpv+  d+++ ++  +++ ++kiDvEGaE evL G +++l    ++ +++Evh  +
  gi|336253741|ref|YP_004596848.1| 179 DDRPGYGSFSLGDDTEETVADVPVRPGDDVIADG-VPKPSVVKIDVEGAEREVLDGLSETLAEGSIRTVFCEVHRHE 254
                                       66666666655559999999**********8888.8**************************************965 PP

                   Methyltransf_21 153 efetelfdeirqflrec 169
                                          + + ++++  l+++
  gi|336253741|ref|YP_004596848.1| 255 ---GVDESDVVGRLEDR 268
                                       ...35556666555555 PP

>> V_cholerae_RfbT  Vibrio cholerae RfbT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   4.4e-09   3.9e-05      72     212 ..     100     236 ..      92     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.4e-09
                   V_cholerae_RfbT  72 wivnhckhdttyidiganvgtfcgiaarhitqgkiiaiepltemensirmnvqlnnplvefhhfgcaigenegenif 148
                                        iv   + d  y d+gan+gt + + a      +iia+ep       +  n  ln+    +  +  a+ +  g   +
  gi|336253741|ref|YP_004596848.1| 100 AIVSELRDDDVYWDVGANIGTHALLPAAAHPGARIIAVEPHHRNVAKLIRNKTLNESD-SVTILPIALSDHTGTATL 175
                                       689999******************999988999*******998777777788888764.566789999999998876 PP

                   V_cholerae_RfbT 149 evyefdnrvsslyfkkntdiadkvknsqvlvrklssldisptnsvvikidaegaeieilnqiye 212
                                            d+r     f    d  + v +  v        d  p  sv +kid egae e+l+ + e
  gi|336253741|ref|YP_004596848.1| 176 --RGADDRPGYGSFSLGDDTEETVADVPVRPGDDVIADGVPKPSV-VKIDVEGAEREVLDGLSE 236
                                       ..5679999999999999999999988887777788899998886.6************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2395.80
//
Query:       gi|336253742|ref|YP_004596849.1|  [L=472]
Description: polysaccharide biosynthesis protein [Halopiger xanaduensis SH-6]
Scores for 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   61.3  14.7      1e-16   61.3  14.7    3.6  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    2.4e-16   59.8   6.4    2.4e-16   59.8   6.4    1.8  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    3.7e-15   56.1  21.4    3.7e-15   56.1  21.4    2.4  3  Polysacc_synt    Polysaccharide biosynthesis protein
    1.7e-06   27.0  16.7    1.7e-06   27.0  16.7    2.9  2  MurJ             Lipid II flippase MurJ


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 ?   -1.5   7.6      0.52   2.3e+03      61     139 ..      12      92 ..       4      96 .. 0.57
   2 ?    2.8   9.2     0.026   1.2e+02       7      85 ..     114     194 ..     109     255 .. 0.79
   3 !   61.3  14.7   2.3e-20     1e-16       1     141 [.     318     453 ..     318     455 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.52
                   Polysacc_synt_C  61 atvlallvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllglllla....alalllavlvgalv 133
                                       a+ +a  v  ++  ++l r+lg  +  l + + ++++++ + +++++ ++  ++ +l++    +  ++++ ++ a++
  gi|336253742|ref|YP_004596849.1|  12 ASQIASSVFGFVATIYLARTLGPGV--LGTYFLVVAVVVWLKVIAFGGVQSAITKRLSEgdepGAYIAAGTGLFAAI 86 
                                       4455555666666777788888777..33333333333333333333333333333333577666888888899999 PP

                   Polysacc_synt_C 134 Ylllll 139
                                       Y++l++
  gi|336253742|ref|YP_004596849.1|  87 YAVLVV 92 
                                       998887 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.026
                   Polysacc_synt_C   7 lsiiflsls.tvlssiLqglgrqkialkalvigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrrll 81 
                                       + ++f++l   ++s+ Lqg +r++i    + + +l   +l++      fg+ G +++ ++a +v+ ++  ++++ + 
  gi|336253742|ref|YP_004596849.1| 114 ILVLFAALLlLFVSATLQGQHRVHISGALSPVDMLSRSGLQIGAAlLGFGLFGLLAGYAVASIVAGLVGAIFVSWKW 190
                                       667777777799***********************999999988877788877777777777777766666665555 PP

                   Polysacc_synt_C  82 gikl 85 
                                       +++ 
  gi|336253742|ref|YP_004596849.1| 191 QLPE 194
                                       5554 PP

  == domain 3  score: 61.3 bits;  conditional E-value: 2.3e-20
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyal 77 
                                       vL+il+ + +++++   + + L+gl+r+++a++++ + ++ +++ln+ l+  +g  Gaa+at+++ lv+  + ++ l
  gi|336253742|ref|YP_004596849.1| 318 VLVILVAARLVYAYGEQFLNALNGLDRPDLAFRINGVFFVTNVGLNFALVATYGWRGAAVATAVSALVTVSIGYWVL 394
                                       6999999999*****99************************************************************ PP

                   Polysacc_synt_C  78 rrllgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllll 141
                                       +r + +++  lr +   +la++ m++vv  + +l+l+ + +   +++  v+vga  Y+++l+l 
  gi|336253742|ref|YP_004596849.1| 395 SRFIPVSF-PLRAVAMQVLATVPMAAVVG-CGRLFLEPSIP---VTVGLVAVGAGTYFAALFLV 453
                                       ********.79****************66.55555544443...6777777*********9986 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   6.4   5.4e-20   2.4e-16       2     282 ..      28     307 ..      27     313 .. 0.84
   2 ?   -3.5   0.8       1.1   4.7e+03     141     163 ..     375     397 ..     349     415 .. 0.54

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 5.4e-20
                   Polysacc_synt_3   2 LARLLspedFGvvaialvvislanlfvdmGlssaliqkedlteedlstvftfnlvlg...llialvlfllapliasf 75 
                                       LAR L p   G + ++++v+  +++++  G++sa+ ++ +  +e    +   + +++   +++ + l+l ++l+  +
  gi|336253742|ref|YP_004596849.1|  28 LARTLGPGVLGTYFLVVAVVVWLKVIAFGGVQSAITKRLSEGDEPGAYIAAGTGLFAaiyAVLVVGLYLGRDLVDAY 104
                                       9***********************************99977777444444444444400044455577889****** PP

                   Polysacc_synt_3  76 ynqpelvtvlrvl..alvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllss 150
                                       ++ p  ++++ vl  al l++ ++++      + + +     + + v ++    + i +Allg+g++ L+ g  ++s
  gi|336253742|ref|YP_004596849.1| 105 IGRPVTIPIILVLfaALLLLFVSATL------QGQHRVHISGALSPVDMLSRSGLQIGAALLGFGLFGLLAGYAVAS 175
                                       ********998762255555555555......5555555556677778888999*********************** PP

                   Polysacc_synt_3 151 llslvllwlaskwrprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvae 227
                                       ++  ++  ++++w+ +l  ++++l ++f +  +  l  l    ++++d+l+ G ++ s  +G+Y++a +lasl +a 
  gi|336253742|ref|YP_004596849.1| 176 IVAGLVGAIFVSWKWQL-PERRHLWSVFDYARYSWLGRLSSRTFSSMDTLVLGVFVASDLIGIYEIAWNLASL-LAV 250
                                       *****************.678*************************************************987.689 PP

                   Polysacc_synt_3 228 itsviakVlfPalSrlqdd..kkklrelylkvlrlialivlPiavglavvaellvkv 282
                                       ++ +i++ +fP +S++ +d  ++++ +l++ +++  +l+ +P +vg  ++ + +++v
  gi|336253742|ref|YP_004596849.1| 251 FSLAIQQTVFPEISSVAEDgdQERIVALLDDAFAYAGLFLIPGLVGCLLIGDFVLRV 307
                                       9***************98622667779999*****************9999988765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.1
                   Polysacc_synt_3 141 ALvigtllssllslvllwlaskw 163
                                       A v   + + ++ ++ +w+ s++
  gi|336253742|ref|YP_004596849.1| 375 AAVATAVSALVTVSIGYWVLSRF 397
                                       33334444444444444444444 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1  21.4   8.2e-19   3.7e-15       5     272 ..       7     265 ..       3     267 .. 0.81
   2 ?    2.1   2.7     0.023     1e+02     155     192 ..     364     397 ..     293     429 .. 0.68
   3 ?   -4.4   0.2       2.2   9.9e+03      34      54 ..     435     455 ..     432     464 .. 0.59

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 8.2e-19
                     Polysacc_synt   5 vivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnv 81 
                                       ++v+++sq+++  ++fv ++ylar+lgp   G + l++a+v+ l +++  G+  a++++ ++  e     ++i   +
  gi|336253742|ref|YP_004596849.1|   7 SFVTFASQIASSVFGFVATIYLARTLGPGVLGTYFLVVAVVVWLKVIAFGGVQSAITKRLSEGDE---PGAYIAAGT 80 
                                       799***********************************************************997...677777777 PP

                     Polysacc_synt  82 llvllvlvllfllllliaa....flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvi 154
                                        l   + ++l++ l+l  +      g+p    ++l+l+++ll      +f++  +qg++r       + v  lsr  
  gi|336253742|ref|YP_004596849.1|  81 GLFAAIYAVLVVGLYLGRDlvdaYIGRPVTIPIILVLFAALL-----LLFVSATLQGQHRVHISGALSPVDMLSRSG 152
                                       777777777777777775533335555555555555555555.....777777888888888888888888888766 PP

                     Polysacc_synt 155 l.vliavflfldivaavlgavlaalvggivslavlrkkfr.prfvilslklvrellsfsapltisslaillytyids 229
                                       l +++a+++f+ ++++++g+++a++v+g+v+++++  k+  p+     +++    + ++ +  +++l++  +  +d+
  gi|336253742|ref|YP_004596849.1| 153 LqIGAALLGFG-LFGLLAGYAVASIVAGLVGAIFVSWKWQlPE-----RRHLWSVFDYARYSWLGRLSSRTFSSMDT 223
                                       61566666666.************************5553222.....3344555666666669************* PP

                     Polysacc_synt 230 illglllgaeavGiYnaayqllvaisgllapivtaalfPvfse 272
                                       ++lg +  ++  GiY  a +l++++ ++  +i + ++fP +s 
  gi|336253742|ref|YP_004596849.1| 224 LVLGVFVASDLIGIYEIAWNLASLLAVFSLAIQQ-TVFPEISS 265
                                       **************************99999999.****9997 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.023
                     Polysacc_synt 155 lvliavflfldivaavlgavlaalvggivslavlrkkf 192
                                       + l+a++++    +a+++++++alv+  ++++vl + f
  gi|336253742|ref|YP_004596849.1| 364 FALVATYGWR---GAAVATAVSALVTVSIGYWVLSR-F 397
                                       4455666666...55555556666666666666552.3 PP

  == domain 3  score: -4.4 bits;  conditional E-value: 2.2
                     Polysacc_synt  34 gfGlvalalaivtllviltdl 54 
                                       ++Glva+ + +++ +  l++ 
  gi|336253742|ref|YP_004596849.1| 435 TVGLVAVGAGTYFAALFLVSG 455
                                       566666666666666666554 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.4      0.75   3.3e+03       5       5 ..      32      32 ..       9      64 .. 0.51
   2 !   27.0  16.7   3.7e-10   1.7e-06     222     428 ..     224     423 ..     108     443 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.75
                              MurJ  5 l 5 
                                      l
  gi|336253742|ref|YP_004596849.1| 32 L 32
                                      1 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 3.7e-10
                              MurJ 222 talAsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltllllipvsfgllv 298
                                       ++l  f+a+  + i++ a+ ++ l l++f+++i  +++P++S +a+++d++ + +ll++a     l lip  +g l+
  gi|336253742|ref|YP_004596849.1| 224 LVLGVFVASDLIGIYEIAWNLASL-LAVFSLAIQQTVFPEISSVAEDGDQERIVALLDDAFAYAGLFLIPGLVGCLL 299
                                       455556777888899999999998.79************************************************** PP

                              MurJ 299 lskpivsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlnillsllllpp 375
                                       +++ +++++         ++ a   vL +  ++ + ya  + +l+++    +   ++ i  +++v+n++l++ l+ +
  gi|336253742|ref|YP_004596849.1| 300 IGDFVLRVYG-------PEFGAGHVVLVILVAARLVYAYGEQFLNALNGLDRPDLAFRINGVFFVTNVGLNFALVAT 369
                                       ***9999875.......45566667888888999999999************************************* PP

                              MurJ 376 lgvvglalatslsaliglvllyvllrkrlk.lteargiktflaklvvllalaav 428
                                       +g  g a+at++sal+ + + y++l +     ++ r++++ + ++v ++a+++ 
  gi|336253742|ref|YP_004596849.1| 370 YGWRGAAVATAVSALVTVSIGYWVLSRFIPvSFPLRAVAMQVLATVPMAAVVGC 423
                                       ***************************998456788889888886655555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 3233.61
//
Query:       gi|336253743|ref|YP_004596850.1|  [L=253]
Description: UTP--glucose-1-phosphate uridylyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-40  137.8   0.0    5.3e-40  137.6   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    2.4e-14   54.0   0.0    2.9e-14   53.7   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    7.2e-07   29.2   0.0    5.4e-06   26.3   0.0    2.0  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.021   14.6   0.0      0.029   14.2   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2


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 !  137.6   0.0   1.2e-43   5.3e-40       2     237 ..       3     226 ..       2     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: 137.6 bits;  conditional E-value: 1.2e-43
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       av+La G+GtRL PLt + +k lv v gk ++i+ ++ +l++ g  e ivv+ +++++++e++  ++++ gv +++a
  gi|336253743|ref|YP_004596850.1|   3 AVVLAAGKGTRLQPLTDDKPKVLVEVDGK-PIIEDVFDNLLEIGASEFIVVVGYQKEQIIERYG-DAYE-GVPITYA 76 
                                       8****************************.*****************88888877777776665.5553.889**** PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECT CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieade 155
                                       +++e+ g+A+A+++a+  ++ ++    +l+Lg D +++ ++ ++v++ +e++a+   ++  vp eea++yGv  ++e
  gi|336253743|ref|YP_004596850.1|  77 HQREQLGLAHAILQAEPHVDGDF----MLMLG-DNVFRANLADVVNRQQEDRADAAFLVEEVPYEEASRYGVLDTNE 148
                                       ********************988....66665.667788**************9999999***************** PP

                                       TSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE.E CS
                   NTP_transferase 156 egrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs.D 231
                                        g++ +  EKP+ ++ s+l+ +G Y+f++ +++   + +++++rge e+ d++  ++++g+   a ++ d  +W+ D
  gi|336253743|ref|YP_004596850.1| 149 YGEIVEVMEKPDDPP-SNLVMTGFYTFTPAIFHAC-HLVQPSDRGEYELPDAIDLLIQSGRTIDA-IRMD--GWRvD 220
                                       ***************.*****************99.89*********************977755.6666..5855* PP

                                       XSSHHH CS
                   NTP_transferase 232 vGtlds 237
                                       vG +++
  gi|336253743|ref|YP_004596850.1| 221 VGYPED 226
                                       **9887 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 !   53.7   0.0   6.4e-18   2.9e-14       1     123 [.       3     131 ..       3     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 6.4e-18
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC..TS-EEE-TTS CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaalarl..gvrvvededp 68 
                                       av+LA+G+++R++     ++K l++++gkp++e v+d+l + g++e +vv+g+  e++ +++ +   gv++++  + 
  gi|336253743|ref|YP_004596850.1|   3 AVVLAAGKGTRLQpltddKPKVLVEVDGKPIIEDVFDNLLEIGASEFIVVVGYqkEQIIERYGDAyeGVPITYAHQR 79 
                                       79**********75443259******************************999444444433222445666555444 PP

                                       .S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEES CS
                      NTP_transf_3  69 .gkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvpty 123
                                        + g +++++ a  ++  +  ++++++D ++  ++ ++ ++++ ++++ad+++++ 
  gi|336253743|ref|YP_004596850.1|  80 eQLGLAHAILQAEPHV--DGDFMLMLGDNVF--RANLADVVNRQQEDRADAAFLVE 131
                                       1789999999999998..67889999***99..77788888888889999888765 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 !   26.3   0.0   1.2e-09   5.4e-06       1      55 [.       1      58 [.       1      67 [. 0.89
   2 ?    0.3   0.0      0.11   4.8e+02     156     219 ..     174     234 ..     151     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.2e-09
                                      EEEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGG CS
                              IspD  1 vvvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvsedd 55
                                      + +v+ AAG+G+R++    ++pK ++e++g++++e   d ll+ +a + ivvv  +++
  gi|336253743|ref|YP_004596850.1|  1 MQAVVLAAGKGTRLQpltDDKPKVLVEVDGKPIIEDVFDNLLEIGASEFIVVVGYQKE 58
                                      579**********9744479****************************9999987765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.11
                                       EEEEEEEHHHHHHHHHHHHHCT---SSHHHHHHHTT--EEEEE--TTG----SHHHHHHHHHHH CS
                              IspD 156 qtPqgFrvdlllaahakgeqegaeitDdaslvekiGlsvkvVeGeednlKittpeDlalAeail 219
                                        tP  F+   l +  ++g    +e  D ++l+ + G ++  +  +   + + +peD   Aea l
  gi|336253743|ref|YP_004596850.1| 174 FTPAIFHACHLVQPSDRG---EYELPDAIDLLIQSGRTIDAIRMDGWRVDVGYPEDRDKAEARL 234
                                       355555555555555555...5779999999999999999999999999999999999999865 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 ?   14.2   0.0   6.4e-06     0.029      42     115 ..      57     130 ..      29     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.4e-06
                                       HHHHHGGGCH..C-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEE CS
                   Glycos_transf_2  42 tveileelak..edprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklvealekdgadvvlgq 115
                                        ++i+e++ +  e+ ++++ ++ e  G+a a+ ++  +++gd++l l  D ++    l ++v++ ++d+ad+++  
  gi|336253743|ref|YP_004596850.1|  57 KEQIIERYGDayEGVPITYAHQREQLGLAHAILQAEPHVDGDFMLMLG-DNVFRA-NLADVVNRQQEDRADAAFLV 130
                                       579999999999999*****************************9995.455554.38888888888777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1942.12
//
Query:       gi|336253744|ref|YP_004596851.1|  [L=284]
Description: transcriptional regulator TrmB [Halopiger xanaduensis SH-6]
Scores for 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-20   70.3   0.0    1.8e-19   69.4   0.0    1.5  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0033   17.2   0.0     0.0059   16.4   0.0    1.5  1  HTH_IclR  IclR helix-turn-helix domain
     0.0051   16.7   0.3      0.038   13.9   0.0    2.4  3  MarR_2    MarR family
  ------ inclusion threshold ------
      0.024   14.7   0.1      0.087   12.9   0.0    2.0  2  HTH_20    Helix-turn-helix domain
      0.075   13.4   0.0       0.13   12.6   0.0    1.3  1  Rrf2      Transcriptional regulator
       0.15   12.2   0.0       0.26   11.4   0.0    1.3  1  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d


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 !   69.4   0.0   6.1e-23   1.8e-19       1      68 []      10      77 ..      10      77 .. 0.99

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 6.1e-23
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                                      Lq l+L+eyEa + + Ll+ g+ ta +i+ ++++p+++vY vL+sL d G++e+++grpk Y++ +pe
  gi|336253744|ref|YP_004596851.1| 10 LQQLDLKEYEATALAHLLSAGRTTAPDISDATDIPQARVYGVLESLADYGFIEVIPGRPKQYQPKSPE 77
                                      899**************************************************************997 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 !   16.4   0.0     2e-06    0.0059       9      49 ..      23      62 ..      20      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2e-06
                                      HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      L +l +a++  t  +++++t++p + v++ L +L   G++e
  gi|336253744|ref|YP_004596851.1| 23 LAHLLSAGRT-TAPDISDATDIPQARVYGVLESLADYGFIE 62
                                      5566667775.999*************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.3e-05     0.038       7      56 ..      19      66 ..      13      69 .. 0.92
   2 ?   -2.9   0.0       2.3   6.7e+03      21      30 ..     193     202 ..     182     206 .. 0.72
   3 ?   -0.3   0.0      0.35     1e+03      50      62 .]     240     252 ..     240     252 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      +a +La+L  +++   t+ ++ +++++++++v  +l+ L + G++e  pg
  gi|336253744|ref|YP_004596851.1| 19 EATALAHLLSAGR--TTAPDISDATDIPQARVYGVLESLADYGFIEVIPG 66
                                      7889*******98..9*****************************98876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                                       EEEHHHHHHH CS
                            MarR_2  21 dltvgelarr 30 
                                         t++e+++r
  gi|336253744|ref|YP_004596851.1| 193 AATQAEIVDR 202
                                       3588998887 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.35
                                       SEEEEESSSSSSS CS
                            MarR_2  50 LverrpgpeDkRa 62 
                                       Lve+++ p+++R+
  gi|336253744|ref|YP_004596851.1| 240 LVEETDVPNHRRQ 252
                                       89**********5 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.9e-05     0.087      16      59 ..      23      66 ..      10      68 .. 0.93
   2 ?   -1.8   0.0       1.1   3.4e+03      17      33 ..     186     202 ..     168     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                                      HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 16 lraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      l++L +a+  ta+++ ++ d++++ ++  L+ L++ g++ev   
  gi|336253744|ref|YP_004596851.1| 23 LAHLLSAGRTTAPDISDATDIPQARVYGVLESLADYGFIEVIPG 66
                                      6788899*********************************9865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                       HHHSTCTTB-HHHHHHH CS
                            HTH_20  17 raLaraegltaselaer 33 
                                       r+L+ ++++t +e+ +r
  gi|336253744|ref|YP_004596851.1| 186 RHLPAEKAATQAEIVDR 202
                                       56777777777776655 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.5e-05      0.13      12      62 ..      21      68 ..      15      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.5e-05
                                      HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT- CS
                              Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkg 62
                                      +al++L +  +    ++ +i++ ++i++  +  +l+ L+  g+++++ G+ 
  gi|336253744|ref|YP_004596851.1| 21 TALAHLLSAGR---TTAPDISDATDIPQARVYGVLESLADYGFIEVIPGRP 68
                                      55555544444...79*********************************85 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.9e-05      0.26      20      52 ..      24      56 ..      19      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.9e-05
                                      HHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHH CS
                             HTH_9 20 etLlrkgrltlrelvkktkLsldqVkksLvvLi 52
                                       +Ll+ gr t+ +++ +t+++   V  +L +L 
  gi|336253744|ref|YP_004596851.1| 24 AHLLSAGRTTAPDISDATDIPQARVYGVLESLA 56
                                      79*********************9999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 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:                        49  (0.002733); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2133.66
//
Query:       gi|336253745|ref|YP_004596852.1|  [L=330]
Description: UDP-glucose 4-epimerase [Halopiger xanaduensis SH-6]
Scores for 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-39  136.4   0.0    1.5e-39  135.9   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    6.9e-30  104.6   0.0    7.9e-30  104.4   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.1e-25   89.4   0.1    2.6e-25   89.1   0.1    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    4.4e-21   75.1   0.0    1.1e-20   73.8   0.0    1.7  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.1e-16   60.0   0.0    1.3e-15   57.3   0.0    2.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    3.2e-08   33.1   0.0    4.5e-05   22.7   0.0    2.6  2  NAD_binding_4    Male sterility protein
    8.2e-08   32.3   0.0    2.3e-07   30.9   0.0    1.9  1  NAD_binding_10   NAD(P)H-binding
    9.3e-05   22.1   0.1    0.00065   19.3   0.0    2.2  2  NmrA             NmrA-like family
     0.0011   19.3   0.1       0.01   16.3   0.0    2.2  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0054   16.9   0.2      0.014   15.5   0.0    1.8  2  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0077   16.5   0.0      0.021   15.1   0.0    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.012   14.7   0.3      0.018   14.1   0.3    1.2  1  Calsequestrin    Calsequestrin
      0.014   15.5   0.0      0.025   14.7   0.0    1.3  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do


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 !  135.9   0.0   1.1e-42   1.5e-39       1     228 [.      14     237 ..      14     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: 135.9 bits;  conditional E-value: 1.1e-42
                                       EEEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S-- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekg..yevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavg 75 
                                       i +tGa+G+iGs +v++l++ +  +++ +ld++ ++++ +++ +++++++d++dr +le++++  ++d+v+hlAav+
  gi|336253745|ref|YP_004596852.1|  14 IAITGAAGYIGSRVVQQLQSTHpnWTLRALDNY-YRGQVESIGETDVTHVDVRDRRRLEEALD--GADIVLHLAAVS 87 
                                       689*****************9988889999999.89999999999******************..9*********** PP

                                       -HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHH CS
                         Epimerase  76 gvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlagekl 152
                                       gv++  e+p   +e n+ gt n++  +rk+g   l+f  S +v G++++ p + ++   p  p + Y+++Kl+ge+ 
  gi|336253745|ref|YP_004596852.1|  88 GVDDCDENPDLAYEVNVTGTNNVAWFCRKTGT-GLVFPFSMAVLGDPEQFPITADL---PRDPFNWYGRTKLLGERA 160
                                       ********************************.************999999*****...99999************* PP

                                       HHHHHHHHT-EEEEEEESEEESTT..S-TTS...TTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHH CS
                         Epimerase 153 veayaaqyglnaiilrlfnlyGpr..ngege...vsrvipalirkilegkqevtllgdgtalRdflyveDvaeaill 224
                                       +e++a+   ++a  +  +nlyG +  +  ++      vi  +++++ +g+ ++t++  gt+ R f++v+Dva+a+++
  gi|336253745|ref|YP_004596852.1| 161 IESFADGA-FPAHLFLKSNLYGDHtvD--ETvvsKPTVINFFVERATAGE-PLTVYEPGTQSRNFVHVKDVARAYVR 233
                                       ****7776.***************642..4431366799**********9.*************************9 PP

                                       HHHH CS
                         Epimerase 225 vleh 228
                                        +e+
  gi|336253745|ref|YP_004596852.1| 234 SAER 237
                                       8887 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 !  104.4   0.0   5.7e-33   7.9e-30       2     331 ..      16     324 ..      15     325 .. 0.82

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 5.7e-33
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       iTG aG+iGs ++++L + + +   + r  ++++ g++e++ +           + ++D++D+++le++l+ +  d 
  gi|336253745|ref|YP_004596852.1|  16 ITGAAGYIGSRVVQQLQSTHPNW--TLRALDNYYRGQVESIGE---------TDVTHVDVRDRRRLEEALDGA--DI 79 
                                       9****************998776..5688889999****9975.........34789***************9..89 PP

                                       EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHH CS
                     GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaa 155
                                       v++LAA s Vd   e+P+  +evnv+Gt ++   +r++g      +++  +  v G++++ p+t + p +P + Y+ 
  gi|336253745|ref|YP_004596852.1|  80 VLHLAAVSGVDDCDENPDLAYEVNVTGTNNVAWFCRKTGT----GLVFPFSMAVLGDPEQFPITADLPRDPFNWYGR 152
                                       *************************************985....566677999************************ PP

                                       HHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCC...HHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHH CS
                     GDP_Man_Dehyd 156 aKlyadwivvnyreayglfavngilfnhesprrgetfvtr...kitravarialgkqevlylGnldakRdwghvkDy 229
                                       +Kl  +  ++++ +   ++a     +n ++ +   + v      i  +v r+++g+ + +++  + + R + hvkD+
  gi|336253745|ref|YP_004596852.1| 153 TKLLGERAIESFADG-AFPAHLFLKSNLYGDHTVDETVVSkptVINFFVERATAGE-PLTVYEPGTQSRNFVHVKDV 227
                                       ***********9985.5788888999999999876654431424556677777776.9999***************9 PP

                                       HHHHHHHHHCSS---EEE-TT.-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB CS
                     GDP_Man_Dehyd 230 veamwlmlqqdkpedyviatg.ethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdl 305
                                       ++a+++  ++  ++  + +tg et ++ +  + +++e+ +t+         +++ +++ +v+   +p+ + ++ v+ 
  gi|336253745|ref|YP_004596852.1| 228 ARAYVRSAERMFTQLANDETGiETCEIAGNEDPSVMEVAETVRDLA-----REELDKTVDVELVENPRSD-ETMVED 298
                                       9998886666555444444443566777777777777777665443.....2334556676666677766.67899* PP

                                       --B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 306 llgdaskakeeLgWkpkvsfeelvre 331
                                        + d+ska+e L+W+++ ++ee vr+
  gi|336253745|ref|YP_004596852.1| 299 FAVDTSKANEVLEWEARHTVEESVRD 324
                                       **********************9997 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 !   89.1   0.1   1.9e-28   2.6e-25       3     249 ..      14     291 ..      12     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 1.9e-28
                                       EEEESTTSHHHHHHHHHCTT..TSEEEEEE-TT..............T--TTSHHHHHHHHHHH--SEEEE------ CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlae..eglevlaltre..............eldltdaeavaellkeakpdvvvnaAAyta 63 
                                       i +tGa G +Gs +++ql++   ++ + al++               ++d++d+ +++e+l+    d+v ++AA   
  gi|336253745|ref|YP_004596852.1|  14 IAITGAAGYIGSRVVQQLQSthPNWTLRALDNYyrgqvesigetdvtHVDVRDRRRLEEALDG--ADIVLHLAAVSG 88 
                                       89****************98435677888877799***************************9..899********* PP

                                       HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH.. CS
                     RmlD_sub_bind  64 vDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla.. 138
                                       vD + +++++ay+vn+++++++A  ++++g  L++  +  V    ++ p + d + +P n YGrtKl+GE+a+++  
  gi|336253745|ref|YP_004596852.1|  89 VDDCDENPDLAYEVNVTGTNNVAWFCRKTGTGLVFPFSMAVLGDPEQFPITADLPRDPFNWYGRTKLLGERAIESfa 165
                                       ******************************************9999999*************************987 PP

                                       ..H-SSEEEEEE-SEESS........SSS-HHHHHHHHHHH-SEEEEES..S-EE--EEHHHHHHHHHHHHHHCHH. CS
                     RmlD_sub_bind 139 ..agkkalivRtswvyge........kgknfvktmlrlakereelkvva..DqlgsPTsardlAevllqllekaaee 203
                                         a + +l +  s +yg+        ++   ++ ++++a+  e+l+v +   q ++  +++d+A++ +  +e++  +
  gi|336253745|ref|YP_004596852.1| 166 dgAFPAHLFLK-SNLYGDhtvdetvvSKPTVINFFVERATAGEPLTVYEpgTQSRNFVHVKDVARAYVRSAERMFTQ 241
                                       76677777665.99**9988888887778888999************9855799***************99998876 PP

                                       GGG....-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--S CS
                     RmlD_sub_bind 204 kel....agvyHlanegetswlefArailkeagadseevkpistaeyptp 249
                                        +      ++  +a+++  s +e+A+ + + a+++  +  +++  e+p++
  gi|336253745|ref|YP_004596852.1| 242 LANdetgIETCEIAGNEDPSVMEVAETVRDLAREELDKTVDVELVENPRS 291
                                       55556578999*********************999988888887777765 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 !   73.8   0.0   8.1e-24   1.1e-20       1     157 [.      15     161 ..      15     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 8.1e-24
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       ++tG+aG++G+++v++L ++++ +++r+lD   + ++    ++++ ++v ++Dv+d  +leeal+g+d+v+hla+++
  gi|336253745|ref|YP_004596852.1|  15 AITGAAGYIGSRVVQQLQSTHPNWTLRALDNYYRGQV----ESIGETDVTHVDVRDRRRLEEALDGADIVLHLAAVS 87 
                                       59****************************9988887....777888888*************************** PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                        v     + d  ++vnv GT+nv   c+k+g + lv+  s+ v g+  ++ +i+       ++  + + y ++K l 
  gi|336253745|ref|YP_004596852.1|  88 GVDDcDENPDLAYEVNVTGTNNVAWFCRKTG-TGLVFPFSMAVLGD-PEQFPIT-----ADLPRDPFNWYGRTKLLG 157
                                       **9978899**********************.679**********9.3333333.....455666667777777777 PP

                         3Beta_HSD 154 Eklv 157
                                       E+++
  gi|336253745|ref|YP_004596852.1| 158 ERAI 161
                                       7766 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   9.7e-19   1.3e-15       1     218 [.      14     236 ..      14     313 .. 0.74

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 9.7e-19
                                       EEEETTTSHHHHHHHHHHHHHB-S.EEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.. CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpk.kiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel 76 
                                       + +tGa+G iGs++v+q+ +++p+ +++ l++      ++e+       ++++  +      dvrd++rle+al+  
  gi|336253745|ref|YP_004596852.1|  14 IAITGAAGYIGSRVVQQLQSTHPNwTLRALDNYYRG--QVESI-----GETDV--T----HVDVRDRRRLEEALD-- 75 
                                       679*****************9997245555544333..33332.....22223..2....469************.. PP

                                       T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEE......EE.......EEEGGGSS--SHHHH CS
                   Polysacc_synt_2  77 kvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkv......vl.......iStDKAvnPtnvmGa 140
                                       + d+v+h AA+  V  ++enp  a + Nv+gt+nv+  + ++g   v      vl       i +D   +P n +G 
  gi|336253745|ref|YP_004596852.1|  76 GADIVLHLAAVSGVDDCDENPDLAYEVNVTGTNNVAWFCRKTGTGLVfpfsmaVLgdpeqfpITADLPRDPFNWYGR 152
                                       *****************************************997654111211223444444789999********* PP

                                       HHHHHHHHHHHGGG--SSS--EEEEEEE-E.....ETTGTTSSHHHHHHHHHTTSSEEES-TT-.EEEEE-HHHHHH CS
                   Polysacc_synt_2 141 tKrlaekllqalakeseekktkfvvvRfGN.....VlgSrGSviplFkkqikeggpvtvTdpem.tRyfmtieeavq 211
                                       tK+l e  + ++a+ +  ++  +    +G       + S+  vi +F ++ ++g+p+tv +p    R f+ +++ ++
  gi|336253745|ref|YP_004596852.1| 153 TKLLGERAIESFADGAFPAHLFLKSNLYGDhtvdeTVVSKPTVINFFVERATAGEPLTVYEPGTqSRNFVHVKDVAR 229
                                       ****************9999888899999644333689**********************99652799999999776 PP

                                       HHHHHHH CS
                   Polysacc_synt_2 212 Lvlqala 218
                                         + +++
  gi|336253745|ref|YP_004596852.1| 230 AYVRSAE 236
                                       5444433 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0013       1.8       1      23 [.      16      38 ..      16      44 .. 0.89
   2 !   22.7   0.0   3.3e-08   4.5e-05      79     208 ..      68     181 ..      55     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0013
                                      EE-TTSHHHHHHHHHHHHHS-.T CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpev 23
                                      +TGa G++G++++++L +t+p+ 
  gi|336253745|ref|YP_004596852.1| 16 ITGAAGYIGSRVVQQLQSTHPNW 38
                                      8***************9999974 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 3.3e-08
                                       HHHHHHHHH--EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS- CS
                     NAD_binding_4  79 edlqelaeevdviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvy 152
                                       ++l+e  +  d+++h aA   +d+   + + +++vNv+Gt +v  +++k+    ++  +S a++ + ++  +     
  gi|336253745|ref|YP_004596852.1|  68 RRLEEALDGADIVLHLAAVSGVDDcdeNPDLAYEVNVTGTNNVAWFCRKTGTG-LVFPFSMAVLGDPEQFPI----- 138
                                       5677888999********8765542216666******************9999.999999999999999765..... PP

                                       H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 153 eegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                                   + +  ++  n Y ++K l+E+ +++ ++   +p+  +  s+++g
  gi|336253745|ref|YP_004596852.1| 139 ------------TADLPRDPFNWYGRTKLLGERAIESFADG-AFPAHLFLKSNLYG 181
                                       ............67778888899*************99965.89988887777777 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 !   30.9   0.0   1.7e-10   2.3e-07       1     109 [.      18     136 ..      18     238 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.7e-10
                                       TTTSHHHHHHHHHHHHC-.T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC... CS
                    NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk... 73 
                                       GA G +G+++v++l + + +++++al  +     ++e+  +++v+++dv d   l+eal+gad+V+  ++ +g    
  gi|336253745|ref|YP_004596852.1|  18 GAAGYIGSRVVQQLQSTHpNWTLRAL--DNYYRGQVESIGETDVTHVDVRDRRRLEEALDGADIVLHLAAVSGVddc 92 
                                       9****************866666665..4444445777789************************766644444346 PP

                                       ..HHHH..........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHH CS
                    NAD_binding_10  74 ..deeg..........aknivdaakeagvkRfvlvsaigvgdevpgef 109
                                         +             ++n++  ++++g+  +   s +  gd   ++f
  gi|336253745|ref|YP_004596852.1|  93 deN--PdlayevnvtgTNNVAWFCRKTGTGLVFPFSMAVLGDP--EQF 136
                                       441..25556666677999999999999988888887777763..333 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.7e-07   0.00065       1      71 [.      14      83 ..      14      98 .. 0.83
   2 ?   -0.6   0.1      0.59   8.1e+02     143     218 ..     230     310 ..     224     323 .. 0.48

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.7e-07
                                      EEESSTTSHHHHHHHHHHHH..HT-EEEEEES-S-SHHHHHHHHSTTEEE.ES-TT-HHHHHHHHTT-SEEEE- CS
                              NmrA  1 IlviGaTGrqGksvvrallk..aghkvralvRdtkselakslkeaGvelv.kgdlddkeslvealkgvdvvfsv 71
                                      I+++Ga+G++G+ vv+ l +   +++ ral    ++    ++++ G + v + d+ d+  l+eal+g+d v   
  gi|336253745|ref|YP_004596852.1| 14 IAITGAAGYIGSRVVQQLQSthPNWTLRAL----DNYYRGQVESIGETDVtHVDVRDRRRLEEALDGADIVLHL 83
                                      89**************98765578888887....5555566777888877799*****************9865 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.59
                                       EEGGG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE.-HHHHHH......HHHHHHHHHHHHHTTEEEEE-SEEE CS
                              NmrA 143 ffmenflsllaqlkvgdtappedkvtllgpgnpkavll.daeeDiG......afvikilkdprklkgkriklagntl 212
                                       ++ +   +++ ql   + +++ +++++ g+++p+ + +  +++D +      ++ ++++++pr  ++ + ++a +t 
  gi|336253745|ref|YP_004596852.1| 230 AYVRSAERMFTQLA--NDETGIETCEIAGNEDPSVMEVaETVRDLAreeldkTVDVELVENPRSDETMVEDFAVDTS 304
                                       55555666666633..3333334566666666655544434444431111111224445555555555555555555 PP

                                       -HHHHH CS
                              NmrA 213 sgneiv 218
                                         ne++
  gi|336253745|ref|YP_004596852.1| 305 KANEVL 310
                                       555544 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 !   16.3   0.0   7.3e-06      0.01       2      71 ..      14      81 ..      13      89 .. 0.68
   2 ?    0.6   0.0      0.53   7.3e+02      28      78 ..     196     246 ..     190     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.3e-06
                                      EEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEE..GGGGGCTT-SEEE CS
                    Semialdhyde_dh  2 vaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkved..vdeeelkevdivf 71
                                      +ai Ga Gy+G+++++ L++ hp+++l +l    r  G+ +++  +  ++++ + v+d    ee+l+++div+
  gi|336253745|ref|YP_004596852.1| 14 IAITGAAGYIGSRVVQQLQStHPNWTLRALDNYYR--GQ-VESIGE--TDVTHVDVRDrrRLEEALDGADIVL 81
                                      89**********************99988755555..32.333322..3444444444434445556666665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.53
                                       EEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHH CS
                    Semialdhyde_dh  28 vvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagv 78 
                                       + ++ ++  aG++l+ + + +++++ + v+dv  + +++++ +f+ l ++ 
  gi|336253745|ref|YP_004596852.1| 196 INFFVERATAGEPLTVYEPGTQSRNFVHVKDVARAYVRSAERMFTQLANDE 246
                                       455666666999999999988888888899988888888888888877765 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     1e-05     0.014       3      80 ..      14      89 ..      12     106 .. 0.81
   2 ?   -2.0   0.1       2.6   3.6e+03      52      75 ..     280     304 ..     237     320 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                                      EEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HHHH CS
                            DapB_N  3 vavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtpeav 80
                                      +a++Ga+G +G++vv+ ++++       a+d+   + + +++ge +++++++v    +lee+l+ ad+++ + + ++v
  gi|336253745|ref|YP_004596852.1| 14 IAITGAAGYIGSRVVQQLQSTHPNWTLRALDNYY-RGQVESIGE-TDVTHVDVRDRRRLEEALDGADIVLHLAAVSGV 89
                                      99*****************976666666777765.566677776.677789999999***********9987776665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.6
                                       --S-BEBSSHHHHHHH.-SEEEE-S CS
                            DapB_N  52 klgvavtddleevlek.advliDFT 75 
                                       +++v++ ++  +  +   d ++D +
  gi|336253745|ref|YP_004596852.1| 280 TVDVELVENPRSDETMvEDFAVDTS 304
                                       3333333333322222345555555 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 !   15.1   0.0   1.5e-05     0.021       1      77 [.      14      84 ..      14      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                      EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77
                                      + i Ga G++G+ v++ l+ +++    +t+   ++    ++ +  +  + + + +d+ +++  L+++l ++d+v++l+
  gi|336253745|ref|YP_004596852.1| 14 IAITGAaGYIGSRVVQQLQSTHPN---WTLRALDNYYRGQV-E--SIGETDVTHVDVRDRRR-LEEALDGADIVLHLA 84
                                      5688999*************9985...66655555543355.3..56889999*********.*************97 PP

>> Calsequestrin  Calsequestrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   1.3e-05     0.018     203     303 ..     180     279 ..     155     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                                       E--HHHHHHCT--TTEEEEE..-TT-SS-EE-SSSS--HHHHHHHHHHCSS-SEEE--CCCHHHHHHS-STSEEEEE CS
                     Calsequestrin 203 tfdkkvakklslklnevdfy..eafmeepvaipdkpyseeelvefvkehrrstlrklkpedmyetweddldgihiva 277
                                         d+ v   +  k   ++f+   a   ep+++ +      ++v  vk+  r+ +r    e m+    +d  gi    
  gi|336253745|ref|YP_004596852.1| 180 YGDHTVDETVVSKPTVINFFveRATAGEPLTVYEPGTQSRNFV-HVKDVARAYVRS--AERMFTQLANDETGIETCE 253
                                       4566666666667777777633467789999987555555555.689999999996..79***************** PP

                                       E--TTSHHHHHHHHHHHHHHHHCCC- CS
                     Calsequestrin 278 faeeadpdgyefleilkavardnten 303
                                       +a + dp  +e  e+++++ar++ ++
  gi|336253745|ref|YP_004596852.1| 254 IAGNEDPSVMEVAETVRDLAREELDK 279
                                       *********************98875 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 ?   14.7   0.0   1.8e-05     0.025       3      79 ..      14      86 ..      12      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                                      EEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEESSGGGGTTESEEEE--S- CS
                           Ldh_1_N  3 vavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvsekeeealkdadvvvitagv 79
                                      +a++GaaG iG+ +  +l++ +    l+ lD      +G++  + +++++  v+v+ ++  eeal +ad+v+  a+v
  gi|336253745|ref|YP_004596852.1| 14 IAITGAAGYIGSRVVQQLQSTHPNWTLRALDNY---YRGQVESIGETDVTH-VDVRDRRRLEEALDGADIVLHLAAV 86
                                      89****************999887778888766...9***********998.9*******************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2298.72
//
Query:       gi|336253746|ref|YP_004596853.1|  [L=321]
Description: NAD-dependent epimerase/dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-49  167.2   0.0    5.1e-49  166.9   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    7.2e-35  120.9   0.0    1.5e-34  119.9   0.0    1.5  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    5.2e-26   91.3   0.0    6.8e-26   90.9   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      5e-13   48.8   0.0    6.2e-13   48.5   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.1e-11   44.4   0.0    1.8e-11   43.7   0.0    1.6  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    6.2e-11   41.9   0.0      8e-07   28.5   0.0    2.3  2  NAD_binding_4    Male sterility protein
    1.1e-10   41.7   0.0    1.5e-10   41.3   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
     0.0004   20.6   0.0    0.00076   19.7   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0011   18.9   0.2     0.0032   17.4   0.2    1.8  1  KR               KR domain
  ------ inclusion threshold ------
      0.017   14.5   0.0      0.026   14.0   0.0    1.3  1  adh_short        short chain dehydrogenase
      0.041   14.0   0.1      0.061   13.4   0.1    1.3  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
      0.091   12.3   0.0        1.8    8.1   0.0    2.4  1  NmrA             NmrA-like family


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 !  166.9   0.0   3.4e-52   5.1e-49       1     241 []       3     241 ..       3     241 .. 0.93

  Alignments for each domain:
  == domain 1  score: 166.9 bits;  conditional E-value: 3.4e-52
                                       EEEETTTSHHHHHHHHHHHHCT.SE.EEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekg.ye.vigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihl 71 
                                       +lVtG+ G+iGsalv +lle   ++ v+++d+l s+s+ +++  +    e+ ++d+++  ++e +++  ++d v+hl
  gi|336253746|ref|YP_004596853.1|   3 VLVTGGCGYIGSALVPKLLEDErVDeVVVFDSLASGSPANLRGCIgdslEFRRGDVREYGDVESAMR--GVDRVVHL 77 
                                       79****************99999555*******999998887777999*******************..9******* PP

                                       -S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHH CS
                         Epimerase  72 AavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKla 148
                                       Aa+ g a +++++++++  n  gt n+l aa k +v+ ++f+sS+  YG+ a++  +ett   + +p +pYa +K+ 
  gi|336253746|ref|YP_004596853.1|  78 AAITGAASTHDRREETFAVNRDGTANVLTAAGKLDVDSVVFASSCNNYGRTASTNIDETT---KQNPLNPYAESKVE 151
                                       *****************************************************7788888...88999********* PP

                                       HHHHHHHHHHHHT-EEEEEEESEEESTT...S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHH CS
                         Epimerase 149 geklveayaaqyglnaiilrlfnlyGpr...ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeai 222
                                       +e+l+ ++ ++yg++ ++lr++++yG     +++  v+++++    + l+++ ++t++gdgt++R+f++veD+a+a+
  gi|336253746|ref|YP_004596853.1| 152 SEQLLADAIDDYGFDGTALRMSTNYGWApgvRFNLVVNHFVF----RSLTER-PLTVYGDGTNWRPFIHVEDAARAY 223
                                       **************************8855777777777766....444456.9*********************** PP

                                       HHHHHHHTT-STTEEEEES CS
                         Epimerase 223 llvlehvdagdkgeiyniG 241
                                        ++l ++++  ++ +yn+G
  gi|336253746|ref|YP_004596853.1| 224 AHALLEPES-WPKTVYNVG 241
                                       ******999.6779****9 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 !  119.9   0.0   9.8e-38   1.5e-34       1     269 [.       4     263 ..       4     305 .. 0.83

  Alignments for each domain:
  == domain 1  score: 119.9 bits;  conditional E-value: 9.8e-38
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+ G+iGs l+ +Lle   +v  +v  +s+ + g+ ++l+     ++ ++l++ +gD+++   +e++++ v  d
  gi|336253746|ref|YP_004596853.1|   4 LVTGGCGYIGSALVPKLLED-ERVDEVVVFDSL-ASGSPANLRG----CIGDSLEFRRGDVREYGDVESAMRGV--D 72 
                                       9*****************97.455555555555.4477777764....57789********************9..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                       +v++LAA    +   +  e+t+ vn  Gt+++L a+ +l ++    +++aS+   YG+++++ ++Ett+ +P +PYa
  gi|336253746|ref|YP_004596853.1|  73 RVVHLAAITGAASTHDRREETFAVNRDGTANVLTAAGKLDVD---SVVFASSCNNYGRTASTNIDETTKQNPLNPYA 146
                                       ***************************************986...5788**************************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                        +K+ ++++  +  + yg+  +  +++ +++   g +f    + ++v r +  +++ +++G++ + R + hv+D ++
  gi|336253746|ref|YP_004596853.1| 147 ESKVESEQLLADAIDDYGFDGTALRMSTNYGWAPGVRFN-LVVNHFVFRSLT-ERPLTVYGDGTNWRPFIHVEDAAR 221
                                       *********************************999976.566777777555.66999******************* PP

                                       HHHHHHHCSS..---..EEE-TT-EEECHHCHHCCHHCCCHH CS
                     GDP_Man_Dehyd 232 amwlmlqqdk..ped..yviatgethsvrefvelaflelgkt 269
                                       a+  +l + +  p++   v at e++++  ++ +   elg +
  gi|336253746|ref|YP_004596853.1| 222 AYAHALLEPEswPKTvyNVGATEENYRIAHIASIVRDELGLE 263
                                       *98887654411222113457777777777777666666654 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 !   90.9   0.0   4.6e-29   6.8e-26       1     225 [.       4     223 ..       4     268 .. 0.80

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 4.6e-29
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihlas 75 
                                       +vtGg+G++G+alv +L++ e++ ev v+D   s +  +    ++  +  +  gDv++  ++e a++gvd v+hla+
  gi|336253746|ref|YP_004596853.1|   4 LVTGGCGYIGSALVPKLLEDERVDEVVVFDSLASGSPANLRGCIGD-SleFRRGDVREYGDVESAMRGVDRVVHLAA 79 
                                       69****************************8887777555544444.3479************************** PP

                         3Beta_HSD  76 lvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKa 151
                                       ++  a+ +++++e   vn  GT nvl a+ k +v  +v+ Ss++  g      + +n dE+++  +++ ++y+esK 
  gi|336253746|ref|YP_004596853.1|  80 ITGAAStHDRREETFAVNRDGTANVLTAAGKLDVDSVVFASSCNNYGR----TASTNIDETTK--QNPLNPYAESKV 150
                                       **9998899**********************************98888....55555678775..56789******* PP

                         3Beta_HSD 152 laEklvlkaNgrtlknggrlyTcaLRpagiyG..egdkllvpllkqlakl..glalfkigdeevlsdrvYvgNvawa 224
                                        +E+l+  a +        +   aLR ++ yG  +g ++ + + + + ++  +  l  +gd  +   ++ v+  a a
  gi|336253746|ref|YP_004596853.1| 151 ESEQLLADAIDD---Y--GFDGTALRMSTNYGwaPGVRFNLVVNHFVFRSltERPLTVYGDGTNWRPFIHVEDAARA 222
                                       ********9993...3..36678999999999444444333322222232113367778888888888888888777 PP

                         3Beta_HSD 225 h 225
                                       +
  gi|336253746|ref|YP_004596853.1| 223 Y 223
                                       6 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 !   48.5   0.0   4.2e-16   6.2e-13       1     231 [.       1     260 [.       1     286 [. 0.78

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 4.2e-16
                                       EEEEEESTTSHHHHHHHHHCTTTSE..EEEEE-TT...................T--TTSHHHHHHHHHHH--SEEE CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeegl..evlaltre...................eldltdaeavaellkeakpdvvv 56 
                                       m++lvtG+ G +Gs+L+ +l e++   ev+ +++                    + d+++   v+++++    d vv
  gi|336253746|ref|YP_004596853.1|   1 MRVLVTGGCGYIGSALVPKLLEDERvdEVVVFDSLasgspanlrgcigdslefrRGDVREYGDVESAMRG--VDRVV 75 
                                       89***************9887754322455555548999************99999************99..677** PP

                                       E------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHH CS
                     RmlD_sub_bind  57 naAAytavDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaG 132
                                       ++AA t      + +e+ +avn ++++++  aa + ++  +++ S+   +  +++++  e+ +++Pln Y+++K++ 
  gi|336253746|ref|YP_004596853.1|  76 HLAAITGAASTHDRREETFAVNRDGTANVLTAAGKLDVdSVVFASSCNNYGRTASTNIDETTKQNPLNPYAESKVES 152
                                       *************************************95589999999999999999******************** PP

                                       HHHHHH....H-SSEEEEEE-SEESS....SSS-HHHHHHHHHHH-SEEEEESS-EE.--.EEHHHHHHHHHHHHHH CS
                     RmlD_sub_bind 133 Eqavla....agkkalivRtswvyge....kgknfvktmlrlakereelkvvaDqlg.sP.TsardlAevllqllek 199
                                       Eq  ++    +g + + +R+s  yg     + +  v+ ++ +  ++ +l+v  D +  +P  +++d A++ +++l +
  gi|336253746|ref|YP_004596853.1| 153 EQLLADaiddYGFDGTALRMSTNYGWapgvRFNLVVNHFVFRSLTERPLTVYGDGTNwRPfIHVEDAARAYAHALLE 229
                                       **887722225556789999999986433222333455666667777888887765425534677888877777666 PP

                                       CHH.GGG-EEEE---BS-EEH.HHHHHHHHHHH CS
                     RmlD_sub_bind 200 aaeekelagvyHlanegetsw.lefArailkea 231
                                         +    + vy +++++e  + + +A  + +e+
  gi|336253746|ref|YP_004596853.1| 230 PES--WPKTVYNVGATEENYRiAHIASIVRDEL 260
                                       654..3466777766665433144555555555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   1.2e-14   1.8e-11       1     128 [.       3     121 ..       3     267 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.2e-14
                                       EEEETTTSHHHHHHHHHHHHH.B-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.. CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkk.kpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel 76 
                                       vlvtG+ G iGs+lv ++l+  ++ +++++++      +    l + +  ++l+++     gdvr+   +e+a++  
  gi|336253746|ref|YP_004596853.1|   3 VLVTGGCGYIGSALVPKLLEDeRVDEVVVFDSLASGSPAN---L-RGCIGDSLEFR----RGDVREYGDVESAMR-- 69 
                                       8******************9879*******9865544322...2.23345688888....9**************.. PP

                                       T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                   Polysacc_synt_2  77 kvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                       +vd v+h AA+           e++  N  gt nv++aa + +v++vv+ S+
  gi|336253746|ref|YP_004596853.1|  70 GVDRVVHLAAITGAASTHDRREETFAVNRDGTANVLTAAGKLDVDSVVFASS 121
                                       ************************************************9996 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   9.6e-05      0.14       1      27 [.       5      31 ..       5      42 .. 0.89
   2 !   28.5   0.0   5.4e-10     8e-07      82     205 ..      65     174 ..      60     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.6e-05
                                      EE-TTSHHHHHHHHHHHHHS-.T.EEEE CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpev.kiyl 27
                                      +TG+ G++G+ L+ kLL++++ v ++++
  gi|336253746|ref|YP_004596853.1|  5 VTGGCGYIGSALVPKLLEDER-VdEVVV 31
                                      7****************9986.657766 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 5.4e-10
                                       HHHHHH--EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS-H. CS
                     NAD_binding_4  82 qelaeevdviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekvyee 154
                                       +  ++ vd ++h aA +   +   + +e ++vN +Gt +vl+ a kl    ++++ S+     ++            
  gi|336253746|ref|YP_004596853.1|  65 ESAMRGVDRVVHLAAITGAASthdRREETFAVNRDGTANVLTAAGKLDVD-SVVFASScNNYGRTA----------- 129
                                       566788*********99877633366779******************999.999999742222223........... PP

                                       .....HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-E CS
                     NAD_binding_4 155 gekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsi 205
                                               + +++++++  n Y  sK+++E+l+ +a +  g+  + +R s+
  gi|336253746|ref|YP_004596853.1| 130 ------STNIDETTKQNPLNPYAESKVESEQLLADAIDDYGFDGTALRMST 174
                                       ......3455678889999***********************999999986 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 !   41.3   0.0     1e-13   1.5e-10       1     145 [.       7     174 ..       7     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1e-13
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT.....HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-.... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.....peklaeleaeeglevvegdvtdvedlaealkgadaVvsal.... 68 
                                       G+ G +G++lv +ll+++ ++ +++  +     p+ l      + le   gdv +  d+++a++g+d Vv  +    
  gi|336253746|ref|YP_004596853.1|   7 GGCGYIGSALVPKLLEDERVDEVVVFDSlasgsPANLRGCI-GDSLEFRRGDVREYGDVESAMRGVDRVVHLAaitg 82 
                                       889**************955555555553333356666555.489**********************7655553554 PP

                                       ..--TCC.....HHHH.......HHHHHHHHHHCT--EEEEEEETTTTS.GCGCHHHHHHH.HCCHHHHHHHHHHHH CS
                    NAD_binding_10  69 ..ggggk.....deeg.......aknivdaakeagvkRfvlvsaigvgd.evpgefgewnk.ellkaylaakraaee 129
                                         +   +     +  +       ++n+++aa + +v  +v+ s+ + +   + ++ +e++k + l++y++ k ++e+
  gi|336253746|ref|YP_004596853.1|  83 aaS---ThdrreE--TfavnrdgTANVLTAAGKLDVDSVVFASSCNNYGrTASTNIDETTKqNPLNPYAESKVESEQ 154
                                       332...1444440..25566666*********************987651556667766652689************ PP

                                       HHHH....SSSEEEEEEE-C CS
                    NAD_binding_10 130 llra....sgldwTivrpgg 145
                                       ll +     g+d T +r++ 
  gi|336253746|ref|YP_004596853.1| 155 LLADaiddYGFDGTALRMST 174
                                       *9886655689999998876 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 !   19.7   0.0   5.1e-07   0.00076       3      80 ..       5      81 ..       3      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.1e-07
                                      EE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG CS
                   Sacchrp_dh_NADP  3 iiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppi 80
                                      + G+ G++G+a++++l++ + vd e++v d   ++  a +    g ++e++  d+ +y + +++++++ d vv+l+  +
  gi|336253746|ref|YP_004596853.1|  5 VTGGcGYIGSALVPKLLEDERVD-EVVVFDSLASGSPANLRGCIGDSLEFRRGDVREYGD-VESAMRGVDRVVHLAAIT 81
                                      55555*****************7.***********99999999*****************.**************9765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   2.2e-06    0.0032       3     139 ..       3     124 ..       2     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-06
                                       EEEETTTSHHHHHHHHHHHHHH.S-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                                KR   3 ylitGGlGgLGlelarwlaekg.arhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78 
                                       +l+tGG+G +G +l+  l+e+    ++v++       + s a+++     g + e+++ Dv +  +ve++++ ++  
  gi|336253746|ref|YP_004596853.1|   3 VLVTGGCGYIGSALVPKLLEDErVDEVVVFDSL---ASGSPANLR--GCIGDSLEFRRGDVREYGDVESAMRGVD-- 72 
                                       69****************998845566666555...233333344..45699*****************999887.. PP

                                       SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHH CS
                                KR  79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiag 139
                                             v+h A ++  +     t ++ e+ +a   +G+ n+ ++  + ++d +v+ SS+ +
  gi|336253746|ref|YP_004596853.1|  73 -----RVVHLAAITGAA----STHDRREETFAVNRDGTANVLTAAGKLDVDSVVFASSCNN 124
                                       .....79******9876....57777888899999***********************976 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.8e-05     0.026       3     118 ..       3     107 ..       1     130 [. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                                       EEEESTTSHHHHHHHHHHHHTT..-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   3 vlvtGassGIGraiakelakeG..akvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklg 76 
                                       vlvtG+++ IG a++ +l+++    +vvv+d+ ++      ++l+ + g+++ + ++Dv+++ +ve +++ +     
  gi|336253746|ref|YP_004596853.1|   3 VLVTGGCGYIGSALVPKLLEDErvDEVVVFDSLASGS---PANLRGCiGDSLEFRRGDVREYGDVESAMRGV----- 71 
                                       9******************987334788888887766...77777777999**********99999988876..... PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHH CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltra 118
                                         d +v+ A+itg +++     ++ e++++vN  g+ ++  a
  gi|336253746|ref|YP_004596853.1|  72 --DRVVHLAAITGAAST----HDRREETFAVNRDGTANVLTA 107
                                       ..556666666333332....344667777777777776665 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 ?   13.4   0.1   4.1e-05     0.061       1      95 [.       1      98 [.       1     121 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                                      EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHH....HCHCCSTS-EEEEESSGGGGTTESEEEE CS
                           Ldh_1_N  1 vkvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldls....histflsvkvkvsekeeealkdadvvvi 75
                                      ++v v+G  G iG++l  +l++ + +de++++D   +   G  ++l     +   f   +v+ +++ e+a++++d vv 
  gi|336253746|ref|YP_004596853.1|  1 MRVLVTGGCGYIGSALVPKLLEDERVDEVVVFDSLAS---GSPANLRgcigDSLEFRRGDVREYGDVESAMRGVDRVVH 76
                                      68*******************************9955...555554411114444555566666699999999999999 PP

                                      --S-SS-TTTT..HHHHHHHHH CS
                           Ldh_1_N 76 tagvprkpGet..RddLlkvNa 95
                                       a+++ +      R++ ++vN 
  gi|336253746|ref|YP_004596853.1| 77 LAAITGAASTHdrREETFAVNR 98
                                      8888765443333666666665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0012       1.8       1     204 [.       3     238 ..       3     263 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0012
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S....-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdt....kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73 
                                       +lv+G+ G++G+++v  ll+++    ++v d+    +  +++       e+  gd+ ++  +++a++gvd v    +
  gi|336253746|ref|YP_004596853.1|   3 VLVTGGCGYIGSALVPKLLEDERVDEVVVFDSlasgSPANLRGCIGDSLEFRRGDVREYGDVESAMRGVDRVVHLAA 79 
                                       68999999999999999998777777777777654444555555556666668888888888888888887766555 PP

                                       GG............S-HHHHHH.HHHHHHHHHS-SEEEEEE---GG.........GT.SSS---TTTHHHHHHHHHH CS
                              NmrA  74 fy............skeiedgk.klvdAakeaGvkhfiySslgddn........drsnaeepavphfdsKaeieeyv 129
                                       ++             +  +dg+ ++  Aa +  v  ++++s  ++         d++ ++ p  p  +sK+e e+ +
  gi|336253746|ref|YP_004596853.1|  80 ITgaasthdrreetFAVNRDGTaNVLTAAGKLDVDSVVFASSCNNYgrtastniDETTKQNPLNPYAESKVESEQLL 156
                                       44555666654333111234431344455555566666655444321111111144455566666666666666655 PP

                                       HHC....TS-EEEEEE-EEGGG-....BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHH CS
                              NmrA 130 ral....gipytfvyagffmenf....lsllaqlkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdpr 198
                                         +    g+  t ++    ++        l+++ +v   +  e  +t+ g+g  + ++++++eD +++ +++l +p+
  gi|336253746|ref|YP_004596853.1| 157 ADAiddyGFDGTALRMSTNYGWApgvrFNLVVNHFVF-RSLTERPLTVYGDGT-NWRPFIHVEDAARAYAHALLEPE 231
                                       5555555443333333222222100001222222222.223333567777776.44444577777777777777777 PP

                                       HH.TTEE CS
                              NmrA 199 kl.kgkr 204
                                        + k+++
  gi|336253746|ref|YP_004596853.1| 232 SWpKTVY 238
                                       7766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2150.78
//
Query:       gi|336253747|ref|YP_004596854.1|  [L=415]
Description: UDP-sulfoquinovose synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-20   73.5   0.1    3.9e-20   72.4   0.1    1.6  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.6e-16   59.1   0.1    2.4e-15   56.8   0.1    2.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    0.00012   21.4   0.0      0.021   14.0   0.1    2.9  2  RmlD_sub_bind    RmlD substrate binding domain
    0.00018   20.7   0.0      0.001   18.3   0.0    2.1  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.025   14.5   0.0    1.3  1  KR               KR domain
      0.032   13.3   0.0       0.11   11.5   0.0    1.8  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras


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 !   72.4   0.1   1.3e-23   3.9e-20       1     225 [.       3     280 ..       3     296 .. 0.79

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 1.3e-23
                                       EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC...........................EEEE-- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledl...........................elveld 49 
                                       ++VtGa G+iG  ++ ++++++ + v+ +d+  +++  ++   +                           ++ve+d
  gi|336253747|ref|YP_004596854.1|   3 VFVTGADGYIGWPTALRIANRTDDrVVLVDNFGRREWVKS---VgstsavpvaeiderleaaedvhgltnlSFVEAD 76 
                                       68********************777******944444444...345699**************************** PP

                                       TT-HHHHHHHHHHHT-SEEEE--S.---H..HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT..EEEEEEEGGGGTS CS
                         Epimerase  50 ltdrsalerlfkeeqpdavihlAa.vggv..aassedpadfieknlqgtlnlleaarkagvk..rllflsSsevYGk 121
                                       l d++a++rl+  ++p+a++h Aa  + +  + + e+++++ ++nlq t+nll  + ++++    ++   ++ vYG+
  gi|336253747|ref|YP_004596854.1|  77 LADKDAVDRLLTVHEPEAIVHTAAqPSAPysQINGERANYTQHNNLQATRNLLWGLEEHDLTdtHFIETTTTGVYGA 153
                                       ************************54443113455789999******************999889999999*****6 PP

                                       CSS.SS........BSTCSTTS--..--SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHH CS
                         Epimerase 122 dae.qp........keettltgpl..kpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvip 187
                                       ++  +p        + e   + p+     s Y ++K +    ++ +++q+++++  +r    yG+    +e++   p
  gi|336253747|ref|YP_004596854.1| 154 PEFpIPeggatmenQGERD-EVPFpaMAGSWYHLTKSHDAANMRLAHDQFDIPISDVRTAITYGAE---TEETAADP 226
                                       6654455555555433333.3466678999************************************...55555555 PP

                                       HHHHHHHT.................TSSSEEEETTST-EEEEEEHHHHHHHHHHH CS
                         Epimerase 188 alirkile.................gkqevtllgdgtalRdflyveDvaeaillv 225
                                       +l++++                   g  + t++g+g+++ +f+  eD++e++ ++
  gi|336253747|ref|YP_004596854.1| 227 RLATRFDFdyyfgvvahrfcaqavaGY-PMTVYGKGEQRKPFIALEDAVEGLARL 280
                                       555555554444444444444333354.**********************98765 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 !   56.8   0.1   8.1e-19   2.4e-15       2     281 ..       5     328 ..       4     351 .. 0.71

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 8.1e-19
                                       EETTTSHHHHHHHHHHHHCT-C.CEEEEE...........EESS-TTHHHH.HCTTT...TTGCCEEEEE--TT-HH CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgye.vhgivr...........rsssfntgrie.hlakdpkeeleenlklhkgDltDss 65 
                                       +TG  G+iG  +a ++ ++  + v+ +++            +s++ +++i+ +l+  ++++  +nl+++++Dl D++
  gi|336253747|ref|YP_004596854.1|   5 VTGADGYIGWPTALRIANRTDDrVVLVDNfgrrewvksvgSTSAVPVAEIDeRLEAAEDVHGLTNLSFVEADLADKD 81 
                                       8999999999999999988655155454444444332222334444455553555566667778************* PP

                                       HHHHHHHHHT-SEEEE--S---HHHHT...TSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSS CS
                     GDP_Man_Dehyd  66 slerllaevqpdevynLAAqshVdvsf...ekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqev 139
                                       +++rll  ++p+++++ AAq   ++s    e + yt  +n+ +t +LL    ++ l+ +++f+ + t  vYG ++  
  gi|336253747|ref|YP_004596854.1|  82 AVDRLLTVHEPEAIVHTAAQPSAPYSQingERANYTQHNNLQATRNLLWGLEEHDLT-DTHFIETTTTGVYGAPE-F 156
                                       ********************88877754557899********************995.8**************96.3 PP

                                       SB-TT..............S-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTS.......... CS
                     GDP_Man_Dehyd 140 pqtEt..............tpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetf.......... 192
                                       p+ E                p  + s Y  +K      ++  +++++++++  ++  +++   +et           
  gi|336253747|ref|YP_004596854.1| 157 PIPEGgatmenqgerdevpFPAMAGSWYHLTKSHDAANMRLAHDQFDIPISDVRTAITYGAETEETAadprlatrfd 233
                                       3333111222244445555666789********************************99999988754444444444 PP

                                       ....CCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHH...HCSS---EEE-TT-EEECHHCHHCC CS
                     GDP_Man_Dehyd 193 ....vtrkitravarialgkqevlylGnldakRdwghvkDyveamwlml...qqdkpedyviatgethsvrefvela 262
                                                 r+ a++ +g  +++++G++++++ +   +D ve++ ++      d+p+d+v+ ++ t  +  +ve+a
  gi|336253747|ref|YP_004596854.1| 234 fdyyFGVVAHRFCAQAVAGY-PMTVYGKGEQRKPFIALEDAVEGLARLAlidPDDRPDDHVVYNQVTRAIS-IVEIA 308
                                       44444456678899999998.9999*******************776442225799*****9998887774.44444 PP

                                       ..HHCCCHHHHHH........ CS
                     GDP_Man_Dehyd 263 ..flelgktiewegkgeeevg 281
                                         ++++ ++   +  ++e+ +
  gi|336253747|ref|YP_004596854.1| 309 etIADVSNEFGLDV-DVEHFE 328
                                       22455555544433.222222 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 !   14.0   0.1   6.9e-06     0.021       1      60 [.       1     100 [.       1     126 [. 0.70
   2 !    3.9   0.0    0.0079        24     215     285 ..     299     368 ..     271     370 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.9e-06
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT........................................T--T CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre........................................eldl 37 
                                       m++ vtGa+G +G+  a ++a++  + + l  +                                        e+dl
  gi|336253747|ref|YP_004596854.1|   1 MTVFVTGADGYIGWPTALRIANRTDDRVVLVDNfgrrewvksvgstsavpvaeiderleaaedvhgltnlsfvEADL 77 
                                       5666677777777644333333222222222222344677777777777777777777777777777777888**** PP

                                       TSHHHHHHHHHHH--SEEEE--- CS
                     RmlD_sub_bind  38 tdaeavaellkeakpdvvvnaAA 60 
                                       +d++av++ll  ++p+++v++AA
  gi|336253747|ref|YP_004596854.1|  78 ADKDAVDRLLTVHEPEAIVHTAA 100
                                       **********************9 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0079
                                       BS-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHHHHH CS
                     RmlD_sub_bind 215 egetswlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevlkel 285
                                       ++++s +e+A+ i++ +++ + +v ++++ e+p++ ++ ++  +++++ +  +  +l++++e++++vl++l
  gi|336253747|ref|YP_004596854.1| 299 TRAISIVEIAETIADVSNEFGLDV-DVEHFENPREEDETHKMEIENDRYADLIDGQLTTFKEGVRDVLDTL 368
                                       4568999************99777.577999************************************9976 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.4e-07     0.001       1     116 [.       3     133 ..       3     148 .. 0.72
   2 ?   -1.2   0.0      0.29   8.6e+02     176     247 ..     239     315 ..     238     326 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.4e-07
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES...-HHH..........HHHHHHH......-TTEEEE....E--TT CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiiller...dElk..........lyeiekeleeelkkkklkveivpvigdvr 64 
                                       v+vtGa G iG     +i++++  +++l+++    E            + ei+++le+  + + l +++  v +d++
  gi|336253747|ref|YP_004596854.1|   3 VFVTGADGYIGWPTALRIANRTDDRVVLVDNfgrREWVksvgstsavpVAEIDERLEAAEDVHGL-TNLSFVEADLA 78 
                                       78999999999999999999999999997642225542111111111145566666655555555.6778889**** PP

                                       -HHHHHHHTT..T-SEEEE------HHHHHHSHHHH...HHHHHHHHHHHHHHHH CS
                   Polysacc_synt_2  65 dkerlekaleelkvdvvfhaAAlKhVPlveenplea...iktNvlgtenvieaai 116
                                       dk+ ++++l+ +++++++h+AA    P  + n   a    ++N  +t+n++    
  gi|336253747|ref|YP_004596854.1|  79 DKDAVDRLLTVHEPEAIVHTAAQPSAPYSQINGERAnytQHNNLQATRNLLWGLE 133
                                       ***************************9998876652225788888888876555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.29
                                       TSSHHHHHHHHHTTSSEEES-TT-EE.EEE-HHHHHH....HHHHHHHH--SS-EEEE--.-EEEHHHHHHHH.... CS
                   Polysacc_synt_2 176 GSviplFkkqikeggpvtvTdpemtR.yfmtieeavq....LvlqalalakggeifvldmGepvkivdlakaliels 247
                                       G v   F +q  +g p+tv  +   R  f+ +e+av+    L l       + ++   ++  +++iv++a+++ ++s
  gi|336253747|ref|YP_004596854.1| 239 GVVAHRFCAQAVAGYPMTVYGKGEQRkPFIALEDAVEglarLALIDPDDRPDDHVVYNQVTRAISIVEIAETIADVS 315
                                       55667788888888888887665544268888888863111333333444445566677778888888888887665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   8.4e-06     0.025       2      90 ..       2     100 ..       1     153 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.4e-06
                                       EEEEETTTSHHHHHHHHHHHHHHS-EEEEE...-SS............--HHHHHHHHHHHHT..T-EEEE----TT CS
                                KR   2 tylitGGlGgLGlelarwlaekgarhlvll...sRsa..........aadedskaliaeleal..gaevevvaaDvs 63 
                                       t+++tG+ G +G  +a  +a++   ++vl+   +R++           + ++ ++++++ e+    ++ ++v+aD++
  gi|336253747|ref|YP_004596854.1|   2 TVFVTGADGYIGWPTALRIANRTDDRVVLVdnfGRREwvksvgstsaVPVAEIDERLEAAEDVhgLTNLSFVEADLA 78 
                                       678*************************9744478779998877666334444456666666543359********* PP

                                       -HHHHHHHHHHHHHHSS---EEEE--- CS
                                KR  64 dkdavealleeikaeeppikGvihaAg 90 
                                       dkdav +ll+  + e      ++h+A 
  gi|336253747|ref|YP_004596854.1|  79 DKDAVDRLLTVHEPE-----AIVHTAA 100
                                       ********9877644.....3666665 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 ?   11.5   0.0   3.6e-05      0.11      22     104 ..      45     133 ..       4     161 .. 0.75
   2 ?   -2.7   0.0      0.77   2.3e+03     177     188 ..     253     264 ..     248     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                         3Beta_HSD  22 elkevrvlDlrespelleelskvnvkkviegDvtdkdkleeal..egvdvvihlas.....lvdvagkltedeimkv 91 
                                       +   v v+ ++e+ e  e+++ + + +++e+D+ dkd +++ l  ++ ++++h+a+     ++++ g  + +  ++ 
  gi|336253747|ref|YP_004596854.1|  45 STSAVPVAEIDERLEAAEDVHGLTNLSFVEADLADKDAVDRLLtvHEPEAIVHTAAqpsapYSQING-ERANYTQHN 120
                                       455677777999999999999999999*************975227899*****9733333445555.455567788 PP

                         3Beta_HSD  92 nvkGTrnvleacv 104
                                       n++ Trn+l    
  gi|336253747|ref|YP_004596854.1| 121 NLQATRNLLWGLE 133
                                       9999999986555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.77
                         3Beta_HSD 177 RpagiyGegdkl 188
                                        p+++yG g+++
  gi|336253747|ref|YP_004596854.1| 253 YPMTVYGKGEQR 264
                                       599*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3007.03
//
Query:       gi|336253748|ref|YP_004596855.1|  [L=41]
Description: hypothetical protein Halxa_2354 [Halopiger xanaduensis SH-6]
Scores for 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:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      127  (0.0070835); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 332.46
//
Query:       gi|336253749|ref|YP_004596856.1|  [L=310]
Description: family 2 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for 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-22   78.4   0.0      9e-22   77.7   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    3.9e-14   53.1   0.1    1.5e-13   51.2   0.1    1.7  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.4e-07   30.5   0.2    5.9e-06   26.0   0.1    2.1  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
    1.9e-05   24.7   0.0    3.2e-05   23.9   0.0    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
     0.0024   17.4   0.0     0.0045   16.5   0.0    1.5  1  Glyco_transf_21  Glycosyl transferase family 21


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 !   77.7   0.0   2.5e-25     9e-22       1     169 [.       4     170 ..       4     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 2.5e-25
                                       EEEEEESS-..TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNe..ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnagl 75 
                                       svvi++y     +   e++es+l+q +y+ +e i++ Dg +    e +ee   + +r++v+ ++envG++ ++n+g+
  gi|336253749|ref|YP_004596856.1|   4 SVVICIYSMdrFEAFSEAVESVLDQ-TYEPVETILIVDGNQTV-YERVEEEWGGHERITVYCNDENVGLSMSRNRGA 78 
                                       78999998888**************.99999999999999444.4444444469*********************** PP

                                       HH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCST CS
                   Glycos_transf_2  76 raatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnls 152
                                       + a+gd+i+flD+D + d++w+++lv  +e++++ +v g+ +   +  ++   +++  + + +  + r +   g + 
  gi|336253749|ref|YP_004596856.1|  79 ELANGDVIAFLDDDAVADEQWVKELVSVYEEHDVEAVGGKMVPQWVAGKPTFLPEE--FYWLVGVTYRGFPNEGAVR 153
                                       ***************************************99998888888888887..6777777777777777777 PP

                                       TCSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 153 feigsaallrrealeel 169
                                          gs+  +r ++l el
  gi|336253749|ref|YP_004596856.1| 154 NTFGSNISFRADVLSEL 170
                                       77777777777777665 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 !   51.2   0.1     4e-17   1.5e-13       4     212 ..       3     215 ..       2     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 4e-17
                   Glyco_tranf_2_3   4 lavlVptfneed..vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksra 78 
                                       ++v+++ +  ++     e +es+l q+y +ve++++vd++++   +v ee     +++r++v+ n++n g  + sr 
  gi|336253749|ref|YP_004596856.1|   3 VSVVICIYSMDRfeAFSEAVESVLDQTYEPVETILIVDGNQTVYERVEEE---WGGHERITVYCNDENVGL-SMSR- 74 
                                       688888888777778999**********************9986664444...455899********9996.8877. PP

                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarral 155
                                        n++ + +++d+++++DdD+v +   +k l+ +++ ++v+avg+++  +      ++l   ++       + + +++
  gi|336253749|ref|YP_004596856.1|  75 -NRGAELANGDVIAFLDDDAVADEQWVKELVSVYEEHDVEAVGGKMVPQWVAGKPTFLPEEFYWLVGVTYRGFPNEG 150
                                       .9********************************99*******9987665555556666767778888888888999 PP

                   Glyco_tranf_2_3 156 gvltlnGsgslirrevlkelegldp.......lflltdDyelglrlrr.agfrtayvpgaavrev 212
                                        v    Gs   +r++vl el+g+dp       + + ++  el+ rlr   ++  +y p+a v + 
  gi|336253749|ref|YP_004596856.1| 151 AVRNTFGSNISFRADVLSELGGFDPnlgrksgKHVQGEETELAARLRTeLNGTLYYTPDAKVKHK 215
                                       8877679999***********88886432221122337777777777756666667787777765 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 !   26.0   0.1   1.6e-09   5.9e-06       1      96 [.       4      97 ..       4     115 .. 0.70
   2 ?    2.6   0.0     0.021        77     165     188 ..     157     179 ..     152     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.6e-09
                   Glyco_tranf_2_2  1 svviplraseerhyieerv..lqkakyydeeielivvddgSsekfleevssii.dl.nllvylkdeddkayslaaarNr 75
                                      svvi+++  ++ +   e v      + y++   +++vd+  +    e v+     + +  vy +de     +l+ +rNr
  gi|336253749|ref|YP_004596856.1|  4 SVVICIYSMDRFEAFSEAVesV-LDQTYEPVETILIVDGNQTVY--ERVEEEWgGHeRITVYCNDE---NVGLSMSRNR 76
                                      89*******9999999999532.233346666667777665544..55555441331445564444...899******* PP

                   Glyco_tranf_2_2 76 GaskaesdlvlFlDaDcfiss 96
                                      Ga+ a++d++ FlD D     
  gi|336253749|ref|YP_004596856.1| 77 GAELANGDVIAFLDDDAVADE 97
                                      **************9987655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.021
                   Glyco_tranf_2_2 165 sssilinrraflevGGyDErfrGh 188
                                       +s+i  +   ++e+GG+D ++ G 
  gi|336253749|ref|YP_004596856.1| 157 GSNISFRADVLSELGGFDPNL-GR 179
                                       6888899999********999.53 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 !   23.9   0.0     9e-09   3.2e-05       1     129 [.      85     221 ..      85     301 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 9e-09
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvm..nvanwleelaalffaedhgkdilvrealgrvvpsvGs 75 
                                       +i++lD+D v +++ ++e+++ +++++v +v g+++++  +     + l   +f + +g   + + + g v   +Gs
  gi|336253749|ref|YP_004596856.1|  85 VIAFLDDDAVADEQWVKELVSVYEEHDVEAVGGKMVPQwvA--GKPTFLPE-EFYWLVGVTYRGFPNEGAVRNTFGS 158
                                       699*********************99**********98542..22222333.34467777777778889999999** PP

                   Glyco_trans_2_3  76 gaflrrsalqevggwdgdes......svsEDfdmglrlq.rkGyrvrfvpeslvkek.spl.t 129
                                       ++++r+++l+e+gg+d + +        +E ++++ rl+ +++ ++++ p++ vk k + + t
  gi|336253749|ref|YP_004596856.1| 159 NISFRADVLSELGGFDPNLGrksgkhVQGEETELAARLRtELNGTLYYTPDAKVKHKiFDYrT 221
                                       *************777433366677689**********7588899999999955443244423 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 !   16.5   0.0   1.2e-06    0.0045      26     121 ..      78     175 ..      63     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-06
                   Glyco_transf_21  26 leaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlqa...klsglg 99 
                                        e a+ d++ ++D+d++++++ ++el+   e+ +v+ V +  v    +g ++ +    ++ l gv+++   + ++++
  gi|336253749|ref|YP_004596856.1|  78 AELANGDVIAFLDDDAVADEQWVKELVSVYEEHDVEAVGGKMVPQWVAGKPT-FLPEEFYWLVGVTYRgfpNEGAVR 153
                                       455999********************************99888887777777.44555666677777744334789* PP

                   Glyco_transf_21 100 favGksmalrreaLeaiGGfea 121
                                         +G+ + +r ++L ++GGf +
  gi|336253749|ref|YP_004596856.1| 154 NTFGSNISFRADVLSELGGFDP 175
                                       ********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2251.30
//
Query:       gi|336253750|ref|YP_004596857.1|  [L=447]
Description: sulfatase [Halopiger xanaduensis SH-6]
Scores for 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   82.7   0.3    7.3e-23   81.4   0.3    1.6  1  Sulfatase     Sulfatase
    1.3e-08   34.8   1.5    1.3e-06   28.3   0.1    2.2  2  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.3   8.2e-27   7.3e-23       3     308 ..      53     344 ..      51     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 8.2e-27
                                       EEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT.... CS
                         Sulfatase   3 vvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg.... 75 
                                       +v i++d l+a+++   +   +ttp+l+      l+ t++++ ++ + p++++lltg yph++g+  +t+  +    
  gi|336253750|ref|YP_004596857.1|  53 IVCIVVDALRADYV---D--DETTPYLA-----SLNGTDAVTPGAWTFPAVSSLLTGIYPHEHGAMKQTDEFDnsdg 119
                                       77788888866553...3..45699997.....78889****************************99999999*** PP

                                       ....HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHCCTTTSEEEETSSSCHHTCCCCCCCCCECTCCCTT CS
                         Sulfatase  76 ....gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyknrgfdrflgfptgsaalkdpekseyngevlrvpp 148
                                           +   ++ +tL e+l +aGY+t                   +gf +   f ++s ++ d+  +++ +       
  gi|336253750|ref|YP_004596857.1| 120 lslpPRMDEDRVTLTEILAGAGYDT------------------YGGFGHDTPFVAVSGRFHDHALYHKMN------- 171
                                       ***9999999***************..................124444444456899999999888875....... PP

                                       TTCSHHHHHHHHHHHHHHCCCTSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCH................. CS
                         Sulfatase 149 eggysddrlldealefllarndkpfflylatlapHappeapdeyakkyatffddgseaar................. 208
                                           + d++l+  le++  ++    f++l++  pH p   p ey kk    +  ++ +++                 
  gi|336253750|ref|YP_004596857.1| 172 ---SDADDVLEDYLEWV--SDRTRTFAFLHLADPHIPVDPPSEYWKKHDIDTSIDDLENWryrtdtdcsedcqsyre 243
                                       ...8999*********8..44689**************999999999655544443333388899999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCG.........HHTTSSSCTTCSSSHHHHBEE CS
                         Sulfatase 209 qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgaslee.........sngplrggkganayeggtrvP 276
                                       + ++ y +sv yvDd+++r+   L  ++ ld+ l+++t+Dhg++l e         + g      g + ye   rvP
  gi|336253750|ref|YP_004596857.1| 244 HRRRLYRASVDYVDDALSRFETGL--ENALDDPLLIVTADHGEALWEqvefdvehfN-GTGCVDHGGAPYEALARVP 317
                                       ************************..999*****************9********63.333333333679******* PP

                                       EEEEETTTSHCEEECSEEEGGGHHHHHHHHTT CS
                         Sulfatase 277 llvwwpgekaprvseelvshiDlfptildlag 308
                                       ll     ++ +      vs+iD++pti d +g
  gi|336253750|ref|YP_004596857.1| 318 LLTNADWTFDS-----DVSLIDIAPTITDSVG 344
                                       *9888777777.....9**********99877 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   1.5e-10   1.3e-06       2      63 ..      54     107 ..      53     117 .. 0.90
   2 !    4.9   0.1    0.0018        16     199     233 ..     251     283 ..     239     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.5e-10
                                       EEEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS- CS
                      Phosphodiest   2 lvislDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGi 63 
                                       + i++D lrad++d+  e++p la+L  +g+ a     +  + Tfp+ +sl+TG yP eHG 
  gi|336253750|ref|YP_004596857.1|  54 VCIVVDALRADYVDD--ETTPYLASL--NGTDAV----TPGAWTFPAVSSLLTGIYPHEHGA 107
                                       78*************..*********..777766....6699*******************6 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES-- CS
                      Phosphodiest 199 dalrrvDkaigdLlealderglsaetniilvSDHG 233
                                       + + +vD+a+ ++  +l+     ++  +i+++DHG
  gi|336253750|ref|YP_004596857.1| 251 ASVDYVDDALSRFETGLENA--LDDPLLIVTADHG 283
                                       67889*************88..67888******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3261.94
//
Query:       gi|336253751|ref|YP_004596858.1|  [L=310]
Description: UDP-glucose 4-epimerase [Halopiger xanaduensis SH-6]
Scores for 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-64  215.6   0.0    8.4e-64  215.3   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.6e-62  210.4   0.0    3.4e-61  207.5   0.0    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.3e-30  106.4   0.0    1.6e-30  106.1   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.9e-17   63.3   0.0    1.2e-16   60.8   0.0    1.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.1e-13   51.5   0.0    1.5e-13   51.0   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    9.7e-12   44.6   0.0    1.1e-11   44.3   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    2.5e-10   40.0   0.1    4.4e-08   32.6   0.1    2.5  1  NAD_binding_4    Male sterility protein
    1.8e-06   27.7   0.1      3e-06   27.0   0.1    1.3  1  NmrA             NmrA-like family
    0.00029   20.3   0.1     0.0005   19.6   0.1    1.4  1  adh_short        short chain dehydrogenase
    0.00041   20.3   1.1     0.0013   18.7   1.1    1.7  1  KR               KR domain
     0.0076   16.5   0.0      0.017   15.4   0.0    1.7  1  TrkA_N           TrkA-N 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 !  215.3   0.0   5.2e-67   8.4e-64       2     240 ..       5     240 ..       4     241 .. 0.95

  Alignments for each domain:
  == domain 1  score: 215.3 bits;  conditional E-value: 5.2e-67
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlAa 73 
                                       +VtGa+GfiGs+lv+ lle+gyev g+d ls+++ ++++e       ++ve+ ++dr+ l+r+++  ++++v+h Aa
  gi|336253751|ref|YP_004596858.1|   5 VVTGAAGFIGSHLVDTLLERGYEVRGIDDLSTGQLENLDEAReheafSFVEGSVRDRDTLARALD--GANCVFHQAA 79 
                                       7*****************************77776666666699*********************..9********* PP

                                       ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHH CS
                         Epimerase  74 vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlage 150
                                       v++va+s++dpa +++ n+ gt  l+e+a +agv+ ++ +sS++vYG + e pk e +   p+ p spYa++K++ e
  gi|336253751|ref|YP_004596858.1|  80 VSSVARSFDDPATVADVNCGGTSMLFEVAADAGVETFVVASSAAVYGSGGELPKREAM---PVDPESPYALSKYYTE 153
                                       **********************************************************...**************** PP

                                       HHHHHHHHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHH CS
                         Epimerase 151 klveayaaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvl 226
                                       + + ++ +qyg++a++lr+fn+yGpr ++++e + v+p++++ + +g+   +++gdg++ Rdf++v Dv++a+++++
  gi|336253751|ref|YP_004596858.1| 154 QAALQLGDQYGIDAVALRYFNVYGPRqDPDSEYAAVVPKFLELMSDGE-RPVIYGDGEQSRDFVFVGDVVDANVRAV 229
                                       **************************999999****************.**************************** PP

                                       HHHTT-STTEEEEE CS
                         Epimerase 227 ehvdagdkgeiyni 240
                                       e        e++n+
  gi|336253751|ref|YP_004596858.1| 230 ESN---CRDEVLNV 240
                                       *93...33456666 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 !  207.5   0.0   2.1e-64   3.4e-61       2     332 .]       6     304 ..       5     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 207.5 bits;  conditional E-value: 2.1e-64
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       +TG aGfiGs+l++ Lle+gyev gi+++    +tg++e+l + +    +e +++++g ++D++ l r+l+ +  + 
  gi|336253751|ref|YP_004596858.1|   6 VTGAAGFIGSHLVDTLLERGYEVRGIDDL----STGQLENLDEAR---EHEAFSFVEGSVRDRDTLARALDGA--NC 73 
                                       9************************9755....456677765433...3468********************9..79 PP

                                       EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHH CS
                     GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaa 155
                                       v++ AA s V++sf++P+++a+vn  Gt  L+e++ ++g+e    f+ aS++ vYG+  e p +E  p++P+sPYa 
  gi|336253751|ref|YP_004596858.1|  74 VFHQAAVSSVARSFDDPATVADVNCGGTSMLFEVAADAGVE---TFVVASSAAVYGSGGELPKREAMPVDPESPYAL 147
                                       ***************************************98...7******************************** PP

                                       HHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TT.SCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 156 aKlyadwivvnyreayglfavngilfnhesprrget.fvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                       +K y ++ + +  ++yg+ av  ++fn ++pr+ ++      +++++  +  g+++v+ +G++++ Rd+ +v D+v+
  gi|336253751|ref|YP_004596858.1| 148 SKYYTEQAALQLGDQYGIDAVALRYFNVYGPRQDPDsEYAAVVPKFLELMSDGERPVI-YGDGEQSRDFVFVGDVVD 223
                                       *********************************9973466789999999999998876.8***************** PP

                                       HHHHHHHCSS-.--EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 232 amwlmlqqdkp.edyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       a +++++++   e  ++a g+  +++++v + +  lg ++e                     + +   rpg+ +   
  gi|336253751|ref|YP_004596858.1| 224 ANVRAVESNCRdEVLNVAGGRRITINDLVSRINDVLGTELEP--------------------I-YDDPRPGDIRHSG 279
                                       *99999876541446788888899998888888888765432....................2.34569******** PP

                                       B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeelvrem 332
                                       +d ska++ ++++p+v++e+++r++
  gi|336253751|ref|YP_004596858.1| 280 ADVSKANRAIEYEPTVDLETGLRRT 304
                                       *********************9986 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 !  106.1   0.0   9.8e-34   1.6e-30       1     230 [.       5     230 ..       5     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 9.8e-34
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD..lrespelleelskvnvkkviegDvtdkdkleealegvdvvihlas 75 
                                       vvtG+aGF+G++lv +L++++   evr +D     + e l+e+++ +  +++eg v+d d+l +al+g+++v+h a+
  gi|336253751|ref|YP_004596858.1|   5 VVTGAAGFIGSHLVDTLLERG--YEVRGIDdlSTGQLENLDEAREHEAFSFVEGSVRDRDTLARALDGANCVFHQAA 79 
                                       8********************..6***99964333446678888999999*************************** PP

                         3Beta_HSD  76 lvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKa 151
                                       ++ va   +   ++ +vn  GT  + e + +agv+++v  Ssa v g    g e+     ++ ++  ++++y+ sK 
  gi|336253751|ref|YP_004596858.1|  80 VSSVARsFDDPATVADVNCGGTSMLFEVAADAGVETFVVASSAAVYGS---GGELP---KREAMPVDPESPYALSKY 150
                                       ****9845667899********************************99...66666...3455666789******** PP

                         3Beta_HSD 152 laEklvlkaNgrtlknggrlyTcaLRpagiyGegdk......llvpllkqlaklglalfkigdeevlsdrvYvgNva 222
                                         E++ l+  +   + g  +  +aLR   +yG++++       +vp + +l+  g+  + +gd e+  d+v+vg v+
  gi|336253751|ref|YP_004596858.1| 151 YTEQAALQLGD---QYG--IDAVALRYFNVYGPRQDpdseyaAVVPKFLELMSDGERPVIYGDGEQSRDFVFVGDVV 222
                                       *******9999...445..899***********986333333577888899999*********************** PP

                         3Beta_HSD 223 wahilAar 230
                                       +a + A+ 
  gi|336253751|ref|YP_004596858.1| 223 DANVRAVE 230
                                       ****9986 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   7.1e-20   1.2e-16       2     251 ..       5     263 ..       4     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 7.1e-20
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T- CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkv 78 
                                       +vtGa+G iGs+lv+++l++  +   + + +  +l ++++  e    ++ ++     v g+vrd+++l++al+  + 
  gi|336253751|ref|YP_004596858.1|   5 VVTGAAGFIGSHLVDTLLERGYEVRGIDDLSTGQLENLDEARE----HEAFS----FVEGSVRDRDTLARALD--GA 71 
                                       69******************99877777777777777777653....33332....457**************..** PP

                                       SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG..............SS--SHHHHH CS
                   Polysacc_synt_2  79 dvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA..............vnPtnvmGat 141
                                       ++vfh AA+  V      p+ + + N  gt+ + e+a +agv+++v+ S+                 v+P + + ++
  gi|336253751|ref|YP_004596858.1|  72 NCVFHQAAVSSVARSFDDPATVADVNCGGTSMLFEVAADAGVETFVVASSAAVygsggelpkreampVDPESPYALS 148
                                       ************************************************98632222222222233448999****** PP

                                       HHHHHHHHHHGGG--SSS--EEEEEEE-EETTGT.......TSSHHHHHHHHHTT.SSEEES-TT-EEEEE-HHHHH CS
                   Polysacc_synt_2 142 KrlaekllqalakeseekktkfvvvRfGNVlgSr.......GSviplFkkqikeg.gpvtvTdpemtRyfmtieeav 210
                                       K ++e+ + +l ++        v+ R+ NV g r         v+p+F + +++g  pv   d e  R f+ + + v
  gi|336253751|ref|YP_004596858.1| 149 KYYTEQAALQLGDQY---GIDAVALRYFNVYGPRqdpdseyAAVVPKFLELMSDGeRPVIYGDGEQSRDFVFVGDVV 222
                                       ********9999998...7999*********987444444458************889******************* PP

                                       HHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH........ CS
                   Polysacc_synt_2 211 qLvlqalalakggeifvldmGepvkivdlakalielsglee 251
                                       +  + a++   + e++ +  G  ++i dl++++ ++ g+e 
  gi|336253751|ref|YP_004596858.1| 223 DANVRAVESNCRDEVLNVAGGRRITINDLVSRINDVLGTEL 263
                                       ********************************999988764 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 !   51.0   0.0   9.3e-17   1.5e-13       1     127 [.       8     152 ..       8     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 9.3e-17
                                       TTTSHHHHHHHHHHHHC-T-EEEEE....ETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtal....vRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk 73 
                                       GA G +G++lv+ ll+r g+ev+ +    + + e l+e +++e+ + veg+v d ++la+al+ga+ V+  ++ ++ 
  gi|336253751|ref|YP_004596858.1|   8 GAAGFIGSHLVDTLLER-GYEVRGIddlsTGQLENLDEAREHEAFSFVEGSVRDRDTLARALDGANCVFHQAAVSSV 83 
                                       9****************.5***98733223346777788899**************************999955555 PP

                                       ....HHHH.........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHH...HCCHHHHHHHHHH CS
                    NAD_binding_10  74 ....deeg.........aknivdaakeagvkRfvlvsaigvgdevpgefgewnk...ellkaylaakraa 127
                                           d+ +         +  + ++a  agv+ fv+ s++ v+ +  ge+++      +  ++y+  k++ 
  gi|336253751|ref|YP_004596858.1|  84 arsfDDPAtvadvncggTSMLFEVAADAGVETFVVASSAAVYGS-GGELPKREAmpvDPESPYALSKYYT 152
                                       44553333567778899************************964.3333322110111223333333333 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 !   44.3   0.0     7e-15   1.1e-11       3     155 ..       4     179 ..       1     278 [. 0.83

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 7e-15
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE-- CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvnaA 59 
                                        +vtGa G +Gs+L++ l e+g+ev +++                      e  ++d++++a++l+ a++  v + A
  gi|336253751|ref|YP_004596858.1|   4 TVVTGAAGFIGSHLVDTLLERGYEVRGIDDLstgqlenldeareheafsfvEGSVRDRDTLARALDGANC--VFHQA 78 
                                       689*************************7667999**************99999***********99655..***** PP

                                       ----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHH CS
                     RmlD_sub_bind  60 AytavDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqa 135
                                       A   v +  ++++  + vn  ++  l e+aa +g+ +++  S+  V+    + p +e  +++P + Y+ +K+  Eqa
  gi|336253751|ref|YP_004596858.1|  79 AVSSVARSFDDPATVADVNCGGTSMLFEVAADAGVeTFVVASSAAVYGSGGELPKREAMPVDPESPYALSKYYTEQA 155
                                       **********************************956999********999************************** PP

                                       HHH....H-SSEEEEEE-SEESSS CS
                     RmlD_sub_bind 136 vla....agkkalivRtswvygek 155
                                        l+    +g +a+ +R   vyg +
  gi|336253751|ref|YP_004596858.1| 156 ALQlgdqYGIDAVALRYFNVYGPR 179
                                       *99444444566778888899873 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   2.7e-11   4.4e-08       1     253 [.       6     221 ..       6     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.7e-11
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TGa GF+G++L+  LL++  e      vR  ++   +  l e+l++ +          e  ++veG + + +    
  gi|336253751|ref|YP_004596858.1|   6 VTGAAGFIGSHLVDTLLERGYE------VRGIDD-LSTGQL-ENLDEARE--------HEAFSFVEGSVRDRD---- 62 
                                       7******************986......999987.344444.44444333........56668******9876.... PP

                                       HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                         +l +  +  ++++h aA  ++ ++ ++   + +vN  Gt  ++e a+      +++  S+a+v+g   +      
  gi|336253751|ref|YP_004596858.1|  63 --TLARALDGANCVFHQAAVSSVARSFDDpatVADVNCGGTSMLFEVAADAGVE-TFVVASSAAVYGSGGE------ 130
                                       ..788888**************9999987666899**************88777.9*********999994...... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHHH CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwingsdlgirgllgl 228
                                                   + +a   + +  Y  sK+  E+   + +++ g+ +v +R  +++g  +   ++    ++  +l l
  gi|336253751|ref|YP_004596858.1| 131 ----------LPKREAMPVDPESPYALSKYYTEQAALQLGDQYGIDAVALRYFNVYGPRQDPDSEYAA-VVPKFLEL 196
                                       ..........4466788899999********************************9944443444444.45555666 PP

                                       HHH-EEES-SB---TT--EEEHHHH CS
                     NAD_binding_4 229 iakgvlpeilgdkeavldlvpvDyv 253
                                       +  g  p i+gd e+  d+v v  v
  gi|336253751|ref|YP_004596858.1| 197 MSDGERPVIYGDGEQSRDFVFVGDV 221
                                       6677777777777777666666555 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   1.9e-09     3e-06       2     103 ..       5     122 ..       4     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.9e-09
                                       EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHH....STTEEEES-TT-HHHHHHHHTT-SEEEE---G CS
                              NmrA   2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslke....aGvelvkgdlddkeslvealkgvdvvfsvtgf 74 
                                       +v+Ga+G +G+++v+ ll++g++vr +  d+++ ++++l e    +   +v+g++ d++ l++al+g++ vf   ++
  gi|336253751|ref|YP_004596858.1|   5 VVTGAAGFIGSHLVDTLLERGYEVRGI-DDLSTGQLENLDEarehEAFSFVEGSVRDRDTLARALDGANCVFHQAAV 80 
                                       69***********************85.67766666666541111567899*********************98887 PP

                                       G.............S-HHHHHHHHHHHHHHHS-SEEEEEE-- CS
                              NmrA  75 y.............skeiedgkklvdAakeaGvkhfiySslg 103
                                                     + +    + l ++a+ aGv+ f+ +s +
  gi|336253751|ref|YP_004596858.1|  81 SsvarsfddpatvaDVNCGGTSMLFEVAADAGVETFVVASSA 122
                                       778888988888555555555778899999999999987755 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   3.1e-07    0.0005       2      71 ..       3      71 ..       2      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.1e-07
                                      EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHH CS
                         adh_short  2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealveka 71
                                      + +vtGa++ IG  ++++l+++G++v  +d  +    e ++e +e+ + + ++++ v+dr+ + ++++ a
  gi|336253751|ref|YP_004596858.1|  3 TTVVTGAAGFIGSHLVDTLLERGYEVRGIDDLSTGQLENLDEAREH-EAFSFVEGSVRDRDTLARALDGA 71
                                      679*************************998888888888998875.78*************99998876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.1   8.1e-07    0.0013       2     143 ..       3     127 ..       2     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.1e-07
                                       EEEEETTTSHHHHHHHHHHHHHH..S-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHH CS
                                KR   2 tylitGGlGgLGlelarwlaekg..arhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeik 76 
                                       t ++tG++G +G +l+++l+e+g   r +  ls        + ++++e ++++   ++v+  v d+d ++++l+ ++
  gi|336253751|ref|YP_004596858.1|   3 TTVVTGAAGFIGSHLVDTLLERGyeVRGIDDLSTG------QLENLDEAREHE-AFSFVEGSVRDRDTLARALDGAN 72 
                                       568********************433444444444......445666666655.5899****************997 PP

                                       HHSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH-- CS
                                KR  77 aeeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgs 143
                                               v+h A v+  +     + +d ++v    + G+  L e+ +d  ++ fv+ SS+a ++gs
  gi|336253751|ref|YP_004596858.1|  73 -------CVFHQAAVSSVA----RSFDDPATVADVNCGGTSMLFEVAADAGVETFVVASSAA-VYGS 127
                                       .......9******98754....589999****************************99976.4565 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     1e-05     0.017       6      58 ..      10      67 ..       4      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                                      -SHHHHHHHHHHHH.TTEEEEEEESSH....HHHHHHHHTT.SEEEES-TTSHHHHHHT CS
                            TrkA_N  6 lGrvGrslaeeLse.ggkdvvvidkde....erveelreeg.levvvgdatdeevLeea 58
                                      +G +G++l+++L e g+ +v +id+      e+++e+re++ + +v g++ d+++L++a
  gi|336253751|ref|YP_004596858.1| 10 AGFIGSHLVDTLLErGY-EVRGIDDLStgqlENLDEAREHEaFSFVEGSVRDRDTLARA 67
                                      6889**********777.5*****98877678899999999899************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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 0.24s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 2310.33
//
Query:       gi|336253752|ref|YP_004596859.1|  [L=410]
Description: group 1 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for 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-30  105.3   0.0    3.7e-30  104.7   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    1.1e-27   97.1   0.0    2.5e-27   95.9   0.0    1.6  1  Glyco_trans_1_4  Glycosyl transferases group 1
    9.5e-08   32.3   0.0      2e-07   31.3   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.016   15.6   1.1      0.027   14.9   0.3    1.8  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain


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 !  104.7   0.0   8.2e-34   3.7e-30       7     162 ..     207     359 ..     201     367 .. 0.94

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 8.2e-34
                                       HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHS CS
                   Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsr 83 
                                        + +++e++ ++ ++grl++eKg+ +l +++++l+    ++v + ++G+g+ +  l+++        +v+++g +++
  gi|336253752|ref|YP_004596859.1| 207 PRGPFRERDHVVGFLGRLDEEKGIRTLAEVAKRLP----DDVTFRFIGDGALRGWLESELSDEIAASTVEVTGWIDH 279
                                       567899***************************96....79************************************ PP

                                       SSHHHHHHCESEEEEEESS.BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH CS
                   Glycos_transf_1  84 edleellknadifvlpsis.EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede 159
                                       ++++  l+   ++v+ps   Eg+++++lEAma+g+pv a+ + g+++vvkdgetG+l + +++ea+a++i+++ +++
  gi|336253752|ref|YP_004596859.1| 280 DEVPDQLTELQLLVMPSAPtEGLPTTILEAMACGTPVYATPVVGVPDVVKDGETGYLMEDTSDEAIARKIQRIQTSD 356
                                       *****************989****************************************************99888 PP

                                       HHH CS
                   Glycos_transf_1 160 elr 162
                                       +lr
  gi|336253752|ref|YP_004596859.1| 357 DLR 359
                                       655 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 !   95.9   0.0   5.5e-31   2.5e-27       2     131 ..     216     352 ..     215     355 .. 0.90

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 5.5e-31
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT.T-T..TEEEE---..THHHHHHHH- CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa.gle.erveftGfv..edlaellaaa 73 
                                       +v++f+Grl +++kg++ l+e +++l  +dv++ ++Gdg  r   le++++ +++ ++ve+tG++  +++++ l + 
  gi|336253752|ref|YP_004596859.1| 216 HVVGFLGRL-DEEKGIRTLAEVAKRLP-DDVTFRFIGDGAlR-GWLESELSdEIAaSTVEVTGWIdhDEVPDQLTEL 289
                                       689******.556**************.55*********965.588877755665256*******9667******** PP

                                       SEEEE--...---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHH CS
                   Glyco_trans_1_4  74 dvfvaPs...egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrL 131
                                       +++v+Ps   eg++ ++lEama+g+pv at+v g+++vv  ge+g+l+++ + ea+a++i+r+
  gi|336253752|ref|YP_004596859.1| 290 QLLVMPSaptEGLPTTILEAMACGTPVYATPVVGVPDVVkdGETGYLMEDTSDEAIARKIQRI 352
                                       *********99**************************************999********986 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 !   31.3   0.0   4.5e-11     2e-07       9      90 ..     300     382 ..     286     384 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 4.5e-11
                   Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehty 83 
                                       e++ + ++Ea+acG+++ +++  g+++ +++g+++ l+e  + e +a+ki++  +++++ r+++++ r  v++e++ 
  gi|336253752|ref|YP_004596859.1| 300 EGLPTTILEAMACGTPVYATPVVGVPDVVKDGETGYLMEdtSDEAIARKIQRIQTSDDL-RSMSHRCRTLVEEEYSF 375
                                       5677889*************99*****************98888899999997666665.66**************9 PP

                   Glyco_trans_1_2  84 dhraeql 90 
                                       + ++e++
  gi|336253752|ref|YP_004596859.1| 376 EGAVERF 382
                                       9999887 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 ?   14.9   0.3     6e-06     0.027      21     144 ..      47     183 ..      18     187 .. 0.66
   2 ?   -2.5   0.0       1.3     6e+03      13      39 ..     265     290 ..     260     336 .. 0.46

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6e-06
                   Glyco_trans_4_4  21 Vtvltpapapgap.eleedgvrvhrlpvprrpspladlaal...ralrrllrqrrerpdvvhahs.ptaglaarlar 92 
                                       + ++t++ ++g+  +++++ v+++   ++ +  p+a +++l   +++ rll  +r+   vv   + +   l++  a+
  gi|336253752|ref|YP_004596859.1|  47 ISLVTAGLPEGSTiREDHEVVELTTANTGESI-PVAAARFLlnqFRMCRLL--ARRDEEVVLFYGaIAYFLPICCAK 120
                                       55666555555442355666666665555443.888888886667888888..777777888777445666666666 PP

                   Glyco_trans_4_4  93 rrrgiplvvtlh........gll..lrrg..sgavrrlyralerrllrradavlvvseaeaeel 144
                                         +g  +v++++         ++  +++g  ++ ++ l++ ler+ +   da+++ ++++a  l
  gi|336253752|ref|YP_004596859.1| 121 -LAGKTVVLEPRgnvpltlrLHWeqRVPGpiARGLAGLVWGLERLGYWLSDAIVTYTPSMASSL 183
                                       .66666666666332222211222233445777788888999******************9866 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                   Glyco_trans_4_4  13 aLaarGheVtvltpapapgapeleedg 39 
                                       + aa  +eVt +++++  +++ l+e +
  gi|336253752|ref|YP_004596859.1| 265 EIAASTVEVTGWIDHDEVPDQ-LTELQ 290
                                       555556666666643333322.22211 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); 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:                         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 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2974.49
//
Query:       gi|336253753|ref|YP_004596860.1|  [L=483]
Description: sulfatase [Halopiger xanaduensis SH-6]
Scores for 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-31  110.5   0.0    1.6e-31  109.9   0.0    1.2  1  Sulfatase      Sulfatase
    8.2e-15   55.2   1.4    2.9e-14   53.4   1.4    1.9  1  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
    3.8e-05   22.5   0.0    9.1e-05   21.2   0.0    1.6  2  DUF229         Protein of unknown function (DUF229)
     0.0011   18.4   0.0     0.0046   16.3   0.0    1.8  2  Metalloenzyme  Metalloenzyme superfamily
     0.0053   15.9   0.0     0.0085   15.2   0.0    1.2  1  DUF1501        Protein of unknown function (DUF1501)
  ------ inclusion threshold ------
      0.061   13.4   0.0       0.11   12.6   0.0    1.3  1  DUF3974        Domain of unknown function (DUF3974)


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.9   0.0   5.4e-35   1.6e-31       1     295 [.       3     346 ..       3     358 .. 0.84

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 5.4e-35
                                       EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHH CS
                         Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgggg 77 
                                       pnv+li++d+++a + +l ++   ttp+l + ae+ +r++++ + +++++ s a+++tg+  ++++v+s +     +
  gi|336253753|ref|YP_004596860.1|   3 PNVLLIVLDSVRARNTSLHEHANDTTPFLNEFAESATRYRQARAPGTTSVTSHASIFTGLHVNEHRVTSAE----AK 75 
                                       9*****************************************************************98887....88 PP

                                       CTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC...CTTTSEEEETSSSCHHTCCCCCCCCCECTCCC..... CS
                         Sulfatase  78 lpqteatLpellkeaGYntaaigkwhlgwssrqsvyk...nrgfdrflgfptgsaalkdpekseyngevlrv..... 146
                                       l +  + + +l  e+GY+t+++   ++ w+      +    +gfd+++g + +   ++ +++s++ ++++++     
  gi|336253753|ref|YP_004596860.1|  76 LSEGATVFERLRDEHGYETGVFS--ENVWITDV---DiglDHGFDTVVGPQDVPYPDALNPRSFVSDRGTGRfteyv 147
                                       888888888999999****6666..55555444...14569********66666666666666666666555***** PP

                                       ...............................TTTTCSHHHHHHHHHHHHHHCCC.TSSEEEEEEE-TTSSSTCTCGG CS
                         Sulfatase 147 ...............................ppeggysddrlldealefllarn.dkpfflylatlapHappeapde 191
                                                                        +g    + ++d++l++ ++++ ++ + + + ++  H p++ ++e
  gi|336253753|ref|YP_004596860.1| 148 reclrddaplrglingaytkissdypsllpsFIDGTSPGNLYTDKFLDW-IDTTvNDEWAACVNLMDAHLPYNPKEE 223
                                       *****************************98667777778899******.57777**************98877777 PP

                                       HTCCGSTTTTCCCCCCH.......................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEE CS
                         Sulfatase 192 yakkyatffddgseaar.......................qlleaylnsveyvDdligrvlaaLeenglldntlvvf 245
                                       + +      dd+    r                          + y+++++++D  ++r+++ Lee g+ld+tlvv+
  gi|336253753|ref|YP_004596860.1| 224 FNEW----GDDLL---RtiedeavdqwqlhcgdglwwrqkAREALYDGAIRQADSYVQRIIDGLEERGVLDDTLVVI 293
                                       7665....22222...12334567778999999999998777789******************************** PP

                                       EESSSSCCCG....HHTTSSSCTTCSSSHHHHBEEEEEEETTTSHCEEECSEEE CS
                         Sulfatase 246 tSDhgaslee....sngplrggkganayeggtrvPllvwwpgekaprvseelvs 295
                                       tSDhg+  +e      ++  g++  + +e  ++vPl+v  pg+  ++ ++ +++
  gi|336253753|ref|YP_004596860.1| 294 TSDHGEGFGErsriRPARIAGHNV-SVHEVLLHVPLVVKRPGQRNAHEVDSVAT 346
                                       ********9998875555666665.889***************99966666555 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   1.4   9.6e-18   2.9e-14       1     234 [.       5     299 ..       5     346 .. 0.71

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 9.6e-18
                                       EEEEEETT-B..TTHHHHHG.STSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTT CS
                      Phosphodiest   1 vlvislDGlr..adlldrla.ellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktg 74 
                                       vl+i+lD++r   + l ++a +++p+l+++a+  ++++       t+++++has+ TGl+  eH +++ +   +++ 
  gi|336253753|ref|YP_004596860.1|   5 VLLIVLDSVRarNTSLHEHAnDTTPFLNEFAESATRYR-QARAPGTTSVTSHASIFTGLHVNEHRVTSAEAKLSEGA 80 
                                       79********444567777766****************.55666799*********************665544444 PP

                                       EEEEEETTTTGGGGGCTT....S-HHHHHHHTHTTCEE.EESETTTTSEBTTCT.SC.TBHHSBTCT.CSTTS.... CS
                      Phosphodiest  75 eyvvfvtededaprwwqg....epiwdtaakarglkaa.alfwpgsevdystyyylvsetppryleddfnakv.... 142
                                          vf + +++  + + +    e +w t +   gl  +   ++   +v+y++     s +++r +  +f+++v    
  gi|336253753|ref|YP_004596860.1|  81 T--VFERLRDE--HGYETgvfsENVWITDVDI-GLDHGfDTVVGPQDVPYPDALNPRSFVSDRGT-GRFTEYVrecl 151
                                       4..33333333..336667888*********9.9985545556669****976555553333333.25555556666 PP

                                       ........................................CHHHHHHHHHHHHH...HHCHTHSHHHHHCT...... CS
                      Phosphodiest 143 ........................................pledkvdkavlqtw...ldaafakvvlekel...... 170
                                                                               ++ d +d+ v ++w   +++ +a+      l      
  gi|336253753|ref|YP_004596860.1| 152 rddaplrglingaytkissdypsllpsfidgtspgnlytdKFLDWIDTTVNDEWaacVNLMDAH------Lpynpke 222
                                       7777777666666666666666666777777555554444333333322333345553333333......1433444 PP

                                       ..SSE..SEE.EEEECCCHHHHHHH-....TTSHH....HHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES--- CS
                      Phosphodiest 171 ..ekp..dll.lvyleetDtvgHkfG....pdspe....vedalrrvDkaigdLlealderglsaetniilvSDHGm 234
                                          ++  dll ++  e++D+ + + G    +  ++       a+r++D+++++++++l+erg+ ++t ++++SDHG 
  gi|336253753|ref|YP_004596860.1| 223 efNEWgdDLLrTIEDEAVDQWQLHCGdglwWRQKArealYDGAIRQADSYVQRIIDGLEERGVLDDTLVVITSDHGE 299
                                       68677775552777789*********9996553334567999**********************************5 PP

>> DUF229  Protein of unknown function (DUF229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.52   1.6e+03     127     139 ..       3      15 ..       2      99 .. 0.56
   2 !   21.2   0.0     3e-08   9.1e-05     295     350 ..     249     305 ..     229     324 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.52
                            DUF229 127 ysVlilglDSlSr 139
                                       ++Vl++ lDS+  
  gi|336253753|ref|YP_004596860.1|   3 PNVLLIVLDSVRA 15 
                                       6666666666633 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 3e-08
                            DUF229 295 fgffwsnslshdkfnll.ealDedllkylkklekkgllentlvlllsDHGlrfgklr 350
                                        g++w ++  +  ++ + +++D+++ +++  le++g+l++tlv++ sDHG  fg+  
  gi|336253753|ref|YP_004596860.1| 249 DGLWWRQKAREALYDGAiRQADSYVQRIIDGLEERGVLDDTLVVITSDHGEGFGERS 305
                                       567788888887777642678*****************************9998765 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.27   8.1e+02       3      36 ..       5      37 ..       3      59 .. 0.67
   2 !   16.3   0.0   1.6e-06    0.0046     120     219 ..     228     338 ..     200     358 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.27
                                      EEEEEETTBB----GGGTTHHHS-..-HHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                     Metalloenzyme  3 vvlvvlDGlGeapadelnaihvAk..tPtldkLkke 36
                                      v+l+vlD++  ++++     ++A+  tP l++++++
  gi|336253753|ref|YP_004596860.1|  5 VLLIVLDSVRARNTSL---HEHANdtTPFLNEFAES 37
                                      899*****98887754...23333348888887766 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-T....TTEEEEEE-SSB--TTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 120 aekaldailsgkfdlvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieq....vdgilvvtADHgnaedmv 192
                                        + +l++i+ ++ d+  ++  +      +   + +  ai +aD+ v++i+d +e+    +d+++v+t+DHg      
  gi|336253753|ref|YP_004596860.1| 228 GDDLLRTIEDEAVDQWQLHCGDGLWWRQKAREALYDGAIRQADSYVQRIIDGLEErgvlDDTLVVITSDHGEGFGER 304
                                       55555666666666666555555444444444556679****************9444456899*******654444 PP

                                       S................-.----EEEEEESTT---- CS
                                       xxxx........xxxxxx.xxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 193 krdk........qplTsH.tlepVPilivgkglapd 219
                                          +        + ++ H +l +VP+++  +g++++
  gi|336253753|ref|YP_004596860.1| 305 S--RirpariagHNVSVHeVLLHVPLVVKRPGQRNA 338
                                       4..344778888555555367899999999987762 PP

>> DUF1501  Protein of unknown function (DUF1501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.9e-06    0.0085     269     302 ..     265     298 ..     246     306 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.9e-06
                           DUF1501 269 lakelDqalaaLlkdLkqrGllddTlVvwagEFG 302
                                        +++ D  ++  +++L++rG lddTlVv +++ G
  gi|336253753|ref|YP_004596860.1| 265 AIRQADSYVQRIIDGLEERGVLDDTLVVITSDHG 298
                                       5589999999*********************988 PP

>> DUF3974  Domain of unknown function (DUF3974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.6e-05      0.11      44      86 ..      17      59 ..       7      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.6e-05
                           DUF3974 44 hesieklsnkstpflkeftkhplfyrwirtegkkeqkvlnvlf 86
                                      + s+++ +n +tpfl+ef++    yr +r+ g     + + +f
  gi|336253753|ref|YP_004596860.1| 17 NTSLHEHANDTTPFLNEFAESATRYRQARAPGTTSVTSHASIF 59
                                      4689999***********************9988776666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); 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:                         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 0.25s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3585.98
//
Query:       gi|336253754|ref|YP_004596861.1|  [L=192]
Description: hypothetical protein Halxa_2360 [Halopiger xanaduensis SH-6]
Scores for 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-12   45.7   5.1    1.3e-09   37.4   2.0    3.8  4  Hexapep        Bacterial transferase hexapeptide (six repeats
    4.5e-09   35.9  15.6      6e-09   35.5   3.3    3.3  4  Hexapep_2      Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
        0.1   12.2   0.1       0.18   11.4   0.1    1.4  1  Mso1_Sec1_bdg  Sec1-binding region of Mso1


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 ?    0.1   0.0      0.13   7.8e+02      11      22 ..      20      31 ..      18      32 .. 0.75
   2 ?    0.4   0.0       0.1   6.1e+02      19      27 ..      38      46 ..      37      49 .. 0.63
   3 !    4.8   0.0    0.0042        25      19      28 ..      60      69 ..      58      76 .. 0.75
   4 !   37.4   2.0   2.2e-13   1.3e-09       4      35 ..     103     134 ..     100     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.13
                                      -TTEEEETTEEE CS
                           Hexapep 11 gpfaviggnVkI 22
                                      g ++++g+++ I
  gi|336253754|ref|YP_004596861.1| 20 GIYSHLGSDAYI 31
                                      778888888776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.1
                                      TEEE-TTEE CS
                           Hexapep 19 nVkIGdnvk 27
                                      ++++G++++
  gi|336253754|ref|YP_004596861.1| 38 GCEVGEGTR 46
                                      566676654 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0042
                                      TEEE-TTEEE CS
                           Hexapep 19 nVkIGdnvkI 28
                                       + IG+n++I
  gi|336253754|ref|YP_004596861.1| 60 QISIGKNCII 69
                                      6778888888 PP

  == domain 4  score: 37.4 bits;  conditional E-value: 2.2e-13
                                       EETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       IG+nv++g  ++++++V IGdnv+Igag+vi 
  gi|336253754|ref|YP_004596861.1| 103 IGDNVFLGERTIVLPDVSIGDNVIIGAGSVIS 134
                                       9*****************************96 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 ?   -1.3   0.0      0.32   1.9e+03      10      20 ..      25      41 ..      24      45 .. 0.55
   2 !    8.0   0.5    0.0004       2.4       2      10 ..      61      69 ..      60      69 .. 0.86
   3 !   35.5   3.3     1e-12     6e-09       3      33 ..     102     134 ..     100     135 .. 0.94
   4 ?   -1.8   0.1      0.45   2.7e+03      12      24 ..     139     152 ..     139     155 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.32
                                      E-TT-EE......SEEE CS
                         Hexapep_2 10 iGanagi......Gvsl 20
                                      +G++a+i      G ++
  gi|336253754|ref|YP_004596861.1| 25 LGSDAYIselesrGCEV 41
                                      57777764444444444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0004
                                      EEE-TT-EE CS
                         Hexapep_2  2 viIGdnCli 10
                                      ++IG+nC+i
  gi|336253754|ref|YP_004596861.1| 61 ISIGKNCII 69
                                      899999998 PP

  == domain 3  score: 35.5 bits;  conditional E-value: 1e-12
                                       EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
                         Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvvit 33 
                                        IGdn+++G + ++   vs+Gdn+++gaG+vi 
  gi|336253754|ref|YP_004596861.1| 102 DIGDNVFLGERTIVlpDVSIGDNVIIGAGSVIS 134
                                       5************9999**************96 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.45
                                       TT-E.ESEEE-TT- CS
                         Hexapep_2  12 anag.iGvslGdnc 24 
                                       +n++ +Gv+ + +c
  gi|336253754|ref|YP_004596861.1| 139 SNSVaVGVPCEVKC 152
                                       58887799765555 PP

>> Mso1_Sec1_bdg  Sec1-binding region of Mso1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.1e-05      0.18      29      40 .]     176     187 ..     174     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                     Mso1_Sec1_bdg  29 YdekgqpfPdWL 40 
                                       Y ++++pfPdWL
  gi|336253754|ref|YP_004596861.1| 176 YRDQNRPFPDWL 187
                                       999********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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 0.20s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1625.00
//
Query:       gi|336253755|ref|YP_004596862.1|  [L=530]
Description: Capsule polysaccharide biosynthesis protein [Halopiger xanaduensis SH-6]
Scores for 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-09   35.3   0.0    1.2e-08   34.8   0.0    1.2  1  Capsule_synth  Capsule polysaccharide biosynthesis protein
    0.00097   18.1   0.0     0.0016   17.3   0.0    1.3  1  Epimerase_2    UDP-N-acetylglucosamine 2-epimerase


Domain annotation for each model (and alignments):
>> Capsule_synth  Capsule polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   1.3e-12   1.2e-08     185     280 ..     343     441 ..     270     469 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.3e-12
                     Capsule_synth 185 padaeliiKtHPldeglikyrrvikgylte.laalkkrvllve...dvnlpsLldqvdgvvvvnStaGleALlhgkp 257
                                        +d +l+iK+HP  +      + i++ l +   +l++   l+e   dv++  L++ +d v v +St+G+eA     p
  gi|336253755|ref|YP_004596862.1| 343 FDDKHLVIKVHPAEKMRGTE-QSITDILDStFDELPDNTTLLEpdtDVDPYELMRSSDIVLVYTSTVGMEATYLDTP 418
                                       36899*******98765555.67777776514678888888865559999*************************** PP

                     Capsule_synth 258 vvtlGravYdiwGltdqrslaef 280
                                       v+t     Y+++G t++ + ++ 
  gi|336253755|ref|YP_004596862.1| 419 VITTADSHYAGKGFTYDPETKDE 441
                                       *****************887764 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.8e-07    0.0016     201     284 ..     334     422 ..     324     428 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-07
                                       HHHHHHHHHHHHHH--EEEEE--..HHHHHHH.......HHHHHH-.TTEEEE----HHHHHHHHHC-SEEEES-HH CS
                       Epimerase_2 201 keilealkalakekdvevvvpvhnnprtrkrl.......leeleel.envtlieplgyldflsllknaklvltdSgG 269
                                       +e +e++++ ++    ++v+ vh ++++r +         ++++el +n tl+ep   +d ++l++++++vl   ++
  gi|336253755|ref|YP_004596862.1| 334 RETVELFETFDD---KHLVIKVHPAEKMRGTEqsitdilDSTFDELpDNTTLLEPDTDVDPYELMRSSDIVLVYTST 407
                                       444555555555...478999997777654434445554555566655***************************** PP

                                       HHHHHHHCT--EEES CS
                       Epimerase_2 270 iqeEapslgvpvvnl 284
                                       +  Ea++l++pv++ 
  gi|336253755|ref|YP_004596862.1| 408 VGMEATYLDTPVITT 422
                                       *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); 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: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 3903.14
//
Query:       gi|336253756|ref|YP_004596863.1|  [L=221]
Description: acylneuraminate cytidylyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-17   63.8   0.0    2.8e-17   63.4   0.0    1.2  1  CTP_transf_3  Cytidylyltransferase
    2.1e-11   44.4   0.0    3.2e-11   43.9   0.0    1.2  1  NTP_transf_3  MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.077   12.8   0.0       0.13   12.1   0.0    1.3  1  DUF2064       Uncharacterized protein conserved in bacteria (


Domain annotation for each model (and alignments):
>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   4.6e-21   2.8e-17       2     127 ..       6     129 ..       5     151 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 4.6e-21
                                       EEEEE-SSSSSSTTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTT..SEEEE--TTCSSHHHH CS
                      CTP_transf_3   2 aIipARsgSkRlpgKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefg..asvlvtrsslesdter 76 
                                       + ++ R+gS+RlpgK+l +l +++ i +v+++   ++++++ +va  +e   +++ e +   +v+   +++ + +er
  gi|336253756|ref|YP_004596863.1|   6 CQVQVRLGSTRLPGKVLYPLESRRVIGWVIDRCTAAETVTDAVVAVGNEPENEAITEWCerNGVRHATGPEGNLLER 82 
                                       5599*******************************************************999*************** PP

                                       HHHHHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTTSSEEEEE CS
                      CTP_transf_3  77 flevvkaflmseneeiivnlqGdnPllqeevikkaietlkenqedylstlv 127
                                        l+v +a++++     +v+++Gd P++++  i++++ +++ n+  y+++  
  gi|336253756|ref|YP_004596863.1|  83 HLAVAEAYSSD----PVVRVTGDCPFVPPAEIDRMVGEHESNDARYTTNVT 129
                                       ***********....***************************987666544 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 !   43.9   0.0   5.3e-15   3.2e-11      13     155 ..      13     163 ..      10     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 5.3e-15
                                       TT....THHHHCCCCCCHHHHHHHHHCTT..-.CEEEEECSH...CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHH CS
                      NTP_transf_3  13 gg....dKallplggkpllervldalraag.v.devvvvggd...eevlaalarlgvrvvededpgkgplaslaaal 80 
                                       g+     K l+pl  ++++ +v+d+ +aa+ v d vv vg++   e++++ ++r gvr ++ +   +g l   + a+
  gi|336253756|ref|YP_004596863.1|  13 GStrlpGKVLYPLESRRVIGWVIDRCTAAEtVtDAVVAVGNEpenEAITEWCERNGVRHATGP---EGNLLERHLAV 86 
                                       54344469*********************547366666666644447888999*9**999998...45555555555 PP

                                       HHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECC..EEEGGGHHHHHHHCTHTTHHHCHH CS
                      NTP_transf_3  81 raaadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpl..lfrarllsalaallgdqgarrllr 155
                                       ++a ++d+v+ +++D+P+++p+ ++r++ ++++++a+ +  ++++ ++  +  ++ +++l++l++l   +  rrl +
  gi|336253756|ref|YP_004596863.1|  87 AEAYSSDPVVRVTGDCPFVPPAEIDRMVGEHESNDARYTTNVTDDMPIGTAvdVIDREVLEELRELGDSHPVRRLRE 163
                                       55559**************************999988888777777755556999**********987777777755 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 ?   12.1   0.0   2.1e-05      0.13       6      90 ..      40     121 ..      34     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                                       HTTSSSEEEEEE----TTHHHHHHHH-TTSEEEE--SSSHHHHHHHHHHHHHHTT-SEEEEE-SS-TT--HHHHHHH CS
                           DUF2064   6 aaadaaevvlaldgaldkalaeqlalakglevlpQqggdlgeRlarafdrafeageepvlliGsDcpqltaalleqA 82 
                                       aa+++++ v+a+ ++ ++++ ++   ++g++  +  +g+l eR  +++++     ++pv+ +  Dcp +++a ++++
  gi|336253756|ref|YP_004596863.1|  40 AAETVTDAVVAVGNEPENEAITEWCERNGVRHATGPEGNLLERHLAVAEAY---SSDPVVRVTGDCPFVPPAEIDRM 113
                                       344556677777777777777766677778888888899988877777777...667****************9998 PP

                                       HHHTTT-S CS
                           DUF2064  83 feaLeead 90 
                                       + + e++d
  gi|336253756|ref|YP_004596863.1| 114 VGEHESND 121
                                       87666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1797.41
//
Query:       gi|336253757|ref|YP_004596864.1|  [L=217]
Description: fumarylacetoacetate (FAA) hydrolase [Halopiger xanaduensis SH-6]
Scores for complete 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-31  109.5   0.1    2.1e-31  109.3   0.1    1.0  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.3   0.1   1.2e-35   2.1e-31      11     217 ..      20     214 ..      10     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 1.2e-35
                                       SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHHHHTTEEE CS
                     FAA_hydrolase  11 ehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsveeAedaiaG 87 
                                       +h+ e +   ++  +   p+   +++ + + +v++g+pi++P ++ +++  +EL +vig +lr++ s +eA d i G
  gi|336253757|ref|YP_004596864.1|  20 SHLDEKE---RTYRW---PD---LWVVPDDGIVPEGEPIEIPPQTDQIKPGCELTAVIGEELRQA-SEAEAWDGIKG 86 
                                       5555533...22333...45...89999999**********************************.9********** PP

                                       EEEEEEEE.-SBGGG---.HH...HHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGGTTTSH CS
                     FAA_hydrolase  88 ytllnDvs.aRdlqaeekapl...gwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkdmifsp 160
                                       +t+ nDv+   d+  +++++      +  k +dtf+pi + +v + + ++ ++le+++rv+ge+  +++t++m f++
  gi|336253757|ref|YP_004596864.1|  87 FTISNDVTaSGDWPGWSDPDHgmvTGVGYKVIDTFSPILTDVVEKRDESHYDNLEVKVRVDGETAVSGSTAQMAFTI 163
                                       ********66788888886662334555566666666666688888888899************************* PP

                                       HHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE CS
                     FAA_hydrolase 161 aeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrV 217
                                       +e+++ +s+++tL+  d+++ G p g     ++++fl d + v++eie++G+l+++V
  gi|336253757|ref|YP_004596864.1| 164 PEMVSFASKVTTLRENDVVALGDP-G-----NPTVFLDDAESVTCEIESIGSLTSPV 214
                                       ************************.4.....799*******************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1849.74
//
Query:       gi|336253758|ref|YP_004596865.1|  [L=337]
Description: pseudaminic acid biosynthesis-associated protein PseG [Halopiger xanaduensis SH-6]
Scores for 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   16.3   0.4       0.02   15.3   0.4    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.031   14.3   0.0    1.2  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
       0.19   11.8   0.0       0.24   11.4   0.0    1.2  1  DUF4778          Domain of unknown function (DUF4778)
        2.1    8.8   4.2       0.79   10.2   0.3    2.4  2  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> 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 !   15.3   0.4   4.4e-06      0.02      36     130 ..     195     296 ..     174     299 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.4e-06
                                       EES---.....HHHHHHHTT-T.TEEEE---THHHHHHHH-SEEEE-----SHHHHHHHHTT-EEEE-TGGG....T CS
                   Glyco_trans_1_4  36 ivGdgp...rpeeleelaagleerveftGfvedlaellaaadvfvaPsegfglkllEamaaglpvVatdvgg....i 105
                                       +vG g    ++++++e aa++++rv+++   edlae +  ad++v +    + +++E +a+g+p+V+ +v      i
  gi|336253758|ref|YP_004596865.1| 195 VVGPGFsaaQERAIREVAADVSARVRVVRDPEDLAERMFCADLAVSTA---STTTYELLALGTPIVSIPVVDnqlpI 268
                                       6776533223356775556888999999999**************998...579**************994323334 PP

                                       TT--.TTSSEE--TT-..HHHHHHHHHH CS
                   Glyco_trans_1_4 106 aevv.gengllvppgd..pealaeailr 130
                                       a+++ ++++ +v ++d  ++a+ +ai r
  gi|336253758|ref|YP_004596865.1| 269 AAALrERDAAIVLERDagESAIRRAIDR 296
                                       4444667776665555355566666655 PP

>> 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 ?   14.3   0.0   6.9e-06     0.031       5     139 ..     169     295 ..     165     313 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.9e-06
                                       EE-SSSHHHHHCCCTSHHHHHHHHHHHHCHHHCCT-E.EC---STT...-TTTTCEEEEEESSSSHHHHHHHH-EEE CS
                   Glyco_tran_28_C   5 tGGSqgaeaLnelvlselkllelksrelqvlhqtGkr.eleevkik...veeltlkvevfefidkmaeaikaadLvI 77 
                                       +GGS  ae L  +vl +     l+     v   +G++ + ++ +      ++++  v+v++  +++ae +  adL +
  gi|336253758|ref|YP_004596865.1| 169 MGGSDTAE-LTPTVLRAFDGVDLT-----VDAVVGPGfSAAQERAIrevAADVSARVRVVRDPEDLAERMFCADLAV 239
                                       56666666.555555555544444.....55555555433333333253334447788888888999********** PP

                                       ECS-CHHHHHHHHTT--EEEE--TT....S-HHHHHHHHHHHHHHSSEEEE-STTCHHHHHH CS
                   Glyco_tran_28_C  78 sRAGagtiaEllalgkplIlvplpeaaenhqdnNakelekagaalvleqkeltpekLeeall 139
                                       s A + t  Ellalg p + +p  +     q   a++l +  aa+vle +   ++ +  a++
  gi|336253758|ref|YP_004596865.1| 240 STAST-TTYELLALGTPIVSIPVVD----NQLPIAAALRERDAAIVLERDAG-ESAIRRAID 295
                                       ***55.668**************99....89999999999999998887665.666666655 PP

>> DUF4778  Domain of unknown function (DUF4778)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.4e-05      0.24     234     276 ..     200     242 ..      84     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.4e-05
                           DUF4778 234 lsserakelreLirklnervglerdlekLleAlkkldLedket 276
                                       +s  +++ +re+ +++++rv++ rd+e+L+e +  +dL  + +
  gi|336253758|ref|YP_004596865.1| 200 FSAAQERAIREVAADVSARVRVVRDPEDLAERMFCADLAVSTA 242
                                       455999*******************************954444 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 ?   -3.0   0.2       2.2   9.8e+03      65      75 ..     144     154 ..     143     160 .. 0.81
   2 ?   10.2   0.3   0.00018      0.79      11      78 ..     242     316 ..     221     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.2
                   Glyco_trans_1_2  65 erraiaeaare 75 
                                       +r++ia++a++
  gi|336253758|ref|YP_004596865.1| 144 LRQEIARRAKR 154
                                       58899999887 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00018
                   Glyco_trans_1_2  11 pnlrlfEaaacGafaltdda....egleelftpgkevilfe...dleelaekiryllanpeerraiaeaarervl 78 
                                        ++ ++E +a G+++++ +       ++  +++ + +i+ e    +  + ++i+++l    +r+++++ +re v 
  gi|336253758|ref|YP_004596865.1| 242 ASTTTYELLALGTPIVSIPVvdnqLPIAAALRERDAAIVLErdaGESAIRRAIDRYLMCASLRAERRRCGRELVD 316
                                       56789*************88987645566777787888888877677899*********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 00:00:00.41
# Mc/sec: 2438.99
//
Query:       gi|336253759|ref|YP_004596866.1|  [L=225]
Description: formyl transferase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-23   80.2   0.4    1.2e-22   79.3   0.4    1.5  1  N_formyltrans_C  N-formyltransferase dimerization C-terminal 
      4e-21   75.6   0.0    5.6e-21   75.1   0.0    1.1  1  Formyl_trans_N   Formyl transferase


Domain annotation for each model (and alignments):
>> N_formyltrans_C  N-formyltransferase dimerization C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   0.4   1.3e-26   1.2e-22       1      52 []     174     224 ..     174     224 .. 0.99

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1.3e-26
                                       HHHHHHB--TT-EEEHHHHHHHHHHT--TT---EEEE-TTS-EEEEEEEEEE CS
                   N_formyltrans_C   1 DykelceidLdkkvtlrElidlLRAltfgpyknAyfiddtGekvFvsleLtk 52 
                                       D+kelc++d+d++v+++E++d+LRAltf+py+nA++++d Ge+++v++++tk
  gi|336253759|ref|YP_004596866.1| 174 DFKELCRLDPDETVRVKEFLDRLRALTFPPYDNAEIEVD-GETYYVDIDITK 224
                                       9**************************************.**********98 PP

>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   6.2e-25   5.6e-21      67     177 ..      36     145 ..      22     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 6.2e-25
                                       CCHHHHHHHHCTT-SEEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSS CS
                    Formyl_trans_N  67 feeelaeelkelkadlivlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeel 143
                                         +e  + ++ +++d+ v  gy +l+p+ +++ +  +++n+Hp+ LP  +Ga++  +++   ++ +Gvt h++d  l
  gi|336253759|ref|YP_004596866.1|  36 TTREQLRTIEDVRPDFLVSCGYRRLVPESILEIPTEGCVNLHPAYLPYNRGANPNVWSIVD-NTPAGVTLHYMDSSL 111
                                       5667788999***********************************************9987.678************ PP

                                       STS-EEEEEEEE--TT--HHHHHHHHHHHHHHHH CS
                    Formyl_trans_N 144 DtGailaqkkveiiaedtkeeleqrvadaehkal 177
                                       DtG+i+a+  v+ + edt ++l++r++da+  ++
  gi|336253759|ref|YP_004596866.1| 112 DTGDIIARRTVPTDFEDTGKDLYRRLEDAQVDLF 145
                                       ***************************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 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:                        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 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1734.89
//
Query:       gi|336253760|ref|YP_004596867.1|  [L=349]
Description: N-acetylneuraminate synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-85  286.4   0.0    1.9e-85  286.2   0.0    1.0  1  NeuB      NeuB family
      1e-10   42.1   0.1    2.3e-10   40.9   0.1    1.7  1  SAF       SAF domain
  ------ inclusion threshold ------
      0.074   13.5   0.4       0.14   12.5   0.1    1.6  2  DUF3486   Protein of unknown function (DUF3486)


Domain annotation for each model (and alignments):
>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.2   0.0   3.2e-89   1.9e-85       1     241 []      37     273 ..      37     273 .. 0.98

  Alignments for each domain:
  == domain 1  score: 286.2 bits;  conditional E-value: 3.2e-89
                                       HHHHHHHHT-SEEEEEE--HHHH--GGGGG--......TT-S-HHHHHHHH---HHHHHHHHHHHHHTT-EEEEEE- CS
                              NeuB   1 lieaAaeagadavKfQtfkaeelvskeakkaeyqkkekekeesqlellkklelseeehkelkeyceekgieflstpf 77 
                                       li++Aa+agadavKfQtf+ae+++ +++ + ey  +    ++s++++++++e+++e+  +l++yc ++g++flstpf
  gi|336253760|ref|YP_004596867.1|  37 LIDVAADAGADAVKFQTFRAEDMYVEDSGEVEYLDD----DRSIYDIIESMEMPYEWIPTLHDYCYDRGVQFLSTPF 109
                                       79************************9999998877....56*********************************** PP

                                       SHHHHHHHHHHT-S-EEE-GGGTT-HHHHHHHHTT-S-EEEE-TT--HHHHHHHHHHH.HHHT--EEEEE----SS- CS
                              NeuB  78 dlesvdlleslgveayKiaSgeltnlpllekiaktgkpvilStGmatleeieeavevlreagaeklvllhCtseYPa 154
                                       d++s+  le++ v+a+K+aS+   ++p+le++a+t+kp+++StG+ +leei+e+v++l+eaga++l+ll+C+++YP+
  gi|336253760|ref|YP_004596867.1| 110 DERSAAELEDY-VPAWKVASYTSSHVPFLEHLAATDKPIVMSTGAHDLEEIAESVTALKEAGADELALLQCVAAYPT 185
                                       ********998.***************************************************************** PP

                                       -GGG--THHHHHHHHH-TSEEEEE--SS.SSHHHHHHHHHT--EEEEEB-S-TT--STTGGG-B-HHHHHHHHHHHH CS
                              NeuB 155 pledvnLkaietlkeafgvpvGySDHtl.giavaiaAvalGAkviEkHftldrnlegpDhkaSlepeelkelveair 230
                                       pl+++n++++etl+e+fgvp+G+SDHtl  ++++ aAvalGA+v+EkHftld+++egpDh+++lep+el+++v++ir
  gi|336253760|ref|YP_004596867.1| 186 PLSEINVRVVETLREKFGVPAGLSDHTLdPVTAPSAAVALGASVVEKHFTLDKSMEGPDHEFALEPDELERMVSSIR 262
                                       ***************************96699********************************************* PP

                                       HHHHHSS--TT CS
                              NeuB 231 nvekalgegek 241
                                       ++e+alg+gek
  gi|336253760|ref|YP_004596867.1| 263 DTESALGTGEK 273
                                       *******9986 PP

>> SAF  SAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.1   3.9e-14   2.3e-10       4      62 ..     290     347 ..     287     348 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3.9e-14
                                       EEESSTB-TT-BEBTTTEEEECECGGCCTSCCCGGHHHHTTEEESS-B-TT-B-BGGGE CS
                               SAF   4 vvAardikaGeviteddltlkrpiashkigllpiaygeviGkratrdikaGepvhahnl 62 
                                       + A+ di aG+ +t d++++ rp+ +  +gl p+ y+ev+G++a+rd+++G  +++ ++
  gi|336253760|ref|YP_004596867.1| 290 IHAVDDIDAGDPLTTDNVKVLRPGER-EPGLEPKFYEEVVGSVAARDLRPGKGITWEDV 347
                                       67999*******************99.*****************************998 PP

>> DUF3486  Protein of unknown function (DUF3486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.2   1.3e+04     117     138 ..      30      51 ..      20      57 .. 0.53
   2 ?   12.5   0.1   2.4e-05      0.14     103     174 ..     237     310 ..     218     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.2
                           DUF3486 117 dpkeakeLakalaklerasvas 138
                                       d + akeL   +a++++ +v+ 
  gi|336253760|ref|YP_004596867.1|  30 DLEIAKELIDVAADAGADAVKF 51 
                                       5555555555555555555554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.4e-05
                           DUF3486 103 ellmaleeeeeeeidpkeakeLakalaklerasvaskkrraeirkeaaeaaaaaaeev.akaaG..lsaetvaki 174
                                       + +m+   + e +++p+e++++ ++++++e+a  + +kr  ++++e  ++a+ a  +v +  aG  l+ + v+ +
  gi|336253760|ref|YP_004596867.1| 237 DKSMEGP-DHEFALEPDELERMVSSIRDTESALGTGEKRVLDAEEELHDKARRAIHAVdDIDAGdpLTTDNVKVL 310
                                       4455544.555669***************************************9999987778877777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2567.93
//
Query:       gi|336253761|ref|YP_004596868.1|  [L=395]
Description: glutamine--scyllo-inositol transaminase [Halopiger xanaduensis SH-6]
Scores for 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-120  401.8   0.0   3.4e-120  401.7   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.2e-08   33.7   0.0      1e-07   31.5   0.0    1.9  2  Aminotran_1_2    Aminotransferase class I and II
    1.4e-07   31.1   0.0    3.4e-07   29.8   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
    8.3e-07   28.3   0.0    1.3e-06   27.6   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
    3.8e-06   25.7   0.0    5.2e-06   25.2   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0097   14.7   0.1      0.018   13.8   0.1    1.4  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain


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 !  401.7   0.0  1.1e-123  3.4e-120       2     360 ..      26     387 ..      25     388 .. 0.96

  Alignments for each domain:
  == domain 1  score: 401.7 bits;  conditional E-value: 1.1e-123
                                       HHHHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHH CS
                   DegT_DnrJ_EryC1   2 ikeeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatan 78 
                                       i+++e++av e+l+++ +t+gp+ve+FE ++a+ +gv+ha+a++sGt+Alhla +a g gpgdeVI+++ltFv+ta+
  gi|336253761|ref|YP_004596868.1|  26 ITDHEKDAVVEALEGDYITRGPTVEAFEDRVADLIGVDHAVATTSGTTALHLAGEAAGFGPGDEVITTPLTFVSTAH 102
                                       678999*********************************************************************** PP

                                       HHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT CS
                   DegT_DnrJ_EryC1  79 avlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg 155
                                       a++++ a+pvf+D+dp+  +idp+a++  ite t++ +p h++G++ad+d+l ++a++h+l vi Da+hA+G t++g
  gi|336253761|ref|YP_004596868.1| 103 AATYTDATPVFADIDPHRRTIDPDAVRDRITEDTAGLVPMHYAGHPADIDELLEVADEHDLTVIWDACHAFGGTWRG 179
                                       ***************************************************************************** PP

                                       EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCEC...CTCSSCECCS..S---B-B-BHHHH CS
                   DegT_DnrJ_EryC1 156 kkvGalgdaavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkr...kaekryvgev..elGynyrlteiqA 227
                                       +++Ga  d+avfSF+p Kn+ttGeGG+vvt+d++lae++r+lr++ ++     +e + + +v   lGyny+ t++qA
  gi|336253761|ref|YP_004596868.1| 180 EPIGAQRDMAVFSFHPVKNVTTGEGGMVVTDDDDLAERLRRLRSFDMNYdvdGHESEPWYQVteGLGYNYNVTDLQA 256
                                       ********************************************999975553333333333668************ PP

                                       HHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE- CS
                   DegT_DnrJ_EryC1 228 AiglaqLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigt 304
                                       A+glaqL+rl+ + +rR+ei+++y+e+++e++   +++ p e++   +hlya+ v+ee+  +r+e+v a+++e++g+
  gi|336253761|ref|YP_004596868.1| 257 ALGLAQLDRLEAFKDRRDEIIARYDEAFNEIDDLRTPPDPLESD-PMYHLYAIEVDEEFGCDRAEFVDAMHAENVGV 332
                                       ********************************987777777777.8******************************* PP

                                       B-SGSCHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 305 rvhypnplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                                       +vhy +plh +p+++ ++++++gd+p +er+++r +sLpl p+++++dv +V++++
  gi|336253761|ref|YP_004596868.1| 333 QVHY-VPLHYHPFFQAEFGYERGDFPRTERVYDRLVSLPLFPAMSDDDVADVIDSI 387
                                       ****.8***********************************************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 !   31.5   0.0   3.4e-11     1e-07      47     192 ..      50     173 ..      24     202 .. 0.86
   2 ?   -0.8   0.0      0.22   6.6e+02     267     308 ..     262     304 ..     246     338 .. 0.66

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3.4e-11
                                       HHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBE CS
                     Aminotran_1_2  47 peleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryply 123
                                        ++e ++a+++g         + av ++sG++al  a +++  + pgde++   +t+ s  +++ + +++ v   ++
  gi|336253761|ref|YP_004596868.1|  50 EAFEDRVADLIG--------VDHAVATTSGTTALHLAGEAAG-FGPGDEVITTPLTFVSTAHAATYTDATPVFADID 117
                                       69**********........9999******************.********************************76 PP

                                       ETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTT CS
                     Aminotran_1_2 124 seedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYag 192
                                        +  +++d +a+ + ++e+++      +++   p +  G  a+ +el ++   a+++ l ++ D  +a 
  gi|336253761|ref|YP_004596868.1| 118 -PHRRTIDPDAVRDRITEDTA------GLV---PMHYAGHPADIDELLEV---ADEHDLTVIWDACHAF 173
                                       .8899*************554......444...88888888888888888...*********9988764 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSSEE CS
                     Aminotran_1_2 267 allkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgmfl 308
                                       +l++ + ++++r+++++r +e ++e+++l  +  + +   m++
  gi|336253761|ref|YP_004596868.1| 262 QLDRLEAFKDRRDEIIARYDEAFNEIDDLRTPPDPLEsDPMYH 304
                                       2333349999999999999999999988865554444345555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   1.1e-10   3.4e-07      16     217 ..      32     216 ..      24     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.1e-10
                                       HHHHCS----CCCT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHH CS
                   Beta_elim_lyase  16 daqaaamlGdesYgedktvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaia 91 
                                       da  +a  Gd    + +tv+++ed+va+l+g ++a+ +++Gt A +++ ++    +g+evi t      f  t  +a
  gi|336253761|ref|YP_004596868.1|  32 DAVVEALEGDY-ITRGPTVEAFEDRVADLIGVDHAVATTSGTTALHLAGEAAGfGPGDEVITTPL---TFVSTAHAA 104
                                       55566666664.45779********************************888779*****87765...455555555 PP

                                       HCC--EEEEE-EBTT.TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                   Beta_elim_lyase  92 elagvklrdlknkea.GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                       ++ +++++ ++++    ++d++++++ i+e     +  +l+ +  + +        ++ ++e+ ++a++++++++ D
  gi|336253761|ref|YP_004596868.1| 105 TYTDATPVFADIDPHrRTIDPDAVRDRITE-----DTAGLVPMHYAGH--------PADIDELLEVADEHDLTVIWD 168
                                       66666666555544439*************.....4679999988766........5788889999*********** PP

                                       ETTHHHHHHHHTS-CHHHHTTSSEEEEESS..STT--SS-EEEEE-HH.... CS
                   Beta_elim_lyase 168 gARfanaakslgeivkemfsyvDsvtmslk..KdllanvGgvlafrddeled 217
                                       ++  +   +  +     + +  D+ ++s+   K++++  Gg+++++dd+l +
  gi|336253761|ref|YP_004596868.1| 169 ACHAFGGTWRGEP----IGAQRDMAVFSFHpvKNVTTGEGGMVVTDDDDLAE 216
                                       **99988855443....33445555555533399999999999999884433 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   4.5e-10   1.3e-06      45     183 ..      49     176 ..      45     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.5e-10
                                       HHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEB CS
                       Aminotran_5  45 veearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipl 121
                                       ve+ +++va+li+++  + +  tsGtt a+ l+  ++   + pgde+++t +   ++     ++a  t a+ +++ +
  gi|336253761|ref|YP_004596868.1|  49 VEAFEDRVADLIGVD--HAVATTSGTT-ALHLAGEAA--GFGPGDEVITTPLTFVSTA----HAATYTDATPVFADI 116
                                       788999********9..5999999999.999988888..49***********888777....888899999999999 PP

                                       ETT.SCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS CS
                       Aminotran_5 122 dee.geldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghi 183
                                       d++  ++d+d++++ ++e+t+ +  +h     G   +++e+ ++a +++  v+ Da+ a+g  
  gi|336253761|ref|YP_004596868.1| 117 DPHrRTIDPDAVRDRITEDTAGLVPMHY---AGHPADIDELLEVADEHDLTVIWDACHAFGGT 176
                                       98625799****************9996...7*************************999854 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 !   25.2   0.0   1.7e-09   5.2e-06      50     179 ..      45     174 ..      27     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.7e-09
                                       --HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHH.TTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEE.EES CS
                   Cys_Met_Meta_PP  50 gnptrsvleeriaaLeggeaalavssGmaAiaaail.allkaGdeivvsddlYggtqrllkkvlkk.lgievk.fvd 123
                                         pt++++e+r+a+L g+++a+a++sG++A+++a   a +  Gde++++   + +t +  +++    +  +++ +  
  gi|336253761|ref|YP_004596868.1|  45 RGPTVEAFEDRVADLIGVDHAVATTSGTTALHLAGEaAGFGPGDEVITTPLTFVSTAHAATYTDATpVFADIDpHRR 121
                                       46*****************************87764145788*************9998877654434445541445 PP

                                       TTSHHHHHHHCCTTEE.EEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT CS
                   Cys_Met_Meta_PP 124 tsdleelekaikentk.lvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp 179
                                       t d+++++  i+e t  lv +   + p    +Di +++++a +++++v+ D++ a +
  gi|336253761|ref|YP_004596868.1| 122 TIDPDAVRDRITEDTAgLVPMHYAGHP----ADIDELLEVADEHDLTVIWDACHAFG 174
                                       678999999999988625545555555....79999999999999999999986655 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   6.1e-06     0.018      55     136 ..      35     117 ..       7     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.1e-06
                                       TGGGBBTTTTBTHHHHH.HHHHHHHCT-SEEEEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEE CS
                          OKR_DC_1  55 vveLgdLldheGaikea.qkyaarvfgadksyfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatP 130
                                       v++L+  ++ +G++ ea ++ +a + g d++   + GT++   +   a   pgd v+    +  S +ha   ++atP
  gi|336253761|ref|YP_004596868.1|  35 VEALEGDYITRGPTVEAfEDRVADLIGVDHAVATTSGTTALHLAGEAAGFGPGDEVITTPLTFVSTAHAATYTDATP 111
                                       556666677889998886889***********************9******************************** PP

                                       EEE--E CS
                          OKR_DC_1 131 vylepe 136
                                       v+   +
  gi|336253761|ref|YP_004596868.1| 112 VFADID 117
                                       **6544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2782.05
//
Query:       gi|336253762|ref|YP_004596869.1|  [L=315]
Description: dTDP-glucose 4,6-dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-59  199.7   0.0    1.3e-58  199.0   0.0    1.3  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.8e-54  184.8   0.0    2.1e-54  184.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.5e-19   68.5   0.0    6.6e-19   68.0   0.0    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.1e-16   60.8   0.0    1.4e-16   60.4   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    2.7e-13   49.7   0.0    4.9e-09   35.7   0.0    2.2  2  NAD_binding_4    Male sterility protein
    1.7e-10   41.1   0.0    3.9e-10   39.9   0.0    1.6  2  NAD_binding_10   NAD(P)H-binding
    5.3e-10   38.9   0.0    5.5e-09   35.6   0.0    2.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    4.9e-06   26.1   0.0    8.5e-05   22.1   0.0    2.3  2  adh_short        short chain dehydrogenase
     0.0004   20.0   0.0    0.00071   19.2   0.0    1.4  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
       0.02   14.8   0.2      0.076   12.9   0.0    2.0  2  KR               KR domain
        0.1   12.1   0.0       0.23   11.0   0.0    1.5  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase


Domain annotation for each model (and alignments):
>> 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 !  199.0   0.0   7.7e-62   1.3e-58       1     331 [.       6     304 ..       6     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 199.0 bits;  conditional E-value: 7.7e-62
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       ++TG aGfiG ++++ Lle+gy v g+++ s + + ++i++  +      +++++l++gD++D + + +l++ v+p 
  gi|336253762|ref|YP_004596869.1|   6 IVTGAAGFIGRWVVRELLERGYSVRGLDDFS-NGSRRNIQAFGD------RDDFELIEGDVCDDATVSELFD-VNPA 74 
                                       59************************98765.567799999875......4579****************96.67** PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S.SSSB-TTS-----SHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq.evpqtEttpfyPrsPY 153
                                       + ++LAA+  V++s+e+P+  +e nv+Gt+++Lea+r++    ++r+  ++t  vY  ++ e  ++E++p++P sPY
  gi|336253762|ref|YP_004596869.1|  75 ACIHLAAEIDVQESLEDPQSHFESNVVGTQTVLEACRRT----ETRLGLVGTCMVYDMADsEEGIDEEHPVKPASPY 147
                                       *************************************96....58************9975788************* PP

                                       HHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                       a +Kl+a+ ++++y++ y+l++v+ + fn+++p+++  +    ++ +  r ++g+ +  ++G++ + Rd +++ D +
  gi|336253762|ref|YP_004596869.1| 148 AGSKLAAENLAESYYHGYDLPVVVLRPFNTYGPYQKTGMAGGVVSIFTDRDLQGE-PLKIFGDGTQSRDLLYATDCA 223
                                       **********************************988777777777777777776.66678**************** PP

                                       HHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       + ++     d       a ge  + ++  ++++ +l + i  e              +++++  +++  ++ev++l 
  gi|336253762|ref|YP_004596869.1| 224 RFIVEGTFCDD------AIGEILNAGTGSDISVNDLAELIASE--------------ETEITHVEHHHPQSEVQTLR 280
                                       ****9888877......78999999999999999999877553..............22334344455679****** PP

                                       B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeelvre 331
                                        d+ska+  L+W+p+vs+ee+v++
  gi|336253762|ref|YP_004596869.1| 281 CDPSKAQAMLDWEPEVSLEEGVDR 304
                                       *********************976 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.5   0.0   1.3e-57   2.1e-54       1     223 [.       5     227 ..       5     243 .. 0.94

  Alignments for each domain:
  == domain 1  score: 184.5 bits;  conditional E-value: 1.3e-57
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE-- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlA 72 
                                       ++VtGa+GfiG+ +v++lle+gy v gld  s++s+++ ++       el+e+d++d++ + +lf+ ++p a ihlA
  gi|336253762|ref|YP_004596869.1|   5 VIVTGAAGFIGRWVVRELLERGYSVRGLDDFSNGSRRNIQAFGdrddfELIEGDVCDDATVSELFD-VNPAACIHLA 80 
                                       68*****************************88888766554488999******************.79******** PP

                                       S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHH CS
                         Epimerase  73 avggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlag 149
                                       a+ +v++s edp+  +e+n++gt+++lea+r+++  rl  ++++ vY   ++  +e   ++ p+kp spYa +Kla+
  gi|336253762|ref|YP_004596869.1|  81 AEIDVQESLEDPQSHFESNVVGTQTVLEACRRTET-RLGLVGTCMVYDMADS--EEGIDEEHPVKPASPYAGSKLAA 154
                                       ***********************************.************8888..5555555699************* PP

                                       HHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHH CS
                         Epimerase 150 eklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeail 223
                                       e+l+e+y + y+l++++lr+fn yGp++ +g   +v++ +  + l+g+ +++++gdgt+ Rd+ly+ D+a+ i+
  gi|336253762|ref|YP_004596869.1| 155 ENLAESYYHGYDLPVVVLRPFNTYGPYQKTGMAGGVVSIFTDRDLQGE-PLKIFGDGTQSRDLLYATDCARFIV 227
                                       ***************************99999****************.**********************987 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 !   68.0   0.0   4.1e-22   6.6e-19       1     189 [.       6     185 ..       6     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 4.1e-22
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk...viegDvtdkdkleeale.gvdvvihl 73 
                                       +vtG+aGF+Gr +v+eL++++    vr lD   + +   +++ ++ ++   +iegDv+d ++++e  + +  + ihl
  gi|336253762|ref|YP_004596869.1|   6 IVTGAAGFIGRWVVRELLERG--YSVRGLDDFSNGSR-RNIQAFGDRDdfeLIEGDVCDDATVSELFDvNPAACIHL 79 
                                       69*******************..5******6555555.4555555555588**************998345789*** PP

                         3Beta_HSD  74 aslvdvag.kltedeimkvnvkGTrnvleacvkagvrv.lvYtSsaevvgpnslgeeilngdEeleyeslhqdaype 148
                                       a+ +dv+      ++  + nv GT++vleac++++ r  lv t     v++   +ee +  dE  e++ ++ ++y+ 
  gi|336253762|ref|YP_004596869.1|  80 AAEIDVQEsLEDPQSHFESNVVGTQTVLEACRRTETRLgLVGTC---MVYDMADSEEGI--DE--EHPVKPASPYAG 149
                                       ******9945567899*******************986233333...344423344444..44..4667899***** PP

                         3Beta_HSD 149 sKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkll 189
                                       sK  aE+l  +        g +l  + LRp   yG+++k+ 
  gi|336253762|ref|YP_004596869.1| 150 SKLAAENLAESYYH-----GYDLPVVVLRPFNTYGPYQKTG 185
                                       *******9765555.....88****************9864 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 !   60.4   0.0   8.7e-20   1.4e-16       2     235 ..       4     265 ..       3     300 .. 0.84

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 8.7e-20
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE- CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvna 58 
                                       +++vtGa G +G+ ++++l e+g++v +l+                      e d+ d ++v el++  +p++ +++
  gi|336253762|ref|YP_004596869.1|   4 TVIVTGAAGFIGRWVVRELLERGYSVRGLDDFsngsrrniqafgdrddfeliEGDVCDDATVSELFDV-NPAACIHL 79 
                                       589**************************6656899*****************************976.9******* PP

                                       -----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-.B-TTS----SSHHHHHHHHHHH CS
                     RmlD_sub_bind  59 AAytavDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrp.YeeddetsPlnvYGrtKlaGEq 134
                                       AA  +v +  +++++ ++ n+ +++++ ea+++++  L  v t  V+d + +++   e+++++P + Y+ +Kla E+
  gi|336253762|ref|YP_004596869.1|  80 AAEIDVQESLEDPQSHFESNVVGTQTVLEACRRTETRLGLVGTCMVYDMADSEEgIDEEHPVKPASPYAGSKLAAEN 156
                                       ************************************************8866555********************** PP

                                       HHHH....H-SSEEEEEE-SEESS.....SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHC CS
                     RmlD_sub_bind 135 avla....agkkalivRtswvyge.....kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqlleka 200
                                         ++    +   ++++R    yg           v+ + ++  + e+lk++ D  q +   +a d A++   ++e  
  gi|336253762|ref|YP_004596869.1| 157 LAESyyhgYDLPVVVLRPFNTYGPyqktgMAGGVVSIFTDRDLQGEPLKIFGDgtQSRDLLYATDCARF---IVEGT 230
                                       *9995544445689***999999833333334688889999999999*999884444445555555555...56788 PP

                                       HH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTT CS
                     RmlD_sub_bind 201 aeekelagvyHlanegetswlefArailkeagads 235
                                        ++ ++ +++ ++    +s  ++A+ i++e  + +
  gi|336253762|ref|YP_004596869.1| 231 FCDDAIGEILNAGTGSDISVNDLAELIASEETEIT 265
                                       88888999999999999999999999998766654 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1     6e-05     0.097       1      20 [.       7      26 ..       7      32 .. 0.90
   2 !   35.7   0.0     3e-12   4.9e-09      90     208 ..      75     179 ..      55     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6e-05
                                      EE-TTSHHHHHHHHHHHHHS CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrtt 20
                                      +TGa GF+G+ ++++LL++ 
  gi|336253762|ref|YP_004596869.1|  7 VTGAAGFIGRWVVRELLERG 26
                                      7****************975 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 3e-12
                                       EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH- CS
                     NAD_binding_4  90 viihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeeklde 163
                                       + ih aA ++++e++++    ++ Nv Gt+ vle +++++    l  v T +v++   +               +++
  gi|336253762|ref|YP_004596869.1|  75 ACIHLAAEIDVQESLEDpqsHFESNVVGTQTVLEACRRTETR--LGLVGTCMVYDMADS---------------EEG 134
                                       679**********99986657899*************77555..******888887774...............689 PP

                                       -EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 164 deraklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                        ++++  + +  Y  sK +aE+l +++ +  +lpvv++Rp + +g
  gi|336253762|ref|YP_004596869.1| 135 IDEEHPVKPASPYAGSKLAAENLAESYYHGYDLPVVVLRPFNTYG 179
                                       999*************************************77766 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 !   39.9   0.0   2.4e-13   3.9e-10       1     144 [.       9     175 ..       9     201 .. 0.78
   2 ?   -2.6   0.0       2.7   4.5e+03     163     178 ..     243     258 ..     236     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.4e-13
                                       TTTSHHHHHHHHHHHHC-T-EEEEE..ETT..HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtal..vRn..peklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk 73 
                                       GA G +Gr +v+ell+r g++v+ l    n     ++++ +++  e++egdv d +++ e ++   a ++ l+++ +
  gi|336253762|ref|YP_004596869.1|   9 GAAGFIGRWVVRELLER-GYSVRGLddFSNgsRRNIQAFGDRDDFELIEGDVCDDATVSELFDVNPAACIHLAAEID 84 
                                       9****************.5****995544433567789999**********************99999999988777 PP

                                       HHHH..............HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHH...CCHHHHHHHHHHHHHHHH CS
                    NAD_binding_10  74 deeg..............aknivdaakeagvkRfvlvsaigvgdevpgefgewnke...llkaylaakraaeellra 133
                                        +e+              ++++++a++++++ R+ lv++  v+d +++e g   ++     ++y+  k aae+l ++
  gi|336253762|ref|YP_004596869.1|  85 VQESledpqshfesnvvgTQTVLEACRRTET-RLGLVGTCMVYDMADSEEGIDEEHpvkPASPYAGSKLAAENLAES 160
                                       333345555678888899**********998.***********9888877665554221334555455555544444 PP

                                       ....SSSEEEEEEE- CS
                    NAD_binding_10 134 ....sgldwTivrpg 144
                                            +l  +++rp 
  gi|336253762|ref|YP_004596869.1| 161 yyhgYDLPVVVLRPF 175
                                       443389999999995 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.7
                                       ----EEEHHHHHHHHH CS
                    NAD_binding_10 163 fkggsisradVAdvlv 178
                                        +g+ is  d+A++++
  gi|336253762|ref|YP_004596869.1| 243 GTGSDISVNDLAELIA 258
                                       468899999**99997 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   3.4e-12   5.5e-09       1     244 [.       5     258 ..       5     281 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 3.4e-12
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       v+vtGa+G iG+ +vr++l++  +   l + +  +  +i+   +   ++    +e   + gdv d ++++++++ ++
  gi|336253762|ref|YP_004596869.1|   5 VIVTGAAGFIGRWVVRELLERGYSVRGLDDFSNGSRRNIQAFGD--RDD----FE--LIEGDVCDDATVSELFD-VN 72 
                                       79*******************98887788888888888887642..222....23..456**************.** PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-S......EEEE........EEEGGGSS--SHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvk......kvvl........iStDKAvnPtnvmGa 140
                                       + +++h AA   V    e p + ++ Nv+gt++v+ea+ +++ +       +v+        i     v+P + +  
  gi|336253762|ref|YP_004596869.1|  73 PAACIHLAAEIDVQESLEDPQSHFESNVVGTQTVLEACRRTETRlglvgtCMVYdmadseegIDEEHPVKPASPYAG 149
                                       **************************************998864222211344322222222333456888888888 PP

                                       HHHHHHHHHHHGGG--SSS--EEEEEE....E-EE..TTGTTSSHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHHHH CS
                   Polysacc_synt_2 141 tKrlaekllqalakeseekktkfvvvR....fGNV..lgSrGSviplFkkqikeggpvtv.TdpemtRyfmtieeav 210
                                       +K++ae l+ ++ +     +  +vv R    +G     g  G v+ +F+++  +g+p+ +  d +  R ++  ++ +
  gi|336253762|ref|YP_004596869.1| 150 SKLAAENLAESYYHGY---DLPVVVLRpfntYGPYqkTGMAGGVVSIFTDRDLQGEPLKIfGDGTQSRDLLYATDCA 223
                                       8888888887776666...5566666622224432224668888888888888888888744677788888888888 PP

                                       HHHHHHH.HH--SS-EEEE--.-EEEHHHHHHHH. CS
                   Polysacc_synt_2 211 qLvlqal.alakggeifvldmGepvkivdlakali 244
                                       +++++ +      gei+    G  +++ dla+ + 
  gi|336253762|ref|YP_004596869.1| 224 RFIVEGTfCDDAIGEILNAGTGSDISVNDLAELIA 258
                                       88877541566678888888888888888887663 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.2e-08   8.5e-05       2      69 ..       4      70 ..       3      84 .. 0.94
   2 ?    1.4   0.0      0.11   1.8e+02     142     164 ..     140     162 ..     135     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.2e-08
                                      EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHH CS
                         adh_short  2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealve 69
                                      +v+vtGa++ IGr +++el+++G++v  +d  ++  ++ ++ +++ ++++  i++Dv d + v++l++
  gi|336253762|ref|YP_004596869.1|  4 TVIVTGAAGFIGRWVVRELLERGYSVRGLDDFSNGSRRNIQAFGD-RDDFELIEGDVCDDATVSELFD 70
                                      89*****************************************98.699***********99998875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.11
                                       B-TTBHHHHHHHHHHHHHHHHHH CS
                         adh_short 142 pvagvaaYsAsKaavagltrsla 164
                                       pv+  ++Y+ sK a + l++s  
  gi|336253762|ref|YP_004596869.1| 140 PVKPASPYAGSKLAAENLAESYY 162
                                       6677899**********999865 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.3e-07   0.00071       1      73 [.       5      80 ..       5      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.3e-07
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEE..ES-S-SHHHHHHHHS.TTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvral..vRdtkselakslkea.Gvelvkgdlddkeslvealkgvdvvfsvtg 73
                                      ++v+Ga+G +G+ vvr ll++g++vr l    + ++ +++++ ++   el++gd+ d++ ++e+++   ++ + ++
  gi|336253762|ref|YP_004596869.1|  5 VIVTGAAGFIGRWVVRELLERGYSVRGLddFSNGSRRNIQAFGDRdDFELIEGDVCDDATVSELFDVNPAACIHLA 80
                                      68*************************944455589999999876257999**********999986555555554 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.7e-05     0.076       2      92 ..       4      83 ..       3     120 .. 0.64
   2 ?   -1.8   0.0       1.5   2.5e+03      45      68 ..     264     289 ..     254     299 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-05
                                      EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR  2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80
                                      t+++tG++G +G+ ++r l+e+g +     + +   ++ s+++i+++ +++ + e+++ Dv d + v++l++       
  gi|336253762|ref|YP_004596869.1|  4 TVIVTGAAGFIGRWVVRELLERGYSV---RGLD-DFSNGSRRNIQAFGDRD-DFELIEGDVCDDATVSELFDVNP---- 73
                                      689*******************9543...2222.23334455555555543.67777777777777777776554.... PP

                                      ---EEEE----- CS
                                KR 81 pikGvihaAgvl 92
                                        + +ih A  +
  gi|336253762|ref|YP_004596869.1| 74 --AACIHLAAEI 83
                                      ..4455555555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                                       HHHHHHT..T-EEEE----TT-HHHH CS
                                KR  45 iaeleal..gaevevvaaDvsdkdav 68 
                                       i+++e++  + ev+++++D s+++a+
  gi|336253762|ref|YP_004596869.1| 264 ITHVEHHhpQSEVQTLRCDPSKAQAM 289
                                       55555543478999999999999987 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 ?   11.0   0.0   0.00014      0.23       1      61 [.       9      70 ..       9      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                      TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHH CS
                      adh_short_C2  1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaevlecDVtdeeqvealve 61
                                      Gaa  IGr ++++l e+G++v   d   ++ +++++++ ++ + e++e DV d+++v +l++
  gi|336253762|ref|YP_004596869.1|  9 GAAGFIGRWVVRELLERGYSVRGLDDFSNGsRRNIQAFGDRDDFELIEGDVCDDATVSELFD 70
                                      88889****************876655555499*******999999*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2254.63
//
Query:       gi|336253763|ref|YP_004596870.1|  [L=375]
Description: polysaccharide biosynthesis protein CapD [Halopiger xanaduensis SH-6]
Scores for 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-90  302.4   0.0    3.4e-90  302.2   0.0    1.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.5e-22   79.5   0.0    2.6e-21   76.2   0.0    2.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    7.5e-22   77.6   0.0    1.2e-21   76.9   0.0    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.5e-16   60.7   0.0    3.3e-16   59.6   0.0    1.7  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      1e-14   54.3   0.0    1.9e-13   50.2   0.0    2.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.1e-12   48.3   0.3    2.3e-12   47.2   0.1    1.7  2  NAD_binding_10   NAD(P)H-binding
    7.4e-09   35.2   0.1    2.6e-05   23.5   0.1    3.2  2  NAD_binding_4    Male sterility protein
    1.2e-08   34.7   0.0    1.8e-08   34.1   0.0    1.3  1  adh_short        short chain dehydrogenase
    3.8e-05   23.4   0.0    6.3e-05   22.6   0.0    1.4  1  NmrA             NmrA-like family
    7.1e-05   23.1   0.0    0.00014   22.1   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0019   17.8   0.0     0.0036   16.9   0.0    1.4  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
     0.0033   17.7   0.1      0.011   16.0   0.0    1.9  2  TrkA_N           TrkA-N domain
     0.0039   17.9   0.0      0.043   14.5   0.0    2.3  2  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.015   15.4   0.1      0.027   14.6   0.1    1.5  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
       0.14   12.7   0.0       0.46   11.1   0.0    1.9  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.2   0.0   2.8e-93   3.4e-90       1     292 [.       7     288 ..       7     290 .. 0.96

  Alignments for each domain:
  == domain 1  score: 302.2 bits;  conditional E-value: 2.8e-93
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vl+tG++Gs+G++l+ ++l+++p+ +++++++E +l e+++++    ++++ ++      gdvrd +rle+a+e  +
  gi|336253763|ref|YP_004596870.1|   7 VLLTGGAGSVGRSLIPRFLEQDPNVVRIFDNNEPALAEVKSQF----DDDRCRFL----AGDVRDGDRLERAME--D 73 
                                       89**************************************998....56677666....9**************..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS--SHHHHHHHHHHHHHHHGGG CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAvnPtnvmGatKrlaekllqalak 154
                                       +dvv+h+AA+KhV ++e+np+ea+ktN lg +n+++aai++ v++vv+ S+DKAvnP n+mG+tK+l ekl++a +k
  gi|336253763|ref|YP_004596870.1|  74 IDVVVHTAAMKHVDVCEYNPFEAVKTNALGLQNIVDAAIDSSVQRVVFTSSDKAVNPANTMGTTKLLGEKLVTAGNK 150
                                       ***************************************************************************** PP

                                       --SSS--EEEEEEE-EETTGTTSSHHHHHHHHHTTSSEEES-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--. CS
                   Polysacc_synt_2 155 eseekktkfvvvRfGNVlgSrGSviplFkkqikeggpvtvTdpemtRyfmtieeavqLvlqalalakggeifvldmG 231
                                       +s++++ +++ vRfGNV++S+ Svip+F +qi++ggpvt+Td+ mtR+f+t ++  +L+ q++  ++gge+fv +m 
  gi|336253763|ref|YP_004596870.1| 151 HSGRQDLRLSSVRFGNVVNSSQSVIPIFADQIRTGGPVTLTDEAMTRFFLTYDDVFDLIAQTIDCMQGGEVFVYKM- 226
                                       ****************************************************************************. PP

                                       -EEEHHHHHHHH...........SSSS-EEE----TT--SS-EEE-GGGGGGEEE-SSEEEE CS
                   Polysacc_synt_2 232 epvkivdlakalielsgleekk.eedieikitGlRpGEklyEeLlieeesveetelekilra 292
                                        +++ivdl +a+ie+   +  +  ++i+++++G RpGE ++Ee+++++e ++++e ++++ +
  gi|336253763|ref|YP_004596870.1| 227 SAMRIVDLTEAMIETLAPQFGHdPAEIDVELIGRRPGETFHEEIMTDREVRRAYENDSMYSI 288
                                       *************8776665543789***************************999999876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.0   2.2e-24   2.6e-21       1     227 [.       7     214 ..       7     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.2e-24
                                       EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC.........EEEE--TT-HHHHHHHHHHHT-SE CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledl.........elveldltdrsalerlfkeeqpda 67 
                                       +l+tG++G +G+ l+ ++le++ + v  +d+++ a +  +   +         ++  +d++d+++ler+++  ++d+
  gi|336253763|ref|YP_004596870.1|   7 VLLTGGAGSVGRSLIPRFLEQDPNvVRIFDNNEPALA--E---VksqfdddrcRFLAGDVRDGDRLERAME--DIDV 76 
                                       699*******************995666666632222..2...123468999*******************..8*** PP

                                       EEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHH CS
                         Epimerase  68 vihlAavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaa 144
                                       v+h Aa ++v++   +p + +++n+ g +n+++aa ++ v+r++f sS+                   ++p +  + 
  gi|336253763|ref|YP_004596870.1|  77 VVHTAAMKHVDVCEYNPFEAVKTNALGLQNIVDAAIDSSVQRVVFTSSDKA-----------------VNPANTMGT 136
                                       ************************************************322.................367788899 PP

                                       HHHHHHHHHHHHHHHHT...-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHH CS
                         Epimerase 145 aKlageklveayaaqyg...lnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDv 218
                                       +Kl+geklv+a ++  g   l+  ++r  n++         ++vip ++ +i +g  +vtl  d    R fl  +Dv
  gi|336253763|ref|YP_004596870.1| 137 TKLLGEKLVTAGNKHSGrqdLRLSSVRFGNVVNSS------QSVIPIFADQIRTGG-PVTLT-DEAMTRFFLTYDDV 205
                                       ***********9999877789**********9887......9**************.99996.68889********* PP

                                       HHHHHHHHH CS
                         Epimerase 219 aeaillvle 227
                                        ++i   ++
  gi|336253763|ref|YP_004596870.1| 206 FDLIAQTID 214
                                       999877665 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 !   76.9   0.0     1e-24   1.2e-21       2     123 ..       9     131 ..       8     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 1e-24
                         3Beta_HSD   2 vtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihlasl 76 
                                       +tGgaG +Gr+l+ ++++ ++ + vr++D +e p l e  s+++ +   ++ gDv+d d+le+a+e++dvv+h+a++
  gi|336253763|ref|YP_004596870.1|   9 LTGGAGSVGRSLIPRFLEQDP-NVVRIFDNNE-PALAEVKSQFDDDRcrFLAGDVRDGDRLERAMEDIDVVVHTAAM 83 
                                       79******************7.99*****765.5565666666666666**************************** PP

                         3Beta_HSD  77 vdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpn 123
                                         v   +++  e  k n  G +n+++a+++++v+++v+tSs ++v p 
  gi|336253763|ref|YP_004596870.1|  84 KHVDVcEYNPFEAVKTNALGLQNIVDAAIDSSVQRVVFTSSDKAVNPA 131
                                       999876888889********************************9983 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 !   59.6   0.0   2.7e-19   3.3e-16       1     130 [.       8     125 ..       8     298 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 2.7e-19
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L TG+aG +G  l+ ++le++ +v+ i ++++  +++++++  +      +++ ++  gD++D ++ler+++++  d
  gi|336253763|ref|YP_004596870.1|   8 LLTGGAGSVGRSLIPRFLEQDPNVVRIFDNNEP-ALAEVKSQFD------DDRCRFLAGDVRDGDRLERAMEDI--D 75 
                                       78************************9877665.4455555443......46899****************998..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEG CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaSts 130
                                        v++ AA++hVdv   +P + +++n+lG +++++a+ +  ++   r++++S++
  gi|336253763|ref|YP_004596870.1|  76 VVVHTAAMKHVDVCEYNPFEAVKTNALGLQNIVDAAIDSSVQ---RVVFTSSD 125
                                       ************************************998764...89999998 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 !   50.2   0.0   1.6e-16   1.9e-13       2     141 ..       6     150 ..       5     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.6e-16
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE- CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvna 58 
                                       ++l+tG+ G +G+ L+ ++ e++ +v+ +  +                    + d++d +++++++++   dvvv++
  gi|336253763|ref|YP_004596870.1|   6 NVLLTGGAGSVGRSLIPRFLEQDPNVVRIFDNnepalaevksqfdddrcrflAGDVRDGDRLERAMED--IDVVVHT 80 
                                       69**************************966669*********************************9..799**** PP

                                       -----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHH CS
                     RmlD_sub_bind  59 AAytavDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqa 135
                                       AA + vD +E ++ +a + na + +++ +aa    ++ +      VF  +       d +++P n+ G tKl+GE+ 
  gi|336253763|ref|YP_004596870.1|  81 AAMKHVDVCEYNPFEAVKTNALGLQNIVDAAIDSSVQRV------VFTSS-------DKAVNPANTMGTTKLLGEKL 144
                                       ******************************988877633......56554.......5689**************** PP

                                       HHHH-S CS
                     RmlD_sub_bind 136 vlaagk 141
                                       v a +k
  gi|336253763|ref|YP_004596870.1| 145 VTAGNK 150
                                       *98665 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 !   47.2   0.1   1.9e-15   2.3e-12       1     120 [.      11     143 ..      11     212 .. 0.77
   2 ?   -2.3   0.0       2.9   3.5e+03      25      42 ..     310     327 ..     304     335 .. 0.71

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.9e-15
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT.HHHCHHHH...CTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.peklaele...aeeglevvegdvtdvedlaealkgadaVvsalggggk 73 
                                       G+ G+vGr l+ + l+++  +v+ +  n +  lae++   ++++++ + gdv d + l++a++++d+Vv +++ ++ 
  gi|336253763|ref|YP_004596870.1|  11 GGAGSVGRSLIPRFLEQD-PNVVRIFDNnEPALAEVKsqfDDDRCRFLAGDVRDGDRLERAMEDIDVVVHTAAMKHV 86 
                                       99***************6.555555555155667666555779************************9999965555 PP

                                       .........HHHH......HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHH CS
                    NAD_binding_10  74 .........deeg......aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkay 120
                                                   +       +nivdaa  + v+R+v+ s+ ++ + ++ + g  +++ll++ 
  gi|336253763|ref|YP_004596870.1|  87 dvceynpfeA--VktnalgLQNIVDAAIDSSVQRVVFTSSDKAVNPAN-TMG--TTKLLGEK 143
                                       4555554440..1444567*********************98875322.222..23444444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.9
                                       EETTHHHCHHHHCTTTCE CS
                    NAD_binding_10  25 lvRnpeklaeleaeegle 42 
                                       +vR++e++++l ++e ++
  gi|336253763|ref|YP_004596870.1| 310 IVRSSEHAEKLTKAEIVD 327
                                       789999999887655544 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   2.2e-08   2.6e-05       1     142 [.       9     131 ..       9     135 .. 0.81
   2 !    7.5   0.0    0.0017       2.1     169     228 ..     127     189 ..     124     213 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.2e-08
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       lTG+ G +G+ L+ + L+++p+     +vR  ++        +e +  e++s++     +r+++++GD+ + +    
  gi|336253763|ref|YP_004596870.1|   9 LTGGAGSVGRSLIPRFLEQDPN-----VVRIFDN--------NEPALAEVKSQFD---DDRCRFLAGDVRDGD---- 65 
                                       8********************8.....5776555........2222345556665...789********9876.... PP

                                       HHHHHHHHHH--EEEE--SS-S.ST.TSSE..EHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfde.pyke..llrvNveGtrevlelakklkklkvllhvST.ayvnge 142
                                         +l++ +e +dv++h aA  ++d  +y+   ++++N +G +++++ a   + +  +++ S+  +vn++
  gi|336253763|ref|YP_004596870.1|  66 --RLERAMEDIDVVVHTAAMKHVDVcEYNPfeAVKTNALGLQNIVDAAIDSSVQ-RVVFTSSdKAVNPA 131
                                       ..99999*************9998755553449****************88777.99999998777765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0017
                                       TTTCCCHHHHHHHHHHHHHHHHHH...HH---EEEEEE-EEE--SSST---TTSHHHHHHHHH CS
                     NAD_binding_4 169 lkglpntYeqsKalaEklvrearr...rsglpvvivRpsiitgesktGwingsdlgirgllgl 228
                                         + +nt   +K l+Eklv + ++   r++l+++ vR ++++ +s++ ++   d + +g  + 
  gi|336253763|ref|YP_004596870.1| 127 AVNPANTMGTTKLLGEKLVTAGNKhsgRQDLRLSSVRFGNVVNSSQSVIPIFADQIRTGGPVT 189
                                       567789999**********7655411156888**********988876555555444555555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.5e-11   1.8e-08       2     146 ..       6     134 ..       5     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.5e-11
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                        vl tG+++ +Gr +  ++++++ +vv  +d++e +l+ev++++ +  ++  ++++Dv+d +++e+++e++      
  gi|336253763|ref|YP_004596870.1|   6 NVLLTGGAGSVGRSLIPRFLEQDPNVVRiFDNNEPALAEVKSQFDD--DRCRFLAGDVRDGDRLERAMEDI------ 74 
                                       79************************99899**99********998..69****************99987...... PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTB CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagv 146
                                        dv+v+ A++    +  +++e +  + +++N  g+ +++ a+++     s  r+v++sS  + +p + +
  gi|336253763|ref|YP_004596870.1|  75 -DVVVHTAAM----KHVDVCEYNPFEAVKTNALGLQNIVDAAIDS----SVQRVVFTSSDKAVNPANTM 134
                                       .*********....45667777756678*************9998....7789******9999887665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   5.3e-08   6.3e-05       1     106 [.       7     128 ..       7     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.3e-08
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S...-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---G CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdt...kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgf 74 
                                       +l +G++G+ G+s++  +l+++ +v  +  +      e+  ++ +    +++gd+ d + l++a+++ dvv  + ++
  gi|336253763|ref|YP_004596870.1|   7 VLLTGGAGSVGRSLIPRFLEQDPNVVRIFDNNepaLAEVKSQFDDDRCRFLAGDVRDGDRLERAMEDIDVVVHTAAM 83 
                                       6889***********999997666555555543777888899******************************99998 PP

                                       G.............S-HHHHHHHHHHHHHHHS-SEEEEEE---GG CS
                              NmrA  75 y.............skeiedgkklvdAakeaGvkhfiySslgddn 106
                                       +             +++    +++vdAa    v+++++ s  +++
  gi|336253763|ref|YP_004596870.1|  84 KhvdvceynpfeavKTNALGLQNIVDAAIDSSVQRVVFTSSDKAV 128
                                       8999*****99986666666689***************9977666 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 !   22.1   0.0   1.2e-07   0.00014       5      77 ..      12      81 ..       7      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.2e-07
                                      --SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77
                                      GaGsvG+++++  +++++    + + d ++  l++++++    r+ + a d+ + +  L++++++ d+vv+ +
  gi|336253763|ref|YP_004596870.1| 12 GAGSVGRSLIPRFLEQDPN--VVRIFDNNEPALAEVKSQFDDDRCRFLAGDVRDGDR-LERAMEDIDVVVHTA 81
                                      67*********99999888..8***********************************.************976 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 !   16.9   0.0     3e-06    0.0036       3     185 ..      13     178 ..      11     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3e-06
                                       TTSHHHHHHHHHHHTT-EEE.EEESSGGHHHHHHHHHHHTTSE...EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE CS
                      adh_short_C2   3 asgIGraiAkalaeeGaevv.ltdlneeakkrveelaeelgae...vlecDVtdeeqvealveevvekfgklDilvn 75 
                                       a ++Gr +  ++ e+  +vv + d ne a   ++e++++++ +   +l+ DV+d + +e+++e+       +D++v+
  gi|336253763|ref|YP_004596870.1|  13 AGSVGRSLIPRFLEQDPNVVrIFDNNEPA---LAEVKSQFDDDrcrFLAGDVRDGDRLERAMED-------IDVVVH 79 
                                       67889999999999999988466777776...566666665443327**********9999887.......9***** PP

                                       -----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  76 nagiapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealt 152
                                        a++ +       ++ + +  +a+++n+ +l +++ aa+       ++v +ss    ++v+  n +g++K   e+l+
  gi|336253763|ref|YP_004596870.1|  80 TAAMKHV------DVCEYNPFEAVKTNALGLQNIVDAAIDSS--VQRVVFTSSD---KAVNPANTMGTTKLLGEKLV 145
                                       ***9887......55444555789**************8743..3579999988...6688889************* PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTH CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgikgf 185
                                        +  ++ g++  R  +v  g +   ++s i+ f
  gi|336253763|ref|YP_004596870.1| 146 TAGNKHSGRQDLRLSSVRFGNVVNSSQSVIPIF 178
                                       *************99999999887777777654 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.9e-06     0.011       5      69 ..      12      80 ..       9     130 .. 0.85
   2 ?   -2.9   0.0       6.5   7.8e+03      96     110 ..     311     325 ..     310     328 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.9e-06
                                      S-SHHHHHHHHHHHHTT.EEEEEEESSHHHHHHHHHTT....SEEEES-TTSHHHHHHTTGGGESEEEE- CS
                            TrkA_N  5 GlGrvGrslaeeLsegg.kdvvvidkdeerveelreeg....levvvgdatdeevLeeagiekadaviaa 69
                                      G+G vGrsl+ ++ e+  + v + d++e +++e++ ++    ++++ gd+ d + Le+a +e++d+v+ +
  gi|336253763|ref|YP_004596870.1| 12 GAGSVGRSLIPRFLEQDpNVVRIFDNNEPALAEVKSQFdddrCRFLAGDVRDGDRLERA-MEDIDVVVHT 80
                                      99**********999553668899**********9998776677*************99.6888888766 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.5
                                       ESSGGGHHHHHHHTT CS
                            TrkA_N  96 aqdpehaellkklga 110
                                       ++++ehae+l k+ +
  gi|336253763|ref|YP_004596870.1| 311 VRSSEHAEKLTKAEI 325
                                       688999999998765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.6e-05     0.043       7      78 ..      12      87 ..       9      98 .. 0.82
   2 ?    0.2   0.0         1   1.2e+03      26      46 ..     231     251 ..     221     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                                      TTSHHHHHHHCTS..T.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG...BSSSTTTEEEEEEESTGGGSS CS
                   Methyltransf_25  7 GtGrltlalakrl..g.kakvtgvDiseemleaareraeeeglnvefvqgdaed...lpfedgsfDlvvssgalhhls 78
                                      G G + + l  r+  +    v  +D +e +l++++++++++  +++f+ gd++d   l+ + + +D+vv + a+ h++
  gi|336253763|ref|YP_004596870.1| 12 GAGSVGRSLIPRFleQdPNVVRIFDNNEPALAEVKSQFDDD--RCRFLAGDVRDgdrLERAMEDIDVVVHTAAMKHVD 87
                                      777788888888775335778889**************766..8********77556889999*******87799987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1
                                       EEESSHHHHHHHHHHHHHTTT CS
                   Methyltransf_25  26 gvDiseemleaareraeeegl 46 
                                        vD++e+m+e+ + ++ ++ +
  gi|336253763|ref|YP_004596870.1| 231 IVDLTEAMIETLAPQFGHDPA 251
                                       69********99988876544 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 ?   14.6   0.1   2.2e-05     0.027       2      82 ..       6      86 ..       5     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                                      EEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCC.STS-EEEEESSGGGGTTESEEEE--S- CS
                           Ldh_1_N  2 kvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistf.lsvkvkvsekeeealkdadvvvitagv 79
                                      +v ++G aG +G sl    ++++    ++++D ++ +l  v   + +     l  +v+ ++  e a++d+dvvv ta++
  gi|336253763|ref|YP_004596870.1|  6 NVLLTGGAGSVGRSLIPRFLEQDPNV-VRIFDNNEPALAEVKSQFDDDRCRfLAGDVRDGDRLERAMEDIDVVVHTAAM 83
                                      6899*************999997766.89*****999999999998877650456777888*****************9 PP

                                      SS- CS
                           Ldh_1_N 80 prk 82
                                      +  
  gi|336253763|ref|YP_004596870.1| 84 KHV 86
                                      865 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 ?   11.1   0.0   0.00038      0.46       6      73 ..      12      85 ..       7      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                                      TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC........-EEECE.CHHHHHHH-SEEEE-S-HHH CS
                     F420_oxidored  6 GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg........vkvtav.dneeaaeeadvvvlavkped 73
                                      GaG++g++l+ ++l+++  p+ ++ + ++n+  ++e ++++          +v  +   e a+e+ dvvv +  +++
  gi|336253763|ref|YP_004596870.1| 12 GAGSVGRSLIPRFLEQD--PNVVR-IFDNNEPALAEVKSQFDddrcrflaGDVRDGdRLERAMEDIDVVVHTAAMKH 85
                                      9****************..66666.5599999999999999988888888444443045667788888886655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 2753.30
//
Query:       gi|336253764|ref|YP_004596871.1|  [L=599]
Description: xenobiotic-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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  116.2   0.0    2.5e-33  115.5   0.0    1.4  1  ABC_tran      ABC transporter
    9.4e-13   48.4   8.5    1.5e-12   47.7   8.5    1.3  1  ABC_membrane  ABC transporter transmembrane region
    4.1e-08   32.9   0.1    2.7e-06   27.0   0.0    2.4  3  SMC_N         RecF/RecN/SMC N terminal domain
    0.00017   21.5   0.0    0.00035   20.5   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
     0.0012   18.5   0.0     0.0029   17.3   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
     0.0055   17.1   0.1      0.016   15.6   0.1    1.9  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.012   15.9   0.1      0.094   13.0   0.1    2.3  1  AAA_22        AAA domain
      0.054   13.1   1.8       0.27   10.8   0.0    2.9  4  AAA_25        AAA domain
       0.07   13.6   0.0       0.13   12.7   0.0    1.5  1  AAA_23        AAA domain
      0.071   12.3   0.0       0.11   11.6   0.0    1.2  1  G-alpha       G-protein alpha subunit
      0.083   12.6   0.1       0.43   10.3   0.0    2.1  3  AAA_30        AAA domain
       0.11   12.5   2.8       0.36   10.8   2.0    2.0  2  Reticulon     Reticulon
       0.15   12.1   0.0       0.37   10.9   0.0    1.7  1  MMR_HSR1      50S ribosome-binding GTPase


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 !  115.5   0.0   1.8e-36   2.5e-33       1     137 []     376     525 ..     376     525 .. 0.88

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 1.8e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ +s+++ +ge va+vG++GaGKSt+++lla+l++p+ Gei+ dg +++e +le++r++i+v+ q+p++f+++ ++
  gi|336253764|ref|YP_004596871.1| 376 LDSLSFEVDRGEFVAFVGQSGAGKSTIVSLLARLYEPDDGEIRADGIPIEEYDLEEWRERIAVVRQQPFIFDDT-LE 451
                                       6899***************************************************************9999999.77 PP

                                       HH.............HHHTC......HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xx.............xxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdee......iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       +n             e   +      ++++++ l + +  d+ +++++  LSgGq+qrvalarallk++++l+lDE+
  gi|336253764|ref|YP_004596871.1| 452 NNvtignrdatradvE---RvceiakVDEFVDDLPNGY--DSQLGDDGVRLSGGQRQRVALARALLKDADFLVLDEA 523
                                       7799998887754441...1455445777777777666..88888999***************************** PP

                                       TT CS
                                       xx RF
                          ABC_tran 136 ta 137
                                       t+
  gi|336253764|ref|YP_004596871.1| 524 TS 525
                                       96 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   8.5   1.1e-15   1.5e-12      37     264 ..      63     305 ..      29     312 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.1e-15
                                       H...................HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSTHHHHHH CS
                      ABC_membrane  37 t...................ealnvysllllllglaqfilallqsyllnvtgerlskrlrrklfkkilrqpmsffdt 94 
                                       t                   + l ++++ +++++ ++f ++++  +l  v+ +r + ++r+++f++ l +++++fd+
  gi|336253764|ref|YP_004596871.1|  63 TeaggllgtfvdiyqfvgipFSLEFLIIGIAGVMTIRFTASFVVAWLKAVLRQRYEEWIRTQAFNAALDANVQYFDE 139
                                       35555555555566666666678999999999999****************************************** PP

                                       SCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane  95 nsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvsaviakilkklkkk 171
                                         + ++l+ + ++++   d++ + + + +  l+++ + l+vmfy+ + +t++ l +l +i +v   +     ++  +
  gi|336253764|ref|YP_004596871.1| 140 EGSDDILNAIITETRYSGDVIKYCV-QALETLFLVGIYLAVMFYIAPEMTVLALLLLGVITYVLRNVIEPAYTVGTR 215
                                       ***************9999999875.88999999999************9888777777777777777777778888 PP

                                       HHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 172 eqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitqllgllsyalalwfGtt 248
                                         +a++++   ++   +gir Vk+fg  e++ + f ++++++  ++i   + +++++ + +l++ l  ++ +++G+ 
  gi|336253764|ref|YP_004596871.1| 216 VAEANERVQESVQAGTQGIRDVKLFGLSEEMFTAFRDSIRQYTDSSINLKRNEAAIQNFYDLAAALTLFALIYVGFI 292
                                       9999999999999999***************************************************99999***99 PP

                                       HHHTTSSTHHHHHHHH CS
                      ABC_membrane 249 lvisgelsvgdlvvfl 264
                                       ++    ls+g l +fl
  gi|336253764|ref|YP_004596871.1| 293 YS---GLSLGALGIFL 305
                                       98...46666665555 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 ?   -3.4   0.0       3.8   5.2e+03      57      89 ..     113     143 ..     103     164 .. 0.68
   2 ?    3.3   0.0     0.034        46      25      42 ..     387     404 ..     357     422 .. 0.87
   3 !   27.0   0.0   1.9e-09   2.7e-06     109     212 ..     452     568 ..     424     573 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.8
                                       TCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  57 rseklsdlihkskekasvkkaeveitfdnedkk 89 
                                        ++++++ i   ++ +++  a+v+  fd+e+++
  gi|336253764|ref|YP_004596871.1| 113 LRQRYEEWIRT-QAFNAALDANVQY-FDEEGSD 143
                                       45677778886.8888888999988.7888776 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.034
                                       SEEEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlld 42 
                                       +f a vG+ G+GKs ++ 
  gi|336253764|ref|YP_004596871.1| 387 EFVAFVGQSGAGKSTIVS 404
                                       68999*********9985 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 1.9e-09
                                       EEEEETTEEE-HHHHHHHHHCTT-STT.................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 109 seykingkevtkkevsellesagiske.................lLSgGektLvalaLlfAiqkvkpaplyllDeid 168
                                       ++++i ++++t+++v+++ e a++++                   LSgG+++ vala        k a + +lDe  
  gi|336253764|ref|YP_004596871.1| 452 NNVTIGNRDATRADVERVCEIAKVDEFvddlpngydsqlgddgvRLSGGQRQRVALAR----ALLKDADFLVLDEAT 524
                                       667888888888888888888888777888888888999999989*******988764....457999********* PP

                                       TTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 169 aaLDeknvkkvaellkeksknaQfivislreemlekadklvgvt 212
                                       + LD +  ++v   +++ + +  +i i++r  ++++ad+++ v 
  gi|336253764|ref|YP_004596871.1| 525 SDLDSSLEREVQASIESMERDYGIIAIAHRLSTVKNADRIYTVD 568
                                       ****************************************9986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.5e-07   0.00035      80     127 ..     366     414 ..     341     421 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.5e-07
                                       EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                       l+  + ++  l++l+ +++  +++++vGqSG+GKSt++  l+   e   
  gi|336253764|ref|YP_004596871.1| 366 LFSYNGDELVLDSLSFEVDRgEFVAFVGQSGAGKSTIVSLLARLYEPDD 414
                                       344444566788999999887*****************99987555555 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 !   17.3   0.0   2.1e-06    0.0029      15      39 ..     379     403 ..     373     415 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-06
                            AAA_29  15 htieidlkgatlltGpsGsGKSTll 39 
                                        ++e+d+ +++ ++G+sG+GKST++
  gi|336253764|ref|YP_004596871.1| 379 LSFEVDRGEFVAFVGQSGAGKSTIV 403
                                       568889777***************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   0.1   1.2e-05     0.016      23      51 ..     385     413 ..     373     545 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekd 51 
                                       r+e v ++G+sG GKs++v  l+r +e d
  gi|336253764|ref|YP_004596871.1| 385 RGEFVAFVGQSGAGKSTIVSLLARLYEPD 413
                                       4489*******************988887 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   6.8e-05     0.094       5     103 ..     386     527 ..     383     548 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.8e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..........................................er 39 
                                         +++ +G+sG+GK+t +  l++ ++ +    +                                           +
  gi|336253764|ref|YP_004596871.1| 386 GEFVAFVGQSGAGKSTIVSLLARLYEPD----DgeiradgipieeydleewreriavvrqqpfifddtlennvtiGN 458
                                       568899*************999999644....233447778888888888877777776666655555543333322 PP

                            AAA_22  40 pevvfvtlpsst...sskdllrellralglelka...erlsseellealeqalraravielliiDEaqh.l 103
                                       ++  + ++   +   + +++  +l + ++++l +   +    ++ + al++al + a+  +l++DEa   l
  gi|336253764|ref|YP_004596871.1| 459 RDATRADVERVCeiaKVDEFVDDLPNGYDSQLGDdgvRLSGGQRQRVALARALLKDAD--FLVLDEATSdL 527
                                       2222444444444444445555555555544444555455555555555666666555..88888886666 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.3   7.3e+03      85     104 ..     112     131 ..     110     146 .. 0.63
   2 ?   -2.2   0.0       1.9   2.6e+03     126     159 ..     335     373 ..     322     374 .. 0.75
   3 ?   10.8   0.0   0.00019      0.27      31      54 ..     384     407 ..     381     416 .. 0.92
   4 ?   -0.7   0.2      0.66   9.1e+02     100     153 ..     474     525 ..     426     551 .. 0.58

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.3
                            AAA_25  85 elrrRlravgealrddarll 104
                                        lr+R++++ ++++++a l+
  gi|336253764|ref|YP_004596871.1| 112 VLRQRYEEWIRTQAFNAALD 131
                                       67888888887774444433 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                            AAA_25 126 ltadvdaleaaieeveg......vrlvviDplsralggde 159
                                       ++++vd+l+a+ e   g      v ++ +D++ + ++gde
  gi|336253764|ref|YP_004596871.1| 335 TQEFVDDLAARSETD-GsrsvavVNHIAVDNVLFSYNGDE 373
                                       567788888888874.347777788999999999999887 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00019
                            AAA_25  31 pagelallaGapgtGKttlaldla 54 
                                        +ge+++++G++g+GK+t+++ la
  gi|336253764|ref|YP_004596871.1| 384 DRGEFVAFVGQSGAGKSTIVSLLA 407
                                       689****************99887 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.66
                            AAA_25 100 darllvldlagveslpLfakdrggtll...tadvdaleaaieevegvrlvviDplsr 153
                                       + +++v dl++  + +L +   +g +l   +++  al++a+ +  +++++v+D  ++
  gi|336253764|ref|YP_004596871.1| 474 KVDEFVDDLPNGYDSQLGD---DGVRLsggQRQRVALARALLK--DADFLVLDEATS 525
                                       3455555555554444433...333331113333344444444..688888887665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.8e-05      0.13      20     123 ..     387     481 ..     368     549 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.8e-05
                            AAA_23  20 gltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvelt.fenkdgrytrsierere 95 
                                        +++++G+ GaGK+Ti+  +   Ly+  p+ +  +  g+  +++ +e +++  a+v+ + f  +d+     +  e +
  gi|336253764|ref|YP_004596871.1| 387 EFVAFVGQSGAGKSTIVSLLA-RLYE--PDDGEIRADGIPIEEYDLEEWRERIAVVRQQpFIFDDT-----L--ENN 453
                                       4789************97664.4777..44555555567777777777777777777666555555.....4..455 PP

                            AAA_23  96 lskkkgkttkkaklelleideleqfise 123
                                       ++ ++ + t+ + ++ +ei++ ++f+++
  gi|336253764|ref|YP_004596871.1| 454 VTIGNRDATRADVERVCEIAKVDEFVDD 481
                                       5566666666666666666666666666 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.3e-05      0.11      27     146 ..     390     551 ..     381     571 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.3e-05
                                       EEEESTTSSHHHHHHHHHHHCS--..........--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT.......HHHC CS
                           G-alpha  27 lllGqseSGKsTilkqlkllykkg..........fseeelatwraviqlnivrsiktilealesleselsesfelqe 93 
                                        ++Gqs+ GKsTi+  l +ly++           ++e +l++wr+  +  +vr+   i++   + + ++ ++   ++
  gi|336253764|ref|YP_004596871.1| 390 AFVGQSGAGKSTIVSLLARLYEPDdgeiradgipIEEYDLEEWRE--RIAVVRQQPFIFDDTLENNVTIGNRDATRA 464
                                       689******************999999999999988888888988..556777777777766666666666666666 PP

                                       -SS-SCCCS-HCHHHH...............................................HHCCHHC..-HCHH CS
                           G-alpha  94 lkerldplkkveasliaklssateee.....................................qeiefnp..raevg 131
                                         er+ ++ kv++   + l ++ +++                                           +  ++ev 
  gi|336253764|ref|YP_004596871.1| 465 DVERVCEIAKVDEF-VDDLPNGYDSQlgddgvrlsggqrqrvalarallkdadflvldeatsdL----DSslEREVQ 536
                                       66666666666654.3445555555555555555555565555555555555444444422222....224444666 PP

                                       HHHHHHCCSHHHHHH CS
                           G-alpha 132 edikaLwndpgiqel 146
                                        +i+++  d+gi ++
  gi|336253764|ref|YP_004596871.1| 537 ASIESMERDYGIIAI 551
                                       666666666666555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.7   3.7e+03     145     165 ..     103     124 ..      93     134 .. 0.75
   2 ?   10.3   0.0   0.00031      0.43      19      48 ..     387     416 ..     381     421 .. 0.85
   3 ?   -2.4   0.0       2.5   3.4e+03      82      98 ..     508     524 ..     486     541 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.7
                            AAA_30 145 gigtaeLtevvRqke.seeraa 165
                                        + +a L+ v Rq+  +++r+ 
  gi|336253764|ref|YP_004596871.1| 103 SFVVAWLKAVLRQRYeEWIRTQ 124
                                       5567889999***876888765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00031
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggr 48 
                                        +++ +G  G+GK+t+++ l++++e + g+
  gi|336253764|ref|YP_004596871.1| 387 EFVAFVGQSGAGKSTIVSLLARLYEPDDGE 416
                                       478899******************987555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.5
                            AAA_30  82 grarlepgtllivDEag 98 
                                       +ra l++++ l+ DEa 
  gi|336253764|ref|YP_004596871.1| 508 ARALLKDADFLVLDEAT 524
                                       44556677888888885 PP

>> Reticulon  Reticulon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.1      0.31   4.2e+02      99     135 ..     163     199 ..      92     203 .. 0.83
   2 ?   10.8   2.0   0.00026      0.36      39     137 ..     189     307 ..     169     314 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.31
                         Reticulon  99 lgedlklflkvalllyilsilgslfslltllyigvvl 135
                                       +++ l++ + v + l ++ ++   +++l ll++gv++
  gi|336253764|ref|YP_004596871.1| 163 CVQALETLFLVGIYLAVMFYIAPEMTVLALLLLGVIT 199
                                       4556889999999999999999999999999999986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00026
                         Reticulon  39 sklllllllvlflwa..............eyagllnkskp................pepelelseesvreladslle 85 
                                         +llll +++++++              e                          +++ + lsee++  + ds+++
  gi|336253764|ref|YP_004596871.1| 189 VLALLLLGVITYVLRnviepaytvgtrvaE---------AnervqesvqagtqgirDVKLFGLSEEMFTAFRDSIRQ 256
                                       333444444555555344444433332222.........13333334445555555569999*************** PP

                         Reticulon  86 llnkalselrrlalgedlklflkvalllyilsilgslfslltllyigvvlaf 137
                                          + ++  r+ a ++++ + l +al l++l ++g + s+l+l ++g++l+ 
  gi|336253764|ref|YP_004596871.1| 257 YTDSSINLKRNEAAIQNFYD-LAAALTLFALIYVGFIYSGLSLGALGIFLLA 307
                                       ***************99998.678899999***************9998875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00027      0.37       2      21 ..     389     408 ..     388     487 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                                       EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                       va+vG++ +GKSt+++ l +
  gi|336253764|ref|YP_004596871.1| 389 VAFVGQSGAGKSTIVSLLAR 408
                                       89************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (599 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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 0.25s 00:00:00.88 Elapsed: 00:00:00.39
# Mc/sec: 4556.84
//
Query:       gi|336253765|ref|YP_004596872.1|  [L=601]
Description: glucosamine--fructose-6-phosphate aminotransferase [Halopiger xanaduensis SH-6]
Scores for 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  128.0   0.2    4.5e-20   71.8   0.1    2.4  2  SIS       SIS domain
    5.9e-22   78.3   0.0    1.2e-21   77.3   0.0    1.5  1  GATase_6  Glutamine amidotransferase domain
    4.6e-19   68.5   0.0    7.5e-19   67.9   0.0    1.4  1  GATase_7  Glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.078   11.9   0.0       0.23   10.3   0.0    1.7  2  GATase_4  Glutamine amidotransferases class-II


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 !   71.8   0.1     1e-23   4.5e-20       6     130 ..     289     412 ..     285     413 .. 0.95
   2 !   53.9   0.0   3.5e-18   1.6e-14       2      85 ..     457     541 ..     456     581 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 1e-23
                                       SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSE CS
                               SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergak 82 
                                       + i ++++Gtsy + +++a  lee++ + + ve ase+  +  +    ++lvi++++sget+d++ a++ a+  ga+
  gi|336253765|ref|YP_004596872.1| 289 EEIQLVACGTSYYASQYAAQLLEEVADVRATVEIASEYEFD-GGRDPWRTLVIAVTQSGETADTLGAIRRAAGAGAR 364
                                       5799*********************************8888.6677779**************************** PP

                                       EEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                               SIS  83 iiaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                       ++a+T+  gs++ read +l i+a+pe++va+tk++++q a l +lav
  gi|336253765|ref|YP_004596872.1| 365 TLAVTNTLGSSVTREADDTLFIRAGPEIGVAATKTFVSQVATLALLAV 412
                                       ******************************************999986 PP

  == domain 2  score: 53.9 bits;  conditional E-value: 3.5e-18
                                       HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHH.HHHHHHHHHH CS
                               SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetk.dlvaaaelak 77 
                                       ++++++ +++G++  y++a+e+alkl+ei++ ++e+ +a+elkhg+lal++++++v+++ + g  + ++ +++ +a+
  gi|336253765|ref|YP_004596872.1| 457 FRDSESFFFVGRRFGYPVALEGALKLKEISYDHAEGFAAGELKHGPLALVTDKTPVLAVLTDGTRAgETMNNVTEAQ 533
                                       789999******************************************************99877625555555*** PP

                                       HTTSEEEE CS
                               SIS  78 ergakiia 85 
                                        rga+ i+
  gi|336253765|ref|YP_004596872.1| 534 TRGAPAIG 541
                                       ****9985 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0   2.6e-25   1.2e-21      13     133 ..      60     188 ..      33     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 2.6e-25
                          GATase_6  13 e..valaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.eelG. 85 
                                       +  ++++H+R++++g ++++ a+P +s++g++++vhNG ++ny++l+ el + +g++f s++Dtev+ +ll +el  
  gi|336253765|ref|YP_004596872.1|  60 DavCGIGHTRWSTHGPPTDANAHPHTSKNGTVAVVHNGIVENYESLKTELVE-AGYEFSSETDTEVIPHLLeRELEd 135
                                       0559*************77666*****************************9.****************99844444 PP

                          GATase_6  86 ........eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafas 133
                                               e+v++ l+G +a+a++++ +++++ +r++   +pl+++  ++g   as
  gi|336253765|ref|YP_004596872.1| 136 ghdllsalERVVDLLEGSYAIAAVQAGTDRIVATRHE---SPLVIGHGDDGSFLAS 188
                                       46788899*****************999999888655...8999998888877777 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.0   1.7e-22   7.5e-19       9     122 ..      77     194 ..      67     195 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 1.7e-22
                          GATase_7   9 seagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnG 76 
                                       ++a+a P + s++g++++v+nG + Ny++l+ eL ++g++f++++Dtev+ +lle+           +e++++ l+G
  gi|336253765|ref|YP_004596872.1|  77 TDANAHPHT-SKNGTVAVVHNGIVENYESLKTELVEAGYEFSSETDTEVIPHLLEReledghdllSALERVVDLLEG 152
                                       566778988.79*******************************************9*********99********** PP

                          GATase_7  77 mfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       ++A+a +++ ++r+++ R    + PL +g+ + d+ ++aS + a+l
  gi|336253765|ref|YP_004596872.1| 153 SYAIAAVQAGTDRIVATRH---ESPLVIGHGD-DGSFLASDVTAFL 194
                                       *******************...7********6.79999**999987 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   5.2e-05      0.23      74     145 ..      64     137 ..      48     166 .. 0.77
   2 ?   -2.5   0.0      0.43   1.9e+03     238     256 ..     209     227 ..     191     239 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.2e-05
                          GATase_4  74 vvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCelleelasrf 145
                                        + H R  t+G  +++n+hp + + +  +    HnG +++y+       e  +e   +TD+E++   l +el+  +
  gi|336253765|ref|YP_004596872.1|  64 GIGHTRWSTHGPPTDANAHPHTSKNG--TVAVVHNGIVENYESLKtelvEAGYEFSSETDTEVIPHLLERELEDGH 137
                                       588*****************998765..45567*****99876554557888999999***988655555555554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.43
                          GATase_4 238 kklepGellvfrdGalvat 256
                                        +le G++ v++dGa v +
  gi|336253765|ref|YP_004596872.1| 209 VSLEAGDVSVYHDGAAVDR 227
                                       4566777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 4428.35
//
Query:       gi|336253766|ref|YP_004596873.1|  [L=390]
Description: glucosamine-1-phosphate N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-45  154.3   0.0    6.1e-45  153.7   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    3.7e-18   66.4   0.1    5.3e-18   65.9   0.1    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
    3.5e-14   51.9  27.6    1.2e-08   34.3   4.3    4.1  4  Hexapep          Bacterial transferase hexapeptide (six repea
    2.1e-08   33.8  23.9    3.4e-05   23.5   3.5    4.3  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase
    8.9e-08   32.1   0.9    8.9e-08   32.1   0.9    1.8  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
      0.007   15.4   0.0      0.021   13.8   0.1    1.8  2  Fucokinase       L-fucokinase
  ------ inclusion threshold ------
      0.067   11.3   6.5      0.035   12.3   4.2    1.5  2  DUF4954          Domain of unknown function (DUF4954)


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 !  153.7   0.0   2.4e-48   6.1e-45       2     245 ..       8     236 ..       7     239 .. 0.93

  Alignments for each domain:
  == domain 1  score: 153.7 bits;  conditional E-value: 2.4e-48
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       av+La G+G RL PLt++++k++vpv+++ +++++++ ++a++g+e+i++v+  ++++++++++++g++++++++++
  gi|336253766|ref|YP_004596873.1|   8 AVVLAAGEGRRLEPLTNRRPKPMVPVANQ-PILEHVVAAIADAGVERIVLVVG-YQQERIRNHFGDGDDWDIDIEYV 82 
                                       89***************************.*****************666655.88999****************** PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECT CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieade 155
                                       +++++ gtA+Av++a+  +  ++     lvL+gD l++  + e v++ ie+++    ++ +++ + a++yGv+++ +
  gi|336253766|ref|YP_004596873.1|  83 VQDKQLGTAHAVLQAQSAISSQF-----LVLNGDRLVETSLVERVRDEIESGN--GPVMTVTRSKHASDYGVVTVAD 152
                                       *******************9776.....9*********999999999999999..888889999***********99 PP

                                       TSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEX CS
                   NTP_transferase 156 egrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDv 232
                                        grv++++EKP+ +  sel+++G+Y f++++++ l    ++ +rge  it +l++++e+  + +a+  ++   W Dv
  gi|336253766|ref|YP_004596873.1| 153 -GRVTDITEKPAPPVTSELINAGVYGFDPSIFDALR--STPTERGELAITTTLKRITEDR-PIQAVRYRG--RWLDV 223
                                       .8*********************************4..6*****************9995.665778888..5**** PP

                                       SSHHHHHHHHHHH CS
                   NTP_transferase 233 Gtldslleanekl 245
                                         l +ll++n+ +
  gi|336253766|ref|YP_004596873.1| 224 SHLWDLLDVNASV 236
                                       ********99876 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 !   65.9   0.1   2.1e-21   5.3e-18       1     128 [.       8     171 ..       8     220 .. 0.75

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2.1e-21
                                       EEEEEESS-TTTT....T.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC.....TS-EEE- CS
                      NTP_transf_3   1 aviLAGGrSsRmg....g.dKallplggkpllervldalraagvdevvvvggd..eevlaalarl.....gvrvved 65 
                                       av+LA+G+++R+     + +K+++p++++p+le+v++a+++agv+++v+v+g+  e +++++ +      ++++v++
  gi|336253766|ref|YP_004596873.1|   8 AVVLAAGEGRRLEpltnRrPKPMVPVANQPILEHVVAAIADAGVERIVLVVGYqqERIRNHFGDGddwdiDIEYVVQ 84 
                                       79**********5444335********************************99655677777555444445777777 PP

                                       TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE............... CS
                      NTP_transf_3  66 edpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeger............... 127
                                       + ++ g++++++ a +a+  ++++lvl +D  l++++lver+++++++ ++ v+ +t+++++               
  gi|336253766|ref|YP_004596873.1|  85 D-KQLGTAHAVLQAQSAI--SSQFLVLNGDR-LVETSLVERVRDEIESGNGPVMTVTRSKHAsdygvvtvadgrvtd 157
                                       6.5899999999999988..7**********.88************9888888888777766666666666666666 PP

                                       .............E CS
                      NTP_transf_3 128 .............g 128
                                                    +
  gi|336253766|ref|YP_004596873.1| 158 itekpappvtselI 171
                                       66666655555551 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   4.3   4.8e-12   1.2e-08       1      35 [.     257     291 ..     257     292 .. 0.95
   2 !   22.4   1.4   2.8e-08   7.1e-05       1      34 [.     275     307 ..     275     308 .. 0.96
   3 !   16.8   1.0   1.6e-06     0.004       2      36 .]     293     326 ..     292     326 .. 0.93
   4 !   11.3   7.3   8.5e-05      0.22       3      36 .]     346     379 ..     344     379 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 4.8e-12
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       ++v+Gs+v+Ig++a+igg + IG+nv+I +++v+ 
  gi|336253766|ref|YP_004596873.1| 257 NAVLGSDVTIGANATIGGSTSIGNNVTIKPNAVVS 291
                                       689******************************97 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 2.8e-08
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       st IG+nv+I p+av+ +n+++ ++++I++g+v+
  gi|336253766|ref|YP_004596873.1| 275 STSIGNNVTIKPNAVV-SNAVVFPDAVIESGAVV 307
                                       689*************.9999************8 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 1.6e-06
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       +v+  +++I ++av+  ++++ +n+++ga+++i+g
  gi|336253766|ref|YP_004596873.1| 293 AVVFPDAVIESGAVV-QDAIVAENARVGANTTITG 326
                                       788899*********.*****************97 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 8.5e-05
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       v+G+n++Ig++ ++ +++++Gd++++ +gv +gg
  gi|336253766|ref|YP_004596873.1| 346 VVGDNAVIGNGGTVEPGTVLGDGATVDHGVSVGG 379
                                       79********888889999999999999998876 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 !   23.5   3.5   1.3e-08   3.4e-05       4      32 ..     260     290 ..     257     292 .. 0.90
   2 ?    4.5   0.5     0.011        29      15      33 ..     306     325 ..     298     326 .. 0.76
   3 !   14.5   5.8   8.4e-06     0.022       4      32 ..     347     377 ..     346     378 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.3e-08
                                       E-TT-EE-TT-EES..EEE-TT-EE-TT-EE CS
                         Hexapep_2   4 IGdnCliGanagiG..vslGdncvvgaGvvi 32 
                                        G ++ iGana+iG  +s+G+n+++ ++ v+
  gi|336253766|ref|YP_004596873.1| 260 LGSDVTIGANATIGgsTSIGNNVTIKPNAVV 290
                                       699**********558*************99 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
                                       EE.SEEE-TT-EE-TT-EE- CS
                         Hexapep_2  15 gi.GvslGdncvvgaGvvit 33 
                                       ++   ++ +n+ vga+ +it
  gi|336253766|ref|YP_004596873.1| 306 VVqDAIVAENARVGANTTIT 325
                                       55566777899999999998 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 8.4e-06
                                       E-TT-EE-TT-EE..SEEE-TT-EE-TT-EE CS
                         Hexapep_2   4 IGdnCliGanagi..GvslGdncvvgaGvvi 32 
                                       +Gdn +iG   ++  G+ lGd+++v+ Gv +
  gi|336253766|ref|YP_004596873.1| 347 VGDNAVIGNGGTVepGTVLGDGATVDHGVSV 377
                                       8*********8877***************88 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 !   32.1   0.9   3.5e-11   8.9e-08       1     133 [.       6     139 ..       6     156 .. 0.76
   2 ?   -1.9   0.1      0.91   2.3e+03      36      73 ..     298     335 ..     282     338 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 3.5e-11
                                       EEEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG.....CCEE CS
                              IspD   1 vvvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld.....ksiq 69 
                                       v +v+ AAG+G+R++   + +pK  + +++q++leh v+a+++   v++iv+vv  ++ e++++  +d      +i+
  gi|336253766|ref|YP_004596873.1|   6 VSAVVLAAGEGRRLEpltNRRPKPMVPVANQPILEHVVAAIAD-AGVERIVLVVGYQQ-ERIRNHFGDgddwdIDIE 80 
                                       679**********86333789*******************999.889******99988.888888888788775677 PP

                                       EEE--SS..HHHHHHHHHHTTSSTTSEEEE--TT-TT--HHHHHHHHHHHHTTCSEEEEEEE-SSE CS
                              IspD  70 lvaGGde..RaesVlnglkalegeakfVLvHDaARpllkaadiaellaaaeqstqgailalpvkDt 133
                                        v+  ++   a++Vl++  a++ +    Lv ++ R l++++ ++++  + e    g  +++ v+ +
  gi|336253766|ref|YP_004596873.1|  81 YVVQDKQlgTAHAVLQAQSAISSQ---FLVLNGDR-LVETSLVERVRDEIES---GNGPVMTVTRS 139
                                       666544322466677777776665...89999999.9999999999988886...55555666554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.91
                                       HHHHCTTTEEEEEEEE-GGGHHHHHHHHGGCCEEEEE- CS
                              IspD  36 dallaskavdkivvvvseddteefeqllldksiqlvaG 73 
                                       da+ +s+av +  +v ++ ++++ ++++++++ ++v+G
  gi|336253766|ref|YP_004596873.1| 298 DAVIESGAVVQDAIVAENARVGANTTITGEPTTMVVDG 335
                                       45666666666667777788899999999988888887 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.82   2.1e+03     136     166 ..     171     201 ..     169     216 .. 0.82
   2 !   13.8   0.1   8.3e-06     0.021     267     340 ..     246     317 ..     219     333 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.82
                        Fucokinase 136 ldsGvvffdhktaekLlklykeskpLdcety 166
                                       +  Gv+ fd++++  L+++ +e + L   t 
  gi|336253766|ref|YP_004596873.1| 171 INAGVYGFDPSIFDALRSTPTERGELAITTT 201
                                       6789999*********999998888877655 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.3e-06
                        Fucokinase 267 kekk..kesavvinSvlessvsvgegsviehs.slkgnvsigsnsivsglelesseeslelpddtilqtlslklske 340
                                       +  +  ++sa+  n+vl s+v++g+++ i  s s+++nv+i+ n +vs+  +  ++    + +  ++q   + ++ +
  gi|336253766|ref|YP_004596873.1| 246 E--ErrEASAIANNAVLGSDVTIGANATIGGStSIGNNVTIKPNAVVSNAVVFPDAV---IESGAVVQDAIVAENAR 317
                                       2..133777777888888888888888887552566888888888888888877644...77777777666666554 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.2   1.4e-05     0.035     181     255 ..     253     325 ..     229     333 .. 0.80
   2 ?   -2.5   0.0       0.4     1e+03     223     243 ..     345     365 ..     332     378 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                           DUF4954 181 kilnagli.kNvkigdyatiegaskl.engtinSskeapveiGegViledfiissGskikdgavisrcfvGqavklk 255
                                        i n  ++   v+ig+ ati g++++ +n ti+ ++     + + V+  d++i+sG+ ++d+ v++++ vG +++++
  gi|336253766|ref|YP_004596873.1| 253 AIANNAVLgSDVTIGANATIGGSTSIgNNVTIKPNA----VVSNAVVFPDAVIESGAVVQDAIVAENARVGANTTIT 325
                                       444444432689***********9994456776654....57899**************************999886 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.4
                           DUF4954 223 gViledfiissGskikdgavi 243
                                       gV+ ++++i +G +++ g+v+
  gi|336253766|ref|YP_004596873.1| 345 GVVGDNAVIGNGGTVEPGTVL 365
                                       677888888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2766.50
//
Query:       gi|336253767|ref|YP_004596874.1|  [L=327]
Description: UDP-glucuronate 5'-epimerase [Halopiger xanaduensis SH-6]
Scores for 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-67  228.0   0.0    2.3e-67  227.8   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.1e-61  207.4   0.0    3.3e-61  206.8   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
      2e-21   76.2   0.0    2.8e-21   75.7   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    7.8e-20   71.1   0.0    9.8e-20   70.8   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.1e-15   57.6   0.0    5.1e-15   55.4   0.0    1.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    5.5e-09   35.6   1.2    8.2e-08   31.7   1.2    2.3  1  NAD_binding_4    Male sterility protein
    4.3e-07   30.0   0.0    2.9e-06   27.3   0.0    2.2  1  NAD_binding_10   NAD(P)H-binding
     0.0016   18.1   0.0     0.0021   17.6   0.0    1.5  1  NmrA             NmrA-like family
     0.0023   17.9   0.0     0.0059   16.5   0.0    1.7  1  KR               KR domain
     0.0037   16.7   0.1      0.015   14.8   0.0    2.1  2  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.069   12.7   0.0        1.2    8.6   0.0    2.1  2  adh_short_C2     Enoyl-(Acyl carrier protein) reductase


Domain annotation for each model (and alignments):
>> 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 !  227.8   0.0   1.4e-70   2.3e-67       1     329 [.       4     306 ..       4     309 .. 0.94

  Alignments for each domain:
  == domain 1  score: 227.8 bits;  conditional E-value: 1.4e-70
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+++e Lle g++v+ ++ ++  +++g  e+  +  +e   +++++++g +tD++ +++++++ +++
  gi|336253767|ref|YP_004596874.1|   4 LVTGGAGFIGSHITEGLLETGHNVITLDVLDPYYDLGIKERNIEICRETGGDRFEFVEGSITDEELVRDIISSNDIE 80 
                                       9*********************************999999888888888899************************* PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        vy+ AAq  V++s+e+P++  e+n +G l+LL a+ ++g++   rf+ aS+s vYG+v+  p++E+++  P+sPY+
  gi|336253767|ref|YP_004596874.1|  81 FVYHQAAQAGVRTSVENPKKPHEINTTGLLNLLVAADDHGIK---RFVNASSSSVYGEVEYLPYDEDHQNVPQSPYG 154
                                       ****************************************85...******************************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                       ++Kl+a++ ++ +++ y++++v+ ++f  ++pr+ ++     it++ +r ++ k + +++G+++++Rd+++++D+v+
  gi|336253767|ref|YP_004596874.1| 155 VTKLTAEHYCRVWNDVYDVPTVSLRYFTVYGPRMRPN---MAITNFTSRCLNAK-PPVIYGDGQQTRDFTYIDDIVD 227
                                       *********************************9555...78999999999988.55669***************** PP

                                       HHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B CS
                     GDP_Man_Dehyd 232 amwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllg 308
                                       a   +l+ d       a+ge+++v++  +++++el ++i+ e            +g + v +++   ++++++ + +
  gi|336253767|ref|YP_004596874.1| 228 ANLSLLETDA------ADGEVMNVGSTGNITIEELAEHIIDE------------TG-TDVGIEYTAAKEADARHTHA 285
                                       *******997......79******************998754............33.35888888999999999*** PP

                                       -THHHHHHH----SS-HHHHH CS
                     GDP_Man_Dehyd 309 daskakeeLgWkpkvsfeelv 329
                                       d +ka+e ++++p++s++e+v
  gi|336253767|ref|YP_004596874.1| 286 DVTKARELIDYEPSTSIREGV 306
                                       *******************98 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.8   0.0     2e-64   3.3e-61       1     241 []       3     246 ..       3     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: 206.8 bits;  conditional E-value: 2e-64
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC............EEEE--TT-HHHHHHHHHHHT- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl............elveldltdrsalerlfkeeqp 65 
                                       +lVtG++GfiGs++++ lle g++vi+ld l      + +e+             e+ve+ +td++ ++++++++++
  gi|336253767|ref|YP_004596874.1|   3 VLVTGGAGFIGSHITEGLLETGHNVITLDVLDPYYDLGIKERNieicretggdrfEFVEGSITDEELVRDIISSNDI 79 
                                       79*****************************88888887777799******************************** PP

                                       SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHH CS
                         Epimerase  66 davihlAavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspY 142
                                       + v+h Aa++gv++s+e+p++  e+n+ g lnll aa ++g+kr++++sSs+vYG+++  p +e+    +  p+spY
  gi|336253767|ref|YP_004596874.1|  80 EFVYHQAAQAGVRTSVENPKKPHEINTTGLLNLLVAADDHGIKRFVNASSSSVYGEVEYLPYDEDH---QNVPQSPY 153
                                       *************************************************************99999...778***** PP

                                       HHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHH CS
                         Epimerase 143 aaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDva 219
                                       +++Kl++e++++ +++ y++++++lr+f++yGpr    +++  i+ + +++l++k + +++gdg++ Rdf y++D++
  gi|336253767|ref|YP_004596874.1| 154 GVTKLTAEHYCRVWNDVYDVPTVSLRYFTVYGPR---MRPNMAITNFTSRCLNAK-PPVIYGDGQQTRDFTYIDDIV 226
                                       **********************************...88****************.********************* PP

                                       HHHHHHHHHHTT-STTEEEEES CS
                         Epimerase 220 eaillvlehvdagdkgeiyniG 241
                                       +a+l +le  da ++ge++n+G
  gi|336253767|ref|YP_004596874.1| 227 DANLSLLET-DA-ADGEVMNVG 246
                                       ********9.44.6799****9 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 !   75.7   0.0   1.7e-24   2.8e-21       1     225 [.       4     229 ..       4     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 1.7e-24
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrlee.lkevrvlD....lrespelleelskvnvkk..viegDvtdkdkleeal..egvd 68 
                                       +vtGgaGF+G+++ + L+++++ + ++ vlD    l ++++  e  ++++ +   ++eg +td++ +++ +  ++++
  gi|336253767|ref|YP_004596874.1|   4 LVTGGAGFIGSHITEGLLETGHnVITLDVLDpyydLGIKERNIEICRETGGDRfeFVEGSITDEELVRDIIssNDIE 80 
                                       69******************98899999999766666666666677777666688**************99224566 PP

                         3Beta_HSD  69 vvihlaslvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqd 144
                                        v h a+   v+  + + ++  ++n  G  n+l a+ ++g++++v  Ss +v g+    e +   dE   +++++q+
  gi|336253767|ref|YP_004596874.1|  81 FVYHQAAQAGVRTsVENPKKPHEINTTGLLNLLVAADDHGIKRFVNASSSSVYGE---VEYLP-YDE--DHQNVPQS 151
                                       688888888887757888999**********************************...44444.455..57899*** PP

                         3Beta_HSD 145 aypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdk...llvpllkqlaklglalfkigdeevlsdrvYv 218
                                       +y  +K  aE++    N+       ++ T++LR  ++yG++ +    ++++  ++++ +   + +gd +++ d++Y 
  gi|336253767|ref|YP_004596874.1| 152 PYGVTKLTAEHYCRVWND-----VYDVPTVSLRYFTVYGPRMRpnmAITNFTSRCLNAK-PPVIYGDGQQTRDFTYI 222
                                       ******************.....45679************9762225666777777777.77899************ PP

                         3Beta_HSD 219 gNvawah 225
                                       + +++a 
  gi|336253767|ref|YP_004596874.1| 223 DDIVDAN 229
                                       *999885 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 !   70.8   0.0     6e-23   9.8e-20       1     243 [.       1     283 [.       1     301 [. 0.86

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 6e-23
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...........................T--TTSHHHHHHHHHHH CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre...........................eldltdaeavaellkea 50 
                                       m++lvtG+ G +Gs++++ l e g++v++l+                             e  +td+e v+++++++
  gi|336253767|ref|YP_004596874.1|   1 MNVLVTGGAGFIGSHITEGLLETGHNVITLDVLdpyydlgikernieicretggdrfefvEGSITDEELVRDIISSN 77 
                                       89****************************99899****************************************** PP

                                       --SEEEE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TTS----SSHHH CS
                     RmlD_sub_bind  51 kpdvvvnaAAytavDkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrpYeeddetsPlnvYG 126
                                       + ++v++ AA   v    +++++ +++n ++  +l  aa  +g++ ++  S+  V+   +  pY ed++  P++ YG
  gi|336253767|ref|YP_004596874.1|  78 DIEFVYHQAAQAGVRTSVENPKKPHEINTTGLLNLLVAADDHGIKrFVNASSSSVYGEVEYLPYDEDHQNVPQSPYG 154
                                       *******************************************9559*********999****************** PP

                                       HHHHHHHHHHHH....H-SSEEEEEE-SEESS.SSS-HH.HHHHHHH..HH-SEEEEESS-EE--EEHHHHHHHHHH CS
                     RmlD_sub_bind 127 rtKlaGEqavla....agkkalivRtswvyge.kgknfv.ktmlrla..kereelkvvaDqlgsPTsardlAevllq 195
                                        tKl  E+  +     +   ++ +R   vyg   + n++ +++ ++   ++   +     q++  T+ +d+ ++ l+
  gi|336253767|ref|YP_004596874.1| 155 VTKLTAEHYCRVwndvYDVPTVSLRYFTVYGPrMRPNMAiTNFTSRClnAKPPVIYGDGQQTRDFTYIDDIVDANLS 231
                                       ********9887443333355679******9854556551455555522444445555669999************* PP

                                       HHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTT.......SEEEEE-C CS
                     RmlD_sub_bind 196 llekaaeekelagvyHlanegetswlefArailkeagads.......eevkpist 243
                                       lle+ a+   + +v  ++++g+++  e+A++i++e+g+d        +e  + +t
  gi|336253767|ref|YP_004596874.1| 232 LLETDAA---DGEVMNVGSTGNITIEELAEHIIDETGTDVgieytaaKEADARHT 283
                                       ****997...6889999********************998765544444444444 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.0   3.1e-18   5.1e-15       1     251 [.       3     268 ..       3     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 3.1e-18
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vlvtG++G iGs++++ +l++  + i l   d +    i++++ e ++++    ++  v g+++d+e +++++++ +
  gi|336253767|ref|YP_004596874.1|   3 VLVTGGAGFIGSHITEGLLETGHNVITLDVLDPYYDLGIKERNIEICRETGG-DRFEFVEGSITDEELVRDIISSND 78 
                                       8********************9888888878888888888886655555444.3335779***************** PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE..............GGGSS--SHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt..............DKAvnPtnvmGa 140
                                       +++v+h AA   V +  enp +  + N +g  n++ aa ++g+k++v  S+              D    P + +G+
  gi|336253767|ref|YP_004596874.1|  79 IEFVYHQAAQAGVRTSVENPKKPHEINTTGLLNLLVAADDHGIKRFVNASSssvygeveylpydeDHQNVPQSPYGV 155
                                       ************************************************9975555555555555567778999**** PP

                                       HHHHHHHHHHHGGG--SSS-..-EEEEEEE-EETTGTTSSHHHHHHHHHTTSSEEES-TT-EEEEE-HHHHHHHHHH CS
                   Polysacc_synt_2 141 tKrlaekllqalakeseekk..tkfvvvRfGNVlgSrGSviplFkkqikeggpvtvTdpemtRyfmtieeavqLvlq 215
                                       tK++ae ++   ++     +   ++ ++ +G  +  +  +  +  + ++++ pv   d + tR f  i++ v+  l+
  gi|336253767|ref|YP_004596874.1| 156 TKLTAEHYCRVWNDVYDVPTvsLRY-FTVYGPRMRPNMAITNFTSRCLNAKPPVIYGDGQQTRDFTYIDDIVDANLS 231
                                       **********999988433332333.444888888888888888888888999*****************9998888 PP

                                       HH.HH--SS-EEEE--.-EEEHHHHHHHH........ CS
                   Polysacc_synt_2 216 al.alakggeifvldmGepvkivdlakalielsglee 251
                                        l + a +ge++ +     ++i +la+++i+ +g+++
  gi|336253767|ref|YP_004596874.1| 232 LLeTDAADGEVMNVGSTGNITIEELAEHIIDETGTDV 268
                                       77245778888877776899*********99888654 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   1.2     5e-11   8.2e-08       1     215 [.       5     195 ..       5     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 5e-11
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSS.HHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaks.gesaeeRleeelekkelfsallkelaerikvveGDlseprlGL 76 
                                       +TG+ GF+G+++ e LL+t  +  i+l v     +  ++eR        e+ +++     +r ++veG +++++l  
  gi|336253767|ref|YP_004596874.1|   5 VTGGAGFIGSHITEGLLETGHN-VITLDVLDPYyDLGIKERNI------EICRET---GGDRFEFVEGSITDEELV- 70 
                                       7*******************98.56666664430334555553......343334...37899********99974. PP

                                       -HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SS CS
                     NAD_binding_4  77 seedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveek 150
                                         +d+   ++ ++ ++h aA+  +  ++++     ++N++G  ++l  a     +  ++  S++ v+ge e      
  gi|336253767|ref|YP_004596874.1|  71 --RDIIS-SNDIEFVYHQAAQAGVRTSVENpkkPHEINTTGLLNLLVAADDHGIK-RFVNASSSSVYGEVEYL---- 139
                                       ..33333.4789********98776665552227899**********99998888.99999999999988843.... PP

                                       S-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-...-SSST-- CS
                     NAD_binding_4 151 vyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg...esktGwi 215
                                                     ++++++  +  Y  +K  aE+ +r +++  ++p+v +R  +++g   ++   ++
  gi|336253767|ref|YP_004596874.1| 140 ------------PYDEDHQNVPQSPYGVTKLTAEHYCRVWNDVYDVPTVSLRYFTVYGprmRPNMAIT 195
                                       ............2334445555569************************9999999985554444333 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 !   27.3   0.0   1.8e-09   2.9e-06       1     130 [.       7     163 ..       7     171 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.8e-09
                                       TTTSHHHHHHHHHHHHC-T-EEEEE.ETT.......HHHCHHHH.....CTTTCEEEE--TT-CCHHHHHHTT-SE. CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtal.vRn.......peklaele.....aeeglevvegdvtdvedlaealkgada. 63 
                                       G+ G +G+++++ ll+ g h+v  l v +       +e+   +e       ++ e veg++td+e +++ ++  d+ 
  gi|336253767|ref|YP_004596874.1|   7 GGAGFIGSHITEGLLETG-HNVITLdVLDpyydlgiKERN--IEicretGGDRFEFVEGSITDEELVRDIISSNDIe 80 
                                       999**************6.888655588833333332222..222232245899******************99973 PP

                                       .EEES---TCC.............HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGC.HHHHHHHHCC.HHHHHHH CS
                    NAD_binding_10  64 .Vvsalggggk.............deegaknivdaakeagvkRfvlvsaigvgdevpg.efgewnkell.kaylaak 124
                                        V+  +++ g              +++g  n++ aa+ +g+kRfv  s+  v+ ev+  + +e  +++  ++y   k
  gi|336253767|ref|YP_004596874.1|  81 fVYHQAAQAGVrtsvenpkkpheiNTTGLLNLLVAADDHGIKRFVNASSSSVYGEVEYlPYDEDHQNVPqSPYGVTK 157
                                       36666633333344444444455555559***********************9887641344444444413333556 PP

                                       HHHHHH CS
                    NAD_binding_10 125 raaeel 130
                                         ae++
  gi|336253767|ref|YP_004596874.1| 158 LTAEHY 163
                                       666665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.3e-06    0.0021       1     101 [.       3     128 ..       3     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEE.ES-S......-SHHHHHHHHST...TEEEES-TT-HHHHHHHHTT-SE CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvral.vRdt......kselakslkeaG...velvkgdlddkeslvealkgvdv 67 
                                       +lv+G++G +G+++++ ll+ gh+v  l v d+      k+ +++   e G    e+v+g++ d+e+++ +++  d 
  gi|336253767|ref|YP_004596874.1|   3 VLVTGGAGFIGSHITEGLLETGHNVITLdVLDPyydlgiKERNIEICRETGgdrFEFVEGSITDEELVRDIISSNDI 79 
                                       79***********************98878888******88888888887733369******************999 PP

                                       EEE---GG...............S-HHHHHHHHHHHHHHHS-SEEEEEE CS
                              NmrA  68 vfsvtgfy...............skeiedgkklvdAakeaGvkhfiySs 101
                                        f+  +++               + ++    +l  Aa   G+k+f+ +s
  gi|336253767|ref|YP_004596874.1|  80 EFVYHQAAqagvrtsvenpkkphEINTTGLLNLLVAADDHGIKRFVNAS 128
                                       9998887778998888888774333333346889999999999998655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.6e-06    0.0059       3     142 ..       3     134 ..       2     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.6e-06
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS...--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHH CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsa.aadedskaliaeleal.gaevevvaaDvsdkdavealleeika 77 
                                       +l+tGG+G +G ++++ l+e g + + l   ++      ++++i+ ++++ g + e+v+  ++d++ v+ ++++ + 
  gi|336253767|ref|YP_004596874.1|   3 VLVTGGAGFIGSHITEGLLETGHNVITLDVLDPyYDLGIKERNIEICRETgGDRFEFVEGSITDEELVRDIISSND- 78 
                                       69********************99999987776344455666888888876779*************999999876. PP

                                       HSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH- CS
                                KR  78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllg 142
                                           i+ v+h A  +      +++ e+ ++  +   +G+ nL  +  d+ ++ fv  SS + ++g
  gi|336253767|ref|YP_004596874.1|  79 ----IEFVYHQAAQAG----VRTSVENPKKPHEINTTGLLNLLVAADDHGIKRFVNASSSS-VYG 134
                                       ....777999987655....45666777777777788999999999999999998887754.455 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   9.3e-06     0.015       2      69 ..       2      75 ..       1     119 [. 0.79
   2 ?   -1.5   0.0      0.87   1.4e+03      53      53 ..     269     269 ..     233     295 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.3e-06
                                      EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHH.....HHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHH CS
                         adh_short  2 vvlvtGassGIGraiakelakeGakvvvvdrseekl.....eevakelkee.gakalaiqvDvtdreevealve 69
                                       vlvtG+++ IG  i + l++ G +v+ +d  +        e+ ++ ++e+ g+++ ++++ +td+e v+++++
  gi|336253767|ref|YP_004596874.1|  2 NVLVTGGAGFIGSHITEGLLETGHNVITLDVLDPYYdlgikERNIEICRETgGDRFEFVEGSITDEELVRDIIS 75
                                      59*************************99976554311111344444555588899999999999988887765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.87
                                       E CS
                         adh_short  53 a 53 
                                        
  gi|336253767|ref|YP_004596874.1| 269 G 269
                                       2 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 ?    8.6   0.0   0.00073       1.2       6     115 ..      12     118 ..       7     168 .. 0.77
   2 ?    1.8   0.0     0.088   1.4e+02      97     146 ..     241     290 ..     225     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00073
                                       HHHHHHHHHHHTT-EEEEEESSGGH.....HHHHHHHHHHTTSE.E..EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   6 IGraiAkalaeeGaevvltdlneea.....kkrveelaeelgae.v..lecDVtdeeqvealveevvekfgklDilv 74 
                                       IG +i + l e G +v+  d+ +       k+r  e+ +e+g + +  +e  +tdee v+++++      + + ++ 
  gi|336253767|ref|YP_004596874.1|  12 IGSHITEGLLETGHNVITLDVLDPYydlgiKERNIEICRETGGDrFefVEGSITDEELVRDIISS-----NDIEFVY 83 
                                       99****************999876442235677777888877665556********999999887.....78999** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalp 115
                                       + a+ a         ts e+ ++ +++n+++l++l+ aa  
  gi|336253767|ref|YP_004596874.1|  84 HQAAQAGV------RTSVENPKKPHEINTTGLLNLLVAADD 118
                                       ****9998......89999*************999998876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.088
                                       HHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHH CS
                      adh_short_C2  97 raldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKa 146
                                       ++++v  ++ + + + a++++ e+g  v + +++a+ + + +++  ++Ka
  gi|336253767|ref|YP_004596874.1| 241 EVMNVGSTGNITIEELAEHIIDETGTDVGIEYTAAKEADARHTHADVTKA 290
                                       68899999999999999999999999999999999999999888888887 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:                      473  (0.0263818); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2279.76
//
Query:       gi|336253768|ref|YP_004596875.1|  [L=246]
Description: glucosamine-1-phosphate N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-42  146.2   0.0    1.4e-42  146.0   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    8.7e-15   55.4   0.0      1e-14   55.2   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    2.2e-06   27.6   0.0    1.2e-05   25.2   0.0    1.9  2  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 !  146.0   0.0   2.3e-46   1.4e-42       2     245 ..       3     234 ..       2     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 146.0 bits;  conditional E-value: 2.3e-46
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       av+La G+GtRL+PLt + +k lv v gk +li+ ++ +l++ g+++++vv+ +++++++e+ ++++++ gv +++a
  gi|336253768|ref|YP_004596875.1|   3 AVVLAAGKGTRLRPLTDDKPKVLVEVDGK-PLIEDVFDNLIEIGVTKLVVVVGYQKEQIIER-YGDEYE-GVPITYA 76 
                                       8****************************.*****************666666666655555.566663.899**** PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECT CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieade 155
                                       +++e+ g+A+A+++a+  ++d++    vl+L gD +++ ++ ++v++ +e++a+   ++  vp+eea++yGv  ++e
  gi|336253768|ref|YP_004596875.1|  77 HQREQLGLAHAILQAEPHIDDDF----VLML-GDNIFRANLADVVNRQREQRADAAFLVEEVPWEEASRYGVCDTNE 148
                                       ********************999....5666.5667788**************999999****************** PP

                                       TSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE.E CS
                   NTP_transferase 156 egrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs.D 231
                                        g++ +  EKP+ ++ s+l+ +G Y+f++ +++   + +++++rge e+ d++  ++++g+   ++++ d  +W+ D
  gi|336253768|ref|YP_004596875.1| 149 YGEIVEVMEKPADPP-SNLVMTGFYTFTPAIFHAC-HLVQPSDRGEYELPDAIDLLIQSGRTI-DAIRMD--GWRiD 220
                                       ***************.*****************99.89*********************9776.556666..6977* PP

                                       XSSHHHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleanekl 245
                                       vG +++  +a+e++
  gi|336253768|ref|YP_004596875.1| 221 VGYPEDRDKAEERI 234
                                       **999877777665 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 !   55.2   0.0   1.7e-18     1e-14       1     124 [.       3     132 ..       3     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.7e-18
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC..TS-EEE-TTS CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaalarl..gvrvvededp 68 
                                       av+LA+G+++R+      ++K l++++gkpl+e v+d+l + gv ++vvv+g+  e++ +++ +   gv++++  + 
  gi|336253768|ref|YP_004596875.1|   3 AVVLAAGKGTRLRpltddKPKVLVEVDGKPLIEDVFDNLIEIGVTKLVVVVGYqkEQIIERYGDEyeGVPITYAHQR 79 
                                       79**********6443325*******************************999544444444332455666665444 PP

                                       .S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESS CS
                      NTP_transf_3  69 .gkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptye 124
                                        + g +++++ a  ++  +d ++++++D ++  ++ ++ ++++ ++++ad+++++ e
  gi|336253768|ref|YP_004596875.1|  80 eQLGLAHAILQAEPHI--DDDFVLMLGDNIF--RANLADVVNRQREQRADAAFLVEE 132
                                       278***********99..79999999***99..566667777767777777776655 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 !   25.2   0.0   1.9e-09   1.2e-05       1      55 [.       1      58 [.       1      74 [. 0.83
   2 ?   -0.4   0.0      0.13     8e+02     156     216 ..     174     231 ..     167     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.9e-09
                                      EEEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGG CS
                              IspD  1 vvvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvsedd 55
                                      + +v+ AAG+G+R++    ++pK ++e++g++l+e   d l + ++ + +vvv  +++
  gi|336253768|ref|YP_004596875.1|  1 MQAVVLAAGKGTRLRpltDDKPKVLVEVDGKPLIEDVFDNLIEIGVTKLVVVVGYQKE 58
                                      579**********7533389***********************887777777765554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.13
                                       EEEEEEEHHHHHHHHHHHHHCT---SSHHHHHHHTT--EEEEE--TTG----SHHHHHHHH CS
                              IspD 156 qtPqgFrvdlllaahakgeqegaeitDdaslvekiGlsvkvVeGeednlKittpeDlalAe 216
                                        tP  F+   l +  ++g    +e  D ++l+ + G ++  +  +   + + +peD   Ae
  gi|336253768|ref|YP_004596875.1| 174 FTPAIFHACHLVQPSDRG---EYELPDAIDLLIQSGRTIDAIRMDGWRIDVGYPEDRDKAE 231
                                       455555555555555555...5779999999999999999999999999999999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1801.88
//
Query:       gi|336253769|ref|YP_004596876.1|  [L=90]
Description: hypothetical protein Halxa_2375 [Halopiger xanaduensis SH-6]
Scores for 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   12.4   0.0       0.23   12.0   0.0    1.2  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg


Domain annotation for each model (and alignments):
>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.3e-05      0.23       5      33 ..      32      60 ..      30      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                         oligo_HPY  5 pssklfdeplHPYTkaLlrsvprldrekd 33
                                      +++++f+ep   Y  +L+ s+p + r++ 
  gi|336253769|ref|YP_004596876.1| 32 TTDTVFREPETQYDYGLAGSIPTEWRQNP 60
                                      7899******************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 723.66
//
Query:       gi|336253770|ref|YP_004596877.1|  [L=305]
Description: NAD-dependent epimerase/dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-47  160.3   0.3    6.1e-47  160.1   0.3    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
      2e-41  142.5   0.2    7.5e-41  140.6   0.2    1.9  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    4.3e-12   45.7   0.2    5.8e-12   45.3   0.2    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    5.8e-12   45.2   0.8    1.7e-11   43.7   0.8    1.8  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      3e-09   36.4   0.0    3.6e-06   26.3   0.0    2.2  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.8e-08   33.9   0.1    1.5e-05   24.4   0.1    2.5  2  NAD_binding_4    Male sterility protein
     0.0086   16.0   0.0      0.016   15.1   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.049   13.5   0.0          3    7.7   0.0    2.4  2  KR               KR domain
      0.089   12.2   0.4        3.1    7.2   0.1    2.6  2  adh_short        short chain dehydrogenase


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 !  160.1   0.3   3.1e-50   6.1e-47       1     241 []       6     234 ..       6     234 .. 0.94

  Alignments for each domain:
  == domain 1  score: 160.1 bits;  conditional E-value: 3.1e-50
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       ilVtG++GfiGs+l+++l++++ +vi++d    +++ ++ +d+e+ve+ +++++    l    ++d+v+hlAa +++
  gi|336253770|ref|YP_004596877.1|   6 ILVTGGAGFIGSNLANELASRN-DVIAVDDCYLGEADNLSDDVEFVEASVLEDD----LPT--DVDVVFHLAALSSY 75 
                                       8******************997.********999999999999********987....555..79************ PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                       a   edp++  + n++g +n +e ar+ g++ ++++s+s++YG  +e p+ e++   p++ n+ Y a+Kla e+++e
  gi|336253770|ref|YP_004596877.1|  76 AMHEEDPTRGTRVNVEGFVNTVEQARQDGCDTVVYASTSSIYGTRTE-PTPEDV---PVAVNTGYEASKLARERYAE 148
                                       ********************************************999.999***...******************** PP

                                       HHHHHHT-EEEEEEESEEESTT....S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHH CS
                         Epimerase 155 ayaaqyglnaiilrlfnlyGpr....ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvle 227
                                       ++ + yg++++ +r f++y  +     ++ge ++vi++++  i++ +    l+gdgt+ Rdf +v+Dv++a+ l++e
  gi|336253770|ref|YP_004596877.1| 149 YFSNHYGMSMCGMRFFSVYQGYegaeGHKGEYANVIAQFADDIAHSR-APELYGDGTQTRDFTHVSDVVRALELAAE 224
                                       *******************555588566777****************.***************************** PP

                                       HHTT-STTEEEEES CS
                         Epimerase 228 hvdagdkgeiyniG 241
                                       h    +  ++yn+G
  gi|336253770|ref|YP_004596877.1| 225 H----ELEGVYNVG 234
                                       *....55679*998 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 !  140.6   0.2   3.8e-44   7.5e-41       1     331 [.       7     299 ..       7     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 140.6 bits;  conditional E-value: 3.8e-44
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+la+ L ++  +v+ +    +  ++g+ ++l +d        ++++++ + + +        +++d
  gi|336253770|ref|YP_004596877.1|   7 LVTGGAGFIGSNLANELASR-NDVIAV----DDCYLGEADNLSDD--------VEFVEASVLEDDL------PTDVD 64 
                                       9******************9.556655....34567788888754........5789988888663......4567* PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        v++LAA s  +   e+P + ++vnv G ++ +e +r+ g++    ++ aSts +YG+ +  p  E+ p+  +  Y 
  gi|336253770|ref|YP_004596877.1|  65 VVFHLAALSSYAMHEEDPTRGTRVNVEGFVNTVEQARQDGCD---TVVYASTSSIYGTRT-EPTPEDVPVAVNTGYE 137
                                       **************************************9986...5789********987.6899************ PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTS....CCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetf....vtrkitravarialgkqevlylGnldakRdwghvk 227
                                       a+Kl+ +  ++ + + yg+ ++  ++f  +  + g++       + i +++  ia+ + + l +G++ ++Rd++hv+
  gi|336253770|ref|YP_004596877.1| 138 ASKLARERYAEYFSNHYGMSMCGMRFFSVYQGYEGAEGhkgeYANVIAQFADDIAHSRAPEL-YGDGTQTRDFTHVS 213
                                       ****************************9999999986222356778888888888888888.7************* PP

                                       HHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--S CS
                     GDP_Man_Dehyd 228 Dyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevd 304
                                       D+v+a+ l+ +++    y+++tg+ +s +e+v+l +  lg +++ e               v+ ++ +       v+
  gi|336253770|ref|YP_004596877.1| 214 DVVRALELAAEHELEGVYNVGTGDRTSFNELVDLLNRTLGTDVDPE--------------YVENPIPED----VYVH 272
                                       ****************************************976553..............223333322....3367 PP

                                       B--B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 305 lllgdaskakeeLgWkpkvsfeelvre 331
                                        +++dask +   gW+p v++ee+v++
  gi|336253770|ref|YP_004596877.1| 273 DTCADASKFRAAAGWEPDVGLEEGVER 299
                                       89**********************986 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 !   45.3   0.2   2.9e-15   5.8e-12       2     232 ..       5     253 ..       4     275 .. 0.74

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.9e-15
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..........T--TTSHHHHHHHHHHH--SEEEE------HHHHH CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre..........eldltdaeavaellkeakpdvvvnaAAytavDkaE 68 
                                       +ilvtG+ G +Gs+La++la+++ +v+a++            ++++ +a+ +++ l  ++ dvv ++AA       E
  gi|336253770|ref|YP_004596877.1|   5 RILVTGGAGFIGSNLANELASRN-DVIAVDDCylgeadnlsdDVEFVEASVLEDDLP-TDVDVVFHLAALSSYAMHE 79 
                                       89*******************99.*****8777886555444444444444444444.4789*************** PP

                                       HSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH....H- CS
                     RmlD_sub_bind  69 seeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla....ag 140
                                       +++ +  +vn+e+  +  e+a++ g  ++++ St  ++ G++++p  ed +++  + Y ++Kla E+  +     +g
  gi|336253770|ref|YP_004596877.1|  80 EDPTRGTRVNVEGFVNTVEQARQDGCdTVVYASTSSIY-GTRTEPTPEDVPVAVNTGYEASKLARERYAEYfsnhYG 155
                                       ************************985799*******9.77799999999999999**********98876444456 PP

                                       SSEEEEEE-SEESS......SSS-HHHHHHHHH.....HH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG CS
                     RmlD_sub_bind 141 kkalivRtswvyge......kgknfvktmlrla.....kereelkvvaDqlgsPTsardlAevllqllekaaeekel 206
                                         ++ +R+  vy        ++ ++++++ + a     ++  el     q++  T++ d+ ++l  ++e+++     
  gi|336253770|ref|YP_004596877.1| 156 MSMCGMRFFSVYQGyegaegHKGEYANVIAQFAddiahSRAPELYGDGTQTRDFTHVSDVVRALELAAEHEL----- 227
                                       677779999999554666665666666666666333333444555555566666666666666655555555..... PP

                                       -EEEE---BS-EEHHHHHHHHHHHHC CS
                     RmlD_sub_bind 207 agvyHlanegetswlefArailkeag 232
                                        gvy ++  + ts  e+ +   +++g
  gi|336253770|ref|YP_004596877.1| 228 EGVYNVGTGDRTSFNELVDLLNRTLG 253
                                       48888888888887777666655555 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 !   43.7   0.8   8.6e-15   1.7e-11       1     230 [.       7     224 ..       7     230 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 8.6e-15
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtGgaGF+G++l +eL +++++  v  + l e ++l+++++ v+   v+e D+           +vdvv+hla+l+
  gi|336253770|ref|YP_004596877.1|   7 LVTGGAGFIGSNLANELASRNDVIAVDDCYLGEADNLSDDVEFVEAS-VLEDDL---------PTDVDVVFHLAALS 73 
                                       69*******************97777777788899998888777776.555554.........3689********99 PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                         a  +    +  +vnv+G  n +e +++ g  ++vY S+ ++ g   + e+     E+   +   +  y  sK   
  gi|336253770|ref|YP_004596877.1|  74 SYAMhEEDPTRGTRVNVEGFVNTVEQARQDGCDTVVYASTSSIYGT--RTEPTP---EDV--PVAVNTGYEASKLAR 143
                                       8877355667889*****************************9999..666655...444..445667788888888 PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiy..........GegdkllvpllkqlaklglalfkigdeevlsdrvYvgN 220
                                       E++        ++n   +  c +R   +y          Ge+ +++ +++  +a+++ a   +gd  ++ d++ v  
  gi|336253770|ref|YP_004596877.1| 144 ERYAEY-----FSNHYGMSMCGMRFFSVYqgyegaeghkGEYANVIAQFADDIAHSR-APELYGDGTQTRDFTHVSD 214
                                       887543.....4444557778888888877666666666677777777777777777.6667788888888888888 PP

                         3Beta_HSD 221 vawahilAar 230
                                       v+ a  lAa 
  gi|336253770|ref|YP_004596877.1| 215 VVRALELAAE 224
                                       8888777775 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00072       1.4       1      21 [.       6      26 ..       6      37 .. 0.88
   2 !   26.3   0.0   1.8e-09   3.6e-06      76     128 ..      61     113 ..      46     123 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00072
                                      EEEETTTSHHHHHHHHHHHHH CS
                   Polysacc_synt_2  1 vlvtGagGsiGselvrqilkk 21
                                      +lvtG++G iGs+l ++++++
  gi|336253770|ref|YP_004596877.1|  6 ILVTGGAGFIGSNLANELASR 26
                                      89*************999876 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.8e-09
                                       .T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                   Polysacc_synt_2  76 lkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                       ++vdvvfh AAl    + ee p+ + + Nv g  n++e a + g ++vv+ St
  gi|336253770|ref|YP_004596877.1|  61 TDVDVVFHLAALSSYAMHEEDPTRGTRVNVEGFVNTVEQARQDGCDTVVYAST 113
                                       689*************************************************9 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0014       2.7       1      21 [.       8      28 ..       8      37 .. 0.86
   2 !   24.4   0.1   7.3e-09   1.5e-05      84     206 ..      59     166 ..      53     219 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0014
                                      EE-TTSHHHHHHHHHHHHHS- CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttp 21
                                      +TG+ GF+G+ L ++L ++++
  gi|336253770|ref|YP_004596877.1|  8 VTGGAGFIGSNLANELASRND 28
                                      7***************98876 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 7.3e-09
                                       HHHH--EEEE--SS-S....STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H.... CS
                     NAD_binding_4  84 laeevdviihsaAtvn...fdepykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegek 157
                                       l   vdv++h aA  +   ++e+  +  rvNveG ++ +e a++     ++++ ST+ ++g+r++   e        
  gi|336253770|ref|YP_004596877.1|  59 LPTDVDVVFHLAALSSyamHEEDPTRGTRVNVEGFVNTVEQARQDGCD-TVVYASTSSIYGTRTEPTPE-------- 126
                                       5678*********9772224556667999**************99888.*******9999999966544........ PP

                                       ..HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EE CS
                     NAD_binding_4 158 eekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsii 206
                                                +    ++++Ye sK + E+  +  +++ g+ ++ +R   +
  gi|336253770|ref|YP_004596877.1| 127 ---------DVPVAVNTGYEASKLARERYAEYFSNHYGMSMCGMRFFSV 166
                                       .........4445555566666666666666655555555555555555 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 !   15.1   0.0   7.9e-06     0.016       1     129 [.      10     144 ..      10     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.9e-06
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT..HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-....... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..peklaeleaeeglevvegdvtdvedlaealkgadaVvsal....... 68 
                                       G+ G +G+ l++el++r+  +v a+  +    ++++l+  + +e ve++v++ +d     +++d+V+  +       
  gi|336253770|ref|YP_004596877.1|  10 GGAGFIGSNLANELASRN--DVIAV-DDcyLGEADNLS--DDVEFVEASVLE-DD---LPTDVDVVFHLAalssyam 77 
                                       999**************6..77775.443456667665..79********94.44...4578999976665666654 PP

                                       ......--TCC...HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHH CS
                    NAD_binding_10  69 ......ggggk...deegaknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaee 129
                                                 +   + eg +n+v+ a++ g   +v+ s+  ++    ++++e +  ++++ ++a + a e
  gi|336253770|ref|YP_004596877.1|  78 heedptR---GtrvNVEGFVNTVEQARQDGCDTVVYASTSSIYGTRTEPTPEDVPVAVNTGYEASKLARE 144
                                       4443321...02335555************************9988888887777777777776555443 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0015         3       4      23 ..       7      26 ..       5      32 .. 0.90
   2 ?    3.3   0.0     0.033        66      81     144 ..      62     120 ..      40     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
                                      EEETTTSHHHHHHHHHHHHH CS
                                KR  4 litGGlGgLGlelarwlaek 23
                                      l+tGG+G +G  la+ la++
  gi|336253770|ref|YP_004596877.1|  7 LVTGGAGFIGSNLANELASR 26
                                      9****************986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.033
                                       ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--T CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsa 144
                                        +  v+h A ++       m +ed ++ ++  v+G  n  e  +++  d +v ++S ++++g++
  gi|336253770|ref|YP_004596877.1|  62 DVDVVFHLAALSSY----AMHEEDPTRGTRVNVEGFVNTVEQARQDGCDTVV-YASTSSIYGTR 120
                                       56667777766654....57889999999999************99999865.78889998876 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0016       3.1       3      28 ..       6      31 ..       4      54 .. 0.85
   2 ?    2.7   0.0     0.037        73      95     161 ..      76     148 ..      40     169 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0016
                                      EEEESTTSHHHHHHHHHHHHTT-EEE CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvv 28
                                      +lvtG+++ IG ++a+ela+++  ++
  gi|336253770|ref|YP_004596877.1|  6 ILVTGGAGFIGSNLANELASRNDVIA 31
                                      89*****************9965444 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.037
                                       GCSHHHHHHHHHHHTHHHHHHHHHHHHH....HHHCTTEEEEEEEEGGG..TSB-TTBHHHHHHHHHHHHHHH CS
                         adh_short  95 elseeewervievNltgvflltravlpa....mlkqssGrIvnvsSvag..kvpvagvaaYsAsKaavagltr 161
                                        + ee+  r   vN+ g +++++++ +      + +s  +I  +    +   vpva+ + Y AsK a + +++
  gi|336253770|ref|YP_004596877.1|  76 AMHEEDPTRGTRVNVEGFVNTVEQARQDgcdtVVYASTSSIYGTRTEPTpeDVPVAVNTGYEASKLARERYAE 148
                                       5555566666666666666666665443111122333333322222222224677888888888888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.37
# Mc/sec: 2440.04
//
Query:       gi|336253771|ref|YP_004596878.1|  [L=431]
Description: nucleotide sugar dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-51  173.0   0.1      8e-51  172.3   0.1    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    1.7e-33  114.7   0.0    2.9e-33  113.9   0.0    1.4  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    4.9e-26   91.2   0.0    1.4e-25   89.7   0.0    1.8  1  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    1.4e-05   25.1   0.0    5.6e-05   23.2   0.0    2.0  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    2.8e-05   23.8   0.0    9.1e-05   22.1   0.0    1.8  2  ApbA            Ketopantoate reductase PanE/ApbA
    3.9e-05   23.6   0.1    7.6e-05   22.7   0.1    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0004   20.9   1.0     0.0068   16.9   0.3    3.1  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0011   18.2   0.1      0.002   17.4   0.1    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0024   18.4   0.8       0.67   10.6   0.0    3.8  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.015   15.5   5.4      0.049   13.9   0.3    3.3  3  TrkA_N          TrkA-N domain
      0.034   14.4   0.1       0.11   12.7   0.1    2.0  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.045   13.6   0.3       0.13   12.1   0.3    1.9  1  Rossmann-like   Rossmann-like domain
      0.053   14.2   0.1        3.7    8.3   0.0    3.4  3  ThiS            ThiS family
      0.054   13.5   0.3       0.17   11.9   0.3    1.9  1  DUF3320         Protein of unknown function (DUF3320)
        0.1   12.0   0.1       0.57    9.5   0.0    2.1  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 !  172.3   0.1   6.7e-54     8e-51       1     186 [.       1     187 [.       1     188 [. 0.96

  Alignments for each domain:
  == domain 1  score: 172.3 bits;  conditional E-value: 6.7e-54
                                       SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveea 77 
                                       m++s+iG+GYvG + aa+la +ghev+ v ide  vd++n+g+ pi e gLee +++++  + l++ttd+++ v ++
  gi|336253771|ref|YP_004596878.1|   1 MNVSIIGSGYVGTTVAACLADLGHEVVNVEIDEDIVDAINAGEAPIHESGLEERIAEHA-GTALRATTDYDE-VLDT 75 
                                       89*******************************************************99.89*********9.99** PP

                                       SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHC...EEEEEE-S---TTHHHHCHHHHHHHHCSS-.TTCEEEE CS
                    UDPG_MGDP_dh_N  78 dvifiaVgTPskkkgkaaDlkyvesaarsiaealkk...gkvvvvkSTvpvgtaeelvkkileeaskkk.gvdfdvv 150
                                       dv++++ +TP+++ + + Dl  + + a+++++al     +++vvvkSTv +gt+ee+v +ilee+s +  g  +dv+
  gi|336253771|ref|YP_004596878.1|  76 DVTLLCLPTPQSD-DGSLDLAPMRAGAEMLGDALAVkddDHLVVVKSTVLPGTTEEVVAPILEEQSGTAiGDGIDVA 151
                                       *************.7778**************99766679*************************9988999***** PP

                                       E------TTSHHHHHHS-S-EEEEESSCHHHHHHHH CS
                    UDPG_MGDP_dh_N 151 snPEflregsavkdllnpdrvviGveekkaeaalee 186
                                       +nPEflr g+av+d+l+pd+vv+G++ ++a++ l++
  gi|336253771|ref|YP_004596878.1| 152 MNPEFLRMGTAVQDFLEPDKVVLGTRTDAAAEQLRD 187
                                       *************************99998877765 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 !  113.9   0.0   2.4e-36   2.9e-33       1      93 [.     206     298 ..     206     299 .. 0.99

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 2.4e-36
                      UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaee 77 
                                       ++AEliK+a+Nafla k+s++N+l+n+++++g+d+ eV+eavgld ri+++f++ glG+GGsc+pkDv+aL a a+e
  gi|336253771|ref|YP_004596878.1| 206 REAELIKYANNAFLASKVSLVNDLGNIAKEYGADAYEVLEAVGLDDRISERFMRSGLGWGGSCFPKDVAALRAGARE 282
                                       68*************************************************************************** PP

                      UDPG_MGDP_dh  78 lgleaelleavrevNe 93 
                                       +g+e+ell+a+++vN+
  gi|336253771|ref|YP_004596878.1| 283 QGYEPELLDAAVAVND 298
                                       ***************8 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 !   89.7   0.0   1.2e-28   1.4e-25       1     102 [.     320     416 ..     320     418 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 1.2e-28
                                       EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--G CS
                    UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehd 77 
                                       a+lGl+fK++tdD+R+S+ald++e L+e+ga v++yDP++ ++ +e++++  ++e++ds+++al+ga+ +v++t+++
  gi|336253771|ref|YP_004596878.1| 320 AVLGLSFKPGTDDIRKSRALDVVEYLRERGAAVVAYDPVAVDNVREQYPD-LEIEYADSAASALEGANGAVVATDWP 395
                                       89********************************************9997.6************************* PP

                                       GGGGS-HHHHHHCCSS-EEEESSS- CS
                    UDPG_MGDP_dh_C  78 efkeldlaklkelmkpavvfDgrnv 102
                                       ef++l++    + m+++v++Dgr++
  gi|336253771|ref|YP_004596878.1| 396 EFDDLTF----DGMAKRVLVDGRRI 416
                                       ****966....66788999999976 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 !   23.2   0.0   4.7e-08   5.6e-05       2      79 ..       3      84 ..       2      95 .. 0.81
   2 ?   -2.2   0.0       3.1   3.7e+03      73     126 ..     115     171 ..     107     183 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.7e-08
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSS..BTTTBTT----...TTEEEES-HHHHHTT--EEEE CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehe..nvkyLpgiklp...enlvattdlaealkgadiivl 75
                                      ++++G+G  Gt++A+ la+ ghev+    +e+ +++in+ +   ++  L++   +   ++l+attd +e+l+  d+ +l
  gi|336253771|ref|YP_004596878.1|  3 VSIIGSGYVGTTVAACLADLGHEVVNVEIDEDIVDAINAGEApiHESGLEERIAEhagTALRATTDYDEVLD-TDVTLL 80
                                      99************************************8654226667777443311167999999999997.777777 PP

                                      ---H CS
                    NAD_Gly3P_dh_N 76 vvPs 79
                                       +P+
  gi|336253771|ref|YP_004596878.1| 81 CLPT 84
                                      7776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.1
                                       EEE---HHHHHHHHHHHCCC--TT-EEEE---SE...ET.TTEEHHHHHHHHH-S-- CS
                    NAD_Gly3P_dh_N  73 ivlvvPsqalrevlkklkgllkkkailvsliKGi...eegtlkllsevieeelkeek 126
                                        ++vv s +l  + +++ + + +++    +  Gi    + +  ++ ++++++l+ +k
  gi|336253771|ref|YP_004596878.1| 115 HLVVVKSTVLPGTTEEVVAPILEEQSGTAIGDGIdvaMNPEFLRMGTAVQDFLEPDK 171
                                       467788888888888888877777777777777765544466777777777777764 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   7.6e-08   9.1e-05       2      90 ..       4      96 ..       3     103 .. 0.87
   2 ?   -2.1   0.0       2.3   2.8e+03      68      96 ..     168     197 ..     151     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.6e-08
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEECEEECCH..SCCCCS-ESEEEE-S CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrppealsae..ekselepidlvivtv 76
                                       i+G+G +G+++aa+La  g++v+ +  ++  ++a++     ++++g +e+i++   ++  +  +  e  + d+ ++++
  gi|336253771|ref|YP_004596878.1|  4 SIIGSGYVGTTVAACLADLGHEVVNVEIDEdIVDAINAGEAPIHESGlEERIAEHAGTALRAttDYDEVLDTDVTLLCL 82
                                      79****************************99***************988888887776666687889999******** PP

                                      SGGGHHHHHHHHGG CS
                              ApbA 77 Kayqteealeeikp 90
                                      ++ q ++   +++p
  gi|336253771|ref|YP_004596878.1| 83 PTPQSDDGSLDLAP 96
                                      **999886555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.3
                                       -ESEEEE-SSGGGHHHHHHH.HGGGECTCE CS
                              ApbA  68 pidlvivtvKayqteealee.ikplldpnt 96 
                                       + d v++ + +  ++e+l++ ++p+l++++
  gi|336253771|ref|YP_004596878.1| 168 EPDKVVLGTRTDAAAEQLRDlYAPILENDS 197
                                       567777777777888888887888888775 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 !   22.7   0.1   6.3e-08   7.6e-05       1      81 [.       2      77 ..       2      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.3e-08
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC- CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavda 79
                                      +v +iG+G +G+ +aa +a  g+eVv v+i+e+++++ ++  +      +++  l+e  +e+a + +++ttd++e+ d+
  gi|336253771|ref|YP_004596878.1|  2 NVSIIGSGYVGTTVAACLADLGHEVVNVEIDEDIVDAINAGEAP-----IHESGLEERIAEHAGTALRATTDYDEVLDT 75
                                      699*****************************999876665544.....333344556667888899999999999988 PP

                                      SE CS
                           3HCDH_N 80 dl 81
                                      d+
  gi|336253771|ref|YP_004596878.1| 76 DV 77
                                      86 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   5.7e-06    0.0068       2      35 ..       3      36 ..       2      67 .. 0.88
   2 ?   -1.9   0.0       4.3   5.2e+03      17      48 ..     106     137 ..     100     161 .. 0.60
   3 ?   -3.0   0.0       9.2   1.1e+04      29      59 ..     151     176 ..     142     182 .. 0.70
   4 ?    0.2   0.0      0.98   1.2e+03      21      46 ..     219     244 ..     208     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.7e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v ++G+Gy+g  +A+ la+lg++V  ve  + + 
  gi|336253771|ref|YP_004596878.1|  3 VSIIGSGYVGTTVAACLADLGHEVVNVEIDEDIV 36
                                      779*********************9999887776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.3
                                       HHHHTTSEEEEEESSSSSSTTSSHHHHHHHHH CS
                         Pyr_redox  17 alaelgkkVtvversdkllrllDeeaskilqe 48 
                                        + + +++ ++v+ ++++l++  ee+ + + e
  gi|336253771|ref|YP_004596878.1| 106 DALAVKDDDHLVVVKSTVLPGTTEEVVAPILE 137
                                       55555666688888888885555444433333 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 9.2
                                       ESSSSSSTTSSHHHHHHHHHHHHHTTEEEEC CS
                         Pyr_redox  29 ersdkllrllDeeaskilqeklekngievll 59 
                                        +++++l      +++++q+ le  ++ + +
  gi|336253771|ref|YP_004596878.1| 151 AMNPEFL-----RMGTAVQDFLEPDKVVLGT 176
                                       5666667.....6888888888877665544 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.98
                                       TTSEEEEEESSSSSSTTSSHHHHHHH CS
                         Pyr_redox  21 lgkkVtvversdkllrllDeeaskil 46 
                                       l++kV++v    ++ + ++++a ++l
  gi|336253771|ref|YP_004596878.1| 219 LASKVSLVNDLGNIAKEYGADAYEVL 244
                                       899***********999999987766 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 !   17.4   0.1   1.7e-06     0.002     145     201 ..       3      64 ..       1      91 [. 0.66

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.7e-06
                                       EEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-....HHHHHHHHHHHHHT.TEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx.xxxxx RF
                       Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgkevtlveardrllrald....kelsaaleealeke.Gvevk 201
                                       + ++G+Gy+G+ +Aa la+lg+ev+ ve  + ++ a +    +  +  lee++ ++ G +++
  gi|336253771|ref|YP_004596878.1|   3 VSIIGSGYVGTTVAACLADLGHEVVNVEIDEDIVDAINageaPIHESGLEERIAEHaGTALR 64 
                                       789********************999998888884444111123333333333333344444 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 !   10.6   0.0   0.00056      0.67       2      72 ..       3      85 ..       2      96 .. 0.74
   2 ?    2.9   0.0      0.14   1.6e+02      21      74 ..     164     226 ..     155     240 .. 0.72
   3 ?   -1.0   0.0       2.3   2.7e+03      44      78 ..     368     401 ..     339     412 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00056
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...................-EEECECHHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...................vkvtavdneeaaee 61
                                      + iiG+G +g ++a  l+  g   he+v + + +++ ++++ ++ +                    ++t+ d+ e+++ 
  gi|336253771|ref|YP_004596878.1|  3 VSIIGSGYVGTTVAACLADLG---HEVVNV-EIDEDIVDAI-NAGEapihesgleeriaehagtaLRATT-DYDEVLD- 74
                                      78*******************...****44.5555544444.3333467788888888888887666666.7777775. PP

                                      -SEEEE-S-HH CS
                     F420_oxidored 62 advvvlavkpe 72
                                      +dv +l++++ 
  gi|336253771|ref|YP_004596878.1| 75 TDVTLLCLPTP 85
                                      88888887765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.14
                                       TTS.-GGCEEEEEESSCCCHHHHHHHHC..........-EEECECHHHHHHH-SEEEE-S-HHHH CS
                     F420_oxidored  21 aga.qpheivvansrnpekaeelaeelg..........vkvtavdneeaaeeadvvvlavkpedv 74 
                                       +++ +p ++v++ +r+   ae+l++ +           v++     +e+++ a+  +la k + v
  gi|336253771|ref|YP_004596878.1| 164 QDFlEPDKVVLG-TRTDAAAEQLRDLYApilendsthlVETDV-REAELIKYANNAFLASKVSLV 226
                                       556678899977.999999999999998777777776544444.667777777777777776655 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.3
                                       HHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHH CS
                     F420_oxidored  44 eelgvkvtavdneeaaeeadvvvlavkpedveevl 78 
                                        +l+++    +++ a+e a+  v+a  +  ++++ 
  gi|336253771|ref|YP_004596878.1| 368 PDLEIEYAD-SAASALEGANGAVVATDWPEFDDLT 401
                                       444455555.7888999999999999988888765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   4.1e-05     0.049       3      59 ..       5      60 ..       3      68 .. 0.81
   2 ?    0.6   0.1      0.54   6.4e+02      15      51 ..     165     199 ..     157     254 .. 0.67
   3 ?    1.2   0.1      0.34   4.1e+02      13      48 ..     341     376 ..     337     390 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                                      EES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTT CS
                            TrkA_N  3 iiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeag 59
                                      iiG G vG+++a  L + g+ +vv ++ de+ v+ + + ++  ++ ++ +e + e+ag
  gi|336253771|ref|YP_004596878.1|  5 IIGSGYVGTTVAACLADlGH-EVVNVEIDEDIVDAINAGEA-PIHESGLEERIAEHAG 60
                                      9****************888.5***********99876554.4566666666666665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.54
                                       HHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTS CS
                            TrkA_N  15 eeLseggkdvvvidkdeerveelreeglevvvgdatd 51 
                                       + L+ ++  vv+  + ++++e+lr+  ++++  d t+
  gi|336253771|ref|YP_004596878.1| 165 DFLEPDK--VVLGTRTDAAAEQLRDLYAPILENDSTH 199
                                       4443333..6666667777888888888888877774 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.34
                                       HHHHHHHTTEEEEEEESSHHHHHHHHHTT..SEEEES- CS
                            TrkA_N  13 laeeLseggkdvvvidkdeerveelreeg..levvvgd 48 
                                       ++e+L+e+g    v+  d+ +v+++re+   le+ ++d
  gi|336253771|ref|YP_004596878.1| 341 VVEYLRERG--AAVVAYDPVAVDNVREQYpdLEIEYAD 376
                                       788999977..688889999999998887444455555 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   9.4e-05      0.11       1      31 [.       5      35 ..       5      75 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.4e-05
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31
                                      I+G+G  G + A+ La+ g++v+ +e  +++
  gi|336253771|ref|YP_004596878.1|  5 IIGSGYVGTTVAACLADLGHEVVNVEIDEDI 35
                                      9*********************999988887 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00011      0.13      12      40 ..       2      30 ..       1      63 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                     Rossmann-like 12 svGiisaGrvGtalgaaleraghvvvgis 40
                                      +v ii++G vGt+++a l+  gh vv + 
  gi|336253771|ref|YP_004596878.1|  2 NVSIIGSGYVGTTVAACLADLGHEVVNVE 30
                                      799**********************9986 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0031       3.7      21      60 ..      12      44 ..      10      49 .. 0.83
   2 ?    1.1   0.0      0.55   6.5e+02      24      64 ..     128     165 ..     123     169 .. 0.79
   3 ?   -1.1   0.0       2.5     3e+03      42      55 ..     290     303 ..     271     322 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0031
                                      TSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGC.CTTTS CS
                              ThiS 21 gstvaelleaLgerypelalerrvavavNgeivpr.lwldt 60
                                      g+tva+ l+ Lg  +      ++v+v+++++iv+  +  ++
  gi|336253771|ref|YP_004596878.1| 12 GTTVAACLADLG--H------EVVNVEIDEDIVDAiNAGEA 44
                                      79*********9..4......88**********99665555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.55
                                       HHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--T CS
                              ThiS  24 vaelleaLgerypelalerrvavavNgeivprlwldtelkd 64 
                                        +e+++ + e++++ a  +++ va+N e+++     t+++d
  gi|336253771|ref|YP_004596878.1| 128 TEEVVAPILEEQSGTAIGDGIDVAMNPEFLRM---GTAVQD 165
                                       56666666666667777899**********99...998887 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.5
                                       TTEEEEETTEEEGC CS
                              ThiS  42 rrvavavNgeivpr 55 
                                          avavN+e  +r
  gi|336253771|ref|YP_004596878.1| 290 LDAAVAVNDEQPRR 303
                                       55688999886555 PP

>> DUF3320  Protein of unknown function (DUF3320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00014      0.17      16      40 ..      36      60 ..      25      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                           DUF3320 16 iakIVevEGPihedeLarRilrawG 40
                                      ++ I + E+Pihe+ L  Ri+++ G
  gi|336253771|ref|YP_004596878.1| 36 VDAINAGEAPIHESGLEERIAEHAG 60
                                      6677789****************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 ?    9.5   0.0   0.00048      0.57      38      70 ..       2      34 ..       1      57 [. 0.83
   2 ?   -0.6   0.0      0.63   7.5e+02      50      74 ..     340     364 ..     338     384 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00048
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                                       v iiG G +G++va +l+ +g +v+ ++  ++
  gi|336253771|ref|YP_004596878.1|  2 NVSIIGSGYVGTTVAACLADLGHEVVNVEIDED 34
                                      689**********************98877654 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.63
                                       HHHHHHHHTT-EEEEESSSHHHHHC CS
                      2-Hacid_dh_C  50 avakrlkafgmkviaydrskkkeee 74 
                                        v ++l++ g+ v+ayd+   ++ +
  gi|336253771|ref|YP_004596878.1| 340 DVVEYLRERGAAVVAYDPVAVDNVR 364
                                       578899999********99776552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 3208.44
//
Query:       gi|336253772|ref|YP_004596879.1|  [L=338]
Description: family 2 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for complete 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-18   67.1   0.1    2.3e-18   66.6   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    2.2e-10   40.8   0.0    3.4e-10   40.2   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0034   17.9   0.0     0.0071   16.8   0.0    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2
     0.0064   16.7   1.8      0.011   16.0   1.8    1.3  1  UPF0060          Uncharacterised BCR, YnfA/UPF0060 family
  ------ inclusion threshold ------
        0.1   13.1   0.0       0.26   11.8   0.0    1.6  1  CoA_binding_2    CoA binding domain
       0.11   11.6   0.0       0.18   11.0   0.0    1.2  1  CobD_Cbib        CobD/Cbib 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 !   66.6   0.1   7.7e-22   2.3e-18       1     129 [.      36     154 ..      36     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 7.7e-22
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       ++ ipt Ne++t+  +++   +q       ++v+D gS D+t+ei++++     +  v+ ++ ++Gk+ a+++++++
  gi|336253772|ref|YP_004596879.1|  36 CILIPTLNEAATIGDVIDGFEEQ---GYTNVVVIDGGSDDDTQEIARDH-----GAQVLVQS-GEGKGQAVREAVDY 103
                                       699********************...88889999999************.....9*******.66************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiern 129
                                        +  y+l lD D ++dp++ e+++e+l + g+  v+g+r++  +++  +  n
  gi|336253772|ref|YP_004596879.1| 104 IDVPYVLMLDGDGTYDPNDAEQMLEPLAQ-GYEHVIGNRFADMDDDAMKALN 154
                                       *****************************.999******9988777666655 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 !   40.2   0.0   1.1e-13   3.4e-10       4     210 ..      35     222 ..      32     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.1e-13
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       + +l+pt+ne++++g+v++ +  q y  + vvv++ +sd++t e a+    ++++   +v+v++      gk +a+ 
  gi|336253772|ref|YP_004596879.1|  35 VCILIPTLNEAATIGDVIDGFEEQGY--TNVVVIDGGSDDDTQEIAR----DHGA---QVLVQSG----EGKGQAVR 98 
                                       789*******************9755..78999999****9988776....4655...6777766....48999999 PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarralgv 157
                                       ea++ ++  +vl++D+D   +P+  +++l  + ++++++v +++f++ ++ ++ al+   f+ r + ++++r+  g+
  gi|336253772|ref|YP_004596879.1|  99 EAVDYIDVPYVLMLDGDGTYDPNDAEQMLEPL-AQGYEHVIGNRFADMDDDAMKALNG--FGNRMI-NRSFRLIHGA 171
                                       *******************************9.*********************9999..666666.4555544443 PP

                   Glyco_tranf_2_3 158 ...ltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavr 210
                                          ++l+G   +++++ +++l  ld    +t   el++++ ++g++t +vp +  +
  gi|336253772|ref|YP_004596879.1| 172 dyeDILSG-YRAFTTDSFDRL-SLDS-DGFTIETELAVECVKHGIDTTVVPVS--Y 222
                                       11366677.358899999999.4444.45666789************999987..4 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 !   16.8   0.0   2.4e-06    0.0071       2      45 ..      43      86 ..      42     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.4e-06
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkelpevkl 45
                                      nea++++ +++  ++ g+++++v+d +s+D+t +i + + +  l
  gi|336253772|ref|YP_004596879.1| 43 NEAATIGDVIDGFEEQGYTNVVVIDGGSDDDTQEIARDHGAQVL 86
                                      9***********************************99855333 PP

>> UPF0060  Uncharacterised BCR, YnfA/UPF0060 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.8   3.6e-06     0.011      38     104 ..     240     309 ..     230     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.6e-06
                           UPF0060  38 aaillavygflatlqp.aafGrvyaa..yGGvfvvlallwglvvdgvkldlydwiGalialvGvlvilya 104
                                       ++i+la+y++  t +p   fG   aa    G  +++ +lw +v  gv  + + ++ a+  l+Gv +++++
  gi|336253772|ref|YP_004596879.1| 240 GTIILALYSLAKTNNPlFYFGSLGAAglVTGSLIAVYVLWEWVQYGVGHNILALVSAAAILLGVQLLMFG 309
                                       689*************88999998884457999***********************************97 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.6e-05      0.26      35     106 ..      13      86 ..       2      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.6e-05
                                       SS-SEETTEES----T......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  35 pkeeeilgekvyaslae.d.pepvdlvdvftppeatpeivkealalgakavwlqpgsedeeaaelaeeagirvv 106
                                         ++ei    + +++ e + +e++ l+  +  ++++ ++++ ++++g   v++  g  d+++ e+a+++g +v+
  gi|336253772|ref|YP_004596879.1|  13 DGSGEITVMSESETTREiSaEEVCILIPTLNEAATIGDVIDGFEEQGYTNVVVIDGGSDDDTQEIARDHGAQVL 86 
                                       5566777777777777655455555666666777788999999****************************997 PP

>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.9e-05      0.18      15     119 ..     230     333 ..     223     337 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.9e-05
                         CobD_Cbib  15 rrllhPvvligklisalekrlrkakkerlaGvllalllvllallvallllllalaall..glvlealllkltlalrs 89 
                                       ++ lhPv+  g++i al ++ ++++     G l a+ lv+++l+++++l   + ++ +   +++ + +++++l+++ 
  gi|336253772|ref|YP_004596879.1| 230 ETNLHPVRDGGTIILALYSLAKTNNPLFYFGSLGAAGLVTGSLIAVYVLWEWV-QYGVghNILALVSAAAILLGVQL 305
                                       4568*************997765556778999999999999999888887754.33233344555666667777777 PP

                         CobD_Cbib  90 Lleevrk.vakalkgdleaaReavsmiVgRd 119
                                       L   v + ++ +l+    + R+++++i +R+
  gi|336253772|ref|YP_004596879.1| 306 LMFGVLSdMLVTLH---REQRRRLEHIARRN 333
                                       76665544666664...68899999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2530.64
//
Query:       gi|336253773|ref|YP_004596880.1|  [L=109]
Description: hypothetical protein Halxa_2382 [Halopiger xanaduensis SH-6]
Scores for 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  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 794.67
//
Query:       gi|336253774|ref|YP_004596881.1|  [L=69]
Description: CopG family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00064   19.6   0.1     0.0011   18.8   0.0    1.5  2  RHH_1         Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.083   13.2   0.1       0.19   12.0   0.1    1.6  2  PG_binding_2  Putative peptidoglycan binding domain
       0.18   11.6   2.7       0.34   10.7   2.7    1.5  1  SHOCT         Short C-terminal domain


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 !   18.8   0.0   1.9e-07    0.0011       2      34 ..       5      38 ..       5      43 .. 0.94
   2 ?   -2.8   0.0       1.2   7.3e+03      14      19 ..      55      60 ..      50      63 .. 0.50

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.9e-07
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlr 34
                                      ++++++++l++r++e ++ +  +S S+l+R +lr
  gi|336253774|ref|YP_004596881.1|  5 TTVSIPKDLADRVEETIDGTSfQSTSDLVRFLLR 38
                                      69****************************8887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                      HHHHHH CS
                             RHH_1 14 Ldelar 19
                                      ++e+ +
  gi|336253774|ref|YP_004596881.1| 55 FEEITE 60
                                      444433 PP

>> PG_binding_2  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.66   3.9e+03      15      24 ..      11      20 ..       4      30 .. 0.65
   2 ?   12.0   0.1   3.2e-05      0.19       8      30 ..      45      67 ..      41      69 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.66
                      PG_binding_2 15 edvaeevqaa 24
                                      +d a+ v++ 
  gi|336253774|ref|YP_004596881.1| 11 KDLADRVEET 20
                                      5666665554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.2e-05
                      PG_binding_2  8 eeervlaedvaeevqaaLsrLGy 30
                                      ++e +l+e++ ee+ ++L++LGy
  gi|336253774|ref|YP_004596881.1| 45 QKEGELTEAEFEEITEQLRGLGY 67
                                      68889****************** PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.7   5.6e-05      0.34      12      22 ..      47      57 ..      46      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.6e-05
                             SHOCT 12 rGeIteEEFea 22
                                      +Ge+te+EFe+
  gi|336253774|ref|YP_004596881.1| 47 EGELTEAEFEE 57
                                      6*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 518.11
//
Query:       gi|336253775|ref|YP_004596882.1|  [L=147]
Description: hypothetical protein Halxa_2384 [Halopiger xanaduensis SH-6]
Scores for 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  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1159.98
//
Query:       gi|336253776|ref|YP_004596883.1|  [L=227]
Description: hypothetical protein Halxa_2385 [Halopiger xanaduensis SH-6]
Scores for 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  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); 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:                         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: 00:00:00.41
# Mc/sec: 1669.16
//
Query:       gi|336253777|ref|YP_004596884.1|  [L=246]
Description: Glyoxalase/bleomycin resistance protein/dioxygenase [Halopiger xanaduensis SH-6]
Scores for 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-10   40.1   0.1    4.1e-06   27.0   0.0    3.0  2  Glyoxalase       Glyoxalase/Bleomycin resistance protein/Diox
    1.9e-08   35.1   4.6    0.00037   21.3   0.8    2.2  2  Glyoxalase_6     Glyoxalase-like domain
  ------ inclusion threshold ------
      0.014   15.4   0.0        3.3    7.7   0.0    3.4  4  Glyoxalase_2     Glyoxalase-like domain
      0.058   13.5   0.2         37    4.5   0.0    3.5  3  DUF397           Domain of unknown function (DUF397)
       0.17   11.8   0.0       0.35   10.8   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain


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 !   27.0   0.0   1.1e-09   4.1e-06       2     128 .]       5     122 ..       4     122 .. 0.88
   2 !    8.5   0.1   0.00061       2.2       5      32 ..     138     164 ..     134     244 .. 0.60

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.1e-09
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEE.EESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdn.teeteglriaffhaggghielvlneapsgaakhvkkieetvhhv 77 
                                       ++++al v+ le + +FY++ L +++ +  +  t e + +++ +++   g   lvl+++++ ++ +       + h+
  gi|336253777|ref|YP_004596884.1|   5 LAWLALEVKYLEPAQRFYAETLEMDVRDGREErTRESGEANGDALTFAAGETDLVLRRPTGVPRGGL------HTHF 75 
                                       6677888999999***************999655666888999999999999999999999999999......589* PP

                                       EEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  78 afialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       af   + e  ++++drl+e+    ++ ++ + fga  s y +DpdG+ +e+
  gi|336253777|ref|YP_004596884.1|  76 AFSIPAAEY-DDWWDRLSERY---DGDLKETQFGAAKSLYLYDPDGNCVEL 122
                                       *****9999.*********98...8888889999999999*******9996 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00061
                                       EEEEESHHHHHHHHHHHHHTSEEEEEEE CS
                        Glyoxalase   5 vallvgdleksldFYtkvLGfklvkktd 32 
                                       v+l v  le++ +FY++ LGf+ v++  
  gi|336253777|ref|YP_004596884.1| 138 VVLEVESLERAESFYAD-LGFETVDRGS 164
                                       56778999*********.******9988 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   6.4e-06     0.023       2     102 ..       8     118 ..       7     122 .. 0.61
   2 !   21.3   0.8     1e-07   0.00037       2     104 ..     138     242 ..     137     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.4e-06
                      Glyoxalase_6   2 vvldaadpaalaaFwaaalgweveree....aaledpegvgpaaedaatllfqrvpe..........paknrvHldl 64 
                                       ++l ++  + + +F+a+ l+++v++ +     +  ++        ++  l f   ++          p +  +H+++
  gi|336253777|ref|YP_004596884.1|   8 LALEVKYLEPAQRFYAETLEMDVRDGReertRESGEA--------NGDALTFAAGETdlvlrrptgvP-RGGLHTHF 75 
                                       677888899999***********99994454222222........33333333333333555444543.457***** PP

                      Glyoxalase_6  65 avedldaevarlvalGArvlreprdgthgr.....vlaDPeGn 102
                                       a + ++ae +   +   ++ + + ++t+ +      l DP+Gn
  gi|336253777|ref|YP_004596884.1|  76 AFSIPAAEYDDWWDRLSERYDGDLKETQFGaakslYLYDPDGN 118
                                       9988877776666555555554444444445556788888887 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1e-07
                      Glyoxalase_6   2 vvldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe.....paknrvHldlav...edld 70 
                                       vvl ++  +++  F+a++ g+e +++ +   + + v++++ +++ l+++  +       a+  vH+dl      ++ 
  gi|336253777|ref|YP_004596884.1| 138 VVLEVESLERAESFYADL-GFETVDRGS---ERRRVRMNGPESMDLALELWEPqlgiaDARGGVHVDLGFeveGEVP 210
                                       789999999999***995.777777773...33444444557777777766666899866778*****554477788 PP

                      Glyoxalase_6  71 aevarlvalGArvlreprdgthgr.vlaDPeGneF 104
                                       ++v ++v+ G r ++++ d+   r v++DP+G+  
  gi|336253777|ref|YP_004596884.1| 211 TQVLEAVRDGVRSVERETDE---RvVVRDPDGHFL 242
                                       **************998886...44*******965 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.073   2.6e+02       6      27 ..      10      31 ..       6      37 .. 0.86
   2 ?    7.7   0.0   0.00091       3.3      99     115 ..     108     124 ..      77     125 .. 0.83
   3 ?    1.0   0.0       0.1   3.8e+02       4      21 ..     138     155 ..     135     164 .. 0.86
   4 ?   -1.8   0.0      0.77   2.8e+03      99     109 ..     231     240 ..     191     244 .. 0.54

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.073
                                      -EES-HHHHHHHHHHTT---EE CS
                      Glyoxalase_2  6 lvvkdieeskkFYedvlelkik 27
                                      l vk +e +++FY + le+ ++
  gi|336253777|ref|YP_004596884.1| 10 LEVKYLEPAQRFYAETLEMDVR 31
                                      56899999*********99885 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00091
                                       EEEEEE-TT--EEEEEE CS
                      Glyoxalase_2  99 rvirfyDpDkhiiEige 115
                                       + +++yDpD++ +E+g+
  gi|336253777|ref|YP_004596884.1| 108 KSLYLYDPDGNCVELGQ 124
                                       5689**********986 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.1
                                       ---EES-HHHHHHHHHHT CS
                      Glyoxalase_2   4 illvvkdieeskkFYedv 21 
                                       ++l v+ +e++ +FY d+
  gi|336253777|ref|YP_004596884.1| 138 VVLEVESLERAESFYADL 155
                                       67899**********986 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.77
                                       EEEEEE-TT-- CS
                      Glyoxalase_2  99 rvirfyDpDkh 109
                                       rv+ + DpD+h
  gi|336253777|ref|YP_004596884.1| 231 RVV-VRDPDGH 240
                                       222.4566666 PP

>> DUF397  Domain of unknown function (DUF397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.027        95      28      45 ..      38      55 ..      10      61 .. 0.77
   2 ?    4.5   0.0      0.01        37       5      19 ..     108     122 ..     107     136 .. 0.75
   3 ?    1.6   0.1     0.082   2.9e+02      26      42 ..     232     245 ..     204     246 .] 0.63

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.027
                            DUF397 28 vRDSkdpdgpvLtftpae 45
                                       R+S + +g +Ltf ++e
  gi|336253777|ref|YP_004596884.1| 38 TRESGEANGDALTFAAGE 55
                                      58888999******9987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.01
                            DUF397   5 KSsySgggggnCVEv 19 
                                       KS y  + +gnCVE+
  gi|336253777|ref|YP_004596884.1| 108 KSLYLYDPDGNCVEL 122
                                       66666676779***9 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.082
                            DUF397  26 vavRDSkdpdgpvLtft 42 
                                       v vRD   pdg  Ltft
  gi|336253777|ref|YP_004596884.1| 232 VVVRD---PDGHFLTFT 245
                                       44555...789999997 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.7e-05      0.35      88     116 ..     139     167 ..     134     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.7e-05
                   Acetyltransf_10  88 eltvnaspyavpfYeklGFkavgeeqeen 116
                                        l+v++   a++fY  lGF++v++  e+ 
  gi|336253777|ref|YP_004596884.1| 139 VLEVESLERAESFYADLGFETVDRGSERR 167
                                       58999999**************8877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 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:                        22  (0.00122706); 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 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1754.31
//
Query:       gi|336253778|ref|YP_004596885.1|  [L=165]
Description: hypothetical protein Halxa_2387 [Halopiger xanaduensis SH-6]
Scores for 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-41  140.9   5.2    4.3e-41  140.6   5.2    1.0  1  DUF892           Domain of unknown function (DUF892)
     0.0011   19.0   9.1     0.0032   17.4   9.1    1.9  1  Ferritin         Ferritin-like domain
  ------ inclusion threshold ------
      0.021   14.8   1.7      0.028   14.3   1.7    1.2  1  TraB             TraB family
      0.034   14.4   4.9       0.12   12.6   0.3    2.6  3  DUF4142          Domain of unknown function (DUF4142)
      0.088   13.5   2.4        8.8    7.1   1.0    2.4  2  Vir_act_alpha_C  Virulence activator alpha C-term
      0.095   13.1   4.8       0.15   12.4   4.5    1.5  1  Rubrerythrin     Rubrerythrin
       0.45   11.5   5.3        0.4   11.7   1.2    2.3  3  FKBP_N           Domain amino terminal to FKBP-type peptidyl-
       0.64   10.6   3.3       0.49   11.0   0.7    2.0  2  MerR-DNA-bind    MerR, DNA binding
       0.81   10.5   6.2       0.14   12.9   1.4    2.0  2  CHIP_TPR_N       CHIP N-terminal tetratricopeptide repeat dom
        2.2    9.0   8.5         52    4.6   0.2    3.2  3  CdiI_2           CdiI immunity protein
          3    7.9   4.9         16    5.6   4.9    2.0  1  DUF4337          Domain of unknown function (DUF4337)


Domain annotation for each model (and alignments):
>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.6   5.2   2.6e-44   4.3e-41       2     151 ..       6     154 ..       5     159 .. 0.96

  Alignments for each domain:
  == domain 1  score: 140.6 bits;  conditional E-value: 2.6e-44
                                       .HHHHHHHHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-------.-HHHHTTT CS
                            DUF892   2 leelfvdeLrDlyaaEkqllkalpkmakaaespeLkaaleqHleeTegqierLeqvferlgesasekkcdameglia 78 
                                        e+lfv  L+ +y+ E++l++al+++ ++++++eLk+ + +H eeT+++i+r+eqvfe+l+++a++++ +++eg+i+
  gi|336253778|ref|YP_004596885.1|   6 TEDLFVSGLKHAYYTEQRLVDALDELESSSSNEELKSGFAEHREETQQHIDRIEQVFEQLDADAEAEEDPVVEGMIQ 82 
                                       68*************************************************************************** PP

                                       -----------THHHHHHH...HHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            DUF892  79 egqelieeaaedeslkdaaliaaaqavehyEiAsYgtLialAeqlgekeaaklLeqtleeekatdekltelae 151
                                         +e+++++++d+ + d + iaa+q+ ehyEiA+Yg Li +A+qlg++++a++Le+t+ ee++  ++l+++ e
  gi|336253778|ref|YP_004596885.1|  83 AHEEFMDQNPSDQ-AIDRFNIAAGQKSEHYEIATYGNLIPMADQLGMDDVADMLEETMREEQDELDTLSQMGE 154
                                       ********77777.788889************************************************99977 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   9.1     2e-06    0.0032      32     135 ..      39     152 ..       8     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH.........C-SSSSCSSHHHH..HHHHHHHHHHHHH CS
                          Ferritin  32 glaeffdeqaeeerehadklaerilalGgtpvltraelee.........ieapkefgsveev..leaalehekkvte 97 
                                       +l+  f e+ ee ++h+d++ +   +l++++ +++  + e          ++ ++ + + +   ++a  ++e + ++
  gi|336253778|ref|YP_004596885.1|  39 ELKSGFAEHREETQQHIDRIEQVFEQLDADAEAEEDPVVEgmiqaheefMDQNPS-DQAIDRfnIAAGQKSEHYEIA 114
                                       5677799**********************77777776666996666655333333.2444441245567899999** PP

                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  98 slrelielaeeegDpatadfledfleeqeeheweleal 135
                                       ++ +li +a++ g +  ad+le+ ++e+++++++l+++
  gi|336253778|ref|YP_004596885.1| 115 TYGNLIPMADQLGMDDVADMLEETMREEQDELDTLSQM 152
                                       **********************************9876 PP

>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.7   1.7e-05     0.028      80     188 ..      54     156 ..       8     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                              TraB  80 lyarlqkalakrglplaaldkmkPwllalllslaelakkkagldpelvDrylaktakragkpvgglEtveeqlslls 156
                                        + r+++++++  l+++a +   P ++  ++++ e++ + ++ + + +Dr+    a  ++ +  ++ t+  ++ + +
  gi|336253778|ref|YP_004596885.1|  54 HIDRIEQVFEQ--LDADAEAEEDP-VVEGMIQAHEEF-MDQNPSDQAIDRFNI--AAGQKSEHYEIATYGNLIPMAD 124
                                       34445555555..44423334478.677777777764.666664555999877..888999***************9 PP

                              TraB 157 slpdeeqlealeetldeleeakdlleelveay 188
                                       +l +++++++leet++e +++ d+l+++ e +
  gi|336253778|ref|YP_004596885.1| 125 QLGMDDVADMLEETMREEQDELDTLSQMGEEF 156
                                       9**************99998888888887755 PP

>> DUF4142  Domain of unknown function (DUF4142)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   7.6e-05      0.12      96     138 ..      18      60 ..      14      61 .. 0.91
   2 ?   -1.3   0.0       1.5   2.4e+03      93     104 ..      78      89 ..      67     119 .. 0.69
   3 ?    3.3   0.2     0.057        92      66      88 ..     136     157 ..     114     159 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.6e-05
                           DUF4142  96 vaahqkavellekaaasgkdaelkafaektlptlqaHleeaea 138
                                       +  +q+ v++l+++ +s +++elk+  +++++  q+H +++e+
  gi|336253778|ref|YP_004596885.1|  18 YYTEQRLVDALDELESSSSNEELKSGFAEHREETQQHIDRIEQ 60 
                                       557899*********************************9987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                           DUF4142  93 eaqvaahqkave 104
                                       e +++ah++ ++
  gi|336253778|ref|YP_004596885.1|  78 EGMIQAHEEFMD 89 
                                       556666666553 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.057
                           DUF4142  66 teldaeaqakldkLkalsgaaFD 88 
                                       +e + e+q++ld L++  g++FD
  gi|336253778|ref|YP_004596885.1| 136 EETMREEQDELDTLSQM-GEEFD 157
                                       45567888899999866.99999 PP

>> Vir_act_alpha_C  Virulence activator alpha C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.0    0.0054       8.8      14      46 ..      34      68 ..      30      90 .. 0.78
   2 ?    5.4   0.0     0.018        30      11      44 ..     122     155 ..     120     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0054
                   Vir_act_alpha_C 14 vldpealieeLerrreeheekLaeyeeieerl..e 46
                                        ++e+l+  ++++ree ++ ++++e+  e+l  +
  gi|336253778|ref|YP_004596885.1| 34 SSSNEELKSGFAEHREETQQHIDRIEQVFEQLdaD 68
                                      56899*********************887777552 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.018
                   Vir_act_alpha_C  11 aaavldpealieeLerrreeheekLaeyeeieer 44 
                                       +a++l+ ++++++Le+  +e +++L+++ ++ e+
  gi|336253778|ref|YP_004596885.1| 122 MADQLGMDDVADMLEETMREEQDELDTLSQMGEE 155
                                       589999*********************9987665 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   4.5   9.3e-05      0.15      24     128 ..      35     144 ..      14     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.3e-05
                                       HHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHH.........HHHHH CS
                      Rubrerythrin  24 akegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLe.........eaieg 91 
                                          ++++++  F e  ee ++H +++++++e+l+ + e e +  v +  +a ++f   +   +         +a + 
  gi|336253778|ref|YP_004596885.1|  35 S--SNEELKSGFAEHREETQQHIDRIEQVFEQLDADAEAEEDPVVEGMIQAHEEFMDQNP--SdqaidrfniAAGQK 107
                                       3..499********************************7777778888888888866654..333566775544444 PP

                                       HHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  92 ayaeeeemyrfyeelaekegneeakklfkklaeaEkk 128
                                        ++ e+  y  +  +a++ g +++++++++ +++E++
  gi|336253778|ref|YP_004596885.1| 108 SEHYEIATYGNLIPMADQLGMDDVADMLEETMREEQD 144
                                       455566778999999****************999986 PP

>> FKBP_N  Domain amino terminal to FKBP-type peptidyl-prolyl isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.1   3.5e+03      25      42 ..       7      24 ..       3      34 .. 0.73
   2 ?   11.7   1.2   0.00025       0.4      16      83 ..      28      94 ..      10     101 .. 0.81
   3 ?    1.4   0.2      0.39   6.3e+02      42      76 ..     122     156 ..      93     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.1
                            FKBP_N 25 kdavlaGlkdalkgkskl 42
                                       d++++Glk+a+  +++l
  gi|336253778|ref|YP_004596885.1|  7 EDLFVSGLKHAYYTEQRL 24
                                      688999999999776664 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00025
                            FKBP_N 16 lkaqgkeldkdavlaGlkdalkgkskltdeeiqevlqalqeklqekqeeeaeknkaegeaFlaenkkk 83
                                      l++ +++ +++++ +G+++  +++++   + i++v+++l++ ++++++   e   ++ e+F+ +n + 
  gi|336253778|ref|YP_004596885.1| 28 LDELESSSSNEELKSGFAEHREETQQH-IDRIEQVFEQLDADAEAEEDPVVEGMIQAHEEFMDQNPSD 94
                                      555567778999999999999888885.699****************99***************9765 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.39
                            FKBP_N  42 ltde.eiqevlqalqeklqekqeeeaeknkaegeaF 76 
                                       ++d+  +++v + l+e ++e+q +e +   + ge+F
  gi|336253778|ref|YP_004596885.1| 122 MADQlGMDDVADMLEETMREEQ-DELDTLSQMGEEF 156
                                       5566678888888888888888.5666666666666 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7    0.0003      0.49      29      63 ..      30      66 ..      22      67 .. 0.83
   2 ?   -0.9   0.1       1.6   2.6e+03      38      49 ..     135     147 ..     118     152 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                                      S..TTTBHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind 29 d..rappcqdvrallarklaeleeriaeLqalraeLa 63
                                      +  ++++ ++++   a++++e +++i++++++ ++L+
  gi|336253778|ref|YP_004596885.1| 30 EleSSSSNEELKSGFAEHREETQQHIDRIEQVFEQLD 66
                                      3346788899999*******************99997 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.6
                                       H.HHHHHHHHHHH CS
                     MerR-DNA-bind  38 r.allarklaele 49 
                                       + +  ++  +el+
  gi|336253778|ref|YP_004596885.1| 135 LeETMREEQDELD 147
                                       2244444444444 PP

>> CHIP_TPR_N  CHIP N-terminal tetratricopeptide repeat domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   8.6e-05      0.14      33      77 ..      22      66 ..      18      71 .. 0.91
   2 ?   -0.3   0.2       1.1   1.8e+03      56      71 ..     133     148 ..      85     157 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.6e-05
                                      HCCCTTCCHGTTTSXCHHHCHHHHHHHHHHHHHHHHHHHHHHHCC CS
                        CHIP_TPR_N 33 erkleeleeeeekeedekleeeeeeieeeaderlaeLnelFaqvd 77
                                      +r +++l+e e+++ +e+l++  +e +ee+++++++++++F+q d
  gi|336253778|ref|YP_004596885.1| 22 QRLVDALDELESSSSNEELKSGFAEHREETQQHIDRIEQVFEQLD 66
                                      567788899999999****************************99 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHH CS
                        CHIP_TPR_N  56 eeieeeaderlaeLne 71 
                                       + +ee  +e+ +eL++
  gi|336253778|ref|YP_004596885.1| 133 DMLEETMREEQDELDT 148
                                       3333333344444433 PP

>> CdiI_2  CdiI immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.032        52      41      66 ..      22      47 ..      15      56 .. 0.85
   2 ?    4.5   0.2     0.034        56      33      63 ..      70     100 ..      52     116 .. 0.77
   3 ?    4.5   0.4     0.035        57      44      74 ..     128     159 ..     112     165 .] 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.032
                            CdiI_2 41 aelideieellassldeeleeaflae 66
                                      ++l+d ++el +ss++eel++ f ++
  gi|336253778|ref|YP_004596885.1| 22 QRLVDALDELESSSSNEELKSGFAEH 47
                                      789************999**999554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.034
                            CdiI_2  33 ssespeevaelideieellassldeeleeaf 63 
                                       + e++  v+ +i+  ee+++++++++  + f
  gi|336253778|ref|YP_004596885.1|  70 EAEEDPVVEGMIQAHEEFMDQNPSDQAIDRF 100
                                       56778899***************88744444 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.035
                            CdiI_2  44 ideieellassldee.leeaflaelgaefdpe 74 
                                       +d++ ++l++  +ee  e ++l+++g+efd+ 
  gi|336253778|ref|YP_004596885.1| 128 MDDVADMLEETMREEqDELDTLSQMGEEFDYG 159
                                       6899999999999998999999*******997 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   4.9    0.0098        16      61     115 ..      30      84 ..      15     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0098
                           DUF4337  61 elllkakaeelaaavdkkiakykkkiarykkekkeikkkAkeleaerdeaneasd 115
                                       el++++++eel++  ++++++++++i+r ++  +++ ++A++ e+ + e + +++
  gi|336253778|ref|YP_004596885.1|  30 ELESSSSNEELKSGFAEHREETQQHIDRIEQVFEQLDADAEAEEDPVVEGMIQAH 84 
                                       3333445999999999**********************99988887766555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1692  (0.0943722); expected 358.6 (0.02)
Passed bias filter:                      876  (0.0488594); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 1196.47
//
Query:       gi|336253779|ref|YP_004596886.1|  [L=64]
Description: hypothetical protein Halxa_2388 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.043   13.5   0.3        1.6    8.5   0.0    2.2  2  DUF3188   Protein of unknown function (DUF3188)
      0.066   13.3   0.7      0.078   13.0   0.7    1.2  1  DUF2892   Protein of unknown function (DUF2892)
       0.13   11.9   2.5       0.15   11.7   2.5    1.0  1  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00027       1.6      28      44 ..      15      31 ..       8      34 .. 0.90
   2 ?    3.2   0.3     0.012        74       3      14 ..      37      48 ..      35      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00027
                           DUF3188 28 PallvGlgLivsgavgr 44
                                      Pal vGl+L++  ++g+
  gi|336253779|ref|YP_004596886.1| 15 PALAVGLFLLLFTWYGI 31
                                      9**********999986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.012
                           DUF3188  3 plLillgllill 14
                                      +lL ++gll+l+
  gi|336253779|ref|YP_004596886.1| 37 LLLTAVGLLGLF 48
                                      79999****998 PP

>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.7   1.3e-05     0.078      14      45 ..      17      48 ..       4      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                           DUF2892 14 ivvGlvllllallglsggwgwllglvGavlll 45
                                      ++vGl+lll+ + g+++  ++ll +vG+  l+
  gi|336253779|ref|YP_004596886.1| 17 LAVGLFLLLFTWYGIQTHNWLLLTAVGLLGLF 48
                                      789***********988878888888887444 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   2.5   2.6e-05      0.15      10      52 ..      17      55 ..      14      63 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.6e-05
                           DUF4131 10 lalllllllllllllrrrprrrvllllllllllallgfalrap 52
                                      la++l+lll+ ++      + + +lll+++ ll+l+ +a+  +
  gi|336253779|ref|YP_004596886.1| 17 LAVGLFLLLFTWY----GIQTHNWLLLTAVGLLGLFLAAQLLL 55
                                      4444444444444....78899999999999999988877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 487.84
//
Query:       gi|336253780|ref|YP_004596887.1|  [L=96]
Description: hypothetical protein Halxa_2389 [Halopiger xanaduensis SH-6]
Scores for 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:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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: 00:00:00.40
# Mc/sec: 711.85
//
Query:       gi|336253781|ref|YP_004596888.1|  [L=151]
Description: Ferritin Dps family protein [Halopiger xanaduensis SH-6]
Scores for complete 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   86.4   0.5      2e-24   86.2   0.5    1.0  1  Ferritin       Ferritin-like domain
    1.7e-10   41.5   0.1    1.9e-10   41.3   0.1    1.0  1  Rubrerythrin   Rubrerythrin
    0.00013   22.6   0.1    0.00021   22.0   0.1    1.5  1  DUF4439        Domain of unknown function (DUF4439)
    0.00055   20.0   2.0     0.0015   18.6   2.0    1.8  1  DUF892         Domain of unknown function (DUF892)
     0.0028   17.8   0.1     0.0038   17.4   0.1    1.3  1  Ferritin_2     Ferritin-like domain
     0.0052   16.7   0.0     0.0059   16.5   0.0    1.1  1  Ferritin-like  Ferritin-like
     0.0055   17.0   0.8        2.7    8.4   0.1    2.3  2  DUF2383        Domain of unknown function (DUF2383)
  ------ inclusion threshold ------
      0.045   13.6   0.3       0.11   12.3   0.2    1.8  1  GatB_Yqey      GatB domain
      0.063   13.7   0.3      0.082   13.4   0.3    1.3  1  T3SSipB        Type III cell invasion protein SipB
      0.076   13.3   0.4        3.4    8.0   0.0    2.2  2  DUF349         Domain of Unknown Function (DUF349)


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.5   1.1e-27     2e-24       2     137 ..       8     146 ..       7     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 1.1e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHH.HHHH...C-S CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltra.elee...iea 74 
                                       ++L e+ +del+  + yl  a +++g++ e++++ ++e ++ee++ha  l er+++l+++p+++++ e  +   +++
  gi|336253781|ref|YP_004596888.1|   8 DLLTEAYNDELETVMNYLTNAIVLDGIHAEEVKASLEEDIQEELDHARILGERLKQLDESPPGSESfEA-KqsgLQP 83 
                                       6899***********************************************************998533.3466777 PP

                                       SSSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  75 pkefgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeehewelealle 137
                                       p + ++v++v+  +l++e++++e++r lie a++++Dp+t+d +  +l+++e h  e++ + +
  gi|336253781|ref|YP_004596888.1|  84 PADTTDVQSVIDGVLQAEEDAIETYRSLIEAADDANDPVTEDVAVTILTDEEAHRTEFRGFQK 146
                                       77767****************************************************998765 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.1     1e-13   1.9e-10       1     134 [.       8     142 ..       8     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1e-13
                                       HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SSBBS------ CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepele.levkekvreyaeak 75 
                                       ++L++A+  E +  + Y   a  ++    +++++ +ee ++eE +Ha+il + l++l+++    e  e + + ++++
  gi|336253781|ref|YP_004596888.1|   8 DLLTEAYNDELETVMNYLTNAIVLDgIHAEEVKASLEEDIQEELDHARILGERLKQLDESPPgSESFEAKQSGLQPP 84 
                                       789**********************999**********************************999999999999999 PP

                                       -TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  76 pkflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlr 134
                                       ++  t  +++++ + +a++  +e yr++ e+a+++ ++ ++++  ++  +E+ H   +r
  gi|336253781|ref|YP_004596888.1|  85 ADT-TDVQSVIDGVLQAEEDAIETYRSLIEAADDANDPVTEDVAVTILTDEEAHRTEFR 142
                                       999.55556666888999999999*******************************9998 PP

>> DUF4439  Domain of unknown function (DUF4439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   1.2e-07   0.00021      53     127 ..      71     149 ..      10     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.2e-07
                           DUF4439  53 gatppaaeaaYelpfevtdaasaarlaaelEedlaaayaalv.aaddadl...RstaadaLteaavraarWraelga 125
                                       +++ +a++++ ++p  +td +s ++ + ++Eed++++y++l+ aadda++    ++a+++Lt+     +++r+  + 
  gi|336253781|ref|YP_004596888.1|  71 SESFEAKQSGLQPPADTTDVQSVIDGVLQAEEDAIETYRSLIeAADDANDpvtEDVAVTILTDEEAHRTEFRGFQKE 147
                                       456788999*********************************77777664222678999999999999999988888 PP

                           DUF4439 126 fP 127
                                       fP
  gi|336253781|ref|YP_004596888.1| 148 FP 149
                                       87 PP

>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.0   8.3e-07    0.0015      31     144 ..      34     139 ..       3     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8.3e-07
                                       -SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-------.-HHHHTTT-----------THHHHHHH...HHHHHHH CS
                            DUF892  31 aespeLkaaleqHleeTegqierLeqvferlgesasekkcdamegliaegqelieeaaedeslkdaaliaaaqaveh 107
                                       ++ +e+ka le++++e  ++++ L + +++l+es+ + +        +  q  ++  a+ +++  +  i    + e 
  gi|336253781|ref|YP_004596888.1|  34 IHAEEVKASLEEDIQEELDHARILGERLKQLDESPPGSE------SFEAKQSGLQPPADTTDVQSV--IDGVLQAEE 102
                                       5669*******************************9999......334444444442333333333..5777999** PP

                                       HHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHH CS
                            DUF892 108 yEiAsYgtLialAeqlgekeaaklLeqtleeekatde 144
                                         i +Y++Li +A+ + ++ + ++  ++l  e+a   
  gi|336253781|ref|YP_004596888.1| 103 DAIETYRSLIEAADDANDPVTEDVAVTILTDEEAHRT 139
                                       *****************************99998765 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   0.1   2.1e-06    0.0038      32     133 ..      32     144 ..       4     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.1e-06
                        Ferritin_2  32 kalldaevrevaeeiakheeaHveflkaale.......Gaaavakptfdf......afdpfadeksflalaavlEdv 95 
                                       ++   +ev++ +ee  ++e +H+++l + l+       G++ ++            +  +++d +s++++    E+ 
  gi|336253781|ref|YP_004596888.1|  32 DGIHAEEVKASLEEDIQEELDHARILGERLKqldesppGSESFE-----AkqsglqPPADTTDVQSVIDGVLQAEED 103
                                       6677788999999999**************98844444444444.....3555558899999*************** PP

                        Ferritin_2  96 gvsAYlgaaplls...nkelltaaasIlsvEArHaavirtl 133
                                       +++ Y + ++  +   ++    +a+ Il++E  H + +r  
  gi|336253781|ref|YP_004596888.1| 104 AIETYRSLIEAADdanDPVTEDVAVTILTDEEAHRTEFRGF 144
                                       *****9877666533377799**************999976 PP

>> Ferritin-like  Ferritin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.3e-06    0.0059       1     104 [.      10     116 ..      10     147 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.3e-06
                                       HHHHHHHHHHHHHHHHHHHHHBS-TTSH.HHHHHHHHHHHHHHHHHHHHHHHHHTT------....-----TT-TB- CS
                     Ferritin-like   1 LqqAielEhstippYLtalySikdgtneeaealilevvkeEMlHltlvaNllnalGgsPvleapdfvpeypatlpgg 77 
                                       L +A + E+ t++ YLt +  ++  ++ee++a ++e ++eE  H+ +    l+ l++sP  +++ ++ +   + p +
  gi|336253781|ref|YP_004596888.1|  10 LTEAYNDELETVMNYLTNAIVLDGIHAEEVKASLEEDIQEELDHARILGERLKQLDESPPGSESFEAKQSGLQPPAD 86 
                                       5678888***************************************************8766554444444333322 PP

                                       GG..-S--SS--SSSHHHHHHHHH.HT--G CS
                     Ferritin-like  78 ve..televkLeplskealetfla.iEaPe 104
                                           +++   + + +++a+et+++ iEa++
  gi|336253781|ref|YP_004596888.1|  87 TTdvQSVIDGVLQAEEDAIETYRSlIEAAD 116
                                       221122333445567777887765367666 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0039         7      27      70 ..      34      77 ..      28      79 .. 0.91
   2 !    8.4   0.1    0.0015       2.7       5      45 ..      93     136 ..      89     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0039
                                      --SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT------------ CS
                           DUF2383 27 vkdpqlktlleriaeereeaaeeLqseiralggepedggslagk 70
                                      ++ +++k+ le+ ++e  ++a+ L +++++l ++p  + s+ +k
  gi|336253781|ref|YP_004596888.1| 34 IHAEEVKASLEEDIQEELDHARILGERLKQLDESPPGSESFEAK 77
                                      677899******************************99999765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHH...HHHHT--SHHHHHHHHHHHHHHHH CS
                           DUF2383   5 aLndLietlkdgeegyk...eaaekvkdpqlktlleriaeeree 45 
                                        +   +++++d++e+y+   eaa++++dp  ++++  i  + e+
  gi|336253781|ref|YP_004596888.1|  93 VIDGVLQAEEDAIETYRsliEAADDANDPVTEDVAVTILTDEEA 136
                                       6777899**********333456666666666666555555555 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   6.4e-05      0.11      80     114 ..      76     110 ..       8     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.4e-05
                                       HHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTT CS
                         GatB_Yqey  80 ieekgLkqisdeeeleklveeviaenpkavedyks 114
                                        ++ gL++  d+  ++++++ v++++++a+e y+s
  gi|336253781|ref|YP_004596888.1|  76 AKQSGLQPPADTTDVQSVIDGVLQAEEDAIETYRS 110
                                       5678*****************************97 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 ?   13.4   0.3   4.6e-05     0.082      76     151 ..      44     122 ..       3     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.6e-05
                                       HHHHHHHHHHHHH...HHTT---------CHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTXXX CS
                           T3SSipB  76 adaatkkvdeaqk...rlkeLaPdePekakleaaeqQagaaadalqadealqKkldaasklsekakakekevDdisa 149
                                        ++ ++ +d+a     rlk+L+   P+    ea++  ++  ad + ++  ++  l a + + e  +++ + +Dd+  
  gi|336253781|ref|YP_004596888.1|  44 EEDIQEELDHARIlgeRLKQLDESPPGSESFEAKQSGLQPPADTTDVQSVIDGVLQAEEDAIETYRSLIEAADDAND 120
                                       3445555555554666*****9999*******999999988********************************9876 PP

                                       XX CS
                           T3SSipB 150 kv 151
                                        v
  gi|336253781|ref|YP_004596888.1| 121 PV 122
                                       65 PP

>> DUF349  Domain of Unknown Function (DUF349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.053        95      19      49 ..      38      68 ..      35      82 .. 0.81
   2 ?    8.0   0.0    0.0019       3.4      26      66 ..      99     148 ..      90     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.053
                            DUF349 19 ahfeeqdaereenlekKealieeaealakst 49
                                      + +++++++ +e l+  + l e++++l++s 
  gi|336253781|ref|YP_004596888.1| 38 EVKASLEEDIQEELDHARILGERLKQLDESP 68
                                      6789999999*****************8764 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0019
                            DUF349  26 aereenlekKealieeaealakstt.........dwksatkrlkelqeeW 66 
                                       +++e+++e  + lie a + +++ t         d ++ + +++ +q+e+
  gi|336253781|ref|YP_004596888.1|  99 QAEEDAIETYRSLIEAADDANDPVTedvavtiltDEEAHRTEFRGFQKEF 148
                                       7899****************999766777777776677799999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1060.68
//
Query:       gi|336253782|ref|YP_004596889.1|  [L=407]
Description: (R)-citramalate synthase [Halopiger xanaduensis SH-6]
Scores for 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-82  275.7   6.6    6.4e-82  275.1   6.6    1.3  1  HMGL-like     HMGL-like
     0.0074   15.7   0.5      0.027   13.9   0.1    2.2  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


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 !  275.1   6.6   7.1e-86   6.4e-82       3     264 .]      24     279 ..      22     279 .. 0.98

  Alignments for each domain:
  == domain 1  score: 275.1 bits;  conditional E-value: 7.1e-86
                                       EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHH CS
                         HMGL-like   3 kivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdik 79 
                                       +++dttLRDGeq++++++s ++k++ia  Lde+g ++iE+gfp+ s  +fe+vr ia++  ++  ++l r ++kdi+
  gi|336253782|ref|YP_004596889.1|  24 RVFDTTLRDGEQSPGTSFSYDDKRQIASILDEMGTHVIEAGFPVNSDAEFEAVRDIASSTSTT-TCGLGRVVDKDIE 99 
                                       579********************************************************9777.9************ PP

                                       HHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHH CS
                         HMGL-like  80 aavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaae 156
                                       aa +     g+++vh+f++ts+++++ +++ +r+ev+++a+e v++++++g  + +s++da+rtd efl++v+ea+ 
  gi|336253782|ref|YP_004596889.1| 100 AALD----SGVEMVHTFVSTSDVQIEDSMHATRDEVVQRAVESVERVKEAGVTCMFSPMDATRTDEEFLIDVIEAVT 172
                                       ****....********************************************************************* PP

                                       HHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB CS
                         HMGL-like 157 eaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGn 233
                                       +aG + ini+Dt Gv+tP+ ++++i+++ ++++  + + vH+H+d+GlA+an+la++eaGad+  ++vn++GeraGn
  gi|336253782|ref|YP_004596889.1| 173 AAGTDWINIPDTCGVATPSRFKAMIEKVEAHTD--ARIDVHTHDDFGLATANALAGIEAGADQAQVSVNSIGERAGN 247
                                       *********************************..****************************************** PP

                                       -BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 234 aaleelvaalealg.vdtgldlqklrsiaalv 264
                                       aa ee+v+a+e l   dtg+d++++++++++v
  gi|336253782|ref|YP_004596889.1| 248 AAYEEFVMAVESLYqTDTGIDTTRITELSEIV 279
                                       ***********9977*************9987 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 !   13.9   0.1     3e-06     0.027      10     151 ..       5     171 ..       3     217 .. 0.83
   2 ?   -1.0   0.1      0.11   9.8e+02      25      42 ..     351     372 ..     331     399 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-06
                                       SEEEEECCTCSHHHHC.....................HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC...... CS
                      AP_endonuc_2  10 dgvElfgrdlvpvsel.....................sdeelrelrkaldelglriaslslftrfgypded...... 59 
                                       +gvE+f  +l++ +e                      s ++ r+++++lde g ++    ++ ++ + +e       
  gi|336253782|ref|YP_004596889.1|   5 RGVEFFQGTLDSTDEIesarvfdttlrdgeqspgtsfSYDDKRQIASILDEMGTHVIEAGFPVNSDAEFEAvrdias 81 
                                       677777777777777777777777777777777777888889************************99999888877 PP

                                       .......HTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEE CS
                      AP_endonuc_2  60 .......erearreesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklal 129
                                                        + + + ie+a + G+++++++++t + + ++s  ++++ ++++  e ++  +++gv+  +
  gi|336253782|ref|YP_004596889.1|  82 ststttcG---L----GRVVDKDIEAALDSGVEMVHTFVSTSDVQIEDSMHATRDEVVQRAVESVERVKEAGVTCMF 151
                                       76664332...2....45589*******************988899999999999999999999999999******* PP

                                       E--TTTTSSSTCHHHHHHHHHH CS
                      AP_endonuc_2 130 Etlagsgvelgdeelarlldav 151
                                        +++ + + +  e l ++++av
  gi|336253782|ref|YP_004596889.1| 152 SPMDATRT-DE-EFLIDVIEAV 171
                                       ***99996.44.5566655555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.11
                                       C....HHHHHHHHHHHHHHTTS CS
                      AP_endonuc_2  25 l....sdeelrelrkaldelgl 42 
                                       l    +d+e+r++ ++++++g 
  gi|336253782|ref|YP_004596889.1| 351 LgfepTDDEVRAVTRRVKDYGA 372
                                       1333345555555555555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2850.24
//
Query:       gi|336253783|ref|YP_004596890.1|  [L=607]
Description: acetolactate synthase, large subunit, biosynthetic type [Halopiger xanaduensis SH-6]
Scores for 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-52  175.8   0.6    3.2e-51  173.4   0.2    2.4  3  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    5.3e-50  169.2   1.8      1e-49  168.2   0.1    2.4  3  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    7.1e-46  155.4   0.1    2.6e-45  153.5   0.0    2.0  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
     0.0018   18.1   0.0     0.0032   17.3   0.0    1.3  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha


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 !  173.4   0.2     7e-55   3.2e-51       2     171 ..      49     216 ..      48     217 .. 0.98
   2 ?   -2.2   0.0      0.62   2.8e+03     114     147 ..     346     379 ..     333     383 .. 0.80
   3 ?   -1.5   0.0      0.38   1.7e+03     118     162 ..     543     582 ..     526     586 .. 0.69

  Alignments for each domain:
  == domain 1  score: 173.4 bits;  conditional E-value: 7e-55
                                       EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHH CS
                      TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatn 78 
                                       ++aea+vraL+++gve++fgv G+ i+p++dal ++ +i++v++ hEqgaa+aAd+y  ++gkpg++l+tsgpGatn
  gi|336253783|ref|YP_004596890.1|  49 NGAEAVVRALENAGVEYAFGVQGGAIMPVYDALYDS-EITHVTMAHEQGAAHAADAYGIVSGKPGICLATSGPGATN 124
                                       79**********************************.5*************************************** PP

                                       CHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EE CS
                      TPP_enzyme_N  79 altalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPv 155
                                       ++t+la+A  d+ Pl++l+g++pt+ +g +++q e+d +++  pvtk + + ++p+++   + +A++ a +grpgP+
  gi|336253783|ref|YP_004596890.1| 125 LVTGLADADMDSDPLVALTGQVPTEFVGNDAFQ-ETDTTGVTTPVTKNNAFASDPDRVGTDVSEAFALASEGRPGPT 200
                                       *********************************.******************************************* PP

                                       EEEEEHHHCC-EEEHH CS
                      TPP_enzyme_N 156 ylelpkdvlleevded 171
                                       +++lpkd+ ++++d++
  gi|336253783|ref|YP_004596890.1| 201 LVDLPKDITKSDTDAE 216
                                       ***********99986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.62
                                       T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHH CS
                      TPP_enzyme_N 114 ldqlalfrpvtkyaervtspeelpealrrAirta 147
                                       +d +++ +++  +   v ++e+++e+l++A++++
  gi|336253783|ref|YP_004596890.1| 346 IDPAEISKNIYADYPLVGDAETVVEQLQEAVDES 379
                                       5777777888888888999999999999999876 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.38
                                       HHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHH CS
                      TPP_enzyme_N 118 alfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkd 162
                                       +l++ +    +r+++ +e++ +++ Ai+       gP ++++  d
  gi|336253783|ref|YP_004596890.1| 543 KLAEAFGAQGYRIDDYDEVADTIESAIAYD-----GPSVIDVHID 582
                                       455566667788888888888888887654.....7777777666 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 ?   -1.7   0.2      0.48   2.2e+03      24      51 ..      85     116 ..      76     129 .. 0.69
   2 ?   -3.0   0.0       1.2   5.6e+03     107     144 ..     342     377 ..     328     381 .. 0.63
   3 !  168.2   0.1   2.3e-53     1e-49       1     153 []     430     579 ..     430     579 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.48
                                       ETTTS-TTTHHHHHHHHHH.....HSTTSEEEE CS
                      TPP_enzyme_C  24 sgglgtmGyglpaAiGakl.....akpdrevva 51 
                                       + +++tm  + +aA++a +      kp+    a
  gi|336253783|ref|YP_004596890.1|  85 EITHVTMAHEQGAAHAADAygivsGKPG-ICLA 116
                                       4589999999999999987554332444.4444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                                       BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHC CS
                      TPP_enzyme_C 107 dlkpvdfaklaealGakgarvekadveeleealkeale 144
                                       +  ++d+a++ + + a+   v +a  e + e+l+ea++
  gi|336253783|ref|YP_004596890.1| 342 IHVDIDPAEISKNIYADYPLVGDA--ETVVEQLQEAVD 377
                                       466788888888876663354444..777777777764 PP

  == domain 3  score: 168.2 bits;  conditional E-value: 2.3e-53
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHST.TSEEEEEEEHHHHHHTGGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakp.drevvaivGDGgflmilqelatavrrnlpit 76 
                                       ++G++++wa +++ +++pr++++s glgtmGyglpaAiGa +a+  d+ev+++ GDG+flm+lq l+ avr++l+it
  gi|336253783|ref|YP_004596890.1| 430 GVGQHQMWACQYWTFTEPRTWVSSHGLGTMGYGLPAAIGARVAADdDQEVICVDGDGSFLMTLQGLSVAVREDLDIT 506
                                       69****************************************754389***************************** PP

                                       EEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                       v vlnNe+ gm++++q+ f+++r+s+ ++  +  + f klaea+Ga+g+r++++  +e++++++ a++ +gp++i+v
  gi|336253783|ref|YP_004596890.1| 507 VAVLNNEYIGMVRQWQDAFFDGRHSASDY--GWMPEFDKLAEAFGAQGYRIDDY--DEVADTIESAIAYDGPSVIDV 579
                                       ************************99885..6666*******************..*******************98 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 !  153.5   0.0   5.8e-49   2.6e-45       1     137 []     237     372 ..     237     372 .. 0.98
   2 ?   -2.9   0.0       1.2   5.2e+03      85     114 ..     552     584 ..     550     586 .. 0.71

  Alignments for each domain:
  == domain 1  score: 153.5 bits;  conditional E-value: 5.8e-49
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealee 77 
                                       +e+aae++++++rpv+l+Gggv+  +ase+ re+a +++iPv+tt+ g g++pedh+l+l m+g+hg+ +an+a+ +
  gi|336253783|ref|YP_004596890.1| 237 VEAAAERIENSERPVMLLGGGVIKGEASEACREFAIEHEIPVITTMPGLGSFPEDHELSLEMAGMHGTGYANMAITH 313
                                       689************************************************************************** PP

                                       -SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  78 aDlvlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                       +D+++ +G+rfdd r tg  ++fapea++ih+didpaei+kn  +d+++vgd+ +++e+L
  gi|336253783|ref|YP_004596890.1| 314 CDTLIGIGTRFDD-RLTGGIETFAPEAELIHVDIDPAEISKNIYADYPLVGDAETVVEQL 372
                                       *************.77888999***********************************998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                                       S-SSSTCCCTT.TTT.TTTTT-.EEEEEESSCC CS
                      TPP_enzyme_M  85 Garfddirttg.sep.efapea.kiihididpa 114
                                       G r dd+  ++ + + ++a ++  +i ++idp+
  gi|336253783|ref|YP_004596890.1| 552 GYRIDDYDEVAdTIEsAIAYDGpSVIDVHIDPQ 584
                                       667777766666555577777788999999986 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 !   17.3   0.0   7.2e-07    0.0032       7      70 ..     220     282 ..     215     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.2e-07
                                       XXXXXXXXXXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEET CS
                             CO_dh   7 PfdeaaianskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvata 70 
                                       P ++    +++ a++e+  + +a+ i   +rP++++G+ v k e  ea     +e +++v+ t 
  gi|336253783|ref|YP_004596890.1| 220 PKTPDTYEVQERADEEIV-EAAAERIENSERPVMLLGGGVIKGEASEACREFAIEHEIPVITTM 282
                                       555567778889999998.99****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 4463.90
//
Query:       gi|336253784|ref|YP_004596891.1|  [L=229]
Description: acetolactate synthase, small subunit [Halopiger xanaduensis SH-6]
Scores for 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-21   74.6   0.1      9e-21   73.9   0.1    1.4  1  ALS_ss_C  Small subunit of acetolactate synthase
    1.8e-14   53.3   0.0    3.1e-14   52.6   0.0    1.4  1  ACT_5     ACT domain
    6.3e-14   51.5   0.1    1.6e-13   50.2   0.0    1.7  2  ACT       ACT domain
     0.0061   17.1   0.0      0.012   16.2   0.0    1.4  1  ACT_4     ACT domain
  ------ inclusion threshold ------
      0.031   14.6   0.2       0.22   11.8   0.1    2.1  2  SbcD_C    Type 5 capsule protein repressor C-terminal domain


Domain annotation for each model (and alignments):
>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.1   2.5e-24     9e-21       1      74 []     125     196 ..     125     196 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 2.5e-24
                                       EEEEEEEEE.-SCHHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHHHHHHHHHS-GGGEEEEEEEEEEEEEST CS
                          ALS_ss_C   1 RElaLiKVkaekeerseileiaeifrakivdvspdsliieltgteekidaliellkpfgilevvRtGrvAleRG 74 
                                       RElaL+KV a +   + + ++a++++a +vd sp++ ++e+tg ++ki+a +e +++fgi e++RtG++Al+RG
  gi|336253784|ref|YP_004596891.1| 125 RELALVKVDARD--PAAVSAVADMYDATTVDSSPETATFEITGARQKIEAAVETFSQFGIREISRTGTTALARG 196
                                       9********965..899********************************************************8 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   8.6e-18   3.1e-14       2      62 .]      54     115 ..      53     115 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 8.6e-18
                             ACT_5   2 apgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvelLsnQleKLidVlkV 62 
                                       +pgvL  v ++++rr F+++sl++ +t d++ +ri+++Ve+ ++ ++++ +Ql+KL+ V++V
  gi|336253784|ref|YP_004596891.1|  54 EPGVLAEVSGLFSRRQFNIESLTVGPTKDDDWARITVVVEEpDPGIDQIKKQLRKLLPVVSV 115
                                       69*******************************************************99987 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   4.3e-17   1.6e-13       1      66 [.      45     110 ..      45     111 .. 0.97
   2 ?   -3.3   0.0       2.3   8.3e+03      44      57 ..     159     172 ..     148     178 .. 0.47

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 4.3e-17
                                       EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT   1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                       tv++ +v+ +PG+La+v+g++++r++Ni+s+++++++d  + +++vv+++ + ++++++++l+kl+
  gi|336253784|ref|YP_004596891.1|  45 TVISALVEHEPGVLAEVSGLFSRRQFNIESLTVGPTKDDDWARITVVVEEPDPGIDQIKKQLRKLL 110
                                       5889999*********************************************************95 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.3
                                       EEEEEEEEHHHHHH CS
                               ACT  44 vfvvivvdeedlee 57 
                                       +++ i++  + +e+
  gi|336253784|ref|YP_004596891.1| 159 ATFEITGARQKIEA 172
                                       33333334444444 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.2e-06     0.012       8      71 ..      46     108 ..      40     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.2e-06
                             ACT_4   8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLra 71 
                                        ++  +e ++g+La+++ ++s  + ni+s+++  +k+d  a+i++ ve  d   ++++ ++Lr+
  gi|336253784|ref|YP_004596891.1|  46 VISALVEHEPGVLAEVSGLFSRRQFNIESLTVGPTKDDDWARITVVVEEPDP-GIDQIKKQLRK 108
                                       57888999*****************************99**99988875443.35555555555 PP

>> SbcD_C  Type 5 capsule protein repressor C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   6.2e-05      0.22      20      59 ..      78     120 ..      51     150 .. 0.73
   2 ?    0.6   0.0       0.2   7.3e+02      38      63 ..     163     189 ..     158     225 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.2e-05
                            SbcD_C  20 epsekpawlevevtdedplp...dlrerlrellegipvevlrl 59 
                                        p + ++w +++v +e+p p   + +++lr+ll+ + v+ l+ 
  gi|336253784|ref|YP_004596891.1|  78 GPTKDDDWARITVVVEEPDPgidQIKKQLRKLLPVVSVRELEP 120
                                       45678**************977677799999999998865554 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.2
                            SbcD_C  38 lpdlrerlrellegipv.evlrlrrtr 63 
                                       ++ +r+++++++e +    + +++rt 
  gi|336253784|ref|YP_004596891.1| 163 ITGARQKIEAAVETFSQfGIREISRTG 189
                                       567899999999998443444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1860.74
//
Query:       gi|336253785|ref|YP_004596892.1|  [L=349]
Description: Ketol-acid reductoisomerase [Halopiger xanaduensis SH-6]
Scores for 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-71  236.7   0.0    1.4e-70  236.1   0.0    1.3  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    1.9e-63  213.1   0.5    2.6e-63  212.6   0.5    1.2  1  IlvC           Acetohydroxy acid isomeroreductase, catalytic 
    2.3e-05   23.9   0.0    4.2e-05   23.0   0.0    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    5.8e-05   23.3   0.0    0.00011   22.5   0.0    1.4  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    0.00011   22.7   0.0    0.00024   21.6   0.0    1.6  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
     0.0028   17.3   0.1     0.0052   16.4   0.1    1.5  1  ApbA           Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.013   15.8   0.1      0.031   14.6   0.1    1.7  1  Mur_ligase     Mur ligase family, catalytic domain


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 !  236.1   0.0   5.5e-74   1.4e-70       2     165 .]      20     183 ..      19     183 .. 0.99

  Alignments for each domain:
  == domain 1  score: 236.1 bits;  conditional E-value: 5.5e-74
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevye 78 
                                       l++ ++av+GyGsqGha+alnl++sg+dvvvglregs s + A+e+g+ev+t  +av++a  + +l+PD++q +vye
  gi|336253785|ref|YP_004596892.1|  20 LDDETVAVLGYGSQGHAHALNLHESGVDVVVGLREGSPSRSAAEEDGLEVATPGDAVAQASYISVLVPDTVQPDVYE 96 
                                       7899************************************************************************* PP

                                       HHTGGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHHH CS
                              IlvN  79 eeiepnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelalay 155
                                       ++iepnl++g++l+fahG+nih+++i+pp+dvdv++vAPk+pGhlvr++ye+ +G+p l+a++qd++g+a+e alay
  gi|336253785|ref|YP_004596892.1|  97 NTIEPNLESGDTLQFAHGLNIHYNQIQPPEDVDVTMVAPKSPGHLVRRNYENDEGTPGLLAIYQDTTGDAEERALAY 173
                                       ***************************************************************************** PP

                                       HHHTTHHHH- CS
                              IlvN 156 akgiGatraG 165
                                       akgiG+traG
  gi|336253785|ref|YP_004596892.1| 174 AKGIGCTRAG 183
                                       *********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 !  212.6   0.5     1e-66   2.6e-63       1     144 []     189     332 ..     189     332 .. 0.99

  Alignments for each domain:
  == domain 1  score: 212.6 bits;  conditional E-value: 1e-66
                                       HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHH CS
                              IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdl 77 
                                       F+eE+e+DlfgEqavLcGgv++lv+ g+etlv+aGyspe+Ayfecl+elklivdl+yegG+++m++s+Sdtaeyg+l
  gi|336253785|ref|YP_004596892.1| 189 FQEEVESDLFGEQAVLCGGVTSLVKHGYETLVDAGYSPEIAYFECLNELKLIVDLMYEGGLSEMWDSVSDTAEYGGL 265
                                       99*************************************************************************** PP

                                       HHHHHHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHTTSHHHHHHHHHHHTSHHHHHHHHHHHCHTT CS
                              IlvC  78 tagprviteevkeemkeileeiqsGefakevieenkagrpelkklrkeeaeheiekvgkklralmpw 144
                                       t+g+++++e+v+e+m+e lee+q+Gef++e+i+en+a+rp++++lr++e++heie vg++lral+ w
  gi|336253785|ref|YP_004596892.1| 266 TRGDEIVDEHVRENMEETLEEVQNGEFTREWILENQAKRPTYSQLRQAEKNHEIEDVGERLRALFAW 332
                                       ***************************************************************9987 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 !   23.0   0.0   1.6e-08   4.2e-05      28     102 ..      14      89 ..       2      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.6e-08
                                       CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S--S CS
                      2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlplt 102
                                       +   ++l ++tv+++G+G+ G+a a  l++ g++v++  r  ++++ ++ee g+e+++  +++a++ ++s+ +p t
  gi|336253785|ref|YP_004596892.1|  14 DADVSTLDDETVAVLGYGSQGHAHALNLHESGVDVVVGLREGSPSRsAAEEDGLEVATPGDAVAQASYISVLVPDT 89 
                                       55667899****************************999999988878889999*******************977 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 !   22.5   0.0   4.1e-08   0.00011       2      86 ..      25     109 ..      24     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.1e-08
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieglle 78 
                                       ++++G G  G+  alnl ++g +v+v  r+ +  +++++e    ++++ ++va++  + ++v+++ + d   + + +
  gi|336253785|ref|YP_004596892.1|  25 VAVLGYGSQGHAHALNLHESGVDVVVGLREGSPSRSAAEEDGLEVATPGDAVAQASYISVLVPDTVQPDVYENTIEP 101
                                       89**************************************9999********************888765555599* PP

                                       C--TT-EE CS
                     NAD_binding_2  79 alkkgdil 86 
                                       +l++gd+l
  gi|336253785|ref|YP_004596892.1| 102 NLESGDTL 109
                                       ***99975 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 !   21.6   0.0   9.4e-08   0.00024       2      81 ..      25      98 ..      24     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 9.4e-08
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlse 80
                                      ++++G+G++g+a a++l ++g    ++vv+  r+ +  +++aee g +v +    +a+++a  + + v+ ++ ++v ++
  gi|336253785|ref|YP_004596892.1| 25 VAVLGYGSQGHAHALNLHESG---VDVVVG-LREGSPSRSAAEEDGLEVAT--PGDAVAQASYISVLVPDTVQPDVYEN 97
                                      89*******************...****88.99999999999999988887..999*999*999999998888888776 PP

                                      C CS
                     F420_oxidored 81 l 81
                                       
  gi|336253785|ref|YP_004596892.1| 98 T 98
                                      5 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1     2e-06    0.0052       1      48 [.      25      77 ..      25     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2e-06
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH.HHHHCEEEEETT...C CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea.lkknGlrltseg...g 48
                                      +a+lG G++G   a +L++ g dv++ lr+     +  +++Gl++ ++g    
  gi|336253785|ref|YP_004596892.1| 25 VAVLGYGSQGHAHALNLHESGVDVVVGLREGsPSRSaAEEDGLEVATPGdavA 77
                                      69***************************99988888999***9999985432 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.2e-05     0.031      16      82 ..      22      78 ..      15      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                      HHHHHHTTSEEEEEESSHCHHHTT-EEEES-HGGGGEE-TS-TTCHHHHHHHHTTEEEEEHHHHHHH CS
                        Mur_ligase 16 alflalkGykvdGsdfieslialGaaavvghdaanivvssiskdnpeleaakepgipvesraeaLae 82
                                      ++ +a  Gy  +G+ ++ +l ++G+ +vvg +++           p   aa e g++v  + +a+a+
  gi|336253785|ref|YP_004596892.1| 22 DETVAVLGYGSQGHAHALNLHESGVDVVVGLREG----------SPSRSAAEEDGLEVATPGDAVAQ 78
                                      478999****************************..........9***********99888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2617.45
//
Query:       gi|336253786|ref|YP_004596893.1|  [L=90]
Description: hypothetical protein Halxa_2395 [Halopiger xanaduensis SH-6]
Scores for 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  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      141  (0.00786435); 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: 0.34u 0.19s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 759.07
//
Query:       gi|336253787|ref|YP_004596894.1|  [L=475]
Description: 3-isopropylmalate dehydratase large subunit [Halopiger xanaduensis SH-6]
Scores for 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-146  487.2   0.0   6.4e-146  487.0   0.0    1.0  1  Aconitase  Aconitase family (aconitate hydratase)
    0.00054   18.8   0.0      0.001   17.9   0.0    1.4  1  DUF521     Protein of unknown function (DUF521)
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.29   11.1   0.0    1.7  1  DUF3944    Domain of unknown function (DUF3944)


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 !  487.0   0.0  1.1e-149  6.4e-146       1     461 []       8     459 ..       8     459 .. 0.94

  Alignments for each domain:
  == domain 1  score: 487.0 bits;  conditional E-value: 1.1e-149
                         Aconitase   1 ekiwdahlvee....egiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeeale 73 
                                       +k+wd+h v++    ++++++   +l+++vt++qa+  l+++  +v+ ++ t at+dh vp+    d+s        
  gi|336253787|ref|YP_004596894.1|   8 DKVWDRHKVTTlptgQDQLFI-GLHLIHEVTSPQAFGMLRERDLEVAYPELTHATVDHIVPTA---DQSR------- 73 
                                       69*****99666643337777.*****************************************...6655....... PP

                         Aconitase  74 knledefernkeryefLksaakafgirvvppg...qGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGg 147
                                          e+  ++  e+++ L+++ ++ gi++ +p    qGIvH++++E+gl++pgkt+v++DSHT+++g++G+la+G+G+
  gi|336253787|ref|YP_004596894.1|  74 -PYEEDAAE--EMMAELEENVREAGIEFSDPTtgdQGIVHVIGPEQGLTQPGKTIVCGDSHTSTHGAFGALAFGIGT 147
                                       .55555555..99******************9999****************************************** PP

                         Aconitase 148 ieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMa 224
                                       +++ +vl++ ++ +++ kv +++++G+l+egv+akD++l++i++l+++g+vg+v E++Ge++esL +e+r++i+NM+
  gi|336253787|ref|YP_004596894.1| 148 SQIRDVLATGTVAMEKQKVRKIQVDGELGEGVEAKDIILEIIRRLGTEGGVGYVYEYAGEAIESLGMEGRMSICNMS 224
                                       ***************************************************************************** PP

                         Aconitase 225 aEvGAttglfpvdektleYLkatgreeaavlveaydkaqalf.elaadedaeydkvleldlstlepsvagpkrPqda 300
                                       +E GA++g++++de+t+e+L+ t+  +++   e++++ + ++ ++++dedaeyd+++++d+++lep v+++++P + 
  gi|336253787|ref|YP_004596894.1| 225 IEGGARAGYVNPDETTYEWLEETDYFQEN--PERFEELKPYWeSIRSDEDAEYDDIVRIDANELEPVVTWGTTPGQG 299
                                       *********************88876665..69*********7799******************************* PP

                         Aconitase 301 vplselvk.k.efkeelekeaaekaley.klkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkp 374
                                       + +++ ++ + ++ e+  +++a++a e+ + ++g ++   ++d+a++gSCTN++++d+r+aa++++     g++v++
  gi|336253787|ref|YP_004596894.1| 300 IGITDPIPaPeDLPEDK-QDTARRAQEHmRVEPGDTMAGYDIDVAFLGSCTNARLPDLRRAARIVE-----GREVHD 370
                                       *******9754777766.45555555555999**********************************.....****** PP

                         Aconitase 375 gvktsvaPGSevvkayleaeGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqg.pntrayLa 449
                                       +v+++v+PGS++v++++e+eGl +++e+aGfe+++agCs+C+g n+d+le +ea++sssNRNF gRqg +++r+ L+
  gi|336253787|ref|YP_004596894.1| 371 DVRAMVVPGSQRVQKQAEEEGLKDTFEEAGFEWRNAGCSMCLGmNEDQLEGDEACASSSNRNFIGRQGsKDGRTVLM 447
                                       *******************************************************************879******* PP

                         Aconitase 450 SPelvvaaAlaG 461
                                        P +v+aaA++G
  gi|336253787|ref|YP_004596894.1| 448 NPRMVAAAAIQG 459
                                       **********98 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.7e-07     0.001     284     360 ..     333     411 ..     298     433 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.7e-07
                            DUF521 284 skakeekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvtt.srevkeeaerlglveklekaGvkvlsdtCm 358
                                       ++    ++d+ +lG c  + l +lr+ a++++g++++++v+ +v+  s+ v+++ae++gl ++ e+aG +  +  C 
  gi|336253787|ref|YP_004596894.1| 333 DTMAGYDIDVAFLGsCTNARLPDLRRAARIVEGREVHDDVRAMVVPgSQRVQKQAEEEGLKDTFEEAGFEWRNAGCS 409
                                       556677899999997899********************998777651666*******************99988886 PP

                            DUF521 359 vv 360
                                       ++
  gi|336253787|ref|YP_004596894.1| 410 MC 411
                                       55 PP

>> DUF3944  Domain of unknown function (DUF3944)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.8e-05      0.29       3      23 ..     338     358 ..     337     360 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.8e-05
                           DUF3944   3 eDkDLeFLkklssedLedLfd 23 
                                       +D D +FL+ ++++ L dL +
  gi|336253787|ref|YP_004596894.1| 338 YDIDVAFLGSCTNARLPDLRR 358
                                       89****************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.37
# Mc/sec: 3876.09
//
Query:       gi|336253788|ref|YP_004596895.1|  [L=211]
Description: 3-isopropylmalate dehydratase, small subunit [Halopiger xanaduensis SH-6]
Scores for complete 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   70.9   0.0    2.1e-19   70.2   0.0    1.3  1  Aconitase_C  Aconitase C-terminal domain
  ------ inclusion threshold ------
      0.094   11.7   0.0       0.14   11.2   0.0    1.3  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.0   2.3e-23   2.1e-19      16     127 ..      22     125 ..       8     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 2.3e-23
                                       HSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE--SSBTBS---TH CS
                       Aconitase_C  16 ksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvviagknfGeGSSReh 92 
                                        + +dtd++ip  f + ++  glg+  + ++r++++++ +     d + ++ ry+  +++++v+   nfG+GSSReh
  gi|336253788|ref|YP_004596895.1|  22 GNDIDTDQIIPARFMKVVTFDGLGEFAFFDVRFDDDDNPK-----DHPMNEDRYQ--DSSVMVVN-SNFGCGSSREH 90 
                                       5678999****************99999999999888853.....6778******..88888888.9********** PP

                                       HHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEE CS
                       Aconitase_C  93 AAkalrllGikaviaeSFerIfennliknglLple 127
                                       A+ al   Gi a+i eSF++If  n +  g+ +++
  gi|336253788|ref|YP_004596895.1|  91 APQALMRWGIDAIIGESFAEIFAGNCLALGIPTVT 125
                                       **************************999997776 PP

>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.5e-05      0.14     102     158 ..     124     181 ..      99     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.5e-05
                                       EE.--S-HHHHHHHH.HTHHHHHHHHHHCSHHCCT-EEEEEEEEE-SSEEEEEEEEE- CS
                       HMG-CoA_red 102 llesvedaaelkkwi.ekkeeleelanaaestsrggglkdievvlagrlvvlrlkvdt 158
                                       ++++ e+++el++w+ e+ +e +e+  +ae+++ gg+  d++v  a+r + ++   dt
  gi|336253788|ref|YP_004596895.1| 124 VTADSETIQELQDWVdEHPDEEIEIDVEAEEVTYGGRTIDVTVDEAQRKALVEGVWDT 181
                                       4568999************************************777777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); 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 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1638.70
//
Query:       gi|336253789|ref|YP_004596896.1|  [L=585]
Description: von Willebrand factor type A [Halopiger xanaduensis SH-6]
Scores for 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-13   49.5   0.0    1.1e-12   48.5   0.0    1.5  1  VWA_2       von Willebrand factor type A domain
    1.4e-12   48.3   0.2    3.2e-12   47.1   0.2    1.6  1  VWA         von Willebrand factor type A domain
    8.5e-09   35.5   0.4    7.5e-08   32.5   0.0    2.1  2  VWA_3       von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.011   15.1   0.2       0.89    8.9   0.0    2.3  2  VWA_CoxE    VWA domain containing CoxE-like protein


Domain annotation for each model (and alignments):
>> 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   2.5e-16   1.1e-12       1     107 []     174     306 ..     174     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 2.5e-16
                             VWA_2   1 lvfvlDtSgSmrng..dy...............gptrleaakdaveallkslp.gdrvglvtfsdgpevliplt... 56 
                                       lv+vlD SgSmr++  dy               +  +++ ak+a+ a+  +l+ +dr+g+v f++++++  pl    
  gi|336253789|ref|YP_004596896.1| 174 LVVVLDISGSMRASfdDYyydqfgnrheaegdtSRPKIDVAKEALAAMTRQLRpDDRLGVVLFNGEAHLAKPLRevd 250
                                       79**********9986669*****999999876677**************995599*****************6533 PP

                             VWA_2  57 .kdkakilnalrnleak...gggtnlaaaLqlarkalkkrr....kgekrvivlitDge 107
                                        +d ++i++ +r+   +   +ggtn+ a+L+l ++++ +      + ++++ +litD++
  gi|336253789|ref|YP_004596896.1| 251 rTDMDAIREHMRE---DveaRGGTNVSAGLELSEELVAEYDdadrEAYENRTILITDAQ 306
                                       3555555555555...45559***************9766667779***********85 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 !   47.1   0.2   7.1e-16   3.2e-12       1     170 [.     173     366 ..     173     372 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 7.1e-16
                                       EEEEEEE-STTS......................CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEET CS
                               VWA   1 DivfvlDgSgsm......................geenfekvkefikklveklevgpegtrvglvqfssevktefsl 55 
                                       ++v+vlD Sgsm                      ++ +++ +ke++  + ++l    +++r+g+v f++e++   +l
  gi|336253789|ref|YP_004596896.1| 173 NLVVVLDISGSMrasfddyyydqfgnrheaegdtSRPKIDVAKEALAAMTRQLR---PDDRLGVVLFNGEAHLAKPL 246
                                       79*************************9999998899999**************...******************** PP

                                       TS.HC.HHHHHHHHHHTGSGGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS....HTHHHHHH CS
                               VWA  56 nd.ys.skeellsalnnlkysgggttntgkalkyaleklfkssagaRenakkviilltdGksndg....dpkeaane 126
                                       ++ ++ + +++ ++ ++ +++  g tn+ ++l+   e + +     Re +++  il+td + n g    d ++a+ e
  gi|336253789|ref|YP_004596896.1| 247 REvDRtDMDAIREHMRE-DVEARGGTNVSAGLELSEELVAEYDDADREAYENRTILITDAQINVGetdaDELQASLE 322
                                       **66688899******9.777777777********************************666654455555555555 PP

                                       HHGC.TEEEEEEEESSSHHHHHHHHHSSSSCHHCEEEESSHHHHH CS
                               VWA 127 akeq.gikvfavGvgnadekelLnkiasepgeghvftvtdfeele 170
                                       a ++ +  + +vGvg + ++el+ ++    g  +++ v++ +e+e
  gi|336253789|ref|YP_004596896.1| 323 ANADrDHHTTVVGVGVDFNAELIDRLTAVRG-ANYYSVHSADEFE 366
                                       5555599*******************99999.9999999988755 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 ?    0.9   0.1     0.089     4e+02       2      16 ..     173     187 ..     172     191 .. 0.89
   2 !   32.5   0.0   1.7e-11   7.5e-08      17     147 ..     210     350 ..     202     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.089
                             VWA_3   2 evvivvDvsssmsae 16 
                                       ++v+v+D+s sm+a+
  gi|336253789|ref|YP_004596896.1| 173 NLVVVLDISGSMRAS 187
                                       79**********986 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 1.7e-11
                             VWA_3  17 n.klvkdaLsvalrqLptndkiavllfgtkprplfpgsravsaaelqealqkike.lelslgasnlegaLk...eal 88 
                                       + + +k+aL ++ rqL + d++ v+lf  ++  l +  r+v+ ++ +++++   e  e+ +g++n+ + L+   e +
  gi|336253789|ref|YP_004596896.1| 210 KiDVAKEALAAMTRQLRPDDRLGVVLFNGEAH-LAKPLREVDRTDMDAIREHMREdVEA-RGGTNVSAGLElseELV 284
                                       34689*************************66.********************997777.***********776333 PP

                             VWA_3  89 rqp....akpgevrsvilltDgssaqge...ervsdlisr.arekirfhalglgsslsaamlqaLAe 147
                                       + +    ++ ++   +il+tD ++  ge   +++ +++++ a ++ +  ++g g + +a+++++L  
  gi|336253789|ref|YP_004596896.1| 285 A-EyddaDREAYENRTILITDAQINVGEtdaDELQASLEAnADRDHHTTVVGVGVDFNAELIDRLTA 350
                                       3.2356799**************9554424466777777524499******************9975 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0002      0.89      57      72 ..     171     186 ..     159     196 .. 0.83
   2 ?    4.0   0.1    0.0063        28      81     144 ..     218     285 ..     205     325 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0002
                          VWA_CoxE  57 prelvllvDvSgSmaa 72 
                                         +lv+++D+SgSm a
  gi|336253789|ref|YP_004596896.1| 171 ALNLVVVLDISGSMRA 186
                                       458***********87 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0063
                          VWA_CoxE  81 lhAllqqlp...rtevfaFdtrlvdlTralrerDpa..eaLarvsaavedlgGgTrigaalaeflelvt 144
                                       l+A+++ql+   r  v++F+ + ++l + lre D++  +a+++  ++  +  GgT+++a+l+   elv+
  gi|336253789|ref|YP_004596896.1| 218 LAAMTRQLRpddRLGVVLFNGE-AHLAKPLREVDRTdmDAIREHMREDVEARGGTNVSAGLELSEELVA 285
                                       6788888777889999999876.567777777666511456655444444789********98888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); 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:                         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 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 4180.52
//
Query:       gi|336253790|ref|YP_004596897.1|  [L=795]
Description: peptidase S8 and S53 subtilisin kexin sedolisin [Halopiger xanaduensis SH-6]
Scores for complete 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-35  122.7   5.7    5.2e-35  121.1   5.7    1.8  1  Peptidase_S8     Subtilase family
      9e-33  112.4  26.5    4.2e-18   65.4   3.8    3.8  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    7.4e-17   61.1   3.7    6.9e-11   42.0   0.3    3.4  3  CarbopepD_reg_2  CarboxypepD_reg-like domain
      1e-06   28.5   0.3      0.055   13.4   0.1    3.7  4  PEGA             PEGA domain
    2.7e-06   27.3   9.5    0.00051   20.0   1.5    4.0  3  Big_1            Bacterial Ig-like domain (group 1)
    7.1e-05   22.8   2.9     0.0043   17.1   0.2    2.7  2  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
    0.00027   20.7   7.0      0.064   12.9   0.5    2.3  2  DUF4249          Domain of unknown function (DUF4249)
     0.0004   20.5   0.4      0.026   14.7   0.1    2.8  2  MG4              Macroglobulin domain MG4
      0.004   17.5  15.8      0.048   14.0   1.9    4.1  3  DUF3869          Domain of unknown function (DUF3869)
  ------ inclusion threshold ------
      0.015   15.1   2.7        3.5    7.5   0.1    3.1  3  DUF824           Salmonella repeat of unknown function (DUF82
      0.086   13.1  10.4       0.23   11.7   1.4    3.3  3  SdrD_B           SdrD B-like domain
        1.6    9.4   5.0        8.7    7.0   0.1    3.6  3  YtkA             YtkA-like


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.1   5.7   3.5e-38   5.2e-35       1     298 []     222     494 ..     222     494 .. 0.78

  Alignments for each domain:
  == domain 1  score: 121.1 bits;  conditional E-value: 3.5e-38
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanap 77 
                                       g+gv vavlD+Gvd +hpd++v              e      +d ++    + +d +g    HGt v Gi+a++ +
  gi|336253790|ref|YP_004596897.1| 222 GEGVRVAVLDSGVDADHPDIEVA-------------E-----WKDFDDNPSAEPVDYDG----HGTQVSGIVAGG-N 275
                                       79*****************9932.............2.....33344444444555556....************.* PP

                                       SSSSSB-SSTTSEEEEEE-SSTTSB-HH.....HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  78 eegekngvapgakilsvkvldtsggsmetg...teliraieeaaedkvdvinmslgestslpktgrsiealainrav 151
                                        +g+  gvap+a++l   v++++++ +  g   +++++++e+a+e+++dvi++slg + +   +++     ai++a+
  gi|336253790|ref|YP_004596897.1| 276 ASGTHIGVAPDATLLHGAVMTDCENRKRCGgrsSTILAGMEWALEEDADVISLSLGWDGHSRASVD-----AIENAR 347
                                       ***************55555555544433323388*********************4444444443.....999*** PP

                                       .CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxx RF
                      Peptidase_S8 152 nkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssd...............gkl 213
                                        + g++vv + GN g          +  +p+++  v++vga++  +++ +fS  G ++d                 +
  gi|336253790|ref|YP_004596897.1| 348 -EAGTVVVGAVGNGG--------EGTSLSPGNAYDVVSVGAIDRSDDVPSFS-GGEEIDtagewrgdapvrwpdSYV 414
                                       .99************........566788999999********888888888.677777777766666555454557 PP

                                       ..-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT.--HHHHHHHHHCCS-EE..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx...xx RF
                      Peptidase_S8 214 kpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpk.ltpetvraallntAqdl...gk 286
                                        pd+vapG++ v++++  +       +y +  GTS  +P++ag +Al++sa  + l+p+++++al+ tA +     +
  gi|336253790|ref|YP_004596897.1| 415 VPDVVAPGVS-VKSATPGG-------GYRTNLGTSLTAPHVAGTVALVQSATAEeLSPDEIKRALEETA-WKpegED 482
                                       8999999998.44444444.......29999*******************66666**************.5556666 PP

                                       ....SSSSSSTT CS
                                       xxxxxxxxxxxx RF
                      Peptidase_S8 287 adniesfaqGaG 298
                                        +++ + ++G G
  gi|336253790|ref|YP_004596897.1| 483 VPAAKDVRYGSG 494
                                       666666666665 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   3.8   2.8e-21   4.2e-18       1      81 [.     510     589 ..     510     590 .. 0.96
   2 !   34.8   2.1   9.7e-12   1.4e-08       1      75 [.     594     667 ..     594     675 .. 0.85
   3 !   23.1   5.2   4.3e-08   6.5e-05       4      81 ..     682     761 ..     679     762 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 2.8e-21
                   CarboxypepD_reg   1 tisGrVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglpp.gtysvtvsapGyatatreevtltagqtt 75 
                                       t+ G+Vtda +gapia+atV+v   ++g  +++ttdadG++ ++gl+  ++y v+v+++Gy+++t  + t++ ++t+
  gi|336253790|ref|YP_004596897.1| 510 TLAGTVTDAeTGAPIANATVEVI--GEGDPYEATTDADGRYEIPGLAGdQEYAVVVERDGYESVTE-TRTVASDETS 583
                                       689*****889************..99**************************************6.69******** PP

                   CarboxypepD_reg  76 tlditL 81 
                                       tld++L
  gi|336253790|ref|YP_004596897.1| 584 TLDVEL 589
                                       ****98 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 9.7e-12
                   CarboxypepD_reg   1 tisGrVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglpp.gtysvtvsapGyatatreevtltagqtt 75 
                                       ti+  Vtda  g +i+ atV++   +   +++     dG++rl+++p+ g+y+++v a+Gy  a+r +v+ +a++++
  gi|336253790|ref|YP_004596897.1| 594 TIEVDVTDAhFGDGIEAATVEAV--GPAGTYTGAHVGDGTYRLENVPTrGEYDLRVGADGYVDAER-AVSFAADTDR 667
                                       68888***967************..666777777789****************************7.6998887654 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 4.3e-08
                   CarboxypepD_reg   4 GrVtdasgapiagatVtvtnadtgtv..astttdadGafrlrglpp..gtysvtvsapGyatatreevtltagqttt 76 
                                        +V  ++ +pi++atVtv++ d+g++  a+ tt +dG+  +  +p    +y v++ ap +++ ++e+  ++ g+t+ 
  gi|336253790|ref|YP_004596897.1| 682 VTVQTEDREPIENATVTVER-DSGVTydANGTTREDGTLEVV-VPGtgESYAVEAAAPEFESNAVETGPVASGETVS 756
                                       588999*************6.5555422888*********97.777899**************************99 PP

                   CarboxypepD_reg  77 lditL 81 
                                       +++ L
  gi|336253790|ref|YP_004596897.1| 757 VTVPL 761
                                       99876 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.3   4.6e-14   6.9e-11       2      79 ..     512     592 ..     511     600 .. 0.87
   2 !   15.8   0.0   6.9e-06      0.01       5      68 ..     599     665 ..     596     685 .. 0.78
   3 ?    2.9   0.1     0.072   1.1e+02       7      34 ..     685     711 ..     681     728 .. 0.76

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 4.6e-14
                   CarbopepD_reg_2   2 sGtVvdketkeplpgatVyvkgtk..kgtvTdenGnFelknlpa.gkytLvvsyvGyktqekkvtvskektldvnil 75 
                                        GtV+d+et+ p++ atV v g +    ++Td++G++e+  l   ++y +vv+  Gy++++++ tv++++t +++++
  gi|336253790|ref|YP_004596897.1| 512 AGTVTDAETGAPIANATVEVIGEGdpYEATTDADGRYEIPGLAGdQEYAVVVERDGYESVTETRTVASDETSTLDVE 588
                                       7*****************996654349*************7765389*********************999999998 PP

                   CarbopepD_reg_2  76 lkee 79 
                                       l+ +
  gi|336253790|ref|YP_004596897.1| 589 LAGN 592
                                       8755 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 6.9e-06
                   CarbopepD_reg_2   5 VvdketkeplpgatVyvkgtkkgtvTde...nGnFelknlpa.gkytLvvsyvGyktqekkvtvskek 68 
                                       V+d++ ++ ++ atV   g  +gt+T +   +G+++l+n+p  g+y L+v + Gy  +e+ v+++ ++
  gi|336253790|ref|YP_004596897.1| 599 VTDAHFGDGIEAATVEAVGP-AGTYTGAhvgDGTYRLENVPTrGEYDLRVGADGYVDAERAVSFAADT 665
                                       78888888888898888664.57777654448********9889******************997653 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.072
                   CarbopepD_reg_2   7 dketkeplpgatVyvkgtkkgtvTdenG 34 
                                       ++e+ ep++ atV+v+    g++ d+nG
  gi|336253790|ref|YP_004596897.1| 685 QTEDREPIENATVTVERD-SGVTYDANG 711
                                       456679*********765.455556666 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.8   2.7e+03      42      56 ..     117     131 ..     116     142 .. 0.83
   2 !   13.4   0.1   3.7e-05     0.055      35      66 ..     558     589 ..     554     592 .. 0.94
   3 !   10.4   0.0   0.00031      0.46      33      58 ..     640     665 ..     624     674 .. 0.87
   4 ?   -2.5   0.0       3.4   5.1e+03      47      66 ..     742     761 ..     728     763 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.8
                              PEGA  42 keGYedlektvtvta 56 
                                       +e Y+++++ vt+++
  gi|336253790|ref|YP_004596897.1| 117 LERYANATEGVTLER 131
                                       789*********984 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.7e-05
                              PEGA  35 nyslrvekeGYedlektvtvtagetvklnltL 66 
                                       +y + ve +GYe +++t tv ++et +l+++L
  gi|336253790|ref|YP_004596897.1| 558 EYAVVVERDGYESVTETRTVASDETSTLDVEL 589
                                       699*************************9998 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00031
                              PEGA  33 aGnyslrvekeGYedlektvtvtage 58 
                                        G+y lrv ++GY d+e+ v++ a++
  gi|336253790|ref|YP_004596897.1| 640 RGEYDLRVGADGYVDAERAVSFAADT 665
                                       69*******************99775 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 3.4
                              PEGA  47 dlektvtvtagetvklnltL 66 
                                       ++++t  v +getv++++ L
  gi|336253790|ref|YP_004596897.1| 742 NAVETGPVASGETVSVTVPL 761
                                       56777788999999999887 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 !   10.0   0.2   0.00044      0.65       7      50 ..     509     550 ..     506     551 .. 0.85
   2 ?   -3.1   0.1       5.7   8.5e+03       8      16 ..     594     602 ..     590     615 .. 0.59
   3 !   20.0   1.5   3.4e-07   0.00051       8      52 ..     679     723 ..     675     730 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00044
                             Big_1   7 ntltatvkDan.gnpvagatVtfsvsggalsassgtTdanGkatv 50 
                                       +tl  tv+Da+ g p+a+atV +   g    + ++tTda+G++++
  gi|336253790|ref|YP_004596897.1| 509 ATLAGTVTDAEtGAPIANATVEVIGEG---DPYEATTDADGRYEI 550
                                       68999****8549**********9777...56699******9875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.7
                             Big_1   8 tltatvkDa 16 
                                       t+ + v+Da
  gi|336253790|ref|YP_004596897.1| 594 TIEVDVTDA 602
                                       344444544 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 3.4e-07
                             Big_1   8 tltatvkDangnpvagatVtfsvsggalsassgtTdanGkatvtl 52 
                                        l +tv+ ++  p+++atVt++ ++g++  ++gtT ++G+ +v +
  gi|336253790|ref|YP_004596897.1| 679 ALAVTVQTEDREPIENATVTVERDSGVTYDANGTTREDGTLEVVV 723
                                       5889999999*****************************998865 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   2.9e-06    0.0043      18      98 ..     514     587 ..     506     592 .. 0.80
   2 ?    5.1   0.3     0.015        23      13      59 ..     677     724 ..     667     745 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.9e-06
                              bMG3  18 wvtsLdsgkPvagaeVrlldkkgevlaegtTDaqGvarfaallargkegaapylvsArkdedlaflkldwergldls 94 
                                        vt  ++g P+a+a+V+++ + +    e+tTDa+G++++++l      g++ y+v++++d+  +++++++ +  ++s
  gi|336253790|ref|YP_004596897.1| 514 TVTDAETGAPIANATVEVIGEGDP--YEATTDADGRYEIPGL-----AGDQEYAVVVERDGYESVTETRTVASDETS 583
                                       588899*************98776..79*************9.....789999999997776666666555555555 PP

                              bMG3  95 rfdv 98 
                                         dv
  gi|336253790|ref|YP_004596897.1| 584 TLDV 587
                                       5555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.015
                              bMG3  13 dkllvwvtsLdsgkPvagaeVrlldkkgevl.aegtTDaqGvarfaal 59 
                                       d +l+++ + ++ +P+++a+V++  ++g +  a+gtT ++G +++  +
  gi|336253790|ref|YP_004596897.1| 677 DAALAVTVQTEDREPIENATVTVERDSGVTYdANGTTREDGTLEVVVP 724
                                       56677777779**************99988757899999998887766 PP

>> DUF4249  Domain of unknown function (DUF4249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   1.1   0.00018      0.27      30     132 ..     496     589 ..     495     611 .. 0.68
   2 !   12.9   0.5   4.3e-05     0.064      57     113 ..     686     744 ..     667     764 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                           DUF4249  30 vnalitaeadtteirlsrsvpvsesdsieevkavtdAtVtlyvnegqeyelsetkagyyssfrlkpgdtyrLeittp 106
                                       v+a+   +a  ++++l  +v+  ++++  +   + +AtV+++ + g  ye +++ +g+y    l   + y + ++  
  gi|336253790|ref|YP_004596897.1| 496 VDAYAAIDAVGQYATLAGTVT--DAETGAP---IANATVEVIGE-GDPYEATTDADGRYEIPGLAGDQEYAVVVER- 565
                                       556666655556666666664..5554444...78********9.989988877777886645555667*******. PP

                           DUF4249 107 dgkeyvsaettvpspppeidtvsaee 132
                                       dg+e v+++ tv s   e+ t+++e 
  gi|336253790|ref|YP_004596897.1| 566 DGYESVTETRTVASD--ETSTLDVEL 589
                                       79*********9733..245555555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.3e-05
                           DUF4249  57 ieevkavtdAtVtlyvnegqeyels.etkag.yyssfrlkpgdtyrLeittpdgkeyvs 113
                                       +e+ +++++AtVt++ ++g++y  + +t ++ ++ +  + +g++y +e+ +p+ + ++ 
  gi|336253790|ref|YP_004596897.1| 686 TEDREPIENATVTVERDSGVTYDANgTTREDgTLEVVVPGTGESYAVEAAAPEFESNAV 744
                                       33457888********99*9997774444445676789*************98544433 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.097   1.4e+02      25      58 ..     519     548 ..     514     551 .. 0.84
   2 !   14.7   0.1   1.7e-05     0.026      18      62 ..     680     723 ..     679     740 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.097
                               MG4  25 pdgspaknvpVkiealkseteekeslttdedGta 58 
                                       + g p++n +V +   +    ++ + ttd+dG+ 
  gi|336253790|ref|YP_004596897.1| 519 ETGAPIANATVEVIG-E---GDPYEATTDADGRY 548
                                       5799********999.4...688899******86 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.7e-05
                               MG4  18 ikVlvkdpdgspaknvpVkiealkseteekeslttdedGtakfsi 62 
                                       + V v+ +d +p++n +V++e  +s+ +++ + tt+edGt ++++
  gi|336253790|ref|YP_004596897.1| 680 LAVTVQTEDREPIENATVTVER-DSGVTYDANGTTREDGTLEVVV 723
                                       579999****************.999***************9998 PP

>> DUF3869  Domain of unknown function (DUF3869)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   1.9   3.2e-05     0.048      21      83 ..     509     581 ..     497     591 .. 0.87
   2 !    8.7   0.1    0.0015       2.2      22      83 ..     594     663 ..     584     667 .. 0.80
   3 ?    0.7   2.8      0.47     7e+02      19      69 ..     676     726 ..     663     761 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-05
                                       EEEEEEE..EETTTTEE-CGCCEEC............CCCCSSEEEECCSCT-EEEEEEECTETTEE.EEEEEE-- CS
                           DUF3869  21 ytisgtvldieattgtdvtdkatis............tssgtatfkggaelaakavkisatGYegik.tatVsvaa 83 
                                       +t++gtv  ++a+tg+ ++ +at++            ++ g   + g a ++ +av++  +GYe ++ t+tV  ++
  gi|336253790|ref|YP_004596897.1| 509 ATLAGTV--TDAETGAPIA-NATVEvigegdpyeattDADGRYEIPGLAGDQEYAVVVERDGYESVTeTRTVASDE 581
                                       7999***..8888999998.788888899999999888899999999999*****************9***98665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0015
                                       EEEEEE..EETTTTEE-CGCCEEC.........CCCCSSEEEECCSCT-EEEEEEECTETTEEEEEEEE-- CS
                           DUF3869  22 tisgtvldieattgtdvtdkatis.........tssgtatfkggaelaakavkisatGYegiktatVsvaa 83 
                                       ti++ v+d+ +++g +++   ++          +  gt  +++ ++ + +++ + a+GY +++ + Vs aa
  gi|336253790|ref|YP_004596897.1| 594 TIEVDVTDAHFGDGIEAATVEAVGpagtytgahVGDGTYRLENVPTRGEYDLRVGADGYVDAE-RAVSFAA 663
                                       7899998888888877774444448888888766777888889999*****************.9998765 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.47
                                       -EEEEEEEE..EETTTTEE-CGCCEECCCCCSSEEEECCS...CT-EEEEEEEC CS
                           DUF3869  19 Akytisgtvldieattgtdvtdkatistssgtatfkggae...laakavkisat 69 
                                         + +++tv + + +  +++t  +t++  sg +t+ ++ +   ++  +v++  t
  gi|336253790|ref|YP_004596897.1| 676 GDAALAVTVQTEDREPIENAT--VTVERDSG-VTYDANGTtreDGTLEVVVPGT 726
                                       456677777666777777777..88887666.6665544433455555555555 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 ?    7.5   0.1    0.0024       3.5      20      35 ..     514     530 ..     500     534 .. 0.85
   2 ?    6.4   0.1    0.0052       7.8      17      42 ..     680     705 ..     678     706 .. 0.88
   3 ?   -3.5   0.0       6.5   9.7e+03       9      19 ..     749     759 ..     748     759 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0024
                            DUF824  20 tvkDasGn.Pvpnapft 35 
                                       tv+Da ++ P++na++ 
  gi|336253790|ref|YP_004596897.1| 514 TVTDAETGaPIANATVE 530
                                       9*************996 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0052
                            DUF824  17 ltitvkDasGnPvpnapftltRgdgk 42 
                                       l +tv   + +P+ na++t+ R++g 
  gi|336253790|ref|YP_004596897.1| 680 LAVTVQTEDREPIENATVTVERDSGV 705
                                       67889989999************985 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.5
                            DUF824   9 aKkGEsiplti 19 
                                       +  GE++ +t+
  gi|336253790|ref|YP_004596897.1| 749 VASGETVSVTV 759
                                       5679*999997 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00015      0.23      21      98 ..     520     598 ..     512     612 .. 0.71
   2 ?    0.4   0.1      0.51   7.6e+02      34      65 ..     618     648 ..     593     679 .. 0.59
   3 ?    5.1   0.4     0.018        26      16      68 ..     684     738 ..     681     752 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                            SdrD_B  21 e.kgisgvtVtLkdakgevvatttTdasGkYkFtnltpGe.YkVefta.pagytvtakkaGsddaldSdadpatglt 94 
                                         + i++ tV+++ + +    + tTda+G+Y+  +l+  + Y V ++    + ++++++ +sd++   d++ a + t
  gi|336253790|ref|YP_004596897.1| 520 TgAPIANATVEVIGEGDPY--EATTDADGRYEIPGLAGDQeYAVVVERdGYESVTETRTVASDETSTLDVELAGNGT 594
                                       3467889999996655544..689************98776999997634444677777888888777776666555 PP

                            SdrD_B  95 ktvt 98 
                                         v+
  gi|336253790|ref|YP_004596897.1| 595 IEVD 598
                                       5555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.51
                            SdrD_B  34 akgevvatttTdasGkYkFtnl.tpGeYkVeft 65 
                                        +g+ +   +   +G+Y+ +n+ t GeY +++ 
  gi|336253790|ref|YP_004596897.1| 618 PAGTYTGAHV--GDGTYRLENVpTRGEYDLRVG 648
                                       3333332222..346666666634566666653 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.018
                            SdrD_B  16 iqdagekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGe.YkVeftapa 68 
                                       +q ++ + i++ tVt+ +++g +  a+ tT ++G+ +      Ge Y Ve +ap+
  gi|336253790|ref|YP_004596897.1| 684 VQTEDREPIENATVTVERDSGVTYdANGTTREDGTLEVVVPGTGEsYAVEAAAPE 738
                                       6788899****************98899******988777666668999998875 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.22   3.2e+02      26      47 ..     515     536 ..     503     564 .. 0.70
   2 ?   -0.9   0.1       1.7   2.6e+03      60      72 ..     623     635 ..     583     647 .. 0.58
   3 ?    7.0   0.1    0.0058       8.7      19      45 ..     675     702 ..     667     727 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.22
                              YtkA  26 vtvtqggkpVedadvkvefwmp 47 
                                       vt+ ++g+p+ +a+v+v ++ +
  gi|336253790|ref|YP_004596897.1| 515 VTDAETGAPIANATVEVIGEGD 536
                                       5688999999999998866655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                              YtkA  60 elkesedGvYeae 72 
                                       +  + +dG Y++e
  gi|336253790|ref|YP_004596897.1| 623 TGAHVGDGTYRLE 635
                                       3444577777776 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0058
                              YtkA  19 agentivvt.vtqggkpVedadvkvefw 45 
                                       +g++++ vt  t++ +p+e+a+v+ve++
  gi|336253790|ref|YP_004596897.1| 675 DGDAALAVTvQTEDREPIENATVTVERD 702
                                       688888887699*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.44
# Mc/sec: 5457.97
//
Query:       gi|336253791|ref|YP_004596898.1|  [L=326]
Description: 3-isopropylmalate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-89  299.8   0.0    3.2e-89  299.5   0.0    1.0  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 !  299.5   0.0   1.8e-93   3.2e-89       2     348 .]       5     322 ..       4     322 .. 0.95

  Alignments for each domain:
  == domain 1  score: 299.5 bits;  conditional E-value: 1.8e-93
                                       EEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSS CS
                            Iso_dh   2 iallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkeke 78 
                                       ia+++gdgiG+ev++aa++vl+a++     ++ef e+++G a+ +etge+lp+et + + +ad+ l+ga g      
  gi|336253791|ref|YP_004596898.1|   5 IAVIPGDGIGQEVTPAAVEVLEALD----VDFEFVEAEAGDAVKEETGEALPQETYDLAASADATLFGAAGETA--- 74 
                                       9**********************99....679*************************************98877... PP

                                       SSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEE CS
                            Iso_dh  79 vrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtk 155
                                             +l Lr  +d f+n+rp+k ++       +++    e+dlv +Re+t+g+Y+g+e   ++      v   t 
  gi|336253791|ref|YP_004596898.1|  75 ---ADVILPLRDAVDSFVNIRPAKAYP---GVDAVRP----ETDLVFLRENTEGVYSGIEDRLTQD-----VSTLTR 136
                                       ...55699******************5...3345665....58*****************999886.....89999* PP

                                       EEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGG CS
                            Iso_dh 156 lyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamqlvkspkq 231
                                       +++e+++e + ++a+e+ +++  +  t+ +Kanv++ ++ l+r+++++va+   +++e +++l+D++a ++  +p+q
  gi|336253791|ref|YP_004596898.1| 137 VVTESASEDLGEFACEYVEDNSYDGFTIAHKANVMRETDgLFRDTIKRVAD--ENGVETDEVLMDAFATHVCLNPEQ 211
                                       **************************************************9..799********************* PP

                                       GSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT-H CS
                            Iso_dh 232 fdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLryslgle 308
                                       fdViv++Nl GD+lSD+aa lvG+lGllpSa++g+ + a+fE+vHG+apdiag ++aNp a+i+Saa++L+y lg +
  gi|336253791|ref|YP_004596898.1| 212 FDVIVCPNLAGDVLSDLAAGLVGGLGLLPSANVGP-ERALFEPVHGTAPDIAGEGVANPAATIISAAMLLEY-LGYD 286
                                       **********************************7.79**********************************.**** PP

                                       HHHHHHHHHHHHHHHHTSCCHHHCTTSTCCCHHHHHHHHH CS
                            Iso_dh 309 eaAdkiekAvekvleagivTkDlageaakevstsefgdav 348
                                       e+ +++++Ave++le+g +T Dl+g a    st+++++a+
  gi|336253791|ref|YP_004596898.1| 287 EEGQAVHEAVEATLEDGPRTPDLGGDA----STEDVTNAI 322
                                       *************************99....999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2419.74
//
Query:       gi|336253792|ref|YP_004596899.1|  [L=703]
Description: beta-glucosidase [Halopiger xanaduensis SH-6]
Scores for complete 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-58  198.5   0.0    3.2e-58  197.1   0.0    1.7  1  Glyco_hydro_3_C  Glycosyl hydrolase family 3 C-terminal domai
      5e-52  177.2   0.0    3.8e-51  174.4   0.0    1.9  2  Glyco_hydro_3    Glycosyl hydrolase family 3 N terminal domai
    1.4e-18   66.7   0.1    2.9e-18   65.7   0.1    1.6  1  Fn3-like         Fibronectin type III-like domain


Domain annotation for each model (and alignments):
>> 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 !  197.1   0.0   5.3e-62   3.2e-58       1     204 []     346     586 ..     346     586 .. 0.91

  Alignments for each domain:
  == domain 1  score: 197.1 bits;  conditional E-value: 5.3e-62
                                       -EEEEEGSS--S-S-STEEEEEESGGGSSS-SS-BSSS----S---HHHHHHHHHHH.................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................... RF
                   Glyco_hydro_3_C   1 iVLLkNennlLPLkkklkkiaviGpnadetlklGggsgtvtvsylvsplegirerles................... 58 
                                       +V+L+N+ ++LPL+ + ++ia++Gpnad++   Gggs++vt+ + +spleg+++r+++                   
  gi|336253792|ref|YP_004596899.1| 346 TVMLQND-GALPLADD-ESIALVGPNADTAKLGGGGSSEVTPFTETSPLEGLEDRAADltfergvepiaessffddg 420
                                       59*****.*****666.5**********9999999*******99************99******************* PP

                                       ........-HHHHHHHHHHHTSEEEEEEEES...SB-TTSCSGHHSSTTHHHHHHHHHHTTSSEEEEEEESSGG--T CS
                                       .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Glyco_hydro_3_C  59 .......eegideaveaakeaDvavvvvgedpeiegEgvDrtdlalpeaqdelikavaaanknvvvvlqsggpvave 128
                                              +++id+av+aa eaD+avvv+++d   ++E  Dr++l+lp+ q+eli+ava+a +++vvvl ++gpva+ 
  gi|336253792|ref|YP_004596899.1| 421 dettdegNASIDAAVTAADEADCAVVVAQDD---ATEFTDRDSLELPGDQNELISAVADAAERTVVVLRTSGPVAM- 493
                                       *******99**********************...******************************************. PP

                                       TTGTTTEEEEEE-S--GCCHHHHHHHHHTTSS---B--SS-EESSSGGG............................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx....xx............. RF
                   Glyco_hydro_3_C 129 pwkeenvkAilaawlpGqegGtaiadvLfGdvnPsGkLpvtfpksledlpd.dyyeek....dt............. 187
                                       pw  e+v+A+l++w+pGq+ G+a+a vLfGd++P+G+Lpvtf +s++d+p+ d         d              
  gi|336253792|ref|YP_004596899.1| 494 PW-LEAVDAVLETWYPGQADGEALAAVLFGDADPGGRLPVTFGQSAADYPTaDEA--AfpgvDDvtsydegvfvgyr 567
                                       77.56********************************************884222..22334115667778899977 PP

                                       ..S.-----SETTTT-BCH CS
                                       .xx.xxxxxxxxxxxxxxx RF
                   Glyco_hydro_3_C 188 .yk.fegtplYpeGlglsY 204
                                         + ++++pl+p+G+glsY
  gi|336253792|ref|YP_004596899.1| 568 yFDeHDREPLFPFGHGLSY 586
                                       6445788899********9 PP

>> Glyco_hydro_3  Glycosyl hydrolase family 3 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.4   0.0   6.4e-55   3.8e-51      62     261 ..      39     233 ..      33     250 .. 0.95
   2 ?    0.4   0.0     0.056   3.4e+02     294     318 ..     288     312 ..     274     313 .. 0.89

  Alignments for each domain:
  == domain 1  score: 174.4 bits;  conditional E-value: 6.4e-55
                                       ....S--EEEE---BTTB---SSS---S-HHHHHHHT-HHHHHHHHHHHHHHHHHHT--EE---B-----STTSSSG CS
                     Glyco_hydro_3  62 srlgiPlllavDqegGlvqrlgegtlfPsalalaatssldlikelgriiakelralgididfaPvvdvnrdprngig 138
                                       +r+giP l  vD   G++   + +t fP+++alaa+++++l++e g ++++e +a + d+ ++P v++ r p+ g++
  gi|336253792|ref|YP_004596899.1|  39 DRVGIPPLRMVDGPLGVRAMAERATAFPASIALAASWNPELAREFGAALGRETAAHDQDVVLGPGVNIVRVPHGGRN 115
                                       699***************999988***************************************************** PP

                                       GGSS-SSHHHHHHHHHHHHHHHHHTT-EEEEEEETTGTT-SSETTTSEEB----HHHHHHTTHHHHHHHH.HTT-SE CS
                     Glyco_hydro_3 139 vrsFsedpelvaalaaamvkGlqgagvaatvKHFpghGdgavdshkelptvdhseeelrevdlvpfqaai.eagvds 214
                                       ++++sedp+l+++ +  +++G+q++gvaatvKH+ +    ++++++  +  d+ e++lre++l  f+aa+ e +v+s
  gi|336253792|ref|YP_004596899.1| 116 FEYYSEDPHLASRTGVGTIEGIQSEGVAATVKHYVAN---NQETNRYEVSADIGERALREIYLPAFRAAVeEGNVHS 189
                                       ************************************5...9999999999999*****************9999*** PP

                                       EEE---B-TTT---BGGG-HHHHIIIIIIIS---SEEEES-TTSHHH CS
                     Glyco_hydro_3 215 VMtaHvqfpaldgtpatgskklltdvLRkelGFdGvvvsDalamkei 261
                                       VMta   ++ ++g  ++ + +ll dvL++e+GFdG+vvsD+++    
  gi|336253792|ref|YP_004596899.1| 190 VMTA---YNRVNGAHMSDHGYLLSDVLKDEWGFDGLVVSDWWGTRST 233
                                       ****...***********************************76554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.056
                                       HHHHHHHTTSS-HHHHHHHHHHHHH CS
                     Glyco_hydro_3 294 alkkavkeGeltearidesvrrvlr 318
                                        l +av+ G++ e+ +de+v r+l 
  gi|336253792|ref|YP_004596899.1| 288 PLREAVEGGDVDESVLDEKVSRLLD 312
                                       5889******************997 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   0.1   4.9e-22   2.9e-18       1      71 []     619     692 ..     619     692 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 4.9e-22
                                       EEEEEEEEESS-STTSBS-EEEEEEEEEE-TT-EEEEEEEEECGGG-EEETTTTE...EE--SCEEEEEEESSS CS
                          Fn3-like   1 evvqlYvsdpessverpvkeLkgFekveLapGesktvtftldrkdlsvwdeekqk...wvvepGeytvlvgtss 71 
                                       evvq+Y+++  + v++p++eL+gFe v+L +Ges+ vt++l+++d++++de ++    w v  G+  + vg+ss
  gi|336253792|ref|YP_004596899.1| 619 EVVQVYAAKAAAPVPTPERELVGFESVSLGAGESTAVTVSLEAEDFAYYDESEDGpdgWTVAHGTNMIAVGRSS 692
                                       8**************************************************9874556**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (703 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 5249.65
//
Query:       gi|336253793|ref|YP_004596900.1|  [L=257]
Description: diphthine synthase [Halopiger xanaduensis SH-6]
Scores for complete 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   80.5   3.1      2e-22   80.2   3.1    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 !   80.2   3.1   1.1e-26     2e-22       1     213 []       1     218 [.       1     218 [. 0.78

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 1.1e-26
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleea.yeeiaealaeal 76 
                                       +l+++G+G+ d   +Tv++  al++ad  +++  ++++++   +++  e++ + + e  ++++a  e+  +a+ ea+
  gi|336253793|ref|YP_004596900.1|   1 MLTFIGLGLYDERSITVEGQTALRNADRAYAEF-YTSKLIGTTIEDL-ESYHDAEIE--VRDRAgVEQEPDAILEAA 73 
                                       799**************************8777.7888887766553.444444444..444441444444444444 PP

                      TP_methylase  77 ragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.........lp 144
                                       ++ +dV++l++GD ++++t+  l   lra+++gie++vi Gv++ +a  + +g+  + +g+++++          l 
  gi|336253793|ref|YP_004596900.1|  74 EN-EDVAFLTAGDTMISTTHVDLR--LRAHDRGIETRVIHGVTAQTATSSLTGLQNYRFGKATTLPfpyahgadgL- 146
                                       44.68******************6..99999*************************************96665443. PP

                      TP_methylase 145 glakeeereleallan....gdtlvllkapr.k.....laelaelLkealyddttpvavveragtedervvrgtlee 211
                                            +++  e + an     +t+v l+    +     ++  aelL+ea y+d+   +vv+rag +d  v  gt++e
  gi|336253793|ref|YP_004596900.1| 147 -----PASVTETIDANradgLHTVVYLDIKAeReeymtADTGAELLAEA-YPDL-VGVVVARAGSPDPLVEAGTMTE 216
                                       .....33333333333444489999996666437899899999999999.7766.889999******9999999999 PP

                      TP_methylase 212 la 213
                                       la
  gi|336253793|ref|YP_004596900.1| 217 LA 218
                                       85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1811.69
//
Query:       gi|336253794|ref|YP_004596901.1|  [L=131]
Description: endoribonuclease L-PSP [Halopiger xanaduensis SH-6]
Scores for 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-28   98.4   0.1    3.2e-28   98.2   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 !   98.2   0.1   1.8e-32   3.2e-28       6     120 ..      13     126 ..       9     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 1.8e-32
                                       TTSSS-BSEEEETTEEEEEEE-SB-TTTSCB..-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGGHHH CS
                     Ribonuc_L-PSP   6 aaaapYsqavkagnlvyvsGqlpldpetgelv.egdveeqtrqalenlkavLaaagaslsdvVkvtvFladiedfae 81 
                                       +++  Ys+av++g +v+vsG++++ + +g++v +gd+++qt+ ale +  +L++ag+sl+dvV+++ +++di+ +++
  gi|336253794|ref|YP_004596901.1|  13 ESTVGYSRAVRVGSQVHVSGTTATGE-DGDVVaPGDPYAQTKYALEVVADALEEAGSSLEDVVRTRLYVTDIDGWEA 88 
                                       56789******************995.777777******************************************** PP

                                       HHHHHHHHSSSSTS--EEEEEE-SBSG.GG-SEEEEEEEE CS
                     Ribonuc_L-PSP  82 vnevyaeafdelkeaParsaveVaaLp.kgakvEIeaiav 120
                                       + ++++e+f +    Pa s+veV++L  ++ +vEIea+a+
  gi|336253794|ref|YP_004596901.1|  89 IGKAHGEVFGDVR--PAASMVEVQRLIdPDHRVEIEAVAI 126
                                       ************5..***********99**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 975.42
//
Query:       gi|336253795|ref|YP_004596902.1|  [L=141]
Description: Rieske (2Fe-2S) iron-sulfur domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-07   29.8   0.1    5.4e-07   29.5   0.1    1.3  1  Rieske    Rieske [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1     3e-11   5.4e-07      34      83 ..      37      89 ..       3      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3e-11
                                      S-EEEEESC-TTTT-BCGGSEEE..TT.EEE-TTT--EEE.TTSBEEE-TTHH CS
                            Rieske 34 gevyAlsdvCtHrgaplsegkid..ekgvleCpcHgwayd.adGkvikgPapr 83
                                      + v    ++CtH+  + ++g++    kg+++Cp Hg+ +d ++G + +g+a +
  gi|336253795|ref|YP_004596902.1| 37 DGVEGWINRCTHEAQRFDTGRGApiRKGQIICPRHGSMFDtCSGYCDNGEAAD 89
                                      45557789********988777555999*******************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 987.96
//
Query:       gi|336253796|ref|YP_004596903.1|  [L=349]
Description: hypothetical protein Halxa_2405 [Halopiger xanaduensis SH-6]
Scores for complete 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-56  191.5   0.0    1.8e-56  191.1   0.0    1.2  1  Met_10           Met-10+ like-protein
    1.3e-13   50.5   0.0    3.5e-13   49.2   0.0    1.7  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    6.9e-07   29.9   0.0    2.3e-06   28.2   0.0    1.9  1  Methyltransf_25  Methyltransferase domain
      3e-06   26.9   0.0    4.2e-06   26.4   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    2.5e-05   24.8   0.0    6.7e-05   23.5   0.0    1.8  1  Methyltransf_11  Methyltransferase domain
    0.00014   21.7   0.0    0.00023   21.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    0.00048   19.6   0.0    0.00073   19.0   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0015   18.1   0.0      0.003   17.1   0.0    1.5  1  MTS              Methyltransferase small domain
     0.0021   17.9   0.1     0.0071   16.2   0.1    1.7  2  Methyltransf_23  Methyltransferase domain
     0.0065   16.1   0.0      0.012   15.2   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0093   15.7   0.0      0.016   14.9   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
       0.13   13.1   0.0       0.39   11.5   0.0    1.9  2  Methyltransf_12  Methyltransferase domain
       0.14   11.4   0.0       0.22   10.9   0.0    1.2  1  DNA_methylase    C-5 cytosine-specific DNA methylase
       0.22   11.4   0.0       0.38   10.7   0.0    1.3  1  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 !  191.1   0.0   1.4e-59   1.8e-56       2     199 .]      78     293 ..      77     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: 191.1 bits;  conditional E-value: 1.4e-59
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       ++e+ G  v+l+ ++   + + +i++++l+   +v+tvl+k s+v+ge+R+++ e+laG+d te++h+E+gc+f lD
  gi|336253796|ref|YP_004596903.1|  78 SYERLGKAVLLDEDDP--DRAWEIADAVLESDlPVETVLNKASKVKGETRVRDWELLAGED-TEVVHREYGCEFALD 151
                                       5788888888765554..44578**************************************.*************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                       +++vyfs++l++Er+r+a++ve ge+  d+fAG+Gpf +p ak  ++ + +++d+nP++++yl+en ++N ve++v+
  gi|336253796|ref|YP_004596903.1| 152 LAEVYFSPRLATERHRVAEQVESGERAFDMFAGVGPFVVPFAK--RGAECVGVDINPAAIEYLRENARRNGVEDRVT 226
                                       *******************************************..99999*************************** PP

                                       EEES-GGG---TT-EE......................EEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 155 pileDgrevireqlad......................rvvmnlpksaieFldkvlaalkdggvihy 199
                                       +i++ +r+++++ +                        r+vmnlp+sa eFld+++a++ d  v hy
  gi|336253796|ref|YP_004596903.1| 227 AICANVRTLVPPRVDAsegegaterdtkgapnyenwadRIVMNLPHSADEFLDTAVAIAGDDCVLHY 293
                                       *********9844333589***********************************************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 !   49.2   0.0   2.7e-16   3.5e-13       1      42 [.       5      46 ..       5      49 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.7e-16
                                      EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S- CS
                            Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkee 42
                                      c++Vp++egE +R  L++++l+d +y I  +d+ lyIP+++ 
  gi|336253796|ref|YP_004596903.1|  5 CVRVPREEGEATRSDLADADLIDDDYEIAVEDGNLYIPITDA 46
                                      ***************************************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.8e-09   2.3e-06       3      59 ..     180     236 ..     178     243 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.8e-09
                                       EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBS CS
                   Methyltransf_25   3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlp 59 
                                       d+ +G G ++  +akr+  a+ +gvDi+++++e+ re+a+++g+  +v+ +++++++l 
  gi|336253796|ref|YP_004596903.1| 180 DMFAGVGPFVVPFAKRG--AECVGVDINPAAIEYLRENARRNGVedRVTAICANVRTLV 236
                                       7889************5..************************************9984 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 !   26.4   0.0   3.3e-09   4.2e-06       4      62 ..     178     236 ..     175     280 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.3e-09
                   Methyltransf_15   4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfell 62 
                                         D+f+G G  v+ fa+ + + ++++in+  ++   +Na+  gv+d++t ++++v +l+
  gi|336253796|ref|YP_004596903.1| 178 AFDMFAGVGPFVVPFAKRGAECVGVDINPAAIEYLRENARRNGVEDRVTAICANVRTLV 236
                                       68***************************************************998855 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   5.3e-08   6.7e-05       5      55 ..     183     235 ..     179     243 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5.3e-08
                                       -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCT CS
                   Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaekl 55 
                                       +G G ++ ++akrga++vgvD++++++++ +e+a+++g+  +v+ ++a++++l
  gi|336253796|ref|YP_004596903.1| 183 AGVGPFVVPFAKRGAECVGVDINPAAIEYLRENARRNGVedRVTAICANVRTL 235
                                       6999**********************************9999999****9997 PP

>> Methyltransf_31  Methyltransferase domain
   #    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       3      63 ..     174     232 ..     172     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.8e-07
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdi 63 
                                       +g r  D  +G G ++  +a++   +ae vG+Di++ aie+ rena+++g++ +v+   +++
  gi|336253796|ref|YP_004596903.1| 174 SGERAFDMFAGVGPFVVPFAKR---GAECVGVDINPAAIEYLRENARRNGVEdRVTAICANV 232
                                       6777889999999999999955...799***********************98888776665 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   5.7e-07   0.00073     157     215 ..     170     227 ..     165     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.7e-07
                              PrmA 157 klvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklev 215
                                       ++v++ge+ +D+ +G G   +  ak ga+  v+vDi++ A++  +eNa++N+ve++++ 
  gi|336253796|ref|YP_004596903.1| 170 EQVESGERAFDMFAGVGPFVVPFAKRGAE-CVGVDINPAAIEYLRENARRNGVEDRVTA 227
                                       568899999****************9986.78***********************9865 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.3e-06     0.003      31      89 ..     174     232 ..     164     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.3e-06
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-ST CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdv 89 
                                         +++ D+ +G+G+  + +ak+  e   + vd++ +A+e  +en+++n++e  v+++  +v
  gi|336253796|ref|YP_004596903.1| 174 SGERAFDMFAGVGPFVVPFAKRGAE--CVGVDINPAAIEYLRENARRNGVEdrVTAICANV 232
                                       456799***************9888..9**********************97666655555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.3   1.6e+03      44      62 ..      69     101 ..      60     155 .. 0.64
   2 !   16.2   0.1   5.5e-06    0.0071       8      62 ..     160     222 ..     152     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                   Methyltransf_23  44 gfsvtgvDlspeaveiae..............k 62 
                                       ++++ g+D+s e  ++a                
  gi|336253796|ref|YP_004596903.1|  69 PADLLGFDPSYERLGKAVlldeddpdraweiaD 101
                                       457888999888777775555444444444440 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 5.5e-06
                   Methyltransf_23   8 elsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae........k 62 
                                       +l+ +++r+++  ++g r  d+ +G+G +   ++++g++++gvD++p+a+e ++        +
  gi|336253796|ref|YP_004596903.1| 160 RLATERHRVAEQVESGERAFDMFAGVGPFVVPFAKRGAECVGVDINPAAIEYLRenarrngvE 222
                                       57788999999889999*********************************9887655444440 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.5e-06     0.012      41     104 ..     174     236 ..     166     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.5e-06
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHH CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleal 104
                                        g+r  D+faG G   +  + Rga ++v v+ +++a++ l+en ++ ++e++++++  +    +
  gi|336253796|ref|YP_004596903.1| 174 SGERAFDMFAGVGPFVVPFAKRGA-ECVGVDINPAAIEYLRENARRNGVEDRVTAICANVRTLV 236
                                       567889*****************5.799********************9998888877766655 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    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      77     116 ..     197     236 ..     171     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                       --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG-- CS
                           UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLr 116
                                       ++ +g+D+++++++  reNa++ gv+d++++ +a+++ L 
  gi|336253796|ref|YP_004596903.1| 197 AECVGVDINPAAIEYLRENARRNGVEDRVTAICANVRTLV 236
                                       6689********************************9986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       6.9   8.8e+03      19      36 ..      68      85 ..      60     107 .. 0.71
   2 ?   11.5   0.0    0.0003      0.39       5      52 ..     183     226 ..     179     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.9
                   Methyltransf_12 19 pdieytgvDispsaieda 36
                                      ++++++g D+s + + +a
  gi|336253796|ref|YP_004596903.1| 68 RPADLLGFDPSYERLGKA 85
                                      567788999998888544 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0003
                   Methyltransf_12   5 cGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnve 52 
                                       +G+G ++ +++++  ++e +gvDi+p+aie  +e  +++     ++v+
  gi|336253796|ref|YP_004596903.1| 183 AGVGPFVVPFAKR--GAECVGVDINPAAIEYLRENARRN--GVEDRVT 226
                                       7999999999999..**************4444444333..3444555 PP

>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00017      0.22       3      43 ..     178     217 ..     177     235 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                                       EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-. CS
                     DNA_methylase   3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk 43 
                                        +d+faG+G f + +++ g ecv  ++i++ a++ ++ n +
  gi|336253796|ref|YP_004596903.1| 178 AFDMFAGVGPFVVPFAKRGAECVG-VDINPAAIEYLRENAR 217
                                       57******************9986.89**********9987 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0003      0.38       7      74 ..     167     232 ..     158     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                   Methyltransf_18   7 aiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdG 74 
                                       ++a+ ve+g+r  D  +  g   +  +k+g   +++ +Din+ ++e  +en++++g+ed++++++++ 
  gi|336253796|ref|YP_004596903.1| 167 RVAEQVESGERAFDMFAGVGPFVVPFAKRG--AECVGVDINPAAIEYLRENARRNGVEDRVTAICANV 232
                                       577777777888887777776666666555..5699***************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2679.86
//
Query:       gi|336253797|ref|YP_004596904.1|  [L=234]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-19   69.4   5.2    4.1e-19   69.1   5.2    1.2  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 !   69.1   5.2   2.3e-23   4.1e-19       2     211 ..       8     205 ..       7     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 2.3e-23
                                       SCCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---.HHHHHHHCCCHCHHHHHHHHHHE.... CS
                              CbiQ   2 ksvlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp.rvlaqalilpllflllgllillfqlit 77 
                                       ++  hrldpr kl++ + +   +   +   +ll ++a+  l+l+ + +p r+ + a++  + f +l l  ll  l  
  gi|336253797|ref|YP_004596904.1|   8 NTLVHRLDPRSKLAVQIGFAATALAHTDARALLALSAVAALVLVAARVPlRRTLYAYR--FAFVILALAPLLAALAL 82 
                                       6899*************99999888888888877766666666666666455555555..77777777777773333 PP

                                       ...EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--H....HHHHHHHHHHHHH CS
                              CbiQ  78 tegefvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPl....elalillLayRfi 150
                                        ++++         + ++G l ++  + R+l +l + ++++ +Tp+ +  ++++r  +P      l + ++L++Rf+
  gi|336253797|ref|YP_004596904.1|  83 GPPWI---------VLEDG-LASARASYRVLLILHVSAAYVRSTPVRDSRAAIQRT-IPGkpgqLLGIGIALVFRFL 148
                                       33333.........55677.7999*******9999******************996.555566889999******** PP

                                       HHHHHHHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                              CbiQ 151 flLleevqrikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                       ++L   +++i++A+++Rlg+     r+ +  + +l+   + ra++ra+r+alAm+aR+++ 
  gi|336253797|ref|YP_004596904.1| 149 PVLQGDIRTIRDAMAARLGTE----RSAVDRASTLALLGLSRAFDRADRLALAMQARCFSW 205
                                       *********************....555667888888899*******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1909.38
//
Query:       gi|336253798|ref|YP_004596905.1|  [L=242]
Description: polyamine-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-30  104.7   0.0    7.2e-30  104.3   0.0    1.1  1  ABC_tran      ABC transporter
    1.1e-09   38.6   0.1    0.00062   19.7   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    8.5e-05   22.1   0.0    0.00047   19.7   0.0    1.8  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00011   22.6   0.2    0.00017   22.0   0.2    1.5  1  AAA_16        AAA ATPase domain
    0.00035   20.3   0.1    0.00058   19.5   0.1    1.3  1  AAA_29        P-loop containing region of AAA domain
    0.00042   20.5   0.2      0.005   17.0   0.2    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
     0.0028   18.2   0.0     0.0038   17.8   0.0    1.2  1  AAA_23        AAA domain
     0.0095   15.2   0.0      0.016   14.5   0.0    1.3  1  Zeta_toxin    Zeta toxin
  ------ inclusion threshold ------
      0.012   15.1   2.7      0.055   13.0   0.0    2.6  2  AAA_25        AAA domain
      0.015   15.1   0.0      0.031   14.0   0.0    1.5  1  AAA_30        AAA domain
      0.026   14.5   0.1      0.044   13.7   0.1    1.3  1  NACHT         NACHT domain
      0.027   13.5   0.5      0.079   12.0   0.0    1.9  3  T2SSE         Type II/IV secretion system protein
      0.033   13.8   0.1      0.062   12.9   0.1    1.5  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.041   14.2   0.2      0.078   13.2   0.1    1.8  1  AAA_22        AAA domain
      0.054   13.7   0.1       0.12   12.6   0.0    1.8  1  AAA_28        AAA domain
      0.068   13.3   0.4       0.11   12.6   0.4    1.8  1  AAA_33        AAA domain
       0.11   12.2   0.0       0.15   11.8   0.0    1.1  1  AAA_15        AAA ATPase domain
       0.14   12.2   0.1        0.4   10.7   0.0    1.8  2  AAA_5         AAA domain (dynein-related subfamily)
       0.14   11.5   0.0       0.22   10.9   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.16    9.4   0.0       0.21    9.0   0.0    1.1  1  DUF3584       Protein of unknown function (DUF3584)
       0.17   11.8   0.0        0.3   11.0   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
        0.2   11.7   0.0       0.33   10.9   0.0    1.3  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei


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 !  104.3   0.0   8.8e-33   7.2e-30       1     136 [.      17     161 ..      17     162 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 8.8e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltv 76 
                                       l+++sl+++ ge v++ G nG+GK+tLl+   gll+p++G++l+dg+++++ +l  +r+++g+++q+    f   tv
  gi|336253798|ref|YP_004596905.1|  17 LEDLSLSIESGEFVVLAGANGSGKTTLLRHCNGLLTPDSGTVLVDGTPVTD-DLVAARSRVGMVFQHpRDQFVAATV 92 
                                       689************************************************.***************6555666678 PP

                                       HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +               e d+++e+al+ +++ + +d+++      LSgG++ rva+a al+ +p+ l+lDEp+
  gi|336253798|ref|YP_004596905.1|  93 GADvafgpenlgleraEIDRRVETALAAVNMAGREDERI----DALSGGEQARVAIAGALAMDPDHLVLDEPF 161
                                       8889***********************************....*****************************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 !   17.1   0.1   4.7e-06    0.0038       1      17 [.      29      45 ..      29      68 .. 0.92
   2 !   19.7   0.0   7.6e-07   0.00062     192     299 ..     107     193 ..      88     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.7e-06
                            AAA_21  1 lnvliGpNgsGKSnLLd 17
                                      + vl G+NgsGK++LL+
  gi|336253798|ref|YP_004596905.1| 29 FVVLAGANGSGKTTLLR 45
                                      689*************7 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 7.6e-07
                            AAA_21 192 lklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEn 268
                                       + +++ ++++ ++++++  ++der+                  + lS G +   a++ al+ ++   + l++DEp +
  gi|336253798|ref|YP_004596905.1| 107 RAEIDRRVETALAAVNMAGREDERI------------------DALSGGEQARVAIAGALAMDP---DHLVLDEPFT 162
                                       5667777777777778888877775..................559*****999**********...77******** PP

                            AAA_21 269 gLHPkllrrllellkelsrngaQviltTHSp 299
                                       gL+  + r++le l++ls  g+ v+l+TH+ 
  gi|336253798|ref|YP_004596905.1| 163 GLDDPARRSVLERLESLSVAGTGVVLATHDL 193
                                       *****************99**********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 !   19.7   0.0   5.8e-07   0.00047      25     212 ..      28     207 ..      18     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.8e-07
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeevsi 99 
                                       +f ++ G+NGSGK+ ll     +L  +s         + l+      +   + + +v ++f+++ ++++  +    +
  gi|336253798|ref|YP_004596905.1|  28 EFVVLAGANGSGKTTLLRHCNGLLTPDSG--------TVLVDGtpVTDDLVAARSRVGMVFQHPRDQFVAATVGADV 96 
                                       6999************8777666665555........5555544334445556899***********9999999999 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                           ++ g  + +i+++  t     ++  +++  +++LSgGe++ va+a  +A+   +p  l +lDe    LD+  +
  gi|336253798|ref|YP_004596905.1|  97 AFGPENLGLERAEIDRRVETALAAVNMAGREDERIDALSGGEQARVAIAGALAM---DPDHL-VLDEPFTGLDDPAR 169
                                       999999999************9999************************99886...45554.79999999999999 PP

                                       HHHHHHHHHHCTT.SEEEEE-SS.HHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxx RF
                             SMC_N 177 kkvaellkekskn.aQfivislr.eemlekadklvgvt 212
                                       + v e+l++ s   + ++  +++ +++l+ ad+lv v+
  gi|336253798|ref|YP_004596905.1| 170 RSVLERLESLSVAgTGVVLATHDlRDVLALADRLVAVR 207
                                       99999999888664555556665356777777777765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   2.1e-07   0.00017      23     107 ..      26     130 ..      16     213 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.1e-07
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdql..esaipysalaqalareellrqllde........ 88 
                                       ++e v+l G+ G+GK++l+r++   l+ d g + + g+ +     +a++++  + +  r++++++   +        
  gi|336253798|ref|YP_004596905.1|  26 SGEFVVLAGANGSGKTTLLRHCNGLLTPDSGTVlVDGTPVTDdlVAARSRVGMVFQHPRDQFVAATVGAdvafgpen 102
                                       4589*******************999999655547777666633222333344444445555554444444443332 PP

                            AAA_16  89 aesaeleawrekleeala..........a 107
                                       +   e+++ +++ e+ala           
  gi|336253798|ref|YP_004596905.1| 103 L-GLERAEIDRRVETALAavnmagredeR 130
                                       2.223344444444444444453333332 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 !   19.5   0.1   7.2e-07   0.00058      17      50 ..      22      55 ..      16      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.2e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++i+  ++++l+G++GsGK+Tll   + lL+p++
  gi|336253798|ref|YP_004596905.1| 22 LSIESGEFVVLAGANGSGKTTLLRHCNGLLTPDS 55
                                      566655599**************99999999986 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 !   17.0   0.2   6.2e-06     0.005      26      89 ..     127     177 ..     107     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.2e-06
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                        ++++ +lSGGe+   a +a+a ala+           ++ ++LDE F +lD+  ++++le le
  gi|336253798|ref|YP_004596905.1| 127 EDERIDALSGGEQ---ARVAIAGALAMD----------PDHLVLDEPFTGLDDPARRSVLERLE 177
                                       47889999*****...788888777653..........5569*****************99765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.7e-06    0.0038      18      45 ..      26      53 ..       8      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.7e-06
                            AAA_23 18 skgltlItGpNGaGKTTildAiklaLyg 45
                                      s  ++++ G NG+GKTT+l+ +   L+ 
  gi|336253798|ref|YP_004596905.1| 26 SGEFVVLAGANGSGKTTLLRHCNGLLTP 53
                                      4467899************998888775 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     2e-05     0.016      18      51 ..      29      62 ..      17      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldp 51
                                       ++l+G+ G+GK++l++  +  l+++++ v +d+
  gi|336253798|ref|YP_004596905.1| 29 FVVLAGANGSGKTTLLRHCNGLLTPDSGTVLVDG 62
                                      799*****************99999999999987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.8e-05     0.055      31      50 ..      25      44 ..      14      52 .. 0.91
   2 ?    0.9   1.1      0.37     3e+02      85     111 ..     109     139 ..     103     225 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.8e-05
                            AAA_25 31 pagelallaGapgtGKttla 50
                                        ge+++laGa g+GKttl+
  gi|336253798|ref|YP_004596905.1| 25 ESGEFVVLAGANGSGKTTLL 44
                                      679***************97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.37
                            AAA_25  85 elrrRlravgeal....rddarllvldlagv 111
                                       e+ rR++ +++a+    r+d+r ++l++ ++
  gi|336253798|ref|YP_004596905.1| 109 EIDRRVETALAAVnmagREDERIDALSGGEQ 139
                                       5666666666666555555555555553211 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.8e-05     0.031      15      50 ..      25      59 ..      20      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.8e-05
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                      +sg+ ++vl G+ G+GKtt+l++ + +++ + g+v+
  gi|336253798|ref|YP_004596905.1| 25 ESGE-FVVLAGANGSGKTTLLRHCNGLLTPDSGTVL 59
                                      4554.99****************9999888766665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.3e-05     0.044       3      19 ..      30      46 ..      28      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.3e-05
                                      EEEEC-TTTCHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqk 19
                                      v+l G++GsGKTtLl++
  gi|336253798|ref|YP_004596905.1| 30 VVLAGANGSGKTTLLRH 46
                                      89*************97 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 ?   12.0   0.0   9.7e-05     0.079     121     154 ..      19      52 ..       8      63 .. 0.81
   2 ?   -2.0   0.0       1.9   1.5e+03     184     205 ..     136     157 ..     113     159 .. 0.69
   3 ?   -2.8   0.0       3.2   2.6e+03     239     267 ..     172     201 ..     169     229 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.7e-05
                             T2SSE 121 vlrkavrerglilvsGgTgsGKttllyallkein 154
                                        l+ ++++   ++++G+ gsGKttll  +   + 
  gi|336253798|ref|YP_004596905.1|  19 DLSLSIESGEFVVLAGANGSGKTTLLRHCNGLLT 52 
                                       577888899999**************87766655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                             T2SSE 184 akvtfadllraaLRlrPDrimv 205
                                       ++ +++ ++  aL ++PD +++
  gi|336253798|ref|YP_004596905.1| 136 GGEQARVAIAGALAMDPDHLVL 157
                                       5556667788899999999887 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.2
                             T2SSE 239 alerLeqlgae.veaaelkssilavvdivv 267
                                       +lerLe l+         ++ +++v+ ++ 
  gi|336253798|ref|YP_004596905.1| 172 VLERLESLSVAgTGVVLATHDLRDVLALAD 201
                                       566666666444222222233333333333 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 ?   12.9   0.1   7.6e-05     0.062       3      20 ..      30      47 ..      28      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.6e-05
                                      EEEEESTTCCHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhl 20
                                      +vl+G  GsGKTtLl+h 
  gi|336253798|ref|YP_004596905.1| 30 VVLAGANGSGKTTLLRHC 47
                                      799************996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   9.6e-05     0.078       4      48 ..      26      63 ..      24     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.6e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlp 48
                                      +  ++v+ G  G+GKTtllr     l+       +++++v+v+ +
  gi|336253798|ref|YP_004596905.1| 26 SGEFVVLAGANGSGKTTLLRHCNGLLT-------PDSGTVLVDGT 63
                                      56799***************9887775.......36666666655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00015      0.12       2      18 ..      30      46 ..      29      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                            AAA_28  2 ivitGgestGKTtllea 18
                                      +v+ G+ ++GKTtll++
  gi|336253798|ref|YP_004596905.1| 30 VVLAGANGSGKTTLLRH 46
                                      89*************87 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   0.00014      0.11       2      19 ..      30      47 ..      29     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                            AAA_33  2 vllvGlpGsGKstlaerl 19
                                      v+l G++GsGK+tl+++ 
  gi|336253798|ref|YP_004596905.1| 30 VVLAGANGSGKTTLLRHC 47
                                      7899***********985 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.15      18      41 ..      21      45 ..      16      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                            AAA_15 18 eidlsee.ltvliGkNnsGKSsile 41
                                      ++++++  + vl G+N+sGK+++l+
  gi|336253798|ref|YP_004596905.1| 21 SLSIESGeFVVLAGANGSGKTTLLR 45
                                      45555545***************96 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   0.00049       0.4       2      31 ..      30      59 ..      29      91 .. 0.80
   2 ?   -2.5   0.0       5.9   4.8e+03      59      72 ..     203     215 ..     189     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00049
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvq 31
                                      v+L G+ G+gK++l ++   +l+    +v+
  gi|336253798|ref|YP_004596905.1| 30 VVLAGANGSGKTTLLRHCNGLLTPDSGTVL 59
                                      79***************9999944444444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.9
                                       ------G-SEEEEE CS
                             AAA_5  59 lvraaregeilvlD 72 
                                       lv a+r g+++v+D
  gi|336253798|ref|YP_004596905.1| 203 LV-AVRDGRVVVDD 215
                                       55.78889998888 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   0.00027      0.22      21      53 ..      26      58 ..      16      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                      Mg_chelatase 21 GgHnlllvGppGsGKtmlakrlpsllpplseee 53
                                       g  ++l+G+ GsGKt l +  ++ll+p s + 
  gi|336253798|ref|YP_004596905.1| 26 SGEFVVLAGANGSGKTTLLRHCNGLLTPDSGTV 58
                                      5556899*******************9877655 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00026      0.21      20      35 ..      30      45 ..      23      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00026
                           DUF3584 20 tnieGtNaaGKTtLlr 35
                                      + + G+N++GKTtLlr
  gi|336253798|ref|YP_004596905.1| 30 VVLAGANGSGKTTLLR 45
                                      6689***********9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00037       0.3      90     120 ..      17      48 ..       4      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinall 120
                                       le+l+  +++ +++vl+G  G GK+tL+ + +
  gi|336253798|ref|YP_004596905.1|  17 LEDLSLSIESgEFVVLAGANGSGKTTLLRHCN 48 
                                       667777777779***************98765 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   0.00041      0.33      18      39 ..      24      47 ..      12      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
                                      H..TEEEEEEESTTSSHHHHHHHH CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrgl 39
                                      +  g++++L G  G+GKTtl r+ 
  gi|336253798|ref|YP_004596905.1| 24 IesGEFVVLAGANGSGKTTLLRHC 47
                                      233789**************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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):              22  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 1962.88
//
Query:       gi|336253799|ref|YP_004596906.1|  [L=195]
Description: BioY protein [Halopiger xanaduensis SH-6]
Scores for complete 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-38  131.7  20.3    2.7e-38  131.1  20.3    1.2  1  BioY         BioY family
  ------ inclusion threshold ------
      0.013   15.6   0.9      0.013   15.6   0.9    2.3  2  DUF2269      Predicted integral membrane protein (DUF2269)
      0.035   14.2  24.4      0.058   13.5  24.4    1.3  1  ECF_trnsprt  ECF transporter, substrate-specific component


Domain annotation for each model (and alignments):
>> BioY  BioY family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.1  20.3   4.6e-42   2.7e-38       2     132 ..      42     187 ..      41     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 131.1 bits;  conditional E-value: 4.6e-42
                              BioY   2 gpvpitlqtlavllaglllgprrgalavllYlllGalglPvfag.ggGlavllgptgGYllGFlvaalvvgll.... 73 
                                       +p pitlq+l+v+lagl+lgp +g+++++lYl++Ga+glPvfag +gG++vl+g t+GYl+++++aa ++gl+    
  gi|336253799|ref|YP_004596906.1|  42 SPAPITLQVLFVFLAGLVLGPIWGTFSLVLYLAAGAVGLPVFAGmNGGPGVLVGQTAGYLWSYPIAAGLIGLAvhrg 118
                                       799*****************************************66*************************999999 PP

                              BioY  74 .......kk.laelllallagllviyalGvlwlalv..lslaaalaagvlpfipgdlvkavlaallaka 132
                                              ++ l  +++al+ag+++iy +Gv ++a++  ++l++a++ag lpfipg+++k+++a++++k+
  gi|336253799|ref|YP_004596906.1| 119 talrdpaAQpLPVVVAALVAGTVLIYGMGVGYMAWLleMNLWEAVTAGALPFIPGEILKMAAAIAIVKS 187
                                       98887632368888*********************77899*************************9986 PP

>> DUF2269  Predicted integral membrane protein (DUF2269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.9   2.2e-06     0.013      64      97 ..      50      83 ..      11      87 .. 0.82
   2 ?    1.5   0.5     0.046   2.8e+02       8      28 ..     137     157 ..     129     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.2e-06
                           DUF2269 64 lwlvhlagwplkqsWlllslvLyllagalwlpVv 97
                                      +++v+lag+ l+  W  +slvLyl+aga+ lpV 
  gi|336253799|ref|YP_004596906.1| 50 VLFVFLAGLVLGPIWGTFSLVLYLAAGAVGLPVF 83
                                      57899***************************97 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.046
                           DUF2269   8 ilsavlllgtgigiafyllra 28 
                                       ++++vl+ g g+g + +ll  
  gi|336253799|ref|YP_004596906.1| 137 VAGTVLIYGMGVGYMAWLLEM 157
                                       567777888888877777654 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5  24.4   9.7e-06     0.058       1     168 [.      17     185 ..      17     187 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.7e-06
                                       HHHHHHHHHHHHHHHHHHH.HEEE.STSEEESHHHHHHHHHHCTTCHHHHHHHHH........HHHHHHHCHT-SST CS
                       ECF_trnsprt   1 kklvitglliAisivlsll.gyiplpnikitiihipvllggllfGpikGailgii........tsvlkailtggtga 68 
                                       +++++++l +A++  +++    ipl +++it+  + v+l+gl++Gpi+G +  ++         +v++ +  gg g 
  gi|336253799|ref|YP_004596906.1|  17 RQFARAALIAALIGASAPVtIPIPLSPAPITLQVLFVFLAGLVLGPIWGTFSLVLylaagavgLPVFAGMN-GGPG- 91 
                                       578999***********9569999999****************************7777766666666666.3333. PP

                                       THHHH......HHHHHHHHCHHHHHHHHHHCCCHTTHHHHHHHHHHHH.CCCCCHHHHHHHCCC.HHHHS....... CS
                       ECF_trnsprt  69 lssfv......piaflsriligliagllykkgkkknlkeivvsfilag.vlgtivatllvllii.lplylklktaka 137
                                        ++++      + + ++++ligl++    ++   +      +++++a+ v+gt++   + ++++ ++l ++l     
  gi|336253799|ref|YP_004596906.1|  92 -VLVGqtagylWSYPIAAGLIGLAVH---RGTALRDPAAQPLPVVVAAlVAGTVLIYGMGVGYMaWLLEMNLW---- 160
                                       .3344778999999999999999888...33333333333555555441445554444444444355555443.... PP

                                       ......--HHHHHHHHHCCTTCCHHHHHHHH CS
                       ECF_trnsprt 138 iaiagkallaailgpiivkglieaiiaaiiv 168
                                              +++a  +p i+ ++++++ a+ iv
  gi|336253799|ref|YP_004596906.1| 161 ------EAVTAGALPFIPGEILKMAAAIAIV 185
                                       ......6777888888888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1436.68
//
Query:       gi|336253800|ref|YP_004596907.1|  [L=1425]
Description: hypothetical protein Halxa_2409 [Halopiger xanaduensis SH-6]
Scores for complete 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-06   28.5   5.4    6.9e-06   26.3   2.5    3.5  2  CARDB         CARDB
    0.00051   20.0   0.2         13    5.6   0.0    4.4  4  EMP24_GP25L   emp24/gp25L/p24 family/GOLD
  ------ inclusion threshold ------
       0.17   12.4   9.7          3    8.4   0.2    5.2  5  DUF4981       Domain of unknown function(DUF4981)
       0.18   11.7   1.0        2.3    8.2   0.1    2.8  2  DUF2536       Protein of unknown function (DUF2536)


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 ?   -0.0   0.1      0.24   1.1e+03      50      86 ..     854     895 ..     825     898 .. 0.73
   2 !   26.3   2.5   1.5e-09   6.9e-06       9      86 ..    1237    1313 ..    1232    1321 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.24
                                       EEEEE...SEE-CTEEEEEEEEEE-S..-S-CEEEEEEEEST CS
                             CARDB  50 gtvtv...psLaagesttvsftwtte..ategevtltvvvDp 86 
                                       ++ ++   p+L+++++++vs+ + ++  a ++++   +v+D+
  gi|336253800|ref|YP_004596907.1| 854 ENESIalePPLENDTTVDVSVRDAATdeALANDSVAYAVADE 895
                                       3333455899***********999986655566666666665 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.5e-09
                                        EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S.-S-CEEEEEE CS
                             CARDB    9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtte.ategevtltv 82  
                                        + + +++++ge++ti++ v+N G +a+++  v+l + g+++++v+v +L++ges+tv+++  t+ +++ge+ +tv
  gi|336253800|ref|YP_004596907.1| 1237 ADTNAPVEQGESLTINADVENVGGEAAEQ-PVTLAVAGTETDSVSV-GLDPGESETVTLNAETAeLEPGEYPITV 1309
                                        56778899***************999887.68899999999*****.****************999999999988 PP

                                        EEST CS
                             CARDB   83 vvDp 86  
                                        + + 
  gi|336253800|ref|YP_004596907.1| 1310 SSEN 1313
                                        7543 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 !    5.6   0.0     0.003        13      30      74 ..     701     743 ..     684     745 .. 0.83
   2 ?    3.7   0.0     0.012        53      20      74 ..     769     840 ..     764     841 .. 0.75
   3 ?   -0.3   0.0       0.2   9.2e+02      26      74 ..     888     942 ..     879     949 .. 0.84
   4 !    4.0   0.0    0.0095        43      18     103 ..    1243    1332 ..    1240    1357 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.003
                       EMP24_GP25L  30 vtdggaaldvdlsvkdpdgngerlvkkkdresegdfsftakesge 74 
                                       v d + + +  l+v+d+ g+ge+lv ++ ++s  d+++ta+ +ge
  gi|336253800|ref|YP_004596907.1| 701 VADDT-DREATLNVTDQTGDGETLVVDEANASV-DYAVTAEYDGE 743
                                       33444.68999****************999888.*******9997 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.012
                       EMP24_GP25L  20 kgtlltgsyqvtdgg..................aaldvdlsvkdpdgngerlvkkkdresegdfsftakesge 74 
                                       +++++ +s+++ + +                  ++ +  l+v d++g+ge+l+ ++ ++s  ++ ++a+ +ge
  gi|336253800|ref|YP_004596907.1| 769 ENATVNVSVRALEDDaelanesiaytvatepsePEPEATLNVSDQEGDGETLLVDDANASV-EYVVSAEYDGE 840
                                       56677777777755556666666666666666689999999*********99999777766.99999998886 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.2
                       EMP24_GP25L  26 gsyqvtdgg......aaldvdlsvkdpdgngerlvkkkdresegdfsfta.kesge 74 
                                       + y v d+g      ++ +  l+v d+ g+ge lv ++ ++s  d++  +  e+ge
  gi|336253800|ref|YP_004596907.1| 888 VAYAVADEGpepgpePEPEATLDVGDQTGSGEALVVDEANASV-DYALAVtDEDGE 942
                                       67889988889999988999**************999888877.888777566666 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.0095
                       EMP24_GP25L   18 lkkgtlltgsyqvtdgg...aaldvdlsvkdpdgngerlvkkkdresegdfsftak....esgeykvCfdnsfst 85  
                                        +++g++lt++ +v++ g   a++ v l v++++ +   +  +   ese  ++ +a+    e+gey + +++++ t
  gi|336253800|ref|YP_004596907.1| 1243 VEQGESLTINADVENVGgeaAEQPVTLAVAGTETDSVSVGLD-PGESE-TVTLNAEtaelEPGEYPITVSSENDT 1315
                                        7899999999999965566778********888755666666.44455.78888877888***********9777 PP

                       EMP24_GP25L   86 ksskkvsfdievgseasd 103 
                                          + +v+++  ++s+a d
  gi|336253800|ref|YP_004596907.1| 1316 V-ETSVTIEAAAESDAGD 1332
                                        5.5788888777766655 PP

>> DUF4981  Domain of unknown function(DUF4981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.012        54      17      71 ..     734     784 ..     722     801 .. 0.71
   2 ?    1.2   0.1      0.12   5.3e+02      19      73 ..     833     884 ..     820     895 .. 0.59
   3 ?   -2.7   0.0       1.9   8.4e+03      24      46 ..     952     976 ..     935    1003 .. 0.69
   4 ?   -1.7   0.0      0.94   4.2e+03      13      50 ..    1195    1237 ..    1185    1268 .. 0.60
   5 ?    8.4   0.2   0.00066         3      24      63 ..    1272    1310 ..    1247    1326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.012
                                       EEEEEEETTEEEEEEEEEE---TT-EEE.EE--S.---TSSEEEEEEEEEESS-BS CS
                           DUF4981  17 lswellkdGkvvasgelelpvaPgesat.vtlpetkeaeeseyfltvsfrlkedtp 71 
                                        +++ + dG+ v+s++++    +g+s++ ++l+ + +  e+ ++++vs+r  ed +
  gi|336253800|ref|YP_004596907.1| 734 YAVTAEYDGERVDSESFD----AGQSVEnLELDLE-PLLEENATVNVSVRALEDDA 784
                                       2334456******99888....8999998999854.44445999****99776543 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                                       EEEEETTEEEEEEEEEE---TT-EEE...EE--S.---TSSEEEEEEEEEES.S-BSSS CS
                           DUF4981  19 wellkdGkvvasgelelpvaPgesat...vtlpetkeaeeseyfltvsfrlk.edtpwa 73 
                                       ++ + dG+ v+s+      a+ge+a+   + l+   ++ e++++++vs+r + +d+++a
  gi|336253800|ref|YP_004596907.1| 833 VSAEYDGERVDSEP----FAAGEAAEnesIALE---PPLENDTTVDVSVRDAaTDEALA 884
                                       33355999999874....455555551004454...44445899999998763455555 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.9
                                       TTEEEEEEEEEE-..--TT-EEEEE CS
                           DUF4981  24 dGkvvasgelelp..vaPgesatvt 46 
                                        G++v++++l+l+  +++ ++ +v 
  gi|336253800|ref|YP_004596907.1| 952 AGETVENESLALEppLEANATLEVA 976
                                       5667777766665445554444443 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.94
                                        GGEEEEEEEEE...TTEEEEEEEEEE-..--TT-EEEEE--S. CS
                           DUF4981   13 sdldlswellk...dGkvvasgelelp..vaPgesatvtlpet 50  
                                        +d +l we+     d ++  + e ++   +aP e a +++  +
  gi|336253800|ref|YP_004596907.1| 1195 DDEQLVWEVDLsryDYEEALTAETATAgeIAPTEPAAYEVSIA 1237
                                        4556667774422222222222333334688877666665433 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.00066
                                        TTEEEEEEEEEE---TT-EEEEE--S.---TSS.EEEEEEE CS
                           DUF4981   24 dGkvvasgelelpvaPgesatvtlpetkeaees.eyfltvs 63  
                                         G++++  ++++ + Pges+tvtl+ ++++ e+ ey +tvs
  gi|336253800|ref|YP_004596907.1| 1272 AGTETD--SVSVGLDPGESETVTLNAETAELEPgEYPITVS 1310
                                        444444..3343488**********9988888899999987 PP

>> DUF2536  Protein of unknown function (DUF2536)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00052       2.3      15      43 ..     636     664 ..     633     670 .. 0.91
   2 ?    0.5   0.1      0.13   5.6e+02      13      60 ..     748     794 ..     745     797 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00052
                           DUF2536  15 FEAedlkeLEkkineqienNkallLeVhs 43 
                                        EA + ++LE +++eq+++ +al+  Vh+
  gi|336253800|ref|YP_004596907.1| 636 LEAGEHEDLEIALDEQLNESQALVAVVHH 664
                                       79*********************888886 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.13
                           DUF2536  13 EfFEA.edlkeLEkkineqienNkallLeVhsvsHqvavdpktgrilYs 60 
                                       E F+A +++++LE  ++  +e+N ++  +V+ ++  + +  +++ i Y+
  gi|336253800|ref|YP_004596907.1| 748 ESFDAgQSVENLELDLEPLLEENATVNVSVRALEDDAEL--ANESIAYT 794
                                       6677746899*****************999999988888..46666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1113  (0.0620782); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); 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: 0.97u 0.28s 00:00:01.25 Elapsed: 00:00:00.49
# Mc/sec: 8690.32
//
Query:       gi|336253801|ref|YP_004596908.1|  [L=96]
Description: hypothetical protein Halxa_2410 [Halopiger xanaduensis SH-6]
Scores for 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:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 686.08
//
Query:       gi|336253802|ref|YP_004596909.1|  [L=47]
Description: hypothetical protein Halxa_2411 [Halopiger xanaduensis SH-6]
Scores for 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   19.6   0.7     0.0011   19.6   0.7    1.0  1  VAPB_antitox  Putative antitoxin
  ------ inclusion threshold ------
      0.029   14.3   3.3        0.1   12.6   1.3    2.0  2  RHH_1         Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.7   1.3e-07    0.0011       2      35 ..       3      36 ..       2      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-07
                      VAPB_antitox  2 tIsIsdevYekLkklKregeSFsdvIerLlekkk 35
                                      t+ +++e+ e+L++l+ ++eS+++++ +L++  +
  gi|336253802|ref|YP_004596909.1|  3 TVELEEETIERLDELRVDDESYDELVTELINIYE 36
                                      7899*************************98444 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 ?   12.6   1.3   1.1e-05       0.1       3      18 ..       3      18 ..       3      21 .. 0.94
   2 ?    2.3   0.1      0.02   1.8e+02       7      18 ..      21      32 ..      18      33 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                                      EEEEEHHHHHHHHHHH CS
                             RHH_1  3 sirldeellerLdela 18
                                      ++ l+ee++erLdel+
  gi|336253802|ref|YP_004596909.1|  3 TVELEEETIERLDELR 18
                                      899***********97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.02
                                      EHHHHHHHHHHH CS
                             RHH_1  7 deellerLdela 18
                                      de+++e++ el+
  gi|336253802|ref|YP_004596909.1| 21 DESYDELVTELI 32
                                      567777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 354.39
//
Query:       gi|336253803|ref|YP_004596910.1|  [L=160]
Description: hypothetical protein Halxa_2412 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.083   12.5   5.0      0.089   12.4   5.0    1.1  1  Chorion_3  Chorion family 3
       0.22   11.4   7.4       0.16   11.9   2.0    2.2  2  Serglycin  Serglycin
       0.44   10.7   4.9        1.5    8.9   1.1    2.1  2  Tubulin    Tubulin/FtsZ family, GTPase domain


Domain annotation for each model (and alignments):
>> Chorion_3  Chorion family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   5.0   1.5e-05     0.089      20      86 ..      81     146 ..      35     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                         Chorion_3  20 YGsagggGGkGsgdlga.gasagleelvnaaaG..GaassgGaiegadaeivaspeeagrlssvqaqlqa 86 
                                        G++g+gGG Gsg + a g++ gl + ++ a G  G+    G+++ga+ e  a+     ++ + q++l++
  gi|336253803|ref|YP_004596910.1|  81 MGGPGAGGGSGSGAGNAsGSGGGLVDSIKGALGlgGDG---GSGQGAKREA-AERLTQEYADELQSKLES 146
                                       68999999999998765267778988888776521554...4556666666.444445566666666665 PP

>> Serglycin  Serglycin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.0   2.7e-05      0.16      76     108 ..      59     100 ..      44     111 .. 0.65
   2 ?    2.8   0.4     0.018   1.1e+02      97     119 ..     115     137 ..     103     157 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                         Serglycin  76 eksqnlndvfplsedy.........sgsgsGsGsGsGsgsgs 108
                                        ++ ++++++p  e++          g+g GsGsG+G  sgs
  gi|336253803|ref|YP_004596910.1|  59 ANTDKVDQIMPELENVdqgmgamggPGAGGGSGSGAGNASGS 100
                                       455667788888888888888887634444444444444443 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.018
                         Serglycin  97 GsGsGsGsgsgsgflteieqeYq 119
                                       G   GsG g++ +  + + qeY 
  gi|336253803|ref|YP_004596910.1| 115 GGDGGSGQGAKREAAERLTQEYA 137
                                       43344555555554455555542 PP

>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.1   0.00026       1.5     103     135 ..      64      96 ..      51      99 .. 0.88
   2 ?    3.5   0.1     0.012        72      80     112 ..     114     146 ..      97     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00026
                                       HHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHH CS
                           Tubulin 103 leeirkevekcdslqgffitaslgGGTGSGlgp 135
                                        ++i+ e+e++d+  g +   + gGG+GSG+g+
  gi|336253803|ref|YP_004596910.1|  64 VDQIMPELENVDQGMGAMGGPGAGGGSGSGAGN 96 
                                       689999*******999999************96 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.012
                                       CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT CS
                           Tubulin  80 kegagnngaggypevgkeaaeeileeirkevek 112
                                         g g++g g+++e ++++++e ++e++ ++e+
  gi|336253803|ref|YP_004596910.1| 114 LGGDGGSGQGAKREAAERLTQEYADELQSKLES 146
                                       456677788888888888888888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1260.92
//
Query:       gi|336253804|ref|YP_004596911.1|  [L=166]
Description: transferase [Halopiger xanaduensis SH-6]
Scores for complete 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   62.6   2.6    2.5e-06   27.0   0.3    3.4  3  Hexapep    Bacterial transferase hexapeptide (six repeats)
      5e-07   29.4   4.2    6.2e-06   25.9   0.4    3.0  3  Hexapep_2  Hexapeptide repeat of succinyl-transferase


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 !   17.3   0.0   3.1e-07    0.0028       3      36 .]      11      44 ..       9      44 .. 0.92
   2 !   17.0   0.0   3.9e-07    0.0035       3      34 ..      50      81 ..      48      83 .. 0.88
   3 !   27.0   0.3   2.8e-10   2.5e-06       2      35 ..      84     117 ..      83     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.1e-07
                                      EEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36
                                      +I + ++++  avi g+V++  ++ ++++++++g
  gi|336253804|ref|YP_004596911.1| 11 QIADSAYVDEAAVIIGDVVVEADASVWPNTTLRG 44
                                      68899999999********************986 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.9e-07
                                      EEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep  3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34
                                      v+G+++ I  +av+++n+++ +++++g+ + +
  gi|336253804|ref|YP_004596911.1| 50 VVGEGANIQDNAVLHENAELEPYATVGHSAIV 81
                                      89999999999999999999999999998877 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 2.8e-10
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +++ + +l+g++a++++++ IG++++++ag+v++
  gi|336253804|ref|YP_004596911.1|  84 ATVAERALVGMNATVLDGARIGEGAVVAAGSVVT 117
                                       6778999*************************97 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 ?    0.0   0.0     0.084   7.5e+02      18      22 ..      23      27 ..      15      42 .. 0.66
   2 !    3.0   0.1    0.0096        86      15      26 ..      52      63 ..      47      70 .. 0.77
   3 !   25.9   0.4   6.9e-10   6.2e-06       6      34 .]      88     118 ..      85     118 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.084
                                      EEE-T CS
                         Hexapep_2 18 vslGd 22
                                      v++Gd
  gi|336253804|ref|YP_004596911.1| 23 VIIGD 27
                                      44444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0096
                                      EESEEE-TT-EE CS
                         Hexapep_2 15 giGvslGdncvv 26
                                      g G ++ dn+v+
  gi|336253804|ref|YP_004596911.1| 52 GEGANIQDNAVL 63
                                      458888888887 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 6.9e-10
                                       TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2   6 dnCliGanagi..GvslGdncvvgaGvvita 34 
                                       ++ l+G na++  G  +G+++vv+aG+v+t+
  gi|336253804|ref|YP_004596911.1|  88 ERALVGMNATVldGARIGEGAVVAAGSVVTE 118
                                       689*******99*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1348.44
//
Query:       gi|336253805|ref|YP_004596912.1|  [L=358]
Description: beta-lactamase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   45.1  13.4    2.8e-11   43.8  10.0    2.8  2  Lactamase_B    Metallo-beta-lactamase superfamily
    1.4e-05   24.7   1.0    2.7e-05   23.8   1.0    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0028   17.1   0.0     0.0059   16.1   0.0    1.5  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 !   43.8  10.0   4.6e-15   2.8e-11       3     182 ..      51     249 ..      49     263 .. 0.68
   2 ?   -0.7   0.1       0.2   1.2e+03     120     143 ..     281     304 ..     270     351 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 4.6e-15
                                       CCSSEEEEEEET.TCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                       Lactamase_B   3 pdpvnsyliegd.ggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78 
                                       ++++ s+li+++ +++iLiDtG + + ++ +   +++  +++++d+++ TH+H+DHiGg + ++e++  +   v ++
  gi|336253805|ref|YP_004596912.1|  51 VGQADSTLIVTPaNETILIDTGDWRDDGQTVI-DYLEAQDIERIDHLVATHGHADHIGGHPAVIEHFEENGEGVGAA 126
                                       78999*****666******************5.*********************************99888888888 PP

                                       HHCCHCHHHHHHHHHCCHH..............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEET CS
                       Lactamase_B  79 apalfmeeaddaasrkgll..............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveyg 141
                                       + ++  +   +++ +  ++              + +    + d     l+ +++  ++  +  g    ++++++ yg
  gi|336253805|ref|YP_004596912.1| 127 YDSGVAHTSATYENYLDAIeehdvdlfqvvagdRLPLESASADGSNATLEATVLNPPEERHSDGVDENSVVLSLAYG 203
                                       88888888877777777777777776666666533333333333333333333333444444444455555556666 PP

                                       TCCEEEECTTTSSHHCCCCCC......TTCEEE-SHCHHHHHHHHH CS
                       Lactamase_B 142 ggkvlftGDallagetgridl.....tlrgaevrdpsdaekyldsl 182
                                       + ++l tGD   + e+ +id        +  +++++++ +++ d +
  gi|336253805|ref|YP_004596912.1| 204 EFTYLTTGDIERTTERRLIDAhgdtlAADAYQAGHHGSSTSSSDPF 249
                                       6666666666666666666666666555555555555555555555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.2
                                       EEEEEHECTTSTSCCEEEEEETTC CS
                       Lactamase_B 120 rralyvtggpghghghgvveyggg 143
                                        r+ +++++ +hg +++ v+ g++
  gi|336253805|ref|YP_004596912.1| 281 ERGIETYWTGVHGDTVITVDGGDD 304
                                       456666666666666666665554 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 !   23.8   1.0   4.5e-09   2.7e-05       3     148 ..      67     218 ..      65     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.5e-09
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EE..EEEEEEHHHHHHCCTTCGH CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkk..lplyapkgvlavleanfvy 76 
                                       iLiD+g d+r   +         +++++id ++ th+H+DH+ g + + e ++++   +    + gv+ + ++   y
  gi|336253805|ref|YP_004596912.1|  67 ILIDTG-DWRDDGQTVIDYL-EAQDIERIDHLVATHGHADHIGGHPAVIEhFEENGegVGAAYDSGVAHTSATYENY 141
                                       666666.4454422222222.467899***********************844433465555578888888888888 PP

                                       HHCHTTTTEEEEEE-TTSEEEE.....CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---H CS
                     Lactamase_B_2  77 laleeepavnvheldwgesfel.....gdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipe 148
                                       l   ee  v++ ++ +g+++ l     ++++ +++at ++   +r+ d   +  + l ++ g+ + + +gD ++++e
  gi|336253805|ref|YP_004596912.1| 142 LDAIEEHDVDLFQVVAGDRLPLesasaDGSNATLEATVLNPPEERHSDGVDENSVVLSLAYGEFTYLTTGDIERTTE 218
                                       87777779999999999998888887744566777776666666655555556666666666666666777777664 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 !   16.1   0.0   9.9e-07    0.0059       6      61 ..      64     118 ..      59     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.9e-07
                     Lactamase_B_6   6 nvkiLlDvG.wdeskvslesalkelekv.iptvdliLLshatlehlGayallyakfks 61 
                                       n +iL+D G w++   + ++++++le   i+++d+ + +h  ++h+G+++ ++ +f++
  gi|336253805|ref|YP_004596912.1|  64 NETILIDTGdWRD---DGQTVIDYLEAQdIERIDHLVATHGHADHIGGHPAVIEHFEE 118
                                       789******4444...4578999999866***********************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2612.62
//
Query:       gi|336253806|ref|YP_004596913.1|  [L=131]
Description: OsmC family protein [Halopiger xanaduensis SH-6]
Scores for 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-11   42.7   0.0    8.1e-11   42.3   0.0    1.2  1  OsmC      OsmC-like protein


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   4.5e-15   8.1e-11       3      97 ..      31     122 ..      28     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 4.5e-15
                                       XSSB-HHHHHHHHHHHHHHHHHHHHTCCCT-.--SCEEEEEEEEEECCECTCEEEEEEEEEEE-SS-H..HHHHHHH CS
                              OsmC   3 gsgpsPeelllaalasCfaitlravakkkgi.kledleveveaerdpegakgiteirlkvevkipgadseeklkkll 78 
                                       +++p+  e+llaa++sC+  +lr   +++g  +l  +e++++++ +++   ++++i ++++v+++ +d  e+ ++++
  gi|336253806|ref|YP_004596913.1|  31 EDAPDTLEALLAAYGSCYVPALRVGGQQRGAdDLGTIEIDITGDLNDDD--KLESIAFDIRVEADVDD--ETGEEIV 103
                                       569999***********************99666999*****9999773..49*********977766..******* PP

                                       HHHHHHSHHHHHHCT-SSS CS
                              OsmC  79 ekaekrCpvsntlkngvkv 97 
                                       e+a + C v+++lk + + 
  gi|336253806|ref|YP_004596913.1| 104 ERAFELCKVHDALKDDLHA 122
                                       *************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1050.38
//
Query:       gi|336253807|ref|YP_004596914.1|  [L=204]
Description: hypothetical protein Halxa_2416 [Halopiger xanaduensis SH-6]
Scores for complete 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   47.1  11.5    2.3e-12   46.6  11.5    1.3  1  YdjM         LexA-binding, inner membrane-associated putative
     0.0048   16.2   3.0      0.006   15.9   3.0    1.2  1  Voltage_CLC  Voltage gated chloride channel
  ------ inclusion threshold ------
      0.028   14.3   0.4      0.058   13.3   0.2    1.6  1  DUF2227      Uncharacterized metal-binding protein (DUF2227)
      0.053   13.5   0.9      0.065   13.2   0.9    1.2  1  DUF1614      Protein of unknown function (DUF1614)


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6  11.5   5.2e-16   2.3e-12       4     141 ..       5     151 ..       1     176 [. 0.80

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 5.2e-16
                              YdjM   4 ltHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllflalla 80 
                                         H+ ++++ ++ +   +g+++    +a+++++A+lPD+D   + l++ l+   +       H g+tH+l+f+al +
  gi|336253807|ref|YP_004596914.1|   5 TGHFGMALVFAAPAWMIWGRRAALGFTAFTLVTAMLPDAD---LVLQHVLPI--S-------HHGITHTLVFVALGG 69 
                                       589999999999999999998878999999999*******...888888877..4.......9************** PP

                              YdjM  81 lvlllllrlfgrsa..................lrlglllllgvlsHlllDlltk....yGvpllwPfskkkvrlsll 135
                                       +v+ +++ ++ + +                  ++++ +l++g +sHl++D+l      ++   +wP+ ++ v ++++
  gi|336253807|ref|YP_004596914.1|  70 AVGGAVASTYLTARlnahrwirsteiesetvfVFATAGLIVGGVSHLFADILSApdiaAPLTPFWPIYSEPVIVDVI 146
                                       ***********999***************998777888****************66666667788887666666655 PP

                              YdjM 136 fiiidp 141
                                        + ++p
  gi|336253807|ref|YP_004596914.1| 147 YY-NSP 151
                                       55.443 PP

>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   3.0   1.3e-06     0.006     158     228 ..      56     124 ..       8     170 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-06
                                       .--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC.CSSSS CS
                       Voltage_CLC 158 alsllelilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgllvgllglllpasvlggg 228
                                       +  ++ l++++l G +gG+++  +    l+++r++r+ e +    ++  a +gl+vg ++ l++  +l+ +
  gi|336253807|ref|YP_004596914.1|  56 HGITHTLVFVALGGAVGGAVASTYLTARLNAHRWIRSTE-IESETVFVFATAGLIVGGVSHLFAD-ILSAP 124
                                       3445678999999***********************995.4445678888888888888777755.66655 PP

>> DUF2227  Uncharacterized metal-binding protein (DUF2227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   1.3e-05     0.058     109     163 ..      72     122 ..      45     126 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                           DUF2227 109 llavlelnwqalvaelkkelkllasllekkekellalllGlelgamlHllsDwvv 163
                                         av++   + l+a+l+ ++++ +s++ ++e++++ +++Gl++g ++Hl++D+++
  gi|336253807|ref|YP_004596914.1|  72 GGAVAS---TYLTARLN-AHRWIRSTEIESETVFVFATAGLIVGGVSHLFADILS 122
                                       333333...33444444.47788888989999********************975 PP

>> DUF1614  Protein of unknown function (DUF1614)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.9   1.4e-05     0.065      30      96 ..      50     128 ..      27     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                           DUF1614  30 kvpvleeeekktvvavNvGGaviPlllslylllrlavs............llaallavlivaavvyllarpvpgvGi 94 
                                        +p+ ++  ++t+v v +GGav  +++s+yl +rl+++            ++ +++a liv  v++l+a++ +   i
  gi|336253807|ref|YP_004596914.1|  50 VLPISHHGITHTLVFVALGGAVGGAVASTYLTARLNAHrwirsteiesetVFVFATAGLIVGGVSHLFADILSAPDI 126
                                       44666777788************************955555555555544444444445555555555555544444 PP

                           DUF1614  95 vv 96 
                                       + 
  gi|336253807|ref|YP_004596914.1| 127 AA 128
                                       44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1491.26
//
Query:       gi|336253808|ref|YP_004596915.1|  [L=242]
Description: hypothetical protein Halxa_2417 [Halopiger xanaduensis SH-6]
Scores for 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-18   67.7   0.9    1.7e-18   67.1   0.9    1.3  1  Lactamase_B_3    Beta-lactamase superfamily domain
    1.1e-14   54.4   1.3    1.6e-14   53.9   1.3    1.2  1  Lactamase_B_2    Beta-lactamase superfamily domain
    2.1e-07   31.2   3.8    2.1e-07   31.2   3.8    1.9  2  Lactamase_B      Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.031   14.0   0.0       0.11   12.2   0.0    1.9  2  Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation 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 !   67.1   0.9   3.8e-22   1.7e-18       1     163 []       2     202 ..       2     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 3.8e-22
                     Lactamase_B_3   1 eltwlghnsflletagarilvDPfkanlgyeppa...eeaDlvlisqaledHahletlkqlaenvkvlee....... 67 
                                       eltw+gh+++ ++++++++l+DPf+ n ++e ++   e++D vl++++++dH  ++   +   +++++++       
  gi|336253808|ref|YP_004596915.1|   2 ELTWHGHSTWHVTVGDTELLIDPFFDNPKTELDPsdvETPDYVLLTHGHADHISHAGEFS---DATLVATpelvsyc 75 
                                       69**********************98666666666689***************9998888...99999998999999 PP

                     Lactamase_B_3  68 .................geslevggleiravatshdavggser....genngflleqd.........gltiyhlGhl 114
                                                        g+++e+g+++++ ++++h+++  +e     g  +gf+++++           t+y  G++
  gi|336253808|ref|YP_004596915.1|  76 edefgyedavggmgmnlGGTVECGDAYVTMHRADHTNGIMTEYdvdaGMPTGFVISDTkptqiadeeSTTFYDAGDT 152
                                       99999999999999998899***************888655443444668999999955666777767888889999 PP

                     Lactamase_B_3 115 ahelsseel.kelgrvDvvltPvggpltlgqeealelakrLkpklvlPmh 163
                                       a   ++ +      ++D   +P+g+++t+g+++a+ ++ +L+ ++ lP h
  gi|336253808|ref|YP_004596915.1| 153 ALMTEMRDViGPYLEPDAAAVPIGDHFTMGPQQAAIAVDWLDVDVALPQH 202
                                       986655554256679********************************977 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 !   53.9   1.3   3.6e-18   1.6e-14       2     201 .]      19     203 ..      18     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 3.6e-18
                                       EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyla 78 
                                        +LiD+++d   + +  l      ++++  d Vllth+H+DH+  +  +       ++l+a++++ ++ e++f y+ 
  gi|336253808|ref|YP_004596915.1|  19 ELLIDPFFD--NP-KTELD----PSDVETPDYVLLTHGHADHISHAGEFSD-----ATLVATPELVSYCEDEFGYED 83 
                                       58*******..55.44554....46799***************76666666.....78**************99865 PP

                                       CHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C..TCCE-TTTSEEEEEECTTEE.........EEEESS-S CS
                     Lactamase_B_2  79 leeepavnvheldwgesfelgdggleitatparhksgr..rldrnagdtlGlriegggkr.........vyyigDtg 144
                                            av    +++g+++e+gd+   +t++ a h+ g   + d +ag   G++i +++ +         +y +gDt+
  gi|336253808|ref|YP_004596915.1|  84 -----AVGGMGMNLGGTVECGDA--YVTMHRADHTNGImtEYDVDAGMPTGFVISDTKPTqiadeesttFYDAGDTA 153
                                       .....55669***********75..5************999999999********55555666666676999***** PP

                                       ---...HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 145 yip...eeigerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                        ++   + ig  l+ +d + ++i+         +++++ p++a+ a++ l++ ++++ H+
  gi|336253808|ref|YP_004596915.1| 154 LMTemrDVIGPYLE-PDAAAVPIG---------DHFTMGPQQAAIAVDWLDVDVALPQHY 203
                                       ***44333665555.9********.........799*********************997 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   3.8   4.6e-11   2.1e-07       4      70 ..       6      66 ..       3      83 .. 0.90
   2 ?   -1.7   0.0      0.56   2.5e+03     149     183 ..     150     194 ..     144     203 .. 0.58

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 4.6e-11
                                      CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCC CS
                       Lactamase_B  4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdv 70
                                       +++++ ++ +++ +LiD+ ++++++ +         + + +d+v+lTH+H+DHi+ +g++ +at v
  gi|336253808|ref|YP_004596915.1|  6 HGHSTWHVTVGDTELLIDPFFDNPKTEL------DPSDVETPDYVLLTHGHADHISHAGEFSDATLV 66
                                      56778888899999*************9......69*************************999866 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.56
                                       CTTTSSHHCCCCCC...........TTCEEE-SHCHHHHHHHHHH CS
                       Lactamase_B 149 GDallagetgridl..........tlrgaevrdpsdaekyldsll 183
                                       GD+ l  e  ++            ++++++++ p++a+ + d+l+
  gi|336253808|ref|YP_004596915.1| 150 GDTALMTEMRDVIGpylepdaaavPIGDHFTMGPQQAAIAVDWLD 194
                                       555554444444445566666666666667777776666666555 PP

>> Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.5e-05      0.11       9      39 ..      60      90 ..      58     101 .. 0.79
   2 ?   -2.7   0.0       1.1   4.9e+03      26      37 ..     116     127 ..     114     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                                      HHTSBHHHHHHHHHHHHHHTTHHHHHHHHHH CS
                   Ribosomal_L12_N  9 ikeltvLElseLvkalEekFGVsAAAPvava 39
                                      ++  t+  + eLv+++E++FG ++A   +++
  gi|336253808|ref|YP_004596915.1| 60 FSDATLVATPELVSYCEDEFGYEDAVGGMGM 90
                                      5677889999*************99666665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                                       HHTTHHHHHHHH CS
                   Ribosomal_L12_N  26 ekFGVsAAAPva 37 
                                       ++++V+A +P +
  gi|336253808|ref|YP_004596915.1| 116 TEYDVDAGMPTG 127
                                       589999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1841.20
//
Query:       gi|336253809|ref|YP_004596916.1|  [L=87]
Description: hypothetical protein Halxa_2418 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.098   12.7   0.1       0.21   11.6   0.1    1.7  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
       0.11   13.2   0.0       0.12   13.1   0.0    1.1  1  Complex1_LYR_2   Complex1_LYR-like


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 ?   11.6   0.1   2.3e-05      0.21      23      47 ..      52      77 ..      15      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.3e-05
                                      EEETT.EEEEEEEETHHHHHHHTTS- CS
                   tRNA_anti-codon 23 lrDgt.griqvvlfreeatklaenlk 47
                                       +D+   +iqv+lf+e++++la++++
  gi|336253809|ref|YP_004596916.1| 52 FEDDDeNEIQVSLFPEQVRELADDIE 77
                                      5555559**************99987 PP

>> Complex1_LYR_2  Complex1_LYR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05      0.12      15      60 ..      36      79 ..       8      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                    Complex1_LYR_2 15 lppelrslgdayvraefrrhkhlknpeeialflknqreYaellery 60
                                      ++ e r++gd +v+  f+   + +n+ ++ lf  + re a+ +er 
  gi|336253809|ref|YP_004596916.1| 36 ESAEGREFGDKRVKLVFED--DDENEIQVSLFPEQVRELADDIERL 79
                                      467899*************..889999*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 710.76
//
Query:       gi|336253810|ref|YP_004596917.1|  [L=716]
Description: OB-fold tRNA/helicase-type nucleic acid binding protein [Halopiger xanaduensis SH-6]
Scores for 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-11   42.8   0.1    1.1e-10   41.3   0.1    1.9  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
    1.9e-08   34.5   0.0    5.7e-08   33.0   0.0    1.9  1  S1               S1 RNA binding domain
    5.8e-05   23.2   0.0    0.00014   22.0   0.0    1.6  1  tRNA_anti_2      OB-fold nucleic acid binding domain
     0.0092   16.0   0.0      0.029   14.4   0.0    1.9  1  S1_2             S1 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 !   41.3   0.1   2.6e-14   1.1e-10       1      76 []     233     305 ..     233     305 .. 0.96
   2 ?   -3.3   0.0         2   9.2e+03       9      32 ..     639     661 ..     637     676 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 2.6e-14
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveeiell 76 
                                       V+++G++t i  r++++   ++lrD+tg++++ +f e+  + + +++++dvv  +G+v+r  g  l++  e +e+l
  gi|336253810|ref|YP_004596917.1| 233 VRLEGEITGI--RQTSGPTVFTLRDETGTVECAAFEEAGVRAYPDVEIDDVVALEGEVERHHGD-LQVETETLEIL 305
                                       899*******..*************************************************999.*9999998886 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2
                                       EEEEEEETTEEEEEEEETTEEEEE CS
                   tRNA_anti-codon   9 sisdrsggkvifidlrDgtgriqv 32 
                                       +++ r++g ++++ + D++  +++
  gi|336253810|ref|YP_004596917.1| 639 RRQ-RDEGPFVTLGVGDDELHVRA 661
                                       454.89999999988888766655 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   1.3e-11   5.7e-08       5      72 ..      38     100 ..      34     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.3e-11
                                       TCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEE CS
                                S1   5 gevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriil 72 
                                       g  + G+V    ++G+fV++g +v+g++++sel+ +     ++    +Gd v+v+vl+v+++ + ++l
  gi|336253810|ref|YP_004596917.1|  38 GRYYRGTVDGYADFGVFVDVGDHVTGLLHRSELDKR----LESLDWEPGDDVYVQVLDVRDNGN-VDL 100
                                       677899****************************98....6999***************99987.776 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 !   22.0   0.0   3.1e-08   0.00014      12      85 ..     223     293 ..     216     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.1e-08
                       tRNA_anti_2  12 elleaelkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgrlsvYeprG 85 
                                       +++++++ + v ++Gei+ + r++sg + ftL+De+ +++++ f+++  +   ++e ++ V ++g+++ +   G
  gi|336253810|ref|YP_004596917.1| 223 DAIDNQVGSVVRLEGEITGI-RQTSGPTVFTLRDETGTVECAAFEEAGVRAYPDVEIDDVVALEGEVERHH--G 293
                                       6788999999**********.767********************977655556688899999999998764..4 PP

>> S1_2  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   6.6e-06     0.029       2      39 ..      38      75 ..      37      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.6e-06
                              S1_2  2 GkintlkvlretdfgyfLqkdesgevlLpkkevpeele 39
                                      G++ + +v+   dfg+f++ ++ ++ lL+ +e+++ le
  gi|336253810|ref|YP_004596917.1| 38 GRYYRGTVDGYADFGVFVDVGDHVTGLLHRSELDKRLE 75
                                      9999*****************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (716 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.40
# Mc/sec: 5314.06
//
Query:       gi|336253811|ref|YP_004596918.1|  [L=191]
Description: hypothetical protein Halxa_2420 [Halopiger xanaduensis SH-6]
Scores for 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-09   36.8   5.0    4.1e-09   35.9   5.0    1.5  1  SHOCT     Short C-terminal domain
      4e-06   26.8   7.2    8.5e-06   25.7   7.2    1.5  1  DUF1707   Domain of unknown function (DUF1707)
  ------ inclusion threshold ------
      0.035   14.1   0.9      0.035   14.1   0.9    1.5  2  GvpG      Gas vesicle protein G
       0.15   11.9   0.1       0.37   10.7   0.1    1.6  1  DUF2631   Protein of unknown function (DUF2631)


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   5.0   9.1e-13   4.1e-09       1      28 []     118     145 ..     118     145 .. 0.98

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 9.1e-13
                             SHOCT   1 daLekLkeLyarGeIteEEFeakKakLL 28 
                                       daLe+L+++ya+Ge+t+E Fe+k ++LL
  gi|336253811|ref|YP_004596918.1| 118 DALETLRDRYAAGELTDEQFERKLERLL 145
                                       89*************************8 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   7.2   1.9e-09   8.5e-06       5      51 ..     113     159 ..     111     159 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.9e-09
                           DUF1707   5 dadReravelLrealaeGrLtldEfdeRleaalaArtrgeLaalvaD 51 
                                       ++dR +a+e Lr+ +a+G Lt + f++ le+ l  +t+++ a+ v+D
  gi|336253811|ref|YP_004596918.1| 113 ESDRRDALETLRDRYAAGELTDEQFERKLERLLHTETLEDVADWVED 159
                                       68***************************************999987 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       2.1   9.6e+03       4      15 ..      37      48 ..      36      49 .. 0.77
   2 ?   14.1   0.9   7.7e-06     0.035      28      64 ..     111     147 ..     105     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.1
                              GvpG  4 lllaPvrgviWi 15
                                      ll+a   g++W+
  gi|336253811|ref|YP_004596918.1| 37 LLVAGFSGLMWL 48
                                      677788899**7 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.7e-06
                              GvpG  28 ddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdr 64 
                                        d+ + r  L +L  +  aGe ++e+F+r+ e+lL  
  gi|336253811|ref|YP_004596918.1| 111 TDESDRRDALETLRDRYAAGELTDEQFERKLERLLHT 147
                                       4666678899************************964 PP

>> DUF2631  Protein of unknown function (DUF2631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   8.2e-05      0.37      33      52 ..      51      70 ..      46      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.2e-05
                           DUF2631 33 triaGlisvlallamliGnh 52
                                      + i+G+i+v+ l+ ml+Gn 
  gi|336253811|ref|YP_004596918.1| 51 FAIVGYIVVVPLITMLFGND 70
                                      689****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 00:00:00.39
# Mc/sec: 1454.59
//
Query:       gi|336253812|ref|YP_004596919.1|  [L=131]
Description: monovalent cation/proton antiporter subunit MnhG/PhaG [Halopiger xanaduensis SH-6]
Scores for 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-25   86.8   7.1    1.1e-24   86.5   7.1    1.1  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit


Domain annotation for each model (and alignments):
>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   7.1     6e-29   1.1e-24       1      78 [.      10      88 ..      10      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 6e-29
                    PhaG_MnhG_YufB  1 llllGalfvllgaigllrlpdvytRlhaatkadtlGlllillGlllrf.slaaslkllliilfllltaPvaahliaraa 78
                                      l+++G++f  +g+igllrlp+vy+R+ha++k++tlG+ +i+l+ ++ f      l +ll i+flllt P++ah+iaraa
  gi|336253812|ref|YP_004596919.1| 10 LVVVGVFFLTVGTIGLLRLPNVYNRMHATSKPTTLGTAAIFLAGFVEFgPGGDGLTALLGIAFLLLTVPTGAHMIARAA 88
                                      79********************************************9977777*************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 965.58
//
Query:       gi|336253813|ref|YP_004596920.1|  [L=97]
Description: multiple resistance and pH regulation protein F [Halopiger xanaduensis SH-6]
Scores for 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-18   64.8   8.9    6.7e-18   64.8   8.9    1.9  2  MrpF_PhaF     Multiple resistance and pH regulation protein F
  ------ inclusion threshold ------
       0.12   11.9   5.9       0.14   11.8   5.9    1.1  1  DUF5336       Family of unknown function (DUF5336)
       0.18   12.2   5.2       0.13   12.6   3.5    1.6  1  IncF          Inclusion membrane protein F


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2     0.095   5.7e+02      28      48 ..       7      27 ..       4      30 .. 0.66
   2 !   64.8   8.9   1.1e-21   6.7e-18       1      52 [.      39      90 ..      39      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.095
                         MrpF_PhaF 28 payldvalvlAllgFvgtvaf 48
                                      pa+l+ ++  Al+   g  ++
  gi|336253813|ref|YP_004596920.1|  7 PALLETVISAALVIVSGLCVL 27
                                      677777777777766665555 PP

  == domain 2  score: 64.8 bits;  conditional E-value: 1.1e-21
                         MrpF_PhaF  1 aDRvvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarfl 52
                                      +DRvvAlD+++t++va+ +l+a+ t+r ++l v lvlA++gF++tva+a+f+
  gi|336253813|ref|YP_004596920.1| 39 PDRVVALDAIATNVVAIAVLFALQTERGLFLTVSLVLAIIGFIATVAVAKFV 90
                                      8**************************************************6 PP

>> DUF5336  Family of unknown function (DUF5336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   5.9   2.4e-05      0.14      76     159 ..      11      96 ..       2      97 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.4e-05
                           DUF5336  76 glglavvllLlagL..lAgvslLPkqksktavaAvlsvlgfLlvlaevinapegvsiawglwvvlvlallqaaaAva 150
                                       ++++  +l+++ gL  l    ++ + ++   v+A+ +++  ++++a +++++++ ++  ++ +vl+++ + a +Ava
  gi|336253813|ref|YP_004596920.1|  11 ETVISAALVIVSGLcvLCSYRVIRGPTNPDRVVALDAIATNVVAIAVLFALQTERGLFLTVSLVLAIIGFIATVAVA 87 
                                       5556666777777644677778888888899*********************9999999999999999999999999 PP

                           DUF5336 151 aLLfeagvi 159
                                           e +vi
  gi|336253813|ref|YP_004596920.1|  88 KFVTEGEVI 96 
                                       988888887 PP

>> IncF  Inclusion membrane protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.5   2.2e-05      0.13      41      98 ..      13      68 ..       7      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                              IncF 41 valaalvlngalcvlslvalcvgatpvgplavlvattlasflcaacvlfiaakdrgwi 98
                                      v  aalv+   lcvl    +     p  p  v+   ++a+ ++a +vlf    +rg  
  gi|336253813|ref|YP_004596920.1| 13 VISAALVIVSGLCVLCSYRVI--RGPTNPDRVVALDAIATNVVAIAVLFALQTERGLF 68
                                      6679999999****9766655..55778999999999*************99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); 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:                         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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 714.92
//
Query:       gi|336253814|ref|YP_004596921.1|  [L=221]
Description: cation antiporter [Halopiger xanaduensis SH-6]
Scores for 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-37  127.7   0.6    3.5e-37  127.4   0.6    1.1  1  MNHE      Na+/H+ ion antiporter subunit


Domain annotation for each model (and alignments):
>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.4   0.6   1.9e-41   3.5e-37       3     145 ..      12     165 ..      11     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 127.4 bits;  conditional E-value: 1.9e-41
                              MNHE   3 llflvWllltgs.......lgelllGlllallvalllrrll.......lplrrvllrllayllvflweivkanldVa 65 
                                       +++++W+++ g        lg++l Gl+++l +a+++rrl+       + +r +++ +  yl+ f+weiv+an d++
  gi|336253814|ref|YP_004596921.1|  12 AFAVLWIFVRGIglspaalLGQFLEGLVIGLPIAFVFRRLYveridlgRGVRALPY-AGLYLATFAWEIVRANADMV 87 
                                       5799******9999999**********************99887776433333355.99999*************** PP

                              MNHE  66 krvlrpklpirpgivkvplrlksdlaltllansitltPGTltvdvdedrrvlyvHvldvedeeeeareeikgrlErr 142
                                       +rvl p +pi+p+++ vplr ++d+a+tllansit+tPGT+ +d+d+++++lyvH+ d +d +e++++ i +++E++
  gi|336253814|ref|YP_004596921.1|  88 YRVLAPGIPIEPEVILVPLRAETDVAITLLANSITITPGTVALDYDAETNALYVHAVDGRD-PEAIAAPI-RQWEDY 162
                                       ***********************************************************99.99998888.569998 PP

                              MNHE 143 lle 145
                                       +le
  gi|336253814|ref|YP_004596921.1| 163 ALE 165
                                       876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1618.05
//
Query:       gi|336253815|ref|YP_004596922.1|  [L=575]
Description: NADH dehydrogenase (quinone) [Halopiger xanaduensis SH-6]
Scores for complete 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-51  175.2  19.0    1.1e-25   90.4   5.0    2.6  2  Proton_antipo_M  Proton-conducting membrane transporter
    0.00063   19.2   2.8    0.00063   19.2   2.8    3.0  3  NADHdeh_related  NADH dehydrogenase I, subunit N related prot
     0.0042   17.1   0.3      0.014   15.4   0.3    1.9  1  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 !   90.4   5.0   1.9e-29   1.1e-25       2     142 ..     156     299 ..     155     317 .. 0.94
   2 !   90.1   6.1   2.4e-29   1.4e-25     148     293 .]     326     479 ..     318     479 .. 0.87

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 1.9e-29
                   Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal....el 74 
                                       +dL+ l++ +E++l+++y+ +++++   + ++A++ ++ l+ll+s ++Llg+  +y++tgtl++ +ls+ l     +
  gi|336253815|ref|YP_004596922.1| 156 GDLFNLFVWFEVMLMASYIFVAYYGGP-QHTRAAFWYVSLNLLASAVFLLGVGGVYAVTGTLNMADLSRRLadpaAF 231
                                       69**********************765.99***************************************99999999 PP

                   Proton_antipo_M  75 glnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavs 142
                                       g++  ++l l+ lll  +++K+++vp+++W+p ay +aP  +sallA+ + k+g++++irl++ ++  
  gi|336253815|ref|YP_004596922.1| 232 GIEPEAALGLYALLLSVFAIKAGLVPFQFWIPTAYRAAPPQISALLAGATKKVGIYAIIRLSFTVFAD 299
                                       9999999999999************************************************9988744 PP

  == domain 2  score: 90.1 bits;  conditional E-value: 2.4e-29
                   Proton_antipo_M 148 qlllilaiismllgslvalaqtdiKrllAySsishlGymlialav..atqy......gveaaiihllthalfkallF 216
                                         l+++a++s+l+g+++a+  ++i  +lAySsi+++G++ i +a+  +t+       ++ aa+++ l h l k llF
  gi|336253815|ref|YP_004596922.1| 326 AALFVMAAASILVGGIGAVGRNSIEGVLAYSSIGQVGFIAIPVAIaaTTASaelrhlALVAALVYALNHTLAKGLLF 402
                                       56899*********************************998777752333211222256799*************** PP

                   Proton_antipo_M 217 llagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvl 292
                                       l++g+v ++ + t  ++++ggLa++ P+la+ ++++ lsl+G+Pp++gF++kfl++ +a ++++  +v++ +v+s+l
  gi|336253815|ref|YP_004596922.1| 403 LAVGAV-RSATGTSRLADLGGLAERSPMLAIPFFIASLSLVGIPPLSGFFGKFLVFDSAARAEAAPVVVLlLVGSLL 478
                                       ***888.667799*************************************************998888887999988 PP

                   Proton_antipo_M 293 t 293
                                       t
  gi|336253815|ref|YP_004596922.1| 479 T 479
                                       7 PP

>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   2.8   1.1e-07   0.00063      80     157 ..     147     224 ..     134     265 .. 0.87
   2 !    6.6   9.3   0.00075       4.5     110     212 ..     376     483 ..     320     487 .. 0.71
   3 ?   -2.5   0.1      0.45   2.7e+03     138     160 ..     516     538 ..     507     546 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.1e-07
                   NADHdeh_related  80 latlgavvtgdvfnftlflaliGianiGivaavkkefvleaafnyGlvaliatlplfggaalilastGtlsifelak 156
                                       l  +ga +tgd+fn  ++  ++ +a    va +       aaf y  + l+a+  ++ g + + a tGtl + +l++
  gi|336253815|ref|YP_004596922.1| 147 LGVTGAFLTGDLFNLFVWFEVMLMASYIFVAYYGGPQHTRAAFWYVSLNLLASAVFLLGVGGVYAVTGTLNMADLSR 223
                                       6789**********988888888999999**********************998888889999************98 PP

                   NADHdeh_related 157 l 157
                                        
  gi|336253815|ref|YP_004596922.1| 224 R 224
                                       6 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00075
                   NADHdeh_related 110 aavkkefvleaafnyGlvaliatlplfggaalilastGtlsifelaklagdvlliaklllv..lGvvGetGvaPf.. 182
                                       +a  ++ +l aa  y l   +a   lf + + + ++tGt  + +l +la   +++a  +++  l +vG   ++ f  
  gi|336253815|ref|YP_004596922.1| 376 SAELRHLALVAALVYALNHTLAKGLLFLAVGAVRSATGTSRLADLGGLAERSPMLAIPFFIasLSLVGIPPLSGFfg 452
                                       344467799************************************99977655444444331134455444444411 PP

                   NADHdeh_related 183 .yaakaeifrapgapyillihlsslllivrv 212
                                        + +     ra+ ap ++l+ + sll+i  +
  gi|336253815|ref|YP_004596922.1| 453 kFLVFDSAARAEAAPVVVLLLVGSLLTIAYA 483
                                       156667889*****************99755 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.45
                   NADHdeh_related 138 gaalilastGtlsifelaklagd 160
                                       +aa++l   G   ++e+a  a +
  gi|336253815|ref|YP_004596922.1| 516 AAAIVLVGVGFEPVYEFADAAAN 538
                                       68888888888888888877765 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 !   15.4   0.3   2.4e-06     0.014      12      44 ..      97     129 ..      89     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.4e-06
                   Proton_antipo_N  12 ieigfllDklsalmllvvtfvsllvhlYSigYM 44 
                                       + i++ +D+lsa ml++v +++   +++S+  +
  gi|336253815|ref|YP_004596922.1|  97 VGITLVVDGLSAFMLTMVAVLGIASLVFSTRVL 129
                                       56899***********************98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 4076.21
//
Query:       gi|336253816|ref|YP_004596923.1|  [L=120]
Description: NADH-ubiquinone oxidoreductase chain 4L [Halopiger xanaduensis SH-6]
Scores for 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-30  103.9   1.2    3.7e-30  103.6   1.2    1.1  1  Oxidored_q2      NADH-ubiquinone/plastoquinone oxidoreductase
  ------ inclusion threshold ------
      0.091   11.6   0.3       0.11   11.3   0.3    1.1  1  Herpes_glycop    Herpesvirus glycoprotein M
       0.18   11.5   0.9        8.1    6.3   0.2    2.4  2  Phage_holin_2_3  Bacteriophage holin family HP1


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 !  103.6   1.2   6.2e-34   3.7e-30       2     103 ..       6     116 ..       5     120 .] 0.94

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 6.2e-34
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.......................TTSCGGH CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvi..........tnpatefadplpqa 68 
                                       l++++++lf++G++++l rr+l++v+ gl +is a+n++l+++g  tegt+                   adpl+qa
  gi|336253816|ref|YP_004596923.1|   6 LAAVVGALFALGTFLLL-RRDLIRVVWGLAIISQAANVYLLAMGGITEGTAETvpvleghghdIHVPVGIADPLVQA 81 
                                       67899************.*******************************9888889***99986667789******* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHSSS-BCCG- CS
                       Oxidored_q2  69 lvLtaivigaaetavgLallvrlyreygtddvqel 103
                                       lvLtaivig+++ta++L+l +r+y+e++t+dv+el
  gi|336253816|ref|YP_004596923.1|  82 LVLTAIVIGFGMTAFALVLSYRVYEEHDTLDVSEL 116
                                       *********************************99 PP

>> Herpes_glycop  Herpesvirus glycoprotein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   1.9e-05      0.11      71     150 ..      20     104 ..       5     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.9e-05
                     Herpes_glycop  71 flespslvfyvvltalvllvvavYylvvgaviskakkkdsslqaserlvsalv..asp...ttlflailslwllqvf 142
                                        l  ++l+ +v   a++  ++ vY l +g+++    +  ++l+  ++++   v  a+p   +++++ai+    + +f
  gi|336253816|ref|YP_004596923.1|  20 LLLRRDLIRVVWGLAIISQAANVYLLAMGGITEGTAETVPVLEGHGHDIHVPVgiADPlvqALVLTAIVIGFGMTAF 96 
                                       555677888899999*******************************999877622677443456778888899**** PP

                     Herpes_glycop 143 vllLsykl 150
                                        l+Lsy+ 
  gi|336253816|ref|YP_004596923.1|  97 ALVLSYRV 104
                                       ******96 PP

>> Phage_holin_2_3  Bacteriophage holin family HP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2    0.0014       8.1      27      41 ..       7      21 ..       5      24 .. 0.92
   2 ?    3.5   0.0      0.01        61      27      47 ..      86     106 ..      81     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0014
                   Phage_holin_2_3 27 AiviGIicgvvTfli 41
                                      A+v+G +++++Tfl+
  gi|336253816|ref|YP_004596923.1|  7 AAVVGALFALGTFLL 21
                                      99***********96 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.01
                   Phage_holin_2_3  27 AiviGIicgvvTfliNwyykr 47 
                                       AiviG  ++++ +++ ++ + 
  gi|336253816|ref|YP_004596923.1|  86 AIVIGFGMTAFALVLSYRVYE 106
                                       899999999999999888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 915.98
//
Query:       gi|336253817|ref|YP_004596924.1|  [L=154]
Description: Na+/H+ antiporter MnhB subunit-like protein [Halopiger xanaduensis SH-6]
Scores for 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-35  122.7   7.8    1.3e-35  122.4   7.8    1.1  1  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   7.8   7.3e-40   1.3e-35       1     124 []       5     146 ..       5     146 .. 0.95

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 7.3e-40
                              MnhB   1 ilrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafglee.lekllrvkla............. 63 
                                       i+rt+ar +vp+il+v+++l+++Ghn PGGGF+gG+++ +a+++lylafgl++ ++ +l ++++             
  gi|336253817|ref|YP_004596924.1|   5 IMRTTARAIVPIILVVAIALFVEGHNLPGGGFIGGVLTVTAFAVLYLAFGLDFlERGVLGRDVEpgkepsrdrvvva 81 
                                       89***************************************************8888887777788899999999*9 PP

                              MnhB  64 prileglglllavltgllglllg..fltslflel.el.llgevelgtallfdlgVylvVvgglll 124
                                       +r+++  gl++av++gl++ll+   fl+++++ + ++ ++g+ve+++a++fd+gVy+vVvggll+
  gi|336253817|ref|YP_004596924.1|  82 YRRIFEYGLAIAVVSGLVPLLFDlpFLSQTYWVFeDVpIYGTVEVASAMAFDFGVYCVVVGGLLT 146
                                       *******************************99966699999********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1218.21
//
Query:       gi|336253818|ref|YP_004596925.1|  [L=804]
Description: NADH dehydrogenase (quinone) [Halopiger xanaduensis SH-6]
Scores for complete 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-69  234.9  16.0    1.1e-69  234.9  16.0    2.6  3  Proton_antipo_M  Proton-conducting membrane transporter
      4e-15   55.7  11.1      4e-15   55.7  11.1    5.4  5  DUF4040          Domain of unknown function (DUF4040)
    4.2e-12   45.9   0.9    4.2e-12   45.9   0.9    2.8  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
     0.0025   17.5   7.5     0.0025   17.5   7.5    5.7  4  Oxidored_q3      NADH-ubiquinone/plastoquinone oxidoreductase


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   1.1      0.53   2.4e+03      37      68 ..      81     112 ..      67     125 .. 0.60
   2 !  234.9  16.0   2.4e-73   1.1e-69       1     282 [.     126     415 ..     126     424 .. 0.92
   3 ?   -2.9   1.3      0.66     3e+03      43      69 ..     643     669 ..     602     682 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.53
                   Proton_antipo_M  37 klflltllgsliLLlgilllynltgtlefeel 68 
                                        ++l + +g li+L++ +++++ +  + f + 
  gi|336253818|ref|YP_004596925.1|  81 FALLASGIGTLIFLYSPAYMHGESHLTRFYAA 112
                                       44555566666666666666665555555433 PP

  == domain 2  score: 234.9 bits;  conditional E-value: 2.4e-73
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg.......tlefeelsk 70 
                                       a +L++++l++El++l++++Lig + ++ +s +A+  ++++t  g l+LL+g+l+l  ++g       t ++ +++ 
  gi|336253818|ref|YP_004596925.1| 126 AANLVAIFLFWELTSLCSFVLIGHYTEDDSSKYAARMAMFITVGGGLFLLVGLLMLSIVAGdaigaaaTFDLVAML- 201
                                       689**********************************************************888864444444444. PP

                   Proton_antipo_M  71 al......elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirllllla 140
                                               e  ++   ++ +llll +g+ +Ksaqvp+h+Wlp+a ++aPtpvsa+l +at+vk+gv+ + r+ +ll 
  gi|336253818|ref|YP_004596925.1| 202 -EnpdamrEGLRERGLFVPVLLLLAIGAGTKSAQVPVHFWLPNA-MAAPTPVSAFLhSATMVKVGVYFVGRVRPLLV 276
                                       .255888666666677777889999*******************.******************************99 PP

                   Proton_antipo_M 141 vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFl 217
                                         ++e+  l+++l++++m + +++a+a td+K+llAyS+ shlG+m+ +++ +++yg ea ++hll halfka+lFl
  gi|336253818|ref|YP_004596925.1| 277 --GEEWLLLFATLGLTTMTVCAIMAVASTDVKELLAYSTASHLGLMVAGFGFTSVYGAEAGVFHLLNHALFKAALFL 351
                                       ..*************************************************************************** PP

                   Proton_antipo_M 218 lagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslil 282
                                       +ag +i ++  tr++++++gL++  Pi+a++ +v++ls+aG+Pp+ gF+sk l++eaav++s++ 
  gi|336253818|ref|YP_004596925.1| 352 IAG-IIAHEAGTRELENLSGLRQDLPITAAMTTVVALSMAGIPPFNGFYSKELLFEAAVEASHYH 415
                                       **5.556667***************************************************9986 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.66
                   Proton_antipo_M  43 llgsliLLlgilllynltgtlefeels 69 
                                        l+ l ++++i+++++ + +l +++l+
  gi|336253818|ref|YP_004596925.1| 643 TLSILGFMVAIFYILGSAPDLALTQLV 669
                                       355666666666666666666666554 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.7      0.28   1.3e+03       2      31 ..     291     322 ..     290     325 .. 0.63
   2 ?   -3.4   4.8       2.6   1.2e+04      18      47 ..     593     622 ..     581     626 .. 0.69
   3 !   55.7  11.1     9e-19     4e-15       2      66 ..     623     686 ..     619     687 .. 0.93
   4 ?   -6.1   3.1         4   1.8e+04      46      59 ..     703     716 ..     700     718 .. 0.61
   5 ?   -3.6   0.8         3   1.3e+04      51      57 ..     766     772 ..     760     780 .. 0.39

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.28
                           DUF4040   2 llvlaalaavlardr..laavillgvvGllva 31 
                                       ++ ++a++av+++d+  l a    + +Gl+va
  gi|336253818|ref|YP_004596925.1| 291 TMTVCAIMAVASTDVkeLLAYSTASHLGLMVA 322
                                       57889999999986511444444555666666 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.6
                           DUF4040  18 aavillgvvGllvallfvllgAPDvAlTqa 47 
                                        a+  + ++G ++a +f l   P vAl  +
  gi|336253818|ref|YP_004596925.1| 593 LALAGFVATGAVTATVFGLETPPAVALVLV 622
                                       466777788888888888877777777665 PP

  == domain 3  score: 55.7 bits;  conditional E-value: 9e-19
                           DUF4040   2 llvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrlp 66 
                                       ++v+a la+v++ +++a v+ l+++G++va++++l +APD+AlTq+ vve+l+++++ll++  +p
  gi|336253818|ref|YP_004596925.1| 623 VAVAAGLAVVTSDSHVAGVLTLSILGFMVAIFYILGSAPDLALTQL-VVETLVLLIFLLVIEEIP 686
                                       5677888888899*********************************.**************9988 PP

  == domain 4  score: -6.1 bits;  conditional E-value: 4
                           DUF4040  46 qaavveglttvlll 59 
                                        +av+++  + +l+
  gi|336253818|ref|YP_004596925.1| 703 SVAVGATAFITVLV 716
                                       56677777766666 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 3
                           DUF4040  51 eglttvl 57 
                                       +   + +
  gi|336253818|ref|YP_004596925.1| 766 ALAAISI 772
                                       2222222 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 !   45.9   0.9   9.5e-16   4.2e-12       2      57 ..      60     113 ..      59     114 .. 0.95
   2 ?   -4.1   0.7         4   1.8e+04      28      39 ..     643     654 ..     641     655 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 9.5e-16
                   Proton_antipo_N   2 ftWlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayl 57 
                                       ftW++  +l+i ++f++D+  +l++l+ +++++l+ lYS  YM+++ + +RF+a l
  gi|336253818|ref|YP_004596925.1|  60 FTWIP--SLEIAMQFYVDGWALLFALLASGIGTLIFLYSPAYMHGESHLTRFYAAL 113
                                       79998..679*******************************************987 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 4
                   Proton_antipo_N  28 vvtfvsllvhlY 39 
                                       + ++++++v ++
  gi|336253818|ref|YP_004596925.1| 643 TLSILGFMVAIF 654
                                       667899999997 PP

>> 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 ?  -10.8  16.6         4   1.8e+04       9      60 ..     127     182 ..       8     302 .. 0.59
   2 ?   -1.9   0.3      0.55   2.5e+03      12      44 ..     320     352 ..     309     356 .. 0.69
   3 ?    2.1   0.6     0.033   1.5e+02      68     141 ..     509     600 ..     426     602 .. 0.70
   4 !   17.5   7.5   5.6e-07    0.0025       2     137 ..     628     777 ..     627     780 .. 0.67

  Alignments for each domain:
  == domain 1  score: -10.8 bits;  conditional E-value: 4
                                       SBHHHHHHHHHHHHHHHHHHHHHT....T-HHHHHHHHHIIIIIHHHHHHHHHHHS CS
                       Oxidored_q3   9 knpvysalfLilsfvgvaglfill....gaeFlallqilvYvGAilvlflFvimll 60 
                                        n+v+  lf  l+ ++ ++l+         ++ a + + + vG+ l l++  +ml+
  gi|336253818|ref|YP_004596925.1| 127 ANLVAIFLFWELTSLCSFVLIGHYteddSSKYAARMAMFITVGGGLFLLVGLLMLS 182
                                       33333333322222222222222212212333333333333333333333333333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.55
                                       HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHI CS
                       Oxidored_q3  12 vysalfLilsfvgvaglfillgaeFlallqilv 44 
                                       + +++ +  +  + ag+f ll+  ++ ++++l+
  gi|336253818|ref|YP_004596925.1| 320 MVAGFGFTSVYGAEAGVFHLLNHALFKAALFLI 352
                                       556667777777778888888776666655554 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.033
                                       -TTCHHHHHHHHHHHHHHHHHHHTT--...................--------TT-HHHHHHHHTTT........T CS
                       Oxidored_q3  68 peslsrslalaalligllllallllllles.............sssavdaqvadvsnieaigsllftk........y 123
                                       p+s+s+++a+ a++ig +lla+ ++  l+              ++++ da    v+n++  g  l ++        y
  gi|336253818|ref|YP_004596925.1| 509 PTSYSPAAAMSAVTIGTGLLAFPFYDRLHRgiraiphtlpptsANWWYDA---VVGNLTGAGAWLGSRvhngllrtY 582
                                       66778888888888888888884443333356666666777774444333...233444443333332222233339 PP

                                       HHHHHHHHHHHHHHHHHH CS
                       Oxidored_q3 124 llpfelasllLLvaliga 141
                                         +++la+  L +a ++a
  gi|336253818|ref|YP_004596925.1| 583 ATWTLLATAALALAGFVA 600
                                       999999999888887776 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 5.6e-07
                                       HHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS----TTCHHHHHHH CS
                       Oxidored_q3   2 allvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeeeepeslsrslala 78 
                                       +l+v+ts + v+ +l L ++ ++va+++il  a+ lal q++v     lvl++F +++ e+  e ++ ++ r  + a
  gi|336253818|ref|YP_004596925.1| 628 GLAVVTSDSHVAGVLTLSILGFMVAIFYILGSAPDLALTQLVV---ETLVLLIFLLVI-EEIPEYYEVEIGRVVRDA 700
                                       689**************************************99...67*********9.565666666666665555 PP

                                       HHHHHHHHHHHHTT--...............--------TT-HHHHHHHHTT.T........THHHHHHHHHHHHHH CS
                       Oxidored_q3  79 alligllllallllllles.........sssavdaqvadvsnieaigsllft.k........yllpfelasllLLva 137
                                       ++ ++++  a++++l+ +          ++++++ +v++ + ++ +  +l++ +         ++++ ++s+l L++
  gi|336253818|ref|YP_004596925.1| 701 VVSVAVGATAFITVLVATDarpdgntdiAEAYANLAVPEGGGTNIVNVTLVDfRgfdtlgelVVVALAAISILTLIV 777
                                       55555555555444444446778877774444455555555555555555542255555533444555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (804 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); 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: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.39
# Mc/sec: 6154.67
//
Query:       gi|336253819|ref|YP_004596926.1|  [L=556]
Description: histone acetyltransferase, ELP3 family [Halopiger xanaduensis SH-6]
Scores for 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   94.7   0.1      9e-26   91.2   0.0    2.3  2  Radical_SAM      Radical SAM superfamily
    1.4e-24   85.9   0.0    2.4e-24   85.1   0.0    1.4  1  Radical_SAM_C    Radical_SAM C-terminal domain
    2.6e-09   37.4   0.0    6.4e-09   36.1   0.0    1.7  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.4e-05   25.1   0.2      3e-05   24.0   0.2    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.08   13.4   0.1       0.17   12.3   0.1    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) 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 !   91.2   0.0   2.5e-29     9e-26       4     164 ..      96     316 ..      93     319 .. 0.95
   2 ?    0.7   0.0      0.17   6.2e+02      81     143 ..     465     525 ..     438     538 .. 0.62

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 2.5e-29
                                       ESEESS-.-TTTSCCTT..................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGST CS
                                       xxxxxxx.xxxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   4 trgCnlr.CsfCarpet..................vrregrgrslsveeileevkelkaekgvkevilgggepllyp 61 
                                        + C+++ C +C+ + +                  + ++++  + +v   le+++e+ +  ++ e+il+gg+ ++++
  gi|336253819|ref|YP_004596926.1|  96 PERCPHGkCLYCPGGPDsefsssqsytgeepaaarGVQNDYDPYGQVTLRLEQLREIGHPVDKVELILMGGTMTARS 172
                                       56788888***************************999*******************99999**************9 PP

                                       THHHHHHHHHHTC..........................................CCTEEEEEEECSSCHGHHHHHH CS
                                       xxxxxxxxxxxxx..........................................xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  62 dfvellerlakla..........................................vpgiritvetngtlpdeekler 96 
                                       + +++++  ++l+                                          v++i +t+et + + d+e+++r
  gi|336253819|ref|YP_004596926.1| 173 HDYQEWFVKRALEamndydvdkepepaegesfaqdpeeyefryledviaenetadVRNIGTTFETKPDWCDPEQIDR 249
                                       99999999999999**************************************9999999999999999999****** PP

                                       HHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  97 llelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleell 164
                                       +l+lg + v++g++++ ++ v + m+rgh+++e ++a ++lr++ +k+ +++++g pG ++e+  e +
  gi|336253819|ref|YP_004596926.1| 250 MLDLGGTKVEVGVQTTYER-VNREMHRGHGVQESMDANQRLRDSAFKVGFHMMPGQPGMSKEMCLEDF 316
                                       *******************.999999***********************************9877665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.17
                                       EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagik 143
                                       ++ +n+++p+ e +++++el+  ++   +  +d+ ++ ++ +rg+++    +a e++++ag +
  gi|336253819|ref|YP_004596926.1| 465 RFPSNPVRPELENAALIRELH--VYGSEVTMGDEGETDQHQHRGYGRRLMEKAEELAADAGYD 525
                                       455666666666666666644..4444444444444444444556666666666666666655 PP

>> 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 !   85.1   0.0   6.8e-28   2.4e-24       1      82 []     327     408 ..     327     408 .. 0.99

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 6.8e-28
                     Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlrelie 77 
                                       pd +K+yp+l++++T  ++++++ge++pl  +e+ +l+a+i+ ++p  +r++R+++dip + + ag+w++nlr+l++
  gi|336253819|ref|YP_004596926.1| 327 PDYLKIYPMLIVRDTATYDWWHRGEFEPLGNDEAAELIAEIKDMIPRYTRLQRVQRDIPADFIDAGVWKSNLRQLAR 403
                                       89*************************************************************************** PP

                     Radical_SAM_C  78 krlke 82 
                                       +r++e
  gi|336253819|ref|YP_004596926.1| 404 QRMEE 408
                                       ***85 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   1.8e-12   6.4e-09      33     117 .]     445     545 ..     414     545 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.8e-12
                                       CEEEEEEETTE..EEEEEEEEEEET....TSTTEEEEEEEEE............SGGGTTSSHHHHHHHHHHHHHHH CS
                    Acetyltransf_1  33 egllvaeedge..liGfisllkipd....ekggvayieslaV............speyrgkGlGsaLlealeerare 91 
                                       e+++++e+ ++  liGf++l+   +    e ++ a i++l+V              +++++G+G++L+e++ee a +
  gi|336253819|ref|YP_004596926.1| 445 EHFISVEDFDKdlLIGFCRLRFPSNpvrpELENAALIRELHVygsevtmgdegeTDQHQHRGYGRRLMEKAEELAAD 521
                                       3444433334447***************977899******************************************* PP

                                       TTESEE.EEEEETTEHHHHHHHH.HTTE CS
                    Acetyltransf_1  92 egikki.vlaveedndaairlYe.klGF 117
                                        g++k+ v+    +  +a+++Y+ klG+
  gi|336253819|ref|YP_004596926.1| 522 AGYDKVsVI----SGIGAREYYRnKLGY 545
                                       *****9455....9********735997 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2   8.3e-09     3e-05      61     111 ..     500     550 ..     499     555 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 8.3e-09
                   Acetyltransf_10  61 peyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYe.klGFkavge 111
                                       ++++++G+g++L+e++ee a ++g+  +++v +   a+++Y+ klG+++ g+
  gi|336253819|ref|YP_004596926.1| 500 DQHQHRGYGRRLMEKAEELAADAGYD-KVSVISGIGAREYYRnKLGYHQDGP 550
                                       589*****************999999.**************7589***9886 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   4.7e-05      0.17      35      74 ..     501     545 ..     478     547 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.7e-05
                                       GGTTSSHHHHHHHH.TT....SEEEEEEEEETHH...HHHHHH.HHTTE CS
                    Acetyltransf_7  35 eyrgkGiGraLlea.ae....kgiileqlelnae...kaikfY.eklGF 74 
                                       +++ +G+Gr+L+e  +e     g+   ++ +       a+++Y  klG+
  gi|336253819|ref|YP_004596926.1| 501 QHQHRGYGRRLMEKaEElaadAGYD--KVSV--IsgiGAREYYrNKLGY 545
                                       79**********9522234444432..1122..1233666677445665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.54u 0.20s 00:00:00.74 Elapsed: 00:00:00.35
# Mc/sec: 4747.85
//
Query:       gi|336253820|ref|YP_004596927.1|  [L=313]
Description: hypothetical protein Halxa_2429 [Halopiger xanaduensis SH-6]
Scores for 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-09   36.2   0.1    5.8e-09   35.7   0.1    1.3  1  Glyco_hydro_43  Glycosyl hydrolases family 43


Domain annotation for each model (and alignments):
>> Glyco_hydro_43  Glycosyl hydrolases family 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.1   3.2e-13   5.8e-09      33     193 ..      92     245 ..      49     280 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 3.2e-13
                                       SEEEEEEESSSSSCEEEEECEESTTTCSTTTEECTEEEEEE..EETTEEEEEEE..EEETTCCCSEEEEEEESSTTS CS
                    Glyco_hydro_43  33 pglrifhSkdLvnWkqvgrvlerrsqlsmkgknasWAPeis..khdgkyylyyt..atkkgeakqgifvvtadspeG 105
                                       + l +++S++Lv W++ + v     q+      + WAP+i     +g y + ++   ++++ ++++i+++  ds e 
  gi|336253820|ref|YP_004596927.1|  92 DALVLWESENLVDWSDQRMVELGDGQFG-----CLWAPDITydAENGDYVVHWSssHRSDEYEEKAIYYARTDSFE- 162
                                       6678899999999999885444444444.....55*****944479********7655666677779999999988. PP

                                       --EECEESSCS.TSSECEEEEEEETTSEEEEEEEEEHCCCSEEEEEEEEEETTTTEEEEEEE.EEEECGCCTCTTBB CS
                    Glyco_hydro_43 106 pwsdpiklkts.gssgiDpslfedddGkkYlvwgqwdkreghseiylaeldddtlklkgekt.klikagtelkglkv 180
                                       ++s+p  l+++ +s+ iD  ++e++ G+ Y++ ++ ++     +i+l++ d +t   +   +  ++++g    ++  
  gi|336253820|ref|YP_004596927.1| 163 TFSEPELLYRKdDSGVIDSAMYEEN-GSYYCFLKSDEN---PTGIILVKSDRPTGPFTRVSAfDRTMEG---LEGAR 232
                                       8********99**************.*******99444...6999999999998876654420333444...58889 PP

                                       EEEEEEEEETTEE CS
                    Glyco_hydro_43 181 tEGPhlykrdgyy 193
                                       +E+P  ++ ++  
  gi|336253820|ref|YP_004596927.1| 233 YEAPTAVRLEDGR 245
                                       9999988876543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2665.67
//
Query:       gi|336253821|ref|YP_004596928.1|  [L=48]
Description: hypothetical protein Halxa_2430 [Halopiger xanaduensis SH-6]
Scores for 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  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 381.25
//
Query:       gi|336253822|ref|YP_004596929.1|  [L=261]
Description: 4-hydroxy-2-oxovalerate aldolase [Halopiger xanaduensis SH-6]
Scores for 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-45  153.2   0.7    6.7e-45  152.9   0.7    1.0  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.9   0.7   3.7e-49   6.7e-45       3     216 ..      15     240 ..      13     244 .. 0.96

  Alignments for each domain:
  == domain 1  score: 152.9 bits;  conditional E-value: 3.7e-49
                                       EEEEESTSHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHHGG CS
                         HpcH_HpaI   3 glflpganaalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqdle 79 
                                       g +++++++a+ae+ a   +D+v+iD E+++   +  +  ++ + a++  da +++   ++VR++++d++ ik+   
  gi|336253822|ref|YP_004596929.1|  15 GTWVALSDPAIAEISAQLAFDAVMIDAEHST---NSIETVTEMARAVDAADADTDTDPGAIVRLSENDPTEIKR--- 85 
                                       78*****************************...5556667888899999999999999***************... PP

                                       HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---...................HCCC-EEEEEE-SHHHHHTHHH CS
                         HpcH_HpaI  80 vldlgaqvvlvPkvetaeealevvsalrepekgirg...................anketrllaqiEsaegvknaee 137
                                       +ld+g+++v+ P+++++e+a+++v+a+r+p++g+rg                   an+et  laqiE++ g +n+ee
  gi|336253822|ref|YP_004596929.1|  86 TLDAGVDGVMAPMIDSPEDARALVEATRYPPEGVRGvgygrgteygeafpehlerANDETLALAQIETESGFENVEE 162
                                       ***************************************************************************** PP

                                       HHTSTTEEEEEE-HHHHHHHTT-TTSTTSHHHHHHHHHHHHTTHCEEEEEEE.E-SSHHHHHHHHHTTHCEEEEEEH CS
                         HpcH_HpaI 138 IaavegldgvflGaeDlsadlgtkrspegtevldareriltaaraagiaaldtvasdiddaegflaegalfvalGfd 214
                                       Iaav+gldg+f+G++Dlsa+l + ++ +g+e l+a +r+l a+ a +   + t+a+++d+ e+ +++g  fv  G+d
  gi|336253822|ref|YP_004596929.1| 163 IAAVDGLDGLFVGPADLSAALDLFGETDGDEFLEAVDRVLEAGHAVDK-PVATLAFEEDEIERWVDRGFDFVLAGVD 238
                                       *********************************************998.99*************************9 PP

                                       HH CS
                         HpcH_HpaI 215 gk 216
                                         
  gi|336253822|ref|YP_004596929.1| 239 ID 240
                                       76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1874.49
//
Query:       gi|336253823|ref|YP_004596930.1|  [L=221]
Description: hypothetical protein Halxa_2432 [Halopiger xanaduensis SH-6]
Scores for 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-28   97.8   0.2    7.7e-28   97.5   0.2    1.1  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 !   97.5   0.2   4.3e-32   7.7e-28       2     152 ..      32     186 ..      31     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 4.3e-32
                           LUD_dom   2 eefienleangaevyyaktaeealelilellkeksvvseggstdlgeiglapalhs..greevldlfeekltreare 76 
                                       e ++ n+e++++ev+++++++ a+e + + ++++  v+ g st+l+eig+ ++l +  g   v + +e+  ++++r 
  gi|336253823|ref|YP_004596930.1|  32 ETVVSNVEERNIEVHVFDDGDAAREHLTDQIPDGAEVMDGHSTTLEEIGFTDVLAEadGFDYVGNALEQIDDEDERS 108
                                       77899*********************************************666654114455666666666999*** PP

                           LUD_dom  77 elrekfltadvgitganfaiAetGtlvlvdnegnr.raltflpkvhivvvginkivpdledavkrlkt..aprnatr 150
                                         r+++ tadv++ gan aiAe+G++      gn+  a  f+ ++ ++v+g+nki  d e av+r+++  +p +  r
  gi|336253823|ref|YP_004596930.1| 109 TRRREATTADVFFDGAN-AIAESGEILGANALGNAvGAWPFGAESLVLVAGTNKIESDWETAVERIREyaLPLEDAR 184
                                       *****************.**************************************************988887777 PP

                           LUD_dom 151 lq 152
                                       +q
  gi|336253823|ref|YP_004596930.1| 185 AQ 186
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:01.03
# Mc/sec: 650.06
//
Query:       gi|336253824|ref|YP_004596931.1|  [L=276]
Description: zinc/iron permease [Halopiger xanaduensis SH-6]
Scores for complete 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   61.0   3.0    1.1e-16   61.0   3.0    2.1  2  Zip       ZIP Zinc transporter


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 !    5.1   3.3   0.00063        11      13      88 ..      16      80 ..       4      88 .. 0.71
   2 !   61.0   3.0   6.3e-21   1.1e-16     185     332 ..     131     270 ..      96     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.00063
                               Zip 13 ilsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealealeesqleeehthplagllvllGfll 88
                                      +++ +g l++ll ++i    s++++   l +a+G+++g a + L+ ++le l+++   e    ++agl++ +Gfll
  gi|336253824|ref|YP_004596931.1| 16 CTTGIGALPLLLTDRI----SHRVYDGSLGLASGIMVGAAVFALVLPGLE-LGSPF--E----VVAGLVAGGGFLL 80
                                      4555666666666654....677999999999*****9999999988888.44442..2....7778877777776 PP

  == domain 2  score: 61.0 bits;  conditional E-value: 6.3e-21
                               Zip 185 raiilllglilHsfidGLAlG...vssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnllfa.ltap 257
                                       ra ++  ++ +H++++GLA+G   +s   + g+++  A+ + ++p ++++ ++ ++ag+s +  +l+ +l++ +  p
  gi|336253824|ref|YP_004596931.1| 131 RAALVGAAITIHNVPEGLAVGiafASGEAALGLAIATAIAVQNVPDGFAMAVPSVRAGISGPRTLLYTTLSGgVPEP 207
                                       5888899***************9667778899*********************************99999972669* PP

                               Zip 258 lGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGfalmlll 332
                                       +++++G++          +++ ++  +++aG ++ v + el+p    +++   ++++   + +++++Gfalml++
  gi|336253824|ref|YP_004596931.1| 208 IAAAVGFA-----LVAFVSNLFPVAAGFAAGAMIAVVFRELVP----SSH---GHGHADIATAAFVVGFALMLIV 270
                                       ********.....8999999***********************....333...456788999**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); 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):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1952.11
//
Query:       gi|336253825|ref|YP_004596932.1|  [L=132]
Description: hypothetical protein Halxa_2434 [Halopiger xanaduensis SH-6]
Scores for 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:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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 0.20s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1075.56
//
Query:       gi|336253826|ref|YP_004596933.1|  [L=217]
Description: hypothetical protein Halxa_2435 [Halopiger xanaduensis SH-6]
Scores for 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  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1610.65
//
Query:       gi|336253827|ref|YP_004596934.1|  [L=718]
Description: Fibronectin-binding A domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-82  276.1   0.0    6.6e-82  275.7   0.0    1.1  1  FbpA       Fibronectin-binding protein A N-terminus (FbpA)
    1.5e-22   80.3   0.0    2.9e-22   79.4   0.0    1.5  1  NFACT-R_1  NFACT protein RNA binding domain
    0.00028   21.0   0.0     0.0018   18.5   0.0    2.4  2  NFACT-R_2  NFACT protein RNA binding domain
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.061   13.2   0.3    2.1  2  DUF2786    Protein of unknown function (DUF2786)
      0.093   12.4   0.7          3    7.5   0.0    2.9  3  LEDGF      Lens epithelium-derived growth factor (LEDGF)
       0.16   12.1   0.1       0.67   10.1   0.0    2.1  2  DUF5590    Domain of unknown function (DUF5590)


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 !  275.7   0.0   2.2e-85   6.6e-82       2     425 ..       9     474 ..       8     492 .. 0.92

  Alignments for each domain:
  == domain 1  score: 275.7 bits;  conditional E-value: 2.2e-85
                                       HHHHHHHHHHHHHHHTTXEEEEEEEEETTEEEEEEE.ETTEEEEEEEEXXTTTXEEEEX..XXXXXXXSSXXHHHHH CS
                              FbpA   2 glvlaavvaELqkellggridkiyqpekdelvltlr.anrgrhkLllsahpsyarihlt..ekpkenpkeppnFcml 75 
                                       +++laa+v+EL + ++g+++dk y++++d ++l++r ++rgr  L  ++  +++r h+   e+  + p +pp+F+m+
  gi|336253827|ref|YP_004596934.1|   9 SVDLAALVEELGA-YEGAKVDKAYLYGDDLVRLKMRdFDRGRTELIFEV-GEVKRAHTVapERVPDAPGRPPQFAMM 83 
                                       799**********.***********************************.********954447899********** PP

                                       HHHHHTTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXB CS
                              FbpA  76 LRkyLkgarivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvRei 152
                                       LR++L+ga    +eq +fdRi+e+++e+      + + ++ivE++g+ +N+ ++d e ++id+++ v+ k    R++
  gi|336253827|ref|YP_004596934.1|  84 LRNRLSGADFAGVEQYEFDRILEFTFERD-----DGTTRIIVELFGQ-GNVAVTDGEYEVIDCLETVRLK---SRTV 151
                                       *****************************.....999**********.**********************...8*** PP

                                       STTXBXXXSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH............. CS
                              FbpA 153 lpgekYelPpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedle 229
                                       +pg+ Ye+P++  + nPl++++ ++f   ++++++d+v++L++++ ++++l+aeel++rag++k+  ++e++e+ ++
  gi|336253827|ref|YP_004596934.1| 152 VPGSRYEFPDT--RTNPLTVSR-DAFYREMDDSDTDVVRTLATQL-NFGGLYAEELCTRAGVEKAMDIAEADEDVYD 224
                                       ***********..*********.9999999999************.******************************* PP

                                       ..HHHHHHHHTXXX....XXEE..........X........SSSEESSX....XTTXX.SSXXXXSXHHHHHHHHTT CS
                              FbpA 230 rlyealqelleeleeekfepqlvlkee.....k........peefsvvp....lkslselekesfdslsealdeyYa 289
                                       r+yea+++l  ++++++f p+l+l+ e     +        +  ++v+p    +++ ++l  e +ds+ +ald+y+ 
  gi|336253827|ref|YP_004596934.1| 225 RIYEAIERLALDIRNGNFDPRLYLEREddddgNgddeddvqERVIDVTPfpleEHEAEGLVGEAYDSFLTALDDYFF 301
                                       ************************99866655155555554555555556675555558888*************** PP

                                       TXXX--SHH....HHHHHHHHH...HHHHHHHHHHHHHHHHHHHHCCGGH.....HHHHCCHH-------------- CS
                              FbpA 290 kkaerdrve....qkrsdlekr...veneleklekklkklekelekaeka.....enyrligelltaylyaikkgms 354
                                       + + +d+ e    ++r d+e++    e+++e+++  ++ +e+e+e+ +++     ++y l++++l+++++a++++  
  gi|336253827|ref|YP_004596934.1| 302 RLELEDEEEpdptEQRPDFEEEiakHERIIEQQQGAIEGFEQEAEQLREKaellyARYGLVDDILSTIRNAREQDRP 378
                                       99888887743336999***99888899*********************99************************** PP

                                       ---------..--........................---------------HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FbpA 355 evelenyyde.ge........................evtIpLdprkspsenAqkyfkkykKlkraveaveeqieet 406
                                       ++e+e+ ++e +e                        + +I L+ r+ + +nA+++++++k++++++e++  +ie t
  gi|336253827|ref|YP_004596934.1| 379 WDEIEERFEEgKErgieaaeavvgidgsegivtvdidGERIDLEARQGVEQNADRLYTEAKRVEEKKEGALAAIEDT 455
                                       **********6559********************99999************************************** PP

                                       HHHHHHHHHHHHHHHT-.- CS
                              FbpA 407 keeleylesveaaleqaes 425
                                       +e le  +   +++e ++ 
  gi|336253827|ref|YP_004596934.1| 456 REDLEEAKRRREQWEAEDA 474
                                       **************94443 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 !   79.4   0.0   9.6e-26   2.9e-22       2     109 .]     508     625 ..     507     625 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 9.6e-26
                         NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylr...lsege....le.eipeelleeaaql 70 
                                       ++wF++sd+ylvi+G+++ +nee++kkyle +d ++h   ++++ ++l+   +   +     + e+p++++eeaaq+
  gi|336253827|ref|YP_004596934.1| 508 FRWFHTSDDYLVIGGRNADQNEEIVKKYLEPGDKVLHTQAHGGPVTVLKatdP---SeassSDiELPDSSIEEAAQF 581
                                       99***********************************************6542...23344458************* PP

                         NFACT-R_1  71 akanSia.gnklssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                       a+++S+  +    + dv+ v  ++++kt++    l++G + ++g
  gi|336253827|ref|YP_004596934.1| 582 AVSYSSVwKDGRYAGDVYAVDSDQVTKTPEsgeyLEKGGFAIRG 625
                                       ********99999*****************9********99986 PP

>> NFACT-R_2  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     6e-07    0.0018       2      58 ..     509     570 ..     509     608 .. 0.72
   2 ?   -2.0   0.0       1.3     4e+03      64     104 .]     670     708 ..     648     708 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6e-07
                         NFACT-R_2   2 RhfrlsekaklIvgReeeEnkfl.kgll.kkdfvslrakshkGplvlid....gelseedlel 58 
                                       R f +s+++ +I gR+++ n+++ k++l  +d v l+++ h Gp+++++     e+s +d+el
  gi|336253827|ref|YP_004596934.1| 509 RWFHTSDDYLVIGGRNADQNEEIvKKYLePGDKV-LHTQAHGGPVTVLKatdpSEASSSDIEL 570
                                       789999************9998747788999999.*************644442333444333 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                         NFACT-R_2  64 arYskgkeeeevevkvkkkegeeekeievkplseeeiekwr 104
                                       +rY++++ ++++  +++++ + e  ++  k +s ++i++++
  gi|336253827|ref|YP_004596934.1| 670 GRYAQADAAKRMYRRFRERFEDE--SFVRKIASPDRIQHFM 708
                                       68999888888777776655555..4667777777777775 PP

>> DUF2786  Protein of unknown function (DUF2786)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.3   6.9e+03      29      39 ..     200     210 ..     200     210 .. 0.88
   2 ?   13.2   0.3   2.1e-05     0.061      17      38 ..     340     361 ..     334     362 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                           DUF2786  29 AqeLmarynld 39 
                                       A+eL++r +++
  gi|336253827|ref|YP_004596934.1| 200 AEELCTRAGVE 210
                                       89*****9985 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.1e-05
                           DUF2786  17 tneaEAeaAlakAqeLmarynl 38 
                                        +e+EAe + +kA+ L ary+l
  gi|336253827|ref|YP_004596934.1| 340 GFEQEAEQLREKAELLYARYGL 361
                                       69******************98 PP

>> LEDGF  Lens epithelium-derived growth factor (LEDGF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.001         3      73      95 ..     339     361 ..     323     392 .. 0.73
   2 ?    2.2   0.0     0.043   1.3e+02      80     118 ..     425     463 ..     364     465 .. 0.87
   3 ?   -2.5   0.0       1.3   3.8e+03      85      98 ..     677     690 ..     675     699 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.001
                             LEDGF  73 vefkekakeirkkAeeiYnkfks 95 
                                         f+++a++ r+kAe +Y ++ +
  gi|336253827|ref|YP_004596934.1| 339 EGFEQEAEQLREKAELLYARYGL 361
                                       569***************99754 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.043
                             LEDGF  80 keirkkAeeiYnkfkslflvpegesnfwekfeeevekfk 118
                                       + + + A+ +Y   k +  ++eg +++ e+ +e +e+ k
  gi|336253827|ref|YP_004596934.1| 425 QGVEQNADRLYTEAKRVEEKKEGALAAIEDTREDLEEAK 463
                                       66899************************9999999877 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.3
                             LEDGF  85 kAeeiYnkfkslfl 98 
                                        A+ +Y +f++ f 
  gi|336253827|ref|YP_004596934.1| 677 AAKRMYRRFRERFE 690
                                       6999******9997 PP

>> DUF5590  Domain of unknown function (DUF5590)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.9   5.7e+03      13      21 ..      25      33 ..      25      35 .. 0.90
   2 ?   10.1   0.0   0.00022      0.67      16      40 ..     506     530 ..     505     532 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.9
                                      EEEEEEEEE CS
                           DUF5590 13 tkvddfylY 21
                                      +kvd++ylY
  gi|336253827|ref|YP_004596934.1| 25 AKVDKAYLY 33
                                      58*****99 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00022
                                       EEEEEEESSSEEEEEEEEETT--EE CS
                           DUF5590  16 ddfylYngketYyvVtGknkkgekv 40 
                                       d+f +++  + Y v+ G n ++++ 
  gi|336253827|ref|YP_004596934.1| 506 DRFRWFHTSDDYLVIGGRNADQNEE 530
                                       89*****************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (718 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); 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):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.42
# Mc/sec: 5074.82
//
Query:       gi|336253828|ref|YP_004596935.1|  [L=87]
Description: hypothetical protein Halxa_2437 [Halopiger xanaduensis SH-6]
Scores for 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  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); 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: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 686.17
//
Query:       gi|336253829|ref|YP_004596936.1|  [L=426]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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-40  136.8  76.2    6.9e-31  107.5  45.5    2.1  2  MFS_1       Major Facilitator Superfamily
    2.4e-05   23.4  22.5    5.1e-05   22.3  12.2    2.2  2  MFS_1_like  MFS_1 like family


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 !  107.5  45.5   7.7e-35   6.9e-31       4     292 ..      49     322 ..      45     325 .. 0.83
   2 !   43.2  22.7   2.6e-15   2.4e-11      33     172 ..     274     415 ..     272     424 .. 0.83

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 7.7e-35
                             MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalgllll 79 
                                         fl+ ++r +++p++  ++ ++ g++p+++gl++t++ +g+a++ lp+G+l +r++r r +l +gl+l++ + +l 
  gi|336253829|ref|YP_004596936.1|  49 FSFLVNTGRIAFAPLVDFFI-QS-GVAPATAGLAATAVWVGSALSRLPTGYLLTRISRHRaLLGMGLFLSVTS-ALT 122
                                       56777778888888888555.44.799*********************************7777777777777.555 PP

                             MFS_1  80 lfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyi 156
                                       ++++++w+ +++ +l Gl++g++f a++ l++++fp+ + g+a+g+ +++++++a+ +p+l ++ +  ++Wr+vf +
  gi|336253829|ref|YP_004596936.1| 123 ALSPGIWFTIAGALLVGLATGIFFIAANPLVSELFPE-RVGLAVGVRGMFSQIAAVTAPILVSVAIVRGSWRLVFGA 198
                                       557*********************************9.*************************************** PP

                             MFS_1 157 laivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw..illialllfffgfsglltllp 231
                                       la++++l+ v fl+ +++ + +++   +++             + a++++  l    ++++ +++ f+++g++ +  
  gi|336253829|ref|YP_004596936.1| 199 LAVLAFLLTVAFLFAVRRAEMPNAGADDRDF------------LAAIRAQWRLIavGIVFVGFTG-FVWQGVFNFYV 262
                                       ********99644444444444444433333............3344444433233344444444.4********** PP

                             MFS_1 232 lylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalgla 292
                                       +yl    g++   ++++ll +l+++g++++++agrl+dr++  + ll +l++++++++++ 
  gi|336253829|ref|YP_004596936.1| 263 TYLGAAKGIP-SETGTTLLTVLFAAGVPSFVIAGRLADRFSYLPVLLATLVGFVACLAAVT 322
                                       **********.7999999***********************99999999999999998875 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 2.6e-15
                             MFS_1  33 eigl.lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlgagalfpaga 107
                                       e g+ llt+ +++ + + +++Grl+drf+  +vll++l++f+++ l+++ ++ +l +++++ v +Gl   +lfp++ 
  gi|336253829|ref|YP_004596936.1| 274 ETGTtLLTVLFAAGVPSFVIAGRLADRFSYLPVLLATLVGFVAC-LAAVtVVEGLVAIAAVTVAMGLIIHCLFPVAD 349
                                       555548888888999999999***********************.44442459999********************* PP

                             MFS_1 108 aliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfyilaivsllafvlfllll 172
                                       a++ d  p+e+r++a++ +sa++ l  + g ++ g++a + lg++avf    ++ +  +v +++l 
  gi|336253829|ref|YP_004596936.1| 350 AYLLDSLPDENRASAYAGFSATMMLIQATGSVAVGAFAqAGLGYTAVFRGYVFFVAAIAVAMAVLA 415
                                       **************************************8888888885555554444444433443 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 !    6.3   3.2   0.00041       3.7     256     346 ..      71     161 ..      42     177 .. 0.73
   2 !   22.3  12.2   5.7e-09   5.1e-05     179     373 ..     195     386 ..     166     398 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00041
                        MFS_1_like 256 gasntllGsl.valgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllw 331
                                       g    ++G + +a+ v + +  + ++  l+++  h+ ll ++l++  ++  l a+    w+++   +L g+++g+++
  gi|336253829|ref|YP_004596936.1|  71 GVAPATAGLAaTAVWVGSALSRLPTGYLLTRISRHRALLGMGLFLS-VTSALTALSPGIWFTIAGALLVGLATGIFF 146
                                       5444555543133444444555556666788888999999999875.55678888899******************* PP

                        MFS_1_like 332 aaaveyvskiapksl 346
                                        aa   vs+++p+++
  gi|336253829|ref|YP_004596936.1| 147 IAANPLVSELFPERV 161
                                       ************986 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 5.7e-09
                        MFS_1_like 179 ysallyvlaallvisllvvlilnetekesklkvtkslqvllnilk.npeviif.llvalilgmswgiienFlflYL. 252
                                       +  +l+vla ll++++l++  +   e  ++    + ++++l+ ++ + ++i++ ++++ + g++w  + nF+  YL 
  gi|336253829|ref|YP_004596936.1| 195 VFGALAVLAFLLTVAFLFA--VRRAEMPNAG---ADDRDFLAAIRaQWRLIAVgIVFVGFTGFVWQGVFNFYVTYLg 266
                                       3456666666666666663..3333333332...233556655551555555535667799***************9 PP

                        MFS_1_like 253 kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgl 329
                                         +g ++++  +l+++  +a +p f++a +l ++++   +l+++l+ +++ +  + ++e ++ +  + v  g+ ++ 
  gi|336253829|ref|YP_004596936.1| 267 AAKGIPSETGTTLLTVLFAAGVPSFVIAGRLADRFSYLPVLLATLVGFVACLAAVTVVEGLVAIAAVTVAMGLIIHC 343
                                       9**************************************************************************** PP

                        MFS_1_like 330 lwaaaveyvskiapksleatgqgllsglyfglGralGsliGGll 373
                                       l+ +a  y  +  p++ +a   + +s++ + l +a Gs++ G++
  gi|336253829|ref|YP_004596936.1| 344 LFPVADAYLLDSLPDENRASAYAGFSAT-MMLIQATGSVAVGAF 386
                                       ******************9999988877.456678888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 3233.32
//
Query:       gi|336253830|ref|YP_004596937.1|  [L=184]
Description: hypothetical protein Halxa_2439 [Halopiger xanaduensis SH-6]
Scores for 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   13.9   6.7       0.87    9.5   0.7    2.1  2  Colicin   Colicin pore forming domain


Domain annotation for each model (and alignments):
>> Colicin  Colicin pore forming domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.7   0.00015       2.6     138     171 ..      23      56 ..      14      68 .. 0.89
   2 ?    9.5   0.7   4.9e-05      0.87     112     163 ..      85     141 ..      73     153 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00015
                           Colicin 138 iaasflssiafalavgtplgilgfalliavvaal 171
                                       +a++f+ +i   l+vg+ lg ++f+ l+ v+a l
  gi|336253830|ref|YP_004596937.1|  23 MAIAFVNAILAGLVVGGELGRISFVALLNVTAGL 56 
                                       89**************************999987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 4.9e-05
                           Colicin 112 leefkiavetGnWkPlfvkveaiaa.g..iaasflssiafalavg..tplgilgfal 163
                                        +ef  ++ tG +  l+v + a++a +   +a +ls+  f +av   +++++++ ++
  gi|336253830|ref|YP_004596937.1|  85 DDEFSQGLATGRFGRLLVLIAAVTAvSllTSAQVLSGTVFQIAVVgvGSIAVVTAII 141
                                       469999********9999988865413115677788888888876455555554432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.19s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 1610.89
//
Query:       gi|336253831|ref|YP_004596938.1|  [L=355]
Description: Pelota-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-24   86.1   0.1    3.2e-24   85.4   0.1    1.3  1  eRF1_1    eRF1 domain 1
    1.3e-23   83.6   0.5    3.6e-23   82.2   0.0    2.0  3  eRF1_3    eRF1 domain 3
      1e-08   35.6   0.2    3.2e-07   30.7   0.2    2.3  1  eRF1_2    eRF1 domain 2


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 !   85.4   0.1   5.3e-28   3.2e-24       2     128 ..       2     128 ..       1     131 [. 0.90

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 5.3e-28
                                       EEEEECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH........--CEEEEEEEEEEEEEEECTT CS
                            eRF1_1   2 kllkrdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqr.esstgsreservklkLtikvekvdfdkd 77 
                                       ++  r+  + g++ vt++pe+ +dlwhl  +++pgd+v+  t+r++qr + +   +  er ++   i v +++f+k 
  gi|336253831|ref|YP_004596938.1|   2 QIKDREQIEGGRERVTVVPESVDDLWHLQYVLEPGDRVAGDTTRRIQRnDDQMRDTGGEREHMWVAIAVDDIEFHKF 78 
                                       555564445899************************************4466667779******************* PP

                                       SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                            eRF1_1  78 agvlrisGkvieenehvklgafhtldlelkrpftiikeewdsfalerLkea 128
                                       a++lr+ G+++  +++ +lg +htl++e  ++++i+k +++  +  rL+ea
  gi|336253831|ref|YP_004596938.1|  79 ANRLRVGGEIVACSREDQLGFHHTLNVEERDELSIEK-RFKPDQEARLEEA 128
                                       *************************************.7888888888876 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.4   8.3e+03      70      89 ..     134     153 ..     105     166 .. 0.59
   2 ?   -3.0   0.1       1.7     1e+04      21      39 ..     227     245 ..     217     247 .. 0.74
   3 !   82.2   0.0   6.1e-27   3.6e-23       3     113 .]     255     354 ..     253     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHTT-EEEEE- CS
                            eRF1_3  70 lieelvenveesgakveiis 89 
                                         +  + +vee +a+v+ + 
  gi|336253831|ref|YP_004596938.1| 134 NPDVAIATVEEGQAHVHTVA 153
                                       44445555666666666554 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                                       SEEESHHHHHHHHHTT-EE CS
                            eRF1_3  21 kavYGveevlkalemgAve 39 
                                       +a+ G + v ++l+ gAv 
  gi|336253831|ref|YP_004596938.1| 227 TAAVGDRGVHEVLKRGAVA 245
                                       6677888899999999986 PP

  == domain 3  score: 82.2 bits;  conditional E-value: 6.1e-27
                                       HHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHH CS
                            eRF1_3   3 qekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenve 79 
                                       +e+++++e++e++a++  ka+YG eev+ka+ +gA+++LL++++  r++   + +   +g     ++ +++lv++ e
  gi|336253831|ref|YP_004596938.1| 255 SEAEYIDELTERMAQG-AKAAYGPEEVRKAADYGAIDRLLILDDRLRKE---RGP---EG--EWNID-VDQLVRTTE 321
                                       6899**********99.9****************************996...333...12..22344.9******** PP

                                       HTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  80 esgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                       + g++v+++sse++ G+ql +++gGiaa+LRy++
  gi|336253831|ref|YP_004596938.1| 322 QKGGEVTVFSSEFPPGQQL-SNLGGIAALLRYRL 354
                                       *******************.************85 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.2   5.4e-11   3.2e-07       2     129 ..     137     246 ..     136     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 5.4e-11
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTES CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklk 78 
                                       v++  ++eg+A++ ++ ++ te +++i+++     ++G+ +         + ++e + ++++ ++++       + +
  gi|336253831|ref|YP_004596938.1| 137 VAIATVEEGQAHVHTVAQYGTEERATITGTT----GKGEYA---------RGRDELFSELGDVLKRQ-------DAD 193
                                       6788899999999999999999999998764....333322.........35678888888887777.......889 PP

                                       EEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC..CHH CS
                            eRF1_2  79 giilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlek..aae 129
                                       +iilagpgf+k++ l+++  ++ + +++i++vd++  g+ g++evl+   +a+
  gi|336253831|ref|YP_004596938.1| 194 AIILAGPGFTKQDALKYIENNEPEVAEKITMVDTAAVGDRGVHEVLKRgaVAD 246
                                       **********************************************9975555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); 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:                         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 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2644.30
//
Query:       gi|336253832|ref|YP_004596939.1|  [L=103]
Description: hypothetical protein Halxa_2441 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.38   10.4   1.0       0.56    9.9   1.0    1.3  1  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.0   3.1e-05      0.56       8      66 ..       4      68 ..       1      71 [. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 3.1e-05
                                      XXXXXXXXXXXXXXXX..XXXXX.....XXX.....................XXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxx..xxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  8 fnllfwligivllavG..vwlrl.....khaeaalacllsesaedpailaillivvGvllfllgfl 66
                                      + l++wl+++++++vG  v + +     +  e+ +  + +   e+p++l+ +l+ vGvll++ g++
  gi|336253832|ref|YP_004596939.1|  4 LVLVLWLLAVLFYGVGdlVTT-VvgtrtDGLEEGQPLTRAIFGEQPSALQFGLFKVGVLLAFYGVF 68
                                      5689************85444.35999744455555566678999*************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 766.72
//
Query:       gi|336253833|ref|YP_004596940.1|  [L=253]
Description: transcriptional regulator TrmB [Halopiger xanaduensis SH-6]
Scores for complete 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-19   69.3   0.0    3.4e-19   68.5   0.0    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00052   19.8   0.0    0.00091   19.0   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
    0.00059   19.9   0.0     0.0011   19.0   0.0    1.4  1  DUF2250          Uncharacterized protein conserved in archaea
    0.00087   19.1   0.0     0.0021   17.9   0.0    1.6  1  MarR_2           MarR family
  ------ inclusion threshold ------
      0.013   15.8   0.1      0.038   14.3   0.0    1.8  2  Penicillinase_R  Penicillinase repressor
      0.019   15.5   0.0       0.09   13.3   0.0    2.2  2  HTH_27           Winged helix DNA-binding domain
      0.036   14.0   0.0       0.18   11.8   0.0    2.1  2  Cdc6_C           CDC6, C terminal winged helix domain
      0.053   13.6   0.0       0.16   12.1   0.0    1.8  1  HTH_20           Helix-turn-helix domain
      0.058   13.3   0.1       0.17   11.8   0.0    1.8  2  MarR             MarR family


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 !   68.5   0.0   1.7e-22   3.4e-19       3      67 ..      14      78 ..      12      79 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 1.7e-22
                                      HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                              TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                       lGL++yEakv++aL +lg  ta+++a +++vprs+vY+v  sLed+Gl e+++++p +Yr+v++
  gi|336253833|ref|YP_004596940.1| 14 GLGLTSYEAKVFIALHRLGAGTARDVADITDVPRSQVYSVADSLEDRGLLEVQQSNPIRYRPVSV 78
                                      69************************************************************986 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 !   19.0   0.0   4.6e-07   0.00091      12      49 ..      28      64 ..      22      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.6e-07
                                      -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      l + + + t +++A+ t++p+S v+    +L+ +G++e
  gi|336253833|ref|YP_004596940.1| 28 LHRLGAG-TARDVADITDVPRSQVYSVADSLEDRGLLE 64
                                      5555555.99***************************8 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 !   19.0   0.0   5.5e-07    0.0011      10      64 ..      21      75 ..      13      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.5e-07
                           DUF2250 10 alkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegktikrte 64
                                      + kv   l+++++  a+ +a+ +++p+++v ++ ++Le+ GLle ++++ i+++ 
  gi|336253833|ref|YP_004596940.1| 21 EAKVFIALHRLGAGTARDVADITDVPRSQVYSVADSLEDRGLLEVQQSNPIRYRP 75
                                      56788889999999*********************************99999876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.1e-06    0.0021       1      55 [.      15      67 ..      15      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                                      TT--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  1 lgltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      lglt  +a v  aL+r + +  t++++a+ +++++s v  + + L+++GL+e + 
  gi|336253833|ref|YP_004596940.1| 15 LGLTSYEAKVFIALHRLGAG--TARDVADITDVPRSQVYSVADSLEDRGLLEVQQ 67
                                      589999999999**999974..*****************************9885 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.9e-05     0.038       1      84 [.      17      97 ..      17     117 .. 0.80
   2 ?   -2.9   0.0       4.1   8.3e+03      11      30 ..     226     245 ..     225     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                      ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE---..-XXXXXXXXXX CS
                   Penicillinase_R  1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplv..seeeavasavk 77
                                      l++ Ea+v  +l+++g  t+++v +  + +    +s V ++   L+++gll+ ++  + ++Y+p+   + +e+++++ +
  gi|336253833|ref|YP_004596940.1| 17 LTSYEAKVFIALHRLGAGTARDVADITDVP----RSQVYSVADSLEDRGLLEVQQ-SNPIRYRPVSvdEARELLREQFE 90
                                      6889********************998887....999***************998.78889**9752133456666666 PP

                                      XXXXXXX CS
                   Penicillinase_R 78 qlldklf 84
                                         d+ f
  gi|336253833|ref|YP_004596940.1| 91 REQDRAF 97
                                      6666655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.1
                                       HHHHHS-EEHHHHHHT--GG CS
                   Penicillinase_R  11 ilwekgeatvkevveeleee 30 
                                       ++w++++++++ +++ +e++
  gi|336253833|ref|YP_004596940.1| 226 AIWSSESLFASVLIQLIEAN 245
                                       68999999988888877765 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   0.0   4.5e-05      0.09      13      54 ..      27      69 ..      22      78 .. 0.85
   2 ?   -3.6   0.0       8.7   1.7e+04      51      62 ..     197     205 ..     193     208 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                            HTH_27 13 r.hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                                      + hr++  +++d+++ ++v  s++ ++ + L+ +GL+e +++ 
  gi|336253833|ref|YP_004596940.1| 27 AlHRLGAGTARDVADITDVPRSQVYSVADSLEDRGLLEVQQSN 69
                                      348999*******************************877763 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.7
                            HTH_27  51 tgdeadrrekrv 62 
                                       t    d+r+ r+
  gi|336253833|ref|YP_004596940.1| 197 TD---DQRSGRI 205
                                       33...4555554 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 ?   11.8   0.0     9e-05      0.18      33      73 ..      41      77 ..      36      87 .. 0.79
   2 ?   -1.4   0.0       1.2   2.4e+03      40      52 ..     127     139 ..     122     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9e-05
                                      T-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEE CS
                            Cdc6_C 33 gvdpltqrevsdllseLemlgileleksskGrregrtrkis 73
                                      +++ + +++v+++ + Le++g+le+++s+      r+r +s
  gi|336253833|ref|YP_004596940.1| 41 DITDVPRSQVYSVADSLEDRGLLEVQQSNP----IRYRPVS 77
                                      6777889********************943....4555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHT CS
                            Cdc6_C  40 revsdllseLeml 52 
                                        +v+dl+s+ e++
  gi|336253833|ref|YP_004596940.1| 127 DRVVDLCSQAEKR 139
                                       5899999998876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.9e-05      0.16      14      57 ..      23      66 ..      19      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.9e-05
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +++ aL+r ++ ta ++a+  d+++++++   + Le+ gL+ev+
  gi|336253833|ref|YP_004596940.1| 23 KVFIALHRLGAGTARDVADITDVPRSQVYSVADSLEDRGLLEVQ 66
                                      56778999999*******************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.8e-05      0.17       3      52 ..      19      68 ..      17      69 .. 0.88
   2 ?   -2.4   0.1       2.4   4.7e+03      46      58 ..     193     205 ..     193     206 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.8e-05
                                      HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR  3 ltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                        + ++   l++ g+ +  + a+   v +s v  v+d Le++Gl+e ++s
  gi|336253833|ref|YP_004596940.1| 19 SYEAKVFIALHRLGAGTARDVADITDVPRSQVYSVADSLEDRGLLEVQQS 68
                                      55666777799999999999***************************998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                                       SEEEEEETTSTTS CS
                              MarR  46 lieRskspeDrRe 58 
                                       +++R+ + +  R+
  gi|336253833|ref|YP_004596940.1| 193 FMRRTDDQRSGRI 205
                                       5667766666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1892.02
//
Query:       gi|336253834|ref|YP_004596941.1|  [L=1045]
Description: Patched family protein [Halopiger xanaduensis SH-6]
Scores for 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  100.6  44.7    2.1e-17   63.1  18.8    3.7  2  MMPL            MMPL family
    1.8e-05   24.6  14.9     0.0039   17.0   2.8    2.3  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
    5.4e-05   21.5  32.6    0.00083   17.6   8.8    3.2  3  Patched         Patched family
    0.00082   18.8   8.6    0.00082   18.8   8.6    2.5  2  SecD_SecF       Protein export membrane protein
  ------ inclusion threshold ------
      0.045   11.4  25.9      0.016   12.9  10.0    2.2  2  ACR_tran        AcrB/AcrD/AcrF family
      0.087   12.8  12.0        1.5    8.8   2.2    3.5  3  RseC_MucC       Positive regulator of sigma(E), RseC/MucC
       0.35   11.2   8.4         18    5.7   1.0    3.7  3  BLOC1_2         Biogenesis of lysosome-related organelles com


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 !   40.1  18.1   8.3e-14   2.1e-10      95     297 ..     352     561 ..     171     564 .. 0.76
   2 !   63.1  18.8   8.1e-21   2.1e-17      72     305 ..     740     997 ..     650    1009 .. 0.69

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 8.3e-14
                              MMPL  95 egdpgsteadesvaairaaveear.......pleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivy 164
                                           ++++++e++ ai +   e +         ++ +  v G +++++++  +   +l++++ ++++ ++v Ll++y
  gi|336253834|ref|YP_004596941.1| 352 STAGADSAGAEEMGAIDDRTVESQleirnlaNAQDGDYVVFGGGIVTDEIDRSMGDSLAIVGPLAMLFVVVALLVAY 428
                                       444455555555555554433333456666544444555667799999999999*********************** PP

                              MMPL 165 rSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedree... 238
                                       r l+  +l ++ ++v l+ ++g+ + +a +++ ++  +v+    vlli+ ++DYa+ ++ R+re++++   + +   
  gi|336253834|ref|YP_004596941.1| 429 RDLLDIILGVVGIAVVLVWTFGF-MGWAGIAFNQMFVAVP----VLLIGLSIDYAIHVFMRHREQRDEAGATGSgsv 500
                                       ***99777666666666666666.8888887777766665....679******************988665533233 PP

                              MMPL 239 ..aviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPA 297
                                         ++  a++++g + +  ++t +i +l+ +v+ ++ ++++G++ ++G++ ++ +  +l+PA
  gi|336253834|ref|YP_004596941.1| 501 reSMTIALGGVGVALVWVTATTVIGFLSNLVSPIGPIREFGIVSSVGIVAALIVFGALIPA 561
                                       33999**********************************************9999999999 PP

  == domain 2  score: 63.1 bits;  conditional E-value: 8.1e-21
                              MMPL  72 s.....................dpdvaaafvSk....Dg...kaaralvtlegdpgsteadesvaairaaveearpl 120
                                       +                     d+d+a++++S     Dg   +aar+++ ++gd++  ++ +++++i+a   + +  
  gi|336253834|ref|YP_004596941.1| 740 DtdddgvpdenvtalydqlfevDEDAASQVISRtdggDGseyDAARLVIGVQGDASPGDTTDEMRDIAA---SIEDG 813
                                       033333333333333333333344466666664322233333689999999987666666555555555...55555 PP

                              MMPL 121 eglkvevtGpaatl....adlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilal 193
                                       +++++  tG +++     +dl d++ ++l ++ v+ ++ + v   ++  S    ++ ll v++s+   lg+     +
  gi|336253834|ref|YP_004596941.1| 814 ADVTAVATGDPIVSyiveQDLLDTVLESLLITLVAVFAFLTVAYWLTGNSASLGIVTLLPVAFSVSWILGT----MY 886
                                       6********99865222266666666666666555555555555566678888999999999999999999....55 PP

                              MMPL 194 llglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarl 270
                                       l g+  +   +g+ + l+i+ G++Y + + +Ry  el++  +  +a+ ++v++tg++ +++++t ++ +  L++a l
  gi|336253834|ref|YP_004596941.1| 887 LIGMPFNVL-TGMITSLTIGLGVAYSIHVSARYSLELERQGNVWSALRTTVTGTGGALLGSAATTVGGFGTLAFAIL 962
                                       667777665.5677899************************************************************ PP

                              MMPL 271 pvlaqvGvaialGvlvdvlivlTllPAllvllGra 305
                                       p+l+q+G+  al++  ++l+++ +lP+llvl  r 
  gi|336253834|ref|YP_004596941.1| 963 PALQQFGIITALTITYAFLASVVVLPSLLVLWTRY 997
                                       ******************************97664 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 !   12.8   4.4   3.2e-05     0.082      10     121 ..     435     551 ..     431     559 .. 0.82
   2 !   17.0   2.8   1.5e-06    0.0039       7     138 ..     865     996 ..     861    1001 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCH.HCHHHHHHHHTTTCH.....HHHHHHHHHH CS
                    Sterol-sensing  10 lagviivllsvasslgllaylgltltliilevlPflvlavgvdnif.vlvkavqrtsrslde.....seriaealge 80 
                                       + gv+ +++ ++ ++g++ + g+ ++ + +  +P l++  ++d    v+++  ++ ++          e +  alg 
  gi|336253834|ref|YP_004596941.1| 435 ILGVVGIAVVLVWTFGFMGWAGIAFNQMFV-AVPVLLIGLSIDYAIhVFMRHREQRDEAGATgsgsvRESMTIALGG 510
                                       4566677777899***************99.99**********654044444444433333366777999******* PP

                                       HCCCCHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH CS
                    Sterol-sensing  81 vgpsilltsltellalllgaltdvpavqeFclfaavavlvd 121
                                       vg++++  ++t ++ +l  +++ +  ++eF + + v+++  
  gi|336253834|ref|YP_004596941.1| 511 VGVALVWVTATTVIGFLSNLVSPIGPIREFGIVSSVGIVAA 551
                                       *************************************9865 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHH.HHHTTTCHHHHHHHHHHHHC CS
                    Sterol-sensing   7 gLglagviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavq.rtsrsldeseriaealgevg 82 
                                        Lg++ ++ v++sv   lg ++++g++++ ++  ++  l +  gv  +  +   +  +++r+ ++ + +  +++ +g
  gi|336253834|ref|YP_004596941.1| 865 SLGIVTLLPVAFSVSWILGTMYLIGMPFNVLTG-MITSLTIGLGVAYSIHVSARYSlELERQGNVWSALRTTVTGTG 940
                                       69999**************************99.9999******998777776665267788888************ PP

                                       CCCHHCCCHHHHHHH.HHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHH CS
                    Sterol-sensing  83 psilltsltellall.lgaltdvpavqeFclfaavavlvdFllqitfFvavLsldir 138
                                        ++l +++t +  +  l+ +  +pa+q+F + +a+ ++  Fl  +++  ++L l +r
  gi|336253834|ref|YP_004596941.1| 941 GALLGSAATTVGGFGtLA-FAILPALQQFGIITALTITYAFLASVVVLPSLLVLWTR 996
                                       ***************555.999*****************************998776 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.033        85      13      83 ..      40     110 ..      30     130 .. 0.78
   2 !   17.6   8.8   3.3e-07   0.00083     257     368 ..     434     551 ..     411     570 .. 0.84
   3 !   11.0  11.3   3.2e-05     0.082     252     384 ..     862     995 ..     820     998 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.033
                           Patched  13 adirslteeevrsekeplkeekffpgkseekaryliitakdresknileesllnevvkindyisenveike 83 
                                       +++ ++++e+  ++  ++ + +f +++ e++  + +i   dr ++n+l ++ l +  + +++i +n +i+e
  gi|336253834|ref|YP_004596941.1|  40 SSLDQFESESDEAQALERIDGNFTSEQQENTTSVQVIARGDRTDENVLAKESLIDSLEFQQEIRTNESINE 110
                                       55556666666666666667778888888777777777778889*******************99977765 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.3e-07
                           Patched 257 ailgvlspvlAivsslGlllwlGfrfnsivtvtPFLvLaiGvDdmflmvaawkrteakls.........vkkrigea 324
                                        ilgv+   +  v  +G++ w G+ fn++   +P L +++ +D +   ++ ++r++ +++         v++ ++ a
  gi|336253834|ref|YP_004596941.1| 434 IILGVVGIAVVLVWTFGFMGWAGIAFNQMFVAVPVLLIGLSIDYA---IHVFMRHREQRDeagatgsgsVRESMTIA 507
                                       467888888889999***************************964...444455555544556779999******** PP

                           Patched 325 lseagvaitiTslTdvlsFgiGaittlpaiqlFciytavailfd 368
                                       l  +gva++  + T v+ F    ++++  i  F i+ +v i+ +
  gi|336253834|ref|YP_004596941.1| 508 LGGVGVALVWVTATTVIGFLSNLVSPIGPIREFGIVSSVGIVAA 551
                                       ********99999*************************999765 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 3.2e-05
                           Patched 252 skpilailgvlspvlAivsslGlllwlGfrfnsivtvtPFLvLaiGvD.dmflmvaawkrteaklsvkkrigealse 327
                                          +l i+ +l    +++  lG+++++G++fn  + ++  L +++Gv   +++ +    ++e++ +v   +  ++  
  gi|336253834|ref|YP_004596941.1| 862 NSASLGIVTLLPVAFSVSWILGTMYLIGMPFNVLTGMITSLTIGLGVAySIHVSARYSLELERQGNVWSALRTTVTG 938
                                       455677888888888888899**************************7244566666667888888*********** PP

                           Patched 328 agvaitiTslTdvlsFgiGaittlpaiqlFciytavailfdfiYqitffaavlaiaa 384
                                       +g a++    T v  Fg  a + lpa+q F i+ta+ i ++f+  ++++ ++l++  
  gi|336253834|ref|YP_004596941.1| 939 TGGALLGSAATTVGGFGTLAFAILPALQQFGIITALTITYAFLASVVVLPSLLVLWT 995
                                       *******************************************99999999998865 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   8.6   3.2e-07   0.00082      39     170 ..     415     550 ..     393     555 .. 0.78
   2 ?    1.2   8.4     0.078     2e+02      19     107 ..     824     917 ..     807     996 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.2e-07
                                       HHHHHHHHHHHHHT-HHHHH.HHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSSHHHHHHHHHHHHH... CS
                         SecD_SecF  39 ialvliliyvalrFewrval.aaiialvhDviitvgvlsllgievdlatvaalLtiiGYSvndtvvvfdrvren... 111
                                       +a++++++ + +++++ + +   ++ ++  ++ t g++ + gi ++  +va    +iG S++  + vf r re+   
  gi|336253834|ref|YP_004596941.1| 415 LAMLFVVVALLVAYRDLLDIiLGVVGIAVVLVWTFGFMGWAGIAFNQMFVAVPVLLIGLSIDYAIHVFMRHREQrde 491
                                       5778888889999999997625677799999*******************************************222 PP

                                       HHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTST CS
                         SecD_SecF 112 lrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGliv 170
                                          +   +++e +  +l    +  +  ++tt++  ++ l+ + + +++f ++  vG+++
  gi|336253834|ref|YP_004596941.1| 492 AGATGSGSVRESMTIALGGVGVALVWVTATTVIGFLSNLVSPIGPIREFGIVSSVGIVA 550
                                       23334445555555555555556677777888888888999999999999999999987 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.078
                                       EEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HH...HHHHHHHH..HHHHHHHHHHHHHHTT----HHH.HHH CS
                         SecD_SecF  19 etvgpsvskelaekavlallialvliliyvalrFewr...valaaiia..lvhDviitvgvlsllgievdlat.vaa 89 
                                         v+  v ++l  +++ +lli+lv+++ ++++++        l+++++  +++ v  ++g + l+g+++++ t ++ 
  gi|336253834|ref|YP_004596941.1| 824 PIVSYIVEQDLLDTVLESLLITLVAVFAFLTVAYWLTgnsASLGIVTLlpVAFSVSWILGTMYLIGMPFNVLTgMIT 900
                                       5688888899999********************9653111233333333379**************99997652444 PP

                                       HHHHTTSSSHHHHHHHHH CS
                         SecD_SecF  90 lLtiiGYSvndtvvvfdr 107
                                        Lt iG  v  ++ v  r
  gi|336253834|ref|YP_004596941.1| 901 SLT-IGLGVAYSIHVSAR 917
                                       444.46666666666555 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  10.0   6.4e-06     0.016     340     485 ..     416     562 ..     404     615 .. 0.85
   2 ?    4.2   7.8    0.0027       6.9     302     484 ..     802     989 ..     782     994 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.4e-06
                                       HHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHTT--BCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          ACR_tran 340 aivLvvlvvflFLqnlratlipaiavPlsllgtfavlkalgfslNlltLfgLvlAiGlvvDdAiVvvEnierkleee 416
                                       a++ vv+ +++  ++l   +  ++ + ++l+ tf ++ + g++ N +     vl iGl +D Ai v     ++  e+
  gi|336253834|ref|YP_004596941.1| 416 AMLFVVVALLVAYRDLLDIILGVVGIAVVLVWTFGFMGWAGIAFNQMFVAVPVLLIGLSIDYAIHVFMRHREQRDEA 492
                                       78899999999999*99999******************************99************9988877777777 PP

                                       TS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHH..HHHHHHHHHHHHHHHHHHHHCCHHHH CS
                          ACR_tran 417 gekpleaalksmkeiqgalvaialvllavflPilflgGveGkl..frqfaltivlaillsvlvaltltPal 485
                                       g++    +++sm+ i+   v++alv + +   i fl+ ++  +   r+f++  ++ i+++++v   l+Pa+
  gi|336253834|ref|YP_004596941.1| 493 GATGSGSVRESMT-IALGGVGVALVWVTATTVIGFLSNLVSPIgpIREFGIVSSVGIVAALIVFGALIPAA 562
                                       8888666666663.555555666666555555666666655554459***************999999986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0027
                                       HHHCCGGGSSTTEEEEEEEESHHHHHHHHH.....HHHHHHHHHHH..HHHHHHHHHHSSHHHHHHHHHHHHHHHHH CS
                          ACR_tran 302 kleeLkeslPegveivvvydrtefvrasie.....eVvktLleaiv..LvvlvvflFLqnlratlipaiavPlsllg 371
                                       ++  +++s+  g++++ v    ++v+  +e     +V ++Ll+ +v   ++l+v   L    a+l +++ +P++  +
  gi|336253834|ref|YP_004596941.1| 802 EMRDIAASIEDGADVTAVATGDPIVSYIVEqdlldTVLESLLITLVavFAFLTVAYWLTGNSASLGIVTLLPVAFSV 878
                                       67777777777777777777666666555421111566666655431134566666667778999999999998888 PP

                                       H..HHHHHHTT--BCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                          ACR_tran 372 t..favlkalgfslNlltLfgLvlAiGlvvDdAiVvvEnierkleeegekpleaalksmkeiqgalvaialvllavf 446
                                          +  ++++g+  N+lt +   l iGl v  +i v    + +le  + +   a + +++  +gal+++a++ +  f
  gi|336253834|ref|YP_004596941.1| 879 SwiLGTMYLIGMPFNVLTGMITSLTIGLGVAYSIHVSARYSLELER-QGNVWSALRTTVTGTGGALLGSAATTVGGF 954
                                       722557************99999999**999999998888888887.444567777888888888888888887777 PP

                                       TGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                          ACR_tran 447 lPilflgGveGklfrqfaltivlaillsvlvaltltPa 484
                                         ++f    +    +qf++  +l i  + l ++++ P+
  gi|336253834|ref|YP_004596941.1| 955 GTLAF---AILPALQQFGIITALTITYAFLASVVVLPS 989
                                       54443...233345666666666666666666666665 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.2   0.00058       1.5      37     111 ..     373     448 ..     368     468 .. 0.83
   2 ?   -1.0   0.0      0.61   1.6e+03      84     119 ..     454     488 ..     445     492 .. 0.70
   3 ?    7.5   2.0    0.0015       3.8      46     109 ..     817     879 ..     800     911 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00058
                         RseC_MucC  37 ekrleveneigakvGdkVevg....ieeksllkaallvYllPllllilgallgsallgssellaalgallglvlgfl 109
                                       e++le++n ++a+ Gd V+ g    ++e +  ++  l+ + Pl++l+++++l  a     +ll ++++++g+++ ++
  gi|336253834|ref|YP_004596941.1| 373 ESQLEIRNLANAQDGDYVVFGggivTDEIDRSMGDSLAIVGPLAMLFVVVALLVAY---RDLLDIILGVVGIAVVLV 446
                                       679999************976332256666777778999********999999888...79*********9999998 PP

                         RseC_MucC 110 iv 111
                                       + 
  gi|336253834|ref|YP_004596941.1| 447 WT 448
                                       86 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.61
                         RseC_MucC  84 lgsallgssellaalgallglvlgflivrllskrlk 119
                                        + ++ +++ ++a+ + l+gl + + i  ++++r +
  gi|336253834|ref|YP_004596941.1| 454 WAGIA-FNQMFVAVPVLLIGLSIDYAIHVFMRHREQ 488
                                       22223.789999999999******999999998844 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0015
                         RseC_MucC  46 igakvGdkVevgieeksllkaallvYllPllllilgallgsallgssellaalgallglvlgfl 109
                                       + +++Gd ++  i e++ll ++l   l+ l+++++++ ++++l+ ++++   ++ ll +++++ 
  gi|336253834|ref|YP_004596941.1| 817 TAVATGDPIVSYIVEQDLLDTVLESLLITLVAVFAFLTVAYWLT-GNSASLGIVTLLPVAFSVS 879
                                       45678**************************************6.5555544444444444433 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 ?    5.7   1.0    0.0069        18      32      80 ..     131     179 ..     121     189 .. 0.80
   2 ?    5.0   0.1     0.011        29      47      81 ..     201     236 ..     193     241 .. 0.73
   3 ?    2.7   0.1     0.059   1.5e+02      34      71 ..     266     305 ..     262     313 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0069
                           BLOC1_2  32 asekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                       + e++++l+++ a+le+ + +lne+++ l++ l++  +++++ +++e++
  gi|336253834|ref|YP_004596941.1| 131 TDERVAALENRSAELEARSAELNETSARLEEGLNETVALQREREQIEAT 179
                                       5678888888888888888888888888888888888888888887776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
                           BLOC1_2  47 ekkleklne.kyeelqpylqqidqiekqvteLeeav 81 
                                       e+  + l+  + +e ++y+ q+ +ie q+ e+e+ +
  gi|336253834|ref|YP_004596941.1| 201 ENATQGLDDgQAAEYEEYVGQLREIESQLFEIEQDA 236
                                       4444444440346*****************999976 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.059
                           BLOC1_2  34 ekykklkdvaaslekkleklnekye..elqpylqqidqie 71 
                                        +y++l+d  + le++  +l+e +e  +l+++++ +++++
  gi|336253834|ref|YP_004596941.1| 266 DEYDALEDDSERLEEDWAALEEDDEqpSLDEQIEALEELD 305
                                       6899999999999999999999888667888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1045 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1379  (0.0769145); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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):               7  [number of targets reported over threshold]
# CPU time: 0.99u 0.31s 00:00:01.30 Elapsed: 00:00:00.46
# Mc/sec: 6816.43
//
Query:       gi|336253835|ref|YP_004596942.1|  [L=317]
Description: methionyl-tRNA formyltransferase-like protein [Halopiger xanaduensis SH-6]
Scores for 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-09   36.6   0.0    4.8e-09   36.2   0.0    1.2  1  Formyl_trans_N  Formyl transferase


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 !   36.2   0.0   2.7e-13   4.8e-09      79     177 ..     138     234 ..     100     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 2.7e-13
                                       T-SEEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE CS
                    Formyl_trans_N  79 kadlivlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkve 155
                                       + d+++  g++ l+ +++++a++++++  Hp+   r++G+ +  + ++ G   +Gvt + +de +D G+i+a  ++ 
  gi|336253835|ref|YP_004596942.1| 138 ECDVVIRFGFG-LIRGAILEAPSHGVVSFHPADIRRYRGLGPP-AIFRDGRSTAGVTLQRLDESIDGGEIVAFGETT 212
                                       67999999999.57889***********************996.679****************************** PP

                                       --TT--HHHHHHHHHHHHHHHH CS
                    Formyl_trans_N 156 iiaedtkeeleqrvadaehkal 177
                                       i    t+ ++ +r+a+++  +l
  gi|336253835|ref|YP_004596942.1| 213 IEDCHTLWDVFDRTATLQIDLL 234
                                       ************9999877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 00:00:00.37
# Mc/sec: 2544.77
//
Query:       gi|336253836|ref|YP_004596943.1|  [L=244]
Description: beta-lactamase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-15   56.7   0.3    2.7e-15   56.4   0.3    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    2.6e-14   53.7   3.0    2.6e-14   53.7   3.0    1.7  2  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.033   14.1   0.0      0.059   13.3   0.0    1.5  1  Lactamase_B_3  Beta-lactamase superfamily domain
      0.041   13.3   0.0      0.066   12.6   0.0    1.2  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
        0.3   10.2   0.3       0.44    9.6   0.3    1.2  1  PDEase_II      cAMP phosphodiesterases class-II


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 !   56.4   0.3   7.6e-19   2.7e-15       1     200 [.      29     208 ..      29     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 7.6e-19
                                       SEEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE.EEEEEEHHHHHHCCTT CS
                     Lactamase_B_2   1 rriLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkk.lplyapkgvlavlean 73 
                                       r +L+D+g +++   l++          + +  Vllth H DH+ +l+ l +   l++++ l++++p+g+   +++ 
  gi|336253836|ref|YP_004596943.1|  29 RTLLVDCGSGVLHR-LQQS-----GVGYENVSTVLLTHHHLDHISDLMPLVKarwLAGEEhLEIVGPQGTKGLVDDL 99 
                                       689*******8766.3332.....234569*********************9988555557**************99 PP

                                       CGHHHCHTT.TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HH CS
                     Lactamase_B_2  74 fvylaleee.pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipee 149
                                       ++ +   e    ++++e++ g +f+++  g+++ a + rh+ +          l++r++    r+ ++gD++ + + 
  gi|336253836|ref|YP_004596943.1| 100 LSVHDYLEGrIDLRIREVHEG-EFSVA--GFDVAAYETRHSVPC---------LAYRFD---DRFTFSGDSEAFGGL 161
                                       988877777788999999955.5***9..788**********97.........******...7************87 PP

                                       HHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 150 igerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                       +    +   +l +d+ + +d        H tpe   +a+   +++r++l+H
  gi|336253836|ref|YP_004596943.1| 162 AN-FAEESAILAHDCSFPDDVD---VSNHPTPETLGKALSGRDIGRVYLTH 208
                                       54.889999999********99...678*********************** PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   3.0   7.1e-18   2.6e-14       4     151 ..      17     155 ..      14     166 .. 0.78
   2 ?   -1.0   0.0      0.41   1.5e+03     105     133 ..     186     214 ..     157     218 .. 0.67

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 7.1e-18
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       ++++ +l+++dg+++L+D+G++    ++       g++ ++v++v+lTH+HlDHi++l+ lv+a++ +  ++ e+  
  gi|336253836|ref|YP_004596943.1|  17 RFQTGILVQDDGRTLLVDCGSGVLHRLQQ-----SGVGYENVSTVLLTHHHLDHISDLMPLVKARWLAGEEHLEIVG 88 
                                       5566689********************97.....7*****************************************9 PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTT CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDa 151
                                          + ++ d+     +    + +   d  + e  ++++++ ++ v    + ++++   +  ++++ f+GD 
  gi|336253836|ref|YP_004596943.1|  89 PQGTKGLVDDLLSVHD----YLEGRIDLRIREVHEGEFSVAGFDVAAYETRHSVPCLAYRFDDRFTFSGDS 155
                                       9999999988888764....444444444444444444444444444445555555556688888888886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.41
                                       CEEEEETTTEECCCTEEEEEHECTTSTSC CS
                       Lactamase_B 105 kpdvdeeeldgnaggrralyvtggpghgh 133
                                       +p + +++ ++ + +++++y t++ +h+ 
  gi|336253836|ref|YP_004596943.1| 186 HPTPETLGKALSGRDIGRVYLTHCYPHTD 214
                                       44555555555666666666666666665 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   1.6e-05     0.059      10      52 ..      22      68 ..      19     154 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                     Lactamase_B_3 10 flletagarilvDPfkanlgyeppa.....eeaDlvlisqaledHahl 52
                                      +l++++g ++lvD +++ +  + ++     e++  vl+++++ dH   
  gi|336253836|ref|YP_004596943.1| 22 ILVQDDGRTLLVDCGSG-VLHRLQQsgvgyENVSTVLLTHHHLDHISD 68
                                      689999*******9974.3333333457779**************753 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 ?   12.6   0.0   1.8e-05     0.066       1      57 [.      23      74 ..      23      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                     Lactamase_B_6  1 lLeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallya 57
                                      l++ d+ ++L+D+G+        + l++     ++v+ +LL+h  l+h++ ++ l++
  gi|336253836|ref|YP_004596943.1| 23 LVQDDGRTLLVDCGSGVL-----HRLQQSGVGYENVSTVLLTHHHLDHISDLMPLVK 74
                                      6788999*******9864.....35777777889****************8766654 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3   0.00012      0.44      79      97 ..      51      69 ..      38      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00012
                                      HTEEEEE-S---GGGTHHH CS
                         PDEase_II 79 nniksylItHsHLDHvsgl 97
                                      +n+ + l+tH HLDH+s l
  gi|336253836|ref|YP_004596943.1| 51 ENVSTVLLTHHHLDHISDL 69
                                      78999***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2057.22
//
Query:       gi|336253837|ref|YP_004596944.1|  [L=243]
Description: rhodopsin [Halopiger xanaduensis SH-6]
Scores for complete 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-58  197.9  22.4    1.8e-58  197.8  22.4    1.0  1  Bac_rhodopsin  Bacteriorhodopsin-like protein


Domain annotation for each model (and alignments):
>> Bac_rhodopsin  Bacteriorhodopsin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.8  22.4     1e-62   1.8e-58       1     221 [.       5     221 ..       5     223 .. 0.98

  Alignments for each domain:
  == domain 1  score: 197.8 bits;  conditional E-value: 1e-62
                                       HHHHHHHHHHHHHHHHHHHHHTTTSSTCCHHHHHHHHHHHHHHHHHHHHHHHTTTTEEEEEETTEEEEEETHHHHHH CS
                     Bac_rhodopsin   1 wtvfsvfallalvatllfvvtsrrvkdgekrkllvipllitaiaavaYltmalglGltgveaefehrqvfyarYidW 77 
                                       + vf+++al+++++t+ f++ +r  ++ e+r++++++ +i+ ia +aY+tma g+G+ +v +    r+vf +rY+dW
  gi|336253837|ref|YP_004596944.1|   5 TLVFWLGALGMAAGTVAFAWGGRS-AAAESRQYYTVLGAISLIATAAYVTMAMGYGWLSVDG----RTVFAPRYVDW 76 
                                       579****************99888.78888********************************....*********** PP

                                       HHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTST CS
                     Bac_rhodopsin  78 llttPllvlvlaelagadrrtllvlvladvvmivgglvgaliestyrwvyftisvaallvvlylllgelaraaksls 154
                                       +lttPll+l+l+ la+ +r++l ++v ++++++ gg++gal ++ +r+++f ++++a++ +lyl+l++++ +a++  
  gi|336253837|ref|YP_004596944.1|  77 ILTTPLLLLYLGWLADINRSRLGLVVGVNTLVMAGGFAGALLTGPVRFALFGVAAVAYVGLLYLILQPMTARANEQA 153
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTSS.CHHHHHHHHHHHHHHHHHHHHHHHHCCHTTCHH CS
                     Bac_rhodopsin 155 serrslfntLrnlvvvlwilYpvawllgeeGngi.qpdveavvygilDlvtkvgfglillaaatslgs 221
                                        ++rslf  Lrnl+v+lw +Ypv+wllg++G g+ +  v+ ++  +lDl+tkvgfgli+l+a ++l+ 
  gi|336253837|ref|YP_004596944.1| 154 DAIRSLFTGLRNLTVILWSVYPVIWLLGTAGFGLlTLPVDVMLTTYLDLLTKVGFGLIALNAGAALEA 221
                                       ************************************************************99888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1802.95
//
Query:       gi|336253838|ref|YP_004596945.1|  [L=565]
Description: methyl-accepting chemotaxis sensory transducer [Halopiger xanaduensis SH-6]
Scores for 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-40  137.3  59.0    5.7e-39  133.7  26.8    4.2  4  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
      2e-30  104.9  20.3      2e-30  104.9  20.3    4.2  3  Htr2            Htr2 transmembrane domain
    1.4e-12   47.8  14.1      6e-10   39.3   0.4    4.6  3  HAMP            HAMP domain
    0.00078   19.9  20.6       0.12   12.9   4.6    4.5  4  NPV_P10         Nucleopolyhedrovirus P10 protein
    0.00098   19.2  31.7      0.014   15.4   2.4    5.3  5  DUF1664         Protein of unknown function (DUF1664)
     0.0018   18.5  41.9     0.0091   16.2   3.6    6.8  7  DUF948          Bacterial protein of unknown function (DUF948
  ------ inclusion threshold ------
      0.012   16.1   4.8      0.012   16.1   4.8    4.6  4  Syntaxin-6_N    Syntaxin 6, N-terminal
      0.013   14.4  36.2       0.18   10.7   6.4    3.1  3  Spc7            Spc7 kinetochore protein
      0.098   12.7  33.4        0.6   10.1   2.2    5.2  5  Laminin_II      Laminin Domain II
       0.12   12.3   9.2        1.1    9.2   0.6    3.8  5  DUF489          Protein of unknown function (DUF489)
       0.19   10.8  15.5       0.43    9.6   0.9    3.1  3  Atg14           Vacuolar sorting 38 and autophagy-related sub
       0.48   10.3  19.8        4.2    7.3   1.1    5.0  6  Sec34           Sec34-like family
       0.52   10.3   7.0        1.8    8.5   0.1    3.6  4  ApoO            Apolipoprotein O
       0.65   10.2  18.8          3    8.0   2.6    4.1  4  Fib_alpha       Fibrinogen alpha/beta chain family
        1.1    7.6   7.7        2.2    6.6   7.7    1.4  1  Cytomega_UL84   Cytomegalovirus UL84 protein
        1.4    9.6  20.6       0.37   11.5   2.6    4.9  3  YabA            Initiation control protein YabA
        1.9    5.9  43.6      0.081   10.4  23.4    2.2  2  DUF3584         Protein of unknown function (DUF3584)
        3.2    7.8  28.6          4    7.5   0.2    5.7  6  COG2            COG (conserved oligomeric Golgi) complex comp
        3.2    7.4  10.4         11    5.7   4.4    3.0  3  DUF4201         Domain of unknown function (DUF4201)
        3.8    7.9  33.6       0.42   11.0  11.9    3.6  3  DUF4200         Domain of unknown function (DUF4200)
        4.1    7.4   9.9        2.6    8.1   0.5    3.1  2  LOH1CR12        Tumour suppressor protein
        4.7    7.3  31.9       0.15   12.2   8.6    3.9  4  Mod_r           Modifier of rudimentary (Mod(r)) protein
        4.9    7.0  34.9        2.8    7.8  14.1    3.3  2  DUF5089         Domain of unknown function (DUF5089)
        5.2    7.8  40.3        8.4    7.1   7.9    5.9  5  DUF883          Bacterial protein of unknown function (DUF883
        5.4    6.7  29.2       0.99    9.1   7.0    3.5  3  LXG             LXG domain of WXG superfamily
        5.8    7.2  35.2        4.7    7.5   1.4    5.1  6  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
        6.5    6.4   9.3        6.1    6.5   0.4    4.0  4  RPW8            Arabidopsis broad-spectrum mildew resistance 
          7    5.8  21.6        3.9    6.6   2.4    3.7  4  TMPIT           TMPIT-like protein


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.5      0.77   4.9e+02     100     142 ..     134     176 ..     106     195 .. 0.49
   2 !   14.8  13.1   2.8e-05     0.018      77     166 ..     226     315 ..     171     319 .. 0.83
   3 !  133.7  26.8   8.9e-42   5.7e-39       6     171 ..     323     488 ..     318     489 .. 0.94
   4 ?   -0.7   0.1       1.7   1.1e+03      75     113 ..     497     535 ..     490     546 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.77
                                       ..........HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH CS
                         MCPsignal 100 keindsvesleetrqrveegselveetgealkeiveavaevad 142
                                       +e++ + e  e  r+r+e+++e++ee++++ ++  e+ a v++
  gi|336253838|ref|YP_004596945.1| 134 EETEAAKEEAERERERAEQALEEAEEARSDAERERERLAAVNA 176
                                       3333344444444444444444444444443333333333333 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  77 VrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaasee 153
                                       + +L  r +  a +++++  ++ ++ ++++++ e++   ++e se +++ +e+++ei++++++++++ +e+aa++++
  gi|336253838|ref|YP_004596945.1| 226 IESLVGRIQGFATDVSDASRDVRANAESVMDASEDVSDTIAEISEGADTQTEKMREIAAEMDDISATTEEMAASAAQ 302
                                       55566666777778888888888888888888888888888888888888888888888888888888888888888 PP

                                       HHHHHHHHHHHHH CS
                         MCPsignal 154 qsasieevnqave 166
                                        +a+++e ++a e
  gi|336253838|ref|YP_004596945.1| 303 VAATSHEAARASE 315
                                       8888888888765 PP

  == domain 3  score: 133.7 bits;  conditional E-value: 8.9e-42
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHH CS
                         MCPsignal   6 easeeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkLAe 82 
                                        a    +e + + +  v+++e+++++ +e+ +i+e+i +ia+QTNlLALNA+iEAA A ++G+GFaVVA+EV++LAe
  gi|336253838|ref|YP_004596945.1| 323 AAIAAMNEVEAQTDASVAAIETLHEEIQEVGEITEIIADIAEQTNLLALNASIEAAHANDEGDGFAVVASEVKSLAE 399
                                       4444444558889999************************************************************* PP

                                       HHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  83 rsaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasie 159
                                       ++++a+ eie+ i+ iq ++ ++v+ + et  r+++g+e+veet ++l+ ive+v+e ++ +q+i+ +++ q++s e
  gi|336253838|ref|YP_004596945.1| 400 ETKEATTEIEDSIEWIQGQTRTTVDDIRETSDRISNGVETVEETVDSLEVIVESVEEANTGIQQINESTDTQAESTE 476
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHH CS
                         MCPsignal 160 evnqaveevakv 171
                                       +v++ ++ va++
  gi|336253838|ref|YP_004596945.1| 477 QVASMIDDVAEI 488
                                       ******999887 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHHHHHHH..............HHHH CS
                         MCPsignal  75 dEVrkLAersaqaakeiealiieiqkeindsvesleetr 113
                                       + V + A+    aa+e+   ++++  +  + +e l++tr
  gi|336253838|ref|YP_004596945.1| 497 SGVADAARSQSTAAREVFGRVEDLSDGAGTLLELLQDTR 535
                                       455566666667888888888888888888777777775 PP

>> Htr2  Htr2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.9  20.3     3e-33     2e-30       1      61 []      21      81 ..      21      81 .. 1.00
   2 ?   -1.1   0.0       3.8   2.4e+03      19      31 ..     185     197 ..     178     203 .. 0.85
   3 ?   -0.7   1.2       2.7   1.7e+03      20      42 ..     489     513 ..     485     517 .. 0.72

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 3e-33
                              Htr2  1 GaiFalviavtvaFGgaaYlevtaalasGDaaavgeaavsaiLGLivLtvinLGLvaatvG 61
                                      GaiFalviavt+aFGgaaYlev+aal+sGDaaavgeaa+saiLGL+vLtvinLGLvaatvG
  gi|336253838|ref|YP_004596945.1| 21 GAIFALVIAVTLAFGGAAYLEVAAALESGDAAAVGEAATSAILGLLVLTVINLGLVAATVG 81
                                      9***********************************************************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.8
                              Htr2  19 YlevtaalasGDa 31 
                                       ++ev a  a+GD 
  gi|336253838|ref|YP_004596945.1| 185 FGEVMARCADGDL 197
                                       89*********95 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.7
                              Htr2  20 levtaalasG..Daaavgeaavsai 42 
                                        e taa asG  Daa  +  a   +
  gi|336253838|ref|YP_004596945.1| 489 SETTAAEASGvaDAARSQSTAAREV 513
                                       5889999998667777777776555 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.4   9.4e-13     6e-10       7      53 .]      85     131 ..      80     131 .. 0.92
   2 !   15.2   0.6   3.3e-05     0.021      15      52 ..     187     227 ..     183     228 .. 0.83
   3 ?   -1.1   0.1       4.1   2.6e+03      11      11 ..     280     280 ..     259     306 .. 0.59

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 9.4e-13
                                       HHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHHH CS
                              HAMP   7 lrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLre 53 
                                        + L  L++ a r+++Gdld++l +++ DEiG+L ++f++M+++Lre
  gi|336253838|ref|YP_004596945.1|  85 AAALSSLSARATRMGEGDLDVDLSTRREDEIGDLYESFDEMRTSLRE 131
                                       566889***************************************95 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.3e-05
                                       HHHHHHTTTBTSSTCCTTSSSH...HHHHHHHHHHHHHHHH CS
                              HAMP  15 raarriaaGdldtrlpvsgrDE...iGeLarafNaMldrLr 52 
                                       ++++r a+Gdl++rl+v+g+ E   +  +a +fN+M+d ++
  gi|336253838|ref|YP_004596945.1| 187 EVMARCADGDLTQRLEVEGDGEteaMESIATSFNEMMDGIE 227
                                       689999****************44445679******99875 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.1
                                       H CS
                              HAMP  11 r 11 
                                       r
  gi|336253838|ref|YP_004596945.1| 280 R 280
                                       2 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.4    0.0018       1.2      11      63 ..     238     291 ..     233     299 .. 0.89
   2 ?    5.9   0.4     0.029        18      11      50 ..     326     365 ..     315     380 .. 0.73
   3 ?   -0.2   0.1       2.2   1.4e+03      26      51 ..     393     419 ..     387     435 .. 0.46
   4 !   12.9   4.6   0.00018      0.12       9      64 ..     433     488 ..     431     496 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0018
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpd.vtelnekLdaqsaqLaeletkvenIqd 63 
                                       +d+++ +  V a  ++v d +e++ d + e++e  d q++++ e+ +++++I+ 
  gi|336253838|ref|YP_004596945.1| 238 TDVSDASRDVRANAESVMDASEDVSDtIAEISEGADTQTEKMREIAAEMDDISA 291
                                       68999999999999***999999865389**********************986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.029
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaq 50 
                                       a+ ++v+ + da  ++++ ++e++++v e++e + ++++q
  gi|336253838|ref|YP_004596945.1| 326 AAMNEVEAQTDASVAAIETLHEEIQEVGEITEIIADIAEQ 365
                                       4667777788888888888888888888888777777666 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.2
                           NPV_P10  26 qvddvqenlpd.vtelnekLdaqsaqL 51 
                                       +v++++e+ ++ +te+++ ++ ++ q 
  gi|336253838|ref|YP_004596945.1| 393 EVKSLAEETKEaTTEIEDSIEWIQGQT 419
                                       555555554431345555554443332 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 0.00018
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                       I + ++ v++ Vd+l+  v++v+e    ++++ne  d q+++ +++ + ++++ +i
  gi|336253838|ref|YP_004596945.1| 433 ISNGVETVEETVDSLEVIVESVEEANTGIQQINESTDTQAESTEQVASMIDDVAEI 488
                                       778899*********************************99999999988888776 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.5      0.13        82      51     116 ..     116     181 ..     107     191 .. 0.67
   2 !   11.5   1.2   0.00035      0.22      38     119 ..     221     302 ..     215     307 .. 0.85
   3 ?    4.0   1.2     0.077        49      68     116 ..     318     365 ..     301     373 .. 0.64
   4 !   15.4   2.4   2.2e-05     0.014      58     122 ..     391     456 ..     386     458 .. 0.87
   5 ?    2.9   0.6      0.16     1e+02      69     101 ..     462     490 ..     456     513 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.13
                           DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                        +++es  + +  L + +++ ++  +e ++  +  ++ ++e++e  s+ +++ e + ++  +le++
  gi|336253838|ref|YP_004596945.1| 116 GDLYESFDEMRTSLRESLEETEAAKEEAERERERAEQALEEAEEARSDAERERERLAAVNAELEAE 181
                                       566777777777777777777777777776666666666666666666666666666666666554 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00035
                           DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                        + d +es+  +++ + ++++++ r+  ++ ++v +  ++++++++ei+e  ++  e+++ei  +++ ++++ e+++
  gi|336253838|ref|YP_004596945.1| 221 EMMDGIESLVGRIQGFATDVSDASRDVRANAESVMDASEDVSDTIAEISEGADTQTEKMREIAAEMDDISATTEEMA 297
                                       58888899999999999999999999999999999999999999999999999999999999999999999999988 PP

                           DUF1664 115 skler 119
                                       ++ ++
  gi|336253838|ref|YP_004596945.1| 298 ASAAQ 302
                                       77655 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.077
                           DUF1664  68 idrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                       +++ ++ + +++e+ +++++ v++++   +ei+ +v ++ e++ +++++
  gi|336253838|ref|YP_004596945.1| 318 LETAEAAIAAMNEVEAQTDASVAAIETLHEEIQ-EVGEITEIIADIAEQ 365
                                       556666677777777777777777666555554.466666666655554 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 2.2e-05
                           DUF1664  58 aatkrhLssridrvdkkldeqke.iskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       a+  + L+++ ++  +++++++e i+ +++  v+++re  ++i++ ve+v+e+v +le  +e++ee
  gi|336253838|ref|YP_004596945.1| 391 ASEVKSLAEETKEATTEIEDSIEwIQGQTRTTVDDIRETSDRISNGVETVEETVDSLEVIVESVEE 456
                                       5566778888888889998888746789*********************************99996 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.16
                           DUF1664  69 drvdkkldeqkeiskeikeevtevredlseige 101
                                       ++++++ d q+e +++    v+++ +d++ei+e
  gi|336253838|ref|YP_004596945.1| 462 QQINESTDTQAESTEQ----VASMIDDVAEISE 490
                                       4444444444444444....4444444443333 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 ?    0.8   0.1       0.9   5.8e+02      30      70 ..     131     171 ..     113     188 .. 0.53
   2 ?    6.7   0.0     0.013       8.6      42      85 ..     205     248 ..     196     252 .. 0.84
   3 ?    5.6   2.1     0.029        19      26      73 ..     263     296 ..     251     322 .. 0.44
   4 ?    4.1   2.1     0.088        56      46      82 ..     318     354 ..     299     371 .. 0.50
   5 !   16.2   3.6   1.4e-05    0.0091      18      88 ..     388     458 ..     386     465 .. 0.84
   6 !    7.8   2.5    0.0059       3.8      44      84 ..     452     492 ..     447     497 .. 0.90
   7 ?    6.6   1.4     0.014         9      28      82 ..     464     522 ..     461     528 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.9
                            DUF948  30 eaaatieelekqvdpilkevedllakvnelledvneklekv 70 
                                       e  +  e  +++++   + +e++l++++e  +d +++ e++
  gi|336253838|ref|YP_004596945.1| 131 ESLEETEAAKEEAERERERAEQALEEAEEARSDAERERERL 171
                                       22222222224444444445555555555555555555555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.013
                            DUF948  42 vdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                        d+ ++ +e + +  ne+++++++ + +++ + + v d+++ v+
  gi|336253838|ref|YP_004596945.1| 205 GDGETEAMESIATSFNEMMDGIESLVGRIQGFATDVSDASRDVR 248
                                       566677888999999***********************999886 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.029
                            DUF948  26 ktldeaaatieelekqvdpilkevedllakvnelledvneklekvdpl 73 
                                       +t+ e+++  ++ ++++++i  e++d+ a+++e              +
  gi|336253838|ref|YP_004596945.1| 263 DTIAEISEGADTQTEKMREIAAEMDDISATTEE--------------M 296
                                       222333333333333333333333333333333..............2 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.088
                            DUF948  46 lkevedllakvnelledvneklekvdplteavadlge 82 
                                       l+ +e+++a +ne+ ++    ++++++l e+++++ge
  gi|336253838|ref|YP_004596945.1| 318 LETAEAAIAAMNEVEAQTDASVAAIETLHEEIQEVGE 354
                                       4444455555555444444444444444444444443 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 1.4e-05
                            DUF948  18 ivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       +vv  ++k++++e++++ +e+e+ ++ i  +++++++ ++e+ + +++ +e+v++ +++++ + esv+e n
  gi|336253838|ref|YP_004596945.1| 388 AVVASEVKSLAEETKEATTEIEDSIEWIQGQTRTTVDDIRETSDRISNGVETVEETVDSLEVIVESVEEAN 458
                                       56778889999999999999999999999999999999999999999999999988888888888887765 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0059
                            DUF948  44 pilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                       + ++e+++ ++++ne ++   e +e+v ++++ va+++e+ 
  gi|336253838|ref|YP_004596945.1| 452 ESVEEANTGIQQINESTDTQAESTEQVASMIDDVAEISETT 492
                                       567999*********999999*****************986 PP

  == domain 7  score: 6.6 bits;  conditional E-value: 0.014
                            DUF948  28 ldeaaatieelekqvdpilkevedllakvne....lledvneklekvdplteavadlge 82 
                                       ++e ++t +e ++qv +++++v+++ +++ +    +++  ++++ +  +++  v+dl++
  gi|336253838|ref|YP_004596945.1| 464 INESTDTQAESTEQVASMIDDVAEISETTAAeasgVADAARSQSTAAREVFGRVEDLSD 522
                                       45555555666666666666666666666552222555666699999999999999886 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 ?    3.0   4.1      0.24   1.5e+02      19      82 ..     117     179 ..     106     189 .. 0.67
   2 ?    5.1   1.6     0.051        33      11      86 ..     248     323 ..     206     333 .. 0.48
   3 ?    0.8   0.4       1.1   7.1e+02      35      65 ..     327     357 ..     291     375 .. 0.49
   4 ?   16.1   4.8   1.9e-05     0.012       1      97 [.     385     484 ..     385     486 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.24
                      Syntaxin-6_N  19 slyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkidekels 82 
                                        ly+++ +++++ ++s  ee + +++e +++ + +e+ le+ ee+ + +e+++++    ++el+
  gi|336253838|ref|YP_004596945.1| 117 DLYESFDEMRTSLRES-LEETEAAKEEAERERERAEQALEEAEEARSDAERERERLAAVNAELE 179
                                       5677777666666554.67777777777777777777777777776666666666555555554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.051
                      Syntaxin-6_N  11 qkslnkaeslyrrwerlledtsss......tseeldetrteLrkalrsiewdledLeetvriveknpsk.fkideke 80 
                                       + +++++    +  ++       +        +   e ++e+ +++++i+ + e++  + + v +  ++  + +e+ 
  gi|336253838|ref|YP_004596945.1| 248 RANAESVMDASEDVSD-------TiaeiseGADTQTEKMREIAAEMDDISATTEEMAASAAQVAATSHEaARASENG 317
                                       2222222222222211.......011111134445555555555555555555555555555554444445555555 PP

                      Syntaxin-6_N  81 lsrrra 86 
                                       l++ +a
  gi|336253838|ref|YP_004596945.1| 318 LETAEA 323
                                       555555 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.1
                      Syntaxin-6_N  35 tseeldetrteLrkalrsiewdledLeetvr 65 
                                         +e++ +++   +a++++ +++++  e  +
  gi|336253838|ref|YP_004596945.1| 327 AMNEVEAQTDASVAAIETLHEEIQEVGEITE 357
                                       4444444444445555555555555444444 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 1.9e-05
                      Syntaxin-6_N   1 DPFfevkeeVqkslnkaeslyrrw..e.rlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskf 74 
                                       D F +v++eV++ ++++++  ++   + +  + ++ +t ++++et++ + + ++++e++++ Le  v+ ve+ ++  
  gi|336253838|ref|YP_004596945.1| 385 DGFAVVASEVKSLAEETKEATTEIedSiEWIQGQTRTTVDDIRETSDRISNGVETVEETVDSLEVIVESVEEANTGI 461
                                       88*******************999542233333333689********************************998887 PP

                      Syntaxin-6_N  75 kidekelsrrrafveevreevke 97 
                                       +  ++  +++ +  e+v + +++
  gi|336253838|ref|YP_004596945.1| 462 QQINESTDTQAESTEQVASMIDD 484
                                       77777777777777777777665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   6.7   0.00066      0.42     159     243 ..     109     192 ..      95     198 .. 0.87
   2 ?   10.7   6.4   0.00028      0.18     136     284 ..     211     358 ..     208     382 .. 0.79
   3 ?    5.7   8.2    0.0092       5.9     177     288 ..     388     498 ..     361     526 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00066
                              Spc7 159 ekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleek 235
                                       +++e+e+ +l+++++e +++l+e le+ ++a+ee ++ ++e+ e++ ee +e+ ++ e+ +++la ++++le+ +e+
  gi|336253838|ref|YP_004596945.1| 109 TRREDEIGDLYESFDEMRTSLRESLEETEAAKEE-AERERERAEQALEEAEEARSDAERERERLAAVNAELEAEAER 184
                                       56789999999**************999997777.666899999999999999999999999999999999999999 PP

                              Spc7 236 ieelkeqk 243
                                       + e+ +++
  gi|336253838|ref|YP_004596945.1| 185 FGEVMARC 192
                                       98887776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00028
                              Spc7 136 llegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelk 212
                                        +e++ ++ +e ++g+e+   +++     ++++  +++++ +++++  e+  +  +e+++   ++ e++re +a+ +
  gi|336253838|ref|YP_004596945.1| 211 AMESIATSFNEMMDGIESLVGRIQGFATDVSDASRDVRANAESVMDASEDVSDTIAEISEGADTQTEKMRE-IAAEM 286
                                       57788888888888888888888888899999999999999999999999999999999988888888885.67777 PP

                              Spc7 213 aeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgw 284
                                        +i++  +e+a   +q+++ + + + ++e+  e+ e+  +a + +e++ + s   +++l+ee +++ e+t++
  gi|336253838|ref|YP_004596945.1| 287 DDISATTEEMAASAAQVAATSHEAARASENGLETAEAAIAAMNEVEAQTDASVAAIETLHEEIQEVGEITEI 358
                                       788888888888888888887777777776666666666677777888999999999999999888888776 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0092
                              Spc7 177 aeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaea 253
                                       a + +e+++l e+ +e ++  ++++e ++ + ++   +i+e ++++++  e +ee  +++e + e+ +e+++ i++ 
  gi|336253838|ref|YP_004596945.1| 388 AVVASEVKSLAEETKEATTEIEDSIEWIQGQTRTTVDDIRETSDRISNGVETVEETVDSLEVIVESVEEANTGIQQI 464
                                       56677888888888887777788888888888888888888888888888888888888888888888888888888 PP

                              Spc7 254 ervleeckgwsesevsrlkeevkaleeltgwkivs 288
                                       ++ ++ + + s+++v ++ + v ++ e+t  +  +
  gi|336253838|ref|YP_004596945.1| 465 NESTDTQAE-STEQVASMIDDVAEISETTAAEASG 498
                                       887775544.4556777778887777777665554 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.6     0.069        44      18      66 ..     125     173 ..     113     190 .. 0.74
   2 ?    5.5   0.3     0.025        16      13      78 ..     217     282 ..     208     285 .. 0.48
   3 ?    4.8   7.6     0.042        27      10     102 ..     270     362 ..     262     377 .. 0.59
   4 ?   10.1   2.2   0.00093       0.6      12      84 ..     391     460 ..     388     467 .. 0.75
   5 ?    5.5   1.4     0.025        16       5      76 ..     461     532 ..     452     545 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.069
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-- CS
                        Laminin_II  18 qlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLek 66 
                                         + l + le+t++  +e++r+ e+ ++ +++a +a  dA+r+   L  
  gi|336253838|ref|YP_004596945.1| 125 MRTSLRESLEETEAAKEEAERERERAEQALEEAEEARSDAERERERLAA 173
                                       5566777888888888888888888888888888888888887776654 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II  13 kevleqlaplsqnlentkeklseinrsvee....tnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                       ++     +++   +e +   +++++++v      + +++++ + a +d+++ + ++ + a+   +k++e+
  gi|336253838|ref|YP_004596945.1| 217 TS----FNEMMDGIESLVGRIQGFATDVSDasrdVRANAESVMDASEDVSDTIAEISEGADTQTEKMREI 282
                                       33....3444444444444444444444440000444555555555555555556666666666666655 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.042
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II  10 etakevleqlaplsqnlentkeklseinrsvee....tnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       e a    e++ +++++++ +++  +e+++s+++     +e ++++ ++++ A+ ++  ++++  q  + +  +++l+
  gi|336253838|ref|YP_004596945.1| 270 EGADTQTEKMREIAAEMDDISATTEEMAASAAQvaatSHEAARASENGLETAEAAIAAMNEVEAQTDASVAAIETLH 346
                                       44444444444444444444444444444433200004556667777888888888888888777777778888888 PP

                                       HH...HHHHHHHHHHHHHHH CS
                        Laminin_II  83 eassslsdniseikelIaqA 102
                                       e+     +++ ei e+Ia  
  gi|336253838|ref|YP_004596945.1| 347 EE----IQEVGEITEIIADI 362
                                       87....45777888888765 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00093
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                       a+ev++  ++ ++ + +++++++ i+++   t   v+d  ++ +  ++ v ++e++++ L+  ++++++ + +
  gi|336253838|ref|YP_004596945.1| 391 ASEVKSLAEETKEATTEIEDSIEWIQGQ---TRTTVDDIRETSDRISNGVETVEETVDSLEVIVESVEEANTG 460
                                       6778888888888888888888888888...777788888888888888888888888888877777776655 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklk 76 
                                       ++++ne++    e +++++  ++ + e  ++ ++++  + + +++ ++a r++   v +L   a  Ll+ l+
  gi|336253838|ref|YP_004596945.1| 461 IQQINESTDTQAESTEQVASMIDDVAEISETTAAEASGVADAARSQSTAAREVFGRVEDLSDGAGTLLELLQ 532
                                       667777777777777777777777777777777787888888899999999999999999988888887765 PP

>> DUF489  Protein of unknown function (DUF489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.9   2.5e+03      49      87 ..     119     157 ..     108     209 .. 0.53
   2 ?   -1.2   0.1       2.7   1.7e+03      86     115 ..     267     296 ..     190     313 .. 0.55
   3 ?    0.0   0.5       1.1   7.3e+02      73     107 ..     316     351 ..     233     375 .. 0.56
   4 ?    9.2   0.6    0.0018       1.1      12     113 ..     390     490 ..     386     503 .. 0.82
   5 ?    7.7   0.1    0.0051       3.3      11      71 ..     477     536 ..     473     544 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.9
                                       TTSGGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHH CS
                            DUF489  49 ygglanlklGletlleqlekekkkkdaeltryalsllal 87 
                                       y++ +++++ l+  le  e+ k++++ e  r   +l + 
  gi|336253838|ref|YP_004596945.1| 119 YESFDEMRTSLRESLEETEAAKEEAERERERAEQALEEA 157
                                       555555555555555444444444444433333333333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.7
                                       HHHHHHHHSTTHHHHHHHHHHTTHHHHTTS CS
                            DUF489  86 alerkLsknkealaklgerieqierqlehf 115
                                       ++++    ++e +++++ +++ i+  +e++
  gi|336253838|ref|YP_004596945.1| 267 EISEGADTQTEKMREIAAEMDDISATTEEM 296
                                       333333344444445555555554444444 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHH.HHHHHHHHSTTHHHHHHHHHHT CS
                            DUF489  73 kdaeltryalsll.alerkLsknkealaklgerieq 107
                                       + +e++  a++ + ++e +   + +a+++l+e+i++
  gi|336253838|ref|YP_004596945.1| 316 NGLETAEAAIAAMnEVEAQTDASVAAIETLHEEIQE 351
                                       222333322222213444444444444444444444 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHS---HHHHHHHHHHHH--S-SSHHHHTTSGGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHHH CS
                            DUF489  12 aaklvqqlArtGqadeealetllkslletdpestedvygglanlklGletlleqlekekkkkdaeltryalsllale 88 
                                        a+ v++lA++ +  ++++e +++ +  ++ ++++d+ + ++++++G+et++e++++ +     ++     ++ +++
  gi|336253838|ref|YP_004596945.1| 390 VASEVKSLAEETKEATTEIEDSIEWIQGQTRTTVDDIRETSDRISNGVETVEETVDSLEV-IVESVEEANTGIQQIN 465
                                       6789**************************************************999877.4445566667777778 PP

                                       HHHHHSTTHHHHHHHHHHTTHHHHT CS
                            DUF489  89 rkLsknkealaklgerieqierqle 113
                                       ++   + e ++++++ i+ +++ +e
  gi|336253838|ref|YP_004596945.1| 466 ESTDTQAESTEQVASMIDDVAEISE 490
                                       8888888888888888887776655 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHHS---HHHHHHHHHHHH--S-SSHHHHTTSGGGGHHHHHHHHHHHHT--S CS
                            DUF489  11 qaaklvqqlArtGqadeealetllkslletdpestedvygglanlklGletlleqlekekk 71 
                                       q a++++++A+  ++ +++ + + +   + +++ + +v+g++++l+ G  tlle l++++ 
  gi|336253838|ref|YP_004596945.1| 477 QVASMIDDVAEISETTAAEASGVAD-AARSQSTAAREVFGRVEDLSDGAGTLLELLQDTRV 536
                                       7888899999988887777766555.467889999*********************98865 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 ?    9.6   0.9   0.00068      0.43      57     128 ..     110     181 ..      70     188 .. 0.66
   2 ?    2.4   0.7       0.1        67      58     124 ..     257     317 ..     213     360 .. 0.57
   3 ?    7.4   1.7    0.0031         2      57     184 ..     379     515 ..     341     522 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00068
                             Atg14  57 qledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleer 128
                                       ++ed+i  + ++ +e+++  +++ e+++  k+  ++ +++ e++ ++ ++ +++  + r++l++++ ele++
  gi|336253838|ref|YP_004596945.1| 110 RREDEIGDLYESFDEMRTSLRESLEETEAAKEEAERERERAEQALEEAEEARSDAERERERLAAVNAELEAE 181
                                       555666666666666666666666666666666666666666666666666666666666666666666554 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.1
                             Atg14  58 ledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqne 124
                                       +++++  + a ++e   ++ ++ ++++  +d++s  ++e+++  +++a+ s++ + R s+     n 
  gi|336253838|ref|YP_004596945.1| 257 ASEDVSDTIAEISEGADTQTEKMREIAAEMDDISATTEEMAASAAQVAATSHEAA-RASE-----NG 317
                                       3334444444455555555555555555555555555555555555555555543.3333.....22 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0031
                             Atg14  57 qledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk......kRrsdleslqnelee 127
                                        ++d+ +  +  ++e ksl ++++e + e++d+++  + +++ +   +++ sd ++      + + d   +  e  e
  gi|336253838|ref|YP_004596945.1| 379 HANDEGDGFAVVASEVKSLAEETKEATTEIEDSIEWIQGQTRTTVDDIRETSDRISngvetvEETVDSLEVIVESVE 455
                                       45666666677788889999999999999999999999998888888888888888777755333333333334444 PP

                             Atg14 128 rrkkqiaklqdaik...rieqklsslssktlesrsslcselaklyglrrtsyergkwvfs 184
                                       + ++ i+++ +++    +++++ +s+ ++ +e + +++ e++ ++++ r++    ++vf 
  gi|336253838|ref|YP_004596945.1| 456 EANTGIQQINESTDtqaESTEQVASMIDDVAEISETTAAEASGVADAARSQSTAAREVFG 515
                                       444455555544442225555555555566666888888888888888866655555555 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.8     0.032        21       7      68 ..     110     171 ..     105     188 .. 0.88
   2 ?    2.3   0.0      0.22   1.4e+02      12      66 ..     216     270 ..     208     278 .. 0.78
   3 ?    4.3   0.4     0.053        34      12      65 ..     251     304 ..     240     316 .. 0.61
   4 ?    3.0   0.3      0.13        83       7      65 ..     274     332 ..     271     334 .. 0.84
   5 ?    3.5   0.2      0.09        58      25      65 ..     320     360 ..     311     370 .. 0.74
   6 ?    7.3   1.1    0.0065       4.2       5      65 ..     426     486 ..     419     491 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.032
                             Sec34   7 skeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekL 68 
                                       ++e+e+ +l e+ de+ ++L+e  e+ ++ +e+ ++ +e++eq lee ++ ++ ae  +e+L
  gi|336253838|ref|YP_004596945.1| 110 RREDEIGDLYESFDEMRTSLRESLEETEAAKEEAERERERAEQALEEAEEARSDAERERERL 171
                                       57889999***************************************999988877766666 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.22
                             Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                        +++ e +d +++++  ++   ++vs+ ++++++++e++++  ++++++  ei+e
  gi|336253838|ref|YP_004596945.1| 216 ATSFNEMMDGIESLVGRIQGFATDVSDASRDVRANAESVMDASEDVSDTIAEISE 270
                                       4455566666777777777778899999999999999999999999999999986 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.053
                             Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                        +++++  +++ ++++e++e  ++ +ek++++ ++++++ + ++++   a ++ 
  gi|336253838|ref|YP_004596945.1| 251 AESVMDASEDVSDTIAEISEGADTQTEKMREIAAEMDDISATTEEMAASAAQVA 304
                                       555666666666666666666666666666666666666666655555555543 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.13
                             Sec34   7 skeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                       +++e+++e+ +++d++  + ee+  +  +v++ +++  +a+e+ le  +      +e+e
  gi|336253838|ref|YP_004596945.1| 274 TQTEKMREIAAEMDDISATTEEMAASAAQVAATSHEAARASENGLETAEAAIAAMNEVE 332
                                       56788999999999999999999999999999999999999999988888777777765 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.09
                             Sec34  25 qLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                       + e     +++v+++t +  +a e+l+ee +++ e++e i 
  gi|336253838|ref|YP_004596945.1| 320 TAEAAIAAMNEVEAQTDASVAAIETLHEEIQEVGEITEIIA 360
                                       45556667788888888888888888888888887777665 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.0065
                             Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                       ++++++++ + +e ++e+ ++Le + e++++ ++  ++++e++++  e+++++ ++ +++ 
  gi|336253838|ref|YP_004596945.1| 426 IRETSDRISNGVETVEETVDSLEVIVESVEEANTGIQQINESTDTQAESTEQVASMIDDVA 486
                                       4444445555555555556666666666666666666666666666666666666666655 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3      0.12        74       8      54 ..     110     156 ..      99     169 .. 0.87
   2 ?   -1.4   0.0       3.2   2.1e+03      31      61 ..     240     270 ..     216     284 .. 0.69
   3 ?   -2.3   0.0       6.5   4.1e+03      28      44 ..     308     324 ..     271     351 .. 0.50
   4 ?    8.5   0.1    0.0028       1.8      11      60 ..     392     448 ..     376     456 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                              ApoO   8 pseeptdrLeegvrslRkslepytsavqdelnkvkskvetaeqsvtd 54 
                                       ++e + + L e++ ++R sl + +++++++ ++++   e aeq +++
  gi|336253838|ref|YP_004596945.1| 110 RREDEIGDLYESFDEMRTSLRESLEETEAAKEEAERERERAEQALEE 156
                                       44778999***********************9999999999998765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.2
                              ApoO  31 tsavqdelnkvkskvetaeqsvtdtiasLke 61 
                                       +s ++  ++   ++v++a + v+dtia+++e
  gi|336253838|ref|YP_004596945.1| 240 VSDASRDVRANAESVMDASEDVSDTIAEISE 270
                                       4444555555566667777777777777655 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.5
                              ApoO  28 epytsavqdelnkvksk 44 
                                       ++ + a ++ l++++ +
  gi|336253838|ref|YP_004596945.1| 308 HEAARASENGLETAEAA 324
                                       33333333333222222 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0028
                              ApoO  11 eptdrLeegvrslRkslepytsavqdel.......nkvkskvetaeqsvtdtiasLk 60 
                                       +++++L+e  +++  ++e+ ++++q ++       +++++++ + +++v++t++sL 
  gi|336253838|ref|YP_004596945.1| 392 SEVKSLAEETKEATTEIEDSIEWIQGQTrttvddiRETSDRISNGVETVEETVDSLE 448
                                       466778888888888888888888888866666668888888888888888888885 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 ?    2.9   0.2      0.17   1.1e+02      34      93 ..     123     185 ..     112     193 .. 0.66
   2 ?    4.4   0.1      0.06        38      26      95 ..     212     281 ..     208     300 .. 0.63
   3 ?    6.6   1.7     0.013         8      23     128 ..     262     365 ..     260     373 .. 0.71
   4 ?    8.0   2.6    0.0047         3      26      96 ..     412     491 ..     404     509 .. 0.54

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.17
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHH CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrl 93 
                                       ++  ++l+++lee +  ++eae+  ++ ++ l+e+++  +d     + +  ++ ele e +r+
  gi|336253838|ref|YP_004596945.1| 123 DEMRTSLRESLEETEAAKEEAERERERAEQALEEAEEARSDAereRERLAAVNAELEAEAERF 185
                                       444456777777777777777777777777777776666654334666777777777777666 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.06
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlke 95 
                                       +++  +++++ ++ +e+ + +i+   +++++ +++++   ++    ++d + +i ++s+  +++ ++++e
  gi|336253838|ref|YP_004596945.1| 212 MESIATSFNEMMDGIESLVGRIQGFATDVSDASRDVRANAESVMDASEDVSDTIAEISEGADTQTEKMRE 281
                                       5556666666667777777777777777777777777776666666666666666666666655555543 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.013
                                       HHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHC CS
                         Fib_alpha  23 qdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketida 99 
                                       +d++ +  +  +++ ek+++  +e+ + + ++ee+  +  ++ +   + ++ ++n ++  +  +   +++++++ da
  gi|336253838|ref|YP_004596945.1| 262 SDTIAEISEGADTQTEKMREIAAEMDDISATTEEMAASAAQVAATSHEAARASENGLETAEAAIA-AMNEVEAQTDA 337
                                       56677777777777777777666666666666666666666666666666666788888888888.88899999999 PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 100 qesnirvLqnvlesneqkiqkLeqdidqk 128
                                        +  i+ L + +++   +i+++  di+++
  gi|336253838|ref|YP_004596945.1| 338 SVAAIETLHEEIQEV-GEITEIIADIAEQ 365
                                       999999999988764.4666666666665 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0047
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH..........HHHHHHHHHHHHHHCCCH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkd..........ndnvikksskeleeeilr 92 
                                       ++  + ++++++++++++ ++isn  +++ee+v +++ ++++ ++ +++          + + +++++++++ ++++
  gi|336253838|ref|YP_004596945.1| 412 IEWIQGQTRTTVDDIRETSDRISNGVETVEETVDSLEVIVESVEEANTGiqqinestdtQAESTEQVASMID-DVAE 487
                                       555555555555555555555555555555555555555444444444322222222222345666666666.6666 PP

                                       HHHH CS
                         Fib_alpha  93 lket 96 
                                       + et
  gi|336253838|ref|YP_004596945.1| 488 ISET 491
                                       6665 PP

>> Cytomega_UL84  Cytomegalovirus UL84 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   7.7    0.0035       2.2     135     193 ..     118     177 ..     107     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0035
                     Cytomega_UL84 135 lgeangesqtapatsqeeetaashepekkkekeekkeeededdrnd.drergilcvvsne 193
                                       l e+  e +t+   s ee  aa  e e+ +e+ e+  ee e+ r d +rer  l+ v  e
  gi|336253838|ref|YP_004596945.1| 118 LYESFDEMRTSLRESLEETEAAKEEAERERERAEQALEEAEEARSDaERERERLAAVNAE 177
                                       55777888999999*************************9999988579**999999877 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.6   0.00058      0.37      14      76 ..     112     174 ..     102     192 .. 0.92
   2 ?    2.6   0.2      0.32     2e+02       5      52 ..     260     307 ..     244     323 .. 0.61
   3 ?   -0.6   5.3       3.3   2.1e+03      72      72 ..     389     389 ..     319     509 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00058
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA  14 eeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarl 76 
                                       e+++++l+e+++e++++l e lee ++ + e e+ rer e++ ++++e +++ ++ +e La +
  gi|336253838|ref|YP_004596945.1| 112 EDEIGDLYESFDEMRTSLRESLEETEAAKEEAERERERAEQALEEAEEARSDAERERERLAAV 174
                                       78899**********************************999999999999999999999876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                       ++ d+++e++e  ++ +e+++e+ +e+ ++    +e+ +   ++  + 
  gi|336253838|ref|YP_004596945.1| 260 DVSDTIAEISEGADTQTEKMREIAAEMDDISATTEEMAASAAQVAATS 307
                                       455666666666666666666666666666666666555555544443 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.3
                                       X CS
                              YabA  72 n 72 
                                        
  gi|336253838|ref|YP_004596945.1| 389 V 389
                                       0 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2  12.1     0.076        49     471     530 ..     120     179 ..      90     201 .. 0.49
   2 ?   10.4  23.4   0.00013     0.081     241     513 ..     213     490 ..     203     534 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.076
                           DUF3584 471 eeadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaerrleqlrqaleele 530
                                       e +de     +e+le+ ea++e++++e+e+++++ +ea+ea+++aer  e l++  +ele
  gi|336253838|ref|YP_004596945.1| 120 ESFDEMRTSLRESLEETEAAKEEAERERERAEQALEEAEEARSDAERERERLAAVNAELE 179
                                       223333333444444444444444444444444444444444444443333333333322 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00013
                           DUF3584 241 ekvrpeieklqeefeql....eslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeaidelnqe 313
                                       e+++ +++++   +e+l    ++    +s  +++++a+ e + +  e+v  + ae+ + ++t+++++ e ++e+  +
  gi|336253838|ref|YP_004596945.1| 213 ESIATSFNEMMDGIESLvgriQGFATDVSDASRDVRANAESVMDASEDVSDTIAEISEGADTQTEKMREIAAEM-DD 288
                                       44455544444444443111155556667778888888899999999999999999999999999999877776.68 PP

                           DUF3584 314 lsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkike 390
                                       +sa+ +++aa  +++ a  +++ +  ++++e+++a   ++ +++++  +  + ++ l e++q+v e ++     +++
  gi|336253838|ref|YP_004596945.1| 289 ISATTEEMAASAAQVAATSHEAARASENGLETAEAAIAAMNEVEAQTDASVAAIETLHEEIQEVGEITEIIADIAEQ 365
                                       99999999999999999999999999999999999999999999999999999999999999999887766666665 PP

                           DUF3584 391 eleeeleklkerleaireekdrl.kaaieealealesqlrkqleaqkeelneeekelesrlselklrlds.atateE 465
                                        +  +l+   e ++a  e+      a + + l +  ++   + e  +e ++ +       + e   r+ + +   eE
  gi|336253838|ref|YP_004596945.1| 366 TNLLALNASIEAAHANDEGDGFAvVASEVKSLAEETKEATTEIEDSIEWIQGQTRTTVDDIRETSDRISNgVETVEE 442
                                       55555555444433333333322234444444444444555666666777777666667777766665541555566 PP

                           DUF3584 466 eleqieeadealekaqeelekaeaevealqaeeeqlrkkrdeadealq 513
                                       ++  +e  +e +e+a+  +++ +++    ++  eq+ +  d   e+ +
  gi|336253838|ref|YP_004596945.1| 443 TVDSLEVIVESVEEANTGIQQINESTDTQAESTEQVASMIDDVAEISE 490
                                       667778888888888888888877766555555555555554444433 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 ?    4.7   5.3     0.045        29      67     114 ..     118     165 ..     113     180 .. 0.84
   2 ?    7.5   0.2    0.0062         4      22     108 ..     165     249 ..     162     270 .. 0.79
   3 ?    6.4   0.3     0.014       9.1      63     129 ..     232     296 ..     228     300 .. 0.61
   4 ?    1.9   1.6      0.33   2.1e+02      66     123 ..     271     325 ..     258     335 .. 0.53
   5 ?    0.6   0.3      0.89   5.7e+02      81     110 ..     327     356 ..     314     379 .. 0.64
   6 ?    5.7   1.8     0.024        15      67     108 ..     408     449 ..     403     512 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.045
                              COG2  67 lqeeleevesplaaarkkvesvreklsereeeveskleeakeleekre 114
                                       l e+ +e++++l +  ++ e+++e+ ++ +e+ e+ leea+e+++  e
  gi|336253838|ref|YP_004596945.1| 118 LYESFDEMRTSLRESLEETEAAKEEAERERERAEQALEEAEEARSDAE 165
                                       5678899**********************************9998764 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0062
                              COG2  22 lrhgvpLeslrrdLeaylkllekellelvnedyadFvslSghLvglqeeleevesplaaarkkvesvreklsereee 98 
                                       +r++  L+ +  +Lea ++   + ++++ + d+   +++ g   g  e++e + ++++++++ +es++  ++   ++
  gi|336253838|ref|YP_004596945.1| 165 ERERERLAAVNAELEAEAERFGEVMARCADGDLTQRLEVEGD--GETEAMESIATSFNEMMDGIESLVGRIQGFATD 239
                                       577889999999999999999999********9999999885..999999999999999999999999999999999 PP

                              COG2  99 veskleeake 108
                                       v++  ++ ++
  gi|336253838|ref|YP_004596945.1| 240 VSDASRDVRA 249
                                       8876555443 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.014
                              COG2  63 hLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkldevvekl 129
                                       + +g+ ++++  + ++ a  + v ++ e +s++++e+++  +   + e++re+   + ++++++e++
  gi|336253838|ref|YP_004596945.1| 232 RIQGFATDVSDASRDVRANAESVMDASEDVSDTIAEISEGADT--QTEKMREIAAEMDDISATTEEM 296
                                       5556666666666666666666666666666666666666543..4456667777777776666665 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.33
                              COG2  66 glqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkld 123
                                       g +++ e+++ ++aa ++++++++e++++  ++v +  +ea+++ e  + l+     +
  gi|336253838|ref|YP_004596945.1| 271 GADTQTEKMR-EIAAEMDDISATTEEMAASAAQVAATSHEAARASE--NGLETAEAAI 325
                                       4445555554.34445566666666666666666665555544433..4444444444 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.89
                              COG2  81 arkkvesvreklsereeeveskleeakele 110
                                       a+++ve+ +++  +++e+++++++e  e++
  gi|336253838|ref|YP_004596945.1| 327 AMNEVEAQTDASVAAIETLHEEIQEVGEIT 356
                                       556666666666666666666666554443 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.024
                              COG2  67 lqeeleevesplaaarkkvesvreklsereeeveskleeake 108
                                       +++++e ++ +  +++++++++ + +s+  e+ve+ ++  + 
  gi|336253838|ref|YP_004596945.1| 408 IEDSIEWIQGQTRTTVDDIRETSDRISNGVETVEETVDSLEV 449
                                       7899999999999999**********9999999999987664 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   4.4     0.017        11      80     135 ..     127     182 ..     118     187 .. 0.75
   2 ?    3.6   0.1     0.074        47      78     166 ..     264     354 ..     256     362 .. 0.81
   3 ?   -1.0   0.0         2   1.3e+03      99     135 ..     436     472 ..     415     492 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.017
                           DUF4201  80 thlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqg 135
                                       t l+e l + e+  +e++ e ++ e+ l++ ++  + ++ er++l + n++l+++ 
  gi|336253838|ref|YP_004596945.1| 127 TSLRESLEETEAAKEEAERERERAEQALEEAEEARSDAERERERLAAVNAELEAEA 182
                                       56777777888888888888888888888888888888888888888888777665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.074
                           DUF4201  78 althlkeklhmleselselkkelkekeerlaklrkelykvk.lerdklrkqneklkqq.ggllrvPaLlkDYdktke 152
                                       +++++ e +++ +++++e   e++++ ++ +++ ++  +v  + ++ +r+  + l++   ++  + ++    d  ++
  gi|336253838|ref|YP_004596945.1| 264 TIAEISEGADTQTEKMREIAAEMDDISATTEEMAASAAQVAaTSHEAARASENGLETAeAAIAAMNEVEAQTDASVA 340
                                       66777778888899999999999999999999999999986257999999999998751567789999999999999 PP

                           DUF4201 153 kveekrksvkkLrr 166
                                        +e +++++++  +
  gi|336253838|ref|YP_004596945.1| 341 AIETLHEEIQEVGE 354
                                       99999999998655 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2
                           DUF4201  99 elkekeerlaklrkelykvklerdklrkqneklkqqg 135
                                         ++ ee+ ++l+  +++v++ ++ +++ ne   +q 
  gi|336253838|ref|YP_004596945.1| 436 GVETVEETVDSLEVIVESVEEANTGIQQINESTDTQA 472
                                       4455556666666666666666666666555555554 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0  11.9   0.00066      0.42      34     105 ..     120     191 ..     108     194 .. 0.85
   2 ?    8.7   3.8    0.0035       2.2      15     102 ..     268     355 ..     255     361 .. 0.89
   3 ?   -1.1   2.3       3.8   2.4e+03      68      68 ..     440     440 ..     392     496 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00066
                           DUF4200  34 eelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekleeklee 105
                                       e +++ +  l+e+l++ +   +e +++r+ra++  ee ++++ + e+e ++l a  ++l++e e++ e +++
  gi|336253838|ref|YP_004596945.1| 120 ESFDEMRTSLRESLEETEAAKEEAERERERAEQALEEAEEARSDAERERERLAAVNAELEAEAERFGEVMAR 191
                                       677888999999****************************************99999999999988776665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0035
                           DUF4200  15 leakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeiet 91 
                                       +++  +   +++++++ + +++ ++ +e+  +++++     e  + +++ l+ ae    +  e ea+     a iet
  gi|336253838|ref|YP_004596945.1| 268 ISEGADTQTEKMREIAAEMDDISATTEEMAASAAQVAATSHEAARASENGLETAEAAIAAMNEVEAQTDASVAAIET 344
                                       555566677899***************************************************************** PP

                           DUF4200  92 lkseiekleek 102
                                       l++ei++  e+
  gi|336253838|ref|YP_004596945.1| 345 LHEEIQEVGEI 355
                                       *****998776 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.8
                           DUF4200  68 a 68 
                                       +
  gi|336253838|ref|YP_004596945.1| 440 V 440
                                       1 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   2.5      0.23   1.4e+02      39     114 ..     295     367 ..     273     377 .. 0.62
   2 ?    8.1   0.5    0.0041       2.6      46     119 ..     389     456 ..     385     463 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.23
                          LOH1CR12  39 HlavcAkavAadqaklverikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiiledivpllEtln 114
                                        +a +A +vAa  ++     +  ++ ++t+ a + ++++  a+  ++++ +++l+++++ +  i e i ++ E+ n
  gi|336253838|ref|YP_004596945.1| 295 EMAASAAQVAATSHEA---ARASENGLETAEAAIAAMNEVEAQTDASVAAIETLHEEIQEVGEITEIIADIAEQTN 367
                                       3444555555544433...344566666666667777777777777777777777777777666555555555544 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0041
                          LOH1CR12  46 avAadqaklverikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiiledivpllEtlnelLde 119
                                        vA++ + l+e++ke  ++i+  ++ ++ + ++      ++  ++e sd +s     +e++v++lE + e ++e
  gi|336253838|ref|YP_004596945.1| 389 VVASEVKSLAEETKEATTEIEDSIEWIQGQTRT------TVDDIRETSDRISNGVETVEETVDSLEVIVESVEE 456
                                       699999*****************9999876654......56777777777777777777777777776655444 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 ?   12.2   8.6   0.00023      0.15      17     120 ..     121     221 ..     106     234 .. 0.75
   2 ?    3.2   0.6      0.13        86      25      81 ..     251     307 ..     231     318 .. 0.71
   3 ?    0.1   6.9       1.2   7.6e+02      11     108 ..     282     379 ..     272     385 .. 0.52
   4 ?    4.2   0.3     0.067        43       9      69 ..     424     484 ..     416     509 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                             Mod_r  17 klealvktlpevkqlkeekeellaeneslaeknlslep...eleelrselqekleelkelekefeekeqeldellqk 90 
                                        ++++        +l+e++ee +a+ e+  ++    e+   e ee rs+ + ++e l+++++e+e+  ++  e++ +
  gi|336253838|ref|YP_004596945.1| 121 SFDEM------RTSLRESLEETEAAKEEAERERERAEQaleEAEEARSDAERERERLAAVNAELEAEAERFGEVMAR 191
                                       33333......3445555555555555444333333334448899******************************** PP

                             Mod_r  91 fspdallarLqtavaeaeeeSealaeefle 120
                                       + +  l +rL+++ +   e  e++a +f e
  gi|336253838|ref|YP_004596945.1| 192 CADGDLTQRLEVEGDGETEAMESIATSFNE 221
                                       ****************************86 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                             Mod_r  25 lpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeeke 81 
                                       +++v +  e+ ++ +ae+ + a+ + ++  e+  + ++++++ ee+++  +++ +  
  gi|336253838|ref|YP_004596945.1| 251 AESVMDASEDVSDTIAEISEGADTQTEKMREIAAEMDDISATTEEMAASAAQVAATS 307
                                       466777778888888888888888888888888888888888888777666665554 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.2
                             Mod_r  11 lledeeklealvktlpevkqlkeekeellaenesla..........eknlslep....eleelrselqekleelkel 73 
                                       +  + + ++a ++++              a+  ++a          e+ l+  +     ++e+ +++ ++   +++l
  gi|336253838|ref|YP_004596945.1| 282 IAAEMDDISATTEEM-------------AASAAQVAatsheaarasENGLETAEaaiaAMNEVEAQTDASVAAIETL 345
                                       333333333333322.............2222222233333333333333332235557777777777777778888 PP

                             Mod_r  74 ekefeekeqeldellqkfspdallarLqtavaeae 108
                                       ++e +e  +   e++ +  ++++l  L++++++a+
  gi|336253838|ref|YP_004596945.1| 346 HEEIQEVGEIT-EIIADIAEQTNLLALNASIEAAH 379
                                       88877776544.67777777777777777776654 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.067
                             Mod_r   9 qelledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqeklee 69 
                                        ++ e  + +++ v+t+ ++v++l+   e+++++n  + + n s  ++ e   +++++ ++ 
  gi|336253838|ref|YP_004596945.1| 424 DDIRETSDRISNGVETVeETVDSLEVIVESVEEANTGIQQINESTDTQAE-STEQVASMIDD 484
                                       56777778888888888666999999999999999888877777644332.33333333333 PP

>> DUF5089  Domain of unknown function (DUF5089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1  13.2      0.49   3.1e+02      15     187 ..     119     303 ..     113     310 .. 0.69
   2 ?    7.8  14.1    0.0043       2.8      15     188 ..     318     500 ..     305     505 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.49
                           DUF5089  15 yetakkarkkLesaartqkkTtkelrkQgekLekakqsaikvhknaekgee....lakkikregkvf.vfkspvvdk 86 
                                       ye   + r  L +++++++++ +e ++ +e  e+a ++a +++ +ae+  e    +  ++++e + f ++ + + d+
  gi|336253838|ref|YP_004596945.1| 119 YESFDEMRTSLRESLEETEAAKEEAERERERAEQALEEAEEARSDAERERErlaaVNAELEAEAERFgEVMARCADG 195
                                       77777888889999999999999999988888888888888888887765421114567777776653456666653 PP

                           DUF5089  87 ..ikkwfkkdkkaeeeveeiknkeeeakeeeedkkeeeefipedkel.....vpgeektdkeLekilnglkslkkea 156
                                          +++  + + + e++e+i++  +e ++  e  + + + +++d ++         e + +  e + +++ ++ + a
  gi|336253838|ref|YP_004596945.1| 196 dlTQRLEVEGDGETEAMESIATSFNEMMDGIESLVGRIQGFATDVSDasrdvRANAESVMDASEDVSDTIAEISEGA 272
                                       32556655666667777777777777765555555555555556666343322223344444578999********* PP

                           DUF5089 157 evQnkeikkqkskikdItkvneksekevkkt 187
                                       ++Q++++ +   ++ dI++++e+  +++ ++
  gi|336253838|ref|YP_004596945.1| 273 DTQTEKMREIAAEMDDISATTEEMAASAAQV 303
                                       ********************99877776665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0043
                           DUF5089  15 yetakkarkkLesaartqkkTtkelrkQgekLekakqsaikvhknaekgeelakkik.......regkvfvfkspvv 84 
                                        eta  a + +++  +++++  + ++   e++++  +    + + ae+ + la +          eg  f   + v 
  gi|336253838|ref|YP_004596945.1| 318 LETAEAAIAAMNEVEAQTDASVAAIETLHEEIQEVGEITEIIADIAEQTNLLALNASieaahanDEGDGF---AVVA 391
                                       5566666666666666666666666555555555555555555555555555544331000000223322...3356 PP

                           DUF5089  85 dkikkwfkkdkkaeeeveeiknkeeeakeeeedkk.eeeefipedkel....vpgeektdkeLekilnglkslkkea 156
                                       +++k+++++ k+a +e+e++ +  + +   + d   e  ++i+++ e+    v++ e   +  e+  +g++++++++
  gi|336253838|ref|YP_004596945.1| 392 SEVKSLAEETKEATTEIEDSIEWIQGQTRTTVDDIrETSDRISNGVETveetVDSLEVIVESVEEANTGIQQINEST 468
                                       789999999999999999999988888333333332555566666555222266666677778888899******** PP

                           DUF5089 157 evQnkeikkqkskikdItkvneksekevkkte 188
                                       ++Q +  ++  s i d+++++e + +e++ + 
  gi|336253838|ref|YP_004596945.1| 469 DTQAESTEQVASMIDDVAEISETTAAEASGVA 500
                                       ************************99998776 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 ?    7.1   7.9     0.013       8.4       3      58 ..     118     172 ..     116     189 .. 0.80
   2 ?    3.8   0.2      0.13        86       7      59 ..     226     277 ..     213     283 .. 0.40
   3 ?    5.7   7.2     0.034        22       2      66 ..     281     343 ..     280     352 .. 0.79
   4 ?    3.4   0.2      0.18   1.1e+02       3      63 ..     397     445 ..     384     463 .. 0.48
   5 ?    4.5   0.4     0.086        55       5      39 ..     476     510 ..     472     526 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                            DUF883   3 leaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaera 58 
                                       l + +++++++l+e l+e++  a+eeae+ Rer+e++le+a e+ +dae++ ++ a
  gi|336253838|ref|YP_004596945.1| 118 LYESFDEMRTSLRESLEETE-AAKEEAERERERAEQALEEAEEARSDAERERERLA 172
                                       56678888999999998877.599****************9999999998755544 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.13
                            DUF883   7 leslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerak 59 
                                       +esl+  ++ ++ + +d +++  ++  e ++++ e++ +++++ +e +  +++
  gi|336253838|ref|YP_004596945.1| 226 IESLVGRIQGFATDVSDASRDVRAN-AESVMDASEDVSDTIAEISEGADTQTE 277
                                       4444444444444444333222222.122333333333333333333333333 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.034
                            DUF883   2 eleaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaad 66 
                                       e++ae++++ a++ee++ +aa+ a+ + e++R+  e+ le+a ++++ a+++v++++++ ++a +
  gi|336253838|ref|YP_004596945.1| 281 EIAAEMDDISATTEEMAASAAQVAATSHEAARAS-ENGLETAEAAIA-AMNEVEAQTDASVAAIE 343
                                       789*********************9999999975.667777776666.55557777777776655 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.18
                            DUF883   3 leaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaae 63 
                                       l++e++++++           e ++++e +  + + ++++ re+ ++ ++  +e ++e ++
  gi|336253838|ref|YP_004596945.1| 397 LAEETKEATT-----------EIEDSIEWIQGQTRTTVDDIRETSDRISN-GVETVEETVD 445
                                       2222222222...........33334444444444444444444333333.3333344444 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.086
                            DUF883   5 aeleslladleellkeaadeageeaeelRerleer 39 
                                       + ++s+++d++e+ +++a+ea   a+++R++ +++
  gi|336253838|ref|YP_004596945.1| 476 EQVASMIDDVAEISETTAAEASGVADAARSQSTAA 510
                                       56789999********************9987654 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.9       2.1   1.3e+03     157     157 ..     150     150 ..     113     190 .. 0.53
   2 ?    9.1   7.0    0.0015      0.99      56     183 ..     223     350 ..     202     360 .. 0.66
   3 ?    8.3   6.6    0.0027       1.8     113     195 ..     399     494 ..     353     500 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.1
                               LXG 157 t 157
                                        
  gi|336253838|ref|YP_004596945.1| 150 A 150
                                       1 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0015
                               LXG  56 adlhlplltslqdlieqyeefLkkikealesvepssngfidedfLeqelenglkkakevteelkdeinkilasvsdi 132
                                        d +  l+ ++q + +++++  ++++++ esv  +s++ + +d +  e++ g +   e+++e + e+++i a++ ++
  gi|336253838|ref|YP_004596945.1| 223 MDGIESLVGRIQGFATDVSDASRDVRANAESVMDASED-V-SDTIA-EISEGADTQTEKMREIAAEMDDISATTEEM 296
                                       34788888999999999999999999999994433333.3.55555.699999999999999999999999888887 PP

                               LXG 133 vslpelddsevkdslqkakkkvqetie....kledfdqeqksalanlesdlkalk 183
                                        + +  +  +  +++++a ++  et e    ++++ ++++++++a++e   ++++
  gi|336253838|ref|YP_004596945.1| 297 -AASAAQVAATSHEAARASENGLETAEaaiaAMNEVEAQTDASVAAIETLHEEIQ 350
                                       .666666666677777776665555541111455555555555555554444443 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0027
                               LXG 113 evteelkdeinkil..............asvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksalanl 175
                                       e+t+e + ei++ +              +++sd +s++  + +e +dsl+   + v+e +++++++++++++  +++
  gi|336253838|ref|YP_004596945.1| 399 EETKEATTEIEDSIewiqgqtrttvddiRETSDRISNGVETVEETVDSLEVIVESVEEANTGIQQINESTDTQAEST 475
                                       33333333333333555566666666668899999999999999999999999999999********9999998777 PP

                               LXG 176 esdlkalktyvseLeemtsk 195
                                       e+ ++++   v+e++e+t  
  gi|336253838|ref|YP_004596945.1| 476 EQ-VASMIDDVAEISETTAA 494
                                       65.55666777888877765 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 ?    5.9   6.2     0.023        15      20     101 ..     109     189 ..     101     193 .. 0.78
   2 ?    5.3   0.3     0.035        23      67     104 ..     249     286 ..     214     292 .. 0.61
   3 ?    7.5   1.4    0.0074       4.7      36      99 ..     242     302 ..     235     310 .. 0.68
   4 ?    5.9   6.1     0.024        15      30     100 ..     278     352 ..     276     355 .. 0.75
   5 ?    0.3   0.2       1.2   7.9e+02      81      99 ..     392     410 ..     370     419 .. 0.55
   6 ?    1.6   2.4      0.49   3.2e+02      40     104 ..     418     482 ..     399     486 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.023
                                       CCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  20 kRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleae 96 
                                       +R+ +++  d + + de r +l+  lee  a + e+ +e ++a ++ e+aee + +++   e+l+a++ael++  ++
  gi|336253838|ref|YP_004596945.1| 109 TRR-EDEIGDLYESFDEMRTSLRESLEETEAAKEEAERERERAEQALEEAEEARSDAERERERLAAVNAELEAEAER 184
                                       554.4455666777888888999999999999999999999998888999999999999999999999888887777 PP

                                       HHHHH CS
                      Seryl_tRNA_N  97 lekll 101
                                       + +++
  gi|336253838|ref|YP_004596945.1| 185 FGEVM 189
                                       66665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.035
                                       S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                      Seryl_tRNA_N  67 edaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                       ++ae++++ ++++++ ++++++  ++ ++++ ++++++
  gi|336253838|ref|YP_004596945.1| 249 ANAESVMDASEDVSDTIAEISEGADTQTEKMREIAAEM 286
                                       45555555555555555555555555555555544433 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0074
                                       HHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  36 ekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelek 99 
                                       ++ r +++ +e++   +  +s +I+++++    a+   ++++e+ +e+++++a+ +e+ a   +
  gi|336253838|ref|YP_004596945.1| 242 DASRDVRANAESVMDASEDVSDTIAEISE---GADTQTEKMREIAAEMDDISATTEEMAASAAQ 302
                                       56677888888888888889999999885...45556666666666666666666665554444 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  30 elleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekl 100
                                       ++ e+ +++  + +++ee+ a   +++++ ++a ++     e ae+ ia ++e+ ++++a  a+ ++l +e++++
  gi|336253838|ref|YP_004596945.1| 278 KMREIAAEMDDISATTEEMAASAAQVAATSHEAARASenglETAEAAIAAMNEVEAQTDASVAAIETLHEEIQEV 352
                                       5566666777777777777766665555444444444444*******************************9975 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  81 eelkaleaelkeleaelek 99 
                                        e+k l +e ke+++e+e+
  gi|336253838|ref|YP_004596945.1| 392 SEVKSLAEETKEATTEIED 410
                                       3334444444444444333 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 0.49
                                       HHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                      Seryl_tRNA_N  40 elqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                       +++++++++++ + ++s+ ++   +  +  e ++++v+e ++ ++++++  ++  +  e++++ i
  gi|336253838|ref|YP_004596945.1| 418 QTRTTVDDIRETSDRISNGVETVEETVDSLEVIVESVEEANTGIQQINESTDTQAESTEQVASMI 482
                                       56778888899999999988888888888888888888888888888888888888877777666 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3       4.5   2.9e+03      42      75 ..     127     157 ..     110     162 .. 0.51
   2 ?    2.3   0.0      0.19   1.2e+02      29      69 ..     211     252 ..     201     270 .. 0.78
   3 ?   -0.4   0.0       1.3   8.1e+02      47      78 ..     324     355 ..     297     372 .. 0.57
   4 ?    6.5   0.4    0.0095       6.1      17      86 ..     420     489 ..     392     494 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.5
                              RPW8  42 eritPvvkeieklnkeldrpreeieeLkklLeka 75 
                                       ++++ +++e e  ++e +r+r   e+ ++ Le+a
  gi|336253838|ref|YP_004596945.1| 127 TSLRESLEETEAAKEEAERER---ERAEQALEEA 157
                                       344444444444444444444...4444444444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.19
                              RPW8  29 dfksilkrLestleritPvvkeieklnkel.drpreeieeLk 69 
                                        ++si  + ++++  i+ +v +i+ + +++ d  r++  + +
  gi|336253838|ref|YP_004596945.1| 211 AMESIATSFNEMMDGIESLVGRIQGFATDVsDASRDVRANAE 252
                                       67899999******************9999888776655544 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.3
                              RPW8  47 vvkeieklnkeldrpreeieeLkklLekaekL 78 
                                        ++ +++++++ d   + ie L +++++  ++
  gi|336253838|ref|YP_004596945.1| 324 AIAAMNEVEAQTDASVAAIETLHEEIQEVGEI 355
                                       44444444444444444555555544444333 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0095
                              RPW8  17 lkaileakkksldfksilkrLestleritPvvkeieklnkeldrpreeieeLkklLekaekLVekcsklk 86 
                                          + + +++s  ++  ++  e+t+ +++ +v+ +e+ n+ +++ +e ++   +  e+  +++   ++++
  gi|336253838|ref|YP_004596945.1| 420 RTTVDDIRETSDRISNGVETVEETVDSLEVIVESVEEANTGIQQINESTDTQAESTEQVASMIDDVAEIS 489
                                       5566677777777777888999999999999999999999999999999999999999999999888886 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.7      0.02        13       9      85 ..     113     188 ..     108     196 .. 0.79
   2 ?    6.6   2.4    0.0062       3.9       7      77 ..     240     309 ..     234     365 .. 0.65
   3 ?    0.3   0.3      0.51   3.3e+02       5      85 ..     343     411 ..     320     427 .. 0.48
   4 ?    4.7   2.4     0.024        15      34      87 ..     418     480 ..     386     531 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.02
                             TMPIT   9 kefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkev 85 
                                       +e+ +l e+++e++++l+e  +  ++ ++e++++++r+++  ++ ++ ++++ e+e+e+++ +++el+ + + + ev
  gi|336253838|ref|YP_004596945.1| 113 DEIGDLYESFDEMRTSLRESLEETEAAKEEAERERERAEQALEEAEEARSDA-ERERERLAAVNAELEAEAERFGEV 188
                                       6677788888888889999999999999999999999999999999988885.577778888888888777776655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0062
                             TMPIT   7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelke 77 
                                       +++  ++++++a++++  +e++s  + ++s+ +++q+++++e+ +++++++++++ e +  +++++++ +e
  gi|336253838|ref|YP_004596945.1| 240 VSDASRDVRANAESVMDASEDVSDTIAEISEGADTQTEKMREIAAEMDDISATTE-EMAASAAQVAATSHE 309
                                       5666677777777788888888888888888888888888888888888777754.222222222222222 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.51
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk....eeeeeeveelkeelke 77 
                                       e+l++e++e+ e  +               +  +i++q+ +l +l++s++  +++ +    +  ++ev++l+ee+ke
  gi|336253838|ref|YP_004596945.1| 343 ETLHEEIQEVGEITE---------------IIADIAEQT-NLLALNASIEAAHANDEgdgfAVVASEVKSLAEETKE 403
                                       223333333333333...............333333332.2334444454444443344444444445555555555 PP

                             TMPIT  78 rkkvlkev 85 
                                       +++ +++ 
  gi|336253838|ref|YP_004596945.1| 404 ATTEIEDS 411
                                       44444433 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.024
                             TMPIT  34 kcskeikkqkkrlkelksslkklkksvk.........eeeeeeveelkeelkerkkvlkeves 87 
                                       +++++++  ++   ++++ +++++++v+         ee ++ +++++e+++++ ++ ++v+s
  gi|336253838|ref|YP_004596945.1| 418 QTRTTVDDIRETSDRISNGVETVEETVDslevivesvEEANTGIQQINESTDTQAESTEQVAS 480
                                       222222222222222222222222222222222223344444445555444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2567  (0.143176); expected 358.6 (0.02)
Passed bias filter:                      776  (0.0432818); expected 358.6 (0.02)
Passed Vit filter:                       162  (0.00903564); expected 17.9 (0.001)
Passed Fwd filter:                        99  (0.00552178); 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: 1.84u 0.40s 00:00:02.24 Elapsed: 00:00:00.62
# Mc/sec: 2743.32
//
Query:       gi|336253839|ref|YP_004596946.1|  [L=225]
Description: abortive infection protein [Halopiger xanaduensis SH-6]
Scores for complete 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-10   41.0   8.0    1.9e-10   41.0   8.0    2.1  2  CPBP           CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
      0.072   13.3   0.6       0.38   11.0   0.1    2.2  3  Glycophorin_A  Glycophorin A
        0.2   11.8   1.1        8.9    6.4   0.1    3.0  2  NDUF_B12       NADH-ubiquinone oxidoreductase B12 subunit fam


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 ?   -0.2   1.6      0.22   1.3e+03      35      73 ..      54     102 ..      26     112 .. 0.61
   2 !   41.0   8.0   3.2e-14   1.9e-10       6      89 ..     128     214 ..     123     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.22
                                       .S-HHHHHHHHHHHHHCSGGG...HHHH..........HHHHHHHHHHHHHH CS
                              CPBP  35 gsstlailissilFglaHlpn...gpsv..........llaalaGlvlgyly 73 
                                        + ++ai++ +i  g+   p    g  +          llaa+aG +l +++
  gi|336253839|ref|YP_004596946.1|  54 QW-LVAIAVIAITVGVEDRPLssiG--FrrpawidlgyLLAAAAGALLVFVF 102
                                       34.5555555555555555554440..1333334444477777777776665 PP

  == domain 2  score: 41.0 bits;  conditional E-value: 3.2e-14
                                       HHHHHHHHHHHHHHHHHHTTCHHHHHHHH..S-HHHHHHHHHHHHHCSGGGHHH..HHHHHHHHHHHHHHHHHTT-H CS
                              CPBP   6 lvfllalllapllEEllfRglllqllqer.gsstlailissilFglaHlpngps..vllaalaGlvlgylylktgsl 79 
                                        +++++++ a+++EE+l+Rg+ +++l e+ gs ++a  ++ ++F+laH++  p   +l +a++  ++ ++yl+ ++l
  gi|336253839|ref|YP_004596946.1| 128 PLAIAMAVTAGVVEEILYRGYAIERLLEYsGSALVAGGFTWLAFTLAHAVAWPLgnLLQVAAVTAIFVVVYLRRRTL 204
                                       567899***********************6666******************555679******************** PP

                                       HHHHHHHHHH CS
                              CPBP  80 laaillHall 89 
                                       ++++ +H+l+
  gi|336253839|ref|YP_004596946.1| 205 VPVVGAHVLV 214
                                       *******985 PP

>> Glycophorin_A  Glycophorin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.22   1.3e+03     101     113 ..      69      81 ..      53      82 .. 0.82
   2 ?   11.0   0.1   6.4e-05      0.38      63      89 ..     131     157 ..     127     162 .. 0.88
   3 ?   -3.6   0.1       2.2   1.3e+04      72      84 ..     190     202 ..     187     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.22
                                       XXXXXXXXXXXXX CS
                     Glycophorin_A 101 edvPLssvEietP 113
                                       ed PLss+    P
  gi|336253839|ref|YP_004596946.1|  69 EDRPLSSIGFRRP 81 
                                       899****988777 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6.4e-05
                                       HHHHHHHHHHHHHHHHHHHHHTHSXXX CS
                     Glycophorin_A  63 iifgvmAgvigtillisYlirRliKKs 89 
                                       i ++v Agv+  il+  Y+i Rl   s
  gi|336253839|ref|YP_004596946.1| 131 IAMAVTAGVVEEILYRGYAIERLLEYS 157
                                       889*******************98655 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHT CS
                     Glycophorin_A  72 igtillisYlirR 84 
                                       +  i+++ Yl rR
  gi|336253839|ref|YP_004596946.1| 190 VTAIFVVVYLRRR 202
                                       5679999998887 PP

>> NDUF_B12  NADH-ubiquinone oxidoreductase B12 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.03   1.8e+02      30      45 ..      55      70 ..      52      74 .. 0.89
   2 ?    6.4   0.1    0.0015       8.9      28      49 ..     125     146 ..     120     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.03
                          NDUF_B12 30 fglavaafaaavgyEh 45
                                      + +a+a++a++vg+E 
  gi|336253839|ref|YP_004596946.1| 55 WLVAIAVIAITVGVED 70
                                      678999*******995 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0015
                          NDUF_B12  28 pGfglavaafaaavgyEhflgs 49 
                                       pG+ la+a+++ a ++E++l+ 
  gi|336253839|ref|YP_004596946.1| 125 PGLPLAIAMAVTAGVVEEILYR 146
                                       9*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1675.41
//
Query:       gi|336253840|ref|YP_004596947.1|  [L=925]
Description: DEAD/H associated domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-51  172.6   0.6    1.6e-50  171.6   0.6    1.5  1  DEAD_assoc     DEAD/H associated
    1.4e-29  103.1   0.0      2e-28   99.3   0.0    2.2  2  DEAD           DEAD/DEAH box helicase
    2.9e-18   66.2   0.1    1.6e-16   60.6   0.0    2.4  2  Helicase_C     Helicase conserved C-terminal domain
      7e-08   32.7   0.0    4.1e-07   30.2   0.0    2.0  2  ResIII         Type III restriction enzyme, res subunit
    0.00028   21.2   0.0     0.0029   17.9   0.0    2.6  1  AAA_22         AAA domain
  ------ inclusion threshold ------
      0.013   14.3   0.0      0.025   13.3   0.0    1.4  1  SNF2_N         SNF2 family N-terminal domain
      0.019   15.3   0.0       0.11   12.8   0.0    2.2  2  AAA_19         AAA domain
      0.094   12.2   0.0        3.8    6.9   0.0    2.4  2  UvrD-helicase  UvrD/REP helicase N-terminal 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 !  171.6   0.6     7e-54   1.6e-50       2     191 .]     693     879 ..     690     879 .. 0.96

  Alignments for each domain:
  == domain 1  score: 171.6 bits;  conditional E-value: 7e-54
                        DEAD_assoc   2 PtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldell 78 
                                       P++  + vEr rde+ +++++vhs +Gr++n++l++lla++++++   +v+va++D+g+vl++pl+++++  l+ ++
  gi|336253840|ref|YP_004596947.1| 693 PDRLSIEVERDRDEY-ERHYYVHSNYGRKFNDGLSRLLAYQCAQEATANVRVAVADNGFVLSMPLNRKVD--LEGIF 766
                                       566667788889998.99**********************************************999975..89*** PP

                        DEAD_assoc  79 ellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrev 155
                                       e l+p++++edl+aal +++l++r Fr +A+r+l++++ry+g +k++++q++++++Ll +a+++++f +++e++re+
  gi|336253840|ref|YP_004596947.1| 767 EDLEPEQVREDLRAALSGTDLLQRYFRINATRSLMILKRYKGYEKSASEQQVSSEMLLGFAEDLENFAVIEETYREI 843
                                       ***************************************************************************** PP

                        DEAD_assoc 156 ledqlDlerlaellrriaageirvvevetprpSpfA 191
                                       led+l++++++++++ i++gei v++  +++p+p A
  gi|336253840|ref|YP_004596947.1| 844 LEDKLNVAEIEAVVEAISEGEIAVERQLLDSPTPRA 879
                                       **************************99*****976 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.0     9e-32     2e-28       1     170 [.      58     246 ..      58     253 .. 0.90
   2 ?    1.1   0.0      0.13   2.9e+02      43      91 ..     309     357 ..     296     380 .. 0.64

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 9e-32
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS......TTSTS-EEEEEESSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet......kgktgpkalivePtreLaeqtlnnlkkfk 71 
                                       t+ Q+ aip i +g++ l++a+TGsGKTla +  +++ +y++        ++   +l+v+P+++La+++++nl+  +
  gi|336253840|ref|YP_004596947.1|  58 TPPQRGAIPKIHEGQNTLICAPTGSGKTLASFTSIINYLYKEdrasedGLENSVYCLYVSPLKSLANDIHRNLEVPL 134
                                       688**************************************999998778999************************ PP

                                       TTST..............SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHH CS
                                       xxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                              DEAD  72 kyid..............lrvlliiggvaardqlskldngvdivvgtpgrlddllstgkln..lsqvrflVlDEadr 132
                                       + i+              +r     g+++ +d ++ l+++++i+ +tp+ l+ ll++ k++  l+ v+++++DE++ 
  gi|336253840|ref|YP_004596947.1| 135 EGIEsvvderdddremgeIRHAIRHGDTSSSDRQKMLEETPHILNTTPETLAILLNSPKFRekLRTVEYVIVDEIHS 211
                                       *888888889998888878887778889999999999999***************77776666************** PP

                                       HHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 133 lldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       l   +++ +++  l++l+ +  d   + + i +SAT++
  gi|336253840|ref|YP_004596947.1| 212 LAAGKRGTHLSVSLERLE-AMVD--HDITRIGCSATIE 246
                                       *****************4.4444..34669******96 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.13
                                       TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardql 91 
                                       + + ++ +l+ + tr+ ae +l+nl+++++ +d + + + +g+  +d +
  gi|336253840|ref|YP_004596947.1| 309 HIQAHTNTLVFTNTRSGAERVLHNLRERFDAYDEENSGCHHGSLSKDVR 357
                                       556677899******************9998773333333333333333 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 ?    2.8   0.0     0.063   1.4e+02      39      62 ..     151     174 ..     123     191 .. 0.82
   2 !   60.6   0.0   7.1e-20   1.6e-16       7     108 ..     303     410 ..     299     413 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.063
                                       TTSTEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  39 kgikvavlhgelpqnereeileqf 62 
                                        +i+ a+ hg++++++r+++le+ 
  gi|336253840|ref|YP_004596947.1| 151 GEIRHAIRHGDTSSSDRQKMLEET 174
                                       38999***************9986 PP

  == domain 2  score: 60.6 bits;  conditional E-value: 7.1e-20
                                       HHHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGT CS
                        Helicase_C   7 lell.kleeeggkilifvntidrlek.vklllekk....gikvavlhgelpqnereeileqfnkgesdvLiatdvae 77 
                                       ++ l ++ + + ++l+f+nt++ +e+ ++ l+e++    + ++ ++hg+l+++ r +i  + ++g+ dv+ +++ +e
  gi|336253840|ref|YP_004596947.1| 303 YKSLhEHIQAHTNTLVFTNTRSGAERvLHNLRERFdaydEENSGCHHGSLSKDVRHDIEGRLKDGSLDVVTSSTSLE 379
                                       5555466688999*********887666666777788889************************************* PP

                                       SSSTSTTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  78 rGidipkvnlVinfdlprnvtsyiqriGRtg 108
                                        Gid+p v+lV++++ p++v+ + qriGR+g
  gi|336253840|ref|YP_004596947.1| 380 LGIDMPHVDLVVQVGSPKSVAALLQRIGRAG 410
                                       ******************************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 !   30.2   0.0   1.8e-10   4.1e-07      22     170 ..      69     246 ..      37     247 .. 0.69
   2 ?   -0.6   0.0      0.51   1.1e+03      55      85 ..     309     348 ..     296     376 .. 0.67

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.8e-10
                                       .TTSEEEEEESTTSTHHHHH.HHHHHHH-S.............-EEEEESSHHHHHHHHHHG.......GGGTGG.. CS
                            ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkee........kflflvprkslleqtleef.......kkflseay 82 
                                       ++ ++ li ++TG+GKTl + +++i +l+k+ + +         +l + p ksl +   +++       +++ +e +
  gi|336253840|ref|YP_004596947.1|  69 HEGQNTLICAPTGSGKTLASfTSIINYLYKEDRASedglensvYCLYVSPLKSLANDIHRNLevplegiESVVDERD 145
                                       4567899*************7777888777766669*****999***************888555555444444443 PP

                                       ........GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T... CS
                            ResIII  83 ke......igkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk... 148
                                       ++         + +gd+ ++  ++  +++ +il tt ++l   +   ++ + + +  + +++i+DE H l+a k   
  gi|336253840|ref|YP_004596947.1| 146 DDremgeiRHAIRHGDTSSSdrQKMLEETPHILNTTPETLAILL---NSPKFREKLRTVEYVIVDEIHSLAAGKrgt 219
                                       33554443222233333333333345666677777777777776...5555566666666************96665 PP

                                       ....TTHHHHHT---.SEEEEEESS-S CS
                            ResIII 149 ....swreilekfke.avllglTATpe 170
                                           s +++  ++++  +++g +AT+e
  gi|336253840|ref|YP_004596947.1| 220 hlsvSLERLEAMVDHdITRIGCSATIE 246
                                       666666666555544599999999985 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.51
                                       ......-EEEEESSHHHHHHHHHHGGGGTGG........G CS
                            ResIII  55 e.....kflflvprkslleqtleefkkflseayke....i 85 
                                             ++l++ +++s  e+ l+++++ ++ +++e    +
  gi|336253840|ref|YP_004596947.1| 309 HiqahtNTLVFTNTRSGAERVLHNLRERFDAYDEEnsgcH 348
                                       2334469999999999999999999888888877655552 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.3e-06    0.0029       5     117 ..      71     233 ..      68     246 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                            AAA_22   5 agilvvtGesGtGKT....tllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellralglelka...... 70 
                                        + +++++++G+GKT    t++ ++l++ d++      ++++  +v++   + +k+l++++ r+l+++l++      
  gi|336253840|ref|YP_004596947.1|  71 GQNTLICAPTGSGKTlasfTSIINYLYKEDRA-----SEDGLEnSVYCLYVSPLKSLANDIHRNLEVPLEGiesvvd 142
                                       67899**********33333444455554432.....233333678888888899********************** PP

                            AAA_22  71 ....................erlsseellealeqalrarav.................ielliiDEaqhlr...s.. 105
                                                           +  +++ +le   + l+++                   +e +i+DE++ l    +  
  gi|336253840|ref|YP_004596947.1| 143 erdddremgeirhairhgdtSSSDRQKMLEETPHILNTTPEtlaillnspkfreklrtVEYVIVDEIHSLAagkRgt 219
                                       9999999999999999888844444444444444444444466666666666777888999********98765256 PP

                            AAA_22 106 ..eealeeLrslln 117
                                            le L  +++
  gi|336253840|ref|YP_004596947.1| 220 hlSVSLERLEAMVD 233
                                       77777888877777 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.1e-05     0.025      47     198 ..      63     221 ..      50     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                                       ..HHHHHTT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--H.HHHHHHHHHHHHH-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                            SNF2_N  47 esaeakqsvrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPa.slldqWeneierhvsss 122
                                       + +++ ++ ++ +++  +G GKT+ + + i   ++ +++d++ ++  + ++  L v+P  sl++   +++e  +++ 
  gi|336253840|ref|YP_004596947.1|  63 GAIPKIHEGQNTLICAPTGSGKTLASFTSII--NYLYKEDRASEDGLENSVYCLYVSPLkSLANDIHRNLEVPLEGI 137
                                       56788899999****************9999..56666666667788888889*****9899988888888888888 PP

                                       -EEE--SSHHHH...........-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGG CS
                                       xxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 123 alrvlvyggqkk...........mkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEght 188
                                       +  v   +++ +            + + +  ++ l ++ +++ tt ++l+   + +k r++l  v  ++v++DE h 
  gi|336253840|ref|YP_004596947.1| 138 ESVVDERDDD-RemgeirhairhGDTSSSDRQKMLEETPHILNTTPETLAILLNSPKFREKLRTV--EYVIVDEIHS 211
                                       7644444444.369******99844444555777788899*************999****99876..69******** PP

                                       T--TTSHHHH CS
                                       xxxxxxxxxx RF
                            SNF2_N 189 lknstskaae 198
                                       l  +++ ++ 
  gi|336253840|ref|YP_004596947.1| 212 LAAGKRGTHL 221
                                       *998765554 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     5e-05      0.11       1     114 [.      61     212 ..      61     222 .. 0.75
   2 ?   -1.0   0.0      0.92   2.1e+03      45      78 ..     316     424 ..     299     464 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTr.vlkhivallvelggvkp......eeillvaftgrAakelrerlaalgae. 68 
                                       qr a+   ++ ++ l+ a+ G+GKT    + i+++l ++ + +         +l v++ +  a+ ++ +l   +++ 
  gi|336253840|ref|YP_004596947.1|  61 QRGAIPkIHEGQNTLICAPTGSGKTLaSFTSIINYLYKEDRASEdglensVYCLYVSPLKSLANDIHRNL---EVPl 134
                                       778885589999*************725788889988888776678887778899999999999999999...5554 PP

                            AAA_19  69 .....................................atTiHrlalldfddlltealelleeaeeekklqeeelliv 108
                                                                             +T H l   ++++++   + ll++ + ++kl+  e++iv
  gi|336253840|ref|YP_004596947.1| 135 egiesvvderdddremgeirhairhgdtsssdrqkmlEETPHIL---NTTPET--LAILLNSPKFREKLRTVEYVIV 206
                                       46777777777777777777777776666666666666666655...444443..355677888999997777**** PP

                            AAA_19 109 DEfqdv 114
                                       DE+  +
  gi|336253840|ref|YP_004596947.1| 207 DEIHSL 212
                                       **8765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.92
                            AAA_19  45 illvaftgrAak....elrerlaalgaeatTiHrlal........................................ 77 
                                        l+ + t+  a+    +lrer +a+++e + +H+ +l                                        
  gi|336253840|ref|YP_004596947.1| 316 TLVFTNTRSGAErvlhNLRERFDAYDEENSGCHHGSLskdvrhdiegrlkdgsldvvtsstslelgidmphvdlvvq 392
                                       55556665544411116788888888888888865555566666666666666555555555555555555555555 PP

                            AAA_19  78 ...............................l 78 
                                                                      l
  gi|336253840|ref|YP_004596947.1| 393 vgspksvaallqrigraghrvgqtvagrviaL 424
                                       55555555555555555555555555555444 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 ?    6.9   0.0    0.0017       3.8       5      41 ..      61      99 ..      57     109 .. 0.76
   2 ?    2.4   0.0      0.04        89      29      81 ..     297     349 ..     296     366 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0017
                                      HHHHHHS..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTS CS
                     UvrD-helicase  5 qreaias..lggpilveAsAGsGKTfvlaerilrlikee 41
                                      qr ai +   g+++l+ A  GsGKT      i++ + +e
  gi|336253840|ref|YP_004596947.1| 61 QRGAIPKihEGQNTLICAPTGSGKTLASFTSIINYLYKE 99
                                      55555554589**************98777777776655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-HH CS
                     UvrD-helicase  29 vlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdder 81 
                                       v+ +r+ + ++e+    ++ lv+T T+  ae   + ++e++    +e+s++++
  gi|336253840|ref|YP_004596947.1| 297 VVQDRFYKSLHEHIQAHTNTLVFTNTRSGAERVLHNLRERFDAYDEENSGCHH 349
                                       6778888999999667788********************99999999988874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (925 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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):               8  [number of targets reported over threshold]
# CPU time: 0.78u 0.29s 00:00:01.07 Elapsed: 00:00:00.50
# Mc/sec: 5553.47
//
Query:       gi|336253841|ref|YP_004596948.1|  [L=126]
Description: hypothetical protein Halxa_2450 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.02   14.2   2.3      0.044   13.1   2.3    1.6  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.3   2.4e-06     0.044       3      50 ..       4      52 ..       1     106 [. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-06
                              YdjM  3 gltHallGaalglalaallgaake.avllavavlg.AllPDiDhpsstlg 50
                                       ++H+++Gaa+  ++ ++l ++   ++ l+++  g A++PD+    s ++
  gi|336253841|ref|YP_004596948.1|  4 AIAHFAFGAAMTTLVITFLVPDVRyPRTLLLLGGGwAMIPDFH-WVSPVA 52
                                      459*****************9988744444444446*****86.333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 913.74
//
Query:       gi|336253842|ref|YP_004596949.1|  [L=328]
Description: AIR synthase-like protein domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   96.4   2.6    3.3e-27   95.5   2.6    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain
    3.8e-16   59.5   0.6    3.8e-16   59.5   0.6    2.0  2  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 !   95.5   2.6   3.7e-31   3.3e-27       1     150 [.     148     298 ..     148     303 .. 0.90

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 3.7e-31
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgala 77 
                                       +pGd++ilt+  G+ g ++++++  ++++  dd  +++++++le   i v++ +   ++ ++a+hD T+GG++  l 
  gi|336253842|ref|YP_004596949.1| 148 EPGDRIILTKAAGIEGTAILAADFADDFDV-DDGTRERAEAFLE--EISVVPDARVVREYASAMHDPTEGGVAAGLL 221
                                       69****************888887777775.5567778888888..6666666666689****************** PP

                                       HHHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESS CS
                            AIRS_C  78 emapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGevtake 149
                                       e+a+as+v++e+d d+vp+++e++      + ++l ++ sG ll +vp+ee d +la+l+ +gl eaa+IG vta++
  gi|336253842|ref|YP_004596949.1| 222 ELARASDVQLEVDRDAVPVREETArlcdaAGVDPLQIFGSGALLATVPREEVDDCLAALANAGL-EAAEIGVVTAGG 297
                                       ****************************************************************.8*********97 PP

                                       S CS
                            AIRS_C 150 e 150
                                       +
  gi|336253842|ref|YP_004596949.1| 298 S 298
                                       5 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 !   59.5   0.6   4.2e-20   3.8e-16       1      93 [.      35     137 ..      35     138 .. 0.92
   2 ?   -1.4   0.1      0.43   3.8e+03      53      76 ..     265     297 ..     246     305 .. 0.59

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 4.2e-20
                                       SSSE........EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC....HHHHHHHHHHHH CS
                              AIRS   1 dDaa........vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp....wleevvrglaea 65 
                                       +Daa        +vv+ d    p+ ++  +  G ++v v+++D+aa GA+P++l+++++lp     le++ ++l+ a
  gi|336253842|ref|YP_004596949.1|  35 EDAAaidwpggdLVVSSD----PISLAASQV-GTLGVYVACNDVAASGADPRWLTVVVMLPdeetSLEAITADLQTA 106
                                       588866666666699999....999999999.********************************************* PP

                                       HHHTT-EEEEEEEEEESS...EEEEEEEEEE CS
                              AIRS  66 aeelgvplvgGdtsfsne...ptisvtavGl 93 
                                       a+e+g+++vgG+++  ++   p++s+ta+G 
  gi|336253842|ref|YP_004596949.1| 107 ADEVGASIVGGHSEYVDQlerPLLSLTAMGA 137
                                       **************9988899********96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.43
                                       C......HHHHHHHHHHHH...HHHTT-EEEEE CS
                              AIRS  53 p......wleevvrglaea...aeelgvplvgG 76 
                                              +++++++ la+a   a+e+gv ++gG
  gi|336253842|ref|YP_004596949.1| 265 LatvpreEVDDCLAALANAgleAAEIGVVTAGG 297
                                       234556644444444444433367788888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2526.57
//
Query:       gi|336253843|ref|YP_004596950.1|  [L=65]
Description: hypothetical protein Halxa_2452 [Halopiger xanaduensis SH-6]
Scores for 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:                       144  (0.00803168); expected 358.6 (0.02)
Passed bias filter:                      134  (0.00747392); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 505.15
//
Query:       gi|336253844|ref|YP_004596951.1|  [L=61]
Description: hypothetical protein Halxa_2453 [Halopiger xanaduensis SH-6]
Scores for 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:                       162  (0.00903564); expected 358.6 (0.02)
Passed bias filter:                      137  (0.00764125); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 455.01
//
Query:       gi|336253845|ref|YP_004596952.1|  [L=287]
Description: phosphoesterase PA-phosphatase-like protein [Halopiger xanaduensis SH-6]
Scores for 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-19   68.7   1.2      4e-19   68.7   1.2    2.1  2  PAP2      PAP2 superfamily
    3.3e-07   30.2  16.5    1.3e-06   28.2  11.2    3.0  2  PAP2_3    PAP2 superfamily


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   1.2   4.5e-23     4e-19       4     129 ..      55     165 ..      52     169 .. 0.83
   2 ?   -1.5   0.2      0.21   1.9e+03      88      91 ..     257     260 ..     202     275 .. 0.63

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 4.5e-23
                              PAP2   4 alllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkrk 80 
                                       ++ +a+a  ++ + ++K l+g pRP  + +++                 +++fPSgH+ +a++++  l++ + r r 
  gi|336253845|ref|YP_004596952.1|  55 VVSYAVAGLGF-VLAIKALFGLPRPPDAVVYEAVELEGA----------NDGFPSGHAFAATVVYGGLCAAYERVRD 120
                                       33344444333.5778****************9999965..........47************************** PP

                              PAP2  81 kiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayr 129
                                       +    +++l + ++++lvalsR++lgvH+l DvlaG+++G+ ++a++ r
  gi|336253845|ref|YP_004596952.1| 121 P----RALLAVGAVVALVALSRVVLGVHYLGDVLAGIALGVGFLAAMGR 165
                                       *....56666666679*************************99987755 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.21
                              PAP2  88 alil 91 
                                       al++
  gi|336253845|ref|YP_004596952.1| 257 ALVA 260
                                       1222 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2  11.2   1.5e-10   1.3e-06      39     188 ..      32     160 ..      20     162 .. 0.71
   2 ?    1.6   0.2     0.022     2e+02      16      51 ..     235     270 ..     230     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.5e-10
                            PAP2_3  39 lhfqvtllvlvllflrrrerlreflttlllatllgllvyalfPaagPrlleeagfvdtvaaaslagalrdgasravl 115
                                       + ++v+l+vl++l+ ++r+r   ++   ++ +  +l++ alf   +P        +d+v                  
  gi|336253845|ref|YP_004596952.1|  32 TVPLVVLAVLFWLAGKDRRRPALVVSYAVAGLGFVLAIKALFGLPRP--------PDAVVYE-------------A- 86 
                                       56889999999998777777777777777777789999999999999........1111111.............1. PP

                            PAP2_3 116 lrgtienglaafPSlHvawallva....lalwrlrrkrllrvlalllnvlmivatvatgnHYlvDviaGvalalvai 188
                                           +e++   fPS H+  a++v+    +a+ r+r+  +  +++ ++++l++++ v++g HYl Dv+aG+al+++ +
  gi|336253845|ref|YP_004596952.1|  87 --VELEGANDGFPSGHAFAATVVYgglcAAYERVRDP-RALLAVGAVVALVALSRVVLGVHYLGDVLAGIALGVGFL 160
                                       ..122334555******99998742211222334444.566666688999**********************98765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.022
                            PAP2_3  16 aalnklllahpalavilalaYaslhfqvtllvlvll 51 
                                       aa+++ll++ +a+  +l   Ya+l  +++l++++++
  gi|336253845|ref|YP_004596952.1| 235 AAVAQLLESVTAVVPLLVGLYAALVAWILLAPVAVA 270
                                       567779999999999999999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2205.77
//
Query:       gi|336253846|ref|YP_004596953.1|  [L=397]
Description: formyl-CoA transferase [Halopiger xanaduensis SH-6]
Scores for 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-124  415.3   0.0   2.7e-124  415.0   0.0    1.0  1  CoA_transf_3  CoA-transferase family III


Domain annotation for each model (and alignments):
>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.0   0.0  1.5e-128  2.7e-124       1     368 []       6     373 ..       6     373 .. 0.98

  Alignments for each domain:
  == domain 1  score: 415.0 bits;  conditional E-value: 1.5e-128
                      CoA_transf_3   1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegre 77 
                                       L++v V+dl+q++ G +++ +L+ lGA+V+kvEpp  g+p+R     +++ge    +++n  K +++l+lk e g+e
  gi|336253846|ref|YP_004596953.1|   6 LEDVDVIDLGQIYNGAYGSLMLSYLGADVTKVEPP-FGEPLRSR-VADGDGEPPELVMLNSTKAGITLNLKAERGKE 80 
                                       899********************************.******86.55557*************************** PP

                      CoA_transf_3  78 llkrLvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdg 154
                                       l+k+Lv++ADV++eNf pg++e +glgye+l++inP+Liya+ sg+G++Gpk++r ++Dl++qa+sG+m++tg pd+
  gi|336253846|ref|YP_004596953.1|  81 LFKDLVRDADVLVENFAPGTMEEFGLGYETLSEINPELIYAHGSGFGEDGPKSDRLAMDLIVQAESGVMDVTGRPDD 157
                                       ***************************************************************************** PP

                      CoA_transf_3 155 pPvkvgvplgDivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgnrdp..aaa 229
                                       pP+k+g++ gD+++g+++a+++laal++r rtG+Gq +++s+ +a+   l  ql++y  + +vp+r+gnr+   a a
  gi|336253846|ref|YP_004596953.1| 158 PPTKTGIAPGDFLGGIHLAAGVLAALYQRARTGEGQFVEASMQDAVYPSLMSQLANYYDDADVPSRTGNRHSslAKA 234
                                       ************************************************************************88999 PP

                      CoA_transf_3 230 pygvyrtkdgwvaiaaatdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaag 306
                                       py++y++ dg+vai +++d++w+alc+a++r++l++d+rfatn +r+e+ + +da+++ew+++rt++e++++l+aag
  gi|336253846|ref|YP_004596953.1| 235 PYNAYEADDGYVAILCTSDDHWRALCEAIDREDLRDDDRFATNVDRVERMETVDAAIEEWTRTRTRDEIETTLSAAG 311
                                       ***************************************************************************** PP

                      CoA_transf_3 307 vpaapvntleevlddpqlaarglvvevddpdygevpvvglpvrlsetparvkraaPklGedt 368
                                       vp++ v++++ev++dp+l +r++vve+d+p+ ge++v+g+p+rlse       +aP+ Ged+
  gi|336253846|ref|YP_004596953.1| 312 VPCGSVQSVKEVIHDPHLEEREMVVEIDHPTEGEIRVPGTPIRLSESAKPDIEPAPRKGEDN 373
                                       ***********************************************99999999*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2975.97
//
Query:       gi|336253847|ref|YP_004596954.1|  [L=477]
Description: acetaldehyde dehydrogenase [Halopiger xanaduensis SH-6]
Scores for complete 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   69.8   0.2    1.1e-17   63.7   0.2    2.1  2  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 !   63.7   0.2   6.1e-22   1.1e-17      25     291 ..      12     278 ..       3     286 .. 0.82
   2 !    3.8   0.0    0.0009        16     375     427 ..     354     410 ..     350     419 .. 0.75

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 6.1e-22
                                       -B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHH..HHTHHHHHHHHHHHH---HHHHHHHHHHHHHHHHH CS
                            Aldedh  25 aataedvdaavaaAkeafkawaklpaeeRaeiLrkaadll..eerkeelaeletletGkplaearaeveeaidvlry 99 
                                       a t+++v a++++A++a+++ ++ + ++  e+++++  ++  e+r+ e++e+ +++tG    e +  ++   +  r 
  gi|336253847|ref|YP_004596954.1|  12 AETSATVGACLERARAAMDEISHYDQAQVDELVQAIGWAIyeEDRAREISEVAVRDTGFGNVEDK--IT---KKRRK 83 
                                       568899******************************99984457899**********94433333..33...34455 PP

                                       HHHHHHHHSE.EE...EEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHHHHH CS
                            Aldedh 100 yaelaekleg.ev...lpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsalll 172
                                       +a+ +++l g  +   ++ +e++ ++   +P+Gvvga++P   P  ++a  +++a+   N++v+ P++    ++ l+
  gi|336253847|ref|YP_004596954.1|  84 TAGTLDDLLGaPSvgvIERDEETGITEIAKPVGVVGAVVPSTNPGTTPANLAMMAVKGRNAIVVSPSPAGRSTCELV 160
                                       55555554443331214556888999999*********************************************999 PP

                                       HHHHHH....TTS-TTSEEE--SS.TCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE CS
                            Aldedh 173 aelfee....aglPkgvlnvvtgs.gsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknpliv 244
                                       +  +++    +g P++++++++ + ++e   +l+  +++d++  tGs +  r+  ++     ++      G++  iv
  gi|336253847|ref|YP_004596954.1| 161 VDYIRDelekVGAPRDLVQMLPAPvEKEKTYELM--DRCDLLQVTGSASNVRRGERS----GTPNYCVGEGNAVSIV 231
                                       98875422227**********9964444444454..58*********8776664443....468888899******* PP

                                       -TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHH CS
                            Aldedh 245 ledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklve 291
                                        + aDl++++++i+k+ ++     C++ + +++ es+yd+ v++l +
  gi|336253847|ref|YP_004596954.1| 232 DATADLEATADRIAKSKTFDYATSCSSDNAAVIVESVYDDAVAALEA 278
                                       ******************************************99876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0009
                                       EEEEEESSHHHHHHHHHS....SSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSS CS
                            Aldedh 375 lsvikfkdeeeaieiaNd....teyGLaagvftkdleraervaerleaGnvyiNdst 427
                                       l+++++ d++ a+e   d       G + g++t++ +++ r+ +++++  + iN+++
  gi|336253847|ref|YP_004596954.1| 354 LTLYEAADFDAALETTSDilafEGSGHSCGLHTTNDDHVDRIGHEIDVARLLINQPQ 410
                                       555566666666665555222235699***************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3448.00
//
Query:       gi|336253848|ref|YP_004596955.1|  [L=498]
Description: hypothetical protein Halxa_2457 [Halopiger xanaduensis SH-6]
Scores for complete 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-126  422.9  38.8   1.5e-126  422.5  38.8    1.1  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 !  422.5  38.8  8.2e-131  1.5e-126       1     409 []      24     447 ..      24     447 .. 0.96

  Alignments for each domain:
  == domain 1  score: 422.5 bits;  conditional E-value: 8.2e-131
                              TctA   1 LllvllGvllGtliGllPGlhatlavalllpltfgldpeaalilllgiyvgaifggsipaillgvPGtpssvatvld 77 
                                       L++++lG+++G+++G++PG++at++++l+ p+t+ ++ +aali+l+++y ga++ggsipail+++PG p sv+t++d
  gi|336253848|ref|YP_004596955.1|  24 LFAIVLGTAIGVIFGAIPGFSATMTIVLFTPITIPFESTAALIFLVSAYGGAVYGGSIPAILINTPGAPGSVVTCWD 100
                                       789************************************************************************** PP

                              TctA  78 gyplakqGrageAlrlaaigSfiGglvsvllllllapllakvalkfgpaeyfalillglvliailseksllkglial 154
                                       gy+l+kqGra  Al+++ai S+++glv++ +ll++ap+++++al+fg++e+f+l++++l++i +  + sl+k+l+a+
  gi|336253848|ref|YP_004596955.1| 101 GYELTKQGRAVYALAVSAIVSGLAGLVAAAFLLVFAPPISEFALNFGSPEMFLLAVFALTIIPAAKGASLTKALLAG 177
                                       ***************************************************************************** PP

                              TctA 155 llglllgtvgldpnsgtpRftfgsielldgislvpvliGlFgiselltsleskskip.............lslkdlk 218
                                       l+gll+gt+g dp+ +++R tfg++ ll+g+++v+vliGlF ++e+++ + ++s+ +                + + 
  gi|336253848|ref|YP_004596955.1| 178 LFGLLIGTIGNDPQLSQSRATFGQTTLLEGVDFVVVLIGLFVLAEVFRLAYRGSTVTgdqnveggmsevyDAARSVA 254
                                       **************************************************987776688888777655442334444 PP

                              TctA 219 kslptilrgsliGtivGilPgvGasiaaflayavakrlskk..pekfgkgaiegvaapeaannaaaggaliplltlg 293
                                       +   +++rg+liGt+vG lPg+Ga++a+f++y++akr++ +  ++kfg+g iegv+a+ ++nna+ ggalip+ltlg
  gi|336253848|ref|YP_004596955.1| 255 ARPLEFARGTLIGTFVGSLPGAGADVANFVSYNEAKRWASDelSDKFGTGIIEGVIAADSSNNATQGGALIPTLTLG 331
                                       56677********************************987623589******************************* PP

                              TctA 294 ipgsgvaavllgallihglqpgpeLftenpelvyallasllianvlllvlgllliklfakllkipkelLlpiilvll 370
                                       ipgsg++a+llga+ +hgl+pgp Lf ++ ++vya+++sl+i+nvl+l+ gl  +++f kl +ip ++++p ++vl+
  gi|336253848|ref|YP_004596955.1| 332 IPGSGSTAALLGAIALHGLNPGPGLFDSSGDIVYAMILSLFIGNVLILIYGLSGSRYFGKLAYIPIRYIIPSVAVLS 408
                                       ***************************************************************************** PP

                              TctA 371 vigayalnnslfdvlvmlifgvlGlllrrlgvplaplvl 409
                                       +ig +a++n  +d++++lifg++G+l+  +++pl+ lvl
  gi|336253848|ref|YP_004596955.1| 409 IIGGFAVRNAPVDLYIVLIFGLVGILFIVYDYPLVSLVL 447
                                       **********************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); 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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:01.15
# Mc/sec: 1313.88
//
Query:       gi|336253849|ref|YP_004596956.1|  [L=196]
Description: hypothetical protein Halxa_2458 [Halopiger xanaduensis SH-6]
Scores for 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-15   56.2   4.4    7.1e-15   55.5   4.4    1.4  1  TctB      Tripartite tricarboxylate transporter TctB family


Domain annotation for each model (and alignments):
>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   4.4     4e-19   7.1e-15       6     134 ..      30     196 .]      13     196 .] 0.68

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 4e-19
                              TctB   6 lllllagvafavgald....tgarvgpgffPlllgvllallgllllv.............................. 48 
                                       l+l+++ +++ +++ +    ++   gp ++    + +la++   +lv                              
  gi|336253849|ref|YP_004596956.1|  30 LVLAFC-LFYYWDTRAlpdlSMLYAGPLLYA---TTALAVI---TLVqqavsldgspdedgdglwtataitdpkpet 99 
                                       344553.333454444333211222222222...2222222...222444566788888888888888999999999 PP

                              TctB  49 ..........aadgekeekearedwrkllklvlallaalllyallleplGfilatalflllll..greerkwlkali 113
                                                 ++ +++++++ ++d +  ++  ++l+ ++ +y+++lep+Gf++at+++l+++l  + +e+++ ++ +
  gi|336253849|ref|YP_004596956.1| 100 gtesepgtasETTADRDAEATATDSPFTVRNAALLIGLTTAYVVVLEPVGFLIATVAYLAATLylF-GEESLFVLTF 175
                                       99999999984444444445555555555555566668888***************7777777653.699******* PP

                              TctB 114 lavvlallvyllFtklLgvpL 134
                                       +++++a+l++++F ++L+vpL
  gi|336253849|ref|YP_004596956.1| 176 YSIGFAFLLWIVFIQWLRVPL 196
                                       ********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1432.57
//
Query:       gi|336253850|ref|YP_004596957.1|  [L=341]
Description: hypothetical protein Halxa_2459 [Halopiger xanaduensis SH-6]
Scores for 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-16   58.3   0.0    8.2e-16   57.9   0.0    1.1  1  TctC            Tripartite tricarboxylate transporter family 
     0.0035   17.0   0.0     0.0071   16.0   0.0    1.5  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
  ------ inclusion threshold ------
      0.058   12.7   1.2       0.13   11.6   1.2    1.6  1  UCR_Fe-S_N      Ubiquitinol-cytochrome C reductase Fe-S subun


Domain annotation for each model (and alignments):
>> TctC  Tripartite tricarboxylate transporter family receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   1.4e-19   8.2e-16       3     196 ..      58     247 ..      57     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.4e-19
                              TctC   3 RvvakklseklgqpvvveNkagaGgiigtdlvakaapDGytillvatslavaphlYkkvpydsekdlqpislvatlp 79 
                                       Rv +   se l   + veN++g    +g + + ++ +DG+t+++  ++ + a +l+++ py+ ++d+ ++ +    p
  gi|336253850|ref|YP_004596957.1|  58 RVTTPTWSELLDIDFAVENHPGGSTQVGGEELYNSEADGFTLAMWNMPQMQATWLFQNAPYR-IEDFDYLGTHHWDP 133
                                       555666788899999***********************************************.9************* PP

                              TctC  80 lvLvvpadspfkdlqelvayakanPgKlsyasaGigtslhLaaellaskagvellhvPYkGssqavsdLlageVdsm 156
                                       +   +p++sp++dl+++v ya++n   +  ++a ig  + L+a l++++ +++l+ v   G+s   +++lag +d  
  gi|336253850|ref|YP_004596957.1| 134 TMWFAPPGSPYEDLEGFVDYARENGATVGITAA-IGN-TALSALLVEETFDLDLTIVNMEGGSGVRQAVLAGDIDAG 208
                                       ***********************9888775432.333.358888889999999999*******************96 PP

                              TctC 157 iaslasalqrikagklralavtsedRsarlPdvptvaEsg 196
                                       +++  + ++      +  l+    + ++  P  p+  E g
  gi|336253850|ref|YP_004596957.1| 209 VNQPWAFNPDYV-DDVISLGSHTAEQQELWPGAPAFGEFG 247
                                       665555444332.234455555555555556666655555 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 !   16.0   0.0   1.2e-06    0.0071      88     170 ..     135     222 ..     133     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-06
                                       EEEEETTSS--SHHHH...GG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEE CS
                    Phosphonate-bd  88 viivradsdiqsledL...kgktiafvspsStsGylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdadaa 161
                                        ++++++s+++ le +   + ++ a v  +++ G  + +alLv e   d+  d++ v + + +++ +avl+gd+da+
  gi|336253850|ref|YP_004596957.1| 135 MWFAPPGSPYEDLEGFvdyARENGATVGITAAIGNTALSALLV-EETFDL--DLTIVNMEGGSGVRQAVLAGDIDAG 208
                                       68999******99977777888889999999***********8.666665..589999******************* PP

                                       E.....EEHHHHHH CS
                    Phosphonate-bd 162 a.....vsadaled 170
                                       +     ++ d ++d
  gi|336253850|ref|YP_004596957.1| 209 VnqpwaFNPDYVDD 222
                                       95555544444444 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.2   2.2e-05      0.13       7      29 ..       4      24 ..       2      27 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.2e-05
                        UCR_Fe-S_N  7 deptRRDFLyiATgavgaVGaaa 29
                                      ++++RR+F+  A+ga+g  G+aa
  gi|336253850|ref|YP_004596957.1|  4 KNTSRREFI--AAGATGLAGTAA 24
                                      689*****9..99****999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2618.51
//
Query:       gi|336253851|ref|YP_004596958.1|  [L=325]
Description: aryl-alcohol dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-68  229.1   0.0    7.3e-68  228.9   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
       0.15   11.6   1.0         10    5.8   0.1    2.6  2  Trimer_CC     Trimerisation motif


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 !  228.9   0.0   8.2e-72   7.3e-68       1     291 [.      15     314 ..      15     317 .. 0.94

  Alignments for each domain:
  == domain 1  score: 228.9 bits;  conditional E-value: 8.2e-72
                                       .EEEE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE... CS
                      Aldo_ket_red   1 elglGtwqlgsk....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv... 70 
                                       +l+lG +++g++    ++ ++ee  e+++ra++ GinffDtA++Y kg+se++lG++l+    +r+  ++atK    
  gi|336253851|ref|YP_004596958.1|  15 RLCLGCMSFGDPdwreWVLEEEEGTEIIDRAIDLGINFFDTANMYSKGESERILGNVLEG--YDRDWPVVATKAyme 89 
                                       59*********9***99*******************************************..************998 PP

                                       --SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--.HHHH CS
                      Aldo_ket_red  71 dlrdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfs.veql 146
                                        + d ++ sgls++ i+++l++sl rLg d+vDl+++Hr+d ++p iee+++al++ v+   +r+iG S+   ++  
  gi|336253851|ref|YP_004596958.1|  90 MDEDNPNASGLSRKAIEQELQNSLDRLGMDTVDLYQIHRWDDETP-IEETMRALDDAVRRQQARYIGASSMWaHQFA 165
                                       88999****************************************.***********************65526666 PP

                                       HHH...HHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------. CS
                      Aldo_ket_red 147 eka...kkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd. 219
                                       e++    + +  ++v+ q +ynl+ ++ee+++l+lc+k+g++++++spl++G+l +  ++ + + ++e+ ++l ++ 
  gi|336253851|ref|YP_004596958.1| 166 ESLhasDRLGLERFVTMQDHYNLVYREEEREMLPLCEKEGIGVMPWSPLARGYLARPAEEIDATARGESGDKLYEHp 242
                                       7776655556667******************************************9999999999999888888889 PP

                                       TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS
                      Aldo_ket_red 220 ertsknldaaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaelde 291
                                        r  + ++ +e++ ela+e+gv++aq+al+++l+++ v  +i+g++++e+le+ ++ale+ lse++ a+l+e
  gi|336253851|ref|YP_004596958.1| 243 YREGGGQEINERVAELAAEKGVTMAQIALAWLLHKDWVDAPIIGTTSVEHLEQAVEALEVSLSESDQAYLEE 314
                                       99999*************************************************************999987 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0011        10      32      45 ..     103     116 ..     101     122 .. 0.87
   2 ?    3.7   0.1    0.0049        44      24      41 ..     135     152 ..     132     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHH CS
                         Trimer_CC  32 qatVQelQkRLDrL 45 
                                       +a+ QelQ  LDrL
  gi|336253851|ref|YP_004596958.1| 103 KAIEQELQNSLDRL 116
                                       5888*********9 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0049
                                       HHHHHHHHHHHHHHHHHH CS
                         Trimer_CC  24 LEEelrkLqatVQelQkR 41 
                                       +EE +r L   V  +Q R
  gi|336253851|ref|YP_004596958.1| 135 IEETMRALDDAVRRQQAR 152
                                       69**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2641.00
//
Query:       gi|336253852|ref|YP_004596959.1|  [L=918]
Description: DNA replication factor Dna2 [Halopiger xanaduensis SH-6]
Scores for 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-39  134.7   0.5    1.2e-18   67.8   0.4    2.6  2  AAA_11           AAA domain
    1.2e-38  132.7   0.0    1.9e-38  132.1   0.0    1.3  1  AAA_12           AAA domain
    1.9e-19   70.3   0.0    6.6e-18   65.3   0.0    2.2  1  Dna2             DNA replication factor Dna2
    3.1e-17   62.9   0.8    9.6e-17   61.3   0.4    2.1  2  AAA_30           AAA domain
    5.6e-14   52.7   0.1    3.7e-13   50.0   0.0    2.1  2  PDDEXK_1         PD-(D/E)XK nuclease superfamily
    5.1e-13   49.6   0.1    2.5e-12   47.3   0.2    2.2  2  AAA_19           AAA domain
    8.3e-07   29.0   0.0     0.0033   17.2   0.0    3.1  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    1.1e-05   25.2   0.0    1.8e-05   24.4   0.0    1.4  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
    5.2e-05   23.4   0.0    0.00032   20.9   0.0    2.2  2  Cas_Cas4         Domain of unknown function DUF83
    7.2e-05   22.7   0.1    0.00027   20.8   0.0    2.0  2  Helicase_RecD    Helicase
    0.00047   20.4   0.0     0.0017   18.6   0.0    2.0  1  AAA_22           AAA domain
    0.00088   19.7   0.4    0.00088   19.7   0.4    2.6  2  AAA_16           AAA ATPase domain
     0.0015   18.6   0.0     0.0032   17.5   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
     0.0072   16.7   0.1         57    4.2   0.0    4.8  4  DUF4350          Domain of unknown function (DUF4350)
     0.0086   15.5   0.1      0.033   13.6   0.1    1.8  2  PhoH             PhoH-like protein
  ------ inclusion threshold ------
      0.011   16.2   0.1      0.037   14.5   0.1    1.9  1  AAA              ATPase family associated with various cellul
      0.012   15.1   0.0       0.03   13.8   0.0    1.6  2  AAA_7            P-loop containing dynein motor region
      0.021   14.5   0.0      0.042   13.6   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.029   14.2   0.0      0.058   13.2   0.0    1.5  1  UvrD_C_2         UvrD-like helicase C-terminal domain
      0.067   12.2   0.0       0.15   11.1   0.0    1.6  1  T2SSE            Type II/IV secretion system protein
      0.069   13.0   0.0        0.2   11.5   0.0    1.8  1  PDZ_6            PDZ domain
      0.081   12.6   0.0       0.42   10.3   0.0    2.0  2  AAA_24           AAA domain
      0.085   13.4   0.1        4.8    7.7   0.0    3.0  2  AAA_18           AAA domain
       0.09   12.4   0.1       0.36   10.4   0.0    2.1  3  SRP54            SRP54-type protein, GTPase domain
      0.099   12.2   0.8       0.23   11.0   0.0    2.1  1  AAA_25           AAA domain
        0.1   11.8   0.0       0.41    9.8   0.0    1.9  1  DUF2075          Uncharacterized conserved protein (DUF2075)
        0.1   12.6   0.1       0.39   10.7   0.0    2.0  2  AAA_5            AAA domain (dynein-related subfamily)
       0.13   12.0   0.0       0.29   10.8   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.21   10.7   0.0          4    6.5   0.0    2.1  2  PIF1             PIF1-like helicase


Domain annotation for each model (and alignments):
>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   2.2e-20   1.4e-17       3     111 ..     540     635 ..     538     643 .. 0.95
   2 !   67.8   0.4     2e-21   1.2e-18     192     258 ..     645     708 ..     638     711 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 2.2e-20
                            AAA_11   3 ndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrgll 79 
                                       n+ q+ea+++a+  ++ +li+GPPGtgKT ti+  ++++          ++++r+L++a +N AvD+ le ll+   
  gi|336253852|ref|YP_004596959.1| 540 NARQNEAVTKAVGAKDCALIHGPPGTGKTYTIARAIRAM---------VERGERVLLSAFTNRAVDNALEALLE--- 604
                                       899************************************.........799***********************... PP

                            AAA_11  80 dsegekykpkivRvgneeeriseavksvslee 111
                                       + eg   + +ivRvg+e+  ++++++++ le+
  gi|336253852|ref|YP_004596959.1| 605 QLEGVIDEDRIVRVGSES-GVRDDMEPYRLER 635
                                       999***************.8999999988876 PP

  == domain 2  score: 67.8 bits;  conditional E-value: 2e-21
                            AAA_11 192 vldeaeivltTlsgagsklleklakkfdvviIDEAaqavEpstliPlrlgakkvvLvGDpkQLpatv 258
                                        l++a++v++T +++gs+ ++++   fd+ ++DEAaq +Ep t  ++ l+ +++vLvGD+ QLp++v
  gi|336253852|ref|YP_004596959.1| 645 ELQNAQVVAATTATCGSRIMKEQ--SFDAALVDEAAQLTEPGTCAAINLA-ERFVLVGDHEQLPPVV 708
                                       699********************..8************************.***************9 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.1   0.0   3.1e-41   1.9e-38       1     198 [.     714     900 ..     714     901 .. 0.88

  Alignments for each domain:
  == domain 1  score: 132.1 bits;  conditional E-value: 3.1e-41
                            AAA_12   1 lerSlferllkkekekvvlLdtqYRmhpeIsrfpsklfYkgkLkdae.svkkrele......aqealeepleplvfi 70 
                                       l++Slferl++ ++e+ v+Ld qYRm+++I  f+s++fY+gkL+ ae  v+ r+l+        +  e+   p+ f+
  gi|336253852|ref|YP_004596959.1| 714 LSESLFERLVDLHPEAGVMLDRQYRMNQRIQAFASREFYDGKLRPAEpAVAARTLNdlegvaRADLPENLRDPVSFV 790
                                       579*****************************************99976777777778887444555666777**** PP

                            AAA_12  71 dvekseeekekkeksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeksekeievnt 147
                                       dve++        ++y+  eEa+ +++l+e++ ++g e+  ++igvi+p+raqv+ ++ ++ +    +    + v+t
  gi|336253852|ref|YP_004596959.1| 791 DVEGDG-------SRYTDGEEAARIAELIEAYEAAGLER--SEIGVIAPFRAQVSEISAHVPD----D----VAVDT 850
                                       **8554.......456778****************9999..****************999883....3....89*** PP

                            AAA_12 148 vdgfQGrekdviilslVRsnekkeigflkderrlNValTRAkskliivGnk 198
                                       vd+fQG+ ++vii+s+  + + +   +++d+rr+NValTR k++l++vG++
  gi|336253852|ref|YP_004596959.1| 851 VDRFQGSSQEVIIVSFTATGSLEGP-IFEDYRRINVALTRPKRALVLVGDS 900
                                       ****************999655443.8**********************97 PP

>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0   1.1e-20   6.6e-18       6     158 ..      66     217 ..      62     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 1.1e-20
                              Dna2   6 ekktvvLrddWaets..vekgdiihivgkfe.eek..iiidn.esnllIlhPdlLvsaTsvanslsClRravLqerl 76 
                                       e  tv+L+++W+++   +e+g+ + +++  + e +  +  +   + +++++P++Lv+ T++ n ++C+R  +L++  
  gi|336253852|ref|YP_004596959.1|  66 EPTTVTLWNKWTKSAelLEPGMELLVTNAEQdEYQgeTQYKTtGDSYVVVEPSFLVNVTAIRNWVECPRLYYLNKLS 142
                                       6679*******9998789******9954443222244555553667*****************************99 PP

                              Dna2  77 kvsgesskamliGtilHelfqkalleeeldkekleelldklleknleelyalglteeeakeeikekleeiekwakky 153
                                        v  + + +++ Gti+He+f ++l+      ++lee +d  ++++  el  lg++ +++ e+++e++ +ie w+++ 
  gi|336253852|ref|YP_004596959.1| 143 GV--PLNYPVVKGTIVHEVFGDLLRG-----RDLEESIDARVDEHGLELGLLGESPDSVAEDVRENAGAIEGWLEQG 212
                                       77..68******************87.....99*****************************************987 PP

                              Dna2 154 vkksn 158
                                         +++
  gi|336253852|ref|YP_004596959.1| 213 RLTED 217
                                       65544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.4   1.5e-19   9.6e-17       3     175 ..     540     757 ..     538     773 .. 0.77
   2 ?   -2.4   0.0       5.4   3.3e+03      37      81 ..     810     859 ..     807     903 .. 0.65

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.5e-19
                            AAA_30   3 naeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.La............... 63 
                                       na Q +av+++++ +d +a+++Gp+GtGKt++++ + +a+ ++g+rv++ A t++a ++ L+               
  gi|336253852|ref|YP_004596959.1| 540 NARQNEAVTKAVGAKD-CALIHGPPGTGKTYTIARAIRAMVERGERVLLSAFTNRAVDNaLEalleqlegvidedri 615
                                       789************9.*******************999999****************9777777666666666666 PP

                            AAA_30  64 ..................eelgieastiakllkrlk............grarlepg.tllivDEagmvdtkqlaall 109
                                                         e +g + +++a+l    +            +r   e++ +  +vDEa+ +    + a +
  gi|336253852|ref|YP_004596959.1| 616 vrvgsesgvrddmepyrlERAGDPEDRLAELQ---NaqvvaattatcgSRIMKEQSfDAALVDEAAQLTEPGTCAAI 689
                                       66665555555555555533333333333333...03346666667664344455679******************* PP

                            AAA_30 110 kaaekagakvilvGDerQlasVeaG......gvlrdlveaagigtaeLtevvRqkeseeraaalalregdae 175
                                       + ae+     +lvGD++Ql++V +       ++++ lv+ +    + L+  +R+++  ++ a++++ +g+ +
  gi|336253852|ref|YP_004596959.1| 690 NLAER----FVLVGDHEQLPPVVRAendlseSLFERLVDLHPEAGVMLDRQYRMNQRIQAFASREFYDGKLR 757
                                       ***98....*************985222222577788777888999********99**********999987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.4
                            AAA_30  37 alreaweaag...grviglAptgkaAkvLaeelg..ieastiakllkrlk 81 
                                       +l ea+eaag    ++ ++Ap  ++  ++++++   ++ +t++++  + +
  gi|336253852|ref|YP_004596959.1| 810 ELIEAYEAAGlerSEIGVIAPFRAQVSEISAHVPddVAVDTVDRFQGSSQ 859
                                       56677777776666777777777777777765543356677776664444 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 !   50.0   0.0     6e-16   3.7e-13       3     254 ..     122     353 ..     121     354 .. 0.66
   2 ?   -1.0   0.7       2.1   1.3e+03      75     120 ..     381     421 ..     357     439 .. 0.57

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 6e-16
                          PDDEXK_1   3 SvsrletfleCplrfflryllglreeeeleapdlGtlvHaaleefyewkkldkedleelleeaveelwpellleeei 79 
                                        v++++ + eCp+ ++l++l g++ ++ + +   Gt+vH+++ ++ +     ++dlee +++ v+e   el+l    
  gi|336253852|ref|YP_004596959.1| 122 NVTAIRNWVECPRLYYLNKLSGVPLNYPVVK---GTIVHEVFGDLLR-----GRDLEESIDARVDEHGLELGLLG-- 188
                                       699********************98999999...********88777.....66888888666665444444444.. PP

                          PDDEXK_1  80 lessarlrylaeklkevlekl.verlaeeleakrgfrpvalel..efggekvrLkGriDrvddkegelriiDyKtgs 153
                                         +s++    ae+++e + +   + ++  l + +++r ++l +   fg     ++Gr D + +       ++ Ktg+
  gi|336253852|ref|YP_004596959.1| 189 --ESPD--SVAEDVRENAGAIeGWLEQGRLTEDDSWRSEQLLIseTFG-----IRGRADAIRRGAP----VELKTGK 252
                                       ..4443..3333333333222123333334444448888888644666.....********87777....9****** PP

                          PDDEXK_1 154 appkskelaelkeglQlllYllalaegeelkeege..pagalylrleepkvkdeevvkkmalteeel...eallqel 225
                                       + +k++   + k+ +Q + Y+l+l+e+   +   +   + +ly +      ++ee+     ++++++   + ll+ +
  gi|336253852|ref|YP_004596959.1| 253 NLKKEP---RFKDKVQAACYALLLEEHG--G---DvdTGTLLYTKN-SALDRNEETGDL--TPAKDFsmgDGLLKFV 318
                                       664444...699999************2..2...222666666655.233333344444..4444444599999999 PP

                          PDDEXK_1 226 eel...aeeil.agefparpskk..CeyCpyksvC 254
                                        +l   +++++ +g++p   +    CeyC  ++ C
  gi|336253852|ref|YP_004596959.1| 319 VRLrneIAAMEmSGDVPTGYEGSakCEYCFEQDTC 353
                                       9995555555555677766554467****777776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.1
                          PDDEXK_1  75 leeeilessarlrylaeklkevleklverlaeeleakrg..frpvale 120
                                       +e+        +r + e+ +ev +++++ +++  ++++   +  + le
  gi|336253852|ref|YP_004596959.1| 381 FERF-------YRAIEEERREVHREYAKLWEQDAQERADddRALINLE 421
                                       2222.......3777777777777777766665555555666666555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.2   4.1e-15   2.5e-12       1     145 [.     543     708 ..     543     709 .. 0.68
   2 ?   -2.0   0.0       6.4     4e+03     125     139 ..     887     901 ..     881     904 .. 0.78

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 4.1e-15
                            AAA_19   1 qreave.al.kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae....... 68 
                                       q+eav+ a+ ++++ l+ ++pGtGKT+++  +++ +ve+g    e++ll aft+rA+++  e+l +   +       
  gi|336253852|ref|YP_004596959.1| 543 QNEAVTkAVgAKDCALIHGPPGTGKTYTIARAIRAMVERG----ERVLLSAFTNRAVDNALEALLE---Qlegvide 612
                                       789995455156788999**********************....89*************9999832...22457776 PP

                            AAA_19  69 ........................atTiHrlalldfddlltealelleeaeeekklqeee..llivDEfqdvd.elq 118
                                                                +   rla+l++ + +  + +       ++ ++e+   + +vDE+ +++ +  
  gi|336253852|ref|YP_004596959.1| 613 drivrvgsesgvrddmepyrleraGDPEDRLAELQNAQVVAATTAT----CGSRIMKEQSfdAALVDEAAQLTePGT 685
                                       6666666666666655555555543333344445555444333322....233333333235999******996666 PP

                            AAA_19 119 yrLlkallgekkklllvGDpdQliyvf 145
                                        + ++     +++++lvGD++Ql++v 
  gi|336253852|ref|YP_004596959.1| 686 CAAIN----LAERFVLVGDHEQLPPVV 708
                                       65444....3357***********985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.4
                            AAA_19 125 llgekkklllvGDpd 139
                                       l+ +k  l+lvGD +
  gi|336253852|ref|YP_004596959.1| 887 LTRPKRALVLVGDSN 901
                                       5666767******98 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 !    6.8   0.0    0.0079       4.9       2      21 ..     558     577 ..     557     604 .. 0.81
   2 !   17.2   0.0   5.4e-06    0.0033      48     120 ..     657     724 ..     635     756 .. 0.76
   3 ?    0.8   0.0      0.56   3.5e+02     183     233 ..     844     897 ..     812     898 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0079
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrt 21 
                                       ++hG pG GK+  i +++r 
  gi|336253852|ref|YP_004596959.1| 558 LIHGPPGTGKTYTIARAIRA 577
                                       79************999998 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.4e-06
                   Viral_helicase1  48 rtvdsflmalvkstkgkililDEylllhaGyilllaalskaklvilfGDplQipfhsrnasfllahlpsslsh 120
                                        t+ s  m   k+++++  ++DE+ +l+  +   +aa++ a+ ++l+GD++Q p   r+++ l  +l+ +l +
  gi|336253852|ref|YP_004596959.1| 657 ATCGSRIM---KEQSFDAALVDEAAQLT--EPGTCAAINLAERFVLVGDHEQLPPVVRAENDLSESLFERLVD 724
                                       44444444...44569***********9..7888*********************999988777777766655 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.56
                   Viral_helicase1 183 r..evttvhevqGltfdkVtlvllketdlelis...esrenllvAlTRhrkslvil 233
                                       +  +v tv   qG++ ++ ++  + + +le      e+     vAlTR +++lv++
  gi|336253852|ref|YP_004596959.1| 844 DdvAVDTVDRFQGSSQEVIIVSFTATGSLE--GpifEDYRRINVALTRPKRALVLV 897
                                       256788999999988665555544333333..23566688899******9999875 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 !   24.4   0.0     3e-08   1.8e-05       2     113 ..     540     672 ..     539     820 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3e-08
                                       SHHHHHHHHS...-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHH........ CS
                     UvrD-helicase   2 npeqreaias...lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRiee........ 67 
                                       n+ q+ea+++    +   l+   +G+GKT+++a  i  +++ +    +r+l++ FTn+A +   e + e        
  gi|336253852|ref|YP_004596959.1| 540 NARQNEAVTKavgAKDCALIHGPPGTGKTYTIARAIRAMVERG----ERVLLSAFTNRAVDNALEALLEqlegvide 612
                                       56788888887544556799999***********999999999....9************99999998867777777 PP

                                       ..............HHHHCCHHCTT-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTT CS
                     UvrD-helicase  68 ..............alkkaeqessdderlrlalqnlseanisTlHsfcqkilkkeanrig 113
                                                     +++  + e+++d   rla+ +  ++   T    +++i+k++ +++ 
  gi|336253852|ref|YP_004596959.1| 613 drivrvgsesgvrdDMEPYRLERAGDPEDRLAELQNAQVVAATTATCGSRIMKEQSFDAA 672
                                       777766666666665555555555555555555555555556666666666666666555 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 ?   -0.8   0.0       2.3   1.4e+03       2      39 ..     123     158 ..     122     179 .. 0.71
   2 !   20.9   0.0   5.1e-07   0.00032      31     161 ..     209     354 ..     199     355 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.3
                          Cas_Cas4   2 gtkiqyyliCkrklwlish.eitleensetvelGkllhe 39 
                                       +t+i+ ++ C+r  +l +  ++ l+     v  G ++he
  gi|336253852|ref|YP_004596959.1| 123 VTAIRNWVECPRLYYLNKLsGVPLNYP---VVKGTIVHE 158
                                       68999999****999988734433333...444888888 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.1e-07
                          Cas_Cas4  31 velGkllheesyerekkevelse....sikiDvvekekeklvvvEvKkskkkeea....aklQllyYlllLekkgve 99 
                                       +e+G+l +++s + e  ++ +se    +++ D ++    +  +vE+K +k+ +++    +k+Q   Y+llLe++g +
  gi|336253852|ref|YP_004596959.1| 209 LEQGRLTEDDSWRSE--QLLISEtfgiRGRADAIR----RGAPVELKTGKNLKKEprfkDKVQAACYALLLEEHGGD 279
                                       577888888777775..455544466699******....8889999999988654222269**************** PP

                          Cas_Cas4 100 ikeGvleypkekkree............velteelreelekaikeieeiissekppk.vkkkkiCkkCayaelCl 161
                                       +++G l y k+    +             ++ + l + + +  +ei ++  s  +p   + + +C+ C  ++ C+
  gi|336253852|ref|YP_004596959.1| 280 VDTGTLLYTKNSALDRneetgdltpakdFSMGDGLLKFVVRLRNEIAAMEMSGDVPTgYEGSAKCEYCFEQDTCM 354
                                       *********987655444566666666666666777777777777777766665554155566777777777775 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   4.4e-07   0.00027       2     105 ..     559     683 ..     558     699 .. 0.67
   2 ?   -2.6   0.0         7   4.3e+03      24      50 ..     820     846 ..     807     872 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.4e-07
                     Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke...................ee 59 
                                       + + +G+GK+ +++ a+ a++++g+ ++l++a ++++v++ +e l ++le +  ++                    e
  gi|336253852|ref|YP_004596959.1| 559 IHGPPGTGKTYTIARAIRAMVERGE-RVLLSAFTNRAVDNALEALLEQLEGVIDEDrivrvgsesgvrddmepyrLE 634
                                       78899******************98.9******************99998776555888888876655555444422 PP

                     Helicase_RecD  60 kkkkaekaelrvr.........kqrieyiapdellklkeqa...........dllvvDEAAaiplp 105
                                       +                      q+ + +a +++      +           d+ +vDEAA++  p
  gi|336253852|ref|YP_004596959.1| 635 R-----------AgdpedrlaeLQNAQVVAATTA------TcgsrimkeqsfDAALVDEAAQLTEP 683
                                       2...........1334333333223332222222......122223344455*********98766 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7
                     Helicase_RecD  24 egksnilvtapskenvktlfeflakgl 50 
                                        ++s+i v ap +++v+++ +++   +
  gi|336253852|ref|YP_004596959.1| 820 LERSEIGVIAPFRAQVSEISAHVPDDV 846
                                       345889999999999999988875554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.7e-06    0.0017       5     103 ..     554     680 ..     550     716 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.7e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsstsskdllrellralglelka........ 70 
                                       + + +++G++GtGKT++++r  +  +e+      + +v+   f + ++++ ++ ll++l   ++    +        
  gi|336253852|ref|YP_004596959.1| 554 KDCALIHGPPGTGKTYTIARAIRAMVER------GERVLlsaFTNRAVDNALEALLEQLEGVID----Edrivrvgs 620
                                       6799******************999876......666663434444444444444444444444....444447777 PP

                            AAA_22  71 .......................erlsseellealeqalrarav....ielliiDEaqhl 103
                                                              ++l++ ++++a +  + +r +      + ++DEa  l
  gi|336253852|ref|YP_004596959.1| 621 esgvrddmepyrleragdpedrlAELQNAQVVAATTATCGSRIMkeqsFDAALVDEAAQL 680
                                       777777777777777777666666666666665555555555556666677777777777 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       6.6   4.1e+03      88      88 ..     398     398 ..     347     512 .. 0.56
   2 !   19.7   0.4   1.4e-06   0.00088      24      89 ..     554     620 ..     541     749 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.6
                            AAA_16  88 e 88 
                                       e
  gi|336253852|ref|YP_004596959.1| 398 E 398
                                       2 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.4e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde..........a 89 
                                         + l++G++G+GK+  + ++ ra+ ++g  +l   ++         a+ +al +  ll+ql+            +
  gi|336253852|ref|YP_004596959.1| 554 KDCALIHGPPGTGKTYTIARAIRAMVERGERVLLSAFTNR-------AVDNAL-E-ALLEQLEGVidedrivrvgS 620
                                       4699**************8888899999755555555544.......122222.2.45555554422224444441 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 !   17.5   0.0   5.2e-06    0.0032      25     146 ..     555     682 ..     530     699 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.2e-06
                                       SEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.........GEEEESSS-B-- CS
                            ResIII  25 krglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke.....igkkvsgdkkka 96 
                                         +li+ + GtGKT+++a++i+++ + g+  ++l+ + ++  ++ +le++ + l+   +e     +g +   + +++
  gi|336253852|ref|YP_004596959.1| 555 DCALIHGPPGTGKTYTIARAIRAMVERGE--RVLLSAFTNRAVDNALEALLEQLEGVIDEdrivrVGSESGVRDDME 629
                                       467899********************866..9***999999888888777555555444444445222222222222 PP

                                       ...................-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS CS
                            ResIII  97 ............kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlga 146
                                                   +  + +n++++ +t+ +  +++         +++++fd  ++DEa  l++
  gi|336253852|ref|YP_004596959.1| 630 pyrleragdpedRLAELQNAQVVAATTATCGSRI---------MKEQSFDAALVDEAAQLTE 682
                                       3444445555555667777777777777777777.........6666677777777655555 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.22   1.3e+02      30      60 ..     104     131 ..      76     133 .. 0.74
   2 ?   -0.0   0.0         2   1.2e+03      12      33 ..     271     295 ..     268     313 .. 0.79
   3 ?    4.2   0.0     0.093        57      52      69 .]     572     589 ..     557     589 .. 0.85
   4 ?    1.8   0.0      0.54   3.3e+02      30      61 ..     886     918 .]     874     918 .] 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.22
                           DUF4350  30 alegedgtllvvapdlrlteeelaallewva 60 
                                       ++  +++ ++vv p + l +  + a+++wv+
  gi|336253852|ref|YP_004596959.1| 104 QYKTTGDSYVVVEPSF-LVN--VTAIRNWVE 131
                                       3445999********5.544..689999997 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2
                           DUF4350  12 elLeaqGvevrrvrkpfd...aleg 33 
                                        lLe++G +v++ + +++   al++
  gi|336253852|ref|YP_004596959.1| 271 LLLEEHGGDVDTGTLLYTknsALDR 295
                                       689*******999888886656655 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.093
                           DUF4350  52 laallewvarGntlvlaa 69 
                                       ++a++++v+rG +++l+a
  gi|336253852|ref|YP_004596959.1| 572 ARAIRAMVERGERVLLSA 589
                                       469************986 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.54
                           DUF4350  30 alegedgtllvvapd.lrlteeelaallewvar 61 
                                       al+++++ l++v++   + t+    ++lew+++
  gi|336253852|ref|YP_004596959.1| 886 ALTRPKRALVLVGDSnALATDPVYGRMLEWARQ 918
                                       8999999999999993444558889*****986 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   5.4e-05     0.033       6      46 ..     540     580 ..     536     589 .. 0.77
   2 ?    0.2   0.0      0.68   4.2e+02      55     101 ..     575     620 ..     572     628 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-05
                                       SHHHHHHH.HHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH   6 tkeQkeyl.ealkkndivfaiGpaGtGKtylavalavealkk 46 
                                       +++Q+e++ +a+ ++d   + Gp GtGKty ++a a++a+ +
  gi|336253852|ref|YP_004596959.1| 540 NARQNEAVtKAVGAKDCALIHGPPGTGKTY-TIARAIRAMVE 580
                                       5667665516777*****************.67888887765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.68
                                       EE-S--TT----SS---------TTTHHHHHHHTTTS-TTCHHHHHH CS
                              PhoH  55 trpaveageelGflpgdleekvdpylrplydaLkdllgaekveklle 101
                                       +r++ve ge++      ++  vd  l++l ++L+ +++++++ ++ +
  gi|336253852|ref|YP_004596959.1| 575 IRAMVERGERVLLSAF-TNRAVDNALEALLEQLEGVIDEDRIVRVGS 620
                                       6899999999975555.7999****************9999877655 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 ?   14.5   0.1     6e-05     0.037       2      22 ..     558     578 ..     557     615 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6e-05
                                       EEESSTTSSHHHHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavakel 22 
                                       l++GppGtGKT+++   ++ +
  gi|336253852|ref|YP_004596959.1| 558 LIHGPPGTGKTYTIARAIRAM 578
                                       89*********7655444443 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 ?   13.8   0.0   4.8e-05      0.03      19      83 ..     540     604 ..     534     608 .. 0.86
   2 ?   -3.4   0.0       9.6   5.9e+03     144     162 ..     644     662 ..     640     664 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.8e-05
                             AAA_7  19 tvrysyllelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiie 83 
                                       ++r++  +++ + +k   l+ Gp GtGKt +i + ++++ ++   +l   f+++   n l  ++e
  gi|336253852|ref|YP_004596959.1| 540 NARQNEAVTKAVGAKDCALIHGPPGTGKTYTIARAIRAMVERGERVLLSAFTNRAVDNALEALLE 604
                                       5778888899999999******************9999998888888888888888888777776 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.6
                             AAA_7 144 keikdvqlvaamgppgggr 162
                                        e+++ q+vaa + + g+r
  gi|336253852|ref|YP_004596959.1| 644 AELQNAQVVAATTATCGSR 662
                                       6899********9999987 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 ?   13.6   0.0   6.8e-05     0.042      43      80 ..     550     587 ..     526     617 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.8e-05
                         IstB_IS21  43 fiekkenivllGpsGvGKshlaialgveavraglsvlf 80 
                                        + +k++ ++ Gp+G+GK++  +   ++ v++g +vl 
  gi|336253852|ref|YP_004596959.1| 550 AVGAKDCALIHGPPGTGKTYTIARAIRAMVERGERVLL 587
                                       57899**************9544444677889999975 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 ?   13.2   0.0   9.4e-05     0.058       2      52 .]     846     897 ..     845     897 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.4e-05
                          UvrD_C_2   2 ayaltihkaQGsefpaVivfdpdlaaarmgel.....rrrlLYtavTRAreklilv 52 
                                       ++++t+ ++QGs  +++iv   +++a   + +       r + +a+TR ++ l+lv
  gi|336253852|ref|YP_004596959.1| 846 VAVDTVDRFQGSSQEVIIV---SFTATG-SLEgpifeDYRRINVALTRPKRALVLV 897
                                       789**********999999...333332.22345777888899**********998 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 ?   11.1   0.0   0.00024      0.15     116     161 ..     541     586 ..     468     590 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderiv 161
                                       ++++e++ kav ++   l+ G+ g+GKt ++  ++  + ++ er++
  gi|336253852|ref|YP_004596959.1| 541 ARQNEAVTKAVGAKDCALIHGPPGTGKTYTIARAIRAMVERGERVL 586
                                       788999**********************999888888888878876 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00033       0.2      16      41 ..     447     470 ..     442     480 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                             PDZ_6  16 lrvGDiilsvNGqpveglsladvaal 41 
                                       lr GD++l+ +G+pv  +   ++a++
  gi|336253852|ref|YP_004596959.1| 447 LREGDLVLASDGHPV--RGQSELARI 470
                                       9**************..887787776 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   0.00068      0.42       5      27 ..     557     586 ..     553     679 .. 0.82
   2 ?   -0.8   0.0       1.7   1.1e+03      26      78 ..     787     855 ..     781     864 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00068
                            AAA_24   5 iliyGpsgiGKTtlakel.......gpkpl 27 
                                        li Gp+g+GKT++++++       g+++l
  gi|336253852|ref|YP_004596959.1| 557 ALIHGPPGTGKTYTIARAiramverGERVL 586
                                       689************999665555555555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                            AAA_24  26 plfidtek.Glksldadkfpdie.................swedfldevvelaaeladyktlviDtidele 78 
                                       + f+d+e+ G++ +d+ +  +i                   ++ f+ +v e++a+ +  + + +Dt+d + 
  gi|336253852|ref|YP_004596959.1| 787 VSFVDVEGdGSRYTDGEEAARIAelieayeaaglerseigVIAPFRAQVSEISAHVP--DDVAVDTVDRFQ 855
                                       558999999999999999998876666666666666666555566666666666666..788899998874 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.49     3e+02      34     110 ..     398     490 ..     368     491 .. 0.67
   2 ?    7.7   0.0    0.0078       4.8       2      29 ..     558     583 ..     558     654 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.49
                            AAA_18  34 englllevdpealdeskrldedkldklldaleenss.................aleegknl.vidghlaeleseaak 92 
                                       e   l+e+d++     +r+d+d+   +l+ +e+ +                  +l+eg+ +   dgh++   se a+
  gi|336253852|ref|YP_004596959.1| 398 EYAKLWEQDAQ-----ERADDDRALINLEFVEKRPLeggrwelrarreggatsKLREGDLVlASDGHPVRGQSELAR 469
                                       33333333333.....6666666555555555555488888999999999998777777653668888888888887 PP

                            AAA_18  93 dikk...vvLtaspeelleRl 110
                                       +      +vLta++ +   Rl
  gi|336253852|ref|YP_004596959.1| 470 IERLddeIVLTADEPVEVTRL 490
                                       6555999*****998766665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0078
                            AAA_18   2 lltGtpGvGKt.tlakeLskrlgfgvnlr 29 
                                       l+ G+pG+GKt t+a++++ + +      
  gi|336253852|ref|YP_004596959.1| 558 LIHGPPGTGKTyTIARAIRAMVER---GE 583
                                       588********8999999877333...22 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00058      0.36       4      49 ..     557     607 ..     554     628 .. 0.75
   2 ?   -3.3   0.1       9.3   5.7e+03      68      94 ..     653     679 ..     644     682 .. 0.72
   3 ?   -3.0   0.0       7.6   4.7e+03      66      90 ..     841     865 ..     832     900 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00058
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE.....ESTSSTTHHHHHH CS
                             SRP54   4 illvGlqGaGKTttlaKLaallkkegkkvllva.....aDtfRaaAveQLk 49 
                                        l+ G+ G+GKT t+a+  + + ++g++vll a     +D    a +eQL+
  gi|336253852|ref|YP_004596959.1| 557 ALIHGPPGTGKTYTIARAIRAMVERGERVLLSAftnraVDNALEALLEQLE 607
                                       6899**************************987111114555555555555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.3
                                       HHHHHHHHHHHHHHTTSSEEEEEE--S CS
                             SRP54  68 paavakeavekakeekidvvlvDTaGr 94 
                                       +a++a  + + +ke+++d+ lvD a +
  gi|336253852|ref|YP_004596959.1| 653 AATTATCGSRIMKEQSFDAALVDEAAQ 679
                                       455566667788999999999998865 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 7.6
                                       SCHHHHHHHHHHHHHHTTSSEEEEE CS
                             SRP54  66 adpaavakeavekakeekidvvlvD 90 
                                       + p +va ++v++++ ++ +v++v 
  gi|336253852|ref|YP_004596959.1| 841 HVPDDVAVDTVDRFQGSSQEVIIVS 865
                                       4578888888999888888888885 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00038      0.23      19      66 ..     540     592 ..     524     667 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00038
                            AAA_25  19 ppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlg....p 66 
                                        ++++  v   + a++ al+ G+pgtGKt        a++ +G+ +l     +
  gi|336253852|ref|YP_004596959.1| 540 NARQNEAVTKAVGAKDCALIHGPPGTGKTYTIARAIRAMVeRGERVLLsaftN 592
                                       5566666777779999***************9999999998888777654443 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00066      0.41       2      47 ..     555     599 ..     554     747 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00066
                           DUF2075   2 avvlVtGvaGtGKtvvllnllaeleddeeertavy.lsvNhplvlvl 47 
                                        + l++G +GtGKt+   +++ ++   e+++++ + +  N++  ++l
  gi|336253852|ref|YP_004596959.1| 555 DCALIHGPPGTGKTYTIARAIRAM--VERGERVLLsAFTNRAVDNAL 599
                                       6899***********999998888..333333322022333333333 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   0.00063      0.39       3      38 ..     558     593 ..     557     600 .. 0.88
   2 ?   -2.6   0.0       8.3   5.1e+03     110     137 ..     691     721 ..     662     722 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00063
                                       EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--H CS
                             AAA_5   3 lLvGppGtgKselaerlaaalnreveyvqltrdtte 38 
                                       l+ GppGtgK+  + r  +a+  + e v+l+++t++
  gi|336253852|ref|YP_004596959.1| 558 LIHGPPGTGKTYTIARAIRAMVERGERVLLSAFTNR 593
                                       688*************99999888888888888875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.3
                                       ....-EEEEEESS--....-TT-TTHHHHTT CS
                             AAA_5 110 llerfrviatanpld...rslnelspalrsR 137
                                       l+erf +++  ++l+   r +n+ls++l  R
  gi|336253852|ref|YP_004596959.1| 691 LAERFVLVGDHEQLPpvvRAENDLSESLFER 721
                                       4566999999999999999999999999888 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 ?   10.8   0.0   0.00047      0.29      29      83 ..     550     607 ..     536     659 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00047
                            RuvB_N  29 reealdhvllyGpPGlGkt.tlakiiakelgvklkitsgPvlekagd..laalltnle 83 
                                          a d  l++GpPG Gkt t+a+ i + ++   ++  +   ++a d  l all +le
  gi|336253852|ref|YP_004596959.1| 550 AVGAKDCALIHGPPGTGKTyTIARAIRAMVERGERVLLSAFTNRAVDnaLEALLEQLE 607
                                       55678999**********9899999999888888888877888877633667777775 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0064         4      25      59 ..     557     591 ..     540     598 .. 0.80
   2 ?    1.7   0.0      0.18   1.1e+02     144     160 ..     695     711 ..     692     720 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0064
                                       EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESS CS
                              PIF1  25 fFvtGsgGtgKtflwkallkklrsegkivlavAss 59 
                                         ++G  GtgKt+   + + ++ ++g+ vl  A +
  gi|336253852|ref|YP_004596959.1| 557 ALIHGPPGTGKTYTIARAIRAMVERGERVLLSAFT 591
                                       4468**************************99987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
                                       EEEE--TTS-----SSS CS
                              PIF1 144 vvlgGDfrQilPviekg 160
                                        vl GD  Q++Pv++  
  gi|336253852|ref|YP_004596959.1| 695 FVLVGDHEQLPPVVRAE 711
                                       699***********764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (918 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:                        83  (0.00462937); 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: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.45
# Mc/sec: 6111.39
//
Query:       gi|336253853|ref|YP_004596960.1|  [L=185]
Description: hypothetical protein Halxa_2462 [Halopiger xanaduensis SH-6]
Scores for 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   23.6  24.0     0.0003   20.3   6.5    2.5  2  SPW              SPW repeat
  ------ inclusion threshold ------
       0.33   11.0   2.4        3.3    7.8   0.0    2.5  3  NVEALA           NVEALA protein
       0.34   11.3   7.1       0.45   10.9   0.2    2.1  2  Phage_holin_5_2  Phage holin family Hol44, in holin superfami
       0.71   10.3   0.0       0.71   10.3   0.0    3.0  4  FeoB_associated  FeoB-associated Cys-rich membrane protein


Domain annotation for each model (and alignments):
>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   6.5   6.7e-08    0.0003       5      41 ..      74     108 ..      72     113 .. 0.90
   2 !    8.7   9.5   0.00027       1.2       4      45 ..     129     168 ..     128     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.7e-08
                               SPW   5 lllGlwlivSPWvlGfsattgaawnnvivGavvavLa 41 
                                        +lG+w+++S  vl f +  +a+wnnv vG++v++ a
  gi|336253853|ref|YP_004596960.1|  74 AVLGAWTALS--VLVFESGEAATWNNVLVGIAVVAAA 108
                                       79********..88889999*************9988 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00027
                               SPW   4 nlllGlwlivSPWvlGfsattgaawnnvivGavvavLalafa 45 
                                       + +lG+wli+S  +l      g++w+ + +G++va La + a
  gi|336253853|ref|YP_004596960.1| 129 VGVLGIWLIISAALLE--MAGGLFWSTLATGLLVAGLAGYNA 168
                                       679************9..6679***************98765 PP

>> NVEALA  NVEALA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.4       2.8   1.2e+04      11      19 ..      71      79 ..      68      86 .. 0.50
   2 ?    7.8   0.0   0.00073       3.3       6      31 ..      98     122 ..      95     126 .. 0.81
   3 ?    2.8   0.0     0.026   1.2e+02       5      27 ..     153     175 ..     151     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.8
                            NVEALA 11 vfavlagtg 19
                                      +++++ g +
  gi|336253853|ref|YP_004596960.1| 71 AIIAVLGAW 79
                                      444444443 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00073
                            NVEALA   6 ilfvlvfavlagtgiyksnkkevsls 31 
                                       +l+ ++++++ag++ y+  ++ + ls
  gi|336253853|ref|YP_004596960.1|  98 VLVGIAVVAAAGYN-YYRLHNDIPLS 122
                                       678899********.77777777665 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.026
                            NVEALA   5 kilfvlvfavlagtgiyksnkke 27 
                                       ++++ l++a lag++ y   ++ 
  gi|336253853|ref|YP_004596960.1| 153 TLATGLLVAGLAGYNAYEAREAR 175
                                       678999*********99887765 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 ?   10.9   0.2    0.0001      0.45      24      67 ..      67     110 ..      56     112 .. 0.70
   2 ?    3.3   2.0     0.023     1e+02      23      67 ..     119     166 ..     116     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                   Phage_holin_5_2  24 PlilgiiGiilgvvivfta..dfqaedilifgaiiqGilsggastg 67 
                                       Pli +ii ++ +  ++ ++   f+  + ++ +++++Gi + +a+ +
  gi|336253853|ref|YP_004596960.1|  67 PLISAIIAVLGA--WTALSvlVFESGEAATWNNVLVGIAVVAAAGY 110
                                       777777777777..333333555555555555********999865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.023
                   Phage_holin_5_2  23 IPlilgiiG..iilgvvivfta....dfqaedilifgaiiqGilsggastg 67 
                                       IPl  g+ +  ++lg ++++++    ++    ++    ++ G+l++g++ +
  gi|336253853|ref|YP_004596960.1| 119 IPLSAGVASlvGVLG-IWLIISaallEMAGGLFWS--TLATGLLVAGLAGY 166
                                       555555555113456.5666644566777777777..9********99855 PP

>> 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 ?   -0.5   0.3      0.37   1.6e+03       4      16 ..      68      80 ..      65      85 .. 0.74
   2 ?   10.3   0.0   0.00016      0.71       2      23 ..      97     118 ..      96     123 .. 0.92
   3 ?   -1.9   0.1         1   4.7e+03       3      10 ..     136     143 ..     128     156 .. 0.63
   4 ?   -0.3   0.1      0.32   1.5e+03       6      18 ..     157     169 ..     152     175 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.37
                   FeoB_associated  4 IVgliiaaavafv 16
                                      ++ +iia++ a+ 
  gi|336253853|ref|YP_004596960.1| 68 LISAIIAVLGAWT 80
                                      6889999887776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00016
                   FeoB_associated   2 tiIVgliiaaavafvirrlikk 23 
                                       +++Vg++++aa+++  +rl+ +
  gi|336253853|ref|YP_004596960.1|  97 NVLVGIAVVAAAGYNYYRLHND 118
                                       89***************99875 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1
                   FeoB_associated   3 iIVgliia 10 
                                       +I+ ++++
  gi|336253853|ref|YP_004596960.1| 136 LIISAALL 143
                                       45555554 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.32
                   FeoB_associated   6 gliiaaavafvir 18 
                                       gl++a+++++  +
  gi|336253853|ref|YP_004596960.1| 157 GLLVAGLAGYNAY 169
                                       7888888888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1403.40
//
Query:       gi|336253854|ref|YP_004596961.1|  [L=92]
Description: hypothetical protein Halxa_2463 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0034   16.9   0.5     0.0056   16.2   0.0    1.6  2  PGPGW     Putative transmembrane protein (PGPGW)


Domain annotation for each model (and alignments):
>> PGPGW  Putative transmembrane protein (PGPGW)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.25   4.5e+03       6      13 ..      37      44 ..      33      46 .. 0.40
   2 !   16.2   0.0   3.1e-07    0.0056      25      51 ..      63      89 ..      58      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.25
                             PGPGW  6 vlGwvvvv 13
                                       lG + ++
  gi|336253854|ref|YP_004596961.1| 37 TLGPAALA 44
                                      33333333 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.1e-07
                             PGPGW 25 GwlvvflGLaiLslefewArrllewlr 51
                                      G+ vv+lG+a+ +l+++ A+ +l++l+
  gi|336253854|ref|YP_004596961.1| 63 GFTVVMLGFAVVALRHHAAEYRLRRLE 89
                                      999********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 704.98
//
Query:       gi|336253855|ref|YP_004596962.1|  [L=184]
Description: hypothetical protein Halxa_2464 [Halopiger xanaduensis SH-6]
Scores for 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   21.0   1.0      0.025   14.6   0.7    2.4  2  HHH_2     Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.041   14.0   0.1      0.086   12.9   0.1    1.3  1  COG2      COG (conserved oligomeric Golgi) complex component,
       0.35   11.0   3.6       0.21   11.7   1.2    1.8  2  DUF5595   Domain of unknown function (DUF5595)


Domain annotation for each model (and alignments):
>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0087        52      39      51 ..      59      71 ..      54      78 .. 0.74
   2 !   14.6   0.7   4.3e-06     0.025      18      43 ..     154     179 ..     152     181 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0087
                             HHH_2 39 evddiGeeiAqsi 51
                                      ev+++G+++A+s 
  gi|336253855|ref|YP_004596962.1| 59 EVRGVGTQVARSL 71
                                      5777777777764 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.3e-06
                             HHH_2  18 lLakrFksldaLkkasleeLlevddi 43 
                                       +La rF++ d+L +a+le+L+e d++
  gi|336253855|ref|YP_004596962.1| 154 DLADRFEEADELLNAELEDLIETDEV 179
                                       79**********************98 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 ?   12.9   0.1   1.4e-05     0.086       9      54 ..     134     178 ..     126     184 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                              COG2   9 gvpdFdpdqFvselrhgvpLeslrrdLeaylkllekellelvnedy 54 
                                        +p+F p ++  + ++  +Le+l +  e+ ++ll++el +l+++d 
  gi|336253855|ref|YP_004596962.1| 134 ESPAFGPMEY-DQYDRPEELEDLADRFEEADELLNAELEDLIETDE 178
                                       56899*****.669*****************************995 PP

>> DUF5595  Domain of unknown function (DUF5595)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.8   1.1e+04      35      46 ..     101     112 ..      97     116 .. 0.49
   2 ?   11.7   1.2   3.4e-05      0.21      28      50 ..     156     178 ..     152     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.8
                           DUF5595  35 daeleskLkely 46 
                                        + l+ +L+ ++
  gi|336253855|ref|YP_004596962.1| 101 AETLSKRLETVL 112
                                       344445555444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.4e-05
                           DUF5595  28 eDtFeeedaeleskLkelynvde 50 
                                       +D Fee d+ l+++L++l + de
  gi|336253855|ref|YP_004596962.1| 156 ADRFEEADELLNAELEDLIETDE 178
                                       8*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1359.50
//
Query:       gi|336253856|ref|YP_004596963.1|  [L=407]
Description: ABC transporter periplasmic protein [Halopiger xanaduensis SH-6]
Scores for 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-16   58.6   0.0    9.3e-16   58.1   0.0    1.3  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.091   12.4   0.1       0.15   11.6   0.1    1.2  1  Clenterotox   Clostridium enterotoxin
       0.12   12.5   0.0       0.84    9.7   0.0    2.1  2  B12-binding   B12 binding 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 !   58.1   0.0   1.6e-19   9.3e-16      47     236 ..     137     349 ..      92     351 .. 0.79

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.6e-19
                                       SSSB-HHHHHHH--SEEEE-GGG.........GGGHHHHHHHS-EEE----TTS.............HHHHHHHHHH CS
                      Peripla_BP_2  47 dgeidvEklaalkPDlvilskgl......gltdedeellksgiptvivessntg.............eslkeqiral 104
                                       ++++d E+l +l+ D+ ++++          +++ +e++ ++ p +   +sn               + l eq++ +
  gi|336253856|ref|YP_004596963.1| 137 SWNPDPEQLYELDSDVHLADPASvlaldgWNQSDVDEIRNNISPWFGNHFSNRHlsppdayageyeyYTLWEQFEKV 213
                                       45555577777777777777666555554344445555555666666666665577888888888889999****** PP

                                       HHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE....EEEE-TTSTTTHHHHT.S--EESTTT--S CS
                      Peripla_BP_2 105 gellgledeaeklvaeidsklaaaksaidsekpkpvlvfggade..ggyvvagsnsyigdllda.lgieniaaeskk 178
                                       + +++ ed++++l++  ++ la ++++++ e ++p++v+gg      +yv++ + +++   +   l+  +++ +   
  gi|336253856|ref|YP_004596963.1| 214 ARVFQAEDRYDALASIREDVLATIEADLPPESERPTVVMGGFSTptEPYVYNVDTPGFLTAHVRpLDPVDAFGDD-V 289
                                       *******************************55555555555554899999999988877776669999999999.* PP

                                       TT-EEE-HHHHHHH--SEEEEEEH..HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-H CS
                      Peripla_BP_2 179 seyeeisaEqilasdpdvifvsgr..aeadnktgleflkenpllaelpAvkngrVyalds 236
                                       s++++i++E++ ++dpd+i+v g   ++ d  t+  +l+++p+ ++l+Av+n r+ya ++
  gi|336253856|ref|YP_004596963.1| 290 SSGAQIDMETLIEADPDAIIVFGGmhPDTDMETVRTELENDPVGQKLTAVQNDRIYAQGA 349
                                       *******************99888899*****************************8766 PP

>> Clenterotox  Clostridium enterotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.6e-05      0.15     125     178 ..     292     345 ..     279     349 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.6e-05
                       Clenterotox 125 etpidedsliqtGpeeeivvgvidPsenieeintaisdtytynipdavnsnpay 178
                                         +id ++li+  p+  iv g ++P++++e + t + ++   +  +av+++ +y
  gi|336253856|ref|YP_004596963.1| 292 GAQIDMETLIEADPDAIIVFGGMHPDTDMETVRTELENDPVGQKLTAVQNDRIY 345
                                       369******************************999887766666666666655 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.17   9.9e+02      66      89 ..     231     255 ..     225     270 .. 0.78
   2 ?    9.7   0.0   0.00014      0.84      75      99 ..     300     324 ..     292     335 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.17
                       B12-binding  66 eavkelvel.lkrirprvkvvvGGa 89 
                                       e+v +++e+ l  +++r  vv+GG 
  gi|336253856|ref|YP_004596963.1| 231 EDVLATIEAdLPPESERPTVVMGGF 255
                                       56777888887788889999***94 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00014
                       B12-binding  75 lkrirprvkvvvGGahpsldpeetl 99 
                                       l +++p++++v+GG hp +d e + 
  gi|336253856|ref|YP_004596963.1| 300 LIEADPDAIIVFGGMHPDTDMETVR 324
                                       56789*************9998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3056.25
//
Query:       gi|336253857|ref|YP_004596964.1|  [L=146]
Description: hypothetical protein Halxa_2466 [Halopiger xanaduensis SH-6]
Scores for 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-05   22.8   0.1    9.6e-05   22.1   0.1    1.4  1  DUF3225   Protein of unknown function (DUF3225)
  ------ inclusion threshold ------
      0.016   15.4   2.1      0.028   14.7   0.7    2.0  2  SnoaL_3   SnoaL-like domain


Domain annotation for each model (and alignments):
>> DUF3225  Protein of unknown function (DUF3225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   1.1e-08   9.6e-05      15      65 ..       8      57 ..       3      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-08
                                      HHHHHHHHHHTT-HHHHHHHB--STT-EEEETTEEEESHHHHH.HHHHHS-- CS
                           DUF3225 15 afarYeaaLvsndvaaldalfwddpktvRyGvgenLyGieair.afRaarps 65
                                      ++++Y +aL +   + l+ +f +++ tv++G+ge L+G +a++ a R++  +
  gi|336253857|ref|YP_004596964.1|  8 VVRDYYDALRRG--ESLEPYFLEADATVKFGIGEALFGSDAVAdALRSQTET 57
                                      566777777665..689************************97246665544 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.7   3.1e-06     0.028       3      99 ..       7     103 ..       5     112 .. 0.74
   2 ?   -0.5   0.0      0.16   1.5e+03     108     119 ..     132     143 ..     127     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-06
                           SnoaL_3   3 alldafyeaaaegdfdalfalwaddivfigtgadelltgreevrrslkqifakgegisfeltdvrvtesgdvawvte 79 
                                       ++++++y+a+++g    l  ++++   ++  g +e l g ++v + l+ + + + ++s e  ++ v++ +  a ++ 
  gi|336253857|ref|YP_004596964.1|   7 DVVRDYYDALRRGE--SLEPYFLEADATVKFGIGEALFGSDAVADALRSQTETTDEWSVESGNLVVEQREAFATFAD 81 
                                       67899******998..7889999555555666788999****************************99888887766 PP

                           SnoaL_3  80 lldv.taa.edgtegegqlrlT 99 
                                       ++ + +++ e g+ +    r +
  gi|336253857|ref|YP_004596964.1|  82 EVAMaWTDtESGARHRFDSRWS 103
                                       6544133333333334444555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.16
                           SnoaL_3 108 gWkivhhhlSvp 119
                                        W  +++h S+p
  gi|336253857|ref|YP_004596964.1| 132 DWLFASMHVSAP 143
                                       799*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1142.56
//
Query:       gi|336253858|ref|YP_004596965.1|  [L=35]
Description: hypothetical protein Halxa_2467 [Halopiger xanaduensis SH-6]
Scores for 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:                       486  (0.0271069); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 265.61
//
Query:       gi|336253859|ref|YP_004596966.1|  [L=320]
Description: hypothetical protein Halxa_2468 [Halopiger xanaduensis SH-6]
Scores for 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-64  215.8   2.9    1.5e-33  116.5   0.7    2.0  2  Zincin_2  Zincin-like metallopeptidase


Domain annotation for each model (and alignments):
>> Zincin_2  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.5   0.7   8.4e-38   1.5e-33       1     189 [.      19     201 ..      19     205 .. 0.91
   2 !  102.1   0.1     2e-33   3.6e-29     210     332 .]     196     315 ..     194     315 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 8.4e-38
                                       --HHHHHHHHHHHHTGGGS--S-HHHHHHHHHHHHHHHHHHHHHHHT---SS--EEEE--HHHHHHHHHHHHHHTTH CS
                          Zincin_2   1 VdwdlaarvArrlaragevdrseaaaavaelreaarlAelwldevtglpaaagsevevvdraeWveatleswrrlle 77 
                                       +dw+ aa+ A+ ++ +g  + + +  +++++++ +r+A+  +++v+gl+ + +++ve+ +r  W++a++++++r+++
  gi|336253859|ref|YP_004596966.1|  19 IDWRSAAEAAKAATDPG--SIDLEPGEAEAYASDVRDARAGVRSVSGLEFDVPETVEIQNRHHWIDANVATFERVMS 93 
                                       8****************..6778899999**********************999*********************98 PP

                                       HHHHHHH---------------HHHHHHHHHHHHHHHHTT--BTTSSH...---.---EEEE-HHHHHHHHHHTT-- CS
                          Zincin_2  78 pvaeklaealaeelaallrqvggavfgaqvGqalgeLssevlgqtdvg...lplapegrllLvapnvaaverelevd 151
                                        + ++ +       ++ +  +++++ +  +  +l++L ++vlgq+d+     + ++e +l++v pn+ +++++levd
  gi|336253859|ref|YP_004596966.1|  94 TLENHAN-------TSTFPGIARTINTGTMTVMLSFLGRNVLGQYDPLllaDTPDDEHALYFVRPNILNAAEALEVD 163
                                       8866555.......4678889999999999******************65544555569****************** PP

                                       HHHHHHHHHHHHHHHHHHHHTSTHHHHHHHHHHHHHHT CS
                          Zincin_2 152 pedvrlwvalrEaaharlFaavpWLrehllsaveeyar 189
                                       ++ +r w+a +E++ha++F a+pWL +hl++++ee ++
  gi|336253859|ref|YP_004596966.1| 164 ADRFRRWIAFHEVTHAAEFGAAPWLSDHLEQRMEEGIA 201
                                       *********************************98665 PP

  == domain 2  score: 102.1 bits;  conditional E-value: 2e-33
                                       ...--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHHHHHHHHHHHHHHTT---- CS
                          Zincin_2 210 leggllelvqtpeqraaldrLeallaLlEGwvdvVmdavgpevlpsvaalrerfrrrratggpaerllrrllGlelk 286
                                       +e+g+ +l q + +r+a++ L a+++++EG+++  md +  +   ++++lr+++++rr+++gp+++l+rrllGl lk
  gi|336253859|ref|YP_004596966.1| 196 MEEGIATLSQGSFDREAFRDLDAAMTVVEGYAELLMDHAFDD---EYEDLRRKLDERRQGRGPLQQLFRRLLGLGLK 269
                                       5678889999999****************************8...9******************************* PP

                                       ---SSHHHHHHHHHHHHH-HHHHGGGGS-GGGS--HHHHH-HHHHH CS
                          Zincin_2 287 lrqyreaaalvravveavGmegrdavWehPdlLPtaeelddpaawv 332
                                        rqy++++++++ vv+++  e+   vWe+P+ LP+++eld p+ w+
  gi|336253859|ref|YP_004596966.1| 270 RRQYERGKNFFEYVVSTRDLETAALVWEGPEYLPSHDELDSPELWL 315
                                       ********************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.51u 0.20s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2396.47
//
Query:       gi|336253860|ref|YP_004596967.1|  [L=104]
Description: hypothetical protein Halxa_2469 [Halopiger xanaduensis SH-6]
Scores for 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   12.5   1.8       0.15   12.2   1.8    1.1  1  BLOC1S3   Biogenesis of lysosome-related organelles complex 1


Domain annotation for each model (and alignments):
>> BLOC1S3  Biogenesis of lysosome-related organelles complex 1 subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.8   8.2e-06      0.15       9      47 ..      46     100 ..      39     104 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.2e-06
                           BLOC1S3   9 EsDsddevyitslsstvasaagtkva................GEasEtddedeae 47 
                                       EsD+d+e++++  +s+  sa g+ va                G+++E+++e++++
  gi|336253860|ref|YP_004596967.1|  46 ESDEDEEAAAADEESGGPSAVGALVAlallvaagvavkryrgGDDEEFEEEEQPD 100
                                       9**********999999999999999999999999999*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 783.03
//
Query:       gi|336253861|ref|YP_004596968.1|  [L=75]
Description: Like-Sm ribonucleoprotein core [Halopiger xanaduensis SH-6]
Scores for 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-19   68.1   0.0    4.6e-19   67.9   0.0    1.1  1  LSM       LSM domain
    1.5e-07   31.4   0.0    1.9e-07   31.1   0.0    1.1  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.0   5.1e-23   4.6e-19       3      67 .]       9      75 .]       7      75 .] 0.89

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 5.1e-23
                                      HHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTET.EEEEE.EEEEEEGGGEEEEEE CS
                               LSM  3 lkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkk.ekrkl.glvliRGnnivlisl 67
                                      l+ +++++vtv+lk+g e++G L+g+Dq+mNlvLed++  + ++  e++ + ++++iRG+n+v+i++
  gi|336253861|ref|YP_004596968.1|  9 LEASLGERVTVRLKSGDEYVGELTGYDQHMNLVLEDATIPVGGTVeEEEPVeDTTIIRGDNVVSITP 75
                                      78899*********************************9887765867777366**********986 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   2.1e-11   1.9e-07       6      79 ..       7      74 ..       2      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.1e-11
                                      HHHHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS...........-EEEEEEE-GGGEEEEX CS
                            SM-ATX  6 flltslvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkkanskssspssgeipdtliikakdivdie 79
                                       +l ++ G++v+v++k+G+ y G +++++    +++vL+ a          + + +++++dt ii+++++v+i+
  gi|336253861|ref|YP_004596968.1|  7 DILEASLGERVTVRLKSGDEYVGELTGYDQ--HMNLVLEDATIPVG----GTVEEEEPVEDTTIIRGDNVVSIT 74
                                      578899************************..*********99998....89999999999**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 603.74
//
Query:       gi|336253862|ref|YP_004596969.1|  [L=58]
Description: 50S ribosomal protein L37e [Halopiger xanaduensis SH-6]
Scores for 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-23   81.0  12.1    5.5e-23   80.9  12.1    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
  ------ inclusion threshold ------
      0.061   13.3   2.1      0.086   12.9   2.1    1.2  1  zinc_ribbon_6   Zinc-ribbon
      0.064   13.3   2.3       0.07   13.1   2.3    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.068   12.6   2.5          3    7.4   0.1    2.3  2  zf-ribbon_3     zinc-ribbon domain
      0.099   12.4   5.5       0.58    9.9   0.6    2.2  2  zinc_ribbon_2   zinc-ribbon domain
       0.49   10.3   5.9        1.2    9.0   0.5    2.2  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.72    9.8   7.1        1.3    9.0   7.0    1.5  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


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 !   80.9  12.1   2.2e-26   5.5e-23       2      53 ..       4      55 ..       3      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 2.2e-26
                    Ribosomal_L37e  2 kGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsaKa 53
                                       Gt+s+Gk++k+ tH++CrrCg++syhv+kk+C+scG+ +sak r+y+W++Ka
  gi|336253862|ref|YP_004596969.1|  4 AGTPSQGKKNKT-THVKCRRCGEKSYHVKKKECSSCGFgKSAKRRDYEWQSKA 55
                                      6********666.**************************************98 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.1   3.4e-05     0.086      23      54 ..      11      39 ..       4      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                     zinc_ribbon_6 23 yknkkvkilCnDCekksevkfhvlglkCkeCg 54
                                       knk++++ C+ C++ks   +hv    C++Cg
  gi|336253862|ref|YP_004596969.1| 11 KKNKTTHVKCRRCGEKS---YHVKKKECSSCG 39
                                      578999*******9886...9**********6 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 ?   13.1   2.3   2.8e-05      0.07      67      94 ..      14      40 ..       9      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
                                      E--EEEETTTS-EEECHHHHHS-TTTSS CS
                              HypA 67 vpvkvrCreCgkefeleekalrCpkCgs 94
                                      +  +v+Cr+Cg++  + +k  +C +Cg 
  gi|336253862|ref|YP_004596969.1| 14 KTTHVKCRRCGEKSYHVKK-KECSSCGF 40
                                      56789******88875543.58****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 ?    5.7   0.3    0.0041        10      11      25 ..      13      26 ..      10      27 .. 0.67
   2 ?    7.4   0.1    0.0012         3       2       9 ..      32      39 ..      31      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0041
                       zf-ribbon_3 11 plssddnvCpyCGtk 25
                                      + ++  ++C  CG+k
  gi|336253862|ref|YP_004596969.1| 13 N-KTTHVKCRRCGEK 26
                                      5.6666788888865 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0012
                       zf-ribbon_3  2 tvrCPnCG 9 
                                      +++C++CG
  gi|336253862|ref|YP_004596969.1| 32 KKECSSCG 39
                                      689****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 ?    9.9   0.6   0.00023      0.58       6      22 ..      10      26 ..      10      27 .. 0.88
   2 ?    5.0   0.4     0.008        20      16      21 ..      35      40 ..      30      42 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00023
                     zinc_ribbon_2  6 GaelqdnakFCpyCGtp 22
                                      G++++ + + C +CG++
  gi|336253862|ref|YP_004596969.1| 10 GKKNKTTHVKCRRCGEK 26
                                      89999999999999986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.008
                     zinc_ribbon_2 16 CpyCGt 21
                                      C+ CG+
  gi|336253862|ref|YP_004596969.1| 35 CSSCGF 40
                                      777775 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 ?    9.0   0.5   0.00048       1.2      14      28 ..       8      24 ..       6      29 .. 0.78
   2 ?    4.5   0.7     0.012        31      23      28 ..      34      39 ..      25      45 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00048
                                      EECSCCCE..EEESSSS CS
                    RNA_POL_M_15KD 14 kedkegkn..feCrqCg 28
                                       ++k++k   + Cr Cg
  gi|336253862|ref|YP_004596969.1|  8 SQGKKNKTthVKCRRCG 24
                                      5566776679******8 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.012
                                      EESSSS CS
                    RNA_POL_M_15KD 23 eCrqCg 28
                                      eC++Cg
  gi|336253862|ref|YP_004596969.1| 34 ECSSCG 39
                                      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 ?    9.0   7.0   0.00051       1.3      25      55 ..      14      41 ..       3      50 .. 0.81
   2 ?    5.7   0.5    0.0054        14      29      43 ..      33      47 ..      32      55 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00051
                    OrfB_Zn_ribbon 25 ayTSktCseCgsknkealsgrtfkCpnCgfe 55
                                        T  +C +Cg+k+++    ++ +C++Cgf 
  gi|336253862|ref|YP_004596969.1| 14 KTTHVKCRRCGEKSYH---VKKKECSSCGFG 41
                                      458899********99...88889*****96 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0054
                    OrfB_Zn_ribbon 29 ktCseCgsknkeals 43
                                      k+Cs Cg  ++ ++ 
  gi|336253862|ref|YP_004596969.1| 33 KECSSCGFGKSAKRR 47
                                      79****998888333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 439.77
//
Query:       gi|336253863|ref|YP_004596970.1|  [L=235]
Description: hypothetical protein Halxa_2472 [Halopiger xanaduensis SH-6]
Scores for complete 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  116.0  15.5    1.5e-33  116.0  15.5    1.8  2  DUF4013   Protein of unknown function (DUF4013)
     0.0042   17.3  11.9     0.0084   16.4   0.3    3.0  3  DUF2189   Predicted integral membrane protein (DUF2189)


Domain annotation for each model (and alignments):
>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0  15.5   1.7e-37   1.5e-33       3     166 ..      25     180 ..      23     182 .. 0.80
   2 ?   -0.3   0.5     0.097   8.7e+02      99     115 ..     186     201 ..     178     209 .. 0.42

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 1.7e-37
                           DUF4013   3 sllliiaivlslvllGYlvrvlrdtirgddelPefddwgkllvdGlkafvvslvYlliplii.alltllvalaslaa 78 
                                        ll+ +++v ++++ GY+vrvl++t +gdde+P f+dwg++l+dG+ka v+ l+Y+l+p+++ ++l+++++l++  +
  gi|336253863|ref|YP_004596970.1|  25 MLLFGFLLVSLFLVWGYVVRVLERTTHGDDEVPRFEDWGEMLIDGAKASVILLAYSLVPIVVgGVLAGIATLVAGGS 101
                                       56777778888888************************************************433333333333333 PP

                           DUF4013  79 gdsaa.gallvlallglllalllvllllllfglllpvalarfartgslsaafnfkeilklikkkigkyiialilllv 154
                                        ds + +a++v++l++++ +       l+ +++++p+a+++fa +g+l a+f+++ i+ ++++  g+y++a++l+l 
  gi|336253863|ref|YP_004596970.1| 102 VDSIGaAAAAVTGLVTFATV-------LV-VAYAVPAAITNFAVEGRLAAGFDVGDIRPILAS--GTYAVAWLLALG 168
                                       33332233444444444444.......44.9****************************9977..69********** PP

                           DUF4013 155 igivlsllaill 166
                                       i+++ s+++++l
  gi|336253863|ref|YP_004596970.1| 169 IVVAGSIVTGAL 180
                                       ********9988 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.097
                           DUF4013  99 llvllllllfglllpva 115
                                       ++v+l+++ +++++ va
  gi|336253863|ref|YP_004596970.1| 186 VGVVLGAI-VAFYALVA 201
                                       23333333.22222222 PP

>> DUF2189  Predicted integral membrane protein (DUF2189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   9.4e-07    0.0084      48     112 ..      25      93 ..       4     102 .. 0.79
   2 ?   -0.7   0.6      0.18   1.6e+03      43      59 ..     110     126 ..      95     138 .. 0.53
   3 !    7.9   0.8   0.00039       3.5      11      67 ..     150     202 ..     139     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.4e-07
                           DUF2189  48 llllglllallfllWvraaallfallfgtapleslsafledvlltpeglaflivg....llvGavlAal 112
                                       +ll+g+ll+ lfl+W +++ +l   + g+ +++ ++++ e ++  ++  ++l+++    ++vG+vlA +
  gi|336253863|ref|YP_004596970.1|  25 MLLFGFLLVSLFLVWGYVVRVLERTTHGDDEVPRFEDWGEMLIDGAKASVILLAYslvpIVVGGVLAGI 93 
                                       899**********************************99988776666666666622224667777766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.18
                           DUF2189  43 anassllllglllallf 59 
                                       a  + l++++ +l++++
  gi|336253863|ref|YP_004596970.1| 110 AAVTGLVTFATVLVVAY 126
                                       22333334444443333 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00039
                           DUF2189  11 vgPllAvglYelSrrlergekvslrdalkalranassllllglllallfllWvraaa 67 
                                       + P+lA g Y+++  l  g  v      ++++   +++ ++g++l +++++++++aa
  gi|336253863|ref|YP_004596970.1| 150 IRPILASGTYAVAWLLALGIVVAG----SIVTGALNAIPFVGVVLGAIVAFYALVAA 202
                                       569***********9998877655....44555556678888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 1665.66
//
Query:       gi|336253864|ref|YP_004596971.1|  [L=399]
Description: threonine synthase [Halopiger xanaduensis SH-6]
Scores for 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-64  216.2   1.9    7.5e-64  216.0   1.9    1.0  1  PALP          Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.023   14.2   2.5      0.064   12.8   2.5    1.8  1  TF_Zn_Ribbon  TFIIB zinc-binding
      0.028   14.4   0.3      0.051   13.6   0.3    1.4  1  DZR           Double zinc ribbon
      0.032   14.3   1.7      0.032   14.3   1.7    2.2  2  Zn-ribbon_8   Zinc ribbon domain
      0.095   12.7   0.2       0.18   11.8   0.2    1.4  1  HypA          Hydrogenase/urease nickel incorporation, metall
       0.19   11.7   0.8        0.4   10.6   0.1    2.0  2  zf-LYAR       LYAR-type C2HC 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 !  216.0   1.9   2.5e-67   7.5e-64       2     294 .]      77     381 ..      76     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 216.0 bits;  conditional E-value: 2.5e-67
                                       GGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaall 77 
                                       t+ +g T lv++p+l++elgv+ +++K+E+ nptg fKdRg + ++++++++ ga  vv as+GN+g+a+Aa+a ++
  gi|336253864|ref|YP_004596971.1|  77 TMDEGATALVDCPNLADELGVErVLVKDEGRNPTGTFKDRGQTVAVTAATQH-GASDVVLASAGNAGQAAAAYAGRA 152
                                       7789************************************************.************************ PP

                                       T-EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHT CS
                              PALP  78 GlkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileql 154
                                       Gl++++++p+ +   ++a+   +G ++ +vgg   +a aa +e+ +e +++y +++f  p++ eg +t+ +Ei+eql
  gi|336253864|ref|YP_004596971.1| 153 GLESHVFLPSRSGFTNKAMVNVHGGDMNVVGGRIGDAGAAYEEAREEHDDWYPLQTFTTPYRHEGKKTMLYEIVEQL 229
                                       ***************************************************************************** PP

                                       T.TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B...SSS.CCSTC CS
                              PALP 155 g.gkpdavvvpvGgGgliaGiaaglke....rrpd..vrvigvepegsdalarslragrrvtvpvs..dtiadglav 222
                                       + + pda+  p+GgG  + G++++  e    +  d  + +++++++g++++ +++++g  +  pv+  dti+ gl++
  gi|336253864|ref|YP_004596971.1| 230 DwETPDAICYPTGGGVGLIGMYKAATEfrelGLIDdlPALYAAQASGCAPIVEAYEEGWDEHEPVEnpDTICGGLEI 306
                                       ************************9998877333368******************9998877777777********* PP

                                       S..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 223 g..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                       +   +s+  +e+++++ + +v+ +d ++lea +++a+++g+ + pssaaa  ++ +l+e+ge+++++++v++ tg
  gi|336253864|ref|YP_004596971.1| 307 PdpGASPWILEAIRATDGGAVATDDPDILEAGVQVAQHAGLEMVPSSAAAASGAwELAERGEFDGDETIVILNTG 381
                                       *99999999***************************************************************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 ?   12.8   2.5   2.1e-05     0.064       2      30 ..      13      38 ..      12      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                                      EETTTTCEECHEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVle 30
                                       C +Cg t   +D++++++ C+dCG Vl+
  gi|336253864|ref|YP_004596971.1| 13 ECVDCGAT---FDAAEATHECPDCGGVLD 38
                                      5*****96...8************99987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   1.7e-05     0.051      15      41 ..      14      40 ..       8      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                               DZR 15 CseCgtklkavaaedrCpsCgekvdpe 41
                                      C +Cg++ +a++a + Cp Cg  +dp+
  gi|336253864|ref|YP_004596971.1| 14 CVDCGATFDAAEATHECPDCGGVLDPT 40
                                      99*******************998886 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.7   1.1e-05     0.032       7      34 ..      13      35 ..      12      38 .. 0.82
   2 ?   -2.4   0.4       1.9   5.6e+03       2       6 ..      39      43 ..      39      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgs 34
                                      +C +Cg +f++         t+ CP+Cg+
  gi|336253864|ref|YP_004596971.1| 13 ECVDCGATFDAAE------ATHeCPDCGG 35
                                      7*********766......5555*****8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.9
                       Zn-ribbon_8  2 PiYeY 6 
                                      P+Y+Y
  gi|336253864|ref|YP_004596971.1| 39 PTYDY 43
                                      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 ?   11.8   0.2   6.1e-05      0.18      71      94 ..      12      35 ..       2      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.1e-05
                                      EEETTTS-EEECHHHHHS-TTTSS CS
                              HypA 71 vrCreCgkefeleekalrCpkCgs 94
                                      ++C +Cg++f+ +e++ +Cp+Cg+
  gi|336253864|ref|YP_004596971.1| 12 LECVDCGATFDAAEATHECPDCGG 35
                                      68*********8876789****97 PP

>> zf-LYAR  LYAR-type C2HC zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00014       0.4       3      14 ..      14      25 ..      12      28 .. 0.83
   2 ?   -2.2   0.1       1.4   4.1e+03       3      10 ..      30      37 ..      29      43 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                           zf-LYAR  3 CiDCsktFdgde 14
                                      C+DC+ tFd  e
  gi|336253864|ref|YP_004596971.1| 14 CVDCGATFDAAE 25
                                      ********9765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                           zf-LYAR  3 CiDCsktF 10
                                      C DC+ + 
  gi|336253864|ref|YP_004596971.1| 30 CPDCGGVL 37
                                      88**9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2848.88
//
Query:       gi|336253865|ref|YP_004596972.1|  [L=233]
Description: Geranylgeranylglyceryl phosphate synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-53  181.9   0.4    1.4e-53  181.7   0.4    1.0  1  PcrB      PcrB family


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 !  181.7   0.4   7.6e-58   1.4e-53       3     224 ..       5     225 ..       3     230 .. 0.94

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 7.6e-58
                                       GGGTSEEEEE-TTSS-CHHHH.HHHHCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TT..SS CS
                              PcrB   3 ileerhltklDPeeenpdEiv.eiviesgtDavmigGsqsvtldntvrllkkvsriklPivlepsnvegvvry..aD 76 
                                       +  + h+ k+DP++++pd +    ++  gtDa+ +gG+ ++t++n + ++    + ++P+  eps ++ v ++  +D
  gi|336253865|ref|YP_004596972.1|   5 WADWDHILKIDPDKDLPDGVTyGDLCATGTDAIEVGGTMGITEENMADVIAACAEHDVPLYQEPSSPDVVIEDdaLD 81 
                                       789***************9862578********************************************99864479 PP

                                       EEEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-B-TTHHHHHHHHHHHHHHTT CS
                              PcrB  77 alFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteakvdlnkediaayallaakllg 153
                                        + +++++n+  + Wi+gah++ ++  ++l   e   +e+Y+v++P++ va+ tea++dl+ +++aaya++a++++g
  gi|336253865|ref|YP_004596972.1|  82 GYLIPTVFNAGSPFWITGAHKEWVRLDRDLD-WERTSTEAYIVMNPEADVATYTEADCDLEADEVAAYATVAERMFG 157
                                       9*******************99988877777.999****************************************** PP

                                       -SEEEEE-TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCCSSEEEE-CHHHHHHHCHHHHHHH CS
                              PcrB 154 lrliYlEasGaledveevialkkklekarlivGGGirsaEkAkevveaADvivvGnvveekderkidaile 224
                                         ++YlE+sG+l+d e v a +   ++++l++GGGi++ ++A+ ++++ADvivvG++ +e++   ida+ e
  gi|336253865|ref|YP_004596972.1| 158 QEIVYLEYSGTLGDEEIVEAASEATDESTLFYGGGIHDYDSAYSMAQYADVIVVGDLAHEEG---IDAVRE 225
                                       ************************************************************99...444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1636.93
//
Query:       gi|336253866|ref|YP_004596973.1|  [L=229]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-15   56.6   0.0    2.6e-15   56.0   0.0    1.3  1  HTH_10         HTH DNA binding domain
     0.0021   17.9   4.8     0.0026   17.6   0.9    2.6  2  BAT            GAF and HTH_10 associated domain
  ------ inclusion threshold ------
      0.029   13.9   0.4      0.066   12.7   0.4    1.7  1  Sigma70_r4     Sigma-70, region 4
      0.034   14.0   0.2      0.079   12.8   0.2    1.6  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
       0.22   11.8   0.0       0.34   11.2   0.0    1.3  1  UPF0122        Putative helix-turn-helix protein, YlxM / p13 


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 !   56.0   0.0   7.1e-19   2.6e-15       2      52 ..     172     222 ..     171     223 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 7.1e-19
                            HTH_10   2 TdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       Td q+e+l+lA+e G+Fd+PR++ l  +A++l Is++++se+Lr+ + +l+
  gi|336253866|ref|YP_004596973.1| 172 TDSQREALALALEHGFFDVPRETGLTTIAETLEISEQAVSERLRRGQARLV 222
                                       9********************************************999997 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.9   7.3e-07    0.0026       4     122 ..       3     139 ..       2     170 .. 0.78
   2 ?   -1.8   0.1      0.69   2.5e+03     115     145 ..     189     219 ..     187     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.3e-07
                               BAT   4 veLeleirdeddvlv.alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtl 79 
                                       v++ +e  ++ ++l  +l a     v+le+  + +  ++++f++++ +d+e+++ a+++  +v++ + +++++d+++
  gi|336253866|ref|YP_004596973.1|   3 VRVAFEAASPKLLLGpTLEAMPSLDVTLERQYALDPAQPVAFCRMRCDDHERLERALAADGTVAEFERLDRSNDRAR 79 
                                       6778888888888888888899999**************************************************** PP

                               BAT  80 leltvs........gpslas.............tlaehGgtvrsaeaedgrarlvvevPpgadv 122
                                       +++t s        g    s             + ++ Gg +   +a++gr+++ +++P++++ 
  gi|336253866|ref|YP_004596973.1|  80 FRVTRSesgggsdlG----SgpesapdvvgayrRWVSVGGELLGGRATNGRWEIDMRFPDREAF 139
                                       **9998455533330....244444444446666777777777777777777777777777665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.69
                               BAT 115 evPpgadvRsvvealeerypdveLvarrere 145
                                       +vP+++ + +++e+le + ++v+ + rr + 
  gi|336253866|ref|YP_004596973.1| 189 DVPRETGLTTIAETLEISEQAVSERLRRGQA 219
                                       7899999999999998888877777666655 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   1.9e-05     0.066       8      48 ..     174     221 ..     169     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   8 rerevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                        +re l l          ++  l  I+e+l iS+ +V+ +++r+  +L
  gi|336253866|ref|YP_004596973.1| 174 SQREALALALehgffdvPRETGLTTIAETLEISEQAVSERLRRGQARL 221
                                       5666666666666666644445889******************97776 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 ?   12.8   0.2   2.2e-05     0.079      21      40 ..     197     216 ..     193     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                     HTH_AsnC-type  21 aeLAervGlSestvlrRvrr 40 
                                       + +Ae + +Se++v +R+rr
  gi|336253866|ref|YP_004596973.1| 197 TTIAETLEISEQAVSERLRR 216
                                       78****************98 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.6e-05      0.34      35      61 ..     195     221 ..     169     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.6e-05
                           UPF0122  35 SlsEiAeefnvsrqavydnikrtekll 61 
                                        l+ iAe+ ++s qav++ ++r ++ l
  gi|336253866|ref|YP_004596973.1| 195 GLTTIAETLEISEQAVSERLRRGQARL 221
                                       5889******************88654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1778.37
//
Query:       gi|336253867|ref|YP_004596974.1|  [L=94]
Description: hypothetical protein Halxa_2476 [Halopiger xanaduensis SH-6]
Scores for 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   84.1   0.0    7.1e-24   83.9   0.0    1.1  1  HalOD1    Halobacterial output domain 1
  ------ inclusion threshold ------
      0.085   13.4   0.0        0.1   13.1   0.0    1.1  1  DUF1499   Protein of unknown function (DUF1499)


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   7.9e-28   7.1e-24       1      75 []      10      84 ..      10      84 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 7.9e-28
                            HalOD1  1 deespstaVveavaavegvdptel.epLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75
                                      d+e+ps++V++ +aa  gvdptel +pLy++ D+ ALdaLf+++++g   + g+++F y++  VtV++dgei+Ve+
  gi|336253867|ref|YP_004596974.1| 10 DDEPPSVRVARELAARDGVDPTELsPPLYHSLDTAALDALFEPTRRGG-LRHGRITFAYNEKWVTVHDDGEITVEQ 84
                                      69**********************777****************66665.6679*********************85 PP

>> DUF1499  Protein of unknown function (DUF1499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05       0.1       7      85 ..      11      86 ..       5      93 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                           DUF1499  7 adpncvssaqaaaaypdiaPltyegdssee.avfaallavvesldpakiegetdgyleaeatsklfgfvDdveirvqpd 84
                                      ++p++v  a + aa++ ++P  ++ +     ++ aal a+ e +++    g + g+++  +  k++   Dd ei+v+++
  gi|336253867|ref|YP_004596974.1| 11 DEPPSVRVARELAARDGVDPTELSPPLYHSlDT-AALDALFEPTRR---GGLRHGRITFAYNEKWVTVHDDGEITVEQS 85
                                      578888776644443336666663211111133.455566666654...55558**********************986 PP

                           DUF1499 85 e 85
                                      +
  gi|336253867|ref|YP_004596974.1| 86 G 86
                                      5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); 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:                         2  (0.000111551); expected 0.2 (1e-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: 700.48
//
Query:       gi|336253868|ref|YP_004596975.1|  [L=84]
Description: hypothetical protein Halxa_2477 [Halopiger xanaduensis SH-6]
Scores for 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:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 678.45
//
Query:       gi|336253869|ref|YP_004596976.1|  [L=227]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-15   56.5   0.3    2.9e-15   55.8   0.3    1.4  1  HTH_10         HTH DNA binding domain
    0.00059   19.4   1.5     0.0095   15.6   0.6    2.8  2  Sigma70_r4_2   Sigma-70, region 4
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.032   14.0   0.1    1.8  1  LexA_DNA_bind  LexA DNA binding domain
      0.011   15.3   0.1      0.028   13.9   0.1    1.8  1  Sigma70_r4     Sigma-70, region 4
      0.016   14.8   0.0       0.03   13.9   0.0    1.5  1  HTH_24         Winged helix-turn-helix DNA-binding
      0.033   13.7   0.0       0.17   11.5   0.0    2.0  1  GerE           Bacterial regulatory proteins, luxR family
      0.051   13.5   0.0       0.11   12.4   0.0    1.5  1  HTH_5          Bacterial regulatory protein, arsR family


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 !   55.8   0.3   1.1e-18   2.9e-15       1      52 [.     166     217 ..     166     218 .. 0.98

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 1.1e-18
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LTd+q+e   lA+e GY++ PR++t +eLA +l++++ t+ ehL+++e kl+
  gi|336253869|ref|YP_004596976.1| 166 LTDRQRELFELALEDGYYEIPRETTHRELAAKLDLAAGTVGEHLQRIEAKLA 217
                                       9*************************************************97 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 ?   -1.3   0.0      0.68   1.7e+03       2      13 ..     132     143 ..     131     144 .. 0.83
   2 !   15.6   0.6   3.7e-06    0.0095      10      54 .]     165     216 ..     164     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.68
                                       HHHHHHHTTS-H CS
                      Sigma70_r4_2   2 qalrealaeLpe 13 
                                       + +++a a+Lpe
  gi|336253869|ref|YP_004596976.1| 132 RSIQRAAAALPE 143
                                       579999999998 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.7e-06
                                       TS-HHHHHHHHHHHTS--.......-HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  10 eLperqreifllrylegl.......sykEIAellgisegtVksrlsRArkkL 54 
                                       +L+ rqre f+l  ++g+       +++E A++l++  gtV  +l+R  +kL
  gi|336253869|ref|YP_004596976.1| 165 TLTDRQRELFELALEDGYyeipretTHRELAAKLDLAAGTVGEHLQRIEAKL 216
                                       589999999***9999977777777**********************99887 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 ?   14.0   0.1   1.3e-05     0.032       3      53 ..     165     215 ..     163     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                                       ---HHHHHHHHH.HHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHT CS
                     LexA_DNA_bind   3 kLTerQrevldl.ikasieetgypPsireiaralglkSpsaveehLkaLerK 53 
                                        LT+rQre+++l +++   e     + re+a +l l+ + +v ehL++ e K
  gi|336253869|ref|YP_004596976.1| 165 TLTDRQRELFELaLEDGYYEIPRETTHRELAAKLDLA-AGTVGEHLQRIEAK 215
                                       69********985788888888889************.9*********9988 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.1e-05     0.028       4      43 ..     165     211 ..     164     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekr 43 
                                       +L++r+re +el          ++ T+ E++++l++  ++V  ++ r
  gi|336253869|ref|YP_004596976.1| 165 TLTDRQRELFELALedgyyeiPRETTHRELAAKLDLAAGTVGEHLQR 211
                                       7***************999998999***************9666666 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 ?   13.9   0.0   1.2e-05      0.03      18      40 ..     189     211 ..     186     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                            HTH_24  18 isqreLAerlglSpstvnrrlkr 40 
                                       ++ reLA +l+l  +tv ++l+r
  gi|336253869|ref|YP_004596976.1| 189 TTHRELAAKLDLAAGTVGEHLQR 211
                                       89*******************98 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.6e-05      0.17      19      47 ..     190     218 ..     164     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.6e-05
                                       -HHHHHHHHTS-HHHHHHHHHHHHHHHT- CS
                              GerE  19 snkeIAeelniSekTVkvhksnimkKLnv 47 
                                       +  e A++l++++ TV  h+++i  KL +
  gi|336253869|ref|YP_004596976.1| 190 THRELAAKLDLAAGTVGEHLQRIEAKLAA 218
                                       67899*********************976 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 ?   12.4   0.0   4.3e-05      0.11      14      39 ..     187     212 ..     183     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                                       SSEEHHHHHHHHTS-HHHHHHHHHHH CS
                             HTH_5  14 gelcvcelaeelglsqstvShHLkkL 39 
                                       +e++  ela++l+l  +tv +HL + 
  gi|336253869|ref|YP_004596976.1| 187 RETTHRELAAKLDLAAGTVGEHLQRI 212
                                       578889*****************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1900.89
//
Query:       gi|336253870|ref|YP_004596977.1|  [L=448]
Description: Unspecific monooxygenase [Halopiger xanaduensis SH-6]
Scores for complete 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-95  320.3   0.0    2.3e-95  320.1   0.0    1.0  1  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.1   0.0   1.3e-99   2.3e-95       1     443 [.      13     427 ..      13     441 .. 0.93

  Alignments for each domain:
  == domain 1  score: 320.1 bits;  conditional E-value: 1.3e-99
                                       --SESEHHCCHCHHHHTTTCCHHHHHHHHHHHH-SEEEEEETTEEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHH CS
                              p450   1 Ppgptplplvgnllqlgrkeelhevlrklqkkygpifrlklgskpvvvlsgpeavkevlikkgeefsgrpdeallat 77 
                                       P gp+ lp+vgn l +   + ++ ++++ +++yg+i  +   + pv+ l++pe++++vl++++++ ++      +++
  gi|336253870|ref|YP_004596977.1|  13 PDGPDGLPIVGNQLAFL--RDPYGFMTRTAREYGDIAYWEDPGGPVFQLNHPEYIEQVLVQNNQNYVK---GDRFQQ 84 
                                       889*************9..689****************************************966666...345555 PP

                                       HHHTTTTSSSTTCGHHHHHHHHHHHHHHHTSHSTTTHHHHHHHHHHHHHHHHHCCCCHCSEEETHHHHHHHHHHHHH CS
                              p450  78 srkpfkgkgvlfangekwkklRrfltptltsfgklsleelveeeaedlveklrkkagesselditellskaaldvig 154
                                         +p  g+g+l+++g+ w+++R+++ p+++ + ++++  ++++ aed ++ +++ ++ +    ++e++ +++l +++
  gi|336253870|ref|YP_004596977.1|  85 TLGPLTGNGILNSEGAVWRRNRHLIQPAFHPDRIREYATMMTDFAEDALADWEDGQTRH----VHEDMMEVTLKIVA 157
                                       668***************************99888*******************99999....************** PP

                                       HHHHSSHHHTTTSSHHHHHHHHHHHHHHHHHCHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHCH CS
                              p450 155 silFgarfdlledeklselvkaveelssllskssvqllllfpllkylptkllrklkeavkklkdlldklieerretl 231
                                       + lFg  +d   d   s l++++e+  sl      +++l+++    +pt+ +r++++a++ l++++ +lie+rr++ 
  gi|336253870|ref|YP_004596977.1| 158 RALFGTDIDEHVDTVGSALEEFMEATESLA-----NFVLPPQ----VPTPARRRIERARENLDEVVYQLIEQRRANP 225
                                       *******99777777777777777774333.....3344444....7***************************988 PP

                                       CHCSCSSCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHCC CS
                              p450 232 dsakksrrdfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklreEidevlg 308
                                        ++     d ++ ll+ + +++ge  +s e+++ +v +ll+aG++Tt+  l+ ++y LaknP+v+e l  E++ vlg
  gi|336253870|ref|YP_004596977.1| 226 TDR-----DVISKLLEVT-DEEGE-AMSTEQIRDEVVTLLLAGHETTALSLTLTFYVLAKNPSVEETLVAELEDVLG 295
                                       777.....*********7.88887.**************************************************** PP

                                       TTTT-HHHHCCT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--G CS
                              p450 309 dkreptyddlqklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdp 385
                                       d+  pt+ddl++l+y+++v+kE++Rl+p+vp ++ Re+ k+ vi+gy ip+G  v +  + +hrdp  +++P  F+p
  gi|336253870|ref|YP_004596977.1| 296 DD-APTMDDLSELTYTEKVVKESMRLYPPVP-GIIREAVKPDVIGGYEIPAGASVRMHQWVVHRDPRWYDDPLAFHP 370
                                       *6.6***************************.********************************************* PP

                                       GGGB-TTSCTESSCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHEEEEESTSTSG CS
                              p450 386 eRFldekgnskrksfaflPFGaGpRnCiGerlArmelklflatlLqnFevelqpetdp 443
                                       eR+ de + s+ ++ a++PF aGpR CiG r+A++e +l+lat+ + + +el p+td 
  gi|336253870|ref|YP_004596977.1| 371 ERWTDEME-SDLPKLAYFPFAAGPRRCIGDRFAMLEARLILATVYRDYHLELEPGTDL 427
                                       *******9.88*****************************************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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 0.23s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3512.69
//
Query:       gi|336253871|ref|YP_004596978.1|  [L=70]
Description: hypothetical protein Halxa_2481 [Halopiger xanaduensis SH-6]
Scores for 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:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 540.90
//
Query:       gi|336253872|ref|YP_004596979.1|  [L=123]
Description: PilT protein domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   23.5   0.2     0.0001   22.8   0.2    1.3  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 !   22.8   0.2   5.6e-09    0.0001       1     111 [.       2     107 ..       2     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.6e-09
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTS..SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCH CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleel..eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpida 75 
                                       ++lD  v+++l+ g e+a   +++le++   + ++s+l++a ++ +l           + +e   + ++l++lp d 
  gi|336253872|ref|YP_004596979.1|   2 VLLDETVVVDLMAGNEDA---VAALEDIdwRDAAVSELTVAQIREGLPE--------SKQTEFDAIVERLEVLPYDF 67 
                                       58999*******999999...5555555569999999999999999999........55555555577899999999 PP

                                       HHHHHHHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.E CS
                               PIN  76 eiaeeaaeialkyg.....llpnDaliaAtAkehgikliat 111
                                       +  ++a + ++++      +++ Da+ia tA+e + +++ t
  gi|336253872|ref|YP_004596979.1|  68 PTGRTAVDEHKRLHgedipIDAVDAMIAGTAIEADEPVL-T 107
                                       999999888888888999****************99998.7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1003.37
//
Query:       gi|336253873|ref|YP_004596980.1|  [L=434]
Description: aspartyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-85  285.4   0.0    5.7e-85  285.1   0.0    1.0  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    5.4e-15   55.1   0.3      1e-14   54.3   0.3    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0011   18.6   0.1        0.2   11.1   0.0    2.4  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
       0.15   12.2   0.4       0.73    9.9   0.1    2.3  3  BOF              Bacterial OB fold (BOF) protein


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 !  285.1   0.0   1.3e-88   5.7e-85       3     313 ..     115     428 ..     113     429 .. 0.96

  Alignments for each domain:
  == domain 1  score: 285.1 bits;  conditional E-value: 1.3e-88
                                       CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                       tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aL 75 
                                        +rl+nr ldlr+++v++++++rs v++avr+ + e + +ei+tP ++ + te+g +lF +       ++f    ++
  gi|336253873|ref|YP_004596980.1| 115 STRLDNRTLDLRKDDVQSIFEIRSGVLNAVRDQFREFDCTEINTPKIVATGTEGGTELFPI-------TYFgeeaFM 184
                                       689**********************************************************.......566666679 PP

                                       -S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  76 tqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakd 152
                                       +qspql+++l++ + ++rvf+i++ FRaE+++t rhl+E t+i++e +f ++ed m+v+e+++ks  + v e+  ++
  gi|336253873|ref|YP_004596980.1| 185 NQSPQLFKQLIAGSNVERVFEIGPIFRAEEHNTPRHLNEATSIDFEGAFCDHEDAMDVAEGIVKSAYEAVQENFGDE 261
                                       **************************************************************************999 PP

                                       CCHTTTTTSEE-SSS.-EEEEHHHHHHHHHTS.........-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBB CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 153 iefvirrnskdlkkp.fkrltykeaieklnei.........gkdldkaderalvkkeknepvfvtdfPaelkpFyar 219
                                       +e      + ++++  f+r++y+eaie++n +         g+dl+++ e al + +    +f+td+P+e+kpFy +
  gi|336253873|ref|YP_004596980.1| 262 LEALGIADEFEVPEGdFPRISYEEAIERINATgeldeqlvwGDDLSTPAEEALGQ-DVGGHYFITDWPSEIKPFYIK 337
                                       9998777666666666************9999**********************9.88899**************** PP

                                       BSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 220 keeddkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvm 296
                                       +++dd++l+ ++Dl+ + +Elv+G +R++++e+l e ++++gld   +++f+ y+++++yG+pph+G+glG +Rl+m
  gi|336253873|ref|YP_004596980.1| 338 DHDDDPELSTGFDLMHPRMELVSGGQREHRHEKLIEGFEQQGLD---PDQFEYYTKMFKYGMPPHAGFGLGGERLLM 411
                                       ********************************************...****************************** PP

                                       HHCT-SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 297 lllgsesIrdviaFPkl 313
                                       +ll++++Ir++++FP+ 
  gi|336253873|ref|YP_004596980.1| 412 TLLNLDNIREAVLFPRD 428
                                       ***************96 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 !   54.3   0.3   2.3e-18     1e-14       1      75 [.      16      94 ..      16      95 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 2.3e-18
                                      EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEE CS
                   tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrr...pggelelkvee 72
                                      VtvaG+v+ i  r+ g+++f++lrD tg+iq+ + +    ++  ++  ++ +++v++v+G v++    p+g +e++ e+
  gi|336253873|ref|YP_004596980.1| 16 VTVAGWVHEI--RDLGGIAFLILRDTTGKIQIKFEKeemdDDLVETGLDVSRESVIKVSGGVEEEpraPTG-VEVTPES 91
                                      9*********..************************999999999999999**************999999.****999 PP

                                      EEE CS
                   tRNA_anti-codon 73 iel 75
                                      +e+
  gi|336253873|ref|YP_004596980.1| 92 LEV 94
                                      997 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 !    4.9   0.0    0.0036        16      91     152 ..     190     254 ..     185     264 .. 0.78
   2 !   11.1   0.0   4.5e-05       0.2     212     234 ..     400     422 ..     389     432 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0036
                                       HHHHHTTS-SSEEEEEEEEEEBSST.-SSSB-SEEEEE..EEEEEETT--HHHHHHHHHHHHHHH CS
                      tRNA-synt_2d  91 qirtlekkkppikiisigrvfRrda.vDathlaeFhqv..eglvvdenvsladlkgvleellkkl 152
                                        +++l + +   +++ ig +fR ++    +hl e +++  eg ++d++  ++   g++++ ++++
  gi|336253873|ref|YP_004596980.1| 190 LFKQLIAGSNVERVFEIGPIFRAEEhNTPRHLNEATSIdfEGAFCDHEDAMDVAEGIVKSAYEAV 254
                                       5566666666779**********99677899988887644799****999999999998877765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.5e-05
                                       EEEEEEHHHHHHHHHT-SSGHHH CS
                      tRNA-synt_2d 212 fafGlGveRlamlkygieDiRel 234
                                       ++fGlG eRl m  +++++iRe 
  gi|336253873|ref|YP_004596980.1| 400 AGFGLGGERLLMTLLNLDNIREA 422
                                       68*******************84 PP

>> BOF  Bacterial OB fold (BOF) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00016      0.73      53      98 ..      35      87 ..       7      90 .. 0.72
   2 ?   -2.7   0.0       1.4   6.3e+03      47      79 ..     127     160 ..     121     164 .. 0.69
   3 ?   -2.4   0.0       1.1   4.9e+03      79      91 ..     288     300 ..     271     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
                                      EEEETTEEEEEE--GGGST......T----TTSEEEEEEEEEEE.TTEEEEEE CS
                               BOF 53 vFrDasGeikveiddrvfn......glevqpkdkvkiqGkvDke.lekaeidv 98
                                      + rD++G+i+++ ++++ +      gl+v  +  +k++G v++e  +++ ++v
  gi|336253873|ref|YP_004596980.1| 35 ILRDTTGKIQIKFEKEEMDddlvetGLDVSRESVIKVSGGVEEEpRAPTGVEV 87
                                      68**********9999886455555899999********99965145555555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                                       EETTEEEEEETTEEEEEE--G.GGSTT----TTS CS
                               BOF  47 iddDeyvFrDasGeikveidd.rvfnglevqpkd 79 
                                       +dd + +F   sG ++ + d+ r+f+ +e++  +
  gi|336253873|ref|YP_004596980.1| 127 KDDVQSIFEIRSGVLNAVRDQfREFDCTEINTPK 160
                                       5666677888888887555443788888888655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.1
                                       SEEEEEEEEEEET CS
                               BOF  79 dkvkiqGkvDkel 91 
                                       ++++ +G++D++l
  gi|336253873|ref|YP_004596980.1| 288 ERINATGELDEQL 300
                                       689999****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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 0.21s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3573.20
//
Query:       gi|336253874|ref|YP_004596981.1|  [L=411]
Description: sodium/hydrogen exchanger [Halopiger xanaduensis SH-6]
Scores for 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-38  131.8  26.5    3.3e-38  131.5  26.5    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
      0.048   12.2   0.1      0.064   11.7   0.1    1.1  1  Acatn           Acetyl-coenzyme A transporter 1


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 !  131.5  26.5   3.7e-42   3.3e-38       3     379 ..       9     397 ..       7     399 .. 0.89

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 3.7e-42
                                       HHHHHHHHHHHHHHHTT....SXHHHHHHHHHHHHTTTTTS.........HHHCHCCHHHHCHHCCHHHHCTCGCCT CS
                    Na_H_Exchanger   3 llillallvgllarrlk....lpeivgliiaGlllGpsglglieps....eedlevlselglilllFlaGleldlre 71 
                                       +++ +a+l+++ + rl     ++ +++++++G+++    l l +p+     ++ e+l e+g+i+ l  aGl++d+  
  gi|336253874|ref|YP_004596981.1|   9 VIVGVAVLGTVALPRLLdnrpVSFPIVYVAFGIVVFSLPLELPAPDplahGTIAEHLTEIGVIVALMGAGLKIDRPP 85 
                                       334435555553555544777999*****************8777789999************************** PP

                                       GCCTHHHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC...CCCTSTCCCCCCHHH CS
                    Na_H_Exchanger  72 lrknlksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailk..eegrvperlgtlllg 146
                                        +k +k++  l+ + + +t+++ ++l ++   +g+++  a+l+ga++++tdpv+++ +     ++  + +++  l +
  gi|336253874|ref|YP_004596981.1|  86 GFKRWKTAWRLLGITMPLTIAAAAVLGWW--AVGLSIPTAVLLGAVIAPTDPVLAADVQVdpPQKGESDEVRFALTS 160
                                       99**************9999995666665..689************************998756666888888899* PP

                                       HHHHHHHHCCCCCHHHHHHTX.XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS....CTHHHHHHHH CS
                    Na_H_Exchanger 147 esvlnDavavvllavllalak.eeaggetslllllliflvvavgglllglvigwllrlitrft....dddrelevll 218
                                       e++lnD++a++++++++a+a+ + a +++ l +l++ +++ +v+g+++g+v+g+ l+++        +  +++  + 
  gi|336253874|ref|YP_004596981.1| 161 EAGLNDGLAFPFTYLAIAMATaGVAPDNWLLEWLAVDVVYKIVVGVAVGWVFGYALAKFVFQYpastQLAKAMGGAE 237
                                       ********************887788888888**********************9999988888999999******* PP

                                       HHHHHHHHHHHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH...HHHHHHHHHHHHHHSXHHHHHXXHHH CS
                    Na_H_Exchanger 219 vlllallaallaellgvsgilgaflaGlvlseyefsnklseklesfre...glfnplfFvlvGlsldlkvlnnhlsv 292
                                       +l+  l+a++l+el g  g +++f+a +++ + e++++ +++l+ f+e    l++ ++ vl+G  +   ++   +  
  gi|336253874|ref|YP_004596981.1| 238 ALAATLIAYGLTELAGGYGFIAVFVAAVAIRGFERDHEYHQELHDFAEvveRLVVAALLVLFGGAIATGLFA--PLT 312
                                       ***************************************************9***************88885..*** PP

                                       HHHHHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTT.SSTTTCSTSXHH CS
                    Na_H_Exchanger 293 lilvllilvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarel.yallivvvlftv 368
                                       ++++ll l+++ll+r+la++l l   g++    +i++fg  ++g++++ la  + ++++ ++   ++++ ++vl+++
  gi|336253874|ref|YP_004596981.1| 313 WRAALLGLALVLLVRPLAGLLGLV--GYPPERNAIAFFGIRGIGSFYY-LAYGVNNAEFDSSGIvWSIVGFAVLVSI 386
                                       *********************886..8888777777777776788875.555556667******************* PP

                                       HHHHHHHHHHH CS
                    Na_H_Exchanger 369 lvqGlslkpll 379
                                       +v+G++ +p++
  gi|336253874|ref|YP_004596981.1| 387 VVHGVTAAPVM 397
                                       *********98 PP

>> Acatn  Acetyl-coenzyme A transporter 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.2e-06     0.064     121     192 ..     168     239 ..     148     288 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.2e-06
                             Acatn 121 LtlvflvLvllcatqDiavDgWaltiLskkslsyastaqtvGlnlGyflsftvflslnssdfvnkylrkvpl 192
                                       L++ f+ L + +at  +a D W l+ L+ + +       +vG  +Gy l+  vf    s+++++    +++l
  gi|336253874|ref|YP_004596981.1| 168 LAFPFTYLAIAMATAGVAPDNWLLEWLAVDVVYKIVVGVAVGWVFGYALAKFVFQYPASTQLAKAMGGAEAL 239
                                       8899*************************9999999999************9*9988888887655443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); 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:                         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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2908.83
//
Query:       gi|336253875|ref|YP_004596982.1|  [L=151]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-38  132.1   0.2    2.3e-38  131.9   0.2    1.0  1  Usp             Universal stress protein family
     0.0045   17.0   0.0      0.007   16.4   0.0    1.2  1  DNA_photolyase  DNA photolyase


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 !  131.9   0.2   2.6e-42   2.3e-38       1     140 [.       1     134 [.       1     135 [. 0.96

  Alignments for each domain:
  == domain 1  score: 131.9 bits;  conditional E-value: 2.6e-42
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+ IlV++Dgs+ ++ A+++Al+ a++++a+l+ l+v+dp ++g  +d++ e + + +e ++  le      aa++
  gi|336253875|ref|YP_004596982.1|   1 MYDEILVPTDGSPGAESAIDHALHIARQNDATLHPLYVVDPADMGDLGDEPAELRAQCSEVTQPVLE------AAQE 71 
                                       9********************************************9999999999999999998886......579* PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       +g k e +v+eg p e i+e+a+   +dliV+G++g+sglsr+llGS++e+v+r+ap+pVl +
  gi|336253875|ref|YP_004596982.1|  72 AGLKAEQHVLEGTPNERIVEYADGAPIDLIVMGTHGKSGLSRVLLGSTAERVVRNAPVPVLTI 134
                                       ************************************************************965 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.8e-07     0.007      15      94 ..      21     103 ..      19     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.8e-07
                                       HHHHHHHCTTSEEEEEEEE-HHHHTCGS-CHHHHHHHHHHHHHHHHHH...HHTT..--EEEEESSHHHHHHHHHHH CS
                    DNA_photolyase  15 pALaaAaasgepvipvfvldpekahklrvgaarvdfllesLadLdeeL...relg..irLvvrrgdpadvlpelake 86 
                                       +AL+ A++++++++p++v+dp+++ +l  g+  +++ +++ +  +  L   +e g   + +v++g+p++ ++e+a  
  gi|336253875|ref|YP_004596982.1|  21 HALHIARQNDATLHPLYVVDPADMGDL--GDEPAELRAQCSEVTQPVLeaaQEAGlkAEQHVLEGTPNERIVEYADG 95 
                                       69********************76666..666666666665555555532233333477799999999999999999 PP

                                       CTECEEEE CS
                    DNA_photolyase  87 lgasavva 94 
                                       + ++ +v+
  gi|336253875|ref|YP_004596982.1|  96 APIDLIVM 103
                                       88888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1230.00
//
Query:       gi|336253876|ref|YP_004596983.1|  [L=129]
Description: hypothetical protein Halxa_2486 [Halopiger xanaduensis SH-6]
Scores for 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  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1130.22
//
Query:       gi|336253877|ref|YP_004596984.1|  [L=277]
Description: GHMP kinase [Halopiger xanaduensis SH-6]
Scores for complete 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-11   44.0   2.3    1.1e-10   41.5   1.6    2.2  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 !   41.5   1.6   6.3e-15   1.1e-10       2      66 .]      80     144 ..      79     144 .. 0.92
   2 ?    0.4   0.0     0.043   7.7e+02      41      61 ..     215     236 ..     190     238 .. 0.72

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 6.3e-15
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                       ++ +s++P+gaG+G S+Ala+++++A+++ ++ +l++++l   a+ + + + ++ gDv a + Gg
  gi|336253877|ref|YP_004596984.1|  80 VEATSDLPLGAGFGVSGALALGTALAANRVFDRKLSMNELVTIAHGAEVQAGTGLGDVVAQARGG 144
                                       7789***************************999999********6665599*********9998 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.043
                                       H.HHHHHHHHHHHHHHSHHHHH CS
                    GHMP_kinases_N  41 l.aleaerlaqggngsggDvaa 61 
                                       l a eae l  +++  +gDvaa
  gi|336253877|ref|YP_004596984.1| 215 LfAREAELLTERVSETIGDVAA 236
                                       3399999999999999****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2113.52
//
Query:       gi|336253878|ref|YP_004596985.1|  [L=985]
Description: hypothetical protein Halxa_2488 [Halopiger xanaduensis SH-6]
Scores for 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-71  233.7   7.2      2e-10   40.4   0.0   13.4 13  DUF1508          Domain of unknown function (DUF1508)
    0.00081   20.2   4.8        3.6    8.4   0.1    5.3  4  FtsQ             Cell division protein FtsQ
     0.0012   19.0   0.2         13    5.9   0.0    4.2  4  Nucleoporin2     Nucleoporin autopeptidase
     0.0017   18.6   6.6         38    4.5   0.0    6.9  8  DDE_Tnp_IS240    DDE domain
  ------ inclusion threshold ------
      0.048   14.8   0.1       0.33   12.1   0.0    2.5  1  PPC              Bacterial pre-peptidase C-terminal domain
      0.087   12.0   2.1       0.13   11.4   2.1    1.2  1  LtrA             Bacterial low temperature requirement A prot
       0.25   10.5   0.0       0.46    9.7   0.0    1.3  1  TolB_like        TolB-like 6-blade propeller-like
       0.34   10.7   0.0       0.34   10.7   0.0    4.2  5  DUF2914          Protein of unknown function (DUF2914)
       0.45   10.7   0.0       0.45   10.7   0.0    6.9  7  DUF2188          Uncharacterized protein conserved in bacteri
       0.55   10.7   2.5        1.9    9.0   0.3    2.3  2  DMRT-like        Doublesex-and mab-3-related transcription fa
        1.4    9.3  10.2         38    4.7   0.0    5.7  6  SPOR             Sporulation related domain
        6.6    6.7   6.8         11    6.0   0.1    3.8  4  DUF615           Protein of unknown function (DUF615)


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 !   10.4   0.0    0.0003      0.45       1      45 [.     183     226 ..     183     229 .. 0.85
   2 !   17.1   0.0   2.4e-06    0.0036       1      48 []     240     288 ..     240     288 .. 0.97
   3 !   12.5   0.0   6.9e-05       0.1       4      36 ..     301     334 ..     299     346 .. 0.84
   4 ?    5.1   0.0     0.014        20       3      36 ..     360     394 ..     359     404 .. 0.87
   5 !   10.6   0.1   0.00026      0.39       2      48 .]     417     464 ..     417     464 .. 0.96
   6 !   31.2   0.0   9.6e-11   1.4e-07       5      47 ..     520     563 ..     518     564 .. 0.95
   7 !   40.4   0.0   1.3e-13     2e-10       3      47 ..     577     622 ..     575     623 .. 0.95
   8 !    6.9   0.0    0.0038       5.7       1      36 [.     634     670 ..     634     678 .. 0.90
   9 !    9.2   0.0    0.0007         1       3      45 ..     692     735 ..     691     736 .. 0.95
  10 !    9.3   0.0   0.00065      0.97       5      46 ..     753     795 ..     751     796 .. 0.90
  11 !   11.1   0.0   0.00018      0.27       2      48 .]     819     866 ..     818     866 .. 0.93
  12 !   31.0   0.0   1.1e-10   1.7e-07       1      46 [.     877     923 ..     877     925 .. 0.92
  13 !   26.2   0.0   3.5e-09   5.2e-06       4      43 ..     938     978 ..     936     981 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                                       ETTTEEEEEEE-TTS-EEEEEEEB.SSHHHHHHHHHHHHHHTTTCC CS
                           DUF1508   1 DknGefrFrLkaaNgevIatsegY.sskaaaenGIesVkknapdae 45 
                                       D++G + ++  +  +e +atseg  +++ +a++GIe+Vk++ ++a 
  gi|336253878|ref|YP_004596985.1| 183 DEQGDWKWNVLH--REALATSEGSaATRPDAREGIERVKSQISSAG 226
                                       678999999999..699***999735899**********9988775 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.4e-06
                                       ETTTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCEEE CS
                           DUF1508   1 DknGefrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaeveD 48 
                                       D++G + ++L  ++g v++t    ++++ +ae+ +   k  +p+a++ +
  gi|336253878|ref|YP_004596985.1| 240 DRDGTWQWTLAREDGSVVGTcDREFDDRDGAEESVSFLKDRGPEADIIE 288
                                       789*******************************************976 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 6.9e-05
                                       TEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHH CS
                           DUF1508   4 GefrFrLkaaNgevIat.segYsskaaaenGIes 36 
                                       + +++ L+++ + v+at   g+++ a+ae++ + 
  gi|336253878|ref|YP_004596985.1| 301 DRWYWQLVDDEHAVLATsDRGHDDQASAEEAART 334
                                       68***************889*********98765 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.014
                                       TTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHH CS
                           DUF1508   3 nGefrFrLkaaNgevIat.segYsskaaaenGIes 36 
                                       ++ + +r++++   vIat   + +++ +ae++ e 
  gi|336253878|ref|YP_004596985.1| 360 GDGWTWRFVDETDTVIATaADTAETRRGAEEAAET 394
                                       578***************99999999999998775 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00026
                                       TTTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCEEE CS
                           DUF1508   2 knGefrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaeveD 48 
                                       +++e+ +rL+++   v+a+  e Y++     +  e   +na da+v++
  gi|336253878|ref|YP_004596985.1| 417 SDEEWEWRLVDESEHVVARgPESYADHGETTRETEQFAENARDADVVE 464
                                       689****************99************************986 PP

  == domain 6  score: 31.2 bits;  conditional E-value: 9.6e-11
                                       EEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCEE CS
                           DUF1508   5 efrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaeve 47 
                                        +++rL+ +++ev+a+  e +++++ a  +Ie+V+++a++a++ 
  gi|336253878|ref|YP_004596985.1| 520 DWHWRLVTDDREVVAAsTEPHADAETATAAIERVREQASEADLI 563
                                       5****************************************986 PP

  == domain 7  score: 40.4 bits;  conditional E-value: 1.3e-13
                                       TTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCEE CS
                           DUF1508   3 nGefrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaeve 47 
                                       +Ge+r+rL +++g+v+a+ +e ++s++ a +++   k++apdae+ 
  gi|336253878|ref|YP_004596985.1| 577 SGEWRWRLIDEDGNVLADsGEEHASRSEAAEAMMTLKEQAPDAELL 622
                                       8******************************************986 PP

  == domain 8  score: 6.9 bits;  conditional E-value: 0.0038
                                       ETTTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHH CS
                           DUF1508   1 DknGefrFrLkaaNgevIat.segYsskaaaenGIes 36 
                                       D+n+e+ +rL ++ g  +a    ++ ++ aa++++++
  gi|336253878|ref|YP_004596985.1| 634 DENDEWGWRLIDEGGKLVAEdPATHPTRDAARDAMNR 670
                                       89*****************999999999999999876 PP

  == domain 9  score: 9.2 bits;  conditional E-value: 0.0007
                                       TTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCC CS
                           DUF1508   3 nGefrFrLkaaNgevIat.segYsskaaaenGIesVkknapdae 45 
                                       ++e+++r++   g ++a    g +++   ++  esV+  a++a+
  gi|336253878|ref|YP_004596985.1| 692 DEEWHWRFVLPSGDTVAVdADGAATRDELRDRLESVRDAAASAQ 735
                                       78***************************************997 PP

  == domain 10  score: 9.3 bits;  conditional E-value: 0.00065
                                       EEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCE CS
                           DUF1508   5 efrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaev 46 
                                        + +rL ++++e +a+   +Y+ ++ a   + +  + a+ a++
  gi|336253878|ref|YP_004596985.1| 753 DWSWRLLDRDREELADaTVTYEGRETALGRVSALTERADAAPI 795
                                       699************************9999988888888877 PP

  == domain 11  score: 11.1 bits;  conditional E-value: 0.00018
                                       TTTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCEEE CS
                           DUF1508   2 knGefrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaeveD 48 
                                       k + +r+ L++a++ v+a+      +k      +e Vk  ap a ++D
  gi|336253878|ref|YP_004596985.1| 819 KTDAWRWDLVDADRDVLASaAGAAPTKDELLSTVEEVKQLAPMAGRVD 866
                                       6688***************999999******************99887 PP

  == domain 12  score: 31.0 bits;  conditional E-value: 1.1e-10
                                       ETTTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCE CS
                           DUF1508   1 DknGefrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaev 46 
                                       D+++ + +rL +++g  +at  e+Y+s aaa++G e V+     a++
  gi|336253878|ref|YP_004596985.1| 877 DEDDRWSWRLLDEDGRPVATgTETYESNAAARKGLEQVRDLIEAASI 923
                                       7899**********************************987777766 PP

  == domain 13  score: 26.2 bits;  conditional E-value: 3.5e-09
                                       TEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTT CS
                           DUF1508   4 GefrFrLkaaNgevIat.segYsskaaaenGIesVkknapd 43 
                                       + + +rL+++ g  +a   ++Y+s+ aa+++++ Vk++apd
  gi|336253878|ref|YP_004596985.1| 938 DGWVWRLVDEYGSRMAEsTQTYESRTAAREAMNDVKSHAPD 978
                                       67**************************************8 PP

>> FtsQ  Cell division protein FtsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         3   4.5e+03      35      80 ..     387     433 ..     358     454 .. 0.66
   2 ?   -0.2   0.0       1.1   1.7e+03      65     104 ..     518     556 ..     516     572 .. 0.70
   3 ?    6.3   0.1     0.011        16      10      84 ..     583     711 ..     572     741 .. 0.43
   4 !    8.4   0.1    0.0024       3.6      38      93 ..     843     907 ..     818     927 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3
                                       ......S-HHHHHCCS-HHHHH..S-SEE-SS-TTEEEE-T.TS-EE CS
                              FtsQ  35 Gpegsekevlevlaelpeelkp.leiseialserrrwqlvlddgvev 80 
                                       G+e++++ +l++l +++  ++   + ++ + +e+ +w+lv ++   v
  gi|336253878|ref|YP_004596985.1| 387 GAEEAAETLLAELSSASVTVSGdPTYEQYTSDEEWEWRLVDESEHVV 433
                                       44444555666666665555556666666888888888887666555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                                       S-TTEEEE-T.TS-EEEEES....TTHHHHHHT-CCHHHC CS
                              FtsQ  65 serrrwqlvlddgvevklgreelaedleeklarlvkilpq 104
                                       +++  w+lv+dd+ ev   + e+ +d e + a+  ++ +q
  gi|336253878|ref|YP_004596985.1| 518 TQDWHWRLVTDDR-EVVAASTEPHADAETATAAIERVREQ 556
                                       57789***99555.55555556777677777766666665 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.011
                                       EEEETT--B-C.........CCBS...S-EEE........................................S-... CS
                              FtsQ  10 alidaeGevfea....deeaedek...lPllt..................................Gpegseke... 42 
                                       +lid++G+v+++      ++  e+   +  l                                   G      +   
  gi|336253878|ref|YP_004596985.1| 583 RLIDEDGNVLADsgeeH-ASRSEAaeaMMTLKeqapdaelleietaafelfvdendewgwrlidegG------Klva 652
                                       67777777776644321.1111111222222222222222222233333333333333333332221......0111 PP

                                       ...........HHHHHCCS-HHHHH.S-SEE.......-SS-TTEEEE-T.TS-EEEEES CS
                              FtsQ  43 ...........vlevlaelpeelkpleisei.......alserrrwqlvlddgvevklgr 84 
                                                  + +++++l e l++ e++ +         +e+  w++vl +g +v +  
  gi|336253878|ref|YP_004596985.1| 653 edpathptrdaARDAMNRLLEHLES-EVRTMddaifqpYADEEWHWRFVLPSGDTVAVDA 711
                                       1222222333333333333333333.3333333344446677777777776666655555 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0024
                                       ...S-HHHHHCCS-HHHHH.......S-SEE....-SS-TTEEEE-T.TS-EEEEES....TTHHH CS
                              FtsQ  38 gsekevlevlaelpeelkp......leisei....alserrrwqlvlddgvevklgreelaedlee 93 
                                        +++e+l+ ++e+ ++l+p      +++++       ++r +w+l+ +dg  v  g e  +++ ++
  gi|336253878|ref|YP_004596985.1| 843 PTKDELLSTVEEV-KQLAPmagrvdFDVASFelvaDEDDRWSWRLLDEDGRPVATGTETYESNAAA 907
                                       3333455555555.44444444566666666777778999999**************877765554 PP

>> Nucleoporin2  Nucleoporin autopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.057        85     122     143 ..     173     194 ..     157     196 .. 0.91
   2 ?   -2.0   0.0       2.4   3.6e+03      56      72 ..     461     477 ..     450     488 .. 0.79
   3 ?    4.0   0.0     0.033        49     102     140 ..     545     583 ..     530     585 .. 0.71
   4 !    5.9   0.0    0.0085        13      96     140 ..     656     700 ..     649     702 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.057
                                       -SSSEEEEEETTTTEEEEEES- CS
                      Nucleoporin2 122 vegteFvsydpetgtwtfkVeH 143
                                        e+++F  ++ e+g w+ +V H
  gi|336253878|ref|YP_004596985.1| 173 LEDAQFAVFRDEQGDWKWNVLH 194
                                       589*****************99 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.4
                                       TTEEEETTEEEESSSCC CS
                      Nucleoporin2  56 kivklekkevtVYpdee 72 
                                       ++v++++ + +VYp +e
  gi|336253878|ref|YP_004596985.1| 461 DVVEIDDAAYEVYPASE 477
                                       69***********9884 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.033
                                       -B---TT-HHHHHHHHHHHH-SSSEEEEEETTTTEEEEE CS
                      Nucleoporin2 102 eeikdkskarvkkhieklkkvegteFvsydpetgtwtfk 140
                                       + +   ++ r +  ++ l + e++ F  y++++g+w+ +
  gi|336253878|ref|YP_004596985.1| 545 TATAAIERVREQASEADLIEFEEAAFQVYEADSGEWRWR 583
                                       333444455666666777777***************976 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.0085
                                       B-TTT--B---TT-HHHHHHHHHHHH-SSSEEEEEETTTTEEEEE CS
                      Nucleoporin2  96 kdkatkeeikdkskarvkkhieklkkvegteFvsydpetgtwtfk 140
                                        ++ t++  +d+ ++ +++++++++++ ++ F  y  e++ w+f 
  gi|336253878|ref|YP_004596985.1| 656 ATHPTRDAARDAMNRLLEHLESEVRTMDDAIFQPYADEEWHWRFV 700
                                       455677777788888888888889999****************95 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.48   7.2e+02      15      53 ..     299     337 ..     295     349 .. 0.82
   2 ?    3.2   0.0     0.062        92      19      93 ..     363     435 ..     358     452 .. 0.76
   3 ?    1.1   0.0      0.28   4.1e+02      18      56 ..     520     558 ..     517     565 .. 0.89
   4 ?    2.0   0.0      0.15   2.3e+02      18      46 ..     579     607 ..     563     629 .. 0.72
   5 ?    4.5   0.0     0.026        38      13      56 ..     633     676 ..     625     687 .. 0.86
   6 ?   -3.1   0.0       5.4   8.1e+03      15      36 ..     750     772 ..     749     780 .. 0.79
   7 ?   -0.1   0.0      0.65   9.7e+02      15      45 ..     878     908 ..     874     921 .. 0.73
   8 ?    1.1   0.0      0.28   4.2e+02      16      49 ..     937     970 ..     934     980 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.48
                     DDE_Tnp_IS240  15 GkwaYlyravDkegrildflvskrRdtkaakaflrkalk 53 
                                       +++++ + +vD e  +l    + + d+++a  + r + +
  gi|336253878|ref|YP_004596985.1| 299 ERDRWYWQLVDDEHAVLATSDRGHDDQASAEEAARTFAE 337
                                       67899************9999999999888877766655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.062
                     DDE_Tnp_IS240  19 YlyravDkegrildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkelkregelfdevshvqvk 93 
                                       + +r vD++  ++  +      +  a  + + +l +   + +++++ + ++y++  +   +e +l de +hv ++
  gi|336253878|ref|YP_004596985.1| 363 WTWRFVDETDTVIATAADTAETRRGAEEAAETLLAEL--SSASVTVSGDPTYEQYTSDEEWEWRLVDESEHVVAR 435
                                       889*****99999988755444444444444445444..566899999999999999988888888888888765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.28
                     DDE_Tnp_IS240  18 aYlyravDkegrildflvskrRdtkaakaflrkalkkek 56 
                                        + +r+v  + +++ +    + d++ a a+++++ ++++
  gi|336253878|ref|YP_004596985.1| 520 DWHWRLVTDDREVVAASTEPHADAETATAAIERVREQAS 558
                                       688******************************998874 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.15
                     DDE_Tnp_IS240  18 aYlyravDkegrildflvskrRdtkaaka 46 
                                       ++ +r++D++g++l     ++  +  a+ 
  gi|336253878|ref|YP_004596985.1| 579 EWRWRLIDEDGNVLADSGEEHASRSEAAE 607
                                       577*********98765555555544444 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.026
                     DDE_Tnp_IS240  13 ikGkwaYlyravDkegrildflvskrRdtkaakaflrkalkkek 56 
                                       + +++++ +r++D+ g+++      +  ++aa+ +++++l++ +
  gi|336253878|ref|YP_004596985.1| 633 VDENDEWGWRLIDEGGKLVAEDPATHPTRDAARDAMNRLLEHLE 676
                                       67788999*********99988888889999*********9984 PP

  == domain 6  score: -3.1 bits;  conditional E-value: 5.4
                     DDE_Tnp_IS240  15 GkwaYlyravDkegr.ildflvs 36 
                                       G + + +r++D + + + d+ v+
  gi|336253878|ref|YP_004596985.1| 750 GTDDWSWRLLDRDREeLADATVT 772
                                       788999*****999877777776 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 0.65
                     DDE_Tnp_IS240  15 GkwaYlyravDkegrildflvskrRdtkaak 45 
                                       +++++ +r++D++gr +      +   +aa+
  gi|336253878|ref|YP_004596985.1| 878 EDDRWSWRLLDEDGRPVATGTETYESNAAAR 908
                                       678999*******998876666555555555 PP

  == domain 8  score: 1.1 bits;  conditional E-value: 0.28
                     DDE_Tnp_IS240  16 kwaYlyravDkegrildflvskrRdtkaakaflr 49 
                                       ++ +++r+vD+ g  +    + +  ++aa+ +++
  gi|336253878|ref|YP_004596985.1| 937 EDGWVWRLVDEYGSRMAESTQTYESRTAAREAMN 970
                                       678********99866666666666666666665 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 ?   12.1   0.0   0.00022      0.33       5      40 ..     697     755 ..     696     772 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                                       EEEEE-TT-EEEEEES-TT..........................SEEEEE-TT..-SS- CS
                               PPC   5 ysfevpagdsltididggti........................dldLylldsngtsvaa 40 
                                       ++f++p+gd++ +d dg ++                        d++++l+d+  t++++
  gi|336253878|ref|YP_004596985.1| 697 WRFVLPSGDTVAVDADGAATrdelrdrlesvrdaaasaqrctigDVTVQLYDAG-TDDWS 755
                                       78****************************************99999***9999.87776 PP

>> LtrA  Bacterial low temperature requirement A protein (LtrA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.1   8.8e-05      0.13     257     337 ..      29     114 ..      15     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.8e-05
                              LtrA 257 ylhllivagiillavglelll.....ahpeelldlaaalllfggvalfllgllllkrvllgsvslsrlvllllllal 328
                                       y++ l+++g+i+ a+g+   +     +  ee+   ++ ++ ++g+a++l g+ l+  v ++ +++s + l ++l+ +
  gi|336253878|ref|YP_004596985.1|  29 YGYWLFILGYIIGAAGVVAFVvgyagSFGEEPIIRVTGVTSAAGLAICLFGIGLMLPVRRRGIQASVVGLFVALVGV 105
                                       55556666666666666665556655334567888999999**************9999999999999988888888 PP

                              LtrA 329 lalalvlaa 337
                                       +a+++v + 
  gi|336253878|ref|YP_004596985.1| 106 AAFGVVYPN 114
                                       888887765 PP

>> TolB_like  TolB-like 6-blade propeller-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0003      0.46     106     170 ..     552     616 ..     520     621 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0003
                         TolB_like 106 elidldksilrildltdstFivsd.ysgdsrfllvdrdgkllkkakeiptlneekekiartalaqa 170
                                       ++ + + s    +++++  F v + +sg+ r+ l+d+dg++l  ++e+   ++e+ ++  t ++qa
  gi|336253878|ref|YP_004596985.1| 552 RVRE-QASEADLIEFEEAAFQVYEaDSGEWRWRLIDEDGNVLADSGEEHASRSEAAEAMMTLKEQA 616
                                       3333.3333346899*****7765278*******************************99999997 PP

>> DUF2914  Protein of unknown function (DUF2914)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.2       8.2   1.2e+04      38      48 ..     182     192 ..     180     194 .. 0.72
   2 ?    2.4   0.0     0.089   1.3e+02      31      58 ..     232     259 ..     216     261 .. 0.85
   3 ?   10.7   0.0   0.00023      0.34      35      57 ..     571     593 ..     568     595 .. 0.88
   4 ?   -3.0   0.1       4.2   6.3e+03      44      59 ..     823     838 ..     822     839 .. 0.86
   5 ?   -3.6   0.1       6.8     1e+04      44      57 ..     882     895 ..     881     896 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 8.2
                           DUF2914  38 peseGkWrVeV 48 
                                       ++++G+W+  V
  gi|336253878|ref|YP_004596985.1| 182 RDEQGDWKWNV 192
                                       45899998655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.089
                           DUF2914  31 ysskqllpeseGkWrVeVeteagqllgr 58 
                                        s  +l+++++G W+ ++  e+g ++g+
  gi|336253878|ref|YP_004596985.1| 232 TSAFRLYEDRDGTWQWTLAREDGSVVGT 259
                                       555667777**************99986 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00023
                           DUF2914  35 qllpeseGkWrVeVeteagqllg 57 
                                       q++++++G+Wr ++++e+g++l+
  gi|336253878|ref|YP_004596985.1| 571 QVYEADSGEWRWRLIDEDGNVLA 593
                                       567779***************97 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 4.2
                           DUF2914  44 WrVeVeteagqllgrl 59 
                                       Wr ++++++  +l+++
  gi|336253878|ref|YP_004596985.1| 823 WRWDLVDADRDVLASA 838
                                       999******9999875 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 6.8
                           DUF2914  44 WrVeVeteagqllg 57 
                                       W  ++++e+g+ ++
  gi|336253878|ref|YP_004596985.1| 882 WSWRLLDEDGRPVA 895
                                       88899999999765 PP

>> DUF2188  Uncharacterized protein conserved in bacteria (DUF2188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.3       8.2   1.2e+04       9      17 ..     245     253 ..     239     255 .. 0.53
   2 ?    4.4   0.3     0.027        41      25      41 ..     322     338 ..     308     348 .. 0.87
   3 ?    2.1   0.1      0.14   2.1e+02      21      47 ..     378     404 ..     359     410 .. 0.82
   4 ?    3.3   2.1     0.061        91      19      59 ..     537     583 ..     521     586 .. 0.86
   5 ?    1.0   0.2      0.32   4.8e+02      11      47 ..     582     621 ..     570     622 .. 0.67
   6 ?   10.7   0.0    0.0003      0.45       6      49 ..     636     681 ..     632     684 .. 0.82
   7 ?    2.6   0.2       0.1   1.5e+02       8      38 ..     939     972 ..     932     979 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8.2
                           DUF2188   9 ggWavkreG 17 
                                       ++W++ re+
  gi|336253878|ref|YP_004596985.1| 245 WQWTLARED 253
                                       346666665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.027
                           DUF2188  25 fdTqeeAieaArelAke 41 
                                       +d q+ A eaAr +A++
  gi|336253878|ref|YP_004596985.1| 322 HDDQASAEEAARTFAER 338
                                       899************87 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.14
                           DUF2188  21 asktfdTqeeAieaArelAkeqggsel 47 
                                       a+ t +T+  A eaA+ l++e   +++
  gi|336253878|ref|YP_004596985.1| 378 AADTAETRRGAEEAAETLLAELSSASV 404
                                       788999************998545555 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.061
                           DUF2188  19 srasktfdTqeeAieaArelAke......qggselvihgrd.Gqirer 59 
                                       + +++  +T  +Aie+ re A e      +  ++  +  +d G++r+r
  gi|336253878|ref|YP_004596985.1| 537 TEPHADAETATAAIERVREQASEadliefE-EAAFQVYEADsGEWRWR 583
                                       567788899************776899977.89999999998999887 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.32
                           DUF2188  11 Wavkre.Ggsra..sktfdTqeeAieaArelAkeqggsel 47 
                                       W + +e G+  a   + + +++eA ea+  l ++  ++el
  gi|336253878|ref|YP_004596985.1| 582 WRLIDEdGNVLAdsGEEHASRSEAAEAMMTLKEQAPDAEL 621
                                       5555554444443367899*******99999877677776 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.0003
                           DUF2188   6 kddggWavkreGgsrask...tfdTqeeAieaArelAkeqggselvi 49 
                                       +d++gW + +eGg+  ++   t++T+++A +a+++l++    se+++
  gi|336253878|ref|YP_004596985.1| 636 NDEWGWRLIDEGGKLVAEdpaTHPTRDAARDAMNRLLEHL-ESEVRT 681
                                       68899******99988643339**************9875.788765 PP

  == domain 7  score: 2.6 bits;  conditional E-value: 0.1
                           DUF2188   8 dggWavkre.Ggsra..sktfdTqeeAieaArel 38 
                                       ++ W + +e G+ +a  ++t++++ +A ea++++
  gi|336253878|ref|YP_004596985.1| 939 GWVWRLVDEyGSRMAesTQTYESRTAAREAMNDV 972
                                       3447777776777777799************986 PP

>> DMRT-like  Doublesex-and mab-3-related transcription factor C1 and C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.45   6.7e+02      47      69 ..     381     404 ..     368     444 .. 0.75
   2 ?    9.0   0.3    0.0012       1.9      47      66 ..     596     615 ..     587     633 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.45
                         DMRT-like  47 asEwqr.klEAAeALlaLrdSpqa 69 
                                       + E  r   EAAe Lla   S+ +
  gi|336253878|ref|YP_004596985.1| 381 TAETRRgAEEAAETLLAELSSASV 404
                                       5566662469******96666554 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0012
                         DMRT-like  47 asEwqrklEAAeALlaLrdS 66 
                                         E+  + EAAeA+++L++ 
  gi|336253878|ref|YP_004596985.1| 596 GEEHASRSEAAEAMMTLKEQ 615
                                       579999************75 PP

>> SPOR  Sporulation related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.026        38      12      45 ..     264     305 ..     263     311 .. 0.88
   2 ?    0.5   0.0      0.53   7.9e+02      14      43 ..     388     411 ..     387     417 .. 0.75
   3 ?   -3.2   0.2       7.8   1.2e+04      52      65 ..     541     554 ..     538     560 .. 0.75
   4 ?   -0.7   0.1       1.3   1.9e+03      52      70 ..     600     617 ..     599     622 .. 0.81
   5 ?   -2.1   0.0       3.4   5.1e+03      53      64 ..     660     671 ..     659     677 .. 0.88
   6 ?    4.4   0.0     0.032        48      50      74 ..     958     981 ..     956     982 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.026
                                       ES-HHHHHHHHHHCCHHT--...........EEECCSSSCEE CS
                              SPOR  12 fsseanAerlaakLrakgfaaav........avvsgggglyr 45 
                                       f +++ Ae+ ++ L+++g++a +        ++++ ++ +y+
  gi|336253878|ref|YP_004596985.1| 264 FDDRDGAEESVSFLKDRGPEADIieiegaafTYTEERDRWYW 305
                                       8899******************98888888888888888885 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.53
                                       -HHHHHHHHHHCCHHT--...EEECCSSSC CS
                              SPOR  14 seanAerlaakLrakgfaaavavvsggggl 43 
                                        e++Ae+l+a+L+++      +v+ +g++ 
  gi|336253878|ref|YP_004596985.1| 388 AEEAAETLLAELSSA------SVTVSGDPT 411
                                       5899*********99......455555444 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 7.8
                                       CTCCHHHHHHHHCH CS
                              SPOR  52 asreeAqaalkkLk 65 
                                       a+ e A aa+++++
  gi|336253878|ref|YP_004596985.1| 541 ADAETATAAIERVR 554
                                       68899999999998 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.3
                                       CTCCHHHHHHHHCHHHHTT CS
                              SPOR  52 asreeAqaalkkLkaaagi 70 
                                       asr+eA++a+  Lk  + +
  gi|336253878|ref|YP_004596985.1| 600 ASRSEAAEAMMTLK-EQAP 617
                                       699**********9.4555 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 3.4
                                       TCCHHHHHHHHC CS
                              SPOR  53 sreeAqaalkkL 64 
                                       +r++A++a+++L
  gi|336253878|ref|YP_004596985.1| 660 TRDAARDAMNRL 671
                                       899*****9988 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.032
                                       SBCTCCHHHHHHHHCHHHHTTS--B CS
                              SPOR  50 pfasreeAqaalkkLkaaagisafv 74 
                                        ++sr +A++a++ +k ++ +++++
  gi|336253878|ref|YP_004596985.1| 958 TYESRTAAREAMNDVK-SHAPDGWI 981
                                       69**************.89999998 PP

>> DUF615  Protein of unknown function (DUF615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3       0.6   8.9e+02      97     138 ..     519     558 ..     517     575 .. 0.67
   2 ?    1.6   0.4      0.17   2.5e+02      71     119 ..     542     600 ..     539     616 .. 0.65
   3 ?    6.0   0.1    0.0074        11      75     122 ..     798     846 ..     753     865 .. 0.76
   4 ?   -3.3   0.0       5.1   7.7e+03      97     131 ..     880     919 ..     876     922 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.6
                            DUF615  97 erwrdrLiaeddaaleelleeypevDrqeLRqlirnarkeke 138
                                       + w  rL+++d++++ +  e  p++D+++  + i ++r++++
  gi|336253878|ref|YP_004596985.1| 519 QDWHWRLVTDDREVVAASTE--PHADAETATAAIERVREQAS 558
                                       56888888888885544333..67777777777777776644 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.17
                            DUF615  71 dveairaalealknk..........seeetaalhelerwrdrLiaeddaaleelleeyp 119
                                       d e   aa+e+++++          +++ + + +   +wr rLi+ed ++l +  ee+ 
  gi|336253878|ref|YP_004596985.1| 542 DAETATAAIERVREQaseadliefeEAAFQVYEADSGEWRWRLIDEDGNVLADSGEEHA 600
                                       56666677777777422233322213333344455558*********999988777765 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0074
                            DUF615  75 iraa.lealknkseeetaalhelerwrdrLiaeddaaleelleeypevD 122
                                       i++a +  +++ s  e+a  ++ + wr  L++ d+++l  ++ ++p  D
  gi|336253878|ref|YP_004596985.1| 798 IEDAvIRVQRDASGDEAASGAKTDAWRWDLVDADRDVLASAAGAAPTKD 846
                                       33332666677899999**********************9999988755 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 5.1
                            DUF615  97 erwrdrLiaed...daaleelleeypev..DrqeLRqlir 131
                                       +rw  rL++ed    a+ +e +e   ++    +++R li 
  gi|336253878|ref|YP_004596985.1| 880 DRWSWRLLDEDgrpVATGTETYESNAAArkGLEQVRDLIE 919
                                       6888999999855545555555554444445566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (985 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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):              12  [number of targets reported over threshold]
# CPU time: 0.81u 0.27s 00:00:01.08 Elapsed: 00:00:00.45
# Mc/sec: 6629.19
//
Query:       gi|336253879|ref|YP_004596986.1|  [L=258]
Description: hypothetical protein Halxa_2489 [Halopiger xanaduensis SH-6]
Scores for 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-77  257.1   2.5    8.1e-77  256.7   2.5    1.1  1  PPS_PS         Phosphopantothenate/pantothenate synthetase
  ------ inclusion threshold ------
      0.077   13.2   0.0       0.13   12.4   0.0    1.4  1  RTT107_BRCT_6  Regulator of Ty1 transposition protein 107 BRC


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 !  256.7   2.5     9e-81   8.1e-77       1     176 []      79     254 ..      79     254 .. 0.99

  Alignments for each domain:
  == domain 1  score: 256.7 bits;  conditional E-value: 9e-81
                            PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeagaeevlgleedaripeleseR 77 
                                       llla+kpv+s+NGN+aaLv+ e+v+La+a+ga+levNlf+rteeR e+ia++l+e+gae+v+gle+darip+l+++R
  gi|336253879|ref|YP_004596986.1|  79 LLLAEKPVLSINGNVAALVPGEMVDLADATGADLEVNLFNRTEERLEAIADHLREHGAEDVKGLEADARIPNLDHQR 155
                                       79*************************************************************************** PP

                            PPS_PS  78 akvskeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkske 154
                                       akv++eGiy+aDvvlvplEDGDRaeaL++mgK+ i+iDLNPlsR+ ++a+++ivdn++Ra+pn+te+++el +++++
  gi|336253879|ref|YP_004596986.1| 156 AKVDAEGIYAADVVLVPLEDGDRAEALEAMGKTEIVIDLNPLSRSPQVAEVPIVDNIIRAVPNMTEHARELADADES 232
                                       ***************************************************************************** PP

                            PPS_PS 155 eleeivkefdnkkvlkealkei 176
                                       e+++iv+ fd++++l++a ++i
  gi|336253879|ref|YP_004596986.1| 233 EVRAIVEAFDREAALEAAEERI 254
                                       ****************998765 PP

>> RTT107_BRCT_6  Regulator of Ty1 transposition protein 107 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.5e-05      0.13      10      68 ..     113     171 ..     109     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                     RTT107_BRCT_6  10 kiNlvsdipggtevissiLkahGikevkvlskklkiedlvknekkkkkekkkspeyvli 68 
                                       ++Nl++  +   e i+  L++hG ++vk l++  +i +l + ++k + e   ++++vl+
  gi|336253879|ref|YP_004596986.1| 113 EVNLFNRTEERLEAIADHLREHGAEDVKGLEADARIPNLDHQRAKVDAEGIYAADVVLV 171
                                       79*****************************9999998888877777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1867.76
//
Query:       gi|336253880|ref|YP_004596987.1|  [L=330]
Description: Bile acid:sodium symporter [Halopiger xanaduensis SH-6]
Scores for complete 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-34  119.7   6.5    2.3e-34  118.8   6.5    1.4  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 !  118.8   6.5   1.3e-38   2.3e-34       2     194 ..      38     223 ..      37     224 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 1.3e-38
                               SBF   2 ilLilmmfpmglkveveklkellkrpkalllglvlqwvikPllmfilakillrdlklepelavGlilvglapggams 78 
                                       ++L++m+f++ + +  ++l++++ +++ +  +l++++v  Pll+ +l  ++lrd+   p l vGl+++ + p++   
  gi|336253880|ref|YP_004596987.1|  38 PILMVMLFAAFAGIPRSQLRAAFGNRRVVGSSLLVNFVWNPLLALGLGAVFLRDH---PALWVGLLMLLVTPCTDWY 111
                                       689****************************************************...******************* PP

                               SBF  79 nvwtylakGdlelsvvlvalstllailltPlllyllaksleqttlkvpieeivksvlivviiPliaGillryillkh 155
                                       +++t++a+G+++l+++l   + +l+++l+P++lyl+a++l    ++ p e +++sv +v+++Pl++   +r +ll++
  gi|336253880|ref|YP_004596987.1| 112 LIFTDIADGNVALATSLLPYNLVLQLILLPVYLYLFAGEL----VDLPLEVLLESVALVLVVPLALAGCVRWVLLRR 184
                                       ****************************************....*********************9999******** PP

                               SBF 156 kGrewfeskllpavspisligllltivvifalkgelive 194
                                       +G+ewf  ++lp++sp+ +  l l i ++fa++ge+++e
  gi|336253880|ref|YP_004596987.1| 185 RGTEWFRRRVLPKLSPLQIGSLCLAIGAMFASQGEVVLE 223
                                       ************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); 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:                         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 0.18s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2626.74
//
Query:       gi|336253881|ref|YP_004596988.1|  [L=214]
Description: hypothetical protein Halxa_2491 [Halopiger xanaduensis SH-6]
Scores for 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  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1570.50
//
Query:       gi|336253882|ref|YP_004596989.1|  [L=64]
Description: hypothetical protein Halxa_2492 [Halopiger xanaduensis SH-6]
Scores for 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-05   23.0  21.2    5.7e-05   22.8  21.2    1.1  1  Gly-zipper_YMGG  YMGG-like Gly-zipper
    0.00031   20.7  18.8    0.00039   20.4  18.8    1.2  1  Gly-zipper_Omp   Glycine zipper
  ------ inclusion threshold ------
      0.048   13.9   8.2      0.055   13.8   8.2    1.1  1  DUF1269          Protein of unknown function (DUF1269)
      0.093   12.5  27.9       0.45   10.3  27.9    1.8  1  Gly-zipper_OmpA  Glycine-zipper domain
        3.7    7.2   7.2        4.3    7.0   7.2    1.0  1  TraT             Enterobacterial TraT complement resistance p
        8.2    6.9  14.9        3.4    8.1   5.0    2.1  2  Romo1            Reactive mitochondrial oxygen species modula


Domain annotation for each model (and alignments):
>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8  21.2   1.9e-08   5.7e-05       4      43 ..      15      55 ..      12      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.9e-08
                                      .XXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG  4 vrGAaiGAaaGAvvGaliG.sgggkGAaiGAaaGalaGgai 43
                                       +GAa GA +G  vG+l+G +gg+ GA++GAa+G laG+a+
  gi|336253882|ref|YP_004596989.1| 15 SKGAAKGAKVGGKVGGLAGpAGGAVGAGVGAATGYLAGTAR 55
                                      69*****************8888788888888888888876 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4  18.8   1.3e-07   0.00039       2      44 ..      17      57 ..      15      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.3e-07
                    Gly-zipper_Omp  2 GaaiGAaaGaliGgavggrgtGaliGAavGaavGgliGaamdk 44
                                      Gaa GA +G+ +Gg +g+  +G ++GA+vGaa G+l G a d+
  gi|336253882|ref|YP_004596989.1| 17 GAAKGAKVGGKVGGLAGP--AGGAVGAGVGAATGYLAGTARDR 57
                                      999**************8..799**************988665 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   8.2   1.8e-05     0.055       1      37 [.      18      52 ..      18      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                           DUF1269  1 AlsGalwGllvGllflnPllGaavGAaaGAlvgalsd 37
                                      A++Ga +G+ vG l+ +P +G avGA++GA++g l+ 
  gi|336253882|ref|YP_004596989.1| 18 AAKGAKVGGKVGGLA-GP-AGGAVGAGVGAATGYLAG 52
                                      799*********988.9*.999**********99874 PP

>> Gly-zipper_OmpA  Glycine-zipper domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  27.9   0.00015      0.45       1      43 [.      19      55 ..      11      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                   Gly-zipper_OmpA  1 vegAavGAalGAaaGAavGaitGsaGtGAaiGAasGavaGllr 43
                                      ++gA vG+ +G +aG a+Ga+      GA++GAa+G +aG++r
  gi|336253882|ref|YP_004596989.1| 19 AKGAKVGGKVGGLAGPAGGAV------GAGVGAATGYLAGTAR 55
                                      456777777777777776666......9************997 PP

>> TraT  Enterobacterial TraT complement resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   7.2    0.0015       4.3      90     130 ..      16      54 ..       9      60 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0015
                              TraT  90 ggalagaaagaaigaanggsagaalggglvGglvgaiagal 130
                                        ga++ga +g ++g++  g ag+a+g+g vG++ g +ag++
  gi|336253882|ref|YP_004596989.1|  16 KGAAKGAKVGGKVGGL-AGPAGGAVGAG-VGAATGYLAGTA 54 
                                       3455566666666655.44444444444.477777777665 PP

>> Romo1  Reactive mitochondrial oxygen species modulator 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   4.4     0.039   1.2e+02       8      25 ..      16      33 ..      10      37 .. 0.62
   2 ?    8.1   5.0    0.0011       3.4       8      27 ..      35      54 ..      34      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.039
                             Romo1  8 mGalmGaaVGlaiGllfG 25
                                       Ga+ Ga VG+ +G l G
  gi|336253882|ref|YP_004596989.1| 16 KGAAKGAKVGGKVGGLAG 33
                                      566666666666666655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0011
                             Romo1  8 mGalmGaaVGlaiGllfGtf 27
                                      +G ++Ga VG+a+G l Gt+
  gi|336253882|ref|YP_004596989.1| 35 AGGAVGAGVGAATGYLAGTA 54
                                      5899*************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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):               6  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 513.05
//
Query:       gi|336253883|ref|YP_004596990.1|  [L=328]
Description: Tyrosyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-47  160.8   0.0    5.6e-47  160.5   0.0    1.1  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.077   12.0   0.3       0.15   11.1   0.2    1.5  1  DUF2156       Uncharacterised conserved protein (DUF2156)
       0.12   11.3   0.0         13    4.6   0.0    2.2  2  tRNA-synt_1f  tRNA synthetases class I (K)


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 !  160.5   0.0   9.3e-51   5.6e-47       7     290 ..      31     312 ..      27     315 .. 0.92

  Alignments for each domain:
  == domain 1  score: 160.5 bits;  conditional E-value: 9.3e-51
                                       EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTT CS
                      tRNA-synt_1b   7 rvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpe 83 
                                       r+y+G +P+g lHlG+l+  +kl++lq+ag+ev++l+aD+hA+++d+   + +++r+ +e+++++    +a gl+ +
  gi|336253883|ref|YP_004596990.1|  31 RAYVGYEPSGVLHLGHLLTANKLIDLQEAGMEVVVLLADVHAYLNDKG--TFEEIRDTAEQMKAQ---FIAYGLEED 102
                                       79**********************************************..9**************...********* PP

                                       TEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGG CS
                      tRNA-synt_1b  84 kaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGsDQ 160
                                       ++e+v++se +  +e+  +l +l  +++lnr  ++ +   +++ ge  +++   Ypl+q++Di +l+ dl +gG DQ
  gi|336253883|ref|YP_004596990.1| 103 QTEFVYGSEFQLDEEYVLDLHELEVSTTLNRAQRAMA---EIQGGETAKVSHVVYPLMQTLDIEYLDLDLAVGGLDQ 176
                                       *******************************999988...88887799***************************** PP

                                       HHHHHHHHHHHHHHHHHSTTSS-EEEEET.-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..... CS
                      tRNA-synt_1b 161 kqnielgrdlarrfnkkevfkkpegltvp.lltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..... 231
                                       ++   l+r+ ++++++      + +l +p + ++++Ge KmS+S g  +I ++d++++ ++k+++a++ + +     
  gi|336253883|ref|YP_004596990.1| 177 RKVHMLAREELPELGYD----VRPALHTPiVADLTSGEGKMSSSGGV-TISMEDSTDELEEKVNSAYCPPTRdpegd 248
                                       ****************9....777777774777888999********.**********************9976666 PP

                                       .SHHHHHHHHHTHHH....CHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 232 .evekllklktelsn....elierleavsgkkpkreaeellaeevtklvhggdlkkalaealne 290
                                        e+  l+   + +++     ++er e+++g  +++++e l+++ +++++h+ d+k  la  l e
  gi|336253883|ref|YP_004596990.1| 249 lENPVLELFEYHVFPrfeeITVERPEKYGGDLTYEAYESLAEDLESGELHPADAKGTLATYLDE 312
                                       6566666556666668866778999*****999**********************999887766 PP

>> DUF2156  Uncharacterised conserved protein (DUF2156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   2.5e-05      0.15      55     113 ..      75     130 ..      49     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.5e-05
                                       GHHHHHHHHHHHHHHCTSEEEEEEE-HHHHHHHHHCTEEEECCCEEEEEEHHHHHTTSG CS
                           DUF2156  55 awpeaieeflelaaehgwrpafygvseelaellaelglsalrlgeeavvdledftLsGk 113
                                       + ++ +ee++++a++ +++++ yg++e+++e+      s+++l ee+v+dl ++++s  
  gi|336253883|ref|YP_004596990.1|  75 NDKGTFEEIRDTAEQMKAQFIAYGLEEDQTEFVYG---SEFQLDEEYVLDLHELEVSTT 130
                                       668899*************************9988...9***************98854 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 ?    4.5   0.0    0.0023        14       8      42 ..      11      47 ..       7      60 .. 0.72
   2 ?    4.6   0.0    0.0022        13     277     302 ..     208     233 ..     202     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0023
                      tRNA-synt_1f  8 aeklie.erkkkka.ekdevvvesGispSGliHiGnl 42
                                      ae++++ e+  + a + +      G+ pSG +H+G l
  gi|336253883|ref|YP_004596990.1| 11 AEEVVTdEEVRELAaDPEGKRAYVGYEPSGVLHLGHL 47
                                      555543133333334667778889***********86 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0022
                      tRNA-synt_1f 277 kggekmssSkGnvltledwlevaepe 302
                                       +g++kmssS G+ +++ed ++ +e++
  gi|336253883|ref|YP_004596990.1| 208 SGEGKMSSSGGVTISMEDSTDELEEK 233
                                       5677**************98776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2400.51
//
Query:       gi|336253884|ref|YP_004596991.1|  [L=56]
Description: hypothetical protein Halxa_2494 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00017   21.4   8.3     0.0014   18.5   8.3    1.9  1  PHD             PHD-finger
    0.00087   19.1   6.5     0.0011   18.9   3.9    1.9  2  C1_1            Phorbol esters/diacylglycerol binding domain 
     0.0041   17.1   8.1     0.0083   16.1   8.1    1.5  1  DZR             Double zinc ribbon
      0.007   16.2   4.3        1.1    9.2   0.1    3.1  3  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0076   16.2   8.3      0.023   14.6   8.3    1.7  1  Prok-RING_1     Prokaryotic RING finger family 1
  ------ inclusion threshold ------
      0.013   15.1   2.8      0.013   15.1   2.8    2.5  2  zinc_ribbon_2   zinc-ribbon domain
      0.017   15.2   1.4      0.017   15.2   1.4    1.9  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.018   15.0   6.3      0.021   14.8   6.3    1.1  1  zf-RING_9       Putative zinc-RING and/or ribbon
      0.028   14.4  14.8       0.26   11.3   6.1    2.8  3  YhfH            YhfH-like protein
      0.029   15.1   6.5      0.039   14.7   1.8    2.0  2  zinc_ribbon_15  zinc-ribbon family
      0.043   13.4   9.1       0.21   11.2   0.2    3.1  3  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.062   13.6   2.2      0.062   13.6   2.2    2.0  2  C1_2            C1 domain
       0.07   13.3   7.8        1.9    8.7   0.9    2.2  2  Ribosomal_L37e  Ribosomal protein L37e
       0.19   11.6   8.0       0.64   10.0   4.3    2.5  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.29   11.1   9.5       0.99    9.4   2.6    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.31   11.1  10.1        9.9    6.2  10.1    2.0  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.47   10.4   5.9      0.099   12.5   2.8    1.5  1  NinF            NinF protein
       0.55   10.8   6.5        2.1    9.0   6.5    1.9  1  Cript           Microtubule-associated protein CRIPT
        1.4    8.9  18.3       0.51   10.3   1.2    3.1  3  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger
        1.8    8.4   8.5         19    5.1   0.2    2.9  2  Ribosomal_S27e  Ribosomal protein S27
          2    8.7   5.2        9.8    6.5   0.1    2.4  2  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 
        2.7    7.9   8.2        3.7    7.5   0.1    2.9  3  ADD_ATRX        Cysteine Rich ADD domain
        5.4    6.6  15.4        3.2    7.3   1.5    2.9  3  DUF2688         Protein of unknown function (DUF2688)
        5.5    7.2  11.2         13    6.1   0.2    3.3  3  zf-CCHC         Zinc knuckle
        5.8    7.1  13.1        1.7    8.9   3.7    2.4  2  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   8.3   1.9e-06    0.0014       1      37 [.       6      41 ..       6      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
                                      SBTTTTSTTSTTSCEEEETTTSCEEETTTSSSTHSHH CS
                               PHD  1 rCavCkkksdeeeelvqCdgCkrwfHqkClkpplese 37
                                      +C  C++   ee+el +C++C+r  H  C +++ + e
  gi|336253884|ref|YP_004596991.1|  6 ICTTCGE-RIEENELQYCETCGRGLHEPCREYETTVE 41
                                      6******.999******************99987744 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 !   18.9   3.9   1.5e-06    0.0011      11      45 ..       4      36 ..       1      43 [. 0.86
   2 ?    2.6   0.1      0.17   1.2e+02       8      19 ..      36      47 ..      34      53 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.5e-06
                                      --B-TTT-SB--SSSS-EEEETTT--EE-CCCCTT CS
                              C1_1 11 ptfCkhCgeflwgkekqglkCswCkllvHkkChek 45
                                       t C++Cge +  +e     C++C++  H+ C e 
  gi|336253884|ref|YP_004596991.1|  4 GTICTTCGERI--EENELQYCETCGRGLHEPCREY 36
                                      588********..8888889************876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.17
                                      -SS--B-TTT-S CS
                              C1_1  8 fkqptfCkhCge 19
                                      ++ +  C  Cg+
  gi|336253884|ref|YP_004596991.1| 36 YETTVECRRCGD 47
                                      566777888876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   8.1   1.2e-05    0.0083       1      36 [.       7      47 ..       5      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
                               DZR  1 CpqCgeelppda.rfCseCgtklkavaa....edrCpsCge 36
                                      C +Cge ++++  ++C++Cg  l ++ +       C +Cg 
  gi|336253884|ref|YP_004596991.1|  7 CTTCGERIEENElQYCETCGRGLHEPCReyetTVECRRCGD 47
                                      99999998755417999999998866668888999999986 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 ?    4.2   0.2     0.058        42      11      19 ..       4      12 ..       3      14 .. 0.72
   2 !    9.2   0.1    0.0016       1.1      11      24 ..      19      32 ..      18      32 .. 0.84
   3 ?    3.7   0.1     0.083        60      28      35 ..      42      49 ..      36      50 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.058
                           DUF35_N 11 gqrCpdCGt 19
                                      g+ C+ CG 
  gi|336253884|ref|YP_004596991.1|  4 GTICTTCGE 12
                                      677888886 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0016
                           DUF35_N 11 gqrCpdCGtvqfPP 24
                                      +q+C  CG+  + P
  gi|336253884|ref|YP_004596991.1| 19 LQYCETCGRGLHEP 32
                                      7*******977766 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.083
                           DUF35_N 28 CphCgsdd 35
                                      C++Cg  +
  gi|336253884|ref|YP_004596991.1| 42 CRRCGDEQ 49
                                      88887665 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 !   14.6   8.3   3.2e-05     0.023       3      41 ..       3      42 ..       1      50 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-05
                       Prok-RING_1  3 tgkkCpvCgkelkeedDiVvCpeCgtpyHraC..yekagkC 41
                                       g++C+ Cg++++e+  +  C +Cg   H  C  ye++ +C
  gi|336253884|ref|YP_004596991.1|  3 LGTICTTCGERIEEN-ELQYCETCGRGLHEPCreYETTVEC 42
                                      5899********988.9***************555555556 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   2.8   1.9e-05     0.013       2      23 .]       7      29 ..       6      29 .. 0.90
   2 ?    3.5   0.6     0.089        64      16      20 ..      42      46 ..      33      48 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                     zinc_ribbon_2  2 CpnCGaelqdnakF.CpyCGtpl 23
                                      C+ CG+ +++n+   C+ CG +l
  gi|336253884|ref|YP_004596991.1|  7 CTTCGERIEENELQyCETCGRGL 29
                                      ********9998888*****876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.089
                     zinc_ribbon_2 16 CpyCG 20
                                      C +CG
  gi|336253884|ref|YP_004596991.1| 42 CRRCG 46
                                      55555 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 ?   15.2   1.4   2.4e-05     0.017       9      31 ..       5      27 ..       2      31 .. 0.92
   2 ?    1.3   0.3      0.53   3.8e+02      24      32 ..      40      48 ..      30      51 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-05
                      NOB1_Zn_bind  9 lrChaCfkvtkdmtkkFCpkCGn 31
                                      + C++C + +++++ ++C++CG 
  gi|336253884|ref|YP_004596991.1|  5 TICTTCGERIEENELQYCETCGR 27
                                      68********************6 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.53
                      NOB1_Zn_bind 24 kFCpkCGnk 32
                                      + C +CG +
  gi|336253884|ref|YP_004596991.1| 40 VECRRCGDE 48
                                      559999975 PP

>> zf-RING_9  Putative zinc-RING and/or ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   6.3   2.9e-05     0.021     154     203 ..       3      47 ..       1      49 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.9e-05
                         zf-RING_9 154 kgfiCelCkseellfpfqlktverCekCkavfHkeClkkkekkecpkcer 203
                                        g+iC +C ++      ++++ + Ce+C+  +H+ C + +++ ec++c  
  gi|336253884|ref|YP_004596991.1|   3 LGTICTTCGER-----IEENELQYCETCGRGLHEPCREYETTVECRRCGD 47 
                                       58899999976.....36799999*************888888*****75 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   6.1   0.00037      0.26      16      34 ..       7      25 ..       5      25 .. 0.93
   2 ?    5.9   7.3     0.018        13      15      37 .]      21      45 ..      18      45 .. 0.89
   3 ?    3.4   0.4      0.11        77      15      22 ..      41      48 ..      39      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                              YhfH 16 CteCGkeieEqaecYgneC 34
                                      Ct+CG+ ieE +  Y ++C
  gi|336253884|ref|YP_004596991.1|  7 CTTCGERIEENELQYCETC 25
                                      ************9998888 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.018
                              YhfH 15 kCteCGkeieEqaecYgn..eCekC 37
                                       C +CG  ++E +  Y++  eC +C
  gi|336253884|ref|YP_004596991.1| 21 YCETCGRGLHEPCREYETtvECRRC 45
                                      6***************985569999 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.11
                              YhfH 15 kCteCGke 22
                                      +C  CG+e
  gi|336253884|ref|YP_004596991.1| 41 ECRRCGDE 48
                                      79999985 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.8   5.5e-05     0.039      66      86 .]       5      26 ..       2      26 .. 0.90
   2 ?    3.3   0.2       0.2   1.4e+02      33      44 ..      35      46 ..      30      53 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.5e-05
                    zinc_ribbon_15 66 keCknCgkeveee.fkyCpkCg 86
                                      ++C  Cg+++ee+  +yC  Cg
  gi|336253884|ref|YP_004596991.1|  5 TICTTCGERIEENeLQYCETCG 26
                                      68********98769******9 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.2
                    zinc_ribbon_15 33 kkkpylacskCk 44
                                      ++++ + c++C+
  gi|336253884|ref|YP_004596991.1| 35 EYETTVECRRCG 46
                                      455566666665 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   0.2    0.0003      0.21       4      18 ..       6      20 ..       4      21 .. 0.92
   2 ?    3.5   0.6     0.074        53       3      13 ..      20      30 ..      18      35 .. 0.77
   3 ?    4.8   0.2      0.03        22       2      10 ..      39      47 ..      38      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                            zf_UBZ  4 lCerCgkeipeselq 18
                                      +C  Cg++i+e+elq
  gi|336253884|ref|YP_004596991.1|  6 ICTTCGERIEENELQ 20
                                      7***********997 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.074
                            zf_UBZ  3 ylCerCgkeip 13
                                      + Ce Cg+ + 
  gi|336253884|ref|YP_004596991.1| 20 QYCETCGRGLH 30
                                      57*****8665 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.03
                            zf_UBZ  2 tylCerCgk 10
                                      t+ C rCg 
  gi|336253884|ref|YP_004596991.1| 39 TVECRRCGD 47
                                      889****96 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.2   8.7e-05     0.062      20      46 ..       6      33 ..       2      34 .. 0.91
   2 ?    2.6   0.3      0.24   1.7e+02      16      27 ..      37      48 ..      34      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.7e-05
                              C1_2 20 nCsaCgrkidgff.YsCseCdfslhvrC 46
                                       C +Cg+ i++++  +C++C   lh+ C
  gi|336253884|ref|YP_004596991.1|  6 ICTTCGERIEENElQYCETCGRGLHEPC 33
                                      6*******99999989*99*******99 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.24
                              C1_2 16 sesfnCsaCgrk 27
                                      + + +C+ Cg +
  gi|336253884|ref|YP_004596991.1| 37 ETTVECRRCGDE 48
                                      66789*999976 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.3    0.0032       2.3      17      47 ..       5      36 ..       1      39 [. 0.82
   2 ?    8.7   0.9    0.0026       1.9      14      27 ..      37      50 ..      28      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0032
                    Ribosomal_L37e 17 ilCrrCgkrsyhvqkktCascGy.psaklrky 47
                                      ++C  Cg+r    + ++C  cG    +  r+y
  gi|336253884|ref|YP_004596991.1|  5 TICTTCGERIEENELQYCETCGRgLHEPCREY 36
                                      89*******************96555556655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0026
                    Ribosomal_L37e 14 ktHilCrrCgkrsy 27
                                      +t + CrrCg + +
  gi|336253884|ref|YP_004596991.1| 37 ETTVECRRCGDEQW 50
                                      57789*****9876 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 ?    3.1   0.1      0.13        90      17      28 ..       2      11 ..       1      18 [. 0.77
   2 ?   10.0   4.3   0.00089      0.64       1      31 [.      19      49 ..      19      53 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
                                      SCCCEEEESSSS CS
                    RNA_POL_M_15KD 17 kegknfeCrqCg 28
                                      k+g++  C +Cg
  gi|336253884|ref|YP_004596991.1|  2 KLGTI--CTTCG 11
                                      67777..88887 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00089
                                      EEBESTTTSBEEEEECSCCCEEEESSSS-EE CS
                    RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYee 31
                                      l+ C +Cg  L  +  +  + +eCr Cg e+
  gi|336253884|ref|YP_004596991.1| 19 LQYCETCGRGLHEPCREYETTVECRRCGDEQ 49
                                      689*****87755555555459*****9775 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 ?    9.4   2.6    0.0014      0.99      29      56 ..       5      29 ..       4      31 .. 0.88
   2 ?    4.8   5.3     0.036        26      31      53 ..      22      46 ..      22      50 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                    OrfB_Zn_ribbon 29 ktCseCgsknkealsgrtfkCpnCgfea 56
                                      + C  Cg++ +e   +++ +C+ Cg  +
  gi|336253884|ref|YP_004596991.1|  5 TICTTCGERIEE---NELQYCETCGRGL 29
                                      57**********...9999*****9765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.036
                    OrfB_Zn_ribbon 31 CseCgsknke..alsgrtfkCpnCg 53
                                      C  Cg+ + e  +  + t++C++Cg
  gi|336253884|ref|YP_004596991.1| 22 CETCGRGLHEpcREYETTVECRRCG 46
                                      6666666666666666666666666 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 ?    6.2  10.1     0.014       9.9      71     101 ..       5      34 ..       1      54 [. 0.72

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                                       EEETTTS-EEECHHHHHS-TTTSSS-EEEEE CS
                              HypA  71 vrCreCgkefeleekalrCpkCgsadveivs 101
                                       + C++Cg+++e++e +  C++Cg+   e  +
  gi|336253884|ref|YP_004596991.1|   5 TICTTCGERIEENELQ-YCETCGRGLHEPCR 34 
                                       689****999988643.59999876555544 PP

>> NinF  NinF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.8   0.00014     0.099      19      38 ..       6      25 ..       3      34 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                              NinF 19 LCanCskkLevdevhvCeeC 38
                                      +C  C++++e +e   Ce C
  gi|336253884|ref|YP_004596991.1|  6 ICTTCGERIEENELQYCETC 25
                                      7******************* PP

>> Cript  Microtubule-associated protein CRIPT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   6.5    0.0029       2.1      46      66 ..       6      26 ..       1      52 [. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0029
                             Cript 46 kCkiCktkveqkgakYCqkCa 66
                                       C++C +++e+++ +YC++C 
  gi|336253884|ref|YP_004596991.1|  6 ICTTCGERIEENELQYCETCG 26
                                      6*******************5 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 ?   10.3   1.2   0.00071      0.51       4      16 ..       4      17 ..       2      20 .. 0.85
   2 ?    4.4   1.3     0.051        37       4      10 ..      20      26 ..      17      29 .. 0.82
   3 ?    5.9   1.2     0.017        12       3      12 ..      36      48 ..      34      48 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00071
                      zf-dskA_traR  4 gs.CeeCGEpIpea 16
                                      g+ C +CGE I e+
  gi|336253884|ref|YP_004596991.1|  4 GTiCTTCGERIEEN 17
                                      667********985 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.051
                      zf-dskA_traR  4 gsCeeCG 10
                                       +Ce+CG
  gi|336253884|ref|YP_004596991.1| 20 QYCETCG 26
                                      68***** PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.017
                      zf-dskA_traR  3 ygs...CeeCGEp 12
                                      y++   C +CG++
  gi|336253884|ref|YP_004596991.1| 36 YETtveCRRCGDE 48
                                      666678*****97 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   3.4     0.069        49      28      39 ..      21      32 ..       7      35 .. 0.90
   2 ?    5.1   0.2     0.026        19      25      34 ..      38      47 ..      34      50 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.069
                                      EESSSTCEEEEE CS
                    Ribosomal_S27e 28 kCisCgkvLveP 39
                                       C++Cg+ L eP
  gi|336253884|ref|YP_004596991.1| 21 YCETCGRGLHEP 32
                                      5********999 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.026
                                      S-EEESSSTC CS
                    Ribosomal_S27e 25 tvvkCisCgk 34
                                      t v+C  Cg 
  gi|336253884|ref|YP_004596991.1| 38 TTVECRRCGD 47
                                      7788888874 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 ?    6.5   0.1     0.014       9.8       5      17 ..       5      17 ..       1      21 [. 0.78
   2 ?    4.0   1.7     0.084        60       7      16 ..      22      31 ..      19      47 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.014
                    Chordopox_RPO7  5 lvCstCGrDlsee 17
                                       +C+tCG+ + e+
  gi|336253884|ref|YP_004596991.1|  5 TICTTCGERIEEN 17
                                      69*****998875 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.084
                    Chordopox_RPO7  7 CstCGrDlse 16
                                      C tCGr l e
  gi|336253884|ref|YP_004596991.1| 22 CETCGRGLHE 31
                                      9*****9987 PP

>> ADD_ATRX  Cysteine Rich ADD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0052       3.7      14      24 ..       7      17 ..       2      21 .. 0.84
   2 ?    3.7   0.1     0.077        55      12      22 ..      20      30 ..      12      36 .. 0.69
   3 ?    3.1   0.5      0.12        86       7      19 ..      35      47 ..      30      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0052
                          ADD_ATRX 14 CtaCgqqvnhf 24
                                      Ct+Cg++++ +
  gi|336253884|ref|YP_004596991.1|  7 CTTCGERIEEN 17
                                      ******99876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.077
                          ADD_ATRX 12 vsCtaCgqqvn 22
                                        C +Cg+ + 
  gi|336253884|ref|YP_004596991.1| 20 QYCETCGRGLH 30
                                      36*****9876 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.12
                          ADD_ATRX  7 eleeivsCtaCgq 19
                                      e e +v+C  Cg 
  gi|336253884|ref|YP_004596991.1| 35 EYETTVECRRCGD 47
                                      56789******96 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   4.5     0.022        16      33      47 ..       2      16 ..       1      25 [. 0.66
   2 ?    0.8   0.4      0.47   3.4e+02      10      18 ..      22      30 ..      19      36 .. 0.82
   3 ?    7.3   1.5    0.0044       3.2       7      15 ..      39      47 ..      34      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.022
                           DUF2688 33 klGdICsdClipEEl 47
                                      klG IC+ C    E 
  gi|336253884|ref|YP_004596991.1|  2 KLGTICTTCGERIEE 16
                                      8********443333 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.47
                           DUF2688 10 CrRCGksls 18
                                      C  CG+ l 
  gi|336253884|ref|YP_004596991.1| 22 CETCGRGLH 30
                                      999**9886 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0044
                           DUF2688  7 tTqCrRCGk 15
                                      t +CrRCG 
  gi|336253884|ref|YP_004596991.1| 39 TVECRRCGD 47
                                      779*****6 PP

>> zf-CCHC  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.054        39       3       8 ..       7      12 ..       6      13 .. 0.88
   2 ?    2.5   1.3      0.24   1.7e+02       2       8 ..      21      27 ..      20      27 .. 0.83
   3 ?    6.1   0.2     0.018        13       2       8 ..      41      47 ..      40      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.054
                                      TSSSSS CS
                           zf-CCHC  3 CynCGe 8 
                                      C +CGe
  gi|336253884|ref|YP_004596991.1|  7 CTTCGE 12
                                      *****9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.24
                                      CTSSSSS CS
                           zf-CCHC  2 kCynCGe 8 
                                       C +CG+
  gi|336253884|ref|YP_004596991.1| 21 YCETCGR 27
                                      6****95 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.018
                                      CTSSSSS CS
                           zf-CCHC  2 kCynCGe 8 
                                       C++CG 
  gi|336253884|ref|YP_004596991.1| 41 ECRRCGD 47
                                      7*****7 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   3.7    0.0023       1.7       8      34 ..       7      27 ..       5      31 .. 0.81
   2 ?    2.7   7.3      0.19   1.4e+02       8      34 ..      22      47 ..      18      49 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0023
                       Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCgs 34
                                      C+ Cg++ e      +++l+ C +Cg 
  gi|336253884|ref|YP_004596991.1|  7 CTTCGERIE------ENELQYCETCGR 27
                                      *****8888......455888****97 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.19
                       Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgs 34
                                      Ce Cg+   + ++  + + t+ C +Cg 
  gi|336253884|ref|YP_004596991.1| 22 CETCGRGLHEPCR--EYETTVeCRRCGD 47
                                      9999998875543..5667888****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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):              25  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 395.75
//
Query:       gi|336253885|ref|YP_004596992.1|  [L=215]
Description: hypothetical protein Halxa_2495 [Halopiger xanaduensis SH-6]
Scores for complete 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  106.1   0.0    2.4e-30  105.7   0.0    1.2  1  DUF305    Domain of unknown function (DUF305)
    1.8e-10   41.2   0.0    5.3e-10   39.7   0.0    1.7  1  DUF4142   Domain of unknown function (DUF4142)


Domain annotation for each model (and alignments):
>> DUF305  Domain of unknown function (DUF305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.0   2.7e-34   2.4e-30       1     151 [.      59     208 ..      59     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 2.7e-34
                                       HHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHT---........-----HHHH CS
                            DUF305   1 DvaFaqdMipHhqqAvemaelaleraedpevralAqdIaaaQqaeiaemqgwleawgqpassagegeaaeaseaeea 77 
                                       Dv+F+q M+ Hh++++e a+l+ er+ + ++r+  q+++++Q++ i++++++l++ g ++ +   + + +a +   +
  gi|336253885|ref|YP_004596992.1|  59 DVTFLQTMAYHHRGGIEAAQLVPERTGHDALREFSQTVIRNQRQGIDRIERILTDAGLEPGQLL-EVDLDAVRDLVT 134
                                       9**********************************************************98777.777777888889 PP

                                       HHTT---HHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHGGGG-----HHHHHHHHHHHHHHHHHHHHHHHH CS
                            DUF305  78 ampgmaseaelaalraasgadfdrlFlelMirhHqgavemaeaalekgedpevrelaeaiieaQqaEieqmqel 151
                                       + pg ++++ela lr+++g++fd  F+e + +hH ga+++++  l++g++p+v+e+a +ii+aQ+a+i qm ++
  gi|336253885|ref|YP_004596992.1| 135 SIPGNLRPNELAYLRTLEGTAFDLRFVERFANHHSGAIQLSQLVLQEGQSPAVEEMATDIIDAQRADIVQMYRW 208
                                       9**********************************************************************998 PP

>> DUF4142  Domain of unknown function (DUF4142)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   5.9e-14   5.3e-10       2     125 ..      58     194 ..      57     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 5.9e-14
                           DUF4142   2 adaeflakaaaaglfeveaaklAlqkaknpevkaFAqqmvadhtkaneeLkalaskkgvtlpd.............s 65 
                                       ad +fl+++a  +   +eaa+l  +++  ++ ++F q++++++++  ++++++ +++g+++ +             +
  gi|336253885|ref|YP_004596992.1|  58 ADVTFLQTMAYHHRGGIEAAQLVPERTGHDALREFSQTVIRNQRQGIDRIERILTDAGLEPGQllevdldavrdlvT 134
                                       5889********************************************************99988555555555544 PP

                           DUF4142  66 teldaeaqakldkLkalsgaaFDkaYleaqvaahqkavellekaaasgkdaelkafaekt 125
                                         + + +  +l+ L++l+g+aFD +++e   + h  a++l +   ++g+ +++ ++a++ 
  gi|336253885|ref|YP_004596992.1| 135 SIPGNLRPNELAYLRTLEGTAFDLRFVERFANHHSGAIQLSQLVLQEGQSPAVEEMATDI 194
                                       44445555666**********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1570.40
//
Query:       gi|336253886|ref|YP_004596993.1|  [L=313]
Description: biotin/acetyl-CoA-carboxylase ligase [Halopiger xanaduensis SH-6]
Scores for 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   56.8   0.0    3.1e-15   56.2   0.0    1.2  1  BPL_LplA_LipB   Biotin/lipoate A/B protein ligase family
    8.7e-13   48.0   0.0    1.6e-12   47.2   0.0    1.4  1  HTH_11          HTH domain
    1.4e-12   47.3   0.3    2.5e-12   46.5   0.3    1.5  1  BPL_C           Biotin protein ligase C terminal domain
    1.8e-07   31.1   0.1    3.4e-06   27.0   0.0    2.3  2  HTH_20          Helix-turn-helix domain
    1.7e-06   27.4   0.0    3.4e-06   26.5   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.3e-05   24.9   0.0    2.2e-05   24.2   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00037   20.3   0.1     0.0013   18.6   0.0    2.0  2  MarR_2          MarR family
      0.007   16.7   0.0      0.012   15.9   0.0    1.4  1  Rrf2            Transcriptional regulator
  ------ inclusion threshold ------
      0.014   15.2   0.1       0.06   13.2   0.1    2.2  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.079   13.2   0.0       0.36   11.0   0.0    2.0  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   1.7e-18   3.1e-15      22     131 .]      98     208 ..      80     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.7e-18
                                       -TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-TTEE CS
                     BPL_LplA_LipB  22 esgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegipvf 94 
                                        s+ +v++++qtgGr    + w  p g++++s++ +p    + +++++ly++  ++a+++a        ++ g+ ++
  gi|336253886|ref|YP_004596993.1|  98 ASDVVVLADEQTGGRgrleREWAAPSGGIWTSVVNRPA---IAPARAPLYTLAASVATARAA-------REAGVDAR 164
                                       577899******************************66...5999*****************.......9******* PP

                                       EETTTEEEE......TTEEEEEEEEEEEE.TTS-EEEEEEEEEE CS
                     BPL_LplA_LipB  95 ikwpnDlyv......ngrKlaGiavtstr.gktlhhivigvgvn 131
                                       ikwpnD++v      ++rKlaGi+++    + ++  +v+g+gvn
  gi|336253886|ref|YP_004596993.1| 165 IKWPNDVVVpvgdegDYRKLAGILTEMEGeTDRVAWLVVGIGVN 208
                                       **************************999888899999999988 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   8.7e-16   1.6e-12       2      54 ..       5      54 ..       4      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 8.7e-16
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgrGY 54
                                      +++ile +  a+gp+sg +LA  L+vSr++v++++++L+e+g++I+s pg GY
  gi|336253886|ref|YP_004596993.1|  5 RRAILEAI--ADGPVSGPDLAASLEVSRAAVWKHVDELREAGFEIDSGPG-GY 54
                                      57788888..8999************************************.*9 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.3   1.4e-15   2.5e-12       1      47 [.     263     309 ..     263     310 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.4e-15
                                       STTSEEEEEETSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEEE CS
                             BPL_C   1 hsGqeVtlededgkveGiavGIdddGaLllktddglqpdinsGdisl 47 
                                       ++Gq+V++ ++ g+v+G av+I++ GaL+l+tddg++ ++++Gd+++
  gi|336253886|ref|YP_004596993.1| 263 TLGQRVRVDRPAGEVVGDAVDITETGALVLETDDGERATVSAGDCEH 309
                                       69*******************************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.9e-09   3.4e-06       9      53 ..       2      45 ..       1      53 [. 0.94
   2 ?    1.5   0.1      0.17   3.1e+02       9      28 ..     229     265 ..     227     266 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.9e-09
                                      -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTT CS
                            HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagL 53
                                      +++Rr+il a+  +++++ ++la+ l++s++ + +H+++L+eag+
  gi|336253886|ref|YP_004596993.1|  2 NETRRAILEAI-ADGPVSGPDLAASLEVSRAAVWKHVDELREAGF 45
                                      79*********.********************************8 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.17
                                       -HHHHHHHHHH.................STCTTB-HH CS
                            HTH_20   9 hPvRrrilraL.................araegltas 28 
                                       + +Rrr+ + L                 +r+ +lt++
  gi|336253886|ref|YP_004596993.1| 229 DVTRRRFVQRLleefdalrsdleavvpaWRDLALTLG 265
                                       569******9977777777777777777776666665 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 !   26.5   0.0   1.9e-09   3.4e-06       1      46 [.       1      45 [.       1      45 [. 0.97

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.9e-09
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGl 46
                                      ++et+r+ILe++ + +  s  +LA  l +S+++v++++++L e+G+
  gi|336253886|ref|YP_004596993.1|  1 MNETRRAILEAIAD-GPVSGPDLAASLEVSRAAVWKHVDELREAGF 45
                                      89**********99.*****************************96 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 !   24.2   0.0   1.2e-08   2.2e-05       1      44 [.       2      45 ..       2      45 .. 0.97

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.2e-08
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGL 44
                                      ++tR+ IL + a+g+ +  +la+ l++s+++v  H   LreaG+
  gi|336253886|ref|YP_004596993.1|  2 NETRRAILEAIADGPVSGPDLAASLEVSRAAVWKHVDELREAGF 45
                                      68****************************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   7.3e-07    0.0013       6      50 ..       4      45 ..       1      45 [. 0.94
   2 ?   -3.5   0.0       5.6     1e+04       5      19 ..     255     269 ..     252     277 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.3e-07
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTS CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGL 50
                                      + + +L a++++p   ++  +la+ l +s++av +++++L +aG+
  gi|336253886|ref|YP_004596993.1|  4 TRRAILEAIADGP---VSGPDLAASLEVSRAAVWKHVDELREAGF 45
                                      77899*******9...***************************96 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.6
                                       HHHHHHHHHHHCTTT CS
                            MarR_2   5 paqarvLaaLgrrpg 19 
                                       pa++++ + Lg r +
  gi|336253886|ref|YP_004596993.1| 255 PAWRDLALTLGQRVR 269
                                       566666666666544 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   6.8e-06     0.012      23      71 ..      14      60 ..       7      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.8e-06
                                      CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHC CS
                              Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakpp 71
                                      ++pvs  ++a++ ++s+  + k + +Lr+ag+ +   G+ GGy La  p
  gi|336253886|ref|YP_004596993.1| 14 DGPVSGPDLAASLEVSRAAVWKHVDELREAGF-EIDSGP-GGYELATVP 60
                                      567999*************************9.9999**.*****9876 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 ?   13.2   0.1   3.4e-05      0.06       3      42 .]       3      41 ..       1      41 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-05
                     HTH_AsnC-type  3 eiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      e+ r+ILea+  d+  s  +LA+ + +S+++v++ v+ L+
  gi|336253886|ref|YP_004596993.1|  3 ETRRAILEAIA-DGPVSGPDLAASLEVSRAAVWKHVDELR 41
                                      66699999997.*********************9988886 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 ?   11.0   0.0    0.0002      0.36      12      51 ..       7      45 ..       5      53 .. 0.87
   2 ?   -1.3   0.0       1.4   2.5e+03      20      38 ..      81      99 ..      66     100 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                                      HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGy 51
                                      +I+++    ++v+  dla  L+vs + V + + +L+++G+
  gi|336253886|ref|YP_004596993.1|  7 AILEAI-ADGPVSGPDLAASLEVSRAAVWKHVDELREAGF 45
                                      566666.67889999***********************97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                                      HSSB-HHHHHHHHTS-HHH CS
                    Fe_dep_repress 20 kkvvktkdlaerLnvspss 38
                                       ++ +t d a++L+v+++s
  gi|336253886|ref|YP_004596993.1| 81 DAIGSTNDRARELAVEGAS 99
                                      5566788899*****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2276.10
//
Query:       gi|336253887|ref|YP_004596994.1|  [L=119]
Description: hypothetical protein Halxa_2497 [Halopiger xanaduensis SH-6]
Scores for 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   16.0   0.2       0.23   11.9   0.1    2.0  2  NYN       NYN domain
      0.075   13.1   0.1        1.2    9.3   0.1    2.2  1  HTH_20    Helix-turn-helix domain
        0.1   12.1   0.1       0.15   11.6   0.1    1.2  1  DUF2587   Protein of unknown function (DUF2587)
       0.13   12.5   0.8       0.21   11.9   0.8    1.4  1  DUF2551   Protein of unknown function (DUF2551)


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.2e-05      0.23     102     136 ..       1      39 [.       1      48 [. 0.77
   2 ?    2.8   0.0     0.034   1.5e+02      48      71 ..      51      75 ..      36      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.2e-05
                               NYN 102 vsgD.gDFaplveklrergkrVevlla...eeastsseL 136
                                       +sgD gDF+ ++e  r r++rV++      +++ t ++L
  gi|336253887|ref|YP_004596994.1|   1 MSGDsGDFETVLELCRDRHRRVVLAVLideQRSLTVNDL 39 
                                       69**9***********99999988776665445555555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.034
                               NYN 48 eqnkfq.dalsstgikvkhkplkkr 71
                                        +++  d+l++++i+++h++l k 
  gi|336253887|ref|YP_004596994.1| 51 SITEVStDVLAQIQISLHHVHLPKM 75
                                      4566677999**********99765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00026       1.2      10      59 ..      18      86 ..       9      87 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00026
                                      HHHHHHHHHH.STCTTB-HHHHHHHH....T..............S-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 10 PvRrrilraL.araegltaselaerl....d..............lskntlsyHLrvLeeagLvevvre 59
                                      + Rr +l+ L  + + lt+++l +++    +              +  +  + HL ++ eagL+e + e
  gi|336253887|ref|YP_004596994.1| 18 RHRRVVLAVLiDEQRSLTVNDLTKTVvkhvSqasitevstdvlaqIQISLHHVHLPKMTEAGLIEYEPE 86
                                      56666666666555555555555555543312333344444444455555567999********99876 PP

>> DUF2587  Protein of unknown function (DUF2587)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.4e-05      0.15      33      83 ..      25      75 ..      18      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.4e-05
                           DUF2587 33 kqlleevraapldeasrerlkeihersikeleeglaPelveelerlslpft 83
                                        l++e r+  +++ +++ +k++ ++si e++  +  +++  l+++ lp  
  gi|336253887|ref|YP_004596994.1| 25 AVLIDEQRSLTVNDLTKTVVKHVSQASITEVSTDVLAQIQISLHHVHLPKM 75
                                      5699******************************999*********99965 PP

>> DUF2551  Protein of unknown function (DUF2551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.8   4.6e-05      0.21       5      47 ..      12      56 ..       8      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                           DUF2551  5 lerDksGiRrevLklflea.kkltveeiyeklkek.fdvsykgva 47
                                      le  ++  Rr vL +++++ ++ltv+++ +++ ++  + s+  v+
  gi|336253887|ref|YP_004596994.1| 12 LELCRDRHRRVVLAVLIDEqRSLTVNDLTKTVVKHvSQASITEVS 56
                                      56667788*********761689*******999984555666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 961.99
//
Query:       gi|336253888|ref|YP_004596995.1|  [L=219]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-15   56.1   0.0      5e-15   55.0   0.0    1.6  1  HTH_10         HTH DNA binding domain
    4.1e-13   49.5   1.9      6e-13   48.9   1.9    1.2  1  BAT            GAF and HTH_10 associated domain
    0.00016   21.1   0.1    0.00068   19.1   0.0    2.0  2  Sigma70_r4     Sigma-70, region 4
  ------ inclusion threshold ------
      0.017   15.0   0.2      0.045   13.6   0.1    1.8  2  MarR_2         MarR family
       0.02   14.7   0.1      0.042   13.7   0.1    1.5  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.026   14.2   0.0        0.4   10.4   0.0    2.3  2  Sigma70_r4_2   Sigma-70, region 4
      0.068   13.8   2.4        2.1    9.0   1.1    2.3  2  SnoaL_2        SnoaL-like domain
      0.085   12.4   0.0       0.17   11.5   0.0    1.5  1  HTH_24         Winged helix-turn-helix DNA-binding


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 !   55.0   0.0   2.2e-18     5e-15       1      52 [.     156     207 ..     156     208 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 2.2e-18
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT  q e+l+lAy+ GYF+ PR+vtl++L +el+Is +++  +Lr+ ++ ++
  gi|336253888|ref|YP_004596995.1| 156 LTTPQQEALALAYDRGYFESPREVTLADLGDELDISSQAVASRLRRGTKHVL 207
                                       899*******************************************988876 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   1.9   2.7e-16     6e-13       7     131 ..       6     132 ..       2     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2.7e-16
                               BAT   7 eleirdeddvlv.alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtllel 82 
                                       ++++ + +++l     ++ d +vele+++p +d  v+ +f+v+g++++++++a++d+++ve++r+v+  +d++ll++
  gi|336253888|ref|YP_004596995.1|   6 TFTVPSGEFPLGsVFEKHPDVTVELERIIPAQD-VVIPYFWVRGTAVDDIESAFADHPGVEEIRFVDSVEDESLLRV 81 
                                       5666666666663456789***********776.6*************************************77655 PP

                               BAT  83 t..vsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealee 131
                                       +  v+ + +++tl+e    + +a+ ++ ++++ ++  +++++ ++ ++++e
  gi|336253888|ref|YP_004596995.1|  82 EwtVEYTGVLQTLTETEIALIKATGTSRQWTFEIRGDDRRAIATFQDRCRE 132
                                       5227788999*************************9999999999999987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.1   2.4e+03       1      11 [.      90     100 ..      90     105 .. 0.74
   2 !   19.1   0.0     3e-07   0.00068       4      46 ..     155     204 ..     154     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                                       HHHHS-HHHHH CS
                        Sigma70_r4   1 aLasLperere 11 
                                       +L++L+e e  
  gi|336253888|ref|YP_004596995.1|  90 VLQTLTETEIA 100
                                       58999998855 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3e-07
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlr 46 
                                        L+  ++e l l +        ++ Tl+++g++l+iS  +V ++++r+ +
  gi|336253888|ref|YP_004596995.1| 155 GLTTPQQEALALAYdrgyfesPREVTLADLGDELDISSQAVASRLRRGTK 204
                                       6888899*******999999999***********************9876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.6   5.9e+03      12      31 ..     113     133 ..     105     136 .. 0.58
   2 ?   13.6   0.1     2e-05     0.045       2      44 ..     155     201 ..     154     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.6
                                       HHHHCTTTSEE.EHHHHHHHH CS
                            MarR_2  12 aaLgrrpgrdl.tvgelarrl 31 
                                       ++++  ++r + t ++ +r+l
  gi|336253888|ref|YP_004596995.1| 113 FEIRGDDRRAIaTFQDRCREL 133
                                       566666665334666656665 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2e-05
                                       T--HHHHHHHHHHHCTTTS.....EEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2   2 gltpaqarvLaaLgrrpgr.....dltvgelarrlglsksavsrilkr 44 
                                       glt  q  +La  ++r+ +     ++t ++l ++l++s +av  +l+r
  gi|336253888|ref|YP_004596995.1| 155 GLTTPQQEALALAYDRG-YfesprEVTLADLGDELDISSQAVASRLRR 201
                                       66666666666666664.45666699*******************998 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 ?   13.7   0.1   1.9e-05     0.042      19      40 ..     180     201 ..     178     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                     HTH_AsnC-type  19 syaeLAervGlSestvlrRvrr 40 
                                       + a+L++++ +S ++v+ R+rr
  gi|336253888|ref|YP_004596995.1| 180 TLADLGDELDISSQAVASRLRR 201
                                       679*****************98 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 ?    1.1   0.0      0.14   3.1e+02       6      23 ..     151     168 ..     150     172 .. 0.87
   2 ?   10.4   0.0   0.00018       0.4      30      53 ..     182     205 ..     178     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.14
                                       HHHTTS-HHHHHHHHHHH CS
                      Sigma70_r4_2   6 ealaeLperqreifllry 23 
                                       ea++ L++ q+e++ l y
  gi|336253888|ref|YP_004596995.1| 151 EAKSGLTTPQQEALALAY 168
                                       78999*********9987 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00018
                                       HHHHHHHT--HHHHHHHHHHHHHH CS
                      Sigma70_r4_2  30 kEIAellgisegtVksrlsRArkk 53 
                                       ++   +l+is+++V srl+R+ k+
  gi|336253888|ref|YP_004596995.1| 182 ADLGDELDISSQAVASRLRRGTKH 205
                                       677789**************9887 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.029        65      45      76 ..      18      49 ..      15      63 .. 0.80
   2 ?    9.0   1.1   0.00093       2.1      49      86 ..      61     111 ..      49     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.029
                                      HHHHHEEEEEEEEEEEEEETTEEEEEEEEEEE CS
                           SnoaL_2 45 alfaafpdlrfeihdvvadgdrvavewtvtgt 76
                                      ++f++ pd+++e+++++  +d v+  + v+gt
  gi|336253888|ref|YP_004596995.1| 18 SVFEKHPDVTVELERIIPAQDVVIPYFWVRGT 49
                                      578899***************99877666665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00093
                                       HEEEEEEEEEEEEEETTEEEEEEEEEEE.............EETTSSEEEE CS
                           SnoaL_2  49 afpdlrfeihdvvadgdrvavewtvtgt.............ipatgrgvtv 86 
                                       + +  ++++ d v+d+    vewtv++t             i+atg+  ++
  gi|336253888|ref|YP_004596995.1|  61 HPGVEEIRFVDSVEDESLLRVEWTVEYTgvlqtlteteialIKATGTSRQW 111
                                       445667889999*****************9999999999999999998887 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 ?   11.5   0.0   7.6e-05      0.17      18      40 ..     179     201 ..     174     201 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.6e-05
                            HTH_24  18 isqreLAerlglSpstvnrrlkr 40 
                                        + ++L ++l++S+++v  rl+r
  gi|336253888|ref|YP_004596995.1| 179 VTLADLGDELDISSQAVASRLRR 201
                                       7999*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1663.61
//
Query:       gi|336253889|ref|YP_004596996.1|  [L=158]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-38  130.6   0.3    6.8e-38  130.3   0.3    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 !  130.3   0.3   3.8e-42   6.8e-38       1     140 [.       1     139 [.       1     140 [. 0.95

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 3.8e-42
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+ IlV++Dgs+e ++Ale+A++la+a++a++++++v+ +  +g  +++   ++ + +  ee +++ +  ++++++
  gi|336253889|ref|YP_004596996.1|   1 MYDCILVPTDGSPEVERALEYAFDLARAHDATIRAVYVVNAAGYGGLPMETAWEGISDALREEGRSAVER-AEELAP 76 
                                       8999********************************************9999988888888777776664.8***** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       ++++ve++v+eg+p+++i+++a   ++dl+V+G++gr+g++rlllGSv+e+v+r++++pVl V
  gi|336253889|ref|YP_004596996.1|  77 EDIDVETKVLEGSPSRVIVQEASPGECDLVVMGTHGRGGIDRLLLGSVTERVVRRCDVPVLTV 139
                                       *************************************************************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 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:                        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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1244.84
//
Query:       gi|336253890|ref|YP_004596997.1|  [L=140]
Description: nucleoside 2-deoxyribosyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-15   55.5   0.0    6.1e-15   55.4   0.0    1.1  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
     0.0037   17.7   0.0     0.0046   17.4   0.0    1.2  1  Glyco_trans_1_4  Glycosyl transferases group 1


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 !   55.4   0.0   6.8e-19   6.1e-15       1     105 [.       3     104 ..       3     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 6.8e-19
                                       EEEESGGGCSCCCHHHHHHHHHHHHTTTTEEE-CC..TT-TT.....--SSHHHHHHHHHHHHHC-SEEEEE--SSS CS
                   Nuc_deoxyrib_tr   1 iYLAgplvFrpdakalaarlkallaengldglaPl..dneaelel.paeetaraiyeadialirqaDavianldpfr 74 
                                       i++ g++   +d+ +l+a+l++ll+++g+ +++++  + ++e+++ +a  t+  i+++d+a++rqaD v+a ++   
  gi|336253890|ref|YP_004596997.1|   3 IFFSGSIRGGRDDVDLYAELIDLLERHGTVLTEHVgtE-DVEEKEaEAGLTDGDIHDQDVAWLRQADGVVAEVTT-- 76 
                                       7899999999*******************999999642.333333589999************************.. PP

                                       SSS--HHHHHHHHHHHHCT-EEEEE-S-GCG CS
                   Nuc_deoxyrib_tr  75 gpeaDsGtafEvGyavalgkpvlayttdare 105
                                          +  G+ +E+G ava +kpvl+++    e
  gi|336253890|ref|YP_004596997.1|  77 ---PSLGVGYEIGRAVAWEKPVLCLYRPDAE 104
                                       ...99******************98765555 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 !   17.4   0.0   5.1e-07    0.0046       4     133 ..       3     137 ..       1     138 [. 0.72

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.1e-07
                                       EEEES---GG.GTHHHHHHHHHHHH.HH.EEEEEES---...HHHHHHHT.T-T.TEEEE---THHHHHHHH-SEEE CS
                   Glyco_trans_1_4   4 ilfvGrleenvkgvdllleavpllrkkd.vrlvivGdgp.rpeeleelaa.gleerveftGfvedlaellaaadvfv 77 
                                       i f G+++  ++ vdl +e + ll ++  v    vG ++ +++e    a+ gl+++ +         ++l++ad +v
  gi|336253890|ref|YP_004596997.1|   3 IFFSGSIRGGRDDVDLYAELIDLLERHGtVLTEHVGTEDvEEKE----AEaGLTDGDIHDQ----DVAWLRQADGVV 71 
                                       78899996677999999999999996645888889955433222....2236654433333....459********* PP

                                       E....-----SHHHHHHHHTT-EEEE-TGGG....TTT--.TTSSE.E--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  78 a....PsegfglkllEamaaglpvVatdvgg....iaevv.gengl.lvppgdpealaeailrLle 133
                                       a    Ps g+g+ +  a a ++pv +   +     ++++v g++++ l++ + p++ a+a+++ l+
  gi|336253890|ref|YP_004596997.1|  72 AevttPSLGVGYEIGRAVAWEKPVLCLYRPDaehdLSAMVrGNDAVeLLEYRRPADVADALEEFLQ 137
                                       *4444446*******************77541223555779877743778889********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1048.78
//
Query:       gi|336253891|ref|YP_004596998.1|  [L=229]
Description: metal dependent phosphohydrolase [Halopiger xanaduensis SH-6]
Scores for 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-11   42.8   2.8    9.9e-11   41.9   2.8    1.4  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 !   41.9   2.8   5.5e-15   9.9e-11       4     121 ..      28     133 ..      27     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 5.5e-15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH... CS
                                HD   4 HsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld... 77 
                                       H  +V  +a rla++ +e+ dr++l +aa +HD G ++++          +++ +H+ +ga+ ++++++r+ ++   
  gi|336253891|ref|YP_004596998.1|  28 HAGRVHDVALRLADECEEPVDRDVLAAAAWFHDAGRPLERA---------GEIDDHAAWGATEAKARLEREVEAasa 95 
                                       677899999********9********************885.........67889****************888*99 PP

                                       ..HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  78 ..ledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                         + +v + ir+h+ +           +++ +lea+++ +aD+l+a
  gi|336253891|ref|YP_004596998.1|  96 drIAAVERCIRAHSIRAS--------SPEPETLEAKLLFDADKLDA 133
                                       999999999999999998........679***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1593.18
//
Query:       gi|336253892|ref|YP_004596999.1|  [L=345]
Description: amidohydrolase [Halopiger xanaduensis SH-6]
Scores for 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   94.7   0.0    1.8e-24   86.8   0.0    2.2  1  Amidohydro_1  Amidohydrolase family
    7.8e-06   25.4   0.0    1.1e-05   24.9   0.0    1.1  1  A_deaminase   Adenosine/AMP deaminase
    1.9e-05   24.3   2.9    0.00069   19.2   0.5    2.6  3  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 !   86.8   0.0   2.9e-28   1.8e-24       1     320 [.      43     314 ..      43     339 .. 0.84

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 2.9e-28
                                       EEEE-EEEEEEECETTECSSS....GHHHHH.............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSST CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl.............vppetaaealesgiktalksGtttvadmgatts 60 
                                       i+lP++I+aH+H+ +s  ++a     le+++             ++ e++  a+++ ++ + ++Gt  ++d+++ ++
  gi|336253892|ref|YP_004596999.1|  43 IILPAFINAHTHIGDSIAKEAgrglSLEELVappdglkhrllrnADREELVSAMRTSLRFMQQGGTAACLDFREGDV 119
                                       79**************99888*999999999*******************************************999 PP

                                       HHHHHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHH CS
                      Amidohydro_1  61 tgiealleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkea 137
                                       +g+e l +a + lp           +  +  +  + s+e+++ag               +++ +   ++ d++ +e 
  gi|336253892|ref|YP_004596999.1| 120 EGVEMLEDAQDGLP-----------I--DALSFARGSIEAMEAG--------------DGFGAS---GANDDTFDEE 166
                                       77776666666663...........3..3555558888888777..............355555...5555555555 PP

                                       HHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHC CS
                      Amidohydro_1 138 lkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeag 214
                                         + +++++p+ iHa+e ++   d+  a +         ++             l+h+vh+ p+ +e+l  +   + 
  gi|336253892|ref|YP_004596999.1| 167 RAATREAGKPFGIHAGEVDES--DIDPALD------LEPDF-------------LVHMVHPQPAHLERLEDD--PVP 220
                                       6566999********886666..4444444......23455.............9*************9999..999 PP

                                       EEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTH CS
                      Amidohydro_1 215 vahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTi 291
                                       ++ cp+sn++ + g+ +  ++ +  +  +lgtD + + ns+++++e+ +++kl+           l++ e+lrmaT 
  gi|336253892|ref|YP_004596999.1| 221 IVVCPRSNLVTDVGLSPYSELNEL-TTLALGTD-NVMLNSPSMFREMEFLAKLSD----------LTADEILRMATV 285
                                       99*******************886.99******.*****************6666..........************ PP

                                       HHHHHTT-TTTSSSS-TTSB--EEEECC..C CS
                      Amidohydro_1 292 ngAkalglddkvGsievGkdADlvvvdl..d 320
                                       ngA++  l  + G +e+Gk+A l v+d+  +
  gi|336253892|ref|YP_004596999.1| 286 NGAEIADL--DYGVLEAGKEARLLVLDGgtN 314
                                       ********..9***************98641 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.9e-09   1.1e-05     178     313 ..     160     289 ..     139     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.9e-09
                                       G..HHHHHCCCCHTT-EEEEEESSSS-CHHHHHHHHCS--SCECE-GGGGGSHHHHHHHHHCT-EEEE-HHHHCCCS CS
                       A_deaminase 178 l..flklraeagkstllltpHaGEagglehvveAllllkaerigHGvrlrkdpvLqyllalaqiplevcPlSNvalg 252
                                       +  f++ ra+ ++++  + +HaGE+ +   +  Al+l + + + H v+   +p+ +++l ++ +p+ vcP SN  + 
  gi|336253892|ref|YP_004596999.1| 160 DdtFDEERAATREAGKPFGIHAGEVDE-SDIDPALDL-EPDFLVHMVHP--QPAHLERLEDDPVPIVVCPRSNLVT- 231
                                       24599999****************865.669999998.*******8876..57789*****************999. PP

                                       ST-TTTT-CHHHHHHTT-EEEE--BSCCCCT-SHHHHHHHHHHHHT--HHHHHHHH.HHHHH CS
                       A_deaminase 253 afleyaenPlkeflerglnvslntDDPlqfgttLieeYaiaaqvfklseedlaela.rNsvk 313
                                          ++   P  e+ ++   ++l+tD+ ++ + ++  e++ +a+   l++ ++ ++a +N+++
  gi|336253892|ref|YP_004596999.1| 232 ---DVGLSPYSEL-NELTTLALGTDNVMLNSPSMFREMEFLAKLSDLTADEILRMAtVNGAE 289
                                       ...7788888886.556789*****************************9998876256665 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.1    0.0025        15      10      53 ..      44      88 ..      42     106 .. 0.70
   2 ?   -0.8   0.0      0.13     8e+02     152     206 ..      85     136 ..      57     177 .. 0.66
   3 !   19.2   0.5   1.1e-07   0.00069     383     466 ..     237     339 ..     129     341 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0025
                      Amidohydro_3 10 vlPGFvDsHtHlaggg.vnl.rllrlpdarvtslegvltavrdqag 53
                                       lP+F+ +HtH+      ++ r+l+l++  v   +g++ ++ ++a 
  gi|336253892|ref|YP_004596999.1| 44 ILPAFINAHTHIGDSIaKEAgRGLSLEE-LVAPPDGLKHRLLRNAD 88
                                      68*********74433344557777777.55556666666655555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.13
                      Amidohydro_3 152 pl.areaeaaavaaalaalasyGitsveagggnvsslddleplfeltaee.klplrv 206
                                       ++ +re++  a+++ l+ + + G  ++    ++   + d+e +  l++++ +lp+++
  gi|336253892|ref|YP_004596999.1|  85 RNaDREELVSAMRTSLRFMQQGGTAAC---LDF--REGDVEGVEMLEDAQdGLPIDA 136
                                       333999999999999999999998888...333..3444444444433321356555 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 1.1e-07
                      Amidohydro_3 383 pwprigaavmrktrrgg............evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld. 446
                                       p++++  + ++  ++++            e+l    +l+  e+l++ T ++A++  l+   G Le+G++A l vld 
  gi|336253892|ref|YP_004596999.1| 237 PYSELNELTTLALGTDNvmlnspsmfremEFLAKLSDLTADEILRMATVNGAEIADLDY--GVLEAGKEARLLVLDg 311
                                       455555555555555555556666667779999*************************9..***************9 PP

                      Amidohydro_3 447 ..adpldvdppelaear......vrltv 466
                                         ++++ + +p +a +r      v++tv
  gi|336253892|ref|YP_004596999.1| 312 gtNNLAGARDPVRAVVRragvddVKETV 339
                                       9966555555544444444444466665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); 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: 00:00:00.42
# Mc/sec: 2475.48
//
Query:       gi|336253893|ref|YP_004597000.1|  [L=403]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for complete 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   93.3  40.8    1.3e-26   93.3  40.8    1.6  2  MFS_1       Major Facilitator Superfamily
    4.1e-05   22.3  16.2    0.00014   20.5   2.7    2.2  2  MFS_2       MFS/sugar transport protein
  ------ inclusion threshold ------
      0.032   12.5   1.5        1.8    6.7   0.5    2.4  2  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 !   93.3  40.8   2.2e-30   1.3e-26       3     353 .]      20     364 ..      15     364 .. 0.85
   2 ?   -2.0   0.2      0.22   1.3e+03     127     145 ..     372     390 ..     366     399 .. 0.72

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 2.2e-30
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       l+++l ++ ++ l + l+ ++  + g++++++g l++++ l+++ ++l +G  +dr+G+ r++ +g+l+++ g +  
  gi|336253893|ref|YP_004597000.1|  20 LSYLLLMFVWFSLPAYLS-TIIAEVGLTGTQAGVLTGAVPLTYIPLALATGLAVDRIGPGRIIGAGVLVYGTGQIGR 95 
                                       567778888888777777.888999************************************************6666 PP

                             MFS_1  80 lfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgg.lla.sslgWravf 154
                                       ++a+ +++ll++ +l G+ga +++ +   l++ +fp+ + gr  +++ +g+s G++l  ++g  ++  +++gWr +f
  gi|336253893|ref|YP_004597000.1|  96 SVAPDFPALLACTILIGVGATTITFGLPKLVSVLFPPAKTGRPSAIYLVGASTGSALVFGVGRpVIGpALGGWRPLF 172
                                       6657777************************************************99887777577777778***** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvl.willialllfffgfsglltll 230
                                       +  ++v++  ++ +l+l+++++ + + +          ++ +++ ++++l+++ l + ++++  +  + + g+  +l
  gi|336253893|ref|YP_004597000.1| 173 FWSGVVAICYGLAWLALVRRTELDGAADDVSFA----LESIASD-LRLVLTHRELqL-VVVIGTMYLLLNHGMQGWL 243
                                       ************999999999999999998888....8888888.********9932.22222222346666***** PP

                             MFS_1 231 plylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvl 307
                                       p++  e +gls + lag + +ll  + +++ l +  l+dr+g rr  l ++++l+++ +  + ++ t  ++l+++++
  gi|336253893|ref|YP_004597000.1| 244 PTI-LESRGLS-AGLAGRATSLLIGAYVAGILSVPELADRFGTRRLALTGCGALACLGVTGVTVGGT--SALAVAGI 316
                                       **7.*******.56777667777777777778**********9666555555555555555555555..88888899 PP

                             MFS_1 308 vliGfglgfvfpsllalasdla..ppeeagtasglfntagslggalgp 353
                                       v  G+g g ++p++ a+  dl   +p+ +gta++++  +g +gg+lgp
  gi|336253893|ref|YP_004597000.1| 317 VATGVGTGGISPLVRAIPPDLEgiGPRLTGTAVSFIFAVGEIGGFLGP 364
                                       99*****************9876699*********************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.22
                             MFS_1 127 sagfslGailgpllgglla 145
                                        a+ s+G+ l+ l+gg+l+
  gi|336253893|ref|YP_004597000.1| 372 DATGSFGPGLAILAGGALV 390
                                       5677788888888888877 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   7.2   0.00051       3.1     223     340 ..       9     127 ..       6     166 .. 0.83
   2 !   20.5   2.7   2.4e-08   0.00014     176     380 ..     172     370 ..     139     385 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00051
                             MFS_2 223 nraflillllfllaalalgvlnglllYyltyv..lg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllga 296
                                        ra+ +++++ l  +l ++v+++l +Y  t +  +g +g++a v++++v +  +  ++    ++ r+g  +++ +g 
  gi|336253893|ref|YP_004597000.1|   9 RRAYALVVAGTLSYLLLMFVWFSLPAYLSTIIaeVGlTGTQAGVLTGAVPLTYIPLALATGLAVDRIGPGRIIGAGV 85 
                                       588999999999999***************9933567888888888888888888888889999************* PP

                             MFS_2 297 lltivllvlvlllqpsnlllflvllviagfgvgvaallpwsmla 340
                                       l++  + ++  ++   +  ++l++++++g+g+ ++++ ++ +++
  gi|336253893|ref|YP_004597000.1|  86 LVYGTGQIGRSVA--PDFPALLACTILIGVGATTITFGLPKLVS 127
                                       ***********99..78999999********9998887666665 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.4e-08
                             MFS_2 176 liialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillllfllaalalgvlnglllYylt 252
                                       ++ + ++++++ +++l+  +r+e + + ++ +    s+  +l+ v+ +r + ++++++ + +l    + g+l   l+
  gi|336253893|ref|YP_004597000.1| 172 FFWSGVVAICYGLAWLALVRRTELDGAADDVSFALESIASDLRLVLTHRELQLVVVIGTMYLLLNHGMQGWLPTILE 248
                                       566777888888888888888888999999999999999************99999998888877777777776666 PP

                             MFS_2 253 yvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvg 329
                                           ++  a   + +++ + ++gi+ ++ la r+g ++++l g  +++ l+v  + +  +  +l+++  v++g+g+g
  gi|336253893|ref|YP_004597000.1| 249 SRGLSAGLAGRATSLLIGAYVAGILSVPELADRFGTRRLALTGCGALACLGVTGVTV-GGTSALAVAGIVATGVGTG 324
                                       655577777778888888999************************************.999999************* PP

                             MFS_2 330 vaallpwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgll 380
                                       ++  l+ ++ +d+        G r +g+++++ +++  +++ +g +++g l
  gi|336253893|ref|YP_004597000.1| 325 GISPLVRAIPPDLEG--I---GPRLTGTAVSFIFAVGEIGGFLGPVLVGTL 370
                                       ************944..4...568888888888888888888888877766 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 ?    6.7   0.5    0.0003       1.8       4      80 ..      16      92 ..      13     101 .. 0.88
   2 ?    4.0   0.0     0.002        12     280     358 ..     206     282 ..     192     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0003
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP  4 vllsllglvqamvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgs 80
                                      v+  l +l+ ++v   +   ++ti  + +l+ ++ g+++ +  +++i l+l  +   +r    r+ig+g+l+ + g 
  gi|336253893|ref|YP_004597000.1| 16 VAGTLSYLLLMFVWFSLPAYLSTIIAEVGLTGTQAGVLTGAVPLTYIPLALATGLAVDRIGPGRIIGAGVLVYGTGQ 92
                                      44445556668888889999****************************************************99986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.002
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 280 lkdfpkalkrllknpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvk 356
                                       l+++ + l+ +l+++ + lv++ +++++ll  G+  +lp  lE++ +lsa  A   t +++i + ++Gil    l  
  gi|336253893|ref|YP_004597000.1| 206 LESIASDLRLVLTHRELQLVVVIGTMYLLLNHGMQGWLPTILESR-GLSAGLAGRAT-SLLIGAYVAGILSVPELAD 280
                                       556677789999*******************************98.88888888886.5677788888877666655 PP

                                       xx RF
                              OATP 357 kl 358
                                       ++
  gi|336253893|ref|YP_004597000.1| 281 RF 282
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 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:                        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: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2891.14
//
Query:       gi|336253894|ref|YP_004597001.1|  [L=814]
Description: cytochrome c oxidase subunit I [Halopiger xanaduensis SH-6]
Scores for 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-124  414.9  70.9   3.6e-124  414.9  70.9    2.9  3  COX1      Cytochrome C and Quinol oxidase polypeptide I
    6.3e-18   65.5  18.2    6.3e-18   65.5  18.2    2.9  3  COX3      Cytochrome c oxidase subunit III


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.9  70.9  4.1e-128  3.6e-124       2     432 .]      22     466 ..      21     466 .. 0.97
   2 ?   -0.0   2.8     0.034     3e+02      81     181 ..     549     667 ..     539     688 .. 0.67
   3 ?   -6.8  16.2         2   1.8e+04       4     173 ..     642     811 ..     639     814 .] 0.58

  Alignments for each domain:
  == domain 1  score: 414.9 bits;  conditional E-value: 4.1e-128
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCTCT......-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS CS
                              COX1   2 igllylilalvlllvggllgllirlqlafp......dletynqlrtlHgnlmiflfatpfilgfgnylvplllgard 72 
                                       +g+ly+++al++ll+gg+++ll+r+ql++p      d  +ynq++t Hg lm+f+f+ p+++gf+ny+vpl++ga+d
  gi|336253894|ref|YP_004597001.1|  22 VGILYIVTALFFLLFGGIMALLFRVQLWQPgglgilDGMEYNQAVTSHGLLMVFWFLSPIATGFANYFVPLQIGAND 98 
                                       89**************************9988877777*************************************** PP

                                       -S-HHHHHHHHHHHHHHHHHHHHHHH..CSS-STTTTTTTC.............SHHHHHHHHHHHHHHHHHHHHHH CS
                              COX1  73 lafprlnalsfwlvvlgvvllllsll..gaattgwteYapls............evdlwllglllvvvssllgainf 135
                                       lafprlna+s+w++++++vl+++s++  ++++ gwt+Yapl+            ++++++l+ +l+v+s+++g +nf
  gi|336253894|ref|YP_004597001.1|  99 LAFPRLNAMSYWFYLFSGVLFAISYFqgHTFAGGWTMYAPLNvpmyttameaaiGGNAAILATILFVLSVTIGTVNF 175
                                       **************************8666************************9999******************* PP

                                       HHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT.-SSSC..E-HHHHHHHHHHHHTHH CS
                              COX1 136 ivtilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrslg.kffsp..gdplldqhlfWffgHpe 209
                                       ++ti++ ra+g+ ++++plf+w++l t++++l+a+ +l +alll+l dr l  +++ +  g+ ll++hlfWffgHpe
  gi|336253894|ref|YP_004597001.1| 176 LTTIHRSRAEGLGLWNMPLFTWSWLLTVWMMLFAFSALLAALLLQLSDRLLLtQYMATdeGSSLLWAHLFWFFGHPE 252
                                       **************************************************9978885567***************** PP

                                       HHHHHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTHHHHHHCC CS
                              COX1 210 VyililpalgivyyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslliavPsglkv 286
                                       Vyi+++palgi+ + + +f+gr+l++ k++++a++l+++ sflvw+HH+f t ++  +k+l +++++ i +P+ l v
  gi|336253894|ref|YP_004597001.1| 253 VYIVFFPALGIMFETFQTFTGRRLVGRKWVIIAMVLVAVQSFLVWMHHMFLTTINLEIKTLYMATTIGISLPFDLMV 329
                                       ***************************************************************************** PP

                                       CHHHHCCTTS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHH CS
                              COX1 287 fnwlatlwrgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyll 363
                                       f++++t+++g++rf+tp+l+++g++vlfi+gG+tGv+l+++ ++y + +tywvvaHfH+v++ +v+ +l++++yy++
  gi|336253894|ref|YP_004597001.1| 330 FSLIYTMVKGRVRFTTPFLYAMGALVLFILGGITGVFLGAVVLDYEFRGTYWVVAHFHYVMVSGVT-ALVGGLYYWW 405
                                       **************************************************************9988.999******* PP

                                       HHHHSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHHHHHH CS
                              COX1 364 pkltgrmlserlaklhfwllfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrtiggvl 432
                                       pkl g+m++e+l+kl+f ++f+G++l+++pm++++    prr+++y       +++q +++ +t+g+++
  gi|336253894|ref|YP_004597001.1| 406 PKLSGKMYDETLGKLSFAIYFVGFNLLYFPMFLAW--ETPRRVFEY------PESYQLYHQSATVGAFV 466
                                       *********************************99..99******9......4699**********986 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.034
                                       HHHH..HHHHHHHHHHHHHHCSS-STTTTTTTC..........SHHHHHHHHHHHHHHHHH.HHHHHHHHHHH.... CS
                              COX1  81 lsfw..lvvlgvvllllsllgaattgwteYapls.........evdlwllglllvvvssll.gainfivtilk.... 141
                                       +s+w   + +gv++l+l+l +++t   +++a+           e+++++  +++++v++l  +++ + +  ++    
  gi|336253894|ref|YP_004597001.1| 549 ASIWpfGIGIGVFVLFLGL-SGITPYLVNFAEARghsvpgtgaEPNIAYPLIAVLGVAILGyTLFEYGRERFNapdm 624
                                       5667666666666677777.555555556665558888888777777777777777777755566666666665555 PP

                                       ...HHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCH CS
                              COX1 142 ...rrapgmtvaklplfvwavlatailillalpvlalalllll 181
                                           r p   v  ++l vw+++a  ++++ a ++ ++ l l++
  gi|336253894|ref|YP_004597001.1| 625 aiaERWPFGGVGTTKLGVWFFIASDVIVFGAAIGAFVFLRLHT 667
                                       5544444334448888899999998888888888877766654 PP

  == domain 3  score: -6.8 bits;  conditional E-value: 2
                                       HHHHHHH.HHHHHHHHHHHHHHHHHCTCT-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS-S-HHHH CS
                              COX1   4 llylila.lvlllvggllgllirlqlafpdletynqlrtlHgnlmiflfatpfilgfgnylvplllgardlafprln 79 
                                       ++++i++ ++++ +++ + +++rl++ + + et     t+ ++   +l++ +f +++++ ++++++++  la+   +
  gi|336253894|ref|YP_004597001.1| 642 VWFFIASdVIVFGAAIGAFVFLRLHTGWENWETIPPSSTVGLINTYVLLTSSFTVVLALVMAERENKRGLLASL-GA 717
                                       45544442555555555666667776677777777777787777777777777888888888888655555544.88 PP

                                       HHHHHHHHHHHHHHHHHHHCSS-STTTTTTTC..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CC...GS CS
                              COX1  80 alsfwlvvlgvvllllsllgaattgwteYapls.evdlwllglllvvvssllgainfivtilkrrapgmtva...kl 152
                                       +l++ l++lgv ++ +s+  +++ g + +++l   v ++  gl+ +   +++g+++   +i++  +   +++    +
  gi|336253894|ref|YP_004597001.1| 718 TLLLGLTFLGVKGWEWSY--EFSHGIYWFTNLHdSVYFVTTGLHAL--HVIFGLLIAGFMIYRVASVDAYLEdhrPV 790
                                       888889999999999998..56666667777775444444455444..22323333333333333333333333344 PP

                                       -HHHHHHHHHHHHHHHHCHHH CS
                              COX1 153 plfvwavlatailillalpvl 173
                                        +f  ++ ++ i++++++p +
  gi|336253894|ref|YP_004597001.1| 791 EFFGLYWHFVDIVWVFLFPLF 811
                                       466556666666667776665 PP

>> COX3  Cytochrome c oxidase subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.8      0.56     5e+03     195     250 ..     158     208 ..     143     211 .. 0.53
   2 ?   -3.5   2.8      0.79   7.1e+03     132     160 ..     286     313 ..     239     404 .. 0.63
   3 !   65.5  18.2   7.1e-22   6.3e-18      77     254 ..     639     812 ..     632     814 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.56
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTT--BSSB-HH.HHHHHHHHHHHHHHHHHHH CS
                              COX3 195 ylatGlhglhviigtillavallrllkyhltknhhlG.feaailywhfvdvvwlfly 250
                                        lat l  l v igt+ ++ ++      h ++   lG +++ ++ w ++  vw++l+
  gi|336253894|ref|YP_004597001.1| 158 ILATILFVLSVTIGTVNFLTTI------HRSRAEGLGlWNMPLFTWSWLLTVWMMLF 208
                                       4555555555555554333333......33344444423455556666666666666 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.79
                                       HHHHHHHHHHHHHHHHHHTTBHHHHHHHH CS
                              COX3 132 iillssGvtvtyahhsliegnrkkalkgl 160
                                       ++l++    + + hh +++  +   +k+l
  gi|336253894|ref|YP_004597001.1| 286 MVLVAVQSFLVWMHHMFLTTIN-LEIKTL 313
                                       3444444444455554433211.111222 PP

  == domain 3  score: 65.5 bits;  conditional E-value: 7.1e-22
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHS--GGGTSSSS-TT-----TTSHHHHHHHHHHHHHHHHHHHHHHHHTTBH CS
                              COX3  77 klGlilfiisevllflalfwaffhsalsPtvelGatwpPvGikavnPlevPllntiillssGvtvtyahhsliegnr 153
                                       klG+ +fi s+v++f a   af    l    e  +t pP          v l+nt +ll+s  tv  a     + n+
  gi|336253894|ref|YP_004597001.1| 639 KLGVWFFIASDVIVFGAAIGAFVFLRLHTGWENWETIPPS-------STVGLINTYVLLTSSFTVVLALVMAERENK 708
                                       89********************998888888777777775.......4699*****************998888899 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH.H-SS-TT..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--BSS CS
                              COX3 154 kkalkgllltillavlftllqaveyl.easftis..dgvyGsvfylatGlhglhviigtillavallrllkyhltkn 227
                                       +  l +l  t+ll++ f++++  e++ e s  i      + sv++++tGlh lhvi g ++  + ++r+++     +
  gi|336253894|ref|YP_004597001.1| 709 RGLLASLGATLLLGLTFLGVKGWEWSyEFSHGIYwfTNLHDSVYFVTTGLHALHVIFGLLIAGFMIYRVASVDAYLE 785
                                       999******************99974244555532256779************************************ PP

                                       B-HHHHHHHHHHHHHHHHHHHHHHHTT CS
                              COX3 228 hhlGfeaailywhfvdvvwlflyvsvy 254
                                        h   e+  lywhfvd+vw+fl+  +y
  gi|336253894|ref|YP_004597001.1| 786 DHRPVEFFGLYWHFVDIVWVFLFPLFY 812
                                       ***********************9888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (814 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.43
# Mc/sec: 5626.30
//
Query:       gi|336253895|ref|YP_004597002.1|  [L=384]
Description: Histidinol-phosphate aminotransferase [Halopiger xanaduensis SH-6]
Scores for 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-66  222.7   0.0    9.4e-66  222.4   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0016   18.4   0.1      0.004   17.1   0.1    1.7  1  FTR              Formylmethanofuran-tetrahydromethanopterin f
     0.0092   14.9   0.0      0.031   13.2   0.0    1.7  1  Alliinase_C      Allinase
  ------ inclusion threshold ------
      0.017   13.7   0.0       0.03   12.8   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
       0.18   11.6   0.0       0.37   10.6   0.0    1.5  1  HTH_38           Helix-turn-helix 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 !  222.4   0.0   2.6e-69   9.4e-66       2     361 ..      31     357 ..      30     358 .. 0.95

  Alignments for each domain:
  == domain 1  score: 222.4 bits;  conditional E-value: 2.6e-69
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       + ++L+sne++++    ++p++a a +e   a +++ +y++   +++l ea+a+ +       +  e +v++ +G +
  gi|336253895|ref|YP_004597002.1|  31 EFVKLASNENPHG----PSPAAAVAIRE---AASSVSSYPKAA-HADLTEAVAERWD------VADE-QVWLANGGD 92 
                                       5799*********....****9999987...9***********.*************......5555.********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                        +++ l +++ l+p+d++lvp+p +a y   +r+++g v++y+l++++df  d++a++e ++ +     + ++++++
  gi|336253895|ref|YP_004597002.1|  93 GALDYLHRAM-LEPDDAVLVPEPGFAYYGMSARYHHGDVREYELSKADDFAQDADAVLEHYDAD-----RDRIVFLT 163
                                       **********.***************************************************95.....668***** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH...HGGSTTSTTEEEEEESSSTTSSGGG- CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavat...ranveeepnllivgslsKafGlaGeR 229
                                       sphNP+G+ ++lee+e l+d +   + l++vDeaY++f+  ++   a+   r +++++++++i++++sKa+GlaG R
  gi|336253895|ref|YP_004597002.1| 164 SPHNPSGSTIPLEEVERLADETSD-ETLIVVDEAYGEFADRDSAL-ALiegRDGFDARDDVAILRTFSKAYGLAGVR 238
                                       ******************988886.9***************8733.33588************************** PP

                                       EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 230 vGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                       +Gy+++ ++++++ +++ +pf  s+++ +a +aa++d++    ++e ++++  + r ++r+ +   +  v++s++++
  gi|336253895|ref|YP_004597002.1| 239 LGYAVVPEEWADAYARVNTPFAASEIACRAGLAAIDDEE----HVERTVETARDARAYMREYI---DAHVWDSEGNF 308
                                       **************************************9....99999999999999999999...899******** PP

                                       EEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHHHHHHH CS
                     Aminotran_1_2 307 flltdlsaetakelskkLleevgvyvtpgtsftvpgrlRitvAglteeeleelve 361
                                       +l+ +++a+   +++++++ + gv+v+ ++sf++pg++Rit+  +teee e++ve
  gi|336253895|ref|YP_004597002.1| 309 VLVEVGDAA---AVAEEMQRR-GVIVRDCSSFGLPGCIRITC--GTEEETERAVE 357
                                       *********...99*******.********************..*********98 PP

>> FTR  Formylmethanofuran-tetrahydromethanopterin formyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.1e-06     0.004       5      65 ..     221     282 ..     218     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                                       TEEE-S-EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHSS-S-TTTSS-E.EEESEEB-GGGS CS
                               FTR   5 gveiedtfaEaFeikvtrviiTaatkkwakeaateatgfatsvigceaE.agiervlspeet 65 
                                       +v i  tf+ a+  + +r+      ++wa++ a+  t fa+s i+c+a  a+i+ + + e+t
  gi|336253895|ref|YP_004597002.1| 221 DVAILRTFSKAYGLAGVRLGYAVVPEEWADAYARVNTPFAASEIACRAGlAAIDDEEHVERT 282
                                       79999*****************************************9964678776665555 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   8.6e-06     0.031     127     211 ..     138     247 ..     100     261 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.6e-06
                                       STT-.........--S..S-EEEEEESS-TTT--.-.-----.....-TT-EEEEEE-TT..-S...TTTS---S-. CS
                       Alliinase_C 127 aaayv........kkknpeefielvtsPnnPdgl.l.reavv.....kgseakviyDlay..YW...Phytpitsk. 182
                                       a +++        + +  ++ i + tsP nP g  +  e+v      +++e+ +++D ay  +      ++ i+ + 
  gi|336253895|ref|YP_004597002.1| 138 ADDFAqdadavleHYDADRDRIVFLTSPHNPSGStIpLEEVErladeTSDETLIVVDEAYgeFAdrdSALALIEGRd 214
                                       33443333333345566788999999999999862322333234454556677889999843221113456666432 PP

                                       ...B--SE.EEEEHHHHHS-GGG-EEEEEES-H CS
                       Alliinase_C 183 ...adedi.mLftlskltGhaGsrlGWalvkdk 211
                                          a +d+ +L t+sk  G aG rlG+a+v ++
  gi|336253895|ref|YP_004597002.1| 215 gfdARDDVaILRTFSKAYGLAGVRLGYAVVPEE 247
                                       222456662688*****************9875 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 ?   12.8   0.0   8.4e-06      0.03      68     176 ..      83     197 ..      63     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.4e-06
                                       SEEEEESSHHHHHHHHHHTTS-TTEEEEEES...TSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCT.TEEE CS
                   Cys_Met_Meta_PP  68 eaalavssGmaAiaaailallkaGdeivvsd...dlYggtqrllkkvlkklgievkfvdtsdleelekaike.ntkl 140
                                       e++ + + G +A++   +a+l+  d ++v +     Yg + r+ +  +++ +++      +d++++ ++ +  + ++
  gi|336253895|ref|YP_004597002.1|  83 EQVWLANGGDGALDYLHRAMLEPDDAVLVPEpgfAYYGMSARYHHGDVREYELSKADDFAQDADAVLEHYDAdRDRI 159
                                       566778889999999999999999999998744458999999999999988876655555666666666654499** PP

                                       EEEESS-TTTT----HHHHHHHHHHTT..-EEEEEGTT CS
                   Cys_Met_Meta_PP 141 vylEtptnpllkvvDiekiaklakkag..vlvvvDntf 176
                                       v+l +p np  +++ +e++ +la + +  +l+vvD ++
  gi|336253895|ref|YP_004597002.1| 160 VFLTSPHNPSGSTIPLEEVERLADETSdeTLIVVDEAY 197
                                       ************************99888******875 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0001      0.37      16      35 ..      11      30 ..       9      30 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0001
                            HTH_38 16 llaeGlslreIArrLgrsps 35
                                       +++G ++ e+Ar+L+r+ps
  gi|336253895|ref|YP_004597002.1| 11 AYEAGRGIEEVARELDRDPS 30
                                      599****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2716.22
//
Query:       gi|336253896|ref|YP_004597003.1|  [L=178]
Description: adenylate kinase [Halopiger xanaduensis SH-6]
Scores for 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-25   87.6   0.3    1.4e-24   87.1   0.3    1.2  1  AAA_18           AAA domain
    0.00022   21.5   5.3     0.0016   18.7   5.3    2.2  1  AAA_28           AAA domain
    0.00039   20.6   1.2       0.33   11.1   0.0    2.3  2  AAA_33           AAA domain
    0.00097   19.4   0.0     0.0025   18.1   0.0    1.6  1  AAA_22           AAA domain
     0.0011   19.4   2.1        1.5    9.2   0.4    2.6  3  AAA_17           AAA domain
     0.0071   16.3   0.0      0.016   15.1   0.0    1.6  1  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.014   15.8   4.9      0.039   14.3   4.9    1.7  1  AAA_16           AAA ATPase domain
      0.015   14.3   0.0      0.034   13.1   0.0    1.6  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.018   14.5   0.0      0.023   14.1   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
      0.022   14.7   0.0      0.069   13.1   0.0    1.8  2  AAA_5            AAA domain (dynein-related subfamily)
      0.024   14.4   0.0      0.054   13.2   0.0    1.6  2  AAA_30           AAA domain
      0.047   13.4   0.7       0.41   10.3   0.1    2.1  2  Thymidylate_kin  Thymidylate kinase
      0.061   13.2   0.0      0.095   12.6   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
      0.065   13.0   0.1       0.12   12.1   0.1    1.5  1  AAA_24           AAA domain
      0.065   13.6   0.0       0.14   12.5   0.0    1.5  1  AAA_19           AAA domain
      0.071   12.9   0.1        4.8    7.0   0.1    2.1  2  dNK              Deoxynucleoside kinase
      0.084   13.0   0.0       0.31   11.1   0.0    1.8  2  DUF87            Helicase HerA, central domain
       0.11   11.8   0.1       0.58    9.4   0.0    2.0  2  Zeta_toxin       Zeta toxin
       0.16   11.7   1.4        3.2    7.4   0.1    2.4  3  CoaE             Dephospho-CoA kinase
       0.16   12.5   0.1        0.4   11.2   0.1    2.0  1  ABC_tran         ABC transporter
        0.2   12.1   0.9       0.28   11.6   0.2    1.8  2  AAA              ATPase family associated with various cellul


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 !   87.1   0.3   1.6e-27   1.4e-24       1     130 []       3     124 ..       3     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.6e-27
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf........gvnlrdvakenglllevdpealdeskrldedkldklldaleenss 69 
                                       +++tGtpG+GKtt ++ L++rl+         +v+l+ v+ ++gl++evd++  +esk++d d l+ +l+  +e   
  gi|336253896|ref|YP_004597003.1|   3 VAITGTPGTGKTTATELLEERLAEddslpdleVVHLNRVLEDEGLYTEVDAD--RESKIADLDALADWLEDRDE--- 74 
                                       78*******************8446999************************..**********5555555555... PP

                            AAA_18  70 aleegknlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeild 130
                                               vi++hla++++++++     vL+++p  l eRl +Rg++eak +en e+e+ld
  gi|336253896|ref|YP_004597003.1|  75 -------AVIESHLAHHFDADRV----AVLRCEPAALEERLLERGETEAKARENAESEALD 124
                                       .......4************998....9******************************985 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   5.3   1.9e-06    0.0016       1      23 [.       2      26 ..       2     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.9e-06
                            AAA_28  1 kivitGgestGKTtlleaLaar..g 23
                                      +++itG+++tGKTt +e L++r  +
  gi|336253896|ref|YP_004597003.1|  2 RVAITGTPGTGKTTATELLEERlaE 26
                                      79*****************987551 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00038      0.33       4      25 ..       5      33 ..       3      79 .. 0.66
   2 !    8.3   0.3    0.0028       2.4      91     137 ..      81     127 ..      78     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                            AAA_33  4 lvGlpGsGKstlaerllkklg.......a 25
                                      + G pG+GK+t  e l ++l+        
  gi|336253896|ref|YP_004597003.1|  5 ITGTPGTGKTTATELLEERLAeddslpdL 33
                                      67**********99998666544444442 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0028
                            AAA_33  91 larrlgvpvrivvvetdeetlkeRlakRaang.ddrsevpeealdrqk 137
                                       la++++ ++r+ v+++ ++ l+eRl +R +++ ++r +++ eald  +
  gi|336253896|ref|YP_004597003.1|  81 LAHHFD-ADRVAVLRCEPAALEERLLERGETEaKARENAESEALDVIL 127
                                       788889.7899*******************987788999999998765 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     3e-06    0.0025       9      38 ..       4      43 ..       2      94 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3e-06
                            AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaee..........e 38
                                      ++tG +GtGKTt  + l e+l e+ +  +          e
  gi|336253896|ref|YP_004597003.1|  4 AITGTPGTGKTTATELLEERLAEDDSLPDlevvhlnrvlE 43
                                      79*******************7766665566665555533 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0021       1.8       1      19 [.       6      24 ..       6      40 .. 0.81
   2 !    9.2   0.4    0.0018       1.5      77     134 ..      63     120 ..      40     124 .. 0.77
   3 ?   -1.6   0.0         4   3.4e+03      28      52 ..     124     148 ..     121     168 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0021
                                      EE-TTSSHHHHHHHHHHHH CS
                            AAA_17  1 lGgPGsGKgtqceklveky 19
                                      +G PG GK+t+ e l e++
  gi|336253896|ref|YP_004597003.1|  6 TGTPGTGKTTATELLEERL 24
                                      69**********9888765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0018
                                       EE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH.TTST-TS-SHHH CS
                            AAA_17  77 dghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd.rtrgrdddnees 134
                                       d  + + e++++ + ++++  + ++ d + +l ++p  + er+l++ +t+  + +n+es
  gi|336253896|ref|YP_004597003.1|  63 DALADWLEDRDE-AVIESHLAHHFDADRVAVLRCEPAALEERLLERgETEAKARENAES 120
                                       555555555554.3467788899999*******************99888888888875 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4
                                       HHHHHHHHTT.TSHSSHHHHCTSHHH CS
                            AAA_17  28 dllreeakrg.glakardemrklple 52 
                                       d++ +ea+++ gl ++  e+++ + e
  gi|336253896|ref|YP_004597003.1| 124 DVILSEAAEQhGL-ESIYEVDTTDRE 148
                                       5555555555244.444444433322 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.9e-05     0.016       1      26 [.       2      27 ..       2      30 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                                      EEEEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkss 26
                                      +v+iTG pG+GKtT  + + e l+++
  gi|336253896|ref|YP_004597003.1|  2 RVAITGTPGTGKTTATELLEERLAED 27
                                      689*************9999999775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   4.9   4.5e-05     0.039      27     157 ..       3     158 ..       2     170 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.5e-05
                            AAA_16  27 vllsGesGvGKsslvrellralekd.................ggiflrgkcdqlesaipy...salaqalareellr 83 
                                       v ++G +G+GK++  + l ++l +d                 +g++++ ++d+ ++ + +   + +++  ++  +++
  gi|336253896|ref|YP_004597003.1|   3 VAITGTPGTGKTTATELLEERLAEDdslpdlevvhlnrvledEGLYTEVDADRESKIADLdalADWLEDRDE-AVIE 78 
                                       689*********************978887777777766665466666666666444444221112222211.3333 PP

                            AAA_16  84 qllde....aesaeleawrekleeala.....................avpelagaeasrllellkrllallsrder 135
                                         l++    +                +                     ++++ + ae+++l   l++++   ++++ 
  gi|336253896|ref|YP_004597003.1|  79 SHLAHhfdaD----------------RvavlrcepaaleerllergetEAKARENAESEALDVILSEAA---EQHGL 136
                                       3333333332................0222222222233333333333222222233334433333333...22222 PP

                            AAA_16 136 plvlvlDdlqwadeaslqllaa 157
                                         +  +D  ++  e+ +++l+a
  gi|336253896|ref|YP_004597003.1| 137 ESIYEVDTTDREPEDVADALEA 158
                                       2455555555555555555555 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 ?   13.1   0.0     4e-05     0.034      31      55 ..       2      26 ..       1      29 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                                      EEEEEE-TTSSHHHHHHHHHHHHHC CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrr 55
                                      +v +tG+PG+Gk t++e l ++l++
  gi|336253896|ref|YP_004597003.1|  2 RVAITGTPGTGKTTATELLEERLAE 26
                                      899***************9999876 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.7e-05     0.023       4      51 ..       3      52 ..       1      84 [. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                                      EEEE--TTSSHHHHHHHHHHHHHH..TT--EEEE-THHHH.TTSSS--GG CS
                             KTI12  4 vvltGlPssGKstrakeLakalee..ekrsvvviddeslgiekdsykdsa 51
                                      v +tG P +GK+t+++ L++ l+e  +  +  v+  + +  ++  y++  
  gi|336253896|ref|YP_004597003.1|  3 VAITGTPGTGKTTATELLEERLAEddSLPDLEVVHLNRVLEDEGLYTEVD 52
                                      789********************966334555555555554444455444 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 ?   13.1   0.0   8.1e-05     0.069       3      46 ..       4      52 ..       2      72 .. 0.77
   2 ?   -0.8   0.0       1.7   1.4e+03      40      54 ..     103     122 ..      75     164 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.1e-05
                                      EEE--SSSSHHHHHHHGGGGB.....S--EEEEE--TT--HHHHH--B- CS
                             AAA_5  3 lLvGppGtgKselaerlaaal.....nreveyvqltrdtteedlkgrre 46
                                       + G pGtgK++ +e l ++l        +e+v l+r ++ e l  +++
  gi|336253896|ref|YP_004597003.1|  4 AITGTPGTGKTTATELLEERLaeddsLPDLEVVHLNRVLEDEGLYTEVD 52
                                      689******************8755444567777777777777766666 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                                       HHH--B--............ CS
                             AAA_5  40 dlkgrreik.....ngttsl 54 
                                        l+ r e++     n + + 
  gi|336253896|ref|YP_004597003.1| 103 RLLERGETEakareNAESEA 122
                                       33333333322222222222 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.3e-05     0.054      22      44 ..       4      26 ..       1      44 [. 0.82
   2 ?   -3.0   0.0       5.8     5e+03     144     157 ..     129     142 ..     118     166 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.3e-05
                            AAA_30 22 vltGpAGtGKttalkalreawea 44
                                      ++tG +GtGKtta + l+e +++
  gi|336253896|ref|YP_004597003.1|  4 AITGTPGTGKTTATELLEERLAE 26
                                      79***********9999776655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.8
                            AAA_30 144 agigtaeLtevvRq 157
                                       ++++++ L++++  
  gi|336253896|ref|YP_004597003.1| 129 EAAEQHGLESIYEV 142
                                       44444445554444 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00048      0.41       3      23 ..       7      27 ..       5      30 .. 0.88
   2 ?    1.6   0.1      0.22   1.9e+02     119     154 ..      88     122 ..      68     155 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00048
                                      ESTTSSHHHHHHHHHHHHHHT CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkee 23
                                      G  G+GKtt +ell erl e 
  gi|336253896|ref|YP_004597003.1|  7 GTPGTGKTTATELLEERLAED 27
                                      888***************986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.22
                                       SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHH CS
                   Thymidylate_kin 119 dltflldvdpevalkRlakrdeldeeeeeqldflrk 154
                                       d +  l ++p+   +Rl +r+e  e+++++    + 
  gi|336253896|ref|YP_004597003.1|  88 DRVAVLRCEPAALEERLLERGET-EAKARENAESEA 122
                                       55667888999999999999993.333332222333 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011     0.095       5      90 ..       3      90 ..       1     106 [. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SS..HHHHHHHHHHHHHHHHHHHHTT-EEEEE- CS
                        APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfs..eedRkenirrvaevaklladaglivlvaf 81
                                      v +tG  g+GK+t ++ le++L e+  s   L+   + + L+ +  ++  ++dR+ +i  +  +a  l d    v+ + 
  gi|336253896|ref|YP_004597003.1|  3 VAITGTPGTGKTTATELLEERLAEDD-SLPDLEVVHLNRVLEDEGLYTevDADRESKIADLDALADWLEDRDEAVIESH 80
                                      679*******************9876.3444555555555554433331268999999999999999999999999888 PP

                                      ---.SHHHHH CS
                        APS_kinase 82 isP.yreeRe 90
                                      ++  + ++R 
  gi|336253896|ref|YP_004597003.1| 81 LAHhFDADRV 90
                                      7742455555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00014      0.12       4      25 ..       2      23 ..       1      82 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                            AAA_24  4 kiliyGpsgiGKTtlakelgpk 25
                                      +++i+G +g+GKTt    l+++
  gi|336253896|ref|YP_004597003.1|  2 RVAITGTPGTGKTTATELLEER 23
                                      89************98888443 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   0.00016      0.14      13      38 ..       3      28 ..       1      40 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                            AAA_19 13 llvtaGpGtGKTrvlkhivallvelg 38
                                      +++t+ pGtGKT+ ++   + l e  
  gi|336253896|ref|YP_004597003.1|  3 VAITGTPGTGKTTATELLEERLAEDD 28
                                      689**********9987777776655 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0056       4.8       2      22 ..       4      24 ..       3      40 .. 0.89
   2 ?    4.6   0.0      0.03        25     119     150 ..      80     114 ..      34     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0056
                                      EEEESTTSSHHHHHHHHHCCS CS
                               dNK  2 vveGnIgaGKstlvklLskkl 22
                                      ++ G+ g GK+t ++lL+++l
  gi|336253896|ref|YP_004597003.1|  4 AITGTPGTGKTTATELLEERL 24
                                      69999*************987 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.03
                                       HCCH...-SEEEEEE--HHHHHHHHHHCTTCCCTT CS
                               dNK 119 elak...pdlliYLkasletclerikkRgreeekk 150
                                       +la+    d +  L++++  ++er+ +Rg++e k 
  gi|336253896|ref|YP_004597003.1|  80 HLAHhfdADRVAVLRCEPAALEERLLERGETEAKA 114
                                       3333444899999*****************99773 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00036      0.31      25      52 ..       2      29 ..       1      36 [. 0.85
   2 ?   -0.9   0.0       1.7   1.5e+03     118     149 ..     102     133 ..      84     165 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00036
                             DUF87 25 HlAilgsTGsGKSntvavLleellekkg 52
                                      ++Ai g+ G+GK++ + +L e+l+e+++
  gi|336253896|ref|YP_004597003.1|  2 RVAITGTPGTGKTTATELLEERLAEDDS 29
                                      79*********************97544 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                             DUF87 118 rsvleealdqakakeekeklssdepvekllee 149
                                       +++le+  ++aka+e+ e+   d ++ + +e+
  gi|336253896|ref|YP_004597003.1| 102 ERLLERGETEAKARENAESEALDVILSEAAEQ 133
                                       44555555555544433333333333333333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00068      0.58      20      44 ..       4      28 ..       2      41 .. 0.77
   2 ?   -0.3   0.2      0.63   5.4e+02      85      99 ..     125     139 ..      84     161 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00068
                        Zeta_toxin 20 llgGqpGAGKselaellkdelerqg 44
                                       + G pG GK+++ ell+++l++++
  gi|336253896|ref|YP_004597003.1|  4 AITGTPGTGKTTATELLEERLAEDD 28
                                      578****************998433 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.63
                        Zeta_toxin  85 ekllqeaiengynii 99 
                                         l ++a ++g + i
  gi|336253896|ref|YP_004597003.1| 125 VILSEAAEQHGLESI 139
                                       222333333444444 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0038       3.2       3      22 ..       3      22 ..       1      27 [. 0.89
   2 ?    2.4   0.1      0.13   1.1e+02      23      55 ..      55      88 ..      45     106 .. 0.81
   3 ?    0.7   0.0      0.41   3.5e+02     114     148 ..      77     113 ..      75     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0038
                                      EEEEESTTSSHHHHHHHHHH CS
                              CoaE  3 vgltGgiasGKstvanlfad 22
                                      v++tG  ++GK+t+++l+++
  gi|336253896|ref|YP_004597003.1|  3 VAITGTPGTGKTTATELLEE 22
                                      99**************9986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.13
                                      TT-EEEEHHHHHHHTTCCTHHHHH.HHHHHHGGG CS
                              CoaE 23 lgvpivDaDlvArqvvepgsealk.kiveeFgee 55
                                         +i D D++A ++   ++++ + +++++F ++
  gi|336253896|ref|YP_004597003.1| 55 RESKIADLDALADWLEDRDEAVIEsHLAHHFDAD 88
                                      567899*********9999988752688899865 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.41
                                       TTTTGGGGS..SEEEEEE--HHHHHHHHHHCCTSTHH CS
                              CoaE 114 vEkqlekli..ervlvvdvelelqveRlvardgvsee 148
                                       +E++l++ +  +rv v+ +e+    eRl++r +++++
  gi|336253896|ref|YP_004597003.1|  77 IESHLAHHFdaDRVAVLRCEPAALEERLLERGETEAK 113
                                       5666666542268999999999999999999776543 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00047       0.4      13      36 ..       2      25 ..       1     159 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00047
                                      EEEEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllk 36
                                      +vai+G  G+GK+t  +ll + l 
  gi|336253896|ref|YP_004597003.1|  2 RVAITGTPGTGKTTATELLEERLA 25
                                      79*************999987765 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   0.2   0.00033      0.28       2      22 ..       4      24 ..       3      77 .. 0.83
   2 ?   -1.8   0.0       4.6   3.9e+03      79     109 ..     116     145 ..     100     164 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                                      EEESSTTSSHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakel 22
                                       ++G+pGtGKT++ + + + l
  gi|336253896|ref|YP_004597003.1|  4 AITGTPGTGKTTATELLEERL 24
                                      579*********988876665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.6
                                       CHHHHHHHHHHHHHHHHTTTSSSTEEEEEEE CS
                               AAA  79 seeeervvnqLlteldgvkkkeskvivigat 109
                                       ++ e+++++++l+e  ++   es +  + +t
  gi|336253896|ref|YP_004597003.1| 116 ENAESEALDVILSEAAEQHGLES-IYEVDTT 145
                                       34444555555555544444433.4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1257.08
//
Query:       gi|336253897|ref|YP_004597004.1|  [L=204]
Description: CDP-alcohol phosphatidyltransferase [Halopiger xanaduensis SH-6]
Scores for 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   40.5   7.5    5.8e-10   39.8   0.7    2.8  3  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
        1.3    9.1   4.6       0.81    9.8   0.8    2.5  2  QCR10            Ubiquinol-cytochrome-c reductase complex sub


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 !   39.8   0.7   6.5e-14   5.8e-10       2      66 .]      27      96 ..      26      96 .. 0.94
   2 ?   -1.0   0.1      0.35   3.2e+03      30      30 ..     120     120 ..      98     164 .. 0.57
   3 !    4.2   0.1    0.0083        75       2      19 ..     170     187 ..     169     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 6.5e-14
                                      -HHHHHHHHHHHHHHHHHGGGS-H.......HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyp.....lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      +P+ ++++ + ++vla++ ++   +     +v+a++l+++ + +D++DG lAR+ ++ s+ G+llD+++D
  gi|336253897|ref|YP_004597004.1| 27 TPDGVSVIAFGMAVLAAVAFFLGGHaspvwYVVAAALVFLNGWLDIVDGALAREQESASSAGDLLDHVLD 96
                                      899**************99999998*****9999999999*****************999********99 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.35
                                       H CS
                   CDP-OH_P_transf  30 a 30 
                                       a
  gi|336253897|ref|YP_004597004.1| 120 A 120
                                       1 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.0083
                                       -HHHHHHHHHHHHHHHHH CS
                   CDP-OH_P_transf   2 lPnaiTllrlllsvlail 19 
                                       +P  +T+++ ll++la++
  gi|336253897|ref|YP_004597004.1| 170 APAGLTIVGWLLVFLAVV 187
                                       7999********999986 PP

>> QCR10  Ubiquinol-cytochrome-c reductase complex subunit (QCR10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.8   9.1e-05      0.81      12      33 ..      29      50 ..      18      51 .. 0.86
   2 ?   -0.9   0.2       0.2   1.8e+03      24      34 ..      59      69 ..      57      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.1e-05
                             QCR10 12 ygptlalfGgaagvavlfftsg 33
                                       g++ ++fG+a ++av+ff++g
  gi|336253897|ref|YP_004597004.1| 29 DGVSVIAFGMAVLAAVAFFLGG 50
                                      58999**************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.2
                             QCR10 24 gvavlfftsgv 34
                                      ++a+l+f++g+
  gi|336253897|ref|YP_004597004.1| 59 VAAALVFLNGW 69
                                      6899***9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1569.55
//
Query:       gi|336253898|ref|YP_004597005.1|  [L=178]
Description: XRE family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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   40.5   0.3    2.9e-10   40.1   0.3    1.2  1  HTH_3         Helix-turn-helix
    7.9e-09   35.4   0.5    1.3e-08   34.8   0.5    1.2  1  HTH_19        Helix-turn-helix domain
    6.2e-08   32.9   0.3      1e-07   32.2   0.3    1.3  1  HTH_31        Helix-turn-helix domain
    3.5e-05   23.6   0.4    5.6e-05   22.9   0.4    1.3  1  HTH_25        Helix-turn-helix domain
     0.0026   15.6  11.2       0.89    7.2  11.5    2.0  2  PI3K_1B_p101  Phosphoinositide 3-kinase gamma adapter protein
  ------ inclusion threshold ------
      0.055   13.4   0.0      0.085   12.8   0.0    1.4  1  HTH_37        Helix-turn-helix domain
        0.2   11.0   4.8       0.23   10.7   4.8    1.1  1  NOA36         NOA36 protein
       0.92    8.0   8.7       0.97    7.9   8.7    1.1  1  Macoilin      Macoilin family
          5    6.7  28.4        1.6    8.3  20.5    2.1  2  Period_C      Period protein 2/3C-terminal region
        6.1    5.6  12.3        7.1    5.4  12.3    1.1  1  Apt1          Golgi-body localisation protein 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 !   40.1   0.3   1.6e-13   2.9e-10       2      52 ..      97     147 ..      96     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.6e-13
                                       HHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEH CS
                             HTH_3   2 kelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsl 52 
                                       + +R+q+glsq +LA +l+ + s i++iE+G++ Ps ++  kl+++L ++l
  gi|336253898|ref|YP_004597005.1|  97 RTAREQKGLSQSDLANELNEKASLIRKIERGDTLPSDRVQSKLERFLEIDL 147
                                       889********************************************9987 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.5   7.1e-12   1.3e-08       2      56 ..      94     147 ..      94     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 7.1e-12
                            HTH_19   2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaell.lkiaealgidl 56 
                                       er++ aRe++gl+q +la++l    s i++iE g +  ps +++  k+ ++l+idl
  gi|336253898|ref|YP_004597005.1|  94 ERVRTAREQKGLSQSDLANELNEKASLIRKIERGDT-LPS-DRVqSKLERFLEIDL 147
                                       8*******************************9976.665.555266666677775 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.3   5.7e-11     1e-07       5      57 ..      95     146 ..      94     150 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 5.7e-11
                            HTH_31   5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57 
                                       ++r++Re+ GLsq ++A  l+  +s ++++E+G   +ps +v  +l r l  d
  gi|336253898|ref|YP_004597005.1|  95 RVRTAREQKGLSQSDLANELNEKASLIRKIERGDT-LPSDRVQSKLERFLEID 146
                                       89*********************************.9****999999998876 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.4   3.1e-08   5.6e-05       3      34 ..      97     128 ..      95     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.1e-08
                                       HHHHHTTT--HHHHHHHSS--HHHHHHHHCT- CS
                            HTH_25   3 raaRearglsleevaketkIrkdylealEedd 34 
                                       r aRe++gls  ++a+e++ ++++++++E++d
  gi|336253898|ref|YP_004597005.1|  97 RTAREQKGLSQSDLANELNEKASLIRKIERGD 128
                                       89****************************97 PP

>> PI3K_1B_p101  Phosphoinositide 3-kinase gamma adapter protein p101 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2  11.5    0.0005      0.89     336     415 ..      32     111 ..       3     126 .. 0.69
   2 !    6.5   0.0   0.00086       1.5       5      47 ..     132     177 ..     128     178 .] 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0005
                      PI3K_1B_p101 336 eeeedslarsstlstvsssskdsmlsllslsssslassvsslssgvdsdyvedsdessssspvaekkekkskkksks 412
                                        ++++s+  s+++st ssss  s++s  s s   + ss+ss ss   sd+++d+de  ++  ++ ++ +++k  s+s
  gi|336253898|ref|YP_004597005.1|  32 VRQTSSSGSSTKYSTGSSSSSSSSSSGDSSSTGGTGSSSSSSSSQRRSDMFDDMDELATDYDERVRTAREQKGLSQS 108
                                       223344467788999999999999999999999999999*****************999887444444444444455 PP

                      PI3K_1B_p101 413 rls 415
                                        l+
  gi|336253898|ref|YP_004597005.1| 109 DLA 111
                                       554 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00086
                      PI3K_1B_p101   5 eDRiqhaLerCLd.gLsk..sstaaqsWnaGlclnrWsLeelvkRd 47 
                                        DR+q  Ler L+  Ls+  ss + ++W+ G +   ++L ++vkR 
  gi|336253898|ref|YP_004597005.1| 132 SDRVQSKLERFLEiDLSAegSSGDDSEWSGGSSSGSYTLGDVVKRK 177
                                       59**********85576511566899******************95 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.7e-05     0.085      23      55 ..      96     128 ..      82     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.7e-05
                                       HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT- CS
                            HTH_37  23 iaeliekrelsqseaaqllgiaqPkvsrllrgk 55 
                                       ++  +e+++lsqs++a+ l+ + + + +++rg+
  gi|336253898|ref|YP_004597005.1|  96 VRTAREQKGLSQSDLANELNEKASLIRKIERGD 128
                                       67789*************************875 PP

>> NOA36  NOA36 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.8   0.00013      0.23     200     287 ..       9      95 ..       1     118 [. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                             NOA36 200 rkgfkyeknkaipcpkcgyetqetkdlslstrslkfgrqkqadgsddddddeedsdydaylkalasgddeddegded 276
                                        k++k e +k   c  c+   +e ++ s s  s k+   + +++s +  +d+++++ ++  ++ +s+++++d  d+ 
  gi|336253898|ref|YP_004597005.1|   9 PKTIKVEGAKLDVCADCTDFGTEVRQTSSSGSSTKYSTGSSSSSSSSSSGDSSSTGGTGSSSSSSSSQRRSDMFDDM 85 
                                       589999***********9888899999*********99998888888887788888777777666655555544433 PP

                             NOA36 277 ddddddeeddd 287
                                       d+    + d+ 
  gi|336253898|ref|YP_004597005.1|  86 DE-LATDYDER 95 
                                       33.22223322 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   8.7   0.00054      0.97     317     369 ..      33      95 ..       5     158 .. 0.44

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00054
                          Macoilin 317 kskssssssssnknskkasagsagssnssskkhsessksvtsssssknskkq................k 369
                                       +++sss ss++ ++ +++s++s++s+ sss +   ss+s +ss+      ++                +
  gi|336253898|ref|YP_004597005.1|  33 RQTSSSGSSTKYSTGSSSSSSSSSSGDSSSTGGTGSSSSSSSSQ------RRsdmfddmdelatdydeR 95 
                                       33333333332222222222233333333332222222222222......2212333333333332221 PP

>> Period_C  Period protein 2/3C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  20.5   0.00088       1.6      18      86 ..      32     102 ..      16     116 .. 0.72
   2 ?    3.5   1.0     0.026        47       4      40 ..     135     170 ..     132     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00088
                          Period_C  18 edsrsgtgsaasgsgasasseslgsgsngcdtsgsgtgssetsntsky....fgSiDssendhkakkkaesee 86 
                                         + s +gs +  s  + ss+s++s+s g ++s +gtgss++s++s++    f  +D   +d  ++++++ e+
  gi|336253898|ref|YP_004597005.1|  32 VRQTSSSGSSTKYS--TGSSSSSSSSSSGDSSSTGGTGSSSSSSSSQRrsdmFDDMDELATDYDERVRTAREQ 102
                                       34444455555544..455566666677899999**********99998999999999988888877766554 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.026
                          Period_C   4 alStsSdlldlllqedsrsgtgsaasgsgasassesl 40 
                                       ++S    +l+++l  ++ sg +s+ sg  +s+ s  l
  gi|336253898|ref|YP_004597005.1| 135 VQSKLERFLEIDLSAEGSSGDDSEWSGG-SSSGSYTL 170
                                       5677778999999999999999999987.45555444 PP

>> Apt1  Golgi-body localisation protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  12.3    0.0039       7.1     329     413 ..      35     122 ..       5     141 .. 0.48

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0039
                              Apt1 329 sssssssssassssssssrssslelrlkptsstssssssessssssskkrsseesslessaservkssr......as 399
                                       +sss ss++ s+ sssss+sss+ ++ +  s+ ++ sss+ssss+ +++   + ++l +  +erv+  r      +s
  gi|336253898|ref|YP_004597005.1|  35 TSSSGSSTKYSTGSSSSSSSSSSGDS-S--STGGTGSSSSSSSSQRRSDMFDDMDELATDYDERVRTAReqkglsQS 108
                                       11122222222222222222222222.1..22222222222222223333334444555555555333344556666 PP

                              Apt1 400 ddleemksRaskym 413
                                       d ++e  ++as  +
  gi|336253898|ref|YP_004597005.1| 109 DLANELNEKASLIR 122
                                       66677766666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1190  (0.0663729); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.37
# Mc/sec: 1427.09
//
Query:       gi|336253899|ref|YP_004597006.1|  [L=214]
Description: triosephosphate isomerase [Halopiger xanaduensis SH-6]
Scores for complete 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-08   34.8   0.0    2.6e-08   33.6   0.0    1.6  2  TIM             Triosephosphate isomerase
    5.1e-05   22.7   1.9    5.1e-05   22.7   1.9    1.7  2  ThiG            Thiazole biosynthesis protein ThiG
     0.0016   17.6   3.7     0.0016   17.6   3.7    1.8  2  FMN_dh          FMN-dependent dehydrogenase
     0.0034   16.6   0.0     0.0089   15.2   0.0    1.7  1  IGPS            Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
      0.063   13.4   2.8       0.11   12.6   0.4    2.4  2  Hydrolase_like  HAD-hyrolase-like
      0.078   12.1   2.2       0.12   11.5   0.5    1.8  2  Glu_synthase    Conserved region in glutamate synthase
       0.15   11.4  10.2      0.066   12.6   7.3    1.6  2  NMO             Nitronate monooxygenase


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 !   33.6   0.0     1e-11   2.6e-08      20     124 ..      18     114 ..       2     125 .. 0.84
   2 ?   -1.6   0.0      0.54   1.4e+03     159     178 ..     129     148 ..     114     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1e-11
                                       HHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHHHHHHTT-SEEEES-HHHHH CS
                               TIM  20 lkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsaemlkdlgvkyviiGHsErrq 96 
                                       +++++   +e+++++++ap++ +le+v++    +  ++ aq v+  + G+ TG + ae ++d+g++ ++i HsE r 
  gi|336253899|ref|YP_004597006.1|  18 AAAVRDVDEETDARIAVAPQAAHLERVAE----TGAETWAQHVDPIDYGSNTGHTLAETVADAGADGTLINHSEQRL 90 
                                       4555666666799************9665....66799**************************************9 PP

                                       HST--HHHHHHHHHHHHHTT-EEEEEE- CS
                               TIM  97 lfkEtdelvakKvkaalksglkpilCvG 124
                                        + +    +   v+aa+ ++l++i+C  
  gi|336253899|ref|YP_004597006.1|  91 KLAD----IDGAVRAAQRADLETIVCAN 114
                                       8876....56667899999999999965 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.54
                                       EEEE--GGGSSSS----HHH CS
                               TIM 159 viAYePvWAiGtgktatpeq 178
                                        +A eP   iGtg+++++ +
  gi|336253899|ref|YP_004597006.1| 129 AVAVEPPELIGTGTPVSQAD 148
                                       588899999***99876544 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.76     2e+03     192     205 ..      72      85 ..      46     125 .. 0.70
   2 !   22.7   1.9     2e-08   5.1e-05     175     215 ..     165     205 ..     137     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.76
                                       HHHHTT-SEEEESH CS
                              ThiG 192 qamelGadavllnt 205
                                       ++ + Gad+ l+n 
  gi|336253899|ref|YP_004597006.1|  72 TVADAGADGTLINH 85 
                                       44566666666664 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 2e-08
                                       SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHH CS
                              ThiG 175 kvPvivDAGigspsdaaqamelGadavllntavaeakdpva 215
                                       +v v+  AGi +  d+++a +lGa++vll++ va+a+dp a
  gi|336253899|ref|YP_004597006.1| 165 DVDVLCGAGISTGDDVVAASDLGAEGVLLASGVAKADDPRA 205
                                       7999**********************************965 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2      0.59   1.5e+03     285     297 ..     118     130 ..      68     141 .. 0.63
   2 !   17.6   3.7   6.2e-07    0.0016     264     301 ..     158     195 ..     144     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.59
                                       HHHHHHHTT-SEE CS
                            FMN_dh 285 DvlkAlalGAdav 297
                                        +  A alG dav
  gi|336253899|ref|YP_004597006.1| 118 QIGAAAALGPDAV 130
                                       3334555555555 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 6.2e-07
                                       HHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESH CS
                            FMN_dh 264 iveavggrievlvDgGirrGsDvlkAlalGAdavllGR 301
                                        +++v+++++vl+  Gi++G Dv+ A  lGA++vll+ 
  gi|336253899|ref|YP_004597006.1| 158 AAANVDDDVDVLCGAGISTGDDVVAASDLGAEGVLLAS 195
                                       46677789**************************9975 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.5e-06    0.0089     151     254 .]      99     210 ..      72     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.5e-06
                                       HHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE-........CHHHHHHCHCC-TTSEEEEESSS- CS
                              IGPS 151 aeaakslglevLvEvhdeeeleralklgakiiGvNnRnLktlevd........lntteeLaklvpkdvllvaeSGik 219
                                       ++aa++ +le +v  ++ +++ +a +lg + + v   +L    +         ++   + a+ v++dv + +  Gi+
  gi|336253899|ref|YP_004597006.1|  99 VRAAQRADLETIVCANNPAQIGAAAALGPDAVAVEPPELIGTGTPvsqadpdiVEDAVDAAANVDDDVDVLCGAGIS 175
                                       5678888899999999999999999999988888888886554430011111134455667778899********** PP

                                       SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHHH CS
                              IGPS 220 tredveklkeegvnafLvGeslmrqedvekairel 254
                                       t +dv + ++ g++++L  + + +++d ++a+++l
  gi|336253899|ref|YP_004597006.1| 176 TGDDVVAASDLGAEGVLLASGVAKADDPRAALEDL 210
                                       *****************************999876 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.44   1.1e+03      35      51 ..      99     115 ..      92     133 .. 0.63
   2 ?   12.6   0.4   4.3e-05      0.11      33      59 ..     178     203 ..     173     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.44
                                       HHHHHHCT-EEEEESSS CS
                    Hydrolase_like  35 iagAnnaGwksvLVltG 51 
                                       +++A++a ++++  +  
  gi|336253899|ref|YP_004597006.1|  99 VRAAQRADLETIVCANN 115
                                       56778888887766554 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.3e-05
                                       THHHHHHHCT-EEEEESSSSS-TTTHH CS
                    Hydrolase_like  33 tDiagAnnaGwksvLVltGvtrpedle 59 
                                       +D+ +A + G+++vL ++Gv +++d +
  gi|336253899|ref|YP_004597006.1| 178 DDVVAASDLGAEGVLLASGVAKADD-P 203
                                       79******************99988.3 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 ?    0.9   0.1     0.079     2e+02     286     311 ..     116     141 ..      17     147 .. 0.78
   2 ?   11.5   0.5   4.7e-05      0.12     268     305 ..     159     196 ..     139     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.079
                                       HHHHHHHHHHT-SEEE-SHHHHHHTT CS
                      Glu_synthase 286 gadvvkalalGAdavgigtaalialg 311
                                       +a++  a+alG dav +    li +g
  gi|336253899|ref|YP_004597006.1| 116 PAQIGAAAALGPDAVAVEPPELIGTG 141
                                       67888999999999999888888877 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.7e-05
                                       HTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHH CS
                      Glu_synthase 268 eeglrdrvsliadGglktgadvvkalalGAdavgigta 305
                                       + ++ d v++    g+ tg+dvv a  lGA+ v ++++
  gi|336253899|ref|YP_004597006.1| 159 AANVDDDVDVLCGAGISTGDDVVAASDLGAEGVLLASG 196
                                       4678899************************9998875 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.52   1.3e+03      22      40 ..      64      82 ..      58      95 .. 0.82
   2 ?   12.6   7.3   2.6e-05     0.066     129     224 ..      99     196 ..      92     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.52
                               NMO 22 iskarLaaavsnaGgLGvl 40
                                       ++  La  v++aG+ G l
  gi|336253899|ref|YP_004597006.1| 64 NTGHTLAETVADAGADGTL 82
                                      5778899999999998877 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.6e-05
                               NMO 129 varlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd.....iPviAaG 200
                                       v + ++a++  i+ +    ++ +++a+G+Da+ v+ pe  G     +v  +    +v+ ++da +     + v+   
  gi|336253899|ref|YP_004597006.1|  99 VRAAQRADLETIVCANNPAQIGAAAALGPDAVAVEPPELIGTGT--PVS-QADPDIVEDAVDAAAnvdddVDVLCGA 172
                                       6677788888888888999999****************988544..333.34555666666665567789******* PP

                               NMO 201 GiidrrgvaaaLalGAsgvqigtr 224
                                       Gi ++ +v aa  lGA+gv +++ 
  gi|336253899|ref|YP_004597006.1| 173 GISTGDDVVAASDLGAEGVLLASG 196
                                       *******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 1759.71
//
Query:       gi|336253900|ref|YP_004597007.1|  [L=138]
Description: hypothetical protein Halxa_2510 [Halopiger xanaduensis SH-6]
Scores for 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   12.9   1.3       0.28   11.0   0.3    2.2  2  Repressor_Mnt  Regulatory protein Mnt


Domain annotation for each model (and alignments):
>> Repressor_Mnt  Regulatory protein Mnt
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   1.6e-05      0.28       2      11 ..      29      38 ..      28      39 .. 0.95
   2 ?    0.0   0.0     0.043   7.7e+02       6      14 ..     116     124 ..     114     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.6e-05
                                      SHHHHHHHHH CS
                     Repressor_Mnt  2 NdAERlADeq 11
                                      N+ ERlADe+
  gi|336253900|ref|YP_004597007.1| 29 NEVERLADEH 38
                                      9********9 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.043
                                       HHHHHHHHH CS
                     Repressor_Mnt   6 RlADeqaEl 14 
                                       Rl D+ +El
  gi|336253900|ref|YP_004597007.1| 116 RLGDDLSEL 124
                                       999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1063.75
//
Query:       gi|336253901|ref|YP_004597008.1|  [L=220]
Description: hypothetical protein Halxa_2511 [Halopiger xanaduensis SH-6]
Scores for 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-08   33.5   0.0    7.4e-08   33.0   0.0    1.2  1  TIR_2            TIR domain
    2.1e-05   24.5   0.0      3e-05   24.0   0.0    1.3  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
     0.0013   19.1   0.0     0.0019   18.5   0.0    1.2  1  DUF1863          MTH538 TIR-like domain (DUF1863)
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.18   11.6   0.0    1.2  1  TIR              TIR domain
       0.18   12.2   0.0       0.31   11.4   0.0    1.3  1  DUF4062          Domain of unknown function (DUF4062)


Domain annotation for each model (and alignments):
>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   2.1e-11   7.4e-08       2      89 ..       7      89 ..       6     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.1e-11
                             TIR_2  2 FiSyssedkewaeklaeaLeaagirvwldrwdlkpgedweeeieeaiessdvvlvvlspaylesewcreeleaaleaae 80
                                      ++S++  d e +++l ++ e+  i v++ +++    ++ +++++  i +sd v++vl++++++++w ++e+ +a +   
  gi|336253901|ref|YP_004597008.1|  7 YVSHAPGDLELVRELFSTVENFPIGVHIAAEE-ADSGRARTRLAGRIANSDLVVAVLTERSATDRWINQEIGYARA--- 81
                                      69************************999977.4566899999********************************7... PP

                             TIR_2 81 egkkrlipv 89
                                       ++ +++p+
  gi|336253901|ref|YP_004597008.1| 82 -KGIPVLPL 89
                                      .45557776 PP

>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   8.5e-09     3e-05      55     128 ..      47     115 ..      16     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 8.5e-09
                                       HHHHHHHC-SEEEEE--SSSSSS--HHHHHHHHHHHHCT-EEEEE-S-GCGHHHHHTS...SB.TTS.B-TTSCHCC CS
                   Nuc_deoxyrib_tr  55 adialirqaDavianldpfrgpeaDsGtafEvGyavalgkpvlayttdarelrervea...lrdadgllvedfglpl 128
                                       + + +i ++D+v+a+l++    ++D  +  E+Gya a g+pvl +++   +      +    +d dg++++ ++lp 
  gi|336253901|ref|YP_004597008.1|  47 RLAGRIANSDLVVAVLTER--SATDRWINQEIGYARAKGIPVLPLSDRDVR------HggyIDDVDGVTIDRSDLPA 115
                                       4456899***********4..69********************99544333......33468899999999888876 PP

>> DUF1863  MTH538 TIR-like domain (DUF1863)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   5.3e-07    0.0019      57     104 ..      41      88 ..      17      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.3e-07
                           DUF1863  57 aedikeairdaldrssvliVLvgsetatsrWvdwEIaaslkkgkrllg 104
                                       + + +++++ ++++s+ ++ +  +  at+rW++ EI ++  kg ++l 
  gi|336253901|ref|YP_004597008.1|  41 SGRARTRLAGRIANSDLVVAVLTERSATDRWINQEIGYARAKGIPVLP 88 
                                       556688999*******************************99998885 PP

>> TIR  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.9e-05      0.18      17      81 ..      17      78 ..       9      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.9e-05
                                      HHHCHHHHHTTCCTTSEEEESSTT--SSS-HHHHHHHHHHCSSEEEEEE-TTHHHHCCCCHHHHH CS
                               TIR 17 fvshllkellekqkgiklfiddrdlepGeaiadelksaIkkSrrlivvlSknyasskwcleElek 81
                                      +v +l+  +  +++ i + i  ++ + G+a  + l   I +S  ++ vl + +a+++w  +E  +
  gi|336253901|ref|YP_004597008.1| 17 LVRELFSTV--ENFPIGVHIAAEEADSGRAR-TRLAGRIANSDLVVAVLTERSATDRWINQEIGY 78
                                      788999999..9999999**97776666666.99************************9999765 PP

>> DUF4062  Domain of unknown function (DUF4062)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.7e-05      0.31       1      63 [.       5      65 ..       5      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.7e-05
                           DUF4062  1 rvFiSStfrdlkeeRealieallelglepvgmeefaardqsqlelcleevdecdifililger 63
                                      + ++S+   dl+  Re    +++++ +  v++ +++a++ +++  +   + ++d+++++l+er
  gi|336253901|ref|YP_004597008.1|  5 QLYVSHAPGDLELVRELF-STVENFPIG-VHIAAEEADSGRARTRLAGRIANSDLVVAVLTER 65
                                      579999999999888766.777755555.99999**************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1735.06
//
Query:       gi|336253902|ref|YP_004597009.1|  [L=245]
Description: heat shock protein DnaJ domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   42.2   0.0    1.2e-10   41.4   0.0    1.3  1  DnaJ             DnaJ domain
  ------ inclusion threshold ------
       0.02   15.2   0.1       0.02   15.2   0.1    3.2  4  Arc_trans_TRASH  Archaeal TRASH domain
      0.037   14.8   1.5      0.037   14.8   1.5    3.5  4  ATPase-cat_bd    Putative metal-binding domain of cation tran
       0.16   11.9   9.4       0.63   10.0   0.0    3.3  3  C1_1             Phorbol esters/diacylglycerol binding domain
       0.59   10.4   0.0       0.59   10.4   0.0    2.3  2  GPR15L           G-protein coupled receptor ligand 15


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   3.2e-14   1.2e-10       4      55 ..     192     240 ..     191     243 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 3.2e-14
                                       HHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTS CS
                              DnaJ   4 eiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsd 55 
                                       ++Lgv++da+ +eI++aY++++++ HPD++   + ++ +F+ +++Aye L  
  gi|336253902|ref|YP_004597009.1| 192 DVLGVESDATLAEIRAAYHQQVKRAHPDRK---SGSRSAFQLVTDAYERLRR 240
                                       79**************************99...677899*********9975 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   5.7e-06      0.02       1      31 [.       8      39 ..       8      43 .. 0.88
   2 ?   -2.7   0.1       2.3   8.1e+03      26      34 ..      62      70 ..      61      72 .. 0.68
   3 ?    3.1   0.9     0.034   1.2e+02      25      31 ..      87      93 ..      84      95 .. 0.83
   4 ?   -3.8   0.8       4.8   1.7e+04      26      31 ..     167     172 ..     167     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.7e-06
                   Arc_trans_TRASH  1 CDYCGkeivg.ePivyklknkvYyvCCktCks 31
                                      CD CG  i + e  ++ + n   ++CC+ C  
  gi|336253902|ref|YP_004597009.1|  8 CDGCGRSIPSeEAATVAMPNGEQVTCCPQCAP 39
                                      ********762689****************75 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.3
                   Arc_trans_TRASH 26 CktCkselk 34
                                      C  C+  + 
  gi|336253902|ref|YP_004597009.1| 62 CDGCRGSFL 70
                                      777776665 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.034
                   Arc_trans_TRASH 25 CCktCks 31
                                      CC++C  
  gi|336253902|ref|YP_004597009.1| 87 CCPSCAA 93
                                      *****76 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 4.8
                   Arc_trans_TRASH  26 CktCks 31 
                                       C  Ck+
  gi|336253902|ref|YP_004597009.1| 167 CRACKE 172
                                       999997 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 ?   14.8   1.5     1e-05     0.037       2      41 ..       8      47 ..       7      52 .. 0.91
   2 ?    0.6   0.1      0.28   9.9e+02      22      33 ..      56      67 ..      47      76 .. 0.80
   3 ?    0.9   3.6      0.22     8e+02       2      33 ..      62      93 ..      61      97 .. 0.86
   4 ?    3.5   0.2     0.032   1.2e+02       1      33 [.     141     172 ..     141     185 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                     ATPase-cat_bd  2 CyHCglpveesaklkaeiegeerefCCkGCqavaqlivea 41
                                      C  Cg +++++++ ++ + + e+ +CC+ C+  a+++ +a
  gi|336253902|ref|YP_004597009.1|  8 CDGCGRSIPSEEAATVAMPNGEQVTCCPQCAPHARAVTDA 47
                                      999***************************9888887765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                     ATPase-cat_bd 22 eerefCCkGCqa 33
                                      ++r+  C GC++
  gi|336253902|ref|YP_004597009.1| 56 DQRRAACDGCRG 67
                                      578889****86 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.22
                     ATPase-cat_bd  2 CyHCglpveesaklkaeiegeerefCCkGCqa 33
                                      C  C+ ++ e++  ++++ +     CC+ C+a
  gi|336253902|ref|YP_004597009.1| 62 CDGCRGSFLEAELEDVRLPDGAVISCCPSCAA 93
                                      8889999999988899999999999*****97 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.032
                     ATPase-cat_bd   1 aCyHCglpveesaklkaeiegeerefCCkGCqa 33 
                                       +C+ C  p+ ++    ++++g++++  C+ C+ 
  gi|336253902|ref|YP_004597009.1| 141 RCSQCTDPIATEPFRVTTVDGRTER-LCRACKE 172
                                       59*******8875444555555555.5688876 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 ?    4.9   0.9    0.0069        25      11      34 ..       5      37 ..       2      41 .. 0.86
   2 ?    0.7   0.4      0.14     5e+02      11      34 ..      59      91 ..      53      95 .. 0.65
   3 ?   10.0   0.0   0.00018      0.63       9      37 ..     137     173 ..     133     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0069
                                      --B-TTT-SB-........-S.SSS-EEEETTT CS
                              C1_1 11 ptfCkhCgefl........wg.kekqglkCswC 34
                                      +t C+ Cg ++         +  + q  +C +C
  gi|336253902|ref|YP_004597009.1|  5 ETGCDGCGRSIpseeaatvAMpNGEQVTCCPQC 37
                                      688********9999999966699999999999 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                                      --B-TTT-SB-........-S.SSS-EEEETTT CS
                              C1_1 11 ptfCkhCgefl........wg.kekqglkCswC 34
                                       + C+ C+ ++        +   + ++ +C  C
  gi|336253902|ref|YP_004597009.1| 59 RAACDGCRGSFleaeledvRLpDGAVISCCPSC 91
                                      678999998886666655533355555555555 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00018
                                       SS--B-TTT-SB-.......-S.SSS-EEEETTT--E CS
                              C1_1   9 kqptfCkhCgefl.......wg.kekqglkCswCkll 37 
                                       ++p++C++C +++        +  +++   C++Ck++
  gi|336253902|ref|YP_004597009.1| 137 DEPARCSQCTDPIatepfrvTTvDGRTERLCRACKEN 173
                                       689**********999999866688888999999987 PP

>> GPR15L  G-protein coupled receptor ligand 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   1.1      0.83     3e+03      34      44 ..      27      37 ..       9      69 .. 0.63
   2 ?   10.4   0.0   0.00016      0.59      36      69 ..     141     176 ..     126     180 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.83
                            GPR15L 34 erklrpCCkrv 44
                                      + ++ +CC + 
  gi|336253902|ref|YP_004597009.1| 27 NGEQVTCCPQC 37
                                      34455566543 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00016
                            GPR15L  36 klrpC..CkrvprlkllnlkgrhvrlCrpcklkpes 69 
                                       +  +C     ++  ++++  gr  rlCr ck++ e+
  gi|336253902|ref|YP_004597009.1| 141 RCSQCtdPIATEPFRVTTVDGRTERLCRACKENAEA 176
                                       44444221122224567777***********98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1936.97
//
Query:       gi|336253903|ref|YP_004597010.1|  [L=153]
Description: hypothetical protein Halxa_2513 [Halopiger xanaduensis SH-6]
Scores for 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-24   84.6  10.3    7.5e-24   84.4  10.3    1.1  1  DUF3054   Protein of unknown function (DUF3054)
  ------ inclusion threshold ------
      0.088   12.8   0.6      0.088   12.8   0.6    2.5  2  DUF3185   Protein of unknown function (DUF3185)


Domain annotation for each model (and alignments):
>> DUF3054  Protein of unknown function (DUF3054)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4  10.3   8.3e-28   7.5e-24       1     109 [.      30     142 ..      30     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 8.3e-28
                           DUF3054   1 lvvDvvavlvfaliGrlsHge.sls.llgvletawPFlvglavgWllvapl...y.earaas.kaaralpagvvvwl 70 
                                       +v+Dvv+++ ++l+G+lsHg  +++ +++ let++PF++    gWllva++   y +a a + ++ r++++++v+w+
  gi|336253903|ref|YP_004597010.1|  30 AVGDVVFLAGLVLVGQLSHGVtPIEqPVAALETVAPFVL----GWLLVAAIaglYtNAGAVAtSVPRTARTTAVTWI 102
                                       699****************9878877*************....****9999999765544442699*********** PP

                           DUF3054  71 vavvvGlllR.allkggvalsFvlValvvlavlLlgwRav 109
                                       +a++vG++lR +l+++++ ++F lV++++++++L+gwR+ 
  gi|336253903|ref|YP_004597010.1| 103 AAANVGFILRnGLFGESTLWPFPLVMTGFGLLVLVGWRVG 142
                                       **********99**************************85 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.6   9.9e-06     0.088      30      59 .]      14      43 ..       8      43 .. 0.89
   2 ?   -0.1   0.3      0.11   9.8e+02      49      57 ..      72      80 ..      58      81 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.9e-06
                           DUF3185 30 seaftGsttdktlllligGgvaaivGlvll 59
                                      +  + G t d+t+lll+ G v +++Glvl+
  gi|336253903|ref|YP_004597010.1| 14 RAEGAGGTADRTTLLLAVGDVVFLAGLVLV 43
                                      5667899*********************85 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.11
                           DUF3185 49 gvaaivGlv 57
                                       vaai+Gl+
  gi|336253903|ref|YP_004597010.1| 72 LVAAIAGLY 80
                                      489999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1271.14
//
Query:       gi|336253904|ref|YP_004597011.1|  [L=71]
Description: hypothetical protein Halxa_2514 [Halopiger xanaduensis SH-6]
Scores for 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   13.0   5.5       0.38   10.6   5.5    2.1  1  PetG      Cytochrome B6-F complex subunit 5


Domain annotation for each model (and alignments):
>> PetG  Cytochrome B6-F complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   5.5   2.1e-05      0.38       9      21 ..       7      19 ..       5      33 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.1e-05
                              PetG  9 iVLGLvpVTlaGL 21
                                      iVLGL+pV l+G 
  gi|336253904|ref|YP_004597011.1|  7 IVLGLIPVALLGI 19
                                      9***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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: 0.36u 0.19s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 592.57
//
Query:       gi|336253905|ref|YP_004597012.1|  [L=332]
Description: Ornithine cyclodeaminase [Halopiger xanaduensis SH-6]
Scores for complete 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-66  224.3   0.2    2.1e-66  224.0   0.2    1.1  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    3.4e-05   24.3   0.0    8.3e-05   23.1   0.0    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00018   21.6   0.0    0.00028   20.9   0.0    1.2  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0062   16.7   0.0       0.01   16.0   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh


Domain annotation for each model (and alignments):
>> 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 !  224.0   0.2   4.7e-70   2.1e-66       4     317 ..       5     314 ..       2     315 .. 0.94

  Alignments for each domain:
  == domain 1  score: 224.0 bits;  conditional E-value: 4.7e-70
                                       EEE-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCC CS
                   OCD_Mu_crystall   4 avltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkks 80 
                                        +lt ++v e+   +d ++av +++r+  +  ++ +pr + +  +  g l    a l+  +      ++++      
  gi|336253905|ref|YP_004597012.1|   5 LFLTSSDVTELATPADYVDAVRDGYRQRGE-GAPAQPRSKFFRSEPAGMLTSYAAVLPDTG-----AMGGYMYSAGF 75 
                                       578999*****9999************999.578888888888887899999999999844.....45666666677 PP

                                       TSSSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEE CS
                   OCD_Mu_crystall  81 glptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikev 157
                                       g      +  L+d e+G plal+d+  +   +T+A++av++  Lar+d  +l+iiG G+qa+ ql a   v++++ v
  gi|336253905|ref|YP_004597012.1|  76 GAEDAWFMTPLFDAESGEPLALLDGASMNPFKTGAAGAVGVDALAREDTDTLGIIGTGAQARGQLWATATVREFTDV 152
                                       8888889999******************************************************************* PP

                                       EEE-SSHHHHHHHHHHCCS..CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB- CS
                   OCD_Mu_crystall 158 riydrdeeaaekfaenlqe.fefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLd 233
                                       r+y  ++e +e+fa       e +v+a++s e av gad+vvt+T+a +p++    ++pG+h++a+g   p+k+eLd
  gi|336253905|ref|YP_004597012.1| 153 RVYSPTPESREAFAADFDDrLEADVRAVDSSEAAVTGADVVVTATTASEPVFDGAALEPGTHVTAMGQYNPEKRELD 229
                                       ******************978******************************************************** PP

                                       HHHHHCCEEEE.SHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHH CS
                   OCD_Mu_crystall 234 ddilkradifv.dseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaakl 309
                                          + ra ++    e ++   G    a+e gv+ ed+++aelge++aG+ pGRtsd eit+fds+G+++e va a+l
  gi|336253905|ref|YP_004597012.1| 230 TTTIERATYVPdLRERATFDAGSFIAALEDGVVTEDHVHAELGEIVAGEAPGRTSDDEITVFDSGGTGIETVAGAHL 306
                                       **********96677788899******************************************************** PP

                                       HHHHHCCC CS
                   OCD_Mu_crystall 310 vyeraeek 317
                                        yera+e+
  gi|336253905|ref|YP_004597012.1| 307 LYERALEE 314
                                       *****985 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 !   23.1   0.0   1.9e-08   8.3e-05       2      69 ..     127     197 ..     126     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.9e-08
                                       EEEETTSHHHHHHHHHHHHTTS.-GGCEEEEEESSCCCHHHHHHHHC......-EEECECHHHHHHH-SEEEE-S CS
                     F420_oxidored   2 igiiGaGnmgealasgllaaga.qpheivvansrnpekaeelaeelg......vkvtavdneeaaeeadvvvlav 69 
                                       +giiG+G ++++ +   ++a + + ++++v  s++pe++e++a+++       v++   + e a++ advvv a 
  gi|336253905|ref|YP_004597012.1| 127 LGIIGTGAQARGQLW--ATATVrEFTDVRVY-SPTPESREAFAADFDdrleadVRAVD-SSEAAVTGADVVVTAT 197
                                       89******9998554..44444478****55.************99999995555555.5566677******986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   6.3e-08   0.00028      13      97 ..     125     211 ..     117     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.3e-08
                                       -EEEEES-SHHH..HHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT-SEEEE-SSSS CS
                      Shikimate_DH  13 kkvlliGaGema..elvakhLlakgvkkvvvaNRtlerakelaeel.kgeeiealkleelkellaeadvvisatase 86 
                                        +  +iG+G  a  +l a++ + +++++v v   t e  +++a ++ +  e+ ++++++ ++++  advv++at ++
  gi|336253905|ref|YP_004597012.1| 125 DTLGIIGTGAQArgQLWATATV-REFTDVRVYSPTPESREAFAADFdDRLEADVRAVDSSEAAVTGADVVVTATTAS 200
                                       5677999998761155555555.68899******************55568999*********************** PP

                                       S-SB-HHHHHC CS
                      Shikimate_DH  87 epilekeevee 97 
                                       ep+++ +++e 
  gi|336253905|ref|YP_004597012.1| 201 EPVFDGAALEP 211
                                       ***99888776 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 !   16.0   0.0   2.3e-06      0.01       2      95 ..     127     224 ..     126     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.3e-06
                                       EEEE--SH..HHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.......EEE-SSHHHHHHHCSEEEE-SSSHHHH CS
                     NAD_binding_2   2 igfiGlGv..MGsnmalnllkagykvavynrtkekveelvaeg.......akaaesieelvasldvvitmvkagkav 69 
                                       +g+iG+G    G+  a+  +++  +v vy  t+e+ e+++a+        ++a++s e++v+++dvv+t  +a+++v
  gi|336253905|ref|YP_004597012.1| 127 LGIIGTGAqaRGQLWATATVREFTDVRVYSPTPESREAFAADFddrleadVRAVDSSEAAVTGADVVVTATTASEPV 203
                                       799999963369999*************************9977889999*****************9988887776 PP

                                       HHHHHSHCCC--TT-EEEE-S---HH CS
                     NAD_binding_2  70 deviegllealkkgdilidgstsspe 95 
                                           +g  +al++g+ +  ++  +pe
  gi|336253905|ref|YP_004597012.1| 204 ---FDG--AALEPGTHVTAMGQYNPE 224
                                       ...344..345555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2667.50
//
Query:       gi|336253906|ref|YP_004597013.1|  [L=158]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-17   62.9   0.0    2.4e-17   62.4   0.0    1.2  1  HTH_10      HTH DNA binding domain
     0.0011   18.9   0.7     0.0016   18.4   0.7    1.3  1  Serglycin   Serglycin
  ------ inclusion threshold ------
      0.013   13.7   4.1      0.015   13.5   4.1    1.0  1  AF-4        AF-4 proto-oncoprotein
      0.014   15.3   0.1       0.03   14.2   0.1    1.6  1  MarR_2      MarR family
      0.049   13.6   0.4       0.11   12.5   0.4    1.5  1  HTH_1       Bacterial regulatory helix-turn-helix protein, ly
       0.05   13.1   0.2       0.11   12.1   0.2    1.6  1  Sigma70_r4  Sigma-70, region 4
       0.11   12.3   0.0        0.2   11.5   0.0    1.3  1  P22_Cro     DNA-binding transcriptional regulator Cro
       0.14   12.1   0.2       0.24   11.4   0.2    1.3  1  HTH_11      HTH domain


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 !   62.4   0.0   1.1e-20   2.4e-17       2      52 ..      60     110 ..      59     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 1.1e-20
                            HTH_10   2 TdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       T+kq e+l lA e+GYFd+PRrv+l+ LA  l Isks++s++Lr+aes+li
  gi|336253906|ref|YP_004597013.1|  60 TPKQWEALELAGELGYFDRPRRVDLETLATVLSISKSAVSQRLRAAESTLI 110
                                       9************************************************98 PP

>> Serglycin  Serglycin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.7   6.9e-07    0.0016      89     107 ..     119     139 ..      87     154 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.9e-07
                         Serglycin  89 edy..sgsgsGsGsGsGsgsg 107
                                       e+   s sgsGsGsGsGs+++
  gi|336253906|ref|YP_004597013.1| 119 ESAadSSSGSGSGSGSGSDAE 139
                                       333224455555555555444 PP

>> AF-4  AF-4 proto-oncoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   4.1   6.6e-06     0.015     451     498 ..     103     150 ..      82     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-06
                              AF-4 451 pssapqstpesvesahsssaeSeSsSeSeSSSeSDSesEssssdsean 498
                                        + ++  ++  ve+a +s a+S+S S+S S S+SD e     +d e  
  gi|336253906|ref|YP_004597013.1| 103 RAAESTLIQAVVEAARESAADSSSGSGSGSGSGSDAEPGATGTDREPV 150
                                       3333344444599******************99999988877877754 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.3e-05      0.03      13      47 ..      72     107 ..      58     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                                       HHHCTTTS.EEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2  13 aLgrrpgr.dltvgelarrlglsksavsrilkrLva 47 
                                       +Lg  +++ ++    la  l +sksavs++l+ +++
  gi|336253906|ref|YP_004597013.1|  72 ELGYFDRPrRVDLETLATVLSISKSAVSQRLRAAES 107
                                       555555556889999*****************9886 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 ?   12.5   0.4   4.8e-05      0.11      20      48 ..      88     116 ..      88     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.8e-05
                                       HHHHTS-HHHHHHHHHHHHHHHTS-SEEE CS
                             HTH_1  20 AeeLglsqpavsrqikrLEeelgvpLfeR 48 
                                       A  L +s +avs+++++ E+ l +  +e 
  gi|336253906|ref|YP_004597013.1|  88 ATVLSISKSAVSQRLRAAESTLIQAVVEA 116
                                       66799***************998887774 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   4.8e-05      0.11      21      44 ..      82     105 ..      57     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.8e-05
                                       --HHHHHHHHTS-HHHHHHHHHHH CS
                        Sigma70_r4  21 lTleEIgerlgiSrerVrqiekrA 44 
                                         le ++ +l iS+++V+q+++ A
  gi|336253906|ref|YP_004597013.1|  82 VDLETLATVLSISKSAVSQRLRAA 105
                                       56999****************987 PP

>> P22_Cro  DNA-binding transcriptional regulator Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.8e-05       0.2      12      29 ..      84     101 ..      83     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.8e-05
                                       HHHHHHHHTS-HHHHHHH CS
                           P22_Cro  12 vekvAkalgvtksAVsqW 29 
                                        e +A +l ++ksAVsq+
  gi|336253906|ref|YP_004597013.1|  84 LETLATVLSISKSAVSQR 101
                                       5789*************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00011      0.24      16      48 ..      82     116 ..      76     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                            HTH_11  16 isgeeLAeeLnvSrrtvrrdIkaLeelg..vpIes 48 
                                       +  e+LA  L++S+++v ++++a e+++  + +e+
  gi|336253906|ref|YP_004597013.1|  82 VDLETLATVLSISKSAVSQRLRAAESTLiqAVVEA 116
                                       7789********************99996655655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1185.97
//
Query:       gi|336253907|ref|YP_004597014.1|  [L=369]
Description: copper-containing nitrite reductase [Halopiger xanaduensis SH-6]
Scores for 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-08   33.9   0.0    5.6e-08   32.8   0.0    1.6  1  Cu-oxidase_3  Multicopper oxidase
    1.1e-06   28.4   0.0    7.7e-06   25.7   0.0    2.4  2  Cu-oxidase_2  Multicopper oxidase
      0.005   16.6   5.3      0.018   14.9   5.3    2.0  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
  ------ inclusion threshold ------
       0.13   11.6   0.8       0.28   10.5   0.8    1.6  1  UCR_Fe-S_N    Ubiquitinol-cytochrome C reductase Fe-S subunit


Domain annotation for each model (and alignments):
>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   1.3e-11   5.6e-08       6     117 ..      94     204 ..      89     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.3e-11
                                       EEECTTEESEEEEEECTSSBS-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSC.SGGG-B-TT-E. CS
                      Cu-oxidase_3   6 tvsplggterevitvNgqfpgptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpg.vtqcpiqpges. 80 
                                       t++++ g++ + +t+ gq+pgp ++vr+gd+v +++   +++++ +  h ++ ++     G+ g      i+pg++ 
  gi|336253907|ref|YP_004597014.1|  94 TAEIEPGVTFDYMTFEGQVPGPMVRVRQGDRVNLTF--DVPDEINLEAHNMDFHAV---YGPGGgADATTIAPGDDp 165
                                       566777777899******************998765..577777777777777766...333330345789998763 PP

                                       EEEEEE--S-SEEEEEEE--TT..HHH.TT-EEEEEEE-H CS
                      Cu-oxidase_3  81 ftyrftvkqqagtlwYhshlsl..qqa.aGlaGaiiiedk 117
                                        + +ft++  ag + Yh  + +  q+  +G++G i++e++
  gi|336253907|ref|YP_004597014.1| 166 AQISFTAEY-AGVFIYHCAIPNmdQHIsSGMFGSILVEPE 204
                                       7899***99.*******99988887778*********997 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.7e-09   7.7e-06      30     136 ..     112     204 ..      75     205 .. 0.73
   2 ?   -2.8   0.0       1.1     5e+03      34      56 ..     264     290 ..     234     291 .. 0.56

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.7e-09
                                       TSSEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEEEEEE CS
                      Cu-oxidase_2  30 entnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwvairfk 106
                                          +++++++g++v ++++ ++++   +  H +df  +  gpg               +   t+  p+++ + i f+
  gi|336253907|ref|YP_004597014.1| 112 VPGPMVRVRQGDRVNLTFDVPDEI--NLEAHNMDFHAV-YGPGG--------------GADATTIAPGDDPAQISFT 171
                                       556788888888888888888888..355566677666.44444..............4578899999********* PP

                                       S.S-EEEEEEESSH...HHHHTT-EEEEEEECH CS
                      Cu-oxidase_2 107 adnpGvwllHCHil...wHldqGmalqfvvrpd 136
                                       a+++Gv+++HC i    +H ++Gm ++++v+p+
  gi|336253907|ref|YP_004597014.1| 172 AEYAGVFIYHCAIPnmdQHISSGMFGSILVEPE 204
                                       ***********987777************9986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                                       EEEEETTEEEEEEEEE-SSS....-EE CS
                      Cu-oxidase_2  34 vitlpkgevveiviqnntkl....pHP 56 
                                       +++++ ge+ ++++ n ++      HP
  gi|336253907|ref|YP_004597014.1| 264 PMHAEVGETARVYFANGGPNllssWHP 290
                                       455555777777777766655444455 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   5.3     4e-06     0.018       3      25 ..       9      31 ..       9      32 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-06
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                      SRR FL++++ a+A+a++g +++
  gi|336253907|ref|YP_004597014.1|  9 SRRRFLQTAGSATALAVAGCLGS 31
                                      9************9998887665 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.8   6.4e-05      0.28       9      29 ..       8      28 ..       1      29 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.4e-05
                        UCR_Fe-S_N  9 ptRRDFLyiATgavgaVGaaa 29
                                       +RR+FL +A +a++  +a++
  gi|336253907|ref|YP_004597014.1|  8 RSRRRFLQTAGSATALAVAGC 28
                                      68*************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2672.13
//
Query:       gi|336253908|ref|YP_004597015.1|  [L=334]
Description: phosphoesterase RecJ domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   47.5   0.1    4.2e-12   46.7   0.1    1.3  1  DHHA1     DHHA1 domain
    1.4e-10   41.3   0.1    2.3e-10   40.6   0.1    1.3  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 !   46.7   0.1   4.7e-16   4.2e-12      38     124 ..     213     306 ..     190     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 4.7e-16
                                       C..TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSHSS-HHHHHHHHHHHTTCCE CS
                             DHHA1  38 k..gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkdgvdagelakeaaaklgggG 111
                                       +    + lva vg++++++al +aad+l++   + +  v+v++  +d +++s+rs++ +v++ge +++ ++ lg  G
  gi|336253908|ref|YP_004597015.1| 213 RerRGSSLVASVGKTAETDALPQAADYLLN--LEgVDTVLVYGIVDDAIRLSGRSIDPRVHMGETLEDGFDGLGAVG 287
                                       3345667777777*****************..888*********************88**********777776666 PP

                                       EEETCEEEEEEE.......H CS
                             DHHA1 112 GGHdlAaGagip.......a 124
                                        GH+ +aG++i+       a
  gi|336253908|ref|YP_004597015.1| 288 -GHHDMAGGRIQlglfadeA 306
                                       .9988888888744554444 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.1   2.5e-14   2.3e-10       3     100 ..      18     158 ..      16     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.5e-14
                                       EEE-ECSSSHHHHHHHHHHHHC................................................ECS--TC CS
                                       xxxxxxxxxxxxxxxxxxxxxx................................................xxxxxxx RF
                               DHH   3 livghknpDtDsigSaialanl................................................lvDhnek 31 
                                       +iv+h npD D+++Sa+al+++                                                 vDh ++
  gi|336253908|ref|YP_004597015.1|  18 AIVCHDNPDPDCLASALALEAIavkqdvddvtivyggeishqqnrafvnmldislepvedaaiddygcigFVDHARP 94 
                                       6999*****************8888888888888888888888888888889999999999999999999******* PP

                                       GGCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  32 sqavegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllg 100
                                           +    ++    i++DHH          +++ +++ +g+ta+i +e+l e ++e+++++a +ll +
  gi|336253908|ref|YP_004597015.1|  95 GANTQL--SDDITPDIVVDHHPGDPGDA---RFTDVRTRYGATATIFVEYLGELGVEPTTRLASALLFA 158
                                       999966..9************9973333...35667788************************999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2619.91
//
Query:       gi|336253909|ref|YP_004597016.1|  [L=158]
Description: heat shock protein Hsp20 [Halopiger xanaduensis SH-6]
Scores for 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   84.7   0.1    5.5e-24   84.3   0.1    1.2  1  HSP20       Hsp20/alpha crystallin family
    1.9e-12   46.5   0.0      3e-12   45.9   0.0    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA
    0.00057   20.9   0.0     0.0008   20.4   0.0    1.3  1  CS          CS domain
  ------ inclusion threshold ------
      0.016   15.3   1.4          5    7.1   0.0    2.8  3  GvpH        GvpH
      0.041   13.7   0.2        2.1    8.1   0.0    2.1  2  DUF2807     Putative auto-transporter adhesin, head GIN domai
       0.16   12.1   0.0         25    5.1   0.0    2.2  2  FKBP26_C    FKBP26_C-terminal


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 !   84.3   0.1   1.8e-27   5.5e-24       3     101 ..      57     157 ..      55     158 .] 0.91

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 1.8e-27
                                       -SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--......---TT----SS---EEEEEE--STTB-TTT-EEE CS
                             HSP20   3 keeeeefevkldvpglkkeelkvkvednrvlvkgehe....eeeedekglikerssrkFsrkftLPenvdadkvkas 75 
                                        +e +ef v++dvpg ++e+l++ + +++++++ge+e    +   de+++++er++++F+r+++LP+ v+ d+v+a+
  gi|336253909|ref|YP_004597016.1|  57 ADEGSEFVVTVDVPGYDTEDLEIRLSGETLSIRGEREheaeQGGADEQYIRRERAVQSFNRQLQLPDPVEVDDVSAT 133
                                       67889********************************8776667899****************************** PP

                                       EETTEEEEEEEBSS--..-------- CS
                             HSP20  76 lkdGvLtvtvpkkepekkkkerkiqi 101
                                       +++G+Ltv +pk+ep  +  + +i+i
  gi|336253909|ref|YP_004597016.1| 134 VNNGILTVRLPKREPSDE--STSIDI 157
                                       ***************955..555555 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 !   45.9   0.0     1e-15     3e-12       2      63 .]      61     143 ..      60     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1e-15
                        ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkig......................nfrRqitLPsvlarkevtsAkfed 56 
                                       +e+v+++d+P+ d+e+++++ sg++L+I+ +                      +f+Rq  LP+ +  ++v sA++++
  gi|336253909|ref|YP_004597016.1|  61 SEFVVTVDVPGYDTEDLEIRLSGETLSIRGEreheaeqggadeqyirreravqSFNRQLQLPDPVEVDDV-SATVNN 136
                                       699*******************************************************************.****** PP

                        ArsA_HSP20  57 gvLeIrF 63 
                                       g L++r+
  gi|336253909|ref|YP_004597016.1| 137 GILTVRL 143
                                       *****96 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.7e-07    0.0008      10      76 .]      61     145 ..      52     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.7e-07
                                       TEEEEEEE-TTCTTTTTCEEEEEETTEEEEEETS.CEEEEECE....................BSS-BETTTEEEEE CS
                                CS  10 deVvvtiyvkkvnikkkdvkvefkerslkvkigk.eklliege....................LfgpIdpeesswti 65 
                                       +e vvt+ v+++  +++d++++++ ++l++   + e +  +g                     L +p+++++ s t+
  gi|336253909|ref|YP_004597016.1|  61 SEFVVTVDVPGY--DTEDLEIRLSGETLSIRG-ErEHEAEQGGadeqyirreravqsfnrqlqLPDPVEVDDVSATV 134
                                       6779*******9..*****************7.43344444447999****************************** PP

                                       ETTEEEEEEEB CS
                                CS  66 eskkveitLkK 76 
                                        +  + + L K
  gi|336253909|ref|YP_004597016.1| 135 NNGILTVRLPK 145
                                       *9999999987 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.29   8.7e+02       5      48 ..       6      44 ..       3      51 .. 0.54
   2 ?    5.7   0.1    0.0048        14      97     124 ..      57      84 ..      48      94 .. 0.84
   3 ?    7.1   0.0    0.0017         5     146     174 ..     126     154 ..     109     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.29
                              GvpH  5 dqsdrlsGlldqlsrlvevlaeleeegGerhessridrGrarid 48
                                      d+ d ++ l+++lsr +e+ a   e      e    d Gr+r d
  gi|336253909|ref|YP_004597016.1|  6 DPFDSITELFERLSRQLETAARSWE-----TEMDVRDGGRSRFD 44
                                      5556666677777777776664322.....22333344555555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0048
                              GvpH  97 sddsdelvvvadlpGvtdedvdvaletd 124
                                       +d++ e+vv  d+pG   ed+++ l  +
  gi|336253909|ref|YP_004597016.1|  57 ADEGSEFVVTVDVPGYDTEDLEIRLSGE 84 
                                       58999***********999999888743 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0017
                              GvpH 146 dvaitdltlrnqvlelrlarsedsdgaed 174
                                       +v   + t++n +l +rl + e+sd +++
  gi|336253909|ref|YP_004597016.1| 126 EVDDVSATVNNGILTVRLPKREPSDESTS 154
                                       5666788*****************98876 PP

>> DUF2807  Putative auto-transporter adhesin, head GIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00072       2.1      17      55 ..      59      97 ..      44     113 .. 0.86
   2 ?    4.0   0.0     0.013        37      30      56 ..     125     151 ..     111     158 .] 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00072
                                      E-SS-EEEEEEEHHHHCCEEEEEETTEEEEEE-TTTTSS CS
                           DUF2807 17 qgdeqsvviegdenllekvevevedgtLkirlekefest 55
                                      +g+e+ v++  +    e++e+  +++tL+ir e+e e +
  gi|336253909|ref|YP_004597016.1| 59 EGSEFVVTVDVPGYDTEDLEIRLSGETLSIRGEREHEAE 97
                                      689999999999999*****************9776655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.013
                                       HHHCCEEEEEETTEEEEEE-TTTTSSB CS
                           DUF2807  30 nllekvevevedgtLkirlekefestk 56 
                                         +++v+ +v++g L++rl k   s +
  gi|336253909|ref|YP_004597016.1| 125 VEVDDVSATVNNGILTVRLPKREPSDE 151
                                       5689**************995544443 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0      0.01        31       8      32 ..      64      88 ..      59      93 .. 0.90
   2 ?    5.1   0.0    0.0083        25      16      36 ..     125     145 ..     118     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.01
                                      HHHHH-TT--..--EEEEETTEEEE CS
                          FKBP26_C  8 lIkryiPnidlekfkieiedktvtI 32
                                      ++ + +P  d+e+++i ++++t++I
  gi|336253909|ref|YP_004597016.1| 64 VVTVDVPGYDTEDLEIRLSGETLSI 88
                                      678889****************999 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0083
                                       --..--EEEEETTEEEEE--T CS
                          FKBP26_C  16 idlekfkieiedktvtIelpe 36 
                                       ++++++  +++++++t+ lp+
  gi|336253909|ref|YP_004597016.1| 125 VEVDDVSATVNNGILTVRLPK 145
                                       799*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1177.12
//
Query:       gi|336253910|ref|YP_004597017.1|  [L=226]
Description: ThiJ/PfpI domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-14   52.3   0.3      3e-12   46.6   0.3    2.1  1  DJ-1_PfpI  DJ-1/PfpI family
    5.3e-09   36.0   0.0      1e-08   35.1   0.0    1.5  1  ThiJ_like  ThiJ/PfpI family-like
  ------ inclusion threshold ------
      0.027   14.7   0.0      0.028   14.7   0.0    1.2  1  ThuA       Trehalose utilisation


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.3     5e-16     3e-12       5     164 ..       6     222 ..       3     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 5e-16
                                       EEEE.TTBEHHHHHHHHHHHHHTTEEEEEEESS....................TSEEEETTSEEEE-SEEGG..GCT CS
                         DJ-1_PfpI   5 vlla.dgvedvElivpvdvlkragikvdvvsvd....................keevkgsrGlkvtvdasld..dvk 58 
                                       +++  +g+   E ++p++ l++ag++++v++++                    +e +++ + ++ +++  +   +++
  gi|336253910|ref|YP_004597017.1|   6 FVVSeEGYWGEECVEPLETLSAAGVEITVATPSgnppkidersidpeevgeetAEHIQEVHETDERLNDPIPtaQAD 82 
                                       44444888889**********************************99997777666666666555555555455777 PP

                                       CCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHH.TT-EEEEETTTHHHHHHTT......TTTTSEE--SGGGHHHH CS
                         DJ-1_PfpI  59 aaeyDalvlpGGragperlrenekvvelvkefae.kgklvaaICagpqlLaaag......vlkgrrvTsypavkdkl 128
                                       a+ yD++v pGG+    ++ +++ ++ l+++++e +++    +C++  +La +       +++gr vT++p+  ++ 
  gi|336253910|ref|YP_004597017.1|  83 AEGYDVVVFPGGHGTEWDVNQDHDARRLLRDAVEgDDGKALVVCHAVGILAFTRdshgafLVNGRDVTGFPNEWEEG 159
                                       889******************************6245677789****999954323334489*********965333 PP

                                       ......................HHTTSEE-SS.....SEEEETTEEEESSGGGHHHHHHHHHH CS
                         DJ-1_PfpI 129 ......................ekagakyvdk.....rvvvdgnlvTsrgpgaaiefalelle 164
                                                             e+ag ++ ++     +v vdg+l+T+rgp+++ + a +lle
  gi|336253910|ref|YP_004597017.1| 160 ivdendlmpsgrklpywvedevEAAGGNWDAEleqdtSVTVDGDLLTARGPESSSAAAQTLLE 222
                                       35555667887666766666666666666666999******************9999999987 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   1.7e-12     1e-08       2     115 ..       9     115 ..       8     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.7e-12
                         ThiJ_like   2 adeGydvtevaipwkvlkdagfsveFvtekgkvpkadekllsgikakllgaskeakdiYkelstlee.Fkeplslss 77 
                                       ++eGy+++e + p+++l  ag++++ +t++g++pk de+ +++         +e+++  +e+ +++e  ++p     
  gi|336253910|ref|YP_004597017.1|   9 SEEGYWGEECVEPLETLSAAGVEITVATPSGNPPKIDERSIDPEE-----VGEETAEHIQEVHETDErLNDPIPT-- 78 
                                       89*************************************999965.....3467888889999999945555444.. PP

                         ThiJ_like  78 esFsleeydlvllpGGsdkavrelleserlhsllveyl 115
                                        + + e yd+v  pGG++    ++ +++   +ll++ +
  gi|336253910|ref|YP_004597017.1|  79 AQADAEGYDVVVFPGGHGTEW-DVNQDHDARRLLRDAV 115
                                       345789***********9876.6666666666666554 PP

>> ThuA  Trehalose utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.6e-06     0.028      29      89 ..      60     131 ..       7     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.6e-06
                                       HHT-EEEEET....TS.G--HHHHHT-SEEEEE-G..GS-H....HHHHH.HHHHHHT..T-EEEEEGGG.G CS
                                       xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx..xxxxxxxxxx.x RF
                              ThuA  29 engfevdate....daavfteenLaqydvvvflstegevld....aaqeaalqryvea..GgGfvglhsA.a 89 
                                       e+  ev++t+    d+ + +++  + ydvvvf + +g+++d    +++++ l+++ve+  G+ +v++h+   
  gi|336253910|ref|YP_004597017.1|  60 EHIQEVHETDerlnDPIPTAQADAEGYDVVVFPGGHGTEWDvnqdHDARRLLRDAVEGddGKALVVCHAVgI 131
                                       333444433323347777888999**********88877762212455567999998766999*****8743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1745.44
//
Query:       gi|336253911|ref|YP_004597018.1|  [L=102]
Description: transcription factor TFIIB cyclin-like protein [Halopiger xanaduensis SH-6]
Scores for 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   24.1   0.2    7.2e-05   22.8   0.2    1.6  1  TFIIB       Transcription factor TFIIB repeat
  ------ inclusion threshold ------
      0.054   13.0   0.0        9.1    5.9   0.0    2.2  2  Sigma70_r4  Sigma-70, region 4


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 !   22.8   0.2     8e-09   7.2e-05       2      70 ..      18      83 ..      17      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8e-09
                                      HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHH CS
                             TFIIB  2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekt 70
                                      +++a++leL+ + +++A+ l+   + +     rs+ +++AA++y +++ ++  rtq  +++ + Vs  +
  gi|336253911|ref|YP_004597018.1| 18 EQVAERLELSTEARSCAVDLFLADVPD---DDRSKRAMLAASVYAGSLVAGDGRTQGAVADAADVSRLS 83
                                      5799*************9998655554...46********************************99766 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0018        16      23      35 ..      17      29 ..      10      30 .. 0.89
   2 ?    5.9   0.0     0.001       9.1      18      39 ..      65      86 ..      49      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0018
                                      HHHHHHHHTS-HH CS
                        Sigma70_r4 23 leEIgerlgiSre 35
                                      le+++erl +S e
  gi|336253911|ref|YP_004597018.1| 17 LEQVAERLELSTE 29
                                      9**********98 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.001
                                      TTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 18 geglTleEIgerlgiSrerVrq 39
                                      g+g+T+  +++  ++Sr  + q
  gi|336253911|ref|YP_004597018.1| 65 GDGRTQGAVADAADVSRLSIQQ 86
                                      89***************88877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.38u 0.19s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 880.93
//
Query:       gi|336253912|ref|YP_004597019.1|  [L=57]
Description: hypothetical protein Halxa_2522 [Halopiger xanaduensis SH-6]
Scores for 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:                       426  (0.0237604); 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:                         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: 00:00:00.39
# Mc/sec: 439.53
//
Query:       gi|336253913|ref|YP_004597020.1|  [L=147]
Description: hypothetical protein Halxa_2523 [Halopiger xanaduensis SH-6]
Scores for 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   18.5  11.9        0.2   11.2   5.9    2.6  2  SPW       SPW repeat
  ------ inclusion threshold ------
      0.097   13.1   3.1       0.12   12.7   3.1    1.1  1  QueT      QueT transporter
        4.4    7.4   8.5        2.1    8.4   3.1    2.2  2  DUF2892   Protein of unknown function (DUF2892)


Domain annotation for each model (and alignments):
>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.3   6.9e-05      0.41       4      43 ..      35      72 ..      30      76 .. 0.84
   2 !   11.2   5.9   3.4e-05       0.2       4      46 ..      91     132 ..      90     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.9e-05
                               SPW  4 nlllGlwlivSPWvlGfsattgaawnnvivGavvavLala 43
                                      + l+Gl l++ P+++   +t  a+wn+  +G  +++La +
  gi|336253913|ref|YP_004597020.1| 35 VALAGLGLVAYPFIFE--STDTATWNDTLTGTGIFLLAGY 72
                                      6788999999999977..5556**************9965 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.4e-05
                               SPW   4 nlllGlwlivSPWvlGfsattgaawnnvivGavvavLalafaa 46 
                                       + +lGlw+ vSP v+   ++  +a++    G++va+L+++ a 
  gi|336253913|ref|YP_004597020.1|  91 AAVLGLWALVSPAVIEMGSS-ELAMTTAGGGLLVAALSAYNAY 132
                                       679***********985555.666777779********99875 PP

>> QueT  QueT transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.1   2.1e-05      0.12      44     138 ..      38     127 ..      26     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                              QueT  44 ailGltiGcliaNllsplgllDvifGslatliaalltyllkkkr...l.laalppvlvnalivgavllelpflltvl 116
                                       a lGl+   +i + + ++++ D + G+   l+a +  y l+k+r   + +a+l+ vl              +   v+
  gi|336253913|ref|YP_004597020.1|  38 AGLGLVAYPFIFESTDTATWNDTLTGTGIFLLAGYNFYRLSKDRlasVgVASLAAVLGLWA---------LVSPAVI 105
                                       4567777778888888999*********************999832212333333333333.........3556899 PP

                              QueT 117 tvglgelivlyvlGlpllkale 138
                                        +g +el+++++ G +l+ al+
  gi|336253913|ref|YP_004597020.1| 106 EMGSSELAMTTAGGGLLVAALS 127
                                       9999999999999999999885 PP

>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2     0.034     2e+02      12      34 ..      34      57 ..      25      74 .. 0.61
   2 ?    8.4   3.1   0.00035       2.1       8      48 ..      79     126 ..      77     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.034
                           DUF2892 12 lrivvGlvllllallglsggw.gw 34
                                      + +++Gl l+++ +++ s+ +  w
  gi|336253913|ref|YP_004597020.1| 34 IVALAGLGLVAYPFIFESTDTaTW 57
                                      445666666666666665555544 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00035
                           DUF2892   8 ldRilrivvGlvllllallglsggw.......gwllglvGavllltgl 48 
                                        dR++++ v++++++l+l++l +++        +    +G++ll+++l
  gi|336253913|ref|YP_004597020.1|  79 KDRLASVGVASLAAVLGLWALVSPAviemgssELAMTTAGGGLLVAAL 126
                                       69*******************99889***9997777888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1226.71
//
Query:       gi|336253914|ref|YP_004597021.1|  [L=164]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-10   39.9   0.5    6.6e-10   39.6   0.5    1.1  1  Usp       Universal stress protein family
     0.0071   16.3   0.0        1.3    8.9   0.0    2.2  2  ETF       Electron transfer flavoprotein domain


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 !   39.6   0.5   7.4e-14   6.6e-10       5     140 ..       3     144 ..       1     145 [. 0.90

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 7.4e-14
                                       EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.......HHHH CS
                               Usp   5 IlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.......akaa 74 
                                        lV++D s  ++ Ale+A  + +a + e+++l+vi++++ +a++ +  +++e  + ++ ++  ++        a+  
  gi|336253914|ref|YP_004597021.1|   3 LLVPFDASRLATDALERATTFGEALEEEVVVLTVIPDDPEYARDRGWITEGEPFAPDAIEAGIRERvmdvapeATFH 79 
                                       69***********************************************************99999*********** PP

                                       HHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  75 aeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       +e    ++ + +   ++ +ei +va e++a+ + +Gs   +++  +   Sv + v+     +V vV
  gi|336253914|ref|YP_004597021.1|  80 TERVSSDEPTATSTTNVVREIRRVAAEIEASVVFIGSENAGSVI-APQSSVGSPVASDQRYDVYVV 144
                                       *************************************9966655.355666666666666666666 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0018        17      15      43 ..      11      39 ..       5      49 .. 0.83
   2 !    8.9   0.0   0.00015       1.3      65     107 ..      84     126 ..      79     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0018
                                      HHHHHHHHHHHHHHHHHT--EEEEEEES. CS
                               ETF 15 pvdlealeaArrlkekaggevtavvvGpp 43
                                      +    ale A  + e++ +ev++++v p+
  gi|336253914|ref|YP_004597021.1| 11 RLATDALERATTFGEALEEEVVVLTVIPD 39
                                      56789***********88*******9775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00015
                                       E-GGGSS--CCHHHHHHHHHHHHC--SEEEEESSCCHHHHHHH CS
                               ETF  65 ddpalagydaeatakalaalikkedpdlvlagataigkqvapr 107
                                       ++++  +  + ++++ ++ +++++++++v++g++  g  +ap+
  gi|336253914|ref|YP_004597021.1|  84 SSDEPTATSTTNVVREIRRVAAEIEASVVFIGSENAGSVIAPQ 126
                                       4555555677799999*********************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1193.34
//
Query:       gi|336253915|ref|YP_004597022.1|  [L=696]
Description: sodium/hydrogen exchanger [Halopiger xanaduensis SH-6]
Scores for 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-50  170.9  49.9    4.5e-50  170.5  49.9    1.1  1  Na_H_Exchanger   Sodium/hydrogen exchanger family
      1e-06   29.3   0.9      2e-06   28.4   0.2    1.8  2  Usp              Universal stress protein 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 !  170.5  49.9     5e-54   4.5e-50       5     377 ..      33     393 ..      26     399 .. 0.89

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 5e-54
                                       HHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHH CS
                    Na_H_Exchanger   5 illallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksill 81 
                                       +l+ l+++l+++r++lp ivg i++G  +Gp g gl+e + e + +l e+g+++l+F aGle++l+++ + +  +++
  gi|336253915|ref|YP_004597022.1|  33 MLVFLTAPLVLQRYRLPGIVGIIVVGAAIGPNGAGLLERD-ETIVLLGEVGIVYLMFVAGLEINLSQFIAYKDRSVV 108
                                       2334445556*****************************9.************************************ PP

                                       HHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCC CS
                    Na_H_Exchanger  82 lallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvl 158
                                       ++ll+++++ ++ G+l+++   l+++l +a lf+ai+s + + ++++i++++g+ + +  t ++g  +++D +a+++
  gi|336253915|ref|YP_004597022.1| 109 FGLLSFVVPQAV-GTLVGV-AALDLSLGAASLFAAIFS-SHTLLAYPIVSRLGIARVESVTATIGGTIVTDTLALLV 182
                                       ************.*****7.78****************.99************************************ PP

                                       CHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXX CS
                    Na_H_Exchanger 159 lavllalakeeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallaellgv 235
                                       lav++a+  + +g  + l      +  +a+++  + l+++ l r + r++++++ +e+l+v++++++aa  a + gv
  gi|336253915|ref|YP_004597022.1| 183 LAVVVAAERGAIGPLFWL----ELTGKLALFFAGVWLLVPRLGRWFFRTVEQESYFEFLFVMVVLFAAASSAAAAGV 255
                                       *****9974444444444....44555666666666666666666666666789*********************** PP

                                       XHHHHHHHHHHHHHHHHHHTT.HHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHH CS
                    Na_H_Exchanger 236 sgilgaflaGlvlseyefsnk.lseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilav 311
                                       +gi+gaflaGl+l++  +++  l  ++e +++ lf+p+f ++vG+ +d+ vl+ +l+ ++++++ l++++ ++++a+
  gi|336253915|ref|YP_004597022.1| 256 EGIIGAFLAGLALNRLVPESGpLMNRIEFVGNALFIPFFLLSVGMLVDVRVLTAGLETVTIAVAFLALVTTTKYAAA 332
                                       **************77777777******************************7799999999*******9******* PP

                                       HHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHHH CS
                    Na_H_Exchanger 312 flllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslkp 377
                                       +l + ++g+++ e ++++ + +++ a ala++++g  +gll+++++++++v++l+  +     ++p
  gi|336253915|ref|YP_004597022.1| 333 WLTAERYGYTHDETMVMFGLSVGQAAAALAIVLIGFETGLLDEAMVNAVVVMILVVSV-----FSP 393
                                       ***************99988999**********************9999999998888.....444 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.2   2.2e-10     2e-06      10     141 .]     428     553 ..     426     553 .. 0.83
   2 ?   -2.8   0.0       0.9   8.1e+03      73     114 ..     612     654 ..     588     661 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.2e-10
                                       -SSHHHHHHHHHHHH....HHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEE CS
                               Usp  10 DgseeskkAlewAle....lakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkv 82 
                                       D +++ +++++ A++    +a++   +l++++v  p++ +++   + e +e e+  +e+e+        a a+++++
  gi|336253915|ref|YP_004597022.1| 428 DRTPNRQRLVDLAVAvrepEAAQ---PLYAATVARPDPGEPARRTEAEIAEIEASFAETEA------YTAGAEVPIE 495
                                       88899999999999966555555...49999999888887777777777777766666655......35799***** PP

                                       EEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  83 evvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                         ++ + d+a++i ++a e+ +  ++vG+ g s   r+ +G v +++l +++  Vlv r
  gi|336253915|ref|YP_004597022.1| 496 LETRIDDDVADGISRAAVENRITTLLVGWDG-SPSPRRTFGTVIDRLLGRTSQQVLVAR 553
                                       *******************************.55555699****************976 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.9
                                       HHHHCTTCEEEEEEEESSHHHHH.HHHHHHTTSSEEEEESCCS CS
                               Usp  73 aaaeaggvkvevvveegdpaeei.levaeeedadliVvGsrgr 114
                                        ++ + +v v+v+  +g p+    l+++ e d   +V ++rg 
  gi|336253915|ref|YP_004597022.1| 612 FELVDPDVPVTVDGADGWPGARDrLRTVGETDLAVLVSARRGA 654
                                       4555666777777777777777766777888888888777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (696 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4810.84
//
Query:       gi|336253916|ref|YP_004597023.1|  [L=658]
Description: acetate/CoA ligase [Halopiger xanaduensis SH-6]
Scores for complete 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-92  310.8   0.0    1.4e-92  310.5   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    4.1e-19   69.3   0.1      8e-19   68.4   0.1    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    4.2e-14   52.2   2.3    9.8e-14   51.0   2.3    1.7  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


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 !  310.5   0.0   2.4e-96   1.4e-92       7     422 ..      95     534 ..      89     535 .. 0.89

  Alignments for each domain:
  == domain 1  score: 310.5 bits;  conditional E-value: 2.4e-96
                                       HSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETT CS
                       AMP-binding   7 ktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnpt 80 
                                        ++++va+ +   +ge++t+TYr+l+ +vn++Aa+Lr lGv+++d+V i+lp+ p + +a+la++++Ga ++++ ++
  gi|336253916|ref|YP_004597023.1|  95 GRKNHVAIRWegkHGEHETYTYRDLYVEVNEFAAALRGLGVEEDDVVTIYLPMIPALPIAMLACARIGAPHSVVFAG 171
                                       577999**8899999************************************************************** PP

                                       S-HHHHHHHHHHHTESEEE.........ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTT CS
                       AMP-binding  81 ltaeelayiledseakvli.........atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseeka 147
                                       l+a++la  ++++e+++li         +   + +  +k+++a+ ++e+  +++v+d+ + +    l ++e ++++ 
  gi|336253916|ref|YP_004597023.1| 172 LSADALATRMDAAESEYLItcdgyyrrgD---AFNqKSKADNARLSVEQDVETVVVDRLGDDLPHVLGDDERDYHDL 245
                                       *******************9998875431...333345556666666777888999999988887887777776655 PP

                                       .S....-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHH CS
                       AMP-binding 148 .e....kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifgli 218
                                        +    + +++++ +++d+++++YTSGTTG+PKGV++ ++ ++a va+ +  +   +++++d++++ +++ +i+g++
  gi|336253916|ref|YP_004597023.1| 246 cReyagETVDPVSRDAEDMLFLMYTSGTTGEPKGVVHATGGYLAHVAWTS--HAvLDITPEDTYWCAADIGWITGHS 320
                                       5167785668889**************************99999988864..33466789***************** PP

                                       HHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS CS
                       AMP-binding 219 lelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllgge 293
                                       + ++++l+ G t v+++++++ +d ++l+e +++  v v++++P++++a+++  ++     +++dlsslrl+ ++ge
  gi|336253916|ref|YP_004597023.1| 321 YIVYGPLALGTTAVMYEGTPDyPDRDRLWEIVDRNAVDVFYTAPTAIRAFMKwGSDYP---DRHDLSSLRLLGSVGE 394
                                       *********************888999*************************665554...678************* PP

                                       -EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEE.CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEE CS
                       AMP-binding 294 plspellrffralfge...evlegYGlTEttgvvtv.lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGe 366
                                       p+sp  + ++r++ g+   +v++++++TEt++v++  lp   d+ k+g +G+ lpg++v++vDe+ g pv++g+ G 
  gi|336253916|ref|YP_004597023.1| 395 PISPRPWNWYREHIGRgdcPVVDTWWQTETGAVIVStLP-GIDEMKPGAAGPGLPGIDVAVVDEA-GDPVEPGQAGY 469
                                       **************99******************55355.6666799*****************9.*********** PP

                                       EEEEET..TS-SEBTT-HHHHHHHEEE.....T.CC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 367 llvrgp..gvmkgYlkkpeataeafds.....e.gr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                       l ++ p  g+++  +  +++ ++ +++     + ++  + +GD + +dedGy+ ++gR++d+i++
  gi|336253916|ref|YP_004597023.1| 470 LTIGRPwpGMARTLYDGDDRFRSEYWDrfsdpDrDEwVYFSGDAAAIDEDGYVTVLGRIDDVINV 534
                                       *****9778*******99999999997788872455589************************98 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 !   68.4   0.1   1.3e-22     8e-19       1      76 []     543     621 ..     543     621 .. 0.93

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 1.3e-22
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       e+Esa++ +++VaeaaVvG + e +G  + a+V  + g+++   +++ +++ +++++gp+a+p+++vf++elpktrs
  gi|336253916|ref|YP_004597023.1| 543 EIESAITDVDGVAEAAVVGRSSEATGTEIYAYVSTAGGHDPdatIRQRIVDSIESTIGPIAKPSEIVFTPELPKTRS 619
                                       8*********************************975543335799******************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|336253916|ref|YP_004597023.1| 620 GK 621
                                       *9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   2.3   1.6e-17   9.8e-14       3      55 .]      35      87 ..      33      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.6e-17
                                      HHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  3 elykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                      e+y+   +d    W+++a+ l+W++p+d+vl+++++pf++WF GGklN++yNc
  gi|336253916|ref|YP_004597023.1| 35 EIYETFERDWPDCWERAADLLSWDEPYDTVLNDENAPFYEWFGGGKLNAAYNC 87
                                      7788888899999**************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (658 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.62u 0.23s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4656.77
//
Query:       gi|336253917|ref|YP_004597024.1|  [L=788]
Description: PAS/PAC sensor protein [Halopiger xanaduensis SH-6]
Scores for complete 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  155.3   7.8    1.1e-45  155.3   7.8    2.9  3  BAT              GAF and HTH_10 associated domain
    1.4e-19   69.6   0.0    3.7e-19   68.3   0.0    1.8  1  HTH_10           HTH DNA binding domain
    1.1e-12   48.1   0.0    2.7e-12   46.9   0.0    1.6  1  PAS_9            PAS domain
      2e-11   44.0   0.0    5.6e-11   42.5   0.0    1.7  2  Phage_integrase  Phage integrase family
    5.6e-10   39.4   1.5    2.6e-09   37.3   0.5    2.8  1  PAS_4            PAS fold
    7.7e-10   38.8   0.0      4e-09   36.5   0.0    2.3  2  PAS              PAS fold
    4.3e-08   33.5   2.4    1.7e-06   28.4   0.3    3.2  2  GAF_2            GAF domain
    1.6e-07   31.7   0.0    2.8e-06   27.7   0.0    2.4  2  GAF_3            GAF domain
     0.0017   18.9   0.0      0.004   17.7   0.0    1.7  1  PAS_10           PAS domain
     0.0035   17.6   0.1     0.0095   16.2   0.1    1.8  1  PAS_3            PAS fold
     0.0064   17.1   0.0      0.021   15.5   0.0    1.9  1  GAF              GAF domain
     0.0087   16.1   0.3       0.05   13.7   0.1    2.5  2  HTH_20           Helix-turn-helix domain
     0.0097   15.9   0.0      0.043   13.9   0.0    2.2  1  PAS_8            PAS domain
  ------ inclusion threshold ------
      0.018   14.5   0.0       0.05   13.1   0.0    1.7  1  Sigma70_r4       Sigma-70, region 4
      0.021   14.5   0.0      0.065   12.9   0.0    1.8  1  Sigma70_r4_2     Sigma-70, region 4
      0.049   13.7   0.8       0.13   12.4   0.8    1.6  1  Cep57_CLD_2      Centrosome localisation domain of PPC89
       0.07   12.8   0.4         12    5.7   0.0    3.1  3  GntR             Bacterial regulatory proteins, gntR family
      0.074   12.9   0.1       0.15   11.9   0.1    1.4  1  Ribosomal_L13e   Ribosomal protein L13e
      0.085   12.7   0.0        0.2   11.5   0.0    1.6  1  HTH_5            Bacterial regulatory protein, arsR family
       0.27   11.1   2.5          2    8.3   0.0    3.5  2  HTH_23           Homeodomain-like domain


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.3   3.8e+03      91     108 ..     146     163 ..     121     166 .. 0.84
   2 ?   -1.8   0.7       2.8   2.5e+03      46      71 ..     455     479 ..     452     510 .. 0.61
   3 !  155.3   7.8   1.2e-48   1.1e-45       1     155 [.     551     705 ..     551     706 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.3
                               BAT  91 stlaehGgtvrsaeaedg 108
                                       ++l++h++ +r++ a +g
  gi|336253917|ref|YP_004597024.1| 146 RALVDHDVNPRAVKAAGG 163
                                       58999**99999999876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.8
                               BAT  46 tvdgadpeevrdaaedldavedvrvv 71 
                                       +++gad e +r+aa d  a   v+v 
  gi|336253917|ref|YP_004597024.1| 455 SAEGADGEPARSAANDGAAA-AVTVE 479
                                       67788888888887743332.22222 PP

  == domain 3  score: 155.3 bits;  conditional E-value: 1.2e-48
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       D+vveLe+++rd+++++v+++++l+cr+el++lvp s+ + l+++ ++ga+p++v ++ae+ ++++d r+v++e dg
  gi|336253917|ref|YP_004597024.1| 551 DRVVELEIACRDDRSFFVDASKQLGCRFELDSLVPVSESTHLYYLDLEGASPADVFELAEADPGITDWRLVETEADG 627
                                       99*************************************************************************** PP

                               BAT  78 tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrref 154
                                        +le+ v+g+ +  tl+e+G+tvr+a++edg+a+++ e++ +ad+R+++++l+++ypd eL+ +re er+v+t+r+f
  gi|336253917|ref|YP_004597024.1| 628 GRLEFVVEGSAPTLTLTEYGVTVREAVVEDGTATITGECAADADLRTIMDGLRAAYPDSELIGKREAERTVQTARQF 704
                                       ***************************************************************************** PP

                               BAT 155 r 155
                                       r
  gi|336253917|ref|YP_004597024.1| 705 R 705
                                       8 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   4.1e-22   3.7e-19       1      52 [.     712     763 ..     712     764 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 4.1e-22
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LTd+q ++l++Ay  GY+d+PR+ t++e+A+++G+s +tl++hLrka+  l+
  gi|336253917|ref|YP_004597024.1| 712 LTDRQEATLRAAYFGGYYDWPRESTAEEIADAMGVSSPTLHNHLRKAQHELL 763
                                       9***********************************************9887 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0     3e-15   2.7e-12       7     103 ..     229     326 ..     224     327 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 3e-15
                             PAS_9   7 dnpdgrilyaNeaalrllGyspeevlgksitdlf....vtdpeanerlraaleqgrkkerevevvlirkngetfwvl 79 
                                        ++dg ++++N++a+ ++Gy + e++g+++++++    v++   ++ l+aale+     +e++   ++k+g++f + 
  gi|336253917|ref|YP_004597024.1| 229 LDEDGYVERWNRSAAAMFGYRAGEIVGTHVSTFYpdeaVEEGAPEQVLSAALEESG---YEDDGWRVHKDGTRFRAT 302
                                       679**9****************************8777777777777777777776...****************** PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDit 103
                                         +sp++dd g+ +g++v+lrDi+
  gi|336253917|ref|YP_004597024.1| 303 EVISPLRDDRGRHRGFAVFLRDIS 326
                                       ***********************9 PP

>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   6.2e-14   5.6e-11       2     167 ..      10     174 ..       9     178 .. 0.88
   2 ?   -3.0   0.0         6   5.4e+03      61      87 ..     689     715 ..     671     725 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 6.2e-14
                                       HHHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGG...EECTTTEEEEEEEECSSSSEEEEECTHH CS
                   Phage_integrase   2 vltedeverllaaleeslkirdklllellyetGlRisEllsLrvkd...ldlengvilvheregKgskeravplsee 75 
                                       vl   ++e+ll+a+e+   +r++l+++l+ + GlR +El++L+v+d   ++++  + lv    +  +  ra  l+ +
  gi|336253917|ref|YP_004597024.1|  10 VLSRRQYEALLDAAET---YREALVVRLCGDVGLRPAELAQLTVDDveqVRIDPPRYLVRVPAIDDRDRRAAYLPTH 83 
                                       68889***********...*************************9955567899999999999999999******** PP

                                       HHHHHHHHHHHHCHCCTTTSBSSBET.TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHH.HHHHHCTSHHH CS
                   Phage_integrase  76 alellkellskaleeaeksellfask.rgkplsrqtvrkafkraveeagiekpltpHtlRhsfat.aLleagvdlrv 150
                                       + + l+++   +    + ++ +f  + r+ ++  ++v ++ + +v   +++ ++++ +lR++fa+ aL+ + v++r+
  gi|336253917|ref|YP_004597024.1|  84 VERELRRYARSN--GLSTDDRIFSVTpRRLQMLVSEVADRASDTVDDPALK-DVSSSDLRRYFARrALVDHDVNPRA 157
                                       ********9999..4444445555445788999999999999999998888.9***********736********** PP

                                       HHHHHT-SSCCHHHHHH CS
                   Phage_integrase 151 vqkllGHssisttqiYt 167
                                       v+ ++G++s +  + Y 
  gi|336253917|ref|YP_004597024.1| 158 VKAAGGWRSFEALEPYL 174
                                       **********9999886 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6
                                       ECSSSSEEEEECTHHHHHHHHHHHHHH CS
                   Phage_integrase  61 egKgskeravplseealellkellska 87 
                                        gK++ er+v   ++  e l++ l ++
  gi|336253917|ref|YP_004597024.1| 689 IGKREAERTVQTARQFREGLEDRLTDR 715
                                       589999999999999999999988888 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.5   2.8e-12   2.6e-09       7     107 ..     225     327 ..     220     330 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.8e-12
                             PAS_4   7 alavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeepiefleelllpgeerhye 82 
                                       al+ ld+dg v+++N++aa++fg+++ e++G ++  ++p+e + ++  +++  ++ +e  +e+   +++ +++r+  
  gi|336253917|ref|YP_004597024.1| 225 ALVRLDEDGYVERWNRSAAAMFGYRAGEIVGTHVSTFYPDEaVEEGAPEQVLSAALEESGYEDDGWRVHKDGTRFRA 301
                                       56789************************************855555666666666668888888888888999999 PP

                             PAS_4  83 lrl.lPlrdesGevigvlvisrDiTe 107
                                       +++ +Plrd++G+ +g+ v++rDi++
  gi|336253917|ref|YP_004597024.1| 302 TEViSPLRDDRGRHRGFAVFLRDISA 327
                                       9998********************86 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   4.4e-12     4e-09      17     113 .]     229     325 ..     223     325 .. 0.88
   2 ?   -2.6   0.0       5.9   5.3e+03      58      80 ..     351     373 ..     343     382 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 4.4e-12
                                       EETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH...HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEE CS
                               PAS  17 vDedgrilyvNaaaeellGlsreevlgkslldliheedda...elaelleqlleqgeesrageisfklrdgrpihle 90 
                                       +Dedg +  +N++a+ ++G+++ e++g +++ +++ e  a     +e+++ ++++ +  ++   ++ + dg+ + + 
  gi|336253917|ref|YP_004597024.1| 229 LDEDGYVERWNRSAAAMFGYRAGEIVGTHVSTFYPDE--AveeGAPEQVLSAALEESGYEDDGWRVHK-DGTRFRAT 302
                                       79******************************99865..44577778888888887777777777777.******** PP

                                       EEEEEEEETTEEEEEEEEEEEES CS
                               PAS  91 vraspvrdaggeilgflgvlrdi 113
                                          sp+rd  g+++gf ++lrdi
  gi|336253917|ref|YP_004597024.1| 303 EVISPLRDDRGRHRGFAVFLRDI 325
                                       **********************8 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.9
                                       HHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS  58 laelleqlleqgeesrageisfk 80 
                                       ++++l+++l+++++ +++e++ +
  gi|336253917|ref|YP_004597024.1| 351 RHRELTRALLDATDHETVETTTC 373
                                       78999999999999999999876 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.099        89      24     120 ..     226     330 ..     211     337 .. 0.55
   2 !   28.4   0.3   1.9e-09   1.7e-06      83     137 ..     481     539 ..     362     540 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.099
                                       EEEEE-TTS-EEEE........EEEES-TTSTT-S-B---TT.HHHHHHHHTS-EEES-..GGG....-S-HHHHHH CS
                             GAF_2  24 yillvdddgglrla........awgeaeeefgaaldrplgeg.lvgealrtgrpvilnd..lee....dpdkkglpa 85 
                                        +  +d+dg+  ++         +g++ +e  + +     +     ea+++g p ++ +  lee    d+ ++ +  
  gi|336253917|ref|YP_004597024.1| 226 LVR-LDEDGY--VErwnrsaaaMFGYRAGEIVGTH----VSTfYPDEAVEEGAPEQVLSaaLEEsgyeDDGWRVHKD 295
                                       443.455666..55333332223333333333333....33324789999998777544334447554444444444 PP

                                       HHHTT--E.EEEEE-T.TS---EEEEES......--H CS
                             GAF_2  86 ghaglrsf.lavPlis.egrvvGvlnlyankppafde 120
                                       g +  + + ++ Pl++ +gr  G+ ++   + +a+ e
  gi|336253917|ref|YP_004597024.1| 296 GTRFRA-TeVISPLRDdRGRHRGFAVF-LRDISAYQE 330
                                       444444.46*******88***999886.466666644 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.9e-09
                                       HHHHHHTT--E....EEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  83 lpaghaglrsf....lavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                         +++++  sf    + vPl +++ v+G l++++++p+afd++++++Le+++++++ +i
  gi|336253917|ref|YP_004597024.1| 481 DVEADVDGTSFdgaiARVPLAYGDTVYGTLAVATERPGAFDDSERAWLETIGRLVGYVI 539
                                       22344444444666699***99889*******9999999*****************998 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.54   4.8e+02      74     101 ..     293     322 ..     241     335 .. 0.70
   2 !   27.7   0.0   3.2e-09   2.8e-06      54     127 ..     461     539 ..     441     541 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.54
                             GAF_3  74 eedglpdraa.lavPLvagr.qviGvlala 101
                                       ++dg++ ra  ++ PL++ r +++G+ ++ 
  gi|336253917|ref|YP_004597024.1| 293 HKDGTRFRATeVISPLRDDRgRHRGFAVFL 322
                                       46778877765889****99******9984 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 3.2e-09
                             GAF_3  54 salarralssgevvse.......psfaeedglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqi 123
                                          ar a++ g ++++       +++++  ++ d+a+  vPL+ g++v+G+la+a+ +p+afd+++++ le+++r++
  gi|336253917|ref|YP_004597024.1| 461 GEPARSAANDGAAAAVtvetdveADVDG--TSFDGAIARVPLAYGDTVYGTLAVATERPGAFDDSERAWLETIGRLV 535
                                       4444445554443333223221144444..567899999*************************************9 PP

                             GAF_3 124 atai 127
                                       +  i
  gi|336253917|ref|YP_004597024.1| 536 GYVI 539
                                       9776 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.5e-06     0.004      10     105 ..     224     325 ..     216     326 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.5e-06
                            PAS_10  10 ieltflDdnlqirrFtpaa.kklfklipadvGrpladihpkkavknv..eeviealrtgekdevevvv.pkngkwvl 82 
                                        +l+ lD++  + r++++a +++  +  + vG +++++ p++av++   e+v+ a  ++   e++ ++  k+g+ + 
  gi|336253917|ref|YP_004597024.1| 224 YALVRLDEDGYVERWNRSAaAMFGYRAGEIVGTHVSTFYPDEAVEEGapEQVLSAALEESGYEDDGWRvHKDGTRFR 300
                                       67889************76156667777889**********887776678898887777776666666368888865 PP

                            PAS_10  83 vr..ylpyrdedgeiaGvvetfvDi 105
                                        +  ++p+rd+ g+ +G  +++ Di
  gi|336253917|ref|YP_004597024.1| 301 ATevISPLRDDRGRHRGFAVFLRDI 325
                                       43339*******************9 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.1e-05    0.0095       3      85 ..     237     318 ..     235     322 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeD..rervrealqealkkgepyegeyRirrkdGeyrwveararvird 77 
                                        ++++   ++Gy++ e+ g+   + +  +p++   e + e++  a+ + + ye +  +++kdG+ +   + ++++rd
  gi|336253917|ref|YP_004597024.1| 237 RWNRSAAAMFGYRAGEIVGT---HVSTFYPDEavEEGAPEQVLSAALEESGYEDDGWRVHKDGTRFRATEVISPLRD 310
                                       69******************...8899999997755566666555555556************************** PP

                             PAS_3  78 engkpvrv 85 
                                       + g+   +
  gi|336253917|ref|YP_004597024.1| 311 DRGRHRGF 318
                                       **997665 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.3e-05     0.021      89     130 ..     494     536 ..     440     539 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-05
                                       EEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHH CS
                               GAF  89 sslvvPlvndgelwGllvlhnpsp.pftreelellqvladqva 130
                                       + + vPl  ++ ++G+l++  ++p  f+++e++ l++++++v+
  gi|336253917|ref|YP_004597024.1| 494 AIARVPLAYGDTVYGTLAVATERPgAFDDSERAWLETIGRLVG 536
                                       7889*****************99999*************9997 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.8   5.2e+03      14      35 ..     102     123 ..     102     141 .. 0.73
   2 !   13.7   0.1   5.6e-05      0.05      24      47 ..     734     757 ..     732     765 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.8
                                       HHHHHHSTCTTB-HHHHHHHHT CS
                            HTH_20  14 rilraLaraegltaselaerld 35 
                                       ri++  +r+  + +se+a+r +
  gi|336253917|ref|YP_004597024.1| 102 RIFSVTPRRLQMLVSEVADRAS 123
                                       5777778888899999999984 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.6e-05
                                       TB-HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_20  24 gltaselaerldlskntlsyHLrv 47 
                                       + ta+e+a+++++s  tl++HLr+
  gi|336253917|ref|YP_004597024.1| 734 ESTAEEIADAMGVSSPTLHNHLRK 757
                                       679*******************97 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.8e-05     0.043      13      54 ..     225     263 ..     213     281 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                             PAS_8  13 giavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrp 54 
                                       +++ +d +g  +  +N++a+ ++Gy+  ++ g    + +  ++p
  gi|336253917|ref|YP_004597024.1| 225 ALVRLDeDGY-VERWNRSAAAMFGYRaGEIVG----THVSTFYP 263
                                       5566785555.999**********99555554....44443333 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.6e-05      0.05       3      44 ..     710     758 ..     710     762 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.6e-05
                                       HHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHH CS
                        Sigma70_r4   3 asLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrA 44 
                                       ++L++r+   l+  +        ++ T eEI++ +g+S  + + ++++A
  gi|336253917|ref|YP_004597024.1| 710 DRLTDRQEATLRAAYfggyydwPRESTAEEIADAMGVSSPTLHNHLRKA 758
                                       68****************99988899************98888888887 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 ?   12.9   0.0   7.2e-05     0.065      27      50 ..     735     758 ..     734     759 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.2e-05
                                       --HHHHHHHHT--HHHHHHHHHHH CS
                      Sigma70_r4_2  27 lsykEIAellgisegtVksrlsRA 50 
                                       ++ +EIA  +g+s+ t  ++l++A
  gi|336253917|ref|YP_004597024.1| 735 STAEEIADAMGVSSPTLHNHLRKA 758
                                       6789******************98 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.8   0.00014      0.13      17      60 ..     323     366 ..     321     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                       Cep57_CLD_2  17 rklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkE 60 
                                       r +++++eel++ ++ERd+ +r+  +A++  +  +a ++a ++E
  gi|336253917|ref|YP_004597024.1| 323 RDISAYQEELESIRSERDGLERRAAIARRHRELTRALLDATDHE 366
                                       56899**********************98766666666666665 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.8   3.4e+03      25      35 ..     177     187 ..     177     191 .. 0.90
   2 ?    5.7   0.0     0.013        12      42      61 ..     223     242 ..     223     244 .. 0.91
   3 ?    3.5   0.0     0.063        56      28      48 ..     738     758 ..     736     763 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.8
                                       --HHHHHHHHT CS
                              GntR  25 PsereLaaefg 35 
                                       P+e eL+++f+
  gi|336253917|ref|YP_004597024.1| 177 PTEAELVDAFE 187
                                       99*******98 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                                       HHHHHHHHHTTSEEEETTCE CS
                              GntR  42 ReALrrLeaeglverrqgrG 61 
                                       R AL rL ++g+ver+++++
  gi|336253917|ref|YP_004597024.1| 223 RYALVRLDEDGYVERWNRSA 242
                                       67***************987 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.063
                                       HHHHHHHTS-HHHHHHHHHHH CS
                              GntR  28 reLaaefgVsrttvReALrrL 48 
                                       +e+a+++gVs +t+   Lr+ 
  gi|336253917|ref|YP_004597024.1| 738 EEIADAMGVSSPTLHNHLRKA 758
                                       79***********98777665 PP

>> Ribosomal_L13e  Ribosomal protein L13e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00017      0.15       4      34 ..     752     782 ..     750     787 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                    Ribosomal_L13e   4 nnhfrKdwqrrvktwfdqparkkrRrearqa 34 
                                       +nh+rK  ++ ++t+fd+p+  +rR   r++
  gi|336253917|ref|YP_004597024.1| 752 HNHLRKAQHELLRTFFDDPSEGHRRTDDRAS 782
                                       79***********************999976 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 ?   11.5   0.0   0.00022       0.2      15      38 ..     734     757 ..     732     757 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                                       SEEHHHHHHHHTS-HHHHHHHHHH CS
                             HTH_5  15 elcvcelaeelglsqstvShHLkk 38 
                                       e ++ e+a+++g+s +t+  HL+k
  gi|336253917|ref|YP_004597024.1| 734 ESTAEEIADAMGVSSPTLHNHLRK 757
                                       66889*****************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.99   8.8e+02      33      46 ..      83      97 ..      81      98 .. 0.80
   2 ?    8.3   0.0    0.0023         2      19      40 ..     736     757 ..     731     762 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.99
                            HTH_23 33 Tvyrwlkryre.eGl 46
                                      +v r l+ry++ +Gl
  gi|336253917|ref|YP_004597024.1| 83 HVERELRRYARsNGL 97
                                      799******876877 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0023
                            HTH_23  19 svreIAreLgvsrrTvyrwlkr 40 
                                       + +eIA+++gvs  T+ + l++
  gi|336253917|ref|YP_004597024.1| 736 TAEEIADAMGVSSPTLHNHLRK 757
                                       678*************987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (788 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); 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: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.42
# Mc/sec: 5690.29
//
Query:       gi|336253918|ref|YP_004597025.1|  [L=658]
Description: acetate/CoA ligase [Halopiger xanaduensis SH-6]
Scores for 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-91  304.5   0.1    1.1e-90  304.3   0.1    1.1  1  AMP-binding    AMP-binding enzyme
    3.8e-22   79.1   2.5    9.3e-22   77.8   2.5    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    2.1e-14   53.1   2.2    6.4e-14   51.6   2.2    1.9  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


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 !  304.3   0.1   1.8e-94   1.1e-90       8     422 ..      95     534 ..      87     535 .. 0.88

  Alignments for each domain:
  == domain 1  score: 304.3 bits;  conditional E-value: 1.8e-94
                                       STTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS CS
                       AMP-binding   8 tpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptl 81 
                                        +++ a+ +    ge +t+TY+el ++v+++Aa Lr lGv+++d+V +++p+ pe+ va+la++++Ga ++++ +++
  gi|336253918|ref|YP_004597025.1|  95 AKNRAAIKWegeLGETRTYTYGELLNEVEAFAATLRDLGVEEDDVVTLYMPMIPELPVAMLACARIGAPHSVVFAGF 171
                                       457788877888789************************************************************** PP

                                       -HHHHHHHHHHHTESEEE.......E..TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTT. CS
                       AMP-binding  82 taeelayiledseakvli.......a..tvdsel.leklleaaakleavklvivldadellkeeelkeeeeseeka. 147
                                       +a++la  ++++++++l+       +  + d++  +++ le+   +++v+ v+v+d+ + + +  l ++++++++  
  gi|336253918|ref|YP_004597025.1| 172 SADALATRMNSADSEYLVtcdgyyrRgdALDHISkANEGLEDV--EHEVSDVVVVDRLGDALNHSLGDNQHDYDELv 246
                                       ********************99987254555555455554444..46899999***999999988888888777655 PP

                                       S....-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHH CS
                       AMP-binding 148 e....kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifglil 219
                                              +e+++ +++d+++++YTSGTTG+PKGV ++++ ++a +a+ +  +   ++k++d++++ +++ +i+g+++
  gi|336253918|ref|YP_004597025.1| 247 AehegASVEPVSRDAEDMLFLMYTSGTTGQPKGVKHTTGGYLAYTAWTS--HSvLDIKPEDTYWCSADIGWITGHSY 321
                                       1577856678899*************************77777655543..33466899****************** PP

                                       HHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS- CS
                       AMP-binding 220 elllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggep 294
                                        ++++l+ G t v+++++++ +++++l++ +ek +v v++++P++++a+++  ++     +++dlsslrl+ ++gep
  gi|336253918|ref|YP_004597025.1| 322 IVYGPLALGTTTVMYEGTPDyPEKDRLWDIVEKNRVDVFYTAPTAIRAFMKwGQQYP---DQHDLSSLRLLGTVGEP 395
                                       ********************66699**************************654444...688************** PP

                                       EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEE.CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEE CS
                       AMP-binding 295 lspellrffralfge...evlegYGlTEttgvvtv.lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGel 367
                                       ++p ++++++++ g+   ++++++++TEt+g++++ lp   ++ k+gs+G+plpg+++ +vD e g +v  g+ G +
  gi|336253918|ref|YP_004597025.1| 396 INPRAWKWYYKHIGNeecPIVDTWWQTETGGMMITtLP-AINTMKPGSAGPPLPGIDAQVVDAE-GDEVDAGKAGYV 470
                                       **************9******************66344.6666799*****************9.99********** PP

                                       EEEET..TS-SEBTT-HHHHHHHEEE......TCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 368 lvrgp..gvmkgYlkkpeataeafds......egr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                        v  p  g+ +  +k++e+    +++       ++  +   D +++d+dGy+ i+gR +d+i++
  gi|336253918|ref|YP_004597025.1| 471 TVNNPwpGMLRTLYKNDERFINEYWDeysdadADEwVYFPEDGAKIDDDGYITILGRVDDVINV 534
                                       ****9778***********9999997788885255489999*********************98 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 !   77.8   2.5   1.6e-25   9.3e-22       1      76 []     543     621 ..     543     621 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.6e-25
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       e+Esa+v +++VaeaaVvG +++vkGea+ ++ +++dg+e+   lee++++ v +++gp+a+p++v+f++elpktrs
  gi|336253918|ref|YP_004597025.1| 543 EIESAVVGVEGVAEAAVVGGDHDVKGEAVYVYAIPEDGYEPnedLEEQVVEGVVDAIGPIARPEEVIFTPELPKTRS 619
                                       8**********************************999533346********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|336253918|ref|YP_004597025.1| 620 GK 621
                                       *9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   2.2   1.1e-17   6.4e-14       4      55 .]      35      86 ..      33      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.1e-17
                                      HHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  4 lykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                      +y+e  e+  + W+++a+ l+We+++d+vl++ ++pf++WF+GG+lN++yNc
  gi|336253918|ref|YP_004597025.1| 35 IYEEFEENWPECWERAADLLSWEEEYDTVLEDGDAPFYEWFTGGELNASYNC 86
                                      7999999999****************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (658 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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 0.25s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4694.85
//
Query:       gi|336253919|ref|YP_004597026.1|  [L=153]
Description: solute symporter protein [Halopiger xanaduensis SH-6]
Scores for 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-22   77.4   0.7    9.9e-22   77.1   0.7    1.1  1  DUF4212   Domain of unknown function (DUF4212)


Domain annotation for each model (and alignments):
>> DUF4212  Domain of unknown function (DUF4212)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.7   5.5e-26   9.9e-22       2      79 .]      51     131 ..      50     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 5.5e-26
                           DUF4212   2 kaYwrenlrlililLviWfvvsfg..lgillaeelnti.rtflgfplgFwfaaqgsilvfvvlifvYalrmdrlDek 75 
                                       ++++r++lr++++ +viW+++++g  ++++la +++t  + +lgfpl+++++a g+++ +++l f+Y +++d+lDek
  gi|336253919|ref|YP_004597026.1|  51 TPFMRDHLRIVWTGFVIWVLAVWGpvTLTYLATDVMTTqMPVLGFPLHYFLVAFGAPTSALILSFWYSRKRDALDEK 127
                                       78**********************99899999999888789************************************ PP

                           DUF4212  76 ygve 79 
                                       yg++
  gi|336253919|ref|YP_004597026.1| 128 YGID 131
                                       **85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1248.94
//
Query:       gi|336253920|ref|YP_004597027.1|  [L=563]
Description: sodium symporter protein [Halopiger xanaduensis SH-6]
Scores for complete 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-51  175.9  31.1    1.8e-51  175.3  31.1    1.3  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 !  175.3  31.1     1e-55   1.8e-51       2     406 .]      53     467 ..      52     467 .. 0.84

  Alignments for each domain:
  == domain 1  score: 175.3 bits;  conditional E-value: 1e-55
                               SSF   2 flagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlrnagalTlpdylskR 78 
                                       ++agrs++ + +g++++a+ +saas++G+a+++a+ G+ ++++ +g + ++ +ll+++a +lr+ g++T pd++  R
  gi|336253920|ref|YP_004597027.1|  53 WVAGRSIGNVENGMAIGANWMSAASYLGMAASIALAGFYGLVYVVGWTTGYFILLIFMAAQLRRFGKYTAPDFVGDR 129
                                       68*************************************************************************** PP

                               SSF  79 fkgkrilvylsalslllvitlklsvdlvggakl....i....elalGln.yetavlllaaltalYtviGGllAvvyt 146
                                       f++    + ++a++++l+ +++ + +  g a      +     l+ Gl+ y++ v++++ +t+ Y  + G+l  + +
  gi|336253920|ref|YP_004597027.1| 130 FNSDT-ARAIAAITTFLIGFVYAIGQAKGMALVglyvFgdygGLIPGLDgYQVMVVAMMTITVGYLTLSGMLGATKN 205
                                       *****.****************9999877775411112111134446666899999999****************** PP

                               SSF 147 dtiqavlmlvgalilliivllevG...gleslvekl...keaapkvvdlltpdslkllrdpltalslwlglvlGvag 217
                                       + +q ++++++ +      l++vG   g+++++ +l   + ++  + ++ +p ++  +   +++      l+ G+ g
  gi|336253920|ref|YP_004597027.1| 206 QAVQYTILIIAFVA----GLYAVGwtqGYSTVLPQLeygMLIDSLGEEFSEPFATSSYYLWVAT---TFSLIVGTCG 275
                                       ********998654....3444444347777765542236777777777776665333333332...245799**** PP

                               SSF 218 lphilvRflaakdakailkgvlkltivlilvligmisiilfaiklagavpkavgte...vgvsniaypeLvvkl..l 289
                                       lph+lvRf+++++ ++++ + + ++ ++ +++  + +   f+ +l   + +a   +   + ++  +++ L+ +l  l
  gi|336253920|ref|YP_004597027.1| 276 LPHVLVRFYTVESERTARWSTVWGLFFICILYWSAPAFAAFGTSLYSENVRATYGDpgmASAASEVIVVLAAQLaeL 352
                                       ********************************988777777777776666544433011334556788888888557 PP

                               SSF 290 pnllaGlllavmlAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgv 366
                                       p+++ Gl+ a  +Aa ++t+++l++++ssa+++D+Y++i+ +  a++++++ v+r+ ++ +++l  l+a++++++ +
  gi|336253920|ref|YP_004597027.1| 353 PQWFVGLVAAGGIAAAIATIAGLFIAGSSAISHDIYTNIINED-ATQRQQILVGRLSIVALGALTTLAALDPASS-I 427
                                       9*****************************************9.999****************************.* PP

                               SSF 367 lklvelafaglasavlavillalfwkrvneqGAlagliiG 406
                                       + lv +afa ++s+ ++++ l+++w+  n+ GAlag+ +G
  gi|336253920|ref|YP_004597027.1| 428 AALVGYAFALAGSVLFPMFFLGMWWENTNRPGALAGMTTG 467
                                       *************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); 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:                         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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 4029.49
//
Query:       gi|336253921|ref|YP_004597028.1|  [L=150]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-36  123.7   1.3    8.7e-36  123.5   1.3    1.0  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.073   13.3   0.0       0.19   11.9   0.0    1.7  2  MGS       MGS-like domain
       0.39   11.2   2.3         11    6.6   0.0    2.6  3  CBS       CBS domain


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 !  123.5   1.3   1.4e-39   8.7e-36       1     140 [.       1     147 [.       1     148 [. 0.98

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 1.4e-39
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH....... CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada....... 70 
                                       my++IlV++Dgse+s++A+ +A++la++++a l++l+v+d+++++ +  +++  + e+    e+e++++        
  gi|336253921|ref|YP_004597028.1|   1 MYEKILVPTDGSETSEAAVAHAIDLAEKYEAGLHALYVVDTDSMSLTLGGEQLDRIEQGRFGEMEEVRERaeratgy 77 
                                       9********************************************************999999999999999***** PP

                                       HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  71 akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                        +++a+++g +++ ++  g p   i+++++++++dl+V+Gs+gr+g++r+llGSv+e+ lr++ +pVlv+
  gi|336253921|ref|YP_004597028.1|  78 VADRAAERGLETVEHISAGRPHSQIADYVDDNGIDLVVMGSHGRTGVRRALLGSVTERTLRSVRVPVLVI 147
                                       99******************************************************************97 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.51   3.1e+03      82      93 ..      14      25 ..       5      58 .. 0.67
   2 ?   11.9   0.0   3.2e-05      0.19      19      85 ..      75     136 ..      73     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.51
                                      HHHHHHHTTSHE CS
                               MGS 82 irraaenidIpl 93
                                      + +aa+ + I l
  gi|336253921|ref|YP_004597028.1| 14 TSEAAVAHAIDL 25
                                      444444444433 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.2e-05
                                       EHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHH.CHHHHHHHH CS
                               MGS  19 TgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatva.kdgykirra 85 
                                       Tg  a+  +e g++    ve+++ g r++   +i d + +++idlv++   +++  ++   g  ++r+
  gi|336253921|ref|YP_004597028.1|  75 TGYVADRAAERGLE---TVEHISAG-RPH--SQIADYVDDNGIDLVVMGSHGRTGVRRaLLGSVTERT 136
                                       56667777888999...99999***.888..79**************988888877765444445555 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0018        11      20      39 ..      24      42 ..      13      47 .. 0.79
   2 ?    3.7   0.4     0.014        85      22      54 ..     103     140 ..      92     143 .. 0.71
   3 ?    0.2   0.2      0.17     1e+03      25      39 ..     137     150 .]     129     150 .] 0.59

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0018
                                      HHHHHHHHHTSSEEEEEETT CS
                               CBS 20 ealelmrekgvsrlPVVded 39
                                      +++e++ e+g+++l+VVd d
  gi|336253921|ref|YP_004597028.1| 24 DLAEKY-EAGLHALYVVDTD 42
                                      566777.888*******866 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.014
                                       HHHHHHHTSSEEEEE.ETTTB......EEEEEEHHHHHHH CS
                               CBS  22 lelmrekgvsrlPVV.dedgk......lvGivtlrDllra 54 
                                       ++   ++g+  l VV  + g+      l+G vt+r l ++
  gi|336253921|ref|YP_004597028.1| 103 ADYVDDNGI-DL-VVmGSHGRtgvrraLLGSVTERTLRSV 140
                                       555555555.44.55566776666678********99876 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.17
                                       HHHHTSSEEEE.E.ETT CS
                               CBS  25 mrekgvsrlPV.V.ded 39 
                                       +r+  v r+PV V ded
  gi|336253921|ref|YP_004597028.1| 137 LRS--V-RVPVlViDED 150
                                       544..6.8888557765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1146.45
//
Query:       gi|336253922|ref|YP_004597029.1|  [L=123]
Description: hypothetical protein Halxa_2532 [Halopiger xanaduensis SH-6]
Scores for 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:                       856  (0.0477439); 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:                         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 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 938.03
//
Query:       gi|336253923|ref|YP_004597030.1|  [L=116]
Description: hypothetical protein Halxa_2533 [Halopiger xanaduensis SH-6]
Scores for 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-22   77.4   0.1    1.1e-21   76.8   0.1    1.3  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.1   6.4e-26   1.1e-21       2      75 .]      40     112 ..      39     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 6.4e-26
                            HalOD1   2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75 
                                       +++ps a+v++vaa+++ dp el+pL++aiD+ ALd+L++  +++++++++  sF+yeg+ Vt  s+g+ieV+p
  gi|336253923|ref|YP_004597030.1|  40 RDQPSLAIVAVVAAAANSDPNELSPLHSAIDTGALDDLLSG-TATDDQKNVCFSFSYEGFAVTTFSEGTIEVKP 112
                                       799**************************************.667789************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 855.48
//
Query:       gi|336253924|ref|YP_004597031.1|  [L=216]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-15   55.6   0.1    5.3e-15   55.0   0.1    1.3  1  HTH_10         HTH DNA binding domain
    4.8e-09   36.3   0.0    7.6e-09   35.6   0.0    1.2  1  BAT            GAF and HTH_10 associated domain
    2.2e-08   33.5   0.1    4.6e-08   32.5   0.1    1.4  1  Sigma70_r4     Sigma-70, region 4
    2.5e-05   23.8   0.0    0.00024   20.7   0.0    2.1  2  Sigma70_r4_2   Sigma-70, region 4
    6.9e-05   22.7   1.1    0.00022   21.1   1.1    1.9  1  MarR_2         MarR family
     0.0091   15.5   0.0      0.017   14.7   0.0    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.025   14.4   0.1      0.039   13.7   0.1    1.3  1  HTH_23         Homeodomain-like domain
      0.036   13.9   0.2      0.071   13.0   0.2    1.5  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.051   13.6   0.1       0.12   12.4   0.1    1.7  1  HTH_Crp_2      Crp-like helix-turn-helix domain
      0.061   13.3   0.0      0.061   13.3   0.0    2.1  3  HTH_11         HTH domain


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 !   55.0   0.1   2.9e-18   5.3e-15       1      52 [.     156     207 ..     156     208 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 2.9e-18
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT+ q+++l lAy  GYFd PR++t +++A+el +s++++s +L++  ++l+
  gi|336253924|ref|YP_004597031.1| 156 LTEGQRSALVLAYSRGYFDSPRKATQDDIADELQVSRQAVSSRLQRGLRRLV 207
                                       9*********************************************999987 PP

>> BAT  GAF and HTH_10 associated 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   7.6e-09       4     142 ..       3     143 ..       2     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 4.2e-12
                               BAT   4 veLeleirdeddvlvalaael.dcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtl 79 
                                       +e  +++  ++++l+++ ++l d ++el+++vp +d+  + +f+++     ++++ ++d  +v++   ++e ++++l
  gi|336253924|ref|YP_004597031.1|   3 IEASFTVPQPEFPLNTIFEQLpDVTIELDRVVP-TDDAIIPYFWIHSKNLGGLTTDLSDDKGVDEFKKIDELEEEML 78 
                                       5777899999999998766644999********.5667*************************************99 PP

                               BAT  80 lelt..vsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarr 142
                                       ++++  ++ +s+++++++  +t+ s   e+ ++++ v+ ++++ + ++ ++++e+   +eL++ +
  gi|336253924|ref|YP_004597031.1|  79 VRIKwnLDHESILTAIVNTEVTLLSGLGEQKNWTFEVRSSDQESLSEFQSYCRENDILIELTQLH 143
                                       99985577**********************************************99888887766 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.1   2.6e-11   4.6e-08       5      48 ..     156     206 ..     155     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 2.6e-11
                                       S-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   5 Lpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       L+e +r  l+l +        ++ T+ +I+++l++Sr +V++++ r+lr+L
  gi|336253924|ref|YP_004597031.1| 156 LTEGQRSALVLAYsrgyfdsPRKATQDDIADELQVSRQAVSSRLQRGLRRL 206
                                       99***************99999***************************98 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 ?    0.5   0.0      0.27   4.8e+02      11      23 ..     156     168 ..     155     172 .. 0.89
   2 !   20.7   0.0   1.3e-07   0.00024      28      54 .]     180     206 ..     179     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.27
                                       S-HHHHHHHHHHH CS
                      Sigma70_r4_2  11 Lperqreifllry 23 
                                       L+e qr +++l y
  gi|336253924|ref|YP_004597031.1| 156 LTEGQRSALVLAY 168
                                       899********87 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.3e-07
                                       -HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsRArkkL 54 
                                       ++++IA +l +s ++V srl+R++++L
  gi|336253924|ref|YP_004597031.1| 180 TQDDIADELQVSRQAVSSRLQRGLRRL 206
                                       679**********************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.1   1.2e-07   0.00022      18      44 ..     176     201 ..     155     216 .] 0.78

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                                       TTSEEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2  18 pgrdltvgelarrlglsksavsrilkr 44 
                                       p r+ t+ ++a++l++s++avs +l+r
  gi|336253924|ref|YP_004597031.1| 176 P-RKATQDDIADELQVSRQAVSSRLQR 201
                                       3.468****************998765 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 !   14.7   0.0   9.6e-06     0.017      17      40 ..     177     201 ..     174     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.6e-06
                            HTH_24  17 r.isqreLAerlglSpstvnrrlkr 40 
                                       r  +q ++A++l +S+++v+ rl+r
  gi|336253924|ref|YP_004597031.1| 177 RkATQDDIADELQVSRQAVSSRLQR 201
                                       448********************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.2e-05     0.039      10      40 ..     164     201 ..     155     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                            HTH_23  10 illllae.......GlsvreIAreLgvsrrTvyrwlkr 40 
                                        +l++ +       ++++ +IA+eL vsr+ v+  l+r
  gi|336253924|ref|YP_004597031.1| 164 LVLAYSRgyfdsprKATQDDIADELQVSRQAVSSRLQR 201
                                       5566664555556689****************955544 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 ?   13.0   0.2   3.9e-05     0.071      18      40 ..     179     201 ..     177     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.9e-05
                     HTH_AsnC-type  18 isyaeLAervGlSestvlrRvrr 40 
                                       ++  ++A+++ +S+++v  R++r
  gi|336253924|ref|YP_004597031.1| 179 ATQDDIADELQVSRQAVSSRLQR 201
                                       67789****************98 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   0.1   6.6e-05      0.12      21      43 ..     178     200 ..     158     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                                       EHHHHHHHHHTTSSHHHHHHHHH CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrils 43 
                                       + tq+++A+ l ++r+ vs  l+
  gi|336253924|ref|YP_004597031.1| 178 KATQDDIADELQVSRQAVSSRLQ 200
                                       68****************98776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       2.8     5e+03      34      46 ..      68      81 ..      68      82 .. 0.66
   2 ?   -2.6   0.1         3   5.4e+03       1      11 [.     131     141 ..     131     144 .. 0.80
   3 ?   13.3   0.0   3.4e-05     0.061      16      37 ..     179     200 ..     173     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.8
                            HTH_11 34 rdIkaLeelg.vpI 46
                                      + I++Lee + v+I
  gi|336253924|ref|YP_004597031.1| 68 KKIDELEEEMlVRI 81
                                      56899966554776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3
                            HTH_11   1 RllqilelLle 11 
                                       R+++il+ L +
  gi|336253924|ref|YP_004597031.1| 131 RENDILIELTQ 141
                                       88999999966 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 3.4e-05
                            HTH_11  16 isgeeLAeeLnvSrrtvrrdIk 37 
                                        + +++A+eL vSr++v  +++
  gi|336253924|ref|YP_004597031.1| 179 ATQDDIADELQVSRQAVSSRLQ 200
                                       6889*************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1696.85
//
Query:       gi|336253925|ref|YP_004597032.1|  [L=43]
Description: hypothetical protein Halxa_2535 [Halopiger xanaduensis SH-6]
Scores for 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:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 364.26
//
Query:       gi|336253926|ref|YP_004597033.1|  [L=239]
Description: hypothetical protein Halxa_2536 [Halopiger xanaduensis SH-6]
Scores for 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-75  253.4   5.7    1.2e-75  253.2   5.7    1.0  1  DUF2270        Predicted integral membrane protein (DUF2270)
  ------ inclusion threshold ------
       0.12   11.7   0.0       0.21   10.9   0.0    1.3  1  7TM_GPCR_Str   Serpentine type 7TM GPCR chemoreceptor Str
        5.5    7.0   6.9       0.74    9.8   0.6    2.4  2  DUF485         Protein of unknown function, DUF485
        6.1    6.4   7.9        3.2    7.3   0.7    2.1  2  MASE3          Membrane-associated sensor domain


Domain annotation for each model (and alignments):
>> DUF2270  Predicted integral membrane protein (DUF2270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.2   5.7   2.6e-79   1.2e-75       1     183 [.      35     213 ..      35     214 .. 0.99

  Alignments for each domain:
  == domain 1  score: 253.2 bits;  conditional E-value: 2.6e-79
                           DUF2270   1 ahlYRgeveratawreRlDrttnWavvvtaallsvalsspeashavlllgmllvlvfLliearryrfydvwrsrvrl 77 
                                       ah+YRge++r+ +wr+RlD+tt+Wav+++aa+l++a+ss++++h++ll+g+++v++fL iearryr+ydv+rsr+r+
  gi|336253926|ref|YP_004597033.1|  35 AHVYRGEIDRVGTWRQRLDQTTTWAVTLMAAILTWAFSSTDNPHYLLLIGIVVVTIFLGIEARRYRDYDVFRSRARV 111
                                       6**************************************************************************** PP

                           DUF2270  78 leenffaealdpeegaeeeeWreeLaedlrkPtlkislleAlgrRLrrnYlwlllvlllawllkitlfkkeeeslee 154
                                       ++en+fa+aldp++g+e+++Wr+eL++d+r+Ptlk+s+ eAl++RL+r+Yl+ll+vll+aw+++it+f++++    +
  gi|336253926|ref|YP_004597033.1| 112 IQENLFANALDPSQGTESHDWRAELSRDYRRPTLKVSVSEALANRLQRVYLALLSVLLVAWVFRITAFAPRQ----D 184
                                       ***********************************************************************9....6 PP

                           DUF2270 155 llerAavgplpGelvllvvalfylallvl 183
                                       +l++A++g++pG +v+++v +fy++ll +
  gi|336253926|ref|YP_004597033.1| 185 WLTTAEIGRIPGIAVVAIVGVFYVVLLGV 213
                                       ************************99875 PP

>> 7TM_GPCR_Str  Serpentine type 7TM GPCR chemoreceptor Str
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.8e-05      0.21      77     152 ..     145     220 ..     136     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.8e-05
                      7TM_GPCR_Str  77 lskevlqillalycglygvsiallavhFiYRYlavtkskklkyfsgkklilwiliplligviwslllyfllspdee 152
                                       l+ +v++ l   +  +y++++++l v +++R +a   ++ + +      i  i+++ ++gv++++ll +++ p+e 
  gi|336253926|ref|YP_004597033.1| 145 LKVSVSEALANRLQRVYLALLSVLLVAWVFRITAFAPRQDWLTTAEIGRIPGIAVVAIVGVFYVVLLGVTFWPRER 220
                                       5566777777788899*******************999988888888999999999****************9986 PP

>> DUF485  Protein of unknown function, DUF485
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3      0.18   8.1e+02      54      72 ..      59      71 ..      49      79 .. 0.54
   2 ?    9.8   0.6   0.00017      0.74       8      77 ..     152     223 ..     150     228 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.18
                            DUF485 54 glllgllqivltflltglY 72
                                      +      + +++ +lt+++
  gi|336253926|ref|YP_004597033.1| 59 A------VTLMAAILTWAF 71
                                      3......333444444444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00017
                            DUF485   8 eLvrkrrrfafpltaiflvvYfgfvllvafapdllatkvgeg...nitvglllgllqivltflltglYvrrAn 77 
                                       +L+++ +r+ + l+ + lv+ +  + ++a  +d+l+t  + g    i v  ++g++ +vl  +  +   r+A+
  gi|336253926|ref|YP_004597033.1| 152 ALANRLQRVYLALLSVLLVAWVFRITAFAPRQDWLTTAEI-GripGIAVVAIVGVFYVVLLGVTFWPRERHAK 223
                                       689999******************************9888.52233445555555555555555555555555 PP

>> MASE3  Membrane-associated sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.7   0.00071       3.2      18      50 ..      58      90 ..      54      95 .. 0.89
   2 ?    2.8   1.3     0.017        74      77     135 ..     161     218 ..     152     223 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00071
                             MASE3 18 ivvallifliawntrkftknnyllflGiaflfv 50
                                       +v+l+ ++++w+  +  + +yll++Gi+++++
  gi|336253926|ref|YP_004597033.1| 58 WAVTLMAAILTWAFSSTDNPHYLLLIGIVVVTI 90
                                      57999***********************98876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.017
                             MASE3  77 qlwiaaRllealslllavlllkrkvlrayavflvyalvtlllllsifypkifPalfieg 135
                                        l +++ ll a+++ + ++ +++++l++ + +  +  +++++++ +fy+ ++  +f++ 
  gi|336253926|ref|YP_004597033.1| 161 YLALLSVLLVAWVFRITAFAPRQDWLTTAE-IGRIPGIAVVAIVGVFYVVLLGVTFWPR 218
                                       567777888899999999999988843333.3344455566667777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1920.75
//
Query:       gi|336253927|ref|YP_004597034.1|  [L=102]
Description: hypothetical protein Halxa_2537 [Halopiger xanaduensis SH-6]
Scores for 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-22   78.3   0.1    5.4e-22   77.9   0.1    1.2  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.1     3e-26   5.4e-22       2      75 .]      22      93 ..      21      93 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 3e-26
                            HalOD1  2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75
                                      ++s+s  V++++ +++g++p+elepL+d++Dp+ALd+++a+  ++e+++  +++F+y+gy+V +++dge ++ p
  gi|336253927|ref|YP_004597034.1| 22 DQSTSAIVIQTITELTGQEPDELEPLWDSVDPEALDSFVAR--AEETETPCRLAFEYQGYTVKIDADGELRIAP 93
                                      7899*************************************..888999*********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 751.26
//
Query:       gi|336253928|ref|YP_004597035.1|  [L=119]
Description: hypothetical protein Halxa_2538 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.083   12.4   0.1       0.12   11.9   0.1    1.1  1  DUF2587   Protein of unknown function (DUF2587)


Domain annotation for each model (and alignments):
>> DUF2587  Protein of unknown function (DUF2587)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.4e-06      0.12      35      81 ..      27      73 ..      20      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-06
                           DUF2587 35 lleevraapldeasrerlkeihersikeleeglaPelveelerlslp 81
                                      l  e r+  l++ +++ lk  h++si e++e +  e++  l+++ lp
  gi|336253928|ref|YP_004597035.1| 27 LAAEQRSLTLNDLAQTVLKYNHQTSITEVSEDVLTEIHLSLHHVHLP 73
                                      55789999***********************************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 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:                        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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 923.01
//
Query:       gi|336253929|ref|YP_004597036.1|  [L=218]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-15   54.3   0.0    1.3e-14   53.7   0.0    1.3  1  HTH_10         HTH DNA binding domain
    7.5e-13   48.6   3.3    9.6e-13   48.3   3.3    1.2  1  BAT            GAF and HTH_10 associated domain
    1.4e-05   24.5   0.1    2.8e-05   23.5   0.1    1.5  1  Sigma70_r4     Sigma-70, region 4
  ------ inclusion threshold ------
       0.04   13.7   0.1      0.075   12.9   0.1    1.4  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain


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 !   53.7   0.0   2.9e-18   1.3e-14       1      51 [.     156     206 ..     156     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2.9e-18
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskl 51 
                                       LTd q e+l lAye GYF+ PR++tl+ L +elGIs++++  ++r  ++ +
  gi|336253929|ref|YP_004597036.1| 156 LTDTQQEALVLAYERGYFESPREATLEVLGEELGISQQAVGSRIRGGINHI 206
                                       9***************************************99999766655 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   3.3   2.2e-16   9.6e-13       4     140 ..       3     141 ..       1     155 [. 0.87

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 2.2e-16
                               BAT   4 veLeleirdeddvlval.aaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtl 79 
                                       +e ++++ +++++l ++  +  d +vele+++p  d  v+ +f+v+g++++++++a++++++ +++r+v+  +d+ l
  gi|336253929|ref|YP_004597036.1|   3 TEATFTVPSDQFPLGTVfNQLPDVTVELERIIPARD-VVIPYFWVRGTEVDDIESAFTEHPGTKEIRLVDSVEDEYL 78 
                                       788999999999999651555799*********777.6*************************************77 PP

                               BAT  80 lelt..vsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLva 140
                                       l+++  ++ ++++++lae  + + +a+ ++ ++++ ++  ++ d+ ++ ++++e    ++L+ 
  gi|336253929|ref|YP_004597036.1|  79 LRVEwaMDYDDVLTVLAETEVPLIEATGTNHQWTFEIRGDDRSDIAEFQQRCRELDIPTTLTE 141
                                       6665226799*****************************************999877777765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   6.3e-09   2.8e-05       4      46 ..     155     204 ..     154     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.3e-09
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlr 46 
                                        L++ ++e l+l +        ++ Tle +ge+lgiS+ +V ++++ +++
  gi|336253929|ref|YP_004597036.1| 155 ALTDTQQEALVLAYergyfesPREATLEVLGEELGISQQAVGSRIRGGIN 204
                                       7*****************999999*****************999998776 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 ?   12.9   0.1   1.7e-05     0.075      18      39 ..     179     200 ..     178     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                     HTH_AsnC-type  18 isyaeLAervGlSestvlrRvr 39 
                                       ++ + L+e++G+S+++v  R+r
  gi|336253929|ref|YP_004597036.1| 179 ATLEVLGEELGISQQAVGSRIR 200
                                       56788***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1730.96
//
Query:       gi|336253930|ref|YP_004597037.1|  [L=82]
Description: hypothetical protein Halxa_2540 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.078   13.1   0.1       0.11   12.7   0.1    1.2  1  ProRS-C_2  Prolyl-tRNA synthetase, C-terminal


Domain annotation for each model (and alignments):
>> ProRS-C_2  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   5.9e-06      0.11      14      45 ..      40      72 ..      30      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.9e-06
                                      HHH.HHHCTTT-SEEEEE--GGG-SHHHHHHHS CS
                         ProRS-C_2 14 eni.keklsekkGvvLvPfneeiYneefeeeid 45
                                      eni k+  +++k vv++ +  ei  ee++e +d
  gi|336253930|ref|YP_004597037.1| 40 ENIdKARHTDEKDVVIIRYSAEINGEEVDELTD 72
                                      6664667788999*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 621.88
//
Query:       gi|336253931|ref|YP_004597038.1|  [L=73]
Description: hypothetical protein Halxa_2541 [Halopiger xanaduensis SH-6]
Scores for 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   12.3   2.2       0.13   12.1   2.2    1.0  1  FA_desaturase  Fatty acid desaturase


Domain annotation for each model (and alignments):
>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.2   7.2e-06      0.13     123     176 ..       4      58 ..       2      69 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-06
                     FA_desaturase 123 rrrapsksrrrkwrllawlllllawlglwlalllllglall.lwlvplllllfll 176
                                       +r++ ++ r+ +w +l+ l+++++w+ ++  + +llg+ +l ++ ++l+ +++++
  gi|336253931|ref|YP_004597038.1|   4 VREWLQTAREERWGILTDLAFAVVWVTIVETINYLLGPPTLvYYTLMLAGIVAYF 58 
                                       6889999999******************999999999998753333322222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 584.12
//
Query:       gi|336253932|ref|YP_004597039.1|  [L=158]
Description: Cupin 2 barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-17   61.1   0.0    8.8e-17   60.6   0.0    1.3  1  Cupin_2       Cupin domain
    3.5e-05   23.4   0.0    6.5e-05   22.5   0.0    1.5  1  Cupin_3       Protein of unknown function (DUF861)
     0.0083   16.0   0.0      0.012   15.6   0.0    1.2  1  AraC_binding  AraC-like ligand binding domain
  ------ inclusion threshold ------
       0.23   11.1   0.0       0.39   10.3   0.0    1.3  1  Cupin_1       Cupin


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 !   60.6   0.0     2e-20   8.8e-17       2      70 ..      39     110 ..      38     111 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 2e-20
                                       EEEEETTE.EEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT..-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   2 lvelppGe.sapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpag..tpHrfrNtgdeparllvv 70 
                                       l+elppG+ s p h+H+ ++e +yVl G g l+ d+ + +l+aGd+v  pa     Hr++N+gd+p+r+l +
  gi|336253932|ref|YP_004597039.1|  39 LYELPPGTrSWPYHYHTANEEALYVLAGDGQLRTDDGPAPLTAGDYVTLPADasGGHRVVNDGDKPLRYLAI 110
                                       689*****9999***************************************9889**************988 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 !   22.5   0.0   1.5e-08   6.5e-05      11      66 ..      39      97 ..      32     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.5e-08
                                      EEEEECEEEEECESS....EEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEEECCCE CS
                           Cupin_3 11 iwectpGkfrltyee....dEfcyileGevkvtpeggetvelraGDlvvlpkglsgtwdv 66
                                      + e  pG+ ++ y +    +E  y+l G  +++ ++g +  l aGD+v+lp++ sg  +v
  gi|336253932|ref|YP_004597039.1| 39 LYELPPGTRSWPYHYhtanEEALYVLAGDGQLRTDDG-PAPLTAGDYVTLPADASGGHRV 97
                                      56777888777664311336777***********666.679************9986665 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 !   15.6   0.0   2.6e-06     0.012      17      74 ..      50     110 ..      38     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-06
                                       EEETT-.SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-..EEEEE-TTSEEEEEEE CS
                      AraC_binding  17 pphvhd.eyvihyvteGtgrlrlngrtydlgpGdlfLlppgep..Hdyesdsedgweyrwl 74 
                                       p+h h  + +  yv++G g+lr +++   l++Gd + lp +    H+   d++++++y  +
  gi|336253932|ref|YP_004597039.1|  50 PYHYHTaNEEALYVLAGDGQLRTDDGPAPLTAGDYVTLPADASggHRVVNDGDKPLRYLAI 110
                                       667777777889***************************9976558888888889888776 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   8.8e-05      0.39      47     111 ..      50     108 ..      48     128 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.8e-05
                                       EEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-..EEEEEEESSSSEEEEE CS
                           Cupin_1  47 lPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPagl..vhfqynsgdepavaiv 111
                                       + hyh+  +e +yvl G g    +       d  + l++Gd + +Pa     h ++n+gd+p+  + 
  gi|336253932|ref|YP_004597039.1|  50 PYHYHTANEEALYVLAGDGQ-LRTD------DGPAPLTAGDYVTLPADAsgGHRVVNDGDKPLR-YL 108
                                       56*****************9.3333......344678888888888755225778888755543.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1367.22
//
Query:       gi|336253933|ref|YP_004597040.1|  [L=200]
Description: tRNA ribose 2'-O-methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-46  155.7   0.0    6.1e-46  155.2   0.0    1.2  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 !  155.2   0.0   3.4e-50   6.1e-46       1     118 [.      58     190 ..      58     191 .. 0.98

  Alignments for each domain:
  == domain 1  score: 155.2 bits;  conditional E-value: 3.4e-50
                                       H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHH..................HC-SE.EEEEE---- CS
                             Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieei..................kkkekdllvvvGaek 59 
                                       +Gg+f+ e+++s k+li++++   g vvhltmyGe++++v ++i                   ++ ++ll+vvG+ek
  gi|336253933|ref|YP_004597040.1|  58 FGGPFEAELTDSPKALIRNWE---GRVVHLTMYGERVQDVEDDIraarsngdesesdvdsegDDEGEPLLIVVGSEK 131
                                       8********************...**********************************9988778889********* PP

                                       --TCHHHHSSEEEESSSS---HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EE CS
                             Trm56  60 vprevyeladynvsvgnqPhsevaalaifldrllegkelekefedaklkviPsergkkv 118
                                       vp++vye ad+nv+v+nqPhseva+la+fldrl+eg+ele+e+e+a+ +viP+e+gk+v
  gi|336253933|ref|YP_004597040.1| 132 VPFDVYEEADWNVGVTNQPHSEVAGLAVFLDRLFEGRELEQEWEGADRTVIPMETGKRV 190
                                       *********************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1546.98
//
Query:       gi|336253934|ref|YP_004597041.1|  [L=643]
Description: hypothetical protein Halxa_2544 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.022   14.6   0.7      0.052   13.4   0.7    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7   2.9e-06     0.052       2      24 ..       7      29 ..       6      30 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      ++RR  LK +A ++A aa +gc+
  gi|336253934|ref|YP_004597041.1|  7 FTRRKYLKLAAIGGASAAIAGCS 29
                                      89********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 4949.08
//
Query:       gi|336253935|ref|YP_004597042.1|  [L=446]
Description: hypothetical protein Halxa_2545 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.02   13.9   0.0      0.084   11.9   0.0    1.9  1  Dyp_perox   Dyp-type peroxidase family
      0.063   13.1   5.6       0.14   12.0   5.6    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> Dyp_perox  Dyp-type peroxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.3e-06     0.084     158     324 ..     235     416 ..     229     419 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.3e-06
                                       TSSBSSTTS--TCHHHHHHHS-CSSSGGGTT-EEEEEEEEEE-HHHHTTS-HHHHH..HHHTB-TTT--BTTTTSTT CS
                         Dyp_perox 158 lGFvDGTeNpkgeeakeavvlikdedewaagGsYvvvrkirhdleaWdrlslkeQe..dviGRrKedgaeldddkea 232
                                       +GF+ G +     +a+e++v+i ++   +agGs +++   ++dle W   s +eQ   + +     + + +++  e+
  gi|336253935|ref|YP_004597042.1| 235 MGFRSGFRES---QATEDRVTIREG--PFAGGSTQHFETLELDLEVWYDESDHEQRvaRLFSPAHAEREAVGEVGER 306
                                       6666666544...44555688****..9***********************99996335677666665555554443 PP

                                       S..............TTTGSSS-TTSHHHHHSGESTTTEC--EE--EEEEEEE-TTSSCEEEEEEEEEESSCHHCHH CS
                         Dyp_perox 233 d..............dseekvipkdsHvrlaklkedgkglkilRralsygeGldkvgkldaGllFiaYqrtlenteq 295
                                                      d + ++     H++     +d    ++lRr ++ ++  d+      G+ F++ qr+++++  
  gi|336253935|ref|YP_004597042.1| 307 LgtetgvasvaddvrD-HARDEGVVGHAQKLARARDDGTPTLLRRDVNTTD--DD----VCGVHFVSLQREMSEFTR 376
                                       3566888888874422.22222334676654445678889999**999999..33....4699*******9999988 PP

                                       HHHHHH...........SCB-GGGGCEEEEEEEEEEE-BH CS
                         Dyp_perox 296 mlqrml...........gktdaLlefikavtgglFfapsg 324
                                       + + ml            +++ +l++ +    g +++p++
  gi|336253935|ref|YP_004597042.1| 377 VREAMLgeefgryglgpRQGNGILRYLRVRRWGSYLVPPR 416
                                       8888887777888887777788888888888888888876 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   5.6   1.6e-05      0.14       3      24 ..      10      31 ..      10      32 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggca 24
                                      SRR F +++ Aa+A aal gc+
  gi|336253935|ref|YP_004597042.1| 10 SRRAFVRAAVAAGASAALVGCL 31
                                      9*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3187.20
//
Query:       gi|336253936|ref|YP_004597043.1|  [L=240]
Description: hypothetical protein Halxa_2546 [Halopiger xanaduensis SH-6]
Scores for 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  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1786.97
//
Query:       gi|336253937|ref|YP_004597044.1|  [L=92]
Description: hypothetical protein Halxa_2547 [Halopiger xanaduensis SH-6]
Scores for 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  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); 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:                         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 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 739.69
//
Query:       gi|336253938|ref|YP_004597045.1|  [L=175]
Description: transcription factor E [Halopiger xanaduensis SH-6]
Scores for 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   68.7   0.0    7.3e-19   67.6   0.1    1.6  2  TFIIE_alpha     TFIIE alpha subunit
     0.0033   17.5   0.1     0.0074   16.4   0.1    1.7  1  Sigma70_r3      Sigma-70 region 3
     0.0054   16.5   1.0      0.027   14.3   0.1    2.3  2  Rad50_zn_hook   Rad50 zinc hook motif
     0.0088   16.0   0.0      0.017   15.1   0.0    1.6  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
  ------ inclusion threshold ------
      0.049   13.8   1.8      0.095   12.8   1.8    1.5  1  Zn-ribbon_8     Zinc ribbon domain
       0.05   13.6   0.3      0.087   12.8   0.3    1.3  1  zinc-ribbons_6  zinc-ribbons
      0.054   12.9   0.1        0.1   12.1   0.1    1.4  1  zf-ribbon_3     zinc-ribbon domain
      0.077   13.1   0.5       0.48   10.5   0.0    2.1  2  HTH_20          Helix-turn-helix domain
       0.11   12.5   0.1       0.17   12.0   0.1    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.12   12.0   0.9        7.5    6.2   0.1    2.5  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.22   11.7   2.2       0.76    9.9   1.5    2.3  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.46   10.0   3.4        2.6    7.6   2.9    2.5  2  TF_Zn_Ribbon    TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.1   4.9e-22   7.3e-19      25     105 .]      33     113 ..      10     113 .. 0.93
   2 ?   -2.2   0.0       2.4   3.6e+03      39      60 ..     136     157 ..     132     169 .. 0.63

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 4.9e-22
                                       TTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHHHHHHHHHC CS
                       TFIIE_alpha  25 kgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevvkkLeekle 101
                                       +gevt+e+la+el ++ln +r++L+ Lye  l++y+r rde+ +w +y w ++y+++++ + +++ ++   Lee  e
  gi|336253938|ref|YP_004597045.1|  33 DGEVTDEELAEELDLELNDVRRALFILYENDLASYRRLRDEDSGWLTYLWTFEYDNIPENLEEEMYRLHDALEERQE 109
                                       79************************************************************************999 PP

                                       CCTS CS
                       TFIIE_alpha 102 keen 105
                                        e n
  gi|336253938|ref|YP_004597045.1| 110 YERN 113
                                       9876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.4
                                       S-HHHHHHHHHHHHHCTSEEEE CS
                       TFIIE_alpha  39 idlnelrklLnrLyearlvkyk 60 
                                       ++ +e ++ L  + ++rlv+  
  gi|336253938|ref|YP_004597045.1| 136 FECPECGSPLESMDNDRLVNAM 157
                                       5566666667777777777654 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1     5e-06    0.0074      20      41 ..      35      56 ..      33      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5e-06
                                      XXXHHHHHHHHTXXHHHHHHHH CS
                        Sigma70_r3 20 ePtpeEiAeeLglseekVrevl 41
                                      e t+eE+AeeL+l++++Vr++l
  gi|336253938|ref|YP_004597045.1| 35 EVTDEELAEELDLELNDVRRAL 56
                                      679****************997 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 ?    0.1   0.1      0.48   7.1e+02      34      49 ..      38      53 ..      33      56 .. 0.78
   2 !   14.3   0.1   1.8e-05     0.027      21      52 .]     137     168 ..     135     168 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.48
                                      HHHHHHHHHHHHHHHH CS
                     Rad50_zn_hook 34 rseLikelqsklerlp 49
                                       +eL++el  +l++++
  gi|336253938|ref|YP_004597045.1| 38 DEELAEELDLELNDVR 53
                                      5899999999999876 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.8e-05
                                       E-TTT--EE-HHHHHHHHHHHHHHHHHHH... CS
                     Rad50_zn_hook  21 cCPlCgReldeehrseLikelqsklerlpeel 52 
                                        CP Cg++l++ +  +L++ + ++le l+eel
  gi|336253938|ref|YP_004597045.1| 137 ECPECGSPLESMDNDRLVNAMDERLEALEEEL 168
                                       5*****************************96 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 !   15.1   0.0   1.2e-05     0.017       1      13 [.     137     149 ..     137     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                    DNA_ligase_ZBD   1 hCPvCGsavvRee 13 
                                       +CP+CGs+++  +
  gi|336253938|ref|YP_004597045.1| 137 ECPECGSPLESMD 149
                                       5********9654 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.8   6.4e-05     0.095       6      37 ..     117     146 ..     109     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.4e-05
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgsevr 37 
                                       Y Ce C  +fe   +++     +CPeCgs+++
  gi|336253938|ref|YP_004597045.1| 117 YLCEICSIRFEFGEAMDF--GFECPECGSPLE 146
                                       67*********6666662..234******886 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   0.3   5.8e-05     0.087       8      42 ..     108     148 ..     103     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                                       S--EE-SSEEE-TTT--......EEEEEEE-SSS-S---EE CS
                    zinc-ribbons_6   8 qelekrgeqyhCeaCqe......dlkkealCpeCeqelevl 42 
                                       qe e+++e y Ce C+        ++    CpeC+++le +
  gi|336253938|ref|YP_004597045.1| 108 QEYERNHEFYLCEICSIrfefgeAMDFGFECPECGSPLESM 148
                                       5667777899*****997767666777789********976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.7e-05       0.1       4      16 ..     137     149 ..     135     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.7e-05
                       zf-ribbon_3   4 rCPnCGaplssdd 16 
                                       +CP+CG+pl+s d
  gi|336253938|ref|YP_004597045.1| 137 ECPECGSPLESMD 149
                                       7******999866 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00032      0.48       9      58 ..       9      69 ..       2      72 .. 0.80
   2 ?    0.3   0.1      0.51   7.6e+02      39      50 ..     155     166 ..     145     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00032
                                      -HHHHHHHHHH...........STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  9 hPvRrrilraL...........araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      +Pv  + l +L           ++++++t +elae+ldl  n +++ L +L e +L   +r
  gi|336253938|ref|YP_004597045.1|  9 DPVIQKYLHELvgpkgmpvaaaPPDGEVTDEELAEELDLELNDVRRALFILYENDLASYRR 69
                                      5555555666677777777777889999***********************9999977666 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.51
                                       HHHHHHHHHHHH CS
                            HTH_20  39 ntlsyHLrvLee 50 
                                       n ++ +L++Lee
  gi|336253938|ref|YP_004597045.1| 155 NAMDERLEALEE 166
                                       789999***998 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   0.00011      0.17      63      95 ..     109     144 ..      85     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                       EEEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS CS
                              HypA  63 eieevpvkvrCreCgkefelee..k.alrCpkCgsa 95 
                                       e+e+ +  + C+ C+ +fe  e  +  ++Cp+Cgs 
  gi|336253938|ref|YP_004597045.1| 109 EYERNHEFYLCEICSIRFEFGEamDfGFECPECGSP 144
                                       5677777889*********655344677******96 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.027        40       2      13 ..     116     127 ..     115     132 .. 0.82
   2 ?    6.2   0.1     0.005       7.5       3      13 ..     136     146 ..     135     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.027
                            zf_UBZ   2 tylCerCgkeip 13 
                                        ylCe C  +++
  gi|336253938|ref|YP_004597045.1| 116 FYLCEICSIRFE 127
                                       69*****99886 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.005
                            zf_UBZ   3 ylCerCgkeip 13 
                                       + C++Cg++++
  gi|336253938|ref|YP_004597045.1| 136 FECPECGSPLE 146
                                       88*****9876 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 ?   -1.7   0.0       2.2   3.2e+03      21      47 ..      74     100 ..      73     114 .. 0.60
   2 ?    9.9   1.5   0.00051      0.76      11      26 ..     130     145 ..     101     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.2
                          zf-Mss51  21 dCGiptycseehwedDyeahleicdtL 47 
                                       d+G+ ty    ++ +  e+ +e +++L
  gi|336253938|ref|YP_004597045.1|  74 DSGWLTYLWTFEYDNIPENLEEEMYRL 100
                                       677777766555555444444444444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00051
                          zf-Mss51  11 apkhvdfeCpdCGipt 26 
                                       +  +  feCp+CG p 
  gi|336253938|ref|YP_004597045.1| 130 EAMDFGFECPECGSPL 145
                                       566778*******997 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.41   6.1e+02      11      25 ..     108     122 ..     105     132 .. 0.80
   2 ?    7.6   2.9    0.0018       2.6      15      36 ..     131     152 ..     117     157 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.41
                                       CHEETSTTCEEESSS CS
                      TF_Zn_Ribbon  11 lveDpergelvCtdC 25 
                                       ++++ ++  ++C+ C
  gi|336253938|ref|YP_004597045.1| 108 QEYERNHEFYLCEIC 122
                                       567777888899877 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0018
                                       TSTTCEEESSSSBEEEECCCCC CS
                      TF_Zn_Ribbon  15 pergelvCtdCGlVlednside 36 
                                       ++   + C++CG+ le +++d 
  gi|336253938|ref|YP_004597045.1| 131 AMDFGFECPECGSPLESMDNDR 152
                                       5555666888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1233.48
//
Query:       gi|336253939|ref|YP_004597046.1|  [L=224]
Description: hypothetical protein Halxa_2549 [Halopiger xanaduensis SH-6]
Scores for 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-95  317.6   0.0    4.6e-95  317.5   0.0    1.0  1  DUF2110   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2110  Uncharacterized protein conserved in archaea (DUF2110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.5   0.0   2.5e-99   4.6e-95       1     223 []       4     222 ..       4     222 .. 0.98

  Alignments for each domain:
  == domain 1  score: 317.5 bits;  conditional E-value: 2.5e-99
                           DUF2110   1 latkvY...dareralesleslvenelkdLdveleisvreddfvkvtleGedeevaanllreefgeitkeveegevy 74 
                                       latk+Y   darer+l+sl+slv+ne++dL+ve+e++vr+ddf++vt+eGed++va+n+lreefgei++++e+ge+y
  gi|336253939|ref|YP_004597046.1|   4 LATKLYvegDARERSLDSLRSLVNNEIGDLEVEFELGVRHDDFPSVTIEGEDATVARNVLREEFGEIVPDLEAGETY 80 
                                       689************************************************************************** PP

                           DUF2110  75 vGtlesldedgfvldigvevripkdelkpLgegspeqiaerFGlvqhlpleveveeveeeekeiearltdeqvdrly 151
                                       vGtles+d++gfvld+g+ vrip+del+ Lg+gsp+qi+erFGlvqh+pl+++++++     e  ++l+de+vdrl+
  gi|336253939|ref|YP_004597046.1|  81 VGTLESWDDEGFVLDAGQAVRIPADELD-LGPGSPTQIRERFGLVQHVPLRFVYGGEG----E-ASTLADEEVDRLF 151
                                       ****************************.*************************7644....3.489********** PP

                           DUF2110 152 ewkkgkedrlivnsatrsevkaalnraGhardivtverlglleqsvvcredtdapGlvaeiGpylpaelkvv 223
                                       ew++g ++rl+vnsatr+ev+a+lnraGha+d vtverlglleqsv+c++dtd+pGl+a++G+ylpael++v
  gi|336253939|ref|YP_004597046.1| 152 EWTRG-DGRLNVNSATRAEVRATLNRAGHAQDYVTVERLGLLEQSVICTDDTDPPGLLASVGEYLPAELRCV 222
                                       *****.*****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1659.79
//
Query:       gi|336253940|ref|YP_004597047.1|  [L=256]
Description: hypothetical protein Halxa_2550 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.002   17.9   0.0       0.57   10.0   0.0    2.9  4  DUF4307   Domain of unknown function (DUF4307)


Domain annotation for each model (and alignments):
>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   3.2e-05      0.57       3      54 ..       3      54 ..       2      56 .. 0.69
   2 ?   -3.0   0.0      0.36   6.4e+03      30      47 ..     102     118 ..      94     123 .. 0.43
   3 ?   -2.8   0.0      0.31   5.6e+03      75      93 ..     135     153 ..     133     155 .. 0.77
   4 !    4.4   0.0    0.0017        31       5      44 ..     206     245 ..     202     249 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.2e-05
                           DUF4307  3 rllvillvvlvvvalalvawigysqgsadvsaevvgfevvddstvevtfeVt 54
                                      r+lv+++++++++a+++    ++   s++   + +++++  ds+++vt++V+
  gi|336253940|ref|YP_004597047.1|  3 RRLVLAVLAVGLLAGTAGCTGFFGGISDEQLDQNASYDDLRDSEANVTVDVE 54
                                      3444455555555555555555555566777799****************96 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.36
                           DUF4307  30 advsaevvgfevvddstv 47 
                                       ++v+++++++e  d s++
  gi|336253940|ref|YP_004597047.1| 102 TEVTGSELNVEQ-DRSST 118
                                       344444444433.22222 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.31
                           DUF4307  75 vGrrevlvpagdertvrvt 93 
                                        Grr++ +pa  e++ rvt
  gi|336253940|ref|YP_004597047.1| 135 AGRRTFQLPAYVEGSYRVT 153
                                       5999999998877777665 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.0017
                           DUF4307   5 lvillvvlvvvalalvawigysqgsadvsaevvgfevvdd 44 
                                       ++ l++++v++++a++a+++ + ++ + + e++gf++  d
  gi|336253940|ref|YP_004597047.1| 206 FAGLIGAVVLLGGAGIAYYYRQIKRLQEQREEMGFDIDID 245
                                       5566777777777777777666688888888888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1935.58
//
Query:       gi|336253941|ref|YP_004597048.1|  [L=168]
Description: CheW domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-14   52.2   0.0    5.5e-14   52.0   0.0    1.0  1  CheW          CheW-like domain
  ------ inclusion threshold ------
      0.083   12.5   0.0        0.1   12.3   0.0    1.3  1  Cytomega_US3  Cytomegalovirus US3 protein


Domain annotation for each model (and alignments):
>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   6.2e-18   5.5e-14       2     129 ..      32     162 ..      31     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 6.2e-18
                                       EEEEEETTEEEEEEGGGEEEEEECCT.BTTTTSS.TTEEEEEEETTEEEEEEEHHHHCTSSSSTT....STCEEEEE CS
                              CheW   2 lllfrlgeetyaiplakvreilevppitpipgap.gavlgvinlrGevipvidLrellglgpees....rentrviv 73 
                                       +l+f+l++e+y++  ++v+++l +++  p++ a  ++ +g +++rGe + v+dL +++  +++++      ++++++
  gi|336253941|ref|YP_004597048.1|  32 VLTFSLASERYCVRTDAVASVLGLSETAPLEDADdPWNAGTVTVRGERVRVVDLPRVFAAERTREtaarI-DDPMLL 107
                                       79********************************9*********************************63.444444 PP

                                       EEET....TEEEEEEESEEEEEEEEECCGEETTTSSTSSTCCCEEEEEECTTSEEEEEE- CS
                              CheW  74 velg....nqvvGllVdevkgiqeivikqiepplglssdlagyisGatklgdgrlvliLD 129
                                       v ++    + ++G lVd v+  ++++  ++e+  +   d ++ + G ++ +dg  +++LD
  gi|336253941|ref|YP_004597048.1| 108 VIDEtdetGAYYGWLVDGVDVTRTVRMADLESTRA---DTKH-VDGRFVFEDG-SAILLD 162
                                       4333357899***********************66...6666.99*****999.666666 PP

>> Cytomega_US3  Cytomegalovirus US3 protein
   #    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      85     114 ..     111     137 ..      60     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
                      Cytomega_US3  85 esyhhdergaylkwnvggypvsrtldvvdi 114
                                       e    de gay+ w v g  v+rt+ + d+
  gi|336253941|ref|YP_004597048.1| 111 E---TDETGAYYGWLVDGVDVTRTVRMADL 137
                                       4...49*********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1230.27
//
Query:       gi|336253942|ref|YP_004597049.1|  [L=230]
Description: CheW protein [Halopiger xanaduensis SH-6]
Scores for complete 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-17   63.9   0.0    1.9e-17   63.2   0.0    1.3  1  CheW      CheW-like domain


Domain annotation for each model (and alignments):
>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0   1.1e-21   1.9e-17       2     104 ..      36     142 ..      35     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.1e-21
                                       EEEEEETTEEEEEEGGGEEEEEECCT..BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTT.STCEEEEEEEE CS
                              CheW   2 lllfrlgeetyaiplakvreilevpp.itpipgapgavlgvinlrGevipvidLrellglgpees.rentrvivvel 76 
                                       l+lf++ge+++a+p+++vr++ ++p+ +t++p++p+av+gv +lrGe+  vid +  +  ++  +    ++++v ++
  gi|336253942|ref|YP_004597049.1|  36 LVLFTVGEHRLAVPVDEVRTTTDLPDeLTSVPRTPPAVEGVTDLRGEITAVIDPSVHFPTDEHGAgAGGEQLLVFDR 112
                                       79**********************666********************************999999988888888885 PP

                                       T..TEEEEEEESEEEEEEEEECCGEETTTS CS
                              CheW  77 g..nqvvGllVdevkgiqeivikqiepplg 104
                                       g  +q +++ Vdev ++++++++++ ++  
  gi|336253942|ref|YP_004597049.1| 113 GadDQSAAIRVDEVLDVESVPERNLLEADD 142
                                       556*********************998843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1639.32
//
Query:       gi|336253943|ref|YP_004597050.1|  [L=120]
Description: response regulator receiver protein [Halopiger xanaduensis SH-6]
Scores for 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  107.4   0.1    4.6e-31  107.3   0.1    1.0  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.027   14.5   0.0    1.2  1  B12-binding   B12 binding domain


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 !  107.3   0.1   5.2e-35   4.6e-31       1     111 [.       5     114 ..       5     115 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 5.2e-35
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       vlivdD++ +r+llrq+le+ +y+  +ea++g+ea++l+ke+++d++++Di mp+++G++++  i++ dp+  vi++
  gi|336253943|ref|YP_004597050.1|   5 VLIVDDSHFMRNLLRQILEQ-EYRILGEASNGAEAVKLYKEHDPDIVMMDIVMPKCNGIKATAAIKKIDPDASVIMC 80 
                                       8******************5.565999************************************************** PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlkal 111
                                       t+ ++ e ++ a+kagad++++Kpf++  ++kal
  gi|336253943|ref|YP_004597050.1|  81 TSVGQREKMKLAVKAGADGYVTKPFEEPSVRKAL 114
                                       ***************************9999886 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     3e-06     0.027      20      87 ..      18      80 ..      13     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-06
                       B12-binding 20 laaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvG 87
                                      l ++l++   e ++lg   + ++ v+  ++++pd+v++ + +  +++++k+++  +k+i+p++ v++ 
  gi|336253943|ref|YP_004597050.1| 18 LRQILEQ---EYRILGEASNGAEAVKLYKEHDPDIVMMDI-VMPKCNGIKATAA-IKKIDPDASVIMC 80
                                      5566666...77888888888*******************.********99875.6688999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 869.17
//
Query:       gi|336253944|ref|YP_004597051.1|  [L=446]
Description: response regulator receiver modulated CheB methylesterase [Halopiger xanaduensis SH-6]
Scores for 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-54  182.3   0.1    1.1e-53  181.5   0.1    1.4  1  CheB_methylest  CheB methylesterase
    2.1e-23   82.6   0.2    4.2e-23   81.7   0.2    1.5  1  Response_reg    Response regulator receiver domain
  ------ inclusion threshold ------
       0.24   12.0   7.3       0.41   11.3   7.3    1.4  1  SRRM_C          Serine/arginine repetitive matrix protein C-t


Domain annotation for each model (and alignments):
>> CheB_methylest  CheB methylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.5   0.1   1.8e-57   1.1e-53       1     170 []     240     420 ..     240     420 .. 0.94

  Alignments for each domain:
  == domain 1  score: 181.5 bits;  conditional E-value: 1.8e-57
                                       EEEEE-TTHHHHHTTTGGGS-TT-SS-EEEEE---TT-HHHHHHHHHHH-SSEEEE--TT-B--TTEEEE--TTSEE CS
                    CheB_methylest   1 vvigaStGGlealkellaalpedfpaavvvvqhmppsftsslaelLnresslkVkeaedgeelepgrvyvapgdkhl 77 
                                       +v+gaStGG++ +++ll++lp  ++a+v++vqhmp++ft ++a++L++  ++ V+ea dg+++ pg+++vapg++hl
  gi|336253944|ref|YP_004597051.1| 240 IVVGASTGGPKIVERLLQRLPIGLDATVLIVQHMPADFTGRFADRLDAMGPYAVSEAGDGDRVGPGEAVVAPGSAHL 316
                                       79*************************************************************************** PP

                                       EEE.............E.E-.-...SS-HHHHHHHHHHHH.GGEEEEE-SBSS-TTHHHHHHHHHTT-EEEEE-GGG CS
                    CheB_methylest  78 lie........lals.a.kkge...rpsiDvlfesaaeaygeraigviLtGmgsDGaeGlkaikeaggltiaqdpes 141
                                       +i         ++l+ a +  +   +p+iDv++e+aa+ +++ ++gv+LtGmg+DGa+G++aik+agg+tiaqd+++
  gi|336253944|ref|YP_004597051.1| 317 EIGadfgdslrVRLDeArR--DygiQPAIDVTMETAADRVDGPLCGVVLTGMGDDGAAGIEAIKAAGGRTIAQDEAT 391
                                       **99999885544444223..1347***************99*********************************** PP

                                       -SSBSHHHHHHHTT--SEEE-GGGHHHHH CS
                    CheB_methylest 142 avvpgmPkaaieagavdevlpleeiaeel 170
                                       + v+g+P +aie+g+vd v+p+ ei++e+
  gi|336253944|ref|YP_004597051.1| 392 SPVFGIPCQAIETGCVDSVAPAPEIVDEI 420
                                       *************************9986 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.2     7e-27   4.2e-23       1     101 [.       4     106 ..       4     112 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 7e-27
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHH..ESEEEEESSCSSSEHHHHHHHHHHCTTTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeek..vdlillDinmpgmdGlellkeireedpelpvi 75 
                                       vl+vdD++ +r+++ ++l +++y +v++a++g+ea+e+++  +  +d++++D++mp+m+G+ ++++i +    +pvi
  gi|336253944|ref|YP_004597051.1|   4 VLVVDDSQFFRTVVGNALSDADY-DVETADTGTEAVEIVRDAAfdPDVVTMDVEMPDMNGIAAVERIMAAT-PTPVI 78 
                                       8**********************.***************766666**********************8877.79*** PP

                                       EEESSTS..HHHHHHHHHCTESEEEESS CS
                      Response_reg  76 iltahse..eedavealkagaddflsKp 101
                                       + +a+++   e + +al+aga dfl+Kp
  gi|336253944|ref|YP_004597051.1|  79 MASAYTDtgAEATLDALEAGAIDFLQKP 106
                                       ***9988778999**************9 PP

>> SRRM_C  Serine/arginine repetitive matrix protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   7.3   6.8e-05      0.41       8      56 ..     140     188 ..     134     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.8e-05
                            SRRM_C   8 rereskskssssekeakrerkrrrrrSySPirkRrRDSPShLeaRRITs 56 
                                       r  +s+ +s+s+ ++a+++ +  r+rS SP  +  R SPS +     Ts
  gi|336253944|ref|YP_004597051.1| 140 RPTSSETRSESTVRSASHSDASPRSRSHSPAARADRSSPSTVGTAGTTS 188
                                       5566777888888888888899******************876655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3449.55
//
Query:       gi|336253945|ref|YP_004597052.1|  [L=1457]
Description: signal transduction histidine kinase CheA [Halopiger xanaduensis SH-6]
Scores for 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-20   71.1   3.9    2.8e-19   69.2   0.2    3.6  3  Hpt           Hpt domain
    3.8e-18   66.0   0.1    1.2e-17   64.5   0.0    1.9  2  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    7.5e-08   32.1   0.6    2.4e-07   30.5   0.6    1.9  1  CheW          CheW-like domain
    1.7e-07   31.5   5.3    4.8e-07   30.1   5.3    1.9  1  H-kinase_dim  Signal transducing histidine kinase, homodimeri
    9.6e-06   25.6   2.1    0.00011   22.2   0.0    3.1  2  P2            P2 response regulator binding domain
     0.0011   18.9   0.8     0.0011   18.9   0.8    4.1  6  HATPase_c_2   Histidine kinase-like ATPase domain
      0.004   17.0   0.0      0.015   15.1   0.0    2.0  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
  ------ inclusion threshold ------
       0.19   11.7   3.7       0.63   10.0   3.7    1.9  1  Serglycin     Serglycin


Domain annotation for each model (and alignments):
>> Hpt  Hpt domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.2   1.2e-22   2.8e-19       1      83 [.       5      97 ..       5     104 .. 0.92
   2 ?    0.2   0.0       0.4   8.9e+02      35      57 ..     402     424 ..     382     442 .. 0.78
   3 ?   -2.0   0.3         2   4.4e+03       9      21 ..    1082    1094 ..    1050    1107 .. 0.55

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.2e-22
                                      HHHHHHHHHHHHHHHHHHHHH........SCCHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHH..HCTSCHHHH CS
                               Hpt  1 ellelfleeaeelleqleqal........dqedlqelaraaHtLKGsagmlGltelaelahelEdlld..ragelelep 69
                                      e++++f++e+ e++++l++al        d++++++++r+aHtLKG +g  Gl+  +elah++Edlld  r g le++p
  gi|336253945|ref|YP_004597052.1|  5 EYWTDFVQESTERITELNNALltlernpdDEAAVEDVFRVAHTLKGNCGAAGLESASELAHAIEDLLDavRGGALEVSP 83
                                      79************************985555*********************************************** PP

                                      HHHHHHHHHHHHHH CS
                               Hpt 70 ellealkallealr 83
                                      el++ + +++++l+
  gi|336253945|ref|YP_004597052.1| 84 ELMDDIFDAVDELE 97
                                      ****7777777765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.4
                                       HHHHHHHHTTBHHHHHHHHHHHH CS
                               Hpt  35 tLKGsagmlGltelaelahelEd 57 
                                        LK    m+G++el++  +elE 
  gi|336253945|ref|YP_004597052.1| 402 ELKDEVEMVGFDELQDELAELEF 424
                                       57888889999999999999986 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2
                                        HHHHHHHHHHHHH CS
                               Hpt    9 eaeelleqleqal 21  
                                        ea+e+ ++le+ l
  gi|336253945|ref|YP_004597052.1| 1082 EADEDRQALETEL 1094
                                        2222222222222 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 !   64.5   0.0   5.2e-21   1.2e-17       3     111 ..    1158    1298 ..    1156    1299 .. 0.87
   2 ?   -3.9   0.0         8   1.8e+04      26      47 ..    1384    1407 ..    1366    1442 .. 0.65

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 5.2e-21
                                        HHHHHHHHHHHHHHHHHH........HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT.............. CS
                         HATPase_c    3 ekrLrqiisnlvdNavkf........atkageieveikaseddlvisveDnGiGipkedlk.............. 55  
                                        ++ L ++++n+vd+ v+         ++ +g +ev+ +++ d+++i+veD+G G++++ +               
  gi|336253945|ref|YP_004597052.1| 1158 SDPLIHLVRNAVDHGVEPpedredaeKPREGAVEVTATRERDRVTITVEDDGSGLDPDRIRseaveadvltedea 1232
                                        577899999999999998888887443355555666554449********************************* PP

                                        ..........GTCS.TTCHHCSTCHTSTSSSHHHHHHHH.HHHHTTTEEEEEEETTTEEEEEEEEESS CS
                         HATPase_c   56 ..........klfe.kfsqddstkrggggtGlGlsivkk.lvelmgGeiwvesepgrGttftftlple 111 
                                                  ++f   +s+ +++ ++ +g+G+G+ +v++ ++e ++G+++++s pg Gtt+t+tlp +
  gi|336253945|ref|YP_004597052.1| 1233 eamadeevydLVFHpGLST-AEEVTDVSGRGVGMDVVDRtVTE-LDGTVSIDSAPGDGTTVTMTLPVS 1298
                                        **********999989999.999999*************5666.*********************975 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 8
                                        EEEEEEEEEE...TEEEEEEEESSS CS
                         HATPase_c   26 eieveikase...ddlvisveDnGi 47  
                                        ++ev ++      +d+ ++++D+ +
  gi|336253945|ref|YP_004597052.1| 1384 TVEVGLEG-AsgdGDVLVRIRDDVR 1407
                                        44555553.1344677788888754 PP

>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.6   1.1e-10   2.4e-07       2     132 ..    1304    1456 ..    1303    1457 .] 0.82

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.1e-10
                                        EEEEEETTEEEEEEGGGEEEEEECCT.BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTT........... CS
                              CheW    2 lllfrlgeetyaiplakvreilevppitpipgapgavlgvinlrGevipvidLrellglgpees........... 65  
                                        +l ++ ++e++++p + v+ + + ++i+ i g p       +  ++ ipvidL e l     +            
  gi|336253945|ref|YP_004597052.1| 1304 ILFVESNGEEFGLPTEVVYDVEPADSIELIDGEPVL----PRDDDDPIPVIDLDETLRTAAVDTdaeteadvavg 1374
                                        688999********************8888888855....67788*************99999988455555555 PP

                                        .STCEEEEEEEET............................TEEEEEEESEEEEEEEEECCGEETTTSSTSSTCC CS
                              CheW   66 .rentrvivvelg............................nqvvGllVdevkgiqeivikqiepplglssdlag 111 
                                                    g                             + v+l  d+v+g+qe+v+k++e   +   + +g
  gi|336253945|ref|YP_004597052.1| 1375 dG----------GsssdddtvevglegasgdgdvlvrirddVRPVALRCDQVHGQQEVVVKPFEGFMR---GIPG 1436
                                        50..........45555555555555556666666666666*************************77...8899 PP

                                        CEEEEEECTTSEEEEEE-CCC CS
                              CheW  112 yisGatklgdgrlvliLDvea 132 
                                         +sGat+ g g++v iLDv  
  gi|336253945|ref|YP_004597052.1| 1437 -LSGATVRGRGKVVNILDVTT 1456
                                        .*****************976 PP

>> H-kinase_dim  Signal transducing histidine kinase, homodimeric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   5.3   2.1e-10   4.8e-07       2      68 ..    1051    1110 ..    1050    1111 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.1e-10
                      H-kinase_dim    2 stlRVdakrlDyLlnlvGElVitkarLnqsleefrfenglkasvtelksslqnlgrisgeLQegvmk 68  
                                        ++lRVd++ +D+Ll lv  lV ++ rL++ +e  +         ++l+ +l+ l+ ++++LQe vm 
  gi|336253945|ref|YP_004597052.1| 1051 QSLRVDVEQVDELLTLVEGLVTSRVRLRHAVEADE-------DRQALETELNALEDLTTDLQETVMD 1110
                                        68***************************998888.......899*********************6 PP

>> P2  P2 response regulator binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0     5e-08   0.00011      20      79 ..     174     233 ..     155     235 .. 0.92
   2 ?    0.8   1.0      0.23   5.1e+02      32      68 ..     718     756 ..     714     764 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5e-08
                                       HHHHHHHHHTTEEEEEES-HHHHHTT-SSSEEEEEEEESS-HHHHHHHHHTSSS-SEEEE CS
                                P2  20 flvfkaLeelgeiiksiPsvedieeekfdegfevvlltkeskeeikealasiseiesvev 79 
                                       +l++kaL +  ++i + P++++ie+  ++++f+ v+++  +++ i++ l+ ++e+ ++e+
  gi|336253945|ref|YP_004597052.1| 174 ILIVKALIDAFDLIGTAPPRDAIEAHAYNGRFDAVFASAVTESAIESGLEPVDEVADFEL 233
                                       79***********************************************99*****9986 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.23
                                       EEEEES-HHHHHTT-S.SSEEEEEEEE.SS-HHHHHHHH CS
                                P2  32 iiksiPsvedieeekf.degfevvllt.keskeeikeal 68 
                                        + s P  e++e+++  ++++e  l t + +++e  ea+
  gi|336253945|ref|YP_004597052.1| 718 RVGSAPADEEVEDGDEdESELETELETpSDTADEAFEAA 756
                                       57899********88878888888854344455544443 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   3.1e+03      91     113 ..     154     185 ..     118     190 .. 0.68
   2 ?   -3.6   0.2       4.6     1e+04      66     101 ..     345     380 ..     340     394 .. 0.71
   3 ?   -3.3   1.4       3.7   8.4e+03      70      95 ..     519     545 ..     487     551 .. 0.72
   4 ?   -3.2   0.5       3.5   7.8e+03      31      98 ..     778     848 ..     753     851 .. 0.67
   5 !   18.9   0.8   5.1e-07    0.0011      50     124 ..    1183    1294 ..    1164    1295 .. 0.80
   6 ?   -3.1   0.1       3.3   7.3e+03      53      78 ..    1382    1409 ..    1372    1420 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                       HATPase_c_2  91 p.........keslkegGrGlalikglvDeve 113
                                       +         + +++    G++++k+l D ++
  gi|336253945|ref|YP_004597052.1| 154 NvylarlsvdESEAEGDNAGILIVKALIDAFD 185
                                       144555555344555556899***99999875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.6
                       HATPase_c_2  66 altvevaDsGpgfdpetlpdpteeepkeslkegGrG 101
                                       a ++  +DsG+  d+e +   +  ++++s+  +G G
  gi|336253945|ref|YP_004597052.1| 345 AAEADSTDSGAERDAESGSVADSGSSSGSESGSGSG 380
                                       566777888888888877777776655555555555 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.7
                       HATPase_c_2  70 evaDsGpg.fdpetlpdpteeepkesl 95 
                                       +vaD++ +  +p++ p+p+ e  +es+
  gi|336253945|ref|YP_004597052.1| 519 TVADEATAtTEPAETPEPESEPESESE 545
                                       688888887777777666554434444 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 3.5
                       HATPase_c_2  31 eirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeep..keslkeg 98 
                                       ++++a +Ea +     a le + ++     +++ ++ ++ v+Ds     d ++ +++  +ep  ++s+ e 
  gi|336253945|ref|YP_004597052.1| 778 DVNFATDEASIASTDDADLESEADSTDAFDDDAIDSDEFDVSDSVTSdADIAEFDEDSFDEPdvSDSDTET 848
                                       56666666666666666666666666666666667777788888888777777777666666444455554 PP

  == domain 5  score: 18.9 bits;  conditional E-value: 5.1e-07
                       HATPase_c_2   50 eap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeep.............................kes 94  
                                        e+p eg vev+++++ +++t++v+D+G g dp  ++ +++e++                              ++
  gi|336253945|ref|YP_004597052.1| 1183 EKPrEGAVEVTATRERDRVTITVEDDGSGLDPDRIRSEAVEADvltedeaeamadeevydlvfhpglstaeeVTD 1257
                                        44556999*************************99999998889*************************977666 PP

                       HATPase_c_2   95 lkegGrGlalikglvDev....ey...dgegnvvtms 124 
                                           +G+G+ ++ + v e+    ++    g+g++vtm+
  gi|336253945|ref|YP_004597052.1| 1258 VSGRGVGMDVVDRTVTELdgtvSIdsaPGDGTTVTMT 1294
                                        7777777778888888886543337666679999997 PP

  == domain 6  score: -3.1 bits;  conditional E-value: 3.3
                       HATPase_c_2   53 egpvevrlesdeea..ltvevaDsGpgf 78  
                                        +++vev le +++   + v+++D+ ++ 
  gi|336253945|ref|YP_004597052.1| 1382 DDTVEVGLEGASGDgdVLVRIRDDVRPV 1409
                                        5677777554444433999999998875 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 !   15.1   0.0   6.9e-06     0.015       7      55 ..    1161    1223 ..    1157    1268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.9e-06
                       HATPase_c_3    7 laelvdNsldAdaen..............vkievnknrgktgeivieDdGkGmseeelkn.alr 55  
                                        l+ lv+N++d   e               v++++ ++r +  +i++eDdG+G++++ +++ a +
  gi|336253945|ref|YP_004597052.1| 1161 LIHLVRNAVDHGVEPpedredaekpregaVEVTATRER-DRVTITVEDDGSGLDPDRIRSeAVE 1223
                                        67799999998777778888888899999*****9998.799***************9985554 PP

>> Serglycin  Serglycin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.7   0.00028      0.63      90     133 ..     363     405 ..     341     418 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00028
                         Serglycin  90 dysgsgsGsGsGsGsgsgsgflteieqeYqpvdendafyynfrp 133
                                       ++++sgs sGs sGsgsgs       +   pv++ da++ +++ 
  gi|336253945|ref|YP_004597052.1| 363 SVADSGSSSGSESGSGSGSAVAD-PGSAEDPVEDADAVFQELKD 405
                                       44566666677777777766544.44444799999988887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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):               8  [number of targets reported over threshold]
# CPU time: 1.24u 0.32s 00:00:01.56 Elapsed: 00:00:00.53
# Mc/sec: 8253.11
//
Query:       gi|336253946|ref|YP_004597053.1|  [L=198]
Description: inhibitor of MCP methylation CheC [Halopiger xanaduensis SH-6]
Scores for 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   49.8   0.1    8.9e-13   47.9   0.0    2.0  2  CheC      CheC-like family
    1.4e-06   28.4   0.1    2.7e-06   27.5   0.1    1.5  1  CheX      Chemotaxis phosphatase CheX


Domain annotation for each model (and alignments):
>> CheC  CheC-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       0.3   2.7e+03      18      27 ..      22      31 ..      20      37 .. 0.78
   2 !   47.9   0.0   9.9e-17   8.9e-13       1      38 []     103     140 ..     103     140 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.3
                                      HHHHHTCCTS CS
                              CheC 18 atalatllnf 27
                                      a+++++l+++
  gi|336253946|ref|YP_004597053.1| 22 ADNMSKLTGQ 31
                                      899**99986 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 9.9e-17
                                       HHHHHHHHHHHHHHHHHHHHHHTCCTS-EEE---EEEE CS
                              CheC   1 melSAlgEigNIlaGsaatalatllnfkidisPPtvvy 38 
                                       m++SA+ E gN++a+++++++a+ l+++idi+ P++vy
  gi|336253946|ref|YP_004597053.1| 103 MARSAVEEMGNMMASGFIDGWADVLGRVIDIAAPQLVY 140
                                       99*********************************997 PP

>> CheX  Chemotaxis phosphatase CheX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1     3e-10   2.7e-06       3      75 ..      60     141 ..      58     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3e-10
                              CheX   3 giiglaGdisGliilsadeelalkias.alg...edeee.ieedvndavgEltNmiaGnak...skl.geevklspP 70 
                                       + + l  + +G+i++ ++e++a+ki++ +l+   +d ++ + +++++av E+ Nm+a ++    +++ g  ++++ P
  gi|336253946|ref|YP_004597053.1|  60 VRVRLLNPPHGHILILFPEASAKKITAiMLDdvvDDMSDvSGKMARSAVEEMGNMMASGFIdgwADVlGRVIDIAAP 136
                                       667788899****************994565243445555678******************8886667999***999 PP

                              CheX  71 lvisg 75 
                                       +++  
  gi|336253946|ref|YP_004597053.1| 137 QLVYA 141
                                       99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1504.31
//
Query:       gi|336253947|ref|YP_004597054.1|  [L=414]
Description: inhibitor of MCP methylation CheC [Halopiger xanaduensis SH-6]
Scores for 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-19   68.8   0.7    4.9e-13   48.8   0.0    2.5  2  CheC      CheC-like family
    1.4e-14   54.0   0.9    8.3e-07   29.1   0.2    2.3  2  CheX      Chemotaxis phosphatase CheX


Domain annotation for each model (and alignments):
>> CheC  CheC-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   2.1e-07    0.0019       1      37 [.     102     138 ..     102     138 .. 0.94
   2 !   48.8   0.0   5.4e-17   4.9e-13       1      37 [.     302     338 ..     302     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.1e-07
                                       HHHHHHHHHHHHHHHHHHHHHHTCCTS-EEE---EEE CS
                              CheC   1 melSAlgEigNIlaGsaatalatllnfkidisPPtvv 37 
                                       m +SA +E+g I+  ++++++a+ l+ +id s+P++v
  gi|336253947|ref|YP_004597054.1| 102 MNRSAATEVGQIMNNGFIDGWADVLETVIDVSTPEFV 138
                                       6789999***************************986 PP

  == domain 2  score: 48.8 bits;  conditional E-value: 5.4e-17
                                       HHHHHHHHHHHHHHHHHHHHHHTCCTS-EEE---EEE CS
                              CheC   1 melSAlgEigNIlaGsaatalatllnfkidisPPtvv 37 
                                       m++SA++E+gNI+a+++++++a+ l+ +id+s+P+++
  gi|336253947|ref|YP_004597054.1| 302 MGRSAITELGNIMASGFLDGWANVLDTTIDHSTPEFI 338
                                       89********************************998 PP

>> CheX  Chemotaxis phosphatase CheX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.2   9.3e-11   8.3e-07       1      77 [.      60     142 ..      60     145 .. 0.91
   2 !   23.4   0.0   5.5e-09   4.9e-05       2      76 ..     256     341 ..     255     363 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 9.3e-11
                              CheX   1 vtgiiglaGdisGliilsadeelalkiasal.gedeee.ieedvndavgEltNmiaGnak...skl.geevklspPl 71 
                                       v + ++l+G+i+G  ++ +++e al+i++ l +e+e +  +e+ ++a+ E+  ++  ++    +++ +  +++s+P+
  gi|336253947|ref|YP_004597054.1|  60 VGVRVELTGAIEGQSVIVFERENALRIVETLvTESEADeFDEMNRSAATEVGQIMNNGFIdgwADVlETVIDVSTPE 136
                                       56789*************************77999888799999****************8886767889******* PP

                              CheX  72 visgke 77 
                                       +++g++
  gi|336253947|ref|YP_004597054.1| 137 FVQGQS 142
                                       ***986 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 5.5e-09
                              CheX   2 tgiiglaGdisGliilsadeelalkiasal...ged....eeeieedvndavgEltNmiaGnak....sklgeevkl 67 
                                        +  ++ G  sG++++ +dee+a +i+ a+   g +    ++  +e+ ++a+ El N++a ++     + l+ +++ 
  gi|336253947|ref|YP_004597054.1| 256 GVAFEFDGVPSGYLLFLFDEESANEIIDAMvptGGSaaggDDGYDEMGRSAITELGNIMASGFLdgwaNVLDTTIDH 332
                                       577899*********************987676433466444489*******************888444499**** PP

                              CheX  68 spPlvisgk 76 
                                       s+P++i++ 
  gi|336253947|ref|YP_004597054.1| 333 STPEFIHDI 341
                                       *****9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3171.39
//
Query:       gi|336253948|ref|YP_004597055.1|  [L=173]
Description: CheD [Halopiger xanaduensis SH-6]
Scores for 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-32  110.9   0.0    3.9e-32  110.6   0.0    1.1  1  CheD      CheD chemotactic sensory transduction


Domain annotation for each model (and alignments):
>> CheD  CheD chemotactic sensory transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   0.0   2.2e-36   3.9e-32       1     109 []      57     161 ..      57     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 2.2e-36
                                       -BS--....SS-TTSCCCBHHHHHHHHHHHHHTTT--GGG-EEEEEE----S.....---SS-HHHHHHHHHHHHHH CS
                              CheD   1 mLPdskeskeksasnpakyadtaielLinellklgakkerleaklaGGAqmfafessksdvlniGerNveavkelLk 77 
                                       mLPd   s+++s+++p+kyadtai++L+++++++ga+   +eak+aGG++mf+f s       +G+rN++a+ke L+
  gi|336253948|ref|YP_004597055.1|  57 MLPDG-DSAANSDRKPGKYADTAIRALLRRMVERGADYTAVEAKIAGGSDMFEFDSF---GDGVGQRNIAAAKEELE 129
                                       9****.7778888*****************************************763...235************** PP

                                       HTT--EEEEEE-SSS-EEEEEETTTTEEEEE- CS
                              CheD  78 eegipivaedvggnygRtvlfdpatgkvlvkk 109
                                       + g+p++aedvgg++gRtv+f pa+g++ vk+
  gi|336253948|ref|YP_004597055.1| 130 KLGVPLIAEDVGGDRGRTVEFTPASGTLRVKT 161
                                       *****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1298.73
//
Query:       gi|336253949|ref|YP_004597056.1|  [L=272]
Description: MCP methyltransferase, CheR-type [Halopiger xanaduensis SH-6]
Scores for 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  161.2   0.0    2.7e-47  160.8   0.0    1.2  1  CheR             CheR methyltransferase, SAM binding domain
    7.3e-11   41.6   3.5    1.2e-10   40.9   1.6    2.3  2  CheR_N           CheR methyltransferase, all-alpha domain
      9e-09   36.0   0.1    3.9e-06   27.5   0.1    2.4  1  Methyltransf_12  Methyltransferase domain
      2e-07   31.6   0.1    0.00091   19.9   0.0    3.0  3  Methyltransf_25  Methyltransferase domain
    4.8e-06   26.4   0.0    0.00023   21.0   0.0    2.2  1  Methyltransf_31  Methyltransferase domain
    7.4e-06   26.5   0.1     0.0041   17.8   0.1    2.7  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.041   13.5   0.0      0.062   12.9   0.0    1.3  1  NodS             Nodulation protein S (NodS)


Domain annotation for each model (and alignments):
>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.8   0.0   1.1e-50   2.7e-47       1     191 [.      69     258 ..      69     262 .. 0.89

  Alignments for each domain:
  == domain 1  score: 160.8 bits;  conditional E-value: 1.1e-50
                                       SS--TTTTCHHHHHHHHCCH.HHHHHHHTSSSEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHH CS
                              CheR   1 neTeffreakhfeelekevlepllakaknekrvriwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvl 77 
                                       n+T ffr+++ ++ +++ +   +l++   +++vriwsa+c++G EpYslAml+++  +  ++ +++il+tDi++ +l
  gi|336253949|ref|YP_004597056.1|  69 NVTGFFRNPDVWAGIRDVLR--TLSAE--NREVRIWSAACADGREPYSLAMLAHDDDQIDES-SISILGTDISEPAL 140
                                       79*************99888..34333..489***********************4444444.9************* PP

                                       HHHHHTEEECCHHTTS-HHH..HHHH..EEEEETTCEEE-HHHHTTEEEEE--TTT-SGGG--EEEEEE-SSGGGC- CS
                              CheR  78 ekAkagvykeeeleglseel..lery..fekseddsykvkkeikelvkFeklnllekksvlgklDvifcrnvliYfd 150
                                       e+A++gvy+e++  ++ ++l  l++y  f ++ed+ y++++++k++v+Fe+++l++  ++++ +D+++crn++iY+d
  gi|336253949|ref|YP_004597056.1| 141 ETAREGVYEESRTVDMADQLsfLDNYseFVEQEDRIYRIDDAVKRTVEFERHDLIN-GDPKSGFDLVVCRNLFIYID 216
                                       ***********998887764225666445699999*********************.99****************** PP

                                       CHHHHHHHHHHHCCEEEEEEEEE-TTB--S.SSCCCCCEEEE CS
                              CheR 151 eetqekvlerfaeklkpgglLllGhsEslk.klkdkfevvks 191
                                       +e ++ +le +a++l+++g+L++G++E+++ +lk  f+v ++
  gi|336253949|ref|YP_004597056.1| 217 NEYKQSMLEVIARSLRQEGYLVIGKAETIPpNLKSAFSVYDA 258
                                       ******************************999999988765 PP

>> CheR_N  CheR methyltransferase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   1.6   4.8e-14   1.2e-10       3      52 ..       6      55 ..       4      56 .. 0.96
   2 ?   -0.9   0.0      0.53   1.4e+03      19      27 ..     217     225 ..     213     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 4.8e-14
                                      HHHHHHHHHHTT-EE--SSTHHHHHTHHHHHHHTTT-SSSHHHHHHTSHS CS
                            CheR_N  3 ferlleliyertGidlsdyKrallkrRlsrRmralglksfeeYldlLrsd 52
                                      f+ ll++++++  +  s+y+ ++l rR+s+Rmr+++ +++++Yl++Lr++
  gi|336253949|ref|YP_004597056.1|  6 FDDLLSFVEHELDFATSHYNDSYLDRRVSSRMRRTQNDTYADYLAFLREN 55
                                      999*********************************************87 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.53
                                       -SSTHHHHH CS
                            CheR_N  19 sdyKrallk 27 
                                       ++yK+++l+
  gi|336253949|ref|YP_004597056.1| 217 NEYKQSMLE 225
                                       68*****97 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   1.5e-09   3.9e-06      25      99 .]     162     237 ..     103     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.5e-09
                   Methyltransf_12  25 gvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl..kdirevldnirklLkpgGrl 99 
                                       ++D  ++++   + ++ ++++     ve+e  dl++ d++s fDlvv+ n++ ++  + ++++l+ i++ L+++G+l
  gi|336253949|ref|YP_004597056.1| 162 FLDNYSEFV-EQEDRIYRIDDAVKRTVEFERHDLINGDPKSGFDLVVCRNLFIYIdnEYKQSMLEVIARSLRQEGYL 237
                                       455555666.666777777777788888888888888888****************99*****************86 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.2   5.6e+03      25      46 ..      40      61 ..      27      76 .. 0.67
   2 !    8.7   0.0    0.0011       2.8      21      45 ..     127     151 ..      99     170 .. 0.67
   3 !   19.9   0.0   3.6e-07   0.00091      28      97 .]     164     235 ..     153     235 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.2
                                      EEEESSHHHHHHHHHHHHHTTT CS
                   Methyltransf_25 25 tgvDiseemleaareraeeegl 46
                                      t  D  +++l+  re+a+e+ +
  gi|336253949|ref|YP_004597056.1| 40 TQNDTYADYLAFLRENADEQTA 61
                                      5557777788888888877655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0011
                                       SSEEEEEESSHHHHHHHHHHHHHTT CS
                   Methyltransf_25  21 kakvtgvDiseemleaareraeeeg 45 
                                       + +++g+Dise +le+are + ee+
  gi|336253949|ref|YP_004597056.1| 127 SISILGTDISEPALETAREGVYEES 151
                                       6899**************9885543 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 3.6e-07
                                       ESSHHHHHHHHHHHHHTTT...TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  28 Diseemleaareraeeegl...nvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                       D  +e++e+  + ++ +++    vef+++d+ + + +++ fDlvv+++ + ++++e  + +l+ iar L+++G
  gi|336253949|ref|YP_004597056.1| 164 DNYSEFVEQEDRIYRIDDAvkrTVEFERHDLINGD-PKSGFDLVVCRNLFIYIDNEYKQSMLEVIARSLRQEG 235
                                       55555555555555444444568999999998876.5569******988*********************998 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   8.9e-08   0.00023       5     113 ..      97     243 ..      93     267 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 8.9e-08
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkae.......vvGiDiseeaielAre..........naqklgldnveFeqgdie 64 
                                       +r+  ++C+ G+  + la ++ ++ +       + G Dise a+e Are          +a+      ++F     e
  gi|336253949|ref|YP_004597056.1|  97 VRIWSAACADGREPYSLAMLAHDDDQidessisILGTDISEPALETAREgvyeesrtvdMAD-----QLSFLDNYSE 168
                                       56666789999999999884444333445556699999999999999998887655444333.....4444443333 PP

                   Methyltransf_31  65 eleklled..........................ekfDlilsnevl..naladpdkileeiervlkpggilliedpr 113
                                         e   ed                          + fDl+++++++   +   +++ le i r l+++g+l+i  + 
  gi|336253949|ref|YP_004597056.1| 169 FVE--QEDriyriddavkrtveferhdlingdpkSGFDLVVCRNLFiyIDNEYKQSMLEVIARSLRQEGYLVIGKAE 243
                                       322..112233344555558888889999999999**********988888889******************98876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.6e-06    0.0041      20      96 .]     129     239 ..     101     239 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                                       EEEEEES-HHHHHHHHHHCCHHT-EEEE..............................TTEECCCT..SS-TT-EEE CS
                   Methyltransf_11  20 rvvgvDlskemlklakekaseeglkvef..............................vvadaekl..pfednsfDl 64 
                                       +++g+D+s+ +l++a+e + ee  +v++                              v+ + ++l    +++ fDl
  gi|336253949|ref|YP_004597056.1| 129 SILGTDISEPALETAREGVYEESRTVDMadqlsfldnysefveqedriyriddavkrtVEFERHDLinGDPKSGFDL 205
                                       56677777777777766666655533334444445666666666666666666655443333333322346678*** PP

                                       EEEES-CCC-..CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  65 vvssevlhhv..edpekalkeiaRvLkpgGllvi 96 
                                       vv+++ + ++  e  ++ l+ iaR L+++G+lvi
  gi|336253949|ref|YP_004597056.1| 206 VVCRNLFIYIdnEYKQSMLEVIARSLRQEGYLVI 239
                                       **********98889999999***********97 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.4e-05     0.062      90     148 ..     186     243 ..     131     247 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                              NodS  90 hiswivsdvqqfstdekfdlivvaevlyyiedvaelraavrnlvsllapdgqlvfGsar 148
                                        + +   d+ + + +  fdl+v+ +++ yi++  + ++ ++ + + l+ +g+lv G a 
  gi|336253949|ref|YP_004597056.1| 186 TVEFERHDLINGDPKSGFDLVVCRNLFIYIDNEYK-QSMLEVIARSLRQEGYLVIGKAE 243
                                       56777889999999****************87655.7899****************885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); 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:                         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 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2089.92
//
Query:       gi|336253950|ref|YP_004597057.1|  [L=423]
Description: hypothetical protein Halxa_2560 [Halopiger xanaduensis SH-6]
Scores for 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  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.36
# Mc/sec: 3486.68
//
Query:       gi|336253951|ref|YP_004597058.1|  [L=259]
Description: hypothetical protein Halxa_2561 [Halopiger xanaduensis SH-6]
Scores for 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   14.7   0.0      0.019   14.0   0.0    1.2  1  TMEM171   Transmembrane protein family 171
      0.023   14.5   0.1      0.048   13.5   0.1    1.5  1  DUF2976   Protein of unknown function (DUF2976)


Domain annotation for each model (and alignments):
>> TMEM171  Transmembrane protein family 171
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.1e-06     0.019      11      47 ..      16      51 ..       8      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-06
                           TMEM171 11 eerdrqvsklifflfvfGavllcvGvllsifgfqaCq 47
                                      +++dr vs li f+ vfG +l +v  +ls+ gfqa +
  gi|336253951|ref|YP_004597058.1| 16 QRDDRAVSELIAFILVFGIILSSVA-ILSVTGFQAME 51
                                      6789**************9988886.57******975 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.3e-06     0.048      27      61 ..      28      63 ..      23      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.3e-06
                           DUF2976 27 gvillgLvlaavaflaVak.aalkkfneisegkaew 61
                                       +++ g++l++va+l V   +a++ ++e++++++  
  gi|336253951|ref|YP_004597058.1| 28 FILVFGIILSSVAILSVTGfQAMEDYQEVEQERNAD 63
                                      57899************86489*******9999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1954.72
//
Query:       gi|336253952|ref|YP_004597059.1|  [L=170]
Description: hypothetical protein Halxa_2562 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.22   11.1   1.2       0.45   10.1   0.1    1.9  2  EF-hand_5  EF hand


Domain annotation for each model (and alignments):
>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.11   1.9e+03       8      12 ..     142     146 ..     139     147 .. 0.52
   2 ?   10.1   0.1   2.5e-05      0.45      10      20 ..     157     167 ..     157     168 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.11
                                       H-SS- CS
                         EF-hand_5   8 iDlNg 12 
                                       +Dl+g
  gi|336253952|ref|YP_004597059.1| 142 ADLDG 146
                                       45555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 2.5e-05
                                       SS-SSCE-HHH CS
                         EF-hand_5  10 lNgDGkIskeE 20 
                                       ++gDG+I++eE
  gi|336253952|ref|YP_004597059.1| 157 ADGDGTITIEE 167
                                       69********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1349.33
//
Query:       gi|336253953|ref|YP_004597060.1|  [L=144]
Description: hypothetical protein Halxa_2563 [Halopiger xanaduensis SH-6]
Scores for 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:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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: 00:00:00.40
# Mc/sec: 1091.66
//
Query:       gi|336253954|ref|YP_004597061.1|  [L=227]
Description: hypothetical protein Halxa_2564 [Halopiger xanaduensis SH-6]
Scores for 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   13.6   0.0       0.03   13.3   0.0    1.1  1  Nramp     Natural resistance-associated macrophage protein
      0.026   14.9   0.1      0.051   13.9   0.1    1.4  1  PXT1      Peroxisomal testis-specific protein 1
      0.039   13.6   0.0       0.11   12.1   0.0    1.8  1  DUF1918   Domain of unknown function (DUF1918)


Domain annotation for each model (and alignments):
>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     5e-06      0.03     114     164 ..      21      73 ..      13      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-06
                             Nramp 114 rklEaliialvlvialsFiaelflvkpdwgevlkglvvPslpg..keslllav 164
                                        +lE +i a+++++a+ F+++ +++ p +g ++  +v  +l++  +++l++a+
  gi|336253954|ref|YP_004597061.1|  21 YTLEGFIGAMIVLMAVLFALQSAVITPTTGGLADRTVQEQLQQetQDALVVAA 73 
                                       579**********************************9999998666666665 PP

>> PXT1  Peroxisomal testis-specific protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   8.5e-06     0.051      11      27 ..      53      69 ..      48      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.5e-06
                              PXT1 11 nhRvvqEdlqqdgrdal 27
                                       +R+vqE+lqq+ +dal
  gi|336253954|ref|YP_004597061.1| 53 ADRTVQEQLQQETQDAL 69
                                      68*************98 PP

>> DUF1918  Domain of unknown function (DUF1918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.9e-05      0.11      14      55 ..      59     100 ..      54     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
                                       TTTS--EEEEEEEE-S-SSS-S-EEEEETTTTEEEEE---SS CS
                           DUF1918  14 rtvgepereGeiveVrgedGaPPYlVRweddgheslvfPGpD 55 
                                       ++++++ +++ +v+  +e G+  Y+ R+ ++++++++f G+D
  gi|336253954|ref|YP_004597061.1|  59 EQLQQETQDALVVAAANETGNLSYTLRYWEEDDDEIIFNGTD 100
                                       45789999*******************999*********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 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:                        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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1756.09
//
Query:       gi|336253955|ref|YP_004597062.1|  [L=162]
Description: hypothetical protein Halxa_2565 [Halopiger xanaduensis SH-6]
Scores for 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   11.4   0.0       0.33   10.7   0.0    1.3  1  DUF1923   Domain of unknown function (DUF1923)


Domain annotation for each model (and alignments):
>> DUF1923  Domain of unknown function (DUF1923)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   1.9e-05      0.33      22      50 ..      58      86 ..      52      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.9e-05
                           DUF1923 22 kiviaanvGkepkeitGGrvwnGkwsdee 50
                                      ++v     G  p ei G  + + kwsd +
  gi|336253955|ref|YP_004597062.1| 58 RVVQNLSTGDSPNEIDGTPIVDDKWSDAQ 86
                                      567777889******************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1286.78
//
Query:       gi|336253956|ref|YP_004597063.1|  [L=690]
Description: type II secretion system F domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-30  103.1  10.5    2.3e-16   59.9   0.5    3.1  3  T2SSF         Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
      0.087   13.0   0.0        0.2   11.8   0.0    1.6  1  MnmE_helical  MnmE helical domain
        0.3   11.4   1.5        1.9    8.8   0.2    2.5  2  Orf78         Orf78 (ac78)
       0.61    9.9   0.0       0.61    9.9   0.0    3.0  3  PMP1_2        ATPase proteolipid family
       0.87    9.9   3.7       0.66   10.3   0.4    2.3  2  DUF2524       Protein of unknown function (DUF2524)
        1.6    8.6   3.8        7.7    6.4   0.2    2.3  2  EMP24_GP25L   emp24/gp25L/p24 family/GOLD


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 !   49.2   0.4   1.6e-16   4.6e-13       5     124 ..     165     290 ..     162     291 .. 0.93
   2 !   59.9   0.5   7.8e-20   2.3e-16       2     123 ..     474     598 ..     474     599 .. 0.95
   3 ?   -2.9   0.2       2.1   6.4e+03      97     119 ..     667     688 ..     663     690 .] 0.53

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.6e-16
                                       HHHHHHTT--HHHHHHHHHHHHS.SHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT CS
                             T2SSF   5 latllsaGvplveaLellaeeae.ngplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageegg 75 
                                       ++ l+ +G++ +e++e++a+ ++ +g++a+e+++i+++ ++   + ++a++    +tps+e++++++ +++++ +gg
  gi|336253956|ref|YP_004597063.1| 165 MYALSVGGLNQLEIIEAMAQADDtYGEVAKEFQSIVKETEYFDvDYRTAIRkqalETPSDELSQFLTDMLSIVNSGG 241
                                       7888999************99999******************964456666777799******************** PP

                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  76 nLaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                       +++ +Le+  e +++ ++++++l +++le   +++++l ++++ll+i++
  gi|336253956|ref|YP_004597063.1| 242 DMENFLEDKKEKHMRTAKQEQELTLETLELFGEMYMTLSLFPLLLIIIM 290
                                       **********************************************997 PP

  == domain 2  score: 59.9 bits;  conditional E-value: 7.8e-20
                                       HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHHH CS
                             T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqlirageeg 74 
                                       lr la++  +G++l+e+L+++++++ +g+la+e++ + +++++G+sl+eal     ++  + ++++ + +++a e++
  gi|336253956|ref|YP_004597063.1| 474 LRKLASANDTGLTLLESLKSVSDTT-SGKLAREFEMMHTKVNYGMSLKEALIefnnKYHIPRLARTTRLITEAQEAS 549
                                       689**********************.**************************7776444479*************** PP

                                       T-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  75 gnLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                        ++++vL+ +a+  e+  +++r++++++   ++++v++++ +l+++ail
  gi|336253956|ref|YP_004597063.1| 550 NQITDVLRTAARASENHDDIERDRKSRTRMQVVIIVMTFMTVLAVIAIL 598
                                       *********************************************9986 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.1
                                       HHHHHHHTTXXXXXXXXXXXXXX CS
                             T2SSF  97 kllaallepllllvvallvllil 119
                                       ++l+ l + ++l+ +al v+++l
  gi|336253956|ref|YP_004597063.1| 667 DILSGLKYAVILATIAL-VGWML 688
                                       55556665555555554.44444 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.8e-05       0.2      19      93 ..     491     567 ..     488     643 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.8e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      MnmE_helical  19 akaalrqleGelskkikelrekllellaeleaaiDFpe.edleelsee.elaekleelkeelekllatakrgellre 93 
                                       +k+     +G+l+++++ +  k+   +++ ea i+F    +++ l +  +l ++ +e+ +++ ++l+ta r +  ++
  gi|336253956|ref|YP_004597063.1| 491 LKSVSDTTSGKLAREFEMMHTKVNYGMSLKEALIEFNNkYHIPRLARTtRLITEAQEASNQITDVLRTAARASENHD 567
                                       677778899***************************997789999888799****************9998765555 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.23     7e+02      44      83 ..     259     292 ..     232     304 .. 0.42
   2 ?    8.8   0.2   0.00065       1.9      29      80 ..     546     598 ..     509     603 .. 0.51

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.23
                             Orf78  44 aeknditekesnaaekaqalnillisllavvcvlvllyvi 83 
                                       ++++++t       e+ +    + ++l  +  +l++++v+
  gi|336253956|ref|YP_004597063.1| 259 KQEQELTL------ETLELFGEMYMTLSLFPLLLIIIMVV 292
                                       11222222......12222222222222222222222222 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00065
                             Orf78  29 ddndkaenkkekksaaeknditekesn.aaekaqalnillisllavvcvlvll 80 
                                       ++++++ ++  +++a+++++ +  e++ +++++ +  i+++++++v++v+ +l
  gi|336253956|ref|YP_004597063.1| 546 QEASNQITDVLRTAARASENHDDIERDrKSRTRMQVVIIVMTFMTVLAVIAIL 598
                                       33333333322222222222222222212333333455666666666666665 PP

>> PMP1_2  ATPase proteolipid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00021      0.61      12      38 ..     438     463 ..     436     465 .. 0.90
   2 ?   -2.2   2.5       1.2   3.6e+03      11      27 ..     583     600 ..     580     603 .. 0.68
   3 ?   -3.2   0.4       2.5   7.4e+03      16      29 ..     669     682 ..     668     687 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00021
                            PMP1_2  12 LvFvLvGLACvAivltilYRkWqeRqR 38 
                                        v+v v L C+Ai l i +R W  R R
  gi|336253956|ref|YP_004597063.1| 438 FVYVYVPLYCMAIPLSI-FREWNVRYR 463
                                       599**********9986.8****9988 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                            PMP1_2  11 iLvFv.LvGLACvAivlt 27 
                                       i+v   +  LA +Ai+ t
  gi|336253956|ref|YP_004597063.1| 583 IIVMTfMTVLAVIAILKT 600
                                       4444314459*****988 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.5
                            PMP1_2  16 LvGLACvAivltil 29 
                                       L GL    i+ ti 
  gi|336253956|ref|YP_004597063.1| 669 LSGLKYAVILATIA 682
                                       55665555666654 PP

>> DUF2524  Protein of unknown function (DUF2524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.4   0.00022      0.66       7      56 ..     178     229 ..     174     234 .. 0.87
   2 ?   -0.8   0.2      0.67     2e+03      48      74 ..     547     575 ..     539     585 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                           DUF2524   7 veellqkceqaieeaeeqfeeakrqehyndeeYteAq..lkLEeavneLekl 56 
                                       + e++ ++++++ e+ ++f++  +  +y d +Y  A   + LE  + eL+++
  gi|336253956|ref|YP_004597063.1| 178 IIEAMAQADDTYGEVAKEFQSIVKETEYFDVDYRTAIrkQALETPSDELSQF 229
                                       55899*******************************6226799999999886 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.67
                           DUF2524  48 eavneLeklaksan..dqQreqLeRarlq 74 
                                       ea+n++++++++a   ++  + +eR r  
  gi|336253956|ref|YP_004597063.1| 547 EASNQITDVLRTAAraSENHDDIERDRKS 575
                                       56666666666553123555555555544 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 ?    6.4   0.2    0.0026       7.7     130     174 ..     251     295 ..     189     296 .. 0.72
   2 ?    3.0   0.5      0.03        89     124     173 ..     550     599 ..     491     606 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0026
                       EMP24_GP25L 130 ikreqkylrereerlrdtnestnsrvvwwsilqllvlvlvavlqv 174
                                        +++++  ++ +e   +t+e   ++++  s++ ll+++++ v+q+
  gi|336253956|ref|YP_004597063.1| 251 KEKHMRTAKQEQELTLETLELFGEMYMTLSLFPLLLIIIMVVMQM 295
                                       35678888888889999***************************8 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.03
                       EMP24_GP25L 124 eekldsikreqkylrereerlrdtnestnsrvvwwsilqllvlvlvavlq 173
                                       ++ +d +++  ++ +++ +  rd    t + vv+  + ++ vl+++a+l 
  gi|336253956|ref|YP_004597063.1| 550 NQITDVLRTAARASENHDDIERDRKSRTRMQVVIIVMTFMTVLAVIAILK 599
                                       44455566667788888999999***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (690 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.43
# Mc/sec: 4829.20
//
Query:       gi|336253957|ref|YP_004597064.1|  [L=1394]
Description: type II secretion system protein E [Halopiger xanaduensis SH-6]
Scores for 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-43  146.4   0.0    1.3e-42  145.7   0.0    1.2  1  T2SSE     Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.022   14.5   0.1    1.5  1  AAA_29    P-loop containing region of AAA domain
      0.014   15.4   0.5      0.038   14.0   0.5    1.7  1  GerPC     Spore germination protein GerPC


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 !  145.7   0.0   2.2e-46   1.3e-42      11     245 ..     421     661 ..     415     684 .. 0.92

  Alignments for each domain:
  == domain 1  score: 145.7 bits;  conditional E-value: 2.2e-46
                             T2SSE  11 dekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllP 86 
                                       d +v di v  +++ v+v    d  ++ +     +++l  ++ ++a+ +++ is++ p +da+lp +g r ++ l  
  gi|336253957|ref|YP_004597064.1| 421 DINVEDISVDGYNSpVFV-YHSDYEQIITNVYHGEDELDDFVVKLAQRSGKGISKRLPQVDATLP-DGSRAQLTLGQ 495
                                       55899*********9***.888887888888888999999999**********************.99999999988 PP

                             T2SSE  87 vvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderiv 161
                                        v +  ++++iR+ +   +t  dl+  ++++ +  ++l   ++++++++++GgT sGKtt+l+a+  +i++s  +iv
  gi|336253957|ref|YP_004597064.1| 496 EVSDhgTNYTIRQFKDVPFTPIDLINWNTFSLDEMAFLWLCIENHKSLIFAGGTASGKTTSLNAVSLFIPSS-AKIV 571
                                       77776799****************************************************************.**** PP

                             T2SSE 162 tvEDpvEiqleganqvqlnak.......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTl 231
                                        +ED++E++l + n ++ +++       +++v+  dll+aaLR+rPD i++GEiR++e  ++ + ++TGH    +T 
  gi|336253957|ref|YP_004597064.1| 572 SIEDTREVELPQRNWIASVTRpsfsddeQGDVDEFDLLEAALRQRPDYIVMGEIRGEEGRTLFQVMSTGHTT-YTTF 647
                                       *******************999*****99*******************************************.**** PP

                             T2SSE 232 HansaagalerLeq 245
                                       Ha+s+ ++l+r  +
  gi|336253957|ref|YP_004597064.1| 648 HADSVDEVLKRFTT 661
                                       **********9764 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 ?   14.5   0.1   3.7e-06     0.022       4      46 ..     517     563 ..     514     571 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.7e-06
                            AAA_29   4 lqlvNWgtfdghtiei.....dlkgatlltGpsGsGKSTllDAiqalL 46 
                                       ++l+NW tf+  ++ +     + + + +++G + sGK+T l A++  +
  gi|336253957|ref|YP_004597064.1| 517 IDLINWNTFSLDEMAFlwlciENHKSLIFAGGTASGKTTSLNAVSL-F 563
                                       89*******98665432222155558999************99874.4 PP

>> GerPC  Spore germination protein GerPC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   6.4e-06     0.038      79     136 ..     287     344 ..     269     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.4e-06
                             GerPC  79 lfqeiqeeveayLeeeapelleelekqyeveldeeyrefileDikkQldsRikyYlkq 136
                                        ++ei++e++a+L+ ++ + ++  ++ ++ + de+ r++++eD  + l +R + Y k 
  gi|336253957|ref|YP_004597064.1| 287 YLNEIEDELQAFLSGKLRTAIKYSDDGIKEKADENGRRIVIEDETRRLLKRYDLYEKT 344
                                       5689*************************************************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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):               3  [number of targets reported over threshold]
# CPU time: 1.05u 0.31s 00:00:01.36 Elapsed: 00:00:00.48
# Mc/sec: 8680.63
//
Query:       gi|336253958|ref|YP_004597065.1|  [L=100]
Description: twin-arginine translocation protein, TatA/E family subunit [Halopiger xanaduensis SH-6]
Scores for 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-14   51.4   2.4    5.6e-14   51.2   2.4    1.3  1  MttA_Hcf106  mttA/Hcf106 family
  ------ inclusion threshold ------
      0.098   12.6   0.7       0.12   12.4   0.7    1.2  1  GP24_25      Tail assembly gene products 24 & 25


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   2.4   6.2e-18   5.6e-14       2      47 ..      15      60 ..      14      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 6.2e-18
                                      -HHHHHHHHHHHHHHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH-- CS
                       MttA_Hcf106  2 gapelliIlvValllFGpkkLPEvaraLGktLreFkkavkeleeen 47
                                      g pelliIl++a+llFG++k+P +ar+ G+++ eF+k     e+e 
  gi|336253958|ref|YP_004597065.1| 15 GGPELLIILFIAILLFGANKIPKLARSTGEAMGEFQKGREKVETEL 60
                                      88**********************************9887777773 PP

>> GP24_25  Tail assembly gene products 24 & 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.7   1.3e-05      0.12      39      71 ..      51      83 ..      35      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                           GP24_25 39 LgkkareavvellkefeeiaeleeddedeLvde 71
                                       g++  e+  e ++e  +  +l+edd+d++vd 
  gi|336253958|ref|YP_004597065.1| 51 KGREKVETELEEMRETGDFDDLDEDDNDDFVDT 83
                                      35566666666666777788999******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 763.42
//
Query:       gi|336253959|ref|YP_004597066.1|  [L=159]
Description: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen [Halopiger xanaduensis SH-6]
Scores for 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-31  107.2   0.0      6e-31  106.9   0.0    1.0  1  AhpC-TSA  AhpC/TSA family
    2.7e-21   75.8   0.0    3.2e-21   75.6   0.0    1.0  1  Redoxin   Redoxin
     0.0012   18.4   0.0     0.0017   18.0   0.0    1.1  1  DUF899    Bacterial protein of unknown function (DUF899)


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 !  106.9   0.0     1e-34     6e-31       2     123 ..       5     135 ..       4     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 1e-34
                                       TSB----EEE..STTCEEEECHHH.TT.SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHH CS
                          AhpC-TSA   2 gdkapdfelk..nadgetvslsdy.kg.kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshk 74 
                                       gd apdf+++  n+d e+++ls+  ++  p+vl f+p+ ++ vCt+e++ +++++ +f +++++v+g+s d+p++++
  gi|336253959|ref|YP_004597066.1|   5 GDSAPDFTAPlaNGDIESFTLSERlEDdAPIVLAFFPGSFTGVCTDEMCTFQDRLANFNDLDATVYGISRDTPFTLN 81 
                                       89********999999*****9987545************************************************* PP

                                       HHHHH-H.SSEEEE-TTSHHHHHTT-EETT.....TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  75 kfiekeslnfpllsDeegkvakaygvlkee.....kglalratfvidkegkiry 123
                                       +f ++++l+f l+sD +++++++y++  +      +g+a r++fv+d +g i+y
  gi|336253959|ref|YP_004597066.1|  82 EFRDQNGLEFGLISDLNKEIIDEYDLEMDFddlgvYGVAKRSVFVVDGDGEITY 135
                                       **************************966599********************99 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.0   5.4e-25   3.2e-21       2     145 ..       4     150 ..       3     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 5.4e-25
                                       TTSBB---ECCEETTCEEEEEHHH..HTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHH CS
                           Redoxin   2 agdkaPdftlplaatdgnsvslse..fkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndaf 75 
                                       +gd+aPdft pla+ d +s++lse    + ++v+ f+pg f+++C+ e++ + + la++ ++ + +v +++ d+   
  gi|336253959|ref|YP_004597066.1|   4 SGDSAPDFTAPLANGDIESFTLSErlEDDAPIVLAFFPGSFTGVCTDEMCtFQDRLANF-NDLDATVYGISRDTPFT 79 
                                       79***********************777888*******************777777888.99999998877777777 PP

                                       HHHHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG..EEE-EEEEEEETTEEEEEEESSSCHTSTTSHHH CS
                           Redoxin  76 vkefwgkeglkfpvlsDgsaaftkalGlrleedaseg..lrtpryavidedgkvvylevepepeteesnaea 145
                                        +ef +++gl f ++sD ++++  +++l+++ d      ++ ++++v+d dg ++y  v ++p + e+++++
  gi|336253959|ref|YP_004597066.1|  80 LNEFRDQNGLEFGLISDLNKEIIDEYDLEMDFDDLGVygVAKRSVFVVDGDGEITYAWVSDDP-GVEPDYDE 150
                                       ******************************999777799*********************999.44777776 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.8e-07    0.0017      88     183 ..      48     145 ..      43     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.8e-07
                            DUF899  88 CslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsleeeq.aseelpglsv 163
                                       C+  +  ++  la+++  d t+  +sr +   l++++++ G ++ ++s+ +++   ++  +++ ++     +   sv
  gi|336253959|ref|YP_004597066.1|  48 CTDEMCTFQDRLANFNDLDATVYGISRDTPFTLNEFRDQNGLEFGLISDLNKEIIDEYDLEMDFDDlGVYGVAKRSV 124
                                       8888889999999***************************************99766666665444256677888** PP

                            DUF899 164 flrdd.grvfhtYstyaRgle 183
                                       f+ d+ g++   +++++ g+e
  gi|336253959|ref|YP_004597066.1| 125 FVVDGdGEITYAWVSDDPGVE 145
                                       ****999*******9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); 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:                         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 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1221.01
//
Query:       gi|336253960|ref|YP_004597067.1|  [L=270]
Description: metal dependent phosphohydrolase [Halopiger xanaduensis SH-6]
Scores for 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   3.2    1.8e-08   34.7   3.2    1.4  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 !   34.7   3.2   9.9e-13   1.8e-08      14     121 ..      90     181 ..      62     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 9.9e-13
                                       HHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH.......HHHHHH CS
                                HD  14 rlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld.......ledvak 83 
                                       + +  +  e+++ ++ laa lHD+G+++++d         e+ ++ +  +a il +v+  + +d         +v++
  gi|336253960|ref|YP_004597067.1|  90 QQGLAE--EDESVIIALAATLHDVGHVVHRD---------EHVYYSIPLAADILDRVLPKF-YDlaetvrvKGEVLH 154
                                       334333..5899999*************999.........466666777777777764444.337999999889*** PP

                                       HHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  84 lirehheswegkkrprglaerqlslearivklaDrlaa 121
                                       +i+ hh  +            +l+ ea ++++aD+l++
  gi|336253960|ref|YP_004597067.1| 155 AILCHHTAET-----------PLTTEAGVIRVADALDM 181
                                       *********9...........***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2050.38
//
Query:       gi|336253961|ref|YP_004597068.1|  [L=74]
Description: hypothetical protein Halxa_2571 [Halopiger xanaduensis SH-6]
Scores for 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-06   25.9   0.1    7.7e-06   25.7   0.1    1.1  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.004   17.0   0.1     0.0051   16.7   0.1    1.2  1  MarR_2           MarR family
     0.0086   15.9   0.2      0.014   15.2   0.2    1.3  1  HTH_IclR         IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.017   15.0   0.0    1.2  1  MarR             MarR family
      0.022   15.1   0.0      0.028   14.7   0.0    1.1  1  Rrf2             Transcriptional regulator
      0.033   13.8   0.0      0.033   13.7   0.0    1.0  1  HTH_42           Winged helix DNA-binding domain
       0.12   12.4   0.1       0.36   10.8   0.1    1.7  1  HTH_36           Helix-turn-helix domain
       0.14   12.6   0.0       0.16   12.3   0.0    1.1  1  Penicillinase_R  Penicillinase repressor


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 !   25.7   0.1   3.4e-09   7.7e-06      13      60 ..      25      72 ..      19      74 .] 0.94

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3.4e-09
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                      vYl+L + g+atade+ ++l+v +s+v ++   L ++G  er+ gr+ 
  gi|336253961|ref|YP_004597068.1| 25 VYLYLEAFGSATADELRSALDVNKSTVLSITGTLRERGHLERRNGRYE 72
                                      9******************************************99976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   2.3e-06    0.0051      17      56 ..      32      69 ..      17      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.3e-06
                                      TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                       +    t+ el  +l++ ks+v  i   L ++G++err g
  gi|336253961|ref|YP_004597068.1| 32 FG--SATADELRSALDVNKSTVLSITGTLRERGHLERRNG 69
                                      33..47*******************************955 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 !   15.2   0.2   6.1e-06     0.014       9      50 ..      29      66 ..      29      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.1e-06
                                      HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      L+a+++a+ +    el  +++++kStv  ++ tL e+G +e+
  gi|336253961|ref|YP_004597068.1| 29 LEAFGSATAD----ELRSALDVNKSTVLSITGTLRERGHLER 66
                                      5666666666....9999********************9998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   7.8e-06     0.017      12      50 ..      29      67 ..      23      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.8e-06
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      l+  g+++  eL ++l v+kstv  ++ +L ++G +eR+
  gi|336253961|ref|YP_004597068.1| 29 LEAFGSATADELRSALDVNKSTVLSITGTLRERGHLERR 67
                                      5667999******************************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.3e-05     0.028      14      61 ..      24      70 ..      21      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                      HHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2 14 llyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                      l+yL +e+ ++ ++++e+ +  ++++s +  i+ +Lr+ g ++ + G+
  gi|336253961|ref|YP_004597068.1| 24 LVYLYLEAFGS-ATADELRSALDVNKSTVLSITGTLRERGHLERRNGR 70
                                      67888888876.9******************************99997 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 ?   13.7   0.0   1.5e-05     0.033     165     214 ..      17      66 ..       3      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                            HTH_42 165 eaealreLvrrylrayGpatvadlaawsgltkarlraalaelvaegelve 214
                                        a  +++Lv  yl+a+G at+++l+  + + k+ +   ++ l+++g l++
  gi|336253961|ref|YP_004597068.1|  17 LASPRAKLVYLYLEAFGSATADELRSALDVNKSTVLSITGTLRERGHLER 66 
                                       4556899***********************************99999986 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00016      0.36       4      55 .]      19      64 ..      19      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                            HTH_36  4 spsaklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                      sp akl++++l +f        ++ + l ++l ++k+Tv ++   L++ G +
  gi|336253961|ref|YP_004597068.1| 19 SPRAKLVYLYLEAFG------SATADELRSALDVNKSTVLSITGTLRERGHL 64
                                      789***********9......35679****************9999999975 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.1e-05      0.16      13      55 ..      30      68 ..      19      72 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                                      HHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEE CS
                   Penicillinase_R 13 wekgeatvkevveeleeekelaysTVktllrrLvkKgllsrek 55
                                       + g+at++e++++     ++++sTV ++ + L ++g+l+r++
  gi|336253961|ref|YP_004597068.1| 30 EAFGSATADELRSA----LDVNKSTVLSITGTLRERGHLERRN 68
                                      55555555555555....5566*****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 581.91
//
Query:       gi|336253962|ref|YP_004597069.1|  [L=65]
Description: XapX domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-06   25.7   1.8    9.7e-06   25.5   1.8    1.1  1  DUF1427   Protein of unknown function (DUF1427)


Domain annotation for each model (and alignments):
>> DUF1427  Protein of unknown function (DUF1427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   1.8   5.4e-10   9.7e-06       3      45 ..       6      49 ..       4      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5.4e-10
                           DUF1427  3 YllslgaGllvGviYsllnvrsPaPPvv.aLvGLlGiLvGeqvv 45
                                       +l+l aGl+ G ++  lnv  PaPP +  ++G++Gi +G +v+
  gi|336253962|ref|YP_004597069.1|  6 TVLALLAGLFTGALFRFLNVPIPAPPELpGIMGIVGIFLGYRVI 49
                                      6899**********************874699********9987 PP



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:                      198  (0.0110436); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 504.97
//
Query:       gi|336253963|ref|YP_004597070.1|  [L=61]
Description: hypothetical protein Halxa_2573 [Halopiger xanaduensis SH-6]
Scores for 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   13.0   0.7       0.12   12.8   0.7    1.0  1  DUF5313   Family of unknown function (DUF5313)


Domain annotation for each model (and alignments):
>> DUF5313  Family of unknown function (DUF5313)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   6.6e-06      0.12      41      92 ..       4      57 ..       1      59 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.6e-06
                           DUF5313 41 raavplvlilavllLlpgslyvrle..mtllillvavlyslalnkesrrhrlak 92
                                       +++++ l+la+llL  g ly      ++l+i l ++ ++++l   +   rl++
  gi|336253963|ref|YP_004597070.1|  4 ERFIQVNLVLAPLLLGAGYLYYESLpvIVLPIGLSYLCFVIVLGFAWGMSRLSM 57
                                      679******************987533889************999999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 471.49
//
Query:       gi|336253964|ref|YP_004597071.1|  [L=611]
Description: succinate dehydrogenase or fumarate reductase, flavoprotein subunit [Halopiger xanaduensis SH-6]
Scores for complete 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-121  406.5   8.3   2.3e-121  405.8   8.3    1.3  1  FAD_binding_2   FAD binding domain
    2.8e-37  127.6   0.2    4.6e-37  126.9   0.2    1.4  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    7.5e-09   35.2   5.4     0.0021   17.4   3.0    2.8  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00083   18.2   0.4    0.00083   18.2   0.4    2.0  2  HI0933_like     HI0933-like protein
     0.0011   18.4   4.1     0.0011   18.4   4.1    2.0  3  FAD_oxidored    FAD dependent oxidoreductase
     0.0015   17.7   4.4     0.0029   16.8   4.4    1.5  1  GIDA            Glucose inhibited division protein A
     0.0025   17.1   1.1     0.0061   15.9   1.1    1.6  1  FAD_binding_3   FAD binding domain
     0.0049   16.5   8.7      0.033   13.8   8.0    2.4  1  DAO             FAD dependent oxidoreductase
     0.0074   15.6   1.9      0.071   12.3   0.4    2.5  2  Thi4            Thi4 family
  ------ inclusion threshold ------
       0.01   15.1   1.6      0.017   14.4   0.5    1.9  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.059   12.7   1.3       0.13   11.5   1.3    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.8   8.3  1.4e-124  2.3e-121       1     417 []       5     387 ..       5     387 .. 0.98

  Alignments for each domain:
  == domain 1  score: 405.8 bits;  conditional E-value: 1.4e-124
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldela 77 
                                       DviV+G+G+AGL+AA++a+eaG+++a+v+k ++++++t +++Ggi+a+l   q    ++d++elh++dt+k++d+l+
  gi|336253964|ref|YP_004597071.1|   5 DVIVVGAGGAGLRAAIAAHEAGADTAIVSKLHPVRSHTGAAEGGINAAL---Q----EGDDWELHAYDTMKGSDYLG 74 
                                       9************************************************...4....5699**************** PP

                                       -HHHHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTC CS
                     FAD_binding_2  78 dqplveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarka 154
                                       d+p+ve+++++ape+   Le++g+pfsr+edg+v +r++Ggls + rt + a+++      tgh+ll++++e++ k+
  gi|336253964|ref|YP_004597071.1|  75 DAPAVETLAKNAPEETMNLEHWGMPFSREEDGRVSQRPFGGLSYP-RTTY-AGAE------TGHHLLHTMYEQVVKR 143
                                       *********************************************.****.9998......**************** PP

                                       TEEEEESEEEEEEEECTT......EEEEEEEEETTTTCEEEEEES.EEEE-----GG..........GSSSBSSGTT CS
                     FAD_binding_2 155 gvdfqerteadeLivedg......rvtGavvenpesgrevrirak.avvlatgGfgrallkellgaaaeaettnapa 224
                                       g+++++++++ +L+++d+      +++G+v  + +sg+++ ++a+ +vvlatgG g+          a+++ttna+ 
  gi|336253964|ref|YP_004597071.1| 144 GIQVYDEWYVMNLVTTDEddpkdrECHGVVGYDVQSGTIEGFKANnGVVLATGGPGQ----------AFDHTTNAVS 210
                                       ***************866668888*********************************..........********** PP

                                       -S-HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH.........GGGS-H CS
                     FAD_binding_2 225 vtGdglalalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm.........nelasr 292
                                       +tGdg+a+a+raga+l+d  me++qfhPtsl+    ++g+Li+e++rgeGgil++++G+rFm         +elasr
  gi|336253964|ref|YP_004597071.1| 211 CTGDGHAMAYRAGAPLED--MEFIQFHPTSLP----STGVLISEGVRGEGGILYNSEGERFMfeygyannsGELASR 281
                                       ******************..************....***************************************** PP

                                       HHHHHHHH.HHHHTTTS..CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEE CS
                     FAD_binding_2 293 dvvsrailekeiaeggs..eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvp 367
                                       dvv+ra l +e+ eg++  +++v ld++h l+++ +  +le+i + a+++++      +d   +p+p       v+p
  gi|336253964|ref|YP_004597071.1| 282 DVVARAEL-TEVGEGRGieDEYVHLDMRH-LGEDRIMDRLENILHLAEDFEG------VDGLVEPMP-------VKP 343
                                       ********.999999999999********.**********************......*********.......*** PP

                                       EEEEES-EEEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHHH CS
                     FAD_binding_2 368 aqhytmgGvetdengrvldadgqpipGLYAaGevaaggvhganrlgGnsl 417
                                       +qhy mgG+e+deng++       ++GLYAaGe+a+++vhg nrlgGn l
  gi|336253964|ref|YP_004597071.1| 344 GQHYAMGGIEVDENGQT------CVNGLYAAGECACVSVHGGNRLGGNAL 387
                                       *****************......*************************87 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.9   0.2   2.8e-40   4.6e-37       1     128 []     482     611 .]     482     611 .] 0.96

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 2.8e-40
                                       .HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S- CS
                    Succ_DH_flav_C   1 rkeLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkES 77 
                                       r +L+++m+++v+vfRteeg k+alk ++e+re+++nv v+d s+++N++l +++e +nl+++Ae+ia +Al R+E 
  gi|336253964|ref|YP_004597071.1| 482 RAKLQQAMTDYVNVFRTEEGVKKALKIIRECREEYQNVYVDDPSRTFNTDLQQTYETRNLIDVAETIALGALVRDEF 558
                                       689************************************************************************** PP

                                       BTTBEBTTS-SEETTT-SEEEEE...TT-SS-EEEEEE--GGG-....-S---SS CS
                    Succ_DH_flav_C  78 rGaHaredfperdDenwlkhtlasldaakeeveleyepveletl....kpkeRsY 128
                                       rGaH+r++++er+D++wlkhtl+s+  +++++++ ++pv le      +pkeRsY
  gi|336253964|ref|YP_004597071.1| 559 RGAHWRKEHQERKDDEWLKHTLISW--NEGDPDIFFRPVILEGEnktyEPKERSY 611
                                       ***********************55..5779********998667778******9 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 !   17.4   3.0   1.3e-06    0.0021       1      30 [.       4      33 ..       4     238 .. 0.77
   2 !   17.3   0.0   1.3e-06    0.0021     256     279 ..     350     383 ..     342     398 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlve 30
                                      +dv+v+G+G AGl+aa+ + +aga++++v+
  gi|336253964|ref|YP_004597071.1|  4 HDVIVVGAGGAGLRAAIAAHEAGADTAIVS 33
                                      59**************************94 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.3e-06
                                       TEEE--TTSBESSTTEEE-GGGC..........T CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..........x RF
                       Pyr_redox_2 256 ggivvdeflrtnvpgiyaiGDva..........g 279
                                       ggi+vde+++t v g+ya+G +a          g
  gi|336253964|ref|YP_004597071.1| 350 GGIEVDENGQTCVNGLYAAGECAcvsvhggnrlG 383
                                       99*********************77776554444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.4   5.1e-07   0.00083       1      32 [.       4      35 ..       4      66 .. 0.85
   2 ?   -1.4   0.1      0.46   7.4e+02     373     388 ..     360     375 ..     346     399 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.1e-07
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                      +dviv+G+G AGl aAi+a+++g++++++ k 
  gi|336253964|ref|YP_004597071.1|  4 HDVIVVGAGGAGLRAAIAAHEAGADTAIVSKL 35
                                      59************************999876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.46
                                       TTSTTEEE-GGGBSEE CS
                       HI0933_like 373 kkvpgLffaGEvlDve 388
                                        +v+gL+ aGE+  v+
  gi|336253964|ref|YP_004597071.1| 360 TCVNGLYAAGECACVS 375
                                       4689*******75443 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   4.1   6.9e-07    0.0011       1      30 [.       5      34 ..       5      38 .. 0.96
   2 ?   -2.4   0.0       1.4   2.3e+03     135     155 ..     204     225 ..     129     227 .. 0.65
   3 ?   -2.8   0.1       1.8     3e+03     238     281 ..     479     521 ..     440     569 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.9e-07
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      Dv+VvG+g aG+ AAiaA +aGa +++v++
  gi|336253964|ref|YP_004597071.1|  5 DVIVVGAGGAGLRAAIAAHEAGADTAIVSK 34
                                      9***************************86 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                      FAD_oxidored 135 rAkvfiDATgdGdlaa.laGvp 155
                                       +    + +TgdG+ +a  aG+p
  gi|336253964|ref|YP_004597071.1| 204 HTTNAVSCTGDGHAMAyRAGAP 225
                                       4455677999997554268877 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.8
                      FAD_oxidored 238 gektdvnwprvstdlienldlpeaeyegreqireeareltqgll 281
                                       +e +  + ++  td+++++   e   ++ + ire  +e+++ ++
  gi|336253964|ref|YP_004597071.1| 479 SE-IRAKLQQAMTDYVNVFRTEEGVKKALKIIRECREEYQNVYV 521
                                       22.33333335566664443333333333334444444444444 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   4.4   1.8e-06    0.0029       1      28 [.       5      32 ..       5      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      dviV+G+G AG+ AA+aa ++Ga+++++
  gi|336253964|ref|YP_004597071.1|  5 DVIVVGAGGAGLRAAIAAHEAGADTAIV 32
                                      8*************************98 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.1   3.7e-06    0.0061       2      34 ..       4      36 ..       3      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.7e-06
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                       dV++VGaG aGl +a   +eaG ++ +v k  
  gi|336253964|ref|YP_004597071.1|  4 HDVIVVGAGGAGLRAAIAAHEAGADTAIVSKLH 36
                                      69***************************9975 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   8.0     2e-05     0.033       1     203 [.       5     198 ..       5     287 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHH..HHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeel..relee 73 
                                       dv+++G+G +Gl +A ++ ++g  ++++ k + +    +g++ g + ++l +        ++ l+a++ +   ++ +
  gi|336253964|ref|YP_004597071.1|   5 DVIVVGAGGAGLRAAIAAHEAGadTAIVSKLHPVR-SHTGAAEGGINAALQEGD------DWELHAYDTMkgSDYLG 74 
                                       8*****************9999*********7777.999999999999886555......78888877775555554 PP

                                       HHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTTSTTTSEEEEETTE...EEEEHHH CS
                               DAO  74 elgididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepalpgllgalfypdt...gqvdpak 147
                                       + ++        +  la ++  +e + +   l + +g +   +++ee  +++    +  g+l yp t   g    ++
  gi|336253964|ref|YP_004597071.1|  75 D-AP-------AVETLAKNA-PEETM-N---L-EHWGMP---FSREEDGRVSQ---RPFGGLSYPRTtyaGAETGHH 131
                                       4.32.......222344332.23333.2...2.337776...67776666664...336888888874423348899 PP

                                       HHHHHHHHHHHTT-EEEESECEEEEEEEE......TCEEEEE..EECTEEEE..EEEE.EEE--GGG CS
                               DAO 148 ltaalaraaealGveilegtevtgleeed......gkvwgve..rttpgend..aada.vVnaaGaw 203
                                       l++ +++++ ++G++++ +  v +l  +d         +gv   ++ +g+++  +a+  vV+a+G  
  gi|336253964|ref|YP_004597071.1| 132 LLHTMYEQVVKRGIQVYDEWYVMNLVTTDeddpkdRECHGVVgyDVQSGTIEgfKANNgVVLATGGP 198
                                       *******************6666652322223555444455454333365532234448*****954 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.4   4.4e-05     0.071      17      48 ..       3      33 ..       1      50 [. 0.75
   2 ?    1.6   0.0     0.083   1.4e+02     206     232 ..     356     383 ..     345     388 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvaile 48
                                      e Dv++vGaG +GL aa    ++ +  +ai+ 
  gi|336253964|ref|YP_004597071.1|  3 EHDVIVVGAGGAGLRAAIAAHEA-GADTAIVS 33
                                      89**************9765555.66666664 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.083
                                       HHECEEETTEEE-T.HHHHHHHT-EB-- CS
                              Thi4 206 kktrevvpnlyvaG.mevaevdganRmG 232
                                       ++ +  v++ly+aG  +   v+g+nR+G
  gi|336253964|ref|YP_004597071.1| 356 ENGQTCVNGLYAAGeCACVSVHGGNRLG 383
                                       678899*******9457789******99 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 ?   14.4   0.5     1e-05     0.017       1      33 [.       7      38 ..       7      42 .. 0.86
   2 ?   -2.1   0.0       1.1   1.8e+03     244     268 ..     174     198 ..     168     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                      i++GaG aGl aai++ +ag  d  i+ k + +
  gi|336253964|ref|YP_004597071.1|  7 IVVGAGGAGLRAAIAAHEAGA-DTAIVSKLHPV 38
                                      89*******************.67898886665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                       Pyr_redox_3 244 eykvktedgkkvevkddvvlatGyk 268
                                        y+v++ + + +++++ vvlatG  
  gi|336253964|ref|YP_004597071.1| 174 GYDVQSGTIEGFKANNGVVLATGGP 198
                                       57888888888999999****9975 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   1.3   8.1e-05      0.13      30      58 ..       5      33 ..       2      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.1e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEE CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlD 58
                                       v+v+G+G aGl A+ +a++ ga++ ++ 
  gi|336253964|ref|YP_004597071.1|  5 DVIVVGAGGAGLRAAIAAHEAGADTAIVS 33
                                      69**********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 4207.94
//
Query:       gi|336253965|ref|YP_004597072.1|  [L=293]
Description: succinate dehydrogenase and fumarate reductase iron-sulfur protein [Halopiger xanaduensis SH-6]
Scores for complete 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  115.4   0.5    3.6e-33  113.8   0.0    2.0  2  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
    4.8e-13   49.4   3.5    1.2e-12   48.0   3.5    1.7  1  Fer4_8    4Fe-4S dicluster domain
    4.4e-08   33.1   3.7    1.1e-07   31.8   3.7    1.7  1  Fer4_10   4Fe-4S dicluster domain
      1e-06   29.2   1.2    2.8e-06   27.8   0.3    2.2  2  Fer4_7    4Fe-4S dicluster domain
    3.1e-05   24.4   3.7    7.7e-05   23.2   3.7    1.7  1  Fer4_17   4Fe-4S dicluster domain
     0.0011   19.1   6.6     0.0011   19.1   6.6    2.3  2  Fer4_9    4Fe-4S dicluster domain
     0.0092   15.7   7.2       0.58    9.9   0.5    2.7  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
  ------ inclusion threshold ------
      0.023   15.6  11.5      0.063   14.2   7.3    3.0  3  Fer4_16   4Fe-4S double cluster binding domain
       0.33   11.5   8.7       0.65   10.6   2.4    2.7  2  Fer4_4    4Fe-4S binding domain
       0.83    9.9   9.5        4.1    7.6   0.2    2.7  3  Fer4_18   4Fe-4S dicluster domain
       0.98    9.3   9.5        3.1    7.8   2.9    2.5  2  Fer4      4Fe-4S binding domain
        1.8    8.8   7.4        3.1    8.0   2.0    2.6  2  Fer4_6    4Fe-4S binding domain
        3.6    8.7  11.9        2.1    9.5   0.4    2.6  2  Fer4_3    4Fe-4S binding domain
        5.4    7.8   9.8         22    5.9   0.1    3.8  3  Fer4_15   4Fe-4S single cluster domain
        6.3    7.0  10.1    1.2e+02    3.0  10.1    2.4  1  Fer4_21   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8   0.0     3e-36   3.6e-33       2     108 ..      56     160 ..      55     161 .. 0.95
   2 ?   -1.1   0.1       1.6   1.9e+03      51      65 ..     197     211 ..     183     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 3e-36
                            Fer2_3   2 lkvkRfdprrdrg.kqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatik 77 
                                       +kv+R+dp+  ++ ++++++++v++e+++tvlda+++ ++e d++l+fr+sCr+++CGs+a+ +nGk++l C+++i+
  gi|336253965|ref|YP_004597072.1|  56 IKVFRYDPEVAAKqEPRFDDFHVPFEKGMTVLDAVMYARDEFDSSLTFRHSCRQAVCGSDAFFVNGKQRLGCKTQIS 132
                                       89******988777*************************************************************** PP

                            Fer2_3  78 dlakqkseieleplpkfpvirDLvvDideml 108
                                       dl++   ++++eplp+ +v++DLvvD+d+++
  gi|336253965|ref|YP_004597072.1| 133 DLEQ---PVRIEPLPHQEVVKDLVVDMDHFY 160
                                       *984...49*******************987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                            Fer2_3  51 sCregiCGscavain 65 
                                       s r   CG+c  ++n
  gi|336253965|ref|YP_004597072.1| 197 SSRCIWCGACMSSCN 211
                                       445567999987777 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   3.5     1e-15   1.2e-12       3      65 .]     198     272 ..     196     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1e-15
                            Fer4_8   3 ekCieCgaCqsaC...........pvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                       ++Ci CgaC+s+C           p++ +++ k+ +d r+  + ++++ + le+e+++w+C+t  +CtevCp++i
  gi|336253965|ref|YP_004597072.1| 198 SRCIWCGACMSSCniaagdneylgPAAINKAyKFAMDDRESEEIKEHRLRILEQEHGVWRCQTQFSCTEVCPKDI 272
                                       79***********77777777777666666669999999998888888888888******************987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   3.7   9.2e-11   1.1e-07       5      56 .]     196     269 ..     192     269 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 9.2e-11
                           Fer4_10   5 dddtCirCgkCvkaCPadl........................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        +++Ci Cg+C+++C  ++                        +s + k+ + ++ +++++v++C++ ++C+e+CP
  gi|336253965|ref|YP_004597072.1| 196 MSSRCIWCGACMSSC--NIaagdneylgpaainkaykfamddrESEEIKEHRLRILEQEHGVWRCQTQFSCTEVCP 269
                                       6789***********..8889*********************9999999**************************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.5   6.6e+03      10      22 ..     110     122 ..     106     157 .. 0.70
   2 !   27.8   0.3   2.3e-09   2.8e-06       1      52 []     199     272 ..     199     272 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.5
                            Fer4_7  10 aaCpvkaieldee 22 
                                       a+C ++a+ ++ +
  gi|336253965|ref|YP_004597072.1| 110 AVCGSDAFFVNGK 122
                                       4566666665543 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 2.3e-09
                            Fer4_7   1 rCigCgaCvaaC................pvkaieldeeenek..gtekv.......eidpekClgCgaCvavCPtga 52 
                                       rCi CgaC++ C                +++ + +d++e+e+  +           e+  ++C++  +C +vCP+++
  gi|336253965|ref|YP_004597072.1| 199 RCIWCGACMSSCniaagdneylgpaainKAYKFAMDDRESEEikE---HrlrileqEHGVWRCQTQFSCTEVCPKDI 272
                                       8***********999988888887765544444455544433221...12345554777899************985 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   3.7   6.5e-08   7.7e-05       1      60 [.     199     272 ..     199     273 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.5e-08
                           Fer4_17   1 rCiqCgyClpeCpsyeaydne..pk..kllraakl..........glleeaekeekaslCieCgeCerkCPqgl 60 
                                       rCi Cg+C+ +C   +  +++  p+  + ++++++          ++l+  e+e+ + +C +   C+++CP+++
  gi|336253965|ref|YP_004597072.1| 199 RCIWCGACMSSCNIAAGDNEYlgPAaiNKAYKFAMddreseeikeHRLRILEQEHGVWRCQTQFSCTEVCPKDI 272
                                       7*************99988754455234555555566555444433444466669*****************98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   2.8   0.00034      0.41      24      47 ..     188     211 ..     177     215 .. 0.68
   2 !   19.1   6.6   9.2e-07    0.0011       1      49 [.     199     271 ..     199     272 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                            Fer4_9  24 rkarlraaseeaCigCgaCveaCp 47 
                                        ++r +++  ++Ci CgaC+  C+
  gi|336253965|ref|YP_004597072.1| 188 PENREKIKMSSRCIWCGACMSSCN 211
                                       344444444478999999999996 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 9.2e-07
                            Fer4_9   1 kCtgCgaCveaC...........pagvvvedaaerkarlraase........................eaCigCgaC 42 
                                       +C+ CgaC+++C           p            a ++a++                         ++C +  +C
  gi|336253965|ref|YP_004597072.1| 199 RCIWCGACMSSCniaagdneylgP-----------AAINKAYKFamddreseeikehrlrileqehgvWRCQTQFSC 264
                                       5***********555555555443...........44444444445555555677899999*****9999999999* PP

                            Fer4_9  43 veaCpkg 49 
                                       +e+Cpk+
  gi|336253965|ref|YP_004597072.1| 265 TEVCPKD 271
                                       *****98 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 !    8.3   1.4    0.0016       1.9       5      47 ..     181     221 ..     177     241 .. 0.79
   2 !    9.9   0.5   0.00048      0.58      25      58 ..     256     290 ..     236     293 .] 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                                       -S-SB----HHHHHHHHTT----TT-HHHHCSTT---HHHHHH CS
                           Fer4_20   5 fkevalglteeealeeAsRClqCkkapcvkgCPveidipefik 47 
                                       ++e +++ +++e ++ +sRC+ C    c+++C +    +e++ 
  gi|336253965|ref|YP_004597072.1| 181 LEEQRQSPENREKIKMSSRCIWC--GACMSSCNIAAGDNEYLG 221
                                       56777778889999*********..78999**99887777765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00048
                                       ---T.T-HHHHCSTT---HHHHHHHHHTT-HHHHH CS
                           Fer4_20  25 lqCk.kapcvkgCPveidipefikkiaegnleeaa 58 
                                        +C+ +  c++ CP +i   e+i++++++ +++ +
  gi|336253965|ref|YP_004597072.1| 256 WRCQtQFSCTEVCPKDIPLTEHIQELKREAVKKNL 290
                                       46873456*******************99998866 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 ?   -1.7   0.1         5     6e+03      17      33 ..      31      47 ..       8      65 .. 0.65
   2 ?   12.3   2.1    0.0002      0.24      30      64 ..     176     210 ..     162     213 .. 0.82
   3 ?   14.2   7.3   5.2e-05     0.063       1      66 [.     199     270 ..     199     271 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5
                           Fer4_16 17 ikekkekeiearecisy 33
                                      ++ek+e +++ ++++++
  gi|336253965|ref|YP_004597072.1| 31 LREKQEGMVDEHAEKEA 47
                                      44455555555555444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0002
                           Fer4_16  30 cisyntaekkdlaedeekckkqeaitgCdiCqdvC 64 
                                         s++ +e+++ +e++ek k+  +++ C++C+  C
  gi|336253965|ref|YP_004597072.1| 176 PDSSELEEQRQSPENREKIKMSSRCIWCGACMSSC 210
                                       3445788999999999******************* PP

  == domain 3  score: 14.2 bits;  conditional E-value: 5.2e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisy..ntaekkdlaedeekckkqeai.tgCd...iCqdvCPa 66 
                                       rC+ Cg+C+++C  +a +++    +++++  +    ++e ++++e++ +  +qe+    C+    C++vCP 
  gi|336253965|ref|YP_004597072.1| 199 RCIWCGACMSSCNIAAGDNEYLGPAAINKAYKFamDDRESEEIKEHRLRILEQEHGvWRCQtqfSCTEVCPK 270
                                       6***************8888444444444333355777777777777777766443466665559******5 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.4   0.00054      0.65       2      14 ..     198     210 ..     197     217 .. 0.93
   2 ?    3.7   0.5     0.091   1.1e+02       7      16 ..     258     270 ..     256     276 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00054
                            Fer4_4   2 erCigCgsCvaaC 14 
                                       +rCi Cg+C+++C
  gi|336253965|ref|YP_004597072.1| 198 SRCIWCGACMSSC 210
                                       79*********** PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.091
                            Fer4_4   7 Cg...sCvaaCPq 16 
                                       C    sC+ +CP 
  gi|336253965|ref|YP_004597072.1| 258 CQtqfSCTEVCPK 270
                                       664336******5 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1         5     6e+03      40      60 ..      32      52 ..      11      58 .. 0.53
   2 ?    7.5   1.0    0.0037       4.4      42      73 ..     180     212 ..     158     220 .. 0.67
   3 ?    7.6   0.2    0.0035       4.1      42      82 ..     239     279 ..     221     282 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5
                           Fer4_18 40 rkkekkalkekeerkekgagd 60
                                      r+k++ ++ e+ e+++++ag+
  gi|336253965|ref|YP_004597072.1| 32 REKQEGMVDEHAEKEAEAAGE 52
                                      223333333444444455555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0037
                           Fer4_18  42 kekkalkekee.rkekgagdcidcescvkvcPt 73 
                                       + +++ ++ e+ +k k ++ ci c++c++ c +
  gi|336253965|ref|YP_004597072.1| 180 ELEEQRQSPENrEKIKMSSRCIWCGACMSSCNI 212
                                       444444444440445677889999999988865 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0035
                           Fer4_18  42 kekkalkekeerkekgagdcidcescvkvcPtgidirkGlq 82 
                                       +e k+++ + +++e+g+  c +  sc +vcP +i + + +q
  gi|336253965|ref|YP_004597072.1| 239 EEIKEHRLRILEQEHGVWRCQTQFSCTEVCPKDIPLTEHIQ 279
                                       344445555567788889999999********998877665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.9    0.0026       3.1       5      18 ..     197     210 ..     194     210 .. 0.89
   2 ?    5.0   0.5      0.02        24      14      21 ..     264     271 ..     263     273 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0026
                                       TTTSSS-THHHHHS CS
                              Fer4   5 eekCigCGaCvevC 18 
                                        ++Ci CGaC++ C
  gi|336253965|ref|YP_004597072.1| 197 SSRCIWCGACMSSC 210
                                       589*********99 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.02
                                       HHHHSTTT CS
                              Fer4  14 CvevCPvg 21 
                                       C evCP +
  gi|336253965|ref|YP_004597072.1| 264 CTEVCPKD 271
                                       ******88 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   2.0    0.0026       3.1       7      19 ..     198     210 ..     196     215 .. 0.88
   2 ?    2.7   0.3      0.13   1.5e+02      15      22 ..     264     271 ..     262     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0026
                            Fer4_6   7 dkCigCgdCvrvC 19 
                                       ++Ci Cg+C++ C
  gi|336253965|ref|YP_004597072.1| 198 SRCIWCGACMSSC 210
                                       79**********9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.13
                            Fer4_6  15 CvrvCPeg 22 
                                       C+ vCP +
  gi|336253965|ref|YP_004597072.1| 264 CTEVCPKD 271
                                       ******75 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   5.7      0.35   4.2e+02       1      11 [.     200     210 ..     200     210 .. 0.88
   2 ?    9.5   0.4    0.0017       2.1       4      14 ..     258     271 ..     255     272 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.35
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C+ CgaC+ +C
  gi|336253965|ref|YP_004597072.1| 200 CIWCGACMSSC 210
                                       666******** PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0017
                            Fer4_3   4 Cg...aCvevCPvg 14 
                                       C+    C evCP++
  gi|336253965|ref|YP_004597072.1| 258 CQtqfSCTEVCPKD 271
                                       765456******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 ?    0.7   1.5      0.74   8.8e+02      37      55 ..      32      50 ..       5      53 .. 0.84
   2 ?    5.9   0.1     0.019        22       6      19 ..     198     211 ..     197     251 .. 0.69
   3 ?    4.5   0.1      0.05        60       6      24 ..     256     274 ..     255     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.74
                           Fer4_15 37 geiaegevpddeeeaaqeA 55
                                      +e +eg+v+++ e++a+ A
  gi|336253965|ref|YP_004597072.1| 32 REKQEGMVDEHAEKEAEAA 50
                                      466889*******999987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.019
                           Fer4_15   6 daCigcglCvaeap 19 
                                       ++Ci cg+C+  + 
  gi|336253965|ref|YP_004597072.1| 198 SRCIWCGACMSSCN 211
                                       69********9995 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.05
                           Fer4_15   6 daCigcglCvaeapevfel 24 
                                       ++C+  + C +++p+ + l
  gi|336253965|ref|YP_004597072.1| 256 WRCQTQFSCTEVCPKDIPL 274
                                       59***********986655 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0  10.1     0.098   1.2e+02       6      22 ..     198     214 ..     193     274 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.098
                           Fer4_21   6 dkCigCgkCliaCedts 22 
                                       ++Ci Cg C+ +C+ ++
  gi|336253965|ref|YP_004597072.1| 198 SRCIWCGACMSSCNIAA 214
                                       68***********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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):              15  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2258.09
//
Query:       gi|336253966|ref|YP_004597073.1|  [L=121]
Description: hypothetical protein Halxa_2576 [Halopiger xanaduensis SH-6]
Scores for 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-10   39.4   6.3    6.5e-10   39.1   6.3    1.1  1  Sdh_cyt   Succinate dehydrogenase/Fumarate reductase transmem
  ------ inclusion threshold ------
       0.29   11.4   2.7          1    9.7   2.7    1.9  1  DUF4536   Domain of unknown function (DUF4536)


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   6.3   7.2e-14   6.5e-10      16     115 ..       8     102 ..       2     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 7.2e-14
                           Sdh_cyt  16 lplgawlsilhritGvallvglllllvwlllalslsspesfarvvallaspiklilllllllallyHllnGiRhllw 92 
                                       +  g + ++l+rit+++l+v +l ++++ l  ++ + + +f    a ++++++++ ++l+l+ +++H++nG++  l+
  gi|336253966|ref|YP_004597073.1|   8 FAPGGTRWLLQRITAAFLVV-VLAFHFFQLHFVTHAAEVTFMGTQARMQNVGYFLTMVLFLITAAFHGVNGVYNALI 83 
                                       4578899*************.66666555666655566677777999999*************************** PP

                           Sdh_cyt  93 Dlglglelesarksalavlalav 115
                                       + gl    e  rk+ ++++++++
  gi|336253966|ref|YP_004597073.1|  84 NQGL----EGTRKKVVLAVLVIA 102
                                       8777....555444433333333 PP

>> DUF4536  Domain of unknown function (DUF4536)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.7   0.00011         1       7      23 ..     100     116 ..     100     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                           DUF4536   7 lvSGsGLigaGvYvyvq 23 
                                       +++G++Li+ GvYv+v+
  gi|336253966|ref|YP_004597073.1| 100 VIAGGALIAQGVYVAVA 116
                                       799***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 884.66
//
Query:       gi|336253967|ref|YP_004597074.1|  [L=142]
Description: succinate dehydrogenase, cytochrome b556 subunit [Halopiger xanaduensis SH-6]
Scores for 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-23   80.6   3.7    1.1e-22   80.4   3.7    1.1  1  Sdh_cyt   Succinate dehydrogenase/Fumarate reductase transmem


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   3.7   5.9e-27   1.1e-22       2     120 ..       4     135 ..       3     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 5.9e-27
                           Sdh_cyt   2 rknrplsphlqlyr.lplgawlsilhritGvallvglllllvwlllalslsspesfarv..........vallas.p 66 
                                       ++nr l +++++++ + +g+w++i+h++tG+ l++ +l++++++l +++++ + +  ++          +++l    
  gi|336253967|ref|YP_004597074.1|   4 SYNRGLIEDFGRWKeFSAGMWAWIFHKFTGWMLIG-YLFTHIAVLSTAIGAASGDASMIqaetdvytttIQGLEElF 79 
                                       689***********889******************.66666654444444444444444669888866555555598 PP

                           Sdh_cyt  67 iklilllllllallyHllnGiRhllwDlglgl.el.esarksalavlalavalvlv 120
                                       i  +l+++ll+++++H+lnG+R+l++Dlg+gl  + +s ++s +++ a++va+v +
  gi|336253967|ref|YP_004597074.1|  80 IVRVLEVGLLAVAVFHILNGLRLLMVDLGIGLeAQdRSFYASLVLTGAITVASVPT 135
                                       999999*********************999998777999************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1160.29
//
Query:       gi|336253968|ref|YP_004597075.1|  [L=367]
Description: succinylglutamate desuccinylase/aspartoacylase [Halopiger xanaduensis SH-6]
Scores for 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-67  225.1   0.0    1.2e-66  224.8   0.0    1.0  1  AstE_AspA      Succinylglutamate desuccinylase / Aspartoacyla
  ------ inclusion threshold ------
       0.13   12.1   0.0       0.41   10.5   0.0    1.8  1  Biotin_lipoyl  Biotin-requiring enzyme


Domain annotation for each model (and alignments):
>> AstE_AspA  Succinylglutamate desuccinylase / Aspartoacylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.8   0.0   1.3e-70   1.2e-66       1     288 [.      69     342 ..      69     343 .. 0.97

  Alignments for each domain:
  == domain 1  score: 224.8 bits;  conditional E-value: 1.3e-70
                                       SS-EEEEEE-SSTT-HHHHHHHHHHHHHHHCCCESCCEEEEEESSHHHHHCTSSSSSTT-S-CTTTTTCCCCCSSTC CS
                         AstE_AspA   1 sgpkvlisAGvHGnElaGvellrqllkqleeadilgeitlvplaNppAiaagsRyipidredLNRaFpgrslgrsld 77 
                                       +gp+v++sA+ HG+El+G+e++r++++++++ +++g+ +++p++N+p++ a++Ry+pi+++dLNR+Fpgr+      
  gi|336253968|ref|YP_004597075.1|  69 PGPTVFLSAAAHGDELNGIEVVREVAHDWDHSELHGTLVCLPVMNVPGFLAQERYLPIYDRDLNRSFPGREGS---- 141
                                       79***********************************************************************.... PP

                                       HHHHHHHHHHHHHHHCHCTCCCGCEEEEEEEESSTBCCSSEEEE---SSHHHHHHHHHHTTTSEEEEEESS--SSHH CS
                         AstE_AspA  78 ealrateaerladalfaaalpeadivlDLHtgtrglkhllfaeadiaeaqlqslallkalglpavllldekesagfl 154
                                            t+a+r+a+++f++ ++++di +D+Ht trg++++l+++a++a++q+   +l+ka+  ++++  + ++++g+l
  gi|336253968|ref|YP_004597075.1| 142 -----TSARRMANQIFTNFIEPCDIGIDFHTSTRGRTNMLHVRANMADPQV--SRLAKAFSSNVII--AGEGPSGTL 209
                                       .....**********************************************..*************..999999*** PP

                                       HHHHHHCTSEEEEEEEES.TTTTCCHHCCHHHHHHHHHHHHCTCHTT-SCC.CEEEEEEEEEEGGSCCCSSCSEEEC CS
                         AstE_AspA 155 etaaeelgalaftlElGgagrlgaedisrtakgvlnvlahigvvagqeavepaklyrvlreldeprdiraeeaGlve 231
                                       +++a  + ++++t+E+G+a+r++  +i+r+ +gv++vla+ g+++++ +v ++ +++v++  de+++ira+++G+v+
  gi|336253968|ref|YP_004597075.1| 210 RREATDADVPTITVEMGEAHRFQRSLIDRALTGVASVLAEFGLHQES-SVHWPGWRTVIDDDDEKTWIRADAGGIVD 285
                                       ***********************************************.9**************************** PP

                                       CCCSTTTTETCTEEEETTEEEEECTSTEEEEESSSSEEEESCCTSCCTTTTEEEEEE CS
                         AstE_AspA 232 fkvklgddveagellakalvldslggekvelrapqdgvivfineaalvekgaalvkv 288
                                       +k+  g+ v  g+++ +++   +++++ v+++ap +g++v+  e++ v +g+ l+++
  gi|336253968|ref|YP_004597075.1| 286 MKHGRGELVREGDVICTITNPFKEEEDIVTVEAPFTGLVVGVLENPVVYPGNPLCHL 342
                                       ***************666655555566788999*********************986 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.6e-05      0.41      15      71 ..     281     340 ..     277     342 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.6e-05
                                       ..ECSESSSTTCEE-TTSEEEEEEC.TTEE...EEEEBSSSEEEEEESSTTTEEE-TTCEEE CS
                     Biotin_lipoyl  15 g.vvevlvkvGdkVkagqvlaevea.mKme...meieapkaGvvkeilvkeGdtvevgdlla 71 
                                       g +v ++   G+ V +g+v++++ +  K e   +++eap +G v+ +l +    v  g +l+
  gi|336253968|ref|YP_004597075.1| 281 GgIVDMKHGRGELVREGDVICTITNpFKEEediVTVEAPFTGLVVGVLEN--PVVYPGNPLC 340
                                       4467789999*************763355433377899999999999877..6777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2710.55
//
Query:       gi|336253969|ref|YP_004597076.1|  [L=249]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-10   40.0   0.0    6.5e-10   39.3   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.2e-09   37.3   0.0    3.2e-09   36.8   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    7.1e-09   36.0   0.1    1.5e-08   34.9   0.1    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    9.6e-06   25.7   0.0    2.1e-05   24.6   0.0    1.6  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00045   20.1   0.0     0.0015   18.5   0.0    1.8  2  FR47             FR47-like protein
     0.0036   17.4   0.0     0.0055   16.9   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.013   15.6   2.7       0.21   11.7   0.5    2.2  2  Acetyltransf_6   Acetyltransferase (GNAT) domain
      0.074   11.6   0.0        1.6    7.2   0.0    2.3  3  AstA             Arginine N-succinyltransferase beta subunit


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 !   39.3   0.0   2.9e-13   6.5e-10      22     117 .]      44     139 ..      18     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 2.9e-13
                                       HH.HHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEE CS
                    Acetyltransf_1  22 ee.feesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikki 97 
                                        + f + +++++   lv+e+dge++Gf +   + +  +g + i  l+V+p++rg+G G +Ll    e + +eg++ +
  gi|336253969|ref|YP_004597076.1|  44 GDgFGDELEDDHAVVLVVERDGEIAGFSQSDLVGQ-QYGSGRILWLHVRPDHRGSGTGVRLLVRTRETLIDEGADHV 119
                                       223333344455556669*****************.89999999******************************999 PP

                                       EEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  98 vlaveedndaairlYeklGF 117
                                       +  v +dn +  ++Y+++GF
  gi|336253969|ref|YP_004597076.1| 120 EGFVLADNAGGNEFYREHGF 139
                                       889************65**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   1.4e-12   3.2e-09      13     117 ..      38     150 ..      20     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.4e-12
                   Acetyltransf_10  13 fkefispealrerieegealllvaeeggkivGvi...el.rdgs..hisllfVdpeyrgqGigkaLleaveeeaekd 83 
                                         ++ + + + +++e+ +a++lv+e++g+i+G+     + ++ +  +i  l V+p++rg G g +Ll + +e + ++
  gi|336253969|ref|YP_004597076.1|  38 AIDQWYGDGFGDELEDDHAVVLVVERDGEIAGFSqsdLVgQQYGsgRILWLHVRPDHRGSGTGVRLLVRTRETLIDE 114
                                       34444457888999999****************9665333333377***************************8888 PP

                   Acetyltransf_10  84 gikl.eltvnasp.yavpfYeklGFkavgeeqeenG 117
                                       g  + e  v a++    +fY+ +GF++ g+ ++e G
  gi|336253969|ref|YP_004597076.1| 115 GADHvEGFVLADNaGGNEFYREHGFEQAGQREVEIG 150
                                       88888********99*************98887755 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   6.7e-12   1.5e-08       3      75 ..      56     140 ..      53     141 .. 0.70

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 6.7e-12
                                       EEEEEEEETTEEEEEEEEEEES.....TCTEEEEE-GGGTTSSHHHHHHH.HTT....SEEE.EE.EEEETHHHHHH CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld.....aeitrlaVdpeyrgkGiGraLle.aae....kgii.le.qlelnaekaik 67 
                                       + v+V+e+dg+i Gf    l++     + i +l V+p++rg G G +Ll   +e    +g   +e  +  ++   ++
  gi|336253969|ref|YP_004597076.1|  56 AVVLVVERDGEIAGFSQSDLVGqqygsGRILWLHVRPDHRGSGTGVRLLVrTREtlidEGADhVEgFVLADNAGGNE 132
                                       6699**********987776669988888888****************95242223344421212222223325567 PP

                                       HHHHTTEE CS
                    Acetyltransf_7  68 fYeklGFe 75 
                                       fY+ +GFe
  gi|336253969|ref|YP_004597076.1| 133 FYREHGFE 140
                                       *******9 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   9.6e-09   2.1e-05       1     127 [.       2     141 ..       2     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 9.6e-09
                                       .EEEE-GGGHHHHHHHHHHHTT----H.........HHHHHHHHHHT......TSEEEEEEETTEEEEEEEEEEEEE CS
                    Acetyltransf_9   1 eirelteedldevlellkyaFqdeespl......e.eireyfrklle......esrvlgaedngelvgqlallplel 64 
                                       eir++t++d+d++ ++  ++   + +++      e  i++++ + ++      ++ vl++e++ge++g  +      
  gi|336253969|ref|YP_004597076.1|   2 EIRTATDDDVDAIRSIAHQSLSSTYTDFlgeetvEsAIDQWYGDGFGdeleddHAVVLVVERDGEIAGFSQ-----S 73 
                                       69****************************99997789999999988555554459999999******875.....6 PP

                                       EETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--...SSH...HHHHTTT-EE CS
                    Acetyltransf_9  65 nvpGktlkaagvtgVavapehrgrgvlskLlaraleemreegqplsllfP...ssi...piYrrfGyei 127
                                        + G+++  + + +  v p+hrg g   +Ll r+ e + +eg+  + +f      +   ++Yr  G+e+
  gi|336253969|ref|YP_004597076.1|  74 DLVGQQYGSGRILWLHVRPDHRGSGTGVRLLVRTRETLIDEGADHVEGFVladN-AggnEFYREHGFEQ 141
                                       899**********************************99999998888875442.13558999999886 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   6.6e-07    0.0015      19      82 ..      79     144 ..      73     147 .. 0.82
   2 ?   -2.7   0.0       2.6   5.9e+03       7      17 ..     203     214 ..     200     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.6e-07
                                       -TT.SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEEEE CS
                              FR47  19 kdg.gelgalqvlpehrrrGlgsrlvkalakeiaerg.ktvllvvvasNtpsirlyeklGfekiee 82 
                                       ++g g +  l v+p+hr+ G g rl     + ++ +g ++v   v a+N    ++y   Gfe++ +
  gi|336253969|ref|YP_004597076.1|  79 QYGsGRILWLHVRPDHRGSGTGVRLLVRTRETLIDEGaDHVEGFVLADNAGGNEFYREHGFEQAGQ 144
                                       4556999***************99888888777776626677889999999**********99855 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.6
                                       T.TT--EEEEEE CS
                              FR47   7 k.elgelaawil 17 
                                         + +el+aw+ 
  gi|336253969|ref|YP_004597076.1| 203 DdDRKELYAWLC 214
                                       338899999985 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.4e-06    0.0055       1     139 [.       3     144 ..       3     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.4e-06
                    Acetyltransf_4   1 iraateeDakeilaiyaeyvvnt...aitfeyevssveefe..kflealdsekeyvflvaesdrivGyaylgqfkkr 72 
                                       ir+at +D ++i+ i ++    t   ++++e ++s++++     f ++l+ +   v+ v+ +++i+G  +   + + 
  gi|336253969|ref|YP_004597076.1|   3 IRTATDDDVDAIRSIAHQSLSSTytdFLGEETVESAIDQWYgdGFGDELEDDHAVVLVVERDGEIAGFSQSDLVGQ- 78 
                                       8***************976333312245588888888755434777777555566666666******999997777. PP

                    Acetyltransf_4  73 akdwkael.svylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgi 139
                                        +++++ +    + + d +  g+g  l+    + l   +    +  + ++n+   +f+ ++GFe +g+
  gi|336253969|ref|YP_004597076.1|  79 -QYGSGRIlWLHV-RPDHRGSGTGVRLLVRTRETLIDEGADHVEGFVLADNAGGNEFYREHGFEQAGQ 144
                                       .666655504455.78999*********************************************9987 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   9.4e-05      0.21      51     132 ..      36     120 ..       1     136 [. 0.76
   2 ?    4.4   0.1     0.017        39      63     106 ..     162     205 ..     122     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.4e-05
                    Acetyltransf_6  51 dpltraflrdllaalaargalrlyvlrldgrpvAva...lglrsgdrlyywlggydpelaklspgllllweliedaa 124
                                       + +  +++ d + +  +++ ++++v++ dg+++++    l+ ++ +    ++  ++p++++ + g  ll ++ e ++
  gi|336253969|ref|YP_004597076.1|  36 ESAIDQWYGDGFGDELEDDHAVVLVVERDGEIAGFSqsdLVGQQYGSGRILWLHVRPDHRGSGTGVRLLVRTRETLI 112
                                       4566778888888888999****************98888888888888999999********************** PP

                    Acetyltransf_6 125 eeGlrrfd 132
                                       +eG ++++
  gi|336253969|ref|YP_004597076.1| 113 DEGADHVE 120
                                       ***99875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.017
                    Acetyltransf_6  63 aalaargalrlyvlrldgrpvAvalglrsgdrlyywlggydpel 106
                                        +l+++g++ + +l+ dg+ v v +g  +++    ++++y+ + 
  gi|336253969|ref|YP_004597076.1| 162 GDLEDEGWGAIDELEIDGETVYVSYGEAARGSRSPFYSAYRDDD 205
                                       367789**************************999999997764 PP

>> AstA  Arginine N-succinyltransferase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00072       1.6       2      76 ..       1      72 [.       1      79 [. 0.66
   2 ?    2.0   0.0     0.027        60     117     162 ..      79     125 ..      74     134 .. 0.80
   3 ?   -3.3   0.0       1.1   2.5e+03      78      91 ..     188     202 ..     178     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00072
                              AstA  2 lviRparesDldallelaeesgvgltsLpadeeaLekkiars.ersfakeveepgeesYlfvledtetgevvGtsa 76
                                      + iR a+ +D+da+ ++a++s     +    ee++e+ i++   + f +e   +++++ ++v+e  ++ge++G s+
  gi|336253969|ref|YP_004597076.1|  1 MEIRTATDDDVDAIRSIAHQSLSSTYTDFLGEETVESAIDQWyGDGFGDE--LEDDHAVVLVVE--RDGEIAGFSQ 72
                                      579*****************854444333444555555544313444443..455556666666..6899999875 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.027
                              AstA 117 ltgaselctlfldpeyrkgglg.rllsrsRflfiaehrerFaekvia 162
                                         g+ ++  l ++p++r++g+g rll r+R  +i e  +  +  v+a
  gi|336253969|ref|YP_004597076.1|  79 QYGSGRILWLHVRPDHRGSGTGvRLLVRTRETLIDEGADHVEGFVLA 125
                                       568889999*********9965499*****99998877776666665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.1
                              AstA  78 eaavGleepfys.yr 91 
                                       eaa G ++pfys yr
  gi|336253969|ref|YP_004597076.1| 188 EAARGSRSPFYSaYR 202
                                       678888888885355 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 1902.28
//
Query:       gi|336253970|ref|YP_004597077.1|  [L=489]
Description: polysaccharide biosynthesis protein [Halopiger xanaduensis SH-6]
Scores for 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-30  104.6  14.5    5.7e-30  104.6  14.5    2.4  2  Polysacc_synt    Polysaccharide biosynthesis protein
    2.1e-24   86.3   2.9    2.1e-24   86.3   2.9    2.2  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    1.8e-19   70.2  20.1    1.8e-19   70.2  20.1    4.0  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    5.7e-06   26.1   1.0    5.7e-06   26.1   1.0    3.7  3  MatE             MatE


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 !  104.6  14.5   1.3e-33   5.7e-30       2     251 ..       9     267 ..       8     287 .. 0.83
   2 ?   -5.4   5.8         4   1.8e+04     153     166 ..     442     457 ..     384     479 .. 0.63

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 1.3e-33
                     Polysacc_synt   2 lkgvivlllsqlitkllafvtlvylari.lgpegfGlvalalaivtllviltdlGlnaalvreiakyrek.kelvsl 76 
                                       ++g+  +l+++ + +l +++ + +lar+ l+p g+G ++ a++i+ + ++++d Gl+ ++ r+i++y+ek    +  
  gi|336253970|ref|YP_004597077.1|   9 VRGFKATLVARAVYMLSSALLMLVLARFlLDPQGYGDLYWAISILAIVQLFADVGLGKSAARYISEYNEKdPGQIPH 85 
                                       5677777888888888899999999987369****************************************666666 PP

                     Polysacc_synt  77 illnvllvllvlvllfllllliaa.....flglpelavlylilalmllllvgvasfrrglfqglermky.aavsqvv 147
                                       +l ++++ +lv+v +++ +ll+++      lg+p +a   l++ + ++++ ++++f    fqg++   y aav+ + 
  gi|336253970|ref|YP_004597077.1|  86 LLRSTMVYKLVVVSVVAYALLLFHdelasMLGEPSAAP-FLAAGVLYVVVKSFQTFAQISFQGFNELGYsAAVQAIG 161
                                       66666666666666666666666666664777777665.5566666667*****************99945688888 PP

                     Polysacc_synt 148 eqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkf.r..prfvilslklvrellsfsapltisslai 221
                                         ++ v +v++++ +f+  ++a++g+ +++ ++g ++la+l++kf r   +  i +  l ++ll++s+plt+++ a+
  gi|336253970|ref|YP_004597077.1| 162 GATRLVFAVGFVLAGFG-ALGALFGYIVGYALAGAFGLAILYFKFyReyDTAEIYEEGLSKRLLKYSVPLTATRSAN 237
                                       88888999999999999.888888888888888888888888888447655555559******************** PP

                     Polysacc_synt 222 llytyidsillglllgaeavGiYnaayqll 251
                                        +  +id++l g +l+++avG+Y+++ q++
  gi|336253970|ref|YP_004597077.1| 238 VVDKQIDTFLVGVFLSSTAVGFYTLGKQIT 267
                                       ***************************997 PP

  == domain 2  score: -5.4 bits;  conditional E-value: 4
                     Polysacc_synt 153 vilvliavflfld..i 166
                                       +i+vli++ ++++  +
  gi|336253970|ref|YP_004597077.1| 442 AIAVLIVTPMVSSfpM 457
                                       3444444444444331 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   2.9   4.7e-28   2.1e-24       1     284 [.      32     331 ..      32     339 .. 0.85
   2 ?   -3.7   4.8       1.2   5.2e+03     185     185 ..     442     442 ..     333     480 .. 0.51

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 4.7e-28
                   Polysacc_synt_3   1 vLAR.LLspedFGvvaialvvislanlfvdmGlssaliqke.dltee........dlstvftfnlvlgllialvlfl 67 
                                       vLAR LL p+ +G +  a+ ++++++lf+d+Gl++   +   + +e+          st+ +  +v++++++++ +l
  gi|336253970|ref|YP_004597077.1|  32 VLARfLLDPQGYGDLYWAISILAIVQLFADVGLGKSAARYIsEYNEKdpgqiphlLRSTMVYKLVVVSVVAYAL-LL 107
                                       89**4579*************************99877655333333456677644566667777777777665.56 PP

                   Polysacc_synt_3  68 lapliasfynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvi 144
                                       + + +as++++p +++ l    l +++++++   +  ++   +    ++++ ++ +  +++a+  +l+g+g+   ++
  gi|336253970|ref|YP_004597077.1| 108 FHDELASMLGEPSAAPFLAAGVLYVVVKSFQTFAQISFQGFNELGYSAAVQAIGGATRLVFAVGFVLAGFGALGALF 184
                                       7899***********************************99999999*************************99999 PP

                   Polysacc_synt_3 145 gtllssllslvllwlaskwrprlkfslksl......kelfsfglklllsnllnylarnldnlliGkvlssaaLGlYs 215
                                       g ++  +l  ++ + ++ ++   + ++ ++      k+l+++++ l+++  +n++ +++d++l+G +lss+a+G+Y+
  gi|336253970|ref|YP_004597077.1| 185 GYIVGYALAGAFGLAILYFKFYREYDTAEIyeeglsKRLLKYSVPLTATRSANVVDKQIDTFLVGVFLSSTAVGFYT 261
                                       99999888888777777777666666665533334489*************************************** PP

                   Polysacc_synt_3 216 vakrlaslpvaeitsviakVlfPalSrlq..ddkkklrelylkvlrlialivlPiavglavvaellvkvll 284
                                        +k+++++++a  +s +   + P + + +  d+ ++ r+ y+ +l  + l+ +P+a+gla+va++++++ +
  gi|336253970|ref|YP_004597077.1| 262 LGKQITDFVLAPAES-LGFTISPNFGEYKanDELEEARRIYESSLTNTLLLYVPAAAGLAIVADPFISLAF 331
                                       *******99998655.66677899998762155689*******************************9987 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.2
                   Polysacc_synt_3 185 l 185
                                        
  gi|336253970|ref|YP_004597077.1| 442 A 442
                                       2 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   1.0      0.15   6.9e+02      91     127 ..      20      52 ..       7      65 .. 0.55
   2 !    9.9   9.0   0.00016      0.72       2      81 ..     125     205 ..     124     228 .. 0.89
   3 ?   -3.0   0.0       1.6     7e+03      80     104 ..     300     322 ..     297     333 .. 0.61
   4 !   70.2  20.1     4e-23   1.8e-19       1     142 [.     340     477 ..     340     478 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.15
                   Polysacc_synt_C  91 llkpllaalvmgivvylllllllgllllaalalllav 127
                                         +++l+++++++v   l+++ll    +  l  ++++
  gi|336253970|ref|YP_004597077.1|  20 A-VYMLSSALLMLV---LARFLLDPQGYGDLYWAISI 52 
                                       3.456666666666...66666666655533333333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00016
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli.plfgivGaaiatvlallvvavlnlyal 77 
                                       La  +l++++ s++t+ +  +qg ++  + + + +ig +  l++ + ++   fg++Ga+++ +++++++ ++ l +l
  gi|336253970|ref|YP_004597077.1| 125 LAAGVLYVVVKSFQTFAQISFQGFNELGYSAAVQAIGGATRLVFAVGFVlAGFGALGALFGYIVGYALAGAFGLAIL 201
                                       5667899999***************************************999***************9998888877 PP

                   Polysacc_synt_C  78 rrll 81 
                                       + ++
  gi|336253970|ref|YP_004597077.1| 202 YFKF 205
                                       7655 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.6
                   Polysacc_synt_C  80 llgiklellrrllkpllaalvmgiv 104
                                       ++  +l   ++ll ++ aa++++iv
  gi|336253970|ref|YP_004597077.1| 300 IYESSL--TNTLLLYVPAAAGLAIV 322
                                       555555..55566677777777776 PP

  == domain 4  score: 70.2 bits;  conditional E-value: 4e-23
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyal 77 
                                       vL+ l+  i+++++++++s  L  lgr+++ ++a   +a+++++lnl+lip +g+vGaaiatvl+  v+ ++nly +
  gi|336253970|ref|YP_004597077.1| 340 VLQALTAFIVLQAITNLTSDSLDYLGRAQARAVAKGGTAAANFGLNLVLIPAMGVVGAAIATVLTHSVYVAVNLYVV 416
                                       79*************************************************************************** PP

                   Polysacc_synt_C  78 rrllgikl.ellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                       + +l +++ +l r++  ++ ++ vm+i+v++++ ++    + +   l++a+++ga+ +++l+++++
  gi|336253970|ref|YP_004597077.1| 417 HSELSLRVrHLARTMGLIFGITGVMAIAVLIVTPMVS---SFP--MLIAAIALGAATWAVLAVASG 477
                                       ********99899999************664444444...444..899*************99876 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   6.6   0.00018      0.82       3     137 ..      16     147 ..      14     187 .. 0.79
   2 !   26.1   1.0   1.3e-09   5.7e-06      10     156 ..     238     386 ..     229     391 .. 0.77
   3 ?   -0.7   3.3      0.21   9.5e+02      16      67 ..     431     483 ..     425     489 .] 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00018
                              MatE   3 alenllesllslidtllvgrl..gskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqgl 76 
                                       +++ ++++l+s++++l+++r+  +++  + +  a+sil ++ +   +gl+ +++  ++ ++ +k++ ++ + lr ++
  gi|336253970|ref|YP_004597077.1|  16 LVARAVYMLSSALLMLVLARFllDPQGYGDLYWAISILAIVQLfADVGLGKSAARYIS-EYNEKDPGQIPHLLRSTM 91 
                                       5778889999999999999999999999999999999999999566999999999998.689*************** PP

                              MatE  77 illlllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrg 137
                                       +  l++  ++a ++llf + ++s+++ + +   la+  l +++      ++q+ ++  ++g
  gi|336253970|ref|YP_004597077.1|  92 VYKLVVVSVVAYALLLFHDELASMLGEPSAAPFLAAGVLYVVV-----KSFQTFAQISFQG 147
                                       ***99999999999************99975555555555443.....3333333333333 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 1.3e-09
                              MatE  10 sllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsli 85 
                                       ++ + idt+lvg + +s+a++ ++++ +i+ ++ +++ +l+  +++  g +      ++a++++  +l  +lll+++
  gi|336253970|ref|YP_004597077.1| 238 VVDKQIDTFLVGVFlSSTAVGFYTLGKQITDFVLAPAESLGFTISPNFGEYKANDELEEARRIYESSLTNTLLLYVP 314
                                       555789*********************************************************************** PP

                              MatE  86 iallvllfseqilsl.ftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllni 156
                                       +a+ + + +++++sl f + e  +++ + +  +++l ++ ++ +  l+   r+++++ +    +++ + ln+
  gi|336253970|ref|YP_004597077.1| 315 AAAGLAIVADPFISLaFPSYEGAIPVLQALTAFIVLQAITNLTSDSLDYLGRAQARAVAKGGTAAANFGLNL 386
                                       999766666666665165556577777777777777777776666666666666665554444444445555 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.21
                              MatE  16 dtllvgrlgskalAavsialsilsllfv.fllglstalttlvgqalGaknfkr 67 
                                       + l+ g  g  a+A++ ++ +++s+ ++  +++l++a+ ++ + a G  ++ +
  gi|336253970|ref|YP_004597077.1| 431 MGLIFGITGVMAIAVLIVTPMVSSFPMLiAAIALGAATWAVLAVASGLVDPGE 483
                                       55667777999999999999999988887889999999888888888666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 3400.85
//
Query:       gi|336253971|ref|YP_004597078.1|  [L=139]
Description: hypothetical protein Halxa_2581 [Halopiger xanaduensis SH-6]
Scores for 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  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); 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 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1051.04
//
Query:       gi|336253972|ref|YP_004597079.1|  [L=274]
Description: Catalase [Halopiger xanaduensis SH-6]
Scores for 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  269.0   0.1    4.2e-80  268.8   0.1    1.0  1  Mn_catalase   Manganese containing catalase
  ------ inclusion threshold ------
      0.011   16.1   0.1      0.027   14.9   0.2    1.6  2  Rubrerythrin  Rubrerythrin
      0.029   14.0   0.1       0.04   13.5   0.1    1.2  1  Foie-gras_1   Foie gras liver health family 1
       0.11   12.5   4.2      0.054   13.4   1.3    2.0  2  Ferritin      Ferritin-like domain


Domain annotation for each model (and alignments):
>> Mn_catalase  Manganese containing catalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.8   0.1   9.3e-84   4.2e-80       1     269 [.       1     268 [.       1     273 [. 0.95

  Alignments for each domain:
  == domain 1  score: 268.8 bits;  conditional E-value: 9.3e-84
                       Mn_catalase   1 mfvhdKkLqylakpdapdpvlAkklqEllGGqfGElsvalrYlfQgfnirdk.ekykdLlmdiatEElgHvEliatm 76 
                                       mf  + +Lqy++ ++ pdp +Ak+lq  +GGq+GE+ val+Y+fQ +  +++ e y++Llm++a+EElgH+E++a+ 
  gi|336253972|ref|YP_004597079.1|   1 MFFQEPELQYEVTVEDPDPHFAKLLQQAIGGQEGEMRVALQYMFQAWALPEEfEAYRNLLMETAAEELGHIEMLASA 77 
                                       9999*********************************************998467********************** PP

                       Mn_catalase  77 iarllegatleqqedveeedeviqsvlggrndsHaivsglgamlvdsaGvpwsadYivasGnliaDlranlaaEaka 153
                                       +++ l g++ e  e+ ee   ++++++ g+n++ +++sgl+am+vds Gvp++++Yi asGnl  Dl+an++aEa +
  gi|336253972|ref|YP_004597079.1|  78 VTKNLRGSPKEMREETEE-TAAVAAAMTGQNPRQYLSSGLSAMPVDSNGVPFTGAYIAASGNLAGDLYANVMAEATG 153
                                       ***************999.66699999************************************************** PP

                       Mn_catalase 154 rlqverlyeltddpgvrdmlsfLlaRelvHqlafekAleeleeeetkvvPvtfakklekqevarkllnlsegee.st 229
                                       r+ ++rl++ tddpg++dmls+L+aR+++Hq+++ +Ale+l++     vP++f++++e+q+v+++++   + e+ + 
  gi|336253972|ref|YP_004597079.1| 154 RTLATRLWDYTDDPGMKDMLSYLIARDTMHQNQWLEALESLDDPV--PVPASFPQEQENQDVNYTFISTRREEQpNP 228
                                       *****************************************9877..79999***************9998887256 PP

                       Mn_catalase 230 egrwakgealdevealevvketkegaaipeLksaPmisrn 269
                                       e  w++gea+d+ + + +++e +  +++    ++P + +n
  gi|336253972|ref|YP_004597079.1| 229 EYPWTQGEAPDGNGTFSYAAEQPGDGEVIAPDPDPSTYNN 268
                                       789******************9999999998999988765 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2     6e-06     0.027       9      72 ..      34      97 ..      23     115 .. 0.73
   2 ?   -3.3   0.0       2.4   1.1e+04      31      54 ..     169     192 ..     150     199 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6e-06
                                      HHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH.CSTTHH.B.SSBBS--- CS
                      Rubrerythrin  9 gEssarrlYkelaekakegypqiaelFeelAeeEreHakilnkllek.lepelelevkekvreya 72
                                      gE      Y++ a  + e+++  ++l+ e+A+eE  H ++l+ ++ k l+++ + e++e++ e a
  gi|336253972|ref|YP_004597079.1| 34 GEMRVALQYMFQAWALPEEFEAYRNLLMETAAEELGHIEMLASAVTKnLRGSPK-EMREETEETA 97
                                      45555567*********************************9988661555555.4555544444 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  31 iaelFeelAeeEreHakilnklle 54 
                                       ++ ++ +l++    H++   ++le
  gi|336253972|ref|YP_004597079.1| 169 MKDMLSYLIARDTMHQNQWLEALE 192
                                       444555555555555555555555 PP

>> Foie-gras_1  Foie gras liver health family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1     9e-06      0.04      90     214 ..      38     195 ..      18     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9e-06
                       Foie-gras_1  90 leeq........pwellhhagyyyqlaakhakerrelaeqia.........ndpeqspassiassayvydty..... 144
                                       + +q        p e++ +  + +  aa+++ + + la++++         + +e++  +++a  ++++++      
  gi|336253972|ref|YP_004597079.1|  38 VALQymfqawalPEEFEAYRNLLMETAAEELGHIEMLASAVTknlrgspkeMREETEETAAVAAAMTGQNPRqylss 114
                                       33335566677788999999999999999999999999999888887665544445556667677776665577999 PP

                       Foie-gras_1 145 ...lapepheeyplsgseekgvahskliidlLekaleeFskrkq..........tRlaeelsleiAeeylrlgdwkk 208
                                            p + + +p +g      a  +l+ dl+ ++++e++ r            + +++ ls+ iA++ ++ ++w +
  gi|336253972|ref|YP_004597079.1| 115 glsAMPVDSNGVPFTGA--YIAASGNLAGDLYANVMAEATGRTLatrlwdytddPGMKDMLSYLIARDTMHQNQWLE 189
                                       97777777778888887..77777788889************99999999999999********************* PP

                       Foie-gras_1 209 alellq 214
                                       ale l+
  gi|336253972|ref|YP_004597079.1| 190 ALESLD 195
                                       ***986 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.3   1.2e-05     0.054      10      56 ..      34      79 ..      22     116 .. 0.79
   2 ?   -1.9   0.1      0.63   2.8e+03     110     133 ..     165     189 ..     157     195 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin 10 deltaayqylamawyvkgpgleglaeffdeqaeeerehadklaeril 56
                                       e+  a+qy+  aw +  +++e+  ++++e a ee++h+++la  + 
  gi|336253972|ref|YP_004597079.1| 34 GEMRVALQYMFQAWAL-PEEFEAYRNLLMETAAEELGHIEMLASAVT 79
                                      479999****888876.578***********************8775 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.63
                                       T-HHHHHHHHHHHHHHHHHH.HHHH CS
                          Ferritin 110 gDpatadfledfleeqeehe.wele 133
                                        Dp++ d+l  +++    h+ ++le
  gi|336253972|ref|YP_004597079.1| 165 DDPGMKDMLSYLIARDTMHQnQWLE 189
                                       5888888886666654444404444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1939.36
//
Query:       gi|336253973|ref|YP_004597080.1|  [L=448]
Description: RimK family alpha-L-glutamate ligase [Halopiger xanaduensis SH-6]
Scores for 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   79.7   0.0    3.6e-22   78.9   0.0    1.4  1  RimK             RimK-like ATP-grasp domain
    6.6e-10   39.0   0.7    1.6e-07   31.3   0.1    2.3  2  Zn_protease      Putative ATP-dependant zinc protease
    3.6e-08   33.0   0.0    6.1e-08   32.3   0.0    1.4  1  GSH-S_ATP        Prokaryotic glutathione synthetase, ATP-gras
    3.4e-07   30.4   0.0    1.5e-06   28.4   0.0    2.1  2  ATP-grasp_3      ATP-grasp domain
    3.5e-05   23.9   1.1    8.4e-05   22.7   1.1    1.6  1  R2K_3            ATP-grasp domain, R2K clade family 3
    0.00063   20.3   0.4     0.0021   18.6   0.2    2.0  2  gag-asp_proteas  gag-polyprotein putative aspartyl protease
     0.0064   16.4   0.2      0.013   15.3   0.2    1.4  1  R2K_2            ATP-grasp domain, R2K clade family 2
  ------ inclusion threshold ------
      0.024   14.4   0.3      0.076   12.8   0.0    2.0  2  DUF5488          Family of unknown function (DUF5488)
      0.046   14.4   2.7      0.066   13.9   0.8    2.3  3  Asp_protease_2   Aspartyl protease
       0.18   11.0   0.0       0.75    9.0   0.0    2.1  1  ATPgrasp_YheCD   YheC/D like ATP-grasp


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0     2e-25   3.6e-22       3     178 ..     100     275 ..      98     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 2e-25
                                       -HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--EEE CS
                              RimK   3 dKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlealkeailvq 79 
                                        Kl +   La +++ +p ++la + +++++   ++  +   v K+  g+ G +       + ++      +   ++q
  gi|336253973|ref|YP_004597080.1| 100 HKLSTATTLAANDVRTPDVTLALNSDQLNAARSRY--GEEAVYKTAIGTHGGGTWKVGPDDPVNPK--VGNRYAFLQ 172
                                       577888899999****************9999999..588999*******9999988877777765..36777799* PP

                                       EE--SS-S..EEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE--..--HHHHHHHHHHHHHCT-SEEEEEEE CS
                              RimK  80 eyieeaen..ediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklq..lseeekelAikaakamelvvaGvDll 152
                                       e i+  +   +d+Rv vvd+e++aa+ r + + d+R+n+ +Gg +e ++  l ee +++A +aa+a++l++aGvDl+
  gi|336253973|ref|YP_004597080.1| 173 ELIDRDDArhRDVRVYVVDGEIIAAMYRYAPDNDWRTNVALGGSVEDATedLPEEARDMARRAADAVGLDYAGVDLV 249
                                       ***98877669***********************************9854489************************ PP

                                       EETTEEEEEEEESS--SHHHHHHHT- CS
                              RimK 153 rakrgllvlEvnsspglekiektlgi 178
                                       + ++g +vlEvn   g +++ + +++
  gi|336253973|ref|YP_004597080.1| 250 EGDEGWFVLEVNPTAGFKGLYQATQV 275
                                       *****************999777766 PP

>> Zn_protease  Putative ATP-dependant zinc protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0061        11       1      32 [.     326     359 ..     326     367 .. 0.84
   2 !   31.3   0.1   8.6e-11   1.6e-07      66     132 ..     369     434 ..     363     436 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0061
                       Zn_protease   1 vvGekEelsLpelkiq..lkakidtgaltsSLsa 32 
                                       v+G +Ee+ L +   +  + ak dtga+  S++ 
  gi|336253973|ref|YP_004597080.1| 326 VIGYTEEVVLSGTSGSksVVAKSDTGATRTSIDT 359
                                       578999999998865546**********999986 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 8.6e-11
                       Zn_protease  66 kvlrivkirqsagd.aekRpViklqlllgpeiekievtLtdRsavkypvllgvralikakaaVDpsrk 132
                                       ++  i++ir+ + + + +RpV+++ +  g++  ++  +++dRs++ ypv lg  ++i  + +VD+sr+
  gi|336253973|ref|YP_004597080.1| 369 PIKSITRIRSGSSKqSRSRPVVDVVVGVGGNQHTVTASVEDRSHMDYPVILG--RDILENYQVDVSRR 434
                                       56778999985554499***********************************..78888999***997 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   3.4e-11   6.1e-08      68     155 ..     165     252 ..     114     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3.4e-11
                                       TTS-EEEEE--G..GGGG-EEEEEEETTEE-SEEEEEE--SS-S---GGGTSCEEE..EE--HHHHHHHHHHHHHHH CS
                         GSH-S_ATP  68 gkepviaqrylp..eikeGDkRillvdGepigyalaRvpaegevRsnlaaggraea..telterdreiaeelapkLk 140
                                       g+++  +q+ ++  ++++ D+R+ +vdGe i  a+ R + +++ R+n+a gg++e   ++l e+ r +a++ a+   
  gi|336253973|ref|YP_004597080.1| 165 GNRYAFLQELIDrdDARHRDVRVYVVDGEIIA-AMYRYAPDNDWRTNVALGGSVEDatEDLPEEARDMARRAAD--- 237
                                       67788889998533899***************.*******************9875115688888888888776... PP

                                       HTT--EEEEEEETTE CS
                         GSH-S_ATP 141 ekGllfvGlDvigdk 155
                                       + Gl ++G+D++++ 
  gi|336253973|ref|YP_004597080.1| 238 AVGLDYAGVDLVEGD 252
                                       569*******99763 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   8.2e-10   1.5e-06       3     156 ..     100     262 ..      98     265 .. 0.73
   2 ?   -1.8   0.0       1.6   2.8e+03      27      64 ..     381     417 ..     369     438 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 8.2e-10
                                       SHHHHHHHHTTT.S---............-EESS--....SSSEEEEESS-------B--SS--TTE........EE CS
                       ATP-grasp_3   3 dKlktykkLkeagvkvP........tkleaeeleee....ekklvvKprdGaggesvrvveekeeae.aaieevelv 66 
                                        Kl t+  L ++ v++P        ++l+a     +     ++ v K + G  g ++ +v  ++  + +  +  + +
  gi|336253973|ref|YP_004597080.1| 100 HKLSTATTLAANDVRTPdvtlalnsDQLNA-----ArsryGEEAVYKTAIGTHGGGTWKVGPDDPVNpKVGNRYAFL 171
                                       5999*************9886654222222.....233348899*******9888888887666555055566679* PP

                                       EE---...SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEE.S----HHHHHHHHHHHHHTTSTT--EEEE CS
                       ATP-grasp_3  67 qefie...GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvt.pietelkeevvelaeevvekleglaGyvG 139
                                       qe i+    ++  v + +      + a+ r   ++ ++ +v  G+++ ++  +l ee++++a+++  ++ gl  y+G
  gi|336253973|ref|YP_004597080.1| 172 QELIDrddARHRDVRVYV-VDGEIIAAMYRYAPDNDWRTNVALGGSVeDATEDLPEEARDMARRAADAV-GL-DYAG 245
                                       ****73335666777755.33456666777777777777555555550566666***************.76.6*** PP

                                       EEEEESS.SEEEEEEES CS
                       ATP-grasp_3 140 vDlvlkdeepyviEvNP 156
                                       vDlv  de+  v+EvNP
  gi|336253973|ref|YP_004597080.1| 246 VDLVEGDEGWFVLEVNP 262
                                       ****************9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                                       SS--SSSEEEEESS-------B--SS--TTE....... CS
                       ATP-grasp_3  27 leeeekklvvKprdGaggesvrvveekeeaeaaieeve 64 
                                        +++ ++ vv  + G+gg++ +v     e+ + +++  
  gi|336253973|ref|YP_004597080.1| 381 SKQSRSRPVVDVVVGVGGNQHTVTASV-EDRSHMDYPV 417
                                       556677778888999999998888877.4555666655 PP

>> R2K_3  ATP-grasp domain, R2K clade family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   1.1   4.7e-08   8.4e-05     116     183 ..     182     262 ..     174     283 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.7e-08
                             R2K_3 116 saEwRvFvvdGevvaas.rYr.............kanddpdl.epdlaafaeavralvgappfyvlDvavtadGrwk 177
                                       +  +Rv+vvdGe++aa  rY              + +d++++ +++++ +a+ ++ +v  +    +D+   ++G w 
  gi|336253973|ref|YP_004597080.1| 182 HRDVRVYVVDGEIIAAMyRYApdndwrtnvalggSVEDATEDlPEEARDMARRAADAV-GLDYAGVDLVEGDEG-WF 256
                                       5789********9987526756666666666555444444447888888888888888.6**************.** PP

                             R2K_3 178 VVEvnd 183
                                       V Evn 
  gi|336253973|ref|YP_004597080.1| 257 VLEVNP 262
                                       *****6 PP

>> gag-asp_proteas  gag-polyprotein putative aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       7.2   1.3e+04      54      74 ..     101     121 ..      72     129 .. 0.59
   2 !   18.6   0.2   1.2e-06    0.0021       9      92 .]     343     426 ..     336     426 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.2
                                       EEEEEEEEEE.EETTEEEEEE CS
                   gag-asp_proteas  54 krvrldsvkiggielrnvsav 74 
                                       k  +  ++  +++++ +v+++
  gi|336253973|ref|YP_004597080.1| 101 KLSTATTLAANDVRTPDVTLA 121
                                       333444555555555555555 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.2e-06
                                       EEEEEEETT-SS-EEEHHHHHHTTGGGGEB..TT--EE-TTST.T-EEEEEEEEEE.EETTEEEEEEEEEESS..SS CS
                   gag-asp_proteas   9 pvkflvDTGAsstiiseelaerlglsrkedkgkvevktangev.eakrvrldsvkiggielrnvsavvlegel..dd 82 
                                       +v +  DTGA++t+i + la  +g  + +     +++ ++ ++ + ++v    v +gg + + v+a+v + +     
  gi|336253973|ref|YP_004597080.1| 343 SVVAKSDTGATRTSIDTGLAADIGAGPIKS--ITRIRSGSSKQsRSRPVVDVVVGVGGNQ-HTVTASVEDRSHmdYP 416
                                       566667*****************9887763..3444444444414455555578998855.56*****998852356 PP

                                       EEEEHHHHHH CS
                   gag-asp_proteas  83 lLLGldfLkr 92 
                                       ++LG d+L++
  gi|336253973|ref|YP_004597080.1| 417 VILGRDILEN 426
                                       7******985 PP

>> R2K_2  ATP-grasp domain, R2K clade family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   7.3e-06     0.013      67     139 ..     185     273 ..     181     278 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.3e-06
                             R2K_2  67 yRlfvldgeiit.vsrYagegrldpdp..................evaeeavaalksalpsayvlDvgvtedgetal 124
                                        R++v+dgeii+ + rYa + + +++                   ++a++a++a++        +D+++ ++ ++ +
  gi|336253973|ref|YP_004597080.1| 185 VRVYVVDGEIIAaMYRYAPDNDWRTNValggsvedatedlpeearDMARRAADAVG---LDYAGVDLVEGDE-GWFV 257
                                       6********9862689*977766555555999999999999777777777777777...5678899998888.9*** PP

                             R2K_2 125 vEandgwa.lglygld 139
                                        E+n+  +  gly++ 
  gi|336253973|ref|YP_004597080.1| 258 LEVNPTAGfKGLYQAT 273
                                       ****976414557765 PP

>> DUF5488  Family of unknown function (DUF5488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       7.2   1.3e+04      35      50 ..      47      62 ..      42      64 .. 0.73
   2 ?   12.8   0.0   4.2e-05     0.076       7      60 ..     353     409 ..     348     417 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 7.2
                           DUF5488 35 ynvsvivntpiGvitn 50
                                       + sv+++  + vi+n
  gi|336253973|ref|YP_004597080.1| 47 TDGSVVLEPSVDVIAN 62
                                      5568888888888887 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.2e-05
                           DUF5488   7 srtsiwtvfmlpimyGpiksmieisrssynvs...vivntpiGvitnaasmaayvnd 60 
                                       +rtsi t +   i  Gpiks+  i   s   s    +v+  +Gv  n  +++a v+d
  gi|336253973|ref|YP_004597080.1| 353 TRTSIDTGLAADIGAGPIKSITRIRSGSSKQSrsrPVVDVVVGVGGNQHTVTASVED 409
                                       79*********************966555544222589999******9999999988 PP

>> Asp_protease_2  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.2   9.2e+03      28      49 ..      73      91 ..      61     123 .. 0.49
   2 ?   -3.3   0.0       8.6   1.5e+04      66      79 ..     180     192 ..     175     199 .. 0.75
   3 ?   13.9   0.8   3.7e-05     0.066      10      89 ..     344     422 ..     333     423 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.2
                    Asp_protease_2 28 aeklglkvreseltvrvsgagg 49
                                      ae+lgl ++     ++v  ++ 
  gi|336253973|ref|YP_004597080.1| 73 AEELGLANTFA---QLVPMLNE 91
                                      56666655553...33333333 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.6
                    Asp_protease_2  66 ltlknvpalvldlg 79 
                                       ++ ++v+++v+d g
  gi|336253973|ref|YP_004597080.1| 180 ARHRDVRVYVVD-G 192
                                       677899999999.3 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 3.7e-05
                    Asp_protease_2  10 vrfllDTGasttlispelaeklglkvreseltvrvsgaggevkarlvrldslklggltlknvpalvldlgeei.dgl 85 
                                       v +  DTGa+ t i++ la+++g  + +s +t+  sg+++++ +r v+   + +gg   + v+a+v d+  ++  ++
  gi|336253973|ref|YP_004597080.1| 344 VVAKSDTGATRTSIDTGLAADIGAGPIKS-ITRIRSGSSKQSRSRPVVDVVVGVGG-NQHTVTASVEDRSHMDyPVI 418
                                       55667*******************99998.45555666666666666666788888.66778888888554442577 PP

                    Asp_protease_2  86 LGmd 89 
                                       LG d
  gi|336253973|ref|YP_004597080.1| 419 LGRD 422
                                       7766 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00042      0.75     103     175 ..     164     229 ..     157     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00042
                    ATPgrasp_YheCD 103 lkkkrylvQqgidlatidgrpfDfRvlvqKngkgkWevtgiaaRiagkgsittnlsrGGtalpleellkkafg 175
                                       ++++   +Q+ id  +   r+ D+Rv v    +g  e+++++ R a++++  tn++ GG++ ++ e l ++  
  gi|336253973|ref|YP_004597080.1| 164 VGNRYAFLQELIDRDD--ARHRDVRVYVV---DG--EIIAAMYRYAPDNDWRTNVALGGSVEDATEDLPEEAR 229
                                       5666667777777654..67778899888...22..5899*********************999988887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3232.42
//
Query:       gi|336253974|ref|YP_004597081.1|  [L=85]
Description: PRC-barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   38.4   0.0    1.2e-09   38.1   0.0    1.1  1  PRC         PRC-barrel domain
  ------ inclusion threshold ------
        0.1   13.2   0.4       0.19   12.4   0.2    1.5  2  Cadherin_4  Bacterial cadherin-like domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   1.3e-13   1.2e-09       1      75 [.       1      83 [.       1      85 [] 0.92

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.3e-13
                                      XEECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT...............-EEEEEGG.CEECCCTE CS
                               PRC  1 edefrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi..........gekevliPfdlavkigkdr 69
                                      ++ + as l Gk+V +++GeklG+++++ ++ ++g+++ + v+  +   +          ++ ++++P +   + ++d+
  gi|336253974|ref|YP_004597081.1|  1 MTTVLASTLSGKPVLSTNGEKLGTIENITMNLASGELEDVFVAPAKE-VPtatarafettDDGTLIVPAG-CMRDVDDY 77
                                      67899***************************************987.4589999999999999999999.99999999 PP

                                      EEETTS CS
                               PRC 70 iivdap 75
                                      ++++ p
  gi|336253974|ref|YP_004597081.1| 78 LLIERP 83
                                      999865 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.68   6.1e+03      20      20 ..      21      21 ..       4      37 .. 0.55
   2 ?   12.4   0.2   2.1e-05      0.19       6      34 ..      41      69 ..      39      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.68
                        Cadherin_4 20 s 20
                                       
  gi|336253974|ref|YP_004597081.1| 21 K 21
                                      1 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.1e-05
                        Cadherin_4  6 tvtgvndaPvavddsatvtedtpltitag 34
                                       v+++   P+a++ ++++t+d++l ++ag
  gi|336253974|ref|YP_004597081.1| 41 FVAPAKEVPTATARAFETTDDGTLIVPAG 69
                                      58999********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       173  (0.00964917); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); 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 0.21s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 670.01
//
Query:       gi|336253975|ref|YP_004597082.1|  [L=712]
Description: Catalase-peroxidase [Halopiger xanaduensis SH-6]
Scores for 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-88  294.2   0.0    9.1e-50  169.5   0.0    2.2  2  peroxidase  Peroxidase


Domain annotation for each model (and alignments):
>> peroxidase  Peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.5   0.0   5.1e-54   9.1e-50       4     228 ..      53     373 ..      50     374 .. 0.88
   2 !  122.8   0.0   9.1e-40   1.6e-35       2     228 ..     380     687 ..     379     688 .. 0.88

  Alignments for each domain:
  == domain 1  score: 169.5 bits;  conditional E-value: 5.1e-54
                                       HHHHCCCC........TTTHCHHHHHHHHHHHTT.......SSTTSCHHHTCCHHCSGGGTTTHHHHHHHHHHHHHC CS
                        peroxidase   4 fvkaalka........drdmgpsllrlafhdcfv.......gGcdgsvlllepektapaNaslrkgldvldaikakl 65 
                                       ++k+++++        ++++gp ++r+a+h++++       gG+ g+ ++++p +++p+N +l+k++++l++ik+k+
  gi|336253975|ref|YP_004597082.1|  53 DLKDLMTTsqdwwpadYGHYGPLFIRMAWHSAGTyrttdgrGGASGGNQRFAPLNSWPDNGNLDKARRLLEPIKQKY 129
                                       555555555556666799**********************9************************************ PP

                                       TT.....S-HHHHHHHHHHHHHHCTT--..--EE---S-SSGGG.S-S............................. CS
                        peroxidase  66 eaacpgvvScADlialaardavelaggplvpvslGRrDatessa.sevsnl.......................... 115
                                       +++    +S+ADli+la+++a+e +g ++  ++ GR+D  e+++ +++ ++                          
  gi|336253975|ref|YP_004597082.1| 130 GRK----LSWADLIVLAGNTALESMGMQTLGWAGGREDEFEPDEaVYW-GPedeweapqhdrvdedgelaeplgatv 201
                                       *95....*********************99**************9999.44567*********************** PP

                                       ..............-.-TS-HHHHHHHHHHHT--HHHHHHH.HGGGGC-EESHH...............SS-GGGT. CS
                        peroxidase 116 ..............PdptasvdelrdkfarkgltdeelvaL.sGaHtiGkahcssfsrly.a...aadpaldaayaa 173
                                                     Pdp +s+d++r+ f r+ ++dee+ aL +G+Ht+Gkah+++ + +  +   a+++ ++ ++  
  gi|336253975|ref|YP_004597082.1| 202 mgliyvdpegpngdPDPMKSADRIRQAFGRMAMSDEETAALiAGGHTFGKAHGATDDDMGpEpeaAPIEDQGLGWTD 278
                                       *******99999999*************************************9877755543556666667777776 PP

                                       ....HHS............EETS-STHHHHHHCC....................................T-EEEHH CS
                        peroxidase 174 e.kCasgnte...lvdld.tptkfdnsyfknlle....................................krgllrs 209
                                       + k ++++t+    +  +  pt +d+sy  nll+                                      +++++
  gi|336253975|ref|YP_004597082.1| 279 SgKGSETTTSgieGAW-NaWPTMWDTSYLDNLLDyeweltespagakqwqpveeeaydtvpdahdpsekhAPMMMTT 354
                                       5444333333343222.2367******************************************************** PP

                                       HHHHHHSCCCHHHHHHCCC CS
                        peroxidase 210 Dqvllsdsetralvekyae 228
                                       D +l++d+e+r+++e + +
  gi|336253975|ref|YP_004597082.1| 355 DVALKRDPEFREIIENFRD 373
                                       ***************9976 PP

  == domain 2  score: 122.8 bits;  conditional E-value: 9.1e-40
                                       HHHHHHCCCC.TTTHCH..HH.......HHHHHHH......................................HTT. CS
                        peroxidase   2 rafvkaalka.drdmgp..sl.......lrlafhd......................................cfv. 29 
                                       +af++a++k  +rdmgp   +       ++++++d                                      + + 
  gi|336253975|ref|YP_004597082.1| 380 DAFARAWYKLiHRDMGPpeRFlgpdvpeETFVWQDpvpdadyeligdeeaeqlkaeiletelsvsqlaktawaA-As 455
                                       6899*************65226889999*********************9999999999999998888776651.15 PP

                                       ........SSTTSCHHHTCCHHCSGGGT..TTHHHHHHHHHHHHHCTT.......S-HHHHHHHHHHHHHHCT.... CS
                        peroxidase  30 ........gGcdgsvlllepektapaNa..slrkgldvldaikakleaacpg.v.vScADlialaardavela.... 90 
                                               gG++g++++lep+++++ N+  +l+++l++l++++++++ + ++ v vS+ADli+l++ +ave+a    
  gi|336253975|ref|YP_004597082.1| 456 tyrdsdkrGGANGARIRLEPQRSWEVNEpaELETVLETLEEVQEEFNGSRSDdVrVSLADLIVLGGYAAVEQAaada 532
                                       68899999***************************************97755545*****************99995 PP

                                       T--...--EE---S-SSGGG.S-S.....-............-TS-HHH.HHHHHHHHT--HHHHHHH.HGGGGC-E CS
                        peroxidase  91 ggp.lvpvslGRrDatessa.sev.snl.P...........dptasvde.lrdkfarkgltdeelvaL.sGaHtiGk 150
                                       g    +p+++GR+Dat++++ +e+ + l P           d ++  ++ l+d +  + lt+ e+++L +G++++G+
  gi|336253975|ref|YP_004597082.1| 533 GYDvEIPFEPGRTDATQDQTdEESfEALkPeidgfrnyfggDYNEPPEDlLVDHADLLDLTASEMTVLvGGLRALGA 609
                                       444555**************888865556466677777777778888888*************************** PP

                                       ESHH...........SS-GGGT....HHS.........EETS-STHHHHHHCC........................ CS
                        peroxidase 151 ahcssfsrlyaaadpaldaayaaekCasgnte.lvdldtptkfdnsyfknlle........................ 202
                                       ++                           + +  v++d+p++++n++f+nll+                        
  gi|336253975|ref|YP_004597082.1| 610 NYQD-------------------------S-DlGVFTDEPETLSNDFFVNLLSmdyeweqasegeevyelidretge 660
                                       **21.........................2.2379999*************************************** PP

                                       .T-EEEHHHHHHHHSCCCHHHHHHCCC CS
                        peroxidase 203 .krgllrsDqvllsdsetralvekyae 228
                                        +++ +r+D+ ++s+s++ra++++ya+
  gi|336253975|ref|YP_004597082.1| 661 vEWTGSRVDLLFGSNSRLRAIADVYAA 687
                                       *************************97 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:                      299  (0.0166769); 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 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 4911.76
//
Query:       gi|336253976|ref|YP_004597083.1|  [L=456]
Description: hypothetical protein Halxa_2586 [Halopiger xanaduensis SH-6]
Scores for 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   5.1        3.9    7.6   0.3    2.7  2  ChapFlgA  Chaperone for flagella basal body P-ring formation


Domain annotation for each model (and alignments):
>> ChapFlgA  Chaperone for flagella basal body P-ring formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.6   0.00064        12       8      69 ..     119     180 ..     117     222 .. 0.82
   2 ?    7.6   0.3   0.00022       3.9       5      67 ..     240     302 ..     236     306 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00064
                          ChapFlgA   8 rpLkrgevitasdlalkkrdlsrlrggvltdeaigkkvkrsiragqpirqnmlekpplVkkg 69 
                                        +L++ge++t + ++++ ++ + ++++ +++e++ +++  +   ++ + ++++++ ++V+++
  gi|336253976|ref|YP_004597083.1| 119 DQLRQGETVTTEIVETQVIEREVVERDTIESEVVDTELADRQVVDSELLSRDIAETEFVTAD 180
                                       68999999999999999999999999999988888887777777777777778888888764 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00022
                          ChapFlgA   5 vaarpLkrgevitasdlalkkrdlsrlrggvltdeaigkkvkrsiragqpirqnmlekpplVk 67 
                                       v + +++++evi+ + ++ k+++ +++r ++++ + +  ++  + r+  ++++++l ++++V 
  gi|336253976|ref|YP_004597083.1| 240 VVQADIAPEEVIEREVIESKRGEGDTVRSELIERRTVEEEIHERTRQQFTLEETDLVESEVVG 302
                                       67889***************************************************9999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); 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:                         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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3294.59
//
Query:       gi|336253977|ref|YP_004597084.1|  [L=203]
Description: HhH-GPD family protein [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.8   0.0    1.7e-15   57.4   0.0    1.2  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei


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 !   57.4   0.0   9.3e-20   1.7e-15       3     105 ..      39     176 ..      37     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 9.3e-20
                                       HHHHTTS-HHHHHHHHHHHHHHHS.HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                           HhH-GPD   3 ailsqqtsderanriierlferfg.fptpedladadeekLrelirelGfyrrKakyikelArilv............ 66 
                                       +i+ qq+s+++a ++ er+fe+ +  +tpe++++a+++ Lr++    G++r+K++y +++Ar+++            
  gi|336253977|ref|YP_004597084.1|  39 SIINQQLSTASAMAVRERVFELLEgEVTPETVLAAEDDALRDA----GLSRSKIEYMRNAARAFQendytrdalady 111
                                       79*********************999*****************....****************************** PP

                                       ............................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHH CS
                                       ............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ............................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleel 105
                                                                    +pdvl+  D+ vrr++++l++  e   ++++ ++++e+
  gi|336253977|ref|YP_004597084.1| 112 sdeevidllteikgigewtanmyllfvlERPDVLPLGDLAVRRGIEQLYGDGEP--DEMTPAEMREI 176
                                       ****************************99*******************99774..45554444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1599.27
//
Query:       gi|336253978|ref|YP_004597085.1|  [L=208]
Description: hypothetical protein Halxa_2588 [Halopiger xanaduensis SH-6]
Scores for 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   24.3   2.1    0.00059   19.7   2.0    2.2  1  DUF2238   Predicted membrane protein (DUF2238)


Domain annotation for each model (and alignments):
>> DUF2238  Predicted membrane protein (DUF2238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   2.0   3.3e-08   0.00059      59     139 ..      91     177 ..      45     178 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.3e-08
                           DUF2238  59 YDrlvHfaqGllla....lvvrelllrkkkl...rkwllllavlvvlaisalYEliEwlvalllggeaaeaflGtqG 128
                                       +D l H +   l+a     v+r + l++ ++   r+++++ +++vvla++ ++El+E+ + ++++ ++++  l++ G
  gi|336253978|ref|YP_004597085.1|  91 WDHLTHAMSASLVAgagyTVARAIELHSDEItipRRFAFVYILVVVLAFAVVWELFEFGLDIVADTTGMTMPLAQHG 167
                                       3444443333332211113444444444444557889**************************99777666666666 PP

                           DUF2238 129 diWDaqkDmll 139
                                        + D+ +D+l+
  gi|336253978|ref|YP_004597085.1| 168 -LDDTVRDLLF 177
                                       .8999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1539.05
//
Query:       gi|336253979|ref|YP_004597086.1|  [L=213]
Description: hypothetical protein Halxa_2589 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.56   10.2   5.8        4.7    7.2   2.7    2.4  2  SK_channel  Calcium-activated SK potassium channel
        2.3    6.7   7.6       0.22   10.0   2.2    1.8  2  DUF5357     Family of unknown function (DUF5357)


Domain annotation for each model (and alignments):
>> SK_channel  Calcium-activated SK potassium channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0    0.0073        65      74     105 ..      65      96 ..      55     100 .. 0.77
   2 ?    7.2   2.7   0.00053       4.7      18      62 ..     107     150 ..     102     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0073
                        SK_channel  74 eiqlflidngaedwrvalsserilkillEllv 105
                                        + + l   +a+dwrv+l +e+++  ll +lv
  gi|336253979|ref|YP_004597086.1|  65 GVVVLLPPGAARDWRVMLPWELLVVALLPILV 96 
                                       556666667899********999999888776 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00053
                        SK_channel  18 faLvlalfGivlmvvetEllalavteklsivslalkvlislsTvi 62 
                                       fa +la+ G++l  v +El ++  ++ ++++++al v+ +++T++
  gi|336253979|ref|YP_004597086.1| 107 FATYLAIAGVALL-VTVELHMFTALRLTHWFAVALVVMTTMATAA 150
                                       77889*****986.679************************9987 PP

>> DUF5357  Family of unknown function (DUF5357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.3     0.045     4e+02      34      66 ..      33      67 ..      30      76 .. 0.77
   2 ?   10.0   2.2   2.5e-05      0.22      34      94 ..     135     196 ..     110     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.045
                           DUF5357 34 vfswll.sllalgvikdiial.vgWlFliagtawy 66
                                      v swll  +l++  +++++ +   Wl ++a+t  +
  gi|336253979|ref|YP_004597086.1| 33 VLSWLLvGVLSAVLVESLLEFdAHWLVFVAATGVV 67
                                      67887625788889999885527899999998765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 2.5e-05
                           DUF5357  34 vfswllsllalgvikdiialvgWlF.liagtawyttddplrvpgtflpvgalitgflvsvfa 94 
                                        f  +l +++++ +     +v W     +gta++tt+++l+++ t ++++ ++ g+l   + 
  gi|336253979|ref|YP_004597086.1| 135 WFAVALVVMTTMATAAAWTVVRWSMdARLGTAYLTTNEQLMIEWTSVTLAGFVAGVLFDSYF 196
                                       46666777777777777778888663569***************************986664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1658.08
//
Query:       gi|336253980|ref|YP_004597087.1|  [L=200]
Description: hypothetical protein Halxa_2590 [Halopiger xanaduensis SH-6]
Scores for 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-06   25.5  19.5    3.3e-05   23.3  14.1    2.9  2  YdjM      LexA-binding, inner membrane-associated putative hy
  ------ inclusion threshold ------
        3.5    7.3   9.7        1.1    8.9   3.7    2.6  3  DUF4184   Domain of unknown function (DUF4184)


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3  14.1   3.7e-09   3.3e-05       1     116 [.       1      94 [.       1     150 [. 0.81
   2 ?    0.6   1.3     0.034   3.1e+02       7      37 ..     136     169 ..     130     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.7e-09
                              YdjM   1 MdgltHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllfla 77 
                                       M+  tHa++G+a+++ l +  ++   +++la+a++g++lPD+D            +++      gHR   H   + a
  gi|336253980|ref|YP_004597087.1|   1 MMLPTHAIVGLAIAAPLVSVAPEF-APAALAGAIVGSVLPDLD------------MYA------GHRRTLHYPTGYA 58 
                                       9999**************999875.56****************............333......5999999999999 PP

                              YdjM  78 llalvlllllrlfgrsalrlgll.lllgvlsHlllDlltk 116
                                       lla+ +l++++l+ +s  +++++ ll+g+  H+  D   +
  gi|336253980|ref|YP_004597087.1|  59 LLAVPALAAAALVPAS-GSFAVAaLLVGAGAHCRMD---R 94 
                                       9999999999999999.5555555999999999888...4 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.034
                              YdjM   7 allGaalglalaallgaakeavllavavlg...A 37 
                                       ++l+++lgl l+  l a++ + +la++++g   A
  gi|336253980|ref|YP_004597087.1| 136 LALAVLLGLPLLVVLEAPFRWLVLAAIAVGgvyA 169
                                       5788999999999999999877777777774554 PP

>> DUF4184  Domain of unknown function (DUF4184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.7   0.00012       1.1       9      69 ..      12      71 ..       6      84 .. 0.78
   2 ?   -0.1   0.0     0.071   6.4e+02     104     120 ..      77      93 ..      72      96 .. 0.80
   3 ?    0.0   0.2     0.065   5.8e+02      58      86 ..     156     183 ..     144     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00012
                           DUF4184  9 aavlplkllkrkrlslsaL...viGslaPDveyflrlkakstltHtllglllvdlplalllalv 69
                                      a++ pl  +    + ++aL   ++Gs+ PD+ ++      +++ H  +g  l+++p   ++alv
  gi|336253980|ref|YP_004597087.1| 12 AIAAPL-VSVAPEFAPAALagaIVGSVLPDLDMYA---GHRRTLHYPTGYALLAVPALAAAALV 71
                                      677777.4444445555553338***********7...56799*************99999887 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.071
                           DUF4184 104 vvvvsaliGaatHvlwD 120
                                       ++v ++l+Ga  H   D
  gi|336253980|ref|YP_004597087.1|  77 FAVAALLVGAGAHCRMD 93 
                                       46777999999999888 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.065
                           DUF4184  58 vdlplalllalvfhlvikkpllallPaal 86 
                                       + ++ a+++  v+ +++++ l+al+P a+
  gi|336253980|ref|YP_004597087.1| 156 WLVLAAIAVGGVY-ALLRRRLAALAPVAF 183
                                       4455555555555.566778888888554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1471.36
//
Query:       gi|336253981|ref|YP_004597088.1|  [L=157]
Description: hypothetical protein Halxa_2591 [Halopiger xanaduensis SH-6]
Scores for 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    8.2   9.9        1.4    8.0   9.9    1.1  1  Astro_capsid_p  Turkey astrovirus capsid protein
        7.5    6.2  15.8        8.7    6.0  15.8    1.1  1  Cwf_Cwc_15      Cwf15/Cwc15 cell cycle control protein


Domain annotation for each model (and alignments):
>> Astro_capsid_p  Turkey astrovirus capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   9.9   0.00016       1.4     232     276 ..      96     147 ..      49     156 .. 0.37

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00016
                                       .XXXXXXXXXX......XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX..XX CS
                    Astro_capsid_p 232 eeisdpsdeed......eevsdeetdtevesde.DeddevdrfDletsyeSe 276
                                       +  ++p   +          sd++tdt+++sd+ D d + d  D +t ++S+
  gi|336253981|ref|YP_004597088.1|  96 DRAVEPVASTPetgrsrGGGSDTDTDTDTDSDDgDTDSDSDSDDGDTDSDSD 147
                                       2233333222211111112233444444443321222223333333333344 PP

>> Cwf_Cwc_15  Cwf15/Cwc15 cell cycle control protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  15.8   0.00098       8.7     107     146 ..     105     151 ..      70     157 .] 0.35

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00098
                                       -.............------------------------------------- CS
                        Cwf_Cwc_15 107 e...........areidaddedseeeeeeeeeesdddsdsdsdddddedet 146
                                       +           +++ d d ++++   ++++++++dd d dsd+dd   +t
  gi|336253981|ref|YP_004597088.1| 105 TpetgrsrgggsDTDTDTDTDSDD--GDTDSDSDSDDGDTDSDSDDG--DT 151
                                       122333332221222233333222..222222222222222222222..22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1216.57
//
Query:       gi|336253982|ref|YP_004597089.1|  [L=383]
Description: Butyryl-CoA dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-52  176.4   3.5    6.7e-52  175.7   3.5    1.3  1  Acyl-CoA_dh_1    Acyl-CoA dehydrogenase, C-terminal domain
    4.1e-36  124.1   0.1    1.3e-35  122.4   0.1    1.9  1  Acyl-CoA_dh_N    Acyl-CoA dehydrogenase, N-terminal domain
    1.4e-28   99.8   4.6    2.2e-28   99.2   4.6    1.3  1  Acyl-CoA_dh_2    Acyl-CoA dehydrogenase, C-terminal domain
    3.8e-26   91.1   0.0    7.8e-26   90.1   0.0    1.6  1  Acyl-CoA_dh_M    Acyl-CoA dehydrogenase, middle domain
  ------ inclusion threshold ------
      0.035   13.2   0.0      0.059   12.5   0.0    1.3  1  HpaB             4-hydroxyphenylacetate 3-hydroxylase C termi
      0.036   14.2   0.7       0.37   11.0   0.2    2.6  3  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.082   13.4   0.4         20    5.8   0.2    2.7  2  S-l_SbsC_C       S-layer protein SbsC C-terminal domain
       0.17   12.0   0.0        0.4   10.8   0.0    1.5  1  2OG-FeII_Oxy_2   2OG-Fe(II) oxygenase superfamily


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.7   3.5     3e-55   6.7e-52       6     150 .]     235     379 ..     233     379 .. 0.98

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 3e-55
                                       HHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH------ CS
                     Acyl-CoA_dh_1   6 vametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagk 82 
                                       + m+ ++ +R+avaa+ +g+a+ a + aleya++r++fgk + ++q++++klaema+++eaar+l+y+aa+ +d+g+
  gi|336253982|ref|YP_004597089.1| 235 QQMQFFDETRVAVAAQGVGIAKGATRAALEYAQDREQFGKSISEFQAIQHKLAEMATDTEAARNLTYKAAWNVDQGE 311
                                       57999************************************************************************ PP

                                       --HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH. CS
                     Acyl-CoA_dh_1  83 pdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrll 150
                                       + ++ asmaK +as++a++vad+a+q++GgaGy ++ pver+yrda++++i+eGt+eiq+n+iar +l
  gi|336253982|ref|YP_004597089.1| 312 DITKLASMAKEYASRVAVDVADEAVQIHGGAGYVDDFPVERFYRDAKITQIYEGTTEIQKNVIAREML 379
                                       *****************************************************************985 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   0.1     6e-39   1.3e-35       1     113 []       6     117 ..       6     117 .. 0.97

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 6e-39
                                       THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HH CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradag 77 
                                       t+eq+++r+++++fae+e+ phaae+d+e++fpr++++++ae+Gl+g ++p eygGag ++l++ai++eel  +d g
  gi|336253982|ref|YP_004597089.1|   6 TDEQRQIREEIQRFAENEIVPHAAEYDREEKFPRDIVDEAAEMGLTGAHIPMEYGGAGYSILDTAIITEELFSYDPG 82 
                                       79*************************************************************************** PP

                                       HHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  78 lalllgvhsslvapailrfGteeqkrryLpklasge 113
                                       +al++ v++s +++ai++fGte+qk+r+L ++a+ge
  gi|336253982|ref|YP_004597089.1|  83 IALSI-VSTSFGCEAIMNFGTEDQKERFLEPVAAGE 117
                                       99866.7899************************98 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   4.6   9.6e-32   2.2e-28       2     133 ..     246     367 ..     245     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 9.6e-32
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                        +aa+ +G+A++a  +++e+a++r +  +g+++++++a+q++lae+a++ +AAr l+++aa+     +++g+ +   
  gi|336253982|ref|YP_004597089.1| 246 AVAAQGVGIAKGATRAALEYAQDREQ--FGKSISEFQAIQHKLAEMATDTEAARNLTYKAAWN----VDQGEDI--- 313
                                       589***********************..***********************************....******9... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                        ++ a++a+ +a++ a++++d++++++Gg ++ ++ p++R++RDa++++++++++
  gi|336253982|ref|YP_004597089.1| 314 -TKLASMAKEYASRVAVDVADEAVQIHGGAGYVDDFPVERFYRDAKITQIYEGTT 367
                                       .99************************************************9875 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.0   3.5e-29   7.8e-26       2      97 .]     122     218 ..     121     218 .. 0.93

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 3.5e-29
                                       EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---..----EEEEEEE..GGGEEE- CS
                     Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd..rarglslflvprdapgvsvr 76 
                                        a++Ep++Gsdv sv+t  ae+dg+e+v+nG+K+witn+   ++++vl++t+ ++  r++g+s ++v++d+ g++ +
  gi|336253982|ref|YP_004597089.1| 122 AAISEPDTGSDVSSVST-RAEKDGDEWVINGNKMWITNGSVGDFFVVLCKTDPDAegRYNGFSQIVVESDRDGFEAE 197
                                       699**************.88999999************************44444699******************* PP

                                       ----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  77 rieeklGlrglptgelvfedv 97 
                                       +i  klG+r  +t+elvf+dv
  gi|336253982|ref|YP_004597089.1| 198 KISGKLGIRASDTAELVFDDV 218
                                       *******************97 PP

>> HpaB  4-hydroxyphenylacetate 3-hydroxylase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.6e-05     0.059      42      76 ..     276     310 ..     272     351 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                                       GGGSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EE- CS
                              HpaB  42 iekfshvqeklgelialrellyalliaaeaeaekd 76 
                                       i++f+++q kl+e+++ +e+ + l+++a+++  + 
  gi|336253982|ref|YP_004597089.1| 276 ISEFQAIQHKLAEMATDTEAARNLTYKAAWNVDQG 310
                                       789**************************998876 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 ?   -2.3   0.0       2.2   4.9e+03      24      41 ..      47      64 ..      29      65 .. 0.72
   2 ?   -1.1   0.0      0.97   2.2e+03      11      35 ..     199     223 ..     191     225 .. 0.81
   3 ?   11.0   0.2   0.00016      0.37      26      57 ..     239     270 ..     232     276 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.2
                   Acetyltransf_CG 24 vldfthTeVpeelrGkGi 41
                                      ++ +t   +p e++G G+
  gi|336253982|ref|YP_004597089.1| 47 EMGLTGAHIPMEYGGAGY 64
                                      566666778999999886 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.97
                   Acetyltransf_CG  11 evafleYevrkegvldfthTeVpee 35 
                                         ++l  +++++ +l+f+ + Vpee
  gi|336253982|ref|YP_004597089.1| 199 ISGKLGIRASDTAELVFDDVRVPEE 223
                                       4578888888999999*99999997 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00016
                   Acetyltransf_CG  26 dfthTeVpeelrGkGiAkkLvkaalddareeg 57 
                                        f+ T V  + +G GiAk  ++aal++a++++
  gi|336253982|ref|YP_004597089.1| 239 FFDETRVAVAAQGVGIAKGATRAALEYAQDRE 270
                                       5899************************9876 PP

>> S-l_SbsC_C  S-layer protein SbsC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.017        38      30      60 ..     109     140 ..     106     143 .. 0.83
   2 ?    5.8   0.2    0.0088        20      31      76 ..     290     336 ..     252     339 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
                        S-l_SbsC_C  30 svetpaagsklsgaaa.aytsgtditditata 60 
                                       + e++aag k+sgaa+ +  +g+d++++   a
  gi|336253982|ref|YP_004597089.1| 109 FLEPVAAGEKISGAAIsEPDTGSDVSSVSTRA 140
                                       57899********999********99776655 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0088
                        S-l_SbsC_C  31 vetpaagsklsgaaa.aytsgtditditatagqyillyeVDasgkiv 76 
                                       ++   a  +l+++aa ++  g+dit+   +a++y   ++VD    +v
  gi|336253982|ref|YP_004597089.1| 290 ATDTEAARNLTYKAAwNVDQGEDITKLASMAKEYASRVAVDVADEAV 336
                                       4444445556666556********************99999887766 PP

>> 2OG-FeII_Oxy_2  2OG-Fe(II) oxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018       0.4     123     144 ..      86     107 ..      79     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                    2OG-FeII_Oxy_2 123 pivSlSLGasatfrfgkesree 144
                                        ivS S+G++a++ fg+e ++e
  gi|336253982|ref|YP_004597089.1|  86 SIVSTSFGCEAIMNFGTEDQKE 107
                                       7***************986554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3028.52
//
Query:       gi|336253983|ref|YP_004597090.1|  [L=657]
Description: 3-hydroxyacyl-CoA dehydrogenase [Halopiger xanaduensis SH-6]
Scores for complete 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-68  230.6   1.6    1.7e-68  230.0   1.6    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    1.9e-61  207.6   0.0    4.2e-61  206.5   0.0    1.5  1  ECH_1           Enoyl-CoA hydratase/isomerase
    1.6e-50  169.7   1.1    1.9e-31  108.6   0.0    3.7  3  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
      1e-36  127.2   0.9    1.7e-32  113.3   0.0    3.1  3  ECH_2           Enoyl-CoA hydratase/isomerase
      4e-08   33.4   0.1    7.8e-08   32.4   0.1    1.5  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    1.7e-07   31.6   0.9    5.8e-07   29.8   0.9    2.0  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    5.2e-05   23.7   3.3    0.00013   22.5   2.0    2.3  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0067   16.0   0.1      0.011   15.3   0.1    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0069   16.5   0.4      0.015   15.4   0.4    1.5  1  OTCace          Aspartate/ornithine carbamoyltransferase, Asp
  ------ inclusion threshold ------
      0.032   13.5   0.1      0.055   12.7   0.1    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.063   12.6   3.9       0.55    9.6   1.9    2.7  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.066   12.5   2.0       0.25   10.6   0.6    2.5  3  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.073   13.6   0.0       0.14   12.7   0.0    1.5  1  XdhC_C          XdhC Rossmann domain
      0.083   12.3   0.2       0.21   11.0   0.2    1.6  1  PALP            Pyridoxal-phosphate dependent enzyme
      0.086   12.2   0.0       0.23   10.9   0.0    1.7  1  DUF3645         Protein of unknown function (DUF3645)
       0.21   11.1   2.0        5.2    6.5   0.3    2.2  2  DLH             Dienelactone hydrolase family
        0.3   10.6   5.9        6.8    6.2   5.9    2.2  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
       0.34   11.0   4.1         36    4.4   3.7    3.0  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> 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 !  230.0   1.6   1.7e-71   1.7e-68       1     179 [.       8     188 ..       8     189 .. 0.99

  Alignments for each domain:
  == domain 1  score: 230.0 bits;  conditional E-value: 1.7e-71
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav 77 
                                       +vav+GaG mG+gia+v+a ag++V++ di+ee+++++ e+ie sl+kl+ek +l+++e++aal+r+++  d++eav
  gi|336253983|ref|YP_004597090.1|   8 TVAVLGAGNMGHGIAEVAAMAGYDVTMRDIKEEFVQNGYEQIEWSLNKLAEKDQLSQDEADAALERVTPLVDMAEAV 84 
                                       69*************************************************************************** PP

                                       .C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-T CS
                           3HCDH_N  78 .dadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrge 153
                                        dad+viEav+E++e+K++v++ele++a+++ai+a+nTSslsi+elae+++rper++g+HFfnPp  m LvEv++g+
  gi|336253983|ref|YP_004597090.1|  85 aDADVVIEAVPEQMEIKKDVYQELEEHANDEAIFATNTSSLSITELAEVTERPERFCGMHFFNPPVRMDLVEVITGA 161
                                       ***************************************************************************** PP

                                       T--HHHHHHHHHHHHHTT-EEEEE.CS CS
                           3HCDH_N 154 kTseetvatvvelakkigktpvvv.kd 179
                                       +T+eet++t+ ela+++gktpv+v kd
  gi|336253983|ref|YP_004597090.1| 162 ETAEETLETIEELAEDFGKTPVRVhKD 188
                                       ************************776 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.5   0.0   4.2e-64   4.2e-61       6     250 ..     411     656 ..     408     657 .] 0.95

  Alignments for each domain:
  == domain 1  score: 206.5 bits;  conditional E-value: 4.2e-64
                                       EEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHC.HHHHHHHCCHHHH CS
                             ECH_1   6 vaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeek.akqallkeevlel 80 
                                       v  i l+rP+ +N++s+ell+El +a+  ledd +vra+ LtG gd+aF+aGad++ ma++    ++++l+ + ++ 
  gi|336253983|ref|YP_004597090.1| 411 VGHIVLDRPHRMNTISNELLAELSEAIDLLEDDDEVRAILLTGeGDRAFSAGADVQSMAAGADpLDAQELSRTGQQT 487
                                       77899******************************************************9987799999******** PP

                                       HHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT- CS
                             ECH_1  81 wtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgk 157
                                       + kl  +++pv+a v G+++gGG+ela ++D+++a++ ++fg++el+lGl+pg ggtq+l  +vG+ +A+ei+l+++
  gi|336253983|ref|YP_004597090.1| 488 FGKLEACDVPVVAGVDGYCLGGGMELATCADLRVASERSEFGQPELNLGLLPGWGGTQRLKHIVGEGRAKEIILTAE 564
                                       ***************************************************************************** PP

                                       EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHH CS
                             ECH_1 158 kisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddik 234
                                       ++ a+  ++ G v+ vv ++ l+ ealela  la  +p +++q+++  + + +d  +++le ea  f +++++dd  
  gi|336253983|ref|YP_004597090.1| 565 RFDAETMAEYGFVNDVVENDALEAEALELASDLA-GGPPIAQQFTKRAMLTGRDDTEAGLEYEASAFGHLMATDDLM 640
                                       **********************************.55556666777777777888899******************* PP

                                       HHHHHHHTCSH----- CS
                             ECH_1 235 eGlqaflEkrkpefed 250
                                       eG++af+  ++pefe+
  gi|336253983|ref|YP_004597090.1| 641 EGITAFMGDGEPEFEG 656
                                       **************97 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.083        83      25      89 ..       2      65 ..       1      72 [. 0.69
   2 !  108.6   0.0   1.9e-34   1.9e-31       1      97 []     191     286 ..     191     286 .. 0.98
   3 !   53.8   0.0   2.2e-17   2.2e-14       5      91 ..     304     390 ..     302     393 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.083
                                      -HHHHHHHHHHHHHHS.SCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HH.HHHHHHTT--BGG CS
                             3HCDH 25 spediDaamrlglGlp.mGpfelldlvgldvakkilevlaeelgerayapspl.leklveagrlgrk 89
                                      + edi +++ lg+G    G+ e++ ++g dv  + ++   ee+ ++ y++ ++ l+kl+e+++l++ 
  gi|336253983|ref|YP_004597090.1|  2 ELEDINTVAVLGAGNMgHGIAEVAAMAGYDVTMRDIK---EEFVQNGYEQIEWsLNKLAEKDQLSQD 65
                                      57999999999998555*************9755544...344444333333327777777777665 PP

  == domain 2  score: 108.6 bits;  conditional E-value: 1.9e-34
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GF+vnR+l+pl+nea++lv e  a+++++D+++++g+GlpmG fel d vg dv +++l++++e+lg   y+p+pll
  gi|336253983|ref|YP_004597090.1| 191 GFIVNRILVPLMNEACWLVSEDEATIAEVDSTTKYGMGLPMGSFELGDQVGNDVSYHVLDYMHEVLGAA-YEPAPLL 266
                                       9****************************************************************9988.8899*** PP

                                       HHHHHTT--BGGGTBSSSBC CS
                             3HCDH  78 eklveagrlgrktgkgfyky 97 
                                       e+ ve+++lg+ktgkgfy+y
  gi|336253983|ref|YP_004597090.1| 267 EEKVENEELGKKTGKGFYDY 286
                                       ******************99 PP

  == domain 3  score: 53.8 bits;  conditional E-value: 2.2e-17
                                       HHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHH CS
                             3HCDH   5 nRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklv 81 
                                        R+la++ nea +l+   va pe+iD+a++lg+G+p Gp +l+d +gl++ +  le  +ee+g ++yap++ l + +
  gi|336253983|ref|YP_004597090.1| 304 RRLLATMANEAAKLIGGDVAPPESIDEAVQLGAGFPDGPVKLVDDYGLETLHETLEDAYEETGHERYAPADYLAERA 380
                                       69******************************************************999**9*************** PP

                                       HTT--BGGGT CS
                             3HCDH  82 eagrlgrktg 91 
                                       eag + +  g
  gi|336253983|ref|YP_004597090.1| 381 EAGGFYESDG 390
                                       *998766655 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3      0.11   1.1e+02     157     252 ..      27     122 ..      17     145 .. 0.67
   2 !  113.3   0.0   1.7e-35   1.7e-32       1     181 [.     411     590 ..     411     596 .. 0.94
   3 !    9.4   0.0   0.00065      0.65     251     310 ..     592     649 ..     587     656 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.11
                                       B-HHHHHHTTS--EE--GGGHHHHHHHHHTT...........--------......----SHHHHHHHHHHHT.-S- CS
                             ECH_2 157 lkgadalaaglathyvpseklealeeaLaelessd...eeaveevleelaeeaeeeeeeselaekreaidrlfsads 230
                                       + g d+   ++ + +v++   e++e +L +l ++d   +++ +++le+++  ++    ++++a+    i+++ ++ +
  gi|336253983|ref|YP_004597090.1|  27 MAGYDVTMRDIKEEFVQNG-YEQIEWSLNKLAEKDqlsQDEADAALERVTPLVDM---AEAVADADVVIEAVPEQME 99 
                                       5566666777777777653.55666555555555544477778888877644443...4566666677777776665 PP

                                       .TTTHHHHHH.T..--SHHHHHH CS
                             ECH_2 231 .veeiveaLekaeaeedewakkt 252
                                         ++++++Le+++++e+ +a++t
  gi|336253983|ref|YP_004597090.1| 100 iKKDVYQELEEHANDEAIFATNT 122
                                       25789999997655555566555 PP

  == domain 2  score: 113.3 bits;  conditional E-value: 1.7e-35
                                       .EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHH CS
                             ECH_2   1 vgvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeY 77 
                                       vg+i L+rp+ +N +s e++ +l+ea++  e+ddev++++l+g+g++af+AG Dv++++  a+  +++  e+ r+  
  gi|336253983|ref|YP_004597090.1| 411 VGHIVLDRPHRMNTISNELLAELSEAIDLLEDDDEVRAILLTGEGDRAFSAGADVQSMAAGADPLDAQ--ELSRTGQ 485
                                       589********************************************************999886655..7999999 PP

                                       HHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH CS
                             ECH_2  78 klnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalT 153
                                       +    ++ +  pvva +dG+++GgG+ l++ + +rv++er+ f  PE ++Gl P  Gg+  L+++ g   ++ + lT
  gi|336253983|ref|YP_004597090.1| 486 QTFGKLEACDVPVVAGVDGYCLGGGMELATCADLRVASERSEFGQPELNLGLLPGWGGTQRLKHIVGeGRAKEIILT 562
                                       ****************************************************************976478999**** PP

                                       ---B-HHHHHHTTS--EE--GGGHHHHH CS
                             ECH_2 154 Garlkgadalaaglathyvpsekleale 181
                                       ++r++++ + + g+ + +v++++lea +
  gi|336253983|ref|YP_004597090.1| 563 AERFDAETMAEYGFVNDVVENDALEAEA 590
                                       **********************998754 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00065
                                       HHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS CS
                             ECH_2 251 ktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvd 310
                                       + ++ l+   P++ ++t +++  gr+ +  +  l+ E  +  +l+a++D++eG++a + d
  gi|336253983|ref|YP_004597090.1| 592 ELASDLAGGPPIAQQFTKRAMLTGRDDT--EAGLEYEASAFGHLMATDDLMEGITAFMGD 649
                                       6678899999****************95..*************************98755 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 !   32.4   0.1   7.8e-11   7.8e-08       2     139 ..       9     167 ..       8     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 7.8e-11
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-H.......HHHHHHHHHSSBTTTBTT----TTEEEES...-HHHHHT CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvree.......elieeineehenvkyLpgiklpenlvatt...dlaealk 68 
                                       +avlGaG+ G  +A v a +g +v++   +e       e+ie   ++  +++ L + + +++l+ +t   d+aea++
  gi|336253983|ref|YP_004597090.1|   9 VAVLGAGNMGHGIAEVAAMAGYDVTMRDIKEefvqngyEQIEWSLNKLAEKDQLSQDEADAALERVTplvDMAEAVA 85 
                                       9**************************9999999988866665555666666777777776655443333******* PP

                                       T--EEEE---HHH..HHHHHHHHCCC--TT-EEEE---SEET.TTEEHHHHHHHHH-S--.........EEEEESS- CS
                    NAD_Gly3P_dh_N  69 gadiivlvvPsqa..lrevlkklkgllkkkailvsliKGieegtlkllsevieeelkeek.........vavlsGps 134
                                       +ad+++ +vP q+   ++v ++l+++ +++ai++  +  ++  +l  ++e  e++ +++          v v++G+ 
  gi|336253983|ref|YP_004597090.1|  86 DADVVIEAVPEQMeiKKDVYQELEEHANDEAIFATNTSSLSITELAEVTERPERFCGMHFfnppvrmdlVEVITGAE 162
                                       **********9963257899*****9999999998888886655555555555555555444456666678888888 PP

                                       -HHHH CS
                    NAD_Gly3P_dh_N 135 lAeEv 139
                                        AeE 
  gi|336253983|ref|YP_004597090.1| 163 TAEET 167
                                       88886 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 !   29.8   0.9   5.8e-10   5.8e-07       2     116 ..       9     150 ..       8     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 5.8e-10
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........................EEE-SSHHHHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........................akaaesieelva 54 
                                       ++++G G+MG+ +a+  + agy+v++ + ++e v++  ++                         ++++ +++e+va
  gi|336253983|ref|YP_004597090.1|   9 VAVLGAGNMGHGIAEVAAMAGYDVTMRDIKEEFVQNGYEQIewslnklaekdqlsqdeadaalerVTPLVDMAEAVA 85 
                                       89****************************9888888887679999999**************************** PP

                                       HCSEEEE-SSSHHHHH.HHHHSHCCC--TT-EEEE.-S---HHHHHHHHHHHHH.TT-EEEEEEE CS
                     NAD_binding_2  55 sldvvitmvkagkavd.eviegllealkkgdilid.gstsspedtrelakelke.kglkfldaPV 116
                                       ++dvvi  v+++ +++ +v+++l e+++ ++i+   +s+ s+++  e++++ ++  g++f++ PV
  gi|336253983|ref|YP_004597090.1|  86 DADVVIEAVPEQMEIKkDVYQELEEHANDEAIFATnTSSLSITELAEVTERPERfCGMHFFNPPV 150
                                       ***********99986268888********99986155667777777777744326777777776 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 !   22.5   2.0   1.3e-07   0.00013       2      86 ..       9     113 ..       8     120 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.3e-07
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.......................-EEECECH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.......................vkvtavdn 55 
                                       ++++GaGnmg+++a+ ++ ag   ++++   + ++e ++   e+++                       v+    d 
  gi|336253983|ref|YP_004597090.1|   9 VAVLGAGNMGHGIAEVAAMAG---YDVT-MRDIKEEFVQNGYEQIEwslnklaekdqlsqdeadaalerVTPLV-DM 80 
                                       89*******************...5555.3355555555554555555555555566**********7666666.99 PP

                                       HHHHHH-SEEEE-S-HHH..HHHHHHHCGHHHH CS
                     F420_oxidored  56 eeaaeeadvvvlavkped..veevlselakdal 86 
                                       +ea+++advv+ av+ ++   ++v +el ++a 
  gi|336253983|ref|YP_004597090.1|  81 AEAVADADVVIEAVPEQMeiKKDVYQELEEHAN 113
                                       **************9776224667777755554 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 !   15.3   0.1   1.1e-05     0.011       2      86 ..       8      96 ..       7     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHH....HHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvd....klnsgkipiyepgLeelvkkavesgrlsfttdvekavee 76
                                      +++v+G+G +G   a v a +g +v++ Di ee v+    +++ +  ++ e+++ +  ++ ++ +r++   d+ +av++
  gi|336253983|ref|YP_004597090.1|  8 TVAVLGAGNMGHGIAEVAAMAGYDVTMRDIKEEFVQngyeQIEWSLNKLAEKDQLSQDEADAALERVTPLVDMAEAVAD 86
                                      699******************************9972222566667788888887777777778999999********* PP

                                      -SEEEE---- CS
                    UDPG_MGDP_dh_N 77 advifiaVgT 86
                                      adv++ aV+ 
  gi|336253983|ref|YP_004597090.1| 87 ADVVIEAVPE 96
                                      *****99985 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 !   15.4   0.4   1.5e-05     0.015       4      97 ..       8     112 ..       5     126 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                                       EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TT..SSH.............-HHHHHHHHHHHHHHT-EEEEESSC CS
                            OTCace   4 kiafvGdkknnvanslikllarlgmdvvlvaPkg..lep.............dkevleeakknakksggsititedl 65 
                                       ++a +G   +n+ ++ ++++a+ g dv++   k+  +++             +k++l++ +++a    +++t   d+
  gi|336253983|ref|YP_004597090.1|   8 TVAVLG--AGNMGHGIAEVAAMAGYDVTMRDIKEefVQNgyeqiewslnklaEKDQLSQDEADA--ALERVTPLVDM 80 
                                       577888..46**********************99974445555666554444334333332222..2356666679* PP

                                       HHHHTT-SEEEE--SSETTCCGGHHHHHHHHC CS
                            OTCace  66 eeavkgaDvvytdvwvsmgeekereerlkklk 97 
                                       +eav++aDvv+  v  +m+ +k+  ++l++++
  gi|336253983|ref|YP_004597090.1|  81 AEAVADADVVIEAVPEQMEIKKDVYQELEEHA 112
                                       ****************9*99888888888776 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 ?   12.7   0.1   5.5e-05     0.055       2     107 ..       8     120 ..       7     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-05
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias........evvkklnqgiell 70 
                                        v+v+G+G  G+  a+ +a ag++vt+ + +++++ +g    ++ l+  ++++++s        e v+ l    e +
  gi|336253983|ref|YP_004597090.1|   8 TVAVLGAGNMGHGIAEVAAMAGYDVTMRDIKEEFVQNGYEQIEWSLNKLAEKDQLSqdeadaalERVTPLVDMAEAV 84 
                                       58999999999999999999999999999999999998888888888888888777888876664444444444444 PP

                                       HCCT.CEEEEESCEEEEETEEECTCEEEEEESEEEE-- CS
                                       xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  71 lgee.vvkidpgkkkvklekkkegdeekiaydklvlAt 107
                                       +++  v++  p++  ++++k++ ++ e+ a d+ + At
  gi|336253983|ref|YP_004597090.1|  85 ADADvVIEAVPEQ--MEIKKDVYQELEEHANDEAIFAT 120
                                       4444344444544..66666666777777777777777 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 ?    9.6   1.9   0.00055      0.55      37      73 ..       7      43 ..       3     124 .. 0.86
   2 ?   -2.8   0.0       3.5   3.5e+03     109     159 ..     302     328 ..     295     334 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00055
                                      SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                                       tv+++G+G++G+ +a++++  g +v++ d +++  +
  gi|336253983|ref|YP_004597090.1|  7 NTVAVLGAGNMGHGIAEVAAMAGYDVTMRDIKEEFVQ 43
                                      59**************************999966333 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.5
                                       BSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSS CS
                      2-Hacid_dh_C 109 inaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeepl 159
                                       +                        e+ Ll+ + ++  + ++ Dv  +e +
  gi|336253983|ref|YP_004597090.1| 302 V------------------------ERRLLATMANEAAKLIGGDVAPPESI 328
                                       3........................44556666666666666666666655 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 ?   10.6   0.6   0.00025      0.25      30      99 ..       8      94 ..       5      97 .. 0.80
   2 ?   -0.9   0.0      0.84   8.4e+02      97     121 ..     289     313 ..     243     323 .. 0.91
   3 ?   -2.4   0.0       2.4   2.4e+03      33      52 ..     317     336 ..     305     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE.................HCHHHHHHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev.................lksqeellaeavk 90
                                      +v v+G+G  G   +++a+  g +Vt+ D++++  ++  + ++ + ++                  +      +aeav+
  gi|336253983|ref|YP_004597090.1|  8 TVAVLGAGNMGHGIAEVAAMAGYDVTMRDIKEEFVQNGYEqIEWS-LNKlaekdqlsqdeadaaleRVTPLVDMAEAVA 85
                                      699***************************998776544433333.222456799999999999876677778999999 PP

                                      H-SEEEE-- CS
                       AlaDh_PNT_C 91 eadvvigtv 99
                                      +advvi +v
  gi|336253983|ref|YP_004597090.1| 86 DADVVIEAV 94
                                      999999886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.84
                                       E---BTTSS---SC-HHHHHTS-TT CS
                       AlaDh_PNT_C  97 gtvlipGkkaPkLvteemvksMkpg 121
                                       g v ip  +   Lv+++ +++M + 
  gi|336253983|ref|YP_004597090.1| 289 GGVDIPTDEQSELVERRLLATMANE 313
                                       6789999***************876 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.4
                                       EESTSHHHHHHHHHHHHTT- CS
                       AlaDh_PNT_C  33 viGgGvaGlqAiatakglga 52 
                                        iGg va  ++i  a++lga
  gi|336253983|ref|YP_004597090.1| 317 LIGGDVAPPESIDEAVQLGA 336
                                       699***************98 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00014      0.14       1      35 [.       9      58 ..       9     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG...............- CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefa...............t 35
                                      ++++Gag++++ +a++aa++g++vt+ d +eef                +
  gi|336253983|ref|YP_004597090.1|  9 VAVLGAGNMGHGIAEVAAMAGYDVTMRDIKEEFVqngyeqiewslnklaE 58
                                      579****************************9886666666665555542 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00021      0.21      55      82 ..       6      33 ..       2      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                                      TSEEEEEBSSHHHHHHHHHHHHHT-EEE CS
                              PALP 55 aktvveassGNhgralAaaaallGlkvt 82
                                        tv++ ++GN+g ++A +aa++G++vt
  gi|336253983|ref|YP_004597090.1|  6 INTVAVLGAGNMGHGIAEVAAMAGYDVT 33
                                      57999********************998 PP

>> DUF3645  Protein of unknown function (DUF3645)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00023      0.23      16      32 ..     521     537 ..     521     537 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                           DUF3645  16 vPserSEFsHpDvvIvL 32 
                                       v serSEF++p+  ++L
  gi|336253983|ref|YP_004597090.1| 521 VASERSEFGQPELNLGL 537
                                       579*********98876 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.3    0.0053       5.2      19      93 ..      24      98 ..       7     105 .. 0.87
   2 ?    3.8   0.1     0.037        37     101     118 ..     501     518 ..     461     533 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0053
                               DLH 19 iqeifGvndnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavaylksvp 93
                                      + ++ G++ +++di+e ++++GY  +   l +  ++d+ +++ea +al+ +   v++++ ++d++  ++++ ++ 
  gi|336253983|ref|YP_004597090.1| 24 VAAMAGYDVTMRDIKEEFVQNGYEQIEWSLNKLAEKDQLSQDEADAALERVTPLVDMAEAVADADVVIEAVPEQM 98
                                      66789*************************9999999999999999**99999999*******998888887776 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.037
                               DLH 101 gvvGfCmGGalalllaae 118
                                       gv G+C+GG + l+  a 
  gi|336253983|ref|YP_004597090.1| 501 GVDGYCLGGGMELATCAD 518
                                       788*******98877665 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 ?    6.2   5.9    0.0068       6.8       7      89 ..       9     116 ..       3     128 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0068
                                       EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-........................HHHHHHHHTT-EEEEHHHHHH CS
                              IlvN   7 iaviGyGsqGhaqalnlrdsgldvvvglregs........................ksvkkAkeegfevltvaeavk 59 
                                       +av+G G+ Gh  a+    +g dv++   +++                          ++ A e+    +++aeav+
  gi|336253983|ref|YP_004597090.1|   9 VAVLGAGNMGHGIAEVAAMAGYDVTMRDIKEEfvqngyeqiewslnklaekdqlsqDEADAALERVTPLVDMAEAVA 85 
                                       666666666666666555555555555444444455555555555555555443223444555556667899***** PP

                                       T-SEEEE-S-HH..HHHHHHHHHTGGG--TT- CS
                              IlvN  60 kadvvmiliPDe..lqkevyeeeiepnlkegk 89 
                                       +advv+  +P++  ++k+vy +e+e++ ++++
  gi|336253983|ref|YP_004597090.1|  86 DADVVIEAVPEQmeIKKDVY-QELEEHANDEA 116
                                       **********9622578999.66776666555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   3.7     0.036        36      43      89 ..      54     100 ..       2     121 .. 0.58
   2 ?   -2.7   0.0       5.7   5.7e+03      88     122 ..     300     333 ..     295     337 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.036
                                       ESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-S CS
                      Shikimate_DH  43 NRtlerakelaeelkgeeiealkleelkellaeadvvisataseepi 89 
                                       N   e+ +   +e +++  ++++l ++ e++a+advvi a+  +  i
  gi|336253983|ref|YP_004597090.1|  54 NKLAEKDQLSQDEADAALERVTPLVDMAEAVADADVVIEAVPEQMEI 100
                                       33344444334444555556889999999999999999988765544 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.7
                                       -SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGG CS
                      Shikimate_DH  88 pilekeeveealkkrkkplllvDiavPRdvepeva 122
                                        ++e++ +  +  +++ +l+  D+a P  ++++v+
  gi|336253983|ref|YP_004597090.1| 300 ELVERRLLATMA-NEAAKLIGGDVAPPESIDEAVQ 333
                                       556666665554.3347778889999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.74u 0.26s 00:00:01.00 Elapsed: 00:00:00.44
# Mc/sec: 4499.84
//
Query:       gi|336253984|ref|YP_004597091.1|  [L=190]
Description: response regulator receiver protein [Halopiger xanaduensis SH-6]
Scores for 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   84.0   4.3    1.6e-23   82.8   4.3    1.7  1  HalX          HalX domain
    2.5e-21   75.9   1.1      3e-21   75.7   0.1    1.6  2  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.072   13.5   0.3       0.26   11.7   0.0    2.0  2  MtrB          Tetrahydromethanopterin S-methyltransferase sub
       0.14   12.2   0.1       0.39   10.8   0.0    1.8  2  DUF772        Transposase domain (DUF772)


Domain annotation for each model (and alignments):
>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   4.3   3.6e-27   1.6e-23       2      68 .]     117     183 ..     116     183 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 3.6e-27
                              HalX   2 rseYdeelqelfaLasKravLeaekseaeLadseeYqeLearleelraqldetldelddaddfealf 68 
                                       rs Y++ +qe++aL+sK+a+Le+ek+e+eL+d+ eY+eL++r+++l++ +det+++++++d+f  +f
  gi|336253984|ref|YP_004597091.1| 117 RSDYESAIQEYYALVSKKALLESEKAERELEDNAEYRELCDRVNDLEQAVDETVTSMSSHDEFVGAF 183
                                       99*************************************************************9887 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.1   6.6e-25     3e-21       1     111 [.       7     111 ..       7     112 .. 0.95
   2 ?   -2.2   0.1         1   4.7e+03       5      34 ..     147     178 ..     146     187 .. 0.50

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6.6e-25
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       vl+vdD+  +++l++ +l++++   v++a dg++ale++  + v ++llD +mpg++G e+l+++ree ++++v+++
  gi|336253984|ref|YP_004597091.1|   7 VLVVDDESRLADLFAAWLQSDWA--VETAYDGEQALEKISDS-VEVVLLDRRMPGLSGDEVLERLREEGYDCRVVMV 80 
                                       8******************8888..**************877.********************************** PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlkal 111
                                       ta + + d    +++g dd+l+Kp++++eLl+++
  gi|336253984|ref|YP_004597091.1|  81 TAVDPDFD---IIEMGFDDYLVKPVSKDELLEMV 111
                                       *9998665...5789****************998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                                       SSSHHHHHHHHHHHH.HTTE.EEEEEESSHHH CS
                      Response_reg   5 dDdplvrellrqlle.eegy.eevaeaedgke 34 
                                       +D+   rel+ ++ + e+ + e+v+++++ +e
  gi|336253984|ref|YP_004597091.1| 147 EDNAEYRELCDRVNDlEQAVdETVTSMSSHDE 178
                                       56666666666654422222244444444444 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.82   3.7e+03      12      41 ..      83     114 ..      78     129 .. 0.58
   2 ?   11.7   0.0   5.8e-05      0.26      31      63 ..     152     184 ..     141     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.82
                              MtrB  12 ldpetgvvaearedvvl..lsldpvleeidkL 41 
                                       +dp+  +++   +d ++  +s d++le +d++
  gi|336253984|ref|YP_004597091.1|  83 VDPDFDIIEMGFDDYLVkpVSKDELLEMVDDV 114
                                       45555566555555544223444555555444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.8e-05
                              MtrB  31 ldpvleeidkLekiaddlvnsLdpetallesyp 63 
                                       ++++ +++++Le+++d+ v+s++ + +++++++
  gi|336253984|ref|YP_004597091.1| 152 YRELCDRVNDLEQAVDETVTSMSSHDEFVGAFQ 184
                                       67899*************************997 PP

>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.4   6.2e+03      19      33 ..      56      70 ..      50      72 .. 0.76
   2 ?   10.8   0.0   8.6e-05      0.39      23      55 ..     138     170 ..     125     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.4
                            DUF772 19 lyglSdreleealre 33
                                      + glS  e+ e+lre
  gi|336253984|ref|YP_004597091.1| 56 MPGLSGDEVLERLRE 70
                                      568888888888886 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 8.6e-05
                            DUF772  23 Sdreleealrenlsfrwflgldlee.dpvpdhst 55 
                                        ++++e++l++n+++r +++  +++ +++ d+++
  gi|336253984|ref|YP_004597091.1| 138 ESEKAERELEDNAEYRELCDR-VNDlEQAVDETV 170
                                       789****************95.333466777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1386.96
//
Query:       gi|336253985|ref|YP_004597092.1|  [L=143]
Description: hypothetical protein Halxa_2595 [Halopiger xanaduensis SH-6]
Scores for 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-12   45.9  10.3    1.7e-06   27.5   0.2    2.3  2  SPW            SPW repeat
     0.0041   17.0   2.4      0.067   13.1   3.1    1.9  1  7TMR-DISM_7TM  7TM diverse intracellular signalling
  ------ inclusion threshold ------
      0.027   14.2   4.5      0.044   13.5   0.2    2.0  2  Cation_efflux  Cation efflux family
        3.2    7.8   6.7        1.1    9.3   0.7    2.6  2  OppC_N         N-terminal TM domain of oligopeptide transport


Domain annotation for each model (and alignments):
>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.2   3.8e-10   1.7e-06       4      43 ..      29      66 ..      26      70 .. 0.90
   2 !   21.1   5.5   3.7e-08   0.00017       2      46 ..      83     126 ..      82     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3.8e-10
                               SPW  4 nlllGlwlivSPWvlGfsattgaawnnvivGavvavLala 43
                                      + l+Gl+l++SP++l   +t +a+wn+  vG  +++La +
  gi|336253985|ref|YP_004597092.1| 29 IALIGLYLVASPFILE--STDAATWNDTLVGTGIFLLAGY 66
                                      679************9..6778**************9965 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 3.7e-08
                               SPW   2 WanlllGlwlivSPWvlGfsattgaawnnvivGavvavLalafaa 46 
                                       ++ +llGlw+ +SP v+   ++  +a+   i G++va+La++ a 
  gi|336253985|ref|YP_004597092.1|  83 GLTVLLGLWALISPAVIEMGSN-ELATGTAISGLAVALLAMYSAY 126
                                       7899*************97666.9999999***********9886 PP

>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   3.1   1.5e-05     0.067      67     148 ..      48     129 ..      24     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                     7TMR-DISM_7TM  67 kllyltlllllilfllFarsflelkkkprllklllllavllsllllllpllpyteslslaqllallvillllligik 143
                                        + ++  l+++++fll  ++f +l+k +       +l+vll+l +l++p++++  s++la+ +a++++ ++ll+++ 
  gi|336253985|ref|YP_004597092.1|  48 AATWNDTLVGTGIFLLAGYNFYRLSKDRLANVGAAGLTVLLGLWALISPAVIEMGSNELATGTAISGLAVALLAMYS 124
                                       334444556666777778889888665477777899999**********************9999999999999999 PP

                     7TMR-DISM_7TM 144 awrkg 148
                                       a+ ++
  gi|336253985|ref|YP_004597092.1| 125 AYANN 129
                                       88443 PP

>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   9.9e-06     0.044     135     196 ..      16      77 ..       4      79 .. 0.72
   2 ?    3.0   0.8     0.016        74      75     121 ..      82     126 ..      75     135 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.9e-06
                     Cation_efflux 135 alkaaalhvlgDaltslgvlvsalvillfnlksg.......plaDpvaslligliilysalkllkesls 196
                                       al++       D++++l +l+++++ +l+  +         ++ D +++  i l+  y+ ++l k+ l 
  gi|336253985|ref|YP_004597092.1|  16 ALNT-------DTMQWLSALIALIGLYLVASPFIlestdaaTWNDTLVGTGIFLLAGYNFYRLSKDRLA 77 
                                       4444.......666666666666666666443335566679************************9875 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.016
                     Cation_efflux  75 gllllglavfllleaiqklikegereihaglalvvalvslvvnlall 121
                                       + l+++l++++l+     +i+ g +e  +g a+ +++v+l+ ++  +
  gi|336253985|ref|YP_004597092.1|  82 AGLTVLLGLWALISPA--VIEMGSNELATGTAISGLAVALLAMYSAY 126
                                       5566666666666655..33224444444444444444444444433 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.1       0.1   4.7e+02      20      36 ..      28      42 ..      24      64 .. 0.62
   2 ?    9.3   0.7   0.00024       1.1       7      36 ..      68      98 ..      59     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.1
                            OppC_N 20 lvilllllliaifaPli 36
                                      l+ l+ l+l+a   P+i
  gi|336253985|ref|YP_004597092.1| 28 LIALIGLYLVA--SPFI 42
                                      23333333332..4666 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00024
                            OppC_N  7 wrrFkrNklAvvglvilllllli.aifaPli 36
                                      ++r+ +++lA vg + l +ll + a++ P +
  gi|336253985|ref|YP_004597092.1| 68 FYRLSKDRLANVGAAGLTVLLGLwALISPAV 98
                                      68*****************888657777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1100.03
//
Query:       gi|336253986|ref|YP_004597093.1|  [L=384]
Description: Butyryl-CoA dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-41  140.7   4.0    8.5e-41  139.7   4.0    1.5  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.3e-27   95.8   0.0    3.7e-27   94.3   0.0    1.8  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    3.2e-24   85.7   0.4    8.5e-24   84.4   0.4    1.8  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    1.1e-16   61.3   6.8    1.9e-16   60.5   6.8    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
       0.13   12.3   0.0        7.3    6.6   0.0    2.5  2  Mor            Mor transcription activator family


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.7   4.0   2.4e-44   8.5e-41       1     148 [.     234     381 ..     234     382 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.7 bits;  conditional E-value: 2.4e-44
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       g Gf  +   +nh+R+ava   lg+a++a+eea+++ ++r++fg+++ ++q+v++ la+m  e e+ar l++ra e+
  gi|336253986|ref|YP_004597093.1| 234 GAGFWMISDFFNHGRVAVAGHGLGMAAAAIEEAWAFTHDREEFGRTINEFQAVQHGLADMLLEFESARTLTWRACEK 310
                                       579999*********************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                       + ++++++  a++aK +a+e+a++va++ mq +Gg+++l+e +++r yrdarv  i+eG++eiqrn+i r+
  gi|336253986|ref|YP_004597093.1| 311 VANDDHAGYWAALAKTKATEAAVDVAEQGMQFHGGRSVLDERRIARVYRDARVPVIYEGANEIQRNLIYRQ 381
                                       ********************************************************************986 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.0     1e-30   3.7e-27       1      97 []     125     222 ..     125     222 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 1e-30
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---..----EEEEEEE..GGGEEE CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd..rarglslflvprdapgvsv 75 
                                       ++a++Ep++Gsd+a+++t  ae++g+e+v+nGeK wi+n+ +a++++v+art++++  r++++slf+vp+d+ g + 
  gi|336253986|ref|YP_004597093.1| 125 GLAVSEPDTGSDLAGMET-RAEKEGDEWVINGEKYWIGNGVEADWVTVYARTDDDEdnRYNNHSLFIVPTDTDGYEA 200
                                       589***************.77888888************************55555699****************** PP

                                       -----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  76 rrieeklGlrglptgelvfedv 97 
                                       ++i+ek+++r  ++++++f+d+
  gi|336253986|ref|YP_004597093.1| 201 EHIPEKMAMRASKQAHITFDDC 222
                                       ********************97 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.4   2.4e-27   8.5e-24       2     113 .]      11     121 ..      10     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 2.4e-27
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                       e  +++++++refa+e+++p+a+e+ ++ge+p++++++  e+Gl++  +pee+gG+g+d  + + ++ee+ radag+
  gi|336253986|ref|YP_004597093.1|  11 EHARDVKQEAREFAREHIEPNAQEYFQSGEYPHDILEAGQEAGLVAQDIPEEWGGRGFDLPQLLALTEEFYRADAGI 87 
                                       677899*********************************************************************** PP

                                       HHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  79 alllgvhsslvapailrfGteeqkrryLpklasge 113
                                       al+l++ s  +++  +++G++eq ++y++++a+ge
  gi|336253986|ref|YP_004597093.1|  88 ALTLQLAS-FGCELTYEYGSDEQCEEYIRPVAEGE 121
                                       **999965.777999******************98 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   6.8   5.4e-20   1.9e-16       3     133 ..     251     371 ..     249     372 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 5.4e-20
                                       HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHH CS
                     Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtved 79 
                                       +a   lG+A aa++e+ +++++r +  +g+++++++a+q+ la++  + ++Ar+l+ ra+++    +a++++     
  gi|336253986|ref|YP_004597093.1| 251 VAGHGLGMAAAAIEEAWAFTHDREE--FGRTINEFQAVQHGLADMLLEFESARTLTWRACEK----VANDDHA---- 317
                                       67789********************..***********************************....6666664.... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  80 raearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                          a++a++ a+e a++++++ ++ +Gg+++++e ++ R++RDa++  +++++n
  gi|336253986|ref|YP_004597093.1| 318 GYWAALAKTKATEAAVDVAEQGMQFHGGRSVLDERRIARVYRDARVPVIYEGAN 371
                                       67899*****************************************99998877 PP

>> Mor  Mor transcription activator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.002       7.3      22      57 ..      39      76 ..      19      83 .. 0.74
   2 ?    3.0   0.0     0.028     1e+02      24      49 ..     323     348 ..     309     380 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.002
                                      S.S-......TTSHHHHHHHHHHHH-SS------SHHH CS
                               Mor 22 geideal..aeqigeevadalaahwGGqqiyiPrgvkl 57
                                      ge+++++  a q +  va+ + ++wGG+ + +P+ + l
  gi|336253986|ref|YP_004597093.1| 39 GEYPHDIleAGQEAGLVAQDIPEEWGGRGFDLPQLLAL 76
                                      5555444226778888*****************97766 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.028
                                       S-....TTSHHHHHHHHHHHH-SS-- CS
                               Mor  24 idealaeqigeevadalaahwGGqqi 49 
                                       + +  a++++ +va++ ++  GG+++
  gi|336253986|ref|YP_004597093.1| 323 LAKTKATEAAVDVAEQGMQFHGGRSV 348
                                       55678999***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); 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:                         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 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2797.04
//
Query:       gi|336253987|ref|YP_004597094.1|  [L=222]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-15   54.8   0.0    9.5e-15   54.1   0.0    1.3  1  HTH_10         HTH DNA binding domain
    2.3e-12   47.1   2.0    3.2e-12   46.6   2.0    1.2  1  BAT            GAF and HTH_10 associated domain
      5e-06   25.9   0.1    1.1e-05   24.8   0.1    1.6  1  Sigma70_r4     Sigma-70, region 4
    0.00026   20.8   0.0    0.00049   19.9   0.0    1.5  1  MarR_2         MarR family
    0.00031   20.5   0.1    0.00058   19.6   0.1    1.4  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0019   17.7   0.0     0.0035   16.9   0.0    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
       0.01   15.5   0.0       0.11   12.2   0.0    2.2  2  Sigma70_r4_2   Sigma-70, region 4
      0.086   12.5   0.0       0.19   11.4   0.0    1.5  1  HTH_50         Helix-turn-helix domain
       0.12   12.3   0.0       0.26   11.2   0.0    1.6  1  HTH_11         HTH domain
       0.21   11.8   0.0       0.36   11.1   0.0    1.3  1  UPF0122        Putative helix-turn-helix protein, YlxM / p13 


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 !   54.1   0.0   5.3e-18   9.5e-15       1      52 [.     156     207 ..     156     208 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 5.3e-18
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT  q e+l lAye GYF+ PR+vt++eL +elGIs++++  +Lr+   +++
  gi|336253987|ref|YP_004597094.1| 156 LTGPQQEALVLAYERGYFNSPRDVTMAELGDELGISQQAVASRLRRGVDQIL 207
                                       7889*****************************************9887776 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   2.0   1.8e-15   3.2e-12       4     131 ..       3     132 ..       1     147 [. 0.83

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.8e-15
                               BAT   4 veLeleirdeddvlvalaae.ldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtl 79 
                                       +e ++++  ++++l ++ ++  d +vele+++p  d  v+ +f+v+g+ ++++++a++d+++v+d+r+v+   d+ l
  gi|336253987|ref|YP_004597094.1|   3 TEATFTVPADEFPLGSVFEQlPDVTVELERIIPARD-VVVPYFWVRGTPVDDIESAFADHPGVTDIRLVDSVADEYL 78 
                                       678888888888888665551699*********777.699***********************************87 PP

                               BAT  80 leltvs..gpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealee 131
                                       l+++++   + ++s+l+e  + + +a+ ++ r+++ v+   + d+ ++ ++++e
  gi|336253987|ref|YP_004597094.1|  79 LRVEWTteYEGVLSVLTETKVPLVKAVGTNRRWTFDVRGDVRSDIAAFQRRCQE 132
                                       77665522679**********************999976666666666555554 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   6.2e-09   1.1e-05       4      47 ..     155     205 ..     154     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.2e-09
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrk 47 
                                        L+  ++e l+l +        ++ T++E+g++lgiS+ +V ++++r++++
  gi|336253987|ref|YP_004597094.1| 155 ALTGPQQEALVLAYergyfnsPRDVTMAELGDELGISQQAVASRLRRGVDQ 205
                                       58888999******999999999************************9986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.7e-07   0.00049      18      47 ..     175     204 ..     137     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.7e-07
                                       TTSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2  18 pgrdltvgelarrlglsksavsrilkrLva 47 
                                        +rd+t++el ++lg+s++av  +l+r v+
  gi|336253987|ref|YP_004597094.1| 175 SPRDVTMAELGDELGISQQAVASRLRRGVD 204
                                       3459**********************9665 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 !   19.6   0.1   3.2e-07   0.00058      19      40 ..     180     201 ..     178     201 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.2e-07
                     HTH_AsnC-type  19 syaeLAervGlSestvlrRvrr 40 
                                       ++aeL++++G+S+++v+ R+rr
  gi|336253987|ref|YP_004597094.1| 180 TMAELGDELGISQQAVASRLRR 201
                                       79******************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 !   16.9   0.0     2e-06    0.0035      18      40 ..     179     201 ..     175     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                            HTH_24  18 isqreLAerlglSpstvnrrlkr 40 
                                        +++eL ++lg+S+++v  rl+r
  gi|336253987|ref|YP_004597094.1| 179 VTMAELGDELGISQQAVASRLRR 201
                                       89*******************98 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 ?    0.5   0.0      0.27   4.8e+02      11      26 ..     156     171 ..     154     174 .. 0.83
   2 ?   12.2   0.0     6e-05      0.11      28      51 ..     180     203 ..     177     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.27
                                       S-HHHHHHHHHHHTS- CS
                      Sigma70_r4_2  11 Lperqreifllryleg 26 
                                       L+  q+e+++l y+ g
  gi|336253987|ref|YP_004597094.1| 156 LTGPQQEALVLAYERG 171
                                       77789******99877 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6e-05
                                       -HHHHHHHHT--HHHHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsRAr 51 
                                       + +E   +lgis ++V srl+R+ 
  gi|336253987|ref|YP_004597094.1| 180 TMAELGDELGISQQAVASRLRRGV 203
                                       6789999***************96 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0001      0.19      29      46 ..     184     201 ..     173     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                            HTH_50  29 lAkrLGvShtaianklrk 46 
                                       l+  LG+S+ a+a +lr+
  gi|336253987|ref|YP_004597094.1| 184 LGDELGISQQAVASRLRR 201
                                       6889************98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.26      12      34 ..     175     197 ..     170     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                            HTH_11  12 argpisgeeLAeeLnvSrrtvrr 34 
                                       +  +++ +eL +eL++S ++v  
  gi|336253987|ref|YP_004597094.1| 175 SPRDVTMAELGDELGISQQAVAS 197
                                       5566****************965 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0002      0.36      32      61 ..     177     206 ..     154     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                           UPF0122  32 dDlSlsEiAeefnvsrqavydnikrtekll 61 
                                        D  ++E+ +e  +s+qav   ++r  +++
  gi|336253987|ref|YP_004597094.1| 177 RDVTMAELGDELGISQQAVASRLRRGVDQI 206
                                       699********************9976554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1678.67
//
Query:       gi|336253988|ref|YP_004597095.1|  [L=440]
Description: integral membrane sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for 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   98.7   0.0    4.8e-28   97.9   0.0    1.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    7.1e-11   42.0   3.3    4.3e-10   39.5   0.0    3.0  3  HisKA        His Kinase A (phospho-acceptor) domain
     0.0016   18.1   0.5      0.028   14.0   0.1    2.2  2  TMEM100      Transmembrane protein 100
     0.0017   18.3   0.0      0.048   13.6   0.0    2.3  1  HATPase_c_5  GHKL domain
      0.003   17.1   6.6     0.0069   16.0   6.6    1.6  1  HisKA_4TM    Archaeal 4TM region of histidine kinase
  ------ inclusion threshold ------
      0.018   15.5   4.0      0.038   14.4   4.0    1.5  1  ZapB         Cell division protein ZapB
       0.05   13.1   0.1        7.4    6.0   0.1    2.4  2  adh_short    short chain dehydrogenase
      0.066   13.0   2.7       0.11   12.4   2.7    1.2  1  KASH_CCD     Coiled-coil region of CCDC155 or KASH


Domain annotation for each model (and alignments):
>> 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 !   97.9   0.0   2.1e-31   4.8e-28       1     110 [.     282     409 ..     282     411 .. 0.86

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 2.1e-31
                                       EHHHHHHHHHHHHHHHHHHHHS.TTTEEEEEEEE.........EE.........TEEEEEEEESSSSSTTHHHTGTC CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfat.kageieveika.........se.........ddlvisveDnGiGipkedlkklf 58 
                                       gde++Lrq+++nl++Na+++++ + ++++v+ ++          e            +isv+D GiGi+++d +++f
  gi|336253988|ref|YP_004597095.1| 282 GDERQLRQVFQNLLSNAIEYSGdEPPRVHVSAERsaeraaeaeGEsggesrgtgAAWTISVRDEGIGIDPDDADRVF 358
                                       79******************55556666666665766665554014556677889********************** PP

                                       STTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  59 ekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       + f++  ++++++ g+G+Gl++++++ve++gGeiwv++epg+G+tf+ftlp 
  gi|336253988|ref|YP_004597095.1| 359 GVFQR-LHSMNEHAGSGIGLALCERIVERHGGEIWVDTEPGEGSTFRFTLPS 409
                                       *****.99999***************************************96 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.7      0.37   8.3e+02      24      52 ..     143     168 ..     136     175 .. 0.49
   2 !   39.5   0.0   1.9e-13   4.3e-10       2      66 ..     174     240 ..     173     241 .. 0.93
   3 ?    0.9   0.0      0.22   4.9e+02      37      59 ..     273     295 ..     261     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.37
                                       HHHHHC..T-HSSCHHHHHHHHHHHHHHH CS
                             HisKA  24 aeaLkregklteelkeyletiesearrld 52 
                                       aeaL      +eelk+  +++e+ + +l+
  gi|336253988|ref|YP_004597095.1| 143 AEALAA---RNEELKRTERRLEEAVAQLE 168
                                       444433...34555555444444444443 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 1.9e-13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l++f+   +H+L  PL  +  ++++++++  ++l+e+  e+++ ++++a+r+d++++ lL++sr ++
  gi|336253988|ref|YP_004597095.1| 174 LEQFAYAASHDLQEPLRMVTSYLQLIEDRygDELDEDCTEFIAYAVDGADRMDAMIDGLLEYSRVDT 240
                                       789***********************88778888899999************************986 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.22
                                       CHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  37 lkeyletiesearrldhlvedlL 59 
                                        +e l t+e  +r+l+++ ++lL
  gi|336253988|ref|YP_004597095.1| 273 TRESLPTVEGDERQLRQVFQNLL 295
                                       6889999**************97 PP

>> TMEM100  Transmembrane protein 100
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.2e-05     0.028      51     100 ..      17      66 ..       3      70 .. 0.85
   2 ?    1.8   0.0     0.072   1.6e+02      71     124 ..     108     165 ..      93     174 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                           TMEM100  51 kscYrCviPfgvvvLvaGvvvtavaytfnshgsvisvlglvLLsa.Glvll 100
                                       + +Yr v   gv++Lv  ++ ++v+ + n        l lvLL + Glv l
  gi|336253988|ref|YP_004597095.1|  17 RYWYRVVPALGVLILVSAIAKATVTLADNGLLLE-AALDLVLLGSlGLVTL 66 
                                       57*****9*********************99988.8999999965488877 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.072
                           TMEM100  71 vtavaytfnshgsvisvlglvLLsaGl....vllassavCWkvrrrrkkerrreseta 124
                                       + +v +tf ++  ++ + +++ L  G+     l+ + a+  + +++++ err e+  a
  gi|336253988|ref|YP_004597095.1| 108 GVTVQFTFGTQAVLLAIGSIAGLGIGVheaqALIRAEALAARNEELKRTERRLEEAVA 165
                                       56789******99999999999999984444578888999999888888888776554 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   2.2e-05     0.048       5      92 ..     286     398 ..     283     406 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.2e-05
                       HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg............................. 52 
                                        l  ++ nlL NAie + + +   + ++++++++ +    ++e +  g                             
  gi|336253988|ref|YP_004597095.1| 286 QLRQVFQNLLSNAIEYSGDEP---PRVHVSAERSAERA-AEAEGESGGesrgtgaawtisvrdegigidpddadrvf 358
                                       6788999*******9988855...78898888766553.34444444456889999999999999988888765444 PP

                       HATPase_c_5  53 .ekkklesskskkeehGiGlksireivkkykgnlsieaedg 92 
                                          ++l+s ++++   GiGl   ++iv++++g++++++e g
  gi|336253988|ref|YP_004597095.1| 359 gVFQRLHS-MNEHAGSGIGLALCERIVERHGGEIWVDTEPG 398
                                       32267777.5568899*******************999865 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   6.6   3.1e-06    0.0069       5     127 ..      24     143 ..      20     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.1e-06
                         HisKA_4TM   5 gvfGlvlaaaaivhhgaeaaaidsvrGPvlalaldGllalglvyagyrlastdlpaeqewtvlvwslgGavvvgavi 81 
                                        ++G+ +  +ai+  ++  a  + +   +l l+l G l l+ +y g +l +t++       +++w  gG  v+g   
  gi|336253988|ref|YP_004597095.1|  24 PALGVLILVSAIAKATVTLADNGLLLEAALDLVLLGSLGLVTLYIGLWLPNTSIRPAFYPRIVAWVGGGIGVMGI-- 98 
                                       5689999999999999999999999999**************************9999999999*8888765555.. PP

                         HisKA_4TM  82 gltvlvrllegrtiaePvf.vvlvaaevGavaGllaGylaararada 127
                                          +++r+l   +  + +f +  v   +G++aGl  G ++a+a   a
  gi|336253988|ref|YP_004597095.1|  99 --VLALRVLHPGVTVQFTFgTQAVLLAIGSIAGLGIGVHEAQALIRA 143
                                       ..55667777666666677245678889*********9998774433 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   4.0   1.7e-05     0.038      16      53 ..     139     176 ..     137     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                              ZapB  16 aidtitlLqmeieeLkeeneelkeenreleeeneqlke 53 
                                       a+ + ++L  ++eeLk+  + l+e  ++le++neql++
  gi|336253988|ref|YP_004597095.1| 139 ALIRAEALAARNEELKRTERRLEEAVAQLEASNEQLEQ 176
                                       55677899****************************97 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1    0.0033       7.4       9      75 ..     129     203 ..     120     208 .. 0.71
   2 ?    4.5   0.0    0.0091        20       8      62 ..     371     425 ..     370     432 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0033
                                       TSHHHHHHHHHHHHTT-EEEE...EESCHHHHHHHHHHHHHT....TSEEEEEE-TTT.SHHHHHHHHHHHHHHH CS
                         adh_short   9 ssGIGraiakelakeGakvvv...vdrseekleevakelkee....gakalaiqvDvt.dreevealvekavkkl 75 
                                       + GIG   a++l+++ a  +    ++r+e++lee++++l++     ++ a+a++ D++   + v  +++ +++++
  gi|336253988|ref|YP_004597095.1| 129 GLGIGVHEAQALIRAEALAARneeLKRTERRLEEAVAQLEASneqlEQFAYAASHDLQePLRMVTSYLQLIEDRY 203
                                       569999999999999987775556899************998443333366666777644455555555555555 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0091
                                       TTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHH CS
                         adh_short   8 assGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdre 62 
                                       a+sGIG+a++++++++    + vd ++ +  +    l + g+   a + Dv++r+
  gi|336253988|ref|YP_004597095.1| 371 AGSGIGLALCERIVERHGGEIWVDTEPGEGSTFRFTLPSRGDASAASAPDVATRA 425
                                       689***********99888888888888888887777777777777777777665 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 ?   12.4   2.7   4.7e-05      0.11      57      95 ..     138     176 ..     135     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.7e-05
                          KASH_CCD  57 qalqkaklleeEleelkalvkeleEkrarlkaqnkqlek 95 
                                       qal +a++l+  +eelk++ ++leE  a+l+a n+qle+
  gi|336253988|ref|YP_004597095.1| 138 QALIRAEALAARNEELKRTERRLEEAVAQLEASNEQLEQ 176
                                       88999********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      696  (0.0388198); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3067.60
//
Query:       gi|336253989|ref|YP_004597096.1|  [L=148]
Description: hypothetical protein Halxa_2599 [Halopiger xanaduensis SH-6]
Scores for 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  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); 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:                         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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1095.62
//
Query:       gi|336253990|ref|YP_004597097.1|  [L=125]
Description: Cupin 2 barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   48.0   0.2      1e-12   47.5   0.2    1.2  1  Cupin_2          Cupin domain
      8e-06   25.8   0.0      1e-05   25.4   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
     0.0002   21.0   0.1     0.0003   20.4   0.1    1.4  1  Cupin_3          Protein of unknown function (DUF861)
    0.00046   20.0   0.0    0.00056   19.7   0.0    1.2  1  EutQ             Ethanolamine utilisation protein EutQ
     0.0034   17.1   0.0      0.004   16.9   0.0    1.1  1  AraC_binding_2   AraC-binding-like domain
     0.0034   17.3   0.0     0.0041   17.0   0.0    1.2  1  MannoseP_isomer  Mannose-6-phosphate isomerase
     0.0071   15.7   0.0     0.0089   15.4   0.0    1.2  1  KduI             KduI/IolB family
  ------ inclusion threshold ------
      0.022   15.0   0.0       0.03   14.5   0.0    1.2  1  CENP-C_C         Mif2/CENP-C like
      0.031   13.9   0.0      0.037   13.6   0.0    1.1  1  Cupin_1          Cupin
      0.063   13.6   0.0      0.087   13.2   0.0    1.2  1  Pirin_C          Pirin C-terminal cupin domain
       0.07   12.9   0.0       0.11   12.3   0.0    1.2  1  FdtA             WxcM-like, C-terminal
      0.079   12.3   0.0       0.11   11.9   0.0    1.2  1  CTP_synth_N      CTP synthase N-terminus
      0.091   12.5   0.0       0.15   11.8   0.0    1.3  1  Cupin_6          Cupin


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 !   47.5   0.2   7.5e-16     1e-12       4      69 ..      36     103 ..      33     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 7.5e-16
                                       EEETTEEEEEECSSSEE..EEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEE CS
                           Cupin_2   4 elppGesapshrHpged..effyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllv 69 
                                       + +pG  +++h H+++d  e+++ +eGe+++ vd+eev +e+Gd++ +p+    ++rN  +e a +lv
  gi|336253990|ref|YP_004597097.1|  36 RCDPGWNSKPHDHTDNDheEVYVLIEGEATVVVDDEEVSMETGDALWIPPESTRQIRNGDEESAFVLV 103
                                       5689**9999999999997999999*********************************9999766654 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 !   25.4   0.0   7.4e-09     1e-05       8      68 ..      35      98 ..      30     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 7.4e-09
                                      ETTSTT-SEEEETT-...SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSE CS
                      AraC_binding  8 eagypdhsfpphvhd...eyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedg 68
                                      ++++p+++ +ph h    + ++ + +eG++++ ++++++ +++Gd +++pp+   +++ ++e++
  gi|336253990|ref|YP_004597097.1| 35 ARCDPGWNSKPHDHTdndHEEVYVLIEGEATVVVDDEEVSMETGDALWIPPESTRQIRNGDEES 98
                                      68999*******9977779********************************9988888877765 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 !   20.4   0.1   2.2e-07    0.0003      20      61 ..      48      88 ..      26     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.2e-07
                                      EECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEE CS
                           Cupin_3 20 rltyeedEfcyileGevkvtpeggetvelraGDlvvlpkgls 61
                                      +++ + +E   ++eGe +v++ + e+v ++ GD++ +p+ ++
  gi|336253990|ref|YP_004597097.1| 48 HTDNDHEEVYVLIEGEATVVV-DDEEVSMETGDALWIPPEST 88
                                      5566678999999********.9999************9884 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     4e-07   0.00056      94     146 ..      52     105 ..      28     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4e-07
                              EutQ  94 nydeidyvieGrldvlidGrkvvaeaGdviliPkgskiefsvtd.eakflyvay 146
                                       +++e+ ++ieG+  v++d  +v+ e+Gd + iP +s  +    d e  f+ v+ 
  gi|336253990|ref|YP_004597097.1|  52 DHEEVYVLIEGEATVVVDDEEVSMETGDALWIPPESTRQIRNGDeESAFVLVSA 105
                                       5789999**************************999877655431456666665 PP

>> AraC_binding_2  AraC-binding-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.9e-06     0.004      34      99 ..      30      97 ..      12     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-06
                    AraC_binding_2 34 lslgrlrygaavsirpsel..ddfylvqlplsGraeveqggrevvlgpgdavvldpgrpyrlrwsadc 99
                                      ++++  r+++ +   p +   +d+  v + ++G+a+v ++++ev  + gda+ + p  + ++r ++  
  gi|336253990|ref|YP_004597097.1| 30 VGVTVARCDPGWNSKPHDHtdNDHEEVYVLIEGEATVVVDDEEVSMETGDALWIPPESTRQIRNGDEE 97
                                      556666666555554444233788899******************************99999987543 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     3e-06    0.0041      84     126 ..      53      95 ..      26     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3e-06
                   MannoseP_isomer  84 raehWvvvkGtakvtvddevlllkenestyiplgaihrlenpG 126
                                         e +v ++G a v vdde++ ++  +  +ip +++ ++ n  
  gi|336253990|ref|YP_004597097.1|  53 HEEVYVLIEGEATVVVDDEEVSMETGDALWIPPESTRQIRNGD 95 
                                       46889********************************999954 PP

>> KduI  KduI/IolB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.5e-06    0.0089      25     111 ..      28     109 ..       7     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.5e-06
                                       CCBECCCEEEECHHCHHCH...GCSEEEEEEEECCEEEECCTT.EEEEE-TTSSGGGS..EEEEE-TT--EEEEE.S CS
                              KduI  25 eyvgfsvlkLaageslele...tedrEvcvvllaGkvtvevageefeelgeRksvFegkpdavYvpkgakvtita.e 97 
                                       e vg++v++ ++g + + +   ++d+E ++vl++G++tv v++ee+  ++          da+++p++++ +i    
  gi|336253990|ref|YP_004597097.1|  28 EQVGVTVARCDPGWNSKPHdhtDNDHEEVYVLIEGEATVVVDDEEV-SME--------TGDALWIPPESTRQIRNgD 95 
                                       6677777777777544333233999****************76333.333........359**************88 PP

                                       STEEEEEEEEE-SS CS
                              KduI  98 tdaevavasapaee 111
                                       ++  ++++sap+ +
  gi|336253990|ref|YP_004597097.1|  96 EESAFVLVSAPSIG 109
                                       8899*****99765 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.2e-05      0.03      23      79 ..      42      98 ..      25     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.2e-05
                                      CCEEEEE--SEEEEEEE.EESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE-SSS-E CS
                          CENP-C_C 23 aeKkkknskkatlvFyV.iqGrvevtvsktsfvigkgsvFqvPagneysieNklnkea 79
                                      ++K + +  +++   yV i+G+  v v +++ ++ +g+   +P  ++ +i+N  ++e+
  gi|336253990|ref|YP_004597097.1| 42 NSKPHDHTDNDHEEVYVlIEGEATVVVDDEEVSMETGDALWIPPESTRQIRNG-DEES 98
                                      56777777777765555389********************************5.4444 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.7e-05     0.037      25     112 ..      23     104 ..       5     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                                       STTTHSSTEEEEEEEE.TTEEEEEEEE.SSS-EEEEE.EESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEE CS
                           Cupin_1  25 lpglntlgisaarvdlepgglllPhyh.pnateiayv.lqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfq 99 
                                        p l t+++++++ +  pg  + Ph h  n +e +yv ++Ge++ ++v  ++        ++ Gd++++P+     +
  gi|336253990|ref|YP_004597097.1|  23 DP-LETEQVGVTVARCDPGWNSKPHDHtDNDHEEVYVlIEGEAT-VVVDDEE------VSMETGDALWIPPESTRQI 91 
                                       46.899999999999999999***9996566776666379***9.5555553......4599*************** PP

                                       EEESSSSEEEEEE CS
                           Cupin_1 100 ynsgdepavaivv 112
                                        n ++e+a+++v+
  gi|336253990|ref|YP_004597097.1|  92 RNGDEESAFVLVS 104
                                       ***8888888776 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 ?   13.2   0.0   6.3e-05     0.087      15      75 ..      48     110 ..      35     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.3e-05
                                       E--TT-EEEEEEEES-E..EESSTTEEE-TTEEEEE-SSSEEEEE--SS-EEEEEEEE----S CS
                           Pirin_C  15 plpegleaavyvleGel..evggerseieeeqlavlgdgdslvvkaeekgarvlLlaGePlge 75 
                                        +++++e + + +eGe+   v++e+ ++e+++ +++ ++++ +++ +++++ ++L++   +ge
  gi|336253990|ref|YP_004597097.1|  48 HTDNDHEEVYVLIEGEAtvVVDDEEVSMETGDALWIPPESTRQIRNGDEESAFVLVSAPSIGE 110
                                       4578888888999**9722455555889999999999*******************9888887 PP

>> FdtA  WxcM-like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.7e-05      0.11      48     110 ..      47     105 ..      38     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.7e-05
                                       EEEESS--EEEEEEES-EEEEEE-SS-EEEEEE-STTEEEEE-TT-EEEEE---TT.-EEEEEE CS
                              FdtA  48 eHahkkleqllialsGsvevllddgkkkkeilldspskglyipkmiWrelinfsed.avllvla 110
                                        H+  + e++ + ++G+ +v++dd + +    ++ +  +l+ip+   r++ n +e+ a +lv a
  gi|336253990|ref|YP_004597097.1|  47 DHTDNDHEEVYVLIEGEATVVVDDEEVS----ME-TGDALWIPPESTRQIRNGDEEsAFVLVSA 105
                                       58888999****************7654....43.56799*********999999955566655 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.6e-05      0.11      26      66 ..      25      65 ..      14      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.6e-05
                                      HHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EE CS
                       CTP_synth_N 26 lksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaet 66
                                      l+++ + vt+ ++DP  n  +      +h Ev+vl +G+ t
  gi|336253990|ref|YP_004597097.1| 25 LETEQVGVTVARCDPGWNSKPHDHTDNDHEEVYVLIEGEAT 65
                                      7788899*****************************99765 PP

>> Cupin_6  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.15      35      96 ..      55     114 ..      34     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                           Cupin_6  35 alhvvlrGscwlidpasgepvrLsagdvvllpggephvladspgtaplaviealgeasglge 96 
                                       +++v+ +G++++++++  e v +++gd++ +p +++ ++  + ++++  +++a ++ ++ ++
  gi|336253990|ref|YP_004597097.1|  55 EVYVLIEGEATVVVDD--EEVSMETGDALWIPPESTRQIRNGDEESAFVLVSAPSIGEEDSD 114
                                       67899********888..88****************99988888776666666555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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):              13  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 905.12
//
Query:       gi|336253991|ref|YP_004597098.1|  [L=142]
Description: transcriptional regulator NikR [Halopiger xanaduensis SH-6]
Scores for 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-21   74.0   2.2    1.2e-20   73.4   2.2    1.3  1  NikR_C           NikR C terminal nickel binding domain
    3.1e-07   30.1   0.0      5e-07   29.4   0.0    1.4  1  RHH_1            Ribbon-helix-helix protein, copG family
     0.0016   18.3   0.0     0.0029   17.5   0.0    1.3  1  RHH_5            CopG-like RHH_1 or ribbon-helix-helix domain
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.041   14.0   0.0    1.5  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
       0.12   12.6   0.1       0.13   12.5   0.1    1.1  1  DUF4276          Domain of unknown function (DUF4276)


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 !   73.4   2.2   3.3e-24   1.2e-20       1      72 [.      54     125 ..      54     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 3.3e-24
                                       EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEE CS
                            NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhv 72 
                                       +G++t+++d++++ ++er+++++he++dl+ s++h h+ +++c+e++vl+Ge e+i++++ k+ra++   ++
  gi|336253991|ref|YP_004597098.1|  54 MGIVTVLFDYETTSVEERMMHLRHEHEDLVASNFHSHVGDHHCMELFVLEGELEDISTFVGKIRATQDALTI 125
                                       79**************************************************************99876555 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 !   29.4   0.0   1.4e-10     5e-07       2      37 ..       4      40 ..       3      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.4e-10
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                      vs+++++ellerLd+ a++ g   rSe++ReA r++l
  gi|336253991|ref|YP_004597098.1|  4 VSVSMPDELLERLDQFADEHGyTGRSEVVREASRNLL 40
                                      9*******************************77766 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     8e-07    0.0029       4      24 ..       4      24 ..       4      27 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8e-07
                             RHH_5  4 vnvtLPeelleeLeewAdeeg 24
                                      v+v+ P+elle+L++ Ade g
  gi|336253991|ref|YP_004597098.1|  4 VSVSMPDELLERLDQFADEHG 24
                                      89****************988 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.2e-05     0.041      92     121 ..       4      34 ..       1      36 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                   HicB_lk_antitox  92 iNitlpervlkriDaavkaag.esRSgflak 121
                                       + +++p+++l+r+D+++ ++g + RS  + +
  gi|336253991|ref|YP_004597098.1|   4 VSVSMPDELLERLDQFADEHGyTGRSEVVRE 34 
                                       789******************5579987765 PP

>> DUF4276  Domain of unknown function (DUF4276)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   3.6e-05      0.13      39      96 ..      44      98 ..      10     118 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
                           DUF4276 39 kkllkqekdedtavttliDlyaldafkrveeleralkedidskgderfipyiql.hefE 96
                                      +    +++d   +vt+l+D+++ + ++r+ +l+++ ++ +    +++f  ++   h++E
  gi|336253991|ref|YP_004597098.1| 44 EDTRLEDRDLMGIVTVLFDYETTSVEERMMHLRHEHEDLV----ASNFHSHVGDhHCME 98
                                      4555566667889**********88888*******77666....788888886514566 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1107.63
//
Query:       gi|336253992|ref|YP_004597099.1|  [L=263]
Description: Creatininase [Halopiger xanaduensis SH-6]
Scores for complete 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-65  221.4   1.0    1.3e-65  221.2   1.0    1.0  1  Creatininase  Creatinine amidohydrolase


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.2   1.0   7.4e-70   1.3e-65       4     240 ..       7     237 ..       4     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: 221.2 bits;  conditional E-value: 7.4e-70
                      Creatininase   4 twpeveealkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTisls 80 
                                        wp+++++++++++a++P+GstEqHGphlp gtD++iaeala+++ e++g   l++P++p+Gvs +h++f GT++++
  gi|336253992|ref|YP_004597099.1|   7 AWPDLADYVADESLAVVPLGSTEQHGPHLPEGTDHMIAEALAREATERTG--FLCTPPIPIGVSSHHRQFHGTMWVD 81 
                                       7***********************************************99..************************* PP

                      Creatininase  81 petliavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaae.aaee 156
                                       + +++++++ + ++l  hG++riv vn+Hggn+a l+e+ r+l+++ +a av+             ++ +++  +  
  gi|336253992|ref|YP_004597099.1|  82 APVFRDYVESLSRNLTYHGIDRIVYVNAHGGNVAHLREVGRRLHEDGTAYAVE-------------WMWDESiPDLI 145
                                       *********************************************99666543.............33444445555 PP

                      Creatininase 157 seeee.gggHAgelEtSlmlalrpelVrmdraedpeeaklakeg.......vstaedaeelspsGvlGdpskataek 225
                                       +e  e  g H+g+ Et+++++++ elV++dr+e++++     +        ++t  da e sp+Gv+Gd+++a +e 
  gi|336253992|ref|YP_004597099.1| 146 EEVFEtPGPHGGPKETAMIMHIANELVHEDRLEEARDGGVVFDYddervhgATTFYDAIENSPNGVFGDQTDAMPEV 222
                                       56666699**************************9999887777999*99978888888889*************** PP

                      Creatininase 226 Gealleaaveelael 240
                                       Ge+l+eaa+++l++l
  gi|336253992|ref|YP_004597099.1| 223 GERLFEAATDQLVAL 237
                                       *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2068.19
//
Query:       gi|336253993|ref|YP_004597100.1|  [L=268]
Description: hypothetical protein Halxa_2603 [Halopiger xanaduensis SH-6]
Scores for 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-21   75.6   3.8    9.9e-14   51.1   0.2    3.0  3  TM_helix         Conserved TM helix
  ------ inclusion threshold ------
       0.11   12.4   0.3       0.25   11.2   0.3    1.6  1  Bacillus_PapR    Bacillus PapR protein
        3.1    7.3   5.9       0.53    9.8   1.6    1.8  2  PMT_4TMC         C-terminal four TMM region of protein-O-mann


Domain annotation for each model (and alignments):
>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.2   1.7e-17   9.9e-14       2      49 ..      15      62 ..      14      63 .. 0.94
   2 !   24.5   0.2   3.3e-09     2e-05       3      41 ..     109     147 ..     107     153 .. 0.89
   3 ?   -2.5   0.0      0.86   5.1e+03      32      45 ..     215     228 ..     207     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.7e-17
                                      XXXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-H CS
                          TM_helix  2 plnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgidd 49
                                      +l++   el++flP+LvgA++IL+vGwi+++++ r+v++l + + +d+
  gi|336253993|ref|YP_004597100.1| 15 WLQEPAAELITFLPRLVGALVILFVGWIVGRLAGRAVRRLADGIELDR 62
                                      77777889*************************************997 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 3.3e-09
                                       XXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TM_helix   3 lnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkl 41 
                                       l++ +++ +s+lP  ++ +l+ ++G+++A f+ +++ + 
  gi|336253993|ref|YP_004597100.1| 109 LSEWVSTAMSYLPAFIAGLLVIVIGFVVADFIGDVIERT 147
                                       667789999**************************9885 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.86
                                       HHHHHHHHHHHHHH CS
                          TM_helix  32 kfvsrlvtkllakt 45 
                                        +vs+ ++ ++ +t
  gi|336253993|ref|YP_004597100.1| 215 DYVSNNIDQWMGRT 228
                                       57888899999876 PP

>> Bacillus_PapR  Bacillus PapR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   4.2e-05      0.25      10      26 ..     199     215 ..     191     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.2e-05
                     Bacillus_PapR  10 vavamLaGvaFGvGqDq 26 
                                        ava+ aGvaFG G   
  gi|336253993|ref|YP_004597100.1| 199 AAVAIGAGVAFGWGGKD 215
                                       48**********98654 PP

>> PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2      0.23   1.4e+03     163     196 ..      75     109 ..      25     112 .. 0.46
   2 ?    9.8   1.6   8.8e-05      0.53     125     186 ..     119     179 ..     116     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.23
                          PMT_4TMC 163 vvllvlviavFiffspltyGlpgts.eevkklkwl 196
                                       ++  +++ a+  + + ++yGl ++  ++  + ++l
  gi|336253993|ref|YP_004597100.1|  75 GTEQAVSSAFGSLAKWFVYGLAILAaANALAIQLL 109
                                       33333333333334444555555544444445555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 8.8e-05
                          PMT_4TMC 125 YlpAllfailllaalldfllkslkkslkkkklvklivvvvllvlviavFiffspltyGlpgt 186
                                       YlpA+++ +l++ + + +  + + + ++++++++ +v++ +++  + +F++f  ++ Gl+  
  gi|336253993|ref|YP_004597100.1| 119 YLPAFIAGLLVIVIGFVVA-DFIGDVIERTRAAAETVYASWFANGARMFLYFTAIVIGLDTM 179
                                       ********99987766554.3555666666899*************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1955.59
//
Query:       gi|336253994|ref|YP_004597101.1|  [L=135]
Description: hypothetical protein Halxa_2604 [Halopiger xanaduensis SH-6]
Scores for 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  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1063.32
//
Query:       gi|336253995|ref|YP_004597102.1|  [L=148]
Description: hypothetical protein Halxa_2605 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.065   13.2   0.5       0.14   12.1   0.5    1.5  1  DUF1467   Protein of unknown function (DUF1467)
        7.2    6.2   8.9         48    3.6   4.9    2.4  2  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF1467  Protein of unknown function (DUF1467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5   1.6e-05      0.14      13      76 ..      68     132 ..      65     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                           DUF1467  13 iWwvvlFa.vLPfgvrtqdeegevkvpGtdasAParprllrkvlitTivaavvfalvlliilsgl 76 
                                        Ww+v+F+  LP  +  + e+  +  +G + + P     l+ ++ + ++ a+  +++++  ++g+
  gi|336253995|ref|YP_004597102.1|  68 RWWTVAFVaFLPYALAAAPESAAAAAAGDAFAGPIVGLALESIVGALVCCAIALTVLYGFARYGI 132
                                       5999999637************999**********999999999999999999999998888775 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   4.9    0.0053        48       4      43 ..      31      79 ..       5     103 .. 0.55
   2 ?    3.5   2.3    0.0056        51      26      58 ..      88     138 ..      66     147 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0053
                           DUF4131  4 plalvllalllllllllllllrr.........rprrrvlllllllllla 43
                                      ++++ l+ +llll l  + +            r+  +++++++++++l 
  gi|336253995|ref|YP_004597102.1| 31 NSPYRLVPALLLLSLGVAGVTDAareygvdrlRTAATRWWTVAFVAFLP 79
                                      3333333333333333333333345555666655666666666666655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0056
                           DUF4131  26 r..................rprrrvllllllllllallgfalrapqpnand 58 
                                       +                    +   +l++++++l++l+gfa +  +p++ +
  gi|336253995|ref|YP_004597102.1|  88 SaaaaaagdafagpivglaLESIVGALVCCAIALTVLYGFARYGIHPGRPS 138
                                       2344444444444444444555556999************99999998855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1073.61
//
Query:       gi|336253996|ref|YP_004597103.1|  [L=982]
Description: multi-sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for complete 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-36  125.0  19.8    3.9e-14   52.8   0.1    5.0  5  PAS_4        PAS fold
    1.7e-27   95.7   0.3    1.8e-07   31.2   0.0    5.3  4  PAS          PAS fold
    1.1e-26   93.6   0.1    2.2e-26   92.5   0.1    1.6  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.8e-23   82.8   0.0    1.4e-05   25.3   0.0    4.7  4  PAS_9        PAS domain
    3.2e-20   71.7   2.6    4.4e-06   26.6   0.0    5.1  4  PAS_8        PAS domain
      3e-14   53.2   0.4    7.2e-06   26.2   0.0    5.4  4  PAS_7        PAS fold
    3.1e-13   50.2   0.6    1.5e-12   48.0   0.1    2.5  2  GAF_2        GAF domain
    1.9e-11   43.8   0.2    1.9e-11   43.8   0.2    2.8  3  HisKA        His Kinase A (phospho-acceptor) domain
    2.5e-07   31.1   0.0    6.4e-07   29.8   0.0    1.8  1  GAF_3        GAF domain
    1.6e-05   24.7   0.0    2.9e-05   23.9   0.0    1.4  1  HATPase_c_5  GHKL domain
    0.00019   21.4   0.9    0.00045   20.2   0.1    2.2  2  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0019   18.4   0.4       0.28   11.5   0.1    4.2  4  PAS_3        PAS fold
     0.0091   16.1   0.0       0.02   15.0   0.0    1.5  1  PAS_11       PAS domain
  ------ inclusion threshold ------
      0.032   14.1   0.0      0.066   13.0   0.0    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
       0.38   10.8   1.4        2.1    8.4   0.2    2.3  2  Holin_BhlA   BhlA holin family


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   1.0    0.0028       3.4       1      72 [.      31     102 ..      31     112 .. 0.89
   2 !   37.5   1.3   1.9e-12   2.3e-09       1     110 []     221     338 ..     221     338 .. 0.95
   3 ?   -3.2   0.0       8.4     1e+04      18      35 ..     344     362 ..     342     406 .. 0.69
   4 !   52.8   0.1   3.3e-17   3.9e-14       3     110 .]     514     613 ..     512     613 .. 0.94
   5 !   37.7   0.1   1.7e-12     2e-09       2     110 .]     630     734 ..     629     734 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0028
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleel 72 
                                       +d++  +++ ld+  r +++  a  el g++++++l++++  ll +++ +rler +r+  + ++p ++ e+ 
  gi|336253996|ref|YP_004597103.1|  31 VDAVDGGVFQLDAANRLVAVDDALLELTGHDRDAVLDEPVSVLLETDAVPRLERRVRARTDDRAPESENETA 102
                                       5788899**********************************999999**********999999888776655 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 1.9e-12
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee......daarleralrrvlegeepieflee 71 
                                       ld   ++++vld+d rv +aN++++++fg++++++lG+  + +  e+      d +++++ +    + ++  e+ e+
  gi|336253996|ref|YP_004597103.1| 221 LDEADVGIFVLDADRRVAWANETIERYFGLERAAVLGRDKHRVIEESiqhrtaDPEGFRDTVLSTYDDGTDRERFEC 297
                                       678899***********************************999999999999********9999999999999999 PP

                             PAS_4  72 lll...pgeerhyelrllPlrdesGe.vigvlvisrDiTerrr 110
                                       +++   +++er++e r +P+  esG  + g ++  +D+T+r+r
  gi|336253996|ref|YP_004597103.1| 298 RVTagdERDERWLEHRSRPI--ESGPyAGGRIECYYDVTDRHR 338
                                       9999****************..899999*************97 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 8.4
                             PAS_4  18 lyaNaaaae.lfgappeel 35 
                                       +++Naa ++ l + + ee+
  gi|336253996|ref|YP_004597103.1| 344 RRLNAAVRDwLEADSNEEA 362
                                       6677777773334444444 PP

  == domain 4  score: 52.8 bits;  conditional E-value: 3.3e-17
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeer 79 
                                       +++d++++ld++ r++++N++a+el+g+p+eel+G+ +++++p + + +l + + +++e++++i+ + +      e 
  gi|336253996|ref|YP_004597103.1| 514 RVSDGFYALDEEWRFTHVNERAEELLGYPREELVGEVVWDVFPGGTRSELIDRYHEAMETQRSISWERYSGS--LEI 588
                                       5799********************************************************998888887666..9** PP

                             PAS_4  80 hyelrllPlrdesGevigvlvisrDiTerrr 110
                                       ++e++++P +       g+ v++rDiTerr+
  gi|336253996|ref|YP_004597103.1| 589 WMEIQIYPSET------GLSVYFRDITERRE 613
                                       ********966......************96 PP

  == domain 5  score: 37.7 bits;  conditional E-value: 1.7e-12
                             PAS_4   2 dslpdalavl.dpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++ p +++ l d+d+r++ +   + e +  ++ +l G+++ +++p++++a+le+  +r  +ge+ ++  e      e
  gi|336253996|ref|YP_004597103.1| 630 ENFPNGVVTLyDEDLRYTLVDGKGFEDLPQSATDLEGRRPSDVFPTPVGAELEELFERSFDGERLVRKIE-----YE 701
                                       68899999999**********995555999*********************************9999999.....79 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       ++++ +++  + de+G+v+  ++i++D+Ter++
  gi|336253996|ref|YP_004597103.1| 702 GQVWRVQAATITDEDGDVLSGMAIAQDVTERKE 734
                                       99*****************************85 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.3e-08   6.4e-05       2      73 ..      26      93 ..      25     151 .. 0.80
   2 !   31.2   0.0   1.5e-10   1.8e-07       6      95 ..     220     316 ..     217     327 .. 0.85
   3 !   28.8   0.0   8.2e-10   9.7e-07       4      71 ..     509     576 ..     506     592 .. 0.90
   4 ?    5.9   0.0      0.01        12       2     113 .]     624     729 ..     623     729 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.3e-08
                                      HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-EC CS
                               PAS  2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesr 73
                                       +ra++++ + ++f +D+  r + v +a  el+G +r+ vl ++++ l+ ++     + +le++ +++++ r
  gi|336253996|ref|YP_004597103.1| 26 YYRALVDAVDGGVFQLDAANRLVAVDDALLELTGHDRDAVLDEPVSVLLETD----AVPRLERRVRARTDDR 93
                                      69********************************************999776....6666666666655544 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 1.5e-10
                                       HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH......HHHHHHHHHHHHTT-ECCCC CS
                               PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda......elaelleqlleqgeesrage 76 
                                       +l+ ++++ifv+D+d r+ ++N+++e+ +Gl+r  vlg+   ++i e  ++       +++ ++  + +g++++ +e
  gi|336253996|ref|YP_004597103.1| 220 VLDEADVGIFVLDADRRVAWANETIERYFGLERAAVLGRDKHRVIEESIQHrtadpeGFRDTVLSTYDDGTDRERFE 296
                                       57889****************************************99998889999899999999999999999999 PP

                                       EEEEC.TTSSEEEEEEEEEE CS
                               PAS  77 isfkl.rdgrpihlevrasp 95 
                                        +++      +++le r +p
  gi|336253996|ref|YP_004597103.1| 297 CRVTAgDERDERWLEHRSRP 316
                                       88887655555666655555 PP

  == domain 3  score: 28.8 bits;  conditional E-value: 8.2e-10
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT- CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgee 71 
                                       ++il    d+  ++De  r+++vN+ aeellG++ree++g+ + d+++  +++el +++++++e++++
  gi|336253996|ref|YP_004597103.1| 509 SEILGRVSDGFYALDEEWRFTHVNERAEELLGYPREELVGEVVWDVFPGGTRSELIDRYHEAMETQRS 576
                                       5666677899*****************************************99999999999998875 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.01
                                       HHHHHHHHSSSEEEEE.ETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   2 dlraileslpdpifvv.DedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       ++r++ e+ p++++ + Ded r ++v  +  e l  s+ ++ g+  +d+++++    + ++   l+e  e+s +ge+
  gi|336253996|ref|YP_004597103.1| 624 RYRTLAENFPNGVVTLyDEDLRYTLVDGKGFEDLPQSATDLEGRRPSDVFPTP----VGAE---LEELFERSFDGER 693
                                       899999999999998736********************************998....4444...4445566666666 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        +++   +   ++v+a++++d++g +l  + +++d+
  gi|336253996|ref|YP_004597103.1| 694 LVRKIEYEGQVWRVQAATITDEDGDVLSGMAIAQDV 729
                                       66666778899*************999888888876 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 !   92.5   0.1   1.9e-29   2.2e-26       1     110 [.     854     963 ..     854     965 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.9e-29
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSS CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtG 75 
                                       gd  +Lrq+++nl++Na+++ + +g  ++ei+as      +isv D GiGi++e+ +++fe f++  +++ ++ gtG
  gi|336253996|ref|YP_004597103.1| 854 GDAGQLRQVFQNLLSNAIEY-SGEGAPTIEISASRegTMWEISVADEGIGIDPEQTDRVFEVFQR-LHSREEHAGTG 928
                                       6899****************.55665666666533369***************************.8889999**** PP

                                       HHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  76 lGlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       +Gl+++k++ve+++Gei+++s+pg+Gtt+ +tlp 
  gi|336253996|ref|YP_004597103.1| 929 IGLTLCKRIVERHDGEIRIDSTPGEGTTVSVTLPV 963
                                       ********************************996 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.4e-06    0.0029       3      91 ..      37     151 ..      35     154 .. 0.84
   2 !   21.0   0.0   2.5e-07    0.0003       1     103 [.     225     334 ..     225     335 .. 0.73
   3 !   25.3   0.0   1.2e-08   1.4e-05       2     104 .]     517     610 ..     516     610 .. 0.78
   4 !   13.0   0.0   7.9e-05     0.094      18     104 .]     652     731 ..     633     731 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.4e-06
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.................... 59 
                                       g++  +  +r++ + +a+l+l+G ++++vl  +++ l+  + +a  rl++ +++ ++                    
  gi|336253996|ref|YP_004597103.1|  37 GVFQLDAANRLVAVDDALLELTGHDRDAVLDEPVSVLL--ETDAVPRLERRVRARTDdrapesenetagadadrrrn 111
                                       566666778899999***********************..6666666666666666666777777777777778889 PP

                             PAS_9  60 ........kerevevvlirkngetfwvlltaspvkdddge 91 
                                               ++ + e++l++ +g  +++++++  ++ d+g 
  gi|336253996|ref|YP_004597103.1| 112 agtgadgkSVATLELDLRTVDGASVPCEVRLNVFRVDEGD 151
                                       9999***************************999999875 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.5e-07
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlf........vtdpeanerlraaleqgrkkerevevvli 69 
                                       ++gi++ + d r+ +aNe+ +r +G  +++vlg++ + ++        ++++  ++++   +++g++ er +  v  
  gi|336253996|ref|YP_004597103.1| 225 DVGIFVLDADRRVAWANETIERYFGLERAAVLGRDKHRVIeesiqhrtADPEGFRDTVLSTYDDGTDRERFECRVTA 301
                                       589**999***9***************************97777866666666666666666666644444444444 PP

                             PAS_9  70 rkngetfwvlltaspvkdddgelvg.iivilrDit 103
                                        +++ + w + + +p+  ++g + g  i +  D+t
  gi|336253996|ref|YP_004597103.1| 302 GDERDERWLEHRSRPI--ESGPYAGgRIECYYDVT 334
                                       4445777777777777..46666666667777766 PP

  == domain 3  score: 25.3 bits;  conditional E-value: 1.2e-08
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkng.etfw 77 
                                       dg+   +++ r +++Ne a++llGy +ee++g  ++d+f  +  ++++l + + +    e ++ +   r +g  ++w
  gi|336253996|ref|YP_004597103.1| 517 DGFYALDEEWRFTHVNERAEELLGYPREELVGEVVWDVF--PGGTRSELIDRYHEAM--ETQRSISWERYSGsLEIW 589
                                       5666666777899**************************..5555555555555555..577788888888868999 PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                        ++ ++p        +g+ v +rDite
  gi|336253996|ref|YP_004597103.1| 590 MEIQIYPSE------TGLSVYFRDITE 610
                                       999999993......445599999997 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 7.9e-05
                             PAS_9  18 eaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddgelvg 94 
                                       +++++l  +s+ ++ g++ +d+f  +     +l++++e+      e+ v  i  +g ++w ++ a+++ d+dg + +
  gi|336253996|ref|YP_004597103.1| 652 KGFEDL-PQSATDLEGRRPSDVF--PTPVGAELEELFERSF--DGERLVRKIEYEG-QVW-RVQAATITDEDGDVLS 721
                                       555555.36899***********..8888888888888888..6777777777766.899.9*************** PP

                             PAS_9  95 iivilrDite 104
                                         +i +D+te
  gi|336253996|ref|YP_004597103.1| 722 GMAIAQDVTE 731
                                       *********8 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   3.2e-06    0.0039       1      46 [.      25      71 ..      25      92 .. 0.76
   2 !   18.1   0.0   1.7e-06     0.002       6      46 ..     220     261 ..     217     282 .. 0.77
   3 !   26.6   0.0   3.7e-09   4.4e-06      10      51 ..     515     557 ..     507     572 .. 0.79
   4 ?    5.1   0.0     0.019        23       1      23 [.     623     646 ..     623     651 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.2e-06
                             PAS_8  1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg 46
                                      +++ral+++++ g++ +d+ +r+v v +a lel+G + + +++e++ 
  gi|336253996|ref|YP_004597103.1| 25 QYYRALVDAVDGGVFQLDAANRLVAVDDALLELTGHDrDAVLDEPVS 71
                                      79****************7778*************765444444444 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.7e-06
                             PAS_8   6 lfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg 46 
                                       +++ +++gi+v+d+++r+ ++N++ ++ +G++ a ++g + +
  gi|336253996|ref|YP_004597103.1| 220 VLDEADVGIFVLDADRRVAWANETIERYFGLErAAVLGRDKH 261
                                       688999*******999**************886555555554 PP

  == domain 3  score: 26.6 bits;  conditional E-value: 3.7e-09
                             PAS_8  10 spdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpv 51 
                                       ++dg   +d+ +r+++vN++a+ellGy+ ++l ge++++++p+
  gi|336253996|ref|YP_004597103.1| 515 VSDGFYALDEEWRFTHVNERAEELLGYPrEELVGEVVWDVFPG 557
                                       789999999878****************777777777655443 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.019
                             PAS_8   1 erlralfesspdgiavvdlgd.ri 23 
                                       +r+r+l e+ p+g++ +++ d r 
  gi|336253996|ref|YP_004597103.1| 623 QRYRTLAENFPNGVVTLYDEDlRY 646
                                       7**************866333354 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.047        56       2      35 ..      32      65 ..      31     110 .. 0.84
   2 !   26.2   0.0     6e-09   7.2e-06       1     112 [.     221     338 ..     221     342 .. 0.78
   3 !   14.3   0.0   2.9e-05     0.035       3     114 ..     514     615 ..     512     616 .. 0.73
   4 ?    0.3   0.0      0.64   7.6e+02     100     114 ..     722     736 ..     679     787 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.047
                             PAS_7  2 enmsqGisvfDadlrLvawNrrylelldlpeelv 35
                                      + ++ G+  +Da++rLva+ +  lel +  ++ v
  gi|336253996|ref|YP_004597103.1| 32 DAVDGGVFQLDAANRLVAVDDALLELTGHDRDAV 65
                                      67899********************998888777 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 6e-09
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaara...gk 74 
                                       l++ + Gi v+Dad r+   N+ + + ++l +  v  g+  + +++   ++   +++  +++v  + +  ++   ++
  gi|336253996|ref|YP_004597103.1| 221 LDEADVGIFVLDADRRVAWANETIERYFGLERAAV-LGRDKHRVIEESIQHRTADPEGFRDTVLSTYDDGTDrerFE 296
                                       577789**************************999.88888888888877777775555555555554444412255 PP

                             PAS_7  75 phsfererpdgrvievrgnpl....pdgGfVttytDiTerrr 112
                                          +   ++d+r++e r++p+      gG +  y D+T+r+r
  gi|336253996|ref|YP_004597103.1| 297 CRVTAGDERDERWLEHRSRPIesgpYAGGRIECYYDVTDRHR 338
                                       56666778999**********5443358***********987 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 2.9e-05
                             PAS_7   3 nmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfe 79 
                                        +s+G+  +D++ r + +N+r  ell++p+e + vg  + +++           g++++ ++r  +a++++++ s e
  gi|336253996|ref|YP_004597103.1| 514 RVSDGFYALDEEWRFTHVNERAEELLGYPREEL-VGEVVWDVFPG---------GTRSELIDRYHEAMETQRSISWE 580
                                       6899***************************99.77777666544.........45555566666666666666666 PP

                             PAS_7  80 rerpd.grvievrgnplpdgGfVttytDiTerrrae 114
                                       r   + + ++e++  p +  G+ + + DiTerr+ +
  gi|336253996|ref|YP_004597103.1| 581 RYSGSlEIWMEIQIYPSE-TGLSVYFRDITERRERQ 615
                                       654431456777777754.57777899999999876 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.64
                             PAS_7 100 fVttytDiTerrrae 114
                                        +++ +D+Ter++ e
  gi|336253996|ref|YP_004597103.1| 722 GMAIAQDVTERKEYE 736
                                       356789999999877 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.1   4.9e+03      18      44 ..     221     244 ..     195     258 .. 0.67
   2 !   48.0   0.1   1.3e-15   1.5e-12       5     137 ..     360     488 ..     356     489 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.1
                                       SS...EEEEEEE-TTS-EEEEEEEES-T CS
                             GAF_2  18 lg.aalgyillvdddgglrlaawgeaee 44 
                                       l+ a++g+++l+   ++   +aw++++ 
  gi|336253996|ref|YP_004597103.1| 221 LDeADVGIFVLDA--DR--RVAWANETI 244
                                       3446666666633..33..345555554 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 1.3e-15
                                       HHHHHHHHHHHHH.SS...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B.---TTHHHHHHHHTS-EEES-GGG-S CS
                             GAF_2   5 eelldlvldelve.lgaa.lgyillvdddgglrlaawgeaeeefgaaldr.plgeglvgealrtgrpvilndleedp 78 
                                       ee ++++++ l+e lg +  g++ ++ +++ lr +  +e+ ++++++++    geg++++a+++g+p +  d+++dp
  gi|336253996|ref|YP_004597103.1| 360 EEAAERACRSLREtLGLEiNGVFTYDSERDALRPVRQSEPAATLFEEPPTfERGEGIAWRAFESGEPELSGDVRSDP 436
                                       899**********56*9956677776677779999999999999999955455**********************99 PP

                                       -HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  79 dkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       d  +    + ++rs+l++P+   g  +Gv+  ++ +p+afde  l+++e  a+ + +a 
  gi|336253996|ref|YP_004597103.1| 437 DVYNP---ETPIRSELVLPV---G-DYGVVIAGSRRPDAFDEGTLSIAEIAASSLETAF 488
                                       87665...6***********...9.9************************999988775 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       5.7   6.8e+03      46      65 ..     341     360 ..     339     362 .. 0.79
   2 !   43.8   0.2   1.6e-14   1.9e-11       2      66 ..     746     812 ..     745     813 .. 0.95
   3 ?   -1.2   0.2       1.8   2.1e+03      32      59 ..     840     867 ..     827     870 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.7
                                       HHHHHHHHHHHHHHHHCCHH CS
                             HisKA  46 searrldhlvedlLdlsrie 65 
                                       ++ rrl++ v d L+  + e
  gi|336253996|ref|YP_004597103.1| 341 DQLRRLNAAVRDWLEADSNE 360
                                       78899999999998876655 PP

  == domain 2  score: 43.8 bits;  conditional E-value: 1.6e-14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l++f+   +H+L  PL  +  ++++L+r+  ++l+++ +e+++ ++++a+r++++++ lL++srie+
  gi|336253996|ref|YP_004597103.1| 746 LEQFAYAASHDLQEPLRMVTSYLQLLERRyaDDLDDDAAEFIDYAVDGAERMREMIDGLLEYSRIET 812
                                       789***********************7777*9*********************************97 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.8
                                       T-HSSCHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  32 klteelkeyletiesearrldhlvedlL 59 
                                       +  e ++e l +++  a +l+++ ++lL
  gi|336253996|ref|YP_004597103.1| 840 SDAEIVAESLPRVRGDAGQLRQVFQNLL 867
                                       456888999999999999*****99997 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   5.4e-10   6.4e-07       3     123 ..     360     484 ..     358     490 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 5.4e-10
                             GAF_3   3 dellekllkllvkllgaevgalllldedgnklqvaagw.dgkpalse..sldedsalarralssgev.vse..psfa 73 
                                       +e +e +++ l ++lg+e+  ++ +d +++ l++++++  ++  ++e  ++++++  a+ra++sge+ +s+  +s +
  gi|336253996|ref|YP_004597103.1| 360 EEAAERACRSLRETLGLEINGVFTYDSERDALRPVRQSePAATLFEEppTFERGEGIAWRAFESGEPeLSGdvRSDP 436
                                       6888999****************************99945555556698999**************94444443333 PP

                             GAF_3  74 e..edglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqi 123
                                       +   + +p r+ l++P+ +    +Gv+ ++s++p afd+ +l+  e  A+ +
  gi|336253996|ref|YP_004597103.1| 437 DvyNPETPIRSELVLPVGD----YGVVIAGSRRPDAFDEGTLSIAEIAASSL 484
                                       3334779************....********************999999866 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.4e-08   2.9e-05       6      92 ..     859     952 ..     855     962 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.4e-08
                       HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ek........kklesskskkeehGiGl 71 
                                       l  ++ nlL NAie + +     + I+++++++  +  is+  +  g   e+        ++l+s  +++   GiGl
  gi|336253996|ref|YP_004597103.1| 859 LRQVFQNLLSNAIEYSGEGA---PTIEISASREGTMWEISVADEGIGidpEQtdrvfevfQRLHS-REEHAGTGIGL 931
                                       6789**********998855...9******************99666555223444434566666.5568899**** PP

                       HATPase_c_5  72 ksireivkkykgnlsieaedg 92 
                                       +  ++iv++++g+++i+   g
  gi|336253996|ref|YP_004597103.1| 932 TLCKRIVERHDGEIRIDSTPG 952
                                       ***************987655 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       5.1   6.1e+03      33      86 ..      47     106 ..      33     115 .. 0.65
   2 !   20.2   0.1   3.7e-07   0.00045      31     123 ..     858     959 ..     831     961 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.1
                       HATPase_c_2  33 rlaveEactNavehayleapegpvevr.....lesdeealtvevaDsGpg.fdpetlpdp 86 
                                        +av+ a+     h ++   ++pv+v      + + e++++++  D++p   + ++++d 
  gi|336253996|ref|YP_004597103.1|  47 LVAVDDALLELTGHDRDAVLDEPVSVLletdaVPRLERRVRARTDDRAPEsENETAGADA 106
                                       577778888888888887778888777444444455566777777777775555555544 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.7e-07
                       HATPase_c_2  31 eirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep....keslkegGrGla 103
                                       ++r + + +++Na+e+  ++ap  ++e++++++++  +++vaD+G g dpe+ ++  e  +     e+    G+Gl 
  gi|336253996|ref|YP_004597103.1| 858 QLRQVFQNLLSNAIEYSGEGAP--TIEISASREGTMWEISVADEGIGIDPEQTDRVFEVFQrlhsREEHAGTGIGLT 932
                                       55666666899***********..9****99****************9999766554443388888899999***** PP

                       HATPase_c_2 104 likglvDev..ey.....dgegnvvtm 123
                                       l k++v+    e+      geg++v++
  gi|336253996|ref|YP_004597103.1| 933 LCKRIVERHdgEIridstPGEGTTVSV 959
                                       ******988665566665566777765 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         2   2.3e+03      48      81 ..     118     151 ..     108     154 .. 0.84
   2 ?    0.8   0.1      0.51   6.1e+02       4      75 ..     240     317 ..     237     322 .. 0.56
   3 !   11.5   0.1   0.00023      0.28       2      55 ..     529     580 ..     528     583 .. 0.85
   4 ?   -2.2   0.0       4.5   5.4e+03      34      55 ..     855     876 ..     853     877 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2
                             PAS_3  48 kgepyegeyRirrkdGeyrwveararvirdengk 81 
                                       ++++ + e  +r+ dG  +  e r +v+r ++g 
  gi|336253996|ref|YP_004597103.1| 118 GKSVATLELDLRTVDGASVPCEVRLNVFRVDEGD 151
                                       34466899999*****************999986 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.51
                             PAS_3   4 vserveeilGyspeellgk.veswl..dlvhp.eDrervrealqealkkge.pyegeyRirrk.dGeyrwveararv 74 
                                       ++e++e+++G++++ +lg+ +++++  ++ h   D e +r+++    ++g+ +  +e R+      + rw+e r r+
  gi|336253996|ref|YP_004597103.1| 240 ANETIERYFGLERAAVLGRdKHRVIeeSIQHRtADPEGFRDTVLSTYDDGTdRERFECRVTAGdERDERWLEHRSRP 316
                                       68888888888888888884222221122222134555555555555555544455666655545566777777776 PP

                             PAS_3  75 i 75 
                                       i
  gi|336253996|ref|YP_004597103.1| 317 I 317
                                       6 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00023
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyege 55 
                                       ++v+er ee+lGy +eel g    + d+     r+++ + ++ea+++++++++e
  gi|336253996|ref|YP_004597103.1| 529 THVNERAEELLGYPREELVGE--VVWDVFPGGTRSELIDRYHEAMETQRSISWE 580
                                       689******************..8888888888888888888888888777665 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 4.5
                             PAS_3  34 Drervrealqealkkgepyege 55 
                                       D  ++r+ +q++l++  +y+ge
  gi|336253996|ref|YP_004597103.1| 855 DAGQLRQVFQNLLSNAIEYSGE 876
                                       78899********999999987 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.7e-05      0.02       8      65 ..     522     575 ..     519     582 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                            PAS_11   8 ldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissnge 65 
                                       ld ++++++v++   ra+  lg+++eelvg +++d +    +s+l + ++e + ++++
  gi|336253996|ref|YP_004597103.1| 522 LDEEWRFTHVNE---RAEELLGYPREELVGEVVWDVFPGGTRSELIDRYHEAM-ETQR 575
                                       799*********...**************************************.4444 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 ?   13.0   0.0   5.5e-05     0.066       9      74 ..     865     928 ..     858     941 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.5e-05
                       HATPase_c_3   9 elvdNsld...AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkG 74 
                                        l+ N+++     a +++i+++++ g   ei++ D+G G+++e+ ++++++ +  +++    + +   G
  gi|336253996|ref|YP_004597103.1| 865 NLLSNAIEysgEGAPTIEISASRE-GTMWEISVADEGIGIDPEQTDRVFEVFQRLHSR----EEHAGTG 928
                                       566777765434567799999996.789*******************99876665552....3333334 PP

>> Holin_BhlA  BhlA holin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.59   7.1e+02      29      60 ..     493     524 ..     490     527 .. 0.87
   2 ?    8.4   0.2    0.0018       2.1      28      53 ..     609     634 ..     601     650 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.59
                        Holin_BhlA  29 kqekreekqeerekkyqeiikkltekfeivee 60 
                                       ++++++ ++++ e ++ ei+ ++++ f  ++e
  gi|336253996|ref|YP_004597103.1| 493 TERRLQRRKHDLETELSEILGRVSDGFYALDE 524
                                       678889999999***************99964 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0018
                        Holin_BhlA  28 kkqekreekqeerekkyqeiikklte 53 
                                        + ++r+ k+eere++y  + +++ +
  gi|336253996|ref|YP_004597103.1| 609 TERRERQRKLEEREQRYRTLAENFPN 634
                                       5678999***********99888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (982 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.45
# Mc/sec: 6529.86
//
Query:       gi|336253997|ref|YP_004597104.1|  [L=178]
Description: hypothetical protein Halxa_2607 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0059   16.9   0.7     0.0091   16.3   0.6    1.5  1  DUF4293   Domain of unknown function (DUF4293)


Domain annotation for each model (and alignments):
>> DUF4293  Domain of unknown function (DUF4293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   5.1e-07    0.0091      43     103 ..      52     112 ..      13     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.1e-07
                           DUF4293  43 taeaetsvnvsvwvlvilllliailaliaIflyknRklQlrlclinllllvllyvllalll 103
                                         ++  +++ + ++ +i ++  a++a++ + +y nR +  +l +++l l +++++++ l++
  gi|336253997|ref|YP_004597104.1|  52 AVAGLATAAADATGATIGATALAVVAVYGLAQYANRVTRRTLAHLSLALWIGFLGVAGLHA 112
                                       344555567777888888999999********************************99943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1375.69
//
Query:       gi|336253998|ref|YP_004597105.1|  [L=225]
Description: O-methyltransferase 3 [Halopiger xanaduensis SH-6]
Scores for 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-23   82.3   0.0    3.6e-23   81.9   0.0    1.2  1  Methyltransf_3   O-methyltransferase
    1.7e-13   51.5   0.0      3e-13   50.7   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
    8.7e-06   25.6   0.0    1.3e-05   25.1   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    0.00022   21.9   0.0    0.00037   21.1   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    0.00092   18.8   0.0     0.0018   17.9   0.0    1.4  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.016   15.0   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.018   15.8   0.0      0.039   14.7   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
       0.14   11.9   0.0       0.19   11.4   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)


Domain annotation for each model (and alignments):
>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   1.6e-26   3.6e-23      30     211 ..      38     223 ..      15     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.6e-26
                                       S--HHHHHHHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES CS
                    Methyltransf_3  30 evsvdegqfLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekielieg 106
                                       +v+++ g fL+++ + ++a r++e G   Gys+   a alP+DG+i+  ++d+++ e+a++++ + g+++   +  g
  gi|336253998|ref|YP_004597105.1|  38 HVGPEVGVFLRFVARASDAERIFEFGSGYGYSAYWFAEALPDDGEIVLTEVDENELELARDYLSRGGYDDVARYELG 114
                                       689999*********************************************************************** PP

                                       -HHHHHHHHHTSSS---EEEEEE-S-GGGHHHHHHHHHHTEEEEEEEEEE-TTGGGGGG........-SS--SHH.H CS
                    Methyltransf_3 107 dalkvLeelvkdkklpefDfifvDaDkssyvnyyeklleLvkvGgliaiDntLWeGkvv........eeddeeak.a 174
                                       dal+++e+   d   + f+ +++D  k+ y + +e + e v vGg+++ Dn++  G +v        e d+++ k  
  gi|336253998|ref|YP_004597105.1| 115 DALETIENY--D---GPFETVLIDHQKHRYLEAFEAVREKVPVGGVVVADNAITAGPIVfddllaalEGDEDVDKtE 186
                                       **9998864..3...56***************************************876233232223344443313 PP

                                       HH.....HHHHHHHHTT-TTEEEEEE-SBT-EEEEEE CS
                    Methyltransf_3 175 lreyravllelnkklaeDprveisllsvgDGitLvrk 211
                                       l e    ++++ + +++Dp  e ++l++g+Gi +  +
  gi|336253998|ref|YP_004597105.1| 187 LDESTRGIVDYLERVKSDPAFETVVLPLGEGIAVSYR 223
                                       45555667788889******************98766 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   1.3e-16     3e-13       2     105 ..      61     160 ..      60     161 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.3e-16
                   Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalareaglddrvrlikadseealaslaagsiDllfiDgg 78 
                                       E G+ +G+s+ w+++al + g+  l+ vd ++  e a+ ++ + g+dd++r   +d+ e++++ + g++  ++iD  
  gi|336253998|ref|YP_004597105.1|  61 EFGSGYGYSAYWFAEALPDDGEIVLTEVDENE-LELARDYLSRGGYDDVARYELGDALETIENYD-GPFETVLID-- 133
                                       99******************************.6778999999**********************.*********.. PP

                   Methyltransf_24  79 haaeavledleallprlapggvvlfdD 105
                                       h+++++le++ea+++++  ggvv+ d+
  gi|336253998|ref|YP_004597105.1| 134 HQKHRYLEAFEAVREKVPVGGVVVADN 160
                                       *************************98 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   5.7e-09   1.3e-05       3      81 ..      55     133 ..      53     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 5.7e-09
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDl 77 
                                       ++ r+ + G+G G+ ++ +ae l +++e+v+ + +e+ +elAr  +++ g+d  ++ e gd+ e +e+   d +f  
  gi|336253998|ref|YP_004597105.1|  55 DAERIFEFGSGYGYSAYWFAEALPDDGEIVLTEVDENELELARDYLSRGGYDdVARYELGDALEtIEN--YDGPFET 129
                                       678999**************99999***************************7788999*****9996..4799*99 PP

                   Methyltransf_31  78 ilsn 81 
                                       +l +
  gi|336253998|ref|YP_004597105.1| 130 VLID 133
                                       8877 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.7e-07   0.00037       1      75 [.      59     138 ..      59     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.7e-07
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBC.CGBSSSTTTEEEEEEEST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl..nvefvqgda.edlpfedgsfDlvvssga 73 
                                       + ++G G G  + ++a++l+ +++++ ++++e+ le ar  +++ g+   ++++ gda e+++  dg f  v++ ++
  gi|336253998|ref|YP_004597105.1|  59 IFEFGSGYGYSAYWFAEALPdDGEIVLTEVDENELELARDYLSRGGYddVARYELGDAlETIENYDGPFETVLIDHQ 135
                                       6799***************559********************9988898999******777999*********9554 PP

                                       .GG CS
                   Methyltransf_25  74 .lh 75 
                                          
  gi|336253998|ref|YP_004597105.1| 136 kHR 138
                                       333 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   7.8e-07    0.0018      31      94 ..      55     121 ..      43     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7.8e-07
                                       TCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle..vevvasdvleeve 94 
                                        ++++  +G+G+G+ + ++a++ p+   ++l++vd + le+a+  l++ + +  +++   d+le++e
  gi|336253998|ref|YP_004597105.1|  55 DAERIFEFGSGYGYSAYWFAEALPDDGeIVLTEVDENELELARDYLSRGGYDdvARYELGDALETIE 121
                                       56789******************98766*******************99999988888899999888 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 ?   15.0   0.0     7e-06     0.016      65     139 ..      46     122 ..      36     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7e-06
                                       HHHHTT.--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEE.EEES-GGGTTGG CS
                              PCMT  65 alelle.lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvi.vvvgDGrkGyee 139
                                       +l ++   ++ +r+ e GsG Gy +  +a+ + ++g +v  e  ++  e a+  l + ++++v+    gD  +  e+
  gi|336253998|ref|YP_004597105.1|  46 FLRFVArASDAERIFEFGSGYGYSAYWFAEALPDDGEIVLTEVDENELELARDYLSRGGYDDVArYELGDALETIEN 122
                                       556665567789********************************9999*******9999998862456777666665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.7e-05     0.039       2      59 ..      61     119 ..      60     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                   Methyltransf_12   2 eiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdll 59 
                                       e+G+G G  +  ++e+l  d e++ ++++++ +e a+  l++ + ++++++el +    
  gi|336253998|ref|YP_004597105.1|  61 EFGSGYGYSAYWFAEALpDDGEIVLTEVDENELELARDYLSRGGYDDVARYELGDALET 119
                                       9****************99**************************99999988765443 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.7e-05      0.19      19      49 ..      47      79 ..      40     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.7e-05
                            DUF938 19 ksylaktte..rvLEiasGtGqHAvffApalpn 49
                                      ++ +a++++  r+ E +sG G  A +fA+alp 
  gi|336253998|ref|YP_004597105.1| 47 LRFVARASDaeRIFEFGSGYGYSAYWFAEALPD 79
                                      555555444459*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1786.45
//
Query:       gi|336253999|ref|YP_004597106.1|  [L=167]
Description: hypothetical protein Halxa_2609 [Halopiger xanaduensis SH-6]
Scores for 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:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); 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 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1354.00
//
Query:       gi|336254000|ref|YP_004597107.1|  [L=325]
Description: ROK family protein [Halopiger xanaduensis SH-6]
Scores for 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-44  150.3   0.0    9.1e-44  150.1   0.0    1.0  1  ROK          ROK family
    0.00044   19.8   0.5     0.0055   16.2   0.1    2.1  2  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
      0.029   14.0   0.1        0.1   12.2   0.1    1.8  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 


Domain annotation for each model (and alignments):
>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.1   0.0   1.5e-47   9.1e-44       1     289 [.       4     310 ..       4     315 .. 0.91

  Alignments for each domain:
  == domain 1  score: 150.1 bits;  conditional E-value: 1.5e-47
                                       EEEEEE-SSEEEEEEEETTS-EEEEEEEEEHCC....HHCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSEEETTCC CS
                               ROK   1 tigidiGgtkialalvdeegeilarekvetpte....tteetlvdaiaelvdeaerkadeliavgigspGlisdksg 73 
                                       ++g+d+G+t++++a+ + +g++    +  tp+     ++ e++  ++ e+ ++a  + d++++ gigs G+ +  +g
  gi|336254000|ref|YP_004597107.1|   4 YAGVDLGATNVRAAVAEGDGTTIGVSRNATPRGptgiDVTEGVLRTLREACTDAGIEPDQIVSAGIGSIGPFDLAEG 80 
                                       68********************9988886665322336778888********************************* PP

                                       EBSSGGC.GCC.CCTTHHHHHHHHHTS.-EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEESSSEEEEEEETTEEE-- CS
                               ROK  74 kivstpn.itw.enfdlvekleerlnv.pvevenDvnaaalaEavfgaskdvenviyvtvgtGvGaGviingklitG 147
                                        ++ ++n ++  + ++l + +e+ ++  +v+++nD  a   +E +  a+ + ++++y+tv+ G+GaGv  +g ++ G
  gi|336254000|ref|YP_004597107.1|  81 AVIDPANlPDSiDRIPLTGPIEKLIDSdEVYLHNDTAAGVIGERF-HADRNPDDMVYITVSSGIGAGVCCDGDILAG 156
                                       *******76778*************9748***************9.9****************************** PP

                                       TTS-TT-GGGSBS-TTS-B.-TTS-BSBHHHCCSHHHHHHCHTC..............CGTTS-HHHHHHHHCTT-H CS
                               ROK 148 rnGvagelGHiqldpegek.cgCGnqgClEtlasgralekraqq..............kgekleakeiiklaekgde 209
                                         G+age+GH  +dp g   cgCG  g +E+++sg+++  +++                  + +ak++++la + de
  gi|336254000|ref|YP_004597107.1| 157 WDGNAGEVGHCIVDPRGRLtCGCGHDGHWEAYCSGNGIPDYVRLlaeddptistdlplDDPDFTAKDVFELAGE-DE 232
                                       **************999877********************9999999*********999999***********9.** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH--SEEEEEHCCC.TSTTHH.HHHHHHHHHCCTTTTCCCT-EEEE-S-STTHHH CS
                               ROK 210 vaeevverlaeylakaiadlinlfdpqaivlgGgvs.eadkll.eairklvkkylnkklevpvveivaaklgdkagl 284
                                        a  ++++la++ a ++a+++  f+p ++ +gG v  + ++l+ ++ir+ v+++++++ ++    i++  lgd+  l
  gi|336254000|ref|YP_004597107.1| 233 LADYAIDQLAHWNAMGVANVVHSFAPIVVSFGGAVAlNNEELVvKPIRERVSEMVMSNVPE----IRVTDLGDDVVL 305
                                       **********************************9735677778**********9987665....556788888888 PP

                                       HHHHH CS
                               ROK 285 lGaaa 289
                                        Ga+a
  gi|336254000|ref|YP_004597107.1| 306 EGALA 310
                                       88876 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 !   16.2   0.1   9.3e-07    0.0055       2      68 ..       6      70 ..       5     144 .. 0.83
   2 ?    2.2   0.0     0.017     1e+02     185     247 ..     228     290 ..     218     312 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.3e-07
                                      EEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..E CS
                       BcrAD_BadFG  2 GiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylv 68
                                      G+D+G+T ++a++ + +g  +g      +    ++++ + + + + l+ea+  ag e+++i++  ++
  gi|336254000|ref|YP_004597107.1|  6 GVDLGATNVRAAVAEGDGTTIGVSRNA-TPRGPTGID-VTEGVLRTLREACTDAGIEPDQIVSAGIG 70
                                      9****************9966654433.333335555.55555678**************9877444 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.017
                                       HHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG-..HHHHHHH.....HHHH-S CS
                       BcrAD_BadFG 185 lsggekaedIlaglhraialrvialisrsggvtdevtltGGvakn..eaavkelrklvkenygev 247
                                         ++e a+  +++l++  a+ v++++++++ +   v + G va n  e +vk +r+ v+e+++  
  gi|336254000|ref|YP_004597107.1| 228 AGEDELADYAIDQLAHWNAMGVANVVHSFAPI--VVSFGGAVALNneELVVKPIRERVSEMVMSN 290
                                       55677777778888888888888888888888..4888888887622458899999999998764 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 ?   12.2   0.1   1.7e-05       0.1       1      76 [.       3      70 ..       3      75 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                                      EEEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEE CS
                            FGGY_N  1 lilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgis 76
                                      ++ g+D+G+t+++a+v + +g+ +++++ + +      +        + + + +++r++++ agi+++qi+  gi+
  gi|336254000|ref|YP_004597107.1|  3 YYAGVDLGATNVRAAVAEGDGTTIGVSRNATPRGPTGID--------VTEGVLRTLREACTDAGIEPDQIVSAGIG 70
                                      799**********************99877654433222........23456666666666666777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2477.84
//
Query:       gi|336254001|ref|YP_004597108.1|  [L=518]
Description: LVIVD repeat-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-18   63.6   0.4    0.00054   19.2   0.0    6.3  6  LVIVD        LVIVD repeat
    2.3e-08   33.4   0.0     0.0019   17.2   0.0    3.9  4  Beta_propel  Beta propeller domain
      0.007   15.2   0.2        4.9    5.9   0.0    3.8  4  SBP56        56kDa selenium binding protein (SBP56)


Domain annotation for each model (and alignments):
>> LVIVD  LVIVD repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   6.4e-06     0.039      13      35 ..      60      81 ..      49      85 .. 0.86
   2 !   10.7   0.0   4.2e-05      0.25      22      42 .]     125     145 ..     121     145 .. 0.90
   3 !    4.0   0.4    0.0052        31       9      28 ..     154     176 ..     148     178 .. 0.69
   4 !   19.2   0.0     9e-08   0.00054       2      40 ..     203     241 ..     202     243 .. 0.92
   5 ?    2.0   0.0     0.021   1.3e+02      23      35 ..     300     312 ..     295     318 .. 0.78
   6 !    5.5   0.0    0.0017        10      20      39 ..     351     370 ..     343     373 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.4e-06
                             LVIVD 13 YaYvAdqdngLvIvDISNpSspt 35
                                       aYvA    g+v vD+S+p  p 
  gi|336254001|ref|YP_004597108.1| 60 TAYVA-ATTGFVTVDVSDPGEPE 81
                                      59***.66***********9885 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4.2e-05
                             LVIVD  22 gLvIvDISNpSsptlkgsydT 42 
                                       g+ + D+S+pS p l  +y T
  gi|336254001|ref|YP_004597108.1| 125 GFAVYDVSDPSEPELLDTYET 145
                                       78899***********99988 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0052
                             LVIVD   9 vsGnYaYvAdqd...ngLvIvDI 28 
                                       + G+Y Y+  ++   n LvI D+
  gi|336254001|ref|YP_004597108.1| 154 LEGDYCYIVGNGqeaNPLVIYDV 176
                                       68******843322266888877 PP

  == domain 4  score: 19.2 bits;  conditional E-value: 9e-08
                             LVIVD   2 GdaqdvavsGnYaYvAdqdngLvIvDISNpSsptlkgsy 40 
                                       ++  dv v ++ aY   +d g   vD+S+p+ p +++++
  gi|336254001|ref|YP_004597108.1| 203 RYLHDVYVQEGIAYLSHWDAGTYLVDVSDPAEPEFISRV 241
                                       6678******************************99988 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.021
                             LVIVD  23 LvIvDISNpSspt 35 
                                        +  D+S+p+ pt
  gi|336254001|ref|YP_004597108.1| 300 IDLYDVSDPAEPT 312
                                       5556*******98 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.0017
                             LVIVD  20 dngLvIvDISNpSsptlkgs 39 
                                       ++g  I D+S+p++p ++ s
  gi|336254001|ref|YP_004597108.1| 351 QGGVKIHDVSDPAAPEEIAS 370
                                       5677889********99876 PP

>> Beta_propel  Beta propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.1e-07    0.0019      16     134 ..      52     165 ..      48     192 .. 0.76
   2 ?    0.5   0.0     0.034     2e+02      95     115 ..     224     244 ..     198     248 .. 0.74
   3 !    9.1   0.0   8.5e-05      0.51     351     404 ..     264     319 ..     250     331 .. 0.78
   4 ?    0.2   0.0     0.042   2.5e+02     385     402 ..     354     371 ..     347     379 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.1e-07
                       Beta_propel  16 ivktDGkyiyvvsg.skvvivd.aeaeelklvs...eiklee..kfkieelyldgdrLvvisseeeeeeseaeeeee 85 
                                       +v  DG    +v      v vd ++++e ++++   ++++++    +  +l +dgdr+vv + ++ ++++       
  gi|336254001|ref|YP_004597108.1|  52 VVVGDGGETAYVAAtTGFVTVDvSDPGEPEILAeerRLSFDDasANELLDLEVDGDRMVVAGPANPSADTFF----- 123
                                       56666655544444255555555555555555433377888877788888999********99977777444..... PP

                       Beta_propel  86 pilskeetkvliyDisdkenpkllreleldGsyvssRkigdklylvssk 134
                                                  +yD+sd+++p+ll ++e   ++++  + gd+ y+v + 
  gi|336254001|ref|YP_004597108.1| 124 -------HGFAVYDVSDPSEPELLDTYETGAHIHNCYLEGDYCYIVGNG 165
                                       .......5799***********************************993 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.034
                       Beta_propel  95 vliyDisdkenpkllreleld 115
                                       ++++D+sd+++p+++++++++
  gi|336254001|ref|YP_004597108.1| 224 TYLVDVSDPAEPEFISRVQQE 244
                                       567777777777777777765 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 8.5e-05
                       Beta_propel 351 IpGySeYLhpydenhLlGiGkeadeegeee..qglklslFDVsDpanpkevakvvi 404
                                       +pG   Y    + + Ll++G+ea  +g  e  +   + l+DVsDpa+p+  a++  
  gi|336254001|ref|YP_004597108.1| 264 LPGNDHYAAVDETGDLLAVGREAWATGSGEpdRPGGIDLYDVSDPAEPTHRATIDA 319
                                       666666666666789*******655555555588889***********99888765 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.042
                       Beta_propel 385 lslFDVsDpanpkevakv 402
                                       +++ DVsDpa+p e+a++
  gi|336254001|ref|YP_004597108.1| 354 VKIHDVSDPAAPEEIASW 371
                                       4568*********99876 PP

>> SBP56  56kDa selenium binding protein (SBP56)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.02   1.2e+02     330     354 ..     127     151 ..     121     179 .. 0.82
   2 ?    1.4   0.0     0.018   1.1e+02     319     348 ..     215     243 ..     205     263 .. 0.79
   3 ?    0.5   0.0     0.034     2e+02     327     346 ..     298     317 ..     296     330 .. 0.85
   4 !    5.9   0.0   0.00081       4.9     321     344 ..     346     369 ..     337     372 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.02
                             SBP56 330 rqydisdpkkPkltgqvrlGGiirk 354
                                         yd+sdp++P+l ++   G  i++
  gi|336254001|ref|YP_004597108.1| 127 AVYDVSDPSEPELLDTYETGAHIHN 151
                                       57***********999999988775 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.018
                             SBP56 319 lyvsnWltGdlrqydisdpkkPkltgqvrl 348
                                        y+s W  G     d+sdp++P+  ++v+ 
  gi|336254001|ref|YP_004597108.1| 215 AYLSHWDAGTY-LVDVSDPAEPEFISRVQQ 243
                                       599***99975.68*********9999975 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.034
                             SBP56 327 GdlrqydisdpkkPkltgqv 346
                                       G +  yd+sdp++P + +++
  gi|336254001|ref|YP_004597108.1| 298 GGIDLYDVSDPAEPTHRATI 317
                                       77899*********998877 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.00081
                             SBP56 321 vsnWltGdlrqydisdpkkPkltg 344
                                        s+W +G ++ +d+sdp+ P++ +
  gi|336254001|ref|YP_004597108.1| 346 YSAWYQGGVKIHDVSDPAAPEEIA 369
                                       489*****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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 0.23s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3937.56
//
Query:       gi|336254002|ref|YP_004597109.1|  [L=143]
Description: F420-dependent protein [Halopiger xanaduensis SH-6]
Scores for 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-18   65.6   0.0    4.4e-18   65.2   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
    1.1e-10   41.6   0.2    1.4e-10   41.3   0.2    1.0  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    8.7e-06   25.4   0.0      1e-05   25.2   0.0    1.1  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like
  ------ inclusion threshold ------
      0.058   13.4   0.0      0.084   12.8   0.0    1.2  1  UspB            Universal stress protein B (UspB)


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 !   65.2   0.0   9.9e-22   4.4e-18       3      87 ..      13      97 ..      11      98 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 9.9e-22
                                      HHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT.GSEEEEEEEE CS
                    Putative_PNPOx  3 eelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde.lgrgvrieGt 80
                                      + ++++l++++++++AT + dG+P++spv+  ++dg+   +f t + + k rn+++++rv+++++d++  +r+v+++G+
  gi|336254002|ref|YP_004597109.1| 13 DPYLDILETESFGHVATLGSDGHPHSSPVWVDHDDGE-AVLFNTLRGRTKERNIRSDSRVSISVVDPDdPYRYVSVRGR 90
                                      668899**************************99999.***************************************** PP

                                      EEEESCH CS
                    Putative_PNPOx 81 aelvsdg 87
                                      ael ++g
  gi|336254002|ref|YP_004597109.1| 91 AELTEEG 97
                                      ***9987 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.2   3.1e-14   1.4e-10       5     137 ..      15     135 ..      12     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 3.1e-14
                                       HHHHHHC-SEEEEEEEE.TTEEEEEEEEEEEE.TTEEEEEEETTSHCCHCCC.T--ECEEEEEEEEEEE-SEGGEEE CS
                      Pyridox_ox_2   5 ilalLdegevgrlafvd.dgepvilPvnyvvd.gdslyfhgakgsrlaaalr.gapvcvvvtevdglvlarsfnsln 78 
                                       +l++L+++++g++a+   dg+p++ Pv +  d g++++f + +g  + + +r +++v+++v + d+           
  gi|336254002|ref|YP_004597109.1|  15 YLDILETESFGHVATLGsDGHPHSSPVWVDHDdGEAVLFNTLRGRTKERNIRsDSRVSISVVDPDD-----P----- 81 
                                       789*************98999******888887788****************66669999999999.....4..... PP

                                       EEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTTGGCSB---CCCCCTEEEEEEEEEEE CS
                      Pyridox_ox_2  79 yrSVvvrGraeevtdeeekaealellvekivpgrwenlrpptrkelkatsvlrlkieev 137
                                       yr V vrGrae+   ee  +e+ + l+++++     +  p+ ++e ++  ++r++ e+v
  gi|336254002|ref|YP_004597109.1|  82 YRYVSVRGRAELT--EEGADEHIDELARQYLD---VEEYPHHDEEDESRVIVRIPAEHV 135
                                       888*********9..55555666667778855...3455999************99877 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 !   25.2   0.0   2.3e-09     1e-05      12      98 ..      21     109 ..      15     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.3e-09
                     Pyrid_ox_like  12 diktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsdesk.kkyvsvsGtaevved 87 
                                         +++ ++t  +dg+ +s P  + ++ + + + f t +   k ++ir ds+v++ ++d+++   yvsv+G+ae+ e+
  gi|336254002|ref|YP_004597109.1|  21 TESFGHVATLGSDGHPHSSPVWVDHD-DGEAVLFNTLRGRTKERNIRSDSRVSISVVDPDDpYRYVSVRGRAELTEE 96 
                                       55666777788899999999988665.56678899***********************987357***********98 PP

                     Pyrid_ox_like  88 ra..kieelWspv 98 
                                        a   i+el  + 
  gi|336254002|ref|YP_004597109.1|  97 GAdeHIDELARQY 109
                                       6511566665554 PP

>> UspB  Universal stress protein B (UspB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.9e-05     0.084      25      77 ..      68     121 ..      61     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                              UspB  25 slrallsvlreadPllyqqvdGrgfftthgqlskqvrll.ryiksreyldhhdp 77 
                                         r+ +sv+   dP  y +v Gr+ +t++g  +    l  +y+  +ey +h ++
  gi|336254002|ref|YP_004597109.1|  68 DSRVSISVVDPDDPYRYVSVRGRAELTEEGADEHIDELArQYLDVEEYPHHDEE 121
                                       568889999999******************999888887369999999866544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1268.07
//
Query:       gi|336254003|ref|YP_004597110.1|  [L=882]
Description: leucyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-60  202.6   0.0    1.2e-40  139.4   0.9    4.6  2  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    4.3e-58  195.9   0.0    7.2e-58  195.1   0.0    1.4  1  tRNA-synt_1_2   Leucyl-tRNA synthetase, Domain 2
    4.2e-30  104.8   0.0    1.6e-21   76.5   0.0    4.5  3  tRNA-synt_1g    tRNA synthetases class I (M)
    1.9e-17   63.6   0.0    3.3e-17   62.8   0.0    1.4  1  Anticodon_1     Anticodon-binding domain of tRNA
    0.00058   18.9   0.0        0.5    9.2   0.0    3.2  3  tRNA-synt_1f    tRNA synthetases class I (K)
     0.0023   17.3   0.0        1.2    8.4   0.1    2.3  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
     0.0032   17.6   0.7     0.0067   16.6   0.0    1.9  2  PknG_rubred     Protein kinase G rubredoxin domain
  ------ inclusion threshold ------
      0.013   15.5   3.3        2.5    8.2   0.5    2.5  2  DZR             Double zinc ribbon
      0.016   14.7  10.2       0.83    9.2   0.6    4.1  3  TF_Zn_Ribbon    TFIIB zinc-binding
      0.062   13.4   6.9       0.17   12.0   0.3    3.2  3  Zn-ribbon_8     Zinc ribbon domain
       0.42   10.7   6.5       0.45   10.6   0.1    3.2  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
        1.5    8.4   7.3         12    5.4   0.2    3.9  4  zf-ribbon_3     zinc-ribbon domain
        1.8    8.8   8.2        4.2    7.6   0.3    3.2  3  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 


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 !  139.4   0.9   8.8e-44   1.2e-40       3     346 ..      15     405 ..      13     415 .. 0.86
   2 !   55.0   0.0   3.1e-18   4.3e-15     416     601 ..     416     609 ..     410     610 .. 0.76

  Alignments for each domain:
  == domain 1  score: 139.4 bits;  conditional E-value: 8.8e-44
                       tRNA-synt_1   3 yekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieak 79 
                                       +  We +dv++    ++   ++++l    Py  G+lH+Gh+ + ++ d   ry+rm+G +vl+ +GwD  Gl+ e +
  gi|336254003|ref|YP_004597110.1|  15 QYVWERDDVYELD--EDAADPTYVLGMF-PYTSGTLHMGHVRNYAITDAYARYRRMQGDDVLHPMGWDAFGLPAENA 88 
                                       568*******988..6777999999875.7********************************************987 PP

                       tRNA-synt_1  80 vekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgli 156
                                         ++                      +w +  + ++r++++ +G  +D++re  T ++e+ +  ++ f+r++++gl+
  gi|336254003|ref|YP_004597110.1|  89 AYERASD-----------------PESWTQACIRRMREELETMGFGYDWSREITTCEPEYYQWNQWLFKRFYEEGLV 148
                                       6665333.................347999999******************************************** PP

                       tRNA-synt_1 157 yrgkklvnwstklktalselEveykdkk................................................. 184
                                          +  vnw+++++t+l+++ v  +++                                                  
  gi|336254003|ref|YP_004597110.1| 149 EYEAASVNWCPDCETVLADAQVAEQETGdrvcwrcetpvgrreldqwfftitdyadelyeglddlegwpdgvreiqr 225
                                       **********************888888899********************************************** PP

                       tRNA-synt_1 185 .....dalihvafpladkeevklv.iaTTtPeTllgdtavavnpeldyvitkeklilaeallkslvkkesek.kile 254
                                            +  + ++f+++ +e++  v +  T+P T+ g t +av p  + +   + l  a+  + + v++  e+   + 
  gi|336254003|ref|YP_004597110.1| 226 nwigrQEGVRITFDVQRGETTDAVdVFSTRPDTIYGATYLAVSPGHELA---RDLADADEDVAEYVERVREQdPDEV 299
                                       ***999999******99998766559*******************5554...4455556666666666644413233 PP

                       tRNA-synt_1 255 dergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynlevinildedgtlteea.... 327
                                        + g e +  ++ +pl+++++p+ +  yv ++ GtG+V   Pah+e D++ +++++l++  ++      +e      
  gi|336254003|ref|YP_004597110.1| 300 GFSGVE-TDATAVHPLTGEELPVYVAGYVLEDVGTGAVMGVPAHNERDHAFAREHDLPIEGVIAPTDATREVDlese 375
                                       344444.356789********************************************66555554444443334568 PP

                       tRNA-synt_1 328 ...........aefeglkvfdarkkvveel 346
                                                  ++++gl+ + ar+ +v++ 
  gi|336254003|ref|YP_004597110.1| 376 pytgegiledsGDYSGLESETARERLVADH 405
                                       9999999*999*************999875 PP

  == domain 2  score: 55.0 bits;  conditional E-value: 3.1e-18
                       tRNA-synt_1 416 iqdWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdkl..kkekgelekdedvlDvW 490
                                        +dW iSRqr+WG++ip+   ++ + v v +e   ++  ++ +++ +  +e+++ ++    +  g  ++++d++D+ 
  gi|336254003|ref|YP_004597110.1| 416 LRDWLISRQRYWGTPIPVVHCDDCGPVLVPDEDLPVELPEFVRTTGNPLEEHDSFRETecPECGGPARRETDTMDTF 492
                                       58************************99988666555555555444444444444444235556899********** PP

                       tRNA-synt_1 491 FsSgswpfstlgypee.....dteelkkffpadmlleGlDiirgWvarlillslaltgse......Pfkevlvhglv 556
                                        +S+      l  p++     dte  ++  p d+++ G       +  + +++ al +        P +e++ +g v
  gi|336254003|ref|YP_004597110.1| 493 VDSSWYYLRFLS-PDYddgpfDTERAEEWMPIDVYVGGDEHAVLHLLYIRFFARALSDLGlldcrePVEELVSQGTV 568
                                       *99765555553.6652223357788899*******998887777777777777766644555555*********99 PP

                       tRNA-synt_1 557 rdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                       +  +G KmS s+gN + p     +yga+  Rl+++  ++  +d ++
  gi|336254003|ref|YP_004597110.1| 569 L-YDGEKMSSSKGNSVTPR----EYGAETTRLFVLsAAHPEQDFEW 609
                                       8.58**************6....7*********9977777888776 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 !  195.1   0.0   5.2e-61   7.2e-58       1     181 [.     225     402 ..     225     406 .. 0.95

  Alignments for each domain:
  == domain 1  score: 195.1 bits;  conditional E-value: 5.2e-61
                     tRNA-synt_1_2   1 rnWIGrseGleiefkvees..eeklevfttrpdtlfGvtfvalapehplveklaekkkelaafieevkkkseserel 75 
                                       rnWIGr+eG++i+f+v+    +++++vf trpdt++G+t++a++p h+l+++la+ ++++a+++e+v++++  e   
  gi|336254003|ref|YP_004597110.1| 225 RNWIGRQEGVRITFDVQRGetTDAVDVFSTRPDTIYGATYLAVSPGHELARDLADADEDVAEYVERVREQDPDEV-- 299
                                       8***************98733469********************************************9998886.. PP

                     tRNA-synt_1_2  76 etkekeGvftglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedeekklees 152
                                            +Gv+t+++a+hP+tge++p++va yvl + gtgavm+vPah++rD++Fa++++lpi+ vi+p+d++++++ +
  gi|336254003|ref|YP_004597110.1| 300 ---GFSGVETDATAVHPLTGEELPVYVAGYVLEDVGTGAVMGVPAHNERDHAFAREHDLPIEGVIAPTDATREVDLE 373
                                       ...569*********************************************************************** PP

                     tRNA-synt_1_2 153 eeayteegilvnsgefdglkskeakekia 181
                                       +e yt+egil +sg+++gl+s++a+e+++
  gi|336254003|ref|YP_004597110.1| 374 SEPYTGEGILEDSGDYSGLESETARERLV 402
                                       ************************99876 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 !   76.5   0.0   1.2e-24   1.6e-21       5     193 ..      38     204 ..      34     246 .. 0.80
   2 !    4.4   0.0    0.0091        13     215     238 ..     409     432 ..     392     442 .. 0.81
   3 !   15.8   0.0   3.3e-06    0.0046     311     371 ..     558     614 ..     524     632 .. 0.80

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.2e-24
                                       E--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHT CS
                      tRNA-synt_1g   5 talpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkkl 81 
                                         +pY++g+lH+Gh++++ ++D++aRy+r++g++vl+  g D++G p e +A ++  +pe  ++   ++++e ++++
  gi|336254003|ref|YP_004597110.1|  38 GMFPYTSGTLHMGHVRNYAITDAYARYRRMQGDDVLHPMGWDAFGLPAENAAYERASDPESWTQACIRRMREELETM 114
                                       568*************************************************************************9 PP

                                       T---SEE..EETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE.-TT CS
                      tRNA-synt_1g  82 nisfdky..grttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqc.eec 155
                                       +  +d    ++t + e ++  q +fk+++e+gl++ ++ ++ +cp++e+ l+d +v        +e+ +gd++  +c
  gi|336254003|ref|YP_004597110.1| 115 GFGYDWSreITTCEPEYYQWNQWLFKRFYEEGLVEYEAASVNWCPDCETVLADAQV--------AEQETGDRVcWRC 183
                                       99998652267889999**************************************8........3455555533666 PP

                                       SSB-E................EEE.EEEEEE-GGGGHH CS
                      tRNA-synt_1g 156 gkkleptelinpksaisgskpevketehlffklskfek 193
                                        + +                   +e +++ff + ++++
  gi|336254003|ref|YP_004597110.1| 184 ETPVGR-----------------RELDQWFFTITDYAD 204
                                       666663.................333444444444444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0091
                                       .HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 215 kewlkegLkdlaisrdldwGipvP 238
                                       +e +   L+d+ isr+  wG p+P
  gi|336254003|ref|YP_004597110.1| 409 EEDVTYRLRDWLISRQRYWGTPIP 432
                                       55566789***************9 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 3.3e-06
                                       --S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHH CS
                      tRNA-synt_1g 311 lpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedf 371
                                        ++++v+++ + ++g+K+S+S+g+ v+++e    + a++ R +++++a  ++D++++ +++
  gi|336254003|ref|YP_004597110.1| 558 PVEELVSQGTVLYDGEKMSSSKGNSVTPRE----YGAETTRLFVLSAAHPEQDFEWTANNV 614
                                       46899*********************9987....578999*99999999999998888776 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 !   62.8   0.0   2.4e-20   3.3e-17       1     145 [.     645     766 ..     645     777 .. 0.81

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 2.4e-20
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       d ++ +e++++++ vte ye++rf++aa+++ e+   +l + y e  +p+             e+++  l tl  l+
  gi|336254003|ref|YP_004597110.1| 645 DEYLAREIDRTIAAVTEEYERFRFHRAATEIREL--AQLLRRYREYDRPHD------------ETYRRGLLTLAALI 707
                                       678999***************************8..8888******98876............9************* PP

                       Anticodon_1  78 aPfmPfitEelwqreeeelgkkesimlaewpe.kaeel.ekeleeeevellkeivkairklrselkikps 145
                                       aP++P++ Ee+w    ++l ++  ++ a+wpe + e   +     +e  l   + ++++++r + +++  
  gi|336254003|ref|YP_004597110.1| 708 APMAPHLGEECW----NKLRGEGLVVEADWPEpEREVDdY----RRERRL---VERTLEDVRDIVDVAAI 766
                                       ************....99999999*******744433331....234444...55666666666666555 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 ?    4.0   0.0     0.014        19      33      69 ..      43      79 ..      19      83 .. 0.86
   2 ?    1.2   0.0       0.1   1.4e+02     104     131 ..      96     123 ..      89     135 .. 0.86
   3 !    9.2   0.0   0.00036       0.5     276     330 ..     569     619 ..     550     644 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.014
                      tRNA-synt_1f 33 pSGliHiGnlrevltadlvaralrkrgeevrlilisD 69
                                      +SG++H+G +r+ + +d+ ar  r +g++v + + +D
  gi|336254003|ref|YP_004597110.1| 43 TSGTLHMGHVRNYAITDAYARYRRMQGDDVLHPMGWD 79
                                      7******************999999999987766666 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.1
                      tRNA-synt_1f 104 hesyaehfnaelvesLdelgievefisa 131
                                        es+ +   ++++e+L+++g+ +++ ++
  gi|336254003|ref|YP_004597110.1|  96 PESWTQACIRRMREELETMGFGYDWSRE 123
                                       589*********************9876 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00036
                      tRNA-synt_1f 276 lkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvd 330
                                       l  gekmssSkGn +t+++      +++  f++  ++P++ ++ + + ++  ++d
  gi|336254003|ref|YP_004597110.1| 569 LYDGEKMSSSKGNSVTPREYG---AETTRLFVLSAAHPEQDFEWTAN-NVRGAYD 619
                                       55677************9854...44444455555688888888777.6766666 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 !    8.4   0.1    0.0009       1.2      13      48 ..      35      72 ..      28      76 .. 0.81
   2 !    6.6   0.0    0.0032       4.4     235     285 ..     556     602 ..     523     618 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0009
                                      EEEEEBTT..S--BHHHHHHHHHHHHHHHHHHHTT-EE CS
                      tRNA-synt_1e 13 YvCGptvy..dashlGhaRslvafDilrrilqalgYdv 48
                                      Yv G+  y   + h+Gh+R++ ++D  +r+ +++g dv
  gi|336254003|ref|YP_004597110.1| 35 YVLGMFPYtsGTLHMGHVRNYAITDAYARYRRMQGDDV 72
                                      5556555522579*****************99999887 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0032
                                       S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-T CS
                      tRNA-synt_1e 235 kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahy 285
                                       ++ v+  + +g +  +gekms s +n +t ++    + +++ Rl++lsa +
  gi|336254003|ref|YP_004597110.1| 556 REPVEELVSQGTVLYDGEKMSSSKGNSVTPRE----YGAETTRLFVLSAAH 602
                                       5667778899******************9875....778888887776544 PP

>> PknG_rubred  Protein kinase G rubredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.9e-06    0.0067      66     108 ..     146     193 ..      91     197 .. 0.82
   2 ?   -3.6   0.1       8.6   1.2e+04     110     123 ..     468     481 ..     461     483 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.9e-06
                                       TTEEEE..------TTGGG-CSS---GGG...-B-TTT--B-S---SS CS
                       PknG_rubred  66 GLveip..rvveadPleAlltnpvvpEsk...RfCwrCGrpvGRseke 108
                                       GLve +  +v+     e +l +  v+E+    R CwrC +pvGR e +
  gi|336254003|ref|YP_004597110.1| 146 GLVEYEaaSVNWCPDCETVLADAQVAEQEtgdRVCWRCETPVGRRELD 193
                                       77765411455555578999*****9964444************9876 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.6
                                       ---SEEE-TTT--E CS
                       PknG_rubred 110 kgaseGtCpkCgsp 123
                                        +  e  Cp+Cg p
  gi|336254003|ref|YP_004597110.1| 468 DSFRETECPECGGP 481
                                       55667789999976 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.5    0.0018       2.5      13      38 ..     156     187 ..     150     191 .. 0.81
   2 ?    7.3   0.1    0.0035       4.8      14      41 ..     435     485 ..     429     488 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0018
                               DZR  13 rfCseCgtklkavaa......edrCpsCgekv 38 
                                       + C++C t l  ++        ++C++C+++v
  gi|336254003|ref|YP_004597110.1| 156 NWCPDCETVLADAQVaeqetgDRVCWRCETPV 187
                                       67*******975544899999999****9987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0035
                               DZR  14 fCseCgtklkavaa.......................edrCpsCgekvdpe 41 
                                        C++Cg  l + ++                       e+ Cp+Cg ++  e
  gi|336254003|ref|YP_004597110.1| 435 HCDDCGPVLVPDEDlpvelpefvrttgnpleehdsfrETECPECGGPARRE 485
                                       69999999976666999999999999999999999*********9887765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.6    0.0006      0.83       3      27 ..     158     185 ..     156     193 .. 0.81
   2 ?    2.5   0.1     0.074     1e+02      22      29 ..     436     443 ..     434     458 .. 0.73
   3 ?    6.8   0.4    0.0034       4.7       3      18 ..     475     491 ..     473     493 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0006
                                       ETTTTC..EE.CHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   3 CPnCgs..tn.lveDpergelvCtdCGl 27 
                                       CP+C +   + +v + e+g+ vC +C++
  gi|336254003|ref|YP_004597110.1| 158 CPDCETvlADaQVAEQETGDRVCWRCET 185
                                       *****9444444999***********53 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.074
                                       ESSSSBEE CS
                      TF_Zn_Ribbon  22 CtdCGlVl 29 
                                       C dCG+Vl
  gi|336254003|ref|YP_004597110.1| 436 CDDCGPVL 443
                                       ******98 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0034
                                       ETTTTCEE.CHEETSTT CS
                      TF_Zn_Ribbon   3 CPnCgstn.lveDperg 18 
                                       CP+Cg++   ++D++ +
  gi|336254003|ref|YP_004597110.1| 475 CPECGGPArRETDTMDT 491
                                       ******88799999965 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.4     0.062        85       7      38 ..     151     189 ..     147     190 .. 0.68
   2 ?   -1.1   0.0       1.6   2.2e+03       7      12 ..     435     440 ..     430     444 .. 0.73
   3 ?   12.0   0.3   0.00013      0.17      14      38 ..     463     484 ..     455     485 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.062
                       Zn-ribbon_8   7 r......CeeCghefevlqsis.dapltaCPeCgsevrr 38 
                                       +      C +C ++    q +  +  + +C +C  +v r
  gi|336254003|ref|YP_004597110.1| 151 EaasvnwCPDCETVLADAQVAEqETGDRVCWRCETPVGR 189
                                       555555599999888888866655556669999887765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                       Zn-ribbon_8   7 rCeeCg 12 
                                       +C++Cg
  gi|336254003|ref|YP_004597110.1| 435 HCDDCG 440
                                       677777 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00013
                       Zn-ribbon_8  14 efevlqsisdapltaCPeCgsevrr 38 
                                         e+  s+    +t+CPeCg+++rr
  gi|336254003|ref|YP_004597110.1| 463 PLEEHDSFR---ETECPECGGPARR 484
                                       555555555...788********99 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 ?   -0.4   3.1      0.86   1.2e+03       2      20 ..     158     183 ..     158     186 .. 0.78
   2 ?   10.6   0.1   0.00033      0.45       1      14 [.     474     487 ..     474     497 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.86
                    DNA_ligase_ZBD   2 CPvCGsavvRee.......geaiyRC 20 
                                       CP C + +   +       + + +RC
  gi|336254003|ref|YP_004597110.1| 158 CPDCETVLADAQvaeqetgDRVCWRC 183
                                       ****9999988878777744555998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00033
                    DNA_ligase_ZBD   1 hCPvCGsavvReeg 14 
                                       +CP+CG ++ Re +
  gi|336254003|ref|YP_004597110.1| 474 ECPECGGPARRETD 487
                                       5*********9976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.073     1e+02      15      26 .]     154     165 ..     152     165 .. 0.82
   2 ?   -0.4   0.0       0.6   8.2e+02      15      24 ..     176     185 ..     172     190 .. 0.61
   3 ?    1.2   0.1      0.19   2.7e+02       3      10 ..     434     441 ..     432     448 .. 0.59
   4 ?    5.4   0.2    0.0088        12       2      11 ..     472     481 ..     471     486 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.073
                       zf-ribbon_3  15 ddnvCpyCGtkl 26 
                                       ++n Cp C t+l
  gi|336254003|ref|YP_004597110.1| 154 SVNWCPDCETVL 165
                                       5788****9987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.6
                       zf-ribbon_3  15 ddnvCpyCGt 24 
                                       +d+vC  C t
  gi|336254003|ref|YP_004597110.1| 176 GDRVCWRCET 185
                                       5555555544 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.19
                       zf-ribbon_3   3 vrCPnCGa 10 
                                       v+C  CG 
  gi|336254003|ref|YP_004597110.1| 434 VHCDDCGP 441
                                       56666665 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0088
                       zf-ribbon_3   2 tvrCPnCGap 11 
                                       +++CP+CG p
  gi|336254003|ref|YP_004597110.1| 472 ETECPECGGP 481
                                       6789999965 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 ?    7.6   0.3    0.0031       4.2      18      40 .]     158     184 ..     156     184 .. 0.91
   2 ?    0.9   0.2      0.38   5.2e+02      17      28 ..     435     446 ..     434     450 .. 0.85
   3 ?    3.5   0.1     0.059        82      16      28 ..     473     485 ..     471     492 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0031
                     Auto_anti-p27  18 CpvCgvPLmrdr....kggkvyCvaCd 40 
                                       Cp+C ++L   +    ++g+ +C +C+
  gi|336254003|ref|YP_004597110.1| 158 CPDCETVLADAQvaeqETGDRVCWRCE 184
                                       **********999988799*******5 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.38
                     Auto_anti-p27  17 tCpvCgvPLmrd 28 
                                       +C++Cg +L+ d
  gi|336254003|ref|YP_004597110.1| 435 HCDDCGPVLVPD 446
                                       9*****999876 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.059
                     Auto_anti-p27  16 etCpvCgvPLmrd 28 
                                       + Cp+Cg P  r+
  gi|336254003|ref|YP_004597110.1| 473 TECPECGGPARRE 485
                                       68******98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (882 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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):              13  [number of targets reported over threshold]
# CPU time: 0.73u 0.26s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 5444.04
//
Query:       gi|336254004|ref|YP_004597111.1|  [L=98]
Description: hypothetical protein Halxa_2614 [Halopiger xanaduensis SH-6]
Scores for 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-26   90.6   0.1      7e-26   90.3   0.1    1.1  1  HalOD1     Halobacterial output domain 1
  ------ inclusion threshold ------
      0.099   13.0   0.1       0.19   12.1   0.1    1.4  1  HTH_31     Helix-turn-helix domain
        1.6    8.7   5.5         13    5.8   0.1    3.0  3  Mago-bind  Mago binding


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.1   1.2e-29     7e-26       3      73 ..      14      89 ..      12      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 1.2e-29
                            HalOD1  3 espstaVveavaavegvdptelep.....LydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieV 73
                                      ++ps aVveava++egv+ptel p     L+ a+Dp+ALd+Lfa+radg+ r+ gs sF y+gy+VtV +dg +  
  gi|336254004|ref|YP_004597111.1| 14 KTPSRAVVEAVADAEGVSPTELRPpeyepLHAAVDPEALDSLFADRADGSPRSHGSTSFHYCGYRVTVGADGSVSL 89
                                      68********************666************************************************986 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.2e-05      0.19      38      61 ..      13      35 ..      11      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.2e-05
                            HTH_31 38 rrgrpspavlealaralgldpaer 61
                                      r   ps+av+ea+a+a g++p e+
  gi|336254004|ref|YP_004597111.1| 13 RK-TPSRAVVEAVADAEGVSPTEL 35
                                      67.5*****************997 PP

>> Mago-bind  Mago binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0021        13      12      17 ..       9      14 ..       8      15 .. 0.91
   2 ?    4.1   0.2    0.0074        44      10      16 ..      59      65 ..      57      67 .. 0.88
   3 ?   -0.2   0.1      0.16   9.8e+02      11      15 ..      83      87 ..      80      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0021
                         Mago-bind 12 DGtvRK 17
                                      DGtvRK
  gi|336254004|ref|YP_004597111.1|  9 DGTVRK 14
                                      *****9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0074
                         Mago-bind 10 RpDGtvR 16
                                      R+DG+ R
  gi|336254004|ref|YP_004597111.1| 59 RADGSPR 65
                                      *****88 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.16
                         Mago-bind 11 pDGtv 15
                                      +DG+v
  gi|336254004|ref|YP_004597111.1| 83 ADGSV 87
                                      8***7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 748.47
//
Query:       gi|336254005|ref|YP_004597112.1|  [L=200]
Description: hypothetical protein Halxa_2615 [Halopiger xanaduensis SH-6]
Scores for 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-38  129.5  12.0    9.1e-38  129.5  12.0    1.4  2  DUF420          Protein of unknown function (DUF420)
      0.004   17.3   1.1      0.004   17.3   1.1    2.2  2  Cytochrom_B561  Eukaryotic cytochrome b561
     0.0079   15.8   1.3     0.0079   15.8   1.3    2.2  2  TM140           TM140 protein family
  ------ inclusion threshold ------
      0.012   15.8  14.0      0.022   15.0   2.2    2.3  2  DUF2306         Predicted membrane protein (DUF2306)
       0.12   11.6   8.9       0.55    9.4   1.2    2.2  2  DUF3413         Domain of unknown function (DUF3413)
        1.5    9.4   5.2       0.23   12.0   0.5    2.0  2  DUF1240         Protein of unknown function (DUF1240)


Domain annotation for each model (and alignments):
>> DUF420  Protein of unknown function (DUF420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.6         5   1.5e+04      83      94 ..      20      31 ..      17      35 .. 0.38
   2 !  129.5  12.0     3e-41   9.1e-38       1     132 []      51     184 ..      51     184 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 5
                            DUF420 83 vLavvvvplvlv 94
                                      +L +v   lv+ 
  gi|336254005|ref|YP_004597112.1| 20 LLTIVGYALVIG 31
                                      333333333333 PP

  == domain 2  score: 129.5 bits;  conditional E-value: 3e-41
                            DUF420   1 lpalnavlnalaavllllglvaikkgkieaHrklmllafvlsalFlvlYllkhalagetkfggpeeegvirpvYlai 77 
                                       l++++av+n++++vll+lg+++i++g++ +Hr +m+ af+l++lFlv+Yl+k+  +ge++f+gp+    + ++Yla+
  gi|336254005|ref|YP_004597112.1|  51 LSHAIAVINSTTTVLLVLGWYWIRRGDVGKHRLAMIGAFALIMLFLVTYLIKVGGGGEKHFVGPDP---VYYAYLAM 124
                                       67999*********************************************************9997...******** PP

                            DUF420  78 LitHivLavvvvplvlvtlvlalkg.....kfekHrkiaritvpiwlyvavtGvvvYllL 132
                                       L++HivL+vv vp+vl++l+l+l++     + ++H++++ri++  w++++v+Gvv+Y+lL
  gi|336254005|ref|YP_004597112.1| 125 LAIHIVLSVVSVPVVLYALILGLTHtpaelRNTAHARVGRIAAASWILSLVLGVVTYVLL 184
                                       **********************************************************98 PP

>> Cytochrom_B561  Eukaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   1.1      0.53   1.6e+03      38      38 ..      53      53 ..      17     101 .. 0.50
   2 !   17.3   1.1   1.3e-06     0.004      34     101 ..     124     188 ..     114     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.53
                                      H CS
                    Cytochrom_B561 38 H 38
                                      H
  gi|336254005|ref|YP_004597112.1| 53 H 53
                                      2 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--SS-SHHHHHHHHHHHHHHHHHHHHHHHHTSS---H CS
                    Cytochrom_B561  34 kkllHlilqllalilavvgllavfksknekeianlyslHswlGlvtvilfllqlvlGfvlfllpklsk 101
                                       + ++H++l ++++ +++ +l++ + ++ +   +  ++ H+++G ++ +  +l+lvlG+v+++l +  +
  gi|336254005|ref|YP_004597112.1| 124 MLAIHIVLSVVSVPVVLYALILGLTHTPA---ELRNTAHARVGRIAAASWILSLVLGVVTYVLLNHVY 188
                                       5689****************998876664...566799***********************9866555 PP

>> TM140  TM140 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.3   2.6e-06    0.0079     112     164 ..      48     100 ..      16     110 .. 0.87
   2 ?    0.4   0.5      0.14   4.2e+02      11      29 ..     127     145 ..     118     170 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-06
                             TM140 112 vgflaassvllagGlglflsyvwkWvrlsllGpgflalvlaqallillllaiv 164
                                       + +l+ +  ++ +  +++l++ w W+r   +G+  la+  a al++l+l++  
  gi|336254005|ref|YP_004597112.1|  48 INLLSHAIAVINSTTTVLLVLGWYWIRRGDVGKHRLAMIGAFALIMLFLVTYL 100
                                       568888889999999******************************99998754 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.14
                             TM140  11 gilvlvvvvisllfyallw 29 
                                       +++vl vv + +++yal+ 
  gi|336254005|ref|YP_004597112.1| 127 IHIVLSVVSVPVVLYALIL 145
                                       4567777778888888864 PP

>> DUF2306  Predicted membrane protein (DUF2306)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   2.2   7.3e-06     0.022      60     104 ..      49      93 ..       6     104 .. 0.78
   2 ?    6.2   4.3    0.0038        11       2      51 ..     126     179 ..     125     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.3e-06
                           DUF2306  60 lvlllgflllallwlvftvlalvairrrdfaaHrawmirsYalal 104
                                        +l+  ++++++ + v +vl++  irr d+ +Hr +mi ++al +
  gi|336254005|ref|YP_004597112.1|  49 NLLSHAIAVINSTTTVLLVLGWYWIRRGDVGKHRLAMIGAFALIM 93 
                                       45566678889999999*************************876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0038
                           DUF2306   2 vlHialalvalllGalqlvkrlr...ak.rpklHrlaGrvyvlavllaalsglf 51 
                                       ++Hi+l++v +++ + +l+ +l    a+ r   H ++Gr+ +++ +l+ + g++
  gi|336254005|ref|YP_004597112.1| 126 AIHIVLSVVSVPVVLYALILGLThtpAElRNTAHARVGRIAAASWILSLVLGVV 179
                                       89*************999999987775557889*********999999888876 PP

>> DUF3413  Domain of unknown function (DUF3413)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.2   0.00018      0.55     113     183 ..      32     102 ..      20     104 .. 0.83
   2 ?    6.6   1.3    0.0013       3.8     130     185 ..     128     183 ..     120     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00018
                           DUF3413 113 pvvlelllngeqselssswllllilvlvilllelllanlvwkklrklkrkklgkpvalvlllaflashlih 183
                                       ++vl++ + ++ ++ + ++l+++i+v+   +  ll+  + w +   + +++l+ + a++l++ fl+++li 
  gi|336254005|ref|YP_004597112.1|  32 TFVLDVPIYPDLTTAQINLLSHAIAVINSTTTVLLVLGWYWIRRGDVGKHRLAMIGAFALIMLFLVTYLIK 102
                                       5677777777777777778888888888888888888888888888999*******************996 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0013
                           DUF3413 130 swllllilvlvilllelllanlvwkklrklkrkklgkpvalvlllaflashlihiw 185
                                       ++ l ++ v+v+l + +l  + +  +lr++ + ++g+++a+ ++l++++  +++++
  gi|336254005|ref|YP_004597112.1| 128 HIVLSVVSVPVVLYALILGLTHTPAELRNTAHARVGRIAAASWILSLVLGVVTYVL 183
                                       466778888888888888888888999999******************99888876 PP

>> DUF1240  Protein of unknown function (DUF1240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.4      0.98   2.9e+03      40      40 ..      77      77 ..      18     103 .. 0.59
   2 ?   12.0   0.5   7.6e-05      0.23       6      68 ..     126     183 ..     122     192 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.98
                           DUF1240 40 d 40
                                      d
  gi|336254005|ref|YP_004597112.1| 77 D 77
                                      1 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.6e-05
                           DUF1240   6 sskvvlllfssPlllYfsvlvvlvaitnklakvndklvkllaiiailsfvlslflslYvdykl 68 
                                       + ++vl ++s+P++lY+++l +    t+  a+++++    +  ia +s +lsl l + v y l
  gi|336254005|ref|YP_004597112.1| 126 AIHIVLSVVSVPVVLYALILGL----THTPAELRNTAHARVGRIAAASWILSLVLGV-VTYVL 183
                                       568999**********987765....5556666666666666666667776666654.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 1578.53
//
Query:       gi|336254006|ref|YP_004597113.1|  [L=170]
Description: pyridoxamine 5'-phosphate oxidase-like FMN-binding protein [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00053   20.0   0.1    0.00074   19.5   0.1    1.2  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    0.00055   20.1   0.0     0.0009   19.4   0.0    1.3  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.082   12.8   0.0       0.14   12.1   0.0    1.4  1  PB1             PB1 domain


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.2e-07   0.00074       1     138 [.       8     141 ..       8     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-07
                                       -HHHHHHHHHC-SE.EEEEEEETTEEEEEEEEEEEE.....TTE...EEEEEETTSHCCHCCCT--.ECEEEEEEEE CS
                      Pyridox_ox_2   1 dreeilalLdegev.grlafvddgepvilPvnyvvd.....gds...lyfhgakgsrlaaalrgap.vcvvvtevdg 67 
                                       +r+ei+ +L+e+ v  rla+ + +   ++ v+ +++     + +   l   +a  + +a +l++ p v+++v+  + 
  gi|336254006|ref|YP_004597113.1|   8 SRDEIETFLEESTVpVRLACRT-PSDQLWMVSLWYRyrsggD-DdwrLQCATAADADIASLLSADPaVAFEVSTNE- 81 
                                       589*******655549******.88899999*9999888642.256688889999999999996566666666522. PP

                                       EEE-SEGGEEE.EEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTT.GGCSB---CCCCCTEEEEEEEEEEEE CS
                      Pyridox_ox_2  68 lvlarsfnsln.yrSVvvrGraeevtdeeekaealellvekivpgr.wenlrpptrkelkatsvlrlkieevs 138
                                                   y  V  +G+a+     + ++e+l++lve+++ g+ ++  r    +e +++  + ++++ vs
  gi|336254006|ref|YP_004597113.1|  82 ----------PpYAGVRGQGTASIE--RDSDKEILRTLVERYLGGTeSQLAR-TLLREDREEVTITIDPAVVS 141
                                       ..........23*999999999999..7788899********9999655555.33333333344566666555 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.5e-07    0.0009       2      87 ..       9      99 ..       8     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.5e-07
                                      HHHHHHHHHHS.SEEEEEEEETTSEEEEEEEEEEEETTT...TEEEEEEETTSHHHHHHHHH-EEEEEEEETT.GSEEE CS
                    Putative_PNPOx  2 deelreflaes.kavvlATvdedGrPnvspvllkagdgr...dgivfatnadsrklrnleenprvallfldde.lgrgv 75
                                      ++e+++fl+es   v+lA+ +++ + +++ +++ +  g     ++  at+ad++ +  l ++p va+ +  +e  + gv
  gi|336254006|ref|YP_004597113.1|  9 RDEIETFLEEStVPVRLACRTPSDQLWMVSLWYRYRSGGdddWRLQCATAADADIASLLSADPAVAFEVSTNEpPYAGV 87
                                      58999****883559*****************8886666666************************************* PP

                                      EEEEEEEEESCH CS
                    Putative_PNPOx 76 rieGtaelvsdg 87
                                      r +Gta +  d 
  gi|336254006|ref|YP_004597113.1| 88 RGQGTASIERDS 99
                                      ******998875 PP

>> PB1  PB1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.3e-05      0.14      13      59 ..      89     136 ..      82     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                                       EE.EEEEGSSS-HHHHHHHHHHHHTSTCCSEEEEEEETTSSEEEESSH CS
                               PB1  13 rr.elsvssnisfeeLrakvekrfklsdedvklkYpdedgdlVtitsD 59 
                                        + ++s+++++  e Lr++ve++++ ++++++ ++  ed ++Vtit D
  gi|336254006|ref|YP_004597113.1|  89 GQgTASIERDSDKEILRTLVERYLGGTESQLARTLLREDREEVTITID 136
                                       4456799999999********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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 0.19s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1468.58
//
Query:       gi|336254007|ref|YP_004597114.1|  [L=257]
Description: ABC-2 type transporter [Halopiger xanaduensis SH-6]
Scores for 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-28   97.1   7.1    9.1e-28   97.1   7.1    1.3  2  ABC2_membrane    ABC-2 type transporter
    3.1e-15   56.1   2.6    3.1e-15   56.1   2.6    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein
    4.2e-07   29.5  10.3    4.2e-07   29.5  10.3    2.0  2  ABC2_membrane_2  ABC-2 family transporter protein
     0.0011   18.2   1.1     0.0016   17.6   1.1    1.2  1  12TM_1           Membrane protein of 12 TMs
  ------ inclusion threshold ------
      0.024   14.6   0.2      0.024   14.6   0.2    3.4  3  OppC_N           N-terminal TM domain of oligopeptide transpo


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 !   97.1   7.1   2.5e-31   9.1e-28       7     209 ..      11     216 ..       6     217 .. 0.93
   2 ?   -4.2   0.1       2.5   9.1e+03     113     118 ..     238     243 ..     227     250 .. 0.39

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 2.5e-31
                     ABC2_membrane   7 lkreflqrwrdpslgllwrliqplllalvfgtvfgnlg.nsedglnr......pgllffsvlflafsaltsvapvfe 76 
                                       ++  +++++r+++   ++ +++p++l+++fg +   ++ + e+ +++      pg l+  vlf+ +s + s  + + 
  gi|336254007|ref|YP_004597114.1|  11 TNAGWRSFIRRRTAV-FFTFFFPVILIVIFGALVR-TDpTGEGLFTEppayyvPGYLAVVVLFTPLSRMGSE-VARH 84 
                                       677899999999888.99****************9.55577777766799999************8888888.**** PP

                     ABC2_membrane  77 rergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrf.flflllllltalaasslgllis 152
                                       re   +e++ ++pl ++++ +la+++v+++++ l++l++l++v++l+g ++  f  l+++++l+ ++++ ++g +++
  gi|336254007|ref|YP_004597114.1|  85 REGNRFEKLATTPL-TRAEWLLAQTVVNAAIIGLASLLILALVVLLTGAEIA-FsPLLVPYVLVGVVCFCGIGAMLG 159
                                       **************.************************************7.7866699999999*********** PP

                     ABC2_membrane 153 alapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                       +++ s++ a++ ++++ lpll+ls  fi+++++p+w+  +  l+Plty+ +++r++ 
  gi|336254007|ref|YP_004597114.1| 160 SYTDSQDGAVTASNAIGLPLLFLSETFISLEQLPGWFEPLVNLSPLTYFARGVRAAT 216
                                       ******************************************************975 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 2.5
                     ABC2_membrane 113 liflli 118
                                       l++l++
  gi|336254007|ref|YP_004597114.1| 238 LAVLAV 243
                                       111111 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 !    3.5   2.8    0.0088        32       4      25 ..      25      46 ..      22      57 .. 0.85
   2 !   56.1   2.6   8.7e-19   3.1e-15     161     344 ..      59     250 ..      55     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0088
                   ABC2_membrane_3  4 liitlllPiilvlllglifsns 25
                                      +++t+++P+il++++g ++ ++
  gi|336254007|ref|YP_004597114.1| 25 VFFTFFFPVILIVIFGALVRTD 46
                                      689*************998766 PP

  == domain 2  score: 56.1 bits;  conditional E-value: 8.7e-19
                   ABC2_membrane_3 161 sflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll...afglgip 234
                                       +++ g+++++++f ++s + +++++ +e +  e + ++++++++ +l+  +  +++  l +llil+l   + g   +
  gi|336254007|ref|YP_004597114.1|  59 YYVPGYLAVVVLFTPLSRMGSEVARHREGNRFEKLATTPLTRAEWLLAQTVVNAAIIGLASLLILALvvlLTG--AE 133
                                       66667************************************************************97443555..66 PP

                   ABC2_membrane_3 235 fgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapgl 311
                                       +  + ll+ ++l++  ++  +g++l+s +++++ a ++  ++ l+l++++  +++le+lp+++  +  + P+++++ 
  gi|336254007|ref|YP_004597114.1| 134 IAFSPLLVPYVLVGVVCFCGIGAMLGSYTDSQDGAVTASNAIGLPLLFLSETFISLEQLPGWFEPLVNLSPLTYFAR 210
                                       66788899************************************99999999999********************** PP

                   ABC2_membrane_3 312 gllrli......tgdplwe......illsliilalfavvylllal 344
                                       g                        +l +l+ila++avv+++l++
  gi|336254007|ref|YP_004597114.1| 211 GVRAATfpeadaA-----AvagvdaTLANLAILAVLAVVTFALGA 250
                                       **99985554441.....155666699***************986 PP

>> 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 ?    0.8   0.6     0.066   2.3e+02       8      35 ..      15      40 ..      12      72 .. 0.74
   2 !   29.5  10.3   1.2e-10   4.2e-07     106     282 ..      90     252 ..      60     257 .] 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.066
                   ABC2_membrane_2  8 frdlvrsrrfllltvllplidvalaylk 35
                                      +r ++r r+ + +t+++p+i   + ++ 
  gi|336254007|ref|YP_004597114.1| 15 WRSFIRRRTAVFFTFFFPVI--LIVIFG 40
                                      67788888888888888888..333333 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 1.2e-10
                   ABC2_membrane_2 106 lkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvlllllvvflalgl 182
                                        + l ++P +R+e ll+  + ++ai      + la++l+  +++l  g ++a++ ll+  v++   +  v+f+++g+
  gi|336254007|ref|YP_004597114.1|  90 FEKLATTPLTRAEWLLAQTVVNAAI------IGLASLLILALVVLLTGAEIAFSPLLVPYVLVG--V--VCFCGIGA 156
                                       5667799****************99......6666666677789999****************9..3..478***** PP

                   ABC2_membrane_2 183 llSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilagsdlna.. 257
                                       +l s + s+  a +++ ++ + l++l+  +   + +l+  +++       l  lsp  ++  ++++ +  ++  a  
  gi|336254007|ref|YP_004597114.1| 157 MLGSYTDSQDGAVTASNAIGLPLLFLSETFI-SLEQLPGWFEP-------LVNLSPLTYFARGVRAATFPEADAAav 225
                                       ***************************9999.66777777777.......666777777777777766666544456 PP

                   ABC2_membrane_2 258 ..lgstatnllilllllavllvlgyvl 282
                                           +t +nl+il +l++v ++lg+ +
  gi|336254007|ref|YP_004597114.1| 226 agVDATLANLAILAVLAVVTFALGARS 252
                                       556677788888888888888888765 PP

>> 12TM_1  Membrane protein of 12 TMs
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.1   4.6e-07    0.0016     261     379 ..      19     148 ..      17     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.6e-07
                            12TM_1 261 llRksqalvlllvPivivlpnvfsivseaqpvl............ltifiialiivlSsvylilllaievsgfsllk 325
                                       + R++ +++++  P++   + + ++v   +++              +++++ l   lS + ++++   e++ f+ l 
  gi|336254007|ref|YP_004597114.1|  19 IRRRTAVFFTFFFPVILIVI-FGALVRTDPTGEglfteppayyvpGYLAVVVLFTPLSRMGSEVARHREGNRFEKLA 94 
                                       569999********987666.67888888877799999**99998899999************************** PP

                            12TM_1 326 aLPlerreillsKlltilliylvvsvvlvllvliykgsnalylliilpspilvv 379
                                         Pl+r e ll   ++ ++i   +s+ +++lv+ + g + ++++ ++p  ++ v
  gi|336254007|ref|YP_004597114.1|  95 TTPLTRAEWLLAQTVVNAAIIGLASLLILALVVLLTGAEIAFSPLLVPYVLVGV 148
                                       ****************9999999***********************99877654 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   6.6e-06     0.024       7      36 ..      15      43 ..      12      62 .. 0.81
   2 ?    3.7   7.0     0.017        60      16      39 ..     113     143 ..     111     166 .. 0.78
   3 ?   -0.6   0.6      0.39   1.4e+03      20      31 ..     235     246 ..     232     254 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.6e-06
                            OppC_N  7 wrrFkrNklAvvglvilllllliaifaPli 36
                                      wr+F r ++Av+  +++ ++l+ +if+ l+
  gi|336254007|ref|YP_004597114.1| 15 WRSFIRRRTAVFFTFFFPVILI-VIFGALV 43
                                      *****************97766.6888777 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.017
                            OppC_N  16 Avvglvillllllia.......ifaPliaPy 39 
                                       A++gl+ ll+l+l++       +f Pl++Py
  gi|336254007|ref|YP_004597114.1| 113 AIIGLASLLILALVVlltgaeiAFSPLLVPY 143
                                       7788888888877752224444778999998 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.39
                            OppC_N  20 lvilllllliai 31 
                                       l+il++l+++ +
  gi|336254007|ref|YP_004597114.1| 235 LAILAVLAVVTF 246
                                       677777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 1930.30
//
Query:       gi|336254008|ref|YP_004597115.1|  [L=327]
Description: phosphonate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-29  100.7   0.0    1.5e-28  100.0   0.0    1.4  1  ABC_tran     ABC transporter
      1e-16   61.6   0.0    1.2e-09   38.4   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00016   22.2   0.1    0.00024   21.7   0.1    1.2  1  AAA_23       AAA domain
    0.00016   21.4   0.6     0.0029   17.4   0.1    2.2  2  AAA_30       AAA domain
    0.00018   21.3   0.0       0.11   12.2   0.0    2.1  2  AAA_15       AAA ATPase domain
    0.00022   21.5   0.0    0.00057   20.2   0.0    1.8  1  AAA_28       AAA domain
    0.00029   20.5   0.1    0.00051   19.7   0.1    1.3  1  AAA_29       P-loop containing region of AAA domain
     0.0066   16.2   0.0       0.13   11.9   0.0    2.1  2  IstB_IS21    IstB-like ATP binding protein
     0.0077   16.2   0.3      0.017   15.1   0.1    1.6  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
     0.0096   16.2   0.0      0.017   15.4   0.0    1.5  1  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.024   14.6   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
      0.019   15.5   0.1        1.5    9.4   0.0    2.9  3  AAA_18       AAA domain
       0.02   15.3   0.3      0.037   14.4   0.1    1.8  1  AAA_16       AAA ATPase domain
      0.021   15.0   1.0      0.057   13.6   0.2    2.3  1  AAA_33       AAA domain
      0.021   14.4   0.0      0.061   12.9   0.0    1.7  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.022   14.2   0.0        0.2   11.0   0.0    2.0  2  SMC_N        RecF/RecN/SMC N terminal domain
      0.029   14.5   0.0      0.085   12.9   0.0    1.8  2  MMR_HSR1     50S ribosome-binding GTPase
      0.029   14.4   0.1        1.1    9.2   0.0    2.5  2  AAA_5        AAA domain (dynein-related subfamily)
      0.033   13.9   0.0       0.18   11.5   0.0    2.0  2  AAA_24       AAA domain
      0.037   14.5   0.0      0.095   13.1   0.0    1.7  2  AAA          ATPase family associated with various cellular a
      0.057   13.0   0.3       0.23   11.0   0.1    2.0  2  AAA_25       AAA domain
        0.1   11.4   0.1       0.15   10.8   0.1    1.2  1  ABC_ATPase   Predicted ATPase of the ABC class
       0.12   11.9   0.1       0.25   10.9   0.1    1.4  1  AAA_27       AAA domain
       0.25   11.0   0.0       0.35   10.6   0.0    1.1  1  DUF2228      Uncharacterised conserved protein (DUF2228)


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 !  100.0   0.0     2e-31   1.5e-28       2     136 ..      21     155 ..      20     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 2e-31
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +  +l++++ge+ a++G+nGaGK+tL+++l+g ++p++Ge ++ g+     ++ + r ++gvlpq+ +  ++lt+re
  gi|336254008|ref|YP_004597115.1|  21 SGATLTIERGEVFALIGPNGAGKTTLVRALTGTTDPDAGEARILGDA----PRAVDRDRLGVLPQDFSPPDRLTARE 93 
                                       6789*************************************777665....566*********************** PP

                                       H........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                ++ ++++++l+ +gl++ +dt      + LSgGq++r ++ ++l+++p+ll+lDEpt
  gi|336254008|ref|YP_004597115.1|  94 LldyyaglyDDARDPADVLADVGLVDSADTWY----EDLSGGQQRRACVGATLVNDPDLLFLDEPT 155
                                       ********777777************999998....*****************************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 !   21.3   0.1   2.6e-07   0.00019       2      22 ..      33      53 ..      32      96 .. 0.79
   2 !   38.4   0.0   1.6e-12   1.2e-09     235     298 ..     126     186 ..      90     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.6e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       +liGpNg+GK++L +al + 
  gi|336254008|ref|YP_004597115.1| 33 FALIGPNGAGKTTLVRALTGT 53
                                      68****************654 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 1.6e-12
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                        +lS G++r +++ + l  ++   +ll++DEp +g++P+  r++++l++el+++g+ v+ltTH+
  gi|336254008|ref|YP_004597115.1| 126 EDLSGGQQRRACVGATLVNDP---DLLFLDEPTTGIDPAGRRTVWRLIEELAAGGTTVVLTTHD 186
                                       578*******66666666666...9**************************************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   3.2e-07   0.00024      20      40 ..      31      51 ..      18      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.2e-07
                            AAA_23 20 gltlItGpNGaGKTTildAik 40
                                       +++++GpNGaGKTT+++A++
  gi|336254008|ref|YP_004597115.1| 31 EVFALIGPNGAGKTTLVRALT 51
                                      5899***************98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   3.8e-06    0.0029      16      64 ..      28      81 ..      21     182 .. 0.61
   2 ?    3.2   0.1     0.083        62      30      70 ..     162     201 ..     128     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.8e-06
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaa.g.grviglAptgkaAkvLa...e 64
                                      ++  v +l Gp G+GKtt+++al+ + + + g  r++g Ap +   ++L+   +
  gi|336254008|ref|YP_004597115.1| 28 ERGEVFALIGPNGAGKTTLVRALTGTTDPDaGeARILGDAPRAVDRDRLGvlpQ 81
                                      4556999****************8887766455899999999988888875551 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.083
                            AAA_30  30 GKttalkalreaweaaggrviglAptgkaAkvLaeelgiea 70 
                                       G  t+ + ++e++ a g +v++ ++  + A++La+ +g+ a
  gi|336254008|ref|YP_004597115.1| 162 GRRTVWRLIEELA-AGGTTVVLTTHDMAEAERLADRVGLLA 201
                                       5556666666654.4789999999999*******9999744 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00014      0.11      22      43 ..      30      50 ..      20      52 .. 0.84
   2 !    7.0   0.0    0.0056       4.2     322     365 ..     144     186 ..     139     188 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                            AAA_15 22 seeltvliGkNnsGKSsileal 43
                                       e +  liG+N++GK+++++al
  gi|336254008|ref|YP_004597115.1| 30 GE-VFALIGPNGAGKTTLVRAL 50
                                      44.889**************98 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0056
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +++++l+++EP + + p   + +++l+ ela  +   v++tTH 
  gi|336254008|ref|YP_004597115.1| 144 NDPDLLFLDEPTTGIDPAGRRTVWRLIEELAAGGT-TVVLTTHD 186
                                       5899******************************7.9******6 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   7.7e-07   0.00057       2     128 ..      33     165 ..      32     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.7e-07
                            AAA_28   2 ivitGgestGKTtlleaLaar......gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaaaa 72 
                                       ++++G+ ++GKTtl++aL+ +      + +++ +a r + +++l    ++     d+l  a+++l+  +  + +a++
  gi|336254008|ref|YP_004597115.1|  33 FALIGPNGAGKTTLVRALTGTtdpdagEARILGDAPRAVDRDRLGVLPQDFSPP-DRL-TARELLDYYAGLYDDARD 107
                                       689****************55456665677889999999988885555444443.444.455678888888899999 PP

                            AAA_28  73 nkvlfcDrglldtla..YarayggeaeaeleaaarekrydlvfllppapeidddgeRr 128
                                       +  ++ D gl+d++   Y + +gg+  ++++ a   +  dl fl +p+  id+ g R+
  gi|336254008|ref|YP_004597115.1| 108 PADVLADVGLVDSADtwYEDLSGGQQRRACVGATLVNDPDLLFLDEPTTGIDPAGRRT 165
                                       999********99844255666666788899999999999999999999888888876 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 !   19.7   0.1   6.9e-07   0.00051      13      43 ..      21      51 ..      18      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.9e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiq 43
                                      +g t++i++ +++ l+Gp+G+GK+Tl+ A++
  gi|336254008|ref|YP_004597115.1| 21 SGATLTIERGEVFALIGPNGAGKTTLVRALT 51
                                      56789999777****************8876 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 !   11.9   0.0   0.00018      0.13      44      68 ..      27      51 ..       7      57 .. 0.87
   2 ?    1.9   0.0      0.22   1.7e+02     106     150 ..     143     186 ..     129     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                      ie+ e ++l+Gp G+GK+ l  al 
  gi|336254008|ref|YP_004597115.1| 27 IERGEVFALIGPNGAGKTTLVRALT 51
                                      8999****************99985 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.22
                         IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlp 150
                                       +  +dll lD+   + +d a +++++++ie+     ++++ +   
  gi|336254008|ref|YP_004597115.1| 143 VNDPDLLFLDEPT-TGIDPAGRRTVWRLIEELAAGGTTVVLTTHD 186
                                       556799****975.689*************987666665554444 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.3e-05     0.017      12      40 ..      23      51 ..       7      57 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-05
                                      HHHHHCH..TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 12 kklakal..gdvilLeGdLGaGKTtlvrgla 40
                                      ++l+  +  g+v++L G+ GaGKTtlvr+l 
  gi|336254008|ref|YP_004597115.1| 23 ATLT--IerGEVFALIGPNGAGKTTLVRALT 51
                                      3333..134889****************986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.3e-05     0.017       6      34 ..      31      59 ..      27     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeak 34
                                       + +++G+ G+GKTtl+r l+ + d +a 
  gi|336254008|ref|YP_004597115.1| 31 EVFALIGPNGAGKTTLVRALTGTTDPDAG 59
                                      5779****************998875554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.2e-05     0.024      98     128 ..      29      59 ..      12      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-05
                                       TTSEEEEECSTTSSHHHHHHHHCTT-----S CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktg 128
                                       ++++ +l+G+ G+GK+tL+ al+++++   g
  gi|336254008|ref|YP_004597115.1|  29 RGEVFALIGPNGAGKTTLVRALTGTTDPDAG 59 
                                       458999*****************98776655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0     0.002       1.5       3      18 ..      35      50 ..      34      83 .. 0.87
   2 ?    1.6   0.0       0.5   3.8e+02      94     113 ..     176     196 ..     159     201 .. 0.77
   3 ?    0.3   0.0       1.3   9.9e+02      75     110 ..     266     306 ..     223     319 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.002
                            AAA_18  3 ltGtpGvGKttlakeL 18
                                      l G+ G+GKttl ++L
  gi|336254008|ref|YP_004597115.1| 35 LIGPNGAGKTTLVRAL 50
                                      89************99 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.5
                            AAA_18  94 ikk.vvLtaspeelleRlekR 113
                                       +++ vvLt+++   +eRl++R
  gi|336254008|ref|YP_004597115.1| 176 GGTtVVLTTHDMAEAERLADR 196
                                       3336***************99 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.3
                            AAA_18  75 knlvidghlaeleseaakdikk.....vvLtaspeelleRl 110
                                         +v+d + a+ + +    +       v+L++ + + +eR 
  gi|336254008|ref|YP_004597115.1| 266 IGIVVDYLEANDLAYTGLSWAEpdletVYLELADATERERT 306
                                       35688888888888888888888888899999998888775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.9e-05     0.037      23      45 ..      29      51 ..      17     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.9e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                      r+e+  l+G+ G GK++lvr+l 
  gi|336254008|ref|YP_004597115.1| 29 RGEVFALIGPNGAGKTTLVRALT 51
                                      558899**************997 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   7.6e-05     0.057       1      21 [.      32      52 ..      32     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.6e-05
                            AAA_33  1 lvllvGlpGsGKstlaerllk 21
                                      ++ l+G++G+GK+tl++ l  
  gi|336254008|ref|YP_004597115.1| 32 VFALIGPNGAGKTTLVRALTG 52
                                      5679*************9864 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 ?   12.9   0.0   8.2e-05     0.061       2      43 ..      32      73 ..      31      82 .. 0.78
   2 ?   -2.0   0.0       3.1   2.3e+03      57      77 ..     174     194 ..     152     224 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.2e-05
                                      EEEEEESTTCCHHHHHHHHH.CT--SS-EEEEESS-SSCHCCC CS
                              cobW  2 vtvltGflGsGKTtLlnhll.enraglklavivNefgevsiDa 43
                                      v+ l G+ G+GKTtL+++l+ +   +   a i+++    ++D+
  gi|336254008|ref|YP_004597115.1| 32 VFALIGPNGAGKTTLVRALTgTTDPDAGEARILGDAP-RAVDR 73
                                      56789**************987777777777777766.55555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.1
                                       TTTTECCHCTT-HHHHHHHHH CS
                              cobW  57 enGciCctlredllkeleale 77 
                                       + G+    l +  ++e+e+l+
  gi|336254008|ref|YP_004597115.1| 174 AAGGTTVVLTTHDMAEAERLA 194
                                       333333333333333333333 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 ?   11.0   0.0   0.00027       0.2      26      44 ..      32      50 ..      19      53 .. 0.83
   2 ?    0.7   0.0       0.4     3e+02     137     198 ..     128     186 ..     110     202 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                                      EEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                      + a++GpNG+GK+ l+ A+
  gi|336254008|ref|YP_004597115.1| 32 VFALIGPNGAGKTTLVRAL 50
                                      6689************998 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.4
                                       S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislr 198
                                       LSgG++  +    + A+   +p  l +lDe    +D + ++ v +l++e     + ++ ++++
  gi|336254008|ref|YP_004597115.1| 128 LSGGQQRRAC---VGATLVNDPD-LLFLDEPTTGIDPAGRRTVWRLIEELAAGgTTVVLTTHD 186
                                       7777765433...3344445554.66799999999***9999999999998762334444443 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   0.0   0.00011     0.085       2      22 ..      33      53 ..      32      71 .. 0.82
   2 ?   -2.6   0.0       7.6   5.6e+03      31      57 ..     177     200 ..     155     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                      EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                      +a++G   +GK+tL++altg+
  gi|336254008|ref|YP_004597115.1| 33 FALIGPNGAGKTTLVRALTGT 53
                                      589****************95 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.6
                                       TSSSSEEEEEEEETTEEEEEEECGGCS CS
                          MMR_HSR1  31 gtTrdinegrvklkgkeielvDtpGli 57 
                                       gtT   +++ ++   +  +l+D +Gl+
  gi|336254008|ref|YP_004597115.1| 177 GTTVVLTTHDMA---EAERLADRVGLL 200
                                       555555555555...233566666654 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 ?    9.2   0.0    0.0015       1.1       4      21 ..      35      52 ..      32      62 .. 0.87
   2 ?    2.3   0.0       0.2   1.5e+02      11      60 ..     162     206 ..     161     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                                      EE--SSSSHHHHHHHGGG CS
                             AAA_5  4 LvGppGtgKselaerlaa 21
                                      L+Gp G gK++l++ l  
  gi|336254008|ref|YP_004597115.1| 35 LIGPNGAGKTTLVRALTG 52
                                      9*************9875 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.2
                                       SHHHHHHHGGGGBS--EEEEE--TT--HHH.HH--B--.........---- CS
                             AAA_5  11 gKselaerlaaalnreveyvqltrdtteed.lkgrreikngttslvdsplv 60 
                                       g++++++ + ++    +++v+ t d+ e++ l  r+ +      l d++lv
  gi|336254008|ref|YP_004597115.1| 162 GRRTVWRLIEELAAGGTTVVLTTHDMAEAErLADRVGL------LADGSLV 206
                                       899**********8888888888888765515444443......5555555 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   0.00023      0.18       4      22 ..      32      50 ..      29     129 .. 0.79
   2 ?   -0.2   0.0      0.94     7e+02     109     133 ..     164     188 ..     161     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                       ++++Gp+g+GKTtl++ l
  gi|336254008|ref|YP_004597115.1| 32 VFALIGPNGAGKTTLVRAL 50
                                      679*************999 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.94
                            AAA_24 109 eefrrllkklqelrknvifiahekt 133
                                       + ++rl++ l + + +v+++ h   
  gi|336254008|ref|YP_004597115.1| 164 RTVWRLIEELAAGGTTVVLTTHDMA 188
                                       678999**************99765 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 ?   13.1   0.0   0.00013     0.095       3      21 ..      35      53 ..      33      75 .. 0.87
   2 ?   -2.3   0.0       7.7   5.7e+03      59      66 ..     146     153 ..     129     194 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                                      EESSTTSSHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavake 21
                                      l+Gp G GKT+l++a+  +
  gi|336254008|ref|YP_004597115.1| 35 LIGPNGAGKTTLVRALTGT 53
                                      89*************9876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.7
                                       SEEEEEET CS
                               AAA  59 psilfiDE 66 
                                       p  lf+DE
  gi|336254008|ref|YP_004597115.1| 146 PDLLFLDE 153
                                       56677776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00031      0.23      30      51 ..      27      48 ..      24      59 .. 0.90
   2 ?   -1.2   0.0       1.8   1.3e+03     179     188 ..     176     185 ..     132     245 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                            AAA_25 30 lpagelallaGapgtGKttlal 51
                                      + +ge+ +l+G+ g+GKttl+ 
  gi|336254008|ref|YP_004597115.1| 27 IERGEVFALIGPNGAGKTTLVR 48
                                      689****************985 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                            AAA_25 179 tgaavllvhH 188
                                        g +v+l+ H
  gi|336254008|ref|YP_004597115.1| 176 GGTTVVLTTH 185
                                       3333333333 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 ?   10.8   0.1    0.0002      0.15     240     267 ..      25      53 ..       6      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                                       EEE-SS.EEEEEE-TTSSHHHHHHHHHHC CS
                        ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAlekG 267
                                       + i +G v++++G++  GK+TL++Al   
  gi|336254008|ref|YP_004597115.1|  25 LTIERGeVFALIGPNGAGKTTLVRALTGT 53 
                                       67999*********************865 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00034      0.25      16      47 ..      22      51 ..       9      53 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                            AAA_27 16 drsldfsaeeadlhliyGpNEAGKstalrAis 47
                                      + +l+++  + ++  ++GpN AGK+t++rA++
  gi|336254008|ref|YP_004597115.1| 22 GATLTIE--RGEVFALIGPNGAGKTTLVRALT 51
                                      5556665..33444456*************96 PP

>> DUF2228  Uncharacterised conserved protein (DUF2228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00047      0.35     121     185 ..     238     304 ..     225     311 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                           DUF2228 121 keisleqkteklkkRkkkvvaktf..hgaGivvpvdkktdvGYReLsesdaelkkllkkieeaknee 185
                                        e+ ++q+ +  ++R++ vv + +  + +Givv++ + +d+ Y  Ls  + +l+ +  ++++a+++e
  gi|336254008|ref|YP_004597115.1| 238 LEYPVDQAADRGRNRDAGVVVREIdpEAIGIVVDYLEANDLAYTGLSWAEPDLETVYLELADATERE 304
                                       56788899999999******99994458***************************999999998443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2204.90
//
Query:       gi|336254009|ref|YP_004597116.1|  [L=380]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-19   68.7   0.0    4.7e-18   65.5   0.0    2.1  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00046   20.4   0.0     0.0085   16.3   0.0    2.3  2  Acetyltransf_1   Acetyltransferase (GNAT) family
     0.0006   20.0   2.1      0.018   15.2   0.4    2.7  2  Acetyltransf_6   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.073   13.5   0.0       0.22   11.9   0.0    1.8  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
        0.1   12.5   0.0        1.1    9.2   0.0    2.2  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
        0.1   12.6   0.1       0.78    9.8   0.0    2.4  3  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   1.6e-21   4.7e-18       1     127 [.      29     158 ..      29     159 .. 0.93
   2 ?    0.6   0.0      0.18   5.5e+02      27      57 ..     232     269 ..     219     271 .. 0.61

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1.6e-21
                                       .EEEE-GGGHHHHHHHHHHHTT----H...HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEE CS
                    Acetyltransf_9   1 eirelteedldevlellkyaFqdeesple.eireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagv 76 
                                       ++r++++ d d+vl+l+++ +++++   + + ++  +++l++  + +ae++ge+v++ +++p++l+ +G++++a   
  gi|336254009|ref|YP_004597116.1|  29 RVRSYEPGDRDGVLSLFERQWGYRPGTDWfDWKYVDDPYLSHVPITLAEQGGEIVAVQGYVPCRLRRGGRIVRALKP 105
                                       589***********************98888778888899999********************************** PP

                                       EEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--..SSHHHHHTTT-EE CS
                    Acetyltransf_9  77 tgVavapehrgrgvlskLlaraleemreegqplsllfP..ssipiYrrfGyei 127
                                       ++  v+p+hr++g+ s++++  +e++r++ + l + fP  +s +  +++G++ 
  gi|336254009|ref|YP_004597116.1| 106 VDAVVHPDHRRQGLYSRITELGIERYRDREAALFFNFPneASLGAQEKLGWSE 158
                                       **************************************555567779999976 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.18
                                       H......HHHHHHHHHHT....TSEEEEEEETTEEEEEE CS
                    Acetyltransf_9  27 pl...e.eireyfrklle....esrvlgaedngelvgql 57 
                                        +   + e+ +y+r lle    ++ +++a+++g+ v+ l
  gi|336254009|ref|YP_004597116.1| 232 NAfhaHrEA-RYYRWLLEapsvDHTAYVARQGGRPVAAL 269
                                       444432232.3445555544447899********99976 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.8e-06    0.0085      16     117 .]      49     156 ..      32     156 .. 0.72
   2 ?    1.6   0.0       0.1     3e+02       4      55 ..     225     276 ..     222     305 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.8e-06
                                       HHHHHHHHHHHH.HHSTTCEEEE....EEETTEEEEEEEEEEEETTSTTEEEEE.....EEEESGGGTTSSHHHHHH CS
                    Acetyltransf_1  16 nedaseeefees.fsleaegllv....aeedgeliGfisllkipdekggvayie.....slaVspeyrgkGlGsaLl 82 
                                       ++ ++  +++++   +++    v    ae +ge+++  ++ +    ++g  +++     + +V+p++r++Gl s+  
  gi|336254009|ref|YP_004597116.1|  49 WGYRPGTDWFDWkYVDDPYLSHVpitlAEQGGEIVAVQGYVPCRL-RRGGRIVRalkpvDAVVHPDHRRQGLYSRIT 124
                                       455555555555333333333333456888888888888888888.334444446888899**************** PP

                                       HHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  83 ealeerareegikkivlaveedndaairlYeklGF 117
                                       e  +er r++++    l    +n+a+ +  eklG+
  gi|336254009|ref|YP_004597116.1| 125 ELGIERYRDREA---ALFFNFPNEASLGAQEKLGW 156
                                       **********77...4444689*999999999986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.1
                                       HHHHHHHHTHHHHHHHHHHHHHHHHHSTTC..EEEEEEETTEEEEEEEEEEEET CS
                    Acetyltransf_1   4 lvellvesffppnedaseeefeesfsleae..gllvaeedgeliGfisllkipd 55 
                                       ++++ v+  f  + +a +++  + ++ +    + +va+ +g++++ +  + ++d
  gi|336254009|ref|YP_004597116.1| 225 VYDSRVPNAFHAHREARYYR--WLLEAPSVdhTAYVARQGGRPVAALVTRSDDD 276
                                       66666655554444444444..22333333658899*******99988777776 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.019        57      15      73 ..      23      82 ..       9     139 .. 0.74
   2 !   15.2   0.4   6.1e-06     0.018      36      96 ..     220     279 ..     201     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.019
                    Acetyltransf_6 15 eelgevrfrvatdpedleallelfraqwarr..pdvfadpltra.flrdllaalaargalrl 73
                                       e++e+r+r   +p d + +l lf++qw+ r  +d f   ++ + +l ++  +la ++ +++
  gi|336254009|ref|YP_004597116.1| 23 VESDEYRVRSY-EPGDRDGVLSLFERQWGYRpgTDWFDWKYVDDpYLSHVPITLA-EQGGEI 82
                                      46677787765.6999999999999999999998999888777734444333443.333333 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 6.1e-06
                    Acetyltransf_6  36 elfraqwarr.pdvfadpltraflrdllaalaargalrlyvlrldgrpvAvalglrsgdrly 96 
                                       +l+++ +  r p+ f+ ++  +++r ll+a+  + +   yv+r +grpvA++++  ++d + 
  gi|336254009|ref|YP_004597116.1| 220 DLLASVYDSRvPNAFHAHREARYYRWLLEAP--SVDHTAYVARQGGRPVAALVTRSDDDGVL 279
                                       566778888999*******************..88899*************99877777655 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.5e-05      0.22       7      48 ..      75     126 ..      65     159 .. 0.68
   2 ?   -3.7   0.0       5.9   1.8e+04       3      16 ..     254     267 ..     253     280 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.5e-05
                                       EEEETTEEE...EEEEEEEES....TCTEE......EEE-GGGTTSSHHHHHHHH CS
                    Acetyltransf_7   7 Vaeddgkiv...Gfialslld....aeitr......laVdpeyrgkGiGraLlea 48 
                                       +ae++g+iv   G++ +        + i r       +V+p++r++G+ +++ e+
  gi|336254009|ref|YP_004597116.1|  75 LAEQGGEIVavqGYVPC---RlrrgGRIVRalkpvdAVVHPDHRRQGLYSRITEL 126
                                       57888888844444333...333353444455555568*********98777775 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.9
                                       EEEEEEEETTEEEE CS
                    Acetyltransf_7   3 gevfVaeddgkivG 16 
                                       ++ +Va+++g++v 
  gi|336254009|ref|YP_004597116.1| 254 HTAYVARQGGRPVA 267
                                       56789988888876 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00036       1.1      33     109 ..      73     159 ..      68     164 .. 0.75
   2 ?    0.7   0.0      0.16   4.7e+02      20     108 ..     240     329 ..     222     346 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00036
                   Acetyltransf_10  33 llvaeeggkiv...Gvi..elrdgshisll......fVdpeyrgqGigkaLleaveeeaekdgikleltvnasp.ya 97 
                                       + +ae+gg+iv   G++  +lr+g++i +       +V+p++r+qG+ +++ e  +e++++++   +l  n  + + 
  gi|336254009|ref|YP_004597116.1|  73 ITLAEQGGEIVavqGYVpcRLRRGGRIVRAlkpvdaVVHPDHRRQGLYSRITELGIERYRDREA--ALFFNFPNeAS 147
                                       5678999999988888888898888777665666779**********99999999999965544..56666555466 PP

                   Acetyltransf_10  98 vpfYeklGFkav 109
                                        +  eklG+ +v
  gi|336254009|ref|YP_004597116.1| 148 LGAQEKLGWSEV 159
                                       666677777665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                   Acetyltransf_10  20 ealreri.e..egealllvaeeggkivGvielrdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvn 92 
                                       +++++++ e  + +++ +va +gg++v ++ +r+++   l+f   ++   G +++ + ++++++  d+     l+v 
  gi|336254009|ref|YP_004597116.1| 240 ARYYRWLlEapSVDHTAYVARQGGRPVAALVTRSDDDGVLVF---DAVPLGSAHEAFADLLAAVVADNADAcVLSVT 313
                                       555555544456678888899999888877554443222222...33333444444444444433444444466666 PP

                   Acetyltransf_10  93 aspyavpfYeklGFka 108
                                       a +   ++  ++GF+ 
  gi|336254009|ref|YP_004597116.1| 314 ARTLPSKLLARFGFVS 329
                                       6666666666666665 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.6   7.8e+03      17      28 ..      75      86 ..      74     103 .. 0.73
   2 ?    9.8   0.0   0.00026      0.78      29      80 ..     110     159 ..     106     168 .. 0.83
   3 ?   -0.8   0.0      0.51   1.5e+03      46      80 ..     296     330 ..     287     335 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.6
                                      EE-TTSSEEEEE CS
                              FR47 17 lrkdggelgalq 28
                                      l+++gge+ a+q
  gi|336254009|ref|YP_004597116.1| 75 LAEQGGEIVAVQ 86
                                      567889998887 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00026
                                       E-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  29 vlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfeki 80 
                                       v+p+hrr+Gl sr+++     i + r+ ++ l  +  N++s    eklG+ + 
  gi|336254009|ref|YP_004597116.1| 110 VHPDHRRQGLYSRITELG---IERyRDREAALFFNFPNEASLGAQEKLGWSEV 159
                                       99***********99865...5555677778889999************9876 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.51
                                       HHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  46 lakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                       l +++++ + ++ ++ v++ t  ++l+ + Gf  +
  gi|336254009|ref|YP_004597116.1| 296 LLAAVVADNADACVLSVTARTLPSKLLARFGFVSY 330
                                       44455555666666666666666677777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2886.12
//
Query:       gi|336254010|ref|YP_004597117.1|  [L=320]
Description: G6PDH family F420-dependent oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-52  176.6   4.3    2.1e-51  175.3   4.3    1.5  1  Bac_luciferase  Luciferase-like monooxygenase
     0.0029   17.8   0.2     0.0047   17.2   0.2    1.2  1  DUF4142         Domain of unknown function (DUF4142)
  ------ inclusion threshold ------
       0.24   11.3   0.3       0.24   11.3   0.3    2.0  2  DpnD-PcfM       DpnD/PcfM-like protein


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.3   4.3   3.4e-55   2.1e-51      11     314 .]       6     294 ..       2     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 175.3 bits;  conditional E-value: 3.4e-55
                    Bac_luciferase  11 qggalgaasaslrylvelaraaEelGfdavwvaehhggpgga....ldaftllaalaaaTerirlgtavtply.trh 82 
                                       +g +l+++++ +++lve+a++aE++Gfd++ +++h +++ +a    +  +++l+a+a+aT+ i++g++vt+++ + h
  gi|336254010|ref|YP_004597117.1|   6 IGYTLSSEEHGPQRLVEIAERAEDAGFDFLSISDHFHPWVSAqgesPFVWSTLGAIANATDEIEVGVGVTCPTiRIH 82 
                                       555555666899********************************99889999*********************9*** PP

                    Bac_luciferase  83 PavlAqqaatLdhlsgGRfglglgtggpaveerrfGv...dhderyarlrEfvevlrrlwrgeevdfeGeffsvkga 156
                                       P+++A ++at+d+l g Rf +g+gtg++ +e+   G    +hd r+++l+E+++v+r+lw+g + +++G++++v++a
  gi|336254010|ref|YP_004597117.1|  83 PVNVAHAVATVDELFGDRFTFGVGTGENLNEHVT-GErwpEHDVRLEMLDEAMDVMRKLWTGQTTSHHGKHYTVENA 158
                                       *******************************777.5559*********************99999*********888 PP

                    Bac_luciferase 157 lllprpgqgpiP.vyvaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivad 232
                                       +l   p+++  P  +  a +p+++e+ a  adgl + g     + e +e ++     ag    d   +++l+ ++ad
  gi|336254010|ref|YP_004597117.1| 159 RLYTCPDEQ--PtTIASAFGPQTAEWVADNADGLWCSG----PKGEPVEAYED----AGG---DGPKYTQLHGCYAD 222
                                       888888655..98999999******************9....33333444443....444...333599******** PP

                    Bac_luciferase 233 teeeAraearaliagldfyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatal.vG.tpeqvaerlaay 307
                                       +eeeA + + + +            ++   +++  qe  ++ ++++aa+ v++e++a++++    +p+++++ l++ 
  gi|336254010|ref|YP_004597117.1| 223 SEEEAVETVYEKW------------PNGSIPGELGQELPTPAHFEQAAQMVEKEDIAEAGTtTSpDPQDHIDSLEQA 287
                                       *********8878............4444466679****************88888888885445888********* PP

                    Bac_luciferase 308 aeagvde 314
                                       ++ag+d+
  gi|336254010|ref|YP_004597117.1| 288 VDAGYDH 294
                                       ****997 PP

>> DUF4142  Domain of unknown function (DUF4142)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   7.9e-07    0.0047      49     109 ..     255     314 ..     252     318 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.9e-07
                           DUF4142  49 eeLkalaskkgvtlpdsteldaeaqakldkLkalsgaaFDkaYleaqvaahqkavelleka 109
                                       e+++++++k++++    t+ +++ q+++d+L+++ +a +D  Y  +  ++++ka+e +e++
  gi|336254010|ref|YP_004597117.1| 255 EQAAQMVEKEDIAEAG-TTTSPDPQDHIDSLEQAVDAGYDHVYFHQIGDEQEKAIEFYEEE 314
                                       6788999999999996.899************************************99974 PP

>> DpnD-PcfM  DpnD/PcfM-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3     4e-05      0.24      17      36 ..     221     240 ..     220     240 .. 0.93
   2 ?   -3.6   0.4       1.8   1.1e+04      21      29 ..     255     263 ..     255     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4e-05
                         DpnD-PcfM  17 AeseeeAerlVeekYkneei 36 
                                       A+seeeA++ V ek+ n+ i
  gi|336254010|ref|YP_004597117.1| 221 ADSEEEAVETVYEKWPNGSI 240
                                       9**************99976 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.8
                         DpnD-PcfM  21 eeAerlVee 29 
                                       e+A ++Ve+
  gi|336254010|ref|YP_004597117.1| 255 EQAAQMVEK 263
                                       78999*997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); 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:                         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: 2330.49
//
Query:       gi|336254011|ref|YP_004597118.1|  [L=371]
Description: Respiratory-chain NADH dehydrogenase domain 51 kDa subunit [Halopiger xanaduensis SH-6]
Scores for 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-18   65.1   0.0      1e-17   64.4   0.0    1.4  1  Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subu
      7e-07   29.1   0.0    1.2e-06   28.4   0.0    1.4  1  RnfC_N        RnfC Barrel sandwich hybrid domain
    0.00019   21.2   0.0    0.00046   20.0   0.0    1.7  1  SLBB          SLBB domain


Domain annotation for each model (and alignments):
>> Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   1.7e-21     1e-17       1     151 [.      25     181 ..      25     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 1.7e-21
                      Complex1_51K   1 vkeagivGrGGagfPthvKlkakakkkkkylivNaaEcEPgltkDrllmreepheileGlkiaaealgaekgvigvr 77 
                                       +++ag+ G+GGagfP++ K+   ++   + l+vN +E+EP ++ D+ l +++++ +   + +    l a+   ++v 
  gi|336254011|ref|YP_004597118.1|  25 IRAAGVAGAGGAGFPSYAKWTDLEA--VDSLLVNHQESEPNYRIDKWLGKTKAETFAALFDA----LLAQAFDLIVV 95 
                                       789********************98..89***********************8887666654....44444433333 PP

                      Complex1_51K  78 dekpeaiealekalaeakaagl.............ldievvklagkYpaGeekaLiesltgrevprgkppadvgvvv 141
                                       + k +  +++ ++l+++++  +               +  +  +++Y  G+e++L++ + g  + +  +p+d g +v
  gi|336254011|ref|YP_004597118.1|  96 SAKWKDRDEYVRELEAETDGTVippdelpldrnaeSGVVFAYTENTYQYGMESVLLKTVDGTVIGND-LPTDYGWLV 171
                                       3334444444444444433222566677888888778999999******************988877.********* PP

                      Complex1_51K 142 nNveTlaavy 151
                                       +N+eTl+++ 
  gi|336254011|ref|YP_004597118.1| 172 QNTETLYNIS 181
                                       ********97 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 !   28.4   0.0     2e-10   1.2e-06      38      86 ..     318     367 ..     291     371 .] 0.82

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2e-10
                            RnfC_N  38 iGapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlva 86 
                                       + +pa+p v+ gd+V  G++ia+ +   +s p has++G+V+a++  ++ 
  gi|336254011|ref|YP_004597118.1| 318 VVEPAEPTVEIGDRVDVGDRIASPSPdGISNPQHASIAGEVTAVSASAIE 367
                                       5689******************9975566***************987765 PP

>> SLBB  SLBB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   7.7e-08   0.00046       1      37 [.     194     230 ..     194     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.7e-08
                                       EEEEESSBSS-EEEEEETT-BHHHHHHTTT-SBSS.. CS
                              SLBB   1 vVtVtGeVkrPgnyevpigttlsdlieqaGGltddad 37 
                                       +V+V+G+V r + +evp gt+ s+l+ +aG +++   
  gi|336254011|ref|YP_004597118.1| 194 YVHVSGDVPRDRFLEVPVGTPASELLRAAGRPPESLP 230
                                       59******************************99844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2786.19
//
Query:       gi|336254012|ref|YP_004597119.1|  [L=220]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-11   43.1   0.0      4e-11   42.5   0.0    1.3  1  HTH_10         HTH DNA binding domain
  ------ inclusion threshold ------
       0.19   11.5   0.0       0.36   10.5   0.0    1.5  1  Sigma70_r4_2   Sigma-70, region 4
       0.27    9.0   0.0       0.49    8.1   0.0    1.4  2  Raffinose_syn  Raffinose synthase or seed imbibition protein 
       0.27   11.6   3.2        9.4    6.7   0.3    2.4  2  HTH_31         Helix-turn-helix domain


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 !   42.5   0.0     9e-15     4e-11       1      53 []     160     212 ..     160     212 .. 0.98

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 9e-15
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LT +q+e++ +A++ GY+   R+ +l+++A++l+ s  t+ e Lr+ae+++++
  gi|336254012|ref|YP_004597119.1| 160 LTRRQFEAVSAAVDCGYYRATRNGSLEDVAERLDCSSGTAGELLRRAERTVMA 212
                                       9*************************************************995 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 ?   10.5   0.0     8e-05      0.36      28      52 ..     184     208 ..     179     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8e-05
                                       -HHHHHHHHT--HHHHHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsRArk 52 
                                       s +++Ae+l++s+gt    l+RA +
  gi|336254012|ref|YP_004597119.1| 184 SLEDVAERLDCSSGTAGELLRRAER 208
                                       6799******************976 PP

>> Raffinose_syn  Raffinose synthase or seed imbibition protein Sip1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       0.3   1.4e+03     195     237 ..      64     106 ..      62     107 .. 0.76
   2 ?    8.1   0.0   0.00011      0.49     386     427 ..     137     178 ..     127     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.3
                     Raffinose_syn 195 Pkivdk.fGwctwdafylevdaegvekGvksledGGvpPkfvii 237
                                       P+++d+ +  c  d+fyl v  e+++   ++++d    P ++ii
  gi|336254012|ref|YP_004597119.1|  64 PTVLDYeLAPCRDDSFYLYVR-ESLTGADRTFVDAVEQPGLIII 106
                                       666665367799999999996.5677777899999999999887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00011
                     Raffinose_syn 386 dGvkvdvlqiletlaeelGGrvelakayyqalessvaknfnd 427
                                       d ++vdv ++ e  a +   rv+l++  ++a+ ++v   +  
  gi|336254012|ref|YP_004597119.1| 137 DTARVDVRSVGEYCAGRIDARVDLTRRQFEAVSAAVDCGYYR 178
                                       7899****************************9998766555 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2    0.0057        26      18      48 ..     133     162 ..     131     174 .. 0.74
   2 ?    6.7   0.3    0.0021       9.4      10      39 ..     178     207 ..     176     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0057
                            HTH_31  18 eevAerlgvsestlsrlEqGrrgrpspavle 48 
                                       ++vA+ ++v +  ++ +  Gr++  + +  +
  gi|336254012|ref|YP_004597119.1| 133 DDVADTARVDVRSVGEYCAGRID-ARVDLTR 162
                                       79********************7.5444333 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0021
                            HTH_31  10 ReraGLsqeevAerlgvsestlsrlEqGrr 39 
                                       R+ ++ s+e+vAerl +s  t + l + ++
  gi|336254012|ref|YP_004597119.1| 178 RATRNGSLEDVAERLDCSSGTAGELLRRAE 207
                                       7777889***********999998888554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1741.89
//
Query:       gi|336254013|ref|YP_004597120.1|  [L=329]
Description: aldo/keto reductase [Halopiger xanaduensis SH-6]
Scores for 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  190.5   0.0    4.6e-56  190.2   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
       0.02   15.2   0.2       0.32   11.3   0.0    2.5  2  HBS1_N        HBS1 N-terminus


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 !  190.2   0.0   5.1e-60   4.6e-56       1     284 [.      15     308 ..      15     317 .. 0.89

  Alignments for each domain:
  == domain 1  score: 190.2 bits;  conditional E-value: 5.1e-60
                                       .EEEE-SSS-ST..TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE.--SSS CS
                      Aldo_ket_red   1 elglGtwqlgsk.eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv.dlrda 75 
                                       e+glGtw++g++ + +++e+  e++r+ale Gi f+DtA+vYg+g+se+ +G++l + r+  ++v +atK  +  d 
  gi|336254013|ref|YP_004597120.1|  15 EVGLGTWNIGGDwGDVDDETGREVVRAALESGIDFIDTADVYGDGRSERHIGHVLDE-REAHDDVTVATKAgRRLDP 90 
                                       68*******************************************************.*************545555 PP

                                       TTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHT CS
                      Aldo_ket_red  76 eiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkk 152
                                       +  ++++ +n+ + +++s++++g d++Dl++lH+p  + ++  ++++ale l++eGki   GvS + ve   ka   
  gi|336254013|ref|YP_004597120.1|  91 HEADRYNYDNLSQFVDRSREYIGEDTLDLVQLHCPPTEAYYQPDTFEALERLKDEGKIARAGVSVEKVEEALKA--V 165
                                       6667899*********************************9***********************6664444444..5 PP

                                       TT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------.......... CS
                      Aldo_ket_red 153 kkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd.......... 219
                                       ++  + +vq+ +n++r++ +e  +e +kk+++++i+  p ++Glltg  ++e++++++++r  +++           
  gi|336254013|ref|YP_004597120.1| 166 EYDVVETVQIIFNPFRQRPKELFFEQAKKNDIGVIVRVPYASGLLTGALEREQEFPEDDHRNFNRQGeafdvgetfa 242
                                       6666889************************************************998888777666******9955 PP

                                       .TS-HHHHHHHHHHHHHHHH..TT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG-.---HH CS
                      Aldo_ket_red 220 .ertsknldaaeelselake..hgvslaqlalryalsqpavgivipgasnieqlednldalel.klsee 284
                                               +  +++++l  +   + ++a+ +lr++l ++av++vipg+++++++e n+++ +l  ls +
  gi|336254013|ref|YP_004597120.1| 243 gV---PYETGHDAVEALEPHvpEDLTMAEFTLRWILDHEAVSTVIPGTTSPDHVESNAAVSDLdSLSHQ 308
                                       44...44445555555555544688************************************88777765 PP

>> HBS1_N  HBS1 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.056     5e+02      11      39 ..      73     115 ..      58     123 .. 0.74
   2 ?   11.3   0.0   3.6e-05      0.32      45      77 ..     153     185 ..     136     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.056
                            HBS1_N  11 eeeee..............eLsdedqarLrscldevrevLgee 39 
                                       e +++              e +   +++L++ +d+ re +ge+
  gi|336254013|ref|YP_004597120.1|  73 EAHDDvtvatkagrrldphEADRYNYDNLSQFVDRSREYIGED 115
                                       3344456677777777777778888899999999999999943 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.6e-05
                            HBS1_N  45 vtekqikeAlwkyyyDvekaldyllnkfkkkkp 77 
                                       v+ ++++eAl   +yDv ++++ ++n f ++++
  gi|336254013|ref|YP_004597120.1| 153 VSVEKVEEALKAVEYDVVETVQIIFNPFRQRPK 185
                                       799***********************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2401.75
//
Query:       gi|336254014|ref|YP_004597121.1|  [L=421]
Description: hypothetical protein Halxa_2624 [Halopiger xanaduensis SH-6]
Scores for complete 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-48  164.5  12.3    1.9e-48  164.5  12.3    1.9  2  DUF418    Protein of unknown function (DUF418)


Domain annotation for each model (and alignments):
>> DUF418  Protein of unknown function (DUF418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.3      0.16     3e+03      53      70 ..     118     135 ..      73     155 .. 0.61
   2 !  164.5  12.3     1e-52   1.9e-48       3     161 ..     236     393 ..     234     395 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.16
                            DUF418  53 svlrylaglllalgyval 70 
                                         l +++ +l+a+g +a 
  gi|336254014|ref|YP_004597121.1| 118 AYLLWYGDILVAYGVCAF 135
                                       233334444444444444 PP

  == domain 2  score: 164.5 bits;  conditional E-value: 1e-52
                            DUF418   3 rkglledpeehkrllrrllligllvglplnlllavlaeaaeesallelllsvlrylaglllalgyvalillllakek 79 
                                        +g+l  +++++r++rrl+++g+  gl++ l+ ++++ea+++ a+ +ll+  ++y+++++la +yv+l++l +++++
  gi|336254014|ref|YP_004597121.1| 236 ERGVLM-NDRSTRFYRRLVAVGASSGLAVILVGVWYIEANDWGAGVALLWRQFNYWGSFALAGAYVGLVMLYCRRRP 311
                                       578888.899******************************************************************* PP

                            DUF418  80 rrrllralaavGRmALTnYllqslictllfygyglglfgslgraallllallifllqllfSklwlrrfrqGPlEwlw 156
                                          ++ralaavGR+A++nY+lq++++t +fyg+glglfg+l r++ll+++++i+++q+ +S  wlr+fr+GPlEwlw
  gi|336254014|ref|YP_004597121.1| 312 DGPVTRALAAVGRTAFSNYILQTVLATSIFYGHGLGLFGRLTRLELLGVVVAIWAVQVPLSVCWLRYFRYGPLEWLW 388
                                       ***************************************************************************** PP

                            DUF418 157 Rrlty 161
                                       R+lty
  gi|336254014|ref|YP_004597121.1| 389 RSLTY 393
                                       ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); 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:                         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 0.22s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3066.42
//
Query:       gi|336254015|ref|YP_004597122.1|  [L=832]
Description: dihydropteroate synthase [Halopiger xanaduensis SH-6]
Scores for 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-79  266.1   1.3    4.5e-79  265.6   1.3    1.2  1  Pterin_bind   Pterin binding enzyme
    7.4e-12   45.7   0.0    1.2e-11   45.0   0.0    1.4  1  Mur_ligase_M  Mur ligase middle domain
    2.5e-09   37.3   0.0    9.9e-09   35.3   0.0    2.0  2  Mur_ligase_C  Mur ligase family, glutamate ligase domain
    0.00076   19.0   5.1      0.043   13.3   0.2    4.1  4  PEP_mutase    Phosphoenolpyruvate phosphomutase
  ------ inclusion threshold ------
       0.08   12.9   0.0       0.15   12.0   0.0    1.4  1  CAT_RBD       CAT RNA binding domain
       0.72    9.6   3.1         15    5.3   0.0    2.9  3  DFP           DNA / pantothenate metabolism flavoprotein


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 !  265.6   1.3   1.5e-82   4.5e-79       1     244 []     572     809 ..     572     809 .. 0.96

  Alignments for each domain:
  == domain 1  score: 265.6 bits;  conditional E-value: 1.5e-82
                                       EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEE CS
                       Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpis 77 
                                       mgilNvtpdsf dgg++ ++++a+a+a++mve+GAd+lD+ggestrPga++v+ eee++rvvpvle++rd  d+pis
  gi|336254015|ref|YP_004597122.1| 572 MGILNVTPDSFHDGGEYDAVEDAVARAEAMVEAGADVLDVGGESTRPGADPVSTEEEIDRVVPVLERVRDF-DIPIS 647
                                       9********************************************************************95.***** PP

                                       EE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHH CS
                       Pterin_bind  78 iDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearv 154
                                       iDt ka va aAl+agadi+Ndvsg+e dp+m  ++a+++a ++vmh+ + +  +  +e++y+dvve+v  +l++rv
  gi|336254015|ref|YP_004597122.1| 648 IDTRKAAVADAALEAGADIINDVSGLE-DPEMRFVAADHDAGLIVMHSIN-APVVPGQEVTYDDVVEDVIDQLSERV 722
                                       ***************************.*********************5.555666667***************** PP

                                       HHHHHTT--GGGEEEETTTTSSTTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHH.CTTCHGHHHHHHHHHH CS
                       Pterin_bind 155 eaaeeaGvaperillDpgigfgkteehnlellrrldelrealevpvllGvSrksflgrll.elgkaeeRdagtaafl 230
                                         ae+aGv++e+i++Dpgigfgk++ +++e+l+rl+e+ +al++pvl G+S ks+   +  e   a +   +t+a++
  gi|336254015|ref|YP_004597122.1| 723 LLAEKAGVDRENIVVDPGIGFGKSARESFEILDRLEEF-RALGCPVLFGHSHKSMFEHVGsE---AGDCLDATVAAS 795
                                       **************************************.*****************997533...669********* PP

                                       HHHHHTT-SEEEES CS
                       Pterin_bind 231 alaaaaGadivrVh 244
                                       alaa++Gad vrVh
  gi|336254015|ref|YP_004597122.1| 796 ALAADRGADLVRVH 809
                                       *************9 PP

>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   4.1e-15   1.2e-11       1     191 [.      44     271 ..      44     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 4.1e-15
                                       EESSS-HHHHHHHHHHHHHCTEEEEETTC............................................SS-T CS
                      Mur_ligase_M   1 vTGtnGKTTtteliaailekagkvigtvg............................................ttnn 33 
                                       v+G+nGK +t++++++ l++ag  +g+                                              t+ +
  gi|336254015|ref|YP_004597122.1|  44 VAGSNGKGSTARMLERTLREAGLSVGLYTsphleelrervrvdgrkiprsavcefvdstqdyltdraadgespTFFE 120
                                       89*******************77777766777**************************************9966555 PP

                                       HHHHHHHHHHHHHTT-SEEEEE--HCHHHC.TTTCCHCBESEEEE---TSTTHHHH.SSHHHHHHHHHHHHHTSETT CS
                      Mur_ligase_M  34 eiglpktlaemekkeaeyavlEvsshglge.krlegllkpdvavitnispdHldfh.gtlenyaeaKaelferlkee 108
                                       +++  ++l +++++++++avlEv+    g+ +  +  ++p + ++t+++ +H + + +t e++a+ Ka+        
  gi|336254015|ref|YP_004597122.1| 121 TMT-ALALWQFDREDVDVAVLEVGIG--GKfDATSV-VDPIASAVTSVTLEHTGILgDTEEEIARDKAHVAPDEA-- 191
                                       555.5555577777************..66344444.9****************99667788******9986444.. PP

                                       CEEEEE.TTSC...CHHHHHCTCCTCEEEEESSSTS..ECEEEE.EEEEETTEEEEEEEEETTEEEEEEESSCSCHH CS
                      Mur_ligase_M 109 giavin.addpyakelikklkkakvkvvtfglekea..edlrak.nieeksegteiellevkggeleieipllGkhn 181
                                         +v+    dp      +++++   +vvt+g+++e+   d+r +   + ++++  +++ + ++  +e ++pl+G+h+
  gi|336254015|ref|YP_004597122.1| 192 -PLVTGvSGDP-----LEAVRDVAGDVVTVGFADEDpePDVRVEyGGRTNHTEAAVSI-DADEWGVETRVPLPGEHQ 261
                                       .4444414566.....455555556799999999997633444433333333333322.24566678999******* PP

                                       HHHHHHHHHH CS
                      Mur_ligase_M 182 vyNalaaiaa 191
                                       ++Na +a+ +
  gi|336254015|ref|YP_004597122.1| 262 AENAGIAATL 271
                                       ****999876 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   3.3e-12   9.9e-09       1      86 [.     292     368 ..     292     372 .. 0.82
   2 ?   -2.7   0.0       2.4   7.3e+03      26      49 ..     389     412 ..     388     426 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 3.3e-12
                                       CTTSSEEEEETTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEEEE CS
                      Mur_ligase_C   1 vkgRlevvgeadgvtvidDyahnpdslsaalkalreiapdkrlilvfgpggelgertrtfhdefgrlasaladslvv 77 
                                       ++gR+ev+++   ++v+ D ahnp++ + + ++l  + ++  l +vfg++ +      ++h e+++++    d +v 
  gi|336254015|ref|YP_004597122.1| 292 WPGRFEVIDT--EPLVVLDGAHNPGACETLASTLGSY-EYDDLRVVFGAMHD------KDHREMAAALPT-PDAVVA 358
                                       79********..99********************777.789********999......446699999998.666666 PP

                                       EESS.-TTST CS
                      Mur_ligase_C  78 lgdy.praed 86 
                                       ++ +  raed
  gi|336254015|ref|YP_004597122.1| 359 TEPSlDRAED 368
                                       5554355555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHHSSSSEEEEEEEE CS
                      Mur_ligase_C  26 slsaalkalreiapdkrlilvfgp 49 
                                       +++aal+++   a+ + ++lv g+
  gi|336254015|ref|YP_004597122.1| 389 AVQAALETALSEADRSDCVLVTGS 412
                                       678999999888888888888885 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.21   6.2e+02     175     219 ..     334     386 ..     330     403 .. 0.65
   2 !   13.3   0.2   1.4e-05     0.043     147     179 ..     582     615 ..     574     638 .. 0.81
   3 !    4.0   0.0    0.0097        29     162     199 ..     656     693 ..     651     712 .. 0.84
   4 ?   -0.9   0.0      0.31   9.2e+02     150     176 ..     783     809 ..     745     824 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.21
                        PEP_mutase 175 vpglqkdaeiaelvaavdvplnvvplkgt........lsvaelaelGvarisl 219
                                       v g+++d++ +e++aa+++p  vv+++++        +  + + ++Gv+ + +
  gi|336254015|ref|YP_004597122.1| 334 VFGAMHDKDHREMAAALPTPDAVVATEPSldraedpaVLADVFDDAGVEDVRI 386
                                       67888888899999999999999995443244555544455555566655555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.4e-05
                        PEP_mutase 147 lll.sagagleeaieRaraYaeAGAdgvfvpglq 179
                                       +    +++++e+a++Ra+a +eAGAd++ v g +
  gi|336254015|ref|YP_004597122.1| 582 FHDgGEYDAVEDAVARAEAMVEAGADVLDVGGES 615
                                       554567899*****************99877665 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0097
                        PEP_mutase 162 araYaeAGAdgvfvpglqkdaeiaelvaavdvplnvvp 199
                                       a+a +eAGAd +  +++ +d+e++ ++a  d+ l+v+ 
  gi|336254015|ref|YP_004597122.1| 656 ADAALEAGADIINDVSGLEDPEMRFVAADHDAGLIVMH 693
                                       6899******************9999999888777776 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.31
                        PEP_mutase 150 sagagleeaieRaraYaeAGAdgvfvp 176
                                       +ag+ l+ +++   + a+ GAd v v+
  gi|336254015|ref|YP_004597122.1| 783 EAGDCLDATVAASALAADRGADLVRVH 809
                                       334444444444455555555555555 PP

>> CAT_RBD  CAT RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.2e-05      0.15      11      39 ..     722     751 ..     714     759 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.2e-05
                                       EEEEE-C..CSEEEEE-TTTTTT--TTSEE CS
                           CAT_RBD  11 vvlakdek.gkEvilmGkGIGFgkkkgdei 39 
                                       v+la++   ++E i++  GIGFgk + + +
  gi|336254015|ref|YP_004597122.1| 722 VLLAEKAGvDRENIVVDPGIGFGKSARESF 751
                                       7888898889**************998876 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0051        15       5      69 ..      27      88 ..      24     112 .. 0.76
   2 ?    3.5   0.4     0.019        56      33      98 ..     595     661 ..     592     682 .. 0.73
   3 ?   -2.6   0.1       1.4   4.2e+03      68      93 ..     772     798 ..     771     816 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0051
                                      EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SH CS
                               DFP  5 kvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesa 69
                                      ++l   G  +E++D V + + +  G ++ +l + ++++G +V l ++p +le+    e+v+v+  
  gi|336254015|ref|YP_004597122.1| 27 RLLAHLGNPHEDVDFVQVAGSNGKGSTARMLERTLREAGLSVGLYTSP-HLEE--LRERVRVDGR 88
                                      667778999*************************************99.4443..2345555554 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.019
                                       HHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHTT-SEEEE....---S--EEES CS
                               DFP  33 yalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveealkeadivim....aAAvaDyrpk 98 
                                       +a Aea++++Ga+V  v g++   t +g++ v+ e+  +    v e++++ di i+     AAvaD   +
  gi|336254015|ref|YP_004597122.1| 595 VARAEAMVEAGADVLDVGGES---TRPGADPVSTEEEIDRVVPVLERVRDFDIPISidtrKAAVADAALE 661
                                       56799**************94...3347775555555555556678888888877522336999997655 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.4
                                       SHHHHHHHHHHHHTT-.SEEEE---S- CS
                               DFP  68 saeemleaveealkea.divimaAAva 93 
                                       s ++m e+v +++ ++ d+ ++a A a
  gi|336254015|ref|YP_004597122.1| 772 SHKSMFEHVGSEAGDClDATVAASALA 798
                                       566788888888777778888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (832 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.43
# Mc/sec: 5758.36
//
Query:       gi|336254016|ref|YP_004597123.1|  [L=125]
Description: Cupin 2 barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-10   38.1   0.7    1.4e-09   37.5   0.7    1.2  1  Cupin_2       Cupin domain
     0.0011   18.8   0.0     0.0014   18.5   0.0    1.1  1  AraC_binding  AraC-like ligand binding domain
     0.0061   16.2   0.1     0.0087   15.7   0.1    1.3  1  Cupin_3       Protein of unknown function (DUF861)
  ------ inclusion threshold ------
       0.16   12.3   0.0       0.24   11.8   0.0    1.2  1  Pirin_C       Pirin C-terminal cupin 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 !   37.5   0.7   3.1e-13   1.4e-09       5      70 ..      35      99 ..      33     100 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 3.1e-13
                                      EETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2  5 lppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70
                                      ++pG+ +p h  pg+d  ++V +G+g+++ ++ e+ +e+Gd+v +pa +  ++r  +de ++ l v
  gi|336254016|ref|YP_004597123.1| 35 FEPGQFIPVHA-PGSDVAIHVRSGTGVVRDGDDEHAVEPGDVVTVPADVDRGVRASEDERLEALLV 99
                                      68999999999.*****************9999****************************99876 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 !   18.5   0.0   3.2e-07    0.0014      14      78 ..      39     103 ..      31     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.2e-07
                                       -SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE-- CS
                      AraC_binding  14 hsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwlyfeg 78 
                                       +  p h ++  v + v +Gtg +r ++ ++ ++pGd++ +p ++    ++++++++e   ++ ++
  gi|336254016|ref|YP_004597123.1|  39 QFIPVHAPGSDVAIHVRSGTGVVRDGDDEHAVEPGDVVTVPADVDRGVRASEDERLEALLVTGPP 103
                                       55566777777778899**************************9988888888888777777666 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 !   15.7   0.1   1.9e-06    0.0087      29      60 ..      52      82 ..      26      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-06
                                      EEEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                           Cupin_3 29 cyileGevkvtpeggetvelraGDlvvlpkgl 60
                                      +++ +G   v++ g  ++++++GD+v++p++ 
  gi|336254016|ref|YP_004597123.1| 52 IHVRSGTGVVRD-GDDEHAVEPGDVVTVPADV 82
                                      589999999988.9999************986 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 ?   11.8   0.0   5.4e-05      0.24      10      72 ..      39     103 ..      33     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.4e-05
                                       -EEEEE--TT-EEEEEEEES-EEESSTT..EEE-TTEEEEE-SSSEEEEE--S.S-EEEEEEEE-- CS
                           Pirin_C  10 aelelplpegleaavyvleGelevgger..seieeeqlavlgdgdslvvkaee.kgarvlLlaGeP 72 
                                       + + +  ++g ++a+ v +G++ v + +  +++e+++++ + +  +  v+a+e ++++ lL+ G P
  gi|336254016|ref|YP_004597123.1|  39 QFIPVH-APGSDVAIHVRSGTGVVRDGDdeHAVEPGDVVTVPADVDRGVRASEdERLEALLVTGPP 103
                                       555555.789999***********98877899*********988888888887799********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 935.98
//
Query:       gi|336254017|ref|YP_004597124.1|  [L=268]
Description: hypothetical protein Halxa_2627 [Halopiger xanaduensis SH-6]
Scores for 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   12.8  10.6        1.9    8.7   3.7    2.8  2  Phage_holin_3_3  LydA holin phage, holin superfamily III


Domain annotation for each model (and alignments):
>> 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 ?    8.7   3.7   0.00011       1.9       2      68 ..       7      74 ..       6      75 .. 0.91
   2 ?    7.3   0.6   0.00028         5      36      69 ..     155     188 ..     143     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00011
                   Phage_holin_3_3  2 liivlAllGGlvsylmrakkg.rrrfsikellleivvSgfvGllvfllceelglsqlltlaiaglsGy 68
                                      +++++A+lGGl++         r   +  e+++ +v++ +vG+l  ++ +++ l  ++ +++a+lsG 
  gi|336254017|ref|YP_004597124.1|  7 TTVAIAALGGLANVAVVLGLYaRGDYPAPEVAVLAVTAFLVGFLPWFATAYTRLLTPAIGFLAALSGT 74
                                      5799*******99877666555899*****************************************96 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00028
                   Phage_holin_3_3  36 vvSgfvGllvfllceelglsqlltlaiaglsGyl 69 
                                        v+++vGl + ll+  +g+ +++++a++ l++++
  gi|336254017|ref|YP_004597124.1| 155 SVAALVGLAATLLVLRAGIRPPAAAAVVFLFAAA 188
                                       589*************************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1955.11
//
Query:       gi|336254018|ref|YP_004597125.1|  [L=261]
Description: ABC transporter-like protein [Halopiger xanaduensis SH-6]
Scores for 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-28   98.9   0.0    4.5e-28   98.5   0.0    1.2  1  ABC_tran    ABC transporter
    2.3e-12   47.4   0.0    2.9e-08   33.9   0.0    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
     0.0019   18.0   0.0        2.3    7.9   0.0    2.2  2  AAA_15      AAA ATPase domain
     0.0089   16.4   0.1      0.016   15.6   0.0    1.5  1  AAA_16      AAA ATPase domain
  ------ inclusion threshold ------
      0.018   15.6   2.0       0.02   15.4   0.3    1.7  2  AAA_23      AAA domain
      0.021   14.5   0.7      0.041   13.6   0.7    1.4  1  AAA_30      AAA domain
      0.088   12.6   0.4       0.15   11.8   0.4    1.3  1  AAA_29      P-loop containing region of AAA domain
      0.088   13.1   0.8       0.43   10.9   0.8    2.1  1  AAA_22      AAA domain
      0.094   12.3   0.0       0.17   11.5   0.0    1.3  1  AAA_27      AAA domain
       0.13   12.7   0.0       0.35   11.3   0.0    1.8  1  AAA         ATPase family associated with various cellular ac
       0.16   11.2   0.2        3.7    6.8   0.1    2.1  2  Zeta_toxin  Zeta toxin
       0.25   10.0   0.0       0.63    8.6   0.0    1.6  2  AAA_13      AAA domain
       0.35   10.5   1.4       0.57    9.8   1.4    1.3  1  SRP54       SRP54-type protein, GTPase 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 !   98.5   0.0   3.2e-31   4.5e-28       2     137 .]      25     167 ..      24     167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 3.2e-31
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +n+++++ +g++++++G+nGaGK+t +++l+ l+kpt+G+ ++ g+++ e  +e +   ig+lp++p + +elt re
  gi|336254018|ref|YP_004597125.1|  25 SNLTMSVDRGTVYGFLGPNGAGKTTTMRMLTTLTKPTSGTARVAGHSIAE--REAVAPYIGYLPEDPPVYDELTGRE 99 
                                       799**********************************************9..************************* PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +             e+de+ie +l++++l  ++++++    + +S+G++q+v + +a+l +p + +lDEpt+
  gi|336254018|ref|YP_004597125.1| 100 QleyaaglrdipedEADERIESLLERFDLLADANKRI----EDYSKGMRQKVGVIQAVLHEPAVAFLDEPTS 167
                                       *************999*********************....*****************************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 !   12.9   0.0   5.1e-05      0.07       3      83 ..      38     114 ..      36     127 .. 0.66
   2 !   33.9   0.0   2.1e-11   2.9e-08     187     299 ..     100     199 ..      90     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-05
                            AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrle 79 
                                       ++ GpNg+GK++ ++ l  l    +   g+  +++ +  +r+    + +y pe p ++    ++ +  +y  glr  
  gi|336254018|ref|YP_004597125.1|  38 GFLGPNGAGKTTTMRMLTTL---TKPTSGTARVAGHSIAEREAVAPYIGYLPEDPPVYDEL-TGREQLEYAAGLRDI 110
                                       689************99888...55555555555555566666666666666666666666.666666666666666 PP

                            AAA_21  80 rsqv 83 
                                        ++ 
  gi|336254018|ref|YP_004597125.1| 111 PEDE 114
                                       6665 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 2.1e-11
                            AAA_21 187 rlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllli 263
                                       +l+    l++i+ +  +e++e+  +++++l            + +  + + S G+++  +++ a+l  +   ++ ++
  gi|336254018|ref|YP_004597125.1| 100 QLEYAAGLRDIPEDEADERIESLLERFDLLA-----------DANKRIEDYSKGMRQKVGVIQAVLHEP---AVAFL 162
                                       5555555555555555555555555555543...........344456667***************999...***** PP

                            AAA_21 264 DEpEngLHPkllrrllellkelsrngaQviltTHS.p 299
                                       DEp +gL+P++ r+  + + +l+++   ++l+TH  p
  gi|336254018|ref|YP_004597125.1| 163 DEPTSGLDPRAARTMRDTIADLADREMTIFLSTHIlP 199
                                       *******************999999*********755 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0     0.002       2.8      28      48 ..      39      59 ..      24      77 .. 0.84
   2 !    7.9   0.0    0.0016       2.3     324     364 ..     157     196 ..     152     197 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.002
                            AAA_15 28 liGkNnsGKSsilealdlFln 48
                                      + G+N++GK++ +++l  + +
  gi|336254018|ref|YP_004597125.1| 39 FLGPNGAGKTTTMRMLTTLTK 59
                                      88**************88776 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0016
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +++ +++EP   L p a + + +++++la+ +   ++++TH
  gi|336254018|ref|YP_004597125.1| 157 PAVAFLDEPTSGLDPRAARTMRDTIADLADREM-TIFLSTH 196
                                       677899**************************7.9****** 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   0.0   1.2e-05     0.016      28     131 ..      38     134 ..      16     193 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                            AAA_16  28 llsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleea 104
                                        + G+ G GK++ +r+l   l+k     ++g+++  + +     +a+  a   ++  l +++   +    re+le a
  gi|336254018|ref|YP_004597125.1|  38 GFLGPNGAGKTTTMRMLT-TLTKP----TSGTARVAGHS-----IAEREAVAPYIGYLPEDPPVYDELTGREQLEYA 104
                                       578***************.68888....66666666222.....344443445555555554444444444444444 PP

                            AAA_16 105 la..avpelagaea.srllellkrllalls 131
                                       ++  ++pe++++e+ ++lle +  l++  +
  gi|336254018|ref|YP_004597125.1| 105 AGlrDIPEDEADERiESLLERFDLLADANK 134
                                       444444445555445444444443333333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.3   1.5e-05      0.02      21      42 ..      36      57 ..      25      79 .. 0.80
   2 ?   -1.2   0.1       1.8   2.5e+03     154     174 ..     118     138 ..      94     154 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                            AAA_23 21 ltlItGpNGaGKTTildAikla 42
                                      ++ + GpNGaGKTT ++ ++  
  gi|336254018|ref|YP_004597125.1| 36 VYGFLGPNGAGKTTTMRMLTTL 57
                                      66799***********999864 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                            AAA_23 154 rleelekeleeledekkllek 174
                                       r+e+l + ++ l d +k +e+
  gi|336254018|ref|YP_004597125.1| 118 RIESLLERFDLLADANKRIED 138
                                       333333333333333333332 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   2.9e-05     0.041      19      54 ..      35      72 ..      19      83 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g.grviglAp 54
                                       v    Gp G+GKtt+++ l+ + +   g  rv+g + 
  gi|336254018|ref|YP_004597125.1| 35 TVYGFLGPNGAGKTTTMRMLTTLTKPTsGtARVAGHSI 72
                                      466678**************999987744456665554 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 ?   11.8   0.4   0.00011      0.15      15      49 ..      27      61 ..      21      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                       t+++d+  ++ + Gp+G+GK+T +  +++l  p+
  gi|336254018|ref|YP_004597125.1| 27 LTMSVDRGTVYGFLGPNGAGKTTTMRMLTTLTKPT 61
                                      577888555999***********997777766665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   0.00031      0.43      11      30 ..      40      59 ..      32     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                            AAA_22 11 tGesGtGKTtllrrlleqld 30
                                       G+ G+GKTt++r+l+   +
  gi|336254018|ref|YP_004597125.1| 40 LGPNGAGKTTTMRMLTTLTK 59
                                      59*************98764 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   0.00012      0.17       9      49 ..      16      57 ..      14      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                            AAA_27  9 eryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      +ryG+ t   +l++s ++  +   +GpN AGK+t++r ++ l
  gi|336254018|ref|YP_004597125.1| 16 KRYGETTAVsNLTMSVDRGTVYGFLGPNGAGKTTTMRMLTTL 57
                                      6889888753799999999999999***********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 ?   11.3   0.0   0.00025      0.35       3      66 ..      39     164 ..      37     196 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................ 37 
                                       + Gp G GKT++++ + + ++  +   ++ g+++ +                                         
  gi|336254018|ref|YP_004597125.1|  39 FLGPNGAGKTTTMRMLTTLTKptSGTARVAGHSIAEReavapyigylpedppvydeltgreqleyaaglrdipedea 115
                                       78**************9998654556777777777445666666666666666666666666666666666666666 PP

                                       ............STTHHHHHHHHHHHHHHHTS........TSEEEEEET CS
                               AAA  38 ............yvgesekkirelfkeakeka........kpsilfiDE 66 
                                                   ++ +++k+i+++ k +++k         +p + f+DE
  gi|336254018|ref|YP_004597125.1| 116 deriesllerfdLLADANKRIEDYSKGMRQKVgviqavlhEPAVAFLDE 164
                                       6666666666665555555555555555555455555555555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0027       3.7      22      49 ..      40      67 ..      20      76 .. 0.77
   2 ?    2.3   0.0     0.064        89     141     177 ..      96     133 ..      92     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0027
                        Zeta_toxin 22 gGqpGAGKselaellkdelerqgnvvrl 49
                                       G  GAGK++++++l++ ++++++  r+
  gi|336254018|ref|YP_004597125.1| 40 LGPNGAGKTTTMRMLTTLTKPTSGTARV 67
                                      5889***********9988877777766 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.064
                        Zeta_toxin 141 ldRyeeevaeg.Rlvpkeehdeafeglresvealeeek 177
                                         R++ e a+g R +p++e de  e l e ++ l+ + 
  gi|336254018|ref|YP_004597125.1|  96 TGREQLEYAAGlRDIPEDEADERIESLLERFDLLADAN 133
                                       568888877777*****************999987654 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00045      0.63      23      41 ..      41      59 ..      34      94 .. 0.83
   2 ?   -2.2   0.0      0.85   1.2e+03     526     573 ..     156     200 ..     150     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00045
                            AAA_13 23 GwNGaGKTtLSrllrslel 41
                                      G NGaGKTt  r+l  l++
  gi|336254018|ref|YP_004597125.1| 41 GPNGAGKTTTMRMLTTLTK 59
                                      89*************9965 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.85
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnlef 573
                                       +  + ++D P S LD  +       i + +   +    +f++TH l  
  gi|336254018|ref|YP_004597125.1| 156 EPAVAFLDEPTSGLDPRAARTMRDTIADLA---DREMTIFLSTHILPV 200
                                       566778999999999988888888887777...777789999997655 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   1.4   0.00041      0.57       3      26 ..      36      59 ..      34      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00041
                                      EEEEEESTTSSHHHHHHHHHHHHH CS
                             SRP54  3 villvGlqGaGKTttlaKLaallk 26
                                      v+ ++G++GaGKTtt+  L  l k
  gi|336254018|ref|YP_004597125.1| 36 VYGFLGPNGAGKTTTMRMLTTLTK 59
                                      56699**********998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1913.58
//
Query:       gi|336254019|ref|YP_004597126.1|  [L=553]
Description: hypothetical protein Halxa_2629 [Halopiger xanaduensis SH-6]
Scores for 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  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 4081.92
//
Query:       gi|336254020|ref|YP_004597127.1|  [L=332]
Description: aryl-alcohol dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-74  250.5   0.0    2.3e-74  250.2   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
      0.014   13.9   0.0      0.021   13.4   0.0    1.1  1  Terminase_1   Phage Terminase


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 !  250.2   0.0   2.6e-78   2.3e-74       1     291 [.      15     326 ..      15     328 .. 0.93

  Alignments for each domain:
  == domain 1  score: 250.2 bits;  conditional E-value: 2.6e-78
                                       .EEEE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-..TTTHHHHHHHHHHHH-TTTGGG-EEEEEE. CS
                      Aldo_ket_red   1 elglGtwqlgsk....eeiskeealellrraleaGinffDtAevY..gkgqseellGealkksrkkreeviiatKv. 70 
                                       +l++Gtw++  +     e+++eea ell++a e+Ginf+DtA+vY   +g+see++Ge+l++  ++re+v+ia+Kv 
  gi|336254020|ref|YP_004597127.1|  15 KLCFGTWRFAMEsdgvVETDREEAHELLDTAWENGINFIDTANVYgdPNGTSEEWIGEWLED--HDREDVVIASKVy 89 
                                       69*******999999999***************************8889*************..************* PP

                                       .....--SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES-- CS
                      Aldo_ket_red  71 .....dlrdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfs 142
                                            ++ +++++sgl +++ir+++e +l rLgtdy+D++++Hr+d ++p i e+l++l+elv+eGk+ ++G S+ +
  gi|336254020|ref|YP_004597127.1|  90 fpfdgWGEPGPNDSGLGRKHIRAQIEGTLDRLGTDYLDVYYIHRWDEDTP-IRETLRTLTELVEEGKVHYLGASSMA 165
                                       ****99********************************************.************************** PP

                                       HHHHHHH....HHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC--- CS
                      Aldo_ket_red 143 veqleka....kkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkd 215
                                       ++ql ka      ++  ++ + q   n ++ +e + +l++c+++++++ +yspl+gG+ltgky++ ed + + p+ +
  gi|336254020|ref|YP_004597127.1| 166 AWQLTKAlwksDVEGLERFDVTQPMVNAVQYDEVSDYLDVCADQDLAVCPYSPLAGGFLTGKYERTEDGGIEAPDGS 242
                                       *******887644444458888888888888888**********************************998777777 PP

                                       ----.......TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTS.TT-SEEEE--SSHHHHHHHHGGGG----HH CS
                      Aldo_ket_red 216 lkrd.......ertsknldaaeelselakehgvslaqlalryalsq.pavgivipgasnieqlednldalelklsee 284
                                        ++           + + d +e+++ +a e + ++aq++lr++++q  ++ ++i+ga++++qle+n++a++l+ls+e
  gi|336254020|ref|YP_004597127.1| 243 RGSLdemfdewYVQENAWDVLEAVEGVADELDATPAQVSLRWLMEQdRFTCVPIVGARTSDQLEENVGAVDLDLSDE 319
                                       6666999*97655566778999************************6678899************************ PP

                                       HHHHHHH CS
                      Aldo_ket_red 285 evaelde 291
                                       +++++++
  gi|336254020|ref|YP_004597127.1| 320 QFERIEA 326
                                       *****97 PP

>> Terminase_1  Phage Terminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.4e-06     0.021     377     439 ..     118     181 ..     113     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-06
                       Terminase_1 377 idklektaldiplvevrqsfaklSnslkeveklvaeerirh.ddnklLavsvnNaelkeddaen 439
                                        d+l   +ld+++++   + + + ++l+ + +lv+e+++++ + + + a++++ a  k d +++
  gi|336254020|ref|YP_004597127.1| 118 LDRLGTDYLDVYYIHRWDEDTPIRETLRTLTELVEEGKVHYlGASSMAAWQLTKALWKSDVEGL 181
                                       699999**********************************945588999*****9999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2472.05
//
Query:       gi|336254021|ref|YP_004597128.1|  [L=58]
Description: hypothetical protein Halxa_2631 [Halopiger xanaduensis SH-6]
Scores for 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:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 458.94
//
Query:       gi|336254022|ref|YP_004597129.1|  [L=142]
Description: hypothetical protein Halxa_2632 [Halopiger xanaduensis SH-6]
Scores for 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:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1064.83
//
Query:       gi|336254023|ref|YP_004597130.1|  [L=481]
Description: protoheme IX farnesyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-56  191.5  26.8    1.6e-56  191.5  26.8    3.0  2  UbiA        UbiA prenyltransferase family
    3.8e-08   32.8  14.5    4.8e-06   25.9   7.8    3.6  4  COX15-CtaA  Cytochrome oxidase assembly protein
  ------ inclusion threshold ------
       0.05   13.4   1.3       0.23   11.3   0.4    2.4  2  Hexapep_2   Hexapeptide repeat of succinyl-transferase


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 ?   -8.6  11.8         3   1.8e+04     194     194 ..     108     108 ..      46     169 .. 0.52
   2 !  191.5  26.8   2.6e-60   1.6e-56       3     247 ..     217     465 ..     214     470 .. 0.93

  Alignments for each domain:
  == domain 1  score: -8.6 bits;  conditional E-value: 3
                              UbiA 194 l 194
                                       l
  gi|336254023|ref|YP_004597130.1| 108 L 108
                                       1 PP

  == domain 2  score: 191.5 bits;  conditional E-value: 2.6e-60
                              UbiA   3 ipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllil 79 
                                       + a++g+alaag+ +d+ +++++l g++la++a+ ++N++++r+iD++m+rt++RPl++ ++ +++al+f+ +l ++
  gi|336254023|ref|YP_004597130.1| 217 LVAAAGMALAAGPALDAYTIVATLGGGVLAIGASGTFNHVLERDIDRRMSRTADRPLATDLVPVRNALAFGGLLTVA 293
                                       467888*********************************************************************** PP

                              UbiA  80 gllllalllnpltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavfll 155
                                       +l++  l++n l+a+lgl+a+l+y vvYt l lK  t+++tv+gg+a++lp+l+gwaavt+++ ++al+la  +fl+
  gi|336254023|ref|YP_004597130.1| 294 SLGVF-LTINRLAAALGLAAILFYsVVYT-LLLKPNTVQNTVIGGFAGALPALIGWAAVTNEIGVPALALAGVIFLW 368
                                       *****.***********************.9********************************************** PP

                              UbiA 156 twaialandlrdregDrkagiktlpvvlGrkaarillalllavllla.llllllalllllylllalllaalallraa 231
                                       t a+++  +l  +++++++g++++pvv G+  +r  ++++la++l++ ++l++l  l+ +y++ ++++++++l+ a+
  gi|336254023|ref|YP_004597130.1| 369 TPAHFYNLALAYKDDYARGGFPMMPVVRGETETRKHIVYYLAATLVStVALAWLTDLGAIYAATVAIFGGVFLWAAV 445
                                       ***********************************64445555555589999999999*****************99 PP

                              UbiA 232 rlvrrrdakkaakff....l 247
                                        l+  +++++a ++f    +
  gi|336254023|ref|YP_004597130.1| 446 VLHFEQTERAAFRSFhasnA 465
                                       99999999999888855554 PP

>> COX15-CtaA  Cytochrome oxidase assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.5   9.3e-08   0.00055       3      48 ..      25      70 ..      23      73 .. 0.91
   2 !   25.9   7.8   8.1e-10   4.8e-06      78     167 ..      72     154 ..      66     175 .. 0.85
   3 ?   -3.3   0.2      0.59   3.5e+03     110     125 ..     207     222 ..     197     244 .. 0.70
   4 ?   -2.5  11.3      0.34   2.1e+03      84     228 ..     304     443 ..     300     480 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.3e-08
                        COX15-CtaA  3 wlllvlllvllvvvlGgltRltdsGlsitdWppctGalppltdeew 48
                                      +l++++l v+l+ ++G+ t +td+   +  Wp+c+  + pl+++++
  gi|336254023|ref|YP_004597130.1| 25 LLTATALGVYLLLIVGATTSITDAASACSTWPTCHAPTDPLNETQL 70
                                      6788999****************************99999888775 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 8.1e-10
                        COX15-CtaA  78 iEwiHRllgrllGllilvpllyflakkrisrelkkllllllllvglQGllGwwmVksgLsekprvspyrlaaHLlla 154
                                       i w HR+ + ++Gll+++ +++++  + ++ ++++ ll+ ++l ++Q  +G+++ ++g         +   +HL+l+
  gi|336254023|ref|YP_004597130.1|  72 IVWGHRIAAVVVGLLVAATAAVAAL-GDATARVRRTLLASAALYVIQVGVGAATATLGA------DAVAPGLHLGLG 141
                                       67*********************98.899*****************************7......89999******* PP

                        COX15-CtaA 155 flllalllwlalr 167
                                       ++++a++++ ++ 
  gi|336254023|ref|YP_004597130.1| 142 VVIFAGVVLALAW 154
                                       ****998875443 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.59
                        COX15-CtaA 110 lkkllllllllvglQG 125
                                       +k++l++ll+lv++ G
  gi|336254023|ref|YP_004597130.1| 207 MKPRLMWLLCLVAAAG 222
                                       5566666666666554 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 0.34
                        COX15-CtaA  84 llgrllGllilvpllyflakkrisrelkkllllllllvglQGllGwwmVksgLsekprvspyrlaaHL.llafllla 159
                                       l + +lGl  ++   ++  +  +++++ +  ++  + ++l +l+Gw+ V+ ++     v  + la    l + + + 
  gi|336254023|ref|YP_004597130.1| 304 L-AAALGLAAILFYSVV-YTLLLKPNTVQNTVIGGFAGALPALIGWAAVTNEI----GVPALALAGVIfLWTPAHFY 374
                                       4.444555443332222.3345788999999999999***************9....45555554422022222222 PP

                        COX15-CtaA 160 lllwlalrllakeae....saeeeaaakklrllallllallllqialGalvagldAglayntfplmggelipd 228
                                        l++ + +  a   +    +++ ++++++ r  +++ la++l+  +  a++  l A++a  t    gg ++ +
  gi|336254023|ref|YP_004597130.1| 375 NLALAYKDDYA---RggfpMMPVVRGETETRKHIVYYLAATLVSTVALAWLTDLGAIYAA-TVAIFGGVFLWA 443
                                       23332222222...2234689999999999999999999999999999999999999998.666666554433 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 ?   11.3   0.4   3.8e-05      0.23       9      32 ..     126     150 ..     123     151 .. 0.94
   2 ?   -0.4   0.0      0.17     1e+03       7      15 ..     331     339 ..     330     347 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.8e-05
                                       EE-TT-EE.SEEE-TT-EE-TT-EE CS
                         Hexapep_2   9 liGanagi.GvslGdncvvgaGvvi 32 
                                        +Ga+a+  G +lG ++v+ aGvv+
  gi|336254023|ref|YP_004597130.1| 126 TLGADAVApGLHLGLGVVIFAGVVL 150
                                       59*****99***************8 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.17
                                       T-EE-TT-E CS
                         Hexapep_2   7 nCliGanag 15 
                                       n++iG +ag
  gi|336254023|ref|YP_004597130.1| 331 NTVIGGFAG 339
                                       99*****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 3481.83
//
Query:       gi|336254024|ref|YP_004597131.1|  [L=122]
Description: hypothetical protein Halxa_2635 [Halopiger xanaduensis SH-6]
Scores for 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  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 919.91
//
Query:       gi|336254025|ref|YP_004597132.1|  [L=305]
Description: hypothetical protein Halxa_2636 [Halopiger xanaduensis SH-6]
Scores for 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-25   89.0   1.7    2.3e-25   89.0   1.7    2.5  2  DUF3267   Putative zincin peptidase


Domain annotation for each model (and alignments):
>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   1.7   1.3e-29   2.3e-25       2     105 ..      76     177 ..      75     179 .. 0.93
   2 ?   -0.2   1.7     0.068   1.2e+03      57      93 ..     215     251 ..     214     255 .. 0.52

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 1.3e-29
                           DUF3267   2 lvlvilHEllHglffklfgkkpkkkvkfgi.klliayatsseallskkqfiiillaPfvllgilllllalllpsstl 77 
                                       +++v+lHE+lHgl++ ++g +p++++++    l++aya + +++ +++q + +llaPfv ++il+++++l++pss  
  gi|336254025|ref|YP_004597132.1|  76 ALVVVLHEALHGLVMTRYGDSPGFGLGVSYfVLPYAYAETRGEF-TRNQLLAMLLAPFVAITILGVAAMLVYPSS-- 149
                                       6899****************999998884445999999999999.*****************************9.. PP

                           DUF3267  78 llllllalnaagsagDlliallllkapk 105
                                       ++l+ la naags+gDl++a++ll++p+
  gi|336254025|ref|YP_004597132.1| 150 VWLIPLATNAAGSIGDLWMAATLLQYPA 177
                                       9*************************97 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.068
                           DUF3267  57 PfvllgilllllalllpsstlllllllalnaagsagD 93 
                                       P+++l+++l+ +a  l+  + l ++ ++  +a+++gD
  gi|336254025|ref|YP_004597132.1| 215 PAIFLTTVLAGAAGTLAVLVGLGIVAVLASLAFGSGD 251
                                       5666666666666665544334444444444444455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2450.46
//
Query:       gi|336254026|ref|YP_004597133.1|  [L=98]
Description: transcriptional regulator PadR family protein [Halopiger xanaduensis SH-6]
Scores for 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   30.4   0.0    4.1e-07   29.9   0.0    1.3  1  PadR        Transcriptional regulator PadR-like family
     0.0015   18.4   0.0     0.0027   17.5   0.0    1.6  1  DUF1495     Winged helix DNA-binding domain (DUF1495)
     0.0085   15.8   0.0      0.021   14.6   0.0    1.5  2  DUF4364     Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.026   14.6   0.0    1.4  1  HTH_20      Helix-turn-helix domain
      0.019   15.1   0.1       0.95    9.6   0.0    2.2  2  Mrr_N       Mrr N-terminal domain
       0.05   13.5   0.0      0.066   13.1   0.0    1.4  1  TrmB        Sugar-specific transcriptional regulator TrmB
      0.067   13.2   0.0       0.17   11.9   0.0    1.6  2  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
       0.15   12.2   0.0        0.3   11.3   0.0    1.5  1  HTH_34      Winged helix DNA-binding domain


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 !   29.9   0.0   1.8e-10   4.1e-07       1      74 [.      16      82 ..      15      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.8e-10
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      +La +e++++ G +++++le +++   ++ + s Y  L+ L + g+ve++ e     +   +YrlT+ G+r+++
  gi|336254026|ref|YP_004597133.1| 16 LLAAAEDGELRGQQLKSRLESHYDD--RIDPKSFYGSLSALVEAGFVEERTE-----GIHDVYRLTESGQRRVR 82
                                      5777888****************99..99999****************9966.....589**********9986 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 !   17.5   0.0   1.2e-06    0.0027      52      87 ..      47      81 ..       2      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.2e-06
                           DUF1495 52 rynsessLielGLveeeeeseglk.lYklteeGieiv 87
                                       y s s+L+e G ve  e  eg++ +Y+lte+G++ v
  gi|336254026|ref|YP_004597133.1| 47 FYGSLSALVEAGFVE--ERTEGIHdVYRLTESGQRRV 81
                                      5888899*******6..56667766********8755 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.75   1.7e+03      61      86 ..      18      43 ..      11      47 .. 0.81
   2 !   14.6   0.0   9.2e-06     0.021      39      70 ..      50      81 ..      45      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.75
                           DUF4364 61 kiTekGketlelfenripksirekid 86
                                      +  e+G+   +++++r+ +++ ++id
  gi|336254026|ref|YP_004597133.1| 18 AAAEDGELRGQQLKSRLESHYDDRID 43
                                      56678888888999999999988887 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9.2e-06
                           DUF4364 39 alseLvesglieeeekenktlykiTekGketl 70
                                       ls Lve+g++ee+++  +++y++Te+G++ +
  gi|336254026|ref|YP_004597133.1| 50 SLSALVEAGFVEERTEGIHDVYRLTESGQRRV 81
                                      699*************************9866 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.1e-05     0.026      12      60 ..      10      66 ..       4      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHH..STCTTB-HHHHHHHH......TS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 12 RrrilraL..araegltaselaerl......dlskntlsyHLrvLeeagLvevvreg 60
                                      Rr+++ +L  a++++l   +l+ rl      ++++++ +  L +L+eag+ve ++eg
  gi|336254026|ref|YP_004597133.1| 10 RRDMCVLLaaAEDGELRGQQLKSRLeshyddRIDPKSFYGSLSALVEAGFVEERTEG 66
                                      6666666666666666677899999766655599999******************98 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.035        78       5      31 ..      13      38 ..      10      47 .. 0.82
   2 ?    9.6   0.0   0.00042      0.95      58      85 ..      51      81 ..      45      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.035
                             Mrr_N  5 mlplLealadgsehrlkeirervaerf 31
                                      m  lL a++dg+++  +++++r+++++
  gi|336254026|ref|YP_004597133.1| 13 MCVLLAAAEDGELRG-QQLKSRLESHY 38
                                      566788888899999.*****999886 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00042
                             Mrr_N 58 rtyLkkagllespkrgv...wkiTekGrevl 85
                                      ++ L++ag++e+ + g+   +++Te G++ +
  gi|336254026|ref|YP_004597133.1| 51 LSALVEAGFVEERTEGIhdvYRLTESGQRRV 81
                                      5789*********9664444*******9865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.9e-05     0.066      37      64 ..      45      73 ..      11      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                                      HCHHHHHHHHHHCTSEEEESST.TTEEEE CS
                              TrmB 37 skvYevLrsLedkGlVerekgr.pklYra 64
                                       + Y +L+ L+++G+Ve + +    +Yr 
  gi|336254026|ref|YP_004597133.1| 45 KSFYGSLSALVEAGFVEERTEGiHDVYRL 73
                                      5779*************999873448876 PP

>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         2   4.6e+03      42      53 ..      23      34 ..      11      36 .. 0.69
   2 ?   11.9   0.0   7.6e-05      0.17       6      37 ..      52      82 ..      51      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2
                                      SS--CCCHHHHH CS
                        HicA_toxin 42 kelkpgtlksIl 53
                                       el+  +lks l
  gi|336254026|ref|YP_004597133.1| 23 GELRGQQLKSRL 34
                                      466666777766 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.6e-05
                                      HHHHHTT-EEEEEETTEEEEE-TTSS-EEEEE CS
                        HicA_toxin  6 klLeklGfevvrqkGSHvrfkhpdkrgivtvp 37
                                      ++L  +Gf+++r++G H +++  + +++  v+
  gi|336254026|ref|YP_004597133.1| 52 SALVEAGFVEERTEGIHDVYRLTESGQR-RVR 82
                                      699******************9444432.455 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 ?   11.3   0.0   0.00013       0.3      38      79 ..      54      91 ..      46      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                            HTH_34 38 LekagYievdkefkgkkprtllriTpeGreafkkyvkaLksl 79
                                      L +ag++e + e      + ++r+T+ G+ +  ++ ++L+++
  gi|336254026|ref|YP_004597133.1| 54 LVEAGFVEERTEGI----HDVYRLTESGQRRVRDHYEWLRER 91
                                      55555555444433....459******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 731.92
//
Query:       gi|336254027|ref|YP_004597134.1|  [L=381]
Description: Butyryl-CoA dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-48  163.8   0.7    4.3e-48  163.3   0.7    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    2.6e-38  131.2   0.1    6.3e-38  129.9   0.0    1.7  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    1.3e-25   90.2   0.3      2e-25   89.6   0.3    1.3  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    1.3e-24   86.2   0.0    2.7e-24   85.2   0.0    1.6  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.3   0.7   9.7e-52   4.3e-48       1     149 [.     230     378 ..     230     379 .. 0.99

  Alignments for each domain:
  == domain 1  score: 163.3 bits;  conditional E-value: 9.7e-52
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       g+Gf +a++tln +R+++aa+ +g+ar+a+e a++ya++r++fg+p++++q++++kla+m ++++aa++l  +aa +
  gi|336254027|ref|YP_004597134.1| 230 GEGFVQALKTLNGGRITIAARGVGIARAAFEAARDYANEREQFGQPIGEFQSIKHKLADMDTKIQAAKMLMHKAADK 306
                                       68*************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                         +g++  ++a+ aKl+ase+ +eva++ +q++Gg+Gy+++ p er+yrda++++i+eGtse++rn+i+++l
  gi|336254027|ref|YP_004597134.1| 307 KIRGENYIKDAAQAKLYASEVSREVANEGIQIHGGYGYTKDFPAERFYRDAKLNEIYEGTSEVLRNTIGDQL 378
                                       ********************************************************************9987 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   0.0   1.4e-41   6.3e-38       1     112 [.       6     117 ..       6     118 .. 0.99
   2 ?   -2.9   0.0       2.4   1.1e+04      34      54 ..     311     331 ..     285     338 .. 0.55

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 1.4e-41
                                       THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HH CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradag 77 
                                       ++eq+++rd+v+ef++ee+ p a+e+d+++efpr+l++++a+lGl+g+++peeygGagldy ++ai +ee++r++ g
  gi|336254027|ref|YP_004597134.1|   6 SPEQQQIRDMVAEFVDEEVVPIADEIDHDDEFPRDLIDEMADLGLMGMPFPEEYGGAGLDYHSYAIGLEEISRGSGG 82 
                                       68*************************************************************************** PP

                                       HHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                     Acyl-CoA_dh_N  78 lalllgvhsslvapailrfGteeqkrryLpklasg 112
                                       l++++++h+sl++++++ fGte+qk++yL +la+g
  gi|336254027|ref|YP_004597134.1|  83 LGTIVAAHTSLAGNMLYDFGTEAQKEEYLVPLAEG 117
                                       *********************************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.4
                                       HHHHHHHHHTTCTSTTS-GGG CS
                     Acyl-CoA_dh_N  34 relwkklaelGllgitvpeey 54 
                                       ++ +k +a++ l++  v  e+
  gi|336254027|ref|YP_004597134.1| 311 ENYIKDAAQAKLYASEVSREV 331
                                       233555555555555555444 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   0.3   4.4e-29     2e-25       1     133 [.     245     367 ..     245     368 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 4.4e-29
                                       .HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----H CS
                     Acyl-CoA_dh_2   1 lgiaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtv 77 
                                       ++iaa  +G+Araa++++ ++a+er +  +g+++ +++ ++++la++ ++++AA++l+++aa++      +g+++  
  gi|336254027|ref|YP_004597134.1| 245 ITIAARGVGIARAAFEAARDYANEREQ--FGQPIGEFQSIKHKLADMDTKIQAAKMLMHKAADK----KIRGENY-- 313
                                       579************************..***********************************....5666666.. PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  78 edraearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                          ++a+ a+++a+e +++++++ ++++Gg++++k+ p +R++RDa+  +++++++
  gi|336254027|ref|YP_004597134.1| 314 --IKDAAQAKLYASEVSREVANEGIQIHGGYGYTKDFPAERFYRDAKLNEIYEGTS 367
                                       ..79********************************************99999886 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.0   6.1e-28   2.7e-24       1      97 []     122     218 ..     122     218 .. 0.94

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 6.1e-28
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE...GGGEEE CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvp.rdapgvsv 75 
                                       afal+E +aGsdv +++t +ae+dg+eyv+nG K wi+n+  a++++++a+ ++p+ +++g+s f+v  + + g+ v
  gi|336254027|ref|YP_004597134.1| 122 AFALSEAGAGSDVPAMET-TAEKDGDEYVVNGGKLWISNGSVADTITLFAK-TDPEaGNKGISSFVVRpEEDDGFIV 196
                                       79****************.99999999************************.555568*********978888**** PP

                                       -----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  76 rrieeklGlrglptgelvfedv 97 
                                       + +eeklG +g+pt+el+f+d+
  gi|336254027|ref|YP_004597134.1| 197 EGTEEKLGDKGCPTAELRFDDM 218
                                       ********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2851.51
//
Query:       gi|336254028|ref|YP_004597135.1|  [L=550]
Description: o-succinylbenzoate--CoA ligase [Halopiger xanaduensis SH-6]
Scores for 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-90  302.6   0.0    4.3e-90  302.3   0.0    1.0  1  AMP-binding    AMP-binding enzyme
    1.6e-23   83.4   0.1    3.1e-23   82.5   0.1    1.5  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 !  302.3   0.0   4.8e-94   4.3e-90       6     422 ..      18     435 ..      12     436 .. 0.84

  Alignments for each domain:
  == domain 1  score: 302.3 bits;  conditional E-value: 4.8e-94
                                       HHSTTSEEEEE..CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETT CS
                       AMP-binding   6 aktpdkvalvd..sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnpt 80 
                                       + + d   + +  +++ q++TY+e+ +r++rlA++L++ G+++gdrV+ +++n  +++ +++a+ ++Ga + ++np 
  gi|336254028|ref|YP_004597135.1|  18 KLYADTEIV-SrnHDGMQRYTYGEYADRTSRLANALEEYGIEQGDRVGTFCWNHSRHFETYFAVPSMGAQLHTINPL 93 
                                       444455555.4488899************************************************************ PP

                                       S-HHHHHHHHHHHTESEEE..ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS CS
                       AMP-binding  81 ltaeelayiledseakvli..atvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeee 155
                                       l+ ++++yi+++++ ++++  +    +l+ ++++a+++ ++v+ v v+ ++e+++ e  + e+  e  +  + + + 
  gi|336254028|ref|YP_004597135.1|  94 LPDAHIRYIVDNADDELIFvdHSFAGKLAGAVADAEGEFDDVDFV-VMGREESDDLEATPYESFIEGRD-AEYDWPD 168
                                       *******************43122333344555555554444444.34444444443333333333332.4667889 PP

                                       -BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEE CS
                       AMP-binding 156 lkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvv 232
                                       ++++++a ++YTSGTTG PKGV ++++ l + + + + ++   + +ddvv+ ++p++h+ ++    ++a + Ga+ v
  gi|336254028|ref|YP_004597135.1| 169 VDEEQPAGMCYTSGTTGDPKGVEYTQQMLWSHTMASQTPQGIPMADDDVVMPVVPMFHVNAW-GMPFTATAGGAKQV 244
                                       **************************99977766655665667888****************.9************* PP

                                       E-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC CS
                       AMP-binding 233 llpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge 309
                                       ++ ++++  p+ l++lie+++vt++agvP v+  l+e  +++    + dls+l++v++gg++ +++++++f ++  e
  gi|336254028|ref|YP_004597135.1| 245 FPGPSPE--PADLADLIETEGVTITAGVPIVWLGLMEYCSEN----QVDLSALETVIVGGSAAPKSMIEWFDDRDVE 315
                                       *999988..7779************************65555....45**************************776 PP

                                       EEEEEEEEGGGSSECEE.........CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE.TTSE.EEEEEEETTS- CS
                       AMP-binding 310 evlegYGlTEttgvvtv.........lpleedkkklgsvGkplpgvevkivDeetgepvp.dgee.Gellvrgpgvm 375
                                        vl+++G+TEt+++ tv         ++ e++  k++++G ++pg e ++v ++ ge+v+ +ge  Gel++rgp+v+
  gi|336254028|ref|YP_004597135.1| 316 -VLHAWGMTETAPIGTVshlradlrdADYETRVDKRSKQGLVMPGLEFRVVGDD-GEEVAwNGEDfGELWIRGPWVA 390
                                       .**************88899****994445666677889*************99.67776477779*********** PP

                                       SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 376 kgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                         Y+ +p+a++  f   ++wl+TGD++++d dGy++iv+R kd+ik+
  gi|336254028|ref|YP_004597135.1| 391 TEYFERPQANEAEFE--DGWLKTGDVVTVDGDGYVKIVDREKDVIKS 435
                                       **************7..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 !   82.5   0.1   3.5e-27   3.1e-23       1      76 []     444     521 ..     444     521 .. 0.94

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 3.5e-27
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE----..--HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgs..ealeeeLkahvrkelgpyavpkkvvfvdelpktrsG 75 
                                       e+E+a+++h++VaeaaVvGvp+e++ e++vafVv+ +g   e l +e+ +h+++e ++++ p++++f++e+pkt++G
  gi|336254028|ref|YP_004597135.1| 444 ELENAIMAHDGVAEAAVVGVPHERWQERPVAFVVPVEGAdrETLVDEITDHLADEYPKWWLPDDIEFIQEIPKTATG 520
                                       89*********************************77843344********************************** PP

                                       - CS
                     AMP-binding_C  76 K 76 
                                       K
  gi|336254028|ref|YP_004597135.1| 521 K 521
                                       9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3962.98
//
Query:       gi|336254029|ref|YP_004597136.1|  [L=216]
Description: NAD-dependent epimerase/dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-47  161.0   0.1    3.4e-47  160.7   0.1    1.1  1  NAD_binding_10   NAD(P)H-binding
    1.6e-16   60.6   0.0    2.2e-16   60.1   0.0    1.1  1  NmrA             NmrA-like family
      4e-10   39.6   0.0    7.2e-10   38.7   0.0    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
    7.5e-07   28.4   0.0      1e-06   28.0   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    0.00023   21.4   0.1     0.0059   16.9   0.0    2.5  2  TrkA_N           TrkA-N domain
      0.007   16.3   0.0        1.3    8.9   0.0    2.5  2  KR               KR domain
  ------ inclusion threshold ------
      0.044   12.9   0.0       0.25   10.5   0.0    2.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
       0.14   11.2   0.1       0.23   10.5   0.1    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
       0.16   11.1   0.0       0.22   10.7   0.0    1.2  1  NAD_binding_4    Male sterility protein


Domain annotation for each model (and alignments):
>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.7   0.1   1.7e-50   3.4e-47       1     182 [.       9     187 ..       9     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 160.7 bits;  conditional E-value: 1.7e-50
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk.... 73 
                                       G +G +G+++++ l++r + e +a++R++++++e+e + g e v++d+t++++l++a++g+ a+v+a+g++g+    
  gi|336254029|ref|YP_004597136.1|   9 GSHGPTGQHVTRLLAER-DAEPRAMIRDESQADEME-SLGGEPVVADLTEPDSLESAVEGCGAIVFAAGSNGEdvyg 83 
                                       89**********99999.7***************98.6999***********************9999999998999 PP

                                       .HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHHHSSSEEEEEEE-CEE-S CS
                    NAD_binding_10  74 .deegaknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellrasgldwTivrpggLtde 149
                                        d++ga+n++daa+++gv Rfv++s++g++d           ++l++yl+ak++a+e+lr+s+l  Tivrpg Lt e
  gi|336254029|ref|YP_004597136.1|  84 vDRDGAINLIDAAEAEGVDRFVMLSSMGADDPES------GPDALRDYLIAKAEADEYLRQSDLSSTIVRPGELTTE 154
                                       99999*************************8433......34789*******************************9 PP

                                       T.--SEEEEETTSS----EEEHHHHHHHHHHHCT CS
                    NAD_binding_10 150 p.ttkyrvvekgepfkggsisradVAdvlvavld 182
                                       + +++ r++ ++ ++ +g i+r+dVA+vlv ++d
  gi|336254029|ref|YP_004597136.1| 155 DgSGELRAA-DSLEMASGDIPREDVARVLVTAID 187
                                       956666665.55668899************9986 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0   1.1e-19   2.2e-16       1     142 [.       5     149 ..       5     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.1e-19
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG.. CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy.. 75 
                                       +lv G+ G  G++v+r l++++ + ra++Rd++  +a+++++ G e v +dl + +sl++a++g  ++ ++ g++  
  gi|336254029|ref|YP_004597136.1|   5 VLVAGSHGPTGQHVTRLLAERDAEPRAMIRDES--QADEMESLGGEPVVADLTEPDSLESAVEGCGAIVFAAGSNge 79 
                                       79****************************975..689999999999******************999999998877 PP

                                       ...S-HHHHHHHHHHHHHHHS-SEEEE.EE---GG.GT.SSS---TTTHHHHHHHHHHHHCTS-EEEEEE- CS
                              NmrA  76 ...skeiedgkklvdAakeaGvkhfiy.SslgddndrsnaeepavphfdsKaeieeyvralgipytfvyag 142
                                          +   +   +l+dAa + Gv +f+  Ss+g+d+ +s + +  ++   +Kae  ey+r++ + +t+v++g
  gi|336254029|ref|YP_004597136.1|  80 dvyGVDRDGAINLIDAAEAEGVDRFVMlSSMGADDPES-GPDALRDYLIAKAEADEYLRQSDLSSTIVRPG 149
                                       77666777779**************9549999999888.5555889999*******************987 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   3.6e-13   7.2e-10       1     172 [.       5     151 ..       5     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 3.6e-13
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       +lV+G +G  G+++++ l+e++ e  ++ r++s+  + +    e v +dlt++++le +++  ++ a++ +A+    
  gi|336254029|ref|YP_004597136.1|   5 VLVAGSHGPTGQHVTRLLAERDAEPRAMIRDESQADEMESLGGEPVVADLTEPDSLESAVE--GCGAIVFAAG---- 75 
                                       79**********************9999888666555554444******************..9*****9977.... PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                           ++ +d++  +  g+ nl++aa + gv+r++ lsS    G+d++  +     +gp    + Y +aK+ ++++++
  gi|336254029|ref|YP_004597136.1|  76 ----SNGEDVYGVDRDGAINLIDAAEAEGVDRFVMLSS---MGADDP--E-----SGP-DALRDYLIAKAEADEYLR 137
                                       ....44566777788999********************...777777..1.....222.47899*********9998 PP

                                       HHHHHHT-EEEEEEESEE CS
                         Epimerase 155 ayaaqyglnaiilrlfnl 172
                                       +     +l+ +i+r+  l
  gi|336254029|ref|YP_004597136.1| 138 QS----DLSSTIVRPGEL 151
                                       54....666688887665 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 !   28.0   0.0     5e-10     1e-06       1     124 [.       6     117 ..       6     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 5e-10
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +v G+ G  G+++ + L +++   e r++ +r++++  +e+++++ +  + +D+t+ d+le a+eg  ++++ a+  
  gi|336254029|ref|YP_004597136.1|   6 LVAGSHGPTGQHVTRLLAERDA--EPRAM-IRDESQA-DEMESLGGE-PVVADLTEPDSLESAVEGCGAIVFAAGS- 76 
                                       699*********9999998885..66665.5555555.788999999.999*******************999653. PP

                         3Beta_HSD  78 dvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpns 124
                                               + ++ v   G  n+++a+   gv ++v  Ss+++  p s
  gi|336254029|ref|YP_004597136.1|  77 -----NG-EDVYGVDRDGAINLIDAAEAEGVDRFVMLSSMGADDPES 117
                                       .....23.44999***************************9866655 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.9e-06    0.0059       2      73 ..       6      77 ..       5      84 .. 0.83
   2 ?    1.5   0.0      0.17   3.3e+02      36      60 ..     190     214 ..     173     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-06
                                      EEES.-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSH CS
                            TrkA_N  2 iiiG.lGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgdd 73
                                      +++G +G +G+++++ L e +  +  +  +de++++e++  g e vv+d t+++ Le+a +e + a++ a+g++
  gi|336254029|ref|YP_004597136.1|  6 LVAGsHGPTGQHVTRLLAErDA-EPRAMIRDESQADEMESLGGEPVVADLTEPDSLESA-VEGCGAIVFAAGSN 77
                                      677779*************555.477778899************************998.67777777776665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.17
                                       HHHHTTSEEEES-TTSHHHHHHTTG CS
                            TrkA_N  36 elreeglevvvgdatdeevLeeagi 60 
                                        ++ + +e++ gd + e++Le+ag 
  gi|336254029|ref|YP_004597136.1| 190 PVSGKTFEILSGDESIEDALEAAGT 214
                                       45667799**************995 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0095        19       2      72 ..       4      64 ..       3      75 .. 0.66
   2 !    8.9   0.0   0.00065       1.3     113     139 ..      86     112 ..      73     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0095
                                      EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHH CS
                                KR  2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdaveall 72
                                      t+l++G  G  G++++r lae+ a+  +++ R+       +++ +e+e+lg e   v aD++++d++e+++
  gi|336254029|ref|YP_004597136.1|  4 TVLVAGSHGPTGQHVTRLLAERDAEPRAMI-RD-------ESQADEMESLGGE--PVVADLTEPDSLESAV 64
                                      689*****************9988754433.22.......1223445554443..3445566666666555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00065
                                       THHHHHHHHHTTTS--SEEEEEEEHHH CS
                                KR 113 vkGawnLhelledesldffvlfSSiag 139
                                        +Ga nL  + e e +d fv++SS+++
  gi|336254029|ref|YP_004597136.1|  86 RDGAINLIDAAEAEGVDRFVMLSSMGA 112
                                       579*********************986 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00012      0.25       2     135 ..       6     116 ..       5     157 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T- CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkv 78 
                                       lv+G+ G  G++++r +++++++    + rdE + +e+e+                pv++d+++ ++le+a+e  ++
  gi|336254029|ref|YP_004597136.1|   6 LVAGSHGPTGQHVTRLLAERDAEPRA-MIRDESQADEMESLG----------G--EPVVADLTEPDSLESAVE--GC 67 
                                       56666666666665555555443322.235555555555422..........2..367788888888888888..77 PP

                                       SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS-- CS
                   Polysacc_synt_2  79 dvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAvnPt 135
                                        +++ aA         +n  ++      g+ n+i+aa + gv+++v++S+  A +P 
  gi|336254029|ref|YP_004597136.1|  68 GAIVFAAG--------SNGEDVYGVDRDGAINLIDAAEAEGVDRFVMLSSMGADDPE 116
                                       77777775........34455555556799*******************98777775 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 ?   10.5   0.1   0.00012      0.23       2      94 ..       4     101 ..       3     110 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHH..HHHHHH.H--S....EEEE------HHHHHHSH CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltreeldltdaeav..aellke.akpd....vvvnaAAytavDkaEsee 71 
                                       ++lv G++G  G++++++lae+++e  a+ r+e + ++ e++  + ++++ ++pd    +v  ++A   v++a s+ 
  gi|336254029|ref|YP_004597136.1|   4 TVLVAGSHGPTGQHVTRLLAERDAEPRAMIRDESQADEMESLggEPVVADlTEPDslesAVEGCGAI--VFAAGSNG 78 
                                       589**************************88866655555542233443312333222366667774..88999999 PP

                                       HHHHHHHTHHHHHHHHHHHHCT- CS
                     RmlD_sub_bind  72 eaayavnaeavealAeaaaavga 94 
                                       e  y v+ +++ +l +aa+a g+
  gi|336254029|ref|YP_004597136.1|  79 EDVYGVDRDGAINLIDAAEAEGV 101
                                       99999999999999999888887 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.22     164     236 ..     113     180 ..      75     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                                       -EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHHHHHH-EEES CS
                     NAD_binding_4 164 deraklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwingsdlgirgllgliakgvlpe 236
                                       d+++++ +  ++Y   Ka+a++ +r+      l  +ivRp+ +t+e  +G +   d  +++  g i ++ + +
  gi|336254029|ref|YP_004597136.1| 113 DDPESGPDALRDYLIAKAEADEYLRQSD----LSSTIVRPGELTTEDGSGELRAAD-SLEMASGDIPREDVAR 180
                                       5566666777899********9999876....899**********99999888888.6666666555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); 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 0.22s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1583.01
//
Query:       gi|336254030|ref|YP_004597137.1|  [L=348]
Description: Squalene/phytoene synthase [Halopiger xanaduensis SH-6]
Scores for 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-54  183.2   2.1    7.7e-54  182.9   2.1    1.1  1  SQS_PSY   Squalene/phytoene synthase
     0.0096   16.2   0.7      0.071   13.4   0.0    2.4  2  UPF0149   Uncharacterised protein family (UPF0149)


Domain annotation for each model (and alignments):
>> SQS_PSY  Squalene/phytoene synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.9   2.1   8.6e-58   7.7e-54       3     262 ..      23     316 ..      21     317 .. 0.86

  Alignments for each domain:
  == domain 1  score: 182.9 bits;  conditional E-value: 8.6e-58
                                       HH-HHHHHHHTTS-HHHHHHHHHHHHHHHHHT-.-----.........------------................. CS
                           SQS_PSY   3 aasksfylaslllppelRdalgalYafcreaddlvDdvseplqarar.ldwwrdavdavya................ 62 
                                        +s++f  ++  l +++ +++++ Y++cr+ad+++D  + p + +   l+++ + +d   a                
  gi|336254030|ref|YP_004597137.1|  23 GVSRTFSITIDRLEEPMSRHICVGYLLCRVADTIEDAGHIPPETQTDlLETYDRLLD-PDAeqpvdafmdevepwip 98 
                                       689************************************666666630444444444.4446888888888777777 PP

                                       ......---------THHHHHHHHHHHT.--HHHHHHHHHHTS--SS-........--SHHHHHHHHHHHHHHHHHH CS
                           SQS_PSY  63 .....edklkpprepvlralaqlirtyk.lpkellleliegmeadlef......tryetlddLeeYcyrvagvVgel 127
                                            +++  +++++vlr +  l ++ + +++e+++el++gm+++ ++       r++tl++LeeYc++ ag+Vg l
  gi|336254030|ref|YP_004597137.1|  99 dertdDWEVVAQTPRVLRTFDSLEEEPReIMREPVRELVDGMAMFTDRyadeggLRLQTLEELEEYCWYAAGTVGTL 175
                                       66554489999************998889******************977777777********************* PP

                                       HHHHH-S....S-HHHHHHHHHHHHHHHHHHHHHT---SH.HHHTT..S-HHHHHHHT--HHHHHHT-.-SHH.HHH CS
                           SQS_PSY 128 clrllgar...rsdralaeaarrlGkalQltnilRdvpeD.aergrvyLPadvlkefgvseedllrkgvrsae.lra 199
                                       ++ l+      +++r+++++ar++ + lQl+ni++dv  D  e+++vyLPa++l+e++v+ e++  ++ ++   + +
  gi|336254030|ref|YP_004597137.1| 176 ITGLVARGaseERAREMRDNARSFALLLQLVNIAKDVEDDyREENNVYLPAEWLAEENVDAEAVT-HE-ANHGgVTN 250
                                       *****87555566699************************777788******************5.55.45566*** PP

                                       HHHHHHHHHHHHHHHHHHTGGGS.-H..HHHHHHHHHHHHHHHHHHHHHHTTT-.TTT------HH CS
                           SQS_PSY 200 llrrlaerArelldearellkqlpdr..rarpalllavalyrailerieaadyd.vlsrrvklsll 262
                                       +++r++ rA+ +ld+a+++l+ +p+r  ++  a+++++ l+  ++++++++++d v+ + vk+s+ 
  gi|336254030|ref|YP_004597137.1| 251 VIKRVTNRAETYLDDAQRYLEIVPERhgNRLSAWAIPFLLAVGTMRELQNRPEDvVREGDVKVSRA 316
                                       **********************98553377889999******************5555****9985 PP

>> UPF0149  Uncharacterised protein family (UPF0149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2     0.057   5.1e+02     121     156 ..     129     163 ..      65     224 .. 0.66
   2 !   13.4   0.0     8e-06     0.071      38     115 ..     225     298 ..     219     344 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.057
                                       SSHHHHHHHHHHHHHCT---TTTS-SSHHHHHHHHH CS
                           UPF0149 121 sseelaelLedlaalarleiaeeeeedeedeealee 156
                                         e ++el++ +a++++  + +e     +++e+lee
  gi|336254030|ref|YP_004597137.1| 129 MREPVRELVDGMAMFTDRYA-DEGGLRLQTLEELEE 163
                                       44666666666666666662.333333333333333 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8e-06
                                       CCCHHHHCCCC.......STCHHHHHHHHHHHHHHHHHHCTTTTS------S-HHHHHHHHHHHHHHHHHHHHHCTT CS
                           UPF0149  38 peeWlpallgeapafsdeeegeallallkrlyneiaaqLadedefefellledladraeplaeWceGFlqGlglagd 114
                                       p+eWl++   +a+a+++e+ +  +++ +kr+ n+ ++ L+d++ + +e + e   +    l++W+  Fl ++g++++
  gi|336254030|ref|YP_004597137.1| 225 PAEWLAEENVDAEAVTHEANHGGVTNVIKRVTNRAETYLDDAQRY-LEIVPE---RHGNRLSAWAIPFLLAVGTMRE 297
                                       789999988888999999999999*****************6543.333333...3445567**********99997 PP

                                       T CS
                           UPF0149 115 d 115
                                        
  gi|336254030|ref|YP_004597137.1| 298 L 298
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2797.50
//
Query:       gi|336254031|ref|YP_004597138.1|  [L=431]
Description: hypothetical protein Halxa_2642 [Halopiger xanaduensis SH-6]
Scores for 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   13.3   0.6       0.45   10.8   0.1    2.1  2  Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen


Domain annotation for each model (and alignments):
>> 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 ?   10.8   0.1   2.5e-05      0.45      40     113 ..      46     118 ..      24     119 .. 0.89
   2 ?    0.2   0.1     0.049   8.7e+02      56      93 ..     148     179 ..     142     187 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.5e-05
                       Myco_19_kDa  40 asgvsavlt.dgdeptvesvgigdvdGftltyaegtgggsaevtkdgntYtitGtaegadsanpaqpvtktFeie 113
                                       ++++ ++++ dgd+  +e v ++d    + +y e+  + + ev  +g+ Y++ G+++    a ++++vt t+ +e
  gi|336254031|ref|YP_004597138.1|  46 PGTLDVYVDgDGDSRWIERVPVNDS--AADRYRENATALEREVDPTGTYYHVVGEGVDRTIALENGTVTVTYAVE 118
                                       6788999**99***********999..58899999988779*****************99999999999999886 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.049
                       Myco_19_kDa  56 esvgigdvdGftltyaegtgggsaevtkdgntYtitGt 93 
                                       + v+i + +G   t+ +++++g   +t+dgnt t  G+
  gi|336254031|ref|YP_004597138.1| 148 DRVTIHTPEG---TVVTNDPSG---ATVDGNTATWDGE 179
                                       5677777744...444444444...5666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.36
# Mc/sec: 3543.93
//
Query:       gi|336254032|ref|YP_004597139.1|  [L=414]
Description: aspartate transaminase [Halopiger xanaduensis SH-6]
Scores for 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-68  229.6   0.0    7.2e-68  229.4   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    2.2e-12   46.6   0.0    7.1e-11   41.7   0.0    2.1  2  Aminotran_5      Aminotransferase class-V
    1.5e-08   34.4   0.4    2.5e-08   33.6   0.4    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    3.4e-05   22.5   0.0    6.5e-05   21.6   0.0    1.5  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0025   17.7   0.2       0.29   10.9   0.1    2.5  2  CPT              Chloramphenicol phosphotransferase-like prot
     0.0045   16.3   0.0     0.0079   15.5   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.019   13.8   0.0      0.047   12.5   0.0    1.7  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase


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 !  229.4   0.0   2.8e-71   7.2e-68       2     362 ..      50     402 ..      49     403 .. 0.95

  Alignments for each domain:
  == domain 1  score: 229.4 bits;  conditional E-value: 2.8e-71
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       d++ L  +e+++d    t+++v++a+ e  +a +++++y+ + g p+l+ea+a+ l+++   ++++++++vv++G  
  gi|336254032|ref|YP_004597139.1|  50 DLVHLEFGEPDFD----TPDHVVEAAVE--AARNGATNYTSNAGMPKLREAIAETLSSERDRPVDPNSEIVVTNGGV 120
                                       6788999******....*********99..9**************************99****************** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       +++ ++i +  ++pgdei+vp+p +++ +  ++l+++  v++p+   e+f+ d e + +a+         t  +l++
  gi|336254032|ref|YP_004597139.1| 121 EALHLAIHAV-ADPGDEIVVPTPAWPNPISQAKLADAVPVEVPMPADEGFEPDPERIVDAIGP------DTAAVLLT 190
                                       **********.9**************************************************9......889***** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSS..HTHHHHGGSTTSTTEEEEEESSSTTSSGGG-E CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsl..davatranveeepnllivgslsKafGlaGeRv 230
                                       sp+NPtG v++ e +e +++ a  ++++++ De+Y ++++++l  +av++    e+++++l  +s+sK ++++G+Rv
  gi|336254032|ref|YP_004597139.1| 191 SPSNPTGRVFPAEAVERVVAAAADRGAYVIADEVYRELAYEELppRAVSLAERNERDDWVLSINSCSKTYAMTGWRV 267
                                       *****************************************997777775666666666****************** PP

                                       EEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSC CS
                     Aminotran_1_2 231 Gyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqs 304
                                       G+++g ++v+sq++ ++ + +s   +++q+a+ +al  +++    ++em++ + +rr++++d+L+++  ++  ++++
  gi|336254032|ref|YP_004597139.1| 268 GWLSGPEDVLSQVETIHESTTScvNTPAQYAAIEALTGPQE---PFDEMQAAFRERRDYVVDRLESIpRVAAAEPEG 341
                                       *****************9999999****************7...8******************************** PP

                                       SSEEEEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 305 gmflltdlsae..takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                       +++ ++d+sa+  + +e++k Ll  + v+  pgt f++  +g+lR+++ + + + le  +++
  gi|336254032|ref|YP_004597139.1| 342 AFYAFVDMSALegSSTEVAKRLLYDHEVVAAPGTAFGAggEGHLRLSF-ANDMARLETGLDR 402
                                       ***********9*99*********************************.7788888877776 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   2.8e-14   7.1e-11      58     177 ..     107     224 ..      62     229 .. 0.74
   2 ?    2.9   0.0     0.017        43     256     363 ..     291     393 ..     260     398 .. 0.73

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 2.8e-14
                                       -STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHH CS
                       Aminotran_5  58 aeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelek 134
                                       ++ ++ei++t G+ ea+ l+++++    +pgdeivv  +  + n +  ++la++  ++v  +p+de+ e d++++ +
  gi|336254032|ref|YP_004597139.1| 107 VDPNSEIVVTNGGVEALHLAIHAV---ADPGDEIVVP-TPAWPNPISQAKLADAVPVEV-PMPADEGFEPDPERIVD 178
                                       45679*******************...89*****986.567888878888888888888.89*************** PP

                                       H--TTEEEEEEESBETTTTEB--HHHHHH...HHHHTT-EEEEE-T CS
                       Aminotran_5 135 llnektklvaithvsnvtGtiqpveeigk...lakkkgalvlvDaa 177
                                       ++ ++t++v +t  sn tG ++p e++ +   +a ++ga+v++D +
  gi|336254032|ref|YP_004597139.1| 179 AIGPDTAAVLLTSPSNPTGRVFPAEAVERvvaAAADRGAYVIADEV 224
                                       *********************9977665510055667999999976 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHH..HCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEE.TTCSHHHHHHHHH CS
                       Aminotran_5 256 agiiglgaaleyl..eeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnf.kgvhaedvatlLd 329
                                       ++  +  aa+e l   +  ++++++  +e ++y+++rl+s+p v  ++  ++ +  + v ++  +g ++e  ++lL 
  gi|336254032|ref|YP_004597139.1| 291 VNTPAQYAAIEALtgPQEPFDEMQAAFRERRDYVVDRLESIPRVAAAE--PEGAFYAFVDMSAlEGSSTEVAKRLLY 365
                                       555555566666654577899**********************99944..567777777776634455555555666 PP

                                       HTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS CS
                       Aminotran_5 330 eegIavrsGhhcaqplmkrlalegtvRaSlyiyn 363
                                       ++++    G +         + eg +R+S+++ +
  gi|336254032|ref|YP_004597139.1| 366 DHEVVAAPGTAFG------AGGEGHLRLSFANDM 393
                                       6677777787777......666677777777665 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 !   33.6   0.4   9.7e-12   2.5e-08      41     144 ..     113     222 ..     107     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 9.7e-12
                                       EEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTT.SSB-GGGCGGG--TTEEEEE CS
                   DegT_DnrJ_EryC1  41 aiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdt.ynidpaaieaaitertkaIl 116
                                        + ++ G +Alhla++a+  +pgde++vp+  +   ++ +  + a+pv v + +d  + +dp++i  ai + t+a+l
  gi|336254032|ref|YP_004597139.1| 113 IVVTNGGVEALHLAIHAVA-DPGDEIVVPTPAWPNPISQAKLADAVPVEVPMPADEgFEPDPERIVDAIGPDTAAVL 188
                                       5778999**********85.78****************************997765389*****************9 PP

                                       ...EB-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 117 ...pVhlyGqva...dmdalkaiaakhglkvieD 144
                                          p +  G+v+    ++++ a aa+ g +vi D
  gi|336254032|ref|YP_004597139.1| 189 ltsPSNPTGRVFpaeAVERVVAAAADRGAYVIAD 222
                                       3334467899883334555556688888888887 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 !   21.6   0.0   2.5e-08   6.5e-05      69     175 ..     112     224 ..      67     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.5e-08
                                       EEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST....TSHHHHHHHCCTTEEEE CS
                   Cys_Met_Meta_PP  69 aalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt....sdleelekaikentklv 141
                                       + ++++ G+ A+++ai a++  Gdeivv + ++    ++ k ++  + +ev +        d+e++  ai + t +v
  gi|336254032|ref|YP_004597139.1| 112 EIVVTNGGVEALHLAIHAVADPGDEIVVPTPAWPNPISQAK-LADAVPVEVPMPADegfePDPERIVDAIGPDTAAV 187
                                       56899****************************98766643.455555555543332344799************** PP

                                       EEESS-TTTT----...HHHHHHHHHHTT-EEEEEGT CS
                   Cys_Met_Meta_PP 142 ylEtptnpllkvvD...iekiaklakkagvlvvvDnt 175
                                       +l +p+np+ +v     +e+++++a ++g+ v+ D +
  gi|336254032|ref|YP_004597139.1| 188 LLTSPSNPTGRVFPaeaVERVVAAAADRGAYVIADEV 224
                                       **********998622266677777777899999976 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.013        34      66      89 ..     117     140 ..      80     163 .. 0.68
   2 !   10.9   0.1   0.00011      0.29      69      94 ..     202     227 ..     163     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHHHTT-EEEEE CS
                               CPT  66 dlllaalyeavaamaraGnnvivD 89 
                                       +  ++al+ a++a+a+ G +++v 
  gi|336254032|ref|YP_004597139.1| 117 NGGVEALHLAIHAVADPGDEIVVP 140
                                       345789****************96 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHTT-EEEEEE--TT CS
                               CPT  69 laalyeavaamaraGnnvivDdvile 94 
                                       ++a+ + vaa a+ G+ vi+D+v+ e
  gi|336254032|ref|YP_004597139.1| 202 AEAVERVVAAAADRGAYVIADEVYRE 227
                                       57999******************976 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.1e-06    0.0079      15     167 ..      68     222 ..      62     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-06
                                       HHHH.HCS----CCCT--HHHHHHHHHHHHHTT-SEEEE.........ES-HHHHHHHHHHHH--TTEEEEEETT-H CS
                   Beta_elim_lyase  15 sdaq.aaamlGdesYgedktvnrLedavaelfgkeaalf.........vpqGtaAnsillkillqrgeevivtepah 81 
                                       ++a   aa  G   Y  + ++ +L +a+ae +  e   +         +  G  A ++++ +++ +g+e++v  pa 
  gi|336254032|ref|YP_004597139.1|  68 VEAAvEAARNGATNYTSNAGMPKLREAIAETLSSERDRPvdpnseivvTNGGVEALHLAIHAVADPGDEIVVPTPAW 144
                                       455548999999******************888888888888888875677999*********************98 PP

                                       HHHSSTTHHHHCC--EEEEE-EBTT..TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHH CS
                   Beta_elim_lyase  82 ihfdetgaiaelagvklrdlknkea..GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaai 156
                                            +  +   a++ +++++ +++   + d+e++ +ai +      ++++++lt   n   G+v + e +++v a 
  gi|336254032|ref|YP_004597139.1| 145 PNPISQAKL---ADAVPVEVPMPADegFEPDPERIVDAIGP------DTAAVLLTSPSNP-TGRVFPAEAVERVVAA 211
                                       777766555...55555555555542267888888888888......4778888888884.8*************** PP

                                       HHHCT-EEEEE CS
                   Beta_elim_lyase 157 akkygiplhlD 167
                                       a ++g  ++ D
  gi|336254032|ref|YP_004597139.1| 212 AADRGAYVIAD 222
                                       *****999887 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.8e-05     0.047      64     276 ..      81     283 ..      68     386 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                                       SSS-TT--HHHHHHHHHHTTS-GGGEEE-SS-HHHHHHHHHHHHHHC--TT-SS-GGGG.--EEEEEES--HHHHHH CS
                    Aminotran_MocR  64 nyGGlaGlpelralfaelldvkaenvlvqnnsslelqglvltlallhGvrdsegpwvkeekvkllvtvpGydrhfll 140
                                       ny   aG+p+lr   ae l  + ++  v  ns + + +  +    lh    +    v+++   ++v++p +      
  gi|336254032|ref|YP_004597139.1|  81 NYTSNAGMPKLREAIAETLSSERDR-PVDPNSEIVVTNGGVE--ALHLAIHA----VADPGDEIVVPTPAWPNPISQ 150
                                       6666777777777777776655443.4455555544433322..22222222....222233466777777666666 PP

                                       HHHHT-EEEEEEEETT.E..E-HHHHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT---SSTT-EEEEE- CS
                    Aminotran_MocR 141 leelGielltvdlqdd.G..pdvdaveklvaedasvkGilavpkysnptGetiseevarrlaalkaaapdfrifadd 214
                                        +      + v++  d G  pd + +   ++ d++   +l+ p  snptG ++ +e + r++a  a      + ad+
  gi|336254032|ref|YP_004597139.1| 151 AKLADAVPVEVPMPADeGfePDPERIVDAIGPDTAA-VLLTSP--SNPTGRVFPAEAVERVVAAAA-DRGAYVIADE 223
                                       555555566677765533447777777777777664.244444..9**************998544.44456789** PP

                                       TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTT.S-TTSS-EEEEE-HHHHHHHHHH CS
                    Aminotran_MocR 215 ayavhdlvaeedkdanivalardaGhpdrafvlastski.tfaGaGvafvassedniawlkky 276
                                        y+  +    e+  +  v+la+     d  + + s sk  +++G  v+ ++  ed +++++  
  gi|336254032|ref|YP_004597139.1| 224 VYRELAY---EELPPRAVSLAERNERDDWVLSINSCSKTyAMTGWRVGWLSGPEDVLSQVETI 283
                                       **96444...66777899999999999999999999994255666788888888877776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.38
# Mc/sec: 3306.00
//
Query:       gi|336254033|ref|YP_004597140.1|  [L=286]
Description: 3-hydroxybutyryl-CoA dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-60  201.9   0.0    9.3e-60  201.6   0.0    1.1  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    3.5e-32  110.9   0.0    1.1e-31  109.3   0.0    1.8  2  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
    0.00037   20.7   0.3    0.00081   19.6   0.2    1.7  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00099   19.1   0.0     0.0015   18.5   0.0    1.3  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
     0.0057   17.2   1.8      0.032   14.8   0.7    2.5  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.091   12.1   0.1       0.16   11.3   0.1    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
       0.11   12.1   0.2       0.55    9.8   0.1    2.0  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,


Domain annotation for each model (and alignments):
>> 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 !  201.6   0.0   3.6e-63   9.3e-60       2     175 ..       9     181 ..       8     186 .. 0.98

  Alignments for each domain:
  == domain 1  score: 201.6 bits;  conditional E-value: 3.6e-63
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavd 78 
                                       ++v+GaGtmG+gia+v+a  g++V++ d++ee++e++ e+i++sle+l+++  l+ e+ e++  ri+ ttdle+++d
  gi|336254033|ref|YP_004597140.1|   9 IGVVGAGTMGSGIAQVAATGGYDVRMRDVEEEFVESGFESIRESLERLENRDDLE-EDPETIRGRIEGTTDLEAFAD 84 
                                       89***************************************************99.99******************* PP

                                       -SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT- CS
                           3HCDH_N  79 adlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekT 155
                                       +dlv+Eav E+l++Kr+vfa+le+++++d+ la+nTS+lsi+ +a++l++perviglHF+nP+p+m+ vEvv gekT
  gi|336254033|ref|YP_004597140.1|  85 CDLVVEAVLEDLDVKREVFADLERVCDDDVPLATNTSTLSITSIAADLEHPERVIGLHFMNPVPIMEGVEVVVGEKT 161
                                       ***************************************************************************** PP

                                       -HHHHHHHHHHHHHTT-EEE CS
                           3HCDH_N 156 seetvatvvelakkigktpv 175
                                       s+e+++ ++++a++++kt+ 
  gi|336254033|ref|YP_004597140.1| 162 SDEATDLAHRIAEDLEKTTW 181
                                       *****************975 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.8   7.1e+03      51      83 ..      13      44 ..       5      52 .. 0.51
   2 !  109.3   0.0   4.2e-35   1.1e-31       1      97 []     188     283 ..     188     283 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.8
                                      HHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHT CS
                             3HCDH 51 gldvakkilevlaeelgerayapsplleklvea 83
                                      g +++ + +  +a++ g  +++  ++ e++ve+
  gi|336254033|ref|YP_004597140.1| 13 GAGTMGSGIAQVAATGGY-DVRMRDVEEEFVES 44
                                      444444444333333333.33334566666555 PP

  == domain 2  score: 109.3 bits;  conditional E-value: 4.2e-35
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GFv+nR+l+p++ne +r+++egva   diD+ m+lg+++pmGp++l+d +gldv+++++e+l+eelg+r y+p+ ll
  gi|336254033|ref|YP_004597140.1| 188 GFVTNRILMPWINEGIRAFDEGVAAKGDIDRGMELGTNVPMGPLRLADHIGLDVCLHASETLHEELGDR-YQPAYLL 263
                                       9*******************************************************************9.8899*** PP

                                       HHHHHTT--BGGGTBSSSBC CS
                             3HCDH  78 eklveagrlgrktgkgfyky 97 
                                       ++ veag+lg+ktgkgfy+y
  gi|336254033|ref|YP_004597140.1| 264 KRKVEAGDLGKKTGKGFYEY 283
                                       ******************98 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 !   19.6   0.2   3.1e-07   0.00081       1      73 [.       8     102 ..       8     145 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.1e-07
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.......................EEE-SSHHHHHH CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.......................akaaesieelva 54 
                                       +ig++G G+MGs +a+  +  gy+v + ++++e ve+  ++                        +++++++e ++a
  gi|336254033|ref|YP_004597140.1|   8 RIGVVGAGTMGSGIAQVAATGGYDVRMRDVEEEFVESGFESIreslerlenrddleedpetirgrIEGTTDLE-AFA 83 
                                       59***************************99877776655544555555566666666666665444444443.444 PP

                                       HCSEEEE-SSSHHHHHHHH CS
                     NAD_binding_2  55 sldvvitmvkagkavdevi 73 
                                       ++d+v+  v ++ +v+  +
  gi|336254033|ref|YP_004597140.1|  84 DCDLVVEAVLEDLDVKREV 102
                                       5566666665555555555 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 !   18.5   0.0   5.9e-07    0.0015       2      98 ..       9     115 ..       8     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.9e-07
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-H.......HHHHHHHHHSSBTTTBTT..----TTEEEES-HHHHHTT CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvree.......elieeineehenvkyLpg..iklpenlvattdlaealkg 69 
                                       i+v+GaG  G+ +A+v a  g +vr+   ee       e i+e  e+ en + L++   ++   ++ ttdl+ a ++
  gi|336254033|ref|YP_004597140.1|   9 IGVVGAGTMGSGIAQVAATGGYDVRMRDVEEefvesgfESIRESLERLENRDDLEEdpETIRGRIEGTTDLE-AFAD 84 
                                       89**************************9999999888777777788899999987556889999999**96.6777 PP

                                       --EEEE---H..HHHHHHHHHHCCC--TT-E CS
                    NAD_Gly3P_dh_N  70 adiivlvvPs..qalrevlkklkgllkkkai 98 
                                       +d++v +v     + rev+++l+ + +++++
  gi|336254033|ref|YP_004597140.1|  85 CDLVVEAVLEdlDVKREVFADLERVCDDDVP 115
                                       9999999965124567777777777666655 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 !   14.8   0.7   1.2e-05     0.032       1      69 [.       8      92 ..       8      97 .. 0.72
   2 ?   -1.1   0.0       1.2     3e+03      27      49 ..     154     175 ..     149     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....................-EEECECHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....................vkvtavdneeaa 59
                                      +ig++GaG mg+++a+ +++ g   ++++   + ++e +e+  e++                      ++++++  ea 
  gi|336254033|ref|YP_004597140.1|  8 RIGVVGAGTMGSGIAQVAATGG---YDVR-MRDVEEEFVESGFESIReslerlenrddleedpetirGRIEGTTDLEAF 82
                                      79**************999999...6666.3355555555444444444445558888888888888777777788888 PP

                                      HH-SEEEE-S CS
                     F420_oxidored 60 eeadvvvlav 69
                                      +++d vv av
  gi|336254033|ref|YP_004597140.1| 83 ADCDLVVEAV 92
                                      8888887665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                                       CEEEEEESSCCCHHHHHHHHC-E CS
                     F420_oxidored  27 eivvansrnpekaeelaeelgvk 49 
                                       e+vv+ +++ ++a+ la ++  +
  gi|336254033|ref|YP_004597140.1| 154 EVVVG-EKTSDEATDLAHRIAED 175
                                       78877.99999999999887644 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 ?   11.3   0.1   6.3e-05      0.16      38      70 ..       8      40 ..       5      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.3e-05
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                                      ++G++G+G +G+ +a++++  g +v + d+ ++
  gi|336254033|ref|YP_004597140.1|  8 RIGVVGAGTMGSGIAQVAATGGYDVRMRDVEEE 40
                                      79***********************99998855 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 ?    9.8   0.1   0.00021      0.55       2      81 ..       8      89 ..       7     107 .. 0.74
   2 ?   -0.3   0.0      0.27     7e+02     136     173 ..     103     140 ..      89     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00021
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHH....HCTTS-SS--T.THHHHHHHHCHTTTEEEES-HHHHHH CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdk....lnsgkipiyep.gLeelvkkavesgrlsfttdvekave 75
                                      +i v+G+G +G   a v a  g +v + D++ee v++    ++++   ++++ +Lee  ++ +  gr+++ttd+e  ++
  gi|336254033|ref|YP_004597140.1|  8 RIGVVGAGTMGSGIAQVAATGGYDVRMRDVEEEFVESgfesIRESLERLENRdDLEEDPETIR--GRIEGTTDLEA-FA 83
                                      89******************************9998521113333333333224555555555..78888888876.77 PP

                                      C-SEEE CS
                    UDPG_MGDP_dh_N 76 eadvif 81
                                      ++d+++
  gi|336254033|ref|YP_004597140.1| 84 DCDLVV 89
                                      777766 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.27
                                       HHHHCSS-TTCEEEEE------TTSHHHHHHS-S-EEE CS
                    UDPG_MGDP_dh_N 136 leeaskkkgvdfdvvsnPEflregsavkdllnpdrvvi 173
                                        ++ ++  + d+ +++n   l   s+  dl +p+rv++
  gi|336254033|ref|YP_004597140.1| 103 FADLERVCDDDVPLATNTSTLSITSIAADLEHPERVIG 140
                                       5555555577888899999999999999*******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2204.43
//
Query:       gi|336254034|ref|YP_004597141.1|  [L=345]
Description: hypothetical protein Halxa_2645 [Halopiger xanaduensis SH-6]
Scores for 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-25   87.9   0.0    1.1e-24   87.5   0.0    1.1  1  Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family
    4.1e-08   33.8   0.1      6e-08   33.3   0.1    1.2  1  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
  ------ inclusion threshold ------
      0.075   12.8   0.0       0.12   12.2   0.0    1.2  1  GxDLY          N-terminus of Esterase_SGNH_hydro-type


Domain annotation for each model (and alignments):
>> 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 !   87.5   0.0   1.9e-28   1.1e-24       2     176 ..     158     338 ..     157     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 1.9e-28
                     Lipase_GDSL_3   2 kpivvYGsSitqGasasRpglaytailsrklgrevvnLgfsGnalleaeladvlaevda.svfvldllpN....asa 73 
                                       ++ + YG+Sit+G ++s   l+y+ +++r+l+++++nLg  G a  +a++ad +a+ d  +v+ l + +N    +sa
  gi|336254034|ref|YP_004597141.1| 158 RRYLAYGTSITEGEAPSAEHLTYVGQTARRLDADLINLGSCGTAYCDAAIADHIAARDDwDVATLSISVNmvgtFSA 234
                                       66789***************************************************9999***********9999** PP

                     Lipase_GDSL_3  74 eeirerleyfvktlrkahPktpi....llvedlsttkglvdeklekeveaknkaleelvkklkkekekklylisske 146
                                       +e+rer++ +v+ +++ahP++p+    ++ +  + ++g  +   ++e e++++ l+ +v +     + +++l+++ e
  gi|336254034|ref|YP_004597141.1| 235 DEFRERAARMVECVASAHPEKPVvpitIFRNGWDVSQGASESGDADECERFREELRAVVDQT---PHDNVHLLEGPE 308
                                       **********************9333335555666666666666777777777777777776...7899******** PP

                     Lipase_GDSL_3 147 llgkdeeatvdgiHpsdlGllryadaleev 176
                                       ll + e  t+d +Hp d  ++ + ++l   
  gi|336254034|ref|YP_004597141.1| 309 LLPTIEGLTTDLVHPGDNAMITMGEHLAAE 338
                                       ********************9999998765 PP

>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.1     1e-11     6e-08       1     174 [.     162     325 ..     162     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1e-11
                                       EEESHHHHTCTTBCCHCHHCCCCCCCHHHTT-EEEEE.EEHCCH-H..HHHHHHHHCTGGG-TSEEEEE--CCCCCT CS
                     Lipase_GDSL_2   1 alGDSiTaGygadgggrsypaylarllaarlgldvvnnlgvsGattallrllerlrdllrlkpdlvtiliGtNDlgr 77 
                                       a+G SiT+G  +++++ +y + +ar+l a l    +n lg  G+   ++++++++   +r ++d+ t++i +N +  
  gi|336254034|ref|YP_004597141.1| 162 AYGTSITEGEAPSAEHLTYVGQTARRLDADL----IN-LGSCGTAYCDAAIADHIA--ARDDWDVATLSISVNMV-G 230
                                       6899*****9877777888888777777777....88.999999998889999888..8999***********98.5 PP

                                       T--HHHHHHH..HHHHHHHHCCC...GEEECEEEEE-TTT-TTSTCC..HHHHHHHHHHHHHHHHHH...CT-EEE- CS
                     Lipase_GDSL_2  78 gvpaaaaaandnleelidalraaapgarilvlgplpptpeaaadare..lnaviaaynealrevaae...egvpfvD 149
                                         +a++++++   +++++ + +a+p+ +++ ++++ ++   ++ a e   ++  ++++e lr+v ++   ++v+++ 
  gi|336254034|ref|YP_004597141.1| 231 TFSADEFRER--AARMVECVASAHPEKPVVPITIFRNGWDVSQGASEsgDADECERFREELRAVVDQtphDNVHLLE 305
                                       5566666777..89****9999********66666666666666666557889999999999999996666666666 PP

                                       HHHHHHHCCCCCGGBBTTS.SSB-H CS
                     Lipase_GDSL_2 150 lhdaladsgerladlladdglHPna 174
                                             ++  +  ++l++d +HP +
  gi|336254034|ref|YP_004597141.1| 306 G-----PELLPTIEGLTTDLVHPGD 325
                                       6.....5555566666666699976 PP

>> GxDLY  N-terminus of Esterase_SGNH_hydro-type
   #    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      23      57 ..      25      59 ..       8      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2e-05
                             GxDLY 23 YeRlpteakkkvrkevwnlsknsaGlavrFktnss 57
                                       +R+p+++++++++  +++ ++ aG+ +rF  + +
  gi|336254034|ref|YP_004597141.1| 25 LQRVPEAIRRELNEGAQSRMRHPAGVELRFVPDGP 59
                                      69****************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2758.80
//
Query:       gi|336254035|ref|YP_004597142.1|  [L=254]
Description: hypothetical protein Halxa_2646 [Halopiger xanaduensis SH-6]
Scores for 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   15.0   0.1        0.1   13.2   0.1    1.9  1  HHH_5            Helix-hairpin-helix domain
       0.04   14.1   0.0      0.071   13.3   0.0    1.4  1  DUF4332          Domain of unknown function (DUF4332)
      0.096   12.5   0.0       0.22   11.4   0.0    1.6  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
       0.47   11.3   4.0       0.16   12.8   0.9    1.7  2  DUF3306          Protein of unknown function (DUF3306)


Domain annotation for each model (and alignments):
>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.3e-05       0.1       5      32 ..     200     227 ..     198     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                                       HTSTT--HHHHHHHHTTT--SHHHHHHS CS
                             HHH_5   5 lsvsGiGpktAlallsaGiesvedlaaa 32 
                                       + v G+Gp +A +l++aG+ s e la  
  gi|336254035|ref|YP_004597142.1| 200 TAVTGVGPDDAETLAEAGVVSAERLATI 227
                                       6899*******************99874 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.6e-05     0.071      57      92 ..     201     236 ..     191     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                           DUF4332  57 rikgigeeyaeLLeaaGvdsvaeLaqrnpanLhqkl 92 
                                       ++ g+g+ +ae L +aGv s++ La+ n+ ++ ++l
  gi|336254035|ref|YP_004597142.1| 201 AVTGVGPDDAETLAEAGVVSAERLATINAFEVAKAL 236
                                       688999999999999999999999998887766655 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 ?   11.4   0.0   4.8e-05      0.22       4      30 ..     200     226 ..     199     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.8e-05
                   DNA_pol_lambd_f   4 tkvyGVGpktAkkwyakGirtledlra 30 
                                       t v+GVGp  A+ + ++G+ + e l +
  gi|336254035|ref|YP_004597142.1| 200 TAVTGVGPDDAETLAEAGVVSAERLAT 226
                                       67*****************99998866 PP

>> DUF3306  Protein of unknown function (DUF3306)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.9   3.7e-05      0.16      51     109 ..      73     140 ..      37     144 .. 0.71
   2 ?   -1.5   0.1         1   4.5e+03      58      58 ..     187     187 ..     155     231 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                           DUF3306  51 e..........aeeaeaeeeletlpdvealtaesdfaaFlakgVseevkraALrklFadphfnvmdgld 109
                                       +          ++++ a+ e++++++ + l++e +++ +l +gV+e++   ALr+ F+ p + + dg d
  gi|336254035|ref|YP_004597142.1|  73 AaadgergrelEADERAALEAADVDPDAVLEKEYSYRMLLDEGVAEST-ADALRRRFSLPWSFEGDGDD 140
                                       122233455568999999******99999****************997.689*****988777666655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1
                           DUF3306  58 e 58 
                                       e
  gi|336254035|ref|YP_004597142.1| 187 E 187
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1822.35
//
Query:       gi|336254036|ref|YP_004597143.1|  [L=279]
Description: deoxyribose-phosphate aldolase/phospho-2-dehydro-3-deoxyheptonate aldolase [Halopiger xanaduensis SH-6]
Scores for 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-41  143.1   0.0    1.2e-41  142.9   0.0    1.1  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 !  142.9   0.0   6.8e-46   1.2e-41       2     235 .]      16     236 ..      15     236 .. 0.94

  Alignments for each domain:
  == domain 1  score: 142.9 bits;  conditional E-value: 6.8e-46
                                       EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTE CS
                              DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqr 78 
                                       +ila+D++ ++++++++ + +   d+ ++++ a+  +  a+++++g++  +   y+ d+ ll+kl+ +      + +
  gi|336254036|ref|YP_004597143.1|  16 LILAMDHGLEHGPVDFE-EVPEKLDPSTVFETATHDAVTAMAVQKGIAEGYYPSYEDDVNLLAKLNGTSNMWMGEPD 91 
                                       59*************99.678999******************************************98888888844 PP

                                       EEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHH CS
                              DeoC  79 dvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvae 155
                                          + +sv  a + GAda++++vy    gs  e ++++e++ v+e+++e++lp++++ y+r++  k++  +p  +  
  gi|336254036|ref|YP_004597143.1|  92 SA-VNWSVDYAAEVGADAIGFTVYS---GSNHEVEMFEEFRDVQEKAREYDLPVVMWSYPRGQGLKNDT-KPGTISY 163
                                       44.6*********************...****************************************9.******* PP

                                       HHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS..SHHHHHHHHHHHHHHHTHCEEEESH CS
                              DeoC 156 AarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv..seedfletvedAvkeagasGvlsGR 230
                                       A+r++ elGaDi Kv++p       +e+ ++ +++++++    vv+sGG+  s+ dfl+tve Av +aga G+++GR
  gi|336254036|ref|YP_004597143.1| 164 ATRIGLELGADIAKVKYP-----GDPEAMAHACKAAGDM--N-VVMSGGSktSDYDFLSTVEAAV-DAGAKGLAVGR 231
                                       ******************.....7788888888888866..4.99********************.*********** PP

                                       HHHTT CS
                              DeoC 231 aifqk 235
                                       +++q+
  gi|336254036|ref|YP_004597143.1| 232 NVWQR 236
                                       ***95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2144.83
//
Query:       gi|336254037|ref|YP_004597144.1|  [L=291]
Description: Fructose-1,6-bisphosphatase class 1 [Halopiger xanaduensis SH-6]
Scores for 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-28   97.8   0.1      8e-28   97.2   0.1    1.2  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain
     0.0054   16.3   0.0     0.0075   15.8   0.0    1.2  1  Inositol_P  Inositol monophosphatase family


Domain annotation for each model (and alignments):
>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.1   8.9e-32     8e-28      50     177 ..      33     154 ..       7     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 8.9e-32
                            FBPase  50 lagaeNvtGdeqkklDvladeiliealkaseevkvlvSEEeeelivlere...kegkyvvafDPlDGSSnidtnvsv 123
                                          +eN tGd q + Dv ad++l + l + e v   +SEE+ e+++ ++     +g y+va+DPlDGSSn++ n ++
  gi|336254037|ref|YP_004597144.1|  33 VEESENPTGDTQLEADVWADDLLGDRLASLEGVGQYASEERAEVVDCGGDpeaDDGVYAVAVDPLDGSSNLESNNAM 109
                                       34679******************************************7651114678******************** PP

                            FBPase 124 GtifsiyrkksedeettidvlqpGkeqvAAgyvvYGsstmlVltlgaGvngFtl 177
                                       Gtif++y           ++   G+ +vAAgyv+YG+ t+lV+++++ v ++ l
  gi|336254037|ref|YP_004597144.1| 110 GTIFGVYD---A------ALPARGERLVAAGYVLYGPITTLVIATEETVAEYEL 154
                                       *******9...2......234579************************999877 PP

>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.4e-07    0.0075      11      98 ..      14     102 ..       4     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.4e-07
                                       HHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCC...CT.SSSS CS
                        Inositol_P  11 elaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakge...kselted 84 
                                       ++ + a e+ +  ++ ++ ++ee++ +   d++ +ad ++++l+ ++la      +  +ee  +  +   + e ++ 
  gi|336254037|ref|YP_004597144.1|  14 TIGRSATEIRQGLIG-RRGAVEESE-NPTGDTQLEADVWADDLLGDRLASLEGVGQYASEERAEVVDcggDPEADDG 88 
                                       445566777777776.888888777.99*********************************9999999988888888 PP

                                       SEEEEEEEEETHHH CS
                        Inositol_P  85 gltwivDPiDGTkn 98 
                                        + + vDP+DG +n
  gi|336254037|ref|YP_004597144.1|  89 VYAVAVDPLDGSSN 102
                                       899********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); 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 0.22s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2138.39
//
Query:       gi|336254038|ref|YP_004597145.1|  [L=74]
Description: hypothetical protein Halxa_2649 [Halopiger xanaduensis SH-6]
Scores for 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  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 580.18
//
Query:       gi|336254039|ref|YP_004597146.1|  [L=391]
Description: hypothetical protein Halxa_2650 [Halopiger xanaduensis SH-6]
Scores for 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  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); 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:                         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 0.21s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 3172.34
//
Query:       gi|336254040|ref|YP_004597147.1|  [L=597]
Description: protionyl-CoA carboxylase [Halopiger xanaduensis SH-6]
Scores for 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-130  434.4   0.0   6.5e-130  434.1   0.0    1.0  1  Carboxyl_trans  Carboxyl transferase domain


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.1   0.0  3.6e-134  6.5e-130      14     493 ..     121     595 ..     101     596 .. 0.92

  Alignments for each domain:
  == domain 1  score: 434.1 bits;  conditional E-value: 3.6e-134
                                       EHTTSGGGEBEHHHHHHHHHHHHHHHHHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGCEEECHHHHHHH CS
                    Carboxyl_trans  14 idllldpgsFgeledlffhrvtelgrkkklprdgvvtgsGaviGravevvaqdktvlggslgpakgekllkaqeeai 90 
                                        ++l+++g F  ++d     + e+   ++lp+dg++tg  + +Gr v+++a+d tv+ gs+  + +ek l+ q++a+
  gi|336254040|ref|YP_004597147.1| 121 DEFLFEDGKFAAFDDWHPDGAGEET-DDRLPADGLITGAATFEGRDVHFMANDYTVKRGSMAAKGVEKFLRMQQRAL 196
                                       3578999999999988776555554.789************************************************ PP

                                       HHTEEEEEEEEE-ES.SSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHHTSEEEEETTEEEE CS
                    Carboxyl_trans  91 kagepligindsgGa.egriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpalgdrvimveetski 166
                                       k+g p++++ ds+G   +++   + +++g+Gk  ++ s +sg++pqi++++g+c++g+aY p ++d++imve+ s++
  gi|336254040|ref|YP_004597147.1| 197 KTGRPVLYLMDSSGGrIDQQTGFFANREGIGKYYYNHSMLSGRVPQICVLYGPCIAGAAYTPVFADFTIMVEGMSAM 273
                                       ************99966655555799*************************************************** PP

                                       ESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGGSS----ECSSGSS CS
                    Carboxyl_trans 167 fltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnresaPivetadepd 243
                                        +++p+++++v+g e+++ eelgG ++h+++sG a+l+aed+e+a el+ +l+ ylP   +n  e++P++e +++ +
  gi|336254040|ref|YP_004597147.1| 274 AIASPRMVQMVTG-EDIDLEELGGPQVHTRESGSADLVAEDEEHARELVARLITYLP---DNADETPPRREGVPPEK 346
                                       *************.*******************************************...55555999999988888 PP

                                       SH....HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--SEEETTEE-HHHHHH CS
                    Carboxyl_trans 244 rd..lieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetrveaGqvlfidsavK 318
                                           ++ +vP+ ++k yD+  vi+r+vdeg+++E++++y++++V++fAr++G+pvG+vAn++++ aG  +f+d+a+K
  gi|336254040|ref|YP_004597147.1| 347 SPagIDAVVPQRPNKGYDMTAVIERVVDEGSYFELQPEYGAEIVTAFARIDGRPVGIVANQPAKRAG-AIFPDAAEK 422
                                       878888*************************************************************.********* PP

                                       HHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEHHHHHTTTGGGSTTT CS
                    Carboxyl_trans 319 aarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayGGayvvmdskingad 395
                                       aa fi+ cda+n+Pl+ l d++Gf+ G+  e++gil +G k+++a + a+vP+ tv++rkayG++ ++m++++++++
  gi|336254040|ref|YP_004597147.1| 423 AAGFIWKCDAFNVPLLYLCDTPGFMAGSGVEKEGILEQGKKMIYATSAATVPQQTVVVRKAYGAGIYAMGGPAYDPE 499
                                       ***************************************************************************** PP

                                       TEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSHHHHHHTT CS
                    Carboxyl_trans 396 lvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargfaDavidpsetrakl 472
                                        v+a p+ +ia++gp+ a+++++ +++a+ +    +++++ +++l+e+ +e + + + a+  ++D++++ps +r++l
  gi|336254040|ref|YP_004597147.1| 500 SVIALPSGEIAIMGPDAAINAVYARKLAEIDDP--EERERQERELREAYREDIDVHRMASEVVIDEIVPPSTLREEL 574
                                       **************************9987733..33344555666666666************************* PP

                                       SSSEEEHGGGHHHHHHHHHHH CS
                    Carboxyl_trans 473 vialelewkkarklparkrrn 493
                                       +++ +++++ +++ p +k++ 
  gi|336254040|ref|YP_004597147.1| 575 AARFAFYEDVEKSVPSKKHGT 595
                                       ******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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 0.25s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 4417.00
//
Query:       gi|336254041|ref|YP_004597148.1|  [L=116]
Description: hypothetical protein Halxa_2652 [Halopiger xanaduensis SH-6]
Scores for 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:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 856.25
//
Query:       gi|336254042|ref|YP_004597149.1|  [L=207]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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   65.1   0.1    1.3e-17   64.8   0.1    1.1  1  Acetyltransf_3  Acetyltransferase (GNAT) domain
    0.00013   22.2   0.1    0.00018   21.7   0.1    1.2  1  Acetyltransf_1  Acetyltransferase (GNAT) family


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.1   1.4e-21   1.3e-17       1     134 [.      13     158 ..      13     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.4e-21
                    Acetyltransf_3   1 RLlLrplteeDleal..fel.rsdpevm...rylpe..pltleeaeewlerawaeeseeegygwaivlkdtg....v 65 
                                       RL L  l++e +++l  + +  sdp+++   +yl++  ++t+ ++ e+le++ ++ + ++g  ++i+ ++++    +
  gi|336254042|ref|YP_004597149.1|  13 RLRLEALRPESVDTLelYDIcSSDPDIEaitEYLTWdpHETPKDTLEFLEHMGEQYESNDGASYVIRPREDEdgasE 89 
                                       999****999777775246625688877443577778899**********9866777788999***76555345775 PP

                    Acetyltransf_3  66 .iGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvlek 134
                                         G+ g+  +++e +++ lg +l++ fwg+Gy  e ++a++e+af++l+le + + ++ +Ne+S r +ek
  gi|336254042|ref|YP_004597149.1|  90 iAGTGGFG-INWEKRTMTLGVWLRKRFWGRGYSGERAAAFVELAFDRLDLELVAVAAHVDNERSNRAIEK 158
                                       47777777.8888888****************************************************99 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   2.1e-08   0.00018      22     114 ..      61     158 ..      39     162 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-08
                                       HH....HHHHHHSTTC.EEEE..EEET.....TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHH CS
                    Acetyltransf_1  22 ee....feesfsleae.gllv..aeed.....geliGfisllkipdekggvayieslaVspeyrgkGlGsaLleale 86 
                                        e    ++es   +++ ++++     +      e++G+ ++ ++++   +++ + +++ ++ ++g+G+  +   a +
  gi|336254042|ref|YP_004597149.1|  61 LEhmgeQYES---NDGaSYVIrpR--EdedgaSEIAGTGGFGINWE---KRTMTLGVWLRKRFWGRGYSGERAAAFV 129
                                       2344333444...66635555642..32345556************...999999********************** PP

                                       HHHHHT.TESEEEEEEETTEHHHHHHHHH CS
                    Acetyltransf_1  87 eraree.gikkivlaveedndaairlYek 114
                                       e a+++  ++ + +a ++dn+++ r  ek
  gi|336254042|ref|YP_004597149.1| 130 ELAFDRlDLELVAVAAHVDNERSNRAIEK 158
                                       ******99999866777999999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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 0.20s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1635.60
//
Query:       gi|336254043|ref|YP_004597150.1|  [L=206]
Description: hypothetical protein Halxa_2654 [Halopiger xanaduensis SH-6]
Scores for 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   49.9   0.1    4.1e-13   49.3   0.1    1.2  1  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 !   49.3   0.1   2.3e-17   4.1e-13       2      77 ..      83     154 ..      82     157 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2.3e-17
                             bPH_2   2 rattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeela 77 
                                        +tt+++t +r++ rsG+l+ + + +ple +q+ + +q  ++r+ g+gt+ +e+aggs     l++ +v+d+  ++
  gi|336254043|ref|YP_004597150.1|  83 TRTTFAVTTHRIATRSGVLGVSVRAVPLECVQNTQRSQHAVGRLVGYGTVTVEVAGGS----DLRFWNVDDPGSIQ 154
                                       5899******************************************************....79999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1521.95
//
Query:       gi|336254044|ref|YP_004597151.1|  [L=213]
Description: hypothetical protein Halxa_2655 [Halopiger xanaduensis SH-6]
Scores for complete 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   60.6   0.0    2.1e-16   59.8   0.0    1.4  1  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 !   59.8   0.0   1.2e-20   2.1e-16       2      77 ..      68     141 ..      67     144 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1.2e-20
                             bPH_2   2 rattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeela 77 
                                        +t+y++t+r ++ ++G+l+r+   i + ++q++s++qs l+  +g+gt++i+taggs+  ve ++ sv+d+++++
  gi|336254044|ref|YP_004597151.1|  68 TNTHYVVTNRALYRKTGVLSRDVKRIEHGKVQDISYSQSALGAHFGYGTVEISTAGGSG--VEMAFKSVADPRAVQ 141
                                       5899******************************************************9..************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1541.80
//
Query:       gi|336254045|ref|YP_004597152.1|  [L=155]
Description: MaoC domain-containing protein dehydratase [Halopiger xanaduensis SH-6]
Scores for complete 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   89.0   0.1    2.2e-25   88.6   0.1    1.1  1  MaoC_dehydratas  MaoC like domain
    2.9e-05   24.2   0.2    0.00014   22.0   0.2    1.8  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.1   2.4e-29   2.2e-25       6     117 ..      11     123 ..       8     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 2.4e-29
                                       TTSEEEEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTT.EGGGEEEE CS
                   MaoC_dehydratas   6 igekvetekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdn.vvarvgei 81 
                                       +ge++e+e+++t++e+d+ ++  ++++ +p+H+d efA+ + fg+++++G++tl+++ ++ + e +d+ +va++  +
  gi|336254045|ref|YP_004597152.1|  11 VGETIEHERRRTISESDNQRFCDMTMNQQPLHLDSEFAADTEFGERVVNGLYTLSLAVGISIPETTDGtIVANLSYD 87 
                                       89*************************************************************************** PP

                                       EEEE-S--BTTCEEEEEEEEEEEEEEEEEEEEEEEE CS
                   MaoC_dehydratas  82 kvrFtkpVlpgdtlkvelevvgkrdvrktkkvevtk 117
                                       +v  ++pV++gdt++++ +v +kr+  +   + vt 
  gi|336254045|ref|YP_004597152.1|  88 DVEHPNPVFHGDTIRARSTVADKRETSDGERGVVTM 123
                                       **********************99988665666555 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   1.5e-08   0.00014       3     131 ..      11     137 ..      10     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.5e-08
                   MaoC_dehydrat_N   3 iGaef.epvkaevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkapellealgidlsrllhg 78 
                                       +G  + ++++ ++++++ ++f+  + + +p++ld e a+++ +++ ++   ++  la      +++   d+  + ++
  gi|336254045|ref|YP_004597152.1|  11 VGETIeHERRRTISESDNQRFCDMTMNQQPLHLDSEFAADTEFGERVVNGLYTLSLAVGI--SIPE-TTDGTIVANL 84 
                                       7888877899****************************************9999999987..4433.2455555566 PP

                   MaoC_dehydrat_N  79 e.qefeyhepiraGDelttesriadvydkkgvGalefivvettvtnqrGepvat 131
                                       +   +e  +p+  GD+++ +s++ad ++  + G+  ++++  +  nq+++ v++
  gi|336254045|ref|YP_004597152.1|  85 SyDDVEHPNPVFHGDTIRARSTVADKRET-SDGERGVVTMHVEAFNQDDDLVCE 137
                                       667889999******************95.48******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1205.79
//
Query:       gi|336254046|ref|YP_004597153.1|  [L=166]
Description: hypothetical protein Halxa_2657 [Halopiger xanaduensis SH-6]
Scores for 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-10   39.8   1.6    9.6e-10   39.1   0.9    1.7  2  Sm_multidrug_ex  Putative small multi-drug export protein


Domain annotation for each model (and alignments):
>> Sm_multidrug_ex  Putative small multi-drug export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.9   5.4e-14   9.6e-10       5     118 ..      40     148 ..      36     151 .. 0.85
   2 ?    0.3   0.1     0.057     1e+03      87      97 ..     144     154 ..     142     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 5.4e-14
                   Sm_multidrug_ex   5 aiplgillgldpllallvsvlgnllpvplillflrkllellkkkkllkklfekleekaekksekiekygflGLllFv 81 
                                        ip++i lgldp+l+ l++++g++ +v  i+l  r+l+ + ++   ++   +   ++ e+ ++  ++yg++GL++  
  gi|336254046|ref|YP_004597153.1|  40 VIPAAIGLGLDPVLTGLAAFAGSVTVVSAIVLAQRRLVAWWAR--RFGGDPADSSDRYERARRLWNRYGLAGLAFAG 114
                                       79***********************************996333..244444555666666666669*********** PP

                   Sm_multidrug_ex  82 aiPLpgTGawtGsliasllglkkkkallaillGvlia 118
                                       +i   + G + ++l+a+  g + + a++++++G   +
  gi|336254046|ref|YP_004597153.1| 115 PI---LAGIHLTALLAATAGSNSRTAIAWLTVGLGAW 148
                                       **...***************************98665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.057
                   Sm_multidrug_ex  87 gTGawtGslia 97 
                                       g Gawt +l+a
  gi|336254046|ref|YP_004597153.1| 144 GLGAWTVALVA 154
                                       679***99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:01.03
# Mc/sec: 486.06
//
Query:       gi|336254047|ref|YP_004597154.1|  [L=466]
Description: succinate-semialdehyde dehydrogenase (NAD(P)(+)) [Halopiger xanaduensis SH-6]
Scores for complete 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-141  472.5   0.0   1.2e-141  472.4   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
      0.018   14.1   0.0      0.029   13.4   0.0    1.2  1  LuxC      Acyl-CoA reductase (LuxC)


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 !  472.4   0.0  1.4e-145  1.2e-141       9     462 .]       3     452 ..       1     452 [. 0.98

  Alignments for each domain:
  == domain 1  score: 472.4 bits;  conditional E-value: 1.4e-145
                                       EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHH CS
                            Aldedh   9 ievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplae 85 
                                       ie++nPatgev+ ++ + + ++ ++ +++A+e+f++w+++p+e+R+++L++a ++l+e+++e ael+t+e+Gkp+ +
  gi|336254047|ref|YP_004597154.1|   3 IESTNPATGEVVDTYDEESDDEREEQLERANETFEEWSETPIETRQQLLARAGEILRENEDEYAELMTREMGKPIGQ 79 
                                       899************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHH.HSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE CS
                            Aldedh  86 araeveeaidvlryyaelaek.legevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKP 161
                                       ar eve+++ v++yyae+a + l+++v++ +e+++++v ++PlG ++aI+PWNfP+  + + +ap laaGN+ +lK 
  gi|336254047|ref|YP_004597154.1|  80 ARDEVEKCAWVCDYYAEHAAEfLQDDVVSGDESARTVVAYQPLGPILAIMPWNFPFWQVFRFAAPNLAAGNVGLLKH 156
                                       ******************9998999**99999********************************************* PP

                                       -TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE-- CS
                            Aldedh 162 aeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGG 238
                                       a+++p +a ++  +f+eag+P+g+++ +  s se+ ++++e+++++ v++tGs   gr +a++a+++lk+ +lElGG
  gi|336254047|ref|YP_004597154.1| 157 ASNVPGCARAIEDVFHEAGFPEGAFTSLLISSSEI-DTVIEDERIAGVTLTGSDGAGRSVAETAGSQLKKNVLELGG 232
                                       ****************************9977766.778899*********************************** PP

                                       -EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHH CS
                            Aldedh 239 knplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPlisea 315
                                        +p++vleda +d++ve ++++ ++n+GQ Ciaa+r++v +++ydefv++++e++ + +vgdp+dedtd+GP+++e+
  gi|336254047|ref|YP_004597154.1| 233 SDPFVVLEDAPMDETVETAAQARLINNGQSCIAAKRFIVVDEVYDEFVDRFIEEMDAQTVGDPMDEDTDIGPQARED 309
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHS CS
                            Aldedh 316 qlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNd 392
                                        +e+++++vee+ e+g ++ lGg   e+ +++g+f+ Ptvl++v+++++  +eE+FGPV++v+++ dee aie+aNd
  gi|336254047|ref|YP_004597154.1| 310 LMEELHDQVEETAEQGGEIELGG---EPMDREGAFYPPTVLTDVPENAPADEEELFGPVATVFRVPDEEAAIEKAND 383
                                       ***********************...899************************************************ PP

                                       SSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                            Aldedh 393 teyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                       t++GL+a+v+t+dler erva+++e G+  +N+  ++++   pfgGvk+Sg+Gre +++g++e++++k +
  gi|336254047|ref|YP_004597154.1| 384 TRFGLGASVWTEDLERGERVARQFESGMAFVNELVKSDPRL-PFGGVKDSGYGRELSRHGIREFVNTKMI 452
                                       ***************************************99.*************************975 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.2e-06     0.029      84     270 ..     116     293 ..      99     323 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-06
                              LuxC  84 yekaqprglvlhvlsgNvpllpvmsilq.glLvknvnllkvSssdpflaaallksladvdenhtladslsvvyfksg 159
                                         ++qp g +l +++ N p   v+  +   l ++nv llk  s+ p+ a a+   + +        +  s +    +
  gi|336254047|ref|YP_004597154.1| 116 VVAYQPLGPILAIMPWNFPFWQVFRFAApNLAAGNVGLLKHASNVPGCARAIEDVFHEAGFPE--GAFTSLL---IS 187
                                       56799****************9998776156689******************99998877654..4444444...44 PP

                              LuxC 160 dtkleeeiv.qnaDvvvawGgeeaikaiseklkp..gkqlikfGakvSfavvdkealeeealdkaaeraAkDiivfd 233
                                       + ++ ++i  +   +v   G++ a ++++e +    +k++++ G    f v++ +      +d+++e aA+   + +
  gi|336254047|ref|YP_004597154.1| 188 SSEIDTVIEdERIAGVTLTGSDGAGRSVAETAGSqlKKNVLELGGSDPFVVLEDAP-----MDETVETAAQARLINN 259
                                       556666665445779999************6654116889**********999877.....9*************** PP

                              LuxC 234 QqAClspqvvfvekddkieidefaeaLaaaLekrari 270
                                        q+C++++   v       +def+ + +++++ ++  
  gi|336254047|ref|YP_004597154.1| 260 GQSCIAAKRFIVV---DEVYDEFVDRFIEEMDAQTVG 293
                                       *****99765555...2479*********99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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 0.25s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 3461.85
//
Query:       gi|336254048|ref|YP_004597155.1|  [L=436]
Description: glutamate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-70  236.9   0.0    3.7e-70  236.4   0.0    1.2  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    1.2e-54  183.6   0.0    2.2e-54  182.8   0.0    1.4  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
     0.0079   15.6   0.0      0.014   14.8   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.014   12.9   0.0      0.027   12.0   0.0    1.3  1  Bac_GDH          Bacterial NAD-glutamate dehydrogenase


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 !  236.4   0.0   8.1e-74   3.7e-70       1     243 []     201     433 ..     201     433 .. 0.98

  Alignments for each domain:
  == domain 1  score: 236.4 bits;  conditional E-value: 8.1e-74
                                       T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HH CS
                     ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldie 77 
                                       GGs +r+ea g++v ++++e +++++ d  e+++va++G+G vg +aa+ l elg +vvavsD +G+iydp+Gld+ 
  gi|336254048|ref|YP_004597155.1| 201 GGSYGREEAPGRSVGIITRETIEYYDWD-PEETTVAVQGFGSVGANAARYLDELGTSVVAVSDVDGAIYDPDGLDTT 276
                                       9***********************9999.9999******************************************** PP

                                       HHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHH CS
                     ELFV_dehydrog  78 ellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeA 154
                                       ++ ++ e  ++v+ y+     + e+++ne  llel+vd+l+P+A+ n++++ena+  ++  + ++vEgAN+ptt+ A
  gi|336254048|ref|YP_004597155.1| 277 DVEDHDETPGMVSGYD-----APETLSNE-ALLELDVDVLIPAAVGNVLTAENAR-DVQ--AGMIVEGANGPTTSRA 344
                                       ****************.....3489***7.*************************.999..9*************** PP

                                       HHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHHH CS
                     ELFV_dehydrog 155 keileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqelvkganiag 231
                                       +ei+ee+gv vvpd++aNaGGVtvS++E+lq+++r sw +e+v+e+l+++m ++++av +e+e+++++++++ +i++
  gi|336254048|ref|YP_004597155.1| 345 DEIFEERGVPVVPDIIANAGGVTVSYFEWLQDINRRSWRHERVNEELETEMLRAWNAVRSEYEDRDVTWRDATYIVA 421
                                       ***************************************************************************** PP

                                       HHHHHHHHHHCT CS
                     ELFV_dehydrog 232 fekvaeamkaqG 243
                                       + ++a a++a+G
  gi|336254048|ref|YP_004597155.1| 422 LSRIAAAHEARG 433
                                       **********99 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 !  182.8   0.0   4.9e-58   2.2e-54       1     130 []      55     183 ..      55     183 .. 0.99

  Alignments for each domain:
  == domain 1  score: 182.8 bits;  conditional E-value: 4.9e-58
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       p +v++v++p++rd+G++e+++gyra+h+s++gP+kGG+R+hp+v++de+  L+++mt+K+a++d+pfGG+kggv +
  gi|336254048|ref|YP_004597155.1|  55 PTSVYRVSIPLERDDGSTEMLTGYRAHHDSVRGPYKGGLRYHPDVTEDECIGLSMWMTWKCAVMDIPFGGGKGGVVV 131
                                       67899************************************************************************ PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeykk 130
                                       +pk+ls++e er+trrf++el+ ++iGp +D+pApD+gt++++maw++d y++
  gi|336254048|ref|YP_004597155.1| 132 NPKDLSRDEKERLTRRFAEELR-PIIGPMTDIPAPDMGTDPQTMAWFMDAYSM 183
                                       **********************.****************************97 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 !   14.8   0.0   3.1e-06     0.014      33      68 ..     228     263 ..     213     282 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-06
                                       -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                      2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrs 68 
                                       + ++ tv++ G+G++G ++a++l ++g  v+a++  
  gi|336254048|ref|YP_004597155.1| 228 DPEETTVAVQGFGSVGANAARYLDELGTSVVAVSDV 263
                                       66899**************************99865 PP

>> Bac_GDH  Bacterial NAD-glutamate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.1e-06     0.027    1050    1099 ..     323     372 ..     319     374 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.1e-06
                           Bac_GDH 1050 ngkelrakvvgEGgNLGltQlgRiEyalkggrintDaiDNsaGVdcSDhE 1099
                                        n+++++a ++ EG+N   t ++   + ++g+ +  D i N++GV +S  E
  gi|336254048|ref|YP_004597155.1|  323 NARDVQAGMIVEGANGPTTSRADEIFEERGVPVVPDIIANAGGVTVSYFE 372 
                                        899********************99********************99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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 0.22s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 3507.05
//
Query:       gi|336254049|ref|YP_004597156.1|  [L=428]
Description: cell division control protein 6-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.3   0.1    2.9e-15   56.0   0.1    1.7  1  Cdc6_C           CDC6, C terminal winged helix domain
    1.1e-12   48.4   0.0    2.6e-12   47.2   0.0    1.6  1  AAA_22           AAA domain
      2e-11   44.6   0.2    6.3e-11   43.0   0.0    1.9  2  AAA_16           AAA ATPase domain
    2.9e-07   30.6   0.0    4.7e-07   29.9   0.0    1.3  1  NACHT            NACHT domain
    4.4e-07   30.4   0.0    1.2e-06   28.9   0.0    1.7  1  AAA              ATPase family associated with various cellul
    2.4e-06   27.1   0.0    4.4e-06   26.2   0.0    1.4  1  TniB             Bacterial TniB protein
    5.6e-06   26.4   0.0    1.5e-05   25.0   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
      4e-05   22.9   0.0    0.00011   21.5   0.0    1.7  2  DUF815           Protein of unknown function (DUF815)
    0.00013   21.7   0.0    0.00029   20.6   0.0    1.6  1  Sigma54_activat  Sigma-54 interaction domain
     0.0014   18.6   0.0     0.0036   17.3   0.0    1.8  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0022   16.9   1.0       0.15   10.8   0.7    2.1  2  AAA_32           AAA domain
     0.0027   17.9   0.0     0.0053   16.9   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
     0.0058   15.5   0.0      0.014   14.2   0.0    1.6  2  DUF2791          P-loop Domain of unknown function (DUF2791)
     0.0069   15.6   0.0      0.011   14.9   0.0    1.3  1  NB-ARC           NB-ARC domain
  ------ inclusion threshold ------
      0.012   15.1   0.1       0.92    8.9   0.0    2.3  2  PhoH             PhoH-like protein
       0.04   13.4   0.0      0.072   12.6   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.052   12.8   0.0      0.072   12.3   0.0    1.4  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.081   13.3   0.0       0.26   11.7   0.0    2.0  2  RNA_helicase     RNA helicase
        0.1   13.1   0.1       0.37   11.3   0.1    2.1  1  ABC_tran         ABC transporter
        1.5    9.0   3.5         20    5.3   0.1    2.9  3  AAA_33           AAA domain


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 !   56.0   0.1   3.3e-18   2.9e-15       1      84 []     311     394 ..     311     394 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 3.3e-18
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L+al++   ++++e+ +t+e+ye+Y  +Ce  + dp+t++  ++ l+e+++lg++e+ek ++Gr++g + +++L +d
  gi|336254049|ref|YP_004597156.1| 311 LYALASRIITGDRETYKTREIYERYVGICELVANDPITENGLYRQLKEQAFLGVIESEKTGGGRSQGSYLLHRLVTD 387
                                       7899988887888888************************************************************* PP

                                       CHHHHHH CS
                            Cdc6_C  78 pddvlea 84 
                                       p+ + +a
  gi|336254049|ref|YP_004597156.1| 388 PKHIVKA 394
                                       **99875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0     3e-15   2.6e-12       7     116 ..      60     175 ..      55     193 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 3e-15
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......erlssee 77 
                                        ++++G +GtGK++  r ++ ++  +a+ ++ + +v++v++++ ++ +   r+l+ +l++e+ +      ++  + e
  gi|336254049|ref|YP_004597156.1|  60 NVMIYGKTGTGKSLISRHVATRARDAAQRNDIDCSVLYVDCSEANTETRATRQLALNLKEETGYqehiplRGVGTME 136
                                       579*******************9777766669***************************99999************* PP

                            AAA_22  78 llealeqalraravielliiDEaqhlrseealeeLrsll 116
                                       +++++++ l+++++  ++i+DE+++l++ ++l +L++  
  gi|336254049|ref|YP_004597156.1| 137 YYQHIWRILDECFDSIVVILDEIDKLDNSNILMQLSRAR 175
                                       **************9***********7688888885544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0     7e-14   6.3e-11       2     152 ..      35     167 ..      34     187 .. 0.72
   2 ?   -1.9   0.1       4.1   3.7e+03     117     147 ..     258     287 ..     201     316 .. 0.54

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 7e-14
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqala 77 
                                        vGR++e++ +++ ++++ +g+p ++v+++G  G+GKs + r+++++++++    ++ +  ++          ++l 
  gi|336254049|ref|YP_004597156.1|  35 IVGRDDEIQSVAAEVGAITRGDPpNNVMIYGKTGTGKSLISRHVATRARDA----AQRNDIDC----------SVL- 96 
                                       69********************************************99999....56666666..........333. PP

                            AAA_16  78 reellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeasl 152
                                           + + ++e++++ + a   k e+ +++  +l+g +    ++++ r+l+ +   ++ +v++lD+++++d +  
  gi|336254049|ref|YP_004597156.1|  97 Y-VDCSEANTETRATRQLALNLKEETGYQEHIPLRGVGTMEYYQHIWRILDECF--DS-IVVILDEIDKLDNSNI 167
                                       2.4555555555555555555555555555566777777777777777774444..45.***********99543 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.1
                            AAA_16 117 srllellkrllallsrderplvlvlDdlqwa 147
                                       +   e lk++ +l++r+++  ++  D++q+a
  gi|336254049|ref|YP_004597156.1| 258 RKAIEILKEAGELARRTGS-EIVSEDHIQQA 287
                                       3333344444444444444.33334444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   5.3e-10   4.7e-07       3      97 ..      61     166 ..      59     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 5.3e-10
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C........ CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse........ 71 
                                       v++ G+ G GK+   +++a+ +++  + ++  + v+++ ++e +++++a    ++l+ +l+e+ + +++        
  gi|336254049|ref|YP_004597156.1|  61 VMIYGKTGTGKSLISRHVATRARDAAQRNDIDCSVLYVDCSEANTETRA---TRQLALNLKEETGYQEHiplrgvgt 134
                                       799**************************999*************9755...7778888888888877788889*** PP

                                       ......CHHHHCCSCCCEEEEEE-STT-SS-T CS
                             NACHT  72 ......vwavllelperlLlilDglDelvtdl 97 
                                             +w +l e +++++ ilD +D+l + +
  gi|336254049|ref|YP_004597156.1| 135 meyyqhIWRILDECFDSIVVILDEIDKLDNSN 166
                                       **999999999999**************9765 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 !   28.9   0.0   1.4e-09   1.2e-06       1     124 [.      61     203 ..      61     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.4e-09
                                       EEEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS..........................STTHH CS
                               AAA   1 vllyGppGtGKTllakavakel.........gvefleisgsellsk..........................yvges 42 
                                       v++yG  GtGK+l+ + va+ +         + ++l +++se   +                             e 
  gi|336254049|ref|YP_004597156.1|  61 VMIYGKTGTGKSLISRHVATRArdaaqrndiDCSVLYVDCSEANTEtratrqlalnlkeetgyqehiplrgvGTMEY 137
                                       689******************8544444333477999999999966799*******************996666666 PP

                                       HHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHH CS
                               AAA  43 ekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpal 119
                                        ++i  +++e+  +    ++++DEid+l +s+          ++ qL ++ + +k++ + + vig++n+++ + + l
  gi|336254049|ref|YP_004597156.1| 138 YQHIWRILDECFDS---IVVILDEIDKLDNSN----------ILMQLSRAREAQKTD-AYIGVIGISNKIQ-YRETL 199
                                       68888888887654...8**********8888..........999*99999999996.66********953.33333 PP

                                       HSTTS CS
                               AAA 120 lrgRf 124
                                         +R+
  gi|336254049|ref|YP_004597156.1| 200 D-ERI 203
                                       3.344 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   4.9e-09   4.4e-06      33     135 ..      56     166 ..      33     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.9e-09
                              TniB  33 krmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkara....... 102
                                       + ++n++++G++ +GK+ i ++ a + +++ + ++  + vl+v++ +  +e r  +++  +l++++  ++       
  gi|336254049|ref|YP_004597156.1|  56 DPPNNVMIYGKTGTGKSLISRHVATRARDAAQRNDIDCSVLYVDCSEANTETRATRQLALNLKEETGYQEhiplrgv 132
                                       45689************************9999999**********************9999999988886666666 PP

                              TniB 103 rvskleqqvlrllrel.kvrvLiiDEihnllags 135
                                        + + +q++ r+l+e+ +  v+i+DEi++l + +
  gi|336254049|ref|YP_004597156.1| 133 GTMEYYQHIWRILDECfDSIVVILDEIDKLDNSN 166
                                       67899999*****99835567788***9987765 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 !   25.0   0.0   1.7e-08   1.5e-05       1      88 [.      60     174 ..      60     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.7e-08
                                       EEEEE--SSSSHHHHHHHGGGGB.........S--EEEEE--TT--HHHHH--B--..........--------... CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.........nreveyvqltrdtteedlkgrreik.ngttslvdsplvraar... 64 
                                       +v++ G++GtgKs +++++a +           ++v+yv +++  te+  + ++ ++ +++t +++ +  r +    
  gi|336254049|ref|YP_004597156.1|  60 NVMIYGKTGTGKSLISRHVATRArdaaqrndiDCSVLYVDCSEANTETRATRQLALNlKEETGYQEHIPLRGVGtme 136
                                       699******************999999999999***********************996666666666666666688 PP

                                       .............G-SEEEEESGGG--.HHHHHHHHHH CS
                             AAA_5  65 .............egeilvlDEverae.sevlnsLlsl 88 
                                                     + +++lDE+++++ s++l+ L + 
  gi|336254049|ref|YP_004597156.1| 137 yyqhiwrildecfDSIVVILDEIDKLDnSNILMQLSRA 174
                                       **************************9999*9999876 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.2e-07   0.00011      26      78 ..      31      83 ..      17      93 .. 0.88
   2 ?   -2.9   0.0       3.2   2.9e+03     168     207 ..     191     229 ..     187     258 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.2e-07
                            DUF815 26 klddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneya 78
                                      + d++vg d++ +++ + + +  +g p nnv+++G+ GtGKS + + + ++++
  gi|336254049|ref|YP_004597156.1| 31 DEDRIVGRDDEIQSVAAEVGAITRGDPPNNVMIYGKTGTGKSLISRHVATRAR 83
                                      56889*************************************98888877665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.2
                            DUF815 168 eeihaseaveeklsLsdRFGl.wlgFykldqeeYleivekl 207
                                       ++i+ +e+++e++  s  FG   l F++ d ++  ei+++ 
  gi|336254049|ref|YP_004597156.1| 191 NKIQYRETLDERIDSS--FGHrELFFHPYDASQLREIMRNR 229
                                       6788888888888644..66425788888887777777655 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.2e-07   0.00029       1      59 [.      35     101 ..      35     112 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.2e-07
                                       ----SHHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHH......HSTTTTS-EEEEETT CS
                   Sigma54_activat   1 ligesealkelleqikkvaktd..lsvlitGesGtGKellaraihe......askrkekpfvavnca 59 
                                       ++g++++++++ +++ ++++ d   +v+i G++GtGK+l++r++ +      +++  + +++ v+c+
  gi|336254049|ref|YP_004597156.1|  35 IVGRDDEIQSVAAEVGAITRGDppNNVMIYGKTGTGKSLISRHVATrardaaQRNDIDCSVLYVDCS 101
                                       68999999********999888779*****************9987333321122222345555555 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 !   17.3   0.0     4e-06    0.0036      10     131 ..      48     163 ..      36     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4e-06
                          ATPase_2  10 eleeilerepneiyfiYGpegsGKtaLlkeiienledkdk......yviyyialreesiskldefie.eeeekkkle 79 
                                       e+  i + +p + ++iYG  g GK+ + ++++++ +d  +       v+y++  +   ++++++ ++ + +e++  +
  gi|336254049|ref|YP_004597156.1|  48 EVGAITRGDPPNNVMIYGKTGTGKSLISRHVATRARDAAQrndidcSVLYVDCSEANTETRATRQLAlNLKEETGYQ 124
                                       4557888999999*******************999887776777779999999999999999988777666666555 PP

                          ATPase_2  80 kalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqkli 131
                                       +++  +++ +              ++ + + + + +    i++i+De+ kl 
  gi|336254049|ref|YP_004597156.1| 125 EHI--PLRGVGT-----------MEYYQHIWRILDECFDSIVVILDEIDKLD 163
                                       555..4444333...........33444444444444445777777777776 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.015        14      30      64 ..      58      91 ..      28     124 .. 0.65
   2 !   10.8   0.7   0.00017      0.15     477     509 ..     257     289 ..     246     294 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.015
                            AAA_32 30 gYNifvlGesgtGrttlvkrlleeiakkeptpdDw 64
                                        N+ + G++gtG++ + +++ + +a+++++ +D+
  gi|336254049|ref|YP_004597156.1| 58 PNNVMIYGKTGTGKSLISRHVAT-RARDAAQRNDI 91
                                      469***********876666655.45555555553 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00017
                            AAA_32 477 fseiadllrEAdywakkegaevveaehVekAle 509
                                        ++ +++l+EA  +a++ g+e+v+++h+++A e
  gi|336254049|ref|YP_004597156.1| 257 ARKAIEILKEAGELARRTGSEIVSEDHIQQAQE 289
                                       56889**************************76 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.9e-06    0.0053       4      84 ..      59     165 ..      56     177 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.9e-06
                                       --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.......... CS
                             AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.......... 70 
                                        ++++ g+tg+Gk+++++ +a   +  +  +   +d+s l   + +e   +     + + + +ee G          
  gi|336254049|ref|YP_004597156.1|  59 NNVMIYGKTGTGKSLISRHVATRAR--DAAQRNDIDCSVLYV-DCSEANTETRATRQLALNLKEETGyqehiplrgv 132
                                       6899***********8888887765..344444455555555.4444444444444455555555555555577779 PP

                                       ....................EEEEETGGG----- CS
                             AAA_2  71 ....................ivllDEidKihpke 84 
                                                           +v lDEidK  + +
  gi|336254049|ref|YP_004597156.1| 133 gtmeyyqhiwrildecfdsiVVILDEIDKLDN-S 165
                                       9****************************998.4 PP

>> 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 !   14.2   0.0   1.6e-05     0.014      16      75 ..      27      84 ..      22     111 .. 0.86
   2 ?   -2.6   0.0       2.1   1.9e+03     223     252 ..     135     163 ..     107     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                           DUF2791 16 GvVPriGleliaVGrereiealledlervaeggaafr.firGeYGsGKtFllqllrerale 75
                                      G VP +      VGr++ei+++  ++ ++++g      +i G+ G+GK+ + + +++ra++
  gi|336254049|ref|YP_004597156.1| 27 GHVPDED---RIVGRDDEIQSVAAEVGAITRGDPPNNvMIYGKTGTGKSLISRHVATRARD 84
                                      6666543...36********************976552788****************9986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.1
                           DUF2791 223 ydylkllaafvrkaGykGLlvvlDElvnly 252
                                       ++y + + +++ ++ ++ ++v+lDE+ +l 
  gi|336254049|ref|YP_004597156.1| 135 MEYYQHIWRILDEC-FDSIVVILDEIDKLD 163
                                       55666666666655.777899999988874 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.3e-05     0.011      22     114 ..      60     161 ..      43     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCCCBT...EEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS.... CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFd...svawvvvsktdkseeiletilkeLslseddleekeeves.... 91 
                                        v ++G+ G GK+ +++++        +r d   sv +v  s+  ++ + +++++ +L+++   +e+ + +      
  gi|336254049|ref|YP_004597156.1|  60 NVMIYGKTGTGKSLISRHVATRARDAAQRNDidcSVLYVDCSEANTETRATRQLALNLKEETGYQEHIPLRGVgtme 136
                                       689***************9988776666555448999*********************9887777777654446777 PP

                                       HHHHHHHHCCCT..TEEEEEEEE-S CS
                            NB-ARC  92 lkrklvrlLltk..rfllvlDDVwe 114
                                         +++ r+L +     +++lD + +
  gi|336254049|ref|YP_004597156.1| 137 YYQHIWRILDECfdSIVVILDEIDK 161
                                       8889999998888566666776643 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0     0.001      0.92      22      46 ..      61      85 ..      47     103 .. 0.84
   2 ?    3.8   0.1     0.039        35     118     145 ..     149     176 ..     143     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.001
                                      EEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH 22 vfaiGpaGtGKtylavalavealkk 46
                                      v++ G++GtGK++++  +a +a  +
  gi|336254049|ref|YP_004597156.1| 61 VMIYGKTGTGKSLISRHVATRARDA 85
                                      8899***********9999887655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.039
                                       B-SEEEEE-SGGG--HHHHHHHHTTB-T CS
                              PhoH 118 lndafvilDEAQnttkeqmkmfltRlGe 145
                                       ++  +vilDE   + ++++ m l+R  e
  gi|336254049|ref|YP_004597156.1| 149 FDSIVVILDEIDKLDNSNILMQLSRARE 176
                                       677899****************999765 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 ?   12.6   0.0     8e-05     0.072      34      68 ..      59      92 ..      55     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8e-05
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltin 68
                                      ++v+++G+tGtGK++i +++ ++   +  + + i 
  gi|336254049|ref|YP_004597156.1| 59 NNVMIYGKTGTGKSLISRHVATRAR-DAAQRNDID 92
                                      589*************999666555.444444444 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.1e-05     0.072       3      33 ..      60      89 ..      58     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.1e-05
                           DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddeeert 33
                                       v++ G++GtGK+++  ++++++ +d+ +r+
  gi|336254049|ref|YP_004597156.1| 60 NVMIYGKTGTGKSLISRHVATRA-RDAAQRN 89
                                      589*******************9.3333332 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   0.00029      0.26       1      26 [.      61      86 ..      61     121 .. 0.85
   2 ?   -2.6   0.0       8.2   7.3e+03      48      74 ..     149     172 ..     133     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                      +++yG++g+GKS++++++a++  ++ 
  gi|336254049|ref|YP_004597156.1| 61 VMIYGKTGTGKSLISRHVATRARDAA 86
                                      689**************999877655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.2
                      RNA_helicase  48 tgqevvvidDfgqvkdeenpsdlaeli 74 
                                        +  vv+ d++ +  ++   ++l++l 
  gi|336254049|ref|YP_004597156.1| 149 FDSIVVILDEIDKLDNS---NILMQLS 172
                                       45567788887777666...6666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00042      0.37      13      80 ..      60     147 ..      56     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00042
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx......... RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren......... 79 
                                        v i G++G+GKS + + +a   ++++ +  +d  ++ + + ++++ e +   q   +l++e+  +e+         
  gi|336254049|ref|YP_004597156.1|  60 NVMIYGKTGTGKSLISRHVATRARDAAQRNDID-CSVLYVDCSEANTETRATRQLaLNLKEETGYQEHiplrgvgtm 135
                                       689****************99999855555444.3344456677777777777764555555546665666666666 PP

                                       ...........H CS
                                       ...........x RF
                          ABC_tran  80 ...........e 80 
                                                  e
  gi|336254049|ref|YP_004597156.1| 136 eyyqhiwrildE 147
                                       555555444441 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.4      0.03        27       2      21 ..      61      80 ..      61      83 .. 0.88
   2 ?    5.3   0.1     0.022        20      81     116 ..      75     110 ..      73     121 .. 0.86
   3 ?   -0.7   0.0       1.7   1.5e+03      18      50 ..     269     301 ..     266     325 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.03
                            AAA_33  2 vllvGlpGsGKstlaerllk 21
                                      v++ G  G+GKs  +++++ 
  gi|336254049|ref|YP_004597156.1| 61 VMIYGKTGTGKSLISRHVAT 80
                                      7899************9985 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.022
                            AAA_33  81 srrerarflklarrlgvpvrivvvetdeetlkeRla 116
                                       sr+   r + +a+r +  +++++v+++e+  + R  
  gi|336254049|ref|YP_004597156.1|  75 SRHVATRARDAAQRNDIDCSVLYVDCSEANTETRAT 110
                                       566668999********************9999965 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.7
                            AAA_33  18 rllkklgavllssdtlrrrlfgtdqqsktdytr 50 
                                       +l++++g +++s+d + ++ ++ + ++++++t 
  gi|336254049|ref|YP_004597156.1| 269 ELARRTGSEIVSEDHIQQAQEVAEINRIEELTS 301
                                       688999999999999999888877776665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 3012.58
//
Query:       gi|336254050|ref|YP_004597157.1|  [L=293]
Description: Citryl-CoA lyase [Halopiger xanaduensis SH-6]
Scores for complete 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  178.3   5.4    2.4e-52  177.3   5.4    1.5  1  HpcH_HpaI       HpcH/HpaI aldolase/citrate lyase family
    1.5e-10   40.8   0.0    5.4e-05   22.5   0.0    2.3  2  C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.3   5.4   2.6e-56   2.4e-52       1     221 []       4     228 ..       4     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 2.6e-56
                                       EEEEEEESTSHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHH CS
                         HpcH_HpaI   1 riglflpganaalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqd 77 
                                       r++lf pg+++++++ a+ +gaD++++DlEdav+  + d+AR+ v+++l+++d+  ++  ev+VRvn+   +++ + 
  gi|336254050|ref|YP_004597157.1|   4 RSVLFTPGDRPEMLRAAPESGADVIVFDLEDAVSPDRIDEARTAVRDVLTDPDFDPDC--EVCVRVNAAPRQFATD- 77 
                                       899***************************************************6666..*******998877766. PP

                                       GG............HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTST CS
                         HpcH_HpaI  78 le............vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaave 142
                                       le             + ++++++ +Pkv  +++++e+v+ l+ ++      ++++++ a +E+a+gv+ a+eIaav+
  gi|336254050|ref|YP_004597157.1|  78 LEavigdvdsdagsNAASQLDAIALPKVAGPADVRELVAELEAID-----DANTVPIFALLETAAGVLAAPEIAAVP 149
                                       444333222444555667899************************.....7899*********************** PP

                                       TEEEEEE-HHHHHHHTT-TTSTTSHHHHHHHHHHHHTTHCEEEEEEE.E-SSHHHHHHHHHTTHCEEEEEEHHHHHH CS
                         HpcH_HpaI 143 gldgvflGaeDlsadlgtkrspegtevldareriltaaraagiaaldtvasdiddaegflaegalfvalGfdgklli 219
                                         d++++GaeDl+ad+g++r++egtevl+arer+++aa a +  a+dt+++d +d+ +++a+ +++++lG+dgkl+i
  gi|336254050|ref|YP_004597157.1| 150 AADALVFGAEDLAADIGATRTAEGTEVLYARERVVLAAAAHDCTAIDTLVTDYEDEAALRADTEFAIELGYDGKLAI 226
                                       ***************************************************************************** PP

                                       HH CS
                         HpcH_HpaI 220 np 221
                                       +p
  gi|336254050|ref|YP_004597157.1| 227 HP 228
                                       *8 PP

>> C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.3e-07    0.0048      10     125 ..       6     122 ..       4     148 .. 0.65
   2 !   22.5   0.0     6e-09   5.4e-05     245     331 ..     198     289 ..     164     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.3e-07
                    C-C_Bond_Lyase  10 tLYmPatrediaekilkqklegltslvlclEDavseeeveaAeenlkellkelaeaekek...ekeelpllFvRvRs 83 
                                        L++P++r+++++       +g+  +v++lEDavs +++++A + ++++l++ +   + +   + ++ p  F     
  gi|336254050|ref|YP_004597157.1|   6 VLFTPGDRPEMLRAAP---ESGADVIVFDLEDAVSPDRIDEARTAVRDVLTDPDFDPDCEvcvRVNAAPRQFATDL- 78 
                                       5899999987766554...578999*************************98776544444455555555554333. PP

                    C-C_Bond_Lyase  84 peqlkellerlge.alelltGfvlPkft.sesleeylealkkan 125
                                        +++ ++ +  g+ a++ l+ + lPk++  + ++e ++ l++++
  gi|336254050|ref|YP_004597157.1|  79 EAVIGDVDSDAGSnAASQLDAIALPKVAgPADVRELVAELEAID 122
                                       33444444444433667777777777741345555555555555 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 6e-09
                    C-C_Bond_Lyase 245 llekdld..glirEvalDkanGlvGKtvIhPsqialvqallvVskeeyedAldilesakg......gvfkseyankm 313
                                       l++++ d   l   ++  ++ G  GK +IhP+q+ +++++++ ++++ e A+++le++++      gvf+++  ++m
  gi|336254050|ref|YP_004597157.1| 198 LVTDYEDeaALRADTEFAIELGYDGKLAIHPAQVGPINEAFTPTADDREWAERVLEAKREadaegrGVFEVD--GEM 272
                                       555444433677777888899**********************************98653344557888888..999 PP

                    C-C_Bond_Lyase 314 nEvkphraWAekilkrak 331
                                       +  +p  a Ae+i +ra+
  gi|336254050|ref|YP_004597157.1| 273 I-DAPLVAQAERIRSRAD 289
                                       9.5899999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2260.85
//
Query:       gi|336254051|ref|YP_004597158.1|  [L=418]
Description: glutamate dehydrogenase (NAD(P)(+)) [Halopiger xanaduensis SH-6]
Scores for 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-74  249.6   0.4      5e-74  249.1   0.4    1.2  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    3.8e-53  178.8   0.0    6.4e-53  178.1   0.0    1.4  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
     0.0022   16.8   0.1     0.0034   16.2   0.1    1.2  1  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
     0.0027   17.1   0.1      0.008   15.6   0.1    1.8  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.016   15.1   0.3        4.7    7.0   0.0    2.2  2  HCV_NS5a_C       HCV NS5a protein C-terminal region


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 !  249.1   0.4   1.4e-77     5e-74       1     243 []     181     415 ..     181     415 .. 0.97

  Alignments for each domain:
  == domain 1  score: 249.1 bits;  conditional E-value: 1.4e-77
                                       T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HH CS
                     ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldie 77 
                                       GGs +r eaTg+++v++++e++++l+ d leg++va++G+Gn g+ aa+l+ e+ga+vva sDssG iy+p+G+d  
  gi|336254051|ref|YP_004597158.1| 181 GGSAGRVEATGRSTVIAAREAFDYLDKD-LEGATVAVQGYGNAGWIAAKLIDEMGATVVAASDSSGGIYNPDGFDPV 256
                                       9***********************9999.************************************************ PP

                                       HHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHH CS
                     ELFV_dehydrog  78 ellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeA 154
                                       + +e+k+e++sv  y++  ++  e i+ne ++l+l+vd+l+P+A++n+id++ a+  ++  ++++ E+AN+p+t++A
  gi|336254051|ref|YP_004597158.1| 257 AAKEHKNETGSVVGYEE--VE--EEITNE-DVLTLDVDLLIPAALENAIDGDLAA-DVE--ADVISEAANGPLTPDA 325
                                       ****************4..33..689997.************************9.899..**************** PP

                                       HHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-T.HHHHHHHH CS
                     ELFV_dehydrog 155 keileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqe.lvkgania 230
                                       + +le+++v+v+pd++aNaGGVtvS++E++qn +r++w+ee+v+e+l++i  ++f+a+ve++ee++ e  +++a+++
  gi|336254051|ref|YP_004597158.1| 326 DAVLEDKDVFVIPDILANAGGVTVSYFEWVQNRQRFYWDEERVNEELEAIIVDAFDALVETYEEHDLEnPRTAAYVV 402
                                       ****************************************************************99999******** PP

                                       HHHHHHHHHHHCT CS
                     ELFV_dehydrog 231 gfekvaeamkaqG 243
                                       ++++va+a  + G
  gi|336254051|ref|YP_004597158.1| 403 AIQRVADAFDEAG 415
                                       ********98876 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 !  178.1   0.0   1.8e-56   6.4e-53       1     129 [.      35     162 ..      35     163 .. 0.99

  Alignments for each domain:
  == domain 1  score: 178.1 bits;  conditional E-value: 1.8e-56
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       pervl+ +++v+ d+G+le +k++r+q++  +gP+kGGiR+hp+v+ devkaL+ +mtyK+a+vd+p+GG+kgg+++
  gi|336254051|ref|YP_004597158.1|  35 PERVLETNLTVELDDGSLERFKAFRSQFNGDRGPYKGGIRYHPDVSRDEVKALSGWMTYKTAIVDIPLGGGKGGIIV 111
                                       89*************************************************************************** PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeyk 129
                                       dp ++se+eler+tr+f++el  ++iG ++DvpApDv+tg+rem+w+ d+y+
  gi|336254051|ref|YP_004597158.1| 112 DPDDYSESELERLTRAFAKELT-PLIGVDRDVPAPDVNTGQREMNWIKDTYE 162
                                       **********************.****************************7 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 !   16.2   0.1   9.5e-07    0.0034     261     306 ..     200     245 ..     186     306 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.5e-07
                                       HHHHHHHHHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS CS
                    Oxidored_nitro 261 daladyheylagkrvaiygdpdrvvalarllkelGmevvaagteta 306
                                       +a+  + + l+g++va+ g++   +  a+l+ e+G++vvaa+ +++
  gi|336254051|ref|YP_004597158.1| 200 EAFDYLDKDLEGATVAVQGYGNAGWIAAKLIDEMGATVVAASDSSG 245
                                       555667899*******************************986555 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 !   15.6   0.1   2.2e-06     0.008      27      68 ..     202     243 ..     186     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.2e-06
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrs 68 
                                        ++l k+l+g tv++ G+G+ G  +ak++ ++g+ v+a + s
  gi|336254051|ref|YP_004597158.1| 202 FDYLDKDLEGATVAVQGYGNAGWIAAKLIDEMGATVVAASDS 243
                                       467889*******************************99876 PP

>> HCV_NS5a_C  HCV NS5a protein C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0013       4.7       7      90 ..     183     265 ..     179     274 .. 0.88
   2 ?    6.0   0.1    0.0026       9.3      56      93 ..     358     395 ..     351     412 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0013
                        HCV_NS5a_C   7 aagrrlargsppsmasssasqlsapslkatctanhdspdaelieanllwrqemggnit.rvesenkvvildsfdplv 82 
                                       +agr  a g    +a+  a +     l  +  a +   +a  i a+l+  +emg  +    +s   +   d fdp+ 
  gi|336254051|ref|YP_004597158.1| 183 SAGRVEATGRSTVIAAREAFDYLDKDLEGATVAVQGYGNAGWIAAKLI--DEMGATVVaASDSSGGIYNPDGFDPVA 257
                                       6999999************999999***9999**************98..79**9876156788889999******* PP

                        HCV_NS5a_C  83 aeederev 90 
                                       a+e + e 
  gi|336254051|ref|YP_004597158.1| 258 AKEHKNET 265
                                       **998875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0026
                        HCV_NS5a_C  56 rqemggnitrvesenkvvildsfdplvaeederevsvp 93 
                                       rq +  +  rv+ e   +i+d+fd lv   +e+++  p
  gi|336254051|ref|YP_004597158.1| 358 RQRFYWDEERVNEELEAIIVDAFDALVETYEEHDLENP 395
                                       5666666789*****************98888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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 0.21s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3218.61
//
Query:       gi|336254052|ref|YP_004597159.1|  [L=664]
Description: xenobiotic-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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  138.2   0.8    4.8e-40  137.9   0.8    1.1  1  ABC_membrane  ABC transporter transmembrane region
    1.4e-28  100.1   0.0    2.5e-28   99.3   0.0    1.4  1  ABC_tran      ABC transporter
    3.5e-05   23.3   0.0     0.0002   20.9   0.0    1.9  2  SMC_N         RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.013   15.2   0.2      0.028   14.2   0.2    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.015   12.9   0.0      0.023   12.3   0.0    1.2  1  DUF3584       Protein of unknown function (DUF3584)
      0.043   13.7   0.0       0.13   12.2   0.0    1.7  2  RsgA_GTPase   RsgA GTPase
      0.052   14.1   0.0       0.14   12.7   0.0    1.8  1  AAA_18        AAA domain
       0.11   12.8   1.6       0.71   10.2   1.6    2.2  1  AAA_16        AAA ATPase 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 !  137.9   0.8   2.2e-43   4.8e-40       1     267 [.      36     326 ..      36     333 .. 0.96

  Alignments for each domain:
  == domain 1  score: 137.9 bits;  conditional E-value: 2.2e-43
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHH.......................HHHHHHHHHHHHHHHHH CS
                      ABC_membrane   1 liliillailagvlsplfplvlgrildtlldkgdpet.......................ealnvysllllllglaq 54 
                                       l++++++++++ ++ ++ +l l+  +d +++++ + +                       + l ++ +l ++++++q
  gi|336254052|ref|YP_004597159.1|  36 LCVGFVSTMINRAARLFPALMLAAAIDLVITQSGSVDqllaatglvptepipadrtgerlSLLYYLGTLTVGAYVVQ 112
                                       6789**************************99766668*******************987777777778889***** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHH CS
                      ABC_membrane  55 filallqsyllnvtgerlskrlrrklfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvg 131
                                       +i+ +l+ y++  t++r+ ++lr ++++++ r+++sff+++++G +++ l++dv++l+d++++ l +++ ++++f  
  gi|336254052|ref|YP_004597159.1| 113 SITHYLSRYFFQTTAQRIQHDLRLDTYDHMQRLSLSFFNDHQTGGMMAILNSDVNRLEDFFNTELRQITEAVMIFGL 189
                                       ***************************************************************************** PP

                                       HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHH CS
                      ABC_membrane 132 glivmfylgwkltlvllailpliilvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfek 208
                                       + ++m+y+ ++l  ++l  +pli+l +a +  ++++  k+  ++va++++ +   l g   Vk+f r + ++ +  +
  gi|336254052|ref|YP_004597159.1| 190 VGGYMLYTEPWLGALVLLPVPLIALATAKFIIWIEPKYKRIRERVAQLNTRLSNNLGGAAIVKSFDRYDVERGRVAE 266
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.TSSTHHHHHHHHHHH CS
                      ABC_membrane 209 aleeakkagikkaianglligitqllgllsyalalwfGttlvis.gelsvgdlvvflslf 267
                                       +++ ++   i +++++ ++++ ++ll+ ++++ +l+ G++ v + g l+ g++vv+ +++
  gi|336254052|ref|YP_004597159.1| 267 QSRGYRDEKIGAITVRKAFFASLRLLVGAMFVSILVAGGYSVVTaGGLTAGTFVVYFMYL 326
                                       *****************************************9999*******88888886 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.0   1.1e-31   2.5e-28       1     137 []     396     578 ..     396     578 .. 0.90

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 1.1e-31
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE................EETTCEGGGB-HHHCCHCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGei................lldgkdlkeqeleslrkei 61 
                                       l+ v+l++++ge+v++ G +G+GKStLlkll + ++ +  +                 ++dg d+++ +l+ lr +i
  gi|336254052|ref|YP_004597159.1| 396 LEGVDLEVEAGETVGFAGTSGSGKSTLLKLLPRFYDVDDRHAladggvdaerggdaavRIDGVDVRDYDLQTLRDRI 472
                                       6789********************************9666666777779999999999******************* PP

                                       EEE-SS--S-TTSBHHHH.................................HHHTC...HHHHHHHSTTGGTTCBGE CS
                                       xxxxxxxxxxxxxxxxxx.................................xxxxx...xxxxxxxxxxxxxxxxxx RF
                          ABC_tran  62 gvlpqepqlfpeltvren.................................esdee...iekalsklglkelkdtvv 102
                                       gv++q+p +f+++ +ren                                 +       +++++++l   +  dt v
  gi|336254052|ref|YP_004597159.1| 473 GVVEQDPYMFSGT-IRENiaygdgeafrtvleagedggdvpadvdrrireaA---IaagAHQFIEELPEGY--DTMV 543
                                       *************.******************99999999986655544433...0455888888888777..9*** PP

                                       STTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 103 ksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       ++++ +LSgGq+qrv++ar++l++p+l++lDE+t+
  gi|336254052|ref|YP_004597159.1| 544 GERGVKLSGGQRQRVSIARTILNDPDLIVLDEATS 578
                                       *********************************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 ?   -0.3   0.0      0.28   6.2e+02      30      41 ..     412     423 ..     398     427 .. 0.83
   2 !   20.9   0.0   8.9e-08    0.0002     103     211 ..     445     620 ..     434     626 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.28
                                       EESTTSSHHHHH CS
                                       xxxxxxxxxxxx RF
                             SMC_N  30 vGpNGSGKsnll 41 
                                        G  GSGKs ll
  gi|336254052|ref|YP_004597159.1| 412 AGTSGSGKSTLL 423
                                       6999*****987 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 8.9e-08
                                       EETTSEEEEEETTEEE-HHHHHHHHHCTT-STT............................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................ RF
                             SMC_N 103 vkrkgeseykingkevtkkevsellesagiske............................................ 135
                                       ++r+g+  ++i+g +v+  +++ l  + g+ ++                                            
  gi|336254052|ref|YP_004597159.1| 445 AERGGDAAVRIDGVDVRDYDLQTLRDRIGVVEQdpymfsgtireniaygdgeafrtvleagedggdvpadvdrrire 521
                                       67899999*********************99999******************************************* PP

                                       ...........................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH CS
                                       ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ...........................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellke 185
                                                                   LSgG+++ v++a        +   l +lDe  +  D +  + + + l+e
  gi|336254052|ref|YP_004597159.1| 522 aaiaagahqfieelpegydtmvgergvKLSGGQRQRVSIART----ILNDPDLIVLDEATSDVDTETEEVIQRNLDE 594
                                       ***********************************9998755....4666779************************ PP

                                       HCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 186 ksknaQfivislreemlekadklvgv 211
                                        + +   +vi++r  ++++ad++v +
  gi|336254052|ref|YP_004597159.1| 595 LTADRTAFVIAHRLSTIRDADRIVVM 620
                                       *********************99865 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 ?   14.2   0.2   1.2e-05     0.028      15      39 ..     399     423 ..     394     425 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                            AAA_29  15 htieidlkgatlltGpsGsGKSTll 39 
                                        ++e++  +++ ++G+sGsGKSTll
  gi|336254052|ref|YP_004597159.1| 399 VDLEVEAGETVGFAGTSGSGKSTLL 423
                                       5667775558889***********8 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     1e-05     0.023       9      41 ..     398     430 ..     394     434 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1e-05
                           DUF3584   9 GrvaeldldghtnieGtNaaGKTtLlrLiPlFY 41 
                                       G+  e++  + +   Gt ++GK tLl+L+P FY
  gi|336254052|ref|YP_004597159.1| 398 GVDLEVEAGETVGFAGTSGSGKSTLLKLLPRFY 430
                                       55558888889999******************* PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         3   6.7e+03      33      63 ..     116     146 ..     110     176 .. 0.76
   2 ?   12.2   0.0   5.8e-05      0.13      98     119 ..     405     426 ..     390     436 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHTT-EEEEEEE-GGG--HHH CS
                       RsgA_GTPase  33 nlldrfLvlaeekgiepvivlnKiDlleeee 63 
                                       + l+r+ ++  +++i+  + l   D +++ +
  gi|336254052|ref|YP_004597159.1| 116 HYLSRYFFQTTAQRIQHDLRLDTYDHMQRLS 146
                                       5789999999999999999888888877765 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.8e-05
                                       TTSEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinal 119
                                       +++t+ ++G SG GKStL++ l
  gi|336254052|ref|YP_004597159.1| 405 AGETVGFAGTSGSGKSTLLKLL 426
                                       458999*************977 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   6.3e-05      0.14       1      20 [.     409     428 ..     409     490 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.3e-05
                            AAA_18   1 IlltGtpGvGKttlakeLsk 20 
                                       ++ +Gt+G+GK+tl k L +
  gi|336254052|ref|YP_004597159.1| 409 VGFAGTSGSGKSTLLKLLPR 428
                                       6789*************933 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.6   0.00032      0.71      25      57 ..     407     439 ..     394     632 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00032
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflr 57 
                                       e v + G sG+GKs+l++ l+r +  d+ ++l+
  gi|336254052|ref|YP_004597159.1| 407 ETVGFAGTSGSGKSTLLKLLPRFYDVDDRHALA 439
                                       567889***************977766555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (664 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.43
# Mc/sec: 4645.90
//
Query:       gi|336254053|ref|YP_004597160.1|  [L=165]
Description: hypothetical protein Halxa_2664 [Halopiger xanaduensis SH-6]
Scores for 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-21   75.0   2.4    6.1e-21   74.8   2.4    1.1  1  DUF2062     Uncharacterized protein conserved in bacteria (DU
  ------ inclusion threshold ------
        0.1   13.0   0.0       0.15   12.5   0.0    1.2  1  RIC3        Resistance to inhibitors of cholinesterase homolo
       0.18   10.5   0.1       0.24   10.1   0.1    1.2  1  DUF2207     Predicted membrane protein (DUF2207)
        3.2    7.8   5.4         16    5.6   1.0    2.8  3  Sec61_beta  Sec61beta family


Domain annotation for each model (and alignments):
>> DUF2062  Uncharacterized protein conserved in bacteria (DUF2062)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   2.4   1.4e-24   6.1e-21       5     146 ..      15     148 ..      11     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.4e-24
                           DUF2062   5 rylllrllrlhlsprsvarGvaiGvfigflPifglqmllaallalllr.vnlpaavagtwisnPltlppiyylaykl 80 
                                       r+ l   +r + +p+++a+++a Gvf+  lP+ g+ + l ++++ l   v++pa +a + + nP+  p +y+++++l
  gi|336254053|ref|YP_004597160.1|  15 REELTAAFREERTPHQIAASFATGVFVTALPTGGFGVGLFFVFCSLWSwVSKPAIFASVAVLNPFVKPAVYVASFQL 91 
                                       56677889999**************************9999999888769*************************** PP

                           DUF2062  81 GalllgeeaealslseleelglewlleslleiglplllGslilglilallgYflvlllwrlyrrrr 146
                                       G l+lg+ +   s     e++    +++  +++  ll+G ++++l+la++gY+l+l++ +lyrrr 
  gi|336254053|ref|YP_004597160.1|  92 GGLVLGTGPVPSS-----EVS----VDQAGTAARQLLVGNVVVALALAAIGYVLLLRVTQLYRRRD 148
                                       *****99988863.....333....45567999******************************985 PP

>> RIC3  Resistance to inhibitors of cholinesterase homologue 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.3e-05      0.15      48      89 ..      13      57 ..       4      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                              RIC3 48 rmrkhmeeaaakek...gikqgkskglvgtllPlYtiGilvfilY 89
                                      r+r++ ++a ++e+    i ++   g++ t lP  ++G+++f+++
  gi|336254053|ref|YP_004597160.1| 13 RAREELTAAFREERtphQIAASFATGVFVTALPTGGFGVGLFFVF 57
                                      56777777777777444466667789*****************99 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   5.3e-05      0.24     402     454 ..      48     162 ..       2     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.3e-05
                           DUF2207 402 llllvll................................................................lvflli 414
                                        ++++l+                                                                lv+ ++
  gi|336254053|ref|YP_004597160.1|  48 GFGVGLFfvfcslwswvskpaifasvavlnpfvkpavyvasfqlgglvlgtgpvpssevsvdqagtaarqlLVGNVV 124
                                       2222222222455566777888999999999999999999999**************************98888888 PP

                           DUF2207 415 lllillliaiivlllfsrllgrrteeGaellakwkgFkky 454
                                       ++l+l+ i+ ++ll  + l +r  ++G+  l+++ ++ +y
  gi|336254053|ref|YP_004597160.1| 125 VALALAAIGYVLLLRVTQLYRR--RDGQLDLHRASALPNY 162
                                       8888888888888888666666..99**999999999998 PP

>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.021        95      24      37 ..      31      44 ..      31      48 .. 0.90
   2 ?   -1.8   0.0      0.72   3.2e+03      30      37 ..      69      76 ..      66      78 .. 0.58
   3 ?    5.6   1.0    0.0036        16      22      39 ..     123     140 ..     122     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.021
                                      HHHHHHHHHHHHHH CS
                        Sec61_beta 24 lvlsvafiasVilL 37
                                      +++s+a +++V +L
  gi|336254053|ref|YP_004597160.1| 31 IAASFATGVFVTAL 44
                                      799********999 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.72
                                      HHHHHHHH CS
                        Sec61_beta 30 fiasVilL 37
                                      + asV +L
  gi|336254053|ref|YP_004597160.1| 69 IFASVAVL 76
                                      44566666 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHHHHHHHHTS CS
                        Sec61_beta  22 vVlvlsvafiasVilLhi 39 
                                       vV++l++a i+ V+lL++
  gi|336254053|ref|YP_004597160.1| 123 VVVALALAAIGYVLLLRV 140
                                       8***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1243.45
//
Query:       gi|336254054|ref|YP_004597161.1|  [L=270]
Description: hypothetical protein Halxa_2665 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0064   16.6   0.2      0.014   15.6   0.2    1.6  1  HupF_HypC    HupF/HypC family
  ------ inclusion threshold ------
      0.034   14.7   0.0      0.074   13.6   0.0    1.6  1  DNA_pol_B_N  DNA polymerase beta N-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 !   15.6   0.2   1.5e-06     0.014      15      65 .]     156     206 ..     140     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-06
                                       TEEEEECTTEEEEEEGTTCTTB-TT-EEEEETTEEEEEE-HHHHHHHHHHH CS
                         HupF_HypC  15 elAlvdvgGvrrevslalveevkvGdyVLvhvGfAiekideeeaeetlell 65 
                                        +A ++++G++ ev+l+++e v+ +  +Lv vG+  +++  +e + +l+l+
  gi|336254054|ref|YP_004597161.1| 156 FTADAEFEGRSVEVDLHVTEAVETDSDLLVTVGVYPQRLRSQEEDDVLALM 206
                                       5999***************************************99999875 PP

>> DNA_pol_B_N  DNA polymerase beta N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.2e-06     0.074       2      78 ..      98     178 ..      97     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.2e-06
                       DNA_pol_B_N   2 vlaapdisWaGrlvdnpvarlgdpsewevtadesaeaaatgad.....ldidtdtgedgeglsvplavrsisIpLtv 73 
                                       vl++p+i+ aGr+  npv ++++ + +e+ a++ +   +   +       +d++t   + ++++++++rs++++L v
  gi|336254054|ref|YP_004597161.1|  98 VLSTPQIELAGRQF-NPVEEMSTTELVELIASNYEGIGNVTLEeeaaiQVLDQATTRSRFTADAEFEGRSVEVDLHV 173
                                       899*********97.9*******9999999977654222221133333236899999999***************** PP

                       DNA_pol_B_N  74 dasaa 78 
                                       +++++
  gi|336254054|ref|YP_004597161.1| 174 TEAVE 178
                                       99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2111.24
//
Query:       gi|336254055|ref|YP_004597162.1|  [L=380]
Description: Butyryl-CoA dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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  161.0   0.4    3.2e-47  160.5   0.4    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    2.6e-38  131.1   0.2    5.8e-38  130.0   0.1    1.7  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    4.3e-25   87.8   0.0    6.7e-25   87.1   0.0    1.3  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    3.1e-15   56.6   0.9    4.9e-15   56.0   0.9    1.3  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.5   0.4   7.2e-51   3.2e-47       1     149 [.     230     378 ..     230     379 .. 0.99

  Alignments for each domain:
  == domain 1  score: 160.5 bits;  conditional E-value: 7.2e-51
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       g+G++++++tl+ +R+++aa + gla+ a+e a +y+ +r++fg+p+ ++++vr+k+++m+ ++e +rll+yraa++
  gi|336254055|ref|YP_004597162.1| 230 GEGWEQTKKTLDGGRISIAALSTGLAQGAYESAKAYSTEREQFGQPISKFDAVRDKIVDMHRKTERSRLLTYRAART 306
                                       69*************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       +dag+p + e+++aKl ase+a+eva++a+q+lGg+Gy+++ + +r+yrda++++igeGtseiq ++i+r l
  gi|336254055|ref|YP_004597162.1| 307 YDAGEPVTRESALAKLEASEAAREVAEDAVQVLGGYGYTTDFAPQRFYRDAKLMEIGEGTSEIQHLVIGREL 378
                                       ********************************************************************9976 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0   0.1   1.3e-41   5.8e-38       2     113 .]       7     118 ..       6     118 .. 0.99
   2 ?   -3.5   0.0       3.6   1.6e+04      28      42 ..     327     341 ..     315     354 .. 0.54

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 1.3e-41
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                       +e++++r+tvr+f+e+e++p a+e+++e++fp+e++++la+l++lg+++ eeygG+g+d+l +a+vaeel+r++ ++
  gi|336254055|ref|YP_004597162.1|   7 DEHRMIRETVRDFCEREIEPIAQEIEDEHRFPEEIFDQLADLDMLGVPIGEEYGGLGGDTLMYALVAEELGRVSGAI 83 
                                       8**************************9************************************************* PP

                                       HHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  79 alllgvhsslvapailrfGteeqkrryLpklasge 113
                                       +l++ +h sl++++i rfGte+qk+r+L++la+ge
  gi|336254055|ref|YP_004597162.1|  84 GLSYVAHVSLASKPIERFGTEAQKDRWLRPLADGE 118
                                       *********************************98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.6
                                       HHTSGHHHHHHHHHH CS
                     Acyl-CoA_dh_N  28 eegefprelwkklae 42 
                                       +++e+ +++++ l+ 
  gi|336254055|ref|YP_004597162.1| 327 AAREVAEDAVQVLGG 341
                                       222444444555554 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.0   1.5e-28   6.7e-25       2      97 .]     123     218 ..     122     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.5e-28
                                       EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE...GGGEEE- CS
                     Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvp.rdapgvsvr 76 
                                        alTEp++Gsd+ +++tta  ++g+e+vlnG+K++itna +a  +lv a t +p  +++g+s+f+v+ r + g++v+
  gi|336254055|ref|YP_004597162.1| 123 WALTEPESGSDASDMDTTA-VKEGDEWVLNGTKQFITNASEAGSILVKAVT-DPGaGYDGISTFIVDpREDDGFEVS 197
                                       599**************66.455556************************4.44458**********88889***** PP

                                       ----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  77 rieeklGlrglptgelvfedv 97 
                                        i++k+Gl+  pt+e+++e+v
  gi|336254055|ref|YP_004597162.1| 198 TIWDKMGLNASPTCEIRLENV 218
                                       *******************97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.9   1.1e-18   4.9e-15       2     127 ..     246     361 ..     245     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 1.1e-18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       +iaa  +G+A++a++++ ++ +er +  +g++++ + a+  ++ ++  + +  r+l++raa++     +ag++v   
  gi|336254055|ref|YP_004597162.1| 246 SIAALSTGLAQGAYESAKAYSTEREQ--FGQPISKFDAVRDKIVDMHRKTERSRLLTYRAART----YDAGEPV--- 313
                                       79************************..***********************************....9*****9... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHC CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaa 127
                                        ++e+++a++ a+e a++++++++++ Gg++++++   qR++RDa+ ++
  gi|336254055|ref|YP_004597162.1| 314 -TRESALAKLEASEAAREVAEDAVQVLGGYGYTTDFAPQRFYRDAKLME 361
                                       .999*****************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); 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:                         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 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2733.49
//
Query:       gi|336254056|ref|YP_004597163.1|  [L=396]
Description: hypothetical protein Halxa_2667 [Halopiger xanaduensis SH-6]
Scores for 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  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.41
# Mc/sec: 2903.62
//
Query:       gi|336254057|ref|YP_004597164.1|  [L=269]
Description: aminoglycoside phosphotransferase [Halopiger xanaduensis SH-6]
Scores for 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-10   39.3   0.0    7.4e-10   38.7   0.0    1.2  1  RIO1             RIO1 family
    8.2e-09   35.7   0.3     0.0025   17.8   0.3    2.3  2  APH              Phosphotransferase enzyme family
    5.5e-06   25.9   0.0    1.1e-05   24.9   0.0    1.4  1  Kdo              Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00026   20.4   0.0    0.00036   20.0   0.0    1.1  1  Pkinase          Protein kinase domain
  ------ inclusion threshold ------
      0.015   14.7   0.0       0.02   14.3   0.0    1.3  1  APH_6_hur        Aminoglycoside/hydroxyurea antibiotic resist
      0.038   13.9   0.0      0.058   13.4   0.0    1.2  1  Kinase-PolyVal   Serine/Threonine/Tyrosine Kinase found in po
       0.12   12.0   0.0       0.18   11.4   0.0    1.3  1  WaaY             Lipopolysaccharide core biosynthesis protein
       0.14   11.3   0.0        3.7    6.6   0.0    2.4  3  Fructosamin_kin  Fructosamine kinase


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 !   38.7   0.0   3.3e-13   7.4e-10      52     150 ..      93     189 ..      86     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 3.3e-13
                                       HHHHHHHHHHHHHHHHTT--S--EEEEET....TEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHT CS
                              RIO1  52 klwaekEfrnLkrleeagvpvPkpielkr....hvlvmefigedgvaapklkdveeeeeaeelyeevleemrklyke 124
                                       + ++e E+++ +r++e+gv++P+pie  +     vlv+e++  +     +++d+      +e ++++ + m + ++e
  gi|336254057|ref|YP_004597164.1|  93 REMVEHEYEATQRMREIGVNAPRPIEAFEvnglGVLVLEYLP-EFESFGTVSDAV----VDERAADLFD-MLATLHE 163
                                       67899********************986544447********.445556777777....4444455555.666789* PP

                                       STEEESS-STTSEEEETTEEEE--GT CS
                              RIO1 125 aglvHaDLSeyNvlvdedkvviIDvs 150
                                       +gl H+DL   N+l+ ++++++ID  
  gi|336254057|ref|YP_004597164.1| 164 HGLAHGDLRAENILLCDGEIYFIDAT 189
                                       ************************65 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.3   1.1e-06    0.0025      31     108 ..      90     164 ..      11     167 .. 0.81
   2 !   17.3   0.0   1.6e-06    0.0036     166     219 ..     164     218 ..     163     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                                       TS-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHC CS
                               APH  31 araaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalhq 107
                                       + + e ++ e++  + +++ gv +P+++      e++gl ++++ey+p      + s+a+ +e +++l ++la lh+
  gi|336254057|ref|YP_004597164.1|  90 STPREMVEHEYEATQRMREIGVNAPRPIE---AFEVNGLGVLVLEYLPEFESFGTVSDAVVDERAADLFDMLATLHE 163
                                       345688999********************...99*************9877777799*******************9 PP

                                       H CS
                               APH 108 v 108
                                       +
  gi|336254057|ref|YP_004597164.1| 164 H 164
                                       7 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.6e-06
                                       EEEE-SS-SGGGEEEC..TTEEEEE---....TT-EEEECCHHHHCCHHHCSCHCCCH CS
                               APH 166 tvllHgDlhpgNllvdpddgrvtGviDf....edaglgpplyDlavllrswtseldpe 219
                                       ++l HgDl+  N+l+   dg++ ++iD     ed ++   +yDla +l+ +  + +++
  gi|336254057|ref|YP_004597164.1| 164 HGLAHGDLRAENILLC--DGEI-YFIDAtsvhEDRVAETTAYDLACALAVLEPRIGAR 218
                                       5789************..9**9.****999999999************7755555443 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   4.7e-09   1.1e-05      51     165 ..      89     187 ..      83     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.7e-09
                               Kdo  51 fklgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkav 127
                                       f+ +r  +  E+++ +r++e gv++p+p+ a +v        +l+ e l ++++  +++         +  +   ++
  gi|336254057|ref|YP_004597164.1|  89 FSTPREMVEHEYEATQRMREIGVNAPRPIEAFEVNGL----GVLVLEYLPEFESFGTVSDA-------VVDERAADL 154
                                       4445555668999****************88766543....48************999885.......666777788 PP

                               Kdo 128 grliaklhragvnHadlyaknillqqeeeeeaeiwliD 165
                                         + a lh+ g+ H+dl a nill  +e     i++iD
  gi|336254057|ref|YP_004597164.1| 155 FDMLATLHEHGLAHGDLRAENILLCDGE-----IYFID 187
                                       899*********************9886.....77777 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.6e-07   0.00036      48     141 ..      99     187 ..      88     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHS..CTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-S CS
                           Pkinase  48 Eikilkklk..hpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHr 122
                                       E +  ++++    n  r +e+fe +   +lvley+++  ++++    g++s++ + + a+ ++  l+ lH++g+ H 
  gi|336254057|ref|YP_004597164.1|  99 EYEATQRMReiGVNAPRPIEAFEVNGLGVLVLEYLPE--FESF----GTVSDAVVDERAADLFDMLATLHEHGLAHG 169
                                       5555555555555555667777777778889999983..3333....347889999999999*************** PP

                                       S-SGGGEEEETTTEEEE-S CS
                           Pkinase 123 DlKpeNiLidekgelKitD 141
                                       Dl  eNiL+  +ge+  +D
  gi|336254057|ref|YP_004597164.1| 170 DLRAENILLC-DGEIYFID 187
                                       ********98.77776665 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 ?   14.3   0.0   8.9e-06      0.02     137     200 ..     142     209 ..     101     243 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.9e-06
                         APH_6_hur 137 gasrlyveaaaiaaeLleepselrpLHgdlhhenvLagerrgWlaidPkglvGer.....gfdlanllr 200
                                       +   +++e aa    +l++ +e ++ Hgdl+ en+L  + +    id   ++ +r     ++dla +l 
  gi|336254057|ref|YP_004597164.1| 142 VSDAVVDERAADLFDMLATLHEHGLAHGDLRAENILLCDGE-IYFIDATSVHEDRvaettAYDLACALA 209
                                       556677888888999*********************99954.445666555544322222777776665 PP

>> Kinase-PolyVal  Serine/Threonine/Tyrosine Kinase found in polyvalent proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.6e-05     0.058     128     155 ..     162     189 ..     159     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                    Kinase-PolyVal 128 kelgliledlhdeNVltkdgtlyfIDtv 155
                                       +e+gl+  dl +eN+l  dg++yfID+ 
  gi|336254057|ref|YP_004597164.1| 162 HEHGLAHGDLRAENILLCDGEIYFIDAT 189
                                       57788899******************86 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.9e-05      0.18      89     180 ..     103     190 ..      85     208 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.9e-05
                              WaaY  89 tdrvrseglaalndfyllaerkilryvkvyimiieyiegielvdm..peiddevkakikqsieklhqlgmvsgdphr 163
                                       t+r+r+ g++a+        +  ++     ++++ey+   e        + de  a++ + + +lh++g+  gd   
  gi|336254057|ref|YP_004597164.1| 103 TQRMREIGVNAPRP------IEAFEVNGLGVLVLEYLPEFESFGTvsDAVVDERAADLFDMLATLHEHGLAHGDLRA 173
                                       55555555555543......3445555566788899887775432113456666778888999************** PP

                              WaaY 164 gnfivkkdevriidlsg 180
                                        n+++ ++e+  id + 
  gi|336254057|ref|YP_004597164.1| 174 ENILLCDGEIYFIDATS 190
                                       *************9764 PP

>> Fructosamin_kin  Fructosamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.3     3e+03     161     196 ..       7      42 ..       2      47 .. 0.79
   2 ?    6.6   0.0    0.0017       3.7      52      97 ..      92     136 ..      77     167 .. 0.73
   3 ?    2.6   0.0     0.029        65     188     221 ..     164     196 ..     143     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                   Fructosamin_kin 161 kekglefakieelvervaellskhqpkpsllHGdLW 196
                                       ++  +e+++ie++v ++a++   + ++   l  d W
  gi|336254057|ref|YP_004597164.1|   7 ARGSIEWGRIERVVRTLADRYDREVVRVEFLEADNW 42 
                                       455678899999999999999999998888888887 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0017
                   Fructosamin_kin  52 alemFeaEaesLealaetqtirvPkvlavGelkdasfLvleyLelk 97 
                                        +em e+E+e  + ++e   ++ P+++ + e++    LvleyL+  
  gi|336254057|ref|YP_004597164.1|  92 PREMVEHEYEATQRMRE-IGVNAPRPIEAFEVNGLGVLVLEYLPEF 136
                                       57899**********55.679**********************853 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.029
                   Fructosamin_kin 188 psllHGdLWsgNaaltkdgepvifdPaayygdrE 221
                                         l HGdL  +N+ l + ge +++d  + + dr 
  gi|336254057|ref|YP_004597164.1| 164 HGLAHGDLRAENILLCD-GEIYFIDATSVHEDRV 196
                                       5689********98775.5599999988888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2131.80
//
Query:       gi|336254058|ref|YP_004597165.1|  [L=511]
Description: aldehyde dehydrogenase [Halopiger xanaduensis SH-6]
Scores for complete 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-143  478.9   0.0   1.5e-143  478.7   0.0    1.0  1  Aldedh         Aldehyde dehydrogenase family
  ------ inclusion threshold ------
      0.026   14.5   0.9      0.054   13.5   0.9    1.4  1  OmdA           Bacteriocin-protection, YdeI or OmpD-Associate
      0.034   13.5   0.0       0.15   11.4   0.0    1.9  2  SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
       0.15   11.1   0.0        0.3   10.1   0.0    1.5  1  LuxC           Acyl-CoA reductase (LuxC)


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 !  478.7   0.0  3.3e-147  1.5e-143       1     459 [.      18     485 ..      18     488 .. 0.97

  Alignments for each domain:
  == domain 1  score: 478.7 bits;  conditional E-value: 3.3e-147
                                       EET-SS.SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHH CS
                            Aldedh   1 wveses.etievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaelet 76 
                                       w+++++ +t+e+ nPatge++a+++++t++dvdaa++aA++af++w++l+  +Rae+L  + + l++r+eel e+ t
  gi|336254058|ref|YP_004597165.1|  18 WTDGSGsDTFESENPATGETLATFRRGTEDDVDAALEAAEDAFEEWRELSYIDRAEYLWDIYHELRDRHEELGEIVT 94 
                                       888888678******************************************************************** PP

                                       HHH---HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEEC.TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHH CS
                            Aldedh  77 letGkplaearaeveeaidvlryyaelaeklegevlpss.egklalvrrePlGvvgaItPWNfPlllaawklapala 152
                                       +e+Gk ++e +a+v+ea ++++++a+ a++ +g+++ps+  +k+a++rr+P Gv+g+ItPWNfP++++ w++a+al+
  gi|336254058|ref|YP_004597165.1|  95 KECGKEISEGKADVTEAWHMVEWAAGNARHPHGDIVPSEiGSKDAYMRRKPRGVIGCITPWNFPVAIPFWHMAIALV 171
                                       **************************************55************************************* PP

                                       TT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHH.HHCT CS
                            Aldedh 153 aGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiaka.aakn 228
                                        GNtvv+KPae+tp++  ++ae++e+ag+P+gv+n+v+g g ++g+a++++ +vd v ftGs evg++ia++  ++ 
  gi|336254058|ref|YP_004597165.1| 172 EGNTVVWKPAEQTPWCGQIIAEMMEDAGIPEGVFNMVQGFG-DAGAAITDDGRVDTVLFTGSAEVGHEIASKvGGEP 247
                                       ***************************************88.6*****************************55588 PP

                                       TSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT CS
                            Aldedh 229 lkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdplded 305
                                        k  + E+GGkn ++++e+aDld av+++v+++f ++GQ+C++ +rl+v+e++ydef e++v+ a+++ vgdpl+ed
  gi|336254058|ref|YP_004597165.1| 248 GKLAACEMGGKNGIVITEEADLDIAVHSAVMSSFKTTGQRCVSSERLIVHEDVYDEFKERFVDIAEDIAVGDPLEED 324
                                       999************************************************************************** PP

                                       -SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TT.....E.SB-SSSTTEE--EEEE.S-TTTSHHHHS---SSEEE CS
                            Aldedh 306 tdvGPliseaqlekvekyveeakeegaklllGge.....reeaglekgyfvePtvla.nvtpdmriaqeEiFGPVls 376
                                       t +GP i+++++ek+++y e a+eeg ++l++       +  +g e+g++v P v + + ++d r+++eE+FGP ++
  gi|336254058|ref|YP_004597165.1| 325 TFMGPAIEADHVEKIRQYNELAREEGGEVLVDRFeleddEIPDGHEDGHWVGPFVYEiDYDTDLRCLKEECFGPHVA 401
                                       *******************************876666666678999*********98689**************999 PP

                                       EEEES.SHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHH CS
                            Aldedh 377 vikfk.deeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkeg 452
                                       +++++ d++ aiei Ndt+yGLa++++++d ++++r+ +r + G  y N ++ ga+ +lpfgGvk+Sg+G  + +e+
  gi|336254058|ref|YP_004597165.1| 402 LVEYSgDIDRAIEIHNDTPYGLAGAIISEDYRQINRFRDRADLGLAYANLPCIGAEVQLPFGGVKKSGNGYPSAREA 478
                                       999998*********************************************************************** PP

                                       HHHTEEE CS
                            Aldedh 453 leeytev 459
                                       +e++te 
  gi|336254058|ref|YP_004597165.1| 479 IEAVTER 485
                                       **99985 PP

>> OmdA  Bacteriocin-protection, YdeI or OmpD-Associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.9   1.2e-05     0.054       6      38 ..      47      79 ..      46      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                              OmdA  6 edlaaaLdadpaakaaFealtpsyrreylrwie 38
                                      +d+ aaL+a ++a + + +l++  r eyl+ i 
  gi|336254058|ref|YP_004597165.1| 47 DDVDAALEAAEDAFEEWRELSYIDRAEYLWDIY 79
                                      7999**************************995 PP

>> SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.4e-05      0.15      42     118 ..      32     112 ..      26     118 .. 0.81
   2 ?   -1.5   0.0       0.3   1.3e+03     132     142 ..     198     208 ..     191     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.4e-05
                     SPOUT_MTase_2  42 kvdayelaeflrgvreGqesRyeiqkksyg..revrkvp..vlvqdlyqlvrkrrkkellivtdPeGeeisevkeel 114
                                       ++ +  la+f rg ++ + + +e  +++++  re++ ++   +++d+y+ +r+r+++   ivt   G+eise k ++
  gi|336254058|ref|YP_004597165.1|  32 PATGETLATFRRGTEDDVDAALEAAEDAFEewRELSYIDraEYLWDIYHELRDRHEELGEIVTKECGKEISEGKADV 108
                                       5667889999999999999999999999863345555542248*************8899**************999 PP

                     SPOUT_MTase_2 115 aeal 118
                                       +ea 
  gi|336254058|ref|YP_004597165.1| 109 TEAW 112
                                       9875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.3
                     SPOUT_MTase_2 132 eGiPkGlfrfa 142
                                        GiP+G+f++ 
  gi|336254058|ref|YP_004597165.1| 198 AGIPEGVFNMV 208
                                       69******875 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   6.6e-05       0.3      80     139 ..     137     196 ..     131     316 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.6e-05
                              LuxC  80 keksyekaqprglvlhvlsgNvpl.lpvmsilqglLvknvnllkvSssdpflaaallksla 139
                                       k+  y+++ prg++  +++ N p+ +p++ ++ +l+ +n  + k+  + p     ++  + 
  gi|336254058|ref|YP_004597165.1| 137 KD-AYMRRKPRGVIGCITPWNFPVaIPFWHMAIALVEGNTVVWKPAEQTPWCGQIIAEMME 196
                                       44.8*******************7589*****************99888877666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 3889.56
//
Query:       gi|336254059|ref|YP_004597166.1|  [L=288]
Description: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-50  170.1   0.0    6.4e-50  169.9   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase
  ------ inclusion threshold ------
       0.05   13.6   0.0        2.1    8.4   0.0    2.6  2  DUF3875       Domain of unknown function, B. Theta Gene descr


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 !  169.9   0.0   7.1e-54   6.4e-50       2     260 ..      20     277 ..      19     278 .. 0.95

  Alignments for each domain:
  == domain 1  score: 169.9 bits;  conditional E-value: 7.1e-54
                                       EEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEE CS
                      CN_hydrolase   2 vAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiav 78 
                                       +A++Q++  a   e n++++++++++Aa +gadL++lPElf++gy  ++++  ++e  +get+ +l+ +a++n++av
  gi|336254059|ref|YP_004597166.1|  20 IALAQIRVEAGRVERNVDRAVSAVERAAARGADLVALPELFNVGYFAFDRYARLSEPFDGETFTALRTAAADNDVAV 96 
                                       799*****9******************************************************************** PP

                                       EEEEEEEEC.........CTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTE CS
                      CN_hydrolase  79 viglierel.........tngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvg 146
                                        +g i ++l         ++  l   nta l+d+ g l   yrK+hLf     + ++ e+el+ pg++++ +  +++
  gi|336254059|ref|YP_004597166.1|  97 LAGSIVEDLaatetvptpADEGL--ANTAALFDAAGDLQLVYRKHHLF-----GYQSAESELLVPGERLETATIEGV 166
                                       ***99987899999**7777777..***********************.....689***********9999999999 PP

                                       EEEEEEGGGGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEE..HCETTEE CS
                      CN_hydrolase 147 kiGaaiCyeigfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvgg..yeqlilw 221
                                        +G+  Cy+ +fpel+r l  +gae+++  s     + ++  ++we+l+rara+en+c+v+ +n +g+    ++ + 
  gi|336254059|ref|YP_004597166.1| 167 TAGVTTCYDLRFPELYRRLVDEGAELVLVPS----AWPYPRIEHWETLSRARAIENQCYVATINGAGTfdTDDGETT 239
                                       *****************************44....45677789**************************9999**** PP

                                       EE--EEEE-TTS-EEEECCSSSTEEEEEEEEHHHHHHHH CS
                      CN_hydrolase 222 pvghSaiidpdGrilaglgeeeegvliaeidladvratr 260
                                        +g S ++dp+G  la  g +  +++ a++d+++v+ +r
  gi|336254059|ref|YP_004597166.1| 240 LLGRSTVYDPWGVSLASSGDDP-TLVAADVDRETVADVR 277
                                       **********************.7***********9987 PP

>> DUF3875  Domain of unknown function, B. Theta Gene description (DUF3875)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.022   1.9e+02      35      44 ..      54      63 ..      51      69 .. 0.82
   2 ?    8.4   0.0   0.00023       2.1      22      41 ..     163     182 ..     150     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.022
                           DUF3875 35 velPEiFtvs 44
                                      v+lPE+F v 
  gi|336254059|ref|YP_004597166.1| 54 VALPELFNVG 63
                                      89*****996 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00023
                           DUF3875  22 ivSkdaditvafevelPEiF 41 
                                       i    a +t ++ ++ PE++
  gi|336254059|ref|YP_004597166.1| 163 IEGVTAGVTTCYDLRFPELY 182
                                       5566799************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2199.75
//
Query:       gi|336254060|ref|YP_004597167.1|  [L=146]
Description: polyketide cyclase/dehydrase [Halopiger xanaduensis SH-6]
Scores for complete 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-17   64.2   1.7    1.7e-17   64.0   1.7    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    1.7e-06   27.9   0.0    2.2e-06   27.5   0.0    1.2  1  COXG             Carbon monoxide dehydrogenase subunit G (Cox
    0.00016   21.9   0.2    0.00021   21.5   0.2    1.2  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.083   13.1   0.5       0.42   10.8   0.5    2.0  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   1.7   3.8e-21   1.7e-17       2     143 .]       3     137 ..       2     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 3.8e-21
                                       EEEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCS.....SEEEEEEEEEETTTT CS
                   Polyketide_cyc2   2 vkvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggr.....gtvreelvevdpegr 73 
                                       v+v +s ++ appe+Vw++++d+en +r ++ v+r++ ++++g+  +v ++v            v+ e v+++p + 
  gi|336254060|ref|YP_004597167.1|   3 VRVDRSFEVSAPPERVWEFIADPENRARAISVVQRYTADDPEGR--RVTWHVELPIPlvrrtVAVETEDVTRRP-PE 76 
                                       79***********************************9998888..7778888776677756558888888889.9* PP

                                       EEEEEEE.SSS-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Polyketide_cyc2  74 llsyrivkpvpvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaakavkgdleagLerLkarle 143
                                        +++ +  + +v  ++++ ++ + +ggtr+++++ +d     g +  p ++k++k++l++ +++L ++le
  gi|336254060|ref|YP_004597167.1|  77 YVKFVG--KSKVLEVTGEHEIVEIDGGTRLENHFVVD-----GKL--PGVEKFFKRNLDDEIRNLHRALE 137
                                       ******..699999********************999.....554..7899***************9997 PP

>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   4.9e-10   2.2e-06       2     110 ..       8     116 ..       7     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 4.9e-10
                                       EEEESS-HHHHHHHHT-HHHHGGGSTTEEEEEEET.TEEEEEEEEESSSSEEEEEEEEEEEEEETTTEEE..EEEEE CS
                              COXG   2 efrvaapkeavwefLndpeklarciPGvksvekeg.deykvkvklkvGplkgsfkarvelselekensttieikGkG 77 
                                       +f+v+ap+e vwef+ dpe+ ar+i  v+ +++ + +  +v+  +++ +  ++ ++ ve +++      ++++ Gk 
  gi|336254060|ref|YP_004597167.1|   8 SFEVSAPPERVWEFIADPENRARAISVVQRYTADDpEGRRVTWHVELPIPLVRRTVAVETEDVTRRPPEYVKFVGKS 84 
                                       79*******************************99999999988888887788888888888877666679999999 PP

                                       E-SSEEEEEEEEEEEEEETTEEEE..EEEEEEEEE CS
                              COXG  78 rgagvaidfalvvlveegggtrls..wsakvnvgg 110
                                       +   v+ + ++v ++   ggtrl+  +++++++ g
  gi|336254060|ref|YP_004597167.1|  85 KVLEVTGEHEIVEID---GGTRLEnhFVVDGKLPG 116
                                       999999888888888...45887522445555555 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   4.6e-08   0.00021       1     129 [.      11     136 ..      11     137 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.6e-08
                                       ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE.....EEEECSTTSSCEEE...EEEEEEEETTTEEECTTCC CS
                    Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaes..glsadlevgfggltesf...tarvtldppeeitfklveg 72 
                                       v+ap++ v++++ad e+  + ++ +++ +  + ++    +  ++e+  + ++++    t++vt+ ppe+        
  gi|336254060|ref|YP_004597167.1|  11 VSAPPERVWEFIADPENRARAISVVQRYTADDPEGRrvTW--HVELPIPLVRRTVaveTEDVTRRPPEY-------- 77 
                                       79************************98888888874444..556666666666655777888888888........ PP

                                       CCCEEEEEEEECTECCEEE.....CEEEEEEEEEEEE-SSCHHHHHHHHHHHHHHHHHHHHH CS
                    Polyketide_cyc  73 dfkslegkWtieslppnsg.....gtrtkvalevdfkfaspllgalvgqvaervldellaal 129
                                          +++gk ++ ++   ++     + +t+++  + ++++ p ++ + +  +++++++l +al
  gi|336254060|ref|YP_004597167.1|  78 --VKFVGKSKVLEVTG-EHeiveiDGGTRLENHFVVDGKLPGVEKFFKRNLDDEIRNLHRAL 136
                                       ..55666666666663.444555555566666666777888888888888888888777766 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5   9.4e-05      0.42       2      38 ..      13      50 ..      12     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.4e-05
                                      S-HHHHHHHHH-HHHHHHH.EEEEEEEE--STTEEEEE CS
                             AHSA1  2 apperVfraltdpellkrW.ftlteaemdlrpGgkfrl 38
                                      apperV++ + dpe  +r    +++ + d  +G ++++
  gi|336254060|ref|YP_004597167.1| 13 APPERVWEFIADPENRARAiSVVQRYTADDPEGRRVTW 50
                                      9*************999853444444444444555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1086.27
//
Query:       gi|336254061|ref|YP_004597168.1|  [L=74]
Description: hypothetical protein Halxa_2672 [Halopiger xanaduensis SH-6]
Scores for 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   0.0      0.005   17.2   0.0    1.2  1  FaeA            FaeA-like protein
     0.0076   16.2   0.0      0.013   15.5   0.0    1.3  1  Put_DNA-bind_N  Putative DNA-binding protein N-terminus
  ------ inclusion threshold ------
       0.08   13.0   0.0       0.13   12.3   0.0    1.4  1  z-alpha         Adenosine deaminase z-alpha domain
      0.097   12.5   0.1       0.38   10.6   0.1    2.0  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.1e-06     0.005       3      60 ..       9      71 ..       7      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHHH.....S----HHHHHHHHTS-HHHHHHHHHHH.HHHSSEEEE--SSSSS-EEEE CS
                              FaeA  3 eeIleylnsi....kapckTreiAdalglsaYQaRyYLeqL.ekegkikrspvrrGvstlWel 60
                                      + Il+yl +     +   + ++iAda+gls  Q+   L  L ek   +     +r  st W++
  gi|336254061|ref|YP_004597168.1|  9 QRILSYLRESaargERYFRAKNIADAIGLSSKQVGARLPHLaEKSDDVDIEKWGRARSTTWKV 71
                                      57999999975554455799****************9*9985788889999999999999987 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.9e-06     0.013      14      44 ..      12      42 ..      10      43 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.9e-06
                                      HHHHHHHHHTT--EE-HHHHHHHCTS-HHHH CS
                    Put_DNA-bind_N 14 lryLeelkeegveriSSteLaealgvtaaqv 44
                                      l+yL+e  ++g+ +  ++ +a+a+g+++ qv
  gi|336254061|ref|YP_004597168.1| 12 LSYLRESAARGERYFRAKNIADAIGLSSKQV 42
                                      79****************************9 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.9e-05      0.13       1      49 [.       3      53 ..       3      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
                                      HHHHHHHHHHHHHHHC-TTCE.....CCHHHHHHHHCC-HHHHHHHHHHHHHTT CS
                           z-alpha  1 iaqeqaekilelLeelgekka.....atalalergLstpkreiNrvLydlerkg 49
                                      ++ +++++il +L+e+    +     a+++a ++gLs   + + + L  l++k 
  gi|336254061|ref|YP_004597168.1|  3 DYSDEEQRILSYLRESA-ARGeryfrAKNIADAIGLS--SKQVGARLPHLAEKS 53
                                      67899**********97.3322334499*********..699999999997654 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 ?   10.6   0.1   8.4e-05      0.38      21      38 ..      29      46 ..       9      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.4e-05
                     HTH_AsnC-type 21 aeLAervGlSestvlrRv 38
                                      + +A+++GlS  +v +R+
  gi|336254061|ref|YP_004597168.1| 29 KNIADAIGLSSKQVGARL 46
                                      57***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 545.13
//
Query:       gi|336254062|ref|YP_004597169.1|  [L=60]
Description: hypothetical protein Halxa_2673 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        1.6    8.6   3.5          2    8.3   3.5    1.1  1  DUF3767   Protein of unknown function (DUF3767)


Domain annotation for each model (and alignments):
>> DUF3767  Protein of unknown function (DUF3767)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.5   0.00011         2      29      67 ..      14      51 ..      12      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00011
                           DUF3767 29 lltGigagavvGglrfvlkknvakaaNWavgafllgsiv 67
                                      l +G ga av+G+l +v++++  +aa W+ ga +l s +
  gi|336254062|ref|YP_004597169.1| 14 LALGCGAIAVLGALLMVIGAPEIQAA-WGFGAAVLFSAI 51
                                      56799***************998887.**9999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 478.80
//
Query:       gi|336254063|ref|YP_004597170.1|  [L=343]
Description: phosphate uptake regulator PhoU [Halopiger xanaduensis SH-6]
Scores for 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-15   56.4   2.7    2.8e-11   43.7   0.0    2.6  2  PhoU            PhoU domain
      9e-07   28.7   0.0      2e-06   27.6   0.0    1.6  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   3.1e-15   2.8e-11       1      89 []     139     231 ..     139     231 .. 0.86
   2 !   10.5   2.3   7.4e-05      0.67       1      88 [.     249     327 ..     249     332 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 3.1e-15
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH.....HHHH.HHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae.....dlre.llsllri 71 
                                       l+r+ ++ ++m  + ++al++++ +la++ ++r++++++++ ++ r +++a+ +  +la+        + l+++++i
  gi|336254063|ref|YP_004597170.1| 139 LERLERTGQTMRGEGIKALAHGNPDLAQRALNRERQANKIFVLLLRLIFTAYQN-PNLARavglsSG-FpLIGYRSI 213
                                       67899999*****************************************99955.445554644422.13699**** PP

                                       HHHHHHHHHHHHHHHHHH CS
                              PhoU  72 ardlERigDhavniaerv 89 
                                       a++lE  +D  ++iae+v
  gi|336254063|ref|YP_004597170.1| 214 AKNLELTADNGEDIAEIV 231
                                       ****************86 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 7.4e-05
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlER 77 
                                       +r++ ++v e+ ++a+ea +++d +  ++v+ +  ei  le+ei  +l e+   ++ l       l ++++  +lE 
  gi|336254063|ref|YP_004597170.1| 249 IRELNDLVDEITSLAVEAAVKRDYDKSNQVRGLFHEISTLEDEILADLPEMP--NEDL-------LRVREVLVSLEQ 316
                                       68999**************************************988843333..3333.......335556667777 PP

                                       HHHHHHHHHHH CS
                              PhoU  78 igDhavniaer 88 
                                        + +a + ae+
  gi|336254063|ref|YP_004597170.1| 317 TAQYAMRNAEI 327
                                       77776666665 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 !   27.6   0.0   2.3e-10     2e-06       5      40 ..      12      48 ..       8      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.3e-10
                                      TEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCC CS
                    MazE_antitoxin  5 nsgavriPkevrfelgireGdevelevdgd.kiilrp 40
                                      +++a+++P+e++ e+ +++Gdev l++ g   + + p
  gi|336254063|ref|YP_004597170.1| 12 STLAMTLPAEWASEHAVEKGDEVSLRTSGKgTLTVMP 48
                                      899************************9986666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2735.61
//
Query:       gi|336254064|ref|YP_004597171.1|  [L=383]
Description: ATP-NAD/AcoX kinase [Halopiger xanaduensis SH-6]
Scores for 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-41  141.8   1.7    7.2e-41  140.3   1.7    1.6  1  NAD_kinase  ATP-NAD kinase
    4.1e-06   26.4   0.7      1e-05   25.1   0.1    2.0  2  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 !  140.3   1.7     8e-45   7.2e-41       2     292 .]       4     382 ..       3     382 .. 0.90

  Alignments for each domain:
  == domain 1  score: 140.3 bits;  conditional E-value: 8e-45
                                       EEEEESSC........................GGTCSHHHHHHHHHHHCT-..EEEEECCGGCCSSSTT--HHHHTT CS
                        NAD_kinase   2 vgivvnpi........................kkeaieraeevarwLldalsrvlevtveeklgeslaeaaefrsev 54 
                                       +g+vvnpi                        ++ a +ra+  +r L ++ ++v   t ++ lge+ a+ a+f++ev
  gi|336254064|ref|YP_004597171.1|   4 LGVVVNPIagmggrvglkgtdgkvpearrlgaEPRAPDRARDALRSLHRRGPDVTVYTAAGVLGEHAARDAGFDPEV 80 
                                       699*************************6666666666666666666666449999999****************** PP

                                       TT--.......................EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHH..............C CS
                        NAD_kinase  55 isvlkkvkttd................dtrkaleafadagvdliivvGGDGTaldvarllqk..............a 101
                                       ++ + + + td                dt +a++af +++vdl+++vGGDGTa dva++l++              +
  gi|336254064|ref|YP_004597171.1|  81 VYDPATDADTDrqatgvdldetettaaDTQAAVRAFLERDVDLVLFVGGDGTAVDVAEVLEDesdskrdsneygagD 157
                                       **9999999999************************************************99888888888887778 PP

                                       T-EEEEEESSS--SS-SE..EGGGHHHHHHHHHHT-SEEEEEEEEE........................EEEEETT CS
                        NAD_kinase 102 eiPvlgvnaGvkgfltef..epeaaaellekllegeirvekrevld........................avimrsk 152
                                       + P lgv+aGvk+++++f  +p++a+++++++ +    ve+rev d                          i+ sk
  gi|336254064|ref|YP_004597171.1| 158 RTPMLGVPAGVKIYSSVFavTPADAGRIAAEFDR----VETREVNDideeayregevrtelkavvpvpvaPDIQSSK 230
                                       9****************************99987....999999998899999999999999999988885555555 PP

                                       E...........EEEEEEESSEEEEEESSSSS-EE..EEEEETTEEEEEEEESEE.....................E CS
                        NAD_kinase 153 gee.....diadiviensvlnevviirgpgstlie..lelyvdtelleadqldgl.....................i 201
                                       +       ++a       + ++ ++++gpg t+     el++d ++l++d+ +++                     i
  gi|336254064|ref|YP_004597171.1| 231 QLSsgsvdSLASGF-AREIDDGRTYVFGPGGTVGAieEELGIDSSPLGVDVWRDGevlardaaesdilavledpvtI 306
                                       54477664455444.5568*************98877**************************************** PP

                                       EE-TGGGGTHHHHTT--EE-TT---EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EE CS
                        NAD_kinase 202 vstPtGstayslsaGgplisPgvlailivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdev 278
                                       v++P+G++++++++G+ +isP+v +          +++++ Vv+s++kl+     +++al +++  e+++ ++++++
  gi|336254064|ref|YP_004597171.1| 307 VVSPIGGQGFVFGRGNHQISPAVIE----------RADELEVVASEEKLD-----GIDALHVDTDGEDVNEELRGWL 368
                                       *************************..........***************.....********************** PP

                                       EEEEESSEEEEEE. CS
                        NAD_kinase 279 rvtasdkkfklirl 292
                                       rv+++++ ++l+++
  gi|336254064|ref|YP_004597171.1| 369 RVRTGRFTTRLVKV 382
                                       ***********986 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       1.1   9.9e+03       4      12 ..       6      14 ..       4      17 .. 0.80
   2 !   25.1   0.1   1.1e-09     1e-05      29      78 ..      95     147 ..      86     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.1
                                      EEE-TTCTT CS
                          DAGK_cat  4 vivNpksGk 12
                                      v+vNp +G 
  gi|336254064|ref|YP_004597171.1|  6 VVVNPIAGM 14
                                      89***9995 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.1e-09
                                       CTCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCT....H CS
                          DAGK_cat  29 agvelelieteepgdakelakeakeegvdlivvaGGDGtvsevlnglle....e 78 
                                        gv+l+ +et+ + d ++ ++   e++vdl++ +GGDGt+  v+++l +    +
  gi|336254064|ref|YP_004597171.1|  95 TGVDLDETETT-AADTQAAVRAFLERDVDLVLFVGGDGTAVDVAEVLEDesdsK 147
                                       45666666666.777899999**************************9954431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3004.32
//
Query:       gi|336254065|ref|YP_004597172.1|  [L=40]
Description: hypothetical protein Halxa_2676 [Halopiger xanaduensis SH-6]
Scores for 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:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 322.14
//
Query:       gi|336254066|ref|YP_004597173.1|  [L=227]
Description: molybdopterin binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-38  129.5   0.1    1.2e-37  128.8   0.1    1.3  1  MoCF_biosynth  Probable molybdopterin binding domain
  ------ inclusion threshold ------
      0.024   14.6   0.3      0.096   12.6   0.0    2.1  2  HTH_15         Helix-turn-helix domain of alkylmercury lyase


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.8   0.1   1.3e-41   1.2e-37       1     141 [.       4     158 ..       4     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 128.8 bits;  conditional E-value: 1.3e-41
                                       EEEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHH CS
                     MoCF_biosynth   1 avitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpea 77 
                                       av+tvGdell+g++++tn+ +l+e+l e+gv v+++t+vpD  ++i++ + +  +e+d++++tGG+Gpt+dDvt e 
  gi|336254066|ref|YP_004597173.1|   4 AVVTVGDELLAGQTTNTNATWLCERLDERGVAVERVTTVPDRVADIARVVNEYRAEYDAVVVTGGLGPTHDDVTMEG 80 
                                       79************************************************5555677******************** PP

                                       HHHHHSEE-HHHHHHHHHHHHHHCC.....................TTSHGGGGGGE.EETTEEEEE-SSHHHHHHH CS
                     MoCF_biosynth  78 laklfekelegfeeafrrvslkpgk.....................pvgvapgailsravgktiigLPGspkavkea 133
                                       +a++++++le++eea+  ++   g                      + gvapga l++     +++LPG+p +++++
  gi|336254066|ref|YP_004597173.1|  81 IAAALGRPLEEHEEALAWLGED-GYsrseliegttklpagaralhnEAGVAPGAALED-----VYVLPGVPTEMQAM 151
                                       *******************999.5569*****************************85.....9************* PP

                                       HHHHHHGG CS
                     MoCF_biosynth 134 leeillpa 141
                                       +e i  pa
  gi|336254066|ref|YP_004597173.1| 152 FEAIA-PA 158
                                       ****8.76 PP

>> HTH_15  Helix-turn-helix domain of alkylmercury lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.1e-05     0.096      35      58 ..      75      98 ..      72     105 .. 0.90
   2 ?   -3.9   0.1       1.6   1.4e+04      42      52 ..     214     224 ..     211     226 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                            HTH_15 35 pVtveeLAaatgrsveevrqaLaa 58
                                       Vt+e++Aaa+gr++ee ++aLa 
  gi|336254066|ref|YP_004597173.1| 75 DVTMEGIAAALGRPLEEHEEALAW 98
                                      59*******************985 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.6
                            HTH_15  42 Aaatgrsveev 52 
                                       A+a+++  e+v
  gi|336254066|ref|YP_004597173.1| 214 AEAAAWLRERV 224
                                       78888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1698.65
//
Query:       gi|336254067|ref|YP_004597174.1|  [L=117]
Description: hypothetical protein Halxa_2678 [Halopiger xanaduensis SH-6]
Scores for 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-07   29.6   0.1    1.1e-06   28.5   0.0    1.6  2  HTH_20    Helix-turn-helix domain
    0.00022   21.1   0.0    0.00042   20.1   0.0    1.6  1  TrmB      Sugar-specific transcriptional regulator TrmB
    0.00042   19.8   0.0    0.00097   18.7   0.0    1.7  2  HTH_24    Winged helix-turn-helix DNA-binding
      0.003   17.2   0.0     0.0055   16.4   0.0    1.4  1  RP-C      Replication protein C N-terminal domain
  ------ inclusion threshold ------
      0.066   13.2   0.0       0.11   12.5   0.0    1.3  1  PadR      Transcriptional regulator PadR-like 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 !   28.5   0.0   3.2e-10   1.1e-06       1      58 [.      13      68 ..      13      70 .. 0.92
   2 ?   -1.8   0.0      0.96   3.4e+03      37      37 ..     103     103 ..      76     117 .] 0.50

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 3.2e-10
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      d++++AL+++  ++il a   + + +a +l e ++++ +t+++++++L++agL++ ++
  gi|336254067|ref|YP_004597174.1| 13 DTVLSALGNKYSAEILCAA--GTPKSAQALSEDIEIPIATCYRRIEELVDAGLLTCEG 68
                                      5789999999999999999..*********************************9886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.96
                                       - CS
                            HTH_20  37 s 37 
                                       +
  gi|336254067|ref|YP_004597174.1| 103 R 103
                                       2 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.2e-07   0.00042      22      58 ..      34      70 ..      25      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-07
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      p++a+ ++e++++p +++Y+ +++L+d+Gl + e ++
  gi|336254067|ref|YP_004597174.1| 34 PKSAQALSEDIEIPIATCYRRIEELVDAGLLTCEGRE 70
                                      789***************************8876554 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   2.7e-07   0.00097      19      47 ..      36      64 ..      26      65 .. 0.91
   2 ?   -2.0   0.0      0.78   2.8e+03      12      19 ..      71      78 ..      69      85 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.7e-07
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      s + L+e + ++++t+ rr+++L+++Gl+
  gi|336254067|ref|YP_004597174.1| 36 SAQALSEDIEIPIATCYRRIEELVDAGLL 64
                                      6789***********************97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.78
                            HTH_24 12 Lqknpris 19
                                      L +++r +
  gi|336254067|ref|YP_004597174.1| 71 LSEKGRRT 78
                                      44444443 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 !   16.4   0.0   1.5e-06    0.0055      48     103 ..      14      66 ..       7      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                              RP-C  48 avLdaLlsftpeddlseearlivfpsNaqLsralglsestlrrhlaaLveaGliir 103
                                       +vL+aL + ++++ l + +++   +s+++Ls+ + ++ +t  r + +Lv+aGl++ 
  gi|336254067|ref|YP_004597174.1|  14 TVLSALGNKYSAEILCAAGTP---KSAQALSEDIEIPIATCYRRIEELVDAGLLTC 66 
                                       689999999999999999988...9****************************985 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     3e-05      0.11      22      66 ..      40      84 ..      34      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                                      CSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S.TSSS-EEEEEES CS
                              PadR 22 lsegllelseGslYpaLkrLekeglvesewees.gegpprkyYrlT 66
                                      lse  +e+  ++ Y+  ++L + gl++ e +e  ++g+++++Yr T
  gi|336254067|ref|YP_004597174.1| 40 LSED-IEIPIATCYRRIEELVDAGLLTCEGRELsEKGRRTNIYRRT 84
                                      4444.7888899***************998876799*******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 925.73
//
Query:       gi|336254068|ref|YP_004597175.1|  [L=165]
Description: queuosine biosynthesis protein QueD [Halopiger xanaduensis SH-6]
Scores for 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-23   81.0   0.0      1e-22   80.4   0.0    1.1  1  PTPS      6-pyruvoyl tetrahydropterin synthase
  ------ inclusion threshold ------
       0.12   12.4   0.1       0.19   11.7   0.1    1.4  1  GYD       GYD domain
       0.13   12.6   0.1       0.19   12.1   0.1    1.2  1  HHH_7     Helix-hairpin-helix motif


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 !   80.4   0.0   1.7e-26     1e-22       6     114 ..      42     158 ..      39     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 1.7e-26
                                       EEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEEC.CCC-CCHHCCS.. CS
                              PTPS   6 feFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkfl.naddpeleell.. 79 
                                       ++++a+Hrl++h+gkc++ HGHny+v vtv ge l ++g+v+d g++ +    +++e+Dh+fl +  dp +e +   
  gi|336254068|ref|YP_004597175.1|  42 IRISAGHRLQHHDGKCARPHGHNYEVAVTVVGE-LTDEGWVADKGDITQ----VIDEWDHRFLlERGDPLIEAFEaa 113
                                       689******************************.************998....899*******999999999888** PP

                                       ............--HHHHHHHHHHHHHHHHGCCCGCEEEEEEEEET CS
                              PTPS  80 ...........spTaEnlaklifeelkerlqekevklskvrvwEtp 114
                                                   pTaE ++ ++ ++l+++l +++v+  +v+v Et 
  gi|336254068|ref|YP_004597175.1| 114 gdadgivvlehPPTAEVMSVVLERKLEAAL-PDTVSEVAVQVNETS 158
                                       **********999*****************.999999999999997 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.3e-05      0.19       4      67 ..      72     136 ..      70     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                               GYD   4 lvnytdegvkgl.kdsperreeakealveslGgkleslyatlGeyDvvvivEapDdetaaalsla 67 
                                       ++++tdeg+ +   d ++ ++e+ +++  + G  l + + + G+ D +v++E p  ++++ + l+
  gi|336254068|ref|YP_004597175.1|  72 VGELTDEGWVADkGDITQVIDEWDHRFLLERGDPLIEAFEAAGDADGIVVLEHPPTAEVMSVVLE 136
                                       67899***99998999**************************************99999998886 PP

>> HHH_7  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.1e-05      0.19       9      42 ..     124     157 ..     117     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                                       -TTGGGS-HHHHHHHHHHHHHHHHHHH-EEHHHH CS
                             HHH_7   9 hPlqellskeellkaletalvdivnlvgvdvnka 42 
                                       hP    + + +l + le+al d v++v+v+vn++
  gi|336254068|ref|YP_004597175.1| 124 HPPTAEVMSVVLERKLEAALPDTVSEVAVQVNET 157
                                       66677788899*********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1342.91
//
Query:       gi|336254069|ref|YP_004597176.1|  [L=262]
Description: Radical SAM domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-27   94.5   0.6    1.7e-26   93.6   0.6    1.5  1  Radical_SAM   Radical SAM superfamily
      4e-15   56.0   0.0    6.3e-15   55.4   0.0    1.3  1  Fer4_14       4Fe-4S single cluster domain
    1.2e-11   45.0   0.0    1.8e-11   44.4   0.0    1.2  1  Fer4_12       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.075   13.0   0.1       0.37   10.7   0.0    1.9  2  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
       0.25   10.8   0.0       0.34   10.3   0.0    1.1  1  Pho86         Inorganic phosphate transporter Pho86


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 !   93.6   0.6   4.8e-30   1.7e-26       2     164 ..      49     233 ..      48     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 4.8e-30
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       v t gCnlrC+fC+ ++t ++e++++++s+eei++ev+++     +++v+l+ggepll+ + vellerl+++   g+
  gi|336254069|ref|YP_004597176.1|  49 VRTSGCNLRCWFCDSYHT-SWEPTHATMSLEEIVAEVESYD----AGHVVLTGGEPLLHEESVELLERLSER---GY 117
                                       789**************9.*********************9....**************************9...** PP

                                       EEEEEECSSCHG...........................HHHHHHHHHTT..-SEEEEEEBSSSHH...HHHHHHTC CS
                                       xxxxxxxxxxxx...........................xxxxxxxxxxx..xxxxxxxxxxxxxx...xxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpd...........................eeklerllelg..vdrvslgleaadde...kvlklmnr 123
                                       ++tvetngt  +                            e++e++ +++  +  ++  +ea+d+    +v +   +
  gi|336254069|ref|YP_004597176.1| 118 HTTVETNGTIYRdapidlasvspklesstptpdrdpkgeGEWAEKHEDARidLEALAALVEAYDSQlkfVVTDDE-D 193
                                       **********99**************************************999999999******9544444444.5 PP

                                       TSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 124 ghtfeevlealeklreagikrvvdrivglpGendeeleell 164
                                       ++++ ++l  l+  +++ i++  d++++++G ++e l e++
  gi|336254069|ref|YP_004597176.1| 194 MPEILDLLGELRGVADVPIRD-GDVLLMPEGATRERLAETR 233
                                       555555666666666666885.99*********99999987 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 !   55.4   0.0   1.8e-18   6.3e-15       1      93 [.      47     129 ..      47     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.8e-18
                           Fer4_14   1 lfvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkee 77 
                                       +fvr+sgCnl C +Cd     + ++++ ++   le+i+++++ ++  +  +vltGGePL++   +e ++l++rl e+
  gi|336254069|ref|YP_004597176.1|  47 VFVRTSGCNLRCWFCDSY---HTSWEPTHATMSLEEIVAEVESYD--AGHVVLTGGEPLLH---EESVELLERLSER 115
                                       6**************964...589999999999999995555555..577*********99...8889********* PP

                           Fer4_14  78 ypekkiwletngtlei 93 
                                       +  ++ ++etngt+  
  gi|336254069|ref|YP_004597176.1| 116 G--YHTTVETNGTIYR 129
                                       *..*********9975 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 !   44.4   0.0   5.1e-15   1.8e-11       1      98 [.      35     130 ..      35     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 5.1e-15
                           Fer4_12   1 lnGeGvrl.....slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeal 72 
                                       l+GeG+ +     ++++sgCnl+C +C    t    ++    +  leei+++++ +    ++l+GGEPll    e+ 
  gi|336254069|ref|YP_004597176.1|  35 LQGEGTLAgvpsvFVRTSGCNLRCWFCDSYHTSWEPTHA---TMSLEEIVAEVESYDAGHVVLTGGEPLL---HEES 105
                                       58899654444337779*********9855543333333...3457899999*99999************...8888 PP

                           Fer4_12  73 lelvkevkeekpekdiwlytgytlee 98 
                                       +el++++ e+++  + ++++g+++ +
  gi|336254069|ref|YP_004597176.1| 106 VELLERLSERGY-HTTVETNGTIYRD 130
                                       9***********.69********987 PP

>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0001      0.37      71     113 ..      80     120 ..      64     125 .. 0.75
   2 ?   -0.1   0.0       0.2   7.3e+02     162     183 ..     183     204 ..     130     243 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0001
                      TP_methylase  71 al..aealragkdVvllvsGDPlvygtgselvealrareagieve 113
                                       ++  +e  +ag   v+l++G Pl++    el+e+l++  +g+++ 
  gi|336254069|ref|YP_004597176.1|  80 IVaeVESYDAG--HVVLTGGEPLLHEESVELLERLSE--RGYHTT 120
                                       33334444555..69**********************..666544 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.2
                      TP_methylase 162 dtlvllkaprklaelaelLkea 183
                                       +  +++++ ++++e+++lL e 
  gi|336254069|ref|YP_004597176.1| 183 QLKFVVTDDEDMPEILDLLGEL 204
                                       4444444444444444444444 PP

>> Pho86  Inorganic phosphate transporter Pho86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   9.6e-05      0.34     165     191 ..     121     147 ..     100     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.6e-05
                             Pho86 165 knteivvYretPIAvislvenkelstk 191
                                        +t+  +Yr++PI ++s++++ e st+
  gi|336254069|ref|YP_004597176.1| 121 VETNGTIYRDAPIDLASVSPKLESSTP 147
                                       5666789*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); 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:                         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 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1971.64
//
Query:       gi|336254070|ref|YP_004597177.1|  [L=250]
Description: exsB protein [Halopiger xanaduensis SH-6]
Scores for 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-74  248.1   0.0    6.8e-74  247.9   0.0    1.0  1  QueC           Queuosine biosynthesis protein QueC
    5.3e-07   29.4   0.0    1.4e-06   28.1   0.0    1.7  2  ThiI           Thiamine biosynthesis protein (ThiI)
    0.00016   20.6   0.0    0.00021   20.2   0.0    1.1  1  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
      0.022   13.9   0.0      0.038   13.1   0.0    1.4  1  NAD_synthase   NAD synthase
      0.026   14.2   0.2      0.037   13.7   0.2    1.2  1  Asn_synthase   Asparagine synthase


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 !  247.9   0.0   1.9e-77   6.8e-74       1     209 [.      20     229 ..      20     230 .. 0.97

  Alignments for each domain:
  == domain 1  score: 247.9 bits;  conditional E-value: 1.9e-77
                                       EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG---- CS
                              QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelgveehkildldllkelggsaLtdee 76 
                                       +avvllSGG+DS+t+++ a+ +g+e++al+ +Ygqr +++ele+a+++a+el+ ++   +++ +l+++g s+Ltd+e
  gi|336254070|ref|YP_004597177.1|  20 RAVVLLSGGMDSATAAYEARGRGYEIYALHTSYGQRtEDRELECARRLADELDAADFLRIETGHLSAIGASSLTDDE 96 
                                       69**********************************99*************************************** PP

                                       -------...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH..HTS- CS
                              QueC  77 ievpkeeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg..edkk 151
                                       ++v ++++e++e+p+++Vp+RN+ +l++a+syaea +++a++iG+++edfsgYPDcr+ef++a+++++ +g   +++
  gi|336254070|ref|YP_004597177.1|  97 MAVADADMESDEIPTSYVPFRNANLLAMAVSYAEANDCDAVFIGAHSEDFSGYPDCRPEFFEAFENVVDVGtkPETD 173
                                       ***********************************************************************765689 PP

                                       -EEE-TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHHHH CS
                              QueC 152 ieieaPlidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRkkgfeea 209
                                       i ieaP++++sK++i+++g el+vp+e+t+sCY+++e   aCg+CdaCa+R ++f+++
  gi|336254070|ref|YP_004597177.1| 174 IAIEAPFVEWSKTDIAERGVELEVPYEHTWSCYRENEP--ACGTCDACAFRLQAFQNV 229
                                       ***********************************555..***************986 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   3.9e-10   1.4e-06       3     115 ..      18     140 ..      16     144 .. 0.68
   2 ?   -3.1   0.0       1.4   4.8e+03     136     155 ..     172     191 ..     166     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.9e-10
                              ThiI   3 qgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaella..eyqtslevklvvv...dfke 74 
                                       ++++++LlSgG+DS  aay +  RG ++ ++h +    t++++ e  ++la+ l   ++    + +l ++   ++++
  gi|336254070|ref|YP_004597177.1|  18 SERAVVLLSGGMDSATAAYEARGRGYEIYALHTSYGQRTEDRELECARRLADELDaaDFLRIETGHLSAIgasSLTD 94 
                                       6899*****************************9999999999*******998851134333344444441115555 PP

                              ThiI  75 vlkeilekv....kekltiv.llkrkmlriAekvaeeegakalvtG 115
                                           + +      + ++  v +    +l +A  +ae ++++a+  G
  gi|336254070|ref|YP_004597177.1|  95 DEMAVADADmesdEIPTSYVpFRNANLLAMAVSYAEANDCDAVFIG 140
                                       4444433323322112333414445678888888888888887666 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                              ThiI 136 vnllilrPLigldKeeiikl 155
                                       ++++i  P +  +K +i + 
  gi|336254070|ref|YP_004597177.1| 172 TDIAIEAPFVEWSKTDIAER 191
                                       67888899999999999875 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   5.7e-08   0.00021       2      64 ..      20      80 ..      19      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.7e-08
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgip 64
                                      + vv+lSgG DS+ aa+  + +gye+ +++    +++++ + ec   + l+d   +a++l i+
  gi|336254070|ref|YP_004597177.1| 20 RAVVLLSGGMDSATAAYEARGRGYEIYALHTSYGQRTEDRELECA--RRLADELDAADFLRIE 80
                                      569***************************999998766664554..4566666677777766 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.1e-05     0.038      18      85 ..      18      85 ..      10     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                                      TSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTS.EEEE---HHHH CS
                      NAD_synthase 18 akgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgi.evktidikpiv 85
                                      ++ +v+ lSGG+DS+++a+ a+      ++ al    ++ ++++++e a+ la++l+  ++  i+  +  
  gi|336254070|ref|YP_004597177.1| 18 SERAVVLLSGGMDSATAAYEARGRG--YEIYALHTSyGQRTEDRELECARRLADELDAaDFLRIETGHLS 85
                                      5678999***********9887654..6788888887889999999999999999864134444444444 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2     1e-05     0.037      21      72 ..      22      73 ..      12      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                      Asn_synthase 21 GalLSGGlDSSliaalaarqsksplktFsigfee.kgsdeakyakevaehlgt 72
                                       +lLSGG+DS++ a+ a+     ++ + +  + +  ++ e++ a+++a++l  
  gi|336254070|ref|YP_004597177.1| 22 VVLLSGGMDSATAAYEARGRG-YEIYALHTSYGQrTEDRELECARRLADELDA 73
                                      689*******99777777765.58888888884459999**********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.75
# Mc/sec: 1011.05
//
Query:       gi|336254071|ref|YP_004597178.1|  [L=76]
Description: hypothetical protein Halxa_2682 [Halopiger xanaduensis SH-6]
Scores for 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:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 566.37
//
Query:       gi|336254072|ref|YP_004597179.1|  [L=334]
Description: NADPH:quinone reductase [Halopiger xanaduensis SH-6]
Scores for 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   80.5   0.1    2.3e-22   79.4   0.1    1.6  1  ADH_zinc_N    Zinc-binding dehydrogenase
    1.1e-22   81.5   0.5      2e-22   80.7   0.2    1.6  2  ADH_zinc_N_2  Zinc-binding dehydrogenase
    1.4e-06   28.1   0.4    4.3e-06   26.6   0.0    2.0  2  ADH_N         Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
      0.073   12.5   0.2       0.14   11.6   0.2    1.4  1  adh_short     short chain dehydrogenase
      0.084   12.8   0.1       0.21   11.5   0.1    1.6  1  ADH_N_2       N-terminal domain of oxidoreductase


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 !   79.4   0.1   6.4e-26   2.3e-22       1     108 [.     160     265 ..     160     283 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 6.4e-26
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       gvG+++vqlA  +Ga v+a+ sse ++ela++lGad++++y+e+d++ ++ e+  g+g+dvvf+ vG  + le+a++
  gi|336254072|ref|YP_004597179.1| 160 GVGHIGVQLADWFGADVTATGSSEANRELAAELGADATVDYTETDVETYVDEHASGGGFDVVFDPVG-DEHLETAFQ 235
                                       9****************************************888***********************.********* PP

                                       CEEEEEEEEECSCTSSEEEEEHHHHHHTT-E CS
                        ADH_zinc_N  78 llkpgGrlvvvGggkgeeefdlrnlllkeks 108
                                       +++p G +v+    +  +++dl++++++++ 
  gi|336254072|ref|YP_004597179.1| 236 AVRPFGSVVTTES-SAAQDLDLAPMHANSLE 265
                                       *********9995.44444888888888776 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.1   1.5e+04      25      38 ..      72      86 ..      57     121 .. 0.65
   2 !   80.7   0.2   5.6e-26     2e-22       1     133 []     192     331 ..     192     331 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.1
                                      EEEES-H.HHHH.HH CS
                      ADH_zinc_N_2 25 vvldtvg.geallea 38
                                       v+d+vg g + +e+
  gi|336254072|ref|YP_004597179.1| 72 GVVDAVGdGVEQFEE 86
                                      566666653333344 PP

  == domain 2  score: 80.7 bits;  conditional E-value: 5.6e-26
                                       TT-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EE CS
                      ADH_zinc_N_2   1 lGAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsv 73 
                                       lGAd  +dy+++d+e    ++++g+g+Dvv+d vg e+l e +++++++ G +v+  ++ +++ +l+p   ++    
  gi|336254072|ref|YP_004597179.1| 192 LGADATVDYTETDVEtyvdEHASGGGFDVVFDPVGDEHL-ETAFQAVRPFGSVVTTESSAAQDLDLAPMHANSLELG 267
                                       8******************99999***********9988.*******999****99854433333333332222333 PP

                                       EE--GGG...-......-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  74 kyeflfsmkas.....aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                        +  ++++  +     ++++ le++a+l+++G+++p++d +++++e+ae hr+ e+g  rGK+ l
  gi|336254072|ref|YP_004597179.1| 268 VVLVILPVLLGdrqdrIGEE-LEDIATLVDKGAIEPHIDDRYSFDEVAEVHRRGEEGDFRGKLLL 331
                                       33333333333778867777.*****************************************976 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.2e-09   4.3e-06       1      63 [.      31      94 ..      31     103 .. 0.92
   2 ?   -2.7   0.0       1.5   5.4e+03      51      62 ..     144     155 ..     139     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.2e-09
                                      TTEEEEEEEEEEE-HHHHHHHTTS.TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-S CS
                             ADH_N  1 pgevlikvkaagiCgsDlhilkgg.kelevklplilGHEivGeveevgpevkklkvGdrVvvep 63
                                      p+e++++v a++++  D++i +g   ++  ++p il  +++G+v++vg++v++++ Gd+V   p
  gi|336254072|ref|YP_004597179.1| 31 PNEIRVEVVASSLNPVDYKIRQGAiPDFAPEFPAILHCDVAGVVDAVGDGVEQFEEGDEVYGMP 94
                                      689********************877888999****************************8765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                                       CS--TT-EEEE- CS
                             ADH_N  51 kklkvGdrVvve 62 
                                       +++ vGd+V+v+
  gi|336254072|ref|YP_004597179.1| 144 STVDVGDEVLVY 155
                                       46899***9986 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   3.8e-05      0.14       3      61 ..     152     208 ..     150     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.8e-05
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSH CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdr 61 
                                       vlv G+++G+G+  ++     Ga+v+++++se++  e+a+el+++ a++ + ++Dv+++
  gi|336254072|ref|YP_004597179.1| 152 VLVYGGAGGVGHIGVQLADWFGADVTATGSSEANR-ELAAELGAD-ATVDYTETDVETY 208
                                       89*************************99997766.9******95.89*******9965 PP

>> ADH_N_2  N-terminal domain of oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.8e-05      0.21      14      91 ..      15      93 ..       7     100 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.8e-05
                           ADH_N_2 14 tesdfeleeeelpelkdGevlvralylSvDPym.RgrmndaksyvepvelgdvmrggavgeVveSknpdfkvGdlVvgl 91
                                      +++ fe +++e+pe+++ e++v++   S+ P   ++r  +  + +++++       ++v + v    ++f++Gd V g+
  gi|336254072|ref|YP_004597179.1| 15 DPDVFEETTVEVPEPGPNEIRVEVVASSLNPVDyKIRQGAIPDFAPEFPAILHCDVAGVVDAVGDGVEQFEEGDEVYGM 93
                                      68899*************************9741445445555555554444444444444445556677777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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:                         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 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2512.58
//
Query:       gi|336254073|ref|YP_004597180.1|  [L=172]
Description: hypothetical protein Halxa_2684 [Halopiger xanaduensis SH-6]
Scores for 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:                       461  (0.0257125); 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):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1364.63
//
Query:       gi|336254074|ref|YP_004597181.1|  [L=422]
Description: iron-containing alcohol dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-61  206.6   3.4    5.7e-61  206.3   3.4    1.0  1  Fe-ADH    Iron-containing alcohol dehydrogenase
    6.9e-10   39.1   0.3      8e-07   29.0   0.0    2.2  2  Fe-ADH_2  Iron-containing alcohol dehydrogenase


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 !  206.3   3.4   6.4e-65   5.7e-61       1     358 [.      29     406 ..      29     413 .. 0.88

  Alignments for each domain:
  == domain 1  score: 206.3 bits;  conditional E-value: 6.4e-65
                                       -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEE.E.EEE-S---HHHHHHHHTT CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievt.vfdgvepnptleeveeaaal 76 
                                       P +i+fg+g++++l+++l++lg++ral+v+++ +     ++d v++ l   g +++ vfd+ +p  +l++  +++a+
  gi|336254074|ref|YP_004597181.1|  29 PATIRFGAGCVADLEDELERLGLERALVVCGSTVGDTPVVIDPVRRGL---GDRLAgVFDETTPKKRLSTALDGVAR 102
                                       889******************************99999999*******...999999******************** PP

                                       S-TT.--EEEEEESHHHHHHHHHHHHHTT............................--EEEEESS-S-S-TT-SEE CS
                            Fe-ADH  77 areegadvviavGGGsviDtAKaialllanpe.....vedyl..gegk...akkkkalpliaiPTtaGtGsevtpla 143
                                       +++e+ad+++a+GGGs++D+A ++++l+a+++      e+++  g  +   +++ + lp++++PTt   G+  +++a
  gi|336254074|ref|YP_004597181.1| 103 VKAEDADALVALGGGSSLDVATVMSVLAARDRsaavlAEELEetG--TidvPDEAELLPVVTVPTTL-AGADLSQVA 176
                                       *****************************9744787444444552..3333556666**********.9******** PP

                                       EEE.-TTS......EEEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHH CS
                            Fe-ADH 144 vitdeeeg......eklsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleair 214
                                        +t + +          +i+dp+l+P++a++Dpel +t+P +v+a ++++ + + +E + + +a+ ++da a+++++
  gi|336254074|ref|YP_004597181.1| 177 GVTASPDSspveaeIGGGISDPRLMPEAAFYDPELAATTPDSVLAGSAMNGFDKGVETLYAANATTITDATARHGLE 253
                                       ***85554456532445899********************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH...... CS
                            Fe-ADH 215 liaknleravadgedleareqmllastlaglaf...snaglgavHalahalgalfgiphglanaillpavlrfna.. 286
                                        + + l+   +  +d    e +l++ +l   +    + + l++vHa++hal+   ++++g+a+a+++p++l++    
  gi|336254074|ref|YP_004597181.1| 254 KLEDGLRAFGEGDRDVGTFETILEGVVLVQYGVsrpEGTTLSIVHAFGHALSRTADVQQGAAHAVVVPHALEYLFer 330
                                       ******99998888**************66655111567788***********88****************999955 PP

                                       .........HHHHHHT.......T--HHHHHHHHHHHHHTT---SHHHHT-TT.-HHHHHHHHHT-TSGGGGSSS- CS
                            Fe-ADH 287 ..eaa.perlaqlaralggesdeeaaeeliealrellkelglptsLselgvde.edldklaeaalkdrslannpre 358
                                         + +  +r   la+alg +++++  ++++ea+ e+ ++l lp +L+ ++ ++ e+++++ae++l dr + n p  
  gi|336254074|ref|YP_004597181.1| 331 eaAGEiDARSGLLANALGVDEAADHGAAVVEAVTEVRDALELPAKLRNVDGPQpEEFRTVAEDVLGDRFMENAPPG 406
                                       43222136667799999888999999***********************955559****************99965 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 !   29.0   0.0     9e-11     8e-07       2      98 ..      34     130 ..      33     138 .. 0.91
   2 !    8.2   0.0    0.0002       1.8     132     241 ..     198     312 ..     158     320 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 9e-11
                          Fe-ADH_2   2 igegaleklgellkelelkkvllvadentkka..agekveeslkeagikvevveeveeeadleeveklvealreket 76 
                                       +g g + +l++ l++l+l+++l+v ++++ ++  + + v++ l ++   + v++e ++++ l+++ + v++++++++
  gi|336254074|ref|YP_004597181.1|  34 FGAGCVADLEDELERLGLERALVVCGSTVGDTpvVIDPVRRGLGDRL--AGVFDETTPKKRLSTALDGVARVKAEDA 108
                                       68899999********************998665999******9994..557999********************** PP

                          Fe-ADH_2  77 dlvvavGgGtiiDiakyvsakl 98 
                                       d++va+GgG+ +D+a ++s  +
  gi|336254074|ref|YP_004597181.1| 109 DALVALGGGSSLDVATVMSVLA 130
                                       *****************99866 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0002
                          Fe-ADH_2 132 kaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwklanevseplaklsaamvqeaaeklvedkketealee 208
                                       +  +P a + D ++ a+ P++ la    +   k + +     a+ +++  a+   +++++ ++++ e  +++   e+
  gi|336254074|ref|YP_004597181.1| 198 PRLMPEAAFYDPELAATTPDSVLAGSAMNGFDKGVETLYAANATTITDATARHGLEKLEDGLRAFGEGDRDVGTFET 274
                                       6678999999999999999998887777888899999999999999*********************999******* PP

                          Fe-ADH_2 209 llealalsgigisrpa...SGsEHliSHaldmlal..k 241
                                       +le+++l   g+srp        H + Hal ++a   +
  gi|336254074|ref|YP_004597181.1| 275 ILEGVVLVQYGVSRPEgttLSIVHAFGHALSRTADvqQ 312
                                       ***************86653347******998875434 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 3524.60
//
Query:       gi|336254075|ref|YP_004597182.1|  [L=762]
Description: AAA ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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-46  158.6   0.0    1.3e-45  155.5   0.0    2.0  2  AAA_12           AAA domain
    8.6e-34  117.5   0.3    1.3e-15   58.0   0.1    2.3  2  AAA_11           AAA domain
    7.5e-15   55.1   0.1    2.1e-14   53.7   0.1    1.7  1  AAA_30           AAA domain
    1.5e-09   38.3   0.0    3.4e-09   37.2   0.0    1.6  1  AAA_19           AAA domain
    1.5e-08   34.7   0.0     0.0005   19.9   0.0    3.2  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00028   21.1   0.2       0.03   14.6   0.0    2.8  2  AAA_22           AAA domain
      0.001   18.8   0.0     0.0027   17.5   0.0    1.6  1  AAA_24           AAA domain
     0.0046   16.3   0.0      0.012   14.8   0.0    1.8  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0059   17.0   0.2      0.069   13.5   0.0    2.4  2  AAA_16           AAA ATPase domain
     0.0061   16.6   0.0      0.022   14.7   0.0    1.9  1  ResIII           Type III restriction enzyme, res subunit
     0.0065   16.3   0.0      0.014   15.2   0.0    1.6  1  Helicase_RecD    Helicase
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.032   13.7   0.0    1.5  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
      0.022   15.2   2.6        0.2   12.1   0.1    3.1  3  AAA              ATPase family associated with various cellul
      0.034   14.0   0.2       0.22   11.4   0.2    2.3  1  UvrD_C_2         UvrD-like helicase C-terminal domain
        0.2   11.1   0.0        2.5    7.5   0.0    2.2  2  PhoH             PhoH-like protein


Domain annotation for each model (and alignments):
>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.34   4.1e+02      37     100 ..     302     361 ..     296     371 .. 0.83
   2 !  155.5   0.0   1.1e-48   1.3e-45       4     197 ..     527     715 ..     524     716 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.34
                            AAA_12  37 lfYkgkLkdaesvkkreleaqealeepleplvfidvekseeekekkeksyiNeeEaelvvklve 100
                                         Y+ +L++ ++v++r+    +al +  + ++f d+ + ++++++   +++ e+E ++ + l+ 
  gi|336254075|ref|YP_004597182.1| 302 VPYDRELEAVKRVRERDDL--RALLTGGTAVTFGDTAGVKSSQQD--VELNQEQELAVSCALLA 361
                                       569999*******999988..999999999*******99999997..67888888887777665 PP

  == domain 2  score: 155.5 bits;  conditional E-value: 1.1e-48
                            AAA_12   4 Slferllkke...kekvvlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkreleaqealeepleplvfidveksee 77 
                                       Slfe+l+  +   +   v L+tqYRmh++++ fp++ fY+ +L+++++v     +           lv +dv +see
  gi|336254075|ref|YP_004597182.1| 527 SLFEHLYADGgvyEGVGVQLRTQYRMHRDVAWFPNRRFYDRALRQGRDVDALADR---------PALVGYDVGGSEE 594
                                       9*******999988999******************************99887777.........45999****9999 PP

                            AAA_12  78 ekekkeksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeksekeievntvdgfQGr 154
                                       + +    s  Ne+Ea+lv++lv++ll++  + e +++ vitpY aqv+ ++ +l+++ e+++ ++++v+t+d+fQG+
  gi|336254075|ref|YP_004597182.1| 595 TVD---RSTKNEAEARLVAHLVSELLEDEDDLEPSDVSVITPYTAQVDAIRGTLRRHLEHERGRAVTVDTIDSFQGS 668
                                       998...59************************9******************************************** PP

                            AAA_12 155 ekdviilslVRsnekkeigfl....kderrlNValTRAkskliivGn 197
                                       ek +i+lslVRsn+++eigfl    +  rrlNVa+TRA++ + ivG+
  gi|336254075|ref|YP_004597182.1| 669 EKTAIVLSLVRSNADGEIGFLgrplDGPRRLNVAMTRAQRYCAIVGD 715
                                       ********************82222468******************7 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   1.5e-18   1.8e-15       2      73 ..     347     409 ..     346     426 .. 0.92
   2 !   58.0   0.1   1.1e-18   1.3e-15     195     257 ..     457     513 ..     451     517 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.5e-18
                            AAA_11   2 lndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDeller 73 
                                       ln++q+ a++ al  +++++i+GPPGtgKT+t+ve++++           +a+  +LvCa SN AvD+l++ 
  gi|336254075|ref|YP_004597182.1| 347 LNQEQELAVSCALLADQLFCIHGPPGTGKTRTLVEVVRRS---------VEAGDDVLVCADSNQAVDNLVAG 409
                                       9***************************************.........799*****************986 PP

  == domain 2  score: 58.0 bits;  conditional E-value: 1.1e-18
                            AAA_11 195 eaeivltTlsgagsklleklakkfdvviIDEAaqavEpstliPlrlgakkvvLvGDpkQLpat 257
                                       +a++v++T+s+a      +l+++fdv++ DEA+qa+ +++ iPl+++ +kv+L+GD+kQLp+ 
  gi|336254075|ref|YP_004597182.1| 457 RADVVAATNSSA-----AALEREFDVLVLDEATQATCTASCIPLSRA-EKVILAGDHKQLPPF 513
                                       699********9.....445557***********************9.**************7 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.1   1.7e-17   2.1e-14       1     132 [.     346     514 ..     346     518 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 1.7e-17
                            AAA_30   1 elnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakll 77 
                                       eln+eQ+ av  +l  ++ + +++Gp+GtGKt +l ++++   +ag +v+++A +++a ++L +++ ++ +  ++ l
  gi|336254075|ref|YP_004597182.1| 346 ELNQEQELAVSCALLADQ-LFCIHGPPGTGKTRTLVEVVRRSVEAGDDVLVCADSNQAVDNLVAGSSTPDAADERSL 421
                                       599*******99988886.*************999999888888999****************99999888889999 PP

                            AAA_30  78 krlk.........................................grarlepg.tllivDEagmvdtkqlaallkaa 112
                                       ++++                                         ++a+le++ ++l+ DEa  +  +     l++a
  gi|336254075|ref|YP_004597182.1| 422 HAYAqhgadefvlrranagnssndvvgrryagcdgradvvaatnsSAAALEREfDVLVLDEATQATCTASCIPLSRA 498
                                       88888999************************************977899999***********9999888888888 PP

                            AAA_30 113 ekagakvilvGDerQlasVe 132
                                       ek    vil+GD++Ql++ +
  gi|336254075|ref|YP_004597182.1| 499 EK----VILAGDHKQLPPFS 514
                                       87....**********9865 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   2.8e-12   3.4e-09       2     143 ..     352     512 ..     351     515 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 2.8e-12
                            AAA_19   2 reave..alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.atTiHrl 75 
                                       + av+   l+++++++ ++pGtGKTr+l+++v+  ve+g    +++l++a  ++A+++l    ++ +a+  + +H+ 
  gi|336254075|ref|YP_004597182.1| 352 ELAVScaLLADQLFCIHGPPGTGKTRTLVEVVRRSVEAG----DDVLVCADSNQAVDNLVAGSSTPDAAdERSLHAY 424
                                       566644357788999************************....78**************986533333247788888 PP

                            AAA_19  76 al.........................ldfddlltealelleeaeeekklqeee.llivDEfqdvdelqyrLlkall 126
                                       a                           + d++ +  ++    +++   l++e+ +l+ DE+ + + ++  +   l 
  gi|336254075|ref|YP_004597182.1| 425 AQhgadefvlrranagnssndvvgrryAGCDGRADVVAA---TNSSAAALEREFdVLVLDEATQATCTASCI--PLS 496
                                       777777899999999988888888888666666633333...3456777888889*******9999666544..222 PP

                            AAA_19 127 gekkklllvGDpdQliy 143
                                        +++k++l GD++Ql++
  gi|336254075|ref|YP_004597182.1| 497 -RAEKVILAGDHKQLPP 512
                                       .3367**********97 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 !    8.5   0.0    0.0012       1.5       3      23 ..     367     394 ..     365     432 .. 0.71
   2 !   19.9   0.0   4.1e-07    0.0005      61     109 ..     473     519 ..     457     586 .. 0.84
   3 ?    2.6   0.0     0.082        98     173     232 ..     641     712 ..     590     714 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
                   Viral_helicase1   3 vhGvpGcGKStlirkllrts.......l 23 
                                       +hG pG GK++ +++++r s       l
  gi|336254075|ref|YP_004597182.1| 367 IHGPPGTGKTRTLVEVVRRSveagddvL 394
                                       9****************99655554333 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 4.1e-07
                   Viral_helicase1  61 tkgkililDEylllhaGyilllaalskaklvilfGDplQipfhsrnasf 109
                                        ++++l+lDE+++++  +   ++ ls+a+ vil GD++Q p  s  ++ 
  gi|336254075|ref|YP_004597182.1| 473 REFDVLVLDEATQAT--CTASCIPLSRAEKVILAGDHKQLPPFSATEEP 519
                                       369**********99..6777*******************988766654 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.082
                   Viral_helicase1 173 tqalkealgvr......evttvhevqGltfdkVtlvllketdlelis......esrenllvAlTRhrkslvi 232
                                        + +++++ ++       v t  + qG++    +l l +++ + +i       +++  l vA+TR+ + + i
  gi|336254075|ref|YP_004597182.1| 641 IRGTLRRHLEHergravTVDTIDSFQGSEKTAIVLSLVRSNADGEIGflgrplDGPRRLNVAMTRAQRYCAI 712
                                       3344555555568888888999999**9888877777777777767789999999***********987776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.5e-05      0.03       6      32 ..     363     389 ..     361     487 .. 0.73
   2 ?    3.4   0.0     0.073        88      56     105 ..     608     668 ..     589     691 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldee 32 
                                       ++ +++G++GtGKT++l +++++ +e+
  gi|336254075|ref|YP_004597182.1| 363 QLFCIHGPPGTGKTRTLVEVVRRSVEA 389
                                       6789***************99997643 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.073
                            AAA_22  56 llrellralglelka...........erlsseellealeqalraravielliiDEaqhlr.s 105
                                       l  +l+++l ++ ++           ++++ ++++ +l+++l++ +  +++ +D ++ +  s
  gi|336254075|ref|YP_004597182.1| 608 LVAHLVSELLEDEDDlepsdvsvitpYTAQVDAIRGTLRRHLEHERG-RAVTVDTIDSFQgS 668
                                       445555555555555777888888889999*****************.********999542 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.3e-06    0.0027       5      86 ..     365     493 ..     362     508 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.3e-06
                            AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfi.........................................dtek 33 
                                       ++i Gp+g+GKT ++ e        g+++l++                                         +  +
  gi|336254075|ref|YP_004597182.1| 365 FCIHGPPGTGKTRTLVEVvrrsveaGDDVLVCadsnqavdnlvagsstpdaaderslhayaqhgadefvlrraNAGN 441
                                       69****************99999999999999999999999999999999999999999999999999999888888 PP

                            AAA_24  34 Glksldadkfpdieswedfldevvel.aaeladyktlviDtideleelclaevi 86 
                                       +++++ ++++  + + +d++ + ++  aa ++++++lv+D ++++   c+a +i
  gi|336254075|ref|YP_004597182.1| 442 SSNDVVGRRYAGCDGRADVVAATNSSaAALEREFDVLVLDEATQA--TCTASCI 493
                                       89999999999888888877777776799999************9..6666665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     1e-05     0.012       2     102 ..     363     488 ..     362     632 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                           DUF2075   2 avvlVtGvaGtGKtvvllnllael.........................edde...eertavylsvNhplvlvlrea 50 
                                       +++ ++G +GtGKt  l++++ +                          +      +er+ +   + ++   vlr+a
  gi|336254075|ref|YP_004597182.1| 363 QLFCIHGPPGTGKTRTLVEVVRRSveagddvlvcadsnqavdnlvagssT--PdaaDERSLHAYAQHGADEFVLRRA 437
                                       6899********************99888888865555444444444441..0332222222222233333456666 PP

                           DUF2075  51 lakkeekkkkkeafeklssfinnlsefkkaeekkeepkedvvivDEAhrllt 102
                                        a+++++   +++ ++ +     +    +  + + e+++dv++ DEA  ++ 
  gi|336254075|ref|YP_004597182.1| 438 NAGNSSNDVVGRRYAGCDGRADVVA-ATNSSAAALEREFDVLVLDEATQATC 488
                                       6666644444444444333333333.25577889999**********88876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   5.8e-05     0.069      26      55 ..     364     395 ..     350     490 .. 0.61
   2 ?    0.6   0.0      0.53   6.4e+02     103     153 ..     615     671 ..     528     689 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.8e-05
                            AAA_16  26 lvllsGesGvGKsslv.rellralekdg.gif 55 
                                       l  ++G++G+GK++ + + ++r++e+ + +++
  gi|336254075|ref|YP_004597182.1| 364 LFCIHGPPGTGKTRTLvEVVRRSVEAGDdVLV 395
                                       5679*********9883555554444322444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.53
                            AAA_16 103 ealaavpelagaea......srllellkrll.allsrderplvlvlDdlqwadeaslq 153
                                       e l++ ++l++++       ++  ++++  l + l++ er   +++D ++ ++ +  +
  gi|336254075|ref|YP_004597182.1| 615 ELLEDEDDLEPSDVsvitpyTAQVDAIRGTLrRHLEH-ERGRAVTVDTIDSFQGSEKT 671
                                       2222444455554466666655566666666444555.77788888888877655544 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 !   14.7   0.0   1.9e-05     0.022      23      71 ..     361     407 ..     337     516 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                                       TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH CS
                            ResIII  23 rdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl 71 
                                        d+ ++i+ + GtGKT++++++++r  ++g+   +l+ +++++ ++ + 
  gi|336254075|ref|YP_004597182.1| 361 ADQLFCIHGPPGTGKTRTLVEVVRRSVEAGD--DVLVCADSNQAVDNLV 407
                                       46779***********************988..9******998777666 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.014       2     103 ..     367     487 ..     366     508 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                     Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke.................eekk 61 
                                       + + +G+GK+ +l  ++ + +++g+ ++lv+a s+++v++l++   +  +a + ++                 +   
  gi|336254075|ref|YP_004597182.1| 367 IHGPPGTGKTRTLVEVVRRSVEAGD-DVLVCADSNQAVDNLVAGSST-PDAADERSlhayaqhgadefvlrraN--- 438
                                       7899*******************98.9**************987743.33333333455767777777664331... PP

                     Helicase_RecD  62 kkaekaelrvr.................kqrieyiapdellklkeqadllvvDEAAaip 103
                                                                   +  +   + +++++l+++ d+lv DEA +  
  gi|336254075|ref|YP_004597182.1| 439 ----------AgnssndvvgrryagcdgRADVVAATNSSAAALEREFDVLVLDEATQAT 487
                                       ..........0222233333357788665555556666667777788*******97655 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 ?   13.7   0.0   2.7e-05     0.032       1      57 [.     347     402 ..     347     418 .. 0.81
   2 ?   -3.2   0.0       3.8   4.6e+03     251     294 ..     469     509 ..     463     510 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-05
                                       SSHHHHHHHHS...-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHH CS
                     UvrD-helicase   1 lnpeqreaias...lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkA 57 
                                       ln+eq+ a+ +     + + +   +G+GKT++l+e++ r ++++    d++lv    n+A
  gi|336254075|ref|YP_004597182.1| 347 LNQEQELAVSCallADQLFCIHGPPGTGKTRTLVEVVRRSVEAG----DDVLVCADSNQA 402
                                       578888888877656777889999*****************999....667766666665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.8
                                       HHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG CS
                     UvrD-helicase 251 ealrerykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQ 294
                                       +al+++++++  DE+  T+ +  +    l++++ ++++ GD kQ
  gi|336254075|ref|YP_004597182.1| 469 AALEREFDVLVLDEA--TQATCTASCIPLSRAE-KVILAGDHKQ 509
                                       556666677777776..4444444444455554.7999999999 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 ?    0.7   0.1      0.55   6.5e+02      63      82 ..     150     170 ..     148     182 .. 0.71
   2 ?   12.1   0.1   0.00017       0.2       2      21 ..     366     385 ..     365     487 .. 0.86
   3 ?   -0.2   0.0         1   1.2e+03      76     121 ..     599     647 ..     591     655 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.55
                                       EEETGGGHHHHH.TTCCCHHH CS
                               AAA  63 fiDEidalaksr.sgseseee 82 
                                       f+DE++++++++ + + +e++
  gi|336254075|ref|YP_004597182.1| 150 FFDELESFVRAEmDAQRDENR 170
                                       9**********9633333333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00017
                                       EEESSTTSSHHHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavake 21 
                                       +++GppGtGKT +   v++ 
  gi|336254075|ref|YP_004597182.1| 366 CIHGPPGTGKTRTLVEVVRR 385
                                       79*********877666655 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1
                                       TCCCHHHHHHHHHHHHHHHHTTTS..SSTEEEEE.EESSGGGSTHHHHS CS
                               AAA  76 gseseeeervvnqLlteldgvkkk..eskvivig.atnrpdkldpallr 121
                                       ++++e e r+v++L++el + +++   s+v vi+  t ++d +   l+r
  gi|336254075|ref|YP_004597182.1| 599 STKNEAEARLVAHLVSELLEDEDDlePSDVSVITpYTAQVDAIRGTLRR 647
                                       3466677777777777776666654546677776356668888777774 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 ?   11.4   0.2   0.00018      0.22       2      52 .]     657     713 ..     656     713 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                          UvrD_C_2   2 ayaltihkaQGsefpaVivfdpdlaaarmgel.........rrrlLYtavTRAreklilv 52 
                                       ++++ti  +QGse  a+++  +  ++a+ g +           r L +a+TRA++ + +v
  gi|336254075|ref|YP_004597182.1| 657 VTVDTIDSFQGSEKTAIVLSLV-RSNAD-G-EigflgrpldGPRRLNVAMTRAQRYCAIV 713
                                       6899*********999999433.34433.2.2356788888888899*******999876 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0021       2.5       6      34 ..     348     377 ..     345     391 .. 0.79
   2 ?    0.8   0.0      0.23   2.8e+02     122     158 ..     477     510 ..     471     529 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0021
                                       SHHHHHHHH.HHHH-SEEEEE--TTSSTTH CS
                              PhoH   6 tkeQkeyle.alkkndivfaiGpaGtGKty 34 
                                       ++eQ+ +++ al + ++ ++ Gp GtGKt 
  gi|336254075|ref|YP_004597182.1| 348 NQEQELAVScALLADQLFCIHGPPGTGKTR 377
                                       6788877762566999************96 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.23
                                       EEEE-SGGG--HHHHHHHHTTB-TT-EEEEEE----- CS
                              PhoH 122 fvilDEAQnttkeqmkmfltRlGenskvvvtGdvtqi 158
                                       +++lDEA  +t +   + l+R     kv+++Gd +q 
  gi|336254075|ref|YP_004597182.1| 477 VLVLDEATQATCTASCIPLSRA---EKVILAGDHKQL 510
                                       5799**9988888888888886...59******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (762 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.40
# Mc/sec: 5750.84
//
Query:       gi|336254076|ref|YP_004597183.1|  [L=426]
Description: OB-fold tRNA/helicase-type nucleic acid binding protein [Halopiger xanaduensis SH-6]
Scores for 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   21.7   8.3       0.13   12.2   0.1    4.3  4  tRNA_anti-codon  OB-fold nucleic acid binding 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 !    5.6   0.1   0.00089        16       1      68 [.      72     139 ..      72     146 .. 0.72
   2 !   12.2   0.1   7.4e-06      0.13       1      74 [.     176     250 ..     176     252 .. 0.85
   3 ?    0.0   0.2     0.048   8.6e+02       1      19 [.     282     298 ..     282     300 .. 0.67
   4 !    5.6   0.1    0.0009        16      21      69 ..     329     400 ..     307     406 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.00089
                                       EEEEEEEEEEE......EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsis......drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelel 68 
                                       Vtv G v +        +++   ++   l D+tg i  +++          l +Gd + +    v++++g+ +el
  gi|336254076|ref|YP_004597183.1|  72 VTVTGVVLTAGkrsiryQGDDHVIVEGRLADDTGVIDYTAWE------DFGLSPGDTITAGnAGVREWDGE-PEL 139
                                       7788888888777774444444555555*************9......77777777777777777777665.666 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.4e-06
                                       EEEEEEEEEEE......EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsis......drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkv 70 
                                       Vt++  v+  +      + ++  +++ +  D++gr+  + ++      a +++eG  vr++  +v++++g  +e++v
  gi|336254076|ref|YP_004597183.1| 176 VTIEVTVVECErrtidgRDGETEILSGVFGDESGRLPFTNWD-----PAPEIEEGNAVRIEnAYVQEFRGV-PEVNV 246
                                       566666666667777776777888999999999999999999.....99**********************.****9 PP

                                       EEEE CS
                   tRNA_anti-codon  71 eeie 74 
                                       +e++
  gi|336254076|ref|YP_004597183.1| 247 SEFS 250
                                       9875 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.048
                                       EEEEEEEEEEEEEEETTEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvi 19 
                                       V v+G v+++  r+g+++i
  gi|336254076|ref|YP_004597183.1| 282 VEVVGNVIAV--RDGSGLI 298
                                       6677777777..6666654 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0009
                                       EEEEETTEEEEEEEET.....................HHHHHHHTTS-...TTSEEEEEEEEEECTTSSEEEE CS
                   tRNA_anti-codon  21 idlrDgtgriqvvlfr.....................eeatklaenlk...eGdvvrvtGrvkrrpggelelk 69 
                                       ++++Dgtg+++++l++                      +++ +a++++   +G  +rv+G ++ ++ g   l 
  gi|336254076|ref|YP_004597183.1| 329 AIVDDGTGTLTAILDDeltedvyggtlddaleqareaMDQEVVADRIReriVGREYRVRGHLSVDEYG-ANLD 400
                                       689*************8888888888887777766665555566666666677777777777777666.5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3287.44
//
Query:       gi|336254077|ref|YP_004597184.1|  [L=627]
Description: hypothetical protein Halxa_2688 [Halopiger xanaduensis SH-6]
Scores for 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   12.5   0.0       0.44   10.8   0.0    1.8  2  DUF4777   Domain of unknown function (DUF4777)


Domain annotation for each model (and alignments):
>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       0.3   5.3e+03      26      44 ..      58      77 ..      58      80 .. 0.79
   2 ?   10.8   0.0   2.5e-05      0.44       7      48 ..     568     611 ..     564     616 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.3
                           DUF4777 26 vervaerydlseeelk.kvV 44
                                      v++++e++ +++e+++ +vV
  gi|336254077|ref|YP_004597184.1| 58 VGTLTEVTSVNDEMVRaRVV 77
                                      67899999*******95555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 2.5e-05
                           DUF4777   7 alvlealkvl..nrPaTldEivervaerydlseeelkkvVkntL 48 
                                       + v+e++++l  +++a   E+ve+va  ++ se+e+++ +++ L
  gi|336254077|ref|YP_004597184.1| 568 DYVVETMADLddGDGADRTELVETVAADTGASEDEVEDAIQDAL 611
                                       789*******98999*************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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):               1  [number of targets reported over threshold]
# CPU time: 1.11u 0.31s 00:00:01.42 Elapsed: 00:00:00.49
# Mc/sec: 3850.44
//
Query:       gi|336254078|ref|YP_004597185.1|  [L=285]
Description: metallophosphoesterase [Halopiger xanaduensis SH-6]
Scores for complete 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-07   31.4   0.0      3e-07   30.8   0.0    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
      1e-05   26.1   0.5    7.7e-05   23.3   0.0    2.0  2  Metallophos    Calcineurin-like phosphoesterase


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 !   30.8   0.0   3.3e-11     3e-07       2     128 ..      27     183 ..      27     194 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3.3e-11
                     Metallophos_2   2 klaiiSDlH.................snldaleavlealkevgvdaiihaGDl..eeeep.....evleellela.. 52 
                                       ++++++D H                 ++ d+ e++ + l+++++d+++++GDl    ++p       le lle    
  gi|336254078|ref|YP_004597185.1|  27 RVLLVADYHagyeaglrsergvdvpsRAPDRRERLCTLLERTAADRLVVCGDLmhSIGDPggaerGELEVLLESVpp 103
                                       58899999999999999999999999889999999*****************6553333344433366666665566 PP

                     Metallophos_2  53 ..pvlaVrGNnDeevveedvlreaaelgtdl.....peeaelel...agek.....vlliHgdplgvkdalaellke 114
                                         +v++V+GN+D++ + +   + +   g+++     p+ a +++   +        v+++Hg+   +++    l   
  gi|336254078|ref|YP_004597185.1| 104 tvDVTVVKGNHDGQLETWFGNDDSDAGGGAIgepgqPDLASVTIvpgD--GididgVGVCHGH--TWPAPA-VLEC- 174
                                       67**********444444444444444444455555566666656553..244788*******..555433.3333. PP

                     Metallophos_2 115 aeegsdvvvcGHtH 128
                                            dvv++GH H
  gi|336254078|ref|YP_004597185.1| 175 -----DVVCLGHEH 183
                                       .....48*****99 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   8.5e-09   7.7e-05       2     123 ..      27     164 ..      27     173 .. 0.68
   2 ?    1.0   0.1     0.055     5e+02     192     204 .]     173     185 ..     163     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.5e-09
                                       EEEEEESBTB...............TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS....HHHHHHHHH.HH CS
                       Metallophos   2 rilvigDlHl...............algggqlddllkllddllreekpdlvllaGDlvdrg....dlekellel.la 58 
                                       r+l+++D H                ++++ + ++l +ll+++     +d ++++GDl +      +     ++  l+
  gi|336254078|ref|YP_004597185.1|  27 RVLLVADYHAgyeaglrsergvdvpSRAPDRRERLCTLLERT----AADRLVVCGDLMHSIgdpgG----AERGeLE 95 
                                       799******999**99*9999888888888888888888777....77888889**8888643332....3333344 PP

                                       HHHHH...TSEEEEEC-TTS.....CHHHHHHHHHHHHHHH......HHHHEHHHCEEETSEEEEEETTEEEEEEEE CS
                       Metallophos  59 alvky...pipvylllGNHe.....gfeeellnkygylgif......sepwrsdaevfnnlplaslgsgslkvlllh 121
                                        l+++    + v +++GNH+     +        +g+   +      +ep + d   + ++p  ++  +   v ++h
  gi|336254078|ref|YP_004597185.1|  96 VLLESvppTVDVTVVKGNHDgqletW--------FGNDDSDagggaiGEPGQPDLASVTIVPGDGIDID--GVGVCH 162
                                       444445447889********554432........22222222223446666666666677777776666..888888 PP

                                       SE CS
                       Metallophos 122 Gg 123
                                       G+
  gi|336254078|ref|YP_004597185.1| 163 GH 164
                                       88 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.055
                                       TESEEEEESSSSE CS
                       Metallophos 192 gvdlvisGHtHvy 204
                                       + d+v+ GH+H++
  gi|336254078|ref|YP_004597185.1| 173 ECDVVCLGHEHPC 185
                                       589********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2188.55
//
Query:       gi|336254079|ref|YP_004597186.1|  [L=176]
Description: oxidoreductase molybdopterin binding protein [Halopiger xanaduensis SH-6]
Scores for complete 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   0.0    5.3e-10   39.2   0.0    1.7  1  Oxidored_molyb  Oxidoreductase molybdopterin binding domain


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   2.9e-14   5.3e-10      26     167 ..      25     139 ..      12     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2.9e-14
                                       EEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHHHHHHHTTB-ETT..EEEEEEEEE CS
                    Oxidored_molyb  26 lslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlrdvLekagvkkpearhvvfegade 102
                                       +  d L +lp +e+ + + Ca+                      + +W Gv++ ++Le+a v  pe++h+ + + d 
  gi|336254079|ref|YP_004597186.1|  25 VDGDSLASLPLQERECEIVCATG------------------DRYTETWYGVPVLELLERASVP-PETTHLLVVSGD- 81 
                                       55666767777777777777773..................346899***************8.**********99. PP

                                       -TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBTTEEEEEEESS- CS
                    Oxidored_molyb 103 eleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvKwlkrievsdee 167
                                            +y a++ +e+al  + lLA+  ng+pL     y  R+v  g  g r vK + rie ++ e
  gi|336254079|ref|YP_004597186.1|  82 -----GYRACVAVETAL--EGLLALGKNGRPLADASDYETRFVAVGADGPRTVKDVGRIEAMTLE 139
                                       .....5***********..89***************************************88766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1309.52
//
Query:       gi|336254080|ref|YP_004597187.1|  [L=98]
Description: hypothetical protein Halxa_2691 [Halopiger xanaduensis SH-6]
Scores for 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   0.1       0.18   12.1   0.1    1.3  1  DUF3910   Protein of unknown function (DUF3910)


Domain annotation for each model (and alignments):
>> DUF3910  Protein of unknown function (DUF3910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   9.9e-06      0.18      18      50 ..      56      88 ..      50      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.9e-06
                           DUF3910 18 ykddvtydataidfslekddnryklivlkheed 50
                                      y ++vt d t+id+  e+dd+ + + +l ++++
  gi|336254080|ref|YP_004597187.1| 56 YAEEVTADVTTIDLQYERDDAGFVFRLLGDRDE 88
                                      899******************998888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 748.48
//
Query:       gi|336254081|ref|YP_004597188.1|  [L=452]
Description: sodium:neurotransmitter symporter [Halopiger xanaduensis SH-6]
Scores for 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  193.2  35.3    3.9e-31  108.4  18.4    2.0  2  SNF       Sodium:neurotransmitter symporter family


Domain annotation for each model (and alignments):
>> SNF  Sodium:neurotransmitter symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   8.9     4e-30   7.2e-26       1     115 [.       4     119 ..       4     125 .. 0.95
   2 !  108.4  18.4   2.2e-35   3.9e-31     182     482 ..     147     433 ..     132     450 .. 0.90

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 4e-30
                               SNF   1 RetwskkldfilsvvGfavgLgnvWRFPYlcyknGGGafliPYlilllvaGiPlfflelalGqytreGaitvwrkic 77 
                                       Re+w ++  fil++vG+avgLgn+WRFPY + + GG afl+ Yl+l+l +G P++ +e+ +G++t++  +++ +++ 
  gi|336254081|ref|YP_004597188.1|   4 RESWATRAGFILAAVGSAVGLGNIWRFPYQVGEYGGAAFLVVYLLLILGIGFPVILVEFVVGRHTERNPVGALKRLG 80 
                                       89*************************************************************************96 PP

                               SNF  78 .PllkgiGyasivvalyvglyYnvilawalfYlfssftt 115
                                          +  iG++ +   +++  yY v+ +w++ Y++  ++ 
  gi|336254081|ref|YP_004597188.1|  81 tGAWTKIGWVFVTAGFIILSYYSVVAGWTVRYVLLGLQG 119
                                       26899***************************9988775 PP

  == domain 2  score: 108.4 bits;  conditional E-value: 2.2e-35
                               SNF 182 lcllvawvvvylailkGvkssgkvvyftatfPyvvllvllvrgvlLpGavkgikfyltpdleklle..pkvWidaat 256
                                       + +++++ +v ++i +G++ s kv+  + +    +l+ l v++ +L+Ga ++  +yl+pd+  + +  +++  +aa+
  gi|336254081|ref|YP_004597188.1| 147 IFMVAVIAIVAFGIERGIELSVKVMVPAII---ALLIGLAVYAFTLEGAGEAYAYYLSPDFGTIASnwTSILPAAAA 220
                                       45677889****************999888...89999*************************98734588899*** PP

                               SNF 257 qiffslgigfGvlialasYnkfennvyrdallvslinsltsvlaglvvFsvlGfmaeeqgekisevaeeGpgLaFia 333
                                       q ff+l++g+Gv+i++asY   + n+ +da +++++++ + ++agl+ F +l f a +         ++Gp+L+F+ 
  gi|336254081|ref|YP_004597188.1| 221 QAFFTLSLGMGVMITYASYLGEDRNLAEDAGIIAFLDTGIAFTAGLIAFPIL-FTAGIPA------GSSGPALIFVS 290
                                       ***************************************************9.7776543......579******** PP

                               SNF 334 ypealtklplsplwsvlFFlmlillgldsqfgtvegiitavvDefkvllrrrelltlivavlaflvglllvtegGiy 410
                                        + a ++lp++ +++ +FF ++ +++l s+++++e++++ ++De  v    r   t+++  ++f+vg+       i 
  gi|336254081|ref|YP_004597188.1| 291 LAAAFAELPFGGILGAIFFGVVSIAALSSAISIMEVVTSYLIDEHGV---DRVPATAMLGTAMFVVGVPAAL--DII 362
                                       ***********************************************...999**************99876..599 PP

                               SNF 411 vltlldkyaaslsllvvvlleaiavawvyglkkflddikemlgfrpllflklcwkfvspllllvlliasivk 482
                                       +++++d +a+ + l++  ll +i + wv   +  ld++ + ++   +l ++++w +  p++++ + ++++  
  gi|336254081|ref|YP_004597188.1| 363 FIDVYDLFANGVLLVLGGLLLSIFIGWVVP-DLALDELGKGITNIGSLGVTWIWLLRIPVIIALIAVVALNA 433
                                       ***************************975.55677888888888888888889999999888887776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3308.18
//
Query:       gi|336254082|ref|YP_004597189.1|  [L=514]
Description: protionyl-CoA carboxylase [Halopiger xanaduensis SH-6]
Scores for complete 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-197  657.4   0.0   1.4e-197  657.2   0.0    1.0  1  Carboxyl_trans  Carboxyl transferase domain
    4.5e-05   23.1   0.0     0.0001   21.9   0.0    1.5  2  MdcE            Malonate decarboxylase gamma subunit (MdcE)
  ------ inclusion threshold ------
       0.39    8.9   1.0       0.52    8.4   1.0    1.1  1  BIV_Env         Bovine immunodeficiency virus surface protein


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  657.2   0.0  2.4e-201  1.4e-197       1     494 []      26     512 ..      26     512 .. 0.99

  Alignments for each domain:
  == domain 1  score: 657.2 bits;  conditional E-value: 2.4e-201
                                       SSCTTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHH.HHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSG CS
                    Carboxyl_trans   1 kehprGkltareridllldpgsFgeledlffhrvtelgr.kkklprdgvvtgsGaviGravevvaqdktvlggslgp 76 
                                       k+h++Gk+tarerid+ ld+g F+e+++l  h+++++g+ ++k+p+dgvvtg+G+v+Gr+v+v+a+d+tv+ggslg+
  gi|336254082|ref|YP_004597189.1|  26 KQHDKGKMTARERIDYFLDEGTFTEFDQLRTHQTSQFGMeERKIPGDGVVTGYGEVNGRTVFVFAHDFTVFGGSLGE 102
                                       69*************************************999*********************************** PP

                                       GGCEEECHHHHHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHH CS
                    Carboxyl_trans  77 akgekllkaqeeaikagepligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpal 153
                                       + +ek++k++++a++ g+p++g+nds+Ga  riqegv+sl+g+ +if++n++asg+Ipqis ++g+caGg++Y+p +
  gi|336254082|ref|YP_004597189.1| 103 VFAEKICKVMDMAMEVGAPVVGLNDSAGA--RIQEGVKSLAGFTEIFRRNQEASGVIPQISGIMGPCAGGAVYSPSI 177
                                       *****************************..********************************************** PP

                                       TSEEEEETTEEEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGG CS
                    Carboxyl_trans 154 gdrvimveetskifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnr 230
                                       +d+++mv++ts++++tGp v k+v+g eevt eelgGa++h+ k+Gva+++ e++e+al+ i++llsylP   +nn 
  gi|336254082|ref|YP_004597189.1| 178 TDFIFMVQDTSHMYITGPGVTKTVTG-EEVTHEELGGAMTHAGKTGVAQFACESEEQALDDIKRLLSYLP---QNNV 250
                                       **************************.*******************************************...9999 PP

                                       SS----ECSSGSSSH.....HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--S CS
                    Carboxyl_trans 231 esaPivetadepdrd...lieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetr 304
                                       e++P+ve++d+pdr+   l++ivP++++kpyD+ +vi  +vdeg+F+E+ e++Ak++VvGf+rl+G++vG+vAn++r
  gi|336254082|ref|YP_004597189.1| 251 EDPPRVEPWDDPDRRderLNDIVPPSPQKPYDMVDVIDSVVDEGSFFEVAENFAKELVVGFGRLDGRSVGIVANQPR 327
                                       **************999999********************************************************* PP

                                       EEETTEE-HHHHHHHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEH CS
                    Carboxyl_trans 305 veaGqvlfidsavKaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayG 381
                                       v+aG  l  ds++K +rf+r+cd +n+P+v+++dv+G+++G++qe+ gi++hGakl++a+aea+vP +tvi+rkayG
  gi|336254082|ref|YP_004597189.1| 328 VNAG-TLTVDSSMKGSRFVRFCDSFNIPIVTFVDVPGYMPGTDQEHRGIIRHGAKLLYAYAEATVPLLTVITRKAYG 403
                                       ****.************************************************************************ PP

                                       HHHHTTTGGGSTTTTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Carboxyl_trans 382 GayvvmdskingadlvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargf 458
                                       Gay+vm sk++gad+++awpta+iaV+gp+gav+il+r+e+++ae    ++++ r + ++ey+ee++npy+a+  gf
  gi|336254082|ref|YP_004597189.1| 404 GAYCVMASKNLGADVNYAWPTAEIAVMGPQGAVNILYRDELEEAE----NPDELRDELIEEYREEFANPYTATDKGF 476
                                       ******************************************999....999************************* PP

                                       HHTTSSHHHHHHTTSSSEEEHGGGHHHHHHHHHHHH CS
                    Carboxyl_trans 459 aDavidpsetraklvialelewkkarklparkrrni 494
                                        D+vi p+etr +l+ +le++++k++++p +k++ni
  gi|336254082|ref|YP_004597189.1| 477 LDDVIVPTETRPRLIDDLEMLETKREQNPDKKHGNI 512
                                       **********************************97 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.92   5.5e+03      94     111 ..     108     125 ..     100     136 .. 0.74
   2 !   21.9   0.0   1.7e-08    0.0001      14     150 ..     304     438 ..     294     448 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.92
                                       HHHHHHHHHHHT--EEEE CS
                              MdcE  94 lakalarArlaGhpvigl 111
                                       + k+++ A   G+pv+gl
  gi|336254082|ref|YP_004597189.1| 108 ICKVMDMAMEVGAPVVGL 125
                                       567778888888888887 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.7e-08
                                       -TTEEEEEEEETTEEEEEEEE---TTSS-B-HHHHHHHHHHHHHHHTSSS--EEEEEEEE--B--SHHHHHHTHHHH CS
                              MdcE  14 aaslkvldgsltlesvrfvaVigdankgevGvdealaLaaaVleaieraekrpilvlvDvasQrlgrrdEllGihea 90 
                                       a +l v  g+l+++sv+ va  +  n g + vd +++ +  V      + + pi+  vDv++   g  +E  Gi   
  gi|336254082|ref|YP_004597189.1| 304 AKELVVGFGRLDGRSVGIVANQPRVNAGTLTVDSSMKGSRFVRFC--DSFNIPIVTFVDVPGYMPGTDQEHRGIIRH 378
                                       5566677899***************************99999765..46789************************* PP

                                       HHHHHHHHHHHHHHT--EEEEEEEEEEHHHHH...HTTTT-SEEEEEET-EEESS-HHHHHHH CS
                              MdcE  91 lahlakalarArlaGhpvigllvGkavsGafl...ahglqanrlialpgvqvavmdkasaArv 150
                                        a l  a+a A +   p+++++  ka  Ga+    +  l a++  a p +++avm+ + a  +
  gi|336254082|ref|YP_004597189.1| 379 GAKLLYAYAEATV---PLLTVITRKAYGGAYCvmaSKNLGADVNYAWPTAEIAVMGPQGAVNI 438
                                       ********99986...9*************8622256799****************8877665 PP

>> BIV_Env  Bovine immunodeficiency virus surface protein (SU)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.0   8.7e-05      0.52       6      47 ..      10      47 ..       1      52 [. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 8.7e-05
                           BIV_Env  6 drvergeeeGesdelrlllqedldkGrltarealdawinnGe 47
                                      +r e++e  G ++     +q++ dkG++tare +d + ++G 
  gi|336254082|ref|YP_004597189.1| 10 ERREEAELGGGEER----IQKQHDKGKMTARERIDYFLDEGT 47
                                      46667776666666....9******************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.38
# Mc/sec: 4070.16
//
Query:       gi|336254083|ref|YP_004597190.1|  [L=116]
Description: hypothetical protein Halxa_2694 [Halopiger xanaduensis SH-6]
Scores for 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:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 896.81
//
Query:       gi|336254084|ref|YP_004597191.1|  [L=262]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-10   41.5   0.0    5.8e-10   39.7   0.0    1.9  3  Methyltransf_25  Methyltransferase domain
    1.1e-09   38.8   0.1    8.1e-09   36.0   0.0    2.4  3  Methyltransf_11  Methyltransferase domain
    1.2e-05   26.0   0.0    2.4e-05   25.0   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    7.9e-05   21.8   0.0    0.00011   21.4   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
  ------ inclusion threshold ------
      0.019   14.3   0.0      0.023   14.0   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
       0.13   11.8   0.0       0.21   11.2   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95


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 ?   -3.2   0.0       4.7   1.4e+04      90      97 .]      22      29 ..      10      29 .. 0.77
   2 !   39.7   0.0   1.9e-13   5.8e-10       1      97 []      48     144 ..      48     144 .. 0.94
   3 ?   -2.2   0.0       2.3   6.9e+03      66      97 .]     187     217 ..     159     217 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.7
                                      HHHEEEEE CS
                   Methyltransf_25 90 arvLkpgG 97
                                      +r L+pgG
  gi|336254084|ref|YP_004597191.1| 22 KRTLRPGG 29
                                      68999999 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 1.9e-13
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH.TTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee.eglnvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       v++++ G G +++ +++r    ++tg++++ e  ++ r+++e+ +++  e+v+g+a d +++ +s D+v+   +l +
  gi|336254084|ref|YP_004597191.1|  48 VVEFAPGVGATARLALDRN-PNSYTGIELDRERAARLRKQLENiDRPVPEIVVGNAADTDLPRNSADAVYGEAMLTM 123
                                       789999*******999995.7********************98777899**********************655999 PP

                                       SSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                        +d   +++l+e++r+L+pgG
  gi|336254084|ref|YP_004597191.1| 124 QPDGGKRAILEEARRLLRPGG 144
                                       99999***************9 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.3
                                       EEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  66 DlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                       D   s  ++ +++++  + al e +rvL ++G
  gi|336254084|ref|YP_004597191.1| 187 DRLES-AGFTVMWRALEPMALLEPRRVLADEG 217
                                       44444.23455555555566667777776665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.8   5.2e+03      85      93 ..      22      30 ..      15      32 .. 0.86
   2 !   36.0   0.0   2.7e-12   8.1e-09       2      93 ..      50     145 ..      49     148 .. 0.87
   3 ?   -1.1   0.0         1   3.1e+03      78      93 ..     203     218 ..     154     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.8
                                      HHHEEEEEE CS
                   Methyltransf_11 85 aRvLkpgGl 93
                                      +R L+pgG 
  gi|336254084|ref|YP_004597191.1| 22 KRTLRPGGE 30
                                      799****96 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 2.7e-12
                                       EET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-.. CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv.. 74 
                                       +++ G G+ a+   +r   +++g++l+ e  ++ +++ ++ +    e+vv++a ++ ++ ns D+v+   +l+    
  gi|336254084|ref|YP_004597191.1|  50 EFAPGVGATARLALDRNpNSYTGIELDRERAARLRKQLENIDRpVPEIVVGNAADTDLPRNSADAVYGEAMLTMQpd 126
                                       567899999999997777***********998887777766657889****************************54 PP

                                       CCHHHHHHHHHHHEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGl 93 
                                          +++l+e++R+L+pgG+
  gi|336254084|ref|YP_004597191.1| 127 GGKRAILEEARRLLRPGGR 145
                                       45789*************8 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1
                                       HHHHHHHHHHEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGl 93 
                                         al e +RvL  +Gl
  gi|336254084|ref|YP_004597191.1| 203 PMALLEPRRVLADEGL 218
                                       4466777888888886 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   8.2e-09   2.4e-05       2      98 ..      50     145 ..      49     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 8.2e-09
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       e+  G+G+++r  l++  + +ytg++++++  ++ +++l  ++ + + ++ + +  + dl+  +s D+v+    l  
  gi|336254084|ref|YP_004597191.1|  50 EFAPGVGATARLALDR-NPNSYTGIELDRERAARLRKQLENID-RPVPEIVVGNAADTDLPR-NSADAVYGEAMLTM 123
                                       8999*******99999.8899***********55555555555.566666666666555554.6******9999999 PP

                   Methyltransf_12  79 l..kdirevldnirklLkpgGr 98 
                                            +r++l+++r+lL+pgGr
  gi|336254084|ref|YP_004597191.1| 124 QpdGGKRAILEEARRLLRPGGR 145
                                       9878899**************8 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   3.6e-08   0.00011      20      94 ..      34     111 ..      30     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.6e-08
                                       HHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHCHTT.TCCCE.EEE-S-CCGHHHHHH CS
                            RrnaAD  20 neIldklnleekltvleigpGkGilTeeLakra.kqvvvlElderLakllqkkls.kdekl.kvvhqDflkfetpee 93 
                                        e l++l +   + v+e +pG+G++ +  ++r  ++++ +Eld++ a++l+k+l+  d+++ ++v  ++ ++++p +
  gi|336254084|ref|YP_004597191.1|  34 RELLEALSIAAADDVVEFAPGVGATARLALDRNpNSYTGIELDRERAARLRKQLEnIDRPVpEIVVGNAADTDLPRN 110
                                       57789999999*************888889************************98555554788888888888875 PP

                                       H CS
                            RrnaAD  94 v 94 
                                        
  gi|336254084|ref|YP_004597191.1| 111 S 111
                                       5 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.7e-06     0.023      51     209 ..      33     194 ..      19     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.7e-06
                                       HHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-.EEEEEE-HHHHHHHHHHS-----TTEEEEES-TTTS--- CS
                    Methyltransf_2  51 akkvleafdleglkslvDvGGGtGalakaivsayPti.kvivfDlpeVveaAkehlsageeervefvgGdffkdslP 126
                                       ++++lea  +     +v+   G+Ga+a+ +    P+  ++i +D  + ++  +++l+   ++  e v G+  +  lP
  gi|336254084|ref|YP_004597191.1|  33 TRELLEALSIAAADDVVEFAPGVGATARLALDRNPNSyTGIELDRERAARL-RKQLENIDRPVPEIVVGNAADTDLP 108
                                       678999999999999******************998526788998776655.555699999999************* PP

                                       ..--SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS---HHHHHH.HHHHHHCSS-----HHHH CS
                    Methyltransf_2 127 ..eaDaillkrvlhDwsdekcvklLkrvkkalpagGkvivveavlgadpsgeletelv.dlimlvqteGkeRteaey 200
                                         +aDa+  + +l    d+  + +L++ ++ l++gG+  v e  l+ + ++e+++++  +   +++   +  te+ +
  gi|336254084|ref|YP_004597191.1| 109 rnSADAVYGEAMLTMQPDGGKRAILEEARRLLRPGGRYGVHELALADGVDDETAVRIRrEAAQVANVRPQPLTESGW 185
                                       888***************************************99999999988877764444444445555555555 PP

                                       HHHHHHCT- CS
                    Methyltransf_2 201 eellseaGf 209
                                        + l++aGf
  gi|336254084|ref|YP_004597191.1| 186 VDRLESAGF 194
                                       555555555 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     7e-05      0.21      12      92 ..      16      95 ..       8     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7e-05
                                      EEEXTTXXXXXSSSHHHHHHHHHHHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT-- CS
                     Cons_hypoth95 12 kLkvlegkstRPttdrvrealFnilaaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkle 90
                                       L++l  +++RP  +     l + l+ +  +  v++   G Ga +  Al R+ ++ + +e d+e ++ l+++le+++  
  gi|336254084|ref|YP_004597191.1| 16 LLATLGKRTLRPGGEALTRELLEALSIAAADD-VVEFAPGVGATARLALDRNPNSYTGIELDRERAARLRKQLENIDRP 93
                                      688888999********999****99777666.99***************************************99966 PP

                                      TT CS
                     Cons_hypoth95 91 ee 92
                                        
  gi|336254084|ref|YP_004597191.1| 94 VP 95
                                      42 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1931.07
//
Query:       gi|336254085|ref|YP_004597192.1|  [L=611]
Description: carbamoyl-phosphate synthase L chain ATP-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-72  242.7   0.1    1.2e-71  240.6   0.1    2.0  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
      3e-45  153.3   0.8      7e-45  152.1   0.5    1.8  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    1.1e-34  118.7   0.0    2.2e-34  117.8   0.0    1.5  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    7.1e-16   57.8   7.3    2.1e-15   56.3   7.3    1.8  1  Biotin_lipoyl    Biotin-requiring enzyme
      1e-07   31.6   3.4     0.0012   18.7   0.4    2.7  2  Biotin_lipoyl_2  Biotin-lipoyl like
    2.4e-06   27.3   0.0    4.7e-06   26.3   0.0    1.4  1  ATP-grasp        ATP-grasp domain
    4.6e-06   26.3   0.0    1.1e-05   25.0   0.0    1.6  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    5.4e-05   23.0   0.0    0.00011   22.1   0.0    1.5  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
     0.0089   16.7   1.8        5.1    7.8   0.1    2.8  2  HlyD_3           HlyD family secretion protein
  ------ inclusion threshold ------
      0.029   13.6   0.7        1.6    7.9   0.1    2.4  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
      0.035   14.0   0.8       0.12   12.3   0.4    2.1  2  RnfC_N           RnfC Barrel sandwich hybrid domain
      0.044   13.7   2.3       0.12   12.2   1.6    2.0  2  GCV_H            Glycine cleavage H-protein


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 !  240.6   0.1   7.9e-75   1.2e-71       2     209 ..     117     333 ..     116     335 .. 0.95
   2 ?   -1.2   0.0      0.81   1.2e+03      82      98 ..     409     425 ..     373     427 .. 0.65

  Alignments for each domain:
  == domain 1  score: 240.6 bits;  conditional E-value: 7.9e-75
                                       HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaaf 78 
                                       k++a++++++++vp+vp+++ pv++ ee+ ++ +e+gyP+ ika  g+GG+Gm+v+r+e+e+++ +++a +e +a f
  gi|336254085|ref|YP_004597192.1| 117 KTKARTIMNEADVPIVPGTTDPVTEPEEVKEFGEEYGYPIAIKAEGGGGGRGMKVVRDESEVEDQLESAKREGQAYF 193
                                       7899************************************************************************* PP

                                       STS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-E CS
                       CPSase_L_D2  79 gnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvv 155
                                        n++v++e++l++p++iEv++l+D++gnv +++er++slq+r+qkvie+ Ps +Ltde r++++eaa + v + +++
  gi|336254085|ref|YP_004597192.1| 194 DNDSVYLERYLEQPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEGPSAALTDELREKIGEAARRGVAAADYT 270
                                       ***************************************************************************** PP

                                       EEEEEEEEEETT.........TTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                       CPSase_L_D2 156 gagtveflldpk.........skeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                       +agtvefl++++         + ++y++EvNtR++ve++++e++TG+d+vk +++ia+ge+++
  gi|336254085|ref|YP_004597192.1| 271 NAGTVEFLVEEEpgrdgplgpDANFYFLEVNTRIQVEHTVTEEITGYDIVKRQIRIAAGEEID 333
                                       *********986333333333468***********************************9875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.81
                                       -EEEEE--SSSEEEEEE CS
                       CPSase_L_D2  82 qvlvekslkgpkeiEve 98 
                                          +e+sl+  +e+E+e
  gi|336254085|ref|YP_004597192.1| 409 DECIERSLRALREYEIE 425
                                       4569**********997 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 !  152.1   0.5   4.7e-48     7e-45       1     110 []       1     111 [.       1     111 [. 0.98

  Alignments for each domain:
  == domain 1  score: 152.1 bits;  conditional E-value: 4.7e-48
                                       ---EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SE CS
                     Biotin_carb_N   1 kikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgada 77 
                                       +++kvl+anrGeiAvr++ra++el++ tva+yse+d+n+ hvr+adea+++gpa+a++sYl+ e++++aa++++ada
  gi|336254085|ref|YP_004597192.1|   1 MFRKVLVANRGEIAVRVMRACEELNVGTVAIYSEADKNAGHVRYADEAYNVGPARAADSYLDHEAVIEAARKADADA 77 
                                       799************************************************************************** PP

                                       EE--SSTTTT-HHHHHHHHH.TT-EESSS-HHHH CS
                     Biotin_carb_N  78 vhpGyGflsEnaefaeavee.agivfiGPsaeal 110
                                       +hpGyGfl+Enaefa++ve+  gi++iGPs++a+
  gi|336254085|ref|YP_004597192.1|  78 IHPGYGFLAENAEFARKVENaDGITWIGPSSDAM 111
                                       *******************7479********998 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   0.0   1.5e-37   2.2e-34       1     108 []     347     455 ..     347     455 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 1.5e-37
                                       EEEEESEETTTTTEE--.CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-E CS
                     Biotin_carb_C   1 eaRinaEdpeknflpss.GkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelr 76 
                                       e+RinaE+++++f+p++ G+++++++p+g gvR+d+++++g+e  ++yDs++aKl+v+ge+r+e+++r  raL+e++
  gi|336254085|ref|YP_004597192.1| 347 EFRINAENAAQDFAPATgGTLETYDPPGGIGVRLDDALRQGDELVTDYDSMIAKLVVWGEDRDECIERSLRALREYE 423
                                       89*************98579********************************************************* PP

                                       EESS-BSHHHHHHHHH-HHHHHT---TTTCCC CS
                     Biotin_carb_C  77 ieGvktnieflrailedeefakgeldtkflee 108
                                       ieG++t i+f+r +l de+f++ +++tk+l+e
  gi|336254085|ref|YP_004597192.1| 424 IEGIPTIIPFHRLMLTDETFVESTHTTKYLDE 455
                                       ******************************85 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   7.3   1.4e-18   2.1e-15       8      73 .]     550     610 ..     542     610 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.4e-18
                                       SEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl   8 iGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                              g ++ + v+vGd+V+ag+vl+++eamKme++i a k G+v+ei v+e+++v+ gd l+++
  gi|336254085|ref|YP_004597192.1| 550 Q------GtILDIEVEVGDEVAAGDVLVVLEAMKMENDIVASKGGTVVEIPVEEDQSVDMGDTLVVL 610
                                       3......446669***************************************************986 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.4   7.8e-07    0.0012       5      39 ..     545     579 ..     543     582 .. 0.87
   2 !   13.2   0.2   4.1e-05     0.061       7      33 ..     584     610 ..     579     611 .] 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.8e-07
                   Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLaelDsralq 39 
                                       + a   G++  + V+ G++V aGdvL++l+  + +
  gi|336254085|ref|YP_004597192.1| 545 VDAEMQGTILDIEVEVGDEVAAGDVLVVLEAMKME 579
                                       667889***********************987665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.1e-05
                   Biotin_lipoyl_2   7 apvsGrVaqlnVkdGqrVkaGdvLael 33 
                                       a+  G+V+++ V++ q V  Gd+L++l
  gi|336254085|ref|YP_004597192.1| 584 ASKGGTVVEIPVEEDQSVDMGDTLVVL 610
                                       56689*******************998 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   3.1e-09   4.7e-06      14     146 ..     139     280 ..     130     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.1e-09
                                       ECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEE CS
                         ATP-grasp  14 veskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlv 82 
                                       v++ ee++e+ ee g+p+ +K + +g  G+G +vvr+e+++e+ le +        ++ +v++E + +  + + v +
  gi|336254085|ref|YP_004597192.1| 139 VTEPEEVKEFGEEYGYPIAIK-AEGGGGGRGMKVVRDESEVEDQLESAkregqayfDNDSVYLERYLEQPRHIEVQI 214
                                       67789****************.89999*******************99999****99*****************999 PP

                                       EEETTC-EEE--EEE.EEEET.TEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEE CS
                         ATP-grasp  83 vrsaeGetafypvve.tvqed.gilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvl 146
                                         +++G+++ +      +q++ + + +   +a+++++  +k+ e a++ v++ ++    +vE+ v 
  gi|336254085|ref|YP_004597192.1| 215 LADEHGNVRHLGERDcSLQRRhQKVIEEGPSAALTDELREKIGEAARRGVAAADYTNAGTVEFLVE 280
                                       99****988764432133433033344444466777788888888888888888888888887665 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 !   25.0   0.0   7.6e-09   1.1e-05      26     164 ..     143     282 ..     125     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 7.6e-09
                                       HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHT.....T-S.CEEEEE--.ESEEEEEEEEETSS CS
                   Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafk.....yde.kvlvEeai.egreievavlgnek 95 
                                       e +++  ee gyp+ +K+   G   G++ v+ e+e+++ +e+a +     +d+ +v  E+++ + r iev +l +e+
  gi|336254085|ref|YP_004597192.1| 143 EEVKEFGEEYGYPIAIKAEGGGGGRGMKVVRDESEVEDQLESAKRegqayFDNdSVYLERYLeQPRHIEVQILADEH 219
                                       56788899********************************99976333334542699*****999************ PP

                                       CEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETT CS
                   Dala_Dala_lig_C  96 levsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDffltee 164
                                        +v ++ge+  +  + + ++k     ++    a+l++e +eki e+a +  +a d +  + v f+++ee
  gi|336254085|ref|YP_004597192.1| 220 GNVRHLGERDCS--LQRRHQKV----IEEGPSAALTDELREKIGEAARRGVAAADYTNAGTVEFLVEEE 282
                                       ********9776..44555665....4556678999999999999999999999999999999999765 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 !   22.1   0.0   7.1e-08   0.00011       2      91 ..     116     206 ..     115     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.1e-08
                                       BHHHHHHHHHHTT--B-..-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TT CS
                            GARS_A   2 sKsfakdllkkagipta..eyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkf 76 
                                       +K+ a++++++a++p+   + + +t+pee+ke+ ee + ++  +Ka+g  +g+g++v+++e+e  + +++  ++ + 
  gi|336254085|ref|YP_004597192.1| 116 EKTKARTIMNEADVPIVpgTTDPVTEPEEVKEFGEEYGYPI-AIKAEGGGGGRGMKVVRDESEVEDQLESAKREGQA 191
                                       688899*********98668899******************.9*********************9999999887777 PP

                                       CCCCSSEEEEE---S CS
                            GARS_A  77 GeagekvviEelleG 91 
                                          +++v +E +le 
  gi|336254085|ref|YP_004597192.1| 192 YFDNDSVYLERYLEQ 206
                                       777899999999974 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0034       5.1       1      30 [.     544     573 ..     544     578 .. 0.90
   2 !    7.4   0.2    0.0048       7.1       2      29 ..     582     609 ..     581     611 .] 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0034
                            HlyD_3   1 tlrApvdGvvvelnveegevvqagdellei 30 
                                       t+ A  +G++ ++ ve+g+ v+agd+l+ +
  gi|336254085|ref|YP_004597192.1| 544 TVDAEMQGTILDIEVEVGDEVAAGDVLVVL 573
                                       578999********************9865 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0048
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdelle 29 
                                       + A+ +G+vve++vee + v  gd+l+ 
  gi|336254085|ref|YP_004597192.1| 582 IVASKGGTVVEIPVEEDQSVDMGDTLVV 609
                                       7899********************9975 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0011       1.6      21      54 ..     544     576 ..     539     581 .. 0.67
   2 ?    4.5   0.1     0.012        17     109     138 ..     580     609 ..     573     611 .] 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23  21 rvsarveGwveklyvnatgdkVkkGqpLaelysp 54 
                                       +v a+++G + +++v+ +gd+V++G+ L+ l++ 
  gi|336254085|ref|YP_004597192.1| 544 TVDAEMQGTILDIEVE-VGDEVAAGDVLVVLEAM 576
                                       4666677777777777.77777777777766654 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 109 vtvkapisGvVteknvreGqyvqpgdtlft 138
                                        ++ a+  G+V+e  v e q v+ gdtl+ 
  gi|336254085|ref|YP_004597192.1| 580 NDIVASKGGTVVEIPVEEDQSVDMGDTLVV 609
                                       57899**********************975 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 ?   -1.2   0.0       1.4   2.1e+03      20      55 ..     238     273 ..     204     275 .. 0.72
   2 ?   12.3   0.4     8e-05      0.12      42      89 ..     554     602 ..     547     611 .] 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.4
                            RnfC_N  20 pieklplpkelvlplsqhiGapakplvkvgdkVlkG 55 
                                       ++ +  + + l+  l+  iG++a+  v+  d+ + G
  gi|336254085|ref|YP_004597192.1| 238 KVIEEGPSAALTDELREKIGEAARRGVAAADYTNAG 273
                                       444444555666678888888888888888877666 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 8e-05
                            RnfC_N  42 akplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlvahgs 89 
                                        ++ v+vgd+V  G+++   e+  +   + as  GtV++i   + ++ +
  gi|336254085|ref|YP_004597192.1| 554 LDIEVEVGDEVAAGDVLVVLEAmKMENDIVASKGGTVVEIPVEEDQSVD 602
                                       56779***********998888567999***********9766555555 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.8   8.7e+03      12      32 ..      96     116 ..      88     122 .. 0.81
   2 ?   12.2   1.6   8.2e-05      0.12      27      74 ..     547     593 ..     542     602 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.8
                                       EETT.EEEEEE-HHHHHHH-S CS
                             GCV_H  12 veedgvatvGitdfaqeelgd 32 
                                       ++ dg++ +G ++ a e lg+
  gi|336254085|ref|YP_004597192.1|  96 ENADGITWIGPSSDAMESLGE 116
                                       467899999999999999987 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 8.2e-05
                                       HHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                             GCV_H  27 qeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvev 74 
                                       +e+ g ++ +e+ evg++v++g+ l ++E+ K+  ++ a   G+vve+
  gi|336254085|ref|YP_004597192.1| 547 AEMQGTILDIEV-EVGDEVAAGDVLVVLEAMKMENDIVASKGGTVVEI 593
                                       677889999998.8********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 4503.12
//
Query:       gi|336254086|ref|YP_004597193.1|  [L=383]
Description: Radical SAM domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-21   74.8   0.0    1.5e-20   74.2   0.0    1.3  1  Radical_SAM   Radical SAM superfamily
    2.9e-05   24.4   0.0    4.4e-05   23.8   0.0    1.2  1  Fer4_12       4Fe-4S single cluster domain
    0.00022   21.6   0.0    0.00056   20.4   0.0    1.7  1  SPASM         Iron-sulfur cluster-binding domain
     0.0013   18.9   0.0     0.0019   18.3   0.0    1.3  1  Fer4_14       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.019   14.9   0.1      0.035   14.0   0.1    1.6  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
      0.057   13.6   0.0        0.1   12.7   0.0    1.3  1  DUF1906       Domain of unknown function (DUF1906)


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 !   74.2   0.0   5.1e-24   1.5e-20       2     166 ..      18     176 ..      17     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 5.1e-24
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpg 77 
                                       +vt++C+l+C +C      +  +++ +ls+ e +++++e+ ae g +  v+l+gg+pl+++d +el++    l   g
  gi|336254086|ref|YP_004597193.1|  18 EVTQACALACDHCRADA--QEKRHPDELSTAEGKRLLEEA-AEFGeGQLVVLSGGDPLVRDDVEELVDYGTDL---G 88 
                                       689*************9..5********************.79999*************99998888888888...* PP

                                       EEEEEEECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpd.eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivgl 152
                                       +r+t++ +gt+    + +e+l+++g+ r++++ + a+   +++ ++  +++fee+++a+e +r+ag++ v +++++ 
  gi|336254086|ref|YP_004597193.1|  89 LRMTITPSGTHSLtADRIEALADAGLKRMAVSFDGASAA-THDDFRgENGSFEETVRAVEDARAAGLP-VQVNTTVC 163
                                       ***********559*************************.777777799*******************.77776666 PP

                                       TTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                       Radical_SAM 153 pGendeeleellel 166
                                       + ++  el e++el
  gi|336254086|ref|YP_004597193.1| 164 R-QTVGELPEIREL 176
                                       5.777777777766 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 !   23.8   0.0   1.5e-08   4.4e-05       9      84 ..      15      89 ..       9     131 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.5e-08
                           Fer4_12  9 slf..vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk.esiegltllGGEPllpenaeallelvkevkeekp 84
                                      +++  ++ C l+C+ C +  +++ ++ +e +++  ++++e++++  + + ++l+GG+Pl+   ++++ elv++    ++
  gi|336254086|ref|YP_004597193.1| 15 LIWevTQACALACDHCRAD-AQEKRHPDELSTAEGKRLLEEAAEfGEGQLVVLSGGDPLV---RDDVEELVDYGTDLGL 89
                                      55666899********955.5555555566666666777776654788************...7777777777666655 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.9e-07   0.00056       6      68 .]     276     331 ..     272     331 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.9e-07
                             SPASM   6 rslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse.eyqefrkskkfplielCrnCp 68 
                                         +f+++ G+V+p  +       + + Gn+r+e+l +I++++  ++ +r+  +++l+  C  Cp
  gi|336254086|ref|YP_004597193.1| 276 GFAFVSHTGEVFPSGFL------PQSAGNVRDEPLTDIYRDSsLFRSLRD--RDNLEGKCGACP 331
                                       5689**********333......58**************888799****4..555566799996 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 !   18.3   0.0   6.5e-07    0.0019       5      74 ..      20      84 ..      16     123 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.5e-07
                           Fer4_14  5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrl 74
                                      +  C l+C  C   ++ k +  + +t e   + l+++ +   + q +vl+GG+PL     +++ +lv++ 
  gi|336254086|ref|YP_004597193.1| 20 TQACALACDHCRADAQEKRHPDELSTAEGK-RLLEEAAEFG-EGQLVVLSGGDPLVR---DDVEELVDYG 84
                                      578********9888666666666665554.5664444444.4677*********66...5556666554 PP

>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.2e-05     0.035      52     116 ..      32      95 ..      14     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                      TP_methylase  52 apmgkekepleeayeeiaeal..aealragkdVvllvsGDPlvygtgselvealrareagieveviP 116
                                       a+  +++ p e   +e  + l  a++  +g + v+l++GDPlv + + elv+  ++   g++  + P
  gi|336254086|ref|YP_004597193.1|  32 ADAQEKRHPDELSTAEGKRLLeeAAEFGEG-QLVVLSGGDPLVRDDVEELVDYGTD--LGLRMTITP 95 
                                       455666677777899999999655555555.5*******************99888..777777766 PP

>> DUF1906  Domain of unknown function (DUF1906)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.5e-05       0.1      28      84 ..      99     156 ..      90     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                           DUF1906  28 knltaeevqdilaaGlrlvpiyqggq..deaadftaaaaqGvadAkdAvaaasalGfpa 84 
                                        +lta+ ++++++aGl+ +++  +g   ++  df+ + +   ++  +Av+ a+a+G+p 
  gi|336254086|ref|YP_004597193.1|  99 HSLTADRIEALADAGLKRMAVSFDGAsaATHDDFRGE-NGSFEETVRAVEDARAAGLPV 156
                                       579*****************99999944444588777.7778**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2807.36
//
Query:       gi|336254087|ref|YP_004597194.1|  [L=119]
Description: phenylacetic acid degradation B [Halopiger xanaduensis SH-6]
Scores for complete 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-08   34.8   0.0    1.9e-08   34.4   0.0    1.3  1  PaaB      Phenylacetic acid degradation B


Domain annotation for each model (and alignments):
>> PaaB  Phenylacetic acid degradation B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0     1e-12   1.9e-08       3      63 ..      20      78 ..      18     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1e-12
                              PaaB  3 plfEVfkrdkeglshqhvgSvhAadaemALlvArdvfvRReeavslwvvkseailastpee 63
                                      p++EVf+rd+eg + +hvgSv A  a+ A ++A  +f      v+lwv +++++++ +  +
  gi|336254087|ref|YP_004597194.1| 20 PQWEVFVRDEEGGPLRHVGSVAAESATDAHEQASRLFGW--YSVDLWVCPADEVVRFSTRA 78
                                      89***********************************85..689*********99877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 930.33
//
Query:       gi|336254088|ref|YP_004597195.1|  [L=156]
Description: flagellin domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   64.6   0.5    1.9e-17   64.0   0.5    1.3  1  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> 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 !   64.0   0.5     1e-21   1.9e-17       2      79 ..      12      91 ..      11      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 1e-21
                           Pilin_N  2 AVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievkidssastgkna.vslehkgGdsidtkdlkivlns 78
                                      AVS+V+Gv+L++aitv+la+v+ +f+++l +++ ++ p a ++++ d++ +++k + ++ +h  Gdsi+ ++l + ++s
  gi|336254088|ref|YP_004597195.1| 12 AVSSVVGVLLLIAITVVLAGVVHTFAFSLaDDTLQTYPTAGVSIDADADCDDEKATgLVATHVAGDSIPANELYLETTS 90
                                      9****************************99999********999888888777778***************9998887 PP

                           Pilin_N 79 e 79
                                      +
  gi|336254088|ref|YP_004597195.1| 91 D 91
                                      6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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: 0.40u 0.19s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1348.89
//
Query:       gi|336254089|ref|YP_004597196.1|  [L=100]
Description: hypothetical protein Halxa_2700 [Halopiger xanaduensis SH-6]
Scores for 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   12.4   0.1       0.18   12.0   0.1    1.2  1  DUF4443   Domain of unknown function (DUF4443)


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 ?   12.0   0.1     1e-05      0.18      62     110 ..      13      60 ..       2      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1e-05
                           DUF4443  62 lrdtmeelamnieevlnfsdgdlivvtwaenpsdamksayhvaltlknd 110
                                        rd  +  + n+e+    +d dl+ v  a++  +a +s yhv l  + d
  gi|336254089|ref|YP_004597196.1|  13 RRDHENSWSANLEQPRHAADRDLV-VEQAKDAVEATESGYHVNLVTHGD 60 
                                       47888888999***********86.67899*************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 770.95
//
Query:       gi|336254090|ref|YP_004597197.1|  [L=140]
Description: hypothetical protein Halxa_2701 [Halopiger xanaduensis SH-6]
Scores for 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-06   26.8   0.1    5.3e-05   23.8   0.1    2.1  1  ThiS      ThiS family


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 !   23.8   0.1     3e-09   5.3e-05       5      74 ..      31     136 ..      27     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3e-09
                                       TCCHHHHT.CEEEEESSTSBHHHHHHHHHHHTCHHG..................................TTTTEEE CS
                              ThiS   5 aelrelag.eeelelaegstvaelleaLgerypela..................................lerrvav 46 
                                       +++re++g  e +   eg+ +++ lea  ++y+ +                                    +   +v
  gi|336254090|ref|YP_004597197.1|  31 GHVREAVGtHELEFTFEGTRLQAFLEAFFAEYDVEDlliaeteeeatahgwaeppeelpgtwrknpegeqTRTYARV 107
                                       78999999888888889999999999999999777789999999999999999**************9998899*** PP

                                       EETTEEEGC.CTTTSB--TTCEEEEEEST CS
                              ThiS  47 avNgeivpr.lwldtelkdgDevailppV 74 
                                        vNg++ +  ++ +tel dgD+va++ p+
  gi|336254090|ref|YP_004597197.1| 108 CVNGKFNELlDGFQTELEDGDRVALIYPF 136
                                       *********88***************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1076.27
//
Query:       gi|336254091|ref|YP_004597198.1|  [L=463]
Description: hypothetical protein Halxa_2702 [Halopiger xanaduensis SH-6]
Scores for 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    8.5   7.5      0.086   12.8   0.8    2.3  2  Sugarporin_N  Maltoporin periplasmic N-terminal extension


Domain annotation for each model (and alignments):
>> Sugarporin_N  Maltoporin periplasmic N-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.8   4.8e-06     0.086       6      39 ..     199     232 ..     197     235 .. 0.92
   2 ?   -4.2   0.9      0.96   1.7e+04       7      22 ..     258     274 ..     256     279 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.8e-06
                      Sugarporin_N   6 lalaialllstaasvaaaasltiEaRLaaLEkrL 39 
                                       la ++++ll ++  +a+ ++ ++E+RL +LE++L
  gi|336254091|ref|YP_004597198.1| 199 LATVLGALLQLTKMFAQWELGALEDRLLQLEQAL 232
                                       889999999999999*****************98 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 0.96
                      Sugarporin_N   7 alaialllstaasv.aa 22 
                                       al+ +l ++t  +v a 
  gi|336254091|ref|YP_004597198.1| 258 ALLAGLVAFTVVVVrAL 274
                                       34444555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3262.96
//
Query:       gi|336254092|ref|YP_004597199.1|  [L=88]
Description: hypothetical protein Halxa_2703 [Halopiger xanaduensis SH-6]
Scores for 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:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 682.12
//
Query:       gi|336254093|ref|YP_004597200.1|  [L=30]
Description: hypothetical protein Halxa_2704 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.75   10.0   4.0        1.1    9.5   4.0    1.4  1  DUF4519   Domain of unknown function (DUF4519)
       0.85    9.6   3.8       0.94    9.5   3.8    1.1  1  OppC_N    N-terminal TM domain of oligopeptide transport perm


Domain annotation for each model (and alignments):
>> DUF4519  Domain of unknown function (DUF4519)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.0   0.00012       1.1      33      54 ..       9      28 ..       4      30 .] 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
                           DUF4519 33 vVlPvlavlillivvfvYlkTr 54
                                      v+l  ++++il++++++Y++T+
  gi|336254093|ref|YP_004597200.1|  9 VAL--FVIVILCLIALLYISTQ 28
                                      444..89999**********98 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.8    0.0001      0.94      18      32 ..       9      23 ..       6      29 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0001
                            OppC_N 18 vglvilllllliaif 32
                                      v+l+++++l lia++
  gi|336254093|ref|YP_004597200.1|  9 VALFVIVILCLIALL 23
                                      99***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (30 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1339  (0.0746835); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 220.08
//
Query:       gi|336254094|ref|YP_004597201.1|  [L=409]
Description: metal dependent phosphohydrolase [Halopiger xanaduensis SH-6]
Scores for 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-12   46.6   1.7    8.6e-12   45.4   1.7    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 !   45.4   1.7   4.8e-16   8.6e-12       1     121 [.      50     162 ..      50     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 4.8e-16
                                       HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHH........HHHCTCCHHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekk........eeefekflaHekvgaeilr 68 
                                       r+eHsl+V++la +  e+l+   +  e++++aaLlHD+G+gpf+++ e          +++++++ a   vg  +lr
  gi|336254094|ref|YP_004597201.1|  50 RFEHSLGVYHLACKALEQLNVeGAQAERVRAAALLHDVGHGPFSHNLEPLthrrtgryHDDVDHLIADGAVGD-VLR 125
                                       79*****************999999********************8888787666554444888888888888.666 PP

                                       HHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  69 evekrlgldledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                       ++ + +    e +a li+   +              ql + +++v+++D+l +
  gi|336254094|ref|YP_004597201.1| 126 DHDLEP----ERIAGLIAGEGRFG------------QLVSGELDVDRMDYLVR 162
                                       666666....68999999999999............69999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2956.92
//
Query:       gi|336254095|ref|YP_004597202.1|  [L=566]
Description: DNA ligase [Halopiger xanaduensis SH-6]
Scores for 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-46  157.6   0.0    5.8e-46  156.7   0.0    1.5  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
    3.7e-39  134.8   0.0      8e-38  130.5   0.0    2.3  2  DNA_ligase_A_N   DNA ligase N terminus
    6.2e-18   65.2   0.0    1.8e-17   63.7   0.0    1.8  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
  ------ inclusion threshold ------
      0.031   14.1   0.0        4.8    7.0   0.0    2.2  2  mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain


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 !  156.7   0.0   1.3e-49   5.8e-46       2     204 .]     233     440 ..     232     440 .. 0.91

  Alignments for each domain:
  == domain 1  score: 156.7 bits;  conditional E-value: 1.3e-49
                                       EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEE..ETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEE CS
                    DNA_ligase_A_M   2 mLAeslksiekalkkleekafivEiKyDGeRaqvhk..egdkvklfSRrlkditaakpelvkalkeafkkdeksvil 76 
                                       mLA+  + + +al++   +++ vE+KyDG+R+q+h   ++d+ ++fSR+++++t+a+pe+++ ++e + +    vil
  gi|336254095|ref|YP_004597202.1| 233 MLAQAGT-VTDALEEW--DEAAVEWKYDGARIQLHHapDDDTTRVFSRNMEEVTDALPEVLEYADETLEEP---VIL 303
                                       8999888.899****8..45559************8789***************************99875...9** PP

                                       EEEEEEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB....... CS
                    DNA_ligase_A_M  77 DGElvavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeil....... 146
                                       DGE+vavd + g +lpfq++ +r+++k++ve++ +e+ ++ ++FD+L+  ge+l++epl  R   L+ +l       
  gi|336254095|ref|YP_004597202.1| 304 DGEVVAVDDD-GGPLPFQEVLKRFRRKHDVEKAREEVTVRPVFFDCLHAGGEDLLEEPLTARHDRLRAVLaedpdav 379
                                       ******9887.99*********************************************************8888888 PP

                                       ..--BTTTEE.E--EEEESSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 147 ..kesedrve.laeslevkdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                         +e+e +ve l+   +++d +e+e++ + a+++g+EG+++Knp+s+Y pg+r+k+w K K
  gi|336254095|ref|YP_004597202.1| 380 teTEDERDVEgLSLLWTTDDPDEIEAIDADALEAGHEGIMLKNPESTYSPGRRGKHWRKRK 440
                                       77555555551444557899**************************************987 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 !  130.5   0.0   1.8e-41     8e-38       2     173 .]       3     184 ..       2     184 .. 0.92
   2 !    5.5   0.0    0.0043        19      65     100 ..     180     215 ..     178     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: 130.5 bits;  conditional E-value: 1.8e-41
                                       CHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT. CS
                    DNA_ligase_A_N   2 FaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealg. 73 
                                       Fa++a+  ++ie+ ++++le++a++++++r+ e    +dl +++r+    ++P++d+++++ig+s++++a+a+a+g 
  gi|336254095|ref|YP_004597202.1|   3 FATFADRAAAIEA-EPADLEIVAHVTDLLRDAE----ADLEIVARFvqgrVFPAWDSTTLDIGPSACYEAIARAAGt 74 
                                       9************.999************9854....59*************************************5 PP

                                       .--HHHHHHHHHHHS-HHHHHHHHH...CCHHHH........------BHHHHHHHHHHHHH-.STTHHHHHHHHHH CS
                    DNA_ligase_A_N  74 .lskkkikdalakvgDlgevaeevl...skrstl........akkspltieevnelLdklaaa.gkgsedekkkilk 137
                                        ++ ++++d+la++g++g+va+++    +   +           +++lt++ev+e+L +laaa g+gs+d+k+++l 
  gi|336254095|ref|YP_004597202.1|  75 nVDADDVEDRLAETGEIGDVAASYDfggQ---QGlgaftggdGGEDDLTVREVYETLCDLAAAeGSGSQDRKVDLLF 148
                                       5556799**************99985433...334679999999999*************9999************* PP

                                       HHHHHS-HHHHHHHHHHHCT---SS--HHHHHHHHH CS
                    DNA_ligase_A_N 138 kllkraspeEakyliriilkdlriglsektvldala 173
                                       +l++r+s+eEa+yl+r++l ++rig++e+ v+da a
  gi|336254095|ref|YP_004597202.1| 149 GLFNRCSSEEARYLARLVLSEMRIGVGEGAVRDAVA 184
                                       *********************************976 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0043
                                       HHHHHHHHT--HHHHHHHHHHHS-HHHHHHHHHCCH CS
                    DNA_ligase_A_N  65 akalaealglskkkikdalakvgDlgevaeevlskr 100
                                       + a+aea+ +++++++ al+  +D+geva  ++++ 
  gi|336254095|ref|YP_004597202.1| 180 RDAVAEAFDVPEEEVERALQVSNDYGEVARIARDEG 215
                                       789***************9999******98777655 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 !   63.7   0.0     4e-21   1.8e-17       2      99 .]     461     550 ..     460     550 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 4e-21
                                       GGSEEEEEEEEEETTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEESEEE CS
                    DNA_ligase_A_C   2 gglvgslllgvyddgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfaeit 78 
                                       ++ +g++ l v+d+++le+vgkv+tG++d++leel++ l+++  ++         +    v +eP++v+eV ++ei+
  gi|336254095|ref|YP_004597202.1| 461 ANFLGTFELSVRDGDDLETVGKVATGITDEKLEELTELLEPHIAAEDGQ------D----VDLEPAVVFEVGYEEIQ 527
                                       67899**********************************6444443333......2....339************** PP

                                       CTSSSTT..EECT-EEEEE-TTS CS
                    DNA_ligase_A_C  79 asgkyka..slRfPrfkrlReDk 99 
                                       +s++y++  +lRfPrf+ +R+Dk
  gi|336254095|ref|YP_004597202.1| 528 TSPTYSSgyALRFPRFLAVRSDK 550
                                       **********************8 PP

>> mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0011       4.8      19      80 ..     251     308 ..     240     315 .. 0.82
   2 ?    4.8   0.0    0.0048        21      88     122 ..     338     372 ..     330     390 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0011
                                       EEEEEESSEEEEEEEEECTEEEEEEETTS-EEEESSST-BTTSSSSTCTSBGGSEEEEEEEE CS
                   mRNA_cap_enzyme  19 vvseKaDGiRylmllteeeegvylidRenevyrvenlrfprekdkeklekvldetllDgElv 80 
                                        v +K DG R+ +    ++++  ++ R++e   v    +p+  +   +e++ +  +lDgE+v
  gi|336254095|ref|YP_004597202.1| 251 AVEWKYDGARIQLHHAPDDDTTRVFSRNMEE--VT-DALPEVLE-YADETLEEPVILDGEVV 308
                                       689***********999999999****9985..55.45777774.345899999******98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0048
                                       EEEEEEEEEEEEEETTEEGTTSBHHHHHHHHHHHT CS
                   mRNA_cap_enzyme  88 kkelryliyDivaingvtvaeeplskRleilkkel 122
                                         ++r + +D+++  g ++ eepl  R + l+  l
  gi|336254095|ref|YP_004597202.1| 338 EVTVRPVFFDCLHAGGEDLLEEPLTARHDRLRAVL 372
                                       467899*********************99887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 4023.72
//
Query:       gi|336254096|ref|YP_004597203.1|  [L=517]
Description: hypothetical protein Halxa_2707 [Halopiger xanaduensis SH-6]
Scores for 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   12.0   0.1       0.92    8.8   0.0    2.1  2  GCS       Glutamate-cysteine ligase


Domain annotation for each model (and alignments):
>> GCS  Glutamate-cysteine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   5.1e-05      0.92     162     218 ..     324     381 ..     308     406 .. 0.80
   2 ?    0.6   0.0     0.016   2.9e+02     307     340 ..     447     479 ..     413     483 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 5.1e-05
                               GCS 162 stdhFeniqstnWqtlrfKpPppesekigWrvefRpmevqltdfenaafsv.fivLlt 218
                                       +  hF     t W+ +r     p++++ + r+efRp+  q t  +  af + f+ Ll 
  gi|336254096|ref|YP_004597203.1| 324 QFPHFRRKHGTYWRWVRPVFGGPTRSAANARIEFRPIPAQPTVRDGTAFLAaFAGLLQ 381
                                       5679999999******95555555666899***************9999651555554 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.016
                               GCS 307 etrkklekylkliskrasgelltaAkwiRefvak 340
                                        ++++ +kyl  +++r++   +t A+w Re v++
  gi|336254096|ref|YP_004597203.1| 447 LNEEEAAKYLYPLRRRVRQ-RVTPASWKREQVRA 479
                                       5677889999999999986.579*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 4072.52
//
Query:       gi|336254097|ref|YP_004597204.1|  [L=330]
Description: LPPG:FO 2-phospho-L-lactate transferase [Halopiger xanaduensis SH-6]
Scores for 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  156.3   0.0    1.3e-45  156.0   0.0    1.1  1  UPF0052   Uncharacterised protein family UPF0052


Domain annotation for each model (and alignments):
>> UPF0052  Uncharacterised protein family UPF0052
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.0   0.0     7e-50   1.3e-45       1     284 [.       2     318 ..       2     327 .. 0.81

  Alignments for each domain:
  == domain 1  score: 156.0 bits;  conditional E-value: 7e-50
                                       EEEEE-CHHHHHHHHHHCCSS..CEEEEEE-----SHHHHHHHHHHTS---HHHHHHHHHH...--S-C........ CS
                           UPF0052   1 vvvlgGGtGlskllrglkevt..aeltavvtvaDdggssGelrrelgllaigDirnvlval...idder........ 64 
                                       v++l+GGtG++kll+g  +v+  +e+t+v +++Dd+++ G       l + +D+++ l++    +d+e+        
  gi|336254097|ref|YP_004597204.1|   2 VTFLSGGTGTPKLLDGAGAVFspEETTIVANTGDDIEIGG-------LFVSPDVDTLLFQGggvLDRETwwgiagdt 71 
                                       789******************99*****************.......*************99999999999998888 PP

                                       ................HHHH...............HCH-B-SS............SSSSTT-BHHHHHHHHHHHHHS CS
                           UPF0052  65 ................llee...............LfqyRfkg............dgdlaghslgnllLaalaeltg 98 
                                                          e               ++++   +            d+d a h+ ++ lL++     g
  gi|336254097|ref|YP_004597204.1|  72 hrtnsalmeladaaglP--EgpqylpedaqtagrdIANW---RrfsgiaefmtigDRDRAVHITRTSLLDQ-----G 138
                                       88666544444444330..03444444444444444444...0333577777777****************.....9 PP

                                       .-HHHHHHHHHHHTT-SSEEEES-SS--EEEEEETTS-EEESTTTGGGG-S....-EEE.EEEESTT----HHHHHH CS
                           UPF0052  99 .sleeaiealskilkvrgrvlPatddpvelsaeledGeeitgeskiseark.lkapikr.vflepegaeaapevlea 172
                                        +l+ea++ l++++++++++lP++ddpv   +++++G +  +e+++   ++  ++++++  f + + ae+ap+vlea
  gi|336254097|ref|YP_004597204.1| 139 hTLSEATQRLADAFDLSVDLLPMSDDPVASLVHTDEGMMHFQEYWV---GRrGEPDVENvEFRGSSTAEPAPGVLEA 212
                                       9*********************************9999555*****...555679****9999************** PP

                                       HHH-SEEEE-SS-IIIIIHHHHTSCCHHHHHHH-SSEEEEE--SB--TTTSTT-BHHHHHHHHHHCH-.....SS.. CS
                           UPF0052 173 ikeAdlivlgpGslytSiiPiLlvpgiaealreskakkvlvsnimtqkGetdgfsvsdhvkaieravg.....kgva 244
                                       +++   +v+gp++++tSi+P+L++pg+a+ l  +++++v+vs++ +      + ++s++++ +++av+     +g a
  gi|336254097|ref|YP_004597204.1| 213 LEDT--VVIGPSNPVTSIGPMLALPGVADSL--AQTTVVAVSPFLG------DEAFSGPAEDLMEAVNaepstEGLA 279
                                       *976..*************************..669*********9......9999999999999999776665555 PP

                                       ..S..-SEEEEE-S---HHHHHHHHTTT--B-B--H.HHHCTT CS
                           UPF0052 245 kay..vdavlvntsevpeellekyaaegkepvelDa.kleklg 284
                                        ay  +da +v+++    + +e ++   ++ +++D  +  k  
  gi|336254097|ref|YP_004597204.1| 280 TAYpfADAYIVDEG----DDVEFDRPTIQTDIKIDSpEDAKRV 318
                                       55598******999....4444455566666777754444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 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:                        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 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2517.44
//
Query:       gi|336254098|ref|YP_004597205.1|  [L=252]
Description: tRNA-dihydrouridine synthase-like protein [Halopiger xanaduensis SH-6]
Scores for 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-09   35.0   0.4    5.1e-08   32.4   0.4    1.8  1  Dus           Dihydrouridine synthase (Dus)
     0.0014   18.1   0.0     0.0025   17.3   0.0    1.5  1  His_biosynth  Histidine biosynthesis protein
     0.0071   16.7   0.2      0.085   13.2   0.1    2.4  2  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
       0.01   15.4   0.5      0.075   12.6   0.4    1.9  2  NmrA          NmrA-like family
      0.023   12.9   2.3      0.028   12.6   2.3    1.0  1  DUF1633       Protein of unknown function (DUF1633)
       0.17   11.0   0.0       0.52    9.4   0.0    1.9  2  IGPS          Indole-3-glycerol phosphate synthase


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 !   32.4   0.4   1.7e-11   5.1e-08      65     230 ..      92     243 ..      84     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.7e-11
                                       HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HH CS
                               Dus  65 pallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenal 141
                                        + +a+aA++  d+g    ++N+ C +++    g G +Llr++d +a  v+++   ++  v vk+r  + d   ++ 
  gi|336254098|ref|YP_004597205.1|  92 REPIADAARVCRDRG-ALLEINAHCRQDELCAVGCGETLLRDADRLAAYVETAA-ETGATVGVKVRAEVSD--VDLP 164
                                       5678999******55.579*******************************9875.5788999999999985..5679 PP

                                       HHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCC CS
                               Dus 142 elakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalg 218
                                        l +++e+aGa+++ v +          +    I++v +a  + viaN +++d e +++ +++ Gad+v +gr +  
  gi|336254098|ref|YP_004597205.1| 165 ALSRRLEDAGAAFVHVDA---------MDSEPVIADVVDATDLFVIANNGVRDDETVREYVDY-GADAVSVGRPS-D 230
                                       9***********998854.........3333679*****************************.*********86.6 PP

                                       STTHHHH.HHHHH CS
                               Dus 219 nPwlfae.stavk 230
                                       nP+++++   av+
  gi|336254098|ref|YP_004597205.1| 231 NPAVLERvRSAVE 243
                                       8999987554544 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   8.4e-07    0.0025      61     120 ..     185     243 ..     144     250 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.4e-07
                                       HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHC CS
                      His_biosynth  61 nldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfg 120
                                          +++ +++++++ v    G+r+ e+v+e+++ gad v++g    +np +++++ ++++
  gi|336254098|ref|YP_004597205.1| 185 SEPVIADVVDATDLFVIANNGVRDDETVREYVDYGADAVSVGRP-SDNPAVLERVRSAVE 243
                                       457899999999999**************************965.578888888777665 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.65   1.9e+03      91     117 ..      70      95 ..      22     114 .. 0.62
   2 !   13.2   0.1   2.8e-05     0.085      80     130 ..     199     245 ..     107     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.65
                                       HHHHHHHHHTT-SEEEEEEBSSSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  91 eeklerllelgvdrvslgleaaddekv 117
                                       +++l++l + +  +  +++ +a+ e++
  gi|336254098|ref|YP_004597205.1|  70 DRQLAALEDVP-IQPGFNVRSATREPI 95 
                                       55555555544.555555555555522 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.8e-05
                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeev 130
                                       +++  ng+++ +e +++ +++g d vs+g  + ++  vl+++ r   +e++
  gi|336254098|ref|YP_004597205.1| 199 FVIANNGVRD-DETVREYVDYGADAVSVGRPSDNPA-VLERV-R-SAVERR 245
                                       4455567775.*************************.**999.5.455554 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.1     3e+02      16      45 ..      78     107 ..      71     120 .. 0.83
   2 ?   12.6   0.4   2.5e-05     0.075      19      75 ..     148     206 ..     135     225 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.1
                                       HHHHHHT-EEEEEES-S-SHHHHHHHHSTT CS
                              NmrA  16 rallkaghkvralvRdtkselakslkeaGv 45 
                                       ++ ++ g++vr  +R++  ++a+   ++G+
  gi|336254098|ref|YP_004597205.1|  78 DVPIQPGFNVRSATREPIADAARVCRDRGA 107
                                       566789***********9999998888887 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.5e-05
                                       HHHT-EEEEEES-S.-SHHHHHHHHSTTEEEES-.TT-HHHHHHHHTT-SEEEE---GG CS
                              NmrA  19 lkaghkvralvRdt.kselakslkeaGvelvkgd.lddkeslvealkgvdvvfsvtgfy 75 
                                       + +g kvra v d+    l++ l++aG+ +v+ d +d++ +++ +++  d++ ++ +  
  gi|336254098|ref|YP_004597205.1| 148 ATVGVKVRAEVSDVdLPALSRRLEDAGAAFVHVDaMDSEPVIADVVDATDLFVIANNGV 206
                                       4488999999999945567899*********666489999*********9976665533 PP

>> DUF1633  Protein of unknown function (DUF1633)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.3   9.4e-06     0.028     308     427 ..      70     192 ..      67     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.4e-06
                           DUF1633 308 drivaalavdpadpvivlpaaqldpleevprlefrpsadlqkknevtkdssstsecgs..saraddlsavvaaarts 382
                                       dr++aal   p +p   + +a  +p+ +  r+     a l+++ +  +d   +  cg      ad l+a v +a ++
  gi|336254098|ref|YP_004597205.1|  70 DRQLAALEDVPIQPGFNVRSATREPIADAARVCRDRGALLEINAHCRQDELCAVGCGEtlLRDADRLAAYVETAAET 146
                                       9*************************************************99999*984334588999999666555 PP

                           DUF1633 383 lav..snasasashpslpevnarpllrrrarllpvvrltaelividq 427
                                        a+   + +a  s   lp+   r l    a ++ v  + +e ++ d 
  gi|336254098|ref|YP_004597205.1| 147 GATvgVKVRAEVSDVDLPALS-RRLEDAGAAFVHVDAMDSEPVIADV 192
                                       554124789999*******99.8888888888888777777665543 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.8   5.4e+03     213     245 ..      13      45 ..       9      51 .. 0.69
   2 ?    9.4   0.0   0.00018      0.52     202     238 ..     189     226 ..     140     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.8
                                       EEESSS-SHHHHHHHCCTT-SEEEESHHHHC-T CS
                              IGPS 213 vaeSGiktredveklkeegvnafLvGeslmrqe 245
                                        ++SG +++e +++ +e    afL G +l +++
  gi|336254098|ref|YP_004597205.1|  13 ASLSGEADAEWARAGAEYAEAAFLGGIALDANS 45 
                                       577777777777777777777788777776554 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00018
                                       HCHCC-.TTSEEEEESSS-SHHHHHHHCCTT-SEEEES CS
                              IGPS 202 Laklvp.kdvllvaeSGiktredveklkeegvnafLvG 238
                                       +a++v+ +d +++a  G+++ e+v+++ + g++a+ vG
  gi|336254098|ref|YP_004597205.1| 189 IADVVDaTDLFVIANNGVRDDETVREYVDYGADAVSVG 226
                                       45566645699************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1796.98
//
Query:       gi|336254099|ref|YP_004597206.1|  [L=134]
Description: hypothetical protein Halxa_2710 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.098   13.7   0.1       0.14   13.2   0.1    1.4  1  SpoIIAA-like  SpoIIAA-like
      0.099   12.0   0.0       0.12   11.7   0.0    1.2  1  SBP_bac_6     Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SpoIIAA-like  SpoIIAA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.5e-05      0.14      29      95 ..      66     131 ..      24     132 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                                       SSSEEEEEEEHHHHHHHCC.....CGGECEEEEE-SS....CC.CCCC.CCHHCCH.-...CCEEEEE..SSHHHHH CS
                      SpoIIAA-like  29 hgkirllvdlediklglah.....lsrfrrvAvvtdk....kw.ikalvallasalfl...slevkvFkleeeeeAl 92 
                                       +   r+l+++               +++r+ A v ++    ++ +    +++++ l     ++e+++F   + ++Al
  gi|336254099|ref|YP_004597206.1|  66 DADKRWLAET--------WipdliDHGVRHGAGVYADsaiaSMdM----EEIEGQLNAidpDFEYRIF--GSDDDAL 128
                                       3444455555........122223578888885555523333333....44444443322256*****..******* PP

                                       HHH CS
                      SpoIIAA-like  93 aWL 95 
                                       +WL
  gi|336254099|ref|YP_004597206.1| 129 EWL 131
                                       **9 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.4e-05      0.12     171     217 ..      16      62 ..       1      79 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.4e-05
                         SBP_bac_6 171 Ped.GalvspifmlvkkgkkkelakafidfllspevqailakaggvfP 217
                                       +e+ G +++++ ++v  ++ ++ a+ ++df+ s+++ +++++  + + 
  gi|336254099|ref|YP_004597206.1|  16 DEEqGVPIFTYNAFVSGEELRDIARTWADFIASEDADQYVVNTES-IS 62 
                                       5555*************99*******************9999886.43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1035.75
//
Query:       gi|336254100|ref|YP_004597207.1|  [L=107]
Description: hypothetical protein Halxa_2711 [Halopiger xanaduensis SH-6]
Scores for 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   12.0   0.5        0.3   11.0   0.0    1.7  2  DUF3695   Protein of unknown function (DUF3695)


Domain annotation for each model (and alignments):
>> DUF3695  Protein of unknown function (DUF3695)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.12   2.2e+03      42      54 ..       4      16 ..       3      34 .. 0.72
   2 ?   11.0   0.0   1.6e-05       0.3      28      57 ..      49      79 ..      38      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.12
                           DUF3695 42 DsLDfrLksrYdh 54
                                      D+L  ++++ Y +
  gi|336254100|ref|YP_004597207.1|  4 DDLNEEIQASYSE 16
                                      7888888888875 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 1.6e-05
                           DUF3695 28 vRrdarff.dpeiPkDsLDfrLksrYdhhre 57
                                      vRr+++   ++ +   +LDf+L+s Yd + +
  gi|336254100|ref|YP_004597207.1| 49 VRRAIHMLfQSTVETGNLDFHLRSAYDVTYD 79
                                      789888877999***************7654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 822.26
//
Query:       gi|336254101|ref|YP_004597208.1|  [L=158]
Description: response regulator receiver protein [Halopiger xanaduensis SH-6]
Scores for 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  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1265.42
//
Query:       gi|336254102|ref|YP_004597209.1|  [L=634]
Description: phosphoesterase RecJ domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   35.2   0.1    1.9e-08   34.1   0.1    1.6  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0021   18.3   0.3     0.0039   17.4   0.3    1.4  1  DHH              DHH family
     0.0051   17.0   0.0      0.011   16.0   0.0    1.5  1  tRNA_anti_2      OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.013   15.8   1.5      0.026   14.9   0.1    2.2  2  S1               S1 RNA binding domain
      0.072   12.7   0.0       0.17   11.5   0.0    1.6  1  Rib_5-P_isom_A   Ribose 5-phosphate isomerase A (phosphoriboi
       0.12   12.5   0.1       0.35   11.0   0.1    1.8  1  S1_2             S1 domain
        3.6    7.6   5.2         14    5.7   0.1    3.1  3  Phe_tRNA-synt_N  Aminoacyl tRNA synthetase class II, N-termin


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 !   34.1   0.1   7.6e-12   1.9e-08       3      73 ..     125     192 ..     123     195 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 7.6e-12
                                       EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEE CS
                   tRNA_anti-codon   3 vaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveei 73 
                                       ++G+v+++  +++g+   + + D+ g + + +f e+  + + ++++GdvvrvtG+++ r+g  +++ v+ +
  gi|336254102|ref|YP_004597209.1| 125 LEGEVVQV--KQTGGPTIFHVADEYGVVPCAAFEEAGVRAYPSVEVGDVVRVTGTPEHREGS-VQIEVDGL 192
                                       78******..**************************************************99.**999876 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   1.5e-06    0.0039       7      57 ..     256     370 ..     252     414 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                                       ECSSSHHHHHHHHHHHH........................................................CECS CS
                                       xxxxxxxxxxxxxxxxx........................................................xxxx RF
                               DHH   7 hknpDtDsigSaialan........................................................llvD 27 
                                        ++ D+D++++a+ ++                                                         l++D
  gi|336254102|ref|YP_004597209.1| 256 RHHADGDGMCAAVPVQIalerfiaevhededaprhlikrlpakapfyemedatrdlnfaledrekhgqqlpllLMLD 332
                                       5789*********9999888888888888888888888888777777777777777777777777777777777*** PP

                                       --TCGGCGCCH..HCCCSEEEEEEE-S---S......S CS
                                       xxxxxxxxxxx..xxxxxxxxxxxxxxxxxx......x RF
                               DHH  28 hneksqavege..akeeaedviiiDHHrlge......e 57 
                                       +++++++v ++  ++  +  ++ iDHH +         
  gi|336254102|ref|YP_004597209.1| 333 NGSTAEDVPAYetLAHYDIPIVAIDHHHPDPdavgdlL 370
                                       *******9887778999999*******99755555551 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 !   16.0   0.0   4.1e-06     0.011      12      92 ..     113     190 ..     105     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.1e-06
                       tRNA_anti_2  12 elleaelkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgrlsvYeprGsyq 88 
                                       ++lea++ +++ ++Ge+ ++k ++ g + f   De   + ++ f+++  +   ++e G+ V v+g+++   ++Gs+q
  gi|336254102|ref|YP_004597209.1| 113 DRLEANVGEQIHLEGEVVQVK-QTGGPTIFHVADEYGVVPCAAFEEAGVRAYPSVEVGDVVRVTGTPEH--REGSVQ 186
                                       5789999999**********5.4689*******************7776655679**********9995..677788 PP

                       tRNA_anti_2  89 live 92 
                                       + v+
  gi|336254102|ref|YP_004597209.1| 187 IEVD 190
                                       7776 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1     1e-05     0.026       6      63 ..      34      82 ..      29      90 .. 0.77
   2 ?   -2.6   0.1       2.8   7.1e+03       8      18 ..     125     135 ..     124     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                                      CEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEE CS
                                S1  6 evveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkv 63
                                      + + +e+  ++++G+fV+l + v+g+v+ s l+          ++ vGde+ v+++ v
  gi|336254102|ref|YP_004597209.1| 34 QPYLAEINGIVDYGVFVDLSESVSGLVHESVLE---------GTFAVGDELVVELESV 82
                                      55779999********************99887.........3466666665555555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.8
                                       EEEEEEEEETT CS
                                S1   8 veGeVtsvtkg 18 
                                       +eGeV++v + 
  gi|336254102|ref|YP_004597209.1| 125 LEGEVVQVKQT 135
                                       58999999875 PP

>> 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 ?   11.5   0.0   6.7e-05      0.17     121     166 ..      11      56 ..       2      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.7e-05
                                       B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEEESEE-S--SEE CS
                    Rib_5-P_isom_A 121 vTdngnlilDvkfeekiedpeelekelksipGVvetGlFlgladkv 166
                                         d   ++ D++ + + +d+e+ +  l +i+G+v+ G+F++l ++v
  gi|336254102|ref|YP_004597209.1|  11 ADDGDSVVYDLDADCTADDLEQDQPYLAEINGIVDYGVFVDLSESV 56 
                                       557778899999977778**********************998765 PP

>> S1_2  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00014      0.35       8      46 ..      39      77 ..      37      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                              S1_2  8 kvlretdfgyfLqkdesgevlLpkkevpeeleiGdeveV 46
                                      +++ + d g+f++ +es+  l++++ ++ ++++Gde+ V
  gi|336254102|ref|YP_004597209.1| 39 EINGIVDYGVFVDLSESVSGLVHESVLEGTFAVGDELVV 77
                                      677789******************************966 PP

>> Phe_tRNA-synt_N  Aminoacyl tRNA synthetase class II, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0055        14      39      58 ..     197     216 ..     194     221 .. 0.89
   2 ?   -0.1   0.0      0.36   9.3e+02      44      66 ..     488     510 ..     478     512 .. 0.88
   3 ?    1.8   0.6     0.088   2.3e+02      45      69 .]     602     626 ..     598     626 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0055
                                       HHCCHHHHCCCCCCCCCHHH CS
                   Phe_tRNA-synt_N  39 GkliNelKqeieealeerke 58 
                                       G+ + +++++ie+aleer e
  gi|336254102|ref|YP_004597209.1| 197 GQDADDARERIETALEERAE 216
                                       9999*************986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.36
                                       HHHCCCCCCCCCHHHCCHCCHHH CS
                   Phe_tRNA-synt_N  44 elKqeieealeerkeeleaaele 66 
                                        +++e+ e+l+++   le +el+
  gi|336254102|ref|YP_004597209.1| 488 RAREEVDEQLAAAMPHLEHEELD 510
                                       699***************99986 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.088
                                       HHCCCCCCCCCHHHCCHCCHHHHHC CS
                   Phe_tRNA-synt_N  45 lKqeieealeerkeeleaaeleakl 69 
                                       +K + ee +e+  e++e+ael++ l
  gi|336254102|ref|YP_004597209.1| 602 VKGKREEVIEALVEKMEEAELDEAL 626
                                       7889999**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); 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: 0.61u 0.23s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4560.20
//
Query:       gi|336254103|ref|YP_004597210.1|  [L=148]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   61.3   0.7    1.6e-16   61.1   0.7    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 !   61.1   0.7   9.1e-21   1.6e-16       3     139 ..       2     145 ..       1     147 [. 0.97

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 9.1e-21
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.......HH CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.......ak 72 
                                       +r lV+   +e++++++++A  la+a +a+++l+h+  +++++a+++a+++ + +   ++ + +++ a       a+
  gi|336254103|ref|YP_004597210.1|   2 DRALVVAEPTEAATELARMAGSLAEAGDAAVVLIHATTDEEYAARKQAMSSIASSGGTYTTDDAREGArqfaqdlAE 78 
                                       7889*********************************************************99999999**9*9999 PP

                                       HHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  73 aaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                       +++   +++ e+   +g++a++ile+a+e+d+d + +  r rs   ++l+G+ +++vl + + pV+v
  gi|336254103|ref|YP_004597210.1|  79 EELSTFDIEYETAGYVGEKADAILEAADEHDCDHVYLPGRERSPTGKALFGDATQRVLLEFDGPVTV 145
                                       999999***********************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1141.07
//
Query:       gi|336254104|ref|YP_004597211.1|  [L=471]
Description: gluconate transporter [Halopiger xanaduensis SH-6]
Scores for 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-95  319.8  33.4    2.8e-95  319.6  33.4    1.0  1  GntP_permease    GntP family permease
      1e-14   54.5  38.6      1e-14   54.5  38.6    2.1  2  CitMHS           Citrate transporter
  ------ inclusion threshold ------
      0.025   14.7   2.8      0.025   14.7   2.8    3.6  4  Na_H_antiport_2  Na+-H+ antiporter family
       0.69   10.1  11.4        2.9    8.1   0.0    4.0  4  Pox_A14          Poxvirus virion envelope protein A14
        1.7    9.0   6.1       0.43   10.9   1.1    2.6  2  DUF3007          Protein of unknown function (DUF3007)


Domain annotation for each model (and alignments):
>> GntP_permease  GntP family permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.6  33.4   7.7e-99   2.8e-95       2     438 ..      14     463 ..      13     466 .. 0.93

  Alignments for each domain:
  == domain 1  score: 319.6 bits;  conditional E-value: 7.7e-99
                     GntP_permease   2 pllivligvilllllviklklnafvaLllvsllvglvsGm.....pldkvvksiekGlGgtlGslaiiiglGamlGk 73 
                                       pll+  ig+++++ l++ l + af+ L+l+ ++vg+v+ +        + ++ +   +G  +  ++i i   a++Gk
  gi|336254104|ref|YP_004597211.1|  14 PLLTFFIGLLVVVALLVWLDFPAFIGLILAGFTVGVVNAVfvpdfGPADAATEVAGAFGDNMTGIGIPILAAAIIGK 90 
                                       689999******************************998722222445677888999******************** PP

                     GntP_permease  74 lledsGaaerialtlikklgkkkvqwalvlagfivgialFfevglvlLiplvfaiakeakisllklgiplvaalavv 150
                                        + +sGaa+ri + +++ lgk + ++al+ ++ +++i++Ff++ + l++pl+ ++ ++ ++    + + + a+ a++
  gi|336254104|ref|YP_004597211.1|  91 SMLESGAAQRIVRGFQNLLGKDNSDIALLGSSSVLAIPVFFDSVFYLMAPLARSMRARVGRDYTLFLVVVGAGAATA 167
                                       **************************************************************9999999******** PP

                     GntP_permease 151 hgllpPhPgplavaellgadiGkvllyGlivaiptviiagpllkkflkevvkeeee......laeeaeeksreekel 221
                                       h+++pP+Pgplava ++g d+G ++ +Gli aip+v +ag +++++++ +            ++e  e   r ++ l
  gi|336254104|ref|YP_004597211.1| 168 HVFVPPTPGPLAVAAQVGSDLGVTIFIGLITAIPAVTLAGLVYGRWINARLDIPLRdtmattTEELQEVADRPTSSL 244
                                       **********************************************999877655555565444555556677899* PP

                     GntP_permease 222 PsfglslltillPvvlmlvktiaelllpkesaale...vvefiGnpvvalliallvaiytlglrrgksikkvldile 295
                                       P++ +sl+ il+ v l+   t+++ ++    a+ +   +v f+G+  val++a +va y+l  ++++++++ ++ l 
  gi|336254104|ref|YP_004597211.1| 245 PGLLASLSPILVAVGLIGSYTVVDSFQDVLPALGSiepIVVFVGDKNVALMLAAVVAAYVLYSHNEMTSSEWSEELT 321
                                       ***********************998655444433444*************************************** PP

                     GntP_permease 296 ealksiaiilliigaGGafkqvlvdsgvgkalaellsnlelspillaflvaallrialGsatVaaltaaglvapiia 372
                                       ealks ++i  i++aGGaf+++l  sg+g++la +l++  + ++++a+l+aa++ria+Gsat a+ltaag++ap++ 
  gi|336254104|ref|YP_004597211.1| 322 EALKSGGNIAAITAAGGAFGAMLAASGIGDYLAGILQEFGIGLLITAWLIAAIVRIAQGSATAAMLTAAGIMAPLTG 398
                                       ***************************************************************************** PP

                     GntP_permease 373 qlpgvnlallvlaigaGslilshvnDagFWlvkeylgltvketlktwtvletilsvvgliivllls 438
                                       ql +v+ a lv+ igaG++i+s+ nD+gFWlvke  glt +etlktwtvl+ti+sv gli++l++s
  gi|336254104|ref|YP_004597211.1| 399 QL-SVSAAYLVMVIGAGGNICSWYNDSGFWLVKEIGGLTQEETLKTWTVLTTIISVSGLITTLVVS 463
                                       **.9999********************************************************876 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5  38.6   2.8e-18     1e-14      16     300 .]      22     412 ..      12     414 .. 0.66
   2 ?    0.3   0.5     0.091   3.3e+02     231     268 ..     423     465 ..     413     468 .. 0.76

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 2.8e-18
                                       xxxxxxxxxxxxx......xxxxxxxxxx.............................xxxxxxxxxxxxxxxxxxx RF
                            CitMHS  16 llvlvllvltiee......alsgiaspii.............................llllgamiigaaleetGlf 57 
                                       llv+v+l++ ++       +l+g+ ++++                             + +l+a iig+ + e+G++
  gi|336254104|ref|YP_004597211.1|  22 LLVVVALLVWLDFpafiglILAGFTVGVVnavfvpdfgpadaatevagafgdnmtgigIPILAAAIIGKSMLESGAA 98 
                                       4444444222222334444777887777788888888888888888888889999999******************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  58 drlaakllrlaggkrdllvllvlltallsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiG 134
                                       +r+++ + +l g+     ++l   + +l+  v +d v+ +m+p++ s+ +r++++ +l+l++++ +a++     +++
  gi|336254104|ref|YP_004597211.1|  99 QRIVRGFQNLLGKDNS-DIALLGSSSVLAIPVFFDSVFYLMAPLARSMRARVGRDYTLFLVVVGAGAAT----AHVF 170
                                       ***********99655.66677777777444546*****************999999986655555554....5667 PP

                                       xxxxxxx............................................................xxxxxxxxxx RF
                            CitMHS 135 tpttraa............................................................arpglslpnl 151
                                        p+t+++                                                            +rp  slp l
  gi|336254104|ref|YP_004597211.1| 171 VPPTPGPlavaaqvgsdlgvtifiglitaipavtlaglvygrwinarldiplrdtmattteelqevaDRPTSSLPGL 247
                                       778888888888***55555555555555555555555555555555555555555555555555555555555555 PP

                                       xx...xxxxxxxx...............................xxxxxxxxxxxxxxxxxxxx.........xxxx RF
                            CitMHS 152 ll...lalllvgl...............................lplvllfmfgvalalpvnap.........kvkk 185
                                       l+   ++l++vgl                               ++l+l++                      +  +
  gi|336254104|ref|YP_004597211.1| 248 LAslsPILVAVGLigsytvvdsfqdvlpalgsiepivvfvgdknVALMLAA------------VvaayvlyshNEMT 312
                                       556554445555544444444445554445554433333344443333333............12333333344445 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxx RF
                            CitMHS 186 qkaiieaiarsllpvatilllaykkveWsvlllfaGvfllvgaleqtGilealadllga.g.gplvalalvlglial 260
                                        ++  e ++++l++ + i            +  ++G+f++  +l ++Gi+++la++l++ g g    l+++++lia+
  gi|336254104|ref|YP_004597211.1| 313 SSEWSEELTEALKSGGNIA----------AITAAGGAFGA--MLAASGIGDYLAGILQEfGiG----LLITAWLIAA 373
                                       5555555555555544444..........23355666666..***************555533....4567****** PP

                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 261 .lsafisnvavaalmapialgmapalgllspsplalalavg 300
                                        ++++++++++a+l+a+++++  p +g ls+s+ +l++++g
  gi|336254104|ref|YP_004597211.1| 374 iVRIAQGSATAAMLTAAGIMA--PLTGQLSVSAAYLVMVIG 412
                                       9********************..632337788889999887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.091
                                       xxx..xxxxxxxxxxx.x.xxxxxxxxxxxxxxx.xxxxxxxx RF
                            CitMHS 231 qtG..ilealadllga.g.gplvalalvlglial.lsafisnv 268
                                       ++G  +++ +++l+++ + + +++l+ ++++++l  ++++s++
  gi|336254104|ref|YP_004597211.1| 423 DSGfwLVKEIGGLTQEeTlKTWTVLTTIISVSGLiTTLVVSSI 465
                                       5666678888888844445777888999999999888888876 PP

>> Na_H_antiport_2  Na+-H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   2.1       1.9   6.9e+03      16      36 ..      32      52 ..      17     104 .. 0.61
   2 ?   14.7   2.8   6.8e-06     0.025      18      84 ..     292     358 ..     283     361 .. 0.86
   3 ?   -2.5   0.6       1.7     6e+03      24      39 ..     387     402 ..     366     416 .. 0.56
   4 ?   -1.3   0.1      0.69   2.5e+03      67      81 ..     448     462 ..     442     467 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.9
                   Na_H_antiport_2 16 lrvnvvlallisalvgGlvgg 36
                                      l +   + l+++ ++ G+v +
  gi|336254104|ref|YP_004597211.1| 32 LDFPAFIGLILAGFTVGVVNA 52
                                      334444444444444444443 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.8e-06
                   Na_H_antiport_2  18 vnvvlallisalvgGlvgglsleetieafasGlgggaevAlsyallGafAvaisksgltdllvkkvi 84 
                                       v ++la +++a v      ++ +e  e +++ l++g ++A   a  Gaf ++++ sg+ d+l+  ++
  gi|336254104|ref|YP_004597211.1| 292 VALMLAAVVAAYVLYSHNEMTSSEWSEELTEALKSGGNIAAITAAGGAFGAMLAASGIGDYLAGILQ 358
                                       5566777777777777788899999*************************************98775 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.7
                   Na_H_antiport_2  24 llisalvgGlvgglsl 39 
                                       l+ + +++ l+g ls+
  gi|336254104|ref|YP_004597211.1| 387 LTAAGIMAPLTGQLSV 402
                                       2333344444444444 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.69
                   Na_H_antiport_2  67 Avaisksgltdllvk 81 
                                         +is sgl ++lv 
  gi|336254104|ref|YP_004597211.1| 448 TTIISVSGLITTLVV 462
                                       567777777776654 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.42   1.5e+03      14      65 ..      15      31 ..       5      36 .. 0.56
   2 ?    8.1   0.0    0.0008       2.9      12      44 ..     282     316 ..     271     323 .. 0.76
   3 ?    6.1   0.9    0.0035        13       9      59 ..     351     402 ..     343     419 .. 0.72
   4 ?   -0.6   0.3      0.42   1.5e+03      40      61 ..     440     461 ..     434     467 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.42
                           Pox_A14 14 vliaGiiLLilacifafvdfskststtdkawralsivsFilgivillglllf 65
                                      +l                                   +F +g++++++ll++
  gi|336254104|ref|YP_004597211.1| 15 LL-----------------------------------TFFIGLLVVVALLVW 31
                                      44...................................455555555555543 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0008
                           Pox_A14  12 stvliaG...iiLLilacifafvdfskststtdkaw 44 
                                         v+++G   ++L+ +a++ a+v +s+++ t+ + w
  gi|336254104|ref|YP_004597211.1| 282 PIVVFVGdknVALMLAAVVAAYVLYSHNEMTS-SEW 316
                                       556676666699****************9965.456 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0035
                           Pox_A14   9 nyystvli.aGiiLLilacifa.fvdfskststtdkawralsivsFilgivil 59 
                                       +y +++l  +Gi LLi+a ++a  v +++ +s+t  ++ a+ i++ ++g +++
  gi|336254104|ref|YP_004597211.1| 351 DYLAGILQeFGIGLLITAWLIAaIVRIAQ-GSATAAMLTAAGIMAPLTGQLSV 402
                                       5666666438********76650555655.555778999*9999998887654 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.42
                           Pox_A14  40 tdkawralsivsFilgivillg 61 
                                       t k+w +l+ +  + g++ +l 
  gi|336254104|ref|YP_004597211.1| 440 TLKTWTVLTTIISVSGLITTLV 461
                                       5667888887777777776653 PP

>> DUF3007  Protein of unknown function (DUF3007)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       1.4     5e+03      38      50 ..      20      32 ..      16      40 .. 0.80
   2 ?   10.9   1.1   0.00012      0.43      12      63 ..     332     383 ..     329     390 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.4
                           DUF3007 38 sqavlvlglvgWv 50
                                      + +++v++l++W+
  gi|336254104|ref|YP_004597211.1| 20 IGLLVVVALLVWL 32
                                      5578889999996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00012
                           DUF3007  12 gvlllgglaylvlqalGldslsagiwsqavlvlglvgWvltYllRvvtkkmT 63 
                                       +++++gg+  ++l a G+ +  agi  +  + l + +W+++ ++R+++++ T
  gi|336254104|ref|YP_004597211.1| 332 AITAAGGAFGAMLAASGIGDYLAGILQEFGIGLLITAWLIAAIVRIAQGSAT 383
                                       578899999999***********************************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3207.55
//
Query:       gi|336254105|ref|YP_004597212.1|  [L=165]
Description: hypothetical protein Halxa_2716 [Halopiger xanaduensis SH-6]
Scores for 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-09   36.6   0.0    4.4e-09   36.2   0.0    1.2  1  Prok-JAB  Prokaryotic homologs of the JAB domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.034   14.1   0.0    1.4  1  RadC      RadC-like 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 !   36.2   0.0   4.9e-13   4.4e-09       8     115 ..      24     126 ..      17     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 4.9e-13
                          Prok-JAB   8 lvaharrahpeEtcGlllgke.....seseevivvplvnewsnrfeipdpedslarlkfearerglevvgiwHSHpg 79 
                                        +++ ++ahp+E  G+l g+e      ++   ++++ + +++     + +    a++k     ++ + +g +HSHp+
  gi|336254105|ref|YP_004597212.1|  24 AIESSEAAHPDEYMGFLRGTEadqlgLDRDGLVITDILVIPG-----TESNSVSATVKTNQIPNDVKALGSVHSHPN 95 
                                       678899*******************97777777777776554.....344444444444999*************** PP

                          Prok-JAB  80 gsarPSetDrrdaaalarvkalliivgdkaeelraw 115
                                       g  rPS++D+ ++ +    + ++ii+g+ +++++ w
  gi|336254105|ref|YP_004597212.1|  96 GVLRPSDADLGTFGR----GSVHIIIGA-PYRRTDW 126
                                       *************98....566666665.4444455 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.8e-06     0.034      28      85 ..      50     105 ..      37     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-06
                                       E-TTSBEEEEEEEEESTT-GGGCSHHHHHHHHHHTT-SEEEEEEE-TTS--S--HHHH CS
                              RadC  28 LdsknrliadeelseGtlnstlvdprevfkealklnAaavilaHnhPsgdlepSeeDi 85 
                                       Ld+   +i+d  +  Gt +  +     v ++ + ++ +a+  +H hP+g l+pS++D+
  gi|336254105|ref|YP_004597212.1|  50 LDRDGLVITDILVIPGTES--NSVSATVKTNQIPNDVKALGSVHSHPNGVLRPSDADL 105
                                       6666666777666666643..333456677778888999999***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1177.49
//
Query:       gi|336254106|ref|YP_004597213.1|  [L=165]
Description: cytidyltransferase-related domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   63.8   0.2    2.2e-17   63.6   0.2    1.1  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.08   12.8   0.1       0.15   12.0   0.1    1.5  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 !   63.6   0.2   2.5e-21   2.2e-17       1     117 [.      29     138 ..      29     160 .. 0.91

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 2.5e-21
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       +a GtFD++H GH ++le+a+++++e liv+v+ + ++++k++p+ +a +R + + +++ vde+i   + ++    +
  gi|336254106|ref|YP_004597213.1|  29 IAQGTFDILHPGHVHYLEEAAAMGDE-LIVIVARKANVDHKEQPICPATQRRDVVGALEAVDEAILGHEEDIFV-PI 103
                                       578***********************.******999999999*******************************9.** PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEE CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsr 117
                                       ++++pd  ++++g+d++ d   + ++e  l+++++ + ++
  gi|336254106|ref|YP_004597213.1| 104 EEIDPD--VIALGHDQHHD---ESAIEAELERRGVDCTVE 138
                                       ******..*********99...889999999888877655 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.6e-05      0.15       5      35 ..      24      54 ..      20      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                           FAD_syn  5 degavvtlGnFDGvHlGHqallkkaveaake 35
                                      + ++v++ G FD +H GH + l++a ++ +e
  gi|336254106|ref|YP_004597213.1| 24 PARTVIAQGTFDILHPGHVHYLEEAAAMGDE 54
                                      5789*******************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1209.44
//
Query:       gi|336254107|ref|YP_004597214.1|  [L=52]
Description: hypothetical protein Halxa_2718 [Halopiger xanaduensis SH-6]
Scores for 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:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 407.93
//
Query:       gi|336254108|ref|YP_004597215.1|  [L=575]
Description: dihydroxy-acid dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-197  655.2   0.7   7.5e-197  655.0   0.7    1.0  1  ILVD_EDD  Dehydratase family
  ------ inclusion threshold ------
       0.16   12.1   0.2        1.7    8.8   0.0    2.3  2  DGC       DGC domain


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 !  655.0   0.7  8.3e-201  7.5e-197       2     517 .]      46     566 ..      45     566 .. 0.98

  Alignments for each domain:
  == domain 1  score: 655.0 bits;  conditional E-value: 8.3e-201
                          ILVD_EDD   2 piigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmleaq 78 
                                       p+ig+ n   +++pc+vhl+e+aea+ egv eagg+p+ef ti++sD+i+mg+egm++sL+sRe+iadsve +  ++
  gi|336254108|ref|YP_004597215.1|  46 PMIGVPNPAADITPCNVHLDEVAEAALEGVDEAGGMPIEFGTITISDAISMGTEGMKASLISREVIADSVELVSFGE 122
                                       99*************************************************************************** PP

                          ILVD_EDD  79 llDalvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaac 153
                                       ++D+lv+i+gCDK++Pg++maa+r+++P++f++gG++++g+++  ++++++vfe vga+a+g++se el+e+e++ac
  gi|336254108|ref|YP_004597215.1| 123 RMDGLVTIGGCDKNMPGMMMAAIRTDLPSVFLYGGSIMPGEHDgrEITIQNVFEGVGAVADGDMSEGELDEMERNAC 199
                                       ***************************************8866679******************************* PP

                          ILVD_EDD 154 pgaGsCsgmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvll 230
                                       pgaGsC+gm+TAntma++ e++G++  gs+s pa+++er e+a+e+g+ +ve+v++  kp+d l+ke+feNAi++++
  gi|336254108|ref|YP_004597215.1| 200 PGAGSCGGMFTANTMASISETIGFAPLGSSSPPAEDDERYEVARESGELAVEVVREGRKPSDFLSKESFENAIALQV 276
                                       ***************************************************************************** PP

                          ILVD_EDD 231 alGGStNavlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvlt 307
                                       a+GGStNavlHllA+A eagv+l+++df+e+s+++p +a+l+P g+  m+dlh++GG+p+vl eLl+a+llhgd+lt
  gi|336254108|ref|YP_004597215.1| 277 AVGGSTNAVLHLLAMAAEAGVDLDIEDFNEISARTPKIADLQPGGERVMNDLHEVGGIPVVLWELLEADLLHGDALT 353
                                       ***************************************************************************** PP

                          ILVD_EDD 308 vtgktlaenleeaev.....keqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseee 379
                                       vtg+tlae+le+ +       + d ++++++p++++g +++L+GnLapeGav+K+++ +  +l++egp r+f++ee+
  gi|336254108|ref|YP_004597215.1| 354 VTGETLAEALERVDPpaiedVDADFLHTVDDPIHERGAIRILTGNLAPEGAVIKITGED--HLEHEGPVRIFENEEN 428
                                       **********884445778899***********************************99..99************** PP

                          ILVD_EDD 380 aveailkgkikagdvvviryeGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGp 456
                                       a++ +++g++++gdv+ ir+eGP+GgpGm+Eml +tsa++g+g  ++val tDGRfSGa++g++ighv+PEAa+gGp
  gi|336254108|ref|YP_004597215.1| 429 AMRYVQEGRVESGDVIGIRNEGPRGGPGMREMLGVTSAVAGQGHAEDVALFTDGRFSGATRGFSIGHVAPEAAVGGP 505
                                       *****99********************************************************************** PP

                          ILVD_EDD 457 ialvedGDiieidiekrtlelevseeelaaRraawkp.ekkvktrgllakyaklvssaseGA 517
                                       ia +edGD+++idi++ +l++++s+ee+++R ++    e++ +t+g+laky + + sa++GA
  gi|336254108|ref|YP_004597215.1| 506 IAALEDGDTVRIDIDDLELSVDLSDEEIERRLEERDLpEPQ-YTTGVLAKYGRDFGSAANGA 566
                                       ********************************877763433.45*****************8 PP

>> DGC  DGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00019       1.7      11      62 ..      85     136 ..      79     148 .. 0.91
   2 ?    0.6   0.0     0.069   6.2e+02       4      48 ..     198     243 ..     197     250 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00019
                               DGC  11 vGqlaneaavklakegeakmiclagvgagveelvelaksarkiiaidGCple 62 
                                        G+++   a+ +  eg  + ++  +v+a++ elv + ++ + +++i GC+++
  gi|336254108|ref|YP_004597215.1|  85 FGTITISDAISMGTEGMKASLISREVIADSVELVSFGERMDGLVTIGGCDKN 136
                                       79999999999****9999999999************************986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.069
                               DGC   4 sCsG.asnvGqlaneaavklakegeakmiclagvgagveelvelak 48 
                                       +C G +s+ G+ + +++  ++++ + + +  ++  a+++e +e+a+
  gi|336254108|ref|YP_004597215.1| 198 ACPGaGSCGGMFTANTMASISETIGFAPLGSSSPPAEDDERYEVAR 243
                                       7***99*******999999999855444444445555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3827.84
//
Query:       gi|336254109|ref|YP_004597216.1|  [L=229]
Description: Molybdopterin-guanine dinucleotide biosynthesis protein A [Halopiger xanaduensis SH-6]
Scores for complete 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-31  110.2   2.9    1.6e-31  109.8   2.9    1.1  1  NTP_transf_3   MobA-like NTP transferase domain
     0.0019   18.2   0.0     0.0088   16.0   0.0    1.9  3  CTP_transf_3   Cytidylyltransferase
  ------ inclusion threshold ------
      0.072   13.3   0.0       0.12   12.6   0.0    1.3  1  CdiA_C_tRNase  CdiA C-terminal tRNase domain


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 !  109.8   2.9   2.7e-35   1.6e-31       1     159 [.      23     191 ..      23     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 2.7e-35
                                       EEEEEESS-TTTTT.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTCT..S-EEE-TTSS-S CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.dKallplggkpllervldalraagvdevvvvggd...eevlaalarlg..vrvvededpgkg 71 
                                       +++ AGG S+R+g  dKa ++l+g+p+++rv+d+l+a+  d vvv++++   ++++aal++    ++++ d+ +++g
  gi|336254109|ref|YP_004597216.1|  23 GLVIAGGYSTRFGDeDKAVADLAGTPMIRRVVDRLAAV-TDAVVVNCREdqrDAITAALEGCApaIEFALDPVEDRG 98 
                                       689**********77***********************.7*******993334566666655345999********* PP

                                       HHHHHHHHHHHH....SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECC..EEEGGGHHHHHH CS
                      NTP_transf_3  72 plaslaaalraaa...dadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpl..lfrarllsalaa 143
                                       p+a++ ++l+a++   + + ++v+acDmP+++p+l+e ll++a++  ad +v++ e+++ +    ++r++ ++++ a
  gi|336254109|ref|YP_004597216.1|  99 PVAGIGTGLEAVGetyGREFAAVVACDMPFVDPDLLELLLERAHDGAADGAVVQLEDGWYQTTqaVYRTDPMARACA 175
                                       ***********887789999***************************************999977888888888887 PP

                                       HCTHTTHHHCHHHHH- CS
                      NTP_transf_3 144 llgdqgarrllrrldr 159
                                        + ++  rr++++l+r
  gi|336254109|ref|YP_004597216.1| 176 ETLESDDRRIVAALER 191
                                       7888999999998866 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.5e-06    0.0088       3      52 ..      24      73 ..      22      91 .. 0.83
   2 ?   -1.2   0.0      0.27   1.6e+03      96     121 ..     122     147 ..     105     182 .. 0.68
   3 ?   -2.0   0.0      0.47   2.8e+03      68      86 ..     176     194 ..     161     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-06
                                      EEEE-SSSSSS..TTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHH CS
                      CTP_transf_3  3 IipARsgSkRl..pgKnlldlggkpliayvleaalkskafekvivaTDseei 52
                                      ++ A   S+R+  ++K+ +dl+g p+i++v++++    + + v+v + +++ 
  gi|336254109|ref|YP_004597216.1| 24 LVIAGGYSTRFgdEDKAVADLAGTPMIRRVVDRLAA--VTDAVVVNCREDQR 73
                                      667777799996668******************988..8899**99977654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.27
                                       E-TT-TT--HHHHHHHHHHHHHSTTS CS
                      CTP_transf_3  96 lqGdnPllqeevikkaietlkenqed 121
                                       +  d P++++ +++ ++e+  +   d
  gi|336254109|ref|YP_004597216.1| 122 VACDMPFVDPDLLELLLERAHDGAAD 147
                                       45578888888888888877766555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.47
                                       TTCSSHHHHHHHHHHHHTT CS
                      CTP_transf_3  68 sslesdterflevvkaflm 86 
                                       + lesd++r+++++++++ 
  gi|336254109|ref|YP_004597216.1| 176 ETLESDDRRIVAALERVDY 194
                                       5678888888888887764 PP

>> CdiA_C_tRNase  CdiA C-terminal tRNase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     2e-05      0.12      34      94 ..     144     206 ..     141     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                     CdiA_C_tRNase  34 GpnkGktvDli..yttdkssakeiekinkffednfeknvevlenhlkkadivplDlRvlteen 94 
                                       G   G+ v l   + + +++ ++ + + +  ++++e     +   l+++d+v +D Rvl e+ 
  gi|336254109|ref|YP_004597216.1| 144 GAADGAVVQLEdgWYQTTQAVYRTDPMARACAETLESDDRRIVAALERVDYVTVDERVLEEAG 206
                                       55556555443224444558999999*********************************9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1683.25
//
Query:       gi|336254110|ref|YP_004597217.1|  [L=108]
Description: hypothetical protein Halxa_2721 [Halopiger xanaduensis SH-6]
Scores for 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:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 789.56
//
Query:       gi|336254111|ref|YP_004597218.1|  [L=339]
Description: beta-ribofuranosylaminobenzene 5'-phosphate synthase protein [Halopiger xanaduensis SH-6]
Scores for 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-07   31.0   1.1    4.3e-07   30.1   0.4    1.9  2  GHMP_kinases_N  GHMP kinases N terminal domain
    1.3e-05   25.5   0.2    2.2e-05   24.7   0.2    1.4  1  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 ?   -2.8   0.0      0.86   7.7e+03      30      53 ..      24      43 ..      16      47 .. 0.56
   2 !   30.1   0.4   4.8e-11   4.3e-07       1      66 []      86     147 ..      86     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.86
                                      HHTTEHHHHHHHHHHHHHHHHHHH CS
                    GHMP_kinases_N 30 allglsleeaklaleaerlaqggn 53
                                      +l  + +   +l+l  erl + g 
  gi|336254111|ref|YP_004597218.1| 24 RLH-VGF--QNLSLARERLYG-GI 43
                                      444.223..577888888876.44 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 4.8e-11
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                       d+ ++ ++P + GLGS++ la+a++aA ++++gl+      a e   ++++g  sg+ va++  Gg
  gi|336254111|ref|YP_004597218.1|  86 DLAVEERLPRHVGLGSGTQLALAVLAATARAYGLE----PRAREHAPAMGRGGRSGVGVATFEAGG 147
                                       578999**************************944....235555577899999***999998776 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 !   24.7   0.2   2.5e-09   2.2e-05       1      79 [.     229     309 ..     229     314 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.5e-09
                    GHMP_kinases_C   1 llealergdlellgellnlsqrs......elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkde 71 
                                       ll+a+ +g+le++ge++ +  r       +   + g+  p   el+eal+++    +++ ++++Gp v++++ d  +
  gi|336254111|ref|YP_004597218.1| 229 LLPAAAEGRLEAFGEAIAEIGRKngawyaDA--QGGVFRPPAGELVEALEDCP-VLSGIGQSSWGPVVYGVT-DSRH 301
                                       578999*********************7655..9*******************.9999*************9.8888 PP

                    GHMP_kinases_C  72 aeqvaral 79 
                                       ae++a a 
  gi|336254111|ref|YP_004597218.1| 302 AEEAAAAA 309
                                       88888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2433.80
//
Query:       gi|336254112|ref|YP_004597219.1|  [L=278]
Description: hypothetical protein Halxa_2723 [Halopiger xanaduensis SH-6]
Scores for complete 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   0.0     0.0011   18.4   0.1    2.2  2  ATPase    KaiC
    0.00011   21.5   0.0     0.0076   15.5   0.0    2.3  2  Rad51     Rad51
  ------ inclusion threshold ------
      0.031   13.8   3.0       0.51    9.9   3.0    2.2  1  AAA_25    AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.8e-07    0.0011       2      46 ..       5      45 ..       4      52 .. 0.86
   2 !    7.3   0.0   0.00043       2.6     107     208 ..     144     248 ..     105     273 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-07
                            ATPase  2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaek 46
                                      + g+  lD+++ gG p g+vvl++Ge+G+G    a +F++++a+ 
  gi|336254112|ref|YP_004597219.1|  5 PLGVARLDRMIGGGAPAGSVVLLAGESGAG----AREFAYTSAVM 45
                                      67999*************************....67777777665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00043
                            ATPase 107 lieelaeaikeika.krvviDsitglayeekeavaReilrqlvrvl..kklgvTailvsekss.seeaaggygveef 179
                                       ++e +a +++e      v++Ds+t l   +++ +  + l  l++ l  +  +   ++   ++s   e ++  +++e 
  gi|336254112|ref|YP_004597219.1| 144 VLEAFAGYLSEHATgDLVIVDSVTDLIAAADDRLGWSDLTVLLKGLarASHRWGGVILLLVNSeLLEPTQLGRLKE- 219
                                       44444444444444377999******99999999888888888888532333334333333332567777788999. PP

                            ATPase 180 ivdgvivLdlkeieeelvRtleivkmRgt 208
                                       + dg++  + ++  +e+ Rt+ +   Rg 
  gi|336254112|ref|YP_004597219.1| 220 ATDGTLLFEWESGGSERARTMVVEQFRGV 248
                                       9************************9986 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.3e-06    0.0076      22      64 ..       7      49 ..       2      80 .. 0.90
   2 !    3.8   0.0    0.0047        28      81     144 ..     100     169 ..      91     191 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-06
                                      S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS- CS
                             Rad51 22 GskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlp 64
                                      G  +lD+++gGG ++gs+  + Ge+++G   +++t +v+  l 
  gi|336254112|ref|YP_004597219.1|  7 GVARLDRMIGGGAPAGSVVLLAGESGAGAREFAYTSAVMNGLA 49
                                      8899**********************************98886 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0047
                                       S---GGGGHHHHHHT.T--HHHHGGGEEEEE--ST......THHHHHHHHTHHHHHHS-EE.EEEEETTTGG CS
                             Rad51  81 gtfrperlveiaery.kldkeevlenvayaRayti......ehqeellqqaaallaedkfa.llivDsvtal 144
                                       +++ +   ve+ae y +l +  v  +   +R   i       ++e++l++ a  l+e+  + l+ivDsvt l
  gi|336254112|ref|YP_004597219.1| 100 TGMDAVEFVELAEEYfQLTP--VPTEWYAERTADItqlgsqTEREDVLEAFAGYLSEHATGdLVIVDSVTDL 169
                                       55666666777766645543..33333333433333344446678899999999999887559******976 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.0   8.5e-05      0.51      23     186 ..      12     203 ..       8     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 8.5e-05
                            AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalava...tGkpwlg.......pvapeqgkVlyvsaEdsedelrrR 89 
                                       +  ++g  pag+++llaG +g+G   +a+  a+      +G   ++       + a+ +g   y+s+ d +  ++  
  gi|336254112|ref|YP_004597219.1|  12 DRMIGGGAPAGSVVLLAGESGAGAREFAYTSAVMNGlaeQGADRFDlhygdleNGATLPGGIHYISFTDERTAVASE 88 
                                       56677888999999999999999777766555532223767666668888776555688999999999999999999 PP

                            AAA_25  90 lravg.eal.....................rddarllvldlagveslpLfakdrggtl.ltadvdaleaaieevegv 143
                                       ++ v+ ++l                     + + ++++   a+   ++L      +++ ++ +++a +  + e++  
  gi|336254112|ref|YP_004597219.1|  89 MSFVMeTDLvetgmdavefvelaeeyfqltPVPTEWYAERTADI--TQLG-----SQTeREDVLEAFAGYLSEHATG 158
                                       99877455588777666666555444444333333333333332..3333.....3334455566667777887889 PP

                            AAA_25 144 rlvviDplsralgg..densnsdvgalvealeriarrtgaavllv 186
                                       +lv++D+++ + ++  d    sd + l++ l+r ++r g  +ll+
  gi|336254112|ref|YP_004597219.1| 159 DLVIVDSVTDLIAAadDRLGWSDLTVLLKGLARASHRWGGVILLL 203
                                       **********88888888899***************999887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2174.16
//
Query:       gi|336254113|ref|YP_004597220.1|  [L=282]
Description: hypothetical protein Halxa_2724 [Halopiger xanaduensis SH-6]
Scores for 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   18.3   1.2     0.0032   17.5   1.2    1.4  1  Erp_C           Erp protein C-terminus
     0.0029   18.1   1.5      0.019   15.5   1.3    2.4  2  Syntaxin-6_N    Syntaxin 6, N-terminal
     0.0081   16.6   0.9      0.034   14.5   0.2    2.2  2  DUF2746         Protein of unknown function (DUF2746)
  ------ inclusion threshold ------
       0.01   15.6   1.8        0.1   12.4   0.3    2.8  2  PSD2            Protein of unknown function (DUF1585)
      0.026   14.6   1.4      0.026   14.6   1.4    2.0  2  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
      0.035   14.1   0.0      0.067   13.2   0.0    1.6  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.038   12.7   0.5       0.05   12.3   0.5    1.1  1  MAP65_ASE1      Microtubule associated protein (MAP65/ASE1 fa
      0.042   13.5   0.0      0.066   12.9   0.0    1.2  1  TackOD1         Thaumarchaeal output domain 1
       0.05   13.3   0.2       0.08   12.7   0.2    1.2  1  DUF713          Protein of unknown function (DUF713)
      0.058   13.5   1.0       0.15   12.2   1.0    1.7  1  Zn-ribbon_8     Zinc ribbon domain
       0.09   12.9   2.9       0.49   10.5   0.4    2.5  2  TolA_bind_tri   TolA binding protein trimerisation
        0.1   13.0   0.1        4.7    7.7   0.0    2.4  2  FlaC_arch       Flagella accessory protein C (FlaC)
       0.12   12.4   0.7        5.6    7.1   0.1    2.5  2  XPA_N           XPA protein N-terminal
       0.26   10.2   3.7       0.46    9.3   3.5    1.5  1  Spc7            Spc7 kinetochore protein
       0.27    9.7   9.0       0.19   10.2   7.3    1.6  2  FUSC            Fusaric acid resistance protein family
       0.29   11.1   2.8        3.9    7.5   0.4    2.3  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.58   10.6   6.3        1.8    9.0   0.2    2.4  2  Latarcin        Latarcin precursor
       0.71   10.3   4.4         12    6.4   3.3    2.6  2  DUF4200         Domain of unknown function (DUF4200)
        1.4    8.9   3.9        1.5    8.8   0.7    2.4  3  DUF2205         Short coiled-coil protein
        4.2    7.9   9.2        2.7    8.5   0.6    2.6  2  DinB_2          DinB superfamily
        8.3    5.8   8.6        1.3    8.5   3.3    2.2  2  MIF4G_like_2    MIF4G like


Domain annotation for each model (and alignments):
>> Erp_C  Erp protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.2   3.7e-06    0.0032      47     137 ..      46     139 ..      27     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.7e-06
                             Erp_C  47 aiyktwgdledeedeglgkllkelsdtrdelrtklnegnkayivlekepklke..nvnvseikedleklkskleevk 121
                                       a+    ++ e  + e++  l  el   rde+r  l++   + i  ++e + k   + +  e + dl  l+++le++ 
  gi|336254113|ref|YP_004597220.1|  46 AVATEGEGAEPADREDIEELRGELETQRDEFRDLLEDVRSRVIQVKRETDAKApaEHDHGEYEADLSSLRADLEDLE 122
                                       555556777888999******************9999999999999999888622567899**************** PP

                             Erp_C 122 kylkde.dkfeeikgyi 137
                                       + ++   ++fee+ +y+
  gi|336254113|ref|YP_004597220.1| 123 DTVDTGfENFEEVLEYL 139
                                       *9986449******997 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 ?    4.4   0.2     0.063        53      34      69 ..      57      92 ..      31     101 .. 0.72
   2 !   15.5   1.3   2.2e-05     0.019       7      66 ..      66     127 ..      63     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.063
                      Syntaxin-6_N 34 stseeldetrteLrkalrsiewdledLeetvrivek 69
                                      + +e+++e+r eL+++ ++ +  led +  v  v++
  gi|336254113|ref|YP_004597220.1| 57 ADREDIEELRGELETQRDEFRDLLEDVRSRVIQVKR 92
                                      368899999999999999999999999888766654 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.2e-05
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrw.erlledtss.stseeldetrteLrkalrsiewdledLeetvri 66 
                                       + e + + ++ + l++   +r+ +++++ + +   ++ + e ++ l+s++ dledLe+tv++
  gi|336254113|ref|YP_004597220.1|  66 RGELETQRDEFRDLLEDVrSRVIQVKREtDAKAPAEHDHGEYEADLSSLRADLEDLEDTVDT 127
                                       667777888888888888557777777766899999999*********************54 PP

>> DUF2746  Protein of unknown function (DUF2746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.2   1.9e+03      39      69 ..      61      90 ..      44      98 .. 0.60
   2 !   14.5   0.2     4e-05     0.034      53      94 ..     105     148 ..      89     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.2
                           DUF2746 39 digeikeqvcnthdtnlrddldsvkadisdl 69
                                      di e++ ++ +t+  ++rd l+ v++ + ++
  gi|336254113|ref|YP_004597220.1| 61 DIEELRGEL-ETQRDEFRDLLEDVRSRVIQV 90
                                      444444443.334445566565555555444 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4e-05
                           DUF2746  53 tnlrddldsvkadisdlkeivlqgfhqvnesin..lerrerieg 94 
                                        +   dl s++ad+ dl++ v  gf + +e ++  ler +r+e 
  gi|336254113|ref|YP_004597220.1| 105 GEYEADLSSLRADLEDLEDTVDTGFENFEEVLEylLERTDRLEE 148
                                       35678*************************98655899999985 PP

>> PSD2  Protein of unknown function (DUF1585)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   0.00012       0.1      36      68 ..      51      83 ..      23      85 .. 0.82
   2 ?    1.3   0.1      0.35     3e+02       5      24 ..     129     148 ..     126     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                              PSD2 36 GRgleasDrcaveeivaalrasgyrlrdlieai 68
                                      G g e++Dr+++ee++ +l+++ + +rdl+e++
  gi|336254113|ref|YP_004597220.1| 51 GEGAEPADREDIEELRGELETQRDEFRDLLEDV 83
                                      8899**************************987 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.35
                              PSD2   5 fegpaeLkqlLlarsdqfar 24 
                                       fe+++e  ++Ll+r+d++ +
  gi|336254113|ref|YP_004597220.1| 129 FENFEEVLEYLLERTDRLEE 148
                                       99*************99876 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.4   3.1e-05     0.026      21     115 ..      59     153 ..      52     163 .. 0.91
   2 ?   -2.0   0.7       4.2   3.6e+03       8      25 ..     251     268 ..     244     274 .. 0.36

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                        TPR_MLP1_2  21 eaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeq 97 
                                       ++++++l+ +le+q+++ ++  ++  + +++ + ++++ + +  ++ e++a++++l+a++e+++ ++++  e+ ee 
  gi|336254113|ref|YP_004597220.1|  59 REDIEELRGELETQRDEFRDLLEDVRSRVIQVKRETDAKAPAEHDHGEYEADLSSLRADLEDLEDTVDTGFENFEEV 135
                                       57899999999999999999999999999999999999999999999999999999999999999999999999999 PP

                        TPR_MLP1_2  98 keelekelselekriedl 115
                                        e l ++ + le+r + l
  gi|336254113|ref|YP_004597220.1| 136 LEYLLERTDRLEERATVL 153
                                       999999999999997655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.2
                        TPR_MLP1_2   8 eeikslkeekeeaeaklq 25 
                                       ++++++ +++e+ +++++
  gi|336254113|ref|YP_004597220.1| 251 STAEDVFAQIESNAETAA 268
                                       222222222222222222 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   0.0   7.8e-05     0.067      70     101 ..     191     223 ..     136     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-05
                                       EEEETTTS-EEECHHH.HHS-TTTSSS-EEEEE CS
                              HypA  70 kvrCreCgkefeleek.alrCpkCgsadveivs 101
                                       +++C++Cg++++++   a +Cp+C s   ++ +
  gi|336254113|ref|YP_004597220.1| 191 TATCEDCGSSVDIALLtAPECPHCASPFADVAE 223
                                       478*********88744889****998777655 PP

>> MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   5.9e-05      0.05      75     174 ..      60     162 ..      58     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS---SS--TSS--HHH...HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        MAP65_ASE1  75 taleelrkekaerlaeflelleqlqklceelgeeplsllidslpklee...leslrkhleelkeekerRleeikelk 148
                                       + +eelr+e++ ++ ef +lle  ++ + +++ e + ++ ++    e+   l+slr  le l+++ +  +e+++e  
  gi|336254113|ref|YP_004597220.1|  60 EDIEELRGELETQRDEFRDLLEDVRSRVIQVKRETDAKAPAEHDHGEYeadLSSLRADLEDLEDTVDTGFENFEEVL 136
                                       579******************************999888888777777888*************9999999999999 PP

                                       HHHHHHHHHHT----SHHHHHHHCT- CS
                        MAP65_ASE1 149 kqIkslmeeLglepktsieedllkes 174
                                       + +++    L+ +++  ++  +   +
  gi|336254113|ref|YP_004597220.1| 137 EYLLERTDRLEERATVLAKAAVDLRD 162
                                       99999999999887777666654444 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.7e-05     0.066       9      96 ..     131     217 ..     125     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.7e-05
                           TackOD1   9 teekllayllsrdeeklepvldpkskelysypllealskekeeseelleelvkrglleeelvdrirlCpsCksg... 82 
                                         e++l+yll+r+  +le++++   k ++  +  +  + ++e+    +++l+   +  ++l  r+ +C+ C s+   
  gi|336254113|ref|YP_004597220.1| 131 NFEEVLEYLLERT-DRLEERATVLAKAAVDLRDHRDAFADRERRRAAADRLK---TAANRLGVRTATCEDCGSSvdi 203
                                       5678999999999.99999999999999999999888876666665555554...4569999**********97444 PP

                           TackOD1  83 hlnvrevCpkCkSi 96 
                                        l    +Cp+C S 
  gi|336254113|ref|YP_004597220.1| 204 ALLTAPECPHCASP 217
                                       699999*****995 PP

>> DUF713  Protein of unknown function (DUF713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   9.4e-05      0.08      22     110 ..      65     148 ..      63     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.4e-05
                            DUF713  22 lklrFeekEqewsdwlkklrepivklknrfsdfeeeikksdkeekklekedleelqselsnLakkvlsaynkLeeaf 98 
                                       l+   e++ +e++d+l+++r+ ++++k++        ++   +  ++e  dl+ l+ +l+ L+  v + ++++ee  
  gi|336254113|ref|YP_004597220.1|  65 LRGELETQRDEFRDLLEDVRSRVIQVKRETDAKA-PAEH---DHGEYEA-DLSSLRADLEDLEDTVDTGFENFEEVL 136
                                       777899*********************9854433.3333...3356665.9999****************9999999 PP

                            DUF713  99 eklkelsekfed 110
                                       e l e +++ e+
  gi|336254113|ref|YP_004597220.1| 137 EYLLERTDRLEE 148
                                       988777776665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.0   0.00018      0.15       8      35 ..     194     217 ..     190     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgse 35 
                                       Ce+Cg+  ++    +    ++CP+C s+
  gi|336254113|ref|YP_004597220.1| 194 CEDCGSSVDIAL-LT---APECPHCASP 217
                                       *****9999443.34...667****986 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 ?   10.5   0.4   0.00057      0.49      32      58 ..      60      86 ..      57     101 .. 0.85
   2 ?    2.0   0.1      0.26   2.2e+02      31      53 ..     108     130 ..     105     152 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00057
                     TolA_bind_tri 32 qelreLRGqiEelqyqleqleerQrdl 58
                                      +++ eLRG++E ++ + ++l+e  r  
  gi|336254113|ref|YP_004597220.1| 60 EDIEELRGELETQRDEFRDLLEDVRSR 86
                                      799****************99988765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.26
                     TolA_bind_tri  31 qqelreLRGqiEelqyqleqlee 53 
                                       +++l++LR ++E+l+  +++  e
  gi|336254113|ref|YP_004597220.1| 108 EADLSSLRADLEDLEDTVDTGFE 130
                                       57999999999999887776555 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 ?    2.6   0.1      0.21   1.8e+02       8      30 ..      61      83 ..      59      92 .. 0.64
   2 ?    7.7   0.0    0.0055       4.7      11      42 ..     106     137 ..     100     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.21
                         FlaC_arch  8 klsklsteletvkkeneelsksv 30
                                      ++++l  elet ++e+ +l ++v
  gi|336254113|ref|YP_004597220.1| 61 DIEELRGELETQRDEFRDLLEDV 83
                                      55666667777777666665555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0055
                         FlaC_arch  11 klsteletvkkeneelsksveelkenVkdlls 42 
                                       + +  l+++++++e+l+++v++  en++++l+
  gi|336254113|ref|YP_004597220.1| 106 EYEADLSSLRADLEDLEDTVDTGFENFEEVLE 137
                                       66788999999999999999999999888885 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.099        85       3      11 ..     193     201 ..     191     207 .. 0.80
   2 ?    7.1   0.1    0.0065       5.6       1      13 [.     208     220 ..     208     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.099
                             XPA_N   3 kCdeCgkef 11 
                                       +C++Cg+  
  gi|336254113|ref|YP_004597220.1| 193 TCEDCGSSV 201
                                       8*****975 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0065
                             XPA_N   1 apkCdeCgkefld 13 
                                       ap+C +C ++f+d
  gi|336254113|ref|YP_004597220.1| 208 APECPHCASPFAD 220
                                       69*********98 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.5   0.00054      0.46     153     251 ..      64     161 ..      56     194 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00054
                              Spc7 153 edkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeql 229
                                       e + +Le q++e+ +ll++++++  ++++e +    a++++ +  +++L +lr +l++l+ +++   ++ +e+ e l
  gi|336254113|ref|YP_004597220.1|  64 ELRGELETQRDEFRDLLEDVRSRVIQVKRETDAKAPAEHDHGE-YEADLSSLRADLEDLEDTVDTGFENFEEVLEYL 139
                                       5556789999999999999999999999998877775555433.478899999999999999987666666666666 PP

                              Spc7 230 eeleekieelkeqkseleeeia 251
                                        e ++++ee ++  +++  +++
  gi|336254113|ref|YP_004597220.1| 140 LERTDRLEERATVLAKAAVDLR 161
                                       6666666666555555555544 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         2   1.7e+03     606     633 ..      26      53 ..      16      60 .. 0.73
   2 ?   10.2   7.3   0.00022      0.19     241     354 ..      61     192 ..      56     201 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2
                              FUSC 606 sarrlrapaaalraldaalaalaaseat 633
                                       ++ r+++p++++r++ +a++a+a++++ 
  gi|336254113|ref|YP_004597220.1|  26 AEDRDESPDDVCRRVVTAAHAVATEGEG 53 
                                       4667778888888888888888887765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00022
                              FUSC 241 llarlraeeaaavpelaallaelaal............eaaaaaealeaalaalrarlralrrale...adadtaal 302
                                         ++lr e +++++e+++ll+++++              a++++ ++ea+l +lra+l++l+   +   +     ++
  gi|336254113|ref|YP_004597220.1|  61 DIEELRGELETQRDEFRDLLEDVRSRviqvkretdakaPAEHDHGEYEADLSSLRADLEDLEDTVDtgfE---NFEE 134
                                       567899999999999****************877776645556666777777777777777777764442...3333 PP

                              FUSC 303 llarlaellaelaqllaslraleaaiaa......arraerlarhrdhlaallnglraa 354
                                       +l+ l+e+ ++l +  + l++ + + ++      +r+++r+a  r  +aa + g+r+a
  gi|336254113|ref|YP_004597220.1| 135 VLEYLLERTDRLEERATVLAKAAVDLRDhrdafaDRERRRAAADRLKTAANRLGVRTA 192
                                       3333333333333322222111111111222344466666666666666666666665 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.078        67       5      11 ..     194     200 ..     190     202 .. 0.81
   2 ?    7.5   0.4    0.0045       3.9       3      10 ..     209     216 ..     204     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.078
                    PhnA_Zn_Ribbon   5 CplCaSe 11 
                                       C+ C+S+
  gi|336254113|ref|YP_004597220.1| 194 CEDCGSS 200
                                       9999997 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0045
                    PhnA_Zn_Ribbon   3 pkCplCaS 10 
                                       p Cp+CaS
  gi|336254113|ref|YP_004597220.1| 209 PECPHCAS 216
                                       99****99 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2    0.0022       1.8      51      78 ..      57      84 ..      52      87 .. 0.89
   2 ?    3.5   1.8      0.12        98      13      73 ..     117     187 ..     108     192 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0022
                          Latarcin 51 edledtEEARgafkklkdkfkkmgeklk 78
                                       d+ed+EE Rg  ++ +d+f+ + e++ 
  gi|336254113|ref|YP_004597220.1| 57 ADREDIEELRGELETQRDEFRDLLEDVR 84
                                      59*******************9999876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
                          Latarcin  13 eLdele.........rgainrklmemvnnlRkvqgRLeemvenlrkved.ledtEEARgafkklkdkfkkm 73 
                                       +L++le          +++   l+e  ++l + +  L++++ +lr   d + d E  R a + lk   +++
  gi|336254113|ref|YP_004597220.1| 117 DLEDLEdtvdtgfenFEEVLEYLLERTDRLEERATVLAKAAVDLRDHRDaFADRERRRAAADRLKTAANRL 187
                                       45555544444444433444556667777777777788888899875543788888888888888777665 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.3     0.014        12      33     101 ..      59     123 ..      57     157 .. 0.50
   2 ?    2.9   0.1      0.16   1.4e+02       6      50 ..     116     160 ..     111     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                           DUF4200  33 eeelekkeqeleedllkfdkflkendakraralkkaeee...rklkkekeaeikklkaeietlkseieklee 101
                                       +e++e+ + ele +  +f   l++  ++ ++  ++++ +   ++ + e+ea++  l+a++e+l+       +
  gi|336254113|ref|YP_004597220.1|  59 REDIEELRGELETQRDEFRDLLEDVRSRVIQVKRETDAKapaEHDHGEYEADLSSLRADLEDLE-------D 123
                                       4555555556666666666666665555554444333321112333344444444444444443.......3 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                           DUF4200   6 remfevqealeakkeeiqrleealkqreeelekkeqeleedllkf 50 
                                        ++++++  +++  e++++  e l +r + le++   l + ++ +
  gi|336254113|ref|YP_004597220.1| 116 ADLEDLEDTVDTGFENFEEVLEYLLERTDRLEERATVLAKAAVDL 160
                                       456667777777777788888888888888887777777666554 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.7    0.0018       1.5      15      47 ..      63      95 ..      54      98 .. 0.88
   2 ?   -0.8   0.1       1.8   1.5e+03      27      41 ..     131     145 ..     108     159 .. 0.59
   3 ?   -0.4   0.1       1.4   1.2e+03       9      37 ..     134     162 ..     126     169 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                           DUF2205 15 rearerLqqqakeLqssLqaLaervdeVkeehd 47
                                      +e r +L++q +e+ + L+++  rv +Vk e d
  gi|336254113|ref|YP_004597220.1| 63 EELRGELETQRDEFRDLLEDVRSRVIQVKRETD 95
                                      58899*************************976 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                           DUF2205  27 eLqssLqaLaervde 41 
                                       ++ + L+ L+er d 
  gi|336254113|ref|YP_004597220.1| 131 NFEEVLEYLLERTDR 145
                                       344444444444444 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.4
                           DUF2205   9 dveklerearerLqqqakeLqssLqaLae 37 
                                       +v +   e  +rL+++a  L +   +L +
  gi|336254113|ref|YP_004597220.1| 134 EVLEYLLERTDRLEERATVLAKAAVDLRD 162
                                       45555556677788888777776666655 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.6    0.0031       2.7      55      89 ..      49      83 ..      21     114 .. 0.70
   2 ?    4.0   1.5     0.077        66      65     108 ..     123     174 ..      96     185 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0031
                            DinB_2 55 aprpgldpltppsaaealaylaevrarllalleal 89
                                      +  +g +p+   +++e++ +l+ +r+++++lle+ 
  gi|336254113|ref|YP_004597220.1| 49 TEGEGAEPADREDIEELRGELETQRDEFRDLLEDV 83
                                      22356666667788888888888888888888875 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.077
                            DinB_2  65 p......psaaealaylaevrarllallealtdadldrpltap..hpglgkl 108
                                       +       +++e+l+yl e  +rl +  + l+ a+ d + +    +++++++
  gi|336254113|ref|YP_004597220.1| 123 DtvdtgfENFEEVLEYLLERTDRLEERATVLAKAAVDLRDHRDafADRERRR 174
                                       3444444799****************99999887766554443335555555 PP

>> MIF4G_like_2  MIF4G like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.3    0.0015       1.3     188     235 ..      48     102 ..      17     151 .. 0.71
   2 ?   -2.8   0.2       4.1   3.5e+03      24      48 ..     247     271 ..     245     276 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0015
                      MIF4G_like_2 188 d.......keeeeeleraeekleaaqkeqkelflivferlveilsesleeletsg 235
                                                ++ e++e+++ +le++++e+++l++ v  r +++  e+  ++ +++
  gi|336254113|ref|YP_004597220.1|  48 AtegegaePADREDIEELRGELETQRDEFRDLLEDVRSRVIQVKRETDAKAPAEH 102
                                       0222344477889999999999999999999999999999999998855543333 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.1
                      MIF4G_like_2  24 kapaeevlelldeikesaeeegsie 48 
                                        a+++  ++++ +i+++ae+ +++e
  gi|336254113|ref|YP_004597220.1| 247 SATESTAEDVFAQIESNAETAAETE 271
                                       5666777777777777776665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1107  (0.0617435); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); 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):              21  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 2125.54
//
Query:       gi|336254114|ref|YP_004597221.1|  [L=211]
Description: hypothetical protein Halxa_2725 [Halopiger xanaduensis SH-6]
Scores for 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  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); 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:                         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: 1633.91
//
Query:       gi|336254115|ref|YP_004597222.1|  [L=107]
Description: transcription termination factor Tfs [Halopiger xanaduensis SH-6]
Scores for 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   60.5   4.0      1e-16   60.5   4.0    3.0  3  TFIIS_C          Transcription factor S-II (TFIIS)
    9.3e-08   31.8   8.6    1.1e-07   31.5   1.6    3.0  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    1.3e-05   24.4  12.5     0.0024   17.2   0.9    3.4  3  zf-ribbon_3      zinc-ribbon domain
    3.8e-05   23.5  12.7     0.0026   17.7   3.1    2.6  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    5.2e-05   23.2  11.1     0.0015   18.5   1.3    2.7  2  DZR              Double zinc ribbon
    0.00039   20.3  12.4     0.0052   16.7   2.2    3.2  3  Prok-RING_1      Prokaryotic RING finger family 1
     0.0012   18.5  10.0        2.5    8.0   0.1    4.3  4  zinc_ribbon_2    zinc-ribbon domain
     0.0026   17.7   6.5     0.0037   17.2   0.4    2.7  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0031   17.0  16.0        1.5    8.4   0.7    4.3  3  TF_Zn_Ribbon     TFIIB zinc-binding
      0.006   16.6   8.8       0.51   10.4   0.8    2.4  2  HypA             Hydrogenase/urease nickel incorporation, met
     0.0061   16.2  10.7       0.31   10.8   0.3    4.1  4  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
     0.0097   15.9  12.0          3    7.9   0.3    4.1  4  ADK_lid          Adenylate kinase, active site lid
  ------ inclusion threshold ------
      0.022   14.7  10.3        4.4    7.4   0.1    4.1  4  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.025   14.5   9.0       0.39   10.7   0.3    3.5  3  zinc_ribbon_4    zinc-ribbon domain
       0.03   14.0   6.0       0.37   10.4   1.3    2.2  2  TackOD1          Thaumarchaeal output domain 1
      0.039   14.1  16.4       0.88    9.7   2.9    3.7  3  Zn-ribbon_8      Zinc ribbon domain
      0.039   13.9  16.0       0.25   11.3   2.7    4.1  4  Nudix_N_2        Nudix N-terminal
      0.079   13.0  12.2         18    5.4   0.1    4.2  4  YhfH             YhfH-like protein
      0.089   12.9  12.9        7.2    6.8   0.3    4.1  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.091   12.4  14.5        1.1    8.9   0.1    4.1  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.11   12.3  12.1       0.39   10.4   0.2    3.7  4  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.15   11.8  14.6        8.4    6.2   0.1    4.3  4  Rubredoxin_2     Rubredoxin metal binding domain
       0.22   11.7   9.8        4.8    7.4   0.1    3.7  3  zf-piccolo       Piccolo Zn-finger
       0.28   11.3   9.5          1    9.5   2.1    2.9  3  DUF2318          Predicted membrane protein (DUF2318)
       0.33   11.2   6.0         38    4.6   0.1    4.0  4  zf-RING_7        C4-type zinc ribbon domain
       0.34   10.5  10.6        4.5    7.0   0.2    4.0  4  GATA             GATA zinc finger
       0.67    9.9  11.5        1.6    8.7   1.5    2.5  2  PHD              PHD-finger
       0.69    9.9  11.0       0.32   11.0   1.7    2.5  2  zinc-ribbons_6   zinc-ribbons
          1    9.1  13.1         16    5.3   2.4    4.1  3  A2L_zn_ribbon    A2L zinc ribbon domain
        1.1    9.3  11.0          3    7.9   1.0    3.1  2  zf-RING_5        zinc-RING finger domain
        1.5    9.2  14.1        7.8    7.0   2.1    3.5  2  Lar_restr_allev  Restriction alleviation protein Lar
        2.1    8.5  14.4        1.9    8.6   1.1    3.8  4  UPF0547          Uncharacterised protein family UPF0547
        2.2    8.2   9.3        1.1    9.2   1.1    2.8  2  C1_1             Phorbol esters/diacylglycerol binding domain
        4.4    7.7  10.7        6.3    7.2   6.1    2.4  2  DnaJ_CXXCXGXG    DnaJ central domain
        6.1    6.8  16.3         29    4.7   0.1    4.1  4  zf-trcl          Probable zinc-ribbon domain
        7.2    6.4  15.7          3    7.6   3.4    3.8  3  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
          9    6.9  12.1         31    5.2   0.2    3.8  4  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
        9.3    6.6  10.2         59    4.1   0.2    4.0  4  Fer4_2           4Fe-4S binding domain
        9.4    7.1  12.9         38    5.1   7.5    2.9  2  zinc_ribbon_15   zinc-ribbon family


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       1.3   6.2e+02       3       8 ..       4       9 ..       2      12 .. 0.69
   2 ?    2.6   0.1      0.27   1.2e+02      30      36 ..      19      25 ..      17      27 .. 0.73
   3 !   60.5   4.0   2.2e-19     1e-16       2      39 .]      67     104 ..      66     104 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.3
                           TFIIS_C 3 CpkCgs 8
                                     C  Cgs
  gi|336254115|ref|YP_004597222.1| 4 CDDCGS 9
                                     777775 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.27
                           TFIIS_C 30 kCtkCgh 36
                                      +Ct+Cg 
  gi|336254115|ref|YP_004597222.1| 19 VCTSCGA 25
                                      7888875 PP

  == domain 3  score: 60.5 bits;  conditional E-value: 2.2e-19
                           TFIIS_C   2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                        C +Cg +ea+++ +Qt saDEp+t+f+kCt+CghrWr
  gi|336254115|ref|YP_004597222.1|  67 VCDECGTQEAWYTLKQTASADEPPTRFFKCTECGHRWR 104
                                       6************************************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 !   31.5   1.6   2.5e-10   1.1e-07       1      35 [.       1      31 [.       1      32 [. 0.95
   2 ?    2.0   0.1      0.43     2e+02      22      29 ..      66      73 ..      57      76 .. 0.69
   3 ?    1.4   0.1      0.65     3e+02      21      28 ..      92     100 ..      85     101 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.5e-10
                                      EEBESTTTSBEEEEECSCCCEEEESSSS-EEESSC CS
                    RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepadq 35
                                      ++FC +Cg+++  ++d+ +    C +Cg+e + d 
  gi|336254115|ref|YP_004597222.1|  1 MQFCDDCGSMMKADGDRMV----CTSCGAETERDR 31
                                      9******************....*******99875 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.43
                                      EEESSSS- CS
                    RNA_POL_M_15KD 22 feCrqCgY 29
                                      + C+ Cg 
  gi|336254115|ref|YP_004597222.1| 66 VVCDECGT 73
                                      45999985 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.65
                                       E.EEESSSS CS
                    RNA_POL_M_15KD  21 n.feCrqCg 28 
                                       + f C  Cg
  gi|336254115|ref|YP_004597222.1|  92 RfFKCTECG 100
                                       457788886 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.9   5.3e-06    0.0024       2      25 ..       1      26 [.       1      27 [. 0.92
   2 !   10.7   0.5   0.00059      0.27       9      25 ..      59      74 ..      59      74 .. 0.90
   3 ?    3.4   0.4      0.12        53      18      24 ..      95     101 ..      94     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.3e-06
                       zf-ribbon_3  2 tvrCPnCGa.p.lssddnvCpyCGtk 25
                                      +++C  CG+   ++ d +vC++CG++
  gi|336254115|ref|YP_004597222.1|  1 MQFCDDCGSmMkADGDRMVCTSCGAE 26
                                      789*******88************85 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00059
                       zf-ribbon_3  9 GaplssddnvCpyCGtk 25
                                      G+p ++ d+vC  CGt+
  gi|336254115|ref|YP_004597222.1| 59 GKP-KATDVVCDECGTQ 74
                                      778.99*********96 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.12
                       zf-ribbon_3  18 vCpyCGt 24 
                                       +C+ CG+
  gi|336254115|ref|YP_004597222.1|  95 KCTECGH 101
                                       5999997 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   3.1   5.6e-06    0.0026      30      60 ..       3      31 ..       2      32 .. 0.94
   2 !   10.4   2.1    0.0011      0.49      23      56 ..      60     103 ..      55     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.6e-06
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfeadrDv 60
                                       C  Cgs +k   +g++++C++Cg+e  rD 
  gi|336254115|ref|YP_004597222.1|  3 FCDDCGSMMKA--DGDRMVCTSCGAETERDR 31
                                      5**********..****************95 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0011
                    OrfB_Zn_ribbon  23 npayTSktCseCgsknke..........alsgrtfkCpnCgfea 56 
                                       +p  T   C eCg +             ++ +r fkC++Cg+++
  gi|336254115|ref|YP_004597222.1|  60 KPKATDVVCDECGTQEAWytlkqtasadEPPTRFFKCTECGHRW 103
                                       6777889999999877666677799999999**********986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.3   3.3e-06    0.0015      13      40 ..       2      29 ..       1      33 [. 0.89
   2 !    8.7   2.7    0.0038       1.8      12      36 ..      65     101 ..      59     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.3e-06
                               DZR 13 rfCseCgtklkavaaedrCpsCgekvdp 40
                                      +fC++Cg+ +ka  +  +C sCg++++ 
  gi|336254115|ref|YP_004597222.1|  2 QFCDDCGSMMKADGDRMVCTSCGAETER 29
                                      7**********9999********98765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0038
                               DZR  12 arfCseCgtk.....lkavaa.......edrCpsCge 36 
                                       + +C+eCgt+     lk++a+         +C +Cg+
  gi|336254115|ref|YP_004597222.1|  65 DVVCDECGTQeawytLKQTASadepptrFFKCTECGH 101
                                       568******9888877655558999888888999987 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 !   16.7   2.2   1.1e-05    0.0052       6      30 ..       3      27 ..       1      34 [. 0.89
   2 !    8.9   0.2     0.003       1.4      21      28 ..      66      73 ..      57      76 .. 0.86
   3 ?    0.4   0.1       1.4   6.3e+02      23      27 ..      96     100 ..      93     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                       Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCgtpy 30
                                       C  Cg  +k + D  vC+ Cg+  
  gi|336254115|ref|YP_004597222.1|  3 FCDDCGSMMKADGDRMVCTSCGAET 27
                                      6*********************965 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.003
                       Prok-RING_1 21 VvCpeCgt 28
                                      VvC+eCgt
  gi|336254115|ref|YP_004597222.1| 66 VVCDECGT 73
                                      89*****9 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.4
                       Prok-RING_1  23 CpeCg 27 
                                       C+eCg
  gi|336254115|ref|YP_004597222.1|  96 CTECG 100
                                       77776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.088        41      14      21 ..       2       9 ..       1      16 [. 0.80
   2 !    8.0   0.1    0.0053       2.5       2       9 ..      20      27 ..      19      33 .. 0.78
   3 ?    4.7   0.1     0.056        26      12      21 ..      64      73 ..      61      74 .. 0.75
   4 ?    5.6   0.8     0.029        14       1       7 [.      95     101 ..      92     102 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.088
                     zinc_ribbon_2 14 kFCpyCGt 21
                                      +FC  CG+
  gi|336254115|ref|YP_004597222.1|  2 QFCDDCGS 9 
                                      58888885 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0053
                     zinc_ribbon_2  2 CpnCGael 9 
                                      C++CGae 
  gi|336254115|ref|YP_004597222.1| 20 CTSCGAET 27
                                      999*9985 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.056
                     zinc_ribbon_2 12 nakFCpyCGt 21
                                      +++ C +CGt
  gi|336254115|ref|YP_004597222.1| 64 TDVVCDECGT 73
                                      5677889988 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.029
                     zinc_ribbon_2   1 fCpnCGa 7  
                                       +C++CG+
  gi|336254115|ref|YP_004597222.1|  95 KCTECGH 101
                                       5666664 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 ?    1.8   1.1      0.54   2.5e+02      17      25 ..      16      24 ..       2      26 .. 0.74
   2 ?    3.3   0.1      0.17        80      17      27 ..      16      26 ..      13      33 .. 0.81
   3 !   17.2   0.4     8e-06    0.0037      19      45 ..      66     101 ..      53     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.54
                     Zn_Tnp_IS1595 17 ngfvCPhCg 25
                                      ++ vC  Cg
  gi|336254115|ref|YP_004597222.1| 16 DRMVCTSCG 24
                                      567788887 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.17
                     Zn_Tnp_IS1595 17 ngfvCPhCgsr 27
                                      ++ vC  Cg +
  gi|336254115|ref|YP_004597222.1| 16 DRMVCTSCGAE 26
                                      6799****976 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 8e-06
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayrikt........rglfqCkeCrk 45 
                                       +vC  Cg +   y++k+         + f+C eC++
  gi|336254115|ref|YP_004597222.1|  66 VVCDECGTQeAWYTLKQtasadeppTRFFKCTECGH 101
                                       89*******77788888*****************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 ?    5.3   0.2     0.031        14      21      30 ..       3      12 ..       2      17 .. 0.85
   2 !    8.4   0.7    0.0033       1.5      15      27 ..      61      73 ..      51      76 .. 0.82
   3 ?    4.6   0.1     0.049        22       1       8 [.      94     101 ..      87     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.031
                                      EESSSSBEEE CS
                      TF_Zn_Ribbon 21 vCtdCGlVle 30
                                      +C dCG+++ 
  gi|336254115|ref|YP_004597222.1|  3 FCDDCGSMMK 12
                                      5******986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0033
                                      TSTTCEEESSSSB CS
                      TF_Zn_Ribbon 15 pergelvCtdCGl 27
                                      p+ +++vC +CG+
  gi|336254115|ref|YP_004597222.1| 61 PKATDVVCDECGT 73
                                      7889********7 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.049
                                       EEETTTTC CS
                      TF_Zn_Ribbon   1 ykCPnCgs 8  
                                       +kC +Cg+
  gi|336254115|ref|YP_004597222.1|  94 FKCTECGH 101
                                       46666665 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   1.8    0.0011      0.53      72      98 ..       3      29 ..       1      42 [. 0.80
   2 !   10.4   0.8    0.0011      0.51      58      94 ..      53     101 ..      39     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                                      EETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 72 rCreCgkefeleekalrCpkCgsadve 98
                                       C++Cg+ ++ + +++ C +Cg++  +
  gi|336254115|ref|YP_004597222.1|  3 FCDDCGSMMKADGDRMVCTSCGAETER 29
                                      6*****99998887899*****98654 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0011
                                       TT-EEEEEEE--EEEETTTS-EEECHH.HHH...........S-TTTSS CS
                              HypA  58 egaeLeieevpvkvrCreCgkefelee.kal...........rCpkCgs 94 
                                       e+a++e + +   v C+eCg++    + k++           +C +Cg+
  gi|336254115|ref|YP_004597222.1|  53 EDANFEGKPKATDVVCDECGTQEAWYTlKQTasadepptrffKCTECGH 101
                                       6788888899999*******8876443322246789999999*****97 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 ?    1.7   0.0      0.45   2.1e+02      23      29 ..       3       9 ..       1      12 [. 0.60
   2 ?    5.7   0.1     0.026        12       4      12 ..      17      25 ..      14      29 .. 0.57
   3 !   10.8   0.3   0.00067      0.31      23      31 ..      67      75 ..      66      76 .. 0.93
   4 ?    2.8   0.4      0.21        94      24      30 ..      96     102 ..      93     103 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.45
                           zf-RRN7 23 yCrrCht 29
                                      +C+ C++
  gi|336254115|ref|YP_004597222.1|  3 FCDDCGS 9 
                                      4555553 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.026
                           zf-RRN7  4 gppCgvCgc 12
                                      +++C  Cg+
  gi|336254115|ref|YP_004597222.1| 17 RMVCTSCGA 25
                                      555555555 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00067
                           zf-RRN7 23 yCrrChtqe 31
                                      +C++C+tqe
  gi|336254115|ref|YP_004597222.1| 67 VCDECGTQE 75
                                      8*******8 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.21
                           zf-RRN7  24 CrrChtq 30 
                                       C++C++ 
  gi|336254115|ref|YP_004597222.1|  96 CTECGHR 102
                                       8888875 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 ?    5.3   0.4     0.042        19      23      29 ..       3       9 ..       2      14 .. 0.83
   2 ?    6.0   0.2     0.026        12       1       9 [.      17      25 ..      17      26 .. 0.89
   3 !    7.9   0.3    0.0064         3      18      29 ..      61      73 ..      51      75 .. 0.77
   4 ?    2.6   0.0       0.3   1.4e+02      17      29 ..      89     101 ..      78     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.042
                                      B-TTT-- CS
                           ADK_lid 23 lCDkCGe 29
                                      +CD+CG+
  gi|336254115|ref|YP_004597222.1|  3 FCDDCGS 9 
                                      7*****8 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.026
                                      EEE-TTT-- CS
                           ADK_lid  1 RrvCpkCGr 9 
                                      R+vC +CG+
  gi|336254115|ref|YP_004597222.1| 17 RMVCTSCGA 25
                                      999999997 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0064
                                      -S.STTB-TTT-- CS
                           ADK_lid 18 Pk.veglCDkCGe 29
                                      Pk ++ +CD+CG 
  gi|336254115|ref|YP_004597222.1| 61 PKaTDVVCDECGT 73
                                      4437889*****7 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.3
                                       --SSTTB-TTT-- CS
                           ADK_lid  17 pPkveglCDkCGe 29 
                                       pP    +C +CG 
  gi|336254115|ref|YP_004597222.1|  89 PPTRFFKCTECGH 101
                                       7777779999995 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.59   2.7e+02      22      27 ..       4       9 ..       3      10 .. 0.85
   2 ?    7.4   0.1    0.0095       4.4      15      28 ..      13      26 ..      13      28 .. 0.89
   3 ?    5.7   0.3     0.032        15      21      28 ..      67      74 ..      65      74 .. 0.89
   4 ?    4.4   0.1      0.08        37      22      29 ..      96     103 ..      90     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.59
                    PhnA_Zn_Ribbon 22 CpeCah 27
                                      C++C++
  gi|336254115|ref|YP_004597222.1|  4 CDDCGS 9 
                                      999986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0095
                    PhnA_Zn_Ribbon 15 edgallvCpeCahE 28
                                      +dg+ +vC  C+ E
  gi|336254115|ref|YP_004597222.1| 13 ADGDRMVCTSCGAE 26
                                      6999*******987 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.032
                    PhnA_Zn_Ribbon 21 vCpeCahE 28
                                      vC+eC+ +
  gi|336254115|ref|YP_004597222.1| 67 VCDECGTQ 74
                                      9****987 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.08
                    PhnA_Zn_Ribbon  22 CpeCahEw 29 
                                       C eC+h w
  gi|336254115|ref|YP_004597222.1|  96 CTECGHRW 103
                                       99****98 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.9      0.23   1.1e+02      19      32 ..      11      24 ..       7      26 .. 0.68
   2 ?    4.5   0.1      0.07        32      25      33 ..      65      73 ..      60      77 .. 0.60
   3 ?   10.7   0.3   0.00085      0.39      26      36 .]      94     104 ..      86     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.23
                     zinc_ribbon_4 19 lpakgvkvrCskCg 32
                                      ++a+g ++ C+ Cg
  gi|336254115|ref|YP_004597222.1| 11 MKADGDRMVCTSCG 24
                                      56666677788887 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.07
                     zinc_ribbon_4 25 kvrCskCgh 33
                                       v C  Cg+
  gi|336254115|ref|YP_004597222.1| 65 DVVCDECGT 73
                                      455555554 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00085
                     zinc_ribbon_4  26 vrCskCghvFr 36 
                                        +C+ Cgh +r
  gi|336254115|ref|YP_004597222.1|  94 FKCTECGHRWR 104
                                       69********7 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.3    0.0008      0.37     147     177 ..       2      32 ..       1      41 [. 0.86
   2 ?    6.6   0.2     0.012       5.7      61     111 ..      53     101 ..      33     104 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0008
                           TackOD1 147 ykCnsCkslfsepevkarClsCekesesddl 177
                                       + C++C+s+++    +++C+sC++e+e d+ 
  gi|336254115|ref|YP_004597222.1|   2 QFCDDCGSMMKADGDRMVCTSCGAETERDRE 32 
                                       67*********************99998875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                           TackOD1  61 krglleeelvdrirlCpsCksghlnvrevCpkCkSidieeqelihhftCgn 111
                                       ++  +e +   + ++C++C +++  ++   ++  S+d   + ++++ +Cg+
  gi|336254115|ref|YP_004597222.1|  53 EDANFEGKPKATDVVCDECGTQEAWYTL--KQTASADEPPTRFFKCTECGH 101
                                       4445566777777889999888776655..688899999999999999997 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   2.9    0.0019      0.88       8      38 ..       4      29 ..       2      31 .. 0.76
   2 ?    4.9   0.4     0.062        28      26      34 ..      65      73 ..      49      77 .. 0.70
   3 ?    7.1   0.7     0.013       5.9       6      14 ..      94     102 ..      90     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0019
                       Zn-ribbon_8  8 CeeCghefevlqsis.dapltaCPeCgsevrr 38
                                      C++Cg     ++  + d +  +C +Cg+e++r
  gi|336254115|ref|YP_004597222.1|  4 CDDCG----SMM--KaDGDRMVCTSCGAETER 29
                                      99999....343..33566778******9998 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.062
                       Zn-ribbon_8 26 ltaCPeCgs 34
                                      +++C eCg 
  gi|336254115|ref|YP_004597222.1| 65 DVVCDECGT 73
                                      556777776 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.013
                       Zn-ribbon_8   6 YrCeeCghe 14 
                                       ++C+eCgh+
  gi|336254115|ref|YP_004597222.1|  94 FKCTECGHR 102
                                       89*****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 ?   11.3   2.7   0.00055      0.25       2      29 ..       3      24 ..       2      25 .. 0.83
   2 ?    8.4   0.4    0.0042         2       3      18 ..      20      35 ..      18      36 .. 0.88
   3 ?    3.5   0.5      0.15        68      24      30 ..      67      73 ..      66      75 .. 0.79
   4 ?    4.0   0.3       0.1        47       3       9 ..      96     102 ..      92     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00055
                                      B-TTT--B-EEE--TT-SS-EEEETTTT CS
                         Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCg 29
                                      FC  CG+ ++          R vC++Cg
  gi|336254115|ref|YP_004597222.1|  3 FCDDCGSMMKADG------DRMVCTSCG 24
                                      9******987644......49******9 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0042
                                      -TTT--B-EEE--TT- CS
                         Nudix_N_2  3 CsqCGtpvelripdgD 18
                                      C++CG+++e+  +++D
  gi|336254115|ref|YP_004597222.1| 20 CTSCGAETERDREQED 35
                                      9999999999998887 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.15
                                      EETTTTE CS
                         Nudix_N_2 24 vCpaCgt 30
                                      vC+ Cgt
  gi|336254115|ref|YP_004597222.1| 67 VCDECGT 73
                                      7888886 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.1
                                       -TTT--B CS
                         Nudix_N_2   3 CsqCGtp 9  
                                       C++CG++
  gi|336254115|ref|YP_004597222.1|  96 CTECGHR 102
                                       8888886 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3     0.044        20      16      24 ..       4      12 ..       1      14 [. 0.88
   2 ?    5.4   0.1     0.038        18      15      24 ..      19      28 ..      17      40 .. 0.69
   3 ?    2.9   0.4      0.24   1.1e+02      15      21 ..      67      73 ..      65      74 .. 0.84
   4 ?    5.3   0.1     0.042        19      15      21 ..      95     101 ..      92     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.044
                              YhfH 16 CteCGkeie 24
                                      C +CG++++
  gi|336254115|ref|YP_004597222.1|  4 CDDCGSMMK 12
                                      ******996 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.038
                              YhfH 15 kCteCGkeie 24
                                      +Ct+CG e e
  gi|336254115|ref|YP_004597222.1| 19 VCTSCGAETE 28
                                      6*****9876 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.24
                              YhfH 15 kCteCGk 21
                                      +C eCG 
  gi|336254115|ref|YP_004597222.1| 67 VCDECGT 73
                                      59***96 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.042
                              YhfH  15 kCteCGk 21 
                                       kCteCG 
  gi|336254115|ref|YP_004597222.1|  95 KCTECGH 101
                                       7*****6 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 ?    6.3   1.8     0.022        10       4      26 .]       4      23 ..       4      23 .. 0.78
   2 ?    3.4   0.9      0.18        81       4       8 ..      20      24 ..      18      27 .. 0.60
   3 ?    2.5   0.3      0.34   1.6e+02       4       9 ..      68      73 ..      66      74 .. 0.83
   4 ?    6.8   0.3     0.016       7.2       1       9 [.      93     101 ..      93     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.022
                            zf-ACC  4 CpsCgemlykkeLernlyVCPkC 26
                                      C+ Cg+m+ +   + + +VC++C
  gi|336254115|ref|YP_004597222.1|  4 CDDCGSMMKA---DGDRMVCTSC 23
                                      9999999987...4677788877 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.18
                            zf-ACC  4 CpsCg 8 
                                      C+sCg
  gi|336254115|ref|YP_004597222.1| 20 CTSCG 24
                                      55555 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.34
                            zf-ACC  4 CpsCge 9 
                                      C++Cg+
  gi|336254115|ref|YP_004597222.1| 68 CDECGT 73
                                      999997 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.016
                            zf-ACC   1 WtKCpsCge 9  
                                       ++KC++Cg+
  gi|336254115|ref|YP_004597222.1|  93 FFKCTECGH 101
                                       79*****95 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0025       1.1       3      15 ..       2      14 ..       1      18 [. 0.82
   2 ?    2.4   0.5      0.27   1.2e+02       3      18 ..      18      33 ..      16      34 .. 0.75
   3 ?    5.9   0.3     0.022       9.9       2      10 ..      65      73 ..      64      74 .. 0.83
   4 ?    4.3   0.3     0.068        31       3      11 ..      94     102 ..      92     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0025
                            zf_UBZ  3 ylCerCgkeipes 15
                                      ++C++Cg+++  +
  gi|336254115|ref|YP_004597222.1|  2 QFCDDCGSMMKAD 14
                                      69*******9876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.27
                            zf_UBZ  3 ylCerCgkeipeselq 18
                                       +C  Cg+e + +  q
  gi|336254115|ref|YP_004597222.1| 18 MVCTSCGAETERDREQ 33
                                      68*****998777555 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.022
                            zf_UBZ  2 tylCerCgk 10
                                       ++C++Cg+
  gi|336254115|ref|YP_004597222.1| 65 DVVCDECGT 73
                                      589****97 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.068
                            zf_UBZ   3 ylCerCgke 11 
                                       + C +Cg++
  gi|336254115|ref|YP_004597222.1|  94 FKCTECGHR 102
                                       89*****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 ?    3.2   2.6      0.16        74       3      25 ..       4      25 ..       3      27 .. 0.77
   2 ?    2.8   0.2      0.21        98       3      11 ..      20      28 ..      18      34 .. 0.71
   3 ?    3.0   0.1      0.18        83      18      25 ..      66      73 ..      60      74 .. 0.75
   4 ?   10.4   0.2   0.00085      0.39      19      26 ..      95     102 ..      89     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.16
                                      -SSS--B----SSS----SSS-- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCGh 25
                                      C +Cg+ ++   gd   C+ CG 
  gi|336254115|ref|YP_004597222.1|  4 CDDCGSMMKA-DGDRMVCTSCGA 25
                                      8888888774.577888999995 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.21
                                      -SSS--B-- CS
                    DNA_RNApol_7kD  3 CgeCgaevs 11
                                      C  Cgae++
  gi|336254115|ref|YP_004597222.1| 20 CTSCGAETE 28
                                      788888776 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.18
                                      ---SSS-- CS
                    DNA_RNApol_7kD 18 iRCkeCGh 25
                                      + C eCG 
  gi|336254115|ref|YP_004597222.1| 66 VVCDECGT 73
                                      55999995 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00085
                                       --SSS--- CS
                    DNA_RNApol_7kD  19 RCkeCGhR 26 
                                       +C+eCGhR
  gi|336254115|ref|YP_004597222.1|  95 KCTECGHR 102
                                       8******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 ?    2.7   0.1      0.23   1.1e+02       3       8 ..       4       9 ..       3      12 .. 0.75
   2 ?    5.5   0.4     0.032        14       2      11 ..      19      28 ..      19      29 .. 0.84
   3 ?    6.2   0.1     0.018       8.4       2      10 ..      67      75 ..      67      81 .. 0.85
   4 ?    5.3   1.0     0.036        17       1       9 [.      94     102 ..      94     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.23
                      Rubredoxin_2 3 CsqCGf 8
                                     C++CG+
  gi|336254115|ref|YP_004597222.1| 4 CDDCGS 9
                                     888886 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.032
                      Rubredoxin_2  2 vCsqCGfesa 11
                                      vC +CG+e+ 
  gi|336254115|ref|YP_004597222.1| 19 VCTSCGAETE 28
                                      7*****9985 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.018
                      Rubredoxin_2  2 vCsqCGfes 10
                                      vC++CG + 
  gi|336254115|ref|YP_004597222.1| 67 VCDECGTQE 75
                                      7*****986 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.036
                      Rubredoxin_2   1 YvCsqCGfe 9  
                                       + C +CG++
  gi|336254115|ref|YP_004597222.1|  94 FKCTECGHR 102
                                       78*****86 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.4     0.069        32      27      44 ..      16      33 ..       1      45 [. 0.68
   2 ?    7.4   0.1      0.01       4.8      12      35 ..      49      72 ..      43      82 .. 0.87
   3 ?    3.2   0.1      0.21        98      15      27 ..      87     100 ..      78     103 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.069
                        zf-piccolo 27 kkqvCnlCGFnptphlte 44
                                       ++vC  CG + + + ++
  gi|336254115|ref|YP_004597222.1| 16 DRMVCTSCGAETERDREQ 33
                                      578999999666555444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.01
                        zf-piccolo 12 vgskeppnyntCteCkkqvCnlCG 35
                                      ++s+e +n++   +   +vC  CG
  gi|336254115|ref|YP_004597222.1| 49 IESSEDANFEGKPKATDVVCDECG 72
                                      5689999***999*********** PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.21
                        zf-piccolo  15 kep.pnyntCteCk 27 
                                       +ep + + +CteC 
  gi|336254115|ref|YP_004597222.1|  87 DEPpTRFFKCTECG 100
                                       333257889****6 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.1    0.0022         1      35      64 ..       2      30 ..       1      36 [. 0.81
   2 ?    5.2   0.1     0.048        22      48      68 ..      62      82 ..      39      91 .. 0.79
   3 ?    1.0   1.0         1   4.7e+02      74      74 ..      88      88 ..      67     106 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0022
                           DUF2318 35 daCevCekkgYvqegeelvCknCgvrfald 64
                                      + C+ C+++  + +g+++vC++Cg + + d
  gi|336254115|ref|YP_004597222.1|  2 QFCDDCGSM-MKADGDRMVCTSCGAETERD 30
                                      579999765.5799**********988766 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.048
                           DUF2318 48 egeelvCknCgvrfaldsige 68
                                      +  ++vC +Cg++ a  ++++
  gi|336254115|ref|YP_004597222.1| 62 KATDVVCDECGTQEAWYTLKQ 82
                                      56789*****99877777764 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1
                           DUF2318 74 n 74
                                      +
  gi|336254115|ref|YP_004597222.1| 88 E 88
                                      0 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 ?    4.6   0.1     0.083        38      25      32 ..       3      10 ..       1      11 [. 0.85
   2 ?    0.6   0.1       1.5   6.9e+02      25      30 ..      19      24 ..      12      25 .. 0.76
   3 ?    4.1   0.1      0.12        53      24      30 ..      66      72 ..      59      73 .. 0.86
   4 ?    2.2   0.0      0.45   2.1e+02      23      30 ..      93     100 ..      77     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.083
                                      E-TTT--E CS
                         zf-RING_7 25 tCpeCGRI 32
                                      +C+ CG +
  gi|336254115|ref|YP_004597222.1|  3 FCDDCGSM 10
                                      8*****87 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.5
                                      E-TTT- CS
                         zf-RING_7 25 tCpeCG 30
                                       C +CG
  gi|336254115|ref|YP_004597222.1| 19 VCTSCG 24
                                      588888 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.12
                                      EE-TTT- CS
                         zf-RING_7 24 vtCpeCG 30
                                      v C+eCG
  gi|336254115|ref|YP_004597222.1| 66 VVCDECG 72
                                      67****9 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.45
                                       -EE-TTT- CS
                         zf-RING_7  23 vvtCpeCG 30 
                                        ++C eCG
  gi|336254115|ref|YP_004597222.1|  93 FFKCTECG 100
                                       589****9 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.28   1.3e+02      23      32 ..       4      13 ..       2      17 .. 0.80
   2 ?    7.0   0.2    0.0098       4.5      17      27 ..      14      24 ..      11      29 .. 0.89
   3 ?    2.9   0.0      0.18        82      22      28 ..      67      73 ..      58      81 .. 0.67
   4 ?    3.8   1.0     0.098        45      23      32 ..      96     105 ..      95     107 .] 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.28
                              GATA 23 CnaCGlyykk 32
                                      C +CG ++k 
  gi|336254115|ref|YP_004597222.1|  4 CDDCGSMMKA 13
                                      999**99886 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0098
                              GATA 17 dgnksLCnaCG 27
                                      dg +++C++CG
  gi|336254115|ref|YP_004597222.1| 14 DGDRMVCTSCG 24
                                      8999******9 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.18
                              GATA 22 LCnaCGl 28
                                      +C  CG+
  gi|336254115|ref|YP_004597222.1| 67 VCDECGT 73
                                      6777775 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.098
                              GATA  23 CnaCGlyykk 32 
                                       C+ CG +++ 
  gi|336254115|ref|YP_004597222.1|  96 CTECGHRWRG 105
                                       999****995 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.8     0.024        11       1      22 [.       3      24 ..       3      27 .. 0.89
   2 ?    8.7   1.5    0.0035       1.6      14      50 ..      64     100 ..      55     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.024
                                      SBTTTTSTTSTTSCEEEETTTS CS
                               PHD  1 rCavCkkksdeeeelvqCdgCk 22
                                      +C+ C++  +++++ ++C +C+
  gi|336254115|ref|YP_004597222.1|  3 FCDDCGSMMKADGDRMVCTSCG 24
                                      6999***888999********7 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0035
                                       CEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTH CS
                               PHD  14 elvqCdgCkrwfHqkClkppleseekpegewlCekCk 50 
                                       + v+Cd+C++    + lk + + +e p++ + C++C 
  gi|336254115|ref|YP_004597222.1|  64 TDVVCDECGTQEAWYTLKQTASADEPPTRFFKCTECG 100
                                       5589******************99999999******5 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.7   0.00071      0.32       3      28 ..       4      29 ..       2      35 .. 0.89
   2 ?    3.5   2.2      0.16        73       2      24 ..      67     101 ..      66     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00071
                                      -SSS-S--EE-SSEEE-TTT--EEEE CS
                    zinc-ribbons_6  3 CpeCqqelekrgeqyhCeaCqedlkk 28
                                      C +C + ++ +g+++ C +C ++ ++
  gi|336254115|ref|YP_004597222.1|  4 CDDCGSMMKADGDRMVCTSCGAETER 29
                                      ********************998765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.16
                                       --SSS-S--EE-S............SEEE-TTT-- CS
                    zinc-ribbons_6   2 kCpeCqqelekrg............eqyhCeaCqe 24 
                                        C eC ++  + +            + ++C +C +
  gi|336254115|ref|YP_004597222.1|  67 VCDECGTQEAWYTlkqtasadepptRFFKCTECGH 101
                                       59999999988887777777777766677777765 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 ?    5.3   2.4     0.035        16      18      31 ..      14      27 ..       4      28 .. 0.75
   2 ?    4.1   0.1     0.087        40      22      29 ..      66      73 ..      62      76 .. 0.75
   3 ?    2.0   0.6       0.4   1.8e+02       5      11 ..      95     101 ..      94     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.035
                     A2L_zn_ribbon 18 eqgylvCieCgasf 31
                                      + + +vC  Cga++
  gi|336254115|ref|YP_004597222.1| 14 DGDRMVCTSCGAET 27
                                      45679******986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.087
                     A2L_zn_ribbon 22 lvCieCga 29
                                       vC eCg+
  gi|336254115|ref|YP_004597222.1| 66 VVCDECGT 73
                                      58888886 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.4
                     A2L_zn_ribbon   5 vCsvCgg 11 
                                       +C+ Cg+
  gi|336254115|ref|YP_004597222.1|  95 KCTECGH 101
                                       7999988 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.0    0.0066         3      24      43 ..       3      24 ..       2      25 .. 0.92
   2 ?    4.0   3.1       0.1        48      24      43 ..      67     100 ..      64     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0066
                         zf-RING_5 24 fCekClkkll..ekeavCpiCr 43
                                      fC++C +  +  + + vC+ C+
  gi|336254115|ref|YP_004597222.1|  3 FCDDCGSMMKadGDRMVCTSCG 24
                                      9*********999*******97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.1
                         zf-RING_5  24 fCekClkkll..............ekeavCpiCr 43 
                                       +C++C +++               ++ ++C+ C+
  gi|336254115|ref|YP_004597222.1|  67 VCDECGTQEAwytlkqtasadeppTRFFKCTECG 100
                                       6888877777777777777777776667777765 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 ?    5.0   4.4     0.067        31       8      42 ..       3      36 ..       2      55 .. 0.59
   2 ?    7.0   2.1     0.017       7.8       6      35 ..      68     100 ..      43     106 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.067
                   Lar_restr_allev  8 fCggravlersqrvvaeigqcvyCadCga.....stpwfk 42
                                      fC   + + ++ +        + C+ Cga      +++  
  gi|336254115|ref|YP_004597222.1|  3 FCDDCGSMMKADGD------RMVCTSCGAeterdREQEDA 36
                                      56666666666333......57899****55555333333 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.017
                   Lar_restr_allev   6 CPfCggravlersqrvvaeigq...cvyCadCg 35 
                                       C+ Cg ++ + + +++++  ++   ++ C++Cg
  gi|336254115|ref|YP_004597222.1|  68 CDECGTQEAWYTLKQTASADEPptrFFKCTECG 100
                                       555555555444444444444455556666565 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2      0.09        41      14      21 ..       1       8 [.       1       8 [. 0.95
   2 ?   -1.1   0.2       4.6   2.1e+03      17      21 ..      20      24 ..      18      26 .. 0.68
   3 ?    3.5   0.1      0.17        78      16      22 ..      67      73 ..      65      74 .. 0.81
   4 ?    8.6   1.1    0.0042       1.9      16      24 ..      95     103 ..      92     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.09
                           UPF0547 14 aqfCphCG 21
                                      +qfC +CG
  gi|336254115|ref|YP_004597222.1|  1 MQFCDDCG 8 
                                      89*****9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.6
                           UPF0547 17 CphCG 21
                                      C  CG
  gi|336254115|ref|YP_004597222.1| 20 CTSCG 24
                                      76677 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.17
                           UPF0547 16 fCphCGy 22
                                      +C +CG+
  gi|336254115|ref|YP_004597222.1| 67 VCDECGT 73
                                      6999998 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0042
                           UPF0547  16 fCphCGyvF 24 
                                       +C +CG+++
  gi|336254115|ref|YP_004597222.1|  95 KCTECGHRW 103
                                       7*******9 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 ?    9.2   1.1    0.0025       1.1      12      36 ..       2      25 ..       1      29 [. 0.85
   2 ?    2.7   1.6      0.26   1.2e+02      14      35 ..      68     100 ..      56     103 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0025
                                      -B-TTT-SB--SSSS-EEEETTT-- CS
                              C1_1 12 tfCkhCgeflwgkekqglkCswCkl 36
                                      +fC+ Cg+++ +     + C+ C+ 
  gi|336254115|ref|YP_004597222.1|  2 QFCDDCGSMM-KADGDRMVCTSCGA 25
                                      79********.77778899999975 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.26
                                       -TTT-SB-...........-SSSS-EEEETTT- CS
                              C1_1  14 CkhCgefl...........wgkekqglkCswCk 35 
                                       C++Cg +             +  ++ +kC++C+
  gi|336254115|ref|YP_004597222.1|  68 CDECGTQEawytlkqtasaDEPPTRFFKCTECG 100
                                       666666655555555555333556778888886 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.1     0.014       6.3       1      64 [.       4      72 ..       4      75 .. 0.56
   2 ?    2.3   2.5      0.47   2.2e+02      12      30 ..      63      82 ..      52     103 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.014
                     DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkGsGvvreeqkt.lgpfvqqsqs....tCpeCeGtGkvikekdkCkkCk 64
                                      C++C    +++g++  C++C+ + +  +eq+  + ++ +q+      + ++ + +Gk  +++  C++C 
  gi|336254115|ref|YP_004597222.1|  4 CDDCGSMMKADGDRMVCTSCGAETERDREQEDaFVTTESQTDDdvieSSEDANFEGKPKATDVVCDECG 72
                                      999*888887899999*****999654444422322222221111114444445555443344677775 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.47
                     DnaJ_CXXCXGXG 12 gkkktCktCkGsGv.vreeq 30
                                      ++   C++C+ +    + +q
  gi|336254115|ref|YP_004597222.1| 63 ATDVVCDECGTQEAwYTLKQ 82
                                      33455777766653123333 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2      0.65     3e+02       7      12 ..       4       9 ..       2      11 .. 0.84
   2 ?    4.7   0.1     0.062        29       5      13 ..      18      26 ..      15      37 .. 0.89
   3 ?    3.0   6.6      0.21        97       5      22 ..      66      83 ..      63      99 .. 0.81
   4 ?    1.8   0.6       0.5   2.3e+02       5      12 ..      94     101 ..      90     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.65
                           zf-trcl  7 CkdCga 12
                                      C dCg+
  gi|336254115|ref|YP_004597222.1|  4 CDDCGS 9 
                                      ****97 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.062
                           zf-trcl  5 ltCkdCgae 13
                                      ++C++Cgae
  gi|336254115|ref|YP_004597222.1| 18 MVCTSCGAE 26
                                      79*****98 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.21
                           zf-trcl  5 ltCkdCgaefvFtageQe 22
                                      ++C +Cg+++ ++   Q 
  gi|336254115|ref|YP_004597222.1| 66 VVCDECGTQEAWYTLKQT 83
                                      69**********988775 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.5
                           zf-trcl   5 ltCkdCga 12 
                                       ++C++Cg 
  gi|336254115|ref|YP_004597222.1|  94 FKCTECGH 101
                                       78999996 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 ?    7.6   3.4    0.0064         3       4      30 ..       2      26 ..       1      27 [. 0.70
   2 ?    2.6   0.2      0.24   1.1e+02      23      29 ..      67      73 ..      65      75 .. 0.86
   3 ?    2.4   0.6      0.28   1.3e+02      24      30 ..      96     102 ..      95     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0064
                     zf-NADH-PPase  4 rFCgrCGaptepaeggwarvCpaCgle 30
                                      +FC  CG+  +++++g  +vC +Cg+e
  gi|336254115|ref|YP_004597222.1|  2 QFCDDCGS--MMKADGDRMVCTSCGAE 26
                                      56666776..34455557*******98 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.24
                     zf-NADH-PPase 23 vCpaCgl 29
                                      vC+ Cg+
  gi|336254115|ref|YP_004597222.1| 67 VCDECGT 73
                                      9****98 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.28
                     zf-NADH-PPase  24 CpaCgle 30 
                                       C  Cg++
  gi|336254115|ref|YP_004597222.1|  96 CTECGHR 102
                                       99***97 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 ?    5.2   0.4     0.067        31       7      17 ..       3      13 ..       1      17 [. 0.86
   2 ?    1.0   0.4       1.4   6.2e+02       5      13 ..      17      25 ..      15      33 .. 0.83
   3 ?    1.4   0.0         1   4.8e+02       6      13 ..      66      73 ..      65      83 .. 0.88
   4 ?    5.2   0.2     0.067        31       6      17 ..      94     105 ..      91     107 .] 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.067
                   Zn_ribbon_recom  7 rCgeCGspmtr 17
                                      +C +CGs m+ 
  gi|336254115|ref|YP_004597222.1|  3 FCDDCGSMMKA 13
                                      8******9986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.4
                   Zn_ribbon_recom  5 llrCgeCGs 13
                                       ++C  CG+
  gi|336254115|ref|YP_004597222.1| 17 RMVCTSCGA 25
                                      589*****8 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1
                   Zn_ribbon_recom  6 lrCgeCGs 13
                                      ++C eCG 
  gi|336254115|ref|YP_004597222.1| 66 VVCDECGT 73
                                      69****96 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.067
                   Zn_ribbon_recom   6 lrCgeCGspmtr 17 
                                        +C eCG++ ++
  gi|336254115|ref|YP_004597222.1|  94 FKCTECGHRWRG 105
                                       79******9875 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.95   4.4e+02       9      14 ..       3       8 ..       1       9 [. 0.81
   2 ?    4.1   0.2      0.13        59       8      15 ..      18      25 ..      11      25 .. 0.80
   3 ?    1.8   0.2      0.66     3e+02       9      15 ..      67      73 ..      62      73 .. 0.84
   4 ?    3.5   0.1      0.19        89       9      14 ..      95     100 ..      87     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.95
                            Fer4_2  9 rCigCg 14
                                       C  Cg
  gi|336254115|ref|YP_004597222.1|  3 FCDDCG 8 
                                      7****9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.13
                            Fer4_2  8 drCigCga 15
                                        C++Cga
  gi|336254115|ref|YP_004597222.1| 18 MVCTSCGA 25
                                      48****95 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.66
                            Fer4_2  9 rCigCga 15
                                       C +Cg+
  gi|336254115|ref|YP_004597222.1| 67 VCDECGT 73
                                      59***95 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.19
                            Fer4_2   9 rCigCg 14 
                                       +C++Cg
  gi|336254115|ref|YP_004597222.1|  95 KCTECG 100
                                       7****9 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   2.9      0.11        52      40      74 ..       4      26 ..       1      33 [. 0.52
   2 ?    5.1   7.5     0.082        38      36      74 ..      16      74 ..      10     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.11
                    zinc_ribbon_15 40 cskCkslleaskelgkeiekkessekkeCknCgke 74
                                      c++C+s+++a+             + ++C +Cg+e
  gi|336254115|ref|YP_004597222.1|  4 CDDCGSMMKADG------------DRMVCTSCGAE 26
                                      444444444444............34555555555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.082
                    zinc_ribbon_15 36 pylacskCkslleaskelgkeiekkesse....................kkeCknCgke 74
                                        ++c++C++  e ++e+++++ ++es++                      +C++Cg++
  gi|336254115|ref|YP_004597222.1| 16 DRMVCTSCGAETERDREQEDAFVTTESQTdddviessedanfegkpkatDVVCDECGTQ 74
                                      5689************9999999998888899**************999999*999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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):              39  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 690.35
//
Query:       gi|336254116|ref|YP_004597223.1|  [L=259]
Description: blue (type 1) copper domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-07   29.6   0.0    1.5e-06   28.6   0.0    1.5  1  Copper-bind  Copper binding proteins, plastocyanin/azurin fam
      0.008   16.0   2.6      0.014   15.2   2.6    1.4  1  TAT_signal   TAT (twin-arginine translocation) pathway signal


Domain annotation for each model (and alignments):
>> 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 !   28.6   0.0   1.6e-10   1.5e-06      12      98 ..      99     184 ..      95     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.6e-10
                                       SEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTT CS
                       Copper-bind  12 lqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHa 88 
                                       ++Fe+  ++v++g+ v f    +  H v   + ++  +    +  +  +  + g+G     +fd++g Y++ C+PH 
  gi|336254116|ref|YP_004597223.1|  99 FVFEPTGLHVEPGDVVRFDL-VAPDHTVTAYHPSLGRQRRVPEGVPAFSSPVLGQGTFWLYRFDQPGVYDVLCAPHE 174
                                       78999999999999999976.7888998888866655555555555558889************************* PP

                                       TTTSEEEEEE CS
                       Copper-bind  89 aagMkgkvtv 98 
                                         gM+g ++v
  gi|336254116|ref|YP_004597223.1| 175 IFGMVGRIVV 184
                                       ********98 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.6   1.6e-06     0.014       2      26 .]       1      25 [.       1      25 [. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaaa 26
                                      ++RR+ LK+++++    +++g++aa
  gi|336254116|ref|YP_004597223.1|  1 MDRRQVLKAAGVTSTVSLAAGLGAA 25
                                      79**************999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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 0.21s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1974.04
//
Query:       gi|336254117|ref|YP_004597224.1|  [L=137]
Description: hypothetical protein Halxa_2728 [Halopiger xanaduensis SH-6]
Scores for complete 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-17   63.7  35.2    1.8e-17   63.5  35.2    1.0  1  DUF5518          Family of unknown function (DUF5518)
  ------ inclusion threshold ------
       0.19   11.5  18.8      0.023   14.5   5.9    2.1  2  DUF4013          Protein of unknown function (DUF4013)
        1.2    9.1  23.6        1.1    9.2   0.7    3.8  4  Rick_17kDa_Anti  Glycine zipper 2TM domain


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5  35.2   3.1e-21   1.8e-17       3     118 .]      30     133 ..      28     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 3.1e-21
                           DUF5518   3 aaliGavvaivlslllglllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllvlllglvaai 79 
                                       +al+G+vv ivls+++g          + +vgG++aGyl+ggd +dg+++GalaGl++ +p+++++l++++  + + 
  gi|336254117|ref|YP_004597224.1|  30 NALVGGVVGIVLSFIPG----------SAFVGGALAGYLEGGDGGDGLRVGALAGLVMLVPMVLFWLFAMT--MVLG 94 
                                       89***************..........***********************************888888885..5567 PP

                           DUF5518  80 gglagfvallvalllvvllllvvllvilgaiGGaiGgll 118
                                       +g+ g+  ++++++++vl++lv+++++l+++G+++Gg+l
  gi|336254117|ref|YP_004597224.1|  95 AGMPGMPGTMGGFVFAVLAFLVLFTLGLSVVGAVVGGVL 133
                                       888888888999999999******************986 PP

>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   5.9   3.9e-06     0.023      29     110 ..      17      91 ..      11      93 .. 0.74
   2 ?    7.7  14.3   0.00049       2.9      45     107 ..      64     124 ..      59     134 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-06
                           DUF4013  29 rgddelPefddwgkllvdGlkafvvslvYllipliialltllvalaslaagdsaagallvlallglllalllvllll 105
                                       ++dd+ P ++   + lv G+    v++v+++ip      ++++ala++++g +++ +l v+al gl++++ +vl++l
  gi|336254117|ref|YP_004597224.1|  17 DKDDSSPGWNTSVNALVGGV----VGIVLSFIPGSA---FVGGALAGYLEGGDGGDGLRVGALAGLVMLVPMVLFWL 86 
                                       67888999998788888887....555555666666...55999999999999999999999999999998666666 PP

                           DUF4013 106 llfgl 110
                                       +++++
  gi|336254117|ref|YP_004597224.1|  87 FAMTM 91 
                                       64443 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00049
                           DUF4013  45 vdGlka.fvvslvYllipliialltllvalaslaagdsaagallvlallglllalllvllllll 107
                                        dGl++ ++ +lv+ l+p+++  + l+++++ l ag+ ++ ++++++++++l++l+l+ l+l +
  gi|336254117|ref|YP_004597224.1|  64 GDGLRVgALAGLVM-LVPMVL--FWLFAMTMVLGAGMPGMPGTMGGFVFAVLAFLVLFTLGLSV 124
                                       59***889999**5.5*****..33333333333333333444444444444444433333332 PP

>> Rick_17kDa_Anti  Glycine zipper 2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00042       2.5      20      36 ..      24      40 ..      19      42 .. 0.81
   2 ?    1.3   9.0     0.053   3.2e+02       7      30 ..      48      74 ..      46      77 .. 0.69
   3 ?   -3.6   0.1       1.8   1.1e+04      13      15 ..      93      95 ..      92      99 .. 0.46
   4 ?    9.2   0.7   0.00018       1.1       4      14 ..     124     134 ..     122     137 .] 0.67

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00042
                   Rick_17kDa_Anti 20 gggrvlGavvGAaaGav 36
                                      g+++++ a+vG+++G v
  gi|336254117|ref|YP_004597224.1| 24 GWNTSVNALVGGVVGIV 40
                                      68888999999999966 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.053
                   Rick_17kDa_Anti  7 AaaGgvaGaai.gg..gggrvlGavvG 30
                                      A +Gg++ + + gg  g+g ++Ga++G
  gi|336254117|ref|YP_004597224.1| 48 AFVGGALAGYLeGGdgGDGLRVGALAG 74
                                      789999999997775555555555555 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.8
                   Rick_17kDa_Anti 13 aGa 15
                                      +Ga
  gi|336254117|ref|YP_004597224.1| 93 LGA 95
                                      333 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.00018
                   Rick_17kDa_Anti   4 liGAaaGgvaG 14 
                                       ++GA++Ggv+ 
  gi|336254117|ref|YP_004597224.1| 124 VVGAVVGGVLA 134
                                       67777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 993.01
//
Query:       gi|336254118|ref|YP_004597225.1|  [L=457]
Description: DNA polymerase IV [Halopiger xanaduensis SH-6]
Scores for 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  130.1   0.0    1.1e-37  129.4   0.0    1.4  1  IMS              impB/mucB/samB family
    1.3e-13   51.7   0.0    1.6e-12   48.2   0.0    2.3  2  IMS_C            impB/mucB/samB family C-terminal domain
    1.5e-05   25.0   0.0    3.5e-05   23.9   0.0    1.6  1  IMS_HHH          IMS family HHH motif
     0.0036   17.9   0.0      0.016   15.8   0.0    2.1  1  HHH_5            Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.025   14.4   0.0      0.055   13.3   0.0    1.5  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
      0.035   14.3   0.0      0.079   13.2   0.0    1.6  1  Cdd1             Pathogenicity locus


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 !  129.4   0.0   3.6e-41   1.1e-37       1     150 []      23     192 ..      23     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 3.6e-41
                                       EEETTHHHHHHHHHT.T-TTS-EEEEET.......TEEEEE-HHHHTTT--TTSBHHHHHTTHTT-EEE........ CS
                               IMS   1 iDmdaFyasverardpeLkgkPvvvaqgsek...rgiviavsyeArayGvkrgmrikeakklcpdlivv........ 66 
                                       +D d+Fyas+er+rdpeL+g+Pvvv+ g e     g v+++syeAr++Gv+++++i+ a++  p    +        
  gi|336254118|ref|YP_004597225.1|  23 VDADCFYASCERLRDPELRGEPVVVGMGYEPgetVGAVATASYEAREFGVESAQAISTALERLPRRAALdpdvedhd 99 
                                       79**************************99988899****************************8555559999999 PP

                                       ............EEE-HHHHHHHHHHHHHHHHH-S..EEEEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH- CS
                               IMS  67 ............kvdlekyrraskkileilkrfispkvekasiDEayldltgleelaesegaalakelrkaikeelg 131
                                                   +vd++ y+++ +++ eil++  ++ v+++siDEayld+t++ +  e+ +  +a+ ++++i  e+g
  gi|336254118|ref|YP_004597225.1| 100 pdltreetgfyrSVDMDFYESVASEVREILHDC-ADVVREVSIDEAYLDVTER-TAWEV-ADGFARHVKDRIRREVG 173
                                       999999999999*********************.77****************4.33444.379************** PP

                                       --EEEEEESSHHHHHHHHH CS
                               IMS 132 ltvsiGiasnkllAKlase 150
                                       +tvs+G a+++ +AK+as+
  gi|336254118|ref|YP_004597225.1| 174 VTVSVGAAPTMSAAKIASD 192
                                       *****************96 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 ?    1.1   0.0      0.21   6.4e+02      38      85 ..      32      85 ..      30     178 .. 0.76
   2 !   48.2   0.0   5.2e-16   1.6e-12       2     115 ..     272     384 ..     271     387 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.21
                             IMS_C 38 arrLrdkglvartitlklrysdfh.....asrsatLpr.ptsdtreileaalkL 85
                                      ++rLrd +l + ++++  +y + +     a+ s    +    ++++i  a+ +L
  gi|336254118|ref|YP_004597225.1| 32 CERLRDPELRGEPVVVGMGYEPGEtvgavATASYEAREfGVESAQAISTALERL 85
                                      689999999999999999998554444443333333222344444444444444 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 5.2e-16
                             IMS_C   2 vearpepksissektfpepyd...esklkkelreLaeelarrLrdkglvartitlklrysdfh.asrsatLprptsd 74 
                                       ve++  pks+s e  f+ep++   +    ++++ La+ +a r +++g + rt+ +k  + +++ ++r ++Lp p +d
  gi|336254118|ref|YP_004597225.1| 272 VEPKGDPKSFSRESAFAEPVSepeP--KYEQIETLAAAVADRAQREGALYRTVGVKAVTPPYDvNTRERSLPGPVDD 346
                                       578899************8885440..567999************************9998889************* PP

                             IMS_C  75 treileaalkLlrrlidepglpirligvsasnlvekaesqa 115
                                       ++++ + a +L+ + +d   +p+r++gv++ nl+ +a++qa
  gi|336254118|ref|YP_004597225.1| 347 PELVDRIANELFAEFED---EPVRKVGVRVANLEFSAADQA 384
                                       ************88877...**************8888876 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.2e-08   3.5e-05       1      32 []     204     235 ..     204     235 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.2e-08
                           IMS_HHH   1 pddvkefLwplpitkipGiGgklgekLeklGi 32 
                                       p++v+efL+pl++  ++G+G++++ +L+ +G+
  gi|336254118|ref|YP_004597225.1| 204 PGEVREFLAPLEVDLLHGVGPVTARELREMGL 235
                                       689*************************9996 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.5e-06     0.016       7      37 ..     219     249 ..     214     255 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.5e-06
                                       STT--HHHHHHHHTTT--SHHHHHHS-HHHH CS
                             HHH_5   7 vsGiGpktAlallsaGiesvedlaaadveeL 37 
                                       + G+Gp+tA+ l + G e+  ++aaad+e L
  gi|336254118|ref|YP_004597225.1| 219 LHGVGPVTARELREMGLETAGEVAAADPEPL 249
                                       67*************************9866 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 ?   13.3   0.0   1.8e-05     0.055       7      30 ..     220     243 ..     219     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                   DNA_pol_lambd_f   7 yGVGpktAkkwyakGirtledlra 30 
                                       +GVGp+tA+++ ++G+ t  ++ a
  gi|336254118|ref|YP_004597225.1| 220 HGVGPVTARELREMGLETAGEVAA 243
                                       9***************99777765 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.7e-05     0.079      11      45 ..     219     253 ..     212     262 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.7e-05
                              Cdd1  11 iPniGkalaedlvelGirsveelkgedpeelyekl 45 
                                       + ++G+ +a++l+e+G+++  e++  dpe l+e++
  gi|336254118|ref|YP_004597225.1| 219 LHGVGPVTARELREMGLETAGEVAAADPEPLVERF 253
                                       678****************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3517.74
//
Query:       gi|336254119|ref|YP_004597226.1|  [L=203]
Description: hypothetical protein Halxa_2731 [Halopiger xanaduensis SH-6]
Scores for 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:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 1727.53
//
Query:       gi|336254120|ref|YP_004597227.1|  [L=210]
Description: hypothetical protein Halxa_2732 [Halopiger xanaduensis SH-6]
Scores for complete 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    1.7e-10   41.1   0.0    1.1  1  UDG       Uracil DNA glycosylase superfamily
  ------ inclusion threshold ------
      0.085   12.4   0.0       0.13   11.8   0.0    1.2  1  DUF4918   Domain of unknown function (DUF4918)


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 !   41.1   0.0   1.9e-14   1.7e-10       1     115 [.      30     149 ..      30     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1.9e-14
                                       HHC-CTT-SEEEEESSTCHH.HHHHSSSS.-.STT--HHHHHHHCCCCCCCHHG...CTEEEEESSS....SECGCT CS
                               UDG   1 pgegppdakvvivGeaPgae.edatglpFsg.ragnllrkllneaglkrdlese...qgvyitnvvkcrppgnrdtp 72 
                                       +g+g+++a+  ++G  Pg + + +tg pF+   ag  +++++ e+g+   +++e   ++++   v  c  p   ++p
  gi|336254120|ref|YP_004597227.1|  30 FGYGDANADFHLIGDHPGVHgGKRTGVPFTEtDAGLAVQDVFRETGFVSGSQDEpdlENLFCSYVHMCCLPN-GHQP 105
                                       69******************9********999***************99887779*9999999999999755.459* PP

                                       TCCCCTCCHHHHHHHHHHHHSSEEEEESHHHHHH...HHHHSCE CS
                               UDG  73 tsaeikacaplleeeiellkprlivllGktaakall.geklgkl 115
                                       t+   +   +++++e+++++ ++++ +G++a +++l + ++++ 
  gi|336254120|ref|YP_004597227.1| 106 TARDYDDLERFFDAELRAINAHILLPVGAQATDHVLqQYTTQRR 149
                                       ****999999************************9952233322 PP

>> DUF4918  Domain of unknown function (DUF4918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.4e-05      0.13      47      77 ..      32      62 ..      27      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.4e-05
                                      --S---EEEEE-S---SSGGGGTSSTT--HH CS
                           DUF4918 47 yndkkkRklilginPgRfgagvtgvpFtdak 77
                                      y d +    ++g  Pg +g+  tgvpFt++ 
  gi|336254120|ref|YP_004597227.1| 32 YGDANADFHLIGDHPGVHGGKRTGVPFTETD 62
                                      8888999999******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.40u 0.17s 00:00:00.57 Elapsed: 00:00:00.32
# Mc/sec: 1934.23
//
Query:       gi|336254121|ref|YP_004597228.1|  [L=316]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-16   58.6   0.0    6.2e-16   57.9   0.0    1.3  1  HTH_10         HTH DNA binding domain
    1.5e-13   50.9   7.3    2.3e-13   50.3   7.3    1.2  1  BAT            GAF and HTH_10 associated domain
    1.3e-07   31.1   0.2    3.2e-07   29.8   0.0    1.7  2  Sigma70_r4     Sigma-70, region 4
     0.0012   18.7   0.3     0.0039   17.0   0.0    2.0  2  MarR_2         MarR family
     0.0013   18.5   0.4     0.0033   17.2   0.4    1.7  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0022   17.5   0.1     0.0043   16.6   0.1    1.5  1  HTH_24         Winged helix-turn-helix DNA-binding
     0.0075   15.9   0.0      0.018   14.7   0.0    1.6  2  Sigma70_r4_2   Sigma-70, region 4
  ------ inclusion threshold ------
      0.074   12.7   0.0       0.19   11.4   0.0    1.6  1  HTH_50         Helix-turn-helix domain


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 !   57.9   0.0   2.8e-19   6.2e-16       1      52 [.     215     266 ..     215     267 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 2.8e-19
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT +q+  + +Aye+GYFd+PR++tl eL ++lGIs+s++s++Lr+    li
  gi|336254121|ref|YP_004597228.1| 215 LTNAQRDLVVAAYEAGYFDVPRKTTLVELGERLGISDSAVSQRLRRGLAELI 266
                                       9********************************************9777665 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   7.3     1e-16   2.3e-13      19     151 ..      78     211 ..      64     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 1e-16
                               BAT  19 alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtlleltvsg..pslastl 93 
                                        l a+ d++v++e +vp  d+++l +++v  + ++ v+d ++d  +v+d+ vv+e +d++l+++++++  + +++++
  gi|336254121|ref|YP_004597228.1|  78 VLDADRDATVSVETTVPA-DEGSLPYLWVPADVADSVVDELDDNGNVTDAAVVDELEDSALVRVEWDDrlDGVLEAI 153
                                       578899***********6.55688*****************************************9753367899** PP

                               BAT  94 aehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtr 151
                                        + ++ v sa+ + +++++++++P+ +d+ +++ a+ e   ++eL + +e   +++ r
  gi|336254121|ref|YP_004597228.1| 154 RSSDAIVTSAAGTASQWTFRLRFPSYEDLSEFYTACVEDDVSIELAQLHEAVGSDQRR 211
                                       *************************************************998887765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.6   5.9e+03      14      22 ..     173     183 ..     172     183 .. 0.84
   2 !   29.8   0.0   1.4e-10   3.2e-07       5      48 ..     215     265 ..     214     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.6
                                       HHHH..TTT-- CS
                        Sigma70_r4  14 elrf..geglT 22 
                                       +lrf  +e+l+
  gi|336254121|ref|YP_004597228.1| 173 RLRFpsYEDLS 183
                                       89**9999986 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.4e-10
                                       S-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   5 Lpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       L+  +r+ ++  +        ++ Tl E+gerlgiS ++V+q+++r+l  L
  gi|336254121|ref|YP_004597228.1| 215 LTNAQRDLVVAAYeagyfdvPRKTTLVELGERLGISDSAVSQRLRRGLAEL 265
                                       888899999999999999988999***********************9876 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       1.4   3.2e+03      41      54 ..     128     141 ..     126     148 .. 0.77
   2 !   17.0   0.0   1.7e-06    0.0039       2      44 ..     214     260 ..     213     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                                       HHHHHHHTTSEEEE CS
                            MarR_2  41 ilkrLvaaGLverr 54 
                                       ++++L++  Lv+ +
  gi|336254121|ref|YP_004597228.1| 128 VVDELEDSALVRVE 141
                                       68999999999987 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.7e-06
                                       T--HHHHHHHHHHHCTTTS.....EEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2   2 gltpaqarvLaaLgrrpgr.....dltvgelarrlglsksavsrilkr 44 
                                       glt aq+++  a + ++ +     + t  el +rlg+s savs++l+r
  gi|336254121|ref|YP_004597228.1| 214 GLTNAQRDLVVAAYEAG-YfdvprKTTLVELGERLGISDSAVSQRLRR 260
                                       77888888877777776.55555566********************98 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 !   17.2   0.4   1.5e-06    0.0033      18      40 ..     238     260 ..     236     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-06
                     HTH_AsnC-type  18 isyaeLAervGlSestvlrRvrr 40 
                                       ++  eL+er+G+S s+v +R+rr
  gi|336254121|ref|YP_004597228.1| 238 TTLVELGERLGISDSAVSQRLRR 260
                                       6789*****************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 !   16.6   0.1   1.9e-06    0.0043      18      40 ..     238     260 ..     235     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.9e-06
                            HTH_24  18 isqreLAerlglSpstvnrrlkr 40 
                                       ++  eL erlg+S s+v++rl+r
  gi|336254121|ref|YP_004597228.1| 238 TTLVELGERLGISDSAVSQRLRR 260
                                       7899*****************98 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 ?   -3.4   0.0       3.6     8e+03      11      27 ..     215     231 ..     215     231 .. 0.81
   2 !   14.7   0.0   8.2e-06     0.018      31      54 .]     242     265 ..     239     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.6
                                       S-HHHHHHHHHHHTS-- CS
                      Sigma70_r4_2  11 Lperqreifllrylegl 27 
                                       L+  qr  ++  y+ g+
  gi|336254121|ref|YP_004597228.1| 215 LTNAQRDLVVAAYEAGY 231
                                       66779999999998875 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 8.2e-06
                                       HHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  31 EIAellgisegtVksrlsRArkkL 54 
                                       E  e+lgis+++V +rl+R+++ L
  gi|336254121|ref|YP_004597228.1| 242 ELGERLGISDSAVSQRLRRGLAEL 265
                                       6679*****************976 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.5e-05      0.19      29      46 ..     243     260 ..     239     260 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.5e-05
                            HTH_50  29 lAkrLGvShtaianklrk 46 
                                       l++rLG+S +a+ ++lr+
  gi|336254121|ref|YP_004597228.1| 243 LGERLGISDSAVSQRLRR 260
                                       799*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); 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:                         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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.34
# Mc/sec: 2820.65
//
Query:       gi|336254122|ref|YP_004597229.1|  [L=170]
Description: hypothetical protein Halxa_2734 [Halopiger xanaduensis SH-6]
Scores for 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   61.3  14.4    3.9e-16   58.8  14.4    1.9  1  YdjM      LexA-binding, inner membrane-associated putative hy
  ------ inclusion threshold ------
       0.83    9.5   2.6        7.6    6.4   0.5    2.4  2  hemP      Hemin uptake protein hemP


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8  14.4   4.4e-20   3.9e-16       2     164 ..       2     161 ..       1     169 [. 0.74

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 4.4e-20
                              YdjM   2 dgltHallGaalglalaallgaake.avllavavlg...AllPDiDhpsstlgrklgllskklaklvgHRgftHSll 74 
                                           H   +++l + l+a  + a   +++l++++++   ++lPD D       ++l+l          HRg tH+ll
  gi|336254122|ref|YP_004597229.1|   2 YQVGHYGAALLLYAPLGAAVSLAGYePAALLGGLVCvglSTLPDCD-------HRLPL-IE-------HRGPTHTLL 63 
                                       55677777777777776666665547899999999999********.......66755.34.......9******** PP

                              YdjM  75 flallalvlllllrlfgrsa.............lrlglllllg...vlsHlllDlltkyGvpllwPfskkkvrlsll 135
                                       f+ l++++l++ +  + +                 +g+++++g   ++sHll+D+lt++G++ +wP+s ++++l+++
  gi|336254122|ref|YP_004597229.1|  64 FAGLVGAALAGTVTVLADASaslltpvggvddaHVVGFAFVVGalsIVSHLLADALTPMGIRPFWPVSRRHYTLRVT 140
                                       *********999998888888***********96667777777555888******************9777777776 PP

                              YdjM 136 fiiidplltllsrrglvalelvllvlylv 164
                                          ++         + v l +v ++++ v
  gi|336254122|ref|YP_004597229.1| 141 RAANTI-------ANYV-LFVVGVGAVAV 161
                                       664443.......2333.33333333333 PP

>> hemP  Hemin uptake protein hemP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.016   1.4e+02      15      25 ..      52      62 ..      47      63 .. 0.86
   2 ?    6.4   0.5   0.00084       7.6      22      30 ..     134     142 ..     133     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.016
                                      EEEETTEEEEE CS
                              hemP 15 lIeHgGetYrL 25
                                      lIeH+G t++L
  gi|336254122|ref|YP_004597229.1| 52 LIEHRGPTHTL 62
                                      7*****99998 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00084
                                       EEEEEE-TT CS
                              hemP  22 tYrLRiTrn 30 
                                       +Y+LR+Tr+
  gi|336254122|ref|YP_004597229.1| 134 HYTLRVTRA 142
                                       7*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); 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):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.19s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 1504.41
//
Query:       gi|336254123|ref|YP_004597230.1|  [L=289]
Description: cytochrome oxidase assembly [Halopiger xanaduensis SH-6]
Scores for complete 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   40.7  26.0    6.3e-07   28.8   9.4    3.3  4  COX15-CtaA    Cytochrome oxidase assembly protein
  ------ inclusion threshold ------
        0.5    9.9  13.0       0.37   10.3   2.3    3.6  4  E1-E2_ATPase  E1-E2 ATPase


Domain annotation for each model (and alignments):
>> COX15-CtaA  Cytochrome oxidase assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   1.7e-07    0.0015       2      38 ..      23      60 ..      22      70 .. 0.92
   2 !   28.8   9.4     7e-11   6.3e-07      77     172 ..      73     161 ..      66     187 .. 0.84
   3 !    3.6   2.9    0.0031        28     124     203 ..     168     248 ..     161     256 .. 0.50
   4 !    3.9   2.7    0.0026        23      86     304 ..     205     256 ..     202     279 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.7e-07
                        COX15-CtaA  2 rwlllvlllvllvvvlGgltRltdsGlsitd.WppctG 38
                                      ++l ++l+lv + ++lG + ++t+sGl + + Wp c G
  gi|336254123|ref|YP_004597230.1| 23 HLLATTLVLVSATILLGIAAKATGSGLACNAnWPRCDG 60
                                      68899************************999****99 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 7e-11
                        COX15-CtaA  77 wiEwiHRllgrllGllilvpllyflakkrisrelkkllllllllvglQGllGwwmVksgLsekprvspyrlaaHLll 153
                                       + EwiHR++++++G+ i+  ++ +++  +++r++++l++l +ll  +Q +lG  +V+            +l++H+ +
  gi|336254123|ref|YP_004597230.1|  73 FYEWIHRFVAMFAGFAIIGSAIAAWRLPSVDRRVTALIVLGTLLTPVQVALGRETVTQY-------TLDILSLHFWT 142
                                       78*******************************************************98.......4579******* PP

                        COX15-CtaA 154 aflllalllwlalrllake 172
                                       a+l++++ ++ ++ +++++
  gi|336254123|ref|YP_004597230.1| 143 AILIFSMFAVATVLVWESS 161
                                       ******9998888877773 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.0031
                        COX15-CtaA 124 QGllGwwmVksgLse.........kprvspyrlaaHLllaflllalllwlalrllakeaesaeeeaaakklrllall 191
                                        G+lG  +V++ L+          +++ sp +  + ++++++lla++++ ++  ++        +   + lr+l+ +
  gi|336254123|ref|YP_004597230.1| 168 TGALGFGLVAVPLHValsptdlglVTDYSPTVQLLQYAATLALLAAIIVATMGSRR--------RFDDRLLRWLLSG 236
                                       56666666666654445555544445555555555555555555555554444322........2444555555555 PP

                        COX15-CtaA 192 llallllqialG 203
                                       + +l+l+ ++lG
  gi|336254123|ref|YP_004597230.1| 237 SAVLVLAVAYLG 248
                                       555555555555 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.0026
                        COX15-CtaA  86 grllGllilvpllyflakkri.srelkkllllllllvglQGllGwwmVksgLsekprvspyrlaaHLllaflllall 161
                                       + +l+ll +++++ +  ++r+ +r l++ll + ++lv++ + lG  +V                             
  gi|336254123|ref|YP_004597230.1| 205 AATLALLAAIIVATMGSRRRFdDRLLRWLLSGSAVLVLAVAYLGRRTVM---------------------------- 253
                                       4455555555555555555553444445555666666666666655554............................ PP

                        COX15-CtaA 162 lwlalrllakeaesaeeeaaakklrllallllallllqialGalvagldAglayntfplmggelipdklplceldwr 238
                                                                                                                    
  gi|336254123|ref|YP_004597230.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                        COX15-CtaA 239 nlfenpatvqfaHRllAilvllvllllailllrkarspklarlavllaallllQvalGistvllav 304
                                                                                                      ++ 
  gi|336254123|ref|YP_004597230.1| 254 ---------------------------------------------------------------TYS 256
                                       ...............................................................333 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.018   1.6e+02     103     140 ..       4      42 ..       1      88 [. 0.77
   2 ?   -1.1   0.1      0.13   1.1e+03     110     144 ..      72     106 ..      67     119 .. 0.72
   3 ?   10.3   2.3   4.1e-05      0.37      95     165 ..     113     184 ..     105     194 .. 0.86
   4 ?    3.6   0.3    0.0048        43     118     159 ..     201     244 ..     197     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.018
                                       -------HHHHHHHHHHHH.HHHHHHHHHHHHHHS-STT CS
                      E1-E2_ATPase 103 eakskktplqkkldklgkv.lvpvvlliallvflialll 140
                                       +++++++ +   +d++g   l ++ l+++ +++l+ +  
  gi|336254123|ref|YP_004597230.1|   4 TSHASRPTFRSLIDRFGFRhLLATTLVLVSATILLGIAA 42 
                                       5668899999999**985548888888888888777654 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSST CS
                      E1-E2_ATPase 110 plqkkldklgkvlvpvvlliallvflialllgksl 144
                                       ++ +++++++++++ ++++ +++++  ++++ + +
  gi|336254123|ref|YP_004597230.1|  72 SFYEWIHRFVAMFAGFAIIGSAIAAWRLPSVDRRV 106
                                       56678889999988888888888777666666655 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 4.1e-05
                                       TTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HHHHHHHHHHHHHS-TTHHH CS
                      E1-E2_ATPase  95 gkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.eallralallvaaiPcaLpl 165
                                       g++ + v+ a  ++t +q  ld l+ ++++++l+++++++++ l+++ sl+  a++ al++ ++a+P   +l
  gi|336254123|ref|YP_004597230.1| 113 GTLLTPVQVALGRETVTQYTLDILSLHFWTAILIFSMFAVATVLVWESSLTaGAVTGALGFGLVAVPLHVAL 184
                                       6667778888889999**********************************9888888999999999977655 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.0048
                                       HHHHHHHHHHHHHHHHHHS-STTTSSTT..HHHHHHHHHHHHHS CS
                      E1-E2_ATPase 118 lgkvlvpvvlliallvflialllgksla..eallralallvaai 159
                                       l ++ ++++ll+a++v+ +   ++ + +  ++ll++ a+lv a+
  gi|336254123|ref|YP_004597230.1| 201 LLQYAATLALLAAIIVATMGSRRRFDDRllRWLLSGSAVLVLAV 244
                                       566777788888888887776666666699*****999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2131.72
//
Query:       gi|336254124|ref|YP_004597231.1|  [L=370]
Description: peptidase M24 [Halopiger xanaduensis SH-6]
Scores for 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   44.0   2.5    2.8e-11   43.5   2.5    1.2  1  Peptidase_M24  Metallopeptidase family M24
    9.4e-06   26.3   0.1    3.4e-05   24.5   0.0    2.0  2  Creatinase_N   Creatinase/Prolidase N-terminal 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 !   43.5   2.5   3.2e-15   2.8e-11       2     191 ..     136     321 ..     135     336 .. 0.72

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 3.2e-15
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSS.SEEEEGGGGG.STTTBCSSSB--TTEE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafp.pivasgenaa.vlhytpndrvlkegdl 76 
                                        +r+ +r ++aa+e v ++++   te+e+a +++ + l++   r++  p   v+ ge+a+ + hytp++   + gd 
  gi|336254124|ref|YP_004597231.1| 136 RYRELGRETAAAVESVCRELRAEDTEHEVASALRVA-LSA---RDIEAPvCLVGGGERAQrYRHYTPTQA--ELGDY 206
                                       799*******************************66.443...44444326788899888889****655..559** PP

                                       EEEEEEEEETTEEEEEEEEEECSSGSH..HHHHHHHHHHHHHHHHHHC-ST.TSBHHHHHHHHHHHHHHTTB.CCGB CS
                     Peptidase_M24  77 vlidagaeydgyasDitrTvlvGkftp..eqrelyeavleaqeaaikavkp.Gvtlseidaaarevlesagl.akff 149
                                        l+ ++ae +g ++ +trTv+++ ++   e  e+ + v++   aa+++v + G t++++  a+++  ++ g+ ++  
  gi|336254124|ref|YP_004597231.1| 207 ALLSVTAERHGLHASCTRTVAFDAPDWleERHEAATRVEATALAATQEVAEnGGTAGDVFGAVQDAYAAVGFeGEWE 283
                                       **********************844335456678888888888888877666***************9988842222 PP

                                       SSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEE CS
                     Peptidase_M24 150 phglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiy 191
                                        h+ G   G   +     +++ ++++  +e  m ++  p + 
  gi|336254124|ref|YP_004597231.1| 284 YHHQGGAAGFAGR---EWIAT-PDHEASVEVPMAYAWNPTVQ 321
                                       3333333332233...23332.44566666666666666555 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   3.8e-09   3.4e-05       2      99 ..       7     112 ..       6     131 .. 0.82
   2 ?   -2.1   0.0      0.63   5.6e+03      82      95 ..     231     244 ..     190     282 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.8e-09
                                       HHHHHHHHHHTT-SEEEEECCHHHHHHHSS......-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH........T CS
                      Creatinase_N   2 lerlralmeekgldallvtspenlrYltGfa...tetgsrglalvvtadga.lllvdalryteaaees.......at 67 
                                       +erl a++e ++lda++  +p ++ +ltG      ++  +g+a+ v  dg+  ++++  ++++  +e+       a 
  gi|336254124|ref|YP_004597231.1|   7 RERLEAVLESRDLDAVWFARPNSFAWLTGGSsviDRESDAGVAA-VGYDGDvRIVTNNIEAARIEAEElpdleadA- 81 
                                       79****************************99988899999999.9999999****************88866333. PP

                                       TSEEEEESTHSSHHHHHHHHHHHHT-EEEE-T CS
                      Creatinase_N  68 veevveyddpvealadllkellesekrvgvel 99 
                                         ++ +y++ +++la++++ ++ + +r + + 
  gi|336254124|ref|YP_004597231.1|  82 -VSIEQYSWHASSLAEAISARVGDDERAAADV 112
                                       .3333333357888888888777777777665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.63
                                       HHHHHHHHHHT-EE CS
                      Creatinase_N  82 adllkellesekrv 95 
                                       +d+l+e+ e++ rv
  gi|336254124|ref|YP_004597231.1| 231 PDWLEERHEAATRV 244
                                       44444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 3012.27
//
Query:       gi|336254125|ref|YP_004597232.1|  [L=210]
Description: transcriptional regulator TrmB [Halopiger xanaduensis SH-6]
Scores for 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   32.1   0.1    1.2e-07   31.5   0.1    1.3  1  TrmB         Sugar-specific transcriptional regulator TrmB
    4.1e-06   26.2   0.0    8.5e-06   25.2   0.0    1.6  1  HTH_24       Winged helix-turn-helix DNA-binding
     0.0024   17.9   0.1     0.0047   17.0   0.1    1.5  1  HTH_20       Helix-turn-helix domain
     0.0061   16.2   0.1      0.015   14.9   0.1    1.6  1  GntR         Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.016   15.0   0.0    1.4  1  HTH_IclR     IclR helix-turn-helix domain
      0.021   14.7   0.0      0.032   14.1   0.0    1.3  1  TFIIE_alpha  TFIIE alpha subunit
      0.081   13.4   0.0       0.13   12.8   0.0    1.4  1  HTH_40       Helix-turn-helix domain
       0.13   12.3   0.0       0.21   11.7   0.0    1.3  1  HTH_9        RNA polymerase III subunit RPC82 helix-turn-heli


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 !   31.5   0.1   5.5e-11   1.2e-07       8      67 ..      55     121 ..      54     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 5.5e-11
                                       HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE--H CS
                              TrmB   8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYravdp 67 
                                       e+ ak+Y+ Ll++  +t +e+a+ +g+  s+v e+L +L + + V+rek+        p+ Y a++p
  gi|336254125|ref|YP_004597232.1|  55 ETRAKIYVHLLANPGSTSEEVAKGTGLYPSTVREALAELHEEDRVTREKRAsegagnnPYEYTAIQP 121
                                       6679*********************************************8889************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 !   25.2   0.0   3.8e-09   8.5e-06       3      47 ..      55      99 ..      53     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.8e-09
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      et+ kI+  L +np+ +  e+A+ +gl pstv++ l +L ee  +
  gi|336254125|ref|YP_004597232.1| 55 ETRAKIYVHLLANPGSTSEEVAKGTGLYPSTVREALAELHEEDRV 99
                                      67789999*******************************999765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.1e-06    0.0047       7      58 ..      52     103 ..      42     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.1e-06
                                       HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20   7 LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58 
                                       L+ ++R++i+ +L  + g t +e+a+  +l ++t++  L++L e + v++++
  gi|336254125|ref|YP_004597232.1|  52 LDTETRAKIYVHLLANPGSTSEEVAKGTGLYPSTVREALAELHEEDRVTREK 103
                                       677*****************************************99888776 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   6.8e-06     0.015      29      60 ..      74     105 ..      71     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.8e-06
                                       HHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                              GntR  29 eLaaefgVsrttvReALrrLeaeglverrqgr 60 
                                       e+a+  g   +tvReAL +L +e+ v+r+++ 
  gi|336254125|ref|YP_004597232.1|  74 EVAKGTGLYPSTVREALAELHEEDRVTREKRA 105
                                       66666777789*****************9985 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 ?   15.0   0.0   7.2e-06     0.016      17      50 ..      68     101 ..      43     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.2e-06
                                       SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       ++ t  e+A+ tgl +Stv+  L+ L+e+  v++
  gi|336254125|ref|YP_004597232.1|  68 PGSTSEEVAKGTGLYPSTVREALAELHEEDRVTR 101
                                       446889*********************9987766 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.4e-05     0.032      16      81 ..      58     124 ..      46     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHH.CTSEEEEEEEE.TTTEEEEEEEEEECCCH CS
                       TFIIE_alpha  16 vlvldvLlekgevteedlakelkidlnelrklLnrLye.arlvkykrrrd.eekswykyywrinyekl 81 
                                       +++   Ll +   t e++ak +++ +  +r++L++L e +r+   kr+ +  + + y+y+  i++ +l
  gi|336254125|ref|YP_004597232.1|  58 AKIYVHLLANPGSTSEEVAKGTGLYPSTVREALAELHEeDRVTREKRASEgAGNNPYEYT-AIQPSEL 124
                                       566667888888999*********************862677777777665555555555.3444444 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.6e-05      0.13       8      41 ..      64      98 ..      57     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                            HTH_40  8 ll.eeglsieeIAkerglkesTIegHLaelieege 41
                                      ll + g + ee+Ak  gl +sT+ + Lael ee++
  gi|336254125|ref|YP_004597232.1| 64 LLaNPGSTSEEVAKGTGLYPSTVREALAELHEEDR 98
                                      555779999***********************964 PP

>> HTH_9  RNA polymerase III subunit RPC82 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   9.3e-05      0.21      14      51 ..      56      93 ..      46      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.3e-05
                                      HHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHH CS
                             HTH_9 14 vvakVvetLlrkgrltlrelvkktkLsldqVkksLvvL 51
                                      + ak++ +Ll++  +t+ e +k t+L ++ V+ +L+ L
  gi|336254125|ref|YP_004597232.1| 56 TRAKIYVHLLANPGSTSEEVAKGTGLYPSTVREALAEL 93
                                      5689*******************************866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.19s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 1853.27
//
Query:       gi|336254126|ref|YP_004597233.1|  [L=822]
Description: type 2 DNA topoisomerase 6 subunit B [Halopiger xanaduensis SH-6]
Scores for 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-62  209.6   0.0      4e-62  208.7   0.0    1.4  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    2.2e-39  134.1   3.9    2.2e-39  134.1   3.9    2.3  3  Top6b_C         Type 2 DNA topoisomerase 6 subunit B C-termin
      2e-13   50.8   0.5    7.9e-13   48.9   0.0    2.2  2  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    2.7e-12   46.7   0.0    9.7e-12   44.9   0.0    1.9  2  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
  ------ inclusion threshold ------
       0.02   14.9   2.7       0.11   12.4   0.0    3.3  3  HATPase_c_2     Histidine kinase-like ATPase domain


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 !  208.7   0.0   1.1e-65     4e-62       1     159 []     524     688 ..     524     688 .. 0.99

  Alignments for each domain:
  == domain 1  score: 208.7 bits;  conditional E-value: 1.1e-65
                    Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydega 77 
                                       P+t+clspi+++lie+gl+ke++++f+a+ +r+++v  g+pf+vE+giayGGe+e+e +a+++RfaNrvPL+y++ga
  gi|336254126|ref|YP_004597233.1| 524 PPTRCLSPITADLIEAGLEKEFDADFYASASRDAEVSGGDPFVVEAGIAYGGEIESEGSAQVMRFANRVPLVYQRGA 600
                                       99*************************************************************************** PP

                    Topo-VIb_trans  78 dvitkavksinwkrYkleq......pedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkyls 148
                                       +++t++vksi w++Y+l+q      p++p+v++vhvast+vPf+se+K+a+a+v+eie+ei+la++e+ar+Lk+y++
  gi|336254126|ref|YP_004597233.1| 601 CATTDVVKSIGWRNYGLDQpggsglPNGPAVIMVHVASTNVPFTSESKDAVANVPEIEDEIELAIREAARDLKSYIN 677
                                       ***************************************************************************** PP

                    Topo-VIb_trans 149 kkekekeekek 159
                                       k+++ +++++k
  gi|336254126|ref|YP_004597233.1| 678 KRQSMQQRRKK 688
                                       ***99998876 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 ?   -2.4   0.0       1.5   5.3e+03      50      70 ..     229     249 ..     221     253 .. 0.88
   2 ?   -4.1   0.0       4.9   1.8e+04      40      74 ..     473     507 ..     472     514 .. 0.76
   3 !  134.1   3.9   6.2e-43   2.2e-39       2     114 .]     709     819 ..     708     819 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.5
                                       --EES-----------EEE-S CS
                           Top6b_C  50 heilpaeieeaspeakvvemd 70 
                                       ++ lp e ee++p+++ ve++
  gi|336254126|ref|YP_004597233.1| 229 TDQLPEETEEIRPHPHGVELG 249
                                       8999*************9998 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 4.9
                                       -------EEE--EES-----------EEE-SSSEE CS
                           Top6b_C  40 fsdkkeefelheilpaeieeaspeakvvemdneyd 74 
                                       f+d+++e  +  i ++ ++ +++ + v e++++ d
  gi|336254126|ref|YP_004597233.1| 473 FGDTARENVVEAIWDVMATVPDDPPLVRELNGDRD 507
                                       67888888888888888888888888888887766 PP

  == domain 3  score: 134.1 bits;  conditional E-value: 6.2e-43
                                       SS---SHHHHHHHTT-EEEEEEE--SSS-EEEEEEE---------EEE--EES-----------EEE-SSSEEE-EE CS
                           Top6b_C   2 reepdidpvvArimgnvlvereveengdgvevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlkWe 78 
                                       r+epdid+++Arim+nvlver+ve ngdg+e+s+ v+N+s+++e++e+++i++ae+ +  ++a+v+emd+e+++kWe
  gi|336254126|ref|YP_004597233.1| 709 RDEPDIDDAIARIMNNVLVERRVEANGDGQEISVVVENNSSTNESLEITDIVSAEPANLPDDATVIEMDGEWFVKWE 785
                                       89*************************************************************************** PP

                                       E---TT-EEEE----SS-GGGS--B----------- CS
                           Top6b_C  79 lsvsageskvleYsvdseaeeelsliveGveeekvT 114
                                       ++v+++++++leY+v+++a+ +l+  v+Gve+ek+T
  gi|336254126|ref|YP_004597233.1| 786 PEVKSDDEAALEYEVSDDATYDLD--VKGVESEKLT 819
                                       ************************..*********9 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 !   48.9   0.0   2.2e-16   7.9e-13       4      97 ..      45     145 ..      42     190 .. 0.76
   2 ?   -1.7   0.4       1.2   4.1e+03      11      44 ..     719     758 ..     710     761 .. 0.61

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2.2e-16
                                       HHHHHHHHHHHHHHHHHHSTTT...EEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCH.....HCSTCHTS CS
                         HATPase_c   4 krLrqiisnlvdNavkfatkag...eieveikaseddlvisveDnGiGipkedlkklfe.kfsq.....ddstkrgg 71 
                                       ++L  +++++vdNa+++a +ag   +i vei+ + d++++ veDnG+G++ke l+k+f+          +++++rg+
  gi|336254126|ref|YP_004597233.1|  45 RGLVTAVKEAVDNALDAAEEAGilpDIYVEIQEEGDYYRLIVEDNGPGLTKESLPKVFGkL-LYgsrfhAREQSRGQ 120
                                       78999***********96677777799*****5559*******************999953.433698889999999 PP

                                       TSSSHHHHHHHH.HHHHTTTEEEEEEE CS
                         HATPase_c  72 ggtGlGlsivkk.lvelmgGeiwvese 97 
                                       +g G+++++  + l++  g   +++s+
  gi|336254126|ref|YP_004597233.1| 121 QGIGISAAVLYSqLTS--GKPAKITSR 145
                                       9999999998765555..433444333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                                       HHHHHHHHHH.....HSTTTEEEEEEEEEE.TEEEEEEEE CS
                         HATPase_c  11 snlvdNavkf.....atkageieveikase.ddlvisveD 44 
                                         ++ N + +     +++++ei+v ++ ++  + +++++D
  gi|336254126|ref|YP_004597233.1| 719 ARIMNNVLVErrveaNGDGQEISVVVENNSsTNESLEITD 758
                                       4444444444444335578888888886324688888877 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 !   44.9   0.0   2.7e-15   9.7e-12       5     123 ..      49     177 ..      46     186 .. 0.83
   2 ?   -3.4   0.1       2.2   7.9e+03      18      40 ..     736     758 ..     733     758 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.7e-15
                       HATPase_c_3   5 kAlaelvdNsldAdaen.....vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGi 75 
                                       +A+ e vdN+ldA  e      +++e++++ g+  ++ +eD+G G+++e l +++ +l   s+  +  ++s+G+ Gi
  gi|336254126|ref|YP_004597233.1|  49 TAVKEAVDNALDAAEEAgilpdIYVEIQEE-GDYYRLIVEDNGPGLTKESLPKVFgKLLYGSRF-HAREQSRGQQGI 123
                                       79***********999999*9999999996.799*******************77589999999.57899******* PP

                       HATPase_c_3  76 GlklAsl....slgkkltvitkkegess..tltldvdkidkenekvleeltvee 123
                                       G+  A+l     +gk +++++++eg s+   ++l vd  ++e e ++ee+t+++
  gi|336254126|ref|YP_004597233.1| 124 GISAAVLysqlTSGKPAKITSRTEGASEaqYFELIVDTDENEPEISVEETTTWD 177
                                       *98887522226899*********999965577777777777788888887765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.2
                       HATPase_c_3  18 daenvkievnknrgktgeivieD 40 
                                       d ++++++v++n + ++++ i+D
  gi|336254126|ref|YP_004597233.1| 736 DGQEISVVVENNSSTNESLEITD 758
                                       66789999999998889999988 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.2e-05      0.11      27     101 ..      42     124 ..      14     128 .. 0.71
   2 ?   -2.8   0.0       1.6   5.6e+03      31      42 ..     307     318 ..     286     319 .. 0.77
   3 ?   -0.2   0.8      0.25   8.8e+02      27      51 ..     656     680 ..     644     757 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                       HATPase_c_2  27 elldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep........kesl 95 
                                       + +  +  av+Ea+ Na  +a + +   ++ v+++ +++  ++ v+D+Gpg + e lp+   + +        ++s+
  gi|336254126|ref|YP_004597233.1|  42 SGARGLVTAVKEAVDNALDAAEEAGILPDIYVEIQEEGDYYRLIVEDNGPGLTKESLPKVFGKLLygsrfharEQSR 118
                                       44557889***************999999999999****************77777665443333566666665556 PP

                       HATPase_c_2  96 kegGrG 101
                                         +G+G
  gi|336254126|ref|YP_004597233.1| 119 GQQGIG 124
                                       666655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                       HATPase_c_2  31 eirlaveEactN 42 
                                       +++ av+Ea +N
  gi|336254126|ref|YP_004597233.1| 307 DLEAAVSEATAN 318
                                       7899*****998 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.25
                       HATPase_c_2  27 elldeirlaveEactNavehaylea 51 
                                       e  dei+la+ Ea      + ++++
  gi|336254126|ref|YP_004597233.1| 656 EIEDEIELAIREAARDLKSYINKRQ 680
                                       456899*****99866555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (822 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); 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):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.26s 00:00:00.96 Elapsed: 00:00:00.37
# Mc/sec: 6574.12
//
Query:       gi|336254127|ref|YP_004597234.1|  [L=363]
Description: type 2 DNA topoisomerase 6 subunit A [Halopiger xanaduensis SH-6]
Scores for 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-15   55.7   0.1    6.5e-15   54.9   0.1    1.5  1  TP6A_N    Type IIB DNA topoisomerase
     0.0069   16.2   0.0      0.012   15.4   0.0    1.3  1  cpYpsA    Circularly permutated YpsA SLOG family


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 !   54.9   0.1   7.3e-19   6.5e-15       1      61 [.      69     135 ..      69     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 7.3e-19
                                       HHHHHHHHHHHHHHHHHHTT--EEHHHHHHH......GGGS-SSHHHHHHHHHHHHHHHTS-GGGGT CS
                            TP6A_N   1 rkfaqllkvlelihelleegkvvTkRdiYYr......dvelFksQaesdrliddievllgvsReeLn 61 
                                       rk+ + ++++e++ e+l e++++T+R++YY       +++ F sQ+es++l++d+e + gv+Re+++
  gi|336254127|ref|YP_004597234.1|  69 RKLLKAVYTIEFLAEQLDEDRSSTLRELYYLseswdnEEAQFSSQDESNSLVEDLEIVSGVTREDFH 135
                                       689999***************************999779***************************9 PP

>> cpYpsA  Circularly permutated YpsA SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.4e-06     0.012      41     103 ..      22      86 ..      14     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-06
                                       TTS--EE-SS--HHHHHHHHHH.TSSEEEEEESSS--HHHHHHHHHHHHTT--EEEEE.TTTS-H CS
                            cpYpsA  41 erYplretessdyaeRtekNvr.dsdgtliltlgklsgGteltvelarelkkpllvvd.lekeae 103
                                       ++++l e+++ +  +Rt+ N++ d d  ++++ ++ s+ ++ +v+ ar+l k +++++ l+++ +
  gi|336254127|ref|YP_004597234.1|  22 DQFELGEIPHMSVPTRTKNNIEyDEDEKVWVYGDRESTRSANSVRGARKLLKAVYTIEfLAEQLD 86 
                                       6799*****************8799********************************94444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.62 Elapsed: 00:00:00.33
# Mc/sec: 3314.32
//
Query:       gi|336254128|ref|YP_004597235.1|  [L=38]
Description: hypothetical protein Halxa_2740 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.058   12.8   0.1      0.082   12.3   0.1    1.3  1  zf_Rg     Reverse gyrase zinc finger


Domain annotation for each model (and alignments):
>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   4.6e-06     0.082       9      24 ..       2      17 ..       1      19 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.6e-06
                             zf_Rg  9 lCPNCgGdisdeRlek 24
                                       C  CgG+i  eRl k
  gi|336254128|ref|YP_004597235.1|  2 TCDACGGEIDGERLYK 17
                                      5999**********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.19s 00:00:00.51 Elapsed: 00:00:00.33
# Mc/sec: 348.91
//
Query:       gi|336254129|ref|YP_004597236.1|  [L=373]
Description: hypothetical protein Halxa_2741 [Halopiger xanaduensis SH-6]
Scores for 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-07   29.1   3.3    5.5e-07   29.1   3.3    2.7  3  zinc_ribbon_2   zinc-ribbon domain
    4.7e-05   22.6   2.6    4.7e-05   22.6   2.6    2.5  2  zf-ribbon_3     zinc-ribbon domain
    0.00034   20.6   0.8    0.00034   20.6   0.8    2.7  2  DZR             Double zinc ribbon
    0.00065   19.5   2.6      0.002   18.0   2.6    1.9  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
    0.00085   19.2  10.9       0.34   10.9   0.1    4.4  4  Nudix_N_2       Nudix N-terminal
     0.0012   19.6   1.5     0.0012   19.6   1.5    2.4  2  zinc_ribbon_15  zinc-ribbon family
  ------ inclusion threshold ------
      0.015   14.9   7.1        1.4    8.7   0.3    3.7  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.035   13.0   0.5      0.055   12.3   0.5    1.3  1  Apt1            Golgi-body localisation protein domain
       0.11   12.2   1.4       0.15   11.7   0.1    1.8  2  DUF2321         Uncharacterized protein conserved in bacteria
       0.26   11.3   0.2       0.26   11.3   0.2    2.4  2  zinc-ribbons_6  zinc-ribbons
        0.3   11.0   2.4       0.57   10.2   0.6    2.2  2  Prok-RING_1     Prokaryotic RING finger family 1
       0.53   10.2   3.7        1.3    9.0   0.2    2.6  2  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.57   10.3   5.6        0.5   10.5   1.9    2.4  2  DUF1272         Protein of unknown function (DUF1272)
        1.2    9.3   3.8        1.2    9.2   0.3    2.5  3  DHHC            DHHC palmitoyltransferase
        1.5    9.2   6.6         32    4.9   0.8    3.2  3  C1_2            C1 domain
        1.5    8.8  10.1        9.1    6.3   0.1    3.8  3  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        4.1    7.0   5.8         16    5.1   2.1    3.1  3  TF_Zn_Ribbon    TFIIB zinc-binding
        8.5    6.3  11.5       0.61   10.0   1.4    2.9  2  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)


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 !   29.1   3.3   5.6e-10   5.5e-07       1      22 [.      13      34 ..      13      35 .. 0.95
   2 ?   -0.2   0.1       0.9     9e+02      13      22 ..     276     285 ..     273     286 .. 0.80
   3 ?   -1.6   0.5       2.4   2.4e+03       1       5 [.     314     318 ..     311     320 .. 0.65

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 5.6e-10
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGtp 22
                                      +C++CG+ l++ +++Cp+CGt 
  gi|336254129|ref|YP_004597236.1| 13 YCSHCGRSLEPPVNYCPNCGTA 34
                                      8*******************96 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.9
                     zinc_ribbon_2  13 akFCpyCGtp 22 
                                       ++ C+ C +p
  gi|336254129|ref|YP_004597236.1| 276 DRPCSVCAEP 285
                                       678***9877 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.4
                     zinc_ribbon_2   1 fCpnC 5  
                                       +C +C
  gi|336254129|ref|YP_004597236.1| 314 YCQRC 318
                                       45555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   2.6   4.7e-08   4.7e-05       1      24 [.      10      33 ..      10      35 .. 0.92
   2 ?   -0.1   0.4      0.69   6.9e+02       4      13 ..     278     287 ..     277     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.7e-08
                       zf-ribbon_3  1 stvrCPnCGaplssddnvCpyCGt 24
                                      +t++C++CG  l++ +n Cp+CGt
  gi|336254129|ref|YP_004597236.1| 10 ETRYCSHCGRSLEPPVNYCPNCGT 33
                                      589*******88***********8 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.69
                       zf-ribbon_3   4 rCPnCGapls 13 
                                        C+ C +p+ 
  gi|336254129|ref|YP_004597236.1| 278 PCSVCAEPVG 287
                                       6****99875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.8   3.4e-07   0.00034      11      40 ..      10      37 ..       5      43 .. 0.65
   2 ?    0.3   1.9      0.76   7.6e+02      11      18 ..     311     318 ..     272     330 .. 0.52

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.4e-07
                               DZR 11 darfCseCgtklkavaaedrCpsCgekvdp 40
                                      + r+Cs+Cg +l+  +  + Cp+Cg++++ 
  gi|336254129|ref|YP_004597236.1| 10 ETRYCSHCGRSLE--PPVNYCPNCGTAIER 37
                                      5667777777775..446667777766655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.76
                               DZR  11 darfCseC 18 
                                       ++ +C++C
  gi|336254129|ref|YP_004597236.1| 311 RNYYCQRC 318
                                       33444444 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 !   18.0   2.6     2e-06     0.002      11      33 ..      11      33 ..       2      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                           DUF35_N 11 gqrCpdCGtvqfPPravCphCgs 33
                                       ++C+ CG+   PP ++Cp+Cg 
  gi|336254129|ref|YP_004597236.1| 11 TRYCSHCGRSLEPPVNYCPNCGT 33
                                      579********9999******95 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0015       1.5       1      11 [.      12      22 ..      12      25 .. 0.88
   2 !   10.9   0.1   0.00034      0.34       1      13 [.      26      38 ..      26      43 .. 0.91
   3 ?    3.2   0.2     0.087        87       3      15 ..     279     291 ..     277     293 .. 0.87
   4 ?    0.7   0.2      0.52   5.2e+02       2       9 ..     314     321 ..     313     326 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                                      -B-TTT--B-E CS
                         Nudix_N_2  1 kFCsqCGtpve 11
                                      ++Cs+CG  +e
  gi|336254129|ref|YP_004597236.1| 12 RYCSHCGRSLE 22
                                      8******9987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00034
                                      -B-TTT--B-EEE CS
                         Nudix_N_2  1 kFCsqCGtpvelr 13
                                      ++C++CGt++e+r
  gi|336254129|ref|YP_004597236.1| 26 NYCPNCGTAIERR 38
                                      7********9987 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.087
                                       -TTT--B-EEE-- CS
                         Nudix_N_2   3 CsqCGtpvelrip 15 
                                       Cs C++pv + i+
  gi|336254129|ref|YP_004597236.1| 279 CSVCAEPVGRGIE 291
                                       ********98775 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.52
                                       B-TTT--B CS
                         Nudix_N_2   2 FCsqCGtp 9  
                                       +C+ C+++
  gi|336254129|ref|YP_004597236.1| 314 YCQRCANA 321
                                       99999975 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.5   1.2e-06    0.0012      62      86 .]       8      32 ..       2      32 .. 0.87
   2 ?    1.1   0.5      0.68   6.7e+02      31      46 ..     306     321 ..     277     334 .. 0.51

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-06
                    zinc_ribbon_15 62 ssekkeCknCgkeveeefkyCpkCg 86
                                      +se+++C++Cg+++e+ ++yCp+Cg
  gi|336254129|ref|YP_004597236.1|  8 RSETRYCSHCGRSLEPPVNYCPNCG 32
                                      56689*******************9 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.68
                    zinc_ribbon_15  31 wkkkkpylacskCksl 46 
                                       ++++   ++c++C + 
  gi|336254129|ref|YP_004597236.1| 306 TGSTGRNYYCQRCANA 321
                                       3333344445555544 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 ?    8.7   0.3    0.0014       1.4       2      12 ..      10      20 ..       9      23 .. 0.80
   2 ?    7.5   0.1    0.0032       3.2       5      16 ..      27      38 ..      26      40 .. 0.83
   3 ?   -0.3   0.4       0.9   8.9e+02       6      13 ..     279     286 ..     279     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0014
                     zf-NADH-PPase  2 thrFCgrCGap 12
                                       +r+C++CG  
  gi|336254129|ref|YP_004597236.1| 10 ETRYCSHCGRS 20
                                      58*******75 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0032
                     zf-NADH-PPase  5 FCgrCGaptepa 16
                                      +C+ CG++ e+ 
  gi|336254129|ref|YP_004597236.1| 27 YCPNCGTAIERR 38
                                      8******98875 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.9
                     zf-NADH-PPase   6 CgrCGapt 13 
                                       C+ C+ p+
  gi|336254129|ref|YP_004597236.1| 279 CSVCAEPV 286
                                       ****9996 PP

>> Apt1  Golgi-body localisation protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   5.5e-05     0.055     321     409 ..      54     182 ..      20     184 .. 0.42

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-05
                              Apt1 321 deesessssss.......ssssssassssssssrssslelrlkptsstssssssessssssskkrsseesslessas 390
                                       ++es              s++ s+a ++s+sss+ss+ + r          ++++ss+++ss++r+ ++++ +    
  gi|336254129|ref|YP_004597236.1|  54 RTES------RqpsvgefSQTRSHAGDRSRSSSSSSQRDAR----------TARTSSTTASSADRDVDPTARK---- 110
                                       1111......0111111222222222222222222222222..........1111122222222222211111.... PP

                              Apt1 391 ervkssr...........................................................asddleemksR 408
                                             +                                                             +d+e m+ R
  gi|336254129|ref|YP_004597236.1| 111 ------QletriaratrdgwelehdfgdhavmvrrtfgdtdehlvvalltvwwtmglgnvlygayrYVEDAERMVLR 181
                                       ......01112222333555555556666666666666666677777777777777777777777766777777777 PP

                              Apt1 409 a 409
                                       a
  gi|336254129|ref|YP_004597236.1| 182 A 182
                                       6 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 ?   11.7   0.1   0.00015      0.15      24      56 ..       9      44 ..       2      51 .. 0.79
   2 ?   -1.8   0.1       2.1   2.1e+03      63      74 ..     309     320 ..     293     322 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                           DUF2321 24 lveeyCekcGekt...itkcpkCsteirGkyyvegv 56
                                      + + yC++cG ++   ++ cp+C+t i+ ++   gv
  gi|336254129|ref|YP_004597236.1|  9 SETRYCSHCGRSLeppVNYCPNCGTAIERRDRSSGV 44
                                      5679******7654449**********988777765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.1
                           DUF2321  63 yevpsyCkkCgk 74 
                                       +  + yC++C++
  gi|336254129|ref|YP_004597236.1| 309 TGRNYYCQRCAN 320
                                       555678888876 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00026      0.26      14      41 ..       9      37 ..       3      43 .. 0.83
   2 ?    1.5   1.8       0.3     3e+02      46      56 ..     310     319 ..     274     326 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                                      SSEEE-TTT--EEEE.EEE-SSS-S---E CS
                    zinc-ribbons_6 14 geqyhCeaCqedlkk.ealCpeCeqelev 41
                                      +e+  C++C ++l+  +++Cp+C+  +e+
  gi|336254129|ref|YP_004597236.1|  9 SETRYCSHCGRSLEPpVNYCPNCGTAIER 37
                                      57789******9985389******99986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.3
                                       TEEEE--TTTT CS
                    zinc-ribbons_6  46 gavdyfCnkcn 56 
                                       g  +y+C++c 
  gi|336254129|ref|YP_004597236.1| 310 GR-NYYCQRCA 319
                                       33.55555553 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 ?   10.2   0.6   0.00057      0.57       5      29 ..      12      34 ..       8      38 .. 0.87
   2 ?   -0.9   0.0       1.6   1.6e+03       5      13 ..     277     285 ..     274     289 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00057
                       Prok-RING_1  5 kkCpvCgkelkeedDiVvCpeCgtp 29
                                        C+ Cg+ l++   +  Cp+Cgt 
  gi|336254129|ref|YP_004597236.1| 12 RYCSHCGRSLEPP--VNYCPNCGTA 34
                                      57**********9..99*******7 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.6
                       Prok-RING_1   5 kkCpvCgke 13 
                                         C+vC ++
  gi|336254129|ref|YP_004597236.1| 277 RPCSVCAEP 285
                                       689999886 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 ?    9.0   0.2    0.0013       1.3       9      37 ..       9      34 ..       4      38 .. 0.83
   2 ?    1.3   0.4      0.33   3.3e+02      14      22 ..     279     299 ..     275     321 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                                      SS--B-TTT-SB--SSSS-EEEETTT--E CS
                              C1_1  9 kqptfCkhCgeflwgkekqglkCswCkll 37
                                      +++ +C+hCg +l   e +   C +C+  
  gi|336254129|ref|YP_004597236.1|  9 SETRYCSHCGRSL---EPPVNYCPNCGTA 34
                                      5789*********...9999999999865 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.33
                                       -TTT-SB-............- CS
                              C1_1  14 CkhCgefl............w 22 
                                       C+ C+e++             
  gi|336254129|ref|YP_004597236.1| 279 CSVCAEPVgrgieriyrsefC 299
                                       888888884444444443330 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.9    0.0005       0.5      28      54 ..      10      38 ..       8      40 .. 0.78
   2 ?   -0.1   0.1         1     1e+03      31      39 ..     314     322 ..     312     331 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                           DUF1272 28 EctFCaeCaeevl..envCPncgGelvkR 54
                                      E  +C++C  ++    n CPncg  + +R
  gi|336254129|ref|YP_004597236.1| 10 ETRYCSHCGRSLEppVNYCPNCGTAIERR 38
                                      667999998876444699*****988877 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                           DUF1272  31 FCaeCaeev 39 
                                       +C++Ca++ 
  gi|336254129|ref|YP_004597236.1| 314 YCQRCANAE 322
                                       899999876 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3    0.0012       1.2       4      33 ..      10      39 ..       7      46 .. 0.92
   2 ?   -0.1   0.0      0.94   9.3e+02      26      51 ..     269     294 ..     265     307 .. 0.82
   3 ?   -3.4   0.2        10   9.9e+03      18      26 ..     311     319 ..     308     321 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                              DHHC  4 elkfCstcniykpprskHcrvCnrcvlrfD 33
                                      e+++Cs c +   p   +c  C+  + r D
  gi|336254129|ref|YP_004597236.1| 10 ETRYCSHCGRSLEPPVNYCPNCGTAIERRD 39
                                      789************************999 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.94
                              DHHC  26 nrcvlrfDHhCpwlnnciGerNykyF 51 
                                       +r+v  +D  C ++   +G+   +++
  gi|336254129|ref|YP_004597236.1| 269 ERFVVAYDRPCSVCAEPVGRGIERIY 294
                                       588999*************9766666 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 10
                              DHHC  18 rskHcrvCn 26 
                                       r ++c++C 
  gi|336254129|ref|YP_004597236.1| 311 RNYYCQRCA 319
                                       567777775 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.8     0.032        32      14      40 ..       7      33 ..       3      38 .. 0.80
   2 ?    3.6   0.1     0.082        81      18      29 ..     276     288 ..     266     301 .. 0.76
   3 ?    2.3   0.1      0.21   2.1e+02      29      38 ..     309     318 ..     302     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.032
                              C1_2 14 dssesfnCsaCgrkidgffYsCseCdf 40
                                       +se++ Cs Cgr+ ++   +C+ C  
  gi|336254129|ref|YP_004597236.1|  7 GRSETRYCSHCGRSLEPPVNYCPNCGT 33
                                      578999********8887778988975 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.082
                              C1_2  18 sfnCsaCgrk.id 29 
                                       +++Cs+C ++ + 
  gi|336254129|ref|YP_004597236.1| 276 DRPCSVCAEPvGR 288
                                       689******9543 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.21
                              C1_2  29 dgffYsCseC 38 
                                       +g +Y+C++C
  gi|336254129|ref|YP_004597236.1| 309 TGRNYYCQRC 318
                                       5667***999 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 ?    0.5   0.3      0.59   5.9e+02       6      12 ..      13      19 ..      13      24 .. 0.80
   2 ?    5.6   0.8     0.015        15       6      20 ..      27      41 ..      27      57 .. 0.88
   3 ?    6.3   0.1    0.0092       9.1      24      31 ..     312     319 ..     303     329 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.59
                    Zn_ribbon_SprT  6 rCtgCgr 12
                                      +C +Cgr
  gi|336254129|ref|YP_004597236.1| 13 YCSHCGR 19
                                      7999996 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.015
                    Zn_ribbon_SprT  6 rCtgCgreythhlsi 20
                                      +C++Cg+ ++++ ++
  gi|336254129|ref|YP_004597236.1| 27 YCPNCGTAIERRDRS 41
                                      7*****999988555 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0092
                    Zn_ribbon_SprT  24 nYrCrrCk 31 
                                       nY+C+rC+
  gi|336254129|ref|YP_004597236.1| 312 NYYCQRCA 319
                                       69999997 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.16   1.5e+02      17      30 ..       8      22 ..       4      26 .. 0.77
   2 ?    5.1   2.1     0.016        16      21      33 ..      27      39 ..      12      45 .. 0.67
   3 ?   -1.7   0.1       2.2   2.2e+03      19      25 ..     312     318 ..     310     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.16
                                      TTCE.EESSSSBEEE CS
                      TF_Zn_Ribbon 17 rgel.vCtdCGlVle 30
                                      r e+ +C+ CG  le
  gi|336254129|ref|YP_004597236.1|  8 RSETrYCSHCGRSLE 22
                                      556669*****8777 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                                      EESSSSBEEEECC CS
                      TF_Zn_Ribbon 21 vCtdCGlVledns 33
                                      +C++CG+ +e ++
  gi|336254129|ref|YP_004597236.1| 27 YCPNCGTAIERRD 39
                                      5666666666554 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.2
                                       CEEESSS CS
                      TF_Zn_Ribbon  19 elvCtdC 25 
                                       +++C +C
  gi|336254129|ref|YP_004597236.1| 312 NYYCQRC 318
                                       7899999 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   1.4   0.00062      0.61      25      49 ..      13      37 ..      11      38 .. 0.92
   2 ?   -0.4   3.0       1.1   1.1e+03      20      31 ..     309     320 ..     275     328 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00062
                                      E-HHHHHHHHHTT-B-TTT--B--E CS
                        zf-C3HC4_3 25 lCeeCaekllkrkkkCpiCrrpiek 49
                                      +C++C ++l+   + Cp C + ie+
  gi|336254129|ref|YP_004597236.1| 13 YCSHCGRSLEPPVNYCPNCGTAIER 37
                                      7********88**********9986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                                       EEEEEE-HHHHH CS
                        zf-C3HC4_3  20 CgHlvlCeeCae 31 
                                       +g  ++C++Ca+
  gi|336254129|ref|YP_004597236.1| 309 TGRNYYCQRCAN 320
                                       445556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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):              18  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2564.58
//
Query:       gi|336254130|ref|YP_004597237.1|  [L=242]
Description: hypothetical protein Halxa_2742 [Halopiger xanaduensis SH-6]
Scores for 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-32  111.3   0.0    5.8e-32  110.8   0.0    1.2  1  Lactamase_B_3  Beta-lactamase superfamily domain
    9.1e-09   35.1   0.3    1.3e-08   34.7   0.3    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 !  110.8   0.0   6.5e-36   5.8e-32       2     163 .]      10     205 ..       9     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 6.5e-36
                     Lactamase_B_3   2 ltwlghnsflleta.garilvDPfka..nlgyeppaeeaDlvlisqaledHahletlkql................. 58 
                                       ++wlg ++++le++ ga+++vDP+ +  ++  ++++++ Dlvl+s++   H++++ ++++                 
  gi|336254130|ref|YP_004597237.1|  10 VDWLGLATVRLEGEtGAVVYVDPGPEryGVLEGQEPRDGDLVLVSHGD--HYDPASIRRVaredalvlvhesidada 84 
                                       89***********76*********76669999999**********998..**********99888888888888888 PP

                     Lactamase_B_3  59 ...........aenvkvleegeslevggleiravatshdavggser.........genngflleqdgltiyhlGhla 115
                                                    +v+ ++ +es+ +g l++ ++++++d+ g+++          ge++gf ++ dg+t y++G+++
  gi|336254130|ref|YP_004597237.1|  85 idgideqpealPYDVERVRADESFVLGPLDLFTTPAYNDPDGPHTDerghpyhreGEGCGFGVTIDGVTAYWPGDTD 161
                                       888877777776677777779*****************5555553334555555599******************** PP

                     Lactamase_B_3 116 helsseelkelgrvDvvltPvggpltlgqeealelakrLkpklvlPmh 163
                                       +    + ++ l +vD++l P+gg++t++++ea+ la +++p lvlP+h
  gi|336254130|ref|YP_004597237.1| 162 A---HPFHADL-DVDLFLPPIGGTYTMDRREAAALAAEMRPGLVLPVH 205
                                       9...5555555.***********************************9 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 !   34.7   0.3   1.4e-12   1.3e-08       3     201 .]      28     206 ..      27     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.4e-12
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylal 79 
                                       + +D+gp+  +  l         +e+++ d+Vl++h+  DH+ +  ++r+ + +++ +++++++ a+  ++++    
  gi|336254130|ref|YP_004597237.1|  28 VYVDPGPERYGV-LEG-------QEPRDGDLVLVSHG--DHY-DPASIRRVAREDALVLVHESIDADAIDGIDEQ-- 91 
                                       568999995555.333.......356778*9999975..899.8999**9776677788*******999996533.. PP

                                       HTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C.......TCCE-TTTSEEEEEECTTEEEEEESS-S---HH CS
                     Lactamase_B_2  80 eeepavnvheldwgesfelgdggleitatparhksgr.......rldrnagdtlGlriegggkrvyyigDtgyipee 149
                                       +e+ + +v+ + ++esf lg+ +  + +tpa  +          +   ++g+ +G+ ++ +g ++y+ gDt   p +
  gi|336254130|ref|YP_004597237.1|  92 PEALPYDVERVRADESFVLGPLD--LFTTPAYNDPDGphtdergHPYHREGEGCGFGVTIDGVTAYWPGDTDAHPFH 166
                                       333679**************866..66666654444335655555555666*********************99966 PP

                                       HHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 150 igerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                       ++  l+ +dl l +i+         + ++++ +ea+++aa+++++ ++++H+
  gi|336254130|ref|YP_004597237.1| 167 AD--LD-VDLFLPPIG---------GTYTMDRREAAALAAEMRPGLVLPVHY 206
                                       44..54.9****9*99.........8999**********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); 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 0.22s 00:00:00.65 Elapsed: 00:00:00.99
# Mc/sec: 737.27
//
Query:       gi|336254131|ref|YP_004597238.1|  [L=325]
Description: transcription initiation factor IIB [Halopiger xanaduensis SH-6]
Scores for 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-38  130.3   0.1    7.6e-20   70.7   0.0    2.2  2  TFIIB            Transcription factor TFIIB repeat
    4.1e-17   61.4   3.3    8.4e-17   60.4   3.3    1.6  1  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00095   19.2   0.0       0.02   15.0   0.0    2.2  2  Cyclin_C         Cyclin, C-terminal domain
  ------ inclusion threshold ------
      0.013   15.4   0.9      0.032   14.1   0.9    1.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.02   14.9   0.8      0.034   14.2   0.8    1.3  1  DZR              Double zinc ribbon
      0.046   12.7   0.2      0.082   11.9   0.2    1.3  1  YopD             YopD protein
       0.05   13.1   4.5        0.1   12.2   0.1    3.2  4  Sigma70_r4       Sigma-70, region 4
       0.19   11.8   6.1       0.99    9.6   1.2    2.4  2  Zn-ribbon_8      Zinc ribbon domain
       0.39   10.9   1.2       0.78    9.9   1.2    1.5  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.43   10.6   2.9        1.4    9.1   2.9    2.0  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
       0.87    9.2   3.3        8.5    6.1   0.2    2.4  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.98    9.2   2.4        4.8    7.0   2.4    1.9  1  A2L_zn_ribbon    A2L zinc ribbon domain
        1.1    9.6   4.4       0.37   11.2   1.0    2.0  1  Lar_restr_allev  Restriction alleviation protein Lar
        1.2    8.6   3.0         12    5.5   3.0    2.1  1  zf-ribbon_3      zinc-ribbon domain
        1.8    8.4   3.7       0.49   10.2   0.4    1.7  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger


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 !   70.7   0.0   6.3e-23   7.6e-20       1      71 []     144     214 ..     144     214 .. 0.97
   2 !   57.7   0.0   7.4e-19   8.8e-16       1      71 []     238     308 ..     238     308 .. 0.99

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 6.3e-23
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i r+a+al+Lpe V++ A  ++++alee++l Grs +g+a A+ly A+r++++ r++ eis+v++V + ++
  gi|336254131|ref|YP_004597238.1| 144 IDRMASALGLPENVRETASVIYRRALEEDLLPGRSIEGVATASLYAAARQAGTPRSLDEISAVSRVDKMEL 214
                                       789***************************************************************99875 PP

  == domain 2  score: 57.7 bits;  conditional E-value: 7.4e-19
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rf++ l+L+++ ++ A el++ a + +v++G+sp g+aAA +y A+++ ++k tq e+s+v+ +se+ti
  gi|336254131|ref|YP_004597238.1| 238 VPRFVSDLDLSDETERMARELLESARKAGVHSGKSPVGLAAAGVYAAALLTNEKVTQNEVSEVASISEVTI 308
                                       689******************************************************************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 !   60.4   3.3     7e-20   8.4e-17       2      43 .]      29      69 ..      28      69 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 7e-20
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      +CP+Cg++ lv D+e++e+vC+dCGlV+e++ id gpewr+f
  gi|336254131|ref|YP_004597238.1| 29 QCPECGGR-LVSDAEHAETVCEDCGLVVEEDEIDRGPEWRAF 69
                                      8******9.8******************************98 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       0.2   2.4e+02      47      85 ..     182     220 ..     180     228 .. 0.88
   2 !   15.0   0.0   1.6e-05      0.02       3      90 ..     234     319 ..     233     325 .] 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.2
                                       HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHH CS
                          Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcvel 85 
                                       +A+a+l++a ++ ++p   +++  +++++k +l   ++ 
  gi|336254131|ref|YP_004597238.1| 182 VATASLYAAARQAGTPRSLDEISAVSRVDKMELTRTYRY 220
                                       79**********999999999999999999999887765 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHH.HCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHH CS
                          Cyclin_C   3 plsFlrrf.lkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgysked 78 
                                       p s++ rf ++   + +d e++ +a+ lle++       + +p  +Aaa +++a    n++  ++++ ++  +s+  
  gi|336254131|ref|YP_004597238.1| 234 PESYVPRFvSDL--DLSD-ETERMARELLESARKAGVHSGKSPVGLAAAGVYAAALLTNEKVTQNEVSEVASISEVT 307
                                       678888997788..6669.****************99999999999999999999999******************* PP

                                       HHHHHHHHHHHH CS
                          Cyclin_C  79 lkpcvelilell 90 
                                       +++ ++ +le++
  gi|336254131|ref|YP_004597238.1| 308 IRNRYKELLEAS 319
                                       ********9987 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 ?   14.1   0.9   2.7e-05     0.032      30      58 ..      29      57 ..      17      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfeadr 58
                                      +C+eCg ++  + ++ + +C++Cg++   
  gi|336254131|ref|YP_004597238.1| 29 QCPECGGRLVSDAEHAETVCEDCGLVVEE 57
                                      8***********************98765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.8   2.8e-05     0.034       9      40 ..      24      57 ..      19      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.8e-05
                               DZR  9 ppdarfCseCgtklkavaa..edrCpsCgekvdp 40
                                      +++++ C+eCg +l + a+  e++C  Cg  v++
  gi|336254131|ref|YP_004597238.1| 24 SEEQEQCPECGGRLVSDAEhaETVCEDCGLVVEE 57
                                      567789*******86555578*******987765 PP

>> YopD  YopD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   6.9e-05     0.082     177     230 ..      96     149 ..      86     155 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.9e-05
                              YopD 177 kisdkdreaiGkvWkaeqvadksklkaldkafesrnskaqvlnaviqsleqman 230
                                       +i+ +d++a Gk   + q +  ++l++ +  f++r+sk + l+ ++  ++ ma 
  gi|336254131|ref|YP_004597238.1|  96 NIGWQDKDAYGKALSSRQRQKMQRLRTWNERFRTRDSKERNLKQALGEIDRMAS 149
                                       78889*****************************************99999996 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.6       3.4   4.1e+03      38      49 ..     110     121 ..     108     122 .. 0.65
   2 ?    0.9   0.0      0.27   3.3e+02      34      46 ..     158     170 ..     148     171 .. 0.89
   3 ?   -2.0   0.0       2.3   2.8e+03      18      28 ..     195     205 ..     190     208 .. 0.79
   4 ?   12.2   0.1   8.4e-05       0.1      18      46 ..     289     317 ..     281     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHHH CS
                        Sigma70_r4  38 rqiekrAlrkLR 49 
                                       ++++++ +++LR
  gi|336254131|ref|YP_004597238.1| 110 SSRQRQKMQRLR 121
                                       466666677776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHH CS
                        Sigma70_r4  34 rerVrqiekrAlr 46 
                                       re+++ i +rAl+
  gi|336254131|ref|YP_004597238.1| 158 RETASVIYRRALE 170
                                       89*********97 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.3
                                       TTT--HHHHHH CS
                        Sigma70_r4  18 geglTleEIge 28 
                                       g +++l EI++
  gi|336254131|ref|YP_004597238.1| 195 GTPRSLDEISA 205
                                       78999999986 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 8.4e-05
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlr 46 
                                        e+ T+ E++e+  iS+ ++r + k+ l+
  gi|336254131|ref|YP_004597238.1| 289 NEKVTQNEVSEVASISEVTIRNRYKELLE 317
                                       5899********************99876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.2   0.00083      0.99      23      36 ..      24      37 ..      12      40 .. 0.66
   2 ?    5.2   0.2      0.02        24      20      34 ..      39      53 ..      36      58 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00083
                       Zn-ribbon_8 23 dapltaCPeCgsev 36
                                       +++++CPeCg+++
  gi|336254131|ref|YP_004597238.1| 24 SEEQEQCPECGGRL 37
                                      344666*****965 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.02
                       Zn-ribbon_8 20 sisdapltaCPeCgs 34
                                      s ++ ++t+C +Cg 
  gi|336254131|ref|YP_004597238.1| 39 SDAEHAETVCEDCGL 53
                                      444778899999985 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 ?    9.9   1.2   0.00065      0.78      16      40 .]      28      52 ..      27      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00065
                     Auto_anti-p27 16 etCpvCgvPLmrdrkggkvyCvaCd 40
                                      e Cp+Cg  L+ d +  +++C  C+
  gi|336254131|ref|YP_004597238.1| 28 EQCPECGGRLVSDAEHAETVCEDCG 52
                                      78************88999**9995 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 ?    9.1   2.9    0.0011       1.4       1      20 [.      29      48 ..      29      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                    DNA_ligase_ZBD  1 hCPvCGsavvReegeaiyRC 20
                                      +CP+CG  +v   + a + C
  gi|336254131|ref|YP_004597238.1| 29 QCPECGGRLVSDAEHAETVC 48
                                      5*********9999888877 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3      0.04        47       2      15 ..      27      40 ..      26      45 .. 0.72
   2 ?    6.1   0.2    0.0071       8.5       4      17 ..      47      60 ..      44      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.04
                            zf_UBZ  2 tylCerCgkeipes 15
                                      + +C++Cg ++ ++
  gi|336254131|ref|YP_004597238.1| 27 QEQCPECGGRLVSD 40
                                      568****9777665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0071
                            zf_UBZ  4 lCerCgkeipesel 17
                                      +Ce+Cg  ++e+e 
  gi|336254131|ref|YP_004597238.1| 47 VCEDCGLVVEEDEI 60
                                      8*********9986 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 ?    7.0   2.4     0.004       4.8       6      30 ..      30      54 ..      26      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.004
                     A2L_zn_ribbon  6 CsvCggngilnseqgylvCieCgas 30
                                      C  Cgg  +  +e+++ vC +Cg++
  gi|336254131|ref|YP_004597238.1| 30 CPECGGRLVSDAEHAETVCEDCGLV 54
                                      778999999999***********86 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 ?   11.2   1.0   0.00031      0.37       3      37 ..      27      62 ..      25      80 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCga........s 37
                                       + CP Cggr v   ++  +        C+dCg          
  gi|336254131|ref|YP_004597238.1| 27 QEQCPECGGRLVSDAEHAET-------VCEDCGLvveedeidR 62
                                      578********999996666.......6*****9544444441 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   3.0    0.0099        12       4      24 ..      29      53 ..      26      55 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0099
                       zf-ribbon_3  4 rCPnCGa.plssd...dnvCpyCGt 24
                                      +CP+CG  ++s+     +vC  CG 
  gi|336254131|ref|YP_004597238.1| 29 QCPECGGrLVSDAehaETVCEDCGL 53
                                      6999998887764222577888886 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 ?   10.2   0.4   0.00041      0.49       1      12 [.      27      38 ..      27      40 .. 0.89
   2 ?   -2.3   0.2       3.2   3.9e+03       3       8 ..      47      52 ..      45      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00041
                                      -EE-SSS--EEE CS
                    zf-C4_Topoisom  1 vekCPkCggdLv 12
                                      +e+CP+Cgg Lv
  gi|336254131|ref|YP_004597238.1| 27 QEQCPECGGRLV 38
                                      589*******99 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.2
                                      E-SSS- CS
                    zf-C4_Topoisom  3 kCPkCg 8 
                                       C+ Cg
  gi|336254131|ref|YP_004597238.1| 47 VCEDCG 52
                                      6****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1177  (0.0656478); expected 358.6 (0.02)
Passed bias filter:                      772  (0.0430587); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2292.20
//
Query:       gi|336254132|ref|YP_004597239.1|  [L=59]
Description: hypothetical protein Halxa_2744 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0025   17.7   3.5       0.21   11.5   0.3    2.1  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
     0.0035   17.2   6.3      0.027   14.4   1.7    1.9  3  zinc_ribbon_4   zinc-ribbon domain
     0.0042   16.8   0.7       0.71    9.6   0.2    2.2  2  Zn_Tnp_IS1      InsA N-terminal domain
     0.0053   16.2   0.6       0.81    9.3   0.1    2.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0061   16.3   0.1     0.0073   16.0   0.1    1.2  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
     0.0072   16.3   0.3     0.0077   16.2   0.3    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.015   15.2   2.9        1.1    9.3   1.1    2.2  2  DUF1610         Domain of unknown function (DUF1610)
      0.025   14.1   0.2      0.025   14.1   0.2    1.0  1  NMD3            NMD3 family
      0.026   14.5   0.3      0.031   14.3   0.3    1.2  1  RNHCP           RNHCP domain
      0.036   14.6   0.4      0.046   14.3   0.4    1.2  1  Stc1            Stc1 domain
       0.04   13.8   1.8        2.8    7.8   0.2    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)
      0.047   13.7   2.2      0.077   13.0   2.2    1.3  1  DZR             Double zinc ribbon
      0.047   13.7   2.0       0.17   11.9   1.8    1.8  2  zinc-ribbons_6  zinc-ribbons
      0.062   13.8   2.5       0.17   12.4   0.3    1.9  2  zf-CHY          CHY zinc finger
      0.067   13.0   1.7        0.5   10.2   0.2    2.2  2  HscB_4_cys      Co-chaperone HscB tetracysteine metal binding
      0.081   13.0   0.4        1.2    9.2   0.0    2.0  2  CpXC            CpXC protein
        0.2   11.6   2.1        2.9    7.8   2.1    2.1  1  HalOD2          Halobacterial output domain 2
       0.27   11.3   4.8       0.38   10.8   0.2    2.1  2  Rubredoxin      Rubredoxin
       0.35   10.3   3.2         17    4.9   1.8    2.4  2  zf_Rg           Reverse gyrase zinc finger
       0.43   10.6   4.8       0.52   10.3   0.6    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.3   0.00024      0.21      19      30 .]       7      18 ..       3      18 .. 0.85
   2 !    7.4   0.3    0.0046       4.1      18      26 ..      29      37 ..      23      39 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                    PhnA_Zn_Ribbon 19 llvCpeCahEwe 30
                                       l+CpeC   w+
  gi|336254132|ref|YP_004597239.1|  7 QLLCPECTKDWQ 18
                                      69******9996 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0046
                    PhnA_Zn_Ribbon 18 allvCpeCa 26
                                      +++ Cp+C+
  gi|336254132|ref|YP_004597239.1| 29 DMFHCPNCH 37
                                      678888887 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.043        38      24      34 ..       6      16 ..       2      18 .. 0.62
   2 !   14.4   1.7   3.1e-05     0.027       5      33 ..      10      38 ..       7      39 .. 0.94
   3 !   10.4   0.2   0.00051      0.46       3      15 ..      31      43 ..      30      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.043
                     zinc_ribbon_4 24 vkvrCskCghv 34
                                      v + C+ C + 
  gi|336254132|ref|YP_004597239.1|  6 VQLLCPECTKD 16
                                      55667777554 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.1e-05
                     zinc_ribbon_4  5 CpsCkakyeiddeklpakgvkvrCskCgh 33
                                      Cp+C +  + ++  lp+++ +  C++C +
  gi|336254132|ref|YP_004597239.1| 10 CPECTKDWQSAPGELPESADMFHCPNCHA 38
                                      ***************************85 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00051
                     zinc_ribbon_4  3 itCpsCkakyeid 15
                                      ++Cp+C+a ++ +
  gi|336254132|ref|YP_004597239.1| 31 FHCPNCHASRRMA 43
                                      68******98865 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 ?    5.7   0.0     0.013        12       3      12 ..       5      14 ..       4      18 .. 0.86
   2 !    9.6   0.2   0.00079      0.71       7      14 ..      32      39 ..      28      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.013
                        Zn_Tnp_IS1  3 sVsihCPrCs 12
                                      +V   CP C 
  gi|336254132|ref|YP_004597239.1|  5 TVQLLCPECT 14
                                      89999****7 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00079
                        Zn_Tnp_IS1  7 hCPrCsst 14
                                      hCP C++ 
  gi|336254132|ref|YP_004597239.1| 32 HCPNCHAS 39
                                      ******96 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.011        10      14      26 ..       2      14 ..       1      18 [. 0.81
   2 !    9.3   0.1    0.0009      0.81       2      19 ..      32      49 ..      31      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                                      ETSTTCEEESSSS CS
                      TF_Zn_Ribbon 14 DpergelvCtdCG 26
                                      D+ +  l+C++C+
  gi|336254132|ref|YP_004597239.1|  2 DETTVQLLCPECT 14
                                      7778888999996 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0009
                                      EETTTTCEECHEETSTTC CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDperge 19
                                       CPnC+ ++   +++r++
  gi|336254132|ref|YP_004597239.1| 32 HCPNCHASRRMAEFMRTD 49
                                      6*****998888888876 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 !   16.0   0.1   8.2e-06    0.0073      19      52 ..       4      38 ..       1      40 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.2e-06
                    zinc_ribbon_10 19 nryalICskChshnGlapkeeleev.kyrCpkCga 52
                                      + + l C++C +    ap e +e    + Cp+C a
  gi|336254132|ref|YP_004597239.1|  4 TTVQLLCPECTKDWQSAPGELPESAdMFHCPNCHA 38
                                      56789*************999999999******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 !   16.2   0.3   8.5e-06    0.0077      66      96 ..       3      40 ..       1      51 [. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.5e-06
                                      EE--EEEETTTS-EEECHH.HHH.......S-TTTSSS- CS
                              HypA 66 evpvkvrCreCgkefelee.kal.......rCpkCgsad 96
                                      e+ v++ C eC k+++++  + l       +Cp+C++++
  gi|336254132|ref|YP_004597239.1|  3 ETTVQLLCPECTKDWQSAPgE-LpesadmfHCPNCHASR 40
                                      67899***********88642.34456677*****9875 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.014        13      15      22 ..       6      13 ..       2      15 .. 0.80
   2 ?    9.3   1.1    0.0012       1.1      16      22 ..      30      36 ..      25      36 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                           DUF1610 15 vvFpCPNC 22
                                      v  +CP+C
  gi|336254132|ref|YP_004597239.1|  6 VQLLCPEC 13
                                      5669**** PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
                           DUF1610 16 vFpCPNC 22
                                       F CPNC
  gi|336254132|ref|YP_004597239.1| 30 MFHCPNC 36
                                      69***** PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   2.8e-05     0.025      11      55 ..       5      50 ..       1      58 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                              NMD3 11 linglCedCllkevditegiek.ievevCkeCgrylpkgkWvkael 55
                                      +++ lC++C ++        ++ +++ +C++C++ ++  ++++ + 
  gi|336254132|ref|YP_004597239.1|  5 TVQLLCPECTKDWQSAPGELPEsADMFHCPNCHASRRMAEFMRTDR 50
                                      4567******9987777666666***********998888877544 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   3.4e-05     0.031       4      43 ..       8      51 ..       5      58 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-05
                             RNHCP  4 ftCeeCgkevekla...agsakrnHCpsCLlskHvde.epgdra 43
                                      + C eC k+ + +    ++sa   HCp+C +s+ + e +  dr 
  gi|336254132|ref|YP_004597239.1|  8 LLCPECTKDWQSAPgelPESADMFHCPNCHASRRMAEfMRTDRD 51
                                      679999988776531125677889*********99886677775 PP

>> Stc1  Stc1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   5.1e-05     0.046      36      73 ..       4      51 ..       1      56 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.1e-05
                                      ...----TTTS-----E..........EE-SSS--EEESTTS-HHHHH CS
                              Stc1 36 akskikCkectakqate..........leCsaCqktkpldeFsksqrr 73
                                      ++ ++ C ect++ +             +C  C+ ++ + eF ++ r 
  gi|336254132|ref|YP_004597239.1|  4 TTVQLLCPECTKDWQSApgelpesadmFHCPNCHASRRMAEFMRTDRD 51
                                      455889*****997777899******9****************99986 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 ?    7.8   0.2    0.0032       2.8      25      39 .]       4      18 ..       2      18 .. 0.86
   2 ?    5.6   0.1     0.016        14       1      10 [.      31      40 ..      31      48 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0032
                           TFIIS_C 25 mtvfykCtkCghrWr 39
                                      +tv   C +C + W+
  gi|336254132|ref|YP_004597239.1|  4 TTVQLLCPECTKDWQ 18
                                      788999********6 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.016
                           TFIIS_C  1 akCpkCgsre 10
                                      + Cp+C+  +
  gi|336254132|ref|YP_004597239.1| 31 FHCPNCHASR 40
                                      57****9765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.2   8.6e-05     0.077      14      37 ..       9      39 ..       4      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.6e-05
                               DZR 14 fCseCgtklkavaa.......edrCpsCgek 37
                                       C+eC ++ ++++        + +Cp+C+++
  gi|336254132|ref|YP_004597239.1|  9 LCPECTKDWQSAPGelpesadMFHCPNCHAS 39
                                      6*******88777789999999******987 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   0.2    0.0053       4.7      26      40 ..       4      18 ..       1      22 [. 0.73
   2 ?   11.9   1.8   0.00019      0.17       2      30 ..       9      44 ..       8      59 .] 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0053
                                      EEEEEE-SSS-S--- CS
                    zinc-ribbons_6 26 lkkealCpeCeqele 40
                                       +++ lCpeC +  +
  gi|336254132|ref|YP_004597239.1|  4 TTVQLLCPECTKDWQ 18
                                      567888999987655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00019
                                      --SSS-S--EE-S.......SEEE-TTT--EEEEEE CS
                    zinc-ribbons_6  2 kCpeCqqelekrg.......eqyhCeaCqedlkkea 30
                                       CpeC +  ++         + +hC +C+++ ++  
  gi|336254132|ref|YP_004597239.1|  9 LCPECTKDWQSAPgelpesaDMFHCPNCHASRRMAE 44
                                      6****999996667899999999*****98766654 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.0    0.0054       4.8      53      73 ..       6      37 ..       1      38 [. 0.69
   2 ?   12.4   0.3   0.00019      0.17      13      38 ..      24      49 ..      15      57 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0054
                            zf-CHY 53 kavlCkkCkk...........efaeyfCpiCk 73
                                      ++ lC +C+k           +++ ++Cp+C+
  gi|336254132|ref|YP_004597239.1|  6 VQLLCPECTKdwqsapgelpeSADMFHCPNCH 37
                                      56678888777777777777666667888887 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00019
                            zf-CHY 13 apcCkklyaCreCHeeledhelerle 38
                                      +p   ++++C +CH++ +  e+ r++
  gi|336254132|ref|YP_004597239.1| 24 LPESADMFHCPNCHASRRMAEFMRTD 49
                                      5677899*******876666666654 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1       0.2   1.8e+02      18      23 ..       8      13 ..       5      14 .. 0.85
   2 ?   10.2   0.2   0.00056       0.5      12      25 ..      25      38 ..      19      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.2
                                      -B-TTT CS
                        HscB_4_cys 18 fFCpqC 23
                                      + Cp C
  gi|336254132|ref|YP_004597239.1|  8 LLCPEC 13
                                      67**** PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00056
                                      SS-S---B-TTT-- CS
                        HscB_4_cys 12 pgrgdefFCpqCRA 25
                                      p  +d f Cp C A
  gi|336254132|ref|YP_004597239.1| 25 PESADMFHCPNCHA 38
                                      5679********87 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.14   1.3e+02      34      46 ..       4      16 ..       1      21 [. 0.68
   2 ?    9.2   0.0    0.0014       1.2      34      50 ..      27      43 ..      24      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.14
                              CpXC 34 slfeatCpkCgat 46
                                      +  +  Cp+C ++
  gi|336254132|ref|YP_004597239.1|  4 TTVQLLCPECTKD 16
                                      5566778888765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0014
                              CpXC 34 slfeatCpkCgatakle 50
                                      s  +++Cp+C+a++++ 
  gi|336254132|ref|YP_004597239.1| 27 SADMFHCPNCHASRRMA 43
                                      56789*******99986 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.1    0.0033       2.9       5      18 ..      10      23 ..       8      45 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0033
                            HalOD2  5 CseCsldWttrhGd 18
                                      C+eC  dW    G+
  gi|336254132|ref|YP_004597239.1| 10 CPECTKDWQSAPGE 23
                                      ********655443 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.7      0.16   1.4e+02      36      42 ..       9      15 ..       6      20 .. 0.79
   2 ?   10.8   0.2   0.00043      0.38      33      45 ..      29      41 ..      17      43 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.16
                                      BBTTTB- CS
                        Rubredoxin 36 vCPdCgv 42
                                       CP+C  
  gi|336254132|ref|YP_004597239.1|  9 LCPECTK 15
                                      6****75 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00043
                                      TT-BBTTTB-BGG CS
                        Rubredoxin 33 ddWvCPdCgveke 45
                                      d ++CP+C +++ 
  gi|336254132|ref|YP_004597239.1| 29 DMFHCPNCHASRR 41
                                      579******9875 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.023        20       5      14 ..       5      14 ..       1      20 [. 0.74
   2 ?    4.9   1.8     0.019        17       9      14 ..      32      37 ..      26      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.023
                             zf_Rg  5 vfeklCPNCg 14
                                       ++ lCP C 
  gi|336254132|ref|YP_004597239.1|  5 TVQLLCPECT 14
                                      67789****7 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.019
                             zf_Rg  9 lCPNCg 14
                                       CPNC+
  gi|336254132|ref|YP_004597239.1| 32 HCPNCH 37
                                      5****8 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 ?    2.7   0.3      0.14   1.3e+02      21      27 ..      10      16 ..       4      23 .. 0.79
   2 ?   10.3   0.6   0.00058      0.52      18      28 ..      30      41 ..      21      53 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.14
                     Zn_Tnp_IS1595 21 CPhCgsr 27
                                      CP C ++
  gi|336254132|ref|YP_004597239.1| 10 CPECTKD 16
                                      9*99865 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00058
                     Zn_Tnp_IS1595 18 gfvCPhCgsr.k 28
                                       f+CP+C+ + +
  gi|336254132|ref|YP_004597239.1| 30 MFHCPNCHASrR 41
                                      499*****8753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 450.57
//
Query:       gi|336254133|ref|YP_004597240.1|  [L=80]
Description: hypothetical protein Halxa_2745 [Halopiger xanaduensis SH-6]
Scores for 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-21   74.6   0.0    5.9e-21   74.5   0.0    1.0  1  UPF0058   Uncharacterised protein family UPF0058
  ------ inclusion threshold ------
      0.048   13.5   0.0      0.052   13.4   0.0    1.1  1  NinB      NinB protein


Domain annotation for each model (and alignments):
>> UPF0058  Uncharacterised protein family UPF0058
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   6.6e-25   5.9e-21       1      73 [.       3      75 ..       3      80 .] 0.91

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 6.6e-25
                                      --HHHHHHHHHHHHHHHHHH.TSTT--TTTTHHHHHH---TT-TTS-HHHHHHHHHHHHHHHHHHHHHHHHCCC CS
                           UPF0058  1 MhKdeLieLHqllvevkkel.eeeevekeefkeYeeLdisPhhihrsKaehkaAifvLgnaiakalsekeessa 73
                                      M+K+eLi+LH ll+ev ++  e +++e + ++eYe+L i+P+ ih+sK++hkaA+f L+  i   ++e+e+++ 
  gi|336254133|ref|YP_004597240.1|  3 MKKQELIHLHGLLAEVSNQCaEWDNCEID-LEEYESLGIRPTSIHKSKTDHKAAVFALAGGITANMREDEQEAV 75
                                      9*******************666677666.***************************************99854 PP

>> NinB  NinB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.8e-06     0.052      47     102 ..      10      68 ..       4      80 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.8e-06
                              NinB  47 llwallkdiarqv.ewagekldaeeWKdllt..aalkqatgeeqevvpgleGgfvvlge 102
                                        l+ ll+++++q+ ew +  +d ee+  l +   ++ +++ +++ +v +l Gg+    +
  gi|336254133|ref|YP_004597240.1|  10 HLHGLLAEVSNQCaEWDNCEIDLEEYESLGIrpTSIHKSKTDHKAAVFALAGGITANMR 68 
                                       69**********868************9865234556668999999******9976555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 605.81
//
Query:       gi|336254134|ref|YP_004597241.1|  [L=171]
Description: hypothetical protein Halxa_2746 [Halopiger xanaduensis SH-6]
Scores for complete 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  128.2   0.2    1.8e-37  127.7   0.2    1.2  1  DUF555       Protein of unknown function (DUF555)
  ------ inclusion threshold ------
       0.04   13.8   5.1      0.041   13.8   5.1    1.1  1  CNDH2_C      Condensin II complex subunit CAP-H2 or CNDH2, C-
       0.24   11.1  15.4       0.33   10.6  15.4    1.2  1  Cwf_Cwc_15   Cwf15/Cwc15 cell cycle control protein
       0.38   10.8   5.3       0.45   10.5   5.3    1.1  1  DUF2076      Uncharacterized protein conserved in bacteria (D
          8    5.8  17.3         10    5.5  17.3    1.1  1  SDA1         SDA1
        8.1    4.5  19.3        9.7    4.3  19.3    1.0  1  Nop14        Nop14-like family


Domain annotation for each model (and alignments):
>> DUF555  Protein of unknown function (DUF555)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7   0.2   6.1e-41   1.8e-37       1     101 []       2     101 ..       2     101 .. 0.99

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 6.1e-41
                            DUF555   1 dyevvleaawivrdvksvddAigiAiseagkrlnpeldfveievgetecPkcgeelesalvvadtalvglllemkvf 77 
                                       +++vv+eaa+ v dv++ d+Ai+iAis++g++lnp+l++vei++ge ++P+ geel +a+++ad+alv+l+lem+vf
  gi|336254134|ref|YP_004597241.1|   2 NCRVVVEAAVPVFDVETEDEAIRIAISKTGEMLNPDLNYVEINMGERTSPS-GEELPPAFIAADEALVALELEMTVF 77 
                                       799***********************************************9.9************************ PP

                            DUF555  78 naeseEhaeriakseigkaledvP 101
                                       n+e+eEha+ria++eig++le++P
  gi|336254134|ref|YP_004597241.1|  78 NVEREEHASRIARKEIGQRLENIP 101
                                       ***********************9 PP

>> CNDH2_C  Condensin II complex subunit CAP-H2 or CNDH2, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   5.1   1.4e-05     0.041      73     168 ..      62     170 ..      17     171 .] 0.63

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                           CNDH2_C  73 d........eleylyqkeakerskarrklar...........eeklkqalleeeeaeeeeevdeqedd.ddneaedg 129
                                                ele+++ + ++e+++ r    r            e  + ++leee+ +ee+e+d+++ + dd + e+ 
  gi|336254134|ref|YP_004597241.1|  62 AadealvalELEMTVFNVEREEHASRIA--RkeigqrlenipLEVTEVEVLEEEDLDEEAEDDAEAGEpDDLDLESE 136
                                       4455555555777776666666665543..33576676666667777777777777777777766443366666666 PP

                           CNDH2_C 130 vdddddfgieleeeeddlkeseeeeeeeeeeeltYeeLv 168
                                       +d+dd+++ +      +++e++  ++e+ e   ++e+Lv
  gi|336254134|ref|YP_004597241.1| 137 SDADDSSEADA-----ESDEESDDDDEDDEVLPEFEDLV 170
                                       66664444444.....33333333445677788899998 PP

>> Cwf_Cwc_15  Cwf15/Cwc15 cell cycle control protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6  15.4   0.00011      0.33      81     148 ..     100     161 ..      60     169 .. 0.35

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                       -...--------------------------..-----------------............---------------- CS
                        Cwf_Cwc_15  81 e...ekekkeeeeeeeeeeakrrkeelleeareidaddedseeeeeeee............eesdddsdsdsddddd 142
                                            +e +                 +lee +++d++ ed+ e  e ++            +e d +sd++sdddd+
  gi|336254134|ref|YP_004597241.1| 100 IpleVTEVE-----------------VLEE-EDLDEEAEDDAEAGEPDDldlesesdaddsSEADAESDEESDDDDE 158
                                       122211111.................2211.2222222222222222223333322221102223333333333333 PP

                                       ------ CS
                        Cwf_Cwc_15 143 edetae 148
                                          ++e
  gi|336254134|ref|YP_004597241.1| 159 ---DDE 161
                                       ...333 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 ?   10.5   5.3   0.00015      0.45     195     257 ..     103     160 ..      68     162 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                           DUF2076 195 saeeeeiinnyyssssladdaedadnasadsfadsdsssdnnadaasdddsdddssddgggDD 257
                                       + +e+e+++++    +l+++aed+ +a++ ++  + +s++++ d++++d+++d++sdd+++DD
  gi|336254134|ref|YP_004597241.1| 103 EVTEVEVLEEE----DLDEEAEDDAEAGEPDDL-DLESESDADDSSEADAESDEESDDDDEDD 160
                                       33444444444....455555555555554433.45666667777778888888888888888 PP

>> SDA1  SDA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  17.3    0.0033        10      72     142 ..     106     160 ..      66     168 .. 0.42

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0033
                              SDA1  72 GleLlekwkeeekkekreeeeedsddeddeedwevesdddseedseggwidvesdeeeieesdesedeeee 142
                                        +e le+++ +e++       ed+ ++ + +d ++es++d  +ds+    d esdee    sd  +d+e++
  gi|336254134|ref|YP_004597241.1| 106 EVEVLEEEDLDEEA-------EDDAEAGEPDDLDLESESDA-DDSS--EADAESDEE----SD--DDDEDD 160
                                       22222222222221.......11122223333333333333.2221..123444433....22..111111 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  19.3    0.0032       9.7     336     399 ..      93     161 ..      63     169 .. 0.47

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0032
                             Nop14 336 lgkglka.....taeee.eeededdfeedddlveseseeeeeeeeedeeeeedeeeeeeeeededdlsdl 399
                                       +g+ l++     t+ e  eeed d++ edd +  + ++ +  e+e+d +++++ ++e++ee+d+dd++d+
  gi|336254134|ref|YP_004597241.1|  93 IGQRLENiplevTEVEVlEEEDLDEEAEDDAEAGEPDDLDL-ESESDADDSSEADAESDEESDDDDEDDE 161
                                       33444325555444444355555555555433333333333.3333333333333333333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1290.66
//
Query:       gi|336254135|ref|YP_004597242.1|  [L=293]
Description: DNA-(apurinic or apyrimidinic site) lyase [Halopiger xanaduensis SH-6]
Scores for 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-15   56.3   0.0    1.2e-14   54.6   0.0    1.8  2  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
    1.7e-06   28.1   0.0    6.8e-06   26.2   0.0    1.8  1  OGG_N     8-oxoguanine DNA glycosylase, N-terminal domain
  ------ inclusion threshold ------
      0.038   14.3   0.1       0.14   12.5   0.1    1.9  2  AlkA_N    AlkA N-terminal 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 ?   -1.3   0.0      0.49   2.9e+03      74      94 ..      50      70 ..      44     101 .. 0.60
   2 !   54.6   0.0   2.1e-18   1.2e-14       1      92 [.     122     259 ..     122     273 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.49
                                      TTSHHHHHHHHHHTTSSSSTT CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD 74 vvDvhvrrilkrlrsikekkt 94
                                      vvD  v r+    + ++ + t
  gi|336254135|ref|YP_004597242.1| 50 VVDGEVIRVRTADGRLEWQST 70
                                      666666666655555554422 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 2.1e-18
                                       HHHHHHTTS-HHHHHHHHHHHHHHHS............HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfg............fptpedladadeekLrelirelGfyrrKakyikelAril 65 
                                       +s+i+s+q +++r+  ++  l++++g            fptpe+la a+e++Lrel    G++ ++a+y+  +A+++
  gi|336254135|ref|YP_004597242.1| 122 ISFICSAQMRVSRIHGMVSTLAREYGtpldvdgrtyyaFPTPEQLATATEAELREL----GLG-YRAPYVVRTAEMV 193
                                       79******************************************************....***.************* PP

                                       H........................................S-SSS--TTSHHHHHHHHHHTTSSSS CS
                                       x........................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  66 v........................................gkpdvlivvDvhvrrilkrlrsikek 92 
                                       +                                        g+ + +++ D++++ +++ +++  ++
  gi|336254135|ref|YP_004597242.1| 194 AdgeahpaearnleyeaardylcqfvgvgdkvadcvllfslGFDE-AVPLDTWIKSAIEDYYPDCDR 259
                                       ****************************************99855.8888*******9998876555 PP

>> 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 !   26.2   0.0   1.1e-09   6.8e-06       9     121 .]      15     121 ..       8     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.1e-09
                                       --HHHHHCSSS-SSEEE-TTS.........-.EEEEETTEEEEEEEETTEEEEET--.............HHHHHHT CS
                             OGG_N   9 ldlkktLkcGQsFrWkktekt.........e.yvgvlgdrvveLkqeeddllyrtlesesstkasseeakeeeteei 75 
                                       +dl  tL++GQ++ W++++++         + y++v++++v+ ++  +  l+++ +                + e +
  gi|336254135|ref|YP_004597242.1|  15 MDLYRTLESGQTYLWRREDGEmyrtepapgTwYSTVVDGEVIRVRTADGRLEWQSTT---------------DAEPT 76 
                                       68999***********88888566555544257777778888888777777777766...............8899* PP

                                       HHHHTTTTS-HHHHHHHHTT.SHHHHHHHCCTTT-------HHHHH CS
                             OGG_N  76 lrdYfnLdvdleelykewskkdplfkksadkftGiRllrqdpwEcL 121
                                       +r+ ++Ld dle ++ + + +dpl++++++ ++G+Rl+    + cL
  gi|336254135|ref|YP_004597242.1|  77 VRRLLRLDDDLEAIV-DAAPDDPLLREAYEAHRGMRLVTDPAFGCL 121
                                       ***************.88999****************998888776 PP

>> AlkA_N  AlkA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.3e-05      0.14      71     111 ..      70     112 ..      40     115 .. 0.84
   2 ?   -1.6   0.0      0.52   3.1e+03       2      13 ..     177     188 ..     176     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                            AlkA_N  71 leaviarvrrllDLdadpeaieaaL..dpllapevaarpGlRv 111
                                        + +  +vrrll Ld d eai +a   dpll++  +a+ G+R+
  gi|336254135|ref|YP_004597242.1|  70 TTDAEPTVRRLLRLDDDLEAIVDAApdDPLLREAYEAHRGMRL 112
                                       5556678**************99999****************8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.52
                            AlkA_N   2 lrLayrpPydwa 13 
                                       l L yr Py ++
  gi|336254135|ref|YP_004597242.1| 177 LGLGYRAPYVVR 188
                                       6799*****765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2021.77
//
Query:       gi|336254136|ref|YP_004597243.1|  [L=107]
Description: hypothetical protein Halxa_2748 [Halopiger xanaduensis SH-6]
Scores for 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-05   24.5   0.1    3.1e-05   24.1   0.1    1.1  1  DUF3784   Domain of unknown function (DUF3784)


Domain annotation for each model (and alignments):
>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   1.7e-09   3.1e-05       3      92 ..      12     102 ..      10     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.7e-09
                           DUF3784   3 lallflilGilflkgkganLiaGYntmskeekekydekklsrfmgivllligilflllgll......saiesealli 73 
                                       +a+++ +lG+l+       LiaGY        +  de +l+ f+g   l +++l++l ++        + + + +++
  gi|336254136|ref|YP_004597243.1|  12 SAGFVGLLGVLIKYFGRVELIAGYD-----PERVADETGLADFIGTNALYVAALLFLVAVAeyaepfGGDGADLVWL 83 
                                       689999******************5.....899*******************9999999999998754445555555 PP

                           DUF3784  74 ialiviiiiviylivyank 92 
                                       ++++ ++++++ +i +a++
  gi|336254136|ref|YP_004597243.1|  84 AFTVGVLGLAVRMIRGARR 102
                                       5666777777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 850.78
//
Query:       gi|336254137|ref|YP_004597244.1|  [L=90]
Description: hypothetical protein Halxa_2749 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0069   16.5   4.3     0.0088   16.2   4.3    1.0  1  FUSC_2    Fusaric acid resistance protein-like


Domain annotation for each model (and alignments):
>> FUSC_2  Fusaric acid resistance protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   4.3   4.9e-07    0.0088      28      85 ..      16      74 ..      13      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.9e-07
                            FUSC_2 28 tlgasltravqRilGtvlGavlallllyllpgn.lalallvfllvfliafflkrnyala 85
                                      + +asl+ +++ ++G +l +v a ++ y+l g   ala++v+l+v++++ ++++ y + 
  gi|336254137|ref|YP_004597244.1| 16 SGRASLRDLLELVVGSILFVVGASAFTYYLLGRtTALAVAVALVVVFAITIVSQAYWGV 74
                                      5679999*******************99888877*******************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1023  (0.0570584); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 749.77
//
Query:       gi|336254138|ref|YP_004597245.1|  [L=82]
Description: hypothetical protein Halxa_2750 [Halopiger xanaduensis SH-6]
Scores for 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:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); 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: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 726.32
//
Query:       gi|336254139|ref|YP_004597246.1|  [L=92]
Description: Acylphosphatase [Halopiger xanaduensis SH-6]
Scores for complete 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   89.6   0.1    1.5e-25   89.4   0.1    1.0  1  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
      0.068   12.7   0.1      0.079   12.5   0.1    1.0  1  Acyl_transf_1    Acyl transferase domain


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.1   1.7e-29   1.5e-25       2      85 .]       8      90 ..       7      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1.7e-29
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      +++v+G+VQgv++R+++r+ A+  g++G+v+Nl+dg+Ve+v+eg+e++v++++e++++g+p+a+v+ veve ++ ++e 
  gi|336254139|ref|YP_004597246.1|  8 HVFVSGNVQGVYYRATTRDTARGEGVDGWVKNLEDGRVEAVFEGPEDAVDAMVEFCREGSPAAEVETVEVEYEDPQGE- 85
                                      789*******************************************************************99999998. PP

                   Acylphosphatase 81 kdFei 85
                                      ++Fei
  gi|336254139|ref|YP_004597246.1| 86 DGFEI 90
                                      ***98 PP

>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   8.8e-06     0.079     124     195 ..      10      84 ..       3      89 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.8e-06
                                       TS-EECCEECS..HHHHHHH....TT.EEEEEEECCCCECCEEHHHHHHHHHHHHHCC.CCEEECCCEECTTCCC CS
                     Acyl_transf_1 124 agpgdmaavel.aeeeeklr..cqddvvgavansprrvvisgsqealrelvervskegvgalvenvnvavhspqv 195
                                        + g+  +v   a+++  +r    d  v     +  + v +g+++a++++ve +++   +a+ve+v+v  + pq 
  gi|336254139|ref|YP_004597246.1|  10 FVSGNVQGVYYrATTRDTARgeGVDGWVKNLEDGRVEAVFEGPEDAVDAMVEFCREGSPAAEVETVEVEYEDPQG 84 
                                       56677777777433333333334555555555566677899****************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 683.72
//
Query:       gi|336254140|ref|YP_004597247.1|  [L=164]
Description: hypothetical protein Halxa_2752 [Halopiger xanaduensis SH-6]
Scores for 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  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); 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:                         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 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1245.21
//
Query:       gi|336254141|ref|YP_004597248.1|  [L=481]
Description: YjeF-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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  142.8   1.9    1.9e-41  142.1   1.9    1.3  1  Carb_kinase   Carbohydrate kinase
    1.3e-39  135.8   0.7    2.6e-39  134.9   0.7    1.5  1  YjeF_N        YjeF-related protein N-terminus
    5.7e-08   32.4   0.1      1e-07   31.6   0.1    1.5  1  HK            Hydroxyethylthiazole kinase family
    8.4e-08   31.9   0.1    2.1e-07   30.6   0.2    1.6  2  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 !  142.1   1.9   4.3e-45   1.9e-41       3     243 ..     230     470 ..     229     471 .. 0.92

  Alignments for each domain:
  == domain 1  score: 142.1 bits;  conditional E-value: 4.3e-45
                                       EEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT....HTTTS....--SSS-SE.EEE CS
                       Carb_kinase   3 vigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll....edeqa.kileklerlda.vvi 73 
                                       +igG   ytGA+ laa+aalr+ga l  va+  + + +++ y++++iv+p++      e+a   le  e +da vv+
  gi|336254141|ref|YP_004597248.1| 230 IIGG-GPYTGAPALAAQAALRAGAELSFVAAPDTVAGEIQGYSEDLIVQPYEedvlTPERAkALLERVEGYDApVVL 305
                                       7888.9**********************************************888845566568999999999899* PP

                                       -TT-SSSHCHHHHCHHHCCCCS-.EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHH CS
                       Carb_kinase  74 GpGLgrdekikklleevlekdep.lviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelare 149
                                       GpGLg+ +++ ++++ +le + +  v+DAd+L+++ +     e +a ++ TP+ +E + + +         ++  ++
  gi|336254141|ref|YP_004597248.1| 306 GPGLGTADETLEAVRRFLESYTGtAVVDADALQVVPE----VETEATLVCTPNRGELAGMGGPDTDDLAAAADEIEA 378
                                       ***********************9************9....59*****************99777455555555567 PP

                                       HHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHC CS
                       Carb_kinase 150 laqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaa 226
                                       +a+ l+ vvl kg++dvi + ++ + i   g++++ +GG+GD+LaG+++alL   e +++aa+aaa ++g a++++a
  gi|336254141|ref|YP_004597248.1| 379 FAADLGHVVLAKGANDVITD-GERTRISRSGTVGMKVGGTGDTLAGIVAALLERTE-PLDAAAAAAHVNGLAGERLA 453
                                       8899*************999.9999999*************************999.******************** PP

                                       CCT-TS-HCHHHHHHHC CS
                       Carb_kinase 227 ekkgvgmlatelskiip 243
                                       ++   g la e++ +ip
  gi|336254141|ref|YP_004597248.1| 454 DRSEHGFLASEMLAEIP 470
                                       **999999999888876 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 !  134.9   0.7   5.8e-43   2.6e-39       2     171 .]      22     184 ..      21     184 .. 0.93

  Alignments for each domain:
  == domain 1  score: 134.9 bits;  conditional E-value: 5.8e-43
                            YjeF_N   2 eeLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeee.kldedaeralel 77 
                                       ++Lme++g+ava+++r+++    ++ +v +++G+gnnGgd+++ Ar+L    ++Vt+lll + e  ++e a++++++
  gi|336254141|ref|YP_004597248.1|  22 KQLMESSGHAVARAVRDAA---APGSSVAIVAGRGNNGGDAFVTARFL--DAYDVTTLLLGRAEnIGTEIARENWDA 93 
                                       69*****************...9*************************..8899999555555549*********** PP

                            YjeF_N  78 lkkaggkvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsg 154
                                       l++a  ++ e +++++ +     ++d+v+DA+lG+g++g+lre++a+++  +n+++a+v++vD+PSG+dad G+ + 
  gi|336254141|ref|YP_004597248.1|  94 LRRADYDTREVTDSSAFDLP---ECDVVVDAMLGTGISGDLREPAATAAAAINDADATVVSVDVPSGFDADGGDHDD 167
                                       ******99998888887653...5***************************************************** PP

                            YjeF_N 155 tavkadvtvtfgapkrg 171
                                       + v+ad +vtf+  k+g
  gi|336254141|ref|YP_004597248.1| 168 NGVEADRVVTFHDAKPG 184
                                       ************99987 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.1   2.3e-11     1e-07     127     234 ..     360     463 ..     285     473 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.3e-11
                                       CSCSSSSSS-SHHHHHHHHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSS CS
                                HK 127 kvkGvDskeaataavaavqkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkd 203
                                        + G D+ + a+ a   +++ A  l+ vv++ G+ Dv++dg+++   ++Gt  + k+ ++G +l+ +vaa l   ++
  gi|336254141|ref|YP_004597248.1| 360 GMGGPDTDDLAA-AADEIEAFAADLGHVVLAKGANDVITDGERTRISRSGTVGM-KVGGTGDTLAGIVAALLE-RTE 433
                                       566777777776.578999**************************99***9877.8*************9986.678 PP

                                       HHHHHHHHHHHHHHHH.HHHHHHHTTHHHHH CS
                                HK 204 kllaaveavllykvAgkeaaarsegsgsFqv 234
                                       +l+aa++a ++  +Ag++ a rse  g   +
  gi|336254141|ref|YP_004597248.1| 434 PLDAAAAAAHVNGLAGERLADRSEH-GFLAS 463
                                       9***************999988764.44444 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.1   4.8e+03      46      93 ..     261     307 ..     242     316 .. 0.66
   2 !   30.6   0.2   4.7e-11   2.1e-07      98     224 ..     326     442 ..     321     445 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHHHHHHTTSSEEEE- CS
                      Phos_pyr_kin  46 elveaqleavledvkvdavKiGmlasaeiievvaeklkkykvpvVlDP 93 
                                       ++v+  ++   ed+ v+     +l + e ++++ e ++ y++pvVl P
  gi|336254141|ref|YP_004597248.1| 261 DTVAGEIQGYSEDLIVQPYEEDVL-TPERAKALLERVEGYDAPVVLGP 307
                                       555555555555555555555555.55666777777788888888877 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 4.7e-11
                                       CTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEE CS
                      Phos_pyr_kin  98 ksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvt 174
                                        +g+++++++a++++ e   + + v tPN  E++ + g + ++++ + +  +++++   + Vl kG +         
  gi|336254141|ref|YP_004597248.1| 326 YTGTAVVDADALQVVPEVETEATLVCTPNRGELAGMGGPDTDDLAAAADEIEAFAADLGHVVLAKGAN--------- 393
                                       57899999******999777888889************99999999999999999988999*****87......... PP

                                       EEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHH CS
                      Phos_pyr_kin 175 dvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkA 224
                                       dv+ dge++++ ++  +   +  GtG+tl+  +aa l + e+l  A + A
  gi|336254141|ref|YP_004597248.1| 394 DVITDGERTRISRSGTVG-MKVGGTGDTLAGIVAALLERTEPLDAAAAAA 442
                                       999999999999999998.99***********************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3408.73
//
Query:       gi|336254142|ref|YP_004597249.1|  [L=180]
Description: molybdenum cofactor biosynthesis protein C [Halopiger xanaduensis SH-6]
Scores for complete 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-48  164.4   0.4    1.7e-48  164.2   0.4    1.0  1  MoaC      MoaC family


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.2   0.4   9.3e-53   1.7e-48       1     135 [.      38     177 ..      38     178 .. 0.98

  Alignments for each domain:
  == domain 1  score: 164.2 bits;  conditional E-value: 9.3e-53
                                       E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEE CS
                              MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkvevelele 77 
                                       mvdv++k++++r+AvA+g+++l+++t+e+i+++++ kGdvla+ar+++++a+K+t+e+ip+cH++p+t+v++++el 
  gi|336254142|ref|YP_004597249.1|  38 MVDVGDKPDSERRAVAAGEIRLQASTVEAIRDDQIGKGDVLATARVGAVQAVKHTWETIPMCHQIPITNVDTDFELG 114
                                       9*************************************************************************987 PP

                                       TTTTEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEES CS
                              MoaC  78 eeeesveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKsg 135
                                         e++ve+e++v+t+gktG+emEAL++v++++ +v+DmvKav+k+       + ie+vr++eK++
  gi|336254142|ref|YP_004597249.1| 115 --EDRVELEVAVETTGKTGCEMEALEGVTTGLNVVWDMVKAVEKDdngqypeTGIENVRVLEKEK 177
                                       ..79****************************************99*****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1400.49
//
Query:       gi|336254143|ref|YP_004597250.1|  [L=339]
Description: 2-nitropropane dioxygenase NPD [Halopiger xanaduensis SH-6]
Scores for 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-64  217.7   3.1    5.5e-63  213.3   3.1    2.0  1  NMO           Nitronate monooxygenase
      5e-09   35.6   8.8      5e-09   35.6   8.8    1.5  2  FMN_dh        FMN-dependent dehydrogenase
    6.8e-09   35.2   6.6      6e-08   32.1   6.6    2.1  1  IMPDH         IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.013   14.9   0.6      0.028   13.9   0.6    1.5  1  His_biosynth  Histidine biosynthesis protein
      0.078   12.2   0.9       0.13   11.4   0.9    1.3  1  DHO_dh        Dihydroorotate dehydrogenase
       0.13   11.4   2.8       0.23   10.6   2.8    1.5  1  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.3   3.1   1.8e-66   5.5e-63       2     329 ..       5     324 ..       4     326 .. 0.89

  Alignments for each domain:
  == domain 1  score: 213.3 bits;  conditional E-value: 1.8e-66
                               NMO   2 slltellkikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvkaltdkPfgvnlflpkkdaad 78 
                                       ++l + l+i++p+vq++ g  ++++LaaavsnaGgLG la     + + ++ i+  +  td+Pf vnl l+ + +  
  gi|336254143|ref|YP_004597250.1|   5 TPLCDALEIEHPIVQAPIGSATNPDLAAAVSNAGGLGHLAVTWRGLEETRDVIHDTRDRTDAPFAVNLALDDATTIV 81 
                                       788999****************************************************************9998877 PP

                               NMO  79 raekykkeleeaalelnieegvrfyrkvevvldekvevvsfgfglpteevvarlkeagvvliptissvkearkvear 155
                                       +        ++  le + e g +              +vsf fg+     v+r ++ag+v++ t++s+ +ar++  +
  gi|336254143|ref|YP_004597250.1|  82 D--------TDDHLETALEAGAP--------------IVSFSFGDA-APYVDRVHDAGAVAMQTVGSAAAAREAVDA 135
                                       7........56677788888888..............*******99.889*************************** PP

                               NMO 156 GaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd..iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltke 230
                                       G D+++ qG eaGGh    ev+   ++aLvp+v+dav   +P++AaGGi d+rgvaaaLalGA g+ +gtrf++t+e
  gi|336254143|ref|YP_004597250.1| 136 GIDVVVTQGLEAGGHVQ-SEVA---TTALVPRVADAVGdaVPIVAAGGIADGRGVAAALALGADGAWLGTRFVATEE 208
                                       ***************99.6665...************889************************************* PP

                               NMO 231 sdakdahkkklleaklddteltsavs....GrpaRalatelleeleeakiatlalpeah.............elakk 290
                                       + ++d  +++l e+ + dte t+ ++    G  +R+la+e le+ ++    +++ +  +             e    
  gi|336254143|ref|YP_004597250.1| 209 AIVHDEYRRRLRESDETDTEYTTLFDkgwpGTAHRVLANETLERWDDDGRPPVGERPGEndviartgdgepiE---R 282
                                       *************************88777999*************966666655443335555555554442...1 PP

                               NMO 291 ....iraalveagnteegllwagqgidrldkiisvkeLiesLv 329
                                           ++   ve+ + e ++l+agq  + +d++ +++ ++e+Lv
  gi|336254143|ref|YP_004597250.1| 283 ydeaLATPDVEG-DIESMALYAGQSVGGVDDVRPAATVVENLV 324
                                       333466666676.*****************************9 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         1   3.1e+03      57      70 ..      13      26 ..      12      54 .. 0.70
   2 !   35.6   8.8   1.7e-12     5e-09     220     304 ..     119     204 ..      85     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1
                                      ESSSEEE--BSTGG CS
                            FMN_dh 57 lslPvliaPvglak 70
                                      +++P++ aP+g a+
  gi|336254143|ref|YP_004597250.1| 13 IEHPIVQAPIGSAT 26
                                      56788888887654 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 1.7e-12
                                       EEEEE-SHHHHHHHHHTTESEEEE--..GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT- CS
                            FMN_dh 220 vvKGvltaedakraveaGvdgivvSN..HGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGA 294
                                        +  v +a+ a++av+aG+d +v      GG+ + + +at    p++++avg+ +++++ gGi  G  v+ AlalGA
  gi|336254143|ref|YP_004597250.1| 119 AMQTVGSAAAAREAVDAGIDVVVTQGleAGGH-VQSEVATTALVPRVADAVGDAVPIVAAGGIADGRGVAAALALGA 194
                                       5556788999**********988764437775.6888999999********************************** PP

                                       SEEEESHHHH CS
                            FMN_dh 295 davllGRpfl 304
                                       d+ +lG  f+
  gi|336254143|ref|YP_004597250.1| 195 DGAWLGTRFV 204
                                       ******8876 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   6.6     2e-11     6e-08      22     246 ..       2     210 ..       1     218 [. 0.74

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2e-11
                                       B--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHH.HHHHHHTSTTSXBXTTSXB-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  22 dlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqae.evkkvkrspnaakdekgrllvga 97 
                                        l+t l++ ++++ P+v a++ + t+ ++A a++++Gg+g +       e+++  ++  +   +a      +l    
  gi|336254143|ref|YP_004597250.1|   2 ALRTPLCDALEIEHPIVQAPIGSATNPDLAAAVSNAGGLGHLAVTWRGLEETRdVIHDTRDRTDA--PFAVNLALDD 76 
                                       58999***********************************9988766544444044444433322..2344455555 PP

                                       EE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEE.EE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                             IMPDH  98 avgvkedalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnvataegakaLieagadav.kvG 173
                                       a  +  d+ +++++ +eag+ ++    + g  +  ++ v+   + +         v +a++a++ ++ag+d+v   G
  gi|336254143|ref|YP_004597250.1|  77 ATTIV-DTDDHLETALEAGAPIV--SFSFGDAAPYVDRVHDAGAVA------MQTVGSAAAAREAVDAGIDVVvTQG 144
                                       55555.67889999999999876..566777777777777665444......44577889999999*****861457 PP

                                       SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 174 iGpGsiCttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEsp 246
                                       + +G      v + + vp+       ++ a    vp++a GGi   + ++ Ala+Gad   lG  + +teE+ 
  gi|336254143|ref|YP_004597250.1| 145 LEAGGHVQSEVATTALVPR-------VADAVGDAVPIVAAGGIADGRGVAAALALGADGAWLGTRFVATEEAI 210
                                       7777766555555444443.......33344556*************************************96 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   9.4e-06     0.028      35     112 ..     129     210 ..     117     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.4e-06
                                       HHHHHHHT-SEEEEEEHHHHC..TTHHHHHHHHHHHHHH-S..SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
                      His_biosynth  35 akryeeegadelhvvDldaak..egreanldlveeiaeevf..ipvqvGGGIrsledveelleagadkviigtaavk 107
                                       a++  ++g+d ++   l+a    +++ a ++lv ++a++v   +p+   GGI +   v+++l +gad   +gt  v 
  gi|336254143|ref|YP_004597250.1| 129 AREAVDAGIDVVVTQGLEAGGhvQSEVATTALVPRVADAVGdaVPIVAAGGIADGRGVAAALALGADGAWLGTRFVA 205
                                       5566677777777777776554477888899*********888******************************9988 PP

                                       -THHH CS
                      His_biosynth 108 npeli 112
                                         e i
  gi|336254143|ref|YP_004597250.1| 206 TEEAI 210
                                       77655 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.9   4.4e-05      0.13     228     285 ..     154     212 ..     112     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.4e-05
                                       HHH.HHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHH CS
                            DHO_dh 228 dia.lkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiak 285
                                       ++a ++++ ++++ + + +pi++ GGi  g+ +   +  GA    ++t +v ++ +i++
  gi|336254143|ref|YP_004597250.1| 154 EVAtTALVPRVADAVGDAVPIVAAGGIADGRGVAAALALGADGAWLGTRFVATEEAIVH 212
                                       4441467899*******************************999999999888887776 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 ?   10.6   2.8   7.7e-05      0.23     270     306 ..     167     203 ..     117     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.7e-05
                                       T-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHH CS
                      Glu_synthase 270 glrdrvsliadGglktgadvvkalalGAdavgigtaa 306
                                        + d v + a+Gg+  g+ v+ alalGAd   +gt  
  gi|336254143|ref|YP_004597250.1| 167 AVGDAVPIVAAGGIADGRGVAAALALGADGAWLGTRF 203
                                       567899***********************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2686.02
//
Query:       gi|336254144|ref|YP_004597251.1|  [L=385]
Description: ArsR family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00052   20.3   5.0      0.003   17.9   0.2    2.8  2  Lar_restr_allev  Restriction alleviation protein Lar
     0.0043   17.1   0.0     0.0093   16.0   0.0    1.6  1  HTH_20           Helix-turn-helix domain
     0.0068   16.4   0.1        1.7    8.7   0.0    2.4  2  Elf1             Transcription elongation factor Elf1 like
  ------ inclusion threshold ------
        3.2    7.8   5.0         17    5.5   0.5    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        5.5    7.2   9.5        1.5    8.9   0.2    3.0  3  DUF1272          Protein of unknown function (DUF1272)
        6.7    6.8   5.6        3.2    7.8   0.9    2.7  3  CpXC             CpXC protein
        7.4    6.8  10.9         12    6.1   0.0    3.6  3  Zn-ribbon_8      Zinc ribbon domain
        7.6    6.0   7.7          7    6.1   1.5    2.7  2  zf-TFIIB         Transcription factor zinc-finger
        8.9    6.5   7.4        5.6    7.2   0.2    3.0  3  zf-Mss51         Zinc-finger of mitochondrial splicing suppre


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 !   17.9   0.2   1.5e-06     0.003       5      35 ..     147     173 ..     146     193 .. 0.93
   2 ?    3.0   0.7     0.065   1.3e+02       6      36 ..     213     254 ..     212     268 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                   Lar_restr_allev   5 pCPfCggravlersqrvvaeigqcvyCadCg 35 
                                       pCPfC  +    rs ++v     +v+Ca C 
  gi|336254144|ref|YP_004597251.1| 147 PCPFCDRETLEARSRDNVV----TVSCAGCD 173
                                       9******************....*******6 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.065
                   Lar_restr_allev   6 CPfCggravlersqrvvaeigq............cvyCadCga 36 
                                       CP Cgg  v    +  +                   +C+ Cg 
  gi|336254144|ref|YP_004597251.1| 213 CPDCGGSVVGRLVEPSPDVA-DelpsehadhvqaELECESCGT 254
                                       99999988755544444322.2355688888888888888887 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.7e-06    0.0093       2      58 ..      36      98 ..      35     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.7e-06
                                      HHHHHHS-HHHHHHHHHH......STCTTB-HHHHHHHHTS-HHH.HHHHHHHHHHCTTEEEEC CS
                            HTH_20  2 qiaeALahPvRrrilraL......araegltaselaerldlsknt.lsyHLrvLeeagLvevvr 58
                                      +++ AL++ vR +il  L      ++ + +++sel e+ d++ +    yHLr+L +  +v+ v+
  gi|336254144|ref|YP_004597251.1| 36 DAFQALGNDVRTGILETLyertsgNGTASASFSELFEASDVDTTAgFAYHLRQL-DGSYVRKVD 98
                                      6799*****************9999999999999999999888888********.888887776 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0   0.00087       1.7      24      53 ..     148     174 ..     130     201 .. 0.87
   2 !    5.3   0.1    0.0099        20      43      60 ..     244     261 ..     231     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00087
                              Elf1  24 CpfCnheksvevkldkkekiaevsCkvCge 53 
                                       CpfC+ e   + +   ++++ +vsC  C  
  gi|336254144|ref|YP_004597251.1| 148 CPFCDRE---TLEARSRDNVVTVSCAGCDR 174
                                       *******...778889999*********86 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0099
                              Elf1  43 iaevsCkvCgesfetkvn 60 
                                        ae++C++Cg+++++ v+
  gi|336254144|ref|YP_004597251.1| 244 QAELECESCGTTTRCPVS 261
                                       688889999888887764 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 ?    3.3   0.3      0.04        80      21      45 ..     148     174 ..     144     175 .. 0.76
   2 ?    5.5   0.5    0.0085        17      20      45 ..     212     254 ..     201     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.04
                     Zn_Tnp_IS1595  21 CPhCgsr..kayriktrglfqCkeCrk 45 
                                       CP+C  +  +a++  +     C+ C +
  gi|336254144|ref|YP_004597251.1| 148 CPFCDREtlEARSRDNVVTVSCAGCDR 174
                                       *****8876666666688888888876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0085
                     Zn_Tnp_IS1595  20 vCPhCgsrkayrikt.................rglfqCkeCrk 45 
                                       +CP Cg++ + r+                      ++C++C++
  gi|336254144|ref|YP_004597251.1| 212 ICPDCGGSVVGRLVEpspdvadelpsehadhvQAELECESCGT 254
                                       5******988887777777888888888877777788888875 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3     0.045        89       3      34 ..     143     174 ..     141     181 .. 0.78
   2 ?    8.9   0.2   0.00077       1.5      41      54 ..     210     223 ..     204     226 .. 0.85
   3 ?   -1.7   0.4       1.6   3.2e+03       7      14 ..     248     255 ..     242     261 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.045
                           DUF1272   3 elrpnCecCdkdlppdseearicsyEctFCae 34 
                                        l + C  Cd++  ++ +   + +  c+ C +
  gi|336254144|ref|YP_004597251.1| 143 ALEDPCPFCDRETLEARSRDNVVTVSCAGCDR 174
                                       67889999999877777788888888887764 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00077
                           DUF1272  41 envCPncgGelvkR 54 
                                       +++CP+cgG +v R
  gi|336254144|ref|YP_004597251.1| 210 DGICPDCGGSVVGR 223
                                       689*******9987 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.6
                           DUF1272   7 nCecCdkd 14 
                                       +Ce C ++
  gi|336254144|ref|YP_004597251.1| 248 ECESCGTT 255
                                       56666543 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.4       2.3   4.6e+03      33      46 ..     162     175 ..     148     177 .. 0.64
   2 ?    1.2   0.1      0.18   3.5e+02      33      46 ..     206     219 ..     201     228 .. 0.84
   3 ?    7.8   0.9    0.0016       3.2       3      62 ..     213     271 ..     212     311 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.3
                              CpXC  33 gslfeatCpkCgat 46 
                                       +++ ++ C  C++t
  gi|336254144|ref|YP_004597251.1| 162 DNVVTVSCAGCDRT 175
                                       45566777777765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.18
                              CpXC  33 gslfeatCpkCgat 46 
                                       g++++  Cp+Cg +
  gi|336254144|ref|YP_004597251.1| 206 GRMRDGICPDCGGS 219
                                       7888889****976 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0016
                              CpXC   3 CpaCgkefeaeiwtsidadedpelkeklldgslfeatCpkCgatakleapllyhdpekel 62 
                                       Cp+Cg +   ++++   +d   el  +  d    e +C++Cg+t++ + +l   d+++ +
  gi|336254144|ref|YP_004597251.1| 213 CPDCGGSVVGRLVEP-SPDVADELPSEHADHVQAELECESCGTTTRCPVSLTLLDHSAVV 271
                                       666666555554442.344445555566666677899**************999965544 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.8      0.17   3.4e+02       8      33 ..     148     173 ..     136     177 .. 0.67
   2 ?    6.1   0.0    0.0062        12      28      38 ..     212     223 ..     198     225 .. 0.72
   3 ?    3.2   0.6     0.048        96       5      14 ..     246     255 ..     239     260 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.17
                       Zn-ribbon_8   8 CeeCghefevlqsisdaplta.CPeCg 33 
                                       C  C++e  + + + d+  t+ C  C 
  gi|336254144|ref|YP_004597251.1| 148 CPFCDRETLEAR-SRDNVVTVsCAGCD 173
                                       777775444444.34666777777775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0062
                       Zn-ribbon_8  28 aCPeCgs.evrr 38 
                                        CP+Cg+  v r
  gi|336254144|ref|YP_004597251.1| 212 ICPDCGGsVVGR 223
                                       5*****955555 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.048
                       Zn-ribbon_8   5 eYrCeeCghe 14 
                                       e +Ce+Cg++
  gi|336254144|ref|YP_004597251.1| 246 ELECESCGTT 255
                                       4456666653 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.5    0.0035         7       2      25 ..     148     172 ..     147     178 .. 0.91
   2 ?    2.4   0.6     0.048        96      22      27 ..     213     218 ..     211     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0035
                          zf-TFIIB   2 CPkCqd.eleeserggveidyCpqC 25 
                                       CP C   +le   r++v    C  C
  gi|336254144|ref|YP_004597251.1| 148 CPFCDReTLEARSRDNVVTVSCAGC 172
                                       ****8658****************9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.048
                          zf-TFIIB  22 CpqCrG 27 
                                       Cp+C+G
  gi|336254144|ref|YP_004597251.1| 213 CPDCGG 218
                                       999999 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 ?   -0.4   0.5      0.64   1.3e+03       2      22 ..     148     172 ..     147     177 .. 0.73
   2 ?    1.7   0.1      0.14   2.8e+02      18      25 ..     212     219 ..     199     221 .. 0.76
   3 ?    7.2   0.2    0.0028       5.6       9      28 ..     239     258 ..     234     268 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.64
                          zf-Mss51   2 CPvpkhkqt....apkhvdfeCpdC 22 
                                       CP+++ +        + v++ C  C
  gi|336254144|ref|YP_004597251.1| 148 CPFCDRETLearsRDNVVTVSCAGC 172
                                       9999755447776777788888887 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                          zf-Mss51  18 eCpdCGip 25 
                                        CpdCG +
  gi|336254144|ref|YP_004597251.1| 212 ICPDCGGS 219
                                       5*****65 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0028
                          zf-Mss51   9 qtapkhvdfeCpdCGiptyc 28 
                                       ++++ + ++eC  CG  t c
  gi|336254144|ref|YP_004597251.1| 239 HADHVQAELECESCGTTTRC 258
                                       44578899*********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3072.60
//
Query:       gi|336254145|ref|YP_004597252.1|  [L=256]
Description: proteasome endopeptidase complex [Halopiger xanaduensis SH-6]
Scores for 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-53  179.9   0.0    4.5e-53  179.6   0.0    1.1  1  Proteasome      Proteasome subunit
    3.5e-12   45.8   0.1    5.6e-12   45.1   0.1    1.3  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 !  179.6   0.0     5e-57   4.5e-53       1     189 [.      33     224 ..      33     225 .. 0.95

  Alignments for each domain:
  == domain 1  score: 179.6 bits;  conditional E-value: 5e-57
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       v++G+ +vG+ ++dgvvlaa kr+   s ll+ +tveKi+++ddh+++a aG aaDar+lv+ ar+eaq++rlryg+
  gi|336254145|ref|YP_004597252.1|  33 VERGSPSVGVVTDDGVVLAARKRVR--SPLLEADTVEKIHRVDDHLAIASAGHAADARQLVDVARREAQRHRLRYGE 107
                                       689**********************..************************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTT..EEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeg..gpeLyqidpsGsyieekdavaiGsgseaaktalek 152
                                       pi  e l++r+a+++q++tq++g rp+gv+ll+agvd +g  gp+Ly++dpsG+ ++++ ava+G+g   ++++le+
  gi|336254145|ref|YP_004597252.1| 108 PIDAELLAKRLADHVQEHTQTGGSRPYGVALLVAGVDLDGadGPQLYEVDPSGTPYGWR-AVAVGNGGRDVRQFLED 183
                                       *************************************776448***************5.***************** PP

                                       HH....STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEE CS
                        Proteasome 153 ey....kedltleeavelavkalkealerdklsgknievav 189
                                             +   +le +  +a++al +++++ +l++++++v +
  gi|336254145|ref|YP_004597252.1| 184 GIaageSTRGDLEWGTATALEALAATSDEPELTPETVDVWT 224
                                       **97766667888889*********************9976 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 !   45.1   0.1   6.3e-16   5.6e-12       1      23 []      10      32 ..      10      32 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 6.3e-16
                    Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                      YDr  t+FSPdGRL+QVEYA +A
  gi|336254145|ref|YP_004597252.1| 10 YDRGHTIFSPDGRLYQVEYAREA 32
                                      9********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1839.45
//
Query:       gi|336254146|ref|YP_004597253.1|  [L=258]
Description: 20S proteasome subunits A and B [Halopiger xanaduensis SH-6]
Scores for complete 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-41  141.8   0.4    2.1e-41  141.5   0.4    1.1  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 !  141.5   0.4   1.2e-45   2.1e-41       1     190 []      44     224 ..      44     224 .. 0.97

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 1.2e-45
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       +k+Gtt+vG++g+dg+vlaad ra+ g + ++++t++Ki  +dd+++vaf+G+++Da+ +vr++rae+++y l+ + 
  gi|336254146|ref|YP_004597253.1|  44 IKTGTTTVGLAGTDGAVLAADARASLGGQFVTNKTARKIDPVDDRTAVAFSGSVSDAQSFVRHLRAELSQYDLERDG 120
                                       699************************************************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTT.SEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpf.gvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktaleke 153
                                       + +ve     +aa++++++ r+  +p+ ++ l++agvd  ++p +yqi   G +++  +++a Gsg + a++ale+ 
  gi|336254146|ref|YP_004597253.1| 121 RASVE-----TAATVAGDLVRR--GPYrILDLVLAGVD--DEPAVYQIGGGGGVMRA-PYAASGSGMQLAYGALEAA 187
                                       *****.....**********99..677479********..559**************.6****************** PP

                                       HSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 154 ykedltleeavelavkalkealerdklsgknievavi 190
                                       y++  ++ e+  +a +a+++a+erd++sg+++++a+i
  gi|336254146|ref|YP_004597253.1| 188 YEPGRSVAELRPIAARAVRSAAERDTASGDGMTIATI 224
                                       **********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1950.82
//
Query:       gi|336254147|ref|YP_004597254.1|  [L=133]
Description: hypothetical protein Halxa_2759 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.066   12.8   0.3       0.17   11.5   0.3    1.6  1  YvrJ      YvrJ protein family
       0.11   12.3   0.9       0.11   12.3   0.9    2.0  2  TatC      Sec-independent protein translocase protein (TatC)
        2.9    6.6   5.6          2    7.1   0.2    2.0  2  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   2.8e-05      0.17       8      19 ..      51      62 ..      50      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.8e-05
                              YvrJ  8 PIaVavYLLvRi 19
                                      PIaV vYLL+R 
  gi|336254147|ref|YP_004597254.1| 51 PIAVPVYLLHRR 62
                                      9**********5 PP

>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.16   9.4e+02     105     118 ..      16      29 ..       3      36 .. 0.61
   2 ?   12.3   0.9   1.9e-05      0.11     182     207 .]      85     110 ..      82     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHTH CS
                              TatC 105 llfllGaafayfvv 118
                                       ++ l+G++++y + 
  gi|336254147|ref|YP_004597254.1|  16 TFLLAGLCLCYAIA 29 
                                       34456888888765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHHHH-S.SHHHHHHHHHH CS
                              TatC 182 aivvilvvaavltPpdvisqlllavP 207
                                       ++ +++vv+ +++Ppd++s +l a+P
  gi|336254147|ref|YP_004597254.1|  85 VVAAVVVVGGIVSPPDPFSVVLYAGP 110
                                       577899*****************998 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2   0.00034         2     385     439 ..      11      69 ..       2      71 .. 0.62
   2 ?    1.8   1.3     0.014        82     385     429 ..      78     120 ..      72     127 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00034
                           DUF2207 385 alglgliilglilillallllvll..........lvfllilllillliaiivlllfsrllgrrte 439
                                       ++ lg ++l+ +++++a      +           + +++++++++ ia+ v+ll +r l+rrt+
  gi|336254147|ref|YP_004597254.1|  11 TAVLGTFLLAGLCLCYA------IaadanarganGSVWGLVAFAVPPIAVPVYLLHRRELPRRTD 69 
                                       22333333333333333......144455589997888888888888888888888899***996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.014
                           DUF2207 385 alglgliilglilillallllvlllvfllilllillliaiivlll 429
                                       a ++g+++++ +++++++++      f ++l  + l+++++ l++
  gi|336254147|ref|YP_004597254.1|  78 AGSIGIGVVAAVVVVGGIVSPP--DPFSVVLYAGPLIVVCVPLAF 120
                                       5556666666666666665554..455555554444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 997.06
//
Query:       gi|336254148|ref|YP_004597255.1|  [L=247]
Description: 3-oxoacyl-(acyl-carrier-protein) reductase [Halopiger xanaduensis SH-6]
Scores for 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-65  218.8   2.2    8.1e-65  218.6   2.2    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.1e-57  194.6   0.8    1.3e-57  194.4   0.8    1.1  1  adh_short        short chain dehydrogenase
    1.2e-21   77.4   0.2    1.6e-21   77.1   0.2    1.2  1  KR               KR domain
     0.0038   16.7   0.1     0.0057   16.1   0.1    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.022   15.0   0.0      0.042   14.1   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> 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 !  218.6   2.2   2.3e-68   8.1e-65       1     233 [.      12     245 ..      12     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: 218.6 bits;  conditional E-value: 2.3e-68
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH..HHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea..kkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilv 74 
                                       G a+gIGr+iA+ l eeGa+vv+ +++ e+  k++v+++++++g++v  ++DVt++eqve++ e + e fg  D+lv
  gi|336254148|ref|YP_004597255.1|  12 GSARGIGRGIAEYLGEEGANVVINYRSSEGaaKEAVDAIETAGGSAVaAQADVTHREQVEHMREVCHEAFGPADVLV 88 
                                       789*************************99988999999999999966***************************** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaale 149
                                       nnagi+ +  ++f+e+sre++dr++dvnl ++f++++++   + +++ g+++n+ssv ++++  +++ y+aaK ++ 
  gi|336254148|ref|YP_004597255.1|  89 NNAGITAD--KQFTEMSREDWDRVMDVNLGGMFNCTQEFYDdIWEAEeGRLINISSVVGKQGNFGQANYAAAKSGMF 163
                                       ********..*******************************9665445***************************** PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEE CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqt 226
                                       ++tr++A el++ g + N+v+pg+++T+++++++  +++l+++ a +pl+rl+++e+va+++ fLa +e+syitG++
  gi|336254148|ref|YP_004597255.1| 164 GFTRTIALELAQGGSTANCVAPGFTRTDMVESVP--EKVLDRIIAGIPLERLAEVEDVAALVRFLAGEESSYITGEV 238
                                       *********************************9..9**************************************** PP

                                       EEESTTG CS
                      adh_short_C2 227 lvvDgGl 233
                                       + ++gG+
  gi|336254148|ref|YP_004597255.1| 239 IDINGGM 245
                                       ******8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.4   0.8   3.7e-61   1.3e-57       2     193 ..       7     199 ..       6     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 194.4 bits;  conditional E-value: 3.7e-61
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       + ++tG ++GIGr ia+ l +eGa+vv+ + +se +++e+++ ++ +g +a+a+q+Dvt+re+ve + e + + +g+
  gi|336254148|ref|YP_004597255.1|   7 TCVITGSARGIGRGIAEYLGEEGANVVInYRSSEGAAKEAVDAIETAGGSAVAAQADVTHREQVEHMREVCHEAFGP 83 
                                       679*************************9999999999*************************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                        dvLvnNAGit +++f e+s e+w+rv++vNl g+f++t+++++ + ++++Gr +n+sSv+gk++++g+a Y+A+K 
  gi|336254148|ref|YP_004597255.1|  84 ADVLVNNAGITADKQFTEMSREDWDRVMDVNLGGMFNCTQEFYDDIWEAEEGRLINISSVVGKQGNFGQANYAAAKS 160
                                       *********************************************99****************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakelrek 193
                                       ++ g+tr++a ela+ g + n+vaPG+++Tdm++++ ek
  gi|336254148|ref|YP_004597255.1| 161 GMFGFTRTIALELAQGGSTANCVAPGFTRTDMVESVPEK 199
                                       *********************************998765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.2   4.4e-25   1.6e-21       2     158 ..       7     164 ..       6     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 4.4e-25
                                       EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHH CS
                                KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikae 78 
                                       t +itG + g+G+ +a+ l e+ga+ +v+  Rs  ++ ++k+ ++++e  g +  +++aDv+++++ve++ e +++ 
  gi|336254148|ref|YP_004597255.1|   7 TCVITGSARGIGRGIAEYLGEEGAN-VVINYRS--SEGAAKEAVDAIETAGGSAVAAQADVTHREQVEHMREVCHEA 80 
                                       569********************96.5666677..56778889********************************** PP

                                       SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHH CS
                                KR  79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaa 151
                                       ++p    ++ Ag+++dk+++em+ ed+++v+   + G+ n  + + d     +   ++ +SS+ g  g++gqanYaa
  gi|336254148|ref|YP_004597255.1|  81 FGPADVLVNNAGITADKQFTEMSREDWDRVMDVNLGGMFNCTQEFYDdiweAEEGRLINISSVVGKQGNFGQANYAA 157
                                       *****************************************999998677666778********************* PP

                                       HHHHHHH CS
                                KR 152 aNaflDa 158
                                       a + + +
  gi|336254148|ref|YP_004597255.1| 158 AKSGMFG 164
                                       *876655 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.6e-06    0.0057       2     118 ..       9     143 ..       8     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-06
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HH...HHHHHHHHH..T-S CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrs...alerlfkee..qpd 66 
                                       ++tG +  iG+ ++++l e+g +v+   r s++ ++++ + +          ++d+t+r+    ++++++e    +d
  gi|336254148|ref|YP_004597255.1|   9 VITGSARGIGRGIAEYLGEEGANVVINYRSSEGAAKEAVDAIetaggsaVAAQADVTHREqveHMREVCHEAfgPAD 85 
                                       79*********************998888877777777666699****98999999999966666788888776789 PP

                                       EEEE--S.---HHH...HHHSHHHHHHHHTHHHHHHHHHHHHH..TCT..EEEEEEEGGG CS
                         Epimerase  67 avihlAa.vggvaa...ssedpadfieknlqgtlnlleaarka..gvk..rllflsSsev 118
                                       + ++ A+  ++ +    s ed  ++++ nl g+ n  ++  +   +++  rl+++sS  v
  gi|336254148|ref|YP_004597255.1|  86 VLVNNAGiTADKQFtemSREDWDRVMDVNLGGMFNCTQEFYDDiwEAEegRLINISS--V 143
                                       999999866665541114444455788888888888887775533222447777777..4 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 ?   14.1   0.0   1.2e-05     0.042       8     100 ..      16     114 ..       9     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...TTTCEEEEE--TTTHHHH..HHHHHTTS....SEEEE CS
                   Sacchrp_dh_NADP   8 svGqavaellarhfdvdaeitvadrskeklealaaka...lgvrfeaialdaenyeav..Laallkeg....dlvvn 75 
                                       ++G+++ae+l +++    ++++  rs e+++++a +a   +g ++ a++ d+  +e+v  + +++ e+    d++vn
  gi|336254148|ref|YP_004597255.1|  16 GIGRGIAEYLGEEGA---NVVINYRSSEGAAKEAVDAietAGGSAVAAQADVTHREQVehMREVCHEAfgpaDVLVN 89 
                                       79**********997...6**********9999988899977777777777777766111555566669999***** PP

                                       -SSGGGHHHHHHHHHHHT-EEEESS CS
                   Sacchrp_dh_NADP  76 lsppissldvlkaCietgvhyvdts 100
                                        ++ + + +  ++ +e   +++d+ 
  gi|336254148|ref|YP_004597255.1|  90 NAGITADKQFTEMSREDWDRVMDVN 114
                                       ***9999999999888777777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1896.57
//
Query:       gi|336254149|ref|YP_004597256.1|  [L=547]
Description: poly(R)-hydroxyalkanoic acid synthase, class III, PhaC subunit [Halopiger xanaduensis SH-6]
Scores for complete 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-24   87.2   0.0      2e-24   86.6   0.0    1.2  1  Abhydrolase_1    alpha/beta hydrolase fold
    4.7e-14   52.4   0.1    7.7e-14   51.7   0.1    1.3  1  PhaC_N           Poly-beta-hydroxybutyrate polymerase (PhaC) 
    2.8e-11   43.9   0.0    7.5e-11   42.5   0.0    1.8  1  HHH_5            Helix-hairpin-helix domain
    9.7e-09   34.8   0.0    7.4e-05   22.1   0.0    2.5  2  Hydrolase_4      Serine aminopeptidase, S33
    7.8e-07   27.9   0.0    4.5e-06   25.4   0.0    1.8  2  DUF3141          Protein of unknown function (DUF3141)
    1.3e-05   24.8   0.0     0.0028   17.2   0.0    2.5  2  DLH              Dienelactone hydrolase family
    9.4e-05   22.6   0.5      0.001   19.3   0.5    2.3  1  DUF4332          Domain of unknown function (DUF4332)
    0.00018   21.0   0.1    0.00051   19.6   0.0    1.8  2  PHB_depo_C       PHB de-polymerase C-terminus
    0.00074   20.2   0.1     0.0015   19.2   0.1    1.5  1  Abhydrolase_6    Alpha/beta hydrolase family
      0.002   18.3   0.0     0.0044   17.2   0.0    1.6  1  Cdd1             Pathogenicity locus
     0.0025   17.6   0.0     0.0059   16.4   0.0    1.6  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
  ------ inclusion threshold ------
      0.071   12.6   0.2       0.49    9.9   0.0    2.2  2  Homez            Homeodomain leucine-zipper encoding, Homez
      0.076   12.7   0.0          8    6.0   0.0    2.3  2  FSH1             Serine hydrolase (FSH1)
       0.16   11.9   0.3       0.82    9.7   0.0    2.4  2  HHH              Helix-hairpin-helix motif


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 !   86.6   0.0   1.6e-27     2e-24       2     252 ..      71     337 ..      70     340 .. 0.89

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 1.6e-27
                                       EEEEE-STTT...CGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSE CS
                     Abhydrolase_1   2 vlvilhGlpg...ssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkl 75 
                                       +++i+ +l +    +d++  r+++++L ++gfdv+l+D+  + + ++++    ddy +  + +++d ++d+  +d +
  gi|336254149|ref|YP_004597256.1|  71 PILIVYALINkpyILDLQPDRSVVRTLLEAGFDVYLIDWGEPSKLDRSLGL--DDYVNRYIDNCVDVVRDRSSQDAI 145
                                       7889999999777788899999****************************9..************************ PP

                                       EEEEETHHHHHHHHHHHHHGGGEEEEEEESE.......CSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHH CS
                     Abhydrolase_1  76 tlvGhSmGGmialayaaeyperVkalvllga.......idpaaslieaqrqqaksfpdffdgyaadcarnpagplla 145
                                       +++G++mGG+++++yaa+ype+V++l l++a             ++ ++++  +++ ++fd++ ad+  + +  l++
  gi|336254149|ref|YP_004597256.1| 146 NVLGYCMGGTMSAMYAALYPEKVRNLGLMAAglcfageGGVLELWGAEDYYDPETVTETFDNVPADFLDT-GFALMD 221
                                       **********************************877777777788888888888888888888877655.555666 PP

                                       CCSCHHHHHHHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHC........THHHHSEE CS
                     Abhydrolase_1 146 delaaleqrhrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlre........lknvlapt 214
                                         ++ ++ + r+ d l+++d++ +f +++++   + +  +  + e + + +  ++l   +         l n+  p+
  gi|336254149|ref|YP_004597256.1| 222 PVANNVTKYVRFYDNLEDEDFVENFARMERWLDEGIDVAGRAYEEFIRDIYQENKLHANELelggervdLANIEMPV 298
                                       666777777777777888*******************9999999999999999999887768999************ PP

                                       EEEEETTCSSSCHHHHHHHHHCHTS.EEEEEEETCSSSH CS
                     Abhydrolase_1 215 lvisgtsDplvppkaledlaqllpk.krlvvisdagHla 252
                                       l i +++D+l+pp+a+  +++++p   +++ ++ +gH+ 
  gi|336254149|ref|YP_004597256.1| 299 LQIVAEYDHLIPPGASKPFNEAIPAeDTEILEFATGHIG 337
                                       **********************99989999999***985 PP

>> PhaC_N  Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.1     6e-17   7.7e-14     116     171 ..      40      95 ..      21      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 6e-17
                            PhaC_N 116 nvattpGkvvfrnelleliqykpttekvlkrPllivPplinkfYilDLkpenslvr 171
                                       +v+ tp +vv++++ lel++y+ +te++++ P+liv +link YilDL+p++s+vr
  gi|336254149|ref|YP_004597256.1|  40 EVGQTPSEVVYEENKLELLHYESQTEEQHDVPILIVYALINKPYILDLQPDRSVVR 95 
                                       6789**************************************************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 !   42.5   0.0   5.8e-14   7.5e-11       2      56 ..     491     545 ..     490     546 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 5.8e-14
                                       HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                       ++L+++sG+G+++A  l+ aGie++++la+ad++eLa+ +G+++ ++e +i+++ 
  gi|336254149|ref|YP_004597256.1| 491 DDLTELSGVGRAYADQLAAAGIETFDQLADADAAELAAETGLSPNRVEDWIEQAA 545
                                       69**************************************************986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.8e-08   7.4e-05      23     110 ..      93     177 ..      90     188 .. 0.80
   2 !   10.0   0.0   0.00029      0.38     187     226 ..     291     330 ..     284     335 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.8e-08
                       Hydrolase_4  23 laeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypd 99 
                                       +++ L ++Gf+vy +D+    + +   g  + +++y+d     v+ v++++++  + +lG  mGG++++ y++ yp+
  gi|336254149|ref|YP_004597256.1|  93 VVRTLLEAGFDVYLIDWGEPSKLDRSLGLDDYVNRYIDN---CVDVVRDRSSQDAINVLGYCMGGTMSAMYAALYPE 166
                                       788999**********85444444555544444555554...477789999************************** PP

                       Hydrolase_4 100 kvaglilsaPa 110
                                       kv+ l l+a+ 
  gi|336254149|ref|YP_004597256.1| 167 KVRNLGLMAAG 177
                                       ***99888875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00029
                       Hydrolase_4 187 aakitlPllllhGeaDkvvdpeasrelyerlgskdktlkl 226
                                        a+i++P+l + +e D++++p+as+ + e+++++d ++  
  gi|336254149|ref|YP_004597256.1| 291 LANIEMPVLQIVAEYDHLIPPGASKPFNEAIPAEDTEILE 330
                                       57899****************************9998765 PP

>> DUF3141  Protein of unknown function (DUF3141)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.19   2.4e+02     131     168 ..     134     171 ..      82     188 .. 0.63
   2 !   25.4   0.0   3.5e-09   4.5e-06     217     317 ..     214     315 ..     203     348 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.19
                           DUF3141 131 kvaelhpeaekPvvignCqaGwavlmlaalapelvGpi 168
                                        v++  ++++   v+g C +G    m aal pe v  +
  gi|336254149|ref|YP_004597256.1| 134 DVVRDRSSQDAINVLGYCMGGTMSAMYAALYPEKVRNL 171
                                       333334444466799*****************987655 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 3.5e-09
                           DUF3141 217 vqnfeklnPantlwskqynlyakvdtea..erylefekwWGghvllnkeeieyivdnLfvGnrlatgelvtsdgvri 291
                                        + f  ++P  +  +k+++ y + ++e   e +  +e+w  + + + ++  e  +++++  n+l ++el +  g+r+
  gi|336254149|ref|YP_004597256.1| 214 DTGFALMDPVANNVTKYVRFYDNLEDEDfvENFARMERWLDEGIDVAGRAYEEFIRDIYQENKLHANEL-ELGGERV 289
                                       5679999*****************99954489*********************************9998.5679*** PP

                           DUF3141 292 DlrnirsPivvfaskgDnitPPqqal 317
                                       Dl ni+ P++   ++ D + PP  + 
  gi|336254149|ref|YP_004597256.1| 290 DLANIEMPVLQIVAEYDHLIPPGASK 315
                                       **********************8765 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.2e-06    0.0028      78     119 ..     125     164 ..     115     171 .. 0.81
   2 ?    4.9   0.0     0.013        17     141     174 ..     292     325 ..     285     358 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-06
                               DLH  78 vlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaev 119
                                       v + ++  v+ ++ ++  s++ + v G+CmGG+++  +aa  
  gi|336254149|ref|YP_004597256.1| 125 VNRYIDNCVDVVRDRS--SQDAINVLGYCMGGTMSAMYAALY 164
                                       4555677788888888..6779**************999976 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.013
                               DLH 141 akikapilalfgeeDefipadevekleealkaan 174
                                       a+i+ p+l +++e D+ ip ++ + ++ea+ a+ 
  gi|336254149|ref|YP_004597256.1| 292 ANIEMPVLQIVAEYDHLIPPGASKPFNEAIPAED 325
                                       789******************9999999996654 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.5   7.9e-07     0.001       2      53 ..     498     544 ..     489     547 .] 0.60

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.9e-07
                           DUF4332   2 gigkeeaekLkkaGikttedLlelgktekgrkalaeklgisernvlklanlA 53 
                                       g+g+++a++L++aGi+t+++L+ +   ++++  la+++g+s ++v +++++A
  gi|336254149|ref|YP_004597256.1| 498 GVGRAYADQLAAAGIETFDQLADA---DAAE--LAAETGLSPNRVEDWIEQA 544
                                       455566666666666666666655...3444..6666666666666666655 PP

>> PHB_depo_C  PHB de-polymerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0     4e-07   0.00051      61     201 ..     225     358 ..     207     360 .. 0.81
   2 ?   -2.2   0.2       1.9   2.4e+03     139     164 ..     485     513 ..     476     519 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4e-07
                        PHB_depo_C  61 rhvkahldlfaslvkgdg.deadkhrefyDeylavlDltaefylqtveevfqefalakgklkvegkrvdlkkikrva 136
                                       + v+++++++ +l ++d  ++  +++++ De    +D++   y + +++++qe +l  ++l+  g+rvdl +i+ + 
  gi|336254149|ref|YP_004597256.1| 225 NNVTKYVRFYDNLEDEDFvENFARMERWLDE---GIDVAGRAYEEFIRDIYQENKLHANELELGGERVDLANIE-MP 297
                                       5566777777777766642555667777777...68999999******************************96.78 PP

                        PHB_depo_C 137 lltveGenDDisglGqtkaaldlctgipesrkahylqegvGhyGvfsGsrfreeivPrvrdfire 201
                                       +l +  e D +  +G    ++ +  +ip++  ++ l+ ++Gh G+   sr ++e+ P v ++ +e
  gi|336254149|ref|YP_004597256.1| 298 VLQIVAEYDHLIPPGA---SKPFNEAIPAED-TEILEFATGHIGMSVSSRSHDELWPEVCEWFEE 358
                                       99999*********95...566778899865.678999*********************998765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                        PHB_depo_C 139 tveGenDDi...sglGqtkaaldlctgip 164
                                       ++e e DD+   sg+G++ a +  ++gi+
  gi|336254149|ref|YP_004597256.1| 485 AIEDETDDLtelSGVGRAYADQLAAAGIE 513
                                       78999999533389999998887777776 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.2e-06    0.0015      20     208 ..      95     336 ..      85     351 .. 0.47

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                       HHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHH.HHHHCCTT........TTSEEEEEETCHHHHHHHHHHCC... CS
                     Abhydrolase_6  20 aallaagvhvlapDlpGhGrsdpppldledladl.aalldelaa......gggpvvlvGHSlGGalalaaapla... 86 
                                       + ll ag+ v+ +D+ G   ++  + +l   +d+  +++d  ++      + +++ ++G+++GG++++++a+l    
  gi|336254149|ref|YP_004597256.1|  95 RTLLEAGFDVYLIDW-GE--PSKLDRSLGL-DDYvNRYIDNCVDvvrdrsSQDAINVLGYCMGGTMSAMYAALYpek 167
                                       6688899999*****.77..6666655554.55543344444333333545566699*******9999944444887 PP

                                       ...EEEEES-...............................----TTT...S----TTHHHHHHTT-CCCCHCCH.. CS
                     Abhydrolase_6  87 .lvvgvlldp....................pp.........talpagl...laaalelllallallrllawlsre.. 128
                                        ++ g++ ++                    p+         +   a++   +                         
  gi|336254149|ref|YP_004597256.1| 168 vRNLGLMAAGlcfageggvlelwgaedyydPEtvtetfdnvP---ADFldtG----------------------Fal 219
                                       655557777744444444444444444433112222121110...1111111......................111 PP

                                       .........S-HSCCCCHHHCCCCHCHCCCGHH..........................HHCCHHC.HTTCCHHTT- CS
                     Abhydrolase_6 129 .........plprlfladedadaawrarlarla..........................allaglg.llpaaawadl 169
                                                 + r + + e  d+++++++ar+                             ++ l+    + ++a +
  gi|336254149|ref|YP_004597256.1| 220 mdpvannvtKYVRFYDNLE--DEDFVENFARMErwldegidvagrayeefirdiyqenkLHANELElGGERVDLANI 294
                                       1111111111111111122..24444444444422222222222222222222222221111122212235577777 PP

                                       TTGCE.EECTT-CHHHHCHHCCCH..STTEEETCE...SSS- CS
                     Abhydrolase_6 170 pvpll.vlggeDplvprllerlla..qagarlpvvlpgaGHl 208
                                        +p+l ++++ D l+p+ + +     ++ ++++++   +GH 
  gi|336254149|ref|YP_004597256.1| 295 EMPVLqIVAEYDHLIPPGASKPFNeaIPAEDTEILEFATGHI 336
                                       777744558888888866554444555666665555577774 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.4e-06    0.0044       3      44 ..     488     529 ..     486     539 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.4e-06
                              Cdd1   3 kalkelqdiPniGkalaedlvelGirsveelkgedpeelyek 44 
                                       ++ ++l+++ ++G+a a++l + Gi+++++l++ d++el ++
  gi|336254149|ref|YP_004597256.1| 488 DETDDLTELSGVGRAYADQLAAAGIETFDQLADADAAELAAE 529
                                       56789*********************************9775 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 !   16.4   0.0   4.6e-06    0.0059       3      35 ..     493     526 ..     492     540 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.6e-06
                   DNA_pol_lambd_f   3 FtkvyGVGpktAkkwyakGirtledlra.krakL 35 
                                       +t+  GVG++ A ++ a+Gi t+++l   + a+L
  gi|336254149|ref|YP_004597256.1| 493 LTELSGVGRAYADQLAAAGIETFDQLADaDAAEL 526
                                       56678*********************88543554 PP

>> Homez  Homeodomain leucine-zipper encoding, Homez
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.52   6.7e+02      42      55 ..     351     364 ..     349     366 .. 0.81
   2 ?    9.9   0.0   0.00038      0.49      22      48 ..     516     542 ..     513     547 .] 0.90

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.52
                             Homez  42 qVrdWFaskeseea 55 
                                       +V +WF+ + + e 
  gi|336254149|ref|YP_004597256.1| 351 EVCEWFEERSNGES 364
                                       799*****988765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00038
                             Homez  22 gllqekDldkLckksklsaqqVrdWFa 48 
                                        +l ++D  +L+ +++ls + V dW +
  gi|336254149|ref|YP_004597256.1| 516 DQLADADAAELAAETGLSPNRVEDWIE 542
                                       6899*********************75 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.023        30      84     128 ..     127     169 ..      94     202 .. 0.79
   2 ?    6.0   0.0    0.0063         8     158     200 ..     292     335 ..     269     336 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.023
                              FSH1  84 egleesldavkdyikengpfdGiiGFSqGaalaallaslleellk 128
                                       + +++++d+v+d  ++      ++G+  G++++a++a+l  e+ +
  gi|336254149|ref|YP_004597256.1| 127 RYIDNCVDVVRDRSSQD--AINVLGYCMGGTMSAMYAALYPEKVR 169
                                       45666666666655444..4789**************99877654 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0063
                              FSH1 158 dkiqtptLhvlGelDtvvdeerseaLaeafkns.skvlkHpggH 200
                                        +i++p+L ++ e D ++++  s+ + ea+  + +++l++  gH
  gi|336254149|ref|YP_004597256.1| 292 ANIEMPVLQIVAEYDHLIPPGASKPFNEAIPAEdTEILEFATGH 335
                                       5789**************************9999********** PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00064      0.82       6      27 ..     486     507 ..     482     510 .. 0.81
   2 ?   -1.5   0.1       2.1   2.8e+03       1      15 [.     514     528 ..     514     528 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00064
                                       HTSSHHHHHTSTT-SHHHHHHH CS
                               HHH   6 ipasreeLlalPGVGpktAeaI 27 
                                       i++  ++L++l+GVG++ A++ 
  gi|336254149|ref|YP_004597256.1| 486 IEDETDDLTELSGVGRAYADQL 507
                                       666789**********999876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                                       SHHHHHTSSHHHHHT CS
                               HHH   1 sleglipasreeLla 15 
                                       +++ l +a+ +eL+a
  gi|336254149|ref|YP_004597256.1| 514 TFDQLADADAAELAA 528
                                       5889999*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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):              14  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 3809.80
//
Query:       gi|336254150|ref|YP_004597257.1|  [L=186]
Description: hypothetical protein Halxa_2762 [Halopiger xanaduensis SH-6]
Scores for complete 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-06   28.0  12.0    1.6e-05   24.2   0.3    2.1  2  PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subuni
     0.0064   16.2   0.3      0.012   15.4   0.3    1.4  1  XFP              D-xylulose 5-phosphate/D-fructose 6-phosphat
  ------ inclusion threshold ------
      0.028   14.2   0.3       0.06   13.0   0.2    1.7  1  BAR_3            BAR domain of APPL family
      0.031   14.1   1.9      0.061   13.2   1.7    1.7  1  Mt_ATP-synt_D    ATP synthase D chain, mitochondrial (ATP5H)
      0.048   13.7   6.8       0.23   11.4   3.9    2.4  2  Phasin           Poly(hydroxyalcanoate) granule associated pr
      0.065   13.3   5.2        3.2    7.8   0.2    2.8  3  COG2             COG (conserved oligomeric Golgi) complex com
      0.079   12.4   0.6       0.15   11.5   0.6    1.8  1  Hs1pro-1_C       Hs1pro-1 protein C-terminus
        0.1   13.2   0.3         23    5.7   0.1    2.4  2  QIL1             MICOS complex subunit MIC13, QIL1
        0.1   12.8   0.1       0.28   11.4   0.0    1.6  2  5_nucleotid_C    5'-nucleotidase, C-terminal domain
       0.13   12.4   3.6       0.27   11.4   1.0    2.6  3  Mating_N         Mating-type protein beta 1
        0.2   11.9   4.4         12    6.3   0.6    3.1  3  DUF948           Bacterial protein of unknown function (DUF94
       0.36   11.4   6.5         10    6.8   0.2    3.3  3  DUF5344          Family of unknown function (DUF5344)
       0.92    9.5   5.0          4    7.4   0.7    2.4  3  Laminin_II       Laminin Domain II
        1.5    9.1  10.8        2.5    8.4   1.6    3.0  2  Phasin_2         Phasin protein


Domain annotation for each model (and alignments):
>> PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   5.9   0.00081         1      35     109 ..      11      84 ..       1      94 [. 0.56
   2 !   24.2   0.3   1.2e-08   1.6e-05     237     311 ..      93     167 ..      85     170 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00081
                   PHA_synth_III_E  35 qwWqavspkeasdaakelmermveqqkayfrlleqfakafadkdasasavedaweqlekaieqlqkafqglisdl 109
                                       q W+a +++  ++++ +++e  ve+q ++++   + + + ++ +  +++ve ++++ e++++  q++++++ ++l
  gi|336254150|ref|YP_004597257.1|  11 QDWNAFVEQ-WNEQFLDALEENVEAQAQFVESWSETVGQATEDNELSEGVEGYAKAYETWMNASQQMVERVNDQL 84 
                                       344444444.56666666666666666666655555555555555555666666666666666666666655544 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1.2e-08
                   PHA_synth_III_E 237 alfdlWveaaeevyaevvaseeyakiygrlvnaqmalkaemqrlveevlealnlPtRsEldtlhkriqelrrevr 311
                                       ++ d+W ++a+e++++v+++  +a++ g+ v    +l+++  +   e+l++l+  t   + ++ +r+ el+r+ +
  gi|336254150|ref|YP_004597257.1|  93 DFRDIWLNTANEAFKDVMSTTAFARMTGETVGDVLELQQQADEAAQETLRMLGFATEEDVVEVGDRLVELERRQH 167
                                       688*********************************************************************876 PP

>> XFP  D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   9.3e-06     0.012      39     100 ..      17      79 ..       3      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.3e-06
                               XFP  39 krqwqeeieee.deelaaeGrvievlsEhlcegllegYlltGrhglfasyEaflrivdsmvnq 100
                                         qw+e++ ++ +e+++a+ + +e  sE + ++  ++ l  G +g  ++yE++++  + mv++
  gi|336254150|ref|YP_004597257.1|  17 VEQWNEQFLDAlEENVEAQAQFVESWSETVGQATEDNELSEGVEGYAKAYETWMNASQQMVER 79 
                                       468999999666999*9*******************************************986 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 ?   13.0   0.2   4.7e-05      0.06      40     110 ..      23      96 ..      17     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-05
                             BAR_3  40 rlieagkaysaaqkqfaqsLrelkkeskgdeetdesLkkfsellqelenehtilldqaqrsikk...pLekFrk 110
                                       + ++a ++ ++aq qf++s +e   + ++d+e++e  +  +++ ++ +n  +++++++++++      +e+Fr 
  gi|336254150|ref|YP_004597257.1|  23 QFLDALEENVEAQAQFVESWSETVGQATEDNELSEGVEGYAKAYETWMNASQQMVERVNDQLEGedvDIEDFRD 96 
                                       67899******************************************************998541114666665 PP

>> Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.7   4.7e-05     0.061      45     142 ..       6     102 ..       1     111 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.7e-05
                                       SS-----HHHHHHHSSSTTHHHHHHHHHHH--------TTTTHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHT CS
                     Mt_ATP-synt_D  45 eelpkIdWayYkknvakeglVdeFekkYealkipypedkyteevdaeekevkkeikefkeeskkrieelekeleklk 121
                                       +++++ dW+++ ++  +e   d +e++ ea    +++ + t    +e +e  + ++ + ++++  ++  ++++e+++
  gi|336254150|ref|YP_004597257.1|   6 QSPQAQDWNAFVEQW-NEQFLDALEENVEAQAQFVESWSETVGQATEDNELSEGVEGYAKAYETWMNASQQMVERVN 81 
                                       566777777777776.55677888888888777777777777777788999************************** PP

                                       -XXXXXXXXXXXXXXXXXXXX CS
                     Mt_ATP-synt_D 122 sllpfeemtmedfaeafPeta 142
                                       + l+ e+ ++edf++ + +ta
  gi|336254150|ref|YP_004597257.1|  82 DQLEGEDVDIEDFRDIWLNTA 102
                                       **************9987776 PP

>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.7     0.064        82      46      97 ..      33      85 ..      15      97 .. 0.62
   2 ?   11.4   3.9   0.00018      0.23      55     123 ..     102     168 ..      46     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.064
                            Phasin 46 klekktkkvaeekleevresvkskveevk..ekaeeqwdklekafdervakaLs 97
                                      +++ +  ++  e++ +++e   + +e v+  +ka e+w +  + + erv++ L+
  gi|336254150|ref|YP_004597257.1| 33 EAQAQFVESWSETVGQATEDN-ELSEGVEgyAKAYETWMNASQQMVERVNDQLE 85
                                      444455555566666666442.33344432267778888888888888888876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00018
                            Phasin  55 aeekleevresvkskveevkekaeeqwdklekafdervakaLsrlgvpsredveaLsarvdeLtkelek 123
                                       a+e+ ++v +  ++++ +++ ++ + + +l++  de  +++L+ lg +++edv ++ +r+ eL+++ + 
  gi|336254150|ref|YP_004597257.1| 102 ANEAFKDVMS--TTAFARMTGETVGDVLELQQQADEAAQETLRMLGFATEEDVVEVGDRLVELERRQHD 168
                                       3333333332..2467888889999999***********************************998765 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 ?    7.8   0.2    0.0025       3.2      33     104 ..      11      85 ..       8      97 .. 0.87
   2 ?    0.4   0.0      0.51   6.5e+02      78     118 ..     102     143 ..      86     149 .. 0.75
   3 ?    5.8   1.1     0.011        14      55      89 ..     150     184 ..     128     186 .] 0.91

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0025
                              COG2  33 rdLeaylkllekellelvnedyad...FvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskle 104
                                       +d +a++++ +++ l+  +e+++    Fv+  ++ vg  +e +e++  ++   k  e  +++ +++ e+v+++le
  gi|336254150|ref|YP_004597257.1|  11 QDWNAFVEQWNEQFLDALEENVEAqaqFVESWSETVGQATEDNELSEGVEGYAKAYETWMNASQQMVERVNDQLE 85 
                                       56678888889999999999996444699999999**************************************98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.51
                              COG2  78 laaarkkvesvreklsereeeveskleeakeleekr.ellkl 118
                                        ++a k+v s+++   ++ e+v + le ++++ e+  e l++
  gi|336254150|ref|YP_004597257.1| 102 ANEAFKDVMSTTAFARMTGETVGDVLELQQQADEAAqETLRM 143
                                       467788888999999999999999998777776655355555 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.011
                              COG2  55 adFvslSghLvglqeeleevesplaaarkkvesvr 89 
                                       +d v+++++Lv l+++ + ve +l ++ +++e+  
  gi|336254150|ref|YP_004597257.1| 150 EDVVEVGDRLVELERRQHDVERKLDRILERLEDED 184
                                       5689*************************999876 PP

>> Hs1pro-1_C  Hs1pro-1 protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6   0.00012      0.15      49      91 ..      56      99 ..      26     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                        Hs1pro-1_C 49 nqtlytihqileswiaaakellkrieerieekefe.kassdvyl 91
                                       + +    +  e+w++a++++++r+++++e ++++ +  +d++l
  gi|336254150|ref|YP_004597257.1| 56 SEGVEGYAKAYETWMNASQQMVERVNDQLEGEDVDiEDFRDIWL 99
                                      44555567789*******************99987344577775 PP

>> QIL1  MICOS complex subunit MIC13, QIL1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.018        23      28      60 ..      17      46 ..       3      51 .. 0.79
   2 ?    5.3   0.0     0.024        31      14      62 ..      63     112 ..      55     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.018
                              QIL1 28 vdevkkklclevpklpsveevkfslveyWNkgV 60
                                      v+++++++   +  l+ + e ++ +ve+W ++V
  gi|336254150|ref|YP_004597257.1| 17 VEQWNEQF---LDALEENVEAQAQFVESWSETV 46
                                      45666666...8999**************9998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.024
                              QIL1  14 eelykkakeyipPyvdevkkklclevpklpsveevkf.slveyWNkgVkk 62 
                                       +++y+ ++++ +  v++v+++l++e ++ +  ++++   + e++++++ +
  gi|336254150|ref|YP_004597257.1|  63 AKAYETWMNASQQMVERVNDQLEGEDVDIEDFRDIWLnTANEAFKDVMST 112
                                       689999999999*************9999999999985666666666655 PP

>> 5_nucleotid_C  5'-nucleotidase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.8   2.3e+03     104     104 ..      56      56 ..      22     103 .. 0.43
   2 ?   11.4   0.0   0.00022      0.28      70     129 ..     112     166 ..     104     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.8
                                       E CS
                     5_nucleotid_C 104 s 104
                                       s
  gi|336254150|ref|YP_004597257.1|  56 S 56 
                                       1 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00022
                                       EEEEEEEEHHHHHHHHHH.HTTTTTS--TT-EEEESEEEEE-TTS-TT--EEEESSS-BE CS
                     5_nucleotid_C  70 tlvvveltGaqlkeaLenesvsaskaasgrflqvsGlrytydlskpagervtslsvtvng 129
                                       t++  ++tG+++ ++Le   +++++ a ++ l + G+  + d+  + g+r+++l+     
  gi|336254150|ref|YP_004597257.1| 112 TTAFARMTGETVGDVLE--LQQQADEAAQETLRMLGFATEEDVV-EVGDRLVELER--RQ 166
                                       677899***********..799***************9999996.67999999944..33 PP

>> Mating_N  Mating-type protein beta 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.0   0.00021      0.27      11      45 ..      10      44 ..       1      58 [. 0.81
   2 ?   -2.0   0.0         3   3.8e+03      67      91 ..     114     138 ..     110     142 .. 0.63
   3 ?   -0.2   0.0      0.85   1.1e+03      72      93 ..     152     173 ..     127     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                          Mating_N 11 DedvrqtLdalrkdFfssLrgesealstFlsawsk 45
                                       +d +  +++ +++F+++L++  ea ++F ++ws+
  gi|336254150|ref|YP_004597257.1| 10 AQDWNAFVEQWNEQFLDALEENVEAQAQFVESWSE 44
                                      556666778899*********************96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3
                          Mating_N  67 sfssliatvssgllelesekeaied 91 
                                        f+ +    + ++lel+++ +++++
  gi|336254150|ref|YP_004597257.1| 114 AFARMTGETVGDVLELQQQADEAAQ 138
                                       5666666666677777776666554 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.85
                          Mating_N  72 iatvssgllelesekeaiedel 93 
                                       +  v + l+ele++++++e++l
  gi|336254150|ref|YP_004597257.1| 152 VVEVGDRLVELERRQHDVERKL 173
                                       4556778888888888888776 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 ?    0.1   0.1      0.75   9.6e+02      59      81 ..      28      50 ..       5      55 .. 0.58
   2 ?    6.3   0.6    0.0091        12      36      68 ..      53      85 ..      21     127 .. 0.75
   3 ?    5.7   0.6     0.014        17      21      70 ..     126     176 ..      98     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.75
                            DUF948 59 lledvneklekvdplteavadlg 81
                                      l e+v+ + + v+++ e v++++
  gi|336254150|ref|YP_004597257.1| 28 LEENVEAQAQFVESWSETVGQAT 50
                                      44556666666666666655554 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0091
                            DUF948 36 eelekqvdpilkevedllakvnelledvnekle 68
                                      +el + v+++ k  e+ ++ +++++e vn++le
  gi|336254150|ref|YP_004597257.1| 53 NELSEGVEGYAKAYETWMNASQQMVERVNDQLE 85
                                      445577777777777777777777777777776 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.014
                            DUF948  21 llklkktldea.aatieelekqvdpilkevedllakvnelledvneklekv 70 
                                       +l+l++ +dea ++t++ l+  +++ + ev d l + ++ + dv++kl+++
  gi|336254150|ref|YP_004597257.1| 126 VLELQQQADEAaQETLRMLGFATEEDVVEVGDRLVELERRQHDVERKLDRI 176
                                       566766666651568899999999999999999999999999999999986 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3     0.013        16      47      80 ..      12      45 ..       7      52 .. 0.86
   2 ?    6.8   0.2    0.0079        10      46      81 ..      53      88 ..      44      92 .. 0.90
   3 ?    0.3   0.1      0.81     1e+03      19      57 ..     100     138 ..      98     164 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                           DUF5344 47 eleeeleellkaYktlllknvedtesaVdslkea 80
                                      + +   e+  +++ ++l++nve+  + V+s +e+
  gi|336254150|ref|YP_004597257.1| 12 DWNAFVEQWNEQFLDALEENVEAQAQFVESWSET 45
                                      5666789999******************998876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0079
                           DUF5344 46 neleeeleellkaYktlllknvedtesaVdslkeaD 81
                                      nel+e  e   kaY+t ++ +++++e++ d+l+ +D
  gi|336254150|ref|YP_004597257.1| 53 NELSEGVEGYAKAYETWMNASQQMVERVNDQLEGED 88
                                      899999************************999988 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.81
                           DUF5344  19 ktaaeelktsipetisgknsldvvekineleeeleellk 57 
                                       +ta e++k  +++t+  + ++++v  + el+++  e+ +
  gi|336254150|ref|YP_004597257.1| 100 NTANEAFKDVMSTTAFARMTGETVGDVLELQQQADEAAQ 138
                                       555666666666777777777777777777777666654 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3     0.056        72      12      70 ..      25      82 ..      13      86 .. 0.75
   2 ?    1.8   0.2      0.18   2.3e+02      13      58 ..      71     117 ..      62     133 .. 0.65
   3 ?    7.4   0.7    0.0032         4      14      76 ..     121     181 ..     100     185 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.056
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTT CS
                        Laminin_II 12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapq 70
                                      + + +e +++ +q +e ++e + ++ ++ +e  e v+ + ka +   ++++++ + +++
  gi|336254150|ref|YP_004597257.1| 25 LDALEENVEAQAQFVESWSETVGQATED-NELSEGVEGYAKAYETWMNASQQMVERVND 82
                                      4566777888888899999999999999.999999998888888888888777776665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  13 kevleqlaplsqnlentkeklseinrs.veetnekvkdankairdAr 58 
                                       ++ ++ ++ ++ +le +  +++ +++  ++  ne  kd + +++ Ar
  gi|336254150|ref|YP_004597257.1|  71 NASQQMVERVNDQLEGEDVDIEDFRDIwLNTANEAFKDVMSTTAFAR 117
                                       45567777777777777777777776524445566666666666665 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0032
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHH CS
                        Laminin_II  14 evleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklk 76 
                                       e+  ++ +l+q+ ++  ++  ++ +    t+e+v +    +++ +r   ++e++++++l++l+
  gi|336254150|ref|YP_004597257.1| 121 ETVGDVLELQQQADEAAQETLRMLGF--ATEEDVVEVGDRLVELERRQHDVERKLDRILERLE 181
                                       44455566666666666655555555..56777778888888888888888888888888876 PP

>> Phasin_2  Phasin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.6    0.0019       2.5      47      94 ..       4      51 ..       1      55 [. 0.83
   2 ?    2.5   1.9      0.14   1.8e+02      24      72 ..      90     139 ..      67     142 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0019
                          Phasin_2 47 akallsakdpqellelqselaqpalekavayarklaelaaktqeeaak 94
                                       ++  +a+d ++++e+++e + +ale+ v+   ++ e  ++t  +a++
  gi|336254150|ref|YP_004597257.1|  4 SQQSPQAQDWNAFVEQWNEQFLDALEENVEAQAQFVESWSETVGQATE 51
                                      677778999999999999999999999999999999999999888875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                          Phasin_2  24 gaeklaelqleaarasleeslaaakal.lsakdpqellelqselaqpale 72 
                                        +e++ + +l++a++++ + ++++  + ++ +++ ++lelq++  ++a+e
  gi|336254150|ref|YP_004597257.1|  90 DIEDFRDIWLNTANEAFKDVMSTTAFArMTGETVGDVLELQQQADEAAQE 139
                                       56777788888888888888887664414446788888888877666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1518  (0.0846673); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); 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):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 1418.01
//
Query:       gi|336254151|ref|YP_004597258.1|  [L=161]
Description: hypothetical protein Halxa_2763 [Halopiger xanaduensis SH-6]
Scores for 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   17.5   0.5     0.0038   16.8   0.5    1.3  1  DUF4795         Domain of unknown function (DUF4795)
     0.0026   17.8   3.6     0.0066   16.6   1.1    2.0  2  ApoLp-III       Apolipophorin-III precursor (apoLp-III)
     0.0062   17.6   2.1      0.067   14.3   0.2    2.1  2  ADH_zinc_N_2    Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.011   15.8   3.1        2.2    8.4   3.4    2.3  2  DUF148          Domain of unknown function DUF148
      0.012   15.3   6.7      0.093   12.4   6.7    2.3  1  YkyA            Putative cell-wall binding lipoprotein
      0.017   15.0  10.4      0.089   12.7  10.5    1.9  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
      0.026   14.8  16.3        1.5    9.2   2.0    3.0  2  Phasin_2        Phasin protein
      0.041   13.9   1.3       0.18   11.8   1.0    2.1  2  DUF1664         Protein of unknown function (DUF1664)
      0.073   13.6   5.4        4.3    7.9   0.1    3.3  3  BMFP            Membrane fusogenic activity
       0.12   12.0   5.7       0.14   11.8   5.7    1.0  1  DUF885          Bacterial protein of unknown function (DUF885
       0.15   12.2   9.1       0.34   11.0   5.1    2.1  2  DUF2959         Protein of unknown function (DUF2959)
       0.19   11.0   1.2       0.25   10.6   1.2    1.1  1  CorA            CorA-like Mg2+ transporter protein
        0.2   12.3   4.9        0.3   11.7   1.7    2.6  3  DUF5344         Family of unknown function (DUF5344)
       0.46    9.9   6.6        1.1    8.7   6.6    1.7  1  CAP_N           Adenylate cyclase associated (CAP) N terminal
       0.52   10.6   4.1          6    7.2   0.9    2.6  3  Cdh1_DBD_1      Chromodomain helicase DNA-binding domain 1
          1    9.3   7.5         17    5.4   1.4    2.8  2  Phasin          Poly(hydroxyalcanoate) granule associated pro
        1.8    9.0   7.2       0.96    9.9   1.4    2.3  2  TBCC_N          Tubulin-specific chaperone C N-terminal domai


Domain annotation for each model (and alignments):
>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.5   3.6e-06    0.0038      71     152 ..      75     153 ..      65     161 .] 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.6e-06
                           DUF4795  71 kadkeaLatkvsrdqfDeakkeLekmleellekleeqeealkkaldtLqeelkekld.rlelepLkeqleerlkelq 146
                                        ad++ L+  v +d +D+++++ ++ le ++e lee eea ++++ + +e +++  d +le     eq+ee++ +++
  gi|336254151|ref|YP_004597258.1|  75 SADFDELRDLV-DDGVDSTTEAQTESLEAAVEALEESEEAYDEFIANYSEVVDTSFDaALEA---HEQVEENVSAVA 147
                                       69*********.888******************************************74443...356666666666 PP

                           DUF4795 147 kelqea 152
                                       +++++ 
  gi|336254151|ref|YP_004597258.1| 148 ENVEQT 153
                                       555532 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.1   6.2e-06    0.0066      18     145 ..      11     141 ..       2     142 .. 0.86
   2 !    7.1   3.4    0.0051       5.4      53     102 ..     107     156 ..      92     161 .] 0.43

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.2e-06
                         ApoLp-III  18 psqeevvetiKensenlvdqlkqvikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQs 94 
                                         q + v+  ++ +  +++  ++ i+ + ++l   sd +e+  + +k ++   +d l+ + Pe     +el+  v +
  gi|336254151|ref|YP_004597258.1|  11 DAQRTAVKQSQTLTHDALEAQQASIGAFADALEGSSDLVESNAELTKGAVHAYFDALEGSLPEDSADFDELRDLVDD 87 
                                       4678899999******************************************************************* PP

                         ApoLp-III  95 gvqslv...kesqklaeslkensqeakeklakaikqayddaveaaqklakqLke 145
                                       gv s+    +es ++a +  e+s+ea ++  +   +++d  ++aa +  +q++e
  gi|336254151|ref|YP_004597258.1|  88 GVDSTTeaqTESLEAAVEALEESEEAYDEFIANYSEVVDTSFDAALEAHEQVEE 141
                                       **9986333466555555557777787887788899********9999999986 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0051
                         ApoLp-III  53 sdeleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvke 102
                                        +e eea +e+ ++ +e++d+   +  e+ ++++e  + v ++v++++ e
  gi|336254151|ref|YP_004597258.1| 107 LEESEEAYDEFIANYSEVVDTSFDAALEAHEQVEENVSAVAENVEQTADE 156
                                       33334444444444444444444444444444444444444444444333 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2   6.3e-05     0.067      37     124 ..      25     112 ..       6     114 .. 0.69
   2 ?    3.2   0.1      0.17   1.8e+02     111     125 ..     128     142 ..     121     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.3e-05
                                       HHHHHHE.EEEEEEEE--.--.S-EEE-CHHHCTTT-EEEE--GGG...-.....-HHHHHHHHHHHHHHH----EE CS
                      ADH_zinc_N_2  37 easlkvl.pggGrlvsig.gpplsaallkpakkrkgrsvkyeflfsmkas....aqadileelaalieeGklrpvvd 107
                                       +++l++  +  G +   + g         ++++++  +  ++ +f++ ++      ad ++el +l+++G   ++  
  gi|336254151|ref|YP_004597258.1|  25 HDALEAQqASIGAFADALeG-----SSDLVESNAELTKGAVHAYFDALEGslpeDSAD-FDELRDLVDDGVDSTTEA 95 
                                       44444444444555554422.....333333445556666677776555568866788.****************** PP

                                       EEEEGGGHHHHHHHHHS CS
                      ADH_zinc_N_2 108 rvfpleeaaeAhryles 124
                                       ++ +le+a+eA++  e+
  gi|336254151|ref|YP_004597258.1|  96 QTESLEAAVEALEESEE 112
                                       *************9986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.17
                                       EGGGHHHHHHHHHSS CS
                      ADH_zinc_N_2 111 pleeaaeAhrylesg 125
                                       ++++a eAh+++e++
  gi|336254151|ref|YP_004597258.1| 128 SFDAALEAHEQVEEN 142
                                       688999999999876 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.021        22      43      99 ..      19      76 ..       9      86 .. 0.78
   2 ?    8.4   3.4    0.0021       2.2      18      82 ..      94     156 ..      79     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.021
                            DUF148 43 kvkaqkeevkknvtavisnLssvqeklea.IldnkslTrkeqkeaieelkkqypkevs 99
                                      + ++ ++ + ++++a i  ++++ e  ++ + +n +lT+ + ++  ++l+ ++p++  
  gi|336254151|ref|YP_004597258.1| 19 QSQTLTHDALEAQQASIGAFADALEGSSDlVESNAELTKGAVHAYFDALEGSLPEDSA 76
                                      55666677777888889999988887766255799******************99855 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0021
                            DUF148  18 aeieeqleawaekygvtdeykefeakvkaqkeevkknvtavisnLssvqekleaIldnkslTrke 82 
                                       + + e lea +e   +++  +++ + +++  e v    +a+++  ++v+e+++a+ +n ++T +e
  gi|336254151|ref|YP_004597258.1|  94 EAQTESLEAAVE--ALEESEEAYDEFIANYSEVVDTSFDAALEAHEQVEENVSAVAENVEQTADE 156
                                       333344444444..677777888888888999999999999999999999999999999999876 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   6.7   8.9e-05     0.093      76     129 ..      70     126 ..       6     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.9e-05
                              YkyA  76 sieeakeefekikeeieei...edeelkkeaeelieameeryeaydklykaYkeale 129
                                       s+ e    f+++++ +++      e++ + +e+ +ea+ee +eayd+++++Y+e+++
  gi|336254151|ref|YP_004597258.1|  70 SLPEDSADFDELRDLVDDGvdsTTEAQTESLEAAVEALEESEEAYDEFIANYSEVVD 126
                                       555666778888888888743334455555666667778888888888888888765 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  10.5   8.5e-05     0.089      64     181 ..      49     157 ..      11     161 .] 0.47

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.5e-05
                                       CCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH- CS
                    Apolipoprotein  64 lgqnleelrqrlapyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkes 140
                                       +++n+e  +  + +y ++l  +l +d+ +         +elr+ ++++v+++ +  ++ +e +++ l+e+ e+  e 
  gi|336254151|ref|YP_004597258.1|  49 VESNAELTKGAVHAYFDALEGSLPEDSADF--------DELRDLVDDGVDSTTEAQTESLEAAVEALEESEEAYDEF 117
                                       444444444444444444444433333333........335555555555555555555555555555555555555 PP

                                       ----..-----SSSHHHHHHHTS-TTSHHHHHS--XXXXXX CS
                    Apolipoprotein 141 laphaeeveerlssrveelrekleeqaeelrerleanleel 181
                                       +a+++ ev ++  + + e+ e++ee+++++ e++e+ ++e+
  gi|336254151|ref|YP_004597258.1| 118 IANYS-EVVDTSFDAALEAHEQVEENVSAVAENVEQTADEF 157
                                       55552.22223333333444444444444444444444444 PP

>> Phasin_2  Phasin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.0    0.0014       1.5       8      48 ..       3      43 ..       1      66 [. 0.70
   2 ?    8.1   6.8     0.003       3.1      38      97 ..      91     155 ..      75     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                          Phasin_2  8 kknlealealaslalegaeklaelqleaarasleeslaaak 48
                                      +  + a++++ ++a++ +++l++ +lea +as+ + ++a++
  gi|336254151|ref|YP_004597258.1|  3 QNPITAFFDAQRTAVKQSQTLTHDALEAQQASIGAFADALE 43
                                      56677888999999999999999999999988888877776 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.003
                          Phasin_2  38 asleeslaaakallsakd.....pqellelqselaqpalekavayarklaelaaktqeeaaklae 97 
                                       +++e++++ ++a+++a       + e+++  se++ +++++a++   ++ e +++++e ++++a 
  gi|336254151|ref|YP_004597258.1|  91 STTEAQTESLEAAVEALEeseeaYDEFIANYSEVVDTSFDAALEAHEQVEENVSAVAENVEQTAD 155
                                       3444444444444444222346799*****************************99999999876 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.26   2.7e+02      97     115 ..      91     109 ..      22     114 .. 0.60
   2 ?   11.8   1.0   0.00017      0.18      47     104 ..      97     158 ..      85     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.26
                           DUF1664  97 seigedvesvkeavegles 115
                                       s+++ + es+++ave le+
  gi|336254151|ref|YP_004597258.1|  91 STTEAQTESLEAAVEALEE 109
                                       2334455566666666654 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00017
                           DUF1664  47 skqleqvseslaatkrhLssridr....vdkkldeqkeiskeikeevtevredlseigedve 104
                                       +++le   e+l++  +   + i++    vd++ d+  e+ ++++e+v++v e+++++ ++++
  gi|336254151|ref|YP_004597258.1|  97 TESLEAAVEALEESEEAYDEFIANysevVDTSFDAALEAHEQVEENVSAVAENVEQTADEFD 158
                                       56666666666666665555554333338999************************999875 PP

>> BMFP  Membrane fusogenic activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.94   9.9e+02      51      71 ..      10      31 ..       9      51 .. 0.71
   2 ?    6.2   0.2     0.014        14      59      77 .]      91     109 ..      75     109 .. 0.79
   3 ?    7.9   0.1    0.0041       4.3       6      43 ..     117     154 ..     113     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.94
                              BMFP 51 Fdvqrevlartre.kleaLear 71
                                      Fd+qr  + + ++   +aLea+
  gi|336254151|ref|YP_004597258.1| 10 FDAQRTAVKQSQTlTHDALEAQ 31
                                      7777777666555133466665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.014
                              BMFP  59 artrekleaLearvaaLEa 77 
                                       + t ++ e+Lea v+aLE+
  gi|336254151|ref|YP_004597258.1|  91 STTEAQTESLEAAVEALEE 109
                                       56889999*********95 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0041
                              BMFP   6 ilddlakkvgdalpaaagvreeieknvravlqealskl 43 
                                       ++ + +++v+ ++ aa +++e +e+nv av++++ ++ 
  gi|336254151|ref|YP_004597258.1| 117 FIANYSEVVDTSFDAALEAHEQVEENVSAVAENVEQTA 154
                                       666778899999*******************9987765 PP

>> DUF885  Bacterial protein of unknown function (DUF885)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   5.7   0.00013      0.14      16     158 ..      20     156 ..       7     161 .] 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                       ----SHHHHHHHHHHHHHHHHHHCT.S-CCHH..HHHHHHHHHHHHHHHHHHHHHHHS..HHHHTT-CCCCHHHHHH CS
                            DUF885  16 lpdlspaaeaaraarlraalaeldaaidrdkl..seerldldllrerleleletaeag..ypleqlralagpvqqlp 88 
                                        + l+ +a +a++a + a+ ++l+     ++l  s++ l+  +++      +++ e +   + +    ++     ++
  gi|336254151|ref|YP_004597258.1|  20 SQTLTHDALEAQQASIGAFADALEG---SSDLveSNAELTKGAVHA----YFDALEGSlpEDSA---DFDELRDLVD 86 
                                       4567777888888888888888843...444422335555555555....44222222222222...2244455577 PP

                                       HHHCGTTSSCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHTT.-S-HHHHHHHHHHHHHHHGTSSHHCCC CS
                            DUF885  89 sllseepfateedleaylarlaavpaaldqaranlregaaaglvpprrqvekvieqlrgllagaaaeasa 158
                                       + ++  + a++e lea ++ l++  +a+d+ +an +e +++   ++ ++ e+v e++++++++ +++a++
  gi|336254151|ref|YP_004597258.1|  87 DGVDSTTEAQTESLEAAVEALEESEEAYDEFIANYSEVVDTSFDAALEAHEQVEENVSAVAENVEQTADE 156
                                       899999999****************************999999998777777777777777766666554 PP

>> DUF2959  Protein of unknown function (DUF2959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.056        59      21      49 ..      25      53 ..      14      83 .. 0.73
   2 ?   11.0   5.1   0.00032      0.34      13      85 ..      82     155 ..      63     159 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.056
                           DUF2959 21 ekardsqeeakeqfksALerfkavvefdg 49
                                      ++a ++q+ +  +f++ALe  + +ve + 
  gi|336254151|ref|YP_004597258.1| 25 HDALEAQQASIGAFADALEGSSDLVESNA 53
                                      57999*************99888887553 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00032
                           DUF2959  13 rdilvdrVekardsqeeakeqfksALerfkavvefdggeLekey.eklnkeyeesekaaeevrerieaveevae 85 
                                       rd++ d V+++ ++q+e+ e+  +ALe+ +++++   ++ +++   ++++++e+ e+  e+v+   e+ve+ a+
  gi|336254151|ref|YP_004597258.1|  82 RDLVDDGVDSTTEAQTESLEAAVEALEESEEAYDEFIANYSEVVdTSFDAALEAHEQVEENVSAVAENVEQTAD 155
                                       77777888888888888888877777777776654444444333034555555555555555555555555554 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.2   0.00024      0.25      90     223 ..      34     158 ..      16     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                              CorA  90 aldevikrlkdeggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrr.lvklrr 165
                                       ++ +++++l+  ++ ++s +el+   + +  d l+  l + +++ del d +     ++ ++++++ +++ l    +
  gi|336254151|ref|YP_004597258.1|  34 SIGAFADALEGSSDLVESNAELTKGAVHAYFDALEGSLPEDSADFDELRDLV-----DDGVDSTTEAQTEsLEAAVE 105
                                       5677778888777888999999999999999999999999999999999999.....999999999995549999** PP

                              CorA 166 alapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtys 223
                                       al +++e++++++a  + +++ d+    ++  l+  e+++e ++a++e +e+  d++ 
  gi|336254151|ref|YP_004597258.1| 106 ALEESEEAYDEFIA--NYSEVVDTS---FDAALEAHEQVEENVSAVAENVEQTADEFD 158
                                       **************..888888888...9***********************999986 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.89   9.4e+02      60      77 ..      46      63 ..      10      66 .. 0.70
   2 ?   11.7   1.7   0.00029       0.3      29      80 ..      91     142 ..      76     149 .. 0.77
   3 ?    0.2   0.1       1.1   1.1e+03      57      69 ..     140     152 ..     129     159 .. 0.51

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.89
                           DUF5344 60 ktlllknvedtesaVdsl 77
                                       +l+++n+e t+ aV  +
  gi|336254151|ref|YP_004597258.1| 46 SDLVESNAELTKGAVHAY 63
                                      568888888888888776 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00029
                           DUF5344  29 ipetisgknsldvvekineleeeleellkaYktlllknvedtesaVdslkea 80 
                                         ++++ ++  ++ve ++e ee++ e + +Y +++  + +++ +a ++ +e+
  gi|336254151|ref|YP_004597258.1|  91 STTEAQTESLEAAVEALEESEEAYDEFIANYSEVVDTSFDAALEAHEQVEEN 142
                                       4555666677789**********************99988887777666665 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.1
                           DUF5344  57 kaYktlllknved 69 
                                       +   +++ +nve+
  gi|336254151|ref|YP_004597258.1| 140 EENVSAVAENVEQ 152
                                       2222333344443 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 ?    8.7   6.6     0.001       1.1      36      94 ..      94     155 ..      10     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.001
                                       XXXXXXXXXXXXXXXSXH....HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH CS
                             CAP_N  36 aaaaaaaaaakaaaaaaaa...ksveaFdelisgsvkefvelskkiggevaeqaelvkkafe 94 
                                       +a++++ +aa +a +++++   ++++++ e++++s++  +e+ ++++++v+  ae v+++ +
  gi|336254151|ref|YP_004597258.1|  94 EAQTESLEAAVEALEESEEaydEFIANYSEVVDTSFDAALEAHEQVEENVSAVAENVEQTAD 155
                                       11112212111111111113459**********************************99865 PP

>> Cdh1_DBD_1  Chromodomain helicase DNA-binding domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.2   1.3e+03      50      89 ..      12      51 ..       6      63 .. 0.64
   2 ?    5.8   0.1     0.016        16      14      75 ..      55     113 ..      51     118 .. 0.56
   3 ?    7.2   0.9    0.0057         6      38      88 ..     108     158 ..     104     161 .] 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.2
                        Cdh1_DBD_1 50 eakklvkeeeekrakeleeleadaeeykeklkkgevkade 89
                                        +  vk++++  ++ le+ +a++ + +++l+ +++ +++
  gi|336254151|ref|YP_004597258.1| 12 AQRTAVKQSQTLTHDALEAQQASIGAFADALEGSSDLVES 51
                                      5556667777777777777777666666666655555544 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.016
                        Cdh1_DBD_1  14 LkyGdlsnkleeliadGtLPeknielleelyeelleeakklvkeeee.krakeleeleadaee 75 
                                       L +G ++  +++l  +G+LPe + + ++el ++l++   ++  e ++   +  +e+le++ e+
  gi|336254151|ref|YP_004597258.1|  55 LTKGAVHAYFDAL--EGSLPEDSAD-FDEL-RDLVDDGVDSTTEAQTeSLEAAVEALEESEEA 113
                                       6678888888887..8999998776.3443.45555544444333330233344444444444 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0057
                        Cdh1_DBD_1  38 elleelyeelleeakklvkeeeekrakeleeleadaeeykeklkkgevkad 88 
                                       e  ee+y+e++++ +++v+++ ++  +  e++e+++++ +e+++++ ++ d
  gi|336254151|ref|YP_004597258.1| 108 EESEEAYDEFIANYSEVVDTSFDAALEAHEQVEENVSAVAENVEQTADEFD 158
                                       566888999999999999998888888888888888888888777766655 PP

>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.4     0.016        17      29      90 ..      12      73 ..       6     115 .. 0.52
   2 ?    5.1   1.9     0.021        22      38      78 ..     115     155 ..     101     161 .] 0.49

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.016
                            Phasin 29 vqeeGsklfeaLvkeGeklekktkkvaeekleevresvkskveevkekaeeqwdklekafde 90
                                      +q+ + k  ++L ++  ++++    +++++le  ++ v+s++e  k  +++  d le  + e
  gi|336254151|ref|YP_004597258.1| 12 AQRTAVKQSQTLTHDALEAQQASIGAFADALEGSSDLVESNAELTKGAVHAYFDALEGSLPE 73
                                      55555555566666666666666666666666666666666666666666666666555533 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.021
                            Phasin  38 eaLvkeGeklekktkkvaeekleevresvkskveevkekae 78 
                                       ++ + + +++ ++  ++a e+ e+v+e+v++ +e+v++ a+
  gi|336254151|ref|YP_004597258.1| 115 DEFIANYSEVVDTSFDAALEAHEQVEENVSAVAENVEQTAD 155
                                       55554444444444444444444444444444444444333 PP

>> TBCC_N  Tubulin-specific chaperone C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.4   0.00091      0.96       8     104 ..      12     110 ..      10     119 .. 0.88
   2 ?    1.7   0.4      0.33   3.4e+02      14      40 ..     133     159 ..     125     161 .] 0.61

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00091
                            TBCC_N   8 qerqeqlekrkeereseaveeekvdsFlkaFteekaaieellesve..esadksklkqkldeitaeiqeLqkllaes 82 
                                       ++r + +++++   ++ ++++ ++ +F++a++ +++ +e++ e  +    a  ++l+ +l e +a+++eL++l+ + 
  gi|336254151|ref|YP_004597258.1|  12 AQRTAVKQSQTLTHDALEAQQASIGAFADALEGSSDLVESNAELTKgaVHAYFDALEGSLPEDSADFDELRDLVDDG 88 
                                       6899999999******************************98888877899999*******************9998 PP

                            TBCC_N  83 smfLpsYdlrsaqealskLkes 104
                                       +   ++ +++s  +a++ L+es
  gi|336254151|ref|YP_004597258.1|  89 VDSTTEAQTESLEAAVEALEES 110
                                       8888888888888888888776 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.33
                            TBCC_N  14 lekrkeereseaveeekvdsFlkaFte 40 
                                       le+ ++ +e+ ++  e+v++ +++F++
  gi|336254151|ref|YP_004597258.1| 133 LEAHEQVEENVSAVAENVEQTADEFDA 159
                                       555556666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1574  (0.0877907); expected 358.6 (0.02)
Passed bias filter:                      738  (0.0411624); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 1280.01
//
Query:       gi|336254152|ref|YP_004597259.1|  [L=103]
Description: hypothetical protein Halxa_2764 [Halopiger xanaduensis SH-6]
Scores for 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   13.6   0.7      0.073   13.0   0.7    1.2  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 ?   13.0   0.7   4.1e-06     0.073       7      33 ..      70      96 ..      66     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-06
                                      EEEEE-CCCHHHCCEECTCEEEEEECT CS
                    MazE_antitoxin  7 gavriPkevrfelgireGdevelevdg 33
                                      g+++iP   r++l+i+eGd v  +v++
  gi|336254152|ref|YP_004597259.1| 70 GRISIPEPEREALDIEEGDIVQTIVVP 96
                                      799******************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      753  (0.041999); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 884.65
//
Query:       gi|336254153|ref|YP_004597260.1|  [L=209]
Description: MaoC domain-containing protein dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-23   81.6   0.0    8.8e-23   80.2   0.0    1.6  2  MaoC_dehydratas  MaoC like domain
    1.6e-07   31.5   0.0    6.2e-07   29.6   0.0    2.0  2  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
     0.0014   18.9   0.1     0.0071   16.7   0.0    2.3  3  4HBT             Thioesterase superfamily
      0.005   17.3   0.0      0.011   16.3   0.0    1.4  1  4HBT_2           Thioesterase-like superfamily


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.39   1.8e+03      59      90 ..      10      41 ..       6      45 .. 0.61
   2 !   80.2   0.0     2e-26   8.8e-23      11     104 ..      85     175 ..      75     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.39
                                      HHHHHHHHHHHHSTTEGGGEEEEEEEE-S--B CS
                   MaoC_dehydratas 59 laivaklveeelgdnvvarvgeikvrFtkpVl 90
                                      +a+++ +++++ ++  ++ + ++++   ++V+
  gi|336254153|ref|YP_004597260.1| 10 FAAMTNAWTAMTQSFLRSATAANRAALSAMVP 41
                                      45666666666666666666666666666665 PP

  == domain 2  score: 80.2 bits;  conditional E-value: 2e-26
                                       EEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S CS
                   MaoC_dehydratas  11 etekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvrFtk 87 
                                        +  e t++ +d++ +a +sgD+n +H+d+efA++++fg++I+hG l+++++++++++  g    + + ++++ F +
  gi|336254153|ref|YP_004597260.1|  85 TF--EKTLSDDDVRAFAQISGDTNRLHLDDEFAAQTRFGERIVHGTLVSGLISAALARLPGL---TIYLSQDLEFRG 156
                                       44..78999*****************************************************...77********** PP

                                       --BTTCEEEEEEEEEE..E CS
                   MaoC_dehydratas  88 pVlpgdtlkvelevvg..k 104
                                       pV +gd++ +++evv+   
  gi|336254153|ref|YP_004597260.1| 157 PVKIGDRVSARVEVVEdlG 175
                                       **************99442 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.11   4.7e+02      85     102 ..      75      92 ..      54      93 .. 0.78
   2 !   29.6   0.0   1.4e-10   6.2e-07      12     100 ..      88     170 ..      76     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.11
                   MaoC_dehydrat_N  85 hepiraGDelttesriad 102
                                        + i +GD +t+e+++ d
  gi|336254153|ref|YP_004597260.1|  75 RNAIGVGDNVTFEKTLSD 92 
                                       458899******998865 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1.4e-10
                   MaoC_dehydrat_N  12 aevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkapellealgidlsrllhgeqefeyhepi 88 
                                        +++ ++vr fa+  g+tn ++ld+e a+++++++ i+  t+++ l  +a  l +  g+    ++ ++q +e+  p+
  gi|336254153|ref|YP_004597260.1|  88 KTLSDDDVRAFAQISGDTNRLHLDDEFAAQTRFGERIVHGTLVSGLISAA--LARLPGL----TIYLSQDLEFRGPV 158
                                       567899*******************************************9..6665555....5799********** PP

                   MaoC_dehydrat_N  89 raGDelttesri 100
                                       + GD+++ + ++
  gi|336254153|ref|YP_004597260.1| 159 KIGDRVSARVEV 170
                                       *******98876 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.4   6.5e+03      36      48 ..      20      32 ..      15      40 .. 0.71
   2 ?   -2.3   0.0       1.3     6e+03      30      51 ..      76      96 ..      65     102 .. 0.64
   3 !   16.7   0.0   1.6e-06    0.0071      36      77 ..     150     192 ..     124     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                                      EEEEESS-BBTTC CS
                              4HBT 36 lsidflrpvrlgd 48
                                      ++  flr+++  +
  gi|336254153|ref|YP_004597260.1| 20 MTQSFLRSATAAN 32
                                      6778999888655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                                      EEEEEEEEEEESS-BBTTCEEE CS
                              4HBT 30 lvvvvelsidflrpvrlgdelt 51
                                       + +v ++++f +    + +++
  gi|336254153|ref|YP_004597260.1| 76 NAIGVGDNVTFEKTLSDD-DVR 96
                                      555667777777777666.455 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 1.6e-06
                                       EEEEESS-BBTTCEEEEEEEEEE.EESSEEEEEEEEEETTSCE CS
                              4HBT  36 lsidflrpvrlgdeltvearvlr.lgrtsavvevevrdedgrl 77 
                                         ++f+ pv++gd++ ++++v++ lg+  + +e ++rde++ +
  gi|336254153|ref|YP_004597260.1| 150 QDLEFRGPVKIGDRVSARVEVVEdLGNDQFRLETRIRDESDDE 192
                                       5689****************8755***************9876 PP

>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.4e-06     0.011      20      98 ..     120     198 ..     103     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.4e-06
                            4HBT_2  20 yleearvkflertglksrsiarrgiglilssahvryrrplkfpdrltvefrv.ididaktliiehrflsnadgkkaa 95 
                                       ++e+ +   l + gl s ++ar+ ++ i  s+ +++r p+k +dr+  ++ v  d   +++++e r+++++d+ +++
  gi|336254153|ref|YP_004597260.1| 120 FGERIVHGTL-VSGLISAALARLPGLTIYLSQDLEFRGPVKIGDRVSARVEVvEDLGNDQFRLETRIRDESDDETVI 195
                                       4444444444.677778888999999**************************666**************87777776 PP

                            4HBT_2  96 rve 98 
                                        +e
  gi|336254153|ref|YP_004597260.1| 196 DGE 198
                                       665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1583.07
//
Query:       gi|336254154|ref|YP_004597261.1|  [L=472]
Description: phosphoglucosamine mutase [Halopiger xanaduensis SH-6]
Scores for 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-31  109.5   0.1    6.3e-31  106.9   0.0    2.1  2  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    3.5e-17   62.9   0.1    9.4e-17   61.5   0.1    1.8  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
      1e-10   41.6   0.0    4.2e-10   39.6   0.0    2.1  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
    0.00038   20.6   0.1      0.001   19.3   0.1    1.7  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet


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 !  106.9   0.0   1.4e-34   6.3e-31       2     135 ..       2     123 ..       1     125 [. 0.94
   2 ?   -0.3   0.0      0.18   8.2e+02      57      88 ..     268     302 ..     247     309 .. 0.79

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 1.4e-34
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB- CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllp 78 
                                        +fgt+G+Rg v  + +tp+l++ +g+a++e       +++ vvGrD+R +++ la+a+ agl ++G++v++lg +p
  gi|336254154|ref|YP_004597261.1|   2 TLFGTAGIRGPVT-D-VTPALALDVGRAAGEP------GATFVVGRDGRETGPALAAAMEAGLESAGADVYRLGQVP 70 
                                       58*********99.4.8************964......567************************************ PP

                                       HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT- CS
                         PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekee 135
                                       tPa+++a +      g+mitaSHnpp++ngiK++   G+++++++e++Ie+++++ +
  gi|336254154|ref|YP_004597261.1|  71 TPALAYASQG---RRGVMITASHNPPTDNGIKLFAD-GVEYDRDAERAIEDAVAADD 123
                                       ********99...68*******************98.**************998765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.18
                                       HHHHHHHHHCCT-CEEEEE...EB-HHHHHHHHHH CS
                         PGM_PMM_I  57 aealaaglaanGvevillg...llptPavsfairk 88 
                                       +++++a++a++ v+  ++g   +++tP +s+ i +
  gi|336254154|ref|YP_004597261.1| 268 EDTVLAVVAEHYVSESDAGdpvVVTTPNASARIDE 302
                                       46788999999999999999999999999987765 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 !   61.5   0.1   2.1e-20   9.4e-17      19     103 .]     168     263 ..     142     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 2.1e-20
                                       H...T-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGG.........G- CS
                        PGM_PMM_II  19 s...glkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkke.........ga 83 
                                       +   gl++++d+++G g+  ++ +l++lg++vv lna+ d++f  + + p++ e+l ++ie +  +         ++
  gi|336254154|ref|YP_004597261.1| 168 RplaGLSIAVDCGNGMGSVATPHVLERLGAEVVALNANVDGHFTARESKPTP-ETLTDFIEFMATDssgaasrnaEF 243
                                       144489***************************************9999999.99***9999999999999998899 PP

                                       SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  84 dlglafDgDaDRlgvvderG 103
                                       dlgla+DgDaDRl+v  ++G
  gi|336254154|ref|YP_004597261.1| 244 DLGLAHDGDADRLVVLGPDG 263
                                       **************997765 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 !   39.6   0.0   9.5e-14   4.2e-10       7      65 ..     406     460 ..     388     468 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 9.5e-14
                                       CC-TT..EECCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEES.SHHHHHHH CS
                        PGM_PMM_IV   7 eekakvvaalaallkvasikeglkilledGrrlavRpSGTepllrvyvEak.sdeelarl 65 
                                       +e    ++a+++ + +  +  g++  + d++++ vRpSGTep++r+y+E+   d+++a+ 
  gi|336254154|ref|YP_004597261.1| 406 TE---LPEAFPDTAVD--TDYGVRLEFDDASWVLVRPSGTEPYVRIYAESEtVDDLIADA 460
                                       33...47788888666..99******************************9777777765 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 !   19.3   0.1   2.2e-07     0.001       3     101 ..     269     372 ..     267     383 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSS..CHHHHHHHHHTT....ECEEEETTCE CS
                       PGM_PMM_III   3 dqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvG..dkyvleemkeeg....avlGgEeSgh 73 
                                       d +la++a+++ +e  +++ +vv+t   s  +++ ++++g+++ +++ G  +  +++e  +++    +v++ E   h
  gi|336254154|ref|YP_004597261.1| 269 DTVLAVVAEHYVSESDAGDPVVVTTPNASARIDERVREAGGRVERVRLGalHEGIARERAQGDedtaVVFAAEPWKH 345
                                       788888888886654555558****************************444446666544437888999**99877 PP

                                       EEETTTBSS--HHHHHHHHHHHHHHHTS CS
                       PGM_PMM_III  74 iifldeattkDGilaallvleilaetgk 101
                                       i    +  + DG+ +a+ v++++a+ g 
  gi|336254154|ref|YP_004597261.1| 346 IHAA-FGGWIDGVASAAVVAALVADAGS 372
                                       6554.44579***********9998763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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 0.20s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3731.07
//
Query:       gi|336254155|ref|YP_004597262.1|  [L=351]
Description: basic membrane lipoprotein [Halopiger xanaduensis SH-6]
Scores for 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-58  196.4   5.8    7.6e-58  195.9   5.8    1.2  1  Bmp           ABC transporter substrate-binding protein PnrA-
    1.6e-05   24.6   9.4    4.5e-05   23.2   9.4    1.7  1  Peripla_BP_4  Periplasmic binding protein domain
  ------ inclusion threshold ------
       0.14   12.1   2.8       0.31   11.0   2.8    1.5  1  TAT_signal    TAT (twin-arginine translocation) pathway signa


Domain annotation for each model (and alignments):
>> Bmp  ABC transporter substrate-binding protein PnrA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.9   5.8   1.3e-61   7.6e-58       2     300 ..      37     349 ..      36     350 .. 0.93

  Alignments for each domain:
  == domain 1  score: 195.9 bits;  conditional E-value: 1.3e-61
                                       EEEEEECSS-TTTSCHHHHHHHHHHHHHHHCTTEEEEEEEEC.GGGHHHHHHHHHHCTT.-SEEEEESCCHHHHHHH CS
                               Bmp   2 vkvavlvegtidDksfnessyeGirrlkkeqnieliskesslltdedyiadlknlkeeg.sdlivatgfalqdalqe 77 
                                       ++ +v + g + D sfn ++ +G++ +++e+ni   + e  +  +++   + ++++e g +dl+  +g+a++dal+e
  gi|336254155|ref|YP_004597262.1|  37 QVGMVYATGGLGDDSFNDMAKQGVEDAQEEFNISYDETEPES--ASEFGGAQRDFAESGdYDLVNCIGYAQKDALSE 111
                                       788999**************************9988888777..7888889999988755***************** PP

                                       HHHH-TTS-EEEESS--TT-STTEEEEEE-HHHHHHHHHHHHHHHHHCTTTTEEC.............SS-SCCCHH CS
                               Bmp  78 vssdfpkvkFliiDavvekeyknvlsvaFrseegaFLaGvaaAlmsktnkigfvg.............Gveipvvks 141
                                        + ++p+++F+i+D  v+++  nv s++F + eg+F +G++a+l+++++     g             G e ++++s
  gi|336254155|ref|YP_004597262.1| 112 NAPEYPDQNFIIVDDEVKED--NVRSYQFGEPEGSFQVGHLAGLLTQEEFSAGAGetnpdanvvgfvgGTETQLIQS 186
                                       ********************..*************************998888889999999999999********* PP

                                       CHHHHHHHHHHH-TT-EEEEEE-SSSS-HHHHHHHHHHHHH.CT--EEEEE-GGGHHHHHHHHHHHCHCTEEEEEES CS
                               Bmp 142 fingFeaGikyvnpdievvvkvagtfsDakkgkslAsslyk.egvdvifpaagkagkgvieaakelglsnyvIgvdk 217
                                       f +gF+aG+  +n+d+evv+ ++g f D + g+++A+ +y+ + +d++f+aag +g+gv++aa+++g    +Igvd+
  gi|336254155|ref|YP_004597262.1| 187 FHAGFQAGVEHANEDAEVVSTYVGGFNDTAGGQQAARTMYQdQDADIVFHAAGRTGIGVFQAAQDEGRF--AIGVDS 261
                                       *****************************************889***********************99..****** PP

                                       --CGCSTT...CCEEEEEEEHHHHHHHHHHHHHCCT---TTEEEEE-CCCTSEEE-...S--TCCHHHHCHHHHHHH CS
                               Bmp 218 dqsylape...nvitsiiknvedlvvsiiekvakgevlaggevitlglkegvvgld...eesdvledekvkeqlkke 288
                                       dqs ++++    ++ s +k v+ +v+ +ie v+++e ++gge+ tlgl+e++vg +   e    + +e +++  + +
  gi|336254155|ref|YP_004597262.1| 262 DQSVSNEDfadVILASMVKRVDTAVYNAIESVVNDE-FQGGETETLGLEEEGVGAVygdEIGGEIPQEITDQVDESR 337
                                       **99998633256677778888899999999****9.*****************99998888889999999999999 PP

                                       HHHHCCCCHHSS CS
                               Bmp 289 nkkiikeisvpa 300
                                       +++i +ei vp+
  gi|336254155|ref|YP_004597262.1| 338 QQIIDGEIDVPS 349
                                       999999999986 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   9.4   7.5e-09   4.5e-05       9     220 ..      49     263 ..      40     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 7.5e-09
                                       STCHHHHHHHHHHHHHHHTTCEEEEEECSTT-HHHHHHHHHHHHHTT.-SEEE.E--SSHHHHHHHHHHHHHTT-EE CS
                      Peripla_BP_4   9 snpffsaaregleeaakelgaevtvvgdaendaaeQvaqiedaiakg.vdgii.vapvdstalapalkkakaaGIpV 83 
                                       +++f + a++g+e+a +e +++++ +  +  +a+e   +  d+ ++g +d++  +  ++ +al++   +  +++  +
  gi|336254155|ref|YP_004597262.1|  49 DDSFNDMAKQGVEDAQEEFNISYDET--EPESASEFGGAQRDFAESGdYDLVNcIGYAQKDALSENAPEYPDQN--F 121
                                       44499999*************99987..5555566666667776666699775589999999**9999999995..5 PP

                                       EEESTTGCTTT-CEEEEEC..-HHHHHHHHHHHHHHHCTTH.......EEEEEETSCCCHHHHHHHHHHHHHHHHH- CS
                      Peripla_BP_4  84 vafdsddapsgerlayvgf..dneaaGelqaeylaeklggk......kgkvvilaGspgdpnaeeriegfrkvlkey 152
                                       + +d ++++++ r++  g    ++++G+l++ +  e   ++      +++vv + G   ++  + + +gf +  + +
  gi|336254155|ref|YP_004597262.1| 122 IIVDDEVKEDNVRSYQFGEpeGSFQVGHLAGLLTQEEFSAGagetnpDANVVGFVGGTETQLIQSFHAGFQAGVEHA 198
                                       88888856666666666642257999*****999999999999999******************************8 PP

                                       T.TCEECCEEESTTTCHHHHHHHHHHHHHTTTECEEEESSCCHHHCHHHHHHHTTTTSTEEEEEES-HH CS
                      Peripla_BP_4 153 p.gikivaevaganwdaekaqqalealltanpldgilaandgmaegalealeaaglagkvvvtgqDatp 220
                                       + + ++v++++g+ +d + +qqa+ ++ + ++ d ++ a + +++g+ +a +++g+      +g+D+++
  gi|336254155|ref|YP_004597262.1| 199 NeDAEVVSTYVGGFNDTAGGQQAARTMYQDQDADIVFHAAGRTGIGVFQAAQDEGRF----AIGVDSDQ 263
                                       88******999999***************6669********************8863....77888776 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.8   5.1e-05      0.31       3      24 ..       4      25 ..       4      26 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.1e-05
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggca 24
                                      +RR  LKg ++a+ A ++g ++
  gi|336254155|ref|YP_004597262.1|  4 NRRAVLKGMGVAGLASMAGCVG 25
                                      7************999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2917.25
//
Query:       gi|336254156|ref|YP_004597263.1|  [L=565]
Description: Monosaccharide-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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  161.9   0.0    1.4e-30  106.6   0.0    2.3  2  ABC_tran     ABC transporter
    1.8e-09   37.8   0.0    0.00017   21.5   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00026   20.7   0.1      0.027   14.2   0.0    2.7  3  AAA_29       P-loop containing region of AAA domain
     0.0015   18.3   0.2      0.011   15.5   0.2    2.1  1  AAA_30       AAA domain
     0.0089   15.9   0.0       0.08   12.8   0.0    2.4  3  RsgA_GTPase  RsgA GTPase
     0.0097   16.2   0.1        3.2    8.0   0.0    2.5  2  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.011   15.2   0.1        4.1    6.8   0.0    2.7  3  SMC_N        RecF/RecN/SMC N terminal domain
      0.017   15.6   0.0      0.032   14.7   0.0    1.4  1  AAA_23       AAA domain
      0.021   14.5   0.0        1.1    8.9   0.0    2.1  2  AAA_15       AAA ATPase domain
      0.034   14.5   0.0       0.12   12.8   0.0    1.9  1  AAA_16       AAA ATPase domain
      0.048   13.8   0.0       0.17   12.0   0.0    2.2  2  MMR_HSR1     50S ribosome-binding GTPase
      0.096   12.3   0.0       0.18   11.4   0.0    1.3  1  AAA_27       AAA domain
       0.13   11.1   1.9       0.16   10.8   0.0    2.0  3  DLIC         Dynein light intermediate chain (DLIC)


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 !  106.6   0.0   9.9e-34   1.4e-30       2     137 .]      59     209 ..      58     209 .. 0.94
   2 !   53.2   0.0     3e-17   4.2e-14       2     136 ..     314     469 ..     313     470 .. 0.83

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 9.9e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       ++v+l +++g+++a++GenGaGK+tL+++l+gl++p+eG++ +dg++ +   ++   ++ +g+++q+  l +++tv+
  gi|336254156|ref|YP_004597263.1|  59 DDVDLRVERGTVHALLGENGAGKTTLMNVLYGLYEPEEGRVVVDGRERSFdSPRDAIDAGVGMIHQHFMLVDTMTVA 135
                                       689*****************************************77766659************************* PP

                                       HH..................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en                  + ++++ ++ +++g + +++ +v    + LS G +qrv++ +al++ +++l+lDEpt
  gi|336254156|ref|YP_004597263.1| 136 ENialgneptkwfgmavdreQVERDVRDLCDRYGFDVDPQARV----EDLSVGVQQRVEILKALFRGADVLILDEPT 208
                                       ***************9887777777999999999999999999....*****************************9 PP

                                       T CS
                                       x RF
                          ABC_tran 137 a 137
                                       a
  gi|336254156|ref|YP_004597263.1| 209 A 209
                                       7 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 3e-17
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS...--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe...pqlfpel 74 
                                       + ++l++++ge+v+i G  G G   L+++++gl +p+eG+i+++g+d+++  ++e+ ++ ++++p++     l    
  gi|336254156|ref|YP_004597263.1| 314 SGIDLDVRAGEIVGIAGVDGNGQAELIEAITGLRTPDEGTITYEGTDVTDwSRRERIEAGMAYIPEDrheRGLVMPF 390
                                       5789**********************************************9999*************5544444444 PP

                                       BHHHH....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEE CS
                                       xxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpklll 131
                                       ++ en                      ++++e+++++++       +++ +++s+SgG +q+  + r + ++p+l++
  gi|336254156|ref|YP_004597263.1| 391 NLVENgvlgsqrspefasggridwaGVRDHAEEIIETYDVRP---PNADADARSFSGGNQQKFIVGREFERDPSLVV 464
                                       455559**9999998888887764444444888888887666...4445578*****************99999998 PP

                                       EESTT CS
                                       xxxxx RF
                          ABC_tran 132 lDEpt 136
                                       +  pt
  gi|336254156|ref|YP_004597263.1| 465 ATHPT 469
                                       76666 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   2.3e-05     0.031       2      23 ..      71      92 ..      70     120 .. 0.82
   2 !   21.5   0.0   1.2e-07   0.00017     234     297 ..     178     238 ..     159     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                       +l G Ng+GK++L+  l++l 
  gi|336254156|ref|YP_004597263.1| 71 HALLGENGAGKTTLMNVLYGLY 92
                                      689****************994 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.2e-07
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       + +lS G+++   +l al+r +   ++l++DEp + L P+ ++ l+++l+el++ g  +i+ TH
  gi|336254156|ref|YP_004597263.1| 178 VEDLSVGVQQRVEILKALFRGA---DVLILDEPTAVLTPQEVEDLYDVLEELTAQGKTIIFITH 238
                                       568899999999********99...9************************************** 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 !   14.2   0.0   1.9e-05     0.027      15      40 ..      61      86 ..      56      98 .. 0.78
   2 ?   -3.8   0.0       8.1   1.1e+04      38      50 ..     203     215 ..     203     216 .. 0.84
   3 ?    3.2   0.0     0.052        72      18      50 ..     319     351 ..     312     357 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllD 40
                                       ++++++  ++ l G++G+GK+Tl+ 
  gi|336254156|ref|YP_004597263.1| 61 VDLRVERGTVHALLGENGAGKTTLMN 86
                                      56677744499*************94 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.1
                            AAA_29  38 llDAiqalLvpak 50 
                                       +lD  +a+L+p++
  gi|336254156|ref|YP_004597263.1| 203 ILDEPTAVLTPQE 215
                                       6888899***986 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.052
                            AAA_29  18 eidlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                       +++  +++ ++G  G+G   l+ Ai+ l +p++
  gi|336254156|ref|YP_004597263.1| 319 DVRAGEIVGIAGVDGNGQAELIEAITGLRTPDE 351
                                       4553448889****************9999987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   7.9e-06     0.011      17      51 ..      67     101 ..      61     255 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.9e-06
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrvig 51 
                                       +  v++l G  G+GKtt++++l  ++e ++grv++
  gi|336254156|ref|YP_004597263.1|  67 RGTVHALLGENGAGKTTLMNVLYGLYEPEEGRVVV 101
                                       456999***********************777765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   5.8e-05      0.08      99     121 ..      68      90 ..      57     105 .. 0.83
   2 ?   -2.6   0.0       3.1   4.3e+03      98     120 ..     322     344 ..     273     353 .. 0.68
   3 ?   -1.0   0.0         1   1.4e+03      33      63 ..     478     508 ..     472     533 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                                       TSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                       + + +l+G+ G+GK+tL+n+l +
  gi|336254156|ref|YP_004597263.1|  68 GTVHALLGENGAGKTTLMNVLYG 90 
                                       57899***************987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.1
                                       TTSEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinall 120
                                       +++++ ++G  G G   Li+a++
  gi|336254156|ref|YP_004597263.1| 322 AGEIVGIAGVDGNGQAELIEAIT 344
                                       23566667777777777777665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHTT-EEEEEEE-GGG--HHH CS
                       RsgA_GTPase  33 nlldrfLvlaeekgiepvivlnKiDlleeee 63 
                                       ++++  L+++ ++g+ +++v +K+D + + +
  gi|336254156|ref|YP_004597263.1| 478 EFIHDRLLELRREGVAILLVSSKLDEVRSLS 508
                                       5666678888999999999999999887665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0023       3.2       6      27 ..      69      90 ..      64     123 .. 0.82
   2 ?    5.6   0.0     0.013        18      70     135 ..     167     242 ..     129     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0023
                            AAA_22  6 gilvvtGesGtGKTtllrrlle 27
                                      ++ ++ Ge G+GKTtl++ l  
  gi|336254156|ref|YP_004597263.1| 69 TVHALLGENGAGKTTLMNVLYG 90
                                      666899**********987655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.013
                            AAA_22  70 a......erlsseellealeqalrarav....ielliiDEaqh.lrseealeeLrsllnlsrkgvqliLvGtpelrk 135
                                       +      + ++ e+l   ++q ++  ++      +li+DE    l +++ +e+L + l+  + + + i+++t++l++
  gi|336254156|ref|YP_004597263.1| 167 RygfdvdPQARVEDLSVGVQQRVEILKAlfrgADVLILDEPTAvL-TPQEVEDLYDVLEELTAQGKTIIFITHKLEE 242
                                       233333346677777777777777777777799**********88.9999999988887788888999999988886 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 ?    6.8   0.0     0.003       4.1      25      44 ..      69      88 ..      56      96 .. 0.78
   2 ?    5.3   0.0    0.0084        12     160     212 ..     200     253 ..     192     260 .. 0.81
   3 ?   -1.9   0.1       1.4   1.9e+03      26      44 ..     325     343 ..     320     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.003
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                       + a++G+NG+GK+ l++ +
  gi|336254156|ref|YP_004597263.1| 69 TVHALLGENGAGKTTLMNVL 88
                                      46899**********99865 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0084
                                       SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 160 plyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvt 212
                                        + +lDe  a L  ++v+ + ++l+e + +   +i i+++ e  ++a   + v 
  gi|336254156|ref|YP_004597263.1| 200 DVLILDEPTAVLTPQEVEDLYDVLEELTAQgKTIIFITHKLEEATHAADAITVL 253
                                       5679**********************9988456777999988877776666654 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.4
                                       EEEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAi 44 
                                       +  i G  G G   l++Ai
  gi|336254156|ref|YP_004597263.1| 325 IVGIAGVDGNGQAELIEAI 343
                                       56799*************9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.4e-05     0.032      21      41 ..      70      89 ..      55     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                            AAA_23 21 ltlItGpNGaGKTTildAikl 41
                                      + ++ G+NGaGKTT+++ + +
  gi|336254156|ref|YP_004597263.1| 70 VHALLGENGAGKTTLMNVL-Y 89
                                      56789***********965.5 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0008       1.1      25      47 ..      70      92 ..      58     117 .. 0.82
   2 ?    3.5   0.0     0.034        46     325     364 ..     200     238 ..     153     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0008
                            AAA_15 25 ltvliGkNnsGKSsilealdlFl 47
                                      +  l G+N++GK++++++l+ + 
  gi|336254156|ref|YP_004597263.1| 70 VHALLGENGAGKTTLMNVLYGLY 92
                                      66899**************9665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.034
                            AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       ++l+++EP a L pq  + l++ l el  ++k  +i+ TH
  gi|336254156|ref|YP_004597263.1| 200 DVLILDEPTAVLTPQEVEDLYDVLEELTAQGK-TIIFITH 238
                                       679****************************9.7888888 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   0.0   8.7e-05      0.12      26      69 ..      70     112 ..      60     247 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.7e-05
                            AAA_16  26 lvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipy 69 
                                       +  l Ge G GK++l++ l+  +e ++  +++ g+ +++  + p+
  gi|336254156|ref|YP_004597263.1|  70 VHALLGENGAGKTTLMNVLYGLYEPEEgRVVVDGRERSF--DSPR 112
                                       45689***************9999997355599999999..3333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.17       3      57 ..      72     135 ..      70     275 .. 0.79
   2 ?   -2.9   0.0       5.1   7.1e+03       2      21 ..     326     345 ..     325     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                       EEEESTTSSHHHHHHHHHT............STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCS CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltg............ekaivsdkpgtTrdinegrvklkgkeielvDtpGli 57 
                                       a++G   +GK+tL+n l g             + +  d p   +d   g ++   +++ lvDt  + 
  gi|336254156|ref|YP_004597263.1|  72 ALLGENGAGKTTLMNVLYGlyepeegrvvvdGRERSFDSPRDAIDAGVGMIH---QHFMLVDTMTVA 135
                                       799***************8777766655553366777777777777777776...689999988753 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.1
                                       EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                       v+i+G    G   Li a+tg
  gi|336254156|ref|YP_004597263.1| 326 VGIAGVDGNGQAELIEAITG 345
                                       78999999999999999998 PP

>> AAA_27  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      0.18      12      47 ..      54      89 ..      50      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                            AAA_27 12 GkftdrsldfsaeeadlhliyGpNEAGKstalrAis 47
                                      G +++  +d++ e+  +h ++G N AGK+t+++ + 
  gi|336254156|ref|YP_004597263.1| 54 GVVANDDVDLRVERGTVHALLGENGAGKTTLMNVLY 89
                                      66788999**********************998665 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.4         2   2.7e+03     416     458 ..       8      51 ..       3      59 .. 0.54
   2 ?   10.8   0.0   0.00012      0.16      30      55 ..      73      98 ..      64     105 .. 0.91
   3 ?   -2.4   0.0       1.2   1.6e+03      27      74 ..     325     371 ..     320     393 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2
                              DLIC 416 gsagagggaa.agrgsnvqdsvkksgkkavltdvqaeldrlsrk 458
                                       ++ ga+ + a + + s+  ++ +  ++ ++ +d +  ld ++++
  gi|336254156|ref|YP_004597263.1|   8 TTDGAAPTDAgSDARSGRRSADQDRDRESTGSDLAVHLDGITKR 51 
                                       33333333330233333444445566677788888888888876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00012
                              DLIC 30 vlGedgsGkttliaklqGveeekkGr 55
                                      +lGe+g+Gkttl+  l G+ e+  Gr
  gi|336254156|ref|YP_004597263.1| 73 LLGENGAGKTTLMNVLYGLYEPEEGR 98
                                      89*******************99998 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.2
                              DLIC  27 svlvlGedgsGkttliaklqGveeekkGrGleylyldvkdedrddltr 74 
                                        v + G dg G++ li  + G+  +  G  + y   dv d  r +   
  gi|336254156|ref|YP_004597263.1| 325 IVGIAGVDGNGQAELIEAITGLRTPDEGT-ITYEGTDVTDWSRRERIE 371
                                       56688999**************9999995.788888888877766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.38
# Mc/sec: 4491.36
//
Query:       gi|336254157|ref|YP_004597264.1|  [L=420]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-45  153.3  30.4    6.7e-45  153.3  30.4    2.0  2  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
        8.9    6.7  12.1       0.19   12.0   4.4    2.2  2  DUF1269       Protein of unknown function (DUF1269)


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.3     0.025   2.2e+02      56      81 ..      28      54 ..      15      85 .. 0.57
   2 !  153.3  30.4   7.5e-49   6.7e-45       2     267 ..      93     380 ..      92     381 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.025
                      BPD_transp_2 56 llallvallvgaavgll.lgllvlrlk 81
                                       +all+a+lvg+++ ++  g+++ r++
  gi|336254157|ref|YP_004597264.1| 28 VAALLAAVLVGGVLVFVsGGIASCRTG 54
                                      344444444444444440344444444 PP

  == domain 2  score: 153.3 bits;  conditional E-value: 7.5e-49
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl...........lllallvallvga 67 
                                       ++++l ++++l++a+l++a+ f +aG++n+g +g++++G+ ++a+ +++  +            ++l++l++ +vg+
  gi|336254157|ref|YP_004597264.1|  93 LARTLQQTTLLVFAGLSVAVAF-RAGLLNIGTQGQLVFGGLATAVTVVYAAAIvpggfvgtivlIPLGVLAGAVVGG 168
                                       567899****************.****************9999999999888899********************** PP

                      BPD_transp_2  68 avglllgllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv......... 135
                                       + g+l g+l+++   +e+i+t++l++v++g+t  +l  +++++ +++  +e++    ++ +     ++         
  gi|336254157|ref|YP_004597264.1| 169 LYGALPGVLKAYADANEVITTIMLNIVAAGVTSAMLSRWFQDPDSSNPRTEPVPEYAEIPNIPYVGFSgsadfslla 245
                                       ********************************************999777776665555444444444557889*** PP

                      BPD_transp_2 136 .llalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvg 211
                                        ++a++l++a+ +++ rt+fG+ lr  g ++ aa++ G++ kr++++++ +sgal+g+aGa+ +l+ +++++   + 
  gi|336254157|ref|YP_004597264.1| 246 fAFAVALMVAIAWVFARTSFGYELRTSGTQPAAAAYGGVDEKRMTVASMTLSGALGGVAGAFWVLMVHGAWLENVPS 322
                                       ***************************************************************************** PP

                      BPD_transp_2 212 lgfnaiaavvlGgagsllgtviGaliigvvksllltllgi....ptelarvllgallilv 267
                                       +gf++ia+ vl+g+ +++g+ ++a+++g+++s +++ +g     p+el  vl+g+++++v
  gi|336254157|ref|YP_004597264.1| 323 IGFDGIAVSVLAGN-NPIGVGAAAFLFGILDS-GGNSIGTatdvPPELVGVLSGLIILFV 380
                                       **************.****************9.555555557779*************98 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.4   2.1e-05      0.19       7      36 ..     146     174 ..     141     205 .. 0.71
   2 ?   -2.5   0.9      0.72   6.5e+03       3       9 ..     304     310 ..     291     350 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                           DUF1269   7 wGllvGllflnPllGaavGAaaGAlvgals 36 
                                        G++vG+++l P lG+++GA +G+l gal 
  gi|336254157|ref|YP_004597264.1| 146 PGGFVGTIVLIP-LGVLAGAVVGGLYGALP 174
                                       5999********.77776666666666653 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.72
                           DUF1269   3 sGalwGl 9  
                                        Ga+w l
  gi|336254157|ref|YP_004597264.1| 304 AGAFWVL 310
                                       2333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3198.10
//
Query:       gi|336254158|ref|YP_004597265.1|  [L=375]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-34  116.8  31.7    9.5e-34  116.8  31.7    1.5  2  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   2.0      0.36   6.5e+03      36      63 ..      31      59 ..      27      62 .. 0.56
   2 !  116.8  31.7   5.3e-38   9.5e-34       5     268 .]      69     354 ..      66     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 0.36
                      BPD_transp_2 36 fmalGayvaalllalllsl.lllallval 63
                                      +++ Ga++a ++++ ll++  ++++l+++
  gi|336254158|ref|YP_004597265.1| 31 LIGAGAVLAVWIVVGLLAPdSWAGVLLSI 59
                                      55566666666666555555555555555 PP

  == domain 2  score: 116.8 bits;  conditional E-value: 5.3e-38
                      BPD_transp_2   5 lltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl........lllallvallvgaavglll 73 
                                       +l+la ++a+aA+G  +   ++Gvin+g++g+++++a+++ ++++ l+           +++llv+ +++++++l++
  gi|336254158|ref|YP_004597265.1|  69 MLRLAVPIALAAIGGIFAE-KSGVINIGIEGLLIVSAFSSIVAVHWLGVGeataglsnHWWGLLVGTIISVLFALIF 144
                                       7899***************.*************************99999*************************** PP

                      BPD_transp_2  74 gllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv............lla 138
                                       ++ ++ +k d++i++l++ ++ +gl+ +  +  ++ +++ s    + +f+++ ++ ls v +            +++
  gi|336254158|ref|YP_004597265.1| 145 AIVCIEFKADQIIAGLAVWLISLGLAPFASQIVFGSPNTAS----VGRFSSVTIPVLSDVPFlgyllfdtepqvYIM 217
                                       **************************955555555555444....33444444444433333444577888998*** PP

                      BPD_transp_2 139 lllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp....nigvg 211
                                       l+ +++ ++ll rt+fGr++ a gen++a + +G++v++v+ +++++sg++Agl Ga +al   +  +     +  g
  gi|336254158|ref|YP_004597265.1| 218 LAGAAVGWYLLARTNFGRWVVASGENPKALDTAGVDVRKVRYAAVLLSGVFAGLGGAGFALGDLGTFAgggdTAING 294
                                       ***********************************************************998666666677677778 PP

                      BPD_transp_2 212 lgfnaiaavvlGgagsllgtviGaliigvvksllltllgi.....ptelarvllgallilvl 268
                                        gf aia  +l+   +++g+++G+++++ ++s + t +++     ptel rv+  + +i+vl
  gi|336254158|ref|YP_004597265.1| 295 RGFIAIATYLLANY-HPIGALLGSFLFAGLDS-IQTGMQAagyaiPTELIRVIPHMTVIVVL 354
                                       9*************.*****************.7777777799999**********999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2987.98
//
Query:       gi|336254159|ref|YP_004597266.1|  [L=140]
Description: cytidine deaminase [Halopiger xanaduensis SH-6]
Scores for 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-17   61.8   0.2    5.6e-17   61.5   0.2    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    4.8e-11   43.0   1.3    6.4e-11   42.6   1.3    1.2  1  dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.26   11.1   0.0    1.6  1  HTH_10           HTH DNA binding domain


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 !   61.5   0.2   9.4e-21   5.6e-17       4     100 ..       9     110 ..       6     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 9.4e-21
                                       HHHHHHHHHHHHHHHH.TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEE.. CS
                   dCMP_cyt_deam_1   4 dekllelalkaakeaq.kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyv.. 77 
                                       +  lle a + +++a+ ++s+ +VGa++++ +  i++g+n e+a++s+ +HAE +A+++a+k+g +++  a ++v  
  gi|336254159|ref|YP_004597266.1|   9 AADLLERAREIQSQAHvPYSEYPVGAALETADGEIFVGCNLENANYSNSLHAEEVAVAEAVKQGYYDF--ARIAVss 83 
                                       5678999***********************88******************************988788..8888888 PP

                                       ....EE--BHHHHHHHHHHT-SEEEEE CS
                   dCMP_cyt_deam_1  78 ....tlePCsmCakaiiqsgikkvvvg 100
                                            ++PC+mC++ ++++  +++vv+
  gi|336254159|ref|YP_004597266.1|  84 grrdGVTPCGMCRQTLAEFCDDDLVVI 110
                                       99999**************98888875 PP

>> dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   1.3   1.1e-14   6.4e-11      43     113 ..       8      79 ..       1      82 [. 0.86

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.1e-14
                                       .S-HHHHHHHHHHTT-B-TTT---EEEEEEETTS-EEEEE-B--TTSTT-B-HHHHHHHHHHH.TT--GGGE CS
                   dCMP_cyt_deam_2  43 kddelkeaAlaaanasyapyskcpsGvaLvtkdgkvyaGsyiEsaAfNpsLpPlqaAlvalvl.ggkefeei 113
                                       ++ +l e+A +   ++++pys+ p G aL+t+dg+++ G  +E+a +  sL++ ++A+ ++v  g  +f +i
  gi|336254159|ref|YP_004597266.1|   8 AAADLLERAREIQSQAHVPYSEYPVGAALETADGEIFVGCNLENANYSNSLHAEEVAVAEAVKqGYYDFARI 79 
                                       3556999*****************************************************999444455555 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   4.4e-05      0.26       5      22 ..      61      78 ..      59      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.4e-05
                            HTH_10  5 qlevlklAyemGYFdyPR 22
                                      +  ++++A+++GY+d  R
  gi|336254159|ref|YP_004597266.1| 61 EEVAVAEAVKQGYYDFAR 78
                                      556899*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1076.45
//
Query:       gi|336254160|ref|YP_004597267.1|  [L=159]
Description: hypothetical protein Halxa_2772 [Halopiger xanaduensis SH-6]
Scores for complete 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-09   38.4   0.7      4e-09   37.1   0.7    1.8  1  DUF488    Protein of unknown function, DUF488


Domain annotation for each model (and alignments):
>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.7   2.2e-13     4e-09      66     122 .]      91     151 ..      52     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.2e-13
                            DUF488  66 dp.rweefferYaaeleskeaakealeelkelakkg..vaLlcaek.dperchrvvlaeyl 122
                                          ++  f e+Y+++le++++a++a+e+l+e +++g  +aL+c+e  +++rchr +l+e l
  gi|336254160|ref|YP_004597267.1|  91 AAwDQVGFDEAYRDHLETSADAQAAIEDLAERLESGesIALVCFENtEKKRCHRTILRERL 151
                                       333467899*********9999***********9999*******9725678*******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1216.55
//
Query:       gi|336254161|ref|YP_004597268.1|  [L=276]
Description: purine or other phosphorylase 1 [Halopiger xanaduensis SH-6]
Scores for 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-47  159.8   1.9    7.7e-47  159.5   1.9    1.0  1  PNP_UDP_1  Phosphorylase superfamily
     0.0037   17.1   0.1     0.0064   16.4   0.1    1.4  1  DAO_C      C-terminal domain of alpha-glycerophosphate oxidas


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 !  159.5   1.9   8.6e-51   7.7e-47       2     225 ..      26     243 ..      25     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: 159.5 bits;  conditional E-value: 8.6e-51
                                       EEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEE CS
                         PNP_UDP_1   2 iaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGt 78 
                                        +++ g+p+++e + +   ++++ + ++r+++++tG+++g+p++++stGiG p+aa +a+ +l   + v+++ir+G+
  gi|336254161|ref|YP_004597268.1|  26 TVLLPGNPERLEKIVDF-WDDHEMRAHHREYRTATGSYEGTPISVTSTGIGSPSAA-IAVEELARVG-VETFIRVGS 99 
                                       58999************.**************************************.9999999855.********* PP

                                       EEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS CS
                         PNP_UDP_1  79 aGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfy 155
                                       +G+l+p++ vGD+vi++  ++++g+s+        +y++  y+a ad e +++l++aae+lg+++h+G++++ad+fy
  gi|336254161|ref|YP_004597268.1| 100 CGALQPEMDVGDLVITTGGVRQEGTSD--------EYVREDYPAAADYEVVSALVAAAERLGYDYHTGITMSADSFY 168
                                       ***************************........9***************************************** PP

                                       -CH............HHHHH.HHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHH CS
                         PNP_UDP_1 156 aet............eaelr.llrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaq 219
                                       a +            ++el   l++ +++++eME++a+ +lA+ +g++++a+++v   +a++        e+   ++
  gi|336254161|ref|YP_004597268.1| 169 AGQgrpgyegfeaagADELVdQLQEANVKNIEMEASAIMTLANVYGLRAGAVCTV---YANRET-----GEFRTEGE 237
                                       ***********9988555557999999****************************...444111.....22222222 PP

                                       HHHHHH CS
                         PNP_UDP_1 220 eaakna 225
                                         a  +
  gi|336254161|ref|YP_004597268.1| 238 SRAAET 243
                                       222222 PP

>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   7.1e-07    0.0064       9      57 ..     182     230 ..     177     258 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.1e-07
                                       TT--.......TT-STTHT--HHHHHHHHHHHGGGHHHHHHHHHHTH.. CS
                             DAO_C   9 vGaenwsknlaaelaqeygldeevaehLaerYGsraeevlelakedekp 57 
                                       +Ga++  ++l+ + ++++++++  +  La+ YG ra +v+++++++e+ 
  gi|336254161|ref|YP_004597268.1| 182 AGADELVDQLQEANVKNIEMEASAIMTLANVYGLRAGAVCTVYANRETG 230
                                       69999999********************************998887753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2059.14
//
Query:       gi|336254162|ref|YP_004597269.1|  [L=254]
Description: mechanosensitive ion channel MscS [Halopiger xanaduensis SH-6]
Scores for 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-17   61.6   0.8    7.5e-17   61.6   0.8    1.7  2  MS_channel  Mechanosensitive ion channel
    2.4e-07   30.6  15.1    3.9e-07   29.9   0.1    3.2  3  TM_helix    Conserved TM helix


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 ?   -4.0   0.8      0.99   8.9e+03      31      41 ..      13      23 ..      10      31 .. 0.58
   2 !   61.6   0.8   8.4e-21   7.5e-17       3     106 ..     143     249 ..     141     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 0.99
                                      HHHHHHHHHHH CS
                        MS_channel 31 lGalglalgla 41
                                       +a+ lalg++
  gi|336254162|ref|YP_004597269.1| 13 IAAAVLALGFV 23
                                      44555555555 PP

  == domain 2  score: 61.6 bits;  conditional E-value: 8.4e-21
                                       HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHH....HHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEE CS
                        MS_channel   3 ilkiliivvgilivlsllgvnvsallavlGalglal....glalkdlisnlvaGiillfekpfkiGDlveigdieGt 75 
                                       ++k+ ++ v++li+l ++gv +  ll +l++ ++++    +  +kd + + +aGi ll+++p+ iGD ++igd +G+
  gi|336254162|ref|YP_004597269.1| 143 LVKYSVLYVAFLIALGQIGVYIYPLLILLAVYAAGIvvvgAVTFKDFLVSSAAGIYLLLNQPYGIGDEIQIGDQAGI 219
                                       789******************9988888888888872233345777777778************************* PP

                                       EEEE-SSEEEEEETTSEEEEEEHHHHHTS-E CS
                        MS_channel  76 VediglrttkirtfdgrivtiPnsslvtsni 106
                                       V+++ l++tki++ + ++ +iPn+ +++++i
  gi|336254162|ref|YP_004597269.1| 220 VQEVDLFVTKIEDDS-EEYIIPNRRVFEEEI 249
                                       ***********9855.5889******99987 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.6   2.9e-05      0.26      18      47 ..      12      41 ..      11      44 .. 0.94
   2 !   29.9   0.1   4.4e-11   3.9e-07       4      46 ..      91     133 ..      90     135 .. 0.90
   3 ?   -5.4   4.3         2   1.8e+04      12      32 ..     162     182 ..     149     186 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.9e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHTS CS
                          TM_helix 18 vgAilILlvGwiiAkfvsrlvtkllaktgi 47
                                      v+A+++L++G++++ +v rl + lla++g+
  gi|336254162|ref|YP_004597269.1| 12 VIAAAVLALGFVVGYLVGRLNKELLAASGV 41
                                      78**************************97 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 4.4e-11
                                       XSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                          TM_helix   4 nnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktg 46 
                                       ++++ ++ +++P++++A+l+L++G+i+A  +  +v+  l++++
  gi|336254162|ref|YP_004597269.1|  91 EAFWFQVTQYIPQVFIAVLVLILGFIVADKAELVVSEYLRSVK 133
                                       57899************************99999998888765 PP

  == domain 3  score: -5.4 bits;  conditional E-value: 2
                                       TTHSHHHHHHHHHHHHHHHHH CS
                          TM_helix  12 sflPnLvgAilILlvGwiiAk 32 
                                        ++  L++ +++ + G ++  
  gi|336254162|ref|YP_004597269.1| 162 VYIYPLLILLAVYAAGIVVVG 182
                                       555555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1955.18
//
Query:       gi|336254163|ref|YP_004597270.1|  [L=270]
Description: hypothetical protein Halxa_2775 [Halopiger xanaduensis SH-6]
Scores for 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-21   74.1   0.0      1e-20   73.5   0.0    1.3  1  DisA_N    DisA bacterial checkpoint controller nucleotide-bin
  ------ inclusion threshold ------
      0.061   13.6   0.0       0.37   11.0   0.0    2.3  2  PK_C      Pyruvate kinase, alpha/beta domain


Domain annotation for each model (and alignments):
>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.0   1.1e-24     1e-20       5     118 ..     140     260 ..     136     261 .. 0.89

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 1.1e-24
                                       HHHHHHT--EEEEEESSSC.........CCTTCCTSEEEEEE--HHHHHHHTSTTSTTCSSEEEE.ETTEEEEEEEE CS
                            DisA_N   5 eelskkkiGaliviereee.........lkeiietgvkldaevskellkeifekksplhDGAvii.rdgrivaagvi 71 
                                       ++ ++k +Gal+v++++ +          + + ++ v++ +++ + +lke+     + +DGA++i ++g+iv+a ++
  gi|336254163|ref|YP_004597270.1| 140 KGQKGKPVGALFVVGDAGKvmnksrplsYNPFEKSHVHVGDPIVNVMLKEF-----SRLDGAFVIsDAGKIVSAYRY 211
                                       5678899***********9666666643357778999**************.....*********88********** PP

                                       E--.TT-TTS.ST-SHHHHHHHHHHHHSSSEEEEE-TTTS-EEEEETTE CS
                            DisA_N  72 Lpl.senkel.kelGtRHraAlgiseetdalvivVSeetgkislakdgk 118
                                       L++ +e  ++ k+lG+RH ++++i+++t+a+ iv Se++g ++ +k g+
  gi|336254163|ref|YP_004597270.1| 212 LEPsAEGIDIpKGLGARHMSGAAITRDTNAVSIVLSESDGLVRAFKAGE 260
                                       ***666778988**********************************998 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.1e-05      0.37      62     104 ..      57      93 ..      11     104 .. 0.73
   2 ?   -0.8   0.0      0.19   1.7e+03      59      89 ..     112     138 ..     100     161 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.1e-05
                                       HHH.HHHHH...TTSHHHHHHHHHHHTTSS-STSEEEEEE-SS CS
                              PK_C  62 pvlvekaktaestdellreavkvakeaglvkkgdevvvtaGtp 104
                                       p++       e+++e++r a++ a+e+ +v++gde+++ +G+ 
  gi|336254163|ref|YP_004597270.1|  57 PLE------FENVSERIRFALEGALEEDVVDDGDELICATGVF 93 
                                       333......678999***********************99974 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.19
                                       TEEHHH.HHHHH...TTSHHHHHHHHHHHTT CS
                              PK_C  59 Gvypvlvekaktaestdellreavkvakeag 89 
                                       G+y + +++        e+++ +++va+e g
  gi|336254163|ref|YP_004597270.1| 112 GIYDLFAQS----RAEPEVIKSVLEVAIELG 138
                                       555554322....223457888888888855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2184.04
//
Query:       gi|336254164|ref|YP_004597271.1|  [L=301]
Description: alpha/beta hydrolase fold protein [Halopiger xanaduensis SH-6]
Scores for 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-23   82.9   6.4    5.9e-23   82.6   6.4    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    8.8e-19   68.1   0.0    1.6e-14   54.2   0.1    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    4.8e-12   45.7   0.1    6.2e-11   42.0   0.1    2.0  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
       0.21   10.2   0.0        7.4    5.2   0.0    2.0  2  Ndr            Ndr family


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   6.4   1.3e-26   5.9e-23       1     219 [.      26     285 ..      26     286 .. 0.60

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 1.3e-26
                                       EEEE--GC.....GC..HHHHHHHHCCTCEEEEE--TTSTS-...GGCS--HHHC.HHHHHHHCCTT..TTSEEEEE CS
                     Abhydrolase_6   1 vlllHGagssassWl..vapLaallaagvhvlapDlpGhGrs...dpppldledl.adlaalldelaagggpvvlvG 71 
                                       ++++HG+++++++W+  v ++    a+++++++pD +GhGr+   d + ++ e   +dl+all++l     +++l G
  gi|336254164|ref|YP_004597271.1|  26 LVFVHGGWLNGTAWQpqVEHF----ADDYRIVTPDVRGHGRTgatDADRYSIELFtDDLEALLAHLE--IERPILCG 96 
                                       79************6235555....999999********94422244445555544666*******7..******** PP

                                       ETCHHHHHHHHHHCC...EEEEES-................................----TTTS----TTHHHHHH CS
                     Abhydrolase_6  72 HSlGGalalaaapla.lvvgvlldp...........................pp...talpagllaaalelllalla 117
                                        SlG +++++   ++ +++g  +dp                           pp   +    g      e++  +++
  gi|336254164|ref|YP_004597271.1|  97 LSLGSMIVQE---YLsRHAGAGMDPdsnssadaaangtvpagailggavrsmPPvdlP---SGV-----EPFVSPGP 162
                                       **********...776555677777666666666666655555555556665332221...222.....22221111 PP

                                       TT-C........CCCHCCH.....S-HSCCCC.HHH.....CCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEE CS
                     Abhydrolase_6 118 llrl........lawlsre.....plprlfla.ded.....adaawrarlarlaallaglgllpaaawadlpvpllv 175
                                       +l +         +++s+        +r++l+ d+d     +da   +   + ++ +++l  + ++++ ++ vp+lv
  gi|336254164|ref|YP_004597271.1| 163 ALGTalsltgpkTTFRSLLqsiraTTGREWLSvDPDvraaaMDAVGEVSREEFRKVFDALVRYDPPDLSGVDVPTLV 239
                                       111111111222233321112122122222221222111112355555555555777777788899*********99 PP

                                       E.CTT-C.HHHHCHHCCCH.STTEEETCE...SSS-HHHHSHHHHHH CS
                     Abhydrolase_6 176 l.ggeDp.lvprllerlla.qagarlpvvlpgaGHlphleepdevae 219
                                       + g++++  v+r  e+++  +a+ r  v+l++aGHl+++++p+++++
  gi|336254164|ref|YP_004597271.1| 240 VhGEQEApQVKRQGEQIASaVADGRR-VTLENAGHLVNQDRPTAFNA 285
                                       94444445666666666667666666.99*************99986 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.1   3.6e-18   1.6e-14       2      94 ..      25     111 ..      24     123 .. 0.95
   2 !   12.2   0.0   2.3e-05       0.1     199     255 ..     217     278 ..     159     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 3.6e-18
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       +lv++hG+  ++  w     ++++a+ +++++++D+rG+g++ +  a   d+y++  + ddl+++l++l +++++l 
  gi|336254164|ref|YP_004597271.1|  25 SLVFVHGGWLNGTAWQP--QVEHFAD-DYRIVTPDVRGHGRTGATDA---DRYSIELFTDDLEALLAHLEIERPILC 95 
                                       79***************..******9.***************99999...9************************** PP

                                       EETHHHHHHHHHHHHH CS
                     Abhydrolase_1  79 GhSmGGmialayaaey 94 
                                       G S+G+mi+ +y++++
  gi|336254164|ref|YP_004597271.1|  96 GLSLGSMIVQEYLSRH 111
                                       **************99 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHC.....THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHH CS
                     Abhydrolase_1 199 klllrlre.....lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafle 255
                                       k+++ l +     l+ v +ptlv++g+++     +++e++a++  + r+v++++agHl++ +
  gi|336254164|ref|YP_004597271.1| 217 KVFDALVRydppdLSGVDVPTLVVHGEQEAPQVKRQGEQIASAVADGRRVTLENAGHLVNQD 278
                                       3333333366677788999************************9999**********99755 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.1   1.4e-14   6.2e-11       7     235 ..      26     276 ..      21     280 .. 0.76

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.4e-14
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGh 83 
                                       +v+vHG      + +  +e++a+ ++ +++ D rGhGr++   ++  s++ ++dDl+a++ +++     ++ +l+G 
  gi|336254164|ref|YP_004597271.1|  26 LVFVHGGWLNGTAWQPQVEHFAD-DYRIVTPDVRGHGRTGATDADRYSIELFTDDLEALLAHLE----IERPILCGL 97 
                                       79999999999999999999875.8***********************************9999....444589*** PP

                       Hydrolase_4  84 SmGGliallyllrypd.............kvaglilsaPalkikakl...........kappllklllkllgkllpk 136
                                       S+G++i+++yl r++                +g + +++ l+ + +            ++ +   +l + l+ + pk
  gi|336254164|ref|YP_004597271.1|  98 SLGSMIVQEYLSRHAGagmdpdsnssadaAANGTVPAGAILGGAVRSmppvdlpsgvePFVSPGPALGTALSLTGPK 174
                                       ***********998887777777777765334555555555555444455566655542222222245555555555 PP

                       Hydrolase_4 137 lqv.......snnlkadslsrdpevvaayeadplvhgkitvrlllelldamkrlee.raakitlPllllhGeaDkvv 205
                                        ++        + +  ++ls dp+v+aa        g+++ + +++++da+ r    + + +++P+l++hGe++   
  gi|336254164|ref|YP_004597271.1| 175 TTFrsllqsiRATTGREWLSVDPDVRAA---AMDAVGEVSREEFRKVFDALVRYDPpDLSGVDVPTLVVHGEQEAPQ 248
                                       5557778899888999999999999993...34457888888889999988887651567788*********99999 PP

                       Hydrolase_4 206 dpeasrelyerlgskdktlklypglyHell 235
                                        +++ ++++ +++  d +  + +++ H + 
  gi|336254164|ref|YP_004597271.1| 249 VKRQGEQIASAVA--DGRRVTLENAGHLVN 276
                                       9999999999988..899999999988765 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0016       7.4      74     117 ..      65     108 ..      40     114 .. 0.81
   2 ?    3.0   0.0    0.0075        33     216     279 ..     231     294 ..     210     296 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0016
                                       -TT-----HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHH CS
                               Ndr  74 pedyqfpslddladqllavldhfklksviglGvgaGAyilarfa 117
                                       ++d    s++  +d+l+a+l h++++  i  G   G  i+  + 
  gi|336254164|ref|YP_004597271.1|  65 ATDADRYSIELFTDDLEALLAHLEIERPILCGLSLGSMIVQEYL 108
                                       45666679999****************************99885 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0075
                                       TSSSS-EEEEEETT.STTHH.HHHHHHHHS-TTTEEEEEETT-TT-HHHH-HHHHHHHHHHHHHHT CS
                               Ndr 216 kklevkvllvvGdk.spfvd.evvevnskldkkkttllkvadsgglvleeqPdklaeslklflkGl 279
                                       ++++v++l+v G++ +p v+ +  +++s++       + ++++g lv +++P +     + fl+Gl
  gi|336254164|ref|YP_004597271.1| 231 SGVDVPTLVVHGEQeAPQVKrQGEQIASAVADG--RRVTLENAGHLVNQDRPTAFNAVSEGFLNGL 294
                                       456789999999762565541456666666544..457789*************999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2412.21
//
Query:       gi|336254165|ref|YP_004597272.1|  [L=523]
Description: xanthine/uracil/vitamin C permease [Halopiger xanaduensis SH-6]
Scores for 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-79  266.8  37.5    5.2e-79  265.7  37.5    1.5  1  Xan_ur_permease  Permease family


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 !  265.7  37.5   2.9e-83   5.2e-79       2     386 ..      28     419 ..      27     421 .. 0.89

  Alignments for each domain:
  == domain 1  score: 265.7 bits;  conditional E-value: 2.9e-83
                                       HHHHHHHHHHHHHHHHHHHHHHTTTS-..........H.HHHHHHHHHHHHHHHHHTTT-----EEE-GGGHH.... CS
                   Xan_ur_permease   2 qllllglQhllamfaalvvvPllvgdalgl.aeelrqlisatllasGiatllqllifgirlpillgssfafvt.... 73 
                                       + ++lg+Qh l+m++a + vPl++++a+g  +  ++q i + +++sGiatl+q++ fg r pi++g  f  ++    
  gi|336254165|ref|YP_004597272.1|  28 ESFVLGVQHYLTMVGANIAVPLILAEAMGMpDDITAQFIGTFFVVSGIATLAQTT-FGNRYPIVQGAPFSMLApala 103
                                       5789***********************999777777*******************.*************99998655 PP

                                       .HHHGGG-......HHHHHHHHHHHHHHHHHHHHHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHTTSS- CS
                   Xan_ur_permease  74 .almialGsa..edieialagllgallvagvlfilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkvgggw 147
                                        +++++ G     d+++al  l+ga++va+ + +l++ +gl+g+l+r++ Pvv++p+++liGlsl + +   + + +
  gi|336254165|ref|YP_004597272.1| 104 iITVVTVGGVggGDWQAALVQLQGAIIVAATVEVLMGYLGLVGKLRRFLSPVVIAPTIMLIGLSLFSAGQ--ITARE 178
                                       5444444444899****************************************************87543..33332 PP

                                       ..BTT.B---HHHHHHHHHHHHHHHHHHHSSSTTTTTHHHHHHHHHHHHHHHHHH....HTTSSHH......HHS-S CS
                   Xan_ur_permease 148 aavegltvvslkllllavvvllvilllsvflkglfsqlpiLigiiagwllalfmg....ivnlspe......vseap 214
                                          ++       ll+l + ++l+      ++   f+++p+ ++++++w++a+++     iv+  p       v++++
  gi|336254165|ref|YP_004597272.1| 179 ---QS-----WWLLGLTLGLILLFSQYLDVKHRAFKLYPVILALVIAWVVAAALSatgvIVDGHPGyvpledVTDTQ 247
                                       ...22.....34444555445555555555999*******************997555666666669***9*77766 PP

                                       S-----------HH..H.HHHHTHHH.HHHHHHHHHHHHHHHHHHTS-TIIIIIHHHHHHHHHHHHHHHHHHT---E CS
                   Xan_ur_permease 215 wfqlpsplkfgtplfnlgliltvlavalvavvesvGdiravakvvgrslkpkpdlrralladGlatllsgllGalpv 291
                                        f + +p+++g+p+f+++ i+ ++a +l+++ves+Gd++ava+++g   + + ++++++  +Gl+ +++g++G+++ 
  gi|336254165|ref|YP_004597272.1| 248 PFLPIYPFQWGAPQFTTAFIVGMFAGVLASIVESIGDYYAVANLTGSGAPSERRINHGIGMEGLMNVFAGIMGTAGS 324
                                       66678*******************************************999************************** PP

                                       EE-HHHHHHHHHHTB--HHHHHHHHHHHHHHT--HHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHTTS-SHH CS
                   Xan_ur_permease 292 ttyaeniGvvaltkvasrrvmvtagvilillglipklaallssIPepvlgGvllvvfgmiaasgvsnlqtvdldsar 368
                                       t+y+eniG + lt+vasr+v+++++++++ +g+++ +++l+++IP+p++gG  +++fg i+a+gvsnl  vdl+s+r
  gi|336254165|ref|YP_004597272.1| 325 TSYSENIGAIGLTGVASRYVVQLGALVMLFVGFVGYFGQLIATIPDPIVGGLFIAMFGQIVAVGVSNLRHVDLESSR 401
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHH---- CS
                   Xan_ur_permease 369 nllivavslvlGlgvatv 386
                                       n++iv+++l++Gl ++++
  gi|336254165|ref|YP_004597272.1| 402 NTFIVGFALFVGLAIPAY 419
                                       **************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); 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:                         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: 0.59u 0.23s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3764.66
//
Query:       gi|336254166|ref|YP_004597273.1|  [L=731]
Description: Magnesium chelatase [Halopiger xanaduensis SH-6]
Scores for complete 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-20   73.2   3.7    2.9e-20   71.9   0.3    3.0  2  AAA_lid_2        AAA lid domain
    1.1e-12   48.5   0.0    2.2e-12   47.6   0.0    1.5  1  VWA_2            von Willebrand factor type A domain
    7.9e-12   45.0   0.0    4.2e-09   36.1   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.6e-10   41.5   0.0    2.6e-10   40.8   0.0    1.3  1  VWA              von Willebrand factor type A domain
    1.3e-07   31.7   0.0    5.9e-05   23.1   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
    2.8e-06   26.9   6.8    4.8e-06   26.1   6.8    1.3  1  VWA_CoxE         VWA domain containing CoxE-like protein
    1.2e-05   24.5   0.0    8.9e-05   21.7   0.0    2.2  2  MCM              MCM P-loop domain
  ------ inclusion threshold ------
       0.01   15.4   0.9       0.02   14.5   0.9    1.5  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      0.018   15.0   0.1      0.035   14.1   0.1    1.4  1  VWA_3            von Willebrand factor type A domain
      0.019   14.6   0.0       0.23   11.1   0.0    2.1  2  Sigma54_activat  Sigma-54 interaction domain
       0.31   11.4   6.1        1.2    9.5   0.2    3.4  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 !   71.9   0.3   1.8e-23   2.9e-20       2      70 ..     270     338 ..     269     341 .. 0.92
   2 ?    0.7   0.2      0.29   4.7e+02      29      46 ..     531     548 ..     525     551 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.8e-23
                         AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegetteeiv 70 
                                       +++a+l++e+gv+g+R+d+a++r+A ++Aalegr++V+  Dv eaa ++L+HRlr  p++++ + ++ +
  gi|336254166|ref|YP_004597273.1| 270 EEIADLCLEAGVDGHRGDVAIARTAMTIAALEGRTTVIGPDVHEAASYALPHRLRSTPFEDEPELDDLL 338
                                       6799***************************************************99999986666665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.29
                         AAA_lid_2  29 lAalegrdyVtpeDvkea 46 
                                        Aa +g+ +V + D+++ 
  gi|336254166|ref|YP_004597273.1| 531 SAAARGESQVEKRDLRQS 548
                                       69*************985 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 !   47.6   0.0   1.4e-15   2.2e-12       1     106 [.     558     658 ..     558     659 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.4e-15
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallk.sl.pgdrvglvtfsd.gpevlipltkdkakilnalrnleakgg 74 
                                       +vf +D S+Smr+       + +ak  v +ll  s+ ++d v+ v+f++ ++ vl+p+t++ +   + l++l   g+
  gi|336254166|ref|YP_004597273.1| 558 IVFAVDASASMRPA------MRTAKGVVLELLRdSYeHRDEVAFVAFAGqDADVLLPPTDSVSLAARHLKDLPS-GD 627
                                       79***********8......************95554599*********88**********************7.6* PP

                             VWA_2  75 gtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                        t l a+L++  ++l++   ++ +v+vl+tDg
  gi|336254166|ref|YP_004597273.1| 628 RTPLPAGLETTADVLERAE-TDASVVVLVTDG 658
                                       ****************997.***********9 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0031         5       4      49 ..      17      64 ..      14      69 .. 0.82
   2 !   36.1   0.0   2.6e-12   4.2e-09      91     159 ..     125     193 ..     115     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0031
                      Mg_chelatase  4 dvkGqeeakraleiaaaGg..HnlllvGppGsGKtmlakrlpsllppl 49
                                       ++Gqe+ kr+l   aa       l++G  G+ K+   + l  llp+ 
  gi|336254166|ref|YP_004597273.1| 17 AIVGQEDLKRVLLCVAANDdlDGALIAGEKGTAKSTAVRGLVDLLPEQ 64
                                      699******9987666654124689*********************86 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 2.6e-12
                      Mg_chelatase  91 vGggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                       + g +   pG +++ah+G+L++DE+  ++ + ++vL +   +g  +++r   +v++pa+f+l+ +mNp 
  gi|336254166|ref|YP_004597273.1| 125 LAGEADFDPGLLARAHRGILYVDEVNLLDDHLVDVLLDAAASGVNRVERDGISVSHPAEFTLIGTMNPE 193
                                       56778999***********************************************************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 !   40.8   0.0   1.6e-13   2.6e-10       2     156 ..     558     706 ..     557     717 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.6e-13
                                       EEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS.EEEEEETTSHCHHHHHHHHHHTGSGGGGS CS
                               VWA   2 ivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfsse.vktefslndysskeellsalnnlkysggg 77 
                                       ivf++D+S sm +  + ++k  + +l+++ +  ++++ v++v f+++ + +  + +d  s + ++++l++l   +g+
  gi|336254166|ref|YP_004597273.1| 558 IVFAVDASASM-RPAMRTAKGVVLELLRDSY--EHRDEVAFVAFAGQdADVLLPPTD--SVSLAARHLKDL--PSGD 627
                                       9**********.999****************..************9989********..6689999****7..5555 PP

                                       SC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS.S.....HTHHHHHHHHGCTEEEEEEEESSSHHHHHH CS
                               VWA  78 ttntgkalkyaleklfkssagaRenakkviilltdGksnd.g.....dpkeaaneakeqgikvfavGvgnadekelL 148
                                        t + ++l+ +++ l +++        +v++l+tdG+ n  +     + ++aa+++ ++g  v++v  g++  +  L
  gi|336254166|ref|YP_004597273.1| 628 RTPLPAGLETTADVLERAETD-----ASVVVLVTDGRANVaEgspteSTRRAARRLARRGAHVVVVDAGDDSRAG-L 698
                                       5569*********88888888.....9********9999854889999999999999**********99999988.9 PP

                                       HHHSSSSC CS
                               VWA 149 nkiasepg 156
                                         +  +++
  gi|336254166|ref|YP_004597273.1| 699 SALVADET 706
                                       88866655 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 !    6.0   0.0    0.0067        11       3      26 ..      41      64 ..      39      78 .. 0.82
   2 !   23.1   0.0   3.6e-08   5.9e-05      25     138 .]      99     205 ..      95     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0067
                                      EEE--SSSSHHHHHHHGGGGBS-- CS
                             AAA_5  3 lLvGppGtgKselaerlaaalnre 26
                                      l+ G++Gt+Ks+ ++ l  +l  +
  gi|336254166|ref|YP_004597273.1| 41 LIAGEKGTAKSTAVRGLVDLLPEQ 64
                                      789*************99999433 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 3.6e-08
                                       --EEEEE--TT--HHHHH--B--............--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..- CS
                             AAA_5  25 reveyvqltrdtteedlkgrreik...ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrlllee 98 
                                       r+v  v l+ + t++ ++g ++++    g++ + ++ l ra r   il++DEv+ ++++ +++Ll        ++e 
  gi|336254166|ref|YP_004597273.1|  99 RPVPLVTLPLGATRDRVVGTLSVEdalAGEADFDPGLLARAHR--GILYVDEVNLLDDHLVDVLLDAAASGVNRVER 173
                                       667778888899***************************8866..7****************************999 PP

                                       SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5  99 ggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                        g  v+++++     f++i+t+np +    +l p+lr+Rf
  gi|336254166|ref|YP_004597273.1| 174 DGISVSHPAE-----FTLIGTMNPEE---GDLRPQLRDRF 205
                                       9999999987.....**********9...77889*****9 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   6.8     3e-09   4.8e-06      15     193 ..     510     695 ..     497     705 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3e-09
                          VWA_CoxE  15 rrrrrkrrrrgrriDlrrtlranlrhgge.lvelvrrkp.re.rkprelvllvDvSgSmaaysa....iflallhAl 84 
                                        r r++     + iD  +++r++ + g   +++  +r+  r    +  +v+ vD S+Sm    +    ++l ll+  
  gi|336254166|ref|YP_004597273.1| 510 SRVRTEPADWDGPIDAAASVRSAAARGESqVEKRDLRQSvRTgDASVTIVFAVDASASMRPAMRtakgVVLELLRDS 586
                                       2356777777899*********999999863333444432321456689**********986652222566666666 PP

                          VWA_CoxE  85 lqqlprtevfaFdtrlvdlTralrerDpaeaLarvsaavedlgGg..TrigaalaeflelvtrpaLsrravvvlvsD 159
                                        + ++++ ++aF  + +d+   l    p++++  +++  +dl +g  T + a+l++ +++ +r      +vvvlv+D
  gi|336254166|ref|YP_004597273.1| 587 YEHRDEVAFVAFAGQDADV--LLP---PTDSVSLAARHLKDLPSGdrTPLPAGLETTADVLERAE-TDASVVVLVTD 657
                                       6777799*****9997777..677...45555555555577544434999************888.899******** PP

                          VWA_CoxE 160 ....glergdreellaelarlvrrarrlvwlnplsdag 193
                                             e+ ++e   ++ +rl rr+ ++v++ + +d +
  gi|336254166|ref|YP_004597273.1| 658 granVAEGSPTESTRRAARRLARRGAHVVVVDAGDDSR 695
                                       777778999999*******************9997765 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.34   5.6e+02      60      77 ..      40      57 ..      10      69 .. 0.55
   2 !   21.7   0.0   5.5e-08   8.9e-05     103     179 ..     122     198 ..     109     211 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.34
                                      EEEEESSTSTHHHHHHHH CS
                               MCM 60 vllvgdpgtaKsqlLkyv 77
                                       l+ g+ gtaKs+ ++ +
  gi|336254166|ref|YP_004597273.1| 40 ALIAGEKGTAKSTAVRGL 57
                                      356666666666665555 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 5.5e-08
                                       EESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSCC CS
                               MCM 103 rdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagryd 179
                                        d   ge  ++ G l  a++G++++De++  +++  ++l++a  +    + + Gi ++ +a+ +++  +np++g   
  gi|336254166|ref|YP_004597273.1| 122 EDALAGEADFDPGLLARAHRGILYVDEVNLLDDHLVDVLLDAAASGVNRVERDGISVSHPAEFTLIGTMNPEEGDLR 198
                                       57778888999*************************************************************99755 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 ?   14.5   0.9   1.2e-05      0.02       9      65 ..     673     730 ..     671     731 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHH CS
                      adh_short_C2   9 aiAkalaeeGaevvltdlneea.kkrveelaeelgaevlecDVtdeeqvealveevve 65 
                                        +A++la++Ga+vv++d+++++ +   + +a+e++ +++ + + ++e+v+++++++++
  gi|336254166|ref|YP_004597273.1| 673 RAARRLARRGAHVVVVDAGDDSrAGLSALVADETDGDLIDLEALSPEAVRTAADRAAS 730
                                       68********************677777778888899***************999875 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 ?   14.1   0.1   2.1e-05     0.035       3     151 ..     558     708 ..     556     710 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                             VWA_3   3 vvivvDvsssmsaen.klvkdaLsvalrqLptndkia.vllfgtkprplfpgsravsaaelqealqkikelelslga 77 
                                       +v++vD+s+sm+    ++    L ++  + +++d++a v+ +g +++ l p  ++vs      a+  +k l+   + 
  gi|336254166|ref|YP_004597273.1| 558 IVFAVDASASMRPAMrTAKGVVLELLRDSYEHRDEVAfVAFAGQDADVLLPPTDSVS-----LAARHLKDLPS-GDR 628
                                       9***********765333344455555569999*88636677899999999999998.....88899999888.999 PP

                             VWA_3  78 snlegaLkealrqp.akpgevrsvilltDgss.aq...geervsdlisr.arekirfhalglgsslsaamlqaLAea 148
                                       ++l + L+++++   +  + ++ v+l+tDg + ++   ++e++  + +r ar+ ++++++  g++  a + +++A +
  gi|336254166|ref|YP_004597273.1| 629 TPLPAGLETTADVLeRAETDASVVVLVTDGRAnVAegsPTESTRRAARRlARRGAHVVVVDAGDDSRAGLSALVADE 705
                                       99******9999553666788889999***97533344446666666664447799999988888777777777777 PP

                             VWA_3 149 sgG 151
                                       + G
  gi|336254166|ref|YP_004597273.1| 706 TDG 708
                                       766 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       0.2   3.3e+02      25      43 ..      40      58 ..      21      72 .. 0.77
   2 ?   11.1   0.0   0.00014      0.23      79     142 ..     126     191 ..     119     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.2
                                      EEEECSTTSSHHHHHHHHH CS
                   Sigma54_activat 25 vlitGesGtGKellaraih 43
                                       li Ge+Gt K++  r + 
  gi|336254166|ref|YP_004597273.1| 40 ALIAGEKGTAKSTAVRGLV 58
                                      79*********99887665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00014
                                       TTTSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHS..EEESBTSSSEEE--EEEEEEES CS
                   Sigma54_activat  79 tGAekekkGlfekadgGtlfLDeigelplelQekLlrvlqeg..evervGsskeikvdvriiaatn 142
                                        G  +   Gl+ +a+ G+l++De++ l+ +l   Ll +  +g  +ver G s ++++++ +i + n
  gi|336254166|ref|YP_004597273.1| 126 AGEADFDPGLLARAHRGILYVDEVNLLDDHLVDVLLDAAASGvnRVERDGISVSHPAEFTLIGTMN 191
                                       55566678***********************99999988775225777788888888888877665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00075       1.2      15      88 ..      28      92 ..      20     178 .. 0.55
   2 ?   -2.5   0.0       3.6   5.9e+03     117     132 ..     239     255 ..     191     307 .. 0.58
   3 ?    2.9   0.4     0.076   1.2e+02      37     153 ..     576     696 ..     571     717 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00075
                            AAA_16 15 alervrsgrpelvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysalaqalareellrqllde 88
                                      +l+ ++ ++    l+ Ge+G+ Ks+ vr l + l ++++++   +g + +           +al   + +r+ + +
  gi|336254166|ref|YP_004597273.1| 28 LLCVAANDDLDGALIAGEKGTAKSTAVRGLVDLLPEQRAVAdcPYGCAPDD----------SALQC-DDCRDRDPD 92
                                      4555555666889******************99999965555544444444..........22211.333333333 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.6
                            AAA_16 117 srllellkrll.allsr 132
                                       +r ++ +++l   ll+ 
  gi|336254166|ref|YP_004597273.1| 239 TRYNDDITALReTLLEA 255
                                       34444444433222222 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.076
                            AAA_16  37 Ksslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala...... 106
                                       K  +++ l++++e ++ + f++   ++       ++l+   +  +l +  l ++ s ++ + ++ le+++       
  gi|336254166|ref|YP_004597273.1| 576 KGVVLELLRDSYEHRDeVAFVAFAGQDA------DVLLPPTDSVSLAARHLKDLPSGDRTPLPAGLETTADvlerae 646
                                       6677777777777775477766666666......3333333344444444444444455555555555554433555 PP

                            AAA_16 107 ...avpelagaea.............srllellkrll.allsrderplvlvlDdlqwadeaslq 153
                                          +                       +  e  +r++ +l++r+++  v+v+D  ++ +    +
  gi|336254166|ref|YP_004597273.1| 647 tdaS--------VvvlvtdgranvaeGSPTESTRRAArRLARRGAH--VVVVDAGDDSR----A 696
                                       5552........0333333345566667777777777566666666..99999666333....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (731 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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):              11  [number of targets reported over threshold]
# CPU time: 0.91u 0.31s 00:00:01.22 Elapsed: 00:00:00.47
# Mc/sec: 4669.35
//
Query:       gi|336254167|ref|YP_004597274.1|  [L=1300]
Description: Cobaltochelatase [Halopiger xanaduensis SH-6]
Scores for 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 1251.4   0.0          0 1251.1   0.0    1.0  1  CobN-Mg_chel   CobN/Magnesium Chelatase
     0.0057   16.4   0.0      0.016   14.9   0.0    1.7  1  LexA_DNA_bind  LexA DNA binding domain


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 ! 1251.1   0.0         0         0       1    1088 [.     109    1266 ..     109    1267 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1251.1 bits;  conditional E-value: 0
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel    1 saYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdake.lfesleeylewykkakkekaptvgi 74  
                                        ++Yl++gg+ N++nl+r+la+++ g ++ e+++p+elp+eg+yhpd++   +e+l   l    +++++++pt+++
  gi|336254167|ref|YP_004597274.1|  109 YEYLEKGGTINVENLCRFLASEYEG-RDLEYDDPAELPTEGVYHPDYPGiGYEEL---L----ETHDSDKPTIAV 175 
                                        58*********************98.7779****************998323333...3....45789******* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel   75 lfyrahllagntavidaliraleerglnvlpvfvssl.dseaqealeelft......kegeekvdalinttsfal 142 
                                        +fy++h++++nt+++da +r lee+g+n+lp+f++ + d+++qe++e ++t      ++ge+ vda+++  +f+l
  gi|336254167|ref|YP_004597274.1|  176 WFYESHWTHENTRYVDAQVRVLEEQGANALPIFCNPAtDTDEQEDAE-WVTdnwlidDDGEPIVDAVLSSFMFSL 249 
                                        ************************************98666666654.4444677799999************** PP

                                        xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  143 vkgpaeeeeeeaeeea....lkelnvPvlqailssqsreeWeessqGlspldlamsvalpEldGriepvvisfke 213 
                                        ++ +++++++++ e+a    l++l+vPvlq+i++++sr+++e+s++G+ + +la+svalpE+dG +++ +is+ke
  gi|336254167|ref|YP_004597274.1|  250 SMDERGRSASDEGESAedvfLDRLGVPVLQTITTMRSRSRYESSDTGVMGFELALSVALPEFDGNVITHPISGKE 324 
                                        *999888777776666899******************************************************** PP

                                        ..xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  214 ..eee..eetevekyepipervervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlL 284 
                                          ++e    ++ +++  i++r+++ ++la +wa+Lr++pn+ek va++l+nypp+++ +g+a gLd+p+S+vnlL
  gi|336254167|ref|YP_004597274.1|  325 rtDDEagIGSAPKHHFSIEDRIDHATRLAVNWAELRHTPNKEKNVAVVLHNYPPSDDGIGTAFGLDSPESTVNLL 399 
                                        873334777888999************************************************************ PP

                                        xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  285 kalkeeGYdv.eelpesgdeLiellleggtndpew...eelkvgaaallpaeeYeewfeeLpeelreeveerWge 355 
                                        ++l+++GY++ +e p++g++L+e+l+++ t + +w   e+++  +++ ++ ++Ye+wf+e +e+ +e+v+e+Wge
  gi|336254167|ref|YP_004597274.1|  400 EELEARGYNLgGEMPDDGQTLVETLTSQLTLEDRWvapEDVRDLSVDVVSPDTYEAWFSEADERFQENVIEEWGE 474 
                                        **********6677*********************9998888799****************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  356 ppgemveeeksgekklvipglqlGnvfvgvQPargyeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvG 430 
                                        +p+          + ++ipg+++Gnv+v+vQP+rg+++dpsk+yhd+dl+P+h+Y+AfY Wlr++f+adavvH+G
  gi|336254167|ref|YP_004597274.1|  475 APD----------RPFAIPGVEFGNVLVTVQPPRGFGMDPSKVYHDSDLQPPHDYYAFYGWLRNTFEADAVVHLG 539 
                                        ***..........79************************************************************ PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  431 kHGtlEwlPGKqvglseecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLee 505 
                                        +HG+lEwlPGK+vgl +e+ Pd l+ d+P++YpYivnnpgEGtqAKRRsyA i+d+ltP+m +a++y+el+eLee
  gi|336254167|ref|YP_004597274.1|  540 THGSLEWLPGKTVGLNGESAPDQLVDDIPNVYPYIVNNPGEGTQAKRRSYAAIVDYLTPVMRSAGTYDELSELEE 614 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  506 lideYeeaesldpe..rlkalreqilelveelnldkdlg.....................leeakeeeeeefeel 557 
                                        l ++Y+ea  +d++  + ++l+  i e+veel+l  +lg                     +e + + ++ +++el
  gi|336254167|ref|YP_004597274.1|  615 LANQYREAGMEDARadDGEHLETLIREKVEELDLAVELGiagtidekadvrgpdeagsslAEGEVDGDDVDIDEL 689 
                                        ********999766547788889***********************************99555678899****** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx RF
                      CobN-Mg_chel  558 lekldgyleelkeaqirdglhilGeapegeqlvdlvvailrleneegesltealaealgldlde....leeksek 628 
                                        +e++++yl+++k++qir glh++ e+p++e+lv+++va++rlen   +sl+e++a alg+d+d+      e +e+
  gi|336254167|ref|YP_004597274.1|  690 VERVHEYLTDVKTTQIRLGLHTMSEPPADERLVEYLVALTRLENPGAPSLRESVAGALGVDYDKmlnaPGEYDEA 764 
                                        ****************************************************************76654445555 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                      CobN-Mg_chel  629 elrtagdalealeeeaeelveelleeeaeeeeaeaeeleeeeeeeee............................ 675 
                                           t+++a + ++e++ elv++l+e++++  e+e+e+  ++e + +                             
  gi|336254167|ref|YP_004597274.1|  765 LGMTYAEAADVVHETSLELVATLAEHDFDIPESEREAGPDDEVNMNLlvvdletigdaraksgahddlrevlafi 839 
                                        567888899999**************999988877777776666666**************************** PP

                                        .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  676 .........eteeEitallraLdGeyippgpsGdptrgraevLPTGrNfysvDpraiPteaAwevGkklaeelle 741 
                                                  +e+Ei ++ +aL+Gey+ppg sG+ptrg  + LPT rNfy++Dpr++P + Aw+vGk++ae +le
  gi|336254167|ref|YP_004597274.1|  840 ceetqprvqGAEDEIPRTADALSGEYVPPGGSGAPTRGGVDLLPTARNFYTLDPRKVPAKPAWQVGKEVAEGVLE 914 
                                        ********7666*************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  742 rylqehgeyPekvglslwgtetmrteGediAqiLallGvrPvwdaagrvvdlelipleeLgRPRiDVtvriSGff 816 
                                        r+++e++eyPe++g++ wgt t+rt+Ge+iAq+La++Gv+P w +agr+ d+e ipleeL+RPRiDVt r+SG+f
  gi|336254167|ref|YP_004597274.1|  915 RHYSENDEYPEEIGVVAWGTPTVRTRGETIAQVLAMMGVEPQWTDAGRIDDVEPIPLEELDRPRIDVTTRVSGLF 989 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  817 RDafpnlielldkavelvaeldEpeedNfvrkhvleeeaeleeke.....eaeeratyRvFgskpGaYgagvqel 886 
                                        RDafp    ++++av++v +ldEp+e+N+v+khv+ee+++l+++e     +a++ a+ RvF+ kpG Ygag +++
  gi|336254167|ref|YP_004597274.1|  990 RDAFPAAAGVIHDAVDAVVDLDEPHEMNYVKKHVEEEAEKLQDEEgldesDARKAAKHRVFTTKPGGYGAGTNKA 1064
                                        ******************************************94445433566********************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  887 iessnWedeedLaeaYlnwssyaYgkgaegeeaeeafearLkrvdvvvqnqdsrehdlldsddyyqflGGltaav 961 
                                        ++++nW+d++dLa +Y++w++ya g++ ++++a++afe+rL++vd++v+ +d+ e d +ds+d y+f+GG++ av
  gi|336254167|ref|YP_004597274.1| 1065 VDEGNWDDRSDLASVYVQWGGYAMGSRGRVSDAHDAFERRLSSVDATVKLEDTMEQDEFDSSDWYAFHGGFISAV 1139
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  962 rslsgkkpeayfgdssnpenpkvrtlkeeiarelrsrvlNPkWiegmmrhGykGafelaatvdnlfgwdatadvv 1036
                                        +++s ++p++y+gdss+p+n+ v t +e++++ +rsrvlNP W+e+m +hGykGa +l+ tvd ++gwdat++vv
  gi|336254167|ref|YP_004597274.1| 1140 SEISSEEPASYVGDSSDPDNVSVYTNEEKVRKAMRSRVLNPDWLESMEEHGYKGAGDLSTTVDVTLGWDATTGVV 1214
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 1037 ddwvyeevaetYvlDeevrefleekNpwAlreiaerLlEaarrglWeaseet 1088
                                        +d ++eevae+Y++D++ +e+l++ NpwAl++i+++LlEa++r+lW+a++et
  gi|336254167|ref|YP_004597274.1| 1215 SDTLWEEVAEKYAFDDARQEWLRDVNPWALESITDTLLEAIERDLWDADDET 1266
                                        **************************************************97 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 !   14.9   0.0   1.8e-06     0.016      22      55 ..     374     407 ..     369     408 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-06
                                       HSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTS CS
                     LexA_DNA_bind  22 tgypPsireiaralglkSpsaveehLkaLerKGy 55 
                                       + ypPs   i+ a+gl Sp++  + L+ Le +Gy
  gi|336254167|ref|YP_004597274.1| 374 HNYPPSDDGIGTAFGLDSPESTVNLLEELEARGY 407
                                       78******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.89u 0.29s 00:00:01.18 Elapsed: 00:00:00.46
# Mc/sec: 8544.75
//
Query:       gi|336254168|ref|YP_004597275.1|  [L=259]
Description: Precorrin-8X methylmutase CbiC/CobH [Halopiger xanaduensis SH-6]
Scores for complete 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  175.0   1.2    1.7e-51  174.7   1.2    1.1  1  CbiC      Precorrin-8X methylmutase
  ------ inclusion threshold ------
       0.19   11.6   0.0       0.32   10.9   0.0    1.2  1  DUF3531   Protein of unknown function (DUF3531)


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 !  174.7   1.2   1.9e-55   1.7e-51       1     195 [.      26     226 ..      26     227 .. 0.93

  Alignments for each domain:
  == domain 1  score: 174.7 bits;  conditional E-value: 1.9e-55
                                       HHHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE-.........TTHHHHHHHHHHCT-EEEESSH CS
                              CbiC   1 eIeaeSfaiideelgeeelseeeeevvrRvihatadfelaellrfs.........pdaveaglealkagapivtDve 68 
                                       +I+++S++i+++ + +e   + +++v ++ +h+++d+e+++l++f+         ++ v+ag++a+ ++a+ivtD++
  gi|336254168|ref|YP_004597275.1|  26 DIAETSMDIVRQFVPDE---TLADRVRQKSVHSMGDIEFQHLIEFTgadglgddeDAPVRAGARAVLEEADIVTDIT 99 
                                       599***********977...8999**********************666666555559******************* PP

                                       HHHCCS-HHHHHTTC-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHH..CTTTCEEEESS-HHHHHHHHHHHHHS. CS
                              CbiC  69 mvkaGitkkrleklgnevlclladpevaelakekgitrsaaamekaae..elegaivviGnAPtALlellelieegk 143
                                       m kaGit++ +++   e + ++ +   aelake+g+tr+aa++ ++ +   ++gai  iGnAPtA ++l+++ie+g+
  gi|336254168|ref|YP_004597275.1| 100 MPKAGITSRGHNC---EKRKAIGHG--AELAKETGMTRTAASVLELDKqgAYDGAIATIGNAPTAAFALADCIENGT 171
                                       ******9998765...788999998..99*****************99899************************97 PP

                                       .HTSEEEE----SCCHHHHHHHHHCSS....S-EEEESSS---HHHHHHHHHHHHH CS
                              CbiC 144 vkpalvigvPvGFvgaaesKealaese....vpyitveGrkGGsavAaaivnaLle 195
                                        +pa+++++PvGFv+a+es+++++e +    vp+it+ Gr+GGs +Aaa++n+L++
  gi|336254168|ref|YP_004597275.1| 172 -RPAAIVATPVGFVKAEESRQRIREVSeeygVPAITNVGRRGGSGLAAALTNELIH 226
                                       .***********************8445678***********************97 PP

>> DUF3531  Protein of unknown function (DUF3531)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.6e-05      0.32      44      90 ..      17      64 ..      14      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.6e-05
                           DUF3531 44 LGgfnaenlqvqesgld.lsyleYdaeeaeeslaalmhnlgdleyqdk 90
                                      LG+   + + ++e+++d ++++  d++ a+++ +  +h +gd+e+q+ 
  gi|336254168|ref|YP_004597275.1| 17 LGATTQNAMDIAETSMDiVRQFVPDETLADRVRQKSVHSMGDIEFQHL 64
                                      89999999*********55677889999999**************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1870.39
//
Query:       gi|336254169|ref|YP_004597276.1|  [L=265]
Description: precorrin-6y C5,15-methyltransferase subunit CbiE [Halopiger xanaduensis SH-6]
Scores for complete 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  126.7   0.7    1.4e-36  126.5   0.7    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 !  126.5   0.7   7.6e-41   1.4e-36       2     212 ..      32     238 ..      31     239 .. 0.94

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 7.6e-41
                      TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal...aea 75 
                                       +y VG+GpG+ e+lT+r+ ra+++adv++g +  + e +++l +e          +++ l+ +y++ a+al    e+
  gi|336254169|ref|YP_004597276.1|  32 VYAVGIGPGNLEYLTPRGERAIREADVIVGFT-TVVEFVEELTDE----------DTDLLTCGYKDEAAALeefGER 97 
                                       8*******************************.******999865..........689*****999999999999** PP

                      TP_methylase  76 lragkdVvllvsGDPlvy..gtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakee 150
                                       ++ag+    + +GDP+ +  + ++++ +a+++++++i+v+++PG+sslq aa+r+++p+++++ v+ +   +l+++ 
  gi|336254169|ref|YP_004597276.1|  98 VAAGESGTAVAMGDPNHSgyQFVGKVQDAVQREDPQIPVRIVPGISSLQVAASRARTPMEDTEFVTLHKSGDLEADM 174
                                       ****************98889***************************************99999999989999999 PP

                      TP_methylase 151 ereleallangdtlvllkapr.k.laelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                       er+ +a+ ++ ++l++l +p  + + ++ae+L+e+  ++d+ ++ v e+++ ++er+ r tl++l
  gi|336254169|ref|YP_004597276.1| 175 ERLAAAVTDDERHLLALPRPYdRmPGDIAEFLLERgADPDL-EALVLEKLTHDEERIHRFTLADL 238
                                       9999999999***********74699*********777755.********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2026.04
//
Query:       gi|336254170|ref|YP_004597277.1|  [L=228]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-26   92.2   0.0      4e-26   91.5   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    5.3e-25   88.0   0.0      1e-24   87.1   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    3.5e-23   82.1   0.0    4.7e-23   81.7   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    8.1e-20   71.3   0.0    1.1e-19   70.9   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    1.7e-18   66.9   0.0    2.6e-18   66.2   0.0    1.3  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.8e-14   54.2   0.0      3e-14   53.5   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    3.6e-07   29.9   0.0    5.5e-07   29.3   0.0    1.2  1  MTS              Methyltransferase small domain
    2.5e-05   23.8   0.0    3.4e-05   23.3   0.0    1.1  1  TehB             Tellurite resistance protein TehB
    6.5e-05   23.0   0.0    0.00017   21.6   0.0    1.6  2  Methyltransf_32  Methyltransferase domain
    9.2e-05   22.1   0.0    0.00013   21.7   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    0.00029   20.6   0.0    0.00069   19.3   0.0    1.6  2  TPMT             Thiopurine S-methyltransferase (TPMT)
    0.00049   19.3   0.0     0.0006   19.0   0.0    1.2  1  DREV             DREV methyltransferase
    0.00062   19.4   0.0    0.00081   19.1   0.0    1.2  1  NodS             Nodulation protein S (NodS)
    0.00065   19.1   0.0    0.00088   18.6   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain
     0.0011   19.3   0.0     0.0017   18.7   0.0    1.3  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
     0.0013   18.1   0.0     0.0027   17.0   0.0    1.4  1  GidB             rRNA small subunit methyltransferase G
     0.0013   18.2   0.0     0.0018   17.8   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0019   18.0   0.0     0.0031   17.3   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0028   17.0   0.0     0.0035   16.7   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0053   16.7   0.0       0.01   15.8   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
      0.056   12.0   0.0       0.12   10.9   0.0    1.6  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
       0.19   11.7   0.0       0.39   10.7   0.0    1.5  1  ADH_zinc_N       Zinc-binding dehydrogenase


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 !   91.5   0.0   4.9e-29     4e-26       1      95 [.      61     155 ..      61     156 .. 0.99

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 4.9e-29
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       LdvGcGtG ++  la+ g++v+gvDls+eml++a++ka +++l+vef+ +dae++p +d+++Dl ++++ + ++++p
  gi|336254170|ref|YP_004597277.1|  61 LDVGCGTGVISLLLADIGHDVTGVDLSEEMLERARAKAGDRDLSVEFRNGDAESIPDPDDTYDLMTARHLVWTLPNP 137
                                       8**************************************************************************** PP

                                       HHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                       ++al+e+ Rv++pgG++v
  gi|336254170|ref|YP_004597277.1| 138 SAALREWQRVVRPGGRVV 155
                                       ***************998 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.0   1.2e-27     1e-24       1      97 []      60     152 ..      60     152 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.2e-27
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       +Ld+GcGtG ++l la+ +  ++vtgvD+seemle+ar++a +++l+vef++gdae++p +d+++Dl++++ +l + 
  gi|336254170|ref|YP_004597277.1|  60 ILDVGCGTGVISLLLADIG--HDVTGVDLSEEMLERARAKAGDRDLSVEFRNGDAESIPDPDDTYDLMTAR-HLVW- 132
                                       8***************995..*************************************************6.4444. PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       + ++  +al+e+ rv++pgG
  gi|336254170|ref|YP_004597277.1| 133 TLPNPSAALREWQRVVRPGG 152
                                       3456779************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.0   5.7e-26   4.7e-23       5     114 ..      58     163 ..      55     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 5.7e-26
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                        r+lD+GCGtG +++ la  +g   +v+G+D see++e+Ar++a +  l+ veF+ gd+e+++    d+++Dl++++
  gi|336254170|ref|YP_004597277.1|  58 QRILDVGCGTGVISLLLA-DIG--HDVTGVDLSEEMLERARAKAGDRDLS-VEFRNGDAESIP--DPDDTYDLMTAR 128
                                       689***************.544..479**********************8.************..579********* PP

                   Methyltransf_31  82 evlnaladpdkileeiervlkpggilliedpr..l 114
                                        ++ +l++p ++l+e +rv++pgg++++ + +   
  gi|336254170|ref|YP_004597277.1| 129 HLVWTLPNPSAALREWQRVVRPGGRVVLIEGHwdF 163
                                       ***************************99988441 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.0   1.3e-22   1.1e-19      21     131 ..      55     168 ..      24     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.3e-22
                   Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdlIvlrevl 92 
                                       ++++r+Ld+GcGtG  + +l++ g++vtgvDls+e+ e+a+      +   ++ + d++++++p++++dl+++r++ 
  gi|336254170|ref|YP_004597277.1|  55 ESPQRILDVGCGTGVISLLLADIGHDVTGVDLSEEMLERARakagdRDLSVEFRNGDAESIPDPDDTYDLMTARHLV 131
                                       6788*****************************************98899999999999****************** PP

                   Methyltransf_23  93 ehvpdppellrqiatllkpgGylllseplaslkedrlll 131
                                        ++p+p ++lr  ++ ++pgG+++l e    +  d++++
  gi|336254170|ref|YP_004597277.1| 132 WTLPNPSAALREWQRVVRPGGRVVLIEG--HWDFDEAFD 168
                                       ***********************99885..344555555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   3.2e-21   2.6e-18       6     153 ..      10     158 ..       5     180 .. 0.85
   2 ?   -3.6   0.0       7.1   5.8e+03     202     221 ..     186     205 ..     183     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 3.2e-21
                                       XXXXXXXXX-HHHHHH..HHHHHHHTTTHHHHHHHHHHH--S...--TTEEEEES-TT-HHHHHHHHHHHHHHEEEE CS
                   Ubie_methyltran   6 eekvkevfesvaskyD..lmndvlslgihrlWkkfveklvav...krgakvlDvagGtgDlafklsdsvgekgkvvv 77 
                                       +e+v++ ++s a++yD     ++    + + W + + + +++    +++++lDv +Gtg +++ l+d      +v++
  gi|336254170|ref|YP_004597277.1|  10 KERVQQYWDSRAESYDgdSHHALQDEAQRDAWLSVLREWTGGgggESPQRILDVGCGTGVISLLLADIG---HDVTG 83 
                                       5689999999999997224566777788999999888887651115667*************9988753...4799* PP

                                       EES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran  78 lDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                       +D++e+mL+ +++k+ ++   ++ef +++ae +p  dd++D++t  + +  +++ + aL+e  rv++pGGr+v +e
  gi|336254170|ref|YP_004597277.1|  84 VDLSEEMLERARAKAGDRD-LSVEFRNGDAESIPDPDDTYDLMTARHLVWTLPNPSAALREWQRVVRPGGRVVLIE 158
                                       **************99886.57****************************************************99 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.1
                                       HHHHHHHHHTTEEEEEEEEE CS
                   Ubie_methyltran 202 etlkeliedaGfksveyesl 221
                                       e+l +++e+ G++ ve+e l
  gi|336254170|ref|YP_004597277.1| 186 EELVDVLEEHGLERVEHEPL 205
                                       67888999999999998765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   3.7e-17     3e-14       1      99 []      61     154 ..      61     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 3.7e-17
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++GcGtG ++  l++   + ++tgvD+s++++e+a++k  +r+ +++++ + +a+++ d d+  ++Dl +a +++ 
  gi|336254170|ref|YP_004597277.1|  61 LDVGCGTGVISLLLADI--GHDVTGVDLSEEMLERARAKAGDRD-LSVEFRNGDAESIPDPDD--TYDLMTARHLVW 132
                                       8*******998888888..**************99999988888.588888888888887776..************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        l+++ ++l++  ++++pgGr+
  gi|336254170|ref|YP_004597277.1| 133 TLPNPSAALREWQRVVRPGGRV 154
                                       ********************85 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   6.8e-10   5.5e-07      33     100 ..      58     124 ..      53     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 6.8e-10
                                       SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST.TS-EEE CS
                               MTS  33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeve.ekkfdl 100
                                       +++lD+GcG+Gv+++ la+   +  vt vd + + le a++ + + +l+ve+++ d+ +  + ++ +dl
  gi|336254170|ref|YP_004597277.1|  58 QRILDVGCGTGVISLLLADIGHD--VTGVDLSEEMLERARAKAGDRDLSVEFRNGDAESIPDpDDTYDL 124
                                       67*****************9888..9*****************************99876654566665 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   4.2e-08   3.4e-05      30      88 ..      56     113 ..      55     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.2e-08
                                       -S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GG CS
                              TehB  30 kpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydin 88 
                                       +p ++ld+gcg g  sl l+ +g+dvt +d  e+ ++  +  +   +l+ ++ +  d +
  gi|336254170|ref|YP_004597277.1|  56 SPQRILDVGCGTGVISLLLADIGHDVTGVDLSEEMLERARAKAGDRDLS-VEFRNGDAE 113
                                       6999**************************9998877766665555555.555555544 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.4   2.7e+03      68      94 ..       7      33 ..       4      46 .. 0.73
   2 !   21.6   0.0     2e-07   0.00017      25      91 ..      56     114 ..      40     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.4
                   Methyltransf_32 68 ekraeklgkkfnkrlsfaelsieeats 94
                                      e+++e++++++++r +  ++++++a +
  gi|336254170|ref|YP_004597277.1|  7 ETVKERVQQYWDSRAESYDGDSHHALQ 33
                                      567888888888888888887776654 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2e-07
                   Methyltransf_32  25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsiee 91 
                                       ++++++DvG+G g  s  la+     ++ v+g+d++ee+ e+a++ a      +  +++f +++ e+
  gi|336254170|ref|YP_004597277.1|  56 SPQRILDVGCGTGVISLLLAD----IGHDVTGVDLSEEMLERARAKAGDRD--L--SVEFRNGDAES 114
                                       5789*****************....89***************999887666..4..55666665555 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.6e-07   0.00013      15     104 ..      58     150 ..      54     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.6e-07
                              MetW  15 srvldlGcGdGellellkeekqvdgrGleldeegvaecva....kGlsviqgdldkdlenfedksfdyvvlsqtlqa 87 
                                        r+ld+GcG G +  ll++  + d  G++l+ee + ++ a    + lsv   + d +    +d+++d++     + +
  gi|336254170|ref|YP_004597277.1|  58 QRILDVGCGTGVISLLLAD-IGHDVTGVDLSEEMLERARAkagdRDLSVEFRNGDAESIPDPDDTYDLMTARHLVWT 133
                                       59*********99988877.7778889999988887766511226799*999999999999**************** PP

                              MetW  88 trnpkevldellrigrr 104
                                       + np+  l+e  r+ r 
  gi|336254170|ref|YP_004597277.1| 134 LPNPSAALREWQRVVRP 150
                                       **********9999764 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.9   3.2e+03      18      33 ..       5      20 ..       3      26 .. 0.78
   2 !   19.3   0.0   8.5e-07   0.00069      37      84 ..      56     103 ..      37     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.9
                                      --SS--HHHHHHHHT. CS
                              TPMT 18 hqeevnpllkkfldal 33
                                      + e v++ +++++d+ 
  gi|336254170|ref|YP_004597277.1|  5 DDETVKERVQQYWDSR 20
                                      7789999999999983 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 8.5e-07
                                       --EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGG CS
                              TPMT  37 aglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepk 84 
                                       + +r+l  +CG ++    lA+ g++v Gv+lse  +e++ ++a+ ++ 
  gi|336254170|ref|YP_004597277.1|  56 SPQRILDVGCGTGVISLLLADIGHDVTGVDLSEEMLERARAKAGDRDL 103
                                       66789999*****************************99888776555 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   7.3e-07    0.0006      92     186 ..      54     156 ..      32     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.3e-07
                              DREV  92 dqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkk........kynvlsalelqetdvkldlilclnl 160
                                       +  ++++ld+G G G i+  +a+  ++v   +lse+m +r + k        +++   a  + + d  +dl+++  l
  gi|336254170|ref|YP_004597277.1|  54 GESPQRILDVGCGTGVISLLLADIGHDVTGVDLSEEMLERARAKagdrdlsvEFRNGDAESIPDPDDTYDLMTARHL 130
                                       56799*********************************999876211111112222223335566778999999999 PP

                              DREV 161 ldrcfdplklledirsalepngrviv 186
                                       +    +p   l++ + + +p grv++
  gi|336254170|ref|YP_004597277.1| 131 VWTLPNPSAALREWQRVVRPGGRVVL 156
                                       99999999999999999999999986 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     1e-06   0.00081      46     143 ..      59     155 ..      34     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                              NodS  46 dalevGcaaGalterlapyckrltvvdvveeaiararervkess.hiswivsdvqqf.stdekfdlivvaevlyyie 120
                                        +l+vGc +G ++  la + + +t vd+ ee ++rar +  +    + +   d + + + d+ +dl+    +++ + 
  gi|336254170|ref|YP_004597277.1|  59 RILDVGCGTGVISLLLADIGHDVTGVDLSEEMLERARAKAGDRDlSVEFRNGDAESIpDPDDTYDLMTARHLVWTLP 135
                                       689***********************************998753267888999998757899999998777766655 PP

                              NodS 121 dvaelraavrnlvsllapdgqlv 143
                                       +     aa+r+  ++++p+g++v
  gi|336254170|ref|YP_004597277.1| 136 N---PSAALREWQRVVRPGGRVV 155
                                       4...4567777777777776665 PP

>> Methyltransf_2  O-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   0.00088      64     170 ..      58     162 ..      50     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                                       SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HH.HHHHHHHHS-----TTEEEEES-TTTS---.--SEEEEESSGG CS
                    Methyltransf_2  64 kslvDvGGGtGalakaivsayPtikvivfDlpe.VveaAkehlsageeervefvgGdffkdslP.eaDaillkrvlh 138
                                       ++++DvG GtG++    +    +  v+  Dl+e   e+A+ +   + + +vef +Gd    s+P   D + l    h
  gi|336254170|ref|YP_004597277.1|  58 QRILDVGCGTGVISLLLADI--GHDVTGVDLSEeMLERARAK-AGDRDLSVEFRNGDAE--SIPdPDDTYDLMTARH 129
                                       6899*******987766665..56778889985378889998.778899********76..***7778888888777 PP

                                       .GS-HHHHHHHHHHHHHH--TT-EEEEEE---- CS
                    Methyltransf_2 139 .DwsdekcvklLkrvkkalpagGkvivveavlg 170
                                         w+  + +  L++ ++ +++gG+v+++e   +
  gi|336254170|ref|YP_004597277.1| 130 lVWTLPNPSAALREWQRVVRPGGRVVLIEGHWD 162
                                       46**************************97655 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.1e-06    0.0017      27      92 ..      21      90 ..       4     107 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.1e-06
                      AdoMet_MTase 27 vestdpl.kfvfedla.iaaylivl..wkktrseeketsfvdvgcgngllvyvlaaegykgygidlrkrk 92
                                       es d   ++  +d a   a+l vl  w      e+++ + dvgcg g++  +la  g+   g+dl    
  gi|336254170|ref|YP_004597277.1| 21 AESYDGDsHHALQDEAqRDAWLSVLreWTGGGGGESPQRILDVGCGTGVISLLLADIGHDVTGVDLSEEM 90
                                      55555431344555441467877763366666679******************************97665 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.3e-06    0.0027      51     158 ..      59     168 ..      53     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.3e-06
                                       .EEEETSTTTTTHHHHHHH-TTSE.EEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC.TTTTT-EEEEEEC-SS CS
                              GidB  51 kviDvGsGaGlPGipLaiarpelk.ltLleslekkiaFLeevkeelklenveivearaee.kqeeekydvvtsRAla 125
                                       +++DvG G G+ ++ La +  ++  + L e    +++       + +l+ ve+ + +ae+  ++ ++yd++t+R l 
  gi|336254170|ref|YP_004597277.1|  59 RILDVGCGTGVISLLLADIGHDVTgVDLSEEMLERAR---AKAGDRDLS-VEFRNGDAESiPDPDDTYDLMTARHLV 131
                                       69***************99999888999999999986...333445666.88********99************875 PP

                                       ....SHHHHHHHHCCCEEEEEEEEEEESS--HHHHHC CS
                              GidB 126 ....slnelteillkllkegglilalKGksaedelee 158
                                           + +      ++++++gg+++++ G+++ de+  
  gi|336254170|ref|YP_004597277.1| 132 wtlpNPSAALREWQRVVRPGGRVVLIEGHWDFDEAFD 168
                                       3222333333444567*****************9865 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.2e-06    0.0018     162     203 ..      57      97 ..      51     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.2e-06
                              PrmA 162 geevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeN 203
                                        +++lDvG+G+G++++  a +g+ +v++vD+ e  ++ a++ 
  gi|336254170|ref|YP_004597277.1|  57 PQRILDVGCGTGVISLLLADIGH-DVTGVDLSEEMLERARAK 97 
                                       5689******************7.69*****99988888765 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 !   17.3   0.0   3.8e-06    0.0031      75     146 ..      58     125 ..      54     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.8e-06
                                       -EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEE CS
                              PCMT  75 arvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdai 146
                                       +r+L+vG+G+G  + +la + ++++   +++ ++e+ e+a+++    dl +v ++ gD +   ++   Yd +
  gi|336254170|ref|YP_004597277.1|  58 QRILDVGCGTGVISLLLADIGHDVT---GVDLSEEMLERARAKAGDRDL-SVEFRNGDAESIPDPDDTYDLM 125
                                       79************99999866655...************998776665.6999999987666666666655 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.2e-06    0.0035      64     110 ..      58     103 ..      29     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.2e-06
                                       -EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-S CS
                              CMAS  64 mtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldl 110
                                       +++Ld+GcG G +    ++  + +v g+ lS+e  ++a+++  ++dl
  gi|336254170|ref|YP_004597277.1|  58 QRILDVGCGTGVISLLLADI-GHDVTGVDLSEEMLERARAKAGDRDL 103
                                       689********999888877.***************99998877775 PP

>> Methyltransf_18  Methyltransferase 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      0.01      16      73 ..      58     111 ..      55     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                   Methyltransf_18  16 srvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsd 73 
                                       +r++D+G+  g++++ l+  ++ + v+ +D++e+ le+a++++ + +l  ++e+r +d
  gi|336254170|ref|YP_004597277.1|  58 QRILDVGCGTGVISLLLA--DIGHDVTGVDLSEEMLERARAKAGDRDL--SVEFRNGD 111
                                       799*********999998..56678*****************999988..57777766 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 ?   10.9   0.0   0.00015      0.12     119     217 ..      58     156 ..      23     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                   Methyltransf_29 119 rtvlDvGCgvasfgayl..lsrdvltlslapkDeheaqvqfaLeRgvpailavlgtkrlpyPsrsfdlihCsrCrid 193
                                       + +lDvGCg    +  l  + +dv+ + l+ +   +a+   a +R +        ++ +p P  ++dl+  +r ++ 
  gi|336254170|ref|YP_004597277.1|  58 QRILDVGCGTGVISLLLadIGHDVTGVDLSEEMLERARA-KAGDRDLSVEFRNGDAESIPDPDDTYDLMT-ARHLVW 132
                                       668888887655554441145788888887665555554.477888888888888888888888888875.677776 PP

                   Methyltransf_29 194 wteedgilllevdRvlRpgGyfvl 217
                                          + ++ l e +Rv+RpgG  vl
  gi|336254170|ref|YP_004597277.1| 133 TLPNPSAALREWQRVVRPGGRVVL 156
                                       667778888888888888887665 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00048      0.39       3      90 ..      66     159 ..      64     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00048
                                       HHHHHHHHH.HTT-EEEEEESSHHHHHHHHH.TT.ESEEEET.....TTC.HHHHHHHHHTTTSSEEEEEESSCSHH CS
                        ADH_zinc_N   3 GlaavqlAk.alGaeviavdsseeklelakk.lG.adeviny.....kea.dlverikeltggegvdvvfecvGsga 70 
                                       G+ ++ l+   +G  v++vd see le a+   G  d  +       ++  d+++    +t     ++v   ++  a
  gi|336254170|ref|YP_004597277.1|  66 GTGVISLLLaDIGHDVTGVDLSEEMLERARAkAGdRDLSVEFrngdaESIpDPDDTYDLMT---ARHLVWTLPNPSA 139
                                       67777776646899*************9998788555555558888888889999999999...8899999999999 PP

                                       HHHHHHHCEEEEEEEEECSC CS
                        ADH_zinc_N  71 tleaalkllkpgGrlvvvGg 90 
                                       +l++  ++++pgGr+v++ g
  gi|336254170|ref|YP_004597277.1| 140 ALREWQRVVRPGGRVVLIEG 159
                                       ****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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):              22  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1699.70
//
Query:       gi|336254171|ref|YP_004597278.1|  [L=60]
Description: hypothetical protein Halxa_2783 [Halopiger xanaduensis SH-6]
Scores for 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  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); 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:                         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: 00:00:00.39
# Mc/sec: 461.25
//
Query:       gi|336254172|ref|YP_004597279.1|  [L=187]
Description: hypothetical protein Halxa_2784 [Halopiger xanaduensis SH-6]
Scores for 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-40  137.2   0.0    5.7e-40  137.0   0.0    1.0  1  DUF1802   Domain of unknown function (DUF1802)


Domain annotation for each model (and alignments):
>> DUF1802  Domain of unknown function (DUF1802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.0   0.0   3.2e-44   5.7e-40       1     173 [.      14     180 ..      14     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 137.0 bits;  conditional E-value: 3.2e-44
                           DUF1802   1 ALkewavaveaLeeGrqivllrKggireergkFeveeeeflLYPtvehqkaellkpeyaallepvasestpekveik 77 
                                       ALke+a +v aL eG q+vl+r+ ++++++      +e+f+LYP+++hq++++++++y+ ++++++++  +  + i+
  gi|336254172|ref|YP_004597279.1|  14 ALKERAGVVSALLEGAQTVLVRHPTLDPGT-----IDERFVLYPAYSHQNPDRYQDRYEGYYHRASTKPDAG-IPIR 84 
                                       9*****************************.....9*****************************7776665.**** PP

                           DUF1802  78 awAeveeavevsdeealealsklhiwteeavedrlkykpkqpltvlllRvyrleepvelpetpeyagckswvdlpes 154
                                        +A+v++ + vs+ +++eal+  +++t++ ++d+  y+p++ l vlllRv +le+p+ ++e+ +y+gc+ w+dl+++
  gi|336254172|ref|YP_004597279.1|  85 GVADVRAEYTVSS-DEVEALATQYVYTPDGLRDK--YDPDDDLRVLLLRVRELESPRLIEERGSYRGCRAWIDLESD 158
                                       *************.99****************65..66**************************************9 PP

                           DUF1802 155 ...eaeeakPVlsdeefeerka 173
                                          ++e+a+PVl+d++f+er+a
  gi|336254172|ref|YP_004597279.1| 159 agiDPEAATPVLDDATFAERRA 180
                                       9******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1468.74
//
Query:       gi|336254173|ref|YP_004597280.1|  [L=437]
Description: Cobyrinic acid A,C-diamide synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-31  109.8   0.0    1.6e-31  109.5   0.0    1.1  1  GATase_3     CobB/CobQ-like glutamine amidotransferase domain
    2.2e-11   43.9   0.0    3.7e-11   43.2   0.0    1.4  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    6.5e-11   42.4   0.0    1.9e-06   27.9   0.0    2.2  2  AAA_26       AAA domain
     0.0023   17.3   0.1     0.0044   16.4   0.1    1.4  1  CTP_synth_N  CTP synthase N-terminus
     0.0097   15.8   0.0      0.021   14.6   0.0    1.5  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 !  109.5   0.0   4.4e-35   1.6e-31       1     194 [.     237     426 ..     237     428 .. 0.89

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 4.4e-35
                          GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeag 75 
                                       ++av+ + a+ + +   ++  ++++ +   f+pl ++ + +d+d v+lpGg++++++ al+   ++  ++ e+a++g
  gi|336254173|ref|YP_004597280.1| 237 TVAVASDAAFCFRYpaTIERFRERA-EVATFSPLAGDPV-PDCDGVYLPGGYPELHADALEST-DTLSELGELASEG 310
                                       5899999999999999999999988.556899*9*****.56***************999887.88899******** PP

                          GATase_3  76 gpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel......aaegeevkGyEiHs 146
                                        pvlg+CGGl+ ++++++++eg+     ++e+ g+L++++e+++ + +   ++e+e+      aa+ge+++G+E+H+
  gi|336254173|ref|YP_004597280.1| 311 LPVLGECGGLMAMSRSLTTAEGE-----RHEMGGILPADVEMHD-RYQALDHVELEAldgtltAAAGETIRGHEFHY 381
                                       **********************9.....****************.77755555555589*9988889********** PP

                          GATase_3 147 Grtilkekakpllkvkvggnng.ekdGavkksedgnvlGtYlHglfdnr 194
                                       ++   + +a+ +++ ++g +++ e+dG+ +     + lGtY+H++ ++ 
  gi|336254173|ref|YP_004597280.1| 382 SSADVDGDARFAFETVRGDGIDgEHDGLTEY----ESLGTYVHVHPESG 426
                                       ****9999999999977777777******77....9********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 !   43.2   0.0     1e-14   3.7e-11       6     126 ..      10     186 ..       5     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 1e-14
                                       SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                              CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................ 54 
                                        ++GvGKT+ ++++ +al ++g+ V++ +a+p+    ++ e   ++  +                            
  gi|336254173|ref|YP_004597280.1|  10 VSSGVGKTVATLSIVQALEDAGYAVQPAKAGPDFIDPSHHEAIAGRPSRtldlwlegedglrrnyrrgegdicvveg 86 
                                       68*******************************9888874444444444667788888888888************* PP

                                       ...........................CCHCCCHHHHHHCHCHHHH.........EEEEEEEEESS...-TTCHHHH CS
                                       ...........................xxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...........................dlkrllellealgkkkall.......lkiagvvlnrvdgeneetllkeal 97 
                                                                  d+k + e+++a   ++++        +++agvv+ r  g ++e+ +++al
  gi|336254173|ref|YP_004597280.1|  87 vmglydgdgsstamvaealdlpvvlvvDAKAGMESVAATALGFEKYaatigrdIDVAGVVAQRAHGGRHEQGIRDAL 163
                                       ***************************77777777766666666656667777************************ PP

                                       HHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  98 eelkqrygvpvlgviprdeavaeaparge 126
                                        +      ++ +g ip ++++ e+p r++
  gi|336254173|ref|YP_004597280.1| 164 PD-----DLEYFGRIPPNDDL-EIPDRHL 186
                                       99.....89**********99.9998885 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   2.8e-05     0.099       3      32 ..       5      34 ..       3      39 .. 0.86
   2 !   27.9   0.0   5.2e-10   1.9e-06      98     195 ..      78     180 ..      50     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.8e-05
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkv 32
                                      +++ g++ gvGKTv +l +v+al++ g+ v
  gi|336254173|ref|YP_004597280.1|  5 FVLGGVSSGVGKTVATLSIVQALEDAGYAV 34
                                      5677999****************9888776 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 5.2e-10
                            AAA_26  98 dadivvVEGagglgvpiteellnadiaknlgapvilVargglg..tinqllltiealr...qknvrvlGvilNkvrn 169
                                       + di vVEG+ gl ++  ++ ++a +a++l++pv+lV+ ++ g  ++++++l  e +     +++ v+Gv++ +   
  gi|336254173|ref|YP_004597280.1|  78 EGDICVVEGVMGLYDG--DGSSTAMVAEALDLPVVLVVDAKAGmeSVAATALGFEKYAatiGRDIDVAGVVAQRAHG 152
                                       679**********998..678999**************9977533799999777766633469***********988 PP

                            AAA_26 170 penvetlekksg..ipvlGvvPylpdle 195
                                        +  + ++ + +  ++ +G++P ++dle
  gi|336254173|ref|YP_004597280.1| 153 GRHEQGIRDALPddLEYFGRIPPNDDLE 180
                                       8999******99779*********9997 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.2e-06    0.0044       4      40 ..       5      41 ..       4      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-06
                                      EEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE- CS
                       CTP_synth_N  4 lvtGGvvSglGkGiiaaslgallksrglkvtlikiDP 40
                                      +v GGv Sg+Gk +++ s+ + l+  g+ v+  k  P
  gi|336254173|ref|YP_004597280.1|  5 FVLGGVSSGVGKTVATLSIVQALEDAGYAVQPAKAGP 41
                                      899****************************999887 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     6e-06     0.021      32      88 ..     275     330 ..     259     349 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6e-06
                                       CC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB CS
                               SNO  32 aevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelene 88 
                                        ++d++ +PGG     +  +e t+ + +l e + ++ ++vlG C Gl+ +s+ l++ 
  gi|336254173|ref|YP_004597280.1| 275 PDCDGVYLPGGYPELHADALESTDTLSELGELASEG-LPVLGECGGLMAMSRSLTTA 330
                                       68************999****************999.**************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3579.65
//
Query:       gi|336254174|ref|YP_004597281.1|  [L=193]
Description: precorrin-6y C5,15-methyltransferase subunit CbiT [Halopiger xanaduensis SH-6]
Scores for 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   20.7   0.1    0.00081   20.1   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
     0.0024   17.5   0.0     0.0037   16.9   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0031   18.1   0.1     0.0093   16.6   0.1    1.7  2  Methyltransf_11  Methyltransferase domain
     0.0077   16.0   0.0      0.013   15.2   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.022   14.3   0.0      0.037   13.6   0.0    1.4  1  GATase_3         CobB/CobQ-like glutamine amidotransferase do
      0.027   14.0   0.1      0.058   12.9   0.0    1.5  2  MTS              Methyltransferase small domain
      0.086   12.4   0.0       0.13   11.8   0.0    1.3  1  DOT1             Histone methylation protein DOT1
      0.089   12.1   0.0       0.14   11.4   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
        0.1   12.4   0.0       0.12   12.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
       0.17   11.6   0.0       0.24   11.1   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase


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 !   20.1   0.1   4.5e-07   0.00081       3      69 ..      37     103 ..      35     136 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.5e-07
                                       EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEE CS
                   Methyltransf_25   3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvv 69 
                                       ++G  tG +t+++a+r   ++vt+++  +e le++++++++++   +++++  +ae+ +   +  D+ +
  gi|336254174|ref|YP_004597281.1|  37 EVGSCTGAVTIEAAQRA--GRVTALERKAERLETTEKNLAANEEsiRADVELRNAEAPEGLPADADALF 103
                                       89**************7..9******************9984444555555555554443333445554 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.1e-06    0.0037      19      90 ..      10      79 ..       3     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.1e-06
                                      XXXXSSSHHHHHHHHHHHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT-- CS
                     Cons_hypoth95 19 kstRPttdrvrealFnilaaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkle 90
                                       +  Pt+++vr  + + la e  + ++ ++ + +Ga+ +EA+ R   +++++e+++e +++ ++nl++ + +
  gi|336254174|ref|YP_004597281.1| 10 AKAGPTKSEVRAVVRSKLALE-PDDHFAEVGSCTGAVTIEAAQRA-GRVTALERKAERLETTEKNLAANEES 79
                                      566799999999999999866.455699**************996.9******************9987633 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.2e-06    0.0093       2      53 ..      37      85 ..      36     117 .. 0.81
   2 ?   -1.1   0.0       1.7   3.1e+03      20      38 ..     128     146 ..     102     169 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.2e-06
                                      EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-....EEEETTEECC CS
                   Methyltransf_11  2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl....kvefvvadae 53
                                      +vG++tG+++ + a+r++rv++++  +e l++ +++   +++            +e
  gi|336254174|ref|YP_004597281.1| 37 EVGSCTGAVTIEAAQRAGRVTALERKAERLETTEKNLAANEEsiraD-------VE 85
                                      79************999***************999998888744333.......33 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                                       EEEEEES-HHHHHHHHHHC CS
                   Methyltransf_11  20 rvvgvDlskemlklakeka 38 
                                       +v  ++++ +++++ +e+ 
  gi|336254174|ref|YP_004597281.1| 128 NVSRLEVAGKATEAFRERD 146
                                       3333333333333333333 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 !   15.2   0.0   7.4e-06     0.013      60     141 ..      18      99 ..       4     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.4e-06
                                       HHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC...SEEEEES-G CS
                              PCMT  60 hmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle...nvivvvgDG 133
                                        + a++   l l++ ++  evGs +G   av+ +  ++ grv ++er +e  e++++nl +++ +   +v ++ ++ 
  gi|336254174|ref|YP_004597281.1|  18 EVRAVVRSKLALEPDDHFAEVGSCTG---AVTIEAAQRAGRVTALERKAERLETTEKNLAANEESiraDVELRNAEA 91 
                                       56678888899**************9...7788899999********************999887778899888888 PP

                                       GGTTGGG- CS
                              PCMT 134 rkGyeeka 141
                                        +G ++ a
  gi|336254174|ref|YP_004597281.1|  92 PEGLPADA 99 
                                       88887766 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 ?   13.6   0.0     2e-05     0.037      23      73 ..      82     131 ..      68     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                          GATase_3  23 pevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaae 73 
                                       ++v++r ++   e l++dad+++l+G+++ ++ l ++ e+g+d+ + + ++
  gi|336254174|ref|YP_004597281.1|  82 ADVELRNAE-APEGLPADADALFLGGSRNFEAVLDHAVETGVDRIVMNVSR 131
                                       456666666.66778899***********************9998887665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.3e-05     0.058      29      83 ..      29      81 ..      21     102 .. 0.82
   2 ?   -2.2   0.0       1.4   2.6e+03      98     104 ..     122     128 ..     110     157 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                                      CCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEE CS
                               MTS 29 kelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankleve 83
                                       e +++ + +G+ +G++++++a++  +  vt+++ +a+ le +++nl+an+ +++
  gi|336254174|ref|YP_004597281.1| 29 LEPDDHFAEVGSCTGAVTIEAAQRAGR--VTALERKAERLETTEKNLAANEESIR 81
                                      556778899**************9999..9********************97743 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                                       EEEEEE- CS
                               MTS  98 fdlivsN 104
                                       +d iv+N
  gi|336254174|ref|YP_004597281.1| 122 VDRIVMN 128
                                       3334333 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.3e-05      0.13      28      66 ..      17      55 ..      11      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.3e-05
                                      HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH-- CS
                              DOT1 28 peflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgc 66
                                       e+ + v +k+ l+++d F + GS  G v++ aa  +g 
  gi|336254174|ref|YP_004597281.1| 17 SEVRAVVRSKLALEPDDHFAEVGSCTGAVTIEAAQRAGR 55
                                      5556677899***********************998774 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.7e-05      0.14      54     120 ..      23      88 ..      14      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.7e-05
                                       HHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES- CS
                              CMAS  54 ileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklld 120
                                       +  kl l+p ++  ++G   G+++++a++r   +v +l   +e+ ++++k++++ + + +++v+l +
  gi|336254174|ref|YP_004597281.1|  23 VRSKLALEPDDHFAEVGSCTGAVTIEAAQR-AGRVTALERKAERLETTEKNLAANEESIRADVELRN 88 
                                       5679**************************.889*******************99999999998865 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.7e-05      0.12       5      80 ..      33     115 ..      29     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaq.klgldnveFeqgdiee...leklled..... 72 
                                        ++ ++G+ tG+ t+e+a+++g   +v+ +++++e +e  ++n++ + ++ ++ +e  ++e+   l+    d     
  gi|336254174|ref|YP_004597281.1|  33 DHFAEVGSCTGAVTIEAAQRAG---RVTALERKAERLETTEKNLAaNEESIRADVELRNAEApegLPA---Dadalf 103
                                       56779*************9865...6**************9965505555566666655555203432...223455 PP

                   Methyltransf_31  73 ....ekfDlils 80 
                                           ++f  +l+
  gi|336254174|ref|YP_004597281.1| 104 lggsRNFEAVLD 115
                                       555555555555 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00013      0.24      50     103 ..      35      87 ..      24     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                   Methyltransf_16  50 vlELGsGtGlvGlavaellpeakviltDleellellkknielnknalkskvkve 103
                                         E+Gs tG v + +a+   +    l    e le  +kn+++n++ ++ +v+ +
  gi|336254174|ref|YP_004597281.1|  35 FAEVGSCTGAVTIEAAQR-AGRVTALERKAERLETTEKNLAANEESIRADVELR 87 
                                       569*************99.3444456667789**********999888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 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:                        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):              10  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 1628.02
//
Query:       gi|336254175|ref|YP_004597282.1|  [L=287]
Description: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-36  126.1   1.1    3.1e-36  125.3   1.1    1.4  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 !  125.3   1.1   1.7e-40   3.1e-36       1     206 [.       2     195 ..       2     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 1.7e-40
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeel..eleapmgkekepleeayeeiaealaea 75 
                                       +ly+VG+GpG ++l+Tvr+  +l+tadvv+ ++++  + +l++++e++   l +pm+k+++ l++a++++a+ +a +
  gi|336254175|ref|YP_004597282.1|   2 TLYGVGLGPGEADLVTVRGKTVLETADVVYSPGRLSRSVALEHVDEDKigDLDFPMTKDEDKLRRAWKAAAAEVAPE 78 
                                       69*******************************669999999999999***************************** PP

                      TP_methylase  76 lragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeer 152
                                       +++g dV++++ GDP+vy+t+++l + + a +++++ e++PGvs+++a a+++gi+++  g  l++        e++
  gi|336254175|ref|YP_004597282.1|  79 AKDG-DVAFVTLGDPNVYSTFGHLRRTIDAFHPDVDLEIVPGVSAVTAFATAMGIEIE-AGAGLALR-------EAA 146
                                       ***9.8***************************************************9.44555555.......222 PP

                      TP_methylase 153 eleallangdtlvllkaprklaelaelLkealyddttpvavveragte.dervvr 206
                                         +     +d+++l+k ++ ++ + e L +a     ++v++++r+ +e +e++v+
  gi|336254175|ref|YP_004597282.1| 147 SGAS-PTGPDRMILFKVTD-APATHEGLVDA----GYDVTYGRRLFMEqGETIVT 195
                                       2222.22378899997777.66666666444....57888888888884488775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); 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: 0.43u 0.18s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 2481.03
//
Query:       gi|336254176|ref|YP_004597283.1|  [L=331]
Description: Precorrin-4 C(11)-methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-38  133.1   0.2    1.8e-38  132.7   0.2    1.2  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
    0.00068   20.0   0.1     0.0016   18.8   0.1    1.8  1  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
       0.01   16.5   0.0      0.036   14.8   0.0    1.9  2  RraB          Regulator of ribonuclease activity B


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 !  132.7   0.2   2.9e-42   1.8e-38       3     212 ..      53     258 ..      51     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 2.9e-42
                      TP_methylase   3 ylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealrag 79 
                                        +VG+GpG+p llTv++ ++l++ad+v+ ++s++ + lld  +       + +  +++ +++ ee    +++a ++g
  gi|336254176|ref|YP_004597283.1|  53 PFVGAGPGNPRLLTVAGKELLEEADLVVHAGSLVNSELLDEYC-------SHADLVNSVGKDLEELIPLMRDAYEEG 122
                                       58*****************************996666654333.......33555778888899999999******* PP

                      TP_methylase  80 kdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl....lpglakeeer 152
                                       ++Vv+l+sGDP +yg++ e ++al+   +g+++  +PGv+s+ aa a l++ lt ++++ +v     + ++ ++ee+
  gi|336254176|ref|YP_004597283.1| 123 RNVVRLHSGDPAIYGAALEQMDALEH--EGVPTYFVPGVTSAFAASATLRTQLTLNEVSNHVAftrpQGKTLEPEED 197
                                       **************************..9************************************997788889999 PP

                      TP_methylase 153 eleallangd.tlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                       ++++++++gd t  ++ +++ + +++++L+e   ++ +tpvav+ +a+++de v +g+++++
  gi|336254176|ref|YP_004597283.1| 198 HISEFVEMGDvTTCIYLGTHAVRDTMDRLLEDgADP-ETPVAVIYHASWPDEDVLVGSIADI 258
                                       999999997725555666668**********96666.66******************99987 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   2.7e-07    0.0016      28     135 ..     105     241 ..      26     255 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.7e-07
                                       HHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.....CCTEEEEEEECSSCHG......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx......... RF
                       Radical_SAM  28 slsveeileevkelkaekgvkevilgggepllypdfvellerlakla.....vpgiritvetngtlpd......... 90 
                                        +++ee++ +++ + +e g ++v l++g+p  y    e +++l ++      vpg++ ++ +++tl +         
  gi|336254176|ref|YP_004597283.1| 105 GKDLEELIPLMRDA-YEEGRNVVRLHSGDPAIYGAALEQMDALEHEGvptyfVPGVTSAFAASATLRTqltlnevsn 180
                                       5688999999999*.7999**************************99999996666666666666655666666666 PP

                                       ...............HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHH CS
                                       ...............xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  91 ...............eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevleale 135
                                                      e+++ +++e+g  ++ ++lg +a+ d    +l+++g ++e  ++++ 
  gi|336254176|ref|YP_004597283.1| 181 hvaftrpqgktlepeEDHISEFVEMGdvTTCIYLGTHAVRDT-MDRLLEDGADPETPVAVIY 241
                                       79999999999******************************9.9999999999998777665 PP

>> RraB  Regulator of ribonuclease activity B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.1   6.3e+03      39      78 ..     114     150 ..     105     154 .. 0.67
   2 ?   14.8   0.0   6.1e-06     0.036       4      49 ..     219     268 ..     216     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                              RraB  39 faeeleklgyevedaeedeedgeevycldlskemsldaee 78 
                                       ++ ++ ++g +v ++   +   +  y + l++ ++l++e 
  gi|336254176|ref|YP_004597283.1| 114 LMRDAYEEGRNVVRLHSGD---PAIYGAALEQMDALEHEG 150
                                       5666666666666666665...568888888888888876 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6.1e-06
                              RraB   4 trevldalledGddldkpreiehhfyfedeedle....kfaeeleklgye 49 
                                        r+++d+lledG d++ p  + +h++ +de+ l     ++ae++e++gy+
  gi|336254176|ref|YP_004597283.1| 219 VRDTMDRLLEDGADPETPVAVIYHASWPDEDVLVgsiaDIAEKVEEAGYR 268
                                       5899**************************98761111455566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2629.36
//
Query:       gi|336254177|ref|YP_004597284.1|  [L=433]
Description: chromosome partitioning ATPase [Halopiger xanaduensis SH-6]
Scores for 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-10   40.6   0.0    5.3e-10   39.5   0.0    1.6  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    8.6e-08   32.2   0.1    9.9e-06   25.5   0.0    2.3  2  AAA_26          AAA domain
    1.8e-07   30.9   0.0      1e-06   28.4   0.0    2.0  1  ParA            NUBPL iron-transfer P-loop NTPase
    1.4e-06   28.1   2.9    0.00063   19.4   0.0    3.4  4  AAA_25          AAA domain
    5.7e-05   23.1   0.0     0.0042   17.0   0.0    2.2  2  AAA_31          AAA domain
      9e-05   22.0   0.0       0.14   11.6   0.0    2.4  2  AP_endonuc_2    Xylose isomerase-like TIM barrel
    0.00011   21.6   0.0    0.00029   20.2   0.0    1.6  2  MipZ            ATPase MipZ
  ------ inclusion threshold ------
      0.011   15.8   2.2      0.021   15.0   1.1    2.0  2  Acetyltransf_6  Acetyltransferase (GNAT) domain
      0.037   13.8   0.0      0.092   12.5   0.0    1.6  1  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
      0.046   13.2   0.0       0.65    9.4   0.0    2.2  2  CBP_BcsQ        Cellulose biosynthesis protein BcsQ


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 !   39.5   0.0   2.9e-13   5.3e-10       1     114 [.       2     186 ..       2     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 2.9e-13
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT..--EEEEEEEESSCCCCHHTTEB-HHHH..................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrg..lrVllvDaDpqannlaileglendiep..................... 54 
                                       iaia+ kGG GK+t++++L +a+ar++     +++DaD q +nl+ +++++ ++ p                     
  gi|336254177|ref|YP_004597284.1|   2 IAIAGSKGGCGKSTVTLGLSTAFARGEplTPAIAIDADRQLPNLH-VMTDRDRE-Ptlaalergvtlkeiaqehpce 76 
                                       89***********************532256789***********.44444444.3588999999999999****** PP

                                       ..........................................................CCHCCCHHHHHHCHCHHHH CS
                                       ..........................................................xxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ..........................................................dlkrllellealgkkkall 73 
                                                                                                 d +r le +e+   + + l
  gi|336254177|ref|YP_004597284.1|  77 stvgivsapkpsdafefdsladhadlegtqvlldcpagagpdlveplrsadgvivvagDSERSLEAAETTIDVARRL 153
                                       ************************99999999999999999999999988888888776666555555555554444 PP

                                       ...EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE- CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  74 .lkiagvvlnrvdgeneetllkealeelkqrygvpvlgvipr 114
                                        + + g vlnr      ++    a e +    gvp+lg +p 
  gi|336254177|ref|YP_004597284.1| 154 gVPVYGAVLNRR-----SAVPDRAAEWR----GVPILGCVPD 186
                                       788888888882.....34444555444....7777777776 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.016        29       3      25 ..       2      24 ..       1      30 [. 0.87
   2 !   25.5   0.0   5.5e-09   9.9e-06     132     192 ..     129     188 ..     118     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.016
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvral 25
                                      i ++g   g GK++v+lgL  a+
  gi|336254177|ref|YP_004597284.1|  2 IAIAGSKGGCGKSTVTLGLSTAF 24
                                      679999*************9887 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 5.5e-09
                            AAA_26 132 ilVarggl.gtinqllltiealrqknvrvlGvilNkvrnpenvetlekksgipvlGvvPylp 192
                                       ++V++g++ ++++++ +ti+++r+ +v+v G +lN+    +  + + +  g+p+lG+vP  p
  gi|336254177|ref|YP_004597284.1| 129 VIVVAGDSeRSLEAAETTIDVARRLGVPVYGAVLNR--RSAVPDRAAEWRGVPILGCVPDRP 188
                                       55666655389************************9..566799999************877 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 !   28.4   0.0   5.6e-10     1e-06       5     176 ..       1     166 [.       1     176 [. 0.76

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.6e-10
                              ParA   5 viavlSgKGGVGKStvavnlAlaLakkg.lkvgl.lDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSig 79 
                                       +ia++ +KGG GKStv+  l++a+a+ + l+ ++ +DaD   p++  +++ ++e p+      +    +g+++  i+
  gi|336254177|ref|YP_004597284.1|   1 MIAIAGSKGGCGKSTVTLGLSTAFARGEpLTPAIaIDADRQLPNLHVMTDRDRE-PT------LAALERGVTLKEIA 70 
                                       599*********************965514444437999887777777776664.33......33345677777777 PP

                              ParA  80 fllesedeavvwrGpmkskaik..qllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvk 154
                                          + e++  +  +p+ s a +   l  +++ +   + ++D+P G g   +  + +   +g+++V+   e +l+ ++
  gi|336254177|ref|YP_004597284.1|  71 QEHPCESTVGIVSAPKPSDAFEfdSLADHADLEGTQV-LLDCPAGAGPDLVEPLRSA--DGVIVVAGDSERSLEAAE 144
                                       7777667777889999888864226666666666665.57*******8766666555..7***************** PP

                              ParA 155 kaiemfkkvkvkvlGvveNmsg 176
                                        +i++++++ v+v G v N   
  gi|336254177|ref|YP_004597284.1| 145 TTIDVARRLGVPVYGAVLNRRS 166
                                       *****************99665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.5e-07   0.00063      37      95 ..       4      62 ..       1     101 [. 0.83
   2 ?   -3.6   0.0       3.9     7e+03      25      42 ..     119     136 ..     117     151 .. 0.83
   3 ?    1.3   0.1      0.13   2.2e+02      21      43 ..     231     253 ..     210     255 .. 0.69
   4 !    6.0   0.5    0.0043       7.6      67     154 ..     262     330 ..     244     338 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.5e-07
                            AAA_25 37 llaGapgtGKttlaldlalavatGkpwlg...pvapeqgkVlyvsaEdsedelrrRlravge 95
                                      +    +g+GK+t++l l+ a a+G+p++    + a +q + l v ++ ++   ++ l+a+ +
  gi|336254177|ref|YP_004597284.1|  4 IAGSKGGCGKSTVTLGLSTAFARGEPLTPaiaIDADRQLPNLHVMTDRDR---EPTLAALER 62
                                      556689*********************99997556699999999999988...566665555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.9
                            AAA_25  25 lvkgllpagelallaGap 42 
                                       lv+ l+ a++++++aG++
  gi|336254177|ref|YP_004597284.1| 119 LVEPLRSADGVIVVAGDS 136
                                       788888888888888875 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.13
                            AAA_25  21 prrwlvkgllpagelallaGapg 43 
                                        ++  ++g lpag++++l+++p+
  gi|336254177|ref|YP_004597284.1| 231 ALDRHLEGGLPAGSVVALVADPA 253
                                       4555566777**********997 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0043
                            AAA_25  67 vapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegv 143
                                       +a+e + +ly+s+ +s++++rr ++ + +++   ++ ++  +ag                + ++++  a +e  +++
  gi|336254177|ref|YP_004597284.1| 262 RATELRGTLYLSTAQSRETVRRAIETTAADA---GEPTIRRVAG----------------DDALEEATALVENLPDA 319
                                       6778899999999999977777777666665...6666666555................46678888999999999 PP

                            AAA_25 144 rlvviDplsra 154
                                       + +++Dp++++
  gi|336254177|ref|YP_004597284.1| 320 ATLIVDPVNEL 330
                                       99999999875 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.4e-06    0.0042       3      44 ..       1      44 [.       1      86 [. 0.68
   2 ?    3.9   0.0     0.025        45     121     162 ..     107     148 ..      93     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.4e-06
                            AAA_31  3 vIaianqKGGvGKTTtsvnlaaalaklg..kkvLlvDlDpQana 44
                                      +Iaia  KGG GK+T ++ l+ a+a+ +     + +D+D Q   
  gi|336254177|ref|YP_004597284.1|  1 MIAIAGSKGGCGKSTVTLGLSTAFARGEplTPAIAIDADRQLPN 44
                                      59***********************6552266789999999633 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.025
                            AAA_31 121 iiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllk 162
                                       +++Dcp   g  ++  L ++d vi++   ++++le +e  ++
  gi|336254177|ref|YP_004597284.1| 107 VLLDCPAGAGPDLVEPLRSADGVIVVAGDSERSLEAAETTID 148
                                       89***************************99**999887766 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 !   11.6   0.0   7.8e-05      0.14      60     114 ..     123     208 ..      85     213 .. 0.70
   2 !    7.8   0.0    0.0011         2     122     194 ..     278     369 ..     269     393 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.8e-05
                                       HTTCS........HHHHHHHHHHHHHHHHHHTBSEEEEEBCC.......................GBCTTTSGHHHH CS
                      AP_endonuc_2  60 erear........reesvdalkraielaaaLGapllvlhpGt.......................agagpkgseeea 105
                                       +r+a+        +e+s++a++ +i+ a++LG+p+      +                        + +++++ ++a
  gi|336254177|ref|YP_004597284.1| 123 LRSADgvivvagdSERSLEAAETTIDVARRLGVPVYGAVLNRrsavpdraaewrgvpilgcvpdrPSPLANDEVAAA 199
                                       4555556666667889***************8888766655566666666666666666666555667777777788 PP

                                       HHHHHHHHH CS
                      AP_endonuc_2 106 werlaesln 114
                                       ++ ++e+l+
  gi|336254177|ref|YP_004597284.1| 200 FDDIVERLR 208
                                       888888876 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0011
                                       HHTSEEEEE--TTTTSSSTC.........HHHHHHHHHHTTTTEEEEEEHHHHHHH..TTTHHHHHHHHHGG..... CS
                      AP_endonuc_2 122 kegvklalEtlagsgvelgd.........eelarlldavdspnvgvclDtgHllia..eedvddalraladr..... 182
                                       +e v+ a+Et+a +  e+           ee+ +l++ +++    +  D+ + l +  +  + ++l++l +r     
  gi|336254177|ref|YP_004597284.1| 278 RETVRRAIETTAADAGEPTIrrvagddalEEATALVENLPD-AATLIVDPVNELERreRSAYVSFLDTLSERlaetg 353
                                       6789999*****9999999999******************7.5*************99999999999999999999* PP

                                       .EEEEEE.EESS...T CS
                      AP_endonuc_2 183 .ikhvHikDakg...d 194
                                        ++++H+ D ++   +
  gi|336254177|ref|YP_004597284.1| 354 gLAILHCLDLDDpanR 369
                                       ******9998885540 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.6e-07   0.00029       3     132 ..       2     136 ..       1     146 [. 0.81
   2 ?   -2.5   0.0       1.4   2.4e+03      63     122 ..     317     375 ..     297     381 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.6e-07
                                       EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T.TT-HHHHHHHHHHHH....HHHHT------EEE-SSS-H CS
                              MipZ   3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldl.rqrtlarylenraat....aerkglsLplpealalseae 74 
                                       i ++  kGG Gkst+++ + +a+++      ai +d+ rq    + + +r       a ++g++L++    +  e+ 
  gi|336254177|ref|YP_004597284.1|   2 IAIAGSKGGCGKSTVTLGLSTAFARGEPLTPAIAIDAdRQLPNLHVMTDRDREptlaALERGVTLKEIAQEHPCEST 78 
                                       788999******************99999999999975888888999888654111134567777776666666677 PP

                                       HHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEESS CS
                              MipZ  75 eaeveeeeeaevaeleelvadleaeldfividtPGsdsalsrlahsladtlvtPlnds 132
                                       +  v+ ++  +  e++ l++++  e   +++d+P    +        ad ++    ds
  gi|336254177|ref|YP_004597284.1|  79 VGIVSAPKPSDAFEFDSLADHADLEGTQVLLDCPAGAGPDLVEPLRSADGVIVVAGDS 136
                                       7788999999999*********************999888888888888887766665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                                       ---EEE-SSS-HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT- CS
                              MipZ  63 plpealalseaeeaeveeeeeaevaeleelvadleaeldfividtPGsdsalsrlahsla 122
                                       p + +l ++ ++e e  +e +a+v+ l++l ++l+++  + ++ +   d++  r a  +a
  gi|336254177|ref|YP_004597284.1| 317 PDAATLIVDPVNELE-RRERSAYVSFLDTLSERLAETGGLAILHCLDLDDPANRAATLRA 375
                                       333333333333322.23445556667777777888888888888888888777776554 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.6   2.8e+03      26      46 ..     195     218 ..     187     250 .. 0.65
   2 ?   15.0   1.1   1.2e-05     0.021       3      80 ..     277     365 ..     275     379 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.6
                    Acetyltransf_6  26 tdpedleallelfraqwarr...p 46 
                                       + +++++ ++e++raq  r    p
  gi|336254177|ref|YP_004597284.1| 195 EVAAAFDDIVERLRAQSPRErapP 218
                                       445666777777777665554442 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.2e-05
                    Acetyltransf_6   3 rRknlrrkrrklee.lgevrfrvatdpedleallelfraqwarr.........pdvfadpltraflrdllaalaa.r 68 
                                        R+++rr++   ++ +ge ++r+ +++++le++ +l++++  +           +   + ++ +fl  l ++la+ +
  gi|336254177|ref|YP_004597284.1| 277 SRETVRRAIETTAAdAGEPTIRRVAGDDALEEATALVENLPDAAtlivdpvneLERRERSAYVSFLDTLSERLAEtG 353
                                       699*******9987699********************888555557777775433334567889***********45 PP

                    Acetyltransf_6  69 galrlyvlrldg 80 
                                       g + l++l ld+
  gi|336254177|ref|YP_004597284.1| 354 GLAILHCLDLDD 365
                                       556688888876 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 ?   12.5   0.0   5.1e-05     0.092       4      62 ..     119     178 ..     118     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-05
                                       HHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EE.EEEGGGTTSS-TTSTTEEEE CS
                      TPP_enzyme_M   4 aaellkaakrpvilvGggvarsgaseelrelaeklgiPv.vttlmgkgvipedhplylgm 62 
                                       ++e l++a  +++++G   ++ +a+e   ++a++lg+Pv    l+ ++++p++   + g+
  gi|336254177|ref|YP_004597284.1| 119 LVEPLRSADGVIVVAGDSERSLEAAETTIDVARRLGVPVyGAVLNRRSAVPDRAAEWRGV 178
                                       5778999999999999999999*****************6677788*****999888774 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00036      0.65       3      52 ..       1      51 [.       1      72 [. 0.70
   2 ?    1.2   0.0      0.12   2.1e+02     118     145 ..     106     133 ..      91     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00036
                          CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhelge..svlviDlspdnlL.rlhFnvdi 52
                                      ++a+ G +GG+G+++++ +L++a+ + +     ++iD+  d +L +lh  +d 
  gi|336254177|ref|YP_004597284.1|  1 MIAIAGSKGGCGKSTVTLGLSTAFARGEPltPAIAIDA--DRQLpNLHVMTDR 51
                                      5899********************98765114455554..4433255555555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                          CBP_BcsQ 118 willDlpagasaltrellaladlvllvv 145
                                        +llD+paga +   e l+ ad v+ v+
  gi|336254177|ref|YP_004597284.1| 106 QVLLDCPAGAGPDLVEPLRSADGVIVVA 133
                                       69*********99999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3136.44
//
Query:       gi|336254178|ref|YP_004597285.1|  [L=423]
Description: hypothetical protein Halxa_2790 [Halopiger xanaduensis SH-6]
Scores for 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   0.8       0.11   12.6   0.1    2.0  2  RcpC          Flp pilus assembly protein RcpC/CpaB
        1.3    8.5   6.0        2.1    7.8   6.0    1.2  1  5TM-5TMR_LYT  5TMR of 5TMR-LYT


Domain annotation for each model (and alignments):
>> RcpC  Flp pilus assembly protein RcpC/CpaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.2e-05      0.11       3     105 ..     207     312 ..     205     315 .. 0.63
   2 ?   -2.8   0.1      0.73   6.5e+03      11      25 ..     381     395 ..     378     406 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
                              RcpC   3 laavlppgkrAvaievdevtgvaglirpGdrVDVlltesekedsesektvaelllqnvrVLavgq...........e 68 
                                       +a+ l++g rAv+++    tg    i+ GdrV + ++   +++s+++ ++++  l+   VLav +           +
  gi|336254178|ref|YP_004597285.1| 207 VATSLSDGARAVTVSGLLPTG----IESGDRVAIGVV---SGGSDGDGSAVTATLEG-DVLAVCRsesaedgasnaR 275
                                       788999999999999886665....899*********...66666666666666655.7999999665555433221 PP

                              RcpC  69 eakkreeedeekkke...........aetastvtLevtpeqaekLala 105
                                            +++      +           +  +  +t+ v   +a +L+ a
  gi|336254178|ref|YP_004597285.1| 276 -----SSS------RstasraadagfEGGPGRLTVRVAASDAGRLLGA 312
                                       .....111......1122222333333335667888888888777766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.73
                              RcpC  11 krAvaievdevtgva 25 
                                       +r v++++ +++g++
  gi|336254178|ref|YP_004597285.1| 381 NRDVTVDTADDNGAS 395
                                       678888888888876 PP

>> 5TM-5TMR_LYT  5TMR of 5TMR-LYT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.0   0.00023       2.1      55     132 ..      15      89 ..       9     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00023
                      5TM-5TMR_LYT  55 GllgGplvGliagliaglhRyllgGftalacgistilagllaGlihrklkrrr.kkltvlvalligllveilqmlli 130
                                       Gll+G+ ++l+ag++a+++ +       la+g++t+ +++ +G+++r +  ++  +  ++va++ ++++ +     i
  gi|336254178|ref|YP_004597285.1|  15 GLLFGFGPALLAGFTAIAVGIGTDRSLPLAAGLATVPIAVGTGVVVRLFDPSAgLEHGPRVAMAATIAGAL----GI 87 
                                       9******************998888999*********************9877888888888888888664....22 PP

                      5TM-5TMR_LYT 131 ll 132
                                       ++
  gi|336254178|ref|YP_004597285.1|  88 VV 89 
                                       22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); 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:                         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: 0.53u 0.20s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3293.03
//
Query:       gi|336254179|ref|YP_004597286.1|  [L=412]
Description: hypothetical protein Halxa_2791 [Halopiger xanaduensis SH-6]
Scores for 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   14.8   0.0      0.039   13.8   0.0    1.6  1  TrkA_C    TrkA-C domain


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 ?   13.8   0.0   2.2e-06     0.039       4      68 ..     335     395 ..     332     397 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-06
                                       EEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                            TrkA_C   4 vtvpagsplvGktlkelnlrargvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                       +tv +g  lvG  ++   l+    +v+ + R+ ++ ++p++  +Le+GD+ ++++sp++la+l+++
  gi|336254179|ref|YP_004597286.1| 335 LTVEPGGSLVGEFVGW--LPG---RVLVLERDgDRQPLPPDRRTLEAGDECWLLASPAELAALEAE 395
                                       6777777777777777..777...6677777778****************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3143.94
//
Query:       gi|336254180|ref|YP_004597287.1|  [L=137]
Description: hypothetical protein Halxa_2792 [Halopiger xanaduensis SH-6]
Scores for 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:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1097.09
//
Query:       gi|336254181|ref|YP_004597288.1|  [L=227]
Description: cobyrinic acid a,c-diamide synthase [Halopiger xanaduensis SH-6]
Scores for 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-10   38.7   2.3    3.8e-05   23.3   0.3    2.4  3  ParA         NUBPL iron-transfer P-loop NTPase
    2.4e-09   37.3   0.0    3.1e-09   37.0   0.0    1.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    8.6e-08   32.3   0.0     0.0021   18.0   0.2    2.1  2  AAA_31       AAA domain
    1.5e-06   27.9   0.1     0.0085   15.6   0.0    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    1.6e-06   27.7   2.9    5.8e-05   22.7   0.2    2.7  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
     0.0001   21.7   0.3       0.06   12.6   0.0    2.2  2  MipZ         ATPase MipZ
    0.00021   21.5   0.8      0.002   18.3   0.8    2.3  1  AAA_33       AAA domain
  ------ inclusion threshold ------
       0.12   11.5   0.6       0.21   10.7   0.6    1.4  1  ArsA_ATPase  Anion-transporting ATPase


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 !   23.3   0.3   1.7e-08   3.8e-05       5      48 ..       2      40 ..       1      57 [. 0.83
   2 !   14.8   0.1   6.6e-06     0.015     113     173 ..     101     159 ..      96     167 .. 0.82
   3 ?   -2.4   0.0       1.2   2.7e+03     204     243 ..     176     218 ..     157     220 .. 0.56

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.7e-08
                              ParA  5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsip 48
                                      ++av+ gKGGVGKSt+a nl  +L +      ++D D+  p++p
  gi|336254181|ref|YP_004597288.1|  2 IVAVAGGKGGVGKSTTAWNLGRELDA-----VVVDGDLAVPDLP 40
                                      799*****************988853.....4666666666555 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6.6e-06
                              ParA 113 DyLiiDlPPGtg.DeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                       D +++D+P G + D+ + +      + av+Vttp ++al d+ ++ +++ ++++++ + v N
  gi|336254181|ref|YP_004597288.1| 101 DHVVVDCPAGLArDVGVELG---CADLAVLVTTPSRAALVDAIRTSDLVASLETPLGAAVLN 159
                                       88999999996536655543...34679************************9998777766 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.2
                              ParA 204 pllgeipldpeireasdeg...kplvlkepeseaakaleeiae 243
                                       +l  ++ l  e +  +d++   +p+  ++p+++a +a++++a+
  gi|336254181|ref|YP_004597288.1| 176 RLGVDVTLVAEQAAVADAQarwQPVRDHRPDAQAVDAYRAVAD 218
                                       4444555544443333333111557777777777777777776 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 !   37.0   0.0   1.4e-12   3.1e-09       1     127 [.       3     199 ..       3     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.4e-12
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH......HTTEB-HHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxx................. RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai......leglendiep................. 54 
                                       +a+a++kGGvGK+t+a nL+r l       ++vD D   + l +                                 
  gi|336254181|ref|YP_004597288.1|   3 VAVAGGKGGVGKSTTAWNLGRELDA-----VVVDGDLAVPDLPSgpdagpD--------Lhdvlagradpleavada 66 
                                       69*******************8887.....************954433330........24466777778999**** PP

                                       .......................................................................CCHCCC CS
                                       .......................................................................xxxxxx RF
                              CbiA  55 .......................................................................dlkrll 60 
                                                                                                              d++r +
  gi|336254181|ref|YP_004597288.1|  67 gpvsvlpsgrtlsgarasslealpsvldrlerrwdhvvvdcpaglardvgvelgcadlavlvttpsraalvDAIRTS 143
                                       ***************************************************************************** PP

                                       HHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  61 ellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                        l+++l ++      +   vln+ d + ++  l + l +++   gv v  ++ +  ava+a ar +p
  gi|336254181|ref|YP_004597288.1| 144 DLVASLETP------LGAAVLNKADRD-THSDLADRLGRRL---GVDVT-LVAEQAAVADAQARWQP 199
                                       *******98......7899****9988.4555666666655...99996.89999999999888666 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   9.6e-07    0.0021       3      26 ..       2      25 ..       1      36 [. 0.91
   2 !   12.3   0.0   5.1e-05      0.12      90     154 ..      78     136 ..      41     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.6e-07
                            AAA_31  3 vIaianqKGGvGKTTtsvnlaaal 26
                                      ++a+a  KGGvGK+Tt+ nl+  l
  gi|336254181|ref|YP_004597288.1|  2 IVAVAGGKGGVGKSTTAWNLGREL 25
                                      799*****************9987 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.1e-05
                            AAA_31  90 LaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayal 154
                                       L++a        ++ e+l ++l++++ ++D +++Dcp  L   +   L  +d  + ++ ++  al
  gi|336254181|ref|YP_004597288.1|  78 LSGARA------SSLEALPSVLDRLERRWDHVVVDCPAGLARDVGVELGCADLAVLVTTPSRAAL 136
                                       444433......335678999*******************9999999999999999888877665 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 !   10.4   0.1   0.00014      0.32       6      24 ..       7      25 ..       1      30 [. 0.79
   2 !   15.6   0.0   3.8e-06    0.0085     174     247 ..     151     223 ..     115     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                         Fer4_NifH  6 yGkGGiGksttsqnlsaal 24
                                       GkGG+Gkstt+ nl   l
  gi|336254181|ref|YP_004597288.1|  7 GGKGGVGKSTTAWNLGREL 25
                                      38************98766 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.8e-06
                         Fer4_NifH 174 vrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilen 247
                                         lg  + n+ + d++++l++++ ++lg++v   v  +  v  a++r + v ++ p+++  + yr++a+++  +
  gi|336254181|ref|YP_004597288.1| 151 TPLGAAVLNKADRDTHSDLADRLGRRLGVDV-TLVAEQAAVADAQARWQPVRDHRPDAQAVDAYRAVADRLERA 223
                                       45889999*999999**************97.689999******************************998765 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.011        26       3      28 ..       2      27 ..       1      34 [. 0.90
   2 !   22.7   0.2   2.6e-08   5.8e-05      99     231 ..      83     218 ..      68     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.011
                          CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhe 28
                                      ++a+ G +GGvG+++ +  L++ l++
  gi|336254181|ref|YP_004597288.1|  2 IVAVAGGKGGVGKSTTAWNLGRELDA 27
                                      7899*****************99976 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 2.6e-08
                          CBP_BcsQ  99 aekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdanchvrLhqqa.lpaaellLiNqfeaa 174
                                       a++ eal + l++l+++++ +++D+pag ++ +   l  adl +lv++p  ++ v   + + l a+    +    + 
  gi|336254181|ref|YP_004597288.1|  83 ASSLEALPSVLDRLERRWDHVVVDCPAGLARDVGVELGCADLAVLVTTPSRAALVDAIRTSdLVASLETPL-GAAVL 158
                                       4667899999*********************99999999***********999875444331333322222.34556 PP

                          CBP_BcsQ 175 sqlqqDllqlWlqslrrllPl...vihrDealaEalaakqPlgeyrpdslaaeevktLan 231
                                        +  +D +    + l r+l +   ++ + +a+a+a a  qP+ + rpd++a+ + + +a 
  gi|336254181|ref|YP_004597288.1| 159 NKADRDTHSDLADRLGRRLGVdvtLVAEQAAVADAQARWQPVRDHRPDAQAVDAYRAVAD 218
                                       78889999999999988887755568899**********************999888776 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0012       2.7       2      21 ..       2      21 ..       1      34 [. 0.85
   2 !   12.6   0.0   2.7e-05      0.06      84     135 ..      84     138 ..      65     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0012
                                      EEEE--SSTTSSHHHHHHHH CS
                              MipZ  2 vivlgnekGGsGksttavhv 21
                                      ++ ++  kGG Gkstta  +
  gi|336254181|ref|YP_004597288.1|  2 IVAVAGGKGGVGKSTTAWNL 21
                                      6789999*********9765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEE...EEEESSHHH CS
                              MipZ  84 aevaeleelvadleaeldfividtPGsdsalsrlahsladtlv...tPlndsfvd 135
                                        + ++l  ++++le++ d +v+d+P    + + +    ad  v   tP   ++vd
  gi|336254181|ref|YP_004597288.1|  84 SSLEALPSVLDRLERRWDHVVVDCPAGLARDVGVELGCADLAVlvtTPSRAALVD 138
                                       445689999****************999999988888888633223787777777 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.8   8.9e-07     0.002       4      33 ..       6      59 ..       3     220 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.9e-07
                            AAA_33  4 lvGlpGsGKstlaerllkklgavllssdt........................l 33
                                        G  G+GKst a++l ++l+av+++ d                          
  gi|336254181|ref|YP_004597288.1|  6 AGGKGGVGKSTTAWNLGRELDAVVVDGDLavpdlpsgpdagpdlhdvlagradP 59
                                      56999***********************95555555555555544444333331 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   9.6e-05      0.21       5      23 ..       5      23 ..       1      30 [. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.6e-05
                                      EEEESTTSSHHHHHHHHHH CS
                       ArsA_ATPase  5 lvgGKGGVGKttvsaatav 23
                                      + gGKGGVGK+t +  ++ 
  gi|336254181|ref|YP_004597288.1|  5 VAGGKGGVGKSTTAWNLGR 23
                                      679*********9877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1800.45
//
Query:       gi|336254182|ref|YP_004597289.1|  [L=324]
Description: aryl-alcohol dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-72  242.8   0.0    4.7e-72  242.7   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family


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 !  242.7   0.0   2.6e-76   4.7e-72       1     291 [.      15     313 ..      15     316 .. 0.95

  Alignments for each domain:
  == domain 1  score: 242.7 bits;  conditional E-value: 2.6e-76
                                       .EEEE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE... CS
                      Aldo_ket_red   1 elglGtwqlgsk....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv... 70 
                                       +++lG +++g++    ++  +ee+ e+++ra++ GinffDtA++Y kg+se+++G+al+     ree ++atK+   
  gi|336254182|ref|YP_004597289.1|  15 RICLGCMSFGDPdwreWVLGEEESTEIIERAIDLGINFFDTANMYSKGESERIFGNALEG---YREESVVATKGyfq 88 
                                       59*********9************************************************...***********997 PP

                                       --SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--.HHHH CS
                      Aldo_ket_red  71 dlrdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfs.veql 146
                                          d++++ gls++ ++++le+sl rLg d vDl+++Hr+d ++p ie +l+al++ v+ G +r++G S+   ++  
  gi|336254182|ref|YP_004597289.1|  89 MREDDPNSGGLSRKAVEQELEASLDRLGMDAVDLYQIHRWDDDTP-IETTLQALDDAVRRGQVRYVGASSMWaHQFA 164
                                       6778899999***********************************.***********************65526667 PP

                                       HHH...HHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------. CS
                      Aldo_ket_red 147 eka...kkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd. 219
                                       e++    + +  ++++ q++ynl+ ++ee+++l+lc+k+gv+++++spl++G+l +  ++ + + ++e++++l ++ 
  gi|336254182|ref|YP_004597289.1| 165 ESLytsDRLGLERFATMQNHYNLVYREEEREMLPLCEKEGVGVMPWSPLARGYLARPHEEIDATTRGETEEHLYEHp 241
                                       7778866666677***********************************************************99999 PP

                                       TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS
                      Aldo_ket_red 220 ertsknldaaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaelde 291
                                        r  + ++ +e++ ela+e+gv++aq+al+++l+++ v  +i+g++++e+le+ ++ale+ ls++++a+l+e
  gi|336254182|ref|YP_004597289.1| 242 YREGGGQEINERVAELAAEKGVTMAQIALSWLLHKDWVDAPIVGTTSVEHLEQAVEALEISLSASDIAYLEE 313
                                       9999*****************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2705.67
//
Query:       gi|336254183|ref|YP_004597290.1|  [L=226]
Description: TenA family transcriptional activator [Halopiger xanaduensis SH-6]
Scores for complete 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  172.0   1.1    1.7e-50  171.8   1.1    1.0  1  TENA_THI-4       TENA/THI-4/PQQC family
  ------ inclusion threshold ------
      0.019   14.8   1.4      0.032   14.0   1.4    1.5  1  Haem_oxygenas_2  Iron-containing redox enzyme


Domain annotation for each model (and alignments):
>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.8   1.1   1.9e-54   1.7e-50       5     209 ..      12     214 ..       8     215 .. 0.96

  Alignments for each domain:
  == domain 1  score: 171.8 bits;  conditional E-value: 1.9e-54
                                       HHHHHHHHCSHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCHHHHHHH CS
                        TENA_THI-4   5 rpiwkeyinHpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgeeielhlr 81 
                                       +++w+    HpFv+ la Gtl  e f ++v qdy yl +++rv+ai++ k+ d+e++  l  ++ +++  e++lh++
  gi|336254183|ref|YP_004597290.1|  12 EQLWEAQKDHPFVRELAAGTLAEEAFLHWVRQDYRYLLDYARVFAIAGTKARDEETMTHLLGVAHEILDFEMDLHRE 88 
                                       678887888******************************************************************** PP

                                       HHHHTT-HHHHHCTTT--HHHHHHHHHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHHS-TSCHHHHHHHHH CS
                        TENA_THI-4  82 laealGlsreelsktkpspatkayvrylldlarrgslaeavaallpclfvyqeiaerlkeklralegpeyyewvkey 158
                                       +a  +G+++ +l++++  p++ ay++yl+++a +gslae++aa +pc  +y  +ae+++e+ +  ++++y++++++y
  gi|336254183|ref|YP_004597290.1|  89 FAADYGVDPADLEAVEKAPTCVAYTNYLVRTAHEGSLAEIAAAIYPCGQGYLDVAEHMAEIAT-DDENPYQPFINKY 164
                                       ***********************************************************9999.66666******** PP

                                       CSHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                        TENA_THI-4 159 aseefraaveeakrllerllakvsdeqleelqeiflkalefetsfltmald 209
                                       +s+efr+av++ ++ ++r+ + +++e  ++++e fl++ ++e +f+ ma++
  gi|336254183|ref|YP_004597290.1| 165 TSDEFREAVDWMRAFVDRCGERYPGE-HDAMREAFLTSAKLEHQFWEMAYT 214
                                       **********************9997.9*********************96 PP

>> Haem_oxygenas_2  Iron-containing redox enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.4   3.6e-06     0.032       2     130 ..      39     156 ..      38     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-06
                   Haem_oxygenas_2   2 eflrqrapyklvfgdwlalvhsrltdrevkrallenlsEElGdgdlernHvelyrrllkalGldeeplealpelpet 78 
                                       +++rq + y l+ ++++a +  + +d+e    ll + +E l d +       l r+++++ G+d+++lea +++p+ 
  gi|336254183|ref|YP_004597290.1|  39 HWVRQDYRYLLDYARVFAIAGTKARDEETMTHLLGVAHEIL-DFE-----MDLHREFAADYGVDPADLEAVEKAPTC 109
                                       89999999999999999999999999999999999999999.555.....6999*********************** PP

                   Haem_oxygenas_2  79 lalinlfeavalsrrllgallGallalEllvsletlklaeelrelgldeeap 130
                                        a+ n++ + ++++  l+++++a +       + +l +ae + e+  d+e+p
  gi|336254183|ref|YP_004597290.1| 110 VAYTNYLVR-TAHEGSLAEIAAAIY----PCGQGYLDVAEHMAEIATDDENP 156
                                       *****9764.555555555666655....33577888888888877777763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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 0.19s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1819.66
//
Query:       gi|336254184|ref|YP_004597291.1|  [L=66]
Description: hypothetical protein Halxa_2796 [Halopiger xanaduensis SH-6]
Scores for 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:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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: 0.34u 0.20s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 565.99
//
Query:       gi|336254185|ref|YP_004597292.1|  [L=131]
Description: signal transduction protein with CBS domains [Halopiger xanaduensis SH-6]
Scores for complete 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   3.1      3e-11   43.6   0.4    2.1  2  CBS           CBS domain
  ------ inclusion threshold ------
       0.11   12.0   0.0        1.5    8.2   0.0    2.0  2  His_biosynth  Histidine biosynthesis protein


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 !   43.6   0.4   3.4e-15     3e-11      10      55 ..       2      46 ..       1      48 [. 0.89
   2 !   40.2   0.1   3.8e-14   3.4e-10       1      54 [.      57     110 ..      57     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 3.4e-15
                                      EEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS 10 vtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      vt++pdt+le ++e+++++ v+++ V+ +d+k+vGivt+rD++ al
  gi|336254185|ref|YP_004597292.1|  2 VTASPDTDLETIAERLESEQVGAI-VITDDEKPVGIVTDRDIALAL 46
                                      8***************6666****.8767889**********9987 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 3.8e-14
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V+ +mt+d+ t++ d+   e+ + ++e++v+r+PVVdedgk+ Gi t  Dl+  
  gi|336254185|ref|YP_004597292.1|  57 VEGVMTEDPATLRSDEEPIEISRAIEEHNVRRFPVVDEDGKPEGIATFDDLVAT 110
                                       6679***********************************************875 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.013   1.2e+02     146     168 ..       7      29 ..       3      47 .. 0.86
   2 ?    8.2   0.0   0.00017       1.5      21      72 ..      64     115 ..      42     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.013
                                       EEEHHHHHHHHHHTT-SEEEEEE CS
                      His_biosynth 146 gldavelakkleelgageilltd 168
                                       + d++ +a++le+ ++g+i++td
  gi|336254185|ref|YP_004597292.1|   7 DTDLETIAERLESEQVGAIVITD 29 
                                       5689999*************998 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00017
                                       STCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH- CS
                      His_biosynth  21 rfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeev 72 
                                          +lr  ++p+e+ ++ ee++++++ vvD d+  eg  +  dlv+++ e++
  gi|336254185|ref|YP_004597292.1|  64 DPATLRSDEEPIEISRAIEEHNVRRFPVVDEDGKPEGIATFDDLVATLGEQL 115
                                       456788999**********************************999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1077.74
//
Query:       gi|336254186|ref|YP_004597293.1|  [L=455]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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  59.5    1.8e-17   63.3  40.8    2.4  2  MFS_1     Major Facilitator Superfamily


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 !   63.3  40.8     1e-21   1.8e-17       2     327 ..      12     339 ..      11     346 .. 0.69
   2 !   22.8  11.7   2.2e-09   3.9e-05      69     172 ..     336     444 ..     330     452 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 1e-21
                             MFS_1   2 llaaflsalarsilgpalplalaed..........lgispse...igllltlyalgaavaslplGrlsdrfGrrrvl 65 
                                       +l+ f  ++++ +l ++lp ++ +           lg++ s+   +gl ++++++++ va++pl++ +drf  r vl
  gi|336254186|ref|YP_004597293.1|  12 YLSRFAEGFGFITLVTLLPYYI-NVleptdttlpvLGLTISAgliVGLYTSGFTIAQTVAVVPLAWAGDRFDKRTVL 87 
                                       6778889999999999999644.33123334444433333334469999999*******************888888 PP

                             MFS_1  66 llglllfalg.lllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllg 141
                                       l+ l l a+  +l+++ + s+ +++++r+lqG+   ++  +g++l+ +++    r+ +ig ++a++ +++i+g l +
  gi|336254186|ref|YP_004597293.1|  88 LVVLGLGAAVyALFPI-VDSSATFIAMRALQGIVVTGSGLMGLSLVGQIADVGTRANYIGKANAANFAASIVGSLSA 163
                                       8888888888344444.366669****************************************************** PP

                             MFS_1 142 gllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialll 218
                                       g l++++g+  +f i+a++++++ +     ++  +p++ r+ +            +p ++ l  ++ +  l ++++ 
  gi|336254186|ref|YP_004597293.1| 164 GSLYEAFGFGPIFTIIAALMVVGWI---GTMRYLEPDETRVYG------------FP-FSDLALNRRI--LTLSSFR 222
                                       **********************977...333333333333322............23.5556667744..3444443 PP

                             MFS_1 219 f..ffgfsglltllplylqevlgls.glllaglllallalvgail....allagrlsdrlgrrrrlllallllllaa 288
                                       f  +f+++++ t++p++   v   s gl ++gl+++l+ ++  +     ++++grlsd +gr  + + ++++  l+a
  gi|336254186|ref|YP_004597293.1| 223 FqyAFAVTLVRTWVPIF-AGVSAASgGLAYGGLAVSLTVAMEKFTnmccQPFTGRLSDGYGRALFVFAGGGAYGLVA 298
                                       33344555599999998.4444444555555544444444433335555************9777777777777777 PP

                             MFS_1 289 lglallavtssavllllvlvl..iGfglgfvfpsllalasd 327
                                       l++ +++ +  av +  ++vl    + +g+v p +l l  +
  gi|336254186|ref|YP_004597293.1| 299 LLVPFAPGIGAAVGAPSAIVLgvPDVLAGLVLPGWLPLSLE 339
                                       77777776633332222333343455555556666555555 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 2.2e-09
                             MFS_1  69 lllfalglllllfa..sslw.lllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllg 141
                                       l l a+ + l lf+  s+ + +l++l  l G++ ++  pa++al+ad  ++    ++ +g+  + +  G++++pllg
  gi|336254186|ref|YP_004597293.1| 336 LSLEAIPAQLTLFGevSPAFlPLVALSGLLGIADSFREPASMALFADEGTEdGGVASSFGIRELIWRPGSVVAPLLG 412
                                       5566777555667555666669*************************999978999999****************** PP

                             MFS_1 142 gllasslgWravfyilaivsllafv.lfllll 172
                                       g+l+  +g  +vfy+ ++++l ++  +f++l+
  gi|336254186|ref|YP_004597293.1| 413 GWLMYEIGMASVFYVGGAFALTGVAtFFVILV 444
                                       **********************9665444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 3700.12
//
Query:       gi|336254187|ref|YP_004597294.1|  [L=1140]
Description: formate dehydrogenase subunit alpha [Halopiger xanaduensis SH-6]
Scores for 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-80  269.7   0.0    5.6e-80  269.4   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    2.8e-28   98.1   0.1    5.5e-28   97.2   0.1    1.5  1  Molydop_binding  Molydopterin dinucleotide binding domain
    8.6e-24   83.4   0.2    2.1e-23   82.2   0.2    1.7  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
    2.1e-12   46.4   1.8    2.1e-12   46.4   1.8    2.2  1  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
    1.4e-11   44.2   0.3    1.4e-11   44.2   0.3    2.3  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
    3.8e-10   39.4  20.2    4.9e-07   29.5   1.0    3.4  2  Fer4_6           4Fe-4S binding domain
    4.4e-09   36.3   8.3    4.4e-09   36.3   8.3    3.2  3  Fer4_21          4Fe-4S dicluster domain
    1.2e-08   35.3   9.9    1.2e-08   35.3   9.9    4.0  3  Fer4_7           4Fe-4S dicluster domain
    4.6e-08   32.6  12.9    8.9e-07   28.5   1.4    3.7  4  Fer4             4Fe-4S binding domain
    4.2e-07   30.0   6.2    4.2e-07   30.0   6.2    4.0  3  Fer4_9           4Fe-4S dicluster domain
    3.1e-05   24.0  22.5    0.00029   20.9  14.1    4.2  4  Fer4_10          4Fe-4S dicluster domain
    7.3e-05   23.1   8.6    7.3e-05   23.1   8.6    3.5  3  Fer4_8           4Fe-4S dicluster domain
     0.0001   23.0  12.0      0.015   16.1   0.6    4.3  3  Fer4_15          4Fe-4S single cluster domain
    0.00032   21.2   8.5      0.082   13.5   0.4    3.1  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
    0.00058   20.7   0.3    0.00058   20.7   0.3    4.1  3  Fer4_16          4Fe-4S double cluster binding domain
     0.0019   18.2  15.4     0.0032   17.5   4.5    4.4  4  Fer4_2           4Fe-4S binding domain
     0.0042   17.9   8.4      0.098   13.5   0.8    3.3  2  Fer4_22          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.017   15.3  14.0      0.023   14.9   0.8    3.0  3  Fer4_18          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.4   0.0   5.6e-83   5.6e-80       1     431 [.     473     906 ..     473     907 .. 0.95

  Alignments for each domain:
  == domain 1  score: 269.4 bits;  conditional E-value: 5.6e-83
                                       B--S-EEEC.....TTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-E CS
                     Molybdopterin   1 RlkyPmvRk.....qargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggk 72 
                                       Rl++P++R      +  g+++F+++sW eAle + + l +++k++g+++  + ss + + +e+ ++ +k+++ + g 
  gi|336254187|ref|YP_004597294.1| 473 RLETPLIRRedagdGPVGRDGFREASWTEALERVYDGLSEIRKEHGSEALSVISS-SKTTNEENFLCQKFARQVLG- 547
                                       9************9999******************************99996555.5666****************. PP

                                       EE-BEECCGGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEE CS
                     Molybdopterin  73 nlsfydwyadlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvi 145
                                        +  +d++a+l+++s++    qt+g++   n +++    d+ ++d  ++ GsN  e +p+l +ri + ++ + a++i
  gi|336254187|ref|YP_004597294.1| 548 -TPHVDNCARLCHSSTVaalkQTVGYGAMTNRINE----DVGETDCYLVTGSNTTESHPVLATRIKQNVRDG-AELI 618
                                       .8*************99777777777755555555....**********************99999998885.**** PP

                                       EECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHH CS
                     Molybdopterin 146 vigpryaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvar 222
                                       v++pr   l+++ad+++ ++pg d+a +++m  +i+++ ++d++f++ +t+ ++e+ + ++  ++e++++ ++v+a+
  gi|336254187|ref|YP_004597294.1| 619 VFDPREIGLAEHADQYVRTTPGEDVAWINGMIRYIVKNDLHDEAFVEERTKHFDELVEKVEPFTPEQVEELTAVPAE 695
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCC CS
                     Molybdopterin 223 iarelarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvll 299
                                          + a+ +a +++  ++ + +gl++++ g+ ++ a++ Lal +gn g+p +g   ++Gq++++g++ ++g  p+ l
  gi|336254187|ref|YP_004597294.1| 696 ELTKAAETIATADT-CIFGWAMGLTQHTTGTRNVLAIADLALVTGNLGKPRAGLSPFRGQNNVQGGGGDMGPAPHNL 771
                                       ****9999999999.************************************************************99 PP

                                       CCCCCTT...HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEE CS
                     Molybdopterin 300 svkslke...ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvld 373
                                       + ++        +kfa+e+ +  +n  + ++ e+ +++ +++++  +++g+np+ + +++ +  +ale ld++ v d
  gi|336254187|ref|YP_004597294.1| 772 PGYQDLGdeeVLEKFADEWGERPPNDVGLRLPEQFHAITDGDLHGTFIMGENPVLSEPNIDNARRALEELDFLAVQD 848
                                       99888776656689*************************************************************** PP

                                       SCSSHHHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                     Molybdopterin 374 grltstalyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                       ++lt++a+yaD++LPaa+  Ek++++tn+e+r+q+ ++av+ppgeak d kIl +La+
  gi|336254187|ref|YP_004597294.1| 849 IFLTESAEYADVVLPAASAAEKSGTFTNTERRIQRVRPAVEPPGEAKADRKILDQLAR 906
                                       *******************************************************997 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.1   5.5e-31   5.5e-28       1     110 [.     993    1098 ..     993    1099 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 5.5e-31
                                        EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEE CS
                   Molydop_binding    1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvv 74  
                                        l+L +gr+l+++h++t+tr+v  l ++ p ++v i+pe A++lG+++++ V+v sr+G+++v+a v+ +  pGvv
  gi|336254187|ref|YP_004597294.1|  993 LTLSSGRVLYHWHTGTMTRRVGTLMNHVPeSFVTIHPEMAEQLGVENDEYVRVQSRQGEIVVKANVEGTSDPGVV 1067
                                        689************************************************************************ PP

                                        EEESSHCC.....S-GHCTS--SCSTTT--CSTT-E CS
                   Molydop_binding   75 fmpfgwweagekggnaNaltddatdplsgtpefksv 110 
                                        f+p+++ +     g++N+lt  ++dp+s +p++k++
  gi|336254187|ref|YP_004597294.1| 1068 FIPMHFRQ-----GAINELTEHELDPTSYIPQYKVT 1098
                                        ******88.....********************986 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 !   82.2   0.2   2.1e-26   2.1e-23       2      81 ..      69     153 ..      68     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 2.1e-26
                            Fer2_4   2 rpvtltfDGkevtvpeGdtvasAllang..vdvprsckygrp...rgelcaggeCrnClVevegepnvracstpved 73 
                                       +p+tl++DG++vtvp+G+t+++A+ ++    ++ ++c+y+r+    + ++++geCr+C V++e+++ v+acs+p+ed
  gi|336254187|ref|YP_004597294.1|  69 EPTTLEIDGTPVTVPPGSTIIDAVEEAEpaDEIAALCYYDRDteqADAIGPRGECRTCTVHTEDHGLVPACSFPAED 145
                                       799***********************99634588*******9888999***************************** PP

                            Fer2_4  74 Glkvetqt 81 
                                       Gl+v+t++
  gi|336254187|ref|YP_004597294.1| 146 GLSVRTDQ 153
                                       ******86 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 !   46.4   1.8   2.1e-15   2.1e-12       1      40 []     160     199 ..     160     199 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.1e-15
                   NADH-G_4Fe-4S_3   1 RktilellLanHpldCltCdknGnCeLQdlayelgveesr 40 
                                       R  +l+l L++H+l C+tC +nG+CeLQd++ e gvee r
  gi|336254187|ref|YP_004597294.1| 160 REVNLDLQLSDHNLRCTTCGQNGRCELQDTSIEQGVEEPR 199
                                       7889*********************************976 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.3   1.4e-14   1.4e-11       3      54 ..     416     469 ..     414     470 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.4e-14
                                       EEEEE-SSBTT--EEEEEEETTEEEEEEE-T..TSTTTTT---HHHHTCHHCCC CS
                    Molybdop_Fe4S4   3 vvktaCpyCgvgCglevhvkdgkivkvegdp..dhpvnegrlCvKGrtllervy 54 
                                       ++ t+C yC vgC +e++ kdg++v v++ +  + p+n   +CvKG++++++v+
  gi|336254187|ref|YP_004597294.1| 416 KAETTCNYCAVGCRFELYGKDGEVVGVRPAEpeSTPANDFSTCVKGKFGYDYVD 469
                                       568*************************98522679999*************97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   2.9   1.1e-07   0.00011       2      20 ..     219     237 ..     218     245 .. 0.89
   2 !   29.5   1.0   4.9e-10   4.9e-07       3      24 .]     264     285 ..     264     285 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCP 20 
                                       ++id++kCi C++Cv +C 
  gi|336254187|ref|YP_004597294.1| 219 IQIDRNKCILCNRCVEACN 237
                                       78****************5 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 4.9e-10
                            Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                       ++d++ C++Cg C++vCP+ga+
  gi|336254187|ref|YP_004597294.1| 264 TFDESTCVSCGHCATVCPTGAL 285
                                       79******************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 !   36.3   8.3   4.4e-12   4.4e-09       2      55 ..     220     283 ..     219     287 .. 0.78
   2 ?    0.3   0.1      0.77   7.6e+02      38      51 ..     415     428 ..     398     431 .. 0.66
   3 ?   -1.5   0.2       2.8   2.8e+03      13      29 ..     553     569 ..     550     591 .. 0.63

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 4.4e-12
                           Fer4_21   2 ridedkCigCgkCliaCedtshqai..........eidaktvl.......kvvedeCvGCnlCssvCPved 55 
                                       +id++kCi C++C+ aC+d  ++ +          +      +       +  e++Cv C  C++vCP+ +
  gi|336254187|ref|YP_004597294.1| 220 QIDRNKCILCNRCVEACNDVQVEGVlrmeghgqdtR------IafqngeeTFDESTCVSCGHCATVCPT-G 283
                                       69********************99987765333322......1355555477899*************7.4 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.77
                           Fer4_21  38 edeCvGCnlCssvC 51 
                                       e+  + Cn C+  C
  gi|336254187|ref|YP_004597294.1| 415 EKAETTCNYCAVGC 428
                                       45556666666655 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.8
                           Fer4_21  13 kCliaCedtshqaieid 29 
                                       +C+  C+ +++ a++ +
  gi|336254187|ref|YP_004597294.1| 553 NCARLCHSSTVAALKQT 569
                                       79999999999998643 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.4       1.2   1.2e+03      27      45 ..     158     185 ..     121     187 .. 0.51
   2 !   35.3   9.9   1.2e-11   1.2e-08       1      52 []     225     284 ..     225     284 .. 0.80
   3 ?    3.6   0.5       0.1     1e+02       4      18 ..     420     434 ..     419     562 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.2
                            Fer4_7  27 gtekveidpe......kClgCga...Cv 45 
                                       + ++v++d +      +C++Cg+   C+
  gi|336254187|ref|YP_004597294.1| 158 EAREVNLDLQlsdhnlRCTTCGQngrCE 185
                                       3344433322112222799997655575 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 1.2e-11
                            Fer4_7   1 rCigCgaCvaaCp....vkaieldeeenek....gtekveidpekClgCgaCvavCPtga 52 
                                       +Ci C++Cv+aC      ++++++ + ++     ++ + ++d+++C++Cg+C++vCPtga
  gi|336254187|ref|YP_004597294.1| 225 KCILCNRCVEACNdvqvEGVLRMEGHGQDTriafQNGEETFDESTCVSCGHCATVCPTGA 284
                                       7***********866667777777664444344444888*******************98 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.1
                            Fer4_7   4 gCgaCvaaCpvkaie 18 
                                        C++C++ C  +   
  gi|336254187|ref|YP_004597294.1| 420 TCNYCAVGCRFELYG 434
                                       6********654433 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2       3.5   3.5e+03       7      13 ..     174     180 ..     172     180 .. 0.86
   2 !   18.6   4.3   1.2e-06    0.0012       1      18 [.     219     236 ..     219     236 .. 0.96
   3 !   28.5   1.4   8.9e-10   8.9e-07       2      23 ..     264     285 ..     263     286 .. 0.94
   4 ?   -2.3   1.2       4.6   4.6e+03      11      18 ..     421     428 ..     419     431 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.5
                                       TSSS-TH CS
                              Fer4   7 kCigCGa 13 
                                       +C+ CG+
  gi|336254187|ref|YP_004597294.1| 174 RCTTCGQ 180
                                       7****95 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.2e-06
                                       EEEETTTSSS-THHHHHS CS
                              Fer4   1 vvideekCigCGaCvevC 18 
                                       ++id +kCi C++Cve+C
  gi|336254187|ref|YP_004597294.1| 219 IQIDRNKCILCNRCVEAC 236
                                       68**************** PP

  == domain 3  score: 28.5 bits;  conditional E-value: 8.9e-10
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       ++de+ C+ CG C+ vCP+gA+
  gi|336254187|ref|YP_004597294.1| 264 TFDESTCVSCGHCATVCPTGAL 285
                                       68*******************8 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4.6
                                       -THHHHHS CS
                              Fer4  11 CGaCvevC 18 
                                       C++C+  C
  gi|336254187|ref|YP_004597294.1| 421 CNYCAVGC 428
                                       99999888 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   3.6       1.6   1.6e+03      33      42 ..     161     184 ..     121     187 .. 0.58
   2 !   30.0   6.2   4.2e-10   4.2e-07       1      50 [.     225     284 ..     211     285 .. 0.77
   3 ?    4.7   0.4     0.035        35       3      23 ..     419     439 ..     419     460 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.6
                            Fer4_9  33 e...........eaCigCga...C 42 
                                       e            +C++Cg+   C
  gi|336254187|ref|YP_004597294.1| 161 EvnldlqlsdhnLRCTTCGQngrC 184
                                       033355566666689999986666 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 4.2e-10
                            Fer4_9   1 kCtgCgaCveaC....pagvvvedaaerkarlraase......eaCigCgaCveaCpkga 50 
                                       kC+ C++CveaC      gv +++  ++  r+  ++       + C++Cg C+ +Cp+ga
  gi|336254187|ref|YP_004597294.1| 225 KCILCNRCVEACndvqVEGVLRMEGHGQDTRIAFQNGeetfdeSTCVSCGHCATVCPTGA 284
                                       7***********888734444444444444443333357888899*************97 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.035
                            Fer4_9   3 tgCgaCveaCpagvvvedaae 23 
                                       t C++C   C ++++ +d   
  gi|336254187|ref|YP_004597294.1| 419 TTCNYCAVGCRFELYGKDGEV 439
                                       57**********999887654 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   3.3       5.9   5.9e+03      36      51 ..     166     184 ..     121     187 .. 0.61
   2 !   20.9  14.1   2.9e-07   0.00029       2      56 .]     219     281 ..     218     281 .. 0.84
   3 !   17.6   1.2   3.1e-06    0.0031       4      23 ..     265     284 ..     262     328 .. 0.78
   4 ?   -1.7   0.4       3.4   3.4e+03      11      19 ..     420     428 ..     415     458 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.9
                           Fer4_10  36 eavrkkvekCtgcg...aC 51 
                                        + ++   +Ct+cg    C
  gi|336254187|ref|YP_004597294.1| 166 LQLSDHNLRCTTCGqngRC 184
                                       4555566778888633355 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.9e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl.........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       ++id+++Ci C++Cv+aC  d+          + + + +a +++++  + + C  cg C+ +CP
  gi|336254187|ref|YP_004597294.1| 219 IQIDRNKCILCNRCVEAC-NDVqvegvlrmeGHGQDTRIAFQNGEETFDESTCVSCGHCATVCP 281
                                       789***************.5559*******75555566666666666788*************9 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 3.1e-06
                           Fer4_10   4 idddtCirCgkCvkaCPadl 23 
                                       +d++tC+ Cg C ++CP+ +
  gi|336254187|ref|YP_004597294.1| 265 FDESTCVSCGHCATVCPTGA 284
                                       6999*************955 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 3.4
                           Fer4_10  11 rCgkCvkaC 19 
                                        C+ C   C
  gi|336254187|ref|YP_004597294.1| 420 TCNYCAVGC 428
                                       688888777 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   2.3      0.48   4.7e+02       7      56 ..     122     180 ..     121     187 .. 0.51
   2 !   23.1   8.6   7.4e-08   7.3e-05       3      64 ..     224     283 ..     222     284 .. 0.69
   3 ?   -0.3   0.0       1.5   1.5e+03      52      62 ..     419     429 ..     364     448 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.48
                            Fer4_8   7 eCgaCq.........saCp.......vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga 56 
                                       eC  C+          aC        ++r+ +++  +ar+ + +  q +++        +Cttcg+
  gi|336254187|ref|YP_004597294.1| 122 ECRTCTvhtedhglvPACSfpaedglSVRTDQDDAAEAREVNLD-LQLSDH------NLRCTTCGQ 180
                                       78888877777777767852233332333333333333333333.444444......678888875 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 7.4e-08
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtk..khlldargeaae.dvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       +kCi C +C +aC  ++ ++  ++  + ++ +++ ++ ee          +C++cg+C++vCp+g
  gi|336254187|ref|YP_004597294.1| 224 NKCILCNRCVEACNDVQVEGvlRMEGHGQDTRIAfQNGEETF-----DESTCVSCGHCATVCPTG 283
                                       69***********86666663344444444444442333333.....3599************87 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.5
                            Fer4_8  52 ttcgaCtevCp 62 
                                       ttc+ C++ C 
  gi|336254187|ref|YP_004597294.1| 419 TTCNYCAVGCR 429
                                       56666666664 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 !   16.1   0.6   1.5e-05     0.015       1      22 [.     219     240 ..     219     262 .. 0.82
   2 !   12.5   0.1   0.00019      0.19       2      32 ..     264     296 ..     264     326 .. 0.60
   3 ?   -1.9   0.2         6     6e+03      27      59 ..     383     421 ..     371     427 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-05
                           Fer4_15   1 VvvDrdaCigcglCvaeapevf 22 
                                       + +Dr++Ci c++Cv+++ +v 
  gi|336254187|ref|YP_004597294.1| 219 IQIDRNKCILCNRCVEACNDVQ 240
                                       68****************7764 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00019
                           Fer4_15   2 vvDrdaCigcglCvaeape..vfeldedglasv 32 
                                       ++D+++C +cg C++++p+  ++e+   ++a++
  gi|336254187|ref|YP_004597294.1| 264 TFDESTCVSCGHCATVCPTgaLVEQGLTDIATM 296
                                       58***************8411233333455544 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 6
                           Fer4_15  27 dglasvllddgeiaeg........evpddeeeaaqeAaraC 59 
                                       +++a+ +++++  + +        +++d +   +++A  +C
  gi|336254187|ref|YP_004597294.1| 383 EHVAERVASESM-S-AgslfavatTIGDARLSRVEKAETTC 421
                                       566655554333.2.23566666799999999999999999 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   0.4   8.2e-05     0.082       1      19 [.     221     239 ..     221     262 .. 0.94
   2 !   10.0   2.4     0.001         1       2      17 ..     266     281 ..     265     283 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.2e-05
                           Fer4_13   1 VDrdtCiacgaCvelaPdv 19 
                                       +Dr++Ci c+ Cve++ dv
  gi|336254187|ref|YP_004597294.1| 221 IDRNKCILCNRCVEACNDV 239
                                       8***************997 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.001
                           Fer4_13   2 DrdtCiacgaCvelaP 17 
                                       D++tC++cg C+ ++P
  gi|336254187|ref|YP_004597294.1| 266 DESTCVSCGHCATVCP 281
                                       889************* 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   0.3    0.0057       5.7       1      12 [.     225     236 ..     208     254 .. 0.88
   2 !   20.7   0.3   5.8e-07   0.00058       1      20 [.     269     288 ..     269     321 .. 0.87
   3 ?   -0.7   0.1       2.9   2.9e+03       4      12 ..     420     428 ..     386     432 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0057
                           Fer4_16   1 rCgtCgkCaevC 12 
                                       +C+ C++C+e+C
  gi|336254187|ref|YP_004597294.1| 225 KCILCNRCVEAC 236
                                       588889998888 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 5.8e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++Cg Ca vCPt+a+ e+
  gi|336254187|ref|YP_004597294.1| 269 TCVSCGHCATVCPTGALVEQ 288
                                       5****************998 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.9
                           Fer4_16   4 tCgkCaevC 12 
                                       tC+ Ca  C
  gi|336254187|ref|YP_004597294.1| 420 TCNYCAVGC 428
                                       455555544 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.8       4.6   4.6e+03      12      17 ..     122     127 ..     121     128 .. 0.81
   2 ?   -0.3   0.9       1.4   1.4e+03       9      16 ..     174     184 ..     168     186 .. 0.77
   3 !   15.7   3.2   1.1e-05     0.011       2      20 ..     218     236 ..     217     237 .. 0.93
   4 !   17.5   4.5   3.2e-06    0.0032       5      22 .]     265     282 ..     263     282 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.6
                            Fer4_2  12 gCgaCv 17 
                                       +C++C+
  gi|336254187|ref|YP_004597294.1| 122 ECRTCT 127
                                       69***6 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                            Fer4_2   9 rCigCg...aC 16 
                                       rC+ Cg    C
  gi|336254187|ref|YP_004597294.1| 174 RCTTCGqngRC 184
                                       8999*755577 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.1e-05
                            Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                       ++++d+++Ci C+ Cv aC
  gi|336254187|ref|YP_004597294.1| 218 AIQIDRNKCILCNRCVEAC 236
                                       699**************** PP

  == domain 4  score: 17.5 bits;  conditional E-value: 3.2e-06
                            Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                       +d+ +C++Cg C ++CP+
  gi|336254187|ref|YP_004597294.1| 265 FDESTCVSCGHCATVCPT 282
                                       89***************7 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.2    0.0066       6.6      76      93 ..     220     237 ..     204     240 .. 0.88
   2 !   13.5   0.8   9.8e-05     0.098      73      94 ..     261     282 ..     250     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0066
                           Fer4_22  76 kfgesgCvGCgRCieacp 93 
                                       ++++++C+ C+RC+eac+
  gi|336254187|ref|YP_004597294.1| 220 QIDRNKCILCNRCVEACN 237
                                       67899************7 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 9.8e-05
                           Fer4_22  73 fkekfgesgCvGCgRCieacpv 94 
                                        +e+f+es+Cv Cg C ++cp+
  gi|336254187|ref|YP_004597294.1| 261 GEETFDESTCVSCGHCATVCPT 282
                                       5677888888888888888886 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   4.0     0.012        12      84      98 ..     225     239 ..     216     248 .. 0.85
   2 ?   14.9   0.8   2.3e-05     0.023      51      81 ..     260     290 ..     241     295 .. 0.77
   3 ?   -3.2   0.0       9.2   9.2e+03      59      72 ..     416     429 ..     387     437 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                           Fer4_18  84 eciscllcidacdkv 98 
                                       +ci c +c++ac++v
  gi|336254187|ref|YP_004597294.1| 225 KCILCNRCVEACNDV 239
                                       7***********998 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.3e-05
                           Fer4_18  51 eerkekgagdcidcescvkvcPtgidirkGl 81 
                                       + +++ +++ c++c++c +vcPtg  + +Gl
  gi|336254187|ref|YP_004597294.1| 260 NGEETFDESTCVSCGHCATVCPTGALVEQGL 290
                                       4445567889**************9999887 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 9.2
                           Fer4_18  59 gdcidcescvkvcP 72 
                                          ++c++c   c 
  gi|336254187|ref|YP_004597294.1| 416 KAETTCNYCAVGCR 429
                                       44467888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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):              18  [number of targets reported over threshold]
# CPU time: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.44
# Mc/sec: 7703.12
//
Query:       gi|336254188|ref|YP_004597295.1|  [L=553]
Description: NADH dehydrogenase (quinone) [Halopiger xanaduensis SH-6]
Scores for 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-19   67.7   0.0    1.8e-18   66.9   0.0    1.4  1  Complex1_51K     Respiratory-chain NADH dehydrogenase 51 Kd s
    3.2e-18   65.6   1.1    3.2e-18   65.6   1.1    1.7  2  NADH_4Fe-4S      NADH-ubiquinone oxidoreductase-F iron-sulfur
  ------ inclusion threshold ------
      0.025   14.5   0.9       0.14   12.0   0.5    2.4  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
      0.034   13.8   0.4      0.088   12.5   0.4    1.8  1  RTP1_C2          Required for nuclear transport of RNA pol II
       0.31   11.3   6.0        0.8   10.0   0.1    3.5  3  acVLRF1          Actinobacteria/chloroflexi VLRF1 release fac


Domain annotation for each model (and alignments):
>> Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.0     5e-22   1.8e-18       1     151 [.     158     334 ..     158     335 .. 0.89

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 5e-22
                      Complex1_51K   1 vkeagivGrGGa....gfPthvKlkakakkkk.......kylivNaaEcEPgltkDrllmreepheileGlkiaaea 66 
                                       v+e g+ GrG +      P+h  +k +++++        ++++vNa+E++    +Dr+l++  + e+++G+ ++ae+
  gi|336254188|ref|YP_004597295.1| 158 VREIGLLGRGRGdwcaDEPVHEEWKLAREAAAeggedrePVVVVNANESDDRNETDRTLLEGAAGEVIDGALAVAEL 234
                                       7899999999863333679******999977799999**************************************** PP

                      Complex1_51K  67 lgaekgvigvrdekpeaiealekalaeakaagl.......ldievvklagkYpaGeekaLiesltgr.evprg.kpp 134
                                       +ga  +v+++++++++a e+ ++a+++a +  l          evv ++++Y+a e ++ +e+++g+ +++++ +pp
  gi|336254188|ref|YP_004597295.1| 235 VGAADVVVYCNENDEQAREQAREAARNAAE-TLgerlereEPPEVVVGPDRYIASEPTMALEAMEGNdRLEARlRPP 310
                                       **************************9975.557899998899************************9444442566 PP

                      Complex1_51K 135 ..advgv.....vvnNveTlaavy 151
                                         a+ g+     vv+   T+a+v 
  gi|336254188|ref|YP_004597295.1| 311 spAEHGLygrptVVHTPRTVAQVR 334
                                       668888899999999999999985 PP

>> NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.4         5   1.8e+04      15      20 ..     128     133 ..     126     135 .. 0.76
   2 !   65.6   1.1   8.9e-22   3.2e-18       4      85 .]     438     516 ..     435     516 .. 0.93

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 5
                                       -S--HH CS
                       NADH_4Fe-4S  15 CGkCtp 20 
                                       CG+C p
  gi|336254188|ref|YP_004597295.1| 128 CGWCEP 133
                                       888876 PP

  == domain 2  score: 65.6 bits;  conditional E-value: 8.9e-22
                                       HHHHHHHHHH--S--HHHHIIIIHHHHHHHHHTBT---HHHHHHHHHHHHHHSS--SSTHHHHHHHHHHHHHHHHHH CS
                       NADH_4Fe-4S   4 rrllefyaaesCGkCtpCreGtkrllelleriaagegteedldlleelaetikgtslCalgdsaanpvlsalrkFre 80 
                                        r  +f+ +e+CG+C+ CreG+++l ++l+++ age +     +++el++++ +ts+C++g++a +p  +a+r+F+ 
  gi|336254188|ref|YP_004597295.1| 438 GRRSNFAMEENCGRCVTCREGSQELTQMLRDVYAGEYRD---AKIRELTRVMGATSICQFGRTAIRPAVTAMREFER 511
                                       56779********************************94...678999999************************** PP

                                       HHHH. CS
                       NADH_4Fe-4S  81 efeah 85 
                                       e+ ah
  gi|336254188|ref|YP_004597295.1| 512 EVAAH 516
                                       *9987 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 ?   12.0   0.5   3.9e-05      0.14       8      55 ..     200     261 ..     196     269 .. 0.78
   2 ?   -1.0   0.0      0.38   1.4e+03       8     145 ..     453     478 ..     364     519 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.9e-05
                   Glyco_tranf_2_3   8 Vptfneed............vlgevlesllaqey..prvevvvvvdesdaetlevaeelaaa 55 
                                       V+++ne+d              gev++ +la ++  ++ +vvv ++e+d+ ++e a+e+a++
  gi|336254188|ref|YP_004597295.1| 200 VVNANESDdrnetdrtllegAAGEVIDGALAVAElvGAADVVVYCNENDEQAREQAREAARN 261
                                       555555555555555555556789******99855799********************8876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.38
                   Glyco_tranf_2_3   8 Vptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealr 84 
                                       V++ + +++l+ +l+++ a ey                                                       
  gi|336254188|ref|YP_004597295.1| 453 VTCREGSQELTQMLRDVYAGEY------------------------------------------------------- 474
                                       4444444444444444444444....................................................... PP

                   Glyco_tranf_2_3  85 avksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerh 145
                                                                                                 + +
  gi|336254188|ref|YP_004597295.1| 475 ---------------------------------------------------------RDAK 478
                                       .........................................................3333 PP

>> RTP1_C2  Required for nuclear transport of RNA pol II C-terminus 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   2.5e-05     0.088      12      28 ..     242     258 ..     241     258 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                           RTP1_C2  12 VedtDtDdlVReHArdv 28 
                                       V+++++D++ Re+Ar +
  gi|336254188|ref|YP_004597295.1| 242 VYCNENDEQAREQAREA 258
                                       9**************86 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       0.2   7.1e+02      49      76 ..      24      51 ..      18     123 .. 0.77
   2 ?   10.0   0.1   0.00022       0.8      52      88 ..     248     289 ..     243     317 .. 0.78
   3 ?    1.5   0.2     0.096   3.4e+02      62      91 ..     330     369 ..     322     396 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.2
                           acVLRF1 49 Rrrenqadalleavaeaaarllaeesae 76
                                      Rrr ++a + ++ +ae+ ++ + e  ++
  gi|336254188|ref|YP_004597295.1| 24 RRRKHRALEEVRSAAEDGDATVLETGPT 51
                                      8999999999999999888877555554 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00022
                           acVLRF1  52 enqadalleavaeaaarllaeesae.....vvlgGdrslvae 88 
                                       ++qa++ ++++a  aa+ l+e+ ++     vv+g dr +++e
  gi|336254188|ref|YP_004597295.1| 248 DEQAREQAREAARNAAETLGERLEReeppeVVVGPDRYIASE 289
                                       789999999999999999976666666777999999987766 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.096
                           acVLRF1  62 vaeaaarllaeesae..........vvlgGdrslvaevle 91 
                                       va+  +++l++++ +          v ++Gd  ++a+v+ 
  gi|336254188|ref|YP_004597295.1| 330 VAQVRQAMLEPHAFDaddadpgtrlVTVTGDVDATATVEL 369
                                       444445555444444444557788899******9999974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 4017.95
//
Query:       gi|336254189|ref|YP_004597296.1|  [L=177]
Description: peptide methionine sulfoxide reductase msrA [Halopiger xanaduensis SH-6]
Scores for 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-66  221.8   1.3    5.1e-66  221.6   1.3    1.0  1  PMSR      Peptide methionine sulfoxide reductase
  ------ inclusion threshold ------
      0.084   12.8   0.4       0.14   12.2   0.4    1.4  1  DUF4298   Domain of unknown function (DUF4298)
       0.13   12.8   0.0        1.2    9.6   0.0    2.4  3  HMA       Heavy-metal-associated 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 !  221.6   1.3   8.5e-70   5.1e-66       2     152 ..       4     154 ..       3     155 .. 0.98

  Alignments for each domain:
  == domain 1  score: 221.6 bits;  conditional E-value: 8.5e-70
                                       EEEE-S-HHHHHHHHCTSTTEEEEEEEEESSS-SS--HHHHHTTTT--EEEEEEEEETTTS-HHHHHHHHHHTS-TT CS
                              PMSR   2 avlagGCFWgveklfeklkGvlstevGYagGktenptYeevcsgktghaEavevvydpekvsleellelffeihDpt 78 
                                       a+++gGCFW+ve++f++l+Gv+s+++GYagG++enptYe vc+g+tghaE+v+++ydp+ v +e+lle+ff+ihDpt
  gi|336254189|ref|YP_004597296.1|   4 ATFGGGCFWCVEAAFKELEGVESVTSGYAGGHVENPTYEAVCRGETGHAEVVQLEYDPDAVAYEDLLEVFFTIHDPT 80 
                                       89*************************************************************************** PP

                                       -SSEETTEESGGG--EEEESSCCHHHHHHHHHHHHHTTHTTSSS---EEEEG-SEEE--CCCTTHHHH-TTS.-- CS
                              PMSR  79 qlnrqgnDvGtqYrsaiyytneeqkevaeevleelqkkkalkkkivteieplkefykaeeyHqqYleknpeg.yc 152
                                       +++r g DvG+qYrsaiy+++++q e+ae++ eel+++  l + ivteiep++efy+aeeyHq+Y+eknp++ yc
  gi|336254189|ref|YP_004597296.1|  81 TKDREGPDVGSQYRSAIYAHDDDQLETAERFAEELENE-GLYEGIVTEIEPVEEFYEAEEYHQDYFEKNPNDaYC 154
                                       *************************************9.88999***************************9999 PP

>> DUF4298  Domain of unknown function (DUF4298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   2.3e-05      0.14      11      53 ..     108     149 ..      96     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHHHTSHHHHHHHTS--S CS
                           DUF4298  11 isallqqLeealeqwkklqkklakLdeYYqseqwredleasnk 53 
                                       ++++ ++Le+    ++ + +++++++e+Y+ e++ +d+ + n 
  gi|336254189|ref|YP_004597296.1| 108 AERFAEELENE-GLYEGIVTEIEPVEEFYEAEEYHQDYFEKNP 149
                                       44444444443.34788999*****************987665 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0002       1.2      10      34 ..       8      32 ..       5      37 .. 0.83
   2 ?   -0.4   0.0      0.27   1.6e+03      37      54 ..      54      71 ..      50      73 .. 0.81
   3 ?   -2.7   0.0       1.5   8.7e+03      43      58 ..     101     117 ..      95     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0002
                               HMA 10 agCaakvekvLselpgVesvkvdla 34
                                      +gC   ve +++el+gVesv+  +a
  gi|336254189|ref|YP_004597296.1|  8 GGCFWCVEAAFKELEGVESVTSGYA 32
                                      688888**************97665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.27
                               HMA 37 tvtVegdaestklrkiie 54
                                       v+ e+d++++ +++++e
  gi|336254189|ref|YP_004597296.1| 54 VVQLEYDPDAVAYEDLLE 71
                                      68999***9988888876 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.5
                               HMA  43 daes.tklrkiieaiek 58 
                                       d+++  + +++ e++e+
  gi|336254189|ref|YP_004597296.1| 101 DDDQlETAERFAEELEN 117
                                       67776777889999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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:                         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 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1388.53
//
Query:       gi|336254190|ref|YP_004597297.1|  [L=222]
Description: 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 1-reductase [Halopiger xanaduensis SH-6]
Scores for 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  187.2   0.2    3.3e-55  187.0   0.2    1.0  1  RibD_C    RibD C-terminal domain


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 !  187.0   0.2   1.8e-59   3.3e-55       2     200 .]       2     215 ..       1     215 [. 0.97

  Alignments for each domain:
  == domain 1  score: 187.0 bits;  conditional E-value: 1.8e-59
                                       EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHH.HTT.GSS- CS
                            RibD_C   2 yvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreae.adaearqp 77 
                                       +v++++a+S+DGkl+ +++e+  i+ge++ ++v++lra++da++vG+gtvlad+p+ltv+ ++ r ++ +d+ea +p
  gi|336254190|ref|YP_004597297.1|   2 HVVVNAATSADGKLSSRRREQIAISGEADFERVDRLRADSDAVVVGAGTVLADDPHLTVKDADLRDQRvEDGEAANP 78 
                                       799************************************************************************** PP

                                       EEEEEETTS-S-TTSHHHHSSS-EEEEESSCSCHHHHHHCC......E.....SE-HHHHHHHHHHTT--EEEEEET CS
                            RibD_C  78 vrvVvdstlrvpldakvltddaptlvatteeadkekveklk......v.....rvdlkelleeLkergirsllveGG 143
                                       vrvVvds+ r+p da++l+d a+t v ++e+a+ +++ +l+      v     rvdl +++++L+e+g+++l+veGG
  gi|336254190|ref|YP_004597297.1|  79 VRVVVDSKARTPVDAEILDDAAETYVCVSEAAPVDRRMDLAnrgaelVtagddRVDLLRAFAALQEAGLERLMVEGG 155
                                       *******************99********************87776638999************************* PP

                                       HHHHHHHHHTTT-SEEEEEEESCE--T.TSBCSSSSST-SS..EEEEEEEEEEETTEEEE CS
                            RibD_C 144 atLagsllraglvDelrlyiaPkllGg.agktlfdgegfka..lklklvksealgegvvl 200
                                       + L+ sl+++glvDelr+++ Pk++Gg +++tl dgegf +  ++l+l ++e+l++gv+l
  gi|336254190|ref|YP_004597297.1| 156 GELIFSLFEDGLVDELRVFVGPKVIGGrDAPTLADGEGFVEdfPTLELESVERLDDGVLL 215
                                       ********************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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 0.20s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1878.61
//
Query:       gi|336254191|ref|YP_004597298.1|  [L=257]
Description: hypothetical protein Halxa_2803 [Halopiger xanaduensis SH-6]
Scores for 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  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2118.45
//
Query:       gi|336254192|ref|YP_004597299.1|  [L=307]
Description: hypothetical protein Halxa_2804 [Halopiger xanaduensis SH-6]
Scores for 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-27   95.9  29.9    9.8e-15   54.9  11.8    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
        0.1   11.9   9.9      0.046   13.1   1.8    2.3  3  TPT       Triose-phosphate Transporter family


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 !   54.9  11.8   1.1e-18   9.8e-15       6     136 ..      13     141 ..       9     142 .. 0.87
   2 !   47.2  10.0   2.7e-16   2.4e-12       2     136 ..     156     290 ..     155     291 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1.1e-18
                              EamA   6 lallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvlafll 81 
                                        + +a++  +++++l ++  +  ++  ++f+r l+ ++++ ++all+ +   a+ls++d++  ++++ ++ ++ f +
  gi|336254192|ref|YP_004597299.1|  13 ALAVAVFAASTSAILVRW--SGAPSSVAAFYRVLFTTAVVAPVALLRHRGEfARLSRSDLAG-AVVAGVALAVHFAA 86 
                                       334455555556666666..6999999*********************9999*******888.555668******** PP

                              EamA  82 ffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       +f +l++ts++  + ++ ++P+f+++ + l+lge+++  +++gi+++++G++ ++
  gi|336254192|ref|YP_004597299.1|  87 WFESLNYTSVAASVTLVQTQPIFVALGAGLVLGERISRETVVGIAVAVVGAAAMS 141
                                       ***************************************************9876 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 2.7e-16
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       lg  lall+a++ a y ++ + + ++vs + +++v + ++++ l+++   +++    ++ ++wll+l +++ ++v++
  gi|336254192|ref|YP_004597299.1| 156 LGNALALLGAVTVAGYVLAGRSIRQRVSLFPYVTVVYAACAATLFLVVGAQGHDYVAYPAREWLLFLGMAVGPGVFG 232
                                       5889*********************************99999999999999999999******************** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       + + ++ lk++++ ++s++ + ePv +++l++lll e +  +++ g +++l G+++++
  gi|336254192|ref|YP_004597299.1| 233 HTVVNWVLKHLESVVVSVAWLGEPVGSALLAALLLAEIPDAITVGGGLVVLGGIYVTT 290
                                       *******************************************************986 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.8   5.1e-06     0.046      30     136 ..      33     141 ..      19     146 .. 0.76
   2 ?   -2.8   0.0      0.34   3.1e+03     269     287 ..     148     166 ..     145     169 .. 0.84
   3 ?    3.5   0.8    0.0042        38      76     137 ..     230     291 ..     171     294 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-06
                               TPT  30 yPltvsavq..llvgsvlilvlwalglkkrpkisseflkailplalvktlghvlavv.slskvaVSfthtvKasePi 103
                                        P+ v+a+   l+ + v++ v++  +  + +++s + l+  ++ +++ +++h++a + sl+ ++V  + t+  ++Pi
  gi|336254192|ref|YP_004597299.1|  33 APSSVAAFYrvLFTTAVVAPVALLRHRGEFARLSRSDLAGAVVAGVA-LAVHFAAWFeSLNYTSVAASVTLVQTQPI 108
                                       56666665333777788888888888888999999977766655544.4555555544888888888888899**** PP

                               TPT 104 FtvilsrlllgeklsllvylsLlpivgGvalas 136
                                       F ++ + l+lge++s   ++ + + v+G a  s
  gi|336254192|ref|YP_004597299.1| 109 FVALGAGLVLGERISRETVVGIAVAVVGAAAMS 141
                                       **********************99999987666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.34
                               TPT 269 npvsllnaiGtavaivGvf 287
                                        p+s  +a+G a+a++G++
  gi|336254192|ref|YP_004597299.1| 148 APLSDATALGNALALLGAV 166
                                       57888899*******9975 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.0042
                               TPT  76 tlghvlavvslskvaVSfthtvKasePiFtvilsrlllgeklsllvylsLlpivgGvalasv 137
                                       ++gh + +  l++       +    eP+ +++l++lll e +    +   l+++gG+ ++++
  gi|336254192|ref|YP_004597299.1| 230 VFGHTVVNWVLKHLESVVVSVAWLGEPVGSALLAALLLAEIPDAITVGGGLVVLGGIYVTTI 291
                                       55555555555544444444445689*****************999999999****999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2566.15
//
Query:       gi|336254193|ref|YP_004597300.1|  [L=210]
Description: lipoprotein [Halopiger xanaduensis SH-6]
Scores for 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   50.5   0.0    3.4e-13   50.1   0.0    1.2  1  NosL        NosL
  ------ inclusion threshold ------
      0.062   13.2   3.8       0.11   12.4   3.8    1.5  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> NosL  NosL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   3.8e-17   3.4e-13       1     124 [.      70     188 ..      70     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 3.8e-17
                              NosL   1 pveltaeaecdvCgMliaehpgpkgqifyededepakFcstrdlfafllepeerkeikaiyvtDmsavdwespdaea 77 
                                       p+++ +++ c+vC M+ a ++g+  q+  e+ +e a F++  +lfa+++ +  ++ ++a +v  ++        a+ 
  gi|336254193|ref|YP_004597300.1|  70 PIAFVDGQHCPVCRMTPASYSGWHCQLAHEN-GEGAVFDTPGCLFAYYAYQPVEEPVTAGWVMGIE--------ADD 137
                                       6788899********************9998.9*****************************9988........99* PP

                              NosL  78 fidakkalyVv..gsdveG..aMGpelvpFsdeadAeaFaaehgGkvlrfe 124
                                       +ida++a+yV+  +s+++   +MGp+  pF+d++dA a+ ++   + l+ e
  gi|336254193|ref|YP_004597300.1| 138 LIDATEAHYVLvtDSEATAdePMGPNPRPFADREDAVAYLEAWEAEDLTEE 188
                                       ********98622555443449*****************998766555554 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.8   1.3e-05      0.11       2      25 ..      11      34 ..      10      35 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      ++RR++L +++ ++A aa+g +++
  gi|336254193|ref|YP_004597300.1| 11 ITRRQLLGAAGTGTAIAAAGCLGG 34
                                      89******8877777777766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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 0.19s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1818.12
//
Query:       gi|336254194|ref|YP_004597301.1|  [L=165]
Description: cyclase/dehydrase [Halopiger xanaduensis SH-6]
Scores for 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-07   30.7   0.1    4.3e-07   30.2   0.1    1.3  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
    0.00016   22.0   1.5    0.00017   21.9   1.5    1.1  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   4.8e-11   4.3e-07       1     106 [.      10     128 ..      10     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4.8e-11
                                       ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...E.................EEECSTTSSCEEEEEEEEEE CS
                    Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaesglsa.................dlevgfggltesftarvtld 60 
                                       v ap+++v++++++v+ + +++p + + +v +  +    +                 +++   +g ++++t+ +t+ 
  gi|336254194|ref|YP_004597301.1|  10 VRAPLEDVWSFHSQVSGLETLTPDWMRLRVESVVG----PdgdpdpdvlevgsevtlSVRPCGAGPRQRWTSVITER 82 
                                       579***********************755554444....22333555555677777788889999*********999 PP

                                       ETTT....EEECTTCCCCCEEEEEEEECTECCEEECEEEEEEEEEEEE-S CS
                    Polyketide_cyc  61 ppee....itfklvegdfkslegkWtieslppnsggtrtkvalevdfkfa 106
                                       +  +     + ++v+g+f++   ++ +   ++   +t +++ +e+ + + 
  gi|336254194|ref|YP_004597301.1|  83 ERGDgaayFRDEMVDGPFDEWTHTHAFYADGE---ATIVRDHVEYAL-PL 128
                                       9999***********************99998...*********998.43 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.5   1.9e-08   0.00017       3     116 ..       3     138 ..       1     165 [] 0.68

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.9e-08
                                       EEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEE.....CSESTSSS.......TTTEEEEECCCS...SEEEEE CS
                   Polyketide_cyc2   3 kvtvsvviaappekVwalvsdfenwprWhpevarve.....leggggpa.......rgvegtvrvggr...gtvree 64 
                                       + ++++++ ap e+Vw++ s+ +++ +  p   r +     +++ g+p        ++v   vr +g+   ++ + +
  gi|336254194|ref|YP_004597301.1|   3 TYERRTRVRAPLEDVWSFHSQVSGLETLTPDWMRLRvesvvGPD-GDPDpdvlevgSEVTLSVRPCGAgprQRWTSV 78 
                                       5678899**************99999866655555411111443.33337899988666788888888998778999 PP

                                       EEEEET..TTTEEEEEEE.SSS-TSEEEEEEEEECCETEEEEEEEEEEE..E--T.....T CS
                   Polyketide_cyc2  65 lvevdp..egrllsyrivkpvpvanyvatwtvtpdgggtrvtwtgefda..gplg.....g 116
                                       ++e++       ++ ++v + p+   + t ++ +dg+ t v+ ++e++   gpl+     +
  gi|336254194|ref|YP_004597301.1|  79 ITERERgdGAAYFRDEMV-DGPFDEWTHTHAFYADGEATIVRDHVEYALplGPLDssgplA 138
                                       999986335555666666.9999999*************9999999995343333332221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); 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: 0.38u 0.18s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1433.53
//
Query:       gi|336254195|ref|YP_004597302.1|  [L=331]
Description: phosphate uptake regulator PhoU [Halopiger xanaduensis SH-6]
Scores for 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-20   72.3   9.1    1.8e-17   63.6   1.8    2.5  2  PhoU            PhoU domain
    4.4e-09   36.1   0.0    1.3e-08   34.6   0.0    1.8  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   1.8     2e-21   1.8e-17       2      88 ..     136     225 ..     135     226 .. 0.86
   2 !   12.7   0.9   1.5e-05      0.13       1      88 [.     240     322 ..     240     323 .. 0.71

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 2e-21
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH....HHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae....dlrellsllriard 74 
                                        rm  i+++ml da++al+e+d+++a++vi+rdd++drl+  ++r  ++a  ++   ae    + ++ +++ + ar 
  gi|336254195|ref|YP_004597302.1| 136 TRMRLIANSMLADAVTALVENDDDIANDVIDRDDDVDRLFLVVSRI-FRATLRSPRAAEelglPREDCFDYHSSARQ 211
                                       79*************************************8888666.777755444444566688889********* PP

                                       HHHHHHHHHHHHHH CS
                              PhoU  75 lERigDhavniaer 88 
                                       lER++Dhav+i++ 
  gi|336254195|ref|YP_004597302.1| 212 LERVADHAVKISQL 225
                                       ***********985 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHHHHHHHHHHCT-H..HHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdt..ela..revierddeidrlekeiersllealakrqplaedlrellsllriar 73 
                                       l +++  ve++l+ +++al+ +d    +a   + +e    id+  ++i++  l+ l     +a+      sl  i  
  gi|336254195|ref|YP_004597302.1| 240 LLELHADVEDILETSMDALFAEDSdeATAqsHDALEAVPAIDEHTRRIDDI-LRDLD--PVMAQ------SLGLILD 307
                                       5789999***********877765223332245566667777777777555.77773..33333......35569** PP

                                       HHHHHHHHHHHHHHH CS
                              PhoU  74 dlERigDhavniaer 88 
                                       +l R +D+  n+ae 
  gi|336254195|ref|YP_004597302.1| 308 SLSRSADYGGNVAET 322
                                       *************95 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 !   34.6   0.0   1.4e-12   1.3e-08       1      43 [.       8      50 ..       8      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.4e-12
                                      EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHH CS
                    MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgdkiilrplks 43
                                      +++G+++ v++Pk+++ +++++ G+ ve++ ++d ++++p+++
  gi|336254195|ref|YP_004597302.1|  8 VTGGSTYTVSLPKDWATDNDVSSGTIVEIYSEDDTLLVTPKSD 50
                                      699*************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2658.94
//
Query:       gi|336254196|ref|YP_004597303.1|  [L=322]
Description: halo transducer protein [Halopiger xanaduensis SH-6]
Scores for 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   22.9   1.6    4.6e-05   22.9   1.6    1.8  2  CorA             CorA-like Mg2+ transporter protein
    0.00063   20.0   0.2       0.22   11.8   0.1    2.8  2  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0029   18.1   0.8        1.2    9.6   0.1    3.2  4  Spectrin         Spectrin repeat
     0.0067   16.4   0.1        1.9    8.5   0.1    2.3  2  Laminin_II       Laminin Domain II
      0.009   16.4   0.0        1.4    9.4   0.0    3.3  3  Snapin_Pallidin  Snapin/Pallidin
  ------ inclusion threshold ------
      0.045   14.2   0.2         14    6.3   0.5    3.8  2  NPV_P10          Nucleopolyhedrovirus P10 protein
      0.096   12.7   0.0        3.3    7.8   0.0    2.9  3  DUF1664          Protein of unknown function (DUF1664)
       0.17   11.7   0.0       0.35   10.7   0.0    1.6  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
       0.87    9.8   7.1       0.28   11.4   0.6    2.8  2  ATG16            Autophagy protein 16 (ATG16)
        1.2    8.9   3.4          1    9.1   0.5    2.4  2  Rbsn             Rabenosyn Rab binding domain


Domain annotation for each model (and alignments):
>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   1.6   2.6e-08   4.6e-05     118     222 ..      96     201 ..      57     211 .. 0.91
   2 ?   -1.8   0.0      0.85   1.5e+03     124     146 ..     258     280 ..     255     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.6e-08
                              CorA 118 eivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrlla..kaddkllddedke 192
                                       + ++ +++ le++e++   l d+l++  +++  ++l++l r++ ++  a+++ +++ ++l     ++d +ld+ d +
  gi|336254196|ref|YP_004597303.1|  96 ARLEGFAARLETVEDRAAGLGDRLQSIVDRKRDGDLYELAREIRQMTAAATEVQRAADDLAFdlESFDAWLDEPD-R 171
                                       5578899**************************************************877768899********9.9 PP

                              CorA 193 ylrdlldelerllemlealrerleslqdty 222
                                       +  dl d+++ l++ l+ l ++++ l ++ 
  gi|336254196|ref|YP_004597303.1| 172 RAGDLADDIDALERSLDELEDVVDGLGSEA 201
                                       ***********************9997765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.85
                              CorA 124 fellekleeeldeledeledstk 146
                                       ++ l++l +++++l ++l d+t+
  gi|336254196|ref|YP_004597303.1| 258 EPRLDELAARRERLGERLADRTE 280
                                       6789999*******999966665 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 ?    5.1   0.0     0.015        28      38      93 ..      52     107 ..      47     109 .. 0.89
   2 !   11.8   0.1   0.00012      0.22      34      93 ..     147     206 ..     132     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.015
                           BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                       +++d++a+++k +   + + e  +  l+   +  + v++L  ++++L+ +  +LE 
  gi|336254196|ref|YP_004597303.1|  52 AVDDALANASKVVTTAETRAELAAAALDDARDAAEPVADLDVVAARLEGFAARLET 107
                                       6778889999999999999999999999999999********************95 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00012
                           BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                       e   + +d a +le++   l+e +     + + id++e++++eLe++v+ L +  ++LE+
  gi|336254196|ref|YP_004597303.1| 147 EVQRAADDLAFDLESFDAWLDEPDRRAGDLADDIDALERSLDELEDVVDGLGSEASDLED 206
                                       4445556666677777777888888888999********************999999985 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.4   2.6e+03      76     103 ..      92     119 ..      54     121 .. 0.62
   2 ?   -0.4   0.0      0.89   1.6e+03      81     103 ..      97     119 ..      69     156 .. 0.60
   3 !    9.6   0.1   0.00068       1.2       7      62 ..     156     209 ..     150     246 .. 0.80
   4 ?    5.0   0.1     0.018        33      72     100 ..     251     279 ..     220     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  76 eeieerleelnerWeeLkelaaerkqkL 103
                                       + + +rle+   r e ++++aa   ++L
  gi|336254196|ref|YP_004597303.1|  92 DVVAARLEGFAARLETVEDRAAGLGDRL 119
                                       5566666666666666666666555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.89
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  81 rleelnerWeeLkelaaerkqkL 103
                                       rle+   r e ++++aa   ++L
  gi|336254196|ref|YP_004597303.1|  97 RLEGFAARLETVEDRAAGLGDRL 119
                                       33333333333333333332222 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00068
                                       HHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin   7 aqdadeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalne 62 
                                       a d++ +++W++e ++ +   dl+ d++++++ l++++++ + l ++   ++++ +
  gi|336254196|ref|YP_004597303.1| 156 AFDLESFDAWLDEPDRRA--GDLADDIDALERSLDELEDVVDGLGSEASDLEDVAD 209
                                       6688999*******9999..999******************999999999999884 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.018
                                       HTTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  72 hsaseeieerleelnerWeeLkelaaerk 100
                                        + + ++e rl+el  r e L e++a+r 
  gi|336254196|ref|YP_004597303.1| 251 ADPPSDVEPRLDELAARRERLGERLADRT 279
                                       4456899******************9996 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1     0.001       1.9      24      95 ..      51     122 ..      30     127 .. 0.78
   2 !    5.7   0.0    0.0075        13       6      71 ..     139     204 ..     129     209 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.001
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTG...GGHHHHHHHHHH...HHHHHHHH CS
                        Laminin_II  24 qnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLl...dklkelkqleeassslsdnisei 95 
                                       + ++   +++s++ +++e   e++ +a    rdA + v +L+ +a +L+   ++l++++ +  +   l+d ++ i
  gi|336254196|ref|YP_004597303.1|  51 AAVDDALANASKVVTTAETRAELAAAALDDARDAAEPVADLDVVAARLEgfaARLETVEDRAAG---LGDRLQSI 122
                                       567888999*******777778888999***************999997222566666666555...88877766 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0075
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       ++    a+ev++   +l+ +le   + l e +r +    ++++++ + +++ ++ v  L  +a +L
  gi|336254196|ref|YP_004597303.1| 139 RQMTAAATEVQRAADDLAFDLESFDAWLDEPDRRAGDLADDIDALERSLDELEDVVDGLGSEASDL 204
                                       233334556666666666666666666666666666666666666666666666665555555555 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00077       1.4      41      89 ..      76     122 ..      62     123 .. 0.88
   2 ?    2.3   0.0      0.12   2.2e+02      15      50 ..     159     194 ..     152     206 .. 0.81
   3 ?   -1.0   0.0       1.3   2.4e+03      31      71 ..     230     270 ..     219     275 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00077
                   Snapin_Pallidin  41 ekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaekL 89 
                                       ++L+++++a+e   ++dl+  a++L  +  r++++++r   l +R++ +
  gi|336254196|ref|YP_004597303.1|  76 AALDDARDAAE--PVADLDVVAARLEGFAARLETVEDRAAGLGDRLQSI 122
                                       55666666666..9*******************************9876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.12
                   Snapin_Pallidin  15 ldeldeklkelrqsQeeLleqldrlnekLkeleeaq 50 
                                       l+ +d+ l e  +   +L++++d l ++L+ele++ 
  gi|336254196|ref|YP_004597303.1| 159 LESFDAWLDEPDRRAGDLADDIDALERSLDELEDVV 194
                                       566666677777777789999********9999875 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.3
                   Snapin_Pallidin  31 eLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkr 71 
                                        Ll++l+ + + L+e +  + a+ ++d+++ ++ L++ + r
  gi|336254196|ref|YP_004597303.1| 230 LLLADLRAELATLREWAGREGADPPSDVEPRLDELAARRER 270
                                       56666777777777776666677777777777777666655 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.5    0.0075        14      11      37 ..     178     204 ..      51     229 .. 0.81
   2 ?   -1.6   0.0       2.1   3.8e+03      18      66 ..     289     299 ..     255     308 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0075
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdv 37 
                                       +di a++  +d l++ vd + ++  d+
  gi|336254196|ref|YP_004597303.1| 178 DDIDALERSLDELEDVVDGLGSEASDL 204
                                       456666666666666666665555554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.1
                           NPV_P10  18 dkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                       d+V a                                      I++ L 
  gi|336254196|ref|YP_004597303.1| 289 DRVAA--------------------------------------IDEALD 299
                                       23333......................................333333 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.21   3.8e+02      88     118 ..      90     120 ..      21     126 .. 0.61
   2 ?    7.8   0.0    0.0018       3.3      49     114 ..     140     205 ..     133     209 .. 0.78
   3 ?   -1.6   0.0       1.4   2.5e+03      61      77 ..     284     300 ..     258     313 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.21
                           DUF1664  88 evtevredlseigedvesvkeavegleskle 118
                                       +++ v   l+ +   +e+v++   gl+ +l+
  gi|336254196|ref|YP_004597303.1|  90 DLDVVAARLEGFAARLETVEDRAAGLGDRLQ 120
                                       3444445555555555555555555555555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0018
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       q++   ++++++ ++L+ ++++ d+ lde  + + +++++++++++ l+e+++ v+ + +  ++le
  gi|336254196|ref|YP_004597303.1| 140 QMTAAATEVQRAADDLAFDLESFDAWLDEPDRRAGDLADDIDALERSLDELEDVVDGLGSEASDLE 205
                                       777788888888888888888888888888888888888888888888888887777666666555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.4
                           DUF1664  61 krhLssridrvdkklde 77 
                                       ++++ +r++ +d+ lde
  gi|336254196|ref|YP_004597303.1| 284 RERFGDRVAAIDEALDE 300
                                       45566666666666666 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 ?   10.7   0.0   0.00019      0.35     110     187 ..     130     207 ..      58     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                          KASH_CCD 110 enikllaekdelkkklkeLlkekaeLkkqlheleellaekealleektkqieeLkltieEyssiieeLraeksrLee 186
                                       ++  l+ e+ ++     e  +  ++L  +l ++++ l e ++ + +   +i+ L+ +++E++ +++ L +e s Le+
  gi|336254196|ref|YP_004597303.1| 130 DLYELAREIRQMTAAATEVQRAADDLAFDLESFDAWLDEPDRRAGDLADDIDALERSLDELEDVVDGLGSEASDLED 206
                                       456678888889999999999****************************************************9997 PP

                          KASH_CCD 187 q 187
                                        
  gi|336254196|ref|YP_004597303.1| 207 V 207
                                       5 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   0.00016      0.28     111     184 ..     131     204 ..      48     206 .. 0.83
   2 ?    0.7   0.8       0.3   5.4e+02     123     144 ..     259     280 ..     231     282 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                             ATG16 111 lqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekENkeL 184
                                       l +l +++++++++  e+++   +l   l++ ++ l e ++   dl D+++aL+  l  +E+  + l  E+++L
  gi|336254196|ref|YP_004597303.1| 131 LYELAREIRQMTAAATEVQRAADDLAFDLESFDAWLDEPDRRAGDLADDIDALERSLDELEDVVDGLGSEASDL 204
                                       56777888888888888888888888888888888888888888******************999999999887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.3
                             ATG16 123 erlaeleaeraaletklkdree 144
                                        rl+el a+r++l ++l+dr+e
  gi|336254196|ref|YP_004597303.1| 259 PRLDELAARRERLGERLADRTE 280
                                       5899999999999999999986 PP

>> Rbsn  Rabenosyn Rab binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.7     3e+03      33      42 .]     132     141 ..     131     141 .. 0.82
   2 ?    9.1   0.5   0.00058         1      23      37 ..     178     192 ..     176     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.7
                              Rbsn  33 kELqeEidrl 42 
                                        EL +Ei ++
  gi|336254196|ref|YP_004597303.1| 132 YELAREIRQM 141
                                       599****986 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00058
                              Rbsn  23 DEvatLeeNLkELqe 37 
                                       D++++Le++L+EL++
  gi|336254196|ref|YP_004597303.1| 178 DDIDALERSLDELED 192
                                       9************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 2403.01
//
Query:       gi|336254197|ref|YP_004597304.1|  [L=222]
Description: phosphate uptake regulator PhoU [Halopiger xanaduensis SH-6]
Scores for 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-39  132.0  10.3    3.8e-22   78.5   0.7    2.1  2  PhoU      PhoU domain
  ------ inclusion threshold ------
      0.083   11.8   0.3        5.2    5.9   0.0    2.1  2  Kre28     Spindle pole body component
        1.2    9.7   5.4       0.63   10.6   0.7    2.4  2  HSCB_C    HSCB C-terminal oligomerisation domain


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.7   6.4e-26   3.8e-22       2      88 ..      18     104 ..      17     105 .. 0.98
   2 !   58.1   3.2   1.6e-19   9.3e-16       4      88 ..     121     209 ..     118     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 6.4e-26
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERi 78 
                                       ++mae+v+++l++al+ale++d+ la++vi+ dd +++ + ++e +++ +la +qp+a+dlr++ ++ +i +dlERi
  gi|336254197|ref|YP_004597304.1|  18 ESMAETVLTQLRRALTALEDGDEALAQAVIDGDDVVNDRYLDLEGDCIDLLALQQPVASDLRFVAASFKILTDLERI 94 
                                       78*************************************************************************** PP

                                       HHHHHHHHHH CS
                              PhoU  79 gDhavniaer 88 
                                       gD a+n+ae+
  gi|336254197|ref|YP_004597304.1|  95 GDLATNLAEY 104
                                       ********97 PP

  == domain 2  score: 58.1 bits;  conditional E-value: 1.6e-19
                                       HHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHH....HHHHHHHHH CS
                              PhoU   4 maeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrells....llriardlE 76 
                                       ++e v e+++ a++a++ +d +++r + +rddeid+l++  +++++++l  r+  a d+++ll+    +l  +rd E
  gi|336254197|ref|YP_004597304.1| 121 IGEDVCEQVRAAVDAYVADDADACRTIAARDDEIDALCQHASEAVVRELIAREVDAWDVERLLDdvsrVLLTIRDVE 197
                                       578899*******************************************5555555556665444444********* PP

                                       HHHHHHHHHHHH CS
                              PhoU  77 RigDhavniaer 88 
                                       RigDhavn+a r
  gi|336254197|ref|YP_004597304.1| 198 RIGDHAVNVAAR 209
                                       **********87 PP

>> Kre28  Spindle pole body component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0   0.00086       5.2     124     175 ..      12      63 ..       4      73 .. 0.89
   2 ?    4.1   0.0    0.0031        19     130     176 ..     119     165 ..      98     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.00086
                             Kre28 124 sleeeVseLedetltekeseieqikgeIkekgkelaekqdqinelyLettne 175
                                       +l  +V+ + + +lt++++ + +++   +  ++ +++  d +n  yL+  ++
  gi|336254197|ref|YP_004597304.1|  12 RLRADVESMAETVLTQLRRALTALEDGDEALAQAVIDGDDVVNDRYLDLEGD 63 
                                       788999*****************************************97664 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0031
                             Kre28 130 seLedetltekeseieqikgeIkekgkelaekqdqinelyLettnei 176
                                       s + +++ ++ +  +++  ++  ++++++a + d+i+ l+  ++ ++
  gi|336254197|ref|YP_004597304.1| 119 SGIGEDVCEQVRAAVDAYVADDADACRTIAARDDEIDALCQHASEAV 165
                                       556688899999999*************************9998775 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.7   0.00011      0.63      25      60 ..       7      43 ..       1      48 [. 0.73
   2 ?    0.9   0.4      0.11   6.6e+02      25      51 ..     143     173 ..     125     190 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH.HTT.-HHHHHH CS
                            HSCB_C 25 keeleelkaeveerieeleaeleeaf.ekk.dleaaad 60
                                       e l++l+a+ve++ e+ +++l++a+ +   d ++a +
  gi|336254197|ref|YP_004597304.1|  7 RESLDRLRADVESMAETVLTQLRRALtA-LeDGDEALA 43
                                      389***********************52.135554443 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.11
                                       H.HHHHHHHHHHHHHHHHHHHHHHHHH...H CS
                            HSCB_C  25 k.eeleelkaeveerieeleaeleeaf...e 51 
                                       +  ++++  +e+++  ++  +++ +++   e
  gi|336254197|ref|YP_004597304.1| 143 AcRTIAARDDEIDALCQHASEAVVRELiarE 173
                                       2455566666666666666666555554331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 1825.48
//
Query:       gi|336254198|ref|YP_004597305.1|  [L=309]
Description: phosphate ABC transporter ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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  109.7   0.0    2.5e-31  109.0   0.0    1.3  1  ABC_tran     ABC transporter
      1e-11   45.2   0.0    8.2e-05   22.5   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.3e-08   33.8   0.0    1.3e-06   28.0   0.0    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    1.8e-05   24.6   0.0    9.3e-05   22.3   0.0    1.9  2  AAA_15       AAA ATPase domain
    0.00016   22.0   0.0    0.00047   20.4   0.0    1.9  1  AAA_22       AAA domain
    0.00016   22.1   0.2    0.00051   20.5   0.2    1.9  1  AAA_16       AAA ATPase domain
    0.00019   21.4   0.0    0.00044   20.2   0.0    1.6  1  RsgA_GTPase  RsgA GTPase
    0.00046   19.9   0.0    0.00096   18.8   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
    0.00075   19.1   0.1      0.022   14.4   0.0    2.2  2  AAA_25       AAA domain
     0.0017   18.9   0.0     0.0038   17.7   0.0    1.6  1  AAA_23       AAA domain
     0.0027   17.7   0.0     0.0044   17.0   0.0    1.3  1  Rad17        Rad17 P-loop domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.019   14.9   0.0    1.3  1  DeoRC        DeoR C terminal sensor domain
      0.014   15.2   0.0       0.36   10.5   0.0    2.2  2  AAA_30       AAA domain
      0.035   14.3   0.0      0.097   12.8   0.0    1.7  1  AAA_33       AAA domain
      0.046   14.3   0.2       0.17   12.5   0.0    2.1  2  AAA_18       AAA domain
      0.059   12.5   0.0      0.077   12.2   0.0    1.2  1  NB-ARC       NB-ARC domain
      0.071   11.9   0.0        1.6    7.4   0.0    2.1  2  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 !  109.0   0.0   2.4e-34   2.5e-31       1     136 [.      65     232 ..      65     233 .. 0.95

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 2.4e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqepql 70 
                                       lk+vs+++ e +++a++G++G+GKSt+l++l ++ +        G+++ldg+d+ +   +l +lrk++g+++q+p+ 
  gi|336254198|ref|YP_004597305.1|  65 LKDVSMEIPEQSVTALIGPSGCGKSTFLRCLNRMNDRirgarVDGTVELDGEDIYQdgVDLVELRKRVGMVFQNPNP 141
                                       79*********************************99888888999********999999***************** PP

                                       -TTSBHHHH..........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHH CS
                                       xxxxxxxxx..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren..........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalar 121
                                       fp++ +ren                           +++ +e+ l++  l e  ++++++++  LSgGq+qr+++ar
  gi|336254198|ref|YP_004597305.1| 142 FPKS-IRENisygprkhgdietgllarltgraepeRESNLVERSLKRAALWEEVNDRLEDNALGLSGGQQQRLCIAR 217
                                       ****.***********************999876545555************************************* PP

                                       HHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxx RF
                          ABC_tran 122 allkkpkllllDEpt 136
                                       +l+  p+++l+DEp 
  gi|336254198|ref|YP_004597305.1| 218 CLAVGPEVILMDEPA 232
                                       **************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 !   20.7   0.0   2.9e-07    0.0003       1      33 [.      77     109 ..      77     152 .. 0.75
   2 !   22.5   0.0   7.8e-08   8.2e-05     219     298 ..     184     262 ..     146     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.9e-07
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdveglt 33 
                                       +++liGp g+GKS++L++l  + + +r ++ ++
  gi|336254198|ref|YP_004597305.1|  77 VTALIGPSGCGKSTFLRCLNRMNDRIRGARVDG 109
                                       69*****************99976543333333 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 7.8e-08
                            AAA_21 219 r...gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv 292
                                       +      ++e +d+ e +a  lS G+++    ++ +l+  +   ++l DEp + L+P +++++ +l+++l++ +  v
  gi|336254198|ref|YP_004597305.1| 184 SlkrAALWEEVNDRLEDNALGLSGGQQQR-LCIARCLAVGP--EVILMDEPASALDPIATSKIEDLIEDLAE-DYTV 256
                                       13337778889999999************.88888998777..9**************************99.**** PP

                            AAA_21 293 iltTHS 298
                                       +++TH+
  gi|336254198|ref|YP_004597305.1| 257 VVVTHN 262
                                       *****8 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 !   28.0   0.0   1.2e-09   1.3e-06      23     213 ..      74     277 ..      63     282 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.2e-09
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--......BTTCS.STTEEEEEEEEEETTEESSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxx.xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk......skeka.svkkaeveitfdnedkklki 92 
                                       ++s+ta++Gp G+GKs +l  +     +r +  +r ++++  +        ++  +    + +v ++f+n++   k 
  gi|336254198|ref|YP_004597305.1|  74 EQSVTALIGPSGCGKSTFLRCL-----NRMNDRIRGARVDGTVELdgediyQDGVDlVELRKRVGMVFQNPNPFPKS 145
                                       6789***************999.....56667888888888887655544322222033456899999999988555 PP

                                       SSSCEEEEEEEETTSEEEE..EETTEEE-H...HHHHHHHHCTT-STT..........CS-HHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx..xxxxxxxxx...xxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxx RF
                             SMC_N  93 ekeevsisrrvkrkgesey..kingkevtk...kevsellesagiske..........lLSgGektLvalaLlfAiq 154
                                        +e++s   r+  + e+    ++ g+   +   + v++ l++a + +e           LSgG+++ + +a  +A+ 
  gi|336254198|ref|YP_004597305.1| 146 IRENISYGPRKHGDIETGLlaRLTGRAEPEresNLVERSLKRAALWEEvndrlednalGLSGGQQQRLCIARCLAVG 222
                                       55555555444444443220033333222211133445555555555566667777668*******99999998874 PP

                                       CCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 155 kvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtk 213
                                          p+ + l+De ++aLD   ++k+ +l++   ++  ++v++++ ++ ++++    v+ 
  gi|336254198|ref|YP_004597305.1| 223 ---PE-VILMDEPASALDPIATSKIEDLIEDLAEDYTVVVVTHNMQQAARVSDQTAVFL 277
                                       ...55.679***********************************999998877777765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   8.9e-08   9.3e-05      13      68 ..      64     121 ..      63     200 .. 0.78
   2 ?    0.1   0.0      0.49   5.2e+02     326     365 ..     225     262 ..     221     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 8.9e-08
                            AAA_15  13 slkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn..kkvikiekedleif 68 
                                       +lkdv++++ e+ +t liG+ ++GKS++l+ l+ + ++ +     + ++ ++ ed+ + 
  gi|336254198|ref|YP_004597305.1|  64 ALKDVSMEIPEQsVTALIGPSGCGKSTFLRCLNRMNDRIRG-ArvDGTVELDGEDIYQD 121
                                       5899999999999********************99996633.14656666666666555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.49
                            AAA_15 326 illiEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++l++EP   L p a + + +l+ +la+d    v++ TH+
  gi|336254198|ref|YP_004597305.1| 225 VILMDEPASALDPIATSKIEDLIEDLAEDYT--VVVVTHN 262
                                       7999**************************6..******7 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.5e-07   0.00047       5      66 ..      75     128 ..      71     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.5e-07
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralgl 66 
                                       +++++++G+sG+GK+t lr l + +d        r + ++v+ +++ + +d++++ +  ++l
  gi|336254198|ref|YP_004597305.1|  75 QSVTALIGPSGCGKSTFLRCLNRMND--------RIRGARVDGTVELDGEDIYQDGVDLVEL 128
                                       7899********************98........7777777777777777777766666555 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   0.2   4.9e-07   0.00051      14      52 ..      63     131 ..      62     282 .. 0.53

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.9e-07
                            AAA_16  14 salervrsgrp..elvllsGesGvGKsslvrellralekd.............................g 52 
                                       +al++v++  p  +++ l+G+sG+GKs+ +r+l  +++++                             +
  gi|336254198|ref|YP_004597305.1|  63 HALKDVSMEIPeqSVTALIGPSGCGKSTFLRCLN-RMNDRirgarvdgtveldgediyqdgvdlvelrkR 131
                                       5778788877788999*****************9.56666443344444444444444444444444431 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.2e-07   0.00044      75     122 ..      50      98 ..      29     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.2e-07
                                       TTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  75 lgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       l +e l v+  + ++l++++ ++ + ++++l+G+SG GKSt++  l+  
  gi|336254198|ref|YP_004597305.1|  50 LAVENLNVHYGDDHALKDVSMEIPEqSVTALIGPSGCGKSTFLRCLNRM 98 
                                       5556666777788899999999988799***************999873 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 !   18.8   0.0   9.1e-07   0.00096      11      39 ..      64      92 ..      57      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.1e-07
                            AAA_29 11 tfdghtieidlkgatlltGpsGsGKSTll 39
                                       +++ ++ei ++++t l+GpsG GKST+l
  gi|336254198|ref|YP_004597305.1| 64 ALKDVSMEIPEQSVTALIGPSGCGKSTFL 92
                                      5667889999888**************98 PP

>> AAA_25  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     0.022      30      50 ..      72      92 ..      63      97 .. 0.89
   2 ?    2.4   0.1     0.094        99      86     148 ..     194     259 ..     181     274 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +p++++++l+G++g+GK+t++
  gi|336254198|ref|YP_004597305.1| 72 IPEQSVTALIGPSGCGKSTFL 92
                                      69*****************97 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.094
                            AAA_25  86 lrrRlravgeal..rddarllvldlagv.eslpLfak..drggtlltadvdaleaaieevegvrlvvi 148
                                       ++ Rl+     l   +++rl +  +  v  ++ L+++   + ++++t+++++l++++ e  ++ +vv+
  gi|336254198|ref|YP_004597305.1| 194 VNDRLEDNALGLsgGQQQRLCIARCLAVgPEVILMDEpaSALDPIATSKIEDLIEDLAE--DYTVVVV 259
                                       44555555544455567888888888888888887762234445589999999999999..4455543 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.6e-06    0.0038       4      40 ..      52      96 ..      49      98 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.6e-06
                            AAA_23  4 ienfrsf.......rdqeidF.skgltlItGpNGaGKTTildAik 40
                                      +en++ +       +d++ +  ++ +t+++Gp G+GK+T+l+++ 
  gi|336254198|ref|YP_004597305.1| 52 VENLNVHygddhalKDVSMEIpEQSVTALIGPSGCGKSTFLRCLN 96
                                      5555555554444455555657889******************85 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.2e-06    0.0044      20      67 ..      49      97 ..      32     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.2e-06
                             Rad17 20 elavhkkkieev.kewlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                      +lav    ++   +++lk  ++e  ++ +  + GPsGCgkst ++ L +
  gi|336254198|ref|YP_004597305.1| 49 KLAVENLNVHYGdDHALKDVSMEIPEQSVTALIGPSGCGKSTFLRCLNR 97
                                      55555555544314577777888887789999*************9976 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.8e-05     0.019      32      73 ..     244     283 ..     238     301 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                             DeoRC  32 lelaraLaekknltvvTnslnvaeeLsekedikvillGGevr 73 
                                       + l++ Lae+ +++vvT++++ a+++s++    v+l+GGe+ 
  gi|336254198|ref|YP_004597305.1| 244 EDLIEDLAEDYTVVVVTHNMQQAARVSDQ--TAVFLTGGELV 283
                                       67999**********************97..9*******975 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00035      0.36      18      49 ..      75     107 ..      66     111 .. 0.84
   2 ?    2.4   0.1       0.1   1.1e+02      90     130 ..     224     267 ..     170     279 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                            AAA_30  18 drvavltGpAGtGKttalkalreaweaa.ggrv 49 
                                       + v++l Gp G GK+t l+ l+++ ++  g rv
  gi|336254198|ref|YP_004597305.1|  75 QSVTALIGPSGCGKSTFLRCLNRMNDRIrGARV 107
                                       56999***************9998877666666 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.1
                            AAA_30  90 tllivDEagmv....dtkqlaallkaaekagakvilvGDerQlas 130
                                       ++++ DE + +    +t+++++l++ +++ + +v++v  + Q a+
  gi|336254198|ref|YP_004597305.1| 224 EVILMDEPASAldpiATSKIEDLIEDLAE-DYTVVVVTHNMQQAA 267
                                       67777776655566678888888888877.555555555555443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.2e-05     0.097       1      24 [.      77     100 ..      77     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.2e-05
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg 24 
                                       ++ l+G++G+GKst+++ l + ++
  gi|336254198|ref|YP_004597305.1|  77 VTALIGPSGCGKSTFLRCLNRMND 100
                                       5679************98866655 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   0.00016      0.17       3      25 ..      80     104 ..      79     149 .. 0.76
   2 ?   -2.8   0.1       8.2   8.7e+03     106     120 ..     164     178 ..     162     188 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                            AAA_18   3 ltGtpGvGKttlakeLskrl.gf.g 25 
                                       l G++G+GK+t+ + L++++  + g
  gi|336254198|ref|YP_004597305.1|  80 LIGPSGCGKSTFLRCLNRMNdRIrG 104
                                       89**************999744462 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.2
                            AAA_18 106 lleRlekRgyeeaki 120
                                       ll Rl  R + e++ 
  gi|336254198|ref|YP_004597305.1| 164 LLARLTGRAEPERES 178
                                       788999999877663 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.3e-05     0.077      15     110 ..      70     229 ..      62     299 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.3e-05
                                       TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE................................. CS
                            NB-ARC  15 kdelqslvvalvGmgGvGKttlakqilnksdeveg.rFdsvawv................................. 57 
                                       ++ +++ v al G  G+GK+t ++  ++  d ++g r d+ + +                                 
  gi|336254198|ref|YP_004597305.1|  70 MEIPEQSVTALIGPSGCGKSTFLRCLNRMNDRIRGaRVDGTVELdgediyqdgvdlvelrkrvgmvfqnpnpfpksi 146
                                       445666799*******************9999999889988888888888888888888888888777777777777 PP

                                       .................................EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCC CS
                            NB-ARC  58 .................................vvsktdkseeiletilkeLslseddleekeeveslkrklvrlLl 101
                                                                         v ++ k   ++e+++ +L+++   l+  +++      + r L 
  gi|336254198|ref|YP_004597305.1| 147 renisygprkhgdietgllarltgraeperesnLVERSLKRAALWEEVNDRLEDNALGLSGGQQQ---RLCIARCLA 220
                                       77777777777777777777777777777777777777777777777777775554444433333...355666666 PP

                                       CTTEEEEEE CS
                            NB-ARC 102 tkrfllvlD 110
                                           ++++D
  gi|336254198|ref|YP_004597305.1| 221 VGPEVILMD 229
                                       666666666 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0015       1.6      80     107 ..      69      95 ..      46     101 .. 0.71
   2 ?    2.2   0.0     0.059        62     224     250 ..     241     268 ..     209     275 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0015
                        Adeno_IVa2  80 slnyglqPviGviyGPtGsGksqllrnl 107
                                       s+++  q v   + GP G+Gks +lr l
  gi|336254198|ref|YP_004597305.1|  69 SMEIPEQSVTA-LIGPSGCGKSTFLRCL 95 
                                       44444555554.56************88 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.059
                        Adeno_IVa2 224 sklsakfkk.ctgfsvlvvlhnlnPrsd 250
                                       sk+ +  +  +  ++v+vv hn++  + 
  gi|336254198|ref|YP_004597305.1| 241 SKIEDLIEDlAEDYTVVVVTHNMQQAAR 268
                                       66666555413579*********87655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.37
# Mc/sec: 2519.06
//
Query:       gi|336254199|ref|YP_004597306.1|  [L=524]
Description: phosphate ABC transporter inner membrane subunit PstA [Halopiger xanaduensis SH-6]
Scores for 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-19   68.9  15.4    4.5e-19   68.9  15.4    4.8  5  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        5.6    7.0   5.4         25    4.9   5.4    2.2  1  TNFR_16_TM    Tumor necrosis factor receptor member 16 trans-


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 ?   -2.4   1.9      0.38   3.4e+03     109     130 ..      47      68 ..      17      82 .. 0.47
   2 ?   -2.2   4.8      0.32   2.9e+03     108     172 ..      46     111 ..      43     115 .. 0.72
   3 ?  -13.1  17.4         2   1.8e+04     109     147 ..      97     130 ..      91     244 .. 0.62
   4 ?   -8.8  10.6         2   1.8e+04      13      44 ..     212     277 ..     194     306 .. 0.48
   5 !   68.9  15.4   5.1e-23   4.5e-19       5     173 ..     299     512 ..     295     523 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.38
                      BPD_transp_1 109 piitglilafggllggavllef 130
                                       ++++ +++a+  +lg+a+l++ 
  gi|336254199|ref|YP_004597306.1|  47 VTVPVAGVALSTALGAALLVLG 68 
                                       2333333333333333333333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.32
                      BPD_transp_1 108 ppiitglilafggllggavlleflgswpG..lgtllleailgydyseisnggvlalviavlllnlva 172
                                       +++++ +++a+  +lg+a+l++ lg   G  l+++l ++  g + s++++++v+++++ +++ +lva
  gi|336254199|ref|YP_004597306.1|  46 TVTVPVAGVALSTALGAALLVLGLG-VVGfgLTSRLGSVDTGPQPSAGLVAAVAFTGVWFAVGSLVA 111
                                       6788889999999999999999998.33444666666666666666666777777777777777776 PP

  == domain 3  score: -13.1 bits;  conditional E-value: 2
                      BPD_transp_1 109 piitglilafggllggavlleflgswpGlgtllleailg 147
                                       +++tg+ +a+g+l+ ga+ l ++gs +        +  +
  gi|336254199|ref|YP_004597306.1|  97 VAFTGVWFAVGSLVAGAAGLGTVGSTTV-----GGVVGA 130
                                       6677777777777777777777774443.....222222 PP

  == domain 4  score: -8.8 bits;  conditional E-value: 2
                      BPD_transp_1  13 nkkldkllrpliivllslPsfvlaillvlvf.....................................v 44 
                                       ++ +   ++++ ivl+ l ++v ++ +   +                                     v
  gi|336254199|ref|YP_004597306.1| 212 GRNVGAYVLIYLIVLSILAVLVGLLAF---VavkglpglfngfsvgggtlirwpfltngaslfadvagV 277
                                       333334444444444444444422222...133466666666666666666666654444433333332 PP

  == domain 5  score: 68.9 bits;  conditional E-value: 5.1e-23
                      BPD_transp_1   5 Gilaa.....lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraal 76 
                                       G+ aa     ++  ++++ ++ + ++ l+s+Ps+v++++  ++++   + + + l+++++l ++++p+v+++ r+a+
  gi|336254199|ref|YP_004597306.1| 299 GVGAAvflseYAEQGRFTGVVEIATNGLWSTPSIVFGLFGAAFLIPRFGNQKSLLAGMLTLGFMLLPLVLITSREAI 375
                                       5555555559*****************************998887777788999*********************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgtllleailgydys 151
                                        ++p++++ a+ alG+s+wq++r vvlP+a+p i tg+il +g++ g+++ ++++++++         ++i g++++
  gi|336254199|ref|YP_004597306.1| 376 LAVPDEYRDASAALGVSKWQTIRSVVLPAAIPGITTGVILGVGRIAGETAPILLTMGGGVlpGKEAAPNVIGGFQLH 452
                                       ********************************************************664466556666666666666 PP

                      BPD_transp_1 152 eis......................................nggvlalviavlllnlvad 173
                                       +                                        +g++l+l+++vl++ ++  
  gi|336254199|ref|YP_004597306.1| 453 ASPpfvtnpallestsalpyqlyalitaglsgniespeqfaWGLALTLLLVVLAFYAIGI 512
                                       555777777777777777777777888888888888877655555555555555555544 PP

>> TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   5.4    0.0028        25      12      28 ..     227     242 ..     220     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0028
                        TNFR_16_TM  12 SILaaVvvgLlaYvifK 28 
                                       SILa V+vgLla+v+ K
  gi|336254199|ref|YP_004597306.1| 227 SILA-VLVGLLAFVAVK 242
                                       8885.9********977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 3701.32
//
Query:       gi|336254200|ref|YP_004597307.1|  [L=377]
Description: phosphate ABC transporter inner membrane subunit PstC [Halopiger xanaduensis SH-6]
Scores for complete 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   64.0  11.6    1.4e-17   64.0  11.6    2.7  3  BPD_transp_1   Binding-protein-dependent transport system inn
  ------ inclusion threshold ------
      0.039   13.0   0.1       0.06   12.4   0.1    1.2  1  DUF2048        Abhydrolase domain containing 18
       0.25   11.9   6.9       0.35   11.5   6.2    1.8  1  Abhydrolase_6  Alpha/beta hydrolase family
          1    9.2   3.9       0.92    9.3   0.1    2.5  3  YlaC           Inner membrane protein YlaC


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 ?   -0.1   9.7      0.15   6.8e+02     108     175 ..      46     106 ..      40     116 .. 0.61
   2 ?    2.3   0.4     0.026   1.2e+02      98     132 ..     142     176 ..     137     180 .. 0.89
   3 !   64.0  11.6   3.2e-21   1.4e-17       1     185 []     168     371 ..     164     371 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.15
                      BPD_transp_1 108 ppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadil 175
                                         +++g  + +++ + +  ++ fl+ ++G g  + +a+ ++ +++++ ++v  +++ ++++ ++   l
  gi|336254200|ref|YP_004597307.1|  46 LAAFAG--FLLASPWAAVPFAAFLA-STGYGWIRYQALTARAITFAM-TTVTLVTLGLIVVFIF---L 106
                                       444445..55555555555555666.3469**************777.4444444444444333...3 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.026
                      BPD_transp_1  98 frkvvlPnalppiitglilafggllggavlleflg 132
                                       +r+ +lP++  +++ + i +++++  g ++++f++
  gi|336254200|ref|YP_004597307.1| 142 VRYSLLPMIHGTVMVTTIATLVAAPLGVAAALFIA 176
                                       677799**************************998 PP

  == domain 3  score: 64.0 bits;  conditional E-value: 3.2e-21
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf......vilsilghlilpviillllsaapyvrli 71 
                                       g+ +++++a     ++++l+ p i++l ++Ps+v +++ + ++       +    g++ l v +++ l+a+p+v+ +
  gi|336254200|ref|YP_004597307.1| 168 GVAAALFIAEIAPPTVRELVKPGIEILAGIPSIVYGFIGFTIInpwasdEFALNGGSTYLFVGLVVGLMALPTVVSV 244
                                       5667777778899***************************999*****97777788********************* PP

                      BPD_transp_1  72 rraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgy 148
                                        ++al s+p++ +  + alGa++wq +  ++lP+a++ + + ++l +g+++g+++++  ++++   + ++ e+i + 
  gi|336254200|ref|YP_004597307.1| 245 AEDALTSVPDSMKDGSVALGATDWQSMTSITLPAAFSGVSAAVLLGVGRAIGETMAATVMLAGI--Q-RIPEPITNV 318
                                       *********************************************************9999543..3.455555555 PP

                      BPD_transp_1 149 dyseis................nggvlalviavlllnlvadilqrlldprvrk 185
                                        y + +                  +++a+++++++ +l++ i  ++++ r+r+
  gi|336254200|ref|YP_004597307.1| 319 FYGYETltsliaanyghannvfESALFAAGVVLFVTVLCLSIASQYIEARMRR 371
                                       55555555668999999999998899999999999999************995 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.3e-05      0.06     177     209 ..      34      66 ..      24      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                           DUF2048 177 plgltGlSmGGhmaslaasnwpkplvlvpclsw 209
                                        l++ GlSmG   a++a+ +++ p + vp+ + 
  gi|336254200|ref|YP_004597307.1|  34 ALAVVGLSMGALLAAFAGFLLASPWAAVPFAAF 66 
                                       69***************************9664 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   6.2   7.7e-05      0.35      54     173 ..      24     142 ..       5     271 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.7e-05
                                       HHHHCCTT..TTSEEEEEETCHHHHHHHHHHCC..EEEEES-..----TTT...............S----TTHHHH CS
                     Abhydrolase_6  54 aalldelaagggpvvlvGHSlGGalalaaaplalvvgvlldppptalpagl...............laaalelllal 115
                                       +++++e    + +  +vG S+G++la++   +      ll++p+ a+p++                 a+a+++    
  gi|336254200|ref|YP_004597307.1|  24 REFVAETE--PEALAVVGLSMGALLAAF---AG----FLLASPWAAVPFAAflastgygwiryqalTARAITF---- 87 
                                       55666664..7778**********9999...55....777776644444444433332221222111111111.... PP

                                       HHTT-CCCCHCCH....S-HSCCCCHHHC.CCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGC CS
                     Abhydrolase_6 116 lallrllawlsre....plprlfladeda.daawrarlarlaallaglgllpaaawadlpvpl 173
                                         + ++ ++++++    +    fl+  +a +++ ++ +    + l ++     ++w ++ +p+
  gi|336254200|ref|YP_004597307.1|  88 --AMTTVTLVTLGlivvF---IFLEAIPAfRYESATVFGVSVPGLGMFT---QTRWSPTSEPV 142
                                       ..1111222222232220...2222111111222222222222222222...33444444444 PP

>> YlaC  Inner membrane protein YlaC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00021      0.92      44      98 ..      72     124 ..      60     138 .. 0.83
   2 ?   -1.9   0.0       0.6   2.7e+03      36      56 ..     225     245 ..     219     251 .. 0.82
   3 ?   -0.7   0.1      0.25   1.1e+03      37      60 ..     343     366 ..     333     370 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00021
                              YlaC  44 vsylavavlllyspylglaslilltvllillsavllldikPvyrfedidvldlrv 98 
                                        +++   +l  ++ ++++++++l+t+ li++  +++l+  P +r+e   v+ + v
  gi|336254200|ref|YP_004597307.1|  72 YGWIRYQALTARAITFAMTTVTLVTLGLIVV--FIFLEAIPAFRYESATVFGVSV 124
                                       57888999999999***99999999988875..8899*********988876655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.6
                              YlaC  36 pylflamlvsylavavlllys 56 
                                        ylf++++v+ +a+  ++ ++
  gi|336254200|ref|YP_004597307.1| 225 TYLFVGLVVGLMALPTVVSVA 245
                                       699999999999998887766 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.25
                              YlaC  37 ylflamlvsylavavlllyspylg 60 
                                        lf a +v +++v+ l + s+y+ 
  gi|336254200|ref|YP_004597307.1| 343 ALFAAGVVLFVTVLCLSIASQYIE 366
                                       578888888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2754.58
//
Query:       gi|336254201|ref|YP_004597308.1|  [L=395]
Description: phosphate ABC transporter substrate-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-22   78.2   0.6    7.9e-22   78.2   0.6    1.8  2  PBP_like_2   PBP superfamily domain
    1.1e-11   44.2   0.1    1.8e-11   43.6   0.1    1.2  1  PBP_like     PBP superfamily domain
  ------ inclusion threshold ------
       0.03   14.6   0.1      0.067   13.5   0.0    1.6  2  Hydrolase    haloacid dehalogenase-like hydrolase
      0.083   12.8   3.1       0.16   11.8   3.1    1.5  1  TAT_signal   TAT (twin-arginine translocation) pathway signal


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.88   3.9e+03      13     250 ..      73      84 ..      59     109 .. 0.56
   2 !   78.2   0.6   1.8e-25   7.9e-22      32     267 ..     138     351 ..     134     365 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.88
                        PBP_like_2  13 fgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangaggliqvp 89 
                                        + Gs+t++p+                                                                  
  gi|336254201|ref|YP_004597308.1|  73 SAEGSSTVYPI------------------------------------------------------------------ 83 
                                       33333333333.................................................................. PP

                        PBP_like_2  90 vaigaialvvnkdnplnlsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqgpwtasgig 166
                                                                                                                    
  gi|336254201|ref|YP_004597308.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                        PBP_like_2 167 asgsegvasavsnngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplawslqpveenia 243
                                                                                                                    
  gi|336254201|ref|YP_004597308.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                        PBP_like_2 244 dgayPls 250
                                             s
  gi|336254201|ref|YP_004597308.1|  84 ------S 84 
                                       ......3 PP

  == domain 2  score: 78.2 bits;  conditional E-value: 1.8e-25
                        PBP_like_2  32 ekaapgakvnyastGSgagikalrngdvdfagsdrplteseia.agwaang.aggliqvpvaigaialvvnkd...n 103
                                       e+++p+++ ++a + Sg+g +a+r+g vd++ s+ p+t++ ++ +     + + + + + v++++  ++v+++    
  gi|336254201|ref|YP_004597308.1| 138 ERSNPPFSTQVALSHSGTGCEAVRDGLVDIGNSSGPITAELDIsE----EErDENYVDHVVGRDGQPVFVSQEvydA 210
                                       6788999999******************************77533....33579*****************997887 PP

                        PBP_like_2 104 pln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqgpwt...asgigasg....seg 172
                                       +++ l+ e++++I++g I nW++ +g+p d+ I vv r +gsgt ++f  +++  ++++               + +
  gi|336254201|ref|YP_004597308.1| 211 GVEqLTGEEIRGIYQGDIANWSE-VGGP-DQEIYVVGRAEGSGTDTTFRLNMLGDADAEmdvD------TrlgqNQQ 279
                                       7779*******************.6666.*******************999998877664332......23344777 PP

                        PBP_like_2 173 vasav.snngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplawslqpveeniadgayP 248
                                       v +++  n++aigy  +a+++   g  +++++  +g++++p      +                   e++i+d +yP
  gi|336254201|ref|YP_004597308.1| 280 VQQVLqDNDNAIGYMALAFAG--SGIQAVAID-FDGTVYEPD----PD------------------AENTIYDAEYP 331
                                       77776799*************..455555432.334444444....22..................346778999** PP

                        PBP_like_2 249 lsrftyiivyqpyayh.gnn 267
                                       l r++++++   +  + g++
  gi|336254201|ref|YP_004597308.1| 332 LNRDLHMYTTITDDTPeGTD 351
                                       ***99999865555554554 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.1   3.9e-15   1.8e-11       5     155 ..     138     307 ..     134     322 .. 0.78

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 3.9e-15
                                       HHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHH CS
                          PBP_like   5 aeknpgvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpk 81 
                                       ++ np ++ +va + sg+G +a+r+g +di++s+ +++   e ++++ ++  d+ ++v   + r+ q + v ++   
  gi|336254201|ref|YP_004597308.1| 138 ERSNPPFSTQVALSHSGTGCEAVRDGLVDIGNSSGPIT--AELDISEEER--DE-NYVDHVVGRDGQPVFVSQEVYD 209
                                       5789999*****************************97..4566664453..44.5777777788888888888555 PP

                                       S.................--BGGGC..-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCC CS
                          PBP_like  82 k.................itnwkdl..adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaa 139
                                       +                 i+nw+++  +d+++ +v+R++GSGt   f   + +   + ++  ++++   ++++v++ 
  gi|336254201|ref|YP_004597308.1| 210 AgveqltgeeirgiyqgdIANWSEVggPDQEIYVVGRAEGSGTDTTFRLNMLG---DADAEMDVDTRLGQNQQVQQV 283
                                       456677777788888888******************************99977...4444445577999******** PP

                                       HCCETTCCE........CCCGG-H CS
                          PBP_like 140 Vaagradvg........vgieava 155
                                        ++++ ++g         gi+ava
  gi|336254201|ref|YP_004597308.1| 284 LQDNDNAIGymalafagSGIQAVA 307
                                       *****9999444444444455555 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   0.0       1.2   5.2e+03     151     180 ..     211     243 ..     186     246 .. 0.64
   2 ?   13.5   0.0   1.5e-05     0.067       1      88 [.     303     386 ..     303     395 .] 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
                                       HHHH.TTGGGESEEEEHHCES...STTTSHHHHH CS
                                       xxxx.xxxxxxxxxxxxxxxx...xxxxxxxxxx RF
                         Hydrolase 151 aanq.lGddyfdaviasdiet...vakpspegkv 180
                                         +q  G + + +++++di     v++p++e++v
  gi|336254201|ref|YP_004597308.1| 211 GVEQlTG-EEIRGIYQGDIANwseVGGPDQEIYV 243
                                       4444344.44445555555556667788877776 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.5e-05
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH....HHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletg....sehpigkalvaaakarsgaltgfatfigrgayaigk 73 
                                       i +v++D+dGT+++  p  e +i  a+ +l++ l++      ++p g  + +aa  +   lt+f++     ++ +  
  gi|336254201|ref|YP_004597308.1| 303 IQAVAIDFDGTVYEPDPDAENTIYDAEYPLNRDLHMYttitDDTPEGTDMREAA-FLNMFLTEFGQ-----QVFVED 373
                                       789***********************9999999999988999999999993333.33345666766.....666666 PP

                                       HHHHHHHHCHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                         Hydrolase  74 pewltaldippdlga 88 
                                       + ++t    ++dl+a
  gi|336254201|ref|YP_004597308.1| 374 ENYITLP--TSDLEA 386
                                       6666655..555555 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.1   3.7e-05      0.16       2      25 ..      12      34 ..      11      36 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      +SRR  L +sA ++AA+++g c++
  gi|336254201|ref|YP_004597308.1| 12 VSRRKYLLASATVGAAGLAG-CSS 34
                                      8*************888655.543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); 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:                         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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2867.91
//
Query:       gi|336254202|ref|YP_004597309.1|  [L=327]
Description: metallophosphoesterase [Halopiger xanaduensis SH-6]
Scores for 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-18   67.2   0.2    3.6e-18   66.8   0.2    1.2  1  Metallophos    Calcineurin-like phosphoesterase
    1.2e-10   41.8   0.6    3.8e-10   40.2   0.6    1.7  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 !   66.8   0.2     4e-22   3.6e-18       2     203 ..      30     236 ..      29     237 .. 0.64

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 4e-22
                                       EEEEEESBTB....TTCCTHHHHHHHHHHHH....HHHTTESEEEEESTSSSSS.HHHHHHHHH.HHHHHHHTSEEE CS
                       Metallophos   2 rilvigDlHl....algggqlddllkllddl....lreekpdlvllaGDlvdrg.dlekellel.laalvkypipvy 68 
                                       +++v+gD+H+      ++  ++++++ l+ +    +++  +dlvl++GDl+ +g +++++ ++  l++l +   p++
  gi|336254202|ref|YP_004597309.1|  30 TLAVVGDPHIatrsQGTYRVFHRTEQRLRAViddvNER-AVDLVLFPGDLTKDGePWNYDRVDAlLEELER---PFI 102
                                       679********999555556666665554443331555.99********999999*********5666666...*** PP

                                       EEC-TTSCHHH.HHHHHHHHHHHH.......HHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHH CS
                       Metallophos  69 lllGNHegfee.ellnkygylgif.......sepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgsl 137
                                       +++GNH+ +++ +  ++ ++ + f       s p+ ++++  + l l+s            +g       +d    +
  gi|336254202|ref|YP_004597309.1| 103 ATPGNHD-LQKcDDDHRCPSATAFgkrygatSFPFHREVGGIDLLVLNS-----------AAG-------PDGPYAE 160
                                       *******.66666666666555552111333333333333333333333...........333.......2222333 PP

                                       HHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESS..........CSSSCSCCHHHHH........HHHHHTTESEE CS
                       Metallophos 138 nleleapepgdewlkdlekrekadwvivlgHsply..........rgsgylfgdeale........dllkkygvdlv 196
                                       +++ + +  + ewl d +  +   ++++ +H pl+                   +a+          ll+++gv lv
  gi|336254202|ref|YP_004597309.1| 161 THRGRLSSAQLEWLDD-RLADASVPIVTCHHNPLPvvtdplchadP-------WRAFTmrdrgrvrSLLERHGVSLV 229
                                       3333333333999999.88889999999999999988864333332.......222224677777788********* PP

                                       EEESSSS CS
                       Metallophos 197 isGHtHv 203
                                       + GH H 
  gi|336254202|ref|YP_004597309.1| 230 VTGHHHL 236
                                       ******7 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 !   40.2   0.6   4.2e-14   3.8e-10       9     164 ..      50     267 ..      30     268 .. 0.70

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 4.2e-14
                     Metallophos_2   9 lHsnldaleavlealkevgvdaiihaGDl.eeeep...evleellela..pvlaVrGNnD................. 62 
                                       +H+  ++l+av+++++e +vd++++ GDl +++ep   + +++lle +  p++a +GN+D                 
  gi|336254202|ref|YP_004597309.1|  50 FHRTEQRLRAVIDDVNERAVDLVLFPGDLtKDGEPwnyDRVDALLEELerPFIATPGNHDlqkcdddhrcpsatafg 126
                                       359999***********************977888555444444443368**********98888777777666666 PP

                     Metallophos_2  63 ............eevveedvlreaaelgtdl.........................peeaelel.......agekvl 95 
                                                   e                 +                          ++a+le+       a + + 
  gi|336254202|ref|YP_004597309.1| 127 krygatsfpfhrE-----------------VggidllvlnsaagpdgpyaethrgrLSSAQLEWlddrladASVPIV 186
                                       6655555555531.................24444444444444444447666664366666643433333444499 PP

                     Metallophos_2  96 liHgdpl..................gvkdalaellkeaeegsdvvvcGHtHvpevekeggv.lvvnPGsvgeprdgd 153
                                        +H+ pl                  +++ ++++ll++   g+ +vv GH H p++ +++g+  ++ P  ++ p    
  gi|336254202|ref|YP_004597309.1| 187 TCHHNPLpvvtdplchadpwraftmRDRGRVRSLLER--HGVSLVVTGHHHLPSLVRRNGLcQLIAPAIASFP---- 257
                                       99999889999999999999***99999999999999..9999**********88888777245555555555.... PP

                     Metallophos_2 154 petyaildtde 164
                                        + y++l++de
  gi|336254202|ref|YP_004597309.1| 258 -QAYCLLEIDE 267
                                       .5777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2453.62
//
Query:       gi|336254203|ref|YP_004597310.1|  [L=92]
Description: hypothetical protein Halxa_2815 [Halopiger xanaduensis SH-6]
Scores for 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   0.1      0.034   14.4   0.1    1.2  1  zf-Di19    Drought induced 19 protein (Di19), zinc-binding
      0.089   13.1   0.1       0.11   12.8   0.1    1.1  1  zf-C2H2_2  C2H2 type zinc-finger (2 copies)


Domain annotation for each model (and alignments):
>> 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 ?   14.4   0.1   3.8e-06     0.034      30      54 .]      43      69 ..      38      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-06
                           zf-Di19 30 kevvCPvCa..ekvtkdlvaHltleha 54
                                      + + CP+C   + +++ ++ Hl+l+h+
  gi|336254203|ref|YP_004597310.1| 43 RTHACPLCGytDDTRDSVFTHLQLSHR 69
                                      567889995446688888888888886 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.2e-05      0.11      44      79 ..      38      72 ..      35      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                         zf-C2H2_2 44 rekieekleClyCekefkslealreHmkkkgHckin 79
                                      re +e+++ C +C+++ ++++++ +H++  +H+k +
  gi|336254203|ref|YP_004597310.1| 38 RESLERTHACPLCGYTDDTRDSVFTHLQ-LSHRKRA 72
                                      67899999********99********96.4566654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 695.35
//
Query:       gi|336254204|ref|YP_004597311.1|  [L=326]
Description: hypothetical protein Halxa_2816 [Halopiger xanaduensis SH-6]
Scores for 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   4.9      0.016   15.6   4.9    2.4  3  YlqD          YlqD protein
      0.039   13.0   0.7      0.054   12.5   0.7    1.1  1  LuxC          Acyl-CoA reductase (LuxC)
       0.04   11.4  10.0     0.0079   13.8   6.1    1.6  2  DUF3584       Protein of unknown function (DUF3584)
      0.086   12.4   5.2      0.033   13.7   2.6    1.6  2  Exonuc_VII_L  Exonuclease VII, large subunit
       0.11   12.6   2.3       0.25   11.3   2.3    1.6  1  Laminin_II    Laminin Domain II
       0.16   11.6   2.0       0.39   10.4   2.0    1.7  1  YkyA          Putative cell-wall binding lipoprotein
          1    9.4   3.8        5.9    6.9   0.3    2.6  3  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
        1.7    7.9  13.1         13    5.0   0.1    2.1  2  DUF4407       Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.5   3.4e+03      25      48 ..      44      67 ..      38      80 .. 0.65
   2 ?   15.6   4.9   7.2e-06     0.016      16      89 ..     146     219 ..     144     233 .. 0.92
   3 ?    0.1   0.1      0.44   9.8e+02      32      56 ..     220     244 ..     218     266 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.5
                              YlqD 25 lqaqieqldkelqqLefqakrlik 48
                                      l ++ e l++e +qL+++++  ++
  gi|336254204|ref|YP_004597311.1| 44 LATAREVLEREDRQLTVEQRAFER 67
                                      556666677777777777765544 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 7.2e-06
                              YlqD  16 klKeelqqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvqkL 89 
                                       ++ e ++++++++  ++ ++ +qL+  ++r +  +++q +++ ++++e+ve e++ + ++ ++l++  e++q+L
  gi|336254204|ref|YP_004597311.1| 146 TWLESIAEEFSEEQAAALEQHAQLHPRLQRSLVTAAEQVVENRAQLRERVETEREAVDDADRELTDVCEDLQSL 219
                                       688999******************************************************************98 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.44
                              YlqD  32 ldkelqqLefqakrlikeikkqsaq 56 
                                       l++ l+qLef+a rl ++  +   +
  gi|336254204|ref|YP_004597311.1| 220 LEQPLAQLEFNALRLTRDRLESLRE 244
                                       5677788888877776555443333 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   2.4e-05     0.054     253     328 ..     152     226 ..     145     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                              LuxC 253 idefaeaLaaaLekrarilpkakldedeaakisskraelklkylladekkvvsskdqkwtvllseeqeelnePlnr 328
                                       ++ef+e  aaaLe++a++ p+++ +   aa+   +    +l+   + e++ v + d + t + ++ q  l++Pl +
  gi|336254204|ref|YP_004597311.1| 152 AEEFSEEQAAALEQHAQLHPRLQRSLVTAAEQVVENRA-QLRERVETEREAVDDADRELTDVCEDLQSLLEQPLAQ 226
                                       68***********************9988876544443.5**************************9******964 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.15   3.3e+02     852     890 ..      44      82 ..      34      87 .. 0.62
   2 ?   13.8   6.1   3.5e-06    0.0079     796     911 ..     136     254 ..     122     274 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.15
                           DUF3584 852 lekerkalekqldqldenlrklrdllsklaelkldadae 890
                                       l ++r+ le    ql+ + r ++ +++++a+l+ +a+ +
  gi|336254204|ref|YP_004597311.1|  44 LATAREVLEREDRQLTVEQRAFERFQRRVAALETAAPRA 82 
                                       455566666666666666666666666666666665555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.5e-06
                           DUF3584 796 vreYraflqetwlkvdslaee.rpalkeqveelesaaeeleqeltrliedtklerkkl....ekerkalekqldqld 867
                                       v +Y++ +  twl+  s+aee  ++ ++ +e+  + + +l+  l ++ e++  +r++l    e+er+a +++  +l+
  gi|336254204|ref|YP_004597311.1| 136 VPHYDDLYDDTWLE--SIAEEfSEEQAAALEQHAQLHPRLQRSLVTAAEQVVENRAQLrervETEREAVDDADRELT 210
                                       778*********87..6666524455566677777777888888777766655555442222788999999999999 PP

                           DUF3584 868 enlrklrdllskl.aelkldadaeqaegelaerlaaleelkrkre 911
                                       +   +l++ll+++ a+l+++a   + +  l+   +++++l ++r+
  gi|336254204|ref|YP_004597311.1| 211 DVCEDLQSLLEQPlAQLEFNALRLTRD-RLESLRERCDDLATERQ 254
                                       999999999999999999988777766.33333333333333333 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 ?   -1.9   0.0      0.87   1.9e+03     180     198 ..      53      71 ..      33      86 .. 0.41
   2 ?   13.7   2.6   1.5e-05     0.033     134     245 ..     151     260 ..     149     313 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.87
                      Exonuc_VII_L 180 speellerkrqrldeleer 198
                                       + +++l+ ++++++++++r
  gi|336254204|ref|YP_004597311.1|  53 REDRQLTVEQRAFERFQRR 71 
                                       1222222222222222221 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.5e-05
                      Exonuc_VII_L 134 aAelvvpdkaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkk 210
                                       +Ae  ++++a  +eq ++l+ rl++++ ++ e+  ++  +l++r+++ +e ++++ ++l+++ e+l++ l++ l   
  gi|336254204|ref|YP_004597311.1| 151 IAEEFSEEQAAALEQHAQLHPRLQRSLVTAAEQVVENRAQLRERVETEREAVDDADRELTDVCEDLQSLLEQPL--- 224
                                       68899999999999999999999999999999999999999999999999999999999999999999555553... PP

                      Exonuc_VII_L 211 rerleelkerl.kekleekkerlkklkerle.lleek 245
                                        ++le  + rl +++le+ +er+++l+++ +  l+++
  gi|336254204|ref|YP_004597311.1| 225 -AQLEFNALRLtRDRLESLRERCDDLATERQtALQRR 260
                                       .333333333333444455555544433322222222 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.3   0.00011      0.25       4      86 ..     151     232 ..     149     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentk.eklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelk 79 
                                       +a+e +e  ++ leq a+l+ +l++     ++++ ++ ++  e v+   +a++dA r+  ++ + ++ Ll++  +l 
  gi|336254204|ref|YP_004597311.1| 151 IAEEFSEEQAAALEQHAQLHPRLQRSLvTAAEQVVENRAQLRERVETEREAVDDADRELTDVCEDLQSLLEQ--PLA 225
                                       6889999999999*******9999865255677777779999******************************..999 PP

                                       HHHHH.. CS
                        Laminin_II  80 qleeass 86 
                                       qle +  
  gi|336254204|ref|YP_004597311.1| 226 QLEFNAL 232
                                       9998843 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.0   0.00017      0.39      39     106 ..     164     232 ..     149     264 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                              YkyA  39 eeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieei.edeelkkeaeel 106
                                       e+  +l    +  +++ +++++en  + +e++e+e+e++++a  e++++ e+++++ e++ ++ e+++l
  gi|336254204|ref|YP_004597311.1| 164 EQHAQLHPRLQRSLVTAAEQVVENRAQLRERVETEREAVDDADRELTDVCEDLQSLlEQPLAQLEFNAL 232
                                       55555555566778999***********************************99995555555565555 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2      0.13     3e+02      53      89 ..     165     201 ..     147     205 .. 0.56
   2 ?    6.9   0.3    0.0026       5.9      17      67 ..     208     259 ..     204     264 .. 0.88
   3 ?   -0.7   0.0       0.6   1.3e+03      32      59 ..     286     313 ..     282     318 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.13
                      Baculo_PEP_C  53 dlksllaeldtrldtlltnLtdalnalqdtlrneLtn 89 
                                       +  +l + l++ l t+++++ +  ++l + +++e ++
  gi|336254204|ref|YP_004597311.1| 165 QHAQLHPRLQRSLVTAAEQVVENRAQLRERVETEREA 201
                                       3345555566666666666666666666666555444 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0026
                      Baculo_PEP_C  17 dLtnvLnairlqnvqilaqla.tlldaietqLnalsedlksllaeldtrldt 67 
                                       +Lt+v +++++++ q laql+ ++l     +L++l e+  +l +e +t+l+ 
  gi|336254204|ref|YP_004597311.1| 208 ELTDVCEDLQSLLEQPLAQLEfNALRLTRDRLESLRERCDDLATERQTALQR 259
                                       9*******************95567777889*************99999986 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.6
                      Baculo_PEP_C  32 ilaqlatlldaietqLnalsedlkslla 59 
                                       ila++a l + ie+   a++ +l++ll+
  gi|336254204|ref|YP_004597311.1| 286 ILAAIADLGAGIERGTAAVDRSLEQLLE 313
                                       4455555555555555555555555543 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1    0.0059        13     130     177 ..      46      93 ..      14     111 .. 0.74
   2 ?    4.4   9.2    0.0091        20     127     236 ..     151     263 ..     143     275 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0059
                           DUF4407 130 altaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttg 177
                                       ++++ l+++++q++  q++++  ++r++al+++a + + +t gtg  +
  gi|336254204|ref|YP_004597311.1|  46 TAREVLEREDRQLTVEQRAFERFQRRVAALETAAPRATAPTAGTGLGA 93 
                                       378899999999999999999999999999999999999988555332 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0091
                           DUF4407 127 laaaltaelaeleaqia....alqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqael 199
                                       +a+++++e+a++ +q a    +lq+ + +a +++ ++ra++++ ++ ++ +   +++   ++++  ++ l++  a+l
  gi|336254204|ref|YP_004597311.1| 151 IAEEFSEEQAAALEQHAqlhpRLQRSLVTAAEQVVENRAQLRERVETEREAVDDADRELTDVCEDLQSLLEQPLAQL 227
                                       44455555555555555333344444444444444444444444443333333333333334444444444433333 PP

                           DUF4407 200 aelkakld......atarlaalraelaeleaerakeraasqaa 236
                                              +       ++rl++lr++ ++l++er+++ ++ +++
  gi|336254204|ref|YP_004597311.1| 228 -------EfnalrlTRDRLESLRERCDDLATERQTALQRRRQE 263
                                       .......244444467778888888888877777766655543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1319  (0.073568); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 2284.67
//
Query:       gi|336254205|ref|YP_004597312.1|  [L=90]
Description: hypothetical protein Halxa_2817 [Halopiger xanaduensis SH-6]
Scores for 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  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 696.42
//
Query:       gi|336254206|ref|YP_004597313.1|  [L=142]
Description: AsnC family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-14   51.1   0.0    1.3e-13   50.3   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    7.7e-12   45.0   0.0    1.3e-11   44.3   0.0    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    1.2e-09   37.9   0.0    2.1e-09   37.0   0.0    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    5.6e-08   32.5   0.0      1e-07   31.6   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
    9.6e-08   31.9   0.2    3.1e-07   30.2   0.0    2.0  1  HTH_11          HTH domain
    4.1e-07   29.9   0.0    7.5e-07   29.0   0.0    1.4  1  HTH_36          Helix-turn-helix domain
      1e-06   28.3   0.0    2.3e-06   27.2   0.0    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
    5.6e-06   26.5   0.1    1.6e-05   25.0   0.1    1.7  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    7.7e-06   25.5   0.0    1.7e-05   24.5   0.0    1.5  1  HTH_23          Homeodomain-like domain
    8.3e-06   25.6   0.0    1.7e-05   24.6   0.0    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
    9.5e-06   25.4   0.0    0.00012   21.9   0.0    2.2  2  MarR_2          MarR family
    1.3e-05   25.5   0.0    2.1e-05   24.8   0.0    1.3  1  FaeA            FaeA-like protein
      4e-05   23.3   0.0    0.00066   19.4   0.0    2.3  2  LacI            Bacterial regulatory proteins, lacI family
    4.2e-05   23.4   0.0    9.6e-05   22.2   0.0    1.6  1  MarR            MarR family
    4.4e-05   23.4   0.0      8e-05   22.5   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    6.1e-05   23.0   0.0    0.00013   21.9   0.0    1.5  1  HTH_20          Helix-turn-helix domain
    7.5e-05   22.8   0.0    0.00017   21.6   0.0    1.6  1  HTH_28          Helix-turn-helix domain
    8.9e-05   22.4   0.0    0.00016   21.6   0.0    1.5  1  HTH_29          Winged helix-turn helix
    0.00012   22.4   0.1    0.00062   20.1   0.0    2.0  2  Rrf2            Transcriptional regulator
    0.00018   21.3   0.1    0.00033   20.5   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00048   19.7   0.1     0.0012   18.4   0.0    1.7  1  GntR            Bacterial regulatory proteins, gntR family
     0.0019   18.0   0.1     0.0049   16.6   0.0    1.7  1  HTH_10          HTH DNA binding domain
     0.0026   17.3   0.0      0.005   16.4   0.0    1.5  1  HTH_47          winged helix-turn-helix
     0.0031   17.1   0.0     0.0064   16.1   0.0    1.6  1  Sigma70_r4_2    Sigma-70, region 4
     0.0053   16.1   0.1     0.0071   15.7   0.1    1.3  1  DUF1670         Protein of unknown function (DUF1670)
     0.0056   16.7   0.0      0.012   15.6   0.0    1.6  1  HTH_Mga         M protein trans-acting positive regulator (MG
     0.0071   16.1   0.1      0.013   15.2   0.1    1.4  1  TetR_N          Bacterial regulatory proteins, tetR family
      0.008   16.0   0.0      0.011   15.6   0.0    1.3  1  TFIIE_alpha     TFIIE alpha subunit
  ------ inclusion threshold ------
      0.015   14.7   0.0      0.022   14.2   0.0    1.3  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.017   15.2   0.0      0.039   14.0   0.0    1.5  1  HTH_3           Helix-turn-helix
      0.025   14.5   0.0      0.046   13.7   0.0    1.4  1  HTH_6           Helix-turn-helix domain, rpiR family
      0.027   14.4   0.0       0.05   13.6   0.0    1.5  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.034   14.1   0.0      0.068   13.2   0.0    1.6  1  HTH_45          Winged helix-turn-helix
      0.038   14.0   0.0      0.065   13.3   0.0    1.5  1  DUF4110         Domain of unknown function (DUF4110)
      0.053   14.0   0.0       0.14   12.7   0.0    1.7  1  HTH_27          Winged helix DNA-binding domain
      0.064   13.7   0.0       0.14   12.6   0.0    1.7  1  HTH_40          Helix-turn-helix domain
      0.076   13.4   0.0       0.13   12.6   0.0    1.4  1  HTH_31          Helix-turn-helix domain
      0.076   12.9   0.2         10    6.1   0.0    2.2  2  DUF3659         Protein of unknown function (DUF3659)
        0.1   12.8   0.0       0.17   12.1   0.0    1.4  1  HTH_17          Helix-turn-helix domain
        0.1   12.1   0.0       0.23   11.0   0.0    1.6  1  Sigma70_r4      Sigma-70, region 4
       0.12   12.6   0.0       0.23   11.7   0.0    1.5  1  AbiEi_4         Transcriptional regulator, AbiEi antitoxin
       0.12   11.3   0.0       0.14   11.1   0.0    1.1  1  TnsD            Tn7-like transposition protein D
       0.12   13.0   0.0       0.25   12.0   0.0    1.5  1  RPA_C           Replication protein A C terminal
       0.13   12.1   0.0       0.25   11.2   0.0    1.5  1  HTH_30          PucR C-terminal helix-turn-helix domain
       0.13   12.0   0.0        0.3   10.9   0.0    1.6  1  MerR            MerR family regulatory protein
       0.14   12.8   0.1       0.46   11.1   0.1    1.9  2  HTH_32          Homeodomain-like domain


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 !   50.3   0.0   3.3e-16   1.3e-13       7      47 ..       9      49 ..       5      50 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 3.3e-16
                            HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +ILe+L++++  s++++Aer g+S++tv++++++LeeeG+I
  gi|336254206|ref|YP_004597313.1|  9 RILEVLEEDAQASYADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      8***************************************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 !   44.3   0.0   3.2e-14   1.3e-11       1      74 [.      69     139 ..      69     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3.2e-14
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       v++ +++++   + e+ +al++l++++ +y+ +Gd+ ++++v+++d ++l ++++e l++++gv+  + s+  e
  gi|336254206|ref|YP_004597313.1|  69 VGIDVSSER---YVEATKALKDLDQIEALYSSSGDHMLMAEVRAEDGDSLGEIISEDLMEIEGVTAAHPSFLQE 139
                                       678899777...99***************************************************999999766 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 !   37.0   0.0   5.5e-12   2.1e-09       7      42 .]       9      44 ..       6      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 5.5e-12
                     HTH_AsnC-type  7 kILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      +ILe L+eda +sya++Aer G+S +tv++ +++Le
  gi|336254206|ref|YP_004597313.1|  9 RILEVLEEDAQASYADIAERAGVSKPTVRKYINQLE 44
                                      8****************************9988887 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 !   31.6   0.0   2.7e-10     1e-07       7      48 ..       9      49 ..       9      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.7e-10
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      +iL+ l+e +q+ + +++A+r+g++k+tv+ +++ L+e+G +
  gi|336254206|ref|YP_004597313.1|  9 RILEVLEEDAQA-SYADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      69*********8.**************************975 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0     8e-10   3.1e-07       4      46 ..       9      50 ..       6      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 8e-10
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                       ile L e++ + s +++Ae+ +vS+ tvr++I +Lee gv +
  gi|336254206|ref|YP_004597313.1|  9 RILEVL-EEDAQASYADIAERAGVSKPTVRKYINQLEEEGVIV 50
                                      799999.99999****************************765 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   1.9e-09   7.5e-07      26      55 .]      20      49 ..      15      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.9e-09
                            HTH_36 26 psqetlakrlglsknTvsraikeLeqlGyi 55
                                      +s++++a+r g+sk Tv+++i+ Le+ G i
  gi|336254206|ref|YP_004597313.1| 20 ASYADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      8************************98865 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 !   27.2   0.0     6e-09   2.3e-06       3      44 ..       8      49 ..       7      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6e-09
                          HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                      + ile l+++   s  +++e+ gvS+ T+R+ +n+Lee+g++
  gi|336254206|ref|YP_004597313.1|  8 DRILEVLEEDAQASYADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      579*************************************98 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 !   25.0   0.1     4e-08   1.6e-05      13      51 ..      10      48 ..       4      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4e-08
                                      HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGy 51
                                      I+++ ee + ++ +d+aer +vs+++V + ++ Le++G 
  gi|336254206|ref|YP_004597313.1| 10 ILEVLEEDAQASYADIAERAGVSKPTVRKYINQLEEEGV 48
                                      788999*******************************95 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   4.2e-08   1.7e-05      16      46 ..      15      48 ..       7      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.2e-08
                            HTH_23 16 e...GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      e    +s+++IA++ gvs+ Tv+++++  +eeG+
  gi|336254206|ref|YP_004597313.1| 15 EedaQASYADIAERAGVSKPTVRKYINQLEEEGV 48
                                      335699***********************99996 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 !   24.6   0.0   4.4e-08   1.7e-05       6      45 ..       9      49 ..       9      50 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.4e-08
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +IL  L+e  +++  ++ae  g+s++tv+ + ++L+e+G++
  gi|336254206|ref|YP_004597313.1|  9 RILEVLEEdAQASYADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      6999****999****************************87 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   3.1e-07   0.00012       9      52 ..       9      50 ..       3      59 .. 0.88
   2 ?    1.0   0.0         1   3.9e+02       7      28 ..     100     119 ..      97     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.1e-07
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      r+L +L        + +++a+r g+sk++v + ++ L++ G ++
  gi|336254206|ref|YP_004597313.1|  9 RILEVLEEDAQ--ASYADIAERAGVSKPTVRKYINQLEEEGVIV 50
                                      78888888887..899*************************986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1
                                       HHHHHHHHHCTTTSEEEHHHHH CS
                            MarR_2   7 qarvLaaLgrrpgrdltvgela 28 
                                       +++++a++++++g   + ge+ 
  gi|336254206|ref|YP_004597313.1| 100 DHMLMAEVRAEDG--DSLGEII 119
                                       68999*******9..5888886 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   5.3e-08   2.1e-05       3      45 ..       8      49 ..       6      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.3e-08
                                      HHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSE CS
                              FaeA  3 eeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegki 45
                                      + Ile l +  a +  ++iA+ +g+s   +R Y++qLe eg i
  gi|336254206|ref|YP_004597313.1|  8 DRILEVLEE-DAQASYADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      789******.*******************************87 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.87   3.4e+02      28      40 ..       4      16 ..       3      18 .. 0.91
   2 !   19.4   0.0   1.7e-06   0.00066       4      22 ..      24      42 ..      22      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.87
                                      HHHHHHHHHHHHH CS
                              LacI 28 eetrerVeaamee 40
                                      ++t +r+++++ee
  gi|336254206|ref|YP_004597313.1|  4 QATEDRILEVLEE 16
                                      79********998 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.7e-06
                                      HHHHHCTS-HHHHHHHCTT CS
                              LacI  4 DVArlAGVSkaTVSrvLnn 22
                                      D+A++AGVSk TV +++n+
  gi|336254206|ref|YP_004597313.1| 24 DIAERAGVSKPTVRKYINQ 42
                                      9***************997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.5e-07   9.6e-05       4      47 ..       6      49 ..       4      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.5e-07
                                      HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      t+ +iL+ l+e  ++s +++a++ gvsk+tv + + +Le++G i
  gi|336254206|ref|YP_004597313.1|  6 TEDRILEVLEEDAQASYADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      55689*************************************87 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 !   22.5   0.0     2e-07     8e-05      21      52 ..      19      50 ..       3      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2e-07
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis 52
                                      + + +++A++ G++  tv + +++L++eg+i 
  gi|336254206|ref|YP_004597313.1| 19 QASYADIAERAGVSKPTVRKYINQLEEEGVIV 50
                                      57899**************************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 !   21.9   0.0   3.4e-07   0.00013      14      54 ..       9      49 ..       7      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.4e-07
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                      ril  L +++ ++ +++aer ++sk t+++ +++Lee g +
  gi|336254206|ref|YP_004597313.1|  9 RILEVLEEDAQASYADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      799**********************************9988 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   4.4e-07   0.00017      12      41 ..      19      48 ..      10      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.4e-07
                            HTH_28 12 GhsvreaArelgisrrtvyrWikryeegGi 41
                                      + s++++A++ g+s  tv++ i+++ee+G+
  gi|336254206|ref|YP_004597313.1| 19 QASYADIAERAGVSKPTVRKYINQLEEEGV 48
                                      459**************************5 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   4.1e-07   0.00016      10      41 ..      18      48 ..       9      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.1e-07
                            HTH_29 10 eGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                          + ++iA++ g+s++tv+++++  ee+G+
  gi|336254206|ref|YP_004597313.1| 18 AQA-SYADIAERAGVSKPTVRKYINQLEEEGV 48
                                      444.599************************5 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.6e-06   0.00062      18      55 ..      12      49 ..       9      53 .. 0.88
   2 ?   -0.1   0.0       3.2   1.2e+03      26      56 ..      61      92 ..      52     108 .. 0.55

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.6e-06
                                      HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglv 55
                                      +  ee+ ++s ++iaer ++s++ ++k +++L+++g++
  gi|336254206|ref|YP_004597313.1| 12 EVLEEDAQASYADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      555667779***************************98 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.2
                                      B-HHHHHH.HHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 26 vsseeiae.rqnispsylekilakLrkaglvk 56
                                      +ss++ia    ++s +     ++ L+  + ++
  gi|336254206|ref|YP_004597313.1| 61 LSSKTIAMvGIDVSSERYVEATKALKDLDQIE 92
                                      67777776334555544444444444444333 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   8.4e-07   0.00033      13      52 ..      10      49 ..       4      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.4e-07
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSE CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlV 52
                                      +  +L +  +a+  +iae++gv++++v +++++Le+ G++
  gi|336254206|ref|YP_004597313.1| 10 ILEVLEEDAQASYADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      5566668889999*************************87 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.1e-06    0.0012      28      54 ..      23      49 ..       5      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.1e-06
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglv 54
                                       ++a++ gVs++tvR+ +++Le+eg++
  gi|336254206|ref|YP_004597313.1| 23 ADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      679**********************98 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.3e-05    0.0049      19      48 ..      15      44 ..      14      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-05
                            HTH_10 19 dyPRrvtlkeLAkelGIskstlsehLrkae 48
                                      +++ +++ +++A++ G+sk+t+ +++++ e
  gi|336254206|ref|YP_004597313.1| 15 EEDAQASYADIAERAGVSKPTVRKYINQLE 44
                                      5677999******************99876 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-05     0.005      30      77 ..       4      50 ..       1      51 [. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                                      ---HHHHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 30 kqaemallwvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                      +++e+++l+vL   D + s  diAer+g++  +v + +++L+e+g+++
  gi|336254206|ref|YP_004597313.1|  4 QATEDRILEVLE-EDAQASYADIAERAGVSKPTVRKYINQLEEEGVIV 50
                                      566788888887.6999*****************************96 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 !   16.1   0.0   1.6e-05    0.0064      28      48 ..      21      41 ..      10      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-05
                                      -HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 28 sykEIAellgisegtVksrls 48
                                      sy++IAe+ g+s  tV++++ 
  gi|336254206|ref|YP_004597313.1| 21 SYADIAERAGVSKPTVRKYIN 41
                                      9*****************985 PP

>> DUF1670  Protein of unknown function (DUF1670)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.8e-05    0.0071      98     146 ..      12      56 ..       3      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                           DUF1670  98 EAyeqealltqsDlalllgvstrtvskqvkeyqeeegivlptrGaikDi 146
                                       E  e +a  + +D+a   gvs+ tv+k+++++ eeeg+++    +  Di
  gi|336254206|ref|YP_004597313.1|  12 EVLEEDAQASYADIAERAGVSKPTVRKYINQL-EEEGVIVG---YSADI 56 
                                       45567888899*********************.9****995...45555 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 !   15.6   0.0   3.1e-05     0.012       2      46 ..       2      45 ..       1      53 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.1e-05
                           HTH_Mga  2 kdikrklkLlelLteneksltldelakeLglseltlqsdiseLne 46
                                      + ++++ ++le L e +   ++ ++a++ g s  t++++i++L e
  gi|336254206|ref|YP_004597313.1|  2 STQATEDRILEVLEE-DAQASYADIAERAGVSKPTVRKYINQLEE 45
                                      567788889999988.9**************************86 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 !   15.2   0.1   3.4e-05     0.013      17      33 ..      20      36 ..      18      39 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.4e-05
                                      --HHHHHHHHTSSHHHH CS
                            TetR_N 17 ttvreIAkrAGvskgal 33
                                      ++ ++IA+rAGvsk+++
  gi|336254206|ref|YP_004597313.1| 20 ASYADIAERAGVSKPTV 36
                                      6779***********98 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.9e-05     0.011      17      57 ..       9      49 ..       3      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-05
                                      HHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSE CS
                       TFIIE_alpha 17 lvldvLlekgevteedlakelkidlnelrklLnrLyearlv 57
                                       +l+vL e+++ +  d+a+  ++ ++ +rk +n+L e++++
  gi|336254206|ref|YP_004597313.1|  9 RILEVLEEDAQASYADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      699***********************************987 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 ?   14.2   0.0   5.6e-05     0.022      13      50 ..       3      42 ..       2      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.6e-05
                      HTH_Tnp_ISL3 13 Tlrleayilellles..rsvkavArqlgvSwtTVwrildr 50
                                      T + e+ ile l e+  +s +++A++ gvS  TV+ ++++
  gi|336254206|ref|YP_004597313.1|  3 TQATEDRILEVLEEDaqASYADIAERAGVSKPTVRKYINQ 42
                                      566788888888888899*****************99887 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0    0.0001     0.039      11      31 ..      21      41 ..      20      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.0001
                                      HHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3 11 sqeeLAeklGvsrstisriEn 31
                                      s +++Ae++Gvs+ t+++++n
  gi|336254206|ref|YP_004597313.1| 21 SYADIAERAGVSKPTVRKYIN 41
                                      5689***************98 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 ?   13.7   0.0   0.00012     0.046      19      59 ..       8      44 ..       2      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00012
                                      HHHHHHHHH-S---TT--HHHHHHHTT--HHHHHHHH---S CS
                             HTH_6 19 kkiaeyilaspdkaielsikalAkaaavSeativrfakkLG 59
                                       +    il+  ++  + s +++A+ a+vS++t+ +   +L 
  gi|336254206|ref|YP_004597313.1|  8 DR----ILEVLEEDAQASYADIAERAGVSKPTVRKYINQLE 44
                                      44....44455555678999*************99877775 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 ?   13.6   0.0   0.00013      0.05      20      40 ..      26      46 ..       9      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00013
                                      HHHHTS-HHHHHHHHHHHHHH CS
                             HTH_1 20 AeeLglsqpavsrqikrLEee 40
                                      Ae+ g+s p+v + i++LEee
  gi|336254206|ref|YP_004597313.1| 26 AERAGVSKPTVRKYINQLEEE 46
                                      9******************96 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00017     0.068      11      50 ..      10      50 ..       8      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                            HTH_45 11 ILeais.egeakkTkimykanLsykllnkYLdmLvekglik 50
                                      ILe+++ + +a+   i  +a  s  +++kY+++L e+g+i 
  gi|336254206|ref|YP_004597313.1| 10 ILEVLEeDAQASYADIAERAGVSKPTVRKYINQLEEEGVIV 50
                                      77777657789999************************993 PP

>> DUF4110  Domain of unknown function (DUF4110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00017     0.065      42      76 ..      60      94 ..      37     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00017
                           DUF4110 42 kkseKelkkeafelAeerywelrpvLeelralede 76
                                      k s+K +   + ++++ery e+ ++L+ l ++e+ 
  gi|336254206|ref|YP_004597313.1| 60 KLSSKTIAMVGIDVSSERYVEATKALKDLDQIEAL 94
                                      3899**********************999999986 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 ?   12.7   0.0   0.00035      0.14       7      48 ..       9      49 ..       4      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00035
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                       +L++++ ++++++ ad+++r  v++ ++ + +++L+e G++
  gi|336254206|ref|YP_004597313.1|  9 RILEVLE-EDAQASYADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      5899999.8999999*************************99 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00035      0.14      13      48 ..      20      61 ..       6     109 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00035
                            HTH_40 13 lsieeIAkerglkesTIegHLaelieeg......eeidlerl 48
                                       s ++IA++ g+++ T+ +++ +l eeg       +id ++l
  gi|336254206|ref|YP_004597313.1| 20 ASYADIAERAGVSKPTVRKYINQLEEEGvivgysADIDPKKL 61
                                      5789***********************844444322222333 PP

>> HTH_31  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   0.00034      0.13      11      36 ..      16      41 ..       9      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00034
                            HTH_31 11 eraGLsqeevAerlgvsestlsrlEq 36
                                      e a  s ++ Aer+gvs+ t++++ +
  gi|336254206|ref|YP_004597313.1| 16 EDAQASYADIAERAGVSKPTVRKYIN 41
                                      6677899***************9976 PP

>> DUF3659  Protein of unknown function (DUF3659)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.073        28      15      38 ..      43      66 ..      35      71 .. 0.84
   2 ?    6.1   0.0     0.027        10      13      36 ..     106     129 ..     104     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.073
                           DUF3659 15 vdeeGnvvGrvveGdlkkLaGkkv 38
                                      + eeG +vG  ++ d+kkL  k++
  gi|336254206|ref|YP_004597313.1| 43 LEEEGVIVGYSADIDPKKLSSKTI 66
                                      5799******7777*****99987 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.027
                           DUF3659  13 evvdeeGnvvGrvveGdlkkLaGk 36 
                                       ev  e+G+ +G++++ dl ++ G 
  gi|336254206|ref|YP_004597313.1| 106 EVRAEDGDSLGEIISEDLMEIEGV 129
                                       68889**************99985 PP

>> HTH_17  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   0.00043      0.17       5      24 ..      23      42 ..      21      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00043
                            HTH_17  5 eEaAelLgvsrstvyrlirr 24
                                      +++Ae  gvs+ tv+++i++
  gi|336254206|ref|YP_004597313.1| 23 ADIAERAGVSKPTVRKYINQ 42
                                      689***************85 PP

>> Sigma70_r4  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    0.0006      0.23      19      39 ..      18      38 ..       6      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0006
                                      TT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 19 eglTleEIgerlgiSrerVrq 39
                                         ++++I+er g+S+ +Vr 
  gi|336254206|ref|YP_004597313.1| 18 AQASYADIAERAGVSKPTVRK 38
                                      5679***************97 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00058      0.23       1      39 [.       8      50 ..       8      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00058
                           AbiEi_4  1 erlpelasrqvGlfttrelea.aGispsa....lrrLvrkGwLv 39
                                      +r++e ++++   ++++++++ aG+s  +    ++ L ++G +v
  gi|336254206|ref|YP_004597313.1|  8 DRILEVLEEDA-QASYADIAErAGVSKPTvrkyINQLEEEGVIV 50
                                      68889998887.99****9999*****98899999999999886 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00035      0.14     191     227 ..      11      47 ..       5      95 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00035
                              TnsD 191 lkeLveeeglslkeiAkelgvdiktVlryakklgllk 227
                                       l+ L e+++ s+++iA+++gv+  tV++y ++l+++ 
  gi|336254206|ref|YP_004597313.1|  11 LEVLEEDAQASYADIAERAGVSKPTVRKYINQLEEEG 47 
                                       66788889***********************998775 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 ?   12.0   0.0   0.00063      0.25      52      97 ..       8      49 ..       1      55 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00063
                                      HHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 52 qqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                                      +++l+++ +    ++  +   ia++ ++s+ +v++ +++L++eG+i
  gi|336254206|ref|YP_004597313.1|  8 DRILEVLEE----DAQASYADIAERAGVSKPTVRKYINQLEEEGVI 49
                                      555555555....33346789***********************99 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 ?   11.2   0.0   0.00064      0.25      10      38 ..      17      45 ..      10      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00064
                                      HTTT-HHHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_30 10 enggnisatAkaLhvHrnTlryRLrriee 38
                                      +++ ++++ A++ +v++ T+r+ ++++ee
  gi|336254206|ref|YP_004597313.1| 17 DAQASYADIAERAGVSKPTVRKYINQLEE 45
                                      567899********************998 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   0.00076       0.3       4      20 ..      24      40 ..      21      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00076
                                      HHHHHHTTTHHHHHHHH CS
                              MerR  4 evAeltGvsprtLRyYE 20
                                      ++Ae++Gvs  t+R Y 
  gi|336254206|ref|YP_004597313.1| 24 DIAERAGVSKPTVRKYI 40
                                      78*************96 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0012      0.46      30      72 ..       3      39 ..       2      40 .. 0.90
   2 ?    2.8   0.0      0.48   1.9e+02       1      18 [.      35      53 ..      35      69 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0012
                            HTH_32 30 sdevrariiallreeprWsprqlaarlaeregvkvShstvyri 72
                                      ++++++ri+++l+e+ + s+  +a+r        vS+ tv+++
  gi|336254206|ref|YP_004597313.1|  3 TQATEDRILEVLEEDAQASYADIAERA------GVSKPTVRKY 39
                                      6899********7788*********99......7******986 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.48
                            HTH_32  1 TvsrwlkRyneeGle.gLk 18
                                      Tv++++++ +eeG+  g+ 
  gi|336254206|ref|YP_004597313.1| 35 TVRKYINQLEEEGVIvGYS 53
                                      9***********9776776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); expected 17.9 (0.001)
Passed Fwd filter:                        46  (0.00256568); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              46  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1071.77
//
Query:       gi|336254207|ref|YP_004597314.1|  [L=107]
Description: hypothetical protein Halxa_2819 [Halopiger xanaduensis SH-6]
Scores for 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   17.2   1.2     0.0039   16.9   1.2    1.0  1  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.2   2.2e-07    0.0039      10      95 ..      10      92 ..       5     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-07
                                      XXXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin 10 llfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcigalkenkcllltfsllllv 88
                                       +++++g ++l +G  + ++   + +a++ ++s +dpa++      vG++ +l+g l ++ a++e +   +  +l  l+
  gi|336254207|ref|YP_004597314.1| 10 AVWFVCGFAILYLGYLIGIRGRAELHADYDESSGVDPAYV---SRWVGATALLMGTLVVLYAIREVRYGFQPAALGGLL 85
                                      6899**********4444466667788888999*******...************************999998888877 PP

                                      XXXXXXX CS
                                      xxxxxxx RF
                       Tetraspanin 89 lfllela 95
                                      + ll l+
  gi|336254207|ref|YP_004597314.1| 86 VALLVLS 92
                                      7777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 807.41
//
Query:       gi|336254208|ref|YP_004597315.1|  [L=369]
Description: hypothetical protein Halxa_2820 [Halopiger xanaduensis SH-6]
Scores for 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-10   39.2  16.1    9.6e-10   38.3  10.5    3.0  3  DZR              Double zinc ribbon
    1.3e-09   37.4  19.5    2.1e-06   27.2   2.7    3.4  3  zinc_ribbon_2    zinc-ribbon domain
    6.5e-08   31.7  27.1    2.7e-05   23.4   3.4    3.9  4  zf-ribbon_3      zinc-ribbon domain
    0.00038   21.2  15.9      0.018   15.8   0.5    3.3  3  zinc_ribbon_15   zinc-ribbon family
      0.003   17.6   5.2      0.003   17.6   5.2    3.2  3  UPF0547          Uncharacterised protein family UPF0547
     0.0037   17.1  17.0      0.029   14.3   3.5    3.2  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0067   16.4   0.7     0.0067   16.4   0.7    2.2  2  RseC_MucC        Positive regulator of sigma(E), RseC/MucC
  ------ inclusion threshold ------
      0.022   14.5   2.3      0.022   14.5   0.4    2.1  2  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l
      0.031   14.2  15.9        1.6    8.7   0.2    5.4  5  Nudix_N_2        Nudix N-terminal
      0.061   13.3   0.1       0.25   11.3   0.0    1.9  2  NinG             Bacteriophage Lambda NinG protein
       0.45   10.3   3.7        1.6    8.5   3.7    1.9  1  Phage_holin_2_3  Bacteriophage holin family HP1
       0.69    9.9  13.5       0.28   11.1   1.7    3.5  3  Prok-RING_1      Prokaryotic RING finger family 1
       0.81    9.8   0.0       0.81    9.8   0.0    2.1  2  Mut7-C           Mut7-C RNAse domain
        2.3    8.9   9.1        2.6    8.8   0.1    3.0  3  zinc-ribbon_6    zinc-ribbon domain
        3.2    8.0  11.4        1.3    9.3   6.0    2.8  3  IBR              IBR domain, a half RING-finger domain
        4.5    7.4  12.0          6    7.0   8.5    2.5  2  DUF1272          Protein of unknown function (DUF1272)
        4.8    7.4  12.0        8.6    6.6   2.4    3.0  2  PHF5             PHF5-like protein
        5.1    7.1  10.8         29    4.6   3.8    3.7  3  C1_1             Phorbol esters/diacylglycerol binding domain
        6.4    6.8  12.7        2.5    8.1   2.2    3.1  3  HypA             Hydrogenase/urease nickel incorporation, met


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 !   38.3  10.5     1e-12   9.6e-10       1      49 []      14      61 ..      14      61 .. 0.97
   2 ?    0.8   0.0      0.54   5.1e+02      28      38 ..     268     278 ..     252     281 .. 0.78
   3 ?    1.3   0.1      0.38   3.6e+02      11      19 ..     304     312 ..     296     317 .. 0.72

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1e-12
                               DZR  1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49
                                      Cp Cg+ +ppda+fC +Cg +l  + ++  C+sCge+ + +++fC +CG
  gi|336254208|ref|YP_004597315.1| 14 CPDCGATVPPDANFCLHCGVELG-TVEPAYCSSCGEAFERDDEFCSNCG 61
                                      **********************5.788*********************9 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.54
                               DZR  28 edrCpsCgekv 38 
                                        +rC+ C+e+ 
  gi|336254208|ref|YP_004597315.1| 268 GERCVVCNEPF 278
                                       67999999875 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.38
                               DZR  11 darfCseCg 19 
                                       ++ +CseC 
  gi|336254208|ref|YP_004597315.1| 304 HNYYCSECA 312
                                       566788885 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   2.7   2.3e-09   2.1e-06       2      22 ..      14      34 ..      13      35 .. 0.94
   2 !   16.5   5.2   5.4e-06    0.0051       1      22 [.      42      63 ..      42      63 .. 0.98
   3 ?    0.9   0.1      0.44   4.2e+02      15      19 ..     307     311 ..     302     316 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.3e-09
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      Cp CGa+++++a+FC +CG +
  gi|336254208|ref|YP_004597315.1| 14 CPDCGATVPPDANFCLHCGVE 34
                                      *******************66 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 5.4e-06
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGtp 22
                                      +C++CG+  + ++ FC++CGtp
  gi|336254208|ref|YP_004597315.1| 42 YCSSCGEAFERDDEFCSNCGTP 63
                                      8********************8 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.44
                     zinc_ribbon_2  15 FCpyC 19 
                                       +C++C
  gi|336254208|ref|YP_004597315.1| 307 YCSEC 311
                                       78888 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   3.9   1.4e-07   0.00013       5      26 .]      14      35 ..      13      35 .. 0.90
   2 !   23.4   3.4   2.9e-08   2.7e-05       4      25 ..      42      63 ..      40      63 .. 0.95
   3 ?    0.4   0.2       0.5   4.7e+02       4      11 ..     270     277 ..     268     281 .. 0.80
   4 ?   -0.5   0.6      0.99   9.3e+02       3       8 ..     306     311 ..     305     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.4e-07
                       zf-ribbon_3  5 CPnCGa.plssddnvCpyCGtkl 26
                                      CP CGa +  +d+n+C +CG +l
  gi|336254208|ref|YP_004597315.1| 14 CPDCGAtV-PPDANFCLHCGVEL 35
                                      ******55.***********875 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 2.9e-08
                       zf-ribbon_3  4 rCPnCGa.plssddnvCpyCGtk 25
                                      +C++CG+   + dd +C +CGt+
  gi|336254208|ref|YP_004597315.1| 42 YCSSCGEaF-ERDDEFCSNCGTP 63
                                      8******99.***********96 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.5
                       zf-ribbon_3   4 rCPnCGap 11 
                                       rC  C++p
  gi|336254208|ref|YP_004597315.1| 270 RCVVCNEP 277
                                       8*****96 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.99
                       zf-ribbon_3   3 vrCPnC 8  
                                       ++C++C
  gi|336254208|ref|YP_004597315.1| 306 YYCSEC 311
                                       79**** PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   1.9e-05     0.018      65      86 .]      11      32 ..       2      32 .. 0.86
   2 !   14.0   1.7   6.7e-05     0.063      66      86 .]      41      61 ..      34      61 .. 0.91
   3 ?   -0.1   1.0       1.7   1.6e+03      65      72 ..     305     312 ..     262     315 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                    zinc_ribbon_15 65 kkeCknCgkeveeefkyCpkCg 86
                                         C++Cg++v ++ ++C +Cg
  gi|336254208|ref|YP_004597315.1| 11 RPPCPDCGATVPPDANFCLHCG 32
                                      678******************9 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6.7e-05
                    zinc_ribbon_15 66 keCknCgkeveeefkyCpkCg 86
                                       +C++Cg++ e + ++C++Cg
  gi|336254208|ref|YP_004597315.1| 41 AYCSSCGEAFERDDEFCSNCG 61
                                      79******************9 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.7
                    zinc_ribbon_15  65 kkeCknCg 72 
                                       +++C++C 
  gi|336254208|ref|YP_004597315.1| 305 NYYCSECA 312
                                       44555554 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   5.2   3.2e-06     0.003       3      21 ..      14      32 ..      13      34 .. 0.97
   2 ?   -1.6   0.4       3.2     3e+03      17      21 ..      43      47 ..      42      52 .. 0.78
   3 ?    3.1   0.1      0.11     1e+02      15      22 ..      55      62 ..      53      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.2e-06
                           UPF0547  3 CPeCeakvPvaaqfCphCG 21
                                      CP C a+vP +a fC hCG
  gi|336254208|ref|YP_004597315.1| 14 CPDCGATVPPDANFCLHCG 32
                                      ******************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.2
                           UPF0547 17 CphCG 21
                                      C+ CG
  gi|336254208|ref|YP_004597315.1| 43 CSSCG 47
                                      999*9 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.11
                           UPF0547 15 qfCphCGy 22
                                      +fC+ CG+
  gi|336254208|ref|YP_004597315.1| 55 EFCSNCGT 62
                                      69*****8 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 !   14.3   3.5     3e-05     0.029      14      33 ..      14      33 ..      14      38 .. 0.93
   2 !    9.9   2.1    0.0007      0.66      13      33 ..      42      62 ..      41      65 .. 0.93
   3 ?   -0.6   0.1       1.3   1.3e+03      27      35 ..     307     315 ..     305     316 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                           DUF35_N 14 CpdCGtvqfPPr.avCphCgs 33
                                      CpdCG+  +PP  ++C hCg+
  gi|336254208|ref|YP_004597315.1| 14 CPDCGAT-VPPDaNFCLHCGV 33
                                      *******.7**********97 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0007
                           DUF35_N 13 rCpdCGtvqfPPr.avCphCgs 33
                                      +C++CG   f +   +C++Cg 
  gi|336254208|ref|YP_004597315.1| 42 YCSSCGEA-FERDdEFCSNCGT 62
                                      8*******.9**********96 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.3
                           DUF35_N  27 vCphCgsdd 35 
                                       +C+ C ++d
  gi|336254208|ref|YP_004597315.1| 307 YCSECARTD 315
                                       566676555 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2       3.2     3e+03      14      24 ..      38      48 ..      32      75 .. 0.68
   2 !   16.4   0.7   7.1e-06    0.0067      68     122 ..     188     242 ..     183     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.2
                         RseC_MucC 14 erksaCgsCaa 24
                                       +   C+sC++
  gi|336254208|ref|YP_004597315.1| 38 VEPAYCSSCGE 48
                                      55566777774 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 7.1e-06
                         RseC_MucC  68 llvYllPllllilgallgsallgssellaalgallglvlgflivrllskrlkkks 122
                                         +Y++   +l++ga+l  ++l+++ +++ l++l+++++g++++  +++r+k+++
  gi|336254208|ref|YP_004597315.1| 188 GSAYVMTATFLFVGAVLSLVALLNGAIVSGLIGLAFAAVGLYVAPAFRRRFKRRH 242
                                       568***************9999****************************99987 PP

>> Phage_holin_2_4  Bacteriophage holin family, superfamily II-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       4.7   4.4e+03      47      61 ..     142     157 ..     137     163 .. 0.62
   2 ?   14.5   0.4   2.4e-05     0.022      18      64 ..     199     245 ..     179     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.7
                   Phage_holin_2_4  47 lLvnWy.YkreanRRa 61 
                                       lL  Wy Y   a+ R+
  gi|336254208|ref|YP_004597315.1| 142 LLYGWYhYSERAEQRH 157
                                       4566863555566554 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.4e-05
                   Phage_holin_2_4  18 ggGavvsfaGflasselialvGlavAliGlLvnWyYkreanRRaaae 64 
                                        +Gav s++  l  + + +l+Gla A +Gl v   ++r   RR+ + 
  gi|336254208|ref|YP_004597315.1| 199 FVGAVLSLVALLNGAIVSGLIGLAFAAVGLYVAPAFRRRFKRRHGIT 245
                                       479****************************************8765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.21     2e+02       3       9 ..      14      20 ..       9      22 .. 0.61
   2 ?    3.9   0.1     0.054        51       1      10 [.      26      35 ..      26      40 .. 0.83
   3 ?    5.7   0.2     0.015        14       2      12 ..      42      52 ..      41      53 .. 0.86
   4 ?    8.7   0.2    0.0017       1.6       2      10 ..      56      64 ..      55      82 .. 0.76
   5 ?    1.2   0.1      0.37   3.5e+02       2       7 ..     307     312 ..     306     316 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.21
                                      -TTT--B CS
                         Nudix_N_2  3 CsqCGtp 9 
                                      C+ CG++
  gi|336254208|ref|YP_004597315.1| 14 CPDCGAT 20
                                      5555544 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.054
                                      -B-TTT--B- CS
                         Nudix_N_2  1 kFCsqCGtpv 10
                                      +FC +CG ++
  gi|336254208|ref|YP_004597315.1| 26 NFCLHCGVEL 35
                                      7******765 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.015
                                      B-TTT--B-EE CS
                         Nudix_N_2  2 FCsqCGtpvel 12
                                      +Cs+CG++ e+
  gi|336254208|ref|YP_004597315.1| 42 YCSSCGEAFER 52
                                      9*****98775 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0017
                                      B-TTT--B- CS
                         Nudix_N_2  2 FCsqCGtpv 10
                                      FCs+CGtp 
  gi|336254208|ref|YP_004597315.1| 56 FCSNCGTPR 64
                                      9******94 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.37
                                       B-TTT- CS
                         Nudix_N_2   2 FCsqCG 7  
                                       +Cs+C+
  gi|336254208|ref|YP_004597315.1| 307 YCSECA 312
                                       9****8 PP

>> NinG  Bacteriophage Lambda NinG protein
   #    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       7      88 ..      41     123 ..      36     128 .. 0.81
   2 ?   -1.0   0.0       1.5   1.4e+03     125     141 ..     270     286 ..     268     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                              NinG   7 rkCkeCkeafkpakatqavCse.ecalalkkaekkaekkrrkeekkeraelkvrkealksrsefikelqkvvnefiR 82 
                                         C +C+eaf++ +++   C++ + +++ ++++ + +++ r+   ++r++ ++  ++++ + +   elq+ + + + 
  gi|336254208|ref|YP_004597315.1|  41 AYCSSCGEAFERDDEFCSNCGTpRKGVESDATRPSRQSRPRSDSSRQRQARRAFERRIQRHLDAGWELQHDYGDRVV 117
                                       67*************9999986155677777888888889999999******9999999999999999988777777 PP

                              NinG  83 lrdkdl 88 
                                       l d+d 
  gi|336254208|ref|YP_004597315.1| 118 LVDRDI 123
                                       777665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                              NinG 125 qCavCnvhlsgnivkYr 141
                                        C+vCn+   g +v+ r
  gi|336254208|ref|YP_004597315.1| 270 RCVVCNEPFDGGLVRRR 286
                                       69999999988888765 PP

>> Phage_holin_2_3  Bacteriophage holin family HP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.7    0.0017       1.6       1      48 [.     183     237 ..     183     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0017
                   Phage_holin_2_3   1 dkysslaAYisSavavvlG.ll...sLseWAiv...iGIicgvvTfliNwyykrk 48 
                                       +++s+++AY+  a+ + +G +l    L + Aiv   iG+++++v + ++  ++r+
  gi|336254208|ref|YP_004597315.1| 183 ERISTGSAYVMTATFLFVGaVLslvALLNGAIVsglIGLAFAAVGLYVAPAFRRR 237
                                       5899***************622333555666652225566777777777777776 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 ?   -0.4   2.3       1.2   1.2e+03      23      28 ..      14      19 ..      12      35 .. 0.74
   2 ?   11.1   1.7    0.0003      0.28       6      29 ..      42      63 ..      38      65 .. 0.90
   3 ?    4.2   0.0     0.045        42       3      17 ..     267     281 ..     265     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                       Prok-RING_1 23 CpeCgt 28
                                      Cp+Cg+
  gi|336254208|ref|YP_004597315.1| 14 CPDCGA 19
                                      777776 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0003
                       Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCgtp 29
                                       C+ Cg++++ +d    C +Cgtp
  gi|336254208|ref|YP_004597315.1| 42 YCSSCGEAFERDDE--FCSNCGTP 63
                                      6**********988..6******9 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.045
                       Prok-RING_1   3 tgkkCpvCgkelkee 17 
                                        g++C vC+++++ +
  gi|336254208|ref|YP_004597315.1| 267 DGERCVVCNEPFDGG 281
                                       5899*******9865 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   1.6       1.9   1.8e+03      89     128 ..      24      59 ..      16      65 .. 0.65
   2 ?    9.8   0.0   0.00085      0.81      89     132 ..     267     314 ..     255     328 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                            Mut7-C  89 elsrCvaCngeleevekeevkervpekvyeeadeftrCek 128
                                         + C++C  el +ve +    +   +++e+ def  C +
  gi|336254208|ref|YP_004597315.1|  24 DANFCLHCGVELGTVEPAYC--SSCGEAFERDDEF--CSN 59 
                                       56789999999999988876..3334445555553..333 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00085
                            Mut7-C  89 elsrCvaCng.....eleevekeevkervpekvyeeadeftrCekCrkv 132
                                         +rCv Cn+      +++ + e+v   +p ++  +++  + C +C + 
  gi|336254208|ref|YP_004597315.1| 267 DGERCVVCNEpfdggLVRRRRDETVVAGLPVRTHAMEH-NYYCSECART 314
                                       468*******7766566677777777777776665544.6789999873 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0028       2.6       4      26 ..      14      36 ..      13      42 .. 0.93
   2 ?    2.9   2.0      0.19   1.8e+02       4      23 ..      43      62 ..      41      73 .. 0.91
   3 ?   -0.9   0.1       2.8   2.7e+03      75      86 ..     304     315 ..     298     321 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0028
                     zinc-ribbon_6  4 CeqCgqllffenssClkCgaalg 26
                                      C  Cg ++  + + Cl+Cg +lg
  gi|336254208|ref|YP_004597315.1| 14 CPDCGATVPPDANFCLHCGVELG 36
                                      9********************99 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                     zinc-ribbon_6  4 CeqCgqllffenssClkCga 23
                                      C++Cg+ +  +++ C +Cg+
  gi|336254208|ref|YP_004597315.1| 43 CSSCGEAFERDDEFCSNCGT 62
                                      9*****************96 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.8
                     zinc-ribbon_6  75 aealCeaCrlnr 86 
                                       ++ +C+ C++++
  gi|336254208|ref|YP_004597315.1| 304 HNYYCSECARTD 315
                                       455677776665 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   6.0    0.0014       1.3      18      55 ..      11      63 ..       5      68 .. 0.78
   2 ?   -0.6   0.0       1.6   1.6e+03      47      58 ..     269     280 ..     263     284 .. 0.77
   3 ?   -2.4   0.1       6.2   5.9e+03      48      52 ..     307     311 ..     297     314 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                               IBR 18 lkwCprpdCeaiiekseg.cks..........vtCskCgf......efCfnCkke 55
                                      +  Cp  dC+a + ++++ c +          + Cs+Cg+      efC+nC+ +
  gi|336254208|ref|YP_004597315.1| 11 RPPCP--DCGATVPPDANfCLHcgvelgtvepAYCSSCGEaferddEFCSNCGTP 63
                                      55799..******99999977788899998888899998633333378****976 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                               IBR  47 efCfnCkkewHe 58 
                                       e C+ C++++ +
  gi|336254208|ref|YP_004597315.1| 269 ERCVVCNEPFDG 280
                                       569999998866 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.2
                               IBR  48 fCfnC 52 
                                       +C++C
  gi|336254208|ref|YP_004597315.1| 307 YCSEC 311
                                       34444 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   8.5    0.0063         6       5      48 ..      11      61 ..       9      64 .. 0.82
   2 ?    0.3   0.1      0.82   7.7e+02      31      39 ..     307     315 ..     296     319 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0063
                           DUF1272  5 rpnCecCdkdlppdseearic.....syEctFCaeCaeevl..envCPncg 48
                                      rp C  C +++ppd++    c     + E ++C++C e+    ++ C ncg
  gi|336254208|ref|YP_004597315.1| 11 RPPCPDCGATVPPDANFCLHCgvelgTVEPAYCSSCGEAFErdDEFCSNCG 61
                                      899************9998884444456789*****9986533689****8 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.82
                           DUF1272  31 FCaeCaeev 39 
                                       +C+eCa + 
  gi|336254208|ref|YP_004597315.1| 307 YCSECARTD 315
                                       899999876 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.4    0.0091       8.6      46      86 ..      14      58 ..       7      68 .. 0.73
   2 ?    4.0   2.3     0.059        56      63      78 ..     299     314 ..     250     320 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0091
                              PHF5 46 cdecsfgkl..eekciicgs.kgvsdayyclecvr.lekdrdGcp 86
                                      c +c  +    ++ c+ cg   g+ +  yc++c +  e+d + c 
  gi|336254208|ref|YP_004597315.1| 14 CPDCGATVPpdANFCLHCGVeLGTVEPAYCSSCGEaFERDDEFCS 58
                                      667765543336779999987888888899999642688888775 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.059
                              PHF5  63 skgvsdayyclecvrl 78 
                                       ++++++ yyc+ec+r+
  gi|336254208|ref|YP_004597315.1| 299 THAMEHNYYCSECART 314
                                       3566799******987 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 ?    4.2   1.6     0.041        39      12      36 ..      26      48 ..      20      50 .. 0.73
   2 ?    4.6   3.8     0.031        29      10      35 ..      39      61 ..      30      63 .. 0.87
   3 ?    3.4   0.1     0.074        69      12      35 ..     269     312 ..     262     315 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.041
                                      -B-TTT-SB--SSSS-EEEETTT-- CS
                              C1_1 12 tfCkhCgeflwgkekqglkCswCkl 36
                                      +fC hCg  l  +      Cs C++
  gi|336254208|ref|YP_004597315.1| 26 NFCLHCGVEL--GTVEPAYCSSCGE 48
                                      6888888888..6666667888876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.031
                                      S--B-TTT-SB--SSSS-EEEETTT- CS
                              C1_1 10 qptfCkhCgeflwgkekqglkCswCk 35
                                      +p++C+ Cge +   e+    Cs+C+
  gi|336254208|ref|YP_004597315.1| 39 EPAYCSSCGEAF---ERDDEFCSNCG 61
                                      799*********...99999999996 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.074
                                       -B-TTT-SB-...................-S.SSS-EEEETTT- CS
                              C1_1  12 tfCkhCgefl...................wg.kekqglkCswCk 35 
                                        +C  C+e++                   ++    + + Cs+C 
  gi|336254208|ref|YP_004597315.1| 269 ERCVVCNEPFdgglvrrrrdetvvaglpvRThAMEHNYYCSECA 312
                                       68999999986666666666666666665333555556666665 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   0.5     0.052        49      72      94 ..      13      33 ..       6      39 .. 0.79
   2 ?    8.1   2.2    0.0027       2.5      71      96 ..      41      64 ..      37      71 .. 0.81
   3 ?    0.4   0.1      0.68   6.4e+02      54      78 ..     289     313 ..     264     317 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.052
                                      EETTTS-EEECHHHHHS-TTTSS CS
                              HypA 72 rCreCgkefeleekalrCpkCgs 94
                                       C +Cg+++  +++   C +Cg 
  gi|336254208|ref|YP_004597315.1| 13 PCPDCGATVPPDAN--FCLHCGV 33
                                      5********98854..6*9**96 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0027
                                      EEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA 71 vrCreCgkefeleekalrCpkCgsad 96
                                      ++C++Cg+ fe +++   C +Cg+ +
  gi|336254208|ref|YP_004597315.1| 41 AYCSSCGEAFERDDE--FCSNCGTPR 64
                                      68*********8743..5*****875 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.68
                                       C.TTTT-EEEEEEE--EEEETTTS- CS
                              HypA  54 gtvlegaeLeieevpvkvrCreCgk 78 
                                       +tv++g  ++ + ++ +++C+eC +
  gi|336254208|ref|YP_004597315.1| 289 ETVVAGLPVRTHAMEHNYYCSECAR 313
                                       5666677777777777888888864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); 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 0.25s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2529.87
//
Query:       gi|336254209|ref|YP_004597316.1|  [L=311]
Description: pyruvate ferredoxin/flavodoxin oxidoreductase subunit beta [Halopiger xanaduensis SH-6]
Scores for complete 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-31  109.6   0.1    1.7e-31  109.1   0.1    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
     0.0079   16.3   2.0      0.025   14.7   2.0    1.9  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit
  ------ inclusion threshold ------
      0.071   13.1   0.0       0.12   12.4   0.0    1.3  1  DUF2487       Protein of unknown function (DUF2487)


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 !  109.1   0.1   2.9e-35   1.7e-31       2     152 ..      61     207 ..      60     208 .. 0.94

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 2.9e-35
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       iGc+             +syl+  g+++ +G++lp+A +akla+pd ev+a  GDG+ + i ++++++ +r+n+++t
  gi|336254209|ref|YP_004597316.1|  61 IGCSGK----------LNSYLDtYGFHTIHGRSLPVARAAKLANPDLEVIAAGGDGDGYGIgGNHFIHTARENHDMT 127
                                       677776..........799999889**************************************************** PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpa 149
                                       ++v+nNe++g+t+gq   ++p+g+k+k++p+g+ ++p+++      +Ga+  ar    ++++ +e++kea+e++g+a
  gi|336254209|ref|YP_004597316.1| 128 YIVFNNEIFGLTKGQtspTSPKGHKSKTQPSGSAKTPIRPLSQSLTAGASyIARTAAVNPNQAKEIIKEAIEHDGFA 204
                                       *****************999************999999999999999***888999999****************** PP

                                       EEE CS
                      TPP_enzyme_C 150 lie 152
                                        ++
  gi|336254209|ref|YP_004597316.1| 205 HVD 207
                                       998 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   2.0   4.3e-06     0.025       1      62 [.     212     279 ..     212     283 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.3e-06
                                       XTTTXSSS.XSXXXXX-EEEGGGS.T---EEHHHHHHHHT----.....-EEEEEEEE.TTS--HHHHHH CS
                        PFO_beta_C   1 CvtFNkvn.TfdwYkervykleed.gyDpsdlekAlekalewgd.....kiplGifYk.eekptyeerle 62 
                                       C+t+Nk    +  Y   + + + d ++D +d+++A e ++e +d      + +G  Y  e++p+y+++ +
  gi|336254209|ref|YP_004597316.1| 212 CPTWNKDArQYVPYI-DIQESD-DyEHDIHDRQEAAEMMRETEDvlnegTVLTGRYYVdEDRPSYTQEKQ 279
                                       888887551222232.334444.348***************888999988***************98765 PP

>> DUF2487  Protein of unknown function (DUF2487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     2e-05      0.12      56     122 ..     175     235 ..     171     252 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                           DUF2487  56 aftYlkeeekeeeverlkeweeelkeegfkhvvfitsdeewkeleeelegkliwvpaiplesldesq 122
                                         +Y+ ++++ +  +  + ++e++++ gf hv f+t   +w++  ++      +vp i +++ d+ +
  gi|336254209|ref|YP_004597316.1| 175 GASYIARTAAVNPNQAKEIIKEAIEHDGFAHVDFLTQCPTWNKDARQ------YVPYIDIQESDDYE 235
                                       568999998888776666778889999***************99998......99999998877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2340.74
//
Query:       gi|336254210|ref|YP_004597317.1|  [L=633]
Description: 2-oxoacid:acceptor oxidoreductase subunit alpha [Halopiger xanaduensis SH-6]
Scores for 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-50  170.2   0.0      1e-49  169.3   0.0    1.4  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    6.6e-47  159.8   0.0    1.4e-46  158.8   0.0    1.5  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    6.4e-12   45.7   0.0    1.2e-11   44.8   0.0    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    0.00086   19.0   0.0     0.0017   18.0   0.0    1.5  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
     0.0044   16.9   0.0      0.011   15.6   0.0    1.6  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
       0.14   12.2   0.1        1.3    9.1   0.0    2.2  2  DUF1664          Protein of unknown function (DUF1664)
       0.17   12.4   0.2       0.84   10.1   0.0    2.3  2  Usp              Universal stress protein family


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 !  169.3   0.0   4.1e-53     1e-49       2     228 ..     234     479 ..     233     482 .. 0.88

  Alignments for each domain:
  == domain 1  score: 169.3 bits;  conditional E-value: 4.1e-53
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +ai ag+++ia+YP+TP ++++  l++  ++ +       q+e+Ei+a++ ++GA+ aG++a+  +Sg G++Lm+e 
  gi|336254210|ref|YP_004597317.1| 234 GAIDAGCRFIAGYPMTPWTDVFTILSQNFPDMGG---ISEQVEDEIAAAALAVGASHAGVKAMSGSSGGGFALMSEP 307
                                       89*****************************995...789************************************* PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvi 150
                                       lgla ++e+P+v+v ++Ra+pstg++++++q+Dl  ++     d++ +v+a++n++ea++ +  Af +A+++++Pv+
  gi|336254210|ref|YP_004597317.1| 308 LGLAEMTETPLVLVEAMRAGPSTGMPTKPEQGDLEHVLytsqgDSQRVVFAPGNIEEAYEQTRLAFDIAWDYQIPVM 384
                                       ***************************************************************************** PP

                                       EEEEHHHH..HEEEEEEC-SGG.GS-----SBXXXXXXXX.................SXXXBXXTXXTSSXXEEESB CS
                             POR_N 151 vlfDgflls.hevekvelpdeedelklikekleeyerkey.................aldpekpiargtaanpdtgl 209
                                       ++ D+ l   ++  +ve+ d+e + +l ++  ee+ ++++                 ++ p++ + +++ ++ +tg 
  gi|336254210|ref|YP_004597317.1| 385 LIYDQKLSGeNTNVDVEFFDREPSPDLGSTLTEEELKEAAhdnsgkfkrfnyedaedGVAPRSLPGQKGGRYLATGN 461
                                       ****988741455578888888444433333322222222456899999999****99******************* PP

                                       XBXTTSXBXXXXHHHHHHH CS
                             POR_N 210 ehrekgneaedaaekvvee 228
                                       eh   g+++ed  +++v +
  gi|336254210|ref|YP_004597317.1| 462 EHSPVGHISED-PDNRVYQ 479
                                       ****9999999.7776655 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.8   0.0   5.5e-50   1.4e-46       1     177 []      14     200 ..      13     200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 158.8 bits;  conditional E-value: 5.5e-50
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEES............. CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllval............. 64 
                                       +G+G+ ++++++aka++r+G++v+++r+y+s+irGgh+y+++r++d+ +v+s++ +++++l+al             
  gi|336254210|ref|YP_004597317.1|  14 SGDGIDSTSQNFAKALMRSGLDVFTHRHYPSRIRGGHTYVEIRAADR-EVQSRG-DGYNFLLALgdsfarnpqeeay 88 
                                       5*********************************************9.9*****.********************** PP

                                       ....SHHHHHHHGGGEEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHH CS
                               POR  65 ....daetlsehldglkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlG 137
                                           + + lse+ld+l++gg+i+y+++ ++++++++  +eer++  ++g++vy++d++ +ake+g+ e+++Nt+++G
  gi|336254210|ref|YP_004597317.1|  89 ygneELKPLSENLDDLREGGVIVYDEGLVSEEDVEELNLEERAE--ENGWHVYPIDLRGLAKEHGR-EVMRNTAGVG 162
                                       **96669999************************9999988655..56******************.********** PP

                                       HHHHHHTS-HHHHHHHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 138 alaallglplealeeaikkrfpkkkeviekNlkafragye 177
                                       ++aall ++le++e+ +++++++  +++e Nl+ + ++ye
  gi|336254210|ref|YP_004597317.1| 163 ITAALLEMDLEHIEDLMEDAMGG--DILESNLEILHEAYE 200
                                       **********************9..7************97 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 !   44.8   0.0   4.6e-15   1.2e-11       1      76 [.     510     585 ..     510     606 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 4.6e-15
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevka 76 
                                       A++ i++ Gs+ g +++av++l ++g++v  l +  + PFPe+e+ e+l++v++ +v+++n++  ++G l +e  +
  gi|336254210|ref|YP_004597317.1| 510 ADYGIITWGSSQGAVEEAVERLNDNGYSVKGLSVSDMMPFPEQEVTEFLESVDEAMVVEMNATAQFRGLLQKELGR 585
                                       89*************************************************************9999**9999765 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 !   18.0   0.0   6.5e-07    0.0017       3     163 ..     227     391 ..     225     399 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.5e-07
                                       HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT..TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHH CS
                      TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeq.girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatn 78 
                                       +++a++    ++g + + g+p +  ++++  ls++  ++  +    E   a+aA ++  ++  + +   +sg G++ 
  gi|336254210|ref|YP_004597317.1| 227 GSNAIAYGAIDAGCRFIAGYPMTPWTDVFTILSQNFpDMGGISEQVEDEIAAAALAVGASHAGVKAMSGSSGGGFAL 303
                                       67777777778999999999999999999999999889999999999999***********9*************** PP

                                       CHHHHHHHHHHT--EEEEEEE--CCCHH......S..TC--T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHH CS
                      TPP_enzyme_N  79 altalaeAkvdriPllvlsgdrptslrg......qgvlqqel..dqlalfrpvtkyaervtspeelpealrrAirta 147
                                       +   l  A  + +Pl+++ + r+  ++g      qg l+++l  +q     +  + ++ + + ee+ e+ r A+++a
  gi|336254210|ref|YP_004597317.1| 304 MSEPLGLAEMTETPLVLVEAMRAGPSTGmptkpeQGDLEHVLytSQG----DSQRVVFAPGNIEEAYEQTRLAFDIA 376
                                       ****************************5544443333333332233....33444688889999999999999999 PP

                                       HSSS--EEEEEEEHHH CS
                      TPP_enzyme_N 148 lsgrpgPvylelpkdv 163
                                         + + Pv l   + +
  gi|336254210|ref|YP_004597317.1| 377 -WDYQIPVMLIYDQKL 391
                                       .888999988766655 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.4e-06     0.011      10      70 ..     510     570 ..     505     575 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.4e-06
                                       SSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEE CS
                   Transketolase_C  10 kdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveea 70 
                                        d  ++++Gs    + eA+e+L+++g+s++ +++  + p+ ++ + e +++ ++ +vve +
  gi|336254210|ref|YP_004597317.1| 510 ADYGIITWGSSQGAVEEAVERLNDNGYSVKGLSVSDMMPFPEQEVTEFLESVDEAMVVEMN 570
                                       56679****************************************************9965 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       0.3   7.7e+02      66      88 ..     475     497 ..     468     532 .. 0.81
   2 ?    9.1   0.0   0.00049       1.3      23      78 ..     538     593 ..     512     600 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.3
                           DUF1664  66 sridrvdkkldeqkeiskeikee 88 
                                       +r+ ++d++l++ ++i +e++ee
  gi|336254210|ref|YP_004597317.1| 475 NRVYQMDRRLEKLEAIREELDEE 497
                                       57777888888888777777765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00049
                           DUF1664  23 wkGwklsdlmfvTkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeq 78 
                                        kG+++sd+m    +  ++++esv + +   +++ a+ +  L++++ r ++kl + 
  gi|336254210|ref|YP_004597317.1| 538 VKGLSVSDMMPFPEQEVTEFLESVDEAMVVEMNATAQFRGLLQKELGRFGEKLTSL 593
                                       59***************************99999**************99999765 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       4.8   1.2e+04      71     101 ..     101     131 ..      79     135 .. 0.53
   2 ?   10.1   0.0   0.00033      0.84      14      79 ..     519     588 ..     518     619 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.8
                                       HHHHHHCTTCEEEEEEEESSHHHHHHHHHHH CS
                               Usp  71 akaaaeaggvkvevvveegdpaeeilevaee 101
                                       + +++e+g+++ +  +++ +  ee+++++++
  gi|336254210|ref|YP_004597317.1| 101 LDDLREGGVIVYDEGLVSEEDVEELNLEERA 131
                                       3345555555555556666666666555554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00033
                                       HHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH....HHHHHHCTT CS
                               Usp  14 eskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada....akaaaeagg 79 
                                       +s+ A+e A+e + ++g  +  l v+d++++++    +  +  +e++  e+ + a+     +k++ + g+
  gi|336254210|ref|YP_004597317.1| 519 SSQGAVEEAVERLNDNGYSVKGLSVSDMMPFPEQEVTEFLESVDEAMVVEMNATAQFrgllQKELGRFGE 588
                                       5899**********************************99999999999999888877766444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); 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: 00:00:00.43
# Mc/sec: 4437.23
//
Query:       gi|336254211|ref|YP_004597318.1|  [L=250]
Description: OsmC family protein [Halopiger xanaduensis SH-6]
Scores for complete 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   61.1   0.0    1.8e-16   60.4   0.0    1.3  1  OsmC             OsmC-like protein
    8.5e-08   31.9   0.0    1.9e-07   30.8   0.0    1.6  2  Biotin_lipoyl    Biotin-requiring enzyme
  ------ inclusion threshold ------
      0.014   16.0   0.3       0.12   13.1   0.1    2.4  3  HlyD_3           HlyD family secretion protein
      0.049   13.5   0.0       0.12   12.2   0.0    1.6  1  Biotin_lipoyl_2  Biotin-lipoyl like


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0     4e-20   1.8e-16       1      97 [.     149     243 ..     148     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 4e-20
                                       TTXSSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECTCEEEEEEEEEEE-SS-H..HHHHHH CS
                              OsmC   1 gdgsgpsPeelllaalasCfaitlravakkkgikledleveveaerdpegakgiteirlkvevkipgadseeklkkl 77 
                                       g+++gp+P++ +l +la+C+++++r  a+k+  ++ +++v++++e +    +   ++++++e +++++d +++l++l
  gi|336254211|ref|YP_004597318.1| 149 GTETGPTPVDVFLGGLAACLSLSVRYQAEKRDAGIGEISVTADGEPERGSVE-QLDVTVRLEADADEID-DDTLERL 223
                                       6788***************************999999999997766655333.4445555555555566.4****** PP

                                       HHHHHHHSHHHHHHCT-SSS CS
                              OsmC  78 lekaekrCpvsntlkngvkv 97 
                                       +e+ae+ C vs +l+ +  +
  gi|336254211|ref|YP_004597318.1| 224 VELAERGCHVSELLRDDLAF 243
                                       **************987655 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   4.3e-11   1.9e-07       7      71 ..      19      78 ..      11      80 .. 0.88
   2 ?   -3.3   0.0       1.9   8.5e+03      26      39 ..     198     211 ..     194     211 .. 0.67

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 4.3e-11
                                      SSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEE CS
                     Biotin_lipoyl  7 miGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdlla 71
                                      + G+     v e++v +Gd+++ag+++aeve   +++ + a  +Gv+   l   G+t   g+++ 
  gi|336254211|ref|YP_004597318.1| 19 TWGT-----VREWHVDEGDSIAAGDPVAEVEFETAVISVDAAGDGVLRRRLSATGSTAPPGTPIG 78
                                      4444.....556************************************999999*****999996 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.9
                                       EE-TTSEEEEEECT CS
                     Biotin_lipoyl  26 kVkagqvlaeveam 39 
                                       +V++ +v + +ea+
  gi|336254211|ref|YP_004597318.1| 198 SVEQLDVTVRLEAD 211
                                       57777777777776 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.6e-05      0.12       7      34 ..      20      47 ..      18      55 .. 0.81
   2 ?   -0.4   0.0      0.41   1.8e+03       7      41 ..      57      91 ..      51      97 .. 0.72
   3 ?   -1.7   0.0         1   4.7e+03      85      96 ..     198     211 ..     168     221 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                            HlyD_3  7 dGvvvelnveegevvqagdelleiippd 34
                                       G+v e++v eg+ ++agd+++e+  + 
  gi|336254211|ref|YP_004597318.1| 20 WGTVREWHVDEGDSIAAGDPVAEVEFET 47
                                      59*********************98554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.41
                            HlyD_3  7 dGvvvelnveegevvqagdelleiippdtllveak 41
                                      dGv+       g+  ++g+++  ++p  + +++++
  gi|336254211|ref|YP_004597318.1| 57 DGVLRRRLSATGSTAPPGTPIGIVAPAGRDIADLE 91
                                      7777777778899999*****99999754444444 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1
                            HlyD_3  85 g..aykvevslenp 96 
                                       +  ++ v+v+le++
  gi|336254211|ref|YP_004597318.1| 198 SveQLDVTVRLEAD 211
                                       12234444444443 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.8e-05      0.12      11      33 ..      21      43 ..      18      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                   Biotin_lipoyl_2 11 GrVaqlnVkdGqrVkaGdvLael 33
                                      G+V +++V +G+ + aGd  ae 
  gi|336254211|ref|YP_004597318.1| 21 GTVREWHVDEGDSIAAGDPVAEV 43
                                      99****************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1884.39
//
Query:       gi|336254212|ref|YP_004597319.1|  [L=260]
Description: PHP domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-05   24.9   0.0    2.5e-05   24.6   0.0    1.3  1  PHP       PHP domain
      0.003   17.3   0.0       0.11   12.3   0.0    2.6  2  PHP_C     PHP-associated


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 !   24.6   0.0   2.8e-09   2.5e-05       1      73 [.       3      91 ..       3     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.8e-09
                                      EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT.....................HHHHHHHHHHHHTTTTS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlf.....................gyvefykaakkkykagi 58
                                      d+H+H++ys   + l    +v++a++ gl+ +++ Dh+n+                         e+++++++++   i
  gi|336254212|ref|YP_004597319.1|  3 DFHIHSNYSDG-DFL--GGMVRAAEAAGLEGVGLADHCNVAprdrlermrglygfnldltyeRRREAIERLRERR--SI 76
                                      79*******88.577..9**********************99999999999999999998886677777775544..68 PP

                                      EEEEEEE........ CS
                                      xxxxxxxxxxxxxxx RF
                               PHP 59 kpiiGleayvaddse 73
                                      ++   +e++  +++e
  gi|336254212|ref|YP_004597319.1| 77 EIYDAVEMDYDPRDE 91
                                      887777766555554 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.021   1.9e+02       5      19 ..     178     192 ..     175     194 .. 0.87
   2 !   12.3   0.0   1.2e-05      0.11       9      33 ..     212     236 ..     208     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.021
                             PHP_C   5 rrArrfAeklglpgt 19 
                                       r Ar fA+ + +p +
  gi|336254212|ref|YP_004597319.1| 178 RVARAFADSRTIPEI 192
                                       78***********87 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.2e-05
                             PHP_C   9 rfAeklglpgtgGSDAHrleeVGra 33 
                                       ++ +++ +++t G D+H ++e+G  
  gi|336254212|ref|YP_004597319.1| 212 EILREHSVAVTVGTDSHEPDEIGDR 236
                                       677999*****************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1894.10
//
Query:       gi|336254213|ref|YP_004597320.1|  [L=383]
Description: chorismate synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-122  408.7   0.0   1.4e-122  408.5   0.0    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 !  408.5   0.0  7.7e-127  1.4e-122       1     327 []      10     354 ..      10     354 .. 0.97

  Alignments for each domain:
  == domain 1  score: 408.5 bits;  conditional E-value: 7.7e-127
                                       SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE CS
                   Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallie 77 
                                       ++vttfGeShg+a+g+++ g+paglel+eediq++LdrR+pgqs +tt+r E D v+i sG+++g+t+Gtpi l+i+
  gi|336254213|ref|YP_004597320.1|  10 FQVTTFGESHGEAMGCTVSGCPAGLELSEEDIQADLDRRKPGQSMITTSRGEPDDVSIKSGIQDGYTTGTPIGLVIQ 86 
                                       89*************************************************************************** PP

                                       -TTS-..SSSSSTSBE-TTSTCHHHHHHC-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE. CS
                   Chorismate_synt  78 NkdqrskdyeeikevpRpgHADltyalkYgirdlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei. 153
                                       Nkd+rs++ye + ++pRp+H+D+ty++k+g+r++ gggrsSaReT+  vaaGa+akklL++ g+e++a+v++ig++ 
  gi|336254213|ref|YP_004597320.1|  87 NKDARSEKYEPFITAPRPSHGDFTYSAKFGTRNWGGGGRSSARETVNWVAAGAIAKKLLEREGVELKAHVNQIGDVe 163
                                       **************************************************************************888 PP

                                       ..........CHHHHHTT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHHTS CS
                   Chorismate_synt 154 ..........ekeaenpvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalmsi 220
                                                 e+++en+vrc+d+e+ae+m+++iee+++egds+Gg + + ++gvp+GlG p fd+l a+L++a+m++
  gi|336254213|ref|YP_004597320.1| 164 apevsfeqlkEHSEENDVRCADPETAEKMQDLIEEYQEEGDSIGGSIYFEARGVPVGLGAPRFDSLSARLGQAMMAV 240
                                       8888888775444788************************************************************* PP

                                       TTEEEEEETTGGGGGGSBHHHHS--EE.......EESS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTTS CS
                   Chorismate_synt 221 pAvkgveiGsGfeaaelkGseanDeiv.......lrktnnaGGieGGisnGepivvrvavKpipsiakeqktvdlet 290
                                       pA+ ++e+G G ea e +G+e nD +        +  +n++GGi+GGis+Gepi+ +v++++  si k+q+t+d et
  gi|336254213|ref|YP_004597320.1| 241 PATTAFEFGLGREAREWTGKERNDDWEfdsegnpTPVENDHGGIQGGISSGEPIYGEVTLHAPTSIPKPQQTADWET 317
                                       **************************96666555449**************************************** PP

                                       -E-EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHHH CS
                   Chorismate_synt 291 keevelevkgrhDpcvvpravvvveamvalvladall 327
                                        e  e +v grhDp++ pr v+vveam+al+l+d++l
  gi|336254213|ref|YP_004597320.1| 318 GELKEEQVIGRHDPVLPPRGVPVVEAMLALTLVDFML 354
                                       **********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2807.95
//
Query:       gi|336254214|ref|YP_004597321.1|  [L=136]
Description: histidine triad (HIT) protein [Halopiger xanaduensis SH-6]
Scores for complete 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   64.2   0.0    1.7e-17   63.9   0.0    1.1  1  HIT       HIT domain
    3.6e-09   37.1   0.0    4.7e-09   36.7   0.0    1.1  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
     0.0006   19.7   0.0    0.00077   19.3   0.0    1.2  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   2.8e-21   1.7e-17       2      97 ..      13     107 ..      12     108 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 2.8e-21
                                       GCC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEES CS
                               HIT   2 keipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinng 78 
                                       +e++++vvyed +++afld +p   gh+Lv+p +h ++l  +++e  a+++++v+ v +a++++++ +g+ v+  +g
  gi|336254214|ref|YP_004597321.1|  13 GEKDAHVVYEDARTIAFLDENPACVGHTLVVPTAHRPDLLVADAETNAAVFETVRTVSTAMEATLEPDGFSVFYSTG 89 
                                       799************************************************************************** PP

                                       GGGT-SSSS-EEEEEEC-T CS
                               HIT  79 ahagqsvahlHiHviprre 97 
                                       +  gq v h H+H++pr+e
  gi|336254214|ref|YP_004597321.1|  90 PIVGQ-VEHAHVHLLPRYE 107
                                       **998.9**********97 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   7.9e-13   4.7e-09       1     100 [.       4     103 ..       4     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 7.9e-13
                                       T-HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T- CS
                            DcpS_C   1 kwvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynev 77 
                                       ++ f++l++g++ + vvyed +++++ D +p+   h lv+p ++ ++l   ++e    + e ++++ +++e     +
  gi|336254214|ref|YP_004597321.1|   4 ECPFCRLIEGEKDAHVVYEDARTIAFLDENPACVGHTLVVPTAHRPDLLVADAETNAAVFETVRTVSTAMEAT---L 77 
                                       589******************************************9999998888888888888887777664...5 PP

                                       EEEEE--SCCCT-...-S-S--EEEE CS
                            DcpS_C  78 daeelrvgvhyqP...svyhlHlHvi 100
                                       +++ + v++   P   +v+h H+H++
  gi|336254214|ref|YP_004597321.1|  78 EPDGFSVFYSTGPivgQVEHAHVHLL 103
                                       89**********************97 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.3e-07   0.00077      12     108 ..       3     104 ..       1     113 [. 0.78

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-07
                                       HH-S----SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHH.HHHHHHHHHHHHHT.. CS
                          CwfJ_C_1  12 dsClfClsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldei.rkfrkalvkmykkq.. 85 
                                       ++C fC   +  +++ +v    ++ + l ++p   gH l++p++H++ ll++d+e+   + +  r   ++m +    
  gi|336254214|ref|YP_004597321.1|   3 EECPFCRLIEGEKDAHVVYEDARTIAFLDENPACVGHTLVVPTAHRPDLLVADAETNAAVfETVRTVSTAMEATLep 79 
                                       78****999999999999999999999**************************988766513344444555333311 PP

                                       T--EEEEEE-..SSS-----EEEEE CS
                          CwfJ_C_1  86 dkdavvfEis..sersvHlaiqvip 108
                                       d   v++ +     +  H++++++p
  gi|336254214|ref|YP_004597321.1|  80 DGFSVFYSTGpiVGQVEHAHVHLLP 104
                                       4446788877777788888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1123.98
//
Query:       gi|336254215|ref|YP_004597322.1|  [L=414]
Description: type I phosphodiesterase/nucleotide pyrophosphatase [Halopiger xanaduensis SH-6]
Scores for 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-32  112.9   1.0      7e-32  111.4   1.0    1.6  1  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
    1.8e-05   24.9   0.0      0.014   15.5   0.1    2.2  2  PglZ             PglZ domain
    0.00011   21.8   0.3       0.38   10.1   0.0    2.2  2  Sulfatase        Sulfatase
     0.0083   15.1   2.2      0.013   14.4   2.2    1.2  1  Alk_phosphatase  Alkaline phosphatase
  ------ inclusion threshold ------
      0.011   15.7   0.3      0.022   14.7   0.3    1.5  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
      0.073   12.4   0.3        0.2   11.0   0.2    1.7  2  Metalloenzyme    Metalloenzyme superfamily
        0.2   11.9   0.5       0.43   10.9   0.5    1.5  1  YqjK             YqjK-like protein


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   1.0   2.7e-35     7e-32       1     356 [.      63     392 ..      63     393 .. 0.78

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 2.7e-35
                                       EEEEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEE CS
                      Phosphodiest   1 vlvislDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgeyv 77 
                                       vlv+++DGl  +  +  +++ p l++L ++g+  p l++v+P++T++++++  TG+ P+eHG++g ++y ++ g   
  gi|336254215|ref|YP_004597322.1|  63 VLVVLIDGLGLNRWKSERDDVPLLKRLTERGTVTP-LTSVYPSETAAAMTTYHTGALPAEHGVIGWNVYEPTVGTSF 138
                                       79*******9766666225****************.*********************************99998864 PP

                                       ...EEETTTTGG......GGGCTTS-HHHHHHHTHTTCEEEESETTTTSEBTTCT.SC.TBHHSBTCT.CSTTSCHH CS
                      Phosphodiest  78 ...vfvtededa......prwwqgepiwdtaakarglkaaalfwpgsevdystyyylvsetppryleddfnakvple 145
                                          +fv +d +        ++ + ep++++++++    ++++++ ++++++            + ++++++  ++l 
  gi|336254215|ref|YP_004597322.1| 139 lalPFVDKDGNPpaglepGDVADAEPWVVDLERD----VDVHYV-TGYPEHEA----------YATNHEYESLEDLG 200
                                       111555555554555554445555**********....778877.57777763..........34444555555555 PP

                                       HHHHHHHHHHHHHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTT CS
                      Phosphodiest 146 dkvdkavlqtwldaafakvvlekelekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsa 222
                                       +++        lda++           p +++ y++++D + H++G   ++ ++al+++ + ++d l+ +d++  ++
  gi|336254215|ref|YP_004597322.1| 201 STLE-----GALDAPA----------SPSYTFAYVPHVDVAAHQHGTTAEQYREALAQACAQLEDALATVDRD-TAE 261
                                       5555.....4456674..........7********************************************99.99* PP

                                       TEEEEEEES---EEEHTTSEEEGGGTSTGGHGEEEEECBHHS.SSEEEEEESTEE.E.CCCTTHHHHHHHHHHTCHH CS
                      Phosphodiest 223 etniilvSDHGmadvsddkvielndlleekgllhlkdegkggakaliainpkare.lnrvaeaeaeevyaelkakle 298
                                       et +++++DHG  d++ d+ ++l ++   +   +  ++g  g++ ++a +p+  + + + +e+ +e+v++ l+  l+
  gi|336254215|ref|YP_004597322.1| 262 ETLVLVTADHGHVDTDPDRNVDLTEFDVLE---ESLERGPDGDPIRYAGSPR--NvHLHLREGTVERVRDALRGRLD 333
                                       ***************967777777665543...4444555566777777777..77999999999999999999955 PP

                                       CCHSTHTTTEEEEEGG.GS-GGGCH....S....TTS-SEEE.EE-TTEEEESSTTCSSBS-SEE--S CS
                      Phosphodiest 299 elrkkegealavylke.aipkrlhy....k....krapdlvl.vadpgwsitskdkpdeyeikgthGy 356
                                       +         +v ++e  + krl      +    +r++dlv+   + g+++ ++++p+e e +g+hG+
  gi|336254215|ref|YP_004597322.1| 334 A---------RVVRREtVLEKRLFGdcepSttfgRRLGDLVVsHRELGVWYGGDYEPEELELVGMHGG 392
                                       5.........444455466666655443314455********************************96 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0019       4.9       2      50 ..      62     112 ..      61     122 .. 0.82
   2 !   15.5   0.1   5.3e-06     0.014     109     170 ..     210     274 ..     182     277 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0019
                              PglZ   2 kvfvIisDalryeaweelkql..LnkedrfeaelsavlgvlPslTklgraa 50 
                                        v v+++D+l+++ w++ ++   L k+ +    +++  +v Ps T  ++  
  gi|336254215|ref|YP_004597322.1|  62 NVLVVLIDGLGLNRWKSERDDvpLLKRLTERGTVTPLTSVYPSETAAAMTT 112
                                       689*************9988523556666677899***********99975 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 5.3e-06
                              PglZ 109 lkdkevvyivhnkvDalgd.kasteqksfeaveeslkelkelvksllee..ngykvlltaDHGfi 170
                                       +    +   ++ +vD  ++ +  t ++  ea +++  +l++ +  +  +  + + vl+taDHG +
  gi|336254215|ref|YP_004597322.1| 210 PASPSYTFAYVPHVDVAAHqHGTTAEQYREALAQACAQLEDALATVDRDtaEETLVLVTADHGHV 274
                                       5556677789999***999566788899999999999999888887544366789********87 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00015      0.38       2      69 ..      62     126 ..      61     144 .. 0.83
   2 !    9.8   0.2   0.00018      0.45     208     251 ..     214     273 ..     170     317 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                                       EEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSS CS
                         Sulfatase   2 nvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvas 69 
                                       nv+++l+d lg + +++  +     p l+rl+e+g++   + +  + ++ ++ +  tg  p+++gv  
  gi|336254215|ref|YP_004597322.1|  62 NVLVVLIDGLGLNRWKSERDD---VPLLKRLTERGTVTPLTSVYPSETAAAMTTYHTGALPAEHGVIG 126
                                       9*********88877777774...679*****999997777766779*****************9865 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00018
                                       H.................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSS CS
                         Sulfatase 208 r.................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhga 251
                                       +                  ++e+y  +++++  ++++ la++ +   +++tlv++t+Dhg+
  gi|336254215|ref|YP_004597322.1| 214 SytfayvphvdvaahqhgTTAEQYREALAQACAQLEDALATV-DRDTAEETLVLVTADHGH 273
                                       044444455555555555778888899999999999999999.9999*************7 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   2.2   5.3e-06     0.013     262     309 ..     223     274 ..     211     289 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.3e-06
                                       HHHHHHT.TTHHHHHHHHHHHHHH.HHHHHHHCHH..CTTEEEEEEESSEES CS
                   Alk_phosphatase 262 IDhaaHe.ndavgalsEvvefdeA.vkaalefakk..eketlvvvTaDHshv 309
                                       +D aaH+ ++++++ +E+++   A ++ al   ++   +etlv+vTaDH hv
  gi|336254215|ref|YP_004597322.1| 223 VDVAAHQhGTTAEQYREALAQACAqLEDALATVDRdtAEETLVLVTADHGHV 274
                                       7888887346788899987654443355555555533489***********7 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 ?   14.7   0.3   8.5e-06     0.022      74     141 ..     186     256 ..     165     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.5e-06
                   2_5_RNA_ligase2  74 vylsvsdsealqalraallealpeagdkedsgeftPHlTiaqsadstsaaelleklaqalpple...fevd 141
                                       +y+  +  e+l++l ++l++al +  + ++ + ++PH+ +a  ++ t a++ +e+laqa  +le   ++vd
  gi|336254215|ref|YP_004597322.1| 186 AYATNHEYESLEDLGSTLEGALDAPASPSYTFAYVPHVDVAAHQHGTTAEQYREALAQACAQLEdalATVD 256
                                       455557899*****************99999******************6666666333333332225554 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.63   1.6e+03       2      16 ..      62      76 ..      61     114 .. 0.77
   2 ?   11.0   0.2     8e-05       0.2     135     189 ..     216     275 ..     185     286 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.63
                                      EEEEEEETTBB---- CS
                                      xxxxxxxxxxxxxxx RF
                     Metalloenzyme  2 kvvlvvlDGlGeapa 16
                                      +v++v++DGlG    
  gi|336254215|ref|YP_004597322.1| 62 NVLVVLIDGLGLNRW 76
                                      5899999**997654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8e-05
                                       EEEEE-HHHHHHHTT..-H....HHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--T CS
                                       xxxxxxxxxxxxxxx..xx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 135 vvvniknaDmvGHtg..dl....eatiaaieaaDeavkeildaieqvdgilvvtADHgnae 189
                                       ++  +++ D ++H+    +    ea ++a+ ++  a++ +  +  +++++++vtADHg  +
  gi|336254215|ref|YP_004597322.1| 216 TFAYVPHVDVAAHQHgtTAeqyrEALAQACAQLEDALATVDRD-TAEETLVLVTADHGHVD 275
                                       4455667777766541144111144455666666666655544.345669********765 PP

>> YqjK  YqjK-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   0.00017      0.43       4      28 ..     233     257 ..     232     261 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                              YqjK   4 qieqQRldLaqaaepwekalapvDr 28 
                                       ++eq R++Laqa +++e+ala vDr
  gi|336254215|ref|YP_004597322.1| 233 TAEQYREALAQACAQLEDALATVDR 257
                                       58999*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2904.23
//
Query:       gi|336254216|ref|YP_004597323.1|  [L=430]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-112  373.7   0.0   1.2e-111  373.5   0.0    1.0  1  EPSP_synthase    EPSP synthase (3-phosphoshikimate 1-carboxyv
  ------ inclusion threshold ------
      0.038   14.5   0.1       0.17   12.4   0.1    2.1  1  Cu_amine_oxidN1  Copper amine oxidase N-terminal 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 !  373.5   0.0  1.3e-115  1.2e-111       4     417 .]       7     419 ..       5     419 .. 0.96

  Alignments for each domain:
  == domain 1  score: 373.5 bits;  conditional E-value: 1.3e-115
                                       SS--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE CS
                     EPSP_synthase   4 gkrlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfea 80 
                                       ++ l+g+ ++p+sks+++ra+l+A  a+g  t+++ L+s+D+r+++ a+  +g+++ +   ++ ++ +eg+ g+ e+
  gi|336254216|ref|YP_004597323.1|   7 PSSLRGTARAPPSKSYTHRAILAAGYADGA-TVRDALWSADTRATARAVELFGGDVDRR--DDGTLAIEGFDGRPEV 80 
                                       6789*****************999998885.79********************999888..5789999********* PP

                                       -HHHHTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS-BE CS
                     EPSP_synthase  81 peelvldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lklkg 156
                                       p ++v+d+ nsgt++rl+ta++ala+g +vLtGdes+r+RP  +ll+a+  lG e e+ +g++ apl v g   +++
  gi|336254216|ref|YP_004597323.1|  81 P-ADVIDCDNSGTTMRLVTAAAALADGTTVLTGDESLRSRPQGPLLEAIADLGGEAESTRGNGQAPLVVTGpISGGE 156
                                       *.7************************************************************************** PP

                                       EEEETSSTTHHHHHHHHHHHTTSBS.EEEEES.-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SS..B--EE CS
                     EPSP_synthase 157 veikaevsSqqvtsllllaallaeg.ttelee.lasepsiddtlkmlkkfgikietsgteesitvkGkek..lpgte 229
                                       v+i ++vsSq++t+ll++ a++ eg ++ le+ l+s+p++d+tl++l++ g++ e+  t++ + v+G+++   ++ e
  gi|336254216|ref|YP_004597323.1| 157 VSIPGDVSSQYITALLMAGAVTEEGiEIDLETeLKSAPYVDITLELLEAYGVDAEK--TDRGFAVEGGQSyrPTDGE 231
                                       ********************99999******************************9..9999********996777* PP

                                       EE--B-HHHHHHHHHHHHHTT-.EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSEEEEEET.TS--BEEEEE CS
                     EPSP_synthase 230 yvvegDassAayflvaAaitgg.evtvenvginslqGdiealdeilekmgaeitqeedasivvgps.glklkdvdie 304
                                       y v+gD ss +y+l+a+ai+ +  v++e++++ s qGd++++d i+ +mga++++ +da ++  ++ +l++++v +e
  gi|336254216|ref|YP_004597323.1| 232 YAVPGDFSSISYPLAAGAIASEdGVRIEGANP-SAQGDTAIVD-IVDRMGADVEWDQDAGTIDVETgSLEGIEVSVE 306
                                       *********************999*****998.5789*88888.**********9988877666666********** PP

                                       BGSTTSBHGGGHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTST CS
                     EPSP_synthase 305 tlpdeaptlavlaafaegttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDh 381
                                       + pd++pt+a+l a+aeg t+i++++++r+ketdr+ ama+eL klG+e++ee+d l+++++e+ l+ga+ve  +Dh
  gi|336254216|ref|YP_004597323.1| 307 DTPDLLPTIATLGAVAEGDTRITNAEHVRYKETDRVSAMAEELGKLGVETTEEQDSLTVHGGESTLEGATVEGRGDH 383
                                       ***************************************************************************** PP

                                       TTTHHHHHHHHHSBSEEEEETTHHHHHHSSSHHHHH CS
                     EPSP_synthase 382 RiamalalaglvaegeveiddiectdksfpefeekL 417
                                       Ri malalaglva+ge++++ ++++d+sfp+f+++L
  gi|336254216|ref|YP_004597323.1| 384 RIIMALALAGLVADGETTVRGADHVDVSFPGFFDVL 419
                                       **********************************87 PP

>> Cu_amine_oxidN1  Copper amine oxidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.8e-05      0.17      11      40 ..     273     303 ..     270     381 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                   Cu_amine_oxidN1  11 aiaealGakvewdeetktVtikkgdkt.ikl 40 
                                        i++ +Ga+vewd++ +t+ +++g+ + i++
  gi|336254216|ref|YP_004597323.1| 273 DIVDRMGADVEWDQDAGTIDVETGSLEgIEV 303
                                       58899****************9977654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3234.01
//
Query:       gi|336254217|ref|YP_004597324.1|  [L=438]
Description: hypothetical protein Halxa_2829 [Halopiger xanaduensis SH-6]
Scores for 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-31  108.9  20.8    2.1e-31  108.9  20.8    2.3  3  DUF389     Domain of unknown function (DUF389)
  ------ inclusion threshold ------
          2    8.1  13.1       0.18   11.5   1.6    2.8  3  CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like


Domain annotation for each model (and alignments):
>> DUF389  Domain of unknown function (DUF389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.27   2.4e+03      29      47 ..     108     126 ..      90     139 .. 0.53
   2 !  108.9  20.8   2.3e-35   2.1e-31       1     142 []     142     286 ..     142     286 .. 0.95
   3 ?   -0.8   0.0      0.16   1.5e+03      32      52 ..     316     336 ..     303     359 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.27
                            DUF389  29 lknlliglllallvgflfg 47 
                                       l+ +l  ++++++++++++
  gi|336254217|ref|YP_004597324.1| 108 LTPELSTYVVMMVLSMFVA 126
                                       3334444444444444433 PP

  == domain 2  score: 108.9 bits;  conditional E-value: 2.3e-35
                            DUF389   1 MlisPlmgpilaiafglvigdrkllrrglknlliglllallvgflfglllplk..vlg.eeelptsemlsrtepnlv 74 
                                       M+i+Pl+gp+l++++g+vi+dr l+rr+lk+++igl + ++++++f+++++++  v    + +  s+++sr +p+l+
  gi|336254217|ref|YP_004597324.1| 142 MVIAPLIGPALGASVGTVINDRALFRRALKQQAIGLGVGVVTATAFAFVIRTAglVSPmIDIFAVSQIESRLTPDLL 218
                                       ***********************************************888555674555788899************ PP

                            DUF389  75 dllvAlasGaagalallsgnssslvGvaIaaaLlPPavnaGlglalgewalalgslllllvNivgIvl 142
                                       +l++A+ +G+aga  l+ g s +lvGv+ a+a++PP+ ++G+g+a+g +a+a+ + +l+lvN++ I++
  gi|336254217|ref|YP_004597324.1| 219 SLVIAVGAGVAGAWTLTAGTSVALVGVMMAVAVVPPLGVVGIGIAWGLPAVAVAAGVLVLVNMLTINI 286
                                       *****************************************************************986 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.16
                            DUF389  32 lliglllallvgflfglllpl 52 
                                        ++  +++l++++++g+++  
  gi|336254217|ref|YP_004597324.1| 316 AVVFAATILVLSAFLGVVTYD 336
                                       344445555555666644322 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 ?   11.5   1.6     2e-05      0.18      80     170 ..      92     198 ..      68     224 .. 0.81
   2 ?   -1.6   2.3       0.2   1.8e+03      98     130 ..     238     278 ..     210     289 .. 0.61
   3 ?    3.6   0.9     0.005        45     105     164 ..     275     336 ..     261     352 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2e-05
                         CPP1-like  80 wvkklqesldtPssedlliraavflvlavltlvapaes.............vpalllalglgasiyflnrKekklgr 143
                                       ++ ++++   + + +dl+ ++++++v++vl+++++++              v+a l+  +lgas+  + + +  + r
  gi|336254217|ref|YP_004597324.1|  92 TTARISREEMQSRAKDLTPELSTYVVMMVLSMFVATAGllldspavvvgsmVIAPLIGPALGASVGTVINDRALFRR 168
                                       455667777788899*******************************99888888888899***************** PP

                         CPP1-like 144 avlltlvgLvvGlllGsllasllqvd...v 170
                                       a+    +gL vG++ ++++a +++++    
  gi|336254217|ref|YP_004597324.1| 169 ALKQQAIGLGVGVVTATAFAFVIRTAglvS 198
                                       ********************9998875442 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.2
                         CPP1-like  98 iraavflvlavltlvapaes........vpalllalglgas 130
                                       +++a+ +v++++++v p            pa+++a g+++ 
  gi|336254217|ref|YP_004597324.1| 238 TSVALVGVMMAVAVVPPLGVvgigiawgLPAVAVAAGVLVL 278
                                       44555555555555555555555555555555555555555 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.005
                         CPP1-like 105 vlavltlvapaesvpalllalglgasiyflnrKek..klgravlltlvgLvvGlllGsllas 164
                                       vl+++ +++ + +++a+l   g     +f+++  +  +  rav+++   Lv++++lG +   
  gi|336254217|ref|YP_004597324.1| 275 VLVLVNMLTINITSLAVLWYKGYRPDTWFQQDEARvtTQKRAVVFAATILVLSAFLGVVTYD 336
                                       3333333333333677888888888888998766544788*****************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 3250.81
//
Query:       gi|336254218|ref|YP_004597325.1|  [L=396]
Description: hypothetical protein Halxa_2830 [Halopiger xanaduensis SH-6]
Scores for 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   13.3   0.0       0.79    9.0   0.0    2.6  3  DUF2092    Predicted periplasmic protein (DUF2092)
      0.098   12.4   0.0        0.5   10.1   0.0    1.9  1  LolA_like  Outer membrane lipoprotein-sorting protein


Domain annotation for each model (and alignments):
>> DUF2092  Predicted periplasmic protein (DUF2092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0     0.099   8.8e+02     164     200 ..      81     123 ..      76     132 .. 0.73
   2 ?    0.2   0.0     0.044   3.9e+02     125     146 ..     142     163 ..     131     168 .. 0.83
   3 ?    9.0   0.0   8.9e-05      0.79     162     209 ..     210     257 ..     197     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.099
                           DUF2092 164 prkivityktdpgapqytaefsd....Wnldpe..ipedtFrf 200
                                        ++i +++ tdp++p   + +++    W+ dpe  + e++F+ 
  gi|336254218|ref|YP_004597325.1|  81 AKRIEVVDSTDPQEPAGAVAVTNrtvtWEYDPErnVVEKQFHP 123
                                       5788889999999999888888888888888864455666655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.044
                           DUF2092 125 ksakyvgtskvngqecehlafr 146
                                          +y gt++v+g e++ +++r
  gi|336254218|ref|YP_004597325.1| 142 YRLEYAGTETVEGREAHAVEAR 163
                                       56789***********998766 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 8.9e-05
                           DUF2092 162 pLprkivityktdpgapqytaefsdWnldpeipedtFrftpPkgArki 209
                                       p+  + v+ + +d+  ++  +++ d  +d+ +++ tF+++pP++A+ +
  gi|336254218|ref|YP_004597325.1| 210 PVGERNVVRDGDDELLHRTAVTYADLSIDEGLSAGTFTYEPPADAEVV 257
                                       5666778888899999999**************************966 PP

>> LolA_like  Outer membrane lipoprotein-sorting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   5.5e-05       0.5      65     177 ..     137     247 ..     126     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.5e-05
                                       -SCCCEEEEEEEEEEETTEEEEEEEEEESS.TTSSECEEEEEEETTT--EEEEEEEETTS-.EEEEEEEEEEEEETT CS
                         LolA_like  65 revedythellgeeevggkdcyvleltpkdaadvsYskivlwvdketylplkvefydksgk.llKtltvsdiekidg 140
                                       +  + y+ e+ g+e+v+g++++ +e+ p +  +++ + i+l+v  + y +      d+++    +t+ ++d  +   
  gi|336254218|ref|YP_004597325.1| 137 NLRDSYRLEYAGTETVEGREAHAVEARPPP--EETGPAIELVVGDSVYAIPLGPSTDLEELtITRTVLIDD--E-YR 208
                                       67899***********************99..577788888887777666666666655431444444442..2.23 PP

                                       EEEEEEEEEEE..TTT--EEEEEEEEEEE--.--GGGCS CS
                         LolA_like 141 rwtptkmtmed..lkkghkTvleisevefdkglpdklFt 177
                                       +++ ++ +++d   +  h+T +++ ++++d+gl++  Ft
  gi|336254218|ref|YP_004597325.1| 209 YPVGERNVVRDgdDELLHRTAVTYADLSIDEGLSAGTFT 247
                                       666788888885445559999999999999999998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 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:                        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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2931.12
//
Query:       gi|336254219|ref|YP_004597326.1|  [L=395]
Description: peptidase M24 [Halopiger xanaduensis SH-6]
Scores for complete 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-51  174.7   0.4    2.6e-51  174.3   0.4    1.2  1  Peptidase_M24  Metallopeptidase family M24
    3.9e-08   34.0   0.0    7.5e-08   33.1   0.0    1.5  1  Creatinase_N   Creatinase/Prolidase N-terminal 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 !  174.3   0.4   2.9e-55   2.6e-51       2     209 .]     155     377 ..     154     377 .. 0.91

  Alignments for each domain:
  == domain 1  score: 174.3 bits;  conditional E-value: 2.9e-55
                                       HHHHHHHHHHHHHHHHHHHHHT.....TC........BHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTB CS
                     Peptidase_M24   2 lirkaariasaaleavleaikp.....gv........terelaaeieattlkrhgarglafppivasgenaavlhyt 65 
                                       +ir+ +r+ +aa++++ e i       g+        t++ +a+eie t l rhg+  +  ++iva+g+ aa +h +
  gi|336254219|ref|YP_004597326.1| 155 QIRRTQRANEAAMARAEELIATadiedGTlvrdgeplTSEFVAEEIEVT-LLRHGCSLD--ETIVACGADAADPHDR 228
                                       79**************8775542223343334444449*********76.9999*9888..79*************9 PP

                                       CSSSB--TTEEEEEEEEEEET..TEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHH CS
                     Peptidase_M24  66 pndrvlkegdlvlidagaeyd..gyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevl 140
                                         + +l++++l++id+ ++ +  gy +D+trT++ G++ +e+r+ y++++ea eaa++a++pG+t++++++aa++v+
  gi|336254219|ref|YP_004597326.1| 229 G-SGPLEADELIVIDIFPKDKetGYFGDMTRTFARGEPGEEARRRYDVTKEAFEAALEAIEPGATGADVHDAACDVI 304
                                       9.69***************889******************************************************* PP

                                       HHTTB.........CCGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                     Peptidase_M24 141 esagl.........akffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                       e+ag+         ++ f h++GHgvGl++h+  psvs  + +g kle+G+++tiEpgiy  p++ggvried+v+vt
  gi|336254219|ref|YP_004597326.1| 305 EAAGYetlrsdpstETGFIHSTGHGVGLDIHEQ-PSVS--P-SGGKLEPGHIITIEPGIY-DPDVGGVRIEDLVVVT 376
                                       **9***********9999*************99.***9..4.59****************.89************** PP

                                       S CS
                     Peptidase_M24 209 e 209
                                       e
  gi|336254219|ref|YP_004597326.1| 377 E 377
                                       7 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   8.4e-12   7.5e-08       4     131 ..       9     146 ..       7     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 8.4e-12
                                       HHHHHHHHTT-SEEEEECC...HHHHHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH.....TTSEEEE CS
                      Creatinase_N   4 rlralmeekgldallvtsp...enlrYltGfatetgsrglalvvtadgalllvdalryteaaees....atveevve 73 
                                        lr++ + +g+d++l+ ++   +++rY++Gf  ++    + l vt dg +llv  l+y++a +es    +t  + ++
  gi|336254219|ref|YP_004597326.1|   9 PLREAVASAGADGYLIDDDatdSDQRYVSGF--TAPDPYQTL-VTDDGVHLLVSGLEYGRATAESgadtVTRRSAYD 82 
                                       5899***************9999********..455555555.9*********************665544444555 PP

                                       EST......HSSHHHHHHHHHHHHT..-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHS CS
                      Creatinase_N  74 ydd......pvealadllkellese..krvgveldaltvafyealkealpdaelvdaselieelRv 131
                                       y++      p  a + +l+  l++   ++v+v  + ++ ++++ l+ +   a  v +++++ee+R+
  gi|336254219|ref|YP_004597326.1|  83 YRElvaehgPHGAKIRMLEAFLADRgvETVAVPRN-FPTGTADGLRDRG-VAVTVESEGVVEEIRA 146
                                       55577777777777777777777767799999887.7999999998886.6788888999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.50
# Mc/sec: 2354.64
//
Query:       gi|336254220|ref|YP_004597327.1|  [L=366]
Description: peptidase S1 and S6 chymotrypsin/Hap [Halopiger xanaduensis SH-6]
Scores for 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   96.7   4.0    4.6e-27   95.8   4.0    1.5  1  Trypsin_2   Trypsin-like peptidase domain
    5.7e-15   55.4   0.2    1.3e-14   54.3   0.2    1.6  1  PDZ_2       PDZ domain
    4.9e-12   46.1   0.4      2e-11   44.2   0.4    1.8  1  Trypsin     Trypsin
     0.0049   16.7   0.9       0.01   15.7   0.0    2.0  2  PDZ_6       PDZ domain
  ------ inclusion threshold ------
       0.03   14.2   1.2      0.086   12.7   1.2    1.8  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


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 !   95.8   4.0   1.3e-30   4.6e-27       1     150 []      82     218 ..      82     218 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 1.3e-30
                         Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgp 77 
                                       G+Gf++++ + ++TnaHvv++a++  v         ++++g++++++vv++d  +DlA ++v +d++    plp+ +
  gi|336254220|ref|YP_004597327.1|  82 GTGFVYDESH-LVTNAHVVGNATELDV---------RFRQGEWRTGTVVGTDVYSDLAAVRV-DDRPEYATPLPFID 147
                                       9*********.****************.........****************777*******.77777777777666 PP

                         Trypsin_2  78 sealkggepvyvvGyplggeksgsvssGivsgvve.sesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                        ++++g+ +v v+G+p g ++  ++++G+vsgv++  +s+ +++ ++ +qtdaa +pG+SGGp++  dG+v+++
  gi|336254220|ref|YP_004597327.1| 148 GDPVVGD-EVLVIGNPYGLDG--TLTTGVVSGVNRsLPSSLGYDIPDAVQTDAAANPGNSGGPIVSLDGEVIAV 218
                                       6667666.************9..9************9***********************************97 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.2   3.6e-18   1.3e-14       1      82 []     252     358 ..     252     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 3.6e-18
                                       ....XX------............-EEEEEE-TTSGGGGT.--T...............T-EEEEETTB--SSHHHH CS
                             PDZ_2   1 pylGvsvsdeed..........tggvlvvsVkeggPaakaglka...............gDvilkvdgkkvksledl 52 
                                       +y+Gvs+  +++           +gv+v  V++ggP+++  l++               gDvi+++++ ++ sledl
  gi|336254220|ref|YP_004597327.1| 252 AYMGVSLATVTPaiaeanglenPRGVIVEGVRSGGPSDGV-LQPstgtaiidgtrvptgGDVIVALNDAEIASLEDL 327
                                       689999999999999999999999***999******9999.9999******************************** PP

                                       HHHHH.TS-TT-EEEEEEEETTEEEEEEEE- CS
                             PDZ_2  53 islll.kkkpGdtVkltvlRdgkkktvevkl 82 
                                        s+l+ +++p++t+++tv Rdg++++v+++l
  gi|336254220|ref|YP_004597327.1| 328 SSYLAlETSPDETISVTVVRDGQEQSVDLTL 358
                                       ****************************997 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.4   5.5e-15     2e-11      18     203 ..      75     226 ..      59     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 5.5e-15
                                       EEETTCEEEEEEEEEETTEEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEE CS
                           Trypsin  18 lsvksgkhlCgGslisenwvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallkl 94 
                                       ++ + g    +G++++e+ ++T+aH+v na++++v++ +       g+ ++++v            ++  D+a +++
  gi|336254220|ref|YP_004597327.1|  75 METTAG--QGTGFVYDESHLVTNAHVVGNATELDVRFRQ-------GEWRTGTVVG---------TDVYSDLAAVRV 133
                                       444443..469******************8888885554.......2212333333.........22346******* PP

                                       SSSSTSBSSBHCCBBCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTT CS
                           Trypsin  95 kepvklgdtvrpiclpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsretcksaykgkvtenmlcagake 171
                                       + +    ++  p+   + +  + vg+++lv+G ++   +g   tl+++ v+ v+r+  +s ++    ++ ++++a  
  gi|336254220|ref|YP_004597327.1| 134 DDR---PEYATPLPFIDGD--PVVGDEVLVIGNPYG-LDG---TLTTGVVSGVNRSLPSS-LGY-DIPDAVQTDA-- 197
                                       ***...8899999999944..49*******999995.566...9***********87777.444.45889*****.. PP

                                       SSSBCTTTTTTSEEEETTTEEEEEEEEESSSS CS
                           Trypsin 172 ggkdacqGDSGGPlvcsdgelvGivswgkgca 203
                                          +a++G+SGGP+v  dge++ ++  g g +
  gi|336254220|ref|YP_004597327.1| 198 ---AANPGNSGGPIVSLDGEVIAVINSGGGDN 226
                                       ...9***************9999998886655 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       1.4   4.9e+03       2      17 ..     279     293 ..     278     294 .. 0.78
   2 !   15.7   0.0   2.8e-06      0.01      19      56 .]     310     347 ..     308     347 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                             PDZ_6   2 VtaVdpgsPAdrAG.lr 17 
                                       V+ V  g+P d  G l+
  gi|336254220|ref|YP_004597327.1| 279 VEGVRSGGPSD--GvLQ 293
                                       889999***99..6555 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.8e-06
                             PDZ_6  19 GDiilsvNGqpveglsladvaallr..gsagesvvlvvrr 56 
                                       GD+i+++N+ ++   sl+d++++l+  +s++e ++++v r
  gi|336254220|ref|YP_004597327.1| 310 GDVIVALNDAEI--ASLEDLSSYLAleTSPDETISVTVVR 347
                                       9***********..*********99889999999999987 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.2   2.4e-05     0.086       2      25 ..       6      28 ..       5      29 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      lSRR  L++ ++aa  +a +gc++
  gi|336254220|ref|YP_004597327.1|  6 LSRRRVLQTLGVAA-TGAIAGCTT 28
                                      7*******777775.666788876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); 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:                         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 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2631.84
//
Query:       gi|336254221|ref|YP_004597328.1|  [L=355]
Description: FAD dependent oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-17   61.5   0.8    1.4e-08   34.5   0.1    2.0  2  Amino_oxidase   Flavin containing amine oxidoreductase
    1.2e-15   57.4   0.2      3e-15   56.2   0.2    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00019   21.2   7.9    0.00032   20.4   5.5    2.1  2  DAO             FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.034   13.4   0.4      0.061   12.5   0.4    1.4  1  Thi4            Thi4 family
      0.054   12.7   2.2       0.82    8.8   0.9    2.5  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
       0.11   13.1   3.5         15    6.3   0.0    3.0  3  DUF2285         Uncharacterized conserved protein (DUF2285)
       0.13   12.9   0.5         11    6.7   0.2    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
       0.15   12.0   0.5        1.1    9.3   0.5    2.1  1  NAD_binding_9   FAD-NAD(P)-binding
        0.2   10.7   9.0       0.65    9.0   1.9    2.8  3  FAD_binding_2   FAD binding domain
       0.23   10.2   0.9        0.4    9.5   0.9    1.3  1  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   3.4e-09   6.1e-06       5      65 ..      15      76 ..      15      91 .. 0.88
   2 !   34.5   0.1   7.6e-12   1.4e-08     197     451 ..     100     352 ..      90     353 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.4e-09
                                      HHHHHHHHTT..EEEEEEESSSSSBTTS-EEEETTEEEESS--EEETTTHHHHHHHHHTTCCC CS
                     Amino_oxidase  5 aaArqLlsaG..fdVtvlEardrvGGRirtvrsdGylielGamwftgagnpllellkelgled 65
                                      aaA+ L +      VtvlE ++ v GR++t+r+dG++++ Ga+ + +++  ++ ll e  le+
  gi|336254221|ref|YP_004597328.1| 15 AAAYALEETLpdATVTVLEKSGGVCGRAATRRRDGVVYDYGANYVKDDDERVTDLLTE-TLET 76
                                      68888877766789*****************************************999.6655 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 7.6e-12
                                       HHTSCCCEETTHTHHHHHHHHHTTTTEEEETSEEEEEEEE.........ETTCEEEEETTSTEE.EESEEEE-S-HH CS
                     Amino_oxidase 197 gfggslllprgGlsqlpealaeelrgldirlntrVkeikr.........egdgvtvtledgevv.eaDaVvvTvplg 263
                                       + +++ ++ r Gl q++++l + + ++d++ +trV ++ r         e+ g +++  dg++  ++Da ++  p +
  gi|336254221|ref|YP_004597328.1| 100 DADEHKWTYRAGLTQIAKRLFA-RTDVDVHRETRVERLVRdaggavnggESAGWRLEDDDGDEWgPFDALLLNPPAP 175
                                       5567889999************.*****************776666644444456665566666************* PP

                                       HHH....SSEEES..CCSHHHHHHHHHSEEEEEEEEEEEESSGGSGCSTSECECECCCEEETTTEEEEECC....EC CS
                     Amino_oxidase 264 vlk....ailfsP..plpdekaeairnlgfgsvnkvilefdrkfwednalgqgvlvseltttlgeafissd....fp 330
                                         +      +++   +l +  ++ai+ +++ ++  + l+++ +  ++         +   t+ + ++ ++      p
  gi|336254221|ref|YP_004597328.1| 176 QTAdllrSAEWDAddGLRETLVDAIDDVPYRTIWTAALHYPFELERP--Y-----YALVNTDKAHEVGWIAreecKP 245
                                       ***999855555566**99**********************777333..2.....1112222222233333334235 PP

                                       CCSTTTEEEEEEEEECHHHHHHHTTS-HHHHHHHHHHHHHHHHT.GTSSTCSEEEEEECCTETTTSSSEEE.BTTHH CS
                     Amino_oxidase 331 srappgkglvllvyvggdaaneleslsdeelvqavlrdLrklfg.eevpepkatlvtrWhtdplargsysyvsvgpg 406
                                       ++ p g +l l+v  + ++  e  + ++ e  +++ r  + l+g +   +p  t +  W+  +l+        +g++
  gi|336254221|ref|YP_004597328.1| 246 DHVPGGESL-LIVQANHEWSVEHYDDPPAENCEELARIAAALLGdDRLADPDWTDHQGWR-YALP-------EAGAQ 313
                                       666666666.****99888888888899999999999999999*6777777777777776.6666.......99988 PP

                                       HHHHHHHHCHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                     Amino_oxidase 407 hedydplakpegdprlffAGehtsreypgtvegAilSGlraAari 451
                                       +  ++   ++    +l+  G++++    g+++ A++SGl++ +ri
  gi|336254221|ref|YP_004597328.1| 314 TGPLRSAEAE----GLYCIGDWVA--GEGRLHAALRSGLEVGERI 352
                                       8888888888....**********..999**********988777 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 !   56.2   0.2   1.7e-18     3e-15       1      67 [.       6      72 ..       6      73 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.7e-18
                                      EE--SHHHHHHHHHHHCC..TEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHHCC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrllre 67
                                      IvGaG+++++aAy+L +   ++ v++lek+ +++Graa+++++gv++dyga+++++  ++++v++ll e
  gi|336254221|ref|YP_004597328.1|  6 IVGAGAAAAAAAYALEETlpDATVTVLEKSGGVCGRAATRRRDGVVYDYGANYVKD--DDERVTDLLTE 72
                                      9****************888************************************..68*****9976 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   5.5   1.8e-07   0.00032       2     113 ..       4     127 ..       3     216 .. 0.69
   2 ?    1.2   1.3      0.12   2.2e+02     246     298 ..     228     289 ..     101     331 .. 0.46

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.8e-07
                                       EEEECTSHHHHHHHHHHHHT.T...EEEEESSSS.TTSSGGGSSEEEEESSS..STHHSTH..HHHHHHHHHHHHHH CS
                               DAO   2 vviiGGGiiGlstAyeLarr.g...Vtllekgdi.agsgaSgrnsgllhsgl..rylpeas..elarlslealeelr 69 
                                       + i+G+G + +++Ay+L +  +   Vt+lek+   +g++a+ r  g+++ +   +   +    ++ +l  e+  e +
  gi|336254221|ref|YP_004597328.1|   4 IGIVGAGAAAAAAAYALEETlPdatVTVLEKSGGvCGRAATRRRDGVVYDYGanY--VKDDdeRVTDLLTET-LETD 77 
                                       77***************7656579********551557**********9966532..332223666888887.6779 PP

                                       HHHHHHSSTTSEEEEEEEEEESSH.....HHHHHHHHHHHHH.HHTTTTE CS
                               DAO  70 eleeelgididyrrtGllslaade.....eelealdkllall.leaglda 113
                                        l + +++ + ++r G +s ++d+     + +++l + +++l ++ ++d+
  gi|336254221|ref|YP_004597328.1|  78 GLVDITEPIWTFDRGGDVSEGRDAdehkwTYRAGLTQIAKRLfARTDVDV 127
                                       99999999999999999999986522222333333333333343344433 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                                       EEETTTTEEEEEE..........TTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGG CS
                               DAO 246 tdddgrgvyvtpr..........kdgrvlvGgtadeesgdddpevdeedidellealrklfPq 298
                                       ++d ++ v  ++r           +  ++v +++++       ++++e ++el + +++l+ +
  gi|336254221|ref|YP_004597328.1| 228 NTDKAHEVGWIAReeckpdhvpgGESLLIVQANHEWSVEHY-DDPPAENCEELARIAAALLGD 289
                                       22222222233322333333311223344455553222222.367777777777777777765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   3.4e-05     0.061      20      53 ..       4      38 ..       1      45 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
                                      EEEE--SHHHHHHHHHHHHC.TTS-EEEEESSSS- CS
                              Thi4 20 vvivGaGssGLtaayylakk.pdlkvailersvsp 53
                                      + ivGaG++  +aay l +  pd  v++le+s  +
  gi|336254221|ref|YP_004597328.1|  4 IGIVGAGAAAAAAAYALEETlPDATVTVLEKSGGV 38
                                      669***************************98555 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 ?    8.8   0.9   0.00046      0.82       2      33 ..       3      37 ..       2     109 .. 0.79
   2 ?    2.6   0.0     0.035        63     181     224 ..     108     160 ..      99     170 .. 0.74
   3 ?   -2.4   0.0       1.2   2.2e+03     268     291 ..     322     342 ..     316     345 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00046
                                      SEEEE--SHHHHHHHHHHHH..HTS-EEEEE.TTH CS
                                      xxxxxxxxxxxxxxxxxxxx..xxxxxxxxx.xxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaq..agakvtlve.leg 33
                                      ++ ++G+G+A+ aaa  l +    a vt++e ++g
  gi|336254221|ref|YP_004597328.1|  3 RIGIVGAGAAAAAAAYALEEtlPDATVTVLEkSGG 37
                                      5679****************766999999985333 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.035
                                       S-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.........EEEEEETTSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxx RF
                       Pyr_redox_2 181 ldkelsaaleealekeGvevklgtsvkeidgnge.........klevvledge 224
                                       +   l++++++ + + +v+v+ +t+v+++ ++             +++++dg+
  gi|336254221|ref|YP_004597328.1| 108 YRAGLTQIAKRLFARTDVDVHRETRVERLVRDAGgavnggesaGWRLEDDDGD 160
                                       557789999******************99988876555554333335555555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.2
                                       STTEEE-GGGCTECCSS--HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 268 vpgiyaiGDvaggkggpelaqaAv 291
                                        +g+y iGD +    g  + +aA 
  gi|336254221|ref|YP_004597328.1| 322 AEGLYCIGDWV---AGEGRLHAAL 342
                                       789******99...5555555555 PP

>> DUF2285  Uncharacterized conserved protein (DUF2285)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2    0.0099        18      58     101 ..     110     147 ..     100     148 .. 0.86
   2 ?   -1.1   0.0       1.6   2.9e+03      73      89 ..     181     198 ..     176     202 .. 0.75
   3 ?    6.3   0.0    0.0084        15      61      82 ..     280     301 ..     274     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0099
                           DUF2285  58 aslreiAevlfgaervaaedWkdsalrsrvrrlvrrgralmrGG 101
                                       a l +iA+ lf + +v      d +   rv+rlvr++   ++GG
  gi|336254221|ref|YP_004597328.1| 110 AGLTQIAKRLFARTDV------DVHRETRVERLVRDAGGAVNGG 147
                                       5567899999999998......679999**********999998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                           DUF2285  73 vaaedW.kdsalrsrvrr 89 
                                       +++++W +d++lr++  +
  gi|336254221|ref|YP_004597328.1| 181 LRSAEWdADDGLRETLVD 198
                                       56779*999999998765 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0084
                           DUF2285  61 reiAevlfgaervaaedWkdsa 82 
                                        +iA++l g++r+a+ dW+d++
  gi|336254221|ref|YP_004597328.1| 280 ARIAAALLGDDRLADPDWTDHQ 301
                                       68****************6654 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0059        11       1      35 [.       3      39 ..       3      47 .. 0.82
   2 ?    3.9   0.0     0.044        80      44      73 ..     114     144 ..     107     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0059
                                      EEEEECSSHHHHHHHHHHHHTT..SEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelg..kkVtvversdkll 35
                                      ++ +vG+G  +  +A al e    + Vtv+e s  ++
  gi|336254221|ref|YP_004597328.1|  3 RIGIVGAGAAAAAAAYALEETLpdATVTVLEKSGGVC 39
                                      688***************9954357899999887766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.044
                                       HHHHHHHHHTTEEEECSEEEEEEEEETTS.E CS
                         Pyr_redox  44 kilqeklekngievllntkveeiegsedg.v 73 
                                       +i ++ + +  ++v+ +t+ve+++ ++ g v
  gi|336254221|ref|YP_004597328.1| 114 QIAKRLFARTDVDVHRETRVERLVRDAGGaV 144
                                       55566667779*************9999866 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 ?    9.3   0.5   0.00059       1.1       2      46 ..       6      47 ..       5     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00059
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrtdq 46
                                      ivGaG++++a++ +L +      + ++t+ ++s+   gr++ +++
  gi|336254221|ref|YP_004597328.1|  6 IVGAGAAAAAAAYALEETL---PDATVTVLEKSGGVCGRAATRRR 47
                                      9**************9996...99********9887688877664 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.9   0.00036      0.65       4      37 ..       6      43 ..       4      78 .. 0.79
   2 ?    5.2   0.1    0.0053       9.5     139     176 ..     111     146 ..      87     156 .. 0.71
   3 ?   -1.8   0.0      0.69   1.2e+03     392     402 ..     322     332 ..     317     344 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00036
                                      EE--SHHHHHHHHHHHH..TTT-EEEEESSSGGGS..G CS
                     FAD_binding_2  4 ViGsGlAGLaAAleaae..aGlkvavvekeqefgg..a 37
                                      ++G+G+A  aAA+++ e    ++v+v+ek + + g  a
  gi|336254221|ref|YP_004597328.1|  6 IVGAGAAAAAAAYALEEtlPDATVTVLEKSGGVCGraA 43
                                      8***************986677*******998777444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0053
                                       HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT.EEEE CS
                     FAD_binding_2 139 tghallarlvesarkagvdfqerteadeLivedg.rvtG 176
                                          ++++rl+++    +vd++ +t++++L+++ g  v+G
  gi|336254221|ref|YP_004597328.1| 111 GLTQIAKRLFART---DVDVHRETRVERLVRDAGgAVNG 146
                                       3344444444444...6**************97757777 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.69
                                       SBTEEE-STCE CS
                     FAD_binding_2 392 ipGLYAaGeva 402
                                        +GLY++G   
  gi|336254221|ref|YP_004597328.1| 322 AEGLYCIGDWV 332
                                       58******876 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.9   0.00022       0.4       1      34 [.       3      35 ..       3      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00022
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                      +i ivG+G a+  aA al+++l + ++vt++e++
  gi|336254221|ref|YP_004597328.1|  3 RIGIVGAGAAAAAAAYALEETLPD-ATVTVLEKS 35
                                      699*******************55.******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 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:                        37  (0.0020637); 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: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 2663.21
//
Query:       gi|336254222|ref|YP_004597329.1|  [L=129]
Description: hypothetical protein Halxa_2834 [Halopiger xanaduensis SH-6]
Scores for 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   12.6   1.8        1.7    8.7   1.8    2.1  1  HTH_20    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 ?    8.7   1.8   9.6e-05       1.7       1      41 [.      26      71 ..      26     104 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 9.6e-05
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHH.....TS-HHHH CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerl.....dlskntl 41
                                      d+++ ALa+  Rr +l +L+ +  ++++e a+++     d s++ +
  gi|336254222|ref|YP_004597329.1| 26 DELLAALADVRRRYVLYYLRNEHQASLTETARQVaawdcDRSPSAV 71
                                      68999***************************99777553333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1072.19
//
Query:       gi|336254223|ref|YP_004597330.1|  [L=162]
Description: AsnC family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for complete 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-13   50.1   0.1    2.8e-13   49.2   0.1    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    4.5e-12   45.6   1.5    1.2e-11   44.3   1.5    1.7  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    2.3e-08   33.8   0.1    6.1e-08   32.5   0.0    1.7  1  HTH_11          HTH domain
    4.2e-06   26.6   0.0    9.6e-06   25.4   0.0    1.6  1  MarR_2          MarR family
      5e-06   26.5   1.2    1.5e-05   25.0   0.0    2.3  2  HTH_20          Helix-turn-helix domain
    1.3e-05   24.8   2.5    0.00018   21.1   0.1    2.6  3  HTH_DeoR        DeoR-like helix-turn-helix domain
      4e-05   23.7   0.0    8.1e-05   22.7   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00023   20.9   0.1    0.00055   19.7   0.1    1.6  1  HTH_30          PucR C-terminal helix-turn-helix domain
    0.00034   20.7   0.0     0.0007   19.7   0.0    1.5  1  HTH_28          Helix-turn-helix domain
    0.00061   19.6   0.0     0.0021   17.9   0.0    1.8  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00091   19.0   0.1     0.0022   17.7   0.0    1.7  1  HTH_IclR        IclR helix-turn-helix domain
     0.0012   18.7   0.0     0.0031   17.4   0.0    1.6  1  MarR            MarR family
     0.0019   17.9   0.1     0.0043   16.8   0.1    1.5  1  HTH_10          HTH DNA binding domain
     0.0027   17.4   0.1     0.0085   15.9   0.0    1.9  1  HTH_23          Homeodomain-like domain
      0.003   17.5   0.0     0.0056   16.7   0.0    1.4  1  HTH_29          Winged helix-turn helix
     0.0051   16.4   0.1      0.014   15.0   0.1    1.7  1  Sigma70_r4_2    Sigma-70, region 4
  ------ inclusion threshold ------
       0.01   15.7   0.2       0.02   14.9   0.2    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
      0.012   15.7   0.2      0.079   13.1   0.0    2.2  2  Sigma70_r3      Sigma-70 region 3
      0.019   14.6   1.2      0.046   13.4   0.1    2.1  2  GntR            Bacterial regulatory proteins, gntR family
      0.019   14.3   0.0      0.041   13.3   0.0    1.6  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.022   14.5   0.0      0.064   13.1   0.0    1.8  1  HTH_8           Bacterial regulatory protein, Fis family
      0.029   14.4   0.0      0.067   13.2   0.0    1.5  1  HTH_Mga         M protein trans-acting positive regulator (MG
      0.034   14.1   0.0      0.089   12.8   0.0    1.7  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.044   13.5   0.0       0.11   12.3   0.0    1.7  1  HTH_38          Helix-turn-helix domain
      0.045   13.7   0.2        0.1   12.6   0.0    1.7  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.05   14.0   0.0       0.13   12.6   0.0    1.7  2  Rrf2            Transcriptional regulator
       0.07   13.3   0.1       0.27   11.4   0.0    1.9  2  HTH_17          Helix-turn-helix domain
      0.075   12.8   0.0       0.17   11.7   0.0    1.6  1  MerR            MerR family regulatory protein
      0.076   13.2   0.0       0.14   12.4   0.0    1.4  1  PaaX            PaaX-like protein
       0.08   12.7   0.1       0.37   10.6   0.0    2.0  2  LexA_DNA_bind   LexA DNA binding domain
       0.12   12.5   0.0       0.25   11.4   0.0    1.5  1  HTH_3           Helix-turn-helix
       0.21   11.6   0.0       0.37   10.8   0.0    1.5  1  HTH_36          Helix-turn-helix domain


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 !   49.2   0.1     5e-16   2.8e-13       1      47 [.       5      52 ..       5      53 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 5e-16
                            HTH_24  1 ldetdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ld+ dr IL lLq+++r ++  e Aerl++Spstv+ r++rLee G++
  gi|336254223|ref|YP_004597330.1|  5 LDDVDRGILFLLQDDARnTTAIEMAERLDVSPSTVRNRIERLEETGVL 52
                                      79********************************************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 !   44.3   1.5   2.1e-14   1.2e-11       1      42 []       5      47 ..       5      47 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 2.1e-14
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisya.eLAervGlSestvlrRvrrLe 42
                                      LD++Dr IL +Lq daR + a e+Aer+ +S+stv++R++rLe
  gi|336254223|ref|YP_004597330.1|  5 LDDVDRGILFLLQDDARNTTAiEMAERLDVSPSTVRNRIERLE 47
                                      8**************9976655********************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   1.1e-10   6.1e-08       5      44 ..      12      51 ..      10      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.1e-10
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      il lL +   + ++ e+Ae+L+vS +tvr++I++Lee+gv
  gi|336254223|ref|YP_004597330.1| 12 ILFLLQDDARNTTAIEMAERLDVSPSTVRNRIERLEETGV 51
                                      66667555555***************************95 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.7e-08   9.6e-06       3      51 ..       5      52 ..       3      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.7e-08
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      l+  ++ +L+ L +  ++  t+ e a+rl++s+s+v ++++rL++ G +
  gi|336254223|ref|YP_004597330.1|  5 LDDVDRGILFLLQDDARN-TTAIEMAERLDVSPSTVRNRIERLEETGVL 52
                                      666678899999999865.7*************************9976 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   2.6e-08   1.5e-05      10      56 ..       7      54 ..       5      58 .. 0.88
   2 ?   -1.0   0.1       3.3   1.9e+03       6      14 ..      74      82 ..      70     106 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.6e-08
                                      HHHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 10 PvRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                       v r+il +L  +a+  ta e aerld+s++t++++++ Lee g +++
  gi|336254223|ref|YP_004597330.1|  7 DVDRGILFLLqDDARNTTAIEMAERLDVSPSTVRNRIERLEETGVLTG 54
                                      5668888888888888999*************************9987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.3
                                      HHS-HHHHH CS
                            HTH_20  6 ALahPvRrr 14
                                      ++a P+Rr 
  gi|336254223|ref|YP_004597330.1| 74 VTAAPTRRH 82
                                      567777773 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 !   21.1   0.1   3.3e-07   0.00018      15      45 ..      23      53 ..      10      55 .. 0.82
   2 ?    2.9   0.1      0.16        91       1      20 [.      81     100 ..      81     102 .. 0.95
   3 ?   -1.8   0.0       4.8   2.7e+03       9      22 ..     111     124 ..     104     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.3e-07
                          HTH_DeoR 15 lsveelvellgvSeaTiRRDLneLeeqgllt 45
                                       +  e +e+l+vS+ T+R+ ++ Lee g+lt
  gi|336254223|ref|YP_004597330.1| 23 TTAIEMAERLDVSPSTVRNRIERLEETGVLT 53
                                      445699**********************986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                          HTH_DeoR   1 Rieqilellkqqgklsveel 20 
                                       R+e+   ll+ +g l+v+el
  gi|336254223|ref|YP_004597330.1|  81 RHEAVESLLEVEGVLEVQEL 100
                                       9*****************98 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.8
                          HTH_DeoR   9 lkqqgklsveelve 22 
                                       +  ++++++ e+++
  gi|336254223|ref|YP_004597330.1| 111 VLARDTCHLSEITQ 124
                                       56678888888887 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 !   22.7   0.0   1.4e-07   8.1e-05      17      51 ..      17      51 ..      10      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.4e-07
                                      HHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress 17 seekkvvktkdlaerLnvspssVsemlkkLekdGy 51
                                      +++    +  ++aerL+vsps+V   +++Le+ G 
  gi|336254223|ref|YP_004597330.1| 17 QDDARNTTAIEMAERLDVSPSTVRNRIERLEETGV 51
                                      556666677799********************996 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 !   19.7   0.1   9.8e-07   0.00055      16      38 ..      26      48 ..      20      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.8e-07
                                      HHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_30 16 satAkaLhvHrnTlryRLrriee 38
                                       ++A++L v++ T+r+R++r+ee
  gi|336254223|ref|YP_004597330.1| 26 IEMAERLDVSPSTVRNRIERLEE 48
                                      589*******************9 PP

>> HTH_28  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   1.3e-06    0.0007      13      47 ..      23      58 ..      12      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-06
                            HTH_28 13 hsvreaArelgisrrtvyrWikryeegG.iagLvpr 47
                                       ++ e A++l +s++tv+  i r+ee G + g +p+
  gi|336254223|ref|YP_004597330.1| 23 TTAIEMAERLDVSPSTVRNRIERLEETGvLTGYWPQ 58
                                      477899**********************44888886 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 !   17.9   0.0   3.7e-06    0.0021       7      45 ..      12      52 ..       8      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.7e-06
                                      HHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  7 ILklLae..gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      IL+lL++  +++++ e ae l++s+stv+    +L+e G++
  gi|336254223|ref|YP_004597330.1| 12 ILFLLQDdaRNTTAIEMAERLDVSPSTVRNRIERLEETGVL 52
                                      9*******999**************************9986 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 !   17.7   0.0     4e-06    0.0022       8      48 ..      12      52 ..       8      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4e-06
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      iL +l   ++  t  e+A+r+++++Stv++ +  L+e G +
  gi|336254223|ref|YP_004597330.1| 12 ILFLLQDDARNTTAIEMAERLDVSPSTVRNRIERLEETGVL 52
                                      677888888889999************************88 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.5e-06    0.0031      15      47 ..      20      52 ..      12      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.5e-06
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGli 47
                                        + + +e+a++l vs+stv + + rLe+ G +
  gi|336254223|ref|YP_004597330.1| 20 ARNTTAIEMAERLDVSPSTVRNRIERLEETGVL 52
                                      5678899**********************9965 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   7.6e-06    0.0043      19      49 ..      18      48 ..      17      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.6e-06
                            HTH_10 19 dyPRrvtlkeLAkelGIskstlsehLrkaes 49
                                      d  R++t+ e+A++l++s+st+ +++++ e+
  gi|336254223|ref|YP_004597330.1| 18 DDARNTTAIEMAERLDVSPSTVRNRIERLEE 48
                                      6789**********************99876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.5e-05    0.0085      24      45 ..      29      50 ..      12      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-05
                            HTH_23 24 AreLgvsrrTvyrwlkryreeG 45
                                      A++L+vs++Tv++ ++r +e G
  gi|336254223|ref|YP_004597330.1| 29 AERLDVSPSTVRNRIERLEETG 50
                                      9****************99898 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   9.9e-06    0.0056      14      41 ..      24      51 ..      11      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.9e-06
                            HTH_29 14 tvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      t  ++A++l++s++tv++ ++r ee+G+
  gi|336254223|ref|YP_004597330.1| 24 TAIEMAERLDVSPSTVRNRIERLEETGV 51
                                      66799*********************95 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 !   15.0   0.1   2.6e-05     0.014      31      49 ..      27      45 ..      24      48 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-05
                                      HHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 31 EIAellgisegtVksrlsR 49
                                      E Ae+l++s++tV++r+ R
  gi|336254223|ref|YP_004597330.1| 27 EMAERLDVSPSTVRNRIER 45
                                      89***************88 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 ?   14.9   0.2   3.5e-05      0.02       9      61 ..      80     129 ..      73     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.5e-05
                                       GTTHHHHHHHHHHTSTTEEEEEEESS.SSSEEEEEEESSHHHHHHHHHHTTTTS CS
                    AsnC_trans_reg   9 hpeqleefeealaelpeVvecyrvtG.dydyllkvvvrdlealerflreklasl 61 
                                       +    +e+ e l e++ V+e+  + G   ++++kv +rd+ +l+++++  +++l
  gi|336254223|ref|YP_004597330.1|  80 R---RHEAVESLLEVEGVLEVQELLGgRENIHIKVLARDTCHLSEITQA-IHEL 129
                                       3...6789999***********9988799*****************877.6665 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00014     0.079      13      42 ..      15      44 ..       5      52 .. 0.87
   2 ?   -0.1   0.0       1.9     1e+03       3      19 ..     119     135 ..     118     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                                      HHHHHSSXXXHHHHHHHHTXXHHHHHHHHH CS
                        Sigma70_r3 13 LeqelgrePtpeEiAeeLglseekVrevle 42
                                      L q+  r+ t+ E Ae+L++s++ Vr+ +e
  gi|336254223|ref|YP_004597330.1| 15 LLQDDARNTTAIEMAERLDVSPSTVRNRIE 44
                                      789999********************8766 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHSS CS
                        Sigma70_r3   3 lnkikraqreLeqelgr 19 
                                       l +i++a++eL  e +r
  gi|336254223|ref|YP_004597330.1| 119 LSEITQAIHELDVEIER 135
                                       67788888888777766 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   8.2e-05     0.046      29      55 ..      27      53 ..      24      54 .. 0.94
   2 ?   -1.3   0.1       3.1   1.7e+03      47      57 ..      88      98 ..      82     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.2e-05
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR 29 eLaaefgVsrttvReALrrLeaeglve 55
                                      e a++++Vs +tvR  + rLe+ g+++
  gi|336254223|ref|YP_004597330.1| 27 EMAERLDVSPSTVRNRIERLEETGVLT 53
                                      789*********************986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.1
                                      HHHHTTSEEEE CS
                              GntR 47 rLeaeglverr 57
                                       Le eg++e++
  gi|336254223|ref|YP_004597330.1| 88 LLEVEGVLEVQ 98
                                      58899999886 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 ?   13.3   0.0   7.2e-05     0.041      17      51 ..       9      46 ..       6      47 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.2e-05
                      HTH_Tnp_ISL3 17 eayilellles.rsvkav..ArqlgvSwtTVwrildry 51
                                      ++ il ll+++ r+ +a+  A++l+vS++TV++++ r+
  gi|336254223|ref|YP_004597330.1|  9 DRGILFLLQDDaRNTTAIemAERLDVSPSTVRNRIERL 46
                                      56677777777766666555**************9985 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 ?   13.1   0.0   0.00011     0.064      23      42 .]      27      46 ..      26      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                      HHHHHHTS-HHHHHHHHHHT CS
                             HTH_8 23 kAArlLGisRrtLyrKLkkY 42
                                      ++A++L++s++t++++++++
  gi|336254223|ref|YP_004597330.1| 27 EMAERLDVSPSTVRNRIERL 46
                                      79***************985 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 ?   13.2   0.0   0.00012     0.067      11      46 ..      13      48 ..      11      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                           HTH_Mga 11 lelLteneksltldelakeLglseltlqsdiseLne 46
                                      l lL + ++ +t  e a++L+ s +t++++i+ L e
  gi|336254223|ref|YP_004597330.1| 13 LFLLQDDARNTTAIEMAERLDVSPSTVRNRIERLEE 48
                                      55777888999999******************9976 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 ?   12.8   0.0   0.00016     0.089      20      39 ..      29      48 ..      20      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                                      HHHHTS-HHHHHHHHHHHHH CS
                             HTH_1 20 AeeLglsqpavsrqikrLEe 39
                                      Ae+L +s+++v  +i rLEe
  gi|336254223|ref|YP_004597330.1| 29 AERLDVSPSTVRNRIERLEE 48
                                      9******************8 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0002      0.11      24      43 ..      26      45 ..       8      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                            HTH_38 24 reIArrLgrspsTIsRElkR 43
                                       e+A rL++spsT+ + + R
  gi|336254223|ref|YP_004597330.1| 26 IEMAERLDVSPSTVRNRIER 45
                                      499***********998877 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 ?   12.6   0.0   0.00019       0.1      22      52 ..      23      53 ..      10      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglis 52
                                       t  e+A++l ++++tv   + +L++ g+++
  gi|336254223|ref|YP_004597330.1| 23 TTAIEMAERLDVSPSTVRNRIERLEETGVLT 53
                                      56679************************98 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00024      0.13      20      56 ..      17      53 ..       2      55 .. 0.83
   2 ?   -1.9   0.0         8   4.5e+03      25      43 ..     132     150 ..     108     160 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00024
                                      SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      +++ +  ++ e+aer ++sps ++  +++L++ g+++
  gi|336254223|ref|YP_004597330.1| 17 QDDARNTTAIEMAERLDVSPSTVRNRIERLEETGVLT 53
                                      333444899************************9875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8
                                       -B-HHHHHHHHTS-HHHHH CS
                              Rrf2  25 pvsseeiaerqnispsyle 43 
                                        ++ +ei +r   sps+ e
  gi|336254223|ref|YP_004597330.1| 132 EIERTEITKRRMRSPSIFE 150
                                       3444555555555555555 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00049      0.27       5      22 ..      26      43 ..      24      54 .. 0.86
   2 ?   -1.3   0.0       4.5   2.5e+03       6      12 ..      96     102 ..      94     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00049
                            HTH_17  5 eEaAelLgvsrstvyrli 22
                                       E+Ae L+vs+stv++ i
  gi|336254223|ref|YP_004597330.1| 26 IEMAERLDVSPSTVRNRI 43
                                      69*************966 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.5
                            HTH_17   6 EaAelLg 12 
                                       E++elLg
  gi|336254223|ref|YP_004597330.1|  96 EVQELLG 102
                                       99****9 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0003      0.17       4      17 ..      27      40 ..      24      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                                      HHHHHHTTTHHHHH CS
                              MerR  4 evAeltGvsprtLR 17
                                      e+Ae+++vsp+t+R
  gi|336254223|ref|YP_004597330.1| 27 EMAERLDVSPSTVR 40
                                      89***********9 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00025      0.14      26      55 ..      25      54 ..      18      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00025
                              PaaX 26 LirllaelGiseslvRaalsRlakaGwlvr 55
                                       i++ + l++s s+vR  + Rl++ G l++
  gi|336254223|ref|YP_004597330.1| 25 AIEMAERLDVSPSTVRNRIERLEETGVLTG 54
                                      599***********************9985 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 ?   10.6   0.0   0.00067      0.37      28      56 ..      25      52 ..      10      55 .. 0.90
   2 ?   -1.2   0.0       3.1   1.8e+03      36      52 ..     142     158 ..     132     160 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00067
                                      HHHHHHHHTS-.HHHHHHHHHHHHHTTSE CS
                     LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyi 56
                                        e+a++l ++ ps+v ++ ++Le  G++
  gi|336254223|ref|YP_004597330.1| 25 AIEMAERLDVS-PSTVRNRIERLEETGVL 52
                                      5699****996.**************997 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.1
                                       TS-.HHHHHHHHHHHHH CS
                     LexA_DNA_bind  36 glkSpsaveehLkaLer 52 
                                       +++Sps  e  L+  +r
  gi|336254223|ref|YP_004597330.1| 142 RMRSPSIFETALESARR 158
                                       67788877777776665 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00045      0.25       7      28 ..      20      41 ..      16      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00045
                                      HTTHHHHHHHHHHTSSHHHHHH CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisr 28
                                      +++ +  e+Ae+l+vs+st+++
  gi|336254223|ref|YP_004597330.1| 20 ARNTTAIEMAERLDVSPSTVRN 41
                                      6899999************975 PP

>> HTH_36  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   0.00065      0.37      30      54 ..      27      51 ..      11      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00065
                            HTH_36 30 tlakrlglsknTvsraikeLeqlGy 54
                                       +a+rl +s +Tv++ i  Le++G 
  gi|336254223|ref|YP_004597330.1| 27 EMAERLDVSPSTVRNRIERLEETGV 51
                                      579********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1320.35
//
Query:       gi|336254224|ref|YP_004597331.1|  [L=243]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-14   52.9   0.1    7.1e-14   52.1   0.1    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.6e-08   34.8   0.0    2.9e-08   34.0   0.0    1.4  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
    1.1e-07   32.1   0.0    2.6e-07   31.0   0.0    1.6  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
      3e-05   24.0   0.0    6.3e-05   22.9   0.0    1.5  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.8e-05   23.4   0.1     0.0017   18.4   0.0    2.4  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    0.00028   21.5   0.1    0.00049   20.8   0.1    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
      0.004   17.3   0.7     0.0098   16.0   0.7    1.7  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.018   15.1   0.0      0.054   13.6   0.0    1.9  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
       0.15   11.8   1.1       0.42   10.4   0.6    1.9  2  PanZ             Acetyltransferase (GNAT) domain, PanZ


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 !   52.1   0.1   3.5e-17   7.1e-14      26     116 ..     122     216 ..      96     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 3.5e-17
                                       HHHHSTTC....EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEE CS
                    Acetyltransf_1  26 esfsleae....gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkiv 98 
                                       +   +++      ++va  +g ++G+  l   + e+++ ++   + V+++yrg+G+Gs+Lle  +e+a  +g++k++
  gi|336254224|ref|YP_004597331.1| 122 NAVTRHNAvrsrVFFVATVEGDVVGWTHLELPQVERRRGTAEQTVGVREAYRGRGIGSKLLERGIEWADANGYRKVY 198
                                       3333333334336777************************************************************* PP

                                       EEEETTEHHHHHHHHHTT CS
                    Acetyltransf_1  99 laveedndaairlYeklG 116
                                         v ++nd+a ++++  G
  gi|336254224|ref|YP_004597331.1| 199 NSVPVTNDRALEFLTDRG 216
                                       *************98777 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.5   6.9e+03      26      44 ..      28      50 ..      12      55 .. 0.59
   2 !   34.0   0.0   1.5e-11   2.9e-08       4     155 .]      87     238 ..      84     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.5
                    Acetyltransf_4 26 t....feyevssveefekfleal 44
                                      +    +ey+  s +ef  +le+l
  gi|336254224|ref|YP_004597331.1| 28 ErhklREYVSLSSDEFGSRLEEL 50
                                      13334777778888888888776 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 1.5e-11
                    Acetyltransf_4   4 ateeDakeilaiyaeyvvntaitfeye.vssveefekflealdsekeyvflvae.sdrivGyaylgqfkkrakdwka 78 
                                        + +D++ + ++  + v  t+    +e v     +e    ++++  ++vf va  ++++vG   l+ ++   +++ a
  gi|336254224|ref|YP_004597331.1|  87 GRHDDFDGLIETIRD-VTDTETYVVAEtVAEELLYENAVTRHNAVRSRVFFVATvEGDVVGWTHLELPQVERRRGTA 162
                                       577888888888865.333333332220333334567777778889999999999*********99444446***** PP

                    Acetyltransf_4  79 elsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiDmiw 155
                                       e +v + +++ + +g+g++l++  ++ + ++++++ + ++ ++n+ + +f+   G++ ++i ++++ +  +  D+++
  gi|336254224|ref|YP_004597331.1| 163 EQTVGV-REAYRGRGIGSKLLERGIEWADANGYRKVYNSVPVTNDRALEFLTDRGWDTEAIRRNHYAIDEELVDEVM 238
                                       ******.589************************************************************9999986 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.3e-10   2.6e-07       4      54 ..     134     195 ..     131     218 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.3e-10
                                       EEEEEEETTEEEEEEEEEEES......TCTEEEEE-GGGTTSSHHHHHHHH.TT....SEEE CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld......aeitrlaVdpeyrgkGiGraLlea.ae....kgii 54 
                                        +fVa  +g +vG   l+l +      + +  + V+++yrg+GiG++Lle  +e    +g++
  gi|336254224|ref|YP_004597331.1| 134 VFFVATVEGDVVGWTHLELPQverrrgTAEQTVGVREAYRGRGIGSKLLERgIEwadaNGYR 195
                                       69***********8877777777765444444*****************9531122344433 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.5   1.1e+04      69      80 ..      14      27 ..      10      41 .. 0.57
   2 !   22.9   0.0   3.2e-08   6.3e-05      11     106 ..     112     217 ..      98     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.5
                   Acetyltransf_10 69 gkaLleaveee..a 80
                                      +++L e+ve++  +
  gi|336254224|ref|YP_004597331.1| 14 SRRLYEYVERHgtV 27
                                      56777777776423 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 3.2e-08
                   Acetyltransf_10  11 etf.kefispealrerieegealllvaeeggkivGvi.....el.rdgs.hisllfVdpeyrgqGigkaLleaveee 79 
                                       et+ +e ++++a++++ +  + +++va+++g +vG       ++ r+++   + + V+++yrg+Gig++Lle+ +e 
  gi|336254224|ref|YP_004597331.1| 112 ETVaEELLYENAVTRHNAVRSRVFFVATVEGDVVGWThlelpQVeRRRGtAEQTVGVREAYRGRGIGSKLLERGIEW 188
                                       66656666667777777888889************997755544434445667779********************* PP

                   Acetyltransf_10  80 aekdgikl.eltvnasp.yavpfYeklGF 106
                                       a+ +g+++   +v  ++  a +f    G+
  gi|336254224|ref|YP_004597331.1| 189 ADANGYRKvYNSVPVTNdRALEFLTDRGW 217
                                       *9999998888888887788888777776 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 ?    2.9   0.0     0.061   1.2e+02      20      44 ..     140     164 ..     118     167 .. 0.85
   2 !   18.4   0.0   8.8e-07    0.0017      30      59 ..     166     195 ..     164     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.061
                   Acetyltransf_CG  20 rkegvldfthTeVpeelrGkGiAkk 44 
                                        +++v+  th e p+  r++G A++
  gi|336254224|ref|YP_004597331.1| 140 VEGDVVGWTHLELPQVERRRGTAEQ 164
                                       46679999***************97 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 8.8e-07
                   Acetyltransf_CG  30 TeVpeelrGkGiAkkLvkaalddareeglk 59 
                                       + V e++rG+Gi++kL ++ +++a ++g++
  gi|336254224|ref|YP_004597331.1| 166 VGVREAYRGRGIGSKLLERGIEWADANGYR 195
                                       5799***********************986 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   2.4e-07   0.00049       4     131 ..      84     211 ..      82     218 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.4e-07
                    Acetyltransf_3   4 LrplteeDlealfelrsdpe.vmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeede 79 
                                       +rp + +D+++l e   d + +++y+   +t++e+  ++e+a ++ ++ ++  + + + +++v+G+  l   + e++
  gi|336254224|ref|YP_004597331.1|  84 IRPGRHDDFDGLIETIRDVTdTETYVV-AETVAEE-LLYENAVTRHNAVRSRVFFVATVEGDVVGWTHLELPQVERR 158
                                       7999999*****974444443777632.2344444.445555556666677666665545549*****998888887 PP

                    Acetyltransf_3  80 e..aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirv 131
                                       +  ae    ++++++g+G+++  ++  +e+a +  g+++++  +  +N +    
  gi|336254224|ref|YP_004597331.1| 159 RgtAEQTVGVREAYRGRGIGSKLLERGIEWA-DANGYRKVYNSVPVTNDRALEF 211
                                       7779999999999******************.7777998988888888777655 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.7   4.9e-06    0.0098      27     131 ..      88     197 ..      73     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.9e-06
                    Acetyltransf_6  27 dpedleallelfraqwarrpdvfadpltra.flrdllaalaargalrlyvlrldgrpvAva...lglrsgdrlyy.w 98 
                                       + +d++ l+e  r+ +   + v a+   ++ ++++++ + +a  + +++v+ ++g +v+     l  + ++r  + +
  gi|336254224|ref|YP_004597331.1|  88 RHDDFDGLIETIRDVTDTETYVVAETVAEElLYENAVTRHNAVRSRVFFVATVEGDVVGWThleLPQVERRRGTAeQ 164
                                       567788888888877666634444443333599*******9999999************985554456666666636 PP

                    Acetyltransf_6  99 lggydpelaklspgllllweliedaaeeGlrrf 131
                                        +g+++++++ ++g  ll + ie+a ++G+r++
  gi|336254224|ref|YP_004597331.1| 165 TVGVREAYRGRGIGSKLLERGIEWADANGYRKV 197
                                       6788*************************9976 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.7e-05     0.054      76     111 ..     163     198 ..      83     219 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                                       EEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEE CS
                    Acetyltransf_9  76 vtgVavapehrgrgvlskLlaraleemreegqplsl 111
                                          V+v   +rgrg+ skLl+r +e ++++g++ ++
  gi|336254224|ref|YP_004597331.1| 163 EQTVGVREAYRGRGIGSKLLERGIEWADANGYRKVY 198
                                       4579*************************9988666 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.36   7.2e+02      58      80 ..     141     163 ..     124     167 .. 0.80
   2 ?   10.4   0.6   0.00021      0.42      65      88 ..     164     187 ..     153     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.36
                              PanZ  58 edkeaelsdlcVRevTRrRGVgs 80 
                                       e+++   ++l   +v RrRG ++
  gi|336254224|ref|YP_004597331.1| 141 EGDVVGWTHLELPQVERRRGTAE 163
                                       5566666899999999***9876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00021
                              PanZ  65 sdlcVRevTRrRGVgsyLleearr 88 
                                       + + VRe  R RG+gs+Lle+  +
  gi|336254224|ref|YP_004597331.1| 164 QTVGVREAYRGRGIGSKLLERGIE 187
                                       4578***************98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1757.97
//
Query:       gi|336254225|ref|YP_004597332.1|  [L=276]
Description: Prephenate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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   41.8   0.7    1.3e-09   37.5   0.7    2.1  1  PDH            Prephenate dehydrogenase
    7.8e-05   23.2   5.2    0.00027   21.5   0.3    2.7  3  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.02   15.7   2.5       0.02   15.7   0.3    2.2  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo


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 !   37.5   0.7   2.2e-13   1.3e-09      37     221 ..      50     216 ..      17     243 .. 0.74

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2.2e-13
                                       ES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S--CHHHHHHHHHCC..GCEEEEEES---S-SSG CS
                               PDH  37 tddieavkeadivvlavPvevilevlkelaphlkedalitDvgsvKekvvreleellkegksfvgghPmaGteksGv 113
                                       +d  +a  + d+v lavP+  + + ++ +a+  + ++ ++Dv++v e   + + e+ +   +  + hP++ +     
  gi|336254225|ref|YP_004597332.1|  50 PDGSDARDDYDVVCLAVPMAHVTDAIATHAS--RAERAVVDVSGVMEPALEVMAEHAP-DLERASLHPLFAP----- 118
                                       3335666778*********************..9************************.556679*******..... PP

                                       GG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEEE--HHHHHHHHHHHTHHHHHHHHHHHHHHHCHHCCC CS
                               PDH 114 daareelfenavviLtPtektdkealekvkelleevgarvilmspeeHDrvvavvshlphvvaialaatlkekknde 190
                                               e+a+  +    + +   ++ +   le +g  +i+++++eHD+++  v+ ++h++  + a +   + +  
  gi|336254225|ref|YP_004597332.1| 119 --------ERAPGSIAVVRDAGGPTIDALLAGLEARGNELIETTASEHDEAMETVQAATHAAVLSFALAA--EPVP- 184
                                       ........55555555556667899***********************************8877665522..2222. PP

                                       CHHHHCGTCCHHHHH....CGGGS-HHHHHHHHHH CS
                               PDH 191 keirklasggfrdvt....RiaksnPelwadille 221
                                            +  ++++ +      + ++ P+++adi+++
  gi|336254225|ref|YP_004597332.1| 185 ---EGFETPIYEGLAtlaeQMTEGTPRVYADIQTA 216
                                       ...23555555544434446667778888888775 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 !   21.5   0.3   4.5e-08   0.00027       4      94 ..       5      89 ..       2      91 .. 0.86
   2 ?    3.4   0.1     0.019   1.1e+02       6      48 ..     131     170 ..     124     183 .. 0.77
   3 ?   -1.8   0.1      0.84     5e+03      54      75 ..     218     239 ..     193     251 .. 0.57

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.5e-08
                                      EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...-EEECECHHHHHHH-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored  4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...vkvtavdneeaaeeadvvvlavkpedveevls 79
                                      i+GaG+mg  + + + aa      + +a + +p+ a+++a++++   v   a d ++a ++ dvv lav++++v+++++
  gi|336254225|ref|YP_004597332.1|  5 IVGAGSMGTWFGRAVEAA------VAFA-DVDPDAAAAAADAVEgaeVAPLAPDGSDARDDYDVVCLAVPMAHVTDAIA 76
                                      78*******999955444......8878.99*********999998866666699***********************9 PP

                                      HCGHHHHTTSEEEEE CS
                     F420_oxidored 80 elakdalkgklvisv 94
                                          ++ +++ v++v
  gi|336254225|ref|YP_004597332.1| 77 TH--ASRAERAVVDV 89
                                      99..77899999998 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.019
                                       TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC- CS
                     F420_oxidored   6 GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgv 48 
                                       ++G  + al+ gl a+g   +e++ ++ ++ ++a e+ +++  
  gi|336254225|ref|YP_004597332.1| 131 AGGPTIDALLAGLEARG---NELIETTASEHDEAMETVQAATH 170
                                       6788999**********...99999999999988888887654 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.84
                                       CHHHHHHH-SEEEE-S-HHHHH CS
                     F420_oxidored  54 dneeaaeeadvvvlavkpedve 75 
                                       d ++a++ea   + a     +e
  gi|336254225|ref|YP_004597332.1| 218 DGADAVSEAAESIAAADADEFE 239
                                       4455555555555555555555 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 ?   15.7   0.3   3.4e-06      0.02       2      84 ..       2      81 ..       1     107 [. 0.71
   2 ?   -0.6   0.1      0.38   2.3e+03      43      54 ..     184     195 ..     139     247 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.4e-06
                                      EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHH.HHHTCT.TESEEEE-S-G.GGHHH CS
                      GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdle.elladp.eidavivatpn.gthee 77
                                       v+i+GaG +g++++r++ ++      va+ d d+ +a a+a++ + + ++ l+ + ++   + d+v+ a+p  +   +
  gi|336254225|ref|YP_004597332.1|  2 DVLIVGAGSMGTWFGRAVEAA------VAFADVDPDAAAAAADAVEGAEVAPLApDGSDARdDYDVVCLAVPMaHVTDA 74
                                      699************888888......7788888888877766665554444332333333499********9622333 PP

                                      HHHHHHH CS
                      GFO_IDH_MocA 78 lakaale 84
                                      +a +a +
  gi|336254225|ref|YP_004597332.1| 75 IATHASR 81
                                      4444433 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.38
                                       HHHTTHEEESSH CS
                      GFO_IDH_MocA  43 aesfgveaysdl 54 
                                        e f+ + y+ l
  gi|336254225|ref|YP_004597332.1| 184 PEGFETPIYEGL 195
                                       333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2031.21
//
Query:       gi|336254226|ref|YP_004597333.1|  [L=527]
Description: type 12 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-11   43.9   0.0    6.9e-11   42.8   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    1.1e-09   38.4   0.0    1.8e-09   37.6   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    6.2e-05   22.4   0.0     0.0001   21.7   0.0    1.2  1  Rsm22            Mitochondrial small ribosomal subunit Rsm22
    6.7e-05   23.5   0.1    0.00043   20.9   0.0    2.4  2  Methyltransf_11  Methyltransferase domain
    0.00026   21.6   0.0    0.00098   19.8   0.0    2.1  1  Methyltransf_25  Methyltransferase domain
     0.0012   18.7   0.0      0.017   14.9   0.0    2.6  2  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0   2.3e-14   6.9e-11       1      97 [.     166     276 ..     166     278 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 2.3e-14
                   Methyltransf_12   1 LeiGcGtGsllrallekl...pdieytgvDispsai..edakeklakrennnnnnvelealdlldldgg........ 64 
                                       L+iG+G+G  +  l+++l     +ey+++++s++a   ed  +++ ++     ++ ++e+ d +  +g         
  gi|336254226|ref|YP_004597333.1| 166 LDIGAGVGGPALGLCDYLpddALLEYHAIEPSAAADvlEDLLAETGRNVHTTIHRTTVEEFDPETVAGDdgfdptap 242
                                       8*****************98899***********99667777777777777777777777776666665999***** PP

                   Methyltransf_12  65 .ssfDlvvasnvlhhlkdirevldnirklLkpgG 97 
                                        + fDlv+a+nvl+ l d+++vl+n+ ++L+p+G
  gi|336254226|ref|YP_004597333.1| 243 dDGFDLVLACNVLSELGDPEAVLRNALEWLAPDG 276
                                       *********************************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0     6e-13   1.8e-09      10     122 ..     147     285 ..     138     360 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 6e-13
                   Methyltransf_23  10 sdklerllpk..lraggrvLdiGcGtG.i...llevl.rengfsvtgvDlspeaveiae........kakkaqkdqf 71 
                                       + +l+ l+++  l ++ rvLdiG+G+G     l+++l  +   ++ ++++s +a  + e        + ++ ++  +
  gi|336254226|ref|YP_004597333.1| 147 QYALNDLAERglLGRDFRVLDIGAGVGgPalgLCDYLpDDALLEYHAIEPSAAADVL-EdllaetgrNVHTTIHRTT 222
                                       44455555444367777**********6555567777444456*******9765554.3699999995555555555 PP

                   Methyltransf_23  72 deqeaae............pqgkfdlIvlrevlehvpdppellrqiatllkpgGylllsepla 122
                                        e++++e            p++ fdl+ + +vl  + dp+++lr++ ++l+p+G +l + p+ 
  gi|336254226|ref|YP_004597333.1| 223 VEEFDPEtvagddgfdptaPDDGFDLVLACNVLSELGDPEAVLRNALEWLAPDGAALAMAPAD 285
                                       5553333444444455555999*********************************99998854 PP

>> Rsm22  Mitochondrial small ribosomal subunit Rsm22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   3.5e-08    0.0001       4     118 ..     131     260 ..     128     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.5e-08
                             Rsm22   4 siaYalarlpatyavlrrvLdelaervpdflPkslldvgegpgtalwaaselwe..eleevlvidaseelleiskel 78 
                                       ++ Ya++ lpa ya+++ +L++laer    +   +ld+g+g+g   +   +  +   l e+  i+ s+++  + + l
  gi|336254226|ref|YP_004597333.1| 131 AAGYAIYHLPAYYAAVQYALNDLAERGLLGRDFRVLDIGAGVGGPALGLCDYLPddALLEYHAIEPSAAADVLEDLL 207
                                       567***********************99999999********99988888888767789***********9999999 PP

                             Rsm22  79 aadapelkeaalrrsvirealeleea.................dLviisyvLleled 118
                                       a+   +++++ +r++v     e+ ++                 dLv    vL el d
  gi|336254226|ref|YP_004597333.1| 208 AETGRNVHTTIHRTTVE----EFDPEtvagddgfdptapddgfDLVLACNVLSELGD 260
                                       99998888875555443....222222245588999999999999999999999977 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.4e-07   0.00043       1      94 [.     166     278 ..     166     280 .. 0.70
   2 ?   -1.6   0.0       1.5   4.5e+03      24      53 ..     411     442 ..     409     449 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
                                       EEET-TTSHHHHHHHHTT.....SEEEEEES-HHHH...HHHHHHCCHHT-..........EEEETTEECC.CTSS- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.....arvvgvDlskeml...klakekaseegl..........kvefvvadae.klpfe 58 
                                       Ld+G+G G  a  l ++       ++ ++++s+++    +l  e +++ +             e v +d   +   +
  gi|336254226|ref|YP_004597333.1| 166 LDIGAGVGGPALGLCDYLpddalLEYHAIEPSAAADvleDLLAETGRNVHTtihrttveefDPETVAGDDGfDPTAP 242
                                       7999999998888885445555788888888888874443333333333334444443444233355555436679* PP

                                       TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  59 dnsfDlvvssevlhhvedpekalkeiaRvLkpgGll 94 
                                       d+ fDlv++ +vl  + dpe++l+++  +L p+G  
  gi|336254226|ref|YP_004597333.1| 243 DDGFDLVLACNVLSELGDPEAVLRNALEWLAPDGAA 278
                                       **********************************86 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                                       EES-HHHHHHHHHHCCHHT-..EEEETTEECC CS
                   Methyltransf_11  24 vDlskemlklakekaseegl..kvefvvadae 53 
                                       +D++ e+ ++ak++  e+++  ++++v a ++
  gi|336254226|ref|YP_004597333.1| 411 IDVALETSDWAKMAEMERHVtnRIDLVAAKLS 442
                                       78888899999999988888777777777666 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.3e-07   0.00098       1      97 []     165     276 ..     165     276 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.3e-07
                                       EEEET-TTSHHHHHHHCTS..T.SSEEEEEESSHHHHHHHHHHHHH..TTTTEEEEESBCCGBS............. CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl..g.kakvtgvDiseemleaareraee..eglnvefvqgdaedlp............. 59 
                                       vLd+G+G G  +l l + l      +++++++s+++ +  +  ++e  ++++ ++++  +e+++             
  gi|336254226|ref|YP_004597333.1| 165 VLDIGAGVGGPALGLCDYLpdDaLLEYHAIEPSAAA-DVLEDLLAEtgRNVHTTIHRTTVEEFDpetvagddgfdpt 240
                                       8***************99864256788888887655.4444444332223344444444444432333355554444 PP

                                       SSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  60 fedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                        +d+ fDlv+++++l+ l d   e++l+++ ++L p+G
  gi|336254226|ref|YP_004597333.1| 241 APDDGFDLVLACNVLSELGD--PEAVLRNALEWLAPDG 276
                                       69*********988999885..569***********99 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   5.8e-06     0.017      71     127 ..     242     297 ..     159     333 .. 0.74
   2 ?   -2.3   0.0       1.1   3.3e+03      56      81 ..     413     440 ..     408     454 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.8e-06
                   Methyltransf_31  71 edekfDlilsnevlnaladpdkileeiervlkpggilliedprllaelpakveeesk 127
                                        d+ fDl+l+ +vl  l dp+++l+++ + l p+g+ l+  p   ++   +++e ++
  gi|336254226|ref|YP_004597333.1| 242 PDDGFDLVLACNVLSELGDPEAVLRNALEWLAPDGAALAMAPA-DKNTSVQLREVER 297
                                       4599*******************************99888877.2333333333333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                   Methyltransf_31  56 veFeqgdiee.lekl.ledekfDlilsn 81 
                                       v +e +d+ + +e+     +++Dl+ ++
  gi|336254226|ref|YP_004597333.1| 413 VALETSDWAKmAEMErHVTNRIDLVAAK 440
                                       6677888888666544333999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3732.82
//
Query:       gi|336254227|ref|YP_004597334.1|  [L=348]
Description: phosphate ABC transporter periplasmic substrate-binding protein [Halopiger xanaduensis SH-6]
Scores for complete 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-07   31.7   0.1    2.2e-07   30.8   0.0    1.4  1  PBP_like_2  PBP superfamily domain


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   1.2e-11   2.2e-07      81     157 ..     162     243 ..     118     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.2e-11
                        PBP_like_2  81 g...aggliqvpvaigaialvvnkd...npln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflf 150
                                       +   + +++++ va+ + a++v+++    +++ l ++++++I++g+ItnW+  +g+p d  I+v++ +d s  + l+
  gi|336254227|ref|YP_004597334.1| 162 SltiGDRFVEHQVATAGSAFIVSPSiidEGVTsLRAAEVRDIYAGEITNWQA-VGGP-DREIRVIAGPDASPPRWLI 236
                                       133446799999999999999999999988889******************9.6666.***********99988777 PP

                        PBP_like_2 151 stalaeq 157
                                        t +  +
  gi|336254227|ref|YP_004597334.1| 237 DTFFDGV 243
                                       7777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); 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 0.22s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2535.01
//
Query:       gi|336254228|ref|YP_004597335.1|  [L=274]
Description: Multifunctional protein surE [Halopiger xanaduensis SH-6]
Scores for 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-48  164.2   0.1    3.6e-48  163.9   0.1    1.1  1  SurE      Survival protein SurE


Domain annotation for each model (and alignments):
>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.9   0.1     2e-52   3.6e-48       1     192 [.       7     197 ..       7     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 163.9 bits;  conditional E-value: 2e-52
                                       EEEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHH CS
                              SurE   1 iLltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvkla 77 
                                       iLltNDDGi++ giral++al+++g +v+vvaP++++S++g+++  ++++ ve     ++e  ya++GtP+dcv  +
  gi|336254228|ref|YP_004597335.1|   7 ILLTNDDGIHSTGIRALYDALSERG-NVTVVAPATDQSACGRSM--SHEVDVE-----THELGYALHGTPSDCVVAG 75 
                                       8*********************877.******************..4444433.....35789************** PP

                                       HHTTTTTS.SSEEEEEEEES---GGGG.GG-HHHHHHHHHHHTTSEEEEEEEESSS.......SS-SSS---HHHHH CS
                              SurE  78 leellkekkpdlVvSGiNhGaNlgtdv.lySGTvgAaleaalegipaiAvSlaskk.......eeekkeedtfeaaa 146
                                       l el ++  pd+Vv+G+N+GaNlg+ v   SGT++Aa+eaa+ ++paiA S+ +         e+ + e  ++++a+
  gi|336254228|ref|YP_004597335.1|  76 LAELGPD--PDIVVAGCNKGANLGEYVlGRSGTISAAVEAAFFDVPAIATSMYVPApgdgaslEAVDLEPADYAEAT 150
                                       *999975..9*****************999***********************9889*9999955555666799999 PP

                                       HHHHHHHTTETTS-...SS-EEEEEEE.SS.GCG-SEEEE-B--CCS CS
                              SurE 147 kvaaklveklieklllekvellnvNvP.eleeeeikgvkvtrlgrrr 192
                                       ++++ lve+ +e+ ++e++ +lnvNvP + +e e + v++tr ++r+
  gi|336254228|ref|YP_004597335.1| 151 RITSFLVEHALETDVFEHAAYLNVNVPvADSEGEPAPVEITRPSQRY 197
                                       9999999*999****************755667777899**999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2107.41
//
Query:       gi|336254229|ref|YP_004597336.1|  [L=85]
Description: selT/selW/selH selenoprotein domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-18   66.5   0.0      2e-18   66.3   0.0    1.0  1  Rdx       Rdx family


Domain annotation for each model (and alignments):
>> Rdx  Rdx family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   1.1e-22     2e-18       1      74 []      12      83 ..      12      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 1.1e-22
                                      EEEEEEETTTTTHHHHHHHHHHHHHHCCCCSSEEEEEEESTT-EEEEETTEEEEEHHHHTSS--HHHHHHHHHH CS
                               Rdx  1 rvtIeYCtqCkwmlraaelaqellstfpeslgevalqpstgGaFeVtldgelvwsrkeeggfpetkelkqrvrd 74
                                      +v+IeYC  C++ +ra++++ +llstf+e+l  v+l ++ +G+F V +d+++++++ e++   +++e+++rvrd
  gi|336254229|ref|YP_004597336.1| 12 TVEIEYCVPCGFLSRAEDVQHALLSTFGEQLDAVTLATGANGVFVVRVDDTVIFDKSEDE--YDVDEIVRRVRD 83
                                      69**********************************************************..9*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 654.29
//
Query:       gi|336254230|ref|YP_004597337.1|  [L=131]
Description: hypothetical protein Halxa_2842 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0037   16.6   0.2     0.0046   16.3   0.2    1.2  1  EAP30     EAP30/Vps36 family


Domain annotation for each model (and alignments):
>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   2.6e-07    0.0046     168     229 ..      27     101 ..       2     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.6e-07
                             EAP30 168 Svptelntdqvevlevakrlvsllaekssg....................ggvtaselaeeeenlgwsvarakeaLe 224
                                       ++  e +td+    ++a +++s+++e + g                    g v++s +   +e++gws +r  ++++
  gi|336254230|ref|YP_004597337.1|  27 TTTDEASTDE----STADETLSYAEEIEYGvderdlqdedkilrllvkrgGRVDQSTV---REETGWSEDRLADVID 96 
                                       5557888888....88888888888888888888889999999999999899******...777************* PP

                             EAP30 225 elere 229
                                       ++e++
  gi|336254230|ref|YP_004597337.1|  97 RMEDD 101
                                       **987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1044.55
//
Query:       gi|336254231|ref|YP_004597338.1|  [L=48]
Description: hypothetical protein Halxa_2843 [Halopiger xanaduensis SH-6]
Scores for complete 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   50.9  20.1    1.5e-13   50.7  20.1    1.1  1  DUF1328         Protein of unknown function (DUF1328)


Domain annotation for each model (and alignments):
>> DUF1328  Protein of unknown function (DUF1328)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7  20.1   8.1e-18   1.5e-13       1      39 []       6      44 ..       6      44 .. 0.98

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 8.1e-18
                           DUF1328  1 liFLviAliAgvLGFgGiagaaagiAkiLFfiFlvlfvi 39
                                      l+F+viA+iAg+LG+gG+ag ++ iAk+L+++Flvl+v+
  gi|336254231|ref|YP_004597338.1|  6 LLFFVIAIIAGALGAGGVAGFSMAIAKWLVILFLVLAVV 44
                                      79************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 345.14
//
Query:       gi|336254232|ref|YP_004597339.1|  [L=124]
Description: hypothetical protein Halxa_2844 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        5.4    5.1  17.5        5.5    5.1  17.5    1.0  1  Nop14       Nop14-like family


Domain annotation for each model (and alignments):
>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  17.5    0.0003       5.5     350     434 ..      39     118 ..       8     124 .] 0.31

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0003
                             Nop14 350 ededdfeedddlveseseeee.eeeeedeeeeedeeeeeeeeededdlsdleseeeeeedeleeelleeekkaaeek 425
                                       ede++   +++ ve++ ee    e ee e++ + e+++ e+e++++ + + ++ e+e+e+     ++e+ ++aa+++
  gi|336254232|ref|YP_004597339.1|  39 EDENE--PESTGVEETPEEPAqPEGEEPEDDPTTENSSGENESESEASTERNDTEDENESS----IVENGTDAATDN 109
                                       22222..222222222222221111111111111111111111111111111111111111....111111111111 PP

                             Nop14 426 kekkkkkkk 434
                                       +++ +++++
  gi|336254232|ref|YP_004597339.1| 110 ETTAQENET 118
                                       111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1391  (0.0775838); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 924.46
//
Query:       gi|336254233|ref|YP_004597340.1|  [L=99]
Description: hypothetical protein Halxa_2845 [Halopiger xanaduensis SH-6]
Scores for 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   21.2   0.2    0.00027   20.6   0.2    1.3  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
     0.0066   15.8   0.7      0.015   14.6   0.7    1.6  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   3.1e-08   0.00027       2      24 ..       1      23 [.       1      25 [. 0.95

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.1e-08
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      ++RR+FL  + A++ ++a+ gc+
  gi|336254233|ref|YP_004597340.1|  1 MNRRSFLTYATAVGTLGAASGCL 23
                                      89********************7 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.7   1.7e-06     0.015      10      28 ..       2      19 ..       1      21 [. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-06
                        UCR_Fe-S_N 10 tRRDFLyiATgavgaVGaa 28
                                      +RR FL +AT avg+ Gaa
  gi|336254233|ref|YP_004597340.1|  2 NRRSFLTYAT-AVGTLGAA 19
                                      7********9.69****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 773.01
//
Query:       gi|336254234|ref|YP_004597341.1|  [L=153]
Description: 30S ribosomal protein S15 [Halopiger xanaduensis SH-6]
Scores for complete 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-21   76.2   0.0    2.4e-21   75.5   0.0    1.3  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    3.1e-15   56.1   0.4    4.7e-15   55.6   0.4    1.2  1  Ribosomal_S15    Ribosomal protein S15
  ------ inclusion threshold ------
      0.074   12.9   0.3       0.13   12.1   0.3    1.4  1  DUF1465          Protein of unknown function (DUF1465)


Domain annotation for each model (and alignments):
>> 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 !   75.5   0.0     4e-25   2.4e-21       4      57 ..       1      54 [.       1      56 [. 0.98

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 4e-25
                                      SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHC CS
                   Ribosomal_S13_N  4 mhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDq 57
                                      mh+r++G+SgS +P+  e+p+W++++++++e+ +v+la++G+ pSqIG++LRD+
  gi|336254234|ref|YP_004597341.1|  1 MHTRRRGSSGSDKPAADEPPEWSDVDADDIEDRVVELAEQGYDPSQIGMKLRDE 54
                                      9****************************************************7 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.4   7.8e-19   4.7e-15      11      75 ..      78     143 ..      70     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 7.8e-19
                                       STT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H.HHHHHHH CS
                     Ribosomal_S15  11 hekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv.erYkkli 75 
                                       ++  t ++++++++l+er+++l+eh+++n++D++++r+L++++sk r+l++Y++  +  ++++++ 
  gi|336254234|ref|YP_004597341.1|  78 ENDATSDIPEDLYNLMERAVRLREHVQQNPQDYQNKRALQNTESKVRRLVDYYRGDELePDFTYTY 143
                                       3445779***********************************************999876777665 PP

>> DUF1465  Protein of unknown function (DUF1465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   2.2e-05      0.13      95     147 ..      76     127 ..      63     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
                                       -----------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX.XXXXXXXX CS
                           DUF1465  95 asdaeavaeLpeelqeLierserLyervrrLdrelreeaeaaeaaenpvaeql 147
                                        ++++a++++pe+l +L+er+ rL e v++  ++ +++++ +++ e++v++++
  gi|336254234|ref|YP_004597341.1|  76 LEENDATSDIPEDLYNLMERAVRLREHVQQNPQDYQNKRALQNT-ESKVRRLV 127
                                       4788999**********************988888887777654.88888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); 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):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1259.89
//
Query:       gi|336254235|ref|YP_004597342.1|  [L=401]
Description: hypothetical protein Halxa_2847 [Halopiger xanaduensis SH-6]
Scores for 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  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 3261.82
//
Query:       gi|336254236|ref|YP_004597343.1|  [L=100]
Description: hypothetical protein Halxa_2848 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0097   15.5   0.3      0.011   15.4   0.3    1.0  1  NLBH      Neuraminyllactose-binding hemagglutinin precursor (
  ------ inclusion threshold ------
       0.17   12.3   2.4       0.27   11.7   2.4    1.6  1  DUF4604   Domain of unknown function (DUF4604)


Domain annotation for each model (and alignments):
>> NLBH  Neuraminyllactose-binding hemagglutinin precursor (NLBH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   1.2e-06     0.011     140     212 ..      24      99 ..      11     100 .] 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-06
                                       TT-TCEEEEEEEEEEEEEEEEE-TTT-...-EEEEEEEE--S-EEEEE..EEEEE--TT-S--TTT---CCC.HHHH CS
                              NLBH 140 pseedldttvDqsaGavklkflEPksg...riihsFaidvgelqaiie..sytlkatnSgglagansvsrtkleknk 211
                                        + +++ ttvD+ +G v  ++    +g     ++++ +++    a+++  + t +at+  g a++   ++t+  +n 
  gi|336254236|ref|YP_004597343.1|  24 DNTDEMATTVDEESGDVVTRIERETTGglhSNVDDYVVNLEVATAVVDaaERTARATDGRGTASEPEHNHTD--TNT 98 
                                       566789***********999877777633356999************9555566666666666555555555..554 PP

                                       H CS
                              NLBH 212 d 212
                                       +
  gi|336254236|ref|YP_004597343.1|  99 N 99 
                                       4 PP

>> DUF4604  Domain of unknown function (DUF4604)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.4     3e-05      0.27      44      69 ..      13      48 ..       1     100 [] 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3e-05
                           DUF4604 44 s..........eeeDeaPqVVvlkeGkhlsaeevev 69
                                      +          ++ De+++ V++++G+++++ e e 
  gi|336254236|ref|YP_004597343.1| 13 DpelvaralrpDNTDEMATTVDEESGDVVTRIERET 48
                                      2445566677799****************8766543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 830.91
//
Query:       gi|336254237|ref|YP_004597344.1|  [L=213]
Description: 30S ribosomal protein S3Ae [Halopiger xanaduensis SH-6]
Scores for 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-60  203.4   0.2    3.3e-60  203.1   0.2    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
       0.24   11.6   0.1       0.24   11.6   0.1    2.4  3  FlaG            FlaG protein


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 !  203.1   0.2   3.7e-64   3.3e-60      11     202 .]      11     191 ..       2     191 .. 0.96

  Alignments for each domain:
  == domain 1  score: 203.1 bits;  conditional E-value: 3.7e-64
                                       CSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCSHTSSSEEEEEEEEEEESSEEEEEE CS
                    Ribosomal_S3Ae  11 kkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtndekeqafrklklkieevqgknaltnF 87 
                                       ++K+Wy+v aP++f ++e+G+t++       +++ek+  r++e++l++L+n+  ++ ++kl +ki++v  ++a+t+F
  gi|336254237|ref|YP_004597344.1|  11 QEKRWYTVLAPEQFDRQELGETPA-------DEPEKVYDRTIETTLGELNNNA-SENNTKLTFKINDVGSDSAYTEF 79 
                                       78**********************.......*********************7.778******************** PP

                                       EEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHHHHS-HHH CS
                    Ribosomal_S3Ae  88 kgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteeaseldlke 164
                                       k ++ltrD+lrslvr++ s+Iea v+v t+D+y ++v +vafT+k+   a +sq+kaIr++mve+++e a+e +++e
  gi|336254237|ref|YP_004597344.1|  80 KEHSLTRDYLRSLVRRGASKIEAYVTVLTTDDYRVQVQPVAFTTKK---ADASQEKAIREQMVEMVEEAAAERTFEE 153
                                       **********************************************...**************************** PP

                                       HHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE-S CS
                    Ribosomal_S3Ae 165 lvkklipeslgkeiekeakkIyplrnveirKvkvlkkP 202
                                       l++ +++  l++ i+ eak+Iyplr+vei+K+ +  +P
  gi|336254237|ref|YP_004597344.1| 154 LISSIVEGRLSSGIYGEAKTIYPLRRVEIQKTTLEAHP 191
                                       *******77***********************987665 PP

>> FlaG  FlaG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.7e-05      0.24      19      58 ..      30      69 ..      20      75 .. 0.84
   2 ?    1.1   0.2     0.049   4.4e+02      20      40 ..     124     144 ..     108     158 .. 0.52
   3 ?   -3.7   0.1       1.6   1.4e+04      18      25 ..     193     200 ..     182     209 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.7e-05
                                      ---SS-------HHHHHHHHHHHHHHHTTSS--EEEEEEE CS
                              FlaG 19 kaekaeeekevseeeleeaveklnkklsslnteleFsvde 58
                                       + +a+e ++v  +++e+++ +ln+++s+ nt+l F++++
  gi|336254237|ref|YP_004597344.1| 30 GETPADEPEKVYDRTIETTLGELNNNASENNTKLTFKIND 69
                                      556677888888899***********************97 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.049
                                       --SS-------HHHHHHHHHH CS
                              FlaG  20 aekaeeekevseeeleeavek 40 
                                       ++ + +++++ +e++ e+ve+
  gi|336254237|ref|YP_004597344.1| 124 KKADASQEKAIREQMVEMVEE 144
                                       222233333333333333433 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 1.6
                                       ----SS-- CS
                              FlaG  18 ekaekaee 25 
                                       e ae++ +
  gi|336254237|ref|YP_004597344.1| 193 EVAEEEAT 200
                                       22233333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1730.36
//
Query:       gi|336254238|ref|YP_004597345.1|  [L=153]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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   30.9   0.0    3.4e-07   30.5   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.5e-07   30.2   0.0    4.3e-07   29.9   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    8.2e-07   29.4   0.0    1.1e-06   29.0   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.039   14.1   0.0      0.053   13.7   0.0    1.2  1  Acetyltransf_4   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 !   30.5   0.0   7.6e-11   3.4e-07      25     112 ..      36     115 ..       8     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 7.6e-11
                                       HHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEE.EEE CS
                    Acetyltransf_1  25 eesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikki.vla 100
                                        +  ++ +e +++a++++e +G  +l          a ++sl+V ++ r  G+G+a  eale r r  gi+ + vl+
  gi|336254238|ref|YP_004597345.1|  36 NDDVREKPEAFYIASDGDERVGIGGLERCGS----DALLRSLVVESDVRSDGYGTAICEALETRGRADGIETLyVLT 108
                                       3446778889999***************999....8**********************************9995665 PP

                                       EETTEHHHHHHH CS
                    Acetyltransf_1 101 veedndaairlY 112
                                       +++       ++
  gi|336254238|ref|YP_004597345.1| 109 TTAAE-----FF 115
                                       54444.....33 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   9.5e-11   4.3e-07      25     111 ..      38     125 ..      15     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 9.5e-11
                   Acetyltransf_10  25 rieegealllvaeeggkivGviel.rdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyav 98 
                                        ++e+   +++a +g++ vG+++l r gs   +  l+V+++ r+ G+g+a+ ea+e++ + dgi+ +l v   ++a 
  gi|336254238|ref|YP_004597345.1|  38 DVREKPEAFYIASDGDERVGIGGLeRCGSdaLLRSLVVESDVRSDGYGTAICEALETRGRADGIE-TLYVLT-TTAA 112
                                       4556667799999***********77776989999************************99*999.777754.5788 PP

                   Acetyltransf_10  99 pfYeklGFkavge 111
                                       +f+   G++++++
  gi|336254238|ref|YP_004597345.1| 113 EFFADRGYERIDR 125
                                       9999999999976 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   2.4e-10   1.1e-06       3      76 .]      44     122 ..      42     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.4e-10
                                       EEEEEEEETTEEEEEEEEEEES.TCTEE.EEE-GGGTTSSHHHHHHHHTT.....SEEEEEEEEE.THHHHHHHHHH CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld.aeitr.laVdpeyrgkGiGraLleaae.....kgiileqlel.naekaikfYek 71 
                                       + +++a d+++ vG  +l++++ + + r l+V  + r  G+G+a+ ea e      gi+ + l++ + ++a++f++ 
  gi|336254238|ref|YP_004597345.1|  44 EAFYIASDGDERVGIGGLERCGsDALLRsLVVESDVRSDGYGTAICEALEtrgraDGIE-T-LYVlT-TTAAEFFAD 117
                                       679***********999999988555557******************833433445654.2.23322.3699***** PP

                                       TTEEE CS
                    Acetyltransf_7  72 lGFee 76 
                                        G+e+
  gi|336254238|ref|YP_004597345.1| 118 RGYER 122
                                       ***85 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05     0.053      49     136 ..      44     122 ..      13     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                    Acetyltransf_4  49 eyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnens 125
                                       e ++ + + d+ vG+  l+   +      a+l  +++e d ++ g+g ++ +ale + ++ +ie+l+  +      +
  gi|336254238|ref|YP_004597345.1|  44 EAFYIASDGDERVGIGGLERCGS-----DALLRSLVVESDVRSDGYGTAICEALETRGRADGIETLYVLTT----TA 111
                                       67888888999999999996666.....67777788889****************************9887....78 PP

                    Acetyltransf_4 126 iqfhkalGFel 136
                                       ++f++  G+e 
  gi|336254238|ref|YP_004597345.1| 112 AEFFADRGYER 122
                                       89999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1309.55
//
Query:       gi|336254239|ref|YP_004597346.1|  [L=449]
Description: tRNA pseudouridine synthase D [Halopiger xanaduensis SH-6]
Scores for 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-166  554.9   0.0   1.2e-166  554.7   0.0    1.0  1  TruD          tRNA pseudouridine synthase D (TruD)
  ------ inclusion threshold ------
       0.15   12.2   0.0       0.28   11.3   0.0    1.4  1  EcoEI_R_C     EcoEI R protein C-terminal
       0.17   12.0   0.6       0.59   10.2   0.3    1.8  2  Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)


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 !  554.7   0.0    2e-170  1.2e-166       2     416 .]      11     440 ..      10     440 .. 0.98

  Alignments for each domain:
  == domain 1  score: 554.7 bits;  conditional E-value: 2e-170
                              TruD   2 lgielyvtdtegigGrlrespeDFiVeEieefsge.eeadegey..lvlrvekrnwdtldlvrelaralgisrkrvg 75 
                                       +g+e+yv+d++g+gG+lr++ + F+V+E+e+f++e ++ad+++y  lv+r+++r+wdt+d++ +l++alg+sr+rv+
  gi|336254239|ref|YP_004597346.1|  11 VGMEYYVSDADGVGGHLRDDDDQFRVRELERFDTEpVDADTDAYphLVVRATLRGWDTNDFATRLSDALGVSRERVN 87 
                                       8*******************************99988888888777******************************* PP

                              TruD  76 faGtKDkrAvTtQlisirkvepeelealeikdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeile 152
                                       +aGtKDk+AvTtQl+s+++++pe+l+  +++++++ev+gra+r+l++GdLaGN+Fe++v+d +++++   +a++i++
  gi|336254239|ref|YP_004597346.1|  88 WAGTKDKYAVTTQLFSVYGADPEDLP--DVNGADIEVLGRAGRSLEFGDLAGNEFELVVSD-PDRPD---NAAAITD 158
                                       **************************..789******************************.87776...******* PP

                              TruD 153 eleekg............gvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaet 217
                                       el+e+g            gvPN+fG+QRFGsrrp+th+vG++iv++d+e+Av++y+g+p+++e+e t+ear++v+et
  gi|336254239|ref|YP_004597346.1| 159 ELREFGgfdgsngqavsvGVPNFFGQQRFGSRRPITHEVGLEIVRDDWEGAVMAYLGRPTDAEPEGTQEARTFVEET 235
                                       ***************************************************************************** PP

                              TruD 218 gdleealeelpkslryErallkrLae.....kpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldep 289
                                       +d++eale++p++lryEr++l++Lae      p+++++Ale+lp+nLqrlFvhA+qSy+FN +lseRlerglp+d+p
  gi|336254239|ref|YP_004597346.1| 236 RDWQEALERFPNRLRYERSMLHELAEcdgepGPEEFRAALERLPSNLQRLFVHAAQSYAFNLMLSERLERGLPFDRP 312
                                       *****************************9999******************************************** PP

                              TruD 290 veGDvvifaeer......lpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegle 360
                                       veGDv++fa+ +      lpdtdrlq+v+e++v +v+r++ergrafvtaplvGtet+la+ge+geier+vl++ +le
  gi|336254239|ref|YP_004597346.1| 313 VEGDVACFADTDapeglvLPDTDRLQRVDERRVGSVTRHCERGRAFVTAPLVGTETDLADGEQGEIERDVLDDLDLE 389
                                       *********9889**************************************************************** PP

                              TruD 361 ledFklpklpelsskGtrRaillrvedlelsaeedeltleFsLpkGsYATvvlrEi 416
                                       ++dF+lp+  e+ s+GtrRa+l+r++    + e+d+l l+F+LpkGsYATvv rE+
  gi|336254239|ref|YP_004597346.1| 390 PDDFDLPG--EFYSSGTRRAMLVRTDL---TLETDPLSLSFALPKGSYATVVAREF 440
                                       ********..**************995...346799*******************7 PP

>> EcoEI_R_C  EcoEI R protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.7e-05      0.28       4      61 ..     225     278 ..     223     300 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.7e-05
                         EcoEI_R_C   4 vekfrkfieenkdsidaLqiiwsdreltkellkeLeekLkepppgitpealweayell 61 
                                       +++ r+f+ee +d  +aL ++ ++    +++l eL+e          pe++++a+e+l
  gi|336254239|ref|YP_004597346.1| 225 TQEARTFVEETRDWQEALERFPNRLRYERSMLHELAEC----DGEPGPEEFRAALERL 278
                                       6899**********************************....77899********999 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.24   1.5e+03     103     125 ..     116     138 ..     110     142 .. 0.86
   2 ?   10.2   0.3   9.9e-05      0.59      26      78 ..     231     283 ..     225     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.24
                                       -HHHHHHHHHHHHHHT--SHHHH CS
                      Spore_III_AB 103 kkedkeilkelgeslgysdregq 125
                                       + +d+e+l + g+sl   d+ g+
  gi|336254239|ref|YP_004597346.1| 116 NGADIEVLGRAGRSLEFGDLAGN 138
                                       6789************9999876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 9.9e-05
                                       HHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHHHHHHHHHHH CS
                      Spore_III_AB  26 rlkeleelkralellegeirygatpLpealeklaeksesplseffeevaerle 78 
                                        ++e +++++ale++ +++ry+++ L e+ e  +e   ++++  +e++ ++l+
  gi|336254239|ref|YP_004597346.1| 231 FVEETRDWQEALERFPNRLRYERSMLHELAECDGEPGPEEFRAALERLPSNLQ 283
                                       57899***********************9888888887777777776666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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 0.20s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 3808.28
//
Query:       gi|336254240|ref|YP_004597347.1|  [L=112]
Description: peptidyl-tRNA hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-40  138.7   0.0    1.1e-40  138.6   0.0    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 !  138.6   0.0   6.2e-45   1.1e-40       1     117 []       1     112 []       1     112 [] 0.97

  Alignments for each domain:
  == domain 1  score: 138.6 bits;  conditional E-value: 6.2e-45
                                       EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-S CS
                              PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglp 77 
                                       +k+++v r+D++m++Gk+aaq+ahA++++++k+ ++     l ++W++ gqkk+vlk ese++L+ela+ a++ g+p
  gi|336254240|ref|YP_004597347.1|   1 MKQAIVARTDIGMGQGKLAAQVAHASLSAYEKADSQ-----LRRQWKDGGQKKVVLKGESERQLHELAEIADSDGIP 72 
                                       69*****************************99996.....5589*999**************************** PP

                                       EEEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                              PTH2  78 aalirDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                       +al+rDag+tq+epgt+T+la+gPa ++ vd+vtg+L l+
  gi|336254240|ref|YP_004597347.1|  73 NALVRDAGHTQLEPGTVTALAVGPAADDRVDRVTGDLSLF 112
                                       *************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 935.82
//
Query:       gi|336254241|ref|YP_004597348.1|  [L=271]
Description: hypothetical protein Halxa_2853 [Halopiger xanaduensis SH-6]
Scores for 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:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2188.89
//
Query:       gi|336254242|ref|YP_004597349.1|  [L=203]
Description: Deoxycytidine triphosphate deaminase [Halopiger xanaduensis SH-6]
Scores for complete 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   60.3   0.0    3.5e-14   52.4   0.0    2.1  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)
    1.7e-13   50.3   0.0    2.5e-13   49.8   0.0    1.2  1  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   3.9e-18   3.5e-14       4     162 ..       2     157 ..       1     159 [. 0.86

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 3.9e-18
                               DCD   4 ilpdqeiealieegaikae.epleeeqiqPaslDLrLgkkayrvrasFlpgkgekvaekleelklhe.ldLtegavl 78 
                                       il+d +i + +e+g +  e  +  e qiqPas+DLrLg++    + + +p  + + +++++e+ +++ +d  ++ +l
  gi|336254242|ref|YP_004597349.1|   2 ILSDADILERLEAGDLVVEpLDEPELQIQPASIDLRLGREFLEFQRTNIPCIHPNSEQEVDEYVTETvVDEGDDFIL 78 
                                       67888887777777764330334458**********************************99888773677799*** PP

                               DCD  79 ekgcvYivplleslaLpadlsaaanpksstGRlDvftRvitdkgeefdeveagYkGplyleispr.sFsilvrkGsr 154
                                         g   +   +e++++p dl a+++ +ss GRl v++   +         + gY+G++ le+s   + ++ + +G+r
  gi|336254242|ref|YP_004597349.1|  79 HPGDFVLGTTHERVEIPPDLIAHVEGRSSLGRLAVVVHATAGL------CDPGYRGQITLELSNLgTAPVALTPGMR 149
                                       **********************************998766554......579**********985489********* PP

                               DCD 155 Lsqirfrr 162
                                       +sq+ f +
  gi|336254242|ref|YP_004597349.1| 150 ISQLTFTE 157
                                       ****9975 PP

>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   2.8e-17   2.5e-13      21     119 ..      73     169 ..      70     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 2.8e-17
                                       SSSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEE..EEEETTBTSEEEEEEEE-SSS-EEE-TT-E CS
                           dUTPase  21 akdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvp..gvidsdyrGevkvvlfnltkkdvkikkgdR 95 
                                        +d+++ pg+ vl +t   +++p +l a + +RS+l ++ ++v+   g+ d  yrG++ + l nl+ ++v ++ g R
  gi|336254242|ref|YP_004597349.1|  73 GDDFILHPGDFVLGTTHERVEIPPDLIAHVEGRSSLGRLAVVVHAtaGLCDPGYRGQITLELSNLGTAPVALTPGMR 149
                                       579*****************************************99******************************* PP

                                       EEEEEEEEBEC.GEEEEESSTTTES CS
                           dUTPase  96 iAqLifarilt.aeleevetlkate 119
                                       i qL f++++t a     e++  +e
  gi|336254242|ref|YP_004597349.1| 150 ISQLTFTELKTeA-----ERPYGSE 169
                                       ********99933.....3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1519.38
//
Query:       gi|336254243|ref|YP_004597350.1|  [L=125]
Description: hypothetical protein Halxa_2855 [Halopiger xanaduensis SH-6]
Scores for 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  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); 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):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 986.21
//
Query:       gi|336254244|ref|YP_004597351.1|  [L=299]
Description: XRE family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for complete 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-53  181.2   0.2    1.7e-53  180.6   0.2    1.3  1  ThiP_synth      Thiamine-phosphate synthase
    1.2e-07   31.6   0.0    2.8e-07   30.5   0.0    1.6  1  HTH_3           Helix-turn-helix
     0.0001   21.7   0.1    0.00026   20.4   0.1    1.7  1  Sigma70_r4      Sigma-70, region 4
    0.00014   22.1   2.0    0.00029   21.1   0.4    2.4  1  HTH_31          Helix-turn-helix domain
    0.00034   20.5   0.0    0.00069   19.5   0.0    1.5  1  HTH_37          Helix-turn-helix domain
    0.00046   19.7   0.0     0.0015   18.1   0.0    1.9  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00055   19.6   0.1     0.0014   18.3   0.1    1.7  1  Sigma70_r4_2    Sigma-70, region 4
    0.00076   19.2   0.0     0.0021   17.8   0.0    1.7  1  HTH_23          Homeodomain-like domain
     0.0011   18.8   0.3     0.0056   16.5   0.0    2.3  2  MarR_2          MarR family
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.037   13.9   0.0    1.8  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.017   15.0   0.0       0.05   13.5   0.0    1.8  1  P22_Cro         DNA-binding transcriptional regulator Cro
      0.037   14.1   0.0      0.078   13.0   0.0    1.5  1  HTH_19          Helix-turn-helix domain
      0.039   13.7   0.7       0.48   10.3   0.0    2.8  2  HTH_IclR        IclR helix-turn-helix domain
      0.046   13.9   0.0       0.13   12.5   0.0    1.8  1  HTH_17          Helix-turn-helix domain
      0.056   13.9   0.0       0.11   12.9   0.0    1.5  1  HTH_26          Cro/C1-type HTH DNA-binding domain
      0.063   13.4   1.8        0.3   11.2   0.0    2.8  3  HTH_28          Helix-turn-helix domain
      0.069   13.0   2.0      0.074   12.9   0.1    2.1  2  HTH_5           Bacterial regulatory protein, arsR family
       0.11   12.2   0.0       0.27   11.0   0.0    1.6  1  HTH_38          Helix-turn-helix domain
       0.15   12.7   0.1        0.5   11.0   0.0    1.8  2  HNF-1_N         Hepatocyte nuclear factor 1 (HNF-1), N termin
       0.15   12.2   0.0       0.35   11.0   0.0    1.6  1  HTH_7           Helix-turn-helix domain of resolvase


Domain annotation for each model (and alignments):
>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.6   0.2   1.9e-56   1.7e-53       1     164 [.     140     296 ..     140     297 .. 0.97

  Alignments for each domain:
  == domain 1  score: 180.6 bits;  conditional E-value: 1.9e-56
                                       HHHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC CS
                        ThiP_synth   1 eleralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkf 77 
                                       +l+r+l++le++++f++liP vgsN+++++pdA++++Dva+vpGRI++vkgr++v++epefg+s+hva+vllaa+++
  gi|336254244|ref|YP_004597351.1| 140 SLRRGLRILENASGFSTLIPAVGSNLVACTPDANDVDDVAGVPGRIFDVKGRTTVPAEPEFGVSEHVATVLLAARRH 216
                                       589************************************************************************** PP

                                       -TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCCS-ECEEEE--BCTB--EEEEEES CS
                        ThiP_synth  78 dpevraainirydekilealeelglkvvefdreeepeevgstmewgvaeaieelevpdviydeGgvGkEpmiyvlgk 154
                                       + ++ aainiryde++l+al+e+++ ++efd++++  +        + +aie++    v+y++Gg+G+Ep iyvlg+
  gi|336254244|ref|YP_004597351.1| 217 GADAAAAINIRYDEDLLAALREADHVAAEFDESDDIAS-------SIGAAIEDEPEASVLYQTGGMGIEPLIYVLGP 286
                                       ***********************************999.......8********4479******************* PP

                                       SHHHHHHHHH CS
                        ThiP_synth 155 daeevvekvl 164
                                       dae+v+++v+
  gi|336254244|ref|YP_004597351.1| 287 DAESVADTVR 296
                                       ******9986 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   3.1e-10   2.8e-07       4      34 ..      24      53 ..      22      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.1e-10
                                      HHHHTTHHHHHHHHHHTSSHHHHHHHHTTSS CS
                             HTH_3  4 lRkqlglsqeeLAeklGvsrstisriEnGer 34
                                      lR ++gl+q e+Ae+lG+s+s++s++  G+ 
  gi|336254244|ref|YP_004597351.1| 24 LR-EQGLTQSEVAEVLGISQSAVSKYAHGDV 53
                                      44.5**********************99944 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1     3e-07   0.00026      18      39 ..      26      47 ..      15      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3e-07
                                      TTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 18 geglTleEIgerlgiSrerVrq 39
                                      ++glT++E++e+lgiS+++V+ 
  gi|336254244|ref|YP_004597351.1| 26 EQGLTQSEVAEVLGISQSAVSK 47
                                      79******************85 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.4   3.3e-07   0.00029      12      56 ..      26      78 ..      19      87 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.3e-07
                            HTH_31 12 raGLsqeevAerlgvsestlsrlEqGrrgrp......spa....vlealaralgl 56
                                      ++GL+q evAe lg+s+s +s++  G  +          +     +e la++l +
  gi|336254244|ref|YP_004597351.1| 26 EQGLTQSEVAEVLGISQSAVSKYAHGDVT-TndriaaD-ErvqtLVEDLAEGLAA 78
                                      78***********************9986.42334430.0334466777777766 PP

>> HTH_37  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   7.7e-07   0.00069      23      56 ..      20      53 ..      15      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.7e-07
                                      HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT-- CS
                            HTH_37 23 iaeliekrelsqseaaqllgiaqPkvsrllrgkl 56
                                      +a  +++++l+qse+a+ lgi+q+ vs+   g++
  gi|336254244|ref|YP_004597351.1| 20 LAGELREQGLTQSEVAEVLGISQSAVSKYAHGDV 53
                                      5667899********************9887776 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 !   18.1   0.0   1.6e-06    0.0015      14      37 ..      25      48 ..      23      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-06
                            HTH_24 14 knprisqreLAerlglSpstvnrr 37
                                      ++ +++q+e+Ae lg+S+s+v+++
  gi|336254244|ref|YP_004597351.1| 25 REQGLTQSEVAEVLGISQSAVSKY 48
                                      5689*****************987 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 !   18.3   0.1   1.5e-06    0.0014      23      48 ..      25      50 ..      23      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                                      HTS---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 23 yleglsykEIAellgisegtVksrls 48
                                      +++gl++ E+Ae+lgis ++V ++ +
  gi|336254244|ref|YP_004597351.1| 25 REQGLTQSEVAEVLGISQSAVSKYAH 50
                                      69*******************98865 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.3e-06    0.0021      13      37 ..      24      48 ..      17      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                            HTH_23 13 llaeGlsvreIAreLgvsrrTvyrw 37
                                      l  +Gl+++e+A+ Lg+s++ v+++
  gi|336254244|ref|YP_004597351.1| 24 LREQGLTQSEVAEVLGISQSAVSKY 48
                                      4556******************987 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   6.3e-06    0.0056      13      40 ..      23      47 ..      12      50 .. 0.77
   2 ?   -3.1   0.0       8.4   7.6e+03       9      19 ..     231     241 ..     231     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.3e-06
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHH CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsr 40
                                      +L+   g  lt++e+a+ lg+s+savs+
  gi|336254244|ref|YP_004597351.1| 23 ELREQ-G--LTQSEVAEVLGISQSAVSK 47
                                      45555.5..*****************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.4
                                       HHHHHHHCTTT CS
                            MarR_2   9 rvLaaLgrrpg 19 
                                       ++LaaL+ ++ 
  gi|336254244|ref|YP_004597351.1| 231 DLLAALREADH 241
                                       68889988875 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 ?   13.9   0.0   4.1e-05     0.037      10      32 ..      30      52 ..      26      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgk 32
                                      +q+++Ae lg+sq+aVs+ ++g 
  gi|336254244|ref|YP_004597351.1| 30 TQSEVAEVLGISQSAVSKYAHGD 52
                                      699****************9985 PP

>> P22_Cro  DNA-binding transcriptional regulator Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.6e-05      0.05      12      30 ..      31      49 ..      30      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                                      HHHHHHHHTS-HHHHHHHH CS
                           P22_Cro 12 vekvAkalgvtksAVsqWg 30
                                      ++ vA++lg+++sAVs+ +
  gi|336254244|ref|YP_004597351.1| 31 QSEVAEVLGISQSAVSKYA 49
                                      789*************984 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.7e-05     0.078      10      36 ..      26      55 ..      23      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.7e-05
                            HTH_19 10 elgltqeelaerlgisrskisaiEng...k 36
                                      e gltq e+ae lgis+s  s++ +g    
  gi|336254244|ref|YP_004597351.1| 26 EQGLTQSEVAEVLGISQSAVSKYAHGdvtT 55
                                      669********************9995443 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 ?   10.3   0.0   0.00053      0.48      16      39 ..      26      49 ..      19      51 .. 0.88
   2 ?    0.3   0.1      0.67     6e+02       1      10 [.     140     149 ..     140     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                                      BSS-BHHHHHHHHTS-HHHHHHHH CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlL 39
                                       q+lt se+A+ +g++ S+v+ + 
  gi|336254244|ref|YP_004597351.1| 26 EQGLTQSEVAEVLGISQSAVSKYA 49
                                      5789****************9876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.67
                                       HHHHHHHHHC CS
                          HTH_IclR   1 sldRalaiLd 10 
                                       sl R+l+iL+
  gi|336254244|ref|YP_004597351.1| 140 SLRRGLRILE 149
                                       799******7 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015      0.13       2      23 ..      29      50 ..      29      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                            HTH_17  2 ltveEaAelLgvsrstvyrlir 23
                                      lt +E+Ae Lg+s+s v ++++
  gi|336254244|ref|YP_004597351.1| 29 LTQSEVAEVLGISQSAVSKYAH 50
                                      7889*************99985 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 ?   12.9   0.0   0.00013      0.11       6      36 ..      24      54 ..      20      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                            HTH_26  6 madrgitkseLargtgisaatlsrlvkgkpe 36
                                      +++ g+t+se+a+ +gis++ +s++ +g ++
  gi|336254244|ref|YP_004597351.1| 24 LREQGLTQSEVAEVLGISQSAVSKYAHGDVT 54
                                      6899**********************99864 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00034       0.3       8      30 ..      23      46 ..      20      49 .. 0.84
   2 ?   -1.9   0.0       4.1   3.7e+03      31      41 ..      92     102 ..      90     118 .. 0.57
   3 ?   -0.6   0.4       1.7   1.5e+03       6      21 ..     209     224 ..     206     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00034
                            HTH_28  8 llaaGh.svreaArelgisrrtvy 30
                                      +l +++ +++e+A+ lgis++ v+
  gi|336254244|ref|YP_004597351.1| 23 ELREQGlTQSEVAEVLGISQSAVS 46
                                      5666666**************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.1
                            HTH_28  31 rWikryeegGi 41 
                                       ++i+ +e+gG+
  gi|336254244|ref|YP_004597351.1|  92 VLIRELESGGD 102
                                       56666666663 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.7
                            HTH_28   6 ikllaaGhsvreaAre 21 
                                       ++l+a+ h +++aA++
  gi|336254244|ref|YP_004597351.1| 209 VLLAARRHGADAAAAI 224
                                       7888888999998875 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 ?   12.9   0.1   8.2e-05     0.074      11      34 ..      24      47 ..      17      48 .. 0.91
   2 ?   -2.9   0.1       7.3   6.5e+03      31      42 ..     140     151 ..     138     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.2e-05
                                      HTTSSEEHHHHHHHHTS-HHHHHH CS
                             HTH_5 11 LaegelcvcelaeelglsqstvSh 34
                                      L+e+ l+ +e ae lg+sqs+vS 
  gi|336254244|ref|YP_004597351.1| 24 LREQGLTQSEVAEVLGISQSAVSK 47
                                      7888999***************96 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.3
                                       HHHHHHHHHHHT CS
                             HTH_5  31 tvShHLkkLrea 42 
                                        +++ L++L++a
  gi|336254244|ref|YP_004597351.1| 140 SLRRGLRILENA 151
                                       556668999886 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0003      0.27      16      39 ..      24      47 ..      21      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                            HTH_38 16 llaeGlslreIArrLgrspsTIsR 39
                                      l+++Gl+++e+A  Lg s s +s+
  gi|336254244|ref|YP_004597351.1| 24 LREQGLTQSEVAEVLGISQSAVSK 47
                                      89******************9885 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 ?   11.0   0.0   0.00056       0.5     152     173 ..      27      48 ..      17      58 .. 0.88
   2 ?   -1.5   0.0       3.6   3.3e+03      17      53 ..     230     265 ..     229     276 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00056
                           HNF-1_N 152 hrIsQrevvdvTGlsQShlSqw 173
                                       + + Q ev++v G+sQS +S++
  gi|336254244|ref|YP_004597351.1|  27 QGLTQSEVAEVLGISQSAVSKY 48 
                                       5689****************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.6
                           HNF-1_N  17 eelihALedldrldrehgekleklrlaegeeadskgg 53 
                                       e l++AL + d++ +e+ e+ + + ++ g++ + +++
  gi|336254244|ref|YP_004597351.1| 230 EDLLAALREADHVAAEFDES-DDIASSIGAAIEDEPE 265
                                       67899999999998888555.6666666766655554 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 ?   11.0   0.0   0.00039      0.35      13      43 ..      20      50 ..      16      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
                                      GGGSSTTTT--STTTSSSS---SSSS--SS- CS
                             HTH_7 13 rvvkLleeGisiskIAkevnisRsTvYRyla 43
                                       +++L+e+G + s++A+ ++is s v +y +
  gi|336254244|ref|YP_004597351.1| 20 LAGELREQGLTQSEVAEVLGISQSAVSKYAH 50
                                      5799********************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2234.09
//
Query:       gi|336254245|ref|YP_004597352.1|  [L=264]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-10   40.8   0.0    9.3e-07   29.4   0.0    2.3  2  Methyltransf_11  Methyltransferase domain
    4.3e-10   39.7   0.0    5.3e-10   39.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.6e-09   37.7   0.0    7.5e-09   36.2   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    1.9e-08   34.3   0.0    3.5e-08   33.4   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    1.6e-07   32.0   0.0    3.1e-07   31.1   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
      2e-05   24.5   0.0      3e-05   23.9   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00012   22.3   0.0    0.00018   21.6   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
     0.0016   17.8   0.0     0.0024   17.3   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
       0.08   12.6   0.0       0.12   12.1   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
       0.13   11.7   0.0        0.2   11.1   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
       0.17   11.0   0.0       0.26   10.4   0.0    1.2  1  Fibrillarin      Fibrillarin


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 !   29.4   0.0   5.7e-10   9.3e-07       2      59 ..      66     125 ..      65     135 .. 0.91
   2 !    9.2   0.0    0.0012       1.9      54      95 ..     142     183 ..     136     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 5.7e-10
                                       EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-T CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfed 59 
                                       ++GcGtG+++ +l +r+   ++vvg+D++  +l++a++ ++e ++ v +v++da++ pf+ 
  gi|336254245|ref|YP_004597352.1|  66 EMGCGTGANLPYLRERVgpeGTVVGLDFTGPVLDRARKLTVEYDN-VHVVRGDATRPPFAG 125
                                       79************7777***********************9995.99********99975 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0012
                                       CTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  54 klpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGllv 95 
                                       +  + ++ +D+ ++++v+  +e+p+ a++ +  ++ pgG++v
  gi|336254245|ref|YP_004597352.1| 142 DAGIDSSDIDALLATFVVGMLENPAGAVDDWCDLVGPGGHVV 183
                                       556677889*******************************98 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   3.3e-13   5.3e-10      14     126 ..      52     193 ..      30     250 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 3.3e-13
                   Methyltransf_23  14 erllpklraggrvLdiGcGtGillevlren.gf..svtgvDlspeaveiae.........................k 62 
                                       + ++ +l++g  v+++GcGtG +l++lre+ g   +v+g D      ++a+                          
  gi|336254245|ref|YP_004597352.1|  52 AAAACRLEPGDTVVEMGCGTGANLPYLRERvGPegTVVGLDFTGPVLDRARkltveydnvhvvrgdatrppfagdtD 128
                                       33334478899****************88856678888999888888888788887775555554433222222221 PP

                   Methyltransf_23  63 akkaqkdqfdeqeaaepqg...................kfdlIvlrevlehvpdppellrqiatllkpgGylllsep 120
                                                         +                    +d   +++v + +++p+ +++   +l+ pgG+++l   
  gi|336254245|ref|YP_004597352.1| 129 ------------------AdtaagagadaledagidssDIDALLATFVVGMLENPAGAVDDWCDLVGPGGHVVLANA 187
                                       ..................12223344555555567777************************************999 PP

                   Methyltransf_23 121 laslke 126
                                       ++s+++
  gi|336254245|ref|YP_004597352.1| 188 ARSDAW 193
                                       998843 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   4.6e-12   7.5e-09       1      63 [.      64     126 ..      64     154 .. 0.87
   2 ?   -1.6   0.0       2.9   4.8e+03      57      97 .]     142     180 ..     133     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 4.6e-12
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTT CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedg 63 
                                       v+++GcGtG ++ +l +r+g +++v+g+D++   l++ar+   e + nv++v+gda++ pf+ +
  gi|336254245|ref|YP_004597352.1|  64 VVEMGCGTGANLPYLRERVGpEGTVVGLDFTGPVLDRARKLTVEYD-NVHVVRGDATRPPFAGD 126
                                       89*****************66********************97654.*************9753 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.9
                                       GBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  57 dlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                       d   +++ +D+ ++++++ +l+++  + a++ +++++ pgG
  gi|336254245|ref|YP_004597352.1| 142 DAGIDSSDIDALLATFVVGMLENP--AGAVDDWCDLVGPGG 180
                                       455566778888887777777654..478888888888887 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   2.2e-11   3.5e-08       3      67 ..      60     122 ..      58     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.2e-11
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieele 67 
                                        g +v++ GCGtG+ +  l e++gp+++vvG+D++  ++ +Ar+     ++dnv++ +gd++  +
  gi|336254245|ref|YP_004597352.1|  60 PGDTVVEMGCGTGANLPYLRERVGPEGTVVGLDFTGPVLDRARKL--TVEYDNVHVVRGDATRPP 122
                                       57899***************************************8..569**********99866 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   1.9e-10   3.1e-07       1      99 []      65     182 ..      65     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.9e-10
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg............ 64 
                                       +e GcGtG++l +l+e+  p+ +++g+D+   ++++a++ + +++n ++ + + +    + +               
  gi|336254245|ref|YP_004597352.1|  65 VEMGCGTGANLPYLRERVgPEGTVVGLDFTGPVLDRARKLTVEYDNVHVVRGDATRPPFAGD--Tdadtaagagada 139
                                       599*******************************8888888888876655555555553332..24699******** PP

                   Methyltransf_12  65 ........ssfDlvvasnvlhhlkdirevldnirklLkpgGrl 99 
                                               s  D+ +a +v+  l++++ ++d   +l+ pgG++
  gi|336254245|ref|YP_004597352.1| 140 ledagidsSDIDALLATFVVGMLENPAGAVDDWCDLVGPGGHV 182
                                       *****************************************85 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 !   23.9   0.0   1.8e-08     3e-05      67     133 ..      54     118 ..      39     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.8e-08
                                       HHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-G CS
                              PCMT  67 ellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDG 133
                                          +l++g+ v+e+G+G+G +   l + vg++g+vv+++ +  + ++a++   + +++nv+vv gD 
  gi|336254245|ref|YP_004597352.1|  54 AACRLEPGDTVVEMGCGTGANLPYLRERVGPEGTVVGLDFTGPVLDRARKL--TVEYDNVHVVRGDA 118
                                       55679***************************************9999874..577899****9996 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.1e-07   0.00018      17      80 ..      57     128 ..      50     209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-07
                                       T-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEES.SSS.....HHH....TTEEEECS-CCCSSHHHHHC CS
                              FtsJ  17 klfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDl.qpm.....apl....pgvttiqgditdpetiekik 80 
                                       + ++pg+tvv+ g+++G+   +l +r+g++g vv++D  +p+     + l    ++v++++gd t+p  +    
  gi|336254245|ref|YP_004597352.1|  57 R-LEPGDTVVEMGCGTGANLPYLRERVGPEGTVVGLDFtGPVldrarK-LtveyDNVHVVRGDATRPPFAGDTD 128
                                       5.789*********************************9999988752.235668**********998776555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.5e-06    0.0024      46     117 ..      59     128 ..      46     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-06
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-E CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsf 117
                                        +g +v+++ +Gtg     l + vg +g+vv+lD+   +L+ ++k   e  + n++ + ++a + pf  d+ 
  gi|336254245|ref|YP_004597352.1|  59 EPGDTVVEMGCGTGANLPYLRERVGPEGTVVGLDFTGPVLDRARKLTVE--YDNVHVVRGDATRPPFAGDTD 128
                                       56899***********************************999876554..679999*****9999998774 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.2e-05      0.12      36      98 ..      56     115 ..      52     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-05
                             GCD14  36 LelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvth 98 
                                        +l+pG  vve G G+g+   ++   v+P G +  ++f     ++ar+   e    ++v+v  
  gi|336254245|ref|YP_004597352.1|  56 CRLEPGDTVVEMGCGTGANLPYLRERVGPEGTVVGLDFTGPVLDRARKLTVE---YDNVHVVR 115
                                       5899**********************************99888888763322...23555555 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012       0.2       4      61 ..      63     119 ..      61     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                       EEEEET-TTSHHHHHHHHH.STTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CC CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkk.nPdknflGiEirvkvvakvlkkiealelkNlrilrgdal 61 
                                       +v+e+GcG G  l  l ++  P+ +++G++   +v++++ k     e+ N++++rgda+
  gi|336254245|ref|YP_004597352.1|  63 TVVEMGCGTGANLPYLRERvGPEGTVVGLDFTGPVLDRARKLT--VEYDNVHVVRGDAT 119
                                       689**********99988736**********999998886654..4789********96 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00016      0.26      66     131 ..      56     121 ..      50     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                                       -S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSG CS
                       Fibrillarin  66 lpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkP 131
                                       + +++g+ v+ +G ++G    ++ + vg+eg+v +++f+  vl    +++ +  n+  + +DA++P
  gi|336254245|ref|YP_004597352.1|  56 CRLEPGDTVVEMGCGTGANLPYLRERVGPEGTVVGLDFTGPVLDRARKLTVEYDNVHVVRGDATRP 121
                                       6789****************************************9******************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.77
# Mc/sec: 1041.59
//
Query:       gi|336254246|ref|YP_004597353.1|  [L=135]
Description: thioesterase superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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-14   53.3   0.1    4.1e-14   52.7   0.1    1.3  1  4HBT         Thioesterase superfamily
    2.9e-14   53.0   0.1    1.7e-06   27.5   0.0    2.0  2  Acyl-ACP_TE  Acyl-ACP thioesterase
    3.1e-13   50.3   0.0    3.9e-13   50.0   0.0    1.1  1  4HBT_2       Thioesterase-like superfamily
  ------ inclusion threshold ------
      0.097   12.9   0.0       0.11   12.7   0.0    1.1  1  4HBT_3       Thioesterase-like 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 !   52.7   0.1   9.1e-18   4.1e-14       1      76 [.      18      96 ..      18      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 9.1e-18
                                      TSSB-HHHHHHHHHHHHHHHHHHTTST...TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSC CS
                              4HBT  1 gGvvhgGvylallDeaagaalrslggr...gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgr 76
                                      +++v+++vy+++++ea+ a++ +  +    +  +v+++l+idf rp +++d+ tv +++++lg++sa++ +++r +++ 
  gi|336254246|ref|YP_004597353.1| 18 MNHVNNAVYASYFEEARVAYVDEVFDVdleNLNFVIAHLEIDFGRPLTIEDDPTVAVEITELGNSSATMAYDLRVDGNS 96
                                      58********************99999999*******************************************988765 PP

>> Acyl-ACP_TE  Acyl-ACP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   1.2     1e-08   4.6e-05     158     184 ..       7      33 ..       2      37 .. 0.89
   2 !   27.5   0.0   3.9e-10   1.7e-06      49     135 ..      44     129 ..      33     135 .] 0.88

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1e-08
                       Acyl-ACP_TE 158 elkvrysDlDlnqHvNNvkYlewilev 184
                                       +  vry DlD+ +HvNN++Y ++ +e+
  gi|336254246|ref|YP_004597353.1|   7 DVDVRYRDLDTMNHVNNAVYASYFEEA 33 
                                       678******************998885 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 3.9e-10
                       Acyl-ACP_TE  49 lkklnlvWvvakyeieierlpefgdkveietwaesenklfcyrdfkvrdekgekiieaksvfvlmdqetrrlsrvtd 125
                                       +   nl  v+a+ ei+  r+   +d  +++ ++   ++  + + + +r  +g+ +++ +s+ v +d et+r+  ++ 
  gi|336254246|ref|YP_004597353.1|  44 VDLENLNFVIAHLEIDFGRPLTIEDDPTVAVEITELGNSSATMAYDLRV-DGNSVATGESTVVFVDPETKRPGPIPS 119
                                       5557999****************************************98.777************************ PP

                       Acyl-ACP_TE 126 eilaeyeees 135
                                       +i++ + e++
  gi|336254246|ref|YP_004597353.1| 120 DIRERIVEHE 129
                                       ****995554 PP

>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   8.7e-17   3.9e-13       1     122 [.      10     124 ..      10     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 8.7e-17
                            4HBT_2   1 vrpndvDlnghlnnarylryleearvkflertglksrsiarrgiglilssahvryrrplkfpdrltvefrvididak 77 
                                       vr +d+D + h+nna y +y+eearv ++  +++    +  +    ++++ ++++ rpl+ +d  tv + +++   +
  gi|336254246|ref|YP_004597353.1|  10 VRYRDLDTMNHVNNAVYASYFEEARVAYV--DEV--FDVDLENLNFVIAHLEIDFGRPLTIEDDPTVAVEITELGNS 82 
                                       7889*************************..677..2333345789******************************* PP

                            4HBT_2  78 tliiehrflsnadgkkaarveerivvmdygkrskkapvPpellka 122
                                       +  +++ ++   dg+ +a++e ++v++d +++ ++ p+P ++++ 
  gi|336254246|ref|YP_004597353.1|  83 SATMAYDLRV--DGNSVATGESTVVFVDPETK-RPGPIPSDIRER 124
                                       ********99..*******************8.9*****999875 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.4e-05      0.11      34     103 ..      54     118 ..      27     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                                       EEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEEEETTEEEEEE..EEEEE---T....---EE------ CS
                            4HBT_3  34 hslhvyFlrpgdag.pviyhvervrdGrsfstrtvelsqggrpifta..tasfgraestgwelepaaapppvp 103
                                       ++l ++F rp   +   ++ ve +  G s +t+   l+ +g+ ++t+  t++f+++e+     +    p p+p
  gi|336254246|ref|YP_004597353.1|  54 AHLEIDFGRPLTIEdDPTVAVEITELGNSSATMAYDLRVDGNSVATGesTVVFVDPET----KR----PGPIP 118
                                       78999***********************************998876533888888885....11....23333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 999.39
//
Query:       gi|336254247|ref|YP_004597354.1|  [L=267]
Description: Arylesterase [Halopiger xanaduensis SH-6]
Scores for 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-31  108.1   0.1      7e-29  101.2   0.1    2.0  1  Abhydrolase_1  alpha/beta hydrolase fold
    3.3e-19   69.1   0.1    7.1e-18   64.7   0.1    2.0  1  Hydrolase_4    Serine aminopeptidase, S33
      3e-18   67.2   0.5    3.7e-18   67.0   0.5    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
     0.0069   16.0   0.2      0.064   12.8   0.2    2.1  1  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.037   14.1   0.0    1.4  1  Abhydrolase_4  TAP-like protein
      0.051   13.2   0.0          2    8.0   0.0    2.7  2  FSH1           Serine hydrolase (FSH1)
      0.098   11.7   0.0       0.14   11.2   0.0    1.1  1  DUF1057        Alpha/beta hydrolase of unknown function (DUF1
       0.18   11.3   0.0        2.9    7.4   0.0    2.1  2  DLH            Dienelactone hydrolase family
        0.2   11.5   0.1        1.3    8.8   0.0    2.2  3  Abhydrolase_2  Phospholipase/Carboxylesterase


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 !  101.2   0.1   3.5e-32     7e-29       2     253 ..      22     251 ..      21     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 3.5e-32
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       ++v+lhG+p ++ ++     + +L ++gf++i++DlrG+g+S+++      dy+ + +add++++ld l+++  tl 
  gi|336254247|ref|YP_004597354.1|  22 PIVFLHGWPLNHRMFEY--QFTDLLEEGFRCIGIDLRGYGESDKPY----GDYSYDRFADDVRAVLDELDIHGATLA 92 
                                       89***************..9999***********************....68************************* PP

                                       EETHHHHHHHHHHHHH.GGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHH CS
                     Abhydrolase_1  79 GhSmGGmialayaaey.perVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqr 154
                                       G+SmGG +a+ y +++   +V++l+ll++          +   +   pdf dg a+ + ++      +d++++   +
  gi|336254247|ref|YP_004597354.1|  93 GFSMGGGTATRYMSRHdEAHVDRLALLAP----------ASPVITEKPDFPDGLAESDVNPLIEGARTDRAKMNAEF 159
                                       *****************9***********..........44444444444444444444433333333333333333 PP

                                       HHHHHHHHH.HCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCH.HH CS
                     Abhydrolase_1 155 hrlvdalkf.pdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvpp.ka 229
                                        + ++  ++  +    ++s g + a + at a  s e+w + d ++  +++        pt +++gt+D ++p+   
  gi|336254247|ref|YP_004597354.1| 160 AAMLFHTDQsDELLHWIWSLG-MEAAGHATIA--SAETWRDADLRPDMDDITV------PTKIYHGTHDEVTPIeIT 227
                                       222222211155556666666.5666666666..8999999999998888777......****************** PP

                                       HHHHHHCHTSEEEEEEETCSSSHH CS
                     Abhydrolase_1 230 ledlaqllpkkrlvvisdagHlaf 253
                                       +e l++ + +++l++++++gH ++
  gi|336254247|ref|YP_004597354.1| 228 GEVLEDGIENAELIRFENSGHGLV 251
                                       *********************776 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.1   3.6e-21   7.1e-18       7     237 ..      23     253 ..      21     255 .. 0.73

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 3.6e-21
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGh 83 
                                       +v++HG     + ++  + +L ++Gf ++++D rG+G+s+   g+  s+d++ dD++a+++++         +l G 
  gi|336254247|ref|YP_004597354.1|  23 IVFLHGWPLNHRMFEYQFTDLLEEGFRCIGIDLRGYGESDKPYGD-YSYDRFADDVRAVLDELD----IHGATLAGF 94 
                                       7999****99*****************************988885.69************9999....334579*** PP

                       Hydrolase_4  84 SmGGliallyllrypd.kvaglilsaPalkikaklk.appllklllkllgkllpklqv...snnlkadslsrdpevv 155
                                       SmGG +a++y+ r+ + +v++l l aPa  + ++ + +p    l+   +++l+   +    ++n +++ +  ++   
  gi|336254247|ref|YP_004597354.1|  95 SMGGGTATRYMSRHDEaHVDRLALLAPASPVITEKPdFPD--GLAESDVNPLIEGARTdraKMNAEFAAMLFHT--- 166
                                       ***********777775899********998887544444..44445566666666663222222222222222... PP

                       Hydrolase_4 156 aayeadplvhgkitvrlllelldam........krleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktl 224
                                          ++d+l+h+  ++++ +  + ++        ++l+ + ++it+P+ ++hG++D+v++ e + e++e    ++ +l
  gi|336254247|ref|YP_004597354.1| 167 --DQSDELLHWIWSLGMEAAGHATIasaetwrdADLRPDMDDITVPTKIYHGTHDEVTPIEITGEVLEDGI-ENAEL 240
                                       ..334455555444444333333330000111135566777888*******************99999877.49999 PP

                       Hydrolase_4 225 klypglyHellnE 237
                                         +++  H l+++
  gi|336254247|ref|YP_004597354.1| 241 IRFENSGHGLVTD 253
                                       9999999999877 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.5   1.8e-21   3.7e-18       1     218 [.      23     259 ..      23     261 .. 0.67

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 1.8e-21
                                       EEEE--GC.....G.CHHHHHHHHCCTCEEEEE--TTSTS-..GGCS--HHH.CHHHHHHHCCTT..TTSEEEEEET CS
                     Abhydrolase_6   1 vlllHGagssassW.lvapLaallaagvhvlapDlpGhGrs..dpppldled.ladlaalldelaagggpvvlvGHS 73 
                                       +++lHG +++++++ +  ++  ll +g++++ +Dl+G+G+s  +  ++++++ ++d++a+ldel+   + + l G S
  gi|336254247|ref|YP_004597354.1|  23 IVFLHGWPLNHRMFeY--QFTDLLEEGFRCIGIDLRGYGESdkPYGDYSYDRfADDVRAVLDELD--IHGATLAGFS 95 
                                       8*****9999999977..99*******************553355668888855666*******6..********** PP

                                       CHHHHHHHHHHCC.........EEEEES-........----TTT.S----TTHHHHHHTT-C..CCCHCCHS-HSCC CS
                     Abhydrolase_6  74 lGGalalaaapla.......lvvgvlldp..pp....talpagl.laaalelllallallrl..lawlsreplprlf 134
                                       +GG  a++   +        +++  ll+p  p+    + +p+gl  +++ +l++++++ +++  +++ +      lf
  gi|336254247|ref|YP_004597354.1|  96 MGGGTATR---YMsrhdeahVDRLALLAPasPVitekPDFPDGLaESDVNPLIEGARTDRAKmnAEFAA----M-LF 164
                                       ********...5555578754444999996533666655555556888888888777766665444443....3.77 PP

                                       CCHHH.CCCCHCHCC...CGHH.HHCC....HHCHTTCCHHTT-TTGC.EEECTT-CHHH.HCHHCCCH..STTEEE CS
                     Abhydrolase_6 135 laded.adaawrarl...arla.alla....glgllpaaawadlpvpl.lvlggeDplvp.rllerlla..qagarl 198
                                       + d + +  +w + l   a +  a+ a    ++++  +++  d++vp+ + +g+ D++ p +   + l   ++ a+l
  gi|336254247|ref|YP_004597354.1| 165 HTDQSdELLHWIWSLgmeA-AGhATIAsaetWRDADLRPDMDDITVPTkIYHGTHDEVTPiEITGEVLEdgIENAEL 240
                                       7766643455555553332.222222222212223335577777777753337999977744444555566699999 PP

                                       TCE...SSS-HHHHSHHHHH CS
                     Abhydrolase_6 199 pvvlpgaGHlphleepdeva 218
                                        + ++++GH +  +e ++++
  gi|336254247|ref|YP_004597354.1| 241 -IRFENSGHGLVTDETEKIN 259
                                       .********55554777766 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.2   3.2e-05     0.064     105     242 ..      91     221 ..      16     229 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                                       EEEECHHHHHHHHHCTT--TT.EEEEEEECE-S-TCCC.CSECTTEEBCCHHHHHHHHHCCCCHHTSSS-STTHHHH CS
                     Peptidase_S15 105 mtGiSYlGttqllaaatgvpa.lkaivpeaaisdlydd.yyregGlvrapgglswedldllaealtsrradegdalk 179
                                         G+S +G t++   +++++a ++ ++ +a+ s + ++   ++ Gl +++ +          ++  + +a+ +++l 
  gi|336254247|ref|YP_004597354.1|  91 LAGFSMGGGTATRYMSRHDEAhVDRLALLAPASPVITEkPDFPDGLAESDVNPLI---EGARTDRAKMNAEFAAMLF 164
                                       5677777777776666554431334444444444444445677777777776555...1111111111111122222 PP

                                       HHHHHHCHCCCCCCTTHHHTHHHHCCCC--SSSHHHHTT-HHHHHCT--S-EEEEEECCSSTT CS
                     Peptidase_S15 180 aaaryeaasdellaeldrqtpveselletgdydafWkdrnlsedadkvkapvllvgGwnDwnv 242
                                       +    + +sdell  +     +e   + t +  + W+d +l+ d+d +++p+ +++G +D +v
  gi|336254247|ref|YP_004597354.1| 165 H----TDQSDELLHWIWSL-GMEAAGHATIASAETWRDADLRPDMDDITVPTKIYHGTHD-EV 221
                                       2....22333333333333.445567889999****************************.55 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05     0.037      38      90 ..     212     265 ..     182     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                     Abhydrolase_4  38 LllqnerDpaTPyegakk.lakalggavlvtvegeGHgalaagntCvdkavdaY 90 
                                        +  +++D +TP e + + l + +++a+l+  e++GHg ++++ + +++ ++++
  gi|336254247|ref|YP_004597354.1| 212 KIYHGTHDEVTPIEITGEvLEDGIENAELIRFENSGHGLVTDETEKINEELADF 265
                                       556799********987725678999*************998888777777665 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.083   1.7e+02       7      27 ..      23      43 ..      20      51 .. 0.89
   2 ?    8.0   0.0     0.001         2      80     131 ..      67     149 ..      52     251 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.083
                              FSH1  7 iLcLhGytqsgeiFraktsal 27
                                      i +LhG+  + ++F++++++l
  gi|336254247|ref|YP_004597354.1| 23 IVFLHGWPLNHRMFEYQFTDL 43
                                      78***************9876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.001
                              FSH1  80 kneyegleesldavkdyikengpfdGiiGFSqGaalaallaslleellkea.......................... 130
                                       + +y+++ + ++av d ++ +g    + GFS G+  a++++s  +e + +                           
  gi|336254247|ref|YP_004597354.1|  67 DYSYDRFADDVRAVLDELDIHG--ATLAGFSMGGGTATRYMSRHDEAHVDRlallapaspvitekpdfpdglaesdv 141
                                       6788899999999999999999..7899*************999987765556666666666655555555555554 PP

                              FSH1 131 .......s 131
                                              +
  gi|336254247|ref|YP_004597354.1| 142 npliegaR 149
                                       44444443 PP

>> DUF1057  Alpha/beta hydrolase of unknown function (DUF1057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.9e-05      0.14      38     119 ..      23     102 ..      10     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.9e-05
                           DUF1057  38 vvalhGsPGshnDfkYirskleelkiRligvnyPGfefvtgylgqkytnaeRnsyskalleelelkgklillghsRG 114
                                       +v lhG P  h+ f Y    l e+  R ig++  G+   ++  g+ y      +   a+l+el+++g   l g s G
  gi|336254247|ref|YP_004597354.1|  23 IVFLHGWPLNHRMFEYQFTDLLEEGFRCIGIDLRGYGESDKPYGD-YSYDRFADDVRAVLDELDIHGA-TLAGFSMG 97 
                                       7899********************************988765554.444444566789*******986.46788988 PP

                           DUF1057 115 cenaL 119
                                       +  a 
  gi|336254247|ref|YP_004597354.1|  98 GGTAT 102
                                       88775 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.086   1.7e+02      99     120 ..      88     109 ..      64     123 .. 0.78
   2 ?    7.4   0.0    0.0014       2.9     140     202 ..     204     263 ..     198     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.086
                               DLH  99 kvgvvGfCmGGalalllaaevp 120
                                          + Gf mGG  a  + ++ +
  gi|336254247|ref|YP_004597354.1|  88 GATLAGFSMGGGTATRYMSRHD 109
                                       55688********999888774 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0014
                               DLH 140 aakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsresyneeaa 202
                                        ++i +p  + +g++De+ p +    + e l++   ++el  +++ gH+ + d+ e+ nee a
  gi|336254247|ref|YP_004597354.1| 204 MDDITVPTKIYHGTHDEVTPIEI---TGEVLEDGIENAELIRFENSGHGLVTDETEKINEELA 263
                                       578999************99984...566677777899******************9999865 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       4.7   9.4e+03      17      22 ..      23      28 ..      21      33 .. 0.88
   2 ?   -0.4   0.0      0.41   8.2e+02     109     121 ..      91     103 ..      79     112 .. 0.81
   3 ?    8.8   0.0   0.00065       1.3     154     213 ..     208     262 ..     183     265 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.7
                                      EEEE-- CS
                     Abhydrolase_2 17 viflHG 22
                                      ++flHG
  gi|336254247|ref|YP_004597354.1| 23 IVFLHG 28
                                      89***9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.41
                                       EEEETHHHHHHHH CS
                     Abhydrolase_2 109 igGFSqGaalaly 121
                                       + GFS+G+  a+ 
  gi|336254247|ref|YP_004597354.1|  91 LAGFSMGGGTATR 103
                                       78*****987765 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00065
                                       GGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS--HHHHHHHHHHH CS
                     Abhydrolase_2 154 tkklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHsideeemqdikefl 213
                                       t  +p +  Hg+ D+v p+ +   + evl++ +++ el  +e+++H  + +e ++i+e l
  gi|336254247|ref|YP_004597354.1| 208 T--VPTKIYHGTHDEVTPIEI---TGEVLEDGIENAELIRFENSGHGLVTDETEKINEEL 262
                                       4..899999*********975...7899**************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2001.33
//
Query:       gi|336254248|ref|YP_004597355.1|  [L=279]
Description: hypothetical protein Halxa_2860 [Halopiger xanaduensis SH-6]
Scores for 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  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2087.64
//
Query:       gi|336254249|ref|YP_004597356.1|  [L=514]
Description: blue (type 1) copper domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-89  299.5  55.8    5.2e-66  223.7  37.3    2.4  2  DUF5059       Domain of unknown function (DUF5059)
    1.2e-09   38.5   0.0      3e-09   37.2   0.0    1.7  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
  ------ inclusion threshold ------
      0.071   13.2   0.1       0.37   10.9   0.1    2.0  1  Cupredoxin_1  Cupredoxin-like domain


Domain annotation for each model (and alignments):
>> DUF5059  Domain of unknown function (DUF5059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.7  37.3   8.7e-70   5.2e-66       2     234 ..      63     297 ..      62     299 .. 0.99
   2 !   82.0  11.6     7e-27   4.2e-23     545     622 .]     296     373 ..     295     373 .. 0.98

  Alignments for each domain:
  == domain 1  score: 223.7 bits;  conditional E-value: 8.7e-70
                           DUF5059   2 vaaewnvyrarLyDavalgeaGktgagaavaqeiferfeqasGeygaheqLeetsesaYegfeealgelr.ealeeg 77 
                                       vaaewn++rar++Da+alg a + +ag +v +++  rfe+a+ e+gaheqLe t+++ Ye feea+ elr e+l+e 
  gi|336254249|ref|YP_004597356.1|  63 VAAEWNAIRARVADALALGIAEEFAAGGTVVGDTLTRFESATAEWGAHEQLEGTDHELYEEFEEAVEELRlEGLDEA 139
                                       9**************************************************************************** PP

                           DUF5059  78 dieeaaeeaekasdnLraaqqalvgeeavqaldllllgsraadaavlaaagafdaaatvaeealerfedaavhdale 154
                                       d e+ +eea +a+++L+aaq+ +++ + + al+++l+g+r+ad+ vla+ag+f aa+t+aee+ er+e a+vhd l 
  gi|336254249|ref|YP_004597356.1| 140 DLERVREEAAIADERLQAAQRERLEGANALALEMALFGARVADVDVLATAGHFGAAETLAEETAERWESATVHDELS 216
                                       ***************************************************************************** PP

                           DUF5059 155 eadgelYeafesalesvasaaeeedaegvkssaaaaldaavdgaYalap.esvagagelaalqargyDaaalaglgG 230
                                         +g+lY afe+ l ++a aa++e++egv+s++ aal aa d+aY+la  +++a a++la++qarg+Daa+l+ l G
  gi|336254249|ref|YP_004597356.1| 217 GTNGDLYAAFEGELPTLAEAASDENGEGVASAVDAALTAAADAAYELAAdDAAAHAAQLATVQARGWDAAVLSDLEG 293
                                       ***********************************************998999************************ PP

                           DUF5059 231 pste 234
                                       + +e
  gi|336254249|ref|YP_004597356.1| 294 VDSE 297
                                       9877 PP

  == domain 2  score: 82.0 bits;  conditional E-value: 7e-27
                           DUF5059 545 gaaaasvvsdvfatfeearvhelLeeaDkeaYeafeaaledyvaaLesgsevdaaveafataalraqfavaGavdaa 621
                                       +++aa+v++d f  fe ar he+LeeaD++aYeafe  le+y++aL++g+ vd+a+  fa aalraqfav+Ga+++a
  gi|336254249|ref|YP_004597356.1| 296 SETAADVMRDTFGRFESARSHEALEEADHDAYEAFEGELEAYIEALAAGEGVDEAAGNFAAAALRAQFAVTGALEEA 372
                                       578************************************************************************** PP

                           DUF5059 622 P 622
                                       P
  gi|336254249|ref|YP_004597356.1| 373 P 373
                                       9 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 !   37.2   0.0   4.9e-13     3e-09       9      99 .]     413     514 .]     406     514 .] 0.79

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 4.9e-13
                                       TETSEEESSEEEEETTEEEEEEEESSSSBEEEEET............TSSTTTGGGTTSCTTC...........EEE CS
                       Copper-bind   9 sgdlqFetkeitvkkgekvtfvnlavmgHNvvldk............dgvpagvdkdkvkaed...........etk 62 
                                         + +Fe+ e+tv++g +v f + ++ +H v   +            +g             d              
  gi|336254249|ref|YP_004597356.1| 413 IHAASFEPDELTVEAGATVAFEHVEGEPHTVTAYEdaipgdatywasGGF------------DsesaaregwenGRG 477
                                       55678******************************555555444443333............133344445555566 PP

                                       EBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEEE CS
                       Copper-bind  63 liggGekdsvtfdeagtYkffCsPHaaagMkgkvtve 99 
                                        i++G+++  tf+ agt +f C PH + g  g ++ve
  gi|336254249|ref|YP_004597356.1| 478 AITEGQAYVRTFEVAGTHEFCCIPHETGGQTGRIVVE 514
                                       899******************************9996 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   6.1e-05      0.37      21      54 ..     407     438 ..     399     513 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.1e-05
                      Cupredoxin_1  21 ktveitvkdggfePskievkagekvklkiknkdk 54 
                                       +  +i++   +feP++++v+ag  v ++ +    
  gi|336254249|ref|YP_004597356.1| 407 ADRVIEIHAASFEPDELTVEAGATVAFEHV--EG 438
                                       4456777778************97766543..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); 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: 0.60u 0.23s 00:00:00.83 Elapsed: 00:00:00.39
# Mc/sec: 3920.93
//
Query:       gi|336254250|ref|YP_004597357.1|  [L=873]
Description: AAA ATPase central domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-79  265.1   0.0    6.3e-39  133.4   0.0    2.4  2  AAA              ATPase family associated with various cellul
    8.6e-11   41.8   0.0    0.00049   19.9   0.0    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.4e-10   38.9   3.7    0.00041   20.1   0.2    2.7  2  AAA_lid_3        AAA+ lid domain
    1.1e-09   38.4   0.0    0.00038   20.5   0.0    3.2  2  AAA_5            AAA domain (dynein-related subfamily)
    9.9e-09   35.5   0.0    0.00094   19.3   0.0    2.7  2  AAA_2            AAA domain (Cdc48 subfamily)
      1e-08   35.5   0.0     0.0052   16.9   0.0    3.7  3  AAA_33           AAA domain
    1.2e-08   35.6  11.8     0.0033   17.8   0.7    5.3  3  AAA_16           AAA ATPase domain
    7.7e-08   33.0   0.0      0.011   16.3   0.0    2.7  2  AAA_18           AAA domain
    1.8e-07   31.5   0.7      0.055   13.8   0.0    3.7  2  AAA_22           AAA domain
    2.5e-07   30.8   0.0      0.035   14.1   0.0    2.4  2  AAA_14           AAA domain
    2.7e-07   30.5   0.4      0.026   14.3   0.2    2.4  2  IstB_IS21        IstB-like ATP binding protein
    1.8e-06   28.3   0.0      0.081   13.3   0.0    2.5  2  RNA_helicase     RNA helicase
    1.4e-05   25.1   0.6        2.9    7.8   0.0    4.3  4  NACHT            NACHT domain
      5e-05   23.2   0.0      0.088   12.5   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    5.7e-05   23.0   0.1       0.18   11.6   0.0    2.5  2  AAA_11           AAA domain
    7.6e-05   23.0   0.5        1.9    8.7   0.0    4.2  3  AAA_28           AAA domain
    9.1e-05   22.9   0.2       0.79   10.2   0.0    2.8  2  AAA_17           AAA domain
     0.0001   21.7   0.4       0.38   10.1   0.0    2.8  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00013   21.9   0.0       0.48   10.3   0.0    2.3  2  Rad17            Rad17 P-loop domain
    0.00029   20.2   0.0       0.58    9.3   0.0    2.2  2  TIP49            TIP49 P-loop domain
    0.00073   19.4   0.0        0.8    9.6   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    0.00078   18.8   0.1        1.2    8.4   0.0    2.6  2  Zeta_toxin       Zeta toxin
     0.0011   18.8   0.0       0.81    9.4   0.0    3.1  3  AAA_24           AAA domain
     0.0014   19.2   0.0        2.5    8.6   0.0    2.7  2  ABC_tran         ABC transporter
     0.0033   17.6   0.0          3    7.9   0.0    2.7  2  SKI              Shikimate kinase
     0.0049   17.2   0.2        2.2    8.5   0.0    2.4  2  Hydin_ADK        Hydin Adenylate kinase-like domain
     0.0052   16.8   0.0          3    7.9   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.008   15.9   0.2        3.6    7.3   0.0    2.6  2  Cytidylate_kin   Cytidylate kinase
       0.01   15.4   0.0        4.5    6.7   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
       0.01   15.4   6.3        3.1    7.3   0.1    4.4  4  AAA_25           AAA domain
      0.011   15.8   0.0          3    8.0   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.013   15.3   0.0         13    5.5   0.0    3.3  3  Bac_DnaA         Bacterial dnaA  protein
      0.015   15.5   0.0        2.2    8.3   0.0    2.6  2  Cytidylate_kin2  Cytidylate kinase-like family
      0.017   14.8   0.1         28    4.4   0.0    3.7  4  Sigma54_activat  Sigma-54 interaction domain
      0.029   14.7   0.3         18    5.7   0.0    2.9  2  AAA_19           AAA domain
      0.037   14.0   0.0        9.1    6.1   0.1    3.1  3  ATPase_2         ATPase domain predominantly from Archaea
      0.062   13.7   0.8       0.43   11.0   0.0    2.5  2  GLTSCR1          Conserved region of unknown function on GLTS
       0.12   11.8   0.6         38    3.6   0.0    3.7  4  SMC_N            RecF/RecN/SMC N terminal domain
       0.22   10.8   0.1         34    3.7   0.0    2.8  3  ATPase           KaiC
       0.26   10.0   0.1        3.6    6.3   0.0    2.1  2  Adeno_IVa2       Adenovirus IVa2 protein
       0.27   10.3   0.1        9.4    5.2   0.1    2.1  2  Parvo_NS1        Parvovirus non-structural protein NS1
       0.67    9.4   1.8         22    4.4   0.0    2.2  2  PhoH             PhoH-like protein


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 !  129.4   0.0   2.5e-40   1.1e-37       1     131 [.     369     496 ..     369     497 .. 0.98
   2 !  133.4   0.0   1.5e-41   6.3e-39       1     131 [.     645     777 ..     645     778 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 2.5e-40
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+GppG+GKT +a a+a el+  fle+  ++l sky+g+ +++++++f+ a+++a p++lf+DEida+a++r+++
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGELDYAFLEVTPADLSSKYMGKPAENVQDVFAIAEANA-PCVLFLDEIDAIASAREDQ 444
                                       79******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       +s++e+ +vnqLltel++v +   +v+v++atn  d++d+a++r gRfd++ie++
  gi|336254250|ref|YP_004597357.1| 445 SSTSERGMVNQLLTELEDVGD---DVLVLAATNLLDDVDDAIVRtGRFDEQIEVP 496
                                       *******************99...6***************************997 PP

  == domain 2  score: 133.4 bits;  conditional E-value: 1.5e-41
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..T CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..s 75 
                                       +llyGppG+GKT +a a+a el+v fle+s ++l sk++g+ ++++++lf+ a+++a p+ +f+DEida+a++r  +
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAGELDVAFLEVSPADLSSKWMGKPAQNVADLFEIARQNA-PCLVFLDEIDAIAGARggH 720
                                       69******************************************************9.****************998 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       gs   +++++vnqLltel+ +++ +++v+v++atnrp ++d+a+lr gRfd++ie++
  gi|336254250|ref|YP_004597357.1| 721 GSGGASQRQMVNQLLTELESLESADEDVVVVAATNRPGDVDDAVLRsGRFDERIEVS 777
                                       889999************************************************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 !   19.9   0.0   1.2e-06   0.00049      33     101 ..     366     442 ..     356     450 .. 0.69
   2 !   18.9   0.0   2.3e-06   0.00096      35      95 ..     644     712 ..     611     716 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.2e-06
                            RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvkl.kit....sgPvleka....gdlaalltnleekdvlfideihrlsrav 100
                                       +  vll+GpPG Gkt +a  +a el+  + ++t    s+  + k+    +d+ a+ ++ ++  vlf+dei  +++a 
  gi|336254250|ref|YP_004597357.1| 366 VSGVLLHGPPGCGKTHVAGALAGELDYAFlEVTpadlSSKYMGKPaenvQDVFAI-AEANAPCVLFLDEIDAIASAR 441
                                       5569*********************977524442222334444441111455554.34556679******9988776 PP

                            RuvB_N 101 e 101
                                       e
  gi|336254250|ref|YP_004597357.1| 442 E 442
                                       6 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.3e-06
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkits.....gPvlekagdlaalltnleekd...vlfideihr 95 
                                        +llyGpPG Gkt +a  +a el+v +   s     +  + k+++ +a l ++ +++   ++f+dei  
  gi|336254250|ref|YP_004597357.1| 644 GILLYGPPGCGKTHVAGALAGELDVAFLEVSpadlsSKWMGKPAQNVADLFEIARQNapcLVFLDEIDA 712
                                       58**********************998776511111344556666666666666554344678888865 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.4   2.1e-06   0.00089       4      41 ..     522     558 ..     519     562 .. 0.85
   2 !   20.1   0.2   9.7e-07   0.00041       3      35 ..     802     834 ..     800     843 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.1e-06
                         AAA_lid_3   4 lkeLAerTeGySGADlaalcreAallAlrrgikeitme 41 
                                       l+ ++ rT+Gy   Dl+ +   Aa++Alr ++   t +
  gi|336254250|ref|YP_004597357.1| 522 LDPVVDRTAGYAASDLEYIATDAARRALRADERIGT-D 558
                                       667899***********************9987644.4 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 9.7e-07
                         AAA_lid_3   3 dlkeLAerTeGySGADlaalcreAallAlrrgi 35 
                                       d++ ++erT Gy   Dla l ++Aa++A+ +g 
  gi|336254250|ref|YP_004597357.1| 802 DWDTVVERTSGYAASDLALLADNAARRAMHDGD 834
                                       7899*************************8874 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 !   20.5   0.0   8.8e-07   0.00038       1     124 [.     368     477 ..     368     485 .. 0.75
   2 !   13.9   0.1   9.6e-05     0.041       2      30 ..     645     673 ..     644     767 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.8e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                       +vlL GppG+gK+ +a  la  l   +++v  ++d++++ +  + e        +d  +  +a+ +++l+lDE++ +
  gi|336254250|ref|YP_004597357.1| 368 GVLLHGPPGCGKTHVAGALAGELDYAFLEVT-PADLSSKYMGKPAE------NVQDVFAIAEANAPCVLFLDEIDAI 437
                                       59*********************99998874.66677777777766......689999999999***********66 PP

                                       -HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                             AAA_5  78 esevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                        s+   + +s  +er +    ++el+++  d     + v+a++n ld
  gi|336254250|ref|YP_004597357.1| 438 ASAR--EDQSSTSERGMVNQLLTELEDVGDD-----VLVLAATNLLD 477
                                       5542..2235566666666666666666664.....66666666666 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 9.6e-05
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEE CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyv 30 
                                       +lL GppG+gK+ +a  la  l   +++v
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAGELDVAFLEV 673
                                       89***************998887666655 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.2e-06   0.00094       2     105 ..     365     462 ..     364     464 .. 0.79
   2 !   13.3   0.0   0.00016      0.07       5     104 ..     644     739 ..     641     750 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.2e-06
                                       ----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGG CS
                             AAA_2   2 piisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEid 78 
                                       p++ +ll gp g+Gkt +a ala  l+     +++ ad s+   ++ +     + ++   ++ +a+   +++lDEid
  gi|336254250|ref|YP_004597357.1| 365 PVSGVLLHGPPGCGKTHVAGALAGELD-YAFLEVTPADLSSKYMGKPA-----ENVQDVFAIAEANAPCVLFLDEID 435
                                       778899*********************.57778888887655553333.....3344444556667778******** PP

                                       G-------------HHHHHHHHHHHH- CS
                             AAA_2  79 KihpkessgadvSregVqrdLLqileg 105
                                        i++ ++ ++  S+ g ++ LL  le+
  gi|336254250|ref|YP_004597357.1| 436 AIASAREDQSSTSERGMVNQLLTELED 462
                                       ****99999999*********987775 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00016
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG-- CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKih 81 
                                        ill gp g+Gkt +a ala  l+v    ++  ad s+   ++ ++++ + +++a+     ++    v+lDEid i+
  gi|336254250|ref|YP_004597357.1| 644 GILLYGPPGCGKTHVAGALAGELDV-AFLEVSPADLSSKWMGKPAQNVADLFEIAR-----QNAPCLVFLDEIDAIA 714
                                       6899********************7.666666667666666666666666555554.....34456*********** PP

                                       --..---------HHHHHHHHHHHH CS
                             AAA_2  82 pk..essgadvSregVqrdLLqile 104
                                           ++ +   S+   ++ LL  le
  gi|336254250|ref|YP_004597357.1| 715 GArgGHGSGGASQRQMVNQLLTELE 739
                                       9888888888999998888886555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.2e-05    0.0052       2      29 ..     369     396 ..     369     483 .. 0.75
   2 ?   -1.6   0.0       6.4   2.7e+03      25      70 ..     537     582 ..     530     587 .. 0.72
   3 !   13.6   0.0   0.00013     0.055       2      33 ..     645     709 ..     645     851 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavlls 29 
                                       vll+G+pG+GK+++a  l+ +l++ +l+
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGELDYAFLE 396
                                       799********************77664 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.4
                            AAA_33  25 avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsag 70 
                                        + +++d++rr+l+++++  +  +  +++++   + + a +al  g
  gi|336254250|ref|YP_004597357.1| 537 LEYIATDAARRALRADERIGTDHLLAAAEEVDSSVPDWAGSALGDG 582
                                       5678899999999998888777777777777776666666666555 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00013
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavl..lssdt...............................l 33 
                                       +ll G+pG+GK+++a  l+ +l++ +  +s  +                               +
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAGELDVAFleVSPADlsskwmgkpaqnvadlfeiarqnapclvfldE 709
                                       6789*******************444024444444444444444444444444444444444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1         9   3.9e+03     163     164 ..     225     226 ..     188     303 .. 0.61
   2 !   17.8   0.7   7.7e-06    0.0033      25      63 ..     367     402 ..     352     470 .. 0.67
   3 !   17.1   0.9   1.3e-05    0.0054      22      63 ..     640     678 ..     631     752 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 9
                            AAA_16 163 es 164
                                       +s
  gi|336254250|ref|YP_004597357.1| 225 KS 226
                                       22 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 7.7e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                       + vll+G++G+GK+ ++ +l+ +l  +   fl+ +  +l
  gi|336254250|ref|YP_004597357.1| 367 SGVLLHGPPGCGKTHVAGALAGELDYA---FLEVTPADL 402
                                       78******************9999877...666666666 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 1.3e-05
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                       g+++ +ll+G++G+GK+ ++ +l+ +l    + fl+    +l
  gi|336254250|ref|YP_004597357.1| 640 GTTGGILLYGPPGCGKTHVAGALAGELD---VAFLEVSPADL 678
                                       67799*****************997776...44777666666 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   0.00014      0.06       1      29 [.     369     418 ..     369     495 .. 0.70
   2 !   16.3   0.0   2.5e-05     0.011       1      76 [.     645     748 ..     645     764 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00014
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlr 29 
                                       +ll G+pG+GKt +a +L+ +l +                     ++ + 
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGELDYaflevtpadlsskymgkpaenVQDVF 418
                                       7899**************99987767777777666666666655444444 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.5e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.........ald 47 
                                       Ill G+pG+GKt +a +L+ +l +                     +  l ++a++n ++l + +e          + 
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAGELDVaflevspadlsskwmgkpaqnVADLFEIARQNAPCLVFLDEidaiagargGHG 721
                                       99****************99886666777888777777777777777777777777777776666666666666666 PP

                            AAA_18  48 eskrldedkldklldaleenssaleegkn 76 
                                       +    +++++++ll++le   s  +++++
  gi|336254250|ref|YP_004597357.1| 722 SGGASQRQMVNQLLTELESLES--ADEDV 748
                                       6666666666666666666654..44444 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   0.00022     0.092       8      51 ..     369     403 ..     367     479 .. 0.60
   2 !   13.8   0.0   0.00013     0.055       5      44 ..     642     672 ..     637     751 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00022
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51 
                                       ++++G++G+GKT+++  l+ +ld           +++vt++ ++
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGELD---------YAFLEVTPADLS 403
                                       589****************9994.........333433333333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00013
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvf 44 
                                        g ++++G++G+GKT+++  l+ +ld         + +++
  gi|336254250|ref|YP_004597357.1| 642 TGGILLYGPPGCGKTHVAGALAGELD---------VAFLE 672
                                       56799**************9999994.........44444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   8.2e-05     0.035       5      80 ..     369     441 ..     367     470 .. 0.84
   2 !   14.1   0.0   8.5e-05     0.036       5      79 ..     645     716 ..     642     750 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.2e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewe 80 
                                       +++ G+  +GKT ++  l+ el      +l+++  d + k + +p+++ + +++ ++++   +lflDEi  + +++
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGELD---YAFLEVTPADLSSKYMGKPAENVQDVFAIAEANAPCVLFLDEIDAIASAR 441
                                       6899***************9988...9999999999999888888877777777755568999******9987765 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8.5e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpew 79 
                                       +++ G+  +GKT ++  l+ el      +l+++  d + k + +p+++   ++e ++++   ++flDEi  + ++
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAGELD---VAFLEVSPADLSSKWMGKPAQNVADLFEIARQNAPCLVFLDEIDAIAGA 716
                                       6799***************9988...8899999999999999999878888888766668999******988654 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 !   13.8   0.0   8.2e-05     0.035      49      70 ..     368     389 ..     363     439 .. 0.88
   2 !   14.3   0.2     6e-05     0.026      48      70 ..     643     665 ..     637     675 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.2e-05
                         IstB_IS21  49 nivllGpsGvGKshlaialgve 70 
                                       +++l Gp+G GK+h+a al+ e
  gi|336254250|ref|YP_004597357.1| 368 GVLLHGPPGCGKTHVAGALAGE 389
                                       789***************9865 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                        +i+l Gp+G GK+h+a al+ e
  gi|336254250|ref|YP_004597357.1| 643 GGILLYGPPGCGKTHVAGALAGE 665
                                       5799***************9865 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   0.00034      0.14       1      26 [.     369     394 ..     369     444 .. 0.75
   2 !   13.3   0.0   0.00019     0.081       1      26 [.     645     670 ..     645     708 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00034
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       ++l+Gp+g+GK+++a  La +l  ++
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGELDYAF 394
                                       689**************999887655 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00019
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       i+lyGp+g+GK+++a  La +l  ++
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAGELDVAF 670
                                       789**************999887555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0069       2.9       3      23 ..     369     389 ..     367     393 .. 0.87
   2 ?    3.4   0.0      0.15        64      59     112 ..     404     460 ..     392     513 .. 0.72
   3 ?    6.3   0.0      0.02       8.5       3      24 ..     645     666 ..     644     673 .. 0.87
   4 ?    2.6   0.0      0.27   1.1e+02      63     127 ..     684     753 ..     669     794 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0069
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l+G++G+GKT+ +  la +
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGE 389
                                       79***********99988865 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.15
                                       CCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHH CS
                             NACHT  59 fsqlpepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLsel 112
                                        + + +pa++v+ v+a ++e     +l lD +D +++  +     +e+  v++lL+el
  gi|336254250|ref|YP_004597357.1| 404 SKYMGKPAENVQDVFA-IAEANAPCVLFLDEIDAIASAREDqsstSERGMVNQLLTEL 460
                                       5556677888888555.66777777777999999999877755566666666666554 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.02
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       ++l G++G+GKT+ +  la ++
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAGEL 666
                                       6899*********999988665 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.27
                                       TS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH...............HHHHHCTTTTT--EEEEEE CS
                             NACHT  63 pepaapvsevwavllelperlLlilDglDelvtdlgq......kekqpvrtlLselirkkllpeasllltv 127
                                        +pa++v     +++++    L  lD +D ++   g       +++q v++lL+el + ++  e  +++++
  gi|336254250|ref|YP_004597357.1| 684 GKPAQNVAD-LFEIARQNAPCLVFLDEIDAIAGARGGhgsggaSQRQMVNQLLTELESLESADEDVVVVAA 753
                                       455555555.66799999999**********9988889999999999999999998766666665555544 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 !   12.5   0.0   0.00021     0.088       2      71 ..     370     434 ..     369     441 .. 0.78
   2 !    8.4   0.0    0.0037       1.6       4      71 ..     648     710 ..     645     715 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       + hG pGcGK+++   l+ +  + + +++p  ++l+   + +p+++v  v ++ +a+ + +   +l+lDE+
  gi|336254250|ref|YP_004597357.1| 370 LLHGPPGCGKTHVAGALAGELdYAFLEVTP--ADLSSKYMGKPAENVQDVFAIAEANAP-C---VLFLDEI 434
                                       68****************995655555555..444444489999999999999998876.4...9999997 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0037
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                        G pGcGK+++   l+ +  + + +++p a l +++  k+ ++    ++ + +++ + +   +++lDE+
  gi|336254250|ref|YP_004597357.1| 648 YGPPGCGKTHVAGALAGELdVAFLEVSP-ADLSSKWMGKPAQNVADLFEIARQNA-P-C---LVFLDEI 710
                                       588*************998989999999.99999996555444333333333322.2.3...7888886 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00041      0.18      20      41 ..     369     390 ..     353     457 .. 0.82
   2 !    8.8   0.0    0.0029       1.2      20      41 ..     645     666 ..     631     767 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00041
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                       +l++GPPG+gKT++  +l  +l
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGEL 390
                                       699**********998888777 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0029
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                        l+ GPPG+gKT++  +l  +l
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAGEL 666
                                       6899*********988877766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0072       3.1       2      22 ..     369     389 ..     368     399 .. 0.83
   2 ?    0.9   0.0       1.1   4.8e+02      91     144 ..     405     460 ..     397     475 .. 0.77
   3 !    8.7   0.0    0.0046       1.9       2      21 ..     645     664 ..     644     717 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0072
                            AAA_28   2 ivitGgestGKTtlleaLaar 22 
                                       + + G++++GKT ++ aLa +
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGE 389
                                       6799**************954 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.1
                            AAA_28  91 ayggeaeaelea..aarekrydlvfllppapeidddgeRredleereaiderlrea 144
                                        y+g+ ++++++  a++e +  +v++l++   i +  e + +  er  ++++l e+
  gi|336254250|ref|YP_004597357.1| 405 KYMGKPAENVQDvfAIAEANAPCVLFLDEIDAIASAREDQSSTSERGMVNQLLTEL 460
                                       5777745556666777788999*******999989999999999999888887764 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0046
                            AAA_28   2 ivitGgestGKTtlleaLaa 21 
                                       i + G++++GKT ++ aLa 
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAG 664
                                       7899**************94 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0022      0.95       2      25 ..     373     396 ..     372     402 .. 0.93
   2 !   10.2   0.0    0.0018      0.79       1      25 [.     648     672 ..     648     676 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0022
                                       E-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthls 25 
                                       G+PG+GK++++  l+ ++++ +l+
  gi|336254250|ref|YP_004597357.1| 373 GPPGCGKTHVAGALAGELDYAFLE 396
                                       9******************99886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0018
                                       EE-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                       +G+PG+GK++++  l+ ++++ +l+
  gi|336254250|ref|YP_004597357.1| 648 YGPPGCGKTHVAGALAGELDVAFLE 672
                                       7*****************9998886 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0027       1.1      25      44 ..     369     388 ..     366     396 .. 0.89
   2 !   10.1   0.0   0.00089      0.38      24      44 ..     644     664 ..     628     671 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0027
                      Mg_chelatase  25 lllvGppGsGKtmlakrlps 44 
                                       +ll GppG+GKt +a +l++
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAG 388
                                       79*************98875 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00089
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlps 44 
                                        +ll+GppG+GKt +a +l++
  gi|336254250|ref|YP_004597357.1| 644 GILLYGPPGCGKTHVAGALAG 664
                                       589*************98875 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0011      0.48      48      75 ..     369     396 ..     364     426 .. 0.86
   2 !    9.1   0.0    0.0026       1.1      48      75 ..     645     672 ..     641     688 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklre 75 
                                       +L+ GP+GCgk+ v   L+ el + + e
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGELDYAFLE 396
                                       5899***************999998776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0026
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklre 75 
                                       +L+ GP+GCgk+ v   L+ el + + e
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAGELDVAFLE 672
                                       5899***********9999998876665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0025       1.1      52      95 ..     368     409 ..     365     419 .. 0.82
   2 !    9.3   0.0    0.0014      0.58      52      95 ..     644     685 ..     639     693 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkk 95 
                                       +vLl Gp+g Gkt +a a++ el     f  ++ +++ s  + k
  gi|336254250|ref|YP_004597357.1| 368 GVLLHGPPGCGKTHVAGALAGELD--YAFLEVTPADLSSKYMGK 409
                                       79********************97..677777777777766665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkk 95 
                                       ++Ll Gp+g Gkt +a a++ el   v f  +s +++ s  + k
  gi|336254250|ref|YP_004597357.1| 644 GILLYGPPGCGKTHVAGALAGELD--VAFLEVSPADLSSKWMGK 685
                                       79********************96..999999988887776655 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 !    9.6   0.0    0.0019       0.8       2      47 ..     369     412 ..     368     478 .. 0.71
   2 !    7.3   0.0    0.0094         4       2      30 ..     645     673 ..     644     759 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0019
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevf 47 
                                       vll+g PG +kt ++ ala  ld  f  + +tp  l s  +G+   
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGELDYAF--LEVTPADLSSKYMGKPAE 412
                                       89******************998887..556777777777776544 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0094
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       +ll g PG +kt ++ ala  ld+ f  +
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAGELDVAFLEV 673
                                       7999*******************999655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0027       1.2      19      41 ..     369     391 ..     360     405 .. 0.83
   2 !    7.5   0.0    0.0051       2.2      19      44 ..     645     668 ..     643     680 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0027
                        Zeta_toxin  19 illgGqpGAGKselaellkdele 41 
                                       +ll G pG+GK+++a +l+ el+
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGELD 391
                                       7999**************99983 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0051
                        Zeta_toxin  19 illgGqpGAGKselaellkdelerqg 44 
                                       ill G pG+GK+++a +l+ el  + 
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAGEL--DV 668
                                       7899**************9998..44 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.032        14       5      22 ..     369     386 ..     367     446 .. 0.84
   2 !    9.4   0.0    0.0019      0.81       5      22 ..     645     662 ..     643     684 .. 0.86
   3 ?   -1.3   0.0       3.6   1.5e+03     108     135 ..     728     758 ..     706     766 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.032
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l+ Gp+g GKT++a  l
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGAL 386
                                       6899*********99766 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0019
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       il+yGp+g GKT++a  l
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGAL 662
                                       89***********99766 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.6
                            AAA_24 108 aeefrrllkklqelrk...nvifiahektrk 135
                                       ++ +++ll+ l++l     +v+++a +    
  gi|336254250|ref|YP_004597357.1| 728 RQMVNQLLTELESLESadeDVVVVAATNRPG 758
                                       5566777777777777888999999887655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0059       2.5      12      38 ..     367     393 ..     360     466 .. 0.82
   2 ?    7.5   0.0     0.013       5.5      15      38 ..     646     669 ..     638     749 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0059
                                       SEEEEEESTTSSHHHHHHHHTTSS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkpt 38 
                                       + v + G+ G+GK+ ++ +lag+l+ +
  gi|336254250|ref|YP_004597357.1| 367 SGVLLHGPPGCGKTHVAGALAGELDYA 393
                                       56889*****************99865 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.013
                                       EEEESTTSSHHHHHHHHTTSS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  15 aivGenGaGKStLlkllagllkpt 38 
                                        + G+ G+GK+ ++ +lag+l+ +
  gi|336254250|ref|YP_004597357.1| 646 LLYGPPGCGKTHVAGALAGELDVA 669
                                       689****************99864 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0071         3       1      23 [.     375     397 ..     375     414 .. 0.92
   2 ?    6.8   0.0     0.016         7       1      23 [.     651     673 ..     651     690 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0071
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ v+ +lA +l++ f+++
  gi|336254250|ref|YP_004597357.1| 375 PGCGKTHVAGALAGELDYAFLEV 397
                                       6*******************875 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ v+ +lA +l++ f+++
  gi|336254250|ref|YP_004597357.1| 651 PGCGKTHVAGALAGELDVAFLEV 673
                                       6******************9875 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 !    8.5   0.0    0.0052       2.2       2      30 ..     369     397 ..     368     399 .. 0.92
   2 ?    6.3   0.0     0.024        10       2      30 ..     645     673 ..     644     676 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0052
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       +++hG+P  GKt+ a +La + + A+l +
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGELDYAFLEV 397
                                       689*****************999999976 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.024
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       i++ G+P  GKt+ a +La + + A+l +
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAGELDVAFLEV 673
                                       7889*********************9987 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.022       9.5      21      47 ..     368     396 ..     337     405 .. 0.80
   2 !    7.9   0.0     0.007         3      21      50 ..     642     674 ..     612     678 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.022
                                       EEEEEESTTSSHHHHHHHHHHHTT--..- CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakalgve..e 47 
                                        +lL+G+ G+GKT+ + +la +l+++  e
  gi|336254250|ref|YP_004597357.1| 368 GVLLHGPPGCGKTHVAGALAGELDYAflE 396
                                       39**************9999998776555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.007
                                       E..EEEEESTTSSHHHHHHHHHHHTT--..---- CS
                              TsaE  21 v..ilLeGdLGaGKTtlvrglakalgve..evkS 50 
                                       +  ilL+G+ G+GKT+ + +la +l+v+  ev S
  gi|336254250|ref|YP_004597357.1| 642 TggILLYGPPGCGKTHVAGALAGELDVAflEV-S 674
                                       2559******************9999987444.4 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0085       3.6       3      28 ..     371     396 ..     369     400 .. 0.92
   2 ?    6.0   0.0      0.02       8.5       3      28 ..     647     672 ..     645     676 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0085
                                       EE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                       + GP g GK  va ala +l++++l+
  gi|336254250|ref|YP_004597357.1| 371 LHGPPGCGKTHVAGALAGELDYAFLE 396
                                       68*********************997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                                       EE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                       + GP g GK  va ala +l++++l+
  gi|336254250|ref|YP_004597357.1| 647 LYGPPGCGKTHVAGALAGELDVAFLE 672
                                       67*********************998 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 ?    6.7   0.0     0.011       4.5      35      65 ..     368     398 ..     362     443 .. 0.74
   2 ?    5.8   0.0     0.021       8.9      36      64 ..     645     673 ..     637     694 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                             AAA_7  35 pvllvGptGtGKtviikdllkkldkekylsl 65 
                                        vll Gp G+GKt ++  l  +ld   + ++
  gi|336254250|ref|YP_004597357.1| 368 GVLLHGPPGCGKTHVAGALAGELDYAFLEVT 398
                                       59**************999999994444433 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.021
                             AAA_7  36 vllvGptGtGKtviikdllkkldkekyls 64 
                                       +ll+Gp G+GKt ++  l  +ld   + +
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAGELDVAFLEV 673
                                       89************999998888555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.028        12      36      54 ..     369     387 ..     354     390 .. 0.88
   2 ?    0.6   0.1      0.82   3.5e+02     127     172 ..     411     456 ..     391     470 .. 0.71
   3 ?    7.3   0.1    0.0072       3.1      36      54 ..     645     663 ..     631     666 .. 0.86
   4 ?    1.0   0.0      0.65   2.8e+02     127     172 ..     687     734 ..     666     753 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.028
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll G+pg+GKt +a  la
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALA 387
                                       69**********9997776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.82
                            AAA_25 127 tadvdaleaaieevegvrlvviDplsralgg.densnsdvgalveal 172
                                       ++ v+++ a +e+ + + ++ +D ++++ ++ + +s++ ++ +v++l
  gi|336254250|ref|YP_004597357.1| 411 AENVQDVFAIAEA-NAPCVLFLDEIDAIASArEDQSSTSERGMVNQL 456
                                       4567777878888.779999******988886444445545555554 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0072
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pg+GKt +a  la
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALA 663
                                       79**********9997776 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.65
                            AAA_25 127 tadvdaleaaieevegvrlvviDplsralgg.densnsdv..galveal 172
                                       ++ v++l + +++ + + lv +D ++++ g+ + + +  +  +++v++l
  gi|336254250|ref|YP_004597357.1| 687 AQNVADLFEIARQ-NAPCLVFLDEIDAIAGArGGHGSGGAsqRQMVNQL 734
                                       5678899999999.77*********999998844444443345555544 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 ?    8.0   0.0     0.007         3      23      81 ..     368     437 ..     365     445 .. 0.56
   2 ?    5.1   0.0     0.055        23      24      42 ..     645     663 ..     640     712 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.007
                                       -EEEEEETT--HHHHHHCC--TTS-.EE--SSTTHHHH...-H....HHHHHHT...TTSEEEEEE-TT- CS
                   Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgp.wleifvverlak...lp....ldlleqa...kggtLylkdiadl 81 
                                        v+l G++G+gk+ vA++L+ +     le++  + ++k    p    +d+++ a    + +L+l +i+ +
  gi|336254250|ref|YP_004597357.1| 368 GVLLHGPPGCGKTHVAGALAGELDYaFLEVTPADLSSKymgKPaenvQDVFAIAeanAPCVLFLDEIDAI 437
                                       59****************9854332022222221122122222222344444334346677777777665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.055
                                       EEEEEETT--HHHHHHCC- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLh 42 
                                       ++l G++G+gk+ vA++L+
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALA 663
                                       799*************997 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.031        13      37      85 ..     369     416 ..     362     525 .. 0.57
   2 ?    4.8   0.0      0.05        21      37      56 ..     645     664 ..     629     674 .. 0.84
   3 ?    0.0   0.0       1.5   6.4e+02     118     179 ..     733     792 ..     725     801 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.031
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHT CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrd 85 
                                       ++++g+ G GktH+  a++ e+   + e     l++ +++ + ++ ++d
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAGELDYAFLEVTPADLSS-KYMGKPAENVQD 416
                                       79************9999988777766666666554.455555555555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.05
                                       EEEE-SSSSSHHHHHHHHHH CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaign 56 
                                       +++yg+ G GktH+  a++ 
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAG 664
                                       79***********9988875 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHTTT-EE.EEEESS-TTT-SS--HHHHH.HHHSSEEEE-----HHHHHHHHHHHH CS
                          Bac_DnaA 118 elfhtfnalleegkqv.vlssDrsPkeleeledrlrs.rfeaGlvvdieppdletrlailkkki 179
                                       +l++ +++l  +++ v v+++   P ++++  + lrs rf+    ++++ppd   r ail+ ++
  gi|336254250|ref|YP_004597357.1| 733 QLLTELESLESADEDVvVVAATNRPGDVDD--AVLRSgRFDE--RIEVSPPDAAARKAILQVHL 792
                                       566666677666655414566677777663..4455436765..6899***********98665 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0053       2.2       8     111 ..     375     478 ..     370     485 .. 0.64
   2 ?    4.4   0.0     0.088        38       8      45 ..     651     688 ..     645     752 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0053
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevde....rsrlssflskllaarvagdtldekldde 80 
                                        G+g++ ++ aLA +L + f++    +  +k +g + e v+ v      +++   fl+++ a   a    + ++ ++
  gi|336254250|ref|YP_004597357.1| 375 PGCGKTHVAGALAGELDYAFLEVTPADLSSKYMGKPAENVQDVFAiaeaNAPCVLFLDEIDAIASAR---EDQSSTS 448
                                       6*********************999999999999999998543332224566667777665554433...3333333 PP

                   Cytidylate_kin2  81 lfeaqervirelaaeesvVivGRgadliLkd 111
                                        + +  ++++el +  + V+v  +a ++L d
  gi|336254250|ref|YP_004597357.1| 449 ERGMVNQLLTELEDVGDDVLV-LAATNLLDD 478
                                       345555555555533233333.345555555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.088
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglsee 45 
                                        G+g++ ++ aLA +L + f++    +  +k +g + +
  gi|336254250|ref|YP_004597357.1| 651 PGCGKTHVAGALAGELDVAFLEVSPADLSSKWMGKPAQ 688
                                       6******************9987666666666555555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.065        28      24      43 ..     368     387 ..     356     408 .. 0.83
   2 ?    0.7   0.0       0.9   3.9e+02      94     142 ..     426     474 ..     412     493 .. 0.63
   3 ?    4.3   0.0     0.068        29      23      42 ..     643     662 ..     621     683 .. 0.74
   4 ?   -1.5   0.0       4.2   1.8e+03     123     143 ..     736     756 ..     696     774 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.065
                                       -EEEECSTTSSHHHHHHHHH CS
                   Sigma54_activat  24 svlitGesGtGKellaraih 43 
                                        vl++G  G+GK+ +a a+ 
  gi|336254250|ref|YP_004597357.1| 368 GVLLHGPPGCGKTHVAGALA 387
                                       69**************8875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.9
                                       TSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSS.SEEE--EEEEEEES CS
                   Sigma54_activat  94 gGtlfLDeigelplelQekLlrvlqegevervGss.keikvdvriiaatn 142
                                         +lfLDei  +  +   +     ++g v+++ ++ + +  dv ++aatn
  gi|336254250|ref|YP_004597357.1| 426 PCVLFLDEIDAIASAREDQ-SSTSERGMVNQLLTElEDVGDDVLVLAATN 474
                                       4689*****9987654333.344455555554433245555666666665 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.068
                                       S-EEEECSTTSSHHHHHHHH CS
                   Sigma54_activat  23 lsvlitGesGtGKellarai 42 
                                         +l+ G  G+GK+ +a a+
  gi|336254250|ref|YP_004597357.1| 643 GGILLYGPPGCGKTHVAGAL 662
                                       579**************887 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 4.2
                                       ESBTSSSEEE--EEEEEEESS CS
                   Sigma54_activat 123 ervGsskeikvdvriiaatne 143
                                       + + s ++ + dv ++aatn+
  gi|336254250|ref|YP_004597357.1| 736 TELESLESADEDVVVVAATNR 756
                                       444455666677888888876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.042        18      13      27 ..     369     383 ..     365     437 .. 0.89
   2 ?    5.6   0.2     0.042        18      13      27 ..     645     659 ..     640     677 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.042
                            AAA_19  13 llvtaGpGtGKTrvl 27 
                                       +l+ ++pG+GKT+v 
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVA 383
                                       7899********986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.042
                            AAA_19  13 llvtaGpGtGKTrvl 27 
                                       +l+ ++pG+GKT+v 
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVA 659
                                       799*********986 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 ?    1.9   0.0      0.42   1.8e+02      23      38 ..     369     384 ..     362     438 .. 0.87
   2 ?    6.1   0.1     0.021       9.1      23      37 ..     645     659 ..     637     672 .. 0.83
   3 ?    1.4   0.0      0.59   2.5e+02     112     165 ..     695     754 ..     670     758 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.42
                          ATPase_2  23 yfiYGpegsGKtaLlk 38 
                                       +++ Gp g+GKt +  
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAG 384
                                       6789********9865 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.021
                          ATPase_2  23 yfiYGpegsGKtaLl 37 
                                       +++YGp g+GKt + 
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVA 659
                                       789*********875 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.59
                          ATPase_2 112 kikkkgkkiiiiiDelqklidlgln........gaellvkeLlnliesltkekhlcvvicls 165
                                       +i ++     +++De+  +   g +        +++++v++Ll+ +esl +  + +vv++++
  gi|336254250|ref|YP_004597357.1| 695 EIARQNAPCLVFLDEIDAIA--GARgghgsggaSQRQMVNQLLTELESLESADEDVVVVAAT 754
                                       45555566889999999999..7778899999999**********************99998 PP

>> GLTSCR1  Conserved region of unknown function on GLTSCR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     0.001      0.43      13      82 ..     170     248 ..     165     251 .. 0.89
   2 ?   -0.5   0.0         4   1.7e+03      74      93 ..     442     461 ..     434     463 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.001
                           GLTSCR1  13 PFasveDavkRLlPYHvfqepkedeedleka.........deefekvaeellkrfqklenkfrklllkeakrespse 80 
                                        F+ v D+++  lP+ v++ +++de+dl  +         d++ +     ++++ +  + ++ ++ ++ea   s+s+
  gi|336254250|ref|YP_004597357.1| 170 SFEGVVDVTRLYLPFWVCEVYRPDERDLIGVvrnledartDDATHGWLSAFFREDKSRLARYAHTSIREAIDRSESA 246
                                       699999*99999*****************5567788888899999999999*******************9888887 PP

                           GLTSCR1  81 ee 82 
                                        +
  gi|336254250|ref|YP_004597357.1| 247 DR 248
                                       66 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 4
                           GLTSCR1  74 krespseeevmlerllleee 93 
                                       + +s ++e+ m+++ll+e e
  gi|336254250|ref|YP_004597357.1| 442 EDQSSTSERGMVNQLLTELE 461
                                       3468999*********9976 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 ?   -0.6   0.0       1.8   7.6e+02      29      44 ..     371     386 ..     363     391 .. 0.87
   2 ?    3.6   0.0     0.089        38     150     169 ..     417     436 ..     414     454 .. 0.93
   3 ?    0.9   0.0      0.59   2.5e+02      27      44 ..     645     662 ..     620     667 .. 0.80
   4 ?    1.4   0.1      0.42   1.8e+02     150     169 ..     693     712 ..     687     714 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.8
                                       EEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                             SMC_N  29 ivGpNGSGKsnlldAi 44 
                                       + Gp G+GK+ +  A+
  gi|336254250|ref|YP_004597357.1| 371 LHGPPGCGKTHVAGAL 386
                                       68*********99887 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.089
                                       HHHHHCCS--SEEEECTTTT CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 150 lfAiqkvkpaplyllDeida 169
                                       +fAi +++  ++ +lDeida
  gi|336254250|ref|YP_004597357.1| 417 VFAIAEANAPCVLFLDEIDA 436
                                       7******************8 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.59
                                       EEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAi 44 
                                         ++Gp G+GK+ +  A+
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGAL 662
                                       5789*********99887 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.42
                                       HHHHHCCS--SEEEECTTTT CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 150 lfAiqkvkpaplyllDeida 169
                                       lf i + +  +l++lDeida
  gi|336254250|ref|YP_004597357.1| 693 LFEIARQNAPCLVFLDEIDA 712
                                       788999999**********8 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.079        34       9      35 ..     356     382 ..     352     387 .. 0.84
   2 ?   -2.1   0.0       4.7     2e+03     125     154 ..     434     463 ..     414     470 .. 0.64
   3 ?    3.6   0.0     0.085        36       9      35 ..     632     658 ..     621     662 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.079
                            ATPase   9 DeilkgGipegrvvlitGepGtGKtif 35 
                                       De+ + G+   + vl+ G pG+GKt +
  gi|336254250|ref|YP_004597357.1| 356 DEFREYGLDPVSGVLLHGPPGCGKTHV 382
                                       6666778888899************76 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.7
                            ATPase 125 iDsitglayeekeavaReilrqlvrvlkkl 154
                                       iD i++  +++++   R  + ql+++l++ 
  gi|336254250|ref|YP_004597357.1| 434 IDAIASAREDQSSTSERGMVNQLLTELEDV 463
                                       444444444445555788888888888765 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.085
                            ATPase   9 DeilkgGipegrvvlitGepGtGKtif 35 
                                       D+  + G+     +l++G pG+GKt +
  gi|336254250|ref|YP_004597357.1| 632 DRYAEYGLGTTGGILLYGPPGCGKTHV 658
                                       55566778888889***********76 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0084       3.6      82     107 ..     360     386 ..     357     402 .. 0.87
   2 ?    1.2   0.1       0.3   1.3e+02      90     107 ..     644     662 ..     633     667 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0084
                        Adeno_IVa2  82 nyglqPviGvi.yGPtGsGksqllrnl 107
                                       +ygl+Pv Gv+ +GP G+Gk+++  +l
  gi|336254250|ref|YP_004597357.1| 360 EYGLDPVSGVLlHGPPGCGKTHVAGAL 386
                                       59*******9638********987666 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.3
                        Adeno_IVa2  90 Gv.iyGPtGsGksqllrnl 107
                                       G+ +yGP G+Gk+++  +l
  gi|336254250|ref|YP_004597357.1| 644 GIlLYGPPGCGKTHVAGAL 662
                                       5526*********987665 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 ?    2.6   0.0      0.14        58     117     136 ..     369     388 ..     366     399 .. 0.90
   2 ?    5.2   0.1     0.022       9.4     117     136 ..     645     664 ..     639     669 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.14
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v+++Gp+ +Gkt +a a+a 
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALAG 388
                                       7899*************985 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.022
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       +++yGp+ +Gkt +a a+a 
  gi|336254250|ref|YP_004597357.1| 645 ILLYGPPGCGKTHVAGALAG 664
                                       89***************985 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.052        22      22      40 ..     369     387 ..     363     392 .. 0.87
   2 ?    3.5   0.7     0.096        41      23      40 ..     646     663 ..     637     669 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.052
                                       EEEE--TTSSTTHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavala 40 
                                       v   Gp G+GKt++a ala
  gi|336254250|ref|YP_004597357.1| 369 VLLHGPPGCGKTHVAGALA 387
                                       5678***********9988 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.096
                                       EEE--TTSSTTHHHHHHH CS
                              PhoH  23 faiGpaGtGKtylavala 40 
                                          Gp G+GKt++a ala
  gi|336254250|ref|YP_004597357.1| 646 LLYGPPGCGKTHVAGALA 663
                                       568***********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (873 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.83u 0.28s 00:00:01.10 Elapsed: 00:00:00.44
# Mc/sec: 5934.03
//
Query:       gi|336254251|ref|YP_004597358.1|  [L=309]
Description: thiazole biosynthesis protein [Halopiger xanaduensis SH-6]
Scores for 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-60  203.8   0.3    1.8e-48  164.8   0.2    2.2  2  Thi4            Thi4 family
    2.9e-11   43.4   0.2    4.5e-11   42.7   0.2    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
      5e-11   42.3   0.2    7.7e-08   31.8   0.2    2.3  2  FAD_binding_2   FAD binding domain
    3.4e-10   40.1   0.4    1.2e-05   25.0   0.2    2.3  2  DAO             FAD dependent oxidoreductase
    1.5e-09   37.6   0.0    3.1e-09   36.5   0.0    1.5  1  FAD_binding_3   FAD binding domain
    2.3e-08   34.2   0.1    4.8e-08   33.1   0.1    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.2e-08   33.2   0.1    7.5e-08   31.9   0.0    1.7  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.2e-07   28.7   0.0    7.2e-07   28.3   0.0    1.2  1  HI0933_like     HI0933-like protein
    4.3e-05   22.9   0.0    8.7e-05   21.9   0.0    1.4  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0002   20.5   0.1     0.0096   15.0   0.0    2.1  2  Lycopene_cycl   Lycopene cyclase protein
     0.0002   21.8   0.7    0.00054   20.5   0.2    2.0  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00029   19.8   0.1      0.075   11.9   0.1    2.1  2  Trp_halogenase  Tryptophan halogenase
     0.0007   19.7   0.0       0.06   13.4   0.0    2.3  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
    0.00077   18.9   0.0     0.0028   17.0   0.0    1.8  2  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0012   18.0   0.1     0.0021   17.2   0.1    1.3  1  GIDA            Glucose inhibited division protein A
     0.0016   18.8   0.0     0.0038   17.7   0.0    1.7  1  NAD_binding_7   Putative NAD(P)-binding
     0.0022   18.0   0.2     0.0067   16.4   0.1    1.8  2  NAD_binding_9   FAD-NAD(P)-binding
     0.0033   16.9   0.1       0.75    9.2   0.1    2.5  2  Glu_dehyd_C     Glucose dehydrogenase C-terminus
  ------ inclusion threshold ------
      0.025   14.9   0.3      0.056   13.7   0.1    1.8  2  TrkA_N          TrkA-N domain
       0.13   11.6   1.7       0.19   11.1   0.5    1.8  2  NMO             Nitronate monooxygenase


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.8   0.2     2e-51   1.8e-48       1     180 [.      16     195 ..      16     218 .. 0.91
   2 !   37.1   0.0   2.1e-12   1.9e-09     190     235 .]     227     272 ..     220     272 .. 0.95

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 2e-51
                                       HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHH CS
                              Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelL 77 
                                       +rai ++  e+++++ +sDv+ivG+G+sGLtaa+ l+++ ++k++++e++  +GGG wlGG l +++ vr+pa+++L
  gi|336254251|ref|YP_004597358.1|  16 TRAIGQEWTEEFMDFSDSDVIIVGGGPSGLTAAKELSER-GVKTMVVEKNNYLGGGFWLGGFLMNKVTVRDPAQQIL 91 
                                       79999**********************************.************************************* PP

                                       HHTT---E..EESSEEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.- CS
                              Thi4  78 delgikye..degdyvvvkdaalftstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvelahdtqscv 152
                                       del++ ++  +  +++++++  ++ s l+ ++++ a++k+ n +   D+++re+++v+G+v+nwt v+    + +cv
  gi|336254251|ref|YP_004597358.1|  92 DELDVSHKqsEDSEGLYIANGPEACSGLIKAACD-AGAKMQNMTEFTDIVIREDHKVSGIVMNWTPVHALPREITCV 167
                                       *****8761145679*******************.***********************************999**** PP

                                       B-EEEEEEEEEE--GSSSTTTTHHHHHH CS
                              Thi4 153 DPlvirakvvvdatGhdgeivavvvkki 180
                                       DP  ++a +v+datGhd+  v+ +  + 
  gi|336254251|ref|YP_004597358.1| 168 DPIAVEADLVIDATGHDAMAVKKLDERG 195
                                       *****************98887666554 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 2.1e-12
                                       ---ECB-HHHHHHHHHHHECEEETTEEE-THHHHHHHT-EB--SB- CS
                              Thi4 190 kgeksldaekaedaivkktrevvpnlyvaGmevaevdganRmGpif 235
                                       +g  s+++ k+eda+v++t  v ++l+++Gm++a  +g++RmGp+f
  gi|336254251|ref|YP_004597358.1| 227 PGHDSMWVGKSEDAVVEHTGLVHDGLIATGMATATTYGLPRMGPTF 272
                                       6889*****************************************9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.2   5.1e-14   4.5e-11       1     145 [.      34     183 ..      34     190 .. 0.65

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 5.1e-14
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrq.rggarlk 76 
                                       Dv++vGGgp+G++AA    ++G k+++ve++++lGG +  g+   +++nk     v+  a+++l++l+  +   +++
  gi|336254251|ref|YP_004597358.1|  34 DVIIVGGGPSGLTAAKELSERGVKTMVVEKNNYLGGGFWLGG---FLMNK---VTVRDPAQQILDELDVsH---KQS 101
                                       9***********************************886555...77777...678888888888886632...222 PP

                      FAD_oxidored  77 krskw..ntfepevakavleemlaeagvtvllntrlveveke.g.............kr.iesvtveskegrktirA 136
                                       ++s+    +  pe+   ++++ ++  g ++  +t++++++ + +             +   +++t+ +    ++++A
  gi|336254251|ref|YP_004597358.1| 102 EDSEGlyIANGPEACSGLIKAACDA-GAKMQNMTEFTDIVIReDhkvsgivmnwtpvHAlPREITCVD---PIAVEA 174
                                       2222222356666666666666644.555555555544444212233333333333311234444444...899*** PP

                      FAD_oxidored 137 kvfiDATgd 145
                                       +++iDATg 
  gi|336254251|ref|YP_004597358.1| 175 DLVIDATGH 183
                                       *******96 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.2   8.6e-11   7.7e-08       1      36 [.      34      69 ..      34     105 .. 0.83
   2 !    8.6   0.0   0.00099      0.89     134     201 ..     105     183 ..      95     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 8.6e-11
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      Dvi++G+G +GL+AA e++e+G k++vvek ++ gg
  gi|336254251|ref|YP_004597358.1| 34 DVIIVGGGPSGLTAAKELSERGVKTMVVEKNNYLGG 69
                                      9*******************************9666 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00099
                                       ......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEE.CTTEEEEEEEEET......TTTCEE......EEEESEEE CS
                     FAD_binding_2 134 r.etlvtghallarlvesarkagvdfqerteadeLiv.edgrvtGavvenp......esgrev......rirakavv 196
                                       +   +++g++ +  l+++a +ag ++q+ te +++++ ed +v+G+v++        +   e       +++a+ v+
  gi|336254251|ref|YP_004597358.1| 105 EgLYIANGPEACSGLIKAACDAGAKMQNMTEFTDIVIrEDHKVSGIVMNWTpvhalpR---EItcvdpiAVEADLVI 178
                                       5567889****************************994566******99767885441...3334455588888888 PP

                                       E---- CS
                     FAD_binding_2 197 latgG 201
                                       +atg 
  gi|336254251|ref|YP_004597358.1| 179 DATGH 183
                                       88885 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.2   1.4e-08   1.2e-05       1      35 [.      34      69 ..      34      77 .. 0.94
   2 !   12.8   0.0   7.3e-05     0.066     143     213 ..     110     191 ..     101     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.4e-08
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                      dv+i+GGG  Gl++A eL++rg  + ++ek++ +g g
  gi|336254251|ref|YP_004597358.1| 34 DVIIVGGGPSGLTAAKELSERGvkTMVVEKNNYLG-G 69
                                      9******************************9988.3 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.3e-05
                                       EEHHHHHHHHHHHHHHTT-EEEESECEEEE.EEEETCEEEEE.EECT.EEE.E..........EEEEEEE--GGGHH CS
                               DAO 143 vdpakltaalaraaealGveilegtevtgl.eeedgkvwgve.rttp.gen.d..........aadavVnaaGawsd 205
                                       ++  +++ +l +aa ++G+++ + te t++  +ed kv+g+  + tp ++  +          +ad v+ a+G+ + 
  gi|336254251|ref|YP_004597358.1| 110 ANGPEACSGLIKAACDAGAKMQNMTEFTDIvIREDHKVSGIVmNWTPvHALpReitcvdpiavEADLVIDATGHDAM 186
                                       588899***********************856677999***99555555554355666888765677******9975 PP

                                       HHHTTCTT CS
                               DAO 206 llgllkel 213
                                        +   k+l
  gi|336254251|ref|YP_004597358.1| 187 AV---KKL 191
                                       55...433 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   3.5e-12   3.1e-09       2      34 ..      33      65 ..      32      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 3.5e-12
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                       dV+IVG+Gp+Gl++a++Lse+Gv++++vek +
  gi|336254251|ref|YP_004597358.1| 33 SDVIIVGGGPSGLTAAKELSERGVKTMVVEKNN 65
                                      69****************************975 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 !   33.1   0.1   5.4e-11   4.8e-08       1      33 [.      37      69 ..      37      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 5.4e-11
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                      IvG+G sGl+aA +L+++g++  ++ek+++lGG
  gi|336254251|ref|YP_004597358.1| 37 IVGGGPSGLTAAKELSERGVKTMVVEKNNYLGG 69
                                      9*******************************9 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 !   31.9   0.0   8.4e-11   7.5e-08       2     108 ..      34     182 ..      33     214 .. 0.65
   2 ?   -2.4   0.0       2.4   2.1e+03     104     124 ..     252     273 ..     236     291 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 8.4e-11
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias..................... 57 
                                       dv+++GgGp Gl+aa++l++ g+k+++v ++++ l+gg +l   l +    ++ a+                     
  gi|336254251|ref|YP_004597358.1|  34 DVIIVGGGPSGLTAAKELSERGVKTMVV-EKNNYLGGGFWLGGFLMNKVTVRDPAQqildeldvshkqsedseglyi 109
                                       8***************************.666666666666666666555555555444457777777777777777 PP

                                       .....................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC..TCEEEEEESEEEE--- CS
                                       .....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .....................evvkklnqgielllgeevvkidpgkkkvklekkke..gdeekiaydklvlAtG 108
                                                            +++++++  ++ + +++v +i +++  v+   ++    d   +++d ++ AtG
  gi|336254251|ref|YP_004597358.1| 110 angpeacsglikaacdagakmQNMTEFTDIVI-REDHKVSGIVMNWTPVHALPREItcVDPIAVEADLVIDATG 182
                                       77777777766666666655433444443333.23335666666666666544332345556666666666666 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                                       EE---.EEE-BCTCTTC.TTBE CS
                                       xxxxx.xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 104 vlAtG.ssprdlgipGvaenvg 124
                                       ++AtG +++ + g+p ++++ g
  gi|336254251|ref|YP_004597358.1| 252 LIATGmATATTYGLPRMGPTFG 273
                                       7999966777779997765554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0     8e-10   7.2e-07       2      43 ..      34      75 ..      33     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 8e-10
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                      dvi++GgG++Gl aA ++++rg +++++ek++ lg  + + G
  gi|336254251|ref|YP_004597358.1| 34 DVIIVGGGPSGLTAAKELSERGVKTMVVEKNNYLGGGFWLGG 75
                                      8*******************************9997776655 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 !   21.9   0.0   9.7e-08   8.7e-05       1      31 [.      36      65 ..      22      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 9.7e-08
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      iI+G+GP Gl+aa el + g++  +++Ek+n
  gi|336254251|ref|YP_004597358.1| 36 IIVGGGPSGLTAAKELSERGVK-TMVVEKNN 65
                                      7999999999999999999994.67999886 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05    0.0096       1      33 [.      34      64 ..      34      72 .. 0.91
   2 ?    3.6   0.0     0.032        28     106     142 ..     148     184 ..     127     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieas 33
                                      Dv+++G+Gp gl  A++l  ++ g+k +++e  
  gi|336254251|ref|YP_004597358.1| 34 DVIIVGGGPSGLTAAKEL--SERGVKTMVVEKN 64
                                      9*****************..9999999999865 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.032
                     Lycopene_cycl 106 eakvesveeeeageslvvleggrkirarlvvdargla 142
                                       ++ v + ++++a  + +++ +   ++a lv+da+g  
  gi|336254251|ref|YP_004597358.1| 148 SGIVMNWTPVHALPREITCVDPIAVEADLVIDATGHD 184
                                       4455666778888899*******************43 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2     6e-07   0.00054       2      35 ..      35      68 ..      34      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6e-07
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v++vGgG +gl +A++l+e g k+ vve ++ l 
  gi|336254251|ref|YP_004597358.1| 35 VIIVGGGPSGLTAAKELSERGVKTMVVEKNNYLG 68
                                      89**************************998876 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   8.3e-05     0.075       1      34 [.      34      64 ..      34      68 .. 0.86
   2 !    6.0   0.0    0.0049       4.4     196     216 ..     170     190 ..     127     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.3e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                      +++ivGGG++G +aA  l++ +   ++  +ve++
  gi|336254251|ref|YP_004597358.1| 34 DVIIVGGGPSGLTAAKELSERG---VKTMVVEKN 64
                                      69*****************998...677777765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0049
                                       -EEE-SEEEE-SGGG-IIIII CS
                    Trp_halogenase 196 reveadlfiDcsGfrgllieq 216
                                         veadl+iD++G+ ++ +++
  gi|336254251|ref|YP_004597358.1| 170 IAVEADLVIDATGHDAMAVKK 190
                                       579***********9988877 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   6.7e-05      0.06       5      41 ..      25      61 ..      21      66 .. 0.90
   2 ?    3.9   0.0     0.057        51      41      92 ..     139     190 ..     125     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-05
                                      HHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEE CS
                      Shikimate_DH  5 kkleslkekkvlliGaGemaelvakhLlakgvkkvvv 41
                                      +++ +++++ v+++G G  +  +ak L+++gvk +vv
  gi|336254251|ref|YP_004597358.1| 25 EEFMDFSDSDVIIVGGGPSGLTAAKELSERGVKTMVV 61
                                      5677899**************************9988 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.057
                                       EEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-H CS
                      Shikimate_DH  41 vaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilek 92 
                                       ++ R+ ++++ ++ +   +++  ++++ ++ +  ead+vi at++  + ++k
  gi|336254251|ref|YP_004597358.1| 139 IVIREDHKVSGIVMNWTPVHALPREITCVDPIAVEADLVIDATGHDAMAVKK 190
                                       556888889999999988889999999999999***********99988876 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.1e-06    0.0028       2      28 ..      43      69 ..      42      72 .. 0.96
   2 ?   -1.2   0.0       1.1   9.7e+02     241     271 ..     162     192 ..     132     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.1e-06
                                      HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGG 28
                                      +GL+aA++L+++G+++ v+E ++ +GG
  gi|336254251|ref|YP_004597358.1| 43 SGLTAAKELSERGVKTMVVEKNNYLGG 69
                                      9*************************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                                       EEEEETTSTEEEESEEEE-S-HHHHHSSEEE CS
                     Amino_oxidase 241 vtvtledgevveaDaVvvTvplgvlkailfs 271
                                         +t++d   veaD V+ ++  ++++ ++++
  gi|336254251|ref|YP_004597358.1| 162 REITCVDPIAVEADLVIDATGHDAMAVKKLD 192
                                       57899999999******99999999944444 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.3e-06    0.0021       1      30 [.      34      63 ..      34      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLith 30
                                      dvi++GgG +G+ AA +++++G+k++ + +
  gi|336254251|ref|YP_004597358.1| 34 DVIIVGGGPSGLTAAKELSERGVKTMVVEK 63
                                      8************************99844 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 !   17.7   0.0   4.2e-06    0.0038       2      40 ..      27      65 ..      27     190 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.2e-06
                     NAD_binding_7  2 fldlkgkkvlvvGgGevAarkvrklleagakvtvvapev 40
                                      f+d+++  v++vGgG+ +++ ++ l e g k  vv ++ 
  gi|336254251|ref|YP_004597358.1| 27 FMDFSDSDVIIVGGGPSGLTAAKELSERGVKTMVVEKNN 65
                                      789********************************9984 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 !   16.4   0.1   7.5e-06    0.0067       2      43 ..      37      73 ..      36      89 .. 0.87
   2 ?   -1.5   0.0       2.4   2.2e+03     140     155 ..     168     183 ..     146     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.5e-06
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvwr 43
                                      ivG+Gp+Gl+++++L +r      ++ ++++++++ g g+ w 
  gi|336254251|ref|YP_004597358.1| 37 IVGGGPSGLTAAKELSER-----GVKTMVVEKNNYlG-GGFWL 73
                                      9***************99.....59999****88856.99885 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                     NAD_binding_9 140 dgaslaadaVvLAlGh 155
                                       d   ++ad V+ A+Gh
  gi|336254251|ref|YP_004597358.1| 168 DPIAVEADLVIDATGH 183
                                       5556789999999998 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.016        14      25      64 ..      26      62 ..      15      67 .. 0.78
   2 !    9.2   0.1   0.00084      0.75      94     134 ..     167     204 ..     130     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.016
                       Glu_dehyd_C 25 safewepesalvlGaGslGLLalalleaeerglervyvlg 64
                                      + ++++ + ++++G G+ GL a+  l+  erg++ + v++
  gi|336254251|ref|YP_004597358.1| 26 EFMDFSDSDVIIVGGGPSGLTAAKELS--ERGVK-TMVVE 62
                                      456789999*************99997..48887.44555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00084
                       Glu_dehyd_C  94 ipeaseemdlvvEaTGsakhafeaiealapnGvaaLlGvpe 134
                                       +  +  e dlv++aTG+ ++a++   +l+  Gv    G+  
  gi|336254251|ref|YP_004597358.1| 167 VDPIAVEADLVIDATGHDAMAVK---KLDERGVLDAPGIED 204
                                       44457899*********998765...566677777666665 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   6.3e-05     0.056       1      30 [.      35      64 ..      35      67 .. 0.91
   2 ?   -2.5   0.0       6.6   5.9e+03      63      75 ..     174     186 ..     171     206 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.3e-05
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESS CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkd 30
                                      +ii+G G  G + a+eLse+g + +v++k+
  gi|336254251|ref|YP_004597358.1| 35 VIIVGGGPSGLTAAKELSERGVKTMVVEKN 64
                                      79*****************7757*****98 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.6
                                       ESEEEE-SSSHHH CS
                            TrkA_N  63 adaviaatgddea 75 
                                       ad+vi atg+d+ 
  gi|336254251|ref|YP_004597358.1| 174 ADLVIDATGHDAM 186
                                       6666666666654 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.1   9.5e+02     137     163 ..      36      62 ..      11      83 .. 0.71
   2 ?   11.1   0.5   0.00022      0.19     113     192 ..     173     249 ..     157     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                               NMO 137 vvliptissvkearkvearGaDalivq 163
                                       +++ +  s  ++a+++ +rG   ++v+
  gi|336254251|ref|YP_004597358.1|  36 IIVGGGPSGLTAAKELSERGVKTMVVE 62 
                                       334445566778888888888888886 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00022
                               NMO 113 kvevvsfgfglpteevvarlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvl 189
                                       ++++v+ + g    ++v++l+e gv+  p i  +ke   + + G D+  + G ++ Gh   + vg k++ a+v++  
  gi|336254251|ref|YP_004597358.1| 173 EADLVIDATGHD-AMAVKKLDERGVLDAPGIEDAKENAGMDQTGDDSYGAPGHDSPGHDS-MWVG-KSEDAVVEHTG 246
                                       566777777777.99********************************************9.7776.55555655555 PP

                               NMO 190 dav 192
                                        ++
  gi|336254251|ref|YP_004597358.1| 247 LVH 249
                                       444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 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:                        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):              20  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2201.33
//
Query:       gi|336254252|ref|YP_004597359.1|  [L=75]
Description: hypothetical protein Halxa_2864 [Halopiger xanaduensis SH-6]
Scores for 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:                       176  (0.0098165); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); 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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 610.62
//
Query:       gi|336254253|ref|YP_004597360.1|  [L=147]
Description: blue (type 1) copper domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-14   53.0   0.1    7.8e-14   51.9   0.1    1.5  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    0.00092   19.3   0.0       0.39   10.9   0.0    2.1  2  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
       0.25   10.5   0.0       0.29   10.3   0.0    1.0  1  ERO1          Endoplasmic Reticulum Oxidoreductin 1 (ERO1)


Domain annotation for each model (and alignments):
>> 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 !   51.9   0.1   1.3e-17   7.8e-14      13      98 ..      48     145 ..      38     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.3e-17
                                       EEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTC............EEEEBSTTEEEEEEEESS CS
                       Copper-bind  13 qFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaed............etkliggGekdsvtfdea 77 
                                       +F ++e +   ge+v+++n+ +  H +   + ++p+g+d +++   +            +    g+ e+++ tf+ +
  gi|336254253|ref|YP_004597360.1|  48 SFVPEEYEATVGETVVWKNTSGADHTITAREASLPEGADYFATGGFEdeqtavdawhdnRGGRLGPRETFEHTFEVP 124
                                       699****************************888888887766543335566777755544567899********** PP

                                       EEEEEEETTTTTTTSEEEEEE CS
                       Copper-bind  78 gtYkffCsPHaaagMkgkvtv 98 
                                       gtY++fC+PH  agM+g+++v
  gi|336254253|ref|YP_004597360.1| 125 GTYTYFCEPHIRAGMVGTIVV 145
                                       *******************98 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0012         7      21      63 ..      38      78 ..      17      90 .. 0.84
   2 !   10.9   0.0   6.4e-05      0.39      70     104 .]     111     145 ..      95     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0012
                      Cupredoxin_1 21 ktveitvkdggfePskievkagekvklkiknkdktpeefesed 63
                                      + ++i ++ ++f P++ e+  ge  ++ +kn++   +++++++
  gi|336254253|ref|YP_004597360.1| 38 NDCSIGMTRNSFVPEEYEATVGE--TVVWKNTSGADHTITARE 78
                                      56789999***************..899***999999888765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 6.4e-05
                      Cupredoxin_1  70 lapgktttitiaplkpGeYeftcdmhm.d.akGkliV 104
                                       l p +t++ t+  + pG+Y+++c+ h    + G+++V
  gi|336254253|ref|YP_004597360.1| 111 LGPRETFEHTF--EVPGTYTYFCEPHIrAgMVGTIVV 145
                                       66778888888..99*********9885579999998 PP

>> ERO1  Endoplasmic Reticulum Oxidoreductin 1 (ERO1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   4.8e-05      0.29      29      78 ..      28      76 ..      19     107 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.8e-05
                              ERO1 29 weddeglCanraCaveeceeeeiPekwraeelsklertlseeeesavkea 78
                                      ++d++++Ca ++C++  + ++ +Pe+ +a+  +++  ++++ ++++++ a
  gi|336254253|ref|YP_004597360.1| 28 FDDEDEFCAGNDCSIGMTRNSFVPEEYEATVGETVVWKNTSGADHTIT-A 76
                                      58999**********************999666665555533322222.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1292.16
//
Query:       gi|336254254|ref|YP_004597361.1|  [L=241]
Description: CDP-alcohol phosphatidyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-10   42.0   3.6    1.2e-10   42.0   3.6    2.8  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 !   42.0   3.6   6.5e-15   1.2e-10       3      66 .]      12      72 ..      11      72 .. 0.91
   2 ?   -0.3   3.0       0.1   1.9e+03      26      44 ..     124     156 ..      78     220 .. 0.67

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 6.5e-15
                                      HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  3 PnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      ++a+T+++ +l+++a++ + ++  + la+ l+l+a+++D+lDG lARr++  ++ G +lDslaD
  gi|336254254|ref|YP_004597361.1| 12 ADAVTIANAALGFVAVV-V-AFVDIALAARLILFAAVADGLDGILARRYGG-TEAGPYLDSLAD 72
                                      789*************7.4.455579***********************99.99*********9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.1
                                       ................HHHHHHHHHHHHHTTHH CS
                   CDP-OH_P_transf  26 p..............lvlailllliasltDalD 44 
                                       +              ++la+ +l +a+l++  D
  gi|336254254|ref|YP_004597361.1| 124 YtaydvaanytegiqTTLAATILGAAILAGVAD 156
                                       255556666666666444444443333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2061.77
//
Query:       gi|336254255|ref|YP_004597362.1|  [L=469]
Description: PBS lyase HEAT domain-containing protein repeat-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-20   72.4   7.7    3.3e-13   49.8   5.3    3.6  3  HEAT_2          HEAT repeats
    2.2e-17   61.9   7.8    4.4e-06   26.9   0.3    6.0  5  HEAT_PBS        PBS lyase HEAT-like repeat
    1.8e-06   27.7   0.2      0.062   13.6   0.1    3.3  3  HEAT            HEAT repeat
    7.6e-06   26.3   3.7      0.011   16.2   0.1    3.4  3  HEAT_EZ         HEAT-like repeat
     0.0017   18.7   0.0        3.1    8.2   0.0    3.3  3  HsbA            Hydrophobic surface binding protein A
     0.0044   17.7   3.3       0.01   16.5   3.3    1.6  1  AATF-Che1       Apoptosis antagonizing transcription factor
  ------ inclusion threshold ------
      0.019   15.0   0.0        1.7    8.8   0.0    3.1  3  Arm             Armadillo/beta-catenin-like repeat
      0.049   14.0   3.3        2.6    8.5   1.0    3.3  2  LPP             Lipoprotein leucine-zipper
      0.087   12.8   2.2       0.27   11.2   1.7    2.0  2  FlxA            FlxA-like protein
       0.13   12.8   0.5       0.13   12.8   0.5    3.3  4  NPV_P10         Nucleopolyhedrovirus P10 protein
       0.13   12.9   0.7        9.4    7.0   0.2    2.9  3  Cytochrom_B562  Cytochrome b562
        1.9    8.7   9.2        7.3    6.8   1.8    2.7  2  FlaG            FlaG protein


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0011       1.7      20      69 ..     307     354 ..     299     356 .. 0.84
   2 !   20.2   0.0     4e-07    0.0006      19      74 ..     333     389 ..     328     391 .. 0.88
   3 !   49.8   5.3   2.2e-16   3.3e-13      11      84 ..     388     461 ..     382     463 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                            HEAT_2  20 airaLgrignpealpaLvellededpavRraaaeaLgaig..dpealpaLke 69 
                                        ++aL r+g++ea++ +v+ ++  d    +aa++ Lg+ig  d+++++ L++
  gi|336254255|ref|YP_004597362.1| 307 CLEALERMGPEEAIDPMVQKANRRD----EAAIRILGKIGveDDQVVDTLLD 354
                                       6899999********9999998777....6899999*999656778888876 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 4e-07
                            HEAT_2  19 aairaLgrig..npealpaLvellededpavRraaaeaLgaigdpealpaLkellddd 74 
                                       aair Lg+ig  +++++++L++++ d++p  +r   +aLg+ig ++a++  ++ l  d
  gi|336254255|ref|YP_004597362.1| 333 AAIRILGKIGveDDQVVDTLLDYV-DSNPTLQRPSFRALGEIGAEDAIQPIADQLVAD 389
                                       89*****8762267**********.8***********************999887666 PP

  == domain 3  score: 49.8 bits;  conditional E-value: 2.2e-16
                            HEAT_2  11 dpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddddvvReaAa 84 
                                         +p+vr  a+raLg ig+++a++ L ++l +de  +vR+ aa+aL +ig+++al++ +e + dd+ ++v+++A+
  gi|336254255|ref|YP_004597362.1| 388 ADEPDVRSWAARALGLIGDTRAIDPLADVLeDDEQDRVRASAAWALNQIGTQDALEIVAE-YEDDRAYLVQAEAE 461
                                       4579**************************445779************************.7899*****99975 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.044        65       5      21 ..     307     323 ..     305     327 .. 0.87
   2 !    6.8   0.0     0.009        13       4      23 ..     333     354 ..     332     358 .. 0.89
   3 !    7.6   0.1     0.005       7.4       7      21 ..     368     382 ..     368     387 .. 0.90
   4 !   26.9   0.3   2.9e-09   4.4e-06       1      27 []     393     419 ..     393     419 .. 0.98
   5 !   15.5   0.2   1.4e-05     0.021       1      20 [.     425     444 ..     425     451 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.044
                                       HHHHHHHCTSGGGHHHH CS
                          HEAT_PBS   5 AakaLgqlgdeeaipaL 21 
                                       +++aL ++g eeai++ 
  gi|336254255|ref|YP_004597362.1| 307 CLEALERMGPEEAIDPM 323
                                       679************86 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.009
                                       HHHHHHHHCTS..GGGHHHHHH CS
                          HEAT_PBS   4 aAakaLgqlgd..eeaipaLle 23 
                                       aA++ Lg++g   ++++++Ll 
  gi|336254255|ref|YP_004597362.1| 333 AAIRILGKIGVedDQVVDTLLD 354
                                       9*****************9986 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.005
                                       HHHHHCTSGGGHHHH CS
                          HEAT_PBS   7 kaLgqlgdeeaipaL 21 
                                       +aLg++g+e+ai+++
  gi|336254255|ref|YP_004597362.1| 368 RALGEIGAEDAIQPI 382
                                       79***********98 PP

  == domain 4  score: 26.9 bits;  conditional E-value: 2.9e-09
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR +Aa+aLg +gd++ai++L  +L+d
  gi|336254255|ref|YP_004597362.1| 393 VRSWAARALGLIGDTRAIDPLADVLED 419
                                       9************************98 PP

  == domain 5  score: 15.5 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHCTSGGGHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipa 20 
                                       vR++Aa+aL q+g+++a+++
  gi|336254255|ref|YP_004597362.1| 425 VRASAAWALNQIGTQDALEI 444
                                       9****************997 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.9   7.4e+03      11      27 ..     357     373 ..     349     375 .. 0.76
   2 !   10.3   0.0   0.00048      0.71       6      27 ..     383     404 ..     379     407 .. 0.80
   3 !   13.6   0.1   4.2e-05     0.062       5      28 ..     413     437 ..     409     439 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.9
                                       -SSHHHHHHHHHHHHHH CS
                              HEAT  11 DpspeVReaAakaLgal 27 
                                       D++p   + +++aLg++
  gi|336254255|ref|YP_004597362.1| 357 DSNPTLQRPSFRALGEI 373
                                       77777777788999998 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00048
                                       HHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   6 lkllsDpspeVReaAakaLgal 27 
                                          l  ++p+VR+ Aa+aLg +
  gi|336254255|ref|YP_004597362.1| 383 ADQLVADEPDVRSWAARALGLI 404
                                       55567899************87 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 4.2e-05
                                       HHHHH.T-SSHHHHHHHHHHHHHHH CS
                              HEAT   5 llkll.sDpspeVReaAakaLgala 28 
                                       l   l  D+  +VR++Aa+aL ++ 
  gi|336254255|ref|YP_004597362.1| 413 LADVLeDDEQDRVRASAAWALNQIG 437
                                       556675789999**********995 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.3     2e+03       5      32 ..     332     355 ..     326     373 .. 0.58
   2 !    9.0   0.4    0.0013         2      24      55 .]     377     404 ..     360     404 .. 0.71
   3 !   16.2   0.1   7.4e-06     0.011      28      55 .]     408     436 ..     407     436 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.3
                           HEAT_EZ   5 raAawaLGrlaggepellqplvpeilpa 32 
                                       +aA++ LG + ++ ++ +      +l++
  gi|336254255|ref|YP_004597362.1| 332 EAAIRILGKIGVEDDQVVD----TLLDY 355
                                       6788888755444444444....44444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                           HEAT_EZ  24 plvpeilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       ++++ i ++L+     d+++VR  Aa+aLg +
  gi|336254255|ref|YP_004597362.1| 377 DAIQPIADQLV----ADEPDVRSWAARALGLI 404
                                       44457777777....3777**********965 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 7.4e-06
                           HEAT_EZ  28 eilpaLlalLnddsd.eVRaaAagaLgnl 55 
                                       +++++L+  L+dd++ +VRa Aa+aL ++
  gi|336254255|ref|YP_004597362.1| 408 RAIDPLADVLEDDEQdRVRASAAWALNQI 436
                                       578999999*999999**********987 PP

>> HsbA  Hydrophobic surface binding protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0021       3.1       6      53 ..      27      74 ..      24      85 .. 0.89
   2 ?   -1.3   0.0       1.9   2.8e+03      65      88 ..     102     125 ..      96     144 .. 0.78
   3 !    6.3   0.0    0.0086        13      41      83 ..     203     244 ..     198     280 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0021
                                      HHHHHHHHHHHHHHHHHHH--SH..HHHHHHHHHHHHHHHHHHHHHHH CS
                              HsbA  6 sdittistavtaldtavnafnGgasalpilsasnalvsaikkattdaq 53
                                      +d+++i t+++al++++ + + +++a++  ++ + ++++i++ ++d +
  gi|336254255|ref|YP_004597362.1| 27 ADLEAIRTQLEALNDDLEGLQSDLEAAETEDDLDVVEADIEEFRADLE 74
                                      79******************77689**************998887765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                                       HHHHHHHHCHHHHHHHHHHHHHTH CS
                              HsbA  65 alaqavqtLepdvkaaldaliaKk 88 
                                       +l++++ ++e dv+++ d+l +K+
  gi|336254255|ref|YP_004597362.1| 102 ELQETYDEIESDVSDLEDDLEDKR 125
                                       677778888888888888888887 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0086
                                       HHHHHHHHHHHHHTS----HHHHHHHHHHHHHCHHHHHHHHHH CS
                              HsbA  41 lvsaikkattdaqasapltdeealalaqavqtLepdvkaalda 83 
                                       l +++++at++++a++   de+a+++a+ ++  ++++++a+d+
  gi|336254255|ref|YP_004597362.1| 203 LGATLDEATAAVDAADLDPDEDAETIAGLLE-ATDEFESAVDD 244
                                       5556666666555555555555555555433.22233333322 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.3     7e-06      0.01      48     129 ..      22     125 ..       6     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7e-06
                         AATF-Che1  48 seefeealeeaekalkklleslleLreelleqneikkla..........................eskeeeekkksk 98 
                                       +ee ++ le+++++l++l ++l  L+++l e  e++                             e +e+e++++++
  gi|336254255|ref|YP_004597362.1|  22 EEEQSADLEAIRTQLEALNDDLEGLQSDL-EAAETE--DdldvveadieefradleeieipeppeE-EEDEDEDDEE 94 
                                       6889999**********************.555533..134799******************9953.4444445555 PP

                         AATF-Che1  99 rkrkkkkkeetsleelwkeleklekalkpfr 129
                                        +  ++++ +++++e+++++++le++l+  r
  gi|336254255|ref|YP_004597362.1|  95 SEPAPEEELQETYDEIESDVSDLEDDLEDKR 125
                                       555566777889999999***9999998766 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.17   2.6e+02      20      39 ..     352     373 ..     346     375 .. 0.85
   2 ?    0.0   0.0      0.67     1e+03      12      37 ..     377     402 ..     373     406 .. 0.87
   3 ?    8.8   0.0    0.0011       1.7      10      36 ..     406     433 ..     402     436 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.17
                                       HTT..TSSHHHHHHHHHHHHHH CS
                               Arm  20 LLs..sedeevqeeAawALsNL 39 
                                       LL+  + ++++q+++ +AL+ +
  gi|336254255|ref|YP_004597362.1| 352 LLDyvDSNPTLQRPSFRALGEI 373
                                       6667789************987 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.67
                                       THHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  12 GavppLvrLLssedeevqeeAawALs 37 
                                        a++p  + L  + ++v+  Aa+AL+
  gi|336254255|ref|YP_004597362.1| 377 DAIQPIADQLVADEPDVRSWAARALG 402
                                       58999999999999****99****98 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0011
                                       HTTHHHHHHHHTT.TSSHHHHHHHHHHH CS
                               Arm  10 eaGavppLvrLLs.sedeevqeeAawAL 36 
                                       +  a++pL + L+ +e ++v+  AawAL
  gi|336254255|ref|YP_004597362.1| 406 DTRAIDPLADVLEdDEQDRVRASAAWAL 433
                                       5669***********************9 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.0    0.0018       2.6       6      36 ..      26      56 ..      23      77 .. 0.88
   2 ?    3.9   0.1     0.046        69      11      31 ..     102     122 ..     101     126 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                               LPP  6 ssqVsqLkskvdqlssdvnsakaaaqaakeE 36
                                      s+++++  ++ ++l++d++ ++++++aa  E
  gi|336254255|ref|YP_004597362.1| 26 SADLEAIRTQLEALNDDLEGLQSDLEAAETE 56
                                      7888888999999999999999999998876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.046
                               LPP  11 qLkskvdqlssdvnsakaaaq 31 
                                       +L++  d+++sdv++++++++
  gi|336254255|ref|YP_004597362.1| 102 ELQETYDEIESDVSDLEDDLE 122
                                       577778888888888888776 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.7   0.00018      0.27       7      87 ..      17      95 ..      11     109 .. 0.78
   2 ?    0.9   0.2       0.3   4.5e+02      38      65 ..      94     121 ..      85     125 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                              FlxA  7 sssssssgsasqiasLqkQiknlqkqLkelses.deltkeekkkqqqliqaQIqqlqaQIaqlqqqqaekaqekqqsek 84
                                         + +++ ++++++++ Q++ l++ L+ l+++ ++  +e      + ++a I+  +a ++ +++ +  +++e +++  
  gi|336254255|ref|YP_004597362.1| 17 EGEAAEEEQSADLEAIRTQLEALNDDLEGLQSDlEAAETE---DDLDVVEADIEEFRADLEEIEIPEPPEEEEDEDEDD 92
                                      555667788899*********************6444444...8999****************9988777777666655 PP

                              FlxA 85 eek 87
                                      ee+
  gi|336254255|ref|YP_004597362.1| 93 EES 95
                                      554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.3
                              FlxA  38 esdeltkeekkkqqqliqaQIqqlqaQI 65 
                                       es+  ++ee ++  ++i++ +++l+  +
  gi|336254255|ref|YP_004597362.1|  94 ESEPAPEEELQETYDEIESDVSDLEDDL 121
                                       3466778888888888888888888766 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   8.4e-05      0.13      11      62 ..      27      77 ..      25      82 .. 0.94
   2 ?   -0.1   0.0      0.89   1.3e+03      19      35 ..     106     122 ..      96     127 .. 0.49
   3 ?   -2.4   0.0       4.5   6.7e+03      35      53 ..     200     216 ..     195     243 .. 0.74
   4 ?   -3.4   0.1       9.2   1.4e+04      22      37 ..     378     393 ..     376     395 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.4e-05
                           NPV_P10 11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62
                                      ad +a+ ++++al++ ++ +q++l+   e ++ Ld   a ++e+ + +e+I+
  gi|336254255|ref|YP_004597362.1| 27 ADLEAIRTQLEALNDDLEGLQSDLEA-AETEDDLDVVEADIEEFRADLEEIE 77
                                      68999********************9.889***************9999996 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.89
                           NPV_P10  19 kVdalqqqvddvqenlp 35 
                                         d +++ v d++++l+
  gi|336254255|ref|YP_004597362.1| 106 TYDEIESDVSDLEDDLE 122
                                       22333333444443333 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.5
                           NPV_P10  35 pdvtelnekLdaqsaqLae 53 
                                       pd  el + Ld+ +a++++
  gi|336254255|ref|YP_004597362.1| 200 PD--ELGATLDEATAAVDA 216
                                       55..778888888887764 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 9.2
                           NPV_P10  22 alqqqvddvqenlpdv 37 
                                       a+q   d++ ++ pdv
  gi|336254255|ref|YP_004597362.1| 378 AIQPIADQLVADEPDV 393
                                       5555556666666665 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0063       9.4       2      69 ..      39     111 ..      19     139 .. 0.79
   2 ?   -1.9   0.0       3.5   5.3e+03      63      81 ..     202     220 ..     199     228 .. 0.80
   3 ?    2.7   0.0      0.13   1.9e+02      18      77 ..     224     278 ..     222     299 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0063
                    Cytochrom_B562   2 lkeeMkqmkkalkqvakaddaeelkkalkelraaaedakeatpsklek.....dseeqkdYqeGldklidqld 69 
                                       l+++ + ++  l++++ +dd + ++++++e+ra  e+ +  +p++ e+     d+e + + +e l++  d+++
  gi|336254255|ref|YP_004597362.1|  39 LNDDLEGLQSDLEAAETEDDLDVVEADIEEFRADLEEIEIPEPPEEEEdededDEESEPAPEEELQETYDEIE 111
                                       6677888999999************************999999777777877744444444555555555444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.5
                    Cytochrom_B562  63 klidqldkaealakagkle 81 
                                       +l ++ld+a a+++a +l+
  gi|336254255|ref|YP_004597362.1| 202 ELGATLDEATAAVDAADLD 220
                                       6778889999999888876 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.13
                    Cytochrom_B562  18 kaddaeelkkalkelraaaedakeatpsklekdseeqkdYqeGldklidqldkaealaka 77 
                                        a++++ l +a +e+++a++da e t  +++     ++  +eG+ +++d +++   +++a
  gi|336254255|ref|YP_004597362.1| 224 DAETIAGLLEATDEFESAVDDATEWTDLEVR-----EQLRREGFFDVLDHIKDFPPELHA 278
                                       57899999999************99995544.....444444444444444444444443 PP

>> FlaG  FlaG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.8    0.0049       7.3       5      53 ..       3      51 ..       1      62 [. 0.87
   2 ?    5.4   1.0     0.014        21      14      52 ..      83     121 ..      74     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0049
                                      HHHHHHHHHHHS-----SS-------HHHHHHHHHHHHHHHTTSS--EE CS
                              FlaG  5 aesakskqqkseeekaekaeeekevseeeleeaveklnkklsslntele 53
                                      +es+  ++++++e++ e aeee+ ++ e + + +e ln++l+ l+++le
  gi|336254255|ref|YP_004597362.1|  3 EESNGDESEAETEAEGEAAEEEQSADLEAIRTQLEALNDDLEGLQSDLE 51
                                      56777888889999999999999999999*************9999886 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.014
                                       HHS-----SS-------HHHHHHHHHHHHHHHTTSS--E CS
                              FlaG  14 kseeekaekaeeekevseeeleeaveklnkklsslntel 52 
                                       ++ee ++e++ee++ + eeel+e+ +++++++s+l+ +l
  gi|336254255|ref|YP_004597362.1|  83 EEEEDEDEDDEESEPAPEEELQETYDEIESDVSDLEDDL 121
                                       56677777778888888888********99999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1284  (0.0716158); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); 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):              12  [number of targets reported over threshold]
# CPU time: 0.84u 0.30s 00:00:01.13 Elapsed: 00:00:00.44
# Mc/sec: 3225.32
//
Query:       gi|336254256|ref|YP_004597363.1|  [L=253]
Description: Zn-dependent hydrolase-like protein [Halopiger xanaduensis SH-6]
Scores for 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-28   98.8   0.1    4.5e-28   98.2   0.1    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
    4.3e-09   36.2   0.3    5.6e-09   35.8   0.3    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 !   98.2   0.1     5e-32   4.5e-28       2     163 .]      10     223 ..       9     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 5e-32
                     Lactamase_B_3   2 ltwlghnsfllet.agarilvDPfkanlgyeppa................eeaDlvlisqaledHahletlkql... 58 
                                       ++wlg+++ ++e  +g++i++DP+++++  + +a                ++ Dlv++++++  H++ + ++++   
  gi|336254256|ref|YP_004597363.1|  10 VSWLGYATARIEApDGTVIYTDPGRYGTLEGTWAdeygeaphpggepydaQDGDLVVVTHDH--HYDDDGVERVaae 84 
                                       89***********559********76555555556777788888999999************..**********987 PP

                     Lactamase_B_3  59 ............................aenvkvleegeslevggleiravatsh........davggsergenngf 99 
                                                                     +v+ +  g++l+v+g+++rav++++        d+++ +++g ++gf
  gi|336254256|ref|YP_004597363.1|  85 datvvvyesvsaeqinaggrdvvepetlPYDVHRIGYGDELAVRGVDVRAVPAYNhldgpntrDGEPIHPEGLGCGF 161
                                       7777777777777777666666666666556666666******************999999988888999999**** PP

                     Lactamase_B_3 100 lleqdgltiyhlGhlahelsseelkelgrvDvvltPvggpltlgqeealelakrLkpklvlPmh 163
                                       ll++dg+  ++ G+ +    +++ +  g+v +++  +  ++t++++ a++la+ L+p+lv+P+h
  gi|336254256|ref|YP_004597363.1| 162 LLTVDGVPCFWTGDSDV--IDAHDDLAGEVSLFMPSIAQNYTMDRHGAADLAETLEPDLVMPIH 223
                                       ****************9..588888899***********************************9 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 !   35.8   0.3   6.2e-13   5.6e-09      19     201 .]      50     224 ..      26     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 6.2e-13
                                       GS--SSS--..SEEEEE-SS--.HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT.TTEEEEEE-TT CS
                     Lactamase_B_2  19 lqPvelrdelppidaVllthaH.yDHlaglltlrelrpkklplyapkgvlavleanfvylaleee.pavnvheldwg 93 
                                        +P+    + ++ d+V++th+H yD   g+  +++   +++++++ ++v+a+  + + +++ e+e  + +vh +  g
  gi|336254256|ref|YP_004597363.1|  50 PHPGGEPYDAQDGDLVVVTHDHhYDDD-GVERVAA---EDATVVVYESVSAEQINAGGRDVVEPEtLPYDVHRIGYG 122
                                       378885666799********9824444.5555555...568999999998876666677777777799********* PP

                                       SEEEECSTTEEEEEEEE-.EE--C.....TCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE- CS
                     Lactamase_B_2  94 esfelgdggleitatpar.hksgr.....rldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadlllldi 164
                                       +++++   g++++a+pa  h  g+     +    +g+ +G++++ +g  ++++gD+  i+++ +++ g + l + + 
  gi|336254256|ref|YP_004597363.1| 123 DELAVR--GVDVRAVPAYnHLDGPntrdgEPIHPEGLGCGFLLTVDGVPCFWTGDSDVIDAH-DDLAGEVSLFM-PS 195
                                       *****9..688*****96144555787766666677************************88.44555566665.53 PP

                                       S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 165 tayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                                +++++++  +a+++a+ l++  +++iH+
  gi|336254256|ref|YP_004597363.1| 196 I--------AQNYTMDRHGAADLAETLEPDLVMPIHY 224
                                       3........26789**********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1903.80
//
Query:       gi|336254257|ref|YP_004597364.1|  [L=605]
Description: phospholipase D/transphosphatidylase [Halopiger xanaduensis SH-6]
Scores for 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-40  136.3   0.0    7.9e-23   80.8   0.0    2.2  2  PLDc_2          PLD-like domain
    1.9e-08   34.1   0.1    7.6e-06   25.9   0.1    2.6  2  PLDc            Phospholipase D Active site motif
    4.3e-06   26.1   0.1      0.073   12.2   0.1    2.4  2  Regulator_TrmB  Archaeal transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.015   14.9   0.0       0.21   11.1   0.0    2.1  2  FAM83           FAM83 A-H


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 !   53.4   0.0   5.1e-18   2.3e-14       3     132 ..     233     362 ..     232     363 .. 0.86
   2 !   80.8   0.0   1.8e-26   7.9e-23       3     133 .]     427     560 ..     425     560 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 5.1e-18
                            PLDc_2   3 qliksAkksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfe.t. 77 
                                       +++++A +++ +a y++ ++++++d+l++aa+rgv+v +l+ s     g+ + a+   l++l  +agv+vrv+    
  gi|336254257|ref|YP_004597364.1| 233 ETLREADERLLLAGYTV-TSDAVADELVAAAERGVDVSVLFES-G-PVGGTPAATEPVLERL-EAAGVDVRVIGgEg 305
                                       6899*************.************************9.3.3344455777777777.*********87514 PP

                            PLDc_2  78 .llgslHaKlylidgktvivGSsNltkrgl..dlnlElnvviedkelakeleeeFerl 132
                                        + +  H K++++d + v+v+S N+ ++g   ++ + ++v++ed+ la+ l+  F ++
  gi|336254257|ref|YP_004597364.1| 306 aRYRYHHPKYAVVD-DSVLVTSENWKPSGIggESSRGWGVRLEDPALAADLATVFRAD 362
                                       43366799*****8.578999*********999999***************9999765 PP

  == domain 2  score: 80.8 bits;  conditional E-value: 1.8e-26
                            PLDc_2   3 qliksAkksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfet.. 77 
                                       +li++A ++i + + ++  + ++l+a+l+aa+rgv+v illds +  + +++ a + +l++++ e+g++++v  +  
  gi|336254257|ref|YP_004597364.1| 427 DLIENADDEILVKQASIDGEFALLEAVLDAARRGVEVDILLDS-TWYHEDENAAVADRLERVAEEEGLPLEVRLAdg 502
                                       79***************666677*******************9.668999999**************9988855334 PP

                            PLDc_2  78 ..llgslHaKlylidgktvivGSsNltkrgldlnlElnvviedkelakeleeeFerlw 133
                                         +++ +HaK+++id+++++vGS+N+++++++ n+E+++ +++  +a++++  F  +w
  gi|336254257|ref|YP_004597364.1| 503 tgRFEKIHAKGIVIDREVAVVGSANWNENSFRNNREVLLALHGDAAAEYYATVFGGDW 560
                                       454489************************************************9999 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0046        21       4      24 ..     310     329 ..     309     331 .. 0.88
   2 !   25.9   0.1   1.7e-09   7.6e-06       6      28 .]     510     532 ..     509     532 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0046
                                       EE---EEEETTTEEEEE---S CS
                              PLDc   4 thHqKivivDdrvafvGgaNL 24 
                                        hH K  +vDd  ++v++ N+
  gi|336254257|ref|YP_004597364.1| 310 YHHPKYAVVDDS-VLVTSENW 329
                                       59**********.99998776 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.7e-09
                                       ---EEEETTTEEEEE---SSHHH CS
                              PLDc   6 HqKivivDdrvafvGgaNLcdgr 28 
                                       H+K++++D +va+vG+aN++ ++
  gi|336254257|ref|YP_004597364.1| 510 HAKGIVIDREVAVVGSANWNENS 532
                                       *******************9875 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   2.9e-05      0.13      16      75 ..     232     299 ..     229     381 .. 0.74
   2 !   12.2   0.1   1.6e-05     0.073       9      59 ..     419     482 ..     412     540 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                                       HHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS........----GGGSSSSEEEEEE CS
                    Regulator_TrmB  16 eelIesAenelivslpselLeelreeliaaaergvtVllliyp........dedleeldleevatevr 75 
                                       +e +++A++ l++++       + +el aaaergv V++l+ +        + ++  ++le   ++vr
  gi|336254257|ref|YP_004597364.1| 232 RETLREADERLLLAGYTVTSDAVADELVAAAERGVDVSVLFESgpvggtpaATEPVLERLEAAGVDVR 299
                                       6899************************************9987777766633344444444444444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHH-SSEEEEEE-G..GGHHHHHHHHHHHHHTT-EEEEEESS............- CS
                    Regulator_TrmB   9 etvierieelIesAenelivslps..elLeelreeliaaaergvtVllliyp............d 59 
                                       +++  r+++lIe+A+ e++v+  s    +  l e   +aa+rgv+V +l+ +            d
  gi|336254257|ref|YP_004597364.1| 419 DNAEPRVADLIENADDEILVKQASidGEFALL-EAVLDAARRGVEVDILLDStwyhedenaavaD 482
                                       7888899************9765522345555.555588899********997776643322222 PP

>> FAM83  FAM83 A-H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.041   1.8e+02     106     175 ..     213     275 ..     166     311 .. 0.71
   2 ?   11.1   0.0   4.7e-05      0.21     149     261 ..     445     551 ..     395     556 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.041
                             FAM83 106 lkgvtrvtvytqppkekaphikevvrkliqkaqkviavvmdvftDvdilkdlleaaskrkvpvyilLdek 175
                                        ++v ++tv++ p+        +v r+++++a + + +  +++t   +  +l+ aa  r+v v +l ++ 
  gi|336254257|ref|YP_004597364.1| 213 STEVDDATVFVLPD------APDVPRETLREADERLLLAGYTVTSDAVADELVAAAE-RGVDVSVLFESG 275
                                       34445555555555......5577899999999999999999999999999998887.779999998765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.7e-05
                             FAM83 149 tDvdilkdlleaaskrkvpvyilLdeknlklf..lemceklq.vnkqhlknlrvRsvkGetyltrsgkkvkGqlkek 222
                                        +  +l+ +l+aa+ r+v v ilLd++  ++     ++++l+ v +++   l+vR   G++   r+      +++ k
  gi|336254257|ref|YP_004597364.1| 445 GEFALLEAVLDAAR-RGVEVDILLDSTWYHEDenAAVADRLErVAEEEGLPLEVRLADGTG---RFE-----KIHAK 512
                                       56778999999987.78*********9887650045556664256677779********98...555.....67899 PP

                             FAM83 223 fllvDgekvlsGsYsftWsssrlhrnlvtvltGqvvesF 261
                                        +++D e +++Gs  +   s r +r+++  l+G+++ ++
  gi|336254257|ref|YP_004597364.1| 513 GIVIDREVAVVGSANWNENSFRNNREVLLALHGDAAAEY 551
                                       9********************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 4528.34
//
Query:       gi|336254258|ref|YP_004597365.1|  [L=144]
Description: DtxR family iron (metal) dependent repressor [Halopiger xanaduensis SH-6]
Scores for 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-17   62.8   0.1    5.7e-17   61.7   0.1    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    1.5e-13   50.6   0.9    3.2e-13   49.6   0.5    1.7  2  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    0.00012   22.0   0.0    0.00018   21.4   0.0    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00014   21.7   0.0    0.00023   21.0   0.0    1.4  1  MarR            MarR family
    0.00017   21.4   0.0    0.00035   20.4   0.0    1.5  1  MarR_2          MarR family
    0.00031   20.7   0.0    0.00073   19.5   0.0    1.6  1  HTH_20          Helix-turn-helix domain
    0.00035   20.4   0.0    0.00058   19.7   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00088   18.8   0.0     0.0016   18.0   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0011   19.4   0.0     0.0021   18.5   0.0    1.5  1  HTH_27          Winged helix DNA-binding domain
     0.0037   17.6   0.0     0.0057   17.0   0.0    1.3  1  Rrf2            Transcriptional regulator
     0.0054   16.6   0.2      0.011   15.6   0.2    1.6  1  HTH_12          Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
      0.018   14.9   0.0       0.15   11.9   0.0    2.1  2  HTH_5           Bacterial regulatory protein, arsR family
      0.019   14.6   0.0      0.052   13.2   0.0    1.8  1  GntR            Bacterial regulatory proteins, gntR family
      0.072   12.3   0.1      0.084   12.1   0.1    1.1  1  DS              Deoxyhypusine synthase
        0.1   12.8   0.0       0.16   12.2   0.0    1.3  1  Rio2_N          Rio2, N-terminal
       0.11   12.5   0.0       0.23   11.4   0.0    1.7  1  HTH_11          HTH domain
       0.11   12.2   0.0       0.18   11.5   0.0    1.4  1  DUF4423         Domain of unknown function (DUF4423)


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 !   61.7   0.1   5.4e-20   5.7e-17       4      60 .]       2      59 ..       1      59 [. 0.97

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 5.4e-20
                                      HHHHHHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  4 estEdYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      +++++YL++IY ++  e ++++t  la  L+vsp+sV em+ kLe+  +ve+ekykg+
  gi|336254258|ref|YP_004597365.1|  2 NTADQYLKAIYLAQRmEDGPASTGTLADLLEVSPASVNEMIGKLEDRDLVEHEKYKGA 59
                                      6889****************************************************97 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 ?   -2.1   0.0       3.9   4.1e+03      22      41 ..      27      46 ..      26      47 .. 0.77
   2 !   49.6   0.5     3e-16   3.2e-13       1      64 [.      62     123 ..      62     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.9
                                      HHHHCT--CCCHHHHCCCCG CS
                     Fe_dep_repr_C 22 LvdvlgvdweeaheeAerlE 41
                                      L+d l+v++  + e   +lE
  gi|336254258|ref|YP_004597365.1| 27 LADLLEVSPASVNEMIGKLE 46
                                      67888899888888777666 PP

  == domain 2  score: 49.6 bits;  conditional E-value: 3e-16
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TT CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPh 64 
                                       Te+G e A ++++ + ++erfL++vl+v  ee  +eA +lE ++++ ++erld++++ peecP+
  gi|336254258|ref|YP_004597365.1|  62 TEEGLERAHDTLQTYCIIERFLTNVLEV--EEFRDEARALESVIDDTVAERLDTIIDRPEECPD 123
                                       9*************************99..9********************************7 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 !   21.4   0.0   1.7e-07   0.00018      21      55 ..      21      56 ..       8      69 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-07
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rgr 55
                                      p +   lA++l +++ +v+ ++++L+++ l++  ++
  gi|336254258|ref|YP_004597365.1| 21 PASTGTLADLLEVSPASVNEMIGKLEDRDLVEhEKY 56
                                      778889**************************5332 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.2e-07   0.00023      15      50 ..      19      54 ..      13      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.2e-07
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                       gp+s   La+ l+vs+++v +++ +Le+++l+e +
  gi|336254258|ref|YP_004597365.1| 19 DGPASTGTLADLLEVSPASVNEMIGKLEDRDLVEHE 54
                                      5899999**************************966 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.3e-07   0.00035      18      54 ..      19      54 ..      10      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.3e-07
                                      TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +g+  + g la+ l +s+++v+ ++ +L+++ Lve +
  gi|336254258|ref|YP_004597365.1| 19 DGP-ASTGTLADLLEVSPASVNEMIGKLEDRDLVEHE 54
                                      554.699***************************987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   6.9e-07   0.00073      20      58 ..      17      55 ..       6      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.9e-07
                                      STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 20 araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      +++++++ + la++l++s+++++  + +Le+ +Lve ++
  gi|336254258|ref|YP_004597365.1| 17 MEDGPASTGTLADLLEVSPASVNEMIGKLEDRDLVEHEK 55
                                      6899********************************875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   5.5e-07   0.00058      19      57 ..      18      56 ..      10      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.5e-07
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      + gpa++ ++a  l+v+ ++v+e++ +Led++lVe ek 
  gi|336254258|ref|YP_004597365.1| 18 EDGPASTGTLADLLEVSPASVNEMIGKLEDRDLVEHEKY 56
                                      789********************************9985 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 !   18.0   0.0   1.5e-06    0.0016      14      48 .]      18      52 ..      12      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                            HTH_24 14 knprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +++  s   LA+ l +Sp+ vn+ + +Le+  l++
  gi|336254258|ref|YP_004597365.1| 18 EDGPASTGTLADLLEVSPASVNEMIGKLEDRDLVE 52
                                      799999999**********************9986 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 !   18.5   0.0     2e-06    0.0021       7      67 ..       6      64 ..       2      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-06
                            HTH_27  7 lvLhlir....hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdk 67
                                      ++L  i+    +++++++   l++ l v+ +++ +++ kL+ ++Lve++++      k  +lT++
  gi|336254258|ref|YP_004597365.1|  6 QYLKAIYlaqrMEDGPASTGTLADLLEVSPASVNEMIGKLEDRDLVEHEKY------KGATLTEE 64
                                      56777777788999********************************66655......45555555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.4e-06    0.0057      15      59 ..      11      55 ..       5      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.4e-06
                                      HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      +yLa++ e++p+s+ ++a+  ++sp  +  ++ kL+  +lv+ ++
  gi|336254258|ref|YP_004597365.1| 11 IYLAQRMEDGPASTGTLADLLEVSPASVNEMIGKLEDRDLVEHEK 55
                                      79***************************************9876 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 !   15.6   0.2   1.1e-05     0.011      39      64 ..      42      67 ..      16      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                            HTH_12 39 LrkleergltrrvgyagreltEkGle 64
                                      + kle+r+l++   y g++ltE Gle
  gi|336254258|ref|YP_004597365.1| 42 IGKLEDRDLVEHEKYKGATLTEEGLE 67
                                      568*********************97 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 ?   11.9   0.0   0.00014      0.15      11      46 ..      17      52 ..       8      53 .. 0.92
   2 ?    0.5   0.0      0.54   5.7e+02      20      31 ..     130     141 ..     129     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                      HTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 11 LaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +++g+++ + la+ l++s++ v +   kL++ +LVe
  gi|336254258|ref|YP_004597365.1| 17 MEDGPASTGTLADLLEVSPASVNEMIGKLEDRDLVE 52
                                      456****************************99997 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.54
                                       HHHHHHTS-HHH CS
                             HTH_5  20 elaeelglsqst 31 
                                       ++++ l++s ++
  gi|336254258|ref|YP_004597365.1| 130 DCCDRLEVSDPA 141
                                       89*******996 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     5e-05     0.052      29      62 ..      26      59 ..      23      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5e-05
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR 29 eLaaefgVsrttvReALrrLeaeglverrqgrGt 62
                                       La+ ++Vs  +v+e + +Le ++lve ++ +G+
  gi|336254258|ref|YP_004597365.1| 26 TLADLLEVSPASVNEMIGKLEDRDLVEHEKYKGA 59
                                      69*************************9998886 PP

>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     8e-05     0.084      74     135 ..      41      99 ..      27     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8e-05
                                DS  74 likalgkktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwsp 135
                                       +i  l+++  ++++++++++L e+g++R +++l   + yc +e++++++l+  e +++ ++ 
  gi|336254258|ref|YP_004597365.1|  41 MIGKLEDRDLVEHEKYKGATLTEEGLERAHDTL---QTYCIIERFLTNVLEVEEFRDEARAL 99 
                                       56667777889999*****************98...68***********9876655554444 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.16      30      71 ..      27      66 ..       7      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                            Rio2_N 30 ieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGy 71
                                      ++ + +++  +v++ + +l +++l++++  ky+G  Lt eG+
  gi|336254258|ref|YP_004597365.1| 27 LADLLEVSPASVNEMIGKLEDRDLVEHE--KYKGATLTEEGL 66
                                      55566677889****************9..7*******9996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022      0.23      11      41 ..      17      47 ..       7      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                            HTH_11 11 eargpisgeeLAeeLnvSrrtvrrdIkaLee 41
                                       ++gp s  +LA+ L+vS + v   I +Le+
  gi|336254258|ref|YP_004597365.1| 17 MEDGPASTGTLADLLEVSPASVNEMIGKLED 47
                                      678899****************999999986 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.18      24      84 ..       9      67 ..       4      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                           DUF4423 24 pvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslt 84
                                       +i+   +++d+ a++ +la+ l   +s + v++ +  L++ +l++ ++ +    te+ l+
  gi|336254258|ref|YP_004597365.1|  9 KAIYLAQRMEDGPASTGTLADLLE--VSPASVNEMIGKLEDRDLVEHEKYKGATLTEEGLE 67
                                      5677777899999***********..********************999888777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1162.17
//
Query:       gi|336254259|ref|YP_004597366.1|  [L=164]
Description: tumor suppressor TSBF1-like protein [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0022   17.7   7.8     0.0034   17.1   7.1    1.7  2  YkyA         Putative cell-wall binding lipoprotein
  ------ inclusion threshold ------
        0.1   12.9   5.0       0.25   11.6   2.2    2.3  2  DUF4226      Domain of unknown function (DUF4226)
       0.21   11.6   1.3        1.2    9.2   0.2    2.6  3  hnRNP_Q_AcD  Heterogeneous nuclear ribonucleoprotein Q acidic
       0.33    9.4   1.5       0.34    9.4   1.5    1.1  1  FUSC         Fusaric acid resistance protein family
       0.41   11.1   4.7        1.3    9.4   1.6    2.2  2  DUF1690      Protein of Unknown function (DUF1690)
        1.9    8.8   6.1          4    7.8   0.8    2.1  2  Cdh1_DBD_1   Chromodomain helicase DNA-binding domain 1


Domain annotation for each model (and alignments):
>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   7.1   1.1e-06    0.0034      83     182 ..      42     151 ..      23     155 .. 0.82
   2 !    5.8   0.7    0.0032       9.7      75     113 ..     122     163 ..     121     164 .] 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                              YkyA  83 efekikeeieei......edeelkkeaeelieameeryeaydklyk....aYkealeldkeLYemLkkeeltleele 149
                                       e  +++e +ee+      e  + ++ +e+li+ ++  + ay+++++    +Y    ++d  LY++L +ee+ ++  +
  gi|336254259|ref|YP_004597366.1|  42 ERAEVDEAVEELlveaseESADHRERLEALIDDLDAETVAYEEINAlvdaQYGPPEDTDGVLYDQLANEETAYKFYD 118
                                       44556666666666656555588999******999999999998862222566666********************* PP

                              YkyA 150 eqiekiNesyeevkeaneqFneatkkyneekke 182
                                       + ie+i  s+ e+    eq+ e +  + ee ke
  gi|336254259|ref|YP_004597366.1| 119 DLIEAIESSDAEFAIDREQLLETLYDIREEEKE 151
                                       *********************999999998876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0032
                              YkyA  75 esieeakeefekikeeieei...edeelkkeaeelieameer 113
                                       e+ie++  ef   +e++ e+     ee k+ +ee+ e+me r
  gi|336254259|ref|YP_004597366.1| 122 EAIESSDAEFAIDREQLLETlydIREEEKEGVEEVTEIMEHR 163
                                       678888888887776654444542455799999999999988 PP

>> DUF4226  Domain of unknown function (DUF4226)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.2   8.5e-05      0.25      23      58 ..      43      78 ..      18      94 .. 0.83
   2 ?    1.9   0.0     0.087   2.6e+02      25      57 ..     115     147 ..      97     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.5e-05
                           DUF4226 23 taelDrqlaevlrsahakaaegrrrLdalqaeidqa 58
                                       ae+D++++e l +a +++a+ r+rL+al  ++d+ 
  gi|336254259|ref|YP_004597366.1| 43 RAEVDEAVEELLVEASEESADHRERLEALIDDLDAE 78
                                      579**************************9998865 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.087
                           DUF4226  25 elDrqlaevlrsahakaaegrrrLdalqaeidq 57 
                                       ++ ++l+e++ s +a+ a +r++L +   +i++
  gi|336254259|ref|YP_004597366.1| 115 KFYDDLIEAIESSDAEFAIDREQLLETLYDIRE 147
                                       555677788888888877777777766666654 PP

>> hnRNP_Q_AcD  Heterogeneous nuclear ribonucleoprotein Q acidic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2   0.00039       1.2       8      39 ..      11      42 ..       2      52 .. 0.88
   2 ?    0.2   0.1      0.25   7.6e+02      21      40 ..      43      62 ..      40      64 .. 0.85
   3 ?   -0.8   0.0      0.52   1.5e+03       8      33 ..      83     108 ..      77     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00039
                       hnRNP_Q_AcD  8 ekLdelfrsgkltasdlDeraleaLkslpeeg 39
                                      ++L +l++ g++ ++ +++ra   L+slp e+
  gi|336254259|ref|YP_004597366.1| 11 HQLARLLQIGVVLEEVVESRAAHHLESLPAEE 42
                                      79***************************986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.25
                       hnRNP_Q_AcD 21 asdlDeraleaLkslpeegA 40
                                      ++++De++ e L + +ee A
  gi|336254259|ref|YP_004597366.1| 43 RAEVDEAVEELLVEASEESA 62
                                      67999999999999999887 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.52
                       hnRNP_Q_AcD   8 ekLdelfrsgkltasdlDeraleaLk 33 
                                       e+ ++l+++ +  ++d D ++ ++L 
  gi|336254259|ref|YP_004597366.1|  83 EEINALVDAQYGPPEDTDGVLYDQLA 108
                                       56778888888888888888877775 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.5   0.00011      0.34     237     325 ..      30      89 ..       3     153 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00011
                              FUSC 237 slarllarlraeeaaavpe.laallaelaaleaaaaaealeaalaalrarlralrraleadadtaalllarlaella 312
                                         a++l+ l+aee+a+v+e +++ll e+ +                              +++ +++ l++l ++l+
  gi|336254259|ref|YP_004597366.1|  30 RAAHHLESLPAEERAEVDEaVEELLVEASE------------------------------ESADHRERLEALIDDLD 76 
                                       334444444444444444444444444444..............................44444444444444444 PP

                              FUSC 313 elaqllaslrale 325
                                       + + ++++++al 
  gi|336254259|ref|YP_004597366.1|  77 AETVAYEEINALV 89 
                                       4444444444443 PP

>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.6   0.00044       1.3      31      90 ..      23      77 ..       6      93 .. 0.74
   2 ?    2.7   0.1     0.053   1.6e+02       3      34 ..     110     142 ..     107     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00044
                           DUF1690 31 lekliqerVaeeLkkLraeeeetlkkfeeklekellkdeadakdelsskalnekieeLrk 90
                                      le+++++r a+ L+ L    +e +++++e++e+ l + +  +++  ++++l+  i++L +
  gi|336254259|ref|YP_004597366.1| 23 LEEVVESRAAHHLESL---PAEERAEVDEAVEELLVEAS--EESADHRERLEALIDDLDA 77
                                      89**************...66666666666666666655..4555666666666666654 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.053
                           DUF1690   3 petpiqfSqslvsqLessketda.sraqalekl 34 
                                       +et  +f ++l++ +ess+ + a  r+q le l
  gi|336254259|ref|YP_004597366.1| 110 EETAYKFYDDLIEAIESSDAEFAiDREQLLETL 142
                                       577788899999999988766554788888764 PP

>> Cdh1_DBD_1  Chromodomain helicase DNA-binding domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.8    0.0013         4      31      79 ..      37      85 ..      16      99 .. 0.88
   2 ?    4.1   0.5     0.018        53      29      81 ..     100     154 ..      97     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0013
                        Cdh1_DBD_1 31 tLPeknielleelyeelleeakklvkeeeekrakeleeleadaeeykek 79
                                      +LP+ +   ++e+ eell ea+++ +++ e+ +  +++l+a+  +y+e 
  gi|336254259|ref|YP_004597366.1| 37 SLPAEERAEVDEAVEELLVEASEESADHRERLEALIDDLDAETVAYEEI 85
                                      89**99******************99999999999****9999888765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.018
                        Cdh1_DBD_1  29 dGtLPe..knielleelyeelleeakklvkeeeekrakeleeleadaeeykeklk 81 
                                       dG+L     n e+  + y++l+e  +++ +e    r++ le l    ee+ke ++
  gi|336254259|ref|YP_004597366.1| 100 DGVLYDqlANEETAYKFYDDLIEAIESSDAEFAIDREQLLETLYDIREEEKEGVE 154
                                       5666542346788899*******99999999999999999999887777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1417  (0.079034); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); 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):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1291.34
//
Query:       gi|336254260|ref|YP_004597367.1|  [L=404]
Description: SufBD protein [Halopiger xanaduensis SH-6]
Scores for 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-63  213.7   2.0      3e-63  213.4   2.0    1.1  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 !  213.4   2.0   1.7e-67     3e-63       3     218 .]     151     375 ..     149     375 .. 0.96

  Alignments for each domain:
  == domain 1  score: 213.4 bits;  conditional E-value: 1.7e-67
                           UPF0051   3 fertlivveegaevtiieey..agc........gvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelt 69 
                                       f++tl+v+ee ++vti+e+              g+ve+++gen++++y ++qn se+a+n++ kr + +  a+++++
  gi|336254260|ref|YP_004597367.1| 151 FNYTLVVAEESSSVTILERQstG-AeqdeqyysGIVEVVAGENSNVQYGSLQNLSEEAYNFALKRGDADTYATIDWI 226
                                       789**************999750.245666777******************************************** PP

                           UPF0051  70 tvslggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrk 146
                                       +v+lg +lt + +s+el+g+ ae+++ g+++++++qh+d++ kv h++++t+++++++gv +d ar+v++g  +v k
  gi|336254260|ref|YP_004597367.1| 227 EVNLGTQLTKSGVSTELNGDSAETQIVGAFYGHNDQHFDLDAKVWHRAEHTTADLVTRGVTDDVARSVYEGVQDVGK 303
                                       ***************************************************************************** PP

                           UPF0051 147 gaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                       +a  t+++q++++L+lsd+++ad+ P+l i+++d +asH AtvG+id e l Y+ sRG++e+ A++++v+gf
  gi|336254260|ref|YP_004597367.1| 304 DAWDTSSYQRENTLMLSDESEADASPKLIINNHDTEASHSATVGQIDREDLLYMTSRGIDERSATNMLVQGF 375
                                       ***********************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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 0.21s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3258.99
//
Query:       gi|336254261|ref|YP_004597368.1|  [L=476]
Description: FeS assembly protein SufB [Halopiger xanaduensis SH-6]
Scores for 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-70  237.9   0.4    1.4e-70  237.4   0.4    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 !  237.4   0.4   7.5e-75   1.4e-70       2     218 .]     222     447 ..     221     447 .. 0.97

  Alignments for each domain:
  == domain 1  score: 237.4 bits;  conditional E-value: 7.5e-75
                           UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakl 66 
                                       qfe+tli++eeg+ev++i   +gc            g ve+fvge+A+++y++vqnws++++nl+tkra +++  ++
  gi|336254261|ref|YP_004597368.1| 222 QFEHTLIIAEEGSEVHYI---EGCsapkygthnlhsGGVEVFVGEDAHVQYSTVQNWSKNTFNLNTKRAIVESGGTM 295
                                       89****************...666666666666777*********************************999999** PP

                           UPF0051  67 elttvslggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkik 143
                                       e++++s+g+k t+ +p + lkg+ga+ +  ++++a+++q +dt+ kv hn+p+tss+i sk+++kd++r+ +rg ++
  gi|336254261|ref|YP_004597368.1| 296 EWVSGSMGSKATMLYPCSILKGRGATDTHITIAFAGEGQDIDTGAKVYHNAPETSSTIESKSISKDGGRTNYRGLVH 372
                                       ***************************************************************************** PP

                           UPF0051 144 vrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                       ++ ga+++++ +e+++L++++++++dt+P++ei++ +v + H+AtvGki +e +fYL+sRGl+ ++A+++iv gf
  gi|336254261|ref|YP_004597368.1| 373 IADGAENSSTAVECDALMFDNESTSDTMPYMEIEESKVDVAHEATVGKIGDEDIFYLQSRGLDDDDAKKMIVAGF 447
                                       **************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.52u 0.20s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3779.74
//
Query:       gi|336254262|ref|YP_004597369.1|  [L=301]
Description: FeS assembly ATPase SufC [Halopiger xanaduensis SH-6]
Scores for complete 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-15   58.1   0.1    5.1e-15   56.2   0.1    1.8  1  ABC_tran  ABC transporter
    4.1e-06   26.4   0.3      0.029   13.8   0.1    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain
    0.00017   22.0   0.1       0.17   12.3   0.0    2.3  2  AAA       ATPase family associated with various cellular acti
     0.0002   21.3   0.5       0.16   11.7   0.1    2.3  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0028   17.7   0.6        2.3    8.2   0.0    2.6  2  AAA_5     AAA domain (dynein-related subfamily)
     0.0035   17.0   0.0     0.0066   16.2   0.0    1.4  1  AAA_29    P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.039   14.2   0.1       0.92    9.8   0.0    2.3  2  AAA_22    AAA domain
      0.065   13.1   0.0       0.11   12.4   0.0    1.3  1  Rad17     Rad17 P-loop domain
      0.092   12.9   0.0       0.15   12.2   0.0    1.4  1  AAA_33    AAA domain
       0.13   12.8   0.4       0.39   11.3   0.1    2.1  2  AAA_18    AAA domain
       0.13   12.0   0.0       0.21   11.4   0.0    1.3  1  Sortase   Sortase domain
       0.15   11.7   1.2       0.51   10.0   0.0    1.9  2  AAA_15    AAA ATPase domain
       0.16   12.5   6.2       0.33   11.4   0.0    2.3  2  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 !   56.2   0.1   3.7e-18   5.1e-15       1     134 [.      21     219 ..      21     222 .. 0.68

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 3.7e-18
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEE..........................EETTCEG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx..........................xxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGei..........................lldgkdl 49 
                                       l+ v+l+++ ge++a++G+nG+GKSt +k++ag+     t Ge+                          l      
  gi|336254262|ref|YP_004597369.1|  21 LEGVDLEVQSGEIHALMGPNGSGKSTTAKVIAGHPAYeiTDGEVllhleenefgdeieidedqrtwdlldL------ 91 
                                       6789*****************************9666669****776666666665544444443333330...... PP

                                       GGB-HHHCCHCEEEE-SS--S-TTSBHHHH............................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
                          ABC_tran  50 keqeleslrkeigvlpqepqlfpeltvren............................................... 79 
                                         ++ e++   i   +q p   +++t+ +                                                
  gi|336254262|ref|YP_004597369.1|  92 --EPNERAALGIFLGFQYPAEIEGVTMTNFlrtalnakieereelfeeeegeeeeadegfetspmegdvdegevgva 166
                                       ..334444444444444444444444333366666666666666666666666688888888888777776666655 PP

                                       HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                       e ++ +++ +++l+++e  +  +++  + +SgG+k+  ++ +a + +p++ +lDE
  gi|336254262|ref|YP_004597369.1| 167 EFQQILQEKMEQLDMDE--KFAQRYLNAGFSGGEKKQNEVLQAAILEPSIAVLDE 219
                                       55555666777777666..33334456***************************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 !   10.9   0.0   0.00016      0.23      25      41 ..      32      48 ..      21      52 .. 0.80
   2 !   13.8   0.1   2.1e-05     0.029     117     202 ..     175     257 ..      98     272 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                                      SEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnll 41
                                      ++ a++GpNGSGKs   
  gi|336254262|ref|YP_004597369.1| 32 EIHALMGPNGSGKSTTA 48
                                      5889**********765 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.1e-05
                                       EE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                             SMC_N 117 evtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQ 191
                                       ++++ ++ e +++  ++   +SgGek+   + L  Ai +    ++ +lDeid+ LD  + + v+e +++ +++  + 
  gi|336254262|ref|YP_004597369.1| 175 KMEQLDMDEKFAQRYLNA-GFSGGEKKQNEV-LQAAILE---PSIAVLDEIDSGLDIDRLQDVSEGINALRDEqgTG 246
                                       444444444444444444.589999887665.4445554...4689*********************9777553366 PP

                                       EEEE-SSHHHC CS
                                       xxxxxxxxxxx RF
                             SMC_N 192 fivislreeml 202
                                       ++ i++ +++l
  gi|336254262|ref|YP_004597369.1| 247 ILQITHYQRIL 257
                                       77777766655 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   0.0   0.00012      0.17       3      21 ..      36      54 ..      34      84 .. 0.85
   2 !    7.5   0.1    0.0039       5.4      36      74 ..     191     227 ..     166     243 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                      EESSTTSSHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavake 21
                                      l+Gp G GK+++ak +a +
  gi|336254262|ref|YP_004597369.1| 36 LMGPNGSGKSTTAKVIAGH 54
                                      89**************987 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0039
                                       SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                               AAA  36 skyvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                       +  ++ +ekk +e++++a   + psi ++DEid+    +
  gi|336254262|ref|YP_004597369.1| 191 NAGFSGGEKKQNEVLQAA-ILE-PSIAVLDEIDSGLDID 227
                                       447778899999999986.444.9*********976655 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 !   11.7   0.1   0.00012      0.16       2      21 ..      34      53 ..      33      84 .. 0.78
   2 !    7.9   0.1    0.0017       2.4     252     299 ..     209     254 ..     116     258 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                            AAA_21  2 nvliGpNgsGKSnLLdaldl 21
                                       +l GpNgsGKS+  + + +
  gi|336254262|ref|YP_004597369.1| 34 HALMGPNGSGKSTTAKVIAG 53
                                      6899*********9998865 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0017
                            AAA_21 252 lralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                       +  +   s+ ++DE+++gL+  +l  + e +++l++  g+ ++  TH  
  gi|336254262|ref|YP_004597369.1| 209 ILEP---SIAVLDEIDSGLDIDRLQDVSEGINALRDeQGTGILQITHYQ 254
                                       3333...9*************9999888777666666567777777755 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 !    7.4   0.1    0.0029         4       4      22 ..      36      54 ..      34     153 .. 0.82
   2 !    8.2   0.0    0.0017       2.3      43      76 ..     187     222 ..     165     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0029
                                      EE--SSSSHHHHHHHGGGG CS
                             AAA_5  4 LvGppGtgKselaerlaaa 22
                                      L Gp G+gKs+ a+ +a  
  gi|336254262|ref|YP_004597369.1| 36 LMGPNGSGKSTTAKVIAGH 54
                                      89***********999865 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0017
                                       --B--...........--------G-SEEEEESGGG CS
                             AAA_5  43 grreik..ngttslvdsplvraaregeilvlDEver 76 
                                       +r+  +  +g+++ ++ +l  a+ e++i+vlDE++ 
  gi|336254262|ref|YP_004597369.1| 187 QRYLNAgfSGGEKKQNEVLQAAILEPSIAVLDEIDS 222
                                       333333566999999999999999**********95 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 !   16.2   0.0   4.8e-06    0.0066      14      37 ..      23      46 ..      17      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.8e-06
                            AAA_29 14 ghtieidlkgatlltGpsGsGKST 37
                                      g ++e++  +++ l+Gp+GsGKST
  gi|336254262|ref|YP_004597369.1| 23 GVDLEVQSGEIHALMGPNGSGKST 46
                                      5677888666*************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00067      0.92       6      25 ..      32      51 ..      27      80 .. 0.86
   2 ?    2.3   0.1      0.14   1.9e+02      84     117 ..     202     241 ..     130     259 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00067
                            AAA_22  6 gilvvtGesGtGKTtllrrl 25
                                       i +++G+ G+GK+t+++ +
  gi|336254262|ref|YP_004597369.1| 32 EIHALMGPNGSGKSTTAKVI 51
                                      67789***********9855 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                            AAA_22  84 qalrarav..ielliiDEaqh.lr..s.eealeeLrslln 117
                                       + + ++a   +++ ++DE++  l+  + +++ e +  l +
  gi|336254262|ref|YP_004597369.1| 202 NEVLQAAIlePSIAVLDEIDSgLDidRlQDVSEGINALRD 241
                                       444444446788999*****99965424333333333333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     8e-05      0.11      33      74 ..      19      60 ..       9      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8e-05
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklr 74
                                      + l+   Le +  +i  + GP G gkst+ kv++   ++++ 
  gi|336254262|ref|YP_004597369.1| 19 KILEGVDLEVQSGEIHALMGPNGSGKSTTAKVIAGHPAYEIT 60
                                      56777789999999******************9987777665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.15       4      51 ..      36      91 ..      33     106 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                            AAA_33  4 lvGlpGsGKstlaerllkklg........avllssdtlrrrlfgtdqqsktdytrv 51
                                      l G++GsGKst a+ ++ + +          +l+++++ + ++ +++q+++d+ ++
  gi|336254262|ref|YP_004597369.1| 36 LMGPNGSGKSTTAKVIAGHPAyeitdgevLLHLEENEFGDEIEIDEDQRTWDLLDL 91
                                      78************999777744444444444555555555555555555555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00028      0.39       3      25 ..      36      62 ..      35     149 .. 0.76
   2 ?   -0.6   0.1       1.3   1.9e+03      55      55 ..     184     184 ..     115     275 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf....g 25
                                      l+G+ G+GK+t ak ++ + ++    g
  gi|336254262|ref|YP_004597369.1| 36 LMGPNGSGKSTTAKVIAGHPAYeitdG 62
                                      89*************987744444441 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                            AAA_18  55 d 55 
                                       +
  gi|336254262|ref|YP_004597369.1| 184 K 184
                                       0 PP

>> Sortase  Sortase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.21      12      76 ..      20      88 ..       7     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                      EEESCSSCHCTTSEEECSTT-BTTSSS.EEEEEEE...BSSTTSTTGGGGGGHTT-EEEEEESSSEEEE CS
                           Sortase 12 vlegtdeedlkagagfldesakpgeag.nfvlaGH...rvgkgavFsdLkklekgdaivvetkkgksyv 76
                                      +leg+d e+   ++  l + +  g+++   v+aGH   + ++g+v  +L++ e gd+i +++++ +++ 
  gi|336254262|ref|YP_004597369.1| 20 ILEGVDLEVQSGEIHALMGPNGSGKSTtAKVIAGHpayEITDGEVLLHLEENEFGDEIEIDEDQRTWDL 88
                                      555555555555555555566678877799*****776599*********************8887765 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   0.0   0.00037      0.51      20      43 ..      27      51 ..      19      86 .. 0.83
   2 ?   -0.2   0.8      0.46   6.3e+02     184     228 ..     153     212 ..     105     250 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                            AAA_15 20 dlsee.ltvliGkNnsGKSsileal 43
                                      ++++  +  l G+N+sGKS+ ++++
  gi|336254262|ref|YP_004597369.1| 27 EVQSGeIHALMGPNGSGKSTTAKVI 51
                                      444444889************9998 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.46
                            AAA_15 184 e.............elknvlksaiiklllis..akRnvsdedsekkssllgklkekilee 228
                                                     e++++l++++++l+ ++  a+R  +  +s  +++  + l+  ile+
  gi|336254262|ref|YP_004597369.1| 153 PmegdvdegevgvaEFQQILQEKMEQLDMDEkfAQRYLNAGFSGGEKKQNEVLQAAILEP 212
                                       023333333344444555555555555554433455555555555555555555555554 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   0.00024      0.33      18      37 ..      30      49 ..       4      53 .. 0.80
   2 ?    0.7   4.6      0.47   6.5e+02     124     190 ..      78     170 ..      56     243 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                            AAA_23 18 skgltlItGpNGaGKTTild 37
                                      s  + ++ GpNG+GK+T   
  gi|336254262|ref|YP_004597369.1| 30 SGEIHALMGPNGSGKSTTAK 49
                                      55678899*********765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.47
                            AAA_23 124 llgskkiilnlilflgqer......................feefelkdkkerleelekeleeledekk.llekl.. 175
                                       +++ +++  +l+++ + er                      f + +l++k e+ eel +e e +e+e++  +e+   
  gi|336254262|ref|YP_004597369.1|  78 EIDEDQRTWDLLDLEPNERaalgiflgfqypaeiegvtmtnFLRTALNAKIEEREELFEEEEGEEEEADeGFETSpm 154
                                       34444444455555555555555555544444444555333222222333333333333322222222212333344 PP

                            AAA_23 176 ..............eqekekekeleelee 190
                                                     +             +
  gi|336254262|ref|YP_004597369.1| 155 egdvdegevgvaefQ-------------Q 170
                                       433333333333221.............2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2128.22
//
Query:       gi|336254263|ref|YP_004597370.1|  [L=912]
Description: DNA polymerase B region [Halopiger xanaduensis SH-6]
Scores for 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-48  163.0   0.0    1.7e-47  162.2   0.0    1.3  1  DNA_pol_B       DNA polymerase family B
      1e-28  100.5   0.0    1.8e-28   99.7   0.0    1.4  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
     0.0079   15.1   0.0      0.088   11.6   0.0    2.1  2  DNA_pol_B_2     DNA polymerase type B, organellar and viral


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 !  162.2   0.0   2.8e-51   1.7e-47      27     380 ..     463     794 ..     451     810 .. 0.82

  Alignments for each domain:
  == domain 1  score: 162.2 bits;  conditional E-value: 2.8e-51
                                       TBE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE-HCCHCCT--BTT...TE CS
                         DNA_pol_B  27 gfilpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlvaseeeakeleaedeylev 103
                                       +f lp ++ +++  e +Y+G+ V+eP++g+ +++v+vlD +SLYP  +   N +++t v  +e + e          
  gi|336254263|ref|YP_004597370.1| 463 RFALP-SKGQQEAGE-EYEGGAVFEPITGV-KENVTVLDLKSLYPMCMTTINASPETKVDPDEYDGET------YVA 530
                                       35566.666644444.7************8.678***********************99888775532......234 PP

                                       EE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HH..HHHHHHHHHHHHHHHHHHHHHHHTSTTSTT- CS
                         DNA_pol_B 104 eveprlvefvkksvregllpklLkdllakRkaikkelkeekdef..ekalldkqQlalKvtaNsvYGftGvansrlp 178
                                        v+++  +f   ++  g++ +++++lla+R++ kkel++e ++   e +++d qQ a+Kv++Ns+YG+ G ++ rl+
  gi|336254263|ref|YP_004597370.1| 531 PVGDDEIHF--RKEPDGVMREMITELLAEREE-KKELRNEYEPGspEYEQYDRQQGAVKVIMNSLYGVSGWEQFRLY 604
                                       566665555..77889**************98.667776666643499***************************** PP

                                       -HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-.SSHHHHHHHHHHHHH CS
                         DNA_pol_B 179 clalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkv.kdveellkigkelae 254
                                        ++ A+ +T++GRe++e t++  ++                  +++v YGDTDSv++el+   + e +l++  e++e
  gi|336254263|ref|YP_004597370.1| 605 DKEAASAITATGREVIEFTETAANEL-----------------DYEVTYGDTDSVMLELGPgVSKEVALETSFEIEE 664
                                       *********************99977.................9***************866999999999999999 PP

                                       HHHT...TS........TTT--EEEEEEEEEEEEE.ETTEEEEEEEEES.STTSEEEEESSGGGSTTS-HHHHHHHH CS
                         DNA_pol_B 255 evsek..lf........kkplklefekvykkllLi.sKKkYaglkvekt.skanklliKGvdlvRrdncklvkevik 319
                                       +++ +   f         + +++efek y +     +KK+Yag ++ k+ ++ n ++i G +  R d ++++kev +
  gi|336254263|ref|YP_004597370.1| 665 HINGRydDFaredlnaeAHRFQIEFEKLYRRFFQAgKKKRYAGHITWKEgKDVNDIDIVGFEYQRSDIAPITKEVQH 741
                                       998631111111111224579**********997725678***776554055567********************** PP

                                       HHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCC CS
                         DNA_pol_B 320 kvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenykskn 380
                                       +v+e+++++     ++e + e+++ ++    e++ +++v+le+  +   + k  +ny++ +
  gi|336254263|ref|YP_004597370.1| 742 RVIEMIVRE----GDIEGAKEYVNGVI----EDVLAGEVSLEEIAIPGGIGKRLDNYDTDT 794
                                       *********....99999999999999....999999999999999999999999996654 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 !   99.7   0.0     3e-32   1.8e-28       4     337 .]      86     380 ..      83     380 .. 0.75

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 3e-32
                                       TTSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTC CS
                    DNA_pol_B_exo1   4 egksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpn 80 
                                       +++   v+v+gf+pyfY+ +++ +++   +e+ ++l++++   ++    ++    +s+ g +     ++k++ ++p+
  gi|336254263|ref|YP_004597370.1|  86 DDELEHVQVVGFRPYFYAPTETLERP--PEEQYERLTGSEE--YD----EDGEHYESIRGEK-----LTKIFGQTPR 149
                                       66667799*************66666..3333333333332..33....3433444555544.....56******** PP

                                       HHHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCEETTTCCS CS
                    DNA_pol_B_exo1  81 elkkirkelspleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddliakpkesep 157
                                       ++ k+r+ +       + ye+d+ +  rflid++++++  ++v+      e+++     ++ + +d++++++  +++
  gi|336254263|ref|YP_004597370.1| 150 DVGKVRDDF-------EHYEADILFPNRFLIDKDVRSG--IRVP------ERRAEDD--SLVVPHDEVESVD--ADA 207
                                       ********9.......48********************..8888......4444443..3445556666654..559 PP

                                       -EEEEEEEEEETEETTSEETTTT..--EEEEEEEE.CCTC.SS.SEE...EEEEECCCTSS----EE--SSTCSTTE CS
                    DNA_pol_B_exo1 158 plrvlsFDIeckskkgkfpdaensedpiiqIscvl.dglgekepear...klftlrecaseeeedfeltpkpeypgv 230
                                       ++rv  FDIe++ ++g fp+  +  +pi+  ++++ d++    +e +   +  +++  ++   e  e++p +   + 
  gi|336254263|ref|YP_004597370.1| 208 NPRVNTFDIEVDDRQG-FPEDGE--EPIV--CLTShDSYR---DEYImwlYEAPIGDGEI-PTEITEYEPIEGAIDH 275
                                       999999**********.******..9996..556645555...22223556666666663.3444778887777889 PP

                                       EEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTCEECCCCESEEEEEEC CS
                    DNA_pol_B_exo1 231 kvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrlnkggrskvseigfskqare 307
                                       +v ++++E ++L +fl ++ + dPdv+tg+N ++FD pY l+R++el+ +  +    ln   +s v+e+  s  + +
  gi|336254263|ref|YP_004597370.1| 276 EVRSYEEEEAMLDDFLAYVEETDPDVLTGWNFEDFDAPYFLDRLEELQGPHHEYD--LNIDRLSRVDEVWRS--NWG 348
                                       ************************************************9777663..344445555555555..666 PP

                                       EEEETTSEEEEHHHHHHHHSSSS..G-SHHHH CS
                    DNA_pol_B_exo1 308 kvkisgrihlDlyrvvkrklklp..sYkLnav 337
                                          ++gri++Dl+  ++r + ++  sY L+av
  gi|336254263|ref|YP_004597370.1| 349 GPDVKGRIVFDLLYGYQRMVFSEldSYRLDAV 380
                                       999***************9766666*****98 PP

>> DNA_pol_B_2  DNA polymerase type B, organellar and viral
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   1.5e-05     0.088     211     245 ..     476     509 ..     464     521 .. 0.86
   2 ?    0.7   0.0      0.03   1.8e+02     373     383 ..     584     594 ..     574     601 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.5e-05
                       DNA_pol_B_2 211 kayrGGrc.ypsvlgiyeeniyvyDvnSlYPsamth 245
                                       + y GG + +p+ +g ++en+ v D +SlYP +mt 
  gi|336254263|ref|YP_004597370.1| 476 EEYEGGAVfEPI-TG-VKENVTVLDLKSLYPMCMTT 509
                                       5699****8888.44.67****************96 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.03
                       DNA_pol_B_2 373 iaKlllNsLYG 383
                                         K ++NsLYG
  gi|336254263|ref|YP_004597370.1| 584 AVKVIMNSLYG 594
                                       57********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (912 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.43
# Mc/sec: 6315.31
//
Query:       gi|336254264|ref|YP_004597371.1|  [L=49]
Description: hypothetical protein Halxa_2876 [Halopiger xanaduensis SH-6]
Scores for 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  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); 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: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 396.83
//
Query:       gi|336254265|ref|YP_004597372.1|  [L=238]
Description: hypothetical protein Halxa_2877 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.057   13.1   0.0      0.077   12.6   0.0    1.1  1  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.3e-06     0.077       9      61 ..     121     174 ..     112     193 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.3e-06
                           DUF4131   9 llalllllllllllllrr..rprrrvllllllllllallgfalrapqpnandlsq 61 
                                       + a+ll++ l llll  +  ++rr  +ll++ l+l+++++  +ra++++ ++ + 
  gi|336254265|ref|YP_004597372.1| 121 INAALLAVSLGLLLLV-FegATRRGGALLAGGLILFGFAVRRYRAYRRSDERADA 174
                                       2233333333333322.24588888888888888888888888888887766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 1891.05
//
Query:       gi|336254266|ref|YP_004597373.1|  [L=168]
Description: hypothetical protein Halxa_2878 [Halopiger xanaduensis SH-6]
Scores for 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:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1371.48
//
Query:       gi|336254267|ref|YP_004597374.1|  [L=894]
Description: DNA double-strand break repair rad50 ATPase [Halopiger xanaduensis SH-6]
Scores for 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   80.2   5.4    2.9e-22   80.2   5.4    7.5  1  AAA_23           AAA domain
      2e-17   64.0   0.0    3.6e-11   43.4   0.0    3.5  2  AAA_15           AAA ATPase domain
    2.3e-12   46.4  63.0    4.7e-08   32.2   4.3    5.1  5  AAA_13           AAA domain
    2.4e-10   40.3  52.7    4.7e-09   36.0  52.7    2.5  1  SMC_N            RecF/RecN/SMC N terminal domain
    1.5e-08   33.9 111.1     0.0029   16.6   0.8    6.0  6  Spc7             Spc7 kinetochore protein
    1.5e-06   27.5  73.3    0.00023   20.4  10.6    5.2  5  Atg14            Vacuolar sorting 38 and autophagy-related su
    1.7e-06   28.1   3.9     0.0019   18.0   5.6    4.2  3  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.3e-05   24.9   0.0    2.5e-05   23.9   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
    0.00017   21.7  58.6     0.0051   16.8   5.0    6.6  6  Laminin_II       Laminin Domain II
     0.0002   20.3   0.6      0.056   12.2   0.1    2.6  2  ABC_ATPase       Predicted ATPase of the ABC class
    0.00024   20.8   0.0    0.00024   20.8   0.0    6.2  8  AAA_27           AAA domain
    0.00067   20.2  24.4    0.00067   20.2  24.4    8.7  5  APG6_N           Apg6 coiled-coil region
     0.0064   16.5   6.4     0.0064   16.5   6.4    6.8  6  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
     0.0064   16.8   1.4     0.0064   16.8   1.4    6.6  6  zf-C4H2          Zinc finger-containing protein
      0.007   16.1  12.0      0.007   16.1  12.0    7.1  6  Laminin_I        Laminin Domain I
  ------ inclusion threshold ------
      0.014   15.4  50.9      0.027   14.5   2.3    7.0  7  DUF1664          Protein of unknown function (DUF1664)
      0.018   12.6 112.0      0.041   11.4  24.3    4.5  5  DUF3584          Protein of unknown function (DUF3584)
       0.02   14.5  52.6      0.031   13.9   6.1    4.4  2  Exonuc_VII_L     Exonuclease VII, large subunit
      0.025   14.3   0.3       0.16   11.6   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.04   14.0 113.7      0.062   13.4  11.6    7.5  8  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.048   13.9   0.5      0.048   13.9   0.5    7.8  8  FliJ             Flagellar FliJ protein
       0.11   12.7   0.0       0.11   12.7   0.0    4.3  3  AAA_33           AAA domain
       0.12   13.2   5.7         11    6.8   0.1    3.9  3  FIVAR            FIVAR domain
       0.14   12.0   0.0       0.14   12.0   0.0    3.1  4  MukB             MukB N-terminal
       0.14   12.1   0.0       0.14   12.1   0.0    2.2  2  NACHT            NACHT domain
       0.68    9.8  97.3      0.011   15.7  19.7    4.5  5  CEP63            Centrosomal protein of 63 kDa
        1.4    8.9   6.4       0.17   11.9   0.4    2.4  2  RepA_C           Plasmid encoded RepA protein
        2.7    7.3  94.5        1.1    8.6  16.1    4.7  4  DUF4407          Domain of unknown function (DUF4407)
        3.6    7.8   0.0        3.6    7.8   0.0    5.1  3  YhzD             YhzD-like protein
          8    5.8  95.6       0.64    9.3   4.9    6.1  6  GAS              Growth-arrest specific micro-tubule binding
        9.3    4.7  66.0       0.13   10.8   0.8    5.9  5  FapA             Flagellar Assembly Protein A


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 !   80.2   5.4     5e-25   2.9e-22       1     197 [.       5     273 ..       5     276 .. 0.56

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 5e-25
                            AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks....grgfeksdveiesegkvka 73 
                                       +++++nf++++d ++ +++g+t+++G NG+GK+T+l+ + +aLyg ++  +r+      +g e+++ve+ + ++++ 
  gi|336254267|ref|YP_004597374.1|   5 RIRLRNFKCYGDADLGLDRGVTVVHGVNGSGKSTLLEGVFFALYGSKALDDRTLddviTTGEEEAEVELWFTHDNRD 81 
                                       79*******************************************76544443333334444444444444455555 PP

                            AAA_23  74 y.veltfenkdgry..trsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqer..... 142
                                       y ve+ ++  ++r   t+++ ++ +++ + ++ ++ + +ell++d+ e f++  + ++ + ++li   +++r     
  gi|336254267|ref|YP_004597374.1|  82 YhVERHLKLRGDRAttTKCVLETPTETIEGARDVRREVTELLRMDA-EAFVNCAYVRQGEVNKLIHASPSDRqdmid 157
                                       5555555554444466666666666666666666666666666665.566666666666666666666666655554 PP

                            AAA_23 143 ...........feefelkdkke...................................................rlee 157
                                                            e                                                   +++ 
  gi|336254267|ref|YP_004597374.1| 158 dllqlgaledyR---------ErasdarlgvksvldgqrevledvrkqverkedkelherlnnlesqraevtdEIDH 225
                                       444444444440.........14444444444444444444444444455554555666666666644444443333 PP

                            AAA_23 158 lekeleeledekkllekl...............eqekekekeleeleeeleeilk 197
                                       +e++ e++++                       e++ + e+ +++l++++ e+++
  gi|336254267|ref|YP_004597374.1| 226 YETQREQAQN-------TldtaedvlerhaetqEEISDLEEGIDDLRSKISETEQ 273
                                       3333333333.......13333333533333334555555555566665555555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   6.3e-14   3.6e-11       1     256 [.       1     368 [.       1     405 [. 0.63
   2 ?   -3.3  17.3       9.5   5.5e+03      74     262 ..     496     704 ..     464     860 .. 0.46

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 6.3e-14
                            AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn...........kkvikiekedle 66 
                                       M++++i+++NF+++ d+++ l+  +tv+ G N+sGKS++le    F+      +                       
  gi|336254267|ref|YP_004597374.1|   1 MRVDRIRLRNFKCYGDADLGLDRGVTVVHGVNGSGKSTLLEGV--FFALY--GSkalddrtlddvI----------- 62 
                                       999**************************************99..55533..22113344444440........... PP

                            AAA_15  67 ifeniseskdikIdvef............................................................ 83 
                                           +  + + +++++f                                                            
  gi|336254267|ref|YP_004597374.1|  63 ----TTGEEEAEVELWFthdnrdyhverhlklrgdratttkcvletptetiegardvrrevtellrmdaeafvncay 135
                                       ....4444444555555555566666666666666699999999999999999999999999999999999999999 PP

                            AAA_15  84 .............................................................aekekakeyektlksk 99 
                                                                                                          +  e+ +  +
  gi|336254267|ref|YP_004597374.1| 136 vrqgevnklihaspsdrqdmiddllqlgaledyrerasdarlgvksvldgqrevledvrkqV-----ERKEDKELHE 207
                                       99999999999999999999999999999999988888888887777776666555442220.....2222222222 PP

                            AAA_15 100 ekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks.kkelpkekeeklekekeelkidkedlkklikk 175
                                       + +  + +  +  ++++ + ++++++ ++ ++  +  + + + + + ++ +e  ++l +++ e++ + ed+k+ i++
  gi|336254267|ref|YP_004597374.1| 208 RLNNLESQRAEVTDEIDHYETQREQAQNTLDTAEDVLERHAETQeEISDLEEGIDDLRSKISETEQQREDAKEQIRE 284
                                       22222224444555666666666666666666666666665544244444444455556666666666677776666 PP

                            AAA_15 176 leeslkkee......elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekleeelteklkeiq 246
                                       le+  ++ +      + +  l++a  +++  +a+ +  + ++e+ ++ l+++   i e++++   +e+l e++++++
  gi|336254267|ref|YP_004597374.1| 285 LETEREELAeeradlLADADLEAANADTDAVEARIEELEARDEELRDDLEEVRVAITETNGE---IERLCEEADDLE 358
                                       66665555566777777777777777777777777777777777777777777777777665...333333333333 PP

                            AAA_15 247 eklkeidkkl 256
                                       +  +e+  + 
  gi|336254267|ref|YP_004597374.1| 359 SQADEARTEA 368
                                       3333333333 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.5
                            AAA_15  74 skdikIdvefaek.ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpk 149
                                       + d +I+  +     +a+ +++ l++++++ ++ l+ +k+++l ++ ++++  l+    + e ++ e ++++ e  +
  gi|336254267|ref|YP_004597374.1| 496 DLDERIERAE--AlREAERRVDRLEENRDNVEQ-LVAEKRESLAERREQREDLLE----DAEEYESEAEEKREEAAE 565
                                       3444444444..234555555556666666665.677777777777777777766....455555555555555555 PP

                            AAA_15 150 ekeeklekekeelkid..kedlkklikkleeslkkee.......elknvlksaiiklllisakRnvsdedsekkssl 217
                                       +++e +ek++e  +i+    ++k++++ l+ + + ++       e++n  +      +l+ ++R+  +++ e k++l
  gi|336254267|ref|YP_004597374.1| 566 LEDEVAEKREELGEINgeRGEIKETLEALRRIAEIDDeredlesEIENYRERRRNWQQLNDERRETLSSKRERKRDL 642
                                       55555555555555554455666666666666666665555555444444444444444444444444444444444 PP

                            AAA_15 218 lgklkekileealqekl.....eeelteklkeiqeklkeidkklaeelk............k 262
                                        ++ +e+ + +a ++k+     +e++  kl++++e  +ei++ +++ ++            +
  gi|336254267|ref|YP_004597374.1| 643 ESEFDEERVATAREDKQnaeqyIEKVDAKLEDLEERRTEIQNAIGAVENeleelerlrdrlE 704
                                       44444444444433333444442222222222222222222222111112222222333331 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.043        25      20      32 ..      27      39 ..      11      84 .. 0.91
   2 !    8.8  16.1   0.00095      0.55     317     455 ..     163     298 ..     117     305 .. 0.83
   3 !    9.1   8.3   0.00076      0.44     329     459 ..     311     444 ..     301     453 .. 0.35
   4 !   13.8  22.4     3e-05     0.017     241     457 ..     442     650 ..     414     655 .. 0.88
   5 !   32.2   4.3   8.1e-11   4.7e-08     302     579 ..     590     865 ..     583     882 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.043
                            AAA_13 20 liYGwNGaGKTtL 32
                                      ++ G NG+GK+tL
  gi|336254267|ref|YP_004597374.1| 27 VVHGVNGSGKSTL 39
                                      799*********9 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00095
                            AAA_13 317 safeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeeke 393
                                        a e+ +e ++++   +++ L+g +++le+ rk++ +  e +++ +++++++++ ae+ + i  +  + ++ ++   
  gi|336254267|ref|YP_004597374.1| 163 GALEDYRERASDARLGVKSVLDGQREVLEDVRKQVER-KEDKELHERLNNLESQRAEVTDEIDHYETQREQAQNTLD 238
                                       44566678888888899999**********9999988.677899999999*************************** PP

                            AAA_13 394 eakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrd 455
                                       +a++ le+h  +e ++e++ +++ +++l  +i+++e++ +++++++++le e +eL ++  d
  gi|336254267|ref|YP_004597374.1| 239 TAEDVLERH--AETQEEISDLEEGIDDLRSKISETEQQREDAKEQIRELETEREELAEERAD 298
                                       *******95..677999999999999999999999999999999999999999999877655 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00076
                            AAA_13 329 eaealeeqLkglqraleaKrkepfk.svelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhl. 403
                                        ++a+e+++++l+ + e+ r+++ + +v +++++++ie++ ++ ++++ +  +     ++l+e+ e  ++++   + 
  gi|336254267|ref|YP_004597374.1| 311 DTDAVEARIEELEARDEELRDDLEEvRVAITETNGEIERLCEEADDLESQADEARTEADDLAERIEGDEDDIADREe 387
                                       33333333333333333333333332333333333333333333333333333333333333333333333322221 PP

                            AAA_13 404 .veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpa 459
                                        +e+le+++++  ++++++  +  ++ + l++ e+e + + +ei +  + +r +++a
  gi|336254267|ref|YP_004597374.1| 388 kLEDLEDDIETAREQFDDAPIEFGDAAAHLEDLESEREDRTDEIGDVTADIRAVENA 444
                                       233333333333333333333333333333333333333333344433333333333 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 3e-05
                            AAA_13 241 adWVkqGlelheassdtCpFCgqplpaerkaaLeahFddefeekqerLekliekveskkselleklkavsdeasens 317
                                       ++ +++G +l e+   +Cp Cgqp++++      ++ dd+ e + ++Lek +e++e ++    + l++ +++a++ +
  gi|336254267|ref|YP_004597374.1| 442 ENAIEEGERLLEEG--NCPTCGQPVKDSPHV---DVLDDKRE-ELSDLEKQLEELEAER----DDLDERIERAEALR 508
                                       56689999999998..9**********9775...45666444.4777888888888887....58889999999999 PP

                            AAA_13 318 afeedkeelkaeaealeeqLkglqraleaKrkepfksve.lesvkakiesikklvaeineliakhNekvanleeeke 393
                                       ++e+ ++ l+++ +++e+   + ++ l ++r++    +e  e++++++e+  ++ ae+++ +a+  e   +++ e+ 
  gi|336254267|ref|YP_004597374.1| 509 EAERRVDRLEENRDNVEQLVAEKRESLAERREQREDLLEdAEEYESEAEEKREEAAELEDEVAEKREELGEINGERG 585
                                       9******************************99999888689*********************************** PP

                            AAA_13 394 eakkklelhl.veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdek 457
                                       e+k+ le+ + ++e+++e + +++++++  +   + ++  +e  + l  ++e+ ++Le +  +e+
  gi|336254267|ref|YP_004597374.1| 586 EIKETLEALRrIAEIDDEREDLESEIENYRERRRNWQQLNDERRETLSSKRERKRDLESEFDEER 650
                                       ******987659******************99999999999999**************9988776 PP

  == domain 5  score: 32.2 bits;  conditional E-value: 8.1e-11
                            AAA_13 302 lleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvel.esvkaki.....esikklva 372
                                        le l  +++        ++++e+l++e+e+ +e+ +++q+  +++r+ ++++ e   +++++        + ++ +
  gi|336254267|ref|YP_004597374.1| 590 TLEALRRIAEI-------DDEREDLESEIENYRERRRNWQQLNDERRETLSSKRERkRDLESEFdeervATAREDKQ 659
                                       44444444444.......445555556666666665555555555555555555532344444432222799999** PP

                            AAA_13 373 eineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeL 449
                                       ++++ i+k  +k ++lee+++e+++++ +  ve+  +el+++ + +++le+ +  le      ++e+++l+    eL
  gi|336254267|ref|YP_004597374.1| 660 NAEQYIEKVDAKLEDLEERRTEIQNAIGA--VENELEELERLRDRLESLEERCDRLE----SLYDEAETLQTTYGEL 730
                                       ****************************9..44335888999999999998887777....6666667777777777 PP

                            AAA_13 450 ekqlrdekpaaeeinkeLkaf...GlgeleLkfeeekkgYrivr..kggsqaa.etLSeGEktaIaf...lYFlksl 517
                                       + +lr+  + +e ++++L++      ++++ + +e +  Yr++   k+g+  + e+LS GE+ +  +   +  + +l
  gi|336254267|ref|YP_004597374.1| 731 RSELRQ--RNVETLERLLNETfelVYQNDSYASIELDGDYRLTVfqKDGEALEpEQLSGGERALFNLslrCAIYRLL 805
                                       777765..3455555555544111167777777777999*98752245554445**********9885555677777 PP

                            AAA_13 518 keddseigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkk 579
                                        e  + +      ++D P   LDs+++   +sl++s    +  ++Q+ +  H  e+   ++ 
  gi|336254267|ref|YP_004597374.1| 806 AEGVEGTAPMPPLILDEPTVFLDSGHVTQLVSLVESMR--ELGVEQIVVVSHDEELVGAADS 865
                                       7777777777889**********************996..899*********9877666555 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 !   36.0  52.7   8.2e-12   4.7e-09       2     214 ..       3     872 ..       2     877 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 8.2e-12
                                       EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkae 78 
                                       + r++++nFk y    ++l +++++t++ G NGSGKs ll+ + F L    +k+l  ++l+d+i+        ++ae
  gi|336254267|ref|YP_004597374.1|   3 VDRIRLRNFKCYG--DADLGLDRGVTVVHGVNGSGKSTLLEGVFFALY--GSKALDDRTLDDVITT-----GEEEAE 70 
                                       689*********5..89999*************************998..6789***********8.....6789** PP

                                       EEEEEEETTEESSSSSSC....EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT................ CS
                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                             SMC_N  79 veitfdnedkklkiekee....vsisrrvkrkgeseykingkevtkkevsellesagiske................ 135
                                       ve+ f++++++ ++e++        ++++   ++ + +i+g +  ++ev+ell++                      
  gi|336254267|ref|YP_004597374.1|  71 VELWFTHDNRDYHVERHLklrgDRATTTKCVLETPTETIEGARDVRREVTELLRMDAEAFVncayvrqgevnkliha 147
                                       *****88888844443321111223333333344556789999999999999987543333689************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|336254267|ref|YP_004597374.1| 148 spsdrqdmiddllqlgaledyrerasdarlgvksvldgqrevledvrkqverkedkelherlnnlesqraevtdeid 224
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|336254267|ref|YP_004597374.1| 225 hyetqreqaqntldtaedvlerhaetqeeisdleegiddlrskiseteqqredakeqireletereelaeeradlla 301
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|336254267|ref|YP_004597374.1| 302 dadleaanadtdavearieeleardeelrddleevrvaitetngeierlceeaddlesqadearteaddlaeriegd 378
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|336254267|ref|YP_004597374.1| 379 eddiadreekledleddietareqfddapiefgdaaahledleseredrtdeigdvtadiravenaieegerlleeg 455
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|336254267|ref|YP_004597374.1| 456 ncptcgqpvkdsphvdvlddkreelsdlekqleeleaerddlderieraealreaerrvdrleenrdnveqlvaekr 532
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|336254267|ref|YP_004597374.1| 533 eslaerreqredlledaeeyeseaeekreeaaeledevaekreelgeingergeiketlealrriaeidderedles 609
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|336254267|ref|YP_004597374.1| 610 eienyrerrrnwqqlnderretlsskrerkrdlesefdeervataredkqnaeqyiekvdakledleerrteiqnai 686
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|336254267|ref|YP_004597374.1| 687 gaveneleelerlrdrlesleercdrleslydeaetlqttygelrselrqrnvetlerllnetfelvyqndsyasie 763
                                       ***************************************************************************** PP

                                       ....................CS-HHHHHHHHHHHHHH........HHCCS--SEEEECTTTTTS-HHHHHHHHHHHH CS
                                       ....................xxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ....................lLSgGektLvalaLlfA........iqkvkpaplyllDeidaaLDeknvkkvaellk 184
                                                           +LSgGe++L  l+L+ A        ++   p p  +lDe    LD  +v+++++l++
  gi|336254267|ref|YP_004597374.1| 764 ldgdyrltvfqkdgealepeQLSGGERALFNLSLRCAiyrllaegVEGTAPMPPLILDEPTVFLDSGHVTQLVSLVE 840
                                       *************************************999999999999**************************** PP

                                       HHCTT..SEEEEE-SSHHHCCC-SCEEEEEEE CS
                                       xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 185 ekskn..aQfivislreemlekadklvgvtkv 214
                                       + ++    Q++v+s++ee++  ad+lv+v k 
  gi|336254267|ref|YP_004597374.1| 841 SMRELgvEQIVVVSHDEELVGAADSLVRVEKD 872
                                       98886669*********************983 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5  23.1   0.00017       0.1     156     259 ..     181     291 ..     177     297 .. 0.77
   2 !    7.3  20.2    0.0034       1.9     141     258 ..     275     390 ..     272     393 .. 0.90
   3 !   16.6   0.8     5e-06    0.0029     192     259 ..     388     454 ..     376     460 .. 0.88
   4 !    8.0   5.3     0.002       1.1     222     265 ..     473     516 ..     469     521 .. 0.88
   5 !    6.6  31.3    0.0052         3     143     280 ..     482     623 ..     480     625 .. 0.84
   6 !   10.4  25.4   0.00038      0.22     146     301 ..     595     757 ..     586     765 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                              Spc7 156 elLekqeeeldellpeleeeka.eleeeleklqeaaeeles.id..keeLeelreelaelkaeie...ekkkelael 225
                                       ++L+ q+e l+++ +++e++++ el+e+l++l+++++e+++ id  +++ e+++++l++++  +e   e ++e+++l
  gi|336254267|ref|YP_004597374.1| 181 SVLDGQREVLEDVRKQVERKEDkELHERLNNLESQRAEVTDeIDhyETQREQAQNTLDTAEDVLErhaETQEEISDL 257
                                       57888999999999999766654999999999997777776666445566778888877766554111678899999 PP

                              Spc7 226 qeqleeleekieelkeqkseleeeiaeaervlee 259
                                       +e +++l++ki+e+++q+++++e+i+e e  +ee
  gi|336254267|ref|YP_004597374.1| 258 EEGIDDLRSKISETEQQREDAKEQIRELETEREE 291
                                       9999999999999999999999999999988887 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0034
                              Spc7 141 kegleenlegleedkelLekqeeel..dellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaei 215
                                       +e ++e++ +le+++e+L+++++ l  d+ l++ ++  +++e+++e+l+++ eel    +++Lee+r +++e + ei
  gi|336254267|ref|YP_004597374.1| 275 REDAKEQIRELETEREELAEERADLlaDADLEAANADTDAVEARIEELEARDEEL----RDDLEEVRVAITETNGEI 347
                                       5778999***********999998776788899999999***********99884....77**************** PP

                              Spc7 216 eekkkelaelqeqleeleekieelkeqkseleeeiaeaervle 258
                                       e++ +e ++l++q +e +++ ++l+e+++  e++ia  e+ le
  gi|336254267|ref|YP_004597374.1| 348 ERLCEEADDLESQADEARTEADDLAERIEGDEDDIADREEKLE 390
                                       ****************************999999998877655 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 5e-06
                              Spc7 192 elesid.keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervlee 259
                                       +le  d ++++e++re+++++  e     + l++l++++e+ +++i ++++ ++ +e++i+e er+lee
  gi|336254267|ref|YP_004597374.1| 388 KLE--DlEDDIETAREQFDDAPIEFGDAAAHLEDLESEREDRTDEIGDVTADIRAVENAIEEGERLLEE 454
                                       333..33789********************************************************998 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.002
                              Spc7 222 laelqeqleeleekieelkeqkseleeeiaeaervleeckgwse 265
                                       l++++e+l +le+++eel++++++l e+i++ae ++e+++++++
  gi|336254267|ref|YP_004597374.1| 473 LDDKREELSDLEKQLEELEAERDDLDERIERAEALREAERRVDR 516
                                       67899999999**********************99999998876 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0052
                              Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqe...aaeelesidkeeLeelreelaelkaeie 216
                                        le++le+le++++ L+++ e +++l  e e++ ++lee+ ++ ++   +++e  +  +e+ e l e+ +e ++e e
  gi|336254267|ref|YP_004597374.1| 482 DLEKQLEELEAERDDLDERIERAEAL-REAERRVDRLEENRDNVEQlvaEKRESLAERREQREDLLEDAEEYESEAE 557
                                       799*****************998765.6678899999999988888432333333456888888999999999**** PP

                              Spc7 217 ekkkelaelqeqleeleekieelkeqkseleeeiaeaervlee..ckgwsesevsrlkeevkalee 280
                                       ek++e ael+++++e++e++ e++ ++ e++e +++ +r+ e   +++  ese+++++e+ ++ ++
  gi|336254267|ref|YP_004597374.1| 558 EKREEAAELEDEVAEKREELGEINGERGEIKETLEALRRIAEIddEREDLESEIENYRERRRNWQQ 623
                                       ***************************************9875226788899***99999888776 PP

  == domain 6  score: 10.4 bits;  conditional E-value: 0.00038
                              Spc7 146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles.idkeeLeelreelaelkaeieekkke 221
                                       ++++++++++e Le++ e+  e   + ++  +e +e+l + +e++++les  d+e+++++re+ +++++ ie+  ++
  gi|336254267|ref|YP_004597374.1| 595 RRIAEIDDEREDLESEIENYRERRRNWQQLNDERRETLSSKRERKRDLESeFDEERVATAREDKQNAEQYIEKVDAK 671
                                       689999******************************************99789************************ PP

                              Spc7 222 laelqeqleeleekieelkeqkseleeeiaeaervleeckgwse..sevsrlkeevkaleeltgwkivsls....gs 292
                                       l++l+e+++e++++i +++++ +ele    + e++ e+c + ++  +e ++l++++ +l +++  + v+      ++
  gi|336254267|ref|YP_004597374.1| 672 LEDLEERRTEIQNAIGAVENELEELERLRDRLESLEERCDRLESlyDEAETLQTTYGELRSELRQRNVETLerllNE 748
                                       ***************************99999999999998775558999999999999988877776655678888 PP

                              Spc7 293 tleltyrse 301
                                       t+el+y+++
  gi|336254267|ref|YP_004597374.1| 749 TFELVYQND 757
                                       899999887 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 !    8.5  15.7    0.0016      0.92      25     134 ..     203     301 ..     191     304 .. 0.83
   2 !   13.7   4.2   4.2e-05     0.024      31     130 ..     305     401 ..     301     403 .. 0.93
   3 !   20.4  10.6     4e-07   0.00023      13     122 ..     457     581 ..     450     594 .. 0.78
   4 ?    0.6   6.7      0.42   2.4e+02      68     110 ..     596     638 ..     583     653 .. 0.74
   5 ?    5.4  10.8     0.014         8      23     151 ..     631     760 ..     629     772 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                             Atg14  25 yelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekk 101
                                        el+erl +l s+++++  +i+ +++++e       +++n+ + +e+   ++a+++e+++ l++ ++ l+++i e+ 
  gi|336254267|ref|YP_004597374.1| 203 KELHERLNNLESQRAEVTDEIDHYETQRE-------QAQNTLDTAEDVLERHAETQEEISDLEEGIDDLRSKISETE 272
                                       57899*****************9999999.......88999999999999999999999999999999999999998 PP

                             Atg14 102 kklaklsdklkkRrsdleslqneleerrkkqia 134
                                       ++ +  ++++    ++le  ++el+e+r++++a
  gi|336254267|ref|YP_004597374.1| 273 QQREDAKEQI----RELETEREELAEERADLLA 301
                                       8888888888....5667778888888888765 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.2e-05
                             Atg14  31 laklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakl 107
                                       l   +++ ++++ +ie+++++ e   +l+d+++  + ++ e+  +i++l e+   l+ + ++ + e ++  +++++ 
  gi|336254267|ref|YP_004597374.1| 305 LEAANADTDAVEARIEELEARDE---ELRDDLEEVRVAITETNGEIERLCEEADDLESQADEARTEADDLAERIEGD 378
                                       5566788999******8888888...*************************************************** PP

                             Atg14 108 sdklkkRrsdleslqneleerrk 130
                                        d++++R ++le l++ +e +r+
  gi|336254267|ref|YP_004597374.1| 379 EDDIADREEKLEDLEDDIETARE 401
                                       ****************9999886 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 4e-07
                             Atg14  13 CesC...lrng.........perlyelrerlaklksekeslkkkiekalegke...eaeqledkiknkkakleelks 74 
                                       C++C   ++ +         +e l +l ++l  l +e++ l ++ie+a++ +e   ++++le++ +n  + + e++ 
  gi|336254267|ref|YP_004597374.1| 457 CPTCgqpVKDSphvdvlddkREELSDLEKQLEELEAERDDLDERIERAEALREaerRVDRLEENRDNVEQLVAEKRE 533
                                       999977777779999999999******************************99333334444444444444444444 PP

                             Atg14  75 liadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslq 122
                                         a+ re+ + l ++ ++  +e eek+++ a+l d+++++r++l  ++
  gi|336254267|ref|YP_004597374.1| 534 SLAERREQREDLLEDAEEYESEAEEKREEAAELEDEVAEKREELGEIN 581
                                       44455555777777788889999*******************998776 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.42
                             Atg14  68 kleelksliadlrerlqelkdklsqlkkeieekkkklaklsdk 110
                                       ++ e+  +++dl++++++ ++++++ ++ ++e++++l+++++ 
  gi|336254267|ref|YP_004597374.1| 596 RIAEIDDEREDLESEIENYRERRRNWQQLNDERRETLSSKRER 638
                                       5667777888888888888888888888888888888888765 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.014
                             Atg14  23 rlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrer....lqelkdklsqlkk 95 
                                        l ++rer ++l se +  ++++  a e k++aeq  +k++ k ++lee +++i+         l+el+ +l+ + +
  gi|336254267|ref|YP_004597374.1| 631 TLSSKRERKRDLESEFD--EERVATAREDKQNAEQYIEKVDAKLEDLEERRTEIQNAIGAveneLEELE-RLRDRLE 704
                                       56666777666666655..46777777777766666666666665555555555544333111144433.2333334 PP

                             Atg14  96 eieekkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikrieqklssls 151
                                       ++ee+  +l++l d+  + + +   l++el++r  + +++l++++++  ++++s  
  gi|336254267|ref|YP_004597374.1| 705 SLEERCDRLESLYDEAETLQTTYGELRSELRQRNVETLERLLNETFELVYQNDSYA 760
                                       566667778888888889999999**********************9888877665 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 !   15.3   0.0   2.2e-05     0.013       1      48 [.      25      61 ..      25      85 .. 0.67
   2 ?   -1.4   0.2       2.9   1.7e+03     101     161 ..     240     300 ..     194     335 .. 0.62
   3 !   18.0   5.6   3.4e-06    0.0019      76     302 ..     617     860 ..     575     861 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsl 48
                                      ++v+ G NgsGKS+LL+   ++              s+  + r  +  
  gi|336254267|ref|YP_004597374.1| 25 VTVVHGVNGSGKSTLLEGVFFALY-----------GSKALDDRTLDDV 61
                                      69999**************88743...........3333344444444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.9
                            AAA_21 101 dkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldgl 161
                                        +++le++ ++  e ++  +g+++ ++k ++ +++ ++ +++ + + t+r + +++  d l
  gi|336254267|ref|YP_004597374.1| 240 AEDVLERHAETQEEISDLEEGIDDLRSKISETEQQREDAKEQIRELETEREELAEERADLL 300
                                       4555666666666666666666666666666666666666666666666555555544444 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 3.4e-06
                            AAA_21  76 lrlersqv....eeklssvetllesgllldkr...sleeedvfnpeargirggvsvfslkelsvsepndlqfgkalt 145
                                        r +++q+    +e+lss+++++++ +  +++   ++ +ed+ n+e + ++++++ + l e   +++n+   +++ +
  gi|336254267|ref|YP_004597374.1| 617 RRRNWQQLnderRETLSSKRERKRDLESEFDEervATAREDKQNAEQYIEKVDAKLEDLEERRTEIQNAIGAVENEL 693
                                       22333333455656666666666665555555111344555555555555555555555555555555555555555 PP

                            AAA_21 146 ditsrawsllllldglrke.rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergv 221
                                       +  +r+++ l++l++  ++ ++++ ++     ++ +++  l+++  + +++ ++ +++++  ++++ ++e++ + + 
  gi|336254267|ref|YP_004597374.1| 694 EELERLRDRLESLEERCDRlESLYDEAETLQTTYGELRSELRQRNVETLERLLNETFELVYQNDSYASIELDGD-YR 769
                                       55555555555554444446555555555555555666666666667777777777777777777777777777.9* PP

                            AAA_21 222 vflengdgqelparelSdGtkrllalltallralkkg.........sllliDEpEngLHPkllrrllellkelsr.n 288
                                        ++  +dg  l + +lS G + l+ l + ++  +  +         + l++DEp  +L+   ++ l+ l+++ ++ +
  gi|336254267|ref|YP_004597374.1| 770 LTVFQKDGEALEPEQLSGGERALFNLSLRCAIYRLLAegvegtapmPPLILDEPTVFLDSGHVTQLVSLVESMRElG 846
                                       ************************999988888888888999******************88888887775555555 PP

                            AAA_21 289 gaQviltTHSplll 302
                                         Q+++++H+ +l+
  gi|336254267|ref|YP_004597374.1| 847 VEQIVVVSHDEELV 860
                                       57********8885 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 !   23.9   0.0   4.3e-08   2.5e-05       2      50 ..       4      51 ..       3      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.3e-08
                            AAA_29  2 krlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                       r++l N   + + ++ +d +g+t++ G +GsGKSTll  + + L+++k
  gi|336254267|ref|YP_004597374.1|  4 DRIRLRNFKCYGDADLGLD-RGVTVVHGVNGSGKSTLLEGVFFALYGSK 51
                                      689999999999999***9.789**********************9987 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.2      0.79   4.6e+02      53      94 ..     189     225 ..     160     236 .. 0.45
   2 !   13.9   4.9     7e-05     0.041       2      71 ..     230     299 ..     229     303 .. 0.79
   3 !   16.8   5.0   8.8e-06    0.0051       5      99 ..     305     403 ..     301     408 .. 0.87
   4 ?    4.2   4.6     0.069        40      46     104 ..     472     533 ..     465     538 .. 0.84
   5 ?    5.6   3.8     0.026        15       5      91 ..     549     635 ..     543     644 .. 0.80
   6 !    8.3   2.2    0.0037       2.1      30      92 ..     658     720 ..     648     732 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.79
                                       XXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHH CS
                        Laminin_II  53 airdArrsvkkLeklapqLldklkelkqleeassslsdnise 94 
                                       +++d+r++v    k+  +L ++l++l+ ++ +   + d+i+ 
  gi|336254267|ref|YP_004597374.1| 189 VLEDVRKQVER--KEDKELHERLNNLESQRAE---VTDEIDH 225
                                       23333333222..1122333333333333333...4444443 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       +e a++ ++ta+ vle  a+ +++++ ++e +  +++++ et+++ +da+++ir+ +++  +L ++  +L
  gi|336254267|ref|YP_004597374.1| 230 REQAQNTLDTAEDVLERHAETQEEISDLEEGIDDLRSKISETEQQREDAKEQIRELETEREELAEERADL 299
                                       5677888888899999999999999999999999999988888888888888888888888886655544 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 8.8e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHH....H CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklk....e 77 
                                       +++an  + +v++ +++l+++ e+++++l+e++  + etn +++ + +  +d +++  +   +a++L ++++     
  gi|336254267|ref|YP_004597374.1| 305 LEAANADTDAVEARIEELEARDEELRDDLEEVRVAITETNGEIERLCEEADDLESQADEARTEADDLAERIEgdedD 381
                                       789*******************************************************************9744335 PP

                                       HHHHHHH...HHHHHHHHHHHH CS
                        Laminin_II  78 lkqleeassslsdniseikelI 99 
                                       +  +ee+ + l d+i+  +e+ 
  gi|336254267|ref|YP_004597374.1| 382 IADREEKLEDLEDDIETAREQF 403
                                       6777777777888888777765 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.069
                                       XXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH......HHHHHHHHHHHHHHHHH CS
                        Laminin_II  46 kvkdankairdArrsvkkLeklapqLldklkelkqleeasss...lsdniseikelIaqARk 104
                                       +++d+ + + d +++  +Le + ++L +++++ + l+ea+     l +n +++ +l+a  R+
  gi|336254267|ref|YP_004597374.1| 472 VLDDKREELSDLEKQLEELEAERDDLDERIERAEALREAERRvdrLEENRDNVEQLVAEKRE 533
                                       56788889999999999999999999999999999999977788899999999999998885 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.026
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       a+e ++ a+e  e  a+l+ ++ + +e+l ein++  e++e ++++ + i++  ++  +Le ++++  ++ ++ +ql
  gi|336254267|ref|YP_004597374.1| 549 AEEYESEAEEKREEAAELEDEVAEKREELGEINGERGEIKETLEAL-RRIAEIDDEREDLESEIENYRERRRNWQQL 624
                                       6677778888899999*******************99999988765.557788888889999888888888888888 PP

                                       HHH....HHHH CS
                        Laminin_II  82 eeasss.lsdn 91 
                                       ++++   ls +
  gi|336254267|ref|YP_004597374.1| 625 NDERREtLSSK 635
                                       77766567665 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0037
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHH CS
                        Laminin_II  30 keklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdni 92 
                                       k+++++  ++v+   e++++  + i+ A  +v +  +++++L d+l++l+++ +  +sl d+ 
  gi|336254267|ref|YP_004597374.1| 658 KQNAEQYIEKVDAKLEDLEERRTEIQNAIGAVENELEELERLRDRLESLEERCDRLESLYDEA 720
                                       444444444444445666677788888888888888889999999999999999888877665 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 !   12.2   0.1   9.7e-05     0.056     240     275 ..      19      54 ..      16      68 .. 0.82
   2 ?    5.4   0.0     0.012       6.8     372     412 ..     831     870 ..     823     882 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.7e-05
                                       EEE-SSEEEEEE-TTSSHHHHHHHHHHCCSEE-TTS CS
                        ABC_ATPase 240 mgipkGvtlIvGggfhGKsTLLeAlekGvynhvpgD 275
                                       +g+ +Gvt++ G +  GKsTLLe +    y   + D
  gi|336254267|ref|YP_004597374.1|  19 LGLDRGVTVVHGVNGSGKSTLLEGVFFALYGSKALD 54 
                                       79********************98877777655555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.012
                                       -B--HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEE CS
                        ABC_ATPase 372 pitplvdrvrelykklgvstilvvggsgdyldvAdtvilme 412
                                        +t lv++v+++ ++lgv  i+vv+  ++++  Ad  +++e
  gi|336254267|ref|YP_004597374.1| 831 HVTQLVSLVESM-RELGVEQIVVVSHDEELVGAADSLVRVE 870
                                       5899*******9.99*********************99877 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   4.1e-07   0.00024       1      55 [.       1      52 [.       1     103 [. 0.87
   2 ?   -2.1   5.3       4.1   2.4e+03     104     196 ..     202     295 ..     183     304 .. 0.71
   3 ?   -1.7   0.3       3.2   1.9e+03     153     197 ..     310     354 ..     290     372 .. 0.55
   4 ?   -1.1   0.1       2.1   1.2e+03     154     185 ..     339     370 ..     311     400 .. 0.48
   5 ?    1.8   0.9      0.27   1.5e+02     155     198 ..     480     522 ..     473     532 .. 0.83
   6 ?    0.4   3.4      0.72   4.2e+02     137     199 ..     517     579 ..     511     587 .. 0.83
   7 ?    1.1   1.1      0.43   2.5e+02     141     198 ..     584     639 ..     568     648 .. 0.71
   8 ?   -2.0   0.6       3.8   2.2e+03     158     164 ..     696     702 ..     652     743 .. 0.50

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.1e-07
                            AAA_27  1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipe 55
                                      Mr++r++L+ +  + d  l ++   +++++++G N +GKst+l+++   l+G ++
  gi|336254267|ref|YP_004597374.1|  1 MRVDRIRLRNFKCYGDADLGLD---RGVTVVHGVNGSGKSTLLEGVFFALYGSKA 52
                                      9********************8...8*************************9654 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                            AAA_27 104 eevlaallggldretFealFgLdh.erLreGGealleaegelgqlLfeasaGlaslrevleaLeaeadelfkprksk 179
                                       ++ l++ l++l+ ++ e    +dh e+ re +++ l++ +++ +   e +  +++l+e +++L+++ +e  ++r+ +
  gi|336254267|ref|YP_004597374.1| 202 DKELHERLNNLESQRAEVTDEIDHyETQREQAQNTLDTAEDVLERHAETQEEISDLEEGIDDLRSKISETEQQREDA 278
                                       55555666666666666666666634456777888888888888888888888888888888888888888888888 PP

                            AAA_27 180 krainealeeleeakke 196
                                       k++i+e ++e ee+ +e
  gi|336254267|ref|YP_004597374.1| 279 KEQIRELETEREELAEE 295
                                       88888888887777665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.2
                            AAA_27 153 aGlaslrevleaLeaeadelfkprkskkrainealeeleeakkel 197
                                       a +  +++ +e+Lea+ +el ++ ++ + ai+e++ e+e++ +e 
  gi|336254267|ref|YP_004597374.1| 310 ADTDAVEARIEELEARDEELRDDLEEVRVAITETNGEIERLCEEA 354
                                       455555555555555555555554444444444444444433333 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2.1
                            AAA_27 154 GlaslrevleaLeaeadelfkprkskkraine 185
                                       ++++ +  +e+L +ead+l ++  ++++++ +
  gi|336254267|ref|YP_004597374.1| 339 AITETNGEIERLCEEADDLESQADEARTEADD 370
                                       33333333333333333333333333333333 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.27
                            AAA_27 155 laslrevleaLeaeadelfkprkskkrainealeeleeakkelr 198
                                       l++l++ le+Leae+d+l ++ ++++ a++ea++++++++++  
  gi|336254267|ref|YP_004597374.1| 480 LSDLEKQLEELEAERDDLDERIERAE-ALREAERRVDRLEENRD 522
                                       6789999***********99999999.99999998888877654 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 0.72
                            AAA_27 137 lleaegelgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelre 199
                                       l e+++++ ql+ e + +la+ re +e+L ++a+e+ ++ ++k+++++e ++e++e ++el e
  gi|336254267|ref|YP_004597374.1| 517 LEENRDNVEQLVAEKRESLAERREQREDLLEDAEEYESEAEEKREEAAELEDEVAEKREELGE 579
                                       557788899999999999999999999999999998888888888999999999998888765 PP

  == domain 7  score: 1.1 bits;  conditional E-value: 0.43
                            AAA_27 141 egelgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelr 198
                                       +ge+ ++L ea   +a++ + +e+Le+e +++ + r+++ +++n++++e  + k+e +
  gi|336254267|ref|YP_004597374.1| 584 RGEIKETL-EALRRIAEIDDEREDLESEIENYRE-RRRNWQQLNDERRETLSSKRERK 639
                                       55555554.77778999999*******9988555.55555588888777666655544 PP

  == domain 8  score: -2.0 bits;  conditional E-value: 3.8
                            AAA_27 158 lrevlea 164
                                       l++++++
  gi|336254267|ref|YP_004597374.1| 696 LERLRDR 702
                                       2222222 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   8.6     0.016         9      32      88 ..     190     241 ..     152     246 .. 0.64
   2 !   20.2  24.4   1.2e-06   0.00067      11     101 ..     209     299 ..     206     303 .. 0.95
   3 ?    2.9  15.5      0.26   1.5e+02      16     127 ..     303     376 ..     299     390 .. 0.46
   4 ?    5.9   6.2     0.029        17      40      95 ..     387     442 ..     373     456 .. 0.61
   5 ?    4.2  13.4       0.1        58      56      92 ..     473     509 ..     446     519 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.016
                            APG6_N  32 lkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaale 88 
                                       l+ ++k+      +++e++el+e+l +le++++e   e++  e++re+ ++ l ++e
  gi|336254267|ref|YP_004597374.1| 190 LEDVRKQV-----ERKEDKELHERLNNLESQRAEVTDEIDHYETQREQAQNTLDTAE 241
                                       33333331.....23455666666666666666666666666666666666666555 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.2e-06
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaal 87 
                                       l++l++q +++++e+d Ye+  ++ +++ +++e+  e ++e++ee+++le+  ++l +++ e+e++re+ ++++++l
  gi|336254267|ref|YP_004597374.1| 209 LNNLESQRAEVTDEIDHYETQREQAQNTLDTAEDVLERHAETQEEISDLEEGIDDLRSKISETEQQREDAKEQIREL 285
                                       789*************************9999999999*************************************** PP

                            APG6_N  88 eeelealeeeeerf 101
                                       e e e+l ee +  
  gi|336254267|ref|YP_004597374.1| 286 ETEREELAEERADL 299
                                       *********98765 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.26
                            APG6_N  16 kqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeele 92 
                                         le+a+++ da e+  ++l+++++e +   ++lee +  + +++ e e+l+ee ++le++ +e + e  +l     
  gi|336254267|ref|YP_004597374.1| 303 ADLEAANADTDAVEARIEELEARDEELR---DDLEEVRVAITETNGEIERLCEEADDLESQADEARTEADDL----- 371
                                       4455555555555555555555544433...34444444444444444444444444444444433333333..... PP

                            APG6_N  93 aleeeeerfwreynelqlelleleeeldsleaqye 127
                                                                     + ++e
  gi|336254267|ref|YP_004597374.1| 372 ------------------------------AERIE 376
                                       ..............................33333 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.029
                            APG6_N  40 keeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeeleale 95 
                                       ++ e+ ++++e ++e++++   e  ++ + L++le+ere+  +e+ + ++  +a+e
  gi|336254267|ref|YP_004597374.1| 387 EKLEDLEDDIETAREQFDDAPIEFGDAAAHLEDLESEREDRTDEIGDVTADIRAVE 442
                                       12222455666666666666666666666666666666666666666666666655 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.1
                            APG6_N  56 leklekeeeelleeLkelekereeleaelaaleeele 92 
                                       l++ ++e ++l+++L+ele+er++l++ ++ +e+  e
  gi|336254267|ref|YP_004597374.1| 473 LDDKREELSDLEKQLEELEAERDDLDERIERAEALRE 509
                                       66778999*********************99887544 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 !    7.3  24.8    0.0077       4.4      13     106 ..     195     292 ..     184     295 .. 0.84
   2 ?    3.7   8.1     0.098        57      46     100 ..     304     358 ..     288     363 .. 0.44
   3 !   16.5   6.4   1.1e-05    0.0064       9     102 ..     358     451 ..     352     456 .. 0.92
   4 ?    2.2  10.2      0.29   1.7e+02      65     113 ..     477     531 ..     471     531 .. 0.73
   5 ?   -0.8  35.9       2.4   1.4e+03       7     135 ..     502     636 ..     498     649 .. 0.86
   6 ?    4.0  16.1     0.081        47      15     106 ..     654     749 ..     648     758 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0077
                    CENP-F_leu_zip  13 Keserkad.sLkdkvenLerelemseenqekvileaEtskaevetlkeeie...elaeelreleldLvalrsekeeL 85 
                                       K++erk+d  L+++ +nLe++  ++  + ++ +++ E++++++ t ++ +e   e +ee ++le  +++lrs   e 
  gi|336254267|ref|YP_004597374.1| 195 KQVERKEDkELHERLNNLESQRAEVTDEIDHYETQREQAQNTLDTAEDVLErhaETQEEISDLEEGIDDLRSKISET 271
                                       7889998846*****************************9999996665552225588999**************** PP

                    CENP-F_leu_zip  86 ekelqkkqervseLeslnssl 106
                                       e++ ++ +e++ eLe+ +++l
  gi|336254267|ref|YP_004597374.1| 272 EQQREDAKEQIRELETEREEL 292
                                       ***************988776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.098
                    CENP-F_leu_zip  46 eaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLe 100
                                       + E + a   ++++ ieel+++ +el+ dL+++r    e + e++   e+ ++Le
  gi|336254267|ref|YP_004597374.1| 304 DLEAANADTDAVEARIEELEARDEELRDDLEEVRVAITETNGEIERLCEEADDLE 358
                                       3344444444444444444444444444444444444443333333333333333 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.1e-05
                    CENP-F_leu_zip   9 lekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeL 85 
                                       +++  e++ +ad L +++e+ e ++ + ee++e+++ + Et++++      e    a++l++le++ ++ + e  ++
  gi|336254267|ref|YP_004597374.1| 358 ESQADEARTEADDLAERIEGDEDDIADREEKLEDLEDDIETAREQFDDAPIEFGDAAAHLEDLESEREDRTDEIGDV 434
                                       66667999*************************************************************99999999 PP

                    CENP-F_leu_zip  86 ekelqkkqervseLesl 102
                                       + +++   + ++e e+l
  gi|336254267|ref|YP_004597374.1| 435 TADIRAVENAIEEGERL 451
                                       99999999999987765 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.29
                    CENP-F_leu_zip  65 aeelreleldLvalrsekeeLeke......lqkkqervseLeslnsslenlleek 113
                                       +eel++le +L++l  e+++L++       l++  +rv+ Le+ +  +e+l+ ek
  gi|336254267|ref|YP_004597374.1| 477 REELSDLEKQLEELEAERDDLDERieraeaLREAERRVDRLEENRDNVEQLVAEK 531
                                       6788888888999988888887641112226678889999999998888888765 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 2.4
                    CENP-F_leu_zip   7 hvlekLKeserkadsLk...dkvenLerelems....eenqekvileaEtskaevetlkeeieelaeelreleldLv 76 
                                       + +e L+e+er+ d L+   d ve+L +e+ +s     e++e++  +aE+   e+e+ +ee  el+ e  e + +L 
  gi|336254267|ref|YP_004597374.1| 502 ERAEALREAERRVDRLEenrDNVEQLVAEKRESlaerREQREDLLEDAEEYESEAEEKREEAAELEDEVAEKREELG 578
                                       56899***********755578****99876543322788999********************************** PP

                    CENP-F_leu_zip  77 alrsekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeLqtql 135
                                       ++  e+ e+++ l+   +r+ e +  +++le+ +e+  + +++ ++  +++ e L++  
  gi|336254267|ref|YP_004597374.1| 579 EINGERGEIKETLE-ALRRIAEIDDEREDLESEIENYRERRRNWQQLNDERRETLSSKR 636
                                       *********66665.5679*****************99999999998888888888765 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.081
                    CENP-F_leu_zip  15 serkadsLkdkvenLerelemseenqek...vileaEtskaevetlkeeieelaeelrelel...dLvalrsekeeL 85 
                                       +++++ + ++ +e+ ++ le++ee +++   +i  +E++ +e+e l++ +e l+e+  +le+   + ++l+    eL
  gi|336254267|ref|YP_004597374.1| 654 AREDKQNAEQYIEKVDAKLEDLEERRTEiqnAIGAVENELEELERLRDRLESLEERCDRLESlydEAETLQTTYGEL 730
                                       55667777888888888888888877541226778899999999999999999987666654333777888888888 PP

                    CENP-F_leu_zip  86 ekelqkkqervseLeslnssl 106
                                         el+  q+ v++Le+l  ++
  gi|336254267|ref|YP_004597374.1| 731 RSELR--QRNVETLERLLNET 749
                                       77765..67788888876554 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       5.3   3.1e+03      44      95 ..      77     128 ..      66     155 .. 0.85
   2 ?    5.5  18.9     0.031        18       3     110 ..     203     310 ..     201     323 .. 0.91
   3 ?    1.5   9.6      0.56   3.2e+02      31     121 ..     280     373 ..     279     380 .. 0.84
   4 !   16.8   1.4   1.1e-05    0.0064       4      72 ..     381     449 ..     378     455 .. 0.94
   5 ?    1.5  10.6      0.53     3e+02       5     103 ..     587     686 ..     585     688 .. 0.85
   6 ?    4.7  12.4     0.056        32      15     113 ..     647     744 ..     632     786 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.3
                           zf-C4H2  44 eqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkee 95 
                                       +  + +Hve   +++ D  +  + + e+ +e+ +  + +++ ++e+ ++  e
  gi|336254267|ref|YP_004597374.1|  77 HDNRDYHVERHLKLRGDRATTTKCVLETPTETIEGARDVRREVTELLRMDAE 128
                                       6679999*99999999999999999999999999999999999998888654 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.031
                           zf-C4H2   3 keirektleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekeksl 79 
                                       ke+ e++++le+ ++++++e++  e++++  +++  + e + +   +  ee+  +++ i++l s i e+e+++e ++
  gi|336254267|ref|YP_004597374.1| 203 KELHERLNNLESQRAEVTDEIDHYETQREQAQNTLDTAEDVLERHAETQEEISDLEEGIDDLRSKISETEQQREDAK 279
                                       788999*********************************************************************** PP

                           zf-C4H2  80 ekakklyeeykklkeevnelrselglekled 110
                                       e++++l +e ++l ee  +l+ +  le  + 
  gi|336254267|ref|YP_004597374.1| 280 EQIRELETEREELAEERADLLADADLEAANA 310
                                       **************99999998888875544 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.56
                           zf-C4H2  31 kcleeykkelelLeqEkmaHve..eLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrse.lg 104
                                       + ++e + e e+L +E+   +   +L   +aD +a+E  i+e e   e+  +  +++   +++   e+++l +e   
  gi|336254267|ref|YP_004597374.1| 280 EQIRELETEREELAEERADLLAdaDLEAANADTDAVEARIEELEARDEELRDDLEEVRVAITETNGEIERLCEEaDD 356
                                       57999************99875227999*********************9999999999999999999999998777 PP

                           zf-C4H2 105 lekledleeeeeellke 121
                                       le+  d + +e + l e
  gi|336254267|ref|YP_004597374.1| 357 LESQADEARTEADDLAE 373
                                       88777766666665555 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 1.1e-05
                           zf-C4H2   4 eirektleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeae 72 
                                       +i ++ ++le+l++ + ++ e++++      +  + le Le+E++   +e+  + aDi a+E+ i+e e
  gi|336254267|ref|YP_004597374.1| 381 DIADREEKLEDLEDDIETAREQFDDAPIEFGDAAAHLEDLESEREDRTDEIGDVTADIRAVENAIEEGE 449
                                       57788899*********************************************************9876 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.53
                           zf-C4H2   5 irektleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinal..Esvikeaeeekeksl 79 
                                       i+e +++l+++ +++ +e e le+e +  +e +++ ++L+ E+++ +   r  ++D+++   E+ +  a+e+k++++
  gi|336254267|ref|YP_004597374.1| 587 IKETLEALRRI-AEIDDEREDLESEIENYRERRRNWQQLNDERRETLSSKRERKRDLESEfdEERVATAREDKQNAE 662
                                       66666666665.5899999******99*****************************9874459999*********** PP

                           zf-C4H2  80 ekakklyeeykklkeevnelrsel 103
                                       + ++k+ ++++ l e+  e+++ +
  gi|336254267|ref|YP_004597374.1| 663 QYIEKVDAKLEDLEERRTEIQNAI 686
                                       ****99999999998877777665 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.056
                           zf-C4H2  15 lknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykk 91 
                                        ++++a++ e  ++ e+ +e++ ++le Le+ +++  + +  +++ +++lE+   + e + e++ ++ ++ly+e + 
  gi|336254267|ref|YP_004597374.1| 647 DEERVATAREDKQNAEQYIEKVDAKLEDLEERRTEIQNAIGAVENELEELERLRDRLE-SLEERCDRLESLYDEAET 722
                                       4678888999999999999999999999999999999999999999999999766665.566778899999999999 PP

                           zf-C4H2  92 lkeevnelrselglekledlee 113
                                       l+++  elrsel  +++e+le 
  gi|336254267|ref|YP_004597374.1| 723 LQTTYGELRSELRQRNVETLER 744
                                       9999999999987766665543 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3  10.7   0.00036      0.21      21     101 ..     190     271 ..     178     274 .. 0.81
   2 !   16.1  12.0   1.2e-05     0.007      14     130 ..     254     371 ..     252     377 .. 0.84
   3 !    7.2   3.9    0.0062       3.6     157     254 ..     358     454 ..     352     457 .. 0.80
   4 !    7.1  10.2    0.0069         4     180     249 ..     471     539 ..     468     545 .. 0.90
   5 ?    1.3   4.3      0.41   2.4e+02     186     220 ..     543     577 ..     540     596 .. 0.74
   6 ?   -1.5   8.0       2.8   1.6e+03     145     201 ..     667     722 ..     652     755 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
                         Laminin_I  21 ledltkeLqeklskesakkskieilekelesLaqeteeLq...kkatqvlakaqkvnaesertlnnakeLaekikkl 94 
                                       led +k+ ++k+ ke    +++++le +  ++  e++ +    ++a+ +l+ a++v ++  +t +++++L+e i +l
  gi|336254267|ref|YP_004597374.1| 190 LEDVRKQVERKEDKE--LHERLNNLESQRAEVTDEIDHYEtqrEQAQNTLDTAEDVLERHAETQEEISDLEEGIDDL 264
                                       788888888877665..3456777778888888887777522278999***************************** PP

                         Laminin_I  95 adnikei 101
                                       + +i+e 
  gi|336254267|ref|YP_004597374.1| 265 RSKISET 271
                                       ****996 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.2e-05
                         Laminin_I  14 pykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkka..tqvlakaqkvnaesertlnnakeLa 88 
                                       +  ++++++dl+++++e +++++  k++i  le e e+La+e   L   a  + + a++  v+a++e+   + +eL 
  gi|336254267|ref|YP_004597374.1| 254 ISDLEEGIDDLRSKISETEQQREDAKEQIRELETEREELAEERADLLADAdlEAANADTDAVEARIEELEARDEELR 330
                                       6679999***********************************9999987611456667788**************** PP

                         Laminin_I  89 ekikkladnikeilekvatlneneealpssklseelaeaqrl 130
                                       +  ++++  i+e +  +++l e++++l  s+ +e+  ea+ l
  gi|336254267|ref|YP_004597374.1| 331 DDLEEVRVAITETNGEIERLCEEADDLE-SQADEARTEADDL 371
                                       ********************99888774.4556666666655 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0062
                         Laminin_I 157 LsrvqtllqklqeenkaLkeal...rdsLaeyeakLsDlrelleeAaaktrdanrlnlanqanlreiekkkeevsee 230
                                        s++     + + e  +L+e +   +d++a+ e+kL+Dl++ +e A ++  da       +a l+++e+  e    e
  gi|336254267|ref|YP_004597374.1| 358 ESQAD----EARTEADDLAERIegdEDDIADREEKLEDLEDDIETAREQFDDAPIEFGDAAAHLEDLESEREDRTDE 430
                                       44444....4466666676666333699*************************999999999999999999988888 PP

                         Laminin_I 231 knqleetlktardsLdaanllLqe 254
                                         ++++ + + ++ + ++++lL+e
  gi|336254267|ref|YP_004597374.1| 431 IGDVTADIRAVENAIEEGERLLEE 454
                                       999999999999999999988876 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0069
                         Laminin_I 180 dsLaeyeakLsDlrelleeAaaktrdanrlnlanqanlreiekkkeevseeknqleetlktardsLdaan 249
                                       d L++  ++LsDl++ lee +a+  d +++  + +++lre+e+++++++e++  +e+++++ r+sL++ +
  gi|336254267|ref|YP_004597374.1| 471 DVLDDKREELSDLEKQLEELEAERDDLDERIER-AEALREAERRVDRLEENRDNVEQLVAEKRESLAERR 539
                                       67888999**************99999998765.678*****************************9865 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.41
                         Laminin_I 186 eakLsDlrelleeAaaktrdanrlnlanqanlrei 220
                                       e+ L+D++e   eA++k  +a +l  +++++ +e+
  gi|336254267|ref|YP_004597374.1| 543 EDLLEDAEEYESEAEEKREEAAELEDEVAEKREEL 577
                                       67799*****************9999998765533 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 2.8
                         Laminin_I 145 eaeaelkaAqkLLsrvqtllqklqeenkaLkealrdsLaeyeakLsDlrelleeAaa 201
                                       +++a+l+  ++   ++q+ +    +e++ L e lrd+L+  e+  + l++l +eA+ 
  gi|336254267|ref|YP_004597374.1| 667 KVDAKLEDLEERRTEIQNAIGAVENELEEL-ERLRDRLESLEERCDRLESLYDEAET 722
                                       333333333333445666666666666666.55666666666666666666666653 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   9.2     0.028        16      38     116 ..     211     288 ..     185     296 .. 0.60
   2 ?    6.7   2.5     0.012       6.8      57     120 ..     285     350 ..     277     364 .. 0.71
   3 ?    2.4   0.4      0.26   1.5e+02      49     113 ..     356     420 ..     350     426 .. 0.68
   4 ?    2.6   1.4      0.23   1.3e+02      49      96 ..     482     514 ..     470     540 .. 0.48
   5 ?    7.8   3.3    0.0058       3.3      55     118 ..     536     598 ..     516     604 .. 0.78
   6 ?   -0.3   0.2       1.8     1e+03      55     102 ..     598     645 ..     586     652 .. 0.75
   7 ?   14.5   2.3   4.7e-05     0.027      56     115 ..     653     715 ..     638     724 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.028
                           DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       +l++  ++v+ ++++  ++ +++++ L    d ++++ + q+eis +++e ++++r+++se++++ e  ke +++le
  gi|336254267|ref|YP_004597374.1| 211 NLESQRAEVTDEIDHYETQREQAQNTLDTAEDVLERHAETQEEIS-DLEEGIDDLRSKISETEQQREDAKEQIRELE 286
                                       555555666666666655555555555555555555554444443.3556666666666666666666666666666 PP

                           DUF1664 115 sk 116
                                       ++
  gi|336254267|ref|YP_004597374.1| 287 TE 288
                                       55 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.012
                           DUF1664  57 laatkrhLssridrv..dkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       l++ +++L+++ + +  d+ l++ ++ + ++++ ++e++   +e+++d+e+v+ a+++ ++++er+
  gi|336254267|ref|YP_004597374.1| 285 LETEREELAEERADLlaDADLEAANADTDAVEARIEELEARDEELRDDLEEVRVAITETNGEIERL 350
                                       555566665443333236778888888888888888888888888888888888888888888776 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.26
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                       +le+  ++ ++  ++L++ri+  ++ + + +e  ++++++++++re+ ++   ++    +  e+l
  gi|336254267|ref|YP_004597374.1| 356 DLESQADEARTEADDLAERIEGDEDDIADREEKLEDLEDDIETAREQFDDAPIEFGDAAAHLEDL 420
                                       45555666666677777788877777777777777788887777777776666665555555555 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.23
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredl 96 
                                       +le+  e+l+a +++L +ri+r ++  +               +++ +
  gi|336254267|ref|YP_004597374.1| 482 DLEKQLEELEAERDDLDERIERAEALRE---------------AERRV 514
                                       3455555555555555555555433222...............22222 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0058
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                       ++ ++++++L ++ ++ +++ +e  e ++e+++ev+e re+l ei+ +  ++ke+ e l  +++
  gi|336254267|ref|YP_004597374.1| 536 AERREQREDLLEDAEEYESEAEEKREEAAELEDEVAEKREELGEINGERGEIKETLEALR-RIA 598
                                       3335688899*********************************************99985.455 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 1.8
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseiged 102
                                       +++ + +++L+s+i++  ++  + +++  e +e +++ re  ++++++
  gi|336254267|ref|YP_004597374.1| 598 AEIDDEREDLESEIENYRERRRNWQQLNDERRETLSSKRERKRDLESE 645
                                       678899999999999999988888888888888888777776666665 PP

  == domain 7  score: 14.5 bits;  conditional E-value: 4.7e-05
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlse...igedvesvkeavegles 115
                                       + ++ k++ ++ i++vd+kl++ +e  +ei++ + +v+++l+e   +++ +es++e    les
  gi|336254267|ref|YP_004597374.1| 653 TAREDKQNAEQYIEKVDAKLEDLEERRTEIQNAIGAVENELEElerLRDRLESLEERCDRLES 715
                                       5567899999**************************998776411155666666666666665 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0075       4.3      17      35 ..      23      41 ..       9      54 .. 0.82
   2 ?    5.3  46.7    0.0048       2.8     635     914 ..     164     452 ..     137     456 .. 0.72
   3 ?    4.0  47.4     0.012         7     240     507 ..     305     576 ..     294     579 .. 0.54
   4 ?    0.1  32.7      0.19   1.1e+02     349     498 ..     469     625 ..     462     631 .. 0.69
   5 ?   11.4  24.3   7.1e-05     0.041     239     408 ..     579     755 ..     576     785 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0075
                           DUF3584 17 dghtnieGtNaaGKTtLlr 35
                                      +g t + G+N++GK tLl 
  gi|336254267|ref|YP_004597374.1| 23 RGVTVVHGVNGSGKSTLLE 41
                                      578999***********96 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0048
                           DUF3584 635 eleeakravaeaatalknard.tlerlqnekesekdklekaiaerkqqaeeqlqkldaqlkqleeqqkaaleelked 710
                                       +le+ ++ +++a+  +k   d ++e l++++++ ++k +k ++er ++ e q+ ++  +++  e q+++a++ l+  
  gi|336254267|ref|YP_004597374.1| 164 ALEDYRERASDARLGVKSVLDgQREVLEDVRKQVERKEDKELHERLNNLESQRAEVTDEIDHYETQREQAQNTLD-- 238
                                       567777777777777777644155667888888888889999999999999999999999999988888877663.. PP

                           DUF3584 711 lseerlekkakwqevvgeldeqlaelkkai...eaartqakarlkeleeaykreLkskdvDpetvkelkr...kiee 781
                                         e  le++a+ qe++++l+e ++ l  +i   e++r+ ak+++ ele+++ +eL++   D  ++++l++   ++ +
  gi|336254267|ref|YP_004597374.1| 239 TAEDVLERHAETQEEISDLEEGIDDLRSKIsetEQQREDAKEQIRELETER-EELAEERADLLADADLEAanaDTDA 314
                                       445556666666666666666666666554111566666777888887764.5788888887777766541125677 PP

                           DUF3584 782 Lekkieriekrreevr....eYraflqetwlkvdslaeerpalkeqveelesaaeeleqeltrliedtklerkklek 854
                                        e++ie+ e r ee+r    e r  + et  +++ l ee + l++q  e +++a +l ++ +  + d   + +kle+
  gi|336254267|ref|YP_004597374.1| 315 VEARIEELEARDEELRddleEVRVAITETNGEIERLCEEADDLESQADEARTEADDLAERIEGDEDDIADREEKLED 391
                                       88888888877665542222678888899999999999999999999999999999999999999999999999999 PP

                           DUF3584 855 erkalekqldqldenlrklrdllsklaelkldadaeqae.gelaerlaaleelkrkrerls 914
                                         + +e + +q d++  ++ d   +l +l+ ++++ + e g++   ++a+e++ ++ erl 
  gi|336254267|ref|YP_004597374.1| 392 LEDDIETAREQFDDAPIEFGDAAAHLEDLESEREDRTDEiGDVTADIRAVENAIEEGERLL 452
                                       9999999999999999899999999988877666665555888888888888877777765 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.012
                           DUF3584 240 iekvrpeieklqeefeqleslelrLsllkgelkadeerlaekqeevqeakaelkqq...lrtledelkeaidelnqe 313
                                       +e+ +++ + +++++e+le   ++L+    e++ ++++ + + e+  e++ +l++q   +rt+ d+l+e+i+  + +
  gi|336254267|ref|YP_004597374.1| 305 LEAANADTDAVEARIEELEARDEELRDDLEEVRVAITETNGEIERLCEEADDLESQadeARTEADDLAERIEGDEDD 381
                                       44444444444444444444444444444444444444444444444444333333111455667777777777777 PP

                           DUF3584 314 lsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkike 390
                                       + + ++kl+  e+++e     +++++da ie   a   +l+ ++se e+   e+  +t  +++v+++ ++ +  ++e
  gi|336254267|ref|YP_004597374.1| 382 IADREEKLEDLEDDIET---AREQFDDAPIEFGDAA-AHLEDLESEREDRTDEIGDVTADIRAVENAIEEGERLLEE 454
                                       77777777777766554...5778******965543.35666778888899999999************99999999 PP

                           DUF3584 391 eleeelek.lker.leaireekdrlkaaieealealesqlrkqlea.qkeelneeekelesrlselklrldsata.. 462
                                        +     +  k++    + + k + + + e++le+le++  +  e  + +e+ +e+++   rl+e    +++  a  
  gi|336254267|ref|YP_004597374.1| 455 GNCPTCGQpVKDSpHVDVLDDKREELSDLEKQLEELEAERDDLDERiERAEALREAERRVDRLEENRDNVEQLVAek 531
                                       77666655144445333444444446666666666666544222210111222222223333333333333333310 PP

                           DUF3584 463 teEeleqieeadealekaqeelekaeaevealqaeeeqlrkkrde 507
                                        e + e+ e+ ++ le a+e   +ae+++e++++ e ++ +kr+e
  gi|336254267|ref|YP_004597374.1| 532 RESLAERREQREDLLEDAEEYESEAEEKREEAAELEDEVAEKREE 576
                                       344556667777778888777666666666666666655555554 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.19
                           DUF3584 349 dldqlpsirseleeleeeldaltekhqdvqekydrrkqkik.eeleeeleklker.leaireekdrl......kaai 417
                                       + d l+  r+el++le++l+ l+ +  d++e+ +r ++ ++ e++ + le+++++ ++ + e+++ l      +++ 
  gi|336254267|ref|YP_004597374.1| 469 HVDVLDDKREELSDLEKQLEELEAERDDLDERIERAEALREaERRVDRLEENRDNvEQLVAEKRESLaerreqREDL 545
                                       67888999999999999999999999999999999988876245567788887775566666666654422223333 PP

                           DUF3584 418 eealealesqlrkqleaqkeelneeekelesrlselklrldsatateEeleqieeadealekaqeelekaeaeveal 494
                                        e+ e+ es+ + ++ ++ +el++e +e +++l+e +  + + + t E l +i+e d++ e  ++e+e+ ++++++ 
  gi|336254267|ref|YP_004597374.1| 546 LEDAEEYESEAE-EKREEAAELEDEVAEKREELGEINGERGEIKETLEALRRIAEIDDEREDLESEIENYRERRRNW 621
                                       333344444444.3334455677777777888888899999999999999999999999999998888888877766 PP

                           DUF3584 495 qaee 498
                                       q+ +
  gi|336254267|ref|YP_004597374.1| 622 QQLN 625
                                       6544 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 7.1e-05
                           DUF3584 239 aiekvrpeieklqeefeqleslelrLsllkgelkadeerlaekqe...evqeakaelkqqlrtledelke.aideln 311
                                       +i+ +r+ei++  e+   ++ +  +   l+ e+++  er ++ q+   e+ e+  +++++ r le+e+ e ++++++
  gi|336254267|ref|YP_004597374.1| 579 EINGERGEIKETLEALRRIAEIDDEREDLESEIENYRERRRNWQQlndERRETLSSKRERKRDLESEFDEeRVATAR 655
                                       57888999999999999999998888888888888777777666512266666677778888899999761568999 PP

                           DUF3584 312 qelsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldalt...ekhqdvqekydrrk 385
                                       +++++a++ +++  ++le lee++ + ++  i  ++++l++l+ +r+ le lee+ d+l+   ++++ +q  y +++
  gi|336254267|ref|YP_004597374.1| 656 EDKQNAEQYIEKVDAKLEDLEERRTEIQN-AIGAVENELEELERLRDRLESLEERCDRLEslyDEAETLQTTYGELR 731
                                       9*************************876.5999999999999999999999988776652227999********** PP

                           DUF3584 386 qkikeeleeeleklker.leaire 408
                                       +++ +++ e le+l ++  e +++
  gi|336254267|ref|YP_004597374.1| 732 SELRQRNVETLERLLNEtFELVYQ 755
                                       ************987774555555 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 ?   13.9   6.1   5.3e-05     0.031     128     246 ..     102     289 ..      96     326 .. 0.43
   2 ?    5.9  14.6     0.014       8.3     142     254 ..     604     732 ..     596     763 .. 0.42

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.3e-05
                      Exonuc_VII_L 128 apTPtaaAelvvpdkaeleeql....................................................... 149
                                        +TPt+  e +  +++e++e l                                                       
  gi|336254267|ref|YP_004597374.1| 102 LETPTETIEGARDVRREVTELLrmdaeafvncayvrqgevnklihaspsdrqdmiddllqlgaledyrerasdarlg 178
                                       67888888888888888866555555555555555555555555555555555555555555554444333333333 PP

                      Exonuc_VII_L 150 ................eelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq..lk 208
                                                       +++er+ +k+++++l++ +++  +++ ++ + e++ e++++ ld +e+ ler+ ++q  ++
  gi|336254267|ref|YP_004597374.1| 179 vksvldgqrevledvrKQVERKEDKELHERLNNLESQRAEVTDEIDHYETQREQAQNTLDTAEDVLERHAETQeeIS 255
                                       33333333333322222222222222222222222222233333334444444444444444444444322222222 PP

                      Exonuc_VII_L 209 kkrerleelkerlkekleekkerlkklkerlelleekk 246
                                         +e ++ l+    +k++e++++ ++ ke++++le+++
  gi|336254267|ref|YP_004597374.1| 256 DLEEGIDDLR----SKISETEQQREDAKEQIRELETER 289
                                       2222222222....222222222222222222222222 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                      Exonuc_VII_L 142 kaeleeqleeler......rlekaikrlleekkqrleklasrl............kspeellerkrqrldeleerle 200
                                       +++le+++e++++      +l+++ +++l++k++r + l+s++            +++e+ +e+   +l++leer +
  gi|336254267|ref|YP_004597374.1| 604 REDLESEIENYRErrrnwqQLNDERRETLSSKRERKRDLESEFdeervataredkQNAEQYIEKVDAKLEDLEERRT 680
                                       56666666666663333334444555666666666666666663322222211112333334444444444444433 PP

                      Exonuc_VII_L 201 ralkkqlkkkrerleelkerlkekleekkerlkklkerlelleekkerleelee 254
                                       + +++++ + +++leel+ rl+++le+ +er+++l++  +++e+ ++++ el +
  gi|336254267|ref|YP_004597374.1| 681 E-IQNAIGAVENELEELE-RLRDRLESLEERCDRLESLYDEAETLQTTYGELRS 732
                                       3.4444444444444444.33333333333333332222222222222222222 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 ?   11.6   0.0   0.00028      0.16       1      16 [.      26      41 ..      26      70 .. 0.89
   2 ?   -0.6   0.1       1.6   9.3e+02     116     183 ..     609     678 ..     601     692 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                   Viral_helicase1  1 ivvhGvpGcGKStlir 16
                                      +vvhGv G+GKStl+ 
  gi|336254267|ref|YP_004597374.1| 26 TVVHGVNGSGKSTLLE 41
                                      69***********986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                   Viral_helicase1 116 ssl.shrvgrrttyllpsdvaeilsak..vgteveversgelkvetepkgqekvlvyltftqalkealgvr 183
                                       s++   r++rr  + l++ + e ls+k   + + e+e+ +e  v+t+ +++++  +y++ + a +e+l +r
  gi|336254267|ref|YP_004597374.1| 609 SEIeNYRERRRNWQQLNDERRETLSSKreRKRDLESEFDEER-VATAREDKQNAEQYIEKVDAKLEDLEER 678
                                       555456888888888999999999999665555666665555.4444444447999999999999999888 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4  11.6   0.00011     0.062      29     117 ..     181     266 ..     161     267 .. 0.77
   2 ?   10.2  22.7   0.00099      0.57       9      96 ..     204     291 ..     198     305 .. 0.69
   3 ?   11.0  11.1   0.00059      0.34       3     102 ..     305     404 ..     301     410 .. 0.84
   4 ?   12.7   7.0   0.00017       0.1       3     110 ..     417     526 ..     415     530 .. 0.88
   5 ?    2.1  29.1      0.32   1.9e+02       2     103 ..     479     579 ..     478     596 .. 0.89
   6 ?   -2.0  27.4       6.1   3.5e+03      10     119 ..     517     625 ..     508     627 .. 0.73
   7 ?    1.6  23.0      0.46   2.7e+02       2     117 ..     603     715 ..     602     732 .. 0.93
   8 ?    2.8  13.2      0.19   1.1e+02      11      92 ..     652     732 ..     648     757 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                        TPR_MLP1_2  29 edlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekel 105
                                       + l  q+e +++  ++   e  + +e  + l++l ++ +e+++ei   ++++e+a+++l+++e  +e +  e ++e+
  gi|336254267|ref|YP_004597374.1| 181 SVLDGQREVLEDVRKQ--VERKEDKELHERLNNLESQRAEVTDEIDHYETQREQAQNTLDTAEDVLE-RHAETQEEI 254
                                       4455556666666663..33456788999*********************************99876.567789*** PP

                        TPR_MLP1_2 106 selekriedlne 117
                                       s+le+ i+dl +
  gi|336254267|ref|YP_004597374.1| 255 SDLEEGIDDLRS 266
                                       *********986 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00099
                        TPR_MLP1_2   9 eikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesaka 85 
                                       e+++ +++ e+++a+++   +  e+q+e+a++  +  e  l  hae+ +e+++l e +++l+++i+e ++++e+ak+
  gi|336254267|ref|YP_004597374.1| 204 ELHERLNNLESQRAEVTDEIDHYETQREQAQNTLDTAEDVLERHAETQEEISDLEEGIDDLRSKISETEQQREDAKE 280
                                       33333444444444444445556778888888888888899999999999999999999999999999999999999 PP

                        TPR_MLP1_2  86 eleeseeswee 96 
                                       ++ e e + ee
  gi|336254267|ref|YP_004597374.1| 281 QIRELETEREE 291
                                       87665544433 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00059
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       l++++++ +++++++ee+ea+ ++l++dle+ +   +e +   er   +  +   +  ++r+e+++l ++i+  +++
  gi|336254267|ref|YP_004597374.1| 305 LEAANADTDAVEARIEELEARDEELRDDLEEVRVAITETNGEIERLCEEADDLESQADEARTEADDLAERIEGDEDD 381
                                       56778888999999999999999999999999999999999999877777777778899999999999999999999 PP

                        TPR_MLP1_2  80 aesakaeleeseesweeqkeele 102
                                         + +++le  e  +e+ +e+++
  gi|336254267|ref|YP_004597374.1| 382 IADREEKLEDLEDDIETAREQFD 404
                                       99999999999999999998876 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00017
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       l+ le+e ++ ++e+ + +a+++++++ +e+ +++++e +     + vk +  v+ l + reel++l+++++el+ae
  gi|336254267|ref|YP_004597374.1| 417 LEDLESEREDRTDEIGDVTADIRAVENAIEEGERLLEEGNCPTCGQPVKDSPHVDVLDDKREELSDLEKQLEELEAE 493
                                       78899999999****************************************************************** PP

                        TPR_MLP1_2  80 aesakaeleesee..sweeqkeelekelselek 110
                                       ++++ + +e++e+  + e++ ++le++ +++e+
  gi|336254267|ref|YP_004597374.1| 494 RDDLDERIERAEAlrEAERRVDRLEENRDNVEQ 526
                                       ********9999722455555788888777776 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.32
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       el+ le+++++l++e ++++++++ + e l++ ++++ + +++  +  ++ ae  ++l++ re+ ++l ++++e ++
  gi|336254267|ref|YP_004597374.1| 479 ELSDLEKQLEELEAERDDLDERIERA-EALREAERRVDRLEENRDNVEQLVAEKRESLAERREQREDLLEDAEEYES 554
                                       899********************997.5699999999999999999999**************************** PP

                        TPR_MLP1_2  79 eaesakaeleeseesweeqkeelek 103
                                       eae+ ++e +e e + +e++eel +
  gi|336254267|ref|YP_004597374.1| 555 EAEEKREEAAELEDEVAEKREELGE 579
                                       ********************99854 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 6.1
                        TPR_MLP1_2  10 ikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakae 86 
                                       +++ +++ e++ a+ ++   + ++q+e + e  + Ye+e  ++ e++   ++l +e++e ++e+ e++ e+ + k++
  gi|336254267|ref|YP_004597374.1| 517 LEENRDNVEQLVAEKRESLAERREQREDLLEDAEEYESEAEEKREEA---AELEDEVAEKREELGEINGERGEIKET 590
                                       33444444555555555555556666666666666888876666655...566789999****************** PP

                        TPR_MLP1_2  87 leese..esweeqkeelekelselekriedlneqN 119
                                       le+ +  ++++ ++e le+e+++ ++r+ + ++ N
  gi|336254267|ref|YP_004597374.1| 591 LEALRriAEIDDEREDLESEIENYRERRRNWQQLN 625
                                       *99883358889****************9999988 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.46
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       e + le+ei++++e+  + ++   + +e l +++e+ ++ +  + +e v  a   ++ q++ + ++++ a++++l++
  gi|336254267|ref|YP_004597374.1| 603 EREDLESEIENYRERRRNWQQLNDERRETLSSKRERKRDLESEFDEERVATA--REDKQNAEQYIEKVDAKLEDLEE 677
                                       7789*******************************************88665..56778999*************** PP

                        TPR_MLP1_2  79 eaesakaeleeseesweeqkeelekelselekriedlne 117
                                       ++ + ++++ + e+++ee  e+l+++l++le+r++ l++
  gi|336254267|ref|YP_004597374.1| 678 RRTEIQNAIGAVENELEE-LERLRDRLESLEERCDRLES 715
                                       ***************987.579*************9975 PP

  == domain 8  score: 2.8 bits;  conditional E-value: 0.19
                        TPR_MLP1_2  11 kslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka...eaesak 84 
                                       ++++e+k++ae+ ++k+  +le  +e+ +e q+     +   +++++el++lr++l++l+++   l++   eae+++
  gi|336254267|ref|YP_004597374.1| 652 ATAREDKQNAEQYIEKVDAKLEDLEERRTEIQN----AIGAVENELEELERLRDRLESLEERCDRLESlydEAETLQ 724
                                       555666666666666666666666666666666....5566666666666666666666655544444111333333 PP

                        TPR_MLP1_2  85 aeleesee 92 
                                       ++  e ++
  gi|336254267|ref|YP_004597374.1| 725 TTYGELRS 732
                                       33333333 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       2.3   1.3e+03      62      80 ..     184     202 ..     175     205 .. 0.82
   2 ?    6.7  15.1     0.014       8.2       9      92 ..     204     292 ..     198     298 .. 0.78
   3 ?    9.0   8.2    0.0027       1.6       3     111 ..     264     367 ..     262     379 .. 0.79
   4 ?   13.9   0.5   8.2e-05     0.048       2      85 ..     328     406 ..     327     411 .. 0.94
   5 ?    2.9   0.0       0.2   1.2e+02       2      56 ..     398     447 ..     397     454 .. 0.84
   6 ?    2.3  18.9      0.33   1.9e+02       7     107 ..     473     567 ..     470     575 .. 0.70
   7 ?   -2.2  17.1       7.8   4.5e+03      11      99 ..     622     710 ..     601     721 .. 0.55
   8 ?    2.1   7.6      0.37   2.1e+02       7      71 ..     651     713 ..     645     748 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.3
                              FliJ  62 aqqkqelaqaekqvekare 80 
                                       + q+++l++ +kqve++++
  gi|336254267|ref|YP_004597374.1| 184 DGQREVLEDVRKQVERKED 202
                                       6799999999999998875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.014
                              FliJ   9 eaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaa.....elrnyqafisaldeaiaqqkqelaqaekqvekare 80 
                                       e + +l++ e++ +e+++++++y+ q ++++++l+ a     +   +q+ is l+e i+ ++++++  e+q+e a+e
  gi|336254267|ref|YP_004597374.1| 204 ELHERLNNLESQRAEVTDEIDHYETQREQAQNTLDTAedvleRHAETQEEISDLEEGIDDLRSKISETEQQREDAKE 280
                                       67788999999999999999999888888875554431111145678899999999999999999999999999999 PP

                              FliJ  81 ewqearqerkkl 92 
                                       +  e + er+ l
  gi|336254267|ref|YP_004597374.1| 281 QIRELETEREEL 292
                                       999999998865 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0027
                              FliJ   3 aareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekar 79 
                                        + +  e ++++++a+e++ ele +r+e++++ ++     + a+l + +a  +a++ +i++++   + ++ ++e+ r
  gi|336254267|ref|YP_004597374.1| 264 LRSKISETEQQREDAKEQIRELETEREELAEERADLL---ADADLEAANADTDAVEARIEELEARDEELRDDLEEVR 337
                                       56778899*********************99999988...99*********************************99 PP

                              FliJ  80 eewqearqerkklekLkerekkeeqkeenrrE 111
                                        +  e + e + l   +e    e q+ e+r E
  gi|336254267|ref|YP_004597374.1| 338 VAITETNGEIERLC--EEADDLESQADEARTE 367
                                       99999988877653..3333334444444433 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 8.2e-05
                              FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqveka 78 
                                       e +  L+e++ ++++ + ++e+l+++ +++++q+ ++       e   + + i+  ++ ia  +++l+++e ++e+a
  gi|336254267|ref|YP_004597374.1| 328 ELRDDLEEVRVAITETNGEIERLCEEADDLESQADEAR-----TEADDLAERIEGDEDDIADREEKLEDLEDDIETA 399
                                       677899*******************************9.....********************************** PP

                              FliJ  79 reewqea 85 
                                       re++  a
  gi|336254267|ref|YP_004597374.1| 400 REQFDDA 406
                                       **98766 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.2
                              FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisa 56 
                                       +a++++  a  e+ +a ++le le++r++   ++ + +     a++r++++ i+ 
  gi|336254267|ref|YP_004597374.1| 398 TAREQFDDAPIEFGDAAAHLEDLESEREDRTDEIGDVT-----ADIRAVENAIEE 447
                                       678888888899999***************99999999.....888888887766 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.33
                              FliJ   7 Laeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewq 83 
                                       L   + el + e++leele +r+++ ++++ +       +lr  ++  ++l+e  +  +q +a +++ + ++re+  
  gi|336254267|ref|YP_004597374.1| 473 LDDKREELSDLEKQLEELEAERDDLDERIERAE------ALREAERRVDRLEENRDNVEQLVAEKRESLAERREQRE 543
                                       5667899999***************88888875......88888888888888888888888888877777776655 PP

                              FliJ  84 earqerkklekLkerekkeeqkee 107
                                             + +e   e++++e+++ e
  gi|336254267|ref|YP_004597374.1| 544 DLLEDAEEYESEAEEKREEAAELE 567
                                       555555555544444444443333 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 7.8
                              FliJ  11 qrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearq 87 
                                       q+  ++ +e l + ++  +++++++ +e  + + ++ +n +++i+++d +++ +++  +  ++++ + ++e+ e ++
  gi|336254267|ref|YP_004597374.1| 622 QQLNDERRETLSSKRERKRDLESEFDEERVATAREDKQNAEQYIEKVDAKLEDLEERRTEIQNAIGAVENELEELER 698
                                       33333444444444444455555555554455555556666666666666665555555555555555555555555 PP

                              FliJ  88 erkklekLkere 99 
                                        r  le L+er+
  gi|336254267|ref|YP_004597374.1| 699 LRDRLESLEERC 710
                                       555555555555 PP

  == domain 8  score: 2.1 bits;  conditional E-value: 0.37
                              FliJ   7 Laeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqa 71 
                                       +a a+  +q+ae+ +e++   +++++++  + +   ++ +  n  + +++l+++++++++ ++++
  gi|336254267|ref|YP_004597374.1| 651 VATAREDKQNAEQYIEKVDAKLEDLEERRTEIQ--NAIGAVENELEELERLRDRLESLEERCDRL 713
                                       555555566666666555555555555555555..333333444444444444444444443333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00019      0.11       1      20 [.      25      44 ..      25     129 .. 0.90
   2 ?   -1.6   1.4       4.6   2.7e+03      31      81 ..     262     311 ..     201     330 .. 0.72
   3 ?   -1.7   0.0       5.1     3e+03      73     110 ..     818     859 ..     771     874 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                            AAA_33  1 lvllvGlpGsGKstlaerll 20
                                      +++++G++GsGKstl+e++ 
  gi|336254267|ref|YP_004597374.1| 25 VTVVHGVNGSGKSTLLEGVF 44
                                      6899************9986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.6
                            AAA_33  31 dtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnls 81 
                                       d+lr+++ +t+qq++    ++++  +++ +ela++++   +++ l a n++
  gi|336254267|ref|YP_004597374.1| 262 DDLRSKISETEQQREDAKEQIRELETER-EELAEERADLLADADLEAANAD 311
                                       5677777777777666555555555555.4666666655555555555555 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5.1
                            AAA_33  73 vildat..nlsrrer...arflklarrlgvpvrivvvetdeet 110
                                       +ild +  +l+  +      +++  r+lgv+  ivvv+ dee+
  gi|336254267|ref|YP_004597374.1| 818 LILDEPtvFLDSGHVtqlVSLVESMRELGVE-QIVVVSHDEEL 859
                                       6777774445544440013445556688877.88888888876 PP

>> FIVAR  FIVAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.5     0.029        17      19      60 ..     221     258 ..     203     270 .. 0.68
   2 ?   -1.3   0.0       6.5   3.8e+03      20      45 ..     430     454 ..     422     459 .. 0.74
   3 ?    6.8   0.1      0.02        11      21      68 ..     643     687 ..     629     690 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.029
                                       CCCCCC-CCHHHHHHHHHHHHHHHC...TSTTTTCCCHHHHH CS
                             FIVAR  19 snysnydqdkkdaynnalsaAnailnktnnpnatveqVnqal 60 
                                        ++  y + + ++ +n l+ A+ +l   +    t+e++ +  
  gi|336254267|ref|YP_004597374.1| 221 DEIDHYET-QREQAQNTLDTAEDVL---ERHAETQEEISDLE 258
                                       44444555.559*************...55588888887655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.5
                                       CCCCC-CCHHHHHHHHHHHHHHHC.. CS
                             FIVAR  20 nysnydqdkkdaynnalsaAnailnk 45 
                                       ++++ ++d+  a +na+++ + +l++
  gi|336254267|ref|YP_004597374.1| 430 EIGDVTADI-RAVENAIEEGERLLEE 454
                                       567778888.8889999999999943 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.02
                                       CCCC-CCHHHHHHHHHHHHHHHC...TSTTTTCCCHHHHHHHHHHHHH CS
                             FIVAR  21 ysnydqdkkdaynnalsaAnailnktnnpnatveqVnqalanlnqain 68 
                                        s+ d++ +++  + +++A++ +   ++ +a  e+ ++  +++++ai 
  gi|336254267|ref|YP_004597374.1| 643 ESEFDEERVATAREDKQNAEQYI---EKVDAKLEDLEERRTEIQNAIG 687
                                       6788999****************...888*****************96 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.14      13      51 ..      10      48 ..       2      69 .. 0.82
   2 ?   -3.0   0.2         9   5.2e+03     145     172 ..     205     231 ..     186     276 .. 0.55
   3 ?   -2.6   0.5       6.7   3.9e+03     137     158 ..     505     526 ..     474     540 .. 0.59
   4 ?   -1.2   0.3       2.5   1.4e+03     137     172 ..     684     718 ..     636     746 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                                      EETTEEEEEE-HHHHHHHHHS--SHHHHHHHHHHHHHHS CS
                              MukB 13 nWnGffartfdldelvttlsGgnGaGksttmaafvtali 51
                                      n++ +      ld+ vt + G nG+Gkst + +++ al 
  gi|336254267|ref|YP_004597374.1| 10 NFKCYGDADLGLDRGVTVVHGVNGSGKSTLLEGVFFALY 48
                                      666666667789*******************99998885 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9
                                       EE--HHHHHHHHHTSTT-EEEE-S-HHH CS
                              MukB 145 rvrelnelkekleelegvrlkkfnsvtd 172
                                          +ln+l ++ +e+ + ++ ++++ ++
  gi|336254267|ref|YP_004597374.1| 205 LHERLNNLESQRAEVTD-EIDHYETQRE 231
                                       33444444444444333.4444444443 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.7
                                       E--SSS--EE--HHHHHHHHHT CS
                              MukB 137 eklddkkarvrelnelkeklee 158
                                       e l + + rv +l+e ++++e+
  gi|336254267|ref|YP_004597374.1| 505 EALREAERRVDRLEENRDNVEQ 526
                                       3334444555555555555555 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 2.5
                                       E--SSS--EE--HHHHHHHHHTSTT-EEEE-S-HHH CS
                              MukB 137 eklddkkarvrelnelkekleelegvrlkkfnsvtd 172
                                       + ++  ++++ el+ l+++le+le+ r  + +s+ d
  gi|336254267|ref|YP_004597374.1| 684 NAIGAVENELEELERLRDRLESLEE-RCDRLESLYD 718
                                       2333334455555556666666555.5555555544 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00024      0.14       2      26 ..      25      49 ..      24      58 .. 0.85
   2 ?   -2.4   0.8       6.8   3.9e+03      88     156 ..     221     298 ..     187     306 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                                      CEEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                      + +++G +GsGK+tLl+++ +a+  
  gi|336254267|ref|YP_004597374.1| 25 VTVVHGVNGSGKSTLLEGVFFALYG 49
                                      579**************99988765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.8
                                       E-STT-SS-TCH.....................HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE--TC CS
                             NACHT  88 DglDelvtdlgq............kekqpvrtlLselirkkllpeasllltvrpralrdleeqleeaivlevegfse 152
                                       D +D  +t+ +q            ++ +++++ +s+l ++  +   + +++ + ++++d++eq++e   +e e++ e
  gi|336254267|ref|YP_004597374.1| 221 DEIDHYETQREQaqntldtaedvlERHAETQEEISDLEEG--IDDLRSKISETEQQREDAKEQIREL-ETEREELAE 294
                                       6666666666666667777777777777778888887777..7777778888888888888888877.777777777 PP

                                       CHHH CS
                             NACHT 153 srrk 156
                                       +r++
  gi|336254267|ref|YP_004597374.1| 295 ERAD 298
                                       7665 PP

>> CEP63  Centrosomal protein of 63 kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   9.0    0.0019       1.1     153     227 ..     182     255 ..     148     256 .. 0.89
   2 ?   15.7  19.7   1.9e-05     0.011     117     266 ..     248     397 ..     246     401 .. 0.82
   3 ?    0.7   0.2      0.71   4.1e+02      33      78 ..     385     430 ..     378     440 .. 0.86
   4 ?    2.0  23.1      0.28   1.6e+02      49     170 ..     471     596 ..     468     601 .. 0.80
   5 ?    2.1  23.4      0.25   1.5e+02     121     255 ..     602     738 ..     594     756 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0019
                             CEP63 153 sleaqrkaLaekleliqsaaykvqlekrkqkLesveldsqseiqrLrskleraqdtleaqelelerLrllveelg 227
                                        l+ qr+ L +  +++++    ++l++r + Les+  ++  ei + +++ e+aq+tl++ e  ler  + +ee+ 
  gi|336254267|ref|YP_004597374.1| 182 VLDGQREVLEDVRKQVER-KEDKELHERLNNLESQRAEVTDEIDHYETQREQAQNTLDTAEDVLERHAETQEEIS 255
                                       589999999999999988.77889******************************************999999875 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.9e-05
                             CEP63 117 eedrvelsrlnskleefrqkslewekqrlqyqkqvasleaqrkaLaekle.liqsaaykvqlekrkqkLesveldsq 192
                                        e + e+s l++ +++ r+k  e e+qr   ++q+  le +r+ Lae+   l+  a  ++  ++ +  +e    + +
  gi|336254267|ref|YP_004597374.1| 248 AETQEEISDLEEGIDDLRSKISETEQQREDAKEQIRELETEREELAEERAdLLADADLEAANADTDA-VEARIEELE 323
                                       5778899***************************************876505555444444444433.243323455 PP

                             CEP63 193 seiqrLrskleraqdtleaqelelerLrllveelgkskrvlleekqeleeelresekqlqvleeekselkqtlq 266
                                       ++ + Lr +le+ +  ++  + e+erL +  ++l  +      e  +l+e+++  e +   +ee +++l+  ++
  gi|336254267|ref|YP_004597374.1| 324 ARDEELRDDLEEVRVAITETNGEIERLCEEADDLESQADEARTEADDLAERIEGDEDDIADREEKLEDLEDDIE 397
                                       66679*********************************9************99999999999998888887765 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.71
                             CEP63  33 letrlkireeeLasarnaldekhkEvgllrqqleelekekqelvak 78 
                                        e +l+  e+++++ar++ d    E g    +le+le e+++++ +
  gi|336254267|ref|YP_004597374.1| 385 REEKLEDLEDDIETAREQFDDAPIEFGDAAAHLEDLESEREDRTDE 430
                                       5788999999****************************99998876 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.28
                             CEP63  49 naldekhkEvgllrqqleelekekqelvakye..qqlqklreelsklkrsyekLqrkqlkearek..eakskeedr. 120
                                       ++ld k +E   l++qleele+e+ +l ++ e  + l++ ++ +++l+++ +   +    e+re   e ++++ed  
  gi|336254267|ref|YP_004597374.1| 471 DVLDDKREELSDLEKQLEELEAERDDLDERIEraEALREAERRVDRLEENRDNVEQLVA-EKRESlaERREQREDLl 546
                                       579*********************99987655226799999999999988877654322.22222234555555551 PP

                             CEP63 121 velsrlnskleefrqkslewekqrlqyqkqvasleaqrkaLaekleliqs 170
                                        + ++++s+ ee r+ ++e e + + +++++  ++ +r  ++e le +++
  gi|336254267|ref|YP_004597374.1| 547 EDAEEYESEAEEKREEAAELEDEVAEKREELGEINGERGEIKETLEALRR 596
                                       568999*************************************9998876 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.25
                             CEP63 121 velsrlnskleefrqkslewekqrlqyqkqvasleaqrkaLaekleliqsaaykvqlekrkqkLesveldsqseiqr 197
                                        e + l+s++e++r++ ++w++ +  +++ ++s  + ++ L  +++  + a+ + ++++ +q +e+v+ + + +++ 
  gi|336254267|ref|YP_004597374.1| 602 DEREDLESEIENYRERRRNWQQLNDERRETLSSKRERKRDLESEFDEERVATAREDKQNAEQYIEKVDAKLE-DLEE 677
                                       5667899***************************************9999999************7775543.4666 PP

                             CEP63 198 LrskleraqdtleaqelelerLrllveelgk...skrvlleekqeleeelresekqlqvle 255
                                        r+++++a   +e +  elerLr ++e l +   + + l +e + l+ +  e   +l++++
  gi|336254267|ref|YP_004597374.1| 678 RRTEIQNAIGAVENELEELERLRDRLESLEErcdRLESLYDEAETLQTTYGELRSELRQRN 738
                                       6777777777777666678899988888877433334555666666555333333332222 PP

>> RepA_C  Plasmid encoded RepA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4    0.0003      0.17      38     106 ..     176     241 ..     171     250 .. 0.88
   2 ?   -1.6   0.8       4.1   2.4e+03      46      95 ..     581     628 ..     554     647 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                            RepA_C  38 rlGlttvsgGarGtlkdireqvsriaaceltvrwedaeslgdektailedkilfederdseqgslfese 106
                                       rlG+++v  G+r  l+d+r qv+r    el  r ++ es   ++ ++ ++  ++e +r++ q++l   e
  gi|336254267|ref|YP_004597374.1| 176 RLGVKSVLDGQREVLEDVRKQVERKEDKELHERLNNLES---QRAEVTDEIDHYETQREQAQNTLDTAE 241
                                       89***************************9988877766...788999***************986555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.1
                            RepA_C  46 gGarGtlkdireqvsriaaceltvrwedaeslgdektailedkilfeder 95 
                                        G+rG++k+  e + ria   +  + ed es  ++  + + ++ + +der
  gi|336254267|ref|YP_004597374.1| 581 NGERGEIKETLEALRRIAE--IDDEREDLESEIENYRERRRNWQQLNDER 628
                                       5999999999999999984..45555555554344334444444444333 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  24.4     0.011       6.2     121     250 ..     195     322 ..     179     325 .. 0.73
   2 ?    8.6  16.1    0.0019       1.1     133     247 ..     303     417 ..     298     447 .. 0.66
   3 ?    4.7  10.5     0.028        16     131     235 ..     420     530 ..     411     538 .. 0.69
   4 ?    1.9  18.1       0.2   1.1e+02     119     235 ..     604     719 ..     586     751 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
                           DUF4407 121 kelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqa 197
                                       k+++++ +++l ++l++le+q+a+   eid  e+++++++++++   d       ++ a   ++    ++ +d+++ 
  gi|336254267|ref|YP_004597374.1| 195 KQVERKEDKELHERLNNLESQRAEVTDEIDHYETQREQAQNTLDTAEDV-----LERHAETQEEISDLEEGIDDLRS 266
                                       3444445555999999999999999999999999999999999966664.....33355556777778888888888 PP

                           DUF4407 198 elaelkakld.atarlaalraelaeleaerakeraa..sqaaaaaddGllarleal 250
                                       ++ e +++++ a++++ +l++e++el++era+  a+   +aa+a+ d + ar+e l
  gi|336254267|ref|YP_004597374.1| 267 KISETEQQREdAKEQIRELETEREELAEERADLLADadLEAANADTDAVEARIEEL 322
                                       88888888778999999999999999999998765500556666666666666655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0019
                           DUF4407 133 aelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld.a 208
                                       a+l++++a+++a +a i+++ear ++lr++++ e+  + +++   +++  ++a+  ++q+d+a++e ++l ++++  
  gi|336254267|ref|YP_004597374.1| 303 ADLEAANADTDAVEARIEELEARDEELRDDLE-EVRVAITETNGEIERLCEEADDLESQADEARTEADDLAERIEgD 378
                                       55666777777777777777777777777766.44444433333567777777778888888888888888887777 PP

                           DUF4407 209 tarlaalraelaeleaerakeraasqaaaaaddGllarl 247
                                       ++++a+++++l++le++++++r+++++a  ++ + +a l
  gi|336254267|ref|YP_004597374.1| 379 EDDIADREEKLEDLEDDIETAREQFDDAPIEFGDAAAHL 417
                                       777888888888888888888877776444333333333 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.028
                           DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld 207
                                       l++e ++ +++i +  a i+a e+++++ ++ +++   +t+g+  + +    ++ + k+++l +++++l+el+a++d
  gi|336254267|ref|YP_004597374.1| 420 LESEREDRTDEIGDVTADIRAVENAIEEGERLLEEGNCPTCGQPVK-DSPHVDVLDDKREELSDLEKQLEELEAERD 495
                                       5566666677777777777777777777777776555555554433.344456777799999999999999999988 PP

                           DUF4407 208 .......atarlaalraelaeleaerakeraasqa 235
                                              ++++l +++++ ++le++r++ ++  ++
  gi|336254267|ref|YP_004597374.1| 496 dlderieRAEALREAERRVDRLEENRDNVEQLVAE 530
                                       88888888888888888888888888877765554 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.2
                           DUF4407 119 eakelkeqlaaa...ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaql 192
                                       +     e l+++   ++++ ++ ++ +++ +++++++++r ++l+ e+++e   t  +    ++  +++ ++ +a+l
  gi|336254267|ref|YP_004597374.1| 604 R-----EDLESEienYRERRRNWQQLNDERRETLSSKRERKRDLESEFDEERVATARED---KQNAEQYIEKVDAKL 672
                                       2.....22222233388888888888888888888888888888888888888655444...555555555555555 PP

                           DUF4407 193 daaqaelaelkakld....atarlaalraelaeleaerakeraasqa 235
                                       ++++++ +e+++ +     + ++l++lr++l++le++ ++ ++  ++
  gi|336254267|ref|YP_004597374.1| 673 EDLEERRTEIQNAIGavenELEELERLRDRLESLEERCDRLESLYDE 719
                                       55555555555555455584455555555555555554444443333 PP

>> YhzD  YhzD-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.8     1e+03      27      42 ..     442     457 ..     436     461 .. 0.87
   2 ?   -1.6   0.0       5.1   2.9e+03      14      22 ..     743     751 ..     740     760 .. 0.83
   3 ?    7.8   0.0    0.0062       3.6       3      20 ..     767     784 ..     766     789 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.8
                              YhzD  27 eeAkekGekkLkekgl 42 
                                       e+A e+Ge++L+e ++
  gi|336254267|ref|YP_004597374.1| 442 ENAIEEGERLLEEGNC 457
                                       68999******99876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.1
                              YhzD  14 eklLdetfe 22 
                                       e lL+etfe
  gi|336254267|ref|YP_004597374.1| 743 ERLLNETFE 751
                                       789*****8 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0062
                              YhzD   3 tYflTvFdksGeklLdet 20 
                                       +Y lTvF+k+Ge l  e+
  gi|336254267|ref|YP_004597374.1| 767 DYRLTVFQKDGEALEPEQ 784
                                       6***********986665 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 ?    7.7  24.8    0.0034         2      32     168 ..     199     336 ..     187     339 .. 0.86
   2 ?    9.3   4.9    0.0011      0.64      33     131 ..     317     412 ..     310     424 .. 0.78
   3 ?    7.9   1.3    0.0031       1.8      27     122 ..     346     438 ..     339     453 .. 0.59
   4 ?   -1.4  22.7       2.1   1.2e+03      28     124 ..     473     572 ..     467     579 .. 0.79
   5 ?    1.2  12.6      0.33   1.9e+02      32     106 ..     560     640 ..     557     650 .. 0.74
   6 ?    6.9  11.6     0.006       3.5      43     134 ..     652     743 ..     640     750 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0034
                               GAS  32 KeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkweh 108
                                       ++e +el ++ +  e + +e++ e  +++ + ++a++ ++  +  l+++ + ++++  l++ + +l +++++++++ 
  gi|336254267|ref|YP_004597374.1| 199 RKEDKELHERLNNLESQRAEVTDEIDHYETQREQAQNTLDTAEDVLERHAETQEEISDLEEGIDDLRSKISETEQQR 275
                                       45668899999999999999999999999999999999999999********************************* PP

                               GAS 109 evleqrfekvekerdelykkfeaaiqevqqktglknl.lLekklkalqeelEkkeaqleev 168
                                       e  ++++ ++e er+el ++  + + ++  ++ +  +  +e ++++l+++ E+    leev
  gi|336254267|ref|YP_004597374.1| 276 EDAKEQIRELETEREELAEERADLLADADLEAANADTdAVEARIEELEARDEELRDDLEEV 336
                                       ********************99999999876665544278888888888877777777766 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
                               GAS  33 eeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehe 109
                                         ieel++++e+ + +l+e+     + + +++++ ee + L+ q+ + + +    + l +r++  e+ + d +++ e
  gi|336254267|ref|YP_004597374.1| 317 ARIEELEARDEELRDDLEEVRVAITETNGEIERLCEEADDLESQADEARTEA---DDLAERIEGDEDDIADREEKLE 390
                                       5689999999999999999999999999999999999999999988776654...5556677777777777777777 PP

                               GAS 110 vleqrfekvekerdelykkfea 131
                                        le+ +e++ +++d+   +f +
  gi|336254267|ref|YP_004597374.1| 391 DLEDDIETAREQFDDAPIEFGD 412
                                       7777777777777776666555 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0031
                               GAS  27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkd 103
                                        I++l ee  +l+ ++++++ e ++++++ +  ++ +   ee++e L+ ++++ ++++   + +  +  ++  +l+d
  gi|336254267|ref|YP_004597374.1| 346 EIERLCEEADDLESQADEARTEADDLAERIEGDEDDIADREEKLEDLEDDIETAREQF---DDAPIEFGDAAAHLED 419
                                       4677777777888888888888888888888888888888888888877776665543...3344444444444444 PP

                               GAS 104 lkwehevleqrfekveker 122
                                       l+ e e   +++  v +++
  gi|336254267|ref|YP_004597374.1| 420 LESEREDRTDEIGDVTADI 438
                                       4444444444444443333 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.1
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyek....dkqslknlkarlkeleke 100
                                        +  +ee+ +l+k+ e+ e e +++ ++ +r  e L++ae+ v++L+++  n e+    +++sl++ +++ ++l + 
  gi|336254267|ref|YP_004597374.1| 473 LDDKREELSDLEKQLEELEAERDDLDERIER-AEALREAERRVDRLEENRDNVEQlvaeKRESLAERREQREDLLED 548
                                       5666899999999999999999999999988.5899999*******9999888762222567788888888888888 PP

                               GAS 101 lkdlkwehevleqrfekvekerde 124
                                        ++ + e+e ++++ +++e+e  e
  gi|336254267|ref|YP_004597374.1| 549 AEEYESEAEEKREEAAELEDEVAE 572
                                       888888888888888888887665 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.33
                               GAS  32 KeeieelkkkeernekelseisqenkrlkepLkkaee......eveeLrkqlknyekdkqslknlkarlkelekelk 102
                                       +ee +el+ + ++++ el ei+ e  ++ke+L+++++      e+e L+ +++ny++ +   ++l+ + +e+ +  +
  gi|336254267|ref|YP_004597374.1| 560 REEAAELEDEVAEKREELGEINGERGEIKETLEALRRiaeiddEREDLESEIENYRERRRNWQQLNDERRETLSSKR 636
                                       79999*************************99987643333337778888888888888877777777776666555 PP

                               GAS 103 dlkw 106
                                       + k 
  gi|336254267|ref|YP_004597374.1| 637 ERKR 640
                                       5444 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.006
                               GAS  43 ernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekve 119
                                       + ++ + ++++q  ++   +L+ +ee + e ++++   e++ ++l++l+ rl++le+   +l+  ++  e   ++  
  gi|336254267|ref|YP_004597374.1| 652 ATAREDKQNAEQYIEKVDAKLEDLEERRTEIQNAIGAVENELEELERLRDRLESLEERCDRLESLYDEAETLQTTYG 728
                                       4556677888999999999**************************************99999999999999999999 PP

                               GAS 120 kerdelykkfeaaiq 134
                                       + r el+++  ++++
  gi|336254267|ref|YP_004597374.1| 729 ELRSELRQRNVETLE 743
                                       999999999888776 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3  12.6      0.17        99     336     412 ..     199     272 ..     177     311 .. 0.70
   2 ?   10.8   0.8   0.00023      0.13     329     434 ..     316     413 ..     297     424 .. 0.70
   3 ?    4.5  14.5     0.019        11     330     419 ..     492     580 ..     450     590 .. 0.66
   4 ?   -0.3  11.8      0.55   3.2e+02     326     420 ..     591     690 ..     570     693 .. 0.69
   5 ?    4.6  10.0     0.017        10     315     441 ..     631     744 ..     623     764 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.17
                              FapA 336 keklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskk 412
                                       +++ kel e+l++le++  +++++i++ +    + ++ ++ +++ + +le   + +ee+++lee +++l +++ + +
  gi|336254267|ref|YP_004597374.1| 199 RKEDKELHERLNNLESQRAEVTDEIDHYET---QREQAQNTLDTAEDVLERHAETQEEISDLEEGIDDLRSKISETE 272
                                       344477777777777777777777777777...34445677777777777777777777777777777777776662 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00023
                              FapA 329 gldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelk 405
                                       + +  el ++ +el+++lee++  +++ + +i++l +         + ++q ++++++   l e++e  e+++++ +
  gi|336254267|ref|YP_004597374.1| 316 EARIEELEARDEELRDDLEEVRVAITETNGEIERLCE------EADDLESQADEARTEADDLAERIEGDEDDIADRE 386
                                       2333344444455666666666666666666666666......2345678999999999****************** PP

                              FapA 406 eeleskkeeakikvnkeiypgvkikigkk 434
                                       e+le+   e  i++ +e ++   i++g++
  gi|336254267|ref|YP_004597374.1| 387 EKLEDL--EDDIETAREQFDDAPIEFGDA 413
                                       *****9..668888888888888888765 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.019
                              FapA 330 ldepelkekl..keleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkel 404
                                        ++ +l+e++  +e  +e e+  ++le+ ++++++l ++k   +  +e++eq + lle+ e++++e ee +ee +el
  gi|336254267|ref|YP_004597374.1| 492 AERDDLDERIerAEALREAERRVDRLEENRDNVEQLVAEK--RESLAERREQREDLLEDAEEYESEAEEKREEAAEL 566
                                       2223333333224444444444555555555577777733..34578888888888888899999999999999999 PP

                              FapA 405 keeleskkeeakikv 419
                                       ++e+++k +e+  ++
  gi|336254267|ref|YP_004597374.1| 567 EDEVAEK-REELGEI 580
                                       9999998.4544444 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.55
                              FapA 326 ievgldepelkeklkeleeeleeleeeleklkkk.......ikklpklkaekqlese.kkeqlkklletkeklkeel 394
                                       +e+  +  e+++++++le e+e+++e+ ++ ++        +++ ++ + + +lese  +e ++ ++e+k++ ++ +
  gi|336254267|ref|YP_004597374.1| 591 LEALRRIAEIDDEREDLESEIENYRERRRNWQQLnderretLSSKRE-R-KRDLESEfDEERVATAREDKQNAEQYI 665
                                       44544456778888999999999977777777777778544333333.3.344444415678899999999999999 PP

                              FapA 395 eeleeelkelkeeleskkeeakikvn 420
                                       e+++++l++l+e+  +  ++a+ +v+
  gi|336254267|ref|YP_004597374.1| 666 EKVDAKLEDLEERRTEI-QNAIGAVE 690
                                       99999999999998888.66666655 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.017
                              FapA 315 klGselgtkteievgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklk 391
                                       +l s+ + k ++e ++d     e+++  +e+ ++ e+++ek+++k++ l++          ++ ++++++ + e+  
  gi|336254267|ref|YP_004597374.1| 631 TLSSKRERKRDLESEFD----EERVATAREDKQNAEQYIEKVDAKLEDLEE----------RRTEIQNAIGAVENEL 693
                                       56667777777777777....666688888888888888888888888887..........5578888888888888 PP

                              FapA 392 eeleeleeelkelkeeleskkeea.kikvnkeiypgvkikigkkkliikre 441
                                       eele l+++l++l+e+ ++ ++   + ++ ++ y + + ++++++ ++ + 
  gi|336254267|ref|YP_004597374.1| 694 EELERLRDRLESLEERCDRLESLYdEAETLQTTYGELRSELRQRNVETLER 744
                                       888888888888888888887777788888888888888888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (894 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2770  (0.154498); expected 358.6 (0.02)
Passed bias filter:                      907  (0.0505884); expected 358.6 (0.02)
Passed Vit filter:                       344  (0.0191868); expected 17.9 (0.001)
Passed Fwd filter:                       217  (0.0121033); 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: 4.19u 0.40s 00:00:04.59 Elapsed: 00:00:00.77
# Mc/sec: 3494.87
//
Query:       gi|336254268|ref|YP_004597375.1|  [L=468]
Description: metallophosphoesterase [Halopiger xanaduensis SH-6]
Scores for 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-12   45.9   0.2    1.5e-11   45.2   0.2    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    2.4e-11   44.1   0.1    4.7e-11   43.2   0.1    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.026   14.7   0.0    1.5  1  Response_reg   Response regulator receiver domain


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 !   45.2   0.2   2.4e-15   1.5e-11       2     123 ..       3     154 ..       2     209 .. 0.71

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 2.4e-15
                                       EEEEEESBTB....TTCCTHHHHHHHHHHHH....HHHTTESEEEEESTSSSSS.....HHHHHHHHHHHHHHHHTS CS
                       Metallophos   2 rilvigDlHl....algggqlddllkllddl....lreekpdlvllaGDlvdrg.....dlekellellaalvkypi 65 
                                       r++++gD+H+       +++ +d+l++++ +     ++ ++d+v++aGDl+++      dl+  +++ l+ l + +i
  gi|336254268|ref|YP_004597375.1|   3 RVIHTGDTHIgyqqYNSPERRRDFLAAFRGVvedaVDD-DVDAVIHAGDLFHDRrpgllDLQG-TIDILRTLADADI 77 
                                       89***********9555555555555554442221777.**********9999999***9999.****9******** PP

                                       EEEEEC-TTS....................CHHHHHHHHHHHHHHH.HHHHEHHHCEEETSEEEEEETTEEEEEEEE CS
                       Metallophos  66 pvylllGNHe....................gfeeellnkygylgif.sepwrsdaevfnnlplaslgsgslkvlllh 121
                                       p+ ++ GNHe                    g + e+    +++g++  +  r+++  +++ p+ +  +   + l+ h
  gi|336254268|ref|YP_004597375.1|  78 PFLAVVGNHEgkrdaqwldlfadlglatrlGADPEVVGDVAFYGLDfVPRSRREDLEYEFEPVPDAADR--TALVSH 152
                                       **********87777777777777777766555555555555555554444555555566666665555..556666 PP

                                       SE CS
                       Metallophos 122 Gg 123
                                       G 
  gi|336254268|ref|YP_004597375.1| 153 GL 154
                                       65 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 !   43.2   0.1   7.8e-15   4.7e-11       2     164 ..       3     223 ..       2     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 7.8e-15
                     Metallophos_2   2 klaiiSDlH.............snldaleavlealkevgvdaiihaGDl.eeeep.........evleellela.pv 54 
                                       ++++  D+H             + l+a + v+e++ + +vda+ihaGDl  ++ p         ++l++l +   p+
  gi|336254268|ref|YP_004597375.1|   3 RVIHTGDTHigyqqynsperrrDFLAAFRGVVEDAVDDDVDAVIHAGDLfHDRRPglldlqgtiDILRTLADADiPF 79 
                                       5788999999999999999888888999999*****************77666666666665557888888888*** PP

                     Metallophos_2  55 laVrGNnD.................eevveedvlreaaelgtdl......................peeaelel... 89 
                                       laV GN++                       +           l                       e+ e e+   
  gi|336254268|ref|YP_004597375.1|  80 LAVVGNHEgkrdaqwldlfadlglaT-----R-----------LgadpevvgdvafygldfvprsrREDLEYEFepv 140
                                       ********877777666665444431.....2...........1333333333346666667665424444444666 PP

                     Metallophos_2  90 ...agekvlliHgdpl...gvkdalaellkeaeegsd.vvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe..ty 157
                                          a++++l+ Hg      +++ + ++ll e++ +++  v++G  H p   + ++ +v + Gs ++++ +++e  +y
  gi|336254268|ref|YP_004597375.1| 141 pdaADRTALVSHGLFEpfaHADWDTERLLAEST-VDFdAVLLGDNHAPDTADVQDAWVTYCGSTERASASEREdrGY 216
                                       7768888******94499988888888888833.3346****************************98888777789 PP

                     Metallophos_2 158 aildtde 164
                                        +++ d+
  gi|336254268|ref|YP_004597375.1| 217 NLVEFDD 223
                                       8888876 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.4e-06     0.026      19      82 ..     212     277 ..     205     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.4e-06
                                       HHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHH.HHHHHCTTTS..EEEEEESSTS CS
                      Response_reg  19 eeegyeevaeaedgkealellkeekvdlillDinmpgmdGlell.keireedpel..pviiltahse 82 
                                       e++gy +  e++d  +  + + +e+ d +++D++++  +G++ + +++r++dp l   v+i+t ++e
  gi|336254268|ref|YP_004597375.1| 212 EDRGY-NLVEFDDEVAISRRAIAETRDFVFVDVELEADEGIDRVqERVRQHDPGLedAVVIVTIEGE 277
                                       57899.9999*******************************86516789999665226999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3586.69
//
Query:       gi|336254269|ref|YP_004597376.1|  [L=89]
Description: hypothetical protein Halxa_2881 [Halopiger xanaduensis SH-6]
Scores for 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-06   27.3   0.0    2.8e-06   26.8   0.0    1.2  1  HTH_24        Winged helix-turn-helix DNA-binding
    0.00058   19.7   0.0    0.00076   19.3   0.0    1.2  1  MarR_2        MarR family
     0.0011   18.6   0.0     0.0016   18.0   0.0    1.2  1  GntR          Bacterial regulatory proteins, gntR family
      0.002   18.0   0.1     0.0027   17.5   0.1    1.3  1  TFIIE_alpha   TFIIE alpha subunit
      0.004   16.8   0.0     0.0066   16.1   0.0    1.4  1  Sigma70_r4_2  Sigma-70, region 4
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.021   15.0   0.0    1.3  1  HTH_28        Helix-turn-helix domain
      0.016   15.2   0.0      0.018   15.0   0.0    1.3  1  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.079   12.9   0.0       0.11   12.4   0.0    1.2  1  MarR          MarR family
      0.099   12.1   0.0       0.13   11.7   0.0    1.1  1  RepL          Firmicute plasmid replication protein (RepL)
      0.099   12.5   0.0       0.18   11.7   0.0    1.4  1  HTH_23        Homeodomain-like domain
       0.11   12.8   0.0       0.15   12.5   0.0    1.2  1  Rrf2          Transcriptional regulator
       0.12   12.4   0.1       0.36   10.8   0.1    2.0  1  HTH_12        Ribonuclease R winged-helix domain
       0.14   11.7   0.1       0.39   10.3   0.1    1.8  2  Sigma70_r4    Sigma-70, region 4


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 !   26.8   0.0   2.1e-09   2.8e-06      11      47 ..      33      69 ..      31      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.1e-09
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +L+ n  ++q+++Ae++ l++ tv++ l+rL ee +I
  gi|336254269|ref|YP_004597376.1| 33 VLEYNDTMTQQQIAEETLLPSRTVRYALNRLDEENVI 69
                                      688899*****************************99 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.5e-07   0.00076       3      55 ..      23      73 ..      21      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.5e-07
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      l+p+   v  +L  ++   +t++++a+++ l+  +v ++l+rL +   +  r 
  gi|336254269|ref|YP_004597376.1| 23 LPPSAKLVAKVLEYNDT--MTQQQIAEETLLPSRTVRYALNRLDEENVIDSRF 73
                                      66666677778889999..**************************99998773 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.2e-06    0.0016      12      56 ..      28      71 ..      26      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                                      HHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR 12 dIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglver 56
                                      ++++++l+ +d++ +++++a+e      tvR AL+rL +e+++ +
  gi|336254269|ref|YP_004597376.1| 28 KLVAKVLEYNDTM-TQQQIAEETLLPSRTVRYALNRLDEENVIDS 71
                                      788999*******.**************************99865 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1     2e-06    0.0027      14      60 ..      26      72 ..      18      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-06
                                      HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE CS
                       TFIIE_alpha 14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkyk 60
                                      +a+lv +vL  +  +t  ++a+e+ +    +r +LnrL e+ +++ +
  gi|336254269|ref|YP_004597376.1| 26 SAKLVAKVLEYNDTMTQQQIAEETLLPSRTVRYALNRLDEENVIDSR 72
                                      5789999*************************************987 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 !   16.1   0.0   4.8e-06    0.0066      23      49 ..      36      62 ..      31      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.8e-06
                                      HTS---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 23 yleglsykEIAellgisegtVksrlsR 49
                                      y + +++++IAe++ ++++tV+++l R
  gi|336254269|ref|YP_004597376.1| 36 YNDTMTQQQIAEETLLPSRTVRYALNR 62
                                      55789******************9987 PP

>> HTH_28  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   1.5e-05     0.021       6      39 ..      33      66 ..      32      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                            HTH_28  6 ikllaaGhsvreaArelgisrrtvyrWikryeeg 39
                                      ++++ + +++ ++A+e  + +rtv+  ++r++e+
  gi|336254269|ref|YP_004597376.1| 33 VLEYNDTMTQQQIAEETLLPSRTVRYALNRLDEE 66
                                      6889999************************997 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 ?   15.0   0.0   1.3e-05     0.018      21      54 ..      39      72 ..      10      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrg 54
                                       +tq+++A+   l   tv  +l++L +e++i+ +
  gi|336254269|ref|YP_004597376.1| 39 TMTQQQIAEETLLPSRTVRYALNRLDEENVIDSR 72
                                      69*****************************943 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.1e-05      0.11      12      57 ..      34      79 ..      29      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.1e-05
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTT CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrR 57
                                      l++++ ++++++a+   + + tv  +l rL +++ i+++ s +D R
  gi|336254269|ref|YP_004597376.1| 34 LEYNDTMTQQQIAEETLLPSRTVRYALNRLDEENVIDSRFSFSDAR 79
                                      789999********************************99999998 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.1e-05      0.13      76     106 ..      40      70 ..      28      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.1e-05
                              RepL  76 atnRelaeetgislktvsetlkileeanilk 106
                                       +t+ ++aeet +  +tv+  l  l+e n++ 
  gi|336254269|ref|YP_004597376.1|  40 MTQQQIAEETLLPSRTVRYALNRLDEENVID 70 
                                       79**************************996 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.18      17      45 ..      39      67 ..      25      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                            HTH_23 17 GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                       +++++IA+e   + rTv+  l+r  ee 
  gi|336254269|ref|YP_004597376.1| 39 TMTQQQIAEETLLPSRTVRYALNRLDEEN 67
                                      689*********************98776 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.15      23      58 ..      37      72 ..      27      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                      CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      + +++ ++iae++ ++ + ++  l++L +++++ s+
  gi|336254269|ref|YP_004597376.1| 37 NDTMTQQQIAEETLLPSRTVRYALNRLDEENVIDSR 72
                                      3459*****************************996 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 ?   10.8   0.1   0.00026      0.36      14      48 ..      40      69 ..      21      80 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                            HTH_12 14 igakeiaeeLkkrgydigeravRyrLrkleerglt 48
                                      +  ++iaee       +  r+vRy L  l+e++ +
  gi|336254269|ref|YP_004597376.1| 40 MTQQQIAEE-----TLLPSRTVRYALNRLDEENVI 69
                                      555555554.....34568************9866 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00028      0.39      17      38 ..      36      57 ..      31      65 .. 0.86
   2 ?   -1.2   0.0       1.1   1.5e+03       5      17 ..      63      73 ..      59      82 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
                                      HTTT--HHHHHHHHTS-HHHHH CS
                        Sigma70_r4 17 fgeglTleEIgerlgiSrerVr 38
                                      + + +T+++I+e+  ++  +Vr
  gi|336254269|ref|YP_004597376.1| 36 YNDTMTQQQIAEETLLPSRTVR 57
                                      7889****************99 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                                      S-HHHHHHHHHHH CS
                        Sigma70_r4  5 Lpererevlelrf 17
                                      L+e   +v+  rf
  gi|336254269|ref|YP_004597376.1| 63 LDE--ENVIDSRF 73
                                      544..45555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 717.29
//
Query:       gi|336254270|ref|YP_004597377.1|  [L=405]
Description: proteasome-activating nucleotidase [Halopiger xanaduensis SH-6]
Scores for 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-45  153.0   1.8    7.6e-45  152.6   0.1    2.1  1  AAA              ATPase family associated with various cellul
      1e-14   54.0   2.2    3.2e-14   52.4   2.2    1.9  1  AAA_lid_3        AAA+ lid domain
    4.8e-09   36.6   0.0    1.7e-08   34.7   0.0    2.0  1  AAA_2            AAA domain (Cdc48 subfamily)
    6.4e-07   29.3   0.0    1.6e-06   27.9   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      4e-06   27.1   0.3    0.00085   19.6   0.0    2.8  2  AAA_22           AAA domain
    5.6e-06   26.4   1.9    1.9e-05   24.6   0.3    2.6  1  AAA_5            AAA domain (dynein-related subfamily)
    1.6e-05   25.4   3.6      0.017   15.6   0.0    2.8  2  AAA_17           AAA domain
      4e-05   24.1   6.6    0.00035   21.0   0.0    3.4  3  AAA_16           AAA ATPase domain
    9.1e-05   22.2   8.3    9.1e-05   22.2   8.3    2.2  1  GrpE             GrpE
    0.00026   21.5   0.5     0.0092   16.5   0.0    3.0  2  AAA_18           AAA domain
    0.00032   20.6   0.8     0.0007   19.5   0.2    2.0  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    0.00051   19.3   0.0     0.0011   18.2   0.0    1.7  1  DUF815           Protein of unknown function (DUF815)
    0.00084   18.6   1.0     0.0026   17.0   0.0    2.2  2  TIP49            TIP49 P-loop domain
     0.0014   18.0   0.2     0.0046   16.4   0.1    1.8  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0015   18.5   0.4     0.0098   15.9   0.0    2.2  2  AAA_14           AAA domain
     0.0016   18.2   0.1      0.045   13.5   0.0    2.6  2  Sigma54_activat  Sigma-54 interaction domain
     0.0034   17.8   0.0     0.0096   16.3   0.0    1.9  1  RNA_helicase     RNA helicase
     0.0035   17.1   0.0     0.0097   15.6   0.0    1.8  1  IstB_IS21        IstB-like ATP binding protein
     0.0067   16.6   1.2      0.023   14.9   0.0    2.4  1  AAA_33           AAA domain
     0.0078   16.0   0.1     0.0078   16.0   0.1    2.9  3  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.011   15.7   0.1       0.12   12.3   0.0    2.4  2  NACHT            NACHT domain
      0.011   15.7   0.0      0.024   14.7   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.013   15.4   0.2      0.059   13.2   0.0    2.3  2  AAA_3            ATPase family associated with various cellul
      0.014   14.5   1.4      0.021   13.9   1.4    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.017   14.6   1.0       0.03   13.8   0.0    2.0  1  AAA_7            P-loop containing dynein motor region
      0.018   15.3   0.0      0.018   15.3   0.0    2.7  2  AAA_28           AAA domain
      0.019   13.8   6.2      0.042   12.7   6.2    1.6  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
      0.024   14.0   0.0        1.7    8.0   0.0    2.6  2  TniB             Bacterial TniB protein
      0.027   13.6   0.0      0.059   12.4   0.0    1.5  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.034   13.3   0.0       0.12   11.5   0.0    2.1  1  NB-ARC           NB-ARC domain
      0.039   14.4   4.7       0.13   12.8   4.7    1.9  1  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
      0.041   13.6   9.0      0.079   12.7   9.0    1.4  1  SHE3             SWI5-dependent HO expression protein 3
      0.045   13.6   0.0       0.11   12.3   0.0    1.8  1  CPT              Chloramphenicol phosphotransferase-like prot
      0.059   13.0   0.0        0.1   12.3   0.0    1.4  1  DUF2334          Uncharacterized protein conserved in bacteri
      0.085   13.0  13.7       0.19   11.8   2.9    2.8  2  bZIP_1           bZIP transcription factor
       0.09   12.9   8.6       0.28   11.3   8.6    1.7  1  ADIP             Afadin- and alpha -actinin-Binding
       0.09   12.3   9.7       0.22   11.1   0.1    3.6  3  AAA_25           AAA domain
        0.1   11.9   9.7       0.34   10.2   0.0    3.7  3  ATPase           KaiC
       0.12   12.5   0.1       0.73    9.9   0.0    2.3  2  Sigma54_activ_2  Sigma-54 interaction domain
       0.16   12.7   2.9        2.9    8.6   3.1    2.6  2  Occludin_ELL     Occludin homology domain
       0.21   11.9   6.6        1.2    9.5   6.6    2.4  1  CLZ              C-terminal leucine zipper domain of cyclic n
       0.24   11.3   4.6        1.9    8.4   0.0    3.5  4  NTPase_1         NTPase
       0.25   11.2   5.1       0.73    9.7   0.0    3.3  5  ATPase_2         ATPase domain predominantly from Archaea
       0.29   11.7   4.9       0.35   11.4   0.0    2.7  1  ABC_tran         ABC transporter
       0.39   10.1  14.5       0.96    8.8  14.5    1.8  1  GAS              Growth-arrest specific micro-tubule binding
       0.49   10.7   2.6        2.1    8.6   0.2    2.4  2  DUF4241          Protein of unknown function (DUF4241)
       0.57   10.3  11.9        1.6    8.9  11.9    1.7  1  Cep57_CLD_2      Centrosome localisation domain of PPC89
       0.73    9.0   5.6       0.19   10.9   0.3    2.2  2  VSG_B            Trypanosomal VSG domain
        1.1    8.9   9.5       0.43   10.3   0.1    2.5  2  AAA_11           AAA domain
        1.9    8.7   7.1        6.6    6.9   6.1    2.6  1  Swi5             Swi5
        1.9    9.0  15.8       0.72   10.4  12.2    2.1  1  APG6_N           Apg6 coiled-coil region
        2.1    9.0   9.8        8.7    7.1   8.2    2.8  1  SlyX             SlyX
        2.3    7.5   8.0       0.78    9.0   4.8    1.8  2  DUF4407          Domain of unknown function (DUF4407)
        2.4    6.9   5.7        1.2    7.8   3.6    1.6  2  Mgr1             Mgr1-like, i-AAA protease complex subunit
        3.2    8.4  10.0         61    4.3   8.8    2.9  2  YabA             Initiation control protein YabA
        3.5    8.1   8.7         42    4.7   0.1    3.4  2  FlaC_arch        Flagella accessory protein C (FlaC)
        7.7    5.4  10.1        2.2    7.2   5.5    2.3  3  DUF3987          Protein of unknown function (DUF3987)


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 !  152.6   0.1   2.4e-47   7.6e-45       1     131 [.     186     318 ..     186     319 .. 0.96

  Alignments for each domain:
  == domain 1  score: 152.6 bits;  conditional E-value: 2.4e-47
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       vllyGppGtGKT+lakava++++++f+++ gsel+ k++ge++k +r+lfk a+e++ p ++fiDEida+a +r   
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVANQTDATFIKMAGSELVHKFIGEGAKLVRDLFKVAREHE-PAVIFIDEIDAIAAKRtes 261
                                       79******************************************************8.****************986 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       ++s + e +r++ qLl+e+dg++++ +++ +i+atnr d+ld+a+lr gRfdr ie++
  gi|336254270|ref|YP_004597377.1| 262 KTSGDAEVQRTMMQLLSEMDGFEDR-GDIRIIAATNRFDMLDRAILRpGRFDRLIEVP 318
                                       666888999***************7.66***************************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 !   52.4   2.2     1e-16   3.2e-14       1      44 [.     341     384 ..     341     385 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 1e-16
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                       dvd++eLAe+ e  SGAD++a+c eA++ A+r++++ei medf+
  gi|336254270|ref|YP_004597377.1| 341 DVDFAELAEEAEEASGADIKAVCTEAGMFAIRDDRTEIQMEDFR 384
                                       9******************************************7 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   5.5e-11   1.7e-08       4     104 ..     184     278 ..     181     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 5.5e-11
                                       --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGG CS
                             AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEid 78 
                                       + +ll gp g+Gkt+laka+a+  ++    ++i +  sel      e ++lv  l        +  e  ++++DEid
  gi|336254270|ref|YP_004597377.1| 184 SGVLLYGPPGTGKTMLAKAVANQTDA----TFIKMAGSELVHkfIGEGAKLVRDL----FKVAREHEPAVIFIDEID 252
                                       568999******************96....9999999999982222233333333....3344556677******** PP

                                       G-------------HHHHHHHHHHHH CS
                             AAA_2  79 KihpkessgadvSregVqrdLLqile 104
                                        i++k+++++     +Vqr ++q+l 
  gi|336254270|ref|YP_004597377.1| 253 AIAAKRTESKTSGDAEVQRTMMQLLS 278
                                       ****87777778889*********95 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 !   27.9   0.0   5.1e-09   1.6e-06      34      99 ..     184     257 ..     156     270 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5.1e-09
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvleka..gdlaalltnl......eekdvlfideihrlsra 99 
                                         vllyGpPG Gkt lak +a++ ++++   +g  l ++  g+ a l+ +l      +e  v+fidei  ++ +
  gi|336254270|ref|YP_004597377.1| 184 SGVLLYGPPGTGKTMLAKAVANQTDATFIKMAGSELVHKfiGEGAKLVRDLfkvareHEPAVIFIDEIDAIAAK 257
                                       469**********************997666665544322355555554442222223446*******988765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.7e-06   0.00085       8      31 ..     186     209 ..     181     223 .. 0.82
   2 ?    4.3   0.1      0.14        44      84     122 ..     236     288 ..     221     296 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.7e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqlde 31 
                                       ++++G++GtGKT+l++ +++q d+
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVANQTDA 209
                                       689******************853 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.14
                            AAA_22  84 qalraravielliiDEaqhlr.....s.........eealeeLrsllnl.srkg 122
                                       + +r++   +++ iDE++ +      s          ++++ L+++  + +r +
  gi|336254270|ref|YP_004597377.1| 236 KVAREHEP-AVIFIDEIDAIAakrteSktsgdaevqRTMMQLLSEMDGFeDRGD 288
                                       44445555.9*********97765541455666666666666655554444555 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 !   24.6   0.3   6.2e-08   1.9e-05       1     124 [.     185     299 ..     185     308 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 6.2e-08
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK++la+ +a  + +++  +++++      l+ +    +++++lv   ++  ar  e++++++DE++
  gi|336254270|ref|YP_004597377.1| 185 GVLLYGPPGTGKTMLAKAVANQTDATFIKMAGSE------LVHKFI--GEGAKLVRDLFK-VARehEPAVIFIDEID 252
                                       59*********************99988877766......666666..333344443333.444469********** PP

                                       G--.HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                             AAA_5  76 rae.sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                        +  + + ++     e +r ++  + e  +++      ++r+ia++n+ d
  gi|336254270|ref|YP_004597377.1| 253 AIAaKRTESKTSGDAEVQRTMMQLLSEMDGFEDR---GDIRIIAATNRFD 299
                                       9985555555555555555554444444444442...2388888888766 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   1.4    0.0056       1.8      35     127 ..      50     136 ..      28     143 .. 0.71
   2 !   15.6   0.0   5.3e-05     0.017       1      69 [.     189     258 ..     189     307 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0056
                                       HTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE-- CS
                            AAA_17  35 krgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpkevleelkpdaiillead 111
                                       ++   +k ++++++l +e kk  q  +  +  +e  ++gv+++ h    +++++l ++++e+ ++l+pda + ++ +
  gi|336254270|ref|YP_004597377.1|  50 EN---NKYQQKLERLTHENKKLKQSPLFVATVQEITDEGVIIKQHG---NNQEALTEVTDEMRDDLEPDARVAVNNS 120
                                       33...344566666666666665655555555556789*******9...57889******************99988 PP

                                       HHHHHHHHHHH.TTST- CS
                            AAA_17 112 peeilerrlkd.rtrgr 127
                                          i++ + +d + r r
  gi|336254270|ref|YP_004597377.1| 121 LS-IVKTLSSDtDVRAR 136
                                       75.66666666334555 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.3e-05
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSHHHHHH.HHHHHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrklpleekk.elqkeaaekiaeea 69 
                                       +G+PG GK+ +++ ++ + + t++ + G+ l      +g++  rd ++ + + e    + +e+ ++ia ++
  gi|336254270|ref|YP_004597377.1| 189 YGPPGTGKTMLAKAVANQTDATFIKMaGSELVHKFIGEGAKLVRDLFKVAREHEPAvIFIDEI-DAIAAKR 258
                                       7***********************877999999988999888888887443333330333333.3444433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.8       6.9   2.2e+03     101     104 ..      44      47 ..       4     130 .. 0.55
   2 !   21.0   0.0   1.1e-06   0.00035      16      49 ..     175     208 ..     153     224 .. 0.78
   3 ?    4.9   0.1     0.097        30     122     149 ..     230     256 ..     216     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 6.9
                            AAA_16 101 leea 104
                                       l++a
  gi|336254270|ref|YP_004597377.1|  44 LLDA 47 
                                       2222 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.1e-06
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellrale 49 
                                       +++v  + p+ vll+G++G+GK+ l+++++++  
  gi|336254270|ref|YP_004597377.1| 175 FDDVGIDPPSGVLLYGPPGTGKTMLAKAVANQTD 208
                                       5555555569*******************97544 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.097
                            AAA_16 122 llkrllallsrderplvlvlDdlqwade 149
                                       l+++l++ +++ ++p v+++D+++ + +
  gi|336254270|ref|YP_004597377.1| 230 LVRDLFKVARE-HEPAVIFIDEIDAIAA 256
                                       55666677887.788*********6544 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   8.3   2.9e-07   9.1e-05       4      69 ..      13      78 ..       9     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.9e-07
                                      ...CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              GrpE  4 eeeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLL 69
                                      +e+e+++++++++lee+le le++ +e+ +kll ++ae  ++++++e+   e kk + + ++ + +
  gi|336254270|ref|YP_004597377.1| 13 DEDEASQQEKIQALEERLEVLESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQSPLFVATV 78
                                      57899********************************************99999998888765544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2      0.86   2.7e+02      49      70 ..      33      60 ..       2     121 .. 0.58
   2 !   16.5   0.0   2.9e-05    0.0092       1      44 [.     186     250 ..     186     343 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.86
                            AAA_18 49 skrldedkldklldaleenss......a 70
                                       +  +e+++dkllda+ en++      +
  gi|336254270|ref|YP_004597377.1| 33 LESQNEEMRDKLLDANAENNKyqqkleR 60
                                      3334444445555555554444444440 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.9e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpe 44 
                                       +ll G+pG+GKt lak++++ + +                     ++ l +va+e+++   + +e
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVANQTdATfikmagselvhkfigegaklVRDLFKVAREHEPAVIFIDE 250
                                       799***************99873336666766666666666666666666666666666555555 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 !   19.5   0.2   2.2e-06    0.0007       1      48 [.      75     120 ..      75     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.2e-06
                                       EEEEEEE-TTSSEEEEE-TT.S-EEEEEE-GGGSSST--TTEEEEEETT CS
                    Prot_ATP_ID_OB   1 VatVsEvlddteraiVktss.deevvvslagavpremLrpgDlVavdkd 48 
                                       VatV E+ d+  ++i+k+++  +e +  +++  + ++L p ++Vav+++
  gi|336254270|ref|YP_004597377.1|  75 VATVQEITDE--GVIIKQHGnNQEALTEVTDEMR-DDLEPDARVAVNNS 120
                                       9*******75..******997889********98.77**********86 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.6e-06    0.0011      16     116 ..     137     251 ..     125     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.6e-06
                            DUF815  16 lepveevdevklddLvgidkqkealventeqfleg.........lpannvLLwGarGtGKSslvkallneyaeegLr 83 
                                       +  v+e  ev+ +d+ g+++q +++ e +e  le           p + vLL+G  GtGK  l ka+ n++ ++ ++
  gi|336254270|ref|YP_004597377.1| 137 VMEVTESPEVSYEDIGGLEEQMQEVRETVEMPLESpemfddvgiDPPSGVLLYGPPGTGKTMLAKAVANQTDATFIK 213
                                       5667888889999999999999999988877665422222222257789************************9988 PP

                            DUF815  84 li..evekedlkelpklvellr...erperfilfvDDL 116
                                       +   e+ ++ + e  klv+ l    +++e  ++f+D +
  gi|336254270|ref|YP_004597377.1| 214 MAgsELVHKFIGEGAKLVRDLFkvaREHEPAVIFIDEI 251
                                       86447888888888888776541215667789999875 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.3       2.6   8.2e+02     231     262 ..      78     109 ..      15     120 .. 0.71
   2 !   17.0   0.0   8.3e-06    0.0026      52      94 ..     185     225 ..     182     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.6
                                       XXXXXXXXXXXXX....XXXXXXXXXXXXXXX CS
                             TIP49 231 vanarpqdllslllqllkskkteiteklreei 262
                                       v +   ++++   + +++   te+t+++r+++
  gi|336254270|ref|YP_004597377.1|  78 VQEITDEGVIIKQHGNNQEALTEVTDEMRDDL 109
                                       33344466666666677777888888888876 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 8.3e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevk 94 
                                       +vLl Gp+gtGkt la a++++   d  f++++gse+    + 
  gi|336254270|ref|YP_004597377.1| 185 GVLLYGPPGTGKTMLAKAVANQT--DATFIKMAGSELVHKFIG 225
                                       79******************975..689********9766555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.5e-05    0.0046      25      43 ..     186     204 ..     183     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKtmlak+++
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVA 204
                                       79*************9875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.3       2.6   8.1e+02      63     119 ..      68     139 ..      18     149 .. 0.53
   2 !   15.9   0.0   3.1e-05    0.0098       5      77 ..     186     255 ..     184     293 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 2.6
                            AAA_14  63 ekktylflDEiqev.............pewekalkslvdeg..knldvivtGSnskllskeiatslagrvae 119
                                        k++ lf   +qe+             +e+ + + + ++++  ++ +v v  S+s ++     t+++ rv e
  gi|336254270|ref|YP_004597377.1|  68 LKQSPLFVATVQEItdegviikqhgnnQEALTEVTDEMRDDlePDARVAVNNSLSIVKTLSSDTDVRARVME 139
                                       244445665666665555555555444333333333333333456777777777777766666666666655 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.1e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                       +++ G+  +GKT+l+k ++++       ++ ++  +   k + + +kl + +++ ++e++  ++f+DEi  + 
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVANQTD---ATFIKMAGSELVHKFIGEGAKLVRDLFKVAREHEPAVIFIDEIDAIA 255
                                       6799**************97777...788888877766655555557777777765667999*******9875 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00014     0.045      22      55 ..     183     213 ..     151     226 .. 0.72
   2 ?    1.9   0.1      0.51   1.6e+02     130     143 ..     284     297 ..     234     318 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00014
                                       SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEE CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfva 55 
                                       ++ vl+ G  GtGK++la+a+ ++++   + f++
  gi|336254270|ref|YP_004597377.1| 183 PSGVLLYGPPGTGKTMLAKAVANQTD---ATFIK 213
                                       378*****************987654...45555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.51
                                       EEE--EEEEEEESS CS
                   Sigma54_activat 130 eikvdvriiaatne 143
                                       e + d+riiaatn+
  gi|336254270|ref|YP_004597377.1| 284 EDRGDIRIIAATNR 297
                                       45679999999997 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.1e-05    0.0096       1      66 [.     186     242 ..     186     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.1e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeen 66 
                                       ++lyGp+g+GK++lak            +++d ++++ + ++ ++++ g+ + ++ D+ +v  e +
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKA---------VANQTDATFIKMAGSELVHKFIGEGAKLVRDLFKVAREHE 242
                                       689**************.........3466677888888888888888888888888888876644 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 !   15.6   0.0   3.1e-05    0.0097      48      71 ..     184     207 ..     173     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.1e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                        +++l Gp+G+GK+ la a++ ++
  gi|336254270|ref|YP_004597377.1| 184 SGVLLYGPPGTGKTMLAKAVANQT 207
                                       6799***************99874 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.2e-05     0.023       2      28 ..     186     212 ..     186     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.2e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavll 28 
                                       vll G+pG+GK+ la+ ++++++a+++
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVANQTDATFI 212
                                       7899***************99988776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.7       2.4   7.7e+02      98     166 ..      44     104 ..      24     147 .. 0.62
   2 !   16.0   0.1   2.5e-05    0.0078       5      75 ..     186     252 ..     183     272 .. 0.65
   3 ?   -1.8   0.1         7   2.2e+03      31      64 ..     364     395 ..     351     400 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.4
                            AAA_24  98 kgdgkG.ygelaeefrrllkklqelrknvifiahektrkdedpegeakytrlepklgkktanelkeevDl 166
                                         d+++   ++++++ rl    ++l++   f+a  ++ +de           ++k++   +++l+e  D+
  gi|336254270|ref|YP_004597377.1|  44 LLDANAeNNKYQQKLERLTHENKKLKQSPLFVATVQEITDEGV---------IIKQHGNNQEALTEVTDE 104
                                       5555566667777777777788888888888888888887754.........344444444555555554 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.5e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtid 75 
                                       +l+yGp+g+GKT+lak    + ++ fi + ++    +++     e+ + ++d ++  +++++   +++iD id
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVanQTDATFIKMAGSELVHKFIG----EGAKLVRDLFKVAREHEP--AVIFIDEID 252
                                       79**************997766666666554332222222....234444444444444444..566666665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 7
                            AAA_24  31 tekGlksldadkfpdieswedfldevvelaaela 64 
                                       te+G+ ++ +d+ + i ++edf+++ ++++ae +
  gi|336254270|ref|YP_004597377.1| 364 TEAGMFAIRDDRTE-I-QMEDFRNAWDKVQAESD 395
                                       78888888888865.4.77778777777766655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00038      0.12       3      22 ..     186     205 ..     184     215 .. 0.90
   2 ?    0.2   0.0       1.9   6.1e+02      76     114 ..     237     278 ..     217     281 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00038
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       v+l G++G GKT+L++ +a 
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVAN 205
                                       799*************9986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.9
                                       HCCSCCCEEEEEE-STT-SS-TCH............HHHHHC CS
                             NACHT  76 llelperlLlilDglDelvtdlgq...kekqpvrtlLselir 114
                                       +++  e +++ +D +D ++++  +   ++ ++v++ + +l++
  gi|336254270|ref|YP_004597377.1| 237 VAREHEPAVIFIDEIDAIAAKRTEsktSGDAEVQRTMMQLLS 278
                                       344556667778999999998888777777777777777765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   7.5e-05     0.024      21      84 ..     178     247 ..     153     263 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.5e-05
                                       E.......EEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEEEE..SSEEEEE-TT-SSTHHHHHCT CS
                              TsaE  21 v.......ilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeYelekeglyHfDlYRledeeeleelg 84 
                                       v       +lL+G+ G+GKT+l++++a++ + + +k     lv+++  e  +l+  Dl+++++e+e   + 
  gi|336254270|ref|YP_004597377.1| 178 VgidppsgVLLYGPPGTGKTMLAKAVANQTDATFIKMAGSELVHKFIGEGAKLV-RDLFKVAREHEPAVIF 247
                                       255556669********************9998888888888888866544454.5777777666655555 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 ?   -1.6   0.0       7.1   2.2e+03      53      88 ..      65     104 ..      51     129 .. 0.61
   2 ?   13.2   0.0   0.00019     0.059       2      30 ..     186     214 ..     185     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 7.1
                             AAA_3  53 efefkkGpvfanll..lade..inrappktqsalleamee 88 
                                       + ++k+ p+f   +  ++de  i +     q al e+ +e
  gi|336254270|ref|YP_004597377.1|  65 NKKLKQSPLFVATVqeITDEgvIIKQHGNNQEALTEVTDE 104
                                       3445555555544433445444455555555555555555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00019
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG++kt+l+ka+a++ d++f ++
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVANQTDATFIKM 214
                                       7999*******************999665 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 ?   13.9   1.4   6.7e-05     0.021      61     117 ..      15      71 ..       8     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.7e-05
                             Atg14  61 kiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsd 117
                                       ++ ++++k++ l  + + l+++++e++dkl   ++e+++ ++kl++l +++kk +++
  gi|336254270|ref|YP_004597377.1|  15 DEASQQEKIQALEERLEVLESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQS 71 
                                       566788899999999999999999999999999999999999999999999865543 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 ?   13.8   0.0   9.7e-05      0.03      35      61 ..     185     210 ..     177     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.7e-05
                             AAA_7  35 pvllvGptGtGKtviikdllkkldkek 61 
                                        vll+Gp GtGKt+++k + ++ d  +
  gi|336254270|ref|YP_004597377.1| 185 GVLLYGPPGTGKTMLAKAVANQTD-AT 210
                                       59*****************99998.33 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   5.6e-05     0.018       2      36 ..     186     221 ..     185     282 .. 0.70
   2 ?   -0.6   0.1       4.5   1.4e+03      31      66 ..     324     358 ..     322     390 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.6e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareile 36 
                                       + + G+++tGKT l++a a++ + + ++ a+ e++ 
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVANQtDATFIKMAGSELVH 221
                                       6799***************77544444444444443 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 4.5
                            AAA_28  31 areileeklakgedalpwvedllafaervleeqlee 66 
                                       +rei+++ + ++ + +++v d+ ++ae+ +e+  ++
  gi|336254270|ref|YP_004597377.1| 324 GREIIFQIHTRNMNVSDDV-DFAELAEEAEEASGAD 358
                                       5777777777777777776.6666666655554443 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   6.2   0.00013     0.042     166     243 ..      16      89 ..      12     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                        Fmp27_WPPW 166 ndpervqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkesees 242
                                       + +++ + + leeRle le+q e++++kl +++ +++k    +++++e+l++e k+lk++  f+ t+ e ++e    
  gi|336254270|ref|YP_004597377.1|  16 EASQQEKIQALEERLEVLESQNEEMRDKLLDANAENNK----YQQKLERLTHENKKLKQSPLFVATVQEITDEGVII 88 
                                       45566677899**********************99999....9******************9999887766666553 PP

                        Fmp27_WPPW 243 s 243
                                       +
  gi|336254270|ref|YP_004597377.1|  89 K 89 
                                       3 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0054       1.7      36      61 ..     184     209 ..     172     222 .. 0.84
   2 ?    2.9   0.0       0.2        62     106     138 ..     229     261 ..     224     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0054
                              TniB  36 pnlllvGdsnnGKtmivekFarlhpp 61 
                                       + +ll+G++ +GKtm+++  a++  +
  gi|336254270|ref|YP_004597377.1| 184 SGVLLYGPPGTGKTMLAKAVANQTDA 209
                                       679**************998877655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.2
                              TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsark 138
                                       kl ++  ++ re ++ v+ iDEi+ + a + ++
  gi|336254270|ref|YP_004597377.1| 229 KLVRDLFKVAREHEPAVIFIDEIDAIAAKRTES 261
                                       5667778899999***********998766655 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 ?   12.4   0.0   0.00019     0.059     117     138 ..     186     207 ..     182     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                       v++yGp+ tGkt+la+a a+ +
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVANQT 207
                                       89****************9976 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00039      0.12      23      47 ..     186     210 ..     181     350 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00039
                                       EEEEESTTSSHHHHHHHHCCSHCCC CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksdev 47 
                                       v l+G +G GKt lak + n+ d +
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVANQTDAT 210
                                       679****************996654 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   4.7    0.0004      0.13       3      52 ..      20      70 ..      18      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0004
                       Fungal_TACC  3 nkrlqelaedLYvqYSsKHEqKVkllkkgye.akyqkkldklelenkslkq 52
                                      ++++q l e L v  S+  E + kll ++ e +kyq+kl++l+ enk+lkq
  gi|336254270|ref|YP_004597377.1| 20 QEKIQALEERLEVLESQNEEMRDKLLDANAEnNKYQQKLERLTHENKKLKQ 70
                                      689************************9987369**************997 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   9.0   0.00025     0.079      10      98 ..      21     111 ..      17     127 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  10 eqiDaLtktnlqLtqqsqeLleklelaqkkeskflenlaslkhENdnL..sslLkRKerrlkdlekelselkesvee 84 
                                       e+i aL + +  L  q++e+ +kl  a++ ++k+ ++l  l hEN +L  s l+    + + d    ++++ ++ e 
  gi|336254270|ref|YP_004597377.1|  21 EKIQALEERLEVLESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLkqSPLFVATVQEITDEGVIIKQHGNNQEA 97 
                                       78999*******************************************44469999999****999*********** PP

                                       HHHHHHHHHHHHHH CS
                              SHE3  85 lklekkqlkkrlen 98 
                                       l++ +++++++le 
  gi|336254270|ref|YP_004597377.1|  98 LTEVTDEMRDDLEP 111
                                       *********99985 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00036      0.11       4      41 ..     186     223 ..     184     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00036
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafveal 41 
                                       +lL G + +GK+ la+a+ +++d+++++++  ++v++ 
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVANQTDATFIKMAGSELVHKF 223
                                       89**************************9987777665 PP

>> DUF2334  Uncharacterized protein conserved in bacteria (DUF2334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00032       0.1      44      85 ..      61     102 ..      16     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00032
                           DUF2334  44 ktgskvnlsenpefvevLkylqakGgeialHGYtHqygtvks 85 
                                        t+++++l+++p fv++++++ ++G +i +HG + +  t  +
  gi|336254270|ref|YP_004597377.1|  61 LTHENKKLKQSPLFVATVQEITDEGVIIKQHGNNQEALTEVT 102
                                       566789**************************9988875333 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.9   0.00061      0.19      25      49 ..      20      44 ..      18      48 .. 0.93
   2 ?    5.6   3.3     0.055        17      40      61 ..      49      70 ..      46      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00061
                                      HHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 25 qaeieeLerrvkaLekeNksLksel 49
                                      q++i++Le+r ++Le++N++++++l
  gi|336254270|ref|YP_004597377.1| 20 QEKIQALEERLEVLESQNEEMRDKL 44
                                      899*******************987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.055
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 40 keNksLkseleelkkevekLks 61
                                      +eN +++++le+l+ e++kLk+
  gi|336254270|ref|YP_004597377.1| 49 AENNKYQQKLERLTHENKKLKQ 70
                                      7999999*********999998 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   8.6   0.00088      0.28      67     123 ..      14      70 ..      10      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00088
                              ADIP  67 aeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlkn 123
                                        + +++q ki+ l+++le le++++    k+ ++++++ + +qkl +++ e+++lk+
  gi|336254270|ref|YP_004597377.1|  14 EDEASQQEKIQALEERLEVLESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQ 70 
                                       678899999999999999999999999999999999999999999999999999985 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3       1.4   4.5e+02      79     137 ..      47     109 ..      12     117 .. 0.55
   2 ?   11.1   0.1    0.0007      0.22      36      53 ..     186     203 ..     180     207 .. 0.87
   3 ?    5.3   0.1     0.041        13     129     164 ..     230     264 ..     206     295 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.4
                            AAA_25  79 aEdsedelrrRlravgeal.rd.darllvldlagv.eslpLfakdrggtl..ltadvdaleaai 137
                                       a   ++  +++l+++ +++ ++ ++ l+v ++ ++ ++  ++ k++g+++  lt+++d++++++
  gi|336254270|ref|YP_004597377.1|  47 ANAENNKYQQKLERLTHENkKLkQSPLFVATV-QEiTDEGVIIKQHGNNQeaLTEVTDEMRDDL 109
                                       33333446666666665555331333444444.3334444444444444434777777766665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0007
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll+G+pgtGKt+la  +
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAV 203
                                       69************9655 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.041
                            AAA_25 129 dvdaleaaieevegvrlvviDplsralggdensnsd 164
                                        v++l ++++e ++++++ iD ++++ +   +s++ 
  gi|336254270|ref|YP_004597377.1| 230 LVRDLFKVARE-HEPAVIFIDEIDAIAAKRTESKTS 264
                                       5788999****.88***********88884444333 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.4      0.41   1.3e+02     135     220 ..      49     141 ..       9     147 .. 0.54
   2 ?   10.2   0.0    0.0011      0.34      14      37 ..     178     201 ..     151     211 .. 0.85
   3 ?    4.2   0.1     0.074        23     106     151 ..     229     280 ..     221     285 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.41
                            ATPase 135 ekeavaReilrqlvrvlkklgvTailvsekss........seeaaggygveefivdgvivLdlkeiee...elvRtl 200
                                       +++++  + l +l+++ kkl++  ++v+ +++        +++++++ ++ e + d  ++ dl+   +    +  +l
  gi|336254270|ref|YP_004597377.1|  49 AENNKYQQKLERLTHENKKLKQSPLFVATVQEitdegviiKQHGNNQEALTE-VTD-EMRDDLEP--DarvAVNNSL 121
                                       4455555566666666666666666666555554444444444444444444.222.22222222..1223445555 PP

                            ATPase 201 eivkmRgtkhskkehpfeIt 220
                                       +ivk  +++++ +  ++e+t
  gi|336254270|ref|YP_004597377.1| 122 SIVKTLSSDTDVRARVMEVT 141
                                       55555555555555555554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                            ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                        Gi   + vl++G pGtGKt++a+
  gi|336254270|ref|YP_004597377.1| 178 VGIDPPSGVLLYGPPGTGKTMLAK 201
                                       478888899*************97 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.074
                            ATPase 106 elieelaeaikeikakrvviDsitglayeeke......avaReilrqlvrvl 151
                                       +l+++l ++ +e +   + iD i+++a + +e      a++ ++++ql++++
  gi|336254270|ref|YP_004597377.1| 229 KLVRDLFKVAREHEPAVIFIDEIDAIAAKRTEsktsgdAEVQRTMMQLLSEM 280
                                       7899999******************944433301111134555555555555 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 ?   -1.4   0.1       7.3   2.3e+03       5      20 ..      21      36 ..      18      39 .. 0.82
   2 ?    9.9   0.0    0.0023      0.73      23      47 ..     185     209 ..     181     260 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 7.3
                                      HHHHHHHHHHHHHHT- CS
                   Sigma54_activ_2  5 aaiqelkerLeqaaqs 20
                                      ++iq+l+erLe+++++
  gi|336254270|ref|YP_004597377.1| 21 EKIQALEERLEVLESQ 36
                                      689********99866 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0023
                                       -EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgp 47 
                                        v+l G++G+gk++ A++ +++   
  gi|336254270|ref|YP_004597377.1| 185 GVLLYGPPGTGKTMLAKAVANQTDA 209
                                       69*****************998654 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.1    0.0094       2.9      22      80 ..      21      79 ..      10      83 .. 0.87
   2 ?    0.3   0.0       3.8   1.2e+03      44      85 ..     258     301 ..     247     305 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0094
                      Occludin_ELL 22 keYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkk 80
                                      ++ ++l+++le ++++ +e++++l +++ ++++y++  e++ +e kklk++p + ++ +
  gi|336254270|ref|YP_004597377.1| 21 EKIQALEERLEVLESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQSPLFVATVQ 79
                                      566789999999****************************************9987765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 3.8
                      Occludin_ELL  44 elkelkegskeykkieeeilqeykklkk..dpeyqekkkrceyL 85 
                                       ++++ + g+ e+++++ ++l+e   ++   d +  ++ +r++ L
  gi|336254270|ref|YP_004597377.1| 258 RTESKTSGDAEVQRTMMQLLSEMDGFEDrgDIRIIAATNRFDML 301
                                       34455556669999999999999999876777778888888877 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 ?    9.5   6.6    0.0039       1.2      16      63 ..      13      60 ..      11      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0039
                               CLZ 16 DeeaakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLkq 63
                                      De++a+++++ + lee++e Les+ e + ++l    ae ++ q+kL++
  gi|336254270|ref|YP_004597377.1| 13 DEDEASQQEKIQALEERLEVLESQNEEMRDKLLDANAENNKYQQKLER 60
                                      89989999999**********************************975 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       3.1   9.8e+02     122     163 ..      68     109 ..      52     113 .. 0.79
   2 ?    1.8   0.1      0.65   2.1e+02     103     124 ..     150     171 ..     118     175 .. 0.86
   3 ?    8.4   0.0     0.006       1.9       2      32 ..     186     216 ..     185     247 .. 0.78
   4 ?   -0.6   0.0       3.4   1.1e+03      94     104 ..     241     251 ..     223     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.1
                                       HTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE--TTTTTTH CS
                          NTPase_1 122 Lksekpvlavihrrkdlalveeirerkdvkvfevteenrdal 163
                                       Lk+++ ++a++++ +d+ ++ + + +++  + evt e rd l
  gi|336254270|ref|YP_004597377.1|  68 LKQSPLFVATVQEITDEGVIIKQHGNNQEALTEVTDEMRDDL 109
                                       777888899999999877777777777888999999999876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.65
                                       --STTGGG-HHHHHHHHHHHTT CS
                          NTPase_1 103 EiGkmElkskkfkeaveevLks 124
                                        iG +E ++++++e+ve  L+s
  gi|336254270|ref|YP_004597377.1| 150 DIGGLEEQMQEVRETVEMPLES 171
                                       59**************998886 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.006
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt l k v+++ +   +k++G
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVANQTDATFIKMAG 216
                                       6788***************999887777777 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 3.4
                                       HHH-EEEE--- CS
                          NTPase_1  94 seadviviDEi 104
                                       +e+ vi iDEi
  gi|336254270|ref|YP_004597377.1| 241 HEPAVIFIDEI 251
                                       56679999999 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 ?   -0.8   0.8       3.8   1.2e+03      98     116 ..      50      68 ..      12     114 .. 0.45
   2 ?    9.7   0.0    0.0023      0.73      23      44 ..     186     207 ..     179     223 .. 0.86
   3 ?   -0.7   0.0       3.5   1.1e+03     112     131 ..     236     255 ..     213     265 .. 0.66
   4 ?    0.6   0.0       1.4   4.4e+02      36      68 ..     230     262 ..     224     284 .. 0.64
   5 ?   -1.7   0.0       6.9   2.2e+03      47      76 ..     323     355 ..     312     394 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.8
                          ATPase_2  98 ksklvfkaielllekikkk 116
                                       ++++ ++++e+l  + kk 
  gi|336254270|ref|YP_004597377.1|  50 ENNKYQQKLERLTHENKKL 68 
                                       2222223333322222222 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0023
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienl 44 
                                       +++YGp g GKt L k ++++ 
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVANQT 207
                                       789*************999987 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 3.5
                          ATPase_2 112 kikkkgkkiiiiiDelqkli 131
                                       k+ ++    +i+iDe+  + 
  gi|336254270|ref|YP_004597377.1| 236 KVAREHEPAVIFIDEIDAIA 255
                                       34444444666667765554 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.4
                          ATPase_2  36 Llkeiienledkdkyviyyialreesiskldef 68 
                                       L++ + +  ++++  vi+++++  ++ ++++++
  gi|336254270|ref|YP_004597377.1| 230 LVRDLFKVAREHEPAVIFIDEIDAIAAKRTESK 262
                                       566666666666677777777777777776666 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 6.9
                          ATPase_2  47 kdkyviyyialreesiskldefie...eeeekk 76 
                                        + ++i+ i  r+ + s   +f e   e ee++
  gi|336254270|ref|YP_004597377.1| 323 EGREIIFQIHTRNMNVSDDVDFAElaeEAEEAS 355
                                       455778888888888888888876653222222 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0011      0.35       8      38 ..     180     210 ..     176     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0011
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpt 38 
                                       + + + v + G+ G+GK+ L+k++a++++ t
  gi|336254270|ref|YP_004597377.1| 180 IDPPSGVLLYGPPGTGKTMLAKAVANQTDAT 210
                                       556667899****************998764 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 ?    8.8  14.5    0.0031      0.96      24      91 ..      19      72 ..      12     139 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0031
                               GAS 24 NLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlk 91
                                      + e+I+ l e +e l+ ++e+++ +l ++++en++++++L+++++e+++L              k++ 
  gi|336254270|ref|YP_004597377.1| 19 QQEKIQALEERLEVLESQNEEMRDKLLDANAENNKYQQKLERLTHENKKL--------------KQSP 72
                                      44555555555555555555555555555555555555555555555555..............5544 PP

>> DUF4241  Protein of unknown function (DUF4241)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.82   2.6e+02     102     135 ..      36      69 ..      17      93 .. 0.66
   2 ?    8.6   0.2    0.0067       2.1      46     123 ..     323     400 ..     303     405 .] 0.70

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.82
                           DUF4241 102 alsefeeslleeepkkdeyddyfeelfekkaeae 135
                                       + +e++++ll+++ ++++y++ +e l++++++ +
  gi|336254270|ref|YP_004597377.1|  36 QNEEMRDKLLDANAENNKYQQKLERLTHENKKLK 69 
                                       4556666888888888888888888666665554 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0067
                           DUF4241  46 edrvaaarlvfsd.epavrwelAllgeqdlaeleegeffgygVDaGlacffDakafealsefeeslleeepkkdeyd 121
                                       e+r +  ++  ++ +       A+l+e+  +e +  ++  +  +aG+ ++ D  +  ++++f++ + + + ++d+ +
  gi|336254270|ref|YP_004597377.1| 323 EGREIIFQIHTRNmNVSDDVDFAELAEEA-EEASGADIKAVCTEAGMFAIRDDRTEIQMEDFRNAWDKVQAESDDAE 398
                                       55566666664443333344445555555.5556667999************************9999999888777 PP

                           DUF4241 122 dy 123
                                       d+
  gi|336254270|ref|YP_004597377.1| 399 DV 400
                                       65 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  11.9     0.005       1.6       4      52 ..      22      70 ..      18      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.005
                       Cep57_CLD_2  4 evktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLka 52
                                       +++L++rL+ l++++++  + l + n+E++ + ++L +   e+ +Lk+
  gi|336254270|ref|YP_004597377.1| 22 KIQALEERLEVLESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQ 70
                                      5778888888888888888888888888888888888888888888875 PP

>> VSG_B  Trypanosomal VSG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.7       1.1   3.5e+02     117     154 ..      13      50 ..       4     105 .. 0.75
   2 ?   10.9   0.3   0.00061      0.19      38     106 ..     316     397 ..     312     405 .] 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.1
                             VSG_B 117 trararanekiqqiaekaaeiyseikkekekakkarae 154
                                        +  a ++ekiq++ e+ + + s+ ++++ k   a+ae
  gi|336254270|ref|YP_004597377.1|  13 DEDEASQQEKIQALEERLEVLESQNEEMRDKLLDANAE 50 
                                       55566777888888888888888877777776655433 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00061
                             VSG_B  38 eaikdeqevtkileeiealnlsladedwlnkfaeeedda.............katktkkaakkncgalkafWkeakk 101
                                       e +k++qe ++i+ +i ++n++++d+  ++++aee+++a                 +   ++ + ++ +++W++ ++
  gi|336254270|ref|YP_004597377.1| 316 EVPKPNQEGREIIFQIHTRNMNVSDDVDFAELAEEAEEAsgadikavcteagMFAIRDDRTEIQMEDFRNAWDKVQA 392
                                       6689999***************************9999988888777666553333445566677777777777777 PP

                             VSG_B 102 aakak 106
                                       + +++
  gi|336254270|ref|YP_004597377.1| 393 ESDDA 397
                                       76665 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   6.6       3.6   1.1e+03      69     178 ..      39      69 ..       8     167 .. 0.56
   2 ?   10.3   0.1    0.0014      0.43      20      41 ..     186     207 ..     156     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.6
                            AAA_11  69 ellerllrglldsegekykpkivRvgneeeriseavksvsleekvekrlekeekaqlakeiskeleklakelrafee 145
                                       e+ ++ll+   ++e +ky+ k+ R+ +e+                                                
  gi|336254270|ref|YP_004597377.1|  39 EMRDKLLD--ANAENNKYQQKLERLTHEN------------------------------------------------ 65 
                                       22222333..3333333333333333333................................................ PP

                            AAA_11 146 eeekeklkkskekskskleqerrklkkerkels 178
                                                                    k+l+
  gi|336254270|ref|YP_004597377.1|  66 -----------------------------KKLK 69 
                                       .............................2221 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0014
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                       +l+ GPPGtgKT    ++ +q 
  gi|336254270|ref|YP_004597377.1| 186 VLLYGPPGTGKTMLAKAVANQT 207
                                       799*********8877777776 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.1     0.021       6.6       2      45 ..      20      63 ..      19      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.021
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHH CS
                              Swi5  2 eaeikeleeqleelekelaelkeelkekkdpeetvkrhIklLhe 45
                                      +++i++lee+le le++ +e++++l + ++ ++  ++++++L  
  gi|336254270|ref|YP_004597377.1| 20 QEKIQALEERLEVLESQNEEMRDKLLDANAENNKYQQKLERLTH 63
                                      789***********************999999999999999965 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  12.2    0.0023      0.72      43      96 ..      17      70 ..       9      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0023
                            APG6_N 43 ekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealee 96
                                       +q+e++++lee+le le++ ee+  +L ++ +e+ + +++l+ l+ e ++l++
  gi|336254270|ref|YP_004597377.1| 17 ASQQEKIQALEERLEVLESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQ 70
                                      236789*********************************************998 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   8.2     0.028       8.7       2      53 ..      20      71 ..      19      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.028
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX  2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53
                                      +e++++LE++l  +e + ee+ d + + + +  + q++l++l+ + k+l++s
  gi|336254270|ref|YP_004597377.1| 20 QEKIQALEERLEVLESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQS 71
                                      5788888888888888888888888888888888888888888777777665 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.8    0.0025      0.78     118     208 ..      14     119 ..       7     166 .. 0.77
   2 ?   -1.9   0.1       5.2   1.7e+03     103     130 ..     246     272 ..     244     307 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0025
                           DUF4407 118 eeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk........gtgttgvaGkgpaak 186
                                       e++++++e+++ al+++l+ le+q+++++ ++  a+a+ ++ ++++++ ++ +k         ++ + +  +g + k
  gi|336254270|ref|YP_004597377.1|  14 EDEASQQEKIQ-ALEERLEVLESQNEEMRDKLLDANAENNKYQQKLERLTHENKklkqsplfVATVQEITDEGVIIK 89 
                                       45555555555.699*****************************999999988899999999444556788999999 PP

                           DUF4407 187 ekkaqldaaqaelaelkakld........a 208
                                       +  ++ +a+++  +e++++l+        +
  gi|336254270|ref|YP_004597377.1|  90 QHGNNQEALTEVTDEMRDDLEpdarvavnN 119
                                       999999999999999999988554443331 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.2
                           DUF4407 103 iFekeIdaelaeeqqeeakelkeqlaaa 130
                                       iF +eIda  a++ +++++  +++++ +
  gi|336254270|ref|YP_004597377.1| 246 IFIDEIDAIAAKRTESKTS-GDAEVQRT 272
                                       6777777655444444433.33443433 PP

>> Mgr1  Mgr1-like, i-AAA protease complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.6    0.0039       1.2     292     382 ..      18     123 ..       1     129 [. 0.64
   2 ?   -2.7   0.0         6   1.9e+03     340     364 ..     320     347 ..     258     349 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0039
                              Mgr1 292 ellekikhteeeleelieknkenrekilkkl...........svekektkekklpl..sskrkeasrgiildedvks 355
                                       + +eki+  ee le l ++n+e r+k l+               ++e++k k+ pl  ++ ++ +  g+i++++ ++
  gi|336254270|ref|YP_004597377.1|  18 SQQEKIQALEERLEVLESQNEEMRDKLLDANaennkyqqkleRLTHENKKLKQSPLfvATVQEITDEGVIIKQHGNN 94 
                                       34455666666666666666666666666555666666655533444444444444104444444599**9998888 PP

                              Mgr1 356 pediD..leeiwslydPWlnLaLdtsLsi 382
                                       +e +    +e++   +P   +a++ sLsi
  gi|336254270|ref|YP_004597377.1|  95 QEALTevTDEMRDDLEPDARVAVNNSLSI 123
                                       887743358999999************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6
                              Mgr1 340 rkeasrgiilde...dvkspediDleei 364
                                        ++++r ii++    +++ ++d+D+ e+
  gi|336254270|ref|YP_004597377.1| 320 PNQEGREIIFQIhtrNMNVSDDVDFAEL 347
                                       4456688888752225566788888775 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   8.8      0.19        61       5      53 ..      25      82 ..      15     111 .. 0.53
   2 ?    2.1   0.0      0.98   3.1e+02       5      39 ..     132     165 ..     129     247 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.19
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.........X CS
                              YabA  5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl.........e 53
                                       l ++le le+q ee+ ++l + ++e ++  ++ ++L+ en+kl++           +
  gi|336254270|ref|YP_004597377.1| 25 ALEERLEVLESQNEEMRDKLLDANAENNKYQQKLERLTHENKKLKQSPlfvatvqeiT 82
                                      3334444445555555555555555555555555566667777777655555544440 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.98
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   5 elfdkleeleeqleelleeleelkeelaelleena 39 
                                       ++ ++++e++e+ e  +e+++ l+e+++e+ e   
  gi|336254270|ref|YP_004597377.1| 132 DVRARVMEVTESPEVSYEDIGGLEEQMQEVRE-TV 165
                                       66788999999999999999999999998765.34 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 ?    3.7   4.0      0.26        81       7      30 ..      21      44 ..      18      71 .. 0.85
   2 ?    4.7   0.1      0.13        42      15      32 ..     150     167 ..     137     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.26
                         FlaC_arch  7 nklsklsteletvkkeneelsksv 30
                                      +k++ l+ +le ++++nee+++++
  gi|336254270|ref|YP_004597377.1| 21 EKIQALEERLEVLESQNEEMRDKL 44
                                      688889999999999999998875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.13
                         FlaC_arch  15 eletvkkeneelsksvee 32 
                                        ++ ++++++e++++ve+
  gi|336254270|ref|YP_004597377.1| 150 DIGGLEEQMQEVRETVEM 167
                                       68899***********98 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.5    0.0071       2.2      69     152 ..      17     105 ..      12     107 .. 0.74
   2 ?   -1.1   0.0       2.4   7.5e+02      41      57 ..     188     204 ..     186     208 .. 0.85
   3 ?   -2.3   0.1       5.3   1.7e+03     132     176 ..     345     388 ..     333     399 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0071
                           DUF3987  69 eeyeeelkeyeaekkaweaelealekkaakak..eakaeealaeleaee...peePklprllvddvTpeaLl.elLa 139
                                       ++ +e++++ e++ +++e+++e+++ k+ +a+  + k +++l+ l+ e+   ++ P l   +v+++T e+++ ++  
  gi|336254270|ref|YP_004597377.1|  17 ASQQEKIQALEERLEVLESQNEEMRDKLLDANaeNNKYQQKLERLTHENkklKQSP-LFVATVQEITDEGVIiKQHG 92 
                                       56688999*******************99998884444444444444444436666.678888******97615666 PP

                           DUF3987 140 engggililsdEg 152
                                       +n++ ++ ++dE+
  gi|336254270|ref|YP_004597377.1|  93 NNQEALTEVTDEM 105
                                       6669999999997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.4
                           DUF3987  41 vvapsGerKSpvdklvl 57 
                                         +p+G++K+ ++k+v+
  gi|336254270|ref|YP_004597377.1| 188 LYGPPGTGKTMLAKAVA 204
                                       569*********99986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.3
                           DUF3987 132 eaLlelLaeng.ggililsdEggiflaaigrydggknldvllkawd 176
                                       + L+e+ +e+    i  + +E+g+f +  +r   + +++ +++awd
  gi|336254270|ref|YP_004597377.1| 345 AELAEEAEEASgADIKAVCTEAGMFAIRDDR--TEIQMEDFRNAWD 388
                                       5555555555434455555666666665333..5555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2045  (0.114061); expected 358.6 (0.02)
Passed bias filter:                      995  (0.0554967); expected 358.6 (0.02)
Passed Vit filter:                       210  (0.0117129); expected 17.9 (0.001)
Passed Fwd filter:                        66  (0.00368119); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              57  [number of targets reported over threshold]
# CPU time: 0.86u 0.28s 00:00:01.14 Elapsed: 00:00:00.42
# Mc/sec: 2874.11
//
Query:       gi|336254271|ref|YP_004597378.1|  [L=45]
Description: hypothetical protein Halxa_2883 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.43   10.8   1.6       0.46   10.7   1.6    1.2  1  MAP17     Membrane-associated protein 117 kDa, PDZK1-interact
       0.47   10.6   2.4       0.46   10.6   2.4    1.1  1  DUF3742   Protein of unknown function (DUF3742)


Domain annotation for each model (and alignments):
>> MAP17  Membrane-associated protein 117 kDa, PDZK1-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.6   5.2e-05      0.46      29      51 ..      10      33 ..       2      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.2e-05
                             MAP17 29 kP.WlvGliAvvgFLflvfvlllv 51
                                      +P Wl+    v+g+L++ +vl ++
  gi|336254271|ref|YP_004597378.1| 10 HPaWLTAASTVAGYLVILAVLTVA 33
                                      588*****************9987 PP

>> DUF3742  Protein of unknown function (DUF3742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.4   5.1e-05      0.46      40      68 ..      13      41 ..       4      45 .] 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.1e-05
                           DUF3742 40 vpaavatavlwvvklavlGvllyvafWla 68
                                      + +a+ t+  ++v lavl v l+v+ Wl 
  gi|336254271|ref|YP_004597378.1| 13 WLTAASTVAGYLVILAVLTVALFVVPWLV 41
                                      5678889999*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 351.08
//
Query:       gi|336254272|ref|YP_004597379.1|  [L=184]
Description: GMP synthase subunit A [Halopiger xanaduensis SH-6]
Scores for complete 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  122.4   0.0    2.3e-35  122.1   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    9.1e-14   51.7   2.8    2.4e-06   27.5   0.0    2.9  3  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.037   13.6   0.4      0.084   12.5   0.4    1.8  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


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 !  122.1   0.0   3.9e-39   2.3e-35       1     187 [.       5     178 ..       5     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 122.1 bits;  conditional E-value: 3.9e-39
                                       EEEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEE CS
                            GATase   1 lliDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGI 77 
                                       +++Dn+ ++t+   +al+ lgv++e++ +d++ e       ++dg+++sgGp    +++++e ++    +++P+LGI
  gi|336254272|ref|YP_004597379.1|   5 VVVDNHGQFTHLERRALRDLGVETELIDNDTPPEDV-----DADGVVLSGGPDMDRIGKSPEYLE----ADMPVLGI 72 
                                       589***************************998888.....79*************999998766....49****** PP

                                       THHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEE CS
                            GATase  78 CLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeel 154
                                       CLGmQl+a+e+g+ v      ++   t  + d +  l+  l+++ +++ +H +ev++   +pag+e ta+s d + +
  gi|336254272|ref|YP_004597379.1|  73 CLGMQLIAEELGGRVGGGDYGGYADVTVDIVDSDDPLTGSLHPDTRVWASHADEVKE---LPAGFELTAES-DVCDV 145
                                       *******************9************999**********************...***********.66778 PP

                                       EEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 155 meiiekknpfvgvQFHPEststpegpellfnfl 187
                                       +++   ++ ++gvQ+HPE+ +t+eg+e+++nf+
  gi|336254272|ref|YP_004597379.1| 146 EAMSDTDRDIYGVQWHPEVAHTEEGEEIFENFI 178
                                       888888888*********************983 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.052   3.1e+02      59      71 ..      42      54 ..      39      56 .. 0.88
   2 !   22.0   0.1   1.8e-08   0.00011     100     125 ..      61      86 ..      58      89 .. 0.91
   3 !   27.5   0.0     4e-10   2.4e-06     166     216 .]     115     163 ..      95     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.052
                     Peptidase_C26 59 ldgllltGgqdve 71
                                       dg++l+Gg+d++
  gi|336254272|ref|YP_004597379.1| 42 ADGVVLSGGPDMD 54
                                      59********975 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.8e-08
                     Peptidase_C26 100 aalergvPilgiCrGlqllnvalGGt 125
                                       + le+++P+lgiC+G+ql++  lGG+
  gi|336254272|ref|YP_004597379.1|  61 EYLEADMPVLGICLGMQLIAEELGGR 86 
                                       56899********************7 PP

  == domain 3  score: 27.5 bits;  conditional E-value: 4e-10
                     Peptidase_C26 166 eeievnslHhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                        +++v   H   +kel  +++ +A ++   +Ea++ ++++  ++gvQwHPE
  gi|336254272|ref|YP_004597379.1| 115 PDTRVWASHADEVKELPAGFELTAESDVCDVEAMSDTDRD--IYGVQWHPE 163
                                       57899999*******************999********88..********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 ?   12.5   0.4   1.4e-05     0.084      70      94 ..      61      85 ..       3     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                          GATase_3 70 eaaeaggpvlgiCGGlqmLGeeied 94
                                      e++ea++pvlgiC G+q+  ee+  
  gi|336254272|ref|YP_004597379.1| 61 EYLEADMPVLGICLGMQLIAEELGG 85
                                      6899***************999855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 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:                        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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1474.20
//
Query:       gi|336254273|ref|YP_004597380.1|  [L=88]
Description: hypothetical protein Halxa_2885 [Halopiger xanaduensis SH-6]
Scores for 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-05   24.0   0.4    5.6e-05   23.4   0.4    1.4  1  DUF3194   Protein of unknown function (DUF3194)


Domain annotation for each model (and alignments):
>> DUF3194  Protein of unknown function (DUF3194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.4   3.1e-09   5.6e-05      10      56 ..       9      52 ..       6      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.1e-09
                                      HHHHHHHHHHHHHHHHTTS-TTTEEEEEEEEEEEESSSEEEEEEEEE CS
                           DUF3194 10 deiseflaeviekkifkkvskkevldlditvevkeneeLdvdvevel 56
                                      de+ + +++++e ++f++  +++v+dld+tv ++ +  L+vdv  +l
  gi|336254273|ref|YP_004597380.1|  9 DEVVQTASDAAEGYVFSQYKQSDVRDLDVTVTFEDG-VLEVDV--YL 52
                                      6888999*************************9766.455555..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 735.45
//
Query:       gi|336254274|ref|YP_004597381.1|  [L=130]
Description: Prefoldin subunit beta [Halopiger xanaduensis SH-6]
Scores for 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-27   93.1  18.4      1e-26   92.9  18.4    1.0  1  Prefoldin_2      Prefoldin subunit
    0.00025   21.3   4.4    0.00025   21.3   4.4    2.6  2  FlaC_arch        Flagella accessory protein C (FlaC)
    0.00033   20.9  11.2    0.00043   20.5  11.2    1.0  1  DUF5082          Domain of unknown function (DUF5082)
    0.00053   19.4   6.5    0.00063   19.1   6.5    1.0  1  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
    0.00068   19.5  16.6      0.032   14.1  16.6    2.6  1  Prefoldin        Prefoldin subunit
    0.00079   19.7   3.8    0.00079   19.7   3.8    2.5  3  CLZ              C-terminal leucine zipper domain of cyclic n
     0.0038   17.2   9.4     0.0051   16.8   9.4    1.2  1  Laminin_II       Laminin Domain II
     0.0074   16.3   6.4     0.0074   16.3   6.4    2.1  2  DHR10            Designed helical repeat protein 10 domain
  ------ inclusion threshold ------
       0.01   16.0   1.6       0.01   16.0   1.6    2.3  2  XhlA             Haemolysin XhlA
      0.018   15.1   7.4      0.018   15.1   7.4    2.2  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.018   12.6   8.3      0.023   12.2   8.3    1.0  1  DUF3584          Protein of unknown function (DUF3584)
      0.022   15.0   2.1      0.022   15.0   2.1    1.9  2  DUF2379          Protein of unknown function (DUF2379)
      0.027   15.1  10.4        0.2   12.2   1.9    2.7  3  DUF5344          Family of unknown function (DUF5344)
      0.027   13.0   0.7      0.034   12.6   0.7    1.1  1  PAF-AH_p_II      Platelet-activating factor acetylhydrolase, 
      0.028   14.1   0.8      0.028   14.1   0.8    1.8  2  DUF4988          Domain of unknown function
      0.046   13.5  15.6      0.068   13.0  15.6    1.2  1  ERM              Ezrin/radixin/moesin family
      0.054   13.5  15.4       0.28   11.2   4.8    2.1  2  Cep57_CLD        Centrosome localisation domain of Cep57
      0.079   13.2   7.2        3.1    8.1   0.1    2.8  3  WXG100           Proteins of 100 residues with WXG
       0.11   12.0   0.1       0.22   11.0   0.1    1.5  1  BRI3BP           Negative regulator of p53/TP53
       0.15   11.5  14.3       0.19   11.1  14.3    1.1  1  HMMR_N           Hyaluronan mediated motility receptor N-term
       0.19   11.8  15.0       0.86    9.7   4.7    2.1  2  BRE1             BRE1 E3 ubiquitin ligase
       0.25   11.4   3.4       0.57   10.3   3.4    1.9  1  SASP             Small, acid-soluble spore proteins, alpha/be
       0.26   10.7   0.4       0.33   10.4   0.4    1.1  1  Fijivirus_P9-2   Fijivirus P9-2 protein
       0.32   10.2  16.4       0.23   10.7   1.7    2.0  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.33   10.8  11.9      0.095   12.6   1.8    2.1  2  Sec34            Sec34-like family
       0.36   10.9  20.7        1.3    9.1   7.0    2.1  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.36   10.1  10.8      0.045   13.1   1.2    2.0  2  TraF_2           F plasmid transfer operon, TraF, protein
       0.61    8.6   6.0       0.88    8.1   6.0    1.2  1  FapA             Flagellar Assembly Protein A
       0.63    8.5   2.1       0.78    8.2   2.1    1.1  1  FUSC             Fusaric acid resistance protein family
       0.63    9.8  10.6       0.83    9.5  10.6    1.1  1  DUF724           Protein of unknown function (DUF724)
       0.64    9.5   4.4        0.8    9.2   4.4    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
       0.83    7.7  16.3        1.1    7.3  16.3    1.1  1  EzrA             Septation ring formation regulator, EzrA
          1    8.6  20.6       0.23   10.7   5.3    2.0  2  DUF3450          Protein of unknown function (DUF3450)
        1.4    9.5   9.9       0.81   10.2   1.1    2.2  2  NPV_P10          Nucleopolyhedrovirus P10 protein
        1.7    6.5   5.9        2.1    6.2   5.9    1.1  1  Prominin         Prominin
        1.8    8.8  18.7          1    9.6   4.3    2.2  2  Spc24            Spc24 subunit of Ndc80
        2.2    8.4   9.8        1.3    9.1   1.2    2.0  2  DUF1664          Protein of unknown function (DUF1664)
        2.6    6.8  19.3        1.9    7.3   6.6    2.0  2  Spc7             Spc7 kinetochore protein
        2.6    8.4  16.1        0.3   11.4   2.8    2.3  2  DUF4164          Domain of unknown function (DUF4164)
        2.6    8.6  14.0        5.7    7.5   2.8    2.4  2  Syntaxin-6_N     Syntaxin 6, N-terminal
        2.8    8.4  18.3    9.4e+02    0.3  18.3    2.2  1  DUF4140          N-terminal domain of unknown function (DUF41
        3.2    8.2  13.3        2.4    8.6   2.9    2.2  2  Snapin_Pallidin  Snapin/Pallidin
        3.7    7.8  15.0        1.1    9.5   1.6    2.2  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
          4    7.7  17.0        1.7    8.9   5.1    2.1  2  Med21            Subunit 21 of Mediator complex
          4    7.0  11.7        6.8    6.2   2.7    2.1  2  Fzo_mitofusin    fzo-like conserved region
        4.5    6.8  10.6        7.2    6.1  10.6    1.2  1  DUF572           Family of unknown function (DUF572)
        4.6    7.7  13.6          5    7.6   3.1    2.3  2  V-SNARE          Vesicle transport v-SNARE protein N-terminus


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 !   92.9  18.4   2.7e-29     1e-26       1     105 [.      10     114 ..      10     115 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 2.7e-29
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketleke 77 
                                       qe+i+++q+lq++ q++a q++++et+l+e+e +l+ele++d++t++y++vG++lv++d +e++++Le++ ++le +
  gi|336254274|ref|YP_004597381.1|  10 QEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELENIDDETTMYRNVGELLVETDYDEAQDDLEDKVDSLEIR 86 
                                       89*************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHCCTS- CS
                       Prefoldin_2  78 iktlekqleklekeleelkeelqkklqq 105
                                       ++tlekq+e+++ ++e l+eel ++l++
  gi|336254274|ref|YP_004597381.1|  87 LETLEKQEERVQDQFESLQEELEELLGG 114
                                       ************************9985 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 ?    0.8   1.8       1.7   6.4e+02      15      24 ..      36      45 ..       8      64 .. 0.55
   2 !   21.3   4.4   6.7e-07   0.00025       3      41 ..      74     112 ..      73     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.7
                         FlaC_arch 15 eletvkkene 24
                                      +l+ +++ ++
  gi|336254274|ref|YP_004597381.1| 36 NLTEAENALD 45
                                      2222222222 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 6.7e-07
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkdll 41 
                                       d+lE k+++l+++let++k+ e ++++ e l+e+ ++ll
  gi|336254274|ref|YP_004597381.1|  74 DDLEDKVDSLEIRLETLEKQEERVQDQFESLQEELEELL 112
                                       79**********************************998 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5  11.2   1.1e-06   0.00043      22     121 ..       9     111 ..       7     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-06
                           DUF5082  22 leekIerLkeaktklsdekeslkqkkkklekplnssesWkGk.eennydgirs..nlessyqtyvdkldelidaiee 95 
                                        +ekIe L+   ++ +++  + ++++++l++ +n  +++ +   e + +  +    +e++y++ +d+l++ +d++e 
  gi|336254274|ref|YP_004597381.1|   9 AQEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELENIdDETTMYRNVGelLVETDYDEAQDDLEDKVDSLEI 85 
                                       69***************************************974444444444589********************* PP

                           DUF5082  96 EIerLenqiseaqgvldtlqsqlnsl 121
                                         e+Le+q +  q   ++lq++l++l
  gi|336254274|ref|YP_004597381.1|  86 RLETLEKQEERVQDQFESLQEELEEL 111
                                       **********************9987 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 !   19.1   6.5   1.6e-06   0.00063       2     113 ..       5     113 ..       4     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-06
                    ALIX_LYPXL_bnd   2 lPpsllekaeevrsqgglqrlekllqdlqelkerneeiLdeieklLdeEe..sedeklrakygtrWtrqpSseltae 76 
                                       lPp+  ek+e+++      +l++  q++   k+++e+ L+e+e+ Lde e  + + ++ ++ g+    ++ +e++  
  gi|336254274|ref|YP_004597381.1|   5 LPPEAQEKIEQLQ------DLQETAQEVAVQKQEAETNLTEAENALDELEniDDETTMYRNVGELLVETDYDEAQDD 75 
                                       7777788888777......9**************************98664555567889999999*********** PP

                    ALIX_LYPXL_bnd  77 lraelqkyreileeAsesDkivrqklqenkedlelL.s 113
                                       l +++++++  le   + ++ v++++++ +e+le+L +
  gi|336254274|ref|YP_004597381.1|  76 LEDKVDSLEIRLETLEKQEERVQDQFESLQEELEELlG 113
                                       *********************************98845 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1  16.6   8.4e-05     0.032      16     117 ..      10     111 ..       8     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.4e-05
                                       HHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  16 keaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiellkkkleelekq 92 
                                       +e+ie l+++ et +++  +++++e+     +++  + e +d++  +     +  ve +++eA + l++k+++le  
  gi|336254274|ref|YP_004597381.1|  10 QEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELENIDDETTMYRNVGELLVETDYDEAQDDLEDKVDSLEIR 86 
                                       789999999999999999999999999999999999999877776555555579*********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  93 lekleeeleklkdqittleanlaql 117
                                       le+le++ e  +dq ++l+++l++l
  gi|336254274|ref|YP_004597381.1|  87 LETLEKQEERVQDQFESLQEELEEL 111
                                       *********************9987 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 ?   -0.8   1.6       5.3     2e+03      35      50 ..      15      26 ..       4      39 .. 0.50
   2 ?    2.2   3.8      0.61   2.3e+02      16      44 ..      20      48 ..      14      51 .. 0.80
   3 !   19.7   3.8   2.1e-06   0.00079      23      62 ..      70     109 ..      61     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 5.3
                               CLZ 35 rLessLeaLqtrlarL 50
                                      +    L+ Lq   + +
  gi|336254274|ref|YP_004597381.1| 15 Q----LQDLQETAQEV 26
                                      3....33444444444 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.61
                               CLZ 16 DeeaakagaeqkeleekverLessLeaLq 44
                                       e+a++   +++e+e+++++ e++L+ L+
  gi|336254274|ref|YP_004597381.1| 20 QETAQEVAVQKQEAETNLTEAENALDELE 48
                                      445556669999**************997 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 2.1e-06
                               CLZ  23 gaeqkeleekverLessLeaLqtrlarLlaeyessqrkLk 62 
                                        + q++le+kv++Le +Le+L+++ +r+ +++es q++L+
  gi|336254274|ref|YP_004597381.1|  70 DEAQDDLEDKVDSLEIRLETLEKQEERVQDQFESLQEELE 109
                                       46799********************************996 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   9.4   1.3e-05    0.0051       4      91 ..      15     107 ..      12     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX--TTTTTGGGHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvk.dankairdArrsvkkLeklapqLldklkelk 79 
                                        +++ +eta+ev  q+++ ++nl + ++ l e+++  +et+   +     +  d  ++  +Le +++ L+ +l++l+
  gi|336254274|ref|YP_004597381.1|  15 QLQDLQETAQEVAVQKQEAETNLTEAENALDELENIDDETTMYRNvGELLVETDYDEAQDDLEDKVDSLEIRLETLE 91 
                                       578999******************9999999999887788877665555667788899999**************** PP

                                       HHHHH.......HHHH CS
                        Laminin_II  80 qleeasss....lsdn 91 
                                       ++ee  +     l ++
  gi|336254274|ref|YP_004597381.1|  92 KQEERVQDqfesLQEE 107
                                       *999955444445555 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 ?    3.3   9.0      0.22        82      22      64 ..      10      52 ..       7      66 .. 0.54
   2 !   16.3   6.4     2e-05    0.0074      60      97 ..      74     111 ..      62     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.22
                             DHR10 22 qakidalqvvekdlrsciklleeieaelakleeakkklkelrd 64
                                      q+ki+ lq++++  +++  + +e+e++l + e a ++l++  d
  gi|336254274|ref|YP_004597381.1| 10 QEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELENIDD 52
                                      4444444444444444444444444444444444444444444 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2e-05
                             DHR10  60 kelrdaleekeielrelerkeerlqrqlenaeeklerl 97 
                                       ++l+d+++++ei+l+ le++eer+q q e+ +e+le l
  gi|336254274|ref|YP_004597381.1|  74 DDLEDKVDSLEIRLETLEKQEERVQDQFESLQEELEEL 111
                                       6899*******************************976 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   6.4      0.14        54       4      47 ..      11      53 ..       8      55 .. 0.56
   2 ?   16.0   1.6   2.7e-05      0.01       9      44 ..      76     111 ..      69     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.14
                              XhlA  4 erlerietkldnleervdkleekaaeaeekiknleedlkklesn 47
                                      e++e+++  +++ + +v   ++ a++ +++++n+ ++l+++ + 
  gi|336254274|ref|YP_004597381.1| 11 EKIEQLQDLQETAQ-EVAVQKQEAETNLTEAENALDELENIDDE 53
                                      44444443333333.46666677777777777777777777665 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.7e-05
                              XhlA   9 ietkldnleervdkleekaaeaeekiknleedlkkl 44 
                                       +e k+d+le r+++le+ +++++ + ++l+e+l++l
  gi|336254274|ref|YP_004597381.1|  76 LEDKVDSLEIRLETLEKQEERVQDQFESLQEELEEL 111
                                       799******************************997 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 ?    2.0   8.4       0.5   1.9e+02      24      68 ..      11      54 ..       7      68 .. 0.50
   2 ?   15.1   7.4   4.7e-05     0.018      17      57 ..      71     111 ..      57     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.5
                    CENP-F_leu_zip 24 dkvenLerelemseenqekvileaEtskaevetlkeeieelaeel 68
                                      +k+e+L+ +l++  ++    + eaEt+  e+e+  +e+e++  e+
  gi|336254274|ref|YP_004597381.1| 11 EKIEQLQ-DLQETAQEVAVQKQEAETNLTEAENALDELENIDDET 54
                                      4555553.3333333333334444455555554444444444443 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.7e-05
                    CENP-F_leu_zip  17 rkadsLkdkvenLerelemseenqekvileaEtskaevetl 57 
                                       + +d L+dkv++Le  le++e++ e+v  + E+ ++e+e+l
  gi|336254274|ref|YP_004597381.1|  71 EAQDDLEDKVDSLEIRLETLEKQEERVQDQFESLQEELEEL 111
                                       5689***********************************97 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   8.3   6.1e-05     0.023     828     930 ..      10     110 ..       5     116 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.1e-05
                           DUF3584 828 esaaeeleqeltrliedtklerkklekerkalekqldqldenlrklrdllsklaelkldadaeqaegelaerlaale 904
                                       ++++e+l+ +l++  +++  + ++ e+++  +e++ld+l+ n+ +  ++ ++++el ++ d ++a+ +l+ +++ le
  gi|336254274|ref|YP_004597381.1|  10 QEKIEQLQ-DLQETAQEVAVQKQEAETNLTEAENALDELE-NIDDETTMYRNVGELLVETDYDEAQDDLEDKVDSLE 84 
                                       44555554.4444455555666666666666666666663.334445577888888888888888888888888888 PP

                           DUF3584 905 elkrkrerlsedvkkalerfkgvlkd 930
                                         ++++e+++e v+ ++e ++  l++
  gi|336254274|ref|YP_004597381.1|  85 IRLETLEKQEERVQDQFESLQEELEE 110
                                       88888888888888888888776655 PP

>> DUF2379  Protein of unknown function (DUF2379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   2.1   5.7e-05     0.022      32      64 ..      19      51 ..       8      78 .. 0.88
   2 ?    0.6   0.1       1.6   6.2e+02      46      74 ..      76     104 ..      50     113 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.7e-05
                           DUF2379 32 LrrtarevaiseadaeeaLateesAlaLlreia 64
                                      L+ ta+eva+++++ae+ L + e+Al  l++i 
  gi|336254274|ref|YP_004597381.1| 19 LQETAQEVAVQKQEAETNLTEAENALDELENID 51
                                      899**********************99988875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.6
                           DUF2379  46 aeeaLateesAlaLlreiarRiregskrL 74 
                                        e+ + + e  l+ l++ ++R+++  + L
  gi|336254274|ref|YP_004597381.1|  76 LEDKVDSLEIRLETLEKQEERVQDQFESL 104
                                       44444444444455555555555554444 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.81   3.1e+02      12      26 ..      13      27 ..       8      29 .. 0.75
   2 ?   12.2   1.9   0.00054       0.2       2      52 ..      24      76 ..      23      84 .. 0.71
   3 ?    8.5   1.1    0.0077       2.9      16      56 ..      74     112 ..      64     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.81
                           DUF5344 12 eqkLselktaaeelk 26
                                       ++L++l+++a+e+ 
  gi|336254274|ref|YP_004597381.1| 13 IEQLQDLQETAQEVA 27
                                      468999999999885 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00054
                           DUF5344  2 gEIklnqaeVeqkLselktaaeelktsipetisgknsld..vvekineleeel 52
                                      +E+ ++++e+e++L+e+++a++el+   +et+  +n ++  v + + e +++l
  gi|336254274|ref|YP_004597381.1| 24 QEVAVQKQEAETNLTEAENALDELENIDDETTMYRNVGEllVETDYDEAQDDL 76
                                      79***********************6666666555654400445555555555 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0077
                           DUF5344  16 selktaaeelktsipetisgknsldvvekineleeeleell 56 
                                       ++l++++++l++ +++   +k + +v++++++l+eeleell
  gi|336254274|ref|YP_004597381.1|  74 DDLEDKVDSLEIRLET--LEKQEERVQDQFESLQEELEELL 112
                                       5677788888555555..666799***************98 PP

>> PAF-AH_p_II  Platelet-activating factor acetylhydrolase, isoform II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.7     9e-05     0.034     167     229 ..      14      84 ..       3      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9e-05
                                       EE-----G.GGHHHHHHHHHHHHHHHHHHHHHHHHHHH.TT-----S....S--SS-..GGGGTT-EEEEE CS
                       PAF-AH_p_II 167 iklrkvke.eeevklrneqvkqRaqEcskaLkllrein.lGepvenv....ldsdfd..lqqlKdnldtsk 229
                                        +l++++e  +ev ++++  +   +E  +aL+ l++i+ + +  +nv    +++d+d    +l d++d  +
  gi|336254274|ref|YP_004597381.1|  14 EQLQDLQEtAQEVAVQKQEAETNLTEAENALDELENIDdETTMYRNVgellVETDYDeaQDDLEDKVDSLE 84 
                                       357788876899**************************888889999999999999976667899888765 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2       2.6   9.8e+02      36      36 ..      31      31 ..       8      62 .. 0.46
   2 ?   14.1   0.8   7.4e-05     0.028       1      31 [.      76     106 ..      76     112 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.6
                           DUF4988 36 g 36
                                      +
  gi|336254274|ref|YP_004597381.1| 31 Q 31
                                      1 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.4e-05
                           DUF4988   1 leddvndlkdrvaaleeqvkelndniealkk 31 
                                       led+v++l+ r ++le+q + ++d++e+l++
  gi|336254274|ref|YP_004597381.1|  76 LEDKVDSLEIRLETLEKQEERVQDQFESLQE 106
                                       89***************************97 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  15.6   0.00018     0.068      97     201 ..       8     111 ..       3     112 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00018
                               ERM  97 eserkeeeaerLkeeleeareaeeeakekllealstpskseseenveeseteeeeensee....esaeletdevekl 169
                                       e ++k e+ + L+e ++e+  +++ea+++l ea ++  + e+    + ++t +   n  e    + ++  +d+ e+ 
  gi|336254274|ref|YP_004597381.1|   8 EAQEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELEN---IDDETTMYR--NVGEllveTDYDEAQDDLED- 78 
                                       667888888999999999999999999988888888842222...222222222..22221111334444444433. PP

                               ERM 170 sleieeeRvtyleks.krlqeqLkeLkseleql 201
                                       + ++ e R++ lek+ +r+q+q + L++ele+l
  gi|336254274|ref|YP_004597381.1|  79 KVDSLEIRLETLEKQeERVQDQFESLQEELEEL 111
                                       556666688888775268999999999999875 PP

>> Cep57_CLD  Centrosome localisation domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.9    0.0057       2.2     114     152 ..       8      46 ..       2      58 .. 0.89
   2 ?   11.2   4.8   0.00072      0.28     134     172 ..      71     109 ..      64     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0057
                         Cep57_CLD 114 elqaklekLekLEkeylrLtatqklaekkikeLeekLke 152
                                       e+q+k e+L++L +  ++++ +++ ae+ + e e+ L e
  gi|336254274|ref|YP_004597381.1|   8 EAQEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDE 46 
                                       7899999*****9999************99999999987 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00072
                         Cep57_CLD 134 atqklaekkikeLeekLkeEehqrklvqdkaaqlqtele 172
                                       ++q   e+k+ +Le +L+  e+q   vqd+ + lq+ele
  gi|336254274|ref|YP_004597381.1|  71 EAQDDLEDKVDSLEIRLETLEKQEERVQDQFESLQEELE 109
                                       578888********************************9 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 ?    6.7   2.2     0.022       8.4       7      38 ..      17      48 ..       7      50 .. 0.75
   2 ?    0.5   0.0       1.8     7e+02      15      36 ..      68      89 ..      65      93 .. 0.57
   3 ?    8.1   0.1    0.0082       3.1      15      45 ..      89     120 ..      79     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.022
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCG CS
                            WXG100  7 eelrqaaarfqkqaeeledelqrlkaevdalq 38
                                      ++l+++a++++ q++e e+ l++ ++ +d+l+
  gi|336254274|ref|YP_004597381.1| 17 QDLQETAQEVAVQKQEAETNLTEAENALDELE 48
                                      67778888888888888888888877777774 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.8
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100 15 rfqkqaeeledelqrlkaevda 36
                                      ++++++++led +++l+  ++ 
  gi|336254274|ref|YP_004597381.1| 68 DYDEAQDDLEDKVDSLEIRLET 89
                                      4556666666666666555444 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0082
                                       HHHHHHHHHHHHHHHHHHHHHHC.GCGCTHHH CS
                            WXG100  15 rfqkqaeeledelqrlkaevdal.qsgWsGaa 45 
                                       ++ kq+e+++d+ ++l+ e+++l ++g  G a
  gi|336254274|ref|YP_004597381.1|  89 TLEKQEERVQDQFESLQEELEELlGGGMGGPA 120
                                       678999*****************999988865 PP

>> BRI3BP  Negative regulator of p53/TP53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00057      0.22     155     178 ..      70      93 ..      54      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00057
                            BRI3BP 155 eesgasleakvrsLerqvrelnkr 178
                                       +e +  le+kv+sLe +++ l+k+
  gi|336254274|ref|YP_004597381.1|  70 DEAQDDLEDKVDSLEIRLETLEKQ 93 
                                       367889****************97 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  14.3   0.00051      0.19     200     300 ..       8     112 ..       1     114 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00051
                            HMMR_N 200 eskakvaqLkeklvslekekieekset....eklleyieelsnvseqlekykldiaql.eellkekndeiesLkssL 271
                                       e+++k+ qL++   ++ +e + +k+e      + ++  +el+n+ ++  +y+   + l e   +e++d++e+   sL
  gi|336254274|ref|YP_004597381.1|   8 EAQEKIEQLQDLQ-ETAQEVAVQKQEAetnlTEAENALDELENIDDETTMYRNVGELLvETDYDEAQDDLEDKVDSL 83 
                                       7899999999764.777777666666610113445667899999999999998777651456888999999999999 PP

                            HMMR_N 272 eekeqelskqvkdlnekckllekekeelv 300
                                       e + ++l+kq +  + + + l++e+eel+
  gi|336254274|ref|YP_004597381.1|  84 EIRLETLEKQEERVQDQFESLQEELEELL 112
                                       99999999999999999999999999765 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.7    0.0023      0.86      18      59 ..       8      49 ..       4      56 .. 0.95
   2 ?    7.9   2.8    0.0081       3.1      43      83 ..      69     110 ..      51     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0023
                              BRE1 18 qlskkvkeltileekklrleaekakadqkyfaamrskdalen 59
                                      ++++k+++l++l+e  + + ++k++a+    +a+++ d len
  gi|336254274|ref|YP_004597381.1|  8 EAQEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELEN 49
                                      689************************************997 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0081
                              BRE1  43 adqkyfaamrskdalenelkkLnkllsKsselieqLke.lek 83 
                                        d+ + +++ + d+le+ l +L k+ ++ ++  e L+e le+
  gi|336254274|ref|YP_004597381.1|  69 YDEAQDDLEDKVDSLEIRLETLEKQEERVQDQFESLQEeLEE 110
                                       567778899999*************************96554 PP

>> SASP  Small, acid-soluble spore proteins, alpha/beta type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.4    0.0015      0.57       4      40 ..       5      41 ..       3     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0015
                                      SSGGGHHHHHHH..HHHHHHHHT---ST.....TSBHHH CS
                              SASP  4 lvpeakeaLdql..KyEvAaElGvslgkdgyngdltsrq 40
                                      l pea+e+++ql    E+A+E+ v+   ++ + +lt  +
  gi|336254274|ref|YP_004597381.1|  5 LPPEAQEKIEQLqdLQETAQEVAVQK--QEAETNLTEAE 41
                                      56**********5558*********6..44555666554 PP

>> Fijivirus_P9-2  Fijivirus P9-2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00085      0.33      26      61 ..      54      90 ..      32      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00085
                    Fijivirus_P9-2 26 ntmh.kvddfvstidvnfsdselddkvddleikiekv 61
                                       tm+ +v +++   d + ++ +l+dkvd lei++e +
  gi|336254274|ref|YP_004597381.1| 54 TTMYrNVGELLVETDYDEAQDDLEDKVDSLEIRLETL 90
                                      4665258899999999999**************9975 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 ?    5.2   7.3     0.028        11      39      83 ..       8      52 ..       2      63 .. 0.87
   2 ?   10.7   1.7   0.00059      0.23      58     101 ..      70     113 ..      58     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.028
                              HemX 39 elqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekele 83
                                      e q+++++l++ ++++++ + qkqe e++l +++++l++le+  +
  gi|336254274|ref|YP_004597381.1|  8 EAQEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELENIDD 52
                                      679999999999999999******************999998655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00059
                              HemX  58 keqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsg 101
                                       +e +++le++++ l+ +le+lek+ e  q q e+lq++l+++ g
  gi|336254274|ref|YP_004597381.1|  70 DEAQDDLEDKVDSLEIRLETLEKQEERVQDQFESLQEELEELLG 113
                                       56789999********************************9876 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   2.6      0.19        72       3      38 ..      14      49 ..      12      68 .. 0.60
   2 ?   12.6   1.8   0.00025     0.095       8      51 ..      69     112 ..      65     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.19
                             Sec34  3 dqLeskeeecdelleqtdealeqLeeleekfksvse 38
                                      +qL++ +e+ +e+  q +ea+++L+e e+  ++ ++
  gi|336254274|ref|YP_004597381.1| 14 EQLQDLQETAQEVAVQKQEAETNLTEAENALDELEN 49
                                      677777777777777777777777766655444332 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00025
                             Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqll 51 
                                       + e  d+l +++d+++  Le+le++ ++v+++ +sl+e+ e+ll
  gi|336254274|ref|YP_004597381.1|  69 YDEAQDDLEDKVDSLEIRLETLEKQEERVQDQFESLQEELEELL 112
                                       567789999*********************************98 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.0    0.0033       1.3      53      92 ..      10      49 ..       8      59 .. 0.86
   2 ?    7.9   5.7     0.008       3.1      96     129 .]      71     104 ..      62     112 .. 0.39

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0033
                        TPR_MLP1_2 53 aedvkelqalreelnelkaeiaelkaeaesakaeleesee 92
                                       e +++lq+l e ++e+  + +e+++++ +a+++l+e e+
  gi|336254274|ref|YP_004597381.1| 10 QEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELEN 49
                                      5789999999999999999999999999999999998875 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.008
                        TPR_MLP1_2  96 eqkeelekelselekriedlneqNklLhdQlEsl 129
                                       e ++ le+++++le r+e l++q +   dQ+Esl
  gi|336254274|ref|YP_004597381.1|  71 EAQDDLEDKVDSLEIRLETLEKQEERVQDQFESL 104
                                       3333333333333333333333333333333332 PP

>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   2.5      0.18        70      37      84 ..      10      56 ..       3      62 .. 0.57
   2 ?   13.1   1.2   0.00012     0.045      32      82 ..      72     115 ..      55     124 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.18
                            TraF_2 37 vDkiDdlsdildgleaavnaasadetqvdeaaddlnalLedlggdgyl 84
                                       +ki++l+d  +++++++ ++++ et+++ea + l ++Le++++++++
  gi|336254274|ref|YP_004597381.1| 10 QEKIEQLQDLQETAQEVAVQKQEAETNLTEAENAL-DELENIDDETTM 56
                                      56777777777766666655554444433333333.356667666654 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00012
                            TraF_2  32 dvdnlvDkiDdlsdildgleaavnaasadetqvdeaaddlnalLedlggdg 82 
                                        +d+l Dk+D+l+ +l+       +++++e  v+++++ l+++Le+l g g
  gi|336254274|ref|YP_004597381.1|  72 AQDDLEDKVDSLEIRLE-------TLEKQEERVQDQFESLQEELEELLGGG 115
                                       34555555555555555.......544444339999999999999987766 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.0    0.0023      0.88     324     411 ..      22     111 ..       5     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0023
                              FapA 324 teievgldepelkekl...keleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleel 397
                                       t  ev+++++e+  +l   ++  +ele++ +e++++++  ++l +    ++ + + ++++++l+  +e l+++ e +
  gi|336254274|ref|YP_004597381.1|  22 TAQEVAVQKQEAETNLteaENALDELENIDDETTMYRNVGELLVE-TDYDEAQDDLEDKVDSLEIRLETLEKQEERV 97 
                                       556677777777777744466666677778999999999888888.5556678888999999999999999999999 PP

                              FapA 398 eeelkelkeelesk 411
                                       ++++++l+eele+ 
  gi|336254274|ref|YP_004597381.1|  98 QDQFESLQEELEEL 111
                                       99999999999876 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.1     0.002      0.78     235     312 ..      19     113 ..       7     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.002
                              FUSC 235 lsslarllarlraeeaaavpelaallaelaal.................eaaaaaealeaalaalrarlralrrale 294
                                       l+++a++ a  ++e ++   e ++ l+el+++                 +  +a+++le+++++l+ rl+ l++++e
  gi|336254274|ref|YP_004597381.1|  19 LQETAQEVAVQKQEAETNLTEAENALDELENIddettmyrnvgellvetDYDEAQDDLEDKVDSLEIRLETLEKQEE 95 
                                       4555555555555444444458888888888899999999999999998556789999999*********9999999 PP

                              FUSC 295 adadtaalllarlaella 312
                                         +d+ + l+++l ell+
  gi|336254274|ref|YP_004597381.1|  96 RVQDQFESLQEELEELLG 113
                                       777777777777777775 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5  10.6    0.0022      0.83      91     185 ..      10     105 ..       7     107 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0022
                            DUF724  91 qsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeid..elekkilelerqlallkekkeaadkeiarlks 165
                                       q+++++L  l++  ++++ +++++e +++e+e++  +le+  d   + +++ el  + +   e +++ + ++ +l+ 
  gi|336254274|ref|YP_004597381.1|  10 QEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELENIDDetTMYRNVGELLVETD-YDEAQDDLEDKVDSLEI 85 
                                       66777777777777777777777777777777777766654331134445555555544.34999999********* PP

                            DUF724 166 eaekleeeledveqeFeava 185
                                         e+le++ e+v+++Fe+++
  gi|336254274|ref|YP_004597381.1|  86 RLETLEKQEERVQDQFESLQ 105
                                       *****************975 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 ?    9.2   4.4    0.0021       0.8     168     257 ..      13     105 ..       2     114 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                      Exonuc_VII_L 168 kqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k....ekleekkerlkklkerl 239
                                        ++l+ l+++ ++   + ++++ +l+e+e+ l++   ++++ +++ ++++ e l +    e  ++ ++++++l+ rl
  gi|336254274|ref|YP_004597381.1|  13 IEQLQDLQETAQEVAVQKQEAETNLTEAENALDE--LENIDDETTMYRNVGELLvEtdydEAQDDLEDKVDSLEIRL 87 
                                       2333333333333333333333344444444444..33455555555555544444333333333334446666666 PP

                      Exonuc_VII_L 240 elleekkerleeleekle 257
                                       e+le+++er++ + e+l+
  gi|336254274|ref|YP_004597381.1|  88 ETLEKQEERVQDQFESLQ 105
                                       667777777666655554 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  16.3     0.003       1.1     326     425 ..      10     110 ..       7     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.003
                                       GGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHH..HHHHHHHHHHHHHHHH CS
                              EzrA 326 keeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeeleel..eekleeieekqeeile 400
                                       +e++++l++  e ++e   + +e e++l e e+ ++ele +++++++ Y ++ e l e+  +e  +++e+k+++++ 
  gi|336254274|ref|YP_004597381.1|  10 QEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELE-NIDDETTMYRNVGELLVETdyDEAQDDLEDKVDSLEI 85 
                                       567777777777777778888999********9999985.789999999999999866411577889********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 401 slkslrkdEkrAreqldeikkelke 425
                                        l++l+k+E+r ++q + +++el+e
  gi|336254274|ref|YP_004597381.1|  86 RLETLEKQEERVQDQFESLQEELEE 110
                                       ***********************98 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   7.5     0.064        24      45      87 ..       8      50 ..       2      67 .. 0.66
   2 ?   10.7   5.3   0.00061      0.23      41      84 ..      68     111 ..      65     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.064
                           DUF3450 45 ekqellaeyralkeeleslevyneqlerlvasqeqeiasleeq 87
                                      e+qe  +++++l+e +++ +v++++ e  ++++e+ +++le+ 
  gi|336254274|ref|YP_004597381.1|  8 EAQEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELENI 50
                                      5667777777777777777777777777777777777776653 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00061
                           DUF3450  41 klddekqellaeyralkeeleslevyneqlerlvasqeqeiasl 84 
                                       ++d+ +++l++++ +l+ +le le+++e+++++ +s+++e+++l
  gi|336254274|ref|YP_004597381.1|  68 DYDEAQDDLEDKVDSLEIRLETLEKQEERVQDQFESLQEELEEL 111
                                       67899999999999999999999999999999999999999987 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.1      0.17        64      25      64 ..      11      50 ..       7      63 .. 0.58
   2 ?   10.2   1.1    0.0021      0.81      15      54 ..      75     111 ..      67     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.17
                           NPV_P10 25 qqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64
                                      ++++++q+  ++ +e+  + ++  ++L+e e+++++ ++i
  gi|336254274|ref|YP_004597381.1| 11 EKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELENI 50
                                      4444444444444445444455555566666655555544 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0021
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLael 54 
                                       +++dkVd+l+ +++ ++++ + v+   +++++++++L+el
  gi|336254274|ref|YP_004597381.1|  75 DLEDKVDSLEIRLETLEKQEERVQ---DQFESLQEELEEL 111
                                       689999999999999999888855...9999999999886 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   5.9    0.0055       2.1     610     702 ..      21     109 ..       4     113 .. 0.44

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0055
                          Prominin 610 sslyleqlckkltkvnletlaekleelanelsngk..knlkqslkneaqdlraiqqelvlplessvkklkksvkkld 684
                                        +     ++k+ +++nl++ ++ l+el n  ++ +  +n+++ l       ++ ++e  + le +v++l+ ++++l+
  gi|336254274|ref|YP_004597381.1|  21 ETAQEVAVQKQEAETNLTEAENALDELENIDDETTmyRNVGELLV------ETDYDEAQDDLEDKVDSLEIRLETLE 91 
                                       233334566666777777777777777766544423322222222......22233333344444444444444444 PP

                          Prominin 685 eensdlqesikkllaave 702
                                       ++++  q++++ l +++e
  gi|336254274|ref|YP_004597381.1|  92 KQEERVQDQFESLQEELE 109
                                       444444444444433333 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   7.2     0.085        32      10      63 ..      13      60 ..       4      73 .. 0.51
   2 ?    9.6   4.3    0.0027         1       8      43 ..      75     110 ..      68     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.085
                             Spc24 10 akelsdleselesleselaelkeeleeleeeseekeservedetllklklYrsL 63
                                      +++l+dl+++++++  +++e +++l+e e+   e e+   +     +  +Yr++
  gi|336254274|ref|YP_004597381.1| 13 IEQLQDLQETAQEVAVQKQEAETNLTEAENALDELEN--ID----DETTMYRNV 60
                                      4455555555555555555555555555555555111..22....333345544 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0027
                             Spc24   8 riakelsdleselesleselaelkeeleeleeesee 43 
                                       ++  ++++le  le le++ ++ ++++e l+ee ee
  gi|336254274|ref|YP_004597381.1|  75 DLEDKVDSLEIRLETLEKQEERVQDQFESLQEELEE 110
                                       677899999999999999999999999999999876 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.7     0.024       9.1      48     123 ..      17      93 ..       9      94 .. 0.81
   2 ?    9.1   1.2    0.0033       1.3      58      98 ..      70     110 ..      56     114 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.024
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeik..eevtevredlseigedvesvkeavegleskleriee 122
                                       ++l++  +++a +k++ + ++ + ++ lde ++i  e++  ++v e+  +++  +e  + +++ v +le +le++e+
  gi|336254274|ref|YP_004597381.1|  17 QDLQETAQEVAVQKQEAETNLTEAENALDELENIDDETTmyRNVGELLVETD-YDEAQDDLEDKVDSLEIRLETLEK 92 
                                       468888899*********************9999876542289999877654.45666778999*********9986 PP

                           DUF1664 123 k 123
                                       +
  gi|336254274|ref|YP_004597381.1|  93 Q 93 
                                       4 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0033
                           DUF1664  58 aatkrhLssridrvdkkldeqkeiskeikeevtevredlse 98 
                                        +++++L++++d+++ +l+  ++  + ++++ ++++e+l+e
  gi|336254274|ref|YP_004597381.1|  70 DEAQDDLEDKVDSLEIRLETLEKQEERVQDQFESLQEELEE 110
                                       55666777777777777777777777777777777776665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   6.6     0.005       1.9     222     264 ..       9      51 ..       4      58 .. 0.78
   2 ?    5.7   4.8     0.016         6     142     179 ..      74     111 ..      65     113 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.005
                              Spc7 222 laelqeqleeleekieelkeqkseleeeiaeaervleeckgws 264
                                        +e+ eql++l+e+ +e++ qk+e+e+++ eae+ l+e ++++
  gi|336254274|ref|YP_004597381.1|   9 AQEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELENID 51 
                                       5677788888888888888888888888888888888877665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                              Spc7 142 egleenlegleedkelLekqeeeldellpeleeekael 179
                                       + le+++++le   e+Lekqee +++  ++l+ee +el
  gi|336254274|ref|YP_004597381.1|  74 DDLEDKVDSLEIRLETLEKQEERVQDQFESLQEELEEL 111
                                       44455555555555555555555555555555554444 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   5.5      0.46   1.8e+02      32      72 ..      14      54 ..       7      57 .. 0.78
   2 ?   11.4   2.8    0.0008       0.3       3      43 ..      66     110 ..      64     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.46
                           DUF4164 32 rkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEv 72
                                      ++ ++l+++ ++++  ++  + +L++ae+ + +le++ +E+
  gi|336254274|ref|YP_004597381.1| 14 EQLQDLQETAQEVAVQKQEAETNLTEAENALDELENIDDET 54
                                      44477888888888888889999999999999999998886 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0008
                           DUF4164   3 tkeleaaltrLeaaldsLEkavdrrleaerkr.....deleaeiea 43 
                                       +++ ++a+++Le ++dsLE +++   ++ ++r     ++l++e+e+
  gi|336254274|ref|YP_004597381.1|  66 ETDYDEAQDDLEDKVDSLEIRLETLEKQ-EERvqdqfESLQEELEE 110
                                       567899*************999874444.44446555666666655 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 ?    7.5   2.8     0.015       5.7      23      62 ..      12      49 ..       6      52 .. 0.79
   2 ?    5.3   9.7     0.077        29       7      79 ..      30     106 ..      30     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.015
                      Syntaxin-6_N 23 rwerlledtssstseeldetrteLrkalrsiewdledLee 62
                                      + e+l++++++   +e+  +++e +++l ++e+ l++Le+
  gi|336254274|ref|YP_004597381.1| 12 KIEQLQDLQET--AQEVAVQKQEAETNLTEAENALDELEN 49
                                      45667777654..789999999999999999999999986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.077
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtss.s......tseeldetrteLrkalrsiewdledLeetvriveknpskfki 76 
                                       k+e + +l +ae+ +++ e++ ++t+  +       + ++de++++L+ +++s+e  le Le+  +   + +++f+ 
  gi|336254274|ref|YP_004597381.1|  30 KQEAETNLTEAENALDELENIDDETTMyRnvgellVETDYDEAQDDLEDKVDSLEIRLETLEKQEE---RVQDQFES 103
                                       57888888888888888888777766653688888999************************9874...44444555 PP

                      Syntaxin-6_N  77 dek 79 
                                        ++
  gi|336254274|ref|YP_004597381.1| 104 LQE 106
                                       555 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 ?    0.3  18.3       2.5   9.4e+02      65      96 ..      66     109 ..       3     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2.5
                           DUF4140  65 e............elkalraeleeledelaaledelaaaearla 96 
                                       e            ++++l+ +le+le++ ++++d+ ++++++l+
  gi|336254274|ref|YP_004597381.1|  66 EtdydeaqddledKVDSLEIRLETLEKQEERVQDQFESLQEELE 109
                                       03333333334547**************************9987 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.8     0.079        30      14      51 ..      15      52 ..       2      62 .. 0.65
   2 ?    8.6   2.9    0.0063       2.4      11      46 ..      76     111 ..      69     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.079
                   Snapin_Pallidin 14 kldeldeklkelrqsQeeLleqldrlnekLkeleeaqe 51
                                      +l++l+e+ +e+  + +e   +l++  ++L+ele++++
  gi|336254274|ref|YP_004597381.1| 15 QLQDLQETAQEVAVQKQEAETNLTEAENALDELENIDD 52
                                      46666666666666666666666666666666666666 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0063
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkel 46 
                                       le k+d l+ +l+ l+++ e +++q ++l+e+L+el
  gi|336254274|ref|YP_004597381.1|  76 LEDKVDSLEIRLETLEKQEERVQDQFESLQEELEEL 111
                                       678899999999999999999999999999999886 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 ?    4.2   5.7      0.13        48      56      93 ..      10      47 ..       3      57 .. 0.55
   2 ?    9.5   1.6     0.003       1.1      66     103 ..      67     107 ..      54     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.13
                                      HHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N 56 skeIgkakkkkedaeeliaevkelkeelkaleaelkel 93
                                      +++I+++ + +e a+e+  + +e  ++l ++e++l+el
  gi|336254274|ref|YP_004597381.1| 10 QEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDEL 47
                                      44444444444445555444455555555554444444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.003
                                       T...S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                      Seryl_tRNA_N  66 k...edaeeliaevkelkeelkaleaelkeleaelekllla 103
                                           e  ++l ++v++l  +l++le++++ +++++e+l  +
  gi|336254274|ref|YP_004597381.1|  67 TdydEAQDDLEDKVDSLEIRLETLEKQEERVQDQFESLQEE 107
                                       445578899999**********************9998765 PP

>> Med21  Subunit 21 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.1    0.0045       1.7      92     138 ..       4      50 ..       3      55 .. 0.92
   2 ?    4.8   4.0     0.082        31      99     140 ..      72     113 ..      68     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0045
                             Med21  92 sLPgigsseeeqeerikeLeeelreveeereekvkekeellkkveel 138
                                       +LP   +++ eq++ ++e ++e++  ++e e  ++e+e+ l+++e++
  gi|336254274|ref|YP_004597381.1|   4 NLPPEAQEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELENI 50 
                                       6999999999********************************99985 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.082
                             Med21  99 seeeqeerikeLeeelreveeereekvkekeellkkveellr 140
                                        +++ e+++++Le  l+  e++ e +  + e l++++eell+
  gi|336254274|ref|YP_004597381.1|  72 AQDDLEDKVDSLEIRLETLEKQEERVQDQFESLQEELEELLG 113
                                       667888999999999999999999999999999999999985 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.7     0.018       6.8     103     148 ..      19      64 ..       7      67 .. 0.82
   2 ?    6.1   2.0     0.019       7.4     109     153 ..      68     109 ..      63     112 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.018
                     Fzo_mitofusin 103 farlcqqvdetekeleeeikelekeiekleevqkkakllrnkasll 148
                                       +++  q+v  +++e e++++e e+ +++le++  +  + rn  +ll
  gi|336254274|ref|YP_004597381.1|  19 LQETAQEVAVQKQEAETNLTEAENALDELENIDDETTMYRNVGELL 64 
                                       556779999999********************99999999876655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.019
                     Fzo_mitofusin 109 qvdetekeleeeikelekeiekleevqkkakllrnkaslleseLe 153
                                       + de++++le+++++le ++e+le+ +++   ++++ ++l++eLe
  gi|336254274|ref|YP_004597381.1|  68 DYDEAQDDLEDKVDSLEIRLETLEKQEER---VQDQFESLQEELE 109
                                       678999**********9998888876665...4555666666655 PP

>> DUF572  Family of unknown function (DUF572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  10.6     0.019       7.2     144     229 ..       8      96 ..       4     114 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                            DUF572 144 ealesLeeLqelnqrqakvdfdanlelrkefreekkereeeeedeealkekislekikllpedeedekkaklle.gk 219
                                       ea+e++e+Lq+l++ +++v +++  ++ + +++e+   e e+ d+e +  +      +ll e++ de +++l +  +
  gi|336254274|ref|YP_004597381.1|   8 EAQEKIEQLQDLQETAQEVAVQKQEAETNLTEAENALDELENIDDETTMYRN---VGELLVETDYDEAQDDLEDkVD 81 
                                       5778899999999999999998888888888888888777777777776444...4577777776656555544233 PP

                            DUF572 220 te.....slfassee 229
                                       +      +l++++e+
  gi|336254274|ref|YP_004597381.1|  82 SLeirleTLEKQEER 96 
                                       322333222222222 PP

>> 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 ?    7.6   3.1     0.013         5       7      45 ..       8      48 ..       4      50 .. 0.76
   2 ?    5.5   2.9     0.056        22      30      73 ..      69     111 ..      67     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.013
                           V-SNARE  7 eiksklarlsslag..eerkaalreiekkldeaeelldqMe 45
                                      e+++k+++l+ l+   +e   + +e+e+ l eae+ ld++e
  gi|336254274|ref|YP_004597381.1|  8 EAQEKIEQLQDLQEtaQEVAVQKQEAETNLTEAENALDELE 48
                                      57889999997765324555566789999999999999987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.056
                           V-SNARE  30 iekkldeaeelldqMelEvrnlpsserasykaklreykselkkl 73 
                                       +++++d++e+ +d++e+ ++ l  ++   ++ ++++ + el++l
  gi|336254274|ref|YP_004597381.1|  69 YDEAQDDLEDKVDSLEIRLETLE-KQEERVQDQFESLQEELEEL 111
                                       67888888888999999888887.77888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2977  (0.166044); expected 358.6 (0.02)
Passed bias filter:                     1358  (0.0757432); expected 358.6 (0.02)
Passed Vit filter:                       223  (0.0124379); expected 17.9 (0.001)
Passed Fwd filter:                        79  (0.00440627); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 0.83u 0.30s 00:00:01.12 Elapsed: 00:00:00.46
# Mc/sec: 855.18
//
Query:       gi|336254275|ref|YP_004597382.1|  [L=124]
Description: hypothetical protein Halxa_2887 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.082   13.1   1.2       0.14   12.4   1.2    1.3  1  DUF2508     Protein of unknown function (DUF2508)


Domain annotation for each model (and alignments):
>> DUF2508  Protein of unknown function (DUF2508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.2   7.7e-06      0.14      13      45 ..      90     122 ..      88     124 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.7e-06
                           DUF2508  13 eedeeLleeIektkeelesakslfensvDlsde 45 
                                       e +eeL++e+ ++++e+  + +++  ++D +++
  gi|336254275|ref|YP_004597382.1|  90 ESNEELVREVRQLRDEMRDQTRALKRIADAIED 122
                                       789**************************8754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1180  (0.0658152); expected 358.6 (0.02)
Passed bias filter:                      756  (0.0421663); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 966.50
//
Query:       gi|336254276|ref|YP_004597383.1|  [L=297]
Description: phosphoesterase PA-phosphatase-like protein [Halopiger xanaduensis SH-6]
Scores for 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   66.7  15.6    2.1e-18   66.7  15.6    1.8  2  PAP2_3        PAP2 superfamily
    2.5e-12   46.7   5.8    2.5e-12   46.7   5.8    2.7  3  PAP2          PAP2 superfamily
  ------ inclusion threshold ------
      0.086   12.5   0.1       0.18   11.5   0.1    1.5  1  NADH_dh_m_C1  NADH dehydrogenase [ubiquinone] 1 subunit C1, m
          1    9.6   8.4          1    9.6   0.1    3.0  3  DUF423        Protein of unknown function (DUF423)
        1.1    7.4  12.3       0.26    9.5   6.5    1.9  2  YfhO          Bacterial membrane protein YfhO
          5    7.3  11.8       0.35   11.0   1.1    3.1  3  Pox_A14       Poxvirus virion envelope protein A14


Domain annotation for each model (and alignments):
>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.4      0.57   1.7e+03      62      78 ..       9      25 ..       3      56 .. 0.66
   2 !   66.7  15.6   7.1e-22   2.1e-18      14     190 .]      87     253 ..      79     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.57
                            PAP2_3 62 flttlllatllgllvya 78
                                      +++++ l++l+g++v++
  gi|336254276|ref|YP_004597383.1|  9 LVAVVTLMVLIGIVVFV 25
                                      44444455555555543 PP

  == domain 2  score: 66.7 bits;  conditional E-value: 7.1e-22
                            PAP2_3  14 weaalnklllahpalavilalaYaslhfqvtllvlvllf.lrrrerlreflttlllatllgllvyalfPaagPrlle 89 
                                       +  +l+  + ++pa++ +++++Y + ++++++ +++  f l++++ lre+l+++ l  +lgl++y+++ a gPr + 
  gi|336254276|ref|YP_004597383.1|  87 FILWLQ--TYETPAATAYFSFIYIYGYVFLLVFPVIAYFaLSNTRPLRELLAAYTLNYALGLVCYIFVIAYGPRNM- 160
                                       455666..778999999999998877766666666666669********************************999. PP

                            PAP2_3  90 eagfvdtvaaaslagalrdgasravllrgtienglaafPSlHvawallvalalwrlrrkrllrvlallln..vlmiv 164
                                             + ++++l   l d +  + +l++ +++    fPSlH+ +a  val+++r+r+    ++la++l+  + ++v
  gi|336254276|ref|YP_004597383.1| 161 ------MPEVTAL---LYDTYPEYQHLTRQVNRNTNVFPSLHASLAGTVALLAYRTRSIY-PKWLAVALAlgISVAV 227
                                       ......2223333...35677777788888889999****************99999888.6666665550056788 PP

                            PAP2_3 165 atvatgnHYlvDviaGvalalvaial 190
                                       +t+++g H ++Dv+aG+ la+v++al
  gi|336254276|ref|YP_004597383.1| 228 STMYLGIHWATDVVAGLGLAYVSVAL 253
                                       9*********************9975 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.3      0.61   1.8e+03      95     103 ..      20      28 ..       5      59 .. 0.55
   2 ?    0.2   0.5      0.19   5.8e+02      78     100 ..     115     155 ..      96     157 .. 0.54
   3 !   46.7   5.8   8.4e-16   2.5e-12      27     133 ..     161     260 ..     131     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.61
                              PAP2  95 avlvalsRl 103
                                        ++v ++R+
  gi|336254276|ref|YP_004597383.1|  20 GIVVFVGRY 28 
                                       222222222 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.19
                              PAP2  78 krkkig..................lvllalillllavlval 100
                                       + +++                   ++ +al l+++++++a+
  gi|336254276|ref|YP_004597383.1| 115 LVFPVIayfalsntrplrellaayTLNYALGLVCYIFVIAY 155
                                       33332122223333344566677666677777777777776 PP

  == domain 3  score: 46.7 bits;  conditional E-value: 8.4e-16
                              PAP2  27 RPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkrkkiglvllalillllavlvalsRl 103
                                        P+++a   ++++  +++ t + ++ ++ fPS H++ a+++all a+  r+ ++k     +++++l+l + va+s +
  gi|336254276|ref|YP_004597383.1| 161 MPEVTALLYDTYPE-YQHLTRQVNRNTNVFPSLHASLAGTVALL-AYRTRSIYPK-----WLAVALALGISVAVSTM 230
                                       45555555555555.55555544888999*******99998764.4455555555.....89999999********* PP

                              PAP2 104 ylgvHflsDvlaGlliGialaalayrlvqk 133
                                       ylg+H+ +Dv+aGl ++++ +ala++lv +
  gi|336254276|ref|YP_004597383.1| 231 YLGIHWATDVVAGLGLAYVSVALAHALVGR 260
                                       ************************998865 PP

>> NADH_dh_m_C1  NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.9e-05      0.18      12      29 ..     212     229 ..     206     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.9e-05
                      NADH_dh_m_C1  12 pnWLkVgLtlGttvflWv 29 
                                       p WL V L+lG +v++ +
  gi|336254276|ref|YP_004597383.1| 212 PKWLAVALALGISVAVST 229
                                       99***********99765 PP

>> DUF423  Protein of unknown function (DUF423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00034         1      48      86 ..       7      47 ..       1      49 [. 0.85
   2 ?   -2.1   0.1       1.5   4.4e+03      26      39 ..     137     150 ..     109     168 .. 0.61
   3 ?    3.9   0.8      0.02        60      29      71 ..     191     232 ..     176     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00034
                            DUF423 48 srllklagllflaGivlFSgslyllaltgk..kvlgaitPi 86
                                      ++l+ +++l++l+Giv+F g   l+a+ g+  + l+ai+P+
  gi|336254276|ref|YP_004597383.1|  7 TQLVAVVTLMVLIGIVVFVGRYRLRATIGEwrERLRAIAPV 47
                                      57889999*****************9988887889999997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                            DUF423  26 qYqlyhalallava 39 
                                        Y l  al+l++  
  gi|336254276|ref|YP_004597383.1| 137 AYTLNYALGLVCYI 150
                                       34444455554444 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.02
                            DUF423  29 lyhalallavallaskaaasrllklagllflaGivlFSgslyl 71 
                                        +ha     vall + +++s ++k+ ++++++Gi +   ++yl
  gi|336254276|ref|YP_004597383.1| 191 SLHASLAGTVALL-AYRTRSIYPKWLAVALALGISVAVSTMYL 232
                                       5788877788888.678999*************9876666665 PP

>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.9     0.022        66     361     458 ..       9     102 ..       1     107 [. 0.60
   2 ?    9.5   6.5   8.7e-05      0.26     338     441 ..     105     229 ..      99     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.022
                              YfhO 361 lkqlkklkllaailllvlllliilllknkksynfltssqlllgllllllalllllllll..kkkkkklvllllllvl 435
                                       l        ++++++l+++++++ +++   +    +++   ++ +  +lal+l+++  +    +++++++   l ++
  gi|336254276|ref|YP_004597383.1|   9 LVA------VVTLMVLIGIVVFVGRYRLRATIGEWRERLRAIAPVTAVLALVLVGSSDIrlIGPELSWIIGWNLTGT 79 
                                       332......33333333333333333333333333444444666666666666665444669999999999999999 PP

                              YfhO 436 vlelggnaylslnkisyssrsey 458
                                       +++l g ++l l++ + ++++ y
  gi|336254276|ref|YP_004597383.1|  80 IFDLEGQFILWLQTYETPAATAY 102
                                       99999999999998887766665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 8.7e-05
                              YfhO 338 fpyRfsfilsflllllaaealkelkqlkklkllaailllvlllliilllknkksynfltssqlll............ 402
                                       f y + +++ +++ ++a+ al++++ l++l  + ++  +++l+++i++++++  + + ++++ll+            
  gi|336254276|ref|YP_004597383.1| 105 FIYIYGYVFLLVFPVIAYFALSNTRPLRELLAAYTLNYALGLVCYIFVIAYGPRNMMPEVTALLYdtypeyqhltrq 181
                                       77889999999****************99999999999999999**********66666666666************ PP

                              YfhO 403 .........gllllllalllllllllkkkkkklvllllllvlvlelgg 441
                                                +l   l++++ ll +  ++++ k+++++l+l++ + +++
  gi|336254276|ref|YP_004597383.1| 182 vnrntnvfpSLHASLAGTVALLAYRTRSIYPKWLAVALALGISVAVST 229
                                       *********99999999999999999**************98776665 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.7      0.09   2.7e+02      48      70 ..       7      29 ..       2      44 .. 0.76
   2 ?   11.0   1.1   0.00012      0.35       9      64 ..     101     154 ..      97     196 .. 0.72
   3 ?   -2.4   0.0       1.9   5.6e+03      44      62 ..     205     223 ..     185     240 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.09
                           Pox_A14 48 sivsFilgivillglllfsmygr 70
                                      + +  ++++++l+g+++f + +r
  gi|336254276|ref|YP_004597383.1|  7 TQLVAVVTLMVLIGIVVFVGRYR 29
                                      55666888999999999987665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00012
                           Pox_A14   9 nyystvliaGiiLLilacifafvdfskststtdkawralsivsFilgivillglll 64 
                                        y+s + i G + L +  ++a++ +s + +  +  + a+  + + lg+v  + ++ 
  gi|336254276|ref|YP_004597383.1| 101 AYFSFIYIYGYVFLLVFPVIAYFALSNTRPLRE--LLAAYTLNYALGLVCYIFVIA 154
                                       79************************9887433..444444555555554444443 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.9
                           Pox_A14  44 wralsivsFilgivillgl 62 
                                       +r+ si    l++++ lg+
  gi|336254276|ref|YP_004597383.1| 205 YRTRSIYPKWLAVALALGI 223
                                       4444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); 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:                         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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2087.45
//
Query:       gi|336254277|ref|YP_004597384.1|  [L=666]
Description: ABC transporter periplasmic protein [Halopiger xanaduensis SH-6]
Scores for 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-46  157.3   0.0      4e-41  141.2   0.0    2.1  2  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.1e-06     0.019     296     364 ..      55     122 ..      35     133 .. 0.76
   2 !  141.2   0.0   2.2e-45     4e-41       2     290 ..     333     660 ..     332     664 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-06
                                       EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHH CS
                         SBP_bac_5 296 klkltlllasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdn 364
                                        l++t+l a g+  + ++a  i+++l+ +Gi+++++  ++++   +   ++dfd+++++  ++  dp++
  gi|336254277|ref|YP_004597384.1|  55 SLTITTLPADGDRESIQLAREIAAALETVGIDASIEMRSNEEFLRAILINQDFDVYVGRHPGG-TDPSY 122
                                       4455555555566666**********************99777778899********988776.44444 PP

  == domain 2  score: 141.2 bits;  conditional E-value: 2.2e-45
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC.....TCTEEEEEEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyasllee.....dqdikkveav 73 
                                       ++p+LA++ we++d g t t+ LR++ +F+D++pltAeDv f+++ l+d + +    +  ++      + +++v  +
  gi|336254277|ref|YP_004597384.1| 333 LQPWLAAD-WEWDDAGETMTVELRENCRFHDDEPLTAEDVRFTYRFLADTGLGDLEVDAPAPlyrgrVDAVESVDRL 408
                                       79******.7***************************************9999988888777999999********* PP

                                       ETTEEEEEESSETT......TTTTHCHHHHHHHGC.......CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEE CS
                         SBP_bac_5  74 ddytvrftlkkpna......lfltllaavpasiak.......kaaekeddkdkdtnekpvgtGPYklkefkpgqkiv 137
                                       dd+ +++t  + +a      + ++l  +++ + a        + a  ++++  ++n +pvg+GPY+++  +  + ++
  gi|336254277|ref|YP_004597384.1| 409 DDHRLEITVDASRAvgeralTVPILPKHIWEPRAAaadvpgyRVALGTSEALVTNNVPPVGSGPYQFATRSEREHVT 485
                                       ************997777754444444444444448889999666777788999*********************** PP

                                       EEE-TTST....TTSCS..SSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHH....HHHTTEEE....... CS
                         SBP_bac_5 138 lernpdYw....gggkp..kldriefkvipdsdaraaalqsGeiddvaepppsdieql....keakglkv....... 197
                                       ler++d +    g  +p   +dr++f + p s+++++ ++++e+d+ +   +s++            +         
  gi|336254277|ref|YP_004597384.1| 486 LERFDDHFtareGVTLPgvTPDRLRFLIDPRSASAIERVETNEADITSTALESYVVDDllgdA----EAGelpedve 558
                                       ******66687755666889************************9986665444444323321....1113445677 PP

                                       EEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH..... CS
                         SBP_bac_5 198 lyespgggvtylafNtkkppfddkrvRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka..... 269
                                       + es +  +++l+fN +k+pf+++r+R+ ++  +D++++v+av+ g+a+p ++++ + +   +   + + ++     
  gi|336254277|ref|YP_004597384.1| 559 VLESESWLFYHLGFNARKAPFSNPRFRRCVAQVLDKQWFVEAVFDGHARPIAAPVTEEWTPDSLRWDGEDPEtpflg 635
                                       7*****************************************************888887777777766555899** PP

                                       ....SHHHHHHHHHHHTT-BCSSTS CS
                         SBP_bac_5 270 ....ydpekAkklLkeaGykdgdgg 290
                                            d+++A++ +++aG+  +++g
  gi|336254277|ref|YP_004597384.1| 636 tdgeIDVAAARNAFESAGFSYDGEG 660
                                       **9999*************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (666 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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 0.26s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4845.18
//
Query:       gi|336254278|ref|YP_004597385.1|  [L=92]
Description: ribonuclease P protein component 4 [Halopiger xanaduensis SH-6]
Scores for 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-13   48.8   0.0    7.7e-13   48.6   0.0    1.1  1  Rpr2       RNAse P Rpr2/Rpp21/SNM1 subunit domain
  ------ inclusion threshold ------
      0.038   14.4   0.6      0.056   13.8   0.6    1.2  1  DUF1771    Domain of unknown function (DUF1771)
      0.057   13.6   2.4        0.9    9.8   0.4    2.5  2  zf-RING_7  C4-type zinc ribbon domain


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 !   48.6   0.0   1.3e-16   7.7e-13       1      88 [.       7      81 ..       7      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.3e-16
                                      HHHHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E....... CS
                              Rpr2  1 rlnfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkka 79
                                      rl+ L+++a+ + a    + +ry+++ +r+v+++++l+lp++++r +C +C+ +l pg++++vr++  +          
  gi|336254278|ref|YP_004597385.1|  7 RLERLHDLASAAAADGDDERARYYVQLARRVAERNRLSLPKQFRRFTCDNCDRYLRPGSNARVRLQDGH---------- 75
                                      78999**9999999***************************************************7522.......... PP

                                      ..EEEEETT CS
                              Rpr2 80 dvlvvtCla 88
                                        +v+tC  
  gi|336254278|ref|YP_004597385.1| 76 --VVITC-D 81
                                      ..46777.4 PP

>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.6   9.4e-06     0.056      16      47 ..       9      40 ..       3      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.4e-06
                           DUF1771 16 nelfekAaeAyrrGdgaaAkelseqGkehgek 47
                                       +l++ A++A + Gd ++A+++++ +++  e+
  gi|336254278|ref|YP_004597385.1|  9 ERLHDLASAAAADGDDERARYYVQLARRVAER 40
                                      578899*********************98875 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 ?    9.8   0.4   0.00015       0.9      24      33 .]      52      61 ..      32      61 .. 0.87
   2 ?    4.2   0.1    0.0084        50      12      27 ..      64      81 ..      60      84 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00015
                                      EE-TTT--EE CS
                         zf-RING_7 24 vtCpeCGRIL 33
                                      +tC++C R L
  gi|336254278|ref|YP_004597385.1| 52 FTCDNCDRYL 61
                                      79******98 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0084
                                      CHHHHHCCS..TB-EE-T CS
                         zf-RING_7 12 qvlselrag..devvtCp 27
                                      ++ +++r +   +v+tC+
  gi|336254278|ref|YP_004597385.1| 64 GSNARVRLQdgHVVITCD 81
                                      55566655543889***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 655.21
//
Query:       gi|336254279|ref|YP_004597386.1|  [L=82]
Description: hypothetical protein Halxa_2891 [Halopiger xanaduensis SH-6]
Scores for complete 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   54.2   0.0    1.4e-14   54.0   0.0    1.0  1  CRS1_YhbY  CRS1 / YhbY (CRM) domain


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 !   54.0   0.0   7.6e-19   1.4e-14       6      84 .]       3      82 .]       1      82 [] 0.93

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 7.6e-19
                         CRS1_YhbY  6 lrrLrhlairlkpkvkiGkaGvtkevvdeiheklkteelvkvkc..egppalnmkrmaeiLeektgglviqrsgtsivL 82
                                       ++L+++a++l+ +v +Gk+G+ ++vvde++++l +  lvkvk+       ++ ++ a+ L+e++++ +++++g+++vL
  gi|336254279|ref|YP_004597386.1|  3 QQELKKRAHDLDVTVWVGKSGI-ESVVDELDDQLSNADLVKVKFlrAARAGSSTEEKAADLAERVNADLVETRGHTAVL 80
                                      579*******************.99*******************98444566799************************ PP

                         CRS1_YhbY 83 YR 84
                                      YR
  gi|336254279|ref|YP_004597386.1| 81 YR 82
                                      *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 647.49
//
Query:       gi|336254280|ref|YP_004597387.1|  [L=317]
Description: mechanosensitive ion channel MscS [Halopiger xanaduensis SH-6]
Scores for complete 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-47  161.7   0.1    1.7e-47  161.7   0.1    1.5  2  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.068   13.3   0.5       0.35   11.1   0.1    2.3  3  HAS-barrel  HAS barrel domain


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 ?   -2.4   0.2      0.31   2.8e+03      23      42 ..      36      56 ..      30      58 .. 0.79
   2 !  161.7   0.1   1.9e-51   1.7e-47       4     206 .]      90     292 ..      88     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.31
                                      -.SCCHHHHHHHHHHHHHHHH CS
                        MS_channel 23 n.vsallavlGalglalglal 42
                                      + ++ l +v+Gal ++l++++
  gi|336254280|ref|YP_004597387.1| 36 EdPALLNSVAGALRFVLAFVV 56
                                      4378888999********985 PP

  == domain 2  score: 161.7 bits;  conditional E-value: 1.9e-51
                                       HHHHHHHHHHHHHHHTTT--..SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS..SEEEEE CS
                        MS_channel   4 lkiliivvgilivlsllgvn..vsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig..dieGtV 76 
                                       ++++i++v+i +++   g+   + ++  +++a++la+gla++++isn+vaGi+++++kpf+iGD++e+   d +G V
  gi|336254280|ref|YP_004597387.1|  90 TRFGILFVAIAVAFGAGGFGnfLVSMAGIAAAGALAIGLAMQNVISNFVAGIFIYTDKPFRIGDWIEWDngDYAGVV 166
                                       78999******9999866655599999999999***********************************9999***** PP

                                       EEE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TT CS
                        MS_channel  77 ediglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkd 153
                                       edi+lr+t++rtfd++++t+Pns l+++ i+N  +  ++ r+k+++g+ y+ d   +e+++ ++ ++++++  + ++
  gi|336254280|ref|YP_004597387.1| 167 EDISLRVTRVRTFDNELLTVPNSVLTDDVIKNPVE-GDKLRLKFVFGIGYDDD---IEQATTIIVDEAERHDGIADE 239
                                       ***********************************.9****************...********************* PP

                                       S-EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 154 kellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                       + + v+l+e+ ds + ++ r+++++ + ++  +++ e +  +k+ ++eegi+i
  gi|336254280|ref|YP_004597387.1| 240 PGPSVRLTELNDSDVGLQSRFWIENPSRSDFVRIKGEYITAVKRRFDEEGIDI 292
                                       *************************999***********************86 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.48   4.3e+03      18      34 ..      53      69 ..      43      76 .. 0.71
   2 ?   11.1   0.1   3.9e-05      0.35      14      80 ..     140     210 ..     126     217 .. 0.81
   3 ?   -1.5   0.0      0.33     3e+03      23      48 ..     265     283 ..     241     308 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.48
                        HAS-barrel 18 egskdvkvGeyVeielp 34
                                        ++ + +G +V+ +l 
  gi|336254280|ref|YP_004597387.1| 53 AFVVVWALGRFVVLPLV 69
                                      44557889999999876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.9e-05
                        HAS-barrel  14 ifrvegskdvkvGeyVeielpdgeivlGmvtdirrgn.......selsndlalvlsleeleeangddevalate 80 
                                        ++++ +k+ ++G+++e +   ++   G+v+di+ +         el+++++ vl+ + +++  ++d++ l+++
  gi|336254280|ref|YP_004597387.1| 140 GIFIYTDKPFRIGDWIEWD---NGDYAGVVEDISLRVtrvrtfdNELLTVPNSVLTDDVIKNPVEGDKLRLKFV 210
                                       56777789***********...5689999999999888888888999999999999888888777777766665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.33
                        HAS-barrel  23 vkvGeyVeielpdgeivlGmvtdirr 48 
                                       ++  ++V+i+++        +t ++r
  gi|336254280|ref|YP_004597387.1| 265 PSRSDFVRIKGE-------YITAVKR 283
                                       555567777755.......3444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2479.18
//
Query:       gi|336254281|ref|YP_004597388.1|  [L=270]
Description: outer membrane lipoprotein-sorting protein-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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   31.2   0.0    5.6e-07   29.1   0.0    2.0  1  DUF2092    Predicted periplasmic protein (DUF2092)
    2.9e-06   27.2   1.1    3.6e-05   23.6   1.1    2.5  1  LolA_like  Outer membrane lipoprotein-sorting protein
     0.0001   21.9   0.1    0.00084   18.9   0.0    2.1  2  MucB_RseB  MucB/RseB N-terminal domain


Domain annotation for each model (and alignments):
>> DUF2092  Predicted periplasmic protein (DUF2092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   9.3e-11   5.6e-07     118     207 ..     146     266 ..     121     268 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 9.3e-11
                           DUF2092 118 edlteevksakyvgtskvngqecehl...............................afrnkdvdwqlWIsqg.dkp 162
                                       ++ ++e+ + +y gt+++ + e+++l                               + +   ++w lWI ++ d+p
  gi|336254281|ref|YP_004597388.1| 146 AAEQRELYDLEYAGTEQIADREAHVLeiepkngtverdvsvlvgntefvvpletapvETDLGVIEWSLWIDAEyDYP 222
                                       3334889999********************************************999999999*******8764667 PP

                           DUF2092 163 LprkivityktdpgapqytaefsdWnldpeipedtFrftpPkgAr 207
                                       L  ++v     + +++ +t+e+++ ++++ ++++ F+f+pP++A+
  gi|336254281|ref|YP_004597388.1| 223 LKERLVYEG-ANGERHELTMEYETVTFNTGFEDERFAFEPPANAT 266
                                       766655444.4556899**************************97 PP

>> LolA_like  Outer membrane lipoprotein-sorting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   1.1   6.1e-09   3.6e-05      11     176 ..      98     257 ..      88     260 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.1e-09
                                       ESTTTTT-EEEEESSSTTEEEEEETTTTCEEEE-G.GGTTSECCTTC.EHHHHC--SCCCEEEEEEEEEEETTEEEE CS
                         LolA_like  11 ePadvkGtafLtlkekdddlWlYlPalkrvrriss.sdksqsfmGsdfsyeDlssrevedythellgeeevggkdcy 86 
                                       + ++v G ++ +     +  W Y+P+ ++     + +  +++ + sd   +D++ ++ e y+ e+ g+e++  ++++
  gi|336254281|ref|YP_004597388.1|  98 SEPSVIGDRYVSN---ASATWNYDPDAETAYYFEPaEPFDDAAVRSD--RADMAAEQRELYDLEYAGTEQIADREAH 169
                                       4446888888888...99***********999986244566667888..99************************** PP

                                       EEEEEESS.TTSSECEEEEEEETTT--EEEEEEEETTS-EEEEEEEEEEEEET.TEEEEEEEEEEE.TTT--EEEEE CS
                         LolA_like  87 vleltpkdaadvsYskivlwvdketylplkvefydksgkllKtltvsdiekid.grwtptkmtmed.lkkghkTvle 161
                                       vle++pk+   v+ +  vl+ ++e  +pl++  ++ +     +++ s + + + ++++ ++++ e    + h+ ++e
  gi|336254281|ref|YP_004597388.1| 170 VLEIEPKN-GTVERDVSVLVGNTEFVVPLETAPVETDL---GVIEWSLWIDAEyDYPLKERLVYEGaNGERHELTME 242
                                       ********.56666666665566666666666666552...233333333333257777888888777778888888 PP

                                       EEEEEE--.--GGGC CS
                         LolA_like 162 isevefdkglpdklF 176
                                       ++ v+f++g++d+ F
  gi|336254281|ref|YP_004597388.1| 243 YETVTFNTGFEDERF 257
                                       888888888888887 PP

>> MucB_RseB  MucB/RseB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.4e-07   0.00084      94     125 ..     146     177 ..      78     179 .. 0.85
   2 ?    0.6   0.0     0.058   3.4e+02     132     149 ..     212     229 ..     210     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.4e-07
                         MucB_RseB  94 lealeehYefrllGreRvAgreaqvvrilPkD 125
                                        ++ +e Y+++ +G e++A+rea+v++i+Pk+
  gi|336254281|ref|YP_004597388.1| 146 AAEQRELYDLEYAGTEQIADREAHVLEIEPKN 177
                                       3477899***********************97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.058
                         MucB_RseB 132 rlwiDeetgLlLksdlld 149
                                        lwiD e   +Lk  l+ 
  gi|336254281|ref|YP_004597388.1| 212 SLWIDAEYDYPLKERLVY 229
                                       69***********99884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); 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:                         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: 00:00:00.40
# Mc/sec: 2042.16
//
Query:       gi|336254282|ref|YP_004597389.1|  [L=312]
Description: hypothetical protein Halxa_2894 [Halopiger xanaduensis SH-6]
Scores for complete 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-41  141.7  35.2    6.1e-23   81.5  11.0    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
       0.12   11.7   5.3       0.22   10.9   5.3    1.6  1  TPT       Triose-phosphate Transporter family


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 !   66.5  16.2     3e-22   2.7e-18       8     137 .]      25     152 ..      19     152 .. 0.95
   2 !   81.5  11.0   6.9e-27   6.1e-23       2     137 .]     168     309 ..     167     309 .. 0.90

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 3e-22
                              EamA   8 llaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffy 84 
                                       l+aa++w+  +v+s +++++++p+tl+f+r+ +++++ll++  ++  ++ ++ ++d+l ++ lg++ t+ +   +f 
  gi|336254282|ref|YP_004597389.1|  25 LAAAVLWGGLYVVSMWGFESIPPVTLAFLRIAVGAAALLLVVRVRYPRR-RFARRDLLGFVALGAVITASM-TTQFL 99 
                                       89************************************99999999999.9*************9888777.8**** PP

                              EamA  85 alkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllill 137
                                       +   t+as+ slit l+P+ft++l+v  lge+lt + ++giv +l+G++l+l+
  gi|336254282|ref|YP_004597389.1| 100 GTAMTTASQGSLITVLTPIFTILLGVTMLGERLTGRLVAGIVGALAGTVLVLT 152
                                       **************************************************986 PP

  == domain 2  score: 81.5 bits;  conditional E-value: 6.9e-27
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl......aklslkdwllllllgl 72 
                                       +gi ++l+a+ +wa+y+v  k l+ ++s l+++++++l+a  +l ++ +l+           ++++  ++++l+lg+
  gi|336254282|ref|YP_004597389.1| 168 IGIGMLLIASATWALYTVRGKPLIDRYSALETATYSTLAAVPMLAALVPLEVALTdaslraIEPTPALVAAVLYLGV 244
                                       78999********************************9888888888544444445444666777777999****** PP

                              EamA  73 lgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllill 137
                                       lgt++a++l+++++++++as++s +++ +Pv+  +l++ +lge+l+ + +lg +++ +Gv+++++
  gi|336254282|ref|YP_004597389.1| 245 LGTAAAWYLWYKGMEYVDASVISAFFFAQPVVGGLLGATVLGEPLGPRFVLGGLVMAAGVYVVST 309
                                       **************************************************************986 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.3   2.4e-05      0.22      31     200 ..      47     223 ..      36     308 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.4e-05
                               TPT  31 PltvsavqllvgsvlilvlwalglkkrpkisseflkailplalvktlghvlavvslskvaVSfthtvKasePiFtvi 107
                                       P+t++ ++++vg   +l++ ++++ +  ++  + l   + l+ v t++  +  +  ++++ S    +  + PiFt++
  gi|336254282|ref|YP_004597389.1|  47 PVTLAFLRIAVGAAALLLVVRVRYPR-RRFARRDLLGFVALGAVITASMTTQFLGTAMTTASQGSLITVLTPIFTIL 122
                                       89999999999999988888888777.56666666666666666677777778889999****************** PP

                               TPT 108 lsrlllgeklsllvylsLlpivgGval........asvtElsFnligfisAlisnltfslrnifsKkllkklkdlda 176
                                       l   +lge+l+  ++  ++  ++G +l        +++   s   ig+   li+  t +l  +  K l+  +  l++
  gi|336254282|ref|YP_004597389.1| 123 LGVTMLGERLTGRLVAGIVGALAGTVLvltgqydlSTLAGGSTPTIGIGMLLIASATWALYTVRGKPLIDRYSALET 199
                                       ***********999999998888876611111111333333444445555555555555555555555555322333 PP

                               TPT 177 lnlfaiitilslllllPvallveg 200
                                        ++ ++ ++  l+ l+P+ +++++
  gi|336254282|ref|YP_004597389.1| 200 ATYSTLAAVPMLAALVPLEVALTD 223
                                       333333333344455566555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2393.12
//
Query:       gi|336254283|ref|YP_004597390.1|  [L=234]
Description: hypothetical protein Halxa_2895 [Halopiger xanaduensis SH-6]
Scores for complete 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-69  233.2   2.2    1.9e-69  232.9   2.2    1.0  1  DUF2270        Predicted integral membrane protein (DUF2270)
  ------ inclusion threshold ------
       0.03   14.1   0.4      0.058   13.1   0.1    1.7  2  PRT_C          Plant phosphoribosyltransferase C-terminal
      0.033   13.3   1.9      0.048   12.7   0.1    1.9  2  Acyl_transf_3  Acyltransferase family


Domain annotation for each model (and alignments):
>> DUF2270  Predicted integral membrane protein (DUF2270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.9   2.2   3.2e-73   1.9e-69       1     184 []      34     212 ..      34     212 .. 0.98

  Alignments for each domain:
  == domain 1  score: 232.9 bits;  conditional E-value: 3.2e-73
                           DUF2270   1 ahlYRgeveratawreRlDrttnWavvvtaallsvalsspeashavlllgmllvlvfLliearryrfydvwrsrvrl 77 
                                       ahlYRgevera +wr+RlD+ttnWav+++aa++++a+s  e shav+l g+++ ++fL+iearr+++yd+wrsrvr+
  gi|336254283|ref|YP_004597390.1|  34 AHLYRGEVERAVSWRDRLDTTTNWAVTIMAAIVAYAFSG-EVSHAVILAGVVMGTAFLFIEARRFQTYDIWRSRVRV 109
                                       6************************************98.89*********************************** PP

                           DUF2270  78 leenffaealdpeegaeeeeWreeLaedlrkPtlkislleAlgrRLrrnYlwlllvlllawllkitlfkkeeeslee 154
                                       l+en+fa+aldp++g+e+++Wr+eL+ed+r+Pt +is++ A+++RLrr+Yl+l++++l++w++++++f++++     
  gi|336254283|ref|YP_004597390.1| 110 LQENLFANALDPSAGVERSAWRAELSEDYRNPTPHISYRGAFSHRLRRVYLPLISAMLASWVFHLWAFNPDT----P 182
                                       ***********************************************************************9....6 PP

                           DUF2270 155 llerAavgplpGelvllvvalfylallvla 184
                                       + e+Aa++ ++G+++++vv ++ylallvla
  gi|336254283|ref|YP_004597390.1| 183 FPESAALPGVDGTVIAAVVGCYYLALLVLA 212
                                       99************************9985 PP

>> PRT_C  Plant phosphoribosyltransferase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.7e-06     0.058      75     121 ..      29      77 ..      16      97 .. 0.79
   2 ?   -2.4   0.0       0.6   3.6e+03     117     128 ..     195     206 ..     162     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.7e-06
                             PRT_C  75 lGdvAtqgEr..lqallswrDpratalflllclvvavvlyvvpfkvlvl 121
                                       lG vA++  r  ++ ++swrD ++t+  + +++++a+v+y+ + +v  +
  gi|336254283|ref|YP_004597390.1|  29 LGSVAAHLYRgeVERAVSWRDRLDTTTNWAVTIMAAIVAYAFSGEVSHA 77 
                                       78888875443377889***********************988765544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.6
                             PRT_C 117 kvlvlllglyll 128
                                        v+++++g+y+l
  gi|336254283|ref|YP_004597390.1| 195 TVIAAVVGCYYL 206
                                       456666677766 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2     0.065   3.9e+02     233     278 ..      62      98 ..      46     116 .. 0.46
   2 ?   12.7   0.1   8.1e-06     0.048      65     107 ..     141     183 ..     128     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.065
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 233 lalillalfgqtdggglvasvliqsaslllvslgimllllllfalp 278
                                       +a+i++++f+               + l+ v++g+++l++ +++++
  gi|336254283|ref|YP_004597390.1|  62 MAAIVAYAFSGE---------VSHAVILAGVVMGTAFLFIEARRFQ 98 
                                       222222222222.........3344445555555555554444444 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.1e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3  65 lyrrrglsklikrRilrlliplliwllliillialvaghiqan 107
                                       ++++ +++ ++ +R++r+++pl+  +l+ ++++   ++  ++ 
  gi|336254283|ref|YP_004597390.1| 141 PTPHISYRGAFSHRLRRVYLPLISAMLASWVFHLWAFNPDTPF 183
                                       5678899999*********************998777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); 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:                         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 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1622.68
//
Query:       gi|336254284|ref|YP_004597391.1|  [L=382]
Description: ferrichrome-binding protein [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.1   0.0    2.6e-15   56.7   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
       0.93    9.4   4.5        1.5    8.8   4.5    1.3  1  TAT_signal    TAT (twin-arginine translocation) pathway signa


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 !   56.7   0.0   2.9e-19   2.6e-15       5     235 ..      66     327 ..      63     330 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 2.9e-19
                                       SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT.........TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GG CS
                      Peripla_BP_2   5 spsvteillalGatdkvvgvdtttsdpldadklee.......aivevgadgeidvEklaalkPDlvilskglgltde 74 
                                        +++ ++ +alG+++ + g + t+++pl+ ++ +        +++ + +++ id E   +l++D+ ++++++ +++ 
  gi|336254284|ref|YP_004597391.1|  66 FSTYGDMGIALGQLEGLQGLIYTDNWPLEFYETLPgvdvsfdDVPQLAGSNGIDKEIFYELDCDVHLMDPNF-VARL 141
                                       5677788899*******************9999999*999*99*****************************.8888 PP

                                       GHHHHHHHS-EEE----TTS................HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT CS
                      Peripla_BP_2  75 deellksgiptvivessntg................eslkeqiralgellgledeaeklvaeidsklaaaksaidse 135
                                       d++ ++ + + ++ + ++ +                ++l+e ++ +++l+++ +++++l a +d+    +++++  e
  gi|336254284|ref|YP_004597391.1| 142 DDNWDDDDFEEIETNVGPIVgnnirrrdenwhdyryYDLYEAFEIVATLFDERERYDELEAIHDEFQSTLEADLLPE 218
                                       88888888888888888777888889999***********************************9999999998888 PP

                                       ..-EEEEEEEETTE......EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH....H CS
                      Peripla_BP_2 136 .kpkpvlvfggade....ggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr....a 203
                                         ++++ +++ + +    ++yv++ +n+++++   +lg+++++  +   +y+e + Eq+l++dpd++++s       
  gi|336254284|ref|YP_004597391.1| 219 dERPEIGLVSINSDfetgSFYVYPLENGNGRKQYQDLGVRDAIGPHLDASYGEWDYEQLLEADPDALVFSYGfshaT 295
                                       544444444444446999****************************9***********************9999966 PP

                                       HHT-S--HHHHT-SHHHHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 204 eadnktgleflkenpllaelpAvkngrVyald 235
                                       +++  ++ + +  +p+ +el Av+n r y+ +
  gi|336254284|ref|YP_004597391.1| 296 ADQFEERMDLMRDDPTGSELAAVQNDRLYRGG 327
                                       66667777888888***************876 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.5   0.00017       1.5       2      24 ..       9      31 ..       8      33 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00017
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                       +RR +L  +A++a   +l+gca
  gi|336254284|ref|YP_004597391.1|  9 PTRRKLLAIGAGTALTSGLAGCA 31
                                      59********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2817.11
//
Query:       gi|336254285|ref|YP_004597392.1|  [L=475]
Description: sodium:neurotransmitter symporter [Halopiger xanaduensis SH-6]
Scores for complete 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-50  172.5  21.7    2.1e-25   89.4   7.9    2.1  2  SNF       Sodium:neurotransmitter symporter family


Domain annotation for each model (and alignments):
>> SNF  Sodium:neurotransmitter symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   5.6   1.2e-29   2.2e-25       1     115 [.       3     119 ..       3     128 .. 0.95
   2 !   89.4   7.9   1.2e-29   2.1e-25     182     482 ..     144     433 ..     124     441 .. 0.85

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1.2e-29
                               SNF   1 RetwskkldfilsvvGfavgLgnvWRFPYlcyknGGGafliPYlilllvaGiPlfflelalGqytreGaitvwrki. 76 
                                       Re+w+++  fil++vG+avgLgn+WRFP+++ +nGG afl+ Yl+++l +G+P +   + +G+++++  +++++ + 
  gi|336254285|ref|YP_004597392.1|   3 RESWTSRTGFILAAVGSAVGLGNLWRFPWMTAENGGSAFLLLYLLIVLGVGVPGLLAAFVIGRRSNRNPVGAFKSLa 79 
                                       89************************************************************************993 PP

                               SNF  77 .cPllkgiGyasivvalyvglyYnvilawalfYlfssftt 115
                                        + ++ ++G   ++ ++++  +Y v+ +w l Y+++s t 
  gi|336254285|ref|YP_004597392.1|  80 gSRVWTVLGALCVLTSVILMSFYSVVGGWILRYFLESATG 119
                                       345799******************************9875 PP

  == domain 2  score: 89.4 bits;  conditional E-value: 1.2e-29
                               SNF 182 lcllvawvvvylailkGvkssgkvvyftatfPyvvllvllvrgvlLpGavkgikfyltpdlekllep..kvWidaat 256
                                       ++l ++ ++v  +i +G++ ++kv++   +   v+l+ l v +   pGa++g +fyl+ d + l e    +   aa 
  gi|336254285|ref|YP_004597392.1| 144 AVLAATSLIVAAGIRRGIEATTKVMMPGIV---VLLIGLAVWAARQPGAAQGYEFYLRFDGTYLAENflAILGSAAG 217
                                       456777889999****************99...99999***************************984457789*** PP

                               SNF 257 qiffslgigfGvlialasYnkfennvyrdallvslinsltsvlaglvvFsvlGfmaeeqgekisevaeeGpgLaFia 333
                                       q +f+l+ig G++i++asY + +  +  da  +++ n  + +laglvvF +l   a+          e Gpg +F+ 
  gi|336254285|ref|YP_004597392.1| 218 QALFTLSIGSGTMITYASYIDDDRSLPLDASAIAVFNLGIGILAGLVVFPLLFSFASG-------PTEGGPGALFVG 287
                                       **************************************************99665543.......4689******** PP

                               SNF 334 ypealtklplsplwsvlFFlmlillgldsqfgtvegiitavvDefkvllrrrelltlivavlaflvg.lllvtegGi 409
                                        + a + lp + l++ +FFl+++l++l+s ++++e  ++ +vDef     +r + t  +++l+ + g +  +     
  gi|336254285|ref|YP_004597392.1| 288 LAGAFASLPGGRLLGGVFFLVVLLAALTSLISMLEIPVSFLVDEFDL---ERSTATGGLFALVAVTGgVNAF---SP 358
                                       ***********************************************...7888777776655555403333...34 PP

                               SNF 410 yvltlldkyaaslsllvvvlleaiavawvyglkkflddikem..lgfrpllflklcwkfvspllllvlliasivk 482
                                        v+tl+ +   +l l++     ++  awv g     + +k    ++   ++ +++++ +v p++ll+++ a +  
  gi|336254285|ref|YP_004597392.1| 359 AVFTLFADQLVNLLLVLGLTGFMVYTAWVLGPAAIDEYLKGAgpISRPLVVPWRYAIGTVFPAFLLFTFYADVAA 433
                                       578888777777767666667778889999988887777765225555567799999999999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3368.07
//
Query:       gi|336254286|ref|YP_004597393.1|  [L=298]
Description: transcriptional regulator-like protein [Halopiger xanaduensis SH-6]
Scores for 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   19.9   0.0     0.0046   16.7   0.0    2.3  2  HTH_IclR        IclR helix-turn-helix domain
    0.00064   19.6   0.0     0.0015   18.4   0.0    1.6  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.022   14.6   0.0       0.04   13.8   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.053   13.8   0.0      0.081   13.2   0.0    1.2  1  Pro-kuma_activ  Pro-kumamolisin, activation domain
       0.08   12.9   0.0       0.15   12.1   0.0    1.3  1  HTH_45          Winged helix-turn-helix
      0.084   12.7   0.0       0.15   11.9   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
      0.099   12.7   0.1       0.23   11.5   0.1    1.6  1  HTH_20          Helix-turn-helix domain
       0.12   12.5   0.2       0.52   10.4   0.1    2.0  2  HemN_C          HemN C-terminal domain


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.1e-06    0.0046       8      50 ..      57      97 ..      51      99 .. 0.88
   2 ?    0.5   0.0      0.25   5.5e+02      31      38 ..     121     128 ..     106     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.1e-06
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      iL+al++ p +   +e+ +r+ ++++t hRl++ L e+G+ve+
  gi|336254286|ref|YP_004597393.1| 57 ILEALRAKPMD--RREIEARLEVSRATSHRLTKWLDEQGFVEK 97
                                      67777766665..89**************************98 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.25
                                       -HHHHHHH CS
                          HTH_IclR  31 pkStvhRl 38 
                                       + StvhR+
  gi|336254286|ref|YP_004597393.1| 121 NVSTVHRM 128
                                       67*****8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   6.8e-07    0.0015       9      56 ..      56     100 ..      52     102 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.8e-07
                                       HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                        +L aL++ p   +  +e+++rl +s+++ +r+ k L ++G+ve++++
  gi|336254286|ref|YP_004597393.1|  56 PILEALRAKP---MDRREIEARLEVSRATSHRLTKWLDEQGFVEKVES 100
                                       6899999999...899****************************9865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.8e-05      0.04      19      58 ..      62     101 ..      58     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                                       HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       + +p++ +ei  +l+v+r++  +  + L + G+Ve++++r
  gi|336254286|ref|YP_004597393.1|  62 RAKPMDRREIEARLEVSRATSHRLTKWLDEQGFVEKVESR 101
                                       678999*******************************987 PP

>> Pro-kuma_activ  Pro-kumamolisin, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.6e-05     0.081      47     100 ..      65     128 ..      60     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                    Pro-kuma_activ  47 hltaeevaelfapseeaidaVrnwLessgiaasr..........hsdtkgwiafsatvaqverl 100
                                        +++ e+++++  s+++++++++wL ++g+  +           ++ t +++ f+a+v++v+r+
  gi|336254286|ref|YP_004597393.1|  65 PMDRREIEARLEVSRATSHRLTKWLDEQGFVEKVesrfrltgrgEAVTDEVLRFEANVSTVHRM 128
                                       578999***********************98777799***********************9975 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.5e-05      0.15      11      73 ..      57     119 ..      55     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.5e-05
                            HTH_45  11 ILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkele 73 
                                       ILea++ +     +i  + + s  + ++  + L e+g+++k ++ ++lT +G+ + +++ ++e
  gi|336254286|ref|YP_004597393.1|  57 ILEALRAKPMDRREIEARLEVSRATSHRLTKWLDEQGFVEKVESRFRLTGRGEAVTDEVLRFE 119
                                       77777777777778877788888888888899**********************999987775 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 ?   11.9   0.0   6.9e-05      0.15       7      47 .]      57      97 ..      56      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.9e-05
                                      HHHHHTTSSEEHHHHHHHHTS-HHHHHHHH.HHHHHTTSEEE CS
                             HTH_5  7 ILklLaegelcvcelaeelglsqstvShHL.kkLreaGLVek 47
                                      IL +L+ +++   e+ + l++s++t Sh L k+L e+G+Vek
  gi|336254286|ref|YP_004597393.1| 57 ILEALRAKPMDRREIEARLEVSRAT-SHRLtKWLDEQGFVEK 97
                                      9**********************87.6666589******997 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0001      0.23      15      59 ..      57     100 ..      56     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                                       HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59 
                                       il aL ra+++   e+ +rl++s++t ++  + L e g+ve v++
  gi|336254286|ref|YP_004597393.1|  57 ILEAL-RAKPMDRREIEARLEVSRATSHRLTKWLDEQGFVEKVES 100
                                       99***.**************9999986665599999*****9976 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00023      0.52      21      64 ..      66     108 ..      57     109 .. 0.84
   2 ?   -1.5   0.0       1.2   2.6e+03      34      54 ..     215     235 ..     211     250 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                            HemN_C  21 ldlaafeqrfgldleellaaaleklqeqGLLeldggrlrltprG 64 
                                       +d +++e+r +++ + + +   ++l eqG++e  ++r+rlt rG
  gi|336254286|ref|YP_004597393.1|  66 MDRREIEARLEVSRATSHRL-TKWLDEQGFVEKVESRFRLTGRG 108
                                       66678999999997777555.9*******************998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                            HemN_C  34 leellaaaleklqeqGLLeld 54 
                                       l+e++   + +++++G L+l+
  gi|336254286|ref|YP_004597393.1| 215 LRETYPTRVTEAIDRGQLTLR 235
                                       566666666677777666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2350.17
//
Query:       gi|336254287|ref|YP_004597394.1|  [L=360]
Description: type 12 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-16   59.0   0.0    6.1e-16   58.6   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    3.6e-12   46.8   0.3    5.7e-12   46.2   0.3    1.3  1  Methyltransf_25  Methyltransferase domain
    1.8e-11   44.7   0.0    3.3e-11   43.8   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    2.7e-10   40.3   0.0    4.1e-10   39.7   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.3e-09   38.6   0.1      2e-09   38.0   0.1    1.3  1  Methyltransf_11  Methyltransferase domain
    5.5e-07   29.3   0.0    8.8e-07   28.6   0.0    1.3  1  MTS              Methyltransferase small domain
    1.1e-06   28.7   0.0      5e-06   26.5   0.0    1.9  2  Methyltransf_18  Methyltransferase domain
    1.3e-05   24.7   0.0      2e-05   24.1   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
    5.9e-05   22.4   0.1    8.8e-05   21.9   0.1    1.2  1  Methyltransf_2   O-methyltransferase domain
      8e-05   22.1   0.0    0.00011   21.6   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    8.5e-05   22.3   0.1    0.00012   21.8   0.1    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    0.00038   19.9   0.1    0.00056   19.4   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00077   20.5   0.9     0.0021   19.0   0.7    1.8  1  Methyltransf_24  Methyltransferase domain
     0.0012   18.7   0.0     0.0019   18.0   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0018   17.6   0.0      0.003   16.9   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.003   17.6   0.0     0.0042   17.1   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.005   16.0   0.0     0.0078   15.4   0.0    1.2  1  Methyltransf_3   O-methyltransferase
     0.0079   15.9   0.0      0.012   15.3   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.019   14.9   0.0       0.13   12.2   0.0    2.1  2  MarR_2           MarR family
      0.099   12.7   0.1       0.38   10.8   0.0    2.0  2  HTH_20           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   6.8e-19   6.1e-16       3     113 ..     180     286 ..     178     335 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 6.8e-19
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDli 78 
                                        g rv D+GCG G+ t  +a e++p++ +v +D+  ++ie+Ar++a++ g+  ++ Fe++ ++e+        +Dl+
  gi|336254287|ref|YP_004597394.1| 180 AGARVADVGCGHGASTVIMA-EAYPNSAFVAVDYHDRSIEVARQRADEAGVAdRIGFEVATATEFTG----TDYDLV 251
                                       6789****************.******************************99***********773....45**** PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedpr 113
                                       + +++ +++ dp  +   + ++l ++g+ ++ +p 
  gi|336254287|ref|YP_004597394.1| 252 TMFDAYHDMGDPVGAASHVREALADDGAWMLVEPF 286
                                       ****************************9998876 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.3   6.3e-15   5.7e-12       1      97 []     184     278 ..     184     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 6.3e-15
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       v d+GcG+G  t  +a++++++ +++vD+ ++ +e ar+ra+e+g+  ++ f+++ a+++   d  +Dlv+++ a+h
  gi|336254287|ref|YP_004597394.1| 184 VADVGCGHGASTVIMAEAYPNSAFVAVDYHDRSIEVARQRADEAGVadRIGFEVATATEFTGTD--YDLVTMFDAYH 258
                                       78*****************99**********************************999988666..******87777 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                        +   d   a ++++++L ++G
  gi|336254287|ref|YP_004597394.1| 259 DMG--DPVGAASHVREALADDG 278
                                       676..56689999999998887 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   3.7e-14   3.3e-11       2      97 ..     186     278 ..     185     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 3.7e-14
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       ++GcG G+ +  ++e+ p++ +++vD++ ++ie a+++  + +   ++++ +e+  + +  g   +Dlv+++++ h 
  gi|336254287|ref|YP_004597394.1| 186 DVGCGHGASTVIMAEAYPNSAFVAVDYHDRSIEVARQRADEAG--VADRIGFEVATATEFTG-TDYDLVTMFDAYHD 259
                                       8*******************************99999988877..68899999999776555.6************* PP

                   Methyltransf_12  79 lkdirevldnirklLkpgG 97 
                                       + d+  + +++r++L+++G
  gi|336254287|ref|YP_004597394.1| 260 MGDPVGAASHVREALADDG 278
                                       *****************99 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   4.6e-13   4.1e-10      16     125 ..     174     290 ..     151     316 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 4.6e-13
                   Methyltransf_23  16 llpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae............kakkaqkdqfdeqeaae 78 
                                       l ++lrag+rv d+GcG+G  + +++e      +++vD  ++ +e a+            +        f    a+e
  gi|336254287|ref|YP_004597394.1| 174 LDARLRAGARVADVGCGHGASTVIMAEAYPnsAFVAVDYHDRSIEVARqradeagvadriG--------FEVATATE 242
                                       44779**************9999997765545899****9999999866666444333222........22222222 PP

                   Methyltransf_23  79 .pqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslk 125
                                            +dl+++++  + + dp  + +++++ l+++G  +l ep a++ 
  gi|336254287|ref|YP_004597394.1| 243 fTGTDYDLVTMFDAYHDMGDPVGAASHVREALADDGAWMLVEPFANDR 290
                                       1555*******************************9999999988764 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.1   2.2e-12     2e-09       2      93 ..     186     279 ..     185     282 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.2e-12
                                       EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       dvGcG G+ +  +a+++  +  v+vD+ ++ +++a+++a e+g+  ++ f va+a++  f    +Dlv+++ + h +
  gi|336254287|ref|YP_004597394.1| 186 DVGCGHGASTVIMAEAYpnSAFVAVDYHDRSIEVARQRADEAGVadRIGFEVATATE--FTGTDYDLVTMFDAYHDM 260
                                       9*************9999**************************9999999999998..89999************* PP

                                       CCHHHHHHHHHHHEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGl 93 
                                        dp  a + ++  L  +G 
  gi|336254287|ref|YP_004597394.1| 261 GDPVGAASHVREALADDGA 279
                                       **********999999996 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   9.9e-10   8.8e-07      30     103 ..     177     253 ..     170     286 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9.9e-10
                                       C..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEE CS
                               MTS  30 e..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdliv 102
                                       +  +  +v+D+GcG G+ ++ +a+++p+ + ++vd + r++e+a++ + + +++  + +    +  e++  ++dl+ 
  gi|336254287|ref|YP_004597394.1| 177 RlrAGARVADVGCGHGASTVIMAEAYPNSAFVAVDYHDRSIEVARQRADEAGVAdrIGFEVATA-TEFTGTDYDLVT 252
                                       4445678******************************************999986544444444.444447888876 PP

                                       E CS
                               MTS 103 s 103
                                       +
  gi|336254287|ref|YP_004597394.1| 253 M 253
                                       6 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   5.6e-09     5e-06      13      76 ..     179     242 ..     171     254 .. 0.87
   2 ?   -0.8   0.0       1.5   1.3e+03     113     135 ..     321     343 ..     309     348 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 5.6e-09
                   Methyltransf_18  13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGle 76 
                                       + g+rvaD+G+ Hg  ++ +++    +  +a+D ++ ++e a++ +++ag+ d+i + ++   e
  gi|336254287|ref|YP_004597394.1| 179 RAGARVADVGCGHGASTVIMAEAYPNSAFVAVDYHDRSIEVARQRADEAGVADRIGFEVATATE 242
                                       6789***************************************************988776655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                   Methyltransf_18 113 lilqpnseaeelRkylvengfki 135
                                        +l ++  +++lR++++e gf+ 
  gi|336254287|ref|YP_004597394.1| 321 PVLGAQAGEARLREVITEGGFTS 343
                                       5899999***********99975 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   2.3e-08     2e-05       5      50 ..     184     229 ..     180     235 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.3e-08
                                       EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTT CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealel 50 
                                       v+++GcG G ++v +A++ P+  f++++ + ++++ + +++++ ++
  gi|336254287|ref|YP_004597394.1| 184 VADVGCGHGASTVIMAEAYPNSAFVAVDYHDRSIEVARQRADEAGV 229
                                       79*********************************99999988765 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   9.8e-08   8.8e-05      63     183 ..     181     301 ..     161     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 9.8e-08
                                       -SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HH.HHHHHHHHS.-----TTEEEEES-TTTS-----SEEEEESSG CS
                    Methyltransf_2  63 lkslvDvGGGtGalakaivsayPtikvivfDlpe.VveaAkehl.sageeervefvgGdffkdslPeaDaillkrvl 137
                                         ++ DvG G Ga    +++ayP+   +  D  +  +e A+++  +ag ++r+ f      + +  + D++ +    
  gi|336254287|ref|YP_004597394.1| 181 GARVADVGCGHGASTVIMAEAYPNSAFVAVDYHDrSIEVARQRAdEAGVADRIGFEVATATEFTGTDYDLVTMFDAY 257
                                       56799**************************97538*******9999******999888886666799********* PP

                                       GGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS---HHHHHHH CS
                    Methyltransf_2 138 hDwsdekcvklLkrvkkalpagGkvivveavlgadpsgeletelvd 183
                                       hD  d   +    +v++al ++G+ ++ve   + + +++l+  + +
  gi|336254287|ref|YP_004597394.1| 258 HDMGDPVGA--ASHVREALADDGAWMLVEPFANDRVEDNLNPIGRA 301
                                       **9987554..689***************99988888777665555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.2e-07   0.00011      58     142 ..     176     262 ..     170     292 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-07
                                       TT--TT-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.--SEEE CS
                              CMAS  58 lelkpGmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde.kvdrvv 132
                                       ++l++G ++ d+GcG G+ ++ ++e y +   v++   +   ++a++r de++++++   +++   ++ +  +d v 
  gi|336254287|ref|YP_004597394.1| 176 ARLRAGARVADVGCGHGASTVIMAEAYpNSAFVAVDYHDRSIEVARQRADEAGVADRIGFEVATATEFTGtDYDLVT 252
                                       5799***********************556789999********************************998999999 PP

                                       EES-GGGTSG CS
                              CMAS 133 svgafehvgk 142
                                        ++a   +g 
  gi|336254287|ref|YP_004597394.1| 253 MFDAYHDMGD 262
                                       9988887775 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.4e-07   0.00012      37     140 ..     177     279 ..     170     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.4e-07
                             GCD14  37 elkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvc.keGfdeevsg 112
                                       +l+ G++v + G G g+ s+ i+    P   + ++++h++ +e ar+   e ++++ +  ++  +   +G d ++  
  gi|336254287|ref|YP_004597394.1| 177 RLRAGARVADVGCGHGA-STVIMAEAYPNSAFVAVDYHDRSIEVARQRADEAGVADRIGFEVATATeFTGTDYDLVT 252
                                       799***********997.889999999*******************************99999888568999***** PP

                             GCD14 113 kvDavfLDlPaPweaiphaakalkkegg 140
                                         Da + D+  P  a  h+ +al ++g+
  gi|336254287|ref|YP_004597394.1| 253 MFDA-YHDMGDPVGAASHVREALADDGA 279
                                       ***9.78****************77765 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   6.2e-07   0.00056     152     229 ..     171     250 ..     169     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.2e-07
                              PrmA 152 lealeklvkegeevlDvGtGSGiLa.iaaakLgakkvvavDiDevAvkvakeNaelNkveakl..evalseellkee 225
                                       l  l++ +++g++v DvG+G G  + i a     +  vavD+ + +++va++ a+  +v++++  eva++ e +  +
  gi|336254287|ref|YP_004597394.1| 171 LDGLDARLRAGARVADVGCGHGASTvIMAEAYPNSAFVAVDYHDRSIEVARQRADEAGVADRIgfEVATATEFT-GT 246
                                       678999****************976256777788889**********************996611443333333.35 PP

                              PrmA 226 kadv 229
                                        +d+
  gi|336254287|ref|YP_004597394.1| 247 DYDL 250
                                       5665 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.7   2.4e-06    0.0021       3     101 ..     187     280 ..     185     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.4e-06
                   Methyltransf_24   3 iGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDll.fiDg 77 
                                       +G+ +G st+++++a  + +    vavd + +  e a++ a+eag++dr+ + +a++ e  +     ++Dl+ ++D+
  gi|336254287|ref|YP_004597394.1| 187 VGCGHGASTVIMAEAYPNSA---FVAVDYHDRsIEVARQRADEAGVADRIGFEVATATEFTG----TDYDLVtMFDA 256
                                       6777*********9988776...7****988656668888888***********99988843....568976378** PP

                   Methyltransf_24  78 ghaaeavledleallprlapggvv 101
                                        h+  +   +  ++++ la++g  
  gi|336254287|ref|YP_004597394.1| 257 YHDMGDPVGAASHVREALADDGAW 280
                                       *******************88765 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 !   18.0   0.0   2.1e-06    0.0019      70     124 ..     175     230 ..     161     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.1e-06
                                       T..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC CS
                              PCMT  70 e..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle 124
                                       +  l++garv +vG+G G  t+++a+   +++  v++++  + +e a+++  + +++
  gi|336254287|ref|YP_004597394.1| 175 DarLRAGARVADVGCGHGASTVIMAEAYPNSA-FVAVDYHDRSIEVARQRADEAGVA 230
                                       45599*********************998877.99***9999999999988776654 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.4e-06     0.003      46     122 ..     179     253 ..     167     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.4e-06
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEE CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvt 121
                                       + ga+v Dv +G g  ++ ++++  +    v +D+ +  ++v+++++ e g+  +i f +a a e+      +D+vt
  gi|336254287|ref|YP_004597394.1| 179 RAGARVADVGCGHGASTVIMAEAYPN-SAFVAVDYHDRSIEVARQRADEAGVAdRIGFEVATATEFT--GTDYDLVT 252
                                       67999************998887655.567889*******************989***999988755..44567776 PP

                                       E CS
                   Ubie_methyltran 122 v 122
                                       +
  gi|336254287|ref|YP_004597394.1| 253 M 253
                                       5 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   4.7e-06    0.0042      26      93 ..     181     244 ..     162     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.7e-06
                   Methyltransf_32  26 altvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieeat 93 
                                         +v+DvG+G g  + ++a       +  +v++d +++ +e a++ra++ g  +++r+ f+ ++ +e t
  gi|336254287|ref|YP_004597394.1| 181 GARVADVGCGHGASTVIMAE---AyPNSAFVAVDYHDRSIEVARQRADEAG--VADRIGFEVATATEFT 244
                                       5789*********9999999...546899**********************..8899988887776655 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   8.7e-06    0.0078      47     110 ..     180     242 ..     173     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.7e-06
                                       T--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHH CS
                    Methyltransf_3  47 nakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalk 110
                                          rv ++G   G s + +a a P+    +a+d      e+a++  + agva++i + ++ a++
  gi|336254287|ref|YP_004597394.1| 180 AGARVADVGCGHGASTVIMAEAYPNS-AFVAVDYHDRSIEVARQRADEAGVADRIGFEVATATE 242
                                       5568999*****************86.689***************************9998875 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.3e-05     0.012      72     124 ..     200     250 ..     177     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                       HHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---E CS
                           UPF0020  72 earaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdv 124
                                       ea ++  ++++D   r ++ ar+ a +agv+d+i f++a a++++  + ++d+
  gi|336254287|ref|YP_004597394.1| 200 EAYPNSAFVAVDYHDRSIEVARQRADEAGVADRIGFEVATATEFT-GT-DYDL 250
                                       34456669***********************************99.55.4665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.13      13      54 ..      47      86 ..      43      91 .. 0.88
   2 ?   -0.2   0.0       1.1   9.7e+02       1      12 [.      92     103 ..      92     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      aL+++++  +t++ela+r++   ++vs  l+   a G+v++ 
  gi|336254287|ref|YP_004597394.1| 47 ALADGGP--FTPAELAERTDTVEPYVSEWLAAGAAGGYVTYD 86
                                      5888888..*****************************9865 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                                       TT--HHHHHHHH CS
                            MarR_2   1 lgltpaqarvLa 12 
                                       +gltp qa +La
  gi|336254287|ref|YP_004597394.1|  92 YGLTPEQAALLA 103
                                       59********97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       5.3   4.7e+03      21      40 ..       7      26 ..       3      28 .. 0.81
   2 ?   10.8   0.0   0.00042      0.38      12      35 ..      41      64 ..      39      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.3
                                      TCTTB-HHHHHHHHTS-HHH CS
                            HTH_20 21 raegltaselaerldlsknt 40
                                       +e++  + l+e+l+++ ++
  gi|336254287|ref|YP_004597394.1|  7 ADEPVDEEKLDELLGMAVAE 26
                                      57899999999999988766 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00042
                                      HHHHHHHHSTCTTB-HHHHHHHHT CS
                            HTH_20 12 RrrilraLaraegltaselaerld 35
                                      R++++ aLa+++++t++elaer d
  gi|336254287|ref|YP_004597394.1| 41 RLGLYEALADGGPFTPAELAERTD 64
                                      99*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2674.21
//
Query:       gi|336254288|ref|YP_004597395.1|  [L=109]
Description: hypothetical protein Halxa_2900 [Halopiger xanaduensis SH-6]
Scores for 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   18.9   2.4    0.00083   18.7   2.4    1.1  1  HAP1_N      HAP1 N-terminal conserved region
     0.0013   18.6   1.5     0.0021   17.9   0.3    1.7  2  DUF1465     Protein of unknown function (DUF1465)
     0.0054   15.4   2.9     0.0057   15.4   2.9    1.1  1  AAA_13      AAA domain
     0.0084   16.4   0.9      0.011   16.0   0.9    1.2  1  BLOC1_2     Biogenesis of lysosome-related organelles complex
  ------ inclusion threshold ------
      0.011   15.3   0.1      0.012   15.1   0.1    1.1  1  Arfaptin    Arfaptin-like domain
      0.021   14.9   0.8       0.03   14.4   0.8    1.2  1  DUF1664     Protein of unknown function (DUF1664)
      0.038   13.9   0.1      0.062   13.2   0.1    1.3  1  GIT_CC      GIT coiled-coil Rho guanine nucleotide exchange f
      0.048   13.3   1.0      0.075   12.7   0.8    1.4  1  DUF4988     Domain of unknown function
      0.064   13.3   0.3       0.16   12.0   0.3    1.7  1  PspB        Phage shock protein B
      0.076   13.5   2.1        0.1   13.1   2.0    1.3  1  DUF16       Protein of unknown function DUF16
      0.084   13.3   0.7       0.11   13.0   0.7    1.4  1  NPV_P10     Nucleopolyhedrovirus P10 protein
      0.091   11.3   0.5      0.095   11.2   0.5    1.0  1  Herpes_UL6  Herpesvirus UL6 like
      0.091   11.9   0.5        0.1   11.8   0.5    1.1  1  Tho2        Transcription factor/nuclear export subunit prote
       0.16   11.7   4.8       0.28   10.8   4.8    1.5  1  CCDC85      CCDC85 family
       0.21   11.8   5.2       0.32   11.2   5.2    1.4  1  Spc24       Spc24 subunit of Ndc80
       0.28   11.8   2.0       0.33   11.6   2.0    1.4  1  YabA        Initiation control protein YabA
        0.3   10.9   6.1      0.046   13.5   2.2    1.7  2  DivIC       Septum formation initiator
        2.1    9.0  10.2        1.8    9.2   6.2    2.4  2  SlyX        SlyX


Domain annotation for each model (and alignments):
>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   2.4   8.3e-07   0.00083      91     137 ..      20      84 ..      16     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.3e-07
                            HAP1_N  91 LlkrNsvLternekLeeqLesareeiaqlrhelslkddLLqlysds..................e 137
                                       + k+ ++L+er  +Lee+++ ++++++++ h+l+ +  LL  ++++                   
  gi|336254288|ref|YP_004597395.1|  20 MYKQVQKLQERIISLEEEMDDTHDTVNRIDHQLTEQRALLLAIAEEqgidgeeilaqaaideaeL 84 
                                       67999*****************************9999988887776887766666666433220 PP

>> DUF1465  Protein of unknown function (DUF1465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   2.1e-06    0.0021      97     150 ..       6      59 ..       2      62 .. 0.90
   2 ?   -0.6   0.0       1.1   1.1e+03      66      86 ..      74      94 ..      73     107 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.1e-06
                                       ---------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX.XXXXXXXXXXX CS
                           DUF1465  97 daeavaeLpeelqeLierserLyervrrLdrelreeaeaaeaaenpvaeqlerL 150
                                       +a++++ L e+++++ ++ ++L+er+ +L++e+ + +++ ++ +++++eq+++L
  gi|336254288|ref|YP_004597395.1|   6 TAKKIQGLSERAEAMYKQVQKLQERIISLEEEMDDTHDTVNRIDHQLTEQRALL 59 
                                       6789999*****************************999988899999998877 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                                      HHHHHHHTTSS-TTTTSSSS- CS
                           DUF1465 66 LlqRAveegelseeqaasekk 86
                                      L q A+ e el++++ +se +
  gi|336254288|ref|YP_004597395.1| 74 LAQAAIDEAELEDADDESEAT 94
                                      778888999988887777665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.9   5.7e-06    0.0057     421     482 ..       6      65 ..       3      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.7e-06
                            AAA_13 421 lekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkafGlgeleLkfeee 482
                                       ++k+i+ l +++++ +++++kl+e+i  Le+++ d + +++ i  +L++   + l L+++ee
  gi|336254288|ref|YP_004597395.1|   6 TAKKIQGLSERAEAMYKQVQKLQERIISLEEEMDDTHDTVNRIDHQLTEQ--RALLLAIAEE 65 
                                       6899*******************************************997..6677777666 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 !   16.0   0.9   1.2e-05     0.011      39      91 ..       3      55 ..       1      59 [. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                           BLOC1_2 39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91
                                      l + a++++  +e+ +++y+++q++ ++i  +e++ ++  ++v+++D+  +e+
  gi|336254288|ref|YP_004597395.1|  3 LGSTAKKIQGLSERAEAMYKQVQKLQERIISLEEEMDDTHDTVNRIDHQLTEQ 55
                                      567889999999999999*****************************988776 PP

>> Arfaptin  Arfaptin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.2e-05     0.012      94     156 ..       4      65 ..       2      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Arfaptin  94 tatgealrllakqgeallkalkrfiselntfvnkaieDTllTikkyedarieYrayllklkea 156
                                        +t+++ + l++++ea+ k+++++++ +   ++  ++DT  T++++ +  +e ra ll + e 
  gi|336254288|ref|YP_004597395.1|   4 GSTAKKIQGLSERAEAMYKQVQKLQERIIS-LEEEMDDTHDTVNRIDHQLTEQRALLLAIAEE 65 
                                       6799*********************99965.6778********************99998775 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.8     3e-05      0.03      74     118 ..       9      53 ..       3      67 .. 0.46

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3e-05
                           DUF1664  74 kldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                       k++  +e ++++ ++v++++e + +++e+++  +++v+ ++++l+
  gi|336254288|ref|YP_004597395.1|   9 KIQGLSERAEAMYKQVQKLQERIISLEEEMDDTHDTVNRIDHQLT 53 
                                       333334444444444444444444444444444444444444433 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 ?   13.2   0.1   6.3e-05     0.062      28      65 ..       6      43 ..       2      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.3e-05
                            GIT_CC 28 seakiqqLlkvNtslsdelrlLQskvqkLqaeNaqlrd 65
                                         kiq L +  + + +++++LQ+ + +L++e ++ +d
  gi|336254288|ref|YP_004597395.1|  6 TAKKIQGLSERAEAMYKQVQKLQERIISLEEEMDDTHD 43
                                      5679999*************************988876 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.8   7.5e-05     0.075       3      45 ..      22      65 ..      20      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.5e-05
                           DUF4988  3 ddvndlkdrvaaleeqvkelndniealk.klleegkviteveen 45
                                      ++v++l++r+ +lee++++  d ++ +  +l+e++ ++  + e+
  gi|336254288|ref|YP_004597395.1| 22 KQVQKLQERIISLEEEMDDTHDTVNRIDhQLTEQRALLLAIAEE 65
                                      689************************62677888888887763 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   0.00016      0.16      41      68 ..      15      42 ..       5      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                              PspB 41 krLeellekAekleeRietLEriLdaes 68
                                      +r e+++++ +kl+eRi +LE+ +d  +
  gi|336254288|ref|YP_004597395.1| 15 ERAEAMYKQVQKLQERIISLEEEMDDTH 42
                                      4557889999999999999999988876 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.0    0.0001       0.1      41      85 ..       8      52 ..       2      66 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                                      HHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HH CS
                             DUF16 41 akvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetl 85
                                      +k++ l e+ +++ ++v+k++e+i  l++e++  ++ +n++d+ l
  gi|336254288|ref|YP_004597395.1|  8 KKIQGLSERAEAMYKQVQKLQERIISLEEEMDDTHDTVNRIDHQL 52
                                      566666666677777777777777777777776666666555444 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.7   0.00011      0.11      13      61 ..      10      55 ..       3      86 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                           NPV_P10 13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenI 61
                                      i+ ++++ +a+ +qv+++qe +     l+e++d+  ++++ ++ ++++ 
  gi|336254288|ref|YP_004597395.1| 10 IQGLSERAEAMYKQVQKLQERIIS---LEEEMDDTHDTVNRIDHQLTEQ 55
                                      555555555666666666554444...5556666666666665555543 PP

>> Herpes_UL6  Herpesvirus UL6 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   9.5e-05     0.095     368     422 ..      18      72 ..      11     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.5e-05
                        Herpes_UL6 368 kcleeqineqfdtiekLkkenelllkklkelekeLerlreeakkeakarevdllt 422
                                       + + +q++++ + i +L++e ++    +++++++L+++r+   + a+++ +d  +
  gi|336254288|ref|YP_004597395.1|  18 EAMYKQVQKLQERIISLEEEMDDTHDTVNRIDHQLTEQRALLLAIAEEQGIDGEE 72 
                                       56889*********************************99888766665555444 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5    0.0001       0.1      49      96 ..      14      61 ..       3      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                              Tho2 49 raaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLkeekkswfk 96
                                      +++a+   k+ ++l+e+i +LeeE++     v+++  +L+e++  +++
  gi|336254288|ref|YP_004597395.1| 14 SERAEAMYKQVQKLQERIISLEEEMDDTHDTVNRIDHQLTEQRALLLA 61
                                      556677789999*****************************9987776 PP

>> CCDC85  CCDC85 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.8   0.00028      0.28     109     147 ..       3      61 ..       1     108 [. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                            CCDC85 109 valylqklkeLearqeellrenleLkelvllLdeekaa....................g 147
                                       ++ + +k++ L +r e++ +  ++L+e ++ L+ee+                      +
  gi|336254288|ref|YP_004597395.1|   3 LGSTAKKIQGLSERAEAMYKQVQKLQERIISLEEEMDDthdtvnridhqlteqralllA 61 
                                       67789******************************999555555555554444443332 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   5.2   0.00032      0.32       8      79 ..       5      82 ..       3     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00032
                             Spc24  8 riakelsdleselesleselaelkeeleeleeeseekeser......vedetllklklYrsLGielekdvnkvlirnk 79
                                      ++ak+++ l + +e++ ++ ++l+e++  leee  + ++++        ++ +l l + ++ Gi+ e+  +++ i++ 
  gi|336254288|ref|YP_004597395.1|  5 STAKKIQGLSERAEAMYKQVQKLQERIISLEEEMDDTHDTVnridhqLTEQRALLLAIAEEQGIDGEEILAQAAIDEA 82
                                      5899****************************9999444442333323344447777777777777666666666655 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.0   0.00034      0.33       8      52 ..       8      52 ..       1     101 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52
                                      +k++ l+e+ e++++++++l+e++ +l ee ++ +   +++ ++l
  gi|336254288|ref|YP_004597395.1|  8 KKIQGLSERAEAMYKQVQKLQERIISLEEEMDDTHDTVNRIDHQL 52
                                      678889999999999999999999999998777666655555555 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.2   4.6e-05     0.046      19      59 ..      10      50 ..       3      66 .. 0.89
   2 ?   -1.7   0.1       2.6   2.6e+03      30      50 ..      81      87 ..      69     101 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.6e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                             DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyiee 59
                                      ++ l +  +a  ++++kl++++ +Le+e +d +++ ++i+ 
  gi|336254288|ref|YP_004597395.1| 10 IQGLSERAEAMYKQVQKLQERIISLEEEMDDTHDTVNRIDH 50
                                      666778889999********************999888875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
                                      HHHHHHHHHHHHHHHHHHCC- CS
                             DivIC 30 qaelaklkaeneeLeaevkdL 50
                                      +              ae++d 
  gi|336254288|ref|YP_004597395.1| 81 E--------------AELEDA 87
                                      3..............333333 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.066        66      30      52 ..       7      29 ..       5      30 .. 0.86
   2 ?    9.2   6.2    0.0018       1.8       1      37 [.      27      63 ..      27      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.066
                                      HHHHHHHHHHHHHHHHT-XXXXX CS
                              SlyX 30 qqqidrlqrqlrllaerlkelee 52
                                      +++i+ l ++ +++++++++l+e
  gi|336254288|ref|YP_004597395.1|  7 AKKIQGLSERAEAMYKQVQKLQE 29
                                      57899999999999999999987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0018
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX  1 leerleeLEiklafqedtieeLndvvaeqqqqidrlq 37
                                      l+er++ LE+++  + dt+++ + +++eq+  + ++ 
  gi|336254288|ref|YP_004597395.1| 27 LQERIISLEEEMDDTHDTVNRIDHQLTEQRALLLAIA 63
                                      689**************************98776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1513  (0.0843884); expected 358.6 (0.02)
Passed bias filter:                      781  (0.0435607); expected 358.6 (0.02)
Passed Vit filter:                       172  (0.0095934); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 786.78
//
Query:       gi|336254289|ref|YP_004597396.1|  [L=326]
Description: cysteine synthase [Halopiger xanaduensis SH-6]
Scores for complete 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  208.7   1.6    1.4e-61  208.5   1.6    1.0  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 !  208.5   1.6   7.6e-66   1.4e-61       3     293 ..      13     306 ..      11     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 208.5 bits;  conditional E-value: 7.6e-66
                                       GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHH.HHTT..TTTSEEEEEBSSHHHHHHHHHHHH CS
                              PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllar.lkeg..tgaktvveassGNhgralAaaaal 76 
                                         ig+TPlvr++       v++++KlE +np+ S+KdR   y+++r l++g   +  t+ve ++GN+g++ A+aa  
  gi|336254289|ref|YP_004597396.1|  13 ETIGRTPLVRVQDGP--ADVRIYAKLETFNPGASVKDRIGRYMVERmLERGdvSPDGTIVEPTAGNTGIGFAIAAEQ 87 
                                       679*********955..6777*************************88888************************** PP

                                       HT-EEEEEEETTS-HHHHHHHHHTT-EEEEE..CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHH CS
                              PALP  77 lGlkvtivvpadaspekvallrllGaevvev..ggdydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEi 150
                                       lGl+++ vvp+  s ek++l+ +lGae++ +  +++  +a ++a+ela+e ++a++ +qf+np++ e+ y+t+++Ei
  gi|336254289|ref|YP_004597396.1|  88 LGLDAIFVVPERFSVEKQQLMDALGAEIINTptEDGMGRAIERAHELAEELDDAVVPQQFSNPLNAEAhYETTAPEI 164
                                       *******************************777779999999********************************** PP

                                       HHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTT CS
                              PALP 151 leqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspse 227
                                       +e ++g++ avv+++G++g+++Gia +  er+pd++v +vepe  + +++++     ++ ++++  ++g++++    
  gi|336254289|ref|YP_004597396.1| 165 YEAVDGEVGAVVAGCGTAGTLMGIAEYALERDPDTHVAAVEPE-GSLYGEAI----GEDREEGEYKIEGIGTHD--L 234
                                       *******************************************.44555555....2333455889*******3..3 PP

                                       CCHHHH.SEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTC......EEEEEEE- CS
                              PALP 228 lafell.drlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkeg......drvvvilt 293
                                       ++ el+  +lvd++ +v de+a++ +++lar+eg++v  s++aa  a+  + a+++++g      d+vv+i++
  gi|336254289|ref|YP_004597396.1| 235 ETNELFdPELVDDVFAVADEAAHAELKRLAREEGHLVASSAGAASVAA-KHVARRIADGdletphDTVVTIFP 306
                                       3333333688899999***********************666666666.455555555545555888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2593.26
//
Query:       gi|336254290|ref|YP_004597397.1|  [L=64]
Description: hypothetical protein Halxa_2902 [Halopiger xanaduensis SH-6]
Scores for 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:                       550  (0.0306766); 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:                         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: 0.33u 0.19s 00:00:00.52 Elapsed: 00:00:00.33
# Mc/sec: 584.12
//
Query:       gi|336254291|ref|YP_004597398.1|  [L=139]
Description: CoA-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-38  131.5   0.3    2.3e-38  131.3   0.3    1.1  1  CoA_binding_2  CoA binding domain
    7.3e-08   33.0   0.0    1.2e-07   32.4   0.0    1.3  1  CoA_binding    CoA binding domain
  ------ inclusion threshold ------
      0.081   12.8   0.0       0.15   11.9   0.0    1.5  1  TusA           Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.3   0.3   3.8e-42   2.3e-38       2     115 ..      20     134 ..      19     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 131.3 bits;  conditional E-value: 3.8e-42
                                       -EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealal 78 
                                       tiaVvG+s++pgk+++ +++yl e+g++v+pVnp ++eilg+++  slae +e++d+v++f+p+e++ +iv++al++
  gi|336254291|ref|YP_004597398.1|  20 TIAVVGCSSTPGKAAHDIPAYLDERGYEVIPVNPFADEILGRPARDSLAEVEEEIDVVCIFRPSEEVGDIVDAALER 96 
                                       8************************************************956**********************888 PP

                                       .--SEEEE-TT---HHHHHHHHHTT-EEE.ES-HHHHH CS
                     CoA_binding_2  79 .gakavwlqpgsedeeaaelaeeagirvvgdrCilveg 115
                                        ++kavw q g++d++aae++ eag +vv+drC++ve+
  gi|336254291|ref|YP_004597398.1|  97 dDVKAVWTQKGIRDDAAAERVLEAGRQVVQDRCMMVEH 134
                                       46***********************************9 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   1.9e-11   1.2e-07       5      91 ..      20     103 ..      17     105 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.9e-11
                                       EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHH CS
                       CoA_binding   5 kviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavde 81 
                                        ++v+G + + ++ + ++   l+ +  +v++vnp   ++e+lg p+ +s++e+ee+  +dv  i+ P+e++ ++vd+
  gi|336254291|ref|YP_004597398.1|  20 TIAVVGCSSTPGKAAHDIPAYLDERGYEVIPVNPF--ADEILGRPARDSLAEVEEE--IDVVCIFRPSEEVGDIVDA 92 
                                       69********************************9..*******************..******************* PP

                                       HHH.TT-SEEE CS
                       CoA_binding  82 lve.agikgiv 91 
                                       ++e   +k ++
  gi|336254291|ref|YP_004597398.1|  93 ALErDDVKAVW 103
                                       **988899887 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.5e-05      0.15      28      57 ..      22      51 ..      12      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                                      -EEEEEESSCHHHHHHHHHHHHHTEEEEEE CS
                              TusA 28 evlevladdpaatediprfakklghelvev 57
                                      +v+   ++   a +dip++++++g+e++ v
  gi|336254291|ref|YP_004597398.1| 22 AVVGCSSTPGKAAHDIPAYLDERGYEVIPV 51
                                      5566667888999*************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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: 0.36u 0.19s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 1220.82
//
Query:       gi|336254292|ref|YP_004597399.1|  [L=210]
Description: hypothetical protein Halxa_2904 [Halopiger xanaduensis SH-6]
Scores for 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-09   35.1   0.0    1.2e-08   34.6   0.0    1.2  1  ATPase     KaiC
    1.2e-06   28.3   0.0    1.8e-06   27.8   0.0    1.3  1  DUF835     Protein of unknown function (DUF835)
     0.0094   15.1   0.0     0.0098   15.1   0.0    1.1  1  PAXNEB     PAXNEB protein
  ------ inclusion threshold ------
      0.035   14.3   0.1      0.079   13.2   0.1    1.6  1  DUF1477    Protein of unknown function (DUF1477)
        0.1   12.3   0.0       0.27   10.9   0.0    1.6  2  IstB_IS21  IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   3.3e-12   1.2e-08      19     188 ..      19     197 ..       7     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 3.3e-12
                            ATPase  19 grvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaees 95 
                                       g+ vli+G p tGK  +a + l +ga++ ++  + vt+  +a ++ e++  ++  le+  +e  + i+d +++++++
  gi|336254292|ref|YP_004597399.1|  19 GTNVLIAGPPLTGKRQLAYEILTNGAVR-NDGSIVVTTKDSADKVLERFDDVDG-LER--DEATIGIVDCVTKQRGI 91 
                                       789*************************.********************97653.343..344599******99987 PP

                            ATPase  96 aee.........kdkedle....elieelaeaikeika..krvviDsitgl.ayeekeavaReilrqlvrvlkklgv 156
                                        +          ++  d+     +l+e l+e  +e ++  +rv++Ds+++l +y++ + v+R  l+ ++ +++  + 
  gi|336254292|ref|YP_004597399.1|  92 GAVeddprikyaSSPIDMTgigiKLSEFLREFYEERGVteNRVLLDSVSTLlMYSDLQTVFR-FLHVFTGRIQSADA 167
                                       665789999999555555511125666666666665557799*********77777666666.79999999999999 PP

                            ATPase 157 TailvsekssseeaaggygveefivdgvivLd 188
                                         + v + s+ ++  + + +++ + dg++ ++
  gi|336254292|ref|YP_004597399.1| 168 MGVYVID-STAHDDQTMNTLKQ-LFDGIVEIE 197
                                       9999999.45556677777777.888887765 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   4.9e-10   1.8e-06      58     136 .]     106     190 ..      85     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 4.9e-10
                            DUF835  58 Ptnlekltetivkflkeaekg......vvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeeke 128
                                       P +++ +  ++++fl+e +++       vl+D++  L+++++ ++v++fl+    ++ + +++ + vid  a +++ 
  gi|336254292|ref|YP_004597399.1| 106 PIDMTGIGIKLSEFLREFYEErgvtenRVLLDSVSTLLMYSDLQTVFRFLHVFTGRIQSADAMGVYVIDSTAHDDQT 182
                                       5555555555555555555545555779************************************************* PP

                            DUF835 129 lalLkref 136
                                       ++ Lk+ f
  gi|336254292|ref|YP_004597399.1| 183 MNTLKQLF 190
                                       ****9977 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.7e-06    0.0098     190     282 ..     115     197 ..      52     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-06
                            PAXNEB 190 qiqqllkkesfsaptkknvlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplsliarsss 266
                                       +++++l++   +++ +    R+++ s    l+       s+ +++++FLh   + ++s  ++ +  + ++ +  + +
  gi|336254292|ref|YP_004597399.1| 115 KLSEFLREFYEERGVT--ENRVLLDSVSTLLM------YSDLQTVFRFLHVFTGRIQSADAMGVYVIDSTAH--DDQ 181
                                       6777777766666666..579*****988888......3689*************************99999..9** PP

                            PAXNEB 267 lvrkieqlvDtvieLe 282
                                        ++ ++ql+D+++e+e
  gi|336254292|ref|YP_004597399.1| 182 TMNTLKQLFDGIVEIE 197
                                       **************97 PP

>> DUF1477  Protein of unknown function (DUF1477)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.2e-05     0.079      49      76 ..     171     198 ..     125     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                           DUF1477  49 fvkklltknslaletlknlfdtiielEr 76 
                                       +v  ++ ++  +++tlk+lfd i+e+E+
  gi|336254292|ref|YP_004597399.1| 171 YVIDSTAHDDQTMNTLKQLFDGIVEIEE 198
                                       5555668999****************96 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 ?   10.9   0.0   7.5e-05      0.27      47     102 ..      19      75 ..       7      86 .. 0.79
   2 ?   -2.1   0.0      0.77   2.7e+03     102     132 ..     161     191 ..     146     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.5e-05
                         IstB_IS21  47 kenivllGpsGvGKshlaia.lgveavraglsvlfvrvedLveelkrarrdgklara 102
                                         n+++ Gp+ +GK  la   l   avr++ s++ ++ +   + l+r ++ + l+r 
  gi|336254292|ref|YP_004597399.1|  19 GTNVLIAGPPLTGKRQLAYEiLTNGAVRNDGSIVVTTKDSADKVLERFDDVDGLERD 75 
                                       68****************86267889**99999988877777777777666666665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.77
                         IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfe 132
                                       ++++  ++ + ++D  +  +   +  ++lf+
  gi|336254292|ref|YP_004597399.1| 161 RIQSADAMGVYVIDSTAHDDQTMNTLKQLFD 191
                                       6777777888888888877777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1591.29
//
Query:       gi|336254293|ref|YP_004597400.1|  [L=286]
Description: Digeranylgeranylglyceryl phosphate synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-46  158.8  18.2    1.6e-46  158.6  18.2    1.0  1  UbiA      UbiA prenyltransferase family


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 !  158.6  18.2   9.2e-51   1.6e-46       4     252 .]      25     272 ..      22     272 .. 0.92

  Alignments for each domain:
  == domain 1  score: 158.6 bits;  conditional E-value: 9.2e-51
                              UbiA   4 palvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilg 80 
                                        +++g+++a+g +  +  +++++++t la +a+na+NdyfDreiD++  + p+R++++G++s + al++++vl++l+
  gi|336254293|ref|YP_004597400.1|  25 LTFIGAFVAGGVTEAPVAVAAAVAATGLAVGAGNAINDYFDREIDRI--NQPERAIPRGAVSARGALAYSLVLFALA 99 
                                       58999****999999988888888888********************..**************************** PP

                              UbiA  81 llllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgsl.sllalllalavfllt 156
                                        +l+ ++l +l++++++++l+++v+Yt+ ++K  + +g+ v++   g  +l+g+aav++     +a++lal+ ++ t
  gi|336254293|ref|YP_004597400.1| 100 TGLA-VTLPLLAIGIAVVNLVALVAYTE-FFKGLPGVGNAVVAYLVGSTFLFGAAAVGEYGdVEPAVVLALLAAIAT 174
                                       ****.**********************8.***************************99877755666666666999* PP

                              UbiA 157 waialandlrdregDrkagiktlpvvlGrkaarillalllavllla.llllllalllllylllalllaalallraar 232
                                       ++  +++d++d+egDr+ g++tlp+ +G+++a+ l+a+lla+++la ++ +ll++++  yll+++++ a++l+ aa 
  gi|336254293|ref|YP_004597400.1| 175 LTREIIKDVEDIEGDRAEGLRTLPIAIGERRAIALSAILLAIAVLAsPVPYLLGYFGVAYLLVVVPADAIMLYAAAE 251
                                       ***********************************666666666666****************************** PP

                              UbiA 233 lvrrrdakkaakff.lflssl 252
                                        v + +a +   ++ +fl+sl
  gi|336254293|ref|YP_004597400.1| 252 SVGDPTAGQSHLKYgMFLASL 272
                                       **9999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.21s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2239.99
//
Query:       gi|336254294|ref|YP_004597401.1|  [L=60]
Description: hypothetical protein Halxa_2906 [Halopiger xanaduensis SH-6]
Scores for 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  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       168  (0.00937029); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); 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: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 515.45
//
Query:       gi|336254295|ref|YP_004597402.1|  [L=119]
Description: hypothetical protein Halxa_2907 [Halopiger xanaduensis SH-6]
Scores for 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   26.7   0.0    5.4e-06   26.1   0.0    1.4  1  HTH_IclR   IclR helix-turn-helix domain
    1.6e-05   24.8   0.0      3e-05   24.0   0.0    1.4  1  HTH_20     Helix-turn-helix domain
     0.0018   17.8   0.3     0.0039   16.7   0.1    1.6  2  HTH_24     Winged helix-turn-helix DNA-binding
     0.0027   17.5   0.1     0.0071   16.1   0.1    1.7  1  HTH_23     Homeodomain-like domain
     0.0036   17.2   0.5     0.0068   16.3   0.1    1.6  2  HTH_11     HTH domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.021   14.7   0.0    1.3  1  TrmB       Sugar-specific transcriptional regulator TrmB
      0.017   15.0   0.1      0.025   14.5   0.1    1.2  1  MarR_2     MarR family
      0.023   14.8   0.1      0.052   13.7   0.1    1.7  2  HTH_28     Helix-turn-helix domain
      0.041   14.1   0.0      0.073   13.3   0.0    1.5  1  HTH_17     Helix-turn-helix domain
      0.044   13.9   0.0      0.061   13.5   0.0    1.3  1  FUR        Ferric uptake regulator family
      0.052   13.6   0.0      0.085   12.9   0.0    1.3  1  HTH_29     Winged helix-turn helix
      0.066   13.1   0.0        0.1   12.5   0.0    1.4  1  HTH_5      Bacterial regulatory protein, arsR family
      0.075   13.0   0.0       0.12   12.4   0.0    1.3  1  HTH_Crp_2  Crp-like helix-turn-helix domain
      0.095   13.2   0.0        0.2   12.1   0.0    1.6  1  HTH_27     Winged helix DNA-binding domain
        0.1   12.4   0.0       0.17   11.7   0.0    1.4  1  TetR_N     Bacterial regulatory proteins, tetR family
       0.12   12.6   0.0       0.21   11.8   0.0    1.4  1  UPF0122    Putative helix-turn-helix protein, YlxM / p13 like


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   4.8e-09   5.4e-06      12      49 ..      39      76 ..      32      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.8e-09
                                      -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      ++e++++ ++se++r +g+++Stv++ + tL++l  ++
  gi|336254295|ref|YP_004597402.1| 39 ISERGRDISVSEVSRLAGVARSTVYNNIDTLERLDVIK 76
                                      6788888**************************98776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.7e-08     3e-05       5      58 ..      24      79 ..      19      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.7e-08
                                      HHHS-HHHHHHHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  5 eALahPvRrrilraL..araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      +++++  R +i  a+   r++  ++se+ ++ +++++t+++++++Le+ + ++ +r
  gi|336254295|ref|YP_004597402.1| 24 YLFGDSARVKIIGAFisERGRDISVSEVSRLAGVARSTVYNNIDTLERLDVIKHTR 79
                                      678999*********99999999*****************************9998 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 !   16.7   0.1   3.5e-06    0.0039       7      48 .]      33      76 ..      28      76 .. 0.89
   2 ?   -2.0   0.0       2.5   2.8e+03      38      46 ..     109     117 ..     108     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.5e-06
                            HTH_24  7 kIL.elLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      kI+   + + +r is +e+++  g+ +stv   ++ Le+  +Ik
  gi|336254295|ref|YP_004597402.1| 33 KIIgAFISERGRdISVSEVSRLAGVARSTVYNNIDTLERLDVIK 76
                                      6665677888889*****************************97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                            HTH_24  38 lkrLeeeGl 46 
                                       l++L++e +
  gi|336254295|ref|YP_004597402.1| 109 LQKLIDEDY 117
                                       789999988 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   6.3e-06    0.0071      17      41 ..      45      69 ..      30      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.3e-06
                            HTH_23 17 GlsvreIAreLgvsrrTvyrwlkry 41
                                       +sv+e++r+ gv r+Tvy+ + + 
  gi|336254295|ref|YP_004597402.1| 45 DISVSEVSRLAGVARSTVYNNIDTL 69
                                      589****************988774 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     6e-06    0.0068       4      42 ..      33      72 ..      31      83 .. 0.88
   2 ?   -1.9   0.0       2.9   3.3e+03       7      23 ..      99     114 ..      96     115 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6e-06
                            HTH_11  4 qilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      +i+  ++++rg  is +e ++  +v r+tv++ I++Le l
  gi|336254295|ref|YP_004597402.1| 33 KIIGAFISERGRdISVSEVSRLAGVARSTVYNNIDTLERL 72
                                      5666777899999************************986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.9
                            HTH_11   7 elLleargpisgeeLAe 23 
                                       elL++ +g +s ++L +
  gi|336254295|ref|YP_004597402.1|  99 ELLYRLEG-VSLQKLID 114
                                       45666666.77777755 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.9e-05     0.021      24      55 ..      47      78 ..      43      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                                      HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVere 55
                                      +++e+++ +gv rs+vY+ +  Le+ ++++  
  gi|336254295|ref|YP_004597402.1| 47 SVSEVSRLAGVARSTVYNNIDTLERLDVIKHT 78
                                      689**********************9999866 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.2e-05     0.025      13      56 ..      38      80 ..      29      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.2e-05
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      ++  r+ rd++v+e+ r  g+ +s+v + ++ L++   +  +++
  gi|336254295|ref|YP_004597402.1| 38 FISERG-RDISVSEVSRLAGVARSTVYNNIDTLERLDVIKHTRD 80
                                      455565.79*************************9999887766 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.7e-05     0.052       2      31 ..      31      64 ..      30      72 .. 0.86
   2 ?   -2.1   0.0       3.9   4.3e+03       1      11 [.      70      80 ..      70      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.7e-05
                            HTH_28  2 Rleiiklla..aGh..svreaArelgisrrtvyr 31
                                      R +ii + +  +G+  sv+e++r+ g+ r+tvy 
  gi|336254295|ref|YP_004597402.1| 31 RVKIIGAFIseRGRdiSVSEVSRLAGVARSTVYN 64
                                      6788888884458899*****************6 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.9
                            HTH_28  1 qRleiikllaa 11
                                      +Rl +ik+  +
  gi|336254295|ref|YP_004597402.1| 70 ERLDVIKHTRD 80
                                      69999998765 PP

>> HTH_17  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   6.5e-05     0.073       3      23 ..      47      67 ..      46      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.5e-05
                            HTH_17  3 tveEaAelLgvsrstvyrlir 23
                                      +v+E+++l gv rstvy+ i+
  gi|336254295|ref|YP_004597402.1| 47 SVSEVSRLAGVARSTVYNNID 67
                                      89***************9665 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.4e-05     0.061      36      68 ..      53      86 ..      31     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.4e-05
                                      TTTT--HHHHHHHHHHHHHTTSEEEEE.ETTSEE CS
                               FUR 36 edpeislaTVYrtLklleeaglvkele.fedges 68
                                      +   +  +TVY+++++le+++++k++  +e+g+s
  gi|336254295|ref|YP_004597402.1| 53 RLAGVARSTVYNNIDTLERLDVIKHTRdIEGGHS 86
                                      5567899****************98741554444 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.6e-05     0.085      11      39 ..      43      72 ..      39      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.6e-05
                            HTH_29 11 Gvs.tvsqiAkllglsrrtvyrwlkrfeeg 39
                                      G + +vs++ +l g+ r+tvy+ ++  e  
  gi|336254295|ref|YP_004597402.1| 43 GRDiSVSEVSRLAGVARSTVYNNIDTLERL 72
                                      55567******************9986654 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 ?   12.5   0.0   9.2e-05       0.1       1      45 [.      28      75 ..      28      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.2e-05
                                      SHHHHHHHHHHTT...SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  1 dptRlkILklLae...gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      d++R+kI+ +  +   +  +v+e ++  g+ +stv      L+ ++++
  gi|336254295|ref|YP_004597402.1| 28 DSARVKIIGAFISergRDISVSEVSRLAGVARSTVYNNIDTLERLDVI 75
                                      789******999999888*****************9999999888776 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    0.0001      0.12      21      57 ..      45      81 ..      27      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rgrri 57
                                      +++  e +++ G+ r+tv   +  L+r  +i+ ++  i
  gi|336254295|ref|YP_004597402.1| 45 DISVSEVSRLAGVARSTVYNNIDTLERLDVIKhTRD-I 81
                                      5788999*************************5453.5 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 ?   12.1   0.0   0.00018       0.2      15      55 ..      41      82 ..      32      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                            HTH_27 15 rrrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdea 55
                                      +r+r++  +++++   v  s++ ++++ L++ +++++t+d +
  gi|336254295|ref|YP_004597402.1| 41 ERGRDISvSEVSRLAGVARSTVYNNIDTLERLDVIKHTRDIE 82
                                      57777777***************************9999954 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 ?   11.7   0.0   0.00016      0.17       9      35 ..      39      64 ..      37      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                      HHHHHTTT--HHHHHHHHTSSHHHHHH CS
                            TetR_N  9 faerGydattvreIAkrAGvskgalYr 35
                                      ++erG d  +v+e+ + AGv+++++Y 
  gi|336254295|ref|YP_004597402.1| 39 ISERGRD-ISVSEVSRLAGVARSTVYN 64
                                      5778877.89****************6 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.21      32      59 ..      44      71 ..      31      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                           UPF0122 32 dDlSlsEiAeefnvsrqavydnikrtek 59
                                       D+S+sE+     v r++vy+ni + e+
  gi|336254295|ref|YP_004597402.1| 44 RDISVSEVSRLAGVARSTVYNNIDTLER 71
                                      59*********************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 904.06
//
Query:       gi|336254296|ref|YP_004597403.1|  [L=93]
Description: hypothetical protein Halxa_2908 [Halopiger xanaduensis SH-6]
Scores for 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  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 736.84
//
Query:       gi|336254297|ref|YP_004597404.1|  [L=761]
Description: hypothetical protein Halxa_2909 [Halopiger xanaduensis SH-6]
Scores for 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-18   64.3   0.0    1.9e-17   63.4   0.0    1.5  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
    0.00035   21.1   0.0    0.00094   19.7   0.0    1.7  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
      0.001   17.6   0.0     0.0017   16.9   0.0    1.2  1  PaRep2b      PaRep2b protein


Domain annotation for each model (and alignments):
>> 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 !   63.4   0.0   3.2e-21   1.9e-17       3     129 ..      25     161 ..      23     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 3.2e-21
                       HATPase_c_3   3 lekAlaelvdNsldAdaen........vkievnknr.gktgeivieDdGkGmseeelknalrlatsskeakrkstsl 70 
                                       + +A  elvdN+ld   +         ++ie+++     ++e+vi+Dd+ G++e++l+  + l++s+ke    + s+
  gi|336254297|ref|YP_004597404.1|  25 PVSAFKELVDNALDNWRRVldgldpvtIEIEYHDGGpDGEDEVVIRDDSGGVEEDDLQILFALGQSKKE--DIAGSI 99 
                                       56899*********877778889995566666654334569****************************..57999* PP

                       HATPase_c_3  71 GkkGiGlklAslslgkkltvitkkegess..tltldvdkidkenekvleeltveeie.evke 129
                                       G +GiG k A+l lg+k+t+ +++    +   +t+d +++++++++++e+ ++e+ie  v+e
  gi|336254297|ref|YP_004597404.1| 100 GAYGIGAKKAILNLGNKATIRSRHMYADTgfGFTIDEEWLQDDEDWTVEKEEYEDIEaGVTE 161
                                       ***********************997777678*********************999854454 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 !   19.7   0.0   1.6e-07   0.00094       9      98 ..      28     123 ..      23     138 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHHHHH....HSTTTEEEEEEEEEE....TEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSH CS
                         HATPase_c   9 iisnlvdNavkf....atkageieveikase....ddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGl 76 
                                       ++++lvdNa+++        + +++ei+ ++    ++ ++ ++D+  G+ ++dl+ lf+   s++++ + + g  G+
  gi|336254297|ref|YP_004597404.1|  28 AFKELVDNALDNwrrvLDGLDPVTIEIEYHDggpdGEDEVVIRDDSGGVEEDDLQILFAlGQSKKEDIAGSIGAYGI 104
                                       57889999999876553344556666665334555899999**************9998555552333333355555 PP

                                       HHHHHHHHHHHTTTEEEEEEET CS
                         HATPase_c  77 GlsivkklvelmgGeiwvesep 98 
                                       G++  k++ + +g + +++s+ 
  gi|336254297|ref|YP_004597404.1| 105 GAK--KAILN-LGNKATIRSRH 123
                                       543..44555.56566655554 PP

>> PaRep2b  PaRep2b protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.8e-07    0.0017     345     434 ..     237     328 ..     235     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.8e-07
                           PaRep2b 345 fireLedvlkrRyGddavkklievlkpAreegtvdlpLaveDergnliArvvdlkvefvk..ngqpvsqcaGedcrl 419
                                       f+r+ e +  +   ++a   l+ ++ + re+ + d +  +  +++ +   v d ++ f +  n+  +++ +G+ +rl
  gi|336254297|ref|YP_004597404.1| 237 FVRRYEGIDLQSKEFEAEVTLNVTVGLMREASAEDSGADIFCQNRLVLSGVTDERAGFGMgsNSSKLGKFSGQHRRL 313
                                       56666666555556777777888888999*****************************8755778899********* PP

                           PaRep2b 420 rvvveYevggerkqf 434
                                       rv++e+e++g+++ +
  gi|336254297|ref|YP_004597404.1| 314 RVIIEFETEGDARIL 328
                                       ***********9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (761 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); 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: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.44
# Mc/sec: 5224.38
//
Query:       gi|336254298|ref|YP_004597405.1|  [L=93]
Description: hypothetical protein Halxa_2910 [Halopiger xanaduensis SH-6]
Scores for 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  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 738.87
//
Query:       gi|336254299|ref|YP_004597406.1|  [L=110]
Description: hypothetical protein Halxa_2911 [Halopiger xanaduensis SH-6]
Scores for 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  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 845.13
//
Query:       gi|336254300|ref|YP_004597407.1|  [L=55]
Description: hypothetical protein Halxa_2912 [Halopiger xanaduensis SH-6]
Scores for 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:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 462.17
//
Query:       gi|336254301|ref|YP_004597408.1|  [L=56]
Description: hypothetical protein Halxa_2913 [Halopiger xanaduensis SH-6]
Scores for 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:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); 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 0.21s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 420.60
//
Query:       gi|336254302|ref|YP_004597409.1|  [L=206]
Description: bacterio-opsin activator-like protein [Halopiger xanaduensis SH-6]
Scores for 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-08   33.4   0.0    6.7e-08   32.5   0.0    1.4  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 !   32.5   0.0   3.7e-12   6.7e-08       5     168 ..      18     190 ..      16     193 .. 0.66

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.7e-12
                                       HHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTT..EEEEE....EEECSSSSEEEEECTHH CS
                   Phage_integrase   5 edeverllaaleeslkirdklllellyetGlRisEllsLrvkdldleng..vilvh....eregKgskeravplsee 75 
                                       +deve + +a+++  + ++ ++++l+   G R+s + s r + ++++ +  ++ ++    +++g ++k r   l+  
  gi|336254302|ref|YP_004597409.1|  18 PDEVEDIAKAART-VDWERGIAMRLMGFVGSRASGVPSARPEGINWNSEgeYWELElkgkNTRGGEKKTRDAYLPGR 93 
                                       6888888888888.888888888888888888888888888888876541144442222222222223344444444 PP

                                       HHHHHHHHHHHHCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-S...........SC--TTHHHHHHHH.H CS
                   Phage_integrase  76 alellkellskaleeaeksellfaskrgkplsrqtvrkafkraveeagie...........kpltpHtlRhsfat.a 140
                                       +  +l  + +++ + a+  +  f+ +     s++++r+++++a+e    +             +++H+lR+s+at +
  gi|336254302|ref|YP_004597409.1|  94 IKDMLDIYADER-SIAD--DEPFVDA-----STSSIRRWVSEAAEDVHSNdgkegtrsdrwLSVSSHDLRRSWAThH 162
                                       444444444444.3333..3334444.....5667777777777764444455588889999************945 PP

                                       HHHHCTSHHHHHHHHT-SSCCHHHHHHC CS
                   Phage_integrase 141 LleagvdlrvvqkllGHssisttqiYth 168
                                       L+ + v++rv ++++G+ss + ++ Y +
  gi|336254302|ref|YP_004597409.1| 163 LVDEDVPVRVMMSIGGWSSYEAIEPYLA 190
                                       9********************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1531.93
//
Query:       gi|336254303|ref|YP_004597410.1|  [L=516]
Description: hypothetical protein Halxa_2915 [Halopiger xanaduensis SH-6]
Scores for 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   27.4   0.2    1.3e-05   25.2   0.1    2.1  2  Mrr_cat   Restriction endonuclease
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.56   10.3   0.0    2.1  2  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.18   1.6e+03       5      25 ..     101     121 ..      97     133 .. 0.77
   2 !   25.2   0.1   1.5e-09   1.3e-05      10     111 ..     327     436 ..     321     439 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.18
                                       -TTCHHHHHHHHHHH.HSSSEE CS
                           Mrr_cat   5 spkeFeklvaellea.lGykev 25 
                                       +   Fe+++ ++l++ +G+k v
  gi|336254303|ref|YP_004597410.1| 101 EESMFEQFAVHILQElHGMK-V 121
                                       5678*******999945877.4 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHHHHHSSS....EEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS..SEEE CS
                           Mrr_cat  10 eklvaellealGyk....eveltgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqeligalkkrgadkgi 82 
                                       e l+ ++ + lG +    +v + +++g   +D+++++ +    r+ +q+K  k+  + k+V + +g + + + ++ +
  gi|336254303|ref|YP_004597410.1| 327 ETLAVKIGRMLGLEfagwRV-RGQKTGGSEVDVVMDEVDTTFGRWQIQCKNIKDDLETKHVAREVGIARMLQTNTIL 402
                                       66666666666666654223.444577778********99999****************************999999 PP

                                       EEESS-B-HHHHHHHHTT--.....EEEE-HHHH CS
                           Mrr_cat  83 fvttsdftkaAreeaeelnk.....ieLldgdeL 111
                                        v  s+++ +A+ +a+++ +     i +l gd+L
  gi|336254303|ref|YP_004597410.1| 403 MVARSGLSGDAKLYANRIMRhenisILFLHGDDL 436
                                       9**************8843223455777777777 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   6.3e-05      0.56       3      31 ..     109     137 ..     107     143 .. 0.92
   2 ?   -1.7   0.0      0.37   3.3e+03       9      25 ..     437     453 ..     437     459 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.3e-05
                                       HHHHHHHCSTTHHHHHHHHHHHHSSBEHH CS
                             HTH_9   3 cteiieehFGevvakVvetLlrkgrltlr 31 
                                       +++i++e+ G  v +++e L+++gr+t +
  gi|336254303|ref|YP_004597410.1| 109 AVHILQELHGMKVIQIIEDLMAEGRQTTN 137
                                       689************************87 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.37
                                       HCSTTHHHHHHHHHHHH CS
                             HTH_9   9 ehFGevvakVvetLlrk 25 
                                       ++F+e+++  +etL ++
  gi|336254303|ref|YP_004597410.1| 437 DQFDERPEHLAETLQDE 453
                                       57**********99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 3871.92
//
Query:       gi|336254304|ref|YP_004597411.1|  [L=327]
Description: DNA methylase N-4/N-6 domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-35  120.6   0.0      1e-34  120.3   0.0    1.1  1  N6_N4_Mtase      DNA methylase
  ------ inclusion threshold ------
       0.13   11.8   0.0       0.23   11.0   0.0    1.3  1  Transglut_core2  Transglutaminase-like superfamily


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 !  120.3   0.0   1.1e-38     1e-34       1     230 [.      41     297 ..      41     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 1.1e-38
                                       EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT.........HHHHH CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk.........elkal 68 
                                       +dl vt+pP++++k+     ++ ++++ +ey +++  +++ v+rvL +dgs +i i+    k          el+  
  gi|336254304|ref|YP_004597411.1|  41 IDLLVTSPPFGLQKK-----KEYGNKDPDEYNDWFMDFADRVYRVLTEDGSWVIDIGGGWEKGkpvrsiyhfELLTR 112
                                       79*************.....99999999*****************************99988899****99999999 PP

                                       HHHHTT-EEEEEEEEEEESSSTTTSTCC......S-B--EEEEEEEESSTT-..---GGGSSBSS-HHHHHHHHHH. CS
                       N6_N4_Mtase  69 adeifggffllnvivwkkpnsmpesnkd......rltsthEyilvfsknkkyllkfnldaikvpyeekdklekrga. 138
                                       ++ ++g f l+++  w +p ++p ++++      r +++  +++++sk+++       d ++v +e +d++++    
  gi|336254304|ref|YP_004597411.1| 113 LAGSDGPFHLAQDFYWYNPAKLPTPAQWvtieriRCKDAVNHVWCLSKTERP----EADNVRVLQEYSDSQKELMEn 185
                                       9999999************666666666666667******************....444444444444444443334 PP

                                       ...CHHHCC-B--BSEE....................E-SCCCTTSTTS-CHH......----SS---HHHHHHHHH CS
                       N6_N4_Mtase 139 ...ytskkkgkkiediW....................dlseiqsnekkskgdt......kkkHpaqkPvallerlIk 186
                                           ++ + g++i+d++                     ++ +          +       + Hpa +P++l+ + I+
  gi|336254304|ref|YP_004597411.1| 186 gykDKKRPSGHDISDKFddpkekgsippnlleiantaSNTHYL---------KackkldVDSHPARFPRQLPDFFIR 253
                                       4477889999*******88888888877777555533333333.........0333445689*************** PP

                                       HHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                       N6_N4_Mtase 187 lstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelae 230
                                        ++++gd+vlD FaGS  T+++a+ lgrk++ +e +e+y+++++
  gi|336254304|ref|YP_004597411.1| 254 FLSEPGDTVLDIFAGSNMTGRVAQDLGRKWLAFELQEKYLQTSK 297
                                       ***************************************99875 PP

>> Transglut_core2  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.6e-05      0.23      74     145 ..     227     297 ..     225     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.6e-05
                   Transglut_core2  74 ylevArrlglplegvgfPgh...flvrvgespegevliDPfnaGrllskedleellraalgaeaeltreflapas 145
                                       yl  +++l+++ ++  fP +   f +r+  s+ g+ ++D f+ G+ ++ + +++l r+ l    el++++l+  +
  gi|336254304|ref|YP_004597411.1| 227 YLKACKKLDVDSHPARFPRQlpdFFIRFL-SEPGDTVLDIFA-GSNMTGRVAQDLGRKWLA--FELQEKYLQTSK 297
                                       8999**************986668***99.9999********.*******99999977654..599999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2401.48
//
Query:       gi|336254305|ref|YP_004597412.1|  [L=195]
Description: hypothetical protein Halxa_2917 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.029   14.0   0.1       0.41   10.3   0.0    2.0  2  PapJ      Pilus-assembly fibrillin subunit, chaperone
       0.08   12.8   0.0       0.18   11.7   0.0    1.5  1  HTH_IclR  IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> PapJ  Pilus-assembly fibrillin subunit, chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.013   1.2e+02      72      99 ..       7      34 ..       2      61 .. 0.73
   2 ?   10.3   0.0   4.6e-05      0.41      90     174 ..      63     147 ..      39     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.013
                              PapJ 72 evklpLrkdngkyvLnlklsrCGdGlse 99
                                       v+ +++++n+  vL l +sr G+G  +
  gi|336254305|ref|YP_004597412.1|  7 RVEGTVLNENDALVLDLFVSRGGEGIDL 34
                                      566678899***************9643 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 4.6e-05
                              PapJ  90 lsrCGdGlselpekrsvasynvvvkqslvlkegkddvlLserklsGlsrkvlrdGdnqlvylvnkeqyekiakaqke 166
                                       l  CG+ ++   +  + +++ ++ ++  +  +g+ + lLs  ++sG +r  +++    l  +v++  +    ++ ++
  gi|336254305|ref|YP_004597412.1|  63 LRDCGEDEAAGGGGSPPKQFRMTSSGYTLHARGDLQSLLSVVRGSGEQRAQIEETVWTLQSRVDRVEEMARRDVDTD 139
                                       6789*99999999999999*************************************9******99888777777777 PP

                              PapJ 167 ataeetsd 174
                                       a+ ee+ d
  gi|336254305|ref|YP_004597412.1| 140 AIREEVND 147
                                       77766655 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     2e-05      0.18       8      49 ..      20      64 ..      18      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                                      HHCT-CTTBSS...-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  8 iLdalaeapqe...ltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +Ld++ ++++e   l+ s ++ +tgl+   v + ++ L + Gy++
  gi|336254305|ref|YP_004597412.1| 20 VLDLFVSRGGEgidLNRSNISSATGLTNGQVQHSTNKLANTGYLR 64
                                      78999888888888999**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1450.85
//
Query:       gi|336254306|ref|YP_004597413.1|  [L=41]
Description: hypothetical protein Halxa_2918 [Halopiger xanaduensis SH-6]
Scores for 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:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 327.21
//
Query:       gi|336254307|ref|YP_004597414.1|  [L=572]
Description: hypothetical protein Halxa_2919 [Halopiger xanaduensis SH-6]
Scores for 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-07   29.0   0.0    3.4e-06   26.5   0.0    2.2  2  HTH_24    Winged helix-turn-helix DNA-binding
    5.5e-06   26.0   0.1      2e-05   24.2   0.0    1.9  2  HTH_23    Homeodomain-like domain
    1.1e-05   25.4   0.0    3.2e-05   23.8   0.0    1.8  1  HTH_29    Winged helix-turn helix
     0.0013   18.8   0.0      0.003   17.7   0.0    1.6  1  HTH_28    Helix-turn-helix domain
     0.0016   18.3   0.0     0.0057   16.5   0.0    1.9  2  MarR_2    MarR family
     0.0039   17.1   0.0     0.0083   16.1   0.0    1.5  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.028   14.4   0.0    1.4  1  HTH_11    HTH domain
      0.054   13.6   0.0       0.13   12.3   0.0    1.6  1  HTH_20    Helix-turn-helix domain
       0.11   12.3   0.0       0.23   11.3   0.0    1.5  1  TrmB      Sugar-specific transcriptional regulator TrmB
       0.13   12.7   0.1       0.59   10.5   0.0    2.1  2  FaeA      FaeA-like protein


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 !   26.5   0.0   1.9e-09   3.4e-06       6      48 .]     405     449 ..     405     449 .. 0.97
   2 ?   -0.8   0.0      0.65   1.2e+03       9      24 ..     555     570 ..     552     572 .] 0.86

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.9e-09
                            HTH_24   6 rkILelLqk..nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       r+IL +L++  + + +++e+ +++gl   tv+ +++r+ e+G+I+
  gi|336254307|ref|YP_004597414.1| 405 RDILLVLYErgDQGATYQEIMDKTGLAYDTVRNYIRRFNEAGIIR 449
                                       78******************************************7 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.65
                            HTH_24   9 LelLqknprisqreLA 24 
                                       L++ +++++i+ +++A
  gi|336254307|ref|YP_004597414.1| 555 LKVAREHGDITDTDIA 570
                                       88899*********99 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.9     7e+03      19      39 ..     312     332 ..     301     335 .. 0.71
   2 !   24.2   0.0   1.1e-08     2e-05      14      46 ..     412     447 ..     405     450 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.9
                            HTH_23  19 svreIAreLgvsrrTvyrwlk 39 
                                       ++ e+A++  v+rr ++ +++
  gi|336254307|ref|YP_004597414.1| 312 PKIEAAAKGTVHRRYLDEVRH 332
                                       566777777789998877765 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1.1e-08
                            HTH_23  14 lae...GlsvreIAreLgvsrrTvyrwlkryreeGl 46 
                                       + +   G++++eI ++ g  + Tv+++++r++e G+
  gi|336254307|ref|YP_004597414.1| 412 YERgdqGATYQEIMDKTGLAYDTVRNYIRRFNEAGI 447
                                       443445***************************997 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.8e-08   3.2e-05      12      41 ..     416     447 ..     407     456 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.8e-08
                            HTH_29  12 vs..tvsqiAkllglsrrtvyrwlkrfeegGl 41 
                                           t ++i+  +gl ++tv+++++rf+e G+
  gi|336254307|ref|YP_004597414.1| 416 DQgaTYQEIMDKTGLAYDTVRNYIRRFNEAGI 447
                                       33459**************************6 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.7e-06     0.003      11      41 ..     417     447 ..     407     453 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-06
                            HTH_28  11 aGhsvreaArelgisrrtvyrWikryeegGi 41 
                                       +G ++ e++ + g+ ++tv+  i+r++e Gi
  gi|336254307|ref|YP_004597414.1| 417 QGATYQEIMDKTGLAYDTVRNYIRRFNEAGI 447
                                       455***************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       3.2   5.8e+03       7      36 ..     323     361 ..     322     362 .. 0.65
   2 !   16.5   0.0   3.2e-06    0.0057       8      56 ..     405     453 ..     401     454 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.2
                                       HHHHHHHHHCTTTS.........EEEHHHHHHHHTSSHH CS
                            MarR_2   7 qarvLaaLgrrpgr.........dltvgelarrlglsks 36 
                                       ++r L +++++  r          l +++l+  l+ + +
  gi|336254307|ref|YP_004597414.1| 323 HRRYLDEVRHHLARicighlrfaGLDANALVSDLHFTAQ 361
                                       678888888887776666665554566666666666655 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.2e-06
                                       HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2   8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                       +++L++L+ r+++  t +e+ +++gl   +v + ++r+ +aG ++++pg
  gi|336254307|ref|YP_004597414.1| 405 RDILLVLYERGDQGATYQEIMDKTGLAYDTVRNYIRRFNEAGIIRKTPG 453
                                       699*********989*******************************987 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.6e-06    0.0083       1      61 [.     397     461 ..     397     471 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                            HTH_45   1 rRskleIiadILeais...egeakkTkimykanLsykllnkYLdmLvekglikk.skekYvlTek 61 
                                       rR +++ + dIL ++    +++a+  +im k  L y+++++Y+    e g+i+k  ++  v+T k
  gi|336254307|ref|YP_004597414.1| 397 RRRQTNSFRDILLVLYergDQGATYQEIMDKTGLAYDTVRNYIRRFNEAGIIRKtPGTPLVITWK 461
                                       566677777888777642245566679*************************6637777888865 PP

>> HTH_11  HTH 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     0.028       3      51 ..     405     453 ..     405     454 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                            HTH_11   3 lqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51 
                                       ++il  L+e  ++  + +e+++++++   tvr++I++ +e+g  I ++pg
  gi|336254307|ref|YP_004597414.1| 405 RDILLVLYERGDQgATYQEIMDKTGLAYDTVRNYIRRFNEAG-IIRKTPG 453
                                       689***************************************.7877777 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.2e-05      0.13      13      57 ..     405     451 ..     401     453 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.2e-05
                                       HHHHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  13 rrilraL..araegltaselaerldlskntlsyHLrvLeeagLvevv 57 
                                       r+il  L  ++++g+t  e+++  +l+  t+++ +r   eag+++ +
  gi|336254307|ref|YP_004597414.1| 405 RDILLVLyeRGDQGATYQEIMDKTGLAYDTVRNYIRRFNEAGIIRKT 451
                                       89999***************************************976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.23      22      64 ..     418     460 ..     407     464 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                       CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                              TrmB  22 patadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64 
                                        at +ei  ++g+ + +v +++r+  ++G++++ +g+p +   
  gi|336254307|ref|YP_004597414.1| 418 GATYQEIMDKTGLAYDTVRNYIRRFNEAGIIRKTPGTPLVITW 460
                                       6899*********************************988765 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.5   4.5e+03      32      38 ..     175     181 ..     163     185 .. 0.50
   2 ?   10.5   0.0   0.00033      0.59      15      49 ..     418     452 ..     405     457 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.5
                                       HHHHHHH CS
                              FaeA  32 aRyYLeq 38 
                                       aR YL  
  gi|336254307|ref|YP_004597414.1| 175 ARIYLRA 181
                                       4555555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00033
                                       ---HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE- CS
                              FaeA  15 pckTreiAdalglsaYQaRyYLeqLekegkikrsp 49 
                                       +++ +ei d +gl+   +R Y+   + +g i+++p
  gi|336254307|ref|YP_004597414.1| 418 GATYQEIMDKTGLAYDTVRNYIRRFNEAGIIRKTP 452
                                       55668*********99*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 00:00:00.45
# Mc/sec: 3857.22
//
Query:       gi|336254308|ref|YP_004597415.1|  [L=383]
Description: integrase protein [Halopiger xanaduensis SH-6]
Scores for 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-07   29.2   0.0    2.9e-06   27.2   0.0    2.0  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
      0.066   13.7   2.6         40    4.8   0.0    3.9  5  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
      0.082   13.2   0.3        2.6    8.4   0.0    3.0  3  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 !   27.2   0.0   4.8e-10   2.9e-06       2     119 ..     153     282 ..     152     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.8e-10
                                       HHHHHHHHHHHHCCGC.HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEE.......EEECSSSSE..E CS
                   Phage_integrase   2 vltedeverllaalee.slkirdklllellyetGlRisEllsLrvkdldlengvilvh.......eregKgske..r 68 
                                       vl+++ v+++l++l++   ++r+  + el  + G R + ++sL+v+d +  ++  +++       e+ +K++k+  r
  gi|336254308|ref|YP_004597415.1| 153 VLDSETVKQILEHLRKyEYATREHVIWELFASAGPRLGGIRSLDVDDYERGDSGPYLKlrhrpdtETTLKNGKDgeR 229
                                       7999************9999999**************************99999999999****999999999999* PP

                                       EEECTHHHHHHHHHHHHHH...CHCCTTTSBSSBETTSSB--HHHHHHHHHHHH CS
                   Phage_integrase  69 avplseealellkellska...leeaeksellfaskrgkplsrqtvrkafkrav 119
                                       +v +se+++e+l ++++++   +e + ++e l+ sk + +l ++t+r ++ ++ 
  gi|336254308|ref|YP_004597415.1| 230 NVFISESLAEVLDDYIKDQredSEDKFGREPLLSSK-QGRLAESTIRNYVYAWT 282
                                       ******************966555556666666666.77888888887776655 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 ?    4.8   0.0    0.0067        40       3      34 ..      40      71 ..      39     100 .. 0.73
   2 ?    4.1   0.0     0.011        65      10      34 ..     101     125 ..      94     135 .. 0.88
   3 ?   -2.9   0.0       1.7   9.9e+03      25      43 ..     158     174 ..     155     178 .. 0.54
   4 ?    1.9   0.0     0.052   3.1e+02      13      25 ..     268     280 ..     263     285 .. 0.84
   5 ?   -2.5   0.1       1.2   7.3e+03       6      23 ..     346     363 ..     344     374 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0067
                   Phage_int_SAM_4  3 erfrealrlaglserTiksYlsaikrflrflk 34
                                      e++ e+ ++++l+++T + + s +  f+++ +
  gi|336254308|ref|YP_004597415.1| 40 EAVNEYFKVRDLKPKTKNKHESSLGFFVDWGE 71
                                      67778888888888888888888888877766 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.011
                   Phage_int_SAM_4  10 rlaglserTiksYlsaikrflrflk 34 
                                       ++++ls++T+++ +  ++ f++ + 
  gi|336254308|ref|YP_004597415.1| 101 QVDELSPKTEETEQKIVRKFIKVCG 125
                                       5789*****************9886 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.7
                   Phage_int_SAM_4  25 aikrflrflkkkapeeltk 43 
                                       ++k++l++l+  + e  t+
  gi|336254308|ref|YP_004597415.1| 158 TVKQILEHLR--KYEYATR 174
                                       5666666665..3444444 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.052
                   Phage_int_SAM_4  13 glserTiksYlsa 25 
                                       +l+e+Ti++Y++a
  gi|336254308|ref|YP_004597415.1| 268 RLAESTIRNYVYA 280
                                       689*******986 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 1.2
                   Phage_int_SAM_4   6 realrlaglserTiksYl 23 
                                        e++  +++ +rT+   +
  gi|336254308|ref|YP_004597415.1| 346 SEKILEKHYDKRTEAEKM 363
                                       566666788888876555 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 ?    8.4   0.0   0.00044       2.6       7      61 ..      44     105 ..      42     125 .. 0.84
   2 ?   -2.7   0.0       1.2   7.4e+03      46      58 ..     156     168 ..     148     176 .. 0.52
   3 ?    1.0   0.1     0.089   5.3e+02      10      24 ..     265     279 ..     263     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00044
                                       HHHHTT-S-HHHHHHHHHHHHHHHHHHHH..TS--TTT--HHHHHHHHHS-----......- CS
                   Phage_int_SAM_1   7 yLikerglspnTlraYrrdLrrflkflae.rgkesleqlttedvraflaeleeeg......l 61 
                                       + +k+r l p+T + ++  L  f+++ +  +g++ ++ l+ +d+ ++ ++++ee       l
  gi|336254308|ref|YP_004597415.1|  44 EYFKVRDLKPKTKNKHESSLGFFVDWGENvAGISEMNFLSGSDLKDYRVWRREESseqvdeL 105
                                       56789*******************************************99999865555555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                                       HHHHHHHHHS--- CS
                   Phage_int_SAM_1  46 tedvraflaelee 58 
                                        e v ++l++l++
  gi|336254308|ref|YP_004597415.1| 156 SETVKQILEHLRK 168
                                       4444444444444 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.089
                                       HTT-S-HHHHHHHHH CS
                   Phage_int_SAM_1  10 kerglspnTlraYrr 24 
                                       k+ +l++ T+r+Y++
  gi|336254308|ref|YP_004597415.1| 265 KQGRLAESTIRNYVY 279
                                       688999*******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); 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:                         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 0.24s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2671.42
//
Query:       gi|336254309|ref|YP_004597416.1|  [L=339]
Description: integrase protein [Halopiger xanaduensis SH-6]
Scores for 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-06   26.8   0.1    4.6e-05   23.3   0.1    2.2  1  Phage_integrase  Phage integrase family
    6.3e-06   26.4   0.3    2.6e-05   24.4   0.1    2.2  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    3.1e-05   24.3   0.1    0.00067   20.1   0.1    2.5  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    0.00014   22.1   0.0    0.00035   20.8   0.0    1.7  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 !   23.3   0.1     1e-08   4.6e-05       3     153 ..     123     307 ..     122     310 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1e-08
                                       HHHHHHHHHHHCCGC.HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEE.....EEECSSSSE..EEEE CS
                   Phage_integrase   3 ltedeverllaalee.slkirdklllellyetGlRisEllsLrvkdldlengvilvh.....eregKgske..ravp 71 
                                       l  + +e++l++l +   + r  ++l+l + t lR + +++ +++d + e++++ +       + +K++ e  r v+
  gi|336254309|ref|YP_004597416.1| 123 LNREHAEAILDHLSKyEYASRAHIVLALQWHTMLRRGAVRAADLQDYHSEDQCLEIRhrpetGTPLKNQEEgeRMVA 199
                                       6678899******997777777888*******************************99999977788877777**** PP

                                       CTHHHHHHHHHHHHHH...CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-S.................... CS
                   Phage_integrase  72 lseealellkellska...leeaeksellfaskrgkplsrqtvrkafkraveeagie.................... 125
                                       ls  ++ ll ++++ +   ++ + +++ l   k + ++   tv  +  +  +  +i+                    
  gi|336254309|ref|YP_004597416.1| 200 LSAPICDLLDDWIDSQrpeVVDEYGRDPLVSTK-QGRIHPVTVTSITYARTRPCDIDapcplnrdpdeceagsyqga 275
                                       **************9988655555555444433.3333333333333333333233333333333333333334444 PP

                                       ....SC--TTHHHHHHHHHHHHHCTSHHHHHH CS
                   Phage_integrase 126 ....kpltpHtlRhsfataLleagvdlrvvqk 153
                                           + +++H  R+ + t  l++ v+++vv++
  gi|336254309|ref|YP_004597416.1| 276 skcpESVSSHAVRRGAITYHLQSDVPTEVVAE 307
                                       45667777777777777777777777777765 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 !   24.4   0.1   5.8e-09   2.6e-05       4      80 ..      16      93 ..      13      97 .. 0.87
   2 ?   -1.3   0.0      0.63   2.8e+03      44      65 ..     123     142 ..      94     152 .. 0.61

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.8e-09
                                      HHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH..TS--TTT--HHHHHHHHHS-----..-----HHHHHHHHHHHHHH CS
                   Phage_int_SAM_1  4 fleyLikerglspnTlraYrrdLrrflkflae.rgkesleqlttedvraflaeleeeg..lsatslarrlsalrsFfqf 79
                                      +l++    r++s+ Tlr++r +L +f+++ +e + + +l++lt +++++f  ++ + +   +  + +  + +lr F +f
  gi|336254309|ref|YP_004597416.1| 16 YLDHR--RREVSESTLRSHRSRLGHFIRWCNEeKSIDNLNELTGRNLHEFRLWRTNMNggIAPVTEKTQMDTLRVFIRF 92
                                      55554..499**********************899999999999999998888887777899999999********999 PP

                                      H CS
                   Phage_int_SAM_1 80 l 80
                                      l
  gi|336254309|ref|YP_004597416.1| 93 L 93
                                      8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.63
                                       --HHHHHHHHHS---------- CS
                   Phage_int_SAM_1  44 lttedvraflaeleeeglsats 65 
                                       l++e+  a+l++l +  +  +s
  gi|336254309|ref|YP_004597416.1| 123 LNREHAEAILDHLSK--YEYAS 142
                                       466777777777777..33333 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 !   20.1   0.1   1.5e-07   0.00067      10      76 ..      20      91 ..      11      95 .. 0.85
   2 !    7.7   0.0    0.0011         5      12      34 ..      72      94 ..      60     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.5e-07
                   Phage_int_SAM_4 10 rlaglserTiksYlsaikrflrflkkk....apeeltkedieaYlnyLanerk.lsastqknalnalsffyk 76
                                      r ++ se+T +s+ s + +f+r++++     + +elt + + ++  +  n +   ++ t k+ +  l++f +
  gi|336254309|ref|YP_004597416.1| 20 RRREVSESTLRSHRSRLGHFIRWCNEEksidNLNELTGRNLHEFRLWRTNMNGgIAPVTEKTQMDTLRVFIR 91
                                      5699********************9435788999***************88879999999999999998866 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0011
                   Phage_int_SAM_4 12 aglserTiksYlsaikrflrflk 34
                                       g+++ T+k+ + +++ f+rfl+
  gi|336254309|ref|YP_004597416.1| 72 GGIAPVTEKTQMDTLRVFIRFLE 94
                                      68999*****************8 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 !   20.8   0.0   7.9e-08   0.00035       7      81 ..      14      91 ..      11     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7.9e-08
                                      HHHTHHHHTTS-HHHHHHHHHHHHHTTTS-..S-..--TTT--HHHHHHHHHHH.HHTS---HHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_5  7 keyiekkkkkgskgtlrnykstlkhlkkFlkkkd..itfeeidkefleeFedYL.kkkkglsentiskyfkklkavln 81
                                      + y+++++++ s++tlr+++s l h+ +++++++   +++e++ + l+eF+ +  + + g+++ t ++++ +l+ +++
  gi|336254309|ref|YP_004597416.1| 14 QLYLDHRRREVSESTLRSHRSRLGHFIRWCNEEKsiDNLNELTGRNLHEFRLWRtNMNGGIAPVTEKTQMDTLRVFIR 91
                                      66889999999*******************65444568****************877889999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2567.61
//
Query:       gi|336254310|ref|YP_004597417.1|  [L=152]
Description: hypothetical protein Halxa_2922 [Halopiger xanaduensis SH-6]
Scores for 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:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1282.27
//
Query:       gi|336254311|ref|YP_004597418.1|  [L=50]
Description: hypothetical protein Halxa_2923 [Halopiger xanaduensis SH-6]
Scores for 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:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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: 0.31u 0.21s 00:00:00.52 Elapsed: 00:00:00.33
# Mc/sec: 454.22
//
Query:       gi|336254312|ref|YP_004597419.1|  [L=139]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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  119.6   2.7    1.5e-34  119.5   2.7    1.0  1  Usp           Universal stress protein family
     0.0081   15.6   0.3     0.0099   15.3   0.3    1.2  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.051   14.3   0.1       0.12   13.0   0.0    1.8  2  PTS_IIB       PTS system, Lactose/Cellobiose specific IIB sub


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 !  119.5   2.7   2.6e-38   1.5e-34       1     140 [.       1     137 [.       1     138 [. 0.98

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 2.6e-38
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+ +lVa+Dgs+++++A+++A+ la++++ +l+ + v+++r+ +  +  d+e+++ +  ++++   ad    +a+a
  gi|336254312|ref|YP_004597419.1|   1 MYDSVLVATDGSDTATAAVDHAITLARQFDIPLYGIVVLESRTEYDNAIVDPEEADRRRRQRAESVLAD---LEAAA 74 
                                       9***************************************************************99998...6**** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       +g + e++++ g p eeil +a e+dad iV+Gsrgrs+++++llGS+ ++v+r+a+ pVlvV
  gi|336254312|ref|YP_004597419.1|  75 EGLALETTIRTGVPHEEILTYAAEQDADVIVIGSRGRSSFKGALLGSTVDAVVRQAERPVLVV 137
                                       **************************************************************9 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 !   15.3   0.3   1.7e-06    0.0099      57     154 ..       8     102 ..       1     107 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-06
                                       THCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCC.......GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSE CS
                      AP_endonuc_2  57 dederearreesvdalkraielaaaLGapllvlhpGt.......agagpkgseeeawerlaeslneladyaekegvk 126
                                        +d  +++     +a+ +ai la+++++pl  + +         a   p++ ++ +++r+ ++l +l + ae     
  gi|336254312|ref|YP_004597419.1|   8 ATDGSDTA----TAAVDHAITLARQFDIPLYGIVVLEsrteydnAIVDPEEADRRRRQRAESVLADLEAAAE----G 76 
                                       44455556....9*****************777766677799998888999999*************99998....7 PP

                                       EEEE--TTTTSSSTCHHHHHHHHHHTTT CS
                      AP_endonuc_2 127 lalEtlagsgvelgdeelarlldavdsp 154
                                       lalEt+ ++gv +  ee++    + d +
  gi|336254312|ref|YP_004597419.1|  77 LALETTIRTGV-PH-EEILTYAAEQDAD 102
                                       9****999996.66.7887777776666 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.77   4.6e+03      55      55 ..      19      19 ..       2      53 .. 0.55
   2 ?   13.0   0.0   2.1e-05      0.12      13      58 ..      65     111 ..      62     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.77
                                      E CS
                           PTS_IIB 55 p 55
                                       
  gi|336254312|ref|YP_004597419.1| 19 V 19
                                      2 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHHHHHCTEEEEETTEE...GGGHHHHHHT-SEEEEEESSG CS
                           PTS_IIB  13 Slmaaeklekaakelgieaegeagv...eleaeeiaddaDlvllapqvr 58 
                                       S++a   le aa+ l +e+++ +gv   e+  ++ ++daD+++++   r
  gi|336254312|ref|YP_004597419.1|  65 SVLA--DLEAAAEGLALETTIRTGVpheEILTYAAEQDADVIVIGSRGR 111
                                       6666..8999***************9997777777777******99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1092.05
//
Query:       gi|336254313|ref|YP_004597420.1|  [L=71]
Description: hypothetical protein Halxa_2925 [Halopiger xanaduensis SH-6]
Scores for 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:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 576.18
//
Query:       gi|336254314|ref|YP_004597421.1|  [L=288]
Description: hypothetical protein Halxa_2926 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        8.4    4.5  13.4         13    3.8  13.4    1.3  1  Nop14     Nop14-like family


Domain annotation for each model (and alignments):
>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8  13.4   0.00075        13     298     407 ..     126     234 ..     109     269 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.00075
                             Nop14 298 edeeeeeekkkkkkkeasaDdldddfvleeeeeeeefglgkglka....taeeeeeededdfeedddlveseseeee 370
                                       +d+ e e+k+ +++++ saD+  ++ + +e +++   g  ++l++          +    df++d ++ +++ e+  
  gi|336254314|ref|YP_004597421.1| 126 DDSVEAESKSGDESAASSADEDSNGAEADEATSDA-GGGTSDLEErlrsA----MSSSLTDFSDDVSQLQERLEALG 197
                                       44444444444444447899888888888766555.33234443233321....22333333333333333333222 PP

                             Nop14 371 ...eeeeedeeeeedeeeeeeeeededdlsdleseeeeee 407
                                          + +e++   e+de+++ e+  ++ ++ ++e+ ++e++
  gi|336254314|ref|YP_004597421.1| 198 gggDADESEAAGESDESAAAES--ESGSEPEDEA-SDESD 234
                                       2222222222222222222222..1111111111.22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.37
# Mc/sec: 2354.30
//
Query:       gi|336254315|ref|YP_004597422.1|  [L=337]
Description: hypothetical protein Halxa_2927 [Halopiger xanaduensis SH-6]
Scores for 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  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1673  (0.0933125); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                       164  (0.00914719); expected 17.9 (0.001)
Passed Fwd filter:                        91  (0.00507558); 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: 1.55u 0.38s 00:00:01.93 Elapsed: 00:00:00.50
# Mc/sec: 2010.69
//
Query:       gi|336254316|ref|YP_004597423.1|  [L=195]
Description: hypothetical protein Halxa_2928 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        2.4    7.4  50.8        3.4    6.9  50.8    1.3  1  BUD22          BUD22
        2.7    7.5  19.5        2.9    7.3  19.5    1.2  1  Lin-8          Ras-mediated vulval-induction antagonist


Domain annotation for each model (and alignments):
>> BUD22  BUD22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  50.8   0.00038       3.4     133     256 ..      79     191 ..      56     195 .] 0.31

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00038
                             BUD22 133 kllgiekkkkkkeeekkkkkkkkkkkkkkeeeeeeesdkeeesedsedeekeeseddeeeeeededdedaee.deed 208
                                       +llg  +      e+++++++++++++++      e+++e+ese+++++e+e+ ++de+e+ee+   ed+ + ++++
  gi|336254316|ref|YP_004597423.1|  79 ELLGTTE------EDEDESEAEESDAEED------EEGAEDESEGEKETEDEAGDEDESEDEEET--EDEADeSADE 141
                                       3333333......1111111111111111......222333333333312222222222222222..2222211222 PP

                             BUD22 209 eeaeerelaqydgllasddeded..eyneetdeesseesdssdssesase 256
                                       + +ee+  ++ d+ l+s d+de+  +++e +d+++s+e d +d++e+a e
  gi|336254316|ref|YP_004597423.1| 142 DTDEEQTDESTDDELESADDDESeaDESETSDDSDSSEGDAEDADEEAAE 191
                                       22222223333334444444444112333333333333333333333333 PP

>> Lin-8  Ras-mediated vulval-induction antagonist
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  19.5   0.00033       2.9     143     259 ..      74     189 ..       9     194 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00033
                             Lin-8 143 diiyegyleaeegedteeeekveveeeaeeqgsmdlketeaeevkeeqmeqsfeeeeeakleeptvniveeeaaara 219
                                       d+ +e++l + e+   +e+e+  +e+ aee+++   +e+e e++ e +   ++e+e+e+++e +  ++++e +++++
  gi|336254316|ref|YP_004597423.1|  74 DMVVEELLGTTEE---DEDESEAEESDAEEDEEGAEDESEGEKETEDEAGDEDESEDEEETEDEADESADEDTDEEQ 147
                                       5555554333222...3333333344444444444345555555555555555566777777777777777777777 PP

                             Lin-8 220 vdqsfgsaeqql..essssrtssassssssaapsstaakdfe 259
                                       +d+s+ ++ +    ++s+++ s++s +s+s++   ++a++ +
  gi|336254316|ref|YP_004597423.1| 148 TDESTDDELESAddDESEADESETSDDSDSSEGDAEDADEEA 189
                                       777777666666334444444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1670  (0.0931452); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                       252  (0.0140554); expected 17.9 (0.001)
Passed Fwd filter:                       116  (0.00646996); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.30u 0.35s 00:00:01.65 Elapsed: 00:00:00.50
# Mc/sec: 1178.96
//
Query:       gi|336254317|ref|YP_004597424.1|  [L=507]
Description: hypothetical protein Halxa_2929 [Halopiger xanaduensis SH-6]
Scores for 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  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2098  (0.117017); expected 358.6 (0.02)
Passed bias filter:                      799  (0.0445647); expected 358.6 (0.02)
Passed Vit filter:                       405  (0.0225891); expected 17.9 (0.001)
Passed Fwd filter:                       225  (0.0125495); 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: 2.99u 0.39s 00:00:03.38 Elapsed: 00:00:00.67
# Mc/sec: 2297.08
//
Query:       gi|336254318|ref|YP_004597425.1|  [L=445]
Description: Pyrrolo-quinoline quinone repeat-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-13   49.0   8.6    2.6e-07   30.5   1.2    2.6  2  PQQ_2     PQQ-like domain
    7.6e-09   35.1   6.2    7.4e-05   22.5   0.1    4.7  5  PQQ       PQQ enzyme repeat
      1e-06   29.0  21.2       0.04   14.4   0.1    7.3  8  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.5   1.3e-08   7.6e-05      17      90 ..      81     169 ..      51     186 .. 0.67
   2 !   30.5   1.2   4.4e-11   2.6e-07      46     219 ..     185     375 ..     180     400 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.3e-08
                             PQQ_2  17 Wrvdlarp.........lgggvsravlsggtlfva..tgggrlvaldaatGkvlWettlegpvvgaplvaegrv... 79 
                                       W+vd+  p           gg +     + t++va  +++g ++++da+tG+++W+++  + v ++  v++      
  gi|336254318|ref|YP_004597425.1|  81 WTVDH--PdhavgiaslEAGGAESDGGTAETIVVAgrGDSGAIAGYDAETGEQRWRYDTAADVGEP--VEDSVFylp 153
                                       66654..122344444544455445556778888867899**********************9999..555555555 PP

                             PQQ_2  80 vvva.....sdgqlia 90 
                                       +vva     + gql+a
  gi|336254318|ref|YP_004597425.1| 154 YVVAleadaETGQLYA 169
                                       4444443333334444 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 4.4e-11
                             PQQ_2  46 grlvaldaatGkvlWettl.egpvvgaplvaegrvvvva.......sdgqlialdaedGkrlWstqqrseepae.lr 113
                                        +++a++ ++G+v+W+++   +p+  +   +++r+ +v         d  l+ l++e+G++ W+ +  +    e  r
  gi|336254318|ref|YP_004597425.1| 185 STVYAFE-SDGTVRWRYETdASPIAMDLAADGERL-AVGynrcmgdHDTGLVVLETESGTLEWTWDPGT----EgDR 255
                                       5899998.***********6667777755555555.4444888866777***************44444....4478 PP

                             PQQ_2 114 ssaspavagdtvvvgessgklvaldpkdGkvlWerelaaprgtsels.........rvgdisgrpvvaegtVyassg 181
                                       ++++ +++g+tv+v+ ++ k   l    G ++W   la p+   +++          v  ++gr+ ++ g++ya + 
  gi|336254318|ref|YP_004597425.1| 256 RVGDVSFDGETVAVASHGDKRGYLLGPGGAERWRVDLAVPT---DIDgetlyaypnHVHANDGRVAFVTGNTYAEES 329
                                       8***************987777777788*********9999...333224556666666666666666666666665 PP

                             PQQ_2 182 qg.........rllaldlatgrrlwskeissinglpildgdllyvvs 219
                                        +         r++a+d + + +lw +++ ++++  +++gd l+   
  gi|336254318|ref|YP_004597425.1| 330 REtenchpnehRIAAFDREAT-PLWDDAVRGFVHGLAAEGDRLVAPC 375
                                       554444444333566676666.4887778877666888887777555 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   1.2e-08   7.4e-05       2      32 ..     110     141 ..     109     144 .. 0.91
   2 ?   -2.8   0.0       1.3   7.5e+03      16      21 ..     161     166 ..     154     167 .. 0.75
   3 !   11.9   0.0   2.7e-05      0.16       9      32 ..     184     206 ..     180     209 .. 0.85
   4 ?   -1.2   0.2      0.38   2.3e+03       9      27 ..     230     248 ..     227     253 .. 0.79
   5 ?   -2.4   0.0      0.91   5.5e+03      20      28 ..     284     292 ..     284     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.2e-08
                                       EEEEE.ETTSEEEEEETTTCCEEEEEESSSCG CS
                               PQQ   2 vvylg.sadGylyAlDadTGkvlWrfktggpv 32 
                                        v++g  + G +  +Da+TG+ +Wr++t ++v
  gi|336254318|ref|YP_004597425.1| 110 IVVAGrGDSGAIAGYDAETGEQRWRYDTAADV 141
                                       588999*********************98876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.3
                                       ETTTCC CS
                               PQQ  16 DadTGk 21 
                                       Da+TG+
  gi|336254318|ref|YP_004597425.1| 161 DAETGQ 166
                                       888886 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 2.7e-05
                                       TSEEEEEETTTCCEEEEEESSSCG CS
                               PQQ   9 dGylyAlDadTGkvlWrfktggpv 32 
                                       + ++yA+  ++G+v+Wr++t++ +
  gi|336254318|ref|YP_004597425.1| 184 HSTVYAFE-SDGTVRWRYETDASP 206
                                       5689****.***********9866 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.38
                                       TSEEEEEETTTCCEEEEEE CS
                               PQQ   9 dGylyAlDadTGkvlWrfk 27 
                                       d+ l+ l  ++G++ W+ +
  gi|336254318|ref|YP_004597425.1| 230 DTGLVVLETESGTLEWTWD 248
                                       56678899999*****855 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 0.91
                                       CCEEEEEES CS
                               PQQ  20 GkvlWrfkt 28 
                                       G ++Wr+++
  gi|336254318|ref|YP_004597425.1| 284 GAERWRVDL 292
                                       899***986 PP

>> PQQ_3  PQQ-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     3e+03      23      38 ..      44      59 ..      34      60 .. 0.81
   2 ?    4.1   0.6     0.012        72       2      40 .]      78     128 ..      78     128 .. 0.64
   3 !   10.1   0.1   0.00016      0.94       1      36 [.     129     190 ..     129     193 .. 0.69
   4 !   14.4   0.1   6.7e-06      0.04       1      39 [.     194     239 ..     194     240 .. 0.84
   5 ?    1.9   0.8     0.057   3.4e+02       1      29 [.     241     272 ..     241     280 .. 0.76
   6 !    7.0   0.0    0.0014       8.5       1      38 [.     284     347 ..     284     348 .. 0.68
   7 ?   -0.7   0.0      0.37   2.2e+03       4      39 ..     352     385 ..     350     386 .. 0.69
   8 ?   -1.7   0.0      0.79   4.7e+03      16      35 ..     410     420 ..     390     422 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.51
                             PQQ_3 23 lvyvgtgdGtlyAlDa 38
                                      l+++g +dG ++A++ 
  gi|336254318|ref|YP_004597425.1| 44 LLVAGRWDGIVTAYER 59
                                      6888888999999975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.012
                             PQQ_3   2 evlWsvqlpg.pvn.ssp....avdgg....lvyvgtg..dGtlyAlDaet 40 
                                       e++W+v+ p+ +v+ +s+    a ++g    +++v++    G +  +Daet
  gi|336254318|ref|YP_004597425.1|  78 EPRWTVDHPDhAVGiASLeaggAESDGgtaeTIVVAGRgdSGAIAGYDAET 128
                                       579999888863333666777733333344445555556999999999998 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00016
                             PQQ_3   1 GevlWsvqlpgpvnssp.........avd......gglvyvgtg...........dGtlyAl 36 
                                       Ge++W++++ ++v+ ++         +v+       g +y+++              t+yA+
  gi|336254318|ref|YP_004597425.1| 129 GEQRWRYDTAADVGEPVedsvfylpyVVAleadaeTGQLYAAARryerdgetrqwHSTVYAF 190
                                       9******9988885544777688888444445555688888887777777777777777766 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 6.7e-06
                             PQQ_3   1 GevlWsvqlpg.pvnsspavdgglvyvgtg......dGtlyAlDae 39 
                                       G+v+W++++++ p+   +a+dg ++ vg        d +l+ l++e
  gi|336254318|ref|YP_004597425.1| 194 GTVRWRYETDAsPIAMDLAADGERLAVGYNrcmgdhDTGLVVLETE 239
                                       9********999************9998767777777777777766 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.057
                             PQQ_3   1 GevlWsv..qlpg.pvnsspavdgglvyvgtg 29 
                                       G++ W+   ++ g + ++ + +dg +v v+++
  gi|336254318|ref|YP_004597425.1| 241 GTLEWTWdpGTEGdRRVGDVSFDGETVAVASH 272
                                       78889997755444666899*******99998 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.0014
                             PQQ_3   1 GevlWsvql..pgpvnssp.........avdgglvyvgtg...............dGtlyAlDa 38 
                                       G ++W+v+l  p ++ + +         a dg++ +v++                 +++ A+D 
  gi|336254318|ref|YP_004597425.1| 284 GAERWRVDLavPTDIDGETlyaypnhvhANDGRVAFVTGNtyaeesretenchpnEHRIAAFDR 347
                                       889****664466777777555556665666667777666777777777777777777777775 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 0.37
                             PQQ_3   4 lWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       lW   + g v  ++a+ g+++++ +   +++  D+e
  gi|336254318|ref|YP_004597425.1| 352 LWDDAVRGFV-HGLAAEGDRLVAPCA-QNFRVRDPE 385
                                       6666666655.578999999999887.666666665 PP

  == domain 8  score: -1.7 bits;  conditional E-value: 0.79
                             PQQ_3  16 spavdgglvyvgtgdGtlyA 35 
                                       ++a+d         d tl A
  gi|336254318|ref|YP_004597425.1| 410 AAATD---------DETLAA 420
                                       33444.........555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3188.90
//
Query:       gi|336254319|ref|YP_004597426.1|  [L=125]
Description: hypothetical protein Halxa_2931 [Halopiger xanaduensis SH-6]
Scores for complete 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  187.0   2.7    1.6e-55  186.8   2.7    1.0  1  DUF3209       Protein of unknown function (DUF3209)
  ------ inclusion threshold ------
      0.028   13.9   0.0      0.033   13.7   0.0    1.0  1  IcmF-related  Intracellular multiplication and human macropha


Domain annotation for each model (and alignments):
>> DUF3209  Protein of unknown function (DUF3209)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.8   2.7   1.8e-59   1.6e-55       1     124 []       1     122 [.       1     122 [. 0.99

  Alignments for each domain:
  == domain 1  score: 186.8 bits;  conditional E-value: 1.8e-59
                                       ---HHHHHHHHHHHHHTT.--GGGCHHHHHHHTTTTTT-HHHHHHHH--SHHHHHHHHHHHHHHHHHHHHH....ST CS
                           DUF3209   1 maCheleaLrlglmnvlgvkdeaerrHaeaEleaeleepgpikalaeAkdlaelerhldaalvdLeeevaktdeddp 77 
                                       m+Che+eaLrlglmnvlgv d+++r+Hae+Ele++le  gpi+ la+A++lae+erhldaalvdLeeeva++d+ddp
  gi|336254319|ref|YP_004597426.1|   1 MSCHEIEALRLGLMNVLGVGDQSAREHAEKELEGHLE--GPIEGLANAESLAEVERHLDAALVDLEEEVATMDSDDP 75 
                                       9************************************..************************************** PP

                                       T-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--XX CS
                           DUF3209  78 eldYlRgrlvavrdaeralkrlveeleallddleelHdtlHeifPvd 124
                                       e+dY+Rgrl+avrdaera++rl++++e+++d+l+++HdtlHe+fPv+
  gi|336254319|ref|YP_004597426.1|  76 EYDYTRGRLLAVRDAERAVQRLRAQGESIVDGLGDAHDTLHETFPVE 122
                                       *********************************************95 PP

>> IcmF-related  Intracellular multiplication and human macrophage-killing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.7e-06     0.033      78     171 ..       7     102 ..       3     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-06
                      IcmF-related  78 eaLKvYlM..Lsdperldaafladwltrdweralegergeqererllehldallaakraiaalspl..dealVaqaR 150
                                       eaL++ lM  L+  ++  +++ ++ l+ ++e+  eg ++ ++ +++ +hlda+l +   +++++ +  d++  + +R
  gi|336254319|ref|YP_004597426.1|   7 EALRLGLMnvLGVGDQSAREHAEKELEGHLEGPIEGLANAESLAEVERHLDAALVDL--EEEVATMdsDDPEYDYTR 81 
                                       6777766644577888889999999999999999999999999***********983..3444455669******** PP

                      IcmF-related 151 aaLrrvplaervYarlkarae 171
                                        +L +v  aer+ +rl+a+ e
  gi|336254319|ref|YP_004597426.1|  82 GRLLAVRDAERAVQRLRAQGE 102
                                       ******************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 943.26
//
Query:       gi|336254320|ref|YP_004597427.1|  [L=412]
Description: cobalamin (vitamin B12) biosynthesis CbiX protein [Halopiger xanaduensis SH-6]
Scores for 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    1.2e-19   70.6   0.1    2.6  3  CbiX             CbiX
    2.4e-08   33.9   0.1    4.3e-08   33.1   0.1    1.3  1  2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
    0.00014   21.3   0.0       0.19   11.0   0.0    2.1  2  CbiK             Cobalt chelatase (CbiK)
    0.00076   19.4   0.0     0.0019   18.1   0.0    1.7  2  Suc_Fer-like     Sucrase/ferredoxin-like
  ------ inclusion threshold ------
       0.16   12.0   0.0         10    6.2   0.0    2.9  3  ETF_alpha        Electron transfer flavoprotein FAD-binding d
       0.18   12.2   0.5        8.1    6.9   0.1    2.3  2  DUF1636          Protein of unknown function (DUF1636)


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 !   70.6   0.1   4.1e-23   1.2e-19       1     106 [.      27     128 ..      27     129 .. 0.98
   2 !   69.0   0.0   1.3e-22   3.8e-19       1     106 [.     154     257 ..     154     258 .. 0.98
   3 ?   -3.3   0.0         4   1.2e+04      86     106 ..     389     409 ..     382     410 .. 0.76

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 4.1e-23
                                       -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT CS
                              CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeele 77 
                                       HGSr+++sne+v++la+ l+ + +  pv  +flel+ep ++ea++ l e  ++r++vv   lfa+ hvk+D+p ++e
  gi|336254320|ref|YP_004597427.1|  27 HGSRREKSNEQVRELAAGLESRLG-IPVDAAFLELAEPAIDEAFAGL-EPVADRVTVVHCSLFAASHVKNDVPLAIE 101
                                       ************************.*******************999.889************************** PP

                                       --SSSS-TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  78 eaeeahpkdveieytepLGthplvaevlk 106
                                       +a+++++    i  + +LG hp++ ++l+
  gi|336254320|ref|YP_004597427.1| 102 QARAEYD--LAIDNGAHLGIHPAILDLLD 128
                                       *******..*****************997 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 1.3e-22
                                       -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT CS
                              CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeele 77 
                                       +GS+dp++n +v+kla+ l e ++f+ ve  f+ ++ep+le++l  l++ + + +vv+P++l +Gv++++ + + ++
  gi|336254320|ref|YP_004597427.1| 154 RGSSDPDANGDVHKLARLLYEGREFDRVEATFIGVTEPTLEDTLHGLSKHRPDAVVVLPYMLGDGVLTQR-VRDWTA 229
                                       7*********************************************************************.****** PP

                                       --SSSS-TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  78 eaeeahpkdveieytepLGthplvaevlk 106
                                       e+++++p  v+   ++pLGt+ ++ +v++
  gi|336254320|ref|YP_004597427.1| 230 EFDDDYP-YVDALAGDPLGTDSRLLDVFA 257
                                       *******.*****************9986 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4
                                       TEEEEE---CCCSCCHHHHHH CS
                              CbiX  86 dveieytepLGthplvaevlk 106
                                       d+e +++++L+ +  v ++++
  gi|336254320|ref|YP_004597427.1| 389 DAERIVSDHLDRDRIVSDLVD 409
                                       667788899999998888876 PP

>> 2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   1.4e-11   4.3e-08      64     142 ..     320     395 ..     315     397 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.4e-11
                                       -SEEEEEE-SHHHHTTTHHHHHHHHHHHHT--TT-B-TTSSEEEEEES--S-GGGSSEEEE..SSSSEEES-HHHHH CS
                   2Fe-2S_thioredx  64 gkyviqvCtttpCalrgseeilealekklgikagettadgkftleeveClGaCanaPvvqi..ndevyedltpekve 138
                                        + ++ vC++ +Ca +gs ++le+l+++++      ++    ++++ +ClG C+ +P+v +  ++  y+d+  e++e
  gi|336254320|ref|YP_004597427.1| 320 PEKHVAVCMNQTCAEMGSPAVLERLRQEVR-----DSEHCDARITRSSCLGRCGDGPMVAVypDGIWYGDVASEDAE 391
                                       6789************************95.....455667788899**************666679********** PP

                                       HHHH CS
                   2Fe-2S_thioredx 139 eile 142
                                       +i++
  gi|336254320|ref|YP_004597427.1| 392 RIVS 395
                                       9987 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   0.00049       1.5     140     217 ..      18      96 ..      11     111 .. 0.88
   2 !   11.0   0.0   6.3e-05      0.19     135     257 ..     140     260 ..     118     264 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00049
                                       TTEEEEEEE---SC.HHHHHHHHHHHHHHHCT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHH CS
                              CbiK 140 kdealvfvgHGteh.esnavyaeldkvlkekdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlvAGdHak 214
                                        dea++++gHG++  +sn+  +el   l+++ +  v  + +e + P ++e  + l+   + +v+++   l A  H+k
  gi|336254320|ref|YP_004597427.1|  18 DDEAVLLIGHGSRReKSNEQVRELAAGLESRLGIPVDAAFLElAEPAIDEAFAGLEP-VADRVTVVHCSLFAASHVK 93 
                                       699********97527999***********99999*****99789*********986.4688999999999****** PP

                                       CCC CS
                              CbiK 215 nDm 217
                                       nD+
  gi|336254320|ref|YP_004597427.1|  94 NDV 96 
                                       *97 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6.3e-05
                                       S----TTEEEEEEE---SC.HHHHHHHHHHHHHHH.CT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS CS
                              CbiK 135 ierarkdealvfvgHGteh.esnavyaeldkvlke.kdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlv 208
                                       ++r + d a+v+ g G++   +n+   +l ++l e ++f++v  + +  + P++e+ ++ l k+   +v ++P+ml 
  gi|336254320|ref|YP_004597427.1| 140 VDREEDDVAVVLCGRGSSDpDANGDVHKLARLLYEgREFDRVEATFIGvTEPTLEDTLHGLSKHRPDAVVVLPYMLG 216
                                       566678999*******87626899999999999998999999877775357************************96 PP

                                       --HHHHCCCCSSSTTSHHHHHHHTT--EEE.----GGGSHHHHHHHHHHH CS
                              CbiK 209 AGdHaknDmasdeedswkealeaaGikvei.ilkgLGeieeirsifikhi 257
                                        G             +w  +++++   v++   + LG ++++ ++f+++ 
  gi|336254320|ref|YP_004597427.1| 217 DGV--LTQR----VRDWTAEFDDDYPYVDAlAGDPLGTDSRLLDVFADRW 260
                                       553..3222....2356666666655554314455666666666666665 PP

>> Suc_Fer-like  Sucrase/ferredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.95   2.9e+03      87     107 ..     129     158 ..      74     162 .. 0.62
   2 !   18.1   0.0   6.5e-07    0.0019      97     192 ..     323     407 ..     165     409 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.95
                      Suc_Fer-like  87 p.........kvrklpekaliLvCshktrD 107
                                       +          v + ++++ + +C+ ++ D
  gi|336254320|ref|YP_004597427.1| 129 DraaaveaelGVDREEDDVAVVLCGRGSSD 158
                                       044445555544455678889999998877 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 6.5e-07
                      Suc_Fer-like  97 liLvCshktrDarCgila.pllrkelerelrekederpggvrvgfisHvGGHkfAgnviiyrkekagqgiwygrvep 172
                                       ++ vC ++     C+ ++ p + ++l++e+r+   +++ ++r+ + s +G     + v +y+ +     iwyg v  
  gi|336254320|ref|YP_004597427.1| 323 HVAVCMNQ----TCAEMGsPAVLERLRQEVRD---SEHCDARITRSSCLGRCGDGPMVAVYPDG-----IWYGDVAS 387
                                       55666554....48888745566777777776...56678999999999988888999999987.....9******* PP

                      Suc_Fer-like 173 edvegiveetilkgkvvkel 192
                                       ed e+iv+++++++++v++l
  gi|336254320|ref|YP_004597427.1| 388 EDAERIVSDHLDRDRIVSDL 407
                                       ****************9986 PP

>> ETF_alpha  Electron transfer flavoprotein FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0034        10       7      38 ..      20      51 ..      17      60 .. 0.91
   2 ?   -1.4   0.0      0.82   2.4e+03      22      40 ..     124     142 ..     113     147 .. 0.83
   3 ?    2.0   0.0     0.071   2.1e+02       8      32 ..     148     172 ..     140     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0034
                                      S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE CS
                         ETF_alpha  7 kvvvsgGrGlkskenlelleelaealgaavga 38
                                      + v+ +G G +++++ e+++ela+ l+  +g+
  gi|336254320|ref|YP_004597427.1| 20 EAVLLIGHGSRREKSNEQVRELAAGLESRLGI 51
                                      78999**********************99986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.82
                                       HHHHHHHHHHHT-EEEE-H CS
                         ETF_alpha  22 lelleelaealgaavgasR 40 
                                       l+ll++ a+a++a++g+ R
  gi|336254320|ref|YP_004597427.1| 124 LDLLDDRAAAVEAELGVDR 142
                                       67899999*******9987 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.071
                                       -EEEE-GGGSSGGGHHHHHHHHHHH CS
                         ETF_alpha   8 vvvsgGrGlkskenlelleelaeal 32 
                                        vv +GrG +++++   +++la+ l
  gi|336254320|ref|YP_004597427.1| 148 AVVLCGRGSSDPDANGDVHKLARLL 172
                                       6999*******99999999999877 PP

>> DUF1636  Protein of unknown function (DUF1636)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.035     1e+02       4      41 ..     272     309 ..     270     316 .. 0.74
   2 ?    6.9   0.1    0.0027       8.1      24      66 ..     339     380 ..     324     396 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.035
                           DUF1636   4 CktCrsseeeeeeegeseGek.Llealqalaeeaeleee 41 
                                       C+tC+ + + e  e+  +G++ +l+al+++ e+++ +e+
  gi|336254320|ref|YP_004597427.1| 272 CDTCKYKVDLEGYEEDVGGARaMLRALAHQ-ETHADRED 309
                                       **********99999999987255566555.44455544 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0027
                           DUF1636  24 kLlealqalaeeaeleeeveiqeveClsaCkrpcavalaapgk 66 
                                       + le+l+++ ++ +++ + +i++ +Cl  C ++  va+  +g 
  gi|336254320|ref|YP_004597427.1| 339 AVLERLRQEVRD-SEHCDARITRSSCLGRCGDGPMVAVYPDGI 380
                                       568889998765.788999**************9999876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); 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:                         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 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3029.21
//
Query:       gi|336254321|ref|YP_004597428.1|  [L=237]
Description: hypothetical protein Halxa_2933 [Halopiger xanaduensis SH-6]
Scores for 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   0.7       0.46   10.4   0.7    1.3  1  Castor1_N  Cytosolic arginine sensor for mTORC1 subunit 1 N-t


Domain annotation for each model (and alignments):
>> Castor1_N  Cytosolic arginine sensor for mTORC1 subunit 1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7   2.5e-05      0.46      35      48 ..      82      95 ..      69     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.5e-05
                         Castor1_N 35 sLTetpedYTiivd 48
                                      s+T+t+++YT+++d
  gi|336254321|ref|YP_004597428.1| 82 SITRTEDEYTLTID 95
                                      9************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1888.14
//
Query:       gi|336254322|ref|YP_004597429.1|  [L=88]
Description: hypothetical protein Halxa_2934 [Halopiger xanaduensis SH-6]
Scores for 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-18   65.4   8.9    7.3e-18   65.1   8.9    1.1  1  Fer4_15   4Fe-4S single cluster domain
     0.0019   18.7   5.9     0.0037   17.8   5.9    1.6  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0086   16.1   0.2        1.8    8.7   0.1    2.1  2  Fer4_19   Divergent 4Fe-4S mono-cluster
  ------ inclusion threshold ------
        1.4    9.1   7.2          8    6.7   0.1    3.5  4  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   8.9   1.6e-21   7.3e-18       1      66 []       6      83 ..       6      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 1.6e-21
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvl.............lddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                      V++++daC+g+++C++++p +f++ edgla+v+             +d++e+  ++++dd++++aq+Aa+aCP+dAI v
  gi|336254322|ref|YP_004597429.1|  6 VTIEKDACDGIFACLTRDP-RFVEGEDGLATVDpdadpvydcegevTDTDERVVATFDDDRIDEAQQAAAACPTDAIAV 83
                                      89****************9.666667*****************999888888999**********************86 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 !   17.8   5.9   8.2e-07    0.0037      37      58 .]      44      83 ..       8      83 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.2e-07
                           Fer4_13 37 s..................eeekadaeeAadaCPvesIgv 58
                                                         ++ +++a++Aa+aCP+++I v
  gi|336254322|ref|YP_004597429.1| 44 YdcegevtdtdervvatfdDDRIDEAQQAAAACPTDAIAV 83
                                      1333344444555666676888****************76 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 !    6.6   0.0    0.0018         8       7      41 ..       5      40 ..       2      59 .. 0.72
   2 !    8.7   0.1   0.00039       1.8      26      62 ..      48      84 ..      43      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0018
                           Fer4_19  7 tiednrelCihsgnCvkglpevFdpkrk..pwikpde 41
                                      +++ +++ C++   C +++p+ F  +++    ++pd+
  gi|336254322|ref|YP_004597429.1|  5 EVTIEKDACDGIFACLTRDPR-FVEGEDglATVDPDA 40
                                      68899************9998.444444123345554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00039
                           Fer4_19 26 pevFdpkrkpwikpdeasteeiievverCPSGALsyv 62
                                      +ev d++++   + d   ++e++++++ CP  A+ + 
  gi|336254322|ref|YP_004597429.1| 48 GEVTDTDERVVATFDDDRIDEAQQAAAACPTDAIAVR 84
                                      578889999888999***************9988765 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0018         8       2      16 ..       6      20 ..       5      21 .. 0.85
   2 ?   -1.3   0.0      0.63   2.8e+03       2       8 ..      34      40 ..      33      40 .. 0.83
   3 ?   -0.8   0.1      0.43   1.9e+03       1       8 [.      58      65 ..      58      65 .. 0.85
   4 ?    4.7   0.3    0.0079        35      17      24 .]      74      81 ..      73      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0018
                            Fer4_6  2 veidpdkCigCgdCv 16
                                      v+i +d+C+g  +C 
  gi|336254322|ref|YP_004597429.1|  6 VTIEKDACDGIFACL 20
                                      89*******988885 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.63
                            Fer4_6  2 veidpdk 8 
                                      +++dpd+
  gi|336254322|ref|YP_004597429.1| 34 ATVDPDA 40
                                      79***95 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.43
                            Fer4_6  1 vveidpdk 8 
                                      v+++d+d+
  gi|336254322|ref|YP_004597429.1| 58 VATFDDDR 65
                                      689**996 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.0079
                            Fer4_6 17 rvCPegai 24
                                      ++CP++ai
  gi|336254322|ref|YP_004597429.1| 74 AACPTDAI 81
                                      79****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 666.45
//
Query:       gi|336254323|ref|YP_004597430.1|  [L=369]
Description: precorrin-3B C17-methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-39  136.1   0.2    1.9e-39  135.8   0.2    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
       0.14   10.7   7.7       0.17   10.5   7.7    1.1  1  Macoilin      Macoilin family
       0.67    9.8   5.6       0.74    9.7   5.6    1.1  1  SPX           SPX domain
       0.87    8.4   9.7          1    8.1   9.7    1.1  1  Apt1          Golgi-body localisation protein domain


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 !  135.8   0.2   4.3e-43   1.9e-39       2     212 ..     117     328 ..     116     329 .. 0.80

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 4.3e-43
                      TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleea..yeeiaeal..ae 74 
                                       l+ VG+GpG+pe +T rA +al +ad+++g++  + e++ d + e+    a+     +  + +  + e++++   ++
  gi|336254323|ref|YP_004597430.1| 117 LIAVGLGPGHPEGMTERAKDALLEADHIVGYT-TYIELIPDEITEQ----AD-----DIYD-TpmCGEVSRTEesID 182
                                       899*****************************.8888886555432....12.....2222.135777777777799 PP

                      TP_methylase  75 alragkdVvllvsGDPlvy...gtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpgl 146
                                       ++ ag dV+++ sGDP+vy   g + e++e   a +  +++ev+PGv+++q++aarlg+pl+++ ++ s++  l ++
  gi|336254323|ref|YP_004597430.1| 183 RALAGNDVAIVGSGDPNVYalaGLALEILESKGATASMVDFEVVPGVPAAQSCAARLGAPLVNDTVSISLSdhLVPM 259
                                       99*****************555555555555555555566*******************************984454 PP

                      TP_methylase 147 akeeereleallangdtlvllkapr.k.....laelaelLkealyddttpvavveragtedervvrgtleel 212
                                        ++e r+ + +++   + + +++p+ +     +++++e+L+++ +d++tpv +v+ ag+ede+v  + l+el
  gi|336254323|ref|YP_004597430.1| 260 PEIESRLHSVASE--NFAITIYNPWsRkrrenFQKACEILLTH-RDPDTPVGIVHGAGREDEQVMITELGEL 328
                                       5566666666666..78888888886467889***********.66677*********************98 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.7   3.7e-05      0.17     298     361 ..      22      92 ..       2     187 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.7e-05
                          Macoilin 298 lsksessgsesellveesvkskssssssssnknskkasagsagssnssskkhsessksvtsss........s 361
                                       + ++++++s+s+++   s++s++  +ss+++ +s ++ +gs+gs  sss k   ss+s +sss        s
  gi|336254323|ref|YP_004597430.1|  22 S-STDETDSSSTTKCGASSSSSEGEASSADSDSSGSKCGGSSGSDDSSSSKCGGSSSSSSSSSsgskcgasS 92 
                                       2.2223334444444444444444444444444555555555555555555554444444444233333321 PP

>> SPX  SPX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.6   0.00016      0.74      62     132 ..      20      99 ..       2     217 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00016
                               SPX  62 e...........rtepstsaaadesgnsaadasssepkdeae......slprrsplsrssrssssygglvssppsan 121
                                                   +t+ + s++++e+++s+ad++        +       ++ ++ +s+s++  ss ++++ss+ s  
  gi|336254323|ref|YP_004597430.1|  20 GasstdetdsssTTKCGASSSSSEGEASSADSD--------SsgskcgGSSGSDDSSSSKCGGSSSSSSSSSSGSKC 88 
                                       022111111100111111111111111111111........011112222222222222222222222222222222 PP

                               SPX 122 sssssddsses 132
                                        +sssddss++
  gi|336254323|ref|YP_004597430.1|  89 GASSSDDSSGN 99 
                                       22222222222 PP

>> Apt1  Golgi-body localisation protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   9.7   0.00023         1     308     389 ..      16      98 ..       2     181 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00023
                              Apt1 308 mvk.ess..seeddesdeesessssssssssssassssssssrssslelrlkptsstssssssessssssskkrsse 381
                                       + k   s  +e+d++s+++  +sssss+ + ssa+s+ss s+  +s+ + ++  ss+++  ss+sssssss ++   
  gi|336254323|ref|YP_004597430.1|  16 TSKcGASstDETDSSSTTKCGASSSSSEGEASSADSDSSGSKCGGSSGSDDS--SSSKCGGSSSSSSSSSSGSKCGA 90 
                                       2222222222222222222222222222222222222222222222221111..22222222222222222222222 PP

                              Apt1 382 esslessa 389
                                       +ss  ss 
  gi|336254323|ref|YP_004597430.1|  91 SSSDDSSG 98 
                                       22222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 2450.49
//
Query:       gi|336254324|ref|YP_004597431.1|  [L=290]
Description: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-45  153.3   0.3    1.1e-44  153.0   0.3    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 !  153.0   0.3     6e-49   1.1e-44       1     212 [.      19     246 ..      19     247 .. 0.81

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 6e-49
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeel.............eleapmgkekepleea 64 
                                       +ly+VG+GpG p+++T rA +++++advv+++  ++ e l+d    +                         +++++
  gi|336254324|ref|YP_004597431.1|  19 TLYVVGIGPGLPDHMTKRAKEVIESADVVIASS-LYQEFLRD----DGtipseertddegiA---------TREDGT 81 
                                       69***************************9999.77777754....2224454224433321.........222222 PP

                      TP_methylase  65 ...........yeeiaealaealragkdVvllvsGDPlvygtgselve.alrareagieveviPGvsslqaaaarlg 129
                                                  + e a+a ++++r+gkdV+++++GDP+vyg  + +++ a ++ + ++++ev+PG++++   aa +g
  gi|336254324|ref|YP_004597431.1|  82 eqeivrstmgrQIELARAAFDYVREGKDVAHVSGGDPSVYGKSDLIFKmAEEESATDVPIEVVPGMTAALGGAANVG 158
                                       3455666676699999999****************************844455567899****************** PP

                      TP_methylase 130 iplteggevlsvl..lpglakeeereleallangdtlvllkapr.klaelaelLkealyddttpvavver.....ag 198
                                       +pl+++++++s++  ++g++++ee++++a+++  d++++l++++ ++++++e+ +e+ + d+  va+v++     ag
  gi|336254324|ref|YP_004597431.1| 159 APLCNDFCTVSLSdkWRGWDEIEEKLRAAAIS--DFVIVLYNCWrNYEQAVEIVREE-RTDDAYVAIVNDagradAG 232
                                       *****************************999..**********77***********.777779****995555556 PP

                      TP_methylase 199 tedervvrgtleel 212
                                       +++e  + +tl+e+
  gi|336254324|ref|YP_004597431.1| 233 RNGESQFITTLGEA 246
                                       66666777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2086.68
//
Query:       gi|336254325|ref|YP_004597432.1|  [L=321]
Description: cobalamin (vitamin B12) biosynthesis CbiG protein [Halopiger xanaduensis SH-6]
Scores for 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-27   94.0   0.0    1.4e-26   92.3   0.0    2.0  1  CbiG_N    Cobalamin synthesis G N-terminal
    1.1e-22   80.8   0.1    2.6e-22   79.5   0.0    1.7  2  CbiG_C    Cobalamin synthesis G C-terminus
    0.00084   20.0   1.4     0.0026   18.4   1.4    1.9  1  AIRS      AIR synthase related protein, N-terminal domain


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 !   92.3   0.0   2.3e-30   1.4e-26       2      82 .]      60     138 ..      59     138 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 2.3e-30
                                       .HHHHCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XX CS
                            CbiG_N   2 llrelfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviT 78 
                                       ++++ + eyd++v ++a+Gi++R  a+ll+dK++Dpa+ vvde+ +++i++++Gh +gAn++A+++a ++ga p++T
  gi|336254325|ref|YP_004597432.1|  60 VFEQYWGEYDCFVGLMASGIAMRKTAHLLDDKWEDPAICVVDEELTWAIPITGGH-HGANQVAQDLA-TMGAVPAMT 134
                                       7899***************************************************.**********5.67******* PP

                                       XXX. CS
                            CbiG_N  79 tatd 82 
                                       ta++
  gi|336254325|ref|YP_004597432.1| 135 TASE 138
                                       **96 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       1.8   1.1e+04      32      53 ..     128     149 ..     116     159 .. 0.54
   2 !   79.5   0.0   4.4e-26   2.6e-22       1     115 [.     203     319 ..     203     320 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
                                       GGEEEEEESSCCSHHHHHHHHH CS
                            CbiG_C  32 eavaalatidlKadepgllela 53 
                                        av a+ t +  a ++g+   a
  gi|336254325|ref|YP_004597432.1| 128 GAVPAMTTASEAAGKQGVESRA 149
                                       3455555555555555554444 PP

  == domain 2  score: 79.5 bits;  conditional E-value: 4.4e-26
                                       EEEEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHHCSCT- CS
                            CbiG_C   1 lvvGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaavevpnps 77 
                                       +v+G G  +g+++e + ea+eeale+ +++ e+v+ + t ++K+de+glle+a++l+l ++tf++e+L + e p+ps
  gi|336254325|ref|YP_004597432.1| 203 VVIGTGSVSGADKERFLEAWEEALEQTDYELEDVEFVGTATRKEDEEGLLEAAQELDLGVVTFDKETLLEHEGPTPS 279
                                       69**********************************************************************99999 PP

                                       CHHHCCCSSS-HHHHHHHHHC...EECSCEEEE.TTEEEEE CS
                            CbiG_C  78 efvkkevGvpsVaEaaAllaa..arllvpKqak.ggvTvAi 115
                                       +  k+ +G p+V+Ea+A++    ++l+++K  + ++vTvAi
  gi|336254325|ref|YP_004597432.1| 280 KS-KELIGWPGVSEASAIAGGrdHELVLKKLSYeDEVTVAI 319
                                       85.68*************997557******9778******9 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 !   18.4   1.4   4.3e-07    0.0026      17      83 ..     106     166 ..      69     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.3e-07
                                       CCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEECHHHHHHHHHHHHHHHTT-EEEEEEEEEESS CS
                              AIRS  17 lvepvhfiGakavavnlsDlaamGArPlalllslalpwleevvrglaeaaeelgvplvgGdtsfsne 83 
                                          p+++ G+ ++ ++++Dla+mGA P + + s a ++     +g+++ a+++++++v Gd++++++
  gi|336254325|ref|YP_004597432.1| 106 WAIPITG-GHHGANQVAQDLATMGAVPAMTTASEAAGK-----QGVESRAKAMDAHVVNGDSTVQTN 166
                                       4557889.********************9999998884.....899***************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2409.42
//
Query:       gi|336254326|ref|YP_004597433.1|  [L=446]
Description: Pyrrolo-quinoline quinone repeat-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-65  221.0  15.3    2.3e-41  141.9   1.7    3.5  3  PQQ_2           PQQ-like domain
    1.7e-58  193.7  44.8      5e-12   45.9   0.4    9.4 10  PQQ_3           PQQ-like domain
    5.4e-42  139.8  14.9    2.9e-09   36.4   0.0    8.5  8  PQQ             PQQ enzyme repeat
  ------ inclusion threshold ------
      0.023   13.5   0.1          2    7.2   0.0    3.0  3  Me-amine-dh_H   Methylamine dehydrogenase heavy chain (MADH)
      0.057   13.3   0.1         13    5.7   0.0    3.6  4  DUF4905         Domain of unknown function (DUF4905)
      0.095   12.7   0.4       0.18   11.8   0.4    1.5  1  PGF-CTERM       PGF-CTERM motif
        4.6    7.6   6.9         64    3.9   0.3    4.6  6  Glyco_hyd_101C  Glycosyl hydrolase 101 beta sandwich domain


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1   1.9e-16     5e-13     172     236 ..      16      90 ..       5      91 .. 0.84
   2 !  141.9   1.7   9.1e-45   2.3e-41       3     237 .]      35     251 ..      33     251 .. 0.93
   3 !   52.3   3.0   2.2e-17   5.5e-14       3     106 ..     235     336 ..     233     410 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.9e-16
                             PQQ_2 172 a.......eg.tVyassgqgrllaldlatgrrlwske.issinglpildgdllyvvsa.gelialdratGavlWk 236
                                       +        g t++as++ g+l+a+d+ tg+rlw+++ ++s+ ++pi+ +++lyv+s+ ++l+ald  tG+ +W+
  gi|336254326|ref|YP_004597433.1|  16 NslqneaaTGpTIFASGYGGNLIAVDALTGERLWERSgPGSPRSSPIVVDGTLYVGSSyERLYALDATTGENVWR 90 
                                       3444333334799******************99************************99***************7 PP

  == domain 2  score: 141.9 bits;  conditional E-value: 9.1e-45
                             PQQ_2   3 gvvsaldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrv 79 
                                       g + a+da tG++lW+ +   + g+ +s + + +gtl+v++ + rl+alda+tG+ +W+++ +gp+ ++p+v +g v
  gi|336254326|ref|YP_004597433.1|  35 GNLIAVDALTGERLWERS---GPGSPRSSPIVVDGTLYVGSSYERLYALDATTGENVWRFDEPGPISSSPTVVDGTV 108
                                       5677*************6...58999999************************************************ PP

                             PQQ_2  80 vvvasdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerelaaprgt 156
                                       +v a d++l+a+dae+G++ W++++ +      r+++sp+v+ dtv++g  +  l a+++++G+  W     +    
  gi|336254326|ref|YP_004597433.1| 109 YVGALDNTLYAVDAETGDEEWEFDLPE-----DRVTSSPTVHNDTVYAGSRDHTLDAVNAETGEHEWTFFDPE---- 176
                                       **********************88888.....899******************************88774444.... PP

                             PQQ_2 157 selsrvgdisgrpvvaegtVyassgqgrllaldlatgrrl.w.skeissinglpildgdllyvvsagelialdratG 231
                                             + ++++p + ++t+y++++++ l a+d +tg+++   +++i++  + p+  +d+ly++  ++l+ald++tG
  gi|336254326|ref|YP_004597433.1| 177 ------DWVDSSPAIYDDTLYVAAYDEALYAVDPETGEQErVvTDSIEGSPS-PVFVDDTLYIHG-DNLYALDPQTG 245
                                       ......34889*****99********************55564888999888.9999*****999.*********** PP

                             PQQ_2 232 avlWkt 237
                                       +++W++
  gi|336254326|ref|YP_004597433.1| 246 EEQWSY 251
                                       ****86 PP

  == domain 3  score: 52.3 bits;  conditional E-value: 2.2e-17
                             PQQ_2   3 gvvsaldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrv 79 
                                       + ++ald+ tG+e W+ d   +++g +  +++++g +f+  gg+ l+a+da+tG++ W  t   p  ++p+v +g+v
  gi|336254326|ref|YP_004597433.1| 235 DNLYALDPQTGEEQWSYDT--SWSGDLLSPTVADGLVFT--GGDGLYAVDAKTGEEQWALTDITPGDTSPTVYDGMV 307
                                       5789*************87..899***9***9*******..8*******************99999999******** PP

                             PQQ_2  80 vvva..sdgqlialdaedGkrlWstqqrs 106
                                       +     sd++++++ a +G+  W+ + + 
  gi|336254326|ref|YP_004597433.1| 308 YTGVggSDQTMYGVHAGTGEIEWELETDF 336
                                       765555999***************44443 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   9.5e-05      0.24      15      38 ..      16      42 ..       5      44 .. 0.82
   2 !   36.9   0.1   1.4e-12   3.5e-09       1      40 []      45      84 ..      45      84 .. 0.97
   3 !   45.9   0.4   1.9e-15     5e-12       1      40 []      85     124 ..      85     124 .. 0.96
   4 !   34.3   0.0     9e-12   2.3e-08       1      40 []     125     165 ..     125     165 .. 0.97
   5 !   31.4   0.3   7.3e-11   1.9e-07       5      40 .]     170     206 ..     166     206 .. 0.89
   6 !   14.5   0.1   1.5e-05     0.038      15      40 .]     219     244 ..     211     244 .. 0.80
   7 !   24.9   1.5   7.9e-09     2e-05       1      40 []     245     283 ..     245     283 .. 0.90
   8 !   19.9   1.9     3e-07   0.00077       1      40 []     284     325 ..     284     325 .. 0.92
   9 ?    1.4   0.0      0.19   4.8e+02       1      21 [.     326     349 ..     326     368 .. 0.58
  10 ?   -3.3   0.2       5.9   1.5e+04      15      25 ..     420     433 ..     414     434 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.5e-05
                             PQQ_3 15 ssp...avdgglvyvgtgdGtlyAlDa 38
                                       s+   a+ g +++++++ G+l A+Da
  gi|336254326|ref|YP_004597433.1| 16 NSLqneAATGPTIFASGYGGNLIAVDA 42
                                      455777899*****************9 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 1.4e-12
                             PQQ_3  1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40
                                      Ge+lW+++ pg   ssp v++g++yvg++  +lyAlDa+t
  gi|336254326|ref|YP_004597433.1| 45 GERLWERSGPGSPRSSPIVVDGTLYVGSSYERLYALDATT 84
                                      9**********888************************98 PP

  == domain 3  score: 45.9 bits;  conditional E-value: 1.9e-15
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       Ge +W+++ pgp+ ssp+v++g+vyvg+ d+tlyA+Daet
  gi|336254326|ref|YP_004597433.1|  85 GENVWRFDEPGPISSSPTVVDGTVYVGALDNTLYAVDAET 124
                                       6778***********************************9 PP

  == domain 4  score: 34.3 bits;  conditional E-value: 9e-12
                             PQQ_3   1 GevlWsvqlpg.pvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       G++ W+++lp+ +v+ssp+v +++vy+g+ d+tl A++aet
  gi|336254326|ref|YP_004597433.1| 125 GDEEWEFDLPEdRVTSSPTVHNDTVYAGSRDHTLDAVNAET 165
                                       8999******99***************************98 PP

  == domain 5  score: 31.4 bits;  conditional E-value: 7.3e-11
                             PQQ_3   5 Wsvqlpg.pvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       W++  p+  v sspa++++++yv+++d  lyA+D+et
  gi|336254326|ref|YP_004597433.1| 170 WTFFDPEdWVDSSPAIYDDTLYVAAYDEALYAVDPET 206
                                       88877776888************************98 PP

  == domain 6  score: 14.5 bits;  conditional E-value: 1.5e-05
                             PQQ_3  15 ssp..avdgglvyvgtgdGtlyAlDaet 40 
                                       +sp  +++++++y+ +   +lyAlD++t
  gi|336254326|ref|YP_004597433.1| 219 GSPspVFVDDTLYIHG--DNLYALDPQT 244
                                       44444*********88..6*******98 PP

  == domain 7  score: 24.9 bits;  conditional E-value: 7.9e-09
                             PQQ_3   1 GevlWsvql..pgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       Ge++Ws+++   g++  sp+v++glv++g+   +lyA+Da+t
  gi|336254326|ref|YP_004597433.1| 245 GEEQWSYDTswSGDLL-SPTVADGLVFTGG--DGLYAVDAKT 283
                                       9******996667886.7***********9..6*******98 PP

  == domain 8  score: 19.9 bits;  conditional E-value: 3e-07
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg..dGtlyAlDaet 40 
                                       Ge++W+ +   p+ +sp+v++g vy+g g  d t+y ++a t
  gi|336254326|ref|YP_004597433.1| 284 GEEQWALTDITPGDTSPTVYDGMVYTGVGgsDQTMYGVHAGT 325
                                       99*****77668889***********************9987 PP

  == domain 9  score: 1.4 bits;  conditional E-value: 0.19
                             PQQ_3   1 GevlWsvqlpg..pvnssp.avdg 21 
                                       Ge+ W+ +++   + ++s+ +v++
  gi|336254326|ref|YP_004597433.1| 326 GEIEWELETDFdeYSGGSAtVVAD 349
                                       899999988542244444435554 PP

  == domain 10  score: -3.3 bits;  conditional E-value: 5.9
                             PQQ_3  15 ssp.avdg..glvy 25 
                                       + p av+g   +vy
  gi|336254326|ref|YP_004597433.1| 420 GVPaAVSGlgTTVY 433
                                       44535554313566 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.3e-07   0.00033       2      37 ..      27      62 ..      26      63 .. 0.89
   2 !   36.4   0.0   1.1e-12   2.9e-09       1      36 [.      66     101 ..      66     103 .. 0.91
   3 !   34.8   0.1   3.7e-12   9.6e-09       1      36 [.     106     141 ..     106     143 .. 0.90
   4 !   14.8   0.0   7.8e-06      0.02       1      36 [.     147     183 ..     147     185 .. 0.87
   5 !    7.8   0.0    0.0013       3.4       1      21 [.     188     208 ..     188     210 .. 0.92
   6 !   13.9   0.1   1.5e-05     0.039       2      31 ..     229     256 ..     228     263 .. 0.81
   7 !   10.9   0.1   0.00013      0.34      12      24 ..     276     288 ..     267     290 .. 0.82
   8 ?    4.0   0.1     0.021        54       6      29 ..     310     335 ..     305     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.3e-07
                                      EEEEEETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ  2 vvylgsadGylyAlDadTGkvlWrfktggpvlslpi 37
                                      ++++  ++G+l A+Da TG+ lW+   +g ++s+pi
  gi|336254326|ref|YP_004597433.1| 27 TIFASGYGGNLIAVDALTGERLWERSGPGSPRSSPI 62
                                      688899******************998888888887 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 1.1e-12
                                       TEEEEE.ETTSEEEEEETTTCCEEEEEESSSCGSSES CS
                               PQQ   1 gvvylg.sadGylyAlDadTGkvlWrfktggpvlslp 36 
                                       g++y+g s+  +lyAlDa+TG+ +Wrf+++gp+ s+p
  gi|336254326|ref|YP_004597433.1|  66 GTLYVGsSYE-RLYALDATTGENVWRFDEPGPISSSP 101
                                       789***6666.************************99 PP

  == domain 3  score: 34.8 bits;  conditional E-value: 3.7e-12
                                       TEEEEEETTSEEEEEETTTCCEEEEEESSSCGSSES CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggpvlslp 36 
                                       g+vy+g  d++lyA+Da+TG++ W+f+++ + + ++
  gi|336254326|ref|YP_004597433.1| 106 GTVYVGALDNTLYAVDAETGDEEWEFDLPEDRVTSS 141
                                       79*************************998877666 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 7.8e-06
                                       TEEEEEETTSEEEEEETTTCCEEEEE.ESSSCGSSES CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrf.ktggpvlslp 36 
                                       ++vy+gs+d +l A++a+TG+  W+f +++++v+s+p
  gi|336254326|ref|YP_004597433.1| 147 DTVYAGSRDHTLDAVNAETGEHEWTFfDPEDWVDSSP 183
                                       69**********************9538888888777 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0013
                                       TEEEEEETTSEEEEEETTTCC CS
                               PQQ   1 gvvylgsadGylyAlDadTGk 21 
                                       +++y++ +d  lyA+D +TG+
  gi|336254326|ref|YP_004597433.1| 188 DTLYVAAYDEALYAVDPETGE 208
                                       689*****************8 PP

  == domain 6  score: 13.9 bits;  conditional E-value: 1.5e-05
                                       EEEEEETTSEEEEEETTTCCEEEEEESSSC CS
                               PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggp 31 
                                       ++y++  + +lyAlD  TG++ W+++t++ 
  gi|336254326|ref|YP_004597433.1| 229 TLYIH--GDNLYALDPQTGEEQWSYDTSWS 256
                                       78888..446*****************986 PP

  == domain 7  score: 10.9 bits;  conditional E-value: 0.00013
                                       EEEEETTTCCEEE CS
                               PQQ  12 lyAlDadTGkvlW 24 
                                       lyA+Da+TG++ W
  gi|336254326|ref|YP_004597433.1| 276 LYAVDAKTGEEQW 288
                                       9*********988 PP

  == domain 8  score: 4.0 bits;  conditional E-value: 0.021
                                       E..ETTSEEEEEETTTCCEEEEEESS CS
                               PQQ   6 g..sadGylyAlDadTGkvlWrfktg 29 
                                       g    d + y + a TG++ W+ +t+
  gi|336254326|ref|YP_004597433.1| 310 GvgGSDQTMYGVHAGTGEIEWELETD 335
                                       44588999999999*******98876 PP

>> Me-amine-dh_H  Methylamine dehydrogenase heavy chain (MADH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00078         2     271     326 ..      77     129 ..      68     148 .. 0.81
   2 ?    2.6   0.0      0.02        52     304     330 ..     190     215 ..     160     228 .. 0.76
   3 ?   -2.0   0.0      0.47   1.2e+03     309     331 ..     271     293 ..     267     303 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00078
                                       EEEEETTT--EEEEEEEEEEESEEEE-SSSS-EEEEEETTTTEEEEEETTT--EEE CS
                     Me-amine-dh_H 271 vfvvdaktgkrlakielgheidsisvsqdakpqlyalstedktlyifdaetgkevs 326
                                       ++ +da+tg+ + +++    i s     d     y + + d tly  daetg+e  
  gi|336254326|ref|YP_004597433.1|  77 LYALDATTGENVWRFDEPGPISSSPTVVDGTV--Y-VGALDNTLYAVDAETGDEEW 129
                                       6789************9999988877777654..4.667799**********9965 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.02
                                       EEEEETTTTEEEEEETTT--EEEEE-- CS
                     Me-amine-dh_H 304 lyalstedktlyifdaetgkevssvne 330
                                       ly +++ d +ly  d+etg++ + v +
  gi|336254326|ref|YP_004597433.1| 190 LY-VAAYDEALYAVDPETGEQERVVTD 215
                                       33.78999***********99888754 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.47
                                       TTTTEEEEEETTT--EEEEE--- CS
                     Me-amine-dh_H 309 tedktlyifdaetgkevssvnel 331
                                       t+   ly  da+tg+e   + ++
  gi|336254326|ref|YP_004597433.1| 271 TGGDGLYAVDAKTGEEQWALTDI 293
                                       67788999999999997766555 PP

>> DUF4905  Domain of unknown function (DUF4905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.053   1.3e+02      69      83 .]      35      49 ..      30      49 .. 0.89
   2 ?   -2.9   0.0       2.5   6.5e+03      71      83 .]      77      89 ..      75      89 .. 0.87
   3 ?    5.7   0.0    0.0052        13      24      63 ..     160     198 ..     147     208 .. 0.80
   4 ?   -0.5   0.0      0.46   1.2e+03      70      83 .]     275     288 ..     272     288 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.053
                           DUF4905 69 kgliaiDiktgkllW 83
                                       +lia+D+ tg+ lW
  gi|336254326|ref|YP_004597433.1| 35 GNLIAVDALTGERLW 49
                                      579***********9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.5
                           DUF4905 71 liaiDiktgkllW 83
                                      l a+D+ tg+ +W
  gi|336254326|ref|YP_004597433.1| 77 LYALDATTGENVW 89
                                      7799****99999 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0052
                           DUF4905  24 aldletgkllfedlvleekwwtgleaiykgvlllhkyekp 63 
                                       a++ etg+  +  +   e+w  +  aiy+++l++  y ++
  gi|336254326|ref|YP_004597433.1| 160 AVNAETGEHEWTFFD-PEDWVDSSPAIYDDTLYVAAYDEA 198
                                       666777777776544.478******************875 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.46
                           DUF4905  70 gliaiDiktgkllW 83 
                                       gl a+D+ktg+  W
  gi|336254326|ref|YP_004597433.1| 275 GLYAVDAKTGEEQW 288
                                       899*******9888 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   7.1e-05      0.18       2      23 .]     417     438 ..     416     438 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.1e-05
                         PGF-CTERM   2 PGFGavlAlaGLLaaalLaRRr 23 
                                       PGFG+  A+ GL  +++ ++Rr
  gi|336254326|ref|YP_004597433.1| 417 PGFGVPAAVSGLGTTVYMLKRR 438
                                       ****************888887 PP

>> Glyco_hyd_101C  Glycosyl hydrolase 101 beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.93   2.4e+03      78      98 ..      72      92 ..      64      95 .. 0.85
   2 ?   -2.7   0.0       2.7   6.9e+03      80      97 ..     114     131 ..     107     141 .. 0.80
   3 ?   -2.3   0.0       2.1   5.3e+03      86     103 ..     161     180 ..     146     189 .. 0.72
   4 ?    3.9   0.3     0.025        64      80     103 ..     234     257 ..     227     261 .. 0.89
   5 ?    1.6   0.0      0.12   3.2e+02      81     110 ..     274     303 ..     265     310 .. 0.85
   6 ?    1.1   0.0      0.18   4.6e+02      79     103 ..     314     338 ..     307     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.93
                                      GGG-EEEEEESS-SEEEEE-- CS
                    Glyco_hyd_101C 78 adeeklYhynpkggtstwkLp 98
                                      ++ e+lY  +++ g+  w+ +
  gi|336254326|ref|YP_004597433.1| 72 SSYERLYALDATTGENVWRFD 92
                                      5679**************976 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                       G-EEEEEESS-SEEEEE- CS
                    Glyco_hyd_101C  80 eeklYhynpkggtstwkL 97 
                                       ++ lY  +++ g  +w+ 
  gi|336254326|ref|YP_004597433.1| 114 DNTLYAVDAETGDEEWEF 131
                                       567999999999999975 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.1
                                       EESS-SEEEEE-..-HHHHT CS
                    Glyco_hyd_101C  86 ynpkggtstwkL..pekwak 103
                                        n++ g+++w+   pe+w +
  gi|336254326|ref|YP_004597433.1| 161 VNAETGEHEWTFfdPEDWVD 180
                                       68999999999744566655 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.025
                                       G-EEEEEESS-SEEEEE--HHHHT CS
                    Glyco_hyd_101C  80 eeklYhynpkggtstwkLpekwak 103
                                        + lY  +p+ g+ +w+ +++w++
  gi|336254326|ref|YP_004597433.1| 234 GDNLYALDPQTGEEQWSYDTSWSG 257
                                       578*******************86 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.12
                                       -EEEEEESS-SEEEEE--HHHHT.S--EEE CS
                    Glyco_hyd_101C  81 eklYhynpkggtstwkLpekwakkssvklY 110
                                       + lY  ++k g+ +w L++   + +s ++Y
  gi|336254326|ref|YP_004597433.1| 274 DGLYAVDAKTGEEQWALTDITPGDTSPTVY 303
                                       669999************988877777777 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.18
                                       GG-EEEEEESS-SEEEEE--HHHHT CS
                    Glyco_hyd_101C  79 deeklYhynpkggtstwkLpekwak 103
                                       +++ +Y   +  g+ +w+L++++ +
  gi|336254326|ref|YP_004597433.1| 314 SDQTMYGVHAGTGEIEWELETDFDE 338
                                       67899999999*********99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3285.78
//
Query:       gi|336254327|ref|YP_004597434.1|  [L=1076]
Description: hypothetical protein Halxa_2939 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.74    9.7   4.0         13    5.7   0.0    2.6  2  Wtap      WTAP/Mum2p family


Domain annotation for each model (and alignments):
>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   3.0    0.0084   1.5e+02      97     152 ..     405     465 ..     403     469 .. 0.82
   2 ?    5.7   0.0   0.00071        13      36      71 ..     711     747 ..     673     814 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.0084
                              Wtap  97 vLeqENeELgkvleegrv.....akLeselalqkkfveelkkaleeleelleeleeevevl 152
                                       +L +E eE++ ++ee+r+     a+++    ++ ++v+e ++   ++e l+e+ +e v+  
  gi|336254327|ref|YP_004597434.1| 405 LLRSELEEMEVMNEEERIpfvesAEVSYTYYAANAHVDEAETYVDQAEHLVEQTDEIVDEA 465
                                       6999*************94443345555678899********************9988765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.00071
                              Wtap  36 pps.ssqlrqvllDPAvnlvfsrlrkeleeaenklee 71 
                                        +s +++++ ++l+PA n +++ lr ele + ++ +e
  gi|336254327|ref|YP_004597434.1| 711 SDSfQEDYDLTALEPAENELIEDLRIELERTHDEFTE 747
                                       3444559999*****************9999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1076 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.84u 0.29s 00:00:01.12 Elapsed: 00:00:00.47
# Mc/sec: 6952.44
//
Query:       gi|336254328|ref|YP_004597435.1|  [L=348]
Description: hypothetical protein Halxa_2940 [Halopiger xanaduensis SH-6]
Scores for 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  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); 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:                         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 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2545.60
//
Query:       gi|336254329|ref|YP_004597436.1|  [L=162]
Description: hypothetical protein Halxa_2941 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.32   11.0   5.8       0.16   11.9   0.7    2.4  3  RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain


Domain annotation for each model (and alignments):
>> RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7     9e-06      0.16      21      55 ..      69     103 ..      68     107 .. 0.86
   2 ?   -2.2   0.0      0.23     4e+03      46      55 ..     134     143 ..     133     147 .. 0.71
   3 ?    0.7   0.3     0.028   5.1e+02      46      57 ..     149     160 ..     138     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9e-06
                     RNase_II_C_S1  21 dPaVeArveggaglplGervrVrLveADvatrrvr 55 
                                       dP    r++++++lp+G++v Vr+++ D ++ r++
  gi|336254329|ref|YP_004597436.1|  69 DPTLRDRIDDTEPLPAGATVYVRITAIDEDANRLT 103
                                       788888998999****************9887765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.23
                     RNase_II_C_S1  46 eADvatrrvr 55 
                                       +A vatr v 
  gi|336254329|ref|YP_004597436.1| 134 DASVATRSVP 143
                                       6888998885 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.028
                     RNase_II_C_S1  46 eADvatrrvrFe 57 
                                       eADv ++++r +
  gi|336254329|ref|YP_004597436.1| 149 EADVRSGTLRVA 160
                                       899999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1205.10
//
Query:       gi|336254330|ref|YP_004597437.1|  [L=314]
Description: hypothetical protein Halxa_2942 [Halopiger xanaduensis SH-6]
Scores for 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  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2271.85
//
Query:       gi|336254331|ref|YP_004597438.1|  [L=577]
Description: hypothetical protein Halxa_2943 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.21   11.5   0.3        0.4   10.5   0.3    1.5  1  CHD5             CHD5-like protein
        1.1    8.9   3.6       0.58    9.9   0.5    2.1  2  Phage_holin_2_2  Phage holin T7 family, holin superfamily II
        1.2    9.1   0.0        1.2    9.1   0.0    3.3  3  LapA_dom         Lipopolysaccharide assembly protein A domain
        2.1    8.3  20.5      0.055   13.4   2.5    3.9  5  T2SSF            Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> CHD5  CHD5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3     9e-05       0.4     127     158 ..     221     251 ..     202     252 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9e-05
                              CHD5 127 pkg.wfPllvewllslplaplgsVSltiWlfac 158
                                         g ++Pl+   +  +p ap+ +VSl+iW+f++
  gi|336254331|ref|YP_004597438.1| 221 AFGiLLPLA--LIALVPAAPMAGVSLNIWMFVL 251
                                       455566666..44459***************96 PP

>> Phage_holin_2_2  Phage holin T7 family, holin superfamily II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.5   0.00013      0.58      10      39 ..     228     255 ..     224     261 .. 0.85
   2 ?   -2.0   0.1      0.66     3e+03      12      33 ..     480     501 ..     470     503 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00013
                   Phage_holin_2_2  10 aaPialvsaaysaGlsldeWvlvatllYtV 39 
                                       +a ialv aa +aG+sl+ W++v+  lY V
  gi|336254331|ref|YP_004597438.1| 228 LALIALVPAAPMAGVSLNIWMFVL--LYDV 255
                                       6779*****************995..6655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.66
                   Phage_holin_2_2  12 PialvsaaysaGlsldeWvlva 33 
                                       P ++ +   +aG+  +e + +a
  gi|336254331|ref|YP_004597438.1| 480 PMVGGATVGMAGMLSAENFDAA 501
                                       5555555558899887777666 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   1.2         1   4.7e+03      16      38 ..      56      79 ..      50      95 .. 0.66
   2 ?   -0.3   0.7      0.21   9.4e+02       6      27 ..     242     265 ..     239     267 .. 0.73
   3 ?    9.1   0.0   0.00026       1.2      18      54 ..     315     351 ..     307     357 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1
                          LapA_dom 16 elpLsllllvafgiGa.llgwlls 38
                                       lpL l  + + ++G+ +l+  l+
  gi|336254331|ref|YP_004597438.1| 56 PLPLLLYGVPFSFVGFfVLTASLA 79
                                      677777777777777764444333 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.21
                          LapA_dom   6 Vtvnfl.faqv.elpLsllllvaf 27 
                                       V++n++ f  + ++ L l+l++a+
  gi|336254331|ref|YP_004597438.1| 242 VSLNIWmFVLLyDVVLPLCLVGAA 265
                                       99****644445888888888775 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00026
                          LapA_dom  18 pLsllllvafgiGallgwllslwsylrlrrelrrlkk 54 
                                       p +l  ++afgiG+ +++l+ ++ +l lr ++r+ ++
  gi|336254331|ref|YP_004597438.1| 315 PAYLAEIAAFGIGLGVALLAVYSPILELRNRVRNVEE 351
                                       789999****************989988888887665 PP

>> 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 ?   -3.0   0.9       1.5   6.6e+03     111     125 .]      51      65 ..      49      65 .. 0.89
   2 ?    7.3   0.2   0.00096       4.3      14     123 ..     119     232 ..     115     235 .. 0.79
   3 ?   -4.2   0.2       3.4   1.5e+04     109     125 .]     322     338 ..     320     338 .. 0.79
   4 ?    2.6   0.2     0.027   1.2e+02      28      67 ..     350     389 ..     341     407 .. 0.70
   5 ?   13.4   2.5   1.2e-05     0.055       9     106 ..     364     468 ..     356     483 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.5
                                       XXXXXXXXXXXXXXX CS
                             T2SSF 111 vallvllillaillp 125
                                       +a++v+l+ll++ +p
  gi|336254331|ref|YP_004597438.1|  51 LAAFVPLPLLLYGVP 65 
                                       89*********9987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00096
                                       -HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.....SHHHHHC.T-TT.TS.-HHHHHHHHHHHHHT-HHHHHHH CS
                             T2SSF  14 plveaLellaeeaengplaeelkriarrlraGg.....slseale.rtpssef.pelvvqlirageeggnLaevLer 83 
                                       +l+ a++ +a++  +gpla+ l++ ++r +        s++e ++ ++p   + ++     +++    g  + +Ler
  gi|336254331|ref|YP_004597438.1| 119 SLENAVRFAARTG-EGPLARSLAAHVTRSKGTPragllSFAEEWApHFP--ALrRSSTLLATAQDAPEGERGRTLER 192
                                       6889999999999.99999999998888887767777788888888887..77566666677777778999****** PP

                                       HHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  84 laeyleeerelrrkllaallepllllvvallvllillail 123
                                       + + + +  +++  +++a +    ++++a+ +ll+l +i 
  gi|336254331|ref|YP_004597438.1| 193 ALSAILDGTRSQMAEFTAAIRAPTTMLFAFGILLPLALIA 232
                                       9999999999998888888877777777777777776664 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 3.4
                                       XXXXXXXXXXXXXXXXX CS
                             T2SSF 109 lvvallvllillaillp 125
                                       +++++ ++++lla++ p
  gi|336254331|ref|YP_004597438.1| 322 AAFGIGLGVALLAVYSP 338
                                       66788899999998876 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.027
                                       SHHHHHHHHHHHHHHHTTSSHHHHHCT-TT.TS-HHHHHH CS
                             T2SSF  28 ngplaeelkriarrlraGgslsealertpssefpelvvql 67 
                                       +  l+++l  i r++++G+s+++a+e   + + +e+  +l
  gi|336254331|ref|YP_004597438.1| 350 EENLTDALYIIGRQVAEGESVEAAIELAADRVADETGEML 389
                                       5667888888899999999999999944432334443333 PP

  == domain 5  score: 13.4 bits;  conditional E-value: 1.2e-05
                                       HHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC.......T-TT.TS-HHHHHHHHHHHHHT-H CS
                             T2SSF   9 lsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale.......rtpssefpelvvqlirageeggnL 77 
                                       ++ G ++++a+el+a+     + +e l+++a   r  + s++ea+          ps   +++++ l  ag+eg + 
  gi|336254331|ref|YP_004597438.1| 364 VAEGESVEAAIELAADRV-ADETGEMLAHAAGVQRRLHtSVEEAFLgdygalrDVPSQRARSMAALLAIAGDEGKPA 439
                                       566778899999999999.88888888888877777776778888888888877777788***************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTX CS
                             T2SSF  78 aevLerlaeyleeerelrrkllaallepl 106
                                       + ++ ++a++lee ++ +++ + +l  + 
  gi|336254331|ref|YP_004597438.1| 440 GRAIVAMADHLEELEDVEAETKRELVRVT 468
                                       ********************999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3872.26
//
Query:       gi|336254332|ref|YP_004597439.1|  [L=650]
Description: type II secretion system protein E [Halopiger xanaduensis SH-6]
Scores for 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-35  120.9   0.0    8.3e-35  120.2   0.0    1.2  1  T2SSE          Type II/IV secretion system protein
     0.0003   21.3   0.0    0.00054   20.5   0.0    1.4  1  ABC_tran       ABC transporter
     0.0049   17.3   0.5      0.032   14.6   0.1    2.3  2  AAA_16         AAA ATPase domain
     0.0088   15.8   0.1      0.024   14.4   0.1    1.8  1  AAA_29         P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.024   14.2   0.2       0.12   11.9   0.1    2.3  3  AAA_25         AAA domain
      0.039   13.5   0.0      0.072   12.7   0.0    1.4  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.059   12.7   0.0       0.11   11.7   0.0    1.4  1  Zeta_toxin     Zeta toxin
       0.07   12.0   0.0       0.11   11.4   0.0    1.2  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.087   12.9   0.0       0.18   11.9   0.0    1.5  1  AAA_14         AAA domain


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 !  120.2   0.0   4.2e-38   8.3e-35       4     252 ..     279     539 ..     277     555 .. 0.91

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 4.2e-38
                             T2SSE   4 lleallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlp...ek 76 
                                       +le l++d+ v+d+    p +   +r   dg+ +++  +l++  +e+l+sri  ++++  s+ +p +da+ +   ++
  gi|336254332|ref|YP_004597439.1| 279 VLEDLFADPAVTDVYATSPVTaNPLRVECDGVAMETNVHLTEIGAEALASRIRRTSGRAFSRAKPTIDATASlanGR 355
                                       578899**********999887788889****************************************99888899* PP

                             T2SSE  77 gvrlrvvllPvvagealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkei 153
                                       g r+ +v+ Pv+ g+ ++ R++s  ++tl  l+a++++ +++a +l+ a++++   l++G+ g GKttll +ll e+
  gi|336254332|ref|YP_004597439.1| 356 GLRIAGVTDPVADGTGFAFRERSDDRFTLPALVANGTVPPAVAGFLSVAIERNAAALIAGTRGAGKTTLLGTLLYEV 432
                                       ***************************************************************************** PP

                             T2SSE 154 nksderivtvEDpvEiqleganqvqlnak........kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnT 222
                                         +  r v++ED+ E+ +++ + v    +          ++  ad+lr+aLRl    ++vGEiR++e++ + +A+  
  gi|336254332|ref|YP_004597439.1| 433 TPD-TRTVLIEDTPELPVAALQSVGRDVQalrtgtgdGPEISPADALRTALRLGDGALVVGEIRGEEAAVLYEAMRV 508
                                       999.9***************999987777788889887899************************************ PP

                             T2SSE 223 GHlgs..lsTlHansaagalerL.eqlgaevea 252
                                       G      l+T+H + a  + er+ ++lg e  +
  gi|336254332|ref|YP_004597439.1| 509 GANANavLGTIHGDGASAVYERVvSDLGVE--P 539
                                       *7642229*************963678844..3 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.7e-07   0.00054       4      59 ..     401     457 ..     400     538 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.7e-07
                                       EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                          ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrk 59 
                                       +s+ ++++    i G  GaGK+tLl +l+ +++p+  ++l+++++      l+s+ +
  gi|336254332|ref|YP_004597439.1| 401 LSVAIERNAAALIAGTRGAGKTTLLGTLLYEVTPDTRTVLIEDTPELPvAALQSVGR 457
                                       58899999*******************************999765443345555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.48   9.5e+02      41     107 ..      72     140 ..      66     240 .. 0.60
   2 !   14.6   0.1   1.6e-05     0.032      25      88 ..     409     465 ..     397     515 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.48
                            AAA_16  41 vrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala......a 107
                                       v++l++  +++++i++r +  q++ +++ +al+ a+   ++++  +++++  +++ +r+ l ea++      a
  gi|336254332|ref|YP_004597439.1|  72 VTALAE--RDADAIVVRSNGLQYRYDAEAAALLGAA-G-RFVELFGSRDDGLARDVARDPLGEAATletrvdA 140
                                       444553..2224677777777773333333333333.2.3333333333333333333333333333333331 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.6e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                        + l+ G +G GK++l+ +ll +++ d   +l +++ +l    p +a +q     + +++l + 
  gi|336254332|ref|YP_004597439.1| 409 AAALIAGTRGAGKTTLLGTLLYEVTPDTRTVLIEDTPEL----P-VAALQSV-G-RDVQALRTG 465
                                       5789*****************999999544433333333....2.2233333.3.455555555 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   0.1   1.2e-05     0.024      17      50 ..     403     436 ..     397     440 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                            AAA_29  17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                       + i+++ a l++G+ G+GK+Tll  + +  +p++
  gi|336254332|ref|YP_004597439.1| 403 VAIERNAAALIAGTRGAGKTTLLGTLLYEVTPDT 436
                                       567766799**************88888888776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.8   5.6e+03      83     113 ..     131     162 ..     129     186 .. 0.72
   2 ?   -3.5   0.0       3.1   6.2e+03       2      29 ..     207     234 ..     206     238 .. 0.86
   3 ?   11.9   0.1   6.2e-05      0.12      24      58 ..     399     433 ..     379     453 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.8
                            AAA_25  83 edelrrRlravgealrddarllvldlagv.es 113
                                       +++l+ R+ a+g  +r+ + l++++++g+  +
  gi|336254332|ref|YP_004597439.1| 131 AATLETRVDAIGDVARESGLLDAVSGVGEyAD 162
                                       56899999999998888999999987775333 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.1
                            AAA_25   2 aeplelsavsvadlaapppprrwlvkgl 29 
                                       a++l+l a++v dl  +p++r+ lv+g+
  gi|336254332|ref|YP_004597439.1| 207 ADRLPLYALEVVDLSLSPAERELLVDGY 234
                                       67888889999999999999*9999986 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 6.2e-05
                            AAA_25  24 wlvkgllpagelallaGapgtGKttlaldlalava 58 
                                         +   + +++ al+aG +g+GKttl+  l ++v+
  gi|336254332|ref|YP_004597439.1| 399 GFLSVAIERNAAALIAGTRGAGKTTLLGTLLYEVT 433
                                       5555568899*****************99999998 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 ?   12.7   0.0   3.6e-05     0.072       3      38 ..     411     446 ..     409     485 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.6e-05
                                       EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SS CS
                              cobW   3 tvltGflGsGKTtLlnhllenraglklavivNefge 38 
                                        +++G  G+GKTtLl +ll +       v++ +  e
  gi|336254332|ref|YP_004597439.1| 411 ALIAGTRGAGKTTLLGTLLYEVTPDTRTVLIEDTPE 446
                                       5799***************55555555566666655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.6e-05      0.11      14      49 ..     406     441 ..     400     444 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                       er ++ l++G  GAGK++l+  l  e++++ + v +
  gi|336254332|ref|YP_004597439.1| 406 ERNAAALIAGTRGAGKTTLLGTLLYEVTPDTRTVLI 441
                                       677899***************999999988877776 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 ?   11.4   0.0   5.5e-05      0.11      16      51 ..     409     444 ..     397     459 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                     TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairargdraivlDl 51 
                                       + +li+Gt G+GKt+ l  ll ++     ++++ D+
  gi|336254332|ref|YP_004597439.1| 409 AAALIAGTRGAGKTTLLGTLLYEVTPDTRTVLIEDT 444
                                       45799********************99999999997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.9e-05      0.18       3      27 ..     409     433 ..     407     454 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.9e-05
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell 27 
                                        + +i G R +GKTtll +l++e  
  gi|336254332|ref|YP_004597439.1| 409 AAALIAGTRGAGKTTLLGTLLYEVT 433
                                       5789**************9998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (650 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 4334.62
//
Query:       gi|336254333|ref|YP_004597440.1|  [L=155]
Description: hypothetical protein Halxa_2945 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.046   13.3   0.0      0.064   12.9   0.0    1.1  1  DUF1449   Protein of unknown function (DUF1449)
       0.22   11.4   0.4       0.43   10.5   0.4    1.5  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> DUF1449  Protein of unknown function (DUF1449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.1e-06     0.064      71     113 ..       6      48 ..       2      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.1e-06
                           DUF1449  71 ilLvlfLtlFglvGlvlqslvasllgallpallaaaialllal 113
                                       + ++l L++Fgl Gl+++ ++ + ++  l   laa+ a+++ l
  gi|336254333|ref|YP_004597440.1|   6 VAVLLTLAIFGLAGLAIDDAAGEATERELRSELAAVEAAAVDL 48 
                                       667889******************************9998876 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 ?   10.5   0.4   4.8e-05      0.43      23      44 ..       2      23 ..       1      29 [. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.8e-05
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                              SecE 23 lkttvvVlvfvvimglflflvD 44
                                      +++ v+Vl++ +i+gl + ++D
  gi|336254333|ref|YP_004597440.1|  2 IRYVVAVLLTLAIFGLAGLAID 23
                                      89*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1244.78
//
Query:       gi|336254334|ref|YP_004597441.1|  [L=232]
Description: hypothetical protein Halxa_2946 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0012   18.3   2.4       0.17   11.1   0.1    2.2  2  Dynamitin        Dynamitin
     0.0014   18.9   1.2      0.076   13.3   0.1    2.4  2  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.003   17.8   1.5      0.051   13.8   0.7    2.5  2  ABC_tran_CTD     ABC transporter C-terminal domain
      0.004   16.8   0.3      0.006   16.3   0.3    1.3  1  Lebercilin       Ciliary protein causing Leber congenital ama
     0.0049   17.0   2.4     0.0076   16.4   1.7    1.6  1  Tropomyosin_1    Tropomyosin like
      0.007   16.4   4.9      0.022   14.9   3.1    2.2  2  Cep57_CLD_2      Centrosome localisation domain of PPC89
     0.0076   16.4   5.9       0.25   11.6   0.3    3.2  3  XhlA             Haemolysin XhlA
     0.0081   14.4   0.0       0.01   14.1   0.0    1.1  1  FPP              Filament-like plant protein, long coiled-coi
      0.009   16.4   0.3        9.7    6.7   0.0    3.1  3  FlaC_arch        Flagella accessory protein C (FlaC)
       0.01   15.7   0.9        4.7    7.2   0.0    2.8  3  HSBP1            Heat shock factor binding protein 1
  ------ inclusion threshold ------
      0.011   15.9   1.4          3    8.1   0.4    2.2  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
      0.017   15.1   3.7      0.025   14.6   3.7    1.3  1  DHR10            Designed helical repeat protein 10 domain
      0.018   14.8   0.5      0.029   14.1   0.5    1.2  1  DUF745           Protein of unknown function (DUF745)
      0.019   15.5   1.0      0.047   14.2   1.1    1.6  1  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.02   14.4  10.6       0.87    9.2   1.0    3.5  3  Trimer_CC        Trimerisation motif
      0.027   15.0   0.7      0.076   13.5   0.7    1.7  1  Spectrin         Spectrin repeat
      0.028   13.8   0.3       0.11   11.8   0.2    1.5  1  DUF3450          Protein of unknown function (DUF3450)
      0.029   14.4   0.5      0.063   13.3   0.4    1.6  1  DUF1664          Protein of unknown function (DUF1664)
      0.037   14.1   2.5        6.4    6.9   0.5    2.6  3  TolA_bind_tri    TolA binding protein trimerisation
      0.041   13.8   0.4        1.6    8.6   0.0    2.2  2  DASH_Spc19       Spc19
      0.043   11.6   2.8      0.079   10.8   2.8    1.3  1  Myosin_tail_1    Myosin tail
      0.047   13.3   6.2       0.42   10.1   0.4    2.2  2  PspA_IM30        PspA/IM30 family
      0.055   13.7   0.1      0.055   13.7   0.1    1.2  1  MutS_III         MutS domain III
      0.056   13.3   0.1      0.059   13.2   0.1    1.1  1  ERM              Ezrin/radixin/moesin family
       0.06   13.7   1.7       0.15   12.3   0.9    2.2  2  Lzipper-MIP1     Leucine-zipper of ternary complex factor MIP
      0.061   13.8   3.1        1.2    9.7   0.6    2.8  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.07   12.0   0.7      0.099   11.5   0.7    1.1  1  Spc7             Spc7 kinetochore protein
      0.074   13.7   4.8        1.9    9.2   1.7    3.1  2  SlyX             SlyX
      0.076   13.0   0.5        6.9    6.7   0.3    2.5  2  Prefoldin_2      Prefoldin subunit
      0.083   12.9   1.5        1.7    8.7   0.1    2.6  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        0.1   12.6   0.1       0.42   10.7   0.1    1.7  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.11   12.3   2.0        9.4    6.1   0.1    2.3  2  DivIC            Septum formation initiator
       0.13   11.7   0.6       0.16   11.4   0.6    1.1  1  Golgin_A5        Golgin subfamily A member 5
       0.13   12.3   1.1       0.35   10.9   0.7    1.9  1  DUF1515          Protein of unknown function (DUF1515)
       0.13   10.8   0.0       0.13   10.8   0.0    1.4  1  DUF3138          Protein of unknown function (DUF3138)
       0.14   12.5   0.1       0.17   12.3   0.1    1.2  1  Fez1             Fez1
       0.15   11.9   0.2       0.34   10.7   0.1    1.6  1  Phage_GP20       Phage minor structural protein GP20
       0.16   11.8   2.6       0.22   11.3   1.3    1.9  2  TRAF_BIRC3_bd    TNF receptor-associated factor BIRC3 binding
       0.17   12.6   3.1        3.7    8.3   0.4    2.4  2  Vir_act_alpha_C  Virulence activator alpha C-term
       0.19   12.1   0.4       0.31   11.5   0.4    1.3  1  Streptin-Immun   Lantibiotic streptin immunity protein
        0.2   11.0   1.6       0.35   10.2   1.5    1.5  1  DUF4407          Domain of unknown function (DUF4407)
       0.27   11.3   0.8        2.6    8.2   0.3    2.2  2  DUF2730          Protein of unknown function (DUF2730)
       0.33   10.3   9.5        4.6    6.5   9.3    2.3  1  Tropomyosin      Tropomyosin
       0.37   11.0   3.9        1.3    9.2   4.0    1.8  1  ATG16            Autophagy protein 16 (ATG16)
       0.38   11.1   6.6          7    7.1   0.1    2.9  3  CLZ              C-terminal leucine zipper domain of cyclic n
       0.49    9.6   4.7         27    4.0   0.1    3.4  3  MRF_C1           Myelin gene regulatory factor -C-terminal do
       0.69    8.4   2.7        0.9    8.0   2.7    1.1  1  FUSC             Fusaric acid resistance protein family
        1.9    8.8  17.2        3.1    8.2   1.5    3.3  3  HalX             HalX domain
        5.1    7.3   6.5         58    3.8   6.4    2.3  1  CENP-Q           CENP-Q, a CENPA-CAD centromere complex subun


Domain annotation for each model (and alignments):
>> Dynamitin  Dynamitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.3    0.0066       2.4     211     254 ..       5      45 ..       1      47 [. 0.89
   2 !   11.1   0.1   0.00048      0.17     207     258 ..      49      98 ..      45     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0066
                         Dynamitin 211 aelekRLaeLEklvGlssesldelsanlkprplletlsrLeakl 254
                                         le+RL++ E++v   ++ ldel +    ++l et+ +Le ++
  gi|336254334|ref|YP_004597441.1|   5 DRLEQRLSAVERVVVDGDAALDELAEV---AALAETVADLETRV 45 
                                       579********************9665...9*********9987 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00048
                         Dynamitin 207 lakiaelekRLaeLEklvGlssesldelsanlkprplletlsrLeaklslLq 258
                                        +++a+le  +  LE  vG+ ++  d+++++   ++ ++t++rLe+++  L+
  gi|336254334|ref|YP_004597441.1|  49 ERRLADLEAAVRSLEGYVGNVESINDDVERQ--AASAVATVDRLERRVDRLE 98 
                                       6899*****************9999988777..999************9885 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 !   13.3   0.1   0.00021     0.076      49      93 ..      27      71 ..      21      73 .. 0.89
   2 ?    3.7   0.1      0.21        78      68      94 ..      74     100 ..      73     102 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00021
                           BLOC1_2 49 kleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93
                                      +l ++ ++ e+++ + +++d+ e+++++Le+av  L+ y+ + E+
  gi|336254334|ref|YP_004597441.1| 27 ELAEVAALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVES 71
                                      677888899999999************************999886 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.21
                           BLOC1_2  68 dqiekqvteLeeavseLDeyskeLEak 94 
                                       d++e+q ++  ++v++L+  + +LE+ 
  gi|336254334|ref|YP_004597441.1|  74 DDVERQAASAVATVDRLERRVDRLEVE 100
                                       566777777777888888888888865 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 !   13.8   0.7   0.00014     0.051      17      68 ..       4      56 ..       2      57 .. 0.94
   2 !    8.6   0.3    0.0058       2.1      12      52 ..      40      81 ..      36     104 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00014
                      ABC_tran_CTD 17 IeaLEeeiaeleaeladpelysdp.eklaelsaeleeleaeLeelyerWeeLe 68
                                      +++LE++++++e  + d +   d+ +++a+l +  ++le+  +e + r   Le
  gi|336254334|ref|YP_004597441.1|  4 LDRLEQRLSAVERVVVDGDAALDElAEVAALAETVADLETRVDEHERRLADLE 56
                                      789******************9999********************99998887 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0058
                      ABC_tran_CTD 12 eleaeIeaLEeeiaeleaeladpely.sdpeklaelsaelee 52
                                       le + ++ E ++a+lea++ + e y  + e +++  +++++
  gi|336254334|ref|YP_004597441.1| 40 DLETRVDEHERRLADLEAAVRSLEGYvGNVESINDDVERQAA 81
                                      688899999999999999999998886666888888877654 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   1.6e-05     0.006     115     186 ..      27     101 ..       2     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-05
                        Lebercilin 115 nLaereeLqkkLeeleakleekeekikeLerkleleek...sfrrqlaaekkktkeaqeevkalqeeierlkqkl 186
                                       +Lae + L++ +++le++++e e+++ +Le  ++ +e    + +      ++++  a ++v++l+++++rl+ +l
  gi|336254334|ref|YP_004597441.1|  27 ELAEVAALAETVADLETRVDEHERRLADLEAAVRSLEGyvgNVESINDDVERQAASAVATVDRLERRVDRLEVEL 101
                                       688999999********************9888777761114444445556777778888999999999998766 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.7   2.1e-05    0.0076      16     101 ..      31     114 ..      14     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.1e-05
                     Tropomyosin_1  16 aeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrkiqlLEeelees 92 
                                       + +l e v +le +  e+e  +++L+  ++ le  v ++e+   +++++   ++++ ++ + l+r+++ LE el++ 
  gi|336254334|ref|YP_004597441.1|  31 VAALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQ---AASAVATVDRLERRVDRLEVELDDV 104
                                       4556788889999999999999999999999999999888765555554...455677899*************975 PP

                     Tropomyosin_1  93 d.kkLkette 101
                                           L+e te
  gi|336254334|ref|YP_004597441.1| 105 RgGVLREPTE 114
                                       4134566555 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.5   5.6e+02      10      23 ..       2      15 ..       1      31 [. 0.81
   2 !   14.9   3.1   5.9e-05     0.022       1      62 [.      34     102 ..      34     111 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.5
                       Cep57_CLD_2 10 nrLdsltrklqvhe 23
                                      ++Ld+l+++l++ e
  gi|336254334|ref|YP_004597441.1|  2 TDLDRLEQRLSAVE 15
                                      78999999999877 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 5.9e-05
                       Cep57_CLD_2   1 LeaevktLqnrLdsltrklqvheeelkrLnk.......ERdsalrqLgvAyeelneLkaevealrkELk 62 
                                       L+ +v  L++r d  +r+l+  e + ++L          +d ++rq  +A  +++ L ++v++l+ EL+
  gi|336254334|ref|YP_004597441.1|  34 LAETVADLETRVDEHERRLADLEAAVRSLEGyvgnvesINDDVERQAASAVATVDRLERRVDRLEVELD 102
                                       678999*****************9999999999999667****************************97 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.44   1.6e+02      11      27 ..       2      18 ..       1      31 [. 0.76
   2 !   11.6   0.3   0.00068      0.25       3      31 ..      35      63 ..      33      74 .. 0.83
   3 ?    4.3   0.2      0.13        47       6      18 ..      87      99 ..      59     106 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.44
                              XhlA 11 tkldnleervdkleeka 27
                                      t+ld le+r++ +e+  
  gi|336254334|ref|YP_004597441.1|  2 TDLDRLEQRLSAVERVV 18
                                      78999999999999875 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00068
                              XhlA  3 kerlerietkldnleervdkleekaaeae 31
                                       e ++ +et++d++e r+ +le   +  e
  gi|336254334|ref|YP_004597441.1| 35 AETVADLETRVDEHERRLADLEAAVRSLE 63
                                      58999****************98877665 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.13
                              XhlA  6 lerietkldnlee 18
                                      + r+e+++d le 
  gi|336254334|ref|YP_004597441.1| 87 VDRLERRVDRLEV 99
                                      3333333333333 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.8e-05      0.01     721     791 ..      34     104 ..       4     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                               FPP 721 lkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaLeveLeee 791
                                       l     + E  ++e +  L+ l+ + + +e  + + + ++ ++e +a+ + a + +l++++++LeveL++ 
  gi|336254334|ref|YP_004597441.1|  34 LAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQAASAVATVDRLERRVDRLEVELDDV 104
                                       45556778888999999999999999999999999999******************************985 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 ?    1.1   0.1       1.5   5.3e+02       3      39 ..       5      40 ..       3      47 .. 0.55
   2 ?    6.7   0.0     0.027       9.7       4      38 ..      40      77 ..      37      82 .. 0.54
   3 ?    5.4   0.0     0.067        24       2      20 ..      87     105 ..      86     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.5
                         FlaC_arch  3 delEnklsklsteletvkkeneelsksveelkenVkd 39
                                      d lE++ls ++  +    + ++el  +v  l e+V d
  gi|336254334|ref|YP_004597441.1|  5 DRLEQRLSAVERVVVDGDAALDELA-EVAALAETVAD 40
                                      6677777777765554455555543.34444444444 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.027
                         FlaC_arch  4 elEnklsklsteletvkk...eneelsksveelkenVk 38
                                      +lE+++++++ +l+ +++   ++e    +ve ++++V+
  gi|336254334|ref|YP_004597441.1| 40 DLETRVDEHERRLADLEAavrSLEGYVGNVESINDDVE 77
                                      56666666666554444400033444456666666664 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.067
                         FlaC_arch   2 idelEnklsklsteletvk 20 
                                       +d lE ++++l++el+ v+
  gi|336254334|ref|YP_004597441.1|  87 VDRLERRVDRLEVELDDVR 105
                                       799************9998 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 ?   -2.0   0.1       9.6   3.5e+03      36      44 ..       4      12 ..       1      17 [. 0.71
   2 ?    7.2   0.0     0.013       4.7      27      46 ..      43      62 ..      34      64 .. 0.76
   3 ?    6.1   0.0     0.027       9.9      27      46 ..      85     104 ..      80     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.6
                             HSBP1 36 iDdLEksia 44
                                      +D LE+ ++
  gi|336254334|ref|YP_004597441.1|  4 LDRLEQRLS 12
                                      788888776 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.013
                             HSBP1 27 sriDdMssriDdLEksiadl 46
                                      +r+D+ ++r+ dLE+ + +l
  gi|336254334|ref|YP_004597441.1| 43 TRVDEHERRLADLEAAVRSL 62
                                      68888888888888877665 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.027
                             HSBP1  27 sriDdMssriDdLEksiadl 46 
                                         +D +++r+D LE  ++d+
  gi|336254334|ref|YP_004597441.1|  85 ATVDRLERRVDRLEVELDDV 104
                                       57899*********999885 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 ?    8.1   0.4    0.0081         3      34      80 ..      13      59 ..       3      78 .. 0.82
   2 ?    6.8   0.0     0.021       7.8       6      41 ..      79     114 ..      75     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0081
                       TMF_TATA_bd 34 elerleaerdeareeivklmkeneelkelkkeleelekeleelqery 80
                                       +er+    d+a +e++++ +  e++++l+++++e e++l++l+   
  gi|336254334|ref|YP_004597441.1| 13 AVERVVVDGDAALDELAEVAALAETVADLETRVDEHERRLADLEAAV 59
                                      56677777899999999999999999999999999999999998765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.021
                       TMF_TATA_bd   6 sagpsvqlverlsseirrlEgElaslkeelerleae 41 
                                       +a + v +v+rl+ ++ rlE+El  ++  + r  +e
  gi|336254334|ref|YP_004597441.1|  79 QAASAVATVDRLERRVDRLEVELDDVRGGVLREPTE 114
                                       5678899****************9988766665555 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 ?   14.6   3.7   6.8e-05     0.025      11     100 ..       4      93 ..       1     101 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.8e-05
                             DHR10  11 laelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrql 87 
                                       l++lE++  +++  +   + +  +l+++ +l+e++++   +++e +++l++l++a+ ++e  +  +e+  + ++rq 
  gi|336254334|ref|YP_004597441.1|   4 LDRLEQRLSAVERVVVDGDAALDELAEVAALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQA 80 
                                       66777777777777777777888999*************************************************** PP

                             DHR10  88 enaeeklerlreq 100
                                       ++a    +rl+++
  gi|336254334|ref|YP_004597441.1|  81 ASAVATVDRLERR 93 
                                       *********9986 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5   7.8e-05     0.029      63     159 ..      10     105 ..       3     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.8e-05
                            DUF745  63 lveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektq 139
                                        +  +e+ + + +a+++e  +  + +e+ a++ ++ +++ ++ l+ l+a++++ +  + n+e++++ +++++a+  +
  gi|336254334|ref|YP_004597441.1|  10 RLSAVERVVVDGDAALDELAEVAALAETVADLETR-VDEHERRLADLEAAVRSLEGYVGNVESINDDVERQAASAVA 85 
                                       34444555555555665555555555555554443.467788999******************************** PP

                            DUF745 140 lleaAkkRveeLkkqlkear 159
                                        ++  ++Rv++L+ +l+++r
  gi|336254334|ref|YP_004597441.1|  86 TVDRLERRVDRLEVELDDVR 105
                                       *************9999877 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 ?   14.2   1.1   0.00013     0.047      14      92 ..       4      87 ..       2     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00013
                      Syntaxin-6_N 14 lnkaeslyrrwerlledtsss.....tseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrraf 87
                                      l+++e+ ++  er+  d++++     +   l et  +L++ +++ e  l dLe +vr +e    +++  +++++r+ a 
  gi|336254334|ref|YP_004597441.1|  4 LDRLEQRLSAVERVVVDGDAAldelaEVAALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQAAS 82
                                      56666666666666666555344555778899**************************999888888888888888776 PP

                      Syntaxin-6_N 88 veevr 92
                                       +++ 
  gi|336254334|ref|YP_004597441.1| 83 AVATV 87
                                      55554 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1       1.1   4.1e+02      42      50 ..       4      12 ..       3      14 .. 0.83
   2 ?    9.2   1.0    0.0024      0.87      23      50 ..      33      60 ..      25      61 .. 0.89
   3 ?    9.0   0.4    0.0028         1      33      46 ..      85      98 ..      82     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.1
                                      HHHHHHHHH CS
                         Trimer_CC 42 LDrLEetvq 50
                                      LDrLE+   
  gi|336254334|ref|YP_004597441.1|  4 LDRLEQRLS 12
                                      8****9865 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0024
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Trimer_CC 23 RLEEelrkLqatVQelQkRLDrLEetvq 50
                                       L E +  L + V e+ +RL  LE +v 
  gi|336254334|ref|YP_004597441.1| 33 ALAETVADLETRVDEHERRLADLEAAVR 60
                                      5789999*****************9985 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0028
                                      HHHHHHHHHHHHHH CS
                         Trimer_CC 33 atVQelQkRLDrLE 46
                                      atV  l +R+DrLE
  gi|336254334|ref|YP_004597441.1| 85 ATVDRLERRVDRLE 98
                                      8************9 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.7   0.00021     0.076       9      95 ..       3      93 ..       1     106 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00021
                                      HHHHHHHHHHHHHHHHCCSSC.SSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT...HTTHHHHHHHHH CS
                          Spectrin  9 dadeleeWieekeellssedl.gkdleevqallkkhkaleaelaaqqervkalnelaeklldeg...hsaseeieerle 83
                                      d+d le+ ++  e+ + + d    +l+ev al ++  +le  ++++++r+ +l++  ++l+ +    +s ++++e + +
  gi|336254334|ref|YP_004597441.1|  3 DLDRLEQRLSAVERVVVDGDAaLDELAEVAALAETVADLETRVDEHERRLADLEAAVRSLEGYVgnvESINDDVERQAA 81
                                      78999999********999998999*****************************9998885443233333355555555 PP

                                      HHHHHHHHHHHH CS
                          Spectrin 84 elnerWeeLkel 95
                                            + L+++
  gi|336254334|ref|YP_004597441.1| 82 SAVATVDRLERR 93
                                      555555555555 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00029      0.11      45     104 ..      23      82 ..       8      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00029
                           DUF3450  45 ekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllek 104
                                        + + lae+ al e +++le   ++ er +a++e+ + sle    ++e i+++++    +
  gi|336254334|ref|YP_004597441.1|  23 AALDELAEVAALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQAAS 82 
                                       566778899999999999999999999999999999999999999999999888765554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   0.00017     0.063      55     122 ..      32      99 ..      12     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00017
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       ++la+t  +L+ r+d+ +++l + +++ ++++  v +v++  ++++++  s  ++v  le +++r+e 
  gi|336254334|ref|YP_004597441.1|  32 AALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQAASAVATVDRLERRVDRLEV 99 
                                       57999999********************************99**********************9985 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 ?    6.9   0.5     0.018       6.4       2      54 ..       7      58 ..       2      63 .. 0.80
   2 ?    3.8   0.2      0.17        60       2      31 ..      34      63 ..      33      81 .. 0.72
   3 ?    6.3   0.1     0.027        10       8      40 ..      75     107 ..      68     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.018
                     TolA_bind_tri  2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleer 54
                                      le+r++ +Er +     + l+ + ++ al + +++L   ++e++ +l +le  
  gi|336254334|ref|YP_004597441.1|  7 LEQRLSAVERVVVD-GDAALDELAEVAALAETVADLETRVDEHERRLADLEAA 58
                                      78888888888877.57888888899999999999999999999999888765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.17
                     TolA_bind_tri  2 ledrvarLErilearsqlllelqqqlealq 31
                                      l + va LE  ++ +++ l +l   + +l+
  gi|336254334|ref|YP_004597441.1| 34 LAETVADLETRVDEHERRLADLEAAVRSLE 63
                                      567788888888888888888877766664 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.027
                     TolA_bind_tri   8 rLErilearsqlllelqqqlealqqelreLRGq 40 
                                        +Er++++   +  +l +++++l+ el++ RG 
  gi|336254334|ref|YP_004597441.1|  75 DVERQAASAVATVDRLERRVDRLEVELDDVRGG 107
                                       5799999988888899***************96 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.035        13      66     110 ..      35      79 ..      30      84 .. 0.83
   2 ?    8.6   0.0    0.0043       1.6      59     117 ..      70     128 ..      67     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.035
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT CS
                        DASH_Spc19  66 eellekaekeleklerreetLkaklelqegrlsnaesskkeeees 110
                                       +e +  +e+ +++ err   L+a ++ +eg + n es +++ e +
  gi|336254334|ref|YP_004597441.1|  35 AETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQ 79 
                                       67788899**********************999987777766655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0043
                                       HHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXX CS
                        DASH_Spc19  59 eeiePqieellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeee 117
                                       e+i+  +e +   a + +++lerr + L+ +l+  +g + ++ +++++e +++ s++++
  gi|336254334|ref|YP_004597441.1|  70 ESINDDVERQAASAVATVDRLERRVDRLEVELDDVRGGVLREPTERETEGTRSGSDSDD 128
                                       68999999**********************99999888888666666666655555544 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.8   0.00022     0.079     513     585 ..      32     104 ..       7     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                     Myosin_tail_1 513 knvekqlstlqaqlsdlkkkleeeasavealeeakkrlqrelealtqrleekaaaydklektkkRlqqeldDl 585
                                        ++   ++ l++++ +  ++l +  +av +le     ++   ++++++  +  a++d+le+  +Rl+ eldD+
  gi|336254334|ref|YP_004597441.1|  32 AALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQAASAVATVDRLERRVDRLEVELDDV 104
                                       4556667778888888888888888888888888888888888888888888899999999999999999997 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.2    0.0014      0.52      84     128 ..      22      66 ..       5      71 .. 0.82
   2 ?   10.1   0.4    0.0012      0.42      22      64 ..      56      98 ..      55     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                         PspA_IM30  84 eLArealaeikslekqaealetqlaqqrsaveqlrkqlealetki 128
                                       ++A   lae + l++++++let +++ +   ++l+++++ le  +
  gi|336254334|ref|YP_004597441.1|  22 DAALDELAEVAALAETVADLETRVDEHERRLADLEAAVRSLEGYV 66 
                                       567777889999999999999999999999999999999998755 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0012
                         PspA_IM30 22 eDPekileqairdmqselakarqalaqviarqkqlerkleeqk 64
                                      e + + le ++ +++s  +++++++a+++a+  +ler++++ +
  gi|336254334|ref|YP_004597441.1| 56 EAAVRSLEGYVGNVESINDDVERQAASAVATVDRLERRVDRLE 98
                                      556688999******************************9876 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   0.00015     0.055      46     135 ..       2      94 ..       1     231 [. 0.59

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00015
                                       S-HHHHHHHHHHHHH.T....TT.HHHHH..HHHTT.---HHHHHHHHHTT---HHHHHHHHHHHHHHHTTTTT--- CS
                                       xxxxxxxxxxxxxxx.xx..xxxxxxxxx..xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III  46 tdleeInaRldaVee.le..neelreelr..ellrr.lpDleRllsrislgkakardlkallealkaleelvallek 116
                                       tdl+++++Rl+aVe+ +   +++  +el   ++l + + Dle  + +      +  dl+a +++l+     v+  ++
  gi|336254334|ref|YP_004597441.1|   2 TDLDRLEQRLSAVERvVVdgDAA-LDELAevAALAEtVADLETRVDEHER---RLADLEAAVRSLEGYVGNVESIND 74 
                                       89************965333111.22222221233335566665543332...223444444444443333333333 PP

                                       SSTHHHHHHHHH..HHHHHHB CS
                                       xxxxxxxxxxxx..xxxxxxx RF
                          MutS_III 117 eklaeseeesla..elleeai 135
                                       + + +  + ++a  ++le+ +
  gi|336254334|ref|YP_004597441.1|  75 DVERQAAS-AVAtvDRLERRV 94 
                                       32222222.222233333322 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   0.00016     0.059       8     113 ..       5     109 ..       2     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00016
                               ERM   8 releerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerkl 84 
                                       ++le+rL  ++  +    +aL e  e    Lae    +e+  ++ e++ a++e++ + l+    + e+  +++er++
  gi|336254334|ref|YP_004597441.1|   5 DRLEQRLSAVERVVVDGDAALDELAEV-AALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQA 80 
                                       67999**99999999999999988776.689********************************************** PP

                               ERM  85 reaeleaarleeeserkeeeaerLkeele 113
                                       + a + + rle+ ++r e e +  +  ++
  gi|336254334|ref|YP_004597441.1|  81 ASAVATVDRLERRVDRLEVELDDVRGGVL 109
                                       *************9999999887776644 PP

>> Lzipper-MIP1  Leucine-zipper of ternary complex factor MIP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4    0.0077       2.8      52      81 ..      23      52 ..       4      54 .. 0.85
   2 ?   12.3   0.9   0.00042      0.15       7      79 ..      32     106 ..      26     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0077
                      Lzipper-MIP1 52 kakellkeiallEeevvkLEqkllsLyrkl 81
                                      +a ++l+e+a l e+v+ LE ++++ +r+l
  gi|336254334|ref|YP_004597441.1| 23 AALDELAEVAALAETVADLETRVDEHERRL 52
                                      56789******************9988887 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00042
                      Lzipper-MIP1   7 ssLeqeveqLqerLqeeeklrraLekal...ssssdgsllslstllpkkakellkeiallEeevvkLEqkllsLyr 79 
                                       ++L + v+ L++r +e+e+  + Le a+   +  + g+  s++  + ++a+   + +  lE  v +LE +l++ + 
  gi|336254334|ref|YP_004597441.1|  32 AALAETVADLETRVDEHERRLADLEAAVrslE-GYVGNVESINDDVERQAASAVATVDRLERRVDRLEVELDDVRG 106
                                       5789999***********999****9996531.234555566666889********************99998765 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.6    0.0032       1.2      12      63 ..      30      71 ..       1      78 [. 0.51
   2 ?    2.5   0.1      0.54     2e+02      20      37 ..      87     104 ..      76     110 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0032
                           NPV_P10 12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63
                                      +++a+ + V  l+++vd+ +  l d          + a++ +le  v n+++
  gi|336254334|ref|YP_004597441.1| 30 EVAALAETVADLETRVDEHERRLAD----------LEAAVRSLEGYVGNVES 71
                                      3333333333333333333333333..........33333333333333333 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.54
                           NPV_P10  20 Vdalqqqvddvqenlpdv 37 
                                       Vd l+ +vd+++ +l dv
  gi|336254334|ref|YP_004597441.1|  87 VDRLERRVDRLEVELDDV 104
                                       666666666666666665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.7   0.00027     0.099     178     259 ..       6      89 ..       2     104 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                              Spc7 178 eleeeleklqeaaeeles.id.keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiae 252
                                       +le++l   ++ + + ++ +d  +e+++l e++a+l++ ++e++++la+l++ + +le  + ++++  +++e + a+
  gi|336254334|ref|YP_004597441.1|   6 RLEQRLSAVERVVVDGDAaLDeLAEVAALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQAAS 82 
                                       56666666666555554444446777777777777777777777777777777777777777777777777777666 PP

                              Spc7 253 aervlee 259
                                       a  ++++
  gi|336254334|ref|YP_004597441.1|  83 AVATVDR 89 
                                       6555443 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.7    0.0051       1.9      26      54 ..      31      59 ..       2      83 .. 0.54
   2 ?    3.9   0.2      0.23        85      31      52 ..      85     106 ..      68     121 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0051
                                      HHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                              SlyX 26 vaeqqqqidrlqrqlrllaerlkeleess 54
                                      va+ +++++ l++++++ ++rl++le++ 
  gi|336254334|ref|YP_004597441.1| 31 VAALAETVADLETRVDEHERRLADLEAAV 59
                                      33344444444444444444444444432 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHT-XXXXX CS
                              SlyX  31 qqidrlqrqlrllaerlkelee 52 
                                        ++drl+r++++l+ +l +++ 
  gi|336254334|ref|YP_004597441.1|  85 ATVDRLERRVDRLEVELDDVRG 106
                                       5688888888888887777665 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.084        31      67      98 ..      34      58 ..      17      68 .. 0.52
   2 ?    6.7   0.3     0.019       6.9      59      96 ..      68     105 ..      30     108 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.084
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2 67 Leerketlekeiktlekqleklekeleelkee 98
                                      L e+       ++ le + +++e++l++l++ 
  gi|336254334|ref|YP_004597441.1| 34 LAET-------VADLETRVDEHERRLADLEAA 58
                                      3333.......333333333333333333333 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.019
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  59 dkeevkeeLeerketlekeiktlekqleklekeleelk 96 
                                       ++e++++++e +++++ + +++le++ ++le el++++
  gi|336254334|ref|YP_004597441.1|  68 NVESINDDVERQAASAVATVDRLERRVDRLEVELDDVR 105
                                       46778888888888888888888888888888887765 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       9.9   3.6e+03      62      72 ..       3      13 ..       2      15 .. 0.74
   2 ?    8.7   0.1    0.0047       1.7      31      67 ..      27      63 ..      22      70 .. 0.81
   3 ?    2.5   0.0       0.4   1.5e+02      41      65 ..      79     103 ..      70     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.9
                        TMF_DNA_bd 62 eleeleerlke 72
                                      +l++le+rl++
  gi|336254334|ref|YP_004597441.1|  3 DLDRLEQRLSA 13
                                      57889999876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0047
                        TMF_DNA_bd 31 lnntikkLrkknkelekeikelkkkleklekeleele 67
                                      + + +  L +++++le+ ++e +++l++le  + +le
  gi|336254334|ref|YP_004597441.1| 27 ELAEVAALAETVADLETRVDEHERRLADLEAAVRSLE 63
                                      5667778888999999999999999999999888887 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.4
                        TMF_DNA_bd  41 knkelekeikelkkkleklekelee 65 
                                       +++ +  ++++l++++++le el+ 
  gi|336254334|ref|YP_004597441.1|  79 QAASAVATVDRLERRVDRLEVELDD 103
                                       5667778899999999999999886 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0021      0.78      46     105 ..      10      70 ..       2      74 .. 0.60
   2 ?   10.7   0.1    0.0011      0.42      22      87 ..      28     101 ..      22     108 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0021
                      Baculo_PEP_C  46 qLnalsedlksllaeldtrldtl..ltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNin 105
                                       +L+a    +++++ + d++ld+l  +++L ++++ l+   d+ + +L  l++ + +L   v+N++
  gi|336254334|ref|YP_004597441.1|  10 RLSA----VERVVVDGDAALDELaeVAALAETVADLEtrvDEHERRLADLEAAVRSLEGYVGNVE 70 
                                       4443....455555566666665223567777777776666666777777777777777777765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0011
                      Baculo_PEP_C  22 LnairlqnvqilaqlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnalq...dtlrneL 87 
                                       L+ + ++  ++ a+l+t +d+ e++L +l+++++sl   + +      +++ +++   +++ +l+   d l+ eL
  gi|336254334|ref|YP_004597441.1|  28 LAEVAALAETV-ADLETRVDEHERRLADLEAAVRSLEGYVGNvesindDVERQAASAVATVDRLErrvDRLEVEL 101
                                       56665555566.999999999999999999999997554444443333333333333333333334444444444 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2      0.03        11      19      50 ..      31      62 ..      24      72 .. 0.64
   2 ?    6.1   0.1     0.026       9.4      21      51 ..      75     105 ..      65     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.03
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkdL 50
                                      + +l + +a+l+  +++   + ++Lea v+ L
  gi|336254334|ref|YP_004597441.1| 31 VAALAETVADLETRVDEHERRLADLEAAVRSL 62
                                      33455556666666666666666666666655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC  21 qlkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                       +++++ a   a++++l  + ++Le e++d +
  gi|336254334|ref|YP_004597441.1|  75 DVERQAASAVATVDRLERRVDRLEVELDDVR 105
                                       789999999***************9999975 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   0.00044      0.16      83     156 ..      26     102 ..       2     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                         Golgin_A5  83 qqqaeaeslreqlqeleeqleeerkakeeveaelerlke...elryleeelvrskatlqsrikdrekeieklrnqlt 156
                                        + ae+  l e +++le++++e +++  ++ea +++l+    +++++++++ r+ a+ ++ + + e+ +++l+ +l 
  gi|336254334|ref|YP_004597441.1|  26 DELAEVAALAETVADLETRVDEHERRLADLEAAVRSLEGyvgNVESINDDVERQAASAVATVDRLERRVDRLEVELD 102
                                       567899*************************99999875222789999***********************998875 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7   0.00095      0.35      35      75 ..      38      78 ..       2      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00095
                           DUF1515 35 rakmyrkmdelvervtalegsvvklkaditsvkevtedvkk 75
                                       a++  ++de   r++ le++v  l++ + +v  + +dv++
  gi|336254334|ref|YP_004597441.1| 38 VADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVER 78
                                      578899*********************************98 PP

>> DUF3138  Protein of unknown function (DUF3138)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00037      0.13      12      74 ..      23      83 ..      14     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00037
                           DUF3138 12 laldglaaaaatadrikalkaqltalqrqvkelraalaaakaaaGgkissqkaaaaaaaaaea 74
                                      +ald la +aa a+ ++ l++++++ +r++++l+aa+ + ++  G  + s++      a a a
  gi|336254334|ref|YP_004597441.1| 23 AALDELAEVAALAETVADLETRVDEHERRLADLEAAVRSLEGYVGN-VESINDDVERQA-ASA 83
                                      59***************************************99998.555554332222.111 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00045      0.17      24     102 ..      29     107 ..       3     162 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00045
                              Fez1  24 aevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelr 100
                                       aev++ ++ +  l +++ e + +l + e+++++le  + + +  ++ +e + + + ++++ l+ +v++le el ++r
  gi|336254334|ref|YP_004597441.1|  29 AEVAALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQAASAVATVDRLERRVDRLEVELDDVR 105
                                       33333333344444444444444444444444444444444444444444444446677777777777777777777 PP

                              Fez1 101 ee 102
                                         
  gi|336254334|ref|YP_004597441.1| 106 GG 107
                                       64 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 ?   10.7   0.1   0.00093      0.34      20      77 ..      31      88 ..      13     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00093
                        Phage_GP20 20 ldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakia 77
                                      ++ + e + +l++++++ +  L dL++++   e    ++e+++ +++++ a + a + 
  gi|336254334|ref|YP_004597441.1| 31 VAALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQAASAVATVD 88
                                      5566777889999999999999999999666666666666666666666665555554 PP

>> TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       8.9   3.3e+03       8      20 ..       6      18 ..       3      19 .. 0.58
   2 ?   11.3   1.3    0.0006      0.22       2      59 ..      41      98 ..      30     101 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 8.9
                     TRAF_BIRC3_bd  8 aLetkvatFEnIV 20
                                       Le+++   E +V
  gi|336254334|ref|YP_004597441.1|  6 RLEQRLSAVERVV 18
                                      5666666655555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0006
                     TRAF_BIRC3_bd  2 lekklsaLetkvatFEnIVsVLnrEverssttieaverqrrldqekieaLekKvrqLe 59
                                      le ++++ e+++a  E  V  L+  v  +++  ++verq + +  +++ Le++v  Le
  gi|336254334|ref|YP_004597441.1| 41 LETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQAASAVATVDRLERRVDRLE 98
                                      789999*************************************************998 PP

>> Vir_act_alpha_C  Virulence activator alpha C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4      0.01       3.7      16      43 ..      33      60 ..      18      68 .. 0.84
   2 ?    5.4   0.1     0.081        30      12      46 ..      64     100 ..      56     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.01
                   Vir_act_alpha_C 16 dpealieeLerrreeheekLaeyeeiee 43
                                        ++++++Le r +ehe++La++e+  +
  gi|336254334|ref|YP_004597441.1| 33 ALAETVADLETRVDEHERRLADLEAAVR 60
                                      5578999****************97655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.081
                   Vir_act_alpha_C  12 aavldpealieeLerrreeheekLaeyeeieerl..e 46 
                                       + v++ e + +++er+ + + ++ +++e++ +rl  e
  gi|336254334|ref|YP_004597441.1|  64 GYVGNVESINDDVERQAASAVATVDRLERRVDRLevE 100
                                       56788999********************998887661 PP

>> Streptin-Immun  Lantibiotic streptin immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00085      0.31      13      83 ..      26      98 ..      18     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00085
                    Streptin-Immun 13 ekiatlnkmaevlvnlkse.deetrrlakydfsklnltesv.tleqiekeieklqnelskkideyeelvrkld 83
                                      ++ a +  +ae + +l++  de++rrla  + +   l   v ++e i+ ++e+       ++d+ e  v +l+
  gi|336254334|ref|YP_004597441.1| 26 DELAEVAALAETVADLETRvDEHERRLADLEAAVRSLEGYVgNVESINDDVERQAASAVATVDRLERRVDRLE 98
                                      566778889999999987549999*************9998679*********99999999*****9999998 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.5   0.00095      0.35     133     208 ..      29     121 ..       4     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00095
                           DUF4407 133 aelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld.. 207
                                       ae+a+l + +a+l++ +d+ e+rl++l+a+++  l+g  g+ ++     +  a ++ a  d+++++++ l+ +ld  
  gi|336254334|ref|YP_004597441.1|  29 AEVAALAETVADLETRVDEHERRLADLEAAVR-SLEGYVGNVESINDDVERQAASAVATVDRLERRVDRLEVELDdv 104
                                       68888999999999999999999999999888.77888888777777777788888888888888888888887777 PP

                           DUF4407 208 ................a 208
                                                       +
  gi|336254334|ref|YP_004597441.1| 105 rggvlrepteretegtR 121
                                       66666655555444440 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3    0.0071       2.6      34      60 ..      37      63 ..      23      97 .. 0.54
   2 ?    1.9   0.1      0.66   2.4e+02      40      74 ..      85     103 ..      68     110 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0071
                           DUF2730 34 dleklaekveendkrlteletkvenLP 60
                                       ++ l+  v+e+++rl++le+ v +L 
  gi|336254334|ref|YP_004597441.1| 37 TVADLETRVDEHERRLADLEAAVRSLE 63
                                      344555566666666666666666653 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.66
                           DUF2730  40 ekveendkrlteletkvenLPtakdlekLklllad 74 
                                        +v++ ++r+++le++++                d
  gi|336254334|ref|YP_004597441.1|  85 ATVDRLERRVDRLEVELD----------------D 103
                                       445555555555555555................4 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   9.3     0.012       4.6     128     215 ..       3      96 ..       2     110 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.012
                       Tropomyosin 128 dLeraeeraeaaeskive....Lee..eLkvvgnnlksLevseekaseredeyeeeirtLeekLkeaeeRaeeAErs 198
                                       dL+r e+r  a e  +v+    L e  e+   ++++ +Le   ++   r  + e ++r+Le    + e   ++ Er+
  gi|336254334|ref|YP_004597441.1|   3 DLDRLEQRLSAVERVVVDgdaaLDElaEVAALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDDVERQ 79 
                                       66777777777766665322224433355666788888888888888888888888888887777777766666666 PP

                       Tropomyosin 199 vqkLekevdrledelea 215
                                       ++   ++vdrle +++ 
  gi|336254334|ref|YP_004597441.1|  80 AASAVATVDRLERRVDR 96 
                                       55444444444444432 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.0    0.0036       1.3      75     177 ..      30      97 ..       2     104 .. 0.43

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0036
                             ATG16  75 kiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekek 151
                                       +++                                   +l e+    e+r++e e++ a+le +++++e  +   e 
  gi|336254334|ref|YP_004597441.1|  30 EVA-----------------------------------ALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVES 71 
                                       222...................................222333333333333333333333333333333333333 PP

                             ATG16 152 lvqdlqDElsaLqlqlnqaEeklrkl 177
                                        ++d+    ++   ++  +E + ++l
  gi|336254334|ref|YP_004597441.1|  72 INDDVERQAASAVATVDRLERRVDRL 97 
                                       33344444444444444444444443 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 ?   -1.3   0.0         8   2.9e+03      60      69 ..       6      15 ..       2      17 .. 0.63
   2 ?    6.3   0.5     0.033        12      15      55 ..      25      60 ..      18      71 .. 0.54
   3 ?    7.1   0.1     0.019         7      17      41 ..      78     102 ..      68     107 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 8
                               CLZ 60 kLkqRitkLE 69
                                      +L+qR++++E
  gi|336254334|ref|YP_004597441.1|  6 RLEQRLSAVE 15
                                      5666666666 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.033
                               CLZ 15 LDeeaakagaeqkeleekverLessLeaLqtrlarLlaeye 55
                                      LDe      ae   l e v  Le++++  + rla L a + 
  gi|336254334|ref|YP_004597441.1| 25 LDEL-----AEVAALAETVADLETRVDEHERRLADLEAAVR 60
                                      5554.....33444445555555555555555555544433 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.019
                               CLZ  17 eeaakagaeqkeleekverLessLe 41 
                                       ++aa+a a+ + le++v+rLe +L+
  gi|336254334|ref|YP_004597441.1|  78 RQAASAVATVDRLERRVDRLEVELD 102
                                       3344555666666666666666665 PP

>> MRF_C1  Myelin gene regulatory factor -C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.19        69      24      35 ..       5      16 ..       1      17 [. 0.87
   2 ?    4.0   0.1     0.073        27      19      35 ..      34      50 ..      29      57 .. 0.82
   3 ?    3.1   0.2      0.15        54      24      35 ..      88      99 ..      86     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.19
                            MRF_C1 24 gnLEtrIeelEk 35
                                      + LE+r++++E+
  gi|336254334|ref|YP_004597441.1|  5 DRLEQRLSAVER 16
                                      67********97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.073
                            MRF_C1 19 LcklTgnLEtrIeelEk 35
                                      L+    +LEtr++e E+
  gi|336254334|ref|YP_004597441.1| 34 LAETVADLETRVDEHER 50
                                      5555579*******986 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.15
                            MRF_C1 24 gnLEtrIeelEk 35
                                      + LE+r+++lE 
  gi|336254334|ref|YP_004597441.1| 88 DRLERRVDRLEV 99
                                      68********95 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.7    0.0024       0.9     227     294 ..      27     102 ..       2     120 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0024
                              FUSC 227 rmlallallsslarllarlraeeaaavpelaallaelaal............eaaaaaealeaalaalrarlralrr 291
                                       +++++ al+  +a+l  r++++e+     la+l a++++l            + +++a+   a +++l++r+++l+ 
  gi|336254334|ref|YP_004597441.1|  27 ELAEVAALAETVADLETRVDEHER----RLADLEAAVRSLegyvgnvesindDVERQAASAVATVDRLERRVDRLEV 99 
                                       333333333333333333333333....3333333333333336666666776667777777888888888877777 PP

                              FUSC 292 ale 294
                                       +l+
  gi|336254334|ref|YP_004597441.1| 100 ELD 102
                                       766 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2       3.7   1.4e+03      38      50 ..       5      17 ..       2      27 .. 0.60
   2 ?    7.3   4.8     0.016         6       7      42 ..      26      57 ..      22      85 .. 0.70
   3 ?    8.2   1.5    0.0083       3.1      37      57 ..      87     107 ..      79     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.7
                              HalX 38 qeLearleelraq 50
                                      ++Le+rl ++++ 
  gi|336254334|ref|YP_004597441.1|  5 DRLEQRLSAVERV 17
                                      4666666666654 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.016
                              HalX  7 eelqelfaLasKravLeaekseaeLadseeYqeLea 42
                                      +el e  aLa+++a Le+ ++e+e+    + ++Lea
  gi|336254334|ref|YP_004597441.1| 26 DELAEVAALAETVADLETRVDEHER----RLADLEA 57
                                      5677778888888888888888777....3444554 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0083
                              HalX  37 YqeLearleelraqldetlde 57 
                                        ++Le+r+++l+ +ld++   
  gi|336254334|ref|YP_004597441.1|  87 VDRLERRVDRLEVELDDVRGG 107
                                       579*************99876 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 ?    3.8   6.4      0.16        58      39      85 ..      29      75 ..      11     147 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.16
                            CENP-Q 39 aqLspelhslelLeaeiekeeralerdyeaLreLeknakaearerke 85
                                      a+++++ +++++Le  +++ er l+  ++a r+Le  + + ++ +++
  gi|336254334|ref|YP_004597441.1| 29 AEVAALAETVADLETRVDEHERRLADLEAAVRSLEGYVGNVESINDD 75
                                      56678889999999999999999999999999999776666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                       158  (0.00881254); 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):              49  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.41
# Mc/sec: 1681.49
//
Query:       gi|336254335|ref|YP_004597442.1|  [L=351]
Description: ATPase-like protein [Halopiger xanaduensis SH-6]
Scores for 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   27.1   0.0    2.1e-05   24.8   0.0    2.0  1  DUF87          Helicase HerA, central domain
    6.4e-05   21.7   0.3      0.032   12.8   0.0    2.2  2  DUF853         Bacterial protein of unknown function (DUF853)
     0.0022   18.4   3.2     0.0097   16.3   0.3    2.4  2  AAA_16         AAA ATPase domain
     0.0038   16.2   0.0        0.3    9.9   0.0    2.1  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
     0.0049   17.3   0.0        4.4    7.7   0.1    2.7  3  AAA            ATPase family associated with various cellular
  ------ inclusion threshold ------
      0.011   16.1   0.1          5    7.4   0.0    2.7  3  AAA_22         AAA domain
       0.02   14.3   0.4        4.5    6.6   0.1    2.5  3  FtsK_SpoIIIE   FtsK/SpoIIIE family
       0.03   14.0   0.0       0.94    9.1   0.0    2.4  3  Zot            Zonular occludens toxin (Zot)
      0.079   12.2   0.0       0.17   11.1   0.0    1.5  1  Zeta_toxin     Zeta toxin


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0     1e-08   2.1e-05      10     108 ..      29     119 ..      18     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1e-08
                             DUF87  10 sevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal..ekllsekvkvitpsps 84 
                                       ++ ++y+dl+    + ++++g+ G+GKS+t +v  eel++  g+  +i+Dp G + ++     + +  v+v+t +  
  gi|336254335|ref|YP_004597442.1|  29 DGADLYVDLDGP--HAMLVVGKRGYGKSYTLGVVAEELARASGVAPVIVDPMGVFETLAdgSTGEPVPVEVVTEP-- 101
                                       556777777666..779************************************9999996544444455566655.. PP

                             DUF87  85 akdkelkinpwsldpeelldllee 108
                                             ++ +++ldp+  + ll+ 
  gi|336254335|ref|YP_004597442.1| 102 ------TVAVDALDPRSWCALLGL 119
                                       ......788888888877777777 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1   0.00096       1.9      25      64 ..      44      84 ..      26     100 .. 0.82
   2 !   12.8   0.0   1.6e-05     0.032     261     339 ..     226     299 ..     217     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00096
                            DUF853 25 liaGatGtGktvtLqvlaeslsea.GvpvfladvkGdLsgi 64
                                      l+ G  G Gk  tL v+ae+l++a Gv+ +++d  G +  +
  gi|336254335|ref|YP_004597442.1| 44 LVVGKRGYGKSYTLGVVAEELARAsGVAPVIVDPMGVFETL 84
                                      799******************97549999999977766555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.6e-05
                            DUF853 261 fffdeahLLfndapkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaad 337
                                       +++deah +f + ++     + +++   r+ Gv + + tq+P+ l +t ++q    v h l a   +d  a+ aa  
  gi|336254335|ref|YP_004597442.1| 226 LLLDEAHAFFAGVAAD---ALHRILTRGRAPGVSLVLATQQPSSLSETAVSQSDVLVAHRLTA--EADLAALEAAQP 297
                                       568*******997765...5556788899*************************999999877..556777777766 PP

                            DUF853 338 tf 339
                                       t+
  gi|336254335|ref|YP_004597442.1| 298 TY 299
                                       66 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   0.3   4.9e-06    0.0097      23     148 ..      39     235 ..      32     259 .. 0.60
   2 ?    3.1   0.5     0.055   1.1e+02     106     144 ..     268     321 ..     202     330 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.9e-06
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekd..........ggiflrgkcdqlesa..ipy......salaqalareel 81 
                                       +p+++l++G +G GKs  +  ++++l ++           g+f ++ +d + ++  +p        + ++al+ ++ 
  gi|336254335|ref|YP_004597442.1|  39 GPHAMLVVGKRGYGKSYTLGVVAEELARAsgvapvivdpMGVF-ETLADGS-TGepVPVevvtepTVAVDALDPRSW 113
                                       6899************************977775555432222.2222222.1233444666664669999999999 PP

                            AAA_16  82 lrqlldeaesa.eleawrekleeala................................................avp 109
                                       ++ l+  +es      wr++ e+a+                                                  v 
  gi|336254335|ref|YP_004597442.1| 114 CALLGLSPESGaGSLVWRAAQESATLeemrdhvaatdapgadkraatnhialaeswgafdpdgldaaelagsavTVV 190
                                       99999884443044455555444444777888888888888888888888888888888888885555555555444 PP

                            AAA_16 110 elagaeasrllellkrll.allsrder.......plvlvlDdlqwad 148
                                       +++g ea  +++++++ + al++  +r          l+lD+++ + 
  gi|336254335|ref|YP_004597442.1| 191 DVSGLEAAPMNAVCRAVAeALYR--ARvtgtidrLPWLLLDEAHAFF 235
                                       44444444444444444422222..2201112212445555555444 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.055
                            AAA_16 106 a................avpelagaeasrllellkrllallsrderplvlvlDdl 144
                                       +                a ++la+ ea +  ++  +l+++l++ ++  v+v+Dd+
  gi|336254335|ref|YP_004597442.1| 268 SetavsqsdvlvahrltAEADLAALEAAQPTYVHESLADRLPT-DPGSVVVIDDA 321
                                       1333444444445666566667777777888888888888899.66699999996 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 !    4.0   0.0    0.0097        19      18      55 ..      43      81 ..      34      85 .. 0.86
   2 !    9.9   0.0   0.00015       0.3     241     288 ..     220     270 ..     196     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0097
                     TrwB_AAD_bind 18 ilivGttGsGKtqalekllra.irargdraivlDltGaf 55
                                      +l+vG  G GK+ +l    ++ +ra g   +++D++G f
  gi|336254335|ref|YP_004597442.1| 43 MLVVGKRGYGKSYTLGVVAEElARASGVAPVIVDPMGVF 81
                                      6789***********999876368999999******987 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00015
                     TrwB_AAD_bind 241 rerrlWfflDElpaL...grleelksllaegRkfGgavvlglqsiaqlrev 288
                                        +r  W++lDE +a     + ++l+++l++gR  G+ +vl+ q+ + l e+
  gi|336254335|ref|YP_004597442.1| 220 IDRLPWLLLDEAHAFfagVAADALHRILTRGRAPGVSLVLATQQPSSLSET 270
                                       56667******999833235799**********************999875 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 !    7.7   0.1    0.0022       4.4       1      23 [.      43      65 ..      43      90 .. 0.80
   2 !    6.4   0.0    0.0058        11      26     125 ..     189     276 ..     166     283 .. 0.76
   3 ?   -1.5   0.0       1.5     3e+03      58      75 ..     311     337 ..     296     351 .] 0.60

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0022
                                      EEEESSTTSSHHHHHHHHHHHHT CS
                               AAA  1 vllyGppGtGKTllakavakelg 23
                                      +l++G  G GK+++   va+el 
  gi|336254335|ref|YP_004597442.1| 43 MLVVGKRGYGKSYTLGVVAEELA 65
                                      89******************984 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0058
                                       EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
                               AAA  26 fleisgsellskyvgesekkirelfkeakeka...kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                                       ++ +sg e     + +  + ++e + +a+      +   l++DE++a++             ++++L + l + +  
  gi|336254335|ref|YP_004597442.1| 189 VVDVSGLEAA--PMNAVCRAVAEALYRARVTGtidRLPWLLLDEAHAFFAGV----------AADALHRILTRGRA- 252
                                       4444444444..5566667777777777777777556899********9998..........89999999999999. PP

                                       SSTEEEEEEESSGGGSTHHHHSTTSS CS
                               AAA 100 eskvivigatnrpdkldpallrgRfd 125
                                          v +++at++p++l++  + +  d
  gi|336254335|ref|YP_004597442.1| 253 -PGVSLVLATQQPSSLSETAV-SQSD 276
                                       .469************99988.5555 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.5
                                       TS.EEEEEETGGGHHHHH........T CS
                               AAA  58 kp.silfiDEidalaksr........s 75 
                                       +p s+++iD++ + + +         +
  gi|336254335|ref|YP_004597442.1| 311 DPgSVVVIDDATETIHAArirrrdtpH 337
                                       466899999976554443254444444 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    0.0025         5       7      33 ..      42      68 ..      37     153 .. 0.75
   2 ?    5.6   0.0    0.0091        18      81     129 ..     206     261 ..     182     266 .. 0.76
   3 ?   -2.6   0.0         3   5.9e+03      85     100 ..     307     321 ..     279     326 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0025
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeea 33
                                       ++v+G  G GK+++l  ++e+l +++
  gi|336254335|ref|YP_004597442.1| 42 AMLVVGKRGYGKSYTLGVVAEELARAS 68
                                      689************999999986544 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0091
                            AAA_22  81 aleqalrarav......ielliiDEaqhlr...seealeeLrsllnlsrkgvqliLvG 129
                                       a+++al +++v       + l++DEa+ ++    ++al  + ++      gv+l+L+ 
  gi|336254335|ref|YP_004597442.1| 206 AVAEALYRARVtgtidrLPWLLLDEAHAFFagvAADALHRILTRGR--APGVSLVLAT 261
                                       45555555555566666788********886554888888888777..8888888865 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3
                            AAA_22  85 alraravielliiDEa 100
                                        l +    ++++iD+a
  gi|336254335|ref|YP_004597442.1| 307 RLPTDPG-SVVVIDDA 321
                                       3333344.78999987 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0046       9.1      28      57 ..      30      58 ..      14     109 .. 0.83
   2 ?    6.6   0.1    0.0022       4.5     155     242 ..     176     265 ..     134     266 .. 0.70
   3 ?   -3.0   0.0       1.9   3.7e+03     109     155 ..     275     320 ..     269     330 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0046
                                      S-EEEEEGGGS-.SEEEE--TTSSHHHHHH CS
                      FtsK_SpoIIIE 28 gnplvldlkkmashllvaGatgsGKStaln 57
                                      g  l++dl +    +lv+G  g GKS +l 
  gi|336254335|ref|YP_004597442.1| 30 GADLYVDLDGPH-AMLVVGKRGYGKSYTLG 58
                                      556777877666.7************9985 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0022
                                       .....................-.----------B-----EEEEEEC-HHHHHHHHHHH.....HHHHHHHHHHHCGG CS
                      FtsK_SpoIIIE 155 nyddlaaeneritsLsnqgpsy.gvhvlvtagrelekrpslvvivderieLrlaapkds.svlvedaivRlarkgra 229
                                       + d+ +  +  +t++   g++   ++ ++ a +e+  r  +   +d +  L l+ +       + da+ R+  +gra
  gi|336254335|ref|YP_004597442.1| 176 GLDAAELAGSAVTVVDVSGLEAaPMNAVCRAVAEALYRARVTGTIDRLPWLLLDEAHAFfAGVAADALHRILTRGRA 252
                                       555555555566666666665415677777777777888888888888888887666555677899*********** PP

                                       GTEEEEEEES--- CS
                      FtsK_SpoIIIE 230 aglHlllatqrls 242
                                        g+ l+latq++s
  gi|336254335|ref|YP_004597442.1| 253 PGVSLVLATQQPS 265
                                       **********998 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHHHTT-SSHHH.HHHHHHHHHHTT---B-TT-.. CS
                      FtsK_SpoIIIE 109 leeLvkemeeryalfreagvrsiaa.ydgeiaedpldifgdvflvlDn 155
                                        + Lv+++  ++a +++  +++ +   ++ + + p+d  +  ++v+D+
  gi|336254335|ref|YP_004597442.1| 275 SDVLVAHRLTAEADLAALEAAQPTYvHESLADRLPTD--PGSVVVIDD 320
                                       5566666666666666666666665333344444444..444555555 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       4.4   8.7e+03       4      15 ..      44      55 ..      43      65 .. 0.78
   2 ?    9.1   0.0   0.00047      0.94      80     133 ..     222     270 ..     200     285 .. 0.84
   3 ?    2.3   0.0     0.058   1.1e+02      68      95 ..     300     327 ..     274     338 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.4
                               Zot  4 lvtGapGsgKts 15
                                      lv G+ G gK++
  gi|336254335|ref|YP_004597442.1| 44 LVVGKRGYGKSY 55
                                      678999999987 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00047
                               Zot  80 kgallviDEcqeifpvrakegrkdpevinaftehRhlgwDivlltqdiskihke 133
                                       +   l++DE++ +f   a+     ++    +t+ R  g  +vl tq++s + + 
  gi|336254335|ref|YP_004597442.1| 222 RLPWLLLDEAHAFFAGVAA-----DALHRILTRGRAPGVSLVLATQQPSSLSET 270
                                       555699********99988.....467799*******************99765 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.058
                               Zot  68 tlkefakwatidkgallviDEcqeifpv 95 
                                         +++a++ ++d g+++viD + e+  +
  gi|336254335|ref|YP_004597442.1| 300 VHESLADRLPTDPGSVVVIDDATETIHA 327
                                       567788899999********99775444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.8e-05      0.17      14      52 ..      38      76 ..      28      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.8e-05
                        Zeta_toxin 14 erPklillgGqpGAGKselaellkdelerqgnvvrldpD 52
                                      + P ++l++G  G GKs+++  +++el+r+++v  +  D
  gi|336254335|ref|YP_004597442.1| 38 DGPHAMLVVGKRGYGKSYTLGVVAEELARASGVAPVIVD 76
                                      679************************998888766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2784.36
//
Query:       gi|336254336|ref|YP_004597443.1|  [L=169]
Description: hypothetical protein Halxa_2948 [Halopiger xanaduensis SH-6]
Scores for 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   16.0   2.5      0.032   14.8   2.5    1.7  1  YtkA             YtkA-like
       0.12   12.6   2.7       0.13   12.5   1.0    1.9  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
        1.1    9.7   5.2       0.54   10.7   3.4    1.4  1  DUF4604          Domain of unknown function (DUF4604)


Domain annotation for each model (and alignments):
>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   2.5   5.4e-06     0.032       5      55 ..      62     114 ..      60     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.4e-06
                              YtkA   5 ddlevelvspe.epkagentivvt.vtqggkpVedadvkvefwmpameGmeem 55 
                                       +d ev+++ ++ ++++ ++++++  v+++g++V+da+v +++    m+G   +
  gi|336254336|ref|YP_004597443.1|  62 TDTEVDVQFDDaTIAEDDDDVSIYvVDEDGNEVTDAVVVAQAGTARMDGALSK 114
                                       5566666665514566666798844************9999999999987654 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.5   8.9e+03      57      70 ..      58      69 ..      57      75 .. 0.60
   2 ?   12.5   1.0   2.2e-05      0.13       2      38 ..      82     117 ..      81     119 .. 0.89
   3 ?   -3.2   0.0       1.8   1.1e+04      69      80 ..     134     146 ..     126     149 .. 0.46

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                   CarboxypepD_reg 57 pGyatatreevtlt 70
                                      +G++t t   v+++
  gi|336254336|ref|YP_004597443.1| 58 DGFQTDTE--VDVQ 69
                                      57888885..4443 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.2e-05
                   CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadG 38 
                                       +s +V+d++g+ ++ a V+++ a+t    ++ + ++G
  gi|336254336|ref|YP_004597443.1|  82 VSIYVVDEDGNEVTDAVVVAQ-AGTARMDGALSKETG 117
                                       7889*****************.588888999999998 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.8
                   CarboxypepD_reg  69 ltagqtt.tldit 80 
                                       l+++q+t t+++t
  gi|336254336|ref|YP_004597443.1| 134 LAPDQSTgTIEFT 146
                                       3333333233443 PP

>> DUF4604  Domain of unknown function (DUF4604)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.4     9e-05      0.54      42      95 ..      72     123 ..      60     151 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9e-05
                           DUF4604  42 des...eeeDeaPqVVvlkeGkhlsaeevevekdaakgkekeeeeeeeeegeeaeed 95 
                                       d     e++D+    Vv+++G+ +   ++ v  +a+++++  +   ++e+g+++e +
  gi|336254336|ref|YP_004597443.1|  72 D-AtiaEDDDDVSIYVVDEDGNEV--TDAVVVAQAGTARM--DGALSKETGDDNEVE 123
                                       3.2577999999****99******..56667788899999..333444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); 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:                         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 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1288.06
//
Query:       gi|336254337|ref|YP_004597444.1|  [L=329]
Description: Na+ ABC efflux pump permease [Halopiger xanaduensis SH-6]
Scores for 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-11   42.0   0.0    9.6e-11   41.4   0.0    1.3  1  ABC2_membrane_3  ABC-2 family transporter protein
    1.5e-06   27.7   7.6    1.9e-06   27.4   7.2    1.4  1  ABC2_membrane_2  ABC-2 family transporter protein
    1.8e-05   24.3   7.7    1.8e-05   24.3   7.7    1.5  2  ABC2_membrane    ABC-2 type transporter
    8.8e-05   22.5   4.0    8.8e-05   22.5   4.0    1.8  1  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> 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 !   41.4   0.0   2.1e-14   9.6e-11      62     299 ..      59     289 ..       2     299 .. 0.70

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 2.1e-14
                   ABC2_membrane_3  62 yevdseeeakkalkngdidgilvipkgfskdllkgesatvtvlinssnlnss...kailnalnsllqqlnasalvlq 135
                                        +  + ++a++a++ gd+ ++l     ++ +l       v v+  +++l+++    +++ al++l +++  ++    
  gi|336254337|ref|YP_004597444.1|  59 ARQYDAASAQQAFDRGDVAAVLRTSRTDEGQL------FVHVTAPEEGLETTllvVQLRDALKDLERTERLANA--- 126
                                       45556667777777777777776555555443......466666666666666666777777776555443332... PP

                   ABC2_membrane_3 136 seatstsaninvestqleeelsnvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskil 211
                                            +++++ v s    ++  +++++++  l+ ++++fi++s+++ s++eE+ ++++ l+ v+++s ++++ +k+ 
  gi|336254337|ref|YP_004597444.1| 127 DAGRLAETPLFVPSAIQASPYVGFTYTVLLpLLCFLPVFISGSIVVDSLIEERDRGTLTLLRVAPLSLTEIVDAKVA 203
                                       3344444444444444577778888875555********************************************** PP

                   ABC2_membrane_3 212 gdflvyllqlllilll.afglgipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffggl 287
                                       ++++++ lq++ +++l a++ g ++    +l+ l+   +l+++ +g+ +  +  + + aq+   + ++++ g++++ 
  gi|336254337|ref|YP_004597444.1| 204 ATAALAPLQAVAWMVLlAVN-GTSIATPTALVTLVAALSLLVVGVGAIVALVAPDRRQAQL---CYSISIVGALVVA 276
                                       **************965777.7999999*******************************97...4444444444444 PP

                   ABC2_membrane_3 288 fp.ledlpsalkw 299
                                        +  e +++++++
  gi|336254337|ref|YP_004597444.1| 277 SLlPEHPANTVAK 289
                                       4414444455554 PP

>> 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 !   27.4   7.2   4.2e-10   1.9e-06      76     215 ..      75     282 ..       3     298 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.2e-10
                   ABC2_membrane_2  76 v............................................................................ 76 
                                                                                                                    
  gi|336254337|ref|YP_004597444.1|  75 Dvaavlrtsrtdegqlfvhvtapeeglettllvvqlrdalkdlerterlanadagrlaetplfvpsaiqaspyvgft 151
                                       03444566666666666777777777777777777777777777777777777777777788888888888876666 PP

                   ABC2_membrane_2  77 ..vstimavlipvi.aalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiil 150
                                         v +++  ++pv+    + +d++ +E++rgTl ll   P s  ei+ +K+ + +a+    a +  ++    +++ +
  gi|336254337|ref|YP_004597444.1| 152 ytVLLPLLCFLPVFiSGSIVVDSLIEERDRGTLTLLRVAPLSLTEIVDAKVAATAAL----APLQAVA---WMVLLA 221
                                       65455555555554478999*******************************999999....4444444...467889 PP

                   ABC2_membrane_2 151 algivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlyg 215
                                       ++g+++a+   l+++va++ ll+    +++g+ ++ va ++r+a +++ + +v  +++ +++  +
  gi|336254337|ref|YP_004597444.1| 222 VNGTSIATPTALVTLVAALSLLV----VGVGAIVALVAPDRRQAQLCYSISIVGALVVASLLPEH 282
                                       99999999999999999996666....89**********99998887666555555665665555 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   1.0       2.7   1.2e+04     114     119 ..      10      15 ..       2      24 .. 0.34
   2 !   24.3   7.7   3.9e-09   1.8e-05      54     170 ..     157     270 ..     134     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 2.7
                     ABC2_membrane 114 iflliv 119
                                       i  + +
  gi|336254337|ref|YP_004597444.1|  10 IAAFSS 15 
                                       111111 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 3.9e-09
                     ABC2_membrane  54 gllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrf 130
                                        ll+f+ +f++ s++  + ++ er+rg+l  ++v+pl sl ++v akv++ ++++ lqa++++++  +  g  +   
  gi|336254337|ref|YP_004597444.1| 157 PLLCFLPVFISGSIVVDS-LIEERDRGTLTLLRVAPL-SLTEIVDAKVAATAALAPLQAVAWMVLLAVN-GTSIATP 230
                                       578999999995666666.******************.**************************77775.6666435 PP

                     ABC2_membrane 131 flflllllltalaasslgllisalapsfedasqlaslvll 170
                                         ++ l+ +++l+++++g +++ +ap+ ++a++  s+ ++
  gi|336254337|ref|YP_004597444.1| 231 TALVTLVAALSLLVVGVGAIVALVAPDRRQAQLCYSISIV 270
                                       8889999999999*******************99888776 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 !   22.5   4.0     2e-08   8.8e-05      55     151 ..     158     252 ..     136     258 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2e-08
                   ABC2_membrane_4  55 tlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsv 131
                                        l +l ++i g i + ++ +E++ +tl  L++ P s t+++ aK+++++ l+ l   v+++  vl+a+  +++++ +
  gi|336254337|ref|YP_004597444.1| 158 LLCFLPVFISGSIVVDSLIEERDRGTLTLLRVAPLSLTEIVDAKVAATAALAPLQ-AVAWM--VLLAVNGTSIATPT 231
                                       233455567788999999*****************************98875444.45454..55555555555554 PP

                   ABC2_membrane_4 132 klvlellkkcl.elgllvffa 151
                                       +lv+ +   +l ++g++ ++a
  gi|336254337|ref|YP_004597444.1| 232 ALVTLVAALSLlVVGVGAIVA 252
                                       444332222220333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2388.25
//
Query:       gi|336254338|ref|YP_004597445.1|  [L=641]
Description: Na+ ABC efflux pump permease [Halopiger xanaduensis SH-6]
Scores for 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-06   27.0   3.9    2.4e-06   27.0   3.9    2.6  2  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
        2.8    7.0  29.2      0.011   14.9  17.0    2.2  2  ABC2_membrane_3  ABC-2 family transporter protein


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 !   27.0   3.9   2.7e-10   2.4e-06      76     217 ..     188     437 ..      56     512 .. 0.67
   2 ?   -3.4   2.9      0.52   4.6e+03     168     206 ..     590     627 ..     570     640 .. 0.60

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.7e-10
                   ABC2_membrane_2  76 v............................................................................ 76 
                                                                                                                    
  gi|336254338|ref|YP_004597445.1| 188 Latlddsgsagsadddtgdgtisddgptsdgarsdtndegdassgddelqvpnvggstgaaettvgapgslsppfpf 264
                                       24444444555566666666666666777777777777777777777778888888888888888888888888888 PP

                   ABC2_membrane_2  77 ..vstimavlipviaalfgada.iagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvll...... 144
                                         +++++ +++p+  ++ ++ + i +E+  +  +llL +P+sR ei++gK + +l++  ++a+a+++++ +      
  gi|336254338|ref|YP_004597445.1| 265 rsLVLAFLFVVPMNFVIQAYGStIMDERIKRRGELLLVSPASRYEIVAGKTLPYLLA--LVAIAAGIAYAIdgglla 339
                                       777778888888888888886549999999999**********************99..678888888888888887 PP

                   ABC2_membrane_2 145 ...........................alaiilalgivlaledllllvvasvlllllvvflalglllSsvarssrea 194
                                                                    ++++a ++ l++ +++  ++  v+ ++   +++  +l+ + ++  ++a
  gi|336254338|ref|YP_004597445.1| 340 vaaalpiallflastfvgamlarsfkeLTFVTVAISVGLTTYAFIPAIFTDVTPIA---LISPLTLIVTALQGESVA 413
                                       77777777777777777777777777766666666666666666666666665555...244444444444444444 PP

                   ABC2_membrane_2 195 aalalglfv.vlailvpivlygva 217
                                       a  +l+  + + + +v  +l+gv+
  gi|336254338|ref|YP_004597445.1| 414 AGEYLFSTLpFYLSAVVCFLLGVG 437
                                       443333333033334444444444 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.52
                   ABC2_membrane_2 168 svlllllvvflalglllSsvarssreaaalalglfvvla 206
                                         ++l+ +++ a+++ +S++   sr +  +alg++++++
  gi|336254338|ref|YP_004597445.1| 590 GAIFLAPLALHAATAIVSAIGA-SRGSVGYALGFVAATL 627
                                       4433433455666666666666.6666666666665554 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 ?   14.9  17.0   1.2e-06     0.011     162     343 ..     267     435 ..     262     462 .. 0.71
   2 ?   -6.7  10.0         2   1.8e+04     218     268 ..     425     504 ..     411     515 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-06
                   ABC2_membrane_3 162 flvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafglgipfgnl 238
                                        ++++++++++ ++++   + i  E+ +r  el+lvs+ s+++++ +k l ++l+    ++++ ++a++  i+ g l
  gi|336254338|ref|YP_004597445.1| 267 LVLAFLFVVPMNFVIQAYGSTIMDERIKRRGELLLVSPASRYEIVAGKTLPYLLAL---VAIAAGIAYA--IDGGLL 338
                                       3444555555555555555688***************************9888776...4445557777..877766 PP

                   ABC2_membrane_3 239 glll.llfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgll 314
                                        ++  l + l +la++++g++l   fk  + + ++i++  l +  +f++ ++++     +  i+ i P++ +  +l 
  gi|336254338|ref|YP_004597445.1| 339 AVAAaLPIALLFLASTFVGAMLARSFKELTFVTVAISV-GL-TTYAFIPAIFTD-----VTPIALISPLTLIVTALQ 408
                                       55445888888999999999999999988665553333.33.334444444444.....556777777777777776 PP

                   ABC2_membrane_3 315 rlitgdplweillsliilalfavvyllla 343
                                         +  +   e+l s +  +l+avv++ll+
  gi|336254338|ref|YP_004597445.1| 409 GESVAA--GEYLFSTLPFYLSAVVCFLLG 435
                                       665444..567777777777777777765 PP

  == domain 2  score: -6.7 bits;  conditional E-value: 2
                   ABC2_membrane_3 218 llqlllilllafgl............................gipfgnlglll.llfllfglayialgyllsslfkn 265
                                        l++++++ll +g+                             ++   + ++l +lf++f++a   l+ +l +++  
  gi|336254338|ref|YP_004597445.1| 425 YLSAVVCFLLGVGIyreedmfaqkpipakvldaiasqidalsRWDARLSPFVLsILFIPFIFAGQLLIVALLFAVPE 501
                                       44445555544444555555555777777777777766665544444556677799999999999999999988877 PP

                   ABC2_membrane_3 266 set 268
                                       +++
  gi|336254338|ref|YP_004597445.1| 502 AVA 504
                                       654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3920.89
//
Query:       gi|336254339|ref|YP_004597446.1|  [L=323]
Description: sulfate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-29  101.4   0.0    1.6e-28   99.9   0.0    1.7  2  ABC_tran  ABC transporter
    2.2e-14   54.0   0.0    8.6e-09   35.6   0.0    2.3  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    2.6e-12   47.3   0.2    4.8e-12   46.4   0.2    1.5  1  DUF4162   Domain of unknown function (DUF4162)
    0.00021   21.1   0.4      0.001   18.8   0.1    2.2  2  AAA_30    AAA domain
     0.0069   16.9   0.5      0.029   14.9   0.1    2.0  2  AAA_23    AAA domain
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.049   13.9   0.0    1.9  1  AAA_22    AAA domain
      0.016   15.0   0.0       0.78    9.4   0.0    2.1  2  AAA_15    AAA ATPase domain
      0.016   14.7   0.0        4.2    6.8   0.0    2.3  2  SMC_N     RecF/RecN/SMC N terminal domain
      0.019   14.7   1.2       0.61    9.8   0.1    2.8  3  AAA_24    AAA domain
      0.026   14.1   0.5      0.053   13.2   0.5    1.4  1  SRP54     SRP54-type protein, GTPase domain
      0.073   11.7   0.1        8.3    4.9   0.0    2.1  2  AAA_13    AAA domain
        0.1   12.4   0.1       0.19   11.5   0.1    1.4  1  AAA_29    P-loop containing region of AAA domain
       0.14   11.8   0.0        0.3   10.7   0.0    1.5  1  AAA_27    AAA domain
       0.19   12.1   0.8       0.91   10.0   0.8    2.1  1  AAA       ATPase family associated with various cellular acti
       0.37   11.0   4.2       0.53   10.5   0.4    2.7  3  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 !   99.9   0.0   1.4e-31   1.6e-28       3     136 ..      21     159 ..      19     160 .. 0.96
   2 ?   -1.3   0.0       2.4   2.9e+03      99     121 ..     244     266 ..     178     291 .. 0.69

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1.4e-31
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                         ++ +++ge+ ++vG+nGaGK+t lk+lagl++pt+G+  + g++  e   + +++++g+lp+e+ l +++t+ + 
  gi|336254339|ref|YP_004597446.1|  21 GSTFAIERGEVFGVVGPNGAGKTTTLKMLAGLVEPTAGTAVVAGRQPGE---PAMQRRLGFLPEESPLYEDMTATDY 94 
                                       5689***************************************999988...9*******************99988 PP

                                       .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                     ++e+i++ l++l+l++ +d+++     ++S+G+k++va+aral+++p++l++DEp 
  gi|336254339|ref|YP_004597446.1|  95 leffadlydvpgeVATERIADTLDRLDLEH-RDRRI----GNMSKGMKRKVAIARALVNDPDVLIFDEPA 159
                                       9**********9999999************.99999....*****************************7 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                                       CBGESTTSGGS-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  99 dtvvksspssLSgGqkqrvalar 121
                                        + ++   ++   Gq++r ++a 
  gi|336254339|ref|YP_004597446.1| 244 SRAIEVTREETNDGQQVRHVVAD 266
                                       33333333444445555544443 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   0.1   5.5e-06    0.0065       2      22 ..      32      52 ..      31      90 .. 0.81
   2 !   35.6   0.0   7.2e-12   8.6e-09     231     300 ..     126     192 ..      74     195 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.5e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       +++GpNg+GK++ L+ l +l
  gi|336254339|ref|YP_004597446.1| 32 FGVVGPNGAGKTTTLKMLAGL 52
                                      689***************988 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 7.2e-12
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                       ++ + ++S G+kr  a++ al  ++   ++l++DEp +gL+P  +  ++e+ +els+ g  ++++ H+ +
  gi|336254339|ref|YP_004597446.1| 126 DRRIGNMSKGMKRKVAIARALVNDP---DVLIFDEPASGLDPLTTNYIIEFTRELSEQGKTIVFSAHNLY 192
                                       467899********99999999999...9**************************************975 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.2     4e-15   4.8e-12       1      80 [.     213     301 ..     213     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 4e-15
                                       E-HHHHHTTS-SSEEEEE...-------..--.-EEEE-TT....S-EEEEE-------------.----EEEEEEE CS
                           DUF4162   1 GtleeiKrsygknrieve...adaeelleepg.veeveeeg....gelelkledeeaanellkal.tsgveirsFee 68 
                                       G+++ei++++g++ ++v    ++ ++l + ++   ev++e+    ++++  + d ++ +++ +a+ ++g++++ ++ 
  gi|336254339|ref|YP_004597446.1| 213 GSVDEIRDEHGGTEYHVYatkDGSDALDDDQSrAIEVTREEtndgQQVRHVVADMASVEAIREAVeAEGGRVTDIQT 289
                                       9*****************9853366666665556666333333446688888888899999999977********** PP

                                       E---HHHHHHHH CS
                           DUF4162  69 eePsLndIFiek 80 
                                       + PsL+dIF+e 
  gi|336254339|ref|YP_004597446.1| 290 KTPSLEDIFLEI 301
                                       **********96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   8.6e-07     0.001      17      96 ..      28     157 ..      22     188 .. 0.61
   2 ?   -0.9   0.0      0.97   1.2e+03      34      49 ..     269     284 ..     239     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.6e-07
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaa.ggrvi.glAptgkaAkv.La.........................e. 64 
                                       +  v  ++Gp G+GKtt+lk l+ ++e   g  v+ g  p + a ++ L+                         + 
  gi|336254339|ref|YP_004597446.1|  28 RGEVFGVVGPNGAGKTTTLKMLAGLVEPTaGTAVVaGRQPGEPAMQRrLGflpeesplyedmtatdyleffadlyDv 104
                                       4568899********************99675555244555555554566555555555444444444333322202 PP

                            AAA_30  65 elgieastiakllkrlk.....................grarlepgtllivDE 96 
                                         ++++++ia  l+rl+                     +ra +++ ++li DE
  gi|336254339|ref|YP_004597446.1| 105 PGEVATERIADTLDRLDlehrdrrignmskgmkrkvaiARALVNDPDVLIFDE 157
                                       11245555555555555666677777777777777777656666668888887 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.97
                            AAA_30  34 alkalreaweaaggrv 49 
                                       +++a+rea+ea+ggrv
  gi|336254339|ref|YP_004597446.1| 269 SVEAIREAVEAEGGRV 284
                                       4567777777777776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.5e-05     0.029      20      38 ..      30      48 ..      12      52 .. 0.82
   2 ?   -0.1   0.0      0.94   1.1e+03      62      62 ..     214     214 ..     106     302 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                            AAA_23 20 gltlItGpNGaGKTTildA 38
                                       ++ ++GpNGaGKTT l  
  gi|336254339|ref|YP_004597446.1| 30 EVFGVVGPNGAGKTTTLKM 48
                                      58999**********9875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.94
                            AAA_23  62 d 62 
                                       +
  gi|336254339|ref|YP_004597446.1| 214 S 214
                                       1 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.1e-05     0.049      10     103 ..      34     162 ..      27     193 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee..............erpevv..fvtlpsstsskdllrellralglelka 70 
                                       v+G+ G+GKTt+l++l+   +  a   +              +r +++  +  l ++++ +d l+ ++  ++++++ 
  gi|336254339|ref|YP_004597446.1|  34 VVGPNGAGKTTTLKMLAGLVEPTAG--TavvagrqpgepamqRRLGFLpeESPLYEDMTATDYLEFFADLYDVPGEV 108
                                       89**************998743333..24577777777765544444444444444446666666666666666665 PP

                            AAA_22  71 ................erlsseellealeqalrarav...........ielliiDEaqh.l 103
                                                       +        +++ + ++  ++           + +li DE    l
  gi|336254339|ref|YP_004597446.1| 109 ateriadtldrldlehR-------DRRIGNMSKGMKRkvaiaralvndPDVLIFDEPASgL 162
                                       55555555533333221.......2222222222222222333355566666666655555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00065      0.78      27      44 ..      33      50 ..      22      60 .. 0.84
   2 ?    3.6   0.0     0.037        45     322     367 ..     148     192 ..     117     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00065
                            AAA_15 27 vliGkNnsGKSsileald 44
                                       ++G+N++GK++ l++l 
  gi|336254339|ref|YP_004597446.1| 33 GVVGPNGAGKTTTLKMLA 50
                                      58*************995 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.037
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                       +++++l+++EP   L p   + +i+  +el++++k  ++++ H+ +
  gi|336254339|ref|YP_004597446.1| 148 NDPDVLIFDEPASGLDPLTTNYIIEFTRELSEQGK-TIVFSAHNLY 192
                                       5899******************************9.8999999976 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 ?    6.8   0.0    0.0035       4.2      26      41 ..      31      46 ..      15      50 .. 0.80
   2 ?    5.6   0.0     0.008       9.6     136     199 ..     131     190 ..     101     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0035
                                      EEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnll 41
                                      +  +vGpNG+GK+  l
  gi|336254339|ref|YP_004597446.1| 31 VFGVVGPNGAGKTTTL 46
                                      4569********9765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.008
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                       ++S G k  va+a       v+   + ++De ++ LD   ++ + e+ +e s++   iv s ++
  gi|336254339|ref|YP_004597446.1| 131 NMSKGMKRKVAIARA----LVNDPDVLIFDEPASGLDPLTTNYIIEFTRELSEQGKTIVFSAHN 190
                                       566666665555433....344445679*******************************98765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00051      0.61       5      22 ..      32      49 ..      28      73 .. 0.84
   2 ?    2.1   0.0      0.11   1.3e+02     109     130 ..     168     189 ..     165     192 .. 0.89
   3 ?   -0.8   0.0      0.87     1e+03     124     163 ..     228     267 ..     201     293 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00051
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      + ++Gp+g+GKTt++k+l
  gi|336254339|ref|YP_004597446.1| 32 FGVVGPNGAGKTTTLKML 49
                                      6799***********998 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                            AAA_24 109 eefrrllkklqelrknvifiah 130
                                       + ++++ + l+e +k+++f ah
  gi|336254339|ref|YP_004597446.1| 168 NYIIEFTRELSEQGKTIVFSAH 189
                                       67899****************9 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.87
                            AAA_24 124 nvifiahektrkdedpegeakytrlepklgkktanelkee 163
                                       +v+++       d+d+ +  + tr e++ g+++   +  +
  gi|336254339|ref|YP_004597446.1| 228 HVYATKDGSDALDDDQSRAIEVTREETNDGQQVRHVVADM 267
                                       4444444444445555444555555555555544444444 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   0.5   4.4e-05     0.053       5      28 ..      33      56 ..      30      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.4e-05
                                      EEEESTTSSHHHHHHHHHHHHHHT CS
                             SRP54  5 llvGlqGaGKTttlaKLaallkke 28
                                       +vG++GaGKTttl  La l++  
  gi|336254339|ref|YP_004597446.1| 33 GVVGPNGAGKTTTLKMLAGLVEPT 56
                                      58************9999877655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0069       8.3      23      39 ..      36      52 ..      31      67 .. 0.85
   2 ?    4.8   0.0    0.0073       8.7     524     578 ..     147     198 ..     139     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0069
                            AAA_13 23 GwNGaGKTtLSrllrsl 39
                                      G NGaGKTt  ++l+ l
  gi|336254339|ref|YP_004597446.1| 36 GPNGAGKTTTLKMLAGL 52
                                      99*******99999987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0073
                            AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevk 578
                                       ++   + ++D P S LD    ++++ + ++     ++ k +  + Hnl+    + 
  gi|336254339|ref|YP_004597446.1| 147 VNDPDVLIFDEPASGLDPLTTNYIIEFTRELS---EQGKTIVFSAHNLYHVESIC 198
                                       567789************************97...999**********9877665 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 ?   11.5   0.1   0.00016      0.19      14      39 ..      21      46 ..      16      60 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTll 39
                                      g t+ i++ +++ ++Gp+G+GK+T l
  gi|336254339|ref|YP_004597446.1| 21 GSTFAIERGEVFGVVGPNGAGKTTTL 46
                                      6788898777999***********87 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00025       0.3      20      47 ..      23      50 ..       9      53 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                            AAA_27 20 dfsaeeadlhliyGpNEAGKstalrAis 47
                                      +f  e+ ++  ++GpN AGK+t+l+ + 
  gi|336254339|ref|YP_004597446.1| 23 TFAIERGEVFGVVGPNGAGKTTTLKMLA 50
                                      3444566677799**********98776 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 ?   10.0   0.8   0.00076      0.91       3      22 ..      34      53 ..      32     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00076
                                      EESSTTSSHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel 22
                                      ++Gp G GKT++ k +a  +
  gi|336254339|ref|YP_004597446.1| 34 VVGPNGAGKTTTLKMLAGLV 53
                                      68**************9875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00044      0.53       4      27 ..      34      62 ..      32      84 .. 0.83
   2 ?   -0.1   0.0      0.79   9.5e+02      26      80 ..     104     157 ..      83     166 .. 0.65
   3 ?   -0.9   0.1       1.5   1.8e+03      33      64 ..     248     279 ..     240     293 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00044
                            AAA_28  4 itGgestGKTtlleaLa.....argypvv 27
                                      ++G+ ++GKTt+l+ La       g+ vv
  gi|336254339|ref|YP_004597446.1| 34 VVGPNGAGKTTTLKMLAglvepTAGTAVV 62
                                      68***************665433377777 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.79
                            AAA_28  26 vvpEaareileeklakgedalpwv.edllafaervleeqleeeaaa.aankvlfcDr 80 
                                       v  E+a+e + + l++     ++  +++ ++ +++ + +++ ++a  ++++vl++D 
  gi|336254339|ref|YP_004597446.1| 104 VPGEVATERIADTLDRLDL--EHRdRRIGNMSKGMKR-KVAIARALvNDPDVLIFDE 157
                                       4467777777777766553..3332455555555443.3333333369999999995 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.5
                            AAA_28  33 eileeklakgedalpwvedllafaervleeql 64 
                                       e+++e++ +g++  + v+d+  +++ +++ ++
  gi|336254339|ref|YP_004597446.1| 248 EVTREETNDGQQVRHVVADMASVEAIREAVEA 279
                                       45555555555544444555555444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 2386.92
//
Query:       gi|336254340|ref|YP_004597447.1|  [L=134]
Description: HxlR family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-20   72.0   0.0    3.2e-20   71.8   0.0    1.1  1  HxlR           HxlR-like helix-turn-helix
    2.4e-06   27.6   0.0    3.3e-06   27.2   0.0    1.2  1  HTH_34         Winged helix DNA-binding domain
    3.9e-05   24.1   0.0    5.5e-05   23.6   0.0    1.2  1  HTH_27         Winged helix DNA-binding domain
    0.00041   20.1   0.0    0.00054   19.8   0.0    1.2  1  HTH_5          Bacterial regulatory protein, arsR family
      0.002   18.1   0.0     0.0031   17.5   0.0    1.3  1  PadR           Transcriptional regulator PadR-like family
     0.0089   15.9   0.0      0.014   15.3   0.0    1.3  1  MarR           MarR family
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.019   14.8   0.0    1.2  1  MarR_2         MarR family
      0.015   15.3   0.1      0.022   14.8   0.1    1.2  1  HTH_20         Helix-turn-helix domain
      0.023   14.8   0.0      0.034   14.3   0.0    1.2  1  Trp_repressor  Trp repressor protein
      0.034   14.1   0.0      0.049   13.6   0.0    1.2  1  HTH_45         Winged helix-turn-helix
      0.042   13.7   0.0      0.057   13.3   0.0    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB
       0.11   12.0   0.0       0.15   11.6   0.0    1.1  1  OGFr_N         Opioid growth factor receptor (OGFr) conserved
       0.12   12.4   0.0       0.16   12.0   0.0    1.2  1  Replic_Relax   Replication-relaxation
       0.24   11.1   0.0       0.33   10.7   0.0    1.2  1  DUF4364        Domain of unknown function (DUF4364)


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 !   71.8   0.0   2.5e-23   3.2e-20       2      89 ..      43     129 ..      42     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 2.5e-23
                                       HHSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHH CS
                              HxlR   2 iggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqe 78 
                                       ig++W+l +l+ell+g++Rf+elkr   +   ++L++ L  L + g++er++ +  P    YsltekG+slepv++e
  gi|336254340|ref|YP_004597447.1|  43 IGSQWRLAVLHELLDGEQRFNELKRST-DANARTLSRVLDDLGEMGFVERRIEEDSPIATYYSLTEKGKSLEPVFDE 118
                                       89***********************99.999********************************************** PP

                                       HHHHHHHHHHC CS
                              HxlR  79 lkkwgeeylee 89 
                                       ++ w+ ++l+e
  gi|336254340|ref|YP_004597447.1| 119 IECWAGSWLDE 129
                                       ********997 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 !   27.2   0.0   2.6e-09   3.3e-06       2      67 ..      48     111 ..      47     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.6e-09
                            HTH_34   2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGre 67 
                                       Rlavl+ L++  e  f+elk ++ a++  Ls  l+ L + g++e+++e ++    t +++T++G++
  gi|336254340|ref|YP_004597447.1|  48 RLAVLHELLDG-EQRFNELKRSTDANARTLSRVLDDLGEMGFVERRIEEDSP-IATYYSLTEKGKS 111
                                       99999999975.569**********************************999.89*********85 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 !   23.6   0.0   4.3e-08   5.5e-05       7      68 .]      50     109 ..      45     109 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.3e-08
                            HTH_27   7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       +vLh +   +++++  +l + ++ ++ + s +l+ L e+G+ver   e +  ++ ++lT+kG
  gi|336254340|ref|YP_004597447.1|  50 AVLHELL--DGEQRFNELKRSTDANARTLSRVLDDLGEMGFVERRIEEDSPIATYYSLTEKG 109
                                       5788898..999999***************************99999877777********9 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 !   19.8   0.0   4.2e-07   0.00054       4      46 ..      48      90 ..      45      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.2e-07
                                      HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      Rl +L+ L +ge+ + el + ++ +  t+S+ L  L e+G+Ve
  gi|336254340|ref|YP_004597447.1| 48 RLAVLHELLDGEQRFNELKRSTDANARTLSRVLDDLGEMGFVE 90
                                      99****************************************7 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.4e-06    0.0031      27      71 ..      69     111 ..      52     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-06
                                       CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                              PadR  27 lelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71 
                                       +++++ +l ++L++L + g+ve++ ee  ++p   yY lT++G++
  gi|336254340|ref|YP_004597447.1|  69 TDANARTLSRVLDDLGEMGFVERRIEE--DSPIATYYSLTEKGKS 111
                                       6777888999**************998..69************95 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05     0.014      16      52 ..      58      94 ..      48      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                      g+++  eL +    +  t++rvld L + G++eR+  
  gi|336254340|ref|YP_004597447.1| 58 GEQRFNELKRSTDANARTLSRVLDDLGEMGFVERRIE 94
                                      5677889999999999******************965 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.5e-05     0.019       8      54 ..      49      92 ..      45      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      + vL++L +++    + +el r ++    ++sr+l++L + G+verr
  gi|336254340|ref|YP_004597447.1| 49 LAVLHELLDGE---QRFNELKRSTDANARTLSRVLDDLGEMGFVERR 92
                                      579*******9...5*******************************9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.7e-05     0.022      12      57 ..      48      92 ..      37      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      R+++l +L  ++++ ++el++  d    tls+ L+ L e g+ve++
  gi|336254340|ref|YP_004597447.1| 48 RLAVLHEL-LDGEQRFNELKRSTDANARTLSRVLDDLGEMGFVERR 92
                                      9*******.***********************************98 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.7e-05     0.034      38      73 ..      48      83 ..      36      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                     Trp_repressor 38 RlqvvkeLLkeelsqreIaeelgvSiAtItRvsrsL 73
                                      Rl v++eLL++e+ ++e++  +++ + t +Rv   L
  gi|336254340|ref|YP_004597447.1| 48 RLAVLHELLDGEQRFNELKRSTDANARTLSRVLDDL 83
                                      999****************************97766 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.8e-05     0.049      11      70 ..      51     117 ..      48     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                            HTH_45  11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli.......kkskekYvlTekGlelleklk 70 
                                       +L+ + +ge++  ++  + + + ++l++ Ld L e g++       +   + Y+lTekG+ l   ++
  gi|336254340|ref|YP_004597447.1|  51 VLHELLDGEQRFNELKRSTDANARTLSRVLDDLGEMGFVerrieedSPIATYYSLTEKGKSLEPVFD 117
                                       6777778888888888999999****************987776433346789******99865555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-05     0.057      20      59 ..      57     100 ..      49     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                                       HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST....T CS
                              TrmB  20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr....p 59 
                                        g+ + +e+ + ++    +  +vL  L ++G+Ver+ ++     
  gi|336254340|ref|YP_004597447.1|  57 DGEQRFNELKRSTDANARTLSRVLDDLGEMGFVERRIEEdspiA 100
                                       6888999999999*********************9876656443 PP

>> OGFr_N  Opioid growth factor receptor (OGFr) conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.15     112     141 ..      59      89 ..      51      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                            OGFr_N 112 kerfenLnekshnnlr.itriLksLgelgye 141
                                       ++rf++L++++  n r + r+L  Lge+g+ 
  gi|336254340|ref|YP_004597447.1|  59 EQRFNELKRSTDANARtLSRVLDDLGEMGFV 89 
                                       68******99987776489**********96 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.16      17      68 ..      67     112 ..      52     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                      Replic_Relax  17 rllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarl 68 
                                       r + a+ r t++r+L +L e g+++r  +++  ++       Y Lt+kG+ l
  gi|336254340|ref|YP_004597447.1|  67 RSTDANAR-TLSRVLDDLGEMGFVERRIEEDSPIAT-----YYSLTEKGKSL 112
                                       44444555.5****************8888666666.....8*******654 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00026      0.33      35      70 ..      75     113 ..      65     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                           DUF4364  35 dlqqalseLvesglieee.ek..enktlykiTekGketl 70 
                                       +l+ +l++L e g++e + e+     t+y++TekGk   
  gi|336254340|ref|YP_004597447.1|  75 TLSRVLDDLGEMGFVERRiEEdsPIATYYSLTEKGKSLE 113
                                       68899**********998655224479********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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):              14  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 998.72
//
Query:       gi|336254341|ref|YP_004597448.1|  [L=148]
Description: hypothetical protein Halxa_2953 [Halopiger xanaduensis SH-6]
Scores for complete 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-48  164.1   0.0    1.9e-48  163.9   0.0    1.0  1  UPF0179      Uncharacterised protein family (UPF0179)
  ------ inclusion threshold ------
      0.012   15.9   0.2      0.021   15.0   0.0    1.5  2  DDE_Tnp_1_6  Transposase DDE domain
      0.015   15.4   0.0      0.024   14.7   0.0    1.4  1  MelC1        Tyrosinase co-factor MelC1


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 !  163.9   0.0   3.2e-52   1.9e-48       2     140 .]       4     144 ..       3     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 163.9 bits;  conditional E-value: 3.2e-52
                           UPF0179   2 itLigkklAkeGteFiylgeaeeCekCklkkvClnLekgrkYrivevrekt.eheCavheegvvaveveeapieali 77 
                                       +tLig++lA++GteF+y+gea+ C +C+++++ClnL++g+kYr+++vrek+ + eCa+h++gv+aveve+a +ea++
  gi|336254341|ref|YP_004597448.1|   4 VTLIGSRLAEPGTEFVYQGEADGCAGCPYRSQCLNLSEGTKYRVTDVREKAqTLECAMHDGGVRAVEVEPAAVEANV 80 
                                       9*************************************************9788*********************** PP

                           UPF0179  78 eskkavegskitleseeCdevecesyelcepeglkegekvkivevlgeiee..ckkgrslkkvel 140
                                       +sk a++gsk++l+   C++vec+s+e+cep+g++ +e+++i e+ g++++  c+ +rsl++vel
  gi|336254341|ref|YP_004597448.1|  81 PSKGAFAGSKASLQ-GPCPYVECPSHEYCEPDGVEFDEEYRIREIRGDPPHdvCHLDRSLELVEL 144
                                       **************.***********************************99**********996 PP

>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.5e-06     0.021      27      62 ..      21      55 ..       6      80 .. 0.71
   2 ?   -3.2   0.0       1.5   9.1e+03      36      44 ..     102     110 ..     100     125 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-06
                       DDE_Tnp_1_6 27 vyrlkdCrgCplreqCtkkkkgrqltirpelselae 62
                                      + ++  C gCp+r+qC + ++g + ++++  +e+a+
  gi|336254341|ref|YP_004597448.1| 21 QGEADGCAGCPYRSQCLNLSEGTKYRVTDV-REKAQ 55
                                      456788**********99966666666655.23333 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.5
                       DDE_Tnp_1_6  36 CplreqCtk 44 
                                       Cp  e C  
  gi|336254341|ref|YP_004597448.1| 102 CPSHEYCEP 110
                                       777777754 PP

>> MelC1  Tyrosinase co-factor MelC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     4e-06     0.024       6      55 ..      85     132 ..      74     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-06
                             MelC1   6 atagaalaglaaasasaaeapakaegsaepesFDevyrGrRiqGlpaegg 55 
                                       a ag+  a+l  + +  +e p+++   +++ +FDe+yr r i+G p +  
  gi|336254341|ref|YP_004597448.1|  85 AFAGSK-ASLQGPCPY-VECPSHEYCEPDGVEFDEEYRIREIRGDPPHDV 132
                                       445555.455555554.489999999******************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); 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:                         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: 1159.61
//
Query:       gi|336254342|ref|YP_004597449.1|  [L=137]
Description: hypothetical protein Halxa_2954 [Halopiger xanaduensis SH-6]
Scores for 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   0.3       0.19   11.9   0.0    1.6  2  DUF2188   Uncharacterized protein conserved in bacteria (DUF2


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 ?   -3.7   0.3      0.76   1.4e+04      11      19 ..      11      19 ..       8      21 .. 0.64
   2 ?   11.9   0.0   1.1e-05      0.19      22      46 ..      83     107 ..      59     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.76
                           DUF2188 11 WavkreGgs 19
                                      Wav   G++
  gi|336254342|ref|YP_004597449.1| 11 WAVWSRGDD 19
                                      888666654 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.1e-05
                           DUF2188  22 sktfdTqeeAieaArelAkeqggse 46 
                                       + +++T++eA e+  elA++ +++e
  gi|336254342|ref|YP_004597449.1|  83 HDRYPTRAEALERTVELARAFDDGE 107
                                       568***************9844555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1117.42
//
Query:       gi|336254343|ref|YP_004597450.1|  [L=690]
Description: serine protein kinase, PrkA [Halopiger xanaduensis SH-6]
Scores for 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-72  241.7   8.2    9.7e-72  241.7   8.2    1.9  2  PrkA      PrkA serine protein kinase C-terminal domain
    3.1e-63  213.9   0.0    4.8e-63  213.2   0.0    1.3  1  AAA_PrkA  PrkA AAA domain
  ------ inclusion threshold ------
      0.057   13.6   0.7        9.1    6.4   0.1    2.7  2  RasGAP_C  RasGAP C-terminus
       0.19   12.2   1.1        1.5    9.4   0.0    2.8  2  AAA_18    AAA domain


Domain annotation for each model (and alignments):
>> PrkA  PrkA serine protein kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2      0.51   2.3e+03     112     148 ..     221     257 ..     205     269 .. 0.71
   2 !  241.7   8.2   2.2e-75   9.7e-72       1     257 []     425     678 ..     425     678 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.51
                              PrkA 112 lyseeeqieelvenYldhveayikkekvkdpiTgeel 148
                                       l ++++  ++ +en ++ +    +++k +   T e +
  gi|336254343|ref|YP_004597450.1| 221 LAYYDDDLQQVLENHVEIIRLVADENKRQALETFEPK 257
                                       4567777888888888888888888875555554433 PP

  == domain 2  score: 241.7 bits;  conditional E-value: 2.2e-75
                              PrkA   1 leKmklYdgeelpdsleeedvkeLreeaee....reGmsGispRyvikilsealssseakeekcinpldvlealeeg 73 
                                       l+K+k Y+ge+  d+ ++ dvk+Lreeae+     eGm G+spR++ + ++ea+++s+++++ +++pl+v++++ee+
  gi|336254343|ref|YP_004597450.1| 425 LSKAKAYNGEI--DEGDDIDVKKLREEAEQkaeiGEGMVGVSPRFIGDEIAEAIMDSKHRQRGFLSPLTVFNFFEEN 499
                                       58********7..899999******9999987767****************************************** PP

                              PrkA  74 lkeheviseeerekyleflevvreeydervkkevqeAllyseeeqieelvenYldhveayikkekvkdpiTgeelep 150
                                       l++h++i+e++ eky ++le+vreey+er+ ++v++Al+y+ +e i+++ e+Y+dhv+ayi++++++d+ Tg+e+ep
  gi|336254343|ref|YP_004597450.1| 500 LEHHGSIPEDNFEKYYRYLETVREEYRERAIEDVRHALAYDVDE-IQRQGEKYMDHVMAYIDDDTIEDELTGREQEP 575
                                       *************************************9966666.******************************** PP

                              PrkA 151 derflrsiEeqigiseeakkdFRrevikelaasalaregkkidytsierlkealekklfedvk...dllklisstkt 224
                                       de+flrs+Ee+++i+e++k+dFR+ev +++  s+ areg++++ +++erl++ale+kl+ed+k   ++++l+s+++ 
  gi|336254343|ref|YP_004597450.1| 576 DETFLRSVEEKLDIPEDRKDDFRQEVSNWV--SRRAREGEAFNPQDNERLRRALERKLWEDKKhniNFSALVSANEF 650
                                       ******************************..*******************************9999******9999 PP

                              PrkA 225 pdkeqqkkveevverLvekfgYceacArevleY 257
                                       +d+e+  ++++++e+     gY+e +A+evle+
  gi|336254343|ref|YP_004597450.1| 651 DDDERSAWIDALMEQ-----GYSEGGAKEVLEF 678
                                       999999999999888.....***********98 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.2   0.0   1.1e-66   4.8e-63       2     355 ..      28     418 ..      27     421 .. 0.87

  Alignments for each domain:
  == domain 1  score: 213.2 bits;  conditional E-value: 1.1e-66
                          AAA_PrkA   2 slaeyleivkedksvaksaaerlldlikdkglelvdtaederlsrifsnetikkypafeedffG..leetiekivey 76 
                                       s+  yle v ed+++a++a++r+ d+  + g +    + +  ++ + + e        e+ f+G  + ++i+  v+ 
  gi|336254343|ref|YP_004597450.1|  28 SFDWYLEEVYEDPKIARNAHQRVADMFDHYGTTY--DETEGMVEYLLASEDPL--HDGENTFYGkvIHQSIHEFVNK 100
                                       6778************************998875..55566666666655443..334557999889********** PP

                          AAA_PrkA  77 fraaaqrleerkqilyllGPvggGksslverlkklleaa......piyal..................egsPvfeeP 129
                                       +++ a+rl  +++i +llGPvg+Gks + +++++ +e++       +y++                   +sP++++P
  gi|336254343|ref|YP_004597450.1| 101 VKSGARRLGPERRIKLLLGPVGSGKSHFDKQVRRYFEDYtlreegRMYTFrwtnlcdvvqdqdpaddtVRSPMNQDP 177
                                       *************************************998999988999999999********9998889******* PP

                          AAA_PrkA 130 lhlipeelrkk....leeeygi....rlegllsP...latkrleeefgGdiekf.....kvekilfsilkrigiakv 190
                                       l l+p e+r+     l+e+++     + +  l P   + + +l + ++ d++++     ++ +++  ++kr+++ ++
  gi|336254343|ref|YP_004597450.1| 178 LVLLPLEQRQRviddLNENLDApytiQNDQALDPeseFYMDKLLAYYDDDLQQVlenhvEIIRLVADENKRQALETF 254
                                       ****9776654111133333324422667778772224467888999999987533322678899999********* PP

                          AAA_PrkA 191 ePgdennqdisalvGkvdirkleeysendpdaysysGalnranrGllefvemfkadikvlhplltatqegnykstek 267
                                       eP d++nqd ++l+G v+ +k++ y e+dp+a+ ysGa+++anrG++   e++k + ++l+ +l atqe+++k  ++
  gi|336254343|ref|YP_004597450.1| 255 EPKDKKNQDETELTGDVNYSKIAIYGESDPRAFDYSGAFCNANRGIFSGEELLKLQREFLYDFLHATQEQTIKP-KN 330
                                       ************************************************************************97.88 PP

                          AAA_PrkA 268 lslipfdgiilahsnesewkkfksnkknealldrivvvkvPyclrvseekkiyekllkeseladahiaPetlevlar 344
                                          i +d++i+  +n  e+k+ k ++k ea+ dr   ++ Py+l  ++e +iy k+l+++++ d ++ P+tle++  
  gi|336254343|ref|YP_004597450.1| 331 NPRIDIDQVIVGRTNMPEYKDKKGDEKMEAFNDRTKRIDFPYVLSYEDEAQIYWKMLNNADVPDINVEPHTLEMAGL 407
                                       899************************************************************************** PP

                          AAA_PrkA 345 fsiltrlkese 355
                                       f +ltr++e++
  gi|336254343|ref|YP_004597450.1| 408 FGVLTRIEEPD 418
                                       *******9986 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.002       9.1      65     122 ..     213     275 ..     204     281 .. 0.76
   2 ?    4.6   0.0    0.0074        33      32      91 ..     470     529 ..     467     575 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.002
                          RasGAP_C  65 knnylesqlesYkayienvleql.........kkkkgklpfskqyfkkrelkksgklpkfgsykysa 122
                                        + y+ + l++Y++ +++vle+          ++k+    +  ++f+ +++k++++++ +g + ys 
  gi|336254343|ref|YP_004597450.1| 213 SEFYMDKLLAYYDDDLQQVLENHveiirlvadENKR----QALETFEPKDKKNQDETELTGDVNYSK 275
                                       456889999**************9999998763332....333456666677777788888888875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0074
                          RasGAP_C  32 neIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYkayienvleqlkkkk 91 
                                       +eIa+ i   +++++   + l + +   ++L+ + +  e+  e+Y +y+e+v+e+  ++ 
  gi|336254343|ref|YP_004597450.1| 470 DEIAEAIMDSKHRQRGFLSPLTVFNFFEENLEHHGSIPEDNFEKYYRYLETVREEYRERA 529
                                       5778888888888888888888888888999999999*****************997765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00034       1.5       2     102 ..     116     244 ..     116     263 .. 0.80
   2 ?   -0.3   0.6      0.34   1.5e+03      42      68 ..     636     666 ..     543     688 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00034
                            AAA_18   2 lltGtpGvGKttlakeLskrl.gf............gvnlrdvakenglllevdpe..aldeskrldedkldkllda 63 
                                       ll G+ G+GK+ + k +++    +            ++nl dv+++ ++ ++        d+   l  +++++++d 
  gi|336254343|ref|YP_004597450.1| 116 LLLGPVGSGKSHFDKQVRRYFeDYtlreegrmytfrWTNLCDVVQDQDPADDTVRSpmNQDPLVLLPLEQRQRVIDD 192
                                       589**************888666688888888999999999999999999888877877777777888999999999 PP

                            AAA_18  64 leenss.........aleegknlvidghlaeleseaakdikk....vvLtas 102
                                       l+en +         al+ ++  ++d +la + ++ +  +      + L a+
  gi|336254343|ref|YP_004597450.1| 193 LNENLDapytiqndqALDPESEFYMDKLLAYYDDDLQQVLENhveiIRLVAD 244
                                       9998888999999988888888899988887766655443334455555555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.34
                            AAA_18  42 dpe....aldeskrldedkldklldaleens 68 
                                        ++    al + +++d+d + +++dal+e+ 
  gi|336254343|ref|YP_004597450.1| 636 KHNinfsALVSANEFDDDERSAWIDALMEQG 666
                                       2223444445566666666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (690 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.60u 0.22s 00:00:00.82 Elapsed: 00:00:00.38
# Mc/sec: 5484.51
//
Query:       gi|336254344|ref|YP_004597451.1|  [L=761]
Description: serine protein kinase, PrkA [Halopiger xanaduensis SH-6]
Scores for 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-54  183.3   1.0    6.5e-54  183.3   1.0    2.6  3  PrkA      PrkA serine protein kinase C-terminal domain
      1e-13   51.0   0.0    1.9e-10   40.2   0.0    3.2  2  AAA_PrkA  PrkA AAA domain


Domain annotation for each model (and alignments):
>> PrkA  PrkA serine protein kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.034     3e+02      67     130 ..     194     255 ..     190     267 .. 0.83
   2 ?   -1.2   0.1      0.14   1.2e+03     179     240 ..     396     458 ..     392     462 .. 0.80
   3 !  183.3   1.0   7.2e-58   6.5e-54       1     252 [.     470     746 ..     470     749 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.034
                              PrkA  67 lealeeglkeheviseeerekyleflevvreeydervkkevqeAllyseeeqieelvenYldhv 130
                                       le l++ l++h  +   + +++  f +++  +++er +++  eAl  +  + ++  v+nY+  v
  gi|336254344|ref|YP_004597451.1| 194 LEDLNAELDDHVPVR--VDAELDPFSREAYDYLEERYRRDGEEALFSAITDDAHLRVKNYVVDV 255
                                       555666666655555..6688888999999999***************************9877 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.14
                              PrkA 179 elaasalaregkkidytsierlkealekklfedvkdllklis.stktpdkeqqkkveevverL 240
                                       el ++ l++e +  + +s+++l + ++  ++  vk+    ++ +++ p   +     +vv+rL
  gi|336254344|ref|YP_004597451.1| 396 ELIRRELTNETEVWEAESYDELEDRIRAPVTVAVKNQAGETTvEEFAPHALEAAALYAVVTRL 458
                                       566788889999999999999999999999999999888888788888888888888888887 PP

  == domain 3  score: 183.3 bits;  conditional E-value: 7.2e-58
                              PrkA   1 leKmklYdgeel.pdsleeedvkeLreeaeereGmsGispRyvikilsealss......seakeekcinpldvleal 70 
                                       ++K+ +Yd+++l ++ +++ +++e+  ++++++G++Gi+++y++++l+e+l++       +  +e++++p+dvl+a+
  gi|336254344|ref|YP_004597451.1| 470 VDKALIYDQGYLqEGDTRR-EKEEFDFDDDNNDGDHGIPVTYTRDTLAELLQTdrdrhhPDLAVEDVVMPRDVLNAM 545
                                       589*********6444444.788887556677*******************9977765437889************* PP

                              PrkA  71 eeglkeheviseeerekyleflevvreeydervkkevqeAllyseeeqieelvenYldhveayikkekvkdpiTgee 147
                                       +egl e++v+s+ er+++++++ +v++++++r++++v eA++ +++++ ee+v++Y++hv+a+ ++e++++++ ge+
  gi|336254344|ref|YP_004597451.1| 546 AEGLAEAPVFSTGERSEFENRVVPVKNYIYDRQESDVIEAIM-HDKRVDEETVAEYVEHVYAWETDEPLYNDR-GER 620
                                       ****************************************99.99****************************.*** PP

                              PrkA 148 lepd..erflrsiEeqig.........iseeakkdFRre.vikelaasalaregkkidyts.....ierlkealekk 207
                                       +epd  +++l+++E+  +         +++e+ ++FRre vi++l+++a++++++++++++     i+ +k++le++
  gi|336254344|ref|YP_004597451.1| 621 VEPDplKMKLFEVEHLGRfsedeyegnLPRESVRNFRREkVITSLNRHAWEHRNEDFSVEDvdltaIPVIKTVLESH 697
                                       ***********************************************************9999999*********** PP

                              PrkA 208 lfedvkdllklisstk....tpdkeqqkkveevverLvekfgYceacAr 252
                                       +++dvk   + +  ++       +e+   +e+++e++v+ fgY+ea+A+
  gi|336254344|ref|YP_004597451.1| 698 DWDDVKRTFEDFDPRQwddpPSGTETAAIKEDTIETMVDLFGYSEASAE 746
                                       ******55555553335654559************************95 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   2.1e-14   1.9e-10       2     280 ..      23     354 ..      22     412 .. 0.78
   2 !    5.7   0.0   0.00064       5.8     332     354 ..     439     461 ..     431     464 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.1e-14
                          AAA_PrkA   2 slaeyleivkedksvaksaaerlldlikdkgl.elvdtaederlsrifsnetikkypafeedffGleetiekiveyf 77 
                                        la y++ + e++++a +a + ll++i+  g  ++v+  e++   r f + +       e+ + G  e+++  v+ +
  gi|336254344|ref|YP_004597451.1|  23 GLAAYVDRIFENPTIASHASKYLLEAIEAAGTrTVVEEGEEKERYRFFDDPHND----GEHAILGNTEVLNGFVDDL 95 
                                       5889****************************6666777777777777765443....445578************* PP

                          AAA_PrkA  78 raaaqrleerkqilyllGPvggGksslverlkklleaa......piyal............................ 120
                                       r+ a +  +  +i+++ GP ++Gks l   l + l ++        y++                            
  gi|336254344|ref|YP_004597451.1|  96 RSIAAGRAKDEKIIWFEGPTATGKSELKRCLVNGLREYsktpegRRYTVewnvttaeagerglsyggdptatddqnw 172
                                       ********************************999998888887678888889999*****************9988 PP

                          AAA_PrkA 121 egsPvfeePlhlipeelrkkleeeygi........rlegllsPla...tkrleeefgGd.........iekfkveki 177
                                        +sPv+ +Pl+++pe++r+ + e+++         r++++l P++   +  lee +  d          ++ ++  +
  gi|336254344|ref|YP_004597451.1| 173 YESPVQAHPLSVFPEDVRQGILEDLNAelddhvpvRVDAELDPFSreaYDYLEERYRRDgeealfsaiTDDAHLRVK 249
                                       89*************99986665555444555566******999622145687777544111111111223334445 PP

                          AAA_PrkA 178 lfsilkrigiakvePgdennqdisalvGkvd...irkleeysendpdaysysGalnranrGllefvemfkadikvlh 251
                                       ++ ++  +g+++++  de  q    lvG+     +++l++  +++p+a+sy+G l+++n G+l  ve      ++l 
  gi|336254344|ref|YP_004597451.1| 250 NYVVDVGQGVGVLHSEDE-GQPKERLVGSWMhgmLQELDSRGRKNPQAFSYDGVLSQGN-GVLTIVEDAAQHADLLQ 324
                                       566677789999987776.68999****975233677888899**************98.9**************** PP

                          AAA_PrkA 252 plltatqegnyksteklsl.ipfdgiilah 280
                                       +ll +  e+++k  + +++ +  + +i++ 
  gi|336254344|ref|YP_004597451.1| 325 KLLNVPDEQSVKLDKGIGMdVDTQMLIISN 354
                                       ************999998834444445443 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.00064
                          AAA_PrkA 332 ahiaPetlevlarfsiltrlkes 354
                                        + aP++le +a ++++trl e+
  gi|336254344|ref|YP_004597451.1| 439 EEFAPHALEAAALYAVVTRLDEE 461
                                       678*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (761 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 5354.63
//
Query:       gi|336254345|ref|YP_004597452.1|  [L=443]
Description: hypothetical protein Halxa_2957 [Halopiger xanaduensis SH-6]
Scores for complete 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-128  429.6   0.1   1.6e-128  429.4   0.1    1.0  1  DUF444         Protein of unknown function (DUF444)
  ------ inclusion threshold ------
       0.15   12.2   0.3        2.4    8.3   0.1    2.7  3  Tautomerase_2  Tautomerase enzyme


Domain annotation for each model (and alignments):
>> DUF444  Protein of unknown function (DUF444)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.4   0.1  1.8e-132  1.6e-128      13     421 .]       3     438 ..       1     438 [. 0.95

  Alignments for each domain:
  == domain 1  score: 429.4 bits;  conditional E-value: 1.8e-132
                            DUF444  13 slenrqRflrrvkeqikeavadavsersikdiskgekikipikdikepefeygkggeregVlpGnkef.keGdkier 88 
                                         ++ +Rf r+v+e+++e++ad+++++++ + s   +i+ip+k +++pefey+ +++++gV++G++++ ++G+++++
  gi|336254345|ref|YP_004597452.1|   3 LRDDLERF-REVGEKRREDLADFIQYGDLGG-SGPGQINIPVKIVSLPEFEYD-QRDKGGVGQGDGDTpDTGQPVGQ 76 
                                       56899***.**********************.9********************.9************99******** PP

                            DUF444  89 peeggggggsgegseaGe.gedefefelsreEfldllfedLeLPdLekkklekveekktkragytrkGspsnldvkr 164
                                       p+ + g+g+ +e++e+Ge g +++++e+++eEf+++l+e+L+L dL++k++++veek++ ++++tr+G++s+ld++r
  gi|336254345|ref|YP_004597452.1|  77 PQPQPGDGDGDEDGEPGEeGGEHEYYEMDPEEFAQELDEELGL-DLDPKGKKVVEEKEGPFTDLTRTGPNSTLDFER 152
                                       ***9999776666999955************************.********************************* PP

                            DUF444 165 tlrealkRrialkrpkeeelre.......leeelaelea.....................eeeekeseeleeleeei 213
                                       +++e+lkR++a+++ +ee lre         ++++e+++                     e+ +++s+e+ e+++e+
  gi|336254345|ref|YP_004597452.1| 153 MFKEGLKRKLAMDF-DEEFLRElckvegiEPRDVFEWARgenlpvsmawieeaykdipddERGKWASIEEVENNVER 228
                                       **************.9999999999999878888888888888888888888777776544447************* PP

                            DUF444 214 eeleerikr.....ipfidelDlRYrrvekepkpesnaVmfclmDvSGSMdetkkdlakrfFilLylFLkrkYekve 285
                                       e+++++i+r     +pf++e D+RYr++e  +++e+n+V+++++DvSGSM+e+k++l++r+F++L+++L+ kY+++e
  gi|336254345|ref|YP_004597452.1| 229 EDVQQKIRRegidhVPFRRE-DERYRHPEIIEEKEKNVVVVNIRDVSGSMREKKRELVERTFTPLDWYLQGKYDNAE 304
                                       ********************.******************************************************** PP

                            DUF444 286 vvFirHtteAkeVdeeeFFysresGGTvvSsalelmkeiieerYppseWNiYaaqasDgdnwseDsekavellaeki 362
                                       +v+i+H++eA+eV++eeFF++r++GGT +Ssa+el++e++e +Yp+s+WN+Y+++a+D++n+s+D+e+ v +++e+i
  gi|336254345|ref|YP_004597452.1| 305 FVYIAHDAEAWEVEREEFFGIRSGGGTKISSAYELAAELLE-EYPWSDWNRYVFAAGDSENSSNDTEERVIPMMEQI 380
                                       ****************************************9.9********************************** PP

                            DUF444 363 lplvqyfaYveitpsaseeeqtlweeyekvaeee.enfamakvkekediypvfrellkke 421
                                          ++++aYve++ps+++ ++t++ee+e+++ ++ +++a+a+v+ ++d++++++e+l++e
  gi|336254345|ref|YP_004597452.1| 381 --PANLHAYVETQPSGNAINATHAEELERHFGTDdDEVAVAYVNGEADVTDAIYEILSTE 438
                                       ..9****************************9998**********************986 PP

>> Tautomerase_2  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.53   4.7e+03      54      68 ..     172     186 ..     165     186 .. 0.79
   2 ?    8.3   0.1   0.00027       2.4      22      79 ..     258     315 ..     242     317 .. 0.83
   3 ?    0.3   0.0     0.086   7.7e+02      52      73 ..     401     422 ..     390     426 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.53
                                       HHHHHHH---GGGEE CS
                     Tautomerase_2  54 erlaaklgirpeDvf 68 
                                       ++l +  gi+p+Dvf
  gi|336254345|ref|YP_004597452.1| 172 RELCKVEGIEPRDVF 186
                                       66777789*****97 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00027
                                       ..TS-TT-EEEEEEEES---HHHHHHHHHHHHHHHHHHH---GGGEEEEEEEE-GGGE CS
                     Tautomerase_2  22 gieRsddlvvieitlsegRseeqKkaLyralaerlaaklgirpeDvfivlvenpkedW 79 
                                         e+++++vv++i   +g  +e+K++L+++ ++ l   l  + ++ + v +  ++e W
  gi|336254345|ref|YP_004597452.1| 258 IEEKEKNVVVVNIRDVSGSMREKKRELVERTFTPLDWYLQGKYDNAEFVYIAHDAEAW 315
                                       468999**************************99999998888888888888888888 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.086
                                       HHHHHHHHH---GGGEEEEEEE CS
                     Tautomerase_2  52 laerlaaklgirpeDvfivlve 73 
                                        ae+l++++g + ++v +  v 
  gi|336254345|ref|YP_004597452.1| 401 HAEELERHFGTDDDEVAVAYVN 422
                                       589*************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3499.62
//
Query:       gi|336254346|ref|YP_004597453.1|  [L=678]
Description: SpoVR family protein [Halopiger xanaduensis SH-6]
Scores for 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-92  308.0   4.8    3.3e-77  259.9   0.9    2.2  2  SpoVR     SpoVR like protein
  ------ inclusion threshold ------
      0.098   12.6   0.0       0.44   10.5   0.0    2.1  1  SOAR      STIM1 Orai1-activating region


Domain annotation for each model (and alignments):
>> SpoVR  SpoVR like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.9   0.9   3.7e-81   3.3e-77       5     322 ..      18     360 ..      14     383 .. 0.81
   2 !   49.7   0.2   2.4e-17   2.2e-13     337     418 .]     495     574 ..     468     574 .. 0.87

  Alignments for each domain:
  == domain 1  score: 259.9 bits;  conditional E-value: 3.7e-81
                             SpoVR   5 keleeakeeieeiakelgLdfypnqfeiitaeqmleaaayvgmPlrysHWsfGkeyeklkksykyglsklaYElViN 81 
                                       ++lee  ee +++a++lgL+ yp+++ ii++++m+e+ ay+g+ +ry+HW++G++y+k++k+ +yg  k  +E+V N
  gi|336254346|ref|YP_004597453.1|  18 TDLEEPVEEARNLAQKLGLEPYPVKYWIIDYDEMNELIAYGGFQSRYPHWRWGMQYDKQRKQGQYGGGKA-FEIVNN 93 
                                       578999999**********************************************************998.****** PP

                             SpoVR  82 sdPciaylleeNslvqqklviAHvygHndFFknNalFkkttda......rkildslalaaerireyee..ryGeeeV 150
                                        +P+ a+l e+N+l++qk vi Hv +H+dFF nN +F   t+        +   +l+ +a+ i +y++   + ++eV
  gi|336254346|ref|YP_004597453.1|  94 DNPAHAFLQESNTLADQKAVITHVEAHSDFFANNEWFGLFTSGradeeqVNAAAMLERHARAIDDYMSdpDIDRAEV 170
                                       ************************************977765433332234556788999*******9778999*** PP

                             SpoVR 151 Eklldaalaleelvdrykrkekkklee.eekrkkereeye.sqvedlwrtleekkkkeeeekek........eekfp 217
                                       Ek +d++l+le+++d+++ ++++ + +   ++ ++ ++   ++ ++l   +e k +  +ee              fp
  gi|336254346|ref|YP_004597453.1| 171 EKWIDHCLSLEDNIDQHRVFQRRLEVDgPGDELEDLDDDLaEKLDELNLSDEIKGEVFDEEW-LeqlegedgGVTFP 246
                                       *****************998654433303333344444334777777444432222222221.123444333449** PP

                             SpoVR 218 eepeedlllFleknap..........eLeeWqrdilrivreeaqYFlPQrqtkimNEGwAsywHstilnel.kltde 283
                                        epe+d+l F++++++          e+eeWqrd+l ++r ea+YF+ Q++tk+mNEGwA+yw st++++     d+
  gi|336254346|ref|YP_004597453.1| 247 DEPEKDILAFVREHGKrydddaeravEMEEWQRDVLDMMRAEAYYFAAQKMTKVMNEGWAAYWESTMMTDEtFAGDD 323
                                       ***********998653333333333699***************************************998456799 PP

                             SpoVR 284 eileflkshsgvvapsksglNPYalGlklfedierrvee 322
                                       e+++++++ ++v+a   +glNPY lG++l+e++e+++++
  gi|336254346|ref|YP_004597453.1| 324 EFMNYADHMAKVLA--SGGLNPYSLGMELWEYVENTTNR 360
                                       ************97..589***************98854 PP

  == domain 2  score: 49.7 bits;  conditional E-value: 2.4e-17
                             SpoVR 337 egreklfevrelekDesfirqyLtkelvrelklfslkkkeeeeeveaiidekgykkvrekLlkqltnaglpaiqved 413
                                       +g +++f++re ++D++f++++Lt+e+++e + f++++++ +   +  + ++  ++v++kLl q+tn+g+p+i v+d
  gi|336254346|ref|YP_004597453.1| 495 AGWDRMFDIRESHNDVTFLDEFLTEEFITENNYFTYEHSQATG--QFHVASDAAEDVKKKLLLQFTNFGKPTIAVYD 569
                                       44469************************************98..889999999*********************** PP

                             SpoVR 414 vdlek 418
                                       +++++
  gi|336254346|ref|YP_004597453.1| 570 GNYNN 574
                                       **985 PP

>> SOAR  STIM1 Orai1-activating region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.9e-05      0.44       7      46 ..     513     552 ..     508     561 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.9e-05
                              SOAR   7 LqqlLqlTyelElkylnkkkqeaekqlqeAkeeveklkkk 46 
                                       L ++L + + +E +y++++ ++a  q+++A +++e +kkk
  gi|336254346|ref|YP_004597453.1| 513 LDEFLTEEFITENNYFTYEHSQATGQFHVASDAAEDVKKK 552
                                       78899999*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); 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: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.38
# Mc/sec: 5361.07
//
Query:       gi|336254347|ref|YP_004597454.1|  [L=231]
Description: HEAT domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-10   41.9  16.1    1.1e-06   29.0   6.5    2.4  2  HEAT_2    HEAT repeats
    2.1e-06   27.5  13.5      0.084   13.2   0.2    4.8  5  HEAT      HEAT repeat
    3.2e-06   27.5  15.1    2.8e-05   24.5   2.5    4.2  4  HEAT_EZ   HEAT-like repeat
    4.3e-06   26.6   3.1       0.34   11.0   0.2    3.4  3  Arm       Armadillo/beta-catenin-like repeat
  ------ inclusion threshold ------
      0.049   12.7   3.1        2.8    7.0   0.9    2.9  2  IFRD      Interferon-related developmental regulator (IFRD)
       0.05   13.2   0.1        8.6    5.8   0.0    2.6  3  MMS19_N   Dos2-interacting transcription regulator of RNA-Pol
       0.21   11.6   0.3        6.4    6.8   0.1    2.6  2  Cnd1      non-SMC mitotic condensation complex subunit 1


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.0     1e-06    0.0026       1      65 [.      46     115 ..      46     118 .. 0.87
   2 !   29.0   6.5   4.2e-10   1.1e-06       8      86 ..     127     226 ..     120     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1e-06
                            HEAT_2   1 ldaLlqalendpdpevrraairaLg.ri.gnpea....lpaLvellededpavRraaaeaLgaigdpealp 65 
                                       l+a l++l +  d +v+r+a+r++     + pea    +  L+ lle +d +  +a+a  L+++++++a++
  gi|336254347|ref|YP_004597454.1|  46 LPAVLAQL-DATDADVQRQAVRTIRaHVdDRPEAciptVSKLRTLLERPDLEYHEAVAYCLAELAEESAAD 115
                                       688999**.9***************5332345666777***************************999876 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 4.2e-10
                            HEAT_2   8 lendpdpevrraairaLgrignpea......lpaLvellededpavRraaaeaLgaig...............dpea 63 
                                       +++ p++   +  +r+L+ i++++       ++aLv+ le++d+ vR++aa aL++++               ++++
  gi|336254347|ref|YP_004597454.1| 127 ATERPSHPATADCCRSLAAIADERPgalvdrVDALVPTLESDDATVRANAALALARVAdgadgpleqtdtpdvLEDV 203
                                       55667777778889******99966667777************************9943444455555544333778 PP

                            HEAT_2  64 lpaLkellddddddvvReaAaea 86 
                                        ++L++l ++d+d++vRe+Aa+a
  gi|336254347|ref|YP_004597454.1| 204 RAILADLERTDPDPDVREWAAQA 226
                                       8999999999***********97 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.2    0.0064        16       2      25 ..      46      69 ..      46      70 .. 0.91
   2 ?    4.3   0.0     0.024        60      17      29 ..      98     110 ..      85     112 .. 0.84
   3 ?   -2.1   0.2       2.7     7e+03      20      28 ..     139     147 ..     137     148 .. 0.80
   4 !   13.2   0.2   3.3e-05     0.084       4      30 ..     160     186 ..     158     187 .. 0.88
   5 !   10.7   0.1   0.00021      0.54      10      23 ..     213     226 ..     205     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0064
                                      HHHHHHHHT-SSHHHHHHHHHHHH CS
                              HEAT  2 lPlllkllsDpspeVReaAakaLg 25
                                      lP++l  l  ++++V + A++++ 
  gi|336254347|ref|YP_004597454.1| 46 LPAVLAQLDATDADVQRQAVRTIR 69
                                      7999**************999985 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHH CS
                              HEAT  17 ReaAakaLgalae 29 
                                        ea+a++L++lae
  gi|336254347|ref|YP_004597454.1|  98 HEAVAYCLAELAE 110
                                       589********98 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.7
                                       HHHHHHHHH CS
                              HEAT  20 AakaLgala 28 
                                       ++++L+a+a
  gi|336254347|ref|YP_004597454.1| 139 CCRSLAAIA 147
                                       788888887 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 3.3e-05
                                       HHHHHHT-SSHHHHHHHHHHHHHHHHC CS
                              HEAT   4 lllkllsDpspeVReaAakaLgalaev 30 
                                       +l+  l+++++ VR++Aa+aL+++a +
  gi|336254347|ref|YP_004597454.1| 160 ALVPTLESDDATVRANAALALARVADG 186
                                       6778899***************99875 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00021
                                       T-SSHHHHHHHHHH CS
                              HEAT  10 sDpspeVReaAaka 23 
                                       +Dp+p+VRe Aa+a
  gi|336254347|ref|YP_004597454.1| 213 TDPDPDVREWAAQA 226
                                       7***********97 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.048   1.2e+02      30      53 ..      46      69 ..      38      70 .. 0.72
   2 ?    3.0   0.0     0.061   1.6e+02       5      31 ..      99     125 ..      90     126 .. 0.87
   3 !   24.5   2.5   1.1e-08   2.8e-05       8      54 ..     140     182 ..     137     183 .. 0.82
   4 !   12.1   2.7   8.2e-05      0.21       3      51 ..     172     226 ..     172     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.048
                           HEAT_EZ 30 lpaLlalLnddsdeVRaaAagaLg 53
                                      lpa la L   +++V+ +A+++++
  gi|336254347|ref|YP_004597454.1| 46 LPAVLAQLDATDADVQRQAVRTIR 69
                                      4555555555555*******9986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.061
                           HEAT_EZ   5 raAawaLGrlaggepellqplvpeilp 31 
                                       +a+a +L++la++ + +++p  +ei+ 
  gi|336254347|ref|YP_004597454.1|  99 EAVAYCLAELAEESAADVAPSADEIVS 125
                                       78888**99**9999999999999985 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 1.1e-08
                           HEAT_EZ   8 awaLGrlaggepellqplvpeilpaLlalLnddsdeVRaaAagaLgn 54 
                                       ++ L+++a ++p +l     + ++aL+++L++d+++VRa+Aa aL++
  gi|336254347|ref|YP_004597454.1| 140 CRSLAAIADERPGALV----DRVDALVPTLESDDATVRANAALALAR 182
                                       5678888999999999....777777777778888**********98 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 8.2e-05
                           HEAT_EZ   3 vRraAawaLGrlaggepellqp.lvpeilpaLlalLnd....dsd.eVRaaAaga 51 
                                       vR++Aa+aL+r+a g++  l++   p++l    a L d    d+d +VR+ Aa a
  gi|336254347|ref|YP_004597454.1| 172 VRANAALALARVADGADGPLEQtDTPDVLEDVRAILADlertDPDpDVREWAAQA 226
                                       8**********66666665554488888888888888888886666******987 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1    0.0002       0.5      14      37 ..      46      69 ..      45      69 .. 0.94
   2 ?    3.9   0.0     0.023        59      14      40 ..      83     109 ..      81     110 .. 0.92
   3 !   11.0   0.2   0.00013      0.34      14      37 ..     158     181 ..     153     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0002
                                      HHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm 14 vppLvrLLssedeevqeeAawALs 37
                                      +p+ ++ L+ +d +vq++A+++++
  gi|336254347|ref|YP_004597454.1| 46 LPAVLAQLDATDADVQRQAVRTIR 69
                                      79999****************996 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.023
                                       HHHHHHHTTTSSHHHHHHHHHHHHHHT CS
                               Arm  14 vppLvrLLssedeevqeeAawALsNLa 40 
                                       v  L +LL+ +d e+ e++a +L+ La
  gi|336254347|ref|YP_004597454.1|  83 VSKLRTLLERPDLEYHEAVAYCLAELA 109
                                       67899******************9997 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00013
                                       HHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  14 vppLvrLLssedeevqeeAawALs 37 
                                       v++Lv  L+s+d +v+ +Aa AL+
  gi|336254347|ref|YP_004597454.1| 158 VDALVPTLESDDATVRANAALALA 181
                                       89********************97 PP

>> IFRD  Interferon-related developmental regulator (IFRD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.012        32     217     246 ..      41      68 ..      26      70 .. 0.78
   2 ?    7.0   0.9    0.0011       2.8     212     279 ..     143     207 ..      78     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.012
                              IFRD 217 eedleealealvelLdssdvevriAAGeai 246
                                       +   e  l+a+ ++Ld +d +v+  A ++i
  gi|336254347|ref|YP_004597454.1|  41 DA--EFNLPAVLAQLDATDADVQRQAVRTI 68 
                                       33..5569***************9887776 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0011
                              IFRD 212 lnkkleedl...eealealvelLdssdvevriAAGeaiALlfElsreedeefeeeeeedteelleqlreLa 279
                                       l+++++e+     + ++alv  L+s+d  vr  A  a+A + + ++ + e    ++  dt+++le +r++ 
  gi|336254347|ref|YP_004597454.1| 143 LAAIADERPgalVDRVDALVPTLESDDATVRANAALALARVADGADGPLE----QT--DTPDVLEDVRAIL 207
                                       444444433555455999999*************9999999998877733....33..5667777776665 PP

>> MMS19_N  Dos2-interacting transcription regulator of RNA-Pol-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.01        27     206     238 ..      42      74 ..      37      92 .. 0.83
   2 ?   -0.5   0.0      0.29   7.4e+02       1      66 [.      83     145 ..      83     150 .. 0.68
   3 ?    5.8   0.0    0.0034       8.6       1      37 [.     158     193 ..     158     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.01
                           MMS19_N 206 aplalplllekLdstsvsakldaLqtlaacvea 238
                                       a++ lp++l +Ld+t  +++++a +t+ a v+ 
  gi|336254347|ref|YP_004597454.1|  42 AEFNLPAVLAQLDATDADVQRQAVRTIRAHVDD 74 
                                       78899**********************998865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.29
                           MMS19_N   1 veaLgeyLtseddkvRakavslLaevlsrlpkkklseeevevLvqFflsrledfavlkealkglla 66 
                                       v++L + L   d +  +    +Lae+++++ ++   + +++ +v F ++r ++ a+   ++++l+a
  gi|336254347|ref|YP_004597454.1|  83 VSKLRTLLERPDLEYHEAVAYCLAELAEESAAD--VAPSADEIVSFATERPSHPATA-DCCRSLAA 145
                                       567777788888888888888899998888754..3345566788888888777664.55555555 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0034
                           MMS19_N   1 veaLgeyLtseddkvRakavslLaevlsrlpkkklse 37 
                                       v aL ++L s+d +vRa+a + La+v+   +  +l++
  gi|336254347|ref|YP_004597454.1| 158 VDALVPTLESDDATVRANAALALARVADGADG-PLEQ 193
                                       6688999*******************876664.5554 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.059   1.5e+02      34     105 ..      57     128 ..      42     152 .. 0.61
   2 ?    6.8   0.1    0.0025       6.4      24      49 ..     159     186 ..     139     226 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.059
                              Cnd1  34 dpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteiseksenaiynllpdiiskls 105
                                       d+ V+++a+ ++   ++         +s+l++lle ++ +  + + ++l e++e+s   +  +  +i+s   
  gi|336254347|ref|YP_004597454.1|  57 DADVQRQAVRTIRAHVDDRPEACIPTVSKLRTLLERPDLEYHEAVAYCLAELAEESAADVAPSADEIVSFAT 128
                                       555555555555333333322223456777777777777777777777777777776666666666666555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0025
                              Cnd1  24 epLrkrLkDedpyVRktaaivvakL..i 49 
                                       + L  +L+ +d++VR +aa+++a++   
  gi|336254347|ref|YP_004597454.1| 159 DALVPTLESDDATVRANAALALARVadG 186
                                       4555566666777777777777766441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 1938.56
//
Query:       gi|336254348|ref|YP_004597455.1|  [L=133]
Description: hypothetical protein Halxa_2960 [Halopiger xanaduensis SH-6]
Scores for 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-36  123.4   0.0    5.7e-36  123.2   0.0    1.0  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.2   0.0   3.2e-40   5.7e-36       1     114 [.      17     127 ..      17     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 3.2e-40
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTTT-GGG.TTS..THHHHHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpeeeYrhn.aegpdnadaHlkssl 76 
                                       ++t+++++av   ++++G+++ f++htta+l+++En +++++eDle++l++lvp+e + h+  +g  nad+Hl+++l
  gi|336254348|ref|YP_004597455.1|  17 EVTDQIAAAVP-DDLESGTCTAFVEHTTAGLVVQEN-ESRLREDLESYLSELVPDEGHAHDqLDG--NADSHLRATL 89 
                                       589****9965.68**********************.*******************889984556..********** PP

                                       H-SEEEEEEETTEE---TTEEEEEEESS-SSEEEEEEE CS
                           UPF0047  77 lgssltipvedgklalGtwqsiylveldgpreRkvvvq 114
                                       +g+++tipv+dg+lalG wqsi++ve+dgpr+R+v v+
  gi|336254348|ref|YP_004597455.1|  90 IGPDVTIPVTDGELALGAWQSILFVECDGPRTRTVSVT 127
                                       ***********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1015.96
//
Query:       gi|336254349|ref|YP_004597456.1|  [L=219]
Description: glycerophosphoryl diester phosphodiesterase [Halopiger xanaduensis SH-6]
Scores for complete 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   93.6   0.1    4.7e-25   88.8   0.1    2.0  1  GDPD      Glycerophosphoryl diester phosphodiesterase family


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.1   2.6e-29   4.7e-25       1     257 [.       6     216 ..       6     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 2.6e-29
                                       TTTTTTTSSTTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECCTTC CS
                              GDPD   1 HRGasgnlpEnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkiaken 77 
                                       HRG+s++ pEnT++++++A ++ ad++EfDv+    g +Vv+HD+++dr+t++ g   v + +leelk+ + +    
  gi|336254349|ref|YP_004597456.1|   6 HRGFSATAPENTIAAIRSA-ADRADAVEFDVRRCGSGELVVVHDETIDRVTGGVG--TVVHSSLEELKTHT-V-L-- 75 
                                       *******************.6779*******************************..***********999.3.2.. PP

                                       CCCSCCCSSGCCB...BHHHHHHH.HHHCCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHTT..STTCSCEE CS
                              GDPD  78 kaqlsenrvrlefpfptleevlkk.pqnvglnieikipmlseakeeeelqivkeilksvdeilkkvlkkadkrkvif 153
                                           s++r+      ptlee ++  p +v           ++ +++e+  i+ ++l+++ ++           +v+ 
  gi|336254349|ref|YP_004597456.1|  76 ---ESGERI------PTLEETIAAlPSDV----------VVNLEMKEL-GIAADVLEAIEDLE---------NRVVT 123
                                       ...256777......*******8744444..........445556677.8***********98.........69999 PP

                                       EESTHHHHHHHHHTCTCTEEEEEEHHHHHHC-E.EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHHHHTT-EEEE CS
                              GDPD 154 ssfnpdilkllrekqpklpllflteggteaeadssleraakfakadallgevsavaeglgdpdlVkraksrglvvhv 230
                                       +sf + +l+ +r +++  p+ +l +   e++       +a ++++d + ++ + +       +lV rak+ gl+vh 
  gi|336254349|ref|YP_004597456.1| 124 TSFLVPELRTMRDLDSGQPTGLLANRHLENPVT-----TAVELGCDVIGANWWRCLTT----RLVPRAKAVGLEVHS 191
                                       ****************99999999988888887.....9****************999....9************** PP

                                       BSB-THSHHHHHHHHCCC-SEEEES-H CS
                              GDPD 231 ytvnnedeeemkrlleagvdgvitDfp 257
                                       +          k+l++ gvd v  D+p
  gi|336254349|ref|YP_004597456.1| 192 WSIERR--LVAKLLERRGVDYVSADRP 216
                                       ******..*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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 0.21s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1807.02
//
Query:       gi|336254350|ref|YP_004597457.1|  [L=147]
Description: response regulator receiver protein [Halopiger xanaduensis SH-6]
Scores for complete 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   77.0   0.0    1.3e-21   76.8   0.0    1.0  1  Response_reg  Response regulator receiver domain


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 !   76.8   0.0   7.4e-26   1.3e-21       1     111 [.      11     130 ..      11     131 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 7.4e-26
                                       EEEESSSHHHHHHHHHHHHHTTEEEEE.EESSHHHHHHHHHHHH......ESEEEEESSCSSSEHHHHHHHHHHCT. CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeeva.eaedgkealellkeek......vdlillDinmpgmdGlellkeireed. 69 
                                       +l+v+D+p  ++l+++++++   e++  +++dg++al ll+ ++      +dl+llD+n+p+m Gle+l+ i++e+ 
  gi|336254350|ref|YP_004597457.1|  11 ILLVEDNPGDVRLIQEAFKDLPTEVTLcVVTDGDDALTLLQDRQaetaplPDLVLLDLNLPRMGGLEFLEAIQDEPa 87 
                                       89*****************8777444469***********88877889****************************9 PP

                                       .TTSEEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  70 .pelpviiltahseeedavealkagaddflsKpfdpeeLlkal 111
                                          lpv++lt+ ++ ed+ e +++ a+ +l+Kp dp+e  +++
  gi|336254350|ref|YP_004597457.1|  88 fARLPVLVLTSSEAYEDVLESYELAANAYLTKPTDPDEFSSMV 130
                                       999**********************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1218.63
//
Query:       gi|336254351|ref|YP_004597458.1|  [L=240]
Description: short-chain dehydrogenase/reductase SDR [Halopiger xanaduensis SH-6]
Scores for 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-40  136.9   0.0    1.5e-39  135.9   0.0    1.4  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    4.9e-37  127.3   0.0    5.8e-37  127.0   0.0    1.1  1  adh_short       short chain dehydrogenase
      6e-08   32.4   0.0    2.4e-07   30.5   0.0    1.9  1  Epimerase       NAD dependent epimerase/dehydratase family
    3.1e-05   24.0   0.0    4.7e-05   23.4   0.0    1.3  1  KR              KR domain
     0.0025   17.3   0.0     0.0037   16.7   0.0    1.2  1  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase
      0.009   15.1   0.1      0.011   14.8   0.1    1.1  1  RmlD_sub_bind   RmlD substrate binding domain
  ------ inclusion threshold ------
      0.019   14.8   0.1      0.038   13.9   0.1    1.5  1  NAD_binding_10  NAD(P)H-binding
      0.091   11.7   0.0       0.13   11.2   0.0    1.2  1  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase


Domain annotation for each model (and alignments):
>> 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 !  135.9   0.0   6.7e-43   1.5e-39       1     229 [.      20     236 ..      20     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: 135.9 bits;  conditional E-value: 6.7e-43
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnna 77 
                                       Ga   +G a++ ++ ++Ga+v+++d+   + ++   l+ + +++++e+D tde++v +lv+ +v++ g++D l+n a
  gi|336254351|ref|YP_004597458.1|  20 GASGALGSAAVDRFRAAGATVCAVDVVAPD-AEDSLLEPDSKTHFYEADLTDESDVSELVASIVDDRGRIDHLLNIA 95 
                                       777889********************9998.33344445556779******************************** PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeg.gsivnlssvgaervvpnynaygaaKaalealtr 153
                                       g  +    p++et+ eef+  +dvnl+ +fl +k+alp+++e+ gsiv +s  ++  + ++   y ++Ka++  lt 
  gi|336254351|ref|YP_004597458.1|  96 GTWTG-GDPIEETDLEEFELLVDVNLKTAFLASKHALPHLQENeGSIVSVSARSSLEGGEGDGPYRITKAGIRILTE 171
                                       ****9.9*******************************998888********************************* PP

                                       HHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEE CS
                      adh_short_C2 154 ylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvv 229
                                       +lA e     +R N+v p++i+T+a++++             a  g +++p e+a++++fL+sd a+ ++G+ + v
  gi|336254351|ref|YP_004597458.1| 172 TLAEENEG-TVRANCVMPSVIDTPANREMM----------PDADHGAWVEPAEIADVMAFLCSDGAAVTSGAAVPV 236
                                       *****999.9***************88764..........334458899**********************99887 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.0   0.0   2.6e-40   5.8e-37       2     191 ..      15     200 ..      14     204 .. 0.95

  Alignments for each domain:
  == domain 1  score: 127.0 bits;  conditional E-value: 2.6e-40
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                       v+++tGas+ +G a ++++ ++Ga+v +vd  + ++e  + e  +   k +++++D+td+++v++lv+ +v++ g++
  gi|336254351|ref|YP_004597458.1|  15 VAVITGASGALGSAAVDRFRAAGATVCAVDVVAPDAEDSLLEPDS---KTHFYEADLTDESDVSELVASIVDDRGRI 88 
                                       89******************************9999777777665...6**************************** PP

                                       SEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  79 dvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       d L n AG  tg  p++e++ ee+e +++vNl+ +fl+++++lp+ l++++G+Iv vs   ++++ +g  +Y  +Ka
  gi|336254351|ref|YP_004597458.1|  89 DHLLNIAGTwTGGDPIEETDLEEFELLVDVNLKTAFLASKHALPH-LQENEGSIVSVSARSSLEGGEGDGPYRITKA 164
                                       *********99**********************************.669**************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakelr 191
                                       +++ lt++la+e + t +r n+v+P ++dT+ ++e  
  gi|336254351|ref|YP_004597458.1| 165 GIRILTETLAEENEGT-VRANCVMPSVIDTPANREMM 200
                                       ************9998.**************999875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.1e-10   2.4e-07       2      73 ..      17      96 ..      16     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.1e-10
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHH....HHH.T-SEEEE-- CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlf....kee.qpdavihlA 72
                                      ++tGa+G +Gsa v+++ ++g +v ++d    + + ++le     +++e+dltd+s++ +l+    ++  ++d+ +++A
  gi|336254351|ref|YP_004597458.1| 17 VITGASGALGSAAVDRFRAAGATVCAVDVVAPDAEDSLLEPDsktHFYEADLTDESDVSELVasivDDRgRIDHLLNIA 95
                                      79*********************9999998666665555555799***********77776511114555777777776 PP

                                      S CS
                         Epimerase 73 a 73
                                      +
  gi|336254351|ref|YP_004597458.1| 96 G 96
                                      6 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.1e-08   4.7e-05       3     150 ..      16     160 ..      14     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.1e-08
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        +itG+ G+LG + ++   + ga+  ++        +d++   ++l + + + ++++aD++d+++v++l+++i ++ 
  gi|336254351|ref|YP_004597458.1|  16 AVITGASGALGSAAVDRFRAAGATVCAVDVVA----PDAE---DSLLEPDSKTHFYEADLTDESDVSELVASIVDDR 85 
                                       68********************9865554333....4444...67888999************************** PP

                                       S---EEEE------.---TTT--HHHHHHHHTTTTHHHHHHH.HHTTT..S--SEEEEEEEHHHHH--TT-HHHH CS
                                KR  80 ppikGvihaAgvlr.dklleemtaedleqvlapKvkGawnLh.elled..esldffvlfSSiagllgsagqanYa 150
                                       ++i   ++ Ag+    +++ee++ e++e ++   +k a     ++l++  e+   +v +S  ++l g  g + Y 
  gi|336254351|ref|YP_004597458.1|  86 GRIDHLLNIAGTWTgGDPIEETDLEEFELLVDVNLKTAFLASkHALPHlqENEGSIVSVSARSSLEGGEGDGPYR 160
                                       ***********9764789*********999888777665443034443545666677777777777777777775 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 !   16.7   0.0   1.6e-06    0.0037       2      79 ..      18      91 ..      17      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.6e-06
                                      EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH.....T CS
                     GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev.....q 75
                                      iTG +G  Gs  ++++ + g +v+ ++  +   +    ++l + p    +++ +++++DltD+s + +l+a++     +
  gi|336254351|ref|YP_004597458.1| 18 ITGASGALGSAAVDRFRAAGATVCAVDVVAPDAE----DSLLE-P----DSKTHFYEADLTDESDVSELVASIvddrgR 87
                                      9************************998877755....55553.3....34679****************987444445 PP

                                      -SEE CS
                     GDP_Man_Dehyd 76 pdev 79
                                      +d  
  gi|336254351|ref|YP_004597458.1| 88 IDHL 91
                                      5555 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 !   14.8   0.1   5.1e-06     0.011       4      76 ..      17     113 ..      14     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-06
                                       EEESTTSHHHHHHHHHCTTTSEEEEEE-TT..................T--TTSHHHHHHHH.....HHH--SEEEE CS
                     RmlD_sub_bind   4 lvtGanGqlGseLakqlaeeglevlaltre..................eldltdaeavaell.....keakpdvvvn 57 
                                       ++tGa+G+lGs+ +++++++g+ v+a++                    e+dltd++ v el+     +  + d + n
  gi|336254351|ref|YP_004597458.1|  17 VITGASGALGSAAVDRFRAAGATVCAVDVVapdaedsllepdskthfyEADLTDESDVSELVasivdDRGRIDHLLN 93 
                                       79*************************88889999***********************9999555544446667777 PP

                                       --.----HHHHHHSHHHHHH CS
                     RmlD_sub_bind  58 aA.AytavDkaEseeeaaya 76 
                                        A  +t  D  E+   ++++
  gi|336254351|ref|YP_004597458.1|  94 IAgTWTGGDPIEETDLEEFE 113
                                       55367888888777666555 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 ?   13.9   0.1   1.7e-05     0.038       1      59 [.      20      79 ..      20      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                                      TTTSHHHHHHHHHHHHC-T-EEEEE.ETTHHHCHHH.HCTTTCEEEE--TT-CCHHHHHHT CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtal.vRnpeklael.eaeeglevvegdvtdvedlaealk 59
                                      GA+G  G+++v++  a+g  +v a+ v  p+  ++l e +++++  e+d+td++d+ e ++
  gi|336254351|ref|YP_004597458.1| 20 GASGALGSAAVDRFRAAG-ATVCAVdVVAPDAEDSLlEPDSKTHFYEADLTDESDVSELVA 79
                                      9****************6.8999987777777766515569999*************9987 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 ?   11.2   0.0   5.8e-05      0.13       1      65 [.      17      79 ..      17      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.8e-05
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk.viegDvtdkdkleeale 65
                                      v+tG++G lG+a v ++  ++   +v ++D++  +   ++l + + k+ + e+D+td+++++e + 
  gi|336254351|ref|YP_004597458.1| 17 VITGASGALGSAAVDRFRAAG--ATVCAVDVVAPDAE-DSLLEPDSKThFYEADLTDESDVSELVA 79
                                      79***************9999..59999999887766.6666655555599*********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 1977.83
//
Query:       gi|336254352|ref|YP_004597459.1|  [L=117]
Description: hypothetical protein Halxa_2964 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0083   15.9   1.5      0.011   15.5   1.5    1.1  1  LAT       Linker for activation of T-cells
  ------ inclusion threshold ------
      0.021   15.4   0.1      0.045   14.4   0.1    1.5  1  HTH_32    Homeodomain-like domain


Domain annotation for each model (and alignments):
>> LAT  Linker for activation of T-cells
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.5   1.2e-06     0.011      85     151 ..       7      83 ..       5      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-06
                               LAT  85 PrsPqppggshr...mpssrqdsdgansvasyene.......elacedadededeeDyhneGylvvLPDsspatsta 151
                                       Pr P  +++s r   +  +++d+++  +va+y  +       e +  d+ + + ++D  n Gy   +P++++ t t 
  gi|336254352|ref|YP_004597459.1|   7 PRPPAALEPSLReslVELAKRDPEALPAVAAYAEDlaawveaERNGSDSSDGDSDDDSDNGGYPPGVPERATVTVTE 83 
                                       8999999999884445679*************9999****888888888888999*************999988874 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   5.1e-06     0.045      23      60 ..       6      50 ..       2      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-06
                            HTH_32 23 rgrpr.klsdevrariiallreep......rWsprqlaarlaere 60
                                      r+rp+  l + +r+ +++l++++p      +  ++ laa++++++
  gi|336254352|ref|YP_004597459.1|  6 RPRPPaALEPSLRESLVELAKRDPealpavAAYAEDLAAWVEAER 50
                                      4677768*************9999988888779999999995544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.38u 0.19s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1007.71
//
Query:       gi|336254353|ref|YP_004597460.1|  [L=79]
Description: hypothetical protein Halxa_2965 [Halopiger xanaduensis SH-6]
Scores for complete 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-06   27.7   0.5    2.6e-06   27.2   0.5    1.1  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.053   14.0   0.1      0.067   13.7   0.1    1.2  1  HTH_27    Winged helix DNA-binding domain


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 !   27.2   0.5   2.9e-10   2.6e-06      13      59 ..      29      75 ..      22      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.9e-10
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                      vY++L + g+at+de+ e l + + +  +vLrsL++ G+Ve+  +++
  gi|336254353|ref|YP_004597460.1| 29 VYVYLAATGSATIDELRETLALKKITLLSVLRSLIRVGIVEKDGSNY 75
                                      9*****************************************98876 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 ?   13.7   0.1   7.4e-06     0.067      16      53 ..      36      73 ..      24      79 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.4e-06
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgd 53
                                       + +++ +l+++l + +++  ++l+ L++ G ve+ g+
  gi|336254353|ref|YP_004597460.1| 36 TGSATIDELRETLALKKITLLSVLRSLIRVGIVEKDGS 73
                                      5678999**************************76665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 700.97
//
Query:       gi|336254354|ref|YP_004597461.1|  [L=451]
Description: glutamine synthetase, type I [Halopiger xanaduensis SH-6]
Scores for 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-140  467.7   0.0   2.7e-140  467.3   0.0    1.1  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    3.6e-32  109.9   0.0    8.6e-32  108.7   0.0    1.7  1  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
    3.9e-05   23.4   0.1     0.0003   20.6   0.1    2.2  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.3   0.0  4.5e-144  2.7e-140       2     345 .]     112     447 ..     111     447 .. 0.98

  Alignments for each domain:
  == domain 1  score: 467.3 bits;  conditional E-value: 4.5e-144
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHH CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrrei 78 
                                       +dPR+vlk+al+r++++G+tv+++pE+EFflf+++ed++            ++++ ++ggyf+vap+d a+d+rr+i
  gi|336254354|ref|YP_004597461.1| 112 GDPRRVLKNALERAEDMGYTVNFAPEPEFFLFEEDEDGN-----------ATTETGDHGGYFDVAPKDLASDVRRDI 177
                                       79***********************************88...........5677899******************** PP

                                       HHHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEE CS
                        Gln-synt_C  79 vealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlS 155
                                       +  le++g+e+eashhEva+gQ+Ein++++dal++aDnv+tf++vv+++A++h+l+atFmpKp++  nGsgmH+h+S
  gi|336254354|ref|YP_004597461.1| 178 IYGLESMGFEIEASHHEVAKGQHEINFEYDDALSTADNVATFRMVVRAIAAQHDLHATFMPKPIPRINGSGMHTHQS 254
                                       ***************************************************************************** PP

                                       EEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-. CS
                        Gln-synt_C 156 lwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa. 231
                                       l+++dg+n+f+dedde +ls++a+++++G+l+ha+a+ta+++ptvnSYkRlvpgyeaPv++aw+ rNRsal+R pa 
  gi|336254354|ref|YP_004597461.1| 255 LMTTDGENAFHDEDDEFNLSDTAHSYLAGILEHAPAITAVANPTVNSYKRLVPGYEAPVYVAWSDRNRSALVRKPAa 331
                                       ****************************************************************************8 PP

                                       TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHC CS
                        Gln-synt_C 232 skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealee 306
                                         + a+r+ElR+pd+s+NPYLa+Aa++ AgldGie+ le+++p+++++ye ++e+r   gi++lP++l eA+eale+
  gi|336254354|ref|YP_004597461.1| 332 RVPAASRIELRSPDPSCNPYLAFAAMIHAGLDGIEQDLECPDPIRENIYEFDDEKReeYGIDTLPSNLGEAVEALEN 408
                                       89***************************************************999999****************** PP

                                       SHHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 307 dellkevlgeevieaylalkraEleeleeevsdwelery 345
                                       de++ ++lge+v  +++++k++E+ee+   vs+we++ry
  gi|336254354|ref|YP_004597461.1| 409 DEVIYNALGEHVAPKFVEAKSQEFEEYLVDVSQWEIDRY 447
                                       ************************************998 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   0.0   1.4e-35   8.6e-32       1      82 [.      21     103 ..      21     104 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 1.4e-35
                                       T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-...EEE CS
                        Gln-synt_N   1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek..ktar 75 
                                       +v f++lqFtDi g++k+v++pa++  e+a++eg+ FDGSsiegf++i+eSDm L+Pd++t++++P+r+++  + ar
  gi|336254354|ref|YP_004597461.1|  21 DVDFLRLQFTDILGTVKNVAVPARQA-EKAFTEGIYFDGSSIEGFVRIQESDMRLVPDPDTFAVLPWRNDEesAAAR 96 
                                       589***********************.******************************************88899*** PP

                                       EEEEEE- CS
                        Gln-synt_N  76 vicdvyd 82 
                                       +icdvyd
  gi|336254354|ref|YP_004597461.1|  97 MICDVYD 103
                                       ******8 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1     5e-08    0.0003       2     103 ..       9     105 ..       8     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5e-08
                                       -........------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-GGGGG--TTS---TT-S-SSS--EEEEE CS
                      Gln-synt_N_2   2 adeavveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGltkatlalserdlidevedlgpvGelrLvp 78 
                                       a+e v+e++ee++v+++++ ++d  G ++  a+p  + e+ +++Gi +    ++++    i+e+       ++rLvp
  gi|336254354|ref|YP_004597461.1|   9 AEEEVLEKIEEEDVDFLRLQFTDILGTVKNVAVPARQAEKAFTEGIYFD--GSSIEGFVRIQES-------DMRLVP 76 
                                       6789*******************************999999***99876..4677778888886.......89**** PP

                                       -GGG-EEE---SS...TTS.EEEEEE-TT CS
                      Gln-synt_N_2  79 dPasavalpyaPd...aaa.llgdlvevd 103
                                       dP ++ +lp   d   aaa ++ d++++ 
  gi|336254354|ref|YP_004597461.1|  77 DPDTFAVLPWRNDeesAAArMICDVYDTS 105
                                       *********87653333336999999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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 0.22s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3336.59
//
Query:       gi|336254355|ref|YP_004597462.1|  [L=88]
Description: hypothetical protein Halxa_2967 [Halopiger xanaduensis SH-6]
Scores for 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   17.4   0.4     0.0013   17.4   0.4    1.0  1  Terminase_GpA   Phage terminase large subunit (GpA)
     0.0049   16.6   0.1      0.009   15.7   0.1    1.4  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
  ------ inclusion threshold ------
      0.035   14.4   4.4       0.31   11.3   3.9    2.1  2  DUF2197         Uncharacterized protein conserved in bacteria


Domain annotation for each model (and alignments):
>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4   2.1e-07    0.0013     195     244 ..      13      59 ..       4      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.1e-07
                     Terminase_GpA 195 rryyvpCphCgelqelsferlkwpegeaeekaryvCphcgslieehhkra 244
                                       r+    C +C++ ++++     w + e+ e++ yvCp c++ i+e+ +r 
  gi|336254355|ref|YP_004597462.1|  13 RKSTLFCRTCDHASPID---GDWRRRERGETVVYVCPVCETRITERPRRD 59 
                                       566677*********99...35888889******************9987 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 !   15.7   0.1   1.5e-06     0.009      11      52 ..       5      50 ..       4      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-06
                    zinc_ribbon_10 11 GddetsaknryalICskChshnGlap....keeleevkyrCpkCga 52
                                      G+ ++++   + l C++C + +        +e+ e+v y+Cp C +
  gi|336254355|ref|YP_004597462.1|  5 GTHKAAVRRKSTLFCRTCDHASPIDGdwrrRERGETVVYVCPVCET 50
                                      555567788899********99665555589999**********86 PP

>> DUF2197  Uncharacterized protein conserved in bacteria (DUF2197)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.3     0.014        82      27      39 ..      12      24 ..       5      40 .. 0.79
   2 ?   11.3   3.9   5.3e-05      0.31       5      46 ..      19      57 ..      16      64 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.014
                           DUF2197 27 rpihtYmCkeCee 39
                                      r++ t +C++C++
  gi|336254355|ref|YP_004597462.1| 12 RRKSTLFCRTCDH 24
                                      6777888888875 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.3e-05
                           DUF2197  5 CvlCdkveeiddesllaKrLrNr.pihtYmCkeCeeRiaektk 46
                                      C  Cd+   id +       r r    +Y+C+ Ce Ri+e+++
  gi|336254355|ref|YP_004597462.1| 19 CRTCDHASPIDGDWRR----RERgETVVYVCPVCETRITERPR 57
                                      6667777777766432....33313568***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 695.10
//
Query:       gi|336254356|ref|YP_004597463.1|  [L=118]
Description: Thioredoxin domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-10   41.3   0.0    1.5e-10   41.0   0.0    1.1  1  Thioredoxin    Thioredoxin
    3.9e-05   23.6   0.0    0.00029   20.8   0.0    1.9  1  TraF           F plasmid transfer operon protein
    0.00086   19.7   0.0      0.049   14.1   0.0    2.2  1  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.015   15.3   0.0    1.2  1  Thioredoxin_3  Thioredoxin domain
      0.048   13.6   0.0      0.081   12.9   0.0    1.4  1  HyaE           Hydrogenase-1 expression protein HyaE
      0.065   12.2   0.0      0.074   12.0   0.0    1.1  1  Phosducin      Phosducin


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 !   41.0   0.0   5.1e-14   1.5e-10      10     102 ..      17     107 ..       9     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 5.1e-14
                                       HHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEE CS
                       Thioredoxin  10 FeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevk 86 
                                        e+ v    +  lveFy   C++C+a++P+l ++a+ ++  v +  ++  +   l++++++e++P l+lf++g+ v+
  gi|336254356|ref|YP_004597463.1|  17 LESFVDR-YDVALVEFYTVGCPKCQAMEPVLGNVARSTA--VPIGMLNPGDDLGLVDRFDIESVPSLLLFRDGEPVA 90 
                                       5566666.7889*************************99..*********************************666 PP

                                       EE.ESS-HHHHHHHHHH CS
                       Thioredoxin  87 ky.egarekeklaaflk 102
                                       ++ +g    ++l++fl+
  gi|336254356|ref|YP_004597463.1|  91 RLaDGFVGGDELVDFLA 107
                                       55155577888888875 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   9.6e-08   0.00029     130     221 ..      25     104 ..      15     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 9.6e-08
                              TraF 130 eygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkv 206
                                       +++L+ Fy  +cp c+a+ p+l ++a+++   + + +             +d g   r+ ++++P l+l++   + v
  gi|336254356|ref|YP_004597463.1|  25 DVALVEFYTVGCPKCQAMEPVLGNVARSTAVPIGMLN-----------PGDDLGLVDRFDIESVPSLLLFRDG-EPV 89 
                                       579999*********************9876554433...........334566677****************.999 PP

                              TraF 207 vpvaaGllsldelee 221
                                       + +a G++  del++
  gi|336254356|ref|YP_004597463.1|  90 ARLADGFVGGDELVD 104
                                       9*******9999986 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.6e-05     0.049       9     105 ..      28     102 ..      24     106 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                     Thioredoxin_2   9 lvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt.i 84 
                                       lv f++++Cp C++++ +l ++             +s    + ++   ++             l+++++++++P+ +
  gi|336254356|ref|YP_004597463.1|  28 LVEFYTVGCPKCQAMEPVLGNV------------ARSTAVPIGMLNPGDDL-----------GLVDRFDIESVPSlL 81 
                                       6678889999999988888888............22333344445555555...........599**********55 PP

                     Thioredoxin_2  85 vfldgkeivarlpGyvpaeel 105
                                       +f dg+ ++    G+v  +el
  gi|336254356|ref|YP_004597463.1|  82 LFRDGEPVARLADGFVGGDEL 102
                                       599999666666777766666 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0     5e-06     0.015       7      55 ..      33      82 ..      25      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5e-06
                                      SSSSTTCHHHHHHHHHHCHCCTCECEEECC.TTHHHHHHCT-SSSSEEEC CS
                     Thioredoxin_3  7 gpgCakCpklekavkeaaaekgikaevekv.tdfeeiekygVmsvPalvi 55
                                      + gC+kC+++e ++  +a +  + + + +   d+  ++++ ++svP+l++
  gi|336254356|ref|YP_004597463.1| 33 TVGCPKCQAMEPVLGNVARSTAVPIGMLNPgDDLGLVDRFDIESVPSLLL 82
                                      789**********************999996777777**********953 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.7e-05     0.081      70     100 ..      63      93 ..      40      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHCCT-TSSSEEEEEETTEEEEEEE CS
                              HyaE  70 eqeealaerfgvlktPsllflrdgeylgvla 100
                                       +++  l +rf +  +Psll++rdge ++ la
  gi|336254356|ref|YP_004597463.1|  63 GDDLGLVDRFDIESVPSLLLFRDGEPVARLA 93 
                                       5666789*****************9888775 PP

>> Phosducin  Phosducin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.5e-05     0.074     148     213 ..      26      91 ..      11     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                                       EEEEEEE-TTSTTHHHHHHHHHHHHHH-TTSEEEEEE.HHHH--TTSS-TTT-SEEEEEETTEEEEE CS
                         Phosducin 148 livvhiyedgvkgtealnssliclaaeyptvkfckvk.asvigasdrfsrdvlpallvykagellsn 213
                                       + +v  y  g + ++a++  l  +a     v +  ++    +g  drf  + +p+ll+++ ge ++ 
  gi|336254356|ref|YP_004597463.1|  26 VALVEFYTVGCPKCQAMEPVLGNVA-RSTAVPIGMLNpGDDLGLVDRFDIESVPSLLLFRDGEPVAR 91 
                                       568999***********99887665.5566777776625789********************97764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 919.80
//
Query:       gi|336254357|ref|YP_004597464.1|  [L=86]
Description: hypothetical protein Halxa_2969 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0021   18.2   0.0     0.0043   17.1   0.0    1.5  2  Mrr_N     Mrr N-terminal domain
     0.0071   16.4   0.0       0.01   15.9   0.0    1.2  1  HTH_20    Helix-turn-helix domain


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 ?   -2.5   0.0      0.67     6e+03       8      25 ..      15      32 ..      13      33 .. 0.63
   2 !   17.1   0.0   4.8e-07    0.0043      58      86 ..      45      73 ..      40      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.67
                             Mrr_N  8 lLealadgsehrlkeire 25
                                      +Le l ++++   ++ir+
  gi|336254357|ref|YP_004597464.1| 15 ILELLCEDEVFEPSQIRD 32
                                      677777766655566665 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.8e-07
                             Mrr_N 58 rtyLkkagllespkrgvwkiTekGrevlk 86
                                      + +L + glle+p  gv+ iT+ G ++l+
  gi|336254357|ref|YP_004597464.1| 45 CRELAERGLLENPMTGVYDITDLGERYLE 73
                                      678999*******************9985 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-06      0.01       9      55 ..       9      55 ..       8      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-06
                                      -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      +Pv  +il +L+++e + +s++ +++ ++   + y+ r+L+e gL+e
  gi|336254357|ref|YP_004597464.1|  9 DPVDDDILELLCEDEVFEPSQIRDEGICRGPHAAYRCRELAERGLLE 55
                                      566669***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 721.27
//
Query:       gi|336254358|ref|YP_004597465.1|  [L=139]
Description: hypothetical protein Halxa_2970 [Halopiger xanaduensis SH-6]
Scores for 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  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1040.10
//
Query:       gi|336254359|ref|YP_004597466.1|  [L=73]
Description: hypothetical protein Halxa_2971 [Halopiger xanaduensis SH-6]
Scores for 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:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 537.61
//
Query:       gi|336254360|ref|YP_004597467.1|  [L=354]
Description: hypothetical protein Halxa_2972 [Halopiger xanaduensis SH-6]
Scores for 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   3.0     0.0027   17.6   3.0    1.7  1  PGF-CTERM    PGF-CTERM motif
  ------ inclusion threshold ------
       0.16   12.1   1.7       0.75   10.0   0.3    2.5  2  DUF4091      Domain of unknown function (DUF4091)
        9.1    5.6  11.9         13    5.1  11.9    1.1  1  SDA1         SDA1


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   3.0   4.5e-07    0.0027       2      21 ..     329     347 ..     328     347 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.5e-07
                         PGF-CTERM   2 PGFGavlAlaGLLaaalLaR 21 
                                       PGFGav A+++L +a  LaR
  gi|336254360|ref|YP_004597467.1| 329 PGFGAVAAVVALSSA-MLAR 347
                                       ************995.7776 PP

>> DUF4091  Domain of unknown function (DUF4091)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.13   7.8e+02      12      34 ..     156     180 ..     141     180 .. 0.79
   2 ?   10.0   0.3   0.00013      0.75       4      43 ..     216     256 ..     213     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.13
                           DUF4091  12 fwnsdpltdtsarg..afpaGDgfl 34 
                                         ++ pl+  ++ +   +p+GDg++
  gi|336254360|ref|YP_004597467.1| 156 EHYDRPLDADQFGTspDVPQGDGYM 180
                                       455678888888888899****985 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00013
                           DUF4091   4 GflyWgydfwns..dpltdtsargafpaGDgflvYP.gedgkp 43 
                                       G+++ + d w    dp++d+++ +  +aG g+ +YP  ++g++
  gi|336254360|ref|YP_004597467.1| 216 GYVQQAHDTWDTdvDPIEDAESYE--EAGGGWTYYPdRSHGQV 256
                                       777788899*9999******9998..9*********4333344 PP

>> SDA1  SDA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  11.9    0.0022        13      58     181 ..     196     311 ..     186     329 .. 0.42

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0022
                              SDA1  58 akkfGeeev.aegieGleLlekwkeeekkekre....eeeedsddeddeedwevesdddseedseggwidves.dee 128
                                       + ++Ge e  +e+ +++eL+  +++ +++ + +    e  + ++ e+   +w    d      s g+ + v + d++
  gi|336254360|ref|YP_004597467.1| 196 EVQYGEAEIaGEHADDIELVGYVQQAHDTWDTDvdpiE--DAESYEEAGGGWTYYPD-----RSHGQVVVVLQlDGD 265
                                       57899999888999999999888877776666544321..11223333334443332.....233343333220222 PP

                              SDA1 129 .eieesdesedeeeeeeeeeekeekeeeeeeeeeeeeeeeeeeeeeekekkkkk 181
                                        +i+ +++ +de+   + +e+  + + +e +e       +e+e+ e ++ ++++
  gi|336254360|ref|YP_004597467.1| 266 kDISLDESTDDETAATDGDENATNSSGDEGNE-------SENESAE-STPSDAN 311
                                       22333333333322222111111111111111.......1111111.1111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2478.80
//
Query:       gi|336254361|ref|YP_004597468.1|  [L=173]
Description: hypothetical protein Halxa_2973 [Halopiger xanaduensis SH-6]
Scores for 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  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1397.64
//
Query:       gi|336254362|ref|YP_004597469.1|  [L=946]
Description: DEAD/H associated domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-37  126.8   0.4    2.8e-36  125.1   0.1    2.1  2  DEAD_assoc     DEAD/H associated
    2.4e-29  102.3   0.0    5.7e-29  101.1   0.0    1.6  2  DEAD           DEAD/DEAH box helicase
    1.9e-22   79.7   0.0    2.3e-21   76.2   0.1    2.5  2  Helicase_C     Helicase conserved C-terminal domain
    3.7e-07   30.3   0.0    7.7e-07   29.3   0.0    1.5  1  ResIII         Type III restriction enzyme, res subunit
      6e-05   22.7   1.7    0.00028   20.5   0.1    2.5  2  AAA_25         AAA domain
    0.00047   20.5   0.0     0.0041   17.5   0.0    2.4  2  AAA_19         AAA domain
     0.0064   16.1   0.0      0.011   15.2   0.0    1.3  1  UvrD-helicase  UvrD/REP helicase N-terminal domain
  ------ inclusion threshold ------
      0.042   12.6   0.0       0.15   10.7   0.0    1.8  2  SNF2_N         SNF2 family N-terminal domain
       0.06   13.4   0.5        0.3   11.1   0.2    2.2  2  HypA           Hydrogenase/urease nickel incorporation, metal
      0.078   13.2   0.3       0.96    9.7   0.3    2.6  1  AAA_22         AAA domain
       0.15   12.2   0.5       0.39   10.9   0.5    1.7  1  Zn-ribbon_8    Zinc ribbon domain
       0.19   11.2   0.2       0.37   10.3   0.2    1.4  1  DUF116         Protein of unknown function DUF116


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 ?   -2.8   0.0       3.2   4.7e+03     148     174 ..     129     155 ..     120     165 .. 0.71
   2 !  125.1   0.1   1.9e-39   2.8e-36       1     188 [.     614     785 ..     614     788 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.2
                        DEAD_assoc 148 lleavrevledqlDlerlaellrriaa 174
                                       +l +  e ++ +l  erl+e+l+++++
  gi|336254362|ref|YP_004597469.1| 129 VLITTPETVQAMLTGERLREALQDVSH 155
                                       566777778888888888888888876 PP

  == domain 2  score: 125.1 bits;  conditional E-value: 1.9e-39
                        DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldel 77 
                                       +Pt+++++ Er  +     ++v++++fG+ +ne+l+++l+a l +r g++v++  ++++i+l++p + +    + e+
  gi|336254362|ref|YP_004597469.1| 614 MPTADRIVLERQGR-----TIVLNACFGHTANETLGRVLSALLGQRAGSSVGLETDPYRIELEVPSSIAT-SDVVEV 684
                                       6***********76.....89*****************************************99665555.34667* PP

                        DEAD_assoc  78 lellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavre 154
                                       le ++pd++e ++e  l++s+ ++ r+ +v a++++l+r++ +        r++ ++Ll++++   d+p+++eavre
  gi|336254362|ref|YP_004597469.1| 685 LEDTDPDHVETIVELGLKNSDALAFRLAQVSAKFGALKRWQGQ-----GSGRISNERLLAALE---DTPMYEEAVRE 753
                                       ****************************************999.....889************...*********** PP

                        DEAD_assoc 155 vledqlDlerlaellrriaageirvvevetprpS 188
                                       v++++lD+er+ ++l+ i++ge+++v+   +  +
  gi|336254362|ref|YP_004597469.1| 754 VFHEDLDIERASAVLAGIQSGELELVTQ--RGRT 785
                                       **************************94..4444 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.1   0.0   3.8e-32   5.7e-29       1     170 [.      29     197 ..      29     202 .. 0.89
   2 ?   -4.2   0.0       8.1   1.2e+04      49      75 ..     265     291 ..     256     312 .. 0.68

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 3.8e-32
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS.TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet.kgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                       t+ Q+ aip +  g++ lv a+TGsGKT+ +++pv+++++ +    +g  al+v+P+r+L +++ ++l+ +++y++l
  gi|336254362|ref|YP_004597469.1|  29 TAPQRLAIPPLAAGQNTLVIAPTGSGKTETAMLPVFDHLVADdGPPEGFGALYVTPLRALNRDMRERLEWWGEYLGL 105
                                       5679***********************************9986678999**************************** PP

                                       EEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  77 rvlliiggvaardqlskldngvdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpq 151
                                       +v +  g++++ +  ++ +n +d++++tp+ ++ +l+ ++l+  l++v+ +V+DE+++l  ++++ ++   l++l++
  gi|336254362|ref|YP_004597469.1| 106 EVDVRHGDTTQYQRGKQAENPPDVLITTPETVQAMLTGERLReaLQDVSHVVIDEVHELAASKRGAQLAIGLERLHD 182
                                       **9888877777777777777*************9966666666*******************************54 PP

                                       HCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              DEAD 152 itcdgklqrqvivlSATlp 170
                                              + q i lSAT+ 
  gi|336254362|ref|YP_004597469.1| 183 L----AGEMQRIGLSATVG 197
                                       4....44466*******96 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 8.1
                                       EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  49 kalivePtreLaeqtlnnlkkfkkyid 75 
                                        +li + tr+ ae   +++k++  +i+
  gi|336254362|ref|YP_004597469.1| 265 STLIFVNTRQTAEALGSRFKELDLPIG 291
                                       567777777777777777777655544 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 ?   -0.2   0.0      0.82   1.2e+03      35      62 ..      99     126 ..      85     138 .. 0.74
   2 !   76.2   0.1   1.6e-24   2.3e-21      13     108 ..     260     355 ..     250     358 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.82
                                       HHHHTTSTEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  35 llekkgikvavlhgelpqnereeileqf 62 
                                         e  g++v v hg+++q +r +  e+ 
  gi|336254362|ref|YP_004597469.1|  99 WGEYLGLEVDVRHGDTTQYQRGKQAENP 126
                                       444449999************9988776 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 1.6e-24
                                       TTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTE CS
                        Helicase_C  13 eeeggkilifvntidrlek.vklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkv 85 
                                        ++++ +lifvnt++++e   +     +   ++ + v+hg+l+++ r+e+ ++f+ ge d L++t+ +e Gid+ +v
  gi|336254362|ref|YP_004597469.1| 260 VADHESTLIFVNTRQTAEAlGSR----FkelDLPIGVHHGSLSKEARIEVEDRFKTGELDGLLCTSSMELGIDVGRV 332
                                       467899*********99654444....33358********************************************* PP

                                       SEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  86 nlVinfdlprnvtsyiqriGRtg 108
                                       ++Vi++  pr+vt++ qriGR+g
  gi|336254362|ref|YP_004597469.1| 333 DHVIQYKSPRQVTRLLQRIGRAG 355
                                       **********************9 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 !   29.3   0.0   5.1e-10   7.7e-07      25     169 ..      43     196 ..      27     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.1e-10
                                       SEEEEEESTTSTHHHHH.HHHHHHH-S........-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--. CS
                            ResIII  25 krglikmaTGtGKTlva.aklierllkkgkee...kflflvprkslleqtleefkkflseaykeigkkvsgdkkka. 96 
                                       ++ l+ ++TG+GKT +a + + ++l    +      +l + p ++l   ++e+++ + +    e   + +gd+ +  
  gi|336254362|ref|YP_004597469.1|  43 QNTLVIAPTGSGKTETAmLPVFDHLVADDGPPegfGALYVTPLRALNRDMRERLEWWGEYLGLE-VDVRHGDTTQYq 118
                                       567899**********96777777777655448999***************9987776654433.333333333333 PP

                                       ........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT---SEEEEE CS
                            ResIII  97 .kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekfkeavllgl 165
                                         +++++  ++l+tt ++++a +   + e+ +   +    ++iDE+H l+a+k         +++ +   e  ++gl
  gi|336254362|ref|YP_004597469.1| 119 rGKQAENPPDVLITTPETVQAML---TGERLREALQDVSHVVIDEVHELAASKrgaqlaiGLERLHDLAGEMQRIGL 192
                                       344578899**************...77777777788889***********86666666677777888888****** PP

                                       ESS- CS
                            ResIII 166 TATp 169
                                       +AT 
  gi|336254362|ref|YP_004597469.1| 193 SATV 196
                                       ***6 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   1.9e-07   0.00028      10     155 ..      20     165 ..      14     182 .. 0.72
   2 ?    0.4   0.2      0.27     4e+02      59     139 ..     516     610 ..     511     628 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.9e-07
                            AAA_25  10 vsvadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEds.ed 84 
                                       +s +++ +p +p+r  ++ l +ag  +l+++++g+GKt  a+  +++ +  ++   g  +pe    lyv    + + 
  gi|336254362|ref|YP_004597469.1|  20 LSERGFSTPTAPQRLAIPPL-AAGQNTLVIAPTGSGKTETAMLPVFDHLvADD---G--PPEGFGALYVTPLRAlNR 90 
                                       567889999***********.69***************887777776662544...5..47999*****99888788 PP

                            AAA_25  85 elrrRlravgeal......rddarllvldlagv...eslpLfakdrggtlltadvdaleaaieevegvrlvviDpls 152
                                       ++r+Rl+++ge l      r+ ++ +   +++     ++ ++++++ ++ lt++  +l++a+++   v +vviD + 
  gi|336254362|ref|YP_004597469.1|  91 DMRERLEWWGEYLglevdvRHGDTTQYQRGKQAenpPDVLITTPETVQAMLTGE--RLREALQD---VSHVVIDEVH 162
                                       *************77777633333333333333202233333444444446664..46666555...89*****987 PP

                            AAA_25 153 ral 155
                                       ++ 
  gi|336254362|ref|YP_004597469.1| 163 ELA 165
                                       765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.27
                            AAA_25  59 tGkpwlg.pvapeqgkVlyvsaEdsedelrrRlravgeal................rddarllvldlagv.eslpLf 117
                                       +G+ w   ++  e gkV +   Ed++ e++ ++ +    +                ++++ ++  d+a v  +l  +
  gi|336254362|ref|YP_004597469.1| 516 RGEMWRIaEIDDEEGKVKVSPIEDPAGEVPSWIGQE---IpvpaavaqevgeiravAQPQLETGADAAAVgRELAHR 589
                                       677776677777999999999999999998888642...22222346666777666666666666666664444444 PP

                            AAA_25 118 akdrggtlltadvdaleaaiee 139
                                       ++  ++ +lt++ d+le++ie+
  gi|336254362|ref|YP_004597469.1| 590 YPA-DEYTLTEACDQLEKQIEA 610
                                       433.333467888888888887 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.7e-06    0.0041       1     115 [.      32     165 ..      32     183 .. 0.69
   2 ?   -0.3   0.0      0.84   1.3e+03      41      82 ..     262     301 ..     247     459 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.7e-06
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkh.ivallvelggvkp..eeillvaftgrAakelrerlaalgae..... 68 
                                       qr a+   ++ ++ lv+a+ G+GKT++ +  +  +lv+  g +p     l v++ +   + +rerl+  g+      
  gi|336254362|ref|YP_004597469.1|  32 QRLAIPpLAAGQNTLVIAPTGSGKTETAMLpVFDHLVADDG-PPegFGALYVTPLRALNRDMRERLEWWGEYlglev 107
                                       6778866888999************9977615567776664.5534677889998888999*****65555477776 PP

                            AAA_19  69 .....atTiHrlal..............ldfddlltealelleeaeeekklqeeellivDEfqdvd 115
                                             t      +              l +++++    ++l  ++ ++ lq+  ++++DE+ ++ 
  gi|336254362|ref|YP_004597469.1| 108 dvrhgDT------TqyqrgkqaenppdvLITTPET--VQAMLTGERLREALQDVSHVVIDEVHELA 165
                                       6666422......2333344666666652222222..234445556778898888******99876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.84
                            AAA_19  41 kpeeillvaftgrAakelrerlaalgaeatTiHrlalldfdd 82 
                                       + e+ l+   t++ a+ l  r ++l++++   H+   l  + 
  gi|336254362|ref|YP_004597469.1| 262 DHESTLIFVNTRQTAEALGSRFKELDLPIGVHHGS--LSKEA 301
                                       44777888888888888888888888888877755..33333 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 !   15.2   0.0   7.7e-06     0.011      11     101 ..      38     165 ..      29     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.7e-06
                                       S..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGG..EEEEESSHHHHHHHHHHHHH................ CS
                     UvrD-helicase  11 s..lggpilveAsAGsGKTfvlaerilrlikeeeiepdr..ilvvTFTnkAaeElkeRiee................ 67 
                                       +   g+++lv+A  GsGKT + +  +  ++ +    p+    l vT  ++  + ++eR+e                 
  gi|336254362|ref|YP_004597469.1|  38 PlaAGQNTLVIAPTGSGKTETAMLPVFDHLVADDGPPEGfgALYVTPLRALNRDMRERLEWwgeylglevdvrhgdt 114
                                       43479**************98666655555555566655569*********************************99 PP

                                       .................HHHHCCHHCTT-HHHHHHHHHCTTSEEEEHHHHH CS
                     UvrD-helicase  68 .................alkkaeqessdderlrlalqnlseanisTlHsfc 101
                                                        ++ +  q  +  erlr+alq +s++ i  +H+++
  gi|336254362|ref|YP_004597469.1| 115 tqyqrgkqaenppdvliTTPETVQAMLTGERLREALQDVSHVVIDEVHELA 165
                                       999999999999988877777777777777*****************9987 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0001      0.15     120     200 ..     101     175 ..      43     195 .. 0.75
   2 ?   -1.3   0.0      0.46   6.8e+02     251     313 ..     879     941 ..     857     944 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0001
                                       TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 120 sssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstska 196
                                       +   l+v v +g++++ ++     ++  +  dv+itt ++++     +  r++l++v    vv+DE h l  s++ a
  gi|336254362|ref|YP_004597469.1| 101 EYLGLEVDVRHGDTTQYQR----GKQAENPPDVLITTPETVQAMLTGERLREALQDV--SHVVIDEVHELAASKRGA 171
                                       4456777777776544333....34445568***********999888999999887..58************9888 PP

                                       HHHH CS
                                       xxxx RF
                            SNF2_N 197 aeav 200
                                       + a+
  gi|336254362|ref|YP_004597469.1| 172 QLAI 175
                                       8776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHTT-STTEE---GGGT--S---EEEEEEEEE--HHHHHHHH............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 251 aqaekgrsrLlqllqrlmlrrakkdveknlPpkteeiiflklskverksYnrllevlrkkala 313
                                       + +++++ r ++l+q+   r++ +   + + p +   i  kl + e ++Y ++l+++r+ a+ 
  gi|336254362|ref|YP_004597469.1| 879 ERMTERAYRAASLVQSHGKRAVTAMAARGVGPHNAAQIINKLRENEDEFYRDILSKEREYART 941
                                       5677777777777777777777777788999999999999***********999998887665 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 ?   -1.4   0.0       1.5   2.3e+03      29      58 ..     558     587 ..     556     615 .. 0.74
   2 ?   11.1   0.2    0.0002       0.3      62      98 ..     815     856 ..     794     867 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
                                       EEEEEETTCT--HHHHHHHHHHHHCC.TTT CS
                              HypA  29 vkvevGelsgvepeaLefafellaegtvle 58 
                                       v  evGe++ v + +Le+  +++a g  l+
  gi|336254362|ref|YP_004597469.1| 558 VAQEVGEIRAVAQPQLETGADAAAVGRELA 587
                                       677999*****9999999988888776655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0002
                                       EEEEEE--EEEETTTS-EEECHH..HHH.....S-TTTSSS-EE CS
                              HypA  62 LeieevpvkvrCreCgkefelee..kal.....rCpkCgsadve 98 
                                        ++++ +v + C++C+ ++++++  k       +Cp+Cgs+++ 
  gi|336254362|ref|YP_004597469.1| 815 ERLQNDRVILLCTHCK-DWKVKTkvK-RvsdqpECPECGSTRIA 856
                                       45778889999****9.666554232.134555*******9875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00064      0.96       6     112 ..      43     180 ..      40     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00064
                            AAA_22   6 gilvvtGesGtGKTtllrr.lleqldeeakaee...erpevvfvtlpsst..sskdllrellralglelka...... 70 
                                       + ++v++++G+GKT ++   +++ l++     +   e+ + ++vt+      + ++ l++  + lgle +       
  gi|336254362|ref|YP_004597469.1|  43 QNTLVIAPTGSGKTETAMLpVFDHLVA-D---DgppEGFGALYVTPLRALnrDMRERLEWWGEYLGLEVDVrhgdtt 115
                                       56899*********8765415555542.2...234578888888876555588888899988988888887889999 PP

                            AAA_22  71 ..................erlsseell.ealeqalraravielliiDEaqhlr.s......eealeeL 112
                                                         ++  +  l  e+l++al++ +    ++iDE++ l  s      +  le L
  gi|336254362|ref|YP_004597469.1| 116 qyqrgkqaenppdvlittPETVQAMLTgERLREALQDVSH---VVIDEVHELAaSkrgaqlAIGLERL 180
                                       9999999999888888843333333446777777777766...99*****997733443443334444 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   0.00026      0.39       8      34 ..     826     852 ..     821     856 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                       Zn-ribbon_8   8 CeeCghefevlqsis.dapltaCPeCgs 34 
                                       C+ C+ +  v  +++  +++++CPeCgs
  gi|336254362|ref|YP_004597469.1| 826 CTHCK-DWKVKTKVKrVSDQPECPECGS 852
                                       88888.6665555554444778*****9 PP

>> DUF116  Protein of unknown function DUF116
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00025      0.37      32      99 ..     813     881 ..     804     902 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                            DUF116  32 kfkkvppekrllllPhClraa.dCpaklteeglnCkrCgkCkigelkklaeklgykvyivtggtlarki 99 
                                         +++++++++ll  hC   + + ++k  ++  +C++Cg  +i++l+  ae++   v  ++ ++  +++
  gi|336254362|ref|YP_004597469.1| 813 VRERLQNDRVILLCTHCKDWKvKTKVKRVSDQPECPECGSTRIASLNPWAEEVVQAVRAAEKDEEQERM 881
                                       45677889999999***8855488888888********************9988777777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (946 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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: 0.74u 0.26s 00:00:01.00 Elapsed: 00:00:00.41
# Mc/sec: 6967.86
//
Query:       gi|336254363|ref|YP_004597470.1|  [L=703]
Description: multi-sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for 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   0.0    2.6e-27   95.6   0.0    2.2  2  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    9.9e-25   86.7   0.0    1.3e-14   54.1   0.0    2.9  2  PAS            PAS fold
    6.6e-22   77.7   0.0    5.6e-10   39.4   0.0    2.6  2  PAS_9          PAS domain
    8.1e-17   61.5   0.0    5.6e-13   49.1   0.0    3.0  2  PAS_4          PAS fold
    1.5e-15   56.7   0.0    7.4e-09   35.4   0.0    2.9  2  PAS_8          PAS domain
    1.7e-14   54.3   0.4    7.4e-14   52.2   0.4    2.2  1  GAF_2          GAF domain
    2.4e-11   43.8   0.0    6.7e-06   26.3   0.0    4.0  3  PAS_3          PAS fold
    2.1e-10   40.5   0.1    2.1e-10   40.5   0.1    2.7  3  HisKA          His Kinase A (phospho-acceptor) domain
    7.3e-10   39.6   0.1    1.5e-09   38.5   0.1    1.6  1  GAF            GAF domain
    8.7e-10   39.0   0.0      2e-09   37.9   0.0    1.7  1  GAF_3          GAF domain
    0.00021   21.1   0.0    0.00039   20.3   0.0    1.4  1  HATPase_c_5    GHKL domain
     0.0014   18.4   0.0     0.0028   17.5   0.0    1.4  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
     0.0027   17.7   0.0     0.0059   16.6   0.0    1.5  1  HATPase_c_2    Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.074   13.1   0.3         11    6.1   0.0    2.3  2  ApoLp-III      Apolipophorin-III precursor (apoLp-III)
       0.24   11.5   1.2       0.43   10.7   1.2    1.4  1  GlnD_UR_UTase  GlnD PII-uridylyltransferase
        9.5    6.4   6.9         13    6.0   2.3    2.3  2  bZIP_2         Basic region leucine zipper


Domain annotation for each model (and alignments):
>> 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 ?    0.6   0.0      0.69   7.8e+02      35      55 ..     561     583 ..     527     586 .. 0.75
   2 !   95.6   0.0   2.3e-30   2.6e-27       1     110 [.     587     696 ..     587     698 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.69
                                       E..TEEEEEEEESSSSSTTHHHT CS
                         HATPase_c  35 e..ddlvisveDnGiGipkedlk 55 
                                       +   dl++++eD+   i+ e l+
  gi|336254363|ref|YP_004597470.1| 561 DvlTDLQVKIEDTDAEITTESLP 583
                                       155799************99987 PP

  == domain 2  score: 95.6 bits;  conditional E-value: 2.3e-30
                                       EHHHHHHHHHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSH CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGl 76 
                                       gd ++Lrq+++nl++Na+++++ + ++++v ++++  + +isveD GiGi++++ +++f  f++  ++++++ gtG+
  gi|336254363|ref|YP_004597470.1| 587 GDDSQLRQLFQNLLSNALEYSGdEPPRVHVAVERNRRTWEISVEDEGIGIDPDETDRVFRVFQR-LHSRDEYPGTGI 662
                                       6899****************66677788888886568***********************9999.889999****** PP

                                       HHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  77 GlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       Gl++++++ve++gG+iwv+sepg+G+tf ft+p 
  gi|336254363|ref|YP_004597470.1| 663 GLALCRRIVERHGGRIWVDSEPGEGSTFAFTIPV 696
                                       *******************************997 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   4.8e-10   5.4e-07       7      72 ..      32      96 ..      26     149 .. 0.67
   2 !   54.1   0.0   1.2e-17   1.3e-14       3     113 .]     168     279 ..     166     279 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.8e-10
                                      HHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.........HHHHHHHHHHHHTT-E CS
                               PAS  7 leslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.........elaelleqlleqgees 72
                                      l +++ + f   e g+i+ vN+a+++l+G+ r+e+ g s+ dl+  +dd          e          + +e+
  gi|336254363|ref|YP_004597470.1| 32 LAAADIAGFRATETGVITDVNDAFASLTGYGRSELEGASITDLVTDDDDIleglvatdaE----------SESEA 96
                                      5566666666789*******************************8776655444444442..........33333 PP

  == domain 2  score: 54.1 bits;  conditional E-value: 1.2e-17
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       ++a+ e+lpd+i+v+D + +i y+N+a+e++lG++++e++g+s +  i++  ++++ ++l+++le+ge+  ++   +
  gi|336254363|ref|YP_004597470.1| 168 FQALAEALPDGIIVLDTNSDIQYANPAIERILGYTPDELVGSSKVNIIPPRLRQTHLDALQRYLETGERHLNWTYVE 244
                                       7999*****************************************999999888********************998 PP

                                       EC...TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  80 kl...rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                            + g +++l v  + ++  g++  +f+g +rdi
  gi|336254363|ref|YP_004597470.1| 245 LPgqhKAGHEVPLAVSLNDFTYDGDR--YFVGLFRDI 279
                                       88***********************9..********8 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   7.4e-12   8.3e-09       9      94 ..      44     145 ..      37     149 .. 0.89
   2 !   39.4   0.0     5e-13   5.6e-10       1     103 [.     176     280 ..     176     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 7.4e-12
                             PAS_9   9 pdgrilyaNeaalrllGyspeevlgksitdlf...............vtdpeanerlraaleqgrkkerevevvlir 70 
                                       + g i+++N+a++ l+Gy++ e+ g sitdl+               ++++ea+ + +a+le+g  ++ + +v l++
  gi|336254363|ref|YP_004597470.1|  44 ETGVITDVNDAFASLTGYGRSELEGASITDLVtddddileglvatdaESESEAETDAAALLESGA-EPVSIPVSLRT 119
                                       678555***************************************99999999999999999999.*********** PP

                             PAS_9  71 kngetfwvlltaspv..kdddgelvg 94 
                                       k ++++ ++l++  +   dd++e+ g
  gi|336254363|ref|YP_004597470.1| 120 KGESYISCDLHLEVFpgPDDEREFGG 145
                                       ***********988855666666655 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 5e-13
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrk..kerevevvlirkng 73 
                                       pdgi++ +++  i yaN+a +r+lGy+p+e++g s  +++     + + + l+++le+g++  +   ve+  ++k g
  gi|336254363|ref|YP_004597470.1| 176 PDGIIVLDTNSDIQYANPAIERILGYTPDELVGSSKVNIIppRLRQTHLDALQRYLETGERhlNWTYVELPGQHKAG 252
                                       79***9889999****************************877777888899999999999*9999*********** PP

                             PAS_9  74 etfwvlltaspvkdddgelvgiivilrDit 103
                                        +++  +++  +  d+++++   +++rDi+
  gi|336254363|ref|YP_004597470.1| 253 HEVPLAVSLNDFTYDGDRYFV--GLFRDIS 280
                                       ****99999999988888888..******8 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0012       1.4      12      49 ..      43      79 ..      33     141 .. 0.83
   2 !   49.1   0.0     5e-16   5.6e-13       2     109 ..     173     283 ..     172     284 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                             PAS_4 12 dpdgrvlyaNaaaaelfgappeellGktlaellpeeda 49
                                       + g+++++N a+a+l g+ + el G +  +l++++  
  gi|336254363|ref|YP_004597470.1| 43 TETGVITDVNDAFASLTGYGRSELEGASITDLVTDD-D 79
                                      5789***************************99885.3 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 5e-16
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.... 74 
                                       ++lpd+++vld+++ ++yaN+a+++++g++p+el+G++   + p+++++ + +al+r le++e++  ++++ l    
  gi|336254363|ref|YP_004597470.1| 173 EALPDGIIVLDTNSDIQYANPAIERILGYTPDELVGSSKVNIIPPRLRQTHLDALQRYLETGERHLNWTYVELpgqh 249
                                       79*******************************************************************99998888 PP

                             PAS_4  75 .pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                         g e+++ ++l+ +   +G+ + +++++rDi+ r+
  gi|336254363|ref|YP_004597470.1| 250 kAGHEVPLAVSLNDF-TYDGD-RYFVGLFRDISPRK 283
                                       888889999999887.56888.99999999998876 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.8e-06    0.0021      19      57 ..      45      83 ..      27      96 .. 0.74
   2 !   35.4   0.0   6.6e-12   7.4e-09       3      54 ..     168     220 ..     166     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-06
                             PAS_8 19 lgdrivdvNqaalellGys.adlkgellgqllpvlrplle 57
                                      +g  i+dvN+a++ l+Gy   +l g+ + +l+++ ++ le
  gi|336254363|ref|YP_004597470.1| 45 TG-VITDVNDAFASLTGYGrSELEGASITDLVTDDDDILE 83
                                      33.4****************99999999766666665554 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 6.6e-12
                             PAS_8   3 lralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrp 54 
                                       ++al e++pdgi+v+d + d i ++N+a +++lGy+ ++l g+   +++p    
  gi|336254363|ref|YP_004597470.1| 168 FQALAEALPDGIIVLDtNSD-IQYANPAIERILGYTpDELVGSSKVNIIPPRLR 220
                                       89**************9999.***************999999888755554444 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.4   6.6e-17   7.4e-14       3     138 .]     311     457 ..     309     457 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 6.6e-17
                                       HHHHHHHHHHHHHHH.SS..EEEEEEE-TTS-....EEEEEEEES-TTS.TT-S-B--...-TT.HHHHHHHHTS-E CS
                             GAF_2   3 dleelldlvldelve.lgaalgyillvdddgg....lrlaawgeaeeef.gaaldrpl...geg.lvgealrtgrpv 69 
                                       d+++lld +++ +++ l+++++ +l+ d+ +g    l ++a+ +  + +   ++ ++l   + + l+++ l++g+p+
  gi|336254363|ref|YP_004597470.1| 311 DVDDLLDKATRLIETaLDVECCLVLETDPSPGdapgLAVRASVGCSDALlENETTPALsssEPAlLAERTLADGEPI 387
                                       89***********9979*********996655555566664444444441444433335546665699********* PP

                                       EES-.GGG-S-HHHHHHHHHTT--EEEEEE.-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  70 ilnd.leedpdkkglpaghaglrsflavPl.isegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       ++++  ++d+  +++ +++ g++s+++v +  ++  + Gvl++y +++++f + d+++Le+ a+++a+ ie
  gi|336254363|ref|YP_004597470.1| 388 VVESfAADDRVERSSVLADTGIQSGMGVTIgPAD-DPWGVLAVYDDQEREFADHDVDFLESTATLLATGIE 457
                                       ****888899999999**************5445.5*******************************9987 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00026      0.29       2      34 ..      49      79 ..      48     143 .. 0.87
   2 !   26.3   0.0   5.9e-09   6.7e-06       3      56 ..     190     242 ..     188     264 .. 0.93
   3 ?    0.4   0.0      0.73   8.2e+02      32      70 ..     638     682 ..     635     683 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                             PAS_3  2 iyvserveeilGyspeellgkveswldlvhpeD 34
                                      + v++++  ++Gy ++el+g   s+ dlv  +D
  gi|336254363|ref|YP_004597470.1| 49 TDVNDAFASLTGYGRSELEGA--SITDLVTDDD 79
                                      579******************..*******999 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 5.9e-09
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegey 56 
                                       y+++++e+ilGy+p+el g+  s  +++ p  r+   +alq++l++ge ++++ y
  gi|336254363|ref|YP_004597470.1| 190 YANPAIERILGYTPDELVGS--SKVNIIPPRLRQTHLDALQRYLETGErHLNWTY 242
                                       89******************..*************************97777666 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.73
                             PAS_3  32 peDrervrealqealkkge.pyege.....yRirrkdGeyrwvea 70 
                                       p++ +rv++ +q++ +++e p +g       Ri+ ++G+ +wv++
  gi|336254363|ref|YP_004597470.1| 638 PDETDRVFRVFQRLHSRDEyPGTGIglalcRRIVERHGGRIWVDS 682
                                       888999999999888666644444455565788888888888875 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.66   7.4e+02      24      53 ..     453     481 ..     447     482 .. 0.75
   2 !   40.5   0.1   1.9e-13   2.1e-10       2      66 ..     479     545 ..     478     546 .. 0.96
   3 ?   -1.7   0.1       2.8   3.2e+03      34      59 ..     575     600 ..     560     605 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.66
                                       HHHHHC..T-HSSCHHHHHHHHHHHHHHHH CS
                             HisKA  24 aeaLkregklteelkeyletiesearrldh 53 
                                       a  ++r +++  +l e ++++e++ +rl++
  gi|336254363|ref|YP_004597470.1| 453 ATGIER-QQYERRLNETVADLEESNERLEQ 481
                                       444555.47888999999999999999976 PP

  == domain 2  score: 40.5 bits;  conditional E-value: 1.9e-13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l++f+   +H+L  PL  ++ ++++ +++  ++l+e+ +e++e ++++a+r++++++ lL +sri++
  gi|336254363|ref|YP_004597470.1| 479 LEQFAYAASHDLQEPLRMVSSYLQLVEDRyvDELDEDAEEFIEFAVDGAERMREMIDGLLAYSRIDS 545
                                       789***********************8888***********************************98 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.8
                                       HSSCHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  34 teelkeyletiesearrldhlvedlL 59 
                                        e   e l t+e    +l++l ++lL
  gi|336254363|ref|YP_004597470.1| 575 AEITTESLPTVEGDDSQLRQLFQNLL 600
                                       46666777788888889999999986 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.1   1.4e-12   1.5e-09       1     131 [.     311     454 ..     311     456 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.4e-12
                                       SHHHHHHHHHHHHHHHHTESEEEEEE........EEETTEEE.............CEEEEECCEEEETTSHHHHHHH CS
                               GAF   1 dleelldtvveelrellgadrvalyl........pdydGlhy.............dipqasrwlfmkngrgicgqvl 56 
                                       d+++lld++++ ++ +l+++ ++++         p   Gl +             ++++a++ +++     ++ ++l
  gi|336254363|ref|YP_004597470.1| 311 DVDDLLDKATRLIETALDVECCLVLEtdpspgdaP---GLAVrasvgcsdallenETTPALSSSEPAL---LAERTL 381
                                       789****************9999976776664331...332233333333222222333333333333...344899 PP

                                       HHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHH CS
                               GAF  57 atgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvav 131
                                       a g+p+v++  ++d+r  +   +++l+ +gi+s ++v +   ++ wG+l++++ ++ +f ++++++l++ a+++a 
  gi|336254363|ref|YP_004597470.1| 382 ADGEPIVVESFAADDRVER---SSVLADTGIQSGMGVTIGPADDPWGVLAVYDDQErEFADHDVDFLESTATLLAT 454
                                       99*******8778888777...99****************999**********44457*************99986 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   1.8e-12     2e-09       1     129 []     311     458 ..     311     458 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.8e-12
                             GAF_3   1 sldellekllkllvkllgaevgalll.....ldedgnklqvaagwdgkpalse.....sld..edsalarralssge 65 
                                       ++d+ll+k+ +l+  +l++e + +l+        d + l+v+a+ + ++al e     +l   e+ +la r+l+ ge
  gi|336254363|ref|YP_004597470.1| 311 DVDDLLDKATRLIETALDVECCLVLEtdpspG--DAPGLAVRASVGCSDALLEnettpALSssEPALLAERTLADGE 385
                                       689*********************99554322..5568888888888888877789997766699999********* PP

                             GAF_3  66 vvsepsfaeedg.........lpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                       ++++ sfa+ d+         +  ++ + v +   + + Gvla++ +++r+f + d+++les A+++at+ier
  gi|336254363|ref|YP_004597470.1| 386 PIVVESFAADDRverssvladTGIQSGMGVTIGPADDPWGVLAVYDDQEREFADHDVDFLESTATLLATGIER 458
                                       *******99888444555333333444666555555899*********************************8 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.5e-07   0.00039       4      92 ..     590     685 ..     588     695 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.5e-07
                       HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ek......kklesskskkeehGi 69 
                                         l  ++ nlL NA+e + + +   + +++ v+++ ++  is+e +  g     +       ++l+s+  +    Gi
  gi|336254363|ref|YP_004597470.1| 590 SQLRQLFQNLLSNALEYSGDEP---PRVHVAVERNRRTWEISVEDEGIGidpdeTDrvfrvfQRLHSRD-EYPGTGI 662
                                       568889**********998866...89******************966656554113443345555544.466799* PP

                       HATPase_c_5  70 Glksireivkkykgnlsieaedg 92 
                                       Gl   r+iv++++g ++++ e g
  gi|336254363|ref|YP_004597470.1| 663 GLALCRRIVERHGGRIWVDSEPG 685
                                       *****************998865 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 !   17.5   0.0   2.5e-06    0.0028      21      74 ..     613     661 ..     591     671 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.5e-06
                       HATPase_c_3  21 nvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrkstslGkkG 74 
                                       +v++ v++nr  t ei++eD+G G++++e ++++r+ +  ++    ++ +   G
  gi|336254363|ref|YP_004597470.1| 613 RVHVAVERNR-RTWEISVEDEGIGIDPDETDRVFRVFQRLHS----RDEYPGTG 661
                                       4999999998.69*******************9997766655....34444445 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.3e-06    0.0059      39     110 ..     599     672 ..     557     685 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.3e-06
                       HATPase_c_2  39 actNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep......keslkegGrGlalikglv 109
                                       +++Na e+  +e p  +v+v++e++ ++ +++v+D+G g dp + ++             ++ +  G+Glal +++v
  gi|336254363|ref|YP_004597470.1| 599 LLSNALEYSGDEPP--RVHVAVERNRRTWEISVEDEGIGIDPDETDRVFR--VfqrlhsRDEYPGTGIGLALCRRIV 671
                                       6899***9999877..9999999****************88876544333..1346777778888999999999988 PP

                       HATPase_c_2 110 D 110
                                       +
  gi|336254363|ref|YP_004597470.1| 672 E 672
                                       6 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.027        31      62      99 ..     460     497 ..     457     526 .. 0.86
   2 ?    6.1   0.0      0.01        11      54      98 ..     557     602 ..     554     609 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.027
                         ApoLp-III  62 evkkkieetadklseenPevkkkaqelqekvQsgvqsl 99 
                                       +    ++et+++l+e+n  +++ a + +  +Q+ ++++
  gi|336254363|ref|YP_004597470.1| 460 QYERRLNETVADLEESNERLEQFAYAASHDLQEPLRMV 497
                                       667899**************************988765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                         ApoLp-III  54 deleealkevkkkieetadklse.enPevkkkaqelqekvQsgvqs 98 
                                       d le +l++++ kie t ++++  + P v+   ++l++ +Q+ +++
  gi|336254363|ref|YP_004597470.1| 557 DVLEDVLTDLQVKIEDTDAEITTeSLPTVEGDDSQLRQLFQNLLSN 602
                                       56899****************98688***************87766 PP

>> GlnD_UR_UTase  GlnD PII-uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.2   0.00039      0.43      34     113 ..     441     521 ..     440     533 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00039
                     GlnD_UR_UTase  34 diefivqvlqlirGgrdpelrerstlealeelver.gllteeeakelreayrflrrlehrLqlladrqthrLpfdee 109
                                       d+ f+  ++ l+  g +++  er++ e++++l+e  + l++  +++ ++ ++ lr++   Lql++dr  ++L +d+e
  gi|336254363|ref|YP_004597470.1| 441 DVDFLESTATLLATGIERQQYERRLNETVADLEESnERLEQFAYAASHDLQEPLRMVSSYLQLVEDRYVDELDEDAE 517
                                       78899999999999999999999999999999987368999999999****************************88 PP

                     GlnD_UR_UTase 110 eqrr 113
                                       e  +
  gi|336254363|ref|YP_004597470.1| 518 EFIE 521
                                       7655 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2      0.18     2e+02      23      41 ..     282     300 ..     282     302 .. 0.93
   2 ?    6.0   2.3     0.012        13      23      46 ..     458     481 ..     457     483 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  23 kkakeeeleervkeLeeeN 41 
                                       +ka e+ l e+v +Le+ N
  gi|336254363|ref|YP_004597470.1| 282 RKAAEQALTEKVVQLESVN 300
                                       799*************988 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  23 kkakeeeleervkeLeeeNaqLrq 46 
                                       + ++e+ l e+v +Lee N++L+q
  gi|336254363|ref|YP_004597470.1| 458 RQQYERRLNETVADLEESNERLEQ 481
                                       679999****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (703 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 5057.16
//
Query:       gi|336254364|ref|YP_004597471.1|  [L=131]
Description: response regulator receiver [Halopiger xanaduensis SH-6]
Scores for complete 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-13   50.6   0.0    2.2e-13   50.3   0.0    1.0  1  Response_reg     Response regulator receiver domain
  ------ inclusion threshold ------
      0.015   15.5   0.1      0.022   15.0   0.1    1.3  1  OKR_DC_1_N       Orn/Lys/Arg decarboxylase, N-terminal domain
      0.022   15.4   0.1      0.032   14.9   0.1    1.3  1  Methyltransf_25  Methyltransferase domain


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 !   50.3   0.0   3.8e-17   2.2e-13       1     101 [.       6     109 ..       6     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 3.8e-17
                                       EEEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHH.HHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSE CS
                      Response_reg   1 vlivdDdplvrellrqlle.eegyeevaeaedgkealell.keekvdlillDinmpgmdGlellkeireed..pelp 73 
                                       vl vdD+  + e +++ l+ e+g+ +v++++++++a   l ++ ++d+++   ++ + +Glel+  +++e   p+lp
  gi|336254364|ref|YP_004597471.1|   6 VLFVDDSDFLTEHVSRTLQsEHGF-DVETVATAADARSTLaDSASFDCVISSYELLEENGLELAASLHDEAtvPDLP 81 
                                       899****************88899.***99999999998845566**********************999989**** PP

                                       EEEEESSTSHHHHHHHHHCTESEEEESS CS
                      Response_reg  74 viiltahseeedavealkagaddflsKp 101
                                        +++t++  e+ + eal+ag++ f+sK 
  gi|336254364|ref|YP_004597471.1|  82 FVLFTGNPLEPLVDEALEAGVSAFVSKS 109
                                       ***************************7 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   3.7e-06     0.022      13      69 ..      23      85 ..      12     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.7e-06
                        OKR_DC_1_N 13 lek.egfevvgvtstdDllsvieqnsriaavvlsvd...deaaelldeire..rnedlPvFll 69
                                      l++ +gf+v +v++  D++s +   ++ ++v+ s++   ++  el + +++  + +dlP  l+
  gi|336254364|ref|YP_004597471.1| 23 LQSeHGFDVETVATAADARSTLADSASFDCVISSYElleENGLELAASLHDeaTVPDLPFVLF 85
                                      554489******************************999777777777754115567776655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   5.3e-06     0.032      22      75 ..       4      61 ..       1      76 [. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.3e-06
                                      SEEEEEESSHHHHHHHHHHHHH.TTTTEEEEE..SBCCGBSSSTTTEEEEEEEST.GG CS
                   Methyltransf_25 22 akvtgvDiseemleaareraee.eglnvefvq..gdaedlpfedgsfDlvvssga.lh 75
                                      ++v+ vD s+ + e++ + +++ +g++ve v   +da++   +++sfD+v+ss++ l+
  gi|336254364|ref|YP_004597471.1|  4 YRVLFVDDSDFLTEHVSRTLQSeHGFDVETVAtaADARSTLADSASFDCVISSYElLE 61
                                      689999999999999999998845668887553378888889999*******977444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 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:                        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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1153.44
//
Query:       gi|336254365|ref|YP_004597472.1|  [L=267]
Description: phosphatidylserine decarboxylase [Halopiger xanaduensis SH-6]
Scores for 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-20   72.8   0.4    3.4e-17   62.7   0.4    2.8  1  PS_Dcarbxylase  Phosphatidylserine decarboxylase
  ------ inclusion threshold ------
      0.044   14.0   0.4         60    3.9   0.0    3.8  4  Peptidase_M23   Peptidase family M23
       0.06   13.3   0.2         15    5.7   0.0    2.8  2  RnfC_N          RnfC Barrel sandwich hybrid domain


Domain annotation for each model (and alignments):
>> PS_Dcarbxylase  Phosphatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.4   5.6e-21   3.4e-17       8     199 ..      42     222 ..      37     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 5.6e-21
                    PS_Dcarbxylase   8 klkdgaRpidddpgaivsPaDgrilqigeieegsviqvKgityslrdLlgeasessadsfkngyfvviyLspgdyHr 84 
                                       +++d++R ++++   +v+PaDgr++     ee                             + + + i++++  +H+
  gi|336254365|ref|YP_004597472.1|  42 FFRDPDRTPPPT--GVVAPADGRVSVL--REE----------------------------GDRVRLGIFMNVWHVHV 86 
                                       678888877443..3788888888887..122............................256899*********** PP

                    PS_Dcarbxylase  85 yhaPvsgkveerrhipGellsvnpsalkelrglftlneRvvlview...........................kGkv 134
                                       ++aP +g+v +++h+ G+    +p++ ke+     +neRv + +e+                               
  gi|336254365|ref|YP_004597472.1|  87 VRAPFAGRVADVEHVSGA---NRPAFSKES----DRNERVHVRLETdspnlpadstdgetdpapdpddyadtpASDA 156
                                       ******************...778888888....889*******955799*********9*9999998765443349 PP

                    PS_Dcarbxylase 135 avvpvGatnvgsivlnvlkgdelkkGeelGyFqfGStvvlvfeag.kfieslvekgqkvkmGeklg 199
                                        v+ ++++++++i+ +v+ +d +++Ge++G+++fGS+v+++f++  ++    ve+g++  +Ge+++
  gi|336254365|ref|YP_004597472.1| 157 EVTLIAGAFARRIHPYVEADDDVERGERIGHIAFGSRVDVLFPPSvDKSAIAVEPGDSTTAGETIV 222
                                       9999***************************************99878899************986 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.016        98      11      29 ..      50      68 ..      46      85 .. 0.74
   2 ?    0.8   0.0     0.096   5.8e+02       6      30 ..      77     101 ..      72     117 .. 0.77
   3 ?    3.9   0.0      0.01        60      56      72 ..     172     188 ..     156     195 .. 0.82
   4 ?    0.4   0.0      0.13   7.5e+02      53      71 ..     205     223 ..     202     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.016
                                      TTT-EEEESSSEEEEEEEE CS
                     Peptidase_M23 11 pkgtpVlAaadGtVvfagk 29
                                      p+ t V+A+adG+V   ++
  gi|336254365|ref|YP_004597472.1| 50 PPPTGVVAPADGRVSVLRE 68
                                      55678*********54443 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.096
                                       EEEEETTT-EEEESSSEEEEEEEEE CS
                     Peptidase_M23   6 idiaapkgtpVlAaadGtVvfagkk 30 
                                       i +++ +   V+A+ +G+V  ++  
  gi|336254365|ref|YP_004597472.1|  77 IFMNVWHVHVVRAPFAGRVADVEHV 101
                                       55555556679********988764 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.01
                                       SS-TTEEE-TTCEEEEE CS
                     Peptidase_M23  56 svkegqkVkaGqvIGtv 72 
                                        v++ + V++G+ IG++
  gi|336254365|ref|YP_004597472.1| 172 YVEADDDVERGERIGHI 188
                                       3999***********97 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.13
                                       SEESS-TTEEE-TTCEEEE CS
                     Peptidase_M23  53 skisvkegqkVkaGqvIGt 71 
                                       s+i+v++g+   aG++I  
  gi|336254365|ref|YP_004597472.1| 205 SAIAVEPGDSTTAGETIVL 223
                                       5688999999999999955 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 ?    4.5   0.0    0.0056        33      45      86 ..      66     104 ..      54     113 .. 0.76
   2 ?    5.7   0.0    0.0024        15      42      62 ..     169     189 ..     152     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0056
                            RnfC_N  45 lvkvgdkVlkGqkiaeaegfvsapvhasvsGtVkaiekrlva 86 
                                       l ++gd+V+ G  +   +      v a+ +G+V ++e++  a
  gi|336254365|ref|YP_004597472.1|  66 LREEGDRVRLGIFMNVWHV---HVVRAPFAGRVADVEHVSGA 104
                                       5567788877766544433...4699***********98765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0024
                            RnfC_N  42 akplvkvgdkVlkGqkiaeae 62 
                                        +p v+ +d V++G++i++  
  gi|336254365|ref|YP_004597472.1| 169 IHPYVEADDDVERGERIGHIA 189
                                       5799*************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); 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:                         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 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2014.51
//
Query:       gi|336254366|ref|YP_004597473.1|  [L=773]
Description: Catalase [Halopiger xanaduensis SH-6]
Scores for 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-172  572.0   0.3   8.1e-172  571.6   0.3    1.1  1  Catalase      Catalase
    1.3e-22   79.8   0.3    2.8e-22   78.7   0.3    1.6  1  Catalase-rel  Catalase-related immune-responsive
    1.6e-21   76.6   0.2    2.5e-21   75.9   0.2    1.3  1  Catalase_C    C-terminal domain found in long catalases
    3.4e-10   40.0   0.6    6.3e-10   39.1   0.6    1.4  1  DJ-1_PfpI     DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> Catalase  Catalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  571.6   0.3  1.8e-175  8.1e-172       1     381 [.      85     478 ..      85     480 .. 0.98

  Alignments for each domain:
  == domain 1  score: 571.6 bits;  conditional E-value: 1.8e-175
                                       B-TTS-B-S-SSS-EEESTTS-BBTT-HHHHHHHHHHHT------SS--SEEEEEEEEEESS-.........-TTT- CS
                          Catalase   1 ttseGapvsdnqnsltagerGplllqdvhlieklahfdreripeRvvhAkGagahgeFevtkd.........isdlt 68 
                                       tt++G++vsd++nsl+agerGp++++d+h++ek+++fd+e ipeRvvhA+G+g hg+F+ ++d         i++lt
  gi|336254366|ref|YP_004597473.1|  85 TTDHGVKVSDTDNSLKAGERGPTIMEDFHFREKMTQFDHESIPERVVHARGTGVHGYFQPYEDpdlgdeyddIEELT 161
                                       899*********************************************************999999999999***** PP

                                       --GGGSSTT-EEEEEEEEE-SS--TT--SSSSS--EEEEEEEETTEEEEEEEESSSS-S-S-GGGHHHHHHHHSB-T CS
                          Catalase  69 kakllskvgkktpvlvRfStvagekgsadtaRdvrGfavkfyTeeGnwDlvgnntpvFfirDpikfpdlihsqkrep 145
                                       kak+l+++++ktpv++RfStv+g++gsadt+RdvrGfa+kfyTeeGnwDlvgnn+pvFfi+D+++fpdl+hs k++p
  gi|336254366|ref|YP_004597473.1| 162 KAKVLTDPDQKTPVFTRFSTVVGSRGSADTVRDVRGFATKFYTEEGNWDLVGNNIPVFFIQDAMEFPDLVHSIKPDP 238
                                       ***************************************************************************** PP

                                       TT-SB..-HHH..HHHHHHT-GGGHHHHHHHHSGGGSBS-GGGS-EE--S-EEEE-TT--EEEEEEEEEETT---B- CS
                          Catalase 146 qtnlk..daam..fwdflslnpeslhqvlilfsdrgipksyrhmngygvhtfklvnkegevvyvkfhfktkqgvknl 218
                                       +  ++  +aa+  fwdf sl+pe +h++++++s r++p+ yr+m+g+gvhtf+lvn+ege+v+vkfh+ ++ ++++l
  gi|336254366|ref|YP_004597473.1| 239 DDGTPqaSAAHdtFWDFASLKPEITHMIMWVLSGRALPRAYRMMQGFGVHTFRLVNEEGESVFVKFHWAPEYDTSQL 315
                                       ***9976333366**************************************************************** PP

                                       -HHHHHHHHHH-TTHHHHHHHHHHHTT---EEEEEEEEEEHHHHTTTHHHHT-TT----TTTS--EEEEEEEEEE-- CS
                          Catalase 219 taeeaeklagedpdyatrdLyeaiekgeypewelyvqvmteeeaeklrfnilDlTkvwpekevplrevGkltLnrnp 295
                                       +++e++k+ag++pd++++dLy+ ie+g  pe+el vq+++ee+ae+++f++lD+Tk++pe+evp+r++Gk+tLn++p
  gi|336254366|ref|YP_004597473.1| 316 VWDETQKIAGKNPDFNRQDLYDVIEAGYEPEFELGVQIFDEEDAEEFDFDVLDPTKIVPESEVPVRPIGKMTLNETP 392
                                       ***************************************************************************** PP

                                       S-HHHHTTT----TT---TTEE--S-HHHHHHHHHHHHHHHHHT.-TTGGGSGGG---..---S----TT-.....S CS
                          Catalase 296 enyFaevEqvafspsnlvpGiepseDklLqgRlfsYadtqryRl.GvnyqqlpvNrpkakvanyqrdGamrveankg 371
                                       +n+FaevEqvaf+p+n+vpGi++s+D+lLqgRlfsY+dtq +R+ ++n++++p+Nrp a+ +n+qr G+mr+e+n+g
  gi|336254366|ref|YP_004597473.1| 393 DNFFAEVEQVAFHPGNVVPGIDFSNDPLLQGRLFSYQDTQLNRFgSANWDEIPINRPIAERHNNQRAGFMRQEINEG 469
                                       ********************************************779**********99999999**********99 PP

                                       -S---SS-S- CS
                          Catalase 372 kepnYepnsl 381
                                       k ++Y+pns+
  gi|336254366|ref|YP_004597473.1| 470 K-ASYKPNSI 478
                                       9.******97 PP

>> Catalase-rel  Catalase-related immune-responsive
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   0.3   6.1e-26   2.8e-22       1      65 []     509     574 ..     509     574 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 6.1e-26
                                       HHGG--SSHHHHHHHHHS-HHHHHHHHHHHHHHHTTSS-HHHHHHHH.HHHHHH-HHHHHHHHHHH CS
                      Catalase-rel   1 sedfddhfsQagllyrsmseeekerlvnniafelskvedeeiqerql.ehfakvDpdlgqrVaeal 65 
                                       se+f++hf Qa+l+++sm+e ek++++++  fel+kv++ ei+er++ + f++vD+++++rVae++
  gi|336254366|ref|YP_004597473.1| 509 SESFQNHFDQARLFWNSMTEPEKQNIIDAAHFELGKVDRVEIRERMVyDLFNNVDHEFAKRVAEGI 574
                                       689***********************************99*******9***************985 PP

>> Catalase_C  C-terminal domain found in long catalases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.2   5.5e-25   2.5e-21       2     151 ..     609     767 ..     608     768 .. 0.83

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 5.5e-25
                        Catalase_C   2 glkVgiLasndseaslaqakalaaalaaegvdvtvvaeklg.....saeg....vnrTYstadaveFDaivvadgae 69 
                                       ++k+++L+++d   + +++++++++l++eg  v++v + lg     +  g     +++ +t+++v+FDa++v +g  
  gi|336254366|ref|YP_004597473.1| 609 TRKIAVLVDDDY--DSDHLETIQSTLQDEGGRVKIVSKVLGdkeaeN--GdtvaADKSHVTTESVLFDAVYVPGG-- 679
                                       89******8655..8999******************99999664331..2564469*******************.. PP

                        Catalase_C  70 slfsakataasslfpagrplqllldayrhgKpigalGsgaealk............aagisa...eepGVyvadsas 131
                                       + +       ++l+++g++ +++ ++++h Kpi+a G+g+++l+                 +   +e+GV++  + +
  gi|336254366|ref|YP_004597473.1| 680 DHV-------DALVEQGNAKHFVAEMFKHKKPIAAAGAGTDLLEavelpgvdvanaR----EgivSEQGVVMDPDGE 745
                                       333.......5789******************************7888866644322....2556899999988866 PP

                        Catalase_C 132 e..alvekvkegLatfrfldRf 151
                                       +  +++e++ +++a++r+++R 
  gi|336254366|ref|YP_004597473.1| 746 DleSFAEEFVDAIAQHRHWERD 767
                                       3337*****************5 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 !   39.1   0.6   1.4e-13   6.3e-10       1     109 [.     610     717 ..     610     725 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.4e-13
                                       EEEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHHHH CS
                         DJ-1_PfpI   1 kkvlvlladgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGragperl 77 
                                       +k++vl+ d++++  l +  + l+ +g +v++vs+  +  +  +G +v +d+s    ++  +Da+ +pGG+   + l
  gi|336254366|ref|YP_004597473.1| 610 RKIAVLVDDDYDSDHLETIQSTLQDEGGRVKIVSKVLGDKEAENGDTVAADKSHVTTESVLFDAVYVPGGDH-VDAL 685
                                       5999***999999888888999******************************99988888************.**** PP

                                       HTSHHHHHHHHHHHHTT-EEEEETTTHHHHHH CS
                         DJ-1_PfpI  78 renekvvelvkefaekgklvaaICagpqlLaa 109
                                       +e+  + ++v e+++ +k++aa +ag+ lL a
  gi|336254366|ref|YP_004597473.1| 686 VEQGNAKHFVAEMFKHKKPIAAAGAGTDLLEA 717
                                       **************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (773 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.41
# Mc/sec: 5601.20
//
Query:       gi|336254367|ref|YP_004597474.1|  [L=119]
Description: hypothetical protein Halxa_2979 [Halopiger xanaduensis SH-6]
Scores for 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  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 945.18
//
Query:       gi|336254368|ref|YP_004597475.1|  [L=220]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-23   82.2   0.4    7.5e-23   81.1   0.1    1.6  2  BAT            GAF and HTH_10 associated domain
    8.8e-18   63.9   0.1    1.9e-17   62.8   0.1    1.6  1  HTH_10         HTH DNA binding domain
    0.00054   20.0   0.1     0.0029   17.7   0.0    2.2  2  HTH_AraC       Bacterial regulatory helix-turn-helix proteins
     0.0019   17.9   0.0     0.0047   16.7   0.0    1.6  1  TetR_N         Bacterial regulatory proteins, tetR family
     0.0032   17.3   0.1     0.0067   16.3   0.1    1.5  1  MarR_2         MarR family
     0.0042   17.1   0.0     0.0088   16.1   0.0    1.5  1  HTH_3          Helix-turn-helix
     0.0045   16.9   0.0     0.0095   15.9   0.0    1.6  1  HTH_Crp_2      Crp-like helix-turn-helix domain
      0.006   16.1   0.0      0.011   15.3   0.0    1.3  1  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.037   14.1   0.0    1.5  1  Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix do
      0.021   14.9   0.0      0.044   13.8   0.0    1.5  1  HTH_20         Helix-turn-helix domain
      0.025   14.4   0.0       0.22   11.3   0.0    2.5  1  HTH_38         Helix-turn-helix domain
      0.026   14.3   0.0      0.063   13.1   0.0    1.6  1  HTH_23         Homeodomain-like domain
       0.03   14.1   0.1      0.055   13.3   0.1    1.4  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.038   13.7   0.1       0.11   12.3   0.1    1.8  1  HTH_psq        helix-turn-helix, Psq domain
      0.042   13.4   0.1       0.11   12.1   0.1    1.7  1  Sigma70_r4     Sigma-70, region 4
      0.087   12.8   0.0       0.18   11.8   0.0    1.4  1  HTH_11         HTH domain
       0.13   12.5   0.0       0.29   11.4   0.0    1.6  1  HTH_17         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.1   7.1e-26   7.5e-23       7     152 ..       6     154 ..       3     156 .. 0.95
   2 ?   -2.0   0.0       2.7   2.8e+03     115     129 ..     175     189 ..     173     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 7.1e-26
                               BAT   7 eleirdeddvlv.alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtllel 82 
                                       e++++++d++++ al+a+ ++ ve+e++v++ +++ + +f+v+g+d+++++da+ d d+v+++  v+e +++ l+++
  gi|336254368|ref|YP_004597475.1|   6 EFSVKSDDLAMHhALTAAPQMVVEIEQVVATMEDRIMPYFWVSGDDQAAFEDAFRDDDSVKNIANVDEVEGARLYRA 82 
                                       8999999999988**************************************************************** PP

                               BAT  83 tvsg..pslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrr 152
                                       ++++  ++++ ++++ G+t+ +a   +++++l++++ ++  +  +  ++ee+  + eL + +e+e+p+ +++
  gi|336254368|ref|YP_004597475.1|  83 EWTDniETIVYAYVDLGATIMRAIGKGEEWDLRMRFDNRDSLSDFQAYCEENDISYELNRIQEQEQPMASAQ 154
                                       *9753357777*********************************************************9987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
                               BAT 115 evPpgadvRsvveal 129
                                       evP+ +  R++++ l
  gi|336254368|ref|YP_004597475.1| 175 EVPRAVTMRELADIL 189
                                       899999999999876 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.1   1.8e-20   1.9e-17       1      53 []     157     209 ..     157     209 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 1.8e-20
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LT+ q+e+l +A+e+GY+++PR vt++eLA++lG+s++tls++ r+a ++li+
  gi|336254368|ref|YP_004597475.1| 157 LTPTQRETLITALEAGYYEVPRAVTMRELADILGVSQQTLSNRFRAAYNNLIT 209
                                       9*************************************************985 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 ?   -1.9   0.0       3.7   3.9e+03      31      39 ..     153     161 ..     152     161 .. 0.86
   2 !   17.7   0.0   2.7e-06    0.0029       9      34 ..     180     205 ..     178     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.7
                                       HHSSS-HHH CS
                          HTH_AraC  31 ketGmtPsq 39 
                                       ++++ tP+q
  gi|336254368|ref|YP_004597475.1| 153 AQYDLTPTQ 161
                                       6899***98 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.7e-06
                                       --HHHHHHHTTSSHHHHHHHHHHHSS CS
                          HTH_AraC   9 ltiediAdelgfSrsyFsrlFkketG 34 
                                        t++++Ad lg+S++++s +F+++++
  gi|336254368|ref|YP_004597475.1| 180 VTMRELADILGVSQQTLSNRFRAAYN 205
                                       699********************996 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 !   16.7   0.0   4.4e-06    0.0047      15      38 ..     178     201 ..     177     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.4e-06
                                       TT--HHHHHHHHTSSHHHHHHHTS CS
                            TetR_N  15 dattvreIAkrAGvskgalYryFp 38 
                                       +a+t+re+A+ +Gvs+ +l  +F+
  gi|336254368|ref|YP_004597475.1| 178 RAVTMRELADILGVSQQTLSNRFR 201
                                       69********************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   6.4e-06    0.0067       2      42 ..     156     200 ..     155     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.4e-06
                                       T--HHHHHHHHHHHCTTTS....EEEHHHHHHHHTSSHHHHHHHH CS
                            MarR_2   2 gltpaqarvLaaLgrrpgr....dltvgelarrlglsksavsril 42 
                                       +ltp+q+  L     ++ +     +t++ela+ lg+s++++s++ 
  gi|336254368|ref|YP_004597475.1| 156 DLTPTQRETLITALEAGYYevprAVTMRELADILGVSQQTLSNRF 200
                                       7888888888887777644777788*****************975 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.4e-06    0.0088      11      32 ..     181     202 ..     175     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.4e-06
                                       HHHHHHHHHTSSHHHHHHHHTT CS
                             HTH_3  11 sqeeLAeklGvsrstisriEnG 32 
                                       +++eLA+ lGvs++t+s+ ++ 
  gi|336254368|ref|YP_004597475.1| 181 TMRELADILGVSQQTLSNRFRA 202
                                       899**************98876 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   0.0     9e-06    0.0095      17      43 ..     175     201 ..     155     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9e-06
                                       EEEEEHHHHHHHHHTTSSHHHHHHHHH CS
                         HTH_Crp_2  17 eielpltqeelAsmlGltretvsrils 43 
                                       e+   +t++elA++lG++++t+s  ++
  gi|336254368|ref|YP_004597475.1| 175 EVPRAVTMRELADILGVSQQTLSNRFR 201
                                       677789*****************8765 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 !   15.3   0.0     1e-05     0.011      18      39 ..     180     201 ..     177     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                            HTH_24  18 isqreLAerlglSpstvnrrlk 39 
                                        ++reLA+ lg+S++t++ r +
  gi|336254368|ref|YP_004597475.1| 180 VTMRELADILGVSQQTLSNRFR 201
                                       79****************9976 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 ?   14.1   0.0   3.6e-05     0.037      12      34 ..     180     201 ..     178     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
                                       -SSCHHHHCCTT--HHHHHHHHH CS
                     Phage_CI_repr  12 vkmqkeLAdlLgiakssvstwvr 34 
                                       v m+ eLAd Lg++++++s++ r
  gi|336254368|ref|YP_004597475.1| 180 VTMR-ELADILGVSQQTLSNRFR 201
                                       5677.***************976 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.2e-05     0.044      22      47 ..     177     202 ..     162     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                                       CTTB-HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_20  22 aegltaselaerldlskntlsyHLrv 47 
                                       ++++t  ela+ l++s++tls+++r+
  gi|336254368|ref|YP_004597475.1| 177 PRAVTMRELADILGVSQQTLSNRFRA 202
                                       7899*******************985 PP

>> HTH_38  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   0.00021      0.22       5      39 ..     157     198 ..     155     199 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                            HTH_38   5 LsleeReeIerllaeGl.......slreIArrLgrspsTIsR 39 
                                       L++++Re++ + l++G+       ++re A +Lg+s +T s+
  gi|336254368|ref|YP_004597475.1| 157 LTPTQRETLITALEAGYyevpravTMRELADILGVSQQTLSN 198
                                       556666666666666644555555899************996 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     6e-05     0.063      19      42 ..     181     205 ..     173     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6e-05
                            HTH_23  19 svreIAreLgvsrrTvy.rwlkryr 42 
                                       + re A++Lgvs++T++ r + +y+
  gi|336254368|ref|YP_004597475.1| 181 TMRELADILGVSQQTLSnRFRAAYN 205
                                       899**************66677775 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 ?   13.3   0.1   5.2e-05     0.055      19      39 ..     181     201 ..     165     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.2e-05
                     HTH_AsnC-type  19 syaeLAervGlSestvlrRvr 39 
                                       +++eLA+ +G+S++t  +R r
  gi|336254368|ref|YP_004597475.1| 181 TMRELADILGVSQQTLSNRFR 201
                                       89****************987 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 ?   12.3   0.1    0.0001      0.11      16      41 ..     179     204 ..     161     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                           HTH_psq  16 kmSirkAArkYgiPrsTLwrrkrgky 41 
                                       ++++r++A++ g++  TL++r+r  y
  gi|336254368|ref|YP_004597475.1| 179 AVTMRELADILGVSQQTLSNRFRAAY 204
                                       599******************99776 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0001      0.11      19      48 ..     178     207 ..     156     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                       TT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  19 eglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       +  T+ E++++lg+S+ + + + + A ++L
  gi|336254368|ref|YP_004597475.1| 178 RAVTMRELADILGVSQQTLSNRFRAAYNNL 207
                                       678***************999999888766 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.18      15      35 ..     179     199 ..     173     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                            HTH_11  15 pisgeeLAeeLnvSrrtvrrd 35 
                                        ++  eLA+ L+vS +t  ++
  gi|336254368|ref|YP_004597475.1| 179 AVTMRELADILGVSQQTLSNR 199
                                       4999*************9886 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00027      0.29       3      20 ..     181     198 ..     179     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                            HTH_17   3 tveEaAelLgvsrstvyr 20 
                                       t  E+A++Lgvs++t+ +
  gi|336254368|ref|YP_004597475.1| 181 TMRELADILGVSQQTLSN 198
                                       889************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1655.37
//
Query:       gi|336254369|ref|YP_004597476.1|  [L=745]
Description: Vesicle-fusing ATPase [Halopiger xanaduensis SH-6]
Scores for 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-95  314.6   0.0    1.6e-46  158.0   0.0    2.3  2  AAA              ATPase family associated with various cellul
      3e-26   90.9   3.5    7.3e-13   48.1   1.8    2.8  2  AAA_lid_3        AAA+ lid domain
    9.3e-23   80.2   1.0    5.2e-22   77.8   0.6    2.5  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.2e-15   57.6   0.0    3.6e-07   30.1   0.0    3.5  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.1e-14   54.2   0.8    1.3e-05   25.6   0.1    4.0  2  AAA_16           AAA ATPase domain
    6.1e-14   52.5   0.0    5.7e-07   29.8   0.0    2.4  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.2e-13   51.4   0.0    6.3e-07   29.6   0.0    2.8  2  AAA_33           AAA domain
    2.7e-12   46.8   0.5    6.7e-05   22.9   0.0    3.8  2  AAA_5            AAA domain (dynein-related subfamily)
    8.3e-10   39.1   0.1     0.0037   17.5   0.0    3.4  2  AAA_22           AAA domain
      8e-09   35.6   0.0     0.0031   17.6   0.0    2.3  2  AAA_14           AAA domain
    1.8e-08   34.0   0.0     0.0025   17.1   0.0    2.3  2  TIP49            TIP49 P-loop domain
    5.5e-08   33.4   0.0      0.012   16.1   0.0    3.0  2  AAA_18           AAA domain
    8.1e-08   31.9   0.3    8.1e-08   31.9   0.3    2.0  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.4e-07   31.9   1.2      0.016   15.5   0.0    3.5  2  AAA_28           AAA domain
    3.1e-07   30.3   0.0      0.025   14.4   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    6.2e-07   29.8   0.0       0.02   15.3   0.0    2.4  2  RNA_helicase     RNA helicase
    8.8e-07   28.8   0.0      0.033   13.9   0.0    2.6  2  IstB_IS21        IstB-like ATP binding protein
    1.5e-06   27.7   0.3      0.062   12.7   0.2    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.6e-06   28.6   0.0      0.044   14.3   0.0    2.5  2  ABC_tran         ABC transporter
    2.5e-06   27.5   0.0       0.11   12.6   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    1.4e-05   24.5   0.0      0.032   13.5   0.0    2.6  2  Zeta_toxin       Zeta toxin
    1.6e-05   24.7   0.0       0.31   10.7   0.0    2.9  2  Sigma54_activat  Sigma-54 interaction domain
    3.7e-05   23.6   0.0       0.26   11.0   0.0    2.5  2  AAA_11           AAA domain
    4.2e-05   23.1   0.0      0.076   12.5   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
    4.8e-05   23.2   0.0        0.3   10.8   0.0    2.7  2  AAA_24           AAA domain
     0.0001   22.7   0.0       0.07   13.5   0.0    2.5  2  AAA_19           AAA domain
    0.00012   21.9   0.1       0.76    9.5   0.0    3.0  2  AAA_30           AAA domain
    0.00015   21.0   0.0       0.29   10.3   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    0.00018   20.7   0.0       0.19   10.8   0.0    2.3  2  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0002   20.8   0.0       0.42    9.8   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0002   21.3   0.3        0.7    9.8   0.1    3.6  3  NACHT            NACHT domain
    0.00021   20.8   0.0       0.79    9.1   0.0    2.5  2  PhoH             PhoH-like protein
    0.00029   21.0   0.0        1.2    9.3   0.0    2.4  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00057   19.1   0.0       0.44    9.7   0.0    2.3  2  NB-ARC           NB-ARC domain
     0.0012   18.3   0.0        1.7    7.9   0.0    2.8  2  ATPase           KaiC
     0.0018   18.1   0.4         11    5.8   0.0    3.9  4  DEAD             DEAD/DEAH box helicase
     0.0034   17.8   0.0        2.1    8.8   0.0    3.6  2  AAA_17           AAA domain
     0.0034   17.0   9.3        1.7    8.2   0.1    4.5  4  AAA_25           AAA domain
     0.0091   16.1   0.0        1.3    9.1   0.0    2.6  2  SKI              Shikimate kinase
     0.0094   15.9   0.0        4.5    7.1   0.0    3.4  3  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.015   14.2   0.0        1.3    7.9   0.0    2.2  2  AFG1_ATPase      AFG1-like ATPase
      0.016   14.6   0.0         12    5.2   0.0    3.5  4  TniB             Bacterial TniB protein
      0.019   14.8   0.1        6.1    6.7   0.0    3.4  3  CPT              Chloramphenicol phosphotransferase-like prot
      0.024   14.4   0.0        8.6    6.0   0.0    2.6  2  Cytidylate_kin   Cytidylate kinase
      0.049   13.5   0.0        8.6    6.2   0.0    2.7  2  NTPase_1         NTPase
      0.059   13.1   0.0        5.8    6.6   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.074   13.1   0.0        6.4    6.9   0.0    2.4  2  Torsin           Torsin
      0.075   12.7   0.0        6.5    6.4   0.0    2.9  3  Zot              Zonular occludens toxin (Zot)
      0.082   13.2   0.0        4.7    7.4   0.0    2.5  2  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.084   12.8   0.0        6.7    6.6   0.0    2.2  2  Rad17            Rad17 P-loop domain
       0.14   12.2   0.0         25    4.8   0.0    2.7  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 !  158.0   0.0   4.6e-49   1.6e-46       1     131 [.     262     390 ..     262     391 .. 0.97
   2 !  154.5   0.0   5.4e-48   1.9e-45       1     131 [.     529     657 ..     529     658 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.0 bits;  conditional E-value: 4.6e-49
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vllyGppGtGKTl+a+ava+e++++f +isg+e++sky gese+++re+f++a+++a p+i+f+DEid++a++r ++
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVDANFETISGPEIMSKYKGESEERLREVFETASANA-PTIIFFDEIDSIAGQR-DD 336
                                       79******************************************************9.****************.89 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + + e+r+v qLlt +dg++ +e+ vivigatnr+d +dpal+r gRfdr+i+i+
  gi|336254369|ref|YP_004597476.1| 337 DGDAENRIVGQLLTLMDGLDAREE-VIVIGATNRVDAIDPALRRgGRFDREIQIG 390
                                       99*******************866.***************************986 PP

  == domain 2  score: 154.5 bits;  conditional E-value: 5.4e-48
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+GppGtGKTlla+a+a e++v+f++++g+e+++ yvgesek ire+f++a+++a psi+f+DEida++++r g+
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAGETDVNFIRVDGPEIIDRYVGESEKAIREVFERARQSA-PSIVFFDEIDAITSAR-GE 603
                                       79******************************************************9.****************.99 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        +e++ervv+qLlteldg++++  +++v++atnr +++dpallr gR+d +++++
  gi|336254369|ref|YP_004597476.1| 604 GHEVTERVVSQLLTELDGMREN-PNLVVLAATNRKEHIDPALLRpGRLDTHVYVG 657
                                       *********************6.66**************************9986 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   1.9e-13   6.7e-11       1      44 [.     413     468 ..     413     469 .. 0.77
   2 !   48.1   1.8   2.1e-15   7.3e-13       1      38 [.     680     717 ..     680     738 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.9e-13
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr............gikeitmedfe 44 
                                       dv+++++A+rT+G++GADl ++  eAa++A+r              ++++ +++f+
  gi|336254369|ref|YP_004597476.1| 413 DVNIDAIARRTHGFVGADLDSVTSEAAMAAIRGrptdtddreewnRNPTVRKRHFD 468
                                       9******************************9855555544444223356666665 PP

  == domain 2  score: 48.1 bits;  conditional E-value: 2.1e-15
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikei 38 
                                       d+d++eLA++ eGy+GADl+al+r A+++A+r++  e+
  gi|336254369|ref|YP_004597476.1| 680 DLDIAELAAELEGYTGADLEALVRDASMRAIREVASEY 717
                                       89*******************************65443 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 !   77.8   0.6   1.5e-24   5.2e-22       2      84 ..      11      92 ..      10      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.5e-24
                                      EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEE CS
                           CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtV 80
                                      L V+ a+++d+grg++ri + + ++lg+ +gd+v i g+ +Tva+ wpa+p+   +++I++d+ tR+nagv++Gd VtV
  gi|336254369|ref|YP_004597476.1| 11 LSVRAAEKRDAGRGVARIPELARRQLGVLSGDTVIIDGEAETVAKMWPADPSVA-ENVIQIDADTRANAGVHVGDAVTV 88
                                      899*************************************************88.************************ PP

                                      EEE- CS
                           CDC48_N 81 rkae 84
                                      r+a+
  gi|336254369|ref|YP_004597476.1| 89 RPAD 92
                                      *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 !   30.1   0.0     1e-09   3.6e-07      34      94 ..     260     328 ..     252     336 .. 0.69
   2 !   22.2   0.0   2.6e-07   9.3e-05      31      96 ..     524     597 ..     518     604 .. 0.68
   3 ?    0.1   0.0       1.7     6e+02      15      38 ..     622     645 ..     613     652 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1e-09
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvleka..gd....laalltnl..eekdvlfideih 94 
                                         vllyGpPG Gkt +a+ +a+e+++++++ sgP +  +  g+    l  ++ +   ++  ++f dei 
  gi|336254369|ref|YP_004597476.1| 260 SGVLLYGPPGTGKTLIARAVANEVDANFETISGPEIMSKykGEseerLREVFETAsaNAPTIIFFDEID 328
                                       569*******************************98543112211114444433211334567777766 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 2.6e-07
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrl 96 
                                       e+   vll+GpPG Gkt la+ +a e +v++    gP +      e ++ +  ++ + +++   ++f dei  +
  gi|336254369|ref|YP_004597476.1| 524 EPPSGVLLHGPPGTGKTLLARALAGETDVNFIRVDGPEIidryvgESEKAIREVFERARQSapSIVFFDEIDAI 597
                                       666789*************************9999997632222222333444444333322257777777655 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.7
                            RuvB_N  15 vkeklkifieaakkreealdhvll 38 
                                       ++e+ ++++ aa +r+e++d  ll
  gi|336254369|ref|YP_004597476.1| 622 MRENPNLVVLAATNRKEHIDPALL 645
                                       67888999************9988 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   3.8e-08   1.3e-05      24     140 ..     258     363 ..     229     372 .. 0.69
   2 !   22.8   0.1   2.7e-07   9.6e-05      14      60 ..     516     559 ..     513     631 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.8e-08
                            AAA_16  24 p.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawre 99 
                                       p + vll+G++G+GK+ ++r++++++ ++ + +++g    +          +  ++e+l +  ++++++a    + +
  gi|336254369|ref|YP_004597476.1| 258 PpSGVLLYGPPGTGKTLIARAVANEVDAN-FETISGPEIMS--------KYKGESEERLREVFETASANAPTIIFFD 325
                                       2599*******************999988.33344444444........3344445455555555555556666667 PP

                            AAA_16 100 kleealaavpelagaeasrllellkrllallsrderplvlv 140
                                       ++++ ++ +++++g++++r+  +l  l++ l  +e+  v+v
  gi|336254369|ref|YP_004597476.1| 326 EIDSIAG-QRDDDGDAENRIVGQLLTLMDGLDAREE--VIV 363
                                       6766666.999999999********99988888777..444 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 2.7e-07
                            AAA_16  14 salervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkc 60 
                                       +++e +++  p+ vll+G++G+GK+ l+r+l+    ++++ f+r + 
  gi|336254369|ref|YP_004597476.1| 516 RLFEETNTEPPSGVLLHGPPGTGKTLLARALAG---ETDVNFIRVDG 559
                                       57788888888******************9994...22244444444 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   1.4e-06    0.0005       5     105 ..     261     354 ..     257     361 .. 0.70
   2 !   29.8   0.0   1.6e-09   5.7e-07       5     101 ..     528     617 ..     524     627 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.4e-06
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-H..HHHTTSEEEEETGGG CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyv..gaeegGivllDEidK 79 
                                        +ll gp g+Gkt++a+a+a+  ++    ++ ++   e++     +   ++++  ++     +a+   i+++DEid 
  gi|336254369|ref|YP_004597476.1| 261 GVLLYGPPGTGKTLIARAVANEVDA----NFETISGPEIMS----KYKGESEERLREVFEtaSANAPTIIFFDEIDS 329
                                       57899******************96....888888888888....33333333333333300334456********* PP

                                       -------------HHHHHHHHHHHH- CS
                             AAA_2  80 ihpkessgadvSregVqrdLLqileg 105
                                       i+  ++      ++ ++  LL +++g
  gi|336254369|ref|YP_004597476.1| 330 IAG-QRDDDGDAENRIVGQLLTLMDG 354
                                       ***.4444444566788889999987 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.6e-09
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidK 79 
                                        +ll gp g+Gkt+la+ala   +v    ++ir+d  e++     + + ++++  ++   +a ++   iv++DEid 
  gi|336254369|ref|YP_004597476.1| 528 GVLLHGPPGTGKTLLARALAGETDV----NFIRVDGPEIID----RYVGESEKAIREVFERARQSApsIVFFDEIDA 596
                                       57999*******************8....************....66666777777888888888899********* PP

                                       -------------HHHHHHHHH CS
                             AAA_2  80 ihpkessgadvSregVqrdLLq 101
                                       i++ + +g++v +  V ++L  
  gi|336254369|ref|YP_004597476.1| 597 ITSARGEGHEVTERVVSQLL-T 617
                                       ***99999999876666655.4 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     4e-06    0.0014       2      47 ..     262     322 ..     262     391 .. 0.74
   2 !   29.6   0.0   1.8e-09   6.3e-07       2      84 ..     529     640 ..     529     686 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt.............d 47 
                                       vll G+pG+GK+  a+ ++++ +  ++++s ++++++++g+ +++++              
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVDanFETISGPEIMSKYKGESEERLRevfetasanaptiI 322
                                       7899***************99999***************9888887744444444444440 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1.8e-09
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt...........................dyt 49 
                                       vll+G+pG+GK+ la+ l+ +++  +++++ +++++r++g+ ++ ++                           +  
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAGETDvnFIRVDGPEIIDRYVGESEKAIRevferarqsapsivffdeidaitsargEGH 605
                                       799********************99********99999997777666677777777889999999999988887666 PP

                            AAA_33  50 rvldrlyqilnelarkalsagrnvildatnlsrre 84 
                                       +v++r+  +l   ++ +++  + v+l atn++++ 
  gi|336254369|ref|YP_004597476.1| 606 EVTERVVSQLLTELDGMRENPNLVVLAATNRKEHI 640
                                       78888888888888888888888999999998875 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 !   22.9   0.0   1.9e-07   6.7e-05       1      77 [.     261     330 ..     261     380 .. 0.72
   2 !   19.0   0.2   3.1e-06    0.0011       1     134 [.     528     644 ..     528     646 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.9e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                       +vlL GppGtgK+ +a+ +a  + +++e++ +++ +++ +  g     +++++l++   + +a+ + i+++DE++ +
  gi|336254369|ref|YP_004597476.1| 261 GVLLYGPPGTGKTLIARAVANEVDANFETISGPEIMSKYK--G-----ESEERLREVFETASANAPTIIFFDEIDSI 330
                                       59******************************99776532..2.....33355566666666778888999998844 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 3.1e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEver 76 
                                       +vlL GppGtgK+ la+ la  +  ++  v +++      ++ r+   ++ ++    ++ ra +  ++i+++DE++ 
  gi|336254369|ref|YP_004597476.1| 528 GVLLHGPPGTGKTLLARALAGETDVNFIRVDGPE------IIDRYV--GESEKAIREVFERARQsAPSIVFFDEID- 595
                                       59********************999999999887......888888..4444555555555555788999999999. PP

                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHH CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspal 134
                                       a +++ ++ + + e+   +l      ++++++     + v+a++n+ +     ++pal
  gi|336254369|ref|YP_004597476.1| 596 AITSARGEGHEVTERVVSQLLTELDGMRENPN-----LVVLAATNRKE----HIDPAL 644
                                       66677777888888877777777777777776.....77777777777....666666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.1e-05    0.0037       8      38 ..     262     305 ..     257     365 .. 0.60
   2 !   16.9   0.0   1.6e-05    0.0057       8      45 ..     529     557 ..     523     631 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.............e 38 
                                       ++++G++GtGKT+ +r ++++ d+  +                e
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVDANFETISgpeimskykgeseE 305
                                       689******************98755544455555555553321 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.6e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfv 45 
                                       ++++G++GtGKT+l+r l+ + d         + +++v
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAGETD---------VNFIRV 557
                                       689***************99984.........444433 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.7e-05     0.013       5      77 ..     262     331 ..     260     376 .. 0.76
   2 !   17.6   0.0   8.8e-06    0.0031       5      80 ..     529     601 ..     527     633 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.7e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                       +++ G+  +GKT +++ +++e      ++  i+  +   k + ++e+ l++++e ++++  t++f+DEi  + 
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVD---ANFETISGPEIMSKYKGESEERLREVFETASANAPTIIFFDEIDSIA 331
                                       6799**************98877...88888888777665555555455566665555699********9884 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 8.8e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewe 80 
                                       +++ G+  +GKT l++ l+ e      +++ ++  +  d+   ++ek +++++e+++++  +++f+DEi  +++++
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAGETD---VNFIRVDGPEIIDRYVGESEKAIREVFERARQSAPSIVFFDEIDAITSAR 601
                                       6899***************8887...67777777777777777777888888888666799********9997665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.2e-06    0.0025      52      93 ..     261     300 ..     258     314 .. 0.84
   2 !   14.4   0.0   4.7e-05     0.017      52     102 ..     528     577 ..     520     586 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslev 93 
                                       +vLl Gp+gtGkt +a a+++e+     f ++sg e+ s   
  gi|336254369|ref|YP_004597476.1| 261 GVLLYGPPGTGKTLIARAVANEVD--ANFETISGPEIMSKYK 300
                                       79********************97..789********99754 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqa 102
                                       +vLl Gp+gtGkt la a++ e  +dv f+ + g e+    v  +e ++ + 
  gi|336254369|ref|YP_004597476.1| 528 GVLLHGPPGTGKTLLARALAGE--TDVNFIRVDGPEIIDRYVGESEkAIREV 577
                                       79******************98..57**********9887777766234444 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   0.00018     0.062       1      25 [.     262     304 ..     262     372 .. 0.63
   2 !   16.1   0.0   3.5e-05     0.012       1      75 [.     529     627 ..     529     654 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00018
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................g 25 
                                       +ll G+pG+GKt +a++++++  ++                  
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVdANfetisgpeimskykgesE 304
                                       799***************9995433455555555554454441 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3.5e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe......aldesk 50 
                                       +ll G+pG+GKt la++L+ ++ +                      +++ + a+++ +++ +++e      a  e +
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAGETDVnfirvdgpeiidryvgesekaIREVFERARQSAPSIVFFDEidaitsARGEGH 605
                                       7899**************88873345777777777777777766655555566666666666666777777777777 PP

                            AAA_18  51 rldedkldklldaleenssaleegk 75 
                                       ++ e ++ +ll++l++ ++   +++
  gi|336254369|ref|YP_004597476.1| 606 EVTERVVSQLLTELDGMRE---NPN 627
                                       7777777777777777643...333 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 !   31.9   0.3   2.3e-10   8.1e-08      12      58 ..     124     169 ..     118     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.3e-10
                                       CCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEE CS
                           CDC48_2  12 rqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielg 58 
                                       +++ +rpv +G+++++e   ++ +++Vv+t+P g+v+it tT i++ 
  gi|336254369|ref|YP_004597476.1| 124 KKLRNRPVRAGEQIRVEGV-GAEPFKVVDTTPEGDVRITSTTTIRIH 169
                                       789***************8.799*********************986 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00022     0.076       2      39 ..     262     304 ..     261     327 .. 0.82
   2 !   15.5   0.0   4.4e-05     0.016       2      38 ..     529     570 ..     528     608 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00022
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileekl 39 
                                       + + G+++tGKT +++a a++   +++++  pE++ ++  e  
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEvdaNFETIsgPEIMSKYKGESE 304
                                       6799***************877889999989999988865555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.4e-05
                            AAA_28   2 ivitGgestGKTtlleaLa.argypvv....pEaareileek 38 
                                       + + G+++tGKT l++aLa +++++ +    pE+  +++ e 
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAgETDVNFIrvdgPEIIDRYVGES 570
                                       6799***************64544433114677777766443 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 !   13.3   0.0   0.00016     0.057       2      30 ..     262     290 ..     261     298 .. 0.91
   2 !   14.4   0.0   7.2e-05     0.025       2      31 ..     529     558 ..     528     579 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00016
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG++ktl+++a+a+ +d++f+ i
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVDANFETI 290
                                       7999**********************987 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.2e-05
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       vll+g PG++ktll++ala   d++f r+ 
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAGETDVNFIRVD 558
                                       89*************************995 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.6e-05      0.02       1      38 [.     262     299 ..     262     334 .. 0.88
   2 !   12.1   0.0   0.00055      0.19       1      68 [.     529     587 ..     529     603 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.6e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrn 38 
                                       ++lyGp+g+GK+++a+ +a+++  ++++++ ++++s+ 
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVDANFETISGPEIMSKY 299
                                       689*******************9999888888887754 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00055
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenps 68 
                                       ++l+Gp+g+GK++la+ La +         +d  ++r    ++ d Y g+    i ++ ++  ++ ps
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAGE---------TDVNFIRVDGPEIIDRYVGESEKAIREVFERARQSAPS 587
                                       689**************5432.........23333466777777777766666666666655444555 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 !   12.0   0.0   0.00038      0.13      48      70 ..     260     282 ..     254     291 .. 0.86
   2 !   13.9   0.0   9.5e-05     0.033      48      70 ..     527     549 ..     512     559 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00038
                         IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                        +++l Gp+G+GK+ +a a++ e
  gi|336254369|ref|YP_004597476.1| 260 SGVLLYGPPGTGKTLIARAVANE 282
                                       5799***************9976 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 9.5e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                        +++l Gp+G+GK+ la al+ e
  gi|336254369|ref|YP_004597476.1| 527 SGVLLHGPPGTGKTLLARALAGE 549
                                       6799****************865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00019     0.066      25      43 ..     262     280 ..     259     305 .. 0.91
   2 !   12.7   0.2   0.00018     0.062      25      43 ..     529     547 ..     527     550 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt++a++++
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVA 280
                                       79*************9875 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00018
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll GppG+GKt+la++l+
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALA 547
                                       79**************986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00084      0.29       7      67 ..     255     313 ..     253     380 .. 0.74
   2 !   14.3   0.0   0.00012     0.044      14      75 ..     529     589 ..     521     643 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00084
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                        +++ + v + G+ G+GK+ +++++a++++ + ++i   g ++ ++ + +++++++ ++++
  gi|336254369|ref|YP_004597476.1| 255 GVEPPSGVLLYGPPGTGKTLIARAVANEVDANFETI--SGPEIMSKYKGESEERLREVFET 313
                                       567777899*********************999999..44444443344444444444444 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00012
                                       EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpelt 75 
                                       v + G+ G+GK+ L+++lag+++     i++dg ++ ++   +++k i+ +++   q  p + 
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAGETDV--NFIRVDGPEIIDRYVGESEKAIREVFERaRQSAPSIV 589
                                       7899*****************975..7888899999998888888888888888555555554 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00034      0.12      20      62 ..     260     302 ..     235     311 .. 0.80
   2 !   12.6   0.0    0.0003      0.11      20      51 ..     527     560 ..     503     576 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00034
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEEEE. CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeYele 62 
                                       + +lL+G+ G+GKT ++r++a++++ +  +++ P   ++++Y+ e
  gi|336254369|ref|YP_004597476.1| 260 SGVLLYGPPGTGKTLIARAVANEVDANfeTISGP--EIMSKYKGE 302
                                       459*********************9988678878..688888765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0003
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                       + +lL+G+ G+GKT l+r+la + +v+  +v  P
  gi|336254369|ref|YP_004597476.1| 527 SGVLLHGPPGTGKTLLARALAGETDVNfiRVDGP 560
                                       349********************99997778777 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0043       1.5      14      41 ..     257     284 ..     249     294 .. 0.86
   2 !   13.5   0.0   9.1e-05     0.032       3      51 ..     516     559 ..     514     566 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0043
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdele 41 
                                       e P  +ll G pG GK+ +a+++++e++
  gi|336254369|ref|YP_004597476.1| 257 EPPSGVLLYGPPGTGKTLIARAVANEVD 284
                                       568889*******************985 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 9.1e-05
                        Zeta_toxin   3 ellkdkkypsqerPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       +l++++   + e P  +ll G pG GK+ la++l+ e+  + n++r+d+
  gi|336254369|ref|YP_004597476.1| 516 RLFEET---NTEPPSGVLLHGPPGTGKTLLARALAGET--DVNFIRVDG 559
                                       556654...479999**********************9..89****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 !   10.7   0.0   0.00089      0.31      22      46 ..     259     283 ..     251     294 .. 0.84
   2 !   10.6   0.0   0.00099      0.35      22      45 ..     526     549 ..     514     571 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00089
                                       SS-EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheas 46 
                                       ++ vl+ G  GtGK+l+ara+ ++ 
  gi|336254369|ref|YP_004597476.1| 259 PSGVLLYGPPGTGKTLIARAVANEV 283
                                       5679****************98765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00099
                                       SS-EEEECSTTSSHHHHHHHHHHH CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraihea 45 
                                       ++ vl++G  GtGK+llara+  +
  gi|336254369|ref|YP_004597476.1| 526 PSGVLLHGPPGTGKTLLARALAGE 549
                                       478****************98654 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0018      0.63      20      42 ..     262     284 ..     240     319 .. 0.74
   2 !   11.0   0.0   0.00074      0.26      19      41 ..     528     550 ..     515     593 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0018
                            AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                       +l+ GPPGtgKT    ++ +++ 
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVD 284
                                       799*********99888888874 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00074
                            AAA_11  19 itliqGPPGtgKTktivellsql 41 
                                        +l++GPPGtgKT    +l  + 
  gi|336254369|ref|YP_004597476.1| 528 GVLLHGPPGTGKTLLARALAGET 550
                                       479**********8777766555 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 !   12.5   0.0   0.00022     0.076      35      63 ..     261     288 ..     250     303 .. 0.86
   2 !    8.1   0.0    0.0051       1.8      35      57 ..     528     550 ..     514     557 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
                             AAA_7  35 pvllvGptGtGKtviikdllkkldkekyl 63 
                                        vll+Gp GtGKt+i++ + +++d  ++ 
  gi|336254369|ref|YP_004597476.1| 261 GVLLYGPPGTGKTLIARAVANEVD-ANFE 288
                                       69******************9999.5555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0051
                             AAA_7  35 pvllvGptGtGKtviikdllkkl 57 
                                        vll Gp GtGKt++++ l  + 
  gi|336254369|ref|YP_004597476.1| 528 GVLLHGPPGTGKTLLARALAGET 550
                                       69************999876665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00087       0.3       5      25 ..     262     281 ..     259     340 .. 0.77
   2 !    9.5   0.0    0.0021      0.73       5      33 ..     529     559 ..     527     610 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00087
                            AAA_24   5 iliyGpsgiGKTtlakelgpk 25 
                                       +l+yGp+g+GKT +a+    +
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAV-AN 281
                                       79***********99987.44 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0021
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtek 33 
                                       +l+ Gp+g+GKT la+ l  + ++ fi +++
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALagETDVNFIRVDG 559
                                       6899************998766666766665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0    0.0002      0.07      13      75 ..     262     324 ..     256     438 .. 0.88
   2 ?    6.7   0.0     0.024       8.5      12      28 ..     528     544 ..     520     601 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0002
                            AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrl 75 
                                       +l+ ++pGtGKT + +++ +++ ++ +    + ++  + g + ++lre  +++ a+a Ti  +
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVDANFETISGPEIMSKYKGESEERLREVFETASANAPTIIFF 324
                                       799**************9999999998888899999999*********999999999998655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.024
                            AAA_19  12 vllvtaGpGtGKTrvlk 28 
                                        +l+ ++pGtGKT + +
  gi|336254369|ref|YP_004597476.1| 528 GVLLHGPPGTGKTLLAR 544
                                       5899*********8765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0022      0.76      21      45 ..     262     286 ..     249     319 .. 0.85
   2 !    8.9   0.0    0.0033       1.2      15      39 ..     523     547 ..     515     553 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0022
                            AAA_30  21 avltGpAGtGKttalkalreaweaa 45 
                                       ++l Gp+GtGKt + +a+++ ++a+
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVDAN 286
                                       6789*************98776655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0033
                            AAA_30  15 tsgdrvavltGpAGtGKttalkalr 39 
                                       t++   ++l+Gp+GtGKt + +al+
  gi|336254369|ref|YP_004597476.1| 523 TEPPSGVLLHGPPGTGKTLLARALA 547
                                       555566899*********9999885 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0036       1.3      52      80 ..     258     286 ..     249     370 .. 0.76
   2 !   10.3   0.0   0.00081      0.29      50     153 ..     523     639 ..     473     647 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0036
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaee 80 
                                       p + vLL+G  GtGK  + +a+ ne+ ++
  gi|336254369|ref|YP_004597476.1| 258 PPSGVLLYGPPGTGKTLIARAVANEVDAN 286
                                       56779*******************99775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00081
                            DUF815  50 glpannvLLwGarGtGKSslvkallneyaeegLrl..ievekedlkelpklvellrerper...filfvDDL..... 116
                                        +p + vLL G  GtGK  l +al  e+  + +r+   e+  + + e +k ++++ er+++    i+f D +     
  gi|336254369|ref|YP_004597476.1| 523 TEPPSGVLLHGPPGTGKTLLARALAGETDVNFIRVdgPEIIDRYVGESEKAIREVFERARQsapSIVFFDEIdaits 599
                                       567789*********************99999888444777777777777666665444331226888887643333 PP

                            DUF815 117 ....sFeeeeeeyksLksvLeGsleakpenvliyaTsNrRh 153
                                           + e +e+   +L + L+G  +++p+ v++ aT  + h
  gi|336254369|ref|YP_004597476.1| 600 argeGHEVTERVVSQLLTELDGM-RENPNLVVLAATNRKEH 639
                                       22222444455557788888874.44555555555544444 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 !   10.8   0.0   0.00054      0.19     117     139 ..     262     284 ..     258     286 .. 0.92
   2 !    7.3   0.0    0.0061       2.1     117     135 ..     529     547 ..     520     553 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00054
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakavp 139
                                       v++yGp+ tGkt +a+a a+ v+
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVD 284
                                       89****************99875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0061
                         Parvo_NS1 117 vwfyGpantGktnlaeaIa 135
                                       v+++Gp+ tGkt la+a+a
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALA 547
                                       899**************98 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0012      0.42       4      26 ..     262     285 ..     260     323 .. 0.78
   2 !    8.4   0.0    0.0031       1.1       4      25 ..     529     550 ..     527     604 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                           DUF2075   4 vlVtGvaGtGKtvvllnllael.e 26 
                                       vl  G +GtGKt+++ ++++e+  
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVdA 285
                                       5778****************9941 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0031
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       vl +G +GtGKt+++ +l+ e 
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAGET 550
                                       6789***********9999887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.02       7.2       3      24 ..     262     283 ..     260     287 .. 0.88
   2 !    9.8   0.1     0.002       0.7       3      21 ..     529     547 ..     527     552 .. 0.90
   3 ?   -0.2   0.0       2.3     8e+02      64     115 ..     569     618 ..     561     665 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.02
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       v+l G++G GKT  ++ +a + 
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEV 283
                                       799*************999875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.002
                                       EEEEC-TTTCHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqkla 21 
                                       v+l+G++G GKT L++ la
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALA 547
                                       79**************998 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.3
                                       S--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCT CS
                             NACHT  64 epaapvsevwavllelperlLlilDglDelvtdlgqkekqpvrtlLselirk 115
                                       e++++++ev++   + + ++   +D +D + +  g+ + + ++++ s+l+++
  gi|336254369|ref|YP_004597476.1| 569 ESEKAIREVFERARQSAPSI-VFFDEIDAITSARGE-GHEVTERVVSQLLTE 618
                                       67777788555444444444.458999999999888.444455555555544 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0022      0.79      22      42 ..     262     282 ..     258     291 .. 0.85
   2 !    8.8   0.0    0.0028      0.97      22      40 ..     529     547 ..     522     554 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0022
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v   Gp GtGKt++a a+a e
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANE 282
                                       5678***********999865 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0028
                                       EEEE--TTSSTTHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavala 40 
                                       v   Gp GtGKt+la ala
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALA 547
                                       5678***********9988 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 !    9.1   0.0    0.0038       1.3      23      49 ..     261     287 ..     255     334 .. 0.60
   2 !    9.3   0.0    0.0033       1.2      22      79 ..     527     595 ..     520     604 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0038
                                       -EEEEEETT--HHHHHHCC--TTS-EE CS
                   Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgpwl 49 
                                        v+l G++G+gk+l+Ar+ +++   + 
  gi|336254369|ref|YP_004597476.1| 261 GVLLYGPPGTGKTLIARAVANEVDANF 287
                                       69****************998755443 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0033
                                       S-EEEEEETT--HHHHHHCC--TTS....-EE--SSTTHHH....H-HHHHHHHT...TTSEEEEEE-T CS
                   Sigma54_activ_2  22 lpvfltGekGsgkelvArlLhknsg....pwleifvverla....klpldlleqa...kggtLylkdia 79 
                                       + v+l G++G+gk+l Ar+L+ +      +++ + +++r +    k+  +++e+a    + + ++ +i+
  gi|336254369|ref|YP_004597476.1| 527 SGVLLHGPPGTGKTLLARALAGETDvnfiRVDGPEIIDRYVgeseKAIREVFERArqsAPSIVFFDEID 595
                                       569*****************8654311114444444444442222233555555433355566666665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0013      0.44      23      53 ..     262     289 ..     251     304 .. 0.87
   2 !    7.1   0.0    0.0078       2.7      21      42 ..     527     548 ..     513     644 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                                       EEEEESTTSSHHHHHHHHCCSHCCCCCCBTE CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksdevegrFds 53 
                                       v l+G +G GKt +a+ + n+   v+ +F+ 
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANE---VDANFET 289
                                       679***************999...7778776 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0078
                                       EEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC  21 lvvalvGmgGvGKttlakqiln 42 
                                         v l+G +G GKt la+    
  gi|336254369|ref|YP_004597476.1| 527 SGVLLHGPPGTGKTLLARALAG 548
                                       3588************997655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0048       1.7      15      37 ..     255     277 ..     226     282 .. 0.76
   2 !    7.0   0.0    0.0093       3.3      22      37 ..     529     544 ..     515     552 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0048
                            ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                       G+   + vl++G pGtGKt++a 
  gi|336254369|ref|YP_004597476.1| 255 GVEPPSGVLLYGPPGTGKTLIAR 277
                                       56666779************985 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0093
                            ATPase  22 vlitGepGtGKtifal 37 
                                       vl+ G pGtGKt++a 
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLAR 544
                                       899**********986 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.5   5.1e+02      17      32 ..     262     277 ..     256     285 .. 0.84
   2 ?    5.8   0.0      0.03        11     106     170 ..     305     369 ..     281     374 .. 0.82
   3 ?    0.3   0.0       1.4   5.1e+02      17      31 ..     529     543 ..     522     550 .. 0.87
   4 ?    5.4   0.0     0.039        14      99     170 ..     564     636 ..     547     641 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.5
                                       EEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                              DEAD  17 vlvaaeTGsGKTlafl 32 
                                       vl+ ++ G+GKTl++ 
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIAR 277
                                       788999******9975 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.03
                                       HHHHHHHHCTSSHCTTEEEEEEETHHHHHHT..TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 106 grlddllstgklnlsqvrflVlDEadrlldq..gfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       +rl ++++t +   +  +++ +DE+d +  q  + +d  nri+ ql +  +   + ++viv+ AT  
  gi|336254369|ref|YP_004597476.1| 305 ERLREVFETAS--ANAPTIIFFDEIDSIAGQrdDDGDAENRIVGQLLTLMDGLDAREEVIVIGATNR 369
                                       67777777777..78888999**********9999999********666555557777******965 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.4
                                       EEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                              DEAD  17 vlvaaeTGsGKTlaf 31 
                                       vl++++ G+GKTl +
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLA 543
                                       8999********976 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.039
                                       SEEEEEHHHHHHHH.HCTSSHCTTEEEEEEETHHHHHHT..TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  99 divvgtpgrlddll.stgklnlsqvrflVlDEadrlldq..gfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       d +vg  ++ ++ + ++ +   s  +++ +DE+d + +   +  +  +r+++ql +  +  +++ +++vl AT  
  gi|336254369|ref|YP_004597476.1| 564 DRYVGESEKAIREVfERAR--QSAPSIVFFDEIDAITSArgEGHEVTERVVSQLLTELDGMRENPNLVVLAATNR 636
                                       5566666666664425444..78889999*********99767788899****976666666777899**99976 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0059       2.1       1      31 [.     265     297 ..     265     336 .. 0.79
   2 ?    4.9   0.0     0.095        33       2      24 ..     533     555 ..     532     682 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0059
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllr 31 
                                       +G+PG GK+ +++ ++ ++  +f+ +s  +++ 
  gi|336254369|ref|YP_004597476.1| 265 YGPPGTGKTLIARAVANEVdaNFETISGPEIMS 297
                                       7**************998766899999555554 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.095
                                       E-TTSSHHHHHHHHHHHHTEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthl 24 
                                       G+PG GK+ +++ l+ + ++ ++
  gi|336254369|ref|YP_004597476.1| 533 GPPGTGKTLLARALAGETDVNFI 555
                                       9***********99998877666 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0058         2      36      54 ..     262     280 ..     256     286 .. 0.86
   2 ?    1.8   0.1      0.42   1.5e+02     128     178 ..     305     354 ..     292     366 .. 0.75
   3 !    8.2   0.1    0.0048       1.7      36      54 ..     529     547 ..     526     551 .. 0.89
   4 ?    1.0   0.0      0.75   2.6e+02     128     184 ..     572     631 ..     557     635 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0058
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pgtGKt +a  +a
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVA 280
                                       69***********997665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.42
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdvgalvealeriarr 178
                                       + ++++ +++ + + +  + +D ++++ g   ++ ++++++v +l  + + 
  gi|336254369|ref|YP_004597476.1| 305 ERLREVFETASA-NAPTIIFFDEIDSIAGQRDDDGDAENRIVGQLLTLMDG 354
                                       456677788888.67************999777777778887777666554 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0048
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll G+pgtGKt la  la
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALA 547
                                       689***********98887 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.75
                            AAA_25 128 advdaleaaieevegvrlvviDplsralgg..densnsd..vgalvealeriarrtgaavl 184
                                        +++++ +++++   +  v +D +++++++  + ++ ++  v++l++ l+ ++++ +  vl
  gi|336254369|ref|YP_004597476.1| 572 KAIREVFERARQ-SAPSIVFFDEIDAITSArgEGHEVTErvVSQLLTELDGMRENPNLVVL 631
                                       567788888888.559999999999888774322222223247777777777776666665 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.12        41       1      20 [.     268     287 ..     268     310 .. 0.90
   2 !    9.1   0.0    0.0037       1.3       1      41 [.     535     580 ..     535     585 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.12
                                       TTSSHHHHHHHHHHHHTSEE CS
                               SKI   1 mGaGKstvGkllAkklglef 20 
                                       +G+GK+ +++++A++++ +f
  gi|336254369|ref|YP_004597476.1| 268 PGTGKTLIARAVANEVDANF 287
                                       69************998877 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0037
                                       TTSSHHHHHHHHHHHHTSEEEEHH..HHHHHHHT...S-HHHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlD..eliekrtg...ksiaeifee 41 
                                       +G+GK+ ++++lA + +++fi +D  e+i + +g   k i+e+fe+
  gi|336254369|ref|YP_004597476.1| 535 PGTGKTLLARALAGETDVNFIRVDgpEIIDRYVGeseKAIREVFER 580
                                       69******************98883357777777333557777765 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 ?    7.1   0.0     0.013       4.5      18      46 ..     257     284 ..     249     313 .. 0.79
   2 ?   -0.2   0.0       2.2   7.7e+02     105     161 ..     306     364 ..     287     368 .. 0.69
   3 ?    3.5   0.0      0.17        58      16      44 ..     522     550 ..     515     630 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienled 46 
                                       ep + +++YGp g GKt + + ++++  d
  gi|336254369|ref|YP_004597476.1| 257 EPPSGVLLYGPPGTGKTLIARAVANEV-D 284
                                       6777789**********8888887776.3 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.2
                          ATPase_2 105 aielllekikkkgkkiiiiiDelqklidlgln.....gaellvkeLlnliesltkekhlcvv 161
                                        + +++e  + ++   ii++De+  +   g +      ++  v +Ll+l++ l ++++++v+
  gi|336254369|ref|YP_004597476.1| 306 RLREVFETASANAP-TIIFFDEIDSIA--GQRdddgdAENRIVGQLLTLMDGLDAREEVIVI 364
                                       44555554444432.7999****9999..544456667788999999999998888887776 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.17
                          ATPase_2  16 erepneiyfiYGpegsGKtaLlkeiienl 44 
                                       ++ep + +++ Gp g GKt L + ++ + 
  gi|336254369|ref|YP_004597476.1| 522 NTEPPSGVLLHGPPGTGKTLLARALAGET 550
                                       67778888999999999999998876555 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.062        22      57      78 ..     254     275 ..     234     294 .. 0.85
   2 ?    7.9   0.0    0.0036       1.3      50      78 ..     516     542 ..     491     553 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.062
                       AFG1_ATPase  57 ksvepvrglYlwGgvGrGKtyl 78 
                                         vep+ g+ l+G+ G GKt +
  gi|336254369|ref|YP_004597476.1| 254 LGVEPPSGVLLYGPPGTGKTLI 275
                                       4689****************86 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0036
                       AFG1_ATPase  50 klfgrkrksvepvrglYlwGgvGrGKtyl 78 
                                       +lf   ++++ep+ g+ l+G+ G GKt l
  gi|336254369|ref|YP_004597476.1| 516 RLFE--ETNTEPPSGVLLHGPPGTGKTLL 542
                                       5565..57899****************88 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.035        12      32      58 ..     256     282 ..     248     297 .. 0.78
   2 ?   -1.0   0.0       2.9     1e+03     105     138 ..     304     336 ..     288     386 .. 0.63
   3 ?    3.8   0.0     0.095        33      26      54 ..     517     545 ..     512     555 .. 0.82
   4 ?   -0.3   0.0       1.7   6.1e+02     106     150 ..     572     616 ..     565     620 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.035
                              TniB  32 rkrmpnlllvGdsnnGKtmivekFarl 58 
                                        + ++ +ll+G++ +GKt i++  a++
  gi|336254369|ref|YP_004597476.1| 256 VEPPSGVLLYGPPGTGKTLIARAVANE 282
                                       5566789*************9987766 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.9
                              TniB 105 skleqqvlrllrelkvrvLiiDEihnllagsark 138
                                       ++  ++v ++ ++  + ++ +DEi+++  g++++
  gi|336254369|ref|YP_004597476.1| 304 EERLREVFETASANAPTIIFFDEIDSIA-GQRDD 336
                                       444455666666677889999**99987.55443 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.095
                              TniB  26 LleypkrkrmpnlllvGdsnnGKtmivek 54 
                                       L+e  + + ++ +ll+G++ +GKt +++ 
  gi|336254369|ref|YP_004597476.1| 517 LFEETNTEPPSGVLLHGPPGTGKTLLARA 545
                                       666667777789************99876 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.7
                              TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLg 150
                                       k+ ++v +  r+  + ++ +DEi+ + +++ +  + +  ++ +L 
  gi|336254369|ref|YP_004597476.1| 572 KAIREVFERARQSAPSIVFFDEIDAITSARGEGHEVTERVVSQLL 616
                                       5556777888999999*********99988887777666666655 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       8.4   2.9e+03     115     143 ..       8      37 ..       8      52 .. 0.79
   2 ?    4.0   0.0      0.11        40       4      30 ..     262     288 ..     260     316 .. 0.89
   3 ?    6.7   0.0     0.017       6.1       4      33 ..     529     558 ..     527     608 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8.4
                                       EEE--HHHHHHHHHHHTS.SSTTHHHHHTT CS
                               CPT 115 GvrcplevlerRelergd.RepGlaalqae 143
                                       Gv  ++  +e+R+++rg  R p la+ q+ 
  gi|336254369|ref|YP_004597476.1|   8 GVSLSVRAAEKRDAGRGVaRIPELARRQLG 37 
                                       8889999999****9996677777776654 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.11
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwl 30 
                                       +lL G + +GK+ +ara+ + +d+ + 
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVDANFE 288
                                       89****************999998875 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.017
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                       +lL+G + +GK+ laral   +d  ++ + 
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAGETDVNFIRVD 558
                                       89****************999999888775 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.025       8.6       4      26 ..     265     287 ..     262     292 .. 0.88
   2 ?    5.6   0.0     0.034        12       3      27 ..     531     555 ..     529     558 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.025
                                       E-STTSSHHHHHHHHHHHHT-EE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglky 26 
                                        GP g+GK  +ara+a+++++++
  gi|336254369|ref|YP_004597476.1| 265 YGPPGTGKTLIARAVANEVDANF 287
                                       6****************998875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.034
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP g+GK  +arala + +++++
  gi|336254369|ref|YP_004597476.1| 531 LHGPPGTGKTLLARALAGETDVNFI 555
                                       68***************99998887 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.025       8.6       2      26 ..     262     286 ..     261     327 .. 0.85
   2 ?    4.6   0.0     0.081        28       2      32 ..     529     559 ..     528     575 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.025
                                       EEEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss 26 
                                       v++ GppG+GKt + + v+++++ +
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVDAN 286
                                       6788***************999655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.081
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt l + ++ + + + ++v+G
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAGETDVNFIRVDG 559
                                       6789**********99999888777777777 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 ?    4.1   0.0     0.093        33       5      71 ..     266     327 ..     262     333 .. 0.65
   2 ?    6.6   0.0     0.016       5.8       2      71 ..     530     594 ..     529     600 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.093
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+ + r ++++   ++ +++   e+ ++ k +++ +  + v +  +a+ +     i+++DE+
  gi|336254369|ref|YP_004597476.1| 266 GPPGTGKTLIARAVANEVdANFETISG-PEIMSKYKGESEERLRE-VFETASANAP----TIIFFDEI 327
                                       78*************996666666655.56666665444444333.3333333333....49999997 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.016
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       + hG pG GK+ l r l+ +     ++v+ p  e++ + + ++++   + ++ + +++       i+++DE+
  gi|336254369|ref|YP_004597476.1| 530 LLHGPPGTGKTLLARALAGETdvNFIRVDGP--EIIDRYVGESEKAIREVFERARQSA-----PSIVFFDEI 594
                                       68****************9977544445555..4444444444444444444444433.....358888887 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.19        66      58      77 ..     264     283 ..     256     289 .. 0.87
   2 ?    6.9   0.0     0.018       6.4      49      76 ..     522     549 ..     515     567 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.19
                                       EEE-TTSSHHHHHHHHHHHH CS
                            Torsin  58 fhGwtGtGknfvaeiiaenl 77 
                                       ++G +GtGk  +a+ +a+++
  gi|336254369|ref|YP_004597476.1| 264 LYGPPGTGKTLIARAVANEV 283
                                       789*************9975 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.018
                                       S-SS-EEEEEEE-TTSSHHHHHHHHHHH CS
                            Torsin  49 kpkkpLvlsfhGwtGtGknfvaeiiaen 76 
                                       +++ p  + +hG +GtGk  +a+ +a +
  gi|336254369|ref|YP_004597476.1| 522 NTEPPSGVLLHGPPGTGKTLLARALAGE 549
                                       5556667789*************99865 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.018       6.5       4      61 ..     263     325 ..     260     338 .. 0.80
   2 ?    2.0   0.0      0.39   1.4e+02       4      18 ..     530     544 ..     528     599 .. 0.58
   3 ?    0.5   0.0       1.2   4.1e+02      57     107 ..     562     611 ..     547     635 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.018
                               Zot   4 lvtGapGsgKts..gavkkdllpalk..egRkiitnidGlrlerieqvlgekvs.tarlirid 61 
                                       l +G+pG+gKt+  +av +++       +g +i+ + +G   er++ v++++   ++ +i+ d
  gi|336254369|ref|YP_004597476.1| 263 LLYGPPGTGKTLiaRAVANEVDANFEtiSGPEIMSKYKGESEERLREVFETASAnAPTIIFFD 325
                                       789********733689998877555347**********99****999999888788899877 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.39
                               Zot   4 lvtGapGsgKtsgav 18 
                                       l +G+pG+gKt+ a 
  gi|336254369|ref|YP_004597476.1| 530 LLHGPPGTGKTLLAR 544
                                       77999*****98763 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.2
                               Zot  57 liridnpegaetlkefakwatidkgallviDEcqeifpvrakegrkdpevi 107
                                       +i+    e+++ + e++ +a+    +++++DE   i ++r + g+++ e++
  gi|336254369|ref|YP_004597476.1| 562 IIDRYVGESEKAIREVFERARQSAPSIVFFDEIDAITSARGE-GHEVTERV 611
                                       55544668888899999999988999*******999888877.66665554 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 ?    3.0   0.0      0.32   1.1e+02       2      30 ..     262     290 ..     261     316 .. 0.87
   2 ?    7.4   0.0     0.013       4.7       2      31 ..     529     558 ..     528     572 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.32
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       +++ G+P +GKt +a ++a + +a + ti
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVDANFETI 290
                                       5789***************9999877666 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.013
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAlltiD 31 
                                       +++hG+P +GKt  a +La + +  ++ +D
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAGETDVNFIRVD 558
                                       689****************99999999888 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.019       6.7      48     112 ..     262     327 ..     254     341 .. 0.83
   2 ?    3.7   0.0      0.15        51      48      76 ..     529     557 ..     514     601 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.019
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqiesfkel 112
                                       +L+ GP+G gk+ + + ++ e   +++  + p  + + +   ++ ++ ++e+ s   + i  f e+
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVDANFETISGPEIMSKYKGeSEERLREVFETASANAPTIIFFDEI 327
                                       5899******************99999999887765544436777899999999999999999887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.15
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrew 76 
                                       +L+ GP+G gk+   + L+ e  ++++  
  gi|336254369|ref|YP_004597476.1| 529 VLLHGPPGTGKTLLARALAGETDVNFIRV 557
                                       6899************9999988777665 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 ?    4.4   0.0     0.093        33      27      51 ..     262     286 ..     235     343 .. 0.89
   2 ?    4.8   0.0      0.07        25      22      45 ..     524     547 ..     498     596 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.093
                                       EEEEESTTSTHHHHHHHHHHHH-S. CS
                            ResIII  27 glikmaTGtGKTlvaaklierllkk 51 
                                       +l+  + GtGKTl+a +++ ++  +
  gi|336254369|ref|YP_004597476.1| 262 VLLYGPPGTGKTLIARAVANEVDAN 286
                                       6677889********9988877665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.07
                                       .TTSEEEEEESTTSTHHHHHHHHH CS
                            ResIII  22 krdkrglikmaTGtGKTlvaakli 45 
                                       +    +l++ + GtGKTl+a +l+
  gi|336254369|ref|YP_004597476.1| 524 EPPSGVLLHGPPGTGKTLLARALA 547
                                       44557899**********997776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (745 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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):              51  [number of targets reported over threshold]
# CPU time: 0.79u 0.27s 00:00:01.06 Elapsed: 00:00:00.42
# Mc/sec: 5297.94
//
Query:       gi|336254370|ref|YP_004597477.1|  [L=44]
Description: hypothetical protein Halxa_2982 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.029   14.2   3.7      0.051   13.4   3.7    1.5  1  zf-C2H2_3  zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.7   2.9e-06     0.051      14      39 ..      13      36 ..       3      37 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-06
                         zf-C2H2_3 14 sqCkeCgMvYnpgspeDeklHkkfHa 39
                                       +C +Cg+++  ++++D+  H+k+++
  gi|336254370|ref|YP_004597477.1| 13 YECETCGLLF--DEKSDATEHEKHCD 36
                                      45******99..6789*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 343.35
//
Query:       gi|336254371|ref|YP_004597478.1|  [L=81]
Description: hypothetical protein Halxa_2983 [Halopiger xanaduensis SH-6]
Scores for 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  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 660.82
//
Query:       gi|336254372|ref|YP_004597479.1|  [L=164]
Description: hypothetical protein Halxa_2984 [Halopiger xanaduensis SH-6]
Scores for 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  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1217.97
//
Query:       gi|336254373|ref|YP_004597480.1|  [L=290]
Description: Shikimate kinase [Halopiger xanaduensis SH-6]
Scores for 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   43.9   1.7    2.1e-11   43.9   1.7    1.9  2  GHMP_kinases_N  GHMP kinases N terminal domain
     0.0014   18.9   0.0     0.0038   17.6   0.0    1.8  1  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 ?   -2.0   0.1       0.5   4.5e+03      21      41 ..      14      37 ..      10      47 .. 0.61
   2 !   43.9   1.7   2.3e-15   2.1e-11       2      66 .]      84     154 ..      83     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.5
                                      HHHHHHHHHHHTTEHHHH...HHH CS
                    GHMP_kinases_N 21 avalvaAllallglslee...akl 41
                                        al++ + +++ ++le+   ++l
  gi|336254373|ref|YP_004597480.1| 14 LNALATGVGSAFAIDLETtasVEL 37
                                      566777777777655544444555 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 2.3e-15
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEH..HHH...HHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallgls..lee...aklaleaerlaqggngsggDv.aasvyGg 66 
                                       ++++se+P+++GL SS+A+a a+v+A l++l++   +e     +l+++a r a++++++ +D+ +as++Gg
  gi|336254373|ref|YP_004597480.1|  84 VRTESEVPMASGLKSSSAAANATVLATLDALEIAesVERveaCRLGVRAARDAGVTVTGAFDDaSASMLGG 154
                                       7899***************************74432222455********************999999998 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 !   17.6   0.0   4.3e-07    0.0038      38      80 ..     234     271 ..     203     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.3e-07
                    GHMP_kinases_C  38 ellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralr 80 
                                        +++al  +++ g++lsG+  Gp+ +a++ d+d  e v+++++
  gi|336254373|ref|YP_004597480.1| 234 PMIDAL--PDVAGVSLSGT--GPSYVAVG-DEDTLETVQERWA 271
                                       677888..66779******..********.***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2275.67
//
Query:       gi|336254374|ref|YP_004597481.1|  [L=126]
Description: chorismate mutase [Halopiger xanaduensis SH-6]
Scores for 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-16   59.9   4.5    2.8e-16   59.6   4.5    1.1  1  CM_2             Chorismate mutase type II
  ------ inclusion threshold ------
       0.02   15.3   0.9      0.035   14.5   0.9    1.4  1  GPS2_interact    G-protein pathway suppressor 2-interacting d
      0.044   14.7   0.3      0.075   14.0   0.3    1.3  1  tRNA_synt_1c_R2  Glutaminyl-tRNA synthetase, non-specific RNA


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 !   59.6   4.5   4.7e-20   2.8e-16       1      71 [.      34     108 ..      34     112 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 4.7e-20
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHHHH....S-HHHHHHHHHHHHHHHH CS
                              CM_2   1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerleega....ldeeaierifreiisasr 71 
                                       R+eI  iD+ei+eL+a+R  +a+ ++++K+e+glp  d+++e++v+er  e+a    +d++ +++ifr +i+  +
  gi|336254374|ref|YP_004597481.1|  34 REEIQTIDREIVELIAQRTYVADTIAQVKEEQGLPTTDEKQEQQVMERAGENAeqfdVDANLVKAIFRLLIELNK 108
                                       99*************************************************77788899************9766 PP

>> GPS2_interact  G-protein pathway suppressor 2-interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.9   5.8e-06     0.035      17      77 ..      19      78 ..      10      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.8e-06
                     GPS2_interact 17 eqeqelvpsrlsKdeLlqnidkvDREiakveqqiskLkkkqkeleeeaakpkeeekpveps 77
                                      e+e   +p  +s deL ++i+ +DREi     q         +++ee   p++ ek++++ 
  gi|336254374|ref|YP_004597481.1| 19 ESE-PRTPDEMSLDELREEIQTIDREIVELIAQRTYVADTIAQVKEEQGLPTTDEKQEQQV 78
                                      333.4568999******************99999999999999999999998777766654 PP

>> tRNA_synt_1c_R2  Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   1.3e-05     0.075       4      78 ..      39     114 ..      37     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                   tRNA_synt_1c_R2   4 evDaqllelLGPKte.aDnlkpkkkkkkkkkkkeekkkaakkakkekeeeesegaetieelegellkfHkpgeNfk 78 
                                        +D +++el+  +t  aD+++++k+++  ++++e++++++ +++ e++e+ + +a+ ++ + + l+++ k + N++
  gi|336254374|ref|YP_004597481.1|  39 TIDREIVELIAQRTYvADTIAQVKEEQGLPTTDEKQEQQVMERAGENAEQFDVDANLVKAIFRLLIELNKIEQNHH 114
                                       79***********9559*********999********999999999999988999999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1432  (0.0798706); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 960.95
//
Query:       gi|336254375|ref|YP_004597482.1|  [L=119]
Description: HxlR family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-14   52.8   0.0    3.1e-14   52.6   0.0    1.1  1  HxlR      HxlR-like helix-turn-helix
    3.3e-06   27.0   0.1    5.1e-06   26.5   0.1    1.3  1  HTH_20    Helix-turn-helix domain
    4.7e-06   26.4   0.0    7.9e-06   25.7   0.0    1.4  1  MarR      MarR family
    2.4e-05   24.1   0.0    3.5e-05   23.6   0.0    1.2  1  MarR_2    MarR family
    0.00011   22.0   0.1    0.00018   21.2   0.1    1.4  1  HTH_IclR  IclR helix-turn-helix domain
    0.00015   21.3   0.0    0.00022   20.7   0.0    1.3  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
       0.06   13.2   0.0      0.085   12.7   0.0    1.3  1  HTH_5     Bacterial regulatory protein, arsR family
      0.061   12.9   0.0      0.077   12.6   0.0    1.1  1  MAGSP     Male accessory gland secretory protein
      0.096   12.7   0.1       0.15   12.0   0.1    1.3  1  HTH_11    HTH domain
       0.12   12.2   0.1       0.19   11.5   0.1    1.3  1  HTH_DeoR  DeoR-like helix-turn-helix domain
       0.12   12.6   0.0       0.15   12.2   0.0    1.2  1  HTH_34    Winged helix DNA-binding domain
       0.16   11.9   0.0       0.25   11.3   0.0    1.3  1  HTH_36    Helix-turn-helix domain


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 !   52.6   0.0   2.1e-17   3.1e-14       2      88 ..      25     113 ..      24     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2.1e-17
                                       HHSTTHHHHHHHHTT...S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHH CS
                              HxlR   2 iggkWkllilvellk...gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepv 75 
                                       +g+  +l il e+++    + Rf+el++ l ++s ++L++rL eL + g++er+ y+e+Pp+veY+ te+ ++l+pv
  gi|336254375|ref|YP_004597482.1|  25 LGKAHTLAILNEIVTtdkQSIRFGELQDSL-ELSPNTLSRRLDELVEVGFLERTQYDEIPPRVEYEETEMVNDLTPV 100
                                       666677788888776322556*********.9********************************************* PP

                                       HHHHHHHHHHHHH CS
                              HxlR  76 lqelkkwgeeyle 88 
                                       +  l+ w e++ +
  gi|336254375|ref|YP_004597482.1| 101 FRGLEIWMERHGS 113
                                       ********99875 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   3.4e-09   5.1e-06       4      57 ..      22      77 ..      19      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.4e-09
                                      HHHHS-HHHHHHHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  4 aeALahPvRrrilraL..araegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +++L+    ++il ++  ++++   ++el + l+ls+ntls++L++L+e+g++e++
  gi|336254375|ref|YP_004597482.1| 22 FSLLGKAHTLAILNEIvtTDKQSIRFGELQDSLELSPNTLSRRLDELVEVGFLERT 77
                                      55566666677777777788888889****************************86 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   5.3e-09   7.9e-06      15      51 ..      42      78 ..      27      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.3e-09
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      +++++  eL++ l++s+ t++r ld+L++ G++eR++
  gi|336254375|ref|YP_004597482.1| 42 KQSIRFGELQDSLELSPNTLSRRLDELVEVGFLERTQ 78
                                      4567777****************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.4e-08   3.5e-05       9      55 ..      32      78 ..      27      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.4e-08
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                       +L+++   + + ++ gel + l ls+ ++sr+l++Lv+ G++er+ 
  gi|336254375|ref|YP_004597482.1| 32 AILNEIVTTDKQSIRFGELQDSLELSPNTLSRRLDELVEVGFLERTQ 78
                                      6999******9999******************************984 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 !   21.2   0.1   1.2e-07   0.00018       6      50 ..      31      76 ..      28      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.2e-07
                                      HHHHC.T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  6 laiLd.alaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      laiL+ ++++  q  ++ el + + l++ t +R L  Lve G++e+
  gi|336254375|ref|YP_004597482.1| 31 LAILNeIVTTDKQSIRFGELQDSLELSPNTLSRRLDELVEVGFLER 76
                                      666651455566667*****************************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 !   20.7   0.0   1.5e-07   0.00022       6      47 ..      31      74 ..      28      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-07
                            HTH_24  6 rkILelLqk..nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++IL+++    + +i   eL + l lSp+t++rrl++L+e G++
  gi|336254375|ref|YP_004597482.1| 31 LAILNEIVTtdKQSIRFGELQDSLELSPNTLSRRLDELVEVGFL 74
                                      77888888777888999**********************98876 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 ?   12.7   0.0   5.7e-05     0.085      16      46 ..      45      75 ..      31      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.7e-05
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 16 lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                        ++el + l+ls+ t+S+ L  L e G++e
  gi|336254375|ref|YP_004597482.1| 45 IRFGELQDSLELSPNTLSRRLDELVEVGFLE 75
                                      5689************************986 PP

>> MAGSP  Male accessory gland secretory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.1e-05     0.077     140     186 ..      23      69 ..      17      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.1e-05
                             MAGSP 140 slllrnhsvslmkeiearktdiikvrqlnldlelelealkrklleln 186
                                       sll + h++ +++ei +   + i+  +l+  lel  ++l r+l el 
  gi|336254375|ref|YP_004597482.1|  23 SLLGKAHTLAILNEIVTTDKQSIRFGELQDSLELSPNTLSRRLDELV 69 
                                       78899**************************************9985 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   9.9e-05      0.15       3      43 ..      31      72 ..      29      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.9e-05
                            HTH_11  3 lqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      l+il  +  ++++ i   eL + L++S  t  r++++L e g
  gi|336254375|ref|YP_004597482.1| 31 LAILNEIVTTDKQsIRFGELQDSLELSPNTLSRRLDELVEVG 72
                                      67899999999999***********************98877 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 ?   11.5   0.1   0.00013      0.19      11      47 ..      41      77 ..      32      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                          HTH_DeoR 11 qqgklsveelvellgvSeaTiRRDLneLeeqglltRt 47
                                      ++++++  el + l+ S++T  R L+eL+e g l+Rt
  gi|336254375|ref|YP_004597482.1| 41 DKQSIRFGELQDSLELSPNTLSRRLDELVEVGFLERT 77
                                      57889999***************************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 ?   12.2   0.0    0.0001      0.15       5      47 ..      33      77 ..      30      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                            HTH_34  5 vlsyLas..vdeadfvelkealeatdgnLsvhlkkLekagYievd 47
                                      +l   ++  ++++ f el+++le++   Ls  l+ L + g++e++
  gi|336254375|ref|YP_004597482.1| 33 ILNEIVTtdKQSIRFGELQDSLELSPNTLSRRLDELVEVGFLERT 77
                                      55544443467899***************************9976 PP

>> HTH_36  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      0.25      30      55 .]      49      74 ..      40      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                            HTH_36 30 tlakrlglsknTvsraikeLeqlGyi 55
                                       l+  l+ls nT sr ++eL++ G++
  gi|336254375|ref|YP_004597482.1| 49 ELQDSLELSPNTLSRRLDELVEVGFL 74
                                      688999****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 903.81
//
Query:       gi|336254376|ref|YP_004597483.1|  [L=258]
Description: NADP oxidoreductase coenzyme F420-dependent [Halopiger xanaduensis SH-6]
Scores for 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-17   61.6   0.1    1.8e-16   60.5   0.1    1.6  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
    2.3e-11   43.3   0.1    5.2e-11   42.2   0.1    1.6  1  HTH_10         HTH DNA binding domain
    0.00062   20.0   0.0     0.0013   18.9   0.0    1.6  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
     0.0011   18.8   0.1      0.016   15.0   0.1    2.4  2  HTH_5          Bacterial regulatory protein, arsR family
     0.0053   16.8   0.1       0.11   12.6   0.1    2.4  1  HTH_3          Helix-turn-helix
     0.0074   15.9   0.1      0.012   15.2   0.1    1.3  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.039   14.0   0.1    1.9  1  HTH_20         Helix-turn-helix domain
      0.025   14.5   0.1      0.052   13.4   0.1    1.6  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.036   14.1   0.0      0.063   13.3   0.0    1.4  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
      0.038   14.1   0.5      0.089   12.9   0.1    1.8  2  Sigma70_r3     Sigma-70 region 3
      0.046   13.3   0.1       0.11   12.1   0.1    1.6  1  Sigma70_r4     Sigma-70, region 4
      0.073   13.0   0.1        0.7    9.8   0.1    2.5  1  MarR_2         MarR family
       0.12   12.3   0.0       0.39   10.7   0.0    1.9  2  HTH_11         HTH domain
       0.17   11.5   0.0       0.32   10.6   0.0    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.17   12.5   0.0        1.5    9.5   0.1    2.2  3  Mga            Mga helix-turn-helix domain
        0.2   12.1   0.2       0.78   10.2   0.2    2.0  1  NAD_binding_7  Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.1   1.6e-19   1.8e-16       5      96 ..       2      86 ..       1      87 [. 0.98

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 1.6e-19
                                      ETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGH CS
                     F420_oxidored  5 iGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlselak 83
                                      iGaGn+g++ a+++++ag   he+++ nsr pe+++ l ++lg ++ a++ +eaa+  +vv  a+++++++++ ++   
  gi|336254376|ref|YP_004597483.1|  2 IGAGNVGSTAAQNFVEAG---HEVMISNSRGPETLTDLVDDLGSNAHAGTVSEAADFGEVVMEAIPFNAYKSLPADT-- 75
                                      9*****************...*****************************************************999.. PP

                                      HHHTTSEEEEESS CS
                     F420_oxidored 84 dalkgklvisvla 96
                                        l +k+vis+++
  gi|336254376|ref|YP_004597483.1| 76 --LGDKIVISASN 86
                                      ..********998 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.1   4.7e-14   5.2e-11       7      52 ..     203     248 ..     200     249 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 4.7e-14
                            HTH_10   7 evlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       ++  +Aye+GY+  + +vt++eLA+el+ s+ +lsehLr+ +++li
  gi|336254376|ref|YP_004597483.1| 203 KATVAAYENGYYSPSQEVTIQELADELDMSEESLSEHLRRGTEQLI 248
                                       66679***********************************999998 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 !   18.9   0.0   1.2e-06    0.0013       4      63 ..       1      63 [.       1      91 [. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                                      EE--SHHHHHHHHHHHHTT-EEEEE-.SSHHHHHHHHHTT..EEE-SSHHHHHHHCSEEEE-S CS
                     NAD_binding_2  4 fiGlGvMGsnmalnllkagykvavyn.rtkekveelvaeg..akaaesieelvasldvvitmv 63
                                      +iG G+ Gs  a+n+++ag++v++ n r +e +++lv++      a +++e+++  +vv+  +
  gi|336254376|ref|YP_004597483.1|  1 MIGAGNVGSTAAQNFVEAGHEVMISNsRGPETLTDLVDDLgsNAHAGTVSEAADFGEVVMEAI 63
                                      7*************************8889999****99545445555666665556666555 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 ?    0.7   0.0      0.43   4.8e+02      12      26 ..      27      41 ..      23      50 .. 0.87
   2 !   15.0   0.1   1.4e-05     0.016      14      37 ..     218     241 ..     216     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.43
                                      TTSSEEHHHHHHHHT CS
                             HTH_5 12 aegelcvcelaeelg 26
                                      ++g+ + ++l+++lg
  gi|336254376|ref|YP_004597483.1| 27 SRGPETLTDLVDDLG 41
                                      469*********998 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.4e-05
                                       SSEEHHHHHHHHTS-HHHHHHHHH CS
                             HTH_5  14 gelcvcelaeelglsqstvShHLk 37 
                                       +e ++ ela+el++s+  +S+HL+
  gi|336254376|ref|YP_004597483.1| 218 QEVTIQELADELDMSEESLSEHLR 241
                                       67799******************9 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   9.5e-05      0.11      23      51 ..     203     232 ..     203     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.5e-05
                                       HHHHHHHHTTSSCSBHH.HHHHHHHHHTSE CS
                             HTH_3  23 rstisriEnGernPsle.tlkklakaLgvs 51 
                                       ++t++++EnG+ +Ps+e t+++la+ L+ s
  gi|336254376|ref|YP_004597483.1| 203 KATVAAYENGYYSPSQEvTIQELADELDMS 232
                                       579*************94577777777665 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 !   15.2   0.1   1.1e-05     0.012      10      76 ..       2      71 ..       1      85 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                                      ES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHT...T-EEEEHHHHHHT-SEEEE-S-HHHHHHH CS
                              IlvN 10 iGyGsqGhaqalnlrdsgldvvvglregsksvkkAkee...gfevltvaeavkkadvvmiliPDelqkev 76
                                      iG G+ G + a+n+ ++g +v++++ +g ++++   ++   + +  tv+ea++  +vvm  iP ++ k++
  gi|336254376|ref|YP_004597483.1|  2 IGAGNVGSTAAQNFVEAGHEVMISNSRGPETLTDLVDDlgsNAHAGTVSEAADFGEVVMEAIPFNAYKSL 71
                                      9**************************99876655443211456789****************8877766 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.5e-05     0.039      19      46 ..     205     241 ..     189     242 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                                       H.........STCTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  19 L.........araegltaselaerldlskntlsyHLr 46 
                                                 ++ +++t  ela++ld+s  +ls HLr
  gi|336254376|ref|YP_004597483.1| 205 TvaayengyySPSQEVTIQELADELDMSEESLSEHLR 241
                                       455555555567789*********************8 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 ?   13.4   0.1   4.6e-05     0.052       5      36 ..       2      34 ..       1      68 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.6e-05
                                      E--SCCHHHHHHHHHHTT-EEEEE-S.-HHHHH CS
                           3HCDH_N  5 iGaGtmGagiaavfasagleVvlvdi.seeale 36
                                      iGaG +G+  a+ f++ag+eV + +   +e+l+
  gi|336254376|ref|YP_004597483.1|  2 IGAGNVGSTAAQNFVEAGHEVMISNSrGPETLT 34
                                      9********************997652345555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.6e-05     0.063      17      67 ..       1      50 [.       1      63 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.6e-05
                                      EES-SHHHHHHHHHHHCCT-CEEEEEE.SSHHHHHHHHHHHT.ET-EEEEGC CS
                      Shikimate_DH 17 liGaGemaelvakhLlakgvkkvvvaN.Rtlerakelaeelkgeeiealkle 67
                                      +iGaG++++ +a++++++g + v++ N R  e   +l+++l+++ ++a +++
  gi|336254376|ref|YP_004597483.1|  1 MIGAGNVGSTAAQNFVEAGHE-VMISNsRGPETLTDLVDDLGSN-AHAGTVS 50
                                      59*****************99.6666659**********99665.5555544 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.6   9.6e+03      53      69 ..      96     112 ..      95     118 .. 0.62
   2 ?   12.9   0.1   7.9e-05     0.089      20      46 ..     219     245 ..     217     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.6
                                       BSSSSTTXBSTTTXBXS CS
                        Sigma70_r3  53 pvgeeedtelgdlledd 69 
                                       +vg++  +   d led+
  gi|336254376|ref|YP_004597483.1|  96 DVGKTHTDLVADHLEDS 112
                                       66666666666666666 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.9e-05
                                       XXXHHHHHHHHTXXHHHHHHHHHHHXX CS
                        Sigma70_r3  20 ePtpeEiAeeLglseekVrevleaare 46 
                                       e t++E+A+eL++see + e l+   e
  gi|336254376|ref|YP_004597483.1| 219 EVTIQELADELDMSEESLSEHLRRGTE 245
                                       679***************999988765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   9.7e-05      0.11      19      48 ..     218     247 ..     212     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.7e-05
                                       TT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  19 eglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       ++ T +E++++l++S+e  + +++r+ ++L
  gi|336254376|ref|YP_004597483.1| 218 QEVTIQELADELDMSEESLSEHLRRGTEQL 247
                                       789*****************9999998776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00062       0.7      18      44 ..     216     242 ..     162     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00062
                                       TTSEEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2  18 pgrdltvgelarrlglsksavsrilkr 44 
                                       p +++t++ela++l++s  ++s +l+r
  gi|336254376|ref|YP_004597483.1| 216 PSQEVTIQELADELDMSEESLSEHLRR 242
                                       44489******************9998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       8.9   9.9e+03      16      28 ..      71      83 ..      67      84 .. 0.77
   2 ?   10.7   0.0   0.00035      0.39      15      33 ..     218     237 ..     214     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.9
                            HTH_11 16 isgeeLAeeLnvS 28
                                      +++++L +++ +S
  gi|336254376|ref|YP_004597483.1| 71 LPADTLGDKIVIS 83
                                      7889999988776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00035
                            HTH_11  15 p.isgeeLAeeLnvSrrtvr 33 
                                       + ++++eLA+eL++S+    
  gi|336254376|ref|YP_004597483.1| 218 QeVTIQELADELDMSEESLS 237
                                       44*************97665 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 ?   10.6   0.0   0.00029      0.32      18      40 ..     220     242 ..     218     242 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                            HTH_24  18 isqreLAerlglSpstvnrrlkr 40 
                                        +++eLA++l++S   ++++l+r
  gi|336254376|ref|YP_004597483.1| 220 VTIQELADELDMSEESLSEHLRR 242
                                       699******************98 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       6.7   7.6e+03      30      46 ..      12      28 ..      10      40 .. 0.77
   2 ?   -0.9   0.0       2.2   2.5e+03      31      52 ..      71      92 ..      65      97 .. 0.78
   3 ?    9.5   0.1    0.0013       1.5      29      59 ..     218     248 ..     214     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.7
                                      EEEHHHHHHHCT--HHH CS
                               Mga 30 evsieelaqelyiSest 46
                                       +++ e   e++iS+s 
  gi|336254376|ref|YP_004597483.1| 12 AQNFVEAGHEVMISNSR 28
                                      57788888999999985 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.2
                                      EEHHHHHHHCT--HHHHHHHHH CS
                               Mga 31 vsieelaqelyiSestlkrkik 52
                                      +    l ++ +iS s+++   +
  gi|336254376|ref|YP_004597483.1| 71 LPADTLGDKIVISASNYYPGRD 92
                                      56778999*******9997655 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0013
                                       SEEEHHHHHHHCT--HHHHHHHHHHHHHHCH CS
                               Mga  29 eevsieelaqelyiSestlkrkikelnklLk 59 
                                       +ev+i+ela+el +Se +l  ++++  + L 
  gi|336254376|ref|YP_004597483.1| 218 QEVTIQELADELDMSEESLSEHLRRGTEQLI 248
                                       789*****************99987665554 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 ?   10.2   0.2    0.0007      0.78      13      75 ..       2     152 ..       1     164 [. 0.58

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0007
                     NAD_binding_7  13 vGgGevAarkvrklleagakvtvvapevkeeleelvk....laeee............................... 54 
                                       +G+G+v+ + +++++eag +v +   +  e l +lv+                                        
  gi|336254376|ref|YP_004597483.1|   2 IGAGNVGSTAAQNFVEAGHEVMISNSRGPETLTDLVDdlgsN---Ahagtvseaadfgevvmeaipfnaykslpadt 75 
                                       8********************997666433333333321110...12333344444455555555555555555555 PP

                     NAD_binding_7  55 ........................................................lekdlegadlviaatddreln 75 
                                                                                               le+d ++ + +++a dd+e +
  gi|336254376|ref|YP_004597483.1|  76 lgdkivisasnyypgrdgltdvgkthtdlvadhledsrvvkafnsiywenlrdgqrLEADPDDRFAIFIAGDDDEAK 152
                                       55555555555566666666666666666666666666666666666666555555566666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 1915.32
//
Query:       gi|336254377|ref|YP_004597484.1|  [L=130]
Description: PilT protein domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   51.6   0.1    1.4e-13   51.4   0.1    1.0  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 !   51.4   0.1   7.9e-18   1.4e-13       3     121 ..       3     124 ..       1     125 [. 0.96

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 7.9e-18
                                       E-HHHHHHHHTTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHH CS
                               PIN   3 lDTsvliallrgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeia 78 
                                        DTs++i+llrg+e+a+++++++e+      ++++++ El+ ++ar   ++  ++++++ l+ l+   +++ d  + 
  gi|336254377|ref|YP_004597484.1|   3 QDTSFIIDLLRGDENAKRLLDIVEKEsRPQKVPSVTVLELYEGVAR---SQVPETKRERILDVLETKHVVSADQTVM 76 
                                       5*************************99999***************...**************************** PP

                                       HHHHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTH.HHHHHH CS
                               PIN  79 eeaaeialkyg.....llpnDaliaAtAkehgikliatfDed.frrvak 121
                                       ++a++++ ++      l   D++iaAtA+ ++ ++i t++++ f+rv+ 
  gi|336254377|ref|YP_004597484.1|  77 RKAGKLSGELInggkqLEREDCIIAATALLNDEPII-TRNTEhFNRVDD 124
                                       *********9999***********************.999888999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 974.66
//
Query:       gi|336254378|ref|YP_004597485.1|  [L=86]
Description: hypothetical protein Halxa_2990 [Halopiger xanaduensis SH-6]
Scores for 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-20   72.8   3.9    4.1e-20   72.3   3.9    1.2  1  VAPB_antitox  Putative antitoxin
  ------ inclusion threshold ------
      0.099   12.7   1.0         11    6.1   0.2    2.3  2  TraY          TraY domain
          4    7.5  10.4       0.27   11.2   0.5    2.9  3  RHH_1         Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   3.9   6.8e-24   4.1e-20       1      69 []       4      66 ..       4      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 6.8e-24
                      VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgilseeeadeiekaskelrkefk 69
                                      KtIs+++e+Ye+Lk++K+egeSFs++++rL+++++      + e++gilseeea  +e+a++e r++++
  gi|336254378|ref|YP_004597485.1|  4 KTISLDEEAYERLKARKKEGESFSETVKRLAGERS------WNEVAGILSEEEASDLESAIEEGRTRSR 66
                                      9*****************************99777......************************9875 PP

>> TraY  TraY domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0036        22       2      18 ..       5      21 ..       5      23 .. 0.87
   2 ?    6.1   0.2    0.0018        11       7      37 ..      48      77 ..      44      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0036
                              TraY  2 tlkLdeetnklLeasae 18
                                      t+ Ldee++++L+a ++
  gi|336254378|ref|YP_004597485.1|  5 TISLDEEAYERLKARKK 21
                                      678*********99886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0018
                              TraY  7 eetnklLeasaersgRSKrkEAqlRLkdHLk 37
                                      ee    Le ++e+ gR+++ E + RL++ L+
  gi|336254378|ref|YP_004597485.1| 48 EEEASDLESAIEE-GRTRSRERSDRLTAELD 77
                                      5555556666665.*************9997 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 ?   11.2   0.5   4.5e-05      0.27       3      23 ..       5      24 ..       5      37 .. 0.78
   2 ?    1.4   1.0     0.056   3.4e+02       6      25 ..      46      66 ..      46      67 .. 0.74
   3 ?   -1.0   0.1      0.32   1.9e+03       2       8 ..      72      78 ..      70      80 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.5e-05
                                      EEEEEHHHHHHHHHHHHHHTS CS
                             RHH_1  3 sirldeellerLdelarrrgr 23
                                      +i+ldee +erL ++++++  
  gi|336254378|ref|YP_004597485.1|  5 TISLDEEAYERLKARKKEG-E 24
                                      8***********9876654.4 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.056
                                      EEHHHHHHHHHHHHHHT.SSH CS
                             RHH_1  6 ldeellerLdelarrrg.rSr 25
                                      l+ee++  L+  +++++ rSr
  gi|336254378|ref|YP_004597485.1| 46 LSEEEASDLESAIEEGRtRSR 66
                                      577888888888888887877 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.32
                                      EEEEEEH CS
                             RHH_1  2 vsirlde 8 
                                      ++  lde
  gi|336254378|ref|YP_004597485.1| 72 LTAELDE 78
                                      4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 590.00
//
Query:       gi|336254379|ref|YP_004597486.1|  [L=267]
Description: hypothetical protein Halxa_2991 [Halopiger xanaduensis SH-6]
Scores for 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   62.8   1.9    1.1e-16   62.0   1.9    1.4  1  Trypsin_2      Trypsin-like peptidase domain
    8.1e-06   25.8   0.4     0.0013   18.6   0.1    2.2  2  Trypsin        Trypsin
     0.0048   15.6   0.5       0.28    9.8   0.2    2.3  3  Peptidase_S46  Peptidase S46
  ------ inclusion threshold ------
      0.024   14.4   0.1       0.16   11.7   0.0    2.0  2  Peptidase_S29  Hepatitis C virus NS3 protease
      0.024   13.8   4.5          1    8.5   0.3    2.2  2  Peptidase_S32  Equine arteritis virus serine endopeptidase S3


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 !   62.0   1.9   3.1e-20   1.1e-16       1     150 []      89     220 ..      89     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 3.1e-20
                         Trypsin_2   1 GsGflvgsd.glilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpel..DlAllkvssderaglpplp 74 
                                       G+G+++++  g+i+Tn Hvv +  + ++          + dg++  a+ v+++ +   D+Al++    +++gl  l 
  gi|336254379|ref|YP_004597486.1|  89 GTGWVLDAAqGYIVTNSHVVIDGRSFTI---------ETFDGETAGATRVGYHQDMipDVALVQT---DSNGLSGLS 153
                                       8**998887579********99999999.........56666666666666665778********...********* PP

                         Trypsin_2  75 lgpsealkggepvyvvGyplggeksgsvssGivsgvvesesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                        g+++al+ g+p++ +G+p+++++   +s G++ ++           +++l  +++ts+G+SGGpl+  +G vvG+
  gi|336254379|ref|YP_004597486.1| 154 TGDESALSDGDPLVTIGHPGRYGDW-IMSIGRYEDHPA--------ASEWLLSTVPTSQGNSGGPLLTLEGDVVGV 220
                                       ******************9999998.99*********9........9****************************8 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0037        13      19      52 ..      81     116 ..      64     171 .. 0.67
   2 !   18.6   0.1   3.7e-07    0.0013     176     205 ..     201     231 ..     192     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0037
                                       EETTCEEEEEEEEEETT..EEEEEGGGTTTGGGEEE CS
                           Trypsin  19 svksgkhlCgGslisen..wvlTAaHCvsnasdvkv 52 
                                        ++s++ + +G ++++   +++T+ H+v + +++++
  gi|336254379|ref|YP_004597486.1|  81 VRGSNGSTGTGWVLDAAqgYIVTNSHVVIDGRSFTI 116
                                       3333345666777766558*********99666655 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.7e-07
                                       CTTTTTTSEEEETTTEEEEEEEEE.SSSSCT CS
                           Trypsin 176 acqGDSGGPlvcsdgelvGivswg.kgcakg 205
                                       + qG+SGGPl++ +g +vG+vs+   g ++g
  gi|336254379|ref|YP_004597486.1| 201 TSQGNSGGPLLTLEGDVVGVVSGTtTGPDDG 231
                                       679*******************986555555 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.0    0.0061        22      21      68 ..      56     109 ..      43     112 .. 0.73
   2 ?   -2.1   0.0      0.32   1.1e+03     237     252 ..     159     174 ..     156     194 .. 0.86
   3 !    9.8   0.2   7.8e-05      0.28     624     651 ..     194     221 ..     166     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0061
                                       HTT--S-HHHHS-SSS--.GGG--EETT..T..EE-EE-.STT-EEEE-HHHHH CS
                     Peptidase_S46  21 elGlklsaekladlrrss.kdAvvsflg..g..CtasfV.SpeGLvlTNHHCay 68 
                                       ++G+  +  + a++++++  dAvv + g  g   t+ +  +++G ++TN H+++
  gi|336254379|ref|YP_004597486.1|  56 ATGFSTDVFERAETTAKAaRDAVVIVRGsnGstGTGWVLdAAQGYIVTNSHVVI 109
                                       48999998888888888889***9975533311455555478*********987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.32
                                       ---TT-EEEEEE---- CS
                     Peptidase_S46 237 GvkegdlvfvlGyPGs 252
                                       ++++gd   ++G+PG+
  gi|336254379|ref|YP_004597486.1| 159 ALSDGDPLVTIGHPGR 174
                                       6789***********8 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 7.8e-05
                                       EEEES----TT-TT-EEE-TTS-EEEEE CS
                     Peptidase_S46 624 nflstnDitGGNSGSPvlngkgelvGla 651
                                        +lst+ +  GNSG P+l  +g++vG++
  gi|336254379|ref|YP_004597486.1| 194 WLLSTVPTSQGNSGGPLLTLEGDVVGVV 221
                                       579***********************97 PP

>> Peptidase_S29  Hepatitis C virus NS3 protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.18   6.5e+02      66      88 ..      90     112 ..      63     120 .. 0.70
   2 ?   11.7   0.0   4.6e-05      0.16     103     126 ..     199     222 ..     180     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.18
                     Peptidase_S29  66 tpCtcgasdlylvtrdadliear 88 
                                       t    +a++ y+vt++  +i++r
  gi|336254379|ref|YP_004597486.1|  90 TGWVLDAAQGYIVTNSHVVIDGR 112
                                       55567788999999999999887 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.6e-05
                     Peptidase_S29 103 lselkGssGsPilCdsGhvvGllv 126
                                       + + +G sG+P+l  +G vvG++ 
  gi|336254379|ref|YP_004597486.1| 199 VPTSQGNSGGPLLTLEGDVVGVVS 222
                                       55678****************986 PP

>> Peptidase_S32  Equine arteritis virus serine endopeptidase S32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.3   0.00028         1      91     138 ..      63     112 ..      55     145 .. 0.76
   2 ?    7.0   0.4   0.00082       2.9     205     229 ..     201     225 ..     190     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00028
                                       XXXXXXXXX---.TTEEEEESSSEEEEEEEECTT.EEEEEEEHHHH-TSE CS
                     Peptidase_S32  91 vleGllRtrkaa.knvvsvvGsslGsGgvftidg.evvvvtashvlgdnk 138
                                       v+e +  t kaa   vv v Gs   +G+ +  d  +  +vt shv+ d++
  gi|336254379|ref|YP_004597486.1|  63 VFERAETTAKAArDAVVIVRGSNGSTGTGWVLDAaQGYIVTNSHVVIDGR 112
                                       566665666655056777888877777778766516689******98765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00082
                                       --GGGTT-EEEETTE.EEEEEEEEE CS
                     Peptidase_S32 205 tkcGDsGspvvdedgelvGvhtGsn 229
                                       t+ G+sG p+++ +g++vGv  G  
  gi|336254379|ref|YP_004597486.1| 201 TSQGNSGGPLLTLEGDVVGVVSGTT 225
                                       889*****************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1930.07
//
Query:       gi|336254380|ref|YP_004597487.1|  [L=181]
Description: hypothetical protein Halxa_2992 [Halopiger xanaduensis SH-6]
Scores for 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  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1394.05
//
Query:       gi|336254381|ref|YP_004597488.1|  [L=70]
Description: hypothetical protein Halxa_2993 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0012   19.1   1.1     0.0016   18.6   1.1    1.2  1  DUF1059    Protein of unknown function (DUF1059)
  ------ inclusion threshold ------
       0.01   16.0   0.1      0.014   15.6   0.1    1.3  1  MmoB_DmpM  MmoB/DmpM family
      0.054   13.7   0.1      0.068   13.4   0.1    1.2  1  DUF5055    Domain of unknown function (DUF5055)


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.1   2.7e-07    0.0016       4      44 ..      16      62 ..      14      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.7e-07
                           DUF1059  4 fkCgDvgpdCgfei..taeteeEvlrkvaeHakaaHg....lteipp 44
                                      ++C   + +C f +  +a++++ +l+  ++H+ ++Hg    l+ei +
  gi|336254381|ref|YP_004597488.1| 16 VACDTEVSGCVFLMrtEADDKDRLLEITRDHVSEQHGkeysLEEIEE 62
                                      67888889998865559********************4444444433 PP

>> MmoB_DmpM  MmoB/DmpM family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1   2.3e-06     0.014      40      67 ..      36      63 ..      25      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-06
                                      EESEEEEEHHHHHHHHTST--HHHHTTS CS
                         MmoB_DmpM 40 aegrleirreeieealGrefdlqelevn 67
                                       ++ lei+r+ ++e+ G+e++l+e+e +
  gi|336254381|ref|YP_004597488.1| 36 KDRLLEITRDHVSEQHGKEYSLEEIEEQ 63
                                      56789********************986 PP

>> DUF5055  Domain of unknown function (DUF5055)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.1e-05     0.068       9      43 ..      33      67 ..      27      70 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                           DUF5055  9 yedkeytleftrrtvkemekkgfvaadieekpmtt 43
                                       +dk+  le+tr  v+e   k +  ++iee+ mt 
  gi|336254381|ref|YP_004597488.1| 33 ADDKDRLLEITRDHVSEQHGKEYSLEEIEEQHMTD 67
                                      589******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 539.29
//
Query:       gi|336254382|ref|YP_004597489.1|  [L=269]
Description: transcriptional regulator-like protein [Halopiger xanaduensis SH-6]
Scores for 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-07   30.6   0.7    7.2e-07   29.0   0.4    2.0  2  MarR_2         MarR family
    1.2e-05   25.0   0.7    2.3e-05   24.1   0.1    1.8  2  HTH_IclR       IclR helix-turn-helix domain
    0.00011   22.0   0.0    0.00021   21.1   0.0    1.5  1  HTH_5          Bacterial regulatory protein, arsR family
    0.00017   21.5   0.2    0.00031   20.6   0.2    1.4  1  HTH_Crp_2      Crp-like helix-turn-helix domain
    0.00018   21.6   0.2      0.002   18.2   0.1    2.2  2  DprA_WH        DprA winged helix domain
    0.00095   19.1   0.1      0.002   18.0   0.1    1.6  1  MarR           MarR family
      0.001   19.1   1.5     0.0044   17.0   0.4    2.5  3  HTH_20         Helix-turn-helix domain
     0.0034   17.8   0.0      0.007   16.8   0.0    1.5  1  HTH_27         Winged helix DNA-binding domain
     0.0038   17.3   0.0     0.0061   16.7   0.0    1.3  1  DUF1724        Domain of unknown function (DUF1724)
  ------ inclusion threshold ------
      0.021   14.4   0.1      0.021   14.4   0.1    1.8  2  HTH_24         Winged helix-turn-helix DNA-binding
      0.035   14.2   0.2      0.065   13.4   0.2    1.3  1  Trp_repressor  Trp repressor protein
      0.059   12.8   0.4       0.15   11.5   0.4    1.8  1  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
       0.13   12.1   1.2       0.39   10.6   1.2    1.8  1  HTH_23         Homeodomain-like domain
       0.16   11.2   0.0       0.28   10.4   0.0    1.3  1  DUF4928        Domain of unknown function (DUF4928)
       0.19   11.9   0.0       0.32   11.2   0.0    1.4  1  HTH_34         Winged helix DNA-binding domain


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 !   29.0   0.4     6e-10   7.2e-07       9      54 ..      24      66 ..      20      72 .. 0.92
   2 ?   -3.6   0.0       8.8   1.1e+04      46      53 ..     179     186 ..     179     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 6e-10
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       vL aL+ rp+   t ++l +r+g s s++sril+ ++++ ++ r 
  gi|336254382|ref|YP_004597489.1| 24 AVLDALAERPR---TRADLRARTGASASTISRILRAFEERNWINRA 66
                                      79********6...*****************************875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.8
                                       HHTTSEEE CS
                            MarR_2  46 vaaGLver 53 
                                       +aaG+v+ 
  gi|336254382|ref|YP_004597489.1| 179 SAAGYVRS 186
                                       589**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 !   24.1   0.1   1.9e-08   2.3e-05       6      50 ..      23      65 ..      21      67 .. 0.93
   2 ?   -3.4   0.0       7.3   8.8e+03       7      17 ..      85      95 ..      85      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.9e-08
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +a+Ldalae+p+    ++l +rtg + St +R+L+ ++e+ ++ +
  gi|336254382|ref|YP_004597489.1| 23 VAVLDALAERPRT--RADLRARTGASASTISRILRAFEERNWINR 65
                                      58**********6..9************************99865 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.3
                                      HHHCT-CTTBS CS
                          HTH_IclR  7 aiLdalaeapq 17
                                      ++Ld +a+++q
  gi|336254382|ref|YP_004597489.1| 85 DLLDRFATERQ 95
                                      68999999886 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 !   21.1   0.0   1.7e-07   0.00021       2      41 ..      20      59 ..      19      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.7e-07
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLre 41
                                      + R+ +L +Lae++++  +l + +g s st+S+ L++ +e
  gi|336254382|ref|YP_004597489.1| 20 EHRVAVLDALAERPRTRADLRARTGASASTISRILRAFEE 59
                                      679******************************9998776 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 !   20.6   0.2   2.6e-07   0.00031       6      54 ..      15      67 ..      13      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.6e-07
                                      HHHHHHCTTT..C.EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE.T CS
                         HTH_Crp_2  6 fLlrlaerag..g.eielpltqeelAsmlGltretvsrilseLkreglisr.g 54
                                      fL+r ++r +  +   e p t+++l ++ G++ +t+sril++++++++i r g
  gi|336254382|ref|YP_004597489.1| 15 FLVRSEHRVAvlDaLAERPRTRADLRARTGASASTISRILRAFEERNWINRaG 67
                                      66665555332223456799*****************************9634 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.7e-06     0.002      11      46 ..      19      54 ..       5      67 .. 0.89
   2 ?    0.9   0.0      0.43   5.1e+02      10      24 ..     159     173 ..     153     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
                           DprA_WH 11 ddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaL 46
                                      ++ + +vL+aL+  P++  +L +rtg++a+++s++L
  gi|336254382|ref|YP_004597489.1| 19 SEHRVAVLDALAERPRTRADLRARTGASASTISRIL 54
                                      67789*****************************99 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.43
                           DprA_WH  10 lddlerrvLaaLgpe 24 
                                        ddl+rr+L+ +++e
  gi|336254382|ref|YP_004597489.1| 159 RDDLRRRILDGMEAE 173
                                       69*******998876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.7e-06     0.002      21      49 ..      37      65 ..      19      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-06
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 21 seLakklgvskstvtrvldrLekkGlieR 49
                                      ++L  + g s st++r+l++ e++++i+R
  gi|336254382|ref|YP_004597489.1| 37 ADLRARTGASASTISRILRAFEERNWINR 65
                                      58999999********************9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.4   3.7e-06    0.0044       9      51 ..      19      60 ..      15      69 .. 0.91
   2 ?   -1.4   0.0       2.2   2.6e+03      13      28 ..      97     113 ..      92     127 .. 0.66
   3 ?   -1.7   0.0       2.6   3.1e+03      11      19 ..     162     170 ..     160     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.7e-06
                                      -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHC CS
                            HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeea 51
                                      ++ R ++l+aL  ++++t ++l +r + s +t+s+ Lr+ ee 
  gi|336254382|ref|YP_004597489.1| 19 SEHRVAVLDAL-AERPRTRADLRARTGASASTISRILRAFEER 60
                                      578********.***************************9996 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                                       HHHHHHH.STCTTB-HH CS
                            HTH_20  13 rrilraL.araegltas 28 
                                       r+i r+L + + g+t++
  gi|336254382|ref|YP_004597489.1|  97 RDIWRWLpSADHGFTVE 113
                                       78999997445555554 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.6
                                       HHHHHHHHH CS
                            HTH_20  11 vRrrilraL 19 
                                        Rrril+  
  gi|336254382|ref|YP_004597489.1| 162 LRRRILDGM 170
                                       688888755 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 !   16.8   0.0   5.8e-06     0.007       7      68 .]      24      76 ..      19      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.8e-06
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +vL  ++  +r+ + adl+ r+  ++s+is +l++ +e+ ++ r gd       r+++T+ G
  gi|336254382|ref|YP_004597489.1| 24 AVLDALA--ERPRTRADLRARTGASASTISRILRAFEERNWINRAGD-------RYEATPLG 76
                                      5677777..888899***************************77666.......58888866 PP

>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.1e-06    0.0061       8      62 .]     207     261 ..     202     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.1e-06
                           DUF1724   8 eeikplsltvtDkflslslfdkdgkydhkdlisfdesAlkWGeeLFeyYlkrSep 62 
                                       +++ p ++ + D+ +++s +d++    +  +  ++++A +W+e  Fe Y++ ++p
  gi|336254382|ref|YP_004597489.1| 207 DDVPPYGVSIFDDRIAISCCDRTTGTVRVLVDTDSPAAREWAESTFEAYRQEARP 261
                                       67889999*************9875555566669******************986 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 ?   14.4   0.1   1.8e-05     0.021      19      47 ..      35      63 ..      18      64 .. 0.82
   2 ?   -2.7   0.9       3.8   4.5e+03       1       9 [.     159     167 ..     159     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      + ++L  r+g S st++r l+ +ee  +I
  gi|336254382|ref|YP_004597489.1| 35 TRADLRARTGASASTISRILRAFEERNWI 63
                                      7899**********************998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.8
                            HTH_24   1 ldetdrkIL 9  
                                       +d+++r+IL
  gi|336254382|ref|YP_004597489.1| 159 RDDLRRRIL 167
                                       6999****9 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   5.5e-05     0.065      37      75 ..      21      59 ..      17      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.5e-05
                     Trp_repressor 37 qRlqvvkeLLkeelsqreIaeelgvSiAtItRvsrsLkt 75
                                      +R+ v+ +L +  ++  ++ + +g+S+ tI+R  r+ + 
  gi|336254382|ref|YP_004597489.1| 21 HRVAVLDALAERPRTRADLRARTGASASTISRILRAFEE 59
                                      799*****************************9998765 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 ?   11.5   0.4   0.00013      0.15      19      50 ..      24      56 ..      22      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                      HTH_Tnp_ISL3 19 yilellles.rsvkavArqlgvSwtTVwrildr 50
                                      ++l +l e+ r++++  +++g S++T+ ril++
  gi|336254382|ref|YP_004597489.1| 24 AVLDALAERpRTRADLRARTGASASTISRILRA 56
                                      6889999************************86 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.2   0.00033      0.39       5      43 ..      20      59 ..      17      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
                            HTH_23  5 reRlrillllae.GlsvreIAreLgvsrrTvyrwlkryre 43
                                      ++R  +l +lae   ++++  ++ g s +T++r+l++++e
  gi|336254382|ref|YP_004597489.1| 20 EHRVAVLDALAErPRTRADLRARTGASASTISRILRAFEE 59
                                      57888888888885599999999***************65 PP

>> DUF4928  Domain of unknown function (DUF4928)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00023      0.28      47      94 ..      43      92 ..      26     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                           DUF4928 47 rGasGatvanilkrhgedrdfakeGGrtsrg..tkelaveivdlldkkpr 94
                                       Gas +t+ +il+ ++e     + G r + +  +  +a  ++dlld+   
  gi|336254382|ref|YP_004597489.1| 43 TGASASTISRILRAFEERNWINRAGDRYEATplGAFVATGLRDLLDRFAT 92
                                      499**************99999****977652267789999**9998655 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 ?   11.2   0.0   0.00027      0.32       2      49 ..      22      68 ..      21      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                            HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49
                                      R avl  La+  + + ++l++ ++a+++ +s  l+++e+ ++i++  +
  gi|336254382|ref|YP_004597489.1| 22 RVAVLDALAERPR-TRADLRARTGASASTISRILRAFEERNWINRAGD 68
                                      6777888877655.4579************************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1907.55
//
Query:       gi|336254383|ref|YP_004597490.1|  [L=271]
Description: hypothetical protein Halxa_2995 [Halopiger xanaduensis SH-6]
Scores for 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:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2024.53
//
Query:       gi|336254384|ref|YP_004597491.1|  [L=194]
Description: hypothetical protein Halxa_2996 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.039   14.1   0.2      0.074   13.2   0.2    1.5  1  UPF0561   Uncharacterised protein family UPF0561


Domain annotation for each model (and alignments):
>> UPF0561  Uncharacterised protein family UPF0561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   4.2e-06     0.074      42     115 ..      40     115 ..      18     118 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-06
                           UPF0561  42 qakekqrrrhtttprrprrpdlqvylpr..srdgsepgsnaeaeesnessssteaettgvelfwldyeadsgdits 115
                                        a   +rrr   +  r r pd  + +    ++ g++++++ e  + +      + e+t   lfw d     g it 
  gi|336254384|ref|YP_004597491.1|  40 LADGANRRRRERATVRNRSPDSTLRTDGgsEQSGTDETATIEFLDRETVRIVGDLEETILSLFWWDESGRVGTITE 115
                                       4677899**************987654410344444444445555555566999************9999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1533.02
//
Query:       gi|336254385|ref|YP_004597492.1|  [L=125]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   54.5   1.5      2e-14   54.3   1.5    1.2  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 !   54.3   1.5   1.1e-18     2e-14      51     141 .]      35     121 ..       4     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1.1e-18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHH CS
                               Usp  51 deeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvse 127
                                       + + e+++++ +ea +     +  + a + +ve++v++gdpa ++ +va+e+dad +VvG+r  +  + + lGS+++
  gi|336254385|ref|YP_004597492.1|  35 AVDDETARQDAREALN----VAPVRLATVGTVETDVRDGDPASVLPDVADEIDADELVVGARSGNPDATAALGSTAQ 107
                                       2222222222222222....468999*************************************888888******** PP

                                       HHHHHTSSEEEEEE CS
                               Usp 128 yvlrhapcpVlvVr 141
                                       +vl+ a+ pV+vV+
  gi|336254385|ref|YP_004597492.1| 108 AVLEAATRPVVVVP 121
                                       *************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1060.62
//
Query:       gi|336254386|ref|YP_004597493.1|  [L=102]
Description: hypothetical protein Halxa_2998 [Halopiger xanaduensis SH-6]
Scores for 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   3.4     0.0015   18.5   3.4    1.0  1  DUF4271          Domain of unknown function (DUF4271)
  ------ inclusion threshold ------
      0.011   15.1   4.1      0.013   14.9   4.1    1.2  1  Glucos_trans_II  Glucosyl transferase GtrII
      0.083   12.6   0.1       0.17   11.6   0.1    1.6  1  DUF5353          Family of unknown function (DUF5353)
       0.21   11.6   1.6        0.3   11.1   0.2    1.9  2  OppC_N           N-terminal TM domain of oligopeptide transpo
        2.1    8.4   4.6        5.3    7.2   0.1    2.3  2  YpmT             Uncharacterized YmpT-like


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 !   18.5   3.4   4.3e-07    0.0015      53     136 ..      15      95 ..       6      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.3e-07
                           DUF4271  53 flllltclllglllylllsefgslfgsylassllllliiflilllylllKlllykllgwlFfdkkkirqwifsylsy 129
                                       +l++ +++l++++  l+  +       y  +   ++l+++++lll+ l+ +l+  ++ +++++++++  ++++++ +
  gi|336254386|ref|YP_004597493.1|  15 LLTVASLFLVAIFGTLIAYQAYRG---YRRNDAPSMLYLAGGLLLLTLCPFLVNVVITTVTDLEQIVTAFLENVSRL 88 
                                       455666666665555555542222...344999******************************************** PP

                           DUF4271 130 lsllgll 136
                                       + ll+++
  gi|336254386|ref|YP_004597493.1|  89 FGLLAIM 95 
                                       *999986 PP

>> Glucos_trans_II  Glucosyl transferase GtrII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   4.1   3.6e-06     0.013     227     282 ..      18      72 ..      11      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-06
                   Glucos_trans_II 227 pkklllililliliilllalllkkkkkkkksllllllllllllpfalnlillkssl 282
                                       + +l+l++i+++li+  ++  ++++   +  +l+  llll l pf++n+++ ++  
  gi|336254386|ref|YP_004597493.1|  18 VASLFLVAIFGTLIAYQAYRGYRRNDAPSMLYLAGGLLLLTLCPFLVNVVI-TTVT 72 
                                       568999******************999988888******************.3333 PP

>> DUF5353  Family of unknown function (DUF5353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.8e-05      0.17       8      32 ..      18      42 ..      15      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.8e-05
                           DUF5353  8 vgNavlvavlsagLGfgAYrkyarG 32
                                      v+ + lva+ ++++++ AYr y r+
  gi|336254386|ref|YP_004597493.1| 18 VASLFLVAIFGTLIAYQAYRGYRRN 42
                                      677899****************997 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   8.3e-05       0.3      20      42 ..      15      37 ..      12      52 .. 0.71
   2 ?   -1.2   0.1      0.58   2.1e+03      26      29 ..      57      60 ..      45      86 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.3e-05
                            OppC_N 20 lvilllllliaifaPliaPydpq 42
                                      l  ++ l+l+aif+ lia   ++
  gi|336254386|ref|YP_004597493.1| 15 LLTVASLFLVAIFGTLIAYQAYR 37
                                      566889***********954432 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.58
                            OppC_N 26 llli 29
                                      l+l+
  gi|336254386|ref|YP_004597493.1| 57 LTLC 60
                                      2222 PP

>> YpmT  Uncharacterized YmpT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.3     0.038   1.3e+02       5      25 ..      13      34 ..      10      65 .. 0.83
   2 ?    7.2   0.1    0.0015       5.3       2      18 ..      83      99 ..      82     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.038
                              YpmT  5 yvyFsllsllfslyFGgl.ayq 25
                                      + + ++ sl +  +FG l ayq
  gi|336254386|ref|YP_004597493.1| 13 FELLTVASLFLVAIFGTLiAYQ 34
                                      77778889999999*9873565 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0015
                              YpmT  2 kriyvyFsllsllfsly 18
                                      +++  +F+ll++++sly
  gi|336254386|ref|YP_004597493.1| 83 ENVSRLFGLLAIMYSLY 99
                                      677789**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 792.33
//
Query:       gi|336254387|ref|YP_004597494.1|  [L=115]
Description: hypothetical protein Halxa_2999 [Halopiger xanaduensis SH-6]
Scores for complete 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   31.8   0.9    1.7e-07   31.2   0.9    1.2  1  HTH_20         Helix-turn-helix domain
    0.00031   20.5   0.1    0.00043   20.1   0.1    1.2  1  MarR_2         MarR family
      0.001   19.2   0.0     0.0012   18.9   0.0    1.2  1  FUR            Ferric uptake regulator family
     0.0033   17.2   0.1     0.0053   16.5   0.1    1.3  1  HTH_IclR       IclR helix-turn-helix domain
     0.0094   15.5   0.0      0.017   14.7   0.0    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.015   15.2   0.0    1.3  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.025   14.5   0.0      0.042   13.8   0.0    1.3  1  HTH_11         HTH domain
       0.03   14.3   0.0      0.043   13.8   0.0    1.4  1  PadR           Transcriptional regulator PadR-like family
      0.049   13.5   0.0      0.077   12.9   0.0    1.4  1  HTH_5          Bacterial regulatory protein, arsR family
      0.053   13.4   0.0      0.091   12.6   0.0    1.5  1  HTH_AsnC-type  AsnC-type 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 !   31.2   0.9   9.5e-11   1.7e-07       3      59 ..      10      65 ..       8      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 9.5e-11
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      ++ +L+++  r+il +  + e+++as l +r+d s  t++++L+ Le   Lv+ ++e
  gi|336254387|ref|YP_004597494.1| 10 VLAVLDDEYAREILTHT-SVEPMSASTLSDRCDASLPTIYRRLDRLEACRLVTEETE 65
                                      7899*************.**********************************99987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   2.4e-07   0.00043      20      58 ..      20      67 ..       8      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.4e-07
                                      S.........EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                            MarR_2 20 r.........dltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                      r         +++++ l +r++ s +++ r+l+rL+a  Lv++++ ++
  gi|336254387|ref|YP_004597494.1| 20 ReilthtsvePMSASTLSDRCDASLPTIYRRLDRLEACRLVTEETELA 67
                                      344444444449******************************998765 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   6.9e-07    0.0012      19      80 ..      21      82 ..       8      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.9e-07
                                      HHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEE.EEETTSEEEEEESSSSSEEE CS
                               FUR 19 kseehlsaeevykelkeedpeislaTVYrtLklleeaglvke.lefedgesryelakkehhdh 80
                                      +  +h s+e +  +  +++ + sl T+Yr L+ le   lv+e +e++ + ++y + +  + dh
  gi|336254387|ref|YP_004597494.1| 21 EILTHTSVEPMSASTLSDRCDASLPTIYRRLDRLEACRLVTEeTELAPDGNHYSVYS-ANLDH 82
                                      4456***********************************975277888888888774.44444 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   0.1   2.9e-06    0.0053      17      50 ..      29      62 ..      21      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.9e-06
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++++ s l++r++ + +t +R L  L+ +++v+ 
  gi|336254387|ref|YP_004597494.1| 29 EPMSASTLSDRCDASLPTIYRRLDRLEACRLVTE 62
                                      78******************************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 !   14.7   0.0   9.5e-06     0.017      18      46 ..      31      59 ..      15      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.5e-06
                            HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGl 46
                                      +s + L++r++ S++t+ rrl+rLe   l
  gi|336254387|ref|YP_004597494.1| 31 MSASTLSDRCDASLPTIYRRLDRLEACRL 59
                                      67788********************8665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   8.4e-06     0.015      21      59 ..      29      73 ..      21      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.4e-06
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......T CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr......p 59
                                      +p++a++++ + + + +++Y+ L +Le + lV+ e +       +
  gi|336254387|ref|YP_004597494.1| 29 EPMSASTLSDRCDASLPTIYRRLDRLEACRLVTEETELapdgnhY 73
                                      799*****************************9997655555544 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.3e-05     0.042      14      42 ..      29      57 ..      19      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                            HTH_11 14 gpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      +p+s+++L+++ + S  t++r++++Le+ 
  gi|336254387|ref|YP_004597494.1| 29 EPMSASTLSDRCDASLPTIYRRLDRLEAC 57
                                      469***********************985 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.4e-05     0.043      29      63 ..      42      76 ..      10      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                                      TTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEE CS
                              PadR 29 lseGslYpaLkrLekeglveseweesgegpprkyY 63
                                      +s  ++Y+ L+rLe+ +lv++e e + +g    +Y
  gi|336254387|ref|YP_004597494.1| 42 ASLPTIYRRLDRLEACRLVTEETELAPDGNHYSVY 76
                                      56669*****************9988777776666 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 ?   12.9   0.0   4.3e-05     0.077      12      46 ..      27      61 ..      16      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.3e-05
                                      TTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 12 aegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      + ++++++ l++  + s +t+ + L +L+ ++LV+
  gi|336254387|ref|YP_004597494.1| 27 SVEPMSASTLSDRCDASLPTIYRRLDRLEACRLVT 61
                                      5589******************************7 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 ?   12.6   0.0   5.1e-05     0.091      18      42 .]      31      55 ..      16      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.1e-05
                     HTH_AsnC-type 18 isyaeLAervGlSestvlrRvrrLe 42
                                      +s + L++r+  S +t+ rR++rLe
  gi|336254387|ref|YP_004597494.1| 31 MSASTLSDRCDASLPTIYRRLDRLE 55
                                      8999********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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 0.21s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 879.52
//
Query:       gi|336254388|ref|YP_004597495.1|  [L=209]
Description: hypothetical protein Halxa_3000 [Halopiger xanaduensis SH-6]
Scores for 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   43.2   1.6    3.5e-11   42.7   1.6    1.3  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   1.6     2e-15   3.5e-11       4     147 ..       4     155 ..       1     180 [. 0.73

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 2e-15
                              YdjM   4 ltHallGaalglalaallgaake.avllavavlgAllPD.iDhpsstlgrklgllskklaklvgHRgftHSllflal 78 
                                         Ha++G ++  ++  l  ++       ++av++++lPD +D     l+ +l  ++           + HS++f++ 
  gi|336254388|ref|YP_004597495.1|   4 WEHAIVGYLVYSLVSRLYYRESPdGPEALAAVVASVLPDvVD---KPLAWELEVFET-------GYALGHSIFFAVP 70 
                                       58************999988777866666777889****999...666667777777.......778********** PP

                              YdjM  79 lalvlllllrlfgrsalrlglllllgvlsHlllDlltk.......yGvpllwPfsk..kkvrlsllfiiidplltll 146
                                       l++++ ll+r++gr+  r+g+++++g+l+Hl  D+l         y+  +lwP+ +  ++ r + lf    + + + 
  gi|336254388|ref|YP_004597495.1|  71 LGIAAGLLTRSLGRT--RAGVAFAIGYLLHLPSDILDGylrggvvYPEIVLWPVATvpTRSRAQGLFDQFFEFFARY 145
                                       **************9..89************9999998887555555588999987554555555544444422222 PP

                              YdjM 147 .........s 147
                                                s
  gi|336254388|ref|YP_004597495.1| 146 rdelvagdlS 155
                                       5555555552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1534.51
//
Query:       gi|336254389|ref|YP_004597496.1|  [L=367]
Description: hypothetical protein Halxa_3001 [Halopiger xanaduensis SH-6]
Scores for 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   16.3   0.0      0.011   15.4   0.0    1.4  1  DUF2334      Uncharacterized protein conserved in bacteria (D
  ------ inclusion threshold ------
      0.016   14.9   1.2      0.056   13.2   0.1    2.2  2  Prenyltrans  Prenyltransferase and squalene oxidase repeat


Domain annotation for each model (and alignments):
>> DUF2334  Uncharacterized protein conserved in bacteria (DUF2334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-06     0.011      54      85 ..     137     171 ..     123     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-06
                           DUF2334  54 npefvevLkylqakGgeialHGYtHqygtvk...s 85 
                                       + e v+v++ l + G+e+++HG  H  + ++   +
  gi|336254389|ref|YP_004597496.1| 137 ADEIVDVIRALDDGGWEVGMHGSYHSADDPErlrE 171
                                       6789**********************997666542 PP

>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       0.1     9e+02      15      21 ..     147     153 ..     145     162 .. 0.81
   2 ?   13.2   0.1   6.2e-06     0.056       5      30 ..     295     320 ..     294     330 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.1
                                       HTTS-BB CS
                       Prenyltrans  15 nedGGwg 21 
                                        +dGGw 
  gi|336254389|ref|YP_004597496.1| 147 LDDGGWE 153
                                       58****6 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.2e-06
                                       HHHHHHHHHSHTTS-BBSSTTSSBBH CS
                       Prenyltrans   5 kavefLlscQnedGGwggrpgsesdt 30 
                                       ++ +++  +  + GGw g+pg  +d+
  gi|336254389|ref|YP_004597496.1| 295 ELYRWVVERALDLGGWVGSPGAFCDA 320
                                       799*******************5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 2948.92
//
Query:       gi|336254390|ref|YP_004597497.1|  [L=451]
Description: hypothetical protein Halxa_3002 [Halopiger xanaduensis SH-6]
Scores for 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  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); 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):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.35
# Mc/sec: 3855.62
//
Query:       gi|336254391|ref|YP_004597498.1|  [L=330]
Description: hypothetical protein Halxa_3003 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        3.1    6.5   5.6        0.8    8.5   2.5    1.5  2  DUF2254   Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.5   4.5e-05       0.8      16      72 ..      23      79 ..      10      86 .. 0.68
   2 ?   -3.7   0.1      0.22     4e+03     260     280 ..     197     217 ..     193     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 4.5e-05
                           DUF2254 16 vllalllllldealslsldleelkegaeaaralLstiagsmltvagfvfSitvvalq 72
                                      vl++++  ll    +l++ le++ ++ +++++l +t++g ++t +++v+Si  ++l+
  gi|336254391|ref|YP_004597498.1| 23 VLTVACFGLLTVFSALDIPLESILADGDTIETLFQTLVGVLITGMTLVVSINQLVLS 79
                                      33333333332222233444455459*************************988886 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.22
                           DUF2254 260 igrertfeqDpefglrqLvEI 280
                                       ++++++++++ + +++ Lv+I
  gi|336254391|ref|YP_004597498.1| 197 WEHQESIDDETRAAIDDLVDI 217
                                       678889999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.23s 00:00:00.69 Elapsed: 00:00:00.35
# Mc/sec: 2799.85
//
Query:       gi|336254392|ref|YP_004597499.1|  [L=372]
Description: hypothetical protein Halxa_3004 [Halopiger xanaduensis SH-6]
Scores for 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   31.6   0.0    3.3e-07   29.7   0.0    2.0  1  DUF354           Protein of unknown function (DUF354)
    1.3e-05   25.3   0.4    2.3e-05   24.5   0.4    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
     0.0042   17.5   0.8     0.0042   17.5   0.8    2.3  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.095   12.7   0.0       0.18   11.8   0.0    1.4  1  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
        0.2   11.2   0.0       0.28   10.7   0.0    1.1  1  Paralemmin       Paralemmin


Domain annotation for each model (and alignments):
>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   9.1e-11   3.3e-07       7     317 ..       6     313 ..       2     341 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 9.1e-11
                            DUF354   7 ltnap.hvryfrdlikkfekeGievlltardsGdlaklvklynfvfksiGk....hGvtlkekliesakrvinlskl 78 
                                       +tn+p hv+ +++ ++++++ G evl+ ard+     l++ y++ +   G     +G  l+    ++a r+i+ ++ 
  gi|336254392|ref|YP_004597499.1|   6 FTNTPaHVHLYKHAVRRLRDRGHEVLVLARDYTCTVDLLEWYELPYAVYGAcdtsKGSLLSRLPAHYA-RAITQAR- 80 
                                       689887**********************************9998777666511104444443333333.3333332. PP

                            DUF354  79 iaevkpdvalakhsvelprvafGlnipvvyvldnehaeaankltlpladeiikpividendlkktGadpnrirryeG 155
                                            pd+ +             l  p+v ++d e a  +  ++ p+a  ++ p +  +       ++ n+   + G
  gi|336254392|ref|YP_004597499.1|  81 --RFDPDLVFGMGGYAA-HTGAVLRTPTVLLIDSEPASFDHTISTPFARAVLTPDTFRK-----NLGR-NHYV-FPG 147
                                       ..345776655544433.3445699*****************************87643.....3445.4554.777 PP

                            DUF354 156 tsevinvqs..yeideeilkdlnlkledektilmrpepslasylda...dchkdvltkiveklkdridilviprdee 227
                                         e + ++   ye +  i + l+l   de+ +++r +    s  d        d   +ive+l + + +lv   de 
  gi|336254392|ref|YP_004597499.1| 148 FKECAYLHPeiYEPNPSIRDRLELG-ADEPYVILRLNA-FGSQHDVgkrGLTADDRRRIVERLGEDATVLVS--DES 220
                                       77776665555************65.667888888877.4554443011345566679*******9998875..455 PP

                            DUF354 228 qkeiyeevdnviviketvdalsllkrsdlviGaGGtmnreaallGipvv...scypqkllsvdkyliekdlmirstd 301
                                        +   e++       ++      l +++l++    tm  eaallG+p++   s   ++ ++    l e++l+ + + 
  gi|336254392|ref|YP_004597499.1| 221 GEADLEGLPARPFDLHPALMHDALAEAELLVADTQTMVTEAALLGTPAIrsnSFVGDDDMGNFVALEEQGLIHNVAS 297
                                       55556777766666667777778899**********************94323344556666666677788888889 PP

                            DUF354 302 vdeivntalrllvdkl 317
                                        d iv+ a+ ll ++ 
  gi|336254392|ref|YP_004597499.1| 298 ADAIVDRAVPLLRSDD 313
                                       9999999998886543 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.4   6.5e-09   2.3e-05      11     101 ..      19     107 ..      13     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6.5e-09
                    Glyco_transf_4  11 LaraLarrGheVtvvtpgddgpleeev...elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaal 84 
                                        +r+L++rGheV v+++++    +  +     +   ++  + +   l r +a++ r+  +++r++pD+v   +    
  gi|336254392|ref|YP_004597499.1|  19 AVRRLRDRGHEVLVLARDYTCTVDLLEwyeLPYAVYGACDTSKGSLLSRLPAHYARAITQARRFDPDLVFGMG---- 91 
                                       6799***************999999955432222223333466677889999*****************6555.... PP

                    Glyco_transf_4  85 gaallalrrrlgiplVl 101
                                       g+a++  +  l+ p+Vl
  gi|336254392|ref|YP_004597499.1|  92 GYAAHTGAV-LRTPTVL 107
                                       555555555.8899887 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 !   17.5   0.8   1.2e-06    0.0042       9      92 ..      18     102 ..      14     141 .. 0.73
   2 ?   -0.0   0.1       0.3   1.1e+03     121     151 ..     238     268 ..     212     271 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.2e-06
                   Glyco_trans_4_4   9 elaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrll.rqrrerpdvvhahspta 84 
                                       + +r+L++rGheV vl+++++   + le+  +++    +  ++++    + ++  +r++ ++rr+ pd+v   + +a
  gi|336254392|ref|YP_004597499.1|  18 HAVRRLRDRGHEVLVLARDYTCTVDLLEWYELPYAVYGACDTSKGSLLSRLPAHYARAItQARRFDPDLVFGMGGYA 94 
                                       6789**************777666656666666655556666654444444444455554559********999777 PP

                   Glyco_trans_4_4  85 glaarlar 92 
                                       +  ++++r
  gi|336254392|ref|YP_004597499.1|  95 AHTGAVLR 102
                                       76666666 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.3
                   Glyco_trans_4_4 121 alerrllrradavlvvseaeaeelralgvpa 151
                                       al + +l+ a ++++ ++ ++ e++ lg pa
  gi|336254392|ref|YP_004597499.1| 238 ALMHDALAEAELLVADTQTMVTEAALLGTPA 268
                                       4567788899999999999999998888887 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 ?   11.8   0.0   5.1e-05      0.18      11     100 ..      12      95 ..       9     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
                                       HHHHHHHHHHHHHCTT-EEEEEEETCCCHHHHHHCCT-EEEE.---GHCTT..CHHHHCCHHHHHHHHHHHHHHHHH CS
                   Glyco_transf_28  11 hvfPalAlakeLkkegheVrylgtkrgleerlveeaglefep.iageklrrklspknlkeilkvlkavvkakkilke 86 
                                       hv ++   +++L+++gheV  l+ +  ++  l e ++l++    a+++ +++l  + +         + +a++  ++
  gi|336254392|ref|YP_004597499.1|  12 HVHLYKHAVRRLRDRGHEVLVLARDYTCTVDLLEWYELPYAVyGACDTSKGSLLSRLPAH-------YARAITQARR 81 
                                       899999999**********99999999999999999999966233446666444444444.......55569999** PP

                                       HHHCCCCCCCCCCC CS
                   Glyco_transf_28  87 akpdavvgtggyvs 100
                                       + pd+v+g+ggy++
  gi|336254392|ref|YP_004597499.1|  82 FDPDLVFGMGGYAA 95 
                                       ************87 PP

>> Paralemmin  Paralemmin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   7.8e-05      0.28     126     172 ..     287     333 ..     270     362 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.8e-05
                        Paralemmin 126 derkVVhevrsedgtvenGvhplSSseVdeLihkadevtlvseakle 172
                                       +e+  +h+v s d++v+ +v  l S++Vde  ++  +++l   ++l+
  gi|336254392|ref|YP_004597499.1| 287 EEQGLIHNVASADAIVDRAVPLLRSDDVDEKWQRRRNAFLADTVNLT 333
                                       68889*****************************9999997666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 3095.00
//
Query:       gi|336254393|ref|YP_004597500.1|  [L=433]
Description: hypothetical protein Halxa_3005 [Halopiger xanaduensis SH-6]
Scores for complete 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   31.3   0.0    4.9e-05   23.0   0.0    2.3  2  Glyco_hydro_76  Glycosyl hydrolase family 76
    0.00028   20.3   0.1     0.0069   15.8   0.0    2.3  2  Pec_lyase       Pectic acid lyase
    0.00061   19.0   0.4     0.0015   17.7   0.4    1.8  1  Glyco_hydro_88  Glycosyl Hydrolase Family 88
  ------ inclusion threshold ------
      0.022   13.4   0.1        4.7    5.7   0.0    2.8  2  LANC_like       Lanthionine synthetase C-like protein


Domain annotation for each model (and alignments):
>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.1e-08   4.9e-05     154     258 ..     167     267 ..     146     319 .. 0.83
   2 !    6.1   0.0    0.0015       6.7     175     222 ..     356     400 ..     350     414 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.1e-08
                                       HHHHHHHHHHHHHHHHH--CHHHHHHHHHHHHHHHHSCSBTTTS-B-SEEETTTCCEEEE---HHHHHHHH.HHHHH CS
                    Glyco_hydro_76 154 isngplfqlaarLarytgnetYlewAekvwdWvedvgliddedwlvyDgasvednctdinklqwtYnqGty.lsgaa 229
                                       +s++++ ++ +r a+++g e+Y+e A+  +d++++    d +  +v  ga+++ +  ++ +  +t n++ +  +  +
  gi|336254393|ref|YP_004597500.1| 167 VSTSCAVKALLRVAEHEGREEYAEIARTAVDFMVE----DLNYREVEEGAKIDYHL-NHPEDSYTINAAALgAQMLV 238
                                       79*********************************....4578999****999997.55666699988765155556 PP

                                       HHHHHH--HHHHHHHHHHHHHHHHHCEEC CS
                    Glyco_hydro_76 230 ylynaTgdekWldrvkgllnatlstffpd 258
                                        ly++ gde+ ++r++++ +++ +  ++ 
  gi|336254393|ref|YP_004597500.1| 239 DLYEYFGDEELRERATKIFDHIAANQTDR 267
                                       799999*************9987766665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHSCSBTTTS-B-SEEETTTCCEEEE---HHHHHH CS
                    Glyco_hydro_76 175 YlewAekvwdWvedvgliddedwlvyDgasvednctdinklqwtYnqG 222
                                        le+Ae++ +Wv ++  ++ e++++y +   +++++ ++ ++w  +qG
  gi|336254393|ref|YP_004597500.1| 356 DLEFAERILRWVLANMQVEGEEGRFYYRK-YRHHTKRVTLMRW--CQG 400
                                       489***********9999**********8.5566677887877..455 PP

>> Pec_lyase  Pectic acid lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.02        91      40      73 ..     168     201 ..     148     207 .. 0.85
   2 !   15.8   0.0   1.5e-06    0.0069      35      96 ..     226     285 ..     202     322 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.02
                         Pec_lyase  40 atvtellflaevykatkdekykdavrkglefllk 73 
                                       +t   ++ l +v ++++ e+y + +r +++f+++
  gi|336254393|ref|YP_004597500.1| 168 STSCAVKALLRVAEHEGREEYAEIARTAVDFMVE 201
                                       67788999999********************986 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.5e-06
                         Pec_lyase  35 tiDndatvtellflaevykatkdekykdavrkglefllkaqYsnGgwpqfyPlkkgYsehit 96 
                                       ti+  a     ++l ++y+  +de+ ++ + k ++++ + q + Ggwp   P+  +  +   
  gi|336254393|ref|YP_004597500.1| 226 TIN--AAALGAQMLVDLYEYFGDEELRERATKIFDHIAANQTDRGGWPYRLPADASHLSMDN 285
                                       443..3444557799**********************************9999888665544 PP

>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.4   3.3e-07    0.0015      34     115 ..     172     269 ..     168     418 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.3e-07
                                       HHHHHHHHHHHH--HHHHHHHHHHHHHCCCTTS-.................CTTSGGGTGHH.HHHHHHHHHH-THH CS
                    Glyco_hydro_88  34 flsglleayeatgdkeyldyakawadslideggk.................telelDdidig.llllllyeltkder 92 
                                       ++++ll+++e+ g++ey ++a + +d ++++ +                   ++ ++++++g ++l++lye  +de+
  gi|336254393|ref|YP_004597500.1| 172 AVKALLRVAEHEGREEYAEIARTAVDFMVEDLNYreveegakidyhlnhpeDSYTINAAALGaQMLVDLYEYFGDEE 248
                                       57899****************99888777766657788899999999999989999999987478999********* PP

                                       HHHHHHHHHHHHHHCS-B.TTS. CS
                    Glyco_hydro_88  93 ykeaaeeladyvlakpprtseGg 115
                                        +e+a +++d + a++ +   Gg
  gi|336254393|ref|YP_004597500.1| 249 LRERATKIFDHIAANQTD--RGG 269
                                       **********77755544..666 PP

>> LANC_like  Lanthionine synthetase C-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0025        11     172     214 ..     234     275 ..     149     287 .. 0.68
   2 ?    5.7   0.0    0.0011       4.7     179     233 ..     348     407 ..     341     425 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0025
                                       HHHHHCCCHT.-HHHHHHHHHHHHHHHHHTS-TGTST--SBCT CS
                         LANC_like 172 alallalykgtksekllelikkllkylkslkfksegnWpdsis 214
                                       a +l +ly+  ++e+l+e ++k+++ +  ++  ++g+Wp ++ 
  gi|336254393|ref|YP_004597500.1| 234 AQMLVDLYEYFGDEELRERATKIFDHIAANQ-TDRGGWPYRLP 275
                                       4456666666777777777777777777777.55777777765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0011
                                       CHT.-HHHHHHHHHHHHHHHHHTS-TGTST....--SBCTTSS-S--...SSSSSHHHHHHH CS
                         LANC_like 179 ykgtksekllelikkllkylkslkfksegn....Wpdsisdknsylv...aWChGapGilla 233
                                         + ++e++le ++++l++++ + +  eg+    +  +   +++++v    WC G    +++
  gi|336254393|ref|YP_004597500.1| 348 ILVFTREGDLEFAERILRWVLANMQV-EGEegrfY-YRKYRHHTKRVtlmRWCQGWMSYATS 407
                                       55668999***************944.33335853.44446666666788*****8777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 3509.12
//
Query:       gi|336254394|ref|YP_004597501.1|  [L=412]
Description: group 1 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for 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-31  108.5   0.0    3.5e-31  108.0   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    3.6e-26   92.2   0.0    5.8e-26   91.5   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.3e-07   31.8   0.1    3.7e-07   30.3   0.1    1.8  2  Glyco_transf_4   Glycosyltransferase Family 4
    4.9e-07   30.3   1.4    4.9e-07   30.3   1.4    2.3  3  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    2.1e-06   28.0   0.0    4.2e-06   27.0   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


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 !  108.0   0.0   9.8e-35   3.5e-31      14     170 ..     235     388 ..     222     390 .. 0.95

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 9.8e-35
                                       T-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHH CS
                   Glycos_transf_1  14 kkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleell 90 
                                        ++ ++ +gr++ eK++ l+++a+a+l+++   +++  ++G g+++  + +++++++l+d++ + g v+  d  +++
  gi|336254394|ref|YP_004597501.1| 235 AEYDFVWLGRFSAEKDPILFVRALAQLEAD-GRDFQAAMVGTGSDRTAVIDEIAARGLEDRIDLPGWVD--DPLSYY 308
                                       56778999*******************987.**************************************..****** PP

                                       HCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHH CS
                   Glycos_transf_1  91 knadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlge 167
                                       +++d+fvl+s++++++++ lEAma+gl+ i+  +g +++vv+dge+G++v+   ++a+a+a+++ l+d+  r++l  
  gi|336254394|ref|YP_004597501.1| 309 RRSDAFVLTSRRDALPLAMLEAMASGLAPIVPRVGSVPDVVTDGENGIVVPDRTPAAFARAMARCLDDPGYRADLAD 385
                                       **************************************************************************999 PP

                                       HHH CS
                   Glycos_transf_1 168 nar 170
                                       +a+
  gi|336254394|ref|YP_004597501.1| 386 AAP 388
                                       887 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 !   91.5   0.0   1.6e-29   5.8e-26       3     134 .]     238     376 ..     236     376 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 1.6e-29
                                       EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT.T-T.TEEEE---THHHHHHHH-SE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa.gleerveftGfvedlaellaaadv 75 
                                       +++++Gr+++ +k   l+++a+++l ++  d++  +vG g+ r + ++e aa gle+r+ + G+v+d  ++++++d 
  gi|336254394|ref|YP_004597501.1| 238 DFVWLGRFSA-EKDPILFVRALAQLEADgrDFQAAMVGTGSdRTAVIDEIAArGLEDRIDLPGWVDDPLSYYRRSDA 313
                                       689*****55.5**************88645********99776666665557************************ PP

                                       EEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       fv++s    ++l++lEama+gl+ ++ +vg +++vv  geng++vp++ p+a+a+a++r+l+d
  gi|336254394|ref|YP_004597501.1| 314 FVLTSrrDALPLAMLEAMASGLAPIVPRVGSVPDVVtdGENGIVVPDRTPAAFARAMARCLDD 376
                                       *****7559********************999**************999***********997 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.1     1e-10   3.7e-07      21     169 ..      90     224 ..      84     225 .. 0.80
   2 ?   -2.6   0.0       1.3   4.7e+03       7      33 ..     366     394 ..     364     406 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1e-10
                    Glyco_transf_4  21 eVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgi 97 
                                       e t+v+ +++++++++     + + vp  +++ l+  l f+ +l +  + +++D v + s  + g+ +lal++ +g 
  gi|336254394|ref|YP_004597501.1|  90 ETTLVCLEPERAIDDA-----EYVQVPEIGPRLLRVLLLFFVALYEGYR-NEYDAVASISLLPYGLYALALKAVYGY 160
                                       5678888888888888.....3334444445666666777777777776.69****888888888888888888999 PP

                    Glyco_transf_4  98 plVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekitVipnGvDle 169
                                       p  l + g +           +++++ a  r+++r+ d++ ++  a a+el++ +gvp+e+i+++ n++D++
  gi|336254394|ref|YP_004597501.1| 161 PAHLGIIGID-------LDHHARQWYGAGPRWAFRQFDAISVPGSAHARELVR-MGVPEERIEILTNAIDVD 224
                                       9988888888.......56677888888899**********************.****************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                    Glyco_transf_4   7 hvleLaraLarrGheVtvv..tpgddgpl 33 
                                       +++ +ar L + G++ ++   +p++++++
  gi|336254394|ref|YP_004597501.1| 366 FARAMARCLDDPGYRADLAdaAPAVRDEF 394
                                       57789999999999999987766666655 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 !   30.3   1.4   1.4e-10   4.9e-07      37     159 ..      62     219 ..      39     220 .. 0.67
   2 ?   -2.0   0.0       1.2   4.4e+03     127     146 ..     308     327 ..     287     341 .. 0.80
   3 ?   -2.0   0.1       1.2   4.2e+03       7      35 ..     367     394 ..     361     404 .. 0.67

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.4e-10
                   Glyco_trans_4_4  37 edgvrvhrlp.vprrp....spladlaal.........................ralrrll........rqrrerpd 75 
                                       +d +rv  +  ++++     +plad+a                           ++l r+l        +  r  +d
  gi|336254394|ref|YP_004597501.1|  62 HDDARVLVITgLSHKNerhyGPLADVA-GettlvcleperaiddaeyvqvpeigPRLLRVLllffvalyEGYRNEYD 137
                                       555555544323333221112333322.0122333444444444444444444444444432333333555699*** PP

                   Glyco_trans_4_4  76 vvhahs.ptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelralgvpa 151
                                        v + s ++ gl+a+++++  g p  + + g +l+++   +r++y a  r+++r++da+ v+  a+a+el+++gvp 
  gi|336254394|ref|YP_004597501.1| 138 AVASISlLPYGLYALALKAVYGYPAHLGIIGIDLDHH---ARQWYGAGPRWAFRQFDAISVPGSAHARELVRMGVPE 211
                                       ******667999999999777****999999888755...999********************************** PP

                   Glyco_trans_4_4 152 drvvvvpn 159
                                       +r++++ n
  gi|336254394|ref|YP_004597501.1| 212 ERIEILTN 219
                                       ***99877 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                   Glyco_trans_4_4 127 lrradavlvvseaeaeelra 146
                                       +rr da++ +s+ +a  l+ 
  gi|336254394|ref|YP_004597501.1| 308 YRRSDAFVLTSRRDALPLAM 327
                                       68888888888888765555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.2
                   Glyco_trans_4_4   7 vaelaraLaarGheVtvltpapapgapel 35 
                                       ++++ar L + G++ ++ ++a++++++e 
  gi|336254394|ref|YP_004597501.1| 367 ARAMARCLDDPGYRADL-ADAAPAVRDEF 394
                                       67788888888888887.55555555544 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 !   27.0   0.0   1.2e-09   4.2e-06       3      86 ..     315     399 ..     313     405 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.2e-09
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarerv 77 
                                       + +sr++ + l ++Ea+a+G   ++ +  ++++ +t+g+ +i++   +++ +a++++++l++p+ r+ +a aa +  
  gi|336254394|ref|YP_004597501.1| 315 VLTSRRDALPLAMLEAMASGLAPIVPRVGSVPDVVTDGENGIVVPdrTPAAFARAMARCLDDPGYRADLADAAPAV- 390
                                       56899999999**********************************999**********************998654. PP

                   Glyco_trans_1_2  78 laehtydhr 86 
                                       + e+ +d +
  gi|336254394|ref|YP_004597501.1| 391 RDEFEMDEA 399
                                       666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3073.15
//
Query:       gi|336254395|ref|YP_004597502.1|  [L=339]
Description: hypothetical protein Halxa_3007 [Halopiger xanaduensis SH-6]
Scores for 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-21   75.2   0.0    1.1e-20   74.3   0.0    1.5  1  Acetyltransf_6  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   5.9e-25   1.1e-20       4     141 ..     163     304 ..     160     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 5.9e-25
                    Acetyltransf_6   4 Rknlrrkrrkleelgevrfrvatdpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrl.d 79 
                                        k+lr+++r++++l+ ++++  ++ + + +++e ++ q+++  d  a p t+ flrdll++l +++++r+yv+r  d
  gi|336254395|ref|YP_004597502.1| 163 SKSLRNEMRRYDDLD-LTIEQ-EGIDSAMRIYEDVVVQYEEY-DDTA-PMTEPFLRDLLSSL-DDDRWRVYVARTpD 234
                                       689**********94.55544.68999999************.8885.**************.69**********9* PP

                    Acetyltransf_6  80 grpvAvalglrsgdrlyywlggydpelaklspgllllweliedaae....eGlrrfdlgggde....eyK 141
                                       g++ +++++l s+d +yyw+gg+ ++++++s++ ll++ ++ed++     e ++ +dl+g+++    eyK
  gi|336254395|ref|YP_004597502.1| 235 GEYKSGIITLFSNDLAYYWQGGVVASYEHVSVNNLLHRVILEDIVTdpelESVTGYDLVGANTerlcEYK 304
                                       **********************************************666669********9984555566 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); 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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.60
# Mc/sec: 1698.16
//
Query:       gi|336254396|ref|YP_004597503.1|  [L=661]
Description: hypothetical protein Halxa_3008 [Halopiger xanaduensis SH-6]
Scores for 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   11.5   9.7        1.3    8.9   9.7    2.1  1  Beta_helix   Right handed beta helix region


Domain annotation for each model (and alignments):
>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   9.7   7.1e-05       1.3      22     111 ..     136     237 ..      49     280 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 7.1e-05
                                       SS-SEEE-SSS-...EEES-EEES-SS-SEEE-TT.............-S-EEES-EEE---SEEE-TT.--S--EE CS
                        Beta_helix  22 ggyGiylrgssn..vvienneiannsgsGiyilgs.............snntisnntisdnngggialf.gasnnli 82 
                                       g +Giy+ ++++  ++i n +i++  ++ iy ++               +++i+n++  d+   +  ++ g++++ +
  gi|336254396|ref|YP_004597503.1| 136 GPTGIYVANAHSgtIRINNVNIQDMPDNAIYGSSPgdlsshpsgggggGDVIITNSYAADCV--ASSFRvGTDGSRV 210
                                       55666666666644444444444444444444444444444455555566777777777666..4444446666666 PP

                                       ES-EEES-SS-SEE-TT-S--EEES-EEE CS
                        Beta_helix  83 enneitdnggsGiylnyssnntienNiid 111
                                       en+     +  G++ +y ++ ++ ++ ++
  gi|336254396|ref|YP_004597503.1| 211 ENCVSVGSDC-GFWAFY-NSPKVVDCDFS 237
                                       6666655543.666665.34444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (661 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); 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:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 4262.65
//
Query:       gi|336254397|ref|YP_004597504.1|  [L=511]
Description: polysaccharide biosynthesis protein [Halopiger xanaduensis SH-6]
Scores for 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-28   99.5  12.8    2.1e-28   99.5  12.8    2.6  2  Polysacc_synt    Polysaccharide biosynthesis protein
    4.5e-19   68.8  21.1    1.8e-15   56.9   0.1    3.1  3  Polysacc_synt_3  Polysaccharide biosynthesis protein
    1.2e-18   67.6  17.8    1.2e-18   67.6  17.8    3.6  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    1.1e-08   34.9   1.4    1.1e-08   34.9   1.4    4.0  4  MatE             MatE
  ------ inclusion threshold ------
      0.027   13.1  28.4      0.034   12.7   7.0    3.6  3  MurJ             Lipid II flippase MurJ


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 !   99.5  12.8   5.9e-32   2.1e-28      19     267 ..      26     303 ..      10     309 .. 0.90
   2 ?   -4.1   6.3       2.2   7.8e+03     148     192 ..     447     491 ..     421     508 .. 0.65

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 5.9e-32
                     Polysacc_synt  19 afvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek......kelvslillnvllvllvlv 89 
                                       ++++l ++  +l++e++Gl++la++i + ++ ++ +G+  ++ r++ + re+          + ++ nv+ + +v+ 
  gi|336254397|ref|YP_004597504.1|  26 GLLVLLLTNVFLTTEEYGLLYLAISICSVAIFFSRMGFAKSAARYVTEFRETdpskipFIVRRALTFNVIAIAVVAG 102
                                       57888888999****************************************99877765566788899999999999 PP

                     Polysacc_synt  90 llfllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldi 166
                                       ++ ++  +iaa +g+p+l+ l+ i +l+++ + +  sf + l qg++r  + a+  +v +l++++ vl+++ l+  +
  gi|336254397|ref|YP_004597504.1| 103 TVLAFRGPIAAQFGEPDLVWLLTIGFLFIV-ARTLHSFGYFLCQGFNRVSWSALLLIVANLGILASVLSLLALGFGV 178
                                       9999******************99999999.*****************************************9999* PP

                     Polysacc_synt 167 vaavlgavlaalvggivslavlrkkfr.........................prfvils.lklvrellsfsapltis 217
                                       ++a++g+v+++ +++ ++l+vl+ ++                           +    +   l+r+++ +s+plt++
  gi|336254397|ref|YP_004597504.1| 179 AGALFGYVVGYALSATLGLTVLY-RWVsgadwnatgetaatgstdgegassaGSDDADEtENLTRRIFEYSLPLTVT 254
                                       ***********************.783357889******************955555555889************** PP

                     Polysacc_synt 218 slaillytyidsillglllgaeavGiYnaayqllvaisgllapivtaalf 267
                                        +a+ ly ++d +l g++l+++avG+Y++a ql+  ++  +++    al 
  gi|336254397|ref|YP_004597504.1| 255 GAASILYKRVDIVLVGAILSPVAVGYYTLAKQLTEFVTAPASSLGF-ALA 303
                                       ********************************99877665555555.555 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 2.2
                     Polysacc_synt 148 eqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkf 192
                                       ++l+r++l++  + ++ ++ ++++   +++++++++  ++  + +
  gi|336254397|ref|YP_004597504.1| 447 RSLFRTALTVCSIAGGMSLIVVLGLPYVSSVASLLAIVLLGVVSW 491
                                       566666666666666666444444444444444444444444334 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   8.3   6.4e-08   0.00023       5     164 ..      36     204 ..      35     216 .. 0.83
   2 !   56.9   0.1   5.1e-19   1.8e-15     174     293 .]     241     361 ..     237     361 .. 0.94
   3 ?   -1.0   0.1      0.22   8.1e+02      82     102 ..     360     380 ..     358     447 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.4e-08
                   Polysacc_synt_3   5 LLspedFGvvaialvvislanlfvdmGlssaliqke.dltee.......dlstvftfnlvlgllialvlfllaplia 73 
                                       +L+ e++G++ +a+ + s+a  f++mG+ +   +   +  e+        ++++ tfn++  +++a  +++++  ia
  gi|336254397|ref|YP_004597504.1|  36 FLTTEEYGLLYLAISICSVAIFFSRMGFAKSAARYVtEFRETdpskipfIVRRALTFNVIAIAVVAGTVLAFRGPIA 112
                                       79**************************98876654344444344556668899*********************** PP

                   Polysacc_synt_3  74 sfynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllss 150
                                         +++p+lv +l++  l ++ ++l s    l +   + +  +   +v+++  +++ + l  lg+gv   ++g ++  
  gi|336254397|ref|YP_004597504.1| 113 AQFGEPDLVWLLTIGFLFIVARTLHSFGYFLCQGFNRVSWSALLLIVANLGILASVLSLLALGFGVAGALFGYVVGY 189
                                       **************999999999999999999988888888888888888888888899999***998888888877 PP

                   Polysacc_synt_3 151 llslv.llwlaskwr 164
                                       +ls+   l++ ++w 
  gi|336254397|ref|YP_004597504.1| 190 ALSATlGLTVLYRWV 204
                                       766540555666665 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 5.1e-19
                   Polysacc_synt_3 174 lkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeitsviakVlfPal..Srlqddkk 248
                                       ++++f+++l l++++ + +l++++d +l+G +ls  a+G+Y+ ak+l+++++a   s++   l Pa+  S+ +d+ +
  gi|336254397|ref|YP_004597504.1| 241 TRRIFEYSLPLTVTGAASILYKRVDIVLVGAILSPVAVGYYTLAKQLTEFVTAPA-SSLGFALAPAYgeSKSSDNLE 316
                                       6899*********************************************998875.67899999*997788999*** PP

                   Polysacc_synt_3 249 klrelylkvlrlialivlPiavglavvaellvkvllGsqWleavp 293
                                       + +e y+++++   l+ +P+a+g+a+va+++v+ ++G+ +l a+p
  gi|336254397|ref|YP_004597504.1| 317 RAAEIYHTTFEYNLLFYVPAAAGIALVADPAVRYVFGDGYLGAIP 361
                                       ***************************************998875 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.22
                   Polysacc_synt_3  82 vtvlrvlalvlilsglssvqe 102
                                       +++++vla  ++l++++++  
  gi|336254397|ref|YP_004597504.1| 360 IPIVQVLAAFVVLQSINKITD 380
                                       577888888888888877654 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 ?   -3.8   8.4       3.5   1.3e+04      36     110 ..      24     108 ..      11     133 .. 0.52
   2 !    5.4  13.0     0.005        18       2      79 ..     124     202 ..     120     210 .. 0.82
   3 !   67.6  17.8   3.3e-22   1.2e-18       2     142 ..     363     499 ..     362     500 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.5
                   Polysacc_synt_C  36 vigalvklilnllli.plfgi..vGaaiatvlallvvavlnlyalrrllgikl.......ellrrll.kpllaalvm 101
                                       v g+lv l+ n++l+  ++g+  + ++i +v+ ++  + +   a+r  + ++         ++rr l   ++a +v+
  gi|336254397|ref|YP_004597504.1|  24 VNGLLVLLLTNVFLTtEEYGLlyLAISICSVAIFFSRMGFAKSAARYVTEFREtdpskipFIVRRALtFNVIAIAVV 100
                                       45667777777777766666434667777777777777777666666777776777655522222222333333333 PP

                   Polysacc_synt_C 102 givvyllll 110
                                       ++ v+  ++
  gi|336254397|ref|YP_004597504.1| 101 AGTVL-AFR 108
                                       33333.333 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.005
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigal.vklilnllliplfgivGaaiatvlallvvavlnlyal 77 
                                       L i  l i+  +l++++  + qg +r+ + ++ l+++ l +   +  ll   fg+ Ga+++ v++++++a l l  l
  gi|336254397|ref|YP_004597504.1| 124 LTIGFLFIVARTLHSFGYFLCQGFNRVSWSALLLIVANLgILASVLSLLALGFGVAGALFGYVVGYALSATLGLTVL 200
                                       6677788899999999999*******99988888877654444444444468********************99999 PP

                   Polysacc_synt_C  78 rr 79 
                                       +r
  gi|336254397|ref|YP_004597504.1| 201 YR 202
                                       88 PP

  == domain 3  score: 67.6 bits;  conditional E-value: 3.3e-22
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalr 78 
                                       +++la  ++++s++ ++   L  lgr++  +++   +a+++++lnl+l+p +g+vGaa++tv++++++  +n+y+++
  gi|336254397|ref|YP_004597504.1| 363 VQVLAAFVVLQSINKITDDALDFLGRARHRALSKGGTAALNFVLNLVLLPTIGVVGAALSTVISYAIMVGINIYLIH 439
                                       79*************************************************************************** PP

                   Polysacc_synt_C  79 rllgikl.ellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                        +l ++l +l+r+ l ++ +a +m+++   ++l l+ +++ a  +ll+ vl+g++ +l+l++ ++
  gi|336254397|ref|YP_004597504.1| 440 SELSLPLrSLFRTALTVCSIAGGMSLI---VVLGLPYVSSVA--SLLAIVLLGVVSWLALAVTSG 499
                                       *******99999999999999999999...888888888755..888888899999999998766 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.69   2.5e+03     124     152 ..      26      54 ..      15      59 .. 0.72
   2 ?    3.6   5.1     0.013        47      63     152 ..      77     161 ..      47     172 .. 0.74
   3 !   34.9   1.4   3.1e-12   1.1e-08       1     159 [.     250     407 ..     250     409 .. 0.92
   4 ?    0.3   4.7      0.13   4.7e+02      71     124 ..     420     473 ..     415     501 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.69
                              MatE 124 alalqlvlsgilrgagktkvplyislisl 152
                                       +l+++l+++ +l + ++  + l+is++s+
  gi|336254397|ref|YP_004597504.1|  26 GLLVLLLTNVFLTTEEYGLLYLAISICSV 54 
                                       55667777778888888888888888876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.013
                              MatE  63 knfkrakealrqglilllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgag 139
                                        ++ ++ +++r++l ++++  +++a  vl+f+ +i+  f+ ++ v      +l i +l+i+a  l+   +  ++g  
  gi|336254397|ref|YP_004597504.1|  77 TDPSKIPFIVRRALTFNVIAIAVVAGTVLAFRGPIAAQFGEPDLVW-----LLTIGFLFIVARTLHSFGYFLCQGFN 148
                                       57889999*******************************9988654.....45555555555555555555555555 PP

                              MatE 140 ktkvplyislisl 152
                                       ++ +++ ++++++
  gi|336254397|ref|YP_004597504.1| 149 RVSWSALLLIVAN 161
                                       5665555555554 PP

  == domain 3  score: 34.9 bits;  conditional E-value: 3.1e-12
                              MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl 76 
                                       P+ ++ ++  l++ +d++lvg + +++a++ +++a ++++++++++ +l+ al++  g +  + n +ra+e++++++
  gi|336254397|ref|YP_004597504.1| 250 PLTVTGAASILYKRVDIVLVGAIlSPVAVGYYTLAKQLTEFVTAPASSLGFALAPAYGESKSSDNLERAAEIYHTTF 326
                                       77888889999****************************************************************** PP

                              MatE  77 illlllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisll 153
                                         +ll+++++a+ + l +++ ++++  d      a  ++++l+ ++++++++ +++ +l+  g+++  +     ++ 
  gi|336254397|ref|YP_004597504.1| 327 EYNLLFYVPAAAGIALVADPAVRYVFGDG--YLGAIPIVQVLAAFVVLQSINKITDDALDFLGRARHRALSKGGTAA 401
                                       ************************99999..5678899999999999999999999999999998888888887778 PP

                              MatE 154 lnipln 159
                                       ln++ln
  gi|336254397|ref|YP_004597504.1| 402 LNFVLN 407
                                       888877 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.13
                              MatE  71 alrqglilllllsliiallvllfseqilslftqdeevlelakrylrililgipa 124
                                       al + +  ++ +++ i l+   +s ++ slf +  +v+++a  + +i++lg+p 
  gi|336254397|ref|YP_004597504.1| 420 ALSTVISYAIMVGINIYLIHSELSLPLRSLFRTALTVCSIAGGMSLIVVLGLPY 473
                                       5555566666666666666666799999**********************9985 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.6     0.096   3.4e+02     370     432 ..      36     106 ..      11     126 .. 0.46
   2 ?    8.6   6.8   0.00017      0.61     191     312 ..     235     356 ..     122     371 .. 0.82
   3 ?   12.7   7.0   9.6e-06     0.034     362     438 ..     400     476 ..     398     489 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.096
                              MurJ 370 llllpplgvvglalatslsaliglvllyvllrkrlk....lteargiktflak....lvvllalaavvill 432
                                       +l    +g+++la++   +a++   + +   + r +     t+ ++i + +++     v+++a++a+ +l 
  gi|336254397|ref|YP_004597504.1|  36 FLTTEEYGLLYLAISICSVAIFFSRMGFAKSAARYVtefrETDPSKIPFIVRRaltfNVIAIAVVAGTVLA 106
                                       33444555555555554444333333333333333333332222333333333223334444444444444 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00017
                              MurJ 191 afrdeglkkflklllptllgvsvsqlnllvdtalAsf.laegsvsilayadrilqlPlglfgvsistvlLPrlSrsa 266
                                       +++++  +++++  lp +++ ++s+l   vd++l  + l +++v ++  a+ + ++  +  + s+  +l P+  +s+
  gi|336254397|ref|YP_004597504.1| 235 DETENLTRRIFEYSLPLTVTGAASILYKRVDIVLVGAiLSPVAVGYYTLAKQLTEFVTAP-ASSLGFALAPAYGESK 310
                                       556777899999********************9987769*****************8885.779************* PP

                              MurJ 267 kekdedevrdllsqairltllllipvsfgllvlskpivsllferGn 312
                                       ++++ + + +   ++    ll  +p+++g++++++p+v+ +f  G 
  gi|336254397|ref|YP_004597504.1| 311 SSDNLERAAEIYHTTFEYNLLFYVPAAAGIALVADPAVRYVFGDGY 356
                                       ******************************************8885 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 9.6e-06
                              MurJ 362 lvlnillsllllpplgvvglalatslsaliglvllyvllrkrlklteargiktflaklvvllalaavvilllssltq 438
                                       + ln +l+l+llp++gvvg al+t++s+ i +++ ++l+  +l+l   ++++t l   +++  +  +v+l+l  +++
  gi|336254397|ref|YP_004597504.1| 400 AALNFVLNLVLLPTIGVVGAALSTVISYAIMVGINIYLIHSELSLPLRSLFRTALTVCSIAGGMSLIVVLGLPYVSS 476
                                       679*************************************************9999966655555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 3600.29
//
Query:       gi|336254398|ref|YP_004597505.1|  [L=608]
Description: hypothetical protein Halxa_3010 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        3.1    6.5  12.3         11    4.6  12.3    1.9  1  DUF2206   Predicted membrane protein (DUF2206)


Domain annotation for each model (and alignments):
>> DUF2206  Predicted membrane protein (DUF2206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  12.3   0.00061        11      19     233 ..     208     473 ..     190     506 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.00061
                           DUF2206  19 lsyivllllalayllliilr....................................................lyike 43 
                                       +s  vl++ +l+yll++++r                                                    +  + 
  gi|336254398|ref|YP_004597505.1| 208 MSQAVLFSALLVYLLVKYVRpgresvsrpasaigvalafvsiatvvyhpqlvahliavflgicalqflarrvASDGR 284
                                       55566666666666666666666666666666666666666666666666666666666666666665444322222 PP

                           DUF2206  44 dksqilnftyvlifvvlalaWYlyissssafktiasivnkilssiateflnptttqglavitkqis......sllht 114
                                       ++ q++   +  + + l l+W    +s+  f    ++++++ s++++ +l+ +  +g  v+++ +s      sl+  
  gi|336254398|ref|YP_004597505.1| 285 MAGQTTLYGHSAFLIGLFLVW----TSNHDF--FSGMFEHFFSAAIEFVLEGRSGAGDTVAVQGASlsaiggSLVEV 355
                                       333333333333333333333....322222..33455566655555555554444433333322211111155555 PP

                           DUF2206 115 vskylhliiqfliviGvlsv.lfl.rkkkyrlsieylai.vlvllvilvasivlpyfas.alntaRlyqilliflap 187
                                        +k+    + f++ +G l++ +++ r++ +  si+   + +l +lv lv ++ + ++a+ +    R++ ++++f+  
  gi|336254398|ref|YP_004597505.1| 356 FFKLFTAQLVFVLLVGALALgVVVrRNSSWFASIRAETMyFLGALVALVPLFGIYFLAPdSTMHFRVFGLMMLFVTL 432
                                       66777777888899*****9866647777766665444414445556666667777777888899*********987 PP

                           DUF2206 188 ffiiGgialiklikkvikksklkskdsiklkiisvflvvllLfn.sG 233
                                       + +i+   + +l  k+   s  +s       +i v +++ll ++ + 
  gi|336254398|ref|YP_004597505.1| 433 LGSIA---IHGLTTKF---SGDRSRFVPGHPVIAVGFALLLVLSlAA 473
                                       66666...55555555...5557888888888888888888888444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); 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):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.25s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 4138.95
//
Query:       gi|336254399|ref|YP_004597506.1|  [L=347]
Description: hypothetical protein Halxa_3011 [Halopiger xanaduensis SH-6]
Scores for complete 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-83  280.5   4.2    1.9e-83  280.3   4.2    1.0  1  DUF1616   Protein of unknown function (DUF1616)
     0.0011   19.2   0.1     0.0027   18.0   0.1    1.6  1  SQAPI     Aspartic acid proteinase inhibitor


Domain annotation for each model (and alignments):
>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.3   4.2   2.1e-87   1.9e-83       3     293 .]      35     336 ..      33     336 .. 0.97

  Alignments for each domain:
  == domain 1  score: 280.3 bits;  conditional E-value: 2.1e-87
                           DUF1616   3 vlalllllailvpvlnetplRivlglplvLflPGYaliaaLFPe..............krdidgieRlaLSfglSia 65 
                                        ++++++l+++v+ + + ++R+++g+pl++++PGYa++aaLFP+               rd++++eR+aL+fglS a
  gi|336254399|ref|YP_004597506.1|  35 GFVAVATLLLTVVDIGSPVVRAAVGFPLLFLAPGYAIVAALFPRaapleastgfgigqMRDVTEVERAALAFGLSFA 111
                                       578889999999999************************************************************** PP

                           DUF1616  66 ivpliglvlnvtpwgirlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleeksesrldkaln 142
                                        +pligl     +++++   ++ ++s+f+ll+++vA+vrR r+p+++r+++ l + + +++++  ++  s + +a+n
  gi|336254399|ref|YP_004597506.1| 112 SLPLIGLTAAALSLEFTGPVVVGAVSGFVLLTVAVATVRRFRVPAQDRYRLRLLRKVGAARAAIVDR-GSIAYTAVN 187
                                       ******************************************************************6.5689***** PP

                           DUF1616 143 vlLvvsivlavaalgyavvaPkegekfTelyllgedgd.elvaenypteltagesqevivgieNhEheevnYtvvvl 218
                                       v+L+vs+v+a++++gya+v+P+++e++T+l llged+  elva+ny+te+++ges ++++ +eN+E+++++Yt vv+
  gi|336254399|ref|YP_004597506.1| 188 VVLIVSMVIALTSVGYALVSPQQAEQYTDLRLLGEDDGgELVAGNYTTEIESGESVPLTIAVENQEGSTTEYTAVVQ 264
                                       ***************************************************************************** PP

                           DUF1616 219 lqevtdeeevevlerteldrrevtladnetweqelevepeatgenlrleflLYkdevpeeptteeayrslhlwVn 293
                                       +q     e+++vlert+++r e+++ d+et + e +v+p+a+ +++r+++lLY+++vp++pt ++ayrs +lwV+
  gi|336254399|ref|YP_004597506.1| 265 EQW---LEDGSVLERTDHQRVEYSVGDGETATAERSVTPTAESGEVRIAVLLYEGDVPDTPTVDNAYRSGYLWVE 336
                                       **9...66778999***********************************************************96 PP

>> SQAPI  Aspartic acid proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1     3e-07    0.0027      37      72 ..     234     269 ..     227     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3e-07
                             SQAPI  37 etQvvsgtnYrLviaakdgsgatknYeavVvEkpwe 72 
                                       +t + sg    L+ia+++++g t++Y avV E+ +e
  gi|336254399|ref|YP_004597506.1| 234 TTEIESGESVPLTIAVENQEGSTTEYTAVVQEQWLE 269
                                       467899999***********************9555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2582.31
//
Query:       gi|336254400|ref|YP_004597507.1|  [L=335]
Description: hypothetical protein Halxa_3012 [Halopiger xanaduensis SH-6]
Scores for complete 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   74.1   0.0    3.1e-20   72.8   0.0    1.7  1  Acetyltransf_6  Acetyltransferase (GNAT) domain
     0.0013   17.8   0.0        1.1    8.1   0.0    2.2  2  FemAB           FemAB family


Domain annotation for each model (and alignments):
>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   0.0   3.5e-24   3.1e-20       7     141 ..     171     304 ..     167     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 3.5e-24
                    Acetyltransf_6   7 lrrkrrkleelgevrfrvatdpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrldgrpv 83 
                                        r+ +r+ ++++e++  v  +pe+++ ++e++ ++++ + d+   + + +f+ dl+++  a g +r y+lr+dg ++
  gi|336254400|ref|YP_004597507.1| 171 ARSNIRNTDDAYEIE--V-GGPEEIRLIHEQVKNRYESQ-DIGF-DVPVEFVLDLAEQS-ANGHVRPYTLRVDGDFI 241
                                       577778888876555..4.79******************.**96.8999********98.6999************* PP

                    Acetyltransf_6  84 Avalglrsgdrlyywlggydpela.klspgllllweliedaaeeGlrrfdlgggde....eyK 141
                                       +++l+l++g++   w+gg++ +++ ++  ++ll w +++d  e+Gl+++dl+g+d+    +yK
  gi|336254400|ref|YP_004597507.1| 242 GGILALEYGGTTGRWMGGVRTDADvDVATNDLLDWSIMQDGLENGLETYDLVGADTrrinRYK 304
                                       ***********************88****************************9975555677 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0   0.00019       1.7     148     182 ..     146     179 ..     138     186 .. 0.89
   2 !    8.1   0.0   0.00012       1.1     337     382 ..     272     312 ..     237     315 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00019
                             FemAB 148 vqprwqlvldleeiteedllksfskktrknikkak 182
                                       + p++++ +dl+  +e+dll +fs+++r ni+++ 
  gi|336254400|ref|YP_004597507.1| 146 ATPEYTYAVDLTL-DEDDLLMTFSSDARSNIRNTD 179
                                       689********98.9999**************986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00012
                             FemAB 337 yllqweaiqeAlergieryNfyGiegkfdgsdGvlrFKtgFngfve 382
                                        ll w ++q+ le+g+e y++ G +    +     r+K +Fn++ +
  gi|336254400|ref|YP_004597507.1| 272 DLLDWSIMQDGLENGLETYDLVGADTRRIN-----RYKAKFNPELR 312
                                       5899******************98776665.....99999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2590.06
//
Query:       gi|336254401|ref|YP_004597508.1|  [L=147]
Description: RDD domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   84.1   1.6    1.1e-23   84.0   1.6    1.0  1  RDD         RDD family
  ------ inclusion threshold ------
       0.25   10.9   0.0        0.4   10.2   0.0    1.4  1  Pex2_Pex12  Pex2 / Pex12 amino terminal region
        2.4    8.6   5.0       0.54   10.6   1.9    1.4  2  DUF2628     Protein of unknown function (DUF2628)


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   1.6   1.9e-27   1.1e-23       2     140 ..      12     140 ..      11     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 1.9e-27
                               RDD   2 aslgrRllAfliDlvllliislllallivallnakasaneavagslllllllvlllvllvyqllllskkgqTlGkll 78 
                                       a+l  R +A+++D+++++i+++++++l+       +s+  a a +   +++++ l++  +y+ + ++k+g T+Gk+l
  gi|336254401|ref|YP_004597508.1|  12 AGLLERGVAWFVDGIVMFILLFVAIVLVLL----LFSPDGAPAEAAEGIAAIIGLVASTAYYMVTEAKWGRTPGKML 84 
                                       78999************************9....78***************************************** PP

                               RDD  79 lglkvvdedgrklglaqaliRalllllllvlglslvlllllligflfvlfsrkrqalhDkla 140
                                       lgl+vv+ dgr+++   a+iR+++++      l+ ++l+  +i++l+vl s+++q+l D+l 
  gi|336254401|ref|YP_004597508.1|  85 LGLRVVHLDGRPCTGSGAVIRNITKV------LGGSSLFPVVIAILLVLSSDDNQRLGDMLG 140
                                       ***********************864......799************************985 PP

>> Pex2_Pex12  Pex2 / Pex12 amino terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   6.7e-05       0.4      34      71 ..      61      95 ..      57     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.7e-05
                        Pex2_Pex12 34 kllldlllelltlksgngTfgeefygLkrvssselkkr 71
                                       l++ +++++ t  ++++T+g ++ gL+ v    l++r
  gi|336254401|ref|YP_004597508.1| 61 GLVASTAYYMVTEAKWGRTPGKMLLGLRVV---HLDGR 95
                                      589999**********************99...44433 PP

>> DUF2628  Protein of unknown function (DUF2628)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.9     9e-05      0.54      43      90 ..      23      70 ..      15      73 .. 0.80
   2 ?   -3.9   0.1         3   1.8e+04      75      80 ..     120     125 ..     111     129 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9e-05
                           DUF2628 43 lkalvllviavavsvvlavlgfsdavrlllalliaillgleanslyyl 90
                                      ++++v++++ +++ v + +l  +d++++  a +ia+++gl a+ +yy 
  gi|336254401|ref|YP_004597508.1| 23 VDGIVMFILLFVAIVLVLLLFSPDGAPAEAAEGIAAIIGLVASTAYYM 70
                                      566777766666666666667899999999*****************7 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3
                           DUF2628  75 liaill 80 
                                       +iaill
  gi|336254401|ref|YP_004597508.1| 120 VIAILL 125
                                       333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1160.87
//
Query:       gi|336254402|ref|YP_004597509.1|  [L=537]
Description: type I phosphodiesterase/nucleotide pyrophosphatase [Halopiger xanaduensis SH-6]
Scores for 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-37  128.7   0.0    3.4e-35  122.3   0.0    2.1  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3   0.0   1.9e-39   3.4e-35       1     332 [.       9     425 ..       9     438 .. 0.85

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 1.9e-39
                                       EEEEEETT-BTTHHHHHG.S.TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTE CS
                      Phosphodiest   1 vlvislDGlradlldrla.e.llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktge 75 
                                       +l++++D +  + l +++ + +lp l++++++gvs+  l++++P+ T++++ sl+TG++Pg+HG++g+  +  ++ +
  gi|336254402|ref|YP_004597509.1|   9 TLLVGIDAACDRVLAPMFeDgDLPALESIYEQGVSSS-LESQIPPWTASAWPSLYTGKNPGKHGVFGFLSF--DGYD 82 
                                       6899*************9769****************.*****************************5555..3333 PP

                                       EEEEETTTTGGGGGCTTS-HHHHHHHTHTTCEEEESETTTTSEBTTCT.SC.........TBHHSBTCT.CSTTS.. CS
                      Phosphodiest  76 yvvfvtededaprwwqgepiwdtaakarglkaaalfwpgsevdystyyylvs........etppryleddfnakv.. 142
                                          +++ ++++   +++  +w+ +    gl++ ++++p + +++   ++l          +++p+ l ++++++   
  gi|336254402|ref|YP_004597509.1|  83 ---WDVVNASD---VRERALWELLDDH-GLTSVVVNVPVTHPPREFDGALIPgytapedpDCHPSGLLEEVRDEIge 152
                                       ...33333333...899**********.*****************99999889999999999999999999999898 PP

                                       ....CHHHHHHHHHHHHH...HHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-T.TSHHHHHHHHHHHHHHHHH CS
                      Phosphodiest 143 ....pledkvdkavlqtw...ldaafakvvlekelekpdlllvyleetDtvgHkfGp.dspevedalrrvDkaigdL 211
                                           p ed +d  +  ++     +  ++ ++ +   +p + ++ + +tD++ H+  p ++++++  +r+vD+ ++ +
  gi|336254402|ref|YP_004597509.1| 153 yrvyPDEDAAD--LGTAYvdcARMRGEAFRYLADRFDPAFGFLEFQGTDSIFHEE-PeNDEAIRSIYREVDRQLATI 226
                                       88773333333..2223311133333333333333789*****************.846****************** PP

                                       HHHHHHTTGTTTEEEEEEES---EEEHTTSEEEGGGTSTGGH................................... CS
                      Phosphodiest 212 lealderglsaetniilvSDHGmadvsddkvielndlleekg................................... 253
                                       le+ d++      ++i++SDHGm++  d + +++nd+l+++g                                   
  gi|336254402|ref|YP_004597509.1| 227 LESHDPD------TVIVASDHGMGPY-DGYEFRVNDYLRDEGlvatenggdgmptwatvrddslkrgedsteydpga 296
                                       *******......5************.5569********************************************** PP

                                       ...........................................GEEEEECBHHS.SSE.....EEEEESTEE.E.CC CS
                      Phosphodiest 254 ...........................................llhlkdegkggakal.....iainpkare.lnrv 281
                                                                                  + +++++++ ++        +++n+++re  + v
  gi|336254402|ref|YP_004597509.1| 297 aeramaaaakagltsqrigrllerlgiydlvaayaptglvnagATQVDFPESTAYVRSrielgVRLNLEGREpNGVV 373
                                       ***************************999999999999999988888888666665588999************** PP

                                       CTTHHHHHHHHHHTCHHCCHSTHTT..TEEEEEGG.GS-GGGCHSTTS-SEEEE CS
                      Phosphodiest 282 aeaeaeevyaelkakleelrkkege..alavylke.aipkrlhykkrapdlvlv 332
                                       +++e+e v++++ ++l + ++++ge  + av+ +e  ++++    ++a d+v +
  gi|336254402|ref|YP_004597509.1| 374 PREEYETVRTRVIDALRSATTPDGEpvFEAVRPREeFFHGPES--EHAVDIVTI 425
                                       ***************99999778888899**999933554433..666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 3779.80
//
Query:       gi|336254403|ref|YP_004597510.1|  [L=265]
Description: zinc/iron permease [Halopiger xanaduensis SH-6]
Scores for complete 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-13   50.3  20.1    2.4e-12   46.7   8.6    3.2  2  Zip       ZIP Zinc transporter


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 !    4.9   3.7   0.00071        13       5      63 ..      11      65 ..       6      90 .. 0.56
   2 !   46.7   8.6   1.4e-16   2.4e-12     182     307 ..     102     237 ..      93     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.00071
                               Zip  5 ilaiiaililsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealea 63
                                      ++a +++ +++ lg l+ l++       s+++  +l  +a+G++l+ + + L+ e+l++
  gi|336254403|ref|YP_004597510.1| 11 FVAGLVTALATGLGALPFLFFES----ISDRRNVVLWGIASGIMLSASVFGLVDEGLAE 65
                                      33333333334444443333332....35566666777777777777777777776654 PP

  == domain 2  score: 46.7 bits;  conditional E-value: 1.4e-16
                               Zip 182 lkvraiilllgl.ilHsfidGLAlG................vssssstgislfiAvllHelpeelglgaiLlkagls 241
                                        +   ++l+lg+  +Hsf++G+A+G                +++    +i++++A+++H++pe+ ++ ++L ++g +
  gi|336254403|ref|YP_004597510.1| 102 ANFKKLVLILGIlTVHSFPEGVAIGvsfadlgleggialfgFTV-PLLAIFMTVAISIHNVPEGTAIAIPLSSMGVD 177
                                       556678899997369**********9864444222222211111.123456789*********************** PP

                               Zip 242 rkkavllnllfaltaplGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnek 307
                                        +k v ++++++l  p+G+++++        + a    ++ ++++aG ++Y  l+e++p E l   
  gi|336254403|ref|YP_004597510.1| 178 DWKLVWWAVFSSLPQPVGAVVAFS-----FVRVAREFLPYGFGFAAGAMIYLVLTEFIP-EALDLG 237
                                       ***********************9.....8899999***********************.876544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1860.84
//
Query:       gi|336254404|ref|YP_004597511.1|  [L=390]
Description: integrase domain-containing protein SAM domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-05   24.8   0.1    7.5e-05   23.0   0.1    2.0  1  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.068   13.6   0.0    2.0  1  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
      0.084   13.1   0.0       0.19   11.9   0.0    1.6  1  DUF5333          Family of unknown function (DUF5333)
      0.099   13.0   0.0       0.34   11.3   0.0    1.8  1  Phage_int_SAM_5  Phage integrase SAM-like domain


Domain annotation for each model (and alignments):
>> 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 !   23.0   0.1   1.7e-08   7.5e-05      26      82 ..      41     102 ..      38     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.7e-08
                                       HHHHHHHHHH..TS--TTT--HHHHHHHHHS-----....-----HHHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_1  26 Lrrflkflae.rgkesleqlttedvraflaeleeeg....lsatslarrlsalrsFfqflvr 82 
                                       L+rf+++l+  +g +s+ +l+te++r++ +el+++     ++ +++  + + +r+F+++  r
  gi|336254404|ref|YP_004597511.1|  41 LERFVDWLEReHGVRSVSALETEHMRSYARELRDRAdrgeYAPATAGTYYAVVRAFLSWCAR 102
                                       89*******99*********************9988899*******************9766 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 ?   13.6   0.0   1.5e-05     0.068      26      82 ..      41     104 ..      32     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                   Phage_int_SAM_4  26 ikrflrflkkk.....apeeltkedieaYlnyLanerk....lsastqknalnalsffykkvlere 82 
                                       ++rf+++l+ +     +++ l++e++++Y   L+ +r     ++++t+ ++ ++ ++f ++ ++ +
  gi|336254404|ref|YP_004597511.1|  41 LERFVDWLE-RehgvrSVSALETEHMRSYARELR-DRAdrgeYAPATAGTYYAVVRAFLSWCARSD 104
                                       789999998.557777*****************9.6667899****************99987765 PP

>> DUF5333  Family of unknown function (DUF5333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.3e-05      0.19      38      72 ..     256     290 ..     251     315 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.3e-05
                           DUF5333  38 seleslkakarelGYseaeieayvddkaekarlra 72 
                                       s + ++++++r++GY ++eiea++++++  +  r+
  gi|336254404|ref|YP_004597511.1| 256 SIASRVRSTLRDRGYDDEEIEALLEERTATELARE 290
                                       5678999*****************99875443333 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 ?   11.3   0.0   7.5e-05      0.34      51      94 ..      41     111 ..      38     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.5e-05
                                       HHHHHHHH...........................HHTS---HHHHHHHHHHHHHHHHHHHHTTS--S-HH CS
                   Phage_int_SAM_5  51 leeFedYL...........................kkkkglsentiskyfkklkavlnkAikegilkknpy 94 
                                       le+F d+L                            ++ +++++t+++y+   +a+l+ + + +i+  np 
  gi|336254404|ref|YP_004597511.1|  41 LERFVDWLerehgvrsvsaletehmrsyarelrdrADRGEYAPATAGTYYAVVRAFLSWCARSDIIAANPA 111
                                       6777777777777777766666666666666565544559******************************4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2793.62
//
Query:       gi|336254405|ref|YP_004597512.1|  [L=623]
Description: NADH dehydrogenase (quinone) [Halopiger xanaduensis SH-6]
Scores for 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-33  113.8  14.6    8.3e-33  113.8  14.6    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 ?   -0.5   1.0     0.032   5.7e+02     247     279 ..      20      51 ..       8      54 .. 0.67
   2 !  113.8  14.6   4.6e-37   8.3e-33       1     274 [.     122     387 ..     122     391 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.032
                   Proton_antipo_M 247 lvllvlllslaGlPptagFlskfliLeaavavs 279
                                       lv++ +ll l+ lP +agF   +l L+a++a+s
  gi|336254405|ref|YP_004597512.1|  20 LVFAAALLVLV-LPRLAGFTVGALSLAAVLAIS 51 
                                       34445555555.889999988888888888776 PP

  == domain 2  score: 113.8 bits;  conditional E-value: 4.6e-37
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       a+d+l l + +El+ + ++l++  ++ +  +++A++ +++    g ++ +l++++ y   g  +f +       + +
  gi|336254405|ref|YP_004597512.1| 122 AGDWLVLLFMWELMAVTSTLVVWHYGGE--AVRAGFRYAVFHGTGGVLVMLAVAVHYVEVG--SFLYA------ANE 188
                                       789******************9988777..9******************************..33333......355 PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqlllila 154
                                        ++  + +ll ++g+ v +a + +h Wlpd y    ++ s++l+  + k ++++l r +++ a  + ++ ++++ ++
  gi|336254405|ref|YP_004597512.1| 189 GIASGIPELLAVLGMGVNVAFIGFHSWLPDTYPRPHIAASVFLSVYTTKTSAFVLYRAFPIGA--ESDLGIYIAYMG 263
                                       7888899999*********************************99999********9999988..99999******* PP

                   Proton_antipo_M 155 iismllgslvalaqtdiKrllAySsishlGymlialav.....atqygveaaiihllthalfkallFllagsviyer 226
                                        +  ++g++ al q d++ ll y   ++lGy++ ++++     +++ + ++a+ hl+  +lfk+llF+++g viy++
  gi|336254405|ref|YP_004597512.1| 264 GLMSVYGATFALLQHDMRALLSYHIQAQLGYIVAGIGMgawmvESELATAGAMSHLFNNILFKSLLFMAVGVVIYRT 340
                                       ********************************9998774444467778899*******************9999988 PP

                   Proton_antipo_M 227 ektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLea 274
                                         ++d+ ++ggL+  mP++a+ + +++ls++++P++ g++sk +++ a
  gi|336254405|ref|YP_004597512.1| 341 -GEEDLYNLGGLWREMPLTAIGFGLGALSITAIPGFNGYVSKGMLFDA 387
                                       .999**************************************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); 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:                         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: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4386.35
//
Query:       gi|336254406|ref|YP_004597513.1|  [L=644]
Description: NADH dehydrogenase (quinone) [Halopiger xanaduensis SH-6]
Scores for 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-52  178.2  18.5    9.8e-52  176.0  18.5    2.0  1  Proton_antipo_M  Proton-conducting membrane transporter
      1e-05   25.5   0.2    3.1e-05   23.9   0.2    1.9  1  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 !  176.0  18.5   1.1e-55   9.8e-52       1     281 [.     135     436 ..     135     451 .. 0.84

  Alignments for each domain:
  == domain 1  score: 176.0 bits;  conditional E-value: 1.1e-55
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgs.liLLlgilllynltg.....tlefeelska 71 
                                       a +L+++++++El +l++y L++ ++++ ++  A+ k++ +t++g  ++LL g +++y+lt+     tl fe+   +
  gi|336254406|ref|YP_004597513.1| 135 AANLVTIFVFYELLSLVTYPLVAHNEDD-EARIAGRKYITYTFFGGgVFLLAGTVMVYWLTSlvqepTLAFEAGGIT 210
                                       689**********************888.88889999999999975277888899*******666666666554433 PP

                   Proton_antipo_M  72 l...elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirllllla.... 140
                                       +    + ++   + ++++ll++g+ vK+a++plh Wl+da + aPtpvs ll A  +vk g++++ r++l +     
  gi|336254406|ref|YP_004597513.1| 211 AlaeAAQAEPVYAQAAFFLLILGFGVKAALMPLHSWLADA-MVAPTPVSGLLhAVAVVKSGAFGISRVILEVYgpgl 286
                                       36755666667788999***********************.***********9999***********9875433332 PP

                   Proton_antipo_M 141 ..........vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllt 207
                                                 + +  +++ ++++a+ ++  +s++a+++  +Kr lAyS+ ++l y++++l++   y++ +a++h+ +
  gi|336254406|ref|YP_004597513.1| 287 iydlpldvpgIGEVGLNIPVALVAAFTLTAASIIAMRKDHLKRRLAYSTTAQLSYIVLGLSLLHPYAIVGALFHIPA 363
                                       2223333333345567899********************************************************** PP

                   Proton_antipo_M 208 halfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavsli 281
                                       ha+ k++lF +ag++ + +++t++i +++g+ k+mP++  ++++++ ++aGlPp agF+skf++L +  +v+  
  gi|336254406|ref|YP_004597513.1| 364 HAFAKLTLFFCAGAI-HVETHTDYISEMAGIGKRMPLTLSAFTIGAAGMAGLPPIAGFVSKFYMLIGTGDVGGS 436
                                       ************766.8888*********************************************887665432 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 !   23.9   0.2   3.5e-09   3.1e-05      12      56 ..      75     121 ..      68     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.5e-09
                   Proton_antipo_N  12 ieigfllDklsalmllvvtfvsllvhlYSigYMa..ddegyqRFfay 56 
                                       ++++++ D+l + ++l+ +f+  +  +Y+ gYM+  d+  ++RFfa 
  gi|336254406|ref|YP_004597513.1|  75 LDFALRADPLGIFFALLASFLWIFTSFYAAGYMRglDEHAQTRFFAA 121
                                       6899*****************************95346689****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 4464.23
//
Query:       gi|336254407|ref|YP_004597514.1|  [L=526]
Description: NADH dehydrogenase (quinone) [Halopiger xanaduensis SH-6]
Scores for 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-58  196.7  15.2    4.7e-58  196.7  15.2    1.9  2  Proton_antipo_M  Proton-conducting membrane transporter
    3.9e-05   23.1   5.8    3.9e-05   23.1   5.8    3.1  3  NADHdeh_related  NADH dehydrogenase I, subunit N related prot


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 ?   -1.1   0.1     0.097   8.7e+02     240     274 ..      85     119 ..      70     124 .. 0.68
   2 !  196.7  15.2   5.3e-62   4.7e-58       2     293 .]     128     426 ..     127     426 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.097
                   Proton_antipo_M 240 kkmPilalvllvlllslaGlPptagFlskfliLea 274
                                        +  i+a++l vl+++  G P    F+s  l+L++
  gi|336254407|ref|YP_004597514.1|  85 IVLLITAVALGVLAFTRRGGPRGNTFYSAYLLLTG 119
                                       44456777777777777777777777777777765 PP

  == domain 2  score: 196.7 bits;  conditional E-value: 5.3e-62
                   Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglns 78 
                                       +d++ l+++lE+++l++y L++   + p+++ A+lk+++l+ ++ ++ L+g++ ++ +tgtl++ el++ +   ++ 
  gi|336254407|ref|YP_004597514.1| 128 GDVFNLFVFLEITSLATYALVASG-DGPEAAVAALKYLILGTVAASMYLIGVAFVFMATGTLNMVELATEI-PDADP 202
                                       58999****************987.888****************************************994.44566 PP

                   Proton_antipo_M  79 lelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.....vssneisqll 150
                                         + +++ +++vg+++K+aq+plh W p ay+ aP  v+ l+Aa++++a+++++ rl++ ++      + + +  ++
  gi|336254407|ref|YP_004597514.1| 203 TLIRAGFAFMIVGFATKVAQWPLHSWQPSAYERAPDGVTPLIAALVSTASAYAFGRLIVTVFevdylAAMPRAGPIV 279
                                       77889999********************************************9998887665555557889999*** PP

                   Proton_antipo_M 151 lilaiismllgslvalaqtdiKrllAySsishlGymlialav....atqygveaaiihllthalfkallFllagsvi 223
                                       ++++ +s+l g+++a+ q+++Kr+lAySs+s+ G++l a +v    +++ ++ +a ihl+ h+l+ka+lFl +  v 
  gi|336254407|ref|YP_004597514.1| 280 VTIGCVSVLAGTVLAVIQREVKRMLAYSSVSQFGLVLAAYGVviagQSETAFVGAAIHLVGHGLLKAGLFLGVALV- 355
                                       **************************************99887878888999*********************666. PP

                   Proton_antipo_M 224 yerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvlt 293
                                            +r++++y+gLa+ +P+ a  ++vlll+l+G+Pp  gF++k++i  +av+ +l+ ++++ +++++lt
  gi|336254407|ref|YP_004597514.1| 356 ATSYGARTVDEYAGLATDRPVAAGSIAVLLLALVGVPPGIGFVGKWYIAVGAVQSELWPVAAViFLSTMLT 426
                                       6667***************************************************9998777757777765 PP

>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.32   2.8e+03     129     143 ..      37      51 ..      35      93 .. 0.68
   2 !   23.1   5.8   4.3e-09   3.9e-05      83     158 ..     122     199 ..     112     228 .. 0.80
   3 !    2.6   6.0    0.0082        74     133     216 ..     346     434 ..     308     437 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.32
                   NADHdeh_related 129 liatlplfggaalil 143
                                        ++tl lfgga  ++
  gi|336254407|ref|YP_004597514.1|  37 GLTTLGLFGGAVYLA 51 
                                       578999999986554 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 4.3e-09
                   NADHdeh_related  83 lgavvtgdvfnftlflaliGianiGivaavkkefvleaafnyGlvaliatlplfggaalilastGtlsifelakl.. 157
                                       lg+ +tgdvfn  +fl +  +a   +va+    ++  aa +y ++  +a+   + g a +  +tGtl + ela    
  gi|336254407|ref|YP_004597514.1| 122 LGISLTGDVFNLFVFLEITSLATYALVASGDGPEAAVAALKYLILGTVAASMYLIGVAFVFMATGTLNMVELATEip 198
                                       57889****************************************999888888888899999*********98744 PP

                   NADHdeh_related 158 a 158
                                        
  gi|336254407|ref|YP_004597514.1| 199 D 199
                                       2 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.0082
                   NADHdeh_related 133 lplfggaalilastGtlsifelaklagdvlliak..lllv...lGvvGetG.vaPfyaakaeifrapgapyillihl 203
                                         lf g al+++s G+ ++ e a+la+d +++a   ++l+   +Gv    G v+ +y+a   + +++  p + +i l
  gi|336254407|ref|YP_004597514.1| 346 AGLFLGVALVATSYGARTVDEYAGLATDRPVAAGsiAVLLlalVGVPPGIGfVGKWYIAVGAV-QSELWPVAAVIFL 421
                                       46899********************99977665312334401155543444367899986655.555669999**** PP

                   NADHdeh_related 204 sslllivrvveil 216
                                       s++l++  ++ +l
  gi|336254407|ref|YP_004597514.1| 422 STMLTLAYAARLL 434
                                       ****998766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); 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:                         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: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 3901.72
//
Query:       gi|336254408|ref|YP_004597515.1|  [L=122]
Description: NADH-ubiquinone oxidoreductase chain 4L [Halopiger xanaduensis SH-6]
Scores for complete 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-28   98.6   4.8    1.7e-28   98.3   4.8    1.1  1  Oxidored_q2      NADH-ubiquinone/plastoquinone oxidoreductase
     0.0099   15.9   2.6     0.0099   15.9   2.6    2.0  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
  ------ inclusion threshold ------
       0.38   10.3   5.1       0.49    9.9   5.1    1.2  1  UNC-50           UNC-50 family
          4    7.0   6.5        3.6    7.2   3.5    2.1  2  Saf_2TM          SAVED-fused 2TM effector domain


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 !   98.3   4.8   3.9e-32   1.7e-28       3     104 ..      15     116 ..      13     117 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 3.9e-32
                                       HHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHH CS
                       Oxidored_q2   3 llliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaa 79 
                                       ++l+++l +iGly+v++++nl+k+lig++l ++a++l++v++++ ++g+ ++     ++a+plpq++vLtaiv+g+a
  gi|336254408|ref|YP_004597515.1|  15 YVLLFVLLGIGLYMVIANENLVKKLIGVSLFQTAIFLFFVAMAYVEGGVSPVVPADGRVASPLPQVIVLTAIVVGIA 91 
                                       78999************************************************************************ PP

                                       HHHHHHHHHHHHHHHSSS-BCCG-- CS
                       Oxidored_q2  80 etavgLallvrlyreygtddvqelr 104
                                        tavgLal++r+y eygt++ + lr
  gi|336254408|ref|YP_004597515.1|  92 LTAVGLALVIRIYSEYGTLREDTLR 116
                                       *******************998876 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 ?   -3.6   9.6       2.5   1.1e+04      49      85 ..      13      55 ..       2      58 .. 0.38
   2 !   15.9   2.6   2.2e-06    0.0099      32     108 ..      37     121 ..      31     122 .] 0.73

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.5
                   Phage_holin_3_6 49 lalllllvalalala.a....lwlaali.vaavllvlagvlal 85
                                      +a +ll+v+l ++l  +      +  li v ++  ++ + +++
  gi|336254408|ref|YP_004597515.1| 13 YAYVLLFVLLGIGLYmVianeNLVKKLIgVSLFQTAIFLFFVA 55
                                      3333333333222211122345555555444444444443333 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.2e-06
                   Phage_holin_3_6  32 ragsgagllgaagvlallalllllvala...........lalaa...lwlaalivaavllvlagvlalvglkklkka 94 
                                       + ++g+ l+  a +l ++a++++  ++                +     l a++v+++l +++++l+++++++    
  gi|336254408|ref|YP_004597515.1|  37 KKLIGVSLFQTAIFLFFVAMAYVEGGVSpvvpadgrvasP---LpqvIVLTAIVVGIALTAVGLALVIRIYSEYGT- 109
                                       5566777777777777777777777773446777664430...14456789999*****************98887. PP

                   Phage_holin_3_6  95 kplpertieelked 108
                                         l e t++e+++d
  gi|336254408|ref|YP_004597515.1| 110 --LREDTLREVRAD 121
                                       ..789999999987 PP

>> UNC-50  UNC-50 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   5.1   0.00011      0.49     134     210 ..      15      90 ..       6     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00011
                            UNC-50 134 ilvllyvlqllllplilkkkfvslllgntlylvaigyYfyitfl.GYnalpflkktevlllpllllavlylitlllg 209
                                       + +l  +l + l+ +i+++++v+ l+g +l+  ai  +f+ + +      p++     ++ pl+ ++vl  i  ++g
  gi|336254408|ref|YP_004597515.1|  15 YVLLFVLLGIGLYMVIANENLVKKLIGVSLFQTAIFLFFVAMAYvEGGVSPVVPADGRVASPLPQVIVLTAI--VVG 89 
                                       33344445566889999999****************999876552445678888888999999988888887..444 PP

                            UNC-50 210 f 210
                                       +
  gi|336254408|ref|YP_004597515.1|  90 I 90 
                                       4 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 ?    1.1   0.6      0.06   2.7e+02      31      63 ..      16      49 ..       5      66 .. 0.54
   2 ?    7.2   3.5   0.00079       3.6      60      90 ..      73     104 ..      35     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.06
                           Saf_2TM 31 alllailgtdwalkialkla.ggslevsfsssei 63
                                      +ll  +lg   ++ ia +   ++ + vs+++  i
  gi|336254408|ref|YP_004597515.1| 16 VLLFVLLGIGLYMVIANENLvKKLIGVSLFQTAI 49
                                      4555555544444444444334444444444443 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00079
                           Saf_2TM  60 sse.ipeivlaiilvigvllivvGavllilry 90 
                                        ++  p++++++++v+g++l++vG+ l i+ y
  gi|336254408|ref|YP_004597515.1|  73 VASpLPQVIVLTAIVVGIALTAVGLALVIRIY 104
                                       5566899*****************99998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); 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:                         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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1064.29
//
Query:       gi|336254409|ref|YP_004597516.1|  [L=184]
Description: Na+/H+ antiporter MnhB subunit-like protein [Halopiger xanaduensis SH-6]
Scores for 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-21   74.7  14.3      1e-20   74.3  14.3    1.1  1  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter
  ------ inclusion threshold ------
          1    9.0  12.7        6.2    6.4  12.7    2.0  1  DUF998    Protein of unknown function (DUF998)


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3  14.3   1.1e-24     1e-20       1     123 [.      18     140 ..      18     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1.1e-24
                              MnhB   1 ilrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafglee.lekllrvklaprileglglllav 76 
                                       ++ t++++++p++l+++l+l+++G ++PGG FqgG i+++ +++l++afg+e  +++l++  l    l++ g+++++
  gi|336254409|ref|YP_004597516.1|  18 VIMTAVKIIAPFTLTYGLFLVFHGADTPGGSFQGGTIVGVTILMLAFAFGIEPtRQWLRNGVL--VGLATGGVAIFA 92 
                                       5789*************************************************5555555553..6*********** PP

                              MnhB  77 ltgllglllg..fltslflelelllg.evelgtallfdlgVylvVvggll 123
                                       ++gl+ ++lg  fl++  +++  +lg ++++g+  +   gV l+V ++++
  gi|336254409|ref|YP_004597516.1|  93 GVGLAMMALGgnFLEYDRIYY--VLGhKQKWGLEAIEVGGVSLIVSSVIV 140
                                       *********99******9998..4442677***************99886 PP

>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  12.7   0.00069       6.2      35      96 ..      43     104 ..      37     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00069
                            DUF998  35 ggpggwlfnaglvllgllvlalavgllraargragragrlllavaglg.lvlagvfptdpggg 96 
                                       ++pgg ++ ++ v +++l+la+a+g+ +  r +++  + + la +g++ ++++g+  +  gg 
  gi|336254409|ref|YP_004597516.1|  43 DTPGGSFQGGTIVGVTILMLAFAFGIEP-TRQWLRNGVLVGLATGGVAiFAGVGLAMMALGGN 104
                                       5899*********************966.999999************9777888777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1421.35
//
Query:       gi|336254410|ref|YP_004597517.1|  [L=179]
Description: multicomponent Na+-H+ antiporter subunit A [Halopiger xanaduensis SH-6]
Scores for 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-18   67.2  14.3      1e-18   67.2  14.3    2.8  3  DUF4040         Domain of unknown function (DUF4040)
  ------ inclusion threshold ------
        1.4    8.5  14.1       0.35   10.4   9.2    2.1  2  Virul_fac_BrkB  Virulence factor BrkB


Domain annotation for each model (and alignments):
>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2  14.3   1.2e-22     1e-18       1      66 [.      10      75 ..      10      76 .. 0.97
   2 ?    0.5   0.4     0.074   6.6e+02      19      30 ..      90     101 ..      82     108 .. 0.54
   3 ?   -0.8   0.6       0.2   1.8e+03       6      30 ..     145     169 ..     142     175 .. 0.55

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.2e-22
                           DUF4040  1 lllvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrlp 66
                                      ++++++a+a++l rd+l+ +i++g+++l++a+l+++l APDvA+T+aa+++g+tt+llll++ r+ 
  gi|336254410|ref|YP_004597517.1| 10 IFILVTAIATALFRDVLSVIIVFGAYSLGMAILYTFLLAPDVAMTEAAIGAGVTTLLLLLTIARTT 75
                                      589************************************************************986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.074
                           DUF4040  19 avillgvvGllv 30 
                                       av+++g++ +++
  gi|336254410|ref|YP_004597517.1|  90 AVVVVGALVVVL 101
                                       444444433333 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.2
                           DUF4040   6 aalaavlardrlaavillgvvGllv 30 
                                       a+laa +  d +  ++++ ++G+ +
  gi|336254410|ref|YP_004597517.1| 145 AVLAAYRGFDTFGEAVVVFAAGIST 169
                                       5555555556666666666666544 PP

>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   9.2   3.9e-05      0.35     154     205 ..      19      69 ..       1      71 [. 0.76
   2 ?    0.6   0.2     0.039   3.5e+02     118     132 ..      92     106 ..      71     172 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.9e-05
                    Virul_fac_BrkB 154 sellllqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwll 205
                                       ++l +  +l+++++++   l +a+lY++l    v + +a++Ga +++ll+ll
  gi|336254410|ref|YP_004597517.1|  19 TAL-FRDVLSVIIVFGAYSLGMAILYTFLLAPDVAMTEAAIGAGVTTLLLLL 69 
                                       223.588999999999*********************************987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.039
                    Virul_fac_BrkB 118 llllllvllllslvl 132
                                       +++++lv++l ++vl
  gi|336254410|ref|YP_004597517.1|  92 VVVGALVVVLCATVL 106
                                       333333333332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1403.12
//
Query:       gi|336254411|ref|YP_004597518.1|  [L=150]
Description: monovalent cation/proton antiporter subunit MnhG/PhaG [Halopiger xanaduensis SH-6]
Scores for 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   85.4   9.7      3e-24   85.0   9.7    1.1  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit
  ------ inclusion threshold ------
      0.065   13.1   0.9      0.085   12.7   0.7    1.3  1  Amastin         Amastin surface glycoprotein
        3.2    7.7   5.5         18    5.3   0.7    2.1  2  SAYSvFN         Uncharacterized conserved domain (SAYSvFN)


Domain annotation for each model (and alignments):
>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0   9.7     5e-28     3e-24       1      78 [.      22     100 ..      22     101 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 5e-28
                    PhaG_MnhG_YufB   1 llllGalfvllgaigllrlpdvytRlhaatkadtlGlllillGlllrf.slaaslkllliilfllltaPvaahliar 76 
                                       ll +G++f+l++++g+lrlpd+y+R h+a+ +dtlG+++ l++++l f +++a++  +l+++f+++t+P+aah+iar
  gi|336254411|ref|YP_004597518.1|  22 LLGFGVFFTLVSTVGVLRLPDIYARAHTASQTDTLGAGFALAAVALAFgWQQAAVYTVLLLFFIFITNPTAAHAIAR 98 
                                       6889********************************************88888************************ PP

                    PhaG_MnhG_YufB  77 aa 78 
                                       +a
  gi|336254411|ref|YP_004597518.1|  99 SA 100
                                       98 PP

>> Amastin  Amastin surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   1.4e-05     0.085      95     145 ..      17      67 ..      10      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                           Amastin  95 wvclllnivsvvtllivwalmvavyy.krfCdalksttakygaGFgLlvvaw 145
                                       w++++l  ++v+++l++++ + ++     +  + ++t+ ++gaGF+L  va 
  gi|336254411|ref|YP_004597518.1|  17 WAIVVLLGFGVFFTLVSTVGVLRLPDiYARAHTASQTD-TLGAGFALAAVAL 67 
                                       999******************99988545555666666.9*******99986 PP

>> SAYSvFN  Uncharacterized conserved domain (SAYSvFN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3    0.0047        28       9      30 ..      17      38 ..      14      42 .. 0.86
   2 ?    5.3   0.7     0.003        18       9      34 ..      65      90 ..      60     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0047
                           SAYSvFN  9 lliaaelefgavfvilsllvli 30
                                      ++i++ l+fg++f ++s+  ++
  gi|336254411|ref|YP_004597518.1| 17 WAIVVLLGFGVFFTLVSTVGVL 38
                                      789999***********98765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.003
                           SAYSvFN  9 lliaaelefgavfvilsllvliftnl 34
                                      +++a  ++ +av+ +l l+++++tn 
  gi|336254411|ref|YP_004597518.1| 65 VALAFGWQQAAVYTVLLLFFIFITNP 90
                                      6778889999**********999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 00:00:00.44
# Mc/sec: 1025.70
//
Query:       gi|336254412|ref|YP_004597519.1|  [L=98]
Description: multiple resistance and pH regulation protein F [Halopiger xanaduensis SH-6]
Scores for complete 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   5.5    1.8e-18   66.6   5.5    2.0  2  MrpF_PhaF  Multiple resistance and pH regulation protein F (M


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.5     0.047   8.5e+02      18      23 ..      22      27 ..      11      35 .. 0.52
   2 !   66.6   5.5     1e-22   1.8e-18       1      51 [.      40      90 ..      40      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.047
                         MrpF_PhaF 18 lallai 23
                                      +++lai
  gi|336254412|ref|YP_004597519.1| 22 FVVLAI 27
                                      222222 PP

  == domain 2  score: 66.6 bits;  conditional E-value: 1e-22
                         MrpF_PhaF  1 aDRvvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarf 51
                                      +DR++A+++lgt++v++lalla+ ++++++ldval++All+F+ ++a+++f
  gi|336254412|ref|YP_004597519.1| 40 QDRLLAVNVLGTNTVVILALLAAGLDQAWFLDVALIYALLNFLMSIAISKF 90
                                      6*************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 771.49
//
Query:       gi|336254413|ref|YP_004597520.1|  [L=354]
Description: cation antiporter [Halopiger xanaduensis SH-6]
Scores for 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-34  116.6   2.5    1.1e-33  116.1   2.5    1.3  1  MNHE      Na+/H+ ion antiporter subunit


Domain annotation for each model (and alignments):
>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1   2.5   5.9e-38   1.1e-33       2     144 ..     181     326 ..     180     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 5.9e-38
                              MNHE   2 lllflvWllltgs..lgelllGlllallvalllrrll.....lplrrv.....llrllayllvflweivkanldVak 66 
                                       ++ f ++l+l +   +++l++G+++a +v+++l+r+          r+     ++r++ y++++lwei+kan++V  
  gi|336254413|ref|YP_004597520.1| 181 AIAFGFYLVLGDPfyWFDLVTGAAVAGIVSIVLARVTftyplD---RIqspirVVRFVIYIPYLLWEILKANIAVSA 254
                                       68899*****999********************9988997662...3333467777********************* PP

                              MNHE  67 rvlrpklpirpgivkvplrlksdlaltllansitltPGTltvdvdedrrvlyvHvldvedeeeeareeikgrlErrl 143
                                       ++lrp++pi+p + +v+ r++s l lt+lansitltPGTltv+  ++++ l+vH+l +   ++++++  +g lE+++
  gi|336254413|ref|YP_004597520.1| 255 VILRPSMPIEPTLTRVNARVRSGLPLTALANSITLTPGTLTVR--ANNQQLLVHTL-I---PAAREDLFDGGLEKAI 325
                                       *******************************************..66777******.2...5555566688888887 PP

                              MNHE 144 l 144
                                       +
  gi|336254413|ref|YP_004597520.1| 326 R 326
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2847.56
//
Query:       gi|336254414|ref|YP_004597521.1|  [L=61]
Description: hypothetical protein Halxa_3026 [Halopiger xanaduensis SH-6]
Scores for 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-16   59.6   4.0    2.6e-16   59.4   4.0    1.1  1  CbtB      Probable cobalt transporter subunit (CbtB)


Domain annotation for each model (and alignments):
>> CbtB  Probable cobalt transporter subunit (CbtB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   4.0   1.5e-20   2.6e-16       3      51 .]      13      61 .]      11      61 .] 0.96

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 1.5e-20
                              CbtB  3 ssasaqrllqlvaAllLGlllvylvgfsqaaalHnaaHDtRHaagfPCH 51
                                      +++++ + + ++++l+++++++++++f q++++H+a+H++RHaag+ CH
  gi|336254414|ref|YP_004597521.1| 13 TARADLSPTEIAVGLAFAAAIAFTLVFLQEPLVHDAMHNFRHAAGIVCH 61
                                      67899999***************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 466.49
//
Query:       gi|336254415|ref|YP_004597522.1|  [L=253]
Description: hypothetical protein Halxa_3027 [Halopiger xanaduensis SH-6]
Scores for complete 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-48  166.1  29.6    1.3e-48  165.9  29.6    1.0  1  CbtA      Probable cobalt transporter subunit (CbtA)
  ------ inclusion threshold ------
      0.017   15.3   0.2      0.017   15.3   0.2    2.4  3  DUF4064   Protein of unknown function (DUF4064)


Domain annotation for each model (and alignments):
>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.9  29.6   1.5e-52   1.3e-48       3     241 ..       4     225 ..       2     227 .. 0.93

  Alignments for each domain:
  == domain 1  score: 165.9 bits;  conditional E-value: 1.5e-52
                              CbtA   3 rlllrgllaGllAGllaflvqrlvvePlilaAeayEeaaaaaeaaeaaaeHehaeaeepelvsrgvqrtlgtvlanv 79 
                                       ++l rg++aGl+AGl+++l+ +lv++Pl ++ ea+ +++a++++        h  a+e++++++++++t+++v ++v
  gi|336254415|ref|YP_004597522.1|   4 DYLKRGVAAGLVAGLAYGLFVALVANPLSQHVEAVGHEHAHEHG--------H--AHEHSHAVSELTTTVVSVGSGV 70 
                                       6899********************************96554332........2..3344556899************ PP

                              CbtA  80 ltgvalglllaavfallegrlgklsaralalllalagflavvlvPflklPpepPgvgaadtieaRqalylatvalsa 156
                                       l+++ lg+++a+++++le++l+++ ++a+a++la+agfl+v+++P+l+lPp +Pg+++   +++Rqalyla+v+++a
  gi|336254415|ref|YP_004597522.1|  71 LWAIFLGGVFAIALYFLEPALPGR-DAAKAYVLAGAGFLTVSATPWLVLPPAAPGAEHLYGVQTRQALYLALVVVGA 146
                                       *********************998.8999************************************************ PP

                              CbtA 157 valalavflarrlaarg.wnavlaaavaflvlvavallalPhvveaPqpeaaesgfpaallaqFrvaslltqavlWa 232
                                       +++a+ v+++rr a+r+  ++v+a+a+++l++ +++ l++P+   + +     sg++a+l+a ++ +++l+qa+lWa
  gi|336254415|ref|YP_004597522.1| 147 IVAAASVLAYRRTAPRHpLAGVVAGAAPLLAIGIALPLLTPTT--VTH-----SGLSADLVAAYQGIVVLSQAALWA 216
                                       ****************88***********************99..666.....89********************** PP

                              CbtA 233 vlGlvfgal 241
                                       +l+++fg l
  gi|336254415|ref|YP_004597522.1| 217 LLAGAFGRL 225
                                       *******87 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   1.9e-06     0.017      12      76 ..       9      86 ..       9     112 .. 0.82
   2 ?   -1.6   0.4      0.37   3.3e+03      71      72 ..     148     149 ..     130     182 .. 0.57
   3 ?   -1.2   0.4      0.27   2.5e+03      55      72 ..     205     220 ..     165     238 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-06
                           DUF4064 12 Ggilgillglllllflfllssgefsqeltee..............qalsgedasavleflstllivlgvialiaivlgi 76
                                      G++ g+++gl+++lf+ l+ +++ sq+ ++               + +  e +++v+++ s++l+++++++++ai+l +
  gi|336254415|ref|YP_004597522.1|  9 GVAAGLVAGLAYGLFVALV-ANPLSQHVEAVghehahehghahehSHAVSELTTTVVSVGSGVLWAIFLGGVFAIALYF 86
                                      6677888888888885555.7788888877789999*999999987788889999999999999999999999999876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.37
                           DUF4064  71 ai 72 
                                        +
  gi|336254415|ref|YP_004597522.1| 148 VA 149
                                       11 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.27
                           DUF4064  55 eflstllivlgvialiai 72 
                                       +++  +l  ++++al+a+
  gi|336254415|ref|YP_004597522.1| 205 GIV--VLSQAALWALLAG 220
                                       322..3333344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 1985.73
//
Query:       gi|336254416|ref|YP_004597523.1|  [L=396]
Description: acetyl-CoA acetyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-76  256.9   0.0    3.1e-76  256.2   0.0    1.3  1  Thiolase_N     Thiolase, N-terminal domain
    1.9e-27   95.3   0.0    3.3e-27   94.6   0.0    1.4  1  Thiolase_C     Thiolase, C-terminal domain
    5.1e-05   23.0   0.3    0.00053   19.6   0.1    2.4  2  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
      0.082   13.1   0.1          1    9.6   0.0    2.3  2  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


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 !  256.2   0.0   6.8e-80   3.1e-76       1     259 [.      11     264 ..      11     265 .. 0.99

  Alignments for each domain:
  == domain 1  score: 256.2 bits;  conditional E-value: 6.8e-80
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSE CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevp 77 
                                       vv+v+++rtp+g+  gsl+d++a+ L+++a+ +lle++ vd +++d v++Gn +qag gq + rq+++++ +p+++ 
  gi|336254416|ref|YP_004597523.1|  11 VVLVDGVRTPHGTLLGSLADVEAVALGRTAVDGLLERVDVDDDAIDWVALGNAIQAGIGQVPGRQVVVESRVPNDTR 87 
                                       89*************************************************************************** PP

                                       EEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSE CS
                        Thiolase_N  78 avtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneeh 154
                                       a+t+n++++Sg++av laa+ iaag+ad +vagG Esm++ap   +   r+g ++gd ++kd +++d+l+d+  ++h
  gi|336254416|ref|YP_004597523.1|  88 ATTINEASGSGMSAVSLAADRIAAGRADLAVAGGFESMTDAPWILP-GYRTGRRYGDVELKDSMLYDSLWDVNLDVH 163
                                       *********************************************9.99**************************** PP

                                       HHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-B CS
                        Thiolase_N 155 mGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkp 231
                                       mG  +e l ++ +i R +qde+A++sh++aa+a+++g F+ eivPv+++g    +tvd+de++r+++t+e La+l +
  gi|336254416|ref|YP_004597523.1| 164 MGEITEGLVDREGIFRVAQDEYALESHRRAAEAIDDGGFDAEIVPVETNG----ETVDTDEGPRPDSTLEDLAELPT 236
                                       ************************************************99....57********************* PP

                                       SSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 232 aFkkeGtvtAgnasqisDGaaavllmse 259
                                        F+++Gt+t gnas++sDGa+avll+ +
  gi|336254416|ref|YP_004597523.1| 237 PFREDGTITPGNASKLSDGAGAVLLADA 264
                                       *************************875 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   0.0   7.3e-31   3.3e-27       2     118 ..     273     390 ..     272     395 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 7.3e-31
                                       --SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH CS
                        Thiolase_C   2 kplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaial 78 
                                       +p+a++++ya++  dp+ ++ +   +++++l+++ l v+d+d++ inEAFaaqa++v+ ++++  ek+N +GGa+a 
  gi|336254416|ref|YP_004597523.1| 273 EPMARLVDYATAYRDPDRFNEAVGDVTEALLERNDLAVDDVDAYWINEAFAAQAVYVMGRVGIPREKLNPQGGAVAF 349
                                       799************************************************************************** PP

                                       -B-TTTHHHHHHHHHHHHHHHC.TTSEEEEEEEETTTEEEE CS
                        Thiolase_C  79 GHPlGasGaRivvtllselkke.ggklgvaalCigggqgva 118
                                       GHP+GasG  ++++l+++l+ + + + gv+ + iggg ++ 
  gi|336254416|ref|YP_004597523.1| 350 GHPIGASGGMLAASLAYQLRDDpDIERGVVGMSIGGGGAIL 390
                                       *******************9874789***********9875 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 !   19.6   0.1   1.2e-07   0.00053     170     207 ..      90     127 ..      84     136 .. 0.87
   2 ?    0.3   0.0     0.097   4.4e+02     233     251 ..     242     265 ..     234     267 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-07
                                       EEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
                     ketoacyl-synt 170 tvdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                                       t+  A  S+  av +a +++ +g+ad+a+aGG e ++ 
  gi|336254416|ref|YP_004597523.1|  90 TINEASGSGMSAVSLAADRIAAGRADLAVAGGFESMTD 127
                                       566677899*************************9876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.097
                                       B.....-SB-BB-EEEEEEEEECH CS
                     ketoacyl-synt 233 a.....dGfvlGEGvGavvLkrle 251
                                       +     +   l++G+Gav+L  ++
  gi|336254416|ref|YP_004597523.1| 242 GtitpgNASKLSDGAGAVLLADAD 265
                                       555555677799********9876 PP

>> 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 ?    1.0   0.0      0.11   4.9e+02       1      71 [.      45     116 ..      45     123 .. 0.71
   2 ?    9.6   0.0   0.00023         1       1      39 [.     303     341 ..     303     393 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.11
                                       HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH.HHH-B-GGGHHHHHHHHHHHTTSS-TT-E CS
                     ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpeekvvvnl.deyGntsaasiplaLdeaveegklkpgdl 71 
                                       Le+ +++ + id++ + +a +  i +v  +  + e +v+++  +++ n ++ s + a + a ++    + dl
  gi|336254416|ref|YP_004597523.1|  45 LERVDVDDDAIDWVALGNAIQAGIGQVPGRQVVVESRVPNDTrATTINEASGSGMSAVSLAADRIAAGRADL 116
                                       567788899999999999999988888888888888888888666667777777777777776444444444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00023
                                       HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB- CS
                     ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpeekvv 39 
                                       Le+++l+++d+da++++ a +     v+ ++g+p+ek  
  gi|336254416|ref|YP_004597523.1| 303 LERNDLAVDDVDAYWINEAFAAQAVYVMGRVGIPREKLN 341
                                       799*********************************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3039.38
//
Query:       gi|336254417|ref|YP_004597524.1|  [L=324]
Description: hypothetical protein Halxa_3030 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.089   12.4   0.3       0.14   11.7   0.3    1.3  1  DUF4689   Domain of unknown function (DUF4689)


Domain annotation for each model (and alignments):
>> DUF4689  Domain of unknown function (DUF4689)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   7.8e-06      0.14      26      59 ..     277     312 ..     255     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.8e-06
                           DUF4689  26 lpcG.pc.ipimlalaslaalfllttavlaerlfrr 59 
                                         cG pc ipi+l+  +  alf + +  la rl+ r
  gi|336254417|ref|YP_004597524.1| 277 TGCGrPCiIPILLSRYVYVALFAVVSVALARRLWHR 312
                                       568879945*************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2401.53
//
Query:       gi|336254418|ref|YP_004597525.1|  [L=356]
Description: dihydroorotate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-86  287.6   0.0    1.1e-85  287.4   0.0    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.018   14.4   0.0       0.03   13.7   0.0    1.3  1  NMO           Nitronate monooxygenase
      0.027   13.9   0.0      0.062   12.7   0.0    1.7  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


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 !  287.4   0.0   1.8e-89   1.1e-85       2     295 .]      51     339 ..      50     339 .. 0.95

  Alignments for each domain:
  == domain 1  score: 287.4 bits;  conditional E-value: 1.8e-89
                                       G-EEETTEEESSSEEE-TTSSTTSSSHHHHHCTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HH CS
                            DHO_dh   2 latkvlglkfknpiglAaGfdkegeeilkllklgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGld 78 
                                       l++++++++f+np+g+AaGfdk++e + +l +lgfg++eig+vtp+pqeGn++Pr+frl ed++++N++G+n +G++
  gi|336254418|ref|YP_004597525.1|  51 LEVDLFDTTFPNPVGVAAGFDKNAEVTRALEALGFGFVEIGTVTPYPQEGNDRPRLFRLREDEAMVNRMGFNGQGME 127
                                       78999************************************************************************ PP

                                       HHHHHHHHHHHHHHCC.CEEEEEEE-TTS..S.HHHHHHHHHHHHGGGESEEEEES-SCTCCTSCCCGCHHHHHHHH CS
                            DHO_dh  79 avlekllkrrkeqeekkelginlskakkt..enavddyvevvrkigpfadilelNvSsPntpglrdlqekeelkail 153
                                        v ++l++    +     lg+n++k  ++  e+a++dy+ v+ +++pfad++++NvS+Pntp   d ++ e+l+ai+
  gi|336254418|ref|YP_004597525.1| 128 RVKARLEEDGTPNV---PLGVNVGKMNSSseEEAIEDYRRVFDRLSPFADYVVVNVSCPNTPDEFDEASPEHLRAIF 201
                                       ******99886644...6*******998867899******************************************9 PP

                                       HHHHHHHH.SSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHH CS
                            DHO_dh 154 lkvvkevs.kvpvlvKlaPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdi 229
                                           +e++ +vp+lvK+ Pd  + +  d +d ++e++ldg+i+tNt++ r+   l s +n+++   GGlsGk++ d+
  gi|336254418|ref|YP_004597525.1| 202 ETLEAENDaDVPILVKIGPDEPENAVLDLVDIVQEFGLDGMIATNTSTGRE--GLAS-PNREE--WGGLSGKPIEDR 273
                                       9888887768*****************************************..7777.55664..9*********** PP

                                       HHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
                            DHO_dh 230 alkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                                       ++ vir++++++++++piIgvGG+ s+  a+ ki+aGAslvq+yt++v++gp  ak+i ++l elL
  gi|336254418|ref|YP_004597525.1| 274 STDVIRTIADYTDGDLPIIGVGGVDSAASAYRKIRAGASLVQLYTGFVYRGPSTAKRINNGLVELL 339
                                       *************************************************************99876 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.1e-06      0.03     166     238 ..     261     333 ..     231     345 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-06
                               NMO 166 eaGGhqGtpevgdkglfaLvpqvldavd..iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakdahk 238
                                       e GG  G  +++    + ++ +++d  d  +P+i  GG+  +      +++GAs vq+ t f+    s+ak + +
  gi|336254418|ref|YP_004597525.1| 261 EWGGLSG-KPIE-DRSTDVIRTIADYTDgdLPIIGVGGVDSAASAYRKIRAGASLVQLYTGFVYRGPSTAKRINN 333
                                       5699999.5665.6778999*****99999*********************************999999998865 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 ?   12.7   0.0     1e-05     0.062       3     152 ..      79     238 ..      27     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
                                       HHHHCT-SEEEEECCTCSHHHHC....................HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC CS
                      AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvsel....................sdeelrelrkaldelglriaslslftrfgypded 59 
                                       a++++Gf +vE+ + +++p   +                      +++++++++l+e g   + l  + +  ++   
  gi|336254418|ref|YP_004597525.1|  79 ALEALGFGFVEIGTVTPYPQEGNdrprlfrlredeamvnrmgfNGQGMERVKARLEEDGTPNVPLGVNVGKMNS--- 152
                                       67889999999999999999877888888888888888888888888888888888888884444444444442... PP

                                       HTTCS.HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTT CS
                      AP_endonuc_2  60 erear.reesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlags 135
                                             +ee++++++r  ++ + + a+++v++++  +  p++ +e+  e+l++ ++ l ++  +++v +++  ++ +
  gi|336254418|ref|YP_004597525.1| 153 ----SsEEEAIEDYRRVFDRLSPF-ADYVVVNVS-CPNTPDEFDEASPEHLRAIFETLEAE-NDADVPILVKIGPDE 222
                                       ....13477899999999999999.777777776.45666666667888888888888777.578899999888888 PP

                                       TSSSTCHHHHHHHHHHT CS
                      AP_endonuc_2 136 gvelgdeelarlldavd 152
                                       + +    +l++++++ +
  gi|336254418|ref|YP_004597525.1| 223 PENAV-LDLVDIVQEFG 238
                                       85555.88888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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: 0.48u 0.19s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2886.19
//
Query:       gi|336254419|ref|YP_004597526.1|  [L=78]
Description: an1-type zinc finger protein [Halopiger xanaduensis SH-6]
Scores for 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-12   46.9   5.3    2.6e-12   46.7   5.3    1.1  1  zf-AN1        AN1-like Zinc finger
  ------ inclusion threshold ------
      0.072   13.5   1.8      0.091   13.1   1.8    1.2  1  Transp_Tc5_C  Tc5 transposase C-terminal domain


Domain annotation for each model (and alignments):
>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   5.3   2.9e-16   2.6e-12       1      37 [.       4      40 ..       4      43 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 2.9e-16
                            zf-AN1  1 CsfksCkkkdflpfkCryCgkvFClkHrlpedHdCkk 37
                                      C++++C+  d++   C+yCg  +C++Hrlpe+HdC+ 
  gi|336254419|ref|YP_004597526.1|  4 CAYPGCSGDDSMKNSCSYCGDGYCSEHRLPENHDCPA 40
                                      ***********************************96 PP

>> Transp_Tc5_C  Tc5 transposase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.8     1e-05     0.091      28      63 .]       2      38 ..       1      38 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                      Transp_Tc5_C 28 edCkiegCselafik..CarCkellCFdHfvvsekhlC 63
                                      +dC+  gCs    +k  C++C +  C +H +  e+h C
  gi|336254419|ref|YP_004597526.1|  2 GDCAYPGCSGDDSMKnsCSYCGDGYCSEHRL-PENHDC 38
                                      79******987777666************98.577777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 680.06
//
Query:       gi|336254420|ref|YP_004597527.1|  [L=455]
Description: dihydroorotase, multifunctional complex type [Halopiger xanaduensis SH-6]
Scores for 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-22   79.0   0.0    5.6e-22   78.5   0.0    1.2  1  Amidohydro_1  Amidohydrolase family
    7.4e-19   68.6   0.8    6.5e-09   35.8   0.0    3.2  3  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.024   15.0   0.3        0.4   11.0   0.2    2.4  2  Urease_alpha  Urease alpha-subunit, N-terminal domain


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 !   78.5   0.0   9.4e-26   5.6e-22       1     344 []      53     436 ..      53     436 .. 0.79

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 9.4e-26
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.....HHHHHHHHHHT CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.....giealleaaee 72 
                                       +++PG++D H+H +             +p+ +++e  es++++a  +G+ttv +m++t++      ++e+ +e  e+
  gi|336254420|ref|YP_004597527.1|  53 VLVPGIVDGHIHNR-------------EPGLEYKEDWESATRAAAAGGVTTVVGMPNTDPVidrpeHLELKFERGED 116
                                       589*********98.............******************************87669988888888888888 PP

                                       SSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEE CS
                      Amidohydro_1  73 lplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpv 148
                                             +++ + s++  +++  ++++ ++++       + + +++  +++++ ++p  +  e+ ea+ + ++ ++ +
  gi|336254420|ref|YP_004597527.1| 117 S-----AHVDFQSYA-VVTSENLDLIPEIDEAG-----ALGFKIFLgSTVGDVPPPNDG--EILEAMAKIRETGKRL 180
                                       3.....677777887.78888888888886664.....444457777888888888887..**************** PP

                                       EEEETSSCHHHHHHHHHHTTTEEEETTTTSTCC.............HHTTTHCCEEEHCTCEEEHHHHHHHHHHHHH CS
                      Amidohydro_1 149 aiHaletkgevedaeaafgetiehgthlevaes.............lglldeiklilahgvhltpteaellkerlke 212
                                        +H  + + +  ++e+  +e+  +  + +  +s             + +++e + +  h+ h++  +a+   +r+ke
  gi|336254420|ref|YP_004597527.1| 181 GFHEENGEIIDHYTEQFKAEGRND--PIDHSHSrpviaeqeavermITFAEE-TGAKIHMFHVSSGSAAEAVARGKE 254
                                       ***966666666788888877777..99998888888888555555444444.444555555553367777888899 PP

                                       HCEE........HHHHHHHH...............SEHHHHHHHHHHHH.TSCEEEEEECT................ CS
                      Amidohydro_1 213 agva........hcpfsnsi...............lrsgrealrkalde.GvkvglgtDga................ 249
                                        gv          + f++++                +++re+l+++  e G++ +++tD+a                
  gi|336254420|ref|YP_004597527.1| 255 RGVDvtaettphYLWFTEEVmrekgnpariqppirDADEREKLWEVGIEdGAIDSIATDHAphtpeekkvddpfgnt 331
                                       999977777776444555558888889999999999999****9987777*****************8888866666 PP

                                       ...TSSCCGGHHHHHHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC... CS
                      Amidohydro_1 250 ...asgnslnlleelrlalklqrgllye.deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl... 319
                                           sg ++ l +e+ ++l        + ++eg l+ +e++r  ++ +A++ g++ ++Gs++vG dAD+++vd+   
  gi|336254420|ref|YP_004597527.1| 332 weaISGFVG-LETEVPVML--------SfVDEGRLTMEEWVRRHSTRPAQIWGMYPQKGSLQVGTDADFTIVDPere 399
                                       655555555.222344444........558899***************************************99876 PP

                                       .CT...........CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 320 .di...........laafvglkkdgnvkkvivkGklv 344
                                        ++            ++f g +  g+ + ++v+G++v
  gi|336254420|ref|YP_004597527.1| 400 wTLesadelhskncVTPFIGESFTGKAVATVVRGEVV 436
                                       62266778899999********************997 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   2.4e-10   1.5e-06       1      48 [.      45      92 ..      45      96 .. 0.95
   2 ?    1.4   0.1     0.029   1.8e+02     262     325 ..     163     224 ..     123     260 .. 0.72
   3 !   35.8   0.0   1.1e-12   6.5e-09     404     473 .]     353     437 ..     328     437 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.4e-10
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltav 48
                                      +v+Da+G++++PG vD H+H  + g+++ + + ++ r+ ++ gv+t+v
  gi|336254420|ref|YP_004597527.1| 45 RVVDAEGKVLVPGIVDGHIHNREPGLEYKEDWESATRAAAAGGVTTVV 92
                                      69**************************99999999*********998 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.029
                      Amidohydro_3 262 dealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegv..tesqierv 325
                                       d+++ e +a+ +e g ++++h    + +d    +++++ +++g++d    +h++ v   ++ +er+
  gi|336254420|ref|YP_004597527.1| 163 DGEILEAMAKIRETGKRLGFHEENGEIID----HYTEQFKAEGRNDPIDHSHSRPViaEQEAVERM 224
                                       66788888888999999998876665555....777777777777754556666666655666665 PP

  == domain 3  score: 35.8 bits;  conditional E-value: 1.1e-12
                      Amidohydro_3 404 pdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpl.dvdppelaear..............vrlt 465
                                       ++ +l++ee+++ ++++pA++ g+   kG+L+vG dAD+++ d ++  +++ ++  + +              +++t
  gi|336254420|ref|YP_004597527.1| 353 DEGRLTMEEWVRRHSTRPAQIWGMYPQKGSLQVGTDADFTIVDPEREwTLESADELHSKncvtpfigesftgkAVAT 429
                                       6789***************************************66651444443333337***************** PP

                      Amidohydro_3 466 vvdGrvvy 473
                                       vv+G+vvy
  gi|336254420|ref|YP_004597527.1| 430 VVRGEVVY 437
                                       *******9 PP

>> Urease_alpha  Urease alpha-subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   6.7e-05       0.4      65     101 ..       2      39 ..       1      56 [. 0.81
   2 ?    1.3   0.0      0.07   4.2e+02      85     107 ..     299     321 ..     296     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.7e-05
                      Urease_alpha  65 alDlvitnavilDatgiv.kadigikdgrivaiGkagn 101
                                       ++Dlv+ n +++  +g +  a +++ dg+iva+G++  
  gi|336254420|ref|YP_004597527.1|   2 TVDLVVRNCTVVTPAGRTpDAGVAVEDGTIVAVGRSDR 39 
                                       58***********9886538**************9864 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.07
                      Urease_alpha  85 digikdgrivaiGkagnpdvmdg 107
                                       ++gi dg i +i+    p++ ++
  gi|336254420|ref|YP_004597527.1| 299 EVGIEDGAIDSIATDHAPHTPEE 321
                                       69***********9999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3274.68
//
Query:       gi|336254421|ref|YP_004597528.1|  [L=321]
Description: UDP-glucose 4-epimerase [Halopiger xanaduensis SH-6]
Scores for 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-57  194.2   0.0    2.9e-57  193.9   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.9e-54  184.0   0.0    1.3e-53  182.6   0.0    1.6  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.5e-19   69.1   0.0    4.2e-18   65.5   0.0    2.4  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    4.8e-19   68.4   0.0    1.2e-18   67.1   0.0    1.6  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    8.4e-13   48.1   0.0      1e-12   47.7   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    6.5e-09   35.3   0.3    1.7e-05   24.2   0.0    2.5  2  NAD_binding_4    Male sterility protein
      1e-06   28.8   0.8    2.6e-06   27.5   0.0    1.9  2  NAD_binding_10   NAD(P)H-binding
      0.002   17.7   0.0      0.004   16.7   0.0    1.5  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.017   15.0   0.4       0.41   10.5   0.4    2.4  1  KR               KR domain
      0.025   14.8   0.0        0.1   12.9   0.0    2.0  2  TrkA_N           TrkA-N 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 !  193.9   0.0   1.6e-60   2.9e-57       1     241 []      11     239 ..      11     239 .. 0.97

  Alignments for each domain:
  == domain 1  score: 193.9 bits;  conditional E-value: 1.6e-60
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       +lVtG++GfiGs+lv+ l+ ++ ev +ld  s++s++ + +d+e+ e+d++d+  l+r+ +  ++d ++h Aav +v
  gi|336254421|ref|YP_004597528.1|  11 VLVTGGAGFIGSHLVDTLAPHN-EVRVLDDFSTGSRSHLPDDVEVFEGDVRDPMLLQRAAR--GVDLIFHHAAVVSV 84 
                                       79*****************876.9***********************************99..9************* PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                        +s++ p +  ++nl+  l +le ar+ ++ r++ +sS+++YG ++e p +e +    ++p+spY+++Kla +++++
  gi|336254421|ref|YP_004597528.1|  85 TQSVDAPRQSNRTNLEAGLLVLEQARQEDA-RVVVASSAAIYGHPEELPVSERA---ATNPTSPYGVQKLALDQYAR 157
                                       ******************************.****************9988888...789***************** PP

                                       HHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT CS
                         Epimerase 155 ayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvda 231
                                        y + y++++++lr+fn+yGpr ++g  s+vi+ +++++ +g+ ++t+ gdg++ Rdf++v+Dv++a+l++++    
  gi|336254421|ref|YP_004597528.1| 158 LYEELYDVPTVALRYFNVYGPR-QQGPYSGVISTFLEQARAGE-PITIEGDGEQTRDFVHVDDVVRANLRAATT--- 229
                                       *********************9.7777****************.******************************... PP

                                       -STTEEEEES CS
                         Epimerase 232 gdkgeiyniG 241
                                        + ge+yniG
  gi|336254421|ref|YP_004597528.1| 230 ANVGEAYNIG 239
                                       67899****9 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 !  182.6   0.0   7.3e-57   1.3e-53       1     331 [.      12     301 ..      12     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 182.6 bits;  conditional E-value: 7.3e-57
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+l++ L     ev +     + f+tg+ +hl +d        +++++gD++D   l+r+ + v  d
  gi|336254421|ref|YP_004597528.1|  12 LVTGGAGFIGSHLVDTLAPH-NEVRV----LDDFSTGSRSHLPDD--------VEVFEGDVRDPMLLQRAARGV--D 73 
                                       9****************985.55644....567899999999764........5799*************9998..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        +++ AA   V +s++ P +  ++n+ + l +Le +r+    +++r++ aS++ +YG+++e p++E+  ++P+sPY+
  gi|336254421|ref|YP_004597528.1|  74 LIFHHAAVVSVTQSVDAPRQSNRTNLEAGLLVLEQARQ----EDARVVVASSAAIYGHPEELPVSERAATNPTSPYG 146
                                       *************************************9....468******************************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                       + Kl+ d+ ++ y+e y++++v  ++fn ++pr++       i++++ ++ +g+ ++++ G+++++Rd+ hv+D+v+
  gi|336254421|ref|YP_004597528.1| 147 VQKLALDQYARLYEELYDVPTVALRYFNVYGPRQQGP-YSGVISTFLEQARAGE-PITIEGDGEQTRDFVHVDDVVR 221
                                       *********************************9776.5589999****99998.77778***************** PP

                                       HHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B CS
                     GDP_Man_Dehyd 232 amwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllg 308
                                       a  ++    +        ge +++++  + ++ +l +ti             ++s++   ++  k  rpg+ +   +
  gi|336254421|ref|YP_004597528.1| 222 ANLRAATTAN-------VGEAYNIGTGDRTSIRDLAETIRDA----------TDSSS---PIVHKDPRPGDIRHSRA 278
                                       *777555433.......4555555555555555555555432..........23334...45556679********* PP

                                       -THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 309 daskakeeLgWkpkvsfeelvre 331
                                       d ska ++Lg++++v++e+++r 
  gi|336254421|ref|YP_004597528.1| 279 DVSKASRDLGFEATVGLESGIRS 301
                                       ********************986 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   2.3e-21   4.2e-18       1     247 [.      11     257 ..      11     275 .. 0.83

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 2.3e-21
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vlvtG++G iGs+lv++++ ++  ++++l+   +         +++l + +++v+     gdvrd   l++a +  +
  gi|336254421|ref|YP_004597528.1|  11 VLVTGGAGFIGSHLVDTLAPHN--EVRVLDDFSTG-------SRSHLPD-DVEVF----EGDVRDPMLLQRAAR--G 71 
                                       89***************99875..66666643332.......2222333.23333....5**************..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEE.............EEEGGGSS--SHHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvl.............iStDKAvnPtnvmGat 141
                                       vd++fh AA+  V      p +  +tN  +   v+e a + + + vv+             +S   A nPt+ +G+ 
  gi|336254421|ref|YP_004597528.1|  72 VDLIFHHAAVVSVTQSVDAPRQSNRTNLEAGLLVLEQARQEDARVVVAssaaiyghpeelpVSERAATNPTSPYGVQ 148
                                       ******************************************99999823332333333334445789********* PP

                                       HHHHHHHHHHGGG--SSS--EEEEEEE-EETTGT..T...SSHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHHHHHH CS
                   Polysacc_synt_2 142 KrlaekllqalakeseekktkfvvvRfGNVlgSr..G...SviplFkkqikeggpvtv.TdpemtRyfmtieeavqL 212
                                       K++ ++++  +++     +   v+ R+ NV g r  G    vi +F +q ++g+p+t+  d e tR f+ +++ v+ 
  gi|336254421|ref|YP_004597528.1| 149 KLALDQYARLYEELY---DVPTVALRYFNVYGPRqqGpysGVISTFLEQARAGEPITIeGDGEQTRDFVHVDDVVRA 222
                                       ********9999988...78999********9874434436*****************5589*************** PP

                                       HHHHHHH--SS-EEEE--.-EEEHHHHHHHH.... CS
                   Polysacc_synt_2 213 vlqalalakggeifvldmGepvkivdlakaliels 247
                                        l a+++a+ ge +    G+ ++i+dla+++ + +
  gi|336254421|ref|YP_004597528.1| 223 NLRAATTANVGEAYNIGTGDRTSIRDLAETIRDAT 257
                                       *****************************995544 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 !   67.1   0.0   6.7e-22   1.2e-18       1     230 [.      12     228 ..      12     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 6.7e-22
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtGgaGF+G++lv +L   +   evrvlD     + +       v+ v egDv+d   l++a +gvd+++h a++v
  gi|336254421|ref|YP_004597528.1|  12 LVTGGAGFIGSHLVDTLAPHN---EVRVLDDFSTGSRSHLPDD--VE-VFEGDVRDPMLLQRAARGVDLIFHHAAVV 82 
                                       69***************9888...7*****6655555333333..33.77*************************** PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                        v++ ++   +  + n++    vle +++ + rv+v  Ssa + g     ee+     +++  ++++++y   K   
  gi|336254421|ref|YP_004597528.1|  83 SVTQsVDAPRQSNRTNLEAGLLVLEQARQEDARVVV-ASSAAIYGH---PEELP---VSERAATNPTSPYGVQKLAL 152
                                       **98678888999******************99877.677766666...55554...235667789999*9999888 PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyGegdk.....llvpllkqlaklglalfkigdeevlsdrvYvgNvawah 225
                                       +++     +       ++ T+aLR   +yG++++     +++++  + a+ g+ +   gd e++ d+v v+ v+ a 
  gi|336254421|ref|YP_004597528.1| 153 DQYARLYEE-----LYDVPTVALRYFNVYGPRQQgpysgVISTF-LEQARAGEPITIEGDGEQTRDFVHVDDVVRAN 223
                                       888766665.....55679***********99873222133444.455788999*********************99 PP

                         3Beta_HSD 226 ilAar 230
                                       + Aa 
  gi|336254421|ref|YP_004597528.1| 224 LRAAT 228
                                       98875 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 !   47.7   0.0   5.8e-16     1e-12       2     236 ..      10     262 ..       9     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 5.8e-16
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHHHHH--SEEEE------ CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre...............eldltdaeavaellkeakpdvvvnaAAyta 63 
                                       ++lvtG+ G +Gs+L++ la ++ ev  l+                 e d++d+  ++++ +    d++ + AA   
  gi|336254421|ref|YP_004597528.1|  10 TVLVTGGAGFIGSHLVDTLAPHN-EVRVLDDFstgsrshlpddvevfEGDVRDPMLLQRAARG--VDLIFHHAAVVS 83 
                                       69******************977.66555433458889*********************9998..899********* PP

                                       HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH.. CS
                     RmlD_sub_bind  64 vDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla.. 138
                                       v +  + ++++++ n ea   + e+a++ +a ++  S+  ++   ++ p +e ++t+P + YG  Kla  q  +   
  gi|336254421|ref|YP_004597528.1|  84 VTQSVDAPRQSNRTNLEAGLLVLEQARQEDARVVVASSAAIYGHPEELPVSERAATNPTSPYGVQKLALDQYARLye 160
                                       ***********************************************************************999843 PP

                                       ..H-SSEEEEEE-SEESSSSS....-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG- CS
                     RmlD_sub_bind 139 ..agkkalivRtswvygekgk....nfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekela 207
                                         +   ++ +R   vyg +++      ++t+l+ a+  e++++  D  q++   +++d+ ++ l ++++a       
  gi|336254421|ref|YP_004597528.1| 161 elYDVPTVALRYFNVYGPRQQgpysGVISTFLEQARAGEPITIEGDgeQTRDFVHVDDVVRANLRAATTANV----G 233
                                       3333456789******9955422226899**************98866899999999999999988888876....8 PP

                                       EEEE---BS-EEHHHHHHHHHHHHCHTTS CS
                     RmlD_sub_bind 208 gvyHlanegetswlefArailkeagadse 236
                                       + y ++  + ts  ++A+ i ++++++s 
  gi|336254421|ref|YP_004597528.1| 234 EAYNIGTGDRTSIRDLAETIRDATDSSSP 262
                                       99********************9999773 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1   0.00037      0.67       1      20 [.      13      32 ..      13      37 .. 0.83
   2 !   24.2   0.0   9.3e-09   1.7e-05      58     212 ..      48     181 ..      34     223 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00037
                                      EE-TTSHHHHHHHHHHHHHS CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrtt 20
                                      +TG+ GF+G++L+  L   +
  gi|336254421|ref|YP_004597528.1| 13 VTGGAGFIGSHLVDTLAPHN 32
                                      7************9987554 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 9.3e-09
                                       HTTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-E CS
                     NAD_binding_4  58 laerikvveGDlseprlGLseedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvl 131
                                       l++ ++v eGD+ +p l      lq+ a+ vd+i+h aA v+++++++      r+N+e+   vle a++  +   +
  gi|336254421|ref|YP_004597528.1|  48 LPDDVEVFEGDVRDPML------LQRAARGVDLIFHHAAVVSVTQSVDAprqSNRTNLEAGLLVLEQARQEDAR--V 116
                                       66777888888887775......8999******************99983335578888888888888877666..5 PP

                                       EEEEEGGGTTS-T.TT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE CS
                     NAD_binding_4 132 lhvSTayvngere.geveekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiit 207
                                       +  S+a+++g+ e   v+e++                  ++ +  Y   K + ++  r + +  ++p+v +R  +++
  gi|336254421|ref|YP_004597528.1| 117 VVASSAAIYGHPEeLPVSERAA-----------------TNPTSPYGVQKLALDQYARLYEELYDVPTVALRYFNVY 176
                                       5556666665555044444444.................44445555555555555555555555555555555555 PP

                                       --SSS CS
                     NAD_binding_4 208 geskt 212
                                       g  ++
  gi|336254421|ref|YP_004597528.1| 177 GPRQQ 181
                                       55555 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 !   27.5   0.0   1.4e-09   2.6e-06       1     130 [.      15     155 ..      15     163 .. 0.67
   2 ?   -1.0   0.2      0.79   1.4e+03      26      61 ..     224     256 ..     209     259 .. 0.59

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.4e-09
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT..HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-....... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..peklaeleaeeglevvegdvtdvedlaealkgadaVvsal....... 68 
                                       G+ G +G++lv+ l+ ++  ev++l  +  + + ++l+  + +ev+egdv d+  l++a +g+d ++  +       
  gi|336254421|ref|YP_004597528.1|  15 GGAGFIGSHLVDTLAPHN--EVRVL-DDfsTGSRSHLP--DDVEVFEGDVRDPMLLQRAARGVDLIFHHAavvsvtq 86 
                                       99************9985..78776.441122333354..79**********************8887776666556 PP

                                       ...--TCC...HHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHH...HHHHCCHHHHHHHHHHHHH CS
                    NAD_binding_10  69 ...ggggk...deegaknivdaakeagvkRfvlvsaigvgdevpgefge...wnkellkaylaakraaeel 130
                                          +++++   + e+   +++ a++++  R+v+ s++ ++  +p+e++     +++  ++y   k a +++
  gi|336254421|ref|YP_004597528.1|  87 svdAPRQSnrtNLEAGLLVLEQARQEDA-RVVVASSAAIYG-HPEELPVserAATNPTSPYGVQKLALDQY 155
                                       6652222222233447778899999988.888888888884.45554430003344556666666666666 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.79
                                       ETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT- CS
                    NAD_binding_10  26 vRnpeklaeleaeeglevvegdvtdvedlaealkga 61 
                                        R +  ++ +   e+ ++ +gd t+  dlae++++a
  gi|336254421|ref|YP_004597528.1| 224 LRAATTAN-V--GEAYNIGTGDRTSIRDLAETIRDA 256
                                       33333333.2..256667778888888888887765 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.3e-06     0.004       1      73 [.      11      80 ..      11      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.3e-06
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73
                                      +lv+G++G +G+++v+ l+   ++vr+l  d  s  ++s     ve+ +gd+ d  +l++a +gvd++f   +
  gi|336254421|ref|YP_004597528.1| 11 VLVTGGAGFIGSHLVDTLAP-HNEVRVL--DDFSTGSRSHLPDDVEVFEGDVRDPMLLQRAARGVDLIFHHAA 80
                                      79**************9876.5689988..66666666666778*************************8766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00023      0.41       2      28 ..      10      36 ..       9     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00023
                                      EEEEETTTSHHHHHHHHHHHHHHS-EE CS
                                KR  2 tylitGGlGgLGlelarwlaekgarhl 28
                                      t+l+tGG+G +G +l+++la + + ++
  gi|336254421|ref|YP_004597528.1| 10 TVLVTGGAGFIGSHLVDTLAPHNEVRV 36
                                      78*****************99875554 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   5.7e-05       0.1       5      59 ..      16      71 ..      11     125 .. 0.76
   2 ?   -0.6   0.0      0.85   1.5e+03      54      69 ..     105     120 ..     101     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-05
                                      S-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHT..T CS
                            TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeea..g 59
                                      G+G +G++l+++L  +++ v v d+     +++  + +ev+ gd+ d+ +L++a  g
  gi|336254421|ref|YP_004597528.1| 16 GAGFIGSHLVDTLAPHNE-VRVLDDFSTGSRSHLPDDVEVFEGDVRDPMLLQRAarG 71
                                      89***********99885.*********************************99443 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.85
                                       HHHHTTGGGESEEEE- CS
                            TrkA_N  54 vLeeagiekadaviaa 69 
                                       vLe+a  e+a++v+a 
  gi|336254421|ref|YP_004597528.1| 105 VLEQARQEDARVVVAS 120
                                       6888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); 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 0.29s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2187.93
//
Query:       gi|336254422|ref|YP_004597529.1|  [L=122]
Description: hypothetical protein Halxa_3035 [Halopiger xanaduensis SH-6]
Scores for 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  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 905.79
//
Query:       gi|336254423|ref|YP_004597530.1|  [L=169]
Description: hypothetical protein Halxa_3036 [Halopiger xanaduensis SH-6]
Scores for 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-05   22.5   0.0    0.00014   21.5   0.0    1.5  1  HTH_IclR   IclR helix-turn-helix domain
     0.0006   19.3   0.1    0.00095   18.7   0.1    1.3  1  HTH_24     Winged helix-turn-helix DNA-binding
     0.0074   16.2   0.0      0.014   15.3   0.0    1.5  1  MarR_2     MarR family
     0.0092   15.9   0.0      0.016   15.1   0.0    1.3  1  MarR       MarR family
  ------ inclusion threshold ------
      0.063   13.3   0.1       0.12   12.4   0.1    1.5  1  HTH_Crp_2  Crp-like helix-turn-helix domain
      0.097   13.1   0.0       0.14   12.6   0.0    1.3  1  BRCT_2     BRCT domain, a BRCA1 C-terminus domain
       0.17   11.8   0.1       0.44   10.5   0.0    1.6  2  TrmB       Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   5.6e-08   0.00014      11      49 ..     102     140 ..     100     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 5.6e-08
                                       T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                       +++e +++++ s + +  +++k++v+RlL+ L+ +G ++
  gi|336254423|ref|YP_004597530.1| 102 LVTENGGRMKQSRIVDSVDWSKAKVSRLLAELEDEGQIT 140
                                       56788999***************************9876 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   0.1   3.7e-07   0.00095      12      48 .]     103     140 ..      97     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.7e-07
                            HTH_24  12 Lqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       + +n++ + q+ + + ++ S++ v+r l +Le+eG I+
  gi|336254423|ref|YP_004597530.1| 103 VTENGGrMKQSRIVDSVDWSKAKVSRLLAELEDEGQIT 140
                                       5676666*****************************96 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   5.4e-06     0.014      16      53 ..     104     141 ..      95     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.4e-06
                                       CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  16 rrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53 
                                        + g+++ ++ +++  + sk+ vsr+l++L++ G +++
  gi|336254423|ref|YP_004597530.1| 104 TENGGRMKQSRIVDSVDWSKAKVSRLLAELEDEGQITK 141
                                       5556679**************************98865 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   6.3e-06     0.016      16      51 ..     108     143 ..     102     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.3e-06
                                       TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  16 gplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                       g +++s + + +  sk+ v+r+l +Le++G i++ +
  gi|336254423|ref|YP_004597530.1| 108 GRMKQSRIVDSVDWSKAKVSRLLAELEDEGQITKLR 143
                                       679***************************999876 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   0.1   4.6e-05      0.12      22      54 ..     110     143 ..      92     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.6e-05
                                       HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                         HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglis.rg 54 
                                       + q  + + +  +   vsr+l+eL++eg i+  +
  gi|336254423|ref|YP_004597530.1| 110 MKQSRIVDSVDWSKAKVSRLLAELEDEGQITkLR 143
                                       6677777788889999**************9533 PP

>> BRCT_2  BRCT domain, a BRCA1 C-terminus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.5e-05      0.14      19      39 ..      94     114 ..      89     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.5e-05
                            BRCT_2  19 psreklkklIeknGGevveti 39 
                                       ++rek+++l+++nGG+++++ 
  gi|336254423|ref|YP_004597530.1|  94 TDREKIRQLVTENGGRMKQSR 114
                                       689**************8887 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.9   4.9e+03      17      35 ..      24      42 ..      22      45 .. 0.77
   2 ?   10.5   0.0   0.00017      0.44      20      55 ..     107     142 ..     100     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.9
                                      HHHHCCCHHCHHCCCTTSS CS
                              TrmB 17 Llklgpatadeiaeelgvp 35
                                      Ll+ g  + + +a+ l +p
  gi|336254423|ref|YP_004597530.1| 24 LLEPGVVNGRSVASPLTLP 42
                                      7888888888888877776 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00017
                                       HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB  20 lgpatadeiaeelgvprskvYevLrsLedkGlVere 55 
                                        g+++ + i   ++ +++kv + L +Led G +++ 
  gi|336254423|ref|YP_004597530.1| 107 GGRMKQSRIVDSVDWSKAKVSRLLAELEDEGQITKL 142
                                       47899999***********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1389.69
//
Query:       gi|336254424|ref|YP_004597531.1|  [L=1000]
Description: hypothetical protein Halxa_3037 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      0.001   19.2   1.2      0.001   19.2   1.2    5.0  5  Big_3_5       Bacterial Ig-like domain (group 3)
      0.006   16.7   0.1       0.11   12.6   0.0    2.7  2  Fn3-like      Fibronectin type III-like domain
  ------ inclusion threshold ------
      0.064   13.4   0.0       0.19   11.9   0.0    1.8  1  Transglut_C   Transglutaminase family, C-terminal ig like dom
      0.076   11.4  63.2     0.0064   15.0  45.2    2.4  2  Glutenin_hmw  High molecular weight glutenin subunit


Domain annotation for each model (and alignments):
>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   2.9      0.39   1.7e+03      10      61 ..      93     146 ..      84     149 .. 0.62
   2 ?   -1.4   2.1      0.61   2.7e+03      23      51 ..     491     519 ..     473     533 .. 0.64
   3 ?   -4.0   0.1         4   1.8e+04      70      87 ..     688     705 ..     686     707 .. 0.45
   4 !   19.2   1.2   2.2e-07     0.001       1      61 [.     861     926 ..     861     930 .. 0.79
   5 ?   -1.3   2.4      0.57   2.6e+03      22      44 ..     932     958 ..     909     972 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.39
                                       EEEEEE--CCCCTTS--EEEEEETT.EE-SS-EE--TT..SEEEEEEE-SS-EEE CS
                           Big_3_5  10 vtltatVtaasggtptGtVtftdgg.ttlgtavllsan..GtAtltvsalaaGth 61 
                                       vt+  + t++ ++++   Vt  +gg +++ + +ll +n  G++  t + l+aGth
  gi|336254424|ref|YP_004597531.1|  93 VTFEEQTTQG-QTVVVDEVTMANGGfVVIHDSSLLVENviGSVIGTSTYLEAGTH 146
                                       3333333333.45677788888877444445555554555888888899999998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.61
                                       TS--EEEEEETTEE-.SS-EE--TTSEEEE CS
                           Big_3_5  23 tptGtVtftdggttl.gtavllsanGtAtl 51 
                                       ++   V+  dggt   ++ ++++  G+At+
  gi|336254424|ref|YP_004597531.1| 491 VVAEDVQMSDGGTDAaANGSTVT-VGQATI 519
                                       45567888887766533344445.467776 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 4
                                       TTS---S--EEEEEEEES CS
                           Big_3_5  70 danyaastssavtvtVtk 87 
                                       d +  + t+ +  vt+++
  gi|336254424|ref|YP_004597531.1| 688 DETTMTDTDGQIEVTIEQ 705
                                       444444444444444444 PP

  == domain 4  score: 19.2 bits;  conditional E-value: 2.2e-07
                                       -S-EETTSEEEEEEE--CCCCTTS--EEEEEETTEE-SS.-EE--TTS.....EEEEEEE-SS-EEE CS
                           Big_3_5   1 ptsvtagqtvtltatVtaasggtptGtVtftdggttlgt.avllsanG.....tAtltvsalaaGth 61 
                                       p+++t g+tv +tat+t  s + +t +++f  +g+ + +  v+l+  G     t  +++s  aaG++
  gi|336254424|ref|YP_004597531.1| 861 PETATIGETVAVTATITNPSDAEATQNIQFRLDGDLIESqEVTLE-GGesqdvTFEIDTSEFAAGNY 926
                                       6899*********************************65266666.346664444445566888887 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 0.57
                                       TTS--EEEEEE....TTEE-SS-EE-- CS
                           Big_3_5  22 gtptGtVtftd....ggttlgtavlls 44 
                                       +++tG V f +    g+t+ gt  + +
  gi|336254424|ref|YP_004597531.1| 932 TDATGEVAFIEltedGDTETGTDDTDT 958
                                       5789****9976665668887765544 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.15   6.8e+02      27      43 ..     139     155 ..     137     157 .. 0.89
   2 !   12.6   0.0   2.5e-05      0.11      21      48 ..     896     923 ..     891     940 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.15
                                       EEE-TT-EEEEEEEEEC CS
                          Fn3-like  27 veLapGesktvtftldr 43 
                                       + L++G  + v++tld+
  gi|336254424|ref|YP_004597531.1| 139 TYLEAGTHENVEITLDE 155
                                       67*************96 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.5e-05
                                       EEEEEEEEE-TT-EEEEEEEEECGGG-E CS
                          Fn3-like  21 LkgFekveLapGesktvtftldrkdlsv 48 
                                       L+  + v+L+ Ges++vtf++d ++++ 
  gi|336254424|ref|YP_004597531.1| 896 LIESQEVTLEGGESQDVTFEIDTSEFAA 923
                                       777899*****************99986 PP

>> Transglut_C  Transglutaminase family, C-terminal ig like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.3e-05      0.19       5      63 ..     858     917 ..     857     937 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.3e-05
                                       EEESSCEBTTSEEEEEEEEEE-SSS-.BEEEEEEEEEEEEECTTTEEEEEEEEEEEEEE- CS
                       Transglut_C   5 ievlesavlgqdltvsvllkNplsee.lkdvklnlcaqtveynGvlaaefkkksleltLe 63 
                                       ++++e+a +g  + v+++++Np+++e +++++ +l +  +e++ v+ +  ++++ +++++
  gi|336254424|ref|YP_004597531.1| 858 FDAPETATIGETVAVTATITNPSDAEaTQNIQFRLDGDLIESQEVTLEGGESQDVTFEID 917
                                       7899*******************8662677887777777777776666666655555554 PP

>> Glutenin_hmw  High molecular weight glutenin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8  10.0     0.013        60     442     498 ..      48     104 ..      26     115 .. 0.76
   2 ?   15.0  45.2   1.4e-06    0.0064     519     617 ..     725     823 ..     710     837 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.013
                      Glutenin_hmw 442 qpgqlqqsaqeqpgqgqqpgqgqqgqqpgqgeqgqqpgqgqpgyyptspqqsgqgqq 498
                                         +q+q +aqeq  ++++ g+   + +p++g+ + + g+gq+  y t  +q+ qgq 
  gi|336254424|ref|YP_004597531.1|  48 VETQAQTQAQEQAQDENDTGDEPIAIEPDEGDGDGDTGDGQQSAYVTFEEQTTQGQT 104
                                       346777888888777888888889999999999999999999999999999999986 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.4e-06
                      Glutenin_hmw 519 qpgqgqpgyyptspqqigqgqqlgqlqqpaqgqqgqqlaqgqqgqqpgqgqqgqqpgqgqqgqqpgqgkqpgqgqpg 595
                                       qp q ++  +p  p+q+ q +q+ q +qp q +q +q  q +q +qp q +q++qp+q++q +qp+q +qp q ++ 
  gi|336254424|ref|YP_004597531.1| 725 QPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQPEQP 801
                                       55555555556666666666656666666666666666666666666666666666666666666666666665555 PP

                      Glutenin_hmw 596 yyptslqqsgqgqqpgqwqqpg 617
                                         p  ++q+ q +qp q +qp 
  gi|336254424|ref|YP_004597531.1| 802 EQPEQPEQPEQPEQPEQPEQPT 823
                                       5566666666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1000 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1109  (0.0618551); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        59  (0.00329076); 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: 1.69u 0.35s 00:00:02.04 Elapsed: 00:00:00.57
# Mc/sec: 5296.07
//
Query:       gi|336254425|ref|YP_004597532.1|  [L=167]
Description: hypothetical protein Halxa_3038 [Halopiger xanaduensis SH-6]
Scores for 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   14.0   0.0       0.19   11.8   0.0    2.1  1  HTH_20    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 ?   11.8   0.0     1e-05      0.19       2      36 ..      15      56 ..      14      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1e-05
                                      HHHHHHS-HHHHHHHHHH.....STCTTB-HHHHHHHHT..S CS
                            HTH_20  2 qiaeALahPvRrrilraL.....araegltaselaerld..l 36
                                      +++++L++  Rr+i ++L       +  + a+e+ae+ +  +
  gi|336254425|ref|YP_004597532.1| 15 EVFHILGNDRRRAIVQLLanesgQVDVSQVATEIAETESdtT 56
                                      799****************99999999999999999874342 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1311.31
//
Query:       gi|336254426|ref|YP_004597533.1|  [L=56]
Description: hypothetical protein Halxa_3039 [Halopiger xanaduensis SH-6]
Scores for 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   0.4     0.0037   17.2   0.4    1.1  1  zf-DNL         DNL zinc finger
     0.0088   16.4   0.4       0.01   16.1   0.4    1.0  1  DUF3268        zinc-finger-containing domain
  ------ inclusion threshold ------
      0.013   15.5   0.4      0.015   15.3   0.4    1.0  1  HypA           Hydrogenase/urease nickel incorporation, metal
      0.018   15.2   1.0       0.03   14.4   1.0    1.4  1  Zn-ribbon_8    Zinc ribbon domain
       0.27   11.2   0.8       0.27   11.2   0.8    2.2  2  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
        0.3   11.4   3.3        3.6    7.9   0.1    2.1  2  zf-LITAF-like  LITAF-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.4   1.3e-06    0.0037       5      36 ..       9      40 ..       7      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                            zf-DNL  5 tCkaCetrsskeiskkaYekGvVivqCpgCkn 36
                                       C++C+t  ++++++   ++G V+  CpgC +
  gi|336254426|ref|YP_004597533.1|  9 RCRNCGTHVTQQFARVFGDNGDVVHGCPGCTT 40
                                      5*****************************86 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   3.4e-06      0.01       3      49 ..       8      51 ..       6      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.4e-06
                           DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkCdayvgvhkgtkip 49
                                       rC+ CG++v+ + a  ++   ++g++++ Cp C +y  ++ g++ p
  gi|336254426|ref|YP_004597533.1|  8 ARCRNCGTHVTQQFA-RVF--GDNGDVVHGCPGCTTYREMQSGSHLP 51
                                      68******9987666.566..47899****************99988 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 ?   15.3   0.4   4.9e-06     0.015      65     103 ..       2      48 ..       1      51 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.9e-06
                                       EEE--EEEETTTS-EEECHHHHH.........S-TTTSSS-EEEEESS CS
                              HypA  65 eevpvkvrCreCgkefeleekal.........rCpkCgsadveivsGe 103
                                       e+  + +rCr+Cg++++++ +++          Cp C + + e++sG+
  gi|336254426|ref|YP_004597533.1|   2 ESSTAGARCRNCGTHVTQQFARVfgdngdvvhGCPGCTTYR-EMQSGS 48 
                                       6788999******99997643235888999999****9975.666665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.0     1e-05      0.03       7      33 ..       9      39 ..       8      45 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                       Zn-ribbon_8  7 rCeeCghefe.vlqsis.dap.lta.CPeCg 33
                                      rC++Cg+  + ++++++ d+   ++ CP C 
  gi|336254426|ref|YP_004597533.1|  9 RCRNCGTHVTqQFARVFgDNGdVVHgCPGCT 39
                                      8*****99999666666655526669****5 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 ?   11.2   0.8   8.9e-05      0.27      11      20 ..       7      16 ..       4      17 .. 0.89
   2 ?    2.8   0.6     0.036   1.1e+02      14      20 ..      35      41 ..      31      42 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.9e-05
                           DUF35_N 11 gqrCpdCGtv 20
                                      g rC++CGt+
  gi|336254426|ref|YP_004597533.1|  7 GARCRNCGTH 16
                                      89*******8 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.036
                           DUF35_N 14 CpdCGtv 20
                                      Cp C t+
  gi|336254426|ref|YP_004597533.1| 35 CPGCTTY 41
                                      7777766 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 ?    4.3   0.5     0.016        49      58      67 ..       9      18 ..       3      20 .. 0.70
   2 ?    7.9   0.1    0.0012       3.6      53      65 ..      29      41 ..      23      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.016
                     zf-LITAF-like 58 yCpnCgallg 67
                                      +C nCg+++ 
  gi|336254426|ref|YP_004597533.1|  9 RCRNCGTHVT 18
                                      5777777764 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0012
                     zf-LITAF-like 53 kdvehyCpnCgal 65
                                       dv h Cp C ++
  gi|336254426|ref|YP_004597533.1| 29 GDVVHGCPGCTTY 41
                                      59********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.32u 0.20s 00:00:00.52 Elapsed: 00:00:00.34
# Mc/sec: 488.46
//
Query:       gi|336254427|ref|YP_004597534.1|  [L=59]
Description: hypothetical protein Halxa_3040 [Halopiger xanaduensis SH-6]
Scores for 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  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 475.07
//
Query:       gi|336254428|ref|YP_004597535.1|  [L=110]
Description: hypothetical protein Halxa_3041 [Halopiger xanaduensis SH-6]
Scores for 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   27.3   0.1      5e-06   26.5   0.1    1.4  1  HTH_20         Helix-turn-helix domain
     0.0015   18.0   0.1     0.0027   17.2   0.1    1.3  1  HTH_24         Winged helix-turn-helix DNA-binding
     0.0026   17.6   0.1     0.0039   17.0   0.1    1.4  1  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0032   17.4   0.1     0.0058   16.5   0.1    1.4  1  HTH_11         HTH domain
     0.0036   17.2   0.0     0.0069   16.2   0.0    1.5  1  MarR_2         MarR family
     0.0079   16.7   0.1      0.013   16.0   0.1    1.3  1  HTH_27         Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.019   14.8   0.0       0.03   14.2   0.0    1.4  1  HTH_5          Bacterial regulatory protein, arsR family
      0.025   14.4   0.0       0.04   13.7   0.0    1.3  1  HTH_IclR       IclR helix-turn-helix domain
      0.036   13.9   0.0      0.066   13.1   0.0    1.6  1  HTH_AsnC-type  AsnC-type 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 !   26.5   0.1   2.5e-09     5e-06       3      55 ..      19      70 ..      17      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.5e-09
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      ++++L+++  r il a  ++++ ta+el +r d s +t++++++ L e +L+ 
  gi|336254428|ref|YP_004597535.1| 19 QLDVLGDECARTILVAT-SDGPKTAKELTKRTDSSSATVYRRINNLLESDLLA 70
                                      678999999********.*********************************75 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 !   17.2   0.1   1.3e-06    0.0027      15      46 ..      37      68 ..      31      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                            HTH_24 15 nprisqreLAerlglSpstvnrrlkrLeeeGl 46
                                      ++  + +eL +r++ S++tv rr+++L e+ l
  gi|336254428|ref|YP_004597535.1| 37 DGPKTAKELTKRTDSSSATVYRRINNLLESDL 68
                                      777899*********************99876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1     2e-06    0.0039      17      51 ..      32      68 ..      29      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2e-06
                                      HH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTS CS
                              TrmB 17 Ll..klgpatadeiaeelgvprskvYevLrsLedkGl 51
                                      L+  + gp+ta+e+ ++++ + ++vY+ +++L++ +l
  gi|336254428|ref|YP_004597535.1| 32 LVatSDGPKTAKELTKRTDSSSATVYRRINNLLESDL 68
                                      5556789*************************99876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   2.9e-06    0.0058      12      40 ..      36      64 ..      30      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.9e-06
                            HTH_11 12 argpisgeeLAeeLnvSrrtvrrdIkaLe 40
                                      ++gp +++eL ++++ S +tv+r+I  L 
  gi|336254428|ref|YP_004597535.1| 36 SDGPKTAKELTKRTDSSSATVYRRINNLL 64
                                      66778********************9994 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.5e-06    0.0069      11      54 ..      32      72 ..      28      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.5e-06
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      L a  ++p    t++el++r++ s ++v r+++ L +  L+ ++
  gi|336254428|ref|YP_004597535.1| 32 LVATSDGPK---TAKELTKRTDSSSATVYRRINNLLESDLLAEC 72
                                      555555555...*************************9999766 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 !   16.0   0.1   6.4e-06     0.013      13      57 ..      34      79 ..      27      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.4e-06
                            HTH_27 13 rhrrrrkkladlcgrlnvedshisyslkkLtekGLv.ertgdeadr 57
                                      +  +++k++++l +r++ +++++   ++ L e +L+ e  + e d+
  gi|336254428|ref|YP_004597535.1| 34 ATSDGPKTAKELTKRTDSSSATVYRRINNLLESDLLaECVRFEDDG 79
                                      45799*******************************7444443333 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 ?   14.2   0.0   1.5e-05      0.03       6      45 ..      30      69 ..      25      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                      HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                       IL + ++g++++ el++ ++ s +tv +  + L e++L+
  gi|336254428|ref|YP_004597535.1| 30 TILVATSDGPKTAKELTKRTDSSSATVYRRINNLLESDLL 69
                                      58888899****************************9996 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   0.0     2e-05      0.04      12      48 ..      33      69 ..      31      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                                      -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      +a+ +++ t +el +rt+ + +tv+R ++ L e  ++
  gi|336254428|ref|YP_004597535.1| 33 VATSDGPKTAKELTKRTDSSSATVYRRINNLLESDLL 69
                                      688899999**********************998877 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 ?   13.1   0.0   3.3e-05     0.066      15      41 ..      37      63 ..      25      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.3e-05
                     HTH_AsnC-type 15 daRisyaeLAervGlSestvlrRvrrL 41
                                      d+  + +eL +r+  S +tv rR++ L
  gi|336254428|ref|YP_004597535.1| 37 DGPKTAKELTKRTDSSSATVYRRINNL 63
                                      8999********************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 900.48
//
Query:       gi|336254429|ref|YP_004597536.1|  [L=91]
Description: transcriptional regulator PadR family protein [Halopiger xanaduensis SH-6]
Scores for 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-14   52.6   0.3    3.7e-14   52.4   0.3    1.1  1  PadR            Transcriptional regulator PadR-like family
     0.0042   17.0   0.1     0.0058   16.6   0.1    1.2  1  HTH_45          Winged helix-turn-helix
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.015   15.7   0.0    1.3  1  HTH_27          Winged helix DNA-binding domain
       0.03   14.6   0.0      0.054   13.8   0.0    1.4  1  DUF4358         Domain of unknown function (DUF4358)
      0.069   13.3   0.0      0.088   13.0   0.0    1.1  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.074   13.2   0.0      0.086   13.0   0.0    1.3  1  HTH_34          Winged helix DNA-binding domain
      0.083   12.7   0.0        0.1   12.5   0.0    1.2  1  DUF1495         Winged helix DNA-binding domain (DUF1495)
      0.096   12.4   0.0       0.12   12.1   0.0    1.2  1  DUF4364         Domain of unknown function (DUF4364)


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 !   52.4   0.3   1.7e-17   3.7e-14       2      75 .]      12      80 ..      11      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 1.7e-17
                                      HHHH..CCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHHH CS
                              PadR  2 Lall..eeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrelae 75
                                      L+++  +++p  G  +++e+e++++   e+++G+lYp+L++L +++lve+ + +    ++++yY++TdaGr++++e
  gi|336254429|ref|YP_004597536.1| 12 LYVIagADRP-SGQTVKDEVEKYYSS--EINHGRLYPNLDTLVNKDLVEKGQLD----RRTNYYAITDAGRQRIEE 80
                                      6666423355.79**********987..***********************998....7*************9985 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.6e-06    0.0058      27      72 ..      34      84 ..      25      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-06
                            HTH_45 27 ykanLsykllnkYLdmLvekgli.....kkskekYvlTekGlelleklkel 72
                                      y+++++  +l   Ld+Lv+k+l+     + +++ Y +T+ G++ +e+ +e 
  gi|336254429|ref|YP_004597536.1| 34 YSSEINHGRLYPNLDTLVNKDLVekgqlDRRTNYYAITDAGRQRIEERREW 84
                                      8889999999999*********98887778999*********999887765 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 ?   15.7   0.0   6.9e-06     0.015      38      68 .]      46      74 ..       4      74 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.9e-06
                            HTH_27 38 slkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +l+ L++k+Lv  ++   drr+  +++Td+G
  gi|336254429|ref|YP_004597536.1| 46 NLDTLVNKDLV--EKGQLDRRTNYYAITDAG 74
                                      799********..444469***********9 PP

>> DUF4358  Domain of unknown function (DUF4358)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.4e-05     0.054      40      96 ..       7      67 ..       3      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                           DUF4358 40 asadevlivkakdeedaeevkkaleerledqkksfedYlpe.....qyaklenavvktkGny 96
                                      ++ d ++++  +d    ++vk+ +e+++++ ++    Y p+     + +++e+ +++++ ny
  gi|336254429|ref|YP_004597536.1|  7 FQRDLLYVIAGADRPSGQTVKDEVEKYYSSEINHGRLY-PNldtlvNKDLVEKGQLDRRTNY 67
                                      6778899****************************999.65223334555555566666665 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 ?   13.0   0.0   3.9e-05     0.088       2      56 ..       6      63 ..       5      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.9e-05
                    B-block_TFIIIC  2 ndqfklLelIa.ssRysGitqsdLa...keskqdprslfyrlksLekkgLIvkqsiids 56
                                       +q+ lL +Ia + R sG t +d +    +s++    l+  l++L +k L++k ++ d+
  gi|336254429|ref|YP_004597536.1|  6 GFQRDLLYVIAgADRPSGQTVKDEVekyYSSEINHGRLYPNLDTLVNKDLVEKGQL-DR 63
                                      57889999997478******998764114566*********************999.43 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 ?   13.0   0.0   3.8e-05     0.086      25      75 ..      37      84 ..      12      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                            HTH_34 25 eatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvka 75
                                      e++ g+L+ +l++L +++ +  +k+  ++ +   + iT++Gr++ ++  ++
  gi|336254429|ref|YP_004597536.1| 37 EINHGRLYPNLDTLVNKDLV--EKGQLDR-RTNYYAITDAGRQRIEERREW 84
                                      68999*********999976..5787777.8889**********9998776 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 ?   12.5   0.0   4.5e-05       0.1      52      87 ..      43      78 ..      26      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-05
                           DUF1495 52 rynsessLielGLveeeeeseglklYklteeGieiv 87
                                       y + + L+++ Lve+ + ++ +++Y +t+ G++  
  gi|336254429|ref|YP_004597536.1| 43 LYPNLDTLVNKDLVEKGQLDRRTNYYAITDAGRQRI 78
                                      5777789********9999*************9755 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.2e-05      0.12      40      71 ..      47      79 ..      24      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.2e-05
                           DUF4364 40 lseLvesglieee.ekenktlykiTekGketle 71
                                      l+ Lv+++l+e+   ++ +++y+iT++G++ +e
  gi|336254429|ref|YP_004597536.1| 47 LDTLVNKDLVEKGqLDRRTNYYAITDAGRQRIE 79
                                      8899999999998666999**********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 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:                        29  (0.00161749); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 752.01
//
Query:       gi|336254430|ref|YP_004597537.1|  [L=332]
Description: hypothetical protein Halxa_3043 [Halopiger xanaduensis SH-6]
Scores for 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-85  285.3   1.3    6.2e-85  285.1   1.3    1.0  1  DUF1616   Protein of unknown function (DUF1616)
  ------ inclusion threshold ------
      0.073   13.6   0.9        1.1    9.7   0.1    2.4  2  DUF4981   Domain of unknown function(DUF4981)


Domain annotation for each model (and alignments):
>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.1   1.3   6.9e-89   6.2e-85       3     293 .]      25     325 ..      22     325 .. 0.96

  Alignments for each domain:
  == domain 1  score: 285.1 bits;  conditional E-value: 6.9e-89
                           DUF1616   3 vlalllllailvpvlnetplRivlglplvLflPGYaliaaLFPe................krdidgieRlaLSfglS 63 
                                        l+++l++++++ v + ++ R+++++plvLflPGYal+++LFP+                 r+id++eRl LSf+lS
  gi|336254430|ref|YP_004597537.1|  25 SLIAALVALVVTGVPAGNAGRLLVAFPLVLFLPGYALVSVLFPAaardgrddaetaierrPRGIDTVERLGLSFALS 101
                                       45566666677777788999****************************************9**************** PP

                           DUF1616  64 iaivpliglvlnvtpwgirlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleeksesrldka 140
                                       iaivp++g+vl +t+wg+ +e+ +++l+++t++la+++++rR+r+p+ +rf+v+l+a +++l++++ +     + +a
  gi|336254430|ref|YP_004597537.1| 102 IAIVPVVGIVLPLTEWGLATESAAAVLAGLTVVLAQLGVIRRLRTPARDRFTVSLTAALTGLRRDEGT-----VATA 173
                                       ***************************************************************99999.....469* PP

                           DUF1616 141 lnvlLvvsivlavaalgyavvaPkegekfTelyllgedgd.elvaenypteltagesqevivgieNhEheevnYtvv 216
                                        +vlLvv+i +a++al   +  P+++ +f+el+l++ed+d +lva++ p+e++ ges +v   ieNhE+ee++Ytvv
  gi|336254430|ref|YP_004597537.1| 174 SSVLLVVAIAVAGGALLAGFLFPASTGGFSELALYTEDEDgDLVAGELPDEVAPGESVPVSFAIENHEGEETSYTVV 250
                                       ***************************************************************************** PP

                           DUF1616 217 vllqevtdeeevevlerteldrrevtladnetweqelevepea.tgenlrleflLYkdevpeeptteeayrslhlwV 292
                                       v++q     e++ev+ertel++++ t+++++t   e e++p+a +ge++r+++lLY++e+p+ept+e+a+ ++++wV
  gi|336254430|ref|YP_004597537.1| 251 VQEQV---LEDGEVVERTELGQIDGTVSADTTGVAEREITPAAgDGETVRISLLLYPGEPPAEPTNENAEADTYFWV 324
                                       ****7...66778999************************************************************* PP

                           DUF1616 293 n 293
                                       +
  gi|336254430|ref|YP_004597537.1| 325 T 325
                                       6 PP

>> DUF4981  Domain of unknown function(DUF4981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00013       1.1      19      62 ..     208     249 ..     200     257 .. 0.72
   2 ?    2.4   0.1     0.024   2.2e+02      20      46 ..     254     283 ..     246     328 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                                       EEEEETTEEEEEEEEEE---TT-EEEEE--S.---TSSEEEEEE CS
                           DUF4981  19 wellkdGkvvasgelelpvaPgesatvtlpetkeaeeseyfltv 62 
                                       ++  +dG +va gel+++vaPges+ v++  ++ + ++e+ +tv
  gi|336254430|ref|YP_004597537.1| 208 YTEDEDGDLVA-GELPDEVAPGESVPVSFAIENHE-GEETSYTV 249
                                       556789****9.899999*******9998754433.33555554 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.024
                                       EEEETTEEEEEEEEEE-...--TT-EEEEE CS
                           DUF4981  20 ellkdGkvvasgelelp...vaPgesatvt 46 
                                       ++l+dG+vv++ el      v + ++ + +
  gi|336254430|ref|YP_004597537.1| 254 QVLEDGEVVERTELGQIdgtVSADTTGVAE 283
                                       678899999976554434445555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2422.20
//
Query:       gi|336254431|ref|YP_004597538.1|  [L=182]
Description: hypothetical protein Halxa_3044 [Halopiger xanaduensis SH-6]
Scores for 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   1.9      0.018   15.3   0.8    1.8  2  DUF3040   Protein of unknown function (DUF3040)
       0.25   11.3   2.7       0.16   11.9   0.9    1.6  2  SLATT_1   SMODS and SLOG-associating 2TM effector domain 1


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 ?   -3.7   0.0       1.7   1.5e+04      37      44 ..      59      66 ..      48      71 .. 0.50
   2 ?   15.3   0.8     2e-06     0.018      36      79 ..     113     161 ..     103     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.7
                           DUF3040 37 rrrslrrl 44
                                        r +rr+
  gi|336254431|ref|YP_004597538.1| 59 VTRTQRRR 66
                                      33333332 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2e-06
                           DUF3040  36 arrrslrrlavlavllfva.GllllvlG.vaaaa...vvlgvvGfvvml 79 
                                       ++r  +r++a +a+l++va ++++l lG v++aa   v+lgv+G++++l
  gi|336254431|ref|YP_004597538.1| 113 SSRAWHRWYAAAATLGAVAfAVAALSLGpVTTAAapaVALGVCGIILAL 161
                                       33444688999999999999********999998999*******99886 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 ?   -2.9   0.0      0.69   6.2e+03      78      95 ..       5      22 ..       2      32 .. 0.64
   2 ?   11.9   0.9   1.8e-05      0.16      13      67 ..     106     160 ..     100     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.69
                           SLATT_1 78 aaaYslaaeeLeiiraal 95
                                       ++++l++ eL ++ ++ 
  gi|336254431|ref|YP_004597538.1|  5 EREHELTQAELFDVFSNA 22
                                      566777777776665555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.8e-05
                           SLATT_1  13 Yrkkaeeneraakrwrlllillellalllaalrafgelsvdlvgvlaavaaalla 67 
                                       Y ++++ ++ra +rw ++ + l+++a ++aal+  ++++ ++ +v+  v++ +la
  gi|336254431|ref|YP_004597538.1| 106 YLDRHHGSSRAWHRWYAAAATLGAVAFAVAALSLGPVTTAAAPAVALGVCGIILA 160
                                       8899999999999999999999999999999995555555555555444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1385.81
//
Query:       gi|336254432|ref|YP_004597539.1|  [L=242]
Description: hypothetical protein Halxa_3045 [Halopiger xanaduensis SH-6]
Scores for 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-28   95.9  14.7    2.6e-09   36.4   0.2    5.2  5  Hexapep    Bacterial transferase hexapeptide (six repeats)
      8e-18   63.9  12.7    1.8e-07   30.8   0.5    4.8  5  Hexapep_2  Hexapeptide repeat of succinyl-transferase


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 !    4.3   0.0    0.0039        35       5      29 ..      57      69 ..      53      71 .. 0.59
   2 !   22.7   0.1   6.4e-09   5.7e-05       2      24 ..      77      99 ..      76     100 .. 0.95
   3 !   12.0   0.2   1.5e-05      0.14      11      35 ..     104     128 ..     103     129 .. 0.80
   4 !   27.9   0.1   1.5e-10   1.3e-06       2      36 .]     131     165 ..     130     165 .. 0.96
   5 !   36.4   0.2     3e-13   2.6e-09       2      35 ..     179     212 ..     178     213 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0039
                                      ETTEEE-TTEEEETTEEE-TTEEEE CS
                           Hexapep  5 GsnvlIgpfaviggnVkIGdnvkIg 29
                                      G+            +++I d++++g
  gi|336254432|ref|YP_004597539.1| 57 GE------------DCTIDDDATVG 69
                                      44............55555555555 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 6.4e-09
                                      EEEETTEEE-TTEEEETTEEE-T CS
                           Hexapep  2 tvIGsnvlIgpfaviggnVkIGd 24
                                      t+IG++++I+++++++g+V+IGd
  gi|336254432|ref|YP_004597539.1| 77 TRIGDGATIRAGSIVYGDVTIGD 99
                                      89********************8 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 1.5e-05
                                       -TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep  11 gpfaviggnVkIGdnvkIgagvvig 35 
                                       g+ + ++++++IGd+v +g  +vi 
  gi|336254432|ref|YP_004597539.1| 104 GHDVLVREGTEIGDDVLVGTKTVID 128
                                       5677788999999999999999886 PP

  == domain 4  score: 27.9 bits;  conditional E-value: 1.5e-10
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       t+IGs+v +  ++++   ++IG+nv +g+g+v+++
  gi|336254432|ref|YP_004597539.1| 131 TTIGSHVSLQTNVYVPTQTTIGSNVFVGPGAVLTN 165
                                       89******************************986 PP

  == domain 5  score: 36.4 bits;  conditional E-value: 3e-13
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       ++I++++ Ig++a+++++V+IG+n+ ++ag+v++
  gi|336254432|ref|YP_004597539.1| 179 PTIEDGASIGANATLLPGVTIGENAFVAAGAVVT 212
                                       79******************************97 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 !   11.8   0.4   1.8e-05      0.16       5      33 ..      57      92 ..      54      93 .. 0.79
   2 !   10.4   0.3   4.6e-05      0.41       1      22 [.      76      99 ..      76     100 .. 0.61
   3 !   16.7   0.1     5e-07    0.0045       2      32 ..     113     145 ..     112     146 .. 0.95
   4 !    9.8   0.0   7.2e-05      0.65       2      15 ..     149     162 ..     148     166 .. 0.77
   5 !   30.8   0.5     2e-11   1.8e-07       3      33 ..     180     212 ..     180     213 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.8e-05
                                      -TT-EE-TT-EES.......EEE-TT-EE-TT-EE- CS
                         Hexapep_2  5 GdnCliGanagiG.......vslGdncvvgaGvvit 33
                                      G++C i  +a++G       + +Gd++++ aG++++
  gi|336254432|ref|YP_004597539.1| 57 GEDCTIDDDATVGygefdepTRIGDGATIRAGSIVY 92
                                      77777777888733355555*************997 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 4.6e-05
                                      .EEE-TT-EE-TT-EE.S.EEE-T CS
                         Hexapep_2  1 pviIGdnCliGanagi.G.vslGd 22
                                      p++IGd   i a +++ G v++Gd
  gi|336254432|ref|YP_004597539.1| 76 PTRIGDGATIRAGSIVyGdVTIGD 99
                                      566666666666666663366666 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 5e-07
                                       EEE-TT-EE-TT-EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2   2 viIGdnCliGanagi.G.vslGdncvvgaGvvi 32 
                                       + IGd++l+G   +i G +++G  + ++ +v++
  gi|336254432|ref|YP_004597539.1| 113 TEIGDDVLVGTKTVIdGrTTIGSHVSLQTNVYV 145
                                       56*************88***************8 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 7.2e-05
                                       EEE-TT-EE-TT-E CS
                         Hexapep_2   2 viIGdnCliGanag 15 
                                       ++IG n+++G+ a+
  gi|336254432|ref|YP_004597539.1| 149 TTIGSNVFVGPGAV 162
                                       67888888888876 PP

  == domain 5  score: 30.8 bits;  conditional E-value: 2e-11
                                       EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
                         Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvvit 33 
                                       +I+d   iGana+   Gv++G+n+ v+aG v+t
  gi|336254432|ref|YP_004597539.1| 180 TIEDGASIGANATLlpGVTIGENAFVAAGAVVT 212
                                       69***********779****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1898.00
//
Query:       gi|336254433|ref|YP_004597540.1|  [L=408]
Description: glutamine--scyllo-inositol transaminase [Halopiger xanaduensis SH-6]
Scores for complete 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-127  425.7   0.0   1.9e-127  425.5   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.7e-08   34.1   0.0    2.5e-08   33.5   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
      6e-05   22.5   0.0    0.00015   21.1   0.0    1.6  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00032   19.8   0.0    0.00049   19.2   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.015   13.9   0.0      0.024   13.2   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


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 !  425.5   0.0  5.4e-131  1.9e-127       4     360 ..      49     401 ..      46     402 .. 0.95

  Alignments for each domain:
  == domain 1  score: 425.5 bits;  conditional E-value: 5.4e-131
                                       HHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHH CS
                   DegT_DnrJ_EryC1   4 eeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanav 80 
                                       ++++++v++vl+sg l  gpev++FE++faay+g++ha+a+s+Gt+Alh aL+algv++gd V++ +++Fva+ana+
  gi|336254433|ref|YP_004597540.1|  49 ADAIDRVRDVLESGALADGPEVRNFESEFAAYCGADHAVATSNGTTALHAALEALGVEEGDAVLTSPFSFVASANAI 125
                                       67899************************************************************************ PP

                                       HHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE..EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT CS
                   DegT_DnrJ_EryC1  81 lelgakpvfvDvdpdtynidpaaieaaitert..kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg 155
                                       + +g kpvf+Dvdp+ty++dp+++++++ er+   + lpVhlyG +adm+al +ia++ +l v+eDa++A+Ga++ g
  gi|336254433|ref|YP_004597540.1| 126 RLAGGKPVFADVDPETYTLDPDDVRRVLSERSdvVGLLPVHLYGLPADMPALCEIADERDLFVLEDACQAHGARITG 202
                                       ********************************66667**************************************** PP

                                       EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHH CS
                   DegT_DnrJ_EryC1 156 kkvGalgdaavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAigla 232
                                        +vG++gdaa+fSFyptKn+ttGeGG+++t+ ++lae+a+ + nhG++++ +  y +   lG+nyr+t i+AAig++
  gi|336254433|ref|YP_004597540.1| 203 DRVGTFGDAACFSFYPTKNMTTGEGGMITTDRDDLAERAQSYINHGRAETGTGGYEHVD-LGHNYRMTAIAAAIGRT 278
                                       ************************************************76666666665.***************** PP

                                       HHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGS CS
                   DegT_DnrJ_EryC1 233 qLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhyp 309
                                       qLerl  +++ Rre a+ y+e+L++l+   e++t+++  +h++h+y+v++ +e  ++rd+l++ l+e+++++ v+y+
  gi|336254433|ref|YP_004597540.1| 279 QLERLPGFNEARRETAAFYDERLSDLPL--ETPTEPRGYRHVYHQYTVRTADE--AERDALAATLEERNVDAAVYYD 351
                                       ***************************6..4555555556***********98..56******************** PP

                                       CHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 310 nplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                                       +p+hrqp+y++  +  ++++p ae++a++vlsLp++p+lte++ + Vvea+
  gi|336254433|ref|YP_004597540.1| 352 TPIHRQPAYETISTA-AAEFPEAEAAADEVLSLPVHPNLTEDERRSVVEAV 401
                                       ***********9765.669******************************98 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 !   33.5   0.0   6.9e-12   2.5e-08      48     187 ..      72     191 ..      44     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 6.9e-12
                                       HHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEE CS
                     Aminotran_1_2  48 eleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplys 124
                                        +e++ a + g        ++ av +++G++al +al++l  ++ gd++l +  ++    n++rl+gg+ v     +
  gi|336254433|ref|YP_004597540.1|  72 NFESEFAAYCG--------ADHAVATSNGTTALHAALEALG-VEEGDAVLTSPFSFVASANAIRLAGGKPVFAD-VD 138
                                       799999*****........999*******************.9*******************************.55 PP

                                       TTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEE CS
                     Aminotran_1_2 125 eedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvD 187
                                       +e+++ld +++ + l+e      +   ++   p +  G  a+ + l+++   a+++ l+++ D
  gi|336254433|ref|YP_004597540.1| 139 PETYTLDPDDVRRVLSE------RSD-VVGLLPVHLYGLPADMPALCEI---ADERDLFVLED 191
                                       9**************98......222.3333456666666666666666...66666666655 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.2e-08   0.00015      27     221 ..      63     247 ..      55     380 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.2e-08
                                       CCT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-E CS
                   Beta_elim_lyase  27 sYgedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlkn 103
                                       + ++ ++v+++e ++a+++g+++a+ + +Gt A + +l++l + +   ++t+p  + f    ++  lag k++ ++ 
  gi|336254433|ref|YP_004597540.1|  63 ALADGPEVRNFESEFAAYCGADHAVATSNGTTALHAALEALGVEEGDAVLTSP--FSFVASANAIRLAGGKPVFADV 137
                                       578899************************************88887877765..6777788888999999988886 PP

                                       BTT.TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHT CS
                   Beta_elim_lyase 104 kea.GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslg 179
                                       + +  ++d++++++++ e+++      ++ l   + +  G +     + ++ +ia+++++ ++ D++    a     
  gi|336254433|ref|YP_004597540.1| 138 DPEtYTLDPDDVRRVLSERSD------VVGLLPVHLY--GLPAD---MPALCEIADERDLFVLEDACQAHGAR---- 199
                                       554399************555......7777777777..77755...56678899999999999999766655.... PP

                                       S-CHHHHTTSSEEEEES..SSTT--SS-EEEEE-HH........HHHH CS
                   Beta_elim_lyase 180 eivkemfsyvDsvtmsl..kKdllanvGgvlafrddel....edylae 221
                                        +  ++    D  ++s+  +K++++  Gg++ +++d+l    + y+++
  gi|336254433|ref|YP_004597540.1| 200 ITGDRVGTFGDAACFSFypTKNMTTGEGGMITTDRDDLaeraQSYINH 247
                                       334455566777776655599999999999999999766666333333 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.4e-07   0.00049      47     182 ..      72     198 ..      67     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBET CS
                       Aminotran_5  47 earekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkviplde 123
                                       + ++++a+  +a+     + ts++t+a+ +++ +l+  +++gd ++++     a  ++++ +    g k +++ +d+
  gi|336254433|ref|YP_004597540.1|  72 NFESEFAAYCGADH---AVATSNGTTALHAALEALG--VEEGDAVLTSPFSFVASANAIRLA----GGKPVFADVDP 139
                                       55666666666665...899***************5..9**********9999888444443....45555777775 PP

                                       .TSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTT CS
                       Aminotran_5 124 .egeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavgh 182
                                        + +ld+d+++  l+e+ ++v +  v    G   ++++++++a +++ +vl Da+qa g 
  gi|336254433|ref|YP_004597540.1| 140 eTYTLDPDDVRRVLSERSDVVGLLPVH-LYGLPADMPALCEIADERDLFVLEDACQAHGA 198
                                       15799********************97.89**************************9876 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 ?   13.2   0.0   6.7e-06     0.024      52     110 ..      68     127 ..      65     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.7e-06
                                       HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHH CS
                   Cys_Met_Meta_PP  52 ptrsvleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrllkk 110
                                       p ++++e++ aa  g+++a+a+s G++A++aa+ al +++Gd +++s   +  + + ++ 
  gi|336254433|ref|YP_004597540.1|  68 PEVRNFESEFAAYCGADHAVATSNGTTALHAALEALgVEEGDAVLTSPFSFVASANAIRL 127
                                       78899****************************9997888****9998777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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 0.26s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3145.31
//
Query:       gi|336254434|ref|YP_004597541.1|  [L=352]
Description: oxidoreductase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-26   93.9   0.2    2.3e-26   93.0   0.2    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      4e-07   29.6   0.0    8.1e-07   28.6   0.0    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    2.9e-06   27.7   0.0    7.2e-06   26.5   0.0    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    4.9e-05   23.6   0.4     0.0005   20.3   0.1    2.2  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      7e-05   22.5   0.0    0.00015   21.4   0.0    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.001   19.5   0.1     0.0022   18.4   0.1    1.5  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
  ------ inclusion threshold ------
       0.01   16.0   0.4       0.01   16.0   0.4    1.7  2  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.033   14.3   0.3       0.26   11.4   0.1    2.2  2  DUF5340          Family of unknown function (DUF5340)
      0.056   13.7   1.3       0.26   11.5   1.3    2.2  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> 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 !   93.0   0.2   1.1e-29   2.3e-26       2     120 .]      15     129 ..      14     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 1.1e-29
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheel 78 
                                       r ++iG+G +g++h+r + e  ++ ++v++ d d+  a +va+++g ea  dleell+  ++d+v+va+p++ h++l
  gi|336254434|ref|YP_004597541.1|  15 RAGVIGVGAMGENHARVYSEL-PNVDLVGVSDHDTDVATEVADEYGTEA-VDLEELLD--RCDVVTVAVPTHVHYDL 87 
                                       789************888888.**************************5.68******..***************** PP

                                       HHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  79 akaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       +  +le  +hvl+EKP+a tve+ ++++ela++++ +++vg+
  gi|336254434|ref|YP_004597541.1|  88 VTTCLEEDVHVLVEKPIAETVEQGRRMAELADERDLVLQVGH 129
                                       ****************************************97 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 !   28.6   0.0   4.1e-10   8.1e-07      37     101 ..      14      81 ..       2      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 4.1e-10
                                       SEEEEES-SHHHHHHHHHHHHT.T-EEEEESSSHHHHH..CHHHHTCEECSHHHHHHH-SEEEE-S-- CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkaf.gmkviaydrskkkee..eeeelgvelvsleellaesDivslhlpl 101
                                        + G+iG+G++G++ a++ +++ ++++++++ + ++ +   ++e+g e v+leell ++D+v++++p 
  gi|336254434|ref|YP_004597541.1|  14 TRAGVIGVGAMGENHARVYSELpNVDLVGVSDHDTDVAteVADEYGTEAVDLEELLDRCDVVTVAVPT 81 
                                       689*****************763779999999888665657899999*******************96 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 !   26.5   0.0   3.6e-09   7.2e-06       3      81 ..      17      91 ..      15     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.6e-09
                                      EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
                     F420_oxidored  3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel 81
                                      g+iG G mge  a+  ++   +   +  +++ + + a+e a+e+g  ++avd ee+++++dvv +av+++++ ++++  
  gi|336254434|ref|YP_004597541.1| 17 GVIGVGAMGENHARVYSELP-NVDLVG-VSDHDTDVATEVADEYG--TEAVDLEELLDRCDVVTVAVPTHVHYDLVTTC 91
                                      9*************777775.555555.6699************9..77778********************9998776 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 !   20.3   0.1   2.5e-07    0.0005       2      75 ..      16      91 ..      15     127 .. 0.84
   2 ?    1.1   0.0      0.19   3.8e+02      52     107 ..     174     234 ..     148     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.5e-07
                                      EEEE--SHHHHHHHHHH..HHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnl..lkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg 75
                                       g+iG+G MG+n a+    l +   v v +++++ ++e+++e  + a ++eel++++dvv + v+   + d v++ 
  gi|336254434|ref|YP_004597541.1| 16 AGVIGVGAMGENHARVYseLPNVDLVGVSDHDTDVATEVADEYGTEAVDLEELLDRCDVVTVAVPTHVHYDLVTTC 91
                                      59*************99444566778899999*********************************99888777655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.19
                                       HHHHCSEEEE-SSSHHHHHHHHHS.....HCCC--TT-EEEE-S---HHHHHHHHHHHHHT CS
                     NAD_binding_2  52 lvasldvvitmvkagkavdevieg.....llealkkgdilidgstsspedtrelakelkek 107
                                       +v+++d+v  m++++++  + +         ++++ +d++   + s +++ + ++  ++++
  gi|336254434|ref|YP_004597541.1| 174 MVHDVDIVGSMLEDTPDALTAMGTedgryATATMEYDDVVATLTASRVTQKKVRKLSVTAR 234
                                       5788899999999988877777666888888889999999999888888888777666665 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 !   21.4   0.0   7.3e-08   0.00015       8      83 ..      17      94 ..      13     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.3e-08
                                      EEES-SHHHHHHHHHHHHTT--EEEEE..-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTGG CS
                              IlvN  8 aviGyGsqGhaqalnlrdsgldvvvgl..regsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeiep 83
                                       viG G+ G+++a+   +      vg+  ++++  ++ A e g e ++++e+ ++ dvv++ +P +++ +++++ +e+
  gi|336254434|ref|YP_004597541.1| 17 GVIGVGAMGENHARVYSELPNVDLVGVsdHDTDVATEVADEYGTEAVDLEELLDRCDVVTVAVPTHVHYDLVTTCLEE 94
                                      69************998865433455500445568999*****************************99998776655 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 !   18.4   0.1   1.1e-06    0.0022       1      93 [.      15      98 ..      15     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvs 79
                                      +++++G  G++G++ +r+ +e p+v+lv ++ ++ +  +++a+ ++    ++ + +e+     l+++d+v  a+p  v+
  gi|336254434|ref|YP_004597541.1| 15 RAGVIG-VGAMGENHARVYSELPNVDLVGVSDHDTDVATEVADEYG----TEAVDLEE----LLDRCDVVTVAVPTHVH 84
                                      579***.9***************************99999999988....44444444....66*************** PP

                                      HHHHHHHHHTTSEE CS
                    Semialdhyde_dh 80 kelapklaeagvkv 93
                                       +l+ +++e++v+v
  gi|336254434|ref|YP_004597541.1| 85 YDLVTTCLEEDVHV 98
                                      *********99987 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   0.4   5.1e-06      0.01       2      96 ..      15     100 ..      14     128 .. 0.83
   2 ?   -3.7   0.0       6.2   1.2e+04      67      86 ..     209     228 ..     201     233 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.1e-06
                                       EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS.--S-BEBSSHHHHHHH-SEEEE-S-H CS
                            DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglg.klgvavtddleevlekadvliDFTtp 77 
                                       + +v+G+ G mG++ +++ +e +++ lv++ d+++      d+ +  ++  + g +   dlee+l+ +dv+      
  gi|336254434|ref|YP_004597541.1|  15 RAGVIGV-GAMGENHARVYSELPNVDLVGVSDHDT------DVAT--EVAdEYGTEAV-DLEELLDRCDVVTVAVPT 81 
                                       6689**9.*************************98......3322..22214555554.9*********99888888 PP

                                       HHHHHHHHHHHHTT-EEEE CS
                            DapB_N  78 eavlenlklalekgvklVi 96 
                                       ++ ++++ ++le+ v++ +
  gi|336254434|ref|YP_004597541.1|  82 HVHYDLVTTCLEEDVHVLV 100
                                       8999********9999865 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.2
                                       H-SEEEE-S-HHHHHHHHHH CS
                            DapB_N  67 kadvliDFTtpeavlenlkl 86 
                                         dv+  +T+  ++ ++++ 
  gi|336254434|ref|YP_004597541.1| 209 YDDVVATLTASRVTQKKVRK 228
                                       45677777777777766654 PP

>> DUF5340  Family of unknown function (DUF5340)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00013      0.26       3      28 ..      76     101 ..      74     114 .. 0.82
   2 ?    0.2   0.0      0.41   8.1e+02      27      57 ..     216     246 ..     208     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                           DUF5340   3 kiplPshiHYEllLqlLErqtlaave 28 
                                       ++ +P h+HY+l+   LE    + ve
  gi|336254434|ref|YP_004597541.1|  76 TVAVPTHVHYDLVTTCLEEDVHVLVE 101
                                       589***************98777766 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.41
                           DUF5340  27 veqnsalreqvqqliitLRKAlaqQkqLEes 57 
                                       ++ ++ ++++v++l +t R  ++    LE+s
  gi|336254434|ref|YP_004597541.1| 216 LTASRVTQKKVRKLSVTARECFVEVDYLEQS 246
                                       4566788999999999999999988888886 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 ?   11.5   1.3   0.00013      0.26       3      97 ..      18      99 ..      16     122 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                      EE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGG CS
                   Sacchrp_dh_NADP  3 iiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppis 81
                                      +iG G++G+  a+++++  +vd  + v d + + + ++a +    +  ++a+d       L++ll   d+v  ++p + 
  gi|336254434|ref|YP_004597541.1| 18 VIGVGAMGENHARVYSELPNVD-LVGVSDHDTDVATEVA-D----EYGTEAVD-------LEELLDRCDVVTVAVPTHV 83
                                      6777777777777777777773.3333333333333333.2....33444443.......78888999***9999999* PP

                                      HHHHHHHHHHHT-EEE CS
                   Sacchrp_dh_NADP 82 sldvlkaCietgvhyv 97
                                      + d++ +C+e  vh++
  gi|336254434|ref|YP_004597541.1| 84 HYDLVTTCLEEDVHVL 99
                                      **************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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: 0.50u 0.20s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2767.35
//
Query:       gi|336254435|ref|YP_004597542.1|  [L=505]
Description: nucleotide sugar dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-41  140.7   0.1    6.5e-41  140.0   0.1    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      4e-20   72.2   0.1    1.8e-19   70.1   0.0    2.1  3  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    3.1e-18   65.8   0.0    5.9e-18   64.9   0.0    1.5  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    8.4e-07   29.3   0.1    2.7e-06   27.6   0.1    1.9  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00059   20.1   0.7     0.0038   17.5   0.7    2.5  1  TrkA_N          TrkA-N domain
    0.00067   19.7   0.1     0.0034   17.4   0.0    2.1  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
  ------ inclusion threshold ------
      0.011   15.6   0.2       0.02   14.8   0.2    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


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 !  140.0   0.1   2.5e-44   6.5e-41       3     182 ..      34     214 ..      32     219 .. 0.96

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 2.5e-44
                                       EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS-.-TTHHHHHHHHCHTTTEEEES-HHHHHHC-S CS
                    UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiy.epgLeelvkkavesgrlsfttdvekaveead 78 
                                       ++v GlG +Gl+ aav+ae   +v+gvDid   v+++nsg+++++ epgL+elv+++v ++rl++ttd   a+++a 
  gi|336254435|ref|YP_004597542.1|  34 VAVYGLGKMGLPLAAVYAETTGNVTGVDIDPDVVETINSGESHVVgEPGLDELVAEQVGTDRLEATTDGAAAAADAR 110
                                       89****************************************98769****************************** PP

                                       EEEE-----B-TTTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE---- CS
                    UDPG_MGDP_dh_N  79 vifiaVgTPskkkgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvsnPEf 155
                                       v++i V+T  ++ +++++l  ves++++ia  l+ g++v+ +ST p+gt+++++++ l+++s  ++ +f+++ +PE+
  gi|336254435|ref|YP_004597542.1| 111 VHVIIVPTLLDE-NDEPNLATVESVVDDIAAGLEPGDLVIAESTLPPGTCRDVLEPHLQQESGLEADEFGLAFCPER 186
                                       ***********9.8888************************************************************ PP

                                       --TTSHHHHHH.S-S-EEEEESSCHHHH CS
                    UDPG_MGDP_dh_N 156 lregsavkdll.npdrvviGveekkaea 182
                                          g a++d+    ++vv+Gv++++++a
  gi|336254435|ref|YP_004597542.1| 187 TSSGRALQDIRgAYPKVVGGVDDESTRA 214
                                       **********83569*********9984 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 ?   -2.8   0.0       3.4   8.6e+03      33      50 ..      11      28 ..       9      56 .. 0.80
   2 ?   -2.5   0.0       2.7   6.9e+03      54      74 ..      96     116 ..      65     137 .. 0.57
   3 !   70.1   0.0     7e-23   1.8e-19       2     104 ..     349     442 ..     348     443 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.4
                                      EEEE-SSTHHCCCCHHGG CS
                    UDPG_MGDP_dh_C 33 vkiyDPkvkeeaveaele 50
                                      v+ yD  v+e+++++ l+
  gi|336254435|ref|YP_004597542.1| 11 VSLYDASVDEARQREALA 28
                                      789999999999887654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.7
                                       CEEES-CHHHHTT-SEEEE-S CS
                    UDPG_MGDP_dh_C  54 vevvdsleealkgadaivilt 74 
                                       +e +++ + a+++a + vi++
  gi|336254435|ref|YP_004597542.1|  96 LEATTDGAAAAADARVHVIIV 116
                                       444444444444444444333 PP

  == domain 3  score: 70.1 bits;  conditional E-value: 7e-23
                                       EE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GG CS
                    UDPG_MGDP_dh_C   2 ilGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehde 78 
                                       +lGl+++++++++R Spaldi++eL+e+ga+v  +DP v++++  a     + + +++le++++  da+v++t+h+ 
  gi|336254435|ref|YP_004597542.1| 349 VLGLTYRPGVEETRASPALDIVDELTERGADVAGVDPLVDPAEYGA-----RPVALEDLEDESDALDAAVVVTPHEG 420
                                       9******************************************998.....3345669******************* PP

                                       GGGS-HHHHHHCCSS-EEEESSS-CC CS
                    UDPG_MGDP_dh_C  79 fkeldlaklkelmkpavvfDgrnvld 104
                                       f+ + +a+l    +p vv+Dgr ++d
  gi|336254435|ref|YP_004597542.1| 421 FDRIPWADL----EPMVVVDGRDAVD 442
                                       ******888....899******9887 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 !   64.9   0.0   2.3e-21   5.9e-18       2      93 ..     235     321 ..     234     322 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 2.3e-21
                      UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeel 78 
                                       tAE++K+++  +++++I ++Nel++l+++lgi v+e i++++  p    ++++pg+GvGG+c+p  +++L+ ++ee 
  gi|336254435|ref|YP_004597542.1| 235 TAEAVKVFEGLYRDVNIGLANELGRLADELGISVREAIDTANDLPM--CQLHDPGPGVGGHCIPYYPHFLLGRTEE- 308
                                       8********************************************9..6***********************9988. PP

                      UDPG_MGDP_dh  79 gleaelleavrevNe 93 
                                         +++l +++r+vN+
  gi|336254435|ref|YP_004597542.1| 309 --PMDLTHTARRVND 321
                                       ..7***********7 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 !   27.6   0.1     1e-09   2.7e-06       2     100 ..      34     162 ..      33     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1e-09
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.....................EEE-SSHHHHHHHCS CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.....................akaaesieelvasld 57 
                                       +++ GlG+MG ++a   ++   +v++++ +++ ve++ + +                     ++a+++ ++++a+++
  gi|336254435|ref|YP_004597542.1|  34 VAVYGLGKMGLPLAAVYAETTGNVTGVDIDPDVVETINSGEshvvgepgldelvaeqvgtdrLEATTDGAAAAADAR 110
                                       7999******************************999988799999**********999999777777777777776 PP

                                       EEEE-S.........SSHHHHHHHHHSHCCC--TT-EEEE-S---HHHHHHH CS
                     NAD_binding_2  58 vvitmv.........kagkavdeviegllealkkgdilidgstsspedtrel 100
                                       v +++v         ++ + v++v++++++ l++gd++i  st  p + r++
  gi|336254435|ref|YP_004597542.1| 111 VHVIIVptlldendePNLATVESVVDDIAAGLEPGDLVIAESTLPPGTCRDV 162
                                       555555112233222245789**********************998877766 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.7   1.5e-06    0.0038       1      85 [.      34     121 ..      34     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEE...EE-SSSH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadav...iaatgdd 73 
                                       +++ GlG++G  la    e  g +v+++d d+++ve++   + +vv   + de v e+ g ++ +a     aa+ d 
  gi|336254435|ref|YP_004597542.1|  34 VAVYGLGKMGLPLAAVYAEtTG-NVTGVDIDPDVVETINSGESHVVGEPGLDELVAEQVGTDRLEATtdgAAAAADA 109
                                       6899***************777.6***************999*****************999988642212333344 PP

                                       HHHHHHHHHHHH CS
                            TrkA_N  74 eanilavllake 85 
                                        + +++v ++ +
  gi|336254435|ref|YP_004597542.1| 110 RVHVIIVPTLLD 121
                                       555555555544 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 !   17.4   0.0   1.3e-06    0.0034       2      79 ..      34     118 ..      33     129 .. 0.85
   2 ?   -1.5   0.0      0.83   2.1e+03      59      84 ..     398     423 ..     394     427 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT--...-....-TTEEEES-HHHHHTT-- CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgik...l....penlvattdlaealkgad 71 
                                       +av G G+ G  lA+v ae++ +v+    +++++e+in+ + +v   pg++         + l+attd a+a+++a+
  gi|336254435|ref|YP_004597542.1|  34 VAVYGLGKMGLPLAAVYAETTGNVTGVDIDPDVVETINSGESHVVGEPGLDelvAeqvgTDRLEATTDGAAAAADAR 110
                                       9**************************************999987655532111211126789************** PP

                                       EEEE---H CS
                    NAD_Gly3P_dh_N  72 iivlvvPs 79 
                                       + v+ vP+
  gi|336254435|ref|YP_004597542.1| 111 VHVIIVPT 118
                                       *******8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.83
                                       EES-HHHHHTT--EEEE---HHHHHH CS
                    NAD_Gly3P_dh_N  59 attdlaealkgadiivlvvPsqalre 84 
                                       a +dl++  +  d  v+v P++ + +
  gi|336254435|ref|YP_004597542.1| 398 ALEDLEDESDALDAAVVVTPHEGFDR 423
                                       668999999999*********98865 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 ?   14.8   0.2   7.7e-06      0.02       2      44 ..      34      76 ..      33     119 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.7e-06
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44
                                      vav G G mG  +aav a++  +V+ vdi+++ +e+ ++  ++
  gi|336254435|ref|YP_004597542.1| 34 VAVYGLGKMGLPLAAVYAETTGNVTGVDIDPDVVETINSGESH 76
                                      9*******************************99887665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3871.95
//
Query:       gi|336254436|ref|YP_004597543.1|  [L=372]
Description: family 2 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for 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-19   69.0   0.0    7.2e-19   68.2   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    6.3e-05   23.0   0.2     0.0002   21.3   0.2    1.7  1  Glyco_tranf_2_3  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 !   68.2   0.0     8e-23   7.2e-19       2     167 ..       9     190 ..       8     192 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 8e-23
                                       EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH..................C-TTEEEEE CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak..................edprvrvir 60 
                                       vv+++y ee+ + +++e + a      ++i+ vDD+S+D++++++++ a+                   + rv  ir
  gi|336254436|ref|YP_004597543.1|   9 VVVTSYEEEAFVGRVIETVPAF----VDRIYAVDDASPDGSWDVIQRVADrineeeepeaelaladggDGRRVVPIR 81 
                                       8*********************....*****************************************9999****** PP

                                       ESSS-HHHHHHHHHHHH--SS...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEE CS
                   Glycos_transf_2  61 reenvGkagalnaglraatgd...yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvge 134
                                       ++en+G+++a+ +g ++a  d   ++++++ D ++dp+ l ++v++   ++ad + g+r  ++ ++  ++  ++v  
  gi|336254436|ref|YP_004597543.1|  82 HDENRGYGAAVKTGYERAAADgidVVAVMNGDGQMDPEILDRIVDPVATGEADYAKGNRLLSPEDREGMSTFRFV-G 157
                                       ******************************************************************999999887.9 PP

                                       EECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHH CS
                   Glycos_transf_2 135 nerlyfkerkrslkgnlsfeigsaallrreale 167
                                       n +l +  +  + ++++ +   ++++++re +e
  gi|336254436|ref|YP_004597543.1| 158 NAMLTGLSKFATGYWTVGDPQNGYTAISRETIE 190
                                       999999999999999999999999999999765 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 !   21.3   0.2   2.3e-08    0.0002       4     128 ..       7     144 ..       4     169 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.3e-08
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaq.e..y......pr...vevvvvvdesdaetlevaeelaaalpdvrvrvvvnar 68 
                                       + v+V++++ee+ +g+v+e + a  +  y      p+   + +  v+d+  +e  ++ae + a+ +d r rvv+  +
  gi|336254436|ref|YP_004597543.1|   7 IGVVVTSYEEEAFVGRVIETVPAFvDriYavddasPDgswDVIQRVADRINEEEEPEAELALADGGDGR-RVVPIRH 82 
                                       789*********777766555432111223332343356555555556644555566654444555544.5555544 PP

                   Glyco_tranf_2_3  69 nlgstgksralnealravk...sdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvflln 128
                                       + + +g+  a++ ++++++    d+v+++++D   +P++l+r++  ++t +++ + ++++l  
  gi|336254436|ref|YP_004597543.1|  83 D-ENRGYGAAVKTGYERAAadgIDVVAVMNGDGQMDPEILDRIVDPVATGEADYAKGNRLLSP 144
                                       4.3467777778888887745667*********************999999999999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2706.66
//
Query:       gi|336254437|ref|YP_004597544.1|  [L=75]
Description: hypothetical protein Halxa_3050 [Halopiger xanaduensis SH-6]
Scores for 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-06   25.4   4.4      1e-05   24.8   4.4    1.3  1  zf-ribbon_3     zinc-ribbon domain
    3.2e-05   23.5   3.6    4.5e-05   23.0   3.6    1.2  1  zinc_ribbon_2   zinc-ribbon domain
    5.8e-05   23.0   0.7    6.6e-05   22.9   0.7    1.1  1  DZR             Double zinc ribbon
    0.00024   21.8   0.2    0.00025   21.8   0.2    1.1  1  zinc_ribbon_15  zinc-ribbon family
    0.00058   19.9   0.6    0.00073   19.5   0.6    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0037   17.1   0.4        2.7    7.9   0.0    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)
  ------ inclusion threshold ------
      0.019   15.1   4.7      0.062   13.4   4.7    1.8  1  Zn-ribbon_8     Zinc ribbon domain
      0.029   14.5   1.7      0.048   13.7   1.7    1.3  1  UPF0547         Uncharacterised protein family UPF0547
      0.043   13.5   0.2      0.053   13.2   0.2    1.1  1  TackOD1         Thaumarchaeal output domain 1
      0.046   13.2   2.7       0.81    9.2   0.1    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.072   13.0   1.6       0.33   10.8   0.1    2.1  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
      0.076   11.8   1.1      0.092   11.5   1.1    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
      0.097   12.6   4.2       0.28   11.1   4.0    1.7  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.099   12.6   2.0       0.92    9.5   0.0    2.2  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.12   12.1   3.2        1.3    8.8   0.1    2.2  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
       0.32   11.3   5.7        1.9    8.9   0.8    2.4  2  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
       0.42   10.5   5.0        2.2    8.2   5.0    1.9  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
        2.3    8.0   6.1         10    5.9   6.1    1.9  1  Rubredoxin_2    Rubredoxin metal binding domain
        2.8    8.7   5.1        8.8    7.1   0.3    2.2  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109


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 !   24.8   4.4   1.1e-08     1e-05       4      25 ..      46      67 ..      45      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.1e-08
                       zf-ribbon_3  4 rCPnCGaplssddnvCpyCGtk 25
                                      +C nCG+++++d+++Cp CG++
  gi|336254437|ref|YP_004597544.1| 46 ECRNCGTNVDADATACPACGSD 67
                                      699****99***********85 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   3.6   4.8e-08   4.5e-05       2      21 ..      47      66 ..      46      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.8e-08
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                      C nCG+ ++ +a+ Cp CG+
  gi|336254437|ref|YP_004597544.1| 47 CRNCGTNVDADATACPACGS 66
                                      *******************7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.7     7e-08   6.6e-05      28      49 .]      44      65 ..      16      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7e-08
                               DZR 28 edrCpsCgekvdpearfCpeCG 49
                                       + C +Cg+ vd++a+ Cp+CG
  gi|336254437|ref|YP_004597544.1| 44 LHECRNCGTNVDADATACPACG 65
                                      6789999999999999999998 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.2   2.6e-07   0.00025      59      86 .]      38      65 ..      12      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.6e-07
                    zinc_ribbon_15 59 kkesse....kkeCknCgkeveeefkyCpkCg 86
                                           +     +eC+nCg++v+++ + Cp Cg
  gi|336254437|ref|YP_004597544.1| 38 G----RsttvLHECRNCGTNVDADATACPACG 65
                                      2....03345899******************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 !   19.5   0.6   7.8e-07   0.00073      66      97 ..      40      69 ..      31      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.8e-07
                                      EE--EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                              HypA 66 evpvkvrCreCgkefeleekalrCpkCgsadv 97
                                      ++ v  +Cr+Cg++++ +  a+ Cp+Cgs d+
  gi|336254437|ref|YP_004597544.1| 40 STTVLHECRNCGTNVDAD--ATACPACGSDDI 69
                                      5667789*****999987..458******986 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 !    7.6   0.1    0.0036       3.4      24      36 ..      40      52 ..      33      54 .. 0.87
   2 !    7.9   0.0    0.0028       2.7       2      14 ..      60      72 ..      59      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0036
                           TFIIS_C 24 pmtvfykCtkCgh 36
                                      ++tv ++C +Cg 
  gi|336254437|ref|YP_004597544.1| 40 STTVLHECRNCGT 52
                                      579999*****96 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0028
                           TFIIS_C  2 kCpkCgsreayff 14
                                       Cp Cgs++++ +
  gi|336254437|ref|YP_004597544.1| 60 ACPACGSDDIVTY 72
                                      6*******99876 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   4.7   6.6e-05     0.062       7      35 ..      46      68 ..      44      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.6e-05
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.e 35
                                      +C++Cg+  +       a+ taCP+Cgs +
  gi|336254437|ref|YP_004597544.1| 46 ECRNCGTNVD-------ADATACPACGSdD 68
                                      7*****7777.......33788*****955 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.7   5.1e-05     0.048       2      21 ..      46      65 ..      45      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-05
                           UPF0547  2 vCPeCeakvPvaaqfCphCG 21
                                      +C  C + v ++a +Cp CG
  gi|336254437|ref|YP_004597544.1| 46 ECRNCGTNVDADATACPACG 65
                                      5999***************9 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   5.7e-05     0.053      71     100 ..      42      71 ..      31      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.7e-05
                           TackOD1  71 drirlCpsCksghlnvrevCpkCkSidiee 100
                                         ++ C++C ++      +Cp C+S di +
  gi|336254437|ref|YP_004597544.1|  42 TVLHECRNCGTNVDADATACPACGSDDIVT 71 
                                       5589**********************9975 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.5    0.0064         6       2      27 ..      46      66 ..      45      66 .. 0.81
   2 ?    9.2   0.1   0.00086      0.81       3      12 ..      61      70 ..      59      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0064
                                      EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                       C nCg+    +D++   + C++CG+
  gi|336254437|ref|YP_004597544.1| 46 ECRNCGTN---VDAD--ATACPACGS 66
                                      5*****85...7777..789****96 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00086
                                      ETTTTCEECH CS
                      TF_Zn_Ribbon  3 CPnCgstnlv 12
                                      CP Cgs+++v
  gi|336254437|ref|YP_004597544.1| 61 CPACGSDDIV 70
                                      ******9976 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 ?   10.8   0.1   0.00035      0.33      14      31 ..      36      54 ..      35      59 .. 0.80
   2 ?    1.4   0.2      0.31     3e+02       4       9 ..      61      66 ..      59      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                                      EECSCCCE.EEESSSS-EE CS
                    RNA_POL_M_15KD 14 kedkegkn.feCrqCgYee 31
                                      ++++++++  eCr+Cg   
  gi|336254437|ref|YP_004597544.1| 36 TDGRSTTVlHECRNCGTNV 54
                                      6788999999*****9765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.31
                                      ESTTTS CS
                    RNA_POL_M_15KD  4 CpkCgN 9 
                                      Cp Cg+
  gi|336254437|ref|YP_004597544.1| 61 CPACGS 66
                                      888885 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.1   9.7e-05     0.092     504     531 ..      41      69 ..      38      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.7e-05
                                       E--EEEETT.--..EESSSB-TTT--BE.E CS
                              NRDD 504 npkidvCnecgy..kgeiekCpkCgseeev 531
                                       ++ +  C++cg+  +   + Cp Cgs++ +
  gi|336254437|ref|YP_004597544.1|  41 TTVLHECRNCGTnvDADATACPACGSDD-I 69 
                                       667789******76666699*****877.4 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 ?   11.1   4.0   0.00029      0.28      41      63 ..      39      61 ..      27      64 .. 0.81
   2 ?    2.0   0.2      0.22     2e+02      30      36 ..      60      66 ..      58      69 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                    OrfB_Zn_ribbon 41 alsgrtfkCpnCgfeadrDvnAa 63
                                      + ++ +++C+nCg+  d+D  A+
  gi|336254437|ref|YP_004597544.1| 39 RSTTVLHECRNCGTNVDADATAC 61
                                      5677889*************998 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.22
                    OrfB_Zn_ribbon 30 tCseCgs 36
                                       C+ Cgs
  gi|336254437|ref|YP_004597544.1| 60 ACPACGS 66
                                      5888887 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 ?    2.6   0.4      0.14   1.3e+02      37      45 ..      44      52 ..      35      53 .. 0.69
   2 ?    9.5   0.0   0.00098      0.92      19      31 ..      59      73 ..      55      75 .] 0.73

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.14
                     Zn_Tnp_IS1595 37 lfqCkeCrk 45
                                      l++C+ C++
  gi|336254437|ref|YP_004597544.1| 44 LHECRNCGT 52
                                      566777764 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00098
                     Zn_Tnp_IS1595 19 fvCPhCgsr..kayr 31
                                        CP+Cgs+    y+
  gi|336254437|ref|YP_004597544.1| 59 TACPACGSDdiVTYS 73
                                      56******9665555 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 ?    3.9   0.6     0.047        44      24      30 ..      47      53 ..      47      55 .. 0.87
   2 ?    8.8   0.1    0.0014       1.3       6      16 ..      60      71 ..      56      75 .] 0.71

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.047
                           zf-RRN7 24 CrrChtq 30
                                      Cr+C+t 
  gi|336254437|ref|YP_004597544.1| 47 CRNCGTN 53
                                      *****95 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0014
                           zf-RRN7  6 pCgvCgc.rsft 16
                                      +C++Cg+ + +t
  gi|336254437|ref|YP_004597544.1| 60 ACPACGSdDIVT 71
                                      7******64444 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 ?    5.1   0.3      0.03        28      19      32 ..      35      51 ..      34      59 .. 0.73
   2 ?    8.9   0.8     0.002       1.9       4      13 ..      59      68 ..      56      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.03
                                      T....S-EE...ETTTT CS
                    Prim_Zn_Ribbon 19 dkdgrGtwf...CrqCg 32
                                      ++dgr+t++   Cr Cg
  gi|336254437|ref|YP_004597544.1| 35 ETDGRSTTVlheCRNCG 51
                                      67889888877788883 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.002
                                      E--TTTT-TT CS
                    Prim_Zn_Ribbon  4 spCPvCGGrD 13
                                       +CP CG+ D
  gi|336254437|ref|YP_004597544.1| 59 TACPACGSDD 68
                                      68*****988 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 ?    8.2   5.0    0.0024       2.2      14      36 ..      47      69 ..      43      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0024
                           DUF35_N 14 CpdCGtvqfPPr.avCphCgsddl 36
                                      C++CGt  + +   +Cp Cgsdd 
  gi|336254437|ref|YP_004597544.1| 47 CRNCGTN-VDADaTACPACGSDDI 69
                                      9999999.688889*******985 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   6.1     0.011        10       1      22 [.      45      66 ..      45      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.011
                      Rubredoxin_2  1 YvCsqCGfesakwfGrCpsCgs 22
                                      ++C++CG    +    Cp+Cgs
  gi|336254437|ref|YP_004597544.1| 45 HECRNCGTNVDADATACPACGS 66
                                      68******************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 ?    4.2   0.6     0.074        70       3      11 ..      45      53 ..      43      58 .. 0.82
   2 ?    7.1   0.3    0.0093       8.8       3      11 ..      59      67 ..      57      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.074
                           zf-ISL3  3 hrCPnCgsk 11
                                      h C+nCg  
  gi|336254437|ref|YP_004597544.1| 45 HECRNCGTN 53
                                      78****975 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0093
                           zf-ISL3  3 hrCPnCgsk 11
                                      ++CP Cgs 
  gi|336254437|ref|YP_004597544.1| 59 TACPACGSD 67
                                      79*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 549.71
//
Query:       gi|336254438|ref|YP_004597545.1|  [L=309]
Description: group 1 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for 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-11   43.5   0.0    7.6e-11   42.6   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.7e-10   40.7   0.0    2.8e-10   40.0   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    2.3e-08   34.2   0.0    5.8e-08   32.9   0.0    1.7  2  Glyco_transf_4   Glycosyltransferase Family 4
    2.8e-08   34.4   0.3    7.5e-08   33.0   0.1    1.8  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    0.00046   20.2   0.0    0.00098   19.2   0.0    1.6  1  Glyco_trans_4_2  Glycosyl transferase 4-like
     0.0038   17.6   0.0     0.0077   16.6   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> 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 !   42.6   0.0   2.6e-14   7.6e-11      63     133 ..     197     274 ..     172     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 2.6e-14
                                       -.....THHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE--TT-HHHHHHHHHHH CS
                   Glyco_trans_1_4  63 v.....edlaellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv.gengllvppgdpealaeailrL 131
                                       v     + ++++++aad ++++s  eg ++++ Ea+a+ lpvV+ dvg ++e + g++  lv+ +d e+l+e + ++
  gi|336254438|ref|YP_004597545.1| 197 VygvdhDTVPDYMNAADALLLTShsEGSPNSVKEALACNLPVVSVDVGDVSERLeGVDPSLVS-EDDEELIEGLREV 272
                                       23446344****************99*********************9999999999999996.68999*9999998 PP

                                       HH CS
                   Glyco_trans_1_4 132 le 133
                                       le
  gi|336254438|ref|YP_004597545.1| 273 LE 274
                                       86 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   9.5e-14   2.8e-10      80     170 ..     199     286 ..     193     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 9.5e-14
                                       CCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHH CS
                   Glycos_transf_1  80 evsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkll 156
                                        v+++ ++ ++++ad+++l+s+sEg + ++ EA+a++lpv+++++g ++e ++  +   lv  +++e+l+e++r++l
  gi|336254438|ref|YP_004597545.1| 199 GVDHDTVPDYMNAADALLLTSHSEGSPNSVKEALACNLPVVSVDVGDVSERLEGVDP-SLVS-EDDEELIEGLREVL 273
                                       467899********************************************9987774.4444.447*********** PP

                                       HSHHHHHHHHHHHH CS
                   Glycos_transf_1 157 edeelrerlgenar 170
                                       e++ +r + +e+ar
  gi|336254438|ref|YP_004597545.1| 274 ESG-ERSNGREAAR 286
                                       **9.5555555555 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   1.9e-11   5.8e-08      37     170 .]      18     139 ..       1     139 [. 0.70
   2 ?   -2.8   0.0       1.9   5.7e+03      45      68 ..     158     181 ..     142     185 .. 0.58

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.9e-11
                    Glyco_transf_4  37 v.....elvvrvprvplpllkrllr..sla.flrrlrrllkre..kpDvvHahspaalgaallalrrrlgiplVltv 103
                                       +     +++v++   p  + ++ ++  s++ +l+++ +++ +   ++D+vHah+  ++  al a     ++p+Vl++
  gi|336254438|ref|YP_004597545.1|  18 QmraleRRGVSFSTLPVSGEGDSGKtrSPTdYLKYFPEVIAEAgnGYDLVHAHYGLTAPMAL-AQ---VRKPVVLSL 90 
                                       455555555555555555544433311333044556677776689*********77765443.33...478****** PP

                    Glyco_transf_4 104 HglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekitVipnGvDler 170
                                        g++           l+  +  + r  +  +d v++ Se++++ l +       + +Vip GvDle+
  gi|336254438|ref|YP_004597545.1|  91 WGSD-----------LYGPVGPVSRTCAPLCDEVVVMSEEMRETLDH-------DCRVIPDGVDLEK 139
                                       ****...........678888999999********************.......368*******985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                    Glyco_transf_4  45 rvplpllkrllrslaflrrlrrll 68 
                                        +  ++++ + r + +++r+rr++
  gi|336254438|ref|YP_004597545.1| 158 EYHVLFPYLPEREVKNYPRARRIV 181
                                       444455666666677777777665 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 !   33.0   0.1   2.5e-11   7.5e-08      23     144 ..       3     124 ..       1     135 [. 0.73
   2 ?   -1.8   0.0       1.2   3.7e+03      37      65 ..     154     179 ..     125     215 .. 0.54

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.5e-11
                   Glyco_trans_4_4  23 vlt...papapg....apeleedgvrvhrlpvprrps...pladlaalralrrllrqrrerpdvvhahs.ptaglaa 88 
                                       vlt    a+ap      ++le++gv    lpv+ +++   ++   ++l  + ++++ +  ++d+vhah+ +ta++a 
  gi|336254438|ref|YP_004597545.1|   3 VLTlttNADAPFmteqMRALERRGVSFSTLPVSGEGDsgkTRSPTDYLKYFPEVIAEAGNGYDLVHAHYgLTAPMAL 79 
                                       44432233333344323348899**********9986332333445788888888889***********77788866 PP

                   Glyco_trans_4_4  89 rlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeel 144
                                       ++ r     p+v++l+g +l ++ g+v        r+++  +d v+v se+++e+l
  gi|336254438|ref|YP_004597545.1|  80 AQVR----KPVVLSLWGSDLYGPVGPV-------SRTCAPLCDEVVVMSEEMRETL 124
                                       6666....6********9887665554.......4677888************998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                   Glyco_trans_4_4  37 edgvrvhrl.pvprrpspladlaalralrr 65 
                                       +d  ++h l p  +++     ++ ++++rr
  gi|336254438|ref|YP_004597545.1| 154 WDSDEYHVLfPYLPER----EVKNYPRARR 179
                                       4455554432322222....2222222222 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 !   19.2   0.0   3.3e-07   0.00098      44     112 ..      26      96 ..       4     101 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.3e-07
                   Glyco_trans_4_2  44 gihvhrlkvd.......rkgpleylkaf.klkklikkikPDvvhahyakpygllgslaarlsgvipvvlsvwGldvl 112
                                       g+ +  l+v+       +++p  ylk+f +++   + +++D+vhahy    gl + +a +    +pvvls wG+d +
  gi|336254438|ref|YP_004597545.1|  26 GVSFSTLPVSgegdsgkTRSPTDYLKYFpEVI-AEAGNGYDLVHAHY----GLTAPMA-LAQVRKPVVLSLWGSDLY 96 
                                       55555555444444444555777777763433.345689********....6777664.556669*********986 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 !   16.6   0.0   2.6e-06    0.0077       3      78 ..     216     289 ..     214     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-06
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervl 78 
                                       L +s+se+    + Ea+ac+ ++++ d  ++ e ++  +  ++ ed eel+e +r++l+  +er+  +eaare v 
  gi|336254438|ref|YP_004597545.1| 216 LLTSHSEGSPNSVKEALACNLPVVSVDVGDVSERLEGVDPSLVSEDDEELIEGLREVLE-SGERSNGREAARE-VS 289
                                       67899999888999*******************997665556666***********986.6666665555554.34 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2251.77
//
Query:       gi|336254439|ref|YP_004597546.1|  [L=482]
Description: hypothetical protein Halxa_3052 [Halopiger xanaduensis SH-6]
Scores for 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  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); 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:                         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: 00:00:00.41
# Mc/sec: 3560.81
//
Query:       gi|336254440|ref|YP_004597547.1|  [L=61]
Description: hypothetical protein Halxa_3053 [Halopiger xanaduensis SH-6]
Scores for 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   14.6   0.2      0.021   14.3   0.2    1.1  1  DUF1129   Protein of unknown function (DUF1129)


Domain annotation for each model (and alignments):
>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   1.2e-06     0.021     150     200 ..       9      59 ..       4      61 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-06
                           DUF1129 150 llilllllvvwlvlftlvallpaviNpvLpplvliiigviafvvryylkkk 200
                                       +l++lll++vw+v+ +l++ll     +v   +  ++ gv+  +  yy++++
  gi|336254440|ref|YP_004597547.1|   9 WLYILLLVLVWVVVASLIELLAFDGDVVSTVVQGAAGGVVFAIGTYYFQRR 59 
                                       799*****************9988888877777888889888899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 495.48
//
Query:       gi|336254441|ref|YP_004597548.1|  [L=393]
Description: alcohol dehydrogenase GroES domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-28   99.3   0.1    2.5e-28   98.1   0.1    1.6  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    7.2e-20   71.3   0.1    8.2e-15   54.9   0.0    2.3  2  ADH_zinc_N       Zinc-binding dehydrogenase
      9e-10   38.3   0.4      2e-09   37.2   0.4    1.6  1  ADH_N_assoc      Alcohol dehydrogenase GroES-associated
  ------ inclusion threshold ------
       0.04   13.2   0.0      0.063   12.6   0.0    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.059   14.1   0.1       0.16   12.7   0.1    1.8  1  Methyltransf_25  Methyltransferase domain
       0.12   13.0   0.0       0.94   10.2   0.0    2.2  1  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.1   8.4e-32   2.5e-28       1     106 [.      29     154 ..      29     157 .. 0.94

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 8.4e-32
                                       TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT- CS
                             ADH_N   1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkege 77 
                                       p++++i+++a++iCgsDlh+++g   + ++ + ++GHE +Gev evg+ev++l+vGdrVvv++++scg+C  C+e+ 
  gi|336254441|ref|YP_004597548.1|  29 PNDAVIEITATAICGSDLHLYNG-YMPGMREGDVIGHEPMGEVIEVGDEVETLEVGDRVVVPFTVSCGSCWFCEEDL 104
                                       5799*******************.8**************************************************** PP

                                       GGG-................TTBEETTTS.....S-SSSBSEEEECGGGE CS
                             ADH_N  78 enlC................eeakllgvs.....ldGgfaeyvvvpekkl 106
                                       ++lC                + a+llg+s     + Gg+aey+ vp +++
  gi|336254441|ref|YP_004597548.1| 105 YSLCdnsnpnaevaraamgqSPAGLLGYShmlggYAGGQAEYLRVPYADI 154
                                       ************99999999778888888888889**********97665 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   2.7e-18   8.2e-15       1      69 [.     200     269 ..     200     280 .. 0.93
   2 !   14.1   0.0   1.2e-05     0.035      71     110 ..     295     335 ..     292     345 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 2.7e-18
                                       HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsg 69 
                                       +vG++ +q A +lGa +via+d+ +e+le+a + Ga e+in + +d+ +r+ e+tgg+g+d  +++vG++
  gi|336254441|ref|YP_004597548.1| 200 PVGQFSIQSAWMLGAeRVIAIDRIQERLEMASDHGAAETINFEHEDVYDRLMEMTGGRGPDRCIDAVGTE 269
                                       7*****************************************444***********************54 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHCEEEEEEEEECSC.TSSEEEEEHHHHHHTT-EEE CS
                        ADH_zinc_N  71 tleaalkllkpgGrlvvvGg.gkgeeefdlrnlllkeksil 110
                                       +l++a+k++++gG+l v G+   + + +++++l+ k ++++
  gi|336254441|ref|YP_004597548.1| 295 VLRQAIKCCRKGGTLSVPGVyIRNSDNVPFGPLMNKALTVK 335
                                       789*****************9999999*********99985 PP

>> ADH_N_assoc  Alcohol dehydrogenase GroES-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.4   6.6e-13     2e-09       1      22 [.       5      26 ..       5      27 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 6.6e-13
                       ADH_N_assoc  1 MKAVTyqGpkdVrVeeVPDPkI 22
                                      M A+T++G kdVr +eVP P+I
  gi|336254441|ref|YP_004597548.1|  5 MEALTWHGEKDVRIDEVPKPEI 26
                                      99*******************9 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 ?   12.6   0.0   2.1e-05     0.063      30      83 ..     192     244 ..     171     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                                       EEEEESTSHHHHHHHHHHHHTT-E.EEEEESSHHHHHHHHHTTTCECEEHCHHHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgak.VtvlDvrparleqleslgakfvevlksqee 83 
                                       +v v G G +G+ +i+ a  lga+ V ++D  ++rle  ++ ga   e+++ ++e
  gi|336254441|ref|YP_004597548.1| 192 TVAVWGCGPVGQFSIQSAWMLGAErVIAIDRIQERLEMASDHGAA--ETINFEHE 244
                                       689*******************96599**********99998776..55555544 PP

>> Methyltransf_25  Methyltransferase 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      0.16       4      58 ..     196     250 ..     193     307 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-05
                                       ET-TT.SHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG.B CS
                   Methyltransf_25   4 lGcGt.GrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaed.l 58 
                                        GcG+ G+++++ a  lg+++v+++D  +e le a  + ++e   ++f++ d+ d l
  gi|336254441|ref|YP_004597548.1| 196 WGCGPvGQFSIQSAWMLGAERVIAIDRIQERLEMASDHGAAE--TINFEHEDVYDrL 250
                                       599988999999999999*********************776..7999999995533 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00032      0.94       4      93 ..     197     308 ..     195     311 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00032
                                       T-T.TSHHHHHHH.HTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC....TS...S-TT-EEEEEEES. CS
                   Methyltransf_11   4 GcG.tGrlaeala.krg.arvvgvDlskemlklakekaseeglkvefvvadaek....lp...fednsfDlvvsse. 69 
                                       GcG  G+++ + a   g +rv+++D  +e l++a++++  e   ++f ++d+ +    +     +d  +D+v     
  gi|336254441|ref|YP_004597548.1| 197 GCGpVGQFSIQSAwMLGaERVIAIDRIQERLEMASDHGAAET--INFEHEDVYDrlmeMTggrGPDRCIDAVGTEAh 271
                                       888777776666644557********************9998..888888887543221122255666666665554 PP

                                       ......-CCC-C.......CHHHHHHHHHHHEEEEEE CS
                   Methyltransf_11  70 ......vlhhve.......dpekalkeiaRvLkpgGl 93 
                                             v + v+       d+  +l+++ +++++gG+
  gi|336254441|ref|YP_004597548.1| 272 gtglkgVTDKVKqemhlqdDRPIVLRQAIKCCRKGGT 308
                                       4444442222212233333666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2827.07
//
Query:       gi|336254442|ref|YP_004597549.1|  [L=334]
Description: NAD-dependent epimerase/dehydratase [Halopiger xanaduensis SH-6]
Scores for complete 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-32  113.3   0.0      2e-32  112.6   0.0    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.7e-24   85.2   0.0    4.9e-24   84.8   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    4.8e-22   78.8   0.0    9.3e-22   77.8   0.0    1.4  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.6e-19   69.8   0.0    3.7e-19   69.3   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    3.2e-18   65.8   0.0    3.7e-11   42.7   0.0    2.2  2  NAD_binding_4    Male sterility protein
    8.7e-11   41.4   0.0    1.3e-10   40.9   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    1.7e-08   34.3   0.0    3.3e-08   33.4   0.0    1.5  2  NmrA             NmrA-like family
    4.1e-07   29.4   0.0    8.8e-07   28.3   0.0    1.5  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.5e-05   24.6   0.0    0.00017   21.1   0.0    2.3  1  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.098   12.6   0.0       0.23   11.4   0.0    1.5  1  KR               KR domain
       0.13   12.6   0.0       0.39   11.0   0.0    1.7  2  TrkA_N           TrkA-N 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 !  112.6   0.0   1.2e-35     2e-32       2     241 .]       8     236 ..       7     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 1.2e-35
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE-- CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihlA 72 
                                        VtGatGf+Gs+l+++ll+ g++v +l+r ss+++  + +d       e++ +d+ d++ l++l++  + dav+hlA
  gi|336254442|ref|YP_004597549.1|   8 AVTGATGFLGSHLCERLLADGWDVRALSRPSSDREVLEGADEgedgalEWYVGDVFDDETLRELVD--GTDAVFHLA 82 
                                       69****************************999998888888************************..9*******7 PP

                                       S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHH..TCTEEEEEEEGGGGTSCSSSSBSTCSTTS--.--SSHHHHHH CS
                         Epimerase  73 avggvaassedpadfieknlqgtlnlleaarka..gvkrllflsSsevYGkdaeqpkeettltgpl.kpnspYaaaK 146
                                       +vg ++a   +p+ + + n  gt ++l+a+r++  gv rl+f s++ +  +++ +p  +++    + +p  +Y  +K
  gi|336254442|ref|YP_004597549.1|  83 GVGLWSA---TPETVKRVNRDGTAHVLKACRASedGVGRLVFTSTAGTRRPNEASPFADES---DVaEPIGAYQSSK 153
                                       6666655...8999999**************8777**********9888888888955555...455999******* PP

                                       HHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHH CS
                         Epimerase 147 lageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeail 223
                                       + +e+lv +ya++ g +a+++ +++++Gpr     + ++ p+l++  le   +  l g g +    + v+Dv+++il
  gi|336254442|ref|YP_004597549.1| 154 AEAEQLVDRYADDEGGDAVTVHPTSVFGPR-----DGSFTPQLLSMGLEPTMPAYLPG-GLS---IVGVSDVVDGIL 221
                                       ******************************.....99****99998777664444444.444...799********* PP

                                       HHHHHHTT-STTEEEEES CS
                         Epimerase 224 lvlehvdagdkgeiyniG 241
                                       ++ e+   g +ge+y +G
  gi|336254442|ref|YP_004597549.1| 222 AAYEK---GGNGEHYILG 236
                                       *****...9999999887 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 !   84.8   0.0     3e-27   4.9e-24       1     193 [.       8     191 ..       8     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 3e-27
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlr.espelleelskvnvkk..viegDvtdkdkleealegvdvvihla 74 
                                       +vtG++GFlG++l+++L+  +  ++vr+l     + e+le + + +        gDv d ++l+e ++g d+v+hla
  gi|336254442|ref|YP_004597549.1|   8 AVTGATGFLGSHLCERLLADG--WDVRALSRPsSDREVLEGADEGEDGAleWYVGDVFDDETLRELVDGTDAVFHLA 82 
                                       69****************999..9****99540455666666655544455999**********************9 PP

                         3Beta_HSD  75 slvdvagkltedeimkvnvkGTrnvleacv..kagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypes 149
                                       ++       t +++ +vn  GT  vl+ac+  + gv +lv+tS+a+   pn ++ ++   dE+   e  +  ay++s
  gi|336254442|ref|YP_004597549.1|  83 GVGLWSA--TPETVKRVNRDGTAHVLKACRasEDGVGRLVFTSTAGTRRPN-EASPFA--DESDVAE--PIGAYQSS 152
                                       9988776..8999****************833468***************5.456776..8887665..6789**** PP

                         3Beta_HSD 150 KalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpll 193
                                       Ka aE+lv +  +    +gg+ +T+   p+ ++G++d  ++p+l
  gi|336254442|ref|YP_004597549.1| 153 KAEAEQLVDRYAD---DEGGDAVTV--HPTSVFGPRDGSFTPQL 191
                                       ********98777...688887775..8*********9988765 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 !   77.8   0.0   5.7e-25   9.3e-22       2     321 ..       9     315 ..       8     320 .. 0.82

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 5.7e-25
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       +TG +Gf Gs+l+e+Ll+ g +v  + r ss    + +e     ++   ++ l+++ gD+ D + l++l++ +  d+
  gi|336254442|ref|YP_004597549.1|   9 VTGATGFLGSHLCERLLADGWDVRALSRPSSDR--EVLEGA---DE-GEDGALEWYVGDVFDDETLRELVDGT--DA 77 
                                       9************************99888874..344443...22.34789********************9..9* PP

                                       EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB.-TTS-----SHHH CS
                     GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpq.tEttpfyPrsPYa 154
                                       v++LA+   V+    +Pe++ +vn  Gt+++L+a+ra + +   r++++St+      +++p+ +E+   +P   Y 
  gi|336254442|ref|YP_004597549.1|  78 VFHLAG---VGLWSATPETVKRVNRDGTAHVLKACRASE-DGVGRLVFTSTAGTRRPNEASPFaDESDVAEPIGAYQ 150
                                       *****7...888999*********************986.4678********88888889997589999******** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EEC.TTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlyl.GnldakRdwghvkDyv 230
                                        +K+ a+++v  y +  g  av+       +pr g +f  ++++ ++     +     yl G l+       v+D+v
  gi|336254442|ref|YP_004597549.1| 151 SSKAEAEQLVDRYADDEGGDAVTVHPTSVFGPRDG-SFTPQLLSMGL-----EPTMPAYLpGGLS----IVGVSDVV 217
                                       *********************************64.46666665554.....3433334448886....679***** PP

                                       HHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH....................TTGGCCCEECGG-- CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevg........rakesgkvvvevdpkyfr 299
                                       +++ ++ +++ + +++i  ge+ + +  v +  ++lg t        + ++        + +++g++v +++++  +
  gi|336254442|ref|YP_004597549.1| 218 DGILAAYEKGGNGEHYILGGENLTYDRAVSRISEHLGGTPARIPVPSTAIHaagpvaeaVGAATGRQVFPFNRRMAK 294
                                       ************************************97655443333333211222211235789999999866665 PP

                                       SS--SB--B-THHHHHHH---- CS
                     GDP_Man_Dehyd 300 pgevdlllgdaskakeeLgWkp 321
                                           ++l+   +ka  eLg++ 
  gi|336254442|ref|YP_004597549.1| 295 -LATERLFYTSEKAADELGYEY 315
                                       .567899999*********985 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 !   69.3   0.0   2.3e-22   3.7e-19       1     144 [.      11     177 ..      11     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 2.3e-22
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH.....CTTTCEEEE--TT-CCHHHHHHTT-SEEEES-.... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaele.....aeeglevvegdvtdvedlaealkgadaVvsal.... 68 
                                       GAtG  G++l+++lla+ g++v+al R +++ + le     ++ +le  +gdv d e+l+e ++g+daV+  +    
  gi|336254442|ref|YP_004597549.1|  11 GATGFLGSHLCERLLAD-GWDVRALSRPSSDREVLEgadegEDGALEWYVGDVFDDETLRELVDGTDAVFHLAgvgl 86 
                                       9****************.5*********999997776555456799***********************99996766 PP

                                       ..--TCC....HHHHHHHHHHHHHH..CT--EEEEEEETTTTSGCGCHHHHHHH.....HCCHHHHHHHHHHHHHHH CS
                    NAD_binding_10  69 ..ggggk....deegaknivdaake..agvkRfvlvsaigvgdevpgefgewnk.....ellkaylaakraaeellr 132
                                         ++ ++    +++g++++++a+++   gv R+v+ s++g+++  p+e +++++     e ++ay   k++ae+l+ 
  gi|336254442|ref|YP_004597549.1|  87 wsATPETvkrvNRDGTAHVLKACRAseDGVGRLVFTSTAGTRR--PNEASPFADesdvaEPIGAYQSSKAEAEQLVD 161
                                       653333356666777*******9973369************97..33333333211122689***********9997 PP

                                       H....SSSEEEEEEE- CS
                    NAD_binding_10 133 a....sgldwTivrpg 144
                                       +     g d + v+p+
  gi|336254442|ref|YP_004597549.1| 162 RyaddEGGDAVTVHPT 177
                                       6444456666666665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0     9e-08   0.00015       1      39 [.       9      45 ..       9      59 .. 0.85
   2 !   42.7   0.0   2.3e-14   3.7e-11      77     209 ..      64     185 ..      62     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 9e-08
                                      EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaee 39
                                      +TGaTGFLG++L e+LL +     + +l R++s+++++e
  gi|336254442|ref|YP_004597549.1|  9 VTGATGFLGSHLCERLLADGW--DVRALSRPSSDREVLE 45
                                      7****************9987..6888888888777665 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 2.3e-14
                                       -HHHHHHHHHH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--..-EEEEEEGGGTTS-TTT--SSS- CS
                     NAD_binding_4  77 seedlqelaeevdviihsaAtvnfdepykellrvNveGtrevlelakklkkl.kvllhvSTayvngeregeveekvy 152
                                       ++e+l+el++ +d+++h a+   + ++ ++++rvN +Gt +vl+ +++ +     l++ ST  + + r +e      
  gi|336254442|ref|YP_004597549.1|  64 DDETLRELVDGTDAVFHLAGVGLWSATPETVKRVNRDGTAHVLKACRASEDGvGRLVFTST--AGTRRPNEA----- 133
                                       6899*******************************************87777245555565..455555433..... PP

                                       H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-...- CS
                     NAD_binding_4 153 eegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg...e 209
                                                   ++++ ++   +Y+ sKa+aE+lv ++++ +g  +v v p+ + g    
  gi|336254442|ref|YP_004597549.1| 134 --------SPFADESDVAEPIGAYQSSKAEAEQLVDRYADDEGGDAVTVHPTSVFGprdG 185
                                       ........44556777788889******************************99985541 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 !   40.9   0.0   7.8e-14   1.3e-10       4     165 ..       8     193 ..       5     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 7.8e-14
                                       EEESTTSHHHHHHHHHCTTTSEEEEEE-TT.....................T--TTSHHHHHHHHHHH--SEEEE-- CS
                     RmlD_sub_bind   4 lvtGanGqlGseLakqlaeeglevlaltre.....................eldltdaeavaellkeakpdvvvnaA 59 
                                        vtGa+G lGs+L ++l ++g++v al+r+                       d+ d e+++el++    d+v ++A
  gi|336254442|ref|YP_004597549.1|   8 AVTGATGFLGSHLCERLLADGWDVRALSRPssdrevlegadegedgalewyVGDVFDDETLRELVDG--TDAVFHLA 82 
                                       79**************************99******************99888*************9..789***** PP

                                       ----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT...-EEEEEEEGGGS-S-TTS-B-.TTS----SSHHHHHHHHH CS
                     RmlD_sub_bind  60 AytavDkaEseeeaayavnaeavealAeaaaavg...alLihvStDyVFdGekkrpYe.eddetsPlnvYGrtKlaG 132
                                           +      +e   +vn ++++++ +a++a +     L++ St      ++++p++ e+d  +P+++Y  +K++ 
  gi|336254442|ref|YP_004597549.1|  83 GVGLWS---ATPETVKRVNRDGTAHVLKACRASEdgvGRLVFTSTAGTRRPNEASPFAdESDVAEPIGAYQSSKAEA 156
                                       877775...5799999**************988633348*******999999999985378999************* PP

                                       HHHHHH....H-SSEEEEEE-SEESSSSS-HHHHHHH CS
                     RmlD_sub_bind 133 Eqavla....agkkalivRtswvygekgknfvktmlr 165
                                       Eq v      +g +a+ v  + v+g ++ +f  ++l+
  gi|336254442|ref|YP_004597549.1| 157 EQLVDRyaddEGGDAVTVHPTSVFGPRDGSFTPQLLS 193
                                       ****986655677899999999999999999887776 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0     2e-11   3.3e-08       2     105 ..       8     127 ..       7     162 .. 0.78
   2 ?   -4.0   0.0       5.2   8.4e+03     193     226 ..     220     254 ..     211     256 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2e-11
                                       EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHST....TEEEES-TT-HHHHHHHHTT-SEEEE---G CS
                              NmrA   2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaG....velvkgdlddkeslvealkgvdvvfsvtgf 74 
                                       +v+GaTG +G+++ + ll++g++vral R ++  ++ + +++G     e   gd+ d+e l+e+++g d+vf   g+
  gi|336254442|ref|YP_004597549.1|   8 AVTGATGFLGSHLCERLLADGWDVRALSRPSSDREVLEGADEGedgaLEWYVGDVFDDETLRELVDGTDAVFHLAGV 84 
                                       79*****************************777777766666222145669********************98875 PP

                                       G.........S-HHHHHHHHHHH...HHHHS-SEEEEEE---G CS
                              NmrA  75 y.........skeiedgkklvdA...akeaGvkhfiySslgdd 105
                                                 +   +dg++ v     a e Gv ++++ s +  
  gi|336254442|ref|YP_004597549.1|  85 GlwsatpetvKRVNRDGTAHVLKacrASEDGVGRLVFTSTAGT 127
                                       5668888877556677776554302245668999998877655 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.2
                                       HHHHHHHH.TTEEEEE-SEEE-HHHHHHHHHHHHT CS
                              NmrA 193 ilkdprkl.kgkriklagntlsgneivelfekkig 226
                                       il   +k  +g+++ l g+ l+++ +v+ +++ +g
  gi|336254442|ref|YP_004597549.1| 220 ILAAYEKGgNGEHYILGGENLTYDRAVSRISEHLG 254
                                       55555566688888889999999999988888776 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   5.4e-10   8.8e-07       3     134 ..       9     130 ..       7     137 .. 0.83
   2 ?   -4.0   0.0       3.7   6.1e+03     132     156 ..     143     167 ..     140     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.4e-10
                                       EETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-S CS
                   Polysacc_synt_2   3 vtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvd 79 
                                       vtGa+G +Gs+l++++l+     ++ l+r       +e     e ++  l+ +    +gdv d e+l+++++  + d
  gi|336254442|ref|YP_004597549.1|   9 VTGATGFLGSHLCERLLADGW-DVRALSRPSSDREVLEGAD--EGEDGALEWY----VGDVFDDETLRELVD--GTD 76 
                                       9***************99754.5777777777766666654..4455567666....***************..*** PP

                                       EEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHH..HTT-SEEEEEEEGGGSS- CS
                   Polysacc_synt_2  80 vvfhaAAlKhVPlveenpleaiktNvlgtenvieaai..eagvkkvvliStDKAvnP 134
                                       +vfh A    V l    p  + + N  gt +v++a+   e gv ++v+ St    +P
  gi|336254442|ref|YP_004597549.1|  77 AVFHLAG---VGLWSATPETVKRVNRDGTAHVLKACRasEDGVGRLVFTSTAGTRRP 130
                                       *****96...899*********************98622568********9766665 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.7
                                       SS--SHHHHHHHHHHHHHHHGGG-- CS
                   Polysacc_synt_2 132 vnPtnvmGatKrlaekllqalakes 156
                                       ++P+ ++  +K+ ae+l+  +a+ +
  gi|336254442|ref|YP_004597549.1| 143 AEPIGAYQSSKAEAEQLVDRYADDE 167
                                       5789999999999999988777655 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.1e-07   0.00017       1     174 [.       5     174 ..       5     179 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.1e-07
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklg 76 
                                       k++ vtGa++ +G  ++++l+++G++v +++r +++  ev++   e     +  + +Dv d e +++lv+       
  gi|336254442|ref|YP_004597549.1|   5 KTAAVTGATGFLGSHLCERLLADGWDVRALSRPSSDR-EVLEGADEGeDGALEWYVGDVFDDETLRELVDGT----- 75 
                                       789**************************99999888.56665555547889999*************9988..... PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBH...... CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagva...... 147
                                         d++ + AG+        l +++ e v  vN  g+ ++ +a+     +   Gr v++s   ++ p++  +      
  gi|336254442|ref|YP_004597549.1|  76 --DAVFHLAGV-------GLWSATPETVKRVNRDGTAHVLKACRAS--EDGVGRLVFTSTAGTRRPNEASPfadesd 141
                                       ..888888888.......4666667777788888888888887666..78888888877666666654432222222 PP

                                       ......HHHHHHHHHHHHHHHHHHHHGGGTEEE CS
                         adh_short 148 ......aYsAsKaavagltrslakelaptgirv 174
                                             aY +sKa  ++l++  a++   + ++v
  gi|336254442|ref|YP_004597549.1| 142 vaepigAYQSSKAEAEQLVDRYADDEGGDAVTV 174
                                       222222666666666666666666666666665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.23       4      85 ..       8      84 ..       6     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                      EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                                KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppi 82
                                       +tG++G LG +l++ l+++g   +  lsR  ++d++  +  +  e  +   e++  Dv d + +++l++  +a +  +
  gi|336254442|ref|YP_004597549.1|  8 AVTGATGFLGSHLCERLLADGW-DVRALSRP-SSDREVLEGAD--EGEDGALEWYVGDVFDDETLRELVDGTDAVF-HL 81
                                      69*******************6.46778888.34444443444..33456899999************99998444.44 PP

                                      -EE CS
                                KR 83 kGv 85
                                      +Gv
  gi|336254442|ref|YP_004597549.1| 82 AGV 84
                                      444 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   0.0   0.00024      0.39       7      58 ..      14      71 ..       8      83 .. 0.77
   2 ?   -2.5   0.0       3.7   6.1e+03      90     107 ..      91     108 ..      87     113 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                      SHHHHHHHHHHHHTTEEEEEEESSH...HHHHHHHHTT....SEEEES-TTSHHHHHHT CS
                            TrkA_N  7 GrvGrslaeeLseggkdvvvidkde...erveelreeg....levvvgdatdeevLeea 58
                                      G +G++l+e+L ++g+dv +  +     e++e + +eg    le++vgd+ d+e+L+e+
  gi|336254442|ref|YP_004597549.1| 14 GFLGSHLCERLLADGWDVRALSRPSsdrEVLEGA-DEGedgaLEWYVGDVFDDETLREL 71
                                      668**********888999998754211445554.444466799************986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.7
                                       SEEEEEESSGGGHHHHHH CS
                            TrkA_N  90 kkiiaraqdpehaellkk 107
                                       ++++ r++++ +a++lk 
  gi|336254442|ref|YP_004597549.1|  91 PETVKRVNRDGTAHVLKA 108
                                       567777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2341.24
//
Query:       gi|336254443|ref|YP_004597550.1|  [L=318]
Description: hypothetical protein Halxa_3056 [Halopiger xanaduensis SH-6]
Scores for 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-06   28.2   0.0    3.3e-06   27.5   0.0    1.4  1  DUF362    Domain of unknown function (DUF362)


Domain annotation for each model (and alignments):
>> DUF362  Domain of unknown function (DUF362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.8e-10   3.3e-06       5     191 ..      58     227 ..      54     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.8e-10
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx...xxxxx RF
                            DUF362   5 pNlgeagnpe.gatthpevvravvellkeagagkiivgdspglyvsrgkahrevaeeagydelae..ga...diadg 75 
                                       p+  ++ +p+ g +t+p+vv a+v +l+++  ++i v+ ++        + +++ +  gy++l+e  +a   d+ad 
  gi|336254443|ref|YP_004597550.1|  58 PDAHYPFHPStGTVTDPAVVGALVAALEDRTDADIAVAGTTNE----IIDLERTGQYLGYRDLLErfDAelvDLADD 130
                                       55566666777999*************9998678999999984....33367788899****999775555777777 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF362  76 legedevvvpvkgkhlkkelkiakavleaDviInlpklKgHalagvtgalKnlfGcisgsgkaeiHskrdsekfaek 152
                                        e + +vv +v+g ++ + +++++ ++   +++ +p l+  + ++v g+++ l  ++  +   ei           +
  gi|336254443|ref|YP_004597550.1| 131 AEPRTDVVREVDG-RSVS-VSVPTRLV-RGAVVTVPTLRPTEDGRVAGGVRRLADLVDSAADPEI-----------T 193
                                       7777777777855.4444.99**9964.568**************************99999999...........5 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF362 153 iadlakalkpdlnvvdgikamegegpsggskelglvlaS 191
                                        + +++a+ p l+v+d+++a+    p     +++ ++a+
  gi|336254443|ref|YP_004597550.1| 194 AVAATQAVDPALSVMDATTAYG-TDPY----AADALFAG 227
                                       899999999*********7765.4442....33344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2374.14
//
Query:       gi|336254444|ref|YP_004597551.1|  [L=366]
Description: oxidoreductase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-23   83.4   0.4    4.3e-23   82.4   0.4    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    1.6e-08   34.6   0.0    5.6e-08   32.8   0.0    1.9  2  GFO_IDH_MocA_C   Oxidoreductase family, C-terminal alpha/beta
     0.0018   18.5   0.1     0.0051   17.1   0.1    1.8  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.007   15.7   0.2      0.051   12.9   0.0    2.2  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.011   16.4   0.1      0.029   15.1   0.1    1.7  1  CoA_binding      CoA binding domain
      0.024   14.6   0.6      0.056   13.4   0.5    1.7  2  ADH_zinc_N       Zinc-binding dehydrogenase
       0.11   12.9   0.0       0.18   12.2   0.0    1.4  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
       0.12   12.8   0.1       0.21   12.0   0.1    1.5  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
       0.14   12.7   0.5       0.29   11.6   0.5    1.5  1  CoA_binding_2    CoA binding domain
       0.16   12.6   1.4       0.32   11.7   1.4    1.5  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> 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 !   82.4   0.4   2.4e-26   4.3e-23       2     120 .]      16     133 ..      15     133 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 2.4e-26
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHHH CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngthee 77 
                                        v++ G+G+ig  hl++  +   + +vva+ d  +e+ e+ ae+ g++  y+d+++ll+ ++ da++va p+ +h++
  gi|336254444|ref|YP_004597551.1|  16 SVGVLGVGNIGMVHLKSASAM-ADVDVVAAADAVPENRER-AERAGADrTYDDYAALLEAEDLDAAVVALPPFLHAD 90 
                                       69*************999999.999**************9.58999998**************************** PP

                                       HHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  78 lakaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                        +++a+eag++v++EKP+a + +ea++++e+ae+ +  v+v++
  gi|336254444|ref|YP_004597551.1|  91 AVERAAEAGVDVFVEKPFARSTAEADRMLEAAEEGDIAVGVDH 133
                                       **********************************999898875 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.5   2.7e+03      63      84 ..      40      61 ..      37      80 .. 0.81
   2 !   32.8   0.0   3.1e-11   5.6e-08      24      84 ..     173     230 ..     145     255 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                                      EEEEEEE.SEEESCTCCSCSEE CS
                    GFO_IDH_MocA_C 63 svvaalgrmrqnaeaaededaa 84
                                       vvaa +++ +n+e+ae+ +a 
  gi|336254444|ref|YP_004597551.1| 40 DVVAAADAVPENRERAERAGAD 61
                                      6899999999999999998877 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 3.1e-11
                                       EECHHHHCCGGSH.HCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCTCCSCSEE CS
                    GFO_IDH_MocA_C  24 agaeakkrwkrrk.kksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaeaaededaa 84 
                                       + ++++ +w  ++ + +gG+l +lgiH +D+l wLfG   +++aa+g +  ++    +edaa
  gi|336254444|ref|YP_004597551.1| 173 PVRDPPASWPLDPdAAGGGSLLELGIHCFDVLEWLFGDLEIESAATGETLDVP----VEDAA 230
                                       567788899999999*******************************9877776....33333 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 !   17.1   0.1   2.8e-06    0.0051       1      96 [.      17     102 ..      17     126 .. 0.83
   2 ?   -3.3   0.0       5.8     1e+04       7     110 ..     335     350 ..     320     357 .. 0.48

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.8e-06
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       v ++G G++G + ++  ++  dvd  ++ ad   e+ e++           +  + ++y+a+L+a  ++ d+ v ++
  gi|336254444|ref|YP_004597551.1|  17 VGVLGVGNIGMVHLKSASAMADVD-VVAAADAVPENRERAER-------AGADRTYDDYAALLEA--EDLDAAVVAL 83 
                                       679********************6.78888888888555542.......2356788999997776..677******* PP

                                       SGGGHHHHHHHHHHHT-EE CS
                   Sacchrp_dh_NADP  78 ppissldvlkaCietgvhy 96 
                                       pp++++d ++ ++e+gv++
  gi|336254444|ref|YP_004597551.1|  84 PPFLHADAVERAAEAGVDV 102
                                       *****************87 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.8
                                       SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGGHH CS
                   Sacchrp_dh_NADP   7 GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppissl 83 
                                       G vG+ ++e                                                                    
  gi|336254444|ref|YP_004597551.1| 335 GEVGRRTLE-------------------------------------------------------------------- 343
                                       333333333.................................................................... PP

                                       HHHHHHHHHT-EEEESS-BCGCCSCHC CS
                   Sacchrp_dh_NADP  84 dvlkaCietgvhyvdtsiskeertnya 110
                                                            ++t+y+
  gi|336254444|ref|YP_004597551.1| 344 --------------------LAETAYE 350
                                       ....................3444444 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 !   12.9   0.0   2.9e-05     0.051      34      92 ..      12      74 ..       4      85 .. 0.71
   2 ?   -0.2   0.0      0.31   5.5e+02     145     162 ..      94     111 ..      87     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                                      GTTSEEEEES-SHHHHHHHHHHHHT.T-EEEEE.SSSHHHHHCHHHHTC..EECSHHHHHHH- CS
                      2-Hacid_dh_C 34 lsgktvGiiGlGrIGqavakrlkaf.gmkviay.drskkkeeeeeelgv..elvsleellaes 92
                                       s   vG++G+G+IG    k ++a+ +++v+a  d  ++++e++e+ g+  ++++  +ll+  
  gi|336254444|ref|YP_004597551.1| 12 SSSLSVGVLGVGNIGMVHLKSASAMaDVDVVAAaDAVPENRERAERAGAdrTYDDYAALLEAE 74
                                      56778*****************97637777765155555555666666654666777777655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.31
                                       SCCEEEES--SSSSSGTC CS
                      2-Hacid_dh_C 145 kiagaalDvfeeeplped 162
                                       + a a++Dvf e p+ ++
  gi|336254444|ref|YP_004597551.1|  94 RAAEAGVDVFVEKPFARS 111
                                       567899999999998744 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.6e-05     0.029       5      91 ..      16     104 ..      12     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                                       EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TT..TTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHH CS
                       CoA_binding   5 kviviGagglgiaglyhfkeklkygikavfgvnpr..kvgtevlglpvyksvdeleektevdvavitvPaesaqeav 79 
                                       +v+v G+g+ g   l + + + ++ ++a+++  p+    ++  +    y++ + l e  + d+av+++P+   ++av
  gi|336254444|ref|YP_004597551.1|  16 SVGVLGVGNIGMVHLKSASAMADVDVVAAADAVPEnrERAERAGADRTYDDYAALLEAEDLDAAVVALPPFLHADAV 92 
                                       79********99999*****************9993233344446677888888888867***************** PP

                                       HHHHHTT-SEEE CS
                       CoA_binding  80 delveagikgiv 91 
                                       ++++eag+ + v
  gi|336254444|ref|YP_004597551.1|  93 ERAAEAGVDVFV 104
                                       ********9876 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   3.1e-05     0.056       5      67 ..      25     108 ..      21     131 .. 0.72
   2 ?   -0.5   0.0      0.63   1.1e+03      27      53 ..      92     122 ..      88     147 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHTT-....EEEE.EESSHHHHHHHHHTTESEEEET....TTC.HHHHHHHHHT...........TTSSEE CS
                        ADH_zinc_N   5 aavqlAkalGa....evia.vdsseeklelakklGadeviny....kea.dlverikelt...........ggegvd 60 
                                       +++  +k + a     v+a +d  +e++e a++ Gad++++      ea dl++++ +l             + gvd
  gi|336254444|ref|YP_004597551.1|  25 IGMVHLKSASAmadvDVVAaADAVPENRERAERAGADRTYDDyaalLEAeDLDAAVVALPpflhadaveraAEAGVD 101
                                       44444443333344677777**********************99994444888888888877777777776567888 PP

                                       EEEESSC CS
                        ADH_zinc_N  61 vvfecvG 67 
                                       v +e + 
  gi|336254444|ref|YP_004597551.1| 102 VFVEKPF 108
                                       8887665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.63
                                       HHHHHHTTESEEEET...TTC.HHHHHHHHH CS
                        ADH_zinc_N  27 lelakklGadeviny...kea.dlverikel 53 
                                       +e a++ G+d+++     +++ + + +++++
  gi|336254444|ref|YP_004597551.1|  92 VERAAEAGVDVFVEKpfaRSTaEADRMLEAA 122
                                       5677788888888776653332333333333 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 ?   12.2   0.0    0.0001      0.18       2      60 ..      16      75 ..      15     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                      EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-.TS-HHHHHHHHHEETTTEC-SS-EEEET CS
                           Gp_dh_N  2 kvainGfGRIGrlvlralleekelevvaind.ltdletlayllkyDsvhgrfkgeveaee 60
                                      +v++ G G IG + l+ + +  +++vva  d + ++++ a     D ++  + + +eae+
  gi|336254444|ref|YP_004597551.1| 16 SVGVLGVGNIGMVHLKSASAMADVDVVAAADaVPENRERAERAGADRTYDDYAALLEAED 75
                                      699****************************88999999999999999999888777774 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 ?   12.0   0.1   0.00012      0.21       2      94 ..      17     103 ..      16     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                       EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEE.GGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkved.vdeeelkevdivflalpag 77 
                                       v+++G  G++G + l+  +   +v++v+++     + ++ ae+      g+d +++d +   e +++d ++ alp  
  gi|336254444|ref|YP_004597551.1|  17 VGVLG-VGNIGMVHLKSASAMADVDVVAAADAVP-ENRERAER-----AGADRTYDDyAALLEAEDLDAAVVALPPF 86 
                                       78888.7888888888777777777777655555.55555555.....4688999997778889************* PP

                                       HHHHHHHHHHHTTSEEE CS
                    Semialdhyde_dh  78 vskelapklaeagvkvi 94 
                                        +++ ++++aeagv v+
  gi|336254444|ref|YP_004597551.1|  87 LHADAVERAAEAGVDVF 103
                                       **************886 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   0.00016      0.29      45     106 ..      66     130 ..      32     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                       S----T....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT....---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  45 vyaslaedpepvdlvdvftppeatpeivkealalgakavwlqpg....sedeeaaelaeeagirvv 106
                                        ya l e  e++d+++v++pp   ++ v+ a+++g+ +++  p     +e + ++e+aee +i v 
  gi|336254444|ref|YP_004597551.1|  66 DYAALLE-AEDLDAAVVALPPFLHADAVERAAEAGVDVFVEKPFarstAEADRMLEAAEEGDIAVG 130
                                       4555554.69***************************99988887777889999999999999876 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   1.4   0.00018      0.32       1     111 [.      21     126 ..      21     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHH CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvl 77 
                                       G+G+iG   l+   +++   ++++va ad+   ++ +r++ +++ ++++d  +l++ +d d  V + ++   a+ v+
  gi|336254444|ref|YP_004597551.1|  21 GVGNIGMVHLKSASAMA---DVDVVAAADAV-PENRERAERAGADRTYDDYAALLEAEDLDAAVVALPPFLHADAVE 93 
                                       78888877777777777...57888888888.77778999****************99988888888999******* PP

                                       HHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS- CS
                     NAD_binding_3  78 kaLkagkdvvtankgaladealyeeLreaaeang 111
                                       +a +ag+dv +    a +  a  ++++eaae+ +
  gi|336254444|ref|YP_004597551.1|  94 RAAEAGVDVFVEKPFARS-TAEADRMLEAAEEGD 126
                                       *********998777777.888999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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:                        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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2774.50
//
Query:       gi|336254445|ref|YP_004597552.1|  [L=316]
Description: polysaccharide deacetylase [Halopiger xanaduensis SH-6]
Scores for 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-06   27.7   0.0      4e-06   26.7   0.0    1.5  1  Polysacc_deac_1  Polysaccharide deacetylase


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 !   26.7   0.0   2.2e-10     4e-06      18     122 ..      31     167 ..       3     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.2e-10
                                       CSCHHHHHHHHHHCT--EEEEE-HHHHCH-...............................HHHHHHHHHTT..EEE CS
                   Polysacc_deac_1  18 rdntteilpvLkkykvkatffvigglvedy...............................pdevremaasG..vei 61 
                                       r ++  +l+++ + +++at+ v+g+l+ +                                pd+v ++  s   +e+
  gi|336254445|ref|YP_004597552.1|  31 RRGWSVMLDLFSEFEIPATWAVVGHLMLEScdgrhaehpapegwferertewadradlrfaPDLVDALLSSEvdHEF 107
                                       6789999******************8544458899999******************************999889*** PP

                                       EE--SS--EG..GGSHHHHHHHHHHHHHHHHHHHHS----EEE-GGGEE-HHHHHHHHHTT.E CS
                   Polysacc_deac_1  62 gnHtinhsnl..krlseeevrreierakdalrkalgreprlfryPygsasatvlevarelgfa 122
                                       ++H+++h  +   +  +e +++e+ r+++ + ++  +   +f yP  +     ++v++++g++
  gi|336254445|ref|YP_004597552.1| 108 ASHSFSHVLFgrPETDRELAEAELRRSTE-IASEWDQSIETFVYPRNDVGH--RDVLADHGVR 167
                                       ********995455555556666666655.688899*********766443..4467777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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 0.20s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2524.42
//
Query:       gi|336254446|ref|YP_004597553.1|  [L=531]
Description: type I phosphodiesterase/nucleotide pyrophosphatase [Halopiger xanaduensis SH-6]
Scores for 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-48  164.7   0.6      2e-46  159.2   0.6    2.1  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.2   0.6   1.1e-50     2e-46       2     312 ..      12     334 ..      11     437 .. 0.71

  Alignments for each domain:
  == domain 1  score: 159.2 bits;  conditional E-value: 1.1e-50
                                       EEEEETT-BTTHHHHHG.S.TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEE CS
                      Phosphodiest   2 lvislDGlradlldrla.e.llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgey 76 
                                        v++lDG++++l+++++ e +lpn+a++++eg s++ l+++ P++T+ ++ s++TG  P++HGi+g++ +   ++ey
  gi|336254446|ref|YP_004597553.1|  12 FVLGLDGVPWRLIEQWSdEgELPNFARMREEGASGT-LESTRPPTTPLAWPSIATGVWPDKHGIYGFQNL---SEEY 84 
                                       599**************989****************.*****************************6655...6666 PP

                                       EEEETTTTGGGGGCTTS-HHHHHHHTHTTCEEEESETTTTSEBTTCT.SC...........TBHHSBTCT.CSTTS. CS
                      Phosphodiest  77 vvfvtededaprwwqgepiwdtaakarglkaaalfwpgsevdystyyylvs..........etppryleddfnakv. 142
                                        +  ++++++   +q++p+w+ ++ a     ++ ++p + +++++ + +v+           t+p+ l d+ +  v 
  gi|336254446|ref|YP_004597553.1|  85 -SHEMYTSHD---IQQPPLWEQLQPA-----HVGNVPMTFPARDIDGSMVTgmmtpstdqeFTHPPDLGDELESRVg 152
                                       .555555555...99***********.....3444455666666666666666667677774555555564444444 PP

                                       ............CHHHHHHHHHHHHHHHCHTHSHHHHHCT....SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHH CS
                      Phosphodiest 143 ............pledkvdkavlqtwldaafakvvlekel....ekpdlllvyleetDtvgHkfGpdspevedalrr 203
                                                   + +d + +av+ ++l++    +v+++++    ++++l++++++++D+++H + +d   +++ +++
  gi|336254446|ref|YP_004597553.1| 153 eyeisldypeyaDRPDEFEEAVS-NMLEQRR--EVMQLQMdragDDWQLFFFVYTAPDRFQHLV-WDMDRLLAHYKK 225
                                       44555566643344444444333.5555443..34444448899******************99.************ PP

                                       HHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEHTTSEEEGGGTSTGGH.GEEEEECBHHS.SSEEEEEESTEE.. CS
                      Phosphodiest 204 vDkaigdLlealderglsaetniilvSDHGmadvsddkvielndlleekg.llhlkdegkggakaliainpkare.. 277
                                       +D+ +gd +++ de+    + ++ +vSDHG++++  +++i++n +le++g l++++deg+ ga a ++i+ ++    
  gi|336254446|ref|YP_004597553.1| 226 LDDLLGDVMDYTDEH----DADLYVVSDHGFGEI--HDLIYVNHILEREGyLFRREDEGTRGALASLGISRDSITnm 296
                                       ***************....***************..***************77777777777777777766655553 PP

                                       E.CCCTTHHHHHHHHHHTCHHCCH.ST.HTT..TEEEEE CS
                      Phosphodiest 278 lnrvaeaeaeevyaelkakleelr.kk.ege..alavyl 312
                                       l+rv +   e  + +l ++l++ + ++ +g+   ++v++
  gi|336254446|ref|YP_004597553.1| 297 LERVGIS-EEMLVSNLPRSLLDTVaEQiPGDhaLYDVDY 334
                                       3333333.3333444433333333333333322444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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 0.27s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3841.37
//
Query:       gi|336254447|ref|YP_004597554.1|  [L=449]
Description: hypothetical protein Halxa_3060 [Halopiger xanaduensis SH-6]
Scores for 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  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3449.90
//
Query:       gi|336254448|ref|YP_004597555.1|  [L=598]
Description: hypothetical protein Halxa_3061 [Halopiger xanaduensis SH-6]
Scores for 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   12.5   0.0       0.11   12.5   0.0    4.5  5  OppC_N    N-terminal TM domain of oligopeptide transport perm


Domain annotation for each model (and alignments):
>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3      0.32   5.7e+03      18      37 ..      12      31 ..       8      38 .. 0.75
   2 ?   -3.3   0.1      0.52   9.4e+03      18      31 ..      46      59 ..      44      66 .. 0.71
   3 ?    0.7   1.1      0.03   5.5e+02      20      37 ..     143     161 ..     140     170 .. 0.75
   4 ?   -1.2   0.5      0.12   2.1e+03      16      28 ..     350     362 ..     349     396 .. 0.73
   5 ?   12.5   0.0   6.2e-06      0.11      13      44 ..     439     470 ..     438     480 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.32
                            OppC_N 18 vglvilllllliaifaPlia 37
                                      vg+v +++ +l+a  +P  a
  gi|336254448|ref|YP_004597555.1| 12 VGFVAVAVGILVARANPATA 31
                                      78888888888887777665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.52
                            OppC_N 18 vglvilllllliai 31
                                      +gl+i l+++++ +
  gi|336254448|ref|YP_004597555.1| 46 AGLAIGLAIAVLGA 59
                                      57777777776654 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.03
                            OppC_N  20 lvillllll.iaifaPlia 37 
                                       l+ +++l++ + ifaPl a
  gi|336254448|ref|YP_004597555.1| 143 LFTIVFLFVpFLIFAPLAA 161
                                       6777777777889999875 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.12
                            OppC_N  16 Avvglvillllll 28 
                                       Av+glv  l++l+
  gi|336254448|ref|YP_004597555.1| 350 AVIGLVAGLFVLV 362
                                       5566555554443 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 6.2e-06
                            OppC_N  13 NklAvvglvilllllliaifa.PliaPydp.qdl 44 
                                       N +A +gl +ll+l l+ ++a Pli  y+p q++
  gi|336254448|ref|YP_004597555.1| 439 NAVASIGLGVLLVLGLLTVYAsPLI--YSPtQHV 470
                                       78999***************87999..8877544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); 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:                         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: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4034.80
//
Query:       gi|336254449|ref|YP_004597556.1|  [L=408]
Description: formyl-CoA transferase [Halopiger xanaduensis SH-6]
Scores for complete 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-124  415.9   0.0   1.7e-124  415.7   0.0    1.0  1  CoA_transf_3  CoA-transferase family III


Domain annotation for each model (and alignments):
>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.7   0.0  9.6e-129  1.7e-124       1     367 [.       4     373 ..       4     374 .. 0.97

  Alignments for each domain:
  == domain 1  score: 415.7 bits;  conditional E-value: 9.6e-129
                      CoA_transf_3   1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpsee..kgesayflavnrnKrsvalDlkseeg 75 
                                       L++vrVldl++vl Gp++t+lLAdlGA+V+k+Epp +gD +R ++p+++  ++ ++yf+++nr+Krs+ lD+++e++
  gi|336254449|ref|YP_004597556.1|   4 LDDVRVLDLTRVLGGPYCTMLLADLGADVVKIEPP-GGDFVRETPPFHDedDSFGGYFQSINRGKRSLELDFTDEDD 79 
                                       89*********************************.***********997777789********************* PP

                      CoA_transf_3  76 rellkrLvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGq....sGpkakrpgyDlvaqaasGlmsl 148
                                       r+ +++Lv+ ADVv+eN+r+g+++++ l+ye+l+++nP+L+ya++ g+G+    + pk+++p++Dlvaqa++G+m+ 
  gi|336254449|ref|YP_004597556.1|  80 RDDFLSLVDAADVVVENYRAGTMAKFDLEYERLAERNPQLVYAALRGFGDprtvESPKQDEPAFDLVAQAMGGVMHQ 156
                                       *************************************************9543336********************* PP

                      CoA_transf_3 149 tgepdgpPvkvgvplgDivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgnrd 225
                                       tg+pdgpP+kvg+++gDi+tg+l av ilaal++rertG Gq +d+++++++++l + ++ +y+ tgevper+gn++
  gi|336254449|ref|YP_004597556.1| 157 TGHPDGPPTKVGFGVGDIFTGVLHAVNILAALHYRERTGVGQFVDTAMYDSMVSLGERAVYQYSYTGEVPERRGNSH 233
                                       ***************************************************************************** PP

                      CoA_transf_3 226 paaapygvyrtkdgwvaiaaatdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlell 302
                                       p++ py++++++dg+v+iaa td++w++lc+ +g+pe+    ++a+ a+rle+r++l++++aew+ +r+aa +le+l
  gi|336254449|ref|YP_004597556.1| 234 PTLFPYNAFEAEDGFVVIAALTDRHWRNLCEHMGEPEW--AVDYADAADRLEHREKLREAIAEWVGSRSAAAVLETL 308
                                       **************************************..7899********************************* PP

                      CoA_transf_3 303 aaagvpaapvntleevlddpqlaarglvvevddpdyge.vpvvglpvrlsetparvkraaPklGed 367
                                       +   vp++p++++++++d ++ ++r+++ve d p+ +e v+  g+p+++++tp+++  +aP l+e+
  gi|336254449|ref|YP_004597556.1| 309 NGS-VPCGPLQDVADIYDCEHAKQREMLVEADLPEADEtVTIAGTPIKMAKTPPEPGDRAPLLDEH 373
                                       987.*******************************8889**************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3022.24
//
Query:       gi|336254450|ref|YP_004597557.1|  [L=406]
Description: hypothetical protein Halxa_3063 [Halopiger xanaduensis SH-6]
Scores for 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-20   74.1   0.0    3.1e-19   69.3   0.0    2.4  2  Acetyltransf_9  Acetyltransferase (GNAT) domain
     0.0059   16.8   0.0       0.32   11.3   0.0    2.4  2  Acetyltransf_1  Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
       0.27   11.2   3.1       0.19   11.7   0.6    2.1  2  SPDY            Domain of unknown function (DUF317)


Domain annotation for each model (and alignments):
>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.0   5.2e-23   3.1e-19       1     127 [.      49     177 ..      49     178 .. 0.90
   2 ?    2.3   0.0     0.027   1.6e+02      32     125 ..     264     353 ..     230     355 .. 0.58

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 5.2e-23
                                       .EEEE-GGGHHHHHHHHHHHTT----H...HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEE CS
                    Acetyltransf_9   1 eirelteedldevlellkyaFqdeesple.eireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagv 76 
                                       +ir+++++d +++lel +++ +d++++ + + +++ ++++++  +++a  +g++vg+   ++lel+ +++tl+a + 
  gi|336254450|ref|YP_004597557.1|  49 TIRPYEPDDREDFLELYDRVLGDRDDE-WfRWKYEDNPYVDHVPMIVATHEGRVVGTKPSFALELRAGNRTLRALQP 124
                                       59*************************.766666667777777********************************** PP

                                       EEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSHHHH..HTTT-EE CS
                    Acetyltransf_9  77 tgVavapehrgrgvlskLlaraleemreegqplsllfPssipiY..rrfGyei 127
                                       ++V+v+ +hr+rg+ s+ ++r+ e++r++ + l + fP ++++    + G++i
  gi|336254450|ref|YP_004597557.1| 125 ADVMVHEDHRRRGLYSRTTERLKERYRDREADLFFNFPNEATLSgsLKHGWRI 177
                                       **************************************888665225667765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.027
                                       HHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT-- CS
                    Acetyltransf_9  32 reyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemreegqp 108
                                       +++ +++   + ++  +d++ ++g+++ ++    +++ t ++     V  a +  +r  l+++lar+l + r+    
  gi|336254450|ref|YP_004597557.1| 264 WRFENPKWTYDAYVASRDGDPIAGVITGTR----TQDGTKETCLTDLVPLARTRERRDGLEAILARVLSDRRDSALL 336
                                       444444444444444444555666655543....3344444444455666677777888888888888888887777 PP

                                       EEEE--SSHHHHHTTT- CS
                    Acetyltransf_9 109 lsllfPssipiYrrfGy 125
                                        + + +  +++ ++fG+
  gi|336254450|ref|YP_004597557.1| 337 AASGRAVDPALLGQFGF 353
                                       77777888888888887 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   5.3e-05      0.32      34      96 ..      91     157 ..      39     168 .. 0.60
   2 ?    3.1   0.0     0.018   1.1e+02      19      60 ..     255     300 ..     236     324 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.3e-05
                                       EEEEEEETTEEEEEEEEEEEETTSTTEEEEE............EEEESGGGTTSSHHHHHHHHHHHHHHHTTESE CS
                    Acetyltransf_1  34 gllvaeedgeliGfisllkipdekggvayie............slaVspeyrgkGlGsaLlealeerareegikk 96 
                                         +va ++g+++G+   +            +            +++V++++r++Gl s+  e l er r+++++ 
  gi|336254450|ref|YP_004597557.1|  91 PMIVATHEGRVVGTKPSFALEL--------RagnrtlralqpaDVMVHEDHRRRGLYSRTTERLKERYRDREADL 157
                                       2333444455555553333333........1333333356666**************************997754 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.018
                                       HHHHH.HHHHHHSTTC...EEEEEEETTE.EEEEEEEEEEETTSTTE CS
                    Acetyltransf_1  19 aseee.feesfsleae...gllvaeedge.liGfisllkipdekggv 60 
                                       a+ +e f+e+ +++++     +va++dg  ++G i+++  +d  +++
  gi|336254450|ref|YP_004597557.1| 255 AHRDEtFYEWRFENPKwtyDAYVASRDGDpIAGVITGTRTQD-GTKE 300
                                       333334666644444445577889999887899999988888.3333 PP

>> SPDY  Domain of unknown function (DUF317)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.1   6.4e+03      19      29 ..     263     277 ..     245     283 .. 0.62
   2 ?   11.7   0.6   3.2e-05      0.19      14      42 ..     376     402 ..     367     403 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                              SPDY  19 e....paaWtiearp 29 
                                       e     + Wt  a++
  gi|336254450|ref|YP_004597557.1| 263 EwrfeNPKWTYDAYV 277
                                       144446677777776 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.2e-05
                              SPDY  14 ededaepaaWtiearpaadgpaWhatFta 42 
                                       +d++  +  Wt+++r  ad+  W++tF +
  gi|336254450|ref|YP_004597557.1| 376 ADDG--GHEWTVAGRAIADPSNWTVTFAE 402
                                       3333..99*******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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 0.27s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 2918.70
//
Query:       gi|336254451|ref|YP_004597558.1|  [L=315]
Description: hypothetical protein Halxa_3064 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.21   11.5   4.4       0.41   10.6   4.4    1.5  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   4.4   2.3e-05      0.41       2      25 ..      22      46 ..      21      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.3e-05
                        TAT_signal  2 lSRRdFLKgsAAaa.AAaalggcaa 25
                                      lSRR+  +  AA+a AA+ lg++++
  gi|336254451|ref|YP_004597558.1| 22 LSRRNYVRSLAAVAtAATSLGAAGS 46
                                      8*********888878888**9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2294.97
//
Query:       gi|336254452|ref|YP_004597559.1|  [L=610]
Description: hypothetical protein Halxa_3065 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.055   13.3   6.7       0.12   12.2   6.7    1.7  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
       0.11   12.5   0.0       0.22   11.5   0.0    1.4  1  MRP-S35     Mitochondrial ribosomal protein MRP-S35
       0.23   11.4   0.4       0.52   10.3   0.0    1.8  2  DUF4957     Domain of unknown function (DUF4957)


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   6.7   2.1e-05      0.12       2      26 .]      30      54 ..      29      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaaa 26
                                      l+RR+ L+ +++++AAaa+ g aaa
  gi|336254452|ref|YP_004597559.1| 30 LDRRSYLRLAGVTTAAAAVTGSAAA 54
                                      68****************9988875 PP

>> MRP-S35  Mitochondrial ribosomal protein MRP-S35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.7e-05      0.22      61      97 ..     474     510 ..     465     516 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                           MRP-S35  61 yqrGarvrlrlkdlelssrflGsktdltlleadavll 97 
                                         +G+ v+  + d   + rf G+ td+t+ e +a++l
  gi|336254452|ref|YP_004597559.1| 474 TISGSTVQSAVTDETQTFRFAGALTDVTFTEGEATVL 510
                                       5689*****************************9876 PP

>> DUF4957  Domain of unknown function (DUF4957)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   8.6e-05      0.52      70     135 ..     152     221 ..      96     224 .. 0.80
   2 ?   -3.3   0.1       1.3     8e+03     101     132 ..     473     503 ..     471     504 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.6e-05
                           DUF4957  70 i.....kdtltiqnCeikdvnkgliydnnkkyviesivinnclvkniessggdiidfkkgfinnltvknST 135
                                       +       ++t+++ ++++ +++  y++n  +   s+ ++nc+ kn++ s++ +   +++ +n++  +  T
  gi|336254452|ref|YP_004597559.1| 152 FyhrtaSCDVTFRQMNVQGWPNNGFYCSN-TASGGSVRFENCYGKNNGVSTYRVAGGNDAIVNSVAYNDDT 221
                                       34444444899999**************9.9999****************999999999999998877666 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.3
                           DUF4957 101 ivinnclvkniessggdiidfkkgfinnltvk 132
                                        +i+ + v+   ++  ++++f  +   ++t++
  gi|336254452|ref|YP_004597559.1| 473 TTISGSTVQSAVTDETQTFRFAGA-LTDVTFT 503
                                       578888888888888888888765.7777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4406.40
//
Query:       gi|336254453|ref|YP_004597560.1|  [L=320]
Description: transcription initiation factor IIB [Halopiger xanaduensis SH-6]
Scores for 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  123.5   0.1    9.1e-18   64.1   0.0    2.2  2  TFIIB           Transcription factor TFIIB repeat
    1.1e-16   60.0   3.4    2.2e-16   59.1   3.4    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0055   16.5   0.0      0.012   15.4   0.0    1.6  1  Cyclin_N        Cyclin, N-terminal domain
  ------ inclusion threshold ------
      0.016   14.9   0.2      0.034   13.9   0.2    1.4  1  Ribosomal_S27e  Ribosomal protein S27
      0.065   13.0   0.6       0.21   11.3   0.6    1.9  1  A2L_zn_ribbon   A2L zinc ribbon domain
       0.11   11.9   0.5        4.7    6.8   0.0    2.4  2  zf-ribbon_3     zinc-ribbon domain
       0.16   12.6   0.7         41    4.9   0.1    2.9  3  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
       0.18   11.8   1.0       0.59   10.2   1.0    1.8  1  DZR             Double zinc ribbon
        1.4    8.6   4.2          9    6.0   1.0    2.9  3  GATA            GATA zinc finger


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 !   64.1   0.0   4.6e-21   9.1e-18       1      71 []     136     206 ..     136     206 .. 0.98
   2 !   57.5   0.0   5.1e-19     1e-15       1      71 []     230     300 ..     230     300 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 4.6e-21
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i r+++al+ p+ V++ A  ++++ale++++ Grs +g+a ++ly Acrke   r+++e+ sv++V + +i
  gi|336254453|ref|YP_004597560.1| 136 IDRMVSALGVPDPVKETASVIYRRALEKDLIRGRSIEGVATSALYTACRKEDIPRSLEEVTSVSRVDQREI 206
                                       789***************************************************************99887 PP

  == domain 2  score: 57.5 bits;  conditional E-value: 5.1e-19
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rf+++l+  + V+ +A+e+++++ e+++++G+sp+g aAA++y A +++ +   q+ +++++q +++t+
  gi|336254453|ref|YP_004597560.1| 230 VPRFCSELDVGKDVETKAVEIIDETTEQGLHSGKSPTGFAAAAIYAAGLLCDETIPQRAVAETAQTTVVTV 300
                                       689**************************************************************999986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   3.4   1.1e-19   2.2e-16       3      43 .]      21      61 ..      20      61 .. 0.99

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 1.1e-19
                                      ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      CP+C ++++v Dp+rge vC++CGlVl +++id+gpewr+f
  gi|336254453|ref|YP_004597560.1| 21 CPDCETDTIVHDPDRGERVCEECGLVLTEDPIDYGPEWRAF 61
                                      ***************************************98 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.9e-06     0.012      47     126 ..     145     221 ..     119     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.9e-06
                                       --TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHTT CS
                          Cyclin_N  47 ltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLetLn 123
                                       +   +  +a +++ R l+k  ++ + ++ v++++L+ A++ e+i p +le+++ ++   ++++ei +  r+i ++L 
  gi|336254453|ref|YP_004597560.1| 145 VPDPVKETASVIYRRALEKDLIRGRSIEGVATSALYTACRKEDI-PRSLEEVTSVS--RVDQREIGRTYRYIADELG 218
                                       55566668999******************************999.9*******995..5999999999999999998 PP

                                       T-- CS
                          Cyclin_N 124 fdl 126
                                        +l
  gi|336254453|ref|YP_004597560.1| 219 INL 221
                                       877 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   1.7e-05     0.034      10      38 ..      21      49 ..      20      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                                      -TTTS-EEEEESS-SS-EEESSSTCEEEE CS
                    Ribosomal_S27e 10 CpdCenetvvFshaatvvkCisCgkvLve 38
                                      CpdCe  t+v +       C+ Cg vL e
  gi|336254453|ref|YP_004597560.1| 21 CPDCETDTIVHDPDRGERVCEECGLVLTE 49
                                      **************9999********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 ?   11.3   0.6   0.00011      0.21       6      30 ..      21      46 ..      16      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                     A2L_zn_ribbon  6 CsvCggngiln.seqgylvCieCgas 30
                                      C  C ++ i+   ++g++vC eCg++
  gi|336254453|ref|YP_004597560.1| 21 CPDCETDTIVHdPDRGERVCEECGLV 46
                                      88899999**999***********86 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.031        62      16      25 ..      18      27 ..      13      28 .. 0.82
   2 ?    6.8   0.0    0.0023       4.7      11      26 .]      33      47 ..      31      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.031
                       zf-ribbon_3 16 dnvCpyCGtk 25
                                      +  Cp C t+
  gi|336254453|ref|YP_004597560.1| 18 AELCPDCETD 27
                                      679****986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0023
                       zf-ribbon_3 11 plssddnvCpyCGtkl 26
                                      p + + +vC  CG +l
  gi|336254453|ref|YP_004597560.1| 33 P-DRGERVCEECGLVL 47
                                      5.899********987 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 ?    4.1   0.1     0.035        69      19      92 ..      63     136 ..      59     140 .. 0.92
   2 ?   -0.6   0.0         1     2e+03      15      36 ..     196     217 ..     191     227 .. 0.87
   3 ?    4.9   0.1      0.02        41      10      42 ..     282     314 ..     280     318 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.035
                    HIP1_clath_bdg  19 rqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaL 92 
                                        q+++e+ r+   l++++++    ++   +++  +  ++ +e + + ++l   ++ +++++  + +l+  l+++
  gi|336254453|ref|YP_004597560.1|  63 AQEHDELSRVGAPLTQSMHDRGLTTTIDWRNKDANGHSMSAEKQGQIHRLRVWQERIRTKNAGERNLKYALSEI 136
                                       5899********************************************************99999999888765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                    HIP1_clath_bdg  15 lsvarqaqeeverekkeleeel 36 
                                        sv+r  q e+ r+ + +++el
  gi|336254453|ref|YP_004597560.1| 196 TSVSRVDQREIGRTYRYIADEL 217
                                       6899*********999998887 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.02
                    HIP1_clath_bdg  10 evtkqlsvarqaqeeverekkeleeelerlkee 42 
                                       e++ q  va  aq  v +++++  e+le++ ++
  gi|336254453|ref|YP_004597560.1| 282 ETIPQRAVAETAQTTVVTVRNRYREQLEAIDQQ 314
                                       7888999**********************9998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.0    0.0003      0.59      11      36 ..      17      45 ..      11      52 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0003
                               DZR 11 darfCseCgtklkavaa....edrCpsCge 36
                                      +a+ C++C t+     +    e++C +Cg 
  gi|336254453|ref|YP_004597560.1| 17 NAELCPDCETDTIVH-DpdrgERVCEECGL 45
                                      566777777775422.23556777777764 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.67   1.3e+03      18      26 ..      16      24 ..      10      27 .. 0.68
   2 ?    6.0   1.0    0.0045         9       3      28 ..      23      45 ..      19      48 .. 0.65
   3 ?    2.4   0.1     0.062   1.2e+02       7      18 ..      86      98 ..      84     101 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.67
                              GATA 18 gnksLCnaC 26
                                       n +LC +C
  gi|336254453|ref|YP_004597560.1| 16 TNAELCPDC 24
                                      456789888 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0045
                              GATA  3 nCgttkTplWRrgpdgnksLCnaCGl 28
                                       C t++     ++pd   ++C+ CGl
  gi|336254453|ref|YP_004597560.1| 23 DCETDT---IVHDPDRGERVCEECGL 45
                                      454444...4455555555******9 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.062
                              GATA  7 tkTplWRrg.pdg 18
                                      t+T +WR+   +g
  gi|336254453|ref|YP_004597560.1| 86 TTTIDWRNKdANG 98
                                      89*****985555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2275.00
//
Query:       gi|336254454|ref|YP_004597561.1|  [L=58]
Description: hypothetical protein Halxa_3068 [Halopiger xanaduensis SH-6]
Scores for 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   14.7   1.7      0.028   14.4   1.7    1.1  1  HUN       HPC2 and ubinuclein domain


Domain annotation for each model (and alignments):
>> HUN  HPC2 and ubinuclein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.7   1.6e-06     0.028       5      36 ..      15      57 ..      14      58 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-06
                               HUN  5 rdddgddtgsgYDieDpFID...........DsElydelvpdi 36
                                      r+ ++d   + YD++D FI            D+++y e++++i
  gi|336254454|ref|YP_004597561.1| 15 RYGHEDEGLELYDEDDEFIGfvpyanlhalvDEDAYGEDERSI 57
                                      56667777889*************************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 429.83
//
Query:       gi|336254455|ref|YP_004597562.1|  [L=130]
Description: hypothetical protein Halxa_3069 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.067   13.1   1.1       0.14   12.1   1.1    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
       0.11   12.8   0.1       0.17   12.2   0.1    1.2  1  Colicin_E5  Colicin E5 ribonuclease domain


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.1   1.5e-05      0.14       4      25 ..       3      23 ..       1      24 [. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                        TAT_signal  4 RRdFLKgsAAaaAAaalggcaa 25
                                      RR  L   A++aA +al+gc++
  gi|336254455|ref|YP_004597562.1|  3 RRRYLT-LAGTAATGALAGCVG 23
                                      555555.677788888***986 PP

>> Colicin_E5  Colicin E5 ribonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.9e-05      0.17      22      69 ..      24      71 ..      22      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                        Colicin_E5 22 evrdvvskgak.tkssddkranktsDglrrndsAtvYgekdgkYvvvnd 69
                                      ev dvv+  +k ++++ ++++++++D l r  sA v +e+dg  +v   
  gi|336254455|ref|YP_004597562.1| 24 EVTDVVEGTTKeASQEANESVDEAMDTLTRPPSADVRVERDGTVIV-RS 71
                                      68889887666155677899999*****************666555.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 926.36
//
Query:       gi|336254456|ref|YP_004597563.1|  [L=654]
Description: type III restriction protein res subunit [Halopiger xanaduensis SH-6]
Scores for 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    3.4e-25   88.7   0.0    1.2  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    3.6e-13   49.9   0.0    8.3e-13   48.7   0.0    1.7  1  ResIII         Type III restriction enzyme, res subunit
    2.7e-12   47.0   0.0    1.7e-11   44.5   0.0    2.1  2  Helicase_C     Helicase conserved C-terminal domain
    3.1e-12   45.9   0.0    3.9e-12   45.6   0.0    1.2  1  SNF2_N         SNF2 family N-terminal domain
    7.7e-07   29.0   0.0    7.5e-06   25.8   0.0    2.3  2  DEAD           DEAD/DEAH box helicase
     0.0024   18.1   0.8      0.052   13.7   0.0    3.3  4  AAA_33         AAA domain
     0.0029   17.5   1.1     0.0077   16.1   0.5    2.1  2  MarR_2         MarR family
     0.0079   15.9   0.0      0.054   13.2   0.0    2.3  2  AAA_30         AAA domain
  ------ inclusion threshold ------
      0.012   15.2   0.4       0.17   11.4   0.0    2.9  3  AAA_25         AAA domain
       0.14   12.6   0.0       0.31   11.5   0.0    1.6  1  AAA            ATPase family associated with various cellular
       0.17   11.4   0.0        0.3   10.6   0.0    1.3  1  DUF4283        Domain of unknown function (DUF4283)


Domain annotation for each model (and alignments):
>> 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 !   88.7   0.0   2.1e-28   3.4e-25      25     202 ..     453     620 ..     430     638 .. 0.89

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 2.1e-28
                     ERCC3_RAD25_C  25 keylkakskkkkllyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkf 101
                                       + y++a+ ++k  +++ n  k+  + +L++ h   + k +vf D +   +e++ +l  p+i Get+++er +++++f
  gi|336254456|ref|YP_004597563.1| 453 NAYVSAEGREKYRIAAENRGKVDEIRYLLSAHP--DSKALVFVDYLEQGRELSDALDAPFISGETRHHERRRLFDEF 527
                                       689999*************************97..5799************************************** PP

                     ERCC3_RAD25_C 102 kknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemays 178
                                       ++n+  + +++s+vgD+ iDlP+a   i  s   gsrrq  qr Gr +r+  +       a  Y L  + t+e  ++
  gi|336254456|ref|YP_004597563.1| 528 RRNE-RDLLVISRVGDEGIDLPTADLAIVASGLGGSRRQGTQRAGRTMRPAGG-------ALVYVLATRGTREEDFA 596
                                       *995.68999****************************************999.......9**************** PP

                     ERCC3_RAD25_C 179 tkrqqflvdqGYafkviteleele 202
                                       +++ q+l  +G + +  t  ++ +
  gi|336254456|ref|YP_004597563.1| 597 RRQLQHLGRKGMTVREQTVERTED 620
                                       *******99999887544433333 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 !   48.7   0.0   5.1e-16   8.3e-13       2     170 ..     262     404 ..     261     405 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 5.1e-16
                                       -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       ++lr+yQ++ +++++e+       +g+++ + G+GKT+ a+ +++++       ++l+lvp+++l  q+ +++++++
  gi|336254456|ref|YP_004597563.1| 262 VTLRDYQQTWVDRFAEA------GEGVFVGPPGSGKTVAAMGAMAHVGG-----ETLVLVPSRDLARQWADTIQEYT 327
                                       689***********855......57**********************99.....6***************9999999 PP

                                       GG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHH CS
                            ResIII  79 seaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreile 155
                                       s   ++ig+   g+k+ +         ++++t+q +  d+     ++  +++ +  ++++DE+ ++ + + +r+   
  gi|336254456|ref|YP_004597563.1| 328 SLGPHQIGQYHGGQKNVR--------PVTIATYQIAGMDR-----HRSLFDDREWGLVVFDECQHVPS-DVYRR-ST 389
                                       999887777777777777........**************.....88999999999************.*****.89 PP

                                       T---SEEEEEESS-S CS
                            ResIII 156 kfkeavllglTATpe 170
                                       ++++  +lgl+A p 
  gi|336254456|ref|YP_004597563.1| 390 HLQSRHRLGLSASPI 404
                                       99**********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 ?   -0.5   0.0      0.97   1.6e+03      13      48 ..     300     339 ..     292     352 .. 0.69
   2 !   44.5   0.0     1e-14   1.7e-11       2     109 ..     473     575 ..     472     577 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.97
                                       TTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEEST CS
                        Helicase_C  13 eeeggkilifvntidrlek.vklllekk...gikvavlhg 48 
                                        ++gg++l+ v+++d + + ++ ++e       ++  +hg
  gi|336254456|ref|YP_004597563.1| 300 AHVGGETLVLVPSRDLARQwADTIQEYTslgPHQIGQYHG 339
                                       57899**********7765555553333444567777776 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 1e-14
                                       HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                       k++ + +ll + + ++k+l+fv + ++    + l  + ++ +  + ge+ + er++ +++f+++e+d+L+ ++v+ +
  gi|336254456|ref|YP_004597563.1| 473 KVDEIRYLL-SAHPDSKALVFVDYLEQG---REL--SDALDAPFISGETRHHERRRLFDEFRRNERDLLVISRVGDE 543
                                       677788888.899*************98...777..67899999********************************* PP

                                       SSTSTTESEEEES.SSSSSHHHHHHHHTTSSS CS
                        Helicase_C  79 GidipkvnlVinf.dlprnvtsyiqriGRtgR 109
                                       Gid+p ++l i   +l  + ++  qr+GRt+R
  gi|336254456|ref|YP_004597563.1| 544 GIDLPTADLAIVAsGLGGSRRQGTQRAGRTMR 575
                                       *********98651566889***********9 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   2.4e-15   3.9e-12      98     227 ..     228     417 ..      45     441 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 2.4e-15
                                       -............................................................................ CS
                                       x............................................................................ RF
                            SNF2_N  98 p............................................................................ 98 
                                       +                                                                            
  gi|336254456|ref|YP_004597563.1| 228 Gseaaikrvlyeagypvqdhrdlesgedleidlevtlrdyqqtwvdrfaeagegvfvgppgsgktvaamgamahvgg 304
                                       15555555555556666666666666666666666666666666666667777777777777777777777777777 PP

                                       .EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS CS
                                       .xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  99 .tLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvl 173
                                        tL++vP+ +l++qW ++i++++s +  ++  y+g++    k         +   v i tY++   +     +rs +
  gi|336254456|ref|YP_004597563.1| 305 eTLVLVPSrDLARQWADTIQEYTSLGPHQIGQYHGGQ----K---------NVRPVTIATYQIAGMDR----HRSLF 364
                                       7*************************99999999974....2.........3579*********9888....9**** PP

                                       -S-S-SEEEES-GGGT--TTSHHHHHHHH---S-EEEE-S--SSS..-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                            SNF2_N 174 kqvewkrvvlDEghtlknstskaaeavskLstsnrwiltGTPiqn..sledlygLl 227
                                        ++ew  vv DE++ + +   + +    +L++++r+ l++ Pi +    +++++L+
  gi|336254456|ref|YP_004597563.1| 365 DDREWGLVVFDECQHVPSDVYRRS---THLQSRHRLGLSASPIREddRQKEIFTLV 417
                                       ****************98755554...5567************9866667777665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.37     6e+02      86     135 ..      64     114 ..      44     123 .. 0.75
   2 !   25.8   0.0   4.6e-09   7.5e-06       2     140 ..     266     387 ..     265     405 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.37
                                       SHHHHHHHHHTTCSEEEEEHHHHHHHHHCTS.SHCTTEEEEEEETHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                              DEAD  86 aardqlskldngvdivvgtpgrlddllstgk.lnlsqvrflVlDEadrlld 135
                                       a+r +l++l+ ++d vv  p+ l dl+++++ + + + r +V+D  d++  
  gi|336254456|ref|YP_004597563.1|  64 AERGDLERLSVSTDPVVWYPSELEDLTDKERvVVFPKRREIVVDRPDQFTR 114
                                       556677788778999**********99655526699999999998777765 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 4.6e-09
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       d+Q+  ++ + + g+ +  ++ GsGKT a++ ++           g  +l+++P+r La+q +++++++++  +   
  gi|336254456|ref|YP_004597563.1| 266 DYQQTWVDRFAEAGEGVFVGPPGSGKTVAAMGAMA--------HVGGETLVLVPSRDLARQWADTIQEYTSL-G--P 331
                                       7899999999999999999************9999........346799********************993.3..3 PP

                                       EEE..ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHH CS
                                       xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lli..iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsd 140
                                       + i  ++g +++    ++   + + ++  +r  +l+     + ++  ++V+DE++ + ++ +++
  gi|336254456|ref|YP_004597563.1| 332 HQIgqYHGGQKNVRPVTI---ATYQIAGMDRHRSLF-----DDREWGLVVFDECQHVPSDVYRR 387
                                       322012222222222222...233333333333333.....34568888888888887776655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.1   5.1e+03      64      99 ..      30      71 ..      18      87 .. 0.68
   2 !   13.7   0.0   3.2e-05     0.052       3      35 ..     282     317 ..     282     357 .. 0.80
   3 ?   -0.1   0.0      0.58   9.4e+02      75     103 ..     506     537 ..     494     545 .. 0.76
   4 ?   -2.9   0.1       4.2   6.8e+03      15      39 ..     595     621 ..     589     635 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.1
                            AAA_33 64 rkalsagrnvildatnlsrrer......arflklarrlgvpv 99
                                      +  +++gr+v++    ++  er      +++++la+r + ++
  gi|336254456|ref|YP_004597563.1| 30 EASQREGRPVLTAGAVARTLERshdavsEQLDRLAERGDLER 71
                                      555677777777666666555555555667888887776554 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.2e-05
                            AAA_33   3 llvGlpGsGKstlaerllkklg...avllssdtlrr 35 
                                       ++vG+pGsGK+  a + +++ g    vl+ s +l r
  gi|336254456|ref|YP_004597563.1| 282 VFVGPPGSGKTVAAMGAMAHVGgetLVLVPSRDLAR 317
                                       69**************99999866555555555555 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.58
                            AAA_33  75 ldatnls....rrerarflklarrlgvpvrivv 103
                                       lda+++s    ++er+r++  +rr + ++++v+
  gi|336254456|ref|YP_004597563.1| 506 LDAPFISgetrHHERRRLFDEFRRNE-RDLLVI 537
                                       68887777776899999999998877.656555 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 4.2
                            AAA_33  15 laerllkklg..avllssdtlrrrlfg 39 
                                       +a+r l++lg  + ++++ t+ r+  +
  gi|336254456|ref|YP_004597563.1| 595 FARRQLQHLGrkGMTVREQTVERTEDE 621
                                       677788888877777777776554444 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.5   4.7e-06    0.0077      17      54 ..      34      72 ..      22      77 .. 0.83
   2 ?   -3.7   0.0       7.1   1.2e+04      17      34 ..     108     124 ..     106     127 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.7e-06
                                      TTTS.EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 17 rpgr.dltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      r+gr  lt+g++ar+l  s+ avs  l+rL ++G +er 
  gi|336254456|ref|YP_004597563.1| 34 REGRpVLTAGAVARTLERSHDAVSEQLDRLAERGDLERL 72
                                      4444357***************************77775 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.1
                                       TTTSEEEHHHHHHHHTSS CS
                            MarR_2  17 rpgrdltvgelarrlgls 34 
                                       rp++ +t ++la+  +l+
  gi|336254456|ref|YP_004597563.1| 108 RPDQ-FTRAQLAQFAHLE 124
                                       4544.8899999988876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.66   1.1e+03      35      82 ..      25      77 ..      23     107 .. 0.67
   2 !   13.2   0.0   3.3e-05     0.054       2      65 ..     264     322 ..     263     390 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.66
                            AAA_30 35 lkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk........g 82
                                      l++  ea +++g++v+     g++A++L+++ ++ ++ +++l +r +        +
  gi|336254456|ref|YP_004597563.1| 25 LAQFHEASQREGRPVLT---AGAVARTLERSHDAVSEQLDRLAERGDlerlsvstD 77
                                      55556666666666554...578889999999999999998887666655554440 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.3e-05
                            AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaee 65 
                                       l++ Q++ v+++++ g+   v +Gp+G+GKt a  +   a+++ gg+ ++l p+   A++ a+ 
  gi|336254456|ref|YP_004597563.1| 264 LRDYQQTWVDRFAEAGE--GVFVGPPGSGKTVAAMG---AMAHVGGETLVLVPSRDLARQWADT 322
                                       7888***********98..999*********87554...4444567778888888888776653 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.43   7.1e+02      81     129 ..     147     196 ..     134     208 .. 0.84
   2 ?   11.4   0.0    0.0001      0.17      25      57 ..     270     302 ..     248     320 .. 0.79
   3 ?   -3.0   0.0       2.8   4.5e+03     139     153 ..     366     379 ..     345     381 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.43
                            AAA_25  81 dsedelrrRlravgealrddarllvldlagv.eslpLfakdrggtlltad 129
                                       ds + l+r +r+++ +++++ ++ v + +++ ++ +L++ ++g t+l+a+
  gi|336254456|ref|YP_004597563.1| 147 DSFEALARTMRQALGQRNEQLEEWVESQWDRaHQFRLYTHEDGYTVLEAK 196
                                       56678999999999999999999999999999999999999988887665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0001
                            AAA_25  25 lvkgllpagelallaGapgtGKttlaldlalav 57 
                                        + +  ++ + ++++G+pg+GKt++a+  +++v
  gi|336254456|ref|YP_004597563.1| 270 TWVDRFAEAGEGVFVGPPGSGKTVAAMGAMAHV 302
                                       4444446788899****************9998 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.8
                            AAA_25 139 evegvrlvviDplsr 153
                                       +  +++lvv+D +++
  gi|336254456|ref|YP_004597563.1| 366 D-REWGLVVFDECQH 379
                                       4.4599*****9887 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 ?   11.5   0.0   0.00019      0.31       3      37 ..     283     318 ..     282     394 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                       EESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSS CS
                               AAA   3 lyGppGtGKTllakavakelg.vefleisgsellsk 37 
                                       ++GppG GKT +a   + ++g  +++ +   +l  +
  gi|336254456|ref|YP_004597563.1| 283 FVGPPGSGKTVAAMGAMAHVGgETLVLVPSRDLARQ 318
                                       89***********99999986244455555555544 PP

>> DUF4283  Domain of unknown function (DUF4283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00018       0.3      25      65 ..     165     205 ..     152     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                           DUF4283  25 salrrvlakaWklkggvkikelgdglflfrfsseedlekvl 65 
                                       ++l++++ ++W  +++++++ ++dg+ +++ +s e + ++ 
  gi|336254456|ref|YP_004597563.1| 165 EQLEEWVESQWDRAHQFRLYTHEDGYTVLEAKSPEVMGNIA 205
                                       6899***************************9998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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: 0.70u 0.25s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 4469.62
//
Query:       gi|336254457|ref|YP_004597564.1|  [L=117]
Description: hypothetical protein Halxa_3071 [Halopiger xanaduensis SH-6]
Scores for 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:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 891.22
//
Query:       gi|336254458|ref|YP_004597565.1|  [L=661]
Description: hypothetical protein Halxa_3072 [Halopiger xanaduensis SH-6]
Scores for complete 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-10   41.9   0.0    1.2e-10   41.9   0.0    2.7  1  DUF87           Helicase HerA, central domain
    1.4e-06   28.8  19.8    4.7e-06   27.1   6.3    2.9  2  SlyX            SlyX
    5.8e-06   25.2   0.1    0.00055   18.7   0.0    2.4  2  DUF853          Bacterial protein of unknown function (DUF853
    0.00078   19.4   4.7    0.00078   19.4   4.7    3.0  2  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
    0.00088   19.6  12.4      0.049   14.0   0.5    3.0  2  FlaC_arch       Flagella accessory protein C (FlaC)
     0.0015   18.6   0.0     0.0029   17.7   0.0    1.7  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0032   17.4   0.1      0.011   15.7   0.0    1.9  1  APS_kinase      Adenylylsulphate kinase
     0.0067   16.6   5.2      0.014   15.6   4.4    1.9  1  Fib_alpha       Fibrinogen alpha/beta chain family
     0.0077   16.6   0.0     0.0077   16.6   0.0    2.9  1  AAA_16          AAA ATPase domain
  ------ inclusion threshold ------
      0.013   16.0   0.0      0.082   13.3   0.0    2.3  1  AAA             ATPase family associated with various cellula
      0.014   14.0   7.8      0.028   13.1   7.8    1.4  1  AAA_13          AAA domain
      0.016   15.1  15.5      0.051   13.5  14.9    2.0  1  Wtap            WTAP/Mum2p family
      0.022   14.4   6.4       0.67    9.5   0.5    2.3  2  DUF4795         Domain of unknown function (DUF4795)
      0.039   14.0  11.8       0.37   10.9   0.9    3.0  2  Med9            RNA polymerase II transcription mediator comp
      0.043   14.1   6.0        2.7    8.3   0.6    2.5  2  KxDL            Uncharacterized conserved protein
      0.048   12.6   2.1       0.45    9.4   0.0    2.8  3  AAA_10          AAA-like domain
      0.072   13.0   0.4       0.17   11.8   0.0    1.8  1  AAA_31          AAA domain
      0.073   13.0   0.6         12    5.8   0.0    2.6  2  ATPase_2        ATPase domain predominantly from Archaea
       0.14   11.9  13.3      0.067   13.0   2.5    3.0  3  Phage_GP20      Phage minor structural protein GP20
       0.19   11.5   0.0          1    9.1   0.0    2.2  2  CLP1_P          mRNA cleavage and polyadenylation factor CLP1
       0.23   11.6  11.4        1.4    9.0   0.5    2.7  2  BRE1            BRE1 E3 ubiquitin ligase
       0.25   11.9   0.0       0.25   11.9   0.0    2.7  1  AAA_18          AAA domain
       0.29   10.4  18.1      0.013   14.9  12.0    1.7  2  DUF4407         Domain of unknown function (DUF4407)
        0.3   11.4   1.5       0.45   10.8   0.0    2.0  1  AAA_22          AAA domain
       0.32   10.1   0.0       0.32   10.1   0.0    2.0  2  ArsA_ATPase     Anion-transporting ATPase
       0.39   11.2  10.9       0.99    9.9   0.8    2.7  2  DUF16           Protein of unknown function DUF16
       0.52   10.3   2.2        7.4    6.6   0.1    2.5  2  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
       0.55   10.5  30.7       0.96    9.7   8.5    3.2  2  ABC_tran_CTD    ABC transporter C-terminal domain
       0.87    8.8   3.1         16    4.7   0.1    2.1  2  TMPIT           TMPIT-like protein
       0.99    9.4  11.6        3.5    7.7   2.1    2.4  2  DUF1664         Protein of unknown function (DUF1664)
          1    9.2   4.3       0.34   10.8   0.3    2.2  2  DUF2570         Protein of unknown function (DUF2570)
        1.1   10.0  20.4         77    3.9  15.1    3.2  2  Ead_Ea22        Ead/Ea22-like protein
        1.1    9.0  18.3       0.17   11.6   5.4    2.4  2  SHE3            SWI5-dependent HO expression protein 3
        1.4    8.9  22.7        1.9    8.5   8.7    3.2  3  Prefoldin_2     Prefoldin subunit
        1.6    8.7  27.3         60    3.6  27.3    2.5  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
        1.8    9.1   3.4         27    5.3   0.2    2.6  2  DUF4094         Domain of unknown function (DUF4094)
        1.9    8.0  25.9       0.03   13.9  18.2    1.7  2  MscS_porin      Mechanosensitive ion channel porin domain
          2    8.9   9.8        3.4    8.1   1.0    3.6  3  TSNAXIP1_N      Translin-associated factor X-interacting N-te
        3.1    7.9  20.6        4.2    7.4   6.9    2.7  2  ADIP            Afadin- and alpha -actinin-Binding
        3.2    7.9  11.3        6.1    6.9   1.6    2.7  2  COG2            COG (conserved oligomeric Golgi) complex comp
        3.2    8.4  10.7       0.14   12.8   0.4    2.7  2  YabA            Initiation control protein YabA
        3.7    7.5   6.2        4.8    7.2   0.8    2.6  2  DUF4446         Protein of unknown function (DUF4446)
        5.4    6.2  11.7        7.8    5.7   4.7    2.4  2  CorA            CorA-like Mg2+ transporter protein
          6    4.7  10.9          9    4.1   1.1    2.0  2  V_ATPase_I      V-type ATPase 116kDa subunit family
        6.5    6.7  14.5        8.6    6.3   3.4    3.2  3  Prefoldin       Prefoldin subunit
        6.7    6.9   7.6         57    3.9   1.1    3.2  3  PilO            Pilus assembly protein, PilO
        6.8    6.2   9.7       0.31   10.6   4.0    1.6  1  Exonuc_VII_L    Exonuclease VII, large subunit
        7.2    6.8   9.3        1.3    9.2   1.8    2.4  2  RasGAP_C        RasGAP C-terminus
        7.3    6.9   9.9         14    6.0   1.9    2.6  2  KLRAQ           Predicted coiled-coil domain-containing prote


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   3.2e-13   1.2e-10      16      78 ..      23      79 ..      11     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 3.2e-13
                             DUF87 16 ldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkv 78
                                      l + +l+t +  + g++GsGKSnt++v+ eell + g+++li+D +GEY+ ++     e++++
  gi|336254458|ref|YP_004597565.1| 23 LPVVELLTGRGFVTGKSGSGKSNTASVIAEELL-EAGYPLLIVDTDGEYYGLK-----EEYEM 79
                                      55667777778899*******************.*****************99.....33333 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   5.6     0.037        14       2      61 ..     299     358 ..     298     361 .. 0.89
   2 !   27.1   6.3   1.3e-08   4.7e-06       2      58 ..     370     426 ..     369     431 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXX.XX CS
                              SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgasea.ee 61 
                                       e+r+ eLE +l   e+ ie+L d++ e +++i+   +q++    r ++ +++ ++ ++ +e
  gi|336254458|ref|YP_004597565.1| 299 ESRILELENELEKKEKRIETLEDEL-ESARDISNAAKQMADALTRPETFQTQLPDRDDgAE 358
                                       78**********************8.889*****************999999996665533 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 1.3e-08
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXX CS
                              SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgase 58 
                                       ee  +eLE+ la  ++ ie+L +++a  +++idrl++  ++l+er++ele+ +g ++
  gi|336254458|ref|YP_004597565.1| 370 EEERDELEETLAERDERIEALEAELASRAETIDRLREANEQLRERVRELEDGDGVDR 426
                                       66779*********************************************9987554 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.5e-06   0.00055      20      67 ..      29      76 ..      10     101 .. 0.87
   2 ?    4.0   0.0     0.041        15     289     360 ..     178     240 ..     170     349 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
                            DUF853 20 anrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiaka 67
                                          G+++G  G Gk  t  v+ae+l eaG p +++d  G+  g+ + 
  gi|336254458|ref|YP_004597565.1| 29 LTGRGFVTGKSGSGKSNTASVIAEELLEAGYPLLIVDTDGEYYGLKEE 76
                                      55679************************************9998765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.041
                            DUF853 289 rskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaadtfranpefdveeaiteLgvGeal 360
                                       r  G G+  ++q P+d+ ++ ++q    v h l     +d+k v   +dt       + eea+ eL+ G+a+
  gi|336254458|ref|YP_004597565.1| 178 RKHGLGIVGISQRPADVKKDFITQANWLVWHRLT--WDNDTKVVGRIIDT-------EYEEAVAELNDGQAF 240
                                       889*********************9999999774..35666666666655.......344555555555555 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.1     0.013       4.9      26      73 ..     293     326 ..     282     339 .. 0.58
   2 !   19.4   4.7   2.1e-06   0.00078       2      46 ..     375     419 ..     374     421 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.013
                        TMF_DNA_bd  26 kkelklnntikkLrkknkelekeikelkkkleklekeleeleerlkea 73 
                                           +++              + i el+++lek+ek +e+le++l++a
  gi|336254458|ref|YP_004597565.1| 293 ERKEREE--------------SRILELENELEKKEKRIETLEDELESA 326
                                       4444444..............445555555555555555555555443 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 2.1e-06
                        TMF_DNA_bd   2 slekklkeKDeqIaqLmeEGekLskkelklnntikkLrkknkele 46 
                                       +le++l+e+De+I++L +E+   + + ++l+++  +Lr+ ++ele
  gi|336254458|ref|YP_004597565.1| 375 ELEETLAERDERIEALEAELASRAETIDRLREANEQLRERVRELE 419
                                       799****************************************99 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 !   12.2   2.0   0.00052      0.19       1      27 [.     301     327 ..     301     337 .. 0.91
   2 !   14.0   0.5   0.00013     0.049       1      35 [.     386     420 ..     386     421 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00052
                         FlaC_arch   1 ridelEnklsklsteletvkkeneels 27 
                                       ri elEn+l+k + ++et+++e+e+ +
  gi|336254458|ref|YP_004597565.1| 301 RILELENELEKKEKRIETLEDELESAR 327
                                       789********************9866 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00013
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelke 35 
                                       ri+ lE +l +   +++ +++ ne+l++ v el++
  gi|336254458|ref|YP_004597565.1| 386 RIEALEAELASRAETIDRLREANEQLRERVRELED 420
                                       89******************************997 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 !   17.7   0.0   7.9e-06    0.0029       4      55 ..      35     150 ..      33     418 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.9e-06
                                       EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                              CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                       + +k+G+GK+ +a  +a  l ++g+  l vD+D +      ++gl+++ e                           
  gi|336254458|ref|YP_004597565.1|  35 VTGKSGSGKSNTASVIAEELLEAGYPLLIVDTDGE------YYGLKEEYEMlhagadeecdiqigpehaeqmatlal 105
                                       689******************************99......777777777778888888866665555555555555 PP

                                       ............................................C CS
                                       ............................................x RF
                              CbiA  55 ............................................d 55 
                                                                                    
  gi|336254458|ref|YP_004597565.1| 106 eenvpiildvsgyieegvadelirkvarqlfvkekklkkpfllvV 150
                                       555555555555555544444444444444444444444444440 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.9e-05     0.011       6      53 ..      34      81 ..      32     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.9e-05
                                      EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSH CS
                        APS_kinase  6 wltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfse 53
                                      ++tG sgsGKs  a  ++++L e g+   ++d d    gL+++  + +
  gi|336254458|ref|YP_004597565.1| 34 FVTGKSGSGKSNTASVIAEELLEAGYPLLIVDTDGEYYGLKEEYEMLH 81
                                      78*******************************999999988765544 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 !   15.6   4.4   3.7e-05     0.014      29     130 ..     308     413 ..     301     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.7e-05
                                       CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHH.HHHHHHHHH...HHHHHHHHHHHHHCCCHHHHHHHCCH CS
                         Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvkeikdslr.ekqkskkdn...dnvikksskeleeeilrlketidaqe 101
                                         ++ +k++e+le+ele++++ ++ a+++  +++   + ++q  ++d    ++ +++    leee  +l+et+ +  
  gi|336254458|ref|YP_004597565.1| 308 ELEKKEKRIETLEDELESARDISNAAKQMADALTRPETfQTQLPDRDDgaeERRLHDEIVALEEERDELEETLAERD 384
                                       5566789****************99999999987543213333333323457888888889**************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 102 snirvLqnvlesneqkiqkLeqdidqker 130
                                       ++i++L   l s  + i +L+++ +q+++
  gi|336254458|ref|YP_004597565.1| 385 ERIEALEAELASRAETIDRLREANEQLRE 413
                                       **********************9999877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.1e-05    0.0077      28     146 ..      34     155 ..      22     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-05
                            AAA_16  28 llsGesGvGKsslvrellralekdg.gif.lrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102
                                       +++G sG+GKs  +  ++++l ++g  ++ + ++ + ++ + +y +l   +++ e   q++ e+   + + +  +le
  gi|336254458|ref|YP_004597565.1|  34 FVTGKSGSGKSNTASVIAEELLEAGyPLLiVDTDGEYYGLKEEYEMLHAGADE-ECDIQIGPEH---AEQMATLALE 106
                                       89**********************65555577777777778889999999967.4444555553...4456666677 PP

                            AAA_16 103 ealaavpelagaea....srllellkrll.allsrderplvlvlDdlqw 146
                                       e++ ++ +++g ++      l ++++r l ++ ++ ++p++lv+++++ 
  gi|336254458|ref|YP_004597565.1| 107 ENVPIILDVSGYIEegvaDELIRKVARQLfVKEKKLKKPFLLVVEEVHE 155
                                       77777888888888666755555555555578888888********995 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 ?   13.3   0.0   0.00022     0.082       3     119 ..      35     198 ..      34     203 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00022
                                       EESSTTSSHHHHHHHHHHHH...THE....................................EEEEETTTCSSS... CS
                               AAA   3 lyGppGtGKTllakavakel...gve....................................fleisgsellsk... 37 
                                       ++G  G GK+ +a+ +a+el   g +                                               +   
  gi|336254458|ref|YP_004597565.1|  35 VTGKSGSGKSNTASVIAEELleaGYPllivdtdgeyyglkeeyemlhagadeecdiqigpehA----------Eqma 101
                                       6899***************75553443333333334444444444444445555555555550..........0555 PP

                                       ..................STTHHHHHHHHHHHHH..HHTS..TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
                               AAA  38 ..................yvgesekkirelfkea..keka..kpsilfiDEidalaksrsgseseeeervvnqLlte 92 
                                                           g + + ir++ +++  kek+  kp  l+++E+++ +++      +   ++ n L++ 
  gi|336254458|ref|YP_004597565.1| 102 tlaleenvpiildvsgyiEEGVADELIRKVARQLfvKEKKlkKPFLLVVEEVHEYIPEG-----GGVGETGNLLIKI 173
                                       55555555555556664344677888999999963355558799**************9.....4445555555555 PP

                                       HHHTTTSSSTEEEEEEESSGGGSTHHH CS
                               AAA  93 ldgvkkkeskvivigatnrpdkldpal 119
                                        ++ +k  + + ++g+++rp ++++ +
  gi|336254458|ref|YP_004597565.1| 174 SKRGRK--HGLGIVGISQRPADVKKDF 198
                                       555555..4699999999998887765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   7.8   7.5e-05     0.028     321     456 ..     286     418 ..     238     422 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.5e-05
                            AAA_13 321 edkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakk 397
                                        d e++++++e  e+++ +l+++le+K k++ +   le+  + +  i+++ +++ +  ++   + ++l ++   a++
  gi|336254458|ref|YP_004597565.1| 286 GDLEKISERKEREESRILELENELEKKEKRIET---LEDELESARDISNAAKQMADALTRPETFQTQLPDRDDGAEE 359
                                       568999**********************99998...9999999999999**************************** PP

                            AAA_13 398 klelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrde 456
                                          ++++  le+e de+++++++ ++ ie le+el+  ++ +  l+e  ++L++++r+ 
  gi|336254458|ref|YP_004597565.1| 360 RRLHDEIVALEEERDELEETLAERDERIEALEAELASRAETIDRLREANEQLRERVREL 418
                                       99999******************************************999999999875 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5  14.9   0.00014     0.051      56     146 ..     303     419 ..     298     423 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00014
                              Wtap  56 srlrkeleeaenkleeaqeeLqalkftpds........................qtGkrLmakcrvLeqENeELgkv 108
                                        +l +ele++e+++e  ++eL++ +   ++                        ++ +rL   +  Le+E +EL+++
  gi|336254458|ref|YP_004597565.1| 303 LELENELEKKEKRIETLEDELESARDISNAakqmadaltrpetfqtqlpdrddgAEERRLHDEIVALEEERDELEET 379
                                       678999999999999999999999988887778888888899999999999999**********************9 PP

                              Wtap 109 lee..grvakLeselalqkkfveelkkaleeleelleele 146
                                       l e  +r++ Le ela + +++++l++a+e+l+e + ele
  gi|336254458|ref|YP_004597565.1| 380 LAErdERIEALEAELASRAETIDRLREANEQLRERVRELE 419
                                       9764479******************************998 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.8     0.008       2.9      14      66 ..     286     338 ..     265     348 .. 0.71
   2 ?    9.5   0.5    0.0018      0.67      11      60 ..     361     410 ..     351     421 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.008
                           DUF4795  14 eaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeevee 66 
                                        ++ek++e++e+ e++  ele++le+kek +e+l++++e  ++     +++++
  gi|336254458|ref|YP_004597565.1| 286 GDLEKISERKEREESRILELENELEKKEKRIETLEDELESARDISNAAKQMAD 338
                                       56677777777777777788888888888888887777766555444444444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0018
                           DUF4795  11 klqeaieklqeelekleekvkelekrledkekklealkkqieelekvkad 60 
                                        l+++i+ l+ee ++lee+ +e ++r+e++e +l +  + i++l+++++ 
  gi|336254458|ref|YP_004597565.1| 361 RLHDEIVALEEERDELEETLAERDERIEALEAELASRAETIDRLREANEQ 410
                                       58899****************************************99964 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.5    0.0073       2.7      41      77 ..     284     320 ..     277     335 .. 0.90
   2 ?   10.9   0.9     0.001      0.37      46      78 ..     374     406 ..     364     408 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0073
                              Med9  41 lirelpgidrsveeqeaeieeleeqlakKrelLkkyk 77 
                                       l+  l+ i++ +e  e +i ele++l+kK++ ++ + 
  gi|336254458|ref|YP_004597565.1| 284 LVGDLEKISERKEREESRILELENELEKKEKRIETLE 320
                                       5667888***********************9998876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.001
                              Med9  46 pgidrsveeqeaeieeleeqlakKrelLkkykn 78 
                                       ++++++ +e++++ie+le +la + e + ++++
  gi|336254458|ref|YP_004597565.1| 374 DELEETLAERDERIEALEAELASRAETIDRLRE 406
                                       5699************************99987 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.6    0.0074       2.7      31      80 ..     276     325 ..     273     327 .. 0.91
   2 ?    8.0   0.5    0.0097       3.5      25      75 ..     369     419 ..     366     421 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0074
                              KxDL  31 eLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkaklak 80 
                                       eL+ + + +   l+k+++r ++    + e+ ++Le+  k+i++l+++l++
  gi|336254458|ref|YP_004597565.1| 276 ELKSVSDALVGDLEKISERKEREESRILELENELEKKEKRIETLEDELES 325
                                       788888888889*********************************99985 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0097
                              KxDL  25 lnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslk 75 
                                       l+++  eL+e  a+ +er + l+a++++ ++++ ++++  e++++++r l+
  gi|336254458|ref|YP_004597565.1| 369 LEEERDELEETLAERDERIEALEAELASRAETIDRLREANEQLRERVRELE 419
                                       899999****************************************99997 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0012      0.45      25      68 ..      34      77 ..      29     155 .. 0.86
   2 ?    1.2   0.0      0.37   1.4e+02     260     290 ..     168     198 ..     126     221 .. 0.78
   3 ?   -1.6   1.2       2.6   9.5e+02     112     195 ..     287     369 ..     272     398 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0012
                            AAA_10 25 liiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketl 68
                                      +++G+ G GKS +a ++   ++ +g  +li+D   e +  ke+ 
  gi|336254458|ref|YP_004597565.1| 34 FVTGKSGSGKSNTASVIAEELLEAGYPLLIVDTDGEYYGLKEEY 77
                                      89********************************9988776654 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.37
                            AAA_10 260 kllkelvRiGRsynaavylvtqsadDvlkee 290
                                       +ll ++ + GR++   ++ ++q + Dv+k+ 
  gi|336254458|ref|YP_004597565.1| 168 NLLIKISKRGRKHGLGIVGISQRPADVKKDF 198
                                       577778888******************9875 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.6
                            AAA_10 112 lllgvkkkesekkaalseaveavlegkqrgllavieelr..kedekvareiarhlesvvkkslaklvfsdgsveeai 186
                                        l++++++++ ++  + e  e+ le+k++ ++ + +el+  ++ +++a+++a+ l  ++ + +   + + ++  e+ 
  gi|336254458|ref|YP_004597565.1| 287 DLEKISERKEREESRILE-LENELEKKEKRIETLEDELEsaRDISNAAKQMADAL--TRPETFQTQLPDRDDGAEER 360
                                       455555555555544444.466667777777777777752233566777777777..44455555444545555555 PP

                            AAA_10 187 slekkvtvl 195
                                       +l+ +++ l
  gi|336254458|ref|YP_004597565.1| 361 RLHDEIVAL 369
                                       555555555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00047      0.17       7      40 ..      35      68 ..      33      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00047
                            AAA_31  7 anqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40
                                      +  K G GK+ t+  +a+ l ++g+  L+vD D 
  gi|336254458|ref|YP_004597565.1| 35 VTGKSGSGKSNTASVIAEELLEAGYPLLIVDTDG 68
                                      56799***************************95 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 ?    5.8   0.0     0.032        12      24      52 ..      34      62 ..      32     158 .. 0.69
   2 ?    4.8   0.2     0.061        22      91     139 ..     288     334 ..     243     345 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.032
                          ATPase_2 24 fiYGpegsGKtaLlkeiienledkdkyvi 52
                                      f++G  gsGK+     i+e+l++ ++  +
  gi|336254458|ref|YP_004597565.1| 34 FVTGKSGSGKSNTASVIAEELLEAGYPLL 62
                                      8********************99987333 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.061
                          ATPase_2  91 leeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngae 139
                                       le+i+++k ++ ++ i +l ++++kk k+i  + Del  ++d+  n a+
  gi|336254458|ref|YP_004597565.1| 288 LEKISERKERE-ESRILELENELEKKEKRIETLEDELESARDIS-NAAK 334
                                       44555555555.89999************************886.4444 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 ?   -2.1   0.0       8.3     3e+03     111     127 ..      64      80 ..      61      84 .. 0.83
   2 ?    4.0   2.1      0.11        39      29      66 ..     304     341 ..     278     356 .. 0.77
   3 ?   13.0   2.5   0.00018     0.067      20      68 ..     366     411 ..     361     420 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8.3
                        Phage_GP20 111 lkedgelkgLdeqikkL 127
                                       ++ dge+ gL+e+ + L
  gi|336254458|ref|YP_004597565.1|  64 VDTDGEYYGLKEEYEML 80 
                                       689*********98777 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.11
                        Phage_GP20  29 tlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknk 66 
                                       +l+++l++++k +e+L+++ + + ++ ++ +++  ++ 
  gi|336254458|ref|YP_004597565.1| 304 ELENELEKKEKRIETLEDELESARDISNAAKQMADALT 341
                                       68999999999999999999999998888888876655 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00018
                        Phage_GP20  20 ldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkka 68 
                                       +  +eeerd+l+e+l++rd+ +e L+++    ++  ++i+ l ++n++ 
  gi|336254458|ref|YP_004597565.1| 366 IVALEEERDELEETLAERDERIEALEAE---LASRAETIDRLREANEQL 411
                                       55789********************998...666666777777777664 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 ?    9.1   0.0    0.0029         1       1      31 [.      37      67 ..      37      70 .. 0.96
   2 ?   -1.6   0.0       5.5     2e+03      97     126 ..     102     132 ..      95     137 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0029
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlD 31
                                      G++ sGKS  a ++++++l++g+  ++vD+D
  gi|336254458|ref|YP_004597565.1| 37 GKSGSGKSNTASVIAEELLEAGYPLLIVDTD 67
                                      8899*************************99 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.5
                            CLP1_P  97 enkkakasgliIntpGwvk.glgaellleli 126
                                       + +  ++ ++i + +G+++ g++ el+ +++
  gi|336254458|ref|YP_004597565.1| 102 TLALEENVPIILDVSGYIEeGVADELIRKVA 132
                                       444557899*********8245667776665 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   4.7     0.046        17       4      57 ..     287     340 ..     284     349 .. 0.84
   2 ?    9.0   0.5    0.0039       1.4      22      80 ..     362     420 ..     356     430 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.046
                              BRE1   4 ELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdal 57 
                                        L+k+++ +e  ++ + ++ +el+  e+++  le e + a+    aa+   dal
  gi|336254458|ref|YP_004597565.1| 287 DLEKISERKEREESRILELENELEKKEKRIETLEDELESARDISNAAKQMADAL 340
                                       689999999999999999999999999999999999999988888877777776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0039
                              BRE1  22 kvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLke 80 
                                       ++ e+ +lee+   le   a+ d+ + a++ +  ++   + +L++ +++ +e + +L++
  gi|336254458|ref|YP_004597565.1| 362 LHDEIVALEEERDELEETLAERDERIEALEAELASRAETIDRLREANEQLRERVRELED 420
                                       56677777777777777777777777777777777777777777777777777777766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00069      0.25       2      79 ..      34     113 ..      34     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00069
                            AAA_18   2 lltGtpGvGKttlakeLskrl.gfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss..aleegk 75 
                                       ++tG++G+GK+  a  ++++l + g+ l  v ++++++   +++    +  +de+ + ++  ++ e+ +  alee+ 
  gi|336254458|ref|YP_004597565.1|  34 FVTGKSGSGKSNTASVIAEELlEAGYPLLIVDTDGEYYGLKEEY-EMLHAGADEECDIQIGPEHAEQMAtlALEENV 109
                                       69*****************9867688888888887777777777.23333344444444444444333344455555 PP

                            AAA_18  76 nlvi 79 
                                       ++++
  gi|336254458|ref|YP_004597565.1| 110 PIIL 113
                                       5555 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9  12.0   3.4e-05     0.013     119     237 ..     290     412 ..     272     420 .. 0.78
   2 ?   -2.8   0.3       8.4   3.1e+03     193     220 ..     627     652 ..     582     660 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.4e-05
                           DUF4407 119 eakelkeqlaaa...ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.gtgttgvaGkgpaakekkaq 191
                                       +++e ke+ ++    l++el++ e++i+ l+ e+++a++  +a+++ a++ + +++ +t+ + ++ +g++ ++  ++
  gi|336254458|ref|YP_004597565.1| 290 KISERKEREESRileLENELEKKEKRIETLEDELESARDISNAAKQMADALTRPETfQTQLP-DRDDGAEERRLHDE 365
                                       44444444444455577888888888888888888888888888888877777666777877.7999********** PP

                           DUF4407 192 ldaaqaelaelkakld.atarlaalraelaeleaerakeraasqaaa 237
                                       + a+++e +el+++l  +++r++al+aela+ ++ +++ r+a+++ +
  gi|336254458|ref|YP_004597565.1| 366 IVALEEERDELEETLAeRDERIEALEAELASRAETIDRLREANEQLR 412
                                       *************9998999999999999999999999998888755 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.4
                           DUF4407 193 daaqaelaelkakldatarlaalraela 220
                                       d++ ++  +l ++  a++++aa+ +e +
  gi|336254458|ref|YP_004597565.1| 627 DRQGERTYALADD--ASQQIAAHLEENE 652
                                       2222222222222..2222222222222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0012      0.45       8     103 ..      33     156 ..      30     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0012
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka............. 70 
                                       ++vtG sG+GK+ ++  ++e+l e+      + +++ v+  ++  ++k+ +++l    ++e++              
  gi|336254458|ref|YP_004597565.1|  33 GFVTGKSGSGKSNTASVIAEELLEA------GYPLLIVDTDGEYyGLKEEYEMLHAGADEECDIqigpehaeqmatl 103
                                       78********************876......8888888888888888888888888888888888888888888888 PP

                            AAA_22  71 ................erlsseellealeqalrarav....ielliiDEaqhl 103
                                                       e++  +el+++++++l  + +    + ll+++E++  
  gi|336254458|ref|YP_004597565.1| 104 aleenvpiildvsgyiEEGVADELIRKVARQLFVKEKklkkPFLLVVEEVHEY 156
                                       88888888888888888888888886666666554445787888888888874 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00089      0.32       5      38 ..      34      67 ..      33      70 .. 0.97
   2 ?   -1.6   0.6       3.3   1.2e+03     155     204 ..     302     353 ..     287     390 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00089
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      +v+GK G GK+  ++ +a +l e g+  l++ tD
  gi|336254458|ref|YP_004597565.1| 34 FVTGKSGSGKSNTASVIAEELLEAGYPLLIVDTD 67
                                      89*******************************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHHHHHCCCSHCHHHHHH..HHHHHHHHHHHHHHHHHHHHTST CS
                       ArsA_ATPase 155 lvklkeklsplakqlvkllglggvsie..ealeeleetkeeikkveeiltdp 204
                                       +++l+++l++  k +  l +  ++  +  +a++++ + + + ++++ +l d 
  gi|336254458|ref|YP_004597565.1| 302 ILELENELEKKEKRIETLEDELESARDisNAAKQMADALTRPETFQTQLPDR 353
                                       3334443333333333333332222222255555555555555555555555 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.4     0.098        36      35      76 ..     287     328 ..     269     355 .. 0.76
   2 ?    9.9   0.8    0.0027      0.99      24      68 ..     375     419 ..     353     434 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.098
                                       HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DUF16  35 rLkkieakvdklgeqinkleqkvekqgekikelkveqkaqge 76 
                                       +L+ki ++ +  + +i +le++ ek++++i+ l+ e +  ++
  gi|336254458|ref|YP_004597565.1| 287 DLEKISERKEREESRILELENELEKKEKRIETLEDELESARD 328
                                       677888888888888888888888888888888888877665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0027
                                       HHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHH CS
                             DUF16  24 qlnefkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelk 68 
                                       +l+e   + ++r++ +ea+++++ e i++l ++ e++ e+++el+
  gi|336254458|ref|YP_004597565.1| 375 ELEETLAERDERIEALEAELASRAETIDRLREANEQLRERVRELE 419
                                       333333334444455555555555555555555555555555444 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.32   1.2e+02      35      73 ..     304     341 ..     279     350 .. 0.80
   2 ?    6.6   0.1      0.02       7.4      34      79 ..     367     418 ..     360     427 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.32
                      Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldtrldtlltnLt 73 
                                       +l++ l++ e+++++l+++l+s   +++++ ++++++Lt
  gi|336254458|ref|YP_004597565.1| 304 ELENELEKKEKRIETLEDELES-ARDISNAAKQMADALT 341
                                       6888888889999999999988.6677777777777776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.02
                      Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnal 79 
                                        +l++  d++e++L + +e++++l ael++      rl ++ ++L + + +l
  gi|336254458|ref|YP_004597565.1| 367 VALEEERDELEETLAERDERIEALEAELASraetidRLREANEQLRERVREL 418
                                       5799999999999999999999999999995555555555555555555555 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 ?    9.7   8.5    0.0026      0.96       6      57 ..     296     350 ..     290     352 .. 0.79
   2 ?    4.9  14.2     0.086        31       8      58 ..     371     419 ..     357     420 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0026
                      ABC_tran_CTD   6 eqre..leeleaeIeaLEeeiaeleaeladpelysdp.eklaelsaeleeleaeL 57 
                                       e+ e  + ele+e+e+ E++i++le+el+++   s+  +++a++ ++ e+ +++L
  gi|336254458|ref|YP_004597565.1| 296 EREEsrILELENELEKKEKRIETLEDELESARDISNAaKQMADALTRPETFQTQL 350
                                       333311447**********************999999788999999888888776 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.086
                      ABC_tran_CTD   8 releeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLe 58 
                                        e +ele+++++ +e+i++leaela+ +  ++ ++l e++++l e   eLe
  gi|336254458|ref|YP_004597565.1| 371 EERDELEETLAERDERIEALEAELASRA--ETIDRLREANEQLRERVRELE 419
                                       4556677777777777777777777666..555666666666666555555 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.8     0.068        25      31      83 ..     280     331 ..     272     353 .. 0.52
   2 ?    4.7   0.1     0.042        16       3      59 ..     365     421 ..     363     437 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.068
                             TMPIT  31 lqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk 83 
                                         ++++ +++k ++r ++ +s++ +l++++ e++e+++e+l++el++++ + +
  gi|336254458|ref|YP_004597565.1| 280 VSDALVGDLEKISERKEREESRILELENEL-EKKEKRIETLEDELESARDISN 331
                                       444444455555555555555555555554.3555555555555555544444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.042
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkks 59 
                                       e+  le+e +eleet  e  +++e l++   + +++i++ ++  ++l++++++l+  
  gi|336254458|ref|YP_004597565.1| 365 EIVALEEERDELEETLAERDERIEALEAELASRAETIDRLREANEQLRERVRELEDG 421
                                       7778999999******9***********99999**************9999999876 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.3     0.024       8.8      44     101 ..     278     334 ..     274     352 .. 0.82
   2 ?    7.7   2.1    0.0096       3.5      62     121 ..     360     419 ..     348     421 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.024
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseige 101
                                       +svs  l    e++++ k++ +sri +++++l++ ++ ++ +++e++++r+  ++  +
  gi|336254458|ref|YP_004597565.1| 278 KSVSDALVGDLEKISERKEREESRILELENELEKKEKRIETLEDELESARDISNA-AK 334
                                       6788888888999********************************9988754433.33 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0096
                           DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       r+L ++i  ++++ de +e+ +e +e +++++ +l++  e ++ ++ea e+l ++++++e
  gi|336254458|ref|YP_004597565.1| 360 RRLHDEIVALEEERDELEETLAERDERIEALEAELASRAETIDRLREANEQLRERVRELE 419
                                       778888888888888888888888888888888888888888888888888888888887 PP

>> DUF2570  Protein of unknown function (DUF2570)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4       7.7   2.8e+03      43      64 ..     313     334 ..     290     353 .. 0.52
   2 ?   10.8   0.3   0.00092      0.34      22      53 ..     384     415 ..     376     420 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.7
                           DUF2570  43 qkanqrLteqLeqerqavekqq 64 
                                       +k  + L ++Le  r   +  +
  gi|336254458|ref|YP_004597565.1| 313 EKRIETLEDELESARDISNAAK 334
                                       2222233333333333333333 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00092
                           DUF2570  22 sqkidsLraenkaqaqlieeqqkanqrLteqL 53 
                                        ++i++L+ae +++a++i + ++an++L e++
  gi|336254458|ref|YP_004597565.1| 384 DERIEALEAELASRAETIDRLREANEQLRERV 415
                                       579*************************9876 PP

>> Ead_Ea22  Ead/Ea22-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  15.1      0.21        77      66     130 ..     299     407 ..     241     497 .. 0.84
   2 ?   -0.4   0.2       4.6   1.7e+03      66      82 ..     641     657 ..     603     660 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.21
                          Ead_Ea22  66 patvlaLLDelekkqqrikeleee.aenedialtvgklrveleaaekrl............................ 113
                                        + +l+L  elekk++ri+ le+e   ++di+ ++ +  ++l   e+ +                            
  gi|336254458|ref|YP_004597565.1| 299 ESRILELENELEKKEKRIETLEDElESARDISNAAKQMADALTRPETFQtqlpdrddgaeerrlhdeivaleeerde 375
                                       56799*******************99999999999999999999888888889999999988888887777777777 PP

                          Ead_Ea22 114 ...............ekenveqadaaeveita 130
                                                      e+e++ +a+ +++ + a
  gi|336254458|ref|YP_004597565.1| 376 leetlaerderiealEAELASRAETIDRLREA 407
                                       76666666666666655555555555555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 4.6
                          Ead_Ea22  66 patvlaLLDelekkqqr 82 
                                        + ++a L+e+ek+++r
  gi|336254458|ref|YP_004597565.1| 641 SQQIAAHLEENEKNEER 657
                                       46677888888877765 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   5.7      0.36   1.3e+02      65      91 ..     296     325 ..     286     349 .. 0.51
   2 ?   11.6   5.4   0.00045      0.17      39     101 ..     358     420 ..     335     435 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.36
                                       HH...HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  65 er...rlkdlekelselkesveelklekkq 91 
                                       er   r+++le+el++ ++++e l+ e + 
  gi|336254458|ref|YP_004597565.1| 296 EReesRILELENELEKKEKRIETLEDELES 325
                                       333335555555555555555555444333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC CS
                              SHE3  39 keskflenlaslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenssa 101
                                        e ++ +++  l +E d L   L  ++ r+  le el++  e ++ l++ ++ql++r++++++
  gi|336254458|ref|YP_004597565.1| 358 EERRLHDEIVALEEERDELEETLAERDERIEALEAELASRAETIDRLREANEQLRERVRELED 420
                                       4557889**************************************************998876 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   8.7    0.0051       1.9      65     100 ..     289     324 ..     287     327 .. 0.93
   2 ?    3.8   1.7      0.15        54       9      39 ..     361     391 ..     357     393 .. 0.72
   3 ?    5.2   5.1     0.054        20      60     101 ..     369     410 ..     366     417 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelkeelq 100
                                       e+  erke+ e +i +le++lek+ek++e l++el 
  gi|336254458|ref|YP_004597565.1| 289 EKISERKEREESRILELENELEKKEKRIETLEDELE 324
                                       67889*****************************97 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   9 qlqqqlqqlaqqikqletqlkelelvleele 39 
                                       +l++++ +l++++++le+ l e ++ +e+le
  gi|336254458|ref|YP_004597565.1| 361 RLHDEIVALEEERDELEETLAERDERIEALE 391
                                       6777788888888888888777777776665 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.054
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelkeelqk 101
                                       +ee ++eLee++++ +++i++le +l +  ++++ l+e + +
  gi|336254458|ref|YP_004597565.1| 369 LEEERDELEETLAERDERIEALEAELASRAETIDRLREANEQ 410
                                       68899999999999999******9999999999999998766 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 ?    3.6  27.3      0.16        60      21     124 ..     297     415 ..     282     429 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.16
                    CENP-F_leu_zip  21 sLkdkvenLerelemseenqekvileaEtskaevetlkeeieela...............eelreleldLvalrsek 82 
                                         + ++++Le ele  e+  e ++ e E+++   ++ k++ + l+               +e r+l+ ++val +e+
  gi|336254458|ref|YP_004597565.1| 297 REESRILELENELEKKEKRIETLEDELESARDISNAAKQMADALTrpetfqtqlpdrddgAEERRLHDEIVALEEER 373
                                       33455555555555555555555555555555555544444444311111111111112246788999999999*** PP

                    CENP-F_leu_zip  83 eeLekelqkkqervseLeslnsslenlleekEqekvqmkees 124
                                       +eLe+ l +  er++ Le+   s  +++ ++ + + q++e+ 
  gi|336254458|ref|YP_004597565.1| 374 DELEETLAERDERIEALEAELASRAETIDRLREANEQLRERV 415
                                       ********************9999999999988888888865 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.074        27      64      86 ..     298     327 ..     267     329 .. 0.69
   2 ?    3.8   0.3      0.21        77      63      84 ..     361     396 ..     330     399 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.074
                           DUF4094  64 thkaiqtL.......dktissLemeLaaar 86 
                                        ++ i  L       +k+i +Le eL++ar
  gi|336254458|ref|YP_004597565.1| 298 EESRILELenelekkEKRIETLEDELESAR 327
                                       333333334444555999********9999 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.21
                           DUF4094  63 kthkaiqtL..............dktissLemeLaa 84 
                                       + h++i +L              d +i +Le eLa+
  gi|336254458|ref|YP_004597565.1| 361 RLHDEIVALeeerdeleetlaerDERIEALEAELAS 396
                                       34444444444444444445999***********94 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9  18.2   8.3e-05      0.03      80     209 ..     288     417 ..     282     419 .. 0.84
   2 ?   -2.5   0.9         8   2.9e+03     195     215 ..     605     625 ..     599     658 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.3e-05
                        MscS_porin  80 leeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrL.nstaaage...alsqaqrt 152
                                       le +  r + ++s+ +el+++l + ++++ +l++ +e a+    +a+q  +++++    +t    +   +   a+  
  gi|336254458|ref|YP_004597565.1| 288 LEKISERKEREESRILELENELEKKEKRIETLEDELESARDISNAAKQMADALTRPEtFQT----QlpdRDDGAEER 360
                                       5666777788999999999999999999999999999999999999999999877111222....123355666777 PP

                        MscS_porin 153 alqaelaaleaqieeleqellsnnnrqeLlklqrdllklriqqleqelqaLqellne 209
                                        l  e  ale + +ele  l+  + r+e l++++   ++ i++l +  ++L+e++ e
  gi|336254458|ref|YP_004597565.1| 361 RLHDEIVALEEERDELEETLAERDERIEALEAELASRAETIDRLREANEQLRERVRE 417
                                       7899*************************************************9976 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8
                        MscS_porin 195 qleqelqaLqellnekRlaea 215
                                       + +q + a+q+ll+e R +  
  gi|336254458|ref|YP_004597565.1| 605 RVDQSMIAVQSLLSELRTESV 625
                                       566666666666666666544 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.77   2.8e+02      47      67 ..     223     243 ..     219     263 .. 0.76
   2 ?    0.9   2.0       1.6   5.7e+02      61      92 ..     291     325 ..     274     342 .. 0.43
   3 ?    8.1   1.0    0.0092       3.4      64     111 .]     358     405 ..     350     405 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.77
                        TSNAXIP1_N  47 IKkEYelyiahllesqreaqy 67 
                                       I  EYe+++a+l ++q   q 
  gi|336254458|ref|YP_004597565.1| 223 IDTEYEEAVAELNDGQAFVQT 243
                                       778***********9976665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.6
                        TSNAXIP1_N  61 sqreaqylkaklktlsessd...kraleleekree 92 
                                        +++++ +++++ +l+++ +   kr+ +le++ e+
  gi|336254458|ref|YP_004597565.1| 291 ISERKEREESRILELENELEkkeKRIETLEDELES 325
                                       33333333333322222222111333333333333 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0092
                        TSNAXIP1_N  64 eaqylkaklktlsessdkraleleekreelralekeskalleeidklr 111
                                       e + l+ +++ l+e+ d+   +l e++e+++ale+e +   e+id+lr
  gi|336254458|ref|YP_004597565.1| 358 EERRLHDEIVALEEERDELEETLAERDERIEALEAELASRAETIDRLR 405
                                       4556789999************************************98 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   6.7     0.088        32      44      88 ..     284     328 ..     279     350 .. 0.77
   2 ?    7.4   6.9     0.011       4.2      65     125 ..     355     415 ..     338     420 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.088
                              ADIP  44 Llqardrdleqreslnetirkleaeierlqskierlktqleqler 88 
                                       L+  +++  e +e  + +i +le+e+e+++++ie l+++le+ + 
  gi|336254458|ref|YP_004597565.1| 284 LVGDLEKISERKEREESRILELENELEKKEKRIETLEDELESARD 328
                                       666677777888999999999999999999999999999987654 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                              ADIP  65 leaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknal 125
                                         ae  rl+ +i  l+++  +le  la   ++   le++l++  +++ +++e ++ l+  +
  gi|336254458|ref|YP_004597565.1| 355 DGAEERRLHDEIVALEEERDELEETLAERDERIEALEAELASRAETIDRLREANEQLRERV 415
                                       4566666666666666666666666666666666666666666666666666666666554 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 ?    5.0   2.5     0.066        24      59     118 ..     279     338 ..     276     350 .. 0.71
   2 ?    6.9   1.6     0.017       6.1      63     112 ..     365     414 ..     361     424 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.066
                              COG2  59 slSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellkl 118
                                       s+S++Lvg  e+++e +   ++   ++e+  ek ++r+e++e++le a+++ ++ + + +
  gi|336254458|ref|YP_004597565.1| 279 SVSDALVGDLEKISERKEREESRILELENELEKKEKRIETLEDELESARDISNAAKQMAD 338
                                       689999997777777777777777777777777777777777777777777777654443 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.017
                              COG2  63 hLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleek 112
                                       + v l+ee +e+e  la+  +++e+++++l+ r e+++   e+ ++l+e 
  gi|336254458|ref|YP_004597565.1| 365 EIVALEEERDELEETLAERDERIEALEAELASRAETIDRLREANEQLRER 414
                                       678899*******************************9988888888775 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.0       1.2   4.2e+02      10      52 ..     288     330 ..     280     353 .. 0.61
   2 ?   12.8   0.4   0.00037      0.14       8      55 ..     371     418 ..     364     437 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  10 leeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                       le+++e+ e+  +++ el++el++  ++ ++Le e e+ r+  
  gi|336254458|ref|YP_004597565.1| 288 LEKISERKEREESRILELENELEKKEKRIETLEDELESARDIS 330
                                       5555566666666666666666666666666666655555554 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXX CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerleee 55 
                                       ++ +elee+l+e  e++e+l++ela+  e  ++L+  ne+lrer++e 
  gi|336254458|ref|YP_004597565.1| 371 EERDELEETLAERDERIEALEAELASRAETIDRLREANEQLRERVREL 418
                                       56689***************************************9543 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.5      0.39   1.4e+02      49      77 ..     297     325 ..     275     344 .. 0.61
   2 ?    7.2   0.8     0.013       4.8      37      72 ..     384     419 ..     358     422 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.39
                           DUF4446  49 ekleeveelkeeseelekeieeleeklkk 77 
                                       ++ +++ el++e e+ ek+ie+le++l++
  gi|336254458|ref|YP_004597565.1| 297 REESRILELENELEKKEKRIETLEDELES 325
                                       34444555555555555555555555544 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.013
                           DUF4446  37 gkdgksleellkekleeveelkeeseelekeieele 72 
                                       +++ + le  l+++ e++++l+e++e+l+++++ele
  gi|336254458|ref|YP_004597565.1| 384 DERIEALEAELASRAETIDRLREANEQLRERVRELE 419
                                       346677888888888888888888888888888876 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.6     0.062        23     192     224 ..     300     332 ..     274     354 .. 0.60
   2 ?    5.7   4.7     0.021       7.8     122     179 ..     361     419 ..     358     438 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.062
                              CorA 192 eylrdlldelerllemlealrerleslqdtyss 224
                                        ++ +l++ele+ ++ +e+l + les +d+ ++
  gi|336254458|ref|YP_004597565.1| 300 SRILELENELEKKEKRIETLEDELESARDISNA 332
                                       334444444444444444444444444444433 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.021
                              CorA 122 rlfellekleeeldeledel.edstkkeilrelaqlr.rrlvklrralapnrevlkrlla 179
                                       rl++++ +leee+dele++l e++++ e l+  ++ r +++ +lr+a  ++re + r l+
  gi|336254458|ref|YP_004597565.1| 361 RLHDEIVALEEERDELEETLaERDERIEALEAELASRaETIDRLREANEQLRERV-RELE 419
                                       7899999*************97777777776555555377999999999999999.5444 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 ?    1.9   9.7      0.11        40      50     150 ..     281     379 ..     269     408 .. 0.67
   2 ?    4.1   1.1     0.025         9      56     104 ..     372     420 ..     355     441 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.11
                        V_ATPase_I  50 ekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleee.eeeeee 125
                                       ++a + + e+ ++++++ee+++ ele+elek+e+++++l+++le+ ++  n ++++   l++ ++f ++  ++++ +
  gi|336254458|ref|YP_004597565.1| 281 SDALVGDLEKISERKEREESRILELENELEKKEKRIETLEDELESARDISNAAKQMADALTRPETFQTQLpDRDDGA 357
                                       455555556678889999999***************************************99998887664333333 PP

                        V_ATPase_I 126 eeseeeeee..keeeeeeeseeeeeee 150
                                        e+++ ++e  + eee    ++e ee+
  gi|336254458|ref|YP_004597565.1| 358 -EERRLHDEivALEEE----RDELEET 379
                                       .222222222322222....2222222 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.025
                        V_ATPase_I  56 eeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelve 104
                                       e+++ e++ a+++++++ le+el +  e + +l+e +e+l+++++el++
  gi|336254458|ref|YP_004597565.1| 372 ERDELEETLAERDERIEALEAELASRAETIDRLREANEQLRERVRELED 420
                                       2222444555555566666666666666666666666666666666555 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   3.4     0.023       8.6      82     116 ..     291     325 ..     288     338 .. 0.89
   2 ?    5.6   1.3     0.039        14      81     117 ..     361     397 ..     356     400 .. 0.89
   3 ?    4.2   0.3      0.11        39       3      34 ..     389     420 ..     384     436 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanlaq 116
                                       + +++e  e+ + +le+elek+ ++i+tle++l+ 
  gi|336254458|ref|YP_004597565.1| 291 ISERKEREESRILELENELEKKEKRIETLEDELES 325
                                       5678889999999*****************99875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.039
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  81 llkkkleelekqlekleeeleklkdqittleanlaql 117
                                        l +++  le+ +++lee l++  ++i+ lea+la +
  gi|336254458|ref|YP_004597565.1| 361 RLHDEIVALEEERDELEETLAERDERIEALEAELASR 397
                                       67888999*************************9986 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                         Prefoldin   3 eeleslqaelaqlkeaieelektletlktlkk 34 
                                       + +++l+++ ++++   e +e+++e++++l++
  gi|336254458|ref|YP_004597565.1| 389 ALEAELASRAETIDRLREANEQLRERVRELED 420
                                       23333444444444444444555555555554 PP

>> PilO  Pilus assembly protein, PilO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.19        70      51      85 ..     165     200 ..     148     202 .. 0.84
   2 ?    3.9   1.1      0.15        57       5      51 ..     309     355 ..     305     359 .. 0.83
   3 ?    0.3   0.9       1.9   7.1e+02      10      46 ..     375     411 ..     366     420 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.19
                              PilO  51 eipsLLedinqaglksgLefelfkpgae.vekefya 85 
                                       e+ +LL +i++ g k+gL +  ++ ++  v+k+f++
  gi|336254458|ref|YP_004597565.1| 165 ETGNLLIKISKRGRKHGLGIVGISQRPAdVKKDFIT 200
                                       6779*******************9987526677766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.15
                              PilO   5 eakekeLkkefeekkekaanLeklkkqleeleeeleellkqLPskke 51 
                                        +k+++  +++e++ e a+++ +  kq+++  ++ e+  +qLP++++
  gi|336254458|ref|YP_004597565.1| 309 LEKKEKRIETLEDELESARDISNAAKQMADALTRPETFQTQLPDRDD 355
                                       45555566789999999**************************9875 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.9
                              PilO  10 eLkkefeekkekaanLeklkkqleeleeeleellkqL 46 
                                       eL+++++e+ e+ ++Le+  +  +e+ ++l+e+ +qL
  gi|336254458|ref|YP_004597565.1| 375 ELEETLAERDERIEALEAELASRAETIDRLREANEQL 411
                                       5555555555555555554444444444444444444 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 ?   10.6   4.0   0.00083      0.31     146     256 ..     292     418 ..     256     428 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00083
                      Exonuc_VII_L 146 eeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldel......eerleralkkq........lk 208
                                        e+ e+ e+r+  ++++ le+k++r+e+l+ +l+s++++ ++++q  d l      +++l      +        l+
  gi|336254458|ref|YP_004597565.1| 292 SERKEREESRI-LELENELEKKEKRIETLEDELESARDISNAAKQMADALtrpetfQTQLPD----RddgaeerrLH 363
                                       22222222222.23455667777777777766655544444444443332111111333332....12222333344 PP

                      Exonuc_VII_L 209 kkrerleelkerlkekleekkerlkklkerle.......lleekkerleeleekl 256
                                        +  +lee +++l+e+l+e++er+++l+++l+       +l+e++e+l+e  ++l
  gi|336254458|ref|YP_004597565.1| 364 DEIVALEEERDELEETLAERDERIEALEAELAsraetidRLREANEQLRERVREL 418
                                       4445555555555444455555554444444433333335666666666555555 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.0      0.92   3.4e+02      32      60 ..     303     331 ..     286     349 .. 0.75
   2 ?    9.2   1.8    0.0035       1.3      33      77 ..     375     419 ..     369     421 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.92
                          RasGAP_C  32 neIakdirnkgrlrekrkeElesleetlk 60 
                                        e+++++ +k++++e  + Eles+++  +
  gi|336254458|ref|YP_004597565.1| 303 LELENELEKKEKRIETLEDELESARDISN 331
                                       46788888999999999999988887655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0035
                          RasGAP_C  33 eIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYk 77 
                                       e++++++++++++e  ++El s  et+++L+e n++l++++++++
  gi|336254458|ref|YP_004597565.1| 375 ELEETLAERDERIEALEAELASRAETIDRLREANEQLRERVRELE 419
                                       788999*********************************998876 PP

>> KLRAQ  Predicted coiled-coil domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.3     0.087        32      24      51 ..     298     325 ..     284     350 .. 0.61
   2 ?    6.0   1.9     0.039        14      25      68 ..     370     420 ..     357     427 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.087
                             KLRAQ  24 EqskeaslkeelkekeqslrkseqEvds 51 
                                       E s+  +l++el +ke+ + + e E++s
  gi|336254458|ref|YP_004597565.1| 298 EESRILELENELEKKEKRIETLEDELES 325
                                       3344445555555555555555555554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.039
                             KLRAQ  25 qskeaslkeelkekeqslrkseqE.......vdsLtFrNkqLekrvellqe 68 
                                        ++ ++l+e+l e+++ +   e+E       +d L   N+qL  rv+ l +
  gi|336254458|ref|YP_004597565.1| 370 EEERDELEETLAERDERIEALEAElasraetIDRLREANEQLRERVRELED 420
                                       556778888888888888888877333222357799999999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (661 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1743  (0.0972168); expected 358.6 (0.02)
Passed bias filter:                      922  (0.0514251); expected 358.6 (0.02)
Passed Vit filter:                       215  (0.0119917); expected 17.9 (0.001)
Passed Fwd filter:                        99  (0.00552178); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              49  [number of targets reported over threshold]
# CPU time: 1.26u 0.32s 00:00:01.58 Elapsed: 00:00:00.52
# Mc/sec: 3853.73
//
Query:       gi|336254459|ref|YP_004597566.1|  [L=55]
Description: hypothetical protein Halxa_3073 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0017   18.6   0.4     0.0017   18.6   0.4    1.0  1  HPP       HPP family


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 !   18.6   0.4   9.3e-08    0.0017      19      61 ..       2      48 ..       1      55 [] 0.73

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.3e-08
                               HPP 19 plaqPrnvvgGhlisalvGvaiaklfgl....sllwlaaalavalai 61
                                      p+  Pr++++G l +alvG+++  l       ++l laa++ v+la+
  gi|336254459|ref|YP_004597566.1|  2 PVLDPRQLIAGFLGAALVGLLASLLTDRiepqRALRLAAGVTVGLAA 48
                                      7889*****************76666557755555456666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 423.99
//
Query:       gi|336254460|ref|YP_004597567.1|  [L=411]
Description: DegT/DnrJ/EryC1/StrS aminotransferase [Halopiger xanaduensis SH-6]
Scores for 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-15   55.5   0.0    4.5e-12   46.0   0.0    2.1  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00032   20.0   0.0    0.00058   19.1   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II


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 !   46.0   0.0     5e-16   4.5e-12      60     171 ..      50     161 ..      27     191 .. 0.90
   2 !    7.6   0.0   0.00023       2.1     239     359 ..     303     408 ..     296     410 .. 0.78

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 5e-16
                                       TTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB--.-HHHHHHHHH CS
                   DegT_DnrJ_EryC1  60 vgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqva.dmdalkaiaa 135
                                       v+pg+ V++p++   a a++ + l ++p +  v   ++ +d a++ea +  +t+a++ V+++G +   ++++ a+a+
  gi|336254460|ref|YP_004597567.1|  50 VEPGQNVLIPAYLPDAVAEPFRDLDLEPRYYRVR-PSFAPDFADLEARLDDETAAVMSVNYFGFPQpGLEEVAALAD 125
                                       789******************************9.68*****************************99********* PP

                                       HCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE-BT CS
                   DegT_DnrJ_EryC1 136 khglkvieDaAhAlGatykgkkvGalgdaavfSFyp 171
                                       + g + i D AhA  +  +g+ +G+ gd+++ S+  
  gi|336254460|ref|YP_004597567.1| 126 ERGCYHIDDNAHAPISVANGRLLGTDGDIGITSLWK 161
                                       *********************************975 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGS CS
                   DegT_DnrJ_EryC1 239 elvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhypnplhrq 315
                                       ++++rRr+++ + ++ La+ +  a+   ++  +      ++v+ +       d+lv+ ++++g+g+ +      ++ 
  gi|336254460|ref|YP_004597567.1| 303 RIRERRRANYRTWRRILADRDDLAV-VYDDLPEGICPQAFPVRAD-----RPDDLVATFETRGVGAYTWP----RLS 369
                                       5789999999999999999997644.4444444478888999999.....6799********99986554....334 PP

                                       CCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 316 pvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVvea 359
                                        ++++       +++ a rl++ +++Lp+++++++ +++++ ++
  gi|336254460|ref|YP_004597567.1| 370 ATVRNDP-----AYETARRLSRTIVALPVHQHIEPSTLEEIGTR 408
                                       4555554.....35789*******************99999766 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 !   19.1   0.0   6.4e-08   0.00058      70     191 ..      32     138 ..      20     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.4e-08
                                       GEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTT CS
                     Aminotran_1_2  70 avvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegn 146
                                          +gsG  al++ l+ l +  pg+++l+p+   + + + +r  ++e ++y+++  ++f  d+ +le+ l++     
  gi|336254460|ref|YP_004597567.1|  32 YTYYGSGKVALRDGLAGLVE--PGQNVLIPAYLPDAVAEPFRDLDLEPRYYRVR--PSFAPDFADLEARLDD----- 99 
                                       6789***************8..******************************88..***************9..... PP

                                       ETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTT CS
                     Aminotran_1_2 147 kktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYa 191
                                        +t  +   + +      ++ + le++++la++++++ + D a+a
  gi|336254460|ref|YP_004597567.1| 100 -ETAAVMSVNYF-----GFPQPGLEEVAALADERGCYHIDDNAHA 138
                                       .66666666665.....4888999999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3172.42
//
Query:       gi|336254461|ref|YP_004597568.1|  [L=543]
Description: type I phosphodiesterase/nucleotide pyrophosphatase [Halopiger xanaduensis SH-6]
Scores for 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-37  129.2   0.0    9.9e-36  124.1   0.0    2.0  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.1   0.0   5.5e-40   9.9e-36       1     345 [.      12     444 ..      12     461 .. 0.85

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 5.5e-40
                                       EEEEEETT-BTTHHHHHG.S.TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTE CS
                      Phosphodiest   1 vlvislDGlradlldrla.e.llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktge 75 
                                       +lv++lD   + +l+ l+   + p l+++++ g+s+p l++++P+ T++++ sl+TG++Pg+HG++++  +   +g 
  gi|336254461|ref|YP_004597568.1|  12 LLVVGLDAGCPPILESLFeSdEVPTLRRILESGSSGP-LESQIPPWTASAWPSLYTGKNPGKHGVFDFLSF---NGY 84 
                                       689999988888888888547****************.*****************************4444...444 PP

                                       EEEEETTTTGGGGGCTTS-HHHHHHHTHTTCEEEESETTTTSEBTTCT.SC.........TBHHSBTCT.CSTTS.. CS
                      Phosphodiest  76 yvvfvtededaprwwqgepiwdtaakarglkaaalfwpgsevdystyyylvs........etppryleddfnakv.. 142
                                       +++ v+++     ++++ p+w+ +    g+++ +++ p + +++   ++l          +++p+ + +d + +   
  gi|336254461|ref|YP_004597568.1|  85 DWNVVNST-----HVRERPVWELLSEH-GITSVVVNLPVTHPAREFDGALIPgmtapedpDCHPDGILEDIKLECgg 155
                                       44555554.....49************.****************999998889999999989888888888887788 PP

                                       ................CHHHHHHHHHHHHHHHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-T.TSHHHHHHHH CS
                      Phosphodiest 143 ................pledkvdkavlqtwldaafakvvlekelekpdlllvyleetDtvgHkfGp.dspevedalr 202
                                                       ++e+++   ++++ +    ++        +p + ++ + +tD+v H+  p d+ ++e+ +r
  gi|336254461|ref|YP_004597568.1| 156 yrvypqsgpepdrsieGYERTIE--LRGKAFRYLCRR-------MEPEFGFLQFQQTDSVFHER-PgDKQAIEAVYR 222
                                       88888888766655555555554..332333333333.......99******************.956999****** PP

                                       HHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEHTTSEEEGGGTSTGGH.......................... CS
                      Phosphodiest 203 rvDkaigdLlealderglsaetniilvSDHGmadvsddkvielndlleekg.......................... 253
                                       +vD+ +++++++ d++      ni++vSDHGm+ v   + +++n++l++ g                          
  gi|336254461|ref|YP_004597568.1| 223 EVDRQLEETIAETDPE------NILIVSDHGMGKV-TGHEFRVNEFLRDRGylrahrggegmpdwskswendllrge 292
                                       ****************......*************.6679************************************* PP

                                       ...........................................................GEEEEECBHHS.SSE... CS
                      Phosphodiest 254 ...........................................................llhlkdegkggakal... 268
                                                                                                  +++++++           
  gi|336254461|ref|YP_004597568.1| 293 dagtheettleramnvaarfgvttqrianaldrvglkepigrqvpndliraaseqvafaDSEVYMR-------Skse 362
                                       ***********************************************9999966666664444444.......3445 PP

                                       ..EEEEESTEE.E.CCCTTHHHHHHHHHHTCHHCCHSTHTT..TEEEEEGG.GS-GGGCHSTTS-SEEE.EE-TTEE CS
                      Phosphodiest 269 ..iainpkare.lnrvaeaeaeevyaelkakleelrkkege..alavylke.aipkrlhykkrapdlvl.vadpgws 338
                                         ++in+++re +++v+e e+e+v++e+ + l+++r+++ge  + av  +e  +++++   +  pd+v   a  ++ 
  gi|336254461|ref|YP_004597568.1| 363 lgLRINLEGREpDGTVPESEYERVRDEVVEELSAVRTPDGEpmFDAVGPREeFFDGPYL--DEGPDIVTvPAAFNNA 437
                                       56*********************************98899999********66999987..9999999945555666 PP

                                       EESSTTC CS
                      Phosphodiest 339 itskdkp 345
                                       i+ + ++
  gi|336254461|ref|YP_004597568.1| 438 IVADLGK 444
                                       6555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3785.04
//
Query:       gi|336254462|ref|YP_004597569.1|  [L=336]
Description: hypothetical protein Halxa_3076 [Halopiger xanaduensis SH-6]
Scores for 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-19   69.5   1.3    4.3e-19   69.1   0.1    1.9  3  Acetyltransf_6  Acetyltransferase (GNAT) domain
    5.1e-06   25.6   0.0    0.00058   18.9   0.0    2.1  2  FemAB           FemAB family


Domain annotation for each model (and alignments):
>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.61   5.5e+03      49      67 ..      26      40 ..      10      65 .. 0.48
   2 ?   -3.1   0.1      0.88   7.8e+03      49      62 ..     101     114 ..      95     133 .. 0.61
   3 !   69.1   0.1   4.8e-23   4.3e-19       5     141 ..     169     305 ..     165     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.61
                    Acetyltransf_6 49 fadpltraflrdllaalaa 67
                                       ++p++ra     + +l a
  gi|336254462|ref|YP_004597569.1| 26 GTNPFFRA----EALRLQA 40
                                      33333333....3333322 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.88
                    Acetyltransf_6  49 fadpltraflrdll 62 
                                       +ad++t++fl+ ++
  gi|336254462|ref|YP_004597569.1| 101 KADQRTQRFLEGAI 114
                                       34445555554444 PP

  == domain 3  score: 69.1 bits;  conditional E-value: 4.8e-23
                    Acetyltransf_6   5 knlrrkrrkleelgevrfrvat.dpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrldg 80 
                                        + r+  r+++e     ++v++ d++d+e+++e ++++++ + + f  +l+ +f+r+++a l ++g++r yv r+dg
  gi|336254462|ref|YP_004597569.1| 169 SDARQNVRNADEDA---YVVEEgDADDIERIVEKVAQRYESQGRSF--HLNPDFVRSAYAVL-PEGSVRPYVCRVDG 239
                                       56677888888863...5555439999***************5555..8999*********9.9************* PP

                    Acetyltransf_6  81 rpvAvalglrsgdrlyywlggydpela.klspgllllweliedaaeeGlrrfdlgggd....eeyK 141
                                       ++++++l+++s+++ y w+gg+ p+ + +l +++ll w +++d  + Gl+r+dl+g+     ++yK
  gi|336254462|ref|YP_004597569.1| 240 EFLGGILVVESDTTRYRWQGGVKPDVDvDLPINDLLDWTVMRDGLRAGLERYDLVGAGvpsiNRYK 305
                                       **************************88**************************985322225676 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   6.4e-08   0.00058     147     197 ..     145     194 ..     138     212 .. 0.85
   2 !    4.6   0.0    0.0013        12     309     381 ..     244     312 ..     238     316 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.4e-08
                             FemAB 147 nvqprwqlvldleeiteedllksfskktrknikkakkkGvkvrrltreeld 197
                                       +v+p +++v+dle+ +eedll+ fs+++r+n+++a +    v+++  ++++
  gi|336254462|ref|YP_004597569.1| 145 TVKPGYTYVVDLEG-SEEDLLNRFSSDARQNVRNADEDAYVVEEGDADDIE 194
                                       589***********.9999*****************999999888877765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0013
                             FemAB 309 aalflcfdqevvylysGsdekfr.kfyapyllqweaiqeAlergieryNfyGiegkfdgsdGvlrFKtgFngfv 381
                                       ++l++++d++ +   +G +++   ++    ll w+++++ l  g+ery++ G          + r+K +Fn+  
  gi|336254462|ref|YP_004597569.1| 244 GILVVESDTTRYRWQGGVKPDVDvDLPINDLLDWTVMRDGLRAGLERYDLVGAG-V----PSINRYKAKFNPRL 312
                                       566666666666666666666542444456899******************953.2....23468888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2451.41
//
Query:       gi|336254463|ref|YP_004597570.1|  [L=427]
Description: hypothetical protein Halxa_3077 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.003   17.7   0.3     0.0059   16.8   0.3    1.4  1  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 !   16.8   0.3   3.3e-07    0.0059       1      78 [.     330     407 ..     330     409 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.3e-07
                             bPH_2   1 yrattytitdrr.vvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeel 76 
                                       y+a ty+i+dr  ++  + + +r+ +++  + + +v+++ +  +rrl ++t++i+  + +r  v++p +   da+++
  gi|336254463|ref|YP_004597570.1| 330 YWAITYRIDDRGnLLASGRLSGRTHRVVDGDGVSTVDVVVTRTDRRLETTTVRIDPVDAER-TVRIPCLADRDARAV 405
                                       78999******9899999999***************************************7.899999999999988 PP

                             bPH_2  77 ae 78 
                                       +e
  gi|336254463|ref|YP_004597570.1| 406 LE 407
                                       75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3222.62
//
Query:       gi|336254464|ref|YP_004597571.1|  [L=96]
Description: hypothetical protein Halxa_3078 [Halopiger xanaduensis SH-6]
Scores for 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   20.9   0.0    0.00034   20.5   0.0    1.2  1  MarR         MarR family
    0.00049   19.9   0.1    0.00065   19.5   0.1    1.3  1  MarR_2       MarR family
     0.0022   17.5   0.0     0.0034   16.9   0.0    1.3  1  HTH_24       Winged helix-turn-helix DNA-binding
     0.0065   16.3   0.0     0.0079   16.0   0.0    1.1  1  TFIIE_alpha  TFIIE alpha subunit
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.013   15.4   0.0    1.2  1  HTH_Crp_2    Crp-like helix-turn-helix domain
      0.013   15.6   0.0       0.02   15.0   0.0    1.3  1  HTH_20       Helix-turn-helix domain
      0.026   14.5   0.0       0.49   10.4   0.0    2.1  1  HTH_36       Helix-turn-helix domain
      0.042   13.7   0.1      0.058   13.3   0.1    1.3  1  TrmB         Sugar-specific transcriptional regulator TrmB
       0.09   12.9   0.0       0.17   12.1   0.0    1.4  1  HTH_28       Helix-turn-helix domain
       0.12   12.6   0.0       0.16   12.1   0.0    1.2  1  DUF2582      Winged helix-turn-helix domain (DUF2582)
       0.16   11.4   0.0       0.17   11.3   0.0    1.1  1  RecA         recA bacterial DNA recombination protein


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 !   20.5   0.0   2.1e-07   0.00034      12      58 ..      43      89 ..      38      90 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.1e-07
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                      l+++g++++ e+a  + + + tv  +l +Le+++ i ++ + eD R+
  gi|336254464|ref|YP_004597571.1| 43 LEYEGAMTQEEIAAESRLCSRTVRYALGKLEDAECIASRVCLEDARQ 89
                                      7899*****************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1     4e-07   0.00065      17      62 .]      45      89 ..      28      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4e-07
                                      TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                            MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkRa 62
                                       +g  +t+ e+a++ +l   +v ++l +L++a  +  r ++eD+R+
  gi|336254464|ref|YP_004597571.1| 45 YEGA-MTQEEIAAESRLCSRTVRYALGKLEDAECIASRVCLEDARQ 89
                                      3443.9**************************************95 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 !   16.9   0.0   2.1e-06    0.0034       9      47 ..      40      78 ..      35      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.1e-06
                            HTH_24  9 LelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +++L+ ++ ++q e+A ++ l + tv++ l +Le+++ I
  gi|336254464|ref|YP_004597571.1| 40 YKVLEYEGAMTQEEIAAESRLCSRTVRYALGKLEDAECI 78
                                      678999999**************************9876 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.8e-06    0.0079      14      65 ..      35      86 ..      29      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.8e-06
                                      HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEET CS
                       TFIIE_alpha 14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrde 65
                                      +a+lv +vL  +g +t e++a e ++    +r +L +L +a  +  +   ++
  gi|336254464|ref|YP_004597571.1| 35 SAKLVYKVLEYEGAMTQEEIAAESRLCSRTVRYALGKLEDAECIASRVCLED 86
                                      678999***********************************99987766655 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 ?   15.4   0.0   8.1e-06     0.013      21      57 ..      48      82 ..      30      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.1e-06
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrri 57
                                       +tqee+A+   l   tv  +l++L+++ +i  +  +
  gi|336254464|ref|YP_004597571.1| 48 AMTQEEIAAESRLCSRTVRYALGKLEDAECIASR--V 82
                                      69*****************************943..4 PP

>> HTH_20  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   1.2e-05      0.02      15      56 ..      39      80 ..      34      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +++ L  ++++t +e+a++ +l   t++y L +Le+a+ + +
  gi|336254464|ref|YP_004597571.1| 39 VYKVLEYEGAMTQEEIAAESRLCSRTVRYALGKLEDAECIAS 80
                                      67788999*****************************87765 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0003      0.49       2      52 ..      31      75 ..      30      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                            HTH_36  2 rLspsaklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeql 52
                                      +L+psakl++  l  +   +     +qe +a+ + l  +Tv+ a+ +Le++
  gi|336254464|ref|YP_004597571.1| 31 ELPPSAKLVYKVL-EYE--GAM---TQEEIAAESRLCSRTVRYALGKLEDA 75
                                      5777777777766.344..455...89*********************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   3.6e-05     0.058      13      53 ..      39      79 ..      32      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      vY++L  +g +t +eia e+ +   +v  +L +Led+  + 
  gi|336254464|ref|YP_004597571.1| 39 VYKVLEYEGAMTQEEIAAESRLCSRTVRYALGKLEDAECIA 79
                                      899999******************************98876 PP

>> HTH_28  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    0.0001      0.17      13      37 ..      49      73 ..      42      80 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                            HTH_28 13 hsvreaArelgisrrtvyrWikrye 37
                                      +++ e+A+e  +++rtv+  + ++e
  gi|336254464|ref|YP_004597571.1| 49 MTQEEIAAESRLCSRTVRYALGKLE 73
                                      59***************77666655 PP

>> DUF2582  Winged helix-turn-helix domain (DUF2582)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0001      0.16      12      46 ..      38      72 ..      34      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                      HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHH CS
                           DUF2582 12 kvwhlLnengeislkelkrktglsdkelalAiGWL 46
                                       v+++L+ +g ++ +e++ ++ l ++ +  A+G L
  gi|336254464|ref|YP_004597571.1| 38 LVYKVLEYEGAMTQEEIAAESRLCSRTVRYALGKL 72
                                      69******************************965 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0001      0.17     143     183 ..      38      79 ..      16      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                                       ---ST.T-----------HHHHHHHHHHHHHHHHHTTT--EE CS
                              RecA 143 lvpka.eieGemgdskvglqarlmsqalrkltgaisksntvv 183
                                       lv k  e eG m++++++ ++rl s+++r   g+++ +++++
  gi|336254464|ref|YP_004597571.1|  38 LVYKVlEYEGAMTQEEIAAESRLCSRTVRYALGKLEDAECIA 79 
                                       44442388****************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 729.04
//
Query:       gi|336254465|ref|YP_004597572.1|  [L=447]
Description: phosphoglucosamine mutase [Halopiger xanaduensis SH-6]
Scores for 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  114.8   0.0    5.9e-33  113.5   0.0    1.7  1  PGM_PMM_I       Phosphoglucomutase/phosphomannomutase, alpha/
    8.3e-22   77.5   0.0    1.6e-21   76.7   0.0    1.5  1  PGM_PMM_III     Phosphoglucomutase/phosphomannomutase, alpha/
    2.9e-21   76.0   2.1    8.3e-21   74.6   0.2    2.5  3  PGM_PMM_II      Phosphoglucomutase/phosphomannomutase, alpha/
    2.6e-14   53.1   1.1      1e-13   51.2   1.1    2.0  1  PGM_PMM_IV      Phosphoglucomutase/phosphomannomutase, C-term
  ------ inclusion threshold ------
      0.089   13.4   0.0       0.26   12.0   0.0    1.8  1  Asp_protease_2  Aspartyl protease
      0.093   12.9   0.3       0.31   11.2   0.3    1.9  1  CinA_KH         Damage-inducible protein CinA KH domain
        1.4    8.8   5.6         32    4.4   0.0    3.7  4  UPF0146         Uncharacterised protein family (UPF0146)


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 !  113.5   0.0   2.3e-36   5.9e-33       4     135 ..       2     127 ..       1     129 [. 0.95

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 2.3e-36
                                       BBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HH CS
                         PGM_PMM_I   4 fgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptP 80 
                                       fgtsG+Rg vg +e+t+ l++ +g+a+a+         +vvvGrD R s++ l +a+a+gl + G++v+ +g+ +tP
  gi|336254465|ref|YP_004597572.1|   2 FGTSGIRGTVG-TEVTAGLALDVGRAVASEGY-----DTVVVGRDVRESGELLVDAVASGLRECGADVLEVGIESTP 72 
                                       9**********.779**********9997665.....58************************************** PP

                                       HHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT- CS
                         PGM_PMM_I  81 avsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekee 135
                                        v+ +i++++adagi++taSHnp+ +ng+K+ +++G  + pe+ e+Ie+++++ +
  gi|336254465|ref|YP_004597572.1|  73 TVARSIEHFGADAGIVVTASHNPAPDNGLKLWNPSGKAFGPEQREAIERRLREDD 127
                                       *************************************************998765 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 !   76.7   0.0   6.1e-25   1.6e-21       2     114 .]     248     354 ..     247     354 .. 0.92

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 6.1e-25
                                       HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETT CS
                       PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifld 78 
                                        d+llal+a++++     ++  v+++v tsla+ +++++ g++l +tkvGd yv+e+  e g+v+GgE Sg +i +d
  gi|336254465|ref|YP_004597572.1| 248 KDALLALFAREAAG---DGD-RVAAPVDTSLAVADALADVGATLTRTKVGDVYVAERTTEDGVVFGGEPSGAWIWPD 320
                                       6999******8855...345.5******************************************************* PP

                                       TBSS--HHHHHHHHHHHHHHHTS-HHHHHHHHHHHH CS
                       PGM_PMM_III  79 eattkDGilaallvleilaetgkslselleellkky 114
                                       e+++ DG laa++++e++a++g +lsel+   +++y
  gi|336254465|ref|YP_004597572.1| 321 ETRCPDGPLAAAKLVELVADRG-PLSELA-GAIERY 354
                                       ********************98.****99.666665 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 ?   -0.3   0.0      0.67   1.7e+03      38      87 ..      76     132 ..      69     133 .. 0.70
   2 !   74.6   0.2   3.2e-24   8.3e-21       6     103 .]     152     243 ..     147     243 .. 0.89
   3 ?   -3.6   0.2         7   1.8e+04      91      98 ..     261     268 ..     261     269 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.67
                                       HHHHHTT-...EEEES-----TT-TTSS----T....T-TTTTHHHHGGGGG-SEEE CS
                        PGM_PMM_II  38 ellkelgv...dvvelnaepdpdfptkapnpee....kealkllielvkkegadlgl 87 
                                       + ++++g+   +vv+  ++p pd + k  np      +e+ +++ +  +++++dlg+
  gi|336254465|ref|YP_004597572.1|  76 RSIEHFGAdagIVVTASHNPAPDNGLKLWNPSGkafgPEQREAIERRLREDDYDLGA 132
                                       556677777777888888888888887777776556666677777778888888876 PP

  == domain 2  score: 74.6 bits;  conditional E-value: 3.2e-24
                                       HGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG CS
                        PGM_PMM_II   6 alkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkeg 82 
                                       a++++vd     +s  +v++d ++Gag +i+ e+l +lg++v +ln ++d++fp++ ++p+e e+l+ l++lv +++
  gi|336254465|ref|YP_004597572.1| 152 AIEAAVD----LESTPSVIVDLGNGAG-TITAEVLADLGCHVRTLNGQQDGSFPGRPSEPNE-ETLETLAALVAETD 222
                                       4555555....3334569*******87.6999******************************.************** PP

                                       -SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  83 adlglafDgDaDRlgvvderG 103
                                       adlg+a+DgDaDR+++vde G
  gi|336254465|ref|YP_004597572.1| 223 ADLGIAHDGDADRMMAVDETG 243
                                       ******************987 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 7
                                       TTS-BEEE CS
                        PGM_PMM_II  91 gDaDRlgv 98 
                                       gD+DR+++
  gi|336254465|ref|YP_004597572.1| 261 GDGDRVAA 268
                                       8****985 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 !   51.2   1.1     4e-17     1e-13       5      72 ..     362     432 ..     359     434 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 4e-17
                                       CHCC-TT......EECCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHHH CS
                        PGM_PMM_IV   5 rveekak....vvaalaallkvasikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevael 72 
                                       +v++ka+    v +++ +++++ ++ +g+++ + dG++l +R+SGT+pl+rv +Ea++ ++++r+ ee +el
  gi|336254465|ref|YP_004597572.1| 362 EVDDKAAvmdaVRTRVSDRYDDVDTLDGVRVETDDGWFL-LRASGTQPLVRVTAEARDADAAERVFEEAREL 432
                                       66666553334667777777777****************.***************************99886 PP

>> Asp_protease_2  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001      0.26      10      61 ..     163     214 ..     153     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                    Asp_protease_2  10 vrfllDTGasttlispelaeklglkvreseltvrvsgaggevkarlvrldsl 61 
                                        ++++D G ++ +i+ e+ ++lg +vr++++++ +s  g  ++  + +l++l
  gi|336254465|ref|YP_004597572.1| 163 PSVIVDLGNGAGTITAEVLADLGCHVRTLNGQQDGSFPGRPSEPNEETLETL 214
                                       579**********************************999988877777665 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00012      0.31      35      67 ..     405     437 ..     401     440 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                       TTEEEEEEE...EEHHHHHHHHH....HHHHHT CS
                           CinA_KH  35 egevtvRltakaaneeeaealiapveeeirerl 67 
                                         +  vR+ta+a+++++ae++ +++ e + ++l
  gi|336254465|ref|YP_004597572.1| 405 GTQPLVRVTAEARDADAAERVFEEARELVGDAL 437
                                       55667******************8887776665 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3     0.039     1e+02      18      47 ..      13      44 ..       7      58 .. 0.76
   2 ?    4.4   0.0     0.012        32      14      38 ..      59      84 ..      48     101 .. 0.80
   3 ?    1.6   0.0     0.095   2.4e+02      11      39 ..     160     188 ..     151     194 .. 0.85
   4 ?   -1.3   0.1      0.73   1.9e+03      24      47 ..     272     295 ..     254     306 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.039
                                      EEET-TT--HHHHHHHHHS-EEEEE..-SS-S CS
                           UPF0146 18 vEvGiGrkldvaealakrgvdlvat..Dikek 47
                                       Ev +G  ldv +a+a  g d v++  D++e+
  gi|336254465|ref|YP_004597572.1| 13 TEVTAGLALDVGRAVASEGYDTVVVgrDVRES 44
                                      599****************8866542266655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.012
                                      SS.EEEEET-TT--HHHHHHHHHS-E CS
                           UPF0146 14 rg.kvvEvGiGrkldvaealakrgvd 38
                                      +g  v EvGi   + va+ + + g d
  gi|336254465|ref|YP_004597572.1| 59 CGaDVLEVGIESTPTVARSIEHFGAD 84
                                      555799**************999866 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.095
                                       HS-SSEEEEET-TT--HHHHHHHHHS-EE CS
                           UPF0146  11 enargkvvEvGiGrkldvaealakrgvdl 39 
                                       e++++ +v++G G+ +  ae la  g+ +
  gi|336254465|ref|YP_004597572.1| 160 ESTPSVIVDLGNGAGTITAEVLADLGCHV 188
                                       678889******************99987 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.73
                                       T--HHHHHHHHHS-EEEEE-SS-S CS
                           UPF0146  24 rkldvaealakrgvdlvatDikek 47 
                                       + l+va+ala  g  l+ t + + 
  gi|336254465|ref|YP_004597572.1| 272 TSLAVADALADVGATLTRTKVGDV 295
                                       556788888888887777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3416.97
//
Query:       gi|336254466|ref|YP_004597573.1|  [L=69]
Description: hypothetical protein Halxa_3080 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0092   15.9   1.6       0.34   10.9   0.1    2.3  2  DUF1610         Domain of unknown function (DUF1610)
  ------ inclusion threshold ------
      0.018   15.1   2.7      0.073   13.2   2.4    1.9  2  Zn-ribbon_8     Zinc ribbon domain
      0.034   13.5   0.9      0.043   13.2   0.1    1.6  2  Vps36-NZF-N     Vacuolar protein sorting 36 NZF-N zinc-finger
      0.038   13.5   1.1        0.3   10.7   0.0    2.1  2  RecR            RecR protein
       0.05   13.9   0.2      0.063   13.6   0.2    1.1  1  DUF3268         zinc-finger-containing domain
      0.054   13.4   0.2      0.059   13.2   0.2    1.0  1  FdhE            Protein involved in formate dehydrogenase for
      0.075   13.3   1.3        5.8    7.3   0.1    2.2  2  zinc_ribbon_9   zinc-ribbon
      0.085   12.8   5.1       0.35   10.8   0.4    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.093   12.8   2.6       0.19   11.8   2.6    1.6  1  DZR             Double zinc ribbon
       0.11   12.8   3.6        0.7   10.2   0.2    2.1  2  zf-LITAF-like   LITAF-like zinc ribbon domain
       0.12   12.1   2.6        1.4    8.8   0.3    2.2  2  zinc_ribbon_2   zinc-ribbon domain
       0.14   11.7   2.7       0.57    9.7   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain


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 ?    4.3   0.1     0.026        39      10      24 .]      15      29 ..      11      29 .. 0.78
   2 !   10.9   0.1   0.00023      0.34      11      22 ..      41      52 ..      37      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.026
                           DUF1610 10 prEravvFpCPNCGE 24
                                       rE+ ++  C NCG+
  gi|336254466|ref|YP_004597573.1| 15 SREHTSAPRCVNCGN 29
                                      57888888899**97 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00023
                           DUF1610 11 rEravvFpCPNC 22
                                       +r vv++CP C
  gi|336254466|ref|YP_004597573.1| 41 DNRDVVHACPDC 52
                                      5788******** PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00056      0.83      22      40 .]      17      35 ..       6      35 .. 0.70
   2 ?   13.2   2.4   4.9e-05     0.073       7      34 ..      23      54 ..      22      59 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00056
                       Zn-ribbon_8 22 sdapltaCPeCgsevrrvi 40
                                         + + C +Cg +v+r++
  gi|336254466|ref|YP_004597573.1| 17 EHTSAPRCVNCGNQVTRQF 35
                                      3444566********9986 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.9e-05
                       Zn-ribbon_8  7 rCeeCghefe.vlqsis.dap.lta.CPeCgs 34
                                      rC +Cg++ + ++++++ d+   ++ CP+C  
  gi|336254466|ref|YP_004597573.1| 23 RCVNCGNQVTrQFARVFgDNRdVVHaCPDCAT 54
                                      8*********9666666655525558****64 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 ?   13.2   0.1   2.9e-05     0.043      27      45 ..      12      33 ..       2      39 .. 0.77
   2 ?   -0.7   0.0      0.64   9.6e+02      30      39 ..      43      52 ..      29      60 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                       Vps36-NZF-N 27 p...nastplPpClaCGvkpdl 45
                                      p   +++t  P C++CG + ++
  gi|336254466|ref|YP_004597573.1| 12 PmtsREHTSAPRCVNCGNQVTR 33
                                      2444899**********76665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.64
                       Vps36-NZF-N 30 stplPpClaC 39
                                      ++ +  C  C
  gi|336254466|ref|YP_004597573.1| 43 RDVVHACPDC 52
                                      3333344444 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4      0.14   2.1e+02      18      24 ..      23      29 ..      18      30 .. 0.85
   2 ?   10.7   0.0    0.0002       0.3       3      27 ..      33      57 ..      31      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.14
                                      E-TTT-- CS
                              RecR 18 hCsrCgn 24
                                      +C +Cgn
  gi|336254466|ref|YP_004597573.1| 23 RCVNCGN 29
                                      699**99 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0002
                                      HHHHHHHHHHHHH-EE-TTT--EES CS
                              RecR  3 eeLaeaLqeakekvrhCsrCgnlte 27
                                      +++a+   + ++ v+ C+ C ++ e
  gi|336254466|ref|YP_004597573.1| 33 RQFARVFGDNRDVVHACPDCATYRE 57
                                      8999*****************9977 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   4.2e-05     0.063       2      49 ..      21      65 ..      20      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
                           DUF3268  2 ttrCpyCGekvilvsaseiYkerskgkllylCpkCdayvgvhkgtkip 49
                                      + rC  CG++v+ +  + ++   ++ ++++ Cp+C +y  ++    ip
  gi|336254466|ref|YP_004597573.1| 21 APRCVNCGNQVTRQF-ARVF--GDNRDVVHACPDCATYREMKTSDFIP 65
                                      579******987655.5677..3455689*********9988776665 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2     4e-05     0.059     205     248 ..      18      60 ..      14      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4e-05
                                       E--TTS-TTT---SS-EEE------C-EEEEEETTTTEEEEEEE CS
                              FdhE 205 hvvRvkCsnCeetkelaylsledekaavkAesCdeChsYlkily 248
                                       h +  +C+nC+++   ++ ++ +++ +v   +C++C +Y+ +  
  gi|336254466|ref|YP_004597573.1|  18 HTSAPRCVNCGNQVTRQFARVFGDNRDV-VHACPDCATYREMKT 60 
                                       555669*************999999885.789*******98765 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.018        27      16      29 ..      16      29 ..      10      31 .. 0.77
   2 ?    7.3   0.1    0.0039       5.8      16      28 ..      40      53 ..      33      54 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.018
                     zinc_ribbon_9 16 pdedsdvlCPhCgg 29
                                      ++++s++ C +Cg+
  gi|336254466|ref|YP_004597573.1| 16 REHTSAPRCVNCGN 29
                                      45777778****98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0039
                     zinc_ribbon_9 16 pdedsdv.lCPhCg 28
                                       d+ + v +CP+C 
  gi|336254466|ref|YP_004597573.1| 40 GDNRDVVhACPDCA 53
                                      566677789****5 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 ?   10.8   0.4   0.00024      0.35       6      18 ..      23      35 ..      23      38 .. 0.93
   2 ?    4.1   0.5      0.03        45       5      16 ..      47      55 ..      46      57 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                    Zn_ribbon_SprT  6 rCtgCgreythhl 18
                                      rC++Cg+++t+++
  gi|336254466|ref|YP_004597573.1| 23 RCVNCGNQVTRQF 35
                                      8**********98 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.03
                    Zn_ribbon_SprT  5 YrCtgCgreyth 16
                                      + C++C    t+
  gi|336254466|ref|YP_004597573.1| 47 HACPDCA---TY 55
                                      67****9...66 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.6   0.00012      0.19      11      36 ..      20      54 ..       8      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                               DZR 11 darfCseCgtklkavaa.........edrCpsCge 36
                                      +a  C +Cg+++ ++ a          ++Cp C +
  gi|336254466|ref|YP_004597573.1| 20 SAPRCVNCGNQVTRQFArvfgdnrdvVHACPDCAT 54
                                      55679999999987777999999999999999987 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 ?    3.7   0.4     0.051        76      58      67 ..      23      32 ..      14      35 .. 0.68
   2 ?   10.2   0.2   0.00047       0.7      51      65 ..      41      55 ..      35      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.051
                     zf-LITAF-like 58 yCpnCgallg 67
                                      +C nCg+++ 
  gi|336254466|ref|YP_004597573.1| 23 RCVNCGNQVT 32
                                      4666666654 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00047
                     zf-LITAF-like 51 slkdvehyCpnCgal 65
                                      + +dv h Cp C ++
  gi|336254466|ref|YP_004597573.1| 41 DNRDVVHACPDCATY 55
                                      568*********875 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3   0.00091       1.4       1       9 [.      23      31 ..      23      33 .. 0.89
   2 ?    3.6   0.1     0.038        57       9      19 ..      42      52 ..      41      55 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00091
                     zinc_ribbon_2  1 fCpnCGael 9 
                                      +C nCG+++
  gi|336254466|ref|YP_004597573.1| 23 RCVNCGNQV 31
                                      6******97 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.038
                     zinc_ribbon_2  9 lqdnakFCpyC 19
                                      + d +  Cp C
  gi|336254466|ref|YP_004597573.1| 42 NRDVVHACPDC 52
                                      66777889988 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00038      0.57       4      13 ..      23      32 ..      21      34 .. 0.83
   2 ?    2.1   0.2     0.092   1.4e+02      18      22 ..      48      52 ..      44      54 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00038
                       zf-ribbon_3  4 rCPnCGapls 13
                                      rC nCG++++
  gi|336254466|ref|YP_004597573.1| 23 RCVNCGNQVT 32
                                      8******766 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.092
                       zf-ribbon_3 18 vCpyC 22
                                      +Cp C
  gi|336254466|ref|YP_004597573.1| 48 ACPDC 52
                                      46666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 529.11
//
Query:       gi|336254467|ref|YP_004597574.1|  [L=393]
Description: glucosamine-1-phosphate N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-37  128.4   0.0    8.3e-37  127.1   0.0    1.6  2  NTP_transferase  Nucleotidyl transferase
    3.8e-16   59.9   0.4    5.5e-16   59.3   0.4    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
    2.2e-12   46.2   9.8    0.00037   20.1   0.4    4.6  6  Hexapep          Bacterial transferase hexapeptide (six repea
     0.0017   18.2   0.0     0.0024   17.6   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0028   17.4   4.8       0.35   10.7   0.3    3.7  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
       0.04   14.2   1.5      0.085   13.2   1.5    1.5  1  Bactofilin       Polymer-forming cytoskeletal
      0.041   12.8   0.0        0.1   11.5   0.0    1.5  2  Fucokinase       L-fucokinase
       0.26    9.4   0.1       0.37    8.9   0.1    1.1  1  DUF4954          Domain of unknown function (DUF4954)


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 !  127.1   0.0   3.7e-40   8.3e-37       1     243 [.       2     221 ..       2     224 .. 0.90
   2 ?   -2.0   0.0      0.99   2.2e+03     120     156 ..     326     363 ..     312     367 .. 0.68

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 3.7e-40
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kav+L  G+GtR++PL+ +++k+++pv++  +l  +t+ +++++g +ei++v+  +++++v+++++++++ gv v++
  gi|336254467|ref|YP_004597574.1|   2 KAVVLTAGEGTRIRPLSASVPKPMLPVADR-PLAAHTVDAAVDAGADEIVLVV-GYRAETVRDYFGSEYR-GVPVSY 75 
                                       79****************************.*****************65555.5999**********95.9***** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       a+++e+ gtAdAv  a+e le  +      vL+gD l++    +a+++  e+      ++ +v+v+e+++yGv  + 
  gi|336254467|ref|YP_004597574.1|  76 AVQEEQAGTADAVNAAREHLEGPF-----AVLNGDNLYD---PAAIDRLFEACP----AVCAVEVDEPSNYGVLSTT 140
                                       ********************9665.....8*********...556666555555....578899***********99 PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       + g+++++vEKP+ ++ ++la++G Y f  ++ + l  d+  ++rge eitd+l ++++e  v   +  +    W+D
  gi|336254467|ref|YP_004597574.1| 141 D-GTITDIVEKPADPP-TNLANAGAYAFPADAREWL--DVPASERGEHEITDVLGRVIDEYAVT-PVTLE---RWMD 209
                                       8.8*************.******************9..79*******************96554.33333...4*** PP

                                       XSSHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleane 243
                                       vG +  lleane
  gi|336254467|ref|YP_004597574.1| 210 VGRPWELLEANE 221
                                       *********996 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.99
                                       HHHHHHHHTHSSTTSEEEEEEESS-.CTTSEEEEECTT CS
                   NTP_transferase 120 eeavkkaiekaakgtvtfgivpvee.ateyGvieadee 156
                                        ++v++ + ++a+++ t+   +v+   +++Gv+  d++
  gi|336254467|ref|YP_004597574.1| 326 GTTVANLRHDEADIEFTVKGDRVSTgRRKFGVVAGDDA 363
                                       56777778888877777777666652578999988865 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 !   59.3   0.4   2.4e-19   5.5e-16       1     127 [.       3     131 ..       3     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 2.4e-19
                                       EEEEEESS-TTTT..T...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHH....HHTTCTS-EEE-T CS
                      NTP_transf_3   1 aviLAGGrSsRmg..g...dKallplggkpllervldalraagvdevvvvggd..eevla....alarlgvrvvede 66 
                                       av+L +G+++R    +   +K++lp++++pl+++++da+ +ag+de+v+v+g+  e v++    ++++ +v+++++e
  gi|336254467|ref|YP_004597574.1|   3 AVVLTAGEGTRIRplSasvPKPMLPVADRPLAAHTVDAAVDAGADEIVLVVGYraETVRDyfgsEYRGVPVSYAVQE 79 
                                       79**********7441458********************************99444455522223344467777776 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeger 127
                                        +++g++ ++ aa +++  + +++vl +D   ++p++++rl++a+      +v+++  +e+
  gi|336254467|ref|YP_004597574.1|  80 -EQAGTADAVNAAREHL--EGPFAVLNGDNL-YDPAAIDRLFEAC-----PAVCAVEVDEP 131
                                       .589************9..69*********5.5**********97.....45555555555 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.1   6.9e+03       5      12 ..       9      16 ..       9      18 .. 0.62
   2 ?   -2.8   0.0       2.7   6.1e+03      11      18 ..      97     104 ..      97     105 .. 0.75
   3 !   14.5   0.3   9.4e-06     0.021      13      36 .]     238     261 ..     232     261 .. 0.92
   4 !   20.1   0.4   1.7e-07   0.00037       2      36 .]     263     297 ..     262     297 .. 0.93
   5 !   14.7   0.2   8.4e-06     0.019       3      36 .]     299     331 ..     297     331 .. 0.84
   6 ?   -1.4   0.0      0.97   2.2e+03       5      23 ..     360     378 ..     358     385 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.1
                                      ETTEEE-T CS
                           Hexapep  5 GsnvlIgp 12
                                      G+++ I+p
  gi|336254467|ref|YP_004597574.1|  9 GEGTRIRP 16
                                      56666666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                                       -TTEEEET CS
                           Hexapep  11 gpfavigg 18 
                                       gpfav+ g
  gi|336254467|ref|YP_004597574.1|  97 GPFAVLNG 104
                                       78999876 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 9.4e-06
                                       TEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  13 faviggnVkIGdnvkIgagvvigg 36 
                                        a++ g+V++ +++++ +gvvi g
  gi|336254467|ref|YP_004597574.1| 238 DAHLEGDVVVEEGATVKPGVVIEG 261
                                       79********************76 PP

  == domain 4  score: 20.1 bits;  conditional E-value: 1.7e-07
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       + I s++++gp+a+++g + I +++k+g+gv +++
  gi|336254467|ref|YP_004597574.1| 263 ALIRSGATVGPNAYVRGATLIDEGAKVGNGVEVKN 297
                                       5699***************************9975 PP

  == domain 5  score: 14.7 bits;  conditional E-value: 8.4e-06
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       v+  ++++g+ +++ g+ ++G++v  gag+++++
  gi|336254467|ref|YP_004597574.1| 299 VLSPGATVGHLSYV-GDSVLGRDVNFGAGTTVAN 331
                                       6667999*******.5555************975 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 0.97
                                       ETTEEE-TTEEEETTEEE- CS
                           Hexapep   5 GsnvlIgpfaviggnVkIG 23 
                                       G++++ g ++ + ++ k+ 
  gi|336254467|ref|YP_004597574.1| 360 GDDAKTGINTSLTPGLKLD 378
                                       8999999999999887765 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 !   17.6   0.0   1.1e-06    0.0024       2      52 ..       2      54 ..       1      93 [. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-06
                                      EEEEECTTSSCTT...-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE- CS
                              IspD  2 vvvipAAGsGkRm...kaglpKqflelkgqtllehtvdallaskavdkivvvvs 52
                                       +v+  AG+G+R+    a +pK  l +++++l +htvda+ + +a d+iv+vv 
  gi|336254467|ref|YP_004597574.1|  2 KAVVLTAGEGTRIrplSASVPKPMLPVADRPLAAHTVDAAVDAGA-DEIVLVVG 54
                                      689*********7332699**********************9665.66666654 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 !    6.1   0.1    0.0043       9.6      18      32 ..     245     259 ..     239     260 .. 0.89
   2 !   10.7   0.3   0.00016      0.35       9      30 ..     270     293 ..     267     297 .. 0.90
   3 ?   -2.4   0.0       1.9   4.2e+03      23      32 ..     297     306 ..     296     307 .. 0.78
   4 ?   -1.0   0.0      0.71   1.6e+03       5      14 ..     318     327 ..     315     329 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0043
                                       EEE-TT-EE-TT-EE CS
                         Hexapep_2  18 vslGdncvvgaGvvi 32 
                                       v ++++++v +Gvvi
  gi|336254467|ref|YP_004597574.1| 245 VVVEEGATVKPGVVI 259
                                       899***********9 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                                       EE-TT-EE.S.EEE-TT-EE-TT- CS
                         Hexapep_2   9 liGanagi.G.vslGdncvvgaGv 30 
                                        +G+na++ G + + ++++vg+Gv
  gi|336254467|ref|YP_004597574.1| 270 TVGPNAYVrGaTLIDEGAKVGNGV 293
                                       69*******98************9 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.9
                                       T-EE-TT-EE CS
                         Hexapep_2  23 ncvvgaGvvi 32 
                                       n+v+++G ++
  gi|336254467|ref|YP_004597574.1| 297 NSVLSPGATV 306
                                       8999999776 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.71
                                       -TT-EE-TT- CS
                         Hexapep_2   5 GdnCliGana 14 
                                       G ++++Ga  
  gi|336254467|ref|YP_004597574.1| 318 GRDVNFGAGT 327
                                       8889999875 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.5   3.8e-05     0.085      20      93 ..     230     306 ..     223     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.8e-05
                        Bactofilin  20 ridGkveGdieakgklvvgeggkvegnika..eevvvaGtvkG.nveaeekvelkktakveGdikaksleieegavf 93 
                                       r+dG v+ d + +g++vv+eg++v+  +      ++ +G   G n ++++   +++ akv   +++k+ ++++ga++
  gi|336254467|ref|YP_004597574.1| 230 RLDGAVSDDAHLEGDVVVEEGATVKPGVVIegPALIRSGATVGpNAYVRGATLIDEGAKVGNGVEVKNSVLSPGATV 306
                                       789999999999*************9866621557777*988879*****************************997 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.31   6.9e+02     280     318 ..     246     285 ..     244     294 .. 0.79
   2 ?   11.5   0.0   4.6e-05       0.1     271     326 ..     290     345 ..     266     350 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.31
                        Fucokinase 280 vlessvsvgegsviehsslk.gnvsigsnsivsgleless 318
                                       v+e++++v++g vie   l  ++ ++g n +v g  l  +
  gi|336254467|ref|YP_004597574.1| 246 VVEEGATVKPGVVIEGPALIrSGATVGPNAYVRGATLIDE 285
                                       6788999999999997666559999999999999887765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.6e-05
                        Fucokinase 271 kesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpd 326
                                        +++ v nSvl+++++vg  s++ +s l+ +v+ g+++ v +l+ ++ + +++++ 
  gi|336254467|ref|YP_004597574.1| 290 GNGVEVKNSVLSPGATVGHLSYVGDSVLGRDVNFGAGTTVANLRHDEADIEFTVKG 345
                                       6788899************************************9998755666665 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00016      0.37     177     259 ..     254     328 ..     227     333 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00016
                           DUF4954 177 gekvkilnaglikN.vkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavisrcfvGqav 252
                                       +  v+i+   li+  +++g+ a+++ga+ +++g          ++G+gV+++++++s G+++ + + + ++++G+ v
  gi|336254467|ref|YP_004597574.1| 254 KPGVVIEGPALIRSgATVGPNAYVRGATLIDEG---------AKVGNGVEVKNSVLSPGATVGHLSYVGDSVLGRDV 321
                                       555555555555432455555555555555444.........58899999999999999999999999999999998 PP

                           DUF4954 253 klkkqfs 259
                                       +++ + +
  gi|336254467|ref|YP_004597574.1| 322 NFGAGTT 328
                                       8876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2830.87
//
Query:       gi|336254468|ref|YP_004597575.1|  [L=603]
Description: glucosamine--fructose-6-phosphate aminotransferase [Halopiger xanaduensis SH-6]
Scores for 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-51  172.7   0.1    1.1e-24   86.8   0.6    2.6  3  SIS       SIS domain
    4.8e-22   78.6   0.2    1.6e-21   76.9   0.1    1.9  2  GATase_6  Glutamine amidotransferase domain
      4e-18   65.5   0.0      8e-18   64.5   0.0    1.5  1  GATase_7  Glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.012   14.4   0.0      0.029   13.1   0.0    1.6  2  GATase_2  Glutamine amidotransferases class-II
      0.014   14.3   0.0      0.023   13.6   0.0    1.2  1  GATase_4  Glutamine amidotransferases class-II
      0.028   14.4   0.1        2.6    8.0   0.0    2.4  2  SIS_2     SIS domain


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 ?   -3.2   0.0       2.4   7.2e+03      86      98 ..     221     233 ..     216     236 .. 0.86
   2 !   86.8   0.6   3.6e-28   1.1e-24       6     130 ..     292     414 ..     288     415 .. 0.91
   3 !   82.5   0.0   7.8e-27   2.3e-23       3     128 ..     459     583 ..     457     585 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.4
                                       EESSTTSHHHHHS CS
                               SIS  86 ITdskgsplarea 98 
                                       +Td +g+p+are 
  gi|336254468|ref|YP_004597575.1| 221 FTDLDGNPIAREP 233
                                       7999******986 PP

  == domain 2  score: 86.8 bits;  conditional E-value: 3.6e-28
                                       SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSE CS
                               SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergak 82 
                                       +++ ++++Gtsy++a++++l+l++ g+   +  +++       +++ded+lvi++++sget+d+++a+++ak+ ga 
  gi|336254468|ref|YP_004597575.1| 292 DSVQLIACGTSYHAALYGSLALNQAGVESTALLANEY-SVA-APPVDEDTLVIAVTQSGETADTLNALRQAKSEGAD 366
                                       5789******************887777666655555.455.6********************************** PP

                                       EEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                               SIS  83 iiaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                       ++++T+  gs++aread al i+a+pe++va+tk++++q ++l +la 
  gi|336254468|ref|YP_004597575.1| 367 TLTVTNVVGSTAAREADDALFIRAGPEIGVAATKTFSSQAVMLTLLAQ 414
                                       *******************************************99986 PP

  == domain 3  score: 82.5 bits;  conditional E-value: 7.8e-27
                                       CTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHT CS
                               SIS   3 akakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelaker 79 
                                        ++++ +++G+G  y++a+e+alk++ei++ ++e+ +++elkhg+lal++++++v+++ + +e  +++++ae+a+ r
  gi|336254468|ref|YP_004597575.1| 459 QDSRSYFFIGRGLGYPVALEGALKFKEITYEHAEGFASGELKHGPLALVTPETPVFAVFTGEEDEKTLKNAEEAQTR 535
                                       578899*********************************************************************** PP

                                       TSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHH CS
                               SIS  80 gakiiaITdskgsplareadlalyinaepetlvastksltaqlaaldal 128
                                       ga+++a++  ++  +++ ad +l+i++ +  l++++ ++++ql++++a+
  gi|336254468|ref|YP_004597575.1| 536 GAPVVAVC-PDDHRAVEVADAHLEIPETDPDLAGLLANVQLQLVSYYAA 583
                                       ********.77778888999**************************986 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.1   5.4e-25   1.6e-21      10     134 .]      62     192 ..      50     192 .. 0.85
   2 ?   -2.1   0.0       1.3     4e+03      82     115 ..     314     347 ..     297     362 .. 0.66

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 5.4e-25
                          GATase_6  10 vedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall..... 81 
                                        e++v+++H+R++++g +++e a+P +  ++ +++vhNG i+ny +l+e l+a kg++f s++Dtev+ +l+     
  gi|336254468|ref|YP_004597575.1|  62 LEGDVGIGHTRWSTHGPPTDENAHPHTDGTEDVAVVHNGIIENYATLKEWLQA-KGHEFTSDTDTEVIPHLIqyyld 137
                                       3557**************88888***888888*********************.****************9977766 PP

                          GATase_6  82 ....eelG.eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                           +e++  +++e l+G +a+ ++ ++e+ l  a  r g +pl+++v+++ +  as+
  gi|336254468|ref|YP_004597575.1| 138 sgldNEAAfRKAVEDLEGSYAVTAMLSDEHVLYAA--RKG-SPLVVGVEDDEFFLASD 192
                                       55544444899999********9999988888777..778.*************9996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                          GATase_6  82 eelGeevlerlrGmfafaiwdkrentlilardrl 115
                                       +++G e  + l+  +++a+   +e+tl++a  + 
  gi|336254468|ref|YP_004597575.1| 314 NQAGVESTALLANEYSVAAPPVDEDTLVIAVTQS 347
                                       5666555566666677777777777777664444 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   2.7e-21     8e-18       9     122 ..      80     197 ..      70     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 2.7e-21
                          GATase_7   9 seagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnG 76 
                                       ++++a P + + ++++++v+nG i Ny  l+e L+akgh+f++++Dtev+ +l+++         +  ++a+e l+G
  gi|336254468|ref|YP_004597575.1|  80 TDENAHPHT-DGTEDVAVVHNGIIENYATLKEWLQAKGHEFTSDTDTEVIPHLIQYyldsgldneAAFRKAVEDLEG 155
                                       456778888.68999*************************************************999********** PP

                          GATase_7  77 mfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       ++A+  + ++e+ l++aR      PL +g ++ d++++aS + a+l
  gi|336254468|ref|YP_004597575.1| 156 SYAVTAMLSDEHVLYAARK---GSPLVVGVED-DEFFLASDVPAFL 197
                                       *******************...59*******6.7*******99987 PP

>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       0.5   1.5e+03      19      49 ..      15      45 ..      10      59 .. 0.84
   2 ?   13.1   0.0   9.8e-06     0.029     198     262 ..      59     129 ..      47     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.5
                                      HHHHHHHHHGGGGS-B-TTSSSBSEEEEEEE CS
                          GATase_2 19 ekalealenleHRGavgadektGDGaGillq 49
                                      e+ l+ lenle+RG  +a     +G+Gi ++
  gi|336254468|ref|YP_004597575.1| 15 ETLLTGLENLEYRGYDSAGVAIQNGSGIDVE 45
                                      56678899*********99999999999765 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.8e-06
                                       STT--BSEEEEEE---SSSS--GGGSSS-S......SEEEEE--TTHHHHHHHHHHHCTT--BT-HH.HHH CS
                          GATase_2 198 deelesalalvHsRfstntfPsWelaqPlR......llaHnGEintlrGnknwmkareaelksellgdele 262
                                       d+ le  + + H+R+st   P+ e a+P         + HnG i      k+w +a+ +e++s++ ++ + 
  gi|336254468|ref|YP_004597575.1|  59 DDPLEGDVGIGHTRWSTHGPPTDENAHPHTdgtedvAVVHNGIIENYATLKEWLQAKGHEFTSDTDTEVIP 129
                                       55678889999*****************85444444799***********************997665554 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.7e-06     0.023      65     186 ..      59     173 ..      30     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.7e-06
                          GATase_4  65 reypiksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCel 137
                                        + p++  + + H R  t+G  ++en+hp +   + ++    HnG +++y+       ++ +e   +TD+E++   +
  gi|336254468|ref|YP_004597575.1|  59 DD-PLEGDVGIGHTRWSTHGPPTDENAHPHTD--GTEDVAVVHNGIIENYATLKewlqAKGHEFTSDTDTEVIPHLI 132
                                       44.7889999*******************987..55678888*****998876655665667777899999764333 PP

                          GATase_4 138 leelasrfekaepsaeeleralaelakeiaelGvfnlllsdgralfaha 186
                                          l+s          + e+a ++ +++++    ++ +lsd + l+a +
  gi|336254468|ref|YP_004597575.1| 133 QYYLDS--------GLDNEAAFRKAVEDLEGSYAVTAMLSDEHVLYAAR 173
                                       333333........33444555555555566666677777777777755 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00088       2.6      85     137 ..     318     371 ..     299     372 .. 0.80
   2 ?    3.8   0.0     0.017        52     119     137 ..     525     543 ..     510     544 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00088
                                       HTT-TTHHHHHHHHTT--TT-EEEE.E-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                             SIS_2  85 lerdegyakqilrlvrlkpgDvLlv.iSnsGnnavvveaaeaakergmkviAlt 137
                                       +e  + +a++++  ++   +D+L++ + +sG+ a  ++a+++ak+ g+ +  +t
  gi|336254468|ref|YP_004597575.1| 318 VESTALLANEYSVAAPPVDEDTLVIaVTQSGETADTLNALRQAKSEGADTLTVT 371
                                       66667777777777777888998872578*******************998887 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHT-EEEEEE CS
                             SIS_2 119 vveaaeaakergmkviAlt 137
                                        ++ ae+a++rg++v+A++
  gi|336254468|ref|YP_004597575.1| 525 TLKNAEEAQTRGAPVVAVC 543
                                       67889************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 4445.84
//
Query:       gi|336254469|ref|YP_004597576.1|  [L=685]
Description: sodium/hydrogen exchanger [Halopiger xanaduensis SH-6]
Scores for complete 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  156.1  50.8    1.5e-45  155.7  50.8    1.1  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
    1.7e-13   51.3   2.5    1.7e-13   51.3   2.5    2.4  2  Usp             Universal stress protein 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 !  155.7  50.8   1.6e-49   1.5e-45       3     379 ..      21     386 ..      19     388 .. 0.92

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 1.6e-49
                                       HHHHHHHHHHH.HHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHH CS
                    Na_H_Exchanger   3 llillallvgl.larrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlks 78 
                                       +++++++lvg  l++rl++p ivg +++G  +Gp  l ++++s + + +l e+gli+llF +Gleld++ +++    
  gi|336254469|ref|YP_004597576.1|  21 TVAMAVFLVGPlLVKRLGQPGIVGVVLFGAAIGPDALEFVSHS-DAIVLLGEVGLIYLLFTVGLELDMQGFKEAPEN 96 
                                       4555555555526*****************************9.********************************* PP

                                       HHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHC CS
                    Na_H_Exchanger  79 illlallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDava 155
                                       + +++l+++ +++v+ G ++ +  +lg++l +all++++++ + + ++++i+ ++g +++r    ++g  +++D +a
  gi|336254469|ref|YP_004597576.1|  97 AAIFGLTSFGLPFVV-GAAVVY-AVLGLNLWAALLLASVFA-SHTLLAYPIVNRLGVTKNRAVAAVFGGILFTDTLA 170
                                       ***************.666664.599************998.99********************************* PP

                                       CCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHT CS
                    Na_H_Exchanger 156 vvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallael 232
                                       +++la++ +++    g+ t +l + + + +v+++g +l ++ ++  r++  f+ +++ +e+l+v++ ++++a lael
  gi|336254469|ref|YP_004597576.1| 171 LIVLAIVTGAV---GGDLTPWLFARVGLSLVVLFGAALFVLPPVSRRFFQTFS-EESYFEFLFVMVAIFATASLAEL 243
                                       **********9...999999999999999999999999999999998888885.*********************** PP

                                       SXXXHHHHHHHHHHHHH.HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHH CS
                    Na_H_Exchanger 233 lgvsgilgaflaGlvls.eyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgri 308
                                       l +  ilgaf+aG++l+ + +++  l  ++e +++ +f+p+f + vG+ +d++v+  +l+ l+++++i+ ++++++ 
  gi|336254469|ref|YP_004597576.1| 244 LELAPILGAFIAGIALNrQIPEGGTLMNRIEFVGNAFFIPFFLLHVGMFVDPTVILDGLETLWIAAVITGIMFATKW 320
                                       *****************555555559999**************************999999999999999999**** PP

                                       HHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHHHHH CS
                    Na_H_Exchanger 309 lavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslkpll 379
                                       +a++l++ +  ++  e+ +i+ + +++ a ala+ ++g +lgl  ++++++++++ ++t +     l+p+l
  gi|336254469|ref|YP_004597576.1| 321 AAAWLVAAVQDYTPTERTVIFGLSTGQAAAALAITLIGYDLGLFGAAVLNAVVLMLVVTAV-----LSPWL 386
                                       ********999999999988877777***********************************.....88876 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   2.5   1.9e-17   1.7e-13       5     141 .]     411     541 ..     409     541 .. 0.91
   2 ?    1.3   0.2     0.049   4.4e+02       8      38 ..     559     589 ..     553     637 .. 0.79

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 1.9e-17
                                       EEEEE-SSHHHH.HHHHHHHHHHHH.CTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   5 IlVavDgseesk.kAlewAlelaka.rgaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                       Il+++ +  + + +++e Al    + +  ++++l+v+ p++++ + + + +a +e le+ +ae          +a++
  gi|336254469|ref|YP_004597576.1| 411 ILLPLSHDADLQrRLVELALVIKGDrSAEPIHVLTVVQPDRDDDATEREIAAVTEDLEKLAAEG--------SAAEV 479
                                       788887666666699******777768889******************************9977........5789* PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++++  ++++++a +i++ a e +ad iV+G+   ++++++++GS  ++vl+ ++ pVlv r
  gi|336254469|ref|YP_004597576.1| 480 PVETEARVNHNVASGIVQGAVEVQADQIVMGWDAARSFRHRIFGSIIDQVLEGTNRPVLVSR 541
                                       ***********************************************************965 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.049
                                       EE-SSHHHHHHHHHHHHHHHHCTSEEEEEEE CS
                               Usp   8 avDgseeskkAlewAlelakargaelillhv 38 
                                       +vD+ e   +A++   +la++ gael ++ v
  gi|336254469|ref|YP_004597576.1| 559 GVDHHEGFYEAVHLVKHLAATLGAELNVIVV 589
                                       67788888899999999********988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.38
# Mc/sec: 5442.21
//
Query:       gi|336254470|ref|YP_004597577.1|  [L=62]
Description: hypothetical protein Halxa_3084 [Halopiger xanaduensis SH-6]
Scores for 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:                      1154  (0.064365); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 540.56
//
Query:       gi|336254471|ref|YP_004597578.1|  [L=268]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-19   67.2   0.0    1.4e-18   66.4   0.0    1.4  1  HTH_10          HTH DNA binding domain
      1e-12   48.2   6.0      1e-12   48.2   6.0    2.4  2  BAT             GAF and HTH_10 associated domain
    2.7e-07   30.0   0.1    8.4e-07   28.4   0.1    1.8  1  Sigma70_r4      Sigma-70, region 4
    7.7e-07   28.6   0.0    4.4e-06   26.1   0.1    2.1  2  HTH_24          Winged helix-turn-helix DNA-binding
    2.5e-06   27.3   0.0    6.9e-06   25.9   0.0    1.8  1  MarR_2          MarR family
    3.2e-05   23.9   0.0    9.2e-05   22.4   0.0    1.7  1  HTH_3           Helix-turn-helix
    0.00035   20.3   0.2      0.001   18.9   0.2    1.8  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    0.00037   20.1   0.2     0.0016   18.1   0.2    2.0  1  Sigma70_r4_2    Sigma-70, region 4
    0.00038   20.8   1.0      0.012   15.9   0.1    3.1  3  HTH_31          Helix-turn-helix domain
    0.00089   19.3   0.0      0.002   18.2   0.0    1.5  1  Phage_CI_repr   Bacteriophage CI repressor helix-turn-helix d
     0.0033   17.3   0.0     0.0064   16.4   0.0    1.4  1  HTH_11          HTH domain
     0.0037   17.2   0.0      0.011   15.7   0.0    1.8  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.004   16.9   0.0       0.01   15.6   0.0    1.7  1  HTH_23          Homeodomain-like domain
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.035   13.7   0.0    1.5  1  HTH_50          Helix-turn-helix domain
      0.022   14.6   0.0      0.042   13.8   0.0    1.5  1  MarR            MarR family
      0.038   13.8   0.0      0.081   12.8   0.0    1.5  1  P22_Cro         DNA-binding transcriptional regulator Cro
      0.038   13.8   0.0       0.08   12.8   0.0    1.4  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.041   13.8   0.0      0.064   13.1   0.0    1.3  1  Sigma70_ECF     ECF sigma factor
      0.043   14.0   0.0      0.089   13.0   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.048   13.6   0.0      0.095   12.7   0.0    1.4  1  HTH_37          Helix-turn-helix domain
      0.048   13.9   0.0       0.13   12.6   0.0    1.7  1  KORA            TrfB plasmid transcriptional repressor
      0.048   13.5   0.0       0.12   12.3   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
      0.082   12.9   0.0        0.3   11.1   0.0    1.9  1  HTH_1           Bacterial regulatory helix-turn-helix protein
       0.12   12.4   0.0       0.28   11.2   0.0    1.6  1  HTH_36          Helix-turn-helix domain
       0.12   12.2   0.3       0.38   10.6   0.0    1.9  2  HTH_38          Helix-turn-helix domain
       0.12   12.6   0.0       0.22   11.8   0.0    1.3  1  UPF0122         Putative helix-turn-helix protein, YlxM / p13
       0.13   12.0   0.0       0.38   10.6   0.0    1.8  1  LacI            Bacterial regulatory proteins, lacI family
       0.15   12.2   0.0       0.31   11.1   0.0    1.6  1  HTH_22          HTH domain
        0.2   11.7   0.0       0.74    9.9   0.0    2.0  1  HTH_19          Helix-turn-helix domain


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 !   66.4   0.0   2.3e-21   1.4e-18       1      51 [.     210     260 ..     210     262 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 2.3e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskl 51 
                                       LT+kq e l++A+e GYFd+PR ++ +eLA++lG+sks++s++Lr+a+  l
  gi|336254471|ref|YP_004597578.1| 210 LTEKQQELLAVAHEEGYFDVPRGISQDELADRLGVSKSAVSQRLRRAIGEL 260
                                       9**********************************************9877 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   2.5      0.28   1.7e+02      49      89 ..      31      68 ..       4      71 .. 0.65
   2 !   48.2   6.0   1.7e-15     1e-12       8     137 ..      61     193 ..      57     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.28
                               BAT 49 gadpeevrdaaedldavedvrvvseeddgtlleltvsgpsl 89
                                      ++d+e+ +daa+   +ve   v se d+g++ +l+++  +l
  gi|336254471|ref|YP_004597578.1| 31 ETDAEAPTDAAA---DVERTGVRSEADGGIVAQLRLDHADL 68
                                      223344444444...67777788888888888888876665 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 1.7e-15
                               BAT   8 leirdeddvlv.alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtllelt 83 
                                       l+++ +d++l  +l +++d +ve e  ++ +++++ vf+tv ga+ +++++a+e+ ++ +d  +v+++ d+ +++++
  gi|336254471|ref|YP_004597578.1|  61 LRLDHADLFLRpTLRRATDVTVEPEYWTSVENDRTFVFLTVYGAEFDAFEAALEADPTAADPVLVDRYTDRRVYRIA 137
                                       566777777777999************************************************************** PP

                               BAT  84 vsgpsl..astlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdve 137
                                       v++ +l  +++ a+ Gg++ +++  ++++ + +++P++ d+ s+ e++++r  + +
  gi|336254471|ref|YP_004597578.1| 138 VADRTLtfVERTAAVGGRLLEMTSCRDGWCVQLRFPSRDDLVSFNEYCRDRGISLT 193
                                       *987653378****************************************976665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.1   1.4e-09   8.4e-07       4      48 ..     209     260 ..     207     261 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.4e-09
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                        L+e+++e l            +g ++ E+++rlg+S+++V+q+++rA+  L
  gi|336254471|ref|YP_004597578.1| 209 ALTEKQQELLAVAHeegyfdvPRGISQDELADRLGVSKSAVSQRLRRAIGEL 260
                                       5899999999999988888888999***********************9765 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 ?   -0.7   0.0       1.7   1.1e+03       3      21 ..     128     146 ..     126     147 .. 0.82
   2 !   26.1   0.1   7.1e-09   4.4e-06      17      40 ..     232     255 ..     230     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.7
                            HTH_24   3 etdrkILelLqknprisqr 21 
                                       +tdr+++++  ++  ++  
  gi|336254471|ref|YP_004597578.1| 128 YTDRRVYRIAVADRTLTFV 146
                                       79******99999888865 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 7.1e-09
                            HTH_24  17 risqreLAerlglSpstvnrrlkr 40 
                                       +isq eLA+rlg+S+s+v++rl+r
  gi|336254471|ref|YP_004597578.1| 232 GISQDELADRLGVSKSAVSQRLRR 255
                                       6**********************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.1e-08   6.9e-06      11      45 ..     217     256 ..     215     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.1e-08
                                       HHHHHCTTTS.....EEEHHHHHHHHTSSHHHHHHHHHHH CS
                            MarR_2  11 LaaLgrrpgr.....dltvgelarrlglsksavsrilkrL 45 
                                       L+a+++++g+      +++ ela+rlg+sksavs++l+r+
  gi|336254471|ref|YP_004597578.1| 217 LLAVAHEEGYfdvprGISQDELADRLGVSKSAVSQRLRRA 256
                                       67788888888776667*********************98 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.5e-07   9.2e-05       8      29 ..     231     252 ..     229     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.5e-07
                                       TTHHHHHHHHHHTSSHHHHHHH CS
                             HTH_3   8 lglsqeeLAeklGvsrstisri 29 
                                       +g+sq eLA++lGvs+s++s+ 
  gi|336254471|ref|YP_004597578.1| 231 RGISQDELADRLGVSKSAVSQR 252
                                       8*******************85 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 !   18.9   0.2   1.6e-06     0.001      18      40 ..     233     255 ..     232     256 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.6e-06
                     HTH_AsnC-type  18 isyaeLAervGlSestvlrRvrr 40 
                                       is  eLA+r+G+S s+v +R+rr
  gi|336254471|ref|YP_004597578.1| 233 ISQDELADRLGVSKSAVSQRLRR 255
                                       6889******************9 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 !   18.1   0.2   2.5e-06    0.0016      26      51 ..     232     257 ..     207     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.5e-06
                                       ---HHHHHHHHT--HHHHHHHHHHHH CS
                      Sigma70_r4_2  26 glsykEIAellgisegtVksrlsRAr 51 
                                       g s++E A +lg+s ++V +rl+RA 
  gi|336254471|ref|YP_004597578.1| 232 GISQDELADRLGVSKSAVSQRLRRAI 257
                                       569*********************95 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.6   3.4e+03      31      50 ..      10      29 ..       9      33 .. 0.73
   2 ?    1.6   0.0      0.57   3.6e+02      23      45 ..      79     100 ..      70     122 .. 0.66
   3 !   15.9   0.1     2e-05     0.012      13      35 ..     231     253 ..     209     267 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.6
                            HTH_31 31 lsrlEqGrrgrpspavleal 50
                                      ls++E+++r+ p  ++ +a 
  gi|336254471|ref|YP_004597578.1| 10 LSDVESAARTDPDAEAADAS 29
                                      67888888877877777665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.57
                            HTH_31  23 rlgvsestlsrlEqGrrgrpspa 45 
                                        + v + +++ +E+ r   + + 
  gi|336254471|ref|YP_004597578.1|  79 DVTVEPEYWTSVENDRT-FVFLT 100
                                       45688999******998.67433 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 2e-05
                            HTH_31  13 aGLsqeevAerlgvsestlsrlE 35 
                                       +G+sq+e+A+rlgvs+s +s+  
  gi|336254471|ref|YP_004597578.1| 231 RGISQDELADRLGVSKSAVSQRL 253
                                       59****************99755 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 !   18.2   0.0   3.2e-06     0.002      13      35 ..     234     255 ..     231     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.2e-06
                                       SSCHHHHCCTT--HHHHHHHHHS CS
                     Phage_CI_repr  13 kmqkeLAdlLgiakssvstwvrR 35 
                                       + q eLAd+Lg++ks vs + rR
  gi|336254471|ref|YP_004597578.1| 234 S-QDELADRLGVSKSAVSQRLRR 255
                                       4.56****************999 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     1e-05    0.0064      16      37 ..     233     254 ..     229     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-05
                            HTH_11  16 isgeeLAeeLnvSrrtvrrdIk 37 
                                       is +eLA++L+vS+++v ++++
  gi|336254471|ref|YP_004597578.1| 233 ISQDELADRLGVSKSAVSQRLR 254
                                       99***************99876 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 !   15.7   0.0   1.8e-05     0.011       8      44 ..     218     255 ..     210     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                                       HHHHCTTTC..EEEEEHHHHHHHHHTTSSHHHHHHHHHH CS
                         HTH_Crp_2   8 lrlaeragg..eielpltqeelAsmlGltretvsrilse 44 
                                       l  a+++ g   +   ++q+elA++lG++ + vs+ l++
  gi|336254471|ref|YP_004597578.1| 218 LAVAHEE-GyfDVPRGISQDELADRLGVSKSAVSQRLRR 255
                                       4555553.33556667******************99986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-05      0.01      16      40 ..     229     255 ..     211     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                            HTH_23  16 e..GlsvreIAreLgvsrrTvyrwlkr 40 
                                       +  G+s+ e A++Lgvs++ v++ l+r
  gi|336254471|ref|YP_004597578.1| 229 VprGISQDELADRLGVSKSAVSQRLRR 255
                                       2559******************88877 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.7e-05     0.035      29      46 ..     238     255 ..     233     255 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-05
                            HTH_50  29 lAkrLGvShtaianklrk 46 
                                       lA rLGvS++a+ ++lr+
  gi|336254471|ref|YP_004597578.1| 238 LADRLGVSKSAVSQRLRR 255
                                       8***************97 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   6.8e-05     0.042      17      40 ..     232     255 ..     210     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.8e-05
                                       TEEHHHHHHHHTS-HHHHHHHHHH CS
                              MarR  17 plsvseLakklgvskstvtrvldr 40 
                                       ++s+ eLa++lgvsks+v+  l+r
  gi|336254471|ref|YP_004597578.1| 232 GISQDELADRLGVSKSAVSQRLRR 255
                                       68999**************99987 PP

>> P22_Cro  DNA-binding transcriptional regulator Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013     0.081      12      29 ..     235     252 ..     234     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                       HHHHHHHHTS-HHHHHHH CS
                           P22_Cro  12 vekvAkalgvtksAVsqW 29 
                                       +  +A  lgv+ksAVsq+
  gi|336254471|ref|YP_004597578.1| 235 QDELADRLGVSKSAVSQR 252
                                       6789*************9 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 ?   12.8   0.0   0.00013      0.08      10      29 ..     234     253 ..     232     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                    YdaS_antitoxin  10 gqkaLAealgvsqqaVsqWl 29 
                                       +q +LA++lgvs++aVsq l
  gi|336254471|ref|YP_004597578.1| 234 SQDELADRLGVSKSAVSQRL 253
                                       899**************976 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.064     118     175 ..     202     256 ..     174     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                       Sigma70_ECF 118 dspdelleLdealerllsldpeqarlvelrkleGlsveEiAeklgvskrtverrlala 175
                                       d++d +++L e  ++ll++  e        +  G s +E+A++lgvsk++v +rl+ a
  gi|336254471|ref|YP_004597578.1| 202 DQDDGVVALTEKQQELLAVAHEEG---YFDVPRGISQDELADRLGVSKSAVSQRLRRA 256
                                       555555555555555555333322...22334699******************99754 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 ?   13.0   0.0   0.00014     0.089      23      45 ..     233     255 ..     230     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                                       B-HHHHHHHHTS-HHHHHHHHHH CS
                    Fe_dep_repress  23 vktkdlaerLnvspssVsemlkk 45 
                                       +++ +la rL+vs+s Vs+ l++
  gi|336254471|ref|YP_004597578.1| 233 ISQDELADRLGVSKSAVSQRLRR 255
                                       67889**************9987 PP

>> HTH_37  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   0.00015     0.095      30      64 ..     231     265 ..     229     267 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                                       CT--HHHHHHHHT--HHHHHHHHTT--TT--HHHH CS
                            HTH_37  30 relsqseaaqllgiaqPkvsrllrgklsrfsldkL 64 
                                       r++sq e+a +lg++++ vs+ lr  + ++++++L
  gi|336254471|ref|YP_004597578.1| 231 RGISQDELADRLGVSKSAVSQRLRRAIGELCESTL 265
                                       789********************999999999998 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00021      0.13      33      57 ..     234     258 ..     231     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                              KORA  33 kqadvatelgltkqavsqavkrvwa 57 
                                       +q ++a++lg++k avsq  +r++ 
  gi|336254471|ref|YP_004597578.1| 234 SQDELADRLGVSKSAVSQRLRRAIG 258
                                       799***************9999875 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 ?   12.3   0.0   0.00019      0.12      20      37 ..     237     254 ..     235     255 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                                       HHHHHHTS-HHHHHHHHH CS
                             HTH_5  20 elaeelglsqstvShHLk 37 
                                       ela+ lg+s+s+vS+ L+
  gi|336254471|ref|YP_004597578.1| 237 ELADRLGVSKSAVSQRLR 254
                                       8**************998 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 ?   11.1   0.0   0.00048       0.3      20      36 ..     239     255 ..     238     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00048
                                       HHHHTS-HHHHHHHHHH CS
                             HTH_1  20 AeeLglsqpavsrqikr 36 
                                       A++Lg+s +avs++++r
  gi|336254471|ref|YP_004597578.1| 239 ADRLGVSKSAVSQRLRR 255
                                       89*************98 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00045      0.28      14      47 ..     217     254 ..     216     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00045
                            HTH_36  14 lasfankngg.cfp...sqetlakrlglsknTvsraik 47 
                                       l++ a ++g+   p   sq+ la rlg+sk+ vs  ++
  gi|336254471|ref|YP_004597578.1| 217 LLAVAHEEGYfDVPrgiSQDELADRLGVSKSAVSQRLR 254
                                       666777788888887779*************7765444 PP

>> HTH_38  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       5.9   3.6e+03       5      21 ..     210     226 ..     209     226 .. 0.88
   2 ?   10.6   0.0   0.00061      0.38      19      43 ..     231     255 ..     229     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.9
                            HTH_38   5 LsleeReeIerllaeGl 21 
                                       L+  + e ++  ++eG+
  gi|336254471|ref|YP_004597578.1| 210 LTEKQQELLAVAHEEGY 226
                                       89999999999999997 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00061
                            HTH_38  19 eGlslreIArrLgrspsTIsRElkR 43 
                                       +G s+ e A rLg+s+s +s  l+R
  gi|336254471|ref|YP_004597578.1| 231 RGISQDELADRLGVSKSAVSQRLRR 255
                                       689*****************99998 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00036      0.22      18      57 ..     210     256 ..     207     263 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00036
                           UPF0122  18 LTekqanylelyyadDl.......SlsEiAeefnvsrqavydnikrt 57 
                                       LTekq++ l +  ++ +       S  E+A++  vs++av++ ++r+
  gi|336254471|ref|YP_004597578.1| 210 LTEKQQELLAVAHEEGYfdvprgiSQDELADRLGVSKSAVSQRLRRA 256
                                       788888877654333222222222999*****************996 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00061      0.38       4      22 ..     237     255 ..     236     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00061
                                       HHHHHCTS-HHHHHHHCTT CS
                              LacI   4 DVArlAGVSkaTVSrvLnn 22 
                                       ++A++ GVSk++VS+ L+ 
  gi|336254471|ref|YP_004597578.1| 237 ELADRLGVSKSAVSQRLRR 255
                                       789999********99986 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00051      0.31      23      58 ..     212     249 ..     204     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00051
                            HTH_22  23 eekieivraLdekGiFllkgav..ekvAekLgiSraTv 58 
                                       e+ +e+ +  +e+G F++ + +  +++A++Lg+S+  v
  gi|336254471|ref|YP_004597578.1| 212 EKQQELLAVAHEEGYFDVPRGIsqDELADRLGVSKSAV 249
                                       67788888889*******99772257*********988 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0012      0.74      11      29 ..     231     249 ..     230     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                            HTH_19  11 lgltqeelaerlgisrski 29 
                                       +g++q+ela+rlg+s+s  
  gi|336254471|ref|YP_004597578.1| 231 RGISQDELADRLGVSKSAV 249
                                       79*************8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2047.32
//
Query:       gi|336254472|ref|YP_004597579.1|  [L=1104]
Description: PAS/PAC sensor protein [Halopiger xanaduensis SH-6]
Scores for 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  153.8  12.6    3.3e-45  153.8  12.6    5.9  6  BAT           GAF and HTH_10 associated domain
    3.2e-20   72.4  10.2    3.7e-07   30.4   0.2    4.6  3  PAS_4         PAS fold
    1.6e-17   63.0   0.0      5e-17   61.5   0.0    1.9  1  HTH_10        HTH DNA binding domain
    1.5e-13   50.7   0.0    1.7e-10   40.9   0.0    2.8  2  PAS           PAS fold
    2.1e-12   47.2   0.0    2.4e-06   27.7   0.0    3.6  3  PAS_9         PAS domain
    3.3e-12   46.1   0.3    0.00062   19.7   0.0    3.8  3  PAS_8         PAS domain
      1e-11   45.0   0.0    3.7e-10   39.9   0.0    2.6  2  PAS_3         PAS fold
    1.1e-11   45.2  16.6    6.9e-10   39.4   0.9    3.9  4  GAF_2         GAF domain
    6.1e-07   29.8   3.6     0.0073   16.7   0.1    3.4  2  GAF_3         GAF domain
    0.00011   22.8   0.2      0.001   19.7   0.0    2.6  2  GAF           GAF domain
     0.0048   16.8   0.0      0.017   15.0   0.0    2.0  1  Sigma70_ECF   ECF sigma factor
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.061   12.9   0.0    2.3  1  Sigma70_r4    Sigma-70, region 4
      0.028   14.5   0.0      0.056   13.6   0.0    1.4  1  PAS_11        PAS domain
      0.038   14.2   0.2        0.1   12.8   0.0    1.8  1  Response_reg  Response regulator receiver domain
      0.078   12.9   0.1         12    5.9   0.0    3.0  2  Stealth_CR3   Stealth protein CR3, conserved region 3
       0.13   12.2   0.0       0.32   10.9   0.0    1.7  1  HTH_5         Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   1.6      0.64   7.1e+02     103     145 ..       5      47 ..       3      57 .. 0.84
   2 ?   -0.8   4.9       1.1   1.2e+03      13      77 ..      88     155 ..      65     176 .. 0.69
   3 ?   -2.8   2.4       4.6   5.2e+03     119     139 ..     523     543 ..     473     572 .. 0.57
   4 ?   -2.3   1.3       3.3   3.7e+03      38      87 ..     638     689 ..     619     699 .. 0.65
   5 ?   -1.5   0.2       1.9   2.1e+03      39      66 ..     825     852 ..     775     862 .. 0.77
   6 !  153.8  12.6   2.9e-48   3.3e-45       1     155 [.     868    1036 ..     868    1037 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.64
                               BAT 103 aeaedgrarlvvevPpgadvRsvvealeerypdveLvarrere 145
                                       a+a+ g++  v+ v ++  + + v+al+++++++ Lv+ r + 
  gi|336254472|ref|YP_004597579.1|   5 ATATVGDVVRVLVVGDSPRIDRTVDALAAAFDSAALVRARSVA 47 
                                       57778888888889999999999*************9999875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                               BAT  13 eddvlvalaaeldcrvele....glvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       +d+++va+a+ + +  +le     +v+++d +++v ++v+ a+ ++ r aae+ ++   +r v e+ d+
  gi|336254472|ref|YP_004597579.1|  88 TDAPIVAVADGASADRALEagatDVVETDDSSAVVAARVRNAA-QRGRLAAETPETDRRARAVLEGSDA 155
                                       5666777777777766666545567888888888888888866.6666666666666667777766663 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.6
                               BAT 119 gadvR.svvealeerypdveLv 139
                                       +advR +vv++l+++  d+eL 
  gi|336254472|ref|YP_004597579.1| 523 EADVRrAVVDGLRAAA-DAELA 543
                                       2333212333333332.33333 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 3.3
                               BAT  38 dgevlvfftvdgadpeevrdaae.dldav.edvrvvseeddgtlleltvsgp 87 
                                         e+++f  +d ++p++++daa+ +ld   e +r  + + d+t+le +++ +
  gi|336254472|ref|YP_004597579.1| 638 STEPMAFEALDLDAPAALADAASlALDRLaERARARDCRRDRTRLESALARD 689
                                       4556666667777777777777765554315567777777777777666554 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 1.9
                               BAT  39 gevlvfftvdgadpeevrdaaedldave 66 
                                       g++++++t   a  e++rda ++l +v+
  gi|336254472|ref|YP_004597579.1| 825 GTLTAYATRPAAFDEDLRDACTHLASVA 852
                                       6777888888888888888888888875 PP

  == domain 6  score: 153.8 bits;  conditional E-value: 2.9e-48
                               BAT    1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseed 75  
                                        D+v eLe+ +rde+++l+a+a+ +++r++++ +vpr+ g+++v++tv++ad+e++r+++e ++ave+ r v++ed
  gi|336254472|ref|YP_004597579.1|  868 DSVAELEIVVRDESEPLSAIARGVGGRIDVRTVVPRTSGGSTVYCTVADADAETIRTTLEGISAVESFREVGDED 942 
                                        99************************************************************************* PP

                               BAT   76 dg..............tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdv 136 
                                        dg              + +e+++s++++a+tlae+Gg++rs++  d+rarlv+e+++++dvRs+v+++e+++p++
  gi|336254472|ref|YP_004597579.1|  943 DGddgddanggtggnrAPFEIRLSESTVAETLAEYGGVLRSIAPVDDRARLVIELASTVDVRSFVRTIERTHPGT 1017
                                        *9999999999**************************************************************** PP

                               BAT  137 eLvarrererpvrtrrefr 155 
                                        eL arrer+r+v  +r f+
  gi|336254472|ref|YP_004597579.1| 1018 ELAARRERDRSVPPARPFD 1036
                                        *************999997 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.2   3.3e-10   3.7e-07       1      91 [.     150     244 ..     150     257 .. 0.85
   2 !   29.0   0.2   8.8e-10   9.9e-07       1     106 [.     269     362 ..     269     365 .. 0.89
   3 !   16.4   0.6   7.4e-06    0.0083       2     105 ..     389     499 ..     388     502 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.3e-10
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll... 74 
                                       l+ + ++++ +d+dg ++ya++a ++ +g++p+el    +  l+ ++d++++++ l++v++     ++  +l+l   
  gi|336254472|ref|YP_004597579.1| 150 LEGSDALVLTVDEDGAITYASPAVESRLGYTPDELERTAFPRLVHPDDRDGVRDLLAAVAAAPFGSSERRTLRLrda 226
                                       6789999***********************************99999***************99888888888899* PP

                             PAS_4  75 pgeerhyelrl.lPlrde 91 
                                       +g++r +el++  +l d+
  gi|336254472|ref|YP_004597579.1| 227 DGRWRLVELTCaDRLADP 244
                                       *********994344343 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 8.8e-10
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       +d+lp ++++l+pd   +yaN+aa++   +++e   G  ++ llpe +++ +++ lr++++++ +++f    ++   
  gi|336254472|ref|YP_004597579.1| 269 VDRLPGPVFALGPDWELRYANPAARQ--FFDGEPRPGTLVWRLLPETVRETFSSRLREAATTGSTVRFDAAIDD--- 340
                                       689********************999..99999999*******************************9996655... PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiT 106
                                        r +e+ + P +d      g+ v++rD++
  gi|336254472|ref|YP_004597579.1| 341 -RRLEVLAAPDDD------GLTVLARDVQ 362
                                       .888888888544......7788888875 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 7.4e-06
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee....daarleralrrvle.......geepie 67 
                                       d+l d++avl  d +++ aNaa  e   a++ +l+G+ +  l+ ++    +++r ++++ r++e       +++++e
  gi|336254472|ref|YP_004597579.1| 389 DALEDGVAVLEGD-TIELANAALLE--LADATTLVGREVDALFDDDlaatVRERARSPIVRWMEpitgrleSDAAAE 462
                                       7889999999998.8*******877..9************9999999888888888888888754421111444444 PP

                             PAS_4  68 fleelll.pgeerhyelrllPlrdesGevigvlvisrDi 105
                                       + e   l  g++r++++++ Pl d++ e   +l+++rD 
  gi|336254472|ref|YP_004597579.1| 463 SSESGGLeAGDGRPVDVFVAPLPDDERE--RTLCVVRDR 499
                                       4444444***************887777..899999885 PP

>> 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   4.4e-20     5e-17       1      53 []    1043    1095 ..    1043    1095 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 4.4e-20
                            HTH_10    1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53  
                                        L+d+ql++l +Ay  G+Fd+PR+ t +e+A++lG+s++t+s hLr a+ kl+e
  gi|336254472|ref|YP_004597579.1| 1043 LSDRQLRTLEAAYYGGFFDWPRESTGEEVAETLGVSQPTFSRHLRLAQHKLFE 1095
                                        89*************************************************85 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   1.5e-13   1.7e-10       3     100 ..     146     244 ..     144     255 .. 0.87
   2 !    6.7   0.0    0.0062         7       3      69 ..     265     329 ..     263     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.5e-13
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                        ra+le +++ ++ vDedg i+y+++a e+ lG++++e+ +  + +l+h++d++  ++ l+ + +++  ++++++++
  gi|336254472|ref|YP_004597579.1| 146 ARAVLEGSDALVLTVDEDGAITYASPAVESRLGYTPDELERTAFPRLVHPDDRD-GVRDLLAAVAAAPFGSSERRTL 221
                                       589*********************************************998775.9999999999999999999999 PP

                                       EC..TTSSEEEEEEEEEEEEETT CS
                               PAS  80 kl..rdgrpihlevraspvrdag 100
                                       +l   dgr + +e++++ ++   
  gi|336254472|ref|YP_004597579.1| 222 RLrdADGRWRLVELTCADRLADP 244
                                       99889999999999987776655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0062
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTH..HHCTTSBGGGGBSTTHHHHHHHHHHHHHHHT CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsr..eevlgkslldliheeddaelaelleqlleqg 69 
                                       +ra ++ lp p+f++  d +  y+N+aa++++  ++    ++ + l + + e+    + ++l++++ +g
  gi|336254472|ref|YP_004597579.1| 265 IRAAVDRLPGPVFALGPDWELRYANPAARQFFDGEPrpGTLVWRLLPETVRET----FSSRLREAATTG 329
                                       58999**************************9655556777777777777776....777777776666 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   2.2e-09   2.4e-06       3      83 ..     155     238 ..     153     254 .. 0.90
   2 ?   -0.2   0.0         1   1.2e+03      12      40 ..     284     310 ..     275     346 .. 0.62
   3 !   14.4   0.0   3.1e-05     0.035       2     102 ..     393     499 ..     392     501 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.2e-09
                             PAS_9   3 gili.dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk....kerevevvlirknge 74 
                                       + ++ +++dg i+ya++a++  lGy+p+e+  + +  l+  +p++++ +r++l +       + +++++ l++ +g+
  gi|336254472|ref|YP_004597579.1| 155 ALVLtVDEDGAITYASPAVESRLGYTPDELERTAFPRLV--HPDDRDGVRDLLAAVAAapfgSSERRTLRLRDADGR 229
                                       5555599********************************..************************************ PP

                             PAS_9  75 tfwvlltas 83 
                                         +v+lt++
  gi|336254472|ref|YP_004597579.1| 230 WRLVELTCA 238
                                       *****9985 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1
                             PAS_9  12 rilyaNeaalrllGyspeevlgksitdlf 40 
                                       ++ yaN+aa++++   p+   g+ ++ l+
  gi|336254472|ref|YP_004597579.1| 284 ELRYANPAARQFFDGEPR--PGTLVWRLL 310
                                       4559********975543..244444444 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 3.1e-05
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.............kereve 65 
                                       dg+++   d +i+ aN a+l+l   ++  ++g+ ++ lf  d++ + ++r+  ++                 + e  
  gi|336254472|ref|YP_004597579.1| 393 DGVAVLEGD-TIELANAALLEL--ADATTLVGREVDALF--DDDLAATVRERARSPIVrwmepitgrlesdAAAESS 464
                                       677775333.599*********..78*************..444444444444444445666688875544333333 PP

                             PAS_9  66 vvlirkng....etfwvlltaspvkdddgelvgiivilrDi 102
                                              g       +v++ ++p+ dd++e ++  +++rD 
  gi|336254472|ref|YP_004597579.1| 465 ESG----GleagDGRPVDVFVAPLPDDERERTL--CVVRDR 499
                                       333....244558899*****************..****96 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   5.5e-07   0.00062       2      47 ..     145     191 ..     144     211 .. 0.78
   2 !   10.3   0.0   0.00049      0.55       4      57 ..     266     318 ..     265     330 .. 0.77
   3 !   11.6   0.1    0.0002      0.23       3      49 ..     384     424 ..     382     453 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.5e-07
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgq 47 
                                       r ra++e s+  ++ vd+++ i+++ +a +  lGy+ ++l +  + +
  gi|336254472|ref|YP_004597579.1| 145 RARAVLEGSDALVLTVDEDGAITYASPAVESRLGYTpDELERTAFPR 191
                                       99***************6666***************88877766632 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00049
                             PAS_8   4 ralfesspdgiavvdlgdrivdvNqaalell.Gysadlkgellgqllpvlrplle 57 
                                       ra+++ +p +++ +  ++ ++++N+aa +++ G +    g l+++llp+   +  
  gi|336254472|ref|YP_004597579.1| 266 RAAVDRLPGPVFALGPDWELRYANPAARQFFdGEP--RPGTLVWRLLPETVRETF 318
                                       8889999999997756679************6655..999999988777666655 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.0002
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGysadlkgellgqll 49 
                                       l++ ++++ dg+av+ +++ i  +N a lel        + l+g+ +
  gi|336254472|ref|YP_004597579.1| 384 LESTIDALEDGVAVLEGDT-IELANAALLELAD-----ATTLVGREV 424
                                       77889********999888.***********84.....444444332 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   3.3e-13   3.7e-10       2      71 ..     167     236 ..     166     241 .. 0.89
   2 ?    1.9   0.0      0.24   2.7e+02      26      72 ..    1009    1055 ..    1000    1062 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 3.3e-13
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqeal..kkgepyegeyRirrkdGeyrwvear 71 
                                       +y+s++ve  lGy+p+el+ +   +  lvhp+Dr+ vr+ l++++    g++     R+r +dG +r ve +
  gi|336254472|ref|YP_004597579.1| 167 TYASPAVESRLGYTPDELERT--AFPRLVHPDDRDGVRDLLAAVAaaPFGSSERRTLRLRDADGRWRLVELT 236
                                       79*******************..*******************88743555566778***********99876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.24
                             PAS_3   26 wldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveara 72  
                                         +++ hp     +r++ ++++   +p++ e R r  d + r +ea +
  gi|336254472|ref|YP_004597579.1| 1009 TIERTHPGTELAARRERDRSVPPARPFDAELRDRLSDRQLRTLEAAY 1055
                                        57889****************9999****************999876 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1         3   3.3e+03      38      65 ..     306     334 ..     294     378 .. 0.52
   2 ?   -1.9   0.1       3.3   3.7e+03      24      44 ..     345     373 ..     312     414 .. 0.48
   3 !   12.0   4.3   0.00018       0.2       2     138 .]     521     664 ..     520     664 .. 0.63
   4 !   39.4   0.9   6.2e-13   6.9e-10      19     137 ..     733     856 ..     723     857 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3
                                       EEEES-TTSTT-S-B---TT.HHHHHHHH CS
                             GAF_2  38 awgeaeeefgaaldrplgeg.lvgealrt 65 
                                       +w+  +e++++ ++++l+e+  +g  +r 
  gi|336254472|ref|YP_004597579.1| 306 VWRLLPETVRETFSSRLREAaTTGSTVRF 334
                                       56666666666665555333223332222 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.3
                                       EEEEE-TTS-EEEE.........EEEES-T CS
                             GAF_2  24 yillvdddgglrla.........awgeaee 44 
                                       +++ +dddg l+++         ++ge+ +
  gi|336254472|ref|YP_004597579.1| 345 VLAAPDDDG-LTVLardvqppetSAGEPAR 373
                                       333344333.33223444444432223322 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEE..............EEEES-TTSTT-S-B---TTHHHHHH CS
                             GAF_2   2 adleelldlvldelvel.gaalgyillvdddgglrla..............awgeaeeefgaaldrplgeglvgeal 63 
                                        ++ ++ ++v+d l+   +a+l+  +lvd+ ++lr a              +  ++++ f++  ++         a 
  gi|336254472|ref|YP_004597579.1| 521 ETEADVRRAVVDGLRAAaDAELAAWYLVDE-DRLRPAamttrdgrpavelpPIERDPPAFDDGDRDES------SAG 590
                                       577888899999999965899776666664.5566555554333322222222222222222222222......333 PP

                                       HHTS-EEES-.GGG-S-HHHHHHHHHTT--E..EEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  64 rtgrpvilnd.leedpdkkglpaghaglrsf..lavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       ++  p+ ++  +  d++    ++++ g+r++  lavP+  ++r v+  +  +++p af++ dl+   +la+ +++a+
  gi|336254472|ref|YP_004597579.1| 591 ASADPFAVDEpTVYDRSALEPALARSGIRAErvLAVPV--DDRAVALAT--STEPMAFEALDLDAPAALADAASLAL 663
                                       334466666644445555556678888888888*****..777777766..899999*******************9 PP

                                       H CS
                             GAF_2 138 e 138
                                       +
  gi|336254472|ref|YP_004597579.1| 664 D 664
                                       6 PP

  == domain 4  score: 39.4 bits;  conditional E-value: 6.2e-13
                                       S..EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B--...-TTHHHHHHHHTS-EEES-GGG-S-HHHHH.HHHHTT CS
                             GAF_2  19 gaalgyillvdddgg.lrlaawgeaeeefgaaldrpl...geglvgealrtgrpvilndleedpdkkglp.aghagl 90 
                                       g++l++i+   ++++ l  a+w+++++ef ++++ pl   ++ ++ + + +++p+i++dle+ +  + ++ a ++g+
  gi|336254472|ref|YP_004597579.1| 733 GVELAWIGRTAAGREtLIAATWAGRDGEFLESASLPLesdADDPAVRTATSREPTIVDDLEAVATADVHReALERGF 809
                                       47899999966554435555*********99998777885555999*************7764444444449***** PP

                                       --EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  91 rsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       r+ l+vP+ +++  +G l+ ya++p afde+ ++  + la+ ++ ai
  gi|336254472|ref|YP_004597579.1| 810 RAALSVPIEHDEFQYGTLTAYATRPAAFDEDLRDACTHLASVAGHAI 856
                                       ********88778********************************98 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.5   0.00019      0.21       9     129 .]     530     665 ..     525     665 .. 0.68
   2 !   16.7   0.1   6.5e-06    0.0073      52     127 ..     773     856 ..     736     858 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                             GAF_3   9 llkllvkllgaevgalllldedgnklqvaagwdgkpalse.sldedsalar.......ralssgevvse.......p 70 
                                       +++ l  + +ae +a++l+ded+ + +++   dg pa++   +++d ++++        a +s  ++++       +
  gi|336254472|ref|YP_004597579.1| 530 VVDGLRAAADAELAAWYLVDEDRLRPAAMTTRDGRPAVELpPIERDPPAFDdgdrdesSAGASADPFAVdeptvydR 606
                                       677788899*************5555555555999999778444555555544433333333333444434333321 PP

                             GAF_3  71 sfae.....edglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                        +a      ++g + + +lavP+ +    + v ++ st+p af a dl+   +lA+ +++a++r
  gi|336254472|ref|YP_004597579.1| 607 -SALepalaRSGIRAERVLAVPVDD----RAVALATSTEPMAFEALDLDAPAALADAASLALDR 665
                                       .222122223557778889999999....889999999***********************997 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 6.5e-06
                             GAF_3  52 edsalarralssgevvse........psfaeedglp.draalavPLvagrqviGvlalastkprafdaedlellesl 119
                                       +d+++ r+a +s+e+ ++        +++++e   +  raal vP+ + +  +G+l ++ t+p afd++ ++   +l
  gi|336254472|ref|YP_004597579.1| 773 ADDPAVRTA-TSREPTIVddleavatADVHREALERgFRAALSVPIEHDEFQYGTLTAYATRPAAFDEDLRDACTHL 848
                                       344433333.3444444423322222666666666546**********99*************************** PP

                             GAF_3 120 Arqiatai 127
                                       A++++ ai
  gi|336254472|ref|YP_004597579.1| 849 ASVAGHAI 856
                                       ****9998 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.9   2.1e+03      53     132 ..     583     662 ..     525     663 .. 0.49
   2 !   19.7   0.0     9e-07     0.001      37     129 ..     763     855 ..     708     859 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.9
                                       H....HHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTES..EEEEEEEEETTEEEEEEEEEESSSCSHHHHHHHHH CS
                               GAF  53 g....qvlatgqplvipdstpdprfaqynrrdllenmgir..sslvvPlvndgelwGllvlhnpsppftreelellq 123
                                       +     + a+ +p  +++      + + +    l++ gir   +l+vP+  d++ ++l + + p + f   +l+   
  gi|336254472|ref|YP_004597579.1| 583 DrdesSAGASADPFAVDE---PTVYDRSALEPALARSGIRaeRVLAVPV--DDRAVALATSTEPMA-FEALDLDAPA 653
                                       133345556667777773...3333333345677789999444555554..555555555555544.6666666666 PP

                                       HHHHHHHHH CS
                               GAF 124 vladqvava 132
                                       +lad +++a
  gi|336254472|ref|YP_004597579.1| 654 ALADAASLA 662
                                       666666666 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 9e-07
                                       EEEECCEEEETTSHHHHHHHHHSSSEEESTGG...TSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEES CS
                               GAF  37 pqasrwlfmkngrgicgqvlatgqplvipdst...pdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnp 110
                                       + as  l+   +++ + +++++++p +++d+    + + + +      + + g+r++l+vP+ +d+  +G+l+++ +
  gi|336254472|ref|YP_004597579.1| 763 ESASLPLESDADDP-AVRTATSREPTIVDDLEavaTADVHRE------ALERGFRAALSVPIEHDEFQYGTLTAYAT 832
                                       33333355555566.4478899*******9443334444555......4569************999********** PP

                                       SS.CS...HHHHHHHHHHHHHHH CS
                               GAF 111 sp.pf...treelellqvladqv 129
                                       +p  f   +r+++  l ++a ++
  gi|336254472|ref|YP_004597579.1| 833 RPaAFdedLRDACTHLASVAGHA 855
                                       **988777778888777777665 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.5e-05     0.017     134     181 ..    1040    1095 ..    1037    1099 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                       Sigma70_ECF  134 ls.ldpeqarlvelrkleGl.......sveEiAeklgvskrtverrlalaRawler 181 
                                         + l+++q+r +e ++  G+       + eE+Ae+lgvs+ t  r+l+la  +l +
  gi|336254472|ref|YP_004597579.1| 1040 RDrLSDRQLRTLEAAYYGGFfdwpresTGEEVAETLGVSQPTFSRHLRLAQHKLFE 1095
                                        55599**************96666665679********************999876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.4e-05     0.061       3      48 ..    1041    1093 ..    1041    1095 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.4e-05
                                        HHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4    3 asLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48  
                                        ++L++r+ + le  +        ++ T eE++e+lg+S+ + +++++ A +kL
  gi|336254472|ref|YP_004597579.1| 1041 DRLSDRQLRTLEAAYyggffdwPRESTGEEVAETLGVSQPTFSRHLRLAQHKL 1093
                                        689************99999998999***************999999999888 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     5e-05     0.056       6      80 ..     158     230 ..     154     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-05
                            PAS_11   6 trldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevi.ssngeatsslyRLrlsqdkf 80 
                                       ++ d dg I+   +     + +lg++ +el ++ + +L+hp+d+  +++ l  v     g ++  + RLr +++++
  gi|336254472|ref|YP_004597579.1| 158 LTVDEDGAITYASP---AVESRLGYTPDELERTAFPRLVHPDDRDGVRDLLAAVAaAPFGSSERRTLRLRDADGRW 230
                                       56799999999999...999*********************************99656678888889999888876 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.9e-05       0.1       1      99 [.      15     114 ..      15     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.9e-05
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSS.....EHHHHHHHHHHCTTTS CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgm.....dGlellkeireedpel 72 
                                       vl+v D+p + + +  l    +      a++ ++ale l e +v+++++  + ++      +G   l+++ ++  + 
  gi|336254472|ref|YP_004597579.1|  15 VLVVGDSPRIDRTVDALAAAFDSAALVRARSVADALERLAETDVHCLVCEFRADRAnadrgNGPSRLERLAART-DA 90 
                                       89********999999999888878999**********************998885555669********9999.99 PP

                                       EEEEEESSTSHHHHHHHHHCTESEEEE CS
                      Response_reg  73 pviiltahseeedavealkagaddfls 99 
                                       p++++    + + a +al+aga d++ 
  gi|336254472|ref|YP_004597579.1|  91 PIVAVA---DGASADRALEAGATDVVE 114
                                       **9998...445699********9985 PP

>> Stealth_CR3  Stealth protein CR3, conserved region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.06        67      16      34 ..     307     325 ..     305     364 .. 0.85
   2 ?    5.9   0.0     0.011        12      13      34 ..     422     443 ..     418     458 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.06
                       Stealth_CR3  16 errfpeelartashrFRsm 34 
                                       +r  pe +++t s+r+R++
  gi|336254472|ref|YP_004597579.1| 307 WRLLPETVRETFSSRLREA 325
                                       67789************97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
                       Stealth_CR3  13 kelerrfpeelartashrFRsm 34 
                                       +e+ + f ++la+t++ r Rs+
  gi|336254472|ref|YP_004597579.1| 422 REVDALFDDDLAATVRERARSP 443
                                       799999**************97 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 ?   10.9   0.0   0.00029      0.32      20      37 ..    1070    1087 ..    1064    1088 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                                        HHHHHHTS-HHHHHHHHH CS
                             HTH_5   20 elaeelglsqstvShHLk 37  
                                        e ae lg+sq+t S+HL+
  gi|336254472|ref|YP_004597579.1| 1070 EVAETLGVSQPTFSRHLR 1087
                                        7899*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.45
# Mc/sec: 7386.61
//
Query:       gi|336254473|ref|YP_004597580.1|  [L=139]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-33  116.1   5.3      2e-33  115.9   5.3    1.0  1  Usp              Universal stress protein family
  ------ inclusion threshold ------
      0.019   15.7   0.2      0.027   15.2   0.2    1.5  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
      0.044   13.7   0.3       0.06   13.2   0.3    1.4  1  ProQ             ProQ/FINO 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 !  115.9   5.3   3.3e-37     2e-33       1     141 []       1     137 [.       1     137 [. 0.87

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 3.3e-37
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCC.CCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavs.dadeeaeeeeleleeaeleadaakaaae 76 
                                       my+ I++a+Dgse +++A e+A+el ++ +a l++l v+++ + ++   d+++  ee e++ + +++e     + a+
  gi|336254473|ref|YP_004597580.1|   1 MYQDIMLATDGSEGARQATEHAIELTRQLEANLHILSVSEDGPHATDTrDEMRHDEEGEAVGAVEAAE-----RTAA 72 
                                       9**************************************99876655404444444444444444444.....567* PP

                                       CTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  77 aggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++g +v+ +v++g p eei+++aee+ +dl+VvG+ grsgl++l++GSv+e v+r++p+pV+vVr
  gi|336254473|ref|YP_004597580.1|  73 DAGLDVTSTVRHGVPQEEIVKAAEENPIDLVVVGTVGRSGLDQLVVGSVAEEVVRNSPVPVVVVR 137
                                       ****************************************************************8 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 ?   15.2   0.2   4.5e-06     0.027      14     106 ..      22     115 ..       5     127 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.5e-06
                                       HHHHHHHCTTTEEEEEEEE.SSTHHHHHHHH.HHHT-SEEEESSHHHHHHHHHHHHHTTSSSEEEESHHHHHHHHCH CS
                   DXP_reductoisom  14 tLdvieenpdkfevvalaa.gsnvellaeqa.kefkpklvavadeeaaeelkealkekelktevlvGeealkelaee 88 
                                       ++++ ++ + + ++ +++  g + +   + + ++ + + v   ++++ ++  + l +  ++++  v +e ++++aee
  gi|336254473|ref|YP_004597580.1|  22 AIELTRQLEANLHILSVSEdGPHATDTRDEMrHDEEGEAVGAVEAAERTAADAGL-DVTSTVRHGVPQEEIVKAAEE 97 
                                       5566666666666666665433333333333033344455444555555555555.356678888889********* PP

                                       TT-SEEEE--SSGGGHHH CS
                   DXP_reductoisom  89 eeadvvvaaivGaaGLkp 106
                                       + +d+vv + vG  GL  
  gi|336254473|ref|YP_004597580.1|  98 NPIDLVVVGTVGRSGLDQ 115
                                       ****************86 PP

>> ProQ  ProQ/FINO family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3     1e-05      0.06      70      98 ..      49      77 ..      13      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                              ProQ 70 egaaRvDLdGnpvgevteehaehAkaqlk 98
                                       +++R+D +G++vg+v+++++++A a l+
  gi|336254473|ref|YP_004597580.1| 49 RDEMRHDEEGEAVGAVEAAERTAADAGLD 77
                                      589*********************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1095.72
//
Query:       gi|336254474|ref|YP_004597581.1|  [L=52]
Description: hypothetical protein Halxa_3088 [Halopiger xanaduensis SH-6]
Scores for 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:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); 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: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 448.74
//
Query:       gi|336254475|ref|YP_004597582.1|  [L=224]
Description: cytochrome c biogenesis protein transmembrane region [Halopiger xanaduensis SH-6]
Scores for 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   33.4  15.4    5.7e-08   32.9  15.4    1.2  1  DsbD      Cytochrome C biogenesis protein transmembrane regio


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9  15.4   3.2e-12   5.7e-08       2     209 ..      14     211 ..      13     217 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.2e-12
                              DsbD   2 flaGllsflsPCilpliPaylsyisgvsvedvktekkkv.kvllkallFvlGlslvfvslglsaaflgqllkdvkev 77 
                                       + aG+ +f+sPC  pl+P y+++  + + +++ +    +  +l + ++  lG+  +f+ l  sa  +g+       +
  gi|336254475|ref|YP_004597582.1|  14 LIAGISTFFSPCAYPLLPGYVGFYVNQTEGERAS----LgGALGRGVVAGLGTLGTFAVLFGSAFWIGHATLSNIVY 86 
                                       89*******************9987666555544....447899999999999999988877777777777444444 PP

                              DsbD  78 irrvaglivillGlhflgvfkievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaaskesl 154
                                        + ++g   +l+G+ +l vf+    +  +l + +  +   svlg  ++G  +al ++ C++P++  v+a a s   +
  gi|336254475|ref|YP_004597582.1|  87 FEPLIGA--LLVGFGLLVVFD----RAPSLSVPLP-QRRSSVLGFGVFGAGYALAAAGCVAPLFVGVVAQALSLP-A 155
                                       4555555..556666677798....3333333333.333446999999999********************9999.7 PP

                              DsbD 155 akgallllvyvlGlaipfllvglllel...lkkklkslkkyskaveiaggvllvllGv 209
                                       a++a ++  yv    i++l+v+l +     l+  +  +  + k ++ ++g +++++G+
  gi|336254475|ref|YP_004597582.1| 156 ASAAAVIGTYVGS--IVVLMVSLTVATgmgLLAGAGRFVTHGKRLKRLAGAIMIVAGL 211
                                       7888888888754..44555555543311245567789999999**********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1935.36
//
Query:       gi|336254476|ref|YP_004597583.1|  [L=190]
Description: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen [Halopiger xanaduensis SH-6]
Scores for 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-13   48.8   0.0    7.3e-13   48.5   0.0    1.1  1  Redoxin        Redoxin
    1.8e-11   44.1   0.0    2.4e-11   43.6   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    2.1e-06   27.6   0.0    1.2e-05   25.2   0.0    1.9  2  Thioredoxin    Thioredoxin
    7.8e-06   26.1   0.0    1.5e-05   25.2   0.0    1.5  1  Thioredoxin_8  Thioredoxin-like
  ------ inclusion threshold ------
      0.019   15.1   0.0      0.029   14.6   0.0    1.3  1  Thioredoxin_7  Thioredoxin-like
        1.6    8.7   5.0        2.8    7.9   5.0    1.4  1  TAT_signal     TAT (twin-arginine translocation) pathway sign


Domain annotation for each model (and alignments):
>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   2.4e-16   7.3e-13      27     143 ..      68     177 ..      52     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 2.4e-16
                                       TTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH..HHHHHHHTT-TSEEEE-TTSHHHHHT CS
                           Redoxin  27 kgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf..vkefwgkeglkfpvlsDgsaaftkal 101
                                       +g+++++  +++ +c +C +++p+l++  e+ ++ +v++v v+    +     ++w++++ ++p+++D+ a++++ +
  gi|336254476|ref|YP_004597583.1|  68 PGRPTFIDLFAT-WCSPCEKQMPALAEAHEQVADADVQFVSVTNEGISHdeLAAWWDEHDGSWPIAVDPAAEVSARY 143
                                       799*********.**************************9987666666878999********************** PP

                                       T-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT.STTSH CS
                           Redoxin 102 Glrleedaseglrtpryavidedgkvvylevepepet.eesna 143
                                                   ++p+ + id+ g+v + + ++ +++  ++++
  gi|336254476|ref|YP_004597583.1| 144 LES---------GYPTAVTIDASGQVLWADDGVKSTDeLVDRI 177
                                       944.........9******************999865555555 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   7.9e-15   2.4e-11      25     122 ..      69     161 ..      62     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 7.9e-15
                                       TSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH..HHHHHHHH-H.SSEEEE-TTSHHHHHTT CS
                          AhpC-TSA  25 gkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe..shkkfiekeslnfpllsDeegkvakayg 99 
                                       g+p+ +  +++ wc +C++++pala+++e+ ++++v+ + v+ +     +++++ ++++  +p++ D+  +v+ +y 
  gi|336254476|ref|YP_004597583.1|  69 GRPTFIDLFAT-WCSPCEKQMPALAEAHEQVADADVQFVSVTNEGIShdELAAWWDEHDGSWPIAVDPAAEVSARYL 144
                                       7899999****.*******************************876666***************************8 PP

                                       -EETTTTECSCEEEEE-TTSBEE CS
                          AhpC-TSA 100 vlkeekglalratfvidkegkir 122
                                                +++++ id+ g + 
  gi|336254476|ref|YP_004597583.1| 145 ES------GYPTAVTIDASGQVL 161
                                       88......999999999999885 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0     4e-09   1.2e-05      17      57 ..      68     109 ..      59     121 .. 0.87
   2 ?   -0.1   0.0      0.31   9.3e+02      58     102 ..     133     178 ..     130     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4e-09
                                       TSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEE CS
                       Thioredoxin  17 ekklvlveFyApwCghCkalaPeleklaeelkd.kvklakvd 57 
                                       + ++ +++ +A+wC +C +  P l+++ e+++d +v+++ v 
  gi|336254476|ref|YP_004597583.1|  68 PGRPTFIDLFATWCSPCEKQMPALAEAHEQVADaDVQFVSVT 109
                                       567899**************************9999999885 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.31
                                       TTTSHHHHHHTT-SSSSEEEEEE.TTEEEEEEESS-HHHHHHHHHH CS
                       Thioredoxin  58 vdenedlakkyevegiPtlklfk.ngkevkkyegarekeklaaflk 102
                                       vd  +++ ++y  +g+Pt + +  +g+     +g ++ ++l++ ++
  gi|336254476|ref|YP_004597583.1| 133 VDPAAEVSARYLESGYPTAVTIDaSGQVLWADDGVKSTDELVDRIE 178
                                       5666777778888899997666515667778888888899988775 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   5.2e-09   1.5e-05       2      95 .]      70     160 ..      69     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.2e-09
                                       SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS.-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT- CS
                     Thioredoxin_8   2 kvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldk.keeefekylkknkkpwlsvpfddkkrnklkkk 77 
                                       + +++  +a+wc+pc++ +p l e +e++  + +v++v+v +   + +e  +   ++  +w       +   ++  +
  gi|336254476|ref|YP_004597583.1|  70 RPTFIDLFATWCSPCEKQMPALAEAHEQVA-DADVQFVSVTNEGiSHDELAAWWDEHDGSWPI---AVDPAAEVSAR 142
                                       788999***********************8.7*********9742555666666655444555...44467888889 PP

                                       S--TT-SEEEEE-TT-BE CS
                     Thioredoxin_8  78 ynvkaiPtlvvldkngev 95 
                                       y  +++Pt v +d +g+v
  gi|336254476|ref|YP_004597583.1| 143 YLESGYPTAVTIDASGQV 160
                                       999999999999988886 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   9.6e-06     0.029      17      60 ..      69     112 ..      65     156 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.6e-06
                                       T--EEEEE--TT-HHHHHHHHH.HHH-HHHHH.HHHT-EEEEESS CS
                     Thioredoxin_7  17 gkpvlvffgaswcftCqalerd.flsdeevkaalaekfvllrvdv 60 
                                       g+p ++++ a+wc++C ++  +  + +e v+  ++ +fv ++ + 
  gi|336254476|ref|YP_004597583.1|  69 GRPTFIDLFATWCSPCEKQMPAlAEAHEQVAD-ADVQFVSVTNEG 112
                                       899***************97662566677777.999999987766 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.0   0.00095       2.8       4      24 ..       3      23 ..       1      24 [. 0.92

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00095
                        TAT_signal  4 RRdFLKgsAAaaAAaalggca 24
                                      RRd L g + a+ +a++g++a
  gi|336254476|ref|YP_004597583.1|  3 RRDVLTGLGSAGVLAGAGAVA 23
                                      ******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); 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:                         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 0.20s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 1664.41
//
Query:       gi|336254477|ref|YP_004597584.1|  [L=278]
Description: electron transport protein SCO1/SenC [Halopiger xanaduensis SH-6]
Scores for complete 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   60.4   0.1    6.1e-15   55.3   0.0    2.1  2  SCO1-SenC   SCO1/SenC
     0.0011   18.8   0.0     0.0016   18.3   0.0    1.3  1  AhpC-TSA    AhpC/TSA family
     0.0032   17.2   0.0     0.0046   16.7   0.0    1.2  1  Redoxin     Redoxin
  ------ inclusion threshold ------
      0.075   12.9   0.1       0.15   11.9   0.1    1.5  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0   1.4e-18   6.1e-15      10     108 ..      70     178 ..      61     188 .. 0.82
   2 ?    3.0   0.0     0.019        87     112     132 ..     228     248 ..     218     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 1.4e-18
                         SCO1-SenC  10 dgeavteedlegk.pslvffgFthCpd.vCpttlanmaevldalgeea..ekvqplfiTvDPerDtpevlkeyleaf 82 
                                        ge++t+++++g+  ++++++Ft+Cpd  Cp+ ++++++++++ +e++  +++ +l +T DPerDtp+vl+ey+ + 
  gi|336254477|ref|YP_004597584.1|  70 AGETITRDQFAGErAIVMTYFFTSCPDgACPALMTRLRRIQEDAAEQGyaDDIALLAMTFDPERDTPDVLEEYAGQQ 146
                                       699********9725667899*****978******************76699**********************999 PP

                         SCO1-SenC  83 dpriig.....ltG.skeeiakaakefrvyve 108
                                       + + ++     l+  ++e+ ++aa++f++  +
  gi|336254477|ref|YP_004597584.1| 147 GVDHEAdnwhfLRPeTNEAARDAADTFGLGLQ 178
                                       88877766777665566777777777766655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.019
                         SCO1-SenC 112 deesdytvdHsssvyLvdpdg 132
                                       +++++yt++H   ++L +++g
  gi|336254477|ref|YP_004597584.1| 228 HDHGEYTFQHINLILLANKQG 248
                                       45669*************998 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.6e-07    0.0016       2      60 ..      57     118 ..      56     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.6e-07
                                       TSB----EEE.STTCEEEECHHHTTSEEEEEEESTST-C..CHHHHHHHHHHCHHHCCCTTE CS
                          AhpC-TSA   2 gdkapdfelk.nadgetvslsdykgkpvvlffypkdwcp..vCttelpalaklyeefkergv 60 
                                       g+++pdf+l+    get++ ++++g+ ++++ y + +cp   C++ + +l++  e+ +e+g+
  gi|336254477|ref|YP_004597584.1|  57 GEEFPDFSLPdPLAGETITRDQFAGERAIVMTYFFTSCPdgACPALMTRLRRIQEDAAEQGY 118
                                       899*******445899*********9999999999999955699999999999999998886 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     1e-06    0.0046       3      68 ..      57     124 ..      56     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-06
                                       TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HH..HHHTHHHHHTHHHHHHCSTT.TEEEE CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPt..Csaehpyleklaellkekgv.dvvav 68 
                                       g+++Pdf+lp+ +  g++++ ++f+g +++v  +  + cP   C a +  l+ ++e ++e g  d +a+
  gi|336254477|ref|YP_004597584.1|  57 GEEFPDFSLPD-PLAGETITRDQFAGERAIVMTYFFTSCPDgaCPALMTRLRRIQEDAAEQGYaDDIAL 124
                                       899********.****************888777776999556***9*9*****999998884255555 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.4e-05      0.15       3      23 ..       2      21 ..       1      23 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggc 23
                                       RR+ L++ +A++ A+ l+gc
  gi|336254477|ref|YP_004597584.1|  2 ERRTYLQALGATGVAG-LAGC 21
                                      5************776.5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1972.23
//
Query:       gi|336254478|ref|YP_004597585.1|  [L=57]
Description: hypothetical protein Halxa_3092 [Halopiger xanaduensis SH-6]
Scores for 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   18.3   3.4      0.048   13.1   0.6    2.1  2  zf-ribbon_3    zinc-ribbon domain
  ------ inclusion threshold ------
      0.012   15.8   3.4        1.7    8.9   0.6    2.2  2  Zn-ribbon_8    Zinc ribbon domain
      0.016   15.5   1.0        3.5    7.9   0.4    2.0  2  zf-LITAF-like  LITAF-like zinc ribbon domain
      0.046   13.8   6.1      0.062   13.4   0.2    2.2  2  UPF0547        Uncharacterised protein family UPF0547
       0.11   12.7   2.2          2    8.7   0.1    2.0  2  E7             E7 protein, Early protein
       0.14   12.2   1.5         11    6.0   0.0    2.0  2  CpXC           CpXC protein
       0.15   11.6   4.2        2.3    7.9   0.1    2.3  2  Sgf11          Sgf11 (transcriptional regulation protein)


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 !    6.3   0.1    0.0026       6.5       5      12 ..      13      21 ..      10      24 .. 0.78
   2 !   13.1   0.6   1.9e-05     0.048       9      26 .]      34      52 ..      34      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0026
                       zf-ribbon_3  5 CPnCGa.pl 12
                                      CP+C++ ++
  gi|336254478|ref|YP_004597585.1| 13 CPECDStIA 21
                                      ****99664 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.9e-05
                       zf-ribbon_3  9 Gap.lssddnvCpyCGtkl 26
                                      G++ l+ + ++C +CG++l
  gi|336254478|ref|YP_004597585.1| 34 GSNrLQGRETCCQNCGHEL 52
                                      56558999********987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0012       3.2      23      35 ..       6      19 ..       1      22 [. 0.69
   2 ?    8.9   0.6   0.00065       1.7       8      16 ..      45      53 ..      35      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0012
                       Zn-ribbon_8 23 daplta.CPeCgse 35
                                      +++ ++ CPeC s+
  gi|336254478|ref|YP_004597585.1|  6 RSAVQVgCPECDST 19
                                      4455677****985 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00065
                       Zn-ribbon_8  8 CeeCghefe 16
                                      C++Cghe e
  gi|336254478|ref|YP_004597585.1| 45 CQNCGHELE 53
                                      788887776 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 ?    6.7   0.0    0.0035       8.9       4      16 ..       9      21 ..       6      31 .. 0.63
   2 ?    7.9   0.4    0.0014       3.5      51      69 ..      37      55 ..      33      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0035
                     zf-LITAF-like  4 tqvdCpaCqqrvv 16
                                      +qv Cp C  ++ 
  gi|336254478|ref|YP_004597585.1|  9 VQVGCPECDSTIA 21
                                      4555666655554 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0014
                     zf-LITAF-like 51 slkdvehyCpnCgallgty 69
                                      +l+  e  C+nCg+ l  y
  gi|336254478|ref|YP_004597585.1| 37 RLQGRETCCQNCGHELELY 55
                                      67778999******99866 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   2.4e-05     0.062       3      13 ..      13      23 ..      12      24 .. 0.91
   2 ?    2.7   1.7     0.052   1.3e+02      17      23 ..      45      51 ..      43      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                           UPF0547  3 CPeCeakvPva 13
                                      CPeC+++++++
  gi|336254478|ref|YP_004597585.1| 13 CPECDSTIAAS 23
                                      ********986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.052
                           UPF0547 17 CphCGyv 23
                                      C  CG++
  gi|336254478|ref|YP_004597585.1| 45 CQNCGHE 51
                                      899**97 PP

>> E7  E7 protein, Early protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00077         2      50      66 ..       6      22 ..       1      33 [. 0.78
   2 ?    4.8   0.3     0.013        32      54      67 ..      42      55 ..      28      57 .] 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00077
                                      .EEEEEEXTTTXXEEEE CS
                                E7 50 gYavevaCprCeqklrl 66
                                        av+v+Cp+C++++  
  gi|336254478|ref|YP_004597585.1|  6 RSAVQVGCPECDSTIAA 22
                                      448*********99965 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.013
                                      EEEXTTTXXEEEEE CS
                                E7 54 evaCprCeqklrlv 67
                                      e++C++C+++l+l 
  gi|336254478|ref|YP_004597585.1| 42 ETCCQNCGHELELY 55
                                      689******99875 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0045        11      34      51 ..       7      24 ..       3      27 .. 0.75
   2 ?    5.8   0.4    0.0053        14      37      50 ..      42      55 ..      35      57 .] 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0045
                              CpXC 34 slfeatCpkCgataklea 51
                                      s  ++ Cp+C+ t++++ 
  gi|336254478|ref|YP_004597585.1|  7 SAVQVGCPECDSTIAASL 24
                                      667788999999987765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0053
                              CpXC 37 eatCpkCgatakle 50
                                      e+ C++Cg++ +l 
  gi|336254478|ref|YP_004597585.1| 42 ETCCQNCGHELELY 55
                                      78999999998775 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1   0.00088       2.3       5      17 ..      11      23 ..       7      23 .. 0.87
   2 ?    4.9   1.0    0.0074        19       5      12 ..      43      50 ..      40      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00088
                                      EE-TTTSSEEEGG CS
                             Sgf11  5 vtCpnCgRqiaas 17
                                      v Cp C+ +iaas
  gi|336254478|ref|YP_004597585.1| 11 VGCPECDSTIAAS 23
                                      78*********98 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0074
                                      EE-TTTSS CS
                             Sgf11  5 vtCpnCgR 12
                                      ++C nCg 
  gi|336254478|ref|YP_004597585.1| 43 TCCQNCGH 50
                                      79****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 438.03
//
Query:       gi|336254479|ref|YP_004597586.1|  [L=405]
Description: peptidase M24 [Halopiger xanaduensis SH-6]
Scores for 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-57  194.1   1.2    5.2e-57  192.9   1.2    1.6  1  Peptidase_M24  Metallopeptidase family M24
    2.2e-22   80.1   0.0      5e-22   79.0   0.0    1.6  1  Creatinase_N   Creatinase/Prolidase N-terminal 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 !  192.9   1.2   5.8e-61   5.2e-57       2     209 .]     170     385 ..     169     385 .. 0.93

  Alignments for each domain:
  == domain 1  score: 192.9 bits;  conditional E-value: 5.8e-61
                                       HHHHHHHHHHHHHHHHHHHHH..TTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEE CS
                     Peptidase_M24   2 lirkaariasaaleavleaik..pgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdl 76 
                                        +r+aa++a+++  ++ e+     g+te+elaaeie+  l++ g++g+af++ivasg+n+a +h++ + r++++gd+
  gi|336254479|ref|YP_004597586.1| 170 TLRRAAELADRVSLEIRERGDdlVGTTEAELAAEIERL-LAEYGGGGPAFETIVASGPNGARPHHHSGAREIERGDP 245
                                       689*************876333349***********77.9999********************************** PP

                                       EEEEEEEEET...........TEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHH CS
                     Peptidase_M24  77 vlidagaeyd...........gyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevles 142
                                       +++d+ga +            +y +D trT++vG++  e+++++e+v eaq+aa++av+pGv+++++d+aarev+e+
  gi|336254479|ref|YP_004597586.1| 246 IVLDFGAFVAadlegdgggtaRYPGDQTRTIVVGEPPTEYERVHEVVAEAQQAAVEAVEPGVPAEAVDRAAREVIED 322
                                       ******9987777777777778************99999************************************** PP

                                       TTBCCGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEES CS
                     Peptidase_M24 143 aglakffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvte 209
                                       ag+++ f h++GHgvGlevh+  p++    +++r+le+Gmvf++Epgiy  +g +gvried+v vte
  gi|336254479|ref|YP_004597586.1| 323 AGYGDAFVHRTGHGVGLEVHEA-PYIV--DGNDRELEPGMVFSVEPGIY-LEGRFGVRIEDLVAVTE 385
                                       ********************98.**87..467*****************.89999***********7 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.0   5.6e-26     5e-22       1     131 [.       8     161 ..       8     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 5.6e-26
                                       HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEE....ESSCEEEEEECTTHHHHHHHH.TTSEEEE CS
                      Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfatetgsrglalvv....tadgalllvdalryteaaeesatveevve 73 
                                       Rl+++r+++ee+++d ++++++ nl YltGf++ + +r+l+l+v    t ++ +l+ +a+++++ a+   +  ev+ 
  gi|336254479|ref|YP_004597586.1|   8 RLAACRRRLEEADADLAVCFPSPNLTYLTGFEESPSERHLLLFVpragTDADPTLVAPAMYEFQLAALPPSTLEVRL 84 
                                       99******************************************7776445558***************77777777 PP

                                       EST...HSSHHHHHHHHH.................HHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHH CS
                      Creatinase_N  74 ydd...pvealadllkel.................lesekrvgveldaltvafyealkealpdaelvdaselieelR 130
                                       + d   p e++a  l+ +                 ++ + +v v+++ ++++f+++l+  lpdae+  as+++e+lR
  gi|336254479|ref|YP_004597586.1|  85 WVDdedPLETVARTLEGYvdvdgarahasedndssAKRGPTVLVDDR-MWATFTQDLRTLLPDAEFGLASAVLEDLR 160
                                       777677888888888888999999999988877655555********.9**************************** PP

                                       S CS
                      Creatinase_N 131 v 131
                                       +
  gi|336254479|ref|YP_004597586.1| 161 I 161
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2889.93
//
Query:       gi|336254480|ref|YP_004597587.1|  [L=548]
Description: alpha,alpha-trehalose-phosphate synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-117  393.0   0.0     2e-117  392.8   0.0    1.0  1  Glyco_transf_20  Glycosyltransferase family 20
     0.0012   19.2   0.0     0.0026   18.2   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
     0.0041   16.7   0.0      0.019   14.5   0.0    1.9  2  Glycos_transf_1  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.8   0.0  3.3e-121    2e-117       3     470 ..      41     518 ..      39     522 .. 0.93

  Alignments for each domain:
  == domain 1  score: 392.8 bits;  conditional E-value: 3.3e-121
                                       EEEEEEE-SEC..EEE-S........SCG..EEECCGSSHHHHHCCCHHCCC-EEEEEEECCES-CCC...HCCCC. CS
                   Glyco_transf_20   3 lvvvsnrlplk..leres.......eeekeeyelkkssgglvsalkglkeetevvwvgwlgvevdesee.akekvs. 68 
                                       l+vvsnr p++   er+         e+++++++++ +ggl   l+++ +e +++w++w   + d + + + + v+ 
  gi|336254480|ref|YP_004597587.1|  41 LIVVSNRQPYRheYERDGdggddgdDESDRSVTVDEPAGGLTAGLDPVVREVDGTWIAWGDGDADFDVAdEDHCVEv 117
                                       7899*****9966555557777776677789999*************************999998888643333435 PP

                                       HHHCCCCCEEEEEE-HHHHHHHCCCHHHHCHHHHHTT-GG....G----HHHHHHHHHHHHHHHHHHHCC--TT-EE CS
                   Glyco_transf_20  69 keleekfsvvpvflsdekveeyyngfsksvLWpllHYklpdsseekefersawdaYvkvnklFAdkiveeikdgdli 145
                                       +  ee +++ ++ ls+e ve+yy gfs++vLWpl+H       +  e  ++++d Y++vn++FAd++ve++ +++++
  gi|336254480|ref|YP_004597587.1| 118 PPGEEAYTLRRIDLSEEAVESYYYGFSNRVLWPLCH----GFGDLVEHRSNDFDWYRTVNERFADAVVEHAAEDSVV 190
                                       678999******************************....45679999999************************** PP

                                       EEESGGGTTHHHHHHHCCTT.SEEEEEE-S----HHHHTTSTTHHHHHHHHTTSSEEEESSHHHHHHHHHHHHHHSS CS
                   Glyco_transf_20 146 wvhDYhLmllPellRkkled.akigfflHiPFPsseifriLpvreeilegllgadliGFhtedyarhFlsccsrllg 221
                                       w++DYh  l+P+l+R+ ++   +++ f HiP+P  e f+  p   ++legllg+dl+GFh + ya+ Fl+c+++   
  gi|336254480|ref|YP_004597587.1| 191 WLQDYHFALAPRLIREGVPAsTTVAQFWHIPWPAPETFQQCPAAGHVLEGLLGNDLLGFHVDWYANTFLDCVEQYFP 267
                                       ******************98799****************************************************99 PP

                                       EEEECTTE.EEEETTEEEEEEE------HHHHHHHCCSCHHHHHHHHHHHHT...TTSEEEEEEEEC-GGG-HHHHH CS
                   Glyco_transf_20 222 leveskrg.gveykgrkvsvkalpigidverlesalkkesvsekvkelkerfe..nkkklilgvDrlDyikGvkqkl 295
                                         +  +r+ +v+y+g++++v a+p g+d +r ++ +++   + +++e++e f+  +++ l lgvDrlDy+kG+++++
  gi|336254480|ref|YP_004597587.1| 268 SATVDRRErTVRYDGHTTRVVATPMGVDADRYDRDARSVG-RAQLAEIREAFGipDDTVLGLGVDRLDYAKGIPERF 343
                                       7777666669*************************99654.6789******973244556689************** PP

                                       HHHHHHHHH-GGGTTTEEEEEEEEB-STTSHHHHHHHHHHHHHHHHHHHHH-BTTB-SEEEEES---HHHHHHHHHH CS
                   Glyco_transf_20 296 laferfLeeypelrgkvvlvqiavpsredveeyqelekeveelvgrINgefgtldytPvvylersldfeeliallaa 372
                                        a+erf+e++p +rg+ ++vq ++psr+d++ yq++  +v   ++rIN +fgt+d++P+vy e  ++ e l+al+++
  gi|336254480|ref|YP_004597587.1| 344 AALERFFERNPDWRGEFTFVQKSTPSRTDIPTYQQYGDHVRSEAERINRRFGTDDWQPIVYTEDYVEHEALCALYRY 420
                                       ***************************************************************************** PP

                                       -SEEEE--SSBSS-CHHHHHHHCSTTT--EEEEETTBGGGGT-TTTSEEE-TT-HHHHHHHHHHHHC--HHHHHHHH CS
                   Glyco_transf_20 373 advllvtslRdGmnlvakeyvvcqqekkgvLiLSeFaGaaqsLkdaailvNPwdieevaeaikeaLkmseeerkkre 449
                                       adv++v+sl dGmnlva+eyv+++ + +g+L+LS++aGa + L  +a+ + P d + +a+ +++aL+m+ +er++r+
  gi|336254480|ref|YP_004597587.1| 421 ADVMVVSSLADGMNLVAQEYVAANVDGDGTLLLSDRAGAHERLGTHALTIDPTDADGTAAQLERALSMPTHERRQRM 497
                                       ***************************************************************************** PP

                                       HHHHHHHHHT-HHHHHHHHHH CS
                   Glyco_transf_20 450 kkllkqvskhdvqsWaesfls 470
                                       ++l ++v  hd + W+  +++
  gi|336254480|ref|YP_004597587.1| 498 QTLRTRVFDHDLEGWMDAQFD 518
                                       ***************998876 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 !   18.2   0.0   4.3e-07    0.0026      54     133 ..     400     487 ..     369     488 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.3e-07
                                       T.TEEEE---..THHHHHHHH-SEEEE--..---SHHHHHHHHTT-....EEEE-TGGGTTT--TTSSEE--TT-HH CS
                   Glyco_trans_1_4  54 eerveftGfv..edlaellaaadvfvaPs..egfglkllEamaagl....pvVatdvggiaevvgengllvppgdpe 122
                                       ++ v    +v  e l +l++ adv+v+ s   g++l++ E+ aa +        +d +g+ e +g+++l ++p d++
  gi|336254480|ref|YP_004597587.1| 400 QPIVYTEDYVehEALCALYRYADVMVVSSlaDGMNLVAQEYVAANVdgdgTLLLSDRAGAHERLGTHALTIDPTDAD 476
                                       444566668875669**************988************87555567777777989988************* PP

                                       HHHHHHHHHHH CS
                   Glyco_trans_1_4 123 alaeailrLle 133
                                         a++++r l+
  gi|336254480|ref|YP_004597587.1| 477 GTAAQLERALS 487
                                       *****999875 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.19   1.2e+03       4      48 ..     313     356 ..     312     357 .. 0.83
   2 !   14.5   0.0   3.1e-06     0.019      80     165 ..     408     497 ..     403     500 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.19
                                       HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCE CS
                   Glycos_transf_1   4 kkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnv 48 
                                       ++r+  g++++  + l v rl++ Kg+     a++++ ++ np++
  gi|336254480|ref|YP_004597587.1| 313 EIREAFGIPDDTVLGLGVDRLDYAKGIPERFAALERFFER-NPDW 356
                                       567788888999999999*********9999999988776.7776 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.1e-06
                                       CCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT-....-EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHH CS
                   Glycos_transf_1  80 evsredleellknadifvlpsisEgfGivllEAmaagl....pviasnaggpaevvkdgetGllvkpnnaealaeai 152
                                       +v++e+l +l+++ad++v++s  +g+ +v+ E+ aa++      + s+  g+ e +  +   l ++p++a+  a+++
  gi|336254480|ref|YP_004597587.1| 408 YVEHEALCALYRYADVMVVSSLADGMNLVAQEYVAANVdgdgTLLLSDRAGAHERLGTHA--LTIDPTDADGTAAQL 482
                                       6789999*****************************986666799999999999888888..99************* PP

                                       HHHHHSH..HHHHHH CS
                   Glycos_transf_1 153 rkllede..elrerl 165
                                       +++l+ +  e+r+r+
  gi|336254480|ref|YP_004597587.1| 483 ERALSMPthERRQRM 497
                                       *****9987777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3947.55
//
Query:       gi|336254481|ref|YP_004597588.1|  [L=290]
Description: trehalose-phosphatase [Halopiger xanaduensis SH-6]
Scores for complete 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-38  132.2   0.0    1.9e-38  131.9   0.0    1.1  1  Trehalose_PPase  Trehalose-phosphatase


Domain annotation for each model (and alignments):
>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.9   0.0   1.1e-42   1.9e-38       1     230 [.      51     268 ..      51     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 131.9 bits;  conditional E-value: 1.1e-42
                                       EEETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHHHH---SSEEEEGGGTEEE-TT--EE CS
                   Trehalose_PPase   1 flDydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeellvkvpelglaaeHGaeirspsgedw 77 
                                       +lD+dGTl piv++pdaa p+++   ++++La++p  ++a++SGr l++++++v+ p + +a++HG+e++  ++  +
  gi|336254481|ref|YP_004597588.1|  51 CLDFDGTLAPIVDEPDAAAPTPANEAAVETLADEPAVTTAVISGRALADVRERVDGPSI-YAGNHGLELERRGS-VA 125
                                       69*******************************************************98.7*********9999.66 PP

                                       E-HHHHTTHHHHHHHHHHHHHHHTTSTT-EEEEETTEEEEE-TT--TT...THH.HHHHHHHHHHHHH.--EEEE-S CS
                   Trehalose_PPase  78 enqaevedlewlkevkeileektertpGsyiEekkfalsvHyrnadde.elqak.elaehlesvltdkpdlevtqgk 152
                                        + ++++  + +++++e le+ +e +p++ iE+k+ + +vH r +++  e  ++ +  e +++   d  +le++ gk
  gi|336254481|ref|YP_004597588.1| 126 VHPVARKRATRIERACEALETVLEPIPNARIEDKRLTATVHVRSVPPAaEPVVErRTREIVDRFGGD--ELEISGGK 200
                                       6679********************************************8555540455555554444..6******* PP

                                       SEEEEE-S---.HHHHHHHHHHTS--------EEEEEE-SSTTHHHHTTS-TT...-EEEEE--TTS---EES-SEE CS
                   Trehalose_PPase 153 kvvevrpqgvs.KGkaverlleslgsadseddfvlciGDdrtDedmFsvlrktkesgvsievsavevgskpskakys 228
                                       +++e+ p++ + KG+a+e +  +l+     d+++l+iGDd tDe++F+++++    g++++v+ +e    ps+a+ +
  gi|336254481|ref|YP_004597588.1| 201 QILEIEPSIPWgKGNALELIDAELPD----DTVALYIGDDTTDESAFRAVEPD---GFGVLVGDDE----PSAASAR 266
                                       ********************999997....5*********************8...9999998886....6666666 PP

                                       ES CS
                   Trehalose_PPase 229 ld 230
                                       ++
  gi|336254481|ref|YP_004597588.1| 267 VA 268
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2174.63
//
Query:       gi|336254482|ref|YP_004597589.1|  [L=118]
Description: hypothetical protein Halxa_3096 [Halopiger xanaduensis SH-6]
Scores for 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-08   32.8   0.0    5.4e-08   32.3   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
      6e-05   22.8   0.0    0.00011   22.0   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0011   18.8   0.0     0.0018   18.1   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.002   18.2   0.0     0.0033   17.5   0.0    1.3  1  DUF2250         Uncharacterized protein conserved in archaea 
     0.0073   16.3   0.0       0.01   15.8   0.0    1.3  1  HTH_20          Helix-turn-helix domain
     0.0076   16.1   0.0      0.012   15.5   0.0    1.3  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.032   14.1   0.0      0.048   13.5   0.0    1.3  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.095   12.9   0.0       0.25   11.5   0.0    1.7  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.15   12.0   0.0       0.23   11.4   0.0    1.3  1  MarR            MarR family
        1.1    9.2   3.9        6.3    6.7   0.1    2.6  3  RelB_N          RelB Antitoxin alpha helical domain


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 !   32.3   0.0     3e-11   5.4e-08       3      48 .]       6      51 ..       4      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3e-11
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       td+ ILe+L++++r   + LAe++g S+ ++n+rl  Le+ Gl++
  gi|336254482|ref|YP_004597589.1|  6 PTDFLILEALEDKGRNVATNLAEHTGKSRKNINTRLPVLEDYGLVE 51
                                      69******************************************96 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 !   22.0   0.0   5.9e-08   0.00011       6      47 .]      10      52 ..       5      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5.9e-08
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                       IL +L++ g   ++ lae++g+s+ ++   L +L++ GLVek
  gi|336254482|ref|YP_004597589.1| 10 LILEALEDkGRNVATNLAEHTGKSRKNINTRLPVLEDYGLVEK 52
                                      7*******99999****************************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 !   18.1   0.0     1e-06    0.0018      12      56 ..      10      54 ..       5      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1e-06
                                      CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                       +  aL  +g+  a+ +ae++g +r +++  L  Led GlVe++ 
  gi|336254482|ref|YP_004597589.1| 10 LILEALEDKGRNVATNLAEHTGKSRKNINTRLPVLEDYGLVEKIG 54
                                      5667777899999*****************************985 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 !   17.5   0.0   1.8e-06    0.0033       7      55 ..       5      53 ..       2      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                           DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerv 55
                                      ++ ++ +l+ l+  + + a ++a+++ +++++++  l  Le+ GL+e+ 
  gi|336254482|ref|YP_004597589.1|  5 QPTDFLILEALEDKGRNVATNLAEHTGKSRKNINTRLPVLEDYGLVEKI 53
                                      567789*****************************************85 PP

>> HTH_20  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   5.8e-06      0.01      13      58 ..       9      54 ..       3      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.8e-06
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                        il aL +++   a+ lae  + s+++++ +L vLe+ gLve  +
  gi|336254482|ref|YP_004597589.1|  9 FLILEALEDKGRNVATNLAEHTGKSRKNINTRLPVLEDYGLVEKIG 54
                                      5589999666667899***************************876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.8e-06     0.012       5      54 ..       6      53 ..       2      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.8e-06
                                      HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      p+++ +L aL + +++   ++ la+++g s+ +++ +l  L++ GLve+ 
  gi|336254482|ref|YP_004597589.1|  6 PTDFLILEALEDKGRN--VATNLAEHTGKSRKNINTRLPVLEDYGLVEKI 53
                                      99***********973..9****************************987 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 ?   13.5   0.0   2.7e-05     0.048       4      38 ..       7      41 ..       6      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                     HTH_AsnC-type  4 iDrkILeaLqedaRisyaeLAervGlSestvlrRv 38
                                      +D  ILeaL+  +R   + LAe +G S+  +  R+
  gi|336254482|ref|YP_004597589.1|  7 TDFLILEALEDKGRNVATNLAEHTGKSRKNINTRL 41
                                      7999************************9999886 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 ?   11.5   0.0   0.00014      0.25      22      51 ..      24      53 ..      18      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                    B-block_TFIIIC 22 sdLakeskqdprslfyrlksLekkgLIvkq 51
                                      + La  ++++ +++  rl +Le++gL++k+
  gi|336254482|ref|YP_004597589.1| 24 TNLAEHTGKSRKNINTRLPVLEDYGLVEKI 53
                                      579999*********************996 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   0.00013      0.23       3      49 ..       6      52 ..       5      55 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  3 ltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      +t f+iL+ l+++g    + La++ g s+ ++ + l  Le+ Gl+e+
  gi|336254482|ref|YP_004597589.1|  6 PTDFLILEALEDKGRNVATNLAEHTGKSRKNINTRLPVLEDYGLVEK 52
                                      689******************************************97 PP

>> RelB_N  RelB Antitoxin alpha helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.043        77      13      21 ..      11      19 ..      10      19 .. 0.93
   2 ?    6.7   0.1    0.0035       6.3      16      24 ..      43      51 ..      41      54 .. 0.87
   3 ?   -3.2   0.1       4.3   7.7e+03       8      15 ..      82      89 ..      80      89 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.043
                                      HHHHH.HHH CS
                            RelB_N 13 IeEiLEDyG 21
                                      I+E+LED G
  gi|336254482|ref|YP_004597589.1| 11 ILEALEDKG 19
                                      89*****98 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0035
                                      HH.HHHHHH CS
                            RelB_N 16 iLEDyGLak 24
                                      +LEDyGL+ 
  gi|336254482|ref|YP_004597589.1| 43 VLEDYGLVE 51
                                      7******95 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.3
                                      HHHHHHHH CS
                            RelB_N  8 eeyekIeE 15
                                      +++e ++E
  gi|336254482|ref|YP_004597589.1| 82 DDFESLIE 89
                                      57887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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):              10  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 905.00
//
Query:       gi|336254483|ref|YP_004597590.1|  [L=268]
Description: peptidase M10A and M12B matrixin and adamalysin [Halopiger xanaduensis SH-6]
Scores for 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   21.3   0.0    0.00024   21.0   0.0    1.2  1  Peptidase_M10  Matrixin
    0.00098   18.8   0.0     0.0014   18.2   0.0    1.2  1  Astacin        Astacin (Peptidase family M12A)
     0.0041   16.1   0.0     0.0056   15.7   0.0    1.2  1  Peptidase_M66  Peptidase M66
     0.0052   17.0   0.0      0.008   16.3   0.0    1.3  1  Reprolysin_5   Metallo-peptidase family M12
     0.0075   15.5   1.3      0.012   14.9   1.3    1.2  1  DUF4953        Met-zincin
     0.0083   16.0   0.0      0.013   15.4   0.0    1.2  1  Peptidase_M43  Pregnancy-associated plasma protein-A
  ------ inclusion threshold ------
      0.012   16.1   0.1      0.017   15.6   0.1    1.5  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
      0.029   14.0   0.0      0.047   13.3   0.0    1.2  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like
      0.032   14.1   0.1      0.062   13.2   0.1    1.5  1  Reprolysin_2   Metallo-peptidase family M12B Reprolysin-like
      0.071   11.7   0.3      0.097   11.3   0.3    1.1  1  Metallopep     Putative peptidase family
       0.19   11.3   1.3       0.31   10.6   1.3    1.2  1  Peptidase_M57  Dual-action HEIGH metallo-peptidase


Domain annotation for each model (and alignments):
>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.5e-07   0.00024     103     126 ..     152     193 ..      59     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.5e-07
                                       ...................SSSEEHHHHHHHHHHHHTTBESX CS
                                       x..................xxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 103 v..................eqgvslflVaaHEiGHalGLeHs 126
                                                          ++++  ++V +HE+GHalGL+H 
  gi|336254483|ref|YP_004597590.1| 152 DggdsepsaepdprriaplTDATRTMQVLVHEVGHALGLRHE 193
                                       13455666666666666667788999***************5 PP

>> Astacin  Astacin (Peptidase family M12A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   8.9e-07    0.0014      75     103 ..     172     200 ..     160     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.9e-07
                                       CCC-SHHHHHHHHHHHHTB--GGGSTTGG CS
                           Astacin  75 kgCeklgiivHElmHalGffHeqsRtdrd 103
                                       +   ++ + vHE++HalG+ He+    rd
  gi|336254483|ref|YP_004597590.1| 172 DATRTMQVLVHEVGHALGLRHEHGVAFRD 200
                                       5667899****************766665 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.5e-06    0.0056     190     218 ..     174     201 ..     138     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.5e-06
                     Peptidase_M66 190 atltgefiHEqGHalGLpHylageaaskg 218
                                        ++ ++++HE+GHalGL H   g a+  g
  gi|336254483|ref|YP_004597590.1| 174 TRTMQVLVHEVGHALGLRH-EHGVAFRDG 201
                                       567899*************.666666555 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.9e-06     0.008     136     160 ..     170     194 ..     123     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.9e-06
                      Reprolysin_5 136 vvstatevqvvaHElGHnfGavHDc 160
                                       +++++ ++qv+ HE+GH++G +H +
  gi|336254483|ref|YP_004597590.1| 170 LTDATRTMQVLVHEVGHALGLRHEH 194
                                       5667899****************76 PP

>> DUF4953  Met-zincin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   1.3   7.1e-06     0.012      15      30 ..     178     193 ..     172     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.1e-06
                           DUF4953  15 fvvaHEvGhtLGLrhN 30 
                                       +v  HEvGh+LGLrh 
  gi|336254483|ref|YP_004597590.1| 178 QVLVHEVGHALGLRHE 193
                                       899************6 PP

>> Peptidase_M43  Pregnancy-associated plasma protein-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.9e-06     0.013      66     106 ..     174     212 ..     168     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.9e-06
                     Peptidase_M43  66 tnksstLthelGhfLgLihtfeggCerGegDkvsDtpsedg 106
                                       t +  +L he+Gh LgL+h      ++G  D v  tp  ++
  gi|336254483|ref|YP_004597590.1| 174 TRTMQVLVHEVGHALGLRHEHGVAFRDG--DAVVATPMISA 212
                                       556789*************999999999..99999998755 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1     1e-05     0.017     108     124 .]     175     193 ..      57     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                      Reprolysin_3 108 a..dtvaHEiGHnfganHt 124
                                       +  +++ HE+GH +g++H+
  gi|336254483|ref|YP_004597590.1| 175 RtmQVLVHEVGHALGLRHE 193
                                       144999************5 PP

>> Reprolysin_4  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.9e-05     0.047     133     153 ..     174     194 ..     164     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
                      Reprolysin_4 133 rdeydifAHEiGHtfGaaHdl 153
                                       + + +++ HE+GH +G+ H+ 
  gi|336254483|ref|YP_004597590.1| 174 TRTMQVLVHEVGHALGLRHEH 194
                                       5688***************85 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.8e-05     0.062     123     147 ..     174     199 ..     166     258 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.8e-05
                      Reprolysin_2 123 tkeidvvaHEvGHaFGatHdndgs.s 147
                                       t+ ++v+ HEvGHa G  H+  +  +
  gi|336254483|ref|YP_004597590.1| 174 TRTMQVLVHEVGHALGLRHEHGVAfR 199
                                       5789***************9876542 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   5.9e-05     0.097     318     339 ..     180     200 ..     172     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.9e-05
                        Metallopep 318 flHEiGHllglpHqedGvmlrd 339
                                        +HE+GH+lgl H + Gv  rd
  gi|336254483|ref|YP_004597590.1| 180 LVHEVGHALGLRHEH-GVAFRD 200
                                       68***********87.999998 PP

>> Peptidase_M57  Dual-action HEIGH metallo-peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.3   0.00019      0.31     135     150 ..     178     193 ..     171     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                     Peptidase_M57 135 hvithelGhtvGlRhs 150
                                        v+ he+Gh++GlRh 
  gi|336254483|ref|YP_004597590.1| 178 QVLVHEVGHALGLRHE 193
                                       5999***********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2119.95
//
Query:       gi|336254484|ref|YP_004597591.1|  [L=92]
Description: hypothetical protein Halxa_3098 [Halopiger xanaduensis SH-6]
Scores for 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  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); 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 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 698.77
//
Query:       gi|336254485|ref|YP_004597592.1|  [L=34]
Description: hypothetical protein Halxa_3099 [Halopiger xanaduensis SH-6]
Scores for 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:                       144  (0.00803168); expected 358.6 (0.02)
Passed bias filter:                      126  (0.00702772); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 282.17
//
Query:       gi|336254486|ref|YP_004597593.1|  [L=194]
Description: hypothetical protein Halxa_3100 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.26    9.3   0.3       0.26    9.3   0.3    1.0  1  AF-4      AF-4 proto-oncoprotein


Domain annotation for each model (and alignments):
>> AF-4  AF-4 proto-oncoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.3   1.5e-05      0.26     468     506 ..     118     156 ..      52     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 1.5e-05
                              AF-4 468 ssaeSeSsSeSeSSSeSDSesEssssdseanepprtatp 506
                                        +a+ +  S S  S +SDSe+ ss +d + n   + + p
  gi|336254486|ref|YP_004597593.1| 118 AEAAAGPESASGGSARSDSEAASSGADAAGNHDGNRRRP 156
                                       3344556788999***************99988766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1456.07
//
Query:       gi|336254487|ref|YP_004597594.1|  [L=254]
Description: hypothetical protein Halxa_3101 [Halopiger xanaduensis SH-6]
Scores for 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  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2015.17
//
Query:       gi|336254488|ref|YP_004597595.1|  [L=325]
Description: cysteine synthase [Halopiger xanaduensis SH-6]
Scores for 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-64  217.2   0.2    4.1e-64  216.8   0.2    1.0  1  PALP        Pyridoxal-phosphate dependent enzyme
      0.005   16.8   0.2      0.011   15.8   0.2    1.7  1  ADH_zinc_N  Zinc-binding dehydrogenase


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 !  216.8   0.2   4.5e-68   4.1e-64       8     281 ..      11     271 ..       7     277 .. 0.92

  Alignments for each domain:
  == domain 1  score: 216.8 bits;  conditional E-value: 4.5e-68
                                       --EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHHHT-EE CS
                              PALP   8 TPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaallGlkv 81 
                                       +Plv++++ +   gv + +K Es+np+gS KdR a  ++ +++++   ++++++ve +sGN+g++l+++aa+ G+++
  gi|336254488|ref|YP_004597595.1|  11 SPLVQVDSPE---GVTVAAKVESFNPGGSAKDRPAREMVRAAEREghiEPGDRLVEPTSGNTGIGLSLVAAARGYDL 84 
                                       6777777765...999*************************88888******************************* PP

                                       EEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHHHHHTT.T CS
                              PALP  82 tivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEileqlg.g 156
                                       tiv+pad+s+e+++ + ++Gae+++v+gd ++a+a+a el+ae  ga+ + qf+np++ e+ y t+g Ei+eq+g +
  gi|336254488|ref|YP_004597595.1|  85 TIVMPADKSEERRQVMAAYGAELELVEGDMEDARARADELEAE--GAVQLGQFENPANPEAhYRTTGEEIVEQVGdR 159
                                       *******************************************..******************************** PP

                                       TEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.CGTTCCHHH CS
                              PALP 157 kpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg.spselafel 232
                                       ++da+v++vG+Gg+i+G+++ l+e++pdv +i+vepe+++ l ++          ++d   +g++ g ++ +l+++l
  gi|336254488|ref|YP_004597595.1| 160 EIDAFVAGVGTGGTISGTGRRLREEFPDVDIIAVEPERNAVLSTGE---------SGDDDFQGMGPGfVSDNLDLDL 227
                                       ******************************************9999.........779999******9999999988 PP

                                       HSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHC CS
                              PALP 233 ldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreage 281
                                       +dr  +    v  e+a e +r+lar+egi+v+ ss+a   +  +r a+e
  gi|336254488|ref|YP_004597595.1| 228 IDRVET----VRLEDAEEECRRLARDEGILVGQSSGATSLVS-QRIARE 271
                                       866555....***********************777765444.455555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   1.2e-06     0.011       1      55 [.      70     126 ..      70     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHHHHHTT-EEEE.EESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTT CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaevia.vdsseeklelakklGadevinykea.dlverikeltg 55 
                                       g+Gl +v++A+ +  ++++ +d see+++ ++ +Ga+  + + ++ d  +r  el  
  gi|336254488|ref|YP_004597595.1|  70 GIGLSLVAAARGYDLTIVMpADKSEERRQVMAAYGAELELVEGDMeDARARADELEA 126
                                       89*************99888***************9988888888898888888873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2209.39
//
Query:       gi|336254489|ref|YP_004597596.1|  [L=124]
Description: hypothetical protein Halxa_3103 [Halopiger xanaduensis SH-6]
Scores for complete 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    2.1e-07   30.9   0.0    1.1  1  Thioredoxin    Thioredoxin
    0.00085   19.1   0.0     0.0015   18.3   0.0    1.3  1  Thioredoxin_9  Thioredoxin
  ------ inclusion threshold ------
      0.022   14.8   0.0      0.035   14.2   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
      0.046   13.9   0.0      0.062   13.5   0.0    1.2  1  Thioredoxin_7  Thioredoxin-like
      0.048   14.0   0.0        3.7    7.9   0.0    2.2  2  Thioredoxin_8  Thioredoxin-like
      0.086   13.3   0.1       0.37   11.2   0.1    1.9  1  Thioredoxin_2  Thioredoxin-like domain
       0.12   12.3   0.0       0.32   10.9   0.0    1.8  1  AhpC-TSA       AhpC/TSA family


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 !   30.9   0.0   8.1e-11   2.1e-07      14      91 ..      21     106 ..      10     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 8.1e-11
                                       HTT...TSSEEEEEEE.-TTSHHHHCHHHHHHHHHHHCTT...TSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTE CS
                       Thioredoxin  14 vak...ekklvlveFy.ApwCghCkalaPeleklaeelkd...kvklakvdvdenedlakkyevegiPtlklfkngk 83 
                                       v     ++++++ + +  +wC  C+al P + ++ ++ +    ++  + vd d++   +++y++e+iPt+++ +++ 
  gi|336254489|ref|YP_004597596.1|  21 VDTleeHNDELVYKVWgGDWCKDCRALLPDFGAALDAAEVpadRIEEIAVDEDKQGPGVDEYGIEYIPTIVVENDDG 97 
                                       4444324555555666359************998777665567***************************8876544 PP

                                       .EEEEEESS CS
                       Thioredoxin  84 .evkkyega 91 
                                        e+ +++++
  gi|336254489|ref|YP_004597596.1|  98 eEITRFVEE 106
                                       366666655 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     6e-07    0.0015      34     116 ..      22     105 ..      11     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6e-07
                                       HHHHT--S-EEEEEE--TT-HHHHHHHHHHHHHHHH-..TTEEEEEE-HHHHHHHT..TTTTT-SS--SSEEEEE-T CS
                     Thioredoxin_9  34 ekiksiekklkilvltedwCgDaavnvPvlakiaeln..pnievkillrdenlelm..dqyltngaraiPtliilde 106
                                       + +++++++l   v   dwC D+++ +P + ++ +++  p   ++ ++ de+++    d+y   g + iPt+++ ++
  gi|336254489|ref|YP_004597596.1|  22 DTLEEHNDELVYKVWGGDWCKDCRALLPDFGAALDAAevPADRIEEIAVDEDKQGPgvDEY---GIEYIPTIVVEND 95 
                                       46677778888889999***********998887665113333444455555544333777...88*********** PP

                                       T--EEEEEES CS
                     Thioredoxin_9 107 egeelgvwge 116
                                       +gee++ ++e
  gi|336254489|ref|YP_004597596.1|  96 DGEEITRFVE 105
                                       *****99987 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.4e-05     0.035       7      56 ..      38      93 ..      32     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                                      SSSSTTCHHHHHHHHHHCHCCTCEC......EEECCTTHHHHHHCT-SSSSEEECT CS
                     Thioredoxin_3  7 gpgCakCpklekavkeaaaekgika......evekvtdfeeiekygVmsvPalvid 56
                                      g  C+ C++l   + +a++  ++ a       v++ ++ + +++yg++ +P++v++
  gi|336254489|ref|YP_004597596.1| 38 GDWCKDCRALLPDFGAALDAAEVPAdrieeiAVDEDKQGPGVDEYGIEYIPTIVVE 93
                                      344*****9999999999999998887776677777888899***********997 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.4e-05     0.062       5      80 ..      16      92 ..      11      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.4e-05
                                      SHHHHHHHHHHHT--EEE.EE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT-.--SSEEEE CS
                     Thioredoxin_7  5 dldealakaaergkpvlv.ffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanilelde.qgvPvvaf 80
                                      ++++a++ ++e +  +   ++g +wc +C+al  df  + + +++ a+++    vd +   + + + ++ +++P++++
  gi|336254489|ref|YP_004597596.1| 16 SYEDAVDTLEEHNDELVYkVWGGDWCKDCRALLPDFGAALDAAEVPADRIEEIAVDEDKQGPGV-DEYGiEYIPTIVV 92
                                      688888888888888877789******************99999999***99999999988877.4444788999986 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0077        20       9      45 ..      37      74 ..      29      78 .. 0.82
   2 ?    7.9   0.0    0.0014       3.7      64      94 ..      68      98 ..      63      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0077
                                      --SSSHHHHHHHHHHHHHHHHHHH.TTSEEEEEEE-SS CS
                     Thioredoxin_8  9 gaswcppckaftpklkelyeklkk.kkkveivyvsldk 45
                                      g +wc++c+a +p   +  +  +  ++++e ++v  dk
  gi|336254489|ref|YP_004597596.1| 37 GGDWCKDCRALLPDFGAALDAAEVpADRIEEIAVDEDK 74
                                      578**********9988888877678888888887776 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0014
                                      .EE-TT-HHHHTT-S--TT-SEEEEE-TT-B CS
                     Thioredoxin_8 64 vpfddkkrnklkkkynvkaiPtlvvldknge 94
                                      +++d++k+    ++y+++ iPt+vv + +ge
  gi|336254489|ref|YP_004597596.1| 68 IAVDEDKQGPGVDEYGIEYIPTIVVENDDGE 98
                                      56677777788899***********999986 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00015      0.37       8      95 ..      31     102 ..      24     109 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                     Thioredoxin_2   8 vlvvft.dpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt 83 
                                       +++ ++  ++C +C++l  ++    d  +        p+  ++ +a++ +k+ +            +++yg++  Pt
  gi|336254489|ref|YP_004597596.1|  31 LVYKVWgGDWCKDCRALLPDFGAALDAAEV-------PADRIEEIAVDEDKQGP-----------GVDEYGIEYIPT 89 
                                       444444488999999998888777455444.......23235556666666665...........5788******** PP

                     Thioredoxin_2  84 ivfldgk.eivar 95 
                                       iv+ + + e+++r
  gi|336254489|ref|YP_004597596.1|  90 IVVENDDgEEITR 102
                                       **99999766665 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013      0.32      27      66 ..      30      71 ..       8     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                                      EEEEEEESTST-CCHHHHHHHHHHCHHHCC..CTTEEEEEEE CS
                          AhpC-TSA 27 pvvlffypkdwcpvCttelpalaklyeefk..ergvevigvs 66
                                       +v  ++ +dwc+ C++ lp++ +++++ +  +  +e i+v 
  gi|336254489|ref|YP_004597596.1| 30 ELVYKVWGGDWCKDCRALLPDFGAALDAAEvpADRIEEIAVD 71
                                      677789****************99986654335555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 953.73
//
Query:       gi|336254490|ref|YP_004597597.1|  [L=452]
Description: metallophosphoesterase [Halopiger xanaduensis SH-6]
Scores for 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   43.9   0.0    0.00026   21.2   0.0    2.2  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    1.2e-09   39.0   0.2    4.8e-08   33.7   0.1    2.1  2  Metallophos    Calcineurin-like phosphoesterase


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 !   20.6   0.0   4.6e-08   0.00041       4     108 ..      11     150 ..       9     171 .. 0.71
   2 !   21.2   0.0   2.9e-08   0.00026     104     150 ..     314     359 ..     279     369 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.6e-08
                     Metallophos_2   4 aiiSDlH..............snldaleavlealkevgvdaiihaGD.................l.eeeepevleel 48 
                                        +iSDlH              + ld le++++  +++  +++i  GD                 +  ++ p+  e+l
  gi|336254490|ref|YP_004597597.1|  11 YVISDLHiggdeqlgevdflpELLDFLERLATTGENA--ELVI-NGDafglweftevagvakfdVlTDRYPDLFEQL 84 
                                       69*********99988877777777777777777777..5555.599888888888777766552344555666666 PP

                     Metallophos_2  49 lela...pvlaVrGNnDeev.veedvlreaaelgtdl.p.eeaelelagekvlliHgdplgvkdal 108
                                       +e     p++  +GN+D+e  + ++  ++ ae++ dl   e+ +  ++++++++ Hg++   ++++
  gi|336254490|ref|YP_004597597.1|  85 RETGesiPITLLPGNHDNELaAYDEYVERLAEYNVDLvRaESITRPVGDRTIYFEHGHQRDPNNRF 150
                                       6655888**********4446556666666666666633355555579999*******87555544 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2.9e-08
                     Metallophos_2 104 vkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgepr 150
                                       ++ a a+ ++++  + +v+++GHtH+p ++  +++++vn G    + 
  gi|336254490|ref|YP_004597597.1| 314 YA-AAAREVFAERPETAVFCYGHTHRPLLKGVDDRVLVNTGTWLKRL 359
                                       33.33344444355556***********************9866655 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.1   5.4e-12   4.8e-08       4     153 ..      11     187 ..       9     222 .. 0.59
   2 ?    3.3   0.0     0.012     1e+02     181     204 .]     316     339 ..     275     339 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 5.4e-12
                                       EEEESBTB.....TTCCTHHHHHHHHHHHHHHHTTESEEEEEST......SSSSS.........HHHHHHHHHHHHH CS
                       Metallophos   4 lvigDlHl.....algggqlddllkllddllreekpdlvllaGD......lvdrg.........dlekellellaal 60 
                                        vi+DlH+       ++  l++ll++l++l+   ++  ++++GD      +   +         +l  ++ +l+++l
  gi|336254490|ref|YP_004597597.1|  11 YVISDLHIggdeqLGEVDFLPELLDFLERLATTGENAELVINGDafglweF---TevagvakfdVLTDRYPDLFEQL 84 
                                       69********8887778888888888888888888888888***5555541...14445555554444344444444 PP

                                       HHH..TSEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE..EEEEEEESE......CEEE CS
                       Metallophos  61 vky..pipvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgs..lkvlllhGg......spel 127
                                        +    ip+ ll+GNH+    + l  y+++ +  + ++ d   + +  +          ++++ hG+         +
  gi|336254490|ref|YP_004597597.1|  85 RETgeSIPITLLPGNHD----NELAAYDEYVERLAEYNVD--LVRAESITR---PVgdRTIYFEHGHqrdpnnR--F 150
                                       444667***********....4444433333333333333..222222222...22346899999996654330..1 PP

                                       ..........THHHHHHHHHHHSCHHHHCC.......HHHHHH CS
                       Metallophos 128 ..........lvsldklgslnleleapepg.......dewlkd 153
                                                 l    + +  ++       g        +wlkd
  gi|336254490|ref|YP_004597597.1| 151 edfgnpyetpLGYYYNTNVTSRA------GrlsgrgrFNWLKD 187
                                       33343333443333333333333......14444458999999 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHTTESEEEEESSSSE CS
                       Metallophos 181 dealedllkkygvdlvisGHtHvy 204
                                         a e + ++++  + ++GHtH++
  gi|336254490|ref|YP_004597597.1| 316 AAAREVFAERPETAVFCYGHTHRP 339
                                       334446699999999999****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3315.33
//
Query:       gi|336254491|ref|YP_004597598.1|  [L=730]
Description: hypothetical protein Halxa_3105 [Halopiger xanaduensis SH-6]
Scores for complete 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-73  246.1   0.0    2.6e-73  245.4   0.0    1.4  1  Thioredox_DsbH  Protein of unknown function, DUF255
    9.4e-11   41.7   0.0      2e-10   40.7   0.0    1.6  1  Thioredoxin_7   Thioredoxin-like
    3.6e-08   33.0   0.2     0.0033   16.7   0.0    3.1  3  GlcNAc_2-epim   N-acylglucosamine 2-epimerase (GlcNAc 2-epime
    0.00013   21.2   0.3     0.0018   17.4   0.0    2.6  3  Glyco_hydro_88  Glycosyl Hydrolase Family 88
     0.0085   15.6   0.1        0.2   11.2   0.0    2.5  3  Glyco_hydro_76  Glycosyl hydrolase family 76
  ------ inclusion threshold ------
       0.02   14.4   0.1        1.6    8.2   0.0    2.9  3  C5-epim_C       D-glucuronyl C5-epimerase C-terminus
       0.11   12.6   0.0       0.23   11.6   0.0    1.5  1  RNA_GG_bind     PHAX RNA-binding domain
          2    8.6   7.1       0.99    9.6   0.9    3.4  4  cwf21           cwf21 domain


Domain annotation for each model (and alignments):
>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.4   0.0   1.2e-76   2.6e-73       1     161 [.       7     168 ..       7     170 .. 0.97

  Alignments for each domain:
  == domain 1  score: 245.4 bits;  conditional E-value: 1.2e-76
                    Thioredox_DsbH   1 knrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvk 77 
                                       +nrl++e spYl+qha+npv+W+pw+e+ale+a+e+d pi+lsiGysachWChvme+esf+de va++lne+fv++k
  gi|336254491|ref|YP_004597598.1|   7 RNRLEDEGSPYLRQHADNPVNWQPWDEQALEAARERDVPIFLSIGYSACHWCHVMEEESFQDEGVAEVLNENFVPIK 83 
                                       69*************************************************************************** PP

                    Thioredox_DsbH  78 vDreerPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweee.reelee 153
                                       vDreerPd+d+iym+++q+++g+ggWPl+ +ltp++kpff gtYfp+e + g+pgfl+++e+i++ w++e ree+e+
  gi|336254491|ref|YP_004597598.1|  84 VDREERPDIDSIYMTVCQLVSGRGGWPLSAWLTPEGKPFFIGTYFPREGQRGQPGFLDLCERISDSWNSEdREEMEH 160
                                       *******************************************************************975499**** PP

                    Thioredox_DsbH 154 eaeellea 161
                                       +a++++ea
  gi|336254491|ref|YP_004597598.1| 161 RADQWTEA 168
                                       99998875 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   9.1e-14     2e-10       2      65 ..      28      91 ..      27     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 9.1e-14
                                      --SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-G CS
                     Thioredoxin_7  2 wlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterda 65
                                      w+ + ++al++a+er  p+++ +g s c+ C+++e++  +de v+++l+e+fv  +vd +er +
  gi|336254491|ref|YP_004597598.1| 28 WQPWDEQALEAARERDVPIFLSIGYSACHWCHVMEEESFQDEGVAEVLNENFVPIKVDREERPD 91
                                      99999*****************************************************999865 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.11   2.4e+02     276     308 ..     220     252 ..     214     266 .. 0.82
   2 !   16.7   0.0   1.5e-06    0.0033     256     330 ..     263     338 ..     248     348 .. 0.86
   3 !   11.7   0.0     5e-05      0.11      91     183 ..     447     540 ..     424     601 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHH--CHHHHHHHHHHHHHH CS
                     GlcNAc_2-epim 276 pqtEalkaaaalaeltgearylewyarvaeyle 308
                                       pq  +l+a+a+++ +tg++ y e  ++ +++++
  gi|336254491|ref|YP_004597598.1| 220 PQPARLQALARAYDRTGREAYREVLEETLDAMA 252
                                       5666799**************999988877764 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.5e-06
                                       SB-.S-B-TTS-BSS--EEHHHHHHHHHHHHHHHHHH--CHHHHHHHHHHHHHHHHTB-TTTSSB-SEE-TTS-.B- CS
                     GlcNAc_2-epim 256 glv.ytldaagkpvddakllWpqtEalkaaaalaeltgearylewyarvaeylerhlidpekGlWfdkldadge.va 330
                                       g++ y +d++ ++++ +k+l   +E   a +++++ltg++ry+e  a+ +++++r   ++e+G  f  lda+ e ++
  gi|336254491|ref|YP_004597598.1| 263 GFHrYCVDRDWTVPHFEKMLYDNAEIPRAFLTGYQLTGDERYAEVVAETLAFVDRE-LTHEEGGFFSTLDAQSEdPE 338
                                       554278**************************************************.7999*********9987554 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 5e-05
                                       HHHHTTT-TTHHHHHHHHHHHHHHHTEETTTTEE--E.E-TTSS-BEEHHHHHHHHHHHHHHHHTT-BTHHHHHHHH CS
                     GlcNAc_2-epim  91 asalaageeeakdlldetlavlekhlweekaglvkee.sdkefsklrgsnpnMhlleAmLalaeatgdkeyleraee 166
                                        +al  g+++++d++ ++l+++  +lw+e ++ ++   +d++++     +    l    L ++eatg+  +l+ a e
  gi|336254491|ref|YP_004597598.1| 447 EAALVLGDDQYADMAVDALDFVRDRLWNESEQRLNRRyKDGDVKVDGYLEDYAFLARGALGCYEATGEVDHLRFALE 523
                                       33678899999999999999999999999888765541444444444455556778889999999999999999999 PP

                                       HHHHHTTTTGGGGTT-- CS
                     GlcNAc_2-epim 167 iaelvisefadaesglv 183
                                       +a++v +ef da  g++
  gi|336254491|ref|YP_004597598.1| 524 LARVVEAEFWDADRGTL 540
                                       99999999999988776 PP

>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.8   3.9e+03      83     113 ..     148     178 ..     143     180 .. 0.77
   2 !   17.4   0.0     8e-07    0.0018      34     118 ..     224     328 ..     203     341 .. 0.88
   3 ?    0.4   0.0      0.12   2.8e+02      33     169 ..     440     476 ..     395     505 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.8
                                       HHHHHH-THHHHHHHHHHHHHHHHCS-B.TT CS
                    Glyco_hydro_88  83 llyeltkderykeaaeeladyvlakpprtse 113
                                       + ++ +++e+++ +a+++++   ++ ++t e
  gi|336254491|ref|YP_004597598.1| 148 DSWNSEDREEMEHRADQWTEAAKDRLEDTPE 178
                                       6799999999999999999976666666655 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 8e-07
                                       HHHHHHHHHHHH--HHHHHHHHHHHHHCCCTTS-.....................CTTSGGGTGHHHHHHHHHHHH- CS
                    Glyco_hydro_88  34 flsglleayeatgdkeyldyakawadslideggk.....................telelDdidigllllllyeltk 89 
                                        l++l++ay+ tg+++y+++++++ d +   g                       +++  D+++i   +l+ y+lt+
  gi|336254491|ref|YP_004597598.1| 224 RLQALARAYDRTGREAYREVLEETLDAMAAGGLYdhvgsgfhrycvdrdwtvphfEKMLYDNAEIPRAFLTGYQLTG 300
                                       6899*******************88888877777778889999999999999999999******************* PP

                                       THHHHHHHHHHHHHHHHCS-B.TTS.B.S CS
                    Glyco_hydro_88  90 derykeaaeeladyvlakpprtseGgfwh 118
                                       dery e + e     ++++   +eGgf+ 
  gi|336254491|ref|YP_004597598.1| 301 DERYAEVVAETLA-FVDRELTHEEGGFFS 328
                                       *************.666777779****86 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHH--HHHHHHHHHHHHHCCCTTS-CTTSGGGTGHHHHHHHHHHHH-THHHHHHHHHHHHHHHHCS- CS
                    Glyco_hydro_88  33 vflsglleayeatgdkeyldyakawadslideggktelelDdidigllllllyeltkderykeaaeeladyvlakpp 109
                                       +++                                                                          
  gi|336254491|ref|YP_004597598.1| 440 LMIA------------------------------------------------------------------------- 443
                                       3333......................................................................... PP

                                       B.TTS.B.SBTTSTTEEETHHHHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHHHBETT CS
                    Glyco_hydro_88 110 rtseGgfwhkkkepeqlWlDgLfMaipllaklskvtgepkyldeaikqflltarhlfdpe 169
                                                                    a+++ v+g+ +y d+a++ ++ ++++l ++ 
  gi|336254491|ref|YP_004597598.1| 444 ---------------------------TCAEAALVLGDDQYADMAVDALDFVRDRLWNES 476
                                       ...........................445555666666666666666666666655544 PP

>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.53   1.2e+03      42      69 ..     225     252 ..     218     281 .. 0.69
   2 ?    0.7   0.0      0.13   2.9e+02      34      67 ..     281     314 ..     255     333 .. 0.81
   3 !   11.2   0.0   8.7e-05       0.2     156     259 ..     438     537 ..     434     554 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHCTTCCCHHHHHHHHHCCC CS
                    Glyco_hydro_76  42 fgalidywrltgdstyndlitqallaqa 69 
                                       ++al  ++++tg + y++++++ l a+a
  gi|336254491|ref|YP_004597598.1| 225 LQALARAYDRTGREAYREVLEETLDAMA 252
                                       5666666777777777777666554443 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.13
                                       GHHHHHHHHHHHHHHHHHCTTCCCHHHHHHHHHC CS
                    Glyco_hydro_76  34 ywWeagalfgalidywrltgdstyndlitqalla 67 
                                       + + ++++  a++  ++ltgd++y +++ + l +
  gi|336254491|ref|YP_004597598.1| 281 MLYDNAEIPRAFLTGYQLTGDERYAEVVAETLAF 314
                                       4788899999999999999999999999886654 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 8.7e-05
                                       HHHHHHHHHHHHHHH--CHHHHHHHHHHHHHHHHSCSBTTTS-B-SEEETTTCCEEEE---HHHHHHHHHHHHHHHH CS
                    Glyco_hydro_76 156 ngplfqlaarLarytgnetYlewAekvwdWvedvgliddedwlvyDgasvednctdinklqwtYnqGtylsgaayly 232
                                       ng +   +a  a + g+++Y++ A    d+v+d +l ++++ + + + + ++   d++   +   ++++  ga   y
  gi|336254491|ref|YP_004597598.1| 438 NGLMIATCAEAALVLGDDQYADMAVDALDFVRD-RLWNESEQRLNRRYK-DG---DVKVDGYLEDYAFLARGALGCY 509
                                       888999999999*********************.899888888888863.33...344445567899********** PP

                                       HHH--HHHHHHHHHHHHHHHHHCEEC.T CS
                    Glyco_hydro_76 233 naTgdekWldrvkgllnatlstffpd.g 259
                                       +aTg+  +l  + +l++ +++ f+++  
  gi|336254491|ref|YP_004597598.1| 510 EATGEVDHLRFALELARVVEAEFWDAdR 537
                                       **********************999863 PP

>> C5-epim_C  D-glucuronyl C5-epimerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.06   1.3e+02      34      62 ..     224     252 ..     219     270 .. 0.77
   2 ?    8.2   0.0   0.00073       1.6      32      76 ..     286     332 ..     281     349 .. 0.85
   3 ?   -0.5   0.0      0.32   7.2e+02      31      61 ..     438     468 ..     430     472 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.06
                         C5-epim_C  34 aisvllrAYeltgdekYlkaakkalksfk 62 
                                        +++l+rAY+ tg e Y ++ ++ l++++
  gi|336254491|ref|YP_004597598.1| 224 RLQALARAYDRTGREAYREVLEETLDAMA 252
                                       5789*************777666666554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00073
                         C5-epim_C  32 gqaisvllrAYeltgdekYlkaakkalksfk..ipvekGGvlktled 76 
                                       +++  ++l  Y+ltgde+Y ++ ++ l++++  ++ e+GG+ +tl+ 
  gi|336254491|ref|YP_004597598.1| 286 AEIPRAFLTGYQLTGDERYAEVVAETLAFVDreLTHEEGGFFSTLDA 332
                                       6778899****************999999862256789999988765 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.32
                         C5-epim_C  31 qgqaisvllrAYeltgdekYlkaakkalksf 61 
                                       +g +i + ++A  + gd++Y ++a  al+++
  gi|336254491|ref|YP_004597598.1| 438 NGLMIATCAEAALVLGDDQYADMAVDALDFV 468
                                       5788999999999*************99986 PP

>> RNA_GG_bind  PHAX RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.23      16      51 ..     227     262 ..     223     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                       RNA_GG_bind  16 liervvkvlGkekalelleeteeieknGGlltadgs 51 
                                        ++r+ ++ G+e  +e+leet +  ++GGl+ + gs
  gi|336254491|ref|YP_004597598.1| 227 ALARAYDRTGREAYREVLEETLDAMAAGGLYDHVGS 262
                                       6899**************************998886 PP

>> cwf21  cwf21 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.39   8.6e+02      16      25 ..       6      26 ..       5      86 .. 0.69
   2 ?   -3.3   0.0       4.8   1.1e+04      16      23 ..     240     247 ..     239     252 .. 0.77
   3 ?    9.6   0.9   0.00044      0.99      15      42 ..     354     418 ..     354     420 .. 0.88
   4 ?   -3.6   0.0         6   1.3e+04      37      44 .]     468     475 ..     465     475 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.39
                             cwf21 16 lrdeLEeeg...........l 25
                                      +r +LE+eg           +
  gi|336254491|ref|YP_004597598.1|  6 ERNRLEDEGspylrqhadnpV 26
                                      799999998555555555550 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.8
                             cwf21  16 lrdeLEee 23 
                                       +r+ LEe 
  gi|336254491|ref|YP_004597598.1| 240 YREVLEET 247
                                       88889885 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00044
                             cwf21  15 elrdeLEeeg.....................................lseeeIeervdelRekLl 42 
                                       e r+ LE+e                                      l+e e+++r++  Re+L 
  gi|336254491|ref|YP_004597598.1| 354 EVREALEDETtadlfcdryditesgnfegrnqpnrvrpiddladeydLEESEVQKRLETAREQLF 418
                                       678999998778899999999999999999999999999999999989***************96 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 6
                             cwf21  37 lRekLlke 44 
                                        R++L++e
  gi|336254491|ref|YP_004597598.1| 468 VRDRLWNE 475
                                       69999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.41
# Mc/sec: 5334.19
//
Query:       gi|336254492|ref|YP_004597599.1|  [L=286]
Description: Fructosamine/Ketosamine-3-kinase [Halopiger xanaduensis SH-6]
Scores for 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-54  183.7   0.0    5.5e-54  183.3   0.0    1.0  1  Fructosamin_kin  Fructosamine kinase
    3.9e-16   59.7   5.6      5e-16   59.3   5.6    1.2  1  APH              Phosphotransferase enzyme family
  ------ inclusion threshold ------
       0.11   11.8   0.0       0.19   11.0   0.0    1.4  1  EcKinase         Ecdysteroid kinase
       0.14   11.7   0.0        4.4    6.9   0.0    2.1  2  RIO1             RIO1 family


Domain annotation for each model (and alignments):
>> Fructosamin_kin  Fructosamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.3   0.0   1.2e-57   5.5e-54       5     285 ..       7     284 ..       4     285 .. 0.88

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 1.2e-57
                   Fructosamin_kin   5 iaqllsealgkafeiteaekveggeineayllseeeqrfFv.klnekealemFeaEaesLealaetqtirvPkvlav 80 
                                       +++ +++al  +++ t+ +++ gg+i +ay++++++    v k+     ++  e Ea  L++lae + + vP+v   
  gi|336254492|ref|YP_004597599.1|   7 VTDAVARALDLEVQPTTVTELRGGQIGSAYRVDRADGPPVVaKV----GETPLEVEAFMLRTLAEESNLPVPEVR-- 77 
                                       566777888888999*****************987776544144....4456689******************96.. PP

                   Fructosamin_kin  81 GelkdasfLvleyLelk.lekkesaaelgqqLaklHraseqkefGfdvdntigktpqpNewqssWaeFfaeqRlgvq 156
                                           d+  Lvley+e +  ++ esa + + +La lH+ ++ + fGf++d++ g ++qpN w++sW++F++eqRl++ 
  gi|336254492|ref|YP_004597599.1|  78 --YADDDLLVLEYVEGTtDHGPESARDAADHLAALHE-NSDDAFGFERDTLTGPVRQPNPWTDSWIDFYREQRLEHV 151
                                       ..568899*******9977889***************.8899*********************************** PP

                   Fructosamin_kin 157 lelakekglefakieelvervaell...skhqpkpsllHGdLWsgNaaltkdgepvifdPaayygdrEvdlamtelf 230
                                         la e g   a++ + +++va+ l    ++   p+l+HGd+W+ N+   + + + ++dPa+yy++ E++la++++ 
  gi|336254492|ref|YP_004597599.1| 152 AALALEGGSLPADLADRIDAVAADLeslLGEPDAPALIHGDVWTTNVLSRDGDVTAFLDPATYYAHPEIELAFIDWT 228
                                       ******99987777777777776652225677889************999999899********************* PP

                   Fructosamin_kin 231 ggfpsefyegYqsivpldegy.eeRkelYqLYhlLnhlnlFgggylsqaqkliqkl 285
                                       + f+++f++ Yq+   l++g+ ++R+ +Y LY lL h++lFgg y++  ++++++l
  gi|336254492|ref|YP_004597599.1| 229 ETFGDAFFDRYQKKRALEPGFfDRRRYVYRLYPLLVHVHLFGGRYVARLEQTLERL 284
                                       ********************72556679*********************9999875 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   5.6   1.1e-19     5e-16       1     230 [.      23     245 ..      23     277 .. 0.79

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 1.1e-19
                                       EEEEE--.SSCEEEEEEETT-.-EEEEEE-TTS-HHHHHHHHHHHHHHH.HTT-B--B-CTTBS-EEETTEEEEEEE CS
                               APH   1 evrelsggasnrtylvttpag.ryvlrrnpparaaeeirrevallrlLa.kagvpvPevlagdtddeeigllfalie 75 
                                       +v+el+gg++   y+v  ++g ++v ++ +++     ++ e+ +lr La ++++pvPev +    d+++    +++e
  gi|336254492|ref|YP_004597599.1|  23 TVTELRGGQIGSAYRVDRADGpPVVAKVGETP-----LEVEAFMLRTLAeESNLPVPEVRY---ADDDL----LVLE 87 
                                       589*****************768888888888.....99999999999945555*******...44444....49** PP

                                       ----EE-SSHHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-....................SHHCHTCCHHHHHHCH CS
                               APH  76 yvpgrsllrklsaaqlpellealgeflaalhqvdpaalpla....................dflaqdlellrqlesa 132
                                       yv+g++ +        pe ++++++ laalh+ + +a +++                    ++++q+le+ +     
  gi|336254492|ref|YP_004597599.1|  88 YVEGTTDHG-------PESARDAADHLAALHENSDDAFGFErdtltgpvrqpnpwtdswidFYREQRLEHVA----- 152
                                       *********.......999**************888888886777777766664444333333333333333..... PP

                                       HHCCCGCCTCC...HHH.HHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHH CS
                               APH 133 tarllaselld...lle.eleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDl 205
                                           la+e +    +l+ ++++ v+a l+ ll  ++++ l+HgD  + N+l +  dg vt+++D  +  +++p  +l
  gi|336254492|ref|YP_004597599.1| 153 ---ALALEGGSlpaDLAdRIDA-VAADLESLLGEPDAPALIHGDVWTTNVLSR--DGDVTAFLDPATY-YAHPEIEL 222
                                       ...3333333333433305555.99999999999*******************..9999******975.778***** PP

                                       HCCHHHCSCHCCCHCHHHHHHHHCS CS
                               APH 206 avllrswtseldpeflaallrayeq 230
                                       a+    wt++++++f +++ +  + 
  gi|336254492|ref|YP_004597599.1| 223 AFID--WTETFGDAFFDRYQKKRAL 245
                                       *876..89*********99887764 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.2e-05      0.19     213     231 ..     184     202 ..     135     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.2e-05
                          EcKinase 213 efnvlnHGDlwvnNimfky 231
                                       +  +l HGD+w++N++ + 
  gi|336254492|ref|YP_004597599.1| 184 DAPALIHGDVWTTNVLSRD 202
                                       45689**********9875 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0   0.00098       4.4      58      91 ..      58      92 ..      47     113 .. 0.78
   2 ?    2.7   0.0     0.019        83     126     148 ..     187     210 ..     166     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00098
                                      HHHHHHHHHHTT.--S--EEEEETTEEEEE--EET CS
                              RIO1 58 EfrnLkrleeag.vpvPkpielkrhvlvmefiged 91
                                      E  +L+ l+e+  +pvP++    ++ lv+e+++  
  gi|336254492|ref|YP_004597599.1| 58 EAFMLRTLAEESnLPVPEVRYADDDLLVLEYVEGT 92
                                      5666777765544*******************933 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.019
                                       TEEESS-STTSEEEETTEE.EE-- CS
                              RIO1 126 glvHaDLSeyNvlvdedkv.viID 148
                                        l+H+D+   Nvl  +++v  ++D
  gi|336254492|ref|YP_004597599.1| 187 ALIHGDVWTTNVLSRDGDVtAFLD 210
                                       69************9996514555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2151.65
//
Query:       gi|336254493|ref|YP_004597600.1|  [L=189]
Description: dihydrofolate reductase [Halopiger xanaduensis SH-6]
Scores for 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-49  165.6   0.0    8.5e-49  165.3   0.0    1.1  1  DHFR_1    Dihydrofolate reductase
  ------ inclusion threshold ------
       0.25   11.2   0.0       0.34   10.7   0.0    1.1  1  ArAE_2    Aromatic acid exporter family member 2


Domain annotation for each model (and alignments):
>> DHFR_1  Dihydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.3   0.0   9.5e-53   8.5e-49       2     145 ..      24     177 ..      23     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 165.3 bits;  conditional E-value: 9.5e-53
                                       EEEEEEEETT-EEEBTTB-SS--HHHHHHHHHHHTTCEEEEEHHHHHCC-....S--TTCEEEEE-S-TT---TTEE CS
                            DHFR_1   2 islivAvaengvIGkdnklpwhlpeDlkrFkklTtgkpvimGrkTfeslg...krpLpnrkniVltrnedlkvegve 75 
                                       ++ ivAva+ngvIGkd+++pwh+p+Dl++Fk++T+++pvimGr T+e +     +pLp+r+++Vlt+++  ++e+++
  gi|336254493|ref|YP_004597600.1|  24 LVGIVAVADNGVIGKDGDMPWHIPADLQHFKETTMDCPVIMGRVTYEGILealGEPLPGRTTVVLTSRDLETPENAV 100
                                       5679*******************************************99756668************9888889*** PP

                                       EESSHHHHC.....CCCTTS...SEEEEEE-HHHHHHCGGG-SEEEEEEESS----SEE-----CCCEEEEEEEEE- CS
                            DHFR_1  76 vvssleeal.....alakee..keevfviGGaeiYkqalpladklylTeidaefegdtffpeideeewelvereehe 145
                                       v+++l+ea+     a+ +++  ++++fv+GGa++Y+q+lp  d+l++Te++ +++gdt+fp++d+++w++++r+eh+
  gi|336254493|ref|YP_004597600.1| 101 VANDLAEAVeaaetAARERHdgADRAFVAGGATVYEQFLPALDRLIVTEVHDAPDGDTVFPDWDRDAWTETDRDEHD 177
                                       *********7665422222256799************************************************9997 PP

>> ArAE_2  Aromatic acid exporter family member 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.8e-05      0.34     148     219 ..      77     147 ..      68     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.8e-05
                            ArAE_2 148 GdpLPeilpapLvkrhlellrkqlkleeseeeadslaealslellrsedgrrfivalsialkildrlDelvl 219
                                       G+pLP  +   L+ r le+ +++  +++   ea++ ae +  e+   +d    + + +++ ++l +lD+l++
  gi|336254493|ref|YP_004597600.1|  77 GEPLPGRTTVVLTSRDLETPENAVVAND-LAEAVEAAETAARERHDGADRAFVAGGATVYEQFLPALDRLIV 147
                                       99**********************9999.5555555566666666666656666678999*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1514.04
//
Query:       gi|336254494|ref|YP_004597601.1|  [L=338]
Description: thymidylate synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-95  319.4   0.0    1.8e-95  319.1   0.0    1.0  1  Thymidylat_synt  Thymidylate synthase


Domain annotation for each model (and alignments):
>> Thymidylat_synt  Thymidylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.1   0.0  9.8e-100   1.8e-95       1     267 [.       2     337 ..       2     337 .. 0.97

  Alignments for each domain:
  == domain 1  score: 319.1 bits;  conditional E-value: 9.8e-100
                                       HHHHHHHHHHHHH-EEEE-TTSSEEEEEEEEEEEEEGGGCB----SSST-...-HHHHHHHHHHHHTT--BTHHHHT CS
                   Thymidylat_synt   1 kqYldlvrkileeGeekedRtgtgtisvfgaqlrfdlsegefPllTtkkv...flksvieEllWflsgetnvkeLqe 74 
                                       +qYldlv+  l+eG+ k++Rtg++tis f++++++dl+eg +PllTtk++   +++s+++E++W+lsge+++++L+ 
  gi|336254494|ref|YP_004597601.1|   2 QQYLDLVDAALSEGTYKPNRTGVDTISSFSEHYEVDLQEG-YPLLTTKQMdgyRWNSMLHEVCWYLSGEEHIRNLR- 76 
                                       69*************************************9.*********9999**********************. PP

                                       TT--TTHHHHHHTTB-SSSHHHHHHHBTST........................TTSSB-HHHHHHHHHHHSTT-ST CS
                   Thymidylat_synt  75 kgvkiWdewadeegdlgpvYGkqwrkfkae........................egkkidqlakvidqlkenpdsRr 127
                                       +++kiWd+wadeeg+l+++YG++wr+++ +                         ++++dql++vid+l+++p+sRr
  gi|336254494|ref|YP_004597601.1|  77 EETKIWDAWADEEGRLDTAYGRFWRRYPIPedgaqlegeswpdetnrwvteeadGRRTFDQLQYVIDTLSDSPNSRR 153
                                       69************************998899999999999999******99988999******************* PP

                                       -EEE---GGGGGGSSS--SEEEEEEEE..SEETEEEEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHT-EEEEEEE CS
                   Thymidylat_synt 128 iivsawnpaeldkmaLppChvlfqfyvkdkkegkLslqlyqRSaDvflGvpFNiasyalLthmlaqvtglkpgelih 204
                                       ++v+aw+pa+     LppCh++f f+v+ +   +L+++l+qRS D++lG+pFNia+yalLt+++aq+tg++pg+++h
  gi|336254494|ref|YP_004597601.1| 154 LVVNAWHPANAAVSTLPPCHYSFVFNVQGD---RLNCHLTQRSGDIALGIPFNIAAYALLTKVVAQQTGFEPGTFAH 227
                                       **********85689************654...5******************************************* PP

                                       EEEEEEEE..................................................GGGHHHHHHHHTS---S-- CS
                   Thymidylat_synt 205 tigdaHiY..................................................snhveqvkeqlereprelp 231
                                       t+ daH+Y                                                  ++hv+++ eql+rep e p
  gi|336254494|ref|YP_004597601.1| 228 TVVDAHVYcgkgergawyadnlealqsrlagvddreeyldvkewleseappeaegderMDHVPGLLEQLSREPLERP 304
                                       ***************************************************************************** PP

                                       EEEE--SSTHSGGG--GGGEEEES----SXXXXXXX CS
                   Thymidylat_synt 232 klelnkekkvsiedfeledfelenYkphpkikakva 267
                                       +le++   +vsi+++ +ed+el++Y++h+ ik+ va
  gi|336254494|ref|YP_004597601.1| 305 TLEVA---DVSIDELAYEDVELTDYESHEGIKFGVA 337
                                       ****6...558*********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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 0.20s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2798.55
//
Query:       gi|336254495|ref|YP_004597602.1|  [L=534]
Description: hypothetical protein Halxa_3109 [Halopiger xanaduensis SH-6]
Scores for 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-38  131.6   0.0    3.6e-38  131.2   0.0    1.2  1  RNase_H_2        RNase_H superfamily
    1.6e-10   41.4   0.0    3.9e-10   40.2   0.0    1.6  1  HHH_5            Helix-hairpin-helix domain
    0.00018   21.2   0.2      0.014   15.2   0.0    2.9  2  HHH              Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.072   12.9   0.0    1.9  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
      0.023   15.3   8.5       0.11   13.1   2.7    3.5  3  SnoaL_2          SnoaL-like domain
      0.067   13.3   0.0       0.15   12.2   0.0    1.5  1  HHH_2            Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2   0.0   1.2e-41   3.6e-38       1     165 [.     305     477 ..     305     478 .. 0.93

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 1.2e-41
                         RNase_H_2   1 lffDiEttGlspkknliyliGvldvdekeiekltqllaeepeeekailelf...lellekkkalvtfngksFDvpfl 74 
                                       l++DiEt+Glsp  ++i+ iGv+d  ++e++ +++  +++p++ +++le+f   l  +++++al+t+ng +FD+++l
  gi|336254495|ref|YP_004597602.1| 305 LCVDIETDGLSP--TIIWQIGVYDPATDEYRAFVE--RDDPSDPASVLEAFcdwLLGVHPDRALLTWNGWRFDYRHL 377
                                       689*********..*****************9987..9*************9999999******************* PP

                         RNase_H_2  75 krlfkkyklde.....eefrhiDLlkelrkkkl......esysLksvekelgierreedlsGsqavklyqeylrtgd 140
                                         ++ k ++++     ++++++DL+ ++ + ++      ++ +L++v+++lg+e + ++l+G+q++++yq+++rtg+
  gi|336254495|ref|YP_004597602.1| 378 DAFVAK-HVPYyleewDSIPKLDLYLWAVRDENailpgrTN-KLEAVATALGYEDAGTGLDGAQTAAAYQRFMRTGE 452
                                       ****43.444445559999*********77666689**999.*********************************** PP

                         RNase_H_2 141 eellekilaYNedDvralatlyekl 165
                                       +  ++++ aY+edD+ral+++ye+l
  gi|336254495|ref|YP_004597602.1| 453 PLEWDRHEAYCEDDCRALWHVYERL 477
                                       ***********************97 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   1.3e-13   3.9e-10       4      51 ..     228     275 ..     227     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.3e-13
                                       HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHH CS
                             HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeri 51 
                                       L svsGiGpktA +l++  +++ ++l++ +ve+La++p +G ++A+++
  gi|336254495|ref|YP_004597602.1| 228 LESVSGIGPKTAERLADRSVTTRAELLETSVERLAELPNVGRDRARKM 275
                                       789******************************************998 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.7e-06     0.014      13      28 ..     228     243 ..     227     244 .. 0.90
   2 ?    2.5   0.0      0.05   1.5e+02       7      25 ..     255     273 ..     251     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-06
                                       HHTSTT-SHHHHHHHH CS
                               HHH  13 LlalPGVGpktAeaIl 28 
                                       L++++G+GpktAe+ +
  gi|336254495|ref|YP_004597602.1| 228 LESVSGIGPKTAERLA 243
                                       89***********875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.05
                                       TSSHHHHHTSTT-SHHHHH CS
                               HHH   7 pasreeLlalPGVGpktAe 25 
                                       + s+e L++lP VG+ +A+
  gi|336254495|ref|YP_004597602.1| 255 ETSVERLAELPNVGRDRAR 273
                                       6799**********98887 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 ?   12.9   0.0   2.4e-05     0.072       4      30 ..     229     255 ..     227     267 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                   DNA_pol_lambd_f   4 tkvyGVGpktAkkwyakGirtledlra 30 
                                        +v G+GpktA+++ ++ ++t  +l++
  gi|336254495|ref|YP_004597602.1| 229 ESVSGIGPKTAERLADRSVTTRAELLE 255
                                       689****************99999987 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.7   3.8e-05      0.11      12      83 ..      24      97 ..      18     145 .. 0.84
   2 ?   -0.0   0.1      0.46   1.4e+03      43      43 ..     157     157 ..      91     228 .. 0.56
   3 ?    3.1   0.1     0.051   1.5e+02      37      73 ..     438     474 ..     419     493 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                                      CHHHHHHTEEEEEEEE.ETTSEEESHHHHHHHHHHHHH..HEEEEEEEEEEEEEETTEEEEEEEEEEEEETTSSE CS
                           SnoaL_2 12 dldalaalfapdvvwe.dpggelrGreairaffralfa..afpdlrfeihdvvadgdrvavewtvtgtipatgrg 83
                                       l+++++++ pd+vw  +p  e +  +a+r++f a      +++ + +ih+ + dg++vav   +++ i+a++++
  gi|336254495|ref|YP_004597602.1| 24 TLEDVDRTLEPDAVWVlGPSREPQTFAAARRAFDASAFhpPLETGDATIHRQAIDGHEVAVAQSARA-IRASPDA 97
                                      689999*********967799999999999988766555799******************9766665.5555544 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.46
                                       H CS
                           SnoaL_2  43 f 43 
                                       +
  gi|336254495|ref|YP_004597602.1| 157 L 157
                                       1 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.051
                                       HHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEE CS
                           SnoaL_2  37 eairaffralfaafpdlrfeihdvvadgdrvavewtv 73 
                                       ++ +a+++++ ++ + l+++ h+ ++++d  a++  +
  gi|336254495|ref|YP_004597602.1| 438 AQTAAAYQRFMRTGEPLEWDRHEAYCEDDCRALWHVY 474
                                       3445567888888899*******99999866555444 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     5e-05      0.15      10      52 ..     233     276 ..     227     281 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5e-05
                             HHH_2  10 hVGektAklLakrFk.sldaLkkasleeLlevddiGeeiAqsiv 52 
                                        +G ktA+ La r   +  +L ++s+e L+e++++G   A++ +
  gi|336254495|ref|YP_004597602.1| 233 GIGPKTAERLADRSVtTRAELLETSVERLAELPNVGRDRARKMH 276
                                       69*********886626678****************99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.37
# Mc/sec: 4279.40
//
Query:       gi|336254496|ref|YP_004597603.1|  [L=899]
Description: hypothetical protein Halxa_3110 [Halopiger xanaduensis SH-6]
Scores for complete 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-20   73.5   0.0    2.2e-19   69.9   0.0    2.2  2  DEAD             DEAD/DEAH box helicase
    7.6e-15   55.4   0.2    7.2e-14   52.3   0.2    2.5  1  DUF1998          Domain of unknown function (DUF1998)
    7.9e-11   42.3   0.0    4.1e-10   40.0   0.0    2.1  2  Helicase_C       Helicase conserved C-terminal domain
    7.5e-09   35.8   0.0    1.1e-08   35.2   0.0    1.3  1  ResIII           Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
        0.1   13.6   3.8       0.16   13.0   0.1    3.1  3  Methyltransf_24  Methyltransferase domain
       0.16   11.8   0.8       0.57   10.1   0.8    2.0  1  TPR_10           Tetratricopeptide repeat


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 !   69.9   0.0   7.5e-23   2.2e-19       2     169 ..      66     238 ..      65     243 .. 0.87
   2 ?    1.0   0.0      0.11   3.2e+02      45      69 ..     325     349 ..     305     378 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 7.5e-23
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS.TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet.kgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       + Qa a++++ ++++v+va  T sGKT ++++ + ++ +e   + +   a ++ Pt++L +++ ++l+ +++ ++l+
  gi|336254496|ref|YP_004597603.1|  66 SHQADALEALAREENVCVATSTSSGKTRIYALQIARNYLEAqARGEDSTAYVLYPTKALSRDQERELNDLFDDLGLE 142
                                       57*********************************99999976777779***********************99977 PP

                                       EE.EEETTSSH.HHHHHHHHTTCSEEEEEHHHHHHHH...HCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHH CS
                                       xx.xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vl.liiggvaa.rdqlskldngvdivvgtpgrlddll...stgkln..lsqvrflVlDEadrlldqgfsdfinriln 147
                                       ++  ++ g+++  + ++++++++d+++++   +   l   ++      ls + ++V+DE +++     + ++  i++
  gi|336254496|ref|YP_004597603.1| 143 ISvRVYDGDTErGQTRRQIREEADVIISNFAGVNTYLhdhDRW--ArfLSACDLVVIDESHTYTGV-HGMHVAWIVR 216
                                       7766677766615566777888********9999988654222..235*****************9.99******** PP

                                       HSHHHCTTSTTTSEEEEEESSB CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 148 qlpqitcdgklqrqvivlSATl 169
                                       +l++  +   ++ q+++ SAT+
  gi|336254496|ref|YP_004597603.1| 217 RLKRVLEYYASDPQFVLTSATI 238
                                       **999999999999*******8 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.11
                                       STS-EEEEEESSHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  45 ktgpkalivePtreLaeqtlnnlkk 69 
                                        +  ++l+ +P+r+Lae  +++++k
  gi|336254496|ref|YP_004597603.1| 325 YHDAQTLLFSPSRKLAELSVKRASK 349
                                       566799**********988887765 PP

>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.2   2.4e-17   7.2e-14       1      83 []     724     846 ..     724     846 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 2.4e-17
                           DUF1998   1 lehalinalplflqcdesdlgteck.........apedep..................................rkr 34 
                                       +eha i ++pl+l++d++dlg+  +         +    p                                  r  
  gi|336254496|ref|YP_004597603.1| 724 AEHATIGVAPLELMVDKRDLGGLATltidshldqS----PtetdgfgtaapdgdapeniaaaeatvreiaqgleRDP 796
                                       69**********************97777666551....04456677778888888999999999********9999 PP

                           DUF1998  35 pariliydavpgGaGiaekaaelleellraalelieecdCee..aGCpaCl 83 
                                         + +iyd+  gG G+a++++e +e ++r+a e+i++cdC +  +GCpaC+
  gi|336254496|ref|YP_004597603.1| 797 ASGWFIYDGIDGGLGFARAIYENFEAVARRAREHIADCDC-GrvDGCPACV 846
                                       99**************************************.4479*****8 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 ?   -1.3   0.0       0.9   2.7e+03      12      60 ..     108     162 ..      96     180 .. 0.61
   2 !   40.0   0.0   1.4e-13   4.1e-10      11     110 ..     322     434 ..     315     435 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.9
                                       HTTTTSEEEEEESSHH...HHHHHHHHHHHT.....TSTEEEESTTSTHHHHHHHHH CS
                        Helicase_C  12 leeeggkilifvntid...rlekvklllekk.....gikvavlhgelpqnereeile 60 
                                        + e++++++  +t+    +  + + l+  +     +i+v v++g+++  + ++ ++
  gi|336254496|ref|YP_004597603.1| 108 ARGEDSTAYVLYPTKAlsrD--QERELNDLFddlglEISVRVYDGDTERGQTRRQIR 162
                                       55566677777777775332..23333333344557899999999876665554443 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 1.4e-13
                                       HHTTTTSEEEEEESSHH....HHHH..........HHHHHHHT.......TSTEEEESTTSTHHHHHHHHHHHHTTS CS
                        Helicase_C  11 kleeeggkilifvntid....rlek..........vklllekk.......gikvavlhgelpqnereeileqfnkge 66 
                                       +l+ ++ ++l+f+++++    +                    +       g  + ++h+  + ++r  + +q + g 
  gi|336254496|ref|YP_004597603.1| 322 HLTYHDAQTLLFSPSRKlaelS--VkraskhrhdnR------RyytnpdrGSAIEPYHAGHSRKKRHGTEHQLKTGV 390
                                       44678899*********55442..122222333333......145556789************************** PP

                                       SSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  67 sdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                        d + +t+++e Gi+i + +  +++++p + +s++q+iGR+gR+
  gi|336254496|ref|YP_004597603.1| 391 LDGVASTNALELGINIGEMDATVQLGYPGQRQSFWQQIGRAGRG 434
                                       *******************************************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 !   35.2   0.0   3.8e-12   1.1e-08       3     169 ..      63     238 ..      61     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 3.8e-12
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S........-EEEEESSHHHHHHHHHHGG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkee...kflflvprkslleqtleefk 75 
                                       +l+++Q++a+e+l+      r+++++++  T +GKT+++ +++++++l+++ +     + +l p+k+l    ++e++
  gi|336254496|ref|YP_004597603.1|  63 DLYSHQADALEALA------REENVCVATSTSSGKTRIYaLQIARNYLEAQARGedsTAYVLYPTKALSRDQERELN 133
                                       57899999999996......89*****************888899998876655888******************** PP

                                       GGTGG.....GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T. CS
                            ResIII  76 kflseayke.igkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk. 148
                                       +++++   e    +++gd+++   +++ ++++++++++   ++  ++  + ++     ++ d+++iDE+H +++ + 
  gi|336254496|ref|YP_004597603.1| 134 DLFDDLGLEiSVRVYDGDTERGqtRRQIREEADVIISNFAGVNTYLH--DHDRWARFLSACDLVVIDESHTYTGVHg 208
                                       ****9988865666777776667778899***************993..3444455566777**********99845 PP

                                       ........TTHHHHHT-..--SEEEEEESS- CS
                            ResIII 149 ........swreilekf..keavllglTATp 169
                                                 +++le++  +++++l  +AT+
  gi|336254496|ref|YP_004597603.1| 209 mhvawivrRLKRVLEYYasDPQFVLT-SATI 238
                                       55666666888889988434466666.7775 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.3e-05      0.16       7      91 ..      89     213 ..      85     221 .. 0.72
   2 ?   -0.6   0.4       0.9   2.7e+03      62      62 ..     522     522 ..     427     639 .. 0.57
   3 ?   -2.7   0.0       4.1   1.2e+04      75      97 ..     806     829 ..     748     844 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-05
                   Methyltransf_24   7 sGvstlwllralrrnga...............grlvavdhdpgaeeaaalareaglddrvrlikads.......... 58 
                                       sG++ ++ l+ +r++ +               ++ ++ d ++   e   l++++gl+  vr+  +d           
  gi|336254496|ref|YP_004597603.1|  89 SGKTRIYALQIARNYLEaqargedstayvlypTKALSRDQER---ELNDLFDDLGLEISVRVYDGDTergqtrrqir 162
                                       666666777766666666666767666666555556666666...77788888888888888888888888888888 PP

                   Methyltransf_24  59 ...................eealaslaagsiDllfiDgghaaeavledleal 91 
                                                          ++  a++  + +Dl++iD +h+++ v     a+
  gi|336254496|ref|YP_004597603.1| 163 eeadviisnfagvntylhdHDRWARFL-SACDLVVIDESHTYTGVHGMHVAW 213
                                       888888777788877766666666777.99*************998875555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.9
                   Methyltransf_24  62 l 62 
                                       l
  gi|336254496|ref|YP_004597603.1| 522 L 522
                                       0 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.1
                   Methyltransf_24  75 iDgghaa.eavledleallprlap 97 
                                       iDgg    +a +e +ea+ +r ++
  gi|336254496|ref|YP_004597603.1| 806 IDGGLGFaRAIYENFEAVARRARE 829
                                       555544325566666666666554 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8   0.00019      0.57       6      35 ..     487     515 ..     485     517 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00019
                            TPR_10   6 nNLanalrqrgrydeAealleealairrrl 35 
                                         La+  ++ gr+++ e+l e+a++++rr+
  gi|336254496|ref|YP_004597603.1| 487 DELAIDESDIGRLADRERL-ERAIEMWRRA 515
                                       689****************.********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (899 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); 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:                         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 0.26s 00:00:00.88 Elapsed: 00:00:00.39
# Mc/sec: 6838.36
//
Query:       gi|336254497|ref|YP_004597604.1|  [L=103]
Description: hypothetical protein Halxa_3111 [Halopiger xanaduensis SH-6]
Scores for 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   14.3   1.7      0.047   13.9   1.7    1.2  1  DUF2304   Uncharacterized conserved protein (DUF2304)


Domain annotation for each model (and alignments):
>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.7   2.6e-06     0.047       9      75 ..      18      85 ..      10      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-06
                           DUF2304  9 vsvllllliirlvrkkklkleysllwlllal.ilivlslfpqiltvlanllGvgrgtnllfllgivfl 75
                                      +  l lll++ ++   + + +y +  + ++  + +vl+l  + l  + +llGvg ++ llf ++ +f+
  gi|336254497|ref|YP_004597604.1| 18 LFGLGLLLLLTKITDTNRSRRYIVPAFCCWGgFHLVLALYEGTLVPVPRLLGVGLAVALLFGFLALFC 85
                                      3445566667777777777788888887776267999*********************9997766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 809.82
//
Query:       gi|336254498|ref|YP_004597605.1|  [L=197]
Description: hypothetical protein Halxa_3112 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.022   13.9   1.3      0.032   13.4   1.3    1.2  1  EutH          Ethanolamine utilisation protein, EutH
       0.28   10.4   4.3       0.33   10.2   4.3    1.2  1  Peptidase_U4  Sporulation factor SpoIIGA
       0.53   10.2   0.0       0.53   10.2   0.0    2.6  3  TraQ          Type-F conjugative transfer system pilin chaper


Domain annotation for each model (and alignments):
>> EutH  Ethanolamine utilisation protein, EutH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.3   5.4e-06     0.032     168     250 ..      88     174 ..      61     182 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.4e-06
                              EutH 168 vnlipviilavllalgL.ifipekmikgfkvfgkvivalitigLalai...vealtgiklipglapieealeivgsi 240
                                       +  + +  la+++++ L +f+p  + + f vf  v++++++  L  ++    + ++g+ ++ + ++++  + +v  +
  gi|336254498|ref|YP_004597605.1|  88 TAYLAIATLALIVVVELeAFAPVELSRRFAVFFAVLTTMAIQALWTVAqfySDRWLGTDFLHSQTELQWDFVVVTAV 164
                                       344555666666666662355666677777777777766665554332111466788999***************** PP

                              EutH 241 aivlaGafpl 250
                                       ++vlaGa+ +
  gi|336254498|ref|YP_004597605.1| 165 GVVLAGAYQV 174
                                       ********76 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.3   5.6e-05      0.33      17     138 ..      44     178 ..      17     188 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.6e-05
                      Peptidase_U4  17 llLlltakllklkikklrlllaAllGalyvvlvlflpklesillsillkilvsllmvliafgpkslk..eflkalll 91 
                                       llL+++a +  l ++ + + +  ll a+  +l ++    +   + + +++++++l ++++ + + +   e+ + +++
  gi|336254498|ref|YP_004597605.1|  44 LLLVIVASIPALAARDWTVTIPWLLSAVA-ALSVVAR-TAGAPFEVTAYLAIATLALIVVVELEAFApvELSRRFAV 118
                                       68999999999999999999888888888.6656664.566889999999999888877655555444478888888 PP

                      Peptidase_U4  92 fylvsfllgGilfalsyll..........lkskn......llvlllgalvaylllkllvkiik 138
                                       f++v  +++  +++   ++          l   +      + +++++a+ ++l   + v++ +
  gi|336254498|ref|YP_004597605.1| 119 FFAVLTTMAIQALWTVAQFysdrwlgtdfL---HsqtelqWDFVVVTAVGVVLAGAYQVYVTR 178
                                       887777776533333333435777665552...045577899999888888888775555443 PP

>> TraQ  Type-F conjugative transfer system pilin chaperone (TraQ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.48   2.9e+03      52      64 ..      38      50 ..      11      59 .. 0.73
   2 ?   -0.1   0.9      0.15   8.7e+02      13      51 ..      62     101 ..      50     105 .. 0.70
   3 ?   10.2   0.0   8.9e-05      0.53      30      62 ..     146     178 ..     115     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.48
                              TraQ 52 liGgyrildalia 64
                                      l+Gg+ +l  ++a
  gi|336254498|ref|YP_004597605.1| 38 LWGGFELLLVIVA 50
                                      6677666665555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.15
                              TraQ  13 vtGlWvlslGvwfhlvarlvyrkPelavlla.eilavglv 51 
                                       vt  W+ls  + + +var      e+   la   la+++v
  gi|336254498|ref|YP_004597605.1|  62 VTIPWLLSAVAALSVVARTAGAPFEVTAYLAiATLALIVV 101
                                       6777999999999999998877666654444145555555 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 8.9e-05
                              TraQ  30 rlvyrkPelavllaeilavglvliGgyrildal 62 
                                          +++ el +    + avg+vl G+y++  + 
  gi|336254498|ref|YP_004597605.1| 146 DFLHSQTELQWDFVVVTAVGVVLAGAYQVYVTR 178
                                       56788999*******************996554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1538.80
//
Query:       gi|336254499|ref|YP_004597606.1|  [L=200]
Description: hypothetical protein Halxa_3113 [Halopiger xanaduensis SH-6]
Scores for 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   14.4   4.6       0.26   11.1   4.6    2.1  1  DUF2238     Predicted membrane protein (DUF2238)
      0.098   13.0  17.7      0.052   13.9   4.8    2.1  2  DUF4233     Protein of unknown function (DUF4233)
       0.43   10.6   2.4       0.45   10.6   0.1    2.3  2  MitoNEET_N  Iron-containing outer mitochondrial membrane prot
        1.8    9.0   6.1         18    5.8   0.4    2.8  2  DUF983      Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> DUF2238  Predicted membrane protein (DUF2238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.6   5.9e-05      0.26      57     112 ..      88     150 ..      43     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.9e-05
                           DUF2238  57 nkYDrlvHfaqGllla......lvvrelllrkkklrk.wllllavlvvlaisalYEliEwlva 112
                                       + YD ++H +   ++a      + ++el  ++ +++  ++ +++v++vla++ ++E++E+++ 
  gi|336254499|ref|YP_004597606.1|  88 QWYDEIAHTVSASVVAgagyaaFRAFELHSDEIDVQPaFRSVFIVVFVLATGVVWEVMEFAFG 150
                                       568888887766554412210145555555666666648********************9875 PP

>> DUF4233  Protein of unknown function (DUF4233)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   4.8   1.2e-05     0.052      12      82 ..      16      83 ..      12      90 .. 0.84
   2 ?    5.0   5.0    0.0066        30      21      90 ..     111     180 ..      96     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                           DUF4233 12 aivvlLallvaiglrdtepatvlsvggvlavallllagllrrpwglalglvlQvlliaagfvvpamfvvgv 82
                                      a+ ++L  lv++g+  + ++ +++++g+la+ + ll + lrr+ g+ ++ +l +++  a++++++ + +g+
  gi|336254499|ref|YP_004597606.1| 16 ALQLALLGLVGYGT--ATAQFAIAATGGLALGITLLPAWLRREYGYSMDAGLVLWIT-AAVILHTAGSLGL 83
                                      66778888889899..55688999999*************************66655.9999999998887 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0066
                           DUF4233  21 vaiglrdtepatvlsvggvlavallllagllrrpwglalglvlQvlliaagfvvp.amfvvgvvFaavWvy 90 
                                        a++l++ e ++  ++  v++v+++l++g++ + + +a+g ++ v  i   +v+  ++ +vg++ +a+W +
  gi|336254499|ref|YP_004597606.1| 111 RAFELHSDEIDVQPAFRSVFIVVFVLATGVVWEVMEFAFGGLVTVYGI-DDIVTDfVFNAVGAIIVAIWGT 180
                                       46677666666666777799****************************.8888888999**********76 PP

>> MitoNEET_N  Iron-containing outer mitochondrial membrane protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       1.1     5e+03      44      53 ..      20      29 ..      16      37 .. 0.73
   2 ?   10.6   0.1    0.0001      0.45      35      62 ..      91     118 ..      80     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                        MitoNEET_N 44 avtaalgYla 53
                                      a ++++gY +
  gi|336254499|ref|YP_004597606.1| 20 ALLGLVGYGT 29
                                      7788899865 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0001
                        MitoNEET_N  35 dwLalvpfaavtaalgYlaykaflpkkk 62 
                                       d +a ++ a+v+a+ gY+a++af ++ +
  gi|336254499|ref|YP_004597606.1|  91 DEIAHTVSASVVAGAGYAAFRAFELHSD 118
                                       55888999***************99876 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0052        23      28      69 ..      32      76 ..      26      87 .. 0.78
   2 ?    5.8   0.4     0.004        18      17      51 ..     114     148 ..     112     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0052
                            DUF983 28 ayfvilivghlvvpla...llvevayepplwvhlliwlpltllls 69
                                      a f i  +g l++++     ++  +y  ++   l++w++ +++l 
  gi|336254499|ref|YP_004597606.1| 32 AQFAIAATGGLALGITllpAWLRREYGYSMDAGLVLWITAAVILH 76
                                      556666666666665544579999999999999999999999875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.004
                            DUF983  17 dlsharaddgPayfvilivghlvvplallvevaye 51 
                                       +l++ + d  Pa+  ++iv++++++ +++  ++++
  gi|336254499|ref|YP_004597606.1| 114 ELHSDEIDVQPAFRSVFIVVFVLATGVVWEVMEFA 148
                                       5677788889***************9999666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1447.11
//
Query:       gi|336254500|ref|YP_004597607.1|  [L=280]
Description: hypothetical protein Halxa_3114 [Halopiger xanaduensis SH-6]
Scores for 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   8.2     0.0056   16.5   8.2    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
     0.0055   16.0   1.3      0.011   15.0   1.3    1.5  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   8.2   6.2e-07    0.0056       3      24 ..       9      30 ..       9      32 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.2e-07
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggca 24
                                      SRR F K++ A+aAA++lg+ +
  gi|336254500|ref|YP_004597607.1|  9 SRRRFVKAGTATAAALGLGATG 30
                                      9******************976 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.3   1.2e-06     0.011       3      29 ..       2      28 ..       1      33 [. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-06
                        UCR_Fe-S_N  3 eaesdeptRRDFLyiATgavgaVGaaa 29
                                      +++sde++RR+F  ++T+ ++a G +a
  gi|336254500|ref|YP_004597607.1|  2 TDQSDEESRRRFVKAGTATAAALGLGA 28
                                      5689********************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.18s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2150.71
//
Query:       gi|336254501|ref|YP_004597608.1|  [L=430]
Description: phosphoribosylamine--glycine ligase [Halopiger xanaduensis SH-6]
Scores for 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-54  182.3   0.2    1.6e-53  181.4   0.0    1.5  2  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 
    6.5e-22   78.1   0.1    1.3e-21   77.1   0.1    1.5  1  GARS_N       Phosphoribosylglycinamide synthetase, N domain
    2.5e-13   50.1   0.1    5.9e-13   48.9   0.1    1.7  1  GARS_C       Phosphoribosylglycinamide synthetase, C domain
    2.2e-05   24.5   0.0    4.1e-05   23.7   0.0    1.4  1  ATP-grasp_3  ATP-grasp domain
  ------ inclusion threshold ------
       0.01   15.1   0.0       0.03   13.6   0.0    1.7  2  ATPgrasp_ST  Sugar-transfer associated ATP-grasp
      0.011   15.3   0.0       0.02   14.4   0.0    1.4  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
       0.55    9.8   2.1       0.63    9.6   0.1    2.2  3  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 ?   -3.9   0.0       3.9     1e+04      23      43 ..      51      71 ..      44      75 .. 0.79
   2 !  181.4   0.0   6.1e-57   1.6e-53       1     194 []     104     291 ..     104     291 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.9
                                      ESSHHHHHHHHHHHSSSEEEE CS
                            GARS_A 23 ftdpeeakeyieeatakalVv 43
                                      +t+p+++ ey e+++a ++V+
  gi|336254501|ref|YP_004597608.1| 51 TTNPKAVVEYAEDVDATIAVI 71
                                      678889999999999888887 PP

  == domain 2  score: 181.4 bits;  conditional E-value: 6.1e-57
                                       HBHHHHHHHHHHTT--B-.-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TT CS
                            GARS_A   1 asKsfakdllkkagipta.eyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkf 76 
                                       ++K+f ++++++ +ip+  ++e+f+d+e+a+++i+e + +   +K++gl++gKgv+v  ++  a +  ke +++  +
  gi|336254501|ref|YP_004597608.1| 104 TDKAFQRRFMQENDIPGCpDFETFDDMEAACDFIDEYDGDL-AIKPAGLTGGKGVKVIGDQVTAEEG-KEYIRESDY 178
                                       69**************987*********************9.9***************998888766.555554554 PP

                                       CCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEE....S-TTS-HHHHHHHHHH CS
                            GARS_A  77 GeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGays....papvvteellekikee 149
                                           +++v+Ee+l GeE++++a+v + ++++ p++qdhkr++egD+gpnTGGmG+ys     +p++te+++e++++ 
  gi|336254501|ref|YP_004597608.1| 179 ----DRIVLEERLIGEEFTVQAFVANGEFRTAPAVQDHKRAYEGDEGPNTGGMGSYSdattHLPFMTEADYEEAVS- 250
                                       ....6****************************************************888889***********99. PP

                                       THHHHHHHHHCTT---EEEEEEEEEEETTEEEEEEEESS--TTCH CS
                            GARS_A 150 ileptveglkkegipfkGvLyaglmlvedgpkvlefnvRfgDpet 194
                                       i+e tv++l+    +++G+Ly+++ml+++gpkv+efn+RfgDpe+
  gi|336254501|ref|YP_004597608.1| 251 IIEATVDALE----DYRGILYGQFMLTAEGPKVVEFNARFGDPEA 291
                                       ********97....49***************************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 !   77.1   0.1   5.1e-25   1.3e-21       2      90 .]       4     103 ..       3     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 5.1e-25
                                       EEEEEESSHHHHHHHHHHTTSTTESEEEEEE..--CGG............TTHHHHHHHHHHCTESEEEE-SHHHHH CS
                            GARS_N   2 kvLvvGsGGRehalawklaqspkvekvyvap..gNagt............edlealvefakeekidlvvvGpeapLv 64 
                                       +vL++G+GGReha+a++l++s+   ++y++   +N+g+            ++ +a+ve+a++ +++++v+Gpe+pL 
  gi|336254501|ref|YP_004597608.1|   4 NVLLIGGGGREHAIARALEDSEA--DLYACAgnRNPGIadiatdfatletTNPKAVVEYAEDVDATIAVIGPESPLE 78 
                                       79*****************9964..688887346788888886666655544458********************** PP

                                       TTHHHHHHHHHT-EEES--CCCCHHH CS
                            GARS_N  65 aGvadaleeekgikvfGpskeaAqlE 90 
                                       aGvad+le++ g+ +fGp+++ A++E
  gi|336254501|ref|YP_004597608.1|  79 AGVADELEAA-GVYAFGPKEDDARIE 103
                                       *******776.**************9 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.1   2.3e-16   5.9e-13       1      79 [.     325     413 ..     325     414 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2.3e-16
                                       EEEEEEEETTTTSS--ST-EEBS.....TTEEEEESSEE.....EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB CS
                            GARS_C   1 avgvvlaskGYPgsyekgkeitg.....egvkvfhagtk.....lvtsGGRvlavvavgetleeArakayeavkkik 67 
                                       +v+ +++++GYP+++e g++++      +++ +++a++      ++t+ +R +avv+++++++e ++ a++a++   
  gi|336254501|ref|YP_004597608.1| 325 TVCKYAVPEGYPTDPEAGAKVKVdeesaGDALLYYASVDerdggIYTTTSRSFAVVGLADSITEGEEIAEDALAVAG 401
                                       69*******************77999998888****988999999*****************************999 PP

                                       -TTEE--STTTH CS
                            GARS_C  68 feglfyRkDIGa 79 
                                        egl++R+DIG+
  gi|336254501|ref|YP_004597608.1| 402 DEGLHMRHDIGK 413
                                       9**********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 !   23.7   0.0   1.6e-08   4.1e-05      28     159 ..     138     287 ..     104     289 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.6e-08
                                       S--SSSEEEEESS-------B--SS--TTE..............EEEE---SEEEEEEEEE.SSSEEEE.EEEEEEE CS
                       ATP-grasp_3  28 eeeekklvvKprdGaggesvrvveekeeaeaaieeve.......lvqefieGkplSvsllsdgekvlvl.avnrqli 96 
                                       +e +  l +Kp+   gg++v v+ ++ +ae+  e++        ++ e + G++++v++ + + ++++  av +   
  gi|336254501|ref|YP_004597608.1| 138 DEYDGDLAIKPAGLTGGKGVKVIGDQVTAEEGKEYIResdydriVLEERLIGEEFTVQAFVANGEFRTApAVQDHKR 214
                                       333778899****************999999988888999***99************97776655554413333333 PP

                                       ET.............TEEEEEEE..S----H.HHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS-- CS
                       ATP-grasp_3  97 ekaeke.........fvyaGnvt..pietel.keevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPRlt 159
                                         +  +          +y+  +t  p+ te   ee+v+++e +v +le+ +G++   ++l+ e+p v+E N+R+ 
  gi|336254501|ref|YP_004597608.1| 215 AYE--GdegpntggmGSYSDATThlPFMTEAdYEEAVSIIEATVDALEDYRGILYGQFMLTAEGPKVVEFNARFG 287
                                       333..145899888866665555226666666899*******************99*****************95 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.2e-05      0.03      43      98 ..     124     179 ..      97     190 .. 0.72
   2 ?   -2.5   0.0       0.9   2.3e+03     249     266 ..     270     286 ..     261     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                       ATPgrasp_ST  43 ikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqdylkssgksalld 98 
                                       +++ ++++++ +f+ e++ +++iKpa   gGkG+ vi ++ +++  k+  ++ ++d
  gi|336254501|ref|YP_004597608.1| 124 FETFDDMEAACDFIDEYDGDLAIKPAGLTGGKGVKVIGDQVTAEEGKEYIRESDYD 179
                                       344478889999*****888*****************7766665555555444444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.9
                       ATPgrasp_ST 249 ivldeekgplllElNarp 266
                                       + l++e+ p ++E Nar 
  gi|336254501|ref|YP_004597608.1| 270 FMLTAEG-PKVVEFNARF 286
                                       5677887.*******985 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 ?   14.4   0.0   7.7e-06      0.02       1      63 [.     105     166 ..     105     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.7e-06
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeel 63 
                                       Dk   ++ +++ ++p  p +++  +++e a ++ +e+     ik+a   GGkG +v+ ++ + 
  gi|336254501|ref|YP_004597608.1| 105 DKAFQRRFMQENDIPGCPDFET-FDDMEAACDFIDEYDGDLAIKPAGLTGGKGVKVIGDQVTA 166
                                       78888999************99.9********************************9887554 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00025      0.63      50      79 ..     176     204 ..     144     219 .. 0.72
   2 ?   -3.2   0.0       2.2   5.6e+03      24      41 ..     242     259 ..     239     265 .. 0.71
   3 ?   -3.6   0.1       2.9   7.4e+03      59      71 ..     385     397 ..     382     404 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00025
                       ATP-grasp_4  50 veeesflvEeyieGeEfavdayfdeeGepv 79 
                                        + +++++Ee + GeEf v a++  +Ge  
  gi|336254501|ref|YP_004597608.1| 176 SDYDRIVLEERLIGEEFTVQAFV-ANGEFR 204
                                       456789*****************.888855 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.2
                       ATP-grasp_4  24 eeewkaavaaieeeleqa 41 
                                       e+++++av+ ie+ ++ +
  gi|336254501|ref|YP_004597608.1| 242 EADYEEAVSIIEATVDAL 259
                                       678888888888776554 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.9
                       ATP-grasp_4  59 eyieGeEfavday 71 
                                       ++ eGeE+a da+
  gi|336254501|ref|YP_004597608.1| 385 SITEGEEIAEDAL 397
                                       56799**999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); 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 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3143.53
//
Query:       gi|336254502|ref|YP_004597609.1|  [L=118]
Description: hypothetical protein Halxa_3116 [Halopiger xanaduensis SH-6]
Scores for 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   14.5   1.2       0.34   11.3   0.5    2.1  2  DUF2939   Protein of unknown function (DUF2939)


Domain annotation for each model (and alignments):
>> DUF2939  Protein of unknown function (DUF2939)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   1.9e-05      0.34       3      52 ..      25      74 ..      24      90 .. 0.79
   2 ?    2.8   0.1    0.0086   1.6e+02      27      47 ..      85     105 ..      70     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.9e-05
                           DUF2939  3 aalgayaasPylalyqlksAararDaaalselVdfpalraslkaqlnael 52
                                      +a g++++  y+a+++  +   + D a+l+  +d ++++  +++   +++
  gi|336254502|ref|YP_004597609.1| 25 IASGGLVLVGYVAVRRALKSQTNADDATLDSAIDAESIKSAVEEDGLQAV 74
                                      6788899999**************************99998887765555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0086
                           DUF2939  27 DaaalselVdfpalraslkaq 47 
                                       + ++l++ Vd ++++ s+ ++
  gi|336254502|ref|YP_004597609.1|  85 NQDELNTPVDTDDVQSSVSEE 105
                                       457899999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 929.93
//
Query:       gi|336254503|ref|YP_004597610.1|  [L=453]
Description: acetylornithine transaminase [Halopiger xanaduensis SH-6]
Scores for complete 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  244.6   0.0    1.9e-71  240.8   0.0    1.9  1  Aminotran_3  Aminotransferase class-III


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 !  240.8   0.0   1.1e-75   1.9e-71      15     405 ..      45     444 ..      35     445 .. 0.81

  Alignments for each domain:
  == domain 1  score: 240.8 bits;  conditional E-value: 1.1e-75
                                       EEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHH.........HHTT-S---TTTCEEHHHHHHHHHH... CS
                       Aminotran_3  15 kaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavke.........qaaklshvsfgaltnepalklaekl... 79 
                                       +a G + tdvdg+ +lD++s  a+++lG+++P v + ++e         + +++     ga   ep +    +l   
  gi|336254503|ref|YP_004597610.1|  45 EAIGPFCTDVDGNVLLDFTSHVAAAPLGYNNPVVREKLEEfdlvdplkiAGQDFYVSTDGA---EPPA--DAELpgp 116
                                       678999**************************99888876222111111222222222222...2222..1122222 PP

                                       ........HHHCT-..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTT CS
                       Aminotran_3  80 ........lklapkgldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkykt 148
                                               ++    ++d+vfl nsG+eAve+ +K++ +          ++  +f+gafHGrtlgals+ +sk+ +++
  gi|336254503|ref|YP_004597610.1| 117 sqlmdrlvAATDHYDMDRVFLSNSGAEAVENGIKICYA-------AGGHRAFTFDGAFHGRTLGALSLNRSKTVHRR 186
                                       23334434445567899********************9.......45556789******************665555 PP

                                       TCTTB-TSEEEE-TTBGGGTB-HH.....HHHHHHHHHHHHHH.CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHH CS
                       Aminotran_3 149 lfgpflpevvrlkypdeevlkene.....eeeaalleeleale.kkkkdevaAvivEpiqgegGvvvaspeflaklr 219
                                       ++ p +p+vv+++yp  e++ en         + ++ +l+  +     deva +i+EpiqgegG+ va +ef + l 
  gi|336254503|ref|YP_004597610.1| 187 GY-PEVPGVVSVPYPGSEAAYENRwltdgPGGNVVADKLHPEQgVIDPDEVAFLILEPIQGEGGYRVAHDEFARDLE 262
                                       55.6789********9999888877765544555666666555566789**************************** PP

                                       HHHHHHT-EEEEE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTT.T-H CS
                       Aminotran_3 220 elckkhdvllivDEvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfg.Gnp 295
                                       +l +++d  ++vDE+q+G+GrTG+l+A++h++++pD++t +K+l  G    a++ + +v     ++  +sT+g G+ 
  gi|336254503|ref|YP_004597610.1| 263 ALRERYDLKVVVDEIQSGVGRTGELWAVDHLDLTPDVITAGKGLRVG----ATISRSDVFPEQ-KSRLSSTWGaGDI 334
                                       ******************************************87766....566666666665.55679***75899 PP

                                       HHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT-..TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHC CS
                       Aminotran_3 296 lacavalavleiieeekllenaqelgaalkegLeelqkky..evikevRgkGlmiaielkeeaevkekeilkkakek 370
                                       +a +  + +l++i+e++ll n+ e g++l++gLe++ ++       +vRg+Glm+a+e+  +++++  ++l++  + 
  gi|336254503|ref|YP_004597610.1| 335 IASMQGALTLDVIHEQNLLSNVLERGQQLRSGLEDAIEDGdlPGAVDVRGRGLMLAVEFDTKERRD--AVLEASFKR 409
                                       99999******************************9988734556689*************99966..8******** PP

                                       TEE-EEETTTEEEE---TT--HHHHHHHHHHHHHH CS
                       Aminotran_3 371 GvlilsaGdnvirllppliitdeeidelleilkka 405
                                       G l+l++G++++rllppl +t+ eid +l  l++a
  gi|336254503|ref|YP_004597610.1| 410 GFLTLGCGHKTLRLLPPLDVTEREIDLGLRLLQEA 444
                                       *****************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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 0.21s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3583.32
//
Query:       gi|336254504|ref|YP_004597611.1|  [L=430]
Description: MgtC/SapB transporter [Halopiger xanaduensis SH-6]
Scores for 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-50  170.3  32.6    4.5e-50  170.3  32.6    2.4  2  DUF4010   Domain of unknown function (DUF4010)
    3.8e-24   85.4  12.7    3.8e-24   85.4  12.7    3.8  3  MgtC      MgtC family


Domain annotation for each model (and alignments):
>> DUF4010  Domain of unknown function (DUF4010)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   6.1      0.38   3.4e+03      79     141 ..      60     121 ..      38     137 .. 0.51
   2 !  170.3  32.6     5e-54   4.5e-50       1     208 [.     194     400 ..     194     402 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.38
                           DUF4010  79 npallvalalpllalallallvaalllrrrekeeeeeelelenPlelksAlkfallfalilll 141
                                       + +++v   l +l+ ++l+++ ++ll+ +   ++e++ l l++ +++  A  +++l+a+  ++
  gi|336254504|ref|YP_004597611.1|  60 SLETAVGEGLLILG-GFLVIVQGVLLAVQGLLGDEDAGLSLTTSVSMLVAYGVGALVAAQYII 121
                                       33333333333333.334444444444444444444447777777777777777777665554 PP

  == domain 2  score: 170.3 bits;  conditional E-value: 5e-54
                           DUF4010   1 VlisaisfagYvalrllgarrGllltgllGGlvSStAvtlslarrskeepelarllaagillAnavmllrvllivav 77 
                                       V++++i++a+Y+++  +g  rG+++tg++GGl+SStAv+ ++ ++++++p++a++++a+illAna+m+ r+l+i++ 
  gi|336254504|ref|YP_004597611.1| 194 VAVAGIGIANYAIVSTYGD-RGIAVTGFFGGLASSTAVVGTMLDHVRQRPDAASYAVAAILLANAAMAARNLAIAVG 269
                                       89*****************.********************************************************* PP

                           DUF4010  78 vnp....allvalalpllalallallvaalllrrrekeeeeeelelenPlelksAlkfallfalilllakaaqeyfG 150
                                       +++    ++lv+ ++pl a++++a+++a l++++ +++e    ++le+P++lk+Al f+++f+++l++  +a++ fG
  gi|336254504|ref|YP_004597611.1| 270 FTIgggsPVLVEAVVPLGAVIVVAFAIAGLTADWGQSSE----MDLESPFSLKNALAFGAVFLVVLVFGSVAESSFG 342
                                       ***99999999999********************99988....889******************************* PP

                           DUF4010 151 daglyalaalsGladvdAitlslarlaaegtlsaataalaillavlsntlvKavlalv 208
                                       + g+ya+a++sG+++++++t+s++ l++ g+l+aa a++ailla++s+++vKa+la++
  gi|336254504|ref|YP_004597611.1| 343 TLGFYATAVASGFVSSAGATTSAVVLYRGGQLAAAEATIAILLATVSSIVVKAMLAAT 400
                                       *******************************************************987 PP

>> MgtC  MgtC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4  12.7   4.2e-28   3.8e-24       1     120 [.      20     142 ..      20     143 .. 0.91
   2 ?   -7.2  10.0         2   1.8e+04      46      61 ..     267     296 ..     191     339 .. 0.53
   3 ?  -10.8  18.1         2   1.8e+04      50     112 ..     337     397 ..     264     403 .. 0.61

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 4.2e-28
                              MgtC   1 LllAlllGlliGleRelrekaaGlRTfaLvalgaalfvllslelaesrvaaqvvsgigflg..agvilkekega... 72 
                                       ++lA +lG+++GleRe+++k+aG+RTf L++l+aa+f++lsle+    v +++++  gfl+   gv+l+ +      
  gi|336254504|ref|YP_004597611.1|  20 IALAGALGMFLGLEREWSQKSAGIRTFSLISLLAAVFTILSLET---AVGEGLLILGGFLVivQGVLLAVQGLLgde 93 
                                       5799************************************8876...899999998899888888888766554676 PP

                              MgtC  73 .kvkglTTaaslwvtaaiGllvglglyllavvatvlvllllallreler 120
                                        +  +lTT++s++v++++G+lv++++++++v+++vl+ lll+l+rel++
  gi|336254504|ref|YP_004597611.1|  94 dAGLSLTTSVSMLVAYGVGALVAAQYIIEGVTVAVLSSLLLVLKRELHE 142
                                       688999*****************************************97 PP

  == domain 2  score: -7.2 bits;  conditional E-value: 2
                              MgtC  46 e..............srvaaqvvsgigflg 61 
                                       +              + v  + v++++f  
  gi|336254504|ref|YP_004597611.1| 267 AvgftigggspvlveAVVPLGAVIVVAFAI 296
                                       022223333222222223333444444444 PP

  == domain 3  score: -10.8 bits;  conditional E-value: 2
                              MgtC  50 aaqvvsgigflgagvilkekegakvkglTTaaslwvtaaiGllvglg...lyllavvatvlvllll 112
                                       a+   s  g lg  +    +   +  g TT+a+++   +   l++++    +lla+v++++v ++l
  gi|336254504|ref|YP_004597611.1| 337 AE---SSFGTLGFYATAVASGFVSSAGATTSAVVLYRGG--QLAAAEatiAILLATVSSIVVKAML 397
                                       33...3334444222222234448899999988877653..4444330014455555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3497.73
//
Query:       gi|336254505|ref|YP_004597612.1|  [L=86]
Description: hypothetical protein Halxa_3119 [Halopiger xanaduensis SH-6]
Scores for 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   18.3   0.3       0.91    9.2   0.2    2.3  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
  ------ inclusion threshold ------
      0.017   15.2   0.3      0.041   14.0   0.3    1.6  1  UPF0547         Uncharacterised protein family UPF0547
      0.023   14.7   0.2       0.04   13.9   0.2    1.4  1  DZR             Double zinc ribbon
       0.05   14.3   0.8       0.05   14.3   0.8    1.8  2  zinc_ribbon_15  zinc-ribbon family
       0.06   12.6   0.3      0.069   12.4   0.3    1.0  1  S_4TM           SMODS-associating 4TM effector domain
       0.11   12.2   1.7       0.94    9.3   0.2    2.1  2  A2L_zn_ribbon   A2L zinc ribbon domain


Domain annotation for each model (and alignments):
>> 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 !    9.2   0.2   0.00031      0.91      17      28 ..      52      63 ..      48      66 .. 0.82
   2 !    7.2   0.0    0.0013       3.9       2      13 ..      70      81 ..      69      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00031
                     zf-NADH-PPase 17 eggwarvCpaCg 28
                                      +++ +r+Cp Cg
  gi|336254505|ref|YP_004597612.1| 52 DAQAMRQCPECG 63
                                      56779******9 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0013
                     zf-NADH-PPase  2 thrFCgrCGapt 13
                                      ++ +C+r+G++ 
  gi|336254505|ref|YP_004597612.1| 70 SYEYCPRDGSRL 81
                                      6779*****986 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   1.4e-05     0.041      13      22 ..      55      64 ..      53      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                           UPF0547 13 aaqfCphCGy 22
                                      a++ Cp+CG+
  gi|336254505|ref|YP_004597612.1| 55 AMRQCPECGF 64
                                      9********9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   1.3e-05      0.04       1      24 [.      59      83 ..      59      86 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                               DZR  1 CpqCgeelppdar.fCseCgtklka 24
                                      Cp+Cg  +++++  +C++ g++l++
  gi|336254505|ref|YP_004597612.1| 59 CPECGFRTTESSYeYCPRDGSRLRE 83
                                      *****997666555*********85 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.49   1.5e+03      13      30 ..      23      40 ..      19      48 .. 0.78
   2 ?   14.3   0.8   1.7e-05      0.05      59      84 ..      50      76 ..      42      78 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.49
                    zinc_ribbon_15 13 elvkkkkvlklffipvfk 30
                                       ++  ++vl ++f+p+++
  gi|336254505|ref|YP_004597612.1| 23 AWIYLETVLLFLFLPFVP 40
                                      566778999999999876 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.7e-05
                    zinc_ribbon_15 59 kkessekkeCknCgkev.eeefkyCpk 84
                                      +++++ +++C++Cg ++ e++++yCp+
  gi|336254505|ref|YP_004597612.1| 50 ASDAQAMRQCPECGFRTtESSYEYCPR 76
                                      45556699******7661566*****7 PP

>> S_4TM  SMODS-associating 4TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   2.3e-05     0.069     175     217 ..      10      52 ..       3      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                             S_4TM 175 vlwillvlvvgliknlslsdlllsvivpllpllllalkeyreq 217
                                       ++ ++l ++v++++ + l+++ll++++p++p+ll   +   + 
  gi|336254505|ref|YP_004597612.1|  10 LAGLALSVLVSVAAWIYLETVLLFLFLPFVPFLLSRSRWTASD 52 
                                       445677888999999*****************99776655555 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 ?    9.3   0.2   0.00031      0.94      19      29 ..      54      64 ..      52      67 .. 0.85
   2 ?    2.6   0.1     0.039   1.2e+02      17      25 ..      67      75 ..      66      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00031
                     A2L_zn_ribbon 19 qgylvCieCga 29
                                      q+ ++C+eCg+
  gi|336254505|ref|YP_004597612.1| 54 QAMRQCPECGF 64
                                      7889******8 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.039
                     A2L_zn_ribbon 17 seqgylvCi 25
                                      +e++y++C+
  gi|336254505|ref|YP_004597612.1| 67 TESSYEYCP 75
                                      689*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 689.70
//
Query:       gi|336254506|ref|YP_004597613.1|  [L=91]
Description: transcriptional regulator PadR family protein [Halopiger xanaduensis SH-6]
Scores for complete 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   66.6   1.9    1.7e-18   66.4   1.9    1.1  1  PadR      Transcriptional regulator PadR-like family
     0.0044   16.8   0.0     0.0065   16.3   0.0    1.3  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
     0.0072   16.3   0.0      0.011   15.8   0.0    1.4  1  HTH_45    Winged helix-turn-helix
     0.0084   16.6   0.2      0.011   16.3   0.2    1.3  1  HTH_27    Winged helix DNA-binding domain
  ------ inclusion threshold ------
       0.02   14.8   0.5        2.1    8.3   0.1    2.6  3  MarR_2    MarR family
        0.1   12.4   0.0       0.17   11.6   0.0    1.3  1  DUF4364   Domain of unknown function (DUF4364)


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 !   66.4   1.9   5.6e-22   1.7e-18       1      74 [.      11      79 ..      11      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 5.6e-22
                                      HHHHH.CCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  1 iLall.eeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      +L+++ +e++ +G++i++elee++e   e+++G+lYp+L++L ++glve+ +++    +++++Y+lT++Grrel+
  gi|336254506|ref|YP_004597613.1| 11 LLYVIaGEEEPHGLAIKEELEEYYEK--EIHHGRLYPNLDTLVDKGLVEKGRRD----RRTNFYTLTRRGRRELE 79
                                      68888777888************986..***********************887....7**************98 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 !   16.3   0.0   2.2e-06    0.0065      53      85 ..      44      76 ..      39      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.2e-06
                           DUF1495 53 ynsessLielGLveeeeeseglklYklteeGie 85
                                      y + + L+ +GLve+   ++ +++Y+lt +G++
  gi|336254506|ref|YP_004597613.1| 44 YPNLDTLVDKGLVEKGRRDRRTNFYTLTRRGRR 76
                                      677789********9999*************97 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.5e-06     0.011      30      67 ..      37      79 ..      25      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.5e-06
                            HTH_45 30 nLsykllnkYLdmLvekgli.....kkskekYvlTekGlelle 67
                                      ++   +l   Ld+Lv+kgl+     + +++ Y+lT +G++ le
  gi|336254506|ref|YP_004597613.1| 37 EIHHGRLYPNLDTLVDKGLVekgrrDRRTNFYTLTRRGRRELE 79
                                      56666777789*********88886678999*******99887 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 !   16.3   0.2   3.6e-06     0.011       9      68 .]      12      74 ..       4      74 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.6e-06
                            HTH_27  9 Lhlir...hrrrrkkladlcgrlnvedshis..yslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      L +i+   ++++ +++++l +++  e  h+    +l+ L+ kGLv  ++ ++drr+ +++lT  G
  gi|336254506|ref|YP_004597613.1| 12 LYVIAgeeEPHGLAIKEELEEYYEKEIHHGRlyPNLDTLVDKGLV--EKGRRDRRTNFYTLTRRG 74
                                      555555544555555577777777666666663489*********..555589*********766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.016        46       2      20 ..       3      21 ..       2      33 .. 0.81
   2 ?    8.3   0.1   0.00071       2.1      42      61 ..      47      64 ..      37      65 .. 0.87
   3 ?   -1.0   0.0      0.58   1.7e+03      25      37 ..      76      88 ..      68      89 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.016
                                      T--HHHHHHHHHHHCTTTS CS
                            MarR_2  2 gltpaqarvLaaLgrrpgr 20
                                      +lt+ q+++L++++ ++++
  gi|336254506|ref|YP_004597613.1|  3 DLTGFQRDLLYVIAGEEEP 21
                                      78999*********99987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00071
                                      HHHHHHTTSEEEEESSSSSS CS
                            MarR_2 42 lkrLvaaGLverrpgpeDkR 61
                                      l+ Lv++GLve+ +   D+R
  gi|336254506|ref|YP_004597613.1| 47 LDTLVDKGLVEKGRR--DRR 64
                                      789********8855..998 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.58
                                      HHHHHHHTSSHHH CS
                            MarR_2 25 gelarrlglsksa 37
                                      +el++r g + ++
  gi|336254506|ref|YP_004597613.1| 76 RELEARRGWEAQY 88
                                      3566666666665 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.6e-05      0.17      40      71 ..      47      79 ..      42      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.6e-05
                           DUF4364 40 lseLvesglieee.ekenktlykiTekGketle 71
                                      l+ Lv++gl+e+  +++ +++y++T +G++ le
  gi|336254506|ref|YP_004597613.1| 47 LDTLVDKGLVEKGrRDRRTNFYTLTRRGRRELE 79
                                      899*********988899**********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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):               6  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 747.24
//
Query:       gi|336254507|ref|YP_004597614.1|  [L=48]
Description: hypothetical protein Halxa_3121 [Halopiger xanaduensis SH-6]
Scores for 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   0.1      0.013   15.9   0.1    1.1  1  DUF2172   Domain of unknown function (DUF2172)
        0.1   12.4   0.3       0.11   12.4   0.3    1.0  1  NMT       Myristoyl-CoA:protein N-myristoyltransferase, N-ter


Domain annotation for each model (and alignments):
>> DUF2172  Domain of unknown function (DUF2172)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.1   1.5e-06     0.013      41      76 ..      12      47 ..       5      48 .] 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-06
                                      HHHGGGEE--TTSTT--B--B-SSS----EE--HHH CS
                           DUF2172 41 eeLkkhlhtlpeqpdaipyrtsyykeeWGFclshee 76
                                      e L++hl +++ + d ++ +++yyk+  G++l++e+
  gi|336254507|ref|YP_004597614.1| 12 EFLTEHLESDEMRHDGVEQMFTYYKRALGWVLEEEH 47
                                      6799****************************9876 PP

>> NMT  Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   1.2e-05      0.11      29      69 ..       1      45 [.       1      48 [] 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                                      TTSHHHHHHHHHHHHHHSSCT....TTSTEEE---HHHHHHHCTS CS
                               NMT 29 ledeeelkevyelLsenYved....ddamfrfkyskeflkWalkp 69
                                      ++deee++e ye+L+e+   d    d     f+y k  l W l+ 
  gi|336254507|ref|YP_004597614.1|  1 MRDEEEIREQYEFLTEHLESDemrhDGVEQMFTYYKRALGWVLEE 45
                                      5799***********99866522214456789*********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 377.29
//
Query:       gi|336254508|ref|YP_004597615.1|  [L=259]
Description: hypothetical protein Halxa_3122 [Halopiger xanaduensis SH-6]
Scores for 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-10   40.6   1.5    4.3e-05   23.7   0.1    2.6  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    8.8e-07   28.8   2.5    2.4e-05   24.2   0.6    3.0  2  Big_1            Bacterial Ig-like domain (group 1)
    3.2e-06   27.0   0.6      0.057   13.4   0.1    2.8  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
    0.00017   21.8   8.8    0.00038   20.7   1.4    2.7  2  Invasin_D3       Invasin, domain 3
     0.0046   16.7   0.1     0.0092   15.8   0.1    1.5  1  DUF824           Salmonella repeat of unknown function (DUF82
     0.0077   16.4   0.3      0.037   14.2   0.1    2.2  2  MG4              Macroglobulin domain MG4
  ------ inclusion threshold ------
      0.013   15.4   0.0       0.12   12.3   0.0    2.4  2  Y_Y_Y            Y_Y_Y domain
      0.022   14.5   2.5          1    9.1   0.9    2.3  2  DUF2606          Protein of unknown function (DUF2606)
       0.15   11.5   2.9       0.18   11.3   1.5    1.7  2  Dioxygenase_C    Dioxygenase
        2.1    6.8  15.2          3    6.3  15.2    1.2  1  UPF0560          Uncharacterised protein family UPF0560


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 !   15.6   0.2   8.2e-06     0.015       1      26 [.      80     105 ..      80     126 .. 0.82
   2 !   23.7   0.1   2.4e-08   4.3e-05      25      81 ..     165     218 ..     158     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.2e-06
                   CarboxypepD_reg   1 tisGrVtdasgapiagatVtvtnadt 26 
                                       t++ +V d +g+p++gatV+v+ ++ 
  gi|336254508|ref|YP_004597615.1|  80 TLTVTVEDDQGEPVEGATVSVEGDGA 105
                                       68899****************96544 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 2.4e-08
                   CarboxypepD_reg  25 dtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttlditL 81 
                                       +tg++ +  td++G+  ++ l+ g+y+vt++++G +     evt++ g++++l++tL
  gi|336254508|ref|YP_004597615.1| 165 GTGESWEDETDENGEVEFEELEDGDYTVTAESDGEEAED--EVTIE-GEDEDLTLTL 218
                                       567788889*************************98888..49999.9999999998 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 !   24.2   0.6   1.3e-08   2.4e-05       4      34 ..      76     107 ..      74     126 .. 0.86
   2 ?    3.3   0.1     0.045        82      39      64 .]     171     194 ..     158     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.3e-08
                             Big_1   4 vdtntltatvkDangnpvagatVtfsvsg.ga 34 
                                       ++t tlt+tv D +g pv+gatV+++ +g g 
  gi|336254508|ref|YP_004597615.1|  76 TETYTLTVTVEDDQGEPVEGATVSVEGDGaGG 107
                                       6889*********************9999654 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.045
                             Big_1  39 sgtTdanGkatvtltstkagtvtvtA 64 
                                       +  Td+nG+++++    + g++tvtA
  gi|336254508|ref|YP_004597615.1| 171 EDETDENGEVEFE--ELEDGDYTVTA 194
                                       678*****98875..55777777776 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00015      0.28       5      31 ..      85     110 ..      81     116 .. 0.81
   2 !   13.4   0.1   3.2e-05     0.057      28      74 ..     172     216 ..     165     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                   CarbopepD_reg_2   5 VvdketkeplpgatVyvkgtkkgtvTd 31 
                                       V +++++ep++gatV+v+g ++g + d
  gi|336254508|ref|YP_004597615.1|  85 V-EDDQGEPVEGATVSVEGDGAGGMMD 110
                                       4.44568*************9998766 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.2e-05
                   CarbopepD_reg_2  28 tvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvni 74 
                                         TdenG+ e+++l++g+yt+++++ G +  e +vt+++e   d+++
  gi|336254508|ref|YP_004597615.1| 172 DETDENGEVEFEELEDGDYTVTAESDGEEA-EDEVTIEGE-DEDLTL 216
                                       57*************************888.689999754.334444 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   1.4   2.1e-07   0.00038      19      60 ..      76     115 ..      65     128 .. 0.82
   2 ?    4.5   1.4     0.025        44      45      91 ..     159     207 ..     122     218 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.1e-07
                        Invasin_D3  19 kststltvtlkDangnpvsgltvtfsttsagtlsavtdngdG 60 
                                       ++t tltvt++D++g+pv g+tv++  + ag  + ++d+ dG
  gi|336254508|ref|YP_004597615.1|  76 TETYTLTVTVEDDQGEPVEGATVSVEGDGAG--GMMDDEMDG 115
                                       67899*********************88555..566666666 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.025
                        Invasin_D3  45 tt..sagtlsavtdngdGtytatLtattagtatitptvnGvaiaatatv 91 
                                       t+    gt ++++d+ d   ++++   + g +t+t++ +G+++++++t+
  gi|336254508|ref|YP_004597615.1| 159 TDdeMGGTGESWEDETDENGEVEFEELEDGDYTVTAESDGEEAEDEVTI 207
                                       3332333666666666666666666667777777777777544444443 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 !   15.8   0.1   5.2e-06    0.0092      13      36 ..      77     100 ..      75     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.2e-06
                            DUF824  13 EsipltitvkDasGnPvpnapftl 36 
                                       E+ +lt+tv D++G+Pv  a++++
  gi|336254508|ref|YP_004597615.1|  77 ETYTLTVTVEDDQGEPVEGATVSV 100
                                       8889****************9987 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   2.1e-05     0.037      16      48 ..      79     120 ..      76     143 .. 0.72
   2 ?   -0.8   0.0      0.95   1.7e+03      50      61 ..     172     183 ..     152     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                               MG4  16 fsikVlvkdpdgspaknvpVkiealk..............seteeke 48 
                                       ++++V v+d +g+p+++ +V++e  +              s    +e
  gi|336254508|ref|YP_004597615.1|  79 YTLTVTVEDDQGEPVEGATVSVEG-DgaggmmddemdgneS----DE 120
                                       9***********************.4455666666544331....22 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.95
                               MG4  50 lttdedGtakfs 61 
                                        +tde+G ++f 
  gi|336254508|ref|YP_004597615.1| 172 DETDENGEVEFE 183
                                       567788877774 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 ?   -0.3   0.0      0.61   1.1e+03      40      53 ..      78      91 ..      72     101 .. 0.72
   2 ?   12.3   0.0   6.9e-05      0.12      19      47 ..     168     196 ..     164     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.61
                                      EEEEEEEEEETTS- CS
                             Y_Y_Y 40 dYtlkVkakdndgq 53
                                      +Ytl+V + d+ g+
  gi|336254508|ref|YP_004597615.1| 78 TYTLTVTVEDDQGE 91
                                      69999999886554 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6.9e-05
                                       SSEEEESSTS.EEEEES--SEEEEEEEEE CS
                             Y_Y_Y  19 keWveasdysqeasytnlppGdYtlkVka 47 
                                       ++W++++d + e+++ +l+ GdYt++++ 
  gi|336254508|ref|YP_004597615.1| 168 ESWEDETDENGEVEFEELEDGDYTVTAES 196
                                       57888888877*************99875 PP

>> DUF2606  Protein of unknown function (DUF2606)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.012        22      39      63 ..      76     100 ..      65     132 .. 0.80
   2 ?    9.1   0.9   0.00057         1      82     107 ..     172     197 ..     150     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.012
                           DUF2606  39 kvvisvtlhvkdkkklPvkdvevil 63 
                                         + ++t+ v+d ++ Pv++  v +
  gi|336254508|ref|YP_004597615.1|  76 TETYTLTVTVEDDQGEPVEGATVSV 100
                                       446789999***********99876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00057
                           DUF2606  82 GktdkeGdvkwdtvrkGdyivaltkn 107
                                         td++G+v +++   Gdy+v    +
  gi|336254508|ref|YP_004597615.1| 172 DETDENGEVEFEELEDGDYTVTAESD 197
                                       47******************976543 PP

>> Dioxygenase_C  Dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.5   9.8e-05      0.18      12      75 ..      61     123 ..      54     134 .. 0.73
   2 ?   -2.0   0.0       1.1     2e+03      80     101 ..     174     195 ..     155     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.8e-05
                                       EEESEEE---S--TT--EEEEEEEEE-TTSSB-TT-EEEEE---TTS--TTS-TTS-SSTTTTE CS
                     Dioxygenase_C  12 ededlarledkgeeegerlvlsGrvldeaGkplagalvelWhanaeGrYshkkeeheapelnlr 75 
                                       e+e++ ++e+  e   e+ +l+ +v d +G+p++ga+v +    a G+ + + +  ++++ n +
  gi|336254508|ref|YP_004597615.1|  61 ENETEDENETDTETDTETYTLTVTVEDDQGEPVEGATVSVEGDGAGGMMDDEMDG-NESDENAT 123
                                       44555555555578889999999****************9887777777777766.55565655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                                       --TTSEEEEEEE----EE--TT CS
                     Dioxygenase_C  80 tdeeGryrirtikPapYpipnd 101
                                       tde+G+ +++ ++ + Y +  +
  gi|336254508|ref|YP_004597615.1| 174 TDENGEVEFEELEDGDYTVTAE 195
                                       7889999998888888887664 PP

>> UPF0560  Uncharacterised protein family UPF0560
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  15.2    0.0016         3     677     802 ..      40     164 ..       8     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0016
                           UPF0560 677 asldsgvd.lneaksgrrgreekkerkekeskkaaeakaysklvyvddleesssesrtavcspednsltplldekae 752
                                        + + g+d +ne+ ++ +  +e++++ e+e+ + +++++y+  v v+d + +  e   a++s e + +  ++d++++
  gi|336254508|ref|YP_004597615.1|  40 ETEEDGMDtTNESDNESELGDENETEDENETDTETDTETYTLTVTVEDDQGEPVE--GATVSVEGDGAGGMMDDEMD 114
                                       34567888567788888888888888888999999******99999965544444..46799999999******999 PP

                           UPF0560 753 krgetlprkgrsrgnssrseespseserdsltspeddsededdaedDqee 802
                                        +++  ++   ++++++++++ +s  +++      dd+e++++a+dD+  
  gi|336254508|ref|YP_004597615.1| 115 GNESDENATDDNETDENETDDNESALNESDAGNETDDNESDENATDDEMG 164
                                       55554444444445555555677888888788888888888888998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1358  (0.0757432); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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):              10  [number of targets reported over threshold]
# CPU time: 1.03u 0.33s 00:00:01.36 Elapsed: 00:00:00.48
# Mc/sec: 1608.00
//
Query:       gi|336254509|ref|YP_004597616.1|  [L=243]
Description: hypothetical protein Halxa_3123 [Halopiger xanaduensis SH-6]
Scores for 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   17.9   0.2      0.012   15.6   0.2    2.1  2  HypA           Hydrogenase/urease nickel incorporation, metal
  ------ inclusion threshold ------
      0.018   14.6   1.5      0.046   13.2   1.5    1.7  1  TF_Zn_Ribbon   TFIIB zinc-binding
      0.019   15.0   0.2      0.034   14.2   0.2    1.3  1  DZR            Double zinc ribbon
       0.09   13.0   0.1       0.19   12.0   0.1    1.5  1  DUF2072        Zn-ribbon containing protein
      0.091   12.8   0.4        0.3   11.1   0.4    1.9  1  DUF1451        Zinc-ribbon containing domain
       0.16   12.4   1.8        3.4    8.2   0.1    2.7  2  zf-IS66        zinc-finger binding domain of transposase IS66
       0.17   12.0   0.2       0.35   10.9   0.2    1.5  1  Zn_Tnp_IS91    Transposase zinc-binding domain
       0.25   11.5   1.5       0.69   10.1   1.5    1.7  1  Zn-ribbon_8    Zinc ribbon domain
        1.9    8.6   4.7        1.3    9.2   0.4    2.2  2  UPF0547        Uncharacterised protein family UPF0547
        1.9    8.5   5.6        8.3    6.5   0.1    2.7  3  Zn_Tnp_IS1595  Transposase zinc-ribbon 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 !   15.6   0.2   6.7e-06     0.012      68      96 ..       4      33 ..       1      53 [. 0.83
   2 ?   -1.1   0.0         1   1.8e+03      15      52 ..     180     217 ..     174     234 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.7e-06
                                      --EEEETTTS-EEECHHH.HHS-TTTSSS- CS
                              HypA 68 pvkvrCreCgkefeleek.alrCpkCgsad 96
                                      + + +C+eCg++++  e+ ++ Cp+Cgs +
  gi|336254509|ref|YP_004597616.1|  4 RGERECKECGTRWSYYETgSIGCPACGSIR 33
                                      56779*********77666899*****974 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                                       HHHHCCTT..EEEEEEEEEETTCT--HHHHHHHHHHHH CS
                              HypA  15 eeeakeaaarkvtkvkvevGelsgvepeaLefafella 52 
                                       e++a e+ +++v+++++  G+++    e+L  a + la
  gi|336254509|ref|YP_004597616.1| 180 ERTALETLGEHVKRIRMLDGDVEPRTAEQLIDATRDLA 217
                                       56665555689999999888888777777766655555 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.5   2.6e-05     0.046       2      36 ..       8      39 ..       7      45 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.6e-05
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCC CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednside 36
                                       C++Cg++     +e+g + C++CG++     ide
  gi|336254509|ref|YP_004597616.1|  8 ECKECGTR--WSYYETGSIGCPACGSIRS-VGIDE 39
                                      5*****98..45599**********9876.55655 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   1.9e-05     0.034      12      37 ..       6      32 ..       3      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                               DZR 12 arfCseCgtklkavaa.edrCpsCgek 37
                                       r C+eCgt+ + +++ ++ Cp+Cg+ 
  gi|336254509|ref|YP_004597616.1|  6 ERECKECGTRWSYYETgSIGCPACGSI 32
                                      688********987779*******985 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   0.00011      0.19       3      68 ..       8      70 ..       7      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                           DUF2072  3 kCtkCekvfedgskeilkGCpsCGgkkFlyvkeeekkedvseekeelvaeaeeeieevldaeetee 68
                                      +C +C++ ++  ++    GCp+CG  + + + e+++++d + + +   +  +++i++v   + +e+
  gi|336254509|ref|YP_004597616.1|  8 ECKECGTRWSYYET-GSIGCPACGSIRSVGIDERTEHTDLQVAFD--LTAVRSDIDDVPTDDLAER 70
                                      69999988766665.456*****************9999887766..3344445566644444444 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00017       0.3     112     140 ..       4      31 ..       1      33 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                           DUF1451 112 lGtlvCekCgkelalkkteeippCpkCga 140
                                        G+ +C++Cg++ ++++t+ i  Cp+Cg+
  gi|336254509|ref|YP_004597616.1|   4 RGERECKECGTRWSYYETGSIG-CPACGS 31 
                                       58899****************5.****96 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 ?    2.8   0.1     0.091   1.6e+02       1       9 [.       6      14 ..       3      19 .. 0.76
   2 ?    8.2   0.1    0.0019       3.4       4      25 ..      26      46 ..      24      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.091
                           zf-IS66  1 prtCpcCGg 9 
                                      +r C++CG+
  gi|336254509|ref|YP_004597616.1|  6 ERECKECGT 14
                                      567888876 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0019
                           zf-IS66  4 CpcCGgllkpigedrvreeldi 25
                                      Cp CG+  + +g d+++e+ d+
  gi|336254509|ref|YP_004597616.1| 26 CPACGS-IRSVGIDERTEHTDL 46
                                      *****8.579****99999987 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 ?   10.9   0.2    0.0002      0.35      40      69 ..       7      35 ..       4      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                       Zn_Tnp_IS91 40 yeCeeCghekivyfsCksrhCpsCqkkate 69
                                       eC+eCg ++++y+  +s  Cp C++ ++ 
  gi|336254509|ref|YP_004597616.1|  7 RECKECG-TRWSYYETGSIGCPACGSIRSV 35
                                      58****9.59999************98765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.5   0.00039      0.69       7      35 ..       8      33 ..       6      35 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00039
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.e 35
                                      +C+eCg++     +      + CP+Cgs +
  gi|336254509|ref|YP_004597616.1|  8 ECKECGTRWSYYET----GSIGCPACGSiR 33
                                      7*****98886654....3456*****955 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4    0.0007       1.3      15      25 ..       7      17 ..       7      18 .. 0.91
   2 ?    0.7   0.4      0.32   5.7e+02      17      21 ..      26      30 ..      24      32 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0007
                           UPF0547 15 qfCphCGyvFq 25
                                      ++C +CG++++
  gi|336254509|ref|YP_004597616.1|  7 RECKECGTRWS 17
                                      69********7 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.32
                           UPF0547 17 CphCG 21
                                      Cp CG
  gi|336254509|ref|YP_004597616.1| 26 CPACG 30
                                      66665 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 ?    3.7   0.8     0.034        61      35      45 ..       4      14 ..       1      15 [. 0.81
   2 ?    6.5   0.1    0.0046       8.3      20      34 ..      25      39 ..      14      43 .. 0.74
   3 ?   -3.1   0.0       4.6   8.2e+03       4      13 ..      73      82 ..      71      86 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.034
                     Zn_Tnp_IS1595 35 rglfqCkeCrk 45
                                      rg  +CkeC++
  gi|336254509|ref|YP_004597616.1|  4 RGERECKECGT 14
                                      7899*****86 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0046
                     Zn_Tnp_IS1595 20 vCPhCgsrkayrikt 34
                                       CP+Cgs ++  i  
  gi|336254509|ref|YP_004597616.1| 25 GCPACGSIRSVGIDE 39
                                      4*****998887765 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4.6
                     Zn_Tnp_IS1595  4 eearalLeal 13
                                      e +r+++ ++
  gi|336254509|ref|YP_004597616.1| 73 ERCRDYVRRR 82
                                      6788887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1773.64
//
Query:       gi|336254510|ref|YP_004597617.1|  [L=297]
Description: Bifunctional protein folD [Halopiger xanaduensis SH-6]
Scores for complete 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-67  225.7   1.1    2.4e-67  225.2   1.1    1.2  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
    2.3e-36  124.6   0.0    3.5e-36  124.0   0.0    1.3  1  THF_DHG_CYH    Tetrahydrofolate dehydrogenase/cyclohydrolase,
  ------ inclusion threshold ------
      0.027   13.8   0.6      0.042   13.1   0.6    1.3  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain


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 !  225.2   1.1     4e-71   2.4e-67       1     158 [.     122     288 ..     122     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 225.2 bits;  conditional E-value: 4e-71
                                       SHHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCT....T-EEEEE-TTSCCH CS
                     THF_DHG_CYH_C   1 hplnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLlek....natVtvchsktkdl 73 
                                       hp n+grlv+g+  ++pctp+gv +ll+++++++eg +v++vGrs+ivgkpla lL +k    natVtvchs+t+dl
  gi|336254510|ref|YP_004597617.1| 122 HPENVGRLVAGDARFRPCTPHGVQKLLEAADVDTEGTDVTIVGRSDIVGKPLANLLIQKaddgNATVTVCHSRTDDL 198
                                       899*******************************************************99999************** PP

                                       HHHHCCSSEEEE-SS-TT-B-GGGS-TT-EEEE---EEC.....-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHH CS
                     THF_DHG_CYH_C  74 aeitreadivvvavGkpelikaemvkegavviDvGinrv.....ekgklvGDvdfeevkevasaitPvpgGVGpmTv 145
                                       ae+tr+adivv+a+G+p+l++++mv egavviDvG+nrv     ++++lvGDv+fe++ke+asaitPvpgGVGpmT 
  gi|336254510|ref|YP_004597617.1| 199 AEKTRSADIVVAAAGVPQLVDGSMVGEGAVVIDVGVNRVdadneKGYELVGDVEFESAKEKASAITPVPGGVGPMTR 275
                                       *****************************************9988899***************************** PP

                                       HHHHHHHHHHHHC CS
                     THF_DHG_CYH_C 146 amllkntleaakr 158
                                       amll nt++aa+ 
  gi|336254510|ref|YP_004597617.1| 276 AMLLYNTVKAASL 288
                                       *********9975 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 !  124.0   0.0   5.8e-40   3.5e-36       1     116 []       4     119 ..       4     119 .. 0.99

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 5.8e-40
                                       E--HHHHHHHHHHHHHHHHHHHHHHT---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHH CS
                       THF_DHG_CYH   1 lldGkalakeireelkeeveklkekgvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellkl 77 
                                       ++dG+a+a++ire+l++ +e+l + g +p+La++l+gddpase+Yv++k++ ceevGies +++++ d+  e+l ++
  gi|336254510|ref|YP_004597617.1|   4 IIDGNAVASQIREDLTDAIETLADAGARPGLATVLMGDDPASETYVNMKQRDCEEVGIESYHVDVDGDAPPETLYDE 80 
                                       79*********************999*************************************************** PP

                                       HHHHHH-TT--EEEE-SS-STTS-HHHHHCCS-GGGBTT CS
                       THF_DHG_CYH  78 ieelneddsvdGilvqlPlpkhidekaileaispeKDVD 116
                                       i eln +d+v+G +vq P+p+h+d ++++ +++p+KDVD
  gi|336254510|ref|YP_004597617.1|  81 IGELNGNDDVHGYIVQAPVPDHVDYREVIRRVDPAKDVD 119
                                       **************************************9 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 ?   13.1   0.6   7.1e-06     0.042      68     130 ..     182     235 ..     157     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.1e-06
                                       HHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEEEETTGG CS
                       AlaDh_PNT_C  68 eslgakfvevlksqeellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgsVivDvAid 130
                                       ++ +a+ v+v +s  + lae+ ++ad+v+ ++ +     P+Lv+ +mv    +g+V++Dv ++
  gi|336254510|ref|YP_004597617.1| 182 DDGNAT-VTVCHSRTDDLAEKTRSADIVVAAAGV-----PQLVDGSMVG---EGAVVIDVGVN 235
                                       444555.99*********************9765.....89******97...6******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2282.72
//
Query:       gi|336254511|ref|YP_004597618.1|  [L=315]
Description: hypothetical protein Halxa_3125 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.47    9.9   3.8       0.71    9.3   3.8    1.2  1  Osteopontin  Osteopontin


Domain annotation for each model (and alignments):
>> Osteopontin  Osteopontin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.8     4e-05      0.71      69     191 ..     148     270 ..     145     299 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXX CS
                       Osteopontin  69 DddddddhvdsqdsvdsddsdetddsdksdeshhsDesDelvtdfptdvpatevf..tpavPtvdtydGRGDsvayg 143
                                       D  dd+d v +       d d t  ++  d   +s   D+++ d p dvp+++v+  ++a+ t d   G GD v+ +
  gi|336254511|ref|YP_004597618.1| 148 DTPDDSDPVAEGTIEHERDGDPTPRPETMDAPIDSLAFDDVMADAPSDVPEADVVgiLEAIETHD-LVGAGDHVTGK 223
                                       55678887776665566677889999***************************952245555544.459****9865 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Osteopontin 144 lrskskkfkksevqypdateeDltskleseelddahkailvaqklkva 191
                                           +   +       da  e l+  le +++d + +a+ va+++++ 
  gi|336254511|ref|YP_004597618.1| 224 PPLSV-DDRAVCLLPDDAWTERLAPALEEHDVDVDLDALEVARTMHRR 270
                                       44433.3334444556788899*********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2563.92
//
Query:       gi|336254512|ref|YP_004597619.1|  [L=231]
Description: hypothetical protein Halxa_3126 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0015   19.2   0.1     0.0026   18.4   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.023   14.5   0.0      0.031   14.1   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
      0.037   14.7   0.0      0.062   14.0   0.0    1.5  1  Methyltransf_11  Methyltransferase domain


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 !   18.4   0.1   4.4e-07    0.0026       1      58 [.      56     105 ..      56     156 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.4e-07
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGB CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedl 58 
                                       vLd+G+G Gr++l+ ++r+   + +++++s+ ++e++r r  e+      +++d+ +l
  gi|336254512|ref|YP_004597619.1|  56 VLDMGAGAGRDALYYQARF---ETVAIEVSDHLVETMRDRGVED-----ARRADMFAL 105
                                       9***************996...9***************998553.....334444333 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.2e-06     0.031      25      62 ..      55     100 ..      21     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.2e-06
                   Methyltransf_23  25 rvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........k 62 
                                        vLd+G+G G+ + +++++ f+ ++++ s+++ve  +          
  gi|336254512|ref|YP_004597619.1|  55 PVLDMGAGAGRDALYYQAR-FETVAIEVSDHLVETMRdrgvedarrA 100
                                       69************99555.9**********9998877764444441 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     1e-05     0.062       1      55 [.      57     105 ..      57     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaekl 55 
                                       Ld+G+G+Gr a +++ r+ ++v++++s+ ++++ +++++e+      ++ad+  l
  gi|336254512|ref|YP_004597619.1|  57 LDMGAGAGRDALYYQARF-ETVAIEVSDHLVETMRDRGVEDA-----RRADMFAL 105
                                       8**************888.9*******************998.....77777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1754.93
//
Query:       gi|336254513|ref|YP_004597620.1|  [L=415]
Description: glycine hydroxymethyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-155  518.2   0.0   1.3e-155  518.0   0.0    1.0  1  SHMT             Serine hydroxymethyltransferase
    8.1e-09   35.2   0.1     0.0021   17.4   0.1    2.1  2  Beta_elim_lyase  Beta-eliminating lyase
    3.4e-08   33.1   0.0    1.2e-07   31.3   0.0    1.7  2  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.021   14.2   0.1      0.028   13.7   0.1    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


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 !  518.0   0.0  2.9e-159  1.3e-155       2     399 .]       7     384 ..       6     384 .. 0.98

  Alignments for each domain:
  == domain 1  score: 518.0 bits;  conditional E-value: 2.9e-159
                                       HHHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHH CS
                              SHMT   2 eesdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakel 78 
                                       +e+dp+va+++++e++rq++++++iasen +s+av++a+Gs ltnkyaeGyPG+ryyGGcef deveela++ra el
  gi|336254513|ref|YP_004597620.1|   7 REVDPDVADALENEVDRQRSTLQMIASENHASEAVIDAQGSALTNKYAEGYPGERYYGGCEFADEVEELAIERATEL 83 
                                       689************************************************************************** PP

                                       CT-STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSS CS
                              SHMT  79 fkldpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketgl 155
                                       f+++    +vnvqp++G+qan+avy a+lepgd+il+ldl +GGhl+hG + ++     +++l+e+ +y+vd+etg+
  gi|336254513|ref|YP_004597620.1|  84 FGAE----HVNVQPHAGTQANQAVYFAMLEPGDKILSLDLNHGGHLSHGHPANF-----TGQLYEVEQYEVDPETGY 151
                                       ****....*********************************************9.....****************** PP

                                       B-HHHHHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESSS CS
                              SHMT 156 idydelekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttthk 232
                                       idy++l ++a ef P +iv+G say+r i+++r++++ad+v+a  l+d+ahi+Glvaagv+psP+  ad+vt  thk
  gi|336254513|ref|YP_004597620.1| 152 IDYESLAEHAAEFEPDIIVSGYSAYPREIEWERIQDVADDVDALHLADIAHITGLVAAGVHPSPVGVADFVTGSTHK 228
                                       ***************************************************************************** PP

                                       TT-S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHH CS
                              SHMT 233 tlrGprgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlkna 309
                                       t+r  rgg++++               ee+++ i+savfPg qGGPl+h +a+kav++kealepef  y++q ++na
  gi|336254513|ref|YP_004597620.1| 229 TIRAGRGGIVMCD--------------EEYADDIDSAVFPGGQGGPLMHNVAGKAVGFKEALEPEFEDYAEQTVANA 291
                                       ************9..............89************************************************ PP

                                       HHHHHHHHHTT-EEGGGS-SSSEEEEEGGGG..TS-HHHHHHHHHHTTEE-EEE--TTS.STTTT-SEEEEESHHHH CS
                              SHMT 310 kalaealkekgyklvsgGtdnhlvlvdlrek..gldGkraekvlekvnitankntvPgd.ksalvtsGlrlGtpalt 383
                                       kal e l e+g++lvsgGtdnhlvlvdlre   +++G +ae++le++ i  n ntvPg+ +s++ +sG+r Gtpalt
  gi|336254513|ref|YP_004597620.1| 292 KALGESLSEHGFSLVSGGTDNHLVLVDLREShpDTSGGDAEEALEEAGIVLNGNTVPGEtRSPFDPSGIRAGTPALT 368
                                       *****************************9733688***************************************** PP

                                       HTT--HHHHHHHHHHH CS
                              SHMT 384 srgfkeedlekvakfi 399
                                       +rgf+eed +kv+++i
  gi|336254513|ref|YP_004597620.1| 369 TRGFDEEDCRKVGDLI 384
                                       ************9876 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   4.7e-07    0.0021      38     120 ..      77     163 ..      35     172 .. 0.74
   2 !   15.8   0.0   1.4e-06    0.0063     188     242 ..     218     326 ..     179     369 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.7e-07
                                       HHHHHHHTT-SEEE.EES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT....TBE CS
                   Beta_elim_lyase  38 edavaelfgkeaal.fvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea....Gkm 109
                                        ++++elfg+e++    + Gt+An+  + ++l++g++++  + +h+     g +a + g  l ++++ e     G++
  gi|336254513|ref|YP_004597620.1|  77 IERATELFGAEHVNvQPHAGTQANQAVYFAMLEPGDKILSLDLNHGGHLSHGHPANFTGQ-LYEVEQYEVdpetGYI 152
                                       367889*****87526778**************************999999999999776.5555544444556*** PP

                                       -HHHHHHHS-- CS
                   Beta_elim_lyase 110 dlekleaaike 120
                                       d e+l+++ +e
  gi|336254513|ref|YP_004597620.1| 153 DYESLAEHAAE 163
                                       *9999987666 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.4e-06
                                       TSSEEEEESSSTT--SS-EEEEE-HH.......................................HHHHHHHHHHHH CS
                   Beta_elim_lyase 188 yvDsvtmslkKdllanvGgvlafrddel...................................edylaerveqrkyl 229
                                       ++D vt s  K + a  Gg+++ +++ +                                   edy ++ v+ +k+l
  gi|336254513|ref|YP_004597620.1| 218 VADFVTGSTHKTIRAGRGGIVMCDEEYAddidsavfpggqggplmhnvagkavgfkealepefEDYAEQTVANAKAL 294
                                       69***********************966************************************************* PP

                                       T---SSTHHHHH.................... CS
                   Beta_elim_lyase 230 ggglrqagvlaa...................l 242
                                       g+ l+++g+  +                    
  gi|336254513|ref|YP_004597620.1| 295 GESLSEHGFSLVsggtdnhlvlvdlreshpdT 326
                                       *********99944444444444444444440 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 ?   -1.7   0.0      0.28   1.3e+03      81     123 ..      25      67 ..      22      73 .. 0.86
   2 !   31.3   0.0   2.7e-11   1.2e-07      44     351 ..      67     367 ..      58     374 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBE CS
                     Aminotran_1_2  81 iealifllklnpgdeilvpdptyasyknilrlsggevvryply 123
                                       +++l ++++ n+ +e +++++  a  +++++ + ge ++  ++
  gi|336254513|ref|YP_004597620.1|  25 RSTLQMIASENHASEAVIDAQGSALTNKYAEGYPGERYYGGCE 67 
                                       6789999999**************9999999999999887665 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 2.7e-11
                                       THHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSE.... CS
                     Aminotran_1_2  44 dglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsgge.... 116
                                       + ++e+ee  ++ +   e    ++  +v+   G++a++++ +++l+  pgd+il+ d++++ +      + ++    
  gi|336254513|ref|YP_004597620.1|  67 EFADEVEELAIERAT--ELFGAEHV-NVQPHAGTQANQAVYFAMLE--PGDKILSLDLNHGGHLSHGHPANFTgqly 138
                                       555555555554444..33336667.**********9999999997..************98766555444441100 PP

                                       .EEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTT CS
                     Aminotran_1_2 117 .vvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYag 192
                                        v +y++ ++e+  +d e+l e  +e+   ++   +i+  +      + + + e+e + d+a+   +l + D a+ +
  gi|336254513|ref|YP_004597620.1| 139 eVEQYEV-DPETGYIDYESLAEHAAEF---EP--DIIV-SGY----SAYPREIEWERIQDVADDVDALHLADIAHIT 204
                                       0444442.3588899999999966664...44..5554.443....3678888************************ PP

                                       CBSSSSHTHHHHGGSTTSTT...EEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHH CS
                     Aminotran_1_2 193 fvfgsldavatranveeepn...llivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaals 265
                                       +           a+v + p    ++++gs  K    aG R G++ +++++++ + +++ p+     l+  ++ +a+ 
  gi|336254513|ref|YP_004597620.1| 205 GLVA--------AGVHPSPVgvaDFVTGSTHKTIR-AG-RGGIVMCDEEYADDIDSAVFPGGQgGPLMHNVAGKAVG 271
                                       ***8........566666666668999**999985.45.77***************999988867778888889999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSSEEEEEETHH...CHHHHHHHHHHTCTEEEEEGGGG CS
                     Aminotran_1_2 266 dallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgmflltdlsae...takelskkLleevgvyvtpgtsf 338
                                        ++  + e+e+ +++  +++k l ++L e g++ ++    + ++l+dl+++   t    +++ lee g+++  +t +
  gi|336254513|ref|YP_004597620.1| 272 FKEALEPEFEDYAEQTVANAKALGESLSEHGFSLVSGGtDNHLVLVDLREShpdTSGGDAEEALEEAGIVLNGNTVP 348
                                       9999989**************************99988789999999999977733333444677779999999999 PP

                                       TS......TTEEEEECTTS CS
                     Aminotran_1_2 339 tv......pgrlRitvAgl 351
                                       +       p+ +R   ++l
  gi|336254513|ref|YP_004597620.1| 349 GEtrspfdPSGIRAGTPAL 367
                                       8877777766677666555 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 ?   13.7   0.1   6.2e-06     0.028      91     201 ..     144     255 ..      82     277 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.2e-06
                                       -B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB--..-HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEE CS
                   DegT_DnrJ_EryC1  91 DvdpdtynidpaaieaaitertkaIlpVhlyGqva..dmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaa 165
                                       +vdp+t  id +++++   e    I++  +   +   + ++++++a++ +   + D Ah  G   +g +   +g a 
  gi|336254513|ref|YP_004597620.1| 144 EVDPETGYIDYESLAEHAAEFEPDIIVSGYSAYPReiEWERIQDVADDVDALHLADIAHITGLVAAGVHPSPVGVAD 220
                                       89********************9999998877777225678*********************999995555555555 PP

                                       EEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTT CS
                   DegT_DnrJ_EryC1 166 vfSFyptKnlttGeGGavvtndeelaekarvlrnhG 201
                                        +     K++ +G GG+v+  dee+a+ +      G
  gi|336254513|ref|YP_004597620.1| 221 FVTGSTHKTIRAGRGGIVMC-DEEYADDIDSAVFPG 255
                                       555556799*******9876.566776666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3208.96
//
Query:       gi|336254514|ref|YP_004597621.1|  [L=765]
Description: hypothetical protein Halxa_3128 [Halopiger xanaduensis SH-6]
Scores for 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  (765 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.39
# Mc/sec: 5823.32
//
Query:       gi|336254515|ref|YP_004597622.1|  [L=272]
Description: hypothetical protein Halxa_3129 [Halopiger xanaduensis SH-6]
Scores for 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  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); 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:                         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 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1972.85
//
Query:       gi|336254516|ref|YP_004597623.1|  [L=234]
Description: ribonuclease P protein component 3 [Halopiger xanaduensis SH-6]
Scores for 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  121.2   0.0    4.9e-35  120.9   0.0    1.0  1  RNase_P_p30  RNase P subunit p30


Domain annotation for each model (and alignments):
>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   0.0   2.7e-39   4.9e-35       5     213 ..       5     203 ..       3     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 2.7e-39
                                       E-SH.........HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H.. CS
                       RNase_P_p30   5 ipwpsddskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpskl. 80 
                                       ++  ++++++ +r ++ +ae+g++gv++ +   a ++ +p+              e +g++++s++++ +++p++  
  gi|336254516|ref|YP_004597623.1|   5 VHAHPEGQSTVARFARAAAEYGFEGVVVRNPAGARADYDPERIR-----------EEYGVDIVSGIEIRADNPQQAs 70 
                                       67778888888899****************99977777777666...........6699***************977 PP

                                       HHHHHHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEESHHHHHS-HHHH CS
                       RNase_P_p30  81 qrlskvrqkfdllavrPttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEinyspllrdsglaR 157
                                       +++ + r   +++ v ++t +++r+a+en +vD++  +++   +  ++h++++aAve+gv++E++++p+lr  g++R
  gi|336254516|ref|YP_004597623.1|  71 GAVGNHRTDETIVTVAGGTPAMNRFAVENEKVDVLARPMAD--DGDVNHVLAKAAVENGVRLEFDLAPVLRTHGGRR 145
                                       ***************************************87..8889****************************** PP

                                       HHHHHHHHHHHHHHHH..--EEEE--BSSGGG---HHHHHHHHHHHT--HHHHHHTTT CS
                       RNase_P_p30 158 rnfisnarkllrltrg..kgvviSSgAesplelRnpydiinLlktlGLeedrakeavs 213
                                       ++ ++ +rkl ++++   +++v+S+ + s+lelR+p+++++L++ +GL+++ ++e + 
  gi|336254516|ref|YP_004597623.1| 146 VRELQSLRKLAEIVDYydAPYVVSATPDSHLELRAPRELAALGEQIGLSSEFVEEGLA 203
                                       *************************************************998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1867.05
//
Query:       gi|336254517|ref|YP_004597624.1|  [L=214]
Description: type 12 methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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   64.3   0.0    2.5e-17   63.4   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.2e-13   51.5   0.1      7e-13   49.0   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
    1.8e-13   50.6   0.0    2.7e-13   50.0   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.5e-10   41.7   0.0    2.6e-10   40.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    2.1e-10   40.4   0.0    3.6e-10   39.6   0.0    1.4  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.4e-07   31.5   0.0      6e-07   29.4   0.0    1.8  2  Methyltransf_23  Methyltransferase domain
    2.8e-06   27.0   0.0    3.8e-06   26.6   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0066   15.9   0.0     0.0092   15.4   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0086   15.2   0.0       0.01   14.9   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0093   15.9   0.0      0.013   15.4   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
     0.0098   15.0   0.0      0.014   14.5   0.0    1.2  1  DREV             DREV methyltransferase
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.018   15.0   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.023   14.0   0.0      0.031   13.6   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.065   13.0   0.0      0.089   12.5   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.086   11.8   0.0        0.2   10.6   0.0    1.4  2  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
       0.16   11.4   0.0       0.25   10.8   0.0    1.3  1  Methyltransf_4   Putative methyltransferase


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 !   63.4   0.0   2.2e-20   2.5e-17       1      90 [.      46     133 ..      46     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 2.2e-20
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                       vLdlG+GtG ++l la+    ++v+g Dise+m+e+a+++a+e+gl n+ef  g +++ +  dg++D+v+s++a+hh
  gi|336254517|ref|YP_004597624.1|  46 VLDLGTGTGAIALPLAEDA--ERVVGRDISEGMMEEAERKADEQGLaNLEFDYGTFREPE-YDGEVDIVTSNFAMHH 119
                                       9****************96..9***********************************966.678************* PP

                                       SSHHHHHHHHHHHH CS
                   Methyltransf_25  77 lsdedlekalkeia 90 
                                       lsd++ ++a++ ia
  gi|336254517|ref|YP_004597624.1| 120 LSDDEKREAIAVIA 133
                                       *****999998776 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   6.2e-16     7e-13       1      81 [.      47     129 ..      47     135 .. 0.91
   2 ?   -0.1   0.0       1.3   1.5e+03      56      80 ..     170     194 ..     159     204 .. 0.71

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 6.2e-16
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-.. CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv.. 74 
                                       Ld+G+GtG++a +la+ ++rvvg D+s+ m++ a++ka e+gl ++ef  +++++ p  d+ +D+v+s++++hh+  
  gi|336254517|ref|YP_004597624.1|  47 LDLGTGTGAIALPLAEDAERVVGRDISEGMMEEAERKADEQGLaNLEFDYGTFRE-PEYDGEVDIVTSNFAMHHLsd 122
                                       8*****************************************9999999999998.8899***************76 PP

                                       CCHHHHH CS
                   Methyltransf_11  75 edpekal 81 
                                       ++ ++a+
  gi|336254517|ref|YP_004597624.1| 123 DEKREAI 129
                                       5555555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                                       SS-TT-EEEEEEES-CCC-CCHHHH CS
                   Methyltransf_11  56 pfednsfDlvvssevlhhvedpeka 80 
                                        ++d+  D+ +s  +++ v+d+  +
  gi|336254517|ref|YP_004597624.1| 170 ALADAFTDAGFSLTAVERVHDQVGV 194
                                       4667777777777777777666544 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   2.4e-16   2.7e-13       2      91 ..      41     124 ..      40     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 2.4e-16
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDl 77 
                                       +++ +vlDlG+GtG++++ la e   +ae vvG Dise + e A+ +a+++gl n+eF  g + e e  + d  +D+
  gi|336254517|ref|YP_004597624.1|  41 ESTDVVLDLGTGTGAIALPLA-E---DAErVVGRDISEGMMEEAERKADEQGLANLEFDYGTFREPE--Y-DGEVDI 110
                                       57789****************.4...4555***********************************66..4.59**** PP

                   Methyltransf_31  78 ilsnevlnaladpd 91 
                                       ++sn ++++l+d +
  gi|336254517|ref|YP_004597624.1| 111 VTSNFAMHHLSDDE 124
                                       ****9999999865 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   2.3e-13   2.6e-10       1      90 [.      47     133 ..      47     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.3e-13
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++G+GtG+++ +l+e+    +++g Dis+ ++   +e+ a+++++ n ++++ +    + dg   +D+v++++++h
  gi|336254517|ref|YP_004597624.1|  47 LDLGTGTGAIALPLAED--AERVVGRDISEGMM-EEAERKADEQGLANLEFDYGTFREPEYDG--EVDIVTSNFAMH 118
                                       8****************..**************.88888888888899999999999888888..8*********** PP

                   Methyltransf_12  78 hl..kdirevldnir 90 
                                       hl  +++re+++ i+
  gi|336254517|ref|YP_004597624.1| 119 HLsdDEKREAIAVIA 133
                                       **9888889988776 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   3.2e-13   3.6e-10      37     134 ..      32     125 ..       5     133 .. 0.86
   2 ?   -3.5   0.0       4.7   5.3e+03     204     217 ..     171     184 ..     162     198 .. 0.59

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 3.2e-13
                                       HHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS CS
                   Ubie_methyltran  37 kfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfe 113
                                       + v++  a+ +   vlD+ +Gtg +a+ l++ ++   +vv+ Di+e m++++e+k+ e+g  n+ef  +   e p+ 
  gi|336254517|ref|YP_004597624.1|  32 SLVIEHAAPESTDVVLDLGTGTGAIALPLAEDAE---RVVGRDISEGMMEEAERKADEQGLANLEFDYGTFRE-PEY 104
                                       46777888889999**************998876...79***************************9998766.889 PP

                                       -T-EEEEEEES-GGG-S-HHH CS
                   Ubie_methyltran 114 ddsfDvvtvsfGlrnvtDklk 134
                                       d+  D+vt  f +  ++D +k
  gi|336254517|ref|YP_004597624.1| 105 DGEVDIVTSNFAMHHLSDDEK 125
                                       9****************9887 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.7
                                       HHHHHHHTTEEEEE CS
                   Ubie_methyltran 204 lkeliedaGfksve 217
                                       l++ + daGf+   
  gi|336254517|ref|YP_004597624.1| 171 LADAFTDAGFSLTA 184
                                       55566666665433 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   5.3e-10     6e-07       7     106 ..      28     133 ..      16     144 .. 0.72
   2 ?   -0.4   0.0      0.79   8.9e+02      34      58 ..     169     193 ..     166     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 5.3e-10
                   Methyltransf_23   7 eelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae........kakkaqkdqfdeq. 74 
                                       ++++ ++ + ++  ++   vLd+G+GtG  +  l+e    v+g D+s+ + e+ae                    + 
  gi|336254517|ref|YP_004597624.1|  28 RACASLVIEHAA-PESTDVVLDLGTGTGAIALPLAEDAERVVGRDISEGMMEEAErkadeqglA-----------Nl 92 
                                       445555533333.588889*********99999*9*999*************985444443331...........02 PP

                   Methyltransf_23  75 .......eaaepqgkfdlIvlrevlehvpd..ppellrqia 106
                                               ++e +g  d++++++ ++h+ d    e+++ ia
  gi|336254517|ref|YP_004597624.1|  93 efdygtfREPEYDGEVDIVTSNFAMHHLSDdeKREAIAVIA 133
                                       23333335556999**************9745556665555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.79
                   Methyltransf_23  34 GillevlrengfsvtgvDlspeave 58 
                                       G l++ + + gfs+t+v+    +v+
  gi|336254517|ref|YP_004597624.1| 169 GALADAFTDAGFSLTAVERVHDQVG 193
                                       7778888888888888888777666 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   3.4e-09   3.8e-06      19     117 ..      30     127 ..      10     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.4e-09
                                       HHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST CS
                               MTS  19 GsklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve 94 
                                        ++l +e+   e ++ vlDlG+G+G++++ la+  ++  v+  d++   +e a++ + +++l+ +e+      e   
  gi|336254517|ref|YP_004597624.1|  30 CASLVIEHAAPESTDVVLDLGTGTGAIALPLAEDAER--VVGRDISEGMMEEAERKADEQGLAnLEFDYGTFREPEY 104
                                       5678889998889999*****************8877..9**********************999**9999999999 PP

                                       TS-EEEEEE---STTTCHCHHHH CS
                               MTS  95 ekkfdlivsNPPfhagkatelav 117
                                       ++++d++ sN  +h+ ++ e++ 
  gi|336254517|ref|YP_004597624.1| 105 DGEVDIVTSNFAMHHLSDDEKRE 127
                                       **********9999877666554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   8.2e-06    0.0092     160     234 ..      41     115 ..      29     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.2e-06
                              PrmA 160 kegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellkeekadvivaNI 234
                                       ++++ vlD+GtG+G +a+  a  +a++vv+ Di e  ++ a++ a+  ++++ +++  + +e   ++++d++ +N 
  gi|336254517|ref|YP_004597624.1|  41 ESTDVVLDLGTGTGAIALPLAE-DAERVVGRDISEGMMEEAERKADEQGLANlEFDYGTFREPEYDGEVDIVTSNF 115
                                       4456899*******99987665.89*******************99999998777654434433368999999985 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   9.3e-06      0.01      22      77 ..      34      88 ..      28     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.3e-06
                                      HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCC CS
                            RrnaAD 22 IldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdek 77
                                      +++++ +e ++ vl++g+G+G+   +La+ a+ vv   + e ++++ + k   ++ 
  gi|336254517|ref|YP_004597624.1| 34 VIEHAAPESTDVVLDLGTGTGAIALPLAEDAERVVGRDISEGMMEEAERKAD-EQG 88
                                      689999*****************************99999999998887554.444 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05     0.013      14      65 ..      42      91 ..      31     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                   Methyltransf_18 14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagled 65
                                      ++++v+D Gt  g +++ l+  + a++v+  Di+eg +e+a+++++++gl +
  gi|336254517|ref|YP_004597624.1| 42 STDVVLDLGTGTGAIALPLA--EDAERVVGRDISEGMMEEAERKADEQGLAN 91
                                      3569**********999999..57899********************99954 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.3e-05     0.014      82     135 ..      33      83 ..      24     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                              DREV  82 laiekespasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkk 135
                                       l+ie+  p+s   +  +ldlG+G G i+  +a+  e+v   ++se m++  ++k
  gi|336254517|ref|YP_004597624.1|  33 LVIEHAAPES---TDVVLDLGTGTGAIALPLAEDAERVVGRDISEGMMEEAERK 83 
                                       6677555555...7789*****************************99887665 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.6e-05     0.018      13      93 ..      30     103 ..      23     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                   Methyltransf_32  13 vakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsi 89 
                                       +a+l+ e a+ ++   v+D+G G g  +  la    +   +vvg d++e ++e+ae+ a++ g  + ++l+f  ++ 
  gi|336254517|ref|YP_004597624.1|  30 CASLVIEHAAPESTDVVLDLGTGTGAIALPLAE---D-AERVVGRDISEGMMEEAERKADEQG--L-ANLEFDYGTF 99 
                                       555555556778889999**************9...4.779*********************9..7.8999998887 PP

                   Methyltransf_32  90 eeat 93 
                                       +e +
  gi|336254517|ref|YP_004597624.1| 100 REPE 103
                                       7654 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    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      53     142 ..      33     122 ..      10     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                                       HHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG..---- CS
                              CMAS  53 lileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyed..ldek 127
                                       l++e +  +  + +Ld+G+G G+++   +e    +vvg  +S+  ++ a+++ de++l++  e ++  +++   d++
  gi|336254517|ref|YP_004597624.1|  33 LVIEHAAPESTDVVLDLGTGTGAIALPLAED-AERVVGRDISEGMMEEAERKADEQGLAN-LEFDYGTFREpeYDGE 107
                                       5566666677899****************99.889**********************765.6777777775224558 PP

                                       -SEEEEES-GGGTSG CS
                              CMAS 128 vdrvvsvgafehvgk 142
                                       vd v s  a+ h+  
  gi|336254517|ref|YP_004597624.1| 108 VDIVTSNFAMHHLSD 122
                                       999988888888765 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 ?   12.5   0.0   7.9e-05     0.089      72     131 ..      41      97 ..      19     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.9e-05
                                       -TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES CS
                              PCMT  72 kkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvg 131
                                       +  + vL++G+G+G  +     l ++  rvv+ + ++ ++eea+r+  +++l+n+ +  g
  gi|336254517|ref|YP_004597624.1|  41 ESTDVVLDLGTGTGAIAL---PLAEDAERVVGRDISEGMMEEAERKADEQGLANLEFDYG 97 
                                       566789********6555...555678899***********************9998766 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 ?   -1.7   0.0         1   1.1e+03      12      45 ..       4      37 ..       2      42 .. 0.81
   2 ?   10.6   0.0   0.00017       0.2     199     252 ..      40      93 ..      31      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1
                   tRNA_U5-meth_tr 12 rlkkllaefeapelevfespeehyrlraefrlwh 45
                                       l++  a f+  + e  es+++ yr  a + + h
  gi|336254517|ref|YP_004597624.1|  4 DLEDHAARFDEMAGEYDESKSDEYRACASLVIEH 37
                                      57777888999999999999*****999988876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00017
                   tRNA_U5-meth_tr 199 qeskgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvq 252
                                        es++ +l+l  G G  +l+la+  e+v+  +i+   +e a    ++  + n++
  gi|336254517|ref|YP_004597624.1|  40 PESTDVVLDLGTGTGAIALPLAEDAERVVGRDISEGMMEEAERKADEQGLANLE 93 
                                       45667789*********************************9999998888876 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00022      0.25       3      54 ..      44      93 ..      42      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                                      EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEE CS
                    Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlr 54
                                       vvl++G+G G + + lA++     ++G +i++ +++++ +k+++++l Nl+
  gi|336254517|ref|YP_004597624.1| 44 DVVLDLGTGTGAIALPLAEDA--ERVVGRDISEGMMEEAERKADEQGLANLE 93
                                      589*********999999875..689************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1665.39
//
Query:       gi|336254518|ref|YP_004597625.1|  [L=167]
Description: ribonuclease P protein component 2 [Halopiger xanaduensis SH-6]
Scores for 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-19   67.9   0.0    9.8e-19   67.5   0.0    1.2  1  RNase_P_Rpp14  Rpp14/Pop5 family


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 !   67.5   0.0   5.5e-23   9.8e-19       1     102 [.      13     113 ..      13     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 5.5e-23
                                       EEEEEEEEESS......-HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTT..TEEEEEEEGGGHHHHHHHHHT CS
                     RNase_P_Rpp14   1 RYllveilypdeeeelteksllkairesvqelfGdyglgklgsslsvkyfspat..staiiRcsresyrlvwaaLtl 75 
                                       RYl+v + +++ +++++++s++++++ + q+l+Gd g++ ++   ++++f+ a   + aii+++r++++ ++aa+++
  gi|336254518|ref|YP_004597625.1|  13 RYLAVGLETWP-DASIDRRSFQREVWYAGQNLLGDPGSADADL--TIVRFDFADgvGEAIIKVRRGETEPARAAVAC 86 
                                       9**********.556999************************9..67777777655899****************** PP

                                       --EETTEEEEEEEEEEESSHHHHHHHT CS
                     RNase_P_Rpp14  76 itkiegrpvvfrvvrvsGTikkaeeea 102
                                       i++i+g  v +r+ ++sGTi++aee++
  gi|336254518|ref|YP_004597625.1|  87 IDEIDGATVGIRIRGISGTIRAAEEKY 113
                                       ************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1253.28
//
Query:       gi|336254519|ref|YP_004597626.1|  [L=254]
Description: proteasome endopeptidase complex subunit alpha [Halopiger xanaduensis SH-6]
Scores for 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-56  188.3   0.0    1.2e-55  188.0   0.0    1.1  1  Proteasome      Proteasome subunit
    8.9e-14   50.9   0.1    1.5e-13   50.1   0.1    1.4  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 !  188.0   0.0   1.3e-59   1.2e-55       1     178 [.      33     206 ..      33     217 .. 0.96

  Alignments for each domain:
  == domain 1  score: 188.0 bits;  conditional E-value: 1.3e-59
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       vk+Gt+++G++++dgvvla+dkr++  s ll++s+veKi+k ddhig+a aG +aDar+l+++ar++ q  +lryg+
  gi|336254519|ref|YP_004597626.1|  33 VKRGTASIGVRTQDGVVLAVDKRVP--SPLLEDSSVEKIHKADDHIGIASAGHVADARQLIDFARRQTQVNQLRYGE 107
                                       79***********************..************************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                       pi ve+l+++v++++q+ytq +g rpfgv+l+++g+  +g+p+L+++dpsG+ +e+k a a+G  +   + +le++y
  gi|336254519|ref|YP_004597626.1| 108 PIGVETLTKEVTDHIQQYTQVGGARPFGVALIVGGIE-NGEPRLFETDPSGTPYEWK-ALAVGADRSDLQDYLEENY 182
                                       ************************************9.889***************8.*****99999********* PP

                                       STTBSHHHHHHHHHHHHHHHHHHB CS
                        Proteasome 155 kedltleeavelavkalkealerd 178
                                        e+ +l+ +++la+ al ++ ++ 
  gi|336254519|ref|YP_004597626.1| 183 DEEADLDGGIQLALDALASVNDGS 206
                                       ******************998865 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 !   50.1   0.1   1.7e-17   1.5e-13       1      23 []      10      32 ..      10      32 .. 0.99

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.7e-17
                    Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                      YDr +t+FSPdGRL+QVEYA +A
  gi|336254519|ref|YP_004597626.1| 10 YDRGITIFSPDGRLYQVEYAREA 32
                                      *********************99 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:                      425  (0.0237046); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1958.16
//
Query:       gi|336254520|ref|YP_004597627.1|  [L=241]
Description: ribosome maturation protein SBDS-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-20   72.9   0.0    2.8e-20   72.2   0.0    1.4  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    1.2e-18   67.2   0.0    3.3e-18   65.8   0.0    1.7  2  SBDS_C    SBDS protein C-terminal domain
  ------ inclusion threshold ------
      0.042   14.3   0.1       0.11   12.9   0.1    1.8  1  RCDG1     Renal cancer differentiation gene 1 protein
      0.049   13.7   0.2       0.82    9.7   0.0    2.2  2  YbjN      Putative bacterial sensory transduction regulator


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 !   72.2   0.0   6.2e-24   2.8e-20       3      88 .]       8      94 ..       6      94 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 6.2e-24
                                      EEEEEEETTEEEEEEE-HHHHHHHHCTT.---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEE CS
                              SBDS  3 sivrykkgkkrFeiavyknklleyregk.eidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGei 80
                                      +++r+++++ rFe++v+++++l  ++g+ + +L++v+++e++F++as+G++  +s+lek+f+t++  eii +++k+Gei
  gi|336254520|ref|YP_004597627.1|  8 VTARLESHGARFEVLVDPDAALAIKRGEfDGELEDVIAAEDVFEDASRGDRPAESDLEKVFDTTDPLEIIPKVIKEGEI 86
                                      789***********************876889*********************************************** PP

                                      E--HHHHH CS
                              SBDS 81 qvsaeerk 88
                                      q +a++r+
  gi|336254520|ref|YP_004597627.1| 87 QITADQRR 94
                                      *****996 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 ?   -1.8   0.0      0.68     3e+03      25      42 ..      75      92 ..      57      99 .. 0.55
   2 !   65.8   0.0   7.3e-22   3.3e-18       2     115 ..     101     219 ..     100     220 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.68
                                      HHHHHHHHHTT----TTS CS
                            SBDS_C 25 tmIekalkelgtsvktnk 42
                                      ++I k +ke  ++++ ++
  gi|336254520|ref|YP_004597627.1| 75 EIIPKVIKEGEIQITADQ 92
                                      344455555555554444 PP

  == domain 2  score: 65.8 bits;  conditional E-value: 7.3e-22
                                       HHHHHHHHHHHEEBTTT.TB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...C CS
                            SBDS_C   2 ekeiieivaeklvnpqt.krpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsik 77 
                                       +++ i+ +++++vnpq  ++p+++++Ie+al+e+g+ v++ ++++sQ+ ++++aL+  ipi+++++ +++++p   +
  gi|336254520|ref|YP_004597627.1| 101 RRQLIDTITRNAVNPQMdNAPHPPERIENALEEAGFTVDPMEPVESQVDDALDALRPVIPIRFEEVTVAVQIP---A 174
                                       6899************9678*****************************************************...5 PP

                                       CCHHHHHHHH.HH.....S.EE.....EEEE.EEGGGHHHHHHHH CS
                            SBDS_C  78 dkilklieqv.esqkvaekewe.....vvvl.iePgaykeleefv 115
                                       +++ ++ +++ +  +++ +ew+     + vl  ++g+++e+ ++v
  gi|336254520|ref|YP_004597627.1| 175 EHAGSAQAKIrQFGELEREEWQsdgswIGVLtFPAGLQNEFYDVV 219
                                       555555555533333333444444554444449999999999987 PP

>> RCDG1  Renal cancer differentiation gene 1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.5e-05      0.11      43      63 ..     135     155 ..     122     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                             RCDG1  43 aptvdPleevelqigdaafsl 63 
                                       + tvdP+e ve q++da  +l
  gi|336254520|ref|YP_004597627.1| 135 GFTVDPMEPVESQVDDALDAL 155
                                       479*************97665 PP

>> YbjN  Putative bacterial sensory transduction regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.054   2.4e+02       3      31 ..       6      32 ..       4      40 .. 0.79
   2 ?    9.7   0.0   0.00018      0.82       1      50 [.     123     181 ..     123     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.054
                                      HHHHHHHHHH--S-EEEEETTEE.EEEEE CS
                              YbjN  3 dlleevLeeagleyertedddgaivvvgt 31
                                      + + + Le++g ++e+  d+d a  +  +
  gi|336254520|ref|YP_004597627.1|  6 EAVTARLESHGARFEVLVDPDAA--LAIK 32
                                      788999*************9999..4333 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHH--S......-EEEEETTEE....EEEEEETTEEEEEEE--SSTT-EE CS
                              YbjN   1 sldlleevLeeagle......yertedddga...ivvvgtwggyrftiallgeseelll 50 
                                       +++++e++Leeag++      +e + dd+ +   +v+  + +++ + +++  e  ++ +
  gi|336254520|ref|YP_004597627.1| 123 PPERIENALEEAGFTvdpmepVESQVDDALDalrPVIPIRFEEVTVAVQIPAEHAGSAQ 181
                                       589************999888888999999999***************99998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1858.04
//
Query:       gi|336254521|ref|YP_004597628.1|  [L=104]
Description: FUN14 family protein [Halopiger xanaduensis SH-6]
Scores for 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   5.7    3.6e-16   59.4   5.7    1.2  1  FUN14     FUN14 family


Domain annotation for each model (and alignments):
>> FUN14  FUN14 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   5.7     2e-20   3.6e-16       1      91 []      13     101 ..      13     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 2e-20
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......x RF
                             FUN14   1 igiGaviGlvtGfalkkvgKlaaiavGggllllqilasqgyikvnwdkiekdveelldrnkdgklgtede......k 71 
                                       +g+G++iG+++Gf +k+v+K++ai+vG++l+++++l+sqg++ v+++++++ +  + +r +        +      +
  gi|336254521|ref|YP_004597628.1|  13 FGGGLAIGALVGFGTKRVAKVLAIVVGIQLMAFRYLESQGIVIVDYERLSAGLVGTGERVD--------GaatpwlE 81 
                                       579***********************************************77764222222........12234566 PP

                                       xxxxxxxxxxxxxxxxxxxx RF
                             FUN14  72 lltenlpfsagFlaGfllGl 91 
                                        + + + ++agF+ Gfl+G+
  gi|336254521|ref|YP_004597628.1|  82 SVLSAVTIGAGFASGFLIGF 101
                                       6777899************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 772.62
//
Query:       gi|336254522|ref|YP_004597629.1|  [L=433]
Description: GTP-binding proten HflX [Halopiger xanaduensis SH-6]
Scores for 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-23   81.3   0.0    1.6e-22   80.0   0.0    1.7  1  GTP-bdg_N     GTP-binding GTPase N-terminal
    2.3e-18   66.3   0.0    5.2e-18   65.2   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
    1.7e-16   60.6   7.9    3.5e-16   59.6   7.9    1.6  1  GTP-bdg_M     GTP-binding GTPase Middle Region
      1e-10   41.5   0.2    3.2e-10   39.9   0.2    1.8  1  GTP_EFTU      Elongation factor Tu GTP binding domain
      2e-08   34.3   0.1     0.0011   18.9   0.1    2.4  2  RsgA_GTPase   RsgA GTPase
    4.9e-06   26.5   0.1    9.8e-06   25.5   0.1    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    9.9e-06   25.3   0.4     0.0019   17.8   0.1    2.4  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
    0.00013   21.5   0.2      0.099   12.2   0.1    2.6  3  FeoB_N        Ferrous iron transport protein B
     0.0033   16.9   0.2        1.1    8.6   0.1    2.5  2  Arf           ADP-ribosylation factor family
     0.0082   16.3   0.1      0.014   15.6   0.1    1.3  1  MnmE_helical  MnmE helical domain
     0.0097   15.2   1.2       0.06   12.6   0.0    2.1  2  DUF2046       Uncharacterized conserved protein H4 (DUF2046)
  ------ inclusion threshold ------
      0.017   15.5   3.0      0.018   15.4   0.7    2.2  2  AAA_16        AAA ATPase domain
      0.034   14.4   0.1         10    6.4   0.0    2.4  2  Roc           Ras of Complex, Roc, domain of DAPkinase
       0.04   14.0   0.0       0.12   12.4   0.0    1.8  1  AAA_14        AAA domain
      0.046   14.3   0.0       0.38   11.3   0.0    2.5  2  AAA_18        AAA domain
      0.048   14.2   0.8        4.3    7.9   0.2    3.1  2  DUF2408       Protein of unknown function (DUF2408)
       0.05   14.1   0.0       0.13   12.7   0.0    1.9  2  ABC_tran      ABC transporter
       0.05   13.4   0.2       0.16   11.8   0.2    1.9  1  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
      0.054   13.1   1.1        1.5    8.4   0.3    3.0  2  AAA_25        AAA domain
       0.11   13.0   1.8         17    5.8   0.0    2.3  2  AAA_23        AAA domain


Domain annotation for each model (and alignments):
>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   1.8e-25   1.6e-22       5      88 ..      17     101 ..      14     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 1.8e-25
                         GTP-bdg_N   5 eEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekel..evkViD 79 
                                       +E+++La++ag++vvge++q+r k dpa  +G+Gk+ee++e++e++ea++vifd++L p q  nL + l  +v+ViD
  gi|336254522|ref|YP_004597629.1|  17 TEIRDLATAAGYTVVGEITQSR-KADPALQLGEGKAEELAEVAERTEATTVIFDNRLGPYQTYNLGQLLpeGVEVID 92 
                                       79*******************7.89******************************************99768***** PP

                         GTP-bdg_N  80 RtqLILdIF 88 
                                       R +LIL+IF
  gi|336254522|ref|YP_004597629.1|  93 RFTLILEIF 101
                                       ********* PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.0   5.8e-21   5.2e-18       2     114 .]     188     320 ..     187     320 .. 0.79

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 5.8e-21
                                       EEEEESTTSSHHHHHHHHHT...............STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg...............ekaivsdkpgtTrdinegrvklkgkeielvDtpGliegasee 63 
                                       va++G++N+GKStL+++l                 ++a+ +dk +tT+ ++++r +++ +++ ++Dt+G+i+  +  
  gi|336254522|ref|YP_004597629.1| 188 VALAGYTNAGKSTLLRRLAAdldvdeneglhrdldATAESQDKLFTTLGTTTRRADIEPRDVLVTDTVGFIS--DLP 262
                                       89****************9555555556666655469*******************999**********887..566 PP

                                       HHHHHHHHH....HHCTSEEEEEEETTTTCSHHHHHHHHHHHHH....TTSEEEEEEES CS
                          MMR_HSR1  64 kglgkafla....leeadlillvvdaseeklkpldeeleellee....akkplilvlnk 114
                                       ++l ++f++    + +adl+llvvd+s e+++++ e+l  + +     ++ p++ vlnk
  gi|336254522|ref|YP_004597629.1| 263 HWLVESFKStldwVYRADLVLLVVDVS-EDIDEIHEKLVTCHDTlyerNEAPIVTVLNK 320
                                       68999999944445569********99.546666655555543344479999999**98 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   7.9   3.9e-19   3.5e-16       1      79 []     104     180 ..     104     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 3.9e-19
                                       H--SHHHHHHHHHHHHHHHHHHHCXXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.... CS
                         GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLeglgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelqrk 77 
                                       rA+t++a+lQVelA+l+y+lpr  +++++l +   + g++G Ge+  e++++ i+++i+++k eLe++++++e++r+
  gi|336254522|ref|YP_004597629.1| 104 RAQTRKAQLQVELAELRYELPRA-EAKTSLAKRDEHPGFMGLGEYD-ESREQDIKDQISRIKDELERIEQTEEQRRE 178
                                       9**********************.55555555444678********.****************************** PP

                                       .T CS
                         GTP-bdg_M  78 kR 79 
                                       +R
  gi|336254522|ref|YP_004597629.1| 179 RR 180
                                       98 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 !   39.9   0.2   3.6e-13   3.2e-10       6     193 ..     188     366 ..     186     367 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 3.6e-13
                                       EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGG CS
                          GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvd 82 
                                       ++++g +++GK+TL+ rL +++  ++++g +++    lD ++e + + +T   +++    + + + + + Dt G ++
  gi|336254522|ref|YP_004597629.1| 188 VALAGYTNAGKSTLLRRLAADLDVDENEGLHRD----LDATAESQDKLFTTLGTTTRRA-DIEPRDVLVTDTVGFIS 259
                                       5678899*****************999777666....************9988888888.8*************985 PP

                                       ....GHHHHHHH....HHT-SEEEEEEETTTBSTHHHHHHH....HHHHHTTTEEEEEEESCGST.HHHHHHHHHHH CS
                          GTP_EFTU  83 ....Fskevirg....lrvlDgavlvvdaveGvepqteevl....rlalkegvpiivfiNKmDrl.kaelkeiveev 146
                                           +  e  ++    +  +D+++lvvd++e++ +  e+++     l  +++ pi++++NK+D + ++el e  +++
  gi|336254522|ref|YP_004597629.1| 260 dlphWLVESFKStldwVYRADLVLLVVDVSEDIDEIHEKLVtchdTLYERNEAPIVTVLNKIDTVdDDELAEKRRAL 336
                                       5555777777776666889*************7777776651111566677888***********888888888888 PP

                                       HHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                          GTP_EFTU 147 kqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                       + +l                  + v +Sa +g +v++ll+ +++ lp
  gi|336254522|ref|YP_004597629.1| 337 S-SL------------AP----NPVTVSAREGTNVEALLDRIDSELP 366
                                       8.56............12....3688999999999999999999887 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   7.7e-05     0.069      67     161 ..     154     257 ..     132     260 .. 0.72
   2 !   18.9   0.1   1.2e-06    0.0011      17      99 ..     280     363 ..     267     366 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.7e-05
                                       HHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT...........-----S---- CS
                       RsgA_GTPase  67 elkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpe...........lelktgevse 132
                                       ++k++++++  e+  ++++ +e+ +e ++    ++++l+G + +GKStL+ +l+ +           +  +t+e ++
  gi|336254522|ref|YP_004597629.1| 154 DIKDQISRIKDELERIEQT-EEQRRERRRDSGFDLVALAGYTNAGKSTLLRRLAADldvdeneglhrDLDATAESQD 229
                                       4555556665555555444.3344444444445799*******************9788888887765566777777 PP

                                       ----------SEEEEEETTTEEEESS-SS CS
                       RsgA_GTPase 133 klgrGkhTTtavellelaegglliDtPGf 161
                                       kl +   TTt++  +e   + l+ Dt Gf
  gi|336254522|ref|YP_004597629.1| 230 KLFTTLGTTTRRADIEPR-DVLVTDTVGF 257
                                       777777788877777766.8888888887 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.2e-06
                                       -EEEEEE..ESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHH CS
                       RsgA_GTPase  17 dqllivv..slkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegle 91 
                                       d +l+vv  s + +e++++l++   +l+e++++++v vlnKiD ++++e l e + +l++l  ++++vsa++++++e
  gi|336254522|ref|YP_004597629.1| 280 DLVLLVVdvSEDIDEIHEKLVTCHDTLYERNEAPIVTVLNKIDTVDDDE-LAEKRRALSSLAPNPVTVSAREGTNVE 355
                                       55555541144446788888888888999********************.*************************** PP

                                       HHHHHCTT CS
                       RsgA_GTPase  92 elkellkd 99 
                                       +l +++++
  gi|336254522|ref|YP_004597629.1| 356 ALLDRIDS 363
                                       *9988765 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 !   25.5   0.1   1.1e-08   9.8e-06      56     103 ..     312     364 ..     282     366 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.1e-08
                      MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare.....pnsvviSaekelnldeLkekiwee 103
                                        p ++vlNKiD+++++el e +r      pn v +Sa++++n+++L+++i +e
  gi|336254522|ref|YP_004597629.1| 312 APIVTVLNKIDTVDDDELAEKRRAlsslaPNPVTVSAREGTNVEALLDRIDSE 364
                                       6899***************99986778889******************99655 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 ?    5.3   0.0     0.015        14       3      21 ..     188     206 ..     186     220 .. 0.82
   2 !   17.8   0.1   2.1e-06    0.0019      70     165 ..     232     335 ..     219     346 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.015
                                       EEEEESTTCCHHHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhll 21 
                                       + l+G+  +GK+tLl++l 
  gi|336254522|ref|YP_004597629.1| 188 VALAGYTNAGKSTLLRRLA 206
                                       5789************997 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.1e-06
                                       HHHHHHHHHHH..TT-SEEEEEECT.TTTHHHHHTT..SHHHHHCCCECEEEEEEETTTH.....CCHCCHHHHHHH CS
                              cobW  70 lkelealeere..erldviliEttG.laePapvaft..eeelksdltldavvavvDaknl....eaeeekieekaed 137
                                         +l    +r   e  dv++  t+G +++   ++++  +++l   +++d v+ vvD+++     +++  + ++++ +
  gi|336254522|ref|YP_004597629.1| 232 FTTLGTTTRRAdiEPRDVLVTDTVGfISDLPHWLVEsfKSTLDWVYRADLVLLVVDVSEDideiHEKLVTCHDTLYE 308
                                       45555555555555679********6555444444458999999*************87655555555566677777 PP

                                       HHHTSSEEEEE-HHHHCHC..HHHHHHH CS
                              cobW 138 qlaaadllvlnKtDlldeeallekleer 165
                                         +a  + vlnK+D++d+++l+ek +  
  gi|336254522|ref|YP_004597629.1| 309 RNEAPIVTVLNKIDTVDDDELAEKRR-A 335
                                       77888899***********8855543.3 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 ?   -3.8   0.0       9.4   8.4e+03      80     106 ..      95     121 ..      91     123 .. 0.73
   2 !    6.9   0.0    0.0045         4       3      21 ..     188     206 ..     186     214 .. 0.90
   3 !   12.2   0.1   0.00011     0.099      78     156 .]     278     361 ..     233     361 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 9.4
                                       SEEEEEEEGGGHHHHHHHHHHHHHTTS CS
                            FeoB_N  80 dvvvnvvdatnlernLyLtlqllelgv 106
                                        +++++       r+ +L ++l+el+ 
  gi|336254522|ref|YP_004597629.1|  95 TLILEIFGQRAQTRKAQLQVELAELRY 121
                                       567777777777888888888888765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0045
                                       EEEEESTTSSHHHHHHHHH CS
                            FeoB_N   3 valvGnpnvGkttlfnalt 21 
                                       val+G  n+Gk+tl+ +l+
  gi|336254522|ref|YP_004597629.1| 188 VALAGYTNAGKSTLLRRLA 206
                                       89*************9986 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00011
                                       SSSEEEEEEEGG....GHHHHHHHHHH.HHHTT.SSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBT CS
                            FeoB_N  78 epdvvvnvvdat....nlernLyLtlq.llelg.vpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkeg 148
                                       ++d+v+ vvd +    +++ +L+   + l e + +p+v +ln+id+++++++    ++Ls+    + v++sa+++++
  gi|336254522|ref|YP_004597629.1| 278 RADLVLLVVDVSedidEIHEKLVTCHDtLYERNeAPIVTVLNKIDTVDDDELAEKRRALSSLA-PNPVTVSAREGTN 353
                                       5677777777542222466666555442566554899****************9999998755.555789******* PP

                                       HHHHHHHH CS
                            FeoB_N 149 ieellkai 156
                                       +e+ll++i
  gi|336254522|ref|YP_004597629.1| 354 VEALLDRI 361
                                       ****9875 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0093       8.3      19      37 ..     190     208 ..     157     227 .. 0.88
   2 !    8.6   0.1    0.0013       1.1      82     141 ..     279     337 ..     271     364 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0093
                                       EEESTTSSHHHHHHHHHHS CS
                               Arf  19 llGLDnaGKtTilkklkle 37 
                                       l G  naGK+T+l +l  +
  gi|336254522|ref|YP_004597629.1| 190 LAGYTNAGKSTLLRRLAAD 208
                                       45899***********876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
                                       ESEEEEEEETT-CTTHHHHHHHHHHHCTS.GCCTTSEEEEEEE-TTSTTSS-HHHHHHHTT CS
                               Arf  82 tdavifvvDsadreRleeakeeLkallee.eelkevallvlaNKqDlpealseeelrellg 141
                                        d v+ vvD+++   ++e +e+L +  ++  e +e++++ + NK+D+ ++ + +e r++l+
  gi|336254522|ref|YP_004597629.1| 279 ADLVLLVVDVSE--DIDEIHEKLVTCHDTlYERNEAPIVTVLNKIDTVDDDELAEKRRALS 337
                                       678899999864..3555555555544431355699***********99988888777664 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.6e-05     0.014      59     131 ..     147     365 ..     141     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx..................................... RF
                      MnmE_helical  59 leelseeelaekleelkeelekllatakr..gellreGik..................................... 96 
                                        +e  e++++++++++k+ele++ +t ++   ++  +G++                                     
  gi|336254522|ref|YP_004597629.1| 147 YDESREQDIKDQISRIKDELERIEQTEEQrrERRRDSGFDlvalagytnagkstllrrlaadldvdeneglhrdlda 223
                                       45788999**************998866510455569**************************************** PP

                                       ............................................................................. RF
                      MnmE_helical  97 ............................................................................. 96 
                                                                                                                    
  gi|336254522|ref|YP_004597629.1| 224 taesqdklfttlgtttrradieprdvlvtdtvgfisdlphwlvesfkstldwvyradlvllvvdvsedideiheklv 300
                                       ***************************************************************99999998888888 PP

                                       .....................xxxxxxx........xxxxxxxx......xxxxxxxxxxxxxxxxxxx.x RF
                      MnmE_helical  97 .....................Dllkeke........ekeeeevl......kiSaktgegieeLeeaike.l 131
                                                            D  +++e        +             ++Sa++g+++e+L+++i + l
  gi|336254522|ref|YP_004597629.1| 301 tchdtlyerneapivtvlnkiDTVDDDElaekrralS------SlapnpvTVSAREGTNVEALLDRIDSeL 365
                                       8888888888888888888884333333333334443......04555559****************7744 PP

>> DUF2046  Uncharacterized conserved protein H4 (DUF2046)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.6      0.23     2e+02     260     283 ..     151     170 ..     102     224 .. 0.60
   2 !   12.6   0.0   6.6e-05      0.06      94     198 ..     270     375 ..     265     398 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.23
                           DUF2046 260 eerqireenvrlqrklqleverre 283
                                        e++i+++  r++  l    er e
  gi|336254522|ref|YP_004597629.1| 151 REQDIKDQISRIKDEL----ERIE 170
                                       2333333333333332....2222 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.6e-05
                           DUF2046  94 ketlalnyeqeeefltndlsrklsqlrqekveleqtlekeqevqvnklmrkieklea.evlakqtkleqlrrekvel 169
                                       k tl   y  +  +l  d+s  ++++++  v    tl +++e  + +++ ki+ ++  e  +k+  l+ l  + v +
  gi|336254522|ref|YP_004597629.1| 270 KSTLDWVYRADLVLLVVDVSEDIDEIHEKLVTCHDTLYERNEAPIVTVLNKIDTVDDdELAEKRRALSSLAPNPVTV 346
                                       7788888999999999***********999*************************86267899************** PP

                           DUF2046 170 entleqeqealvnrlWkrldkleaekrll 198
                                             + eal++r+   l   e e+ +l
  gi|336254522|ref|YP_004597629.1| 347 SAREGTNVEALLDRIDSELPDWEEERLML 375
                                       ***99*********999999999887776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2       1.3   1.2e+03      73     107 ..      88     138 ..      22     178 .. 0.55
   2 ?   15.4   0.7     2e-05     0.018      18     158 ..     179     336 ..     156     347 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                            AAA_16  73 aqalareellrqlldeaesaeleawrekleeala....................a 107
                                       +++++r +l+ ++  +     ++  +++l+ +la                     
  gi|336254522|ref|YP_004597629.1|  88 VEVIDRFTLILEIFGQ----RAQTRKAQLQVELAelryelpraeaktslakrdeH 138
                                       5555555666666655....33344444444444333444333333333333330 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2e-05
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesael 94 
                                       r r+++  lv l G+   GKs+l+r+l+  l  d+    +g  ++l         a+a ++++l++ l++ ++ a+ 
  gi|336254522|ref|YP_004597629.1| 179 RRRDSGFDLVALAGYTNAGKSTLLRRLAADLDVDE---NEGLHRDL--------DATAESQDKLFTTLGTTTRRADI 244
                                       34444449********************9888774...55555555........566666789********999999 PP

                            AAA_16  95 eawrekleeala..............................avpelagaeasrllellkrll.allsrderplvlv 140
                                       e+ +   +++++                              +v+e+       ++e+l  +   l++r+e p+v v
  gi|336254522|ref|YP_004597629.1| 245 EPRDVLVTDTVGfisdlphwlvesfkstldwvyradlvllvvDVSEDI----DEIHEKLVTCHdTLYERNEAPIVTV 317
                                       999999999888888888888888888888888887775444333333....5677777777777888889999999 PP

                            AAA_16 141 lDdlqwadeaslql.laaL 158
                                       l  ++ +d++ l+   +aL
  gi|336254522|ref|YP_004597629.1| 318 LNKIDTVDDDELAEkRRAL 336
                                       9999999997776544444 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.019        17       2      22 ..     188     208 ..     187     256 .. 0.85
   2 ?    6.4   0.0     0.011        10      68     119 ..     268     322 ..     261     323 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.019
                                       EEEESSTTSSHHHHHHCHCT- CS
                               Roc   2 vvlvGdsgvGKtsllkrfved 22 
                                       v l G +++GK++ll+r+  d
  gi|336254522|ref|YP_004597629.1| 188 VALAGYTNAGKSTLLRRLAAD 208
                                       568899***********9865 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                                       CTTTT-HHHHCTSCEEEEEEE.GHHHHCHHHHHHHHHHH...CSSS-EEEEEE-TT CS
                               Roc  68 rfrslhplylreaalailvyd.srssenlkeWlkelkkv...agkspvilvgnkiD 119
                                        f+s+ +  +r a+l++lv+d s++ ++++e l  +++    ++++p++ v nkiD
  gi|336254522|ref|YP_004597629.1| 268 SFKSTLDWVYR-ADLVLLVVDvSEDIDEIHEKLVTCHDTlyeRNEAPIVTVLNKID 322
                                       56666665555.55777777746667888887777776533356789********9 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013      0.12       5      83 ..     188     265 ..     185     282 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqevpewe 80 
                                       +++ G   +GK+tll++l+ +l v++++ l  +ld   +++ + +++l +  ++  ++   + +l+ D +  ++++ 
  gi|336254522|ref|YP_004597629.1| 188 VALAGYTNAGKSTLLRRLAADLDVDENEGLHRDLDATAESQDKLFTTLGTTTRRAdIE--PRDVLVTDTVGFISDLP 262
                                       78999999***********9999*************9999888887666666665333..46667777777666666 PP

                            AAA_14  81 kal 83 
                                       ++l
  gi|336254522|ref|YP_004597629.1| 263 HWL 265
                                       655 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   0.00043      0.38       1      25 [.     188     215 ..     188     291 .. 0.75
   2 ?   -1.4   0.0       3.7   3.3e+03      38      70 ..     306     347 ..     284     375 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf...g 25 
                                       ++l+G+  +GK+tl ++L+  l +    
  gi|336254522|ref|YP_004597629.1| 188 VALAGYTNAGKSTLLRRLAADLDVdenE 215
                                       689***************9887443331 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.7
                            AAA_18  38 llevdpe....aldeskrldedkldklldaleenss.....a 70 
                                       l+e++++     l++ + +d+d l++  +al   +      +
  gi|336254522|ref|YP_004597629.1| 306 LYERNEApivtVLNKIDTVDDDELAEKRRALSSLAPnpvtvS 347
                                       444444445555555566666666666666555555555553 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0048       4.3      15      65 ..     116     186 ..     102     238 .. 0.64
   2 ?    2.8   0.0      0.18   1.6e+02      14      58 ..     328     372 ..     285     381 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0048
                           DUF2408  15 LvsirrsLlslaakskaeeakesee................vkeelkelkeeLkkieskrde......egkFk 65 
                                       L ++r +L    ak++  + +e  +                +k++++++k+eL++ie++ ++      +  F 
  gi|336254522|ref|YP_004597629.1| 116 LAELRYELPRAEAKTSLAKRDE--HpgfmglgeydesreqdIKDQISRIKDELERIEQTEEQrrerrrDSGFD 186
                                       5555555555555555542222..24577777777777777****************8554422233344554 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.18
                           DUF2408  14 kLvsirrsLlslaakskaeeakeseevkeelkelkeeLkkieskr 58 
                                       +L + rr L+sla +  + +a+e ++v++ l+++ +eL + e++r
  gi|336254522|ref|YP_004597629.1| 328 ELAEKRRALSSLAPNPVTVSAREGTNVEALLDRIDSELPDWEEER 372
                                       556667777777777777767777777777777777777777665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       7.1   6.4e+03      79      92 ..     153     166 ..      95     180 .. 0.48
   2 ?   12.7   0.0   0.00015      0.13      13      44 ..     187     218 ..     183     338 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.1
                                       HHHHTCHHHHHHHS CS
                                       xxxxxxxxxxxxxx RF
                          ABC_tran  79 nesdeeiekalskl 92 
                                       ++ +++i+++ ++l
  gi|336254522|ref|YP_004597629.1| 153 QDIKDQISRIKDEL 166
                                       13333333333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00015
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeill 44 
                                       +va+ G + aGKStLl+ la  l+ +e e l 
  gi|336254522|ref|YP_004597629.1| 187 LVALAGYTNAGKSTLLRRLAADLDVDENEGLH 218
                                       699*****************999987766533 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 ?   11.8   0.2   0.00018      0.16      14      58 .]     279     322 ..     276     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                              NOG1  14 adavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                       ad+vl ++D+se+     e+ +   ++++e+ + +p+++vlnKiD
  gi|336254522|ref|YP_004597629.1| 279 ADLVLLVVDVSEDIDEIHEKLVTCHDTLYERNE-APIVTVLNKID 322
                                       689**********99888888899999999966.**********9 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.17   1.6e+02     125     150 ..      46      70 ..       5      72 .. 0.70
   2 ?    8.4   0.3    0.0016       1.5      34      56 ..     186     208 ..     156     300 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.17
                            AAA_25 125 lltadvdaleaaieevegvrlvviDp 150
                                       l +++ ++l++++e++ ++  v++D+
  gi|336254522|ref|YP_004597629.1|  46 LGEGKAEELAEVAERT-EATTVIFDN 70 
                                       2478899999999995.5******98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0016
                            AAA_25  34 elallaGapgtGKttlaldlala 56 
                                       +l++laG + +GK+tl+  la++
  gi|336254522|ref|YP_004597629.1| 186 DLVALAGYTNAGKSTLLRRLAAD 208
                                       6899*************999987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.4     0.026        24     131     197 ..      93     171 ..      24     181 .. 0.56
   2 ?    5.8   0.0     0.019        17      21      37 ..     187     203 ..     182     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.026
                            AAA_23 131 ilnlilflgqerfeefelkdkke.rleelekeleeledekkllekl.............eqekekekeleeleeele 193
                                       +++lil +  +r+  + +k++++ +l+el+ el  +e++ +l ++               +e++ +++++ +++ele
  gi|336254522|ref|YP_004597629.1|  93 RFTLILEIFGQRA--QTRKAQLQvELAELRYELPRAEAKTSLAKRDehpgfmglgeydeSREQDIKDQISRIKDELE 167
                                       3434433333332..22333333455555555555555555555557777777777776455555556666666666 PP

                            AAA_23 194 eilk 197
                                        i++
  gi|336254522|ref|YP_004597629.1| 168 RIEQ 171
                                       5554 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.019
                            AAA_23  21 ltlItGpNGaGKTTild 37 
                                       l+++ G + aGK+T+l+
  gi|336254522|ref|YP_004597629.1| 187 LVALAGYTNAGKSTLLR 203
                                       78999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 3102.27
//
Query:       gi|336254523|ref|YP_004597630.1|  [L=385]
Description: protanoyl-CoA C-acyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-56  190.9   0.0    3.3e-56  190.5   0.0    1.1  1  Thiolase_N       Thiolase, N-terminal domain
    1.2e-07   31.4   0.1    4.2e-07   29.7   0.1    1.8  2  Thiolase_C       Thiolase, C-terminal domain
     0.0072   16.3   0.1         13    5.8   0.0    3.3  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
  ------ inclusion threshold ------
       0.17   11.4   4.1       0.58    9.7   0.8    2.4  3  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal 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 !  190.5   0.0   7.3e-60   3.3e-56       1     260 []       4     222 ..       4     222 .. 0.99

  Alignments for each domain:
  == domain 1  score: 190.5 bits;  conditional E-value: 7.3e-60
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-TT CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipee 75 
                                       v+i+++++t++g+     +d+++ +Ll+ea+ ++le+agvd+++v++++v+n++++ +egq+ +++++a +++   +
  gi|336254523|ref|YP_004597630.1|   4 VAIIGSSMTQFGQ-----RDAWVLDLLSEAGLECLEDAGVDASDVEHLYVSNMASGeFEGQTgVMNALAQDIDA-VP 74 
                                       79***********.....*************************************99****************9.** PP

                                       SEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTT CS
                        Thiolase_N  76 vpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafne 152
                                       +++++v++++sSg +++++a+qs+a+g++d+++++G+E+m++++t e+tdv+++l++++e+++++++p+        
  gi|336254523|ref|YP_004597630.1|  75 AYTQRVDQTSSSGGAGIYAAWQSVASGASDMTMLVGGEKMTHKTTGEATDVIASLTHPAEYKHGVTLPS-------- 143
                                       *********************************************************************........ PP

                                       SEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS CS
                        Thiolase_N 153 ehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLakl 229
                                        ++Glta++++++++++Re+++++Avk+h+++++++ka+ F++e+              d ++ ++s+++a++L+ +
  gi|336254523|ref|YP_004597630.1| 144 -FAGLTARHYLERFDAPRESLAKVAVKNHKNGVDNPKAQ-FRKEV--------------DLETVLESPIVADPLRLY 204
                                       .**************************************.*****..............99**************** PP

                                       -BSSSTTSS-BTTSB--BEEEEEEEEEEEHH CS
                        Thiolase_N 230 kpaFkkeGtvtAgnasqisDGaaavllmses 260
                                                    ++++i+DG+aa++l++es
  gi|336254523|ref|YP_004597630.1| 205 -------------DFCPITDGSAALMLCPES 222
                                       .............***************986 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.57   2.5e+03      30      45 ..      31      46 ..      17      62 .. 0.82
   2 !   29.7   0.1   9.3e-11   4.2e-07      30     120 ..     264     377 ..     243     380 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.57
                                      HHHHHHT--GGGESEE CS
                        Thiolase_C 30 kvlkkagltvedidlf 45
                                      ++l++ag++ +d++ +
  gi|336254523|ref|YP_004597630.1| 31 ECLEDAGVDASDVEHL 46
                                      6899999999999865 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 9.3e-11
                                       HHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G...................GGBSTT--HHHH-B-TTTHHH CS
                        Thiolase_C  30 kvlkkagltvedidlfEinEAFaaqaLavakaldldl...................ekvNvnGGaialGHPlGasGa 87 
                                        + +  g + +did+ E+++ F+   +  ++ l++++                     +N  GG  + GHPlGasG+
  gi|336254523|ref|YP_004597630.1| 264 GAYEMSGRDPDDIDVAELHDMFTILEFLQMEGLGFAEqgeawklveegyterdtgeLPINTSGGLKSKGHPLGASGV 340
                                       5667889999**************************9***************999778******************* PP

                                       HHHHHHHHHHHHCTT....SEEEEEEEETTTEEEEEE CS
                        Thiolase_C  88 Rivvtllselkkegg....klgvaalCigggqgvalv 120
                                        ++v + ++l  e g       v   C+ gg g+ ++
  gi|336254523|ref|YP_004597630.1| 341 AQAVEIYEQLMGEAGprqvDADVGLTCNVGGFGNCVI 377
                                       *****99999866541111455666899999998876 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.053   2.4e+02      31      48 ..      30      47 ..      19      81 .. 0.83
   2 !    4.8   0.0    0.0062        28      28      52 ..     260     284 ..     231     289 .. 0.67
   3 !    5.8   0.0     0.003        13      87     112 ..     331     356 ..     309     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.053
                                      HHHHHHHT--GGGEEEEE CS
                   Ketoacyl-synt_C 31 ekalaeagvdpedvdyve 48
                                       ++l++agvd++dv+++ 
  gi|336254523|ref|YP_004597630.1| 30 LECLEDAGVDASDVEHLY 47
                                      589***********9654 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0062
                                       HHHHHHHHHHT--GGGEEEEE-SS- CS
                   Ketoacyl-synt_C  28 raiekalaeagvdpedvdyveahgt 52 
                                       +  e a++++g dp+d+d+ e h+ 
  gi|336254523|ref|YP_004597630.1| 260 ESGEGAYEMSGRDPDDIDVAELHDM 284
                                       345789*****************97 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.003
                                       H-B-GGGHHHHHHHHHHHHHHHTEE- CS
                   Ketoacyl-synt_C  87 iGHleaAaGvaelikvvlalkhgvip 112
                                        GH ++A+Gva+++ +  +l  ++ p
  gi|336254523|ref|YP_004597630.1| 331 KGHPLGASGVAQAVEIYEQLMGEAGP 356
                                       5************9998887666555 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 ?   -2.8   0.0      0.84   3.8e+03       1      12 [.       1      12 [.       1      28 [. 0.82
   2 ?    2.6   0.1     0.018        82      91     126 ..      24      59 ..       9      84 .. 0.73
   3 ?    9.7   0.8   0.00013      0.58     172     218 ..      81     127 ..      74     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.84
                                      X--EEEEEEEEE CS
                     ketoacyl-synt  1 aepvaivGmgar 12
                                      +e+vai+G +++
  gi|336254523|ref|YP_004597630.1|  1 MERVAIIGSSMT 12
                                      689****99986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHH CS
                     ketoacyl-synt  91 llleaawealedagltpeeldgsrvgvfiGvgagdy 126
                                       ll ea  e+ledag+++ ++++  v +++  + + +
  gi|336254523|ref|YP_004597630.1|  24 LLSEAGLECLEDAGVDASDVEHLYVSNMASGEFEGQ 59 
                                       6789999**********9998877777766666633 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00013
                                       ESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTT CS
                     ketoacyl-synt 172 dtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaag 218
                                       d   sS+ + + aa+qs+ sg +d+    G e +++  +  + + ++
  gi|336254523|ref|YP_004597630.1|  81 DQTSSSGGAGIYAAWQSVASGASDMTMLVGGEKMTHKTTGEATDVIA 127
                                       55678889999*************97777777788887777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2853.53
//
Query:       gi|336254524|ref|YP_004597631.1|  [L=120]
Description: hypothetical protein Halxa_3138 [Halopiger xanaduensis SH-6]
Scores for 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-06   26.3   0.9    7.7e-06   25.8   0.9    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated


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 !   25.8   0.9   4.3e-10   7.7e-06       4      63 ..      33      91 ..      30      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.3e-10
                                      E-G.G-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT......-EE-EEEEEEES..TT-B-EEE CS
                     OB_aCoA_assoc  4 lsg.rGtvysftvvhrappgfaeeaPyvvgvVeLde...gvrimarlvgvdpdevriGmrVrav 63
                                      ls  +++v+++t+  + p   + ++P ++++Ve+d     vr +++l+  d   v+ G++Vr v
  gi|336254524|ref|YP_004597631.1| 33 LSEyTAEVVTWTTSTATP--PGVREPNHLAIVEFDVdgeSVRAIGQLTTGD---VETGDEVRPV 91
                                      66669*************..679************9777888999999888...669****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 941.17
//
Query:       gi|336254525|ref|YP_004597632.1|  [L=99]
Description: hypothetical protein Halxa_3140 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.03   14.6   0.0      0.046   14.1   0.0    1.3  1  DUF3268       zinc-finger-containing domain


Domain annotation for each model (and alignments):
>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.6e-06     0.046       4      37 ..       2      38 ..       1      54 [. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-06
                           DUF3268  4 rCpyCGekvilvs...aseiYkerskgkllylCpkCd 37
                                       C +CG++v++ +   a+ i++  + ++  +lC++C 
  gi|336254525|ref|YP_004597632.1|  2 ECLFCGQPVQFSQhkmAHRIFELSDPEDNWWLCRDCA 38
                                      7*******99876222568998888999********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 779.79
//
Query:       gi|336254526|ref|YP_004597633.1|  [L=270]
Description: hypothetical protein Halxa_3141 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0047   16.1   0.1      0.029   13.5   0.0    1.9  2  APG17         Autophagy protein Apg17
  ------ inclusion threshold ------
       0.78   10.3   2.8        1.8    9.1   0.9    2.3  2  COMP          Cartilage oligomeric matrix protein
       0.89    9.8   6.9          8    6.7   0.4    3.3  3  Cnn_1N        Centrosomin N-terminal motif 1
        8.2    6.7   7.2        7.7    6.8   0.4    3.3  4  DUF4148       Domain of unknown function (DUF4148)


Domain annotation for each model (and alignments):
>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   6.6e-06     0.029      75     158 ..       3     127 ..       1     154 [. 0.67
   2 !    4.1   0.8    0.0047        21      48     160 ..      79     228 ..      75     252 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-06
                                       HHHHHHHHHHHHHHHHHHHHHTSS-TTS.....................STGGGCS--TTTTHHHHHHHHH...... CS
                             APG17  75 dlikeldaanerLektlekLrktkvepsfrpegee..............ktLlDFvdedsveelkealkes...... 131
                                       d +++l +a ++L++tle Lr+    ++ r+ g +              + Ll F de +v +   al++s      
  gi|336254526|ref|YP_004597633.1|   3 DQDDDLADAIRELTRTLEDLRQELDRSDRRTGG-RgrrgwrpplrpptpRELLAFADEVAVPAALAALESSiralka 78 
                                       67899****************877777755555.56*************************9999999999455555 PP

                                       ......................HHHHHHHHHHHHTTHH..HHHHHHHHH CS
                             APG17 132 ......................idelqaaqkkldssllefdtdlrelkk 158
                                                             ++  ++a    +++l+++dt l+el++
  gi|336254526|ref|YP_004597633.1|  79 fqrglklvrterdvrdrtsdaaTAGSERADRLRKTTLERLDTALAELQR 127
                                       5555555555555555544433333333333333334444444444444 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0047
                                       HHHHHHHHHHIIIIIIIIIIIIIIIIIHHHHHHHHHHHHHHHHHHHHHTSS-TTS..............STGGGCS- CS
                             APG17  48 lkqQlkllekirkslerklekgkeefkdlikeldaanerLektlekLrktkvepsfrpegee.......ktLlDFvd 117
                                        ++ lkl+++ r+   r+ + +    ++ ++ +++  erL++ l++L+    e ++  ++e+       + L+D vd
  gi|336254526|ref|YP_004597633.1|  79 FQRGLKLVRTERDVRDRTSDAATAGSERADRLRKTTLERLDTALAELQRAASEGTLPADDEArslltdaRELRDEVD 155
                                       56667777777777777778888888899999999999999999999999999997777755888888888888888 PP

                                       -TTTTHHHHHHHHH..............................HHHHHHHHHHHHTTHH..HHHHHHHHHHH CS
                             APG17 118 edsveelkealkes..............................idelqaaqkkldssllefdtdlrelkkel 160
                                        +  e+  +   ++                               +  ++  ++ ++s+   d +l++lk+++
  gi|336254526|ref|YP_004597633.1| 156 ARLREATSDGTSTEpgsdsdssavqidieegapdgaetdqdeseGAAADEESESNSNSNIDVDAELETLKDQY 228
                                       7777666666655555555666666666666666666665544433333333444444445555566666555 PP

>> COMP  Cartilage oligomeric matrix protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.9    0.0004       1.8       1      24 [.       3      26 ..       3      29 .. 0.94
   2 ?   -0.0   0.0      0.28   1.3e+03      18      31 ..     148     161 ..     142     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0004
                              COMP  1 DvtkqLlrqLseltqllkeLreel 24
                                      D+++ L+  ++elt+ l++Lr el
  gi|336254526|ref|YP_004597633.1|  3 DQDDDLADAIRELTRTLEDLRQEL 26
                                      8999*****************998 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.28
                              COMP  18 keLreelrqQvkEi 31 
                                       +eLr+e+    +E+
  gi|336254526|ref|YP_004597633.1| 148 RELRDEVDARLREA 161
                                       699**998888886 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 ?    4.7   0.1    0.0076        34      36      64 ..       3      31 ..       1      34 [. 0.80
   2 ?    0.2   0.2      0.19   8.4e+02      35      55 ..     130     157 ..     103     164 .. 0.57
   3 ?    6.7   0.4    0.0018         8      33      64 ..     202     233 ..     189     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0076
                            Cnn_1N 36 eqkeellkenielkveveslqkelkekkk 64
                                      +q ++l +   el  ++e+l++el++ ++
  gi|336254526|ref|YP_004597633.1|  3 DQDDDLADAIRELTRTLEDLRQELDRSDR 31
                                      46778888888999999999999998776 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.19
                            Cnn_1N  35 e.......eqkeellkenielkvevesl 55 
                                       +       ++ ++ll    el++ev   
  gi|336254526|ref|YP_004597633.1| 130 SegtlpadDEARSLLTDARELRDEVDAR 157
                                       1233334455555666666666665554 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0018
                            Cnn_1N  33 lseeqkeellkenielkveveslqkelkekkk 64 
                                        ++e++e+  ++ni++  e+e+l+++  + ++
  gi|336254526|ref|YP_004597633.1| 202 AADEESESNSNSNIDVDAELETLKDQYAADDE 233
                                       345999******************99877666 PP

>> DUF4148  Domain of unknown function (DUF4148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.87   3.9e+03      13      20 ..      62      69 ..      56     102 .. 0.65
   2 ?    6.8   0.4    0.0017       7.7      35      51 ..     123     139 ..     121     142 .. 0.88
   3 ?    2.2   0.0     0.047   2.1e+02      30      50 ..     151     173 ..     151     177 .. 0.79
   4 ?   -2.7   0.1       1.6     7e+03      33      41 ..     217     225 ..     216     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.87
                           DUF4148 13 avaaaaal 20
                                       +aa aal
  gi|336254526|ref|YP_004597633.1| 62 VPAALAAL 69
                                      34444444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0017
                           DUF4148  35 aELaqaeaaGylpsgds 51 
                                       aEL++a + G+lp++d+
  gi|336254526|ref|YP_004597633.1| 123 AELQRAASEGTLPADDE 139
                                       9************9774 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.047
                           DUF4148  30 RAqVraELaqaeaaGylps..gd 50 
                                       R +V a L +a ++G++++  +d
  gi|336254526|ref|YP_004597633.1| 151 RDEVDARLREATSDGTSTEpgSD 173
                                       899************77653354 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.6
                           DUF4148  33 VraELaqae 41 
                                       V aEL+ ++
  gi|336254526|ref|YP_004597633.1| 217 VDAELETLK 225
                                       89***9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1026  (0.0572257); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.21s 00:00:00.74 Elapsed: 00:00:00.35
# Mc/sec: 2303.91
//
Query:       gi|336254527|ref|YP_004597634.1|  [L=246]
Description: hypothetical protein Halxa_3142 [Halopiger xanaduensis SH-6]
Scores for 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  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1860.83
//
Query:       gi|336254528|ref|YP_004597635.1|  [L=252]
Description: hypothetical protein Halxa_3143 [Halopiger xanaduensis SH-6]
Scores for 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  119.0   0.0    2.5e-34  118.6   0.0    1.1  1  RNase_H_2       RNase_H superfamily
  ------ inclusion threshold ------
      0.017   14.8   0.0      0.022   14.5   0.0    1.3  1  DNA_pol_A_exo1  3'-5' exonuclease


Domain annotation for each model (and alignments):
>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   0.0   2.8e-38   2.5e-34       1     165 [.      87     236 ..      87     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 2.8e-38
                         RNase_H_2   1 lffDiEttGlspkknliyliGvldvdekeiekltqllaeepeeekailelflellekkkalvtfngksFDvpflkrl 77 
                                       +f+DiEttGl+ + + ++++++++  ++e++++++   ++ + e+   e     le  + lvtfng++FDvpfl++ 
  gi|336254528|ref|YP_004597635.1|  87 CFLDIETTGLDASCDDVTTVSLHR--GDETKTFVK--GRDLTSERLERE-----LEASSLLVTFNGARFDVPFLETC 154
                                       69**********999999999997..555565664..555555555555.....99********************* PP

                         RNase_H_2  78 fkkykldeeefrhiDLlkelrkkklesysLksvekelgierreedlsGsqavklyqeylrtgdeellekilaYNedD 154
                                       + ++++d   ++h+DL++++++ +l++ +Lk++e+elgi+r+ +dlsG++av+l++ey ++gde++le++++YN++D
  gi|336254528|ref|YP_004597635.1| 155 Y-DIDVD---VPHLDLMYPCKQVGLDG-GLKAIERELGIDRDMPDLSGRDAVRLWHEY-ERGDESALETLVEYNRAD 225
                                       *.65555...7****************.******************************.69**************** PP

                         RNase_H_2 155 vralatlyekl 165
                                       + ++  l+e++
  gi|336254528|ref|YP_004597635.1| 226 TKNMRPLVETV 236
                                       ****9999875 PP

>> DNA_pol_A_exo1  3'-5' exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.4e-06     0.022      25     101 ..      89     160 ..      77     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-06
                                       EEEEEE-SSSTTSSEEEEEEEEECSSEEEEEECTTTTTT-HGHHHHHHHT-TTSEEEESSHHHHHHHHHHHHTS--S CS
                    DNA_pol_A_exo1  25 vDtEttsldlisatlvliliqlgekeeayiidplelgddvalealkrlledenitkvghnakfDlevlardfgiele 101
                                       +D Ett+ld   + + ++ ++l +++e+  +++    +    e l r le +++ + + +a+fD+ +l ++++i++ 
  gi|336254528|ref|YP_004597635.1|  89 LDIETTGLDA--SCDDVTTVSLHRGDETKTFVKGRDLT---SERLERELEASSLLVTFNGARFDVPFLETCYDIDVD 160
                                       799*******..88888888888887777766555555...7******************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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 0.19s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2007.13
//
Query:       gi|336254529|ref|YP_004597636.1|  [L=133]
Description: thioesterase superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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   60.6   0.0    2.5e-16   60.3   0.0    1.1  1  4HBT_2       Thioesterase-like superfamily
    9.8e-14   51.5   0.1    1.3e-13   51.1   0.1    1.2  1  4HBT         Thioesterase superfamily
    2.2e-09   37.0   0.0    4.3e-09   36.0   0.0    1.5  1  Acyl-ACP_TE  Acyl-ACP thioesterase
  ------ inclusion threshold ------
      0.072   13.0   1.4       0.22   11.4   0.1    2.1  2  3-alpha      3-alpha domain


Domain annotation for each model (and alignments):
>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   5.6e-20   2.5e-16       1     121 [.      13     126 ..      13     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 5.6e-20
                            4HBT_2   1 vrpndvDlnghlnnarylryleearvkfle.rtglksrsiarrgiglilssahvryrrplkfpdrltvefrvidida 76 
                                       vr +d+D++gh+nna+y  yle+ar+ +++ + g+   s+     g +l+  +++y rp+     +t  +rv +  +
  gi|336254529|ref|YP_004597636.1|  13 VRLRDIDFMGHVNNATYATYLEQAREAYFTdVLGV---SLV--DTGTVLATLEIDYARPIDADADVTAALRVPELGT 84 
                                       899***********************988435555...333..3499****************************** PP

                            4HBT_2  77 ktliiehrflsnadgkkaarveerivvmdygkrskkapvPpellk 121
                                       ++l ie++++   dg +aa++++++v++d +++ ++ p+P+e ++
  gi|336254529|ref|YP_004597636.1|  85 SSLPIEYEIRA--DGELAATARTVQVLVDEETG-DSRPLPDEWRR 126
                                       *********99..*******************9.******99766 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.1   2.9e-17   1.3e-13       1      75 [.      21      98 ..      21     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 2.9e-17
                                      TSSB-HHHHHHHHHHHHHHHHHHTTST...TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTS CS
                              4HBT  1 gGvvhgGvylallDeaagaalrslggr...gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedg 75
                                      +G+v++++y+++l++a+ a+++   g    +++ v + l+id+ rp+  + ++t+  rv +lg++s+ +e+e+r++++
  gi|336254529|ref|YP_004597636.1| 21 MGHVNNATYATYLEQAREAYFTDVLGVslvDTGTVLATLEIDYARPIDADADVTAALRVPELGTSSLPIEYEIRADGE 98
                                      7***********************9999**********************************************9976 PP

>> Acyl-ACP_TE  Acyl-ACP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   9.6e-13   4.3e-09     158     244 ..      10     105 ..       2     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 9.6e-13
                       Acyl-ACP_TE 158 elkvrysDlDlnqHvNNvkYlewi........levlpleilkkhe.lkkitlkYekevqlgdkveilte.iaesees 224
                                        + vr  D+D+ +HvNN++Y  ++         +vl+ +++++ + l+ ++++Y +++  + +v+   + ++  ++s
  gi|336254529|ref|YP_004597636.1|  10 GIDVRLRDIDFMGHVNNATYATYLeqareayfTDVLGVSLVDTGTvLATLEIDYARPIDADADVTAALRvPELGTSS 86 
                                       689***************99876522222222688999999886527899**************987776889999* PP

                       Acyl-ACP_TE 225 lktkheirlseGeeiakakt 244
                                       l +++eir++ Ge  a a+t
  gi|336254529|ref|YP_004597636.1|  87 LPIEYEIRAD-GELAATART 105
                                       **********.999998887 PP

>> 3-alpha  3-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1     5e-05      0.22       2      32 ..      54      85 ..      54      85 .. 0.94
   2 ?   -0.0   0.2      0.19   8.3e+02      29      35 ..     120     126 ..     119     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5e-05
                                      BHHHHHHHHHTS---HH.HHHHHHTSTT--HH CS
                           3-alpha  2 tVarvnallyhdkldre.alrrllelpaLsps 32
                                      tV   +++ y ++ d++ +  ++l++p+L++s
  gi|336254529|ref|YP_004597636.1| 54 TVLATLEIDYARPIDADaDVTAALRVPELGTS 85
                                      899999***********************976 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.19
                                       --HHHHH CS
                           3-alpha  29 LspsWrk 35 
                                       L+++Wr+
  gi|336254529|ref|YP_004597636.1| 120 LPDEWRR 126
                                       99****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1047.60
//
Query:       gi|336254530|ref|YP_004597637.1|  [L=96]
Description: hypothetical protein Halxa_3145 [Halopiger xanaduensis SH-6]
Scores for complete 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  105.7   1.5    1.3e-30  105.5   1.5    1.1  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5   1.5   7.2e-35   1.3e-30       1      75 []      12      91 ..      12      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 7.2e-35
                            HalOD1  1 deespstaVveavaavegvdptelep.....LydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVe 74
                                      d++s+s+aV++ava+ egvdpt++ep     Lydai+p+ALd+Lfa+r+dg+ar++g+v+Fty++y+V+V+sdg++eV+
  gi|336254530|ref|YP_004597637.1| 12 DDQSLSFAVISAVAEREGVDPTDIEPpeyeaLYDAINPEALDSLFAPRTDGTARTTGRVEFTYCDYHVVVTSDGDVEVH 90
                                      689*********************888***************************************************8 PP

                            HalOD1 75 p 75
                                      +
  gi|336254530|ref|YP_004597637.1| 91 D 91
                                      5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 831.70
//
Query:       gi|336254531|ref|YP_004597638.1|  [L=437]
Description: hypothetical protein Halxa_3146 [Halopiger xanaduensis SH-6]
Scores for 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   12.1   0.0       0.31   11.2   0.0    1.3  1  baeRF_family5  Bacterial archaeo-eukaryotic release factor fa


Domain annotation for each model (and alignments):
>> baeRF_family5  Bacterial archaeo-eukaryotic release factor family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.7e-05      0.31      28      89 ..      76     139 ..      69     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.7e-05
                     baeRF_family5  28 eyeldletedWrekkgpskaerssgsgs..kdefeerfeenqqRwyKslaskleklakerewee 89 
                                        +e+d +t dWr  +   +++   g ++  + +++e  ++   R   +l++ +++ a++ +we+
  gi|336254531|ref|YP_004597638.1|  76 IFEWDADTGDWRPANTGTTENPVPGTTHleRADISEVNNAFVARDSDELQAVIDRAADSAGWEK 139
                                       69***********9997777777777776699999***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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 0.16s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 3757.56
//
Query:       gi|336254532|ref|YP_004597639.1|  [L=77]
Description: hypothetical protein Halxa_3147 [Halopiger xanaduensis SH-6]
Scores for 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:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); 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 0.20s 00:00:00.52 Elapsed: 00:00:00.34
# Mc/sec: 687.12
//
Query:       gi|336254533|ref|YP_004597640.1|  [L=176]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-20   73.6   0.1    1.9e-20   73.2   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    9.5e-14   51.4   0.0    1.5e-13   50.8   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.8e-12   46.9   0.0    3.6e-12   46.5   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.1e-09   38.1   0.0    1.8e-09   37.4   0.0    1.4  1  FR47             FR47-like protein
    1.3e-08   35.6   0.1    1.6e-08   35.4   0.1    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    2.1e-07   31.1   0.1    4.1e-07   30.1   0.1    1.5  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    4.6e-06   26.7   0.0      1e-05   25.5   0.0    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    4.8e-05   23.1   0.2    6.4e-05   22.7   0.2    1.5  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
     0.0018   18.2   0.0     0.0038   17.2   0.0    1.5  1  Acetyltransf_13  ESCO1/2 acetyl-transferase
     0.0024   17.6   0.1     0.0054   16.4   0.0    1.6  2  PanZ             Acetyltransferase (GNAT) domain, PanZ
  ------ inclusion threshold ------
      0.027   14.6   0.0      0.029   14.5   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
      0.048   13.7   0.0      0.081   12.9   0.0    1.4  1  ZNRF_3_ecto      ZNRF-3 Ectodomain
       0.15   11.5   0.0       0.46    9.9   0.0    1.8  1  Acetyltransf_15  Putative acetyl-transferase
       0.16   12.1   9.0      0.037   14.2   4.3    2.0  2  Acetyltransf_6   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 !   73.2   0.1   1.5e-23   1.9e-20      23     117 .]      44     145 ..      17     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 1.5e-23
                                       HHHHH..HHSTTCEEEE..EEETTEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT CS
                    Acetyltransf_1  23 efees..fsleaegllv..aeedgeliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLlealeeraree 92 
                                       +++e   +++ ++gllv  a  d++l+Gf+s++       ++  ++ i  ++V p++rg+G+G aLlea+e+ + ++
  gi|336254533|ref|YP_004597640.1|  44 RMRETlaAHQATDGLLVarAGADDTLVGFVSFSLEHGtleLDATRGTISNIYVEPTHRGRGIGAALLEAAEDALADR 120
                                       22222223335557777688888************99***999*****************************99999 PP

                                       TESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  93 gikkivlaveedndaairlYeklGF 117
                                       g++ + l+v +dn+aa+r+Y++ GF
  gi|336254533|ref|YP_004597640.1| 121 GAEVVILEVMADNEAARRFYREQGF 145
                                       ****9***************65**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   1.2e-16   1.5e-13      37     110 ..      64     149 ..      23     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.2e-16
                   Acetyltransf_10  37 eeggkivGvi.........el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfY 101
                                         ++++vG++         el  +++ is ++V+p +rg+Gig+aLlea+e+++ ++g ++  l+v a++ +a++fY
  gi|336254533|ref|YP_004597640.1|  64 GADDTLVGFVsfslehgtlELdATRGTISNIYVEPTHRGRGIGAALLEAAEDALADRGAEVvILEVMADNeAARRFY 140
                                       44466666663222222226655556***************************99999999*********9****** PP

                   Acetyltransf_10 102 eklGFkavg 110
                                       + +GF a  
  gi|336254533|ref|YP_004597640.1| 141 REQGFDAFR 149
                                       *****9875 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   2.8e-15   3.6e-12      10      74 ..      63     145 ..      31     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.8e-15
                                       ET..TEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHHHTT.....SEEEEEEEEE..THHHHHHH CS
                    Acetyltransf_7  10 dd..gkivGfialslld.........aeitrlaVdpeyrgkGiGraLleaae.....kgiileqlel..naekaikf 68 
                                        +  +  vGf+++sl+          + i +++V p +rg+GiG aLleaae     +g +++ le+  ++e+a++f
  gi|336254533|ref|YP_004597640.1|  63 AGadDTLVGFVSFSLEHgtleldatrGTISNIYVEPTHRGRGIGAALLEAAEdaladRGAEVVILEVmaDNEAARRF 139
                                       4455888999999999999998877677777******************833455666733222233434448888* PP

                                       HHHTTE CS
                    Acetyltransf_7  69 YeklGF 74 
                                       Y+  GF
  gi|336254533|ref|YP_004597640.1| 140 YREQGF 145
                                       ****** PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   1.4e-12   1.8e-09      20      81 ..      87     149 ..      71     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.4e-12
                                       TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEE.EETT-HHHHHHHHHHT-EEEE CS
                              FR47  20 dggelgalqvlpehrrrGlgsrlvkalakeiaergktvllv.vvasNtpsirlyeklGfekie 81 
                                         g ++ ++v+p+hr+rG g  l +a   ++a rg +v+++ v a+N++++r+y   Gf + +
  gi|336254533|ref|YP_004597640.1|  87 TRGTISNIYVEPTHRGRGIGAALLEAAEDALADRGAEVVILeVMADNEAARRFYREQGFDAFR 149
                                       4599*******************************98765538999*************8765 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.1   1.2e-11   1.6e-08       2     137 ..       5     145 ..       4     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.2e-11
                    Acetyltransf_3   2 LlLrplteeDlealfe.lrsdpevmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleee 77 
                                       +++ p+t++D+ea++e ++   + +r++      ++ + ++++++a+ ++ +g+  a    d+  +G+v++   ++ 
  gi|336254533|ref|YP_004597640.1|   5 VTIEPATSDDVEAVAElWVRLARGQRAYDSYVRADANRNRMRETLAAHQATDGLLVARAGADDTLVGFVSFSLEHGT 81 
                                       6899**********996777777777654544455556666666766666677444433344436*******88887 PP

                    Acetyltransf_3  78 dee....aelg.ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                        e     + ++ +++ p ++g+G++   ++a+ +++ ++ g+e ++ ++ ++Nea +r ++  Gf
  gi|336254533|ref|YP_004597640.1|  82 LELdatrGTISnIYVEPTHRGRGIGAALLEAAEDAL-ADRGAEVVILEVMADNEAARRFYREQGF 145
                                       766988877766889999****************99.6666*********************999 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   3.2e-10   4.1e-07       2     126 ..       7     146 ..       6     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.2e-10
                                       EEEE-GGGHHHHHHHHHHHTT----H...........HHHHHHHHHHTTSEEEEEEE..TTEEEEEEEEEEEEEEET CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespl........e.eireyfrklleesrvlgaed..ngelvgqlallplelnvp 67 
                                       i ++t++d+++v+el+ +    ++ +         + ++re +      +  l+a+   +++lvg +  ++le  + 
  gi|336254533|ref|YP_004597640.1|   7 IEPATSDDVEAVAELWVRLARGQRAYDsyvradanRnRMRETLAAHQATDGLLVARAgaDDTLVGFV-SFSLEHGTL 82 
                                       7889999999999999776666555555667665544555555555556667777768888898854.456666666 PP

                                       TEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-E CS
                    Acetyltransf_9  68 GktlkaagvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGye 126
                                       +   + + ++ + v p+hrgrg+  +Ll++a + ++++g+++++l       +++++Yr  G++
  gi|336254533|ref|YP_004597640.1|  83 ELDATRGTISNIYVEPTHRGRGIGAALLEAAEDALADRGAEVVILEVmadneAARRFYREQGFD 146
                                       6666669**************************************8877988889****99996 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 !   25.5   0.0   8.1e-09     1e-05       8      62 ..      66     126 ..      59     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 8.1e-09
                   Acetyltransf_CG   8 egeevafleYevrkeg......vldfthTeVpeelrGkGiAkkLvkaalddareeglkvvp 62 
                                       +++ v+f++++ +++       + ++  ++V++ +rG+Gi+++L +aa d   ++g  vv+
  gi|336254533|ref|YP_004597640.1|  66 DDTLVGFVSFSLEHGTleldatRGTISNIYVEPTHRGRGIGAALLEAAEDALADRGAEVVI 126
                                       46789999999333334444447799999***************************99986 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2     5e-08   6.4e-05      88     139 ..      97     147 ..      13     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5e-08
                                       SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EE CS
                    Acetyltransf_8  88 eaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfek 139
                                       e+++rg+g+++all+a  + ++ad++++ v++E  ++Ne+a+r+++++Gf  
  gi|336254533|ref|YP_004597640.1|  97 EPTHRGRGIGAALLEAAED-ALADRGAEVVILEVMADNEAARRFYREQGFDA 147
                                       899***********99765.56777*************************75 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     3e-06    0.0038       7      31 ..      91     115 ..      86     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3e-06
                   Acetyltransf_13   7 isriWvssshRrkgiAtkLldaare 31 
                                       is i+v ++hR +gi  +Ll+aa +
  gi|336254533|ref|YP_004597640.1|  91 ISNIYVEPTHRGRGIGAALLEAAED 115
                                       9********************9975 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.4   1.8e+03      60      89 ..      14      43 ..       6      74 .. 0.60
   2 !   16.4   0.0   4.2e-06    0.0054      54     122 ..      81     147 ..      42     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.4
                              PanZ 60 keaelsdlcVRevTRrRGVgsyLleearrq 89
                                      ++ ++ +l VR    +R   sy   +a r+
  gi|336254533|ref|YP_004597640.1| 14 DVEAVAELWVRLARGQRAYDSYVRADANRN 43
                                      555556666665555554444444444333 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.2e-06
                              PanZ  54 kveledkeaelsdlcVRevTRrRGVgsyLleearrqaPevkswvlaeedvkeldlavlqaflealgfaa 122
                                        +el+++ +++s++ V    R RG+g  Lle a + + +  + v+  e ++  d++++++f +++gf+a
  gi|336254533|ref|YP_004597640.1|  81 TLELDATRGTISNIYVEPTHRGRGIGAALLEAAEDALADRGAEVVILEVMA--DNEAARRFYREQGFDA 147
                                       46788999***********************99999977777777776644..6678888888888865 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.3e-05     0.029      78     138 ..      90     149 ..       9     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                    Acetyltransf_4  78 aelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvg 138
                                        +  +y+   + + +g+g +l++a e+ l+  + e    e++++ne++  f+ + GF+  +
  gi|336254533|ref|YP_004597640.1|  90 TISNIYVE-PTHRGRGIGAALLEAAEDALADRGAEVVILEVMADNEAARRFYREQGFDAFR 149
                                       46678995.89**********************************************9765 PP

>> ZNRF_3_ecto  ZNRF-3 Ectodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.3e-05     0.081      18      86 ..      89     158 ..      81     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.3e-05
                       ZNRF_3_ecto  18 gfisivkLeqpelepksClslldkaklal.erGatavifdisddaeaaeqLkqeasLkrPvvlikgadae 86 
                                       g is + +e++++      +ll+ a  al +rGa+ vi+++  d+eaa ++ +e++++   v ++ + a 
  gi|336254533|ref|YP_004597640.1|  89 GTISNIYVEPTHRGRGIGAALLEAAEDALaDRGAEVVILEVMADNEAARRFYREQGFDAFRVTMERSLAD 158
                                       5667777788888888888999999999658*****************9999998887766666665555 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00036      0.46      75     136 ..      91     145 ..      78     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00036
                   Acetyltransf_15  75 iYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksMnisfalYyslgF 136
                                       i ++yv++ +rg+G+   lLe + ++l      +  ++++L + +     + + ++Y++ gF
  gi|336254533|ref|YP_004597640.1|  91 ISNIYVEPTHRGRGIGAALLEAAEDAL----ADRGAEVVILEVMADN---EAARRFYREQGF 145
                                       6689*****************997666....3444556666655432...345566666666 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   4.3   2.9e-05     0.037      21     130 ..       6     124 ..       2     133 .. 0.75
   2 ?    1.3   0.6      0.27   3.5e+02      19      38 ..     124     143 ..     108     171 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-05
                    Acetyltransf_6  21 rfrvatdpedleallelfraqwarr...pdvfadpltraflrdllaalaargalrlyvlrldgrpvAva.lglrsgd 93 
                                       +++  ++++d+ea+ el++++ +++    ++ + +++r  +r+ laa  a + l +  + +d+++v+++ + l++g+
  gi|336254533|ref|YP_004597640.1|   6 TIEP-ATSDDVEAVAELWVRLARGQrayDSYVRADANRNRMRETLAAHQATDGLLVARAGADDTLVGFVsFSLEHGT 81 
                                       4444.47899999999999888888788666666777777888888888899999999999*******977777766 PP

                    Acetyltransf_6  94 ......rlyywlggydpelaklspgllllweliedaaeeGlrr 130
                                             r     + + p +++ ++g  ll  + +++a++G ++
  gi|336254533|ref|YP_004597640.1|  82 leldatRGTISNIYVEPTHRGRGIGAALLEAAEDALADRGAEV 124
                                       5555445556677778888888888888888888888888765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.27
                    Acetyltransf_6  19 evrfrvatdpedleallelf 38 
                                        v ++v +d e+++++++  
  gi|336254533|ref|YP_004597640.1| 124 VVILEVMADNEAARRFYREQ 143
                                       33447777777777776643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1311.33
//
Query:       gi|336254534|ref|YP_004597641.1|  [L=211]
Description: signal transduction protein with CBS domains [Halopiger xanaduensis SH-6]
Scores for complete 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-22   79.5   7.2    3.2e-14   53.1   1.2    2.2  2  CBS              CBS domain
  ------ inclusion threshold ------
      0.012   15.3   0.8      0.019   14.6   0.8    1.4  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
      0.036   14.0   1.3      0.062   13.2   0.3    1.9  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.062   13.4   1.0       0.12   12.5   1.0    1.4  1  Zn-ribbon_8      Zinc ribbon domain
      0.089   12.0   0.2       0.21   10.8   0.1    1.5  1  Thi4             Thi4 family
       0.12   12.1   1.0       0.22   11.2   1.0    1.3  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.46   10.0   7.2        1.6    8.3   3.6    3.0  3  TF_Zn_Ribbon     TFIIB zinc-binding
       0.47   10.4   2.8        1.3    9.0   2.8    1.7  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon


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 !   30.0   0.5   2.4e-10   5.3e-07       1      56 [.       7      61 ..       7      62 .. 0.94
   2 !   53.1   1.2   1.4e-17   3.2e-14       1      54 [.      71     123 ..      71     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.4e-10
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                      V+d+ t+d+v v++++t++ a++lmr+++ s+++VV + +  vGi t+ Dll++++
  gi|336254534|ref|YP_004597641.1|  7 VTDVLTTDYVGVSESDTVRGAVQLMRDERASCVLVVRGAD-AVGIMTEWDLLDLVA 61
                                      789***********************99999*****8788.***********9876 PP

  == domain 2  score: 53.1 bits;  conditional E-value: 1.4e-17
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllra 54 
                                       Vgd+mt++v++v pd +l +a+ lm++++++ + VV dedg + G+vt+rD++ a
  gi|336254534|ref|YP_004597641.1|  71 VGDVMTTPVISVAPDRSLTDAASLMTRENIRNV-VVeDEDG-VRGVVTQRDVIAA 123
                                       89*******************************.9978888.**********987 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 ?   14.6   0.8   8.4e-06     0.019       5      27 ..     184     208 ..     180     211 .] 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.4e-06
                           zf-RRN7   5 ppCgvCgc..rsftlddGfyyCrrC 27 
                                        +C++Cg+   s ++ +G+ +C  C
  gi|336254534|ref|YP_004597641.1| 184 GVCEACGSlaESLRESNGQLVCPDC 208
                                       69*******99***********877 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 ?   -1.7   0.0       1.3   2.8e+03      53      63 ..     113     123 ..     112     125 .. 0.83
   2 ?   13.2   0.3   2.8e-05     0.062      23      54 ..     178     210 ..     165     211 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                    OrfB_Zn_ribbon  53 gfeadrDvnAa 63 
                                       g++ +rDv Aa
  gi|336254534|ref|YP_004597641.1| 113 GVVTQRDVIAA 123
                                       67889***998 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.8e-05
                    OrfB_Zn_ribbon  23 npayTSktCseCgsknke.alsgrtfkCpnCgf 54 
                                       +++ T   C  Cgs  +  + s+ +++Cp+C +
  gi|336254534|ref|YP_004597641.1| 178 DEYTTQGVCEACGSLAESlRESNGQLVCPDCRT 210
                                       56668889***********************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 ?   12.5   1.0   5.3e-05      0.12       8      33 ..     186     209 ..     179     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-05
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCg 33 
                                       Ce+Cg+  e l++++   + +CP+C 
  gi|336254534|ref|YP_004597641.1| 186 CEACGSLAESLRESN--GQLVCPDCR 209
                                       ***********9877..3667****5 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   9.5e-05      0.21     113     155 ..      92     134 ..      76     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.5e-05
                                       EEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-E CS
                              Thi4 113 vkllnavaveDlivregegvaGvvinwtlvelahdtqscvDPl 155
                                       + l++   + +++v +++gv+Gvv++  +++ a + q+ v P 
  gi|336254534|ref|YP_004597641.1|  92 ASLMTRENIRNVVVEDEDGVRGVVTQRDVIAAASSFQATVAPR 134
                                       56788888999**********************9999999885 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   9.6e-05      0.22       9      28 ..     186     205 ..     185     208 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.6e-05
                                       -TTT--EEEECC--SS-EEE CS
                   Desulfoferrod_N   9 CevCGniVeVleaGgGeLVC 28 
                                       Ce CG   e l +  G+LVC
  gi|336254534|ref|YP_004597641.1| 186 CEACGSLAESLRESNGQLVC 205
                                       ******************** PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.34   7.7e+02      28      38 ..     104     114 ..     103     118 .. 0.84
   2 ?    5.1   0.4    0.0071        16      18      30 ..     182     194 ..     178     197 .. 0.76
   3 ?    8.3   3.6   0.00071       1.6       2      25 ..     185     208 ..     184     211 .] 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.34
                                       EEEECCCCCCC CS
                      TF_Zn_Ribbon  28 Vlednsidegp 38 
                                       V+ed++ + g+
  gi|336254534|ref|YP_004597641.1| 104 VVEDEDGVRGV 114
                                       9*****99887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0071
                                       TCEEESSSSBEEE CS
                      TF_Zn_Ribbon  18 gelvCtdCGlVle 30 
                                       +  vC++CG++ e
  gi|336254534|ref|YP_004597641.1| 182 TQGVCEACGSLAE 194
                                       5559*****9866 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00071
                                       EETTTTC.EECHEETSTTCEEESSS CS
                      TF_Zn_Ribbon   2 kCPnCgs.tnlveDpergelvCtdC 25 
                                       +C  Cgs  +  + +++g lvC+dC
  gi|336254534|ref|YP_004597641.1| 185 VCEACGSlAE-SLRESNGQLVCPDC 208
                                       7999999665.667899******** PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.8   0.00058       1.3       5      25 ..     186     208 ..     181     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00058
                    PhnA_Zn_Ribbon   5 CplCaS.eytY.edgallvCpeC 25 
                                       C+ C+S  +++ e +  lvCp+C
  gi|336254534|ref|YP_004597641.1| 186 CEACGSlAESLrESNGQLVCPDC 208
                                       999999433447*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1713.65
//
Query:       gi|336254535|ref|YP_004597642.1|  [L=254]
Description: GTP cyclohydrolase III [Halopiger xanaduensis SH-6]
Scores for 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  314.9   0.2    3.8e-94  314.6   0.2    1.0  1  GCH_III   GTP cyclohydrolase III
    1.2e-10   41.7   0.1    2.7e-05   24.4   0.0    2.1  2  GGDEF_2   GGDEF-like domain
      0.002   18.5   0.0      0.036   14.4   0.0    2.1  2  mCpol     minimal CRISPR polymerase domain


Domain annotation for each model (and alignments):
>> GCH_III  GTP cyclohydrolase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.6   0.2   6.3e-98   3.8e-94       1     235 [.       6     245 ..       6     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 314.6 bits;  conditional E-value: 6.3e-98
                                       -EEEEETTHHHHCCSSS---HHHHHHHHHHHHHHHHHHHHTTT-EEE-TTSSEEEEE-TT--HHHHHHHHHHHHHHS CS
                           GCH_III   1 mtviqidnYgpWtvepaprreadlqalqarlyadlqkelaardGlvfatRfDnllaitngidleehkRiqesirnry 77 
                                       +t++qidnYgpWtv+p prre+dlq++q+rlyad+ ++++ardG+vf+tRfDn++a+tng+  e+h+R+qesi+nry
  gi|336254535|ref|YP_004597642.1|   6 VTLLQIDNYGPWTVTPEPRRETDLQTMQSRLYADISQFVGARDGYVFFTRFDNMIAVTNGLSREDHERLQESIGNRY 82 
                                       589************************************************************************** PP

                                       SS-EEEEEEEESSHHHHHHHHHHHHHHH--TT-TT----EE...E.S---SS--EEEEEEEETTHHHHTTTTS-HHH CS
                           GCH_III  78 pvtvsmgigaaetPldaleaaseaLreagsaqdeeRkevls...v.delvtegyvqiahiDinnitgtltdivsavr 150
                                       pvt s+g++++ tP++al+ a++ L+eagsaqd++R+evl+   + d+  t+g vqiah+D+ n+tgt+td   a++
  gi|336254535|ref|YP_004597642.1|  83 PVTLSLGVATGTTPVQALSDATTQLQEAGSAQDKDRREVLEgrvIeDGHRTDGDVQIAHFDVINATGTYTDELNAFD 159
                                       ****************************************8443356679*************************** PP

                                       HHHHHHHHHHHHHHHH.HTTT---EEEETTEEEEE-TT--HHHHHHHHHHHHHHHS--EEEEEEEESSHHHHHHHHH CS
                           GCH_III 151 tylevnkvkaklakkl.ekegallqfiGGDnilavcneleeedvldiinevkekvdvdlkaGiGiadtaedaaalad 226
                                       t +e+++  a l++++ ++++ l +f+GGDn++ vc++lee d  ++i +v e+vdvdl++G+G++d a++a+  a+
  gi|336254535|ref|YP_004597642.1| 160 TFIEIEQGYAELMRHMrHTHDSLSFFVGGDNVIVVCPDLEEPDYEEAIHHVAEAVDVDLQVGVGRGDSAHEAGYAAK 236
                                       ***************999*********************************************************** PP

                                       HHHHHHHTT CS
                           GCH_III 227 eaLeeiRgk 235
                                       +aLe++R+ 
  gi|336254535|ref|YP_004597642.1| 237 HALETCRAD 245
                                       *******54 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.4e-06     0.014      31     113 ..      30     113 ..       4     115 .. 0.78
   2 !   24.4   0.0   4.5e-09   2.7e-05      36     115 ..     166     243 ..     125     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-06
                           GGDEF_2  31 eedaerllraleealralgpdalvavrgdrlvlllpaedeedaeallerlarrlgg.lsvriGiG.spveglaglrr 105
                                       ++ ++rl++ +++++ a+  ++++++r d+ +++  + ++ed e+l+e + +r++  ls+ ++ G +pv+ l+++ +
  gi|336254535|ref|YP_004597642.1|  30 QTMQSRLYADISQFVGAR-DGYVFFTRFDNMIAVTNGLSREDHERLQESIGNRYPVtLSLGVATGtTPVQALSDATT 105
                                       334556888888888876.699999*******************************555555555447999999999 PP

                           GGDEF_2 106 SyreArrA 113
                                        ++eA  A
  gi|336254535|ref|YP_004597642.1| 106 QLQEAGSA 113
                                       99999877 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 4.5e-09
                           GGDEF_2  36 rllraleealralgpdalvavrgdrlvlllpaedeedaeallerlarrlgglsvriGiGspveglaglrrSyreArr 112
                                       + +++l +++r+++ +  ++v gd++++++p  +e+d e++++++a++++  ++ +G+G+  ++++++  + + A++
  gi|336254535|ref|YP_004597642.1| 166 QGYAELMRHMRHTHDSLSFFVGGDNVIVVCPDLEEPDYEEAIHHVAEAVDV-DLQVGVGR-GDSAHEAGYAAKHALE 240
                                       46889999***9999999********************************9.*******9.6788888888888877 PP

                           GGDEF_2 113 Alr 115
                                       ++r
  gi|336254535|ref|YP_004597642.1| 241 TCR 243
                                       766 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.043   2.6e+02      39      96 ..      40      99 ..      26     116 .. 0.65
   2 !   14.4   0.0     6e-06     0.036      29     106 ..     161     241 ..     133     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.043
                             mCpol 39 lkkllkdelgasvifaaGDsilaksslee.dllvelsrvyqkitgltvSiGv..Gktlrea 96
                                      +++++       v f   D+++a ++  + ++   l++   +   +t S+Gv  G t  +a
  gi|336254535|ref|YP_004597642.1| 40 ISQFVGAR-DGYVFFTRFDNMIAVTNGLSrEDHERLQESIGNRYPVTLSLGVatGTTPVQA 99
                                      55555555.6778999999999999743334455555555555567777665225555443 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6e-06
                             mCpol  29 skevkeaikklkkllkdelgasvifaaGDsilaksslee..dllvelsrvyqkit.gltvSiGvGktlrealiaLkk 102
                                         e+++   +l +++ ++      f++GD++++ ++  e  d++  +++v ++    l v +G G++++ea  a k 
  gi|336254535|ref|YP_004597642.1| 161 FIEIEQGYAELMRHMRHTHDSLSFFVGGDNVIVVCPDLEepDYEEAIHHVAEAVDvDLQVGVGRGDSAHEAGYAAKH 237
                                       45778888888899999955555799*********865566777777777777768999************999998 PP

                             mCpol 103 Aksk 106
                                       A  +
  gi|336254535|ref|YP_004597642.1| 238 ALET 241
                                       8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2018.93
//
Query:       gi|336254536|ref|YP_004597643.1|  [L=108]
Description: hypothetical protein Halxa_3151 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.071   13.8   0.0      0.092   13.5   0.0    1.1  1  HOCHOB          Homeobox-cysteine loop-homeobox
       0.11   13.0   0.7       0.11   13.0   0.7    1.9  2  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5


Domain annotation for each model (and alignments):
>> HOCHOB  Homeobox-cysteine loop-homeobox
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     1e-05     0.092      33      86 ..      19      72 ..      18      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1e-05
                            HOCHOB 33 RfselRllkkekCeknDtCekvakyfeskekydglldektlellkeeFekliea 86
                                      R  ++R++++++ e++D    va++++++ +y   ++++ + +++e+Fe + ++
  gi|336254536|ref|YP_004597643.1| 19 RKYDMRIIADKVDEEEDFPMNVAEFVDEYGDYPIRINHERVVAMREIFEYVDAE 72
                                      55799********************************************98654 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 ?   -1.4   0.1       0.4   3.5e+03      17      20 ..      32      35 ..      29      53 .. 0.56
   2 ?   13.0   0.7   1.3e-05      0.11       8      22 ..      64      78 ..      57      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.4
                                      HHTT CS
                    RNA_pol_Rpb2_5 17 EEet 20
                                      EEe+
  gi|336254536|ref|YP_004597643.1| 32 EEED 35
                                      4443 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.3e-05
                                      TSEEEEEHHHHTT-- CS
                    RNA_pol_Rpb2_5  8 gvvEylDaeEEetam 22
                                      ++ Ey+DaeE+et++
  gi|336254536|ref|YP_004597643.1| 64 EIFEYVDAEEFETIL 78
                                      678**********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 833.96
//
Query:       gi|336254537|ref|YP_004597644.1|  [L=640]
Description: gamma-glutamyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-141  470.3   0.0   9.1e-141  470.1   0.0    1.1  1  G_glu_transpept  Gamma-glutamyltranspeptidase
  ------ inclusion threshold ------
      0.072   12.5   2.4       0.18   11.2   2.4    1.7  1  UCR_Fe-S_N       Ubiquitinol-cytochrome C reductase Fe-S subu


Domain annotation for each model (and alignments):
>> G_glu_transpept  Gamma-glutamyltranspeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.1   0.0    1e-144  9.1e-141       2     512 .]      88     608 ..      87     608 .. 0.96

  Alignments for each domain:
  == domain 1  score: 470.1 bits;  conditional E-value: 1e-144
                                       HHHHTT--HHHHHHHHHHHHHHHSTTT-STTSEEEEEEEETTSCEEEEEEE--BB-TT--TTTT...TSCBCCHHHH CS
                   G_glu_transpept   2 evLrkGGnAvDAavAaalclgvvepqssGiGGGgfllvydaktkkvealdaretAPaaatkdmf...dkegdsklsk 75 
                                       +vL +GGnA+DAavA++++l+vv pq+sGiGGGgf++vyda++ +v+ ++ re+AP++a+++mf    +  d + + 
  gi|336254537|ref|YP_004597644.1|  88 RVLAEGGNAIDAAVAVQYVLNVVSPQASGIGGGGFMVVYDAESDSVHCINSRERAPRDAHPEMFldnGEPRDFDEAI 164
                                       79**************************************************************9877777788888 PP

                                       SSGGG-BB--HHHHHHHHHHHH-SS-HHHHHHHHHHHHHH-EE--HHHHHHHHHCHHHHHTSHHHHHHHEE.TTSE- CS
                   G_glu_transpept  76 tgalavgVPGevagleeahkkyGklpwadllepaiklareGfpvsealaralaeaeerlkkdpelaklFlp.egevl 151
                                       +  +a+gVPG++++le+a +++G+ p ++l+ pai+la  Gf+v+e+l++++ae++++++    ++++Fl+ +g+v+
  gi|336254537|ref|YP_004597644.1| 165 QRSEAIGVPGTLDALETARERFGSRPRQRLIRPAIQLAAGGFTVDEYLSEVIAENRDKFNDA--AREVFLDaNGNVP 239
                                       8889*****************************************************99987..889****88999* PP

                                       -TTSEE--HHHHHHHHHHHHHTTHHHHSSHHHHHHHHHHHHT..T-S--HHHHHH---EEES-EEEEETTCEEEEE- CS
                   G_glu_transpept 152 kagellkqpalAktLerlaeeGaeaFYkGelAeklvaelqka..gGiltaeDLanykvevreplsadyrggytvyep 226
                                       ++g++l++++lA+tLe++ ++G++aFY+G +A++++a+++    g  + ++DLa+y+v + ep++ +  + + v +p
  gi|336254537|ref|YP_004597644.1| 240 QPGDTLTNEDLARTLELIRRDGRDAFYEGPIARDIAATVEGLegGPGIDERDLAEYSVTIDEPVRKEAYDFEIVGQP 316
                                       ***************************************995425569******************99888999999 PP

                                       TTCSHHHHHHHHHHHHCTTTGGGCTTTCHHHHHHHHHHHHHHHHHHHHH-SSTTTSSSGHCHHHHHT-HHHHHHHHT CS
                   G_glu_transpept 227 ppssggivllqiLnilegfdlkslssnsaetlhllvEamklayadRsrylgDpdfvknptelveellskeyakerak 303
                                        p sg +++++i+++le +d ++++ + +e++hl++Ea ++a adR++y+gDp+fv++p   ve ll+++++++ra+
  gi|336254537|ref|YP_004597644.1| 317 VPTSGPTTIAMIMRMLEFLDIEEYDIRAPEKYHLIAEANRVAWADRDQYMGDPEFVDVP---VEGLLDDDFLRQRAS 390
                                       99999999************************************************988...*************** PP

                                       T.BTTB..SG....................GGCSCGGCSCG.TTEEEEEEEEETTS-EEEEEEEESSTTTTSEBETT CS
                   G_glu_transpept 304 lIkdkaatps....................seyykaaeaaeesggTthlsvvDregnaVSltstinllFGsgvvvpg 360
                                       +I+ +   ++                    ++  ++a +a + ++T+h++++Dr+gn+VS+t+ti++l Gsg +v g
  gi|336254537|ref|YP_004597644.1| 391 RIDLDGVIADyaageqvppgvppgaperftPDWAATASTADPVSSTAHFTTADRHGNVVSYTTTIEQLMGSGKMVSG 467
                                       *******9999**************999987777888888889********************************** PP

                                       TTEBE--GGGGSBSTS..TTSCSTTSTTB--TT----B----EEEEETTEEEEEEEEESGGGHHHHHHHHHHHHHTT CS
                   G_glu_transpept 361 tGilLnnemddfstgvenafgldpspanaiePgkRplssmaPtivlkdgkpvlvlGaaGGsriisavlqvlvnvldl 437
                                        G++Lnne++df+        ++p  +n+++P+kRplss++Pt+v++dg+p ++ G++GG +ii++v q++++ l++
  gi|336254537|ref|YP_004597644.1| 468 RGFMLNNELTDFD--------FEPGGPNQVQPRKRPLSSTSPTMVFRDGEPIFTAGSPGGFTIITSVQQAILHRLVY 536
                                       *************........******************************************************** PP

                                       -S-HHHHHHS--EEESSSSTEEEESTTS.HHHHHHHHHTTSEEEESSSTCCCEEEEEEEETTTEEEEEE-TTTTT CS
                   G_glu_transpept 438 gldlqeavdaprihhqllpdkvevEegfseevveeLearGhkvkevedsssvvaavavakekgvleaasDprkdg 512
                                       gl++ ea+++p i        v +E+ ++e+ ve  earG+    ++++++ v+++ v+   + +++a+Dp +dg
  gi|336254537|ref|YP_004597644.1| 537 GLEPLEAIQEPSIFSA-RDFDVMWEPDVPEAAVEYGEARGQPWADEPEEIGNVQVMDVR--PDGFTGAADPTRDG 608
                                       ***************6.3459**********************9999999999999997..9*********9986 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.4     2e-05      0.18       6      30 ..      12      36 ..       8      41 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2e-05
                        UCR_Fe-S_N  6 sdeptRRDFLyiATgavgaVGaaaa 30
                                      s   +RR+FL +A +++ga   +aa
  gi|336254537|ref|YP_004597644.1| 12 SSRIDRRRFLALAGASAGALSLGAA 36
                                      56789**************754443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 4935.43
//
Query:       gi|336254538|ref|YP_004597645.1|  [L=689]
Description: hypothetical protein Halxa_3153 [Halopiger xanaduensis SH-6]
Scores for 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  (689 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 5175.71
//
Query:       gi|336254539|ref|YP_004597646.1|  [L=390]
Description: formyl-CoA transferase [Halopiger xanaduensis SH-6]
Scores for 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-125  418.0   0.0   3.8e-125  417.8   0.0    1.0  1  CoA_transf_3    CoA-transferase family III
  ------ inclusion threshold ------
      0.081   13.0   0.7       0.19   11.8   0.1    1.9  3  DUF3850         Domain of unknown function (DUF3850)
       0.18   11.9   0.1        0.3   11.1   0.1    1.3  1  MPTase-PolyVal  Metallopeptidase superfamily domain


Domain annotation for each model (and alignments):
>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.8   0.0  6.4e-129  3.8e-125       1     367 [.       4     375 ..       4     376 .. 0.97

  Alignments for each domain:
  == domain 1  score: 417.8 bits;  conditional E-value: 6.4e-129
                      CoA_transf_3   1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpsee....kgesayflavnrnKrsvalDlkse 73 
                                       L+ +rVldl+qvlaGp++t+lLAd+GA+V+k+E+p +gD +R  +p+ +    +  ++yf++vnr+K+s+ lD++++
  gi|336254539|ref|YP_004597646.1|   4 LSNLRVLDLTQVLAGPYCTMLLADMGADVVKIERP-GGDLIRSNPPYVDdpeeEAYGGYFQSVNRGKKSLELDFNDD 79 
                                       789********************************.***********9999999999******************** PP

                      CoA_transf_3  74 egrellkrLvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGq..sG..pkakrpgyDlvaqaasGlm 146
                                       e+r+ +++Lv++ADVvieN+r+g++e++ lgye+lr+ nP+Liy s+ g+G+  +G   ++ +p++Dl+aqa +G+m
  gi|336254539|ref|YP_004597646.1|  80 EDRADFLSLVEEADVVIENYRAGTMEKYDLGYETLREHNPQLIYSSIRGFGDprTGetHRQGQPSFDLIAQALGGVM 156
                                       ***************************************************965675566667************** PP

                      CoA_transf_3 147 sltgepdgpPvkvgvplgDivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgn 223
                                        +tg++dgpP+kvg+++gD +t++l +++ilaa+ +re+tG+Gq +d+ +++++l++++ ++ +++ tge+p+rqgn
  gi|336254539|ref|YP_004597646.1| 157 EITGQEDGPPTKVGPGIGDLFTATLNCIGILAAVNHREQTGEGQYVDTGMYDSMLSMTERAIYQQSYTGEAPTRQGN 233
                                       ***************************************************************************** PP

                      CoA_transf_3 224 rdpaaapygvyrtkdgwvaiaaatdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewle 300
                                       ++p++ py++++t+dg+ ++aa++ ++w++lc al+rp+l   +++ t a+rle+r+el+a++a w+a  +++++++
  gi|336254539|ref|YP_004597646.1| 234 SHPTLFPYDAFETADGYAVVAAFGTNHWRELCSALDRPDL--AEEYPTAADRLEHREELRAQIADWAADLETDDLVD 308
                                       ***************************************9..68899999999************************ PP

                      CoA_transf_3 301 llaaagvpaapvntleevlddpqlaarglvvevddpdyge.vpvvglpvrlsetparvkraaPklGed 367
                                       +l+   vpaapv+t ee++ddp++++r+++v v++p  ge v+  g+p+++ +tp++++ +aP l+e+
  gi|336254539|ref|YP_004597646.1| 309 RLEGR-VPAAPVQTTEEIFDDPHVRDRDMLVPVEQPGTGEdVEIAGNPIKMTATPPEPRGRAPLLDEH 375
                                       **987.*******************************9999**************************9 PP

>> DUF3850  Domain of unknown function (DUF3850)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.1e-05      0.19       9      41 ..      60      91 ..      56     107 .. 0.84
   2 ?   -3.6   0.0         2   1.2e+04      40      53 ..     215     228 ..     210     231 .. 0.64
   3 ?   -3.8   0.0       2.4   1.4e+04      21      37 ..     322     338 ..     320     341 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.1e-05
                           DUF3850  9 eyfeaVvsGkKtfeirknDrdyqvGDlLvLkei 41
                                       yf++V +GkK+ e+  nD++    D+L L e 
  gi|336254539|ref|YP_004597646.1| 60 GYFQSVNRGKKSLELDFNDDE-DRADFLSLVEE 91
                                      69*****************99.66799998874 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2
                           DUF3850  40 eideedgeytGrev 53 
                                       e    ++ ytG++ 
  gi|336254539|ref|YP_004597646.1| 215 ERAIYQQSYTGEAP 228
                                       44445789999875 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.4
                           DUF3850  21 feirknDrdyqvGDlLv 37 
                                       +e   +D +++ +D+Lv
  gi|336254539|ref|YP_004597646.1| 322 TEEIFDDPHVRDRDMLV 338
                                       56677899999999986 PP

>> MPTase-PolyVal  Metallopeptidase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1     5e-05       0.3      32      86 ..     238     296 ..     208     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5e-05
                    MPTase-PolyVal  32 lPekeaFeeaesyyatllHelvHwtghesRldrd.lskr...fgseayarEElvAelga 86 
                                       l + +aFe+a+ y+ +++  + Hw +  s ldr  l+++     ++   rEEl+A+++ 
  gi|336254539|ref|YP_004597646.1| 238 LFPYDAFETADGYAVVAAFGTNHWRELCSALDRPdLAEEyptAADRLEHREELRAQIAD 296
                                       556789***************************75776622234566789*****9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 3169.24
//
Query:       gi|336254540|ref|YP_004597647.1|  [L=146]
Description: methylaspartate mutase S chain [Halopiger xanaduensis SH-6]
Scores for 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-17   63.1   1.4      3e-17   62.8   1.4    1.1  1  B12-binding  B12 binding domain
  ------ inclusion threshold ------
      0.011   15.6   0.2       0.25   11.3   0.0    2.1  2  ADH_zinc_N   Zinc-binding dehydrogenase


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 !   62.8   1.4   3.4e-21     3e-17       2     120 ..       4     125 ..       3     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 3.4e-21
                       B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkri 78 
                                       +v+l+++g+d+h +G+ +l +a+++agf+V++lg+++++e++++a+ a+++++v++S+l+++  ++++   e l+ +
  gi|336254540|ref|YP_004597647.1|   4 TVVLGVIGSDAHVVGITILEQAFSAAGFDVVNLGVQTSQEEFAEAAVAHDAEAVLVSSLYGHAEQDCQGFHEVLEDA 80 
                                       699***********************************************************************9** PP

                       B12-binding  79 rprvkvvvGGahpsldpeetleak.....lgiddvvvgegedaleal 120
                                       + ++ + +GG  + + ++++ +++     lg +d v+   +d+ ea+
  gi|336254540|ref|YP_004597647.1|  81 GVEAVTYIGGNLA-VGQDDFEQTRrtfreLG-FDRVFDSETDPEEAI 125
                                       **********985.33333333334458899.888999999999987 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.013   1.1e+02       9      67 ..      24      81 ..      16      88 .. 0.52
   2 ?   11.3   0.0   2.8e-05      0.25      16      54 ..      92     129 ..      80     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.013
                                      HHH.HTT-EEEE..EESSHHHHHHHHH.TTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSC CS
                        ADH_zinc_N  9 lAk.alGaevia..vdsseeklelakk.lGadevinykeadlverikeltggegvdvvfecvG 67
                                       A  a+G+ v+   v  s+e ++ a+    a++v+ +   +l  + ++ +  +g++ v+e +G
  gi|336254540|ref|YP_004597647.1| 24 QAFsAAGFDVVNlgVQTSQEEFAEAAVaHDAEAVLVS---SLYGHAEQDC--QGFHEVLEDAG 81
                                      4443777777763344444444444432457777666...4555555555..35555555555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.8e-05
                                       EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHT CS
                        ADH_zinc_N  16 eviavdsseeklelakklGadevinykeadlverikelt 54 
                                         ++ d  e+ ++  ++lG d+v+++++ d++e+i++l 
  gi|336254540|ref|YP_004597647.1|  92 LAVGQDDFEQTRRTFRELGFDRVFDSET-DPEEAIAALR 129
                                       56777888999999************66.******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1044.58
//
Query:       gi|336254541|ref|YP_004597648.1|  [L=485]
Description: methylaspartate mutase, E subunit [Halopiger xanaduensis SH-6]
Scores for complete 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-206  686.1   0.0   1.7e-206  685.9   0.0    1.0  1  Met_asp_mut_E  Methylaspartate mutase E chain (MutE)


Domain annotation for each model (and alignments):
>> Met_asp_mut_E  Methylaspartate mutase E chain (MutE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  685.9   0.0  9.5e-211  1.7e-206       1     441 []      41     473 ..      41     473 .. 1.00

  Alignments for each domain:
  == domain 1  score: 685.9 bits;  conditional E-value: 9.5e-211
                     Met_asp_mut_E   1 lPeekrfakklekakeegktllqpragvalldehiellktleeegeadllpttiDsytRqnryeeaeegieesleag 77 
                                       lP++krfa++le+a++    llqpragv++l+++i+ll++l+ eg+adllpttiDsytR+n+ye+a+eg+e+++e++
  gi|336254541|ref|YP_004597648.1|  41 LPDRKRFADVLESADK---PLLQPRAGVPRLEDQIDLLEYLHGEGKADLLPTTIDSYTRDNEYEKAQEGLEKARETD 114
                                       79************99...9********************************************************* PP

                     Met_asp_mut_E  78 kslLNGfPavnhGvkacRkvveavdvpvqvrhgtpdarllaeitlagGftsfegggisynipyakkvsleetiekwq 154
                                       +++LNGfPavnhGv++cR+++ea+d+p++vrhgtpdarlla+it+agGf+sfegg+isynipy+k++ leetie+wq
  gi|336254541|ref|YP_004597648.1| 115 EDTLNGFPAVNHGVEGCRELIEAIDAPIEVRHGTPDARLLAAITFAGGFQSFEGGPISYNIPYTKRHGLEETIERWQ 191
                                       ***************************************************************************** PP

                     Met_asp_mut_E 155 yvdrLvglyeEnGvsinrepfgpltgtlvPpsisiavaiiEallaaeqGvksitvgygqvgnlvqDvaalraleela 231
                                       +vdrL+g+y+E+Gv+inrepfgpltgtlvPpsi+ia+++iE+ laa+qGv+sit+gygqvgn+vqDvaal+al++l 
  gi|336254541|ref|YP_004597648.1| 192 FVDRLAGAYTERGVRINREPFGPLTGTLVPPSIAIAIMLIEGKLAATQGVRSITLGYGQVGNVVQDVAALNALQKLG 268
                                       ***************************************************************************** PP

                     Met_asp_mut_E 232 eeylkkfgyedvvvttvlhqwmGgfPqdeakafgvislgaavaalakatkvivKtphEalgvptkeanaaglratkq 308
                                       +e+l     ++vvvttv+h+wmGgfP dea+a+gvi lg ++aa+a+++kvi+K+p+E++gvptkeanaaglr+t+q
  gi|336254541|ref|YP_004597648.1| 269 DEFLP----DEVVVTTVFHEWMGGFPPDEARANGVIGLGGMTAAIAQPDKVITKSPQEFQGVPTKEANAAGLRTTRQ 341
                                       *****....9******************************************************************* PP

                     Met_asp_mut_E 309 vlnlledqkleeteeleeekelikketraildkvlelgdGDvavgavrafeaGvlDvPFapskanagkvlparDneG 385
                                       v++++ +q++ +++ +eee+eli++etr+++d+vle+ dGDv++g+++af++G+lDvPFaps++++g+vlparD++G
  gi|336254541|ref|YP_004597648.1| 342 VIDMAIEQDI-DIDGIEEEQELIERETRCLMDTVLEHDDGDVVQGTLKAFDTGALDVPFAPSDSAKGAVLPARDDDG 417
                                       **********.****************************************************************** PP

                     Met_asp_mut_E 386 avrllefgnlplseeikefhrekleeRakaegRevsfqmvidDvyaiskgrLvgrp 441
                                       +vr++e+g+l+++++ike+h+++l++Ra++egR++sf+mv+dDv ais+g+L+grp
  gi|336254541|ref|YP_004597648.1| 418 RVRIFEWGDLAMDDDIKEIHKARLSRRADTEGRDQSFRMVADDVDAISDGKLIGRP 473
                                       *******************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3745.60
//
Query:       gi|336254542|ref|YP_004597649.1|  [L=432]
Description: methylaspartate ammonia-lyase [Halopiger xanaduensis SH-6]
Scores for complete 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-114  381.7   0.0   1.7e-114  381.1   0.0    1.2  1  MAAL_C    Methylaspartate ammonia-lyase C-terminus
    4.6e-69  231.1   0.4    8.1e-69  230.3   0.4    1.4  1  MAAL_N    Methylaspartate ammonia-lyase N-terminus
    4.6e-13   49.2   0.1    7.9e-13   48.5   0.1    1.4  1  MR_MLE_C  Enolase C-terminal domain-like
  ------ inclusion threshold ------
      0.026   15.3   0.6        0.4   11.5   0.3    2.8  2  ASL_C2    Argininosuccinate lyase C-terminal
        4.7    7.2   9.1        1.5    8.9   1.8    2.6  2  DUF2514   Protein of unknown function (DUF2514)


Domain annotation for each model (and alignments):
>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.1   0.0  4.8e-118  1.7e-114       3     247 ..     167     413 ..     165     415 .. 0.98

  Alignments for each domain:
  == domain 1  score: 381.1 bits;  conditional E-value: 4.8e-118
                            MAAL_C   3 akepvpilaqsgddrylnvdkmiikrvdvlPhalinnveklGeegekLldYvewlkeRieklgseeykptlhiDvyg 79 
                                       a+epvp+++qsgddry+n++km +k+v+vlPh+lin++ek+Ge+ge+Ll+Yvewl++R ++lg ++y+p++hiDvyg
  gi|336254542|ref|YP_004597649.1| 167 ATEPVPVFGQSGDDRYTNAEKMFVKGVPVLPHGLINSREKIGEDGETLLEYVEWLRTRSQELGPDGYEPRFHIDVYG 243
                                       579************************************************************************** PP

                            MAAL_C  80 tlgkvfdd..deervadylakleeaaapyklliegPldagskeeqierlaelreklkekgikvelvaDeWcntledi 154
                                       ++g++f    d+ +v+dy+a+leeaaapy++++egP+dag ++eqi+++ elre l+++g++v++vaDeWcntled+
  gi|336254542|ref|YP_004597649.1| 244 MIGEIFGApyDRAEVVDYFADLEEAAAPYPIQVEGPMDAGGRAEQIAAMVELREGLRDAGVDVDIVADEWCNTLEDV 320
                                       ******98779999*************************************************************** PP

                            MAAL_C 155 refvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvsarvsvhvalatrpaqlLakPGlGvDe 231
                                       r+fvda+aadlvqiktPDlGgi+++  av yc+ ++++aylGG+cnet++sar+++hvalat++aq+LakPG+G+De
  gi|336254542|ref|YP_004597649.1| 321 RAFVDAGAADLVQIKTPDLGGIHRSGRAVRYCEGTDTRAYLGGTCNETETSARACAHVALATDAAQVLAKPGMGFDE 397
                                       ***************************************************************************** PP

                            MAAL_C 232 GlmivtnemnRalall 247
                                       G+miv+nem+R++a +
  gi|336254542|ref|YP_004597649.1| 398 GYMIVENEMRRTIARR 413
                                       *************976 PP

>> MAAL_N  Methylaspartate ammonia-lyase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.3   0.4   2.3e-72   8.1e-69       2     158 ..       6     162 ..       5     163 .. 0.99

  Alignments for each domain:
  == domain 1  score: 230.3 bits;  conditional E-value: 2.3e-72
                            MAAL_N   2 kikdvlaseglsgfffdDqkAikagakedgfayegepvtpgFksvrqagesisvllvledgqvavGdcaavqysgag 78 
                                       +i++++a++g+sgfffdDq+Aik+ga++dgf+y+gepv +gF+++rqage+++v ++ledg+v++Gdcaavqysgag
  gi|336254542|ref|YP_004597649.1|   6 RITAIHATPGYSGFFFDDQRAIKQGAQQDGFTYDGEPVMEGFDEIRQAGETLIVDVELEDGTVVRGDCAAVQYSGAG 82 
                                       799************************************************************************** PP

                            MAAL_N  79 gRdplflaeefipvvekevapaLvgrdltsfrelaeeleslkedgkrlhtavrYGvsQalLdAaakaekttmaevva 155
                                       gRdplf+aee++p+ve+ va+aL+grd+t+f ++ae+le+l++dg+rlhta+rYGvsQalL+Aaa a++tt+++v+a
  gi|336254542|ref|YP_004597649.1|  83 GRDPLFRAEEYAPLVEGPVAEALEGRDATEFLANAETLEELQVDGDRLHTAIRYGVSQALLAAAASATGTTRTDVLA 159
                                       ***************************************************************************** PP

                            MAAL_N 156 eey 158
                                       +++
  gi|336254542|ref|YP_004597649.1| 160 DAL 162
                                       975 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 !   48.5   0.1   2.2e-16   7.9e-13      57     184 ..     253     393 ..     192     409 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 2.2e-16
                                       SBHHHHHHHHHHHGG.GT..ESEEESSSST...TTHHHHHHHHHH...HH..SSEEEESTTSSSHHHHHHHHHHTSE CS
                          MR_MLE_C  57 wdlatAirvarelee.ld..llwlEEPvpp...eddleglaelra...ra..sipiaagEslysradfrelleagav 122
                                       +d+a+ + +   lee     +  +E P+ +    ++++++ elr+   +a  ++ i+a+E + +++d+r++++aga+
  gi|336254542|ref|YP_004597649.1| 253 YDRAEVVDYFADLEEaAApyPIQVEGPMDAggrAEQIAAMVELREglrDAgvDVDIVADEWCNTLEDVRAFVDAGAA 329
                                       677777777777755433336678999988777678**********9844699************************ PP

                                       SEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBS.CS.SHHHHHHHHHHHHTTTTBEEEEEEGG CS
                          MR_MLE_C 123 divqpdvsrvgGitearkvaalaeafgvpvapHs.gs.gglglaaslhlaaaipnllileyfld 184
                                       d vq++    gGi ++ + ++ +e  + +  +++ ++ +  +  a++h+a a++ +++l  +  
  gi|336254542|ref|YP_004597649.1| 330 DLVQIKTPDLGGIHRSGRAVRYCEGTDTRAYLGGtCNeTETSARACAHVALATDAAQVLAKPGM 393
                                       *****************************999996666899***********988777666555 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.35   1.3e+03      23      37 ..     343     357 ..     342     370 .. 0.83
   2 ?   11.5   0.3   0.00011       0.4       3      46 ..     380     423 ..     379     432 .] 0.82

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHTT- CS
                            ASL_C2  23 eivgravrlaeekgk 37 
                                       + +gravr++e +++
  gi|336254542|ref|YP_004597649.1| 343 HRSGRAVRYCEGTDT 357
                                       668*******97765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00011
                                       THHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHH CS
                            ASL_C2   3 tATdlADyLvrkGlpFReAHeivgravrlaeekgkeleeltlee 46 
                                       +ATd A +L++ G+ F e + iv +  r+ ++++ ++e+   ++
  gi|336254542|ref|YP_004597649.1| 380 LATDAAQVLAKPGMGFDEGYMIVENEMRRTIARRERAEQSRADA 423
                                       7**********************999999888887777665555 PP

>> DUF2514  Protein of unknown function (DUF2514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.8   0.00041       1.5      86     129 ..     119     163 ..     101     169 .. 0.84
   2 ?    2.4   0.3      0.04   1.4e+02      16      49 ..     393     426 ..     382     432 .] 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00041
                           DUF2514  86 aadrLrqeaakL.aaaksavaadsaaaargkaaaraavvLadlLs 129
                                       + + L+ + + L  a +  v++   aaa++ +++   +vLad L+
  gi|336254542|ref|YP_004597649.1| 119 TLEELQVDGDRLhTAIRYGVSQALLAAAASATGTTRTDVLADALE 163
                                       3478999999998888999***********************986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.04
                           DUF2514  16 wGfahGrskeeaewekrwadrdaedsqakviaee 49 
                                       +Gf  G   +e+e ++  a+r++++++   +a++
  gi|336254542|ref|YP_004597649.1| 393 MGFDEGYMIVENEMRRTIARRERAEQSRADAATD 426
                                       6889999999999999999888765444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 3448.52
//
Query:       gi|336254543|ref|YP_004597650.1|  [L=364]
Description: MaoC domain-containing protein dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-08   32.5   0.0    5.3e-05   22.8   0.0    2.3  2  MaoC_dehydratas  MaoC like domain
    4.5e-06   26.8   0.0      0.022   14.9   0.0    2.5  2  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   5.9e-09   5.3e-05      28     106 ..      58     137 ..      34     151 .. 0.75
   2 !    7.6   0.1    0.0003       2.7      37     106 ..     258     325 ..     227     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.9e-09
                                       HHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S.--BTTCEEEEEEEEEE CS
                   MaoC_dehydratas  28 lvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvrFtk.pVlpgdtlkvelevvg 103
                                         + ++ p  +  ++A++ gf++p  h  + +a+  + ++e+l ++   ++g  +vrF++ pV pg +l+ve evvg
  gi|336254543|ref|YP_004597650.1|  58 SQTLNHDPAYWRTDAARERGFDEPPIHPDYLTAATLGTTVEDLSEKGGYFLGRTDVRFPGaPVSPGTELRVESEVVG 134
                                       55778999999999********6655555555555555666666667789********965***************9 PP

                                       EEE CS
                   MaoC_dehydratas 104 krd 106
                                        + 
  gi|336254543|ref|YP_004597650.1| 135 TAT 137
                                       654 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0003
                                       GT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S--BTTCEEEEEEEEEEEEE CS
                   MaoC_dehydratas  37 HvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvrFtkpVlpgdtlkvelevvgkrd 106
                                       H ++++ + a+ g +++ G +t +++ ++  ++ ++     vg+++ +F   V pgdt+++ + v + +d
  gi|336254543|ref|YP_004597650.1| 258 HHNADAMADAPSGDIVTYGDVTRSTALGHARSDEQT--WREVGFDDESFHTFVTPGDTVYAFTRVLEAED 325
                                       666666667777778888888888887777777666..7889*****************99887777554 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.5e-06     0.022      22      69 ..      56     101 ..      54     161 .. 0.75
   2 !    9.3   0.0   0.00013       1.1      83     130 ..     303     351 ..     298     352 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-06
                   MaoC_dehydrat_N  22 fakavgetnpayldeeaaraagyrsliaPptflivlatkapellealg 69 
                                       +++ + + +pay+  +aar+ g++++++ p++l+++        e+l+
  gi|336254543|ref|YP_004597650.1|  56 WMSQTLNHDPAYWRTDAARERGFDEPPIHPDYLTAATLGT--TVEDLS 101
                                       556667889************************9998766..445554 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00013
                   MaoC_dehydrat_N  83 eyhepiraGDelttesriadvydkkg.vGalefivvettvtnqrGepva 130
                                        +h  + +GD+++  +r+ + +d  +  +++  ++ e++  nqr+epv 
  gi|336254543|ref|YP_004597650.1| 303 SFHTFVTPGDTVYAFTRVLEAEDDSSsPDEAGTVRFEHVAFNQRDEPVY 351
                                       589999*****************9899********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2794.98
//
Query:       gi|336254544|ref|YP_004597651.1|  [L=352]
Description: HpcH/HpaI aldolase [Halopiger xanaduensis SH-6]
Scores for 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-15   55.7   0.0    1.4e-14   53.8   0.0    2.0  1  HpcH_HpaI        HpcH/HpaI aldolase/citrate lyase family
  ------ inclusion threshold ------
      0.058   11.6   0.0       0.63    8.2   0.0    2.1  3  Malate_synthase  Malate synthase


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   1.5e-18   1.4e-14      20     189 ..      42     220 ..      34     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.5e-18
                                       C--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SST..TH...HHHHHHGG....HHHTTSSE CS
                         HpcH_HpaI  20 agaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsl..ds...elikqdle....vldlgaqv 87 
                                       + +D+++ DlEd++a   K++     +++++q+    + + e+  Rv +   d    e +++++     ++  ++++
  gi|336254544|ref|YP_004597651.1|  42 QAPDWLVPDLEDGTAPDMKAEGL---ENTIEQVPR-YEFPGEIWPRVEWSyeDGtyrEKGREQIDrlasAIGDEIEG 114
                                       578***********999999654...555555555.34556889999864212211133444444666889999*** PP

                                       EEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH...TSTTEEEEEE-HHHHHHHTT-T CS
                         HpcH_HpaI  88 vlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIa...avegldgvflGaeDlsadlgtk 161
                                       v+vPkv   e+++ + +a++e+e++ +  ++++ l + +E+ ++ ++++eIa   +  +l ++++G+ D++a+lg +
  gi|336254544|ref|YP_004597651.1| 115 VVVPKVGRLEDVRRAAEAVAEAEREHGYPDGSIGLSIIVETGRARSDLREIAkfgEDSRLTALVFGPVDYTAELGGR 191
                                       ****************************************************766667*****************98 PP

                                       TSTTS.HHHHHHHHHHHHTTHCEEEEEEE CS
                         HpcH_HpaI 162 rspeg.tevldareriltaaraagiaald 189
                                       +  +g + +    e++   a aag+  ++
  gi|336254544|ref|YP_004597651.1| 192 DLGDGrPRWDGLLEALSNEASAAGLLSIG 220
                                       76554144445666666666666665554 PP

>> Malate_synthase  Malate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0     7e-05      0.63     207     276 ..     115     185 ..     111     188 .. 0.87
   2 ?   -2.9   0.0      0.17   1.5e+03     349     368 ..     244     263 ..     237     272 .. 0.75
   3 ?    0.3   0.0     0.017   1.6e+02     409     447 ..     273     311 ..     259     315 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 7e-05
                                       EEE-S-SSHHHHHHHHHHHHHHHHHCTSSTTSCEEEEEE-SHHHHTTHHHHHHCTTT.TEEEEEE-CHHHH CS
                   Malate_synthase 207 ivlPKmegpqEaalwnevFsraedllglprgtikatvliEtlraslnldeiiyelrd.rvaglNcGrlDyi 276
                                       +v PK+   ++++ ++e    ae   g p g+i  ++++Et ra  +l+ei +   d r++ l  G  Dy+
  gi|336254544|ref|YP_004597651.1| 115 VVVPKVGRLEDVRRAAEAVAEAEREHGYPDGSIGLSIIVETGRARSDLREIAKFGEDsRLTALVFGPVDYT 185
                                       578***********************************************987655436677777777776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.17
                                       HCHHHHHCT-SEEEESSHHH CS
                   Malate_synthase 349 dKlrevraGadgaWvahPtl 368
                                       + ++e+r G dg+W   P  
  gi|336254544|ref|YP_004597651.1| 244 QIEHEARLGLDGSWSLYPKQ 263
                                       5567999*******888864 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHCT-SSEEETTEEESHHHH CS
                   Malate_synthase 409 eteeglrnnvqvglqYvvaWlrgvGcvpiihLmEDaATa 447
                                        t ++l+++v+ + ++ +a  +g+G+v i   m D AT 
  gi|336254544|ref|YP_004597651.1| 273 PTPDELERDVHKIERFNEAKREGTGAVTIDGQMVDEATF 311
                                       577899999999999999999****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2585.76
//
Query:       gi|336254545|ref|YP_004597652.1|  [L=171]
Description: OsmC family protein [Halopiger xanaduensis SH-6]
Scores for complete 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   63.7   0.0    3.8e-17   62.6   0.0    1.5  2  OsmC      OsmC-like protein
  ------ inclusion threshold ------
        0.1   12.8   0.1       0.21   11.8   0.1    1.5  1  CARM1     Coactivator-associated arginine methyltransferase 1


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.93   8.4e+03      57      63 ..      24      30 ..      14      46 .. 0.53
   2 !   62.6   0.0   4.2e-21   3.8e-17       1     100 []      60     166 ..      60     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.93
                                      EEEEEEE CS
                              OsmC 57 irlkvev 63
                                      ++l+++ 
  gi|336254545|ref|YP_004597652.1| 24 AQLTLTA 30
                                      3333333 PP

  == domain 2  score: 62.6 bits;  conditional E-value: 4.2e-21
                                       TTXSSB-HHHHHHHHHHHHHHHHHHHHTCCCT---.SCEEEEEEEEEECCECT........CEEEEEEEEEEE-SS- CS
                              OsmC   1 gdgsgpsPeelllaalasCfaitlravakkkgikl.edleveveaerdpegak........giteirlkvevkipga 68 
                                       g+g+g  +++lll ala+C ++t++ava++  i+   d++ve++++ d +g+         g++++rl+v+v+ +++
  gi|336254545|ref|YP_004597652.1|  60 GPGTGACSGDLLLGALAACSQLTAQAVAENFDIGDdVDISVEASGDLDLRGTMgvdedapvGFEDLRLDVTVE-GDI 135
                                       67889999***********************66443566888888***99999*******************6.666 PP

                                       H..HHHHHHHHHHHHHSHHHHHHCT-SSSEEE CS
                              OsmC  69 dseeklkkllekaekrCpvsntlkngvkvele 100
                                         ee+ ++l +++e++C v++tl+n+++ve+e
  gi|336254545|ref|YP_004597652.1| 136 G-EETKAALRKYTERYCVVYQTLENPPDVETE 166
                                       6.68888888889****************986 PP

>> CARM1  Coactivator-associated arginine methyltransferase 1 N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.3e-05      0.21      21      48 ..       5      32 ..       2      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                             CARM1 21 qrhseqqplrlevkttedaaeialsnte 48
                                       +h eq+pl+ e +t+++aa+++l+ t 
  gi|336254545|ref|YP_004597652.1|  5 DLHEEQKPLKREYETNPEAAQLTLTATG 32
                                      5799********************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1325.90
//
Query:       gi|336254546|ref|YP_004597653.1|  [L=444]
Description: hypothetical protein Halxa_3161 [Halopiger xanaduensis SH-6]
Scores for 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-47  159.6   1.5    7.8e-47  159.2   1.5    1.1  1  DUF21      Cyclin M transmembrane N-terminal domain
    4.3e-21   74.7   1.1    1.5e-20   73.0   1.1    2.0  1  CorC_HlyC  Transporter associated domain
    3.6e-16   59.3   5.4    1.1e-08   35.3   1.0    2.7  2  CBS        CBS 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 !  159.2   1.5   1.3e-50   7.8e-47       3     176 .]      14     205 ..      12     205 .. 0.98

  Alignments for each domain:
  == domain 1  score: 159.2 bits;  conditional E-value: 1.3e-50
                             DUF21   3 ivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvell 79 
                                       +++l++l++ff++aE+A+v+++++ +e+++++g+++++ l + ++n++++L+t+++g+t+++++l++l++++++ ll
  gi|336254546|ref|YP_004597653.1|  14 AFVLVALNGFFVAAEFAYVRVRSSAVEQMVAEGRSGSALLADAVDNLDDYLATTQLGITIASLGLGWLGEPAVAALL 90 
                                       68999************************************************************************ PP

                             DUF21  80 ae...........galavviatvivtllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwllskllnli 145
                                       ++           + +++++ + ++t+l++vfgE++Pk++a+++ae++al+++p++++++++++P +++++  +n +
  gi|336254546|ref|YP_004597653.1|  91 EPvlapllpegvlHLVSFAVGFGFITFLHVVFGELAPKTIAIAQAERVALLVSPLMKFFYYIFFPGIIVFNGTANRF 167
                                       **********999888999999999**************************************************** PP

                             DUF21 146 l.......esesepavseeelkklveeseeegvieeee 176
                                       +        se+++++se el+++++ s ++g+i+++e
  gi|336254546|ref|YP_004597653.1| 168 TrllgvppASETDETLSETELRTVLARSGQSGEIDTSE 205
                                       ********9*************************9987 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   1.1   2.5e-24   1.5e-20       3      79 ..     361     435 ..     359     437 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 2.5e-24
                                       ECTTEEEEETT-BHHHHHHHHTSTTHHCT-SBHHHHHHHHH-S---TT-EEEEEETTEEEEEEEEETTCEEEEEEEE CS
                         CorC_HlyC   3 ldegsylvdGslpldeleeelglelpeedyeTlgGlllellgriPkegesvevdleglrftVlemdgrrIkkvrvek 79 
                                       +++g+y+vdG +++  ++e+l+++++ +++ T+gGl+l++lgr+P++g+++evd  ++ ++V +++g r++++ v+ 
  gi|336254546|ref|YP_004597653.1| 361 RGDGTYVVDGGVTVSTVNERLDTDFEADEFGTIGGLVLDRLGRVPEVGDRIEVD--DYALEVAAVEGSRVDSLVVRE 435
                                       789**********************************************88888..****************99976 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   1.0   1.9e-12   1.1e-08       1      56 [.     220     279 ..     220     280 .. 0.89
   2 !   25.4   0.2   2.4e-09   1.4e-05       2      56 ..     291     344 ..     290     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.9e-12
                                       HHHH..SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 Vgdi..mtrdvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllrall 56 
                                       V+d+  +++d +tv  d +++e+  l+ e+g++r+PVV  d+ +++vG v  +D+lral 
  gi|336254546|ref|YP_004597653.1| 220 VRDVmvPRPDAITVASDRPVAEVRSLILESGHTRYPVVdaDDPDQVVGFVDAKDVLRALD 279
                                       78984466688***************88***99*****8877779*************95 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 2.4e-09
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrl.PVVdedgklvGivtlrDllrall 56 
                                       gdi  rd++ vp++t++ ++le++ +++v +l  V+de g + G+vt +D+l+ ++
  gi|336254546|ref|YP_004597653.1| 291 GDI-ARDLPIVPETTSVVDLLEQFQRERV-QLaAVIDEWGVFEGLVTVEDVLEEVV 344
                                       676.7999****************99999.9966**9888999*********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2897.27
//
Query:       gi|336254547|ref|YP_004597654.1|  [L=249]
Description: hypothetical protein Halxa_3162 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00013   21.8   0.0    0.00028   20.7   0.0    1.4  1  DUF2064   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2064  Uncharacterized protein conserved in bacteria (DUF2064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.6e-08   0.00028      22     110 ..      79     167 ..      73     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.6e-08
                                       TTHHHHHHHH-TTSEEEE--SSSHHHHHHHHHHHHHHTT-S.EEEEE-SS-TT--HHHHHHHHHHTTT-SEEEEEBT CS
                           DUF2064  22 dkalaeqlalakglevlpQqggdlgeRlarafdrafeagee.pvlliGsDcpqltaalleqAfeaLeeadaVlgpae 97 
                                       ++ +a++l++++++++++Q g++  +R+ + +++ +e +e  +v ++    p ++++ +++A+ +L+++da+lgp++
  gi|336254547|ref|YP_004597654.1|  79 RELAAAALETTDDVRFERQVGSSHSARIGNTVTHLLEREEAgSVGVLEPTAPLVSRSEIDSAAMSLRRYDAILGPST 155
                                       555666779999***********************8888889*********************************** PP

                                       TSSEEEEEEEG-G CS
                           DUF2064  98 DGGYyllGlkkrl 110
                                        G  y+ G+++ +
  gi|336254547|ref|YP_004597654.1| 156 GGRAYVAGFTE-P 167
                                       *9999999994.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1934.15
//
Query:       gi|336254548|ref|YP_004597655.1|  [L=74]
Description: hypothetical protein Halxa_3163 [Halopiger xanaduensis SH-6]
Scores for 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  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); 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 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 589.89
//
Query:       gi|336254549|ref|YP_004597656.1|  [L=265]
Description: alpha/beta hydrolase fold protein [Halopiger xanaduensis SH-6]
Scores for 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-23   83.5   7.2    3.7e-23   83.3   7.2    1.1  1  Abhydrolase_6   Alpha/beta hydrolase family
    3.4e-23   82.6   0.0    1.4e-20   74.1   0.0    2.1  2  Abhydrolase_1   alpha/beta hydrolase fold
    4.6e-19   68.6   0.1    7.6e-19   67.9   0.1    1.4  1  Hydrolase_4     Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.031   14.1   0.1       0.07   13.0   0.0    1.6  2  Ser_hydrolase   Serine hydrolase
      0.079   12.5   0.0        0.2   11.2   0.0    1.7  1  Abhydro_lipase  Partial alpha/beta-hydrolase lipase region
       0.11   12.7   0.0       0.16   12.1   0.0    1.4  1  Thioesterase    Thioesterase domain
       0.14   11.6   0.0        0.6    9.5   0.0    2.0  2  Peptidase_S9    Prolyl oligopeptidase family
       0.15   11.7   0.2       0.39   10.3   0.1    1.7  1  Esterase        Putative esterase


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   7.2   1.6e-26   3.7e-23       1     219 [.      30     257 ..      30     258 .. 0.66

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 1.6e-26
                                       EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH...CHHHHHHHCCTT..TTSEEEEEETC CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldled...ladlaalldelaagggpvvlvGHSl 74 
                                       v+l+HG   +++ W   +L   la++++v+a+D++GhGr+d p ++++    +adl+ ++del+   +++vlvGHS+
  gi|336254549|ref|YP_004597656.1|  30 VVLAHGMYDNGRRWV--RLGSELADDYEVIAYDARGHGRTDAPETGYDMtnrVADLVGIVDELG--LPNPVLVGHSM 102
                                       8*****99999***8..999999*********************999667789**********5..9999******* PP

                                       HHH.HHHHHHHCC..EE.EEES-..----TTTS----TTHHHHHHTT-C..CCCHCCHS-HSCCCCHHHCCCCHCHC CS
                     Abhydrolase_6  75 GGa.lalaaaplalvvg.vlldppptalpagllaaalelllallallrl..lawlsreplprlfladedadaawrar 147
                                       G+a +a+aaa+++++ + ++l++  +a     +++ +e ++ + + l++    ++ +  + ++ ++d+da+++  +r
  gi|336254549|ref|YP_004597656.1| 103 GAAtVACAAADHPDLPRaLVLEA--PARFREAPQMDMETARERSRKLVReaQDLSLE-ERIDQHYDDVDAEPEQIRR 176
                                       *6659999999995555566666..14444445666666665555333333233322.2334555555532222222 PP

                                       CCGHH.......HHCCHHCHTTCCHHTT-TTGCEEE....CTT-CHHHHCHHCCCHSTTEEETCE...SSS-HHHHS CS
                     Abhydrolase_6 148 larla.......allaglgllpaaawadlpvpllvl....ggeDplvprllerllaqagarlpvvlpgaGHlphlee 213
                                       la +        a  a+   l ++ +  +++p+l l      +D++    ++++  +a++rl v +p+aGH+++ ++
  gi|336254549|ref|YP_004597656.1| 177 LAVATgecsprvAMYAQEHRLVVETFDEITCPTLSLrpdlDVADRTSDLNAAER--LASERL-VHVPDAGHYVFRDA 250
                                       211112233211222233344599*********876543335566333112233..478***.************88 PP

                                       H.HHHHH CS
                     Abhydrolase_6 214 p.devae 219
                                         +++ae
  gi|336254549|ref|YP_004597656.1| 251 YdAALAE 257
                                       8777776 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.0     6e-24   1.4e-20       1     126 [.      28     150 ..      28     163 .. 0.92
   2 !    7.0   0.0    0.0018         4     206     253 ..     193     247 ..     154     251 .. 0.71

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 6e-24
                                       SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEE CS
                     Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltl 77 
                                       p++v+ hG+ +++  w +  l++ La+ +++vi++D rG+g+++++ +     y + +  +dl  i+d lg+ +++l
  gi|336254549|ref|YP_004597656.1|  28 PPVVLAHGMYDNGRRWVR--LGSELAD-DYEVIAYDARGHGRTDAPET----GYDMTNRVADLVGIVDELGLPNPVL 97 
                                       89****************..******9.*******************5....67776678888899*********** PP

                                       EEETHHHHHHHHHHHHHGGGEEEEEEESE....CSSCCHHHHHHHHHHHHHHC CS
                     Abhydrolase_1  78 vGhSmGGmialayaaeyperVkalvllga....idpaaslieaqrqqaksfpd 126
                                       vGhSmG ++++ +aa++p+  +alvl ++     +p ++++ a ++++k + +
  gi|336254549|ref|YP_004597656.1|  98 VGHSMGAATVACAAADHPDLPRALVLEAParfrEAPQMDMETARERSRKLVRE 150
                                       *****************************999999999999999998887655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0018
                                       C........THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHH CS
                     Abhydrolase_1 206 e........lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlaf 253
                                       +        ++++++ptl +  + D ++  + l   ++ l ++rlv+++dagH++f
  gi|336254549|ref|YP_004597656.1| 193 QehrlvvetFDEITCPTLSLRPDLDVADRTSDLNAAER-LASERLVHVPDAGHYVF 247
                                       15556666678899999999777776665555544444.5566***********98 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.1   3.4e-22   7.6e-19       7     169 ..      30     178 ..      28     251 .. 0.63

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 3.4e-22
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelplfllG 82 
                                       vvl+HG+ +  +r  +l+ +La+ +++v+a+D+rGhGr++ +++g   +++  v+Dl  +v+++  ++p    +l+G
  gi|336254549|ref|YP_004597656.1|  30 VVLAHGMYDNGRRWVRLGSELAD-DYEVIAYDARGHGRTDaPETG--YDMTNRVADLVGIVDELGLPNP----VLVG 99 
                                       9********************86.8**************977777..6888899********9996664....78** PP

                       Hydrolase_4  83 hSmGGliallyllrypdkvaglilsaPalkikaklk.appllklllkllgkllpklqvsnnlkadslsrdpevvaay 158
                                       hSmG+++++ +++++pd  ++l+l aPa   +a+   +  + +  ++ l + +++l+++++++ +         + +
  gi|336254549|ref|YP_004597656.1| 100 HSMGAATVACAAADHPDLPRALVLEAPARFREAPQMdMETARER-SRKLVREAQDLSLEERIDQH--------YDDV 167
                                       *****************999********5444332223333332.23333333444444444433........3333 PP

                       Hydrolase_4 159 eadplvhgkit 169
                                       +a+p  ++++ 
  gi|336254549|ref|YP_004597656.1| 168 DAEPEQIRRLA 178
                                       33333333333 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.1e-05      0.07      56     102 ..      94     139 ..      77     183 .. 0.78
   2 ?   -2.7   0.0       2.1   4.6e+03     129     153 ..     224     245 ..     218     253 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                                       TEEEEEETCHHHHHHHHHHHTTSSSEEEEEEET--SGGS..TT.GGG CS
                     Ser_hydrolase  56 kvvlvAHSlgclavlhaaelqlakkvagalLVapadveeeaaklael 102
                                       + vlv HS+g+++v+ aa + +++  ++ +L apa  +e ++++ e+
  gi|336254549|ref|YP_004597656.1|  94 NPVLVGHSMGAATVACAA-ADHPDLPRALVLEAPARFREAPQMDMET 139
                                       349************999.8888888999999***996444444333 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.1
                                       -HHHHHHHHHHCT-EEEEETT-TTS CS
                     Ser_hydrolase 129 sfeeaeelaeawgaelvdlgeaGHi 153
                                       + ++ae+la++   +lv+++ aGH 
  gi|336254549|ref|YP_004597656.1| 224 DLNAAERLASE---RLVHVPDAGHY 245
                                       55555555543...67888888885 PP

>> Abhydro_lipase  Partial alpha/beta-hydrolase lipase region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.1e-05       0.2      41      62 ..      24      45 ..      16      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.1e-05
                    Abhydro_lipase 41 lekkpvVlLqHGLlasSevwvl 62
                                      ++++p+V L HG+ ++   wv 
  gi|336254549|ref|YP_004597656.1| 24 TGEGPPVVLAHGMYDNGRRWVR 45
                                      6789****************96 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     7e-05      0.16      15      84 ..      42     112 ..      28     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7e-05
                                       GGHHHHHHCTTCEEEEEEECSTTSTSHHHCTTCHHHHHHHHHHHHHHH-SSS.SE.EEEEETHHH.HHHHHHH CS
                      Thioesterase  15 vfrslasklsdpvvevlavqlpgrerdepplesieelaaeyaealrqiqpeg.Py.alfGhSlGg.llAfevA 84 
                                          +l s+l d+  ev+a+ ++g++  + ++e+  ++ +++a+ +  + + g P  +l+GhS+G+ ++A ++A
  gi|336254549|ref|YP_004597656.1|  42 RWVRLGSELADD-YEVIAYDARGHG-RTDAPETGYDMTNRVADLVGIVDELGlPNpVLVGHSMGAaTVACAAA 112
                                       56789999***8.9**********7.67777888899999999988888888854389******824665555 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.59   1.3e+03     161     189 ..      39      67 ..      18      90 .. 0.64
   2 ?    9.5   0.0   0.00027       0.6      67      97 ..      96     126 ..      77     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.59
                                       HHHHHHHHHH--S-SEEEEEETTS-SSTT CS
                      Peptidase_S9 161 ealklvaaLqkkgknvlllifpdegHgvg 189
                                       ++ ++v+   +  +++++  +   gHg  
  gi|336254549|ref|YP_004597656.1|  39 NGRRWVRLGSELADDYEVIAYDARGHGRT 67 
                                       44455555555556666677777777544 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00027
                                       EEEEETHHHHHHHHHHHH-GGG-SEEEEESE CS
                      Peptidase_S9  67 aitGgSyGGyltgaalnqrpdlFkaavaevp 97 
                                       ++ G+S G  ++++a++++pdl +a+v e+p
  gi|336254549|ref|YP_004597656.1|  96 VLVGHSMGAATVACAAADHPDLPRALVLEAP 126
                                       678************************9998 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00017      0.39     118     139 ..      96     117 ..      59     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00017
                                       EEEEETHHHHHHHHHHHCSTTT CS
                          Esterase 118 avaGqSmGGlgALilalkhpdr 139
                                       +++G+SmG+ +  ++a++hpd+
  gi|336254549|ref|YP_004597656.1|  96 VLVGHSMGAATVACAAADHPDL 117
                                       79******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2258.54
//
Query:       gi|336254550|ref|YP_004597657.1|  [L=218]
Description: uracil-DNA glycosylase superfamily [Halopiger xanaduensis SH-6]
Scores for 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-18   66.4   0.0    3.6e-18   66.0   0.0    1.2  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 !   66.0   0.0     2e-22   3.6e-18       2     132 ..      34     186 ..      33     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 2e-22
                                       HC-CTT-SEEEEESSTCHHHHHHSSSS.-.STT........--HHHHHHHCCCCCCCHHG.....CTEEEEESSS.. CS
                               UDG   2 gegppdakvvivGeaPgaeedatglpFsg.rag........nllrkllneaglkrdlese.....qgvyitnvvkcr 64 
                                       g+g+  a+ ++vGe+P    d+tg p ++ + g          lr++l+++ l   +        ++vy tn+ +cr
  gi|336254550|ref|YP_004597657.1|  34 GYGDVGADFLFVGEQPTSAADETGVPLVAgPDGdaeaetggADLRRILERLALCDATSPReepllENVYCTNLTRCR 110
                                       899************************9864446666677799*******6555533333699************** PP

                                       ..SECGCTTCCCCTCCHHHHHHHHHHHHSSEEEEESHHHHHH...........HHHHSCESCCCSCT..SEEEEES- CS
                               UDG  65 ppgnrdtptsaeikacaplleeeiellkprlivllGktaakall.........geklgklrgklleak.irvlplph 131
                                        p+ r  pt++ei +c p+l++ei+ ++p++++ +G+ a+  l          + +l++++ + ++ +  +++p+  
  gi|336254550|ref|YP_004597657.1| 111 EPE-R-PPTDEEIGNCEPYLNAEIRMINPEILIPVGERALTELGkeytttpveELELSDAHATTIRGRgFELVPMIA 185
                                       877.7.8***********************************83333455553335556666666665566666655 PP

                                       S CS
                               UDG 132 P 132
                                       P
  gi|336254550|ref|YP_004597657.1| 186 P 186
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1684.83
//
Query:       gi|336254551|ref|YP_004597658.1|  [L=86]
Description: hypothetical protein Halxa_3166 [Halopiger xanaduensis SH-6]
Scores for 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  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.33u 0.19s 00:00:00.52 Elapsed: 00:00:00.33
# Mc/sec: 781.57
//
Query:       gi|336254552|ref|YP_004597659.1|  [L=357]
Description: ParA/MinD ATPase-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-100  335.9   0.0   1.6e-100  335.7   0.0    1.1  1  ParA            NUBPL iron-transfer P-loop NTPase
    1.1e-15   57.5   1.5    2.1e-15   56.7   0.8    1.9  2  FeS_assembly_P  Iron-sulfur cluster assembly protein
    6.2e-15   55.4   0.0    4.7e-14   52.5   0.0    2.1  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    2.4e-10   40.6   0.2    9.3e-09   35.4   0.1    2.1  2  AAA_31          AAA domain
      6e-08   32.3   0.0    8.2e-08   31.9   0.0    1.2  1  MipZ            ATPase MipZ
    3.1e-06   26.8   0.0       0.01   15.3   0.1    2.2  2  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
    0.00015   21.2   0.0    0.00025   20.4   0.0    1.3  1  VirC1           VirC1 protein
    0.00023   20.4   3.6    0.00058   19.1   1.0    2.1  2  ArsA_ATPase     Anion-transporting ATPase
     0.0058   16.2   0.0      0.013   15.1   0.0    1.5  1  AAA_25          AAA domain
  ------ inclusion threshold ------
      0.017   15.1   0.1      0.063   13.2   0.0    1.9  2  DUF1610         Domain of unknown function (DUF1610)
      0.041   13.4   0.8       0.26   10.7   0.3    2.0  2  CBP_BcsQ        Cellulose biosynthesis protein BcsQ
       0.05   13.4   0.0          4    7.2   0.1    2.4  2  AAA_26          AAA domain
       0.11   12.2   0.0       0.22   11.3   0.0    1.4  1  CLP1_P          mRNA cleavage and polyadenylation factor CLP1
       0.15   11.9   0.0       0.41   10.5   0.0    1.7  2  APS_kinase      Adenylylsulphate kinase


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 !  335.7   0.0  1.2e-103  1.6e-100       2     245 ..      92     333 ..      91     334 .. 0.98

  Alignments for each domain:
  == domain 1  score: 335.7 bits;  conditional E-value: 1.2e-103
                              ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSi 78 
                                       vk+viav+SgKGGVGKStvavnlA+ L++ g++vgl+DaD+yGp++pr+++++e  + +++++l+P e++g+k+mS+
  gi|336254552|ref|YP_004597659.1|  92 VKNVIAVASGKGGVGKSTVAVNLAAGLSQLGARVGLFDADVYGPNVPRMVDADEPPMATEDETLMPPEKYGVKLMSM 168
                                       9*****************************************************988888999************** PP

                              ParA  79 gfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkk 155
                                       +fl+  ed++v+wrGpm++k+i+ql +dvewg+lDyL++DlPPGtgD+qlt++q++p++gaviVttpq+val+d++k
  gi|336254552|ref|YP_004597659.1| 169 AFLTG-EDDPVIWRGPMVHKVITQLTEDVEWGHLDYLVVDLPPGTGDTQLTMLQTMPVTGAVIVTTPQDVALDDARK 244
                                       ****9.*********************************************************************** PP

                              ParA 156 aiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepes 232
                                       ++emf + ++ vlG+ eNms f+cp+cg++++ifg+ggg+++a+e+++p+lg+ipldp++re +d+gkp+vl++ +s
  gi|336254552|ref|YP_004597659.1| 245 GLEMFAQHDTVVLGIAENMSSFACPDCGSQHDIFGSGGGREFADEHDMPFLGSIPLDPSVREGGDSGKPTVLDD-DS 320
                                       *********************************************************************99986.99 PP

                              ParA 233 eaakaleeiaekv 245
                                       e+ +++++i+e+v
  gi|336254552|ref|YP_004597659.1| 321 EVGESFRTITENV 333
                                       *********9998 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.8   1.6e-18   2.1e-15       1      62 [.       3      64 ..       3      76 .. 0.93
   2 ?   -2.5   0.0       4.8   6.2e+03      40      58 ..     229     247 ..     227     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 1.6e-18
                                      HHHHHHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--SSTT-TTHHHHHHHHHHHHC CS
                    FeS_assembly_P  1 keavlaaLrtVtDPelgvdlvslglvreidieggkVsvditltypacslaeairadaeaalr 62
                                      ++av++ LrtV DPelg d+vslglv +i+++g++Vsvd++l+ p  +  ++i+a+a++ l 
  gi|336254552|ref|YP_004597659.1|  3 EDAVRDRLRTVEDPELGDDIVSLGLVNDIAVDGDEVSVDLALGAPYSPTESDIAAEAREVLI 64
                                      689******************************************************99885 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.8
                                       E--SSTT-TTHHHHHHHHH CS
                    FeS_assembly_P  40 itltypacslaeairadae 58 
                                       + +t+p+  ++++ r+ +e
  gi|336254552|ref|YP_004597659.1| 229 VIVTTPQDVALDDARKGLE 247
                                       6789999999999998776 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 !   52.5   0.0   3.7e-17   4.7e-14       1     126 [.      96     312 ..      96     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 3.7e-17
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx...................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep...................... 54 
                                       ia+as+kGGvGK+t+a+nLa+ l++ g rV l+DaD+ ++n    ++ +e    p                      
  gi|336254552|ref|YP_004597659.1|  96 IAVASGKGGVGKSTVAVNLAAGLSQLGARVGLFDADVYGPNVPRmVDADE----Ppmatedetlmppekygvklmsm 168
                                       89***************************************993333333....2466699999************* PP

                                       ........................................................................CCHCC CS
                                       ........................................................................xxxxx RF
                              CbiA  55 ........................................................................dlkrl 59 
                                                                                                               d+ ++
  gi|336254552|ref|YP_004597659.1| 169 afltgeddpviwrgpmvhkvitqltedvewghldylvvdlppgtgdtqltmlqtmpvtgavivttpqdvaldDARKG 245
                                       *********************************************************************99999999 PP

                                       CHHHHHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  60 lellealgkkkall...lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparge 126
                                       le++++ +++  +l    ++ ++     +++ ++   + + +e   ++ +p+lg+ip d +v e   +g+
  gi|336254552|ref|YP_004597659.1| 246 LEMFAQHDTV--VLgiaENMSSFACPDCGSQ-HDIFGSGGGREFADEHDMPFLGSIPLDPSVREGGDSGK 312
                                       9999888876..3446677777777777777.56666666666667778999999999998888877777 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.1   7.3e-12   9.3e-09       2      40 ..      94     132 ..      93     145 .. 0.94
   2 ?    3.1   0.0     0.062        79     108     160 ..     190     245 ..     162     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 7.3e-12
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                        vIa+a  KGGvGK+T +vnlaa l++lg +v l D+D 
  gi|336254552|ref|YP_004597659.1|  94 NVIAVASGKGGVGKSTVAVNLAAGLSQLGARVGLFDADV 132
                                       59***********************************96 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.062
                            AAA_31 108 kellekvk.deYDyiiiDcpPsLglltenaLva..sdsviipvqaeayaleGleql 160
                                       ++l e+v+  + Dy ++D pP  g    + L +      +i++ +++ al+ +++ 
  gi|336254552|ref|YP_004597659.1| 190 TQLTEDVEwGHLDYLVVDLPPGTGDTQLTMLQTmpVTGAVIVTTPQDVALDDARKG 245
                                       555555552357*********99866665554411344567777888887766555 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   6.4e-11   8.2e-08       2     116 ..      95     218 ..      94     267 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 6.4e-11
                                       EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT------EEE-SSS-HHHHT CS
                              MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkglsLplpealalseaeeaev 78 
                                       vi ++  kGG Gkst+av +a  L++ Garv+  d d+    + r ++     ++ ++ +L  pe + ++  ++a +
  gi|336254552|ref|YP_004597659.1|  95 VIAVASGKGGVGKSTVAVNLAAGLSQLGARVGLFDADVYGPNVPRMVDADEPPMATEDETLMPPEKYGVKLMSMAFL 171
                                       7999********************************************99999999999999999999998888888 PP

                                       TS-HHHHHHH.......HHHHHHHHHH.H-SEEEEE--.SS--HHHH CS
                              MipZ  79 eeeeeaevae.......leelvadlea.eldfividtP.Gsdsalsr 116
                                       ++e++  + +       +++l++d+e  +ld++v+d P G+ ++   
  gi|336254552|ref|YP_004597659.1| 172 TGEDDPVIWRgpmvhkvITQLTEDVEWgHLDYLVVDLPpGTGDTQLT 218
                                       88777654322221111556666666425799999986354333222 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 !   15.3   0.1   7.9e-06      0.01       6      33 ..     100     127 ..      94     133 .. 0.86
   2 !    9.3   0.0   0.00054      0.69     194     259 ..     284     348 ..     243     353 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.9e-06
                         Fer4_NifH   6 yGkGGiGksttsqnlsaalaemgkkvli 33 
                                        GkGG+Gkst + nl+a l++ g +v +
  gi|336254552|ref|YP_004597659.1| 100 SGKGGVGKSTVAVNLAAGLSQLGARVGL 127
                                       5**********************99955 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00054
                         Fer4_NifH 194 ekfaeelgtkvlevvPrdeivrkaelrkk.tvieyapeseqakeyrelarkilenkklviPkplsed 259
                                       ++fa+e +++ l  +P+d  vr+     k tv   +++se+++ +r + +++++n   v  + +s+ 
  gi|336254552|ref|YP_004597659.1| 284 REFADEHDMPFLGSIPLDPSVREGGDSGKpTVL--DDDSEVGESFRTITENVANNTGIVHRRSVSQS 348
                                       57999*****************98655541554..6778889*************998888888775 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.9e-07   0.00025       2      40 ..      94     132 ..      93     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.9e-07
                             VirC1   2 klitfcslkGGaGkttalmglcsalasdgkrvalfeade 40 
                                       ++i+++s kGG Gk+t  + l + l + g rv+lf+ad 
  gi|336254552|ref|YP_004597659.1|  94 NVIAVASGKGGVGKSTVAVNLAAGLSQLGARVGLFDADV 132
                                       6899*********************************96 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.0   4.5e-07   0.00058       5      34 ..      98     127 ..      93     132 .. 0.86
   2 ?    1.6   0.1       0.1   1.3e+02     117     148 ..     193     226 ..     177     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.5e-07
                                       EEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                       ArsA_ATPase   5 lvgGKGGVGKttvsaatavklsekgkkvll 34 
                                       + +GKGGVGK+tv+  +a+ ls+ g +v l
  gi|336254552|ref|YP_004597659.1|  98 VASGKGGVGKSTVAVNLAAGLSQLGARVGL 127
                                       569*********************999855 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.1
                                       HHHHHCSSSSEEEEESBS.CCHT.CGGGGHHHHH CS
                       ArsA_ATPase 117 lkyvkeeeydvvvlDtaP.TGht.lrllslpevl 148
                                       ++ v+  + d++v+D +P TG+t l +l++  v 
  gi|336254552|ref|YP_004597659.1| 193 TEDVEWGHLDYLVVDLPPgTGDTqLTMLQTMPVT 226
                                       5555667789******998999867888765555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.9e-06     0.013      23      58 ..      86     119 ..      69     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.9e-06
                            AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalava 58 
                                       +++++g+  ++ +a+  G +g+GK+t+a++la+ ++
  gi|336254552|ref|YP_004597659.1|  86 EQVLPGV--KNVIAVASGKGGVGKSTVAVNLAAGLS 119
                                       5566666..7889999****************9887 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.3   4.2e+03       8      14 ..     155     161 ..     154     163 .. 0.84
   2 ?   13.2   0.0   4.9e-05     0.063      12      23 ..     261     272 ..     256     273 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.3
                           DUF1610   8 laprEra 14 
                                       l p+E++
  gi|336254552|ref|YP_004597659.1| 155 LMPPEKY 161
                                       78****9 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.9e-05
                           DUF1610  12 EravvFpCPNCG 23 
                                       E+ ++F+CP CG
  gi|336254552|ref|YP_004597659.1| 261 ENMSSFACPDCG 272
                                       778********9 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3    0.0002      0.26       3      38 ..      95     130 ..      93     135 .. 0.90
   2 ?    0.7   0.0      0.24   3.1e+02     110     142 ..     194     227 ..     181     241 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                          CBP_BcsQ   3 vlalqGvRGGvGttsllaaLawalhelgesvlviDl 38 
                                       v+a+   +GGvG++++++ La  l +lg +v + D+
  gi|336254552|ref|YP_004597659.1|  95 VIAVASGKGGVGKSTVAVNLAAGLSQLGARVGLFDA 130
                                       78888889***********************88886 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.24
                          CBP_BcsQ 110 kelk.eqyrwillDlpagasaltrellaladlvl 142
                                       + ++ ++ +++++Dlp g+ +++ ++l++  ++ 
  gi|336254552|ref|YP_004597659.1| 194 EDVEwGHLDYLVVDLPPGTGDTQLTMLQTMPVTG 227
                                       4444678899*******99999888888765543 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0031         4       3      35 ..      96     128 ..      94     130 .. 0.91
   2 ?    3.6   0.0      0.04        51     132     195 ..     229     305 ..     214     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0031
                            AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyf 35 
                                       i v++   gvGK++v+  L++ l++ g++vg f
  gi|336254552|ref|YP_004597659.1|  96 IAVASGKGGVGKSTVAVNLAAGLSQLGARVGLF 128
                                       67889999**********************976 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.04
                            AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNk..vrnpe...........nvetlekksgipvlGvvPylpdle 195
                                       ++V+++++ +++++   +e++ q++  vlG+  N   ++ p+             +++   + +p lG++P +p+++
  gi|336254552|ref|YP_004597659.1| 229 VIVTTPQDVALDDARKGLEMFAQHDTVVLGIAENMssFACPDcgsqhdifgsgGGREFADEHDMPFLGSIPLDPSVR 305
                                       7888899999999999999999999999999988733222224444555566666666666689*******999876 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 ?   11.3   0.0   0.00017      0.22       1      34 [.     101     134 ..     101     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGq 34 
                                       G+  +GKST+a +L+  + + g ++ + D+Dv  
  gi|336254552|ref|YP_004597659.1| 101 GKGGVGKSTVAVNLAAGLSQLGARVGLFDADVYG 134
                                       66789**************************975 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.4   6.9e+03      34      52 ..      31      49 ..      22      57 .. 0.76
   2 ?   10.5   0.0   0.00032      0.41       6      40 ..      98     132 ..      93     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.4
                                      EEEEHHHHTTTTTTT--SS CS
                        APS_kinase 34 ylLdGdnvRhgLnkdLgfs 52
                                      + +dGd+v  +L  + ++s
  gi|336254552|ref|YP_004597659.1| 31 IAVDGDEVSVDLALGAPYS 49
                                      5689999999998766665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00032
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase   6 wltGlsgsGKstianalekkLvekgisvylLdGdn 40 
                                         +G  g GKst+a++l+  L + g +v l d d+
  gi|336254552|ref|YP_004597659.1|  98 VASGKGGVGKSTVAVNLAAGLSQLGARVGLFDADV 132
                                       568999**********************9999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2745.76
//
Query:       gi|336254553|ref|YP_004597660.1|  [L=111]
Description: hypothetical protein Halxa_3168 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.044   13.9   0.0       0.42   10.7   0.1    2.1  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
      0.045   13.2   0.1       0.12   11.8   0.1    1.7  1  zf-ribbon_3     zinc-ribbon domain
      0.055   13.4   0.3       0.17   11.8   0.1    2.0  2  Nudix_N_2       Nudix N-terminal
      0.071   12.9   0.1       0.22   11.3   0.0    1.8  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
       0.16   12.2   0.2        2.4    8.3   0.1    2.1  2  Acetone_carb_G  Acetone carboxylase gamma subunit


Domain annotation for each model (and alignments):
>> 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 ?   10.7   0.1   0.00012      0.42      13      27 ..       7      21 ..       2      25 .. 0.82
   2 ?    0.5   0.0      0.18   6.5e+02      21      37 ..      77      93 ..      75      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                          zf-Mss51 13 khvdfeCpdCGipty 27
                                        v+++Cp+CG ++ 
  gi|336254553|ref|YP_004597660.1|  7 VTVRYTCPHCGAVVS 21
                                      579********9875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.18
                          zf-Mss51 21 dCGiptycseehwedDy 37
                                       CG p y +  ++e+  
  gi|336254553|ref|YP_004597660.1| 77 GCGRPFYLNFVRYEQGV 93
                                      5******9988888765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.3e-05      0.12       4      12 ..      12      20 ..      10      23 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                       zf-ribbon_3  4 rCPnCGapl 12
                                      +CP+CGa++
  gi|336254553|ref|YP_004597660.1| 12 TCPHCGAVV 20
                                      788888865 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.8e-05      0.17      22      31 ..      10      19 ..       3      27 .. 0.78
   2 ?   -3.0   0.0         2   7.1e+03       6       9 ..      78      81 ..      77      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
                                      EEEETTTTEE CS
                         Nudix_N_2 22 RlvCpaCgti 31
                                      R++Cp+Cg++
  gi|336254553|ref|YP_004597660.1| 10 RYTCPHCGAV 19
                                      8888888876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2
                                      T--B CS
                         Nudix_N_2  6 CGtp 9 
                                      CG p
  gi|336254553|ref|YP_004597660.1| 78 CGRP 81
                                      8876 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 ?   11.3   0.0   6.1e-05      0.22      39      53 ..       5      19 ..       1      20 [. 0.82
   2 ?   -1.4   0.0      0.54   1.9e+03      43      48 ..      57      62 ..      49      67 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.1e-05
                    zinc_ribbon_10 39 eleevkyrCpkCgal 53
                                      +  +v+y Cp+Cga+
  gi|336254553|ref|YP_004597660.1|  5 DTVTVRYTCPHCGAV 19
                                      56789********86 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.54
                    zinc_ribbon_10 43 vkyrCp 48
                                      +++ C 
  gi|336254553|ref|YP_004597660.1| 57 IEFLCG 62
                                      555553 PP

>> Acetone_carb_G  Acetone carboxylase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00067       2.4      75      93 ..       8      26 ..       2      28 .. 0.83
   2 ?    2.0   0.0     0.063   2.3e+02      62      92 ..      43      73 ..      28      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00067
                                      EEEEE-TTT--EEEEEEE- CS
                    Acetone_carb_G 75 irEyycPecgtllevEalt 93
                                       + y cP+cg+++  E ++
  gi|336254553|ref|YP_004597660.1|  8 TVRYTCPHCGAVVSLERPP 26
                                      567**********999876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.063
                                      SSTTTS--TTT-EEEEEE-TTT--EEEEEEE CS
                    Acetone_carb_G 62 yekllapdpewqrirEyycPecgtllevEal 92
                                      y +   pd e     E++c e g + + E  
  gi|336254553|ref|YP_004597660.1| 43 YAAPDDPDRESADGIEFLCGEDGPVTDLEGE 73
                                      555567888888889******9999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 835.01
//
Query:       gi|336254554|ref|YP_004597661.1|  [L=111]
Description: hypothetical protein Halxa_3169 [Halopiger xanaduensis SH-6]
Scores for 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:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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: 883.10
//
Query:       gi|336254555|ref|YP_004597662.1|  [L=283]
Description: initiation factor 2B-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-48  165.9   0.7    1.3e-48  165.7   0.7    1.0  1  IF-2B          Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.047   13.8   2.4      0.068   13.3   1.9    1.5  1  ApoLp-III      Apolipophorin-III precursor (apoLp-III)
       0.46   11.1   2.2        2.8    8.5   0.5    2.3  2  MerR-DNA-bind  MerR, DNA binding


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 !  165.7   0.7   2.1e-52   1.3e-48       2     278 ..      14     279 ..      13     282 .. 0.94

  Alignments for each domain:
  == domain 1  score: 165.7 bits;  conditional E-value: 2.1e-52
                                       S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHH CS
                             IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakks 78 
                                       +++s  +a+ a+++l e +++ +  +v+e  ++l++++ +L+ a+P+  sl+ air++ k+++ + +  +v+e k+ 
  gi|336254555|ref|YP_004597662.1|  14 THSSSVVAVHAAQALEELLDR-EFATVDEYLRDLERNGTVLRRANPSHASLQTAIREIVKDVT-DADPDTVEEGKEL 88 
                                       67899999******9887765.669***********************************877.556678999**** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHH CS
                             IF-2B  79 liekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLv 155
                                         +ki+ +++++e  +++ +++  e+++dg t+lT+ +s+tv+e l++a  ++k++ V+v+E rPr  Gr+ta +L+
  gi|336254555|ref|YP_004597662.1|  89 TAKKIDAVVSRVESGKRLAAENTVEHLEDGATLLTHDYSSTVIEALEQATAAGKTLDVYVTEARPRYIGRKTARTLA 165
                                       ****************************************************************************9 PP

                                       H.TTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGG CS
                             IF-2B 156 q.agipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqlded 231
                                       + +g+++tlitd+a ++ ++e  d v+vG d i+e+  ++n++GT  +A  A++ ++pv vv   +k++ +   + +
  gi|336254555|ref|YP_004597662.1| 166 DlEGVDTTLITDNAHGVYLEE-CDRVVVGMDCIVEDT-LYNRVGTFPIASTANRLDVPVTVVGSASKIVSE---GFV 237
                                       768******************.**************9.******************************999...777 PP

                                       SSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTE CS
                             IF-2B 232 ifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevG 278
                                         +e+r   e+++   e       +v np +D tP el++ +IT++G
  gi|336254555|ref|YP_004597662.1| 238 FENEFRSGSEVMPEPAE-----GFAVENPNYDATPVELLESVITDEG 279
                                       789********998874.....679********************99 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.9   1.1e-05     0.068      33     144 ..       4     116 ..       2     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                         ApoLp-III  33 nlvdqlkqvikslqeelkk.ksdeleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqklae 108
                                       + v+++++++   ++ ++  + ++lee+l+   + + e   +l+  n  v + a+   +++Q++++++vk++  ++ 
  gi|336254555|ref|YP_004597662.1|   4 ETVEEIQEMQTHSSSVVAVhAAQALEELLDREFATVDEYLRDLER-NGTVLRRANPSHASLQTAIREIVKDVTDADP 79 
                                       679999999999998888767889999999999999999999999.999***********************99986 PP

                         ApoLp-III 109 s.lkensqeakeklakaikqayddaveaaqklakqLk 144
                                       + ++e ++ + +k+ + +  +      aa+++ ++L+
  gi|336254555|ref|YP_004597662.1|  80 DtVEEGKELTAKKIDAVVSRVESGKRLAAENTVEHLE 116
                                       5166666667777877777777777777777777776 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.5   0.00047       2.8      16      63 ..       5      54 ..       4      56 .. 0.87
   2 ?    1.7   0.1     0.062   3.7e+02      20      55 ..      67     103 ..      64     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00047
                                      -HHHHHHHHHHHHS..TTTBHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind 16 sLdeIrelLalydd..rappcqdvrallarklaeleeriaeLqalraeLa 63
                                      +++eI+e+ +   +    +++q++++ll+r  a ++e +++L++  + L+
  gi|336254555|ref|YP_004597662.1|  5 TVEEIQEMQTHSSSvvAVHAAQALEELLDREFATVDEYLRDLERNGTVLR 54
                                      6799*****9988888889999999*****************99766665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.062
                                       HHHHH.HHHHSTTTBHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind  20 IrelL.alyddrappcqdvrallarklaeleeriaeL 55 
                                       Ire+  ++ d + ++ ++ ++l+a+k++ +  r +  
  gi|336254555|ref|YP_004597662.1|  67 IREIVkDVTDADPDTVEEGKELTAKKIDAVVSRVESG 103
                                       99999666777889999999********998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); 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:                         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 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2253.98
//
Query:       gi|336254556|ref|YP_004597663.1|  [L=234]
Description: hypothetical protein Halxa_3171 [Halopiger xanaduensis SH-6]
Scores for 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-32  112.6   0.1    3.6e-32  112.3   0.1    1.0  1  ThuA      Trehalose utilisation


Domain annotation for each model (and alignments):
>> ThuA  Trehalose utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   0.1     2e-36   3.6e-32       2     210 .]       4     220 ..       3     220 .. 0.78

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 2e-36
                                       EEEEE-..-.SHHHH-...HHHHHH-..........HHHT-....EE.EEETTS.G..--HHHHHT-SEEEEE-..G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxx....xx.xxxxxxxx..xxxxxxxxxxxxxxxx..x RF
                              ThuA   2 VLvfsgtagerhdsieaaieaieklg..........kengf....ev.datedaav..fteenLaqydvvvfls..t 59 
                                       V+v+++   +rh+++++ ++a+   g          +        ev +at+d+ +  +te++L+ +dv+ +++  +
  gi|336254556|ref|YP_004597663.1|   4 VTVWNE---FRHEQEDEDAAAVYPDGihatladaleG---HdpvdEVqTATLDEPEhgLTEDVLEATDVLFWWGhiA 74 
                                       999999...7999988777888777766666665532...144568877777764478****************554 PP

                                       ..GS-HHHHHH.HHHHHHTT-EEEEEGGG.GS.....HHHH.HH-SEEEEE..T............TSGGGTT--.S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThuA  60 egevldaaqeaalqryveaGgGfvglhsA.adaeerskwfsgLiGarfvgh..ppvqeatvkvedrshpateglpee 133
                                       ++ev d+ +++ +q++v +G+G+++lhs+ ++     k f++L+G++ + +   + ++ ++ v+d+ hp++ g++e 
  gi|336254556|ref|YP_004597663.1|  75 HDEVEDEIVDR-VQERVLEGMGLIVLHSGhFS-----KIFKRLMGTTCDLQwrEDGATERLWVVDPGHPIVDGIDEC 145
                                       67888888888.*****************777.....87777****5554432344567777************988 PP

                                       EEEE.EEEEE..-.S---SE..EEEEE...............ETE...TTEEEEEE----TTS.GGG-HHHHHHHHH CS
                                       xxxx.xxxxx..x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                              ThuA 134 wert.dewYn..f.kpnprgvhvlatvdestydpngadhPiaWcreydgkGrvFytalGhtee.syeepefrkhllg 205
                                       +e++ +e+Y+  f  p+p+  ++++t+ ++   + g+ +    c +  gkGr+Fy+++Gh++  +ye++e+r++l++
  gi|336254556|ref|YP_004597663.1| 146 IELPqTEMYGepFdVPEPD--RLVFTSWFE---G-GEVFRSGCCYQR-GKGRIFYFRPGHETFpIYENEEIRRVLRN 215
                                       **********844444444..69**99444...2.445555555555.99*************************** PP

                                       HHHHC CS
                                       xxxxx RF
                              ThuA 206 glkWa 210
                                       +++Wa
  gi|336254556|ref|YP_004597663.1| 216 AVEWA 220
                                       ****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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: 0.40u 0.19s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1977.07
//
Query:       gi|336254557|ref|YP_004597664.1|  [L=371]
Description: oxidoreductase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-28   99.8   0.9    3.8e-28   98.7   0.3    1.8  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    2.5e-08   33.9   0.0    4.8e-08   33.0   0.0    1.5  1  GFO_IDH_MocA_C   Oxidoreductase family, C-terminal alpha/beta
    0.00044   20.5   0.1    0.00099   19.3   0.1    1.7  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0017   18.9   0.0     0.0036   17.8   0.0    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0027   18.3   0.5     0.0046   17.6   0.5    1.4  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
     0.0028   17.0   0.0     0.0057   16.0   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.021   14.4   0.1      0.041   13.4   0.1    1.5  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.094   13.0   0.1       0.29   11.4   0.1    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.095   13.4   0.2       0.36   11.5   0.1    2.0  2  CoA_binding      CoA binding domain


Domain annotation for each model (and alignments):
>> 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 !   98.7   0.3   1.9e-31   3.8e-28       2     120 .]       7     123 ..       6     123 .. 0.98
   2 ?   -1.2   0.0       1.7   3.4e+03      25      65 ..     315     344 ..     288     364 .. 0.44

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 1.9e-31
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheel 78 
                                        ++++G+G +g  h+r++ e   ++ vva  d  +e+++++a++f+++ y+ +e+ll+++++daviv+tpn+ he +
  gi|336254557|ref|YP_004597664.1|   7 GIGVVGLGGMGHLHARAVEEL--GASVVAGADLVPEQQQRFADEFNAATYETHEDLLENDDVDAVIVTTPNRFHEPI 81 
                                       69*************999999..99**************************************************** PP

                                       HHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  79 akaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       + aaleag hvl+EKPla t+e a++++++a++++ +++vg+
  gi|336254557|ref|YP_004597664.1|  82 TVAALEAGRHVLVEKPLAHTLESAERVARTAAESDAICMVGF 123
                                       ****************************************96 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                                       TEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCT.TESE CS
                      GFO_IDH_MocA  25 leevvalldpdaeraeavaesfgveaysdleelladp.eida 65 
                                       ++ + a+ +  +++  +vae++ v            +  ida
  gi|336254557|ref|YP_004597664.1| 315 EQFLRAIRSDAPPETNTVAEALTV------------QrVIDA 344
                                       223333333333333333333333............323444 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   2.4e-11   4.8e-08       6      86 ..     140     238 ..     137     268 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.4e-11
                                       TTTTSSEEEEEEEEECBEEECHHHHCCGGSH.HCSTSHHHHTCHHHHHHHHHHHTSEEEEEE.....EEE.SEEESC CS
                    GFO_IDH_MocA_C   6 ngklGevvsvdvwtldtragaeakkrwkrrk.kksgGvlgdlgiHdiDllqwLfGqppsvva.....algrmrqnae 76 
                                        g++Ge ++v+   +  r+g + + +w  ++   +gG+l d+g+H +Dl+ + +  p +v++      ++++r+   
  gi|336254557|ref|YP_004597664.1| 140 RGRFGELTHVE-ANYVRRRGVPGPGSWFTDPdLAGGGALLDIGVHALDLALYALDFPEIVEVsgtarTTFGTREEYA 215
                                       699*******9.99999*******************************************99666444444444444 PP

                                       TCCSCSEEE.............E CS
                    GFO_IDH_MocA_C  77 aaededaav.............m 86 
                                       ++e ++++               
  gi|336254557|ref|YP_004597664.1| 216 DPEGFGDNWdaesetyevddsvS 238
                                       44444444144444444444444 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     5e-07   0.00099       2      69 ..       8      77 ..       7     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5e-07
                                      EEEE--SHHHHHHHHHHHHTT-EEE.EE-SSHHHHHHHHHTT.EEE-SSHHHHHHHCSEEEE-SSSHHHH CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkagykva.vynrtkekveelvaeg.akaaesieelvasldvvitmvkagkav 69
                                      ig++GlG MG+  a+ +++ g +v+ + ++ +e+ +++++e  a ++e+ e+l+++ dv  ++v+  +  
  gi|336254557|ref|YP_004597664.1|  8 IGVVGLGGMGHLHARAVEELGASVVaGADLVPEQQQRFADEFnAATYETHEDLLENDDVDAVIVTTPNRF 77
                                      9********************99752689***********955999********9986655555555544 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 !   17.8   0.0   1.8e-06    0.0036       2      78 ..       8      82 ..       7      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH..H-SEEEE-S-HHHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae..eadvvvlavkpedveevl 78
                                      ig++G G mg+  a+ + + g    ++v +++  pe+ + +a+e+++ + + ++e+++e  + d v+++ + + +e + 
  gi|336254557|ref|YP_004597664.1|  8 IGVVGLGGMGHLHARAVEELG---ASVVAGADLVPEQQQRFADEFNAATYE-THEDLLEndDVDAVIVTTPNRFHEPIT 82
                                      9********************...****9*****************76666.9*****955566799999988877765 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 !   17.6   0.5   2.3e-06    0.0046       1     106 [.       7     111 ..       7     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.3e-06
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTH CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrd.sllskdrkallasealtldlddliahldpdvvVEcasseavaelv 76 
                                       G+G++G + + +l + + e el  + va +d   ++++r a+  ++a+++  +dl+++ d+d v+  ++ +  + + 
  gi|336254557|ref|YP_004597664.1|   7 GIGVVGLGGMGHLHARAVE-ELGASVVAGADlVPEQQQRFADEFNAATYETHEDLLENDDVDAVIVTTPNRFHEPIT 82 
                                       99****************9.999999999997666666777777889999999****999*****9*********** PP

                                       HHHHHTTEEEE-S--CGGG-HHHHHHHTSS CS
                     NAD_binding_3  77 lkaLkagkdvvtankgaladealyeeLrea 106
                                       ++aL+ag +v++    a + ++  e+ +  
  gi|336254557|ref|YP_004597664.1|  83 VAALEAGRHVLVEKPLAHT-LESAERVART 111
                                       ***********99888888.4444554444 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 !   16.0   0.0   2.9e-06    0.0057      39      98 ..       8      70 ..       4      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-06
                                      EEEES-SHHHHHHHHHHHHTT-EEEE.ESSSHHHHH..CHHHHTCEECSHHHHHHH-SEEEE- CS
                      2-Hacid_dh_C 39 vGiiGlGrIGqavakrlkafgmkvia.ydrskkkee..eeeelgvelvsleellaesDivslh 98
                                      +G++GlG +G+  a+ ++++g+ v+a  d  +++++  ++e + +++++ e+ll++ D+  + 
  gi|336254557|ref|YP_004597664.1|  8 IGVVGLGGMGHLHARAVEELGASVVAgADLVPEQQQrfADEFNAATYETHEDLLENDDVDAVI 70
                                      8*********************77652677777666766666677999******987763333 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 ?   13.4   0.1   2.1e-05     0.041       7      77 ..       8      82 ..       4     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                                      EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-H.HHHHHHHTT-EEEEHHH.HHH..T-SEEEE-S-HHHHHHHH CS
                              IlvN  7 iaviGyGsqGhaqalnlrdsgldvvvglregsk.svkkAkeegfevltvae.avk..kadvvmiliPDelqkevy 77
                                      i v+G G  Gh +a+ + + g  vv g     + + + A e +  +++++e + +  + d v++ +P+++++ + 
  gi|336254557|ref|YP_004597664.1|  8 IGVVGLGGMGHLHARAVEELGASVVAGADLVPEqQQRFADEFNAATYETHEdLLEndDVDAVIVTTPNRFHEPIT 82
                                      89************************9865443144445555544544444144411456799999999998776 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 ?   11.4   0.1   0.00014      0.29       1      97 [.       8      93 ..       8     120 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS..SEEEE-S CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg..dlvvnls 77
                                      + ++G G++G+  a+ +++ +     ++ ad   e+ ++ a+       e+ a + e +e+    ll+    d+v+  +
  gi|336254557|ref|YP_004597664.1|  8 IGVVGLGGMGHLHARAVEELGAS--VVAGADLVPEQQQRFAD-------EFNAATYETHED----LLENDdvDAVIVTT 73
                                      56888888888888888888876..34444444444444443.......344555555555....5555445******* PP

                                      SGGGHHHHHHHHHHHT-EEE CS
                   Sacchrp_dh_NADP 78 ppissldvlkaCietgvhyv 97
                                      p+ +++++  a++e+g h++
  gi|336254557|ref|YP_004597664.1| 74 PNRFHEPITVAALEAGRHVL 93
                                      ******************98 PP

>> CoA_binding  CoA 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      0.36       6      89 ..       8      92 ..       4      95 .. 0.66
   2 ?   -2.1   0.0       3.3   6.6e+03       6      25 ..     118     137 ..     114     142 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                      EEEETTTSHHHHHHHHHHHHHHECEEEEEEC-..TTTTTCEET..TEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHH CS
                       CoA_binding  6 viviGagglgiaglyhfkeklkygikavfgvn..prkvgtevl..glpvyksvdeleektevdvavitvPaesaqeavd 80
                                      ++v+G gg+   g +h +   + g ++v+g +  p++  +  +  +   y++ ++l e+ +vd+ ++t+P+++ + +++
  gi|336254557|ref|YP_004597664.1|  8 IGVVGLGGM---GHLHARAVEELGASVVAGADlvPEQQQRFADefNAATYETHEDLLENDDVDAVIVTTPNRFHEPITV 83
                                      678888888...4455555555555555554322665444444444445556677777657****************** PP

                                      HHHHTT-SE CS
                       CoA_binding 81 elveagikg 89
                                      +++eag  +
  gi|336254557|ref|YP_004597664.1| 84 AALEAGRHV 92
                                      ***999665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.3
                                       EEEETTTSHHHHHHHHHHHH CS
                       CoA_binding   6 viviGagglgiaglyhfkek 25 
                                       ++ +G++++  a ++ f+e+
  gi|336254557|ref|YP_004597664.1| 118 ICMVGFHNRHAASMVMFEEQ 137
                                       78899999955555666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2818.80
//
Query:       gi|336254558|ref|YP_004597665.1|  [L=243]
Description: proteasome endopeptidase complex subunit beta [Halopiger xanaduensis SH-6]
Scores for complete 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-44  152.2   0.1    1.3e-44  152.0   0.1    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 !  152.0   0.1     7e-49   1.3e-44       2     188 ..      46     224 ..      45     226 .. 0.95

  Alignments for each domain:
  == domain 1  score: 152.0 bits;  conditional E-value: 7e-49
                                       HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                        Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                       k+Gtt++Gi+++dgvv+a+d+ra+ g   +s+++v+K+ +i+++ +++++G+++ a+ +++ +rae++ly+ r g++
  gi|336254558|ref|YP_004597665.1|  46 KTGTTTIGITTTDGVVIATDMRASLGGRFVSNKNVQKVEQIHPTGALTLVGSVGGAQSFISTLRAEVNLYESRRGEN 122
                                       79*************************************************************************** PP

                                       TCHHHHHHHHHHHHHHHHHHCTTTTT.SEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  79 ipverlvarvaaklqaytqrsgrrpf.gvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                       ++++     + a l+++ +r+  +pf  ++ +++gvde+g  ++++idp+G ++e++ ++++Gsg + a+++le+ey
  gi|336254558|ref|YP_004597665.1| 123 MSID-----ALASLAGNFARG--GPFfAIHPILGGVDEDG-SHVFSIDPAGGVMEDD-YTVTGSGMQLAYGLLEQEY 190
                                       ****.....778888888888..455169********998.8**************6.******************* PP

                                       STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEE CS
                        Proteasome 155 kedltleeavelavkalkealerdklsgknieva 188
                                       ++dl+ +ea ++a +a+k+a+erd+ sg+++ ++
  gi|336254558|ref|YP_004597665.1| 191 EDDLSNDEATTIAASAIKSAAERDTGSGNGVFLC 224
                                       *****************************98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1850.12
//
Query:       gi|336254559|ref|YP_004597666.1|  [L=56]
Description: hypothetical protein Halxa_3174 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.046   13.5   0.5      0.081   12.8   0.5    1.4  1  Ost4      Oligosaccaryltransferase


Domain annotation for each model (and alignments):
>> Ost4  Oligosaccaryltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   4.5e-06     0.081       7      23 ..      13      29 ..      12      30 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.5e-06
                                      HHHHHHHHHHHHHHHHH CS
                              Ost4  7 LytLAnfLGsaamlLIV 23
                                      Ly+L+++ G++am L V
  gi|336254559|ref|YP_004597666.1| 13 LYQLCIVVGILAMPLAV 29
                                      9************7755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 428.76
//
Query:       gi|336254560|ref|YP_004597667.1|  [L=117]
Description: hypothetical protein Halxa_3175 [Halopiger xanaduensis SH-6]
Scores for 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-47  158.1   0.1      7e-47  157.9   0.1    1.1  1  DUF555    Protein of unknown function (DUF555)


Domain annotation for each model (and alignments):
>> DUF555  Protein of unknown function (DUF555)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.9   0.1   3.9e-51     7e-47       1     101 []       3     104 ..       3     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 157.9 bits;  conditional E-value: 3.9e-51
                            DUF555   1 dyevvleaawivrdvksvddAigiAiseagkrlnpe.ldfveievgetecPkcgeelesalvvadtalvglllemkv 76 
                                       +y v++eaaw+vrdv+++ddAig+A+seagkrln+e +d+ve+evg t cP+cge+++sa+++adtalvgl+lem+v
  gi|336254560|ref|YP_004597667.1|   3 NYLVAMEAAWLVRDVEEIDDAIGVAVSEAGKRLNSEdMDYVEVEVGATGCPACGEPFDSAFIAADTALVGLALEMEV 79 
                                       79*********************************99**************************************** PP

                            DUF555  77 fnaeseEhaeriakseigkaledvP 101
                                       +na+ eEha+riakse+g al+dvP
  gi|336254560|ref|YP_004597667.1|  80 YNADGEEHASRIAKSEVGGALRDVP 104
                                       ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 962.52
//
Query:       gi|336254561|ref|YP_004597668.1|  [L=179]
Description: XRE family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-22   78.7   0.1    7.2e-11   42.4   0.0    2.3  2  CBS         CBS domain
    6.3e-12   45.7   2.5    1.2e-11   44.8   2.5    1.5  1  HTH_31      Helix-turn-helix domain
    8.3e-12   45.0   0.3      2e-11   43.8   0.3    1.6  1  HTH_3       Helix-turn-helix
    1.6e-07   31.3   0.0      3e-07   30.3   0.0    1.4  1  HTH_19      Helix-turn-helix domain
    7.3e-05   22.6   1.1    0.00036   20.3   0.1    2.5  3  HTH_25      Helix-turn-helix domain
     0.0001   22.2   0.1    0.00031   20.6   0.1    1.8  1  HTH_37      Helix-turn-helix domain
     0.0037   17.2   0.1      0.012   15.5   0.0    2.0  2  Pou         Pou domain - N-terminal to homeobox domain
     0.0046   17.4   0.1       0.01   16.3   0.0    1.7  2  HTH_26      Cro/C1-type HTH DNA-binding domain
  ------ inclusion threshold ------
      0.053   13.1   0.2        1.2    8.8   0.0    2.6  2  HTH_24      Winged helix-turn-helix DNA-binding
      0.099   12.2   0.1        1.3    8.6   0.1    2.7  3  Sigma70_r4  Sigma-70, region 4
       0.27   11.5   3.0       0.28   11.5   0.9    2.1  2  DUF3618     Protein of unknown function (DUF3618)


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 !   42.4   0.0   4.4e-14   7.2e-11       2      53 ..      67     117 ..      66     120 .. 0.94
   2 !   34.0   0.0   1.8e-11   2.9e-08       1      54 [.     127     177 ..     127     179 .] 0.91

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 4.4e-14
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       +d+m++ vv+v+p++ ++ea+++m+e+++s+l V+  +g +vG ++++Dl+ 
  gi|336254561|ref|YP_004597668.1|  67 ADLMNESVVSVSPNDAVKEAARKMEEEAYSQLAVI-QEGIPVGSISESDLVH 117
                                       79**********************8888*******.7*************87 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 1.8e-11
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V++ m++ ++tv+ d+tl e+ +l+  +++ +++++ e g+ vGi+t+ D+++ 
  gi|336254561|ref|YP_004597668.1| 127 VEEHMSESFPTVSKDATLDEISNLL--EHYKAVMIT-EAGETVGIITEADIASR 177
                                       6777*********************..55*9**888.9*************975 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   2.5   7.3e-15   1.2e-11       6      61 ..       9      63 ..       7      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 7.3e-15
                            HTH_31  6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpaer 61
                                      Lr++R++ GL+q e+Ae + vs+  + r+E G  + p++++l+++++al   ++++
  gi|336254561|ref|YP_004597668.1|  9 LRQRRTELGLTQSELAEKADVSQPLIARIEGGDVD-PRLSTLRRIVNALEQAESDV 63
                                      9*********************************7.*************9655544 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.3   1.2e-14     2e-11       1      48 [.       9      56 ..       9      61 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.2e-14
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaL 48
                                      l+++R +lgl+q eLAek++vs+  i+riE G+  P+l+tl ++ +aL
  gi|336254561|ref|YP_004597668.1|  9 LRQRRTELGLTQSELAEKADVSQPLIARIEGGDVDPRLSTLRRIVNAL 56
                                      89********************************************98 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.9e-10     3e-07       4      54 ..       9      58 ..       8      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.9e-10
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgi 54
                                      L++ R elgltq elae++++s+  i+ iE+g   +p  ++l++i++al++
  gi|336254561|ref|YP_004597668.1|  9 LRQRRTELGLTQSELAEKADVSQPLIARIEGGDV-DPRLSTLRRIVNALEQ 58
                                      7899****************************99.**************97 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.2e-07   0.00036       2      36 ..       9      43 ..       8      45 .. 0.96
   2 ?   -1.0   0.0      0.98   1.6e+03      25      37 ..      51      63 ..      45      70 .. 0.81
   3 ?   -2.4   0.0       2.7   4.5e+03      29      38 ..      89      98 ..      88     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.2e-07
                                      HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25  2 LraaRearglsleevaketkIrkdylealEeddfd 36
                                      Lr++R ++gl+  e+a++  +++ ++ ++E +d+d
  gi|336254561|ref|YP_004597668.1|  9 LRQRRTELGLTQSELAEKADVSQPLIARIEGGDVD 43
                                      9******************************9986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.98
                                      HHHHHHHCT--TT CS
                            HTH_25 25 dylealEeddfda 37
                                      +++ alE+ ++d 
  gi|336254561|ref|YP_004597668.1| 51 RIVNALEQAESDV 63
                                      6899999998875 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.7
                                      HHHCT--TTS CS
                            HTH_25 29 alEeddfdal 38
                                      ++Ee+ +++l
  gi|336254561|ref|YP_004597668.1| 89 KMEEEAYSQL 98
                                      7999999998 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   1.9e-07   0.00031      23      73 ..       9      58 ..       6      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.9e-07
                                      HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT--HHHHHHHHHHTTE CS
                            HTH_37 23 iaeliekrelsqseaaqllgiaqPkvsrllrgklsrfsldkLlnlltalGq 73
                                      +++ + +++l+qse+a++  ++qP + r++ g+++  +l++L+++++al q
  gi|336254561|ref|YP_004597668.1|  9 LRQRRTELGLTQSELAEKADVSQPLIARIEGGDVD-PRLSTLRRIVNALEQ 58
                                      678999************************88887.5999******99976 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 !   15.5   0.0   7.6e-06     0.012      12      50 ..       8      40 ..       5      60 .. 0.84
   2 ?   -3.8   0.0       7.9   1.3e+04      29      42 ..      85      98 ..      82     100 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.6e-06
                               Pou 12 efkqkRiklgltQadvglaLgklygkefSqttIcrFEkL 50
                                       ++q+R++lgltQ++++++       ++Sq  I r+E  
  gi|336254561|ref|YP_004597668.1|  8 DLRQRRTELGLTQSELAEK------ADVSQPLIARIEGG 40
                                      79************99987......78999999999965 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.9
                               Pou 29 laLgklygkefSqt 42
                                      +a +k+  +++Sq 
  gi|336254561|ref|YP_004597668.1| 85 EAARKMEEEAYSQL 98
                                      55566667777875 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 !   16.3   0.0   6.2e-06      0.01       2      51 ..       9      57 ..       8      68 .. 0.89
   2 ?   -3.6   0.0       9.8   1.6e+04      41      50 ..     142     151 ..     137     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.2e-06
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLg 51
                                      Lr+   + g+t+seLa+++++s++ ++r+  g +  ++l+tL +i +aL+
  gi|336254561|ref|YP_004597668.1|  9 LRQRRTELGLTQSELAEKADVSQPLIARIEGGDV-DPRLSTLRRIVNALE 57
                                      6777778899***********************6.************998 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.8
                            HTH_26  41 dtLdkiCdaL 50 
                                        tLd i + L
  gi|336254561|ref|YP_004597668.1| 142 ATLDEISNLL 151
                                       5788887776 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   0.00072       1.2      17      36 ..      17      36 ..      17      37 .. 0.89
   2 ?    1.4   0.0      0.15   2.4e+02      32      44 ..      47      59 ..      46      60 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00072
                            HTH_24 17 risqreLAerlglSpstvnr 36
                                      +++q+eLAe+ ++S++ + r
  gi|336254561|ref|YP_004597668.1| 17 GLTQSELAEKADVSQPLIAR 36
                                      69************998876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.15
                            HTH_24 32 stvnrrlkrLeee 44
                                      st++r ++ Le++
  gi|336254561|ref|YP_004597668.1| 47 STLRRIVNALEQA 59
                                      7899999999986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00078       1.3      16      38 ..      12      35 ..       9      39 .. 0.77
   2 ?   -2.7   0.0       2.7   4.3e+03       4      16 ..      55      67 ..      53      73 .. 0.76
   3 ?   -0.5   0.0      0.57   9.2e+02      19      30 ..     140     151 ..     134     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00078
                                      HH.TTT--HHHHHHHHTS-HHHHH CS
                        Sigma70_r4 16 rf.geglTleEIgerlgiSrerVr 38
                                      r+ + glT++E++e+ ++S+  + 
  gi|336254561|ref|YP_004597668.1| 12 RRtELGLTQSELAEKADVSQPLIA 35
                                      445779*************96555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                      HS-HHHHHHHHHH CS
                        Sigma70_r4  4 sLpererevlelr 16
                                       L++ e +v++  
  gi|336254561|ref|YP_004597668.1| 55 ALEQAESDVVRAA 67
                                      6888899998865 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.57
                                       TT--HHHHHHHH CS
                        Sigma70_r4  19 eglTleEIgerl 30 
                                       ++ Tl EI++ l
  gi|336254561|ref|YP_004597668.1| 140 KDATLDEISNLL 151
                                       578*****9876 PP

>> DUF3618  Protein of unknown function (DUF3618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.9   0.00017      0.28       9      32 ..       7      30 ..       7      31 .. 0.93
   2 ?   -3.1   0.0       5.9   9.7e+03      20      26 ..     142     148 ..     141     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                           DUF3618  9 rdIertRaeLaeTvdeLaaradPk 32
                                      +d  + R eL+ T  eLa++ad++
  gi|336254561|ref|YP_004597668.1|  7 ADLRQRRTELGLTQSELAEKADVS 30
                                      68899*****************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.9
                           DUF3618  20 eTvdeLa 26 
                                       +T+de++
  gi|336254561|ref|YP_004597668.1| 142 ATLDEIS 148
                                       7999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1338.41
//
Query:       gi|336254562|ref|YP_004597669.1|  [L=121]
Description: transcriptional regulator TrmB [Halopiger xanaduensis SH-6]
Scores for 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-10   40.4   0.2    3.4e-10   39.8   0.2    1.2  1  HTH_20    Helix-turn-helix domain
      2e-06   27.6   0.0    2.8e-06   27.1   0.0    1.2  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.023   14.5   0.0    1.4  1  HTH_IclR  IclR helix-turn-helix domain
      0.013   15.3   0.0      0.023   14.6   0.0    1.4  1  MarR_2    MarR family
      0.036   14.4   0.0      0.058   13.7   0.0    1.3  1  Rrf2      Transcriptional regulator
      0.044   13.7   0.0      0.065   13.1   0.0    1.3  1  HTH_5     Bacterial regulatory protein, arsR family
      0.082   12.7   0.1       0.12   12.2   0.1    1.3  1  DUF742    Protein of unknown function (DUF742)


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 !   39.8   0.2   1.3e-13   3.4e-10       3      56 ..      17      68 ..      15      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1.3e-13
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      i  AL++   rri + L  +e+lta e+a++ d++ ++ ++ L+ L++a+Lv+ 
  gi|336254562|ref|YP_004597669.1| 17 IVAALDDDACRRIIAVL--EEPLTADEIADEADVPLSSTYKKLDRLADADLVTE 68
                                      678**************..*********************************85 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.1e-09   2.8e-06      19      58 ..      33      72 ..      29      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.1e-09
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       ++p+tadeia e++vp s+ Y+ L +L d++lV+   g 
  gi|336254562|ref|YP_004597669.1| 33 LEEPLTADEIADEADVPLSSTYKKLDRLADADLVTEANGI 72
                                      589*******************************987665 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 ?   14.5   0.0   8.9e-06     0.023      12      49 ..      30      67 ..      28      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.9e-06
                                      -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +a   ++lt  e+A+++++p S+++  L  L    +v+
  gi|336254562|ref|YP_004597669.1| 30 IAVLEEPLTADEIADEADVPLSSTYKKLDRLADADLVT 67
                                      6667899******************9999999888876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   8.9e-06     0.023      16      54 ..      34      69 ..      19      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.9e-06
                                      CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 16 rrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       +p   lt+ e+a++ +++ s++ + l+rL +a Lv++ 
  gi|336254562|ref|YP_004597669.1| 34 EEP---LTADEIADEADVPLSSTYKKLDRLADADLVTEA 69
                                      444...9*****************************875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.3e-05     0.058      23      60 ..      34      71 ..      28      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                                      CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvksvrG 60
                                      eep++++eia++ +++ s   k l +L+ a+lv+   G
  gi|336254562|ref|YP_004597669.1| 34 EEPLTADEIADEADVPLSSTYKKLDRLADADLVTEANG 71
                                      4589*****************************98888 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 ?   13.1   0.0   2.5e-05     0.065      10      46 ..      31      67 ..      27      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                                      HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 10 lLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++ e++l++ e+a+e +++ s +   L +L +a+LV+
  gi|336254562|ref|YP_004597669.1| 31 AVLEEPLTADEIADEADVPLSSTYKKLDRLADADLVT 67
                                      57899*******************************7 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.7e-05      0.12      43      91 ..      24      72 ..       7      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.7e-05
                            DUF742 43 pehrailrLcreplsVaelaAelklPvgvvrvLlsdLldaglltvrapv 91
                                      + +r+i++  +epl+  e+a e ++P++ +   l  L+da+l+t  + +
  gi|336254562|ref|YP_004597669.1| 24 DACRRIIAVLEEPLTADEIADEADVPLSSTYKKLDRLADADLVTEANGI 72
                                      5789*************************************99876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); 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:                         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: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 980.40
//
Query:       gi|336254563|ref|YP_004597670.1|  [L=258]
Description: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP [Halopiger xanaduensis SH-6]
Scores for 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-52  176.5   0.0    6.8e-52  176.2   0.0    1.1  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
  ------ inclusion threshold ------
       0.06   13.4   0.0      0.077   13.1   0.0    1.4  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 !  176.2   0.0   7.6e-56   6.8e-52       3     172 .]      64     258 .]      62     258 .] 0.91

  Alignments for each domain:
  == domain 1  score: 176.2 bits;  conditional E-value: 7.6e-56
                    CobA_CobO_BtuR   3 glihvytGdGKGKttAAlGlalRalgaglkvlvvqFlKg.eke....sgElaalkkl.eielerlgkegfv.kmeee 72 
                                       gl++v++GdGKGKttA lG+ +Ra+g+g++v+++qF+Kg +++     gE++a+++l +i++e+lg++g++ + + +
  gi|336254563|ref|YP_004597670.1|  64 GLVQVWWGDGKGKTTATLGMGVRAAGHGYRVHMLQFMKGgASSvdavRGEYNAIAALpGISYENLGHYGWHgMADGS 140
                                       99*************************************544367779*********66************878889 PP

                    CobA_CobO_BtuR  73 ekeedaaaakealekakealas.eeyd................lvvlDEinyalklglldeeevlellkkkpeklel 132
                                       ++e+++a+a+++le+a+e+la+ +e+d                +++lDE++ya++ gl++e++vlel+++kp++lel
  gi|336254563|ref|YP_004597670.1| 141 DEEDHEAQAQAGLERARELLAAaGEADletpfpldgpadegvhMLILDEVLYAADRGLITEDDVLELIEEKPADLEL 217
                                       99999**************988454555666666666666666********************************** PP

                    CobA_CobO_BtuR 133 vlTG.rnapeelleaADlvtemkkvkHpydkgikarkGiey 172
                                       vl+G +++p+ l e+ADl+t+++k+kHp+d+g++ar+G e+
  gi|336254563|ref|YP_004597670.1| 218 VLSGsHSEPSYLEERADLITNVRKEKHPIDAGQRARRGTEF 258
                                       ****8899999*****************************8 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 ?   13.1   0.0   8.6e-06     0.077       9      34 ..      73      98 ..      71     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.6e-06
                                      TSSHHHHHHHHHHHHHHTT--EEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  9 GvGKTtlaanLaralarrglrVllvD 34
                                      G GKTt ++++++  a +g+rV ++ 
  gi|336254563|ref|YP_004597670.1| 73 GKGKTTATLGMGVRAAGHGYRVHMLQ 98
                                      88********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.42u 0.18s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 2245.60
//
Query:       gi|336254564|ref|YP_004597671.1|  [L=255]
Description: phosphonate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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   83.1   0.0    4.6e-23   82.3   0.0    1.4  1  ABC_tran     ABC transporter
    7.6e-11   42.4   0.1    4.1e-05   23.5   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00025   21.6   0.1    0.00039   21.0   0.1    1.2  1  AAA_23       AAA domain
     0.0016   18.2   0.0          1    9.0   0.0    2.1  2  AAA_15       AAA ATPase domain
     0.0088   15.8   0.0       0.02   14.6   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.023   14.4   0.0       0.05   13.3   0.0    1.5  1  AAA_30       AAA domain
      0.026   14.4   0.0      0.044   13.6   0.0    1.3  1  MukB         MukB N-terminal
      0.031   13.3   0.1      0.046   12.7   0.1    1.2  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.034   14.0   0.0       0.38   10.6   0.0    2.1  2  RsgA_GTPase  RsgA GTPase
      0.059   12.9   0.0      0.098   12.2   0.0    1.3  1  AAA_27       AAA domain
      0.066   11.9   0.1        6.4    5.3   0.0    2.0  2  AAA_13       AAA domain
      0.073   13.4   0.0       0.13   12.6   0.0    1.8  1  AAA_16       AAA ATPase domain
      0.074   13.2   0.0       0.24   11.6   0.0    1.8  1  AAA_33       AAA domain
      0.091   12.2   0.0        8.2    5.8   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
       0.11   12.1   0.0       0.21   11.2   0.0    1.4  1  SRP54        SRP54-type protein, GTPase domain
       0.15   12.3   0.1       0.48   10.6   0.0    1.8  2  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 !   82.3   0.0   4.1e-26   4.6e-23       2     136 ..      20     162 ..      19     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 4.1e-26
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + +++++ +ge+ +++G+nGaGK+t l++l+g+ +p++G++++ + d       ++r+++g++p+  +  + lt re
  gi|336254564|ref|YP_004597671.1|  20 DGMTFDVDRGEVFGFLGPNGAGKTTTLRALTGQIRPDAGDVRVLDCDPVAA-PIETRRRVGIVPERGSPPSFLTPRE 95 
                                       789**************************************9986666663.5568999*******88888888888 PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                     + +e+ e + ++lg   + dt      + LS Gq+q+v++a+a+l +p+ +l+DEp 
  gi|336254564|ref|YP_004597671.1|  96 YlefvgdvrdlepeYVRERTELWSDRLGFCSKLDTLH----TDLSRGQQQKVMIAQAFLHEPDAVLIDEPL 162
                                       7888999888888777888888999999888888887....*****************************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 !   17.3   0.0     3e-06    0.0033       2      23 ..      32      53 ..      31      89 .. 0.79
   2 !   23.5   0.0   3.7e-08   4.1e-05     234     299 ..     132     194 ..      73     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                       ++ GpNg+GK++ L+al +  
  gi|336254564|ref|YP_004597671.1| 32 FGFLGPNGAGKTTTLRALTGQI 53
                                      5789**************7653 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 3.7e-08
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                        ++lS G+++   ++ a+l  +   + +liDEp ++L+P +++ + ++l + ++ +  v+++TH+ 
  gi|336254564|ref|YP_004597671.1| 132 HTDLSRGQQQKVMIAQAFLHEP---DAVLIDEPLANLDPLVQEQVKRFLVAYAADDNAVFVSTHNI 194
                                       5689999999966666666666...88**********************6666669********95 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   3.5e-07   0.00039      14      40 ..      23      50 ..       6      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.5e-07
                            AAA_23 14 eidFsk.gltlItGpNGaGKTTildAik 40
                                      ++d ++  ++ + GpNGaGKTT l+A++
  gi|336254564|ref|YP_004597671.1| 23 TFDVDRgEVFGFLGPNGAGKTTTLRALT 50
                                      566655369*****************97 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0028       3.2      28      43 ..      34      49 ..      23      51 .. 0.86
   2 !    9.0   0.0   0.00089         1     324     365 ..     153     193 ..     100     197 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0028
                            AAA_15 28 liGkNnsGKSsileal 43
                                      + G+N++GK++ l+al
  gi|336254564|ref|YP_004597671.1| 34 FLGPNGAGKTTTLRAL 49
                                      88************99 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00089
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++ +li+EP a+L p  q+++ + l   a d++  v+++TH+
  gi|336254564|ref|YP_004597671.1| 153 PDAVLIDEPLANLDPLVQEQVKRFLVAYAADDN-AVFVSTHN 193
                                       56799*************************998.9******8 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 !   14.6   0.0   1.8e-05      0.02      12      43 ..      19      50 ..      16      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiq 43
                                       dg t+++d+ +++ + Gp+G+GK+T l A++
  gi|336254564|ref|YP_004597671.1| 19 VDGMTFDVDRGEVFGFLGPNGAGKTTTLRALT 50
                                      5788999997779*************998876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-05      0.05      20      52 ..      31      63 ..      17      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvigl 52
                                      v    Gp G+GKtt+l+al+  ++ + g+v +l
  gi|336254564|ref|YP_004597671.1| 31 VFGFLGPNGAGKTTTLRALTGQIRPDAGDVRVL 63
                                      66678**************99998887777665 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.9e-05     0.044      20      56 ..      22      59 ..      16      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
                                      EEE-HHH.HHHHHHS--SHHHHHHHHHHHHHHS--TTT CS
                              MukB 20 rtfdlde.lvttlsGgnGaGksttmaafvtaliPdlsl 56
                                       tfd+d+  v  + G nGaGk+tt+ a+   + Pd   
  gi|336254564|ref|YP_004597671.1| 22 MTFDVDRgEVFGFLGPNGAGKTTTLRALTGQIRPDAGD 59
                                      589999856999*****************999999765 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 ?   12.7   0.1   4.1e-05     0.046      26      68 ..      26      68 ..      15      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                                      -S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--- CS
                              MeaB 26 aGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPs 68
                                        r +v G+ G  GaGk t++ al+ ++r     v vl  DP 
  gi|336254564|ref|YP_004597671.1| 26 VDRGEVFGFLGPNGAGKTTTLRALTGQIRPDAGDVRVLDCDPV 68
                                      568899*************************99********96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00034      0.38      90     131 ..      19      61 ..       3      64 .. 0.77
   2 ?    1.0   0.0      0.32   3.6e+02      30      60 ..     168     198 ..     147     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       ++ ++  ++  ++  ++G+ G+GK+t + al+++ +   g+v+
  gi|336254564|ref|YP_004597671.1|  19 VDGMTFDVDRgEVFGFLGPNGAGKTTTLRALTGQIRPDAGDVR 61 
                                       555555555558899*****************99887777765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.32
                                       --HHHHHHHHHHHHHTT-EEEEEEE-GGG-- CS
                       RsgA_GTPase  30 lslnlldrfLvlaeekgiepvivlnKiDlle 60 
                                       l +++++rfLv++ + +  + +    iD++ 
  gi|336254564|ref|YP_004597671.1| 168 LVQEQVKRFLVAYAADDNAVFVSTHNIDVAA 198
                                       5567899999999998888888777777665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.8e-05     0.098      19      47 ..      22      50 ..       8      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.8e-05
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAis 47
                                      ++f+ ++ ++   +GpN AGK+t+lrA++
  gi|336254564|ref|YP_004597671.1| 22 MTFDVDRGEVFGFLGPNGAGKTTTLRALT 50
                                      66666666666779*************97 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0096        11      23      38 ..      36      51 ..      30      60 .. 0.84
   2 ?    5.3   0.0    0.0057       6.4     526     576 ..     152     199 ..     142     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0096
                            AAA_13 23 GwNGaGKTtLSrllrs 38
                                      G NGaGKTt  r+l  
  gi|336254564|ref|YP_004597671.1| 36 GPNGAGKTTTLRALTG 51
                                      99*******9888865 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0057
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffke 576
                                       +   v iD P   LD  ++  v  ++ +++   ++ + +f++THn++   e
  gi|336254564|ref|YP_004597671.1| 152 EPDAVLIDEPLANLDPLVQEQVKRFLVAYA---ADDNAVFVSTHNIDVAAE 199
                                       566799********************9999...88889*******987655 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   0.0   0.00012      0.13      27      58 ..      32      65 ..      17     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                            AAA_16 27 vllsGesGvGKsslvrellralekd..ggiflrg 58
                                        + G+ G GK++ +r+l  +++ d  ++ +l +
  gi|336254564|ref|YP_004597671.1| 32 FGFLGPNGAGKTTTLRALTGQIRPDagDVRVLDC 65
                                      5578******************999532333333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00021      0.24       4      39 ..      34      79 ..      31     222 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                            AAA_33  4 lvGlpGsGKstlaerllkklg.....avllssdt.....lrrrlfg 39
                                      + G++G+GK+t ++ l  +       + +l+ d      + rr +g
  gi|336254564|ref|YP_004597671.1| 34 FLGPNGAGKTTTLRALTGQIRpdagdVRVLDCDPvaapiETRRRVG 79
                                      78*************9554433444322233332333333333333 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 ?    5.8   0.0    0.0073       8.2      29      44 ..      34      49 ..       4      54 .. 0.80
   2 ?    4.6   0.0     0.017        19     136     212 ..     134     207 ..      77     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0073
                                      EEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 29 ivGpNGSGKsnlldAi 44
                                       +GpNG+GK+  l A+
  gi|336254564|ref|YP_004597671.1| 34 FLGPNGAGKTTTLRAL 49
                                      58********999887 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.017
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH.HHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk.eksknaQfivislreemlekadklvgv 211
                                        LS+G+++ v++a  f ++  +p   +l+De  a+LD    ++v ++l   + ++  ++v +++ ++ ++  + vg+
  gi|336254564|ref|YP_004597671.1| 134 DLSRGQQQKVMIAQAF-LH--EPD-AVLIDEPLANLDPLVQEQVKRFLVaYAADDNAVFVSTHNIDVAAEICTRVGI 206
                                       6999999888888765.23..333.3689*********999999998872455668999999999888887777776 PP

                                       E CS
                                       x RF
                             SMC_N 212 t 212
                                        
  gi|336254564|ref|YP_004597671.1| 207 V 207
                                       5 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00019      0.21       5      33 ..      33      61 ..      30      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                             SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvl 33
                                       ++G++GaGKTttl  L  +++ ++ +v 
  gi|336254564|ref|YP_004597671.1| 33 GFLGPNGAGKTTTLRALTGQIRPDAGDVR 61
                                      589***********999887776655555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00043      0.48       4      21 ..      34      51 ..      32      64 .. 0.85
   2 ?   -1.6   0.0       2.4   2.7e+03      51      55 ..     160     164 ..     104     198 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00043
                            AAA_28  4 itGgestGKTtlleaLaa 21
                                      ++G+ ++GKTt+l+aL+ 
  gi|336254564|ref|YP_004597671.1| 34 FLGPNGAGKTTTLRALTG 51
                                      78**************84 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.4
                            AAA_28  51 dllaf 55 
                                       ++la 
  gi|336254564|ref|YP_004597671.1| 160 EPLAN 164
                                       33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 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:                        73  (0.00407162); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2092.74
//
Query:       gi|336254565|ref|YP_004597672.1|  [L=496]
Description: hypothetical protein Halxa_3180 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.76   10.3   6.1       0.23   11.9   1.9    2.3  2  Sigma_M_inh  Sigma-M inhibitor


Domain annotation for each model (and alignments):
>> Sigma_M_inh  Sigma-M inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.9   1.3e-05      0.23      11      76 ..      91     165 ..      87     184 .. 0.60
   2 ?   -1.8   0.1      0.25   4.5e+03      44      60 ..     303     319 ..     278     341 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                       Sigma_M_inh  11 nvfgwvsv...gtavlsll...llnlailsdviaysyk.mlpfamaavplgvvelf..ikkgrtglgllgvvlnl 76 
                                       nvfg +s+    +a l l    ll l +l d+ +y    +lp+a+aavpl v+     +  g t       vl l
  gi|336254565|ref|YP_004597672.1|  91 NVFGRLSLvlsTAATLPLSrrrLLGLFLLKDTAFYGLVfVLPMAIAAVPLEVLTSAseLTTGATLSSAAVAVLAL 165
                                       78888775221234444422338999*********975379**********986531133444433333334444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.25
                       Sigma_M_inh  44 lpfamaavplgvvelfi 60 
                                       + fa+ a  +gvve + 
  gi|336254565|ref|YP_004597672.1| 303 ILFALVAALVGVVESIT 319
                                       45888888888888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3705.01
//
Query:       gi|336254566|ref|YP_004597673.1|  [L=367]
Description: hypothetical protein Halxa_3181 [Halopiger xanaduensis SH-6]
Scores for 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-06   26.7   0.0    1.8e-05   25.0   0.0    1.8  2  Iron_transport  Fe2+ transport protein


Domain annotation for each model (and alignments):
>> Iron_transport  Fe2+ transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   9.9e-10   1.8e-05      77     116 ..     122     162 ..     108     186 .. 0.82
   2 ?   -2.2   0.0      0.23   4.2e+03      94     131 ..     312     347 ..     293     351 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 9.9e-10
                                       T----EEEE-EEEEE.TTEEEEEEEE--T-SEEEEEEEEEE CS
                    Iron_transport  77 ksgeaksgtlmpmva.sDgphYganvklkgvgkYkltleie 116
                                       + + + + tl pm +   g+hYg+nv+l+g g+Y++t+++ 
  gi|336254566|ref|YP_004597673.1| 122 DGERVDRRTLWPMLSqRMGFHYGDNVALAGGGTYEVTVRVG 162
                                       44778889999*875167*******************9985 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.23
                                       EEEEEEEE--T-SEE.EEEEEEEE---TTT-EEE-STTT CS
                    Iron_transport  94 gphYganvklkgvgk.YkltleieppekkefgrHvdket 131
                                       g hYg  ++  ++++  ++ +++epp+    +rH   et
  gi|336254566|ref|YP_004597673.1| 312 GHHYGLALEGLEADRvEDISFTLEPPQV---ARHEGYET 347
                                       7888865543223331356788888876...56666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2723.58
//
Query:       gi|336254567|ref|YP_004597674.1|  [L=164]
Description: hypothetical protein Halxa_3182 [Halopiger xanaduensis SH-6]
Scores for 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-41  139.4  11.4    9.4e-41  139.2  11.4    1.0  1  DUF2243       Predicted membrane protein (DUF2243)
  ------ inclusion threshold ------
       0.39   11.0   4.6       0.23   11.7   2.9    1.5  1  Peptidase_A8  Signal peptidase (SPase) II


Domain annotation for each model (and alignments):
>> DUF2243  Predicted membrane protein (DUF2243)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2  11.4   1.1e-44   9.4e-41       1     139 [.      14     150 ..      14     151 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 1.1e-44
                           DUF2243   1 agillGvglggfvDgivlHqlLqwHhllssvlpaktvstlelnllsDGlfhaatlvlvvaglvllararrreevals 77 
                                       ag ++G+g+g+++D +++Hq+Lq+Hhlls ++++ t++++++n+++DGlf a +l ++++g+++l+r+++ ++++ls
  gi|336254567|ref|YP_004597674.1|  14 AGGTIGFGFGAVLDVVIFHQILQTHHLLSGFYDPYTYDGVRTNVMFDGLFTAGMLAITAIGFAMLWRVVNGTDARLS 90 
                                       6899************************************************************************* PP

                           DUF2243  78 srallgavllGaGlFnlvdgvvdHkllgiHqvregeelllydlvflalgvlllvvGllllrr 139
                                       +ral+g+++lGaG+Fn++dg+vdH +l++H+v +g+   +++ ++++++vl+l +G+++lr+
  gi|336254567|ref|YP_004597674.1|  91 TRALVGSTVLGAGAFNVFDGIVDHYVLDLHNVVHGT--EAWNPHWVVVSVLMLGLGAIILRS 150
                                       ********************************9766..89******************9986 PP

>> Peptidase_A8  Signal peptidase (SPase) II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.9   2.6e-05      0.23      58     118 ..      67     129 ..      31     151 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.6e-05
                      Peptidase_A8  58 llslvvill.livlllkk..kkkskllrialalilgGalGNliDrllygkVvDfldfslelief 118
                                       +l++ +i++ +++ ++ +  +++ ++ ++  + +lg+++ N++D ++ ++V D  ++ + +  +
  gi|336254567|ref|YP_004597674.1|  67 MLAITAIGFaMLWRVV-NgtDARLSTRALVGSTVLGAGAFNVFDGIVDHYVLDLHNVVHGTEAW 129
                                       2233344441444333.34544455566677889999999*************99975444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1261.78
//
Query:       gi|336254568|ref|YP_004597675.1|  [L=547]
Description: Cobyric acid synthase [Halopiger xanaduensis SH-6]
Scores for complete 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  132.8   0.0    2.1e-38  131.9   0.0    1.5  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
    3.1e-22   79.0   0.0    5.1e-22   78.3   0.0    1.3  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
    1.4e-18   67.4   0.0    9.5e-18   64.7   0.0    2.2  1  AAA_26    AAA domain


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 !  131.9   0.0   3.5e-42   2.1e-38       1     195 [.     286     488 ..     286     489 .. 0.88

  Alignments for each domain:
  == domain 1  score: 131.9 bits;  conditional E-value: 3.5e-42
                          GATase_3   1 kiavirlpaisnytdldpLeaepevrvrfvplkdeslg..............edadlvilpGgkdtiqdlallresg 63 
                                       +iav+r p+isn tdl++L+aep v v fvp+  ++ +               dad+v+lpG+k+t++dl +lr+s 
  gi|336254568|ref|YP_004597675.1| 286 RIAVPRFPRISNATDLEALAAEPGVSVVFVPVAADDGTgddavqtqakplerVDADAVVLPGTKNTVDDLLALRASP 362
                                       69*****************************9888887899*********9967*********************** PP

                          GATase_3  64 ldeaikeaaeaggpvlgiCGGlqmLGeeiedp..egvegeageveglglLdietefekekltgqvegevel...... 132
                                       + +ai+++   +gpv+g CGG+qmLGe+i+++  eg++g    veglglL++et+fe +k++++ ++ v+       
  gi|336254568|ref|YP_004597675.1| 363 VGDAIRAF---DGPVVGLCGGYQMLGERITNAglEGTDGVDDVVEGLGLLPVETRFEADKRLERRTVPVDGaatpll 436
                                       ******96...89****************87511445556679****************999998888777999999 PP

                          GATase_3 133 .aaeg.eevkGyEiHsGrtilkekakpllkvkvggnngekdGavkksedgnvlGtYlHglfdnrn 195
                                        a +g ++ +GyEiH Grt   e++++ l+         +  a    ++g+vlGtYlHglfdn +
  gi|336254568|ref|YP_004597675.1| 437 aAIDGdATASGYEIHAGRTRALEDVTQPLED--------AS-A----AHGTVLGTYLHGLFDNAA 488
                                       84445599************99988887776........22.2....34699**********975 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 !   78.3   0.0   8.6e-26   5.1e-22       1     116 [.       5     253 ..       5     260 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 8.6e-26
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep................... 54 
                                       +++a+t + vGK+t+aa+L+r+la+rg  V++++a++++nn+++      g+                         
  gi|336254568|ref|YP_004597675.1|   5 LLVAGTASHVGKSTVAAGLCRLLADRGVAVAPFKAQNMSNNARVvvrpERGND----Gettdghaardgttdgdrwg 77 
                                       589***************************************97654433333....14566999************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|336254568|ref|YP_004597675.1|  78 eigvsqfvqaraarttpttdhnpvllkprgdaesqlvlqgeahdhvpvgtyydeywdrarecavgsyrrlaadndvi 154
                                       ***************************************************************************** PP

                                       ...................................CCHCCCHHHHHHCHCHHHH.......EEEEEEEEESS...-T CS
                                       ...................................xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...................................dlkrllellealgkkkall.....lkiagvvlnrvdgeneet 91 
                                                                          d++r ++ +++l+++ +ll      +++g v+++++g+    
  gi|336254568|ref|YP_004597675.1| 155 vaegagsiaeinlhdrdlanvetarfadaeilllvDIER-GGAFASLYGTIELLpddlrERVVGAVVTKFRGD--RS 228
                                       ***************************************.99999*******99*******************..9* PP

                                       TCHHHHHHHHHHCTS-EEEEEE--C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  92 llkealeelkqrygvpvlgviprde 116
                                       ll+ ++e ++ r+gvp+lgv+p+d+
  gi|336254568|ref|YP_004597675.1| 229 LLEPGIEAIESRTGVPILGVLPYDD 253
                                       ***********************97 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   1.6e-21   9.5e-18       1     191 [.       3     252 ..       3     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.6e-21
                            AAA_26   1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie..........................ede..... 46 
                                       rt++v+gt  +vGK++v++gL+r l ++gv v+ fK  +  ++                          + +     
  gi|336254568|ref|YP_004597675.1|   3 RTLLVAGTASHVGKSTVAAGLCRLLADRGVAVAPFKAQNMSNNarvvvrpergndgettdghaardgttD-Gdrwge 78 
                                       79**********************************97777778899*9999998888777777666650.155556 PP

                            AAA_26  47 ..dselikellgldqtyelpeplalsaplspelaarqegedid...lekiv...............kelekdadivv 103
                                          s++++  +  ++++ + +p++l+ +   e +  ++ge+ d   + ++                ++l++d+d++v
  gi|336254568|ref|YP_004597675.1|  79 igVSQFVQARAARTTPTTDHNPVLLKPRGDAESQLVLQGEAHDhvpVGTYYdeywdrarecavgsyRRLAADNDVIV 155
                                       66*****998888889999******988655555555555555444333336666**********999********* PP

                            AAA_26 104 VEGagglgvpitee..llnadiaknlgapvilVarggl.gtinqllltiealrqk.nvrvlGvilNkvrnpe..... 171
                                        EGag++ +  +++  l n++ a+  +a+++l++ +++ g+++ l+ tie+l +    rv+G ++ k+r ++     
  gi|336254568|ref|YP_004597675.1| 156 AEGAGSIAEINLHDrdLANVETARFADAEILLLVDIERgGAFASLYGTIELLPDDlRERVVGAVVTKFRGDRsllep 232
                                       ********8866665689******************99569***********7642668************777778 PP

                            AAA_26 172 nvetlekksgipvlGvvPyl 191
                                        +e++e+ +g+p+lGv+Py+
  gi|336254568|ref|YP_004597675.1| 233 GIEAIESRTGVPILGVLPYD 252
                                       ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 4121.56
//
Query:       gi|336254569|ref|YP_004597676.1|  [L=129]
Description: CopG/Arc/MetJ family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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   12.9   0.0       0.18   11.8   0.0    1.6  1  RHH_1     Ribbon-helix-helix protein, copG 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 ?   11.8   0.0     1e-05      0.18       3      28 ..       5      31 ..       5      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1e-05
                                      EEEEEHHHHHHHHHHHHHHT.SSHHHH CS
                             RHH_1  3 sirldeellerLdelarrrg.rSrSel 28
                                      ++r ++e++e++d+l++++   S+Se+
  gi|336254569|ref|YP_004597676.1|  5 TVRYPDEVVEEIDALVEDGMfESKSEF 31
                                      67789**************99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 965.15
//
Query:       gi|336254570|ref|YP_004597677.1|  [L=83]
Description: hypothetical protein Halxa_3185 [Halopiger xanaduensis SH-6]
Scores for 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  107.4   0.1    2.6e-31  107.2   0.1    1.0  1  MTH865    MTH865-like family


Domain annotation for each model (and alignments):
>> MTH865  MTH865-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.2   0.1   1.5e-35   2.6e-31       1      69 [.       6      74 ..       6      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 1.5e-35
                                      HHHHHHHHHHTTSSSTTBHHHHHHHH-TTSS-----BTTB---TTTTGGGS-GGGSB-SHHHHHHHHHH CS
                            MTH865  1 elkeqivealegadFPikspeeLlaalPkGaettceagdvevtagelgkklkdsdFPyksaedladdiv 69
                                      el++q+++a+egad+P++sp++L++alP+G++t++e+gd+++ta+el++k++  dFPy+++e+l+dd++
  gi|336254570|ref|YP_004597677.1|  6 ELRQQMIDAFEGADYPVSSPMDLVPALPNGPGTKFESGDFSMTAMELNTKVSGGDFPYDDPESLVDDLL 74
                                      79*****************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 664.76
//
Query:       gi|336254571|ref|YP_004597678.1|  [L=690]
Description: PAS/PAC sensor protein [Halopiger xanaduensis SH-6]
Scores for 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-44  150.1   8.3    4.4e-44  150.1   8.3    3.8  4  BAT           GAF and HTH_10 associated domain
    1.1e-18   66.7   0.0    5.4e-18   64.5   0.0    2.2  2  HTH_10        HTH DNA binding domain
    4.4e-14   52.7   0.7    4.4e-14   52.7   0.7    3.7  4  PAS_4         PAS fold
    4.1e-13   49.8   1.0    4.1e-13   49.8   1.0    3.0  4  GAF_2         GAF domain
    9.2e-05   22.4   0.8     0.0031   17.5   0.1    2.8  2  H_kinase_N    Signal transduction histidine kinase
    0.00017   22.3   0.0    0.00058   20.5   0.0    2.1  1  GAF           GAF domain
    0.00021   21.7   0.1     0.0005   20.4   0.1    1.6  1  GAF_3         GAF domain
    0.00084   19.6   0.0     0.0027   17.9   0.0    2.0  1  PAS_9         PAS domain
     0.0015   18.0   0.0     0.0082   15.6   0.0    2.3  2  Sigma70_r4    Sigma-70, region 4
     0.0017   18.0   0.0      0.006   16.2   0.0    2.0  2  Sigma70_r4_2  Sigma-70, region 4
  ------ inclusion threshold ------
      0.066   12.7   0.0       0.19   11.2   0.0    1.8  1  Autoind_bind  Autoinducer binding domain
       0.15   11.9   0.3       0.95    9.4   0.0    2.4  3  HTH_5         Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.9       2.7     4e+03      50      76 ..      38      64 ..      29     100 .. 0.72
   2 ?   -0.2   0.3      0.55   8.3e+02     110     134 ..      82     106 ..      79     112 .. 0.87
   3 ?   -1.8   0.8       1.6   2.5e+03      51      77 ..     353     379 ..     336     422 .. 0.58
   4 !  150.1   8.3   2.9e-47   4.4e-44       1     155 [.     465     618 ..     465     619 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.7
                               BAT 50 adpeevrdaaedldavedvrvvseedd 76
                                       ++++++da+e++d+ e+ +v + +d+
  gi|336254571|ref|YP_004597678.1| 38 IAAARLADALETVDGAESREVPGNGDS 64
                                      566778888888888877666555554 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.55
                               BAT 110 arlvvevPpgadvRsvvealeeryp 134
                                       a +v+e  ++ ++R+++e+++++ +
  gi|336254571|ref|YP_004597678.1|  82 AAVVLETDDRSELRTLLERVRDAAD 106
                                       568999999**********999865 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.6
                               BAT  51 dpeevrdaaedldavedvrvvseeddg 77 
                                       d+ +  +   d+da e ++v ++ ++g
  gi|336254571|ref|YP_004597678.1| 353 DATAYMAHSRDVDAAEHCSVTRAAETG 379
                                       445555555666666666666666554 PP

  == domain 4  score: 150.1 bits;  conditional E-value: 2.9e-47
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       D+vveLe++i+  + +  +l+++ dc+++le++ ++s g++ +f+tvdg d e+v + a+++d++e++r+++++ ++
  gi|336254571|ref|YP_004597678.1| 465 DTVVELEFRIDGGETFSFDLSEAYDCTCSLEWVGTSSRGKTFQFVTVDGLDGETVLEEAQAHDSIEECRLIHDGTSQ 541
                                       9**************************************************************************** PP

                               BAT  78 tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrref 154
                                       +++e+++  +s ++tla+hG+t+r+++++dg +++ vev+++a+vR++++al+  y+++eLvarre++rpvrt++e 
  gi|336254571|ref|YP_004597678.1| 542 CTIEMRL-AESGVRTLANHGATIRDVAVNDGVGTCLVEVSQDANVREIADALSVIYENTELVARREVDRPVRTAAER 617
                                       *******.78899*************************************************************997 PP

                               BAT 155 r 155
                                       r
  gi|336254571|ref|YP_004597678.1| 618 R 618
                                       6 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.7   2.5e+03      21      35 ..     580     594 ..     578     602 .. 0.79
   2 !   64.5   0.0   3.6e-21   5.4e-18       1      52 [.     625     676 ..     625     677 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.7
                            HTH_10  21 PRrvtlkeLAkelGI 35 
                                       + +++++e+A++l +
  gi|336254571|ref|YP_004597678.1| 580 SQDANVREIADALSV 594
                                       67899******9977 PP

  == domain 2  score: 64.5 bits;  conditional E-value: 3.6e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT++ql++l++Ay +G+Fd+PR+ t +e+A++++++++t+++hLrk +++++
  gi|336254571|ref|YP_004597678.1| 625 LTERQLTTLRVAYYAGFFDWPRESTGEEIAEAMDVTPPTMHQHLRKGMKTIL 676
                                       9*********************************************999886 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       6.8     1e+04      43     107 ..     132     153 ..     118     155 .. 0.57
   2 !   52.7   0.7   2.9e-17   4.4e-14       3     109 ..     170     278 ..     168     279 .. 0.94
   3 ?    2.5   0.1      0.11   1.7e+02      47      74 ..     363     390 ..     349     404 .. 0.80
   4 ?   -2.8   0.0       5.1   7.7e+03      45      65 ..     600     620 ..     575     626 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.8
                             PAS_4  43 llpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlrdesGevigvlvisrDiTe 107
                                       ++                                          P+ d++  v+ +l+ + D T+
  gi|336254571|ref|YP_004597678.1| 132 YA------------------------------------------PV-DRDDAVDRILEAAADGTD 153
                                       44..........................................44.444444444444444444 PP

  == domain 2  score: 52.7 bits;  conditional E-value: 2.9e-17
                             PAS_4   3 slpdalavldpdgrvlyaNaa..aaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                        lpd  +v+++dg++l+a  +  aael+ ++ ++l+G++l++ +p++  a l+  ++r+ e+e+ ++ + e  +  +
  gi|336254571|ref|YP_004597678.1| 170 ELPDEAFVIGEDGTYLDAQIRpdAAELYTVSSDDLIGRRLEDAFPDDTVAKLRGCMDRAFETETIQSVEYEAETTEG 246
                                       689999************99999****************************************************** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +r +e r++P++++  + ++v++++rDiTer+
  gi|336254571|ref|YP_004597678.1| 247 WRRFEARVVPIDERIDGQRAVVWLARDITERA 278
                                       ***********7765446************97 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.11
                             PAS_4  47 edaarleralrrvlegeepiefleelll 74 
                                       ++ a+ ++ ++r++e++e++++ ++l +
  gi|336254571|ref|YP_004597678.1| 363 DVDAAEHCSVTRAAETGETQITDHILET 390
                                       466788999***********99998776 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 5.1
                             PAS_4  45 peedaarleralrrvlegeep 65 
                                          ++++++r++r ++e + +
  gi|336254571|ref|YP_004597678.1| 600 ELVARREVDRPVRTAAERRNR 620
                                       444788899999999988765 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.7   2.6e+03      23      64 ..      83     126 ..      74     133 .. 0.64
   2 ?   -2.6   0.0       4.2   6.2e+03       3      17 ..     136     150 ..     134     169 .. 0.83
   3 !   49.8   1.0   2.8e-16   4.1e-13       3     137 ..     313     453 ..     311     454 .. 0.76
   4 ?   -2.5   0.0         4   5.9e+03      38      73 ..     641     678 ..     619     688 .. 0.49

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.7
                                       EEEEEE-TTS-EEEEEEEES-TTSTT-S-B--.-TT.HHHHHHH CS
                             GAF_2  23 gyillvdddgglrlaawgeaeeefgaaldrpl.geg.lvgealr 64 
                                       +++l+ dd+ +lr++  + +++ +  a+  p+ g+  l++ a+r
  gi|336254571|ref|YP_004597678.1|  83 AVVLETDDRSELRTLLERVRDAADAPAIAAPPaGSEpLAAAAVR 126
                                       56667777777777755555555555555555466645777766 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.2
                                       HHHHHHHHHHHHHHH CS
                             GAF_2   3 dleelldlvldelve 17 
                                       d ++ +d++l+++++
  gi|336254571|ref|YP_004597678.1| 136 DRDDAVDRILEAAAD 150
                                       679999999999988 PP

  == domain 3  score: 49.8 bits;  conditional E-value: 2.8e-16
                                       HHHHHHHHHHHHHHHSS..EEEEEEE-.TTS-EEEE.EEEES-TTSTT-S-B--.-TTHHHHHHHHTS-EEES-.GG CS
                             GAF_2   3 dleelldlvldelvelgaalgyillvd.ddgglrla.awgeaeeefgaaldrpl.geglvgealrtgrpvilnd.le 75 
                                       + + + ++v+++lv+    +g + +   +d+ l ++  +g a++   ++ d +  +++ v +a++tg+  i ++ le
  gi|336254571|ref|YP_004597678.1| 313 TRDAIEQQVCEQLVDSELYCGALIVERaADDTLAYRiGAGDATAYMAHSRDVDAaEHCSVTRAAETGETQITDHiLE 389
                                       567888999999999444466665644255555555544444444444444455245589**************888 PP

                                       G..-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  76 e..dpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       +   pd  +++a++ ++r+++avP+++e+ ++Gvl++ a++ +af++++ + +e+l+e+i++ i
  gi|336254571|ref|YP_004597678.1| 390 TepLPDDLQEAAREDDVRATIAVPITYEDATYGVLSVLASRTDAFTDSEAAAFELLGETIGFTI 453
                                       855555555559999************99********************************987 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 4
                                       EEEES-TTSTT-S-B---TT.H.HHHHHHHTS-EEES- CS
                             GAF_2  38 awgeaeeefgaaldrplgeg.l.vgealrtgrpvilnd 73 
                                        +  ++e+ g+++  +++   + + + lr+g ++iln 
  gi|336254571|ref|YP_004597678.1| 641 FFDWPRESTGEEIAEAMDVTpPtMHQHLRKGMKTILNE 678
                                       33344444444444444444454667788887777777 PP

>> H_kinase_N  Signal transduction histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.1e-06    0.0031      52     135 ..     187     283 ..     171     289 .. 0.77
   2 ?    2.2   0.1      0.11   1.6e+02      75     133 ..     379     437 ..     354     444 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.1e-06
                                       EEE--SSS-..-S--S--TT-EE-G........GGSHHHHHHHH----------.------.---EEEEEE.EE.TE CS
                        H_kinase_N  52 aqarPttgp..tlyqeDvVGevvee........eeeplvdraleegrivrekdp.dwsggv.pvreeaiPVrrr.gk 115
                                       aq+rP  ++  t+ ++D++G+++e+        + +  +dra+e+++i+  + + ++++g+   + +++P+ +r + 
  gi|336254571|ref|YP_004597678.1| 187 AQIRPDAAElyTVSSDDLIGRRLEDafpddtvaKLRGCMDRAFETETIQSVEYEaETTEGWrRFEARVVPIDERiDG 263
                                       999**98765599************7777777679***********7766554303344446999******888978 PP

                                       EEEEEEEE--GGGS----HH CS
                        H_kinase_N 116 viAVltretnlssartpsrl 135
                                         AV+   ++++++ +++r+
  gi|336254571|ref|YP_004597678.1| 264 QRAVVWLARDITERAKRERE 283
                                       88999999999976666554 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.11
                                       GGSHHHHHHHH-------------------EEEEEE.EETEEEEEEEEE--GGGS---- CS
                        H_kinase_N  75 eeeplvdraleegrivrekdpdwsggvpvreeaiPVrrrgkviAVltretnlssartps 133
                                       +e +  d  le++   ++ ++  +++      a+P++ ++ + +Vl++  + + a t s
  gi|336254571|ref|YP_004597678.1| 379 GETQITDHILETEPLPDDLQEAAREDDVRATIAVPITYEDATYGVLSVLASRTDAFTDS 437
                                       333334444445555555554444444455779***99988888888766666555555 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   3.9e-07   0.00058      53     131 ..     371     451 ..     249     453 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.9e-07
                                       H..HHHHHSSSEEESTGG...TSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHH CS
                               GAF  53 g..qvlatgqplvipdst...pdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellq 123
                                          ++++tg++ + +++    p p+      ++ +++  +r+ ++vP++ ++ ++G+l++   ++  ft++e + ++
  gi|336254571|ref|YP_004597678.1| 371 SvtRAAETGETQITDHILetePLPDD----LQEAAREDDVRATIAVPITYEDATYGVLSVLASRTdAFTDSEAAAFE 443
                                       24367777777777764422244444....448899**************************55558*********9 PP

                                       HHHHHHHH CS
                               GAF 124 vladqvav 131
                                        l++ ++ 
  gi|336254571|ref|YP_004597678.1| 444 LLGETIGF 451
                                       99998875 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   3.3e-07    0.0005      49     127 ..     363     453 ..     319     454 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.3e-07
                             GAF_3  49 sld.edsalarralssgevvsepsfaeedglpd...........raalavPLvagrqviGvlalastkprafdaedl 113
                                        +d ++ +   ra+++ge +++    e++ lpd           ra +avP++ ++ ++Gvl +  +++ af+++++
  gi|336254571|ref|YP_004597678.1| 363 DVDaAEHCSVTRAAETGETQITDHILETEPLPDdlqeaareddvRATIAVPITYEDATYGVLSVLASRTDAFTDSEA 439
                                       45544444445888999999996666655555555555555556999****************97778899****** PP

                             GAF_3 114 elleslArqiatai 127
                                       + +e l+  i+  i
  gi|336254571|ref|YP_004597678.1| 440 AAFELLGETIGFTI 453
                                       ********999766 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.8e-06    0.0027      20     104 .]     193     276 ..     173     276 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-06
                             PAS_9  20 alrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdd.dgelv 93 
                                       a++l+  s+++++g++++d f  +t ++ +  +++a+e+ +   ++ve++  + +g + + +++++p+ +  dg   
  gi|336254571|ref|YP_004597678.1| 193 AAELYTVSSDDLIGRRLEDAFpdDTVAKLRGCMDRAFETET--IQSVEYEAETTEGWRRF-EARVVPIDERiDGQRA 266
                                       67787789*************55555555555555555555..999********995555.8999999555444433 PP

                             PAS_9  94 giivilrDite 104
                                        ++++ rDite
  gi|336254571|ref|YP_004597678.1| 267 -VVWLARDITE 276
                                       .78*******8 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.3   3.4e+03      26      40 ..     445     459 ..     441     460 .. 0.87
   2 !   15.6   0.0   5.5e-06    0.0082       2      46 ..     622     673 ..     621     675 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.3
                                       HHHHHTS-HHHHHHH CS
                        Sigma70_r4  26 IgerlgiSrerVrqi 40 
                                       +ge+ g + ++V+ +
  gi|336254571|ref|YP_004597678.1| 445 LGETIGFTIMAVKNR 459
                                       799*********988 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.5e-06
                                       HHHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                        Sigma70_r4   2 LasLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlr 46 
                                       L++L+er+ + l+  +        ++ T eEI+e ++++  + +q+++++++
  gi|336254571|ref|YP_004597678.1| 622 LDELTERQLTTLRVAYyagffdwPRESTGEEIAEAMDVTPPTMHQHLRKGMK 673
                                       9***************9***9998999**********************997 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 ?   -3.1   0.0       4.5   6.8e+03       7      21 ..     621     635 ..     620     641 .. 0.69
   2 !   16.2   0.0     4e-06     0.006      27      53 ..     648     674 ..     646     675 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.5
                                       HHTTS-HHHHHHHHH CS
                      Sigma70_r4_2   7 alaeLperqreifll 21 
                                        l+eL+erq + +  
  gi|336254571|ref|YP_004597678.1| 621 ILDELTERQLTTLRV 635
                                       799999999665555 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 4e-06
                                       --HHHHHHHHT--HHHHHHHHHHHHHH CS
                      Sigma70_r4_2  27 lsykEIAellgisegtVksrlsRArkk 53 
                                       ++ +EIAe +++++ t+ ++l++++k 
  gi|336254571|ref|YP_004597678.1| 648 STGEEIAEAMDVTPPTMHQHLRKGMKT 674
                                       5779*********************96 PP

>> Autoind_bind  Autoinducer binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.19      61     141 ..     372     445 ..     331     450 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                       HHHHHHHCSSEEEEECGGCCCCCSHHHHHHHHHHHHTT-SEEEEEEEEETTSSEEEEEEEESSSSCCHHHHHHHHHH CS
                      Autoind_bind  61 vvreaarssspfvWsddllaaelspaarrfldeardfGlrsGltvpvhgprgrlaalslageerdldaaeaaearar 137
                                       v+r+a ++ +  + +++l++   +p  +++ ++ar+ ++r+ ++vp+   +  +++ls+ +++ d   ++   ++a+
  gi|336254571|ref|YP_004597678.1| 372 VTRAA-ETGETQITDHILET---EPLPDDLQEAAREDDVRATIAVPITYEDATYGVLSVLASRTDAFTDS---EAAA 441
                                       44444.34445667777777...888999****************************9977777666654...5566 PP

                                       HHHH CS
                      Autoind_bind 138 lqll 141
                                       ++ll
  gi|336254571|ref|YP_004597678.1| 442 FELL 445
                                       6655 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 ?   -2.3   0.0       2.9   4.4e+03      14      26 ..     581     593 ..     576     594 .. 0.79
   2 ?   -1.7   0.1       1.9   2.8e+03       3      17 ..     617     631 ..     616     632 .. 0.85
   3 ?    9.4   0.0   0.00063      0.95      19      38 ..     651     670 ..     646     670 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.9
                                       SSEEHHHHHHHHT CS
                             HTH_5  14 gelcvcelaeelg 26 
                                       + + v e+a++l 
  gi|336254571|ref|YP_004597678.1| 581 QDANVREIADALS 593
                                       668899***9996 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
                                       HHHHHHHHHTTSSEE CS
                             HTH_5   3 tRlkILklLaegelc 17 
                                        R +IL  L e++l+
  gi|336254571|ref|YP_004597678.1| 617 RRNRILDELTERQLT 631
                                       799******998876 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00063
                                       HHHHHHHTS-HHHHHHHHHH CS
                             HTH_5  19 celaeelglsqstvShHLkk 38 
                                        e+ae+++++++t  +HL+k
  gi|336254571|ref|YP_004597678.1| 651 EEIAEAMDVTPPTMHQHLRK 670
                                       59****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (690 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 4756.35
//
Query:       gi|336254572|ref|YP_004597679.1|  [L=392]
Description: tRNA sulfurtransferase [Halopiger xanaduensis SH-6]
Scores for 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-43  148.3   0.0      3e-43  147.7   0.0    1.2  1  ThiI           Thiamine biosynthesis protein (ThiI)
    6.4e-17   62.0   0.0    1.3e-16   61.0   0.0    1.5  1  THUMP          THUMP domain
    2.3e-05   24.0   0.0       0.23   10.9   0.0    2.5  2  QueC           Queuosine biosynthesis protein QueC
    0.00058   18.8   0.0    0.00081   18.3   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
      0.049   13.4   0.1       0.59    9.9   0.1    2.3  1  ATP_bind_3     PP-loop family


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 !  147.7   0.0   8.3e-47     3e-43       1     190 [.     182     370 ..     182     376 .. 0.93

  Alignments for each domain:
  == domain 1  score: 147.7 bits;  conditional E-value: 8.3e-47
                              ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlk 77 
                                       g+q++v+a++SgGiDSpVaay ++kRG  vv v+++   + + + + +  + ++ l++y  + +++++ ++  e+++
  gi|336254572|ref|YP_004597679.1| 182 GAQETVIAMISGGIDSPVAAYEMMKRGAPVVPVYVDLGAYGGIDHEARAMETVRTLSRYAPNFDMQVYKIPGGETVD 258
                                       789*********************************9999999999999999*********9999999999999999 PP

                              ThiI  78 eilekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiik 154
                                        ++++++++ +++ l+r ++r+Ae++ae+ +a+ +vtGe++gq +Sqtl+Nl v+s +++l+i rPL++ dK++i++
  gi|336254572|ref|YP_004597679.1| 259 LLVNEMEQG-RMLSLRRFFYRAAETLAERVDAHGIVTGEAVGQKSSQTLQNLAVTSRATDLPIHRPLLTRDKQDIVA 334
                                       988887655.78899************************************************************** PP

                              ThiI 155 lAkeigtyeisiekedkCsvlakhPttkakleevek 190
                                        A+ei+t+  s++   +  v + + +t+a+le + +
  gi|336254572|ref|YP_004597679.1| 335 RAREIDTFTDSTIDAGCNRVAPDRAETNARLEPLLE 370
                                       ***********99887777777999*9999987655 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   3.7e-20   1.3e-16       2     143 ..      34     171 ..      33     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 3.7e-20
                                       HHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHH CS
                             THUMP   2 eieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkk 78 
                                       ++e+ll++  +  e++++ ++r ++ +       + e++  a   a+g+++ +    ++ ++  +ilea  ei ++ 
  gi|336254572|ref|YP_004597679.1|  34 NLEALLEDRSIPGEVERR-WNRPLIHTEPD----AVEAATAAAADAFGVVSASAC-LTTSTEKGEILEALAEIAREC 104
                                       8999*******9997777.55656555444....556666666777777777776.********************* PP

                                       HHHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT....-EE-SSS-SEEEEEEEETTEEEEEEE CS
                             THUMP  79 feeeketFaVrvkrrgkhfeftsreinrevGkaivektg....lkVdlenPdivvrveiikdkayisid 143
                                       + ++  tFaV ++r +k++ ++s e++r  G ai+e+ +    ++Vdl++Pd+++ ve+++++a+i+++
  gi|336254572|ref|YP_004597679.1| 105 YGGG--TFAVDARRANKELPYGSEELARDGGTAIWEAVEdefePEVDLDDPDLTFGVEVRDEAAFIYLE 171
                                       *999..*****************************99999999***********************986 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   6.4e-05      0.23       2      36 ..     187     221 ..     186     266 .. 0.80
   2 !   10.4   0.0   9.4e-05      0.34     138     180 ..     304     346 ..     273     354 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.4e-05
                                       EEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T CS
                              QueC   2 avvllSGGlDSttvlalakkegkevealtfdYgqr 36 
                                       ++ ++SGG+DS ++++ ++k+g+ v  + +d g  
  gi|336254572|ref|YP_004597679.1| 187 VIAMISGGIDSPVAAYEMMKRGAPVVPVYVDLGAY 221
                                       6889*********************9999987755 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9.4e-05
                                       HHHHHHHHHHHTS--EEE-TTTT--HHHHHHHHHHTTHHHHH- CS
                              QueC 138 kalnkalnlgedkkieieaPlidlsKaeivklgkelgvpleet 180
                                       ++l++++ +++++++ i+ Pl++ +K++iv+++ e++  ++ t
  gi|336254572|ref|YP_004597679.1| 304 QTLQNLAVTSRATDLPIHRPLLTRDKQDIVARAREIDTFTDST 346
                                       44555555568899*********************99777666 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.3e-07   0.00081       2      67 ..     186     250 ..     185     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.3e-07
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplev 67 
                                       +v++ +SgG+DS vaa+ + ++g  v+ v++ l +  +  + e  a e +++ +r a ++++++++
  gi|336254572|ref|YP_004597679.1| 186 TVIAMISGGIDSPVAAYEMMKRGAPVVPVYVDLGAYGGIDH-EARAMETVRTLSRYAPNFDMQVYK 250
                                       7999**************************99988844444.666777777777777777777665 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00016      0.59     121     168 ..     301     346 ..     186     349 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
                                       --CCHHH-S-SEEEETTCCEE-CCCT--HHHHHHHHHHTT---B--CG CS
                        ATP_bind_3 121 sglaglagikeaseiasirlvRPlLkvskeeleeylkekkikwveDes 168
                                       ++ ++l+ ++  s+ ++  + RPlL+  k+++ +  + ++i+ ++D++
  gi|336254572|ref|YP_004597679.1| 301 KSSQTLQNLAVTSRATDLPIHRPLLTRDKQDIVA--RAREIDTFTDST 346
                                       344566666667777799**************98..555688888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 3188.76
//
Query:       gi|336254573|ref|YP_004597680.1|  [L=418]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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-44  150.4  54.4    3.1e-26   92.1  27.6    2.1  2  MFS_1       Major Facilitator Superfamily
     0.0019   17.1  19.5      0.022   13.7   0.1    3.3  3  MFS_1_like  MFS_1 like family
     0.0027   16.1   2.2      0.003   15.9   0.7    1.7  2  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 !   92.1  27.6   5.2e-30   3.1e-26       3     226 ..      17     239 ..      15     258 .. 0.82
   2 !   59.7  24.8   3.9e-20   2.3e-16      26     172 ..     249     400 ..     224     416 .. 0.78

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 5.2e-30
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                        ++f+++++ ++++p+lp  l+e lgis+  +g++l++  ++ +va+ p+G+l+dr+G r+ +++gl++ +l+ +++
  gi|336254573|ref|YP_004597680.1|  17 ASTFFVGFGGGVVFPILP-NLGEVLGISAFMVGIILSANRFTRLVANAPAGSLVDRIGTRKPFIAGLAIEGLA-TFG 91 
                                       689***************.9*****************************************************.555 PP

                             MFS_1  80 l...fa.........ss...lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllg 141
                                           +a         ++   +w ++v+r+l G+g++++f+++++++ad++  + rg  +g++ ag+ +G+  g +lg
  gi|336254573|ref|YP_004597680.1|  92 YvvaLAagrsvlwflPNvpeFW-FMVARILWGVGSALVFATAYTITADVSEADSRGTSMGIVRAGITFGFPAGLVLG 167
                                       5333334554445553333244.****************************************************** PP

                             MFS_1 142 gllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialll 218
                                       gl+++ +g   +f+++a+++ la v+++l +pe++++++ ks            ++p w +  + p    +l++ l+
  gi|336254573|ref|YP_004597680.1| 168 GLVSDIWGNVEAFVLAAAFAGLASVIAYLIVPETHVDSEQKS------------VKP-WDIETTVP----ALTVGLV 227
                                       *************************98888888887777774............334.66666777....6666666 PP

                             MFS_1 219 fffgfsg....l 226
                                       +f  +++    l
  gi|336254573|ref|YP_004597680.1| 228 NFGLYFAyigvL 239
                                       665555543322 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 3.9e-20
                             MFS_1  26 d.....lgisp.seigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw.lllvlrvlq 95 
                                       +     +g+++  + g+l+++  l  +v++l +G+lsd +G+r  ++lg+ll+++ ++++l +  ++ +l+++ +l 
  gi|336254573|ref|YP_004597680.1| 249 EraiviFGLDAqGSSGMLMAVTVLSGSVFTLGGGALSDAVGARVPVMLGFLLTSFVGFVALATGRSFeVLVLACLLI 325
                                       344444444440458999**************************666666666666455553477888********* PP

                             MFS_1  96 GlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                       G+g+g++     al+ad++p+e+ gra+g  +++  +G  lgpl++  l+++++++ v+ + ai+ +la+v+  ll 
  gi|336254573|ref|YP_004597680.1| 326 GAGQGGVGGPLTALLADLTPEERVGRAMGTNNVFGDVGGGLGPLVSLPLVDLVSFEFVYGLSAILPVLAGVV--LLA 400
                                       *********************************************************************994..332 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 !   13.7   0.1   3.6e-06     0.022       7      77 ..      19      97 ..      13     112 .. 0.74
   2 !    5.5   4.1    0.0011       6.4     312     383 ..     111     180 ..      87     185 .. 0.78
   3 !    6.1   4.9    0.0007       4.2     259     370 ..     260     371 ..     176     386 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-06
                        MFS_1_like  7 lyFfffaalgsllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkk.........vvilslllsa 76
                                      ++F+ f+  g ++P l    +  g++a  +gii+++  +t++++    g l+Dr+g rk+         ++ ++ ++++
  gi|336254573|ref|YP_004597680.1| 19 TFFVGFGG-GVVFPILPNLGEVLGISAFMVGIILSANRFTRLVANAPAGSLVDRIGTRKPfiaglaiegLATFGYVVAL 96
                                      66666665.6677777777778899999********************************7666666664444444444 PP

                        MFS_1_like 77 v 77
                                      +
  gi|336254573|ref|YP_004597680.1| 97 A 97
                                      4 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0011
                        MFS_1_like 312 nawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                       ++w  +++ +L g+  +l++a+a +  +++     ++t +g++ +  + +G   G ++GGl+ d+ + + +F
  gi|336254573|ref|YP_004597680.1| 111 EFW-FMVARILWGVGSALVFATAYTITADVSEADSRGTSMGIVRAG-ITFGFPAGLVLGGLVSDIWGNVEAF 180
                                       445.56689*********************************9743.5666677888888887777766666 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0007
                        MFS_1_like 259 ntllGslvalgvvaeiplfffaeklleklGhvklliiallay.ilrfllyaiienawlvlpievLhgisfgllwaaa 334
                                       +   G+l+a++v++  ++ + +  l + +G+++ +++++l++ ++ f+ +a+ +++ +++++ +L g+  g + + +
  gi|336254573|ref|YP_004597680.1| 260 QGSSGMLMAVTVLSGSVFTLGGGALSDAVGARVPVMLGFLLTsFVGFVALATGRSFEVLVLACLLIGAGQGGVGGPL 336
                                       334577888888888888999************9999998762578***************************9*** PP

                        MFS_1_like 335 veyvskiapksleatgqgllsglyfglGralGsliG 370
                                       +   ++++p++  ++ +g  + +   +G++lG l++
  gi|336254573|ref|YP_004597680.1| 337 TALLADLTPEERVGRAMGTNNVF-GDVGGGLGPLVS 371
                                       **********9999999976554.558888888876 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 ?   -2.4   0.0      0.18   1.1e+03      14      82 ..      23      93 ..      11      98 .. 0.62
   2 !   15.9   0.7     5e-07     0.003     133     198 ..     112     177 ..      98     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.18
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                              OATP 14 amvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggr..ghrPrwigigallmalgsll 82
                                      ++ +g++  ++ ++    +++   +g+i+s+n  + +++ +  + + +r  +++P + g+++  +a + ++
  gi|336254573|ref|YP_004597680.1| 23 GFGGGVVFPILPNLGEVLGISAFMVGIILSANRFTRLVANAPAGSLVDRigTRKPFIAGLAIEGLATFGYV 93
                                      66666666677777777788888888888888888887777666666665445666666665555555555 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 5e-07
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 133 llfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllklyvdi 198
                                       ++f++a +l G+G++++++ +++   D ++  +  + +gi+ a  ++G   G +lG+l+  ++ ++
  gi|336254573|ref|YP_004597680.1| 112 FWFMVARILWGVGSALVFATAYTITADVSEADSRGTSMGIVRAGITFGFPAGLVLGGLVSDIWGNV 177
                                       389********************************************************9999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); 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:                         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: 0.52u 0.20s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 3376.91
//
Query:       gi|336254574|ref|YP_004597681.1|  [L=401]
Description: S-adenosylmethionine synthase [Halopiger xanaduensis SH-6]
Scores for 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-173  576.7   6.9   2.4e-173  576.5   6.9    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
     0.0055   17.4   1.0      0.015   16.0   0.0    2.3  3  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 
  ------ inclusion threshold ------
      0.011   16.0   0.3       0.34   11.3   0.1    2.4  2  DUF961           Bacterial protein of unknown function (DUF96
       0.73   10.3   7.1        4.7    7.7   1.8    3.4  2  Asp23            Asp23 family, cell envelope-related function


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 !  576.5   6.9  5.3e-177  2.4e-173       1     396 []       4     397 ..       4     397 .. 0.99

  Alignments for each domain:
  == domain 1  score: 576.5 bits;  conditional E-value: 5.3e-177
                                       --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEE CS
                   AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGG 77 
                                       rni+ve +++++ve+qevEivErKGiGHPD+i+Dg+aeavs+al++ey++++g++lh+n+D+++lvaGe++p+fgGG
  gi|336254574|ref|YP_004597681.1|   4 RNIRVEPIDRHAVEDQEVEIVERKGIGHPDTICDGVAEAVSEALAQEYIDRVGEVLHFNTDETQLVAGEAAPAFGGG 80 
                                       79*************************************************************************** PP

                                       EEEE-EEEEEEEEEEEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BE CS
                   AdoMet_Synthase  78 eviepieillsgratkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevpla 154
                                       ev++pi++l++gratk+++g++ip+e+ial+aa+eyl++++++l++ +d++vdvklg+gs dL++vf +++ +vp+a
  gi|336254574|ref|YP_004597681.1|  81 EVVDPIYLLIVGRATKHYDGQTIPAETIALRAAREYLESEIPQLNVGEDIVVDVKLGEGSGDLQEVFGEDEVSVPMA 157
                                       *********************************************************************999***** PP

                                       SSSEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHH CS
                   AdoMet_Synthase 155 NDtSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevke 231
                                       NDtSfgvg+apl+e+e++vle+e+ ln  e+ +++p +G D+K+mg Re+++i++Tva+a++d++++dl+eY+++ +
  gi|336254574|ref|YP_004597681.1| 158 NDTSFGVGHAPLTETEQIVLEAESRLNG-EFADENPYLGPDVKLMGKREGDTIDVTVAAAMIDEHIADLDEYIDAVD 233
                                       ***************************7.99********************************************** PP

                                       HHHHHHHHHHHHHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-T CS
                   AdoMet_Synthase 232 eikeeveelakkltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNP 308
                                       ++++ ve++a+++t+ rev+v+vNtaD++ee+s+yltvtGtsaE+gDdGsvGRGNR+nGlitpnr+ms+EA++GKNP
  gi|336254574|ref|YP_004597681.1| 234 AVEAFVEDVATEHTD-REVNVHVNTADDYEEGSIYLTVTGTSAEQGDDGSVGRGNRANGLITPNRSMSMEATSGKNP 309
                                       **************9.************************************************************* PP

                                       TT-HHHHHHHHHHHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT-H CS
                   AdoMet_Synthase 309 vsHvGKiYnvlaneiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideeleki 385
                                       v+H+GKiYn+l++eia+e+v+ev+g++++ vrllsqiG+pid+P+va+v+v++++gv+le+ve+++e+i+d+el+++
  gi|336254574|ref|YP_004597681.1| 310 VNHIGKIYNLLSTEIAEEVVAEVDGIRDLRVRLLSQIGRPIDQPHVADVHVVTDDGVTLEDVESDIENIVDRELANV 386
                                       ***************************************************************************** PP

                                       HHHHHHHTTT- CS
                   AdoMet_Synthase 386 eeiteeliegk 396
                                       ++it+++i+g+
  gi|336254574|ref|YP_004597681.1| 387 TDITRQVIDGE 397
                                       ********986 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 !   16.0   0.0   3.3e-06     0.015      11      55 ..      29      73 ..      22     108 .. 0.80
   2 ?   -2.9   0.1       2.5   1.1e+04      60      74 ..     228     242 ..     208     258 .. 0.50
   3 ?   -3.4   0.0       3.6   1.6e+04      39      69 ..     300     327 ..     295     336 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.3e-06
                   S-AdoMet_synt_N 11 eGHPDkvadqisdaildailkedpkarvacet.lvttglvvvagei 55
                                       GHPD ++d +++a+ +a l+++   rv     + t+++ +vage 
  gi|336254574|ref|YP_004597681.1| 29 IGHPDTICDGVAEAVSEA-LAQEYIDRVGEVLhFNTDETQLVAGEA 73
                                      6***********998766.888888888644314455577788876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.5
                   S-AdoMet_synt_N  60 kvdiekivrevikei 74 
                                       ++d  ++v   ++++
  gi|336254574|ref|YP_004597681.1| 228 YIDAVDAVEAFVEDV 242
                                       333333333333333 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.6
                   S-AdoMet_synt_N  39 acetlvttglvvvageittkakvdiekivre 69 
                                       ++e++  ++ v  +g+i +  +++i +   e
  gi|336254574|ref|YP_004597681.1| 300 SMEATSGKNPVNHIGKIYNLLSTEIAE---E 327
                                       556666666666666664443333333...2 PP

>> DUF961  Bacterial protein of unknown function (DUF961)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   7.7e-05      0.34      36      99 ..     193     260 ..     171     261 .. 0.87
   2 ?    2.3   0.0     0.046   2.1e+02      21      55 ..     297     331 ..     293     339 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.7e-05
                            DUF961  36 vkartyklyssaqgedieVtipaeagvkef....eyedeVkLvnpkieavgnsingravvnyklkAdd 99 
                                        ++ ++kl+ +++g++i Vt++a+   +++    ey d+V  v+  +e v+++  +r+v+  + +Add
  gi|336254574|ref|YP_004597681.1| 193 YLGPDVKLMGKREGDTIDVTVAAAMIDEHIadldEYIDAVDAVEAFVEDVATEHTDREVNVHVNTADD 260
                                       4577899******************99999999********************999887777667777 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.046
                            DUF961  21 eevkvedeekngetevkartyklyssaqgedieVt 55 
                                       + + +e + +++  + ++++y+l s + +e++   
  gi|336254574|ref|YP_004597681.1| 297 RSMSMEATSGKNPVNHIGKIYNLLSTEIAEEVVAE 331
                                       66778888888889999**********99998655 PP

>> Asp23  Asp23 family, cell envelope-related function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3     0.029   1.3e+02      43     105 ..     189     256 ..     170     258 .. 0.66
   2 ?    7.7   1.8     0.001       4.7      61      97 ..     355     391 ..     318     395 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.029
                             Asp23  43 kenltkgvkvev.geekqvavdlyvvve.YGvkipevaenvq..ekVkeaveem.tglevseVnvhVq 105
                                        en+  g +v+  g+ ++ ++d++v ++  + +i+++ e +   ++V++ ve++ t+ +  eVnvhV+
  gi|336254574|ref|YP_004597681.1| 189 DENPYLGPDVKLmGKREGDTIDVTVAAAmIDEHIADLDEYIDavDAVEAFVEDVaTEHTDREVNVHVN 256
                                       45555554444313366678888887652578888887766422689999998537888899****97 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.001
                             Asp23  61 avdlyvvveYGvkipevaenvqekVkeaveemtglev 97 
                                         d++vv + Gv +++v +++++ V +++ ++t+++ 
  gi|336254574|ref|YP_004597681.1| 355 VADVHVVTDDGVTLEDVESDIENIVDRELANVTDITR 391
                                       68*******************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3047.68
//
Query:       gi|336254575|ref|YP_004597682.1|  [L=212]
Description: adenylyl cyclase CyaB [Halopiger xanaduensis SH-6]
Scores for 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-34  118.5   8.4    1.2e-33  116.5   8.4    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 !  116.5   8.4   6.9e-38   1.2e-33       1     179 []       1     205 [.       1     205 [. 0.87

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 6.9e-38
                                       EEEEEEEEEE-.HHHHHHHHHH............HHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEE....... CS
                              CYTH   1 miEvEvKflvs.aaeyedlelr............laelrakeettveqrdtYydtpdrdlartdeaLRiR....... 57 
                                       m+EvEvK++ +   ++   ++r            ++ l+a  ++tv q+dtYyd+p+r++ +tdeaLRiR       
  gi|336254575|ref|YP_004597682.1|   1 MYEVEVKVPADpDLAAV--RERlergggsdgadeARRLEADRAETVVQEDTYYDAPHRSFPETDEALRIRrestpgs 75 
                                       67788887775322222..222234566666556677899999********************************** PP

                                       ..EETTTEEE.EEEEEECSSST...EEEEEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEE....T CS
                              CYTH  58 ..raegdgee.ltlKgpgvdge...reevegevsreEyeeplsdaaeaaelldglglepvasvkklRrkykl....e 124
                                          a +d e+ +t+Kgp++d+e   ree+e++v+         d +++ ++l  lg+ p+a+v+k+R+ y +    +
  gi|336254575|ref|YP_004597682.1|  76 esDAAEDAESrITYKGPLLDDEsksREEIETAVA---------DGEKMDAVLTNLGFAPAATVRKEREHYTValavD 143
                                       **666999999***********************.........*****************************66651 PP

                                       T........EEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHHHHHTTEEGGGBSCSHH CS
                              CYTH 125 g........vevalDaveflegeevEiElevedeeevkeaaekllallrelglssaskirrsy 179
                                       +         +++lDav+++ ge+vE+E+ ve e+++++a++ ++a+l+ l l++ ++ir+sy
  gi|336254575|ref|YP_004597682.1| 144 DdgdertytYTITLDAVDDV-GEYVEVETDVEREADLETARRGAYAVLESLDLDPDDQIRTSY 205
                                       166789999***********.****************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1722.66
//
Query:       gi|336254576|ref|YP_004597683.1|  [L=327]
Description: FKBP-type peptidylprolyl isomerase [Halopiger xanaduensis SH-6]
Scores for complete 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   31.5   0.3    4.4e-07   30.1   0.2    1.8  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
  ------ inclusion threshold ------
       0.06   13.0   0.2       0.16   11.7   0.2    1.7  1  ScdA_N    Domain of Unknown function (DUF542)


Domain annotation for each model (and alignments):
>> 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 !   30.1   0.2   4.9e-11   4.4e-07       5      74 ..      30     119 ..      26     170 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.9e-11
                                       B-TTCEEEEEEEEEET.TSSEEEEH.............CCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEG CS
                            FKBP_C   5 akegdtVtvhykgkle.dgkvfdss.............rsrakplefkvGsgqvikGfeealegmkvGekrtltipp 67 
                                        ++gd+V+++y+++   +++++d++              ++ kp ++++G+g++ ++ ee ++g + G + t+t+p 
  gi|336254576|ref|YP_004597683.1|  30 LQNGDFVEIEYTAYTVdGDQLVDTTdpevaeeegvddqGQEFKPRTIVLGEGHIFEAVEEDIVGSEPGAEGTVTVPA 106
                                       689************8457777777888887777655455999********************************** PP

                                       GGTTTT......T CS
                            FKBP_C  68 elaYge......k 74 
                                       e a+ge      +
  gi|336254576|ref|YP_004597683.1| 107 EDAFGEydpddvQ 119
                                       *****95554440 PP

>> ScdA_N  Domain of Unknown function (DUF542)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   1.7e-05      0.16      31      55 ..     301     325 ..     299     326 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.7e-05
                            ScdA_N  31 kvsLaeAckekgidleevlaeLeal 55 
                                          ++eA++++++d++e+++eLe +
  gi|336254576|ref|YP_004597683.1| 301 GGDIEEALEDADVDADEIVEELEGA 325
                                       55799*****************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 2484.53
//
Query:       gi|336254577|ref|YP_004597684.1|  [L=208]
Description: hypothetical protein Halxa_3193 [Halopiger xanaduensis SH-6]
Scores for 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-07   29.8   0.0     0.0004   19.8   0.0    2.2  2  ATPase    KaiC


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   8.4e-05       1.5       2      25 ..       6      29 ..       5      62 .. 0.93
   2 !   19.8   0.0   2.2e-08    0.0004     121     222 ..     100     198 ..      78     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 8.4e-05
                            ATPase  2 ktgIeglDeilkgGipegrvvlit 25
                                      +tgI  lD+ l+gG+p g+v+  t
  gi|336254577|ref|YP_004597684.1|  6 ETGIDVLDRKLDGGLPPGSVIAFT 29
                                      7******************99765 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.2e-08
                            ATPase 121 krvviDsitglayeekeavaReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelv 197
                                        +++iD+ ++l +++++++  + l  l++++ ++g  a+l + k  ++  a++ +  + ++d ++ L+ +   +el+
  gi|336254577|ref|YP_004597684.1| 100 ANLIIDTMNTL-ERTDTDEYIDFLNDLKTRMVETGSIAVLHCLK-AQDPPANRARTFH-AADAIFDLTTDITGTELE 173
                                       689********.999999999*******************9995.5568999999999.9***************** PP

                            ATPase 198 RtleivkmRgtkhskkehpfeItee 222
                                        +l i k R  +  ++ + +e tee
  gi|336254577|ref|YP_004597684.1| 174 NHLTIPKFRNGGQPTEAIKLELTEE 198
                                       ***************9999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1623.77
//
Query:       gi|336254578|ref|YP_004597685.1|  [L=313]
Description: aspartate carbamoyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-45  154.8   0.0    7.6e-45  152.6   0.0    2.0  2  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    1.8e-31  109.4   0.0    2.4e-31  108.9   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
  ------ inclusion threshold ------
        0.2   10.8   0.0       0.28   10.3   0.0    1.2  1  DUF2586   Protein of unknown function (DUF2586)


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 !  152.6   0.0   1.3e-48   7.6e-45       2     148 .]       5     144 ..       4     144 .. 0.93
   2 ?   -0.5   0.0      0.18   1.1e+03      52      89 ..     163     193 ..     152     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 152.6 bits;  conditional E-value: 1.3e-48
                                       -BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSC CS
                          OTCace_N   2 hllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediq 78 
                                       hl++ ++ls+ +ie++ld+aae+ ++++     +  +gk l+llF+epStRT++Sfe+A+krlGg+v+ +++   ++
  gi|336254578|ref|YP_004597685.1|   5 HLITSKQLSRGDIETVLDRAAEIDADRA--AVADRHAGKLLGLLFFEPSTRTKMSFETAMKRLGGDVVDMGS---VE 76 
                                       99**********************9986..7888889**********************************4...57 PP

                                       TTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  79 lssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       +ssv+kg  E+l+Dt+rv+++y+da+v+Rhp++  +    ++ +vp++Nagdg+g+HPtQ+L+Dl+tire
  gi|336254578|ref|YP_004597685.1|  77 SSSVKKG--ETLADTVRVIEGYADALVLRHPKQGAATMASEFVDVPLLNAGDGAGHHPTQTLLDLYTIRE 144
                                       8999***..**********************775566556666*************************98 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHTTSEEEEEESTTTSCT.TTGGSTTSSC CS
                          OTCace_N  52 RTrvSfevAakrlGgkvlslseaediql.ssvskgrkEs 89 
                                       RT  S   A ++  ++  ++s +e++ql         E 
  gi|336254578|ref|YP_004597685.1| 163 RTVHSLAYALTNFDASQHFIS-PESLQLpR-------EV 193
                                       777777777777777777777.55555522.......33 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 !  108.9   0.0     4e-35   2.4e-31       2     156 ..     150     299 ..     149     300 .. 0.93

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 4e-35
                                       C.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE CS
                            OTCace   2 glkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvyt 77 
                                       +l+i ++Gd k++++++sl+++l+ ++++ ++++P++l+   ev+  +++   ++g++i  +e+lee++   Dv+y 
  gi|336254578|ref|YP_004597685.1| 150 DLTIGIMGDlKYGRTVHSLAYALTNFDASQHFISPESLQLPREVVYDLHQ---QQGAQIREHESLEEVLPSLDVLYV 223
                                       789**********************************9999999966655...68********************** PP

                                       --SSETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHH CS
                            OTCace  78 dvwvsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhti 150
                                       ++++     +er+   ++++k+++ yq+++e l++a +d+ v+H+LP  r +E++ e+++ +++++feqa N++ ++
  gi|336254578|ref|YP_004597685.1| 224 TRIQ-----RERFpdeNEYQKVAGeYQIDAETLEAAGDDLTVMHPLP--RVDEIAPEIDETDHAAYFEQAHNGVPVR 293
                                       ****.....5555555889999989**********************..**************************** PP

                                       HHHHHH CS
                            OTCace 151 kAllvl 156
                                       +All l
  gi|336254578|ref|YP_004597685.1| 294 MALLDL 299
                                       ***987 PP

>> DUF2586  Protein of unknown function (DUF2586)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   4.8e-05      0.28     220     273 ..     220     273 ..     208     294 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.8e-05
                           DUF2586 220 latlkalekaRysvpqwypdydGvYwsDgnlLdvegGDyqvienlRvvdkvaRk 273
                                       +  ++ ++++R+     y    G Y  D+++L++ g D +v+  l  vd +a +
  gi|336254578|ref|YP_004597685.1| 220 VLYVTRIQRERFPDENEYQKVAGEYQIDAETLEAAGDDLTVMHPLPRVDEIAPE 273
                                       5566778999********************************999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2346.42
//
Query:       gi|336254579|ref|YP_004597686.1|  [L=163]
Description: aspartate carbamoyltransferase regulatory chain [Halopiger xanaduensis SH-6]
Scores for 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  112.9   0.5    8.1e-33  112.5   0.5    1.1  1  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    5.4e-12   45.4   0.2    1.1e-11   44.5   0.2    1.5  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 !  112.5   0.5   9.1e-37   8.1e-33       1      94 []      16     108 ..      16     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 9.1e-37
                                       X-----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT- CS
                              PyrI   1 lkvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapna 77 
                                       l+v+ki++G+ViDH++ g+al+vl +L++d+ +++e+v+i++nv+s++l +Kdi+k+eg+els++e+d+l+liap+a
  gi|336254579|ref|YP_004597686.1|  16 LRVSKIRDGTVIDHVHGGQALNVLAILGIDG-SEGEEVSIGMNVPSDRLARKDIVKVEGRELSQDEVDVLSLIAPDA 91 
                                       689***************************8.66679**************************************** PP

                                       EEEEEETTEEEEEE--. CS
                              PyrI  78 tiniIkdgevveKkkve 94 
                                       tini++++ev+eK++ve
  gi|336254579|ref|YP_004597686.1|  92 TINIVREYEVIEKHRVE 108
                                       **************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 !   44.5   0.2   1.2e-15   1.1e-11       2      46 ..     113     155 ..     112     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.2e-15
                                       EESSS--S-TTBGGGT.TS-.-EEEEEETTTTEEEETTT--EEEHH CS
                            PyrI_C   2 iegvlkCpNpnCItnn.epveskFkvedkekvklkCkYCekeisee 46 
                                       +egvl+CpN  CIt   epv+s+F+v ++    ++C YCe++++ e
  gi|336254579|ref|YP_004597686.1| 113 VEGVLSCPNRGCITTGdEPVTSRFEVLED---GVRCAYCETIVRDE 155
                                       89**************99*******8554...48*******99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1193.34
//
Query:       gi|336254580|ref|YP_004597687.1|  [L=37]
Description: hypothetical protein Halxa_3196 [Halopiger xanaduensis SH-6]
Scores for 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  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 309.66
//
Query:       gi|336254581|ref|YP_004597688.1|  [L=279]
Description: hypothetical protein Halxa_3197 [Halopiger xanaduensis SH-6]
Scores for 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  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 2276.20
//
Query:       gi|336254582|ref|YP_004597689.1|  [L=58]
Description: hypothetical protein Halxa_3198 [Halopiger xanaduensis SH-6]
Scores for 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:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); 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: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 487.03
//
Query:       gi|336254583|ref|YP_004597690.1|  [L=313]
Description: hypothetical protein Halxa_3199 [Halopiger xanaduensis SH-6]
Scores for 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  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); 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):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 2274.47
//
Query:       gi|336254584|ref|YP_004597691.1|  [L=222]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   65.6   0.1    4.4e-18   64.8   0.1    1.4  1  HTH_10         HTH DNA binding domain
    7.7e-12   45.3   0.8    1.3e-11   44.6   0.8    1.5  1  BAT            GAF and HTH_10 associated domain
    0.00032   20.5   0.3     0.0012   18.6   0.0    2.0  2  MarR_2         MarR family
     0.0013   18.3   0.0     0.0024   17.4   0.0    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.021   14.6   0.1      0.045   13.6   0.1    1.5  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.026   14.6   0.0      0.079   13.1   0.0    1.8  2  Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix do
      0.033   14.4   0.0      0.055   13.7   0.0    1.3  1  UPF0122        Putative helix-turn-helix protein, YlxM / p13 
      0.035   13.8   0.0      0.087   12.6   0.0    1.7  1  HTH_psq        helix-turn-helix, Psq domain
      0.036   13.6   0.1      0.069   12.7   0.1    1.5  1  Sigma70_r4     Sigma-70, region 4


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 !   64.8   0.1   2.2e-21   4.4e-18       1      52 [.     152     203 ..     152     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 2.2e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT +q+e+l +A++ GYF+ PR+v+++eL++elGIs ++lse+Lr+a + l+
  gi|336254584|ref|YP_004597691.1| 152 LTARQYETLVAAIDHGYFEIPREVSMQELSDELGISHQALSERLRRAYRALV 203
                                       9**********************************************99887 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.8   6.6e-15   1.3e-11      30     131 ..      30     129 ..      22     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 6.6e-15
                               BAT  30 leglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtlleltvsgp..slastlaehGgtvrsae 104
                                       +e+++++s+ ++    +++ga+++ev++a+++   +e+++++s ++d++l+ ++++ +  ++++++ e Ggtv sa+
  gi|336254584|ref|YP_004597691.1|  30 MERVIASSGHGL----WLSGASQDEVEAALSESTEIEEYTMISSDGDRWLYDIEFDPDtvDPFTVVLEEGGTVLSAS 102
                                       555555555554....899*******************************99998543114677************* PP

                               BAT 105 aedgrarlvvevPpgadvRsvvealee 131
                                       a+++++ l v+v +++ v +++++l +
  gi|336254584|ref|YP_004597691.1| 103 ASNDTWLLSVRVVDRESVSTLYDRLVD 129
                                       ***********************9976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   2.3e+03      33      47 ..     115     129 ..     111     132 .. 0.87
   2 !   18.6   0.0   6.2e-07    0.0012       3      45 ..     152     198 ..     151     201 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                       SSHHHHHHHHHHHHH CS
                            MarR_2  33 lsksavsrilkrLva 47 
                                       +++ +vs + +rLv+
  gi|336254584|ref|YP_004597691.1| 115 VDRESVSTLYDRLVD 129
                                       789999999999997 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 6.2e-07
                                       --HHHHHHHHHHHCTTTS.....EEEHHHHHHHHTSSHHHHHHHHHHH CS
                            MarR_2   3 ltpaqarvLaaLgrrpgr.....dltvgelarrlglsksavsrilkrL 45 
                                       lt  q+  L a  +++ +     +++++el ++lg+s++a+s +l+r+
  gi|336254584|ref|YP_004597691.1| 152 LTARQYETLVAAIDHG-YfeiprEVSMQELSDELGISHQALSERLRRA 198
                                       5555555555555554.44555589*********************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 !   17.4   0.0   1.2e-06    0.0024      18      40 ..     175     197 ..     172     200 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-06
                            HTH_24  18 isqreLAerlglSpstvnrrlkr 40 
                                        s++eL+++lg+S +++++rl+r
  gi|336254584|ref|YP_004597691.1| 175 VSMQELSDELGISHQALSERLRR 197
                                       79********************8 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 ?   13.6   0.1   2.3e-05     0.045      19      40 ..     176     197 ..     174     198 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                     HTH_AsnC-type  19 syaeLAervGlSestvlrRvrr 40 
                                       s++eL++++G+S ++  +R+rr
  gi|336254584|ref|YP_004597691.1| 176 SMQELSDELGISHQALSERLRR 197
                                       89*******************9 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 ?   -2.6   0.0       3.1   6.1e+03      26      35 ..     117     126 ..     115     129 .. 0.83
   2 ?   13.1   0.0     4e-05     0.079      12      36 ..     175     198 ..     173     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.1
                                       HHHHHHHHHS CS
                     Phage_CI_repr  26 kssvstwvrR 35 
                                       + svst++ R
  gi|336254584|ref|YP_004597691.1| 117 RESVSTLYDR 126
                                       6899999987 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4e-05
                                       -SSCHHHHCCTT--HHHHHHHHHSS CS
                     Phage_CI_repr  12 vkmqkeLAdlLgiakssvstwvrRd 36 
                                       v+mq eL+d+Lgi+++ +s + rR 
  gi|336254584|ref|YP_004597691.1| 175 VSMQ-ELSDELGISHQALSERLRRA 198
                                       7788.****************9995 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.8e-05     0.055      14      64 ..     157     205 ..     144     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-05
                           UPF0122  14 YqsLLTekqanylelyyadDlSlsEiAeefnvsrqavydnikrteklleky 64 
                                       Y++L+      y+e  +  + S++E+ +e  +s+qa+++ ++r+ + l + 
  gi|336254584|ref|YP_004597691.1| 157 YETLVAAIDHGYFE--IPREVSMQELSDELGISHQALSERLRRAYRALVTS 205
                                       55555555556665..46789**********************98887665 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 ?   12.6   0.0   4.4e-05     0.087       5      42 ..     160     200 ..     157     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                           HTH_psq   5 laaAleavv....nGkmSirkAArkYgiPrsTLwrrkrgkys 42 
                                       l aA+++      ++ +S+++++++ gi++  L++r+r+ y 
  gi|336254584|ref|YP_004597691.1| 160 LVAAIDHGYfeipRE-VSMQELSDELGISHQALSERLRRAYR 200
                                       556665544455456.9**********************986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.5e-05     0.069      19      48 ..     173     202 ..     151     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                                       TT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  19 eglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       ++ +++E++++lgiS  + + +++rA r L
  gi|336254584|ref|YP_004597691.1| 173 REVSMQELSDELGISHQALSERLRRAYRAL 202
                                       6889**********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1644.78
//
Query:       gi|336254585|ref|YP_004597692.1|  [L=277]
Description: NifC-like ABC-type porter [Halopiger xanaduensis SH-6]
Scores for 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-16   58.6  13.7    6.4e-16   58.6  13.7    2.0  2  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 ?    0.3   0.2     0.028     5e+02      53      71 ..      29      47 ..      12      81 .. 0.66
   2 !   58.6  13.7   3.6e-20   6.4e-16       4     175 ..      85     270 ..      82     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.028
                      BPD_transp_1 53 ilpviillllsaapyvrli 71
                                      +l +++ll+++++p+v+++
  gi|336254585|ref|YP_004597692.1| 29 ALLGAVLLAYFLVPFVVFV 47
                                      3344444444444444444 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 3.6e-20
                      BPD_transp_1   4 lGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf...........vilsilghlilpviillllsaap 66 
                                       +G+ +a    + ++++++l+   + ++l +P++v ++ll+ v+           ++   l+++  +vi++ ++ aap
  gi|336254585|ref|YP_004597692.1|  85 FGVPLAyvlSRASFRGKRLVEAAVVIPLVVPPIVGGVLLLTVVgrytpigaaaaALGVPLTDSRAGVILAQTFVAAP 161
                                       5555555555999*********************9999999999********97555566777788*********** PP

                      BPD_transp_1  67 yvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtlll 142
                                       y +++ +a+++ ++  l+eaar +G ++ +++r v lP+a   i++g++l+f+++lg++ ++ +++ +p  + t++ 
  gi|336254585|ref|YP_004597692.1| 162 YLVVTAKAGFDGVDPRLEEAARSMGYGPLETIRAVSLPLARNAIAAGIVLTFVRALGEFGATMMVAYNPRtMPTQIR 238
                                       ******************************************************************66658999999 PP

                      BPD_transp_1 143 eailgydyseisnggvlalviavlllnlvadil 175
                                        a+++  + +i   ++lal++++ll ++++++l
  gi|336254585|ref|YP_004597692.1| 239 VAYISEGLEAIV-PIALALLAVTLLAVVAVRAL 270
                                       999999999888.77777777777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2135.13
//
Query:       gi|336254586|ref|YP_004597693.1|  [L=339]
Description: family 1 extracellular solute-binding protein [Halopiger xanaduensis SH-6]
Scores for complete 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-28  100.1   0.2    2.1e-28   99.6   0.2    1.1  1  SBP_bac_11  Bacterial extracellular solute-binding protein
    1.6e-05   25.0   0.0    0.00035   20.6   0.0    2.2  2  SBP_bac_1   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   0.2   2.3e-32   2.1e-28       1     218 [.      42     289 ..      42     291 .. 0.93

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 2.3e-32
                                       .EEEE-SSTHHHHH.HHHHHHHHHH---EEEEESSHHHHHHHHHHH...-SEEEESSH.HHHHHHHHGGGGGGG-EE CS
                        SBP_bac_11   1 ltvaaagslaaalr.elaaaFeahtgvkvevsaggsgklarqiadga.rpDvwipassawlellaaaglvqaesavp 75 
                                       ++v++agsla +l+  + +aF+++tg+ +e+++ gs++++r+++dg+ rpDv i+a+ + l++  + ++++  +  +
  gi|336254586|ref|YP_004597693.1|  42 VRVLSAGSLASVLEnGVGPAFRSETGIGYEGEYHGSNAVVRMVRDGTkRPDVAISADIGLLRDRLRPDYAD--WDLT 116
                                       589***********66******************************99***********************..**** PP

                                       EEEEEEEEEESTT-......TT---SHHHHHHSS-.-EEEE--T-TTTTHH.HHHHGGG--....HHHHHHHHHTEE CS
                        SBP_bac_11  76 lassplviavpkgn......pkkikgwadLlkpgl.klavadPttspsGlaalalleaaga....qellkalekkvv 141
                                       +a + +vi++  ++      +++  + +  +++g  ++a++dP  +p G++a+ l+e a +    +++ +++ ++v 
  gi|336254586|ref|YP_004597693.1| 117 FAANEVVIVYASETalgarlADGEPWYEVFADAGPdEIAISDPDLDPLGYRAVLLFELAARehglEGFRESMLERVY 193
                                       **************66655445666777788888889********************88555555789999999997 PP

                                       EEESSHHHHHHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--...........................EE CS
                        SBP_bac_11 142 klgessrqlltaveageadagivyeseakaaengdkleavylpeglnl.d.......................pldy 194
                                         ++++ qll+ +eag+ + +++y++ a     + +l++ +lp+ +n+ +                       p++y
  gi|336254586|ref|YP_004597693.1| 194 -REPDEAQLLAGLEAGNRACAVAYKNMAV----ERDLPYRTLPDAYNFgNpdyasqyadasyttddgyttrgsPVVY 265
                                       .67889***********************....99************988*************************** PP

                                       EEEEEE-TT--HHHHHHHHHTTSH CS
                        SBP_bac_11 195 paavlkkaakreaAraFlafLrsp 218
                                       +a+v+++++ ++a r+F++fL+s 
  gi|336254586|ref|YP_004597693.1| 266 GATVCTTGDAQAAGREFVDFLASN 289
                                       **********************96 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.015   1.4e+02       2      71 ..      48     102 ..      47     155 .. 0.83
   2 !   20.6   0.0   3.9e-08   0.00035     220     311 ..     195     289 ..     186     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.015
                                       GSHHHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSB CS
                         SBP_bac_1   2 gsltegaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakagll 71 
                                       gsl++   l+  v  af   ++gi  e e+ gs+++       +  G++ +Dv+++        a+ gll
  gi|336254586|ref|YP_004597693.1|  48 GSLAS--VLENGVGPAFRS-ETGIGYEGEYHGSNAVVR----MVRDGTKRPDVAIS--------ADIGLL 102
                                       56666..777778789977.89****************....******888***99........333443 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.9e-08
                                       CSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE...EEEEEEEEBT CS
                         SBP_bac_1 220 nkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi...lgayglaipk 293
                                       + d+a++la +eaG+ a a+++ ++a   ++ +   ++a +  +p+    +a   ++++++++    +++yg ++ +
  gi|336254586|ref|YP_004597693.1| 195 EPDEAQLLAGLEAGNRACAVAYKNMAVERDLPYRTLPDAYNFGNPDYASQYADASYTTDDGYTTrgsPVVYGATVCT 271
                                       5799************************************************************************* PP

                                       TCSTHHHHHHHHHHHTSH CS
                         SBP_bac_1 294 gsknpeaAkkFldfllsp 311
                                       + + ++a ++F+dfl+s+
  gi|336254586|ref|YP_004597693.1| 272 TGDAQAAGREFVDFLASN 289
                                       ****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2484.34
//
Query:       gi|336254587|ref|YP_004597694.1|  [L=186]
Description: molybdopterin-guanine dinucleotide biosynthesis protein B [Halopiger xanaduensis SH-6]
Scores for 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-23   81.3   0.0    1.9e-17   63.4   0.0    2.1  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
    0.00014   22.3   0.1     0.0044   17.4   0.0    2.2  2  AAA_16        AAA ATPase domain
    0.00065   19.3   0.0     0.0012   18.4   0.0    1.5  1  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0045   16.5   0.0     0.0066   15.9   0.0    1.3  1  SRPRB         Signal recognition particle receptor beta subun
     0.0049   16.5   0.0      0.021   14.4   0.0    1.8  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.005   17.4   0.0      0.025   15.1   0.0    1.9  2  AAA_18        AAA domain
     0.0098   15.6   0.0      0.017   14.8   0.0    1.4  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
  ------ inclusion threshold ------
      0.036   14.0   0.0      0.098   12.6   0.0    1.7  2  RsgA_GTPase   RsgA GTPase
      0.045   13.9   0.0       0.11   12.7   0.0    1.7  1  AAA_33        AAA domain
      0.091   13.0   0.0       0.15   12.4   0.0    1.5  2  AAA_22        AAA domain
        0.1   12.3   0.0       0.15   11.8   0.0    1.2  1  AAA_24        AAA domain
        0.1   12.3   0.0       0.21   11.3   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
        0.1   12.7   0.0       0.24   11.5   0.0    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
       0.11   12.7   0.0       0.16   12.2   0.0    1.3  1  Roc           Ras of Complex, Roc, domain of DAPkinase
       0.12   11.4   0.0       0.17   10.9   0.0    1.2  1  T2SSE         Type II/IV secretion system protein
       0.13   12.2   0.0       0.26   11.2   0.0    1.5  1  NACHT         NACHT domain
       0.14   11.6   0.0       0.18   11.2   0.0    1.2  1  TniB          Bacterial TniB protein
       0.14   12.2   0.0       0.25   11.4   0.0    1.3  1  AAA_14        AAA domain
       0.17   11.8   0.0       0.29   11.0   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
       0.17   11.9   0.0       0.26   11.3   0.0    1.3  1  AAA_5         AAA domain (dynein-related subfamily)
       0.17   12.3   0.0       0.24   11.8   0.0    1.3  1  RNA_helicase  RNA helicase
       0.17   11.6   0.0       0.26   11.0   0.0    1.3  1  PRK           Phosphoribulokinase / Uridine kinase family


Domain annotation for each model (and alignments):
>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   2.4e-20   1.9e-17       2      67 ..      12      76 ..      11      92 .. 0.87
   2 !   16.1   0.0   9.9e-06    0.0081      78     109 ..     113     146 ..     103     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 2.4e-20
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlvasker 67
                                      ++++g s+sGKTtL+e+l+p l++ + rv+t+K  hh++++d+pg D++rhr  GA++v+ +++e 
  gi|336254587|ref|YP_004597694.1| 12 VCLAGPSDSGKTTLVEELVPRLAEDD-RVATVKSIHHDIEIDTPGADTHRHRTTGAETVVGITPEL 76
                                      789*******************8765.9******************************98776665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 9.9e-06
                              MobB  78 elsleellarlse..vDlvlvEGfkkealpkiev 109
                                         +l+  l+rl++  +D+vlvEGf +++lp i v
  gi|336254587|ref|YP_004597694.1| 113 MRALASTLERLERrgYDIVLVEGFSASPLPTILV 146
                                       456888899996668***************9977 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.4e-06    0.0044      21      57 ..       4      43 ..       1      74 [. 0.76
   2 ?    2.9   0.0      0.15   1.2e+02       7      34 ..     111     138 ..     110     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.4e-06
                            AAA_16 21 sgrp..elvllsGesGvGKsslvrellralekdg.giflr 57
                                      ++rp  ++v l G+s +GK++lv+el  +l +d+ + +++
  gi|336254587|ref|YP_004597694.1|  4 DSRPrlRAVCLAGPSDSGKTTLVEELVPRLAEDDrVATVK 43
                                      4555669****************99887777774244444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.15
                            AAA_16   7 eeleqLlsalervrsgrpelvllsGesG 34 
                                       +e+++L+s+ler+ + +  +vl+ G s+
  gi|336254587|ref|YP_004597694.1| 111 REMRALASTLERLERRGYDIVLVEGFSA 138
                                       6899**********9999******9886 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 !   18.4   0.0   1.5e-06    0.0012       2      55 ..       8      63 ..       7      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                                      CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH..HHHSTHCHSHHHHHHTSC CS
                          GTP_EFTU  2 rirnigiighvDhGKtTLtdrLlyktgaiskkgeka..eeervlDtlkeErergiT 55
                                      r+r ++++g  D+GKtTL+++L+ ++ ++++ ++++   ++  +Dt  ++  r  T
  gi|336254587|ref|YP_004597694.1|  8 RLRAVCLAGPSDSGKTTLVEELVPRLAEDDRVATVKsiHHDIEIDTPGADTHRHRT 63
                                      5799********************99999998888755445557766666666555 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 !   15.9   0.0   8.1e-06    0.0066       4      40 ..      10      50 ..       7      65 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.1e-06
                                      -EEEEE-STTSSHHHHHHHHHHS....S---B---SS-EEE CS
                             SRPRB  4 pavllvGlsdsGKTslftrLttd....svkktvtSqessaa 40
                                      +av l+G+sdsGKT+l + L           tv S++  + 
  gi|336254587|ref|YP_004597694.1| 10 RAVCLAGPSDSGKTTLVEELVPRlaedDRVATVKSIHHDIE 50
                                      7899***********98866544222277778877765554 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 !   14.4   0.0   2.6e-05     0.021       3      43 ..      12      53 ..      10      72 .. 0.86
   2 ?   -0.3   0.0      0.88   7.1e+02      69      99 ..     116     143 ..     111     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-05
                                      EEEEESTTCCHHHHHHHHH.CT--SS-EEEEESS-SSCHCCC CS
                              cobW  3 tvltGflGsGKTtLlnhll.enraglklavivNefgevsiDa 43
                                      + l+G+  sGKTtL+++l+ + +++ ++a +     +++iD 
  gi|336254587|ref|YP_004597694.1| 12 VCLAGPSDSGKTTLVEELVpRLAEDDRVATVKSIHHDIEIDT 53
                                      67999999************999******9988777777775 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.88
                                       HHHHHHHHHHHHTT-SEEEEEECT.TTTHHHH CS
                              cobW  69 llkelealeereerldviliEttG.laePapv 99 
                                       l  +le+le+r   +d++l+E  G  a+P p 
  gi|336254587|ref|YP_004597694.1| 116 LASTLERLERRG--YDIVLVE--GfSASPLPT 143
                                       566788888888..99***99..445666655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.1e-05     0.025       1      27 [.      12      41 ..      12      64 .. 0.74
   2 ?   -0.2   0.0       1.6   1.3e+03     107     115 ..     120     128 ..     102     143 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf...gvn 27
                                      ++l+G++ +GKttl +eL  rl+    +  
  gi|336254587|ref|YP_004597694.1| 12 VCLAGPSDSGKTTLVEELVPRLAEddrVAT 41
                                      79****************998732355444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
                            AAA_18 107 leRlekRgy 115
                                       leRle+Rgy
  gi|336254587|ref|YP_004597694.1| 120 LERLERRGY 128
                                       456666655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.1e-05     0.017       3      49 ..      11      59 ..       9      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                         PduV-EutP  3 killiGkvgsGKttLtqalkgeelkYkktqaiefsde.v.iDtPGeyle 49
                                       + l G+++sGKttL ++l  +  + ++  +++  ++ + iDtPG   +
  gi|336254587|ref|YP_004597694.1| 11 AVCLAGPSDSGKTTLVEELVPRLAEDDRVATVKSIHHdIeIDTPGADTH 59
                                      68899***************999999888888754331359****7555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012     0.098     100     131 ..      10      43 ..       5      64 .. 0.76
   2 ?   -3.2   0.0       8.6     7e+03      63      82 ..     114     133 ..     109     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                       SEEEEECSTTSSHHHHHHHHCTT-..----S--- CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpel..elktgevs 131
                                       + ++l+G+S  GK+tL+++l+p+l  + +++ v+
  gi|336254587|ref|YP_004597694.1|  10 RAVCLAGPSDSGKTTLVEELVPRLaeDDRVATVK 43 
                                       5689******************742255555554 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.6
                                       HHHHHHHHHHHHTTSEEEE- CS
                       RsgA_GTPase  63 eeleelkeelealgyevllv 82 
                                       ++l ++ e+le+ gy+++lv
  gi|336254587|ref|YP_004597694.1| 114 RALASTLERLERRGYDIVLV 133
                                       45677788888888888876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013      0.11       3      25 ..      13      40 ..      12     140 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                            AAA_33  3 llvGlpGsGKstlaerllkklg.....a 25
                                       l G++ sGK+tl+e+l+ +l+     a
  gi|336254587|ref|YP_004597694.1| 13 CLAGPSDSGKTTLVEELVPRLAeddrvA 40
                                      678**************97666644431 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00018      0.15       8      37 ..      12      41 ..       8     133 .. 0.78
   2 ?   -2.2   0.0       5.7   4.6e+03     108     129 ..     119     147 ..     108     150 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaee 37
                                      +++ G+s +GKTtl+++l+ +l e+   ++
  gi|336254587|ref|YP_004597694.1| 12 VCLAGPSDSGKTTLVEELVPRLAEDDRVAT 41
                                      6899***************99976444433 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.7
                            AAA_22 108 aleeL.rsllnl......srkgvqliLvG 129
                                        le L r+ +++      s ++++ iLvG
  gi|336254587|ref|YP_004597694.1| 119 TLERLeRRGYDIvlvegfSASPLPTILVG 147
                                       45555555555566666677778888887 PP

>> AAA_24  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      0.15       5      27 ..      12      34 ..       9      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                            AAA_24  5 iliyGpsgiGKTtlakelgpkpl 27
                                      +++ Gps +GKTtl+ el p+ +
  gi|336254587|ref|YP_004597694.1| 12 VCLAGPSDSGKTTLVEELVPRLA 34
                                      89***************966654 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   0.00026      0.21      24      39 ..      11      26 ..       2      32 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                            AAA_29 24 atlltGpsGsGKSTll 39
                                      a+ l+Gps sGK+Tl+
  gi|336254587|ref|YP_004597694.1| 11 AVCLAGPSDSGKTTLV 26
                                      5789***********8 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00029      0.24       2      55 ..      12      55 ..      11      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                                      EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGG CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpG 55
                                      v+++G + +GK+tL+  l+ + a  +d   +T + +++ ++        +DtpG
  gi|336254587|ref|YP_004597694.1| 12 VCLAGPSDSGKTTLVEELVPRLA--EDDRVATVKSIHHDIE--------IDTPG 55
                                      899****************8744..5566667777777666........56666 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.16       2      36 ..      12      46 ..      11      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEE CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdf 36
                                      v+l G s +GKt+l++++v +  ++++ +t+    
  gi|336254587|ref|YP_004597694.1| 12 VCLAGPSDSGKTTLVEELVPRLAEDDRVATVKSIH 46
                                      7899***************9999999988876544 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 ?   10.9   0.0   0.00021      0.17     132     163 ..      12      42 ..       6      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                             T2SSE 132 ilvsGgTgsGKttllyallkeinksderivtv 163
                                       + ++G+  sGKttl+  l+  ++++ +r+ tv
  gi|336254587|ref|YP_004597694.1|  12 VCLAGPSDSGKTTLVEELVPRLAED-DRVATV 42 
                                       6789*******************99.899887 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   0.00031      0.26       1      28 [.      10      37 ..      10      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                                      SCEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklalawaegk 28
                                      r v+l G++ sGKTtL+++l+  +ae++
  gi|336254587|ref|YP_004597694.1| 10 RAVCLAGPSDSGKTTLVEELVPRLAEDD 37
                                      6799*****************9999876 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.18      30      57 ..       4      31 ..       1      60 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                              TniB 30 pkrkrmpnlllvGdsnnGKtmivekFar 57
                                       +r r + + l+G+s+ GKt++ve+   
  gi|336254587|ref|YP_004597694.1|  4 DSRPRLRAVCLAGPSDSGKTTLVEELVP 31
                                      5689999****************98764 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    0.0003      0.25       4      37 ..      11      43 ..       9      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyin 37
                                      ++++ G+  +GKTtl+++l+ +l  +++++  ++
  gi|336254587|ref|YP_004597694.1| 11 AVCLAGPSDSGKTTLVEELVPRLA-EDDRVATVK 43
                                      7899***************97776.666666555 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 ?   11.0   0.0   0.00035      0.29      25      51 ..      14      39 ..       5      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                          ATPase_2 25 iYGpegsGKtaLlkeiienledkdkyv 51
                                      + Gp  sGKt+L+ e++ +l + d +v
  gi|336254587|ref|YP_004597694.1| 14 LAGPSDSGKTTLVEELVPRLAEDD-RV 39
                                      56*****************97644.44 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 ?   11.3   0.0   0.00032      0.26       2      37 ..      12      50 ..      11      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                                      EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT-- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtt 37
                                      v+L Gp+ +gK++l+e+l  +l    r  +++ ++ d++
  gi|336254587|ref|YP_004597694.1| 12 VCLAGPSDSGKTTLVEELVPRLaedDRVATVKSIHHDIE 50
                                      9*******************9999777777788888776 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    0.0003      0.24       1      25 [.      12      36 ..      12      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                      ++l Gps  GK+tl++eL+ +l+++
  gi|336254587|ref|YP_004597694.1| 12 VCLAGPSDSGKTTLVEELVPRLAED 36
                                      6899***************999954 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00032      0.26       3      55 ..      13      65 ..      11      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                               PRK  3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkr 55
                                       +ag+S +Gktt+ ++l+ ++++    a++     ++++d    d++ ++  +
  gi|336254587|ref|YP_004597694.1| 13 CLAGPSDSGKTTLVEELVPRLAEDDRVATVKSIHHDIEIDTPGADTHRHRTTG 65
                                      689*******************9888877777777788887777777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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):              22  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1354.83
//
Query:       gi|336254588|ref|YP_004597695.1|  [L=280]
Description: anaerobic dehydrogenase-like protein [Halopiger xanaduensis SH-6]
Scores for 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   0.2    1.4e-19   70.4   0.3    1.6  2  Nitrate_red_del  Nitrate reductase delta subunit


Domain annotation for each model (and alignments):
>> Nitrate_red_del  Nitrate reductase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.14   2.6e+03      59      79 ..      19      39 ..      13      47 .. 0.79
   2 !   70.4   0.3   7.9e-24   1.4e-19       6     136 ..      51     183 ..      30     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.14
                   Nitrate_red_del 59 llfgestlevrefyrqaglev 79
                                      l f+++t ++re++++ ++++
  gi|336254588|ref|YP_004597695.1| 19 LAFDRPTDDLREAMESDEFDE 39
                                      568899999999998877765 PP

  == domain 2  score: 70.4 bits;  conditional E-value: 7.9e-24
                   Nitrate_red_del   6 aeveealaelaeal.....aa..ededllelaaeYtrLFlgpgrrsasPyesvYlsekkgllfgestlevrefyrqa 75 
                                       ++++ea       +     ++  + ++ ++    Y++LF   +++++  ye  Y  ++   ++ ++ ++++ fy ++
  gi|336254588|ref|YP_004597695.1|  51 DDLREA-------AetvaaESpnDPDAIEDCYSTYAALFGFEQGGEIQQYEVEYGPGTL-VTNTDKLADIAGFYGAF 119
                                       334443.......2444442246999*************999**************444.6677777********** PP

                   Nitrate_red_del  76 glevaeefneppDHlaveLeflahLaereaeaeea...eeaealleaqkafleehllpWlpefa 136
                                       +l+ +e+ +e  DHl+veLef++hLa ++a   e+   +  e + +aq++fle+hl +Wlp+f 
  gi|336254588|ref|YP_004597695.1| 120 DLDLEEGNRERVDHLCVELEFVSHLALQTAYLAETgdeKGVEIVTNAQADFLEDHLGRWLPRFR 183
                                       *******************************98889988889999******************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2048.61
//
Query:       gi|336254589|ref|YP_004597696.1|  [L=397]
Description: Selenate reductase [Halopiger xanaduensis SH-6]
Scores for 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-32  109.6   7.0    6.9e-32  109.6   7.0    1.8  2  Fer4_11   4Fe-4S dicluster domain
      2e-07   31.5  18.3    8.6e-05   23.1   7.0    3.5  3  Fer4_7    4Fe-4S dicluster domain
    1.5e-05   25.0  21.2     0.0018   18.3   7.4    3.3  3  Fer4_10   4Fe-4S dicluster domain
    1.5e-05   25.0  16.7      0.016   15.4   5.1    3.4  4  Fer4_9    4Fe-4S dicluster domain
    0.00041   20.3  23.4      0.013   15.6   1.2    4.6  4  Fer4_2    4Fe-4S binding domain
    0.00066   19.4  18.9      0.036   13.9   0.9    4.7  4  Fer4      4Fe-4S binding domain
    0.00098   19.2  20.2      0.019   15.1   0.7    3.3  3  Fer4_21   4Fe-4S dicluster domain
     0.0014   19.1   8.4      0.061   13.9   0.2    3.7  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0076   16.3  25.4       0.27   11.4   0.7    4.6  4  Fer4_6    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.31   12.0  16.5        4.9    8.2   0.7    3.7  3  Fer4_16   4Fe-4S double cluster binding domain
        0.4   11.2   0.0        0.4   11.2   0.0    3.9  2  Fer4_8    4Fe-4S dicluster domain
       0.55   10.8  19.4       0.75   10.4   0.1    3.9  4  Fer4_17   4Fe-4S dicluster domain
        1.8    8.8   9.3         31    4.8   0.0    2.5  2  Fer4_18   4Fe-4S dicluster domain
          2    8.6   8.4      0.056   13.5   1.3    2.1  1  Fer4_19   Divergent 4Fe-4S mono-cluster


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       3.4   4.4e+03      70      75 ..      34      39 ..      16      52 .. 0.62
   2 !  109.6   7.0   5.4e-35   6.9e-32       2      99 ..     163     259 ..     162     260 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.4
                           Fer4_11 70 kCdmcl 75
                                      kC  c 
  gi|336254589|ref|YP_004597696.1| 34 KCIACQ 39
                                      444442 PP

  == domain 2  score: 109.6 bits;  conditional E-value: 5.4e-35
                           Fer4_11   2 ewlflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrv 78 
                                       ++++lp+ C+hC+ ++C+  +p++ai+k++e+G+Vllde++++ +++e+v+acPy +  +n  +++++kC +c+++v
  gi|336254589|ref|YP_004597696.1| 163 WFFYLPRVCNHCTFAACAGGCPVQAIYKRQEDGIVLLDEESCQ-SFQECVRACPYGKSIYNPVEMNSQKCVGCYPKV 238
                                       5799**************************************8.********************************* PP

                           Fer4_11  79 eaGllpacvescptgalnfgd 99 
                                       e+Gl+p+c+e+c ++++++g+
  gi|336254589|ref|YP_004597696.1| 239 EQGLVPQCFENCLGKIRMHGW 259
                                       *****************9986 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.4   0.00034      0.44      31      50 ..      28      47 ..       8      56 .. 0.75
   2 !   23.1   7.0   6.7e-08   8.6e-05       2      51 ..     171     217 ..     170     218 .. 0.90
   3 ?    3.7   0.1     0.072        92      31      48 ..     224     250 ..     221     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00034
                            Fer4_7 31 veidpekClgCgaCvavCPt 50
                                      +++d +kC+ C+ C   C t
  gi|336254589|ref|YP_004597696.1| 28 AVFDLNKCIACQTCSLSCKT 47
                                      46788899999999999976 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 6.7e-08
                            Fer4_7   2 CigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       C +C   aC+  Cpv+ai+ ++e   +    v +d+e+C++ ++Cv++CP+g
  gi|336254589|ref|YP_004597696.1| 171 CNHCTfaACAGGCPVQAIYKRQE---D--GIVLLDEESCQSFQECVRACPYG 217
                                       ****766************9886...4..48999****************97 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.072
                            Fer4_7  31 veidpekClgCg.........aCvavC 48 
                                       ve++++kC+gC+         +C + C
  gi|336254589|ref|YP_004597696.1| 224 VEMNSQKCVGCYpkveqglvpQCFENC 250
                                       577888999995444444444677766 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.3   7.3e-05     0.094       3      25 ..      29      51 ..      27      71 .. 0.72
   2 !   18.3   7.4   1.4e-06    0.0018       6      56 .]     168     215 ..     165     215 .. 0.95
   3 !   13.4   5.8     5e-05     0.064       2      55 ..     197     250 ..     196     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-05
                           Fer4_10  3 vidddtCirCgkCvkaCPadlts 25
                                      v+d ++Ci C++C  +C +++t+
  gi|336254589|ref|YP_004597696.1| 29 VFDLNKCIACQTCSLSCKTTWTN 51
                                      7899*************443333 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.4e-06
                           Fer4_10   6 ddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +  C +C+  +C   CP+     +a++++ e++ v  + e+C+   +Cv+aCP
  gi|336254589|ref|YP_004597696.1| 168 PRVCNHCTfaACAGGCPV-----QAIYKRQEDGIVLLDEESCQSFQECVRACP 215
                                       578*****99********.....9****************************9 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 5e-05
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgc......g...aCveaC 55 
                                       v +d+++C   ++Cv+aCP+          +s+ ++v+ +++kC gc      g   +C e C
  gi|336254589|ref|YP_004597696.1| 197 VLLDEESCQSFQECVRACPY---------GKSIYNPVEMNSQKCVGCypkveqGlvpQCFENC 250
                                       67899***************.........8889999999999999995555542566888888 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.3   6.2e-05      0.08       1      16 [.      34      49 ..      13      67 .. 0.72
   2 !   15.4   5.1   1.2e-05     0.016       2      49 ..     171     217 ..     170     220 .. 0.89
   3 ?    4.3   7.4     0.035        45       2      46 ..     204     250 ..     203     254 .. 0.78
   4 ?    2.6   0.3      0.12   1.5e+02       1      24 [.     230     262 ..     230     271 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.2e-05
                            Fer4_9  1 kCtgCgaCveaCpagv 16
                                      kC+ C++C  +C+++ 
  gi|336254589|ref|YP_004597696.1| 34 KCIACQTCSLSCKTTW 49
                                      5777777777775544 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.2e-05
                            Fer4_9   2 CtgCg..aCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       C+ C+  aC   Cp +++ +++  +++ l+++   +C + ++Cv aCp g
  gi|336254589|ref|YP_004597696.1| 171 CNHCTfaACAGGCPVQAIYKRQEDGIVLLDEE---SCQSFQECVRACPYG 217
                                       99**6447******************999764...8************85 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.035
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.........CveaC 46 
                                       C + ++Cv+aCp+g  ++  +e   +       +C+gC           C+e C
  gi|336254589|ref|YP_004597696.1| 204 CQSFQECVRACPYGKSIYNPVEMNSQ-------KCVGCYPkveqglvpqCFENC 250
                                       444467*******9988888776655.......5****9888888888888888 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.12
                            Fer4_9   1 kCtgC.........gaCveaCpagvvvedaaer 24 
                                       kC+gC          +C e C  ++ +  +++r
  gi|336254589|ref|YP_004597696.1| 230 KCVGCypkveqglvPQCFENCLGKIRMHGWVNR 262
                                       699996666665554599999666665555544 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.2   9.8e-06     0.013       3      21 ..      28      46 ..      26      47 .. 0.89
   2 !    7.1   2.5    0.0049       6.2       4      21 ..     165     184 ..     164     185 .. 0.86
   3 ?    4.5   0.2     0.034        43      14      22 .]     208     216 ..     196     216 .. 0.71
   4 ?    6.1   0.7      0.01        13       2      14 ..     223     235 ..     222     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.8e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      +v+d ++Ci+C +C  +C 
  gi|336254589|ref|YP_004597696.1| 28 AVFDLNKCIACQTCSLSCK 46
                                      689************9996 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0049
                            Fer4_2   4 vvdtdrCigCg..aCvsaCP 21 
                                       ++ ++ C++C   aC   CP
  gi|336254589|ref|YP_004597696.1| 165 FYLPRVCNHCTfaACAGGCP 184
                                       68899*****777******9 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.034
                            Fer4_2  14 gaCvsaCPa 22 
                                         Cv aCP+
  gi|336254589|ref|YP_004597696.1| 208 QECVRACPY 216
                                       47******5 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.01
                            Fer4_2   2 pvvvdtdrCigCg 14 
                                       pv+ ++++C+gC 
  gi|336254589|ref|YP_004597696.1| 223 PVEMNSQKCVGCY 235
                                       57889*******7 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.9   2.8e-05     0.036       2      19 ..      29      46 ..      28      47 .. 0.90
   2 ?    5.1   1.2     0.016        21      13      24 .]     178     189 ..     177     189 .. 0.92
   3 !    7.4   0.3    0.0031       3.9      13      21 ..     209     217 ..     197     217 .. 0.81
   4 ?    3.4   0.1      0.06        76       4      11 ..     227     234 ..     224     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                                      EEETTTSSS-THHHHHST CS
                              Fer4  2 videekCigCGaCvevCP 19
                                      v+d +kCi+C +C   C 
  gi|336254589|ref|YP_004597696.1| 29 VFDLNKCIACQTCSLSCK 46
                                      89************9995 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                                       HHHHHSTTTEEE CS
                              Fer4  13 aCvevCPvgAIt 24 
                                       aC+  CPv AI+
  gi|336254589|ref|YP_004597696.1| 178 ACAGGCPVQAIY 189
                                       7*********96 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0031
                                       HHHHHSTTT CS
                              Fer4  13 aCvevCPvg 21 
                                       +Cv +CP+g
  gi|336254589|ref|YP_004597696.1| 209 ECVRACPYG 217
                                       7******97 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.06
                                       ETTTSSS- CS
                              Fer4   4 deekCigC 11 
                                       +  kC+gC
  gi|336254589|ref|YP_004597696.1| 227 NSQKCVGC 234
                                       778***** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.7   1.5e-05     0.019       1      21 [.      28      48 ..      28      60 .. 0.89
   2 !   11.9   5.4   0.00015      0.19      11      54 ..     171     217 ..     168     222 .. 0.71
   3 ?    1.8   0.5       0.2   2.6e+02      35      44 ..     225     234 ..     220     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                           Fer4_21  1 AridedkCigCgkCliaCedt 21
                                      A++d +kCi C+ C ++C++t
  gi|336254589|ref|YP_004597696.1| 28 AVFDLNKCIACQTCSLSCKTT 48
                                      77899*************976 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00015
                           Fer4_21  11 CgkCl.iaCedts.hqaieidaktvlkv.vedeCvGCnlCssvCPve 54 
                                       C++C+  aC  ++ +qai + ++  + +  e++C   + C+  CP  
  gi|336254589|ref|YP_004597696.1| 171 CNHCTfAACAGGCpVQAIYKRQEDGIVLlDEESCQSFQECVRACPYG 217
                                       666641356554438***87777666551699*************75 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.2
                           Fer4_21  35 kvvedeCvGC 44 
                                       ++ +++CvGC
  gi|336254589|ref|YP_004597696.1| 225 EMNSQKCVGC 234
                                       4567889999 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 !   13.9   0.2   4.8e-05     0.061       2      31 ..      31      60 ..      30      78 .. 0.86
   2 ?    1.8   0.3      0.28   3.6e+02      48      56 ..     180     188 ..     172     190 .. 0.80
   3 ?    6.2   0.2     0.012        15       2      17 ..     200     215 ..     199     217 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                           Fer4_13  2 DrdtCiacgaCvelaPdvFeeddeggasvv 31
                                      D ++Ciac++C   +  +   ++ +++++ 
  gi|336254589|ref|YP_004597696.1| 31 DLNKCIACQTCSLSCKTTWTNNEGQEHMFW 60
                                      7789****************9998877664 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.28
                           Fer4_13  48 adaCPvesI 56 
                                       a +CPv++I
  gi|336254589|ref|YP_004597696.1| 180 AGGCPVQAI 188
                                       458*****9 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.012
                           Fer4_13   2 DrdtCiacgaCvelaP 17 
                                       D+++C + + Cv ++P
  gi|336254589|ref|YP_004597696.1| 200 DEESCQSFQECVRACP 215
                                       89*************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 !   11.4   0.7   0.00021      0.27       2      20 ..      28      46 ..      28      51 .. 0.92
   2 ?    2.4   4.4      0.14   1.8e+02       9      24 .]     171     188 ..     168     188 .. 0.86
   3 !    8.1   0.4    0.0023         3      14      22 ..     209     217 ..     200     220 .. 0.84
   4 !    7.8   0.8    0.0028       3.6       2      14 ..     224     236 ..     223     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                            Fer4_6  2 veidpdkCigCgdCvrvCP 20
                                      +++d +kCi C  C   C 
  gi|336254589|ref|YP_004597696.1| 28 AVFDLNKCIACQTCSLSCK 46
                                      68*************9996 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.14
                            Fer4_6   9 CigCgd..CvrvCPegai 24 
                                       C++C    C+  CP +ai
  gi|336254589|ref|YP_004597696.1| 171 CNHCTFaaCAGGCPVQAI 188
                                       999966689999*****8 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0023
                            Fer4_6  14 dCvrvCPeg 22 
                                       +Cvr+CP+g
  gi|336254589|ref|YP_004597696.1| 209 ECVRACPYG 217
                                       7******97 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0028
                            Fer4_6   2 veidpdkCigCgd 14 
                                       ve + +kC+gC++
  gi|336254589|ref|YP_004597696.1| 224 VEMNSQKCVGCYP 236
                                       899********97 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 ?    5.9   0.2      0.02        25       1      14 [.      34      47 ..       3      68 .. 0.74
   2 ?    8.2   0.7    0.0038       4.9       2      22 ..     171     193 ..     170     202 .. 0.80
   3 ?    4.9   4.3      0.04        51       2      32 ..     204     233 ..     203     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                           Fer4_16  1 rCgtCgkCaevCPt 14
                                      +C+ C+ C  +C t
  gi|336254589|ref|YP_004597696.1| 34 KCIACQTCSLSCKT 47
                                      36666666666655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0038
                           Fer4_16   2 CgtCgk..CaevCPtnaikekke 22 
                                       C  C+   Ca  CP++ai +++e
  gi|336254589|ref|YP_004597696.1| 171 CNHCTFaaCAGGCPVQAIYKRQE 193
                                       88887444**********98855 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.04
                           Fer4_16   2 CgtCgkCaevCPtna.ikekkekeiearecis 32 
                                       C++ ++C+ +CP +  i ++   e+++++c+ 
  gi|336254589|ref|YP_004597696.1| 204 CQSFQECVRACPYGKsIYNP--VEMNSQKCVG 233
                                       9999********96437777..6777777765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00031       0.4       2      17 ..      32      47 ..      18      90 .. 0.81
   2 ?   -2.5  11.1       5.6   7.2e+03       5      63 ..     171     216 ..     168     218 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                            Fer4_8  2 lekCieCgaCqsaCpv 17
                                      l+kCi C+ C  +C +
  gi|336254589|ref|YP_004597696.1| 32 LNKCIACQTCSLSCKT 47
                                      6788888888888853 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.6
                            Fer4_8   5 CieCg..aCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       C++C   aC   Cpv    k+       e  +  +  ++       +sC++ ++C+++Cp 
  gi|336254589|ref|YP_004597696.1| 171 CNHCTfaACAGGCPVQAIYKRQ------E-DG-IVLLDE-------ESCQSFQECVRACPY 216
                                       6666444666666644333221......1.12.333344.......689999999999996 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00058      0.75       1      18 [.      34      51 ..       5      74 .. 0.74
   2 ?    6.0   1.0     0.014        18       2      24 ..     171     195 ..     170     201 .. 0.86
   3 ?    6.8   1.0    0.0078        10      44      59 ..     202     217 ..     199     219 .. 0.90
   4 ?   -2.6   0.5       6.8   8.6e+03      45      49 ..     230     234 ..     224     255 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00058
                           Fer4_17  1 rCiqCgyClpeCpsyeay 18
                                      +Ci C+ C  +C + + +
  gi|336254589|ref|YP_004597696.1| 34 KCIACQTCSLSCKTTWTN 51
                                      466666666666665554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.014
                           Fer4_17   2 CiqCgy..ClpeCpsyeaydnepkk 24 
                                       C++C +  C+  Cp  ++y+ +++ 
  gi|336254589|ref|YP_004597696.1| 171 CNHCTFaaCAGGCPVQAIYKRQEDG 195
                                       ****9777********999988765 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0078
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                       ++C + +eC+r+CP+g
  gi|336254589|ref|YP_004597696.1| 202 ESCQSFQECVRACPYG 217
                                       5899**********96 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 6.8
                           Fer4_17  45 lCieC 49 
                                       +C++C
  gi|336254589|ref|YP_004597696.1| 230 KCVGC 234
                                       44444 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.024        31      59      74 ..      33      48 ..       4      59 .. 0.76
   2 ?    4.3   6.4     0.034        43      57      92 ..     200     235 ..     171     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.024
                           Fer4_18 59 gdcidcescvkvcPtg 74
                                      ++ci+c++c   c t 
  gi|336254589|ref|YP_004597696.1| 33 NKCIACQTCSLSCKTT 48
                                      5677777777777665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.034
                           Fer4_18  57 gagdcidcescvkvcPtgidirkGlqleciscllci 92 
                                       ++  c + + cv+ cP g  i + + ++  +c  c 
  gi|336254589|ref|YP_004597696.1| 200 DEESCQSFQECVRACPYGKSIYNPVEMNSQKCVGCY 235
                                       56789999*******************999998885 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 ?   13.5   1.3   4.4e-05     0.056      12      57 ..     168     217 ..     165     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.4e-05
                           Fer4_19  12 relCihsgn..Cvkglp..evFdpkrkpwikpdeasteeiievverCPSG 57 
                                       + +C+h ++  C  g p  ++++ ++++++  de+s ++ +e v+ CP G
  gi|336254589|ref|YP_004597696.1| 168 PRVCNHCTFaaCAGGCPvqAIYKRQEDGIVLLDEESCQSFQECVRACPYG 217
                                       67899876433887654338****************************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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):              14  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3010.97
//
Query:       gi|336254590|ref|YP_004597697.1|  [L=1188]
Description: molybdopterin oxidoreductase [Halopiger xanaduensis SH-6]
Scores for complete 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-34  119.4   0.1      4e-30  105.1   0.0    2.2  2  Molybdopterin    Molybdopterin oxidoreductase
    0.00016   21.7   0.3    0.00087   19.3   0.0    2.4  3  Molydop_binding  Molydopterin dinucleotide binding domain
     0.0062   16.5   0.1      0.017   15.1   0.1    1.8  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   1.2e-05     0.074       1      41 [.     149     211 ..     149     215 .. 0.96
   2 !  105.1   0.0   6.7e-34     4e-30      70     406 ..     281     735 ..     256     743 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.2e-05
                                       B--S-EEEC......................TTTTTSEEEE--HHHHHHHHHHHHHHHHHHCS CS
                     Molybdopterin   1 RlkyPmvRk......................qargeGkFvrvsWdeAleliaaslkytikkyg 41 
                                       R+k Pm+R                        +rge++Fv+vs +eA e+ a+ ++++ ++y 
  gi|336254590|ref|YP_004597697.1| 149 RVKAPMIREgfkqwvddgfprdddgsmpteyAQRGEDDFVEVSQEEAHEYAAQTFLELAQQYS 211
                                       9******************************99************************999986 PP

  == domain 2  score: 105.1 bits;  conditional E-value: 6.7e-34
                                       T-EEE-BEECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEE CS
                     Molybdopterin  70 ggknlsfydwyadlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakviv 146
                                       g   l +y+   dlpp+++   ++   + ++    +l+++e +d i+l G N  +  + +  + + +a+ k+ k+  
  gi|336254590|ref|YP_004597697.1| 281 GAMGLDNYSFHTDLPPGHT---MV---TGQQTVDFDLASIEYADHIVLDGINYLTSKMAD-CHWLTEAKLKGSKLTG 350
                                       55558899999*****995...33...33445677788***************9999999.8999888888899999 PP

                                       ECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCS........... CS
                     Molybdopterin 147 igpryaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleee........... 212
                                       i ++y+++++++de + ++p+td al+l+ + vi+++ ++d+      +y+++ td pllv  +++           
  gi|336254590|ref|YP_004597697.1| 351 IFTDYNATASKCDELITVRPATDSALFLGAARVIMEQELYDT------EYVRKHTDLPLLVRMDDNellrasdvfsd 421
                                       99999999**********************************......*************999988********** PP

                                       ............................................................................. CS
                     Molybdopterin 213 ............................................................................. 212
                                                                                                                    
  gi|336254590|ref|YP_004597697.1| 422 yepadlekteavaddadrpgvdvtdiddqviteelrrewgdfvvrndesgefesvtrddvgddfdvpatiegefeve 498
                                       ***************************************************************************** PP

                                       ............................HHHHHHCCHHHHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHH CS
                     Molybdopterin 213 ............................tgkkkevvariarelarnaaktagksmiivGaglnhrqdgdaiyravin 261
                                                                   t++ ++   + + +la+++a+++++ m + G+g nh ++ d++ ra++ 
  gi|336254590|ref|YP_004597697.1| 499 ladgstvevrtvfdlikehltetwdlesTAEVTGTDPQAVENLAQDFADNQQSTMLLTGMGPNHYANADQHGRAAFL 575
                                       ***************************************************************************** PP

                                       HHHHCTHCSSTTCEEEEESS...CTTHHHCHHHHTCCTTCCCCCCCTT...................HHHHHCCCT. CS
                     Molybdopterin 262 LallvgnvgqpgGgwahlnG...qlilagaaekvgalpvllsvkslke...................ekikfaaeq. 315
                                       La l+ nvg + G+++++ G     +++g ++ + + p +++ +   e                   + +k+  e  
  gi|336254590|ref|YP_004597697.1| 576 LASLTRNVGYQTGNVGSYSGnyrMAYFNGVGQYANEDPFDPELDPDAEartdkrwdahsahfytnldKPLKVDGEYf 652
                                       ********************555346667777777777777766666677777777766666667654444444433 PP

                                       TTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHH..CSSEEEEEESCSSHHHHTSSEEEEBE CS
                     Molybdopterin 316 pgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekale..kldlvvvldgrltstalyaDiiLPaa 390
                                       +g+   +++ ++++ s   +        +lg  +       + +ekal+  + +++ + +  ++ t++y+Di++Pa 
  gi|336254590|ref|YP_004597697.1| 653 QGDSHMHTPTKSIWVSGSNS--------ILG--NAK--GAYKIIEKALRtgDIEAFFTNEWWWSMTCEYSDIVFPAD 717
                                       67777777777777665444........233..111..222222334444499************************ PP

                                       -CCGSE..EEEE-TTSEE CS
                     Molybdopterin 391 twyEke..dlytndegrf 406
                                       +w E++  d++ +   +f
  gi|336254590|ref|YP_004597697.1| 718 SWAEHHvhDITASVTNPF 735
                                       ****75115555555555 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.1   6.3e+03      20      42 ..     176     198 ..     173     200 .. 0.75
   2 ?   -3.5   0.0       1.7     1e+04      43      54 ..     498     509 ..     496     511 .. 0.86
   3 !   19.3   0.0   1.4e-07   0.00087      28      53 ..     989    1013 ..     971    1016 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                                       CCHHHHCSSS-EEEEEHHHHHHH CS
                   Molydop_binding  20 pvlrlakpepevveinpedAaal 42 
                                       p++++++ e+++ve+++e A ++
  gi|336254590|ref|YP_004597697.1| 176 PTEYAQRGEDDFVEVSQEEAHEY 198
                                       55666666669******999876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.7
                                       T--TT-EEEEEE CS
                   Molydop_binding  43 GikdGdlVeves 54 
                                       +++dG +Vev++
  gi|336254590|ref|YP_004597697.1| 498 ELADGSTVEVRT 509
                                       799*******97 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 1.4e-07
                                        SS-EEEEEHHHHHHHT--TT-EEEEE CS
                   Molydop_binding   28 epevveinpedAaalGikdGdlVeve 53  
                                        e  +ve+npedA++ +++dGd V+v 
  gi|336254590|ref|YP_004597697.1|  989 E-GYVEMNPEDAREEDLQDGDYVWVD 1013
                                        3.59********************95 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.9e-06     0.017      13      55 .]      92     146 ..      85     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.9e-06
                                       T--EEEEEEETTEEE............EEEE-TTSTTTTT---HHHHTCHHCCCB CS
                    Molybdop_Fe4S4  13 vgCglevhvkdgkiv............kvegdpdhpvnegrlCvKGrtllervyn 55 
                                        +C le++vk+g+i+              +g+++++    r+C KG ++ er yn
  gi|336254590|ref|YP_004597697.1|  92 HNCYLEATVKNGQITrlgpsmnygeatDLQGNQSSQRWDPRVCNKGLAMVERFYN 146
                                       68**********************99999****999999************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 0.73u 0.28s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 7600.07
//
Query:       gi|336254591|ref|YP_004597698.1|  [L=433]
Description: ParA/MinD ATPase-like protein [Halopiger xanaduensis SH-6]
Scores for 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-51  173.8   0.0    5.3e-51  173.4   0.0    1.1  1  ParA            NUBPL iron-transfer P-loop NTPase
    5.5e-11   42.6   0.0    9.9e-11   41.8   0.0    1.5  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    6.7e-07   29.4   1.0    1.9e-06   27.9   0.4    1.8  2  AAA_31          AAA domain
    0.00036   19.9   0.3    0.00057   19.2   0.3    1.2  1  MipZ            ATPase MipZ
     0.0025   17.1   0.1     0.0064   15.8   0.1    1.6  2  VirC1           VirC1 protein
     0.0029   16.9   0.8     0.0044   16.2   0.8    1.2  1  ArsA_ATPase     Anion-transporting ATPase
     0.0054   16.9   1.4     0.0054   16.9   1.4    2.9  3  FeS_assembly_P  Iron-sulfur cluster assembly protein
     0.0063   16.0   0.4      0.013   15.0   0.2    1.5  2  CBP_BcsQ        Cellulose biosynthesis protein BcsQ
  ------ inclusion threshold ------
      0.012   14.7   0.2      0.018   14.2   0.2    1.2  1  LpxK            Tetraacyldisaccharide-1-P 4'-kinase
      0.024   14.4   0.3       0.21   11.4   0.2    2.2  2  AAA_26          AAA 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 !  173.4   0.0     3e-54   5.3e-51       2     222 ..      99     316 ..      98     336 .. 0.87

  Alignments for each domain:
  == domain 1  score: 173.4 bits;  conditional E-value: 3e-54
                              ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqs.ekkliPveakgikvmS 77 
                                       v ++iav S+KGGVGK+tv+v+lA aL++ gl+vg++Da +y p+ p+ll++e+  +++s + k +Pve++gi+v+S
  gi|336254591|ref|YP_004597698.1|  99 VDSIIAVGSAKGGVGKTTVTVSLARALSEAGLDVGVFDANVYAPDAPDLLEAEGP-VQSSpSGKPMPVEVDGIQVVS 174
                                       789***************************************************7.4555477899*********** PP

                              ParA  78 igfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvk 154
                                       i+++ e  d +v wrG+m++ ++k+ll d++w++ D+L++DlPPG gD+  t++q+ pl+g ++V+tp +  +  ++
  gi|336254591|ref|YP_004597698.1| 175 IELIAE--DGPVAWRGAMVHDVVKDLLGDAAWDDRDVLLVDLPPGIGDAVYTIVQQAPLDGGLLVSTPTDEGVRATQ 249
                                       **9998..********************************************************************* PP

                              ParA 155 kaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdeg 222
                                       +++++++  +v+ +Gvv N+ g v +  g   +   +  ++++ e+  +  l  +p+dp++re +++ 
  gi|336254591|ref|YP_004597698.1| 250 RTAALYTANDVPTVGVVPNVVGSVADAAGPFDDADPETIADDVVEA-AYADLEPVPFDPALREPTEAS 316
                                       ********************99999876655554444444444443.445577888888888877654 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 !   41.8   0.0   5.5e-14   9.9e-11       1      85 [.     103     271 ..     103     314 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 5.5e-14
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ia+ s kGGvGKTt++++Laral+++gl+V ++Da + a+ +  l   e+ ++                        
  gi|336254591|ref|YP_004597698.1| 103 IAVGSAKGGVGKTTVTVSLARALSEAGLDVGVFDANVYAPDAPDLLEAEGPVQSspsgkpmpvevdgiqvvsielia 179
                                       7899*********************************9999885555555554477788888888888888887888 PP

                                       ................................................................CCHCCCHHHHHHC CS
                                       ................................................................xxxxxxxxxxxxx RF
                              CbiA  55 ................................................................dlkrllellealg 67 
                                                                                                       ++ r  +  +al+
  gi|336254591|ref|YP_004597698.1| 180 edgpvawrgamvhdvvkdllgdaawddrdvllvdlppgigdavytivqqapldggllvstptdeGV-RATQRTAALY 255
                                       877777777777777777777777777777777777777777777777777777777777666544.3355555555 PP

                                       HCHHHH..EEEEEEEEES CS
                                       xxxxxxxxxxxxxxxxxx RF
                              CbiA  68 kkkalllkiagvvlnrvd 85 
                                       + +   +  +gvv+n v+
  gi|336254591|ref|YP_004597698.1| 256 TAND--VPTVGVVPNVVG 271
                                       5433..667777777665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.4   1.1e-09   1.9e-06       3      38 ..     102     137 ..     100     141 .. 0.92
   2 ?   -0.9   0.0      0.75   1.3e+03     114     132 ..     203     221 ..     171     230 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.1e-09
                            AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDl 38 
                                       +Ia+   KGGvGKTT +v la al+++g  v + D+
  gi|336254591|ref|YP_004597698.1| 102 IIAVGSAKGGVGKTTVTVSLARALSEAGLDVGVFDA 137
                                       8***************************99988776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.75
                            AAA_31 114 vkdeYDyiiiDcpPsLgll 132
                                         d+ D+ ++D pP +g  
  gi|336254591|ref|YP_004597698.1| 203 AWDDRDVLLVDLPPGIGDA 221
                                       4567799999999988755 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   3.2e-07   0.00057       2      37 ..     102     137 ..     101     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.2e-07
                                       EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE- CS
                              MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidl 37 
                                       +i +g  kGG Gk+t++v +a aL+++G+ v++ d 
  gi|336254591|ref|YP_004597698.1| 102 IIAVGSAKGGVGKTTVTVSLARALSEAGLDVGVFDA 137
                                       799*****************************9996 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   3.6e-06    0.0064       3      40 ..     102     139 ..     101     144 .. 0.92
   2 ?   -3.0   0.0         2   3.6e+03      71      90 ..     292     311 ..     279     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.6e-06
                             VirC1   3 litfcslkGGaGkttalmglcsalasdgkrvalfeade 40 
                                       +i++ s kGG Gktt  ++l  al   g  v++f+a+ 
  gi|336254591|ref|YP_004597698.1| 102 IIAVGSAKGGVGKTTVTVSLARALSEAGLDVGVFDANV 139
                                       68899******************************975 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2
                             VirC1  71 lleaayeeaegeGfdyalad 90 
                                       ++eaay + e   fd al +
  gi|336254591|ref|YP_004597698.1| 292 VVEAAYADLEPVPFDPALRE 311
                                       5899*****99999999976 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.8   2.5e-06    0.0044       7      32 ..     107     132 ..     101     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                                       EESTTSSHHHHHHHHHHHHHHTTS-E CS
                       ArsA_ATPase   7 gGKGGVGKttvsaatavklsekgkkv 32 
                                       + KGGVGKttv  ++a  lse g +v
  gi|336254591|ref|YP_004597698.1| 107 SAKGGVGKTTVTVSLARALSEAGLDV 132
                                       56*******************99876 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.4     3e-06    0.0054      16      72 ..      26      82 ..      10      84 .. 0.86
   2 ?   -3.3   0.0       6.1   1.1e+04      47      62 ..     325     340 ..     320     349 .. 0.71
   3 ?   -1.7   0.0       1.8   3.3e+03      25      41 ..     366     382 ..     363     388 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3e-06
                                      TSSBCCCCT---EEEE-T-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEE CS
                    FeS_assembly_P 16 lgvdlvslglvreidieggkVsvditltypacslaeairadaeaalralpgvevveV 72
                                      +g d vs  l++++++e+g V++++      + la+ + ++++ a  a  gv  v+V
  gi|336254591|ref|YP_004597698.1| 26 MGGDPVSEQLIEDVAVEDGIVTFTVDFEPVSRVLADRLTDQLRGAGLATDGVVHVRV 82
                                      5999************************88888******************666665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.1
                                       -TTHHHHHHHHHHHHC CS
                    FeS_assembly_P  47 cslaeairadaeaalr 62 
                                       + +++++ra +e+ l+
  gi|336254591|ref|YP_004597698.1| 325 ERAIADLRATVESFLE 340
                                       5577888888888776 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.8
                                       ---EEEE-T-EEEEEE- CS
                    FeS_assembly_P  25 lvreidieggkVsvdit 41 
                                       +v e+ +++g Vsv ++
  gi|336254591|ref|YP_004597698.1| 366 VVTELGVTEGPVSVVMR 382
                                       78999999999999986 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   7.2e-06     0.013       3      39 ..     102     138 ..     101     144 .. 0.91
   2 ?   -4.0   0.0       4.5   8.1e+03     117     138 ..     208     229 ..     204     240 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.2e-06
                          CBP_BcsQ   3 vlalqGvRGGvGttsllaaLawalhelgesvlviDls 39 
                                       ++a+   +GGvG+t+++++La+al e g  v v D++
  gi|336254591|ref|YP_004597698.1| 102 IIAVGSAKGGVGKTTVTVSLARALSEAGLDVGVFDAN 138
                                       68888899**********************9999986 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 4.5
                          CBP_BcsQ 117 rwillDlpagasaltrellala 138
                                       + +l+Dlp g  + + +++++a
  gi|336254591|ref|YP_004597698.1| 208 DVLLVDLPPGIGDAVYTIVQQA 229
                                       5678888888777766666655 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   9.8e-06     0.018      37      70 ..     102     134 ..      79     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.8e-06
                                       EEEEEESBSS-HSHHHHHHHHHHHTTTS..-EEE CS
                              LpxK  37 VivVGNitvGGtGKTPlvialvkllqarglkvgv 70 
                                       +i VG    GG GKT +++ l+++l+++gl vgv
  gi|336254591|ref|YP_004597698.1| 102 IIAVGSA-KGGVGKTTVTVSLARALSEAGLDVGV 134
                                       7889985.5***********************98 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00012      0.21       7      35 ..     107     135 ..     102     137 .. 0.88
   2 ?    0.4   0.0      0.27   4.8e+02     135     166 ..     238     269 ..     219     312 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                            AAA_26   7 gtdtgvGKTvvslgLvralkrkgvkvgyf 35 
                                       +   gvGKT+v+  L+ral++ g  vg+f
  gi|336254591|ref|YP_004597698.1| 107 SAKGGVGKTTVTVSLARALSEAGLDVGVF 135
                                       66779*******************99998 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.27
                            AAA_26 135 argglgtinqllltiealrqknvrvlGvilNk 166
                                        +++++ + ++  t++++  ++v+ +Gv+ N 
  gi|336254591|ref|YP_004597698.1| 238 STPTDEGVRATQRTAALYTANDVPTVGVVPNV 269
                                       44444444444445555555555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2988.95
//
Query:       gi|336254592|ref|YP_004597699.1|  [L=157]
Description: cyclase/dehydrase [Halopiger xanaduensis SH-6]
Scores for 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   15.6   0.9       0.02   15.2   0.9    1.2  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.9   1.1e-06      0.02       3     128 ..       3     142 ..       1     151 [. 0.65

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-06
                                       EEEEEEEESS-HHHHHHHHTTTTGGG....GT-T.TEEEEECSESTSSS.......TTTEEEEECCCS.SEEEEEEE CS
                   Polyketide_cyc2   3 kvtvsvviaappekVwalvsdfenwp....rWhp.evarveleggggpa.......rgvegtvrvggr.gtvreelv 66 
                                       +++++ vi+a+ e+Vw++    +++      W+   va + +++ gg+        ++++ +++ +++ ++++++++
  gi|336254592|ref|YP_004597699.1|   3 TTRRTSVIDADFETVWSFYDGVDELEiltpDWMGlKVAHSIGPE-GGRNpdgyytgTEIHLEMQPVRLlPRMEWVVE 78 
                                       6788999**************99998443347665555554555.33335788955444555554444955666666 PP

                                       EEE.T.TTTEEEEEE..E..SSS-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHHHHH CS
                   Polyketide_cyc2  67 evd.p.egrllsyri..v.kpvpvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaakavk 128
                                        vd + +  + ++    v +  p ++ + t ++++ g+ t v+ +++++    +g ++ p+aa +++
  gi|336254592|ref|YP_004597699.1|  79 IVDrEvSDDRATFVDeqVaGRGPYERWRHTHRFADLGDATVVHDRIDYRT---PGVGDLPLAAPLLA 142
                                       554223333333333224789999999****************9999994...24444445555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 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:                        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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1130.50
//
Query:       gi|336254593|ref|YP_004597700.1|  [L=301]
Description: UbiA prenyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-29  100.9  19.8    9.6e-29  100.4  19.8    1.2  1  UbiA       UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.42   10.7   6.1        3.7    7.7   0.8    2.6  2  DUF3742    Protein of unknown function (DUF3742)


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 !  100.4  19.8   1.1e-32   9.6e-29       4     238 ..      39     272 ..      36     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 1.1e-32
                              UbiA   4 palvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilg 80 
                                        a+vg++l  +gs+d+ ++ l+++ ++la + ++++N + D+e+D++  +    P+ +     +  + ++ + ++++
  gi|336254593|ref|YP_004597700.1|  39 LAFVGVVLH-PGSFDWATATLAAVVMVLAYGIVYLYNYFTDVEEDRL--NDSYNPVLDETYR-RVIIGYICAAVVAT 111
                                       456666666.999**********************************..999*****99988.77777888888888 PP

                              UbiA  81 llllalllnpltallgllalllyvvYt.g.lrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavfll 155
                                       ++++a+ l+p  ++++l++l  +v+Y+ + lr+K+r +l++vv++++ g ++l+     tg + +l +++ +++++ 
  gi|336254593|ref|YP_004597700.1| 112 VGISAVSLGPIPLAVVLFYLCTGVAYStPpLRFKKRFVLKNVVVALFSGPLLLVMTSSLTGRIAVLDVVMVAFFGIT 188
                                       9999************************99*******************9999999999999977777777777*** PP

                              UbiA 156 twaialandlrdregDrkagiktlpvvlGrkaarillalllavllla.llllllalllllylllalllaalallraa 231
                                       ++++ ++ d+rd++gDrkag++t p+vlG + +  +++++++v ll+ ++ ++l+++ + yl +++++++ + ++ a
  gi|336254593|ref|YP_004597700.1| 189 ALTTSIVGDFRDVDGDRKAGVRTVPIVLGVRGTGHYVLAWTLVQLLVlVVPVWLGYVDPRYLPVLVAMLPRLRFVYA 265
                                       **********************************9844444444444467788888888777777776665555544 PP

                              UbiA 232 rlvrrrd 238
                                       +  r+r+
  gi|336254593|ref|YP_004597700.1| 266 MYARDRE 272
                                       4444433 PP

>> DUF3742  Protein of unknown function (DUF3742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.4    0.0028        25      45      78 ..      30      65 ..      17      86 .. 0.82
   2 ?    7.7   0.8   0.00041       3.7      54      80 ..     216     242 ..     203     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0028
                           DUF3742 45 atavlwvvklavlGvllyvaf..Wlalllvvvvlva 78
                                      +++ + +v la +Gv l+     W +  l++vv+v+
  gi|336254593|ref|YP_004597700.1| 30 VRPAVNCVTLAFVGVVLHPGSfdWATATLAAVVMVL 65
                                      567889***********9543249988999888875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00041
                           DUF3742  54 lavlGvllyvafWlalllvvvvlvawa 80 
                                       l v G++ yv +W+++ l+v+v+ +w+
  gi|336254593|ref|YP_004597700.1| 216 LGVRGTGHYVLAWTLVQLLVLVVPVWL 242
                                       67889***********88888887785 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2375.53
//
Query:       gi|336254594|ref|YP_004597701.1|  [L=283]
Description: hypothetical protein Halxa_3210 [Halopiger xanaduensis SH-6]
Scores for 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-05   22.7   4.2    0.00012   22.1   2.3    2.3  2  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.075   12.9   0.1         12    5.9   0.0    2.5  2  HTH_5     Bacterial regulatory protein, arsR family
        7.1    6.7   6.0        1.3    9.1   1.2    2.2  2  YyzF      YyzF-like protein


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 !   22.1   2.3     2e-08   0.00012       2      58 ..       7      82 ..       6      84 .. 0.88
   2 ?   -1.9   0.0      0.59   3.5e+03      38      50 ..     158     171 ..     145     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2e-08
                                      HHHHHHS-HHHHHHHHHH.STCTTB-HHHHHHHH........T..........S-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  2 qiaeALahPvRrrilraL.araegltaselaerl........d..........lskntlsyHLrvLeeagLvevvr 58
                                      ++++++a+P  r+il  L   a++lt+sel +rl        d          ++ +  +++L +LeeagLve  r
  gi|336254594|ref|YP_004597701.1|  7 RVLRLIADPRNRAILTVLnDAAQPLTVSELLDRLvtaeteicDsvateadrkrIRISLHHNRLPKLEEAGLVEYDR 82
                                      6899**************99**************9887666516667777788********************876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.59
                                       HHHHHHHH.HHHHH CS
                            HTH_20  38 kntlsyHL.rvLee 50 
                                       ++ + +H+ ++Le+
  gi|336254594|ref|YP_004597701.1| 158 QSACLDHVdEALER 171
                                       77899999888887 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 ?    5.9   0.0    0.0019        12       1      24 [.      14      39 ..      14      42 .. 0.88
   2 ?    4.4   0.0    0.0059        35      36      47 .]      69      80 ..      65      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0019
                                      SHHHHHHHHHHTT..SSEEHHHHHHH CS
                             HTH_5  1 dptRlkILklLae..gelcvcelaee 24
                                      dp  + IL  L++  ++l+v+el + 
  gi|336254594|ref|YP_004597701.1| 14 DPRNRAILTVLNDaaQPLTVSELLDR 39
                                      677789****************9775 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0059
                                      HHHHHHTTSEEE CS
                             HTH_5 36 LkkLreaGLVek 47
                                      L kL+eaGLVe+
  gi|336254594|ref|YP_004597701.1| 69 LPKLEEAGLVEY 80
                                      669*******96 PP

>> YyzF  YyzF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.2   0.00022       1.3       1      16 [.     160     175 ..     160     177 .. 0.92
   2 ?   -1.3   0.3      0.39   2.3e+03       4      16 ..     266     278 ..     265     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00022
                              YyzF   1 vCeeHvElAlDefVde 16 
                                       +C +Hv++Al++ Vd+
  gi|336254594|ref|YP_004597701.1| 160 ACLDHVDEALERDVDV 175
                                       6***********9996 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.39
                              YyzF   4 eHvElAlDefVde 16 
                                       +H++   +ef+d+
  gi|336254594|ref|YP_004597701.1| 266 DHLDYQCEEFLDD 278
                                       6999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2335.68
//
Query:       gi|336254595|ref|YP_004597702.1|  [L=103]
Description: hypothetical protein Halxa_3211 [Halopiger xanaduensis SH-6]
Scores for complete 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   66.5   0.2    2.5e-18   66.1   0.2    1.2  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.2   1.4e-22   2.5e-18       1      67 [.      27      91 ..      27      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 1.4e-22
                            HalOD1  1 deespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrs 67
                                      d+e pst Vv+a a +++++p +lepLyd+iDpd Ld +f+s  ++ ++  ++ +F y+g++VtV+ 
  gi|336254595|ref|YP_004597702.1| 27 DDEAPSTGVVKATAILTDTSPLDLEPLYDVIDPDHLDGMFQS--SDGGTVFIETRFVYCGCTVTVTP 91
                                      689***************************************..444567799************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 892.95
//
Query:       gi|336254596|ref|YP_004597703.1|  [L=116]
Description: hypothetical protein Halxa_3212 [Halopiger xanaduensis SH-6]
Scores for 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   11.7   0.0       0.17   11.3   0.0    1.1  1  NQRA      Na(+)-translocating NADH-quinone reductase subunit 


Domain annotation for each model (and alignments):
>> NQRA  Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.6e-06      0.17     209     253 ..      31      77 ..      18      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.6e-06
                              NQRA 209 lhefsGphPaglvgthihfi..dpvskektvwtisyqdviaiGklfl 253
                                       +++f G++ aglv + +  +  ++v ++ + w+i y+  ++iG lfl
  gi|336254596|ref|YP_004597703.1|  31 TNQFYGEFEAGLVLIALTALifASVASKAKYWNIPYTAAVVIGGLFL 77 
                                       689**********99998764478999******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.20s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 1015.81
//
Query:       gi|336254597|ref|YP_004597704.1|  [L=482]
Description: phosphoesterase RecJ domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   73.9   1.8    2.2e-20   73.1   0.8    2.0  1  TrkA_N           TrkA-N domain
    1.2e-13   51.1   2.9    3.8e-12   46.3   1.2    2.4  2  DHH              DHH family
    2.2e-09   37.8   0.3    8.2e-09   35.9   0.1    2.1  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    3.8e-08   33.6   0.1    1.5e-07   31.8   0.1    2.1  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    4.3e-07   29.7   0.0    1.2e-06   28.2   0.0    1.8  2  ApbA             Ketopantoate reductase PanE/ApbA
      1e-05   26.0   0.2      5e-05   23.7   0.0    2.2  2  DHHA1            DHHA1 domain
    4.5e-05   23.7   0.0    9.4e-05   22.6   0.0    1.6  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    6.2e-05   23.4   0.2    0.00022   21.6   0.2    2.0  1  NAD_binding_7    Putative NAD(P)-binding
    6.2e-05   23.1   0.0    0.00018   21.6   0.0    1.7  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0001   22.2   1.7     0.0001   22.2   1.7    1.8  2  NAD_binding_10   NAD(P)H-binding
    0.00014   21.5   0.0    0.00036   20.2   0.0    1.7  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00015   21.4   0.2     0.0003   20.4   0.2    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
     0.0002   20.9   0.2    0.00047   19.7   0.1    1.6  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00052   19.4   0.0     0.0012   18.2   0.0    1.5  1  FAD_binding_3    FAD binding domain
     0.0025   17.2   0.0     0.0072   15.7   0.0    1.7  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0058   16.5   0.0      0.014   15.3   0.0    1.7  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0063   16.5   0.0      0.012   15.6   0.0    1.5  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
     0.0075   15.6   0.2       0.02   14.2   0.2    1.7  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
       0.01   15.3   1.0      0.034   13.6   0.1    2.4  4  adh_short        short chain dehydrogenase
       0.03   14.8   0.4       0.11   13.0   0.0    2.2  2  XdhC_C           XdhC Rossmann domain
      0.034   13.7   5.0      0.041   13.4   0.4    2.9  3  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
       0.04   13.5   0.7      0.089   12.3   0.1    1.8  2  DAO              FAD dependent oxidoreductase
       0.15   12.3   0.0       0.39   11.0   0.0    1.7  1  NAD_binding_8    NAD(P)-binding Rossmann-like 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 !   73.1   0.8   2.8e-23   2.2e-20       1     116 []      13     126 ..      13     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 2.8e-23
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       ++i+G+G vG+++aeeL e+gkdv++id+de+rve+lr++ l++  +d  ++e+ +   +++ d+v+++++d e+n 
  gi|336254597|ref|YP_004597704.1|  13 YAILGCGSVGYAVAEELVEQGKDVLIIDRDESRVESLRDQDLDARTADIREPEAADL--VAERDVVLILASDVESNK 87 
                                       68*****************7779******************************9775..7999************** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                        av+++++ n+++ ++ara+dp   + l++lgad vi+p
  gi|336254597|ref|YP_004597704.1|  88 QAVEHIRDQNDGQFVVARASDPVSGDELEELGADIVINP 126
                                       *************************************98 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.064        50      25      55 ..      15      45 ..       5      90 .. 0.84
   2 !   46.3   1.2   4.9e-15   3.8e-12       3     101 .]     162     299 ..     160     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.064
                                      ECS--TCGGCGCCHHCCCSEEEEEEE-S--- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH 25 lvDhneksqavegeakeeaedviiiDHHrlg 55
                                      ++ +++   av++e+ e+++dv+iiD  ++ 
  gi|336254597|ref|YP_004597704.1| 15 ILGCGSVGYAVAEELVEQGKDVLIIDRDESR 45
                                      567889999999**************88775 PP

  == domain 2  score: 46.3 bits;  conditional E-value: 4.9e-15
                                       EEE-ECSSSHHHHHHHHHHHHC................................................ECS--TC CS
                                       xxxxxxxxxxxxxxxxxxxxxx................................................xxxxxxx RF
                               DHH   3 livghknpDtDsigSaialanl................................................lvDhnek 31 
                                       +i++  +pD Dsi+Sa a++++                                                +vDh ++
  gi|336254597|ref|YP_004597704.1| 162 AIITQDSPDPDSIASAAAMQAIadhlgvesdiiylgdvghqenrafvnllgidlvqwdeiedyavydtvaMVDHATS 238
                                       688999***************6666666666677777777777777777777777777777777777777*****99 PP

                                       GGCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  32 sqavegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                       +++  +         ++iDHH++++++e    ++ ++++++st++i++++++e + ++s+e+a++ll gi
  gi|336254597|ref|YP_004597704.1| 239 DEMDLP-------VDVVIDHHEPESDYEPE--FVDIRPNMSSTSTIMTKYIQEFDMNVSEEVATALLYGI 299
                                       999999.......889*******8555444..77889*******************************98 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 !   35.9   0.1   1.1e-11   8.2e-09       2      92 ..      13     103 ..      12     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.1e-11
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....-EEECECHHHHHHH-SEE.EE-S-HHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....vkvtavdneeaaeeadvv.vlavkped 73 
                                        +i+G+G++g a+a+ l+++g   ++++++ +r+++++e+l+++      +++ + +++++++e dvv +la   e 
  gi|336254597|ref|YP_004597704.1|  13 YAILGCGSVGYAVAEELVEQG---KDVLII-DRDESRVESLRDQDLdartADIREPEAADLVAERDVVlILASDVES 85 
                                       59*******************...****99.***********77667999999999999*******98468999*** PP

                                       HHHHHHHCGHHHHTTSEEE CS
                     F420_oxidored  74 veevlselakdalkgklvi 92 
                                        +++++ + +d+  g++v+
  gi|336254597|ref|YP_004597704.1|  86 NKQAVEHI-RDQNDGQFVV 103
                                       ******99.8889999998 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 !   31.8   0.1   1.9e-10   1.5e-07       3      87 ..      15      91 ..      13      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.9e-10
                                      EE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG. CS
                   Sacchrp_dh_NADP  3 iiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppi. 80
                                      i+G+GsvG avae+l+++++    + ++dr+++++e l    + ++++a++ d+ ++ea  a l++e+d+v+ l+ ++ 
  gi|336254597|ref|YP_004597704.1| 15 ILGCGSVGYAVAEELVEQGKD---VLIIDRDESRVESL----RDQDLDARTADIREPEA--ADLVAERDVVLILASDVe 84
                                      9*****************985...**********7666....7889************9..***************995 PP

                                      GHHHHHH CS
                   Sacchrp_dh_NADP 81 ssldvlk 87
                                      s+ + ++
  gi|336254597|ref|YP_004597704.1| 85 SNKQAVE 91
                                      5555555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.5e-09   1.2e-06       2      74 ..      14      78 ..      13     106 .. 0.77
   2 ?   -3.3   0.0       7.8   6.1e+03     120     144 ..     382     407 ..     367     413 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.5e-09
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlviv 74
                                      ailG+G++G  +a +L ++g dv +i+r++ r+e+l++++l+ ++ +    +r+pea++ +     ++ d+v++
  gi|336254597|ref|YP_004597704.1| 14 AILGCGSVGYAVAEELVEQGKDVLIIDRDEsRVESLRDQDLDARTAD----IREPEAADLV-----AERDVVLI 78
                                      8******************************************9999....7777777776.....34444443 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.8
                                       EEEEEEE-EEEEEETTEEEECS.--E CS
                              ApbA 120 vlggvtthgatregpgevhhag.kge 144
                                        l gvtt  ++  ++ ++ +ag +++
  gi|336254597|ref|YP_004597704.1| 382 NLEGVTTTAVFGIADETIFLAGrSKD 407
                                       57789999998888888888885554 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.6   2.8e+03      28      62 ..      87     122 ..      65     134 .. 0.57
   2 !   23.7   0.0   6.4e-08     5e-05      23     119 ..     343     435 ..     326     463 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.6
                                       HHHHHTCEEECTCEEEEEECHCCHHHHHHHHH.HHH CS
                             DHHA1  28 eellekaeevkgvkvlvaevgeewdagalgia.adk 62 
                                       ++++e +++ ++ +++va+ ++ +  + l+++ ad 
  gi|336254597|ref|YP_004597704.1|  87 KQAVEHIRDQNDGQFVVARASDPVSGDELEELgADI 122
                                       233333333337777777777777777777774444 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 6.4e-08
                                       HHHHHHHHHHTCEEEC.TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSH.SS-H CS
                             DHHA1  23 aklkaeellekaeevk.gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkd.gvda 96 
                                        +++ae++ ++    + + + lv++ g   d+ al +aa+ l++   + ++ ++v++  ++++ + +rsk d ++++
  gi|336254597|ref|YP_004597704.1| 343 LDVLAEAIANR----DvQGSHLVSNAGFVRDREALTQAASHLLN--LEgVTTTAVFGIADETIFLAGRSK-DiRINI 412
                                       45555555544....248888999999*****************..777777788877777********9.66**** PP

                                       HHHHHHHHHHTTCCEEEE.TCEEE CS
                             DHHA1  97 gelakeaaaklgggGGGH.dlAaG 119
                                       g+++ +a+ ++g    GH  +A++
  gi|336254597|ref|YP_004597704.1| 413 GKVLADAYGEMGETA-GHsTQASA 435
                                       ******999999888.88666654 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 !   22.6   0.0   1.2e-07   9.4e-05       2      78 ..      13      95 ..      12     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.2e-07
                                      EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.....EEE-S.SHHHHHHHCSEEEE-SSSHHHHHHHHH CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.....akaae.sieelvasldvvitmvkagkavdevie 74
                                      ++++G G  G   a++l+++g +v +++r++++ve+l ++      a++ e ++++lva+ dvv+++ ++ +  ++ +e
  gi|336254597|ref|YP_004597704.1| 13 YAILGCGSVGYAVAEELVEQGKDVLIIDRDESRVESLRDQDldartADIREpEAADLVAERDVVLILASDVESNKQAVE 91
                                      799*************************************988555333221455788888999999888777777777 PP

                                      SHCC CS
                     NAD_binding_2 75 glle 78
                                       + +
  gi|336254597|ref|YP_004597704.1| 92 HIRD 95
                                      7544 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 !   21.6   0.2   2.8e-07   0.00022      11      94 ..      14     108 ..      10     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.8e-07
                     NAD_binding_7  11 lvvGgGevAarkvrklleagakvtvvapevkeele.........elvklaeeelekdlegadlviaatddrelneri 78 
                                        + G G+v++  ++ l+e+g++v +++ + ++ +e         ++ +++e e+ + +++ d+v++  +d e n++ 
  gi|336254597|ref|YP_004597704.1|  14 AILGCGSVGYAVAEELVEQGKDVLIIDRD-ESRVEslrdqdldaRTADIREPEAADLVAERDVVLILASDVESNKQA 89 
                                       699**************************.444444555444333333444555666999***************** PP

                     NAD_binding_7  79 aeaaka...rrilvnvadk 94 
                                       +e +++    + +v +a +
  gi|336254597|ref|YP_004597704.1|  90 VEHIRDqndGQFVVARASD 108
                                       *999773323445555555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.3e-07   0.00018      16      83 ..      14      80 ..       7     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.3e-07
                                      EEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-S CS
                      Shikimate_DH 16 lliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisat 83
                                       ++G G ++  va+ L+++g + v+++ R+ +r+++l+++  ++++  ++  e  +l+ae dvv++  
  gi|336254597|ref|YP_004597704.1| 14 AILGCGSVGYAVAEELVEQGKD-VLIIDRDESRVESLRDQDLDARTADIREPEAADLVAERDVVLILA 80
                                      699**************99977.****************998888999999999*********98543 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 !   22.2   1.7   1.3e-07    0.0001       4     162 ..      19     169 ..      17     187 .. 0.72
   2 ?   -3.1   0.0       7.6   5.9e+03      52      69 ..     344     361 ..     327     389 .. 0.54

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.3e-07
                                       SHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCHHHHHHH CS
                    NAD_binding_10   4 GkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkdeegakn 80 
                                       G+vG ++++el+++g  +v ++ R+++++++l+ ++ l++ ++d+ ++e+ a+ ++  d+V++ ++      e+ k+
  gi|336254597|ref|YP_004597704.1|  19 GSVGYAVAEELVEQG-KDVLIIDRDESRVESLR-DQDLDARTADIREPEA-ADLVAERDVVLILASDV----ESNKQ 88 
                                       99************6.8***************8.69**********8877.9***********99954....45677 PP

                                       HHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHH.CCHHHHHHHHHHHHHHHHSSSEEEEEEE-CEE-ST--SEEE CS
                    NAD_binding_10  81 ivdaakeagvkRfvlvsaigvgdevpgefgewnke.llkaylaakraaeellrasgldwTivrpggLtdepttkyrv 156
                                       +v+  + ++  +fv+  a +    + +e++e+  + ++++     + a + l++ +l++   + + L +e +t+  +
  gi|336254597|ref|YP_004597704.1|  89 AVEHIRDQNDGQFVVARASDPV--SGDELEELGADiVINPSSVIAESALRALESGELEYNAGKLADLLEETSTRLAI 163
                                       7777777777777776665432..12334443333255666666666777777777777777777777777666666 PP

                                       EETTSS CS
                    NAD_binding_10 157 vekgep 162
                                       ++++ p
  gi|336254597|ref|YP_004597704.1| 164 ITQDSP 169
                                       666554 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.6
                                       CHHHHHHTT-SEEEES-- CS
                    NAD_binding_10  52 edlaealkgadaVvsalg 69 
                                       + laea+++ d+  s l 
  gi|336254597|ref|YP_004597704.1| 344 DVLAEAIANRDVQGSHLV 361
                                       455555555554333332 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 !   20.2   0.0   4.6e-07   0.00036       4      57 ..      14      72 ..      11      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.6e-07
                                      EEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-.....SS--TTHHHHHHH CS
                    UDPG_MGDP_dh_N  4 sviGlGYvGlvtaavlaeighevigvDideekvdklnsgki.....piyepgLeelvkk 57
                                      +++G G vG   a  l e+g++v+++D de++v++l+ +++      i ep+ ++lv++
  gi|336254597|ref|YP_004597704.1| 14 AILGCGSVGYAVAEELVEQGKDVLIIDRDESRVESLRDQDLdartaDIREPEAADLVAE 72
                                      799********************************998765111115666666666665 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 !   20.4   0.2   3.9e-07    0.0003       8      84 ..      14      96 ..      10     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.9e-07
                                      EEES-SHHHHHHHHHHHHTT--EEEEE-TT-......HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHH CS
                              IlvN  8 aviGyGsqGhaqalnlrdsgldvvvglregs......ksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeee 80
                                      a++G+Gs G a a++l ++g dv +  r++s       +   A+ + ++  ++a++v++ dvv+il+ D   ++   e+
  gi|336254597|ref|YP_004597704.1| 14 AILGCGSVGYAVAEELVEQGKDVLIIDRDESrveslrDQDLDARTADIREPEAADLVAERDVVLILASDVESNKQAVEH 92
                                      9*************************9999955433223346888888889999***************8887776677 PP

                                      TGGG CS
                              IlvN 81 iepn 84
                                      i+++
  gi|336254597|ref|YP_004597704.1| 93 IRDQ 96
                                      7765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1     6e-07   0.00047       8      93 ..      19      98 ..      14     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6e-07
                                      SHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.---HHHHHHSHH CS
                         Epimerase  8 GfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.vggvaassedpa 85
                                      G +G a++++l e+g +v+ +dr++s+ ++ r++dl+  ++d+++++a + + +    d+v+ lA  v +    ++++ 
  gi|336254597|ref|YP_004597704.1| 19 GSVGYAVAEELVEQGKDVLIIDRDESRVESLRDQDLDARTADIREPEAADLVAE---RDVVLILASdVES----NKQAV 90
                                      99******************************************9997666555...5999999664444....44444 PP

                                      HHHHHHTH CS
                         Epimerase 86 dfieknlq 93
                                      + i++   
  gi|336254597|ref|YP_004597704.1| 91 EHIRDQND 98
                                      44554444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.5e-06    0.0012       5      52 ..      14      61 ..      11      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                                      EEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHH CS
                     FAD_binding_3  5 lIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmel 52
                                      +I G G +G   a +L e+G +v+++++ +++v+  r + l+ rt ++
  gi|336254597|ref|YP_004597704.1| 14 AILGCGSVGYAVAEELVEQGKDVLIIDRDESRVESLRDQDLDARTADI 61
                                      799**********************************99999999765 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   9.3e-06    0.0072      39     109 ..      13      90 ..       7     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.3e-06
                                       EEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.......CHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTS CS
                      2-Hacid_dh_C  39 vGiiGlGrIGqavakrlkafgmkviaydrskkkee.......eeeelgvelvsleellaesDivslhlpltpetrhl 108
                                        +i+G+G++G ava+ l + g +v+++dr +++ e       ++++  ++  +  +l+ae D+v + +   +++++ 
  gi|336254597|ref|YP_004597704.1|  13 YAILGCGSVGYAVAEELVEQGKDVLIIDRDESRVEslrdqdlDARTADIREPEAADLVAERDVVLILASDVESNKQA 89 
                                       58***************************999776665554445555556667888999999999998888877776 PP

                                       B CS
                      2-Hacid_dh_C 109 i 109
                                       +
  gi|336254597|ref|YP_004597704.1|  90 V 90 
                                       5 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 !   15.3   0.0   1.8e-05     0.014       3      41 ..      14      52 ..      12      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                                      EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHH CS
                           3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdiseealekalek 41
                                      a++G+G +G  +a+ ++++g +V ++d++e+++e+ +++
  gi|336254597|ref|YP_004597704.1| 14 AILGCGSVGYAVAEELVEQGKDVLIIDRDESRVESLRDQ 52
                                      89******************************9998765 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 !   15.6   0.0   1.6e-05     0.012       3      46 ..      14      57 ..      12      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                                      EEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTT CS
                    NAD_Gly3P_dh_N  3 avlGaGswGtalAkvlaenghevrlwvreeelieeineehenvk 46
                                      a+lG Gs G a+A  l e+g++v ++ r+e  +e+++++  + +
  gi|336254597|ref|YP_004597704.1| 14 AILGCGSVGYAVAEELVEQGKDVLIIDRDESRVESLRDQDLDAR 57
                                      89********************************9998876655 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 !   14.2   0.2   2.5e-05      0.02      28      96 ..      10      77 ..       1      95 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                      --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH..TTTCECEEHCHHHHHHHHHHHH-SEEE CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles..lgakfvevlksqeellaeavkeadvvi 96
                                       +   ++G G +G + ++  ++ g +V ++D +++r e l++  l a+   +    e + a+ v+e dvv 
  gi|336254597|ref|YP_004597704.1| 10 ISDYAILGCGSVGYAVAEELVEQGKDVLIIDRDESRVESLRDqdLDAR---TADIREPEAADLVAERDVVL 77
                                      45789************************************9555555...66777777788888888774 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.3e-05     0.034      10      63 ..      19      66 ..      14      96 .. 0.80
   2 ?   -1.3   0.0       1.7   1.3e+03      21      51 ..      70     102 ..      61     123 .. 0.63
   3 ?   -3.2   0.0         6   4.7e+03      39      72 ..     149     184 ..     141     193 .. 0.64
   4 ?   -3.1   0.0       5.6   4.3e+03      81      94 ..     360     373 ..     346     395 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                                      SHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHH CS
                         adh_short 10 sGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdree 63
                                      + +G+a+a+el+++G +v+++dr e+++e + ++      ++ a ++D+++ e+
  gi|336254597|ref|YP_004597704.1| 19 GSVGYAVAEELVEQGKDVLIIDRDESRVESLRDQ------DLDARTADIREPEA 66
                                      468***********************99776665......34555666655555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.7
                                       HHTT-EEEEEESCHHHHHHHHHHHHHT..TSEE CS
                         adh_short  21 akeGakvvvvdrseekleevakelkee..gaka 51 
                                       ++e   v+++++  e  ++++++++++  g+ +
  gi|336254597|ref|YP_004597704.1|  70 VAERDVVLILASDVESNKQAVEHIRDQndGQFV 102
                                       444444555777777778888888877533333 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6
                                       HHHHHHHHTTSEEEEEE-TTTSHHHHH..HHHHHHH CS
                         adh_short  39 evakelkeegakalaiqvDvtdreeve..alvekav 72 
                                       ++a+ l+e+++++ +i+ D  d +++   a++++++
  gi|336254597|ref|YP_004597704.1| 149 KLADLLEETSTRLAIITQDSPDPDSIAsaAAMQAIA 184
                                       455666666778888888888877775113344444 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 5.6
                                       EEE---SS--SSGG CS
                         adh_short  81 LvnNAGitgsgpfs 94 
                                       Lv NAG  +++++ 
  gi|336254597|ref|YP_004597704.1| 360 LVSNAGFVRDREAL 373
                                       67777774333332 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014      0.11       2      74 ..      14     104 ..      13     130 .. 0.77
   2 ?   -1.2   0.1       3.6   2.8e+03      18      18 ..     209     209 ..     146     292 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG..........-GGG-TT-SE...............-EEEE--S- CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefa..........tkerfpeade...............tavvvlthd 53 
                                       +i+G g v+ a+a+ + + g +v ++d +e+            +        +               ++v++l  d
  gi|336254597|ref|YP_004597704.1|  14 AILGCGSVGYAVAEELVEQGKDVLIIDRDESRVeslrdqdldaR--------TadirepeaadlvaerDVVLILASD 82 
                                       699***************************64436655554441........0455556667788899********* PP

                                       HHHHHHHHHHHSS.S--SEEEE CS
                            XdhC_C  54 hklDaealeaalr.kkaayigl 74 
                                        +  ++a+e++ + ++ +++ +
  gi|336254597|ref|YP_004597704.1|  83 VESNKQAVEHIRDqNDGQFVVA 104
                                       *********9986333556655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.6
                                       H CS
                            XdhC_C  18 a 18 
                                       +
  gi|336254597|ref|YP_004597704.1| 209 N 209
                                       3 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 ?   13.4   0.4   5.2e-05     0.041       5      60 ..      20      71 ..      15     106 .. 0.89
   2 ?   -0.4   0.1      0.87   6.8e+02      34     113 ..     150     236 ..     142     242 .. 0.64
   3 ?    0.0   0.0      0.67   5.2e+02      53     112 ..     340     397 ..     337     425 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-05
                                      SHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHH CS
                      adh_short_C2  5 gIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealv 60
                                      ++G+a+A++l e+G +v++ d++e++   ve+l ++ + ++  +D++++e+ + ++
  gi|336254597|ref|YP_004597704.1| 20 SVGYAVAEELVEQGKDVLIIDRDESR---VESLRDQ-DLDARTADIREPEAADLVA 71
                                      89**********************98...8888875.7778999999988877655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.87
                                       HHHHHHHTTSE.E.EE--TTSHHHHH..HHHHHHHHHH.SSEEEE.EE-----EG.CSS-GGGH-HHHHHHHHHHHT CS
                      adh_short_C2  34 veelaeelgae.v.lecDVtdeeqve..alveevvekf.gklDil.vnnagiapk.lkgpfletsreefdraldvnl 103
                                       +++l ee++++ + +  D  d+++++  a+++++++++  + Di+ +  +g+ ++    ++l ++  ++d++ d  +
  gi|336254597|ref|YP_004597704.1| 150 LADLLEETSTRlAiITQDSPDPDSIAsaAAMQAIADHLgVESDIIyLGDVGHQENrAFVNLLGIDLVQWDEIEDYAV 226
                                       55666666666424777777777765114556666666435565414567777776667777778888888888888 PP

                                       HHHHHHHHHH CS
                      adh_short_C2 104 yslfllakaa 113
                                       y +++++ +a
  gi|336254597|ref|YP_004597704.1| 227 YDTVAMVDHA 236
                                       8888887776 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHH CS
                      adh_short_C2  53 eeqvealveevvekfgklDilvnnagiapklkgpfletsreefdraldvnlyslfllaka 112
                                       +e+++ l+e+++++  +   lv nag++++   ++l+   +++ +   v ++++f +a +
  gi|336254597|ref|YP_004597704.1| 340 PETLDVLAEAIANRDVQGSHLVSNAGFVRD--REALTQAASHLLNLEGVTTTAVFGIADE 397
                                       566777777888887778889999**9999..7777777777777777777777766655 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00011     0.089       1      29 [.      12      42 ..      12      54 .. 0.93
   2 ?   -2.9   0.0         5   3.9e+03     124     154 ..     350     379 ..     292     396 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      d +i G G +G ++A eL ++g  V++++++
  gi|336254597|ref|YP_004597704.1| 12 DYAILGCGSVGYAVAEELVEQGkdVLIIDRD 42
                                      789******************99*******9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5
                                       HSTTSTTTSEEEEETTEEEE.EHHHHHHHHHH CS
                               DAO 124 lepalpgllgalfypdtgqv.dpakltaalar 154
                                       ++   ++++g+ ++ ++g v d ++lt+a  +
  gi|336254597|ref|YP_004597704.1| 350 IA--NRDVQGSHLVSNAGFVrDREALTQAASH 379
                                       22..2366777667777777455555555444 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 ?   11.0   0.0    0.0005      0.39       1      28 [.      15      42 ..      15      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0005
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      I+G G  G + A +L ++g+dvl++++ 
  gi|336254597|ref|YP_004597704.1| 15 ILGCGSVGYAVAEELVEQGKDVLIIDRD 42
                                      89************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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: 0.56u 0.22s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3611.35
//
Query:       gi|336254598|ref|YP_004597705.1|  [L=218]
Description: hypothetical protein Halxa_3214 [Halopiger xanaduensis SH-6]
Scores for 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  113.0  25.9    1.3e-18   66.6   8.3    2.6  2  UPF0126   UPF0126 domain


Domain annotation for each model (and alignments):
>> UPF0126  UPF0126 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   6.0   2.6e-19   4.6e-15       3      76 ..      17      88 ..      15      89 .. 0.90
   2 !   66.6   8.3   7.2e-23   1.3e-18       2      76 ..     103     175 ..     102     177 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 2.6e-19
                                      HHHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHTTSSSSGHHHSSTCHHHHHHHHHHHHHHH CS
                           UPF0126  3 ldaiGlaafavsGalvAlkkgldllgvvvlGvvTAvgGGvlRDvllgrevPvvllreelyataallgalvvvll 76
                                      +++iGl+afa++G  +A+++++dl+g++v+G++ A++GG +RD+l+ r vP++l +++l +++ llg+ ++++l
  gi|336254598|ref|YP_004597705.1| 17 MNTIGLVAFALVGSTKAIREEFDLFGIAVVGLTMAFAGGATRDLLVTR-VPLAL-QSPLEIALGLLGVGLAIAL 88
                                      899********************************************6.***99.5578888888888877765 PP

  == domain 2  score: 66.6 bits;  conditional E-value: 7.2e-23
                                       HHHHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHTTSSSSGHHHSSTCHHHHHHHHHHHHHHH CS
                           UPF0126   2 ildaiGlaafavsGalvAlkkgldllgvvvlGvvTAvgGGvlRDvllgrevPvvllreelyataallgalvvvll 76 
                                       + daiGlaafa +Ga+vA +++++++gvv ++++ AvgGG   D+ll+r  P++l+++ +ya++a+lg+ +++++
  gi|336254598|ref|YP_004597705.1| 103 VSDAIGLAAFATTGAIVATEANVSAFGVVTVATINAVGGGAFADILLDR-SPFILFED-FYASCAVLGGSAYWVA 175
                                       68**********************************************7.9*****98.*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); 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):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1725.67
//
Query:       gi|336254599|ref|YP_004597706.1|  [L=100]
Description: PRC-barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-11   42.6   1.9    6.3e-11   42.2   1.9    1.1  1  PRC       PRC-barrel domain
  ------ inclusion threshold ------
      0.014   15.5   0.4      0.026   14.6   0.4    1.4  1  RcnB      Nickel/cobalt transporter regulator


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   1.9   7.1e-15   6.3e-11       6      76 ..      11      85 ..       9      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 7.1e-15
                                      S---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT...........-EEEEEGG.CEECCCTEEEETTS- CS
                               PRC  6 asdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi......gekevliPfdlavkigkdriivdapk 76
                                      +++++G+eVy++ G  +G+++D+ ++++++ v++l ++  +  ++       +  v++P++ +v++++d+++v++  
  gi|336254599|ref|YP_004597706.1| 11 ITSIVGREVYSNGGVFVGEIEDLQLNIDGQVVTGLALGNLNS-ELfteearSGQGVIVPYR-WVRSVGDVVLVNEVV 85
                                      789***********************************9988.555***************.***********9865 PP

>> RcnB  Nickel/cobalt transporter regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.4   2.9e-06     0.026      30      44 ..      69      83 ..      67      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.9e-06
                              RcnB 30 yrWvriggdyvLvai 44
                                      yrWvr  gd+vLv+ 
  gi|336254599|ref|YP_004597706.1| 69 YRWVRSVGDVVLVNE 83
                                      9************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 832.47
//
Query:       gi|336254600|ref|YP_004597707.1|  [L=388]
Description: DRTGG domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-37  127.1   0.0    1.3e-36  126.3   0.0    1.4  1  AAA_26    AAA domain
    3.7e-29  100.6   0.1    1.3e-28   98.8   0.0    1.9  2  DRTGG     DRTGG domain
    0.00091   19.3   0.0      0.003   17.6   0.0    1.9  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   0.0   2.1e-40   1.3e-36       2     196 ..      36     243 ..      35     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 2.1e-40
                            AAA_26   2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie......ededselikellgldqtyelpeplalsap 72 
                                       ti+v++ +++vGKT+++l+L+r  +++g  vgy+KP +t +e       ded+ l++ell+ld++++++ep+++s  
  gi|336254600|ref|YP_004597707.1|  36 TILVSSLEESVGKTAITLALARLAQAEGEGVGYMKPKGTRLEsnvgktLDEDPMLARELLDLDAEMHDLEPVVYSPT 112
                                       8*****************************************888885588************************99 PP

                            AAA_26  73 lspelaarqegedidlekiv...kelekdadivvVEGagglgvpiteellnadiaknlgapvilVarggl.gtinql 145
                                       + +++   +e+ d   e++    ++l++d+d ++VEG g++ v+ + +l+++d+a+ l+a v+lVa++++ g ++++
  gi|336254600|ref|YP_004597707.1| 113 FIEQAIRGREDPDELRERVGeafDSLAADTDRMFVEGGGEYEVGGIVDLTDVDVAELLDARVLLVAPYKQpGDVDDV 189
                                       87777665555454444444666*********************************************8889***** PP

                            AAA_26 146 lltiealrqknvrvlGvilNkvrnpe......nvetlekksgipvlGvvPylpdlea 196
                                       l++++a+ +   r +Gv++N v++++      +v  + +   +pv+Gv+P++++l  
  gi|336254600|ref|YP_004597707.1| 190 LAAADAFGD---RFAGVVFNDVPDAAydqletDVVPFLEGRDVPVFGVLPSERTLAG 243
                                       *******99...8********99994445556999999999***********99975 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       0.4   2.4e+03       1      28 [.     165     193 ..     165     206 .. 0.66
   2 !   98.8   0.0   2.2e-32   1.3e-28       1     103 [.     248     352 ..     248     354 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.4
                                       HHHHHTT-EEEE--..SS--.E-EEEE-S CS
                             DRTGG   1 eiaealgaevlnggeeelrr.vekvvvga 28 
                                       ++ae l+a+vl     ++   v++v+ +a
  gi|336254600|ref|YP_004597707.1| 165 DVAELLDARVLLVAPYKQPGdVDDVLAAA 193
                                       57777888877766655555555555555 PP

  == domain 2  score: 98.8 bits;  conditional E-value: 2.2e-32
                                       HHHHHTT-EEEE--..SS--E-EEEE-SS-HHHHHHHHHT..SEEEEEETT-HHHHHHHTT-T.EEEEEEETT---- CS
                             DRTGG   1 eiaealgaevlnggeeelrrvekvvvgamsvenmlerlke..gdlvivpGDRediqlaaleag.iaalilTggleps 74 
                                       ++a++lga+vl+++  +   ve+++vgam ++++l+r+++  +++vi++GDR++i++aalea  +++lilTgg++ps
  gi|336254600|ref|YP_004597707.1| 248 DLASELGASVLVENG-DDSFVERFSVGAMGADSALRRFRRtkNAAVITGGDRAEIHTAALEAPgVRCLILTGGHRPS 323
                                       799***********5.5557*******************999********************99************* PP

                                       HHHHHHHHHHT--EEE-SS-HHHHHHHHH CS
                             DRTGG  75 eevlklaeeaglpvlsveldtfttakrin 103
                                        +vl  a+e+g+pvlsv++dt+tt++r +
  gi|336254600|ref|YP_004597707.1| 324 GAVLGQAAEKGVPVLSVQTDTLTTVERAE 352
                                       *************************9987 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 !   17.6   0.0   5.1e-07     0.003       2     115 ..      38     238 ..      37     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.1e-07
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       ++ s    vGKT ++++Lar+ + +g  V   +  p ++ l++  g+  d++p                        
  gi|336254600|ref|YP_004597707.1|  38 LVSSLEESVGKTAITLALARLAQAEGEGVGYMK--PKGTRLESNVGKTLDEDPmlarelldldaemhdlepvvyspt 112
                                       56666678*************************..66666665567777777788999******************* PP

                                       ........................................................................CCHCC CS
                                       ........................................................................xxxxx RF
                              CbiA  55 ........................................................................dlkrl 59 
                                                                                                               d++ +
  gi|336254600|ref|YP_004597707.1| 113 fieqairgredpdelrervgeafdslaadtdrmfvegggeyevggivdltdvdvaelldarvllvapykqpgDVDDV 189
                                       ****************************************************************************9 PP

                                       CHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  60 lellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprd 115
                                       l  + a+g +      +agvv+n v   ++++l+ + +  l+    vpv+gv+p  
  gi|336254600|ref|YP_004597707.1| 190 LAAADAFGDR------FAGVVFNDVPDAAYDQLETDVVPFLE-GRDVPVFGVLPSE 238
                                       ********87......89*********999999999888875.3499999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2905.38
//
Query:       gi|336254601|ref|YP_004597708.1|  [L=701]
Description: CoA-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-74  248.1   0.1    1.5e-73  246.9   0.1    1.6  1  ATP-grasp_5    ATP-grasp domain
    3.4e-54  182.4   1.2    2.2e-52  176.5   0.1    2.7  3  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    2.1e-24   86.2   0.8    2.7e-23   82.7   0.1    3.1  3  CoA_binding_2  CoA binding domain
    3.3e-12   46.9   0.1    1.3e-11   45.0   0.1    2.1  1  CoA_binding    CoA binding domain
     0.0002   21.0   0.0    0.00045   19.8   0.0    1.6  1  ATP-grasp_2    ATP-grasp domain
  ------ inclusion threshold ------
      0.045   14.2   0.3         17    5.7   0.0    3.9  4  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
      0.065   13.2   0.0       0.17   11.9   0.0    1.7  1  HRDC           HRDC 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 !  246.9   0.1   5.9e-77   1.5e-73       8     222 .]     479     693 ..     472     693 .. 0.96

  Alignments for each domain:
  == domain 1  score: 246.9 bits;  conditional E-value: 5.9e-77
                       ATP-grasp_5   8 tlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeei 84 
                                       +     e+++lleaygip++   ++++++ a e+ae+i+  vv+Kivspdi+hK+d+gGv++++ d e+v +a+e++
  gi|336254601|ref|YP_004597708.1| 479 DNRLGVESMDLLEAYGIPTPAGDIVDDPDRAREVAESIDGDVVMKIVSPDITHKSDIGGVKVGVGD-EDVYDAYEDL 554
                                       444478*********************************************************997.89******** PP

                       ATP-grasp_5  85 lervkekspeariegvlVqemakr.ggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlarelier 160
                                       ++r+++++p+a i gv+Vqem ++ +++E ivg+++Dp+FGp++lfGlGG+ ve l+d++v+++p+ + +ar++i++
  gi|336254601|ref|YP_004597708.1| 555 VSRARNYQPDATIIGVQVQEMLDVgESTETIVGMNRDPQFGPLLLFGLGGIFVETLEDTSVRVAPIGEDEARDMIDE 631
                                       *********************8888**************************************************** PP

                       ATP-grasp_5 161 tkaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDarirl 222
                                       ++a++ll+g rg+++ad++a++e+++rlsqLv+d+p I eld+nPl++ ++gv a+D r+++
  gi|336254601|ref|YP_004597708.1| 632 IQAAPLLRGARGREPADVDAIVETVQRLSQLVTDFPSILELDVNPLVAGPDGVQAIDLRLTV 693
                                       ***********************************************************987 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 ?    3.8   0.0     0.018        45      72     101 ..      79     110 ..      73     122 .. 0.84
   2 !  176.5   0.1   8.7e-56   2.2e-52       2     138 .]     152     288 ..     151     288 .. 0.99
   3 ?   -2.9   0.0       2.1   5.3e+03      42      61 ..     359     378 ..     351     419 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.018
                      Succ_CoA_lig  72 lsaarraark..kpvvvlksGrseagaraaas 101
                                       l+++r+++++  k vvv+ +G se+g + a+ 
  gi|336254601|ref|YP_004597708.1|  79 LETVRELSEAgtKNVVVITAGFSETGGEGAKR 110
                                       788899998888*************9987765 PP

  == domain 2  score: 176.5 bits;  conditional E-value: 8.7e-56
                      Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarra 78 
                                       G+i+++sqSGa+++a+ldwa+++g+gf+ vvs+Gn++ +d++d++e +++dp+t+vi+ ylE+i+dg++f+++ar++
  gi|336254601|ref|YP_004597708.1| 152 GSISFMSQSGAFITAVLDWANEEGIGFKDVVSVGNKSVLDETDFVEEWGDDPDTDVIIGYLEDIDDGQEFVRTAREV 228
                                       99*************************************************************************** PP

                      Succ_CoA_lig  79 arkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                       + + p+v++ksGr++aga+aa+shtga+ags+++++a ++qaGv+r++s++elfd+a++l
  gi|336254601|ref|YP_004597708.1| 229 TDDTPIVLVKSGRTDAGAQAASSHTGAIAGSERAYEAGLEQAGVIRAESVQELFDYARAL 288
                                       *********************************************************986 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.1
                      Succ_CoA_lig  42 vadlleylaedpetkvilly 61 
                                       +++ le   +dp++ + +++
  gi|336254601|ref|YP_004597708.1| 359 FGEALEIALDDPNVGSAVVV 378
                                       77788888888877655443 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.1   1.1e-26   2.7e-23       2     114 ..      12     134 ..      11     136 .. 0.96
   2 ?   -1.6   0.0       1.4   3.6e+03      81     103 ..     154     176 ..     147     189 .. 0.82
   3 ?   -1.1   0.0         1   2.6e+03      54     103 ..     370     427 ..     341     435 .. 0.66

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 1.1e-26
                                       -EEEET--S-TTSHHHHHHHHHHH..HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHH CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle..hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkeal 76 
                                       t+ VvGa d++g  g+ +l++l++  +g ++vp+npk++e+lg ++y+++a+   p+dl +v++pp +++e+v+e++
  gi|336254601|ref|YP_004597708.1|  12 TVGVVGATDREGAVGRAILENLQSdfEG-EIVPINPKRDEVLGLECYEDVAS-APPIDLGVVVVPPPVVLETVRELS 86 
                                       788**********************999.**********************6.58********************** PP

                                       HH--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  77 algakavwlqpg..........sedeeaaelaeeagirvvgdrCilve 114
                                       ++g+k v++  +           +++e+ e+a+e++++vvg+++++++
  gi|336254601|ref|YP_004597708.1|  87 EAGTKNVVVITAgfsetggegaKRERELREIAAEYDLNVVGPNSLGIM 134
                                       ****999999988*********************************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                                       SEEEE-TT---HHHHHHHHHTT- CS
                     CoA_binding_2  81 kavwlqpgsedeeaaelaeeagi 103
                                        +++ q+g++  +++++a+e+gi
  gi|336254601|ref|YP_004597708.1| 154 ISFMSQSGAFITAVLDWANEEGI 176
                                       567889999999******99887 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1
                                       .T--EEEE-S-HHHHGGGHHHHHHH........--SEEEE-TT---HHHHHHHHHTT- CS
                     CoA_binding_2  54 epvdlvdvftppeatpeivkealal........gakavwlqpgsedeeaaelaeeagi 103
                                        +v +++v+  p+a++e+ + a+++        ++ +  l+ g++ ++a e++++ gi
  gi|336254601|ref|YP_004597708.1| 370 PNVGSAVVVAAPTAVLEYDDLAETViekrdeyeKPVVTSLMGGARARAAEEVLRAFGI 427
                                       4555777777777777654444333333554444666667777888888888888777 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.1   5.1e-15   1.3e-11       3      96 .]      10      99 ..       8      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 5.1e-15
                                      TEEEEEETTTSHHHHHHHHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHH CS
                       CoA_binding  3 dtkviviGagglgiaglyhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavd 80
                                      +  v+v+Ga+ +++a++  + e+l+  ++ +++++np+   +evlgl++y++v+ ++     d +v++vP++ + e+v 
  gi|336254601|ref|YP_004597708.1| 10 PETVGVVGATDREGAVGRAILENLQSDFEgEIVPINPK--RDEVLGLECYEDVASAPPI---DLGVVVVPPPVVLETVR 83
                                      5689*************9999999*9***9********..**********999999998...***************** PP

                                      HHHHTT-SEEEEESST CS
                       CoA_binding 81 elveagikgiviiteg 96
                                      el eag k +v+it+g
  gi|336254601|ref|YP_004597708.1| 84 ELSEAGTKNVVVITAG 99
                                      **************86 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.8e-07   0.00045       6     201 ..     485     678 ..     483     679 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.8e-07
                                       HHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE.--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE CS
                       ATP-grasp_2   6 qakeilakygvkvpegevaesaeeaeeaakklgekelvvKa.QvlaGGRGKagGvklvkskeeakeaakellgkelv 81 
                                       +++++l+ yg+++p g +++++++a+e+a+++++++ v+K     +  +   gGvk+    e++++a ++l++    
  gi|336254601|ref|YP_004597708.1| 485 ESMDLLEAYGIPTPAGDIVDDPDRAREVAESIDGDV-VMKIvSPDITHKSDIGGVKVGVGDEDVYDAYEDLVSRARN 560
                                       5889******************************99.777413344555556******************9987665 PP

                                       -TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB-.-HH CS
                       ATP-grasp_2  82 tkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakgl.kee 157
                                        +q +    ++  v v+e+ld+ + +   + + r+ +   +++   GG+ +E++ +++  +++ +  d a ++ +e 
  gi|336254601|ref|YP_004597708.1| 561 -YQPD---ATIIGVQVQEMLDVGESTETIVGMNRDPQFGPLLLFGLGGIFVETLEDTS-VRVAPIGEDEARDMiDEI 632
                                       .6664...46777888888898887777777888888877888888999998875544.566666666655541556 PP

                                       HHHHHHHHC.T--CHHHHHHHHHHHHHHHHHHHTTEEE.EEEEEEE CS
                       ATP-grasp_2 158 qareiakkl.glekelvkkaakiikklyklfveldatl.vEiNPLv 201
                                       qa  +++ + g e   v+ +++++++l +l+++    l +++NPLv
  gi|336254601|ref|YP_004597708.1| 633 QAAPLLRGArGREPADVDAIVETVQRLSQLVTDFPSILeLDVNPLV 678
                                       6666666541566678888888888888888887655437888887 PP

>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.21   5.5e+02     125     151 ..     156     186 ..      76     207 .. 0.58
   2 ?    2.0   0.0     0.094   2.4e+02      68     143 ..     237     345 ..     214     370 .. 0.68
   3 ?   -2.8   0.0       2.9   7.4e+03     122     150 ..     456     489 ..     413     509 .. 0.65
   4 ?    5.7   0.0    0.0067        17      80     108 ..     543     581 ..     528     683 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHHHCT-EEE-H....H CS
                     Lipase_GDSL_2 125 lnaviaaynealrevaaeegvpfvDl....h 151
                                       + ++  a+  a+ ++a+eeg+ f D+    +
  gi|336254601|ref|YP_004597708.1| 156 FMSQSGAFITAVLDWANEEGIGFKDVvsvgN 186
                                       4566777888888888999988888866652 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.094
                                       EE--CCCCCTT--HHHHHHH.....................HHHHHHHHCCC..........GEEE.......CEEE CS
                     Lipase_GDSL_2  68 iliGtNDlgrgvpaaaaaand...................nleelidalraa.......apgaril.......vlgp 111
                                       +  G  D+g+++ ++++ a +                    ++el d +ra+       + g+ ++       vl++
  gi|336254601|ref|YP_004597708.1| 237 VKSGRTDAGAQAASSHTGAIAgserayeagleqagviraeSVQELFDYARALsglpepdSDGVAVItnaggpgVLTT 313
                                       44455554444444444444455555555566666666666777777777777766444444455578888888889 PP

                                       EE-TTT-TTSTCCHHHHHHHHHHHHHHHHHHC CS
                     Lipase_GDSL_2 112 lpptpeaaadarelnaviaaynealrevaaee 143
                                        ++++++ ++a++++++i++++ea+ e a+ +
  gi|336254601|ref|YP_004597708.1| 314 DAVGDSTLEMADFTDETIDELAEAMPEEANVY 345
                                       99999999999999999999999998888764 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.9
                                       TCC.HHHHHHHHHHHHHHHHHH....CT-EEE-H CS
                     Lipase_GDSL_2 122 are.lnaviaaynealrevaae....egvpfvDl 150
                                       ++  ++  +++++++l+++a++     gv+  Dl
  gi|336254601|ref|YP_004597708.1| 456 EPAqFDVDRERARKILARAADRddnrLGVESMDL 489
                                       2222555666666666666666544455555555 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0067
                                       -HHHHHHH..HHHHHHHHCCC...GEEE............C CS
                     Lipase_GDSL_2  80 paaaaaandnleelidalraaapgaril............v 108
                                        +++++ +  +e l++++r+  p+a+i+             
  gi|336254601|ref|YP_004597708.1| 543 GDEDVYDA--YEDLVSRARNYQPDATIIgvqvqemldvgeS 581
                                       44455555..******************7755544444440 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.6e-05      0.17      27      64 ..     326     363 ..     326     365 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.6e-05
                                       S-HHHHHHHHHH---SHHHHHTSTTT-HHHHHHHHHHH CS
                              HRDC  27 fpdktLleiAeklPttleeLlqiegvgkrklekygeei 64 
                                       f+d+t+ e+Ae++P  ++    i+ +g++ ++++ge++
  gi|336254601|ref|YP_004597708.1| 326 FTDETIDELAEAMPEEANVYNPIDAIGDADVDRFGEAL 363
                                       89*********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (701 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); 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 0.22s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 5463.71
//
Query:       gi|336254602|ref|YP_004597709.1|  [L=356]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-56  189.5  33.4    7.4e-56  189.5  33.4    1.5  2  ABC-3      ABC 3 transport family
    5.3e-06   25.6  33.4    5.3e-06   25.6  33.4    1.9  2  FecCD      FecCD transport family
  ------ inclusion threshold ------
        5.1    7.3   5.7       0.85    9.8   0.9    2.1  2  DUF2407_C  DUF2407 C-terminal domain


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2      0.52   3.1e+03      59     212 ..      34      51 ..      24      76 .. 0.48
   2 !  189.5  33.4   1.2e-59   7.4e-56       1     257 [.      80     345 ..      80     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.52
                             ABC-3  59 gailvgliaavalellkrktklkedtaigivlsvflalglvlvslikkskvdldsyLfGniltisqedliliaiiea 135
                                       +a+++++++ val +l                                                             
  gi|336254602|ref|YP_004597709.1|  34 AALAAAMVGFVALDWL------------------------------------------------------------- 49 
                                       3333333333333333............................................................. PP

                             ABC-3 136 vvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrsles 212
                                                                                                                  ++
  gi|336254602|ref|YP_004597709.1|  50 ---------------------------------------------------------------------------RH 51 
                                       ...........................................................................33 PP

  == domain 2  score: 189.5 bits;  conditional E-value: 1.2e-59
                             ABC-3   1 qyeflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvn......lllgailvgliaaval 71 
                                       q+ f+ r +++++ ++++++l+g+++v r+++l+g++l+H a++Gva++++++        ll+ a++vg+++a+a+
  gi|336254602|ref|YP_004597709.1|  80 QHAFMWRQIATGVCIGIVAPLVGTYLVHRQMALIGETLAHTAFAGVAVGLIFTGLtgwsgsLLWIALVVGVLGALAV 156
                                       6789************************************************9888899999*************** PP

                             ABC-3  72 ellkrktklkedtaigivlsvflalglvlvslikk...skvdldsyLfGniltisqedliliaiieavvllllllfw 145
                                       ++l+++t    d+ i+i+l+ ++a+g +l+s  ++   ++ d++ yLfGn+  ++ +   ++ai+++ v++++   +
  gi|336254602|ref|YP_004597709.1| 157 QWLTEHTTAFGDVPIAIMLTGSFAVGTLLISWGRSsmsIAIDIEGYLFGNLSVVTADGARMMAILSVAVVAVVAATY 233
                                       *******************************9988778999************************************ PP

                             ABC-3 146 kelllitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillgl 222
                                       k+ll+itfde+ A+v+ l+v+ ++ ll++++a+ vv a+q+ GviLv+ +l+iP atA +++rs+++ l ++il+g 
  gi|336254602|ref|YP_004597709.1| 234 KQLLFITFDEQAARVARLNVRWYNTLLIVMTAVVVVGAMQVLGVILVAGMLVIPVATASQIARSFRETLYCSILFGQ 310
                                       ***************************************************************************** PP

                             ABC-3 223 vsvvaGlllSyyldlatGavivlvatllfllallv 257
                                        +++ G +l   ldl++G++i++va+l++l+++++
  gi|336254602|ref|YP_004597709.1| 311 CAILGGFALALGLDLPSGGSIIVVAILFYLCSIAL 345
                                       ******************************99875 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   1.0      0.22   1.3e+03      82      96 ..      33      46 ..      25     108 .. 0.47
   2 !   25.6  33.4   8.9e-10   5.3e-06      82     286 ..     120     323 ..     112     346 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.22
                             FecCD 82 gaalgavlalllllg 96
                                      +aal+a+++ ++  +
  gi|336254602|ref|YP_004597709.1| 33 VAALAAAMVGFVA-L 46
                                      3333333333333.2 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 8.9e-10
                             FecCD  82 gaalgavlalllllgslslfalplaaflgallalllvllla..rkrkgasplkliLaG.iavsallsaltsllllll 155
                                        a +g++++l+++ ++  + +l+++a++ ++l++l v +l+  +   g  p+ ++L+G +av++ll +     + + 
  gi|336254602|ref|YP_004597709.1| 120 TAFAGVAVGLIFTGLTGWSGSLLWIALVVGVLGALAVQWLTehTTAFGDVPIAIMLTGsFAVGTLLISWGRSSMSI- 195
                                       678899999999855555668999999***********99966666677889999999789999999999888877. PP

                             FecCD 156 neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvallt 232
                                           + +i  +l+G+ls ++ + + ++++l++++++++++ +++l  ++++++ A+   +nv+ ++ ll++++a+++
  gi|336254602|ref|YP_004597709.1| 196 ----AIDIEGYLFGNLSVVTADGARMMAILSVAVVAVVAATYKQLLFITFDEQAARVARLNVRWYNTLLIVMTAVVV 268
                                       ....568********************************************************************** PP

                             FecCD 233 avavalvGpigFvG.LivPhiarllvgadhrkllplsallGallllladllarll 286
                                         a+ + G+i   G L++P      + +++r +l +s+l+G + +l    la  l
  gi|336254602|ref|YP_004597709.1| 269 VGAMQVLGVILVAGmLVIPVATASQIARSFRETLYCSILFGQCAILGGFALALGL 323
                                       **************4466888888889***************9999887776555 PP

>> DUF2407_C  DUF2407 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.9   0.00014      0.85      91     137 ..      86     132 ..      66     135 .. 0.91
   2 ?   -1.6   0.3      0.48   2.9e+03      95     118 ..     144     166 ..     138     180 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00014
                         DUF2407_C  91 edlliGlliGfflglfalllllkeegllnkrqkmaviaGvlvnlvlg 137
                                       +++  G++iG++ +l++  l+ ++ +l+ +      +aGv+v l+++
  gi|336254602|ref|YP_004597709.1|  86 RQIATGVCIGIVAPLVGTYLVHRQMALIGETLAHTAFAGVAVGLIFT 132
                                       56778************99999999*****************99986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.48
                         DUF2407_C  95 iGlliGfflglfalllllkeegll 118
                                       i+l++G +lg +a+ +l+++ + +
  gi|336254602|ref|YP_004597709.1| 144 IALVVG-VLGALAVQWLTEHTTAF 166
                                       455566.57888999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2667.08
//
Query:       gi|336254603|ref|YP_004597710.1|  [L=252]
Description: phosphonate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-31  108.3   0.0    5.7e-31  107.9   0.0    1.2  1  ABC_tran      ABC transporter
    1.1e-12   48.5   0.2    1.2e-05   25.3   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00025   20.6   0.1       0.15   11.5   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00044   20.7   0.5    0.00093   19.6   0.5    1.5  1  AAA_16        AAA ATPase domain
    0.00082   19.7   0.5     0.0084   16.4   0.5    2.1  1  AAA_22        AAA domain
     0.0011   18.7   0.2     0.0021   17.8   0.2    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0034   17.0   0.0     0.0056   16.3   0.0    1.3  1  Peripla_BP_4  Periplasmic binding protein domain
     0.0038   17.7   0.0     0.0054   17.3   0.0    1.4  1  AAA_23        AAA domain
      0.005   16.6   0.0      0.017   14.9   0.0    1.6  2  AAA_15        AAA ATPase domain
  ------ inclusion threshold ------
      0.011   16.0   0.1      0.051   13.7   0.1    2.0  1  AAA_33        AAA domain
       0.03   14.2   0.1      0.098   12.6   0.0    1.8  2  NTPase_1      NTPase
      0.053   13.4   0.0       0.28   11.1   0.0    2.1  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.055   12.8   0.0        0.1   12.0   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.085   13.1   2.0       0.62   10.3   0.4    2.5  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.086   12.8   0.1       0.21   11.6   0.1    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
       0.15   11.6   0.7       0.29   10.7   0.2    1.7  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.16   12.4   0.0       0.95    9.9   0.0    2.0  2  AAA           ATPase family associated with various cellular 
       0.25   10.9   5.8        2.8    7.5   0.0    2.9  3  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 !  107.9   0.0   5.7e-34   5.7e-31       2     136 ..      27     173 ..      26     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 5.7e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.vr 77 
                                       ++vsl++++g  ++++G+nG+GK+tLl+l++gll+p++G+++l g+++++    +  ++ig+++q+++   ++  v 
  gi|336254603|ref|YP_004597710.1|  27 DDVSLTVEAGDFLGLIGPNGSGKTTLLRLMLGLLSPDSGSVELFGRPVDD---FERGERIGYVSQQATSGGGTMpVT 100
                                       89************************************************...778899*******77777664333 PP

                                       HH..................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        +                  e+++ +++al+++g+++l+d+ +    ++LSgGq+qr  +aral+++++ll lDEpt
  gi|336254603|ref|YP_004597710.1| 101 VRecvrmgrfahvghsrltdEDRAIADEALETVGITDLADQQL----NQLSGGQRQRAYIARALASEADLLALDEPT 173
                                       3355************997666666******************....*****************************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 !   25.3   0.0   1.2e-08   1.2e-05       2      24 ..      39      61 ..      38      91 .. 0.79
   2 !   21.5   0.0   1.7e-07   0.00017     220     295 ..     129     201 ..     104     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.2e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                       +liGpNgsGK++LL+++ +l +
  gi|336254603|ref|YP_004597710.1| 39 LGLIGPNGSGKTTLLRLMLGLLS 61
                                      68****************99975 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.7e-07
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvilt 295
                                        + ++  +d  + ++++lS G+++ ++++ al++ +   +ll++DEp  g + +    +++ll++l+r g+ +il 
  gi|336254603|ref|YP_004597710.1| 129 ALETVGITDLADQQLNQLSGGQRQRAYIARALASEA---DLLALDEPTVGVDAESRDAFYQLLESLNRDGITIILI 201
                                       666677788888999**********88888888888...9*********************************986 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 !   11.5   0.0   0.00015      0.15      26      45 ..      38      57 ..      25      70 .. 0.80
   2 !    7.4   0.0    0.0027       2.7     134     203 ..     143     209 ..      78     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                      EEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAil 45
                                      f  ++GpNGSGK+ ll  +l
  gi|336254603|ref|YP_004597710.1| 38 FLGLIGPNGSGKTTLLRLML 57
                                      7789*********9987665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0027
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemle 203
                                        ++LSgG+++ + +a  +A    + a l  lDe     D++ + ++ +ll++ + +   +i i ++ ++++
  gi|336254603|ref|YP_004597710.1| 143 LNQLSGGQRQRAYIARALA----SEADLLALDEPTVGVDAESRDAFYQLLESLNRDgITIILIEHDIGVVT 209
                                       458******9999988877....56789***********************88766477777777766554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.5   9.3e-07   0.00093      26     169 ..      38     198 ..      23     201 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.3e-07
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggif.lrgkcdql.esa..ipy.............salaqalareellrql 85 
                                        + l+G+ G+GK++l+r  l  l+ d g + l g+ ++  e++  i y             +++ ++  r + ++ +
  gi|336254603|ref|YP_004597710.1|  38 FLGLIGPNGSGKTTLLRLMLGLLSPDSGSVeLFGRPVDDfERGerIGYvsqqatsgggtmpVTVRECV-RMGRFAHV 113
                                       46689****************99999777778888888853333322222222333333223344555.55555555 PP

                            AAA_16  86 ldeaesaeleawrekleeala.......avpelagaeasrllellkrllallsrderplvlvlDdlq.wadeaslql 154
                                       +    ++e +a +++ +e+++       + ++l+g   +r ++ ++r+l  +s+ ++  +l lD+    +d++s+++
  gi|336254603|ref|YP_004597710.1| 114 GHSRLTDEDRAIADEALETVGitdladqQLNQLSGG--QRQRAYIARAL--ASE-AD--LLALDEPTvGVDAESRDA 183
                                       555444444444444444444454444444444444..44444444555..333.44..777777666788888888 PP

                            AAA_16 155 laaLlrlleskpllv 169
                                       +++Ll++l+++ +++
  gi|336254603|ref|YP_004597710.1| 184 FYQLLESLNRDGITI 198
                                       888888887755544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5   8.4e-06    0.0084       7     128 ..      38     201 ..      33     205 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.4e-06
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee............erpevvfvtlpsst.....sskdllrellralgl 66 
                                       +l ++G+ G+GKTtllr +l  l  ++   e            er ++v+ +++s++     + ++ + ++ r+ ++
  gi|336254603|ref|YP_004597710.1|  38 FLGLIGPNGSGKTTLLRLMLGLLSPDSGSVElfgrpvddfergERIGYVSQQATSGGgtmpvTVRE-CVRMGRFAHV 113
                                       6779****************9996555555589999999988855555555555555442222222.2233333333 PP

                            AAA_22  67 elka...........................erlsseellealeqalraravielliiDEaqh.lr..seealeeLr 113
                                       ++++                           +    ++ ++++++al + a+  ll +DE    ++  s +a+ +L 
  gi|336254603|ref|YP_004597710.1| 114 GHSRltdedraiadealetvgitdladqqlnQLSGGQRQRAYIARALASEAD--LLALDEPTVgVDaeSRDAFYQLL 188
                                       3333555566666666633333333344333333333333444444444444..66666655555565588888888 PP

                            AAA_22 114 sllnlsrkgvqliLv 128
                                       + ln  r+g+++iL+
  gi|336254603|ref|YP_004597710.1| 189 ESLN--RDGITIILI 201
                                       8888..888888887 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 !   17.8   0.2   2.1e-06    0.0021      15      50 ..      29      64 ..      24      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.1e-06
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                       +++++  ++  l+Gp+GsGK+Tll  +  lL p++
  gi|336254603|ref|YP_004597710.1| 29 VSLTVEAGDFLGLIGPNGSGKTTLLRLMLGLLSPDS 64
                                      5566665557889************88888888875 PP

>> Peripla_BP_4  Periplasmic binding protein 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    0.0056      15     105 ..     121     223 ..     111     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.6e-06
                                       HHHHHHHHHHHHTTCEEEEE.ECSTT-H.HHHHHHHHHHHHTT-SEEE.......E--SSHHHHHHHHHHHHHTT-E CS
                      Peripla_BP_4  15 aaregleeaakelgaevtvv.gdaenda.aeQvaqiedaiakgvdgii.......vapvdstalapalkkakaaGIp 82 
                                       ++r  ++ea+++ g++   + + ++ +  ++Q a i  a+a+ +d+++       v++ + +a ++ l+ ++  GI 
  gi|336254603|ref|YP_004597710.1| 121 EDRAIADEALETVGITDLADqQLNQLSGgQRQRAYIARALASEADLLAldeptvgVDAESRDAFYQLLESLNRDGIT 197
                                       56667889999999999998877888888****************9998888888999999**************** PP

                                       EEEESTT...GCTTT-CEEEEEC-HH CS
                      Peripla_BP_4  83 Vvafdsd...dapsgerlayvgfdne 105
                                       ++ +  d   +++ ++r+a++++  +
  gi|336254603|ref|YP_004597710.1| 198 IILIEHDigvVTDRADRIACINTELY 223
                                       *******9999999999999988766 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.4e-06    0.0054      24      44 ..      41      61 ..      28     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.4e-06
                            AAA_23 24 ItGpNGaGKTTildAiklaLy 44
                                      ++GpNG+GKTT+l+ +   L 
  gi|336254603|ref|YP_004597710.1| 41 LIGPNGSGKTTLLRLMLGLLS 61
                                      78***********97766665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.7e-05     0.017      22      49 ..      36      62 ..      27      77 .. 0.83
   2 ?   -1.6   0.0       1.7   1.7e+03     290     333 ..     139     173 ..     117     200 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                            AAA_15 22 seeltvliGkNnsGKSsilealdlFlnn 49
                                       + +  liG+N+sGK+++l+++  +l+ 
  gi|336254603|ref|YP_004597710.1| 36 GD-FLGLIGPNGSGKTTLLRLMLGLLSP 62
                                      45.7779*************99887775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
                            AAA_15 290 eelplnknGsGvqrllllillileaekkdekeeknvilliEEPE 333
                                        ++ ln+ + G+++  +++   + a++        ++l+++EP 
  gi|336254603|ref|YP_004597710.1| 139 ADQQLNQLSGGQRQRAYIAR--ALASEA-------DLLALDEPT 173
                                       56788888889999888874..444444.......567777775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.2e-05     0.051       4      96 ..      41     192 ..      39     214 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-05
                            AAA_33   4 lvGlpGsGKstlaerllkklgavllssdt................................................ 32 
                                       l+G++GsGK+tl++ +l      lls d+                                                
  gi|336254603|ref|YP_004597710.1|  41 LIGPNGSGKTTLLRLML-----GLLSPDSgsvelfgrpvddfergerigyvsqqatsgggtmpvtvrecvrmgrfah 112
                                       69***********9887.....4455555333333333355555555555555555555555555555444433333 PP

                            AAA_33  33 ........lrrrlfgtdqqskt.................dytrvldr.lyqilnelarkalsagrn.vildatnls. 81 
                                               +                              d +++++    q++++++++al+++++ + ld + +  
  gi|336254603|ref|YP_004597710.1| 113 vghsrltdE------------DraiadealetvgitdlaD-QQLNQLsGGQRQRAYIARALASEADlLALDEPTVGv 176
                                       333222221............0333333333333333321.122221122344455555555555523336664432 PP

                            AAA_33  82 .rrerarflklarrlg 96 
                                        ++ r++f +l++ l+
  gi|336254603|ref|YP_004597710.1| 177 dAESRDAFYQLLESLN 192
                                       1566666666666555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.9e-05     0.098       4      74 ..      41     110 ..      39     136 .. 0.79
   2 ?   -1.2   0.0       1.6   1.6e+03      90     103 ..     157     171 ..     145     211 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.9e-05
                                       EE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-.------EEEEEET.T--EEEEEETT---SSEETTE CS
                          NTPase_1   4 iTGppGvGKtTlvkkvlellkssgvkvgGfyteevr.eggrrigFkivdlasgeegiLarveakreprvgky 74 
                                       + Gp G+GKtTl++ +l ll+ +  +v+ f  +    e+g+rig+   + +sg  ++   v+  +++r+g++
  gi|336254603|ref|YP_004597710.1|  41 LIGPNGSGKTTLLRLMLGLLSPDSGSVELFGRPVDDfERGERIGYVSQQATSGGGTMPVTVR--ECVRMGRF 110
                                       669*****************988877777766655569999****99999888766655555..67777776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                                       HHHH.HHH-EEEE-- CS
                          NTPase_1  90 rkal.seadviviDE 103
                                        +al sead++ +DE
  gi|336254603|ref|YP_004597710.1| 157 ARALaSEADLLALDE 171
                                       444447888888888 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 ?   11.1   0.0   0.00028      0.28       2      32 ..      39      69 ..      38     133 .. 0.82
   2 ?    0.1   0.0      0.71   7.1e+02      19      37 ..     187     205 ..     183     252 .] 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgt 32
                                      lg++g +gsGKTtLl  ++  l+    +v +
  gi|336254603|ref|YP_004597710.1| 39 LGLIGPNGSGKTTLLRLMLGLLSPDSGSVEL 69
                                      799*************999999877666655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.71
                              MobB  19 lipelkarglrvgtiKhah 37 
                                       l++ l++ g+++ +i h+ 
  gi|336254603|ref|YP_004597710.1| 187 LLESLNRDGITIILIEHDI 205
                                       6666777777777666653 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001       0.1       7      49 ..      21      63 ..      15      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                      Mg_chelatase  7 GqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllppl 49
                                      G++ a   + +++  g  l l+Gp GsGKt l + + +ll+p 
  gi|336254603|ref|YP_004597710.1| 21 GEQLAVDDVSLTVEAGDFLGLIGPNGSGKTTLLRLMLGLLSPD 63
                                      555666666667767777889******************9875 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 ?   -3.0   0.1         9     9e+03      29      43 ..      87     100 ..      78     103 .. 0.72
   2 ?   10.3   0.4   0.00063      0.62      28      89 ..     141     189 ..     126     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9
                           SbcCD_C  29 ssgtlSGGekqflay 43 
                                       s ++ SGG + ++++
  gi|336254603|ref|YP_004597710.1|  87 SQQATSGGGT-MPVT 100
                                       4567899988.6665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00063
                           SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       ++ ++lSGG++   ay+a a+a     s+        +l++LDE   ++D+es+++  +lle
  gi|336254603|ref|YP_004597710.1| 141 QQLNQLSGGQR-QRAYIARALA-----SE-------ADLLALDEPTVGVDAESRDAFYQLLE 189
                                       66778888888.5566665522.....33.......47999***********9999998886 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 ?   11.6   0.1   0.00021      0.21       4      24 ..      41      62 ..      39      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                                      EE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5  4 LvGppGtgKselaerlaaal.n 24
                                      L+Gp G+gK++l + ++ +l  
  gi|336254603|ref|YP_004597710.1| 41 LIGPNGSGKTTLLRLMLGLLsP 62
                                      9***************999863 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 ?   10.7   0.2   0.00029      0.29       4      21 ..      40      57 ..      37      67 .. 0.84
   2 ?   -2.8   0.0         4     4e+03      27      37 ..     196     206 ..     182     235 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                                      EEEESTTCCHHHHHHHHH CS
                              cobW  4 vltGflGsGKTtLlnhll 21
                                      +l G+ GsGKTtLl+ +l
  gi|336254603|ref|YP_004597710.1| 40 GLIGPNGSGKTTLLRLML 57
                                      789***********9876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4
                                       S-EEEEESS-S CS
                              cobW  27 lklavivNefg 37 
                                         + +i+ ++g
  gi|336254603|ref|YP_004597710.1| 196 ITIILIEHDIG 206
                                       44444444444 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 ?    9.9   0.0   0.00095      0.95       3      21 ..      41      59 ..      39      90 .. 0.85
   2 ?    0.1   0.0      0.98   9.8e+02      14      64 ..     156     201 ..     130     219 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00095
                                      EESSTTSSHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavake 21
                                      l+Gp G GKT+l + +   
  gi|336254603|ref|YP_004597710.1| 41 LIGPNGSGKTTLLRLMLGL 59
                                      89**********9987665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.98
                                       HHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEE CS
                               AAA  14 lakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfi 64 
                                       +a+a+a+e  +++l ++ +++   +  es + + +l++++ +    +i++i
  gi|336254603|ref|YP_004597710.1| 156 IARALASE--ADLLALDEPTVG--VDAESRDAFYQLLESLNRDG-ITIILI 201
                                       45555555..233444444433..22334444444444443333.455555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0028       2.8      31      50 ..      34      53 ..      28      73 .. 0.89
   2 ?    0.3   0.1      0.44   4.4e+02     127     188 ..     152     203 ..     108     204 .. 0.57
   3 ?    4.5   0.5     0.023        23     173     188 ..     235     250 ..     207     252 .] 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0028
                            AAA_25 31 pagelallaGapgtGKttla 50
                                       ag++  l+G+ g+GKttl+
  gi|336254603|ref|YP_004597710.1| 34 EAGDFLGLIGPNGSGKTTLL 53
                                      6899999***********97 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.44
                            AAA_25 127 tadvdaleaaieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                       ++++  +++a+ + e ++l+ +D    ++g d +s ++  +l+e l+r     g++++l+ H
  gi|336254603|ref|YP_004597710.1| 152 QRAY--IARALAS-E-ADLLALDE--PTVGVDAESRDAFYQLLESLNR----DGITIILIEH 203
                                       3333..5555555.3.67777774..4566666666666666666655....4677777766 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.023
                            AAA_25 173 eriarrtgaavllvhH 188
                                       + +++++ga+ ++vhH
  gi|336254603|ref|YP_004597710.1| 235 DALREAYGATGTVVHH 250
                                       7899************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1817.29
//
Query:       gi|336254604|ref|YP_004597711.1|  [L=385]
Description: metal ion ABC transporter periplasmic protein [Halopiger xanaduensis SH-6]
Scores for complete 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-41  143.0   4.9    1.4e-41  142.7   4.9    1.1  1  ZnuA        Zinc-uptake complex component A periplasmic
  ------ inclusion threshold ------
      0.048   13.5   3.2        0.1   12.5   3.2    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
       0.15   11.3  15.7       0.21   10.8  15.7    1.1  1  Zip         ZIP Zinc transporter
       0.17   10.6   5.1       0.25   10.1   5.1    1.3  1  SAPS        SIT4 phosphatase-associated protein
          1    8.6  14.7        1.4    8.2  14.7    1.1  1  BUD22       BUD22
        1.4    7.1  15.1        1.7    6.8  15.1    1.1  1  CDC45       CDC45-like protein
        2.3    7.6  22.2        3.1    7.1  22.2    1.1  1  SDA1        SDA1


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.7   4.9   5.3e-45   1.4e-41       2     208 ..      41     323 ..      41     379 .. 0.81

  Alignments for each domain:
  == domain 1  score: 142.7 bits;  conditional E-value: 5.3e-45
                                       EESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTTCCCE.EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                              ZnuA   2 vattsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssqatrv.ev 77 
                                       +a +++l+d+ ++vaGd+   +  v++g+  H +ep+    +++a+++++vy      +w ++++++++ + ++ ++
  gi|336254604|ref|YP_004597711.1|  41 YAAFFALQDWSEHVAGDQLSFENPVEAGQIGHGWEPQGDLTADIADSEVFVYLDSPEFAWAQDVASQLETDYDHvTL 117
                                       58899***********************************************9855555*****9888654443477 PP

                                       EETTTTC.....................CSEBCSS.......................................... CS
                                       xxxxxxx.....................xxxxxxx.......................................... RF
                              ZnuA  78 idlsegv.....................eeeeeee.......................................... 91 
                                       id  +g+                     +     +                                          
  gi|336254604|ref|YP_004597711.1| 118 IDGMDGIedellafdeahdhdhgseddhD-----Hegdhahedeeehdhetndsteshdeheghddhadhedehdhd 189
                                       77666556777777755555555544440.....1444455555566667788888888888888888899999999 PP

                                       .............ESTGGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSGTEGE CS
                                       .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA  92 .............DpHiWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireelaeipeekrk 155
                                                    DpH+W++p +a+ +v +iad+L+eadp+n+dty++na+ay+++L ++d+++++ +ae+ ++   
  gi|336254604|ref|YP_004597711.1| 190 hnhedetddaefhDPHVWVDPVLAQDVVGTIADGLAEADPDNEDTYRENADAYAQRLADVDDQLESLVAEADRDV-A 265
                                       9********************************************************************999665.9 PP

                                       EEESSSTTHHHHHHTT-EEEEEESSSSS....HHHHHHHHHHHHHTT-SEEEEET.TS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx.xx RF
                              ZnuA 156 lvtthdafgylarayglevagiagiste....aaqiaalieeikeagvkaifvep.la 208
                                       ++  hd+f+y +++yg+e+ + + +s++    a+q+a+ i+ i+e+++++i+++p  +
  gi|336254604|ref|YP_004597711.1| 266 VLAGHDSFRYIEERYGFELHTPVDVSPNaevtAGQLADTIDLIDEHEIETILYDPfET 323
                                       99***************************************************99533 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.2   4.1e-05       0.1       1      26 []       2      27 ..       2      28 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                        TAT_signal  1 klSRRdFLKgsAAaaAAaalggcaaa 26
                                      +lSRR+ L ++A+  A+  l+g+a++
  gi|336254604|ref|YP_004597711.1|  2 NLSRRSVLHAGAGSLALSSLAGLAGC 27
                                      58********************9986 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  15.7   8.2e-05      0.21     112     203 ..     135     225 ..     126     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.2e-05
                               Zip 112 kkasssssesaakksvsndkveeseekedhvaeadtdadskeelrngkqeksesekeqaseeedkeklaslkvraii 188
                                       +++++ s+  ++++  ++++ ee+++ e +++ + +d+ +++ +++++++ +++++++++ e d+ + +   v +  
  gi|336254604|ref|YP_004597711.1| 135 HDHDHGSEDDHDHEGDHAHEDEEEHDHETNDSTESHDEHEGHDDHADHEDEHDHDHNHED-ETDDAEFHDPHVWVDP 210
                                       567888888889999999999999999999999999999999999999999999999987.6666666666666666 PP

                               Zip 189 lllglilHsfidGLA 203
                                       +l  +++  + dGLA
  gi|336254604|ref|YP_004597711.1| 211 VLAQDVVGTIADGLA 225
                                       777777777777776 PP

>> SAPS  SIT4 phosphatase-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.1   9.9e-05      0.25     274     347 ..     132     205 ..      70     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.9e-05
                              SAPS 274 easkeesaesedltdkdedvsleesksakdenkesdesesdtaeesseededdasseesalaeeteeklrkkpv 347
                                       ++++++++ sed +d++ d ++e++++++ e+++s es+++++ +++++d++d++++++  ++et+++  ++p 
  gi|336254604|ref|YP_004597711.1| 132 DEAHDHDHGSEDDHDHEGDHAHEDEEEHDHETNDSTESHDEHEGHDDHADHEDEHDHDHNHEDETDDAEFHDPH 205
                                       34555666777777777777777777777778888888888888888888888888888888888877766665 PP

>> BUD22  BUD22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  14.7   0.00053       1.4     145     250 ..     140     252 ..     111     288 .. 0.43

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00053
                             BUD22 145 eeekkkkkkkkkkkkkkeeee...eeesdkeeesedsedeekeeseddeeeeeededdedaee.............. 204
                                        +e + + + +++ +++ee++   ++++++++e e+ +d          ++++ede d+d ++              
  gi|336254604|ref|YP_004597711.1| 140 GSEDDHDHEGDHAHEDEEEHDhetNDSTESHDEHEGHDD----------HADHEDEHDHDHNHedetddaefhdphv 206
                                       222222222222222222222111222222222222222..........2222222222222211111122445666 PP

                             BUD22 205 .....................deedeeaeerelaqydgllasddededeyneetdeesseesdssds 250
                                                            d                      ++ed y e+ d  +++ +d +d+
  gi|336254604|ref|YP_004597711.1| 207 wvdpvlaqdvvgtiadglaeaD---------------------PDNEDTYRENADAYAQRLADVDDQ 252
                                       5555555544444444444432.....................333333333333333333333333 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  15.1   0.00068       1.7     102     184 ..     113     195 ..      81     256 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00068
                             CDC45 102 erivvfDDgd.ieeeleeereayealeeeeesdeedeeeeeeddddeeeeeeeeedeedeeedeeeskkkrksksde 177
                                       ++++ +D  d ie+el +  ea  + +  e+++ ++e ++ ++d++e+++e ++++e+++e+++++++ ++++++d+
  gi|336254604|ref|YP_004597711.1| 113 DHVTLIDGMDgIEDELLAFDEAHDHDHGSEDDH-DHEGDHAHEDEEEHDHETNDSTESHDEHEGHDDHADHEDEHDH 188
                                       566666666656666665555444444444433.2222222222222222222222333333333323333333333 PP

                             CDC45 178 eeesddd 184
                                       +++++d+
  gi|336254604|ref|YP_004597711.1| 189 DHNHEDE 195
                                       3221111 PP

>> SDA1  SDA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  22.2    0.0012       3.1      58     161 ..     109     226 ..      99     271 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0012
                              SDA1  58 akkfGeeevaegieGle..Llekwkeeekkekreeeeedsddeddeedwevesdddseedseggwidvesdeeeiee 132
                                       +  + +++  +g +G+e  Ll+ +++ + +  +   e+d+d+e d++++++e++d++ +ds ++    ++de  +  
  gi|336254604|ref|YP_004597711.1| 109 ETDYDHVTLIDGMDGIEdeLLAFDEAHDHDHGS---EDDHDHEGDHAHEDEEEHDHETNDS-TE----SHDEH-EGH 176
                                       556777777788899999666665555544433...3332333333333333333332333.22....22222.222 PP

                              SDA1 133 sdesedeeeeeeeeeekeekeeeeeeee.........................e 161
                                       +d+ ++e+e +++++ ++e ++     e                         e
  gi|336254604|ref|YP_004597711.1| 177 DDHADHEDEHDHDHNHEDETDDA----EfhdphvwvdpvlaqdvvgtiadglaE 226
                                       22223332222222222222222....122235666666666666666555431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1027  (0.0572815); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); 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):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 2696.02
//
Query:       gi|336254605|ref|YP_004597712.1|  [L=397]
Description: ribonuclease BN [Halopiger xanaduensis SH-6]
Scores for 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-45  155.3  25.1    2.7e-45  155.0  25.1    1.1  1  Virul_fac_BrkB  Virulence factor BrkB
    4.6e-06   26.7   4.7    7.4e-06   26.0   4.7    1.2  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
    0.00013   21.8   8.0     0.0002   21.2   8.0    1.1  1  ERM             Ezrin/radixin/moesin family
    0.00016   22.0   7.1    0.00016   22.0   7.1    2.2  2  ZapB            Cell division protein ZapB
    0.00078   19.1   6.3      0.001   18.7   6.3    1.1  1  Filament        Intermediate filament protein
    0.00094   19.2   5.7     0.0016   18.5   5.7    1.4  1  bZIP_1          bZIP transcription factor
      0.002   18.7   3.1     0.0041   17.7   2.8    1.7  2  YabA            Initiation control protein YabA
     0.0052   17.2   0.9     0.0052   17.2   0.9    2.1  2  Enkurin         Calmodulin-binding
  ------ inclusion threshold ------
      0.016   15.3   8.6      0.023   14.8   8.6    1.2  1  ADIP            Afadin- and alpha -actinin-Binding
      0.019   15.0   8.7      0.027   14.5   8.7    1.1  1  Rootletin       Ciliary rootlet component, centrosome cohesio
      0.029   14.7   2.4      0.055   13.8   2.4    1.4  1  TSC22           TSC-22/dip/bun family
      0.041   12.1   1.3      0.055   11.6   1.3    1.1  1  EzrA            Septation ring formation regulator, EzrA
      0.086   12.2   7.9       0.25   10.7   7.9    1.6  1  GAS             Growth-arrest specific micro-tubule binding
      0.093   12.9   0.4      0.093   12.9   0.4    2.3  2  JIP_LZII        JNK-interacting protein  leucine zipper II
       0.11   12.8   0.5       0.81   10.1   0.3    2.1  2  FlaC_arch       Flagella accessory protein C (FlaC)
       0.13   12.4   0.8       0.28   11.3   0.1    1.7  2  DUF2053         Predicted membrane protein (DUF2053)
       0.16   12.2   6.3       0.59   10.3   5.0    2.0  2  Cnn_1N          Centrosomin N-terminal motif 1
       0.16   11.8   6.3       0.11   12.3   3.0    1.9  2  KASH_CCD        Coiled-coil region of CCDC155 or KASH
       0.17   12.0   0.4       0.33   11.0   0.4    1.5  1  DUF1664         Protein of unknown function (DUF1664)
       0.22   12.0   3.1        2.8    8.4   0.6    2.2  2  Fungal_TACC     Fungal Transforming acidic coiled-coil (TACC)
       0.24   10.4   1.0       0.34    9.9   1.0    1.1  1  Perilipin       Perilipin family
       0.86    9.5  12.9        2.5    7.9  12.9    1.6  1  CortBP2         Cortactin-binding protein-2
       0.92    9.8   4.7       0.46   10.7   1.0    2.1  2  HALZ            Homeobox associated leucine zipper
        1.1    9.3   7.4          4    7.5   7.5    2.0  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
        1.6    8.8  11.0          1    9.4   7.1    2.0  2  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
        1.8    9.1  17.2        1.4    9.4  14.2    1.9  2  APG6_N          Apg6 coiled-coil region
        2.9    8.3   7.8        4.2    7.8   5.9    1.7  1  CENP-H          Centromere protein H (CENP-H)
        3.9    7.3  13.1        1.7    8.5   4.2    2.7  2  DivIC           Septum formation initiator
        5.8    7.1  16.2        8.4    6.6   5.5    2.5  2  Cep57_CLD_2     Centrosome localisation domain of PPC89
        6.9    7.6  11.3         10    7.1   2.0    2.2  2  PRKG1_interact  cGMP-dependent protein kinase interacting dom
        9.1    5.3   7.3         13    4.7   7.3    1.1  1  Atg14           Vacuolar sorting 38 and autophagy-related sub
        9.5    6.1   8.1         16    5.4   0.6    2.7  2  betaPIX_CC      betaPIX coiled coil


Domain annotation for each model (and alignments):
>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.0  25.1   4.9e-48   2.7e-45       2     254 ..      21     257 ..      20     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 155.0 bits;  conditional E-value: 4.9e-48
                    Virul_fac_BrkB   2 eddlsllAaalayytllSlfPlllvllavlgllglddelqeqlldllaevlpegaaevvedilqrllnqaslgllgl 78 
                                       +++++ +Aa++ay +++Sl Pll++++ +++++g +d+++ +++++ +++lpe+++ +ve+ +++   +a  +++gl
  gi|336254605|ref|YP_004597712.1|  21 QKNVTFMAASIAYQAFISLLPLLVLVFFLVTIVG-GDQFATEVTAATEGFLPESGQLIVENAIEDSPASAGSSIIGL 96 
                                       78999*************************9976.79****************99********99999999****** PP

                    Virul_fac_BrkB  79 avllwsasggvsalrralnkiygveesrsflrkrllsllllllllvllllslvlsvflqslllasapllglglelse 155
                                       +vllw a++++++l++a+ +iy+++   s++ ++ + l+++ +l+ +ll+++++s++l +        +++      
  gi|336254605|ref|YP_004597712.1|  97 VVLLWGALKIFRGLDTAFSEIYETTAESSLIDQLRDGLIVFGALGGALLAAVAASIVLAF--------FPAIP---- 161
                                       ************************776788888888888888888888888888888866........44332.... PP

                    Virul_fac_BrkB 156 llllqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwllvkilfslylsnfasynaiYGslgalii 232
                                         +++ll+ ++++++l++af+ +Y+++p++ v+ r++lpGa++aa++w++++ lf++y+s fa+ ++  G+lga+++
  gi|336254605|ref|YP_004597712.1| 162 --FISLLQPILLAIVLTVAFLPMYYYFPDADVSAREVLPGAAVAAVGWTALQSLFQVYVS-FAGSSESAGPLGAILL 235
                                       ..367777778999999******************************************9.5889999********* PP

                    Virul_fac_BrkB 233 lllWlylsalilLlGaelnael 254
                                       ll Wly+ +lilLlG ++na+ 
  gi|336254605|ref|YP_004597712.1| 236 LLTWLYFGGLILLLGGVVNAVS 257
                                       *******************985 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 !   26.0   4.7   1.3e-08   7.4e-06      49     122 ..     297     374 ..     290     385 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.3e-08
                    CENP-F_leu_zip  49 tskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnssle....nlleekEqekvqmk 121
                                       +++ e e l +++ + ++e+ +l++dL+a rs +  Le  + +  +r++ Le++n +le    +l +e+Eqe+ q+ 
  gi|336254605|ref|YP_004597712.1| 297 DARREREHLTAQLGTVSRERDQLQHDLEAQRSRRYRLEDRVGELDSRIDALEATNRDLEseneRLRRELEQERQQEP 373
                                       689999***********************************************999987222134456677766655 PP

                    CENP-F_leu_zip 122 e 122
                                       e
  gi|336254605|ref|YP_004597712.1| 374 E 374
                                       4 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   8.0   3.6e-07    0.0002      45     132 ..     298     385 ..     294     393 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.6e-07
                               ERM  45 aeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerLkeeleeareaeee 121
                                       a++e+e L+++   + +e ++l+++ e++ + +++le+++ e ++++  le  ++  e+e+erL++ele+ r++e e
  gi|336254605|ref|YP_004597712.1| 298 ARREREHLTAQLGTVSRERDQLQHDLEAQRSRRYRLEDRVGELDSRIDALEATNRDLESENERLRRELEQERQQEPE 374
                                       7899************************************************************************* PP

                               ERM 122 akekllealst 132
                                        +++l+e ls 
  gi|336254605|ref|YP_004597712.1| 375 WRRRLREGLSH 385
                                       *****998876 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.6     0.092        52      27      61 ..     295     329 ..     294     334 .. 0.90
   2 !   22.0   7.1   2.9e-07   0.00016      18      64 ..     335     381 ..     332     387 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.092
                              ZapB  27 ieeLkeeneelkeenreleeeneqlkeereawqer 61 
                                       i++ ++e e l+ +   +++e +ql+++ ea+++r
  gi|336254605|ref|YP_004597712.1| 295 IDDARREREHLTAQLGTVSRERDQLQHDLEAQRSR 329
                                       567789999**********************9988 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.9e-07
                              ZapB  18 dtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64 
                                       d++ +L  +i++L++ n+ l++en++l++e+eq++++  +w++rl+ 
  gi|336254605|ref|YP_004597712.1| 335 DRVGELDSRIDALEATNRDLESENERLRRELEQERQQEPEWRRRLRE 381
                                       78889****************************************97 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   6.3   1.9e-06     0.001      46     140 ..     277     372 ..     258     392 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.9e-06
                                       X.XXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  46 sklkelyekeleelrk.qldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkdldeatlarvd 121
                                       +   + +e+  e+ r   +d++ +er++l ++l+++  e ++l++ +e + ++r  +E+ + +l   +d++  +  d
  gi|336254605|ref|YP_004597712.1| 277 TDAVDEFETIPESKRPpMIDDARREREHLTAQLGTVSRERDQLQHDLEAQRSRRYRLEDRVGELDSRIDALEATNRD 353
                                       55555555554544433699********************************************************* PP

                                       XXXXXXXXXXXXXXXXXXX CS
                          Filament 122 LekkvesLkeelaflkkvh 140
                                       Le++ e L+ el+  ++  
  gi|336254605|ref|YP_004597712.1| 354 LESENERLRRELEQERQQE 372
                                       *************998865 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   5.7   2.9e-06    0.0016      15      61 ..     324     370 ..     303     372 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.9e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  15 eaArrsRqRKqaeieeLerrvkaLekeNksLkseleelkkevekLks 61 
                                       ea+r  R R + ++ eL +r +aLe+ N +L se+e+l+ e e+ ++
  gi|336254605|ref|YP_004597712.1| 324 EAQRSRRYRLEDRVGELDSRIDALEATNRDLESENERLRRELEQERQ 370
                                       5666666688889***************************9998776 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       3.7     2e+03      23      48 ..     301     326 ..     294     332 .. 0.59
   2 !   17.7   2.8   7.3e-06    0.0041       5      74 ..     318     387 ..     314     390 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  23 eleelkeelaelleenaeLelenekl 48 
                                       e e+l ++l ++  e ++L+ + e  
  gi|336254605|ref|YP_004597712.1| 301 EREHLTAQLGTVSRERDQLQHDLEAQ 326
                                       55566666666666666666555444 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 7.3e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLa 74 
                                       +l + le+  ++  +l ++++el +++ +l   n++Le ene+lr++le+e+++e e +++l+eg ++++
  gi|336254605|ref|YP_004597712.1| 318 QLQHDLEAQRSRRYRLEDRVGELDSRIDALEATNRDLESENERLRRELEQERQQEPEWRRRLREGLSHVR 387
                                       5566666666777788999*****************************9999999999999998887765 PP

>> Enkurin  Calmodulin-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.9   9.3e-06    0.0052      18      96 ..     266     349 ..     260     351 .. 0.88
   2 ?    0.4   2.1       1.6   8.9e+02       8      37 ..     348     377 ..     347     389 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9.3e-06
                           Enkurin  18 eeeeekeeaekkeappgmrllseeerqellegLkkkweelnkeyqslp.....llidtlskrqrKeklEkeLkqlEk 89 
                                        ++e++ +a++ +a +++++++e++r  +++  ++++e+l+ ++  ++     l+ d  ++r+r+ +lE +  +l+ 
  gi|336254605|ref|YP_004597712.1| 266 DAAEDEDAADETDAVDEFETIPESKRPPMIDDARREREHLTAQLGTVSrerdqLQHDLEAQRSRRYRLEDRVGELDS 342
                                       4455556666666679********************************99999999999****************** PP

                           Enkurin  90 dikllek 96 
                                        i  le 
  gi|336254605|ref|YP_004597712.1| 343 RIDALEA 349
                                       **99986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.6
                           Enkurin   8 kkrkkeleeeeeeeekeeaekkeappgmrl 37 
                                       + ++++le+e+e+ ++e +++++++p++r+
  gi|336254605|ref|YP_004597712.1| 348 EATNRDLESENERLRRELEQERQQEPEWRR 377
                                       556667777777777776666665555554 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   8.6   4.1e-05     0.023      54     117 ..     308     371 ..     294     388 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-05
                              ADIP  54 qreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekee 117
                                       q  ++++++ +l++++e ++s+  rl++++ +l++++++++a+ r+le ++++l + l +e+++
  gi|336254605|ref|YP_004597712.1| 308 QLGTVSRERDQLQHDLEAQRSRRYRLEDRVGELDSRIDALEATNRDLESENERLRRELEQERQQ 371
                                       33467788899***********************************************999986 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   8.7   4.8e-05     0.027      64     135 ..     303     378 ..     259     388 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.8e-05
                         Rootletin  64 eesadl........eealakLeeErqrseklaqvnslLreqleearqaneaLtedlqkltkdwerlreeleqkekew 132
                                       e+ + +        +++ + Le  r r  +l++    L   +++ +++n+ L++++++l++++e+ r++    e ew
  gi|336254605|ref|YP_004597712.1| 303 EHLTAQlgtvsrerDQLQHDLEAQRSRRYRLEDRVGELDSRIDALEATNRDLESENERLRRELEQERQQ----EPEW 375
                                       2222223555555599***********************************************976665....5555 PP

                         Rootletin 133 ree 135
                                       r++
  gi|336254605|ref|YP_004597712.1| 376 RRR 378
                                       554 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.4   9.8e-05     0.055      14      47 ..     335     368 ..     331     374 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.8e-05
                             TSC22  14 EeVevLkekIkeLeernseleeENslLkalaspe 47 
                                       + V +L ++I  Le++n+ le+EN+ L++ + +e
  gi|336254605|ref|YP_004597712.1| 335 DRVGELDSRIDALEATNRDLESENERLRRELEQE 368
                                       6799999*********************999887 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.3   9.8e-05     0.055     347     428 ..     303     384 ..     295     396 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 347 relekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkel 423
                                       + l+++l +++++ ++l+++le++     +l++++ el+++++++e    +++ + + lr++ ++ r+q  e++++l
  gi|336254605|ref|YP_004597712.1| 303 EHLTAQLGTVSRERDQLQHDLEAQRSRRYRLEDRVGELDSRIDALEATNRDLESENERLRRELEQERQQEPEWRRRL 379
                                       44455555555555555555555555555555555555555555555555555555555555555555555555555 PP

                                       HHHHH CS
                              EzrA 424 keikr 428
                                       +e  +
  gi|336254605|ref|YP_004597712.1| 380 REGLS 384
                                       55555 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 ?   10.7   7.9   0.00045      0.25      50     135 ..     296     385 ..     290     388 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                               GAS  50 seisqenkrlkepLkkaeeeveeLrkqlknyekdkqslk....nlkarlkelekelkdlkwehevleqrfekveker 122
                                       +++  e ++l+ +L ++ +e+++L+++l+ +++ + +l+    +l +r+  le   +dl+ e+e l+ ++e+  ++ 
  gi|336254605|ref|YP_004597712.1| 296 DDARREREHLTAQLGTVSRERDQLQHDLEAQRSRRYRLEdrvgELDSRIDALEATNRDLESENERLRRELEQERQQE 372
                                       6788999**********************999999887633336888999999999999999999999998888888 PP

                               GAS 123 delykkfeaaiqe 135
                                        e++++ ++ + +
  gi|336254605|ref|YP_004597712.1| 373 PEWRRRLREGLSH 385
                                       8888887776655 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   0.00017     0.093      28      68 ..     302     342 ..     301     345 .. 0.94
   2 ?    3.1   3.0      0.19     1e+02      37      65 ..     353     381 ..     342     383 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00017
                          JIP_LZII  28 kddLIarvdeLtsereiLreEleslqkakerlesrikelEe 68 
                                       +++L a++   + er+ L+++le+ ++ + rle+r+ el+ 
  gi|336254605|ref|YP_004597712.1| 302 REHLTAQLGTVSRERDQLQHDLEAQRSRRYRLEDRVGELDS 342
                                       78999*********************************986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.19
                          JIP_LZII  37 eLtsereiLreEleslqkakerlesrike 65 
                                       +L se+e Lr Ele+ +++  + + r++e
  gi|336254605|ref|YP_004597712.1| 353 DLESENERLRRELEQERQQEPEWRRRLRE 381
                                       58899999999999999888888887776 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 ?   -0.4   0.0       2.7   1.5e+03      10      31 ..     303     324 ..     292     325 .. 0.74
   2 ?   10.1   0.3    0.0014      0.81       5      36 ..     333     364 ..     331     369 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.7
                         FlaC_arch  10 sklsteletvkkeneelsksve 31 
                                       + l  +l+tv +e ++l+ ++e
  gi|336254605|ref|YP_004597712.1| 303 EHLTAQLGTVSRERDQLQHDLE 324
                                       4566788888888888887776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0014
                         FlaC_arch   5 lEnklsklsteletvkkeneelsksveelken 36 
                                       lE ++++l+++++ ++++n +l+++ e+l ++
  gi|336254605|ref|YP_004597712.1| 333 LEDRVGELDSRIDALEATNRDLESENERLRRE 364
                                       77777888888888888888887777777654 PP

>> DUF2053  Predicted membrane protein (DUF2053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       3.6     2e+03      34      68 ..      27      60 ..      15      98 .. 0.64
   2 ?   11.3   0.1    0.0005      0.28      21     121 ..     123     220 ..     107     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.6
                           DUF2053 34 vvlailaylltqlvKmlllAtlfpafdteeldliq 68
                                      ++ +i++ ++ +l+ +l+l  ++ ++ ++  ++ +
  gi|336254605|ref|YP_004597712.1| 27 MAASIAYQAFISLLPLLVLVFFLVTI-VGGDQFAT 60
                                      33344444556666666666665444.34444444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0005
                           DUF2053  21 kasslseykafskvvlailaylltqlvKmlllAtlfpafdteeldliqeilkalvdlldliglylvLssvagkkikl 97 
                                       ++s + + +    v+ a++  ll+ ++  ++lA + pa+    ++l+q il a+v ++ ++ +y+       +  ++
  gi|336254605|ref|YP_004597712.1| 123 ESSLIDQLRDGLIVFGALGGALLAAVAASIVLAFF-PAI--PFISLLQPILLAIVLTVAFLPMYYYFPDADVSAREV 196
                                       45556666778888888899999999999999987.665..5579********************999966666566 PP

                           DUF2053  98 eskvlavgiGWalaeslltrllpl 121
                                            ++++GW+  +sl++ ++++
  gi|336254605|ref|YP_004597712.1| 197 LPGAAVAAVGWTALQSLFQVYVSF 220
                                       68889999**********988876 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 ?    1.7   0.2      0.52   2.9e+02      36      63 ..     300     327 ..     281     337 .. 0.62
   2 ?   10.3   5.0     0.001      0.59      22      64 ..     329     370 ..     312     374 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.52
                            Cnn_1N  36 eqkeellkenielkveveslqkelkekk 63 
                                       +++e l +++  +  e+ +lq++l++ +
  gi|336254605|ref|YP_004597712.1| 300 REREHLTAQLGTVSRERDQLQHDLEAQR 327
                                       4555566666666666666666666554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.001
                            Cnn_1N  22 riyfLeerleklseeqkeellkenielkveveslqkelkekkk 64 
                                       r y Le+r+ +l++  +++l+++n +l+ e+e l++el++ ++
  gi|336254605|ref|YP_004597712.1| 329 RRYRLEDRVGELDS-RIDALEATNRDLESENERLRRELEQERQ 370
                                       56889999999999.***********************99876 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 ?    1.6   0.3      0.37   2.1e+02      93     126 ..     298     331 ..     294     336 .. 0.83
   2 ?   12.3   3.0    0.0002      0.11      19      75 ..     332     389 ..     321     396 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.37
                          KASH_CCD  93 lekenqsLiakiesLqeenikllaekdelkkklk 126
                                       + +e+++L+a++ +   e  +l+ + ++ +++  
  gi|336254605|ref|YP_004597712.1| 298 ARREREHLTAQLGTVSRERDQLQHDLEAQRSRRY 331
                                       5799999999999999999999999998887765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0002
                          KASH_CCD  19 kLaeenskLkkavetaeetnakLteeieeLkkklks.tQqalqkaklleeEleelkal 75 
                                       +L++ +  L   +++ e tn  L  e+e L++ l    Qq  +  + l e l  +++l
  gi|336254605|ref|YP_004597712.1| 332 RLEDRVGELDSRIDALEATNRDLESENERLRRELEQeRQQEPEWRRRLREGLSHVRTL 389
                                       8999*****************************9652688889999999988888765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00059      0.33      39     101 ..     305     370 ..     299     385 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00059
                           DUF1664  39 lsdavesvskqleqvseslaatkr...hLssridrvdkkldeqkeiskeikeevtevredlseige 101
                                       l+  + +vs++ +q++++l+a++    +L++r+ ++d+++d+ +++ +++++e +++r++l++ ++
  gi|336254605|ref|YP_004597712.1| 305 LTAQLGTVSRERDQLQHDLEAQRSrryRLEDRVGELDSRIDALEATNRDLESENERLRRELEQERQ 370
                                       5666677888888888777766542228*************************9999999998665 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.18     1e+02      52      73 ..     300     321 ..     296     333 .. 0.62
   2 ?    8.4   0.6     0.005       2.8      38      66 ..     342     370 ..     338     375 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.18
                       Fungal_TACC  52 qeieqLkkqleaerkEKqeLlk 73 
                                       +e e+L+ ql ++ +E+++L +
  gi|336254605|ref|YP_004597712.1| 300 REREHLTAQLGTVSRERDQLQH 321
                                       5666666666666666666643 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.005
                       Fungal_TACC  38 kkldklelenkslkqeieqLkkqleaerk 66 
                                       +++d le  n+ l++e e+L+++le er+
  gi|336254605|ref|YP_004597712.1| 342 SRIDALEATNRDLESENERLRRELEQERQ 370
                                       6899***********************97 PP

>> Perilipin  Perilipin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.0   0.00061      0.34     203     288 ..     298     381 ..     273     389 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00061
                                       HHHHTT-EEEEGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--...---------------- CS
                         Perilipin 203 eqkkkpsyfvRLGsLSaklrerAyqhsleklrqakqraqealaqlsstldLielakkglsaanqklseaqekllqsw 279
                                         ++++ ++  LG++S +  +  +qh le+ r+ + r ++ + +l s +d +e +   l++ n++l ++ e+ +q+ 
  gi|336254605|ref|YP_004597712.1| 298 ARREREHLTAQLGTVSRERDQ--LQHDLEAQRSRRYRLEDRVGELDSRIDALEATNRDLESENERLRRELEQERQQE 372
                                       456778889999999987655..89**************************************************** PP

                                       --------- CS
                         Perilipin 280 lewkkkqqe 288
                                        ew+++ +e
  gi|336254605|ref|YP_004597712.1| 373 PEWRRRLRE 381
                                       ***998765 PP

>> CortBP2  Cortactin-binding protein-2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  12.9    0.0045       2.5      65     170 ..     270     385 ..     260     390 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0045
                           CortBP2  65 aksketsesevkklyekqlaeLekliekqreaqermleqLaaaekrhrkvleeLeeekrkheedtaqgddv...... 135
                                        +++++++++v + ++ + ++   +i+  r+  e++++qL ++ ++  ++ ++Le ++ ++ +  ++  ++      
  gi|336254605|ref|YP_004597712.1| 270 DEDAADETDAVDEFETIPESKRPPMIDDARREREHLTAQLGTVSRERDQLQHDLEAQRSRRYRLEDRVGELdsrida 346
                                       3444555555555556666777789*******************************999886654443222111111 PP

                           CortBP2 136 ....tylLekererLkqeleqekaqkkklekelkkllek 170
                                              Le e erL++eleqe++q+ + ++ l++ l++
  gi|336254605|ref|YP_004597712.1| 347 leatNRDLESENERLRRELEQERQQEPEWRRRLREGLSH 385
                                       111135699****************99888887776665 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       2.3   1.3e+03      15      34 ..     303     322 ..     299     328 .. 0.67
   2 ?   10.7   1.0   0.00083      0.46      13      36 ..     343     366 ..     332     369 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.3
                              HALZ  15 daLksdydsLkkenekLkae 34 
                                       + L+++   + +e+++L+  
  gi|336254605|ref|YP_004597712.1| 303 EHLTAQLGTVSRERDQLQHD 322
                                       55666666777777777755 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00083
                              HALZ  13 sYdaLksdydsLkkenekLkaelq 36 
                                       + daL + +  L+ ene+L+ el+
  gi|336254605|ref|YP_004597712.1| 343 RIDALEATNRDLESENERLRRELE 366
                                       458888888888888888888886 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 ?    7.5   7.5    0.0072         4      66     145 ..     301     384 ..     207     390 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0072
                           UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkee.......ldakeeelerlkeenqqLqekleaiaedfee 135
                                       e ++l ++   ++ ++   ++ +  le  +++  +L+++       +da e + + l+ en+ L+ +le+  ++  e
  gi|336254605|ref|YP_004597712.1| 301 EREHLTAQLGTVSRER---DQLQHDLEAQRSRRYRLEDRvgeldsrIDALEATNRDLESENERLRRELEQERQQEPE 374
                                       3444444444444444...5555566666666666666677778779999999999999999999999998888888 PP

                           UPF0242 136 lkleleeqLa 145
                                        ++ l e L 
  gi|336254605|ref|YP_004597712.1| 375 WRRRLREGLS 384
                                       8888877775 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   7.1    0.0018         1      59     127 ..     295     366 ..     284     367 .. 0.78
   2 ?    1.8   4.0      0.41   2.3e+02      71     108 ..     349     386 ..     347     390 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                        TPR_MLP1_2  59 lqalreelnelkaeiaelkaeaesakaeleesees...weeqkeelekelselekriedlneqNklLhdQlE 127
                                       + ++r e ++l+a++ ++  e+++++++le++++    +e +  el+++++ le+   dl++ N+ L   lE
  gi|336254605|ref|YP_004597712.1| 295 IDDARREREHLTAQLGTVSRERDQLQHDLEAQRSRryrLEDRVGELDSRIDALEATNRDLESENERLRRELE 366
                                       67899999*********************9998742226677777777777777777777777777766666 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.41
                        TPR_MLP1_2  71 aeiaelkaeaesakaeleeseesweeqkeelekelsel 108
                                       a+ ++l++e+e+++ ele+++++  e + +l++ ls +
  gi|336254605|ref|YP_004597712.1| 349 ATNRDLESENERLRRELEQERQQEPEWRRRLREGLSHV 386
                                       66789999999999999999999999999999888766 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.3     0.005       2.8      55      96 ..     282     335 ..     260     339 .. 0.74
   2 ?    9.4  14.2    0.0025       1.4      18     101 ..     295     375 ..     294     387 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.005
                            APG6_N  55 e............leklekeeeelleeLkelekereeleaelaaleeelealee 96 
                                       e            +++ ++e+e l ++L  + +er++l+ +l+a+++   +le+
  gi|336254605|ref|YP_004597712.1| 282 EfetipeskrppmIDDARREREHLTAQLGTVSRERDQLQHDLEAQRSRRYRLED 335
                                       14455556777889999**************************99998888875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0025
                            APG6_N  18 leqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeeleal 94 
                                       +++a++er+ +++ l ++ +e+++ +   ++le+ + +  +le+   el + +++le+++++le+e + l++ele+ 
  gi|336254605|ref|YP_004597712.1| 295 IDDARREREHLTAQLGTVSRERDQLQ---HDLEAQRSRRYRLEDRVGELDSRIDALEATNRDLESENERLRRELEQE 368
                                       58999***************988876...588888888888999999999999999999999999999999999988 PP

                            APG6_N  95 eeeeerf 101
                                        ++e + 
  gi|336254605|ref|YP_004597712.1| 369 RQQEPEW 375
                                       8887554 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 ?    7.8   5.9    0.0075       4.2      17      68 ..     332     383 ..     309     389 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0075
                            CENP-H  17 klsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeel 68 
                                       +l+  + el ++++ +e+ n++l+ +n+ l +el+++++++ +++ +l+e l
  gi|336254605|ref|YP_004597712.1| 332 RLEDRVGELDSRIDALEATNRDLESENERLRRELEQERQQEPEWRRRLREGL 383
                                       3444555666667777777777777777777777766666666665555544 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.7     0.018        10      18      46 ..     308     336 ..     295     337 .. 0.55
   2 ?    8.5   4.2     0.003       1.7      15      52 ..     326     363 ..     323     378 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC  18 aykqlkqeiaalqaelaklkaeneeLeae 46 
                                       ++  + +e+++lq++l++++ ++ +Le++
  gi|336254605|ref|YP_004597712.1| 308 QLGTVSRERDQLQHDLEAQRSRRYRLEDR 336
                                       33345556666666666666666666655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.003
                                       XXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                             DivIC  15 gllaykqlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                       + +++++l+  + +l   +++l a+n++Le+e ++L+ 
  gi|336254605|ref|YP_004597712.1| 326 QRSRRYRLEDRVGELDSRIDALEATNRDLESENERLRR 363
                                       67888999999999999999999999999999999964 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.7     0.034        19      30      58 ..     299     327 ..     295     339 .. 0.90
   2 ?    6.6   5.5     0.015       8.4      46      67 .]     350     371 ..     342     371 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.034
                       Cep57_CLD_2  30 nkERdsalrqLgvAyeelneLkaevealr 58 
                                       ++ER+    qLg   +e ++L+  +ea r
  gi|336254605|ref|YP_004597712.1| 299 RREREHLTAQLGTVSRERDQLQHDLEAQR 327
                                       799*******************9999987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                       Cep57_CLD_2  46 elneLkaevealrkELkeqrae 67 
                                       ++++L +e+e+lr+EL+ +r++
  gi|336254605|ref|YP_004597712.1| 350 TNRDLESENERLRRELEQERQQ 371
                                       5789***********9999875 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.0     0.018        10       7      48 ..     296     336 ..     293     355 .. 0.74
   2 ?    4.9   2.7     0.087        49       9      35 ..     354     380 ..     349     390 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.018
                    PRKG1_interact   7 eeekeenerLkreLeelekelselkseleklkqqrqesvskr 48 
                                        ++++e+e+L ++L ++++e ++l+  le  + +r+ ++++r
  gi|336254605|ref|YP_004597712.1| 296 DDARREREHLTAQLGTVSRERDQLQHDLEAQR-SRRYRLEDR 336
                                       57899*********************999976.444444444 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.087
                    PRKG1_interact   9 ekeenerLkreLeelekelselksele 35 
                                        ++enerL+reLe+ +++  e + +l 
  gi|336254605|ref|YP_004597712.1| 354 LESENERLRRELEQERQQEPEWRRRLR 380
                                       578************999999888776 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 ?    4.7   7.3     0.023        13      29     106 ..     307     381 ..     295     391 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.023
                             Atg14  29 erlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkkla 105
                                        +l  +  e+++l+  +e+  ++++   +led++  +  +++ l ++ +dl++++++l+  l+q +++  e +++l+
  gi|336254605|ref|YP_004597712.1| 307 AQLGTVSRERDQLQHDLEAQRSRRY---RLEDRVGELDSRIDALEATNRDLESENERLRRELEQERQQEPEWRRRLR 380
                                       4555666777778877777777777...8888888888888888888888888888888888888888888777776 PP

                             Atg14 106 k 106
                                       +
  gi|336254605|ref|YP_004597712.1| 381 E 381
                                       5 PP

>> betaPIX_CC  betaPIX coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.6     0.029        16      42      75 ..     307     340 ..     303     352 .. 0.81
   2 ?    1.7   3.8       0.4   2.2e+02      45      64 ..     352     371 ..     343     388 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.029
                        betaPIX_CC  42 devqelkqenkklkksleeEqkaRkdLEkvvrkl 75 
                                        ++ ++ +e  +l++ le  +  R +LE  v  l
  gi|336254605|ref|YP_004597712.1| 307 AQLGTVSRERDQLQHDLEAQRSRRYRLEDRVGEL 340
                                       67888999**********98888889**988665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.4
                        betaPIX_CC  45 qelkqenkklkksleeEqka 64 
                                       + l+ en +l++ le+E++ 
  gi|336254605|ref|YP_004597712.1| 352 RDLESENERLRRELEQERQQ 371
                                       67999**********99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1563  (0.0871772); expected 358.6 (0.02)
Passed bias filter:                      854  (0.0476323); expected 358.6 (0.02)
Passed Vit filter:                       209  (0.0116571); 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: 0.68u 0.25s 00:00:00.93 Elapsed: 00:00:00.42
# Mc/sec: 2857.01
//
Query:       gi|336254606|ref|YP_004597713.1|  [L=181]
Description: Ferritin Dps family protein [Halopiger xanaduensis SH-6]
Scores for complete 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-32  112.8   3.0    1.6e-32  112.4   3.0    1.1  1  Ferritin  Ferritin-like domain
     0.0068   16.7   0.5        3.2    8.2   0.0    2.7  3  DUF2383   Domain of unknown function (DUF2383)


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4   3.0   1.7e-36   1.6e-32       2     139 ..      31     172 ..      30     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 1.7e-36
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH....C-S CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee....iea 74 
                                       +aLn  la+ +++++q ++++w+v+g ++  l+ef++e +e+  e ad++aer +alGg+pv+ +  le+    +  
  gi|336254606|ref|YP_004597713.1|  31 DALNTELANAYVLYHQLKKHHWVVEGAEFLPLHEFLEEAYEHVEEGADEIAERAQALGGVPVSGPTNLEKratvE-- 105
                                       79********************************************************************77753.. PP

                                       SSS....CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  75 pke....fgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                              + +v+ +++++le + +++es+r+ ielae  gD+at ++l ++l + ee  +++e++le+ 
  gi|336254606|ref|YP_004597713.1| 106 --FegedVYDVRTMFRNDLEIYGDIIESMRDSIELAENLGDHATSELLREILVDLEEDGHHFEHYLEDD 172
                                       ..2333344*********************************************************986 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.39   3.5e+03      21      34 ..       8      21 ..       2      40 .. 0.58
   2 !    8.2   0.0   0.00035       3.2      31      66 ..      61      96 ..      28     102 .. 0.89
   3 !    6.4   0.1    0.0013        11       8      46 ..     127     165 ..     120     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.39
                                      HHHHHT--SHHHHH CS
                           DUF2383 21 keaaekvkdpqlkt 34
                                      ++ a+ v++++l+ 
  gi|336254606|ref|YP_004597713.1|  8 RQSADTVEENELRL 21
                                      56666666666653 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00035
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHCT-------- CS
                           DUF2383 31 qlktlleriaeereeaaeeLqseiralggepedggs 66
                                       l ++le+  e  ee a+e++++++algg p +g +
  gi|336254606|ref|YP_004597713.1| 61 PLHEFLEEAYEHVEEGADEIAERAQALGGVPVSGPT 96
                                      57889999999********************99977 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHH CS
                           DUF2383   8 dLietlkdgeegykeaaekvkdpqlktlleriaeereea 46 
                                       d+ie ++d++e  ++  +++ ++ l+++l +  e+  ++
  gi|336254606|ref|YP_004597713.1| 127 DIIESMRDSIELAENLGDHATSELLREILVDLEEDGHHF 165
                                       89*************************998887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1344.27
//
Query:       gi|336254607|ref|YP_004597714.1|  [L=54]
Description: hypothetical protein Halxa_3223 [Halopiger xanaduensis SH-6]
Scores for 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:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 427.91
//
Query:       gi|336254608|ref|YP_004597715.1|  [L=179]
Description: Appr-1-p processing domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-29  100.9   0.0    6.8e-29  100.3   0.0    1.3  1  Macro     Macro domain


Domain annotation for each model (and alignments):
>> Macro  Macro domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.0   3.8e-33   6.8e-29       1     118 []      19     131 ..      19     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 3.8e-33
                                       EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEES.E-TTTSTSTTHHH CS
                             Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvg.plftsskskeeee 76 
                                       VnAa ++l +g+gvaga+ r ag++++ee+ e     g+++lGe++vt+ay+l+a+yvih+++ p +  ++++ ++e
  gi|336254608|ref|YP_004597715.1|  19 VNAAGTSLRMGSGVAGALRRGAGEEINEEAMET----GPVDLGEVAVTDAYDLDAEYVIHAAAmPHY--GDGQATAE 89 
                                       9********************************....************************664555..49****** PP

                                       HHHHHHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHHH CS
                             Macro  77 llakayknalelaeekgiksvafPaistGifgvpweeaarva 118
                                       ++++a++nale+a++ +++sv++Pa+++G+ g+++ e a+++
  gi|336254608|ref|YP_004597715.1|  90 SVRDATRNALEQADDLRCRSVVLPALGCGVAGFDLAEGAEII 131
                                       *************************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1399.37
//
Query:       gi|336254609|ref|YP_004597716.1|  [L=120]
Description: hypothetical protein Halxa_3225 [Halopiger xanaduensis SH-6]
Scores for 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   0.2       0.11   12.5   0.2    1.4  1  CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit
      0.067   13.1   0.9      0.067   13.1   0.9    1.9  2  TAT_signal    TAT (twin-arginine translocation) pathway signa


Domain annotation for each model (and alignments):
>> CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.2e-05      0.11       6      27 ..       1      22 [.       1      24 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                      CytB6-F_Fe-S  6 msrRqllNlllvGaialtaaaa 27
                                      m +Rq+l  + v a+++ta+ +
  gi|336254609|ref|YP_004597716.1|  1 MDKRQFLASIAVTAVGMTAGCL 22
                                      99****************9865 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.9   7.5e-06     0.067       2      26 .]       1      24 [.       1      24 [. 0.85
   2 ?   -2.4   0.1      0.55     5e+03      18      23 ..     106     111 ..     105     112 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.5e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaaa 26
                                      ++ R+FL  s A++A ++++gc+aa
  gi|336254609|ref|YP_004597716.1|  1 MDKRQFLA-SIAVTAVGMTAGCLAA 24
                                      56799999.9999999999*99975 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.55
                        TAT_signal  18 aalggc 23 
                                       +algg 
  gi|336254609|ref|YP_004597716.1| 106 TALGGT 111
                                       677774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 910.27
//
Query:       gi|336254610|ref|YP_004597717.1|  [L=334]
Description: phosphoribosylformylglycinamidine cyclo-ligase [Halopiger xanaduensis SH-6]
Scores for 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-22   78.4   0.2    1.3e-21   77.4   0.0    1.6  2  AIRS_C    AIR synthase related protein, C-terminal domain
    2.5e-13   50.5   0.8    4.8e-13   49.6   0.8    1.4  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 ?   -2.5   0.1      0.55   4.9e+03      64      92 ..       1      29 [.       1      50 [. 0.62
   2 !   77.4   0.0   1.4e-25   1.3e-21       2     153 ..     173     328 ..     172     330 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.55
                                      EEE--TTHHHHHHHHHHHTTTEEEEEECG CS
                            AIRS_C 64 ahDvTgGGLlgalaemapasgvgaeidld 92
                                      ++D  + G + a  e +  ++ g+ i+++
  gi|336254610|ref|YP_004597717.1|  1 MTDPADDGSAAADEERLTYADTGVDIEAS 29
                                      56666666666666666666666666655 PP

  == domain 2  score: 77.4 bits;  conditional E-value: 1.4e-25
                                       TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT......TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHH CS
                            AIRS_C   2 pGdvliltgslGlggagtslkrkileeegldds......avqlgdvlleptliyvkralaalkglvkaahDvTgGGL 72 
                                       +Gd+l++ +s G++++g+ l+r+ ++++++  +      ++ +g++ll pt+iy  +++++ +++v+aa++vTgGG 
  gi|336254610|ref|YP_004597717.1| 173 VGDALVGFPSNGIHSNGLTLAREAVTRDHEYTDefpldpERTIGEELLRPTRIYTDLLEPMHEHDVRAAAHVTGGGW 249
                                       8****************************98779****9999********************************987 PP

                                       HHHHHHHHHTTTEEEEEECG..THHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEE CS
                            AIRS_C  73 lgalaemapasgvgaeidld..kvpifdele.....splemllsensGrllvavppeea.davlaileeeglpeaav 141
                                       + +l +m +    + +id +  + p+f+ ++     +++em++++n+G ++v++ pe++ d ++a+ +       +v
  gi|336254610|ref|YP_004597717.1| 250 T-NLLRMGER---EYVIDDPlpAQPVFEFVQaegnvTDEEMHCTFNMGTGFVVALPEDRaDDLVAETD------GRV 316
                                       6.67788555...47777777799999999999**************************555555544......589 PP

                                       EEEEEESSSEEE CS
                            AIRS_C 142 IGevtakeelsv 153
                                       IG+v++++++++
  gi|336254610|ref|YP_004597717.1| 317 IGRVEDGNSVEI 328
                                       *******98776 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 !   49.6   0.8   5.4e-17   4.8e-13       5      93 ..      59     160 ..      29     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 5.4e-17
                                       EEEEEEEEE.EECC....TCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-E CS
                              AIRS   5 vvvttdshnrpvlv....epvhfiGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvp 72 
                                       ++++td++++++lv    e++ +iG  ++a+n++Dl+a G +P+a++++la+        +e+ +gla ++ee++  
  gi|336254610|ref|YP_004597717.1|  59 LALATDGVGTKLLVaeaiEDYSTIGIDCIAMNVNDLVAAGVEPVAFVDYLAIDepdedLTNEIGEGLAVGLEEADLT 135
                                       5999*********9766667777***********************************99***************** PP

                                       EEEEEEEEESS....EEEEEEEEEE CS
                              AIRS  73 lvgGdtsfsne....ptisvtavGl 93 
                                       ++gG+t++++e    + ++ t+ Gl
  gi|336254610|ref|YP_004597717.1| 136 MLGGETAVMPEvvkgFDLAGTCAGL 160
                                       *********9999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.47
# Mc/sec: 2130.92
//
Query:       gi|336254611|ref|YP_004597718.1|  [L=196]
Description: hypothetical protein Halxa_3227 [Halopiger xanaduensis SH-6]
Scores for 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-06   25.7  20.0    4.3e-05   22.9  16.2    2.7  2  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9  16.2   2.4e-09   4.3e-05       1     114 [.       1      98 [.       1     107 [. 0.87
   2 ?   -0.3   0.1     0.033   5.8e+02      36      47 ..     146     167 ..     114     193 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.4e-09
                              YdjM   1 MdgltHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllfla 77 
                                       M+  tHal+G+al++++    gaa+ a +l++a++g+++PD+D+++           +       HR   H  + l+
  gi|336254611|ref|YP_004597718.1|   1 MMATTHALMGVALVALVFPEVGAAPTAGVLLAAFVGGIVPDLDMGA-----------A-------HRKTLHFPVCLP 59 
                                       99**********************99*****************443...........3.......**********99 PP

                              YdjM  78 llalvlllllrlfgrsalrlgll...lllgvlsHlllDll 114
                                       ++++++ + l   g++   l+l+   +l+++++H ++D++
  gi|336254611|ref|YP_004597718.1|  60 VATALVGGGLLASGAT-GGLALGllaFLVSAALHSAIDVF 98 
                                       9999999999888888.4444444367777999****987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.033
                              YdjM  36 g.......AllPDiD...hpss 47 
                                       g       A+ P iD    +++
  gi|336254611|ref|YP_004597718.1| 146 GtvairaaATTPAIDrllLGTL 167
                                       1222233344444443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1426.82
//
Query:       gi|336254612|ref|YP_004597719.1|  [L=196]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-12   48.2   0.0    1.4e-12   47.9   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      5e-09   36.5   0.0    7.9e-09   35.8   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.5e-07   31.4   0.0    3.5e-07   31.0   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    3.6e-06   26.9   0.0    1.2e-05   25.2   0.0    1.8  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
    6.1e-06   26.1   0.0      1e-05   25.4   0.0    1.3  1  FR47             FR47-like protein
    0.00034   20.7   0.0    0.00047   20.2   0.0    1.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0035   16.9   0.0     0.0042   16.6   0.0    1.3  1  Acetyltransf_15  Putative acetyl-transferase
     0.0052   16.9   0.0     0.0096   16.0   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
     0.0076   16.4   0.0      0.011   15.9   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.19   11.5   0.0       0.29   10.9   0.0    1.2  1  Big_3_4          Domain of unknown function


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 !   47.9   0.0   7.9e-16   1.4e-12      24     117 .]      75     174 ..      33     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 7.9e-16
                                       HHHHHHSTTCEEEEEEETTEEEEEEEEEEEET........TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT CS
                    Acetyltransf_1  24 feesfsleaegllvaeedgeliGfisllkipd........ekggvayieslaVspeyrgkGlGsaLlealeeraree 92 
                                        e s   +a+ l++++ +g ++G + l+ +          ++ + ay+++l+V+p+yr++G Gs+Ll  +++ +r++
  gi|336254612|ref|YP_004597719.1|  75 DEAS---DADLLVLGRLEGDVVGQVFLNRDETdvhelearLSIDGAYVWRLYVDPDYRNRGFGSKLLAGAMDAVRDR 148
                                       2233...4556666***********65555559999999988999******************************** PP

                                       .TESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  93 .gikkivlaveedndaairlYeklGF 117
                                        g  ++++ + +dn +++rl+e +GF
  gi|336254612|ref|YP_004597719.1| 149 wGPVELYALIADDNLPSRRLFEGHGF 174
                                       8777788889999********77999 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   4.4e-12   7.9e-09      13      76 .]      91     176 ..      78     176 .. 0.66

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 4.4e-12
                                       EEEEEEEEEEES..............TCTEEEEE-GGGTTSSHHHHHHH.H...TT..SE.EEEEEEEE...THH.H CS
                    Acetyltransf_7  13 kivGfialslld..............aeitrlaVdpeyrgkGiGraLle.a...ae..kg.iileqlel...nae.k 64 
                                        +vG++ l +++              a+ +rl+Vdp+yr++G G++Ll+ a   ++  +g ++l+       +++ +
  gi|336254612|ref|YP_004597719.1|  91 DVVGQVFLNRDEtdvhelearlsidgAYVWRLYVDPDYRNRGFGSKLLAgAmdaVRdrWGpVELY---AliaDDNlP 164
                                       5556555555556666666666666678888*****************87544411445532222...123322358 PP

                                       HHHHHHHTTEEE CS
                    Acetyltransf_7  65 aikfYeklGFee 76 
                                       +++++e +GF++
  gi|336254612|ref|YP_004597719.1| 165 SRRLFEGHGFVP 176
                                       899*******85 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0     2e-10   3.5e-07       5     137 ..      36     174 ..      33     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2e-10
                    Acetyltransf_3   5 rplteeDlealfelrsdpevmry.lpepltleeaeewlerawaeeseeegygwaivlkdtg.viGsvglrdleeede 79 
                                       r++ e+D e+++  ++d e  r  ++ +++++  ++ +   ++++ e ++  +++  + +g v+G v l++ e + +
  gi|336254612|ref|YP_004597719.1|  36 RRPAESD-EPFA--ANDDESSRLeFTVHESPAGVDADVP--YKPD-EASDADLLVLGRLEGdVVGQVFLNRDETDVH 106
                                       5555666.6665..5677777665666777777777777..7654.45555777756555427****9998888888 PP

                    Acetyltransf_3  80 e..........aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                       e              ++++p+++++G+++  ++++++++ ++ g  +l+a i+ +N  S+r++e  Gf
  gi|336254612|ref|YP_004597719.1| 107 ElearlsidgaYVWRLYVDPDYRNRGFGSKLLAGAMDAVRDRWGPVELYALIADDNLPSRRLFEGHGF 174
                                       8899988885555556667889********************9************************9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.97   1.7e+03      81      98 ..      48      66 ..      44      68 .. 0.73
   2 !   25.2   0.0     7e-09   1.2e-05      47     111 ..     111     179 ..      87     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.97
                   Acetyltransf_10 81 ekdgikl.eltvnaspyav 98
                                      ++d+++  e+tv++sp+ v
  gi|336254612|ref|YP_004597719.1| 48 NDDESSRlEFTVHESPAGV 66
                                      455566689*****99876 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 7e-09
                   Acetyltransf_10  47 el.rdgshisllfVdpeyrgqGigkaLleaveee.aekdgikl..eltvnaspyavpfYeklGFkavge 111
                                       +l  dg ++ +l+Vdp+yr +G g++Ll  + ++  +++g+ +  +l ++ +   ++++e +GF++ ++
  gi|336254612|ref|YP_004597719.1| 111 RLsIDGAYVWRLYVDPDYRNRGFGSKLLAGAMDAvRDRWGPVElyALIADDNLPSRRLFEGHGFVPESR 179
                                       5556778999*******************99999455566655655555555599*********98776 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   5.6e-09     1e-05      16      77 ..     111     174 ..     100     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5.6e-09
                                       EEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS.-.S-EEEEEETT-HHHHHHHHHHT- CS
                              FR47  16 ilrkdggelgalqvlpehrrrGlgsrlvkalakeiaer.g.ktvllvvvasNtpsirlyeklGf 77 
                                       +l  dg ++  l+v+p+ r+rG+gs+l +    +++ r g  ++ ++++ +N ps+rl+e  Gf
  gi|336254612|ref|YP_004597719.1| 111 RLSIDGAYVWRLYVDPDYRNRGFGSKLLAGAMDAVRDRwGpVELYALIADDNLPSRRLFEGHGF 174
                                       56667889999*****************99999**995232578899*************9998 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.6e-07   0.00047      21     106 ..      57     151 ..      50     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.6e-07
                                       TT----H.....HHHHHHHHHHTTSEEEEEEE.TTEEEEEEEEEEEEEEETT..EEEEE..EEEEEEEE-CCGTTS- CS
                    Acetyltransf_9  21 Fqdeespl..e.eireyfrklleesrvlgaed.ngelvgqlallplelnvpG..ktlka..agvtgVavapehrgrg 89 
                                       F ++esp+  + +   y+ +  ++++ l++ + +g++vgq+ l++ e  v++  ++l +  a+v    v+p++r+rg
  gi|336254612|ref|YP_004597719.1|  57 FTVHESPAgvDaD-VPYKPDEASDADLLVLGRlEGDVVGQVFLNRDETDVHEleARLSIdgAYVWRLYVDPDYRNRG 132
                                       5566666665433.4566777777788777777*****************997344333449999************ PP

                                       HHHHHHHHHHHHHHHT..T CS
                    Acetyltransf_9  90 vlskLlaraleemree..g 106
                                       + skLla a++ +r++   
  gi|336254612|ref|YP_004597719.1| 133 FGSKLLAGAMDAVRDRwgP 151
                                       *************998434 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.3e-06    0.0042      46     103 ..      90     147 ..      56     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.3e-06
                   Acetyltransf_15  46 eeLvasvfivkkkyyslvssilieknvleiYtlyvsekyrgkGlakklLeeslkelkk 103
                                       +  v++vf++++     +   + + ++  ++ lyv+++yr++G+  klL  ++++++ 
  gi|336254612|ref|YP_004597719.1|  90 GDVVGQVFLNRDETDVHELEARLSIDGAYVWRLYVDPDYRNRGFGSKLLAGAMDAVRD 147
                                       66788888888877666666788889999********************999988764 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 !   16.0   0.0   5.3e-06    0.0096      28      56 ..     120     148 ..     102     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.3e-06
                   Acetyltransf_CG  28 thTeVpeelrGkGiAkkLvkaalddaree 56 
                                       +  +V++ +r +G+++kL   a+d +r++
  gi|336254612|ref|YP_004597719.1| 120 WRLYVDPDYRNRGFGSKLLAGAMDAVRDR 148
                                       5679*********************9986 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     6e-06     0.011      68     141 ..     107     181 ..     102     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6e-06
                    Acetyltransf_4  68 qfkkr.akdwkaelsvylaerdnnkeglgrelidaleqvl.keqnienllaeiaspnensiqfhkalGFelvgifk 141
                                       ++++r   d++  +  y++  d +++g g++l++  ++    + +  +l+a ia +n +s  +++ +GF  + +f+
  gi|336254612|ref|YP_004597719.1| 107 ELEARlSIDGAYVWRLYVD-PDYRNRGFGSKLLAGAMDAVrDRWGPVELYALIADDNLPSRRLFEGHGFVPESRFR 181
                                       5667777788999*****6.89***************99999***************************8777766 PP

>> Big_3_4  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016      0.29       6      56 ..      85     138 ..      83     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                           Big_3_4   6 fGkvdg...ievefdrseGdiWnvpvPldedGeyvvellaedeaGnqayiakll 56 
                                        G+++g    +v ++r e d+ ++   l +dG yv  l+ + +  n+ + +kll
  gi|336254612|ref|YP_004597719.1|  85 LGRLEGdvvGQVFLNRDETDVHELEARLSIDGAYVWRLYVDPDYRNRGFGSKLL 138
                                       56666522237899********************************99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1435.57
//
Query:       gi|336254613|ref|YP_004597720.1|  [L=233]
Description: CDP-alcohol phosphatidyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-06   28.7   1.4    1.7e-06   28.7   1.4    2.5  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
       0.16   12.0   0.0       0.24   11.4   0.0    1.3  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


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 !   28.7   1.4   1.9e-10   1.7e-06       3      66 .]      41     102 ..      39     102 .. 0.93
   2 ?    0.2   0.6      0.15   1.3e+03      13      13 ..     167     167 ..     109     228 .. 0.55

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.9e-10
                                       HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf   3 PnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66 
                                       ++  +l++ll++ +a+ll+++ +p  ++++ ++ a+l+D lDG lARr    s++G  +Ds++D
  gi|336254613|ref|YP_004597720.1|  41 ADYCSLASLLFAWAATLLIVSGDP-NWGVVAMFGAFLFDKLDGALARRGYG-SDYGLEIDSFID 102
                                       67889************9999999.9999999*****************77.99*******998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
                                       H CS
                   CDP-OH_P_transf  13 l 13 
                                        
  gi|336254613|ref|YP_004597720.1| 167 V 167
                                       1 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.6e-05      0.24      82     109 ..     204     231 ..     195     233 .] 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.6e-05
                                       -THHHH-B-GGGHHHHHHHHHHHHHHHT CS
                   Ketoacyl-synt_C  82 SvKsniGHleaAaGvaelikvvlalkhg 109
                                       + K+ +GH++ A G ++++ v+lal+ g
  gi|336254613|ref|YP_004597720.1| 204 CYKTDVGHALVAIGGIAAAVVCLALEFG 231
                                       68**********************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1780.05
//
Query:       gi|336254614|ref|YP_004597721.1|  [L=299]
Description: PHP domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   56.2   1.4    4.4e-15   55.2   1.4    1.6  1  PHP_C     PHP-associated
      1e-07   32.4   0.0    1.9e-07   31.6   0.0    1.5  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 !   55.2   1.4     5e-19   4.4e-15       1      56 []     193     258 ..     193     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 5e-19
                             PHP_C   1 geaNrrArrfAeklglpgtgGSDAHrleeVGrayTef...eepia..........tpdelleairegrt 56 
                                       g++Nr+A+rfAe +g++g++GSDAH+++ VGra+T++   +   a          +   +leai  grt
  gi|336254614|ref|YP_004597721.1| 193 GVRNRQAARFAENRGFAGVAGSDAHTARLVGRAVTDVhleS---AavpdgdptaiDRGRILEAIADGRT 258
                                       579**********************************6651...3344555544455999999999997 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   2.1e-11   1.9e-07       1      74 [.      62     143 ..      62     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.1e-11
                                       EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE........... CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                               PHP   1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse... 73 
                                       dlHvHt  s   d +l   +++++a++ gl+ i++TDh+ + + + ++  a    + g+ +i G+e++  d+++   
  gi|336254614|ref|YP_004597721.1|  62 DLHVHTAESyDCDTPL--VDVLERAADAGLDGICVTDHDAIEQSLAAATIA---PEYGLFAIPGVEVSTRDGHVlal 133
                                       89*******8887888..******************************999...5558********88888876666 PP

                                       .......... CS
                                       .........x RF
                               PHP  74 .........k 74 
                                                +
  gi|336254614|ref|YP_004597721.1| 134 gvetrpepgR 143
                                       6655555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2243.77
//
Query:       gi|336254615|ref|YP_004597722.1|  [L=208]
Description: peptidase M50 [Halopiger xanaduensis SH-6]
Scores for 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   26.0  15.8     0.0032   16.8   0.8    3.2  2  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
       0.93    9.8   6.6       0.87    9.9   5.5    1.8  1  DUF3021        Protein of unknown function (DUF3021)


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 !    8.2   8.3   0.00015       1.3       3     106 ..      61     144 ..      59     150 .. 0.69
   2 !   16.8   0.8   3.6e-07    0.0032     191     219 ..     156     184 ..     148     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00015
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....X CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   3 illlgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaf 79 
                                       ++ +g+  ++HEl+H +vA   g  + ef   + + l+      +  ++ + p G+ V  +g+              
  gi|336254615|ref|YP_004597722.1|  61 LVTVGVAFLLHELAHKVVAVEYGQ-IAEFRADY-QMLFLALMSALAGFLFAAP-GA-VYHRGQI------------- 120
                                       577889999999999999998886.44666665.3344444444444455555.33.4444444............. PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  80 lkkspwqrllivlAGplanfilailvf 106
                                          +  + ++i+lAGp++n++la+l+f
  gi|336254615|ref|YP_004597722.1| 121 ---TQRENAIIALAGPITNLLLALLFF 144
                                       ...456789***************998 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.6e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 191 flqllalisvnLgilNLlPipvLDGghll 219
                                       + q+  +i++ L+ +N++P+ +LDG  +l
  gi|336254615|ref|YP_004597722.1| 156 IGQMGLWINLFLAAFNMIPFGPLDGRSVL 184
                                       668899*******************9887 PP

>> DUF3021  Protein of unknown function (DUF3021)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   5.5   9.7e-05      0.87      32      83 ..      75     140 ..      39     207 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.7e-05
                           DUF3021  32 l..............estavlkqvllsaliGvlfalaslifeserlsllkqtlihflvvlllvlll 83 
                                       +                +++l  +l+sal G+lfa ++++++  ++  + + +i +   ++ +ll+
  gi|336254615|ref|YP_004597722.1|  75 HkvvaveygqiaefrADYQMLFLALMSALAGFLFAAPGAVYHRGQITQRENAIIALAGPITNLLLA 140
                                       1334455666666778899*************************9999888885544433333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1588.38
//
Query:       gi|336254616|ref|YP_004597723.1|  [L=591]
Description: TraB determinant protein [Halopiger xanaduensis SH-6]
Scores for 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-27   95.9   0.0    1.5e-16   61.1   0.0    2.1  2  TraB       TraB family
  ------ inclusion threshold ------
      0.031   14.6   0.5      0.086   13.2   0.5    1.7  1  RRM_4      RNA recognition motif of the spliceosomal PrP8
        0.6    9.9   0.0        0.6    9.9   0.0    3.1  3  PAP2       PAP2 superfamily


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 !   61.1   0.0   2.5e-20   1.5e-16       8     153 ..      20     154 ..      16     165 .. 0.90
   2 !   32.6   0.0   1.3e-11   7.6e-08     181     252 ..     323     389 ..     307     393 .. 0.75

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 2.5e-20
                              TraB   8 ggttsyLfGTiHvskksvyplspeveealeksdtvvvEldlsdd..tdeatqkelaklkllpdgktlsdllseelya 82 
                                       +  ++ ++GT+Hvs+ sv+++ ++v++  e++d+v+vEld+ ++   +  t ++l +++ll+ g+t+ ++l   +++
  gi|336254616|ref|YP_004597723.1|  20 DEGSVTVLGTAHVSQASVDDVHEAVDR--ERPDVVAVELDEGRYrqMQGGTPDDLEAKDLLS-GNTVFQFLAYWMLS 93 
                                       333489*********************..9***********999878888999********9.************** PP

                              TraB  83 rlqkalakrglplaaldkmkPwllalllslaelakkkagldpelvDrylaktakragkpvgglEtveeqls 153
                                        +q++l + ++++      +P  +a + + ++  ++++g + +lvDr+++ t +r + ++++ E+++ + +
  gi|336254616|ref|YP_004597723.1|  94 YVQSRLGD-QFDI------EP--GADMKAGIDA-AERNGSGVALVDRDIQVTIQRFWQRLSFTEKLKMVGG 154
                                       ********.9***......9*..8888888886.5899999999*********************997655 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 1.3e-11
                              TraB 181 leelveaykegdleal.eleaeaeeefpelkevlldeRnrrwaekieallkepgsvfvaVGagHlaGedgvla 252
                                       +ee+++    gd+ +  +  +e+++ +p   ++l+deR+++ a+++ +l +++  v+++VGagH aG++ +l+
  gi|336254616|ref|YP_004597723.1| 323 IEEMTD----GDVVSAmM--EEFRQFSPGGANALIDERDAYIAHNLHELREQGYDVLAIVGAGHKAGIERYLQ 389
                                       333333....44433322..6999999999******************99999***************98876 PP

>> RRM_4  RNA recognition motif of the spliceosomal PrP8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   1.4e-05     0.086      42      75 ..     172     204 ..     167     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                             RRM_4  42 syGlirGlqfssfvvqyyglvldllllGlerase 75 
                                       + G++ Gl f+ f++ y+g v dll+lG++ ++ 
  gi|336254616|ref|YP_004597723.1| 172 AAGVLFGLVFTMFLAPYFG-VADLLMLGITGSTT 204
                                       5799***************.68******997765 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0001       0.6       6      83 ..      28     104 ..      23     190 .. 0.75
   2 ?   -4.4   1.5       2.6   1.6e+04     113     127 ..     290     304 ..     289     309 .. 0.74
   3 ?   -5.1   8.6         3   1.8e+04      65     117 ..     423     474 ..     418     481 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0001
                              PAP2   6 llalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkrkki 82 
                                       ++a +++a +  v   +v+r RP+++a+e +     +++ + +++   + + Sg ++f f+++ +l+++  r+  ++
  gi|336254616|ref|YP_004597723.1|  28 GTAHVSQASVDDV-HEAVDRERPDVVAVELDEGRYRQMQGGTPDDLEAKDLLSGNTVFQFLAYWMLSYVQSRLGDQF 103
                                       4455555555444.8899*****************8888877775555568*****************999887776 PP

                              PAP2  83 g 83 
                                       +
  gi|336254616|ref|YP_004597723.1| 104 D 104
                                       5 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 2.6
                              PAP2 113 vlaGlliGialaala 127
                                       vlaGl +Gia++al+
  gi|336254616|ref|YP_004597723.1| 290 VLAGLGVGIAVGALL 304
                                       678888888888765 PP

  == domain 3  score: -5.1 bits;  conditional E-value: 3
                              PAP2  65 falalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGl 117
                                       f+++++l  + +   ++  ++ +a++l+  ++ +al+Rl+ g+ ++s+ ++Gl
  gi|336254616|ref|YP_004597723.1| 423 FVAFFFLLVMAGVQNAFLLKLFAAWFLFNGTFAFALARLA-GARWTSAGVGGL 474
                                       4444444444333333333688889999999999999986.566777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4120.86
//
Query:       gi|336254617|ref|YP_004597724.1|  [L=158]
Description: thioesterase superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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-15   56.4   0.3    4.1e-15   55.9   0.3    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 !   55.9   0.3   2.3e-19   4.1e-15       3      74 ..      25      95 ..      23      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 2.3e-19
                                      SB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETT CS
                              4HBT  3 vvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrded 74
                                      v hgG++++++De++++ +++  g+ ++v++   ++df rp+ +gd+ +++a v  +g++s++v+    +ed
  gi|336254617|ref|YP_004597724.1| 25 VAHGGNVMKWMDEVGAMSAMRFSGE-TCVTAHVNRMDFERPIPVGDTAYITAYVYDAGTSSVKVRLVTERED 95
                                      78**********************9.**************************************98777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1229.15
//
Query:       gi|336254618|ref|YP_004597725.1|  [L=350]
Description: peptidase U61 LD-carboxypeptidase A [Halopiger xanaduensis SH-6]
Scores for 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   90.2   0.0    1.4e-25   89.7   0.0    1.2  1  Peptidase_S66   LD-carboxypeptidase N-terminal domain
    3.4e-24   85.7   0.0    5.3e-24   85.1   0.0    1.3  1  Peptidase_S66C  LD-carboxypeptidase C-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_S66  LD-carboxypeptidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.0   1.6e-29   1.4e-25       1     121 []      16     135 ..      16     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 1.6e-29
                                       EEEE-SSS-GGGSSH.H.HHHHHHHHHHHC.TEEEEEGCTC--TTTTCSS-HHHHHHHHHHHHC-TTECEEEES--S CS
                     Peptidase_S66   1 iaivapSsglkkeeeke.eleraievleel.glevvlgksaaksagylagtdeeRaadLnealadpeikaiicarGG 75 
                                       ia+vapSs+ ++e   +  ++ ++e+l+e  +le+v+ ++++ + + la ++e+Ra+dL +a+adp+i+ +i+++GG
  gi|336254618|ref|YP_004597725.1|  16 IAVVAPSSNPTDE--FPhVYDLGLERLREVfDLEPVEYPTVSMAPDALADDPEARARDLIDAFADPDIDGVIALIGG 90 
                                       89*****998644..555*********7744*****88877555668****************************** PP

                                       S-CHHCHHHH-HCCHHCS--EEEE-CCHHHHHHHHHHCHTBSEEE- CS
                     Peptidase_S66  76 ygaarllpyldfdaikknpkiliGySDiTalhlalyaktglvtlhg 121
                                       ++ +r+l++l+ d +++np  + GySD T++ l+l++ +g+v+++g
  gi|336254618|ref|YP_004597725.1|  91 NDQIRVLEHLEPDVLQENPTRFYGYSDNTNVALYLWN-LGIVSYYG 135
                                       ************************************9.6*****98 PP

>> Peptidase_S66C  LD-carboxypeptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   5.9e-28   5.3e-24       1     124 []     209     340 ..     209     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 5.9e-28
                                       EEEEEEEEHHHH.HCCTTSTTS--.-TT..EEEEEE--TT..HHHHHHHHHHHHCTSTTGGG--EEEEEE--..... CS
                    Peptidase_S66C   1 eGrliGGnlsvl.asllgtpylpe.kdlkgkILflEdvse..spyridrmLtqlkeagvldkvkGivlGrftkp... 70 
                                       +Gr++GG+l++l +++l+ +ylp+ + l+g++L +E+ +e  +p+ ++  L++l+e+g+l++++G+++Gr   p   
  gi|336254618|ref|YP_004597725.1| 209 SGRVWGGCLEILnQQFLADRYLPDdNVLDGTVLAIETSEElpAPSWVEGVLRALGERGLLERFAGVLVGR---Paar 282
                                       6***********88889999***97777*********55599***************************5...4345 PP

                                       ....G......CC...---HHHHHHHHHT-GGGTTS-EEEEESESSSBS---EEETSEEEE CS
                    Peptidase_S66C  71 ....eek...eeeeekeeykealeevlaeiledlkiPvlynldiGHtspnltlplGakael 124
                                           + +   ++e+++++++ea+e v+a   ++  +P+ +++d+GHt p++++p+G+++e+
  gi|336254618|ref|YP_004597725.1| 283 shleD-RpaeRREQYRTQQREAIEGVFA--EYNPAAPIAFDVDFGHTWPTTPIPIGGRVEI 340
                                       77751.1456889999999*******97..56788***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2831.15
//
Query:       gi|336254619|ref|YP_004597726.1|  [L=69]
Description: 17 kDa surface antigen [Halopiger xanaduensis SH-6]
Scores for 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-07   30.0  15.1    4.3e-07   29.6  15.1    1.2  1  Gly-zipper_YMGG  YMGG-like Gly-zipper
    5.6e-06   26.1  15.0    8.1e-06   25.6  15.0    1.3  1  Rick_17kDa_Anti  Glycine zipper 2TM domain
     0.0012   18.8  33.9      0.011   15.7   6.1    2.0  2  Gly-zipper_Omp   Glycine zipper
     0.0064   16.8   1.1     0.0067   16.7   1.1    1.1  1  DUF456           Protein of unknown function (DUF456)
  ------ inclusion threshold ------
      0.066   12.6   7.5      0.075   12.4   7.5    1.0  1  DUF3482          Domain of unknown function (DUF3482)
      0.095   12.4   3.6        0.1   12.3   3.6    1.1  1  TraT             Enterobacterial TraT complement resistance p
       0.14   12.5   0.2       0.14   12.5   0.2    1.5  2  ATP-synt_E       ATP synthase E chain
        1.4    8.8  20.4        1.5    8.6  19.1    1.7  1  Gly-zipper_OmpA  Glycine-zipper domain
        1.7    8.8  11.2        2.6    8.2  11.2    1.3  1  Bacteriocin_IIc  Bacteriocin class II with double-glycine lea


Domain annotation for each model (and alignments):
>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6  15.1   2.2e-10   4.3e-07       2      39 ..      10      48 ..       9      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.2e-10
                                      ...XXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG  2 gavrGAaiGAaaGAvvGaliG.sgggkGAaiGAaaGala 39
                                      +++r AaiGA++GA++Gal+  +++++G aiG+ +Gal+
  gi|336254619|ref|YP_004597726.1| 10 RRARYAAIGAGIGAGIGALFSrNAASTGGAIGGLVGALV 48
                                      57899****************888889999999999986 PP

>> Rick_17kDa_Anti  Glycine zipper 2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6  15.0   4.1e-09   8.1e-06       2      38 ..      14      49 ..      13      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.1e-09
                   Rick_17kDa_Anti  2 GaliGAaaGgvaGaaigggggrvlGavvGAaaGavaG 38
                                      +a+iGA++G+ +Ga++++ + +++G+++G+++Ga+++
  gi|336254619|ref|YP_004597726.1| 14 YAAIGAGIGAGIGALFSR-NAASTGGAIGGLVGALVA 49
                                      69**************88.9***************97 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   6.1   5.5e-06     0.011      19      42 ..      10      33 ..       3      36 .. 0.84
   2 !   14.4  19.8   1.5e-05     0.029       1      34 [.      17      48 ..      15      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.5e-06
                    Gly-zipper_Omp 19 grgtGaliGAavGaavGgliGaam 42
                                       r++ a+iGA++Ga +G+l +++ 
  gi|336254619|ref|YP_004597726.1| 10 RRARYAAIGAGIGAGIGALFSRNA 33
                                      47899*************999886 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.5e-05
                    Gly-zipper_Omp  1 iGaaiGAaaGaliGgavggrgtGaliGAavGaav 34
                                      iGa+iGA +Gal+  ++    tG +iG+ vGa+v
  gi|336254619|ref|YP_004597726.1| 17 IGAGIGAGIGALFSRNAA--STGGAIGGLVGALV 48
                                      788888888888888777..48888999999887 PP

>> DUF456  Protein of unknown function (DUF456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.1   3.3e-06    0.0067      61      97 ..      13      52 ..       3      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.3e-06
                            DUF456 61 krgligaivGaivGffllp...plGlllgpflgaflgEll 97
                                      ++++iga++Ga +G+++       G  +g ++ga+++E  
  gi|336254619|ref|YP_004597726.1| 13 RYAAIGAGIGAGIGALFSRnaaSTGGAIGGLVGALVAETR 52
                                      7899**********988776545***************43 PP

>> DUF3482  Domain of unknown function (DUF3482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   7.5   3.8e-05     0.075     154     203 ..      15      64 ..       7      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.8e-05
                           DUF3482 154 aaaGAaaGagiDlavgGltLGaaaaiGalaGglaatlkrygkrllaklkG 203
                                       aa GA +Gagi +++      ++ aiG+l+G+l+a ++   ++  +k+k 
  gi|336254619|ref|YP_004597726.1|  15 AAIGAGIGAGIGALFSRNAASTGGAIGGLVGALVAETRDTAGEYVEKAKN 64 
                                       899********************************999998888888765 PP

>> TraT  Enterobacterial TraT complement resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.6   5.1e-05       0.1      92     128 ..      15      49 ..       2      61 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.1e-05
                              TraT  92 alagaaagaaigaanggsagaalggglvGglvgaiag 128
                                       a+ ga++ga+iga+   s +aa  gg++Gglvga++ 
  gi|336254619|ref|YP_004597726.1|  15 AAIGAGIGAGIGAL--FSRNAASTGGAIGGLVGALVA 49 
                                       67899999999999..555566666677777776554 PP

>> ATP-synt_E  ATP synthase E chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   6.9e-05      0.14       6      26 ..       5      25 ..       1      36 [. 0.85
   2 ?   -2.2   0.0       2.7   5.4e+03      51      57 ..      58      64 ..      48      68 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.9e-05
                        ATP-synt_E  6 vsPlinvlRysaLalGvvyGa 26
                                      +  +++ +Ry+a ++G+ +G+
  gi|336254619|ref|YP_004597726.1|  5 ITTVVRRARYAAIGAGIGAGI 25
                                      667899**************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.7
                        ATP-synt_E 51 liekaka 57
                                       +ekak+
  gi|336254619|ref|YP_004597726.1| 58 YVEKAKN 64
                                      3444443 PP

>> Gly-zipper_OmpA  Glycine-zipper domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  19.1   0.00077       1.5       2      39 ..      13      48 ..      12      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00077
                   Gly-zipper_OmpA  2 egAavGAalGAaaGAavGaitGsaGtGAaiGAasGava 39
                                      + Aa+GA++GA  GA++   +  a+tG aiG+ +Ga++
  gi|336254619|ref|YP_004597726.1| 13 RYAAIGAGIGAGIGALFSRNA--ASTGGAIGGLVGALV 48
                                      77**************76665..788999998888875 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 ?    8.2  11.2    0.0013       2.6      27      58 ..      14      48 ..       6      49 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                   Bacteriocin_IIc 27 givggalaGaatGaa...tlgilgaavGavvGavv 58
                                       ++ ga +Ga++Ga     +  +g+a+G++vGa+v
  gi|336254619|ref|YP_004597726.1| 14 YAAIGAGIGAGIGALfsrNAASTGGAIGGLVGALV 48
                                      55667777777777766655556666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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):               9  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 534.12
//
Query:       gi|336254620|ref|YP_004597727.1|  [L=260]
Description: HAD-superfamily hydrolase [Halopiger xanaduensis SH-6]
Scores for complete 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-24   86.2   0.0    4.5e-24   84.5   0.0    1.9  2  Hydrolase_6      Haloacid dehalogenase-like hydrolase
    2.9e-21   75.3   0.7    9.3e-21   73.7   0.5    2.0  2  Hydrolase_like   HAD-hyrolase-like
    1.6e-07   31.9   1.3    1.8e-06   28.4   1.3    2.5  1  Hydrolase        haloacid dehalogenase-like hydrolase
    5.7e-05   23.3   0.1    0.00051   20.2   0.0    2.2  2  HAD_2            Haloacid dehalogenase-like hydrolase
     0.0073   15.9   0.0      0.012   15.2   0.0    1.3  1  PGP_phosphatase  Mitochondrial PGP phosphatase
  ------ inclusion threshold ------
      0.027   14.2   0.0      0.059   13.1   0.0    1.5  2  Hydrolase_3      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 !   84.5   0.0   1.5e-27   4.5e-24       2     100 ..       8     106 ..       7     107 .. 0.98
   2 ?   -2.1   0.0       1.4   4.2e+03       9      28 ..     153     172 ..     147     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 1.5e-27
                                       EEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHHS CS
                       Hydrolase_6   2 lfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkrk 78 
                                       ++D+dG+++rgd+++pga + ++al++ag   vl++Nn ++  ++y +kl  +gvd+++e+v+tsat++a+yl++++
  gi|336254620|ref|YP_004597727.1|   8 ILDVDGTIIRGDELLPGATDGIRALEDAGCSWVLCSNNPTRGGDHYREKLAPFGVDVDPERVLTSATITAAYLADIH 84 
                                       79*************************************************************************** PP

                                       XXXEEEEESXHHHHHHHHHTTX CS
                       Hydrolase_6  79 adkkvlvigeeglreelkeagf 100
                                       +d+ v+++g+ +l+e+l+eag+
  gi|336254620|ref|YP_004597727.1|  85 PDDAVYLVGGRRLEELLEEAGV 106
                                       ********************97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                                       SEETTEE-TTHHHHHHHHHH CS
                       Hydrolase_6   9 Lwrgdkaipgaaealnalra 28 
                                       +  +d aipg+  +l a++a
  gi|336254620|ref|YP_004597727.1| 153 IPVDDGAIPGSGAILAAMEA 172
                                       55678999999999998875 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    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       8      23 ..     126     141 ..     125     154 .. 0.64
   2 !   73.7   0.5   3.1e-24   9.3e-21       2      74 ..     182     255 ..     181     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.2
                                       HHHHHHHHHH---GGG CS
                    Hydrolase_like   8 emydfalevlgsdpee 23 
                                       ++yd+ +e+l +  ++
  gi|336254620|ref|YP_004597727.1| 126 FSYDALREALRALEGD 141
                                       6788888888554444 PP

  == domain 2  score: 73.7 bits;  conditional E-value: 3.1e-24
                                       .STTSSHHHHHHHHHH.---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like   2 lgKPepemydfalevl.gsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                       lgKP++++ ++a+e l + dpee+l++GDrl+tDi+ + +aG++++ VltGvt+++dl+e +  p+yv+++lae
  gi|336254620|ref|YP_004597727.1| 182 LGKPSATAAEAAVELLdDPDPEETLVVGDRLDTDIELGARAGMTTAVVLTGVTDRADLAESAVDPDYVLESLAE 255
                                       7***************6667***************************************************998 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   1.3   5.9e-10   1.8e-06       2     210 .]       5     223 ..       4     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.9e-10
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH...HHHHHHHHHETTTE........ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx........ RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar...sgaltgfatfigrg........ 67 
                                       ++ ++D+dGT+++g   +  +++ +                     +a ++    +  ++++ t   rg        
  gi|336254620|ref|YP_004597727.1|   5 EAAILDVDGTIIRGDELLPGATDGI---------------------RALEDAgcsWVLCSNNPT---RGgdhyrekl 57 
                                       6889***********7777777777.....................444444443555566666...3333455555 PP

                                       ...............................HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHH CS
                                       ...............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ...............................ayaigkpewltaldippdlgaaigsaqsqgrtvallqaralavfti 113
                                                                      +y++g +++ + l             +++g     + + a+ v+  
  gi|336254620|ref|YP_004597727.1|  58 apfgvdvdpervltsatitaayladihpddaVYLVGGRRLEELL-------------EEAGVALTADPDAADVVVGS 121
                                       55544444444444444445556666666666666666666666.............33333333333345555555 PP

                                       HHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH.TT..GGGESEEEEHHCES.STTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                         Hydrolase 114 adplkvkpeaaeavasLkaagievvlltgdnpetaeraanq.lG..ddyfdaviasdiet.vakpspegkvaaireL 186
                                        d  + ++ ++ea+++L    ++ +    d   +++  a    G    +++av +++ ++  +kps  + +aa++ L
  gi|336254620|ref|YP_004597727.1| 122 FDDEFSYDALREALRALEGD-VPFYGTDPDTTIPVDDGAIPgSGaiLAAMEAVAGREPDAiLGKPSATAAEAAVELL 197
                                       577799************43.555555556666677555555889777779999999999***************** PP

                                       T.STGGGEEEEESSHH.HHHHHHHTT CS
                                       x.xxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 187 q.gkpeevamVGDgvn.DaaalaaAg 210
                                          +pee+++VGD++  D++ +a+Ag
  gi|336254620|ref|YP_004597727.1| 198 DdPDPEETLVVGDRLDtDIELGARAG 223
                                       8677********************98 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.16   4.8e+02       2      16 ..       8      22 ..       7      49 .. 0.83
   2 !   20.2   0.0   1.7e-07   0.00051     131     178 .]     180     229 ..     165     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.16
                             HAD_2  2 iFDlDgTlldteeli 16
                                      i D+DgT++   el+
  gi|336254620|ref|YP_004597727.1|  8 ILDVDGTIIRGDELL 22
                                      78******9766665 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.7e-07
                             HAD_2 131 vekkKPdpeviekalekl.klkkeeviyvGDsp.tDieaakkagikviav 178
                                       +   KP+++  e+a+e l + ++ee+++vGD   tDie + +ag+++++v
  gi|336254620|ref|YP_004597727.1| 180 AILGKPSATAAEAAVELLdDPDPEETLVVGDRLdTDIELGARAGMTTAVV 229
                                       45569*************779*************************9976 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     4e-06     0.012     135     167 ..     201     233 ..     184     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-06
                   PGP_phosphatase 135 eadeiavvgDRllTdvllanmmGslgvwlrdgv 167
                                       +++e +vvgDRl Td+ l+++ G ++ ++  gv
  gi|336254620|ref|YP_004597727.1| 201 DPEETLVVGDRLDTDIELGARAGMTTAVVLTGV 233
                                       689********************9888887777 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     2e-05     0.059       2      52 ..       8      57 ..       7      63 .. 0.91
   2 ?   -3.0   0.0       1.6   4.8e+03     202     227 ..     201     227 ..     196     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                                      EEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHC CS
                       Hydrolase_3  2 alDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleel 52
                                      +lD+DGT+++ d+ + + + + i+ l+++g+  v+++ +++r+  ++ e+l
  gi|336254620|ref|YP_004597727.1|  8 ILDVDGTIIRGDELL-PGATDGIRALEDAGCSWVLCSNNPTRGGDHYREKL 57
                                      68*******999876.78889*********************999999987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.6
                                       -GGGEEEEESS.GGGHHHHHHSSEEEE CS
                       Hydrolase_3 202 sleeviafGDg.eNDieMLeaaglgvA 227
                                       ++ee++++GD  + Die+  +ag+  A
  gi|336254620|ref|YP_004597727.1| 201 DPEETLVVGDRlDTDIELGARAGMTTA 227
                                       689999****83468888777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2118.39
//
Query:       gi|336254621|ref|YP_004597728.1|  [L=149]
Description: hypothetical protein Halxa_3237 [Halopiger xanaduensis SH-6]
Scores for 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-09   34.8   0.3    1.5e-08   34.1   0.3    1.4  1  SHOCT           Short C-terminal domain
     0.0014   18.7   7.5     0.0078   16.3   7.3    2.1  1  DUF1707         Domain of unknown function (DUF1707)
  ------ inclusion threshold ------
       0.03   13.4   0.0      0.036   13.1   0.0    1.0  1  Ric8            Guanine nucleotide exchange factor synembryn
      0.058   13.4   1.5      0.097   12.7   1.4    1.5  1  GvpG            Gas vesicle protein G
       0.11   12.3   0.1       0.14   11.9   0.1    1.2  1  Peptidase_M48   Peptidase family M48
       0.16   11.6   0.0       0.23   11.1   0.0    1.2  1  tRNA_anti-like  tRNA_anti-like


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.3   4.9e-12   1.5e-08       1      27 [.      88     114 ..      88     115 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 4.9e-12
                             SHOCT   1 daLekLkeLyarGeIteEEFeakKakL 27 
                                       d+  +L+e+ya+G +++EEFeak ++L
  gi|336254621|ref|YP_004597728.1|  88 DPVTQLQERYAAGDLSDEEFEAKLERL 114
                                       67789********************99 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   7.3   2.6e-06    0.0078       6      44 ..      85     122 ..      71     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.6e-06
                           DUF1707   6 adReravelLrealaeGrLtldEfdeRleaalaArtrge 44 
                                       +dR+ +  +L+e +a+G L+ +Ef+  le+   A  r++
  gi|336254621|ref|YP_004597728.1|  85 DDRDPV-TQLQERYAAGDLSDEEFEAKLERLIDANERAD 122
                                       566654.67*************************99998 PP

>> Ric8  Guanine nucleotide exchange factor synembryn
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05     0.036     382     444 ..      68     126 ..      45     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                              Ric8 382 yssdsedsdteeykqakraiNPiTGqveeeeeenpleeMTeeEKErEAerLfvlfdrlektgv 444
                                       +s +++++ t+++++a+++ +P+T q++e        ++++eE E+  erL++  +r  + gv
  gi|336254621|ref|YP_004597728.1|  68 RSAETDADRTATASAAADDRDPVT-QLQERYA-A--GDLSDEEFEAKLERLIDANERADRAGV 126
                                       455556788999999*********.6666666.3..37**********************998 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.4   3.2e-05     0.097      36      72 ..      89     125 ..      65     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                              GvpG  36 eLaaLqqeLdaGeIdeeeFdrrEeelLdrLealerle 72 
                                         ++Lq +  aG+ ++eeF+++ e+l+d+ e  +r+ 
  gi|336254621|ref|YP_004597728.1|  89 PVTQLQERYAAGDLSDEEFEAKLERLIDANERADRAG 125
                                       4689***********************9988666554 PP

>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   4.6e-05      0.14     114     176 ..      32     108 ..       9     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                                       -S---HHHHHHHHHHTT................HHHHHHHHHHHHHHHHTTT.HHHHHHHHHHHHHHTT--S---HH CS
                                       xxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 114 ldalavliglliillfl................alSRkrEyqADeagvellkrakdlvraliklakdlerqdvsasl 174
                                       + a +v+ +l  +ll+l                a  R+ E+ AD+ +   ++  +d+ + + +l+++++  d s+++
  gi|336254621|ref|YP_004597728.1|  32 VLAGPVYGVLTLALLVLsfilvwgltrseetddAQARSAETDADRTATASAA--ADDRDPVTQLQERYAAGDLSDEE 106
                                       4444444444433333344477899*********************988777..88999999999999999988887 PP

                                       HH CS
                                       xx RF
                     Peptidase_M48 175 rs 176
                                       ++
  gi|336254621|ref|YP_004597728.1| 107 FE 108
                                       75 PP

>> tRNA_anti-like  tRNA_anti-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.6e-05      0.23       9      70 ..      41     103 ..      37     110 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX---HHHHHTS-...............EEEHHHHH CS
                    tRNA_anti-like   9 lviilivilllfvialvaqaaesardkekaekedadatlaeakakpeavaekas.qisArdLl 70 
                                       l ++l+v++++ v+ l + ++++  ++ +ae +   +++a a a+   + +++  +++A dL 
  gi|336254621|ref|YP_004597728.1|  41 LTLALLVLSFILVWGLTRSEETDDAQARSAETDADRTATASAAADDRDPVTQLQeRYAAGDLS 103
                                       678999999999**9998888776666666665555555567777777777764267777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); 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):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 1271.98
//
Query:       gi|336254622|ref|YP_004597729.1|  [L=154]
Description: hypothetical protein Halxa_3238 [Halopiger xanaduensis SH-6]
Scores for 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   10.8   0.0       0.19   10.4   0.0    1.1  1  Peptidase_C57  Vaccinia virus I7 processing peptidase


Domain annotation for each model (and alignments):
>> Peptidase_C57  Vaccinia virus I7 processing peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0     1e-05      0.19     137     186 ..      75     126 ..      66     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 1e-05
                     Peptidase_C57 137 FsqldlkvDdl.srkgi.ktGenekvvklkikpdkkaWlsnksienlvapla 186
                                       Fsq+d + Dd+  r g+   G  e   + +++pd ++W + +si+  ++++ 
  gi|336254622|ref|YP_004597729.1|  75 FSQFDFFWDDFaDRVGYhAPGIPEDWQAREYHPDLDTWGTVSSINAELTEFG 126
                                       9**********556788667************************98888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1186.00
//
Query:       gi|336254623|ref|YP_004597730.1|  [L=46]
Description: hypothetical protein Halxa_3239 [Halopiger xanaduensis SH-6]
Scores for 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   16.9   5.1      0.011   15.9   5.1    1.5  1  Zn-ribbon_8    Zinc ribbon domain
     0.0059   16.6   0.8     0.0059   16.6   0.8    1.0  1  HypA           Hydrogenase/urease nickel incorporation, metal
  ------ inclusion threshold ------
      0.014   15.2   1.6       0.13   12.1   0.1    2.1  2  TFIIS_C        Transcription factor S-II (TFIIS)
      0.024   14.7   3.9        2.1    8.5   0.1    2.2  2  UPF0547        Uncharacterised protein family UPF0547
      0.088   12.5   4.4        2.8    7.8   0.5    2.1  2  A2L_zn_ribbon  A2L zinc ribbon domain
       0.23   10.2   0.8       0.21   10.4   0.8    1.0  1  NRDD           Anaerobic ribonucleoside-triphosphate reductas
       0.53   10.1   5.9        5.3    6.8   5.9    2.0  1  Rubredoxin_2   Rubredoxin metal binding domain


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 !   15.9   5.1   4.2e-06     0.011       6      37 ..      14      39 ..      13      41 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.2e-06
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgsevr 37
                                      Y+C++Cgh+ ++        l+ CPeC + vr
  gi|336254623|ref|YP_004597730.1| 14 YECRDCGHRETAES------LESCPECDGVVR 39
                                      9******9888554......888****98555 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 !   16.6   0.8   2.3e-06    0.0059      71      98 ..      14      40 ..       7      46 .] 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.3e-06
                                      EEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 71 vrCreCgkefeleekalrCpkCgsadve 98
                                      ++Cr+Cg++ + e+  ++Cp+C++   +
  gi|336254623|ref|YP_004597730.1| 14 YECRDCGHRETAESL-ESCPECDGVVRN 40
                                      79*****99887753.58****986555 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 ?   12.1   0.1     5e-05      0.13      25      37 ..      10      22 ..       8      24 .. 0.82
   2 ?    2.7   0.2     0.044   1.1e+02       2       7 ..      30      35 ..      29      38 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5e-05
                           TFIIS_C 25 mtvfykCtkCghr 37
                                         +y+C +Cghr
  gi|336254623|ref|YP_004597730.1| 10 DRSYYECRDCGHR 22
                                      5679********8 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.044
                           TFIIS_C  2 kCpkCg 7 
                                       Cp+C+
  gi|336254623|ref|YP_004597730.1| 30 SCPECD 35
                                      599997 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.9    0.0018       4.5      16      23 ..      15      22 ..      12      22 .. 0.88
   2 ?    8.5   0.1   0.00082       2.1       2       7 ..      30      35 ..      26      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                           UPF0547 16 fCphCGyv 23
                                      +C++CG++
  gi|336254623|ref|YP_004597730.1| 15 ECRDCGHR 22
                                      8*****95 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00082
                           UPF0547  2 vCPeCe 7 
                                       CPeC+
  gi|336254623|ref|YP_004597730.1| 30 SCPECD 35
                                      599998 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   0.5    0.0011       2.8      18      28 ..      10      20 ..       7      24 .. 0.87
   2 ?    4.8   4.9    0.0091        23       3      27 ..      13      34 ..      12      37 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                     A2L_zn_ribbon 18 eqgylvCieCg 28
                                      +++y+ C +Cg
  gi|336254623|ref|YP_004597730.1| 10 DRSYYECRDCG 20
                                      68999999999 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0091
                     A2L_zn_ribbon  3 lkvCsvCggngilnseqgylvCieC 27
                                      +++C  Cg+     ++ + ++C+eC
  gi|336254623|ref|YP_004597730.1| 13 YYECRDCGHRE---TAESLESCPEC 34
                                      67777777765...56899999999 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.8     8e-05      0.21     509     526 ..      15      35 ..       7      45 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8e-05
                                       EETT.--..EESS...SB-TTT- CS
                              NRDD 509 vCnecgy..kgei...ekCpkCg 526
                                        C++cg+  +      e+Cp+C+
  gi|336254623|ref|YP_004597730.1|  15 ECRDCGHreT--AeslESCPECD 35 
                                       6******642..335799****8 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.9    0.0021       5.3       1      20 [.      14      34 ..      14      36 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0021
                      Rubredoxin_2  1 YvCsqCGfe.sakwfGrCpsC 20
                                      Y+C++CG++ +a  +  Cp+C
  gi|336254623|ref|YP_004597730.1| 14 YECRDCGHReTAESLESCPEC 34
                                      9******96256677777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 376.52
//
Query:       gi|336254624|ref|YP_004597731.1|  [L=60]
Description: hypothetical protein Halxa_3240 [Halopiger xanaduensis SH-6]
Scores for 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   15.1   0.1      0.029   14.7   0.1    1.3  1  zf-Di19        Drought induced 19 protein (Di19), zinc-bindin
      0.074   13.0   0.3       0.12   12.3   0.1    1.5  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> 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 ?   14.7   0.1   3.2e-06     0.029       4      24 ..      14      36 ..      11      47 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-06
                           zf-Di19  4 tCPyCgkeltv..keLveHvede 24
                                       CP+Cg+el+   + +v+H++++
  gi|336254624|ref|YP_004597731.1| 14 VCPFCGDELQSpgAGFVDHIDEN 36
                                      7*****97665227899999986 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 ?   12.3   0.1   1.4e-05      0.12      15      27 ..       9      21 ..       5      31 .. 0.85
   2 ?   -2.4   0.0      0.54   4.9e+03      24      27 ..      39      42 ..      35      49 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                     Zn_Tnp_IS1595 15 WpngfvCPhCgsr 27
                                      W +  vCP+Cg +
  gi|336254624|ref|YP_004597731.1|  9 WVDPIVCPFCGDE 21
                                      9999*******76 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.54
                     Zn_Tnp_IS1595 24 Cgsr 27
                                      C++r
  gi|336254624|ref|YP_004597731.1| 39 CEHR 42
                                      3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 517.17
//
Query:       gi|336254625|ref|YP_004597732.1|  [L=406]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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-38  130.2  58.2    2.9e-34  118.6  46.3    2.0  2  MFS_1      Major Facilitator Superfamily
    1.2e-06   27.5  12.6     0.0012   17.7   0.4    3.5  3  LacY_symp  LacY proton/sugar symporter
  ------ inclusion threshold ------
       0.83    8.1  32.1        1.7    7.1  26.1    2.4  2  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 !  118.6  46.3   4.8e-38   2.9e-34       6     340 ..      19     351 ..      13     352 .. 0.82
   2 !   23.9  10.3   2.9e-09   1.7e-05      92     177 ..     318     403 ..     311     406 .] 0.93

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 4.8e-38
                             MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                       fl+ l r+++ p++  a ++++g+s +++g+++t+++l++a++++p G+l+dr+G+  v+ +g+++ a ++l l+ +
  gi|336254625|ref|YP_004597732.1|  19 FLAKLLRYAFPPLFG-AFQTSYGVSNATLGTAFTGFMLVYAAMQFPSGVLADRLGSVAVVTAGAAIAATAALTLI-I 93 
                                       666677888999999.99****************************************************44444.4 PP

                             MFS_1  83 .sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgg...llasslg..Wrav 153
                                        +++ +l+++ +++G+g+g+  ++++ l+++ +p  + gra+g++ +   ++ +++p +      l+ ++g  Wr++
  gi|336254625|ref|YP_004597732.1|  94 dAPFLVLVAAMLVMGAGTGTHKTVSVRLLSRAYPA-RTGRALGVFDTVGTFSGVVAPTAVVtvaGLSFAFGesWRLI 169
                                       47888******************************.***********8888888887665522234444449***** PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvp....awkallkdpvlwillialllfffgfsgl 226
                                       f+++++v+l ++v   l+ ++ p++ +++++++     + +++       +  l++d+ +  + +  +lf+f ++gl
  gi|336254625|ref|YP_004597732.1| 170 FLLAGVVGLTLAV---LFRVRVPKRVPTEATADG----AASGFDAidigTYARLFRDRRFSTFALLTILFSFTYNGL 239
                                       *************...666666666666666666....33333334467688888888885355555555569**** PP

                             MFS_1 227 ltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavll 303
                                       ++++plyl +  g++   +ag+l+++++l++  ++l +g lsdrlgr +++   l+++++a+++++ l  t  ++ll
  gi|336254625|ref|YP_004597732.1| 240 VAFVPLYLTDAAGFA-DATAGVLYSAFFLAS-LVQLGTGELSDRLGRLPIIAGLLAVATAALIAFISLTGTAGPILL 314
                                       ***************.478887777777777.4579***********777777777777777777777777777777 PP

                             MFS_1 304 llvlvliGfglgfvfpsllalasdlappeeagtasgl 340
                                          lv +G+g+  ++p   a+++ ++p + ag  +g+
  gi|336254625|ref|YP_004597732.1| 315 GGTLVAVGVGSHGFRPVRGAYLMTVIPDDVAGGGLGV 351
                                       779999***88889******************99987 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 2.9e-09
                             MFS_1  92 rvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlf 168
                                        v  G+g+ ++ p+ +a++  + p++  g ++g++ ++   + +l+p++ g +++++g+r +f++la+    a vl+
  gi|336254625|ref|YP_004597732.1| 318 LVAVGVGSHGFRPVRGAYLMTVIPDDVAGGGLGVVRTMLMGAGALAPAIVGTVSELAGFRPAFWLLAASVTGATVLA 394
                                       6889***********************************************************************98 PP

                             MFS_1 169 llllpeepp 177
                                       ++ll+++++
  gi|336254625|ref|YP_004597732.1| 395 VFLLVTDHR 403
                                       888877665 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   6.8   1.9e-06     0.011      18     237 ..      17     237 ..       2     240 .. 0.71
   2 !   17.7   0.4   2.1e-07    0.0012       5      72 ..     218     284 ..     217     324 .. 0.83
   3 !    4.6   0.0     0.002        12     366     402 ..     364     400 ..     355     404 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-06
                         LacY_symp  18 fyffimsayfplfpvw..lkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvlfapfli 92 
                                       ++f+   + +++ p++  ++   g+s++ +G+ f+   l+   +q   G++ d+lG    +  +    +  +a + +
  gi|336254625|ref|YP_004597732.1|  17 IWFLAKLLRYAFPPLFgaFQTSYGVSNATLGTAFTGFMLVYAAMQFPSGVLADRLGSVAVV--TAGAAIAATAALTL 91 
                                       444444444444444422567889****************9999999*********75433..33333344444444 PP

                         LacY_symp  93 yvfepllqlnilvGalvGgvflGlvysagagai.eayiekvsraskfeyGkarvfGclGyalcaslaGilfsidp.. 166
                                        + +p+l l  ++ +lv g   G   +    ++  ay  +  ra          +G +  +   ++aG+ f+  +  
  gi|336254625|ref|YP_004597732.1|  92 IIDAPFLVL--VAAMLVMGAGTGTHKTVSVRLLsRAYPARTGRALGVFDTVGTFSGVVAPTAVVTVAGLSFAFGEsw 166
                                       444454432..23333333334444444444432689999999998755555677999999999*****99986522 PP

                         LacY_symp 167 slvfwlasgfalilllllllskpdksssakvadalGankeafslrlalelfkdrklwvfvlyvvGvasvyd 237
                                       +l f la  ++l l++l  +  p++  +   ad      +a+ + + + lf+dr++ +f l ++  + +y+
  gi|336254625|ref|YP_004597732.1| 167 RLIFLLAGVVGLTLAVLFRVRVPKRVPTEATADGAASGFDAIDIGTYARLFRDRRFSTFALLTILFSFTYN 237
                                       699************99998888888888888888888899999******************998888887 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.1e-07
                         LacY_symp   5 kntnfylfalffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGl 72 
                                       +++ f +fal   ++ f +    ++ p++l++  g++++  G+++s+  l s+  q   G +sd+lG 
  gi|336254625|ref|YP_004597732.1| 218 RDRRFSTFALLTILFSFTYNGLVAFVPLYLTDAAGFADATAGVLYSAFFLASL-VQLGTGELSDRLGR 284
                                       5678999***************************************9988776.58889*******93 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.002
                         LacY_symp 366 stlaGklydkvGfqtaylvlgiivlsltlisvftlsk 402
                                        +++G++ + +Gf+ a+ +l++ v   t+++vf l +
  gi|336254625|ref|YP_004597732.1| 364 PAIVGTVSELAGFRPAFWLLAASVTGATVLAVFLLVT 400
                                       57899****************************9976 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6  10.5      0.26   1.6e+03     228     340 ..      14     123 ..       9     132 .. 0.76
   2 ?    7.1  26.1   0.00028       1.7      28     333 ..      39     328 ..      38     371 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.26
                             MFS_2 228 illllfllaalalgvlnglllYyltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllv 304
                                       + ++ fl+++l++++     ++   y + n++  ++f++ +++  +++ +   +la rlg  +++ +ga++++   +
  gi|336254625|ref|YP_004597732.1|  14 TAAIWFLAKLLRYAFPPLFGAFQTSYGVSNATLGTAFTG-FMLVYAAMQFPSGVLADRLGSVAVVTAGAAIAATAAL 89 
                                       566777777777777777788888888999999999999.555555556668999******9999999999876655 PP

                             MFS_2 305 lvlllqpsnlllflvllviagfgvgvaallpwsmla 340
                                        +++   +  l++++++++ g g+g++ ++   +l+
  gi|336254625|ref|YP_004597732.1|  90 TLIID--APFLVLVAAMLVMGAGTGTHKTVSVRLLS 123
                                       55555..78888888888889999998888776666 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00028
                             MFS_2  28 lglsaalvglvllvarlvDaitDpivGtlidktstrwGrrrPwlllsaiila.vsiillftppelsqsakfiwllvt 103
                                       +g+s+a +g+++  ++lv a + + +G+l+d++          + ++a i+a ++++l+        +a f++l+++
  gi|336254625|ref|YP_004597732.1|  39 YGVSNATLGTAFTGFMLVYAAMQFPSGVLADRLGS----VA-VVTAGAAIAAtAALTLII-------DAPFLVLVAA 103
                                       68899999999999999999999999999997655....44.444444333302223322.......2556677777 PP

                             MFS_2 104 yillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailafllvlilgglkserkgylifaliial 180
                                       ++++   + + +  +v l++ + + ++ R  l ++  + +  g v+ ++++++  l ++      + ++++ l+  +
  gi|336254625|ref|YP_004597732.1| 104 MLVMGAGTGTHKTVSVRLLSRAYPARTGRA-LGVFDTVGTFSGVVAPTAVVTVAGLSFAF----GESWRLIFLLAGV 175
                                       777766666666666666555534444443.34444444444444444444444433433....4457777777777 PP

                             MFS_2 181 Lmllgviivvlgtkervemrkkekteqkeklslle..qlkevfrnraflillllfllaalalgvlnglllYyltyvl 255
                                       + l ++++    + +rv   ++ ++++++ + +++     ++fr+r f +++ll +l++++++ l + + +ylt+  
  gi|336254625|ref|YP_004597732.1| 176 VGLTLAVLFRVRVPKRVPT-EATADGAASGFDAIDigTYARLFRDRRFSTFALLTILFSFTYNGLVAFVPLYLTDAA 251
                                       7777777777777888886.555666666666653226789************************************ PP

                             MFS_2 256 gngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaa 332
                                       g+++a + +l+ ++ +a l+ +    l  rlg+  +++  ++++ + l+ ++ l ++   + l+  +++ +gvg+++
  gi|336254625|ref|YP_004597732.1| 252 GFADATAGVLYSAFFLASLVQLGTGELSDRLGRLPIIAGLLAVATAALIAFISL-TGTAGPILLGGTLVAVGVGSHG 327
                                       ******99***9**********************99999998888888888888.5555555555555555555444 PP

                             MFS_2 333 l 333
                                       +
  gi|336254625|ref|YP_004597732.1| 328 F 328
                                       3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2753.95
//
Query:       gi|336254626|ref|YP_004597733.1|  [L=503]
Description: phosphoenolpyruvate carboxykinase (ATP) [Halopiger xanaduensis SH-6]
Scores for complete 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-59  202.1   0.0    2.6e-59  201.1   0.0    1.5  1  PEPCK_ATP  Phosphoenolpyruvate carboxykinase


Domain annotation for each model (and alignments):
>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.1   0.0   1.5e-63   2.6e-59      63     463 ..      68     460 ..      22     462 .. 0.85

  Alignments for each domain:
  == domain 1  score: 201.1 bits;  conditional E-value: 1.5e-63
                                       BEEE-HHHHHHHHHHHHHHHHTS-EEEEEEEE-SSTTT-EEEEEEES-HHHHHHHH.HHSBGGS-S-TTT---SEEE CS
                         PEPCK_ATP  63 nkpiseekfealkekvleylkekelyvvdafagadpkyrlkvrviterawqalfvk.nllirpteeeleefepdfti 138
                                       +++++++ +  l e +++   ++e+ +vd+ +g +p+ ++ +r+++ +  +++ +    l++p +      epd+  
  gi|336254626|ref|YP_004597733.1|  68 DHEFTDRDH-DLLEAAVDRAGDREMVCVDRLMGRHPDATFCCRLFVPVDHARIALAwANLFEPADGR----EPDLYT 139
                                       455555554.456778899999**********************99988887766544445665444....8****9 PP

                                       EEETT----HHHH--SSS-EEEEETTTTEEEEES---THHHHHHHHHHHHHHHHHTT-EEEEEEEEE.......-T. CS
                         PEPCK_ATP 139 lnapefkadpekdglnsetvvalnlekklvlilgteYaGEikKsifsvmnyllpkkgvlsmhcsanv.......gek 208
                                       ++ p+            et++ +  ++ ++ +lgt+Y GE kKs++++ +y ++++g l++h++++        g+ 
  gi|336254626|ref|YP_004597733.1| 140 VQDPD----------YDETAIRVLPDEGVTAVLGTDYIGEAKKSFLRLFMYRIKQRGGLGLHAGSKRvrvrdadGDL 206
                                       99999..........6799**********************************************976777554333 PP

                                       TS-EE.EEEE-TTSSHHHHH......-BTTB.-EEESSEEEE-SS-.EEES-S.EEEEE-TT--TTTSHHHHHHHS. CS
                         PEPCK_ATP 209 kgdva.lfFGLSGtGKTtLs......adper.kligdDehgwsdeg.vfnieg.GcYaKtidLskekepeiynair. 274
                                       +  v+ +f GLS+tGK tL+      +dpe  +++ dD  g+  +g v + eg G+++Kti+L+ e++pe+y+a++ 
  gi|336254626|ref|YP_004597733.1| 207 R-TVGqVFMGLSATGKSTLTshgcwlEDPEDaSMLQDDVCGLLPDGtVAGSEGeGLFIKTIGLDPEEQPELYAAATh 282
                                       3.4557**************9***99787752688999999999976*****98*******************9997 PP

                                       TT-EEES-EE-TTT--EETT--SS-S--EEEEEGGGSSSB-TTSEE--EEEEEEEE--TTS-S-SEEEE-HHHHHHH CS
                         PEPCK_ATP 275 fgavlENvvldeetrevdfddtslteNtrvaypiehienakeesvaghpkniifLtadafgvlPpvskLtkeqamyh 351
                                         avlENv++d+ +++v+fd++++t+N+r+ + ++ +e+a ee   ++ ++i+f+t++   ++Ppv+kL+ ++a++ 
  gi|336254626|ref|YP_004597733.1| 283 ESAVLENVAVDD-DGNVHFDEDRYTSNSRAIVRRDRLESADEEIDLERLDQIFFITRNP--LMPPVAKLDDREAAVA 356
                                       99********75.6889**********************8887777***********99..9*************** PP

                                       HHH-EEEE-----------EEEE-GGG-GGG-SS-HHHHHHHHHHHHHHH--EEEEEE-SEESSSTTTSEE--HHHH CS
                         PEPCK_ATP 352 FlsGytakvaGtergvtepeatFsacfgapFlplhpteyaelLaeklekhnakvyLvNtGwtggaygvgkrislkat 428
                                       F++G++++++  +    +   +   + ++pF++ ++ e+++++++ +++ +a++y++NtG+ g    + k i ++++
  gi|336254626|ref|YP_004597733.1| 357 FMLGESIETSAGDPS--RAGESIRVVGTNPFIIGSEGEEGNIFQDLIDELDAECYIINTGYLGD---ESKDIGVEES 428
                                       *******99865544..233345667789*********************************99...7899****** PP

                                       HHHHHHHHTTCCCTS-EEE-TTT--EEES-BTTC- CS
                         PEPCK_ATP 429 raiikaildgeleavefekdpvfglevptevpgvp 463
                                        +i++++++g++   e++ d+  gl++p +vpg++
  gi|336254626|ref|YP_004597733.1| 429 VTILTEAARGTI---EWTDDERTGLTIPDSVPGLD 460
                                       ************...89****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3685.85
//
Query:       gi|336254627|ref|YP_004597734.1|  [L=64]
Description: hypothetical protein Halxa_3243 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.044   14.2   0.3      0.049   14.0   0.3    1.1  1  PBP1_TM      Transmembrane domain of transglycosylase PBP1 at
      0.049   13.7   0.1      0.052   13.6   0.1    1.1  1  DUF2505      Protein of unknown function (DUF2505)
       0.18   11.5   0.0        0.2   11.3   0.0    1.0  1  DCAF15_WD40  DDB1-and CUL4-substrate receptor 15, WD repeat


Domain annotation for each model (and alignments):
>> PBP1_TM  Transmembrane domain of transglycosylase PBP1 at N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   8.2e-06     0.049      18      55 ..       5      42 ..       1      50 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.2e-06
                           PBP1_TM 18 akparkkasrrrrrdddyddeyddeedDdddddeeeev 55
                                       +++ +++  r  r + +d+e +  + Dddddd e++v
  gi|336254627|ref|YP_004597734.1|  5 VRAPTARVCERCERAEYWDEELEAWQIDDDDDDGEKQV 42
                                      56677777777889999999999999999999999887 PP

>> DUF2505  Protein of unknown function (DUF2505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   8.8e-06     0.052       2      36 ..       1      35 [.       1      50 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.8e-06
                           DUF2505  2 vsaeypapvdrvyaaltdeeywearleevgaeese 36
                                      +sa++ ap +rv + +  +eyw++ le+++ ++ +
  gi|336254627|ref|YP_004597734.1|  1 MSAQVRAPTARVCERCERAEYWDEELEAWQIDDDD 35
                                      58999***********************9855443 PP

>> DCAF15_WD40  DDB1-and CUL4-substrate receptor 15, WD repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.4e-05       0.2     132     175 ..       5      54 ..       3      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.4e-05
                       DCAF15_WD40 132 vavPslepCkdCkklaesseee........dleeeletalsleClehgltvh 175
                                       v+ P ++ C+ C+++++  +ee        d+++++++  + +Cl h+  ++
  gi|336254627|ref|YP_004597734.1|   5 VRAPTARVCERCERAEY-WDEEleawqiddDDDDGEKQVGNPHCL-HEWDIN 54 
                                       789***********884.44445899999888889999999***9.555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 499.38
//
Query:       gi|336254628|ref|YP_004597735.1|  [L=103]
Description: CutA1 divalent ion tolerance protein [Halopiger xanaduensis SH-6]
Scores for 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-29  100.6   0.0    3.8e-29  100.5   0.0    1.0  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 !  100.5   0.0   2.1e-33   3.8e-29       3      98 ..       4      97 ..       2      98 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 2.1e-33
                                      EEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEE CS
                             CutA1  3 vlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpeii 81
                                      v++tap  + a++la++lv+e+laACvn l+ ++S+YrW+g+i++d+Ev+ll+kt++e +++l +rv+elhpy+vp+i 
  gi|336254628|ref|YP_004597735.1|  4 VYITAP-PDRADELAERLVDERLAACVNRLS-TTSTYRWEGEIHHDDEVVLLAKTTDEAYDDLADRVRELHPYDVPCIE 80
                                      899999.789********************9.*********************************************** PP

                                      EEEESEEEHHHHHHHHH CS
                             CutA1 82 alpieagseaYlkWiee 98
                                       ++  +  e++++W +e
  gi|336254628|ref|YP_004597735.1| 81 RFDEADLLESFAEWRAE 97
                                      **************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.19s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 882.30
//
Query:       gi|336254629|ref|YP_004597736.1|  [L=158]
Description: 50S ribosomal protein L11 [Halopiger xanaduensis SH-6]
Scores for complete 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   76.4   0.0    2.7e-21   75.8   0.0    1.3  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
    3.9e-17   61.9   0.1      6e-17   61.2   0.1    1.3  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain


Domain annotation for each model (and alignments):
>> 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 !   75.8   0.0   3.1e-25   2.7e-21       2      70 .]      68     135 ..      67     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 3.1e-25
                                       --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                     Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                       +Ppt+ l+k +ag e+gsg+p+k++v+++s++qv++IA++K++dl a+ + ++a+k+++gt+ smG+++
  gi|336254629|ref|YP_004597736.1|  68 VPPTAELIKDEAGFETGSGEPQKDFVADLSVDQVKQIAEQKHPDLLAY-DTKNAAKEVVGTCASMGVTI 135
                                       6*********************************************99.******************97 PP

>> 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 !   61.2   0.1   6.7e-21     6e-17       5      65 .]       2      62 ..       1      62 [. 0.97

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 6.7e-21
                   Ribosomal_L11_N  5 vkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyqdrsf 65
                                      ++++++ vp+G+A p+PplGp LGp  + ++ +++e+n++T+ + g+ +pV++  ++d sf
  gi|336254629|ref|YP_004597736.1|  2 AGTIEVLVPGGQADPGPPLGPELGPTPVDVQAVVQEINDQTEAFDGTEVPVTVDYEDDGSF 62
                                      689**************************************99************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1186.55
//
Query:       gi|336254630|ref|YP_004597737.1|  [L=202]
Description: hypothetical protein Halxa_3246 [Halopiger xanaduensis SH-6]
Scores for 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:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1562.75
//
Query:       gi|336254631|ref|YP_004597738.1|  [L=210]
Description: 50S ribosomal protein L1 [Halopiger xanaduensis SH-6]
Scores for 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-41  139.8   0.0    1.2e-40  139.5   0.0    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 !  139.5   0.0   6.5e-45   1.2e-40       5     204 .]      18     205 ..      12     205 .. 0.95

  Alignments for each domain:
  == domain 1  score: 139.5 bits;  conditional E-value: 6.5e-45
                                       S-SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHH CS
                      Ribosomal_L1   5 akkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkky 81 
                                        +++f+e+v++a+nl++++ +++++r+ ++++Lp ++g+e++i++i+++++a     a+e    ++v++++++ +  
  gi|336254631|ref|YP_004597738.1|  18 PNRNFTETVDLAINLRDLDLNEPSNRVDESVVLPSGTGQETRIVVIAEGETAV---RAEEVA--DEVLSGDDVADLD 89 
                                       4789**********************************************999...888888..9*********999 PP

                                       T-HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEE CS
                      Ribosomal_L1  82 ksfeakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtcls 158
                                           + + +++e d+f+a++++m+ + ++LG ++g+r+kmP p   +    edv + v+++++ tv +r+ +  +++
  gi|336254631|ref|YP_004597738.1|  90 --DDEAKDMADETDFFIAEEAMMQDIARHLGTILGPRGKMPDPL--S--PDEDVVETVNRLKN-TVQLRSGDRRTFH 159
                                       ..46999*************************************..3..378***********.************* PP

                                       EEEEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS- CS
                      Ribosomal_L1 159 vkvGklsftaeelaeNieavvkalvekvpkkwkniksiylkttmsp 204
                                         vG+ +++ae++a+Ni+ +++ l  +++k+ +ni ++y+kttm+p
  gi|336254631|ref|YP_004597738.1| 160 TLVGSEEMDAEDVADNIDVILRRLHADLEKGPQNIDAVYVKTTMGP 205
                                       *********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1640.31
//
Query:       gi|336254632|ref|YP_004597739.1|  [L=350]
Description: Acidic ribosomal protein P0-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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   83.0   0.0    2.3e-23   82.2   0.0    1.4  1  Ribosomal_L10    Ribosomal protein L10
    1.9e-16   59.8   0.0    3.8e-16   58.8   0.0    1.5  1  RL10P_insert     Insertion domain in 60S ribosomal protein L1
  ------ inclusion threshold ------
       0.58    9.9   9.6       0.86    9.3   9.6    1.3  1  Cwf_Cwc_15       Cwf15/Cwc15 cell cycle control protein
       0.69   10.1  13.0        1.3    9.3  13.0    1.5  1  RNA_pol_3_Rpc31  DNA-directed RNA polymerase III subunit Rpc3
        1.5    8.4   5.4        2.2    7.8   5.4    1.2  1  PPP4R2           PPP4R2


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2   0.0   6.5e-27   2.3e-23       3      97 ..      13     105 ..      11     107 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 6.5e-27
                                       CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.SSCGCCSSSE CS
                     Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeeklkellkgpv 79 
                                       +++K e v+el +ll +y+sv +v ++g++++qlq++R++l ++ ael+v +ntl  rAle++g++ +l ++++g v
  gi|336254632|ref|YP_004597739.1|  13 PQWKREEVDELADLLADYESVGIVGLTGIPSKQLQDMRRDLYGT-AELRVSRNTLQIRALEDAGYD-DLVDHVEGHV 87 
                                       69*****************************************9.********************9.8********* PP

                                       EEEEESS-TCHHHHCCCC CS
                     Ribosomal_L10  80 alvftnedpvalakvlee 97 
                                       +lv tn++p+ l+k le+
  gi|336254632|ref|YP_004597739.1|  88 GLVATNDNPFTLYKELEA 105
                                       **************9987 PP

>> 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 !   58.8   0.0   1.1e-19   3.8e-16       3      71 .]     114     182 ..     113     182 .. 0.99

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.1e-19
                      RL10P_insert   3 aGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                        G++A++d++ip+g+++  Pg+++ eL+++g ++++++G i + ed +v ++Ge+++++ a++L+ Lgi
  gi|336254632|ref|YP_004597739.1| 114 EGEVAPNDIVIPEGDTGIDPGPFVGELQSIGANARIEDGSIQVMEDSTVLEAGEEVSADLANVLNELGI 182
                                       59******************************************************************9 PP

>> Cwf_Cwc_15  Cwf15/Cwc15 cell cycle control protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   9.6   0.00024      0.86      94     144 ..     289     340 ..     218     348 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00024
                                       --------------....----------------------------------- CS
                        Cwf_Cwc_15  94 eeeakrrkeelleea..reidaddedseeeeeeeeeesdddsdsdsddddded 144
                                         e+ +  e+  +ea  +++d+d+ ++e+ +e+ ++e   d d d+dd+dd d
  gi|336254632|ref|YP_004597739.1| 289 LPEELQDVEAPAAEAdaAAADEDEGEDESADEDADTEAG-DADTDDDDEDDGD 340
                                       222222222222222113455555555444433333333.3333333333334 PP

>> RNA_pol_3_Rpc31  DNA-directed RNA polymerase III subunit Rpc31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  13.0   0.00035       1.3     169     214 ..     271     340 ..     211     342 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00035
                   RNA_pol_3_Rpc31 169 elleklkelaeeeddee.....................ekkekedeeeee...eeeeddefddddedggD 214
                                       +++++l +la ++ddee                     +++e+ede  +e    e  d + dddded+gD
  gi|336254632|ref|YP_004597739.1| 271 KADAQLRALAAQIDDEEalpeelqdveapaaeadaaaaDEDEGEDESADEdadTEAGDADTDDDDEDDGD 340
                                       3444444455555554455555555555555555555533333333333333457888888888888887 PP

>> PPP4R2  PPP4R2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   5.4    0.0006       2.2     187     262 ..     265     338 ..     227     343 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0006
                            PPP4R2 187 ipwvdekteselspfikeidsimsvnlgfedeeekeeddneseesaseseeiteekdesvkveekdddeeddeedt 262
                                       +p + +k++ +l +  ++id       + +d e+ +   + + + a e+e + e++de+ ++e+ d d +dd+ed+
  gi|336254632|ref|YP_004597739.1| 265 MPDLVSKADAQLRALAAQIDDEEALPEELQDVEAPAA--EADAAAADEDEGEDESADEDADTEAGDADTDDDDEDD 338
                                       5566666677777777777765444433333333333..3445666666667777777777777666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.36
# Mc/sec: 2889.73
//
Query:       gi|336254633|ref|YP_004597740.1|  [L=116]
Description: 50S ribosomal protein L12P [Halopiger xanaduensis SH-6]
Scores for 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   60.0  17.1    3.3e-16   59.7  17.1    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
     0.0076   14.8   2.6     0.0089   14.6   2.6    1.0  1  RRN3           RNA polymerase I specific transcription initia
  ------ inclusion threshold ------
        2.4    7.8   6.9          3    7.5   6.9    1.2  1  Cwf_Cwc_15     Cwf15/Cwc15 cell cycle control protein
          4    6.7   8.6        4.6    6.5   8.6    1.1  1  NOA36          NOA36 protein
        5.7    6.8   9.5        7.3    6.4   9.5    1.2  1  Sigma70_ner    Sigma-70, non-essential region
        6.5    5.8   9.4        6.8    5.7   9.4    1.1  1  DUF2457        Protein of unknown function (DUF2457)


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 !   59.7  17.1   1.1e-19   3.3e-16       1      85 [.      16     107 ..      16     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.1e-19
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.. CS
                     Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeee. 76 
                                       e++++n++ vl aagv+ve++rvk+lv+ale++di+++++++aa   +a++aaa +aaa++a+  +ee+++ee  + 
  gi|336254633|ref|YP_004597740.1|  16 EINEDNLTDVLDAAGVDVEESRVKALVAALEDVDIDDAVEEAAAV--PAGGAAAGGAAAGGAEGGDEEEEAEETSDv 90 
                                       699***************************************999..888999999999999999999999988889 PP

                                       .......XX--SS--.S CS
                     Ribosomal_60s  77 .......EeedddmG.f 85 
                                              E++d+d+G +
  gi|336254633|ref|YP_004597740.1|  91 pdttdddEDDDEDEGaG 107
                                       99999755555598843 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 !   14.6   2.6     3e-06    0.0089     178     263 ..       1     103 [.       1     110 [. 0.63

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-06
                              RRN3 178 vtYirnllklteycpelsedileliverlikiDVe......iqveledlddeedeeleeelee.............. 234
                                       ++Y+   l l e  +e++ed l+ +++  + +DVe      +   led+d ++  e+  ++ +              
  gi|336254633|ref|YP_004597740.1|   1 MEYVYAALILNESGEEINEDNLTDVLDA-AGVDVEesrvkaLVAALEDVDIDDAVEEAAAVPAggaaaggaaaggae 76 
                                       57************************95.68***6555444557777666555554444444488899****99875 PP

                              RRN3 235 ..deddedddeddeesdlddlssdeeaeede 263
                                         d   e+++++ e+sd  d+++d+e+++++
  gi|336254633|ref|YP_004597740.1|  77 ggD---EEEEAE-ETSDVPDTTDDDEDDDED 103
                                       432...222222.333444433333333332 PP

>> Cwf_Cwc_15  Cwf15/Cwc15 cell cycle control protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   6.9     0.001         3     109     145 ..      46     104 ..      10     108 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.001
                                       .-----------------......................------------------- CS
                        Cwf_Cwc_15 109 reidaddedseeeeeeee......................eesdddsdsdsdddddede 145
                                       +++d dd  +e+                            e+sd  +  d+d+dddede
  gi|336254633|ref|YP_004597740.1|  46 EDVDIDDAVEEAAAVPAGgaaaggaaaggaeggdeeeeaeETSDVPDTTDDDEDDDEDE 104
                                       45666665554433333366666666666666655433323333355555666666666 PP

>> NOA36  NOA36 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   8.6    0.0015       4.6     262     301 ..      65     104 ..      26     110 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0015
                             NOA36 262 alasgddeddegdedddddddeedddeeeddedeeeeeee 301
                                       a a+g+     +  d++++ +e +d  +  d+de+++e+e
  gi|336254633|ref|YP_004597740.1|  65 AAAGGAAAGGAEGGDEEEEAEETSDVPDTTDDDEDDDEDE 104
                                       2222222222233334444444444333333333333333 PP

>> Sigma70_ner  Sigma-70, non-essential region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   9.5    0.0024       7.3      16      55 ..      32     103 ..      13     113 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0024
                       Sigma70_ner  16 eageirLrdiidGflD................................eeeeeeeeeeeedeeeeeeeeddd 55 
                                         +e r++ ++ ++ D                                eeee+ee ++  d+++++e++d+d
  gi|336254633|ref|YP_004597740.1|  32 DVEESRVKALVAALEDvdiddaveeaaavpaggaaaggaaaggaeggdEEEEAEETSDVPDTTDDDEDDDED 103
                                       4566777777777766888889999999******99999999976654333444444444444444433333 PP

>> DUF2457  Protein of unknown function (DUF2457)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   9.4    0.0023       6.8      54      84 ..      75     103 ..      26     111 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0023
                           DUF2457  54 eeeeeddeedeeddddddddedddedddeed 84 
                                        e  +++ee ee  +d  d +dddeddde d
  gi|336254633|ref|YP_004597740.1|  75 AEGGDEEEEAEET-SDVPDTTDDDEDDDE-D 103
                                       2222333333332.222233332222222.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 999.88
//
Query:       gi|336254634|ref|YP_004597741.1|  [L=301]
Description: lycopene cyclase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   14.2   4.9      0.065   13.2   4.9    1.5  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)
      0.063   12.5  11.1       0.15   11.3  11.2    1.7  1  SLAC1        Voltage-dependent anion channel
       0.14   10.4   3.3       0.19   10.0   3.3    1.2  1  DUF2070      Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   4.9   1.1e-05     0.065      61      79 ..     277     295 ..     268     301 .] 0.52

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                       Trypan_PARP  61 pepepepepepepepepep 79 
                                        e+epepepe epep+p+ 
  gi|336254634|ref|YP_004597741.1| 277 REREPEPEPELEPEPNPDA 295
                                       3444444444444444433 PP

>> SLAC1  Voltage-dependent anion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3  11.2   2.5e-05      0.15      19     128 ..      80     184 ..      43     249 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.5e-05
                             SLAC1  19 llkalparglrii.slilfllalvlfllllvlyllrfilypeavrkelrhpveslflgtfpmglltilnglllvl.p 93 
                                       ++ ++p      +  +++f+l  +l +l+lvl+ +r+    ++ r elr p +   +g+ +  ++t++ g++l+   
  gi|336254634|ref|YP_004597741.1|  80 IW-HTP------LeEYLFFVLQPILTALVLVLVGFRLSASDRSSRVELRLPRRHRIAGATAGLAVTVV-GWALLGpG 148
                                       44.323......44899999*******************************96666665443336666.55555534 PP

                             SLAC1  94 gewlatlalvllWigvllslltavvvvfllftek.e 128
                                       +++  +l + llW g +l+l +av+ ++l+ +++  
  gi|336254634|ref|YP_004597741.1| 149 STETYYLGALLLWAGPILALQWAVGATYLWANRRlV 184
                                       47888899999*****************99666532 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.3   3.2e-05      0.19      13     177 ..      36     251 ..       8     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.2e-05
                           DUF2070  13 swkvsllliillalligllaflssk........................lfgillfglp....alvaflltlpvlri 61 
                                       +w++ +   + +++++++++++ +                         l+++l+f l     a   ++l+l   r+
  gi|336254634|ref|YP_004597741.1|  36 RWRRRVGTGLAIIVALAVVYTTPWTnlliprgvwwygegvvrgtiwhtpLEEYLFFVLQpiltA---LVLVLVGFRL 109
                                       6665555555555555555555555678888999999999999998999666666666543332...3333222222 PP

                           DUF2070  62 lggr......ltykrslflalltelivviisllaillsallqalvllalvls......................lal 110
                                       + +       l + r   +a +t+ ++v ++  a+l    +++++l al+l                       +al
  gi|336254634|ref|YP_004597741.1| 110 SASDrssrveLRLPRRHRIAGATAGLAVTVVGWALLGPGSTETYYLGALLLWagpilalqwavgatylwanrrlVAL 186
                                       22223345568888888888888888888888888888878666666666666899999999999999999999999 PP

                           DUF2070 111 vfalrllvlvavsdesllkav.lpaliqpllailllvlyfspesfllllllslifalavylfivvvdr 177
                                       +++l++l l++ ++  l + +  ++ +++  ++l+ +++   e +l++l++ ++++ +++l+ +vv+r
  gi|336254634|ref|YP_004597741.1| 187 AIGLPTLYLWLADRIALERGLwHISETHTTGYALAGLPL---EEALFFLVTNAFVVQGIVLYAWVVER 251
                                       999999999999999999988344445555555555555...99**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2213.10
//
Query:       gi|336254635|ref|YP_004597742.1|  [L=353]
Description: beta-carotene 15,15'-monooxygenase [Halopiger xanaduensis SH-6]
Scores for 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-83  278.6  19.6      7e-83  278.2  19.6    1.2  1  BCD       Beta-carotene 15,15'-dioxygenase
      0.002   18.3   1.7     0.0032   17.7   1.7    1.5  1  Patatin   Patatin-like phospholipase


Domain annotation for each model (and alignments):
>> BCD  Beta-carotene 15,15'-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.2  19.6   7.8e-87     7e-83       2     268 .]      59     344 ..      58     344 .. 0.96

  Alignments for each domain:
  == domain 1  score: 278.2 bits;  conditional E-value: 7.8e-87
                               BCD   2 lvvllGlpHGAlDhlv.arallrkrslrsllrfivlYlllaaavvalwllaPvlaLalFllvsvlHfGqgdl..... 72 
                                       +vv+lGlpHGA+Dhlv +r+++r ++ r+l++++++Yl++++a++alw++aP++++alF+l++++H+Gqgd+     
  gi|336254635|ref|YP_004597742.1|  59 SVVVLGLPHGAVDHLVlPRSRGRPVTSRALAAVGGCYLAIGGAYAALWFVAPAVSFALFILLTLVHWGQGDVyalce 135
                                       79*************************************************************************** PP

                               BCD  73 .agtehlktraqrallalvrGglvllvpllahpeevaeifsalvglfepaallavaaaialfrl......avgvvll 142
                                        +++++l+t+a++ l+++vrGgl++lvpl+a+p+++a ++ +lvglf+p+a++a+  a+   r+      avg+++l
  gi|336254635|ref|YP_004597742.1| 136 lTDVSYLETPAHKGLALVVRGGLPMLVPLVAFPDQYAFVAGTLVGLFDPGAAAALEGAF---RPtvryavAVGFGAL 209
                                       *************************************************9777666655...444457889999999 PP

                               BCD 143 lalllalglgrlrarls...daaetalllalfavvppllafglYFclwHSlrhvarllav......alrkgrlkasl 210
                                       +a++lalg++r++a +    da+et+ l+a+fa+vpp+la+glYF  wHS+rh+ r+l +      al +g+ + ++
  gi|336254635|ref|YP_004597742.1| 210 IAATLALGYRRTDALEPwliDAGETLGLTAFFAAVPPILAIGLYFTGWHSVRHIVRTLLIddaavaALADGDARGAI 286
                                       99999999999999888*****************************************99***************** PP

                               BCD 211 krflrkaapltlatilllallyvllpksaslleslvalififlaalTlPHvvvvslld 268
                                        rf+r+aaplt+ +++++a+l+v++p++++++++++al+++++a+lTlPHvvvvslld
  gi|336254635|ref|YP_004597742.1| 287 GRFARDAAPLTAGSLVVFAALAVAVPRTPATVPDAAALYLVGVAVLTLPHVVVVSLLD 344
                                       *******************************************************997 PP

>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.7   3.6e-07    0.0032       7      54 ..     176     224 ..     175     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.6e-07
                           Patatin   7 Gsr.gafslgalkaLkkelgerfdiisGtSaGAiialllalgrdpaalv 54 
                                       G++ g+f +ga +aL+ +  + +++ +++  GA+ia+ lalg+ + +  
  gi|336254635|ref|YP_004597742.1| 176 GTLvGLFDPGAAAALEGAFRPTVRYAVAVGFGALIAATLALGYRRTDAL 224
                                       67779*************************************8876644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2494.79
//
Query:       gi|336254636|ref|YP_004597743.1|  [L=423]
Description: hypothetical protein Halxa_3252 [Halopiger xanaduensis SH-6]
Scores for complete 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-64  218.1  45.6      2e-64  217.8  45.6    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 !  217.8  45.6   1.1e-68     2e-64       1     409 []      29     413 ..      29     413 .. 0.93

  Alignments for each domain:
  == domain 1  score: 217.8 bits;  conditional E-value: 1.1e-68
                              TctA   1 LllvllGvllGtliGllPGlhatlavalllpltfgl..dpeaalilllgiyvgaifggsipaillgvPGtpssvatv 75 
                                       L++ l+G+llG ++Gl+PGlha++++ ll+ +++ +  +p+ + +++l++ v+++f++++pa+ lgvP ++++++t+
  gi|336254636|ref|YP_004597743.1|  29 LAWTLAGCLLGSCSGLVPGLHANNFALLLAGVAPAVpgPPLFVGCAMLAAGVVHTFLNAVPAMALGVP-DAEMAITA 104
                                       789*******************************554599****************************.******** PP

                              TctA  76 ldgyplakqGrageAlrlaaigSfiGglvsvllllllapllakvalkfgpaeyfalillglvliailse...ksllk 149
                                       l+g++++++Gr+ eA+rl+a+gS++++l +v+l+++++  ++  a++ + + +++l+l+++v+++i se   ++++ 
  gi|336254636|ref|YP_004597743.1| 105 LPGHRMVLEGRGYEAIRLSALGSILAVLAAVPLAVPITRGVT--AVYPTVRAHLSLVLAAVVVALIASErtsRRMVG 179
                                       ******************************************..************************99999**** PP

                              TctA 150 glialllglllgtvgldpnsgtpRftfgsielldgislvpvliGlFgiselltsleskskip.......lslkdlkk 219
                                       g ++++l+  lg+++ld ++++p        l +g +l p++ GlFg++ l++ +  +  ip          k+l  
  gi|336254636|ref|YP_004597743.1| 180 GTLSFALAAGLGWLTLDLEPNAP--------LEAGGTLAPLFAGLFGAPVLIDAIFGT-GIPpqegdgiAASKRL-- 245
                                       *******************8777........************************864.5554555432122222.. PP

                              TctA 220 slptilrgsliGtivGilPgvGasiaaflayavakrlskkpekfgkgaiegvaapeaannaaaggaliplltlgipg 296
                                       + +t+l+g+l+G++vG++Pgv+a+iaa++   v           g  ++ +++a++++ +a++++al++l+++g p+
  gi|336254636|ref|YP_004597743.1| 246 VGTTALAGALAGAVVGYIPGVSAAIAAVAVLVVVPG--------GASDRGYIVATSGVDTANTIFALFALVAIGQPR 314
                                       4478999**************************886........679****************************** PP

                              TctA 297 sgvaavllgallihglqpgpeLftenpelvyallasllianvlllvlgllliklfakll.kipkelLlpiilvllvi 372
                                        gv++++  +                p  + +l+as++ia +l +vl++++++ + +++ ++ ++ L++++l+ll++
  gi|336254636|ref|YP_004597743.1| 315 TGVMVAFERVN--------------APLELPILIASVVIAGLLGFVLVIVVGDAYLEVVgRLTYWKLSAAVLALLLV 377
                                       ****9999964..............5667899*************************888***************** PP

                              TctA 373 gayalnnslfdvlvmlifgvlGlllrrlgvplaplvl 409
                                       ++ ++++  ++++++++++++Gl++ rl+ ++++l++
  gi|336254636|ref|YP_004597743.1| 378 LSLLFAGP-IGIAIFVVATAIGLVPVRLRARRVHLMG 413
                                       ********.**************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); 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:                         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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3121.82
//
Query:       gi|336254637|ref|YP_004597744.1|  [L=277]
Description: photosystem I assembly BtpA [Halopiger xanaduensis SH-6]
Scores for 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-83  279.0   4.7    3.8e-83  278.8   4.7    1.0  1  BtpA            BtpA family
     0.0026   17.5   0.6      0.018   14.8   0.0    2.0  2  4HFCP_synth     4-HFC-P synthase
     0.0077   15.4   0.1      0.017   14.3   0.1    1.4  1  TGT             Queuine tRNA-ribosyltransferase
  ------ inclusion threshold ------
      0.012   15.1   5.6      0.088   12.2   1.3    2.6  3  PcrB            PcrB family
      0.023   13.6   1.2      0.037   12.9   1.2    1.4  1  Trp_syntA       Tryptophan synthase alpha chain
       0.12   12.6   3.3        1.2    9.4   0.3    2.8  3  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain


Domain annotation for each model (and alignments):
>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.8   4.7   1.3e-86   3.8e-83       3     253 ..      15     270 ..      13     271 .. 0.97

  Alignments for each domain:
  == domain 1  score: 278.8 bits;  conditional E-value: 1.3e-86
                              BtpA   3 kpvigvvHLkpLPgsaeykanleevidkAvkeakaleegGvDavilenygdaPflke.vdpetvaamtvivkevksd 78 
                                       +pv+g+vHL++LPg + ++++  ++ ++A+++a+ le gG+D+++len+gdaPf  e v + +va mt ++++v+++
  gi|336254637|ref|YP_004597744.1|  15 RPVLGMVHLPALPGAPAFDGDRAAIRERALEDARRLEGGGIDGIVLENFGDAPFYPEsVPNHVVAEMTAVASAVTDA 91 
                                       79***************************************************87664888999************* PP

                              BtpA  79 vsiplGvnvLrndavaalaiAkavgakFiRvnvltgvalsdeGilegkaaellrykkllesrvkiladvavkhavpl 155
                                       v +p+G+nvLrnda aal+iA a+ga+F+Rvnv +g+a++d+G+leg a+e++r++ +++++v+iladv+vkha+p+
  gi|336254637|ref|YP_004597744.1|  92 VDVPVGINVLRNDAGAALSIAAAAGAEFVRVNVHVGTAATDQGVLEGRAHETVRLRDRIDADVAILADVHVKHATPI 168
                                       ***************************************************************************** PP

                              BtpA 156 verdlesavkdtvergladavilsGkatGgevdleelklaketvk...vkvlvgsGvseenlekllsi.adGvivgt 228
                                       +e+++e+a+++tv rg ad+vi+sG  tG e++le+++++++++      v+vgsGv+ e ++  + + adG ivgt
  gi|336254637|ref|YP_004597744.1| 169 GETEIEHAALETVGRGRADGVIVSGSGTGAETSLEDVERVADALAgreASVIVGSGVTPETIADCVAAgADGAIVGT 245
                                       ******************************************9988999*************99886559******* PP

                              BtpA 229 sikkdGkianaiDkervrkivelae 253
                                        +k +G+++na+ +erv+ +ve+a+
  gi|336254637|ref|YP_004597744.1| 246 ALKEGGETTNAVSRERVESLVEAAR 270
                                       *********************9985 PP

>> 4HFCP_synth  4-HFC-P synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3     0.097   2.9e+02      67     128 ..     105     164 ..      71     191 .. 0.54
   2 !   14.8   0.0   5.9e-06     0.018     133     178 ..     228     273 ..     198     277 .] 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.097
                                       HHHHHHHHHHTT-SEEEEEE-S--SHHHHHHHHHHHHHHHHHH-TTSEEEEEEETTGGGTT- CS
                       4HFCP_synth  67 vslaalgaaaagvdyvKvGlaglkkeeealealkavvkavkeedkekkvvavlyaDaervas 128
                                       + +a   aaaag+++v+v +  +++++  + +l+  ++++ + + +     ++ aD + v++
  gi|336254637|ref|YP_004597744.1| 105 AGAALSIAAAAGAEFVRVNVH-VGTAATDQGVLEGRAHETVRLRDRIDADVAILADVH-VKH 164
                                       334445578999999999865.344444444444322222222222233344556665.444 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5.9e-06
                                       GHHHHHHHHT-SEEEEE-SS-SS--HHHHS-HHHHHHHHHHHHHTT CS
                       4HFCP_synth 133 ellelaaeagaagvmlDTadKdgkslldflseeelaefveeareag 178
                                       e+++   +aga+g+++ Ta K+g+++++ +s e+++++ve+ar a+
  gi|336254637|ref|YP_004597744.1| 228 ETIADCVAAGADGAIVGTALKEGGETTNAVSRERVESLVEAARTAD 273
                                       566777899*********************************9876 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   5.8e-06     0.017     182     244 ..     178     239 ..     167     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.8e-06
                                       HHHHHHH--SEEEE-SSSSSSHHHHHHHHHHHHGGGS-TTS-EEETTB-.SHHHHHHHHHTT-- CS
                               TGT 182 aeelakrdfdgyaigGlsvgeekeellevveavtellpedkprylmGvg.tPedlleavalGvD 244
                                       +e + +  +dg+ ++G   g   e+ le ve+v++ l  +   ++ G g tPe+++++va+G+D
  gi|336254637|ref|YP_004597744.1| 178 LETVGRGRADGVIVSGSGTGA--ETSLEDVERVADALAGREASVIVGSGvTPETIADCVAAGAD 239
                                       4444444579******77777..899***********9999999999999*************9 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.6   4.8e+03     176     190 ..      42      56 ..      33      57 .. 0.82
   2 ?    5.7   0.2     0.003       8.9      17      41 ..     172     199 ..     156     211 .. 0.71
   3 ?   12.2   1.3     3e-05     0.088     163     217 ..     197     253 ..     195     261 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.6
                                       HHHSSSEEEEESS-- CS
                              PcrB 176 kklekarlivGGGir 190
                                       + le+ar + GGGi+
  gi|336254637|ref|YP_004597744.1|  42 RALEDARRLEGGGID 56 
                                       5689999999***97 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.003
                                       S-CHHHHHHHHCTT-SEEEEECST...C CS
                              PcrB  17 enpdEiveiviesgtDavmigGsq...s 41 
                                       e    ++e+v ++ +D+v+++Gs    +
  gi|336254637|ref|YP_004597744.1| 172 EIEHAALETVGRGRADGVIVSGSGtgaE 199
                                       444567899*************974333 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 3e-05
                                       TSSS-HHHHHHHHHHHS..SSEEEEESS--SHHHHHHHHCCSSEEEE-CHHHHHHHC CS
                              PcrB 163 Galedveevialkkkle..karlivGGGirsaEkAkevveaADvivvGnvveekder 217
                                       Ga   +e v ++   l   +a +ivG G+  + +A  v+  AD  +vG++++e +e+
  gi|336254637|ref|YP_004597744.1| 197 GAETSLEDVERVADALAgrEASVIVGSGVTPETIADCVAAGADGAIVGTALKEGGET 253
                                       66666677777777775226789******988888888877***********98854 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.2   1.2e-05     0.037     176     250 ..     196     268 ..     160     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                                       SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHHHHHHHCTTTSHHHHHHHHHHH CS
                         Trp_syntA 176 TgaenavaaevdelverlkkltavPvavGFGistkeqvkqvakvadGvivGSalvkkieeeaeekeqalekleel 250
                                       Tgae++  ++v+++  +l   + + v vG G+  +  ++ va++adG+ivG al +  e++ + +++ +e l e 
  gi|336254637|ref|YP_004597744.1| 196 TGAETS-LEDVERVADALAGRE-ASVIVGSGVTPETIADCVAAGADGAIVGTALKEGGETTNAVSRERVESLVEA 268
                                       555554.456777777776665.7899*****9999999999***********9877776666666666665555 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0       0.1     3e+02      23      35 ..      54      66 ..      36      98 .. 0.78
   2 ?    9.4   0.3    0.0004       1.2      13      58 ..     175     222 ..     159     231 .. 0.72
   3 ?    0.5   0.1      0.23   6.7e+02      10      30 ..     224     244 ..     221     272 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.1
                                      T--EEEEEEBTTT CS
                    Asparaginase_C 23 gakGvvlegtGvG 35
                                      g++G+vle +G  
  gi|336254637|ref|YP_004597744.1| 54 GIDGIVLENFGDA 66
                                      78********976 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0004
                                       HHHHHHHHHTT--EEEEEEBTTTB--H..HHHHHHHHHHTTT-EEEEE CS
                    Asparaginase_C  13 tkvlkallkkgakGvvlegtGvGnlps..allealkeakargivvvat 58 
                                        + l+ + + +a+Gv++ g G+G+ +s  ++ +++  +  r+  v++ 
  gi|336254637|ref|YP_004597744.1| 175 HAALETVGRGRADGVIVSGSGTGAETSleDVERVADALAGREASVIVG 222
                                       334444445579*************99977777777777777777765 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.23
                                       T--HHHHHHHHHTT--EEEEE CS
                    Asparaginase_C  10 gmdtkvlkallkkgakGvvle 30 
                                       g++++++  ++++ga+G ++ 
  gi|336254637|ref|YP_004597744.1| 224 GVTPETIADCVAAGADGAIVG 244
                                       788999999999999998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); 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):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2325.19
//
Query:       gi|336254638|ref|YP_004597745.1|  [L=370]
Description: NADPH dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-65  219.5   0.0    9.9e-65  219.0   0.0    1.2  1  Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase famil
  ------ inclusion threshold ------
      0.077   12.1   0.0       0.14   11.2   0.0    1.5  1  Dus           Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.0   0.0   1.1e-68   9.9e-65       1     339 [.       3     352 ..       3     355 .. 0.83

  Alignments for each domain:
  == domain 1  score: 219.0 bits;  conditional E-value: 1.1e-68
                                       CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGG CS
                      Oxidored_FMN   1 kLFkPikignmtLknRivmapmtrlraldkgnvledlaaeyysqraeipvtliiteaafvnpksggfdnapgiwdee 77 
                                       +LF  + + + ++ nR++++pm+++ +  +g  ++++   +   ra ++ ++++tea++v+p +++++ + giw++e
  gi|336254638|ref|YP_004597745.1|   3 DLFSDLSLRDLEVPNRLAVSPMCQYTCDADG-LPTEWHRVHLGSRAVGGAGIVMTEATAVEPRGRITPHDLGIWSDE 78 
                                       599999*************************.78889999************************************* PP

                                       GHHHHHHHHHHHHHTT-EEEEEEE--GGGS..SCSTCEC................SS.ESSSSSTTT-......... CS
                      Oxidored_FMN  78 qieewrklteavhengskvvvqlwhlGreakseyladqe..............vdspsdpvaldaqee......... 131
                                       ++e+++++te v+++g+  ++ql+h+G +a s +++ ++                                      
  gi|336254638|ref|YP_004597745.1|  79 HAEALQPITEFVRDQGGVPGIQLAHAGHKA-SKTRPWDGnvpiapdetdpdgaA-------------Gwevlspspd 141
                                       ******************************.66666666433333333333330.............2556666666 PP

                                       ......S...CS-EE--HHHHHHHHHHHHHHHHHHHHTT-SEEEEEE-CTSHHHHHH-TTT----STTSSSHHHHHH CS
                      Oxidored_FMN 132 .....esaeevykkeltkeeikqliqefveAAkraieAgfDgVeihganGYLlnqFlspksnkrtDeygGslenRar 203
                                                +   ++ ++++i+ +i+++  AA+r+ eAgf + e+h+a+GYLl++Flsp +n+r D ygGs enR r
  gi|336254638|ref|YP_004597745.1| 142 ayppfPGDRPA-MRKADQDDIEGVIDAYRAAAERSLEAGFEIAEVHAAHGYLLHEFLSPVTNDRDDDYGGSFENRTR 217
                                       66654344444.6899************************************************************* PP

                                       HHHHHHHHHHHHH-SSS.EEEEEECE--STTS--.HHHH.HHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHH CS
                      Oxidored_FMN 204 FllevvdaVkeavgeer.vgyRlSpedvvekgld.faet.aqkivllkelekrlkdgkklalvhaaeprkrgagsvr 277
                                        ++evv+aV+++   e+ +++R+S  d ve+ +   +++    +  l+el+++l+d++++ l h ++   + +g  +
  gi|336254638|ref|YP_004597745.1| 218 LVREVVKAVRDVWPDEKpIFVRISGTDWVEDRESwDIDQsVRLAGDLAELGVDLLDVSSGGL-HPDQ---QVPGGPN 290
                                       ************************99988765431344456667778888899998888876.4444...3444444 PP

                                       CCTTHHHHHHCCCH.SSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCT CS
                      Oxidored_FMN 278 teqekntefvkevw.kkplitvgriadeekaaeivaegeadLvamgRefladpdlveklkkgl 339
                                       ++    +e v+e   + ++ +vg+ +++e+a+  v +g+adLv +gRefl+dp +  +++ +l
  gi|336254638|ref|YP_004597745.1| 291 FQV-PLAEAVREGTdDLAVGAVGGVTEPEQADALVRNGRADLVLVGREFLRDPYFGLRAAGEL 352
                                       442.33567776551689***********************************9988877655 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.5e-05      0.14     176     239 ..     297     361 ..     199     370 .] 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.5e-05
                                       HHHHHH-S.S-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHHHHHHHHSC------ CS
                               Dus 176 kevkqavs.ipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfaestavktgeaepapp 239
                                       ++v++    + v a G+++++e+a+a +++  ad v++gr+ l++P++  + +   +g a++++p
  gi|336254638|ref|YP_004597745.1| 297 EAVREGTDdLAVGAVGGVTEPEQADALVRNGRADLVLVGREFLRDPYFGLRAAGELEGDAAEKWP 361
                                       567777778899999***************99**************9876544555556666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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 0.20s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 3152.55
//
Query:       gi|336254639|ref|YP_004597746.1|  [L=187]
Description: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen [Halopiger xanaduensis SH-6]
Scores for complete 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   60.8   0.0    1.5e-16   60.4   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    1.5e-13   50.7   0.0    1.8e-13   50.4   0.0    1.1  1  Redoxin        Redoxin
     0.0034   16.8   0.0     0.0044   16.4   0.0    1.1  1  TatD_DNase     TatD related DNase
     0.0047   16.8   0.0      0.025   14.4   0.0    1.9  1  TraF           F plasmid transfer operon protein
     0.0079   16.6   0.0      0.013   15.9   0.0    1.3  1  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.026   14.8   0.0      0.038   14.3   0.0    1.2  1  Thioredoxin_8  Thioredoxin-like
      0.064   12.5   0.0      0.083   12.2   0.0    1.2  1  T4_deiodinase  Iodothyronine deiodinase


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 !   60.4   0.0   5.9e-20   1.5e-16       2     113 ..      13     125 ..      12     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 5.9e-20
                                       TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH....... CS
                          AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe....... 71 
                                       gd+apdfel+  dget++l+ ++++ ++l++++ ++cp+++++   l++l++e++   v v+g+++++ e       
  gi|336254639|ref|YP_004597746.1|  13 GDAAPDFELPGVDGETYTLESFADSEALLVVFTCNHCPYAQAKFDLLNELADEYD--EVAVVGINPNDAEeypddsf 87 
                                       99********************9977777777777********************..89*******99999****** PP

                                       .HHHHHHHH-H.SSE.EEE-TTSHHHHHTT-EETTTTECSCEEE CS
                          AhpC-TSA  72 .shkkfiekeslnfp.llsDeegkvakaygvlkeekglalratf 113
                                        ++++f+e+ +++++ +l De+++va +yg++       ++  f
  gi|336254639|ref|YP_004597746.1|  88 eKMQEFVEDGRVQYNaYLRDESQAVAAEYGAVC------TPDPF 125
                                       ************9964899*************4......44444 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   7.1e-17   1.8e-13       2     121 ..      12     127 ..      11     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 7.1e-17
                                       TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH... CS
                           Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf... 75 
                                       agd+aPdf+lp+   dg++++l++f++  ++++++++++cP+ +a+   l++la++     v vv+++ ++ +    
  gi|336254639|ref|YP_004597746.1|  12 AGDAAPDFELPG--VDGETYTLESFADSEALLVVFTCNHCPYAQAKFDLLNELADE--YDEVAVVGINPNDAEEypd 84 
                                       8*********99..*********************************999999999..4568999999998888899 PP

                                       .....HHHHHHHTT-TSEE.EE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEE CS
                           Redoxin  76 .....vkefwgkeglkfpv.lsDgsaaftkalGlrleedaseglrtpryavi 121
                                            ++ef+++  +++   l D+s+a+++++G+          +tp  +++
  gi|336254639|ref|YP_004597746.1|  85 dsfekMQEFVEDGRVQYNAyLRDESQAVAAEYGAV---------CTPDPFLF 127
                                       999*9*******66666554*************88.........55555555 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.7e-06    0.0044      38      88 ..      49      99 ..      18     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-06
                                      G....GGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHHHHHCCCTSE CS
                        TatD_DNase 38 s....kdskavlelakkypnkvyavlGiHPnevdeasedlleelkelanvkhskv 88
                                           ++++ + ela +y++  +av+Gi Pn+++e  +d +e+++e+  v++ +v
  gi|336254639|ref|YP_004597746.1| 49 CpyaqAKFDLLNELADEYDE--VAVVGINPNDAEEYPDDSFEKMQEF--VEDGRV 99
                                      244434777999*******9..9************************..998877 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   9.7e-06     0.025     123     169 ..      30      78 ..      25     143 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.7e-06
                              TraF 123 alkklakeygLlfFyr.gkcpyceaqapilqafadky.glevraVsvdg 169
                                       +l++ a++ +Ll+++  ++cpy +a  + l+++ad+y + +v+ ++ ++
  gi|336254639|ref|YP_004597746.1|  30 TLESFADSEALLVVFTcNHCPYAQAKFDLLNELADEYdEVAVVGINPND 78 
                                       5777777767666555599******************556666665443 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.1e-06     0.013       6      98 ..      38     140 ..      34     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.1e-06
                     Thioredoxin_2   6 kpvlvvftdpdCpyCkklkkelkelddvtvrvllfp...lkpsfepkavaiwcakekkkafkd.............i 66 
                                       + +lvvft ++Cpy ++   +++ l+++ + +  ++   ++p+    a++   +  +  ++++              
  gi|336254639|ref|YP_004597746.1|  38 EALLVVFTCNHCPYAQA---KFDLLNELADEYDEVAvvgINPN---DAEEYPDDSFE--KMQEfvedgrvqynaylR 106
                                       5789**********998...55555555555333333344444...22222222222..244466678888888989 PP

                     Thioredoxin_2  67 eenvelarkygvrgtPt.ivfldgk.eivarlpG 98 
                                       +e++++a +yg   tP+ ++f  ++ e  ++++G
  gi|336254639|ref|YP_004597746.1| 107 DESQAVAAEYGAVCTPDpFLFAREDgEFRLVYQG 140
                                       *****************55566555777777777 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.5e-05     0.038       4      85 ..      40     123 ..      37     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                                       EEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-.......SS-HHHHHHHGGGS-TTSEE.EE-T...T- CS
                     Thioredoxin_8   4 vlLyfgaswcppckaftpklkelyeklkkkkkveivyvsl.......dkkeeefekylkknkkpwlsvpfdd...kk 70 
                                       +l++f  ++cp  +a    l+el +++   + v +v ++        d + e++++++++      +v+++    ++
  gi|336254639|ref|YP_004597746.1|  40 LLVVFTCNHCPYAQAKFDLLNELADEY---DEVAVVGINPndaeeypDDSFEKMQEFVEDG-----RVQYNAylrDE 108
                                       799************************...69********545544444445555555544.....44444411134 PP

                                       HHHHTT-S--TT-SE CS
                     Thioredoxin_8  71 rnklkkkynvkaiPt 85 
                                       +++++ +y+  + P 
  gi|336254639|ref|YP_004597746.1| 109 SQAVAAEYGAVCTPD 123
                                       677788888777665 PP

>> T4_deiodinase  Iodothyronine deiodinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.2e-05     0.083      72     135 ..       9      70 ..       2     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-05
                     T4_deiodinase  72 qvkeGgdaPnsevvrvsgteschildfaqgnrPlvlnfGsatcPpflaklsafkrlveefssva 135
                                       + + G+ aP+ e+  v+g     +  fa+++  lv+ f    cP   ak++ ++ l +e+  va
  gi|336254639|ref|YP_004597746.1|   9 ELEAGDAAPDFELPGVDGET-YTLESFADSEALLVV-FTCNHCPYAQAKFDLLNELADEYDEVA 70 
                                       5689**************98.899999999876665.99*********************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1405.79
//
Query:       gi|336254640|ref|YP_004597747.1|  [L=199]
Description: hypothetical protein Halxa_3256 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.39   10.1   0.2       0.39   10.1   0.2    2.4  3  SeqA_N        SeqA protein N-terminal domain
       0.64    8.7   7.5       0.74    8.5   7.5    1.1  1  SAPS          SIT4 phosphatase-associated protein
       0.66    9.3   3.7       0.83    8.9   3.7    1.1  1  DUF4407       Domain of unknown function (DUF4407)
        2.2    6.7  11.4        2.3    6.7  11.4    1.1  1  RRN3          RNA polymerase I specific transcription initiat
        2.8    6.0  19.0          3    6.0  19.0    1.0  1  Nop14         Nop14-like family


Domain annotation for each model (and alignments):
>> SeqA_N  SeqA protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00011      0.39       1      21 [.       1      21 [.       1      24 [. 0.84
   2 ?   -1.5   0.2      0.45   1.6e+03       4       8 ..      53      57 ..      52      60 .. 0.85
   3 ?   -3.7   0.6       2.1   7.7e+03      22      26 ..      80      84 ..      78      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
                            SeqA_N  1 MKtIevDeeLYrYIasntqai 21
                                      MKt e+ +e Y +I    q+i
  gi|336254640|ref|YP_004597747.1|  1 MKTLEITDEQYAFIQRLRQEI 21
                                      **************7666665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.45
                            SeqA_N  4 IevDe 8 
                                      Ie+De
  gi|336254640|ref|YP_004597747.1| 53 IEIDE 57
                                      9***9 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.1
                            SeqA_N 22 GESaS 26
                                      GESa 
  gi|336254640|ref|YP_004597747.1| 80 GESAG 84
                                      9*995 PP

>> SAPS  SIT4 phosphatase-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.5   0.00021      0.74     246     343 ..      31     163 ..      14     185 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00021
                              SAPS 246 ivkerDevrerlleel...............tseeealedvs.............................deaske 278
                                        v+erD++   + + +               +                                        e++++
  gi|336254640|ref|YP_004597747.1|  31 FVRERDAIQFLIDNIDgeadvdieideafhsS---------AtadvagsvgaaieagagesageevsydetAEPTDP 98 
                                       56666666665555444443333333222220.........122222444444444444444444446442333333 PP

                              SAPS 279 esaesedltdkdedvsleesksakdenkesdesesdtaeesseededdasseesalaeeteeklr 343
                                       ++a+++d++ ++++ ++ +++++++++++ d+ ++  ++es+++d+d++ +e   l e++++k +
  gi|336254640|ref|YP_004597747.1|  99 DEAADDDTDAATDSSTSTDDADEEADSDDADADSDAGDNESGDADDDEMLDEMMSLLETHDDKWE 163
                                       33333333333333333333333334666666666667777777777777777777777777665 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.7   0.00023      0.83     133     252 ..      33     156 ..       4     171 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00023
                           DUF4407 133 aelaeleaqiaalqaeidaaearldalraeaqkeldgtk......gtgttgvaGkgpaakekkaqldaaqaelaelk 203
                                        e ++++  i+++++e d   +  +a    a++ + g        g+g    aG++ +++e  +  d  +a+ ++ +
  gi|336254640|ref|YP_004597747.1|  33 RERDAIQFLIDNIDGEADVDIEIDEAFHSSATADVAGSVgaaieaGAG--ESAGEEVSYDETAEPTDPDEAADDDTD 107
                                       444555555555555555544444444555555555555777744555..568999999999999999999999999 PP

                           DUF4407 204 akldatarlaalraelaeleaerakeraasqaaaaaddGllarlealdr 252
                                       a  d+++ ++++++e+++ +a++++++ ++++  a+dd +l+++  l +
  gi|336254640|ref|YP_004597747.1| 108 AATDSSTSTDDADEEADSDDADADSDAGDNESGDADDDEMLDEMMSLLE 156
                                       9999**************************************9877655 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 ?    6.7  11.4   0.00064       2.3     234     295 ..      86     161 ..      25     194 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00064
                              RRN3 234 e...............deddedddedd..eesdlddlssdeeaeedeekdeeeeslkkikelvekLDailtllfehl 293
                                       e                +dd d++ d+  +++d+d+++++++a+ d++   + ++ +   +  e LD++++ll +h 
  gi|336254640|ref|YP_004597747.1|  86 EvsydetaeptdpdeaADDDTDAATDSstSTDDADEEADSDDADADSD---AGDNESGDADDDEMLDEMMSLLETHD 159
                                       033333333322211111122222222222222222222222222222...22333566677788999999998887 PP

                              RRN3 294 ek 295
                                       +k
  gi|336254640|ref|YP_004597747.1| 160 DK 161
                                       77 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  19.0   0.00083         3     336     440 ..      71     167 ..      19     193 .. 0.42

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00083
                             Nop14 336 lgkglka..........taeee.eeededdfeedddlveseseeeeeeeeedeeeeedeeeeeeeeededdlsdles 401
                                       +g+ ++a          + +e  e  d d+  +dd++ +++s+   ++++ dee ++d+ +       ++d+ d+e 
  gi|336254640|ref|YP_004597747.1|  71 VGAAIEAgagesageevSYDETaEPTDPDEAADDDTDAATDSST--STDDADEEADSDDAD------ADSDAGDNE- 138
                                       44444223333222222111111222222222222112222211..112222221111111......112222222. PP

                             Nop14 402 eeeeeedeleeel...leeekkaaeekkekkkkkkkseekak 440
                                       + + ++de+ +e+   le++++             k ee+++
  gi|336254640|ref|YP_004597747.1| 139 SGDADDDEMLDEMmslLETHDD-------------KWEESSS 167
                                       2333334433332233222222.............2222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1086  (0.0605723); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1449.53
//
Query:       gi|336254641|ref|YP_004597748.1|  [L=161]
Description: AsnC family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for complete 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   47.4   0.7    2.5e-12   46.6   0.1    1.7  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    1.2e-06   28.0   0.1    3.9e-06   26.3   0.1    1.9  2  HTH_24          Winged helix-turn-helix DNA-binding
    1.5e-05   25.3   0.1    0.00049   20.5   0.2    2.4  2  HTH_27          Winged helix DNA-binding domain
    3.9e-05   23.4   0.9    7.8e-05   22.4   0.3    1.8  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
     0.0021   17.9   1.1     0.0027   17.6   0.1    1.7  2  MarR_2          MarR family
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.025   14.7   0.0    1.3  1  FeoC            FeoC like transcriptional regulator
      0.015   15.3   0.1      0.033   14.2   0.1    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.03   14.4   0.4      0.053   13.7   0.4    1.3  1  DprA_WH         DprA winged helix domain
      0.037   13.9   0.4      0.066   13.1   0.4    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.057   13.8   0.0       0.13   12.6   0.0    1.6  1  Rrf2            Transcriptional regulator
      0.089   12.6   0.3       0.29   10.9   0.1    2.0  2  She9_MDM33      She9 / Mdm33 family
       0.13   12.3   0.1       0.78    9.8   0.0    2.0  2  HTH_54          ParA helix turn helix domain


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 ?   -2.4   0.1       3.1   4.7e+03      14      23 ..      30      39 ..      22      46 .. 0.57
   2 !   46.6   0.1   1.7e-15   2.5e-12       2      74 ..      69     139 ..      66     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.1
                                      HHHHHHHHTS CS
                    AsnC_trans_reg 14 eefeealael 23
                                      +e+e++++el
  gi|336254641|ref|YP_004597748.1| 30 DEVEAVIEEL 39
                                      3444444433 PP

  == domain 2  score: 46.6 bits;  conditional E-value: 1.7e-15
                                       EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       +v+l+++    + +++e+la++p+V+ +  v+Gdyd+ ++v   ++++ ++f++ek+a +p++++t t+ v+ 
  gi|336254641|ref|YP_004597748.1|  69 NVRLDRET--GYGDIAERLARFPQVKALRLVSGDYDFDMEVEGDSIREVSQFISEKVAPVPEITQTVTHYVMT 139
                                       56666555..999**********************************************************95 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 !   26.3   0.1   2.6e-09   3.9e-06       5      48 .]       3      46 ..       2      46 .. 0.97
   2 ?   -2.2   0.0       2.1   3.1e+03      20      27 ..      78      85 ..      73      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.6e-09
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +r++LelL++n+r s +++A++++l    v + +++Le +G+++
  gi|336254641|ref|YP_004597748.1|  3 EREVLELLRENARYSTADIARMTDLEEDEVEAVIEELEAAGVVR 46
                                      799***************************************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                            HTH_24 20 qreLAerl 27
                                      + ++Aerl
  gi|336254641|ref|YP_004597748.1| 78 YGDIAERL 85
                                      5799**98 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 !   20.5   0.2   3.3e-07   0.00049       5      48 ..       3      45 ..       1      50 [. 0.94
   2 ?    2.5   0.0      0.14   2.1e+02       3      27 ..      88     118 ..      86     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.3e-07
                            HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                      ++ vL+l+r +++r + ad+++++++e   +  ++++L+++G+v
  gi|336254641|ref|YP_004597748.1|  3 EREVLELLR-ENARYSTADIARMTDLEEDEVEAVIEELEAAGVV 45
                                      7899*****.*********************************9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                            HTH_27   3 rqqalvLhlir......hrrrrkkladlcgr 27 
                                       ++q+  L+l+       ++++++++++++++
  gi|336254641|ref|YP_004597748.1|  88 FPQVKALRLVSgdydfdMEVEGDSIREVSQF 118
                                       7899999999999999999999999999986 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 !   22.4   0.3   5.2e-08   7.8e-05       6      41 ..       4      39 ..       3      40 .. 0.88
   2 ?   -2.4   0.0       2.9   4.3e+03      20      27 ..      78      85 ..      73      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.2e-08
                     HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      r  Le+L+e+aR s a++A+++ l e++v + ++ L
  gi|336254641|ref|YP_004597748.1|  4 REVLELLRENARYSTADIARMTDLEEDEVEAVIEEL 39
                                      6679************************98766666 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.9
                     HTH_AsnC-type 20 yaeLAerv 27
                                      y ++Aer+
  gi|336254641|ref|YP_004597748.1| 78 YGDIAERL 85
                                      67899987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.8e-06    0.0027       6      52 ..       2      46 ..       1      65 [. 0.90
   2 ?   -3.0   0.1       4.7     7e+03      25      31 ..      79      85 ..      79      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.8e-06
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +++ vL  L+ + +   + +++ar ++l+   v  ++++L+aaG v+
  gi|336254641|ref|YP_004597748.1|  2 SEREVLELLRENAR--YSTADIARMTDLEEDEVEAVIEELEAAGVVR 46
                                      6899********98..7****************************96 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.7
                                      HHHHHHH CS
                            MarR_2 25 gelarrl 31
                                      g++a+rl
  gi|336254641|ref|YP_004597748.1| 79 GDIAERL 85
                                      6999998 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   1.7e-05     0.025       4      47 ..       5      48 ..       4      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                              FeoC  4 elkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekv 47
                                      e+ e+l+e+ r s  +++r  + +++ +ea +e +++ G v+  
  gi|336254641|ref|YP_004597748.1|  5 EVLELLRENARYSTADIARMTDLEEDEVEAVIEELEAAGVVRGY 48
                                      677899*********************************99865 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 ?   14.2   0.1   2.2e-05     0.033      20      67 ..      14      59 ..       2      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHHHHH CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrgrririldleaLra 67
                                       + + +++A+m  l    v  ++ eL+ +g+++      + d+++L++
  gi|336254641|ref|YP_004597748.1| 14 ARYSTADIARMTDLEEDEVEAVIEELEAAGVVRGY--QAVVDWDKLED 59
                                      478999**************************944..4799***9986 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   3.5e-05     0.053      14      56 ..       3      46 ..       1      48 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-05
                           DprA_WH 14 errvLaaLgpePv.hvDqLvrrtglpaaevsaaLleLELaGlve 56
                                      er vL++L   ++ +  +++r t l+ +ev a+  eLE aG v+
  gi|336254641|ref|YP_004597748.1|  3 EREVLELLRENARySTADIARMTDLEEDEVEAVIEELEAAGVVR 46
                                      899*****886555***************************997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   4.4e-05     0.066      14      53 ..       7      46 ..       2      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                                      CHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 14 YlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                         L ++ + ++ +ia+++++++  v  v+++Le +G+V+
  gi|336254641|ref|YP_004597748.1|  7 LELLRENARYSTADIARMTDLEEDEVEAVIEELEAAGVVR 46
                                      44455999999***************************96 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.8e-05      0.13      18      56 ..       8      46 ..       5      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.8e-05
                                      HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      ++ +e+   s+++ia+++++++  +e ++++L+ ag+v+
  gi|336254641|ref|YP_004597748.1|  8 ELLRENARYSTADIARMTDLEEDEVEAVIEELEAAGVVR 46
                                      555666679****************************98 PP

>> She9_MDM33  She9 / Mdm33 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0002      0.29      70     113 ..       2      45 ..       1      66 [. 0.84
   2 ?   -0.1   0.0      0.45   6.7e+02      53      53 ..      94      94 ..      50     146 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                        She9_MDM33  70 sqrevneLLqRkssWspedlerftelyrkdhanekeeeeakekl 113
                                       s rev eLL+    +s++d++r t+l  ++ +   ee ea+  +
  gi|336254641|ref|YP_004597748.1|   2 SEREVLELLRENARYSTADIARMTDLEEDEVEAVIEELEAAGVV 45 
                                       78************************999988887777776555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.45
                        She9_MDM33 53 v 53
                                      +
  gi|336254641|ref|YP_004597748.1| 94 L 94
                                      0 PP

>> HTH_54  ParA 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   0.00052      0.78      27      56 ..      15      44 ..       2      51 .. 0.90
   2 ?   -0.2   0.0      0.68     1e+03      31      58 ..     121     148 ..     113     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00052
                            HTH_54 27 tyskaalaklpklsrrkvdkavsemeaeGy 56
                                       ys a +a+++ l   +v++ ++e+ea+G 
  gi|336254641|ref|YP_004597748.1| 15 RYSTADIARMTDLEEDEVEAVIEELEAAGV 44
                                      79**************************96 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.68
                            HTH_54  31 aalaklpklsrrkvdkavsemeaeGyef 58 
                                        ++a +p++++    + ++  +++G+e+
  gi|336254641|ref|YP_004597748.1| 121 EKVAPVPEITQTVTHYVMTSYKENGIEL 148
                                       5678888999998888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      757  (0.0422221); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1307.85
//
Query:       gi|336254642|ref|YP_004597749.1|  [L=386]
Description: aspartate transaminase [Halopiger xanaduensis SH-6]
Scores for 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-69  232.7   0.0    8.2e-69  232.5   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    5.5e-07   29.1   0.0    1.3e-06   27.9   0.0    1.5  2  Beta_elim_lyase  Beta-eliminating lyase
    4.2e-05   22.7   0.0    7.5e-05   21.9   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.017   14.4   0.0      0.034   13.5   0.0    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.076   11.7   0.0       0.11   11.2   0.0    1.1  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major 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 !  232.5   0.0   2.3e-72   8.2e-69       2     362 ..      29     377 ..      28     378 .. 0.94

  Alignments for each domain:
  == domain 1  score: 232.5 bits;  conditional E-value: 2.3e-72
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       +vi Lg++e+++     t+ +++ a++   +  ++ ++y+ ++g  el+ea+ +++ ++  l + ++ +++v+ Ga+
  gi|336254642|ref|YP_004597749.1|  29 EVISLGVGEPDFS----TPWAARDAAIT--SLEQGKTSYTANRGKRELREAISDYVADRFDLGYGADEEIIVTAGAS 99 
                                       79***********....*********98..88888899*******************999***************** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       ++ ++++++l ++pgd + + +p+y sy++++  +ggev ++p+++e+df+l++eale+a ++      +  +++++
  gi|336254642|ref|YP_004597749.1| 100 EAVDLAFRAL-VDPGDTVAIAQPSYISYEPGVIFAGGEVLPVPTKKEDDFRLTVEALEAAGAS------EADLLVLC 169
                                       **********.9***********************************************9999......7899**** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvG 231
                                        p+NPtG+++ +e+le ++++a+++ l ++ De+Ya++ +g  ++++ +a++    + +++ +++sKa +++G+R+G
  gi|336254642|ref|YP_004597749.1| 170 YPNNPTGAIMREEDLEPVAEFAREHDLTVLADEIYAELTYGGNEHTS-IATLPGMRErTIVFNGFSKAHAMTGLRLG 245
                                       *****************************************998888.55555555559****************** PP

                                       EEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 232 yilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                       y+lg a+vv +++k+++      ++ +q+a+++al+  +    ++ em++++ +rr+++ ++++e+g +v++ ++++
  gi|336254642|ref|YP_004597749.1| 246 YALGPADVVGAMNKIHQYTMLsaPTTAQHAALEALDSCDG---DVREMVAQYDRRRQFVLSRFREIGMDVFEAKGAF 319
                                       ***************9976666***************997...9********************************* PP

                                       EEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 307 flltdlsae.takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                       +++ ++++  ta+e++++ l e+gv+v+pg  f++  +g+lR+++ ++  ++l+e++++
  gi|336254642|ref|YP_004597749.1| 320 YCFPEVPEGwTAEEFAEAVLREQGVAVVPGDVFGAggEGHLRVSY-ATGLDDLREALNR 377
                                       *******99*********77777**********************.6666667777766 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   3.7e-10   1.3e-06      13     167 ..      45     201 ..      40     202 .. 0.84
   2 ?   -2.8   0.0      0.81   2.9e+03      39      70 ..     307     342 ..     277     350 .. 0.66

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.7e-10
                                       HHHHHH.HCS----CCCT--HHHHHHHHHHHH........HTT-SEEEEES-H.HHHHHHHHHHH--TTEEEEEETT CS
                   Beta_elim_lyase  13 amsdaq.aaamlGdesYgedktvnrLedavae........lfgkeaalfvpqG.taAnsillkillqrgeevivtep 79 
                                       a +da  + +++G  sY  +++ ++L +a+ +         +g++  + v+ G   A  +++++l+ +g+ v + +p
  gi|336254642|ref|YP_004597749.1|  45 AARDAAiTSLEQGKTSYTANRGKRELREAISDyvadrfdlGYGADEEIIVTAGaSEAVDLAFRALVDPGDTVAIAQP 121
                                       456666699***********************9999998878888888888873579999***************** PP

                                       -HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHH CS
                   Beta_elim_lyase  80 ahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaai 156
                                       + i  +e g i + ++v +++ k++++  +++e+leaa +       +  l++l   nn   G ++  e l+ va++
  gi|336254642|ref|YP_004597749.1| 122 SYI-SYEPGVIFAGGEVLPVPTKKEDDFRLTVEALEAAGAS------EADLLVLCYPNNP-TGAIMREEDLEPVAEF 190
                                       976.5888888666777777777777677788888877666......5679999999995.8*************** PP

                                       HHHCT-EEEEE CS
                   Beta_elim_lyase 157 akkygiplhlD 167
                                       a++++++++ D
  gi|336254642|ref|YP_004597749.1| 191 AREHDLTVLAD 201
                                       ********998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.81
                                       HHHHHHTT-SEEEE....ES-HHHHHHHHHHHH--T CS
                   Beta_elim_lyase  39 davaelfgkeaalf....vpqGtaAnsillkillqr 70 
                                       +   ++f++++a++    vp G  A++++ ++l ++
  gi|336254642|ref|YP_004597749.1| 307 EIGMDVFEAKGAFYcfpeVPEGWTAEEFAEAVLREQ 342
                                       334457777777766667777777777776666544 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.1e-08   7.5e-05      60     175 ..      88     201 ..      55     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.1e-08
                                       TGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE..EBETTSCBEGGGHHH CS
                       Aminotran_5  60 seeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi..pldeegeldldelek 134
                                        +eeii+t G++ea+ l+ ++l   ++pgd++ + +  + +   p +  a   g +v  +  +++++ +l++++le+
  gi|336254642|ref|YP_004597749.1|  88 ADEEIIVTAGASEAVDLAFRAL---VDPGDTVAIAQPSYISYE-PGVIFA---GGEVLPVptKKEDDFRLTVEALEA 157
                                       358*******************...**************9999.777776...444443312778889999****** PP

                                       H--TTEEEEEEESBETTTTEB...--HHHHHHHHHHTT-EEEEE CS
                       Aminotran_5 135 llnektklvaithvsnvtGti...qpveeigklakkkgalvlvD 175
                                       + + +++l+ ++  +n tG i   +++e +++ a++++  vl+D
  gi|336254642|ref|YP_004597749.1| 158 AGASEADLLVLCYPNNPTGAImreEDLEPVAEFAREHDLTVLAD 201
                                       ********************7233578889999********999 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   0.0   9.4e-06     0.034      38     144 ..      89     201 ..      47     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.4e-06
                                       -SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-.TTTSSB-GGGCGGG--TTEE CS
                   DegT_DnrJ_EryC1  38 vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvd.pdtynidpaaieaaitertk 113
                                       ++  i ++ +++A+ la ral v+pgd+V +++ ++++    v+ +g ++ +v  + +d++ ++++a+eaa  ++  
  gi|336254642|ref|YP_004597749.1|  89 DEEIIVTAGASEAVDLAFRAL-VDPGDTVAIAQPSYISYEPGVIFAGGEVLPVPTKkEDDFRLTVEALEAAGASEAD 164
                                       56678889999*********9.99*****************************9862579***********888885 PP

                                       EEE...EB-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 114 aIl...pVhlyGqva...dmdalkaiaakhglkvieD 144
                                         +   p +  G+++   d++ + + a++h+l v+ D
  gi|336254642|ref|YP_004597749.1| 165 LLVlcyPNNPTGAIMreeDLEPVAEFAREHDLTVLAD 201
                                       44422256777887767799999*********99998 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.1e-05      0.11      79     129 ..      86     136 ..      71     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                                       CT-SEEEEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EE CS
                          OKR_DC_1  79 fgadksyfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgat 129
                                       +gad+  +v+ G s +      a++ pgd+v +      S e +++++g +
  gi|336254642|ref|YP_004597749.1|  86 YGADEEIIVTAGASEAVDLAFRALVDPGDTVAIAQPSYISYEPGVIFAGGE 136
                                       89**********************************999999999999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.34
# Mc/sec: 3356.99
//
Query:       gi|336254643|ref|YP_004597750.1|  [L=427]
Description: acetyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-23   84.1   0.4    3.3e-23   82.7   0.4    1.8  1  Acetyltransf_17  Acetyltransferase (GNAT) domain
    1.9e-23   82.9   0.0    2.9e-23   82.2   0.0    1.3  1  SCP2_2           Sterol carrier protein domain
    3.9e-22   78.7   0.0    7.8e-22   77.7   0.0    1.6  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0052   17.0   0.0        2.2    8.5   0.0    2.4  2  Acetyltransf_1   Acetyltransferase (GNAT) family


Domain annotation for each model (and alignments):
>> Acetyltransf_17  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.4   7.5e-27   3.3e-23       2     116 .]     198     310 ..     197     310 .. 0.92

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 7.5e-27
                                       EBE--HHHHHHHHHTTTTSTGCSEEEEEE.TTSEETEEEEEEEETTE.TTC.EEEEEEEEESSHHHHHHHHHHHHCG CS
                   Acetyltransf_17   2 aleRseawWrrrllkrrearegalayvvyrdddgpeGyllYrvkeesgaeg.tleVrelvaltpeayraLlrflash 77 
                                       aleR+++wWr rl+++++   +  +y++ rd+d  +Gyl+Y+++++++++g t+ V e ++++++a  aLl+f+ +h
  gi|336254643|ref|YP_004597750.1| 198 ALERDREWWRCRLFENHD--TDPFVYAYERDGD-VRGYLIYTIDDDPTRDGrTMDVFEPAFADHDALLALLSFCHKH 271
                                       79*********9999986..5568888866554.8********999989999************************* PP

                                       TGTESEEEEEEESTT-SCGGGCSSGG..EECEEEEEEEEE CS
                   Acetyltransf_17  78 dslveeveawkappddplpllledpri.keaarpgamlRi 116
                                       ds+ve+v+  ++p+d pl  + + p++ ++++++g m+Ri
  gi|336254643|ref|YP_004597750.1| 272 DSQVERVR-LRLPADVPLLDIAQRPDAvETTVETGPMVRI 310
                                       ********.*****************99999********9 PP

>> SCP2_2  Sterol carrier protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2   0.0   6.5e-27   2.9e-23       1     103 [.     313     423 ..     313     424 .. 0.87

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 6.5e-27
                                       HHHHHHHS--SS-S.SEEEEEEEE-TTSGGGSEEEEEEEETTSEE..EECSCE-......SCE..EEEEHHHHHHHH CS
                            SCP2_2   1 veaalearpyekee.kgeltleveDpllpwnngrfrltiedgkge..evgkeee......ada.dltldiqtLaqll 67 
                                       v++al+a++y+  +  +++tl+v+Dp+++wn+g f l++++g+g+  +    +       +++ d +ldi++L+ql+
  gi|336254643|ref|YP_004597750.1| 313 VAEALSAVSYPDLAaPASITLSVTDPVADWNEGAFALSVSEGRGTcdR---VAAdagsdpDPDaDAHLDIGALSQLV 386
                                       789*******5333689***************************6542...33345678866669************ PP

                                       TTSS-HHHHHHTTSSB.SSHHHHHHHHHHS-SS--B- CS
                            SCP2_2  68 lGyrsaseLarlgrie.gaeealatldalfpkekpyl 103
                                       +Gyrsa++L r+gr+e g++++l+tl+alf++ + yl
  gi|336254643|ref|YP_004597750.1| 387 VGYRSATDLERTGRLEtGDSATLETLEALFSETAVYL 423
                                       ****************888899**********99997 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.0   1.7e-25   7.8e-22      52     127 ..      71     146 ..       9     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 1.7e-25
                                       EEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSHHHHHTTT-EE CS
                    Acetyltransf_9  52 elvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemreegqplsllfPssipiYrrfGyei 127
                                       +  ++++ ++le +v+G+  ++ag+++Va+ pehr+ g++  +l+r+lee+r++g+++++l+P+++++Yr+fG+++
  gi|336254643|ref|YP_004597750.1|  71 DPRCVCRHYWLEARVRGELHPTAGLAAVATPPEHRRGGYVGTMLERSLEEYRDRGDRFAVLWPFEYAFYRQFGWDT 146
                                       4678899*******************************************************************86 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0005       2.2      58     116 ..      90     143 ..      21     144 .. 0.82
   2 !    6.3   0.0    0.0024        11      23      56 ..     199     241 ..     179     253 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0005
                                       TTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTT CS
                    Acetyltransf_1  58 ggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklG 116
                                        ++a +  +a  pe+r+ G+  ++le  +e+ r++g +  vl+ +e      ++Y+++G
  gi|336254643|ref|YP_004597750.1|  90 HPTAGLAAVATPPEHRRGGYVGTMLERSLEEYRDRGDRFAVLWPFE-----YAFYRQFG 143
                                       36788889************99999999999****87655664433.....66774477 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0024
                                       H...HHHH....HHSTTC..EEEEEEETTEEEEEEEEEEEETT CS
                    Acetyltransf_1  23 e...fees....fsleae..gllvaeedgeliGfisllkipde 56 
                                           +e++    f++++   + +++e+dg + G++ +++++d+
  gi|336254643|ref|YP_004597750.1| 199 LerdREWWrcrlFENHDTdpFVYAYERDGDVRGYLIYTIDDDP 241
                                       2222333355555555552255559999***********9993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); 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:                         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 0.23s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3546.08
//
Query:       gi|336254644|ref|YP_004597751.1|  [L=185]
Description: intracellular protease, PfpI family [Halopiger xanaduensis SH-6]
Scores for 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-47  160.7   0.5    2.9e-47  160.5   0.5    1.0  1  DJ-1_PfpI   DJ-1/PfpI family
    4.2e-06   26.5   0.5    2.3e-05   24.1   0.5    1.9  1  Catalase_C  C-terminal domain found in long catalases
  ------ inclusion threshold ------
      0.021   14.5   0.0      0.036   13.7   0.0    1.4  1  ThiJ_like   ThiJ/PfpI family-like
      0.023   14.3   0.0      0.033   13.8   0.0    1.3  1  GATase_3    CobB/CobQ-like glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.5   0.5   6.4e-51   2.9e-47       2     164 ..      12     180 ..      11     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 160.5 bits;  conditional E-value: 6.4e-51
                                       EEEEEEE.TTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTS.....EEEE-SEEGGGCTCCG-SEEEE--BHH CS
                         DJ-1_PfpI   2 kvlvlla.dgvedvElivpvdvlkragikvdvvsvdkeevkgsrG.....lkvtvdaslddvkaaeyDalvlpGGra 72 
                                       +v+v++a +g+e++E+++p ++ ++ag +vdv + +++e ++ +        + v++++d+v+a++yDa+++pGG+ 
  gi|336254644|ref|YP_004597751.1|  12 TVAVFIApEGTEEIEFTEPKEAVAEAGATVDVLGSETGEAQTVNNdleesDAYEVEKTFDEVSADDYDAVIVPGGTV 88 
                                       68899998****************************66665555445577899************************ PP

                                       HHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEEEE CS
                         DJ-1_PfpI  73 gperlrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlvTs 149
                                       g+++lr+ne +vel+++++++gk+ + IC+gp+lL++a+v++gr++Tsyp++++++++ag ++vd++vv d+ lvTs
  gi|336254644|ref|YP_004597751.1|  89 GADTLRANEDAVELLRSHVTAGKPAGVICHGPWLLVEADVVDGRTLTSYPSLQTDIRNAGGEWVDEEVVDDDGLVTS 165
                                       ***************************************************************************** PP

                                       SSGGGHHHHHHHHHH CS
                         DJ-1_PfpI 150 rgpgaaiefalelle 164
                                       r+p+++++f+  +le
  gi|336254644|ref|YP_004597751.1| 166 RNPDDLEAFCDGILE 180
                                       **********99998 PP

>> Catalase_C  C-terminal domain found in long catalases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.5     5e-09   2.3e-05       4     115 ..      12     126 ..      10     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5e-09
                        Catalase_C   4 kVgiLasndseaslaqakalaaalaaegvdvtvvaeklg..........saeg....vnrTYstadaveFDaivvad 66 
                                       +V++ + ++ +++++  ++ ++a+a++g++v+v++++ g          +  +    v++T+   +a ++Da++v +
  gi|336254644|ref|YP_004597751.1|  12 TVAVFIAPEGTEEIE-FTEPKEAVAEAGATVDVLGSETGeaqtvnndleE--SdayeVEKTFDEVSADDYDAVIVPG 85 
                                       677777766655554.4566999999999999998776644433344331..1445699****************** PP

                        Catalase_C  67 gaeslfsakataasslfpagrplqllldayrhgKpigalGsgaealkaa 115
                                       g+          a++l  ++++++ll+     gKp g++ +g  +l +a
  gi|336254644|ref|YP_004597751.1|  86 GT--------VGADTLRANEDAVELLRSHVTAGKPAGVICHGPWLLVEA 126
                                       *3........356688999999999999999999999998887666555 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.1e-06     0.036      27      95 ..      16      88 ..       3     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.1e-06
                         ThiJ_like 27 Fvtekgk....vpkadekll.sgikakllgask.eakdiYkelstleeFkeplslssesFsleeydlvllpGGsd 95
                                      F++++g+      ++ e +   g++  +lg++  ea+ + ++l ++++++  +++ +   s ++yd+v +pGG+ 
  gi|336254644|ref|YP_004597751.1| 16 FIAPEGTeeieFTEPKEAVAeAGATVDVLGSETgEAQTVNNDLEESDAYEVEKTFDE--VSADDYDAVIVPGGTV 88
                                      788887777777777777777899999***98758889999*********9999976..5689**********74 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 ?   13.8   0.0   7.4e-06     0.033      33      88 ..      71     123 ..      53     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.4e-06
                          GATase_3  33 kdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmL 88 
                                        + s  +d+d+vi+pGg   + +  l ++++  e ++++++ag+p   iC G  +L
  gi|336254644|ref|YP_004597751.1|  71 DEVSA-DDYDAVIVPGGT--VGADTLRANEDAVELLRSHVTAGKPAGVICHGPWLL 123
                                       33444.78*********5..66666777777*******************987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1395.12
//
Query:       gi|336254645|ref|YP_004597752.1|  [L=645]
Description: PAS sensor protein [Halopiger xanaduensis SH-6]
Scores for 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-25   88.6   9.5      2e-14   53.8   0.2    3.2  3  PAS_4      PAS fold
      1e-17   64.1   0.2    3.4e-09   36.7   0.1    2.7  2  PAS        PAS fold
    3.5e-15   56.1   0.0    5.5e-09   36.2   0.1    2.7  2  PAS_9      PAS domain
    6.3e-13   49.2   1.3    1.1e-12   48.4   0.3    2.0  2  GAF_2      GAF domain
    2.6e-12   46.4   0.5      5e-07   29.6   0.2    2.9  2  PAS_8      PAS domain
    5.8e-06   26.7   0.0    1.5e-05   25.3   0.0    1.7  1  GAF_3      GAF domain
    0.00022   21.7   0.0    0.00046   20.7   0.0    1.5  1  HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like A
  ------ inclusion threshold ------
      0.066   13.4   3.6        1.7    8.8   0.1    3.8  3  PAS_7      PAS fold
       0.07   13.3   0.5       0.26   11.5   0.0    2.1  2  HEXIM      Hexamethylene bis-acetamide-inducible protein


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.2     1e-17     2e-14       1     110 []       9     110 ..       9     110 .. 0.97
   2 !   39.7   0.7   2.3e-13   4.6e-10       1     110 []     122     235 ..     122     235 .. 0.89
   3 ?   -2.0   0.1         2   4.1e+03      52      74 ..     381     403 ..     367     449 .. 0.61

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1e-17
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ld++ da+++ld+d+r++y+Na+a++l++++++el+G+ +++ +pe + +++ +   r+++++ p++f+ +++    
  gi|336254645|ref|YP_004597752.1|   9 LDRITDAFFALDTDFRFTYLNARAESLLKRSRAELIGRVMWDEFPETVETQFPDGFHRAMDEQVPVSFEVYHTQ--L 83 
                                       78999************************************99***************************8888..* PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       e ++e  ++P +       g+ v++rD+Ter+r
  gi|336254645|ref|YP_004597752.1|  84 ETWFEAKAYPSET------GLSVYMRDVTERKR 110
                                       **********966......************97 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 2.3e-13
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee......daarleralrrvlegeepieflee 71 
                                       +++++d+++ ld++  ++ +N a+++++ga++e+l+G++++ +lpe       da ++ ra++    g +  ++le 
  gi|336254645|ref|YP_004597752.1| 122 VEAISDGVVTLDRNREIVSVNGAMERILGADREDLIGEHVE-ILPELaaidddDAVEIGRAITDIDIGTAETRRLEA 197
                                       6899************************************9.66766677788999999999999988877777776 PP

                             PAS_4  72 lll..pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       + +  +g er  e+r++P++d   ++  v +++rD+T++++
  gi|336254645|ref|YP_004597752.1| 198 PFTaaDGTERMGEFRFVPIED---DAATVACVLRDVTDQHE 235
                                       66679**************99...7788**********985 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2
                             PAS_4  52 leralrrvlegeepiefleelll 74 
                                        ++al+r+ +++   e++ el +
  gi|336254645|ref|YP_004597752.1| 381 TRAALDRADRERVLRERTAELER 403
                                       44444444444444444443333 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   9.9e-09     2e-05       7      67 ..       9      69 ..       8      78 .. 0.90
   2 !   36.7   0.1   1.7e-12   3.4e-09       4     113 .]     119     230 ..     116     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 9.9e-09
                                      HHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHH CS
                               PAS  7 leslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlle 67
                                      l+ ++d+ f++D d r++y Na ae+ll  sr e++g+ + d+++e+ + ++++ +++++ 
  gi|336254645|ref|YP_004597752.1|  9 LDRITDAFFALDTDFRFTYLNARAESLLKRSRAELIGRVMWDEFPETVETQFPDGFHRAMD 69
                                      56789*****************************************988888888887775 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 1.7e-12
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSB...GGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgks...lldliheeddaelaelleqlleqgeesragei 77 
                                        a++e++ d+++ +D++ +i+ vN a+e++lG +re+++g++   l +l   +dd  +a ++ +++ +   ++a+ +
  gi|336254645|ref|YP_004597752.1| 119 AAVVEAISDGVVTLDRNREIVSVNGAMERILGADREDLIGEHveiLPELAAIDDD--DAVEIGRAITDIDIGTAETR 193
                                       589*************************************973325666777766..77777777777777777777 PP

                                       EEEC....TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfkl....rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +++      dg+++  e r +p+ d       + +vlrd+
  gi|336254645|ref|YP_004597752.1| 194 RLEApftaADGTERMGEFRFVPIEDDAA---TVACVLRDV 230
                                       777777779***9999999999999988...899999997 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.3e-06    0.0046       2     104 .]      14     107 ..      13     107 .. 0.84
   2 !   36.2   0.1   2.8e-12   5.5e-09       2     104 .]     127     232 ..     126     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-06
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       d+++  ++d+r +y N  a+ ll  s++e++g+ ++d f    + +  + +++a+++    + ++ev ++  +    
  gi|336254645|ref|YP_004597752.1|  14 DAFFALDTDFRFTYLNARAESLLKRSRAELIGRVMWDEFpeTVETQFPDGFHRAMDEQV--PVSFEVYHTQLET--- 85 
                                       6788778***************************9999988778888888888888888..8888888888855... PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       w++++a+p        +g+ v +rD+te
  gi|336254645|ref|YP_004597752.1|  86 WFEAKAYPSE------TGLSVYMRDVTE 107
                                       9999999983......445588999987 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 2.8e-12
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgrk...kerevevvlirkn 72 
                                       dg++  + + +i+++N a++r+lG ++e+++g +++ l    + d++++ ++ +a+ +++    + r+ e  ++  +
  gi|336254645|ref|YP_004597752.1| 127 DGVVTLDRNREIVSVNGAMERILGADREDLIGEHVEILPelaAIDDDDAVEIGRAITDIDIgtaETRRLEAPFTAAD 203
                                       89999889999***********************888888887777777777777777777888************* PP

                             PAS_9  73 getfwvlltaspvkdddgelvgiivilrDite 104
                                       g++ + +++++p+ dd      ++++lrD+t+
  gi|336254645|ref|YP_004597752.1| 204 GTERMGEFRFVPIEDDA---ATVACVLRDVTD 232
                                       *************6653...4456******96 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.3   5.6e-16   1.1e-12       2     137 ..     254     385 ..     253     386 .. 0.85
   2 ?   -2.8   0.0       3.7   7.4e+03      31      31 ..     449     449 ..     410     500 .. 0.57

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 5.6e-16
                                       HHHHHHHHHHHHHHHHS.S...EEEEEEE-TTS-EEEE.EEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GG CS
                             GAF_2   2 adleelldlvldelvel.gaa.lgyillvdddgglrla.awgeaeeefgaaldrplgeglvgealrtgrpvilndle 75 
                                        d+ee+  +++    +l +    g+ ll +++g+l+ +   ++a +efg+ ++  +geglv+ea++ g    ++dl+
  gi|336254645|ref|YP_004597752.1| 254 DDPEEICAIAVHSGSDLlDLPiSGVWLLEEEHGYLEPVaGTAGAHDEFGGLPRFYPGEGLVWEAFEAGDVERFDDLA 330
                                       57899999999999996686634566666778887755688899999999999999*************99988844 PP

                                       G-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  76 edpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       +   +  l   + ++rs+++ P+   g ++Gvl  +a +p++fde+d+elL++l e    a+
  gi|336254645|ref|YP_004597752.1| 331 A---QEELYNPETPIRSEIIAPI---G-THGVLMTGALEPNRFDETDVELLSTLVENTRAAL 385
                                       4...67778899***********...9.**************************99888877 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.7
                                       T CS
                             GAF_2  31 d 31 
                                       +
  gi|336254645|ref|YP_004597752.1| 449 R 449
                                       1 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0     2e-05      0.04       7      50 ..       9      54 ..       4      72 .. 0.72
   2 !   29.6   0.2   2.5e-10     5e-07       2      54 ..     117     169 ..     116     182 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                             PAS_8  7 fesspdgiavvdlgdrivdvNqaalellGys.adlkgellg.qllp 50
                                      ++ + d+ + +d++ r+++ N +a+ ll  s a+l+g +++ ++++
  gi|336254645|ref|YP_004597752.1|  9 LDRITDAFFALDTDFRFTYLNARAESLLKRSrAELIGRVMWdEFPE 54
                                      677899***9*96669************966777777766632222 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 2.5e-10
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrp 54 
                                       ++ a++e+++dg++ +d+++ iv vN a++++lG + +dl+ge + ++lp+l  
  gi|336254645|ref|YP_004597752.1| 117 QHAAVVEAISDGVVTLDRNREIVSVNGAMERILGADrEDLIGEHV-EILPELAA 169
                                       5789*************5556*************55555555555.55555544 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   7.5e-09   1.5e-05       1     119 [.     255     377 ..     255     386 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 7.5e-09
                             GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagw.dgkpalsesld...edsalarralssgevvsepsfa 73 
                                       +++e+++++++ +++ll++ ++ ++ll+e+  +l ++ag+ ++++ +   l+    ++ l ++a++ g v  + + a
  gi|336254645|ref|YP_004597752.1| 255 DPEEICAIAVHSGSDLLDLPISGVWLLEEEHGYLEPVAGTaGAHDEFG-GLPrfyPGEGLVWEAFEAGDVERFDDLA 330
                                       689*************************************88888886.4443469*************98887776 PP

                             GAF_3  74 ee.....dglpdraalavPLvagrqviGvlalastkprafdaedlellesl 119
                                       ++     + +p r+ +++P+ +     Gvl+ +  +p  fd++d+ell++l
  gi|336254645|ref|YP_004597752.1| 331 AQeelynPETPIRSEIIAPIGT----HGVLMTGALEPNRFDETDVELLSTL 377
                                       642233366999********99....9****99999999*********987 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 !   20.7   0.0   2.3e-07   0.00046       2     106 ..     525     629 ..     524     635 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE......EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTST CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveika......seddlvisveDnGiGipkedlkklfekfsqddstkrggg 72 
                                       d++r+ +++  + d  +  + + ++++v i++      +     +  +D+   + +  +++l ++ ++     +++ 
  gi|336254645|ref|YP_004597752.1| 525 DSDRFVHLLETAFDDVASRSRSRSDVTVWIDVigvedaD-RSRGFFMRDDAAEVHPGTHDRLLDPSTD-----DETA 595
                                       789999999999999999877888888888876664322.3555558888888888888877766555.....7888 PP

                                       SSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEE CS
                         HATPase_c  73 gtGlGlsivkklvelmgGeiwvesepgrGttftf 106
                                        +GlGl++vk+++e ++ ++++e  +++Gt++ +
  gi|336254645|ref|YP_004597752.1| 596 IEGLGLALVKAIAEAHDWTLSIERGSEGGTRIEI 629
                                       99********************99999****987 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.061   1.2e+02       3      32 ..      11      40 ..       9     113 .. 0.52
   2 ?    8.8   0.1   0.00087       1.7       1     114 [.     122     237 ..     122     238 .. 0.67
   3 ?   -3.7   0.1       6.4   1.3e+04      52      73 ..     383     404 ..     372     409 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.061
                             PAS_7  3 nmsqGisvfDadlrLvawNrrylelldlpe 32
                                       +++++  +D d r +  N r  +ll+ ++
  gi|336254645|ref|YP_004597752.1| 11 RITDAFFALDTDFRFTYLNARAESLLKRSR 40
                                      566666666666666666666666665443 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00087
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefg..agdveaeverrlaaaragkp 75 
                                       +e +s+G++ +D++ ++v +N  + ++l+  +e + +g ++e l +  a   + +   g++   ++  +a+ r+  +
  gi|336254645|ref|YP_004597752.1| 122 VEAISDGVVTLDRNREIVSVNGAMERILGADREDL-IGEHVEILPELAAIDDDDAveIGRAITDIDIGTAETRRL-E 196
                                       5889**************************99988.777777666655444333311444444444445555544.4 PP

                             PAS_7  76 hsfererpdgrvievrgnplpd.gGfV.ttytDiTerrrae 114
                                         f     ++r+ e+r  p++d   +V  +  D+T++++ e
  gi|336254645|ref|YP_004597752.1| 197 APFTAADGTERMGEFRFVPIEDdAATVaCVLRDVTDQHEYE 237
                                       44556677888888888888662333314678888888776 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 6.4
                             PAS_7  52 gefgagdveaeverrlaaarag 73 
                                        +++++d+e  +++r+a+++++
  gi|336254645|ref|YP_004597752.1| 383 AALDRADRERVLRERTAELERR 404
                                       3444556666666666655554 PP

>> HEXIM  Hexamethylene bis-acetamide-inducible protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.26     103     132 ..      17      47 ..       8      51 .. 0.86
   2 ?   -1.6   0.4       1.4   2.8e+03      63      70 ..     435     442 ..     382     488 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                             HEXIM 103 f.lekeFsetYeevhaerLqnmsKqeLiqey 132
                                       f l  +F  tY +++ae+L + s+ eLi  +
  gi|336254645|ref|YP_004597752.1|  17 FaLDTDFRFTYLNARAESLLKRSRAELIGRV 47 
                                       35789***********************765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                             HEXIM  63 erresrtr 70 
                                       err+s++r
  gi|336254645|ref|YP_004597752.1| 435 ERRSSSSR 442
                                       11111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 4700.47
//
Query:       gi|336254646|ref|YP_004597753.1|  [L=208]
Description: HalX domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   60.7   8.7    2.8e-16   59.6   8.7    1.6  1  HalX      HalX domain


Domain annotation for each model (and alignments):
>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   8.7   1.5e-20   2.8e-16       2      58 ..     130     189 ..     129     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 1.5e-20
                              HalX   2 rseYdeelqelfaLasKravLeaekseaeLadseeYqeLearleelraqldetlde...l 58 
                                        ++Yd++l+++++LasKra+L++  ++aeLa+s +Y++Le+rl+  ra++det+++   +
  gi|336254646|ref|YP_004597753.1| 130 QATYDDQLRTFYELASKRALLDRDRPDAELAASRRYAALEDRLAVARARADETVADvlaF 189
                                       689****************************************************95443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 1808.65
//
Query:       gi|336254647|ref|YP_004597754.1|  [L=724]
Description: phosphoribosylformylglycinamidine synthase 2 [Halopiger xanaduensis SH-6]
Scores for 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-41  140.6   9.6    1.8e-32  112.7   1.6    2.6  3  AIRS_C          AIR synthase related protein, C-terminal doma
    2.4e-39  133.9   9.0    1.5e-22   80.1   0.1    3.0  3  AIRS            AIR synthase related protein, N-terminal doma
    4.3e-07   30.4   0.1    1.1e-06   29.0   0.1    1.8  1  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe
  ------ inclusion threshold ------
       0.35   11.3   2.2        1.3    9.4   0.0    2.5  2  GHMP_kinases_C  GHMP kinases C terminal


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 ?   -3.2   0.0       1.8   8.1e+03     109     130 ..      39      67 ..       6      70 .. 0.62
   2 !  112.7   1.6   3.9e-36   1.8e-32       1     149 [.     198     348 ..     198     352 .. 0.95
   3 !   32.5   0.6   1.8e-11   8.2e-08      14     151 ..     580     696 ..     563     700 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.8
                                       C.......STTTEEEEEEEHGGHHHHHHH CS
                            AIRS_C 109 s.......ensGrllvavppeeadavlai 130
                                       s       ++s++  v+v p +++av+a+
  gi|336254647|ref|YP_004597754.1|  39 SsrpllsaFESEGEQVVVGPGDDAAVVAL 67 
                                       14444444666666677777777787775 PP

  == domain 2  score: 112.7 bits;  conditional E-value: 3.9e-36
                                       STTEEEEEEET....SSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHH CS
                            AIRS_C   1 kpGdvliltgs....lGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaalkglvkaahDvTgGGL 72 
                                       +pG++l+l+g+    +Glgga+ ++++ + e+++++d+ avq+gd+++e+ li++++ l+++ gl+ +a+D+++ GL
  gi|336254647|ref|YP_004597754.1| 198 EPGNKLVLVGNgtgrDGLGGAS-FASEDLSEDAETEDRpAVQVGDPYAEKLLIEANEQLIEE-GLIESARDLGAAGL 272
                                       69********************.6666677777776677**********************8.************** PP

                                       HHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESS CS
                            AIRS_C  73 lgalaemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtake 149
                                        ga +e+++++g+gaei+l++v  +++ +++le+ll+e+++r++  v+pe+ ++v +i+e+ +l  ++vIGevt+++
  gi|336254647|ref|YP_004597754.1| 273 GGASSELVAKGGLGAEIELERVHQREPNMNALEILLAESQERMCYEVAPENVERVAEIAERFDL-GCSVIGEVTDGN 348
                                       ****************************************************************.7********987 PP

  == domain 3  score: 32.5 bits;  conditional E-value: 1.8e-11
                                       CTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEE CS
                            AIRS_C  14 lggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeid 90 
                                       lgg+  +l+r  + +++ +     +gd++++   ++ +++ a + +   a+hDv++GGL++alaem+ +   g+e++
  gi|336254647|ref|YP_004597754.1| 580 LGGSE-YLARF-DGSDAFP---ALPGDPAAL---VRTVAEVAND-DATLAIHDVSHGGLAVALAEMVSDE-AGLEVS 646
                                       55666.33332.2223333...237777777...4444444554.6789********************7.999999 PP

                                       CGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSE CS
                            AIRS_C  91 ldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeel 151
                                       l+   + d+    + +l+ e  Gr+l+  ++++a  v+++++    p +  +G +t +++l
  gi|336254647|ref|YP_004597754.1| 647 LP---ADDP----TGALFHEQPGRVLIQTAAPDA--VREAFDGVA-P-VVSLGSATTDGRL 696
                                       96...6666....579*****************9..888888654.4.7778887777766 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 !   80.1   0.1   3.3e-26   1.5e-22       1      93 [.      60     185 ..      60     186 .. 0.88
   2 ?   -1.8   0.0       1.1   5.1e+03      24      40 ..     267     283 ..     244     287 .. 0.65
   3 !   56.8   2.3   6.1e-19   2.7e-15       1      92 [.     429     545 ..     429     546 .. 0.91

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 3.3e-26
                                       SSSEE.....................EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC... CS
                              AIRS   1 dDaav.....................vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp... 53 
                                       dDaav                     ++ ++shn+p++v+p+++ +a++v+++++D ++mGA P+al +sl ++   
  gi|336254647|ref|YP_004597754.1|  60 DDAAVvalpdntddeesgdetqdtyiTMGIESHNHPSYVDPFDG-AATGVGGIVRDTLSMGAYPIALADSLYFGafd 135
                                       68884444455555555555555555889***************.******************************** PP

                                       ......HHHHHHHHHHHHHHHTT-EEEEEEEEEESS....EEEEEEEEEE CS
                              AIRS  54 ......wleevvrglaeaaeelgvplvgGdtsfsne....ptisvtavGl 93 
                                              +e+vv+g++++++++gvp+v G + f+++    p+++v++vGl
  gi|336254647|ref|YP_004597754.1| 136 rehskyLFEGVVEGISHYGNCIGVPTVAGSVDFHPDyegnPLVNVACVGL 185
                                       **********************************9999***********7 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHTTT CS
                              AIRS  24 iGakavavnlsDlaamG 40 
                                       +Ga +++++ s l+a G
  gi|336254647|ref|YP_004597754.1| 267 LGAAGLGGASSELVAKG 283
                                       46777777777777766 PP

  == domain 3  score: 56.8 bits;  conditional E-value: 6.1e-19
                                       SSSE..........EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHH CS
                              AIRS   1 dDaa..........vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleev 58 
                                       dDaa          +++++   ++ +  +p+++ ++ ++ +n+ ++aa GA+Pla++++l+ +          ++++
  gi|336254647|ref|YP_004597754.1| 429 DDAAiiavreagtgLAISAGAAPNWTDAAPYEG-ARAVALENATNVAAKGATPLAAVDCLNGGnpekpdvygGFKGI 504
                                       7888555444444448899989999999*****.******************************************* PP

                                       HHHHHHHHHHTT-EEEEEEEEEESS.......EEEEEEEEE CS
                              AIRS  59 vrglaeaaeelgvplvgGdtsfsne.......ptisvtavG 92 
                                       v+gla++++ l++p+vgG++s +n+       pt+++++vG
  gi|336254647|ref|YP_004597754.1| 505 VDGLADMCATLEAPVVGGNVSLYNDsvtgpipPTPTLAMVG 545
                                       ***********************999**************9 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 !   29.0   0.1   2.5e-10   1.1e-06      11      49 ..       2      37 ..       1      38 [. 0.91

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.5e-10
                    FGAR-AT_linker 11 aLsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrH 49
                                      +L+d++ + +++    lgr+Pt +E  +f   wSEHC +
  gi|336254647|ref|YP_004597754.1|  2 SLADSDRELVVDE---LGREPTRAEAALFENLWSEHCAY 37
                                      6888888888888...9********************99 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 ?    0.3   0.5       0.2   9.2e+02      39      57 ..     260     276 ..     256     277 .. 0.89
   2 ?    9.4   0.0   0.00029       1.3       8      55 ..     299     342 ..     290     343 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.2
                    GHMP_kinases_C  39 llealselGalgaklsGaG 57 
                                       l+e++++lG  +a+l Ga+
  gi|336254647|ref|YP_004597754.1| 260 LIESARDLG--AAGLGGAS 276
                                       89*******..*****996 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00029
                    GHMP_kinases_C   8 gdlellgellnlsqrselkavvgilppeleellealselGalgaklsG 55 
                                        ++++l+ ll +sq+   + ++++ p+++e++ e++++ + lg ++ G
  gi|336254647|ref|YP_004597754.1| 299 PNMNALEILLAESQE---RMCYEVAPENVERVAEIAERFD-LGCSVIG 342
                                       688999*********...99********************.9988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (724 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 5332.58
//
Query:       gi|336254648|ref|YP_004597755.1|  [L=126]
Description: hypothetical protein Halxa_3264 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.008   16.1   4.8      0.008   16.1   4.8    1.9  2  DUF2975   Protein of unknown function (DUF2975)
  ------ inclusion threshold ------
      0.014   15.5   0.8      0.014   15.5   0.8    2.3  2  BofA      SigmaK-factor processing regulatory protein BofA


Domain annotation for each model (and alignments):
>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   4.8   8.9e-07     0.008      50     117 ..      15      85 ..       7      92 .. 0.91
   2 ?    0.2   0.3     0.069   6.2e+02      77      92 ..      97     110 ..      89     126 .] 0.39

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.9e-07
                           DUF2975  50 vFspanvrrLrriglaliaaalllaagivalallaelelap.....gvvllllgvafaslvigllvlvlaell 117
                                       +F+p  +rrLr    al ++ l++aa ++++ +++e  l+p     + + +l gva+a++  +++v+v+ ++l
  gi|336254648|ref|YP_004597755.1|  15 AFDPPGSRRLRLAFAALWVVDLIAAASFFVVSYASE--LNPvtvffYDLFGLAGVALAAVCYAAVVVVVGNVL 85 
                                       7999999**********999****************..99999999999999999999999*******99998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.069
                           DUF2975  77 ivalallaelelapgv 92 
                                       +v+l+ + +  l++ v
  gi|336254648|ref|YP_004597755.1|  97 AVVLYAAFA--LNNVV 110
                                       222222222..22222 PP

>> BofA  SigmaK-factor processing regulatory protein BofA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.8   1.6e-06     0.014      29      69 ..      26      70 ..      22      75 .. 0.79
   2 ?    1.0   1.5     0.057   5.1e+02      26      37 ..      92     103 ..      73     125 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-06
                              BofA 29 lGlvlLflvNllgavfglh....ipiNlitaliagflGipGvilL 69
                                      l +++L++v+l++a+  +       +N++t++   ++G+ Gv+l 
  gi|336254648|ref|YP_004597755.1| 26 LAFAALWVVDLIAAASFFVvsyaSELNPVTVFFYDLFGLAGVALA 70
                                      6899******8855544442255689****************985 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.057
                              BofA  26 navlGlvlLflv 37 
                                       ++v G+v+L+++
  gi|336254648|ref|YP_004597755.1|  92 RFVAGAVVLYAA 103
                                       567777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1008.60
//
Query:       gi|336254649|ref|YP_004597756.1|  [L=485]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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   52.8  55.0    2.8e-08   33.1  29.5    2.4  3  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.16   12.1   0.4        7.8    6.7   0.1    2.4  2  SH3_12    Xrn1 SH3-like 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 !   21.9  12.4   8.1e-09   7.2e-05     202     297 ..      58     149 ..      39     159 .. 0.83
   2 !   33.1  29.5   3.1e-12   2.8e-08       1     226 [.      66     303 ..      66     328 .. 0.73
   3 !   21.6  22.5   9.8e-09   8.8e-05      28     176 ..     318     480 ..     290     484 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.1e-09
                             MFS_1 202 allkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrll 278
                                       al +d    +l +a++ f++gf++++ +lp y +  lg sg + +gl+  ++ +++a     +g++sdr+g+r +l+
  gi|336254649|ref|YP_004597756.1|  58 ALERDVL--VLSLAMFAFSLGFQMTSRFLPDY-MVALGASG-FVVGLFGTFGNIISALYPYPGGAISDRIGSRYALT 130
                                       3333333..48889999999************.*******8.999999********999****************** PP

                             MFS_1 279 lallllllaalglallavt 297
                                       l+++l +l+++ +++++ +
  gi|336254649|ref|YP_004597756.1| 131 LFGFLSTLGFAVWLVAGQF 149
                                       ************9998866 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 3.1e-12
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalgl 76 
                                       l+la f  +l++ +++ +lp  ++ +lg+s+ ++gl  t+  + +a+  +p+G++sdr+G+r  + l+g+l+++ ++
  gi|336254649|ref|YP_004597756.1|  66 LSLAMFAFSLGFQMTSRFLP-DYMVALGASGFVVGLFGTFGNIISALYPYPGGAISDRIGSRYaLTLFGFLSTLGFA 141
                                       57899***************.77899*************************************88888888888885 PP

                             MFS_1  77 llll...f...a.....sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllg 141
                                       ++l+   f   +     +  w +++v+ vl+ +  ++++ a+ a++ + + +++ + +++   ++   ++++gp+l+
  gi|336254649|ref|YP_004597756.1| 142 VWLVagqFgpiPvgpvtIEPWlWIFVGLVLAQAWKSFGLGASFAVVKQATDPSRLAAGFASTETFRRTAFLIGPVLA 218
                                       5555366654414455644566999999999999******************************************* PP

                             MFS_1 142 gllasslg.....Wravfyilaivsllafv.lfllllpeepperkrkspkeee...kgtgpaplvpawkallkdpvl 209
                                       ++l+ +       +++v  ++ ++++l+ v   +l+   e++  + ++++e+     ++ p pl+p   +l+ d   
  gi|336254649|ref|YP_004597756.1| 219 AALIGLHPdftvsFQYVLAVAVAFGALGTVvQHVLYDSSEDSIGGSFAGIEQIvrdLRDMPDPLRP---LLVGDT-- 290
                                       ****44447888888888888888888877544466677777777777777733333333333333...222222.. PP

                             MFS_1 210 willialllfffgfsgl 226
                                          l+ ++ + ++++++
  gi|336254649|ref|YP_004597756.1| 291 ---LVRFANG-MVYTFF 303
                                       ...2222222.222222 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 9.8e-09
                             MFS_1  28 g...........ispse.igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll....fasslw.l 87 
                                       +           +sp++ +g ll++ +l+a++ ++p++ +++r+G ++v+ lg++++a++ ++l+    f+++   +
  gi|336254649|ref|YP_004597756.1| 318 TiavggfsypidLSPQAfFGYLLGVEMLVALLVMVPAAKVAERVGLKPVVALGFAVYAIFPIVLInvpeFTANTAtA 394
                                       044444444444444444999***************************************44444555555777779 PP

                             MFS_1  88 llvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                       ++++ +++Gl   a++p+  ali+  + +   gr++g +++  +  +i  ++lgg+l + ++ +++f i+a++++++
  gi|336254649|ref|YP_004597756.1| 395 MILVFAFSGLRF-AGLPSHKALIVGPAEQGAGGRVTGTYYLLRNTIVIPSAALGGYLWEFISAELAFTIAAVIGVVG 470
                                       **********96.9*************************************************************** PP

                             MFS_1 165 fvlfllllpeep 176
                                          +++ll+ e+
  gi|336254649|ref|YP_004597756.1| 471 --TGYFLLFGEE 480
                                       ..5556666555 PP

>> SH3_12  Xrn1 SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.013   1.2e+02      18      30 ..      88     103 ..      83     126 .. 0.80
   2 ?    6.7   0.1   0.00087       7.8      14      41 ..     237     256 ..     232     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.013
                            SH3_12  18 sVPlGlrGtVVg...r 30 
                                       +V lG+ G VVg   +
  gi|336254649|ref|YP_004597756.1|  88 MVALGASGFVVGlfgT 103
                                       599********96550 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00087
                            SH3_12  14 dngksVPlGlrGtVVgrsdtlleVlfDe 41 
                                          ++V +G+ GtVV+       Vl+D 
  gi|336254649|ref|YP_004597756.1| 237 A--VAVAFGALGTVVQH------VLYDS 256
                                       4..469**********3......66654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3518.42
//
Query:       gi|336254650|ref|YP_004597757.1|  [L=132]
Description: regulatory protein ArsR [Halopiger xanaduensis SH-6]
Scores for 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-12   44.9   0.9    1.8e-11   43.9   0.9    1.5  1  HTH_20    Helix-turn-helix domain
    1.1e-08   34.8   0.4    2.1e-08   33.9   0.3    1.6  2  HTH_5     Bacterial regulatory protein, arsR family
     0.0013   18.3   0.1     0.0029   17.2   0.1    1.5  1  GntR      Bacterial regulatory proteins, gntR family
     0.0019   17.9   0.0     0.0035   17.1   0.0    1.3  1  DUF4423   Domain of unknown function (DUF4423)
      0.004   17.0   0.0     0.0086   15.9   0.0    1.6  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0074   16.2   0.3      0.023   14.6   0.3    1.9  1  MarR_2    MarR family
  ------ inclusion threshold ------
      0.013   15.2   0.9      0.052   13.2   0.7    2.0  1  RP-C      Replication protein C N-terminal domain
        1.1    9.7   5.0          4    7.9   3.2    2.3  2  Nnf1      Nnf1


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 !   43.9   0.9   8.1e-15   1.8e-11       2      61 .]      48     108 ..      47     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 8.1e-15
                                       HHHHHHS-HHHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20   2 qiaeALahPvRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       ++++ALa+++R+ri raL a +e+l++ el++ +++s + ls+ L +L++a Lv  ++ gr
  gi|336254650|ref|YP_004597757.1|  48 DVLSALANETRYRIVRALvAAEEELCVCELDAIVGVSESGLSHALSELVDAKLVADRKDGR 108
                                       799******************************************************9997 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 ?   -2.0   0.0       1.5   3.5e+03       4      13 ..      46      55 ..      44      56 .. 0.76
   2 !   33.9   0.3   9.5e-12   2.1e-08       1      45 [.      55     101 ..      55     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                                      HHHHHHHHTT CS
                             HTH_5  4 RlkILklLae 13
                                       l++L++La+
  gi|336254650|ref|YP_004597757.1| 46 ELDVLSALAN 55
                                      5889999986 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 9.5e-12
                                       SHHHHHHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5   1 dptRlkILklLae..gelcvcelaeelglsqstvShHLkkLreaGLV 45 
                                       ++tR +I+++L    +elcvcel +++g+s+s +Sh L+ L +a LV
  gi|336254650|ref|YP_004597757.1|  55 NETRYRIVRALVAaeEELCVCELDAIVGVSESGLSHALSELVDAKLV 101
                                       58*********887699***************************998 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.3e-06    0.0029      10      55 ..      58     102 ..      51     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                                       HHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR  10 redIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55 
                                       r +I++  +++++ L  + eL a  gVs + +  AL++L+ ++lv 
  gi|336254650|ref|YP_004597757.1|  58 RYRIVRALVAAEEEL-CVCELDAIVGVSESGLSHALSELVDAKLVA 102
                                       678999999******.****************************96 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.6e-06    0.0035      19      79 ..      55     112 ..      44     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.6e-06
                           DUF4423  19 ssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqt 79 
                                       ++  y ++r+l++++++   + el  +++  +s++  ++al+ L++++l+   +dg++++ 
  gi|336254650|ref|YP_004597757.1|  55 NETRYRIVRALVAAEEE-LCVCELDAIVG--VSESGLSHALSELVDAKLVADRKDGRWKKY 112
                                       5677899*********9.***********..************************999875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.8e-06    0.0086      16      66 ..      64     116 ..      55     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.8e-06
                                       HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE-- CS
                              TrmB  16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravd 66 
                                       aL+ +++++ + e+  ++gv++s    +L++L+d+ lV  +k gr k+Yra++
  gi|336254650|ref|YP_004597757.1|  64 ALVaAEEELCVCELDAIVGVSESGLSHALSELVDAKLVADRKdGRWKKYRATN 116
                                       7887899999****************************999967799***986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.3     1e-05     0.023       6      58 ..      45     108 ..      44     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHCTTTS...........EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                            MarR_2   6 aqarvLaaLgrrpgr...........dltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58 
                                       ++++vL aL+++ ++           +l v el +  g+s s +s +l +Lv+a Lv  r++ +
  gi|336254650|ref|YP_004597757.1|  45 TELDVLSALANETRYrivralvaaeeELCVCELDAIVGVSESGLSHALSELVDAKLVADRKDGR 108
                                       5677777777777667777777777789999**************************9988644 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 ?   13.2   0.7   2.3e-05     0.052      76     118 ..      76     118 ..      28     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                              RP-C  76 qLsralglsestlrrhlaaLveaGliirrDspngkRyarrdre 118
                                       +L   +g+ses l++ l++Lv+a l++ r     k y+  +r+
  gi|336254650|ref|YP_004597757.1|  76 ELDAIVGVSESGLSHALSELVDAKLVADRKDGRWKKYRATNRA 118
                                       4556789**********************99999999887765 PP

>> Nnf1  Nnf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.2    0.0018         4       8      43 ..       2      36 ..       1      69 [. 0.85
   2 ?    1.4   0.0      0.18     4e+02       6      39 ..      61      96 ..      56     121 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                                      HHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH CS
                              Nnf1  8 kqmvefleesiraefeeIleerdvvekLneLDdlie 43
                                      +q++++l+   ++e+ e ++ +d++ +L eLD+l +
  gi|336254650|ref|YP_004597757.1|  2 AQATKRLQRYLEEELGE-CRDEDIECRLEELDALEA 36
                                      799**************.999***********9865 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.18
                                      HHHHHHHHHHHHHHHHHHHHH..HHTTHHHHHHHHH CS
                              Nnf1  6 vhkqmvefleesiraefeeIl..eerdvvekLneLD 39
                                      + + +v+  ee +  e+++I+   e ++   L+eL 
  gi|336254650|ref|YP_004597757.1| 61 IVRALVAAEEELCVCELDAIVgvSESGLSHALSELV 96
                                      667778888889999999995337888888898884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1073.71
//
Query:       gi|336254651|ref|YP_004597758.1|  [L=143]
Description: protein tyrosine phosphatase [Halopiger xanaduensis SH-6]
Scores for complete 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-28  100.3   0.1    1.6e-28   99.8   0.1    1.2  1  LMWPc     Low molecular weight phosphotyrosine protein phosph
  ------ inclusion threshold ------
       0.17   12.1   0.2       0.17   12.1   0.2    2.1  2  DUF2526   Protein of unknown function (DUF2526)


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 !   99.8   0.1   1.8e-32   1.6e-28       1     142 []      13     140 ..      13     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 1.8e-32
                                       EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTSTTT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHHH CS
                             LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgalvgkradpravevlkekgislsghvarqlskeelae 77 
                                       ++fvC++N++RS+mA+a++++e+e++g+++ +e+ S Gt   +++ +++++v+++ e gi+ls++++r+++ e+l+e
  gi|336254651|ref|YP_004597758.1|  13 IAFVCVQNAGRSQMATAFAERERERRGADH-IEIVSGGTD--PADAVHEEVVAAMDELGIDLSDRTPREITPEDLQE 86 
                                       79***********************98877.*********..*********************************** PP

                                       SSEEEESSHHHHHHHHHHCCTTGGGGEEEGGGGSSTSS---HTTSSHHHHHHHHHHHHHHHHHHH CS
                             LMWPc  78 lDlilamdeenkreleslapekekakvkllgeyteqldieDPyygeieafeevldeieeavkkll 142
                                       + ++++m  +++  +++   ++e          ++++d+ DP ++++++++e++deie +v++l+
  gi|336254651|ref|YP_004597758.1|  87 CEYVITMGCSAE-GVCPATWSGE----------NRDWDLTDPHGKDEKTVREIRDEIEARVEALF 140
                                       *******66666.6888888844..........479*************************9986 PP

>> DUF2526  Protein of unknown function (DUF2526)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.9e-05      0.17      13      33 ..      54      74 ..      40      84 .. 0.84
   2 ?   -1.1   0.1      0.25   2.2e+03       4      12 ..     129     137 ..     117     142 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
                           DUF2526 13 aalaesviahmnellialsdd 33
                                      +a++e+v+a m+el i lsd 
  gi|336254651|ref|YP_004597758.1| 54 DAVHEEVVAAMDELGIDLSDR 74
                                      789****************95 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.25
                           DUF2526   4 ledvkvrvd 12 
                                       ++++++rv+
  gi|336254651|ref|YP_004597758.1| 129 RDEIEARVE 137
                                       344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1069.98
//
Query:       gi|336254652|ref|YP_004597759.1|  [L=228]
Description: PHP domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-22   79.4   1.3    2.6e-22   78.3   1.3    1.6  1  PHP_C            PHP-associated
    2.3e-08   34.5   0.1    3.2e-08   34.0   0.1    1.5  1  PHP              PHP domain
  ------ inclusion threshold ------
       0.14   12.7   0.1       0.33   11.5   0.1    1.9  1  Glyco_tranf_2_4  Glycosyl transferase family 2


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 !   78.3   1.3   4.3e-26   2.6e-22       1      56 []     140     195 ..     140     195 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 4.3e-26
                             PHP_C   1 geaNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleairegrt 56 
                                       g+aNr+A+rfA++++lp+t+GSDAH+ e+VG+a T ++++++++d++leair g+t
  gi|336254652|ref|YP_004597759.1| 140 GRANRQADRFARARDLPRTAGSDAHISEMVGQAITRVDADERSADAILEAIRDGKT 195
                                       689***************************************************98 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.1   5.4e-12   3.2e-08       1      58 [.       5      58 ..       5     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 5.4e-12
                                      EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagi 58
                                      +lH+H++ s   g  s+e ++++a++ gl+aia+TDh+++++ +e++++a +    g+
  gi|336254652|ref|YP_004597759.1|  5 ELHAHSSLSYD-GRDSVELILEQAEAVGLDAIAVTDHDEIDASLEAAERAPD---YGL 58
                                      79*******66.66677*******************************9933...344 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 ?   11.5   0.1   5.5e-05      0.33       9      48 ..      22      61 ..      15     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.5e-05
                   Glyco_tranf_2_4  9 eflahhlalgfdrilvydndstDgtrailkelpevkllhv 48
                                        l+ ++a+g d+i v+d+d  D + +  ++ p++ l+ +
  gi|336254652|ref|YP_004597759.1| 22 LILEQAEAVGLDAIAVTDHDEIDASLEAAERAPDYGLVGI 61
                                      568899*************************999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); 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:                         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 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1696.23
//
Query:       gi|336254653|ref|YP_004597760.1|  [L=378]
Description: asparagine synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-33  117.4   6.8    1.1e-21   77.9   1.4    2.1  2  Asn_synthase   Asparagine synthase
  ------ inclusion threshold ------
      0.037   12.8   0.0      0.051   12.4   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
      0.059   12.5   0.0       0.12   11.5   0.0    1.5  1  NAD_synthase   NAD synthase
       0.32   11.4   1.7        1.1    9.6   1.6    1.9  1  SIMPL          Protein of unknown function (DUF541)


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 !   77.9   1.4   2.5e-25   1.1e-21       2     142 ..     118     252 ..     117     276 .. 0.89
   2 !   43.1   0.5   9.6e-15   4.3e-11     212     307 ..     264     356 ..     252     375 .. 0.80

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 2.5e-25
                      Asn_synthase   2 lrelLedaVkrrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelv 78 
                                       l+++++ a +    ad+++++ +SGG+DS+l+a l+++        + +gf  ++s ++++a+ +ae++g + t ++
  gi|336254653|ref|YP_004597760.1| 118 LDDAIRTATDAARTADREIAVAFSGGVDSALVAELLDAP------LYVVGF--PDSHDVEAARTAAEAMGRDLTVVE 186
                                       78899999999999**********************995......59****..************************ PP

                      Asn_synthase  79 lteeelldalpdviyhlee..pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaa 142
                                       l++++l++a+p++++++ +   +  + a+plyl+ +++ ++ +  +  G+GaDElfgGY+   +  
  gi|336254653|ref|YP_004597760.1| 187 LEPADLERAVPEIVRATGRtnAMDVQIALPLYLVGERVAADSYDALAVGQGADELFGGYEKVVRLD 252
                                       ****************9999999999*********************************9544443 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 9.6e-15
                      Asn_synthase 212 yldlktllpgdllrkDrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLRealegylPeeileRpKegf 288
                                       +++  + lp++l r   +  a glE   P+l++r+ve+alrlp++l  ++++ K+ +R+++++ylP e++eR K+++
  gi|336254653|ref|YP_004597760.1| 264 VREQIESLPDQLPRDVLTIRATGLEPVAPLLHDRVVEAALRLPDDLLADEETRKRGFRQVAARYLPGEVAERDKKAV 340
                                       555556677777777778899******************************************************** PP

                      Asn_synthase 289 sapvgewklkgelrelaee 307
                                       ++++      +el +la++
  gi|336254653|ref|YP_004597760.1| 341 QYGSLVA---RELDRLARQ 356
                                       *955544...455555555 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.1e-05     0.051       2      25 ..     135     158 ..     134     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgy 25 
                                       +++va+SgGVDS+++a ll    y
  gi|336254653|ref|YP_004597760.1| 135 EIAVAFSGGVDSALVAELLDAPLY 158
                                       699***************987655 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.7e-05      0.12      19      84 ..     134     190 ..     115     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.7e-05
                                       SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHH CS
                      NAD_synthase  19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpi 84 
                                       +++ +  SGGvDS+lva l    l       + +P    + +dve+a++ ae +g + ++++++p+
  gi|336254653|ref|YP_004597760.1| 134 REIAVAFSGGVDSALVAELLDAPL-----YVVGFP----DSHDVEAARTAAEAMGRDLTVVELEPA 190
                                       5678899**********9987777.....445555....456777777777777777777777665 PP

>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.6   0.00026       1.1     115     151 ..     100     137 ..      77     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00026
                             SIMPL 115 fslsdedel.rdeareeAvkdArakAealAkalgvklg 151
                                       f+l d+d+    ea  eA++dA+++A ++A+++++++ 
  gi|336254653|ref|YP_004597760.1| 100 FTLPDPDPEpDHEAALEALDDAIRTATDAARTADREIA 137
                                       5566665552459*********************9983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); 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:                         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: 2775.87
//
Query:       gi|336254654|ref|YP_004597761.1|  [L=111]
Description: Cupin 2 barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-10   38.9   2.3    7.8e-10   38.3   2.3    1.2  1  Cupin_2     Cupin domain
     0.0093   15.4   0.0     0.0094   15.4   0.0    1.1  1  PCO_ADO     PCO_ADO
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.012   15.2   0.0    1.2  1  Cupin_1     Cupin
      0.016   14.9   0.1       0.02   14.6   0.1    1.1  1  DMSP_lyase  Dimethlysulfonioproprionate lyase
       0.03   14.0   0.2      0.047   13.4   0.2    1.4  1  Cupin_3     Protein of unknown function (DUF861)


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 !   38.3   2.3   2.2e-13   7.8e-10       4      68 ..      39     103 ..      37     107 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 2.2e-13
                                       EEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEE CS
                           Cupin_2   4 elppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparll 68 
                                        l pG++ ++h H +++ +f+VleG +++  dge  e+ea  +v+ ++g+ H+ +N++de ++++
  gi|336254654|ref|YP_004597761.1|  39 ALGPGAELEPHEHAESTNVFHVLEGSVTVLQDGESEEIEAPGVVHHERGVDHGAKNETDERVVFT 103
                                       578**********************************************************9985 PP

>> PCO_ADO  PCO_ADO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.6e-06    0.0094      27      78 ..      16      67 ..       3     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.6e-06
                           PCO_ADO 27 skskppvtyltlyetdsfslgvFvlppgaviPLHdHPgMtvlskllyGslhi 78
                                      ++ +  v  ++l  td++ +  F l pga +  H+H + t +  +l Gs+ +
  gi|336254654|ref|YP_004597761.1| 16 EPADGEVETTELVVTDDVLVKAFALGPGAELEPHEHAESTNVFHVLEGSVTV 67
                                      566788999*****************************************98 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   3.5e-06     0.012      34      69 ..      34      69 ..      21     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.5e-06
                                      EEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEE CS
                           Cupin_1 34 saarvdlepgglllPhyhpnateiayvlqGegrvgf 69
                                       +  ++l pg+ l+Ph h  +t ++ vl+G+++v +
  gi|336254654|ref|YP_004597761.1| 34 LVKAFALGPGAELEPHEHAESTNVFHVLEGSVTVLQ 69
                                      45567789***********************99654 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   5.4e-06      0.02      89     157 ..      27      95 ..      20     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.4e-06
                        DMSP_lyase  89 lekrddvalGlvllaPkvrYPdHhhaa.eelYlvlsggaefrqgeaewlsrgiGevifnepgikhamrsa 157
                                       l+  ddv +    l+P  +   H+ha+  +++ vl g++ + q+++   + ++ +v+++e+g+ h  + +
  gi|336254654|ref|YP_004597761.1|  27 LVVTDDVLVKAFALGPGAELEPHEHAEsTNVFHVLEGSVTVLQDGE-SEEIEAPGVVHHERGVDHGAKNE 95 
                                       667788888899999**99999****9999*******977766554.3799**************87665 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 ?   13.4   0.2   1.3e-05     0.047      22      59 ..      51      87 ..      42     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                      CESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TT CS
                           Cupin_3 22 tyeedEfcyileGevkvtpeggetvelraGDlvvlpkg 59
                                      + e +  +++leG v+v   +ge  e++a ++v  + g
  gi|336254654|ref|YP_004597761.1| 51 HAESTNVFHVLEGSVTVLQ-DGESEEIEAPGVVHHERG 87
                                      56667889***********.888888888777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 884.39
//
Query:       gi|336254655|ref|YP_004597762.1|  [L=363]
Description: ParA/MinD ATPase-like protein [Halopiger xanaduensis SH-6]
Scores for 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-90  300.8   0.1    8.8e-90  300.4   0.1    1.1  1  ParA             NUBPL iron-transfer P-loop NTPase
    1.1e-12   48.1   0.0    1.9e-12   47.3   0.0    1.4  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    3.2e-11   43.5   0.2    3.9e-08   33.4   0.3    2.2  2  AAA_31           AAA domain
    7.4e-07   28.6   2.6    0.00029   20.1   0.7    2.9  3  ArsA_ATPase      Anion-transporting ATPase
    1.7e-06   28.1   0.3      8e-06   25.9   0.1    2.1  2  FeS_assembly_P   Iron-sulfur cluster assembly protein
    0.00012   21.5   0.3    0.00022   20.6   0.2    1.5  2  MipZ             ATPase MipZ
    0.00056   19.8   0.1       0.68    9.7   0.0    2.3  2  AAA_26           AAA domain
     0.0016   17.8   0.0     0.0031   16.9   0.0    1.4  1  VirC1            VirC1 protein
     0.0079   15.7   0.4        0.6    9.5   0.8    2.1  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
  ------ inclusion threshold ------
      0.032   13.9   0.2      0.051   13.2   0.2    1.3  1  SRP54            SRP54-type protein, GTPase domain
      0.034   13.6   0.1      0.088   12.2   0.2    1.6  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
      0.049   13.7   0.8       0.15   12.2   0.3    2.0  2  DUF1490          Protein of unknown function (DUF1490)
      0.087   12.0   0.1       0.23   10.6   0.1    1.6  2  NB-ARC           NB-ARC domain
      0.097   12.6   0.0       0.18   11.7   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
       0.15   11.9   0.2       0.37   10.7   0.2    1.6  1  NTPase_1         NTPase
       0.16   11.3   0.0       0.27   10.5   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family


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 !  300.4   0.1   7.8e-93   8.8e-90       2     244 ..      92     332 ..      91     334 .. 0.96

  Alignments for each domain:
  == domain 1  score: 300.4 bits;  conditional E-value: 7.8e-93
                              ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSi 78 
                                       v++viav+SgKGGVGK+tva+n+A+ L+k+g+ vgllDaDi+Gp++p++l ve+e   + ++ ++P +++g++v+S+
  gi|336254655|ref|YP_004597762.1|  92 VRNVIAVASGKGGVGKTTVAANIAAGLEKRGAMVGLLDADIHGPNVPKILPVESEPGVTPDEDIVPPRSDGVRVISM 168
                                       89****************************************************855555999************** PP

                              ParA  79 gfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkk 155
                                       gf++e+ed++ + rGpm++k++ ++l+ vewg lDyLi+DlPPGtgD++l ++q++p++gav+Vttpqe+al+d++k
  gi|336254655|ref|YP_004597762.1| 169 GFMMEEEDDPAILRGPMVNKFMMKFLEGVEWGRLDYLIVDLPPGTGDATLNLLQSMPVTGAVVVTTPQEMALEDTRK 245
                                       ***************************************************************************** PP

                              ParA 156 aiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepes 232
                                       +i+mf+k +++vlGvveNms fvcp+cg+++ +fg++g++++ +++++pllg+ip++p++   + eg   ++k++es
  gi|336254655|ref|YP_004597762.1| 246 GIQMFNKHDTPVLGVVENMSSFVCPSCGDQHGLFGTEGADTIVDNYDAPLLGRIPIHPDFGADGSEGP--IVKDDES 320
                                       *************************************************************9999998..5566789 PP

                              ParA 233 eaakaleeiaek 244
                                       ++++++e+++++
  gi|336254655|ref|YP_004597762.1| 321 PVQEHVEDVVAE 332
                                       999999998865 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 !   47.3   0.0   1.7e-15   1.9e-12       1     117 [.      96     304 ..      96     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.7e-15
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ia+as+kGGvGKTt+aan+a+ l +rg  V l+DaD  ++n    + l  + ep                       
  gi|336254655|ref|YP_004597762.1|  96 IAVASGKGGVGKTTVAANIAAGLEKRGAMVGLLDADIHGPNVP--KILPVESEPgvtpdedivpprsdgvrvismgf 170
                                       89***************************************99..44444444477888888999999999999999 PP

                                       .......................................................................CCHCCC CS
                                       .......................................................................xxxxxx RF
                              CbiA  55 .......................................................................dlkrll 60 
                                                                                                              d  +++
  gi|336254655|ref|YP_004597762.1| 171 mmeeeddpailrgpmvnkfmmkflegvewgrldylivdlppgtgdatlnllqsmpvtgavvvttpqemaleDTRKGI 247
                                       99999999999999999999999999999999999999999999999999999999999988888888888777778 PP

                                       HHHHHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CC CS
                                       xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  61 ellealgkkkall...lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdea 117
                                       +++++ +++  +l    ++ ++v    + + +     e+ +++   y  p+lg ip   +
  gi|336254655|ref|YP_004597762.1| 248 QMFNKHDTP--VLgvvENMSSFVCPSCGDQ-HGLFGTEGADTIVDNYDAPLLGRIPIHPD 304
                                       888777765..3344555555555555444.67777777777777777777777776655 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.3   3.5e-11   3.9e-08       2      40 ..      94     132 ..      93     140 .. 0.94
   2 !    7.8   0.0    0.0025       2.8     107     166 ..     190     252 ..     150     260 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.5e-11
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                        vIa+a  KGGvGKTT + n+aa l k+g  v l D+D 
  gi|336254655|ref|YP_004597762.1|  94 NVIAVASGKGGVGKTTVAANIAAGLEKRGAMVGLLDADI 132
                                       59***********************************96 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0025
                            AAA_31 107 lkellekvk.deYDyiiiDcpPsLglltenaLvas..dsviipvqaeayaleGleqllktiee 166
                                       + ++le v+  + Dy i+D pP  g  t n L +      ++++ ++++ale  ++ ++++++
  gi|336254655|ref|YP_004597762.1| 190 MMKFLEGVEwGRLDYLIVDLPPGTGDATLNLLQSMpvTGAVVVTTPQEMALEDTRKGIQMFNK 252
                                       4566666663468*****************997641145688888999999887777666665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.7   2.6e-07   0.00029       5      35 ..      98     128 ..      94     133 .. 0.84
   2 ?    2.1   0.0     0.082        92     115     144 ..     192     223 ..     180     229 .. 0.74
   3 !    5.3   0.0    0.0085       9.6     205     243 ..     225     263 ..     217     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.6e-07
                                       EEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                       ArsA_ATPase   5 lvgGKGGVGKttvsaatavklsekgkkvlli 35 
                                       + +GKGGVGKttv+a +a+ l + g  v l+
  gi|336254655|ref|YP_004597762.1|  98 VASGKGGVGKTTVAANIAAGLEKRGAMVGLL 128
                                       569******************9999877666 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.082
                                       HHHHHHHCSSSSEEEEESBS.CCH.TCGGGGH CS
                       ArsA_ATPase 115 ellkyvkeeeydvvvlDtaP.TGh.tlrllsl 144
                                       ++l+ v+    d++++D +P TG+ tl ll+ 
  gi|336254655|ref|YP_004597762.1| 192 KFLEGVEWGRLDYLIVDLPPgTGDaTLNLLQS 223
                                       34444456678********9889658999974 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0085
                                       TTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                       ArsA_ATPase 205 ertsfrlVvipEklslkEteRaikeLkkygikvdavivN 243
                                         t  ++V++p +++l++t++ i+ ++k +  v  v+ N
  gi|336254655|ref|YP_004597762.1| 225 PVTGAVVVTTPQEMALEDTRKGIQMFNKHDTPVLGVVEN 263
                                       568889***********************9999888876 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   7.2e-09     8e-06       8      55 ..      12      59 ..       8      68 .. 0.87
   2 ?   -1.5   0.0       2.6   2.9e+03      40      58 ..     230     248 ..     226     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7.2e-09
                                      HTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--SSTT-TTHHHHHH CS
                    FeS_assembly_P  8 LrtVtDPelgvdlvslglvreidieggkVsvditltypacslaeaira 55
                                      L+++ DP +g d+v lglv +++i++ +++++++   p  ++  ++ +
  gi|336254655|ref|YP_004597762.1| 12 LEDIEDPDIGEDIVTLGLVNDVVIDDETARISLAFNAPYAPSEMELGN 59
                                      899***********************9999999999888886555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.6
                                       E--SSTT-TTHHHHHHHHH CS
                    FeS_assembly_P  40 itltypacslaeairadae 58 
                                       + +t+p+++++e+ r+ ++
  gi|336254655|ref|YP_004597762.1| 230 VVVTTPQEMALEDTRKGIQ 248
                                       77999****9999998765 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2     2e-07   0.00022       2      40 ..      95     133 ..      94     145 .. 0.93
   2 ?   -3.8   0.0       5.7   6.4e+03      99     112 ..     201     215 ..     174     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2e-07
                                       EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TT CS
                              MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlr 40 
                                       vi ++  kGG Gk+t+a  +a  L k+Ga v+ +d d+ 
  gi|336254655|ref|YP_004597762.1|  95 VIAVASGKGGVGKTTVAANIAAGLEKRGAMVGLLDADIH 133
                                       7999*******************************9975 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.7
                                       H-SEEEEE--.SS-- CS
                              MipZ  99 eldfividtP.Gsds 112
                                       +ld++++d P G+ +
  gi|336254655|ref|YP_004597762.1| 201 RLDYLIVDLPpGTGD 215
                                       679999997525544 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.3     0.003       3.4       3      33 ..      96     126 ..      94     128 .. 0.89
   2 !    9.7   0.0   0.00061      0.68     132     194 ..     230     305 ..     223     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.003
                            AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkvg 33 
                                       i v++   gvGKT+v++ +++ l+++g+ vg
  gi|336254655|ref|YP_004597762.1|  96 IAVASGKGGVGKTTVAANIAAGLEKRGAMVG 126
                                       67889999******************99887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00061
                            AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNk....vrnp...........envetlekksgipvlGvvPylpd 193
                                       ++V+++++ +++++   i+++ +++ +vlGv+ N     +  p           e  +t+  +   p+lG++P  pd
  gi|336254655|ref|YP_004597762.1| 230 VVVTTPQEMALEDTRKGIQMFNKHDTPVLGVVENMssfvC--PscgdqhglfgtEGADTIVDNYDAPLLGRIPIHPD 304
                                       789999999***********************99844321..25676666666669999999999********9988 PP

                            AAA_26 194 l 194
                                        
  gi|336254655|ref|YP_004597762.1| 305 F 305
                                       6 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.7e-06    0.0031       2      41 ..      94     133 ..      93     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.7e-06
                             VirC1   2 klitfcslkGGaGkttalmglcsalasdgkrvalfeaden 41 
                                       ++i+++s kGG Gktt    + + l  +g  v+l++ad  
  gi|336254655|ref|YP_004597762.1|  94 NVIAVASGKGGVGKTTVAANIAAGLEKRGAMVGLLDADIH 133
                                       6899*********************************965 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.8   0.00054       0.6       3      38 ..      95     130 ..      93     134 .. 0.90
   2 ?    3.6   0.0     0.036        40     102     145 ..     187     231 ..     160     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00054
                          CBP_BcsQ   3 vlalqGvRGGvGttsllaaLawalhelgesvlviDl 38 
                                       v+a+   +GGvG+t+++a +a  l++ g  v ++D+
  gi|336254655|ref|YP_004597762.1|  95 VIAVASGKGGVGKTTVAANIAAGLEKRGAMVGLLDA 130
                                       78888889*********************9999886 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.036
                          CBP_BcsQ 102 aeallaalkelk.eqyrwillDlpagasaltrellaladlvllvv 145
                                       ++ ++++l+ ++ ++ +++++Dlp g+ + t +ll+   ++ +vv
  gi|336254655|ref|YP_004597762.1| 187 NKFMMKFLEGVEwGRLDYLIVDLPPGTGDATLNLLQSMPVTGAVV 231
                                       5567778888888999***************99999766554433 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   0.2   4.5e-05     0.051       6      39 ..      99     132 ..      93     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.5e-05
                                       EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54   6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39 
                                         G  G+GKTt +a +aa l+k+g  v l  aD+
  gi|336254655|ref|YP_004597762.1|  99 ASGKGGVGKTTVAANIAAGLEKRGAMVGLLDADI 132
                                       45899************************99997 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 ?   12.2   0.2   7.9e-05     0.088       6      31 ..     100     125 ..      94     136 .. 0.85
   2 ?   -2.9   0.0       3.3   3.6e+03     197     256 ..     288     349 ..     278     360 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.9e-05
                         Fer4_NifH   6 yGkGGiGksttsqnlsaalaemgkkv 31 
                                        GkGG+Gk+t ++n++a l ++g  v
  gi|336254655|ref|YP_004597762.1| 100 SGKGGVGKTTVAANIAAGLEKRGAMV 125
                                       5********************99877 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.3
                         Fer4_NifH 197 aeelgtkvlevvPrdeivrkaelrkktvieyapese..qakeyrelarkilenkklviPkpl 256
                                       +++ + ++l  +P + +      +  +v + ++  +  + +   e a++i e+++ ++ +  
  gi|336254655|ref|YP_004597762.1| 288 VDNYDAPLLGRIPIHPDFGADGSEGPIVKDDESPVQehVEDVVAEAADRIGEANRRTVAEHT 349
                                       55555666666666666555555555555443332222445556666666666655555444 PP

>> DUF1490  Protein of unknown function (DUF1490)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       6.1   6.8e+03      34      52 ..     224     244 ..     218     248 .. 0.53
   2 ?   12.2   0.3   0.00013      0.15      64      80 ..     325     341 ..     318     348 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.1
                           DUF1490  34 aplreaaVaat..alglrgaR 52 
                                       +p+  a V +t  +++l  +R
  gi|336254655|ref|YP_004597762.1| 224 MPVTGAVVVTTpqEMALEDTR 244
                                       455544444433345555555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                           DUF1490  64 kvaDvvaeAreriGeea 80 
                                       +v DvvaeA +riGe  
  gi|336254655|ref|YP_004597762.1| 325 HVEDVVAEAADRIGEAN 341
                                       689***********964 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.7   1.9e+03     109     149 ..      30      70 ..      26      78 .. 0.78
   2 ?   10.6   0.1   0.00021      0.23      23      42 ..      97     116 ..      89     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                                       EEEE-SHHHH.....HHHHCHTTSEEEEEESBCCCCCCS-S CS
                            NB-ARC 109 lDDVweeedwdkigvvlparenrlrvllTTRdeevanavsa 149
                                         DV+   +  +i++++ a    +++ l  R +e++++v+ 
  gi|336254655|ref|YP_004597762.1|  30 VNDVVIDDETARISLAFNAPYAPSEMELGNRIRELCDEVGL 70 
                                       56666666666999999999999999999999999999876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00021
                                       EEEEESTTSSHHHHHHHHCC CS
                            NB-ARC  23 valvGmgGvGKttlakqiln 42 
                                          +G+gGvGKtt+a++i  
  gi|336254655|ref|YP_004597762.1|  97 AVASGKGGVGKTTVAANIAA 116
                                       4458*************975 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.18       6      39 ..      98     131 ..      93     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                        APS_kinase   6 wltGlsgsGKstianalekkLvekgisvylLdGd 39 
                                         +G  g GK+t+a +++  L+++g  v lLd d
  gi|336254655|ref|YP_004597762.1|  98 VASGKGGVGKTTVAANIAAGLEKRGAMVGLLDAD 131
                                       568999**************************88 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00033      0.37       5      30 ..     100     125 ..      96     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                                       E--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1   5 TGppGvGKtTlvkkvlellkssgvkv 30 
                                       +G+ GvGKtT+  +++  l+++g  v
  gi|336254655|ref|YP_004597762.1| 100 SGKGGVGKTTVAANIAAGLEKRGAMV 125
                                       7999*****************99877 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00024      0.27      46      93 ..     201     248 ..     185     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHH CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklk 93 
                                       +    ++D+  GtgD +++l++s+  +g vvv   +e+ L+ ++k ++
  gi|336254655|ref|YP_004597762.1| 201 RLDYLIVDLPPGTGDATLNLLQSMPVTGAVVVTTPQEMALEDTRKGIQ 248
                                       4445799**************************999999999888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2743.02
//
Query:       gi|336254656|ref|YP_004597763.1|  [L=103]
Description: hypothetical protein Halxa_3272 [Halopiger xanaduensis SH-6]
Scores for 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   7.0      0.083   12.7   7.0    1.1  1  Bax1-I    Inhibitor of apoptosis-promoting Bax1
        0.9    9.6   6.2       0.17   11.9   1.0    2.0  2  DUF997    Protein of unknown function (DUF997)


Domain annotation for each model (and alignments):
>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   7.0   9.2e-06     0.083      31      98 ..      24      86 ..       8      93 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.2e-06
                            Bax1-I 31 qlflslhivlflvvilaplalvflslsaarlkkkssalalallllftlleGlslspillvytgaiilq 98
                                      + f++++++l++ vil+p+++++++ +++   +++     + ll+ + l Gl+ s+++ ++  ++++ 
  gi|336254656|ref|YP_004597763.1| 24 TGFPNTGTWLIFAVILVPVYVMIIA-WFVGSPRNT----KTGLLGVSYLVGLTTSMWVGMFFLTVLIG 86
                                      5688999***************845.444555444....45777788888888888888876555443 PP

>> DUF997  Protein of unknown function (DUF997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.0   1.9e-05      0.17      35      62 ..      20      51 ..      11      53 .. 0.81
   2 ?    0.4   0.4     0.072   6.5e+02      19      27 ..      74      82 ..      59      95 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                            DUF997 35 y.yilglP...lWfflscillpilfivlvill 62
                                      + +++g+P    W+++++il+p+ ++++++++
  gi|336254656|ref|YP_004597763.1| 20 TaGVTGFPntgTWLIFAVILVPVYVMIIAWFV 51
                                      348999995556*****************986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.072
                            DUF997 19 wwllfaYgl 27
                                      +w+++++++
  gi|336254656|ref|YP_004597763.1| 74 MWVGMFFLT 82
                                      344444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 764.26
//
Query:       gi|336254657|ref|YP_004597764.1|  [L=104]
Description: hypothetical protein Halxa_3273 [Halopiger xanaduensis SH-6]
Scores for 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   14.1   9.4      0.037   13.9   9.4    1.1  1  Bax1-I    Inhibitor of apoptosis-promoting Bax1
      0.081   13.2   5.1      0.091   13.0   5.1    1.1  1  DUF996    Protein of unknown function (DUF996)
        3.3    7.5   5.1        2.9    7.7   0.2    2.1  2  Lig_chan  Ligand-gated ion channel
        8.5    6.7  10.2       0.16   12.2   3.2    1.7  2  Ost5      Oligosaccharyltransferase subunit 5


Domain annotation for each model (and alignments):
>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   9.4   8.3e-06     0.037      13     100 ..       3      90 ..       1      95 [. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.3e-06
                            Bax1-I  13 lgllltalvaavvlsspa.....qlflslhivlflvvilaplalvflslsaarlkkkssalalallllftlleGlsl 84 
                                       ++ +l+a+++ v++  +      + f++ ++++++ +il+p++++++++ +  + k + +   + ll+ + l+Gl+ 
  gi|336254657|ref|YP_004597764.1|   3 FATTLAAAASSVLYHGYDgtegfTGFVNEGTWVIFALILVPIYIMLIAW-F--TGKPRDT--KTGLLGVSYLAGLTT 74 
                                       4444443333333333337999999********************8453.3..4444555..568999999999999 PP

                            Bax1-I  85 spillvytgaiilqaf 100
                                       s+++ ++  ++++  +
  gi|336254657|ref|YP_004597764.1|  75 SMWVGMFFLTVLIGIL 90 
                                       9999999766665544 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   5.1     2e-05     0.091      62     128 ..      24      90 ..       1      92 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                            DUF996  62 gleeaas...lilllllvliiayvlliisavflkksyellgkrtgvklFetagllyfiGaiLtivlvGli 128
                                       g++         ++++++li++ + +++ a+f  k  ++    +gv+++    + +++G + + vl+G++
  gi|336254657|ref|YP_004597764.1|  24 GFT---GfvnEGTWVIFALILVPIYIMLIAWFTGKPRDTKTGLLGVSYLAGLTTSMWVGMFFLTVLIGIL 90 
                                       223...1444678999999*************************************************97 PP

>> Lig_chan  Ligand-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2   0.00064       2.9      67      94 ..      23      50 ..       1      62 [. 0.70
   2 ?    1.9   1.1      0.04   1.8e+02       2      20 ..      74      92 ..      73      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00064
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Lig_chan 67 rsvsgRivvavWwffvlillssYtAnLa 94
                                      + ++g +  ++W++f+lil+  Y+  +a
  gi|336254657|ref|YP_004597764.1| 23 EGFTGFVNEGTWVIFALILVPIYIMLIA 50
                                      5566666678999999999999985444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.04
                                      XXXXXXXXTXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxx RF
                          Lig_chan  2 levWlsvlvalilvsivlf 20
                                      +++W+ ++++ +l++i+++
  gi|336254657|ref|YP_004597764.1| 74 TSMWVGMFFLTVLIGILFY 92
                                      689***********99876 PP

>> Ost5  Oligosaccharyltransferase subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.6       1.3   5.9e+03      48      56 ..       5      13 ..       2      16 .. 0.58
   2 ?   12.2   3.2   3.6e-05      0.16       3      71 ..      25      89 ..      23      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                              Ost5 48 lllalvASl 56
                                      ++la++AS 
  gi|336254657|ref|YP_004597764.1|  5 TTLAAAASS 13
                                      455666654 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.6e-05
                              Ost5  3 fsppvppslqptlafvllligllltalfflyevtstkkkrslvkelllalvASlflG..fGvvflllavGV 71
                                      f+  v+  +  ++a++l+ i ++l+a+f      + k+ ++ +  l ++ +A l+    +G++fl   +G+
  gi|336254657|ref|YP_004597764.1| 25 FTGFVNEGTWVIFALILVPIYIMLIAWF------TGKPRDTKTGLLGVSYLAGLTTSmwVGMFFLTVLIGI 89
                                      899999**********************......6677777888888888888887755689999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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: 759.42
//
Query:       gi|336254658|ref|YP_004597765.1|  [L=469]
Description: polysulfide reductase NrfD [Halopiger xanaduensis SH-6]
Scores for 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-19   69.6  17.7    3.5e-19   69.6  17.7    1.7  2  NrfD      Polysulphide reductase, NrfD


Domain annotation for each model (and alignments):
>> NrfD  Polysulphide reductase, NrfD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6  17.7   1.9e-23   3.5e-19       9     309 ..      62     391 ..      56     394 .. 0.80
   2 !    1.9   2.9    0.0078   1.4e+02      14     113 ..     339     431 ..     335     442 .. 0.74

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.9e-23
                              NrfD   9 vvWglliavylFligisAgalilaillklfkkkegkslkliirtgallaalavlagllilvldlgrperflklll.y 84 
                                         Wgl+i  +++ +gi+ g +il+++++l+  +++ +   i+r++ +l ++ + a+   +++++grp+r++  ++ +
  gi|336254658|ref|YP_004597765.1|  62 STWGLYIGAFIWWVGIAHGGIILSAAVRLLGMERYMP---IARLAEMLTLAGLSAAGFYILVHMGRPDRMVTSVIgH 135
                                       57******************************99888...666677776777777677777********99999777 PP

                              NrfD  85 ynfs...Simswgvlllslyivvlvlyllvifekdlaakg..lpa.............lgilaklisla........ 135
                                       y ++   S+++w+v++ ++y+v+ + yl + ++ d+  +   lp              +g+++  + +         
  gi|336254658|ref|YP_004597765.1| 136 YHITvnnSPLVWDVTVITAYFVMTATYLGLTLRYDVSRLRddLPSfepkvggvqlpdlYGLVYDALTIGytekedev 212
                                       7774445**************************99999997755455555555555554455554444477888888 PP

                              NrfD 136 .ervakilaiialilavll..gsytgfllsavlsrplwnspllpvlFlasaiasGlavlllasllaarfekese..d 207
                                        er++ +la +++i+a ll  g++  +l+s + + p w +++ ++ Fl  a++s+++ ++l+s+ + r  + ++   
  gi|336254658|ref|YP_004597765.1| 213 iERMVWWLAAAVIIMAPLLlhGGVIPWLFSLLPAMPSWTGAIQGPQFLSIALTSAISGVILLSYAFRRAYDWDHiiT 289
                                       899999******9999665447899*************************************999888776433223 PP

                              NrfD 208 ....agllkklellvilteagllvilfvglaleggekiealeaalsggfl.tvlFwlgvvllglaiplllslavprl 279
                                           +gll  l+++ +l++ ++l  l+ g  l+++ ++ a++  l   ++ t++     ++lg ++ ++l+ + p l
  gi|336254658|ref|YP_004597765.1| 290 ddifRGLLLWLGFFCLLFLWFQLQQLVNGSFLGPLDQAHATAGKLGHPIYiTSML----MVLGTLAFIFLQGIRPAL 362
                                       01114555566666666777777789889999*****999999999966643443....357888999**9999999 PP

                              NrfD 280 renvavvviasilalvgvlllrfllliagq 309
                                        ++++++  a+ ++l  ++l+++l ++ g 
  gi|336254658|ref|YP_004597765.1| 363 FSKKRAL-AAGFVVLTATFLEKLLFVVEGF 391
                                       9999999.8899999999999998888775 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.0078
                              NrfD  14 liavylFligisAgalilaillklfkkkegkslkliirtgallaalavlagllilvldlgrpe.rflklllyynfsS 89 
                                       +i  +l ++g+ A  ++  i + lf kk++     ++ t+        l  ll++v    +p   +++ +  + f+S
  gi|336254658|ref|YP_004597765.1| 339 YITSMLMVLGTLAFIFLQGIRPALFSKKRALAAGFVVLTAT------FLEKLLFVVEGFLHPTfDIYANVPGTYFPS 409
                                       44457777789999999999999999988766444433333......344567777777788888899999999999 PP

                              NrfD  90 imswgvlllslyivvlvlyllvif 113
                                        + w  l l++ i+++vl+ l+i 
  gi|336254658|ref|YP_004597765.1| 410 AIEW--LSLAGTIGLVVLFFLSIS 431
                                       9999..899999999999988774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3504.79
//
Query:       gi|336254659|ref|YP_004597766.1|  [L=559]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-36  124.0   6.4    1.8e-36  124.0   6.4    2.7  2  Ferredoxin_N  N-terminal region of 4Fe-4S ferredoxin iron-sul
    3.9e-14   53.0  23.0    1.1e-05   25.9   1.6    4.2  4  Fer4_7        4Fe-4S dicluster domain
    1.3e-12   47.7  17.6    3.2e-08   33.5   0.3    3.6  3  Fer4_10       4Fe-4S dicluster domain
    2.5e-11   43.6   6.0    2.5e-11   43.6   6.0    2.9  3  Fer4_11       4Fe-4S dicluster domain
    1.7e-07   30.7  34.1    0.00013   21.7   3.5    5.0  5  Fer4          4Fe-4S binding domain
      6e-07   29.5  26.7    0.00054   20.1   8.3    3.7  5  Fer4_9        4Fe-4S dicluster domain
    1.1e-06   28.5  37.0     0.0015   18.5   2.9    4.8  5  Fer4_6        4Fe-4S binding domain
    1.2e-05   25.1  10.1    0.00034   20.5   1.9    4.6  4  Fer4_2        4Fe-4S binding domain
    0.00024   21.5  23.8      0.053   14.0   8.4    3.5  3  Fer4_8        4Fe-4S dicluster domain
     0.0012   19.7  40.7       0.17   12.9   2.2    4.3  4  Fer4_3        4Fe-4S binding domain
     0.0062   17.5  25.9          1   10.4   0.0    4.8  4  Fer4_16       4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.019   15.4  30.3       0.16   12.6   3.3    4.4  4  Fer4_4        4Fe-4S binding domain
      0.022   14.9  21.9       0.33   11.1   8.6    3.7  3  Fer4_21       4Fe-4S dicluster domain
      0.024   15.2  26.1       0.84   10.2   7.5    4.1  3  Fer4_17       4Fe-4S dicluster domain
      0.094   12.5   0.7        1.3    8.8   0.1    3.0  2  SHOCT         Short C-terminal domain
        4.9    8.0  22.1       0.38   11.5   0.4    4.7  4  Fer4_15       4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Ferredoxin_N  N-terminal region of 4Fe-4S ferredoxin iron-sulfur binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.0   6.4   1.6e-39   1.8e-36       1      65 []       9      73 ..       9      73 .. 0.99
   2 ?   -0.0   0.2      0.88   9.9e+02       8      28 ..     397     417 ..     389     426 .. 0.85

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 1.6e-39
                      Ferredoxin_N  1 hplgeeweeeleemLddteYDaeLGlemarDAvrvtkGeLseaeFhekYheaVlaEFgeDeRPta 65
                                      hplg+ewe+eleemLddteYD+eLG++ma+DA+rvtkGeLseaeFhekYhe+V++EFgeD+RPta
  gi|336254659|ref|YP_004597766.1|  9 HPLGSEWEDELEEMLDDTEYDTELGMKMAQDAMRVTKGELSEAEFHEKYHEDVMEEFGEDNRPTA 73
                                      89*************************************************************96 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.88
                      Ferredoxin_N   8 eeeleemLddteYDaeLGlem 28 
                                       ++++e+ L+  e D++L   m
  gi|336254659|ref|YP_004597766.1| 397 DDDFESALEALEIDSDLVSVM 417
                                       7899************97766 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   2.1   0.00023      0.26      30      50 ..     158     178 ..     142     180 .. 0.74
   2 !   15.8  13.0   1.4e-05     0.015       1      52 []     165     237 ..     165     237 .. 0.69
   3 !   25.9   1.6   9.9e-09   1.1e-05       2      41 ..     254     325 ..     253     335 .. 0.60
   4 !   13.3   0.0   8.3e-05     0.094       3      26 ..     338     361 ..     336     383 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                            Fer4_7  30 kveidpekClgCgaCvavCPt 50 
                                        ++id e+C gC +C+++C +
  gi|336254659|ref|YP_004597766.1| 158 GMTIDLERCDGCLSCMTACAS 178
                                       3799***************65 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.4e-05
                            Fer4_7   1 rCigCgaCvaaC........pvkaieldeeenek...........gtekveidpekClgCga..CvavCPtga 52 
                                       rC gC  C+ aC         v+++++  +e+e            g  + ++  + C++C+   C++vCPt a
  gi|336254659|ref|YP_004597766.1| 165 RCDGCLSCMTACasendldqGVNWMYVMAFEDELtaggspapdvmGGVEQNMLVRPCQHCTDapCEKVCPTTA 237
                                       8***********88877776477777665544333333333322232444788889*****999******986 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 9.9e-09
                            Fer4_7   2 CigCgaCvaaCpvkaield......eeenek........................gtekv.........eidpekCl 39 
                                       CigC++C++aCp+++ +++                                    g             ++ ++kC+
  gi|336254659|ref|YP_004597766.1| 254 CIGCRYCQVACPYGVNYFQwdepdvA----HeeitghggaevddpkeithaeyenG---EdrwvdsrspRGTMSKCT 323
                                       ************88888774443330....23344444333333333333333332...033355555599999999 PP

                            Fer4_7  40 gC 41 
                                        C
  gi|336254659|ref|YP_004597766.1| 324 MC 325
                                       99 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 8.3e-05
                            Fer4_7   3 igCgaCvaaCpvkaieldeeenek 26 
                                       +g+ aC++aCp +ai++ ++++e+
  gi|336254659|ref|YP_004597766.1| 338 VGTTACERACPPNAIQFGNVKSER 361
                                       6899*************9876655 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8  11.7   2.1e-05     0.023       2      56 .]     159     234 ..     158     234 .. 0.87
   2 !    6.5   3.6    0.0082       9.2       8      23 ..     220     237 ..     212     245 .. 0.77
   3 !   33.5   0.3   2.9e-11   3.2e-08       3      56 .]     248     348 ..     246     348 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl....................tsvgakgeaseeeavrkkvekCtgcg..aCveaCP 56 
                                       + id ++C +C  C++aC a+                      + +  +  +++ +++  v  C++c+   C ++CP
  gi|336254659|ref|YP_004597766.1| 159 MTIDLERCDGCLSCMTAC-ASEndldqgvnwmyvmafedeltAGGSPAPDVMGGVEQNMLVRPCQHCTdaPCEKVCP 234
                                       679***************.4447******************666666677777777788********888******9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0082
                           Fer4_10   8 tCirCg..kCvkaCPadl 23 
                                        C +C+   C k+CP+++
  gi|336254659|ref|YP_004597766.1| 220 PCQHCTdaPCEKVCPTTA 237
                                       599999889999**9944 PP

  == domain 3  score: 33.5 bits;  conditional E-value: 2.9e-11
                           Fer4_10   3 vidddtCirCgkCvkaCPadl................................tsvgakgeaseeeavrkkvekCtg 47 
                                         d d Ci+C+ C+ aCP+ +                                +  ++++   ++   r+ ++kCt+
  gi|336254659|ref|YP_004597766.1| 248 LTDYDVCIGCRYCQVACPYGVnyfqwdepdvaheeitghggaevddpkeithaEYENGEDRWVDSRSPRGTMSKCTM 324
                                       6799***************99*****************************99444444444455566677******* PP

                           Fer4_10  48 c...............gaCveaCP 56 
                                       c               +aC +aCP
  gi|336254659|ref|YP_004597766.1| 325 CpsmqdgqqgeeyvgtTACERACP 348
                                       *9999999999998877******9 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3       2.5   2.8e+03      68      79 ..     163     174 ..     152     185 .. 0.63
   2 !   43.6   6.0   2.2e-14   2.5e-11       4      65 ..     215     275 ..     212     280 .. 0.92
   3 !    7.9   0.4     0.003       3.3      65      99 ..     316     356 ..     309     357 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.5
                           Fer4_11  68 vekCdmcldrve 79 
                                       +e+Cd+cl+ ++
  gi|336254659|ref|YP_004597766.1| 163 LERCDGCLSCMT 174
                                       455666654443 PP

  == domain 2  score: 43.6 bits;  conditional E-value: 2.2e-14
                           Fer4_11   4 lflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneet 65 
                                       ++l + C+hC+++pC +++p++a + ++++G+Vl+d + +  ++r ++ acPy + + ++++
  gi|336254659|ref|YP_004597766.1| 215 NMLVRPCQHCTDAPCEKVCPTTARHTRDKDGLVLTDYDVCI-GCRYCQVACPYGVNYFQWDE 275
                                       678899**********************************7.**************999876 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.003
                           Fer4_11  65 tgkvekCdmcldrv..eaGl....lpacvescptgalnfgd 99 
                                        g+++kC+mc + +  ++G+    ++ac ++cp +a++fg+
  gi|336254659|ref|YP_004597766.1| 316 RGTMSKCTMCPSMQdgQQGEeyvgTTACERACPPNAIQFGN 356
                                       5789******77651134443333589*******9999996 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.5   6.7e-06    0.0075       2      18 ..     160     176 ..     159     176 .. 0.95
   2 ?    4.4   0.5     0.031        35      14      22 ..     229     237 ..     228     239 .. 0.87
   3 !   21.7   3.5   1.1e-07   0.00013       4      21 ..     250     267 ..     247     268 .. 0.91
   4 ?   -1.2   0.3       1.9   2.1e+03       6      11 ..     320     325 ..     318     325 .. 0.87
   5 !    8.6   1.1    0.0015       1.7      13      24 .]     342     353 ..     341     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.7e-06
                                       EEETTTSSS-THHHHHS CS
                              Fer4   2 videekCigCGaCvevC 18 
                                       +id e+C gC  C+ +C
  gi|336254659|ref|YP_004597766.1| 160 TIDLERCDGCLSCMTAC 176
                                       79*************** PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.031
                                       HHHHSTTTE CS
                              Fer4  14 CvevCPvgA 22 
                                       C++vCP+ A
  gi|336254659|ref|YP_004597766.1| 229 CEKVCPTTA 237
                                       ******965 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 1.1e-07
                                       ETTTSSS-THHHHHSTTT CS
                              Fer4   4 deekCigCGaCvevCPvg 21 
                                       d++ CigC +C  +CP+g
  gi|336254659|ref|YP_004597766.1| 250 DYDVCIGCRYCQVACPYG 267
                                       99**************99 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 1.9
                                       TTSSS- CS
                              Fer4   6 ekCigC 11 
                                       +kC+ C
  gi|336254659|ref|YP_004597766.1| 320 SKCTMC 325
                                       89**99 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0015
                                       HHHHHSTTTEEE CS
                              Fer4  13 aCvevCPvgAIt 24 
                                       aC+ +CP +AI+
  gi|336254659|ref|YP_004597766.1| 342 ACERACPPNAIQ 353
                                       7*********95 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   3.0    0.0015       1.7      33      48 ..     157     178 ..     137     182 .. 0.70
   2 !   11.0  11.7   0.00032      0.36       1      49 [.     165     236 ..     165     238 .. 0.75
   3 ?    4.8   4.2     0.028        32       2      20 ..     221     241 ..     220     251 .. 0.68
   4 !   20.1   8.3   4.8e-07   0.00054       2      51 .]     254     352 ..     253     352 .. 0.93
   5 ?    6.0   2.2     0.012        14       1      26 [.     321     361 ..     321     367 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0015
                            Fer4_9  33 e......eaCigCgaCveaCpk 48 
                                       +      e+C gC +C+ aC +
  gi|336254659|ref|YP_004597766.1| 157 WgmtidlERCDGCLSCMTACAS 178
                                       3556666789999999999975 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00032
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.....................eaCigCga..CveaCpkg 49 
                                       +C gC +C++aC ++   ++ ++ +  +  ++e                       C +C +  C+++Cp++
  gi|336254659|ref|YP_004597766.1| 165 RCDGCLSCMTACASENDLDQGVNWMYVMAFEDEltaggspapdvmggveqnmlvRPCQHCTDapCEKVCPTT 236
                                       5***********65555444444444443333467778888888888888889988**************97 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.028
                            Fer4_9   2 CtgCga..CveaCpagvvved 20 
                                       C  C+   C+++Cp+++   +
  gi|336254659|ref|YP_004597766.1| 221 CQHCTDapCEKVCPTTARHTR 241
                                       777765558888887776555 PP

  == domain 4  score: 20.1 bits;  conditional E-value: 4.8e-07
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase..................................eaCigCga... 41 
                                       C+gC++C+ aCp+gv+  ++ e  +++++                                     ++C++C +   
  gi|336254659|ref|YP_004597766.1| 254 CIGCRYCQVACPYGVNYFQWDEPDVAHEEITGhggaevddpkeithaeyengedrwvdsrsprgtmSKCTMCPSmqd 330
                                       ***********99999999888888887766689999999999*****************************9999* PP

                            Fer4_9  42 ............CveaCpkgai 51 
                                                   C+ aCp +ai
  gi|336254659|ref|YP_004597766.1| 331 gqqgeeyvgttaCERACPPNAI 352
                                       ******************9987 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.012
                            Fer4_9   1 kCtgC...............gaCveaCpagvvvedaaerka 26 
                                       kCt C               +aC++aCp ++++  +++ ++
  gi|336254659|ref|YP_004597766.1| 321 KCTMCpsmqdgqqgeeyvgtTACERACPPNAIQFGNVKSER 361
                                       57777777777666666665679999999999887777665 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.6   7.1e-06    0.0079       3      20 ..     160     177 ..     159     180 .. 0.91
   2 !    8.3   4.2    0.0023       2.5       8      21 ..     220     235 ..     219     238 .. 0.90
   3 !   18.5   2.9   1.3e-06    0.0015       5      23 ..     250     268 ..     247     269 .. 0.91
   4 ?   -2.0   0.2       4.2   4.7e+03       7      12 ..     320     325 ..     319     325 .. 0.83
   5 ?    6.2   0.9      0.01        12      14      24 .]     342     352 ..     340     352 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.1e-06
                            Fer4_6   3 eidpdkCigCgdCvrvCP 20 
                                       +id ++C+gC  C+++C 
  gi|336254659|ref|YP_004597766.1| 160 TIDLERCDGCLSCMTACA 177
                                       89***************6 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0023
                            Fer4_6   8 kCigCgd..CvrvCPe 21 
                                       +C +C d  C++vCP+
  gi|336254659|ref|YP_004597766.1| 220 PCQHCTDapCEKVCPT 235
                                       6****999*******7 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 1.3e-06
                            Fer4_6   5 dpdkCigCgdCvrvCPega 23 
                                       d+d CigC+ C ++CP+g+
  gi|336254659|ref|YP_004597766.1| 250 DYDVCIGCRYCQVACPYGV 268
                                       8899*************97 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 4.2
                            Fer4_6   7 dkCigC 12 
                                       +kC+ C
  gi|336254659|ref|YP_004597766.1| 320 SKCTMC 325
                                       799999 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.01
                            Fer4_6  14 dCvrvCPegai 24 
                                       +C+r+CP +ai
  gi|336254659|ref|YP_004597766.1| 342 ACERACPPNAI 352
                                       7******9998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.4   2.4e-06    0.0027       3      20 ..     159     176 ..     157     178 .. 0.91
   2 ?    3.5   5.3     0.078        87      10      22 .]     221     235 ..     217     235 .. 0.80
   3 !   20.5   1.9     3e-07   0.00034       4      22 .]     248     266 ..     245     266 .. 0.89
   4 ?   -2.2   4.8       5.3   5.9e+03      15      21 ..     342     348 ..     309     349 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.4e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                       + +d +rC gC +C +aC
  gi|336254659|ref|YP_004597766.1| 159 MTIDLERCDGCLSCMTAC 176
                                       679*************** PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.078
                            Fer4_2  10 CigCg..aCvsaCPa 22 
                                       C +C   +C ++CP+
  gi|336254659|ref|YP_004597766.1| 221 CQHCTdaPCEKVCPT 235
                                       7778556*******7 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 3e-07
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                         d d CigC+ C+ aCP+
  gi|336254659|ref|YP_004597766.1| 248 LTDYDVCIGCRYCQVACPY 266
                                       5699**************5 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 5.3
                            Fer4_2  15 aCvsaCP 21 
                                       aC  aCP
  gi|336254659|ref|YP_004597766.1| 342 ACERACP 348
                                       8999999 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   7.8   0.00062       0.7       2      63 ..     163     235 ..     162     237 .. 0.60
   2 !   14.0   8.4   4.8e-05     0.053       3      62 ..     252     348 ..     250     351 .. 0.58
   3 ?    1.0   0.4      0.54     6e+02       9      17 ..     341     353 ..     338     390 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00062
                            Fer4_8   2 lekCieCgaCqsaCp...............vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga..CtevC 61 
                                       le+C +C  C++aC                +++++     ++  ++++ v      e++  +  C++c    C++vC
  gi|336254659|ref|YP_004597766.1| 163 LERCDGCLSCMTACAsendldqgvnwmyvmAFEDELTAGGSPAPDVMGGV------EQNMLVRPCQHCTDapCEKVC 233
                                       799***********744444444443222233333333333333333322......2255699*****9999***** PP

                            Fer4_8  62 pv 63 
                                       p+
  gi|336254659|ref|YP_004597766.1| 234 PT 235
                                       *7 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.8e-05
                            Fer4_8   3 ekCieCgaCqsaCp............vlrr..........tk.khlldargeaaedvqeeqvlee....eealwsCt 52 
                                       + Ci+C +Cq aCp            v+++           + k++ +a++e+ e +++     +    + ++ +Ct
  gi|336254659|ref|YP_004597766.1| 252 DVCIGCRYCQVACPygvnyfqwdepdVAHEeitghggaevDDpKEITHAEYENGE-DRWV----DsrspRGTMSKCT 323
                                       56***********966655555555522223333222222222333333333333.3333....14455999***** PP

                            Fer4_8  53 tcga...............CtevCp 62 
                                       +c +               C+++Cp
  gi|336254659|ref|YP_004597766.1| 324 MCPSmqdgqqgeeyvgttaCERACP 348
                                       **88777777777777777777777 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.54
                            Fer4_8   9 gaCqsaCp....v 17 
                                        aC+ aCp     
  gi|336254659|ref|YP_004597766.1| 341 TACERACPpnaiQ 353
                                       4677777654441 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   4.5     0.063        71       1      11 [.     166     176 ..     166     179 .. 0.91
   2 !    9.5   5.3    0.0018       2.1       1      13 [.     221     235 ..     221     237 .. 0.84
   3 !   10.9   5.1   0.00067      0.75       1      14 [.     254     267 ..     254     268 .. 0.95
   4 !   12.9   2.2   0.00015      0.17       1      15 []     322     351 ..     322     351 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.063
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C+gC  C+ +C
  gi|336254659|ref|YP_004597766.1| 166 CDGCLSCMTAC 176
                                       ****88***** PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0018
                            Fer4_3   1 CtgCg..aCvevCPv 13 
                                       C++C   +C++vCP+
  gi|336254659|ref|YP_004597766.1| 221 CQHCTdaPCEKVCPT 235
                                       ****6668******7 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00067
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+gC+ C ++CP+g
  gi|336254659|ref|YP_004597766.1| 254 CIGCRYCQVACPYG 267
                                       ****99******98 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 0.00015
                            Fer4_3   1 CtgCg...............aCvevCPvgA 15 
                                       Ct+C                aC+++CP++A
  gi|336254659|ref|YP_004597766.1| 322 CTMCPsmqdgqqgeeyvgttACERACPPNA 351
                                       ****447889999*****99********98 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 ?    5.1   0.3      0.04        45      53      64 ..     165     176 ..     141     184 .. 0.71
   2 ?    3.4   4.9      0.14   1.5e+02       2      17 ..     221     238 ..     220     249 .. 0.85
   3 !    8.7   4.2     0.003       3.3       2      30 ..     254     283 ..     253     328 .. 0.53
   4 !   10.4   0.0    0.0009         1       6      37 ..     341     369 ..     338     384 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.04
                           Fer4_16  53 aitgCdiCqdvC 64 
                                       ++ gC  C+++C
  gi|336254659|ref|YP_004597766.1| 165 RCDGCLSCMTAC 176
                                       455555555555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.14
                           Fer4_16   2 CgtCgk..CaevCPtnai 17 
                                       C+ C+   C +vCPt a 
  gi|336254659|ref|YP_004597766.1| 221 CQHCTDapCEKVCPTTAR 238
                                       99**9999*******985 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.003
                           Fer4_16   2 CgtCgkCaevCPtnaikek.kekeiearec 30 
                                       C++C+ C  +CP ++   +  e+ ++ +e 
  gi|336254659|ref|YP_004597766.1| 254 CIGCRYCQVACPYGVNYFQwDEPDVAHEEI 283
                                       999999999999987444423444444443 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0009
                           Fer4_16   6 gkCaevCPtnaikekkekeiearecisyntae 37 
                                       ++C  +CP nai+     +++++++ +y+ +e
  gi|336254659|ref|YP_004597766.1| 341 TACERACPPNAIQFG---NVKSERSDAYQHRE 369
                                       68***********99...67777777774443 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.7    0.0082       9.1       2      14 ..     164     176 ..     163     179 .. 0.90
   2 ?    4.2   1.9      0.07        78       4      16 ..     221     235 ..     214     241 .. 0.88
   3 ?   12.6   3.3   0.00014      0.16       2      17 .]     252     267 ..     251     268 .. 0.92
   4 ?    7.5   0.7    0.0059       6.6       2      15 ..     320     348 ..     319     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0082
                            Fer4_4   2 erCigCgsCvaaC 14 
                                       erC gC sC+ aC
  gi|336254659|ref|YP_004597766.1| 164 ERCDGCLSCMTAC 176
                                       9************ PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.07
                            Fer4_4   4 CigCgs..CvaaCPq 16 
                                       C++C    C+ +CP+
  gi|336254659|ref|YP_004597766.1| 221 CQHCTDapCEKVCPT 235
                                       99999778******6 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00014
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       + CigC+ C  aCP+g
  gi|336254659|ref|YP_004597766.1| 252 DVCIGCRYCQVACPYG 267
                                       88************86 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0059
                            Fer4_4   2 erCigCgs...............CvaaCP 15 
                                       ++C+ C+s               C++aCP
  gi|336254659|ref|YP_004597766.1| 320 SKCTMCPSmqdgqqgeeyvgttaCERACP 348
                                       68999997778888888888888****** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.5    0.0018         2       3      19 ..     161     177 ..     145     187 .. 0.70
   2 ?   11.1   8.6    0.0003      0.33       8      52 ..     221     265 ..     215     270 .. 0.74
   3 ?    2.7   0.4      0.12   1.4e+02      39      58 ..     335     353 ..     320     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
                           Fer4_21   3 idedkCigCgkCliaCe 19 
                                       id ++C gC +C++aC 
  gi|336254659|ref|YP_004597766.1| 161 IDLERCDGCLSCMTACA 177
                                       55566666666666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0003
                           Fer4_21   8 CigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                       C +C+   C ++C++t+      d++  + +  d C+GC  C   CP
  gi|336254659|ref|YP_004597766.1| 221 CQHCTDapCEKVCPTTARHT--RDKDGLVLTDYDVCIGCRYCQVACP 265
                                       77776444888888766554..344455566789************* PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.12
                           Fer4_21  39 deCvGCnlCssvCPvedcie 58 
                                       +e vG + C   CP  ++i+
  gi|336254659|ref|YP_004597766.1| 335 EEYVGTTACERACP-PNAIQ 353
                                       67788899999999.57775 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   7.5   0.00075      0.84       1      58 [.     165     235 ..     165     238 .. 0.78
   2 ?    6.6  11.0      0.01        12       2      61 .]     221     269 ..     220     269 .. 0.79
   3 ?    5.4  11.2     0.024        27       2      20 ..     254     272 ..     253     352 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00075
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraakl............glleeaekeekaslCieCge..CerkCPq 58 
                                       rC +C  C+ +C s ++ d+   ++++ +++              ++++e+++ +  C +C    Ce++CP 
  gi|336254659|ref|YP_004597766.1| 165 RCDGCLSCMTACASENDLDQ-GVNWMYVMAFedeltaggspapDVMGGVEQNMLVRPCQHCTDapCEKVCPT 235
                                       7************9888555.4455555555556777777777788889999*******997555******6 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                           Fer4_17   2 CiqCgy..ClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgld 61 
                                       C++C    C+++Cp+ +++  +++ l+                 + Ci+C+ C+ +CP+g++
  gi|336254659|ref|YP_004597766.1| 221 CQHCTDapCEKVCPTTARHTRDKDGLVLT-------------DYDVCIGCRYCQVACPYGVN 269
                                       88888667888888888888877777665.............3578*************985 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.024
                           Fer4_17   2 CiqCgyClpeCpsyeaydn 20 
                                       Ci+C+yC  +Cp++ +y +
  gi|336254659|ref|YP_004597766.1| 254 CIGCRYCQVACPYGVNYFQ 272
                                       9999999999999777332 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0012       1.3      12      23 ..      45      56 ..      40      59 .. 0.86
   2 ?    0.4   0.1      0.53   5.9e+02      14      21 ..     296     303 ..     295     304 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0012
                             SHOCT 12 rGeIteEEFeak 23
                                      +Ge++e+EF +k
  gi|336254659|ref|YP_004597766.1| 45 KGELSEAEFHEK 56
                                      8********998 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.53
                             SHOCT  14 eIteEEFe 21 
                                       eIt +E+e
  gi|336254659|ref|YP_004597766.1| 296 EITHAEYE 303
                                       8******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 ?   -1.9   0.2       5.3     6e+03      33      53 ..      42      62 ..      34      84 .. 0.65
   2 ?   10.6   0.7   0.00065      0.73       2      19 ..     160     177 ..     159     200 .. 0.82
   3 ?   11.5   0.4   0.00034      0.38       2      47 ..     248     294 ..     247     303 .. 0.71
   4 ?   -1.3   0.4       3.3   3.7e+03      57      65 ..     345     353 ..     340     354 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.3
                           Fer4_15 33 llddgeiaegevpddeeeaaq 53
                                      ++++ge++e+e+ ++ +e++ 
  gi|336254659|ref|YP_004597766.1| 42 RVTKGELSEAEFHEKYHEDVM 62
                                      455566666666666555553 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00065
                           Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                       ++D ++C+gc  C++++ 
  gi|336254659|ref|YP_004597766.1| 160 TIDLERCDGCLSCMTACA 177
                                       79**************95 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00034
                           Fer4_15   2 vvDrdaCigcglCvaea...pevfeldedglasvllddgeiaegevpdd 47 
                                         D d Cigc  C  ++    ++f+ de ++a   +++   + +ev+d 
  gi|336254659|ref|YP_004597766.1| 248 LTDYDVCIGCRYCQVACpygVNYFQWDEPDVAHEEITGH--GGAEVDDP 294
                                       5699*************6665899999998884444322..23355554 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.3
                           Fer4_15  57 raCPvdAIr 65 
                                       raCP  AI+
  gi|336254659|ref|YP_004597766.1| 345 RACPPNAIQ 353
                                       89*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 4266.13
//
Query:       gi|336254660|ref|YP_004597767.1|  [L=114]
Description: Cupin 2 barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-08   34.0   0.2    2.3e-08   33.6   0.2    1.3  1  Cupin_2    Cupin domain
  ------ inclusion threshold ------
      0.023   14.9   0.0      0.032   14.4   0.0    1.2  1  Pirin_C_2  Quercetinase C-terminal cupin domain
      0.026   14.2   0.0       0.06   13.0   0.0    1.4  1  Cupin_3    Protein of unknown function (DUF861)
      0.028   13.8   0.0       0.05   13.0   0.0    1.5  1  DUF2917    Protein of unknown function (DUF2917)
      0.045   14.0   0.0      0.063   13.5   0.0    1.2  1  CENP-C_C   Mif2/CENP-C like
      0.095   12.7   0.0       0.11   12.4   0.0    1.2  1  HutD       HutD
       0.12   12.7   0.0       0.17   12.3   0.0    1.2  1  Pirin_C    Pirin C-terminal cupin 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 !   33.6   0.2   8.9e-12   2.3e-08       4      51 ..      37      86 ..      34     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 8.9e-12
                                      EEETTEEEEEECSSSEEEEEEEEESEEEEEEC..TEEEEEETTEEEEE-T CS
                           Cupin_2  4 elppGesapshrHpgedeffyVleGegeltvd..geeveleaGdsvyfpa 51
                                       l+ G+++ +h Hp+ + +f+VleG++ +t++  ++++e+ aG+++ f+ 
  gi|336254660|ref|YP_004597767.1| 37 ALEEGDEIAPHQHPDREIVFHVLEGRVSITLGddDHDHEVAAGELIRFDG 86
                                      57899999**********************663455***********986 PP

>> Pirin_C_2  Quercetinase C-terminal cupin 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     0.032      22      83 ..      35     102 ..      30     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                         Pirin_C_2  22 aakldegesleyelaagrkaYlqvieGevev......ngeslaagDGlaiedesslsltaeedaevLl 83 
                                       ++ l+eg+++  + +++r++  +v+eG+v++      +++++aag  + ++++++++ ta +d+ ++l
  gi|336254660|ref|YP_004597767.1|  35 RLALEEGDEIAPHQHPDREIVFHVLEGRVSItlgdddHDHEVAAGELIRFDGAQDIAPTALADTTAVL 102
                                       6789***************************666655589999*************999999876655 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 ?   13.0   0.0   2.4e-05      0.06      26      56 ..      52      84 ..      45      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                      EEEE.EEEECEEEEEET.TTEEEEEETTEEEEE CS
                           Cupin_3 26 dEfc.yileGevkvtpe.ggetvelraGDlvvl 56
                                       E++ ++leG+v++t   +  ++e+ aG l+++
  gi|336254660|ref|YP_004597767.1| 52 REIVfHVLEGRVSITLGdDDHDHEVAAGELIRF 84
                                      56666**********9425555******99887 PP

>> DUF2917  Protein of unknown function (DUF2917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.9e-05      0.05      13      52 ..      50      89 ..      32      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                           DUF2917 13 aragqeLrvreGrvWvTregdpeDhwLqaGqslrlargqr 52
                                      + +  + +v eGrv +T   d +Dh  +aG+ +r  ++q 
  gi|336254660|ref|YP_004597767.1| 50 PDREIVFHVLEGRVSITLGDDDHDHEVAAGELIRFDGAQD 89
                                      45555556***********************998887776 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.4e-05     0.063      17      51 ..      36      70 ..      33      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.4e-05
                                      EEE-TCCCEEEEE--SEEEEEEEEESEEEEEETTE CS
                          CENP-C_C 17 lkLppgaeKkkknskkatlvFyViqGrvevtvskt 51
                                      l L+ g+e  +++  +  +vF+V++Grv +t+ + 
  gi|336254660|ref|YP_004597767.1| 36 LALEEGDEIAPHQHPDREIVFHVLEGRVSITLGDD 70
                                      567778888888889999*************9875 PP

>> HutD  HutD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.4e-05      0.11     124     174 ..      43      93 ..      23     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.4e-05
                                       EEEEEE.--SEEEEEESSS-EEEEETTE..EEEE-TT-EEEEES--EEEEE CS
                              HutD 124 kaaasasgastvllfllkgqlevtlsveaadetlaagdalllegeaalele 174
                                       + a ++++++ +++++l+g++++tl+ +++d+++aag+ ++++g + +  +
  gi|336254660|ref|YP_004597767.1|  43 EIAPHQHPDREIVFHVLEGRVSITLGDDDHDHEVAAGELIRFDGAQDIAPT 93 
                                       445556677888999999999999999999999999999999998844443 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 ?   12.3   0.0   6.6e-05      0.17       4      69 ..      36     105 ..      33     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.6e-05
                                       EEE-TT-EEEEE--TT-EEEEEEEES-EEESSTT....EEE-TTEEEEE-SSSEEEEE--SS-EEEEEEE CS
                           Pirin_C   4 ltleagaelelplpegleaavyvleGelevgger....seieeeqlavlgdgdslvvkaeekgarvlLla 69 
                                       l le+g e++    ++ e +  vleG++++   +    +e+++++l+ ++  +++  +a ++++ vl+la
  gi|336254660|ref|YP_004597767.1|  36 LALEEGDEIAPHQHPDREIVFHVLEGRVSITLGDddhdHEVAAGELIRFDGAQDIAPTALADTTAVLVLA 105
                                       78999****99999*************987644445889******************9999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 856.52
//
Query:       gi|336254661|ref|YP_004597768.1|  [L=224]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-19   68.5   0.4    7.6e-19   67.3   0.0    1.8  2  HTH_10          HTH DNA binding domain
    0.00016   21.8   0.0      0.085   13.0   0.1    2.2  2  HTH_Tnp_1_2     Helix-turn-helix of insertion element transpo
     0.0014   18.5   0.8     0.0034   17.3   0.2    1.9  2  BAT             GAF and HTH_10 associated domain
      0.005   16.7   0.0      0.011   15.6   0.0    1.6  1  PuR_N           Bacterial purine repressor, N-terminal
     0.0061   16.6   0.1      0.013   15.6   0.1    1.5  1  NYD-SP28        Sperm tail
     0.0082   15.9   0.3      0.069   13.0   0.0    2.3  2  HTH_IclR        IclR helix-turn-helix domain
     0.0091   15.5   0.3       0.02   14.4   0.0    1.8  1  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.037   13.9   0.0    1.9  1  MarR_2          MarR family
      0.022   15.0   0.1         19    5.6   0.0    3.4  4  HTH_Tnp_Tc3_2   Transposase
      0.027   14.7   0.0      0.059   13.6   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.058   13.6   0.0       0.11   12.7   0.0    1.5  1  UPF0122         Putative helix-turn-helix protein, YlxM / p13
      0.073   13.1   0.5       0.22   11.6   0.2    1.9  1  HTH_20          Helix-turn-helix domain
      0.079   13.1   0.0       0.19   11.8   0.0    1.6  1  Phage_CI_repr   Bacteriophage CI repressor helix-turn-helix d
        0.1   12.5   0.0       0.25   11.3   0.0    1.7  1  MarR            MarR family
       0.11   12.5   0.0       0.23   11.5   0.0    1.5  1  HTH_35          Winged helix-turn-helix DNA-binding
       0.12   12.5   0.2        5.1    7.3   0.0    2.6  2  PilN            Fimbrial assembly protein (PilN)


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 ?   -1.9   0.0       2.6     3e+03      25      33 ..     120     128 ..     118     129 .. 0.83
   2 !   67.3   0.0   6.8e-22   7.6e-19       1      53 []     150     202 ..     150     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.6
                            HTH_10  25 tlkeLAkel 33 
                                       +l+eLA++l
  gi|336254661|ref|YP_004597768.1| 120 RLAELAEQL 128
                                       6899***98 PP

  == domain 2  score: 67.3 bits;  conditional E-value: 6.8e-22
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       L+++qlev+++A+e+GY+d+PR+++l eLA+ l+I+kst se L +ae+ +i+
  gi|336254661|ref|YP_004597768.1| 150 LSERQLEVVAAAVEKGYYDTPRQCSLTELAEHLDIAKSTCSETLHRAEEAIIK 202
                                       89***********************************************9985 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 !    6.8   0.0    0.0062         7      29      57 ..      55      83 ..      51     112 .. 0.88
   2 !   13.0   0.1   7.6e-05     0.085       7      45 ..     146     191 ..     140     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0062
                                      HHHHHHHHTS-HHHHHHHHH-HHHHHHHH CS
                       HTH_Tnp_1_2 29 ldeiaeevgvsrsTlykWkkkkeFieyvn 57
                                      +d+++e+ ++ + Tl +W ++++ +++  
  gi|336254661|ref|YP_004597768.1| 55 VDDMTEHPQITELTLAQWSDNEATVHFET 83
                                      589******************99998865 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.6e-05
                                       H...S-HHHHHHHHHHHHHHH....--S-HHHHHHHHTS-HHHHHH CS
                       HTH_Tnp_1_2   7 e...LtakQkkaaellvendy....ekltldeiaeevgvsrsTlyk 45 
                                       e   L+++Q+ ++   ve+ y     + +l+e+ae++ +++sT  +
  gi|336254661|ref|YP_004597768.1| 146 EsqlLSERQLEVVAAAVEKGYydtpRQCSLTELAEHLDIAKSTCSE 191
                                       44559*****************99999**************99755 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2     3e-06    0.0034      19     116 ..      18     114 ..       3     130 .. 0.73
   2 ?   -2.0   0.0       2.7     3e+03     126     145 ..     137     156 ..     135     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3e-06
                               BAT  19 alaae.ldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtlleltvsgpslastla 94 
                                       +l++e  d+++++   vp sd ++ ++++++g ++ e++d  +++++++++++ + +d+++++ ++++ p l    +
  gi|336254661|ref|YP_004597768.1|  18 QLSTEyPDATFRVLAGVPGSDTGF-ALVRIAGSKVPEIVDDMTEHPQITELTLAQWSDNEATVHFETTAPLL-LFSS 92 
                                       5555526999********999877.99*****999999999999**********************966655.5444 PP

                               BAT  95 ehGgtvrsaeaedgrarlvvev 116
                                       +  g++ ++ +e  +++ ++ev
  gi|336254661|ref|YP_004597768.1|  93 QESGMPIELPVEIADGEATIEV 114
                                       4455555554444444444444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
                               BAT 126 vealeerypdveLvarrere 145
                                       ++ ++er  + +L++ r+ e
  gi|336254661|ref|YP_004597768.1| 137 IDNVRERLHESQLLSERQLE 156
                                       57899999999999999866 PP

>> PuR_N  Bacterial purine repressor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.9e-06     0.011      17      49 ..     170     201 ..     159     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.9e-06
                             PuR_N  17 PnklisltyfaerfeaAKSsiSeDlaiikeale 49 
                                       P +++slt++ae++++AKS+ Se l+  +ea+ 
  gi|336254661|ref|YP_004597768.1| 170 P-RQCSLTELAEHLDIAKSTCSETLHRAEEAII 201
                                       4.4689*****************9987777665 PP

>> NYD-SP28  Sperm tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.1e-05     0.013      29      85 ..     153     210 ..     134     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                          NYD-SP28  29 ksseekfeeinekWreilrknkpqeLrkeleeqkqaceelideK.dklikelqeeLke 85 
                                       ++ e   +++++ +  + r++   eL ++l++ k++c+e +++  +++ik++ e+L  
  gi|336254661|ref|YP_004597768.1| 153 RQLEVVAAAVEKGYYDTPRQCSLTELAEHLDIAKSTCSETLHRAeEAIIKRFVEDLPG 210
                                       333333456677777999************************9867899*****9965 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 ?   -0.0   0.1       0.7   7.8e+02      20      28 ..     120     128 ..     115     129 .. 0.81
   2 !   13.0   0.0   6.2e-05     0.069      15      37 ..     169     191 ..     158     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.7
                                       BHHHHHHHH CS
                          HTH_IclR  20 tlselArrt 28 
                                       +l+elA+++
  gi|336254661|ref|YP_004597768.1| 120 RLAELAEQL 128
                                       79*****97 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.2e-05
                                       TBSS-BHHHHHHHHTS-HHHHHH CS
                          HTH_IclR  15 apqeltlselArrtglpkStvhR 37 
                                       +p+  +l+elA++++++kSt + 
  gi|336254661|ref|YP_004597768.1| 169 TPRQCSLTELAEHLDIAKSTCSE 191
                                       57778***************765 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 !   14.4   0.0   1.8e-05      0.02      15      43 ..     169     198 ..     166     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                            HTH_24  15 npr.isqreLAerlglSpstvnrrlkrLee 43 
                                        pr +s +eLAe+l++ +st+++ l r ee
  gi|336254661|ref|YP_004597768.1| 169 TPRqCSLTELAEHLDIAKSTCSETLHRAEE 198
                                       67779*****************97766665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.3e-05     0.037      20      48 ..     171     199 ..     157     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                                       SEEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2  20 rdltvgelarrlglsksavsrilkrLvaa 48 
                                       r ++ +ela++l++ ks+ s +l r+++a
  gi|336254661|ref|YP_004597768.1| 171 RQCSLTELAEHLDIAKSTCSETLHRAEEA 199
                                       45799*********************987 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.8   6.5e+03       4      20 ..      16      32 ..      16      35 .. 0.85
   2 ?    0.5   0.0      0.63   7.1e+02       3      35 ..      53      84 ..      52      89 .. 0.78
   3 ?    5.6   0.0     0.017        19      16      48 ..     121     153 ..     118     159 .. 0.85
   4 ?    3.9   0.0     0.056        63      12      42 ..     171     196 ..     165     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.8
                     HTH_Tnp_Tc3_2  4 IvrlvrkdPritlreLa 20
                                      I +l ++ P +t+r La
  gi|336254661|ref|YP_004597768.1| 16 IQQLSTEYPDATFRVLA 32
                                      77899999999999886 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.63
                     HTH_Tnp_Tc3_2  3 rIvrlvrkdPritlreLanelkeeGksvsreTi 35
                                      +Iv  +++ P+it   La+ + +++ +v+ eT 
  gi|336254661|ref|YP_004597768.1| 53 EIVDDMTEHPQITELTLAQWS-DNEATVHFETT 84
                                      588899999***999998877.55777777775 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.017
                     HTH_Tnp_Tc3_2  16 lreLanelkeeGksvsreTirrrLrkaglkkrk 48 
                                       l+eLa++l++ G + +   +r rL++++l + +
  gi|336254661|ref|YP_004597768.1| 121 LAELAEQLEHFGLQYRIDNVRERLHESQLLSER 153
                                       5799****777****************997765 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.056
                     HTH_Tnp_Tc3_2  12 PritlreLanelkeeGksvsreTirrrLrka 42 
                                       ++ +l+eLa++l      + ++T + +L++a
  gi|336254661|ref|YP_004597768.1| 171 RQCSLTELAEHL-----DIAKSTCSETLHRA 196
                                       779*********.....77777777777765 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 ?   13.6   0.0   5.2e-05     0.059      24      47 ..     174     197 ..     168     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.2e-05
                                       -HHHHHHHHTS-HHHHHHHHHHHH CS
                    Fe_dep_repress  24 ktkdlaerLnvspssVsemlkkLe 47 
                                       + ++lae L++++s+ se+l + e
  gi|336254661|ref|YP_004597768.1| 174 SLTELAEHLDIAKSTCSETLHRAE 197
                                       5689****************9966 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001      0.11      16      64 ..     148     204 ..     142     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                           UPF0122  16 sLLTekqanylel.....yyad..DlSlsEiAeefnvsrqavydnikrtek.lleky 64 
                                       +LL e+q +++       yy+     Sl+E+Ae+ ++ +++ +++++r+e+ +++++
  gi|336254661|ref|YP_004597768.1| 148 QLLSERQLEVVAAavekgYYDTprQCSLTELAEHLDIAKSTCSETLHRAEEaIIKRF 204
                                       67888888776432222377643378**********************986145555 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00019      0.22      22      46 ..     170     194 ..     148     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                                       CTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  22 aegltaselaerldlskntlsyHLr 46 
                                       ++  +++elae ld++k+t+s  L+
  gi|336254661|ref|YP_004597768.1| 170 PRQCSLTELAEHLDIAKSTCSETLH 194
                                       56789****************9996 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 ?   11.8   0.0   0.00017      0.19      16      33 ..     176     193 ..     173     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                                       HHHHCCTT--HHHHHHHH CS
                     Phage_CI_repr  16 keLAdlLgiakssvstwv 33 
                                        eLA++L+iaks+ s   
  gi|336254661|ref|YP_004597768.1| 176 TELAEHLDIAKSTCSETL 193
                                       59***********99655 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00023      0.25      17      40 ..     172     195 ..     167     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                                       TEEHHHHHHHHTS-HHHHHHHHHH CS
                              MarR  17 plsvseLakklgvskstvtrvldr 40 
                                       ++s++eLa++l + kst +++l+r
  gi|336254661|ref|YP_004597768.1| 172 QCSLTELAEHLDIAKSTCSETLHR 195
                                       599******************998 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.23      14      39 ..     171     196 ..     156     207 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                            HTH_35  14 rgttLaalsreaglssstlsnaltrp 39 
                                       r+ +L++l++++++++st+s++l+r 
  gi|336254661|ref|YP_004597768.1| 171 RQCSLTELAEHLDIAKSTCSETLHRA 196
                                       889*********************96 PP

>> PilN  Fimbrial assembly protein (PilN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0046       5.1       6      25 ..       6      40 ..       3      87 .. 0.65
   2 ?    2.6   0.0      0.13   1.5e+02      26      63 ..     112     162 ..      92     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0046
                              PilN  6 LsravPkgvwltsisqegn...............q 25
                                      L+ ++P+++w++++s e                 +
  gi|336254661|ref|YP_004597768.1|  6 LTVTMPDQLWIQQLSTEYPdatfrvlagvpgsdtG 40
                                      8889**********988765555555555555551 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                              PilN  26 ltitGsAvsndeVaefmrnLeg................spffknidlksaeqkt 63 
                                       +++tG   s d++ae+ ++Le                 s+++++ +l+ + ++ 
  gi|336254661|ref|YP_004597768.1| 112 IEVTG---SRDRLAELAEQLEHfglqyridnvrerlheSQLLSERQLEVVAAAV 162
                                       44444...5599999999999888888888888888888888888887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 1826.75
//
Query:       gi|336254662|ref|YP_004597769.1|  [L=74]
Description: hypothetical protein Halxa_3278 [Halopiger xanaduensis SH-6]
Scores for 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-19   68.1   0.1    5.2e-19   67.9   0.1    1.0  1  DUF2249   Uncharacterized conserved protein (DUF2249)
    0.00037   20.3   0.0    0.00051   19.8   0.0    1.4  1  TusA      Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.1   5.8e-23   5.2e-19       1      69 [.       9      72 ..       9      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 5.8e-23
                           DUF2249  1 tlDvRelppperhaaIfeafeaLapGetlelvndhdPkpLlyqLearrpgffsweylergpgewrvlit 69
                                      tlDvRe+  + ++  I++a+++L +Ge+lel+++++PkpL+++Le r  g+ ++e ++r+ g+w+vli+
  gi|336254662|ref|YP_004597769.1|  9 TLDVREI-DGPPFDDIMSALRTLNAGERLELIAPFEPKPLYNVLESR--GY-TYESEQRD-GVWHVLIE 72
                                      79*****.566************************************..**.99986665.59***996 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.7e-08   0.00051      17      69 ..      23      72 ..       8      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.7e-08
                                      HHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEE CS
                              TusA 17 lkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivir 69
                                      ++ al++l++ge+le++a  ++  + + + ++++g++  e e++dg+++++i+
  gi|336254662|ref|YP_004597769.1| 23 IMSALRTLNAGERLELIAPFEP--KPLYNVLESRGYT-YESEQRDGVWHVLIE 72
                                      6789**************9886..78**********9.77789********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 578.92
//
Query:       gi|336254663|ref|YP_004597770.1|  [L=77]
Description: hypothetical protein Halxa_3279 [Halopiger xanaduensis SH-6]
Scores for 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-26   90.5   0.9    5.1e-26   90.3   0.9    1.0  1  DUF2249   Uncharacterized conserved protein (DUF2249)


Domain annotation for each model (and alignments):
>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.9   2.9e-30   5.1e-26       2      70 .]       4      74 ..       3      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 2.9e-30
                           DUF2249  2 lDvRelppperhaaIfeafeaLapGetlelvndhdPkpLlyqLearr..pgffsweylergpgewrvlitk 70
                                      lDvR++pp +rh++I+e+fe+LapGetl++vndh+PkpL+y+++a++  ++++++e+++ gp+e+++++ k
  gi|336254663|ref|YP_004597770.1|  4 LDVRDIPPVNRHPTIHEEFEDLAPGETLTIVNDHEPKPLFYEFQAEVesFDADNYEVERVGPEEFVAKFPK 74
                                      9**********************************************999999*************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 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:                        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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 613.03
//
Query:       gi|336254664|ref|YP_004597771.1|  [L=91]
Description: hypothetical protein Halxa_3280 [Halopiger xanaduensis SH-6]
Scores for complete 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-13   50.2   0.2    2.1e-13   49.9   0.2    1.1  1  DUF2249   Uncharacterized conserved protein (DUF2249)
     0.0052   16.6   0.0     0.0077   16.0   0.0    1.3  1  TusA      Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.2   2.3e-17   2.1e-13       1      66 [.      21      84 ..      21      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 2.3e-17
                           DUF2249  1 tlDvRelppperhaaIfeafeaLapGetlelvndhdPkpLlyqLearrpgffsweylergpge.wrv 66
                                      t+DvR l ppe++++++e++ +L +  +l+  nd+ P++L++ Le+r  g+ ++e +e + ++ +++
  gi|336254664|ref|YP_004597771.1| 21 TIDVRSLGPPEPLKRTLETLVDLSDETVLVQRNDRVPQFLFPKLEDR--GY-AHESVELEGEDeVVT 84
                                      79*********************************************..**.777777665551544 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.6e-07    0.0077       1      62 [.      20      80 ..      20      87 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.6e-07
                                      EEEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-..GCC CS
                              TusA  1 ielDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelvevee..edg 62
                                      +++D+r l  PePl +++++l  l ++ vl v  +d+ + + +   ++ +g++ ++ve   e +
  gi|336254664|ref|YP_004597771.1| 20 ETIDVRSLGPPEPLKRTLETLVDLSDETVL-VQRNDRVP-QFLFPKLEDRGYAHESVELegE-D 80
                                      58*********************9887777.88888876.5666668889998888866433.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.31u 0.21s 00:00:00.52 Elapsed: 00:00:00.34
# Mc/sec: 796.75
//
Query:       gi|336254665|ref|YP_004597772.1|  [L=304]
Description: Soluble epoxide hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-25   88.3   0.1      2e-24   86.7   0.1    1.7  1  Abhydrolase_1  alpha/beta hydrolase fold
      3e-20   73.8  12.2    3.8e-20   73.4  12.2    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.2e-12   47.7   0.1    9.2e-12   44.7   0.1    1.9  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.089   12.9   0.0       0.12   12.4   0.0    1.3  1  Thioesterase   Thioesterase domain


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 !   86.7   0.1   4.4e-28     2e-24       1     257 []      43     290 ..      43     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 4.4e-28
                                       SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEE CS
                     Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltl 77 
                                       p++v+lhG+p+ ++ w+e   +  L ++g++v+++D+rG+  S+++       y+   + +d+  +  + + d  ++
  gi|336254665|ref|YP_004597772.1|  43 PLVVLLHGFPEFWYGWHE--QIGPLVDAGYRVLVPDQRGYNLSEKPAPV--RAYHQKQLSRDIVELIGSADRDAAHV 115
                                       78****************..66677777*******************97..89************************ PP

                                       EEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHH CS
                     Abhydrolase_1  78 vGhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqr 154
                                       vGh++GGm+a+ +a+++ e V++l+ ++a    +++   qr+ + ++  + + ++a+c++ p  p l+ ++   ++ 
  gi|336254665|ref|YP_004597772.1| 116 VGHDWGGMVAWDLALRHHEVVDRLAIVNA----PHPTVFQRHLRSNPAQMRRSWYAACFQVPRLPELCCRYDDFRLL 188
                                       *****************************....99*********************************999999999 PP

                                       HHHHHHHHHHCHHHCCHHHHHHHCHHHHHHH....HHHHHHHHHCCHHHHHHHHHC..THHHHSEEEEEEETTCSSS CS
                     Abhydrolase_1 155 hrlvdalkfpdkskrfpssgsdnasslatga....lksieqwpttdsaklllrlre..lknvlaptlvisgtsDplv 225
                                        r++     + +s     s+ d +++  +++    l ++  w+    ++      +   + v aptl+ +gt+D + 
  gi|336254665|ref|YP_004597772.1| 189 ERAL-----RGTSAPGTFSDADLEHYRRAWSrdgaLTAMINWYRASARYGT----NppRDRVEAPTLLAWGTDDAAL 256
                                       8887.....444444444444444444444300003333333333333333....244468999************* PP

                                       CHHHHHHHHHCHTS..EEEEEEETCSSSHHHHSH CS
                     Abhydrolase_1 226 ppkaledlaqllpk..krlvvisdagHlaflegp 257
                                         +  +d+ + + +   rl+ ++++ H+++ e+p
  gi|336254665|ref|YP_004597772.1| 257 GTELVVDSYDYCARegRRLELFEGTSHWVQHEEP 290
                                       *999999999988888**************9986 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4  12.2   8.5e-24   3.8e-20       1     218 [.      45     294 ..      45     296 .. 0.62

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 8.5e-24
                                       EEEE--GC.....GC..HHHHHHHHCCTCEEEEE--TTS.TS-GGCS--HHHC......HHHHHHHCCTT..TTSEE CS
                     Abhydrolase_6   1 vlllHGagssassWl..vapLaallaagvhvlapDlpGh.Grsdpppldledl......adlaalldelaagggpvv 68 
                                       v+llHG++   + W+  + ++ +l  ag++vl+pD +G+    + +p  ++++      +d+++l+ +   ++++++
  gi|336254665|ref|YP_004597772.1|  45 VVLLHGFP---EFWYgwHEQIGPLVDAGYRVLVPDQRGYnL--SEKPAPVRAYhqkqlsRDIVELIGSA--DRDAAH 114
                                       8*****99...6665557899******************54..55555554433322235556666666..58888* PP

                                       EEEETCHHHHHHHHHHCC.......EE.EEES-..----TTTS----TTHHHHHH.......TT-C.......CCCH CS
                     Abhydrolase_6  69 lvGHSlGGalalaaapla.....lvvg.vlldppptalpagllaaalelllalla.......llrl.......lawl 125
                                       +vGH++GG++a+    la     +v +  ++++p +++  + l+  ++++++ +        +  l       + ++
  gi|336254665|ref|YP_004597772.1| 115 VVGHDWGGMVAWD---LAlrhheVVDRlAIVNAPHPTVFQRHLRSNPAQMRRSWYaacfqvpR--LpelccryDDFR 186
                                       *************...44444566666777777554555555555555555555545544431..234566663333 PP

                                       CCH......S-HSCCCCHHHCCCCHCHCCCGHHHHCCHHCHTT.......CCHHTT-TTGCEEECTT-C.......H CS
                     Abhydrolase_6 126 sre......plprlfladedadaawrarlarlaallaglgllp.......aaawadlpvpllvlggeDp.......l 182
                                        +e      ++p +f + +   +++r++++r  al+a+  +++        ++  ++ +p+l+ +g+D+       +
  gi|336254665|ref|YP_004597772.1| 187 LLEralrgtSAPGTFSDADL--EHYRRAWSRDGALTAMINWYRasarygtNPPRDRVEAPTLLAWGTDDaalgtelV 261
                                       22233556666667777666..9999999999988887776653222221224444444445547666657555432 PP

                                       HHHCHHCCCH...STTEEETCE...SSS-HHHHSHHHHH CS
                     Abhydrolase_6 183 vprllerlla...qagarlpvvlpgaGHlphleepdeva 218
                                             +      ++g+rl ++++g++H+++ eep+++ 
  gi|336254665|ref|YP_004597772.1| 262 -----VDSYDycaREGRRL-ELFEGTSHWVQHEEPERLT 294
                                       .....333334458999**.***************8765 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.1   2.1e-15   9.2e-12       3     238 ..      41     289 ..      39     290 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.1e-15
                       Hydrolase_4   3 pkavvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelpl 78 
                                       ++ +vvl+HG+ e     +e +  L+++G+ v+  D+rG+  se ++ ++  + +++ +D+ +++  +     +   
  gi|336254665|ref|YP_004597772.1|  41 NDPLVVLLHGFPEFWYGWHEQIGPLVDAGYRVLVPDQRGYNLSEkPAPVRAYHQKQLSRDIVELIGSAD----RDAA 113
                                       5679****************************************9888999999*******99998877....3446 PP

                       Hydrolase_4  79 fllGhSmGGliallyllrypdkva.glilsaPalkikaklk.appllklllkllgkllpklqv.............. 139
                                        ++Gh +GG++a  ++lr+++ v+  +i+ aP   + ++    +p++   + + + +++  ++              
  gi|336254665|ref|YP_004597772.1| 114 HVVGHDWGGMVAWDLALRHHEVVDrLAIVNAPHPTVFQRHLrSNPAQMR-RSWYAACFQVPRLpelccryddfrlle 189
                                       78*******************9**6667777765554443223333333.222222222222256888999999998 PP

                       Hydrolase_4 140 .snnlkadslsrdpevvaayeadplvhgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelye 215
                                          +  ++  +   + ++ y++     g++t+ + +    a   ++   +++++P+ll  G++D     e   + y+
  gi|336254665|ref|YP_004597772.1| 190 rALRGTSAPGTFSDADLEHYRRAWSRDGALTAMINWYRASARYGTNPPRDRVEAPTLLAWGTDDAALGTELVVDSYD 266
                                       74455555556666777888888888888888777777777777888889999************************ PP

                       Hydrolase_4 216 rlgskdktlklypglyHellnEp 238
                                        ++++  +l+l++g  H + +E+
  gi|336254665|ref|YP_004597772.1| 267 YCAREGRRLELFEGTSHWVQHEE 289
                                       *****************998885 PP

>> Thioesterase  Thioesterase 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      0.12      58     120 ..     103     162 ..      73     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.8e-05
                                       HHHHH-SSSSEEEEEETHHHHHHHHHHHHHHHCT-SEEEEEEESCCCCCCHHCHHCCCHTTHH CS
                      Thioesterase  58 alrqiqpegPyalfGhSlGgllAfevArqLesqGlavkslflidssapseteaqeasrraede 120
                                       +l  + +++  +++Gh  Gg++A ++A +     + v +l ++ +++p + +++ +s+ a+++
  gi|336254665|ref|YP_004597772.1| 103 ELIGSADRDAAHVVGHDWGGMVAWDLALRH---HEVVDRLAIVNAPHPTVFQRHLRSNPAQMR 162
                                       55667778899****************875...568999999999999999999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2189.24
//
Query:       gi|336254666|ref|YP_004597773.1|  [L=369]
Description: copper-containing nitrite reductase [Halopiger xanaduensis SH-6]
Scores for 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   38.5   0.0    2.3e-09   37.3   0.0    1.6  2  Cu-oxidase_3  Multicopper oxidase
    1.4e-06   28.0   0.0    5.1e-06   26.3   0.0    2.0  2  Cu-oxidase_2  Multicopper oxidase
     0.0046   16.7   0.2      0.011   15.5   0.2    1.7  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
  ------ inclusion threshold ------
      0.015   15.7   0.2      0.054   14.0   0.0    2.0  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
       0.09   12.9   0.0       0.17   12.0   0.0    1.5  1  Cupredoxin_1  Cupredoxin-like domain


Domain annotation for each model (and alignments):
>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   6.4e-13   2.3e-09       4     118 ..      86     199 ..      83     200 .. 0.83
   2 ?   -3.1   0.0       2.2   7.8e+03      29      44 ..     259     274 ..     237     296 .. 0.59

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 6.4e-13
                                       EEEEECTTEESEEEEEECTSSBS-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSCS.GGG-B-TT- CS
                      Cu-oxidase_3   4 ektvsplggterevitvNgqfpgptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpgv.tqcpiqpge 79 
                                       + t++++ g++ + +t+ gq+pgp ++vr+gd+v +++  +++e+t +  h ++ ++     G+ g+     ++pg+
  gi|336254666|ref|YP_004597773.1|  86 RVTAEIEPGVTFDYMTFEGQVPGPMVRVRKGDRVNLTF--EVPEETNLEAHNVDFHAV---YGPGGGaEATTVAPGD 157
                                       56777788888999******************987776..79***********99998...4554440456678865 PP

                                       E.EEEEEE--S-SEEEEEEE--TT..HHH.TT-EEEEEEE-HH CS
                      Cu-oxidase_3  80 s.ftyrftvkqqagtlwYhshlsl..qqa.aGlaGaiiiedke 118
                                       +  + +ft++  ag + Yh  + +  q+  aG++G+i++e++e
  gi|336254666|ref|YP_004597773.1| 158 EpAEISFTAEY-AGAFVYHCAIPNmdQHIsAGMFGTILVEPEE 199
                                       52889*****9.*******99988887778**********986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.2
                                       EEEETT-EEEEEEEE- CS
                      Cu-oxidase_3  29 ievregdtvvvnvtNk 44 
                                       +e++ g+t +v + N 
  gi|336254666|ref|YP_004597773.1| 259 MEAEVGETARVYFANG 274
                                       4445555555555554 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.4e-09   5.1e-06      30     136 ..     106     198 ..      69     199 .. 0.72
   2 ?   -3.2   0.0       1.8   6.4e+03      34      56 ..     258     284 ..     232     285 .. 0.58

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.4e-09
                                       TSSEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEEEEEE CS
                      Cu-oxidase_2  30 entnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwvairfk 106
                                          ++++++kg++v ++++ ++++   +  H +df  +  gpg               +   t+  p+++ + i f+
  gi|336254666|ref|YP_004597773.1| 106 VPGPMVRVRKGDRVNLTFEVPEET--NLEAHNVDFHAV-YGPGG--------------GAEATTVAPGDEPAEISFT 165
                                       556777788888888888887777..455677777777.44444..............56889999*********** PP

                                       S.S-EEEEEEESSH...HHHHTT-EEEEEEECH CS
                      Cu-oxidase_2 107 adnpGvwllHCHil...wHldqGmalqfvvrpd 136
                                       a+++G++++HC i    +H ++Gm ++++v+p+
  gi|336254666|ref|YP_004597773.1| 166 AEYAGAFVYHCAIPnmdQHISAGMFGTILVEPE 198
                                       ***********987777************9986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.8
                                       EEEEETTEEEEEEEEE-SSS....-EE CS
                      Cu-oxidase_2  34 vitlpkgevveiviqnntkl....pHP 56 
                                       +++++ ge+ ++++ n ++      HP
  gi|336254666|ref|YP_004597773.1| 258 AMEAEVGETARVYFANGGPNftsaLHP 284
                                       345555777778777766655444566 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   3.2e-06     0.011       3      24 ..       7      27 ..       6      29 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.2e-06
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggca 24
                                      +RR+F+++ +A++  a  +gc+
  gi|336254666|ref|YP_004597773.1|  7 NRRQFMQALGATGVVA-IAGCL 27
                                      8***********9666.66665 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 ?   14.0   0.0   1.5e-05     0.054      18      99 .]     110     196 ..      89     196 .. 0.77
   2 ?   -1.6   0.1         1   3.7e+03      47      73 ..     226     252 ..     212     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                                       EEEEETTEEEEEEEE.....SSSSBEEEEET.TSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEET.T. CS
                       Copper-bind  18 eitvkkgekvtfvnl.....avmgHNvvldk.dgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCs.P. 86 
                                        ++v kg+ v+ +       +  +HNv +++  g   g++++ v ++de        + s t + ag++ ++C+ P 
  gi|336254666|ref|YP_004597773.1| 110 MVRVRKGDRVNLTFEvpeetNLEAHNVDFHAvYGPGGGAEATTVAPGDEP------AEISFTAEYAGAFVYHCAiPn 180
                                       588999999887666677889999****9995233346777788887655......566666678999*******99 PP

                                       ...TTTTTSEEEEEEE CS
                       Copper-bind  87 ...HaaagMkgkvtve 99 
                                          H +agM g++ ve
  gi|336254666|ref|YP_004597773.1| 181 mdqHISAGMFGTILVE 196
                                       999**********986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                                       TTTGGGTTSCTTCEEEEBSTTEEEEEE CS
                       Copper-bind  47 pagvdkdkvkaedetkliggGekdsvt 73 
                                       ++ +d d +k ed t+++ +G+++ +t
  gi|336254666|ref|YP_004597773.1| 226 HHAFDFDGMKTEDPTYVVFNGQAYGLT 252
                                       445677778888899999999998776 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.7e-05      0.17      37      96 ..     111     180 ..      75     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.7e-05
                      Cupredoxin_1  37 ievkagekvklkiknkdktp...eefesed......lgeekvlapgkt.ttitiaplkpGeYeftcdmhm 96 
                                       + v +g +v l+++   +t    +++ ++         e +++apg++ ++i ++++++G + ++c + +
  gi|336254666|ref|YP_004597773.1| 111 VRVRKGDRVNLTFEVPEETNleaHNVDFHAvygpggGAEATTVAPGDEpAEISFTAEYAGAFVYHCAIPN 180
                                       7899**************95555999999999999866778888886539****************9644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2718.64
//
Query:       gi|336254667|ref|YP_004597774.1|  [L=44]
Description: hypothetical protein Halxa_3283 [Halopiger xanaduensis SH-6]
Scores for 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-05   22.2   1.2    0.00013   21.7   1.2    1.3  1  VATC      Vms1-associating treble clef domain


Domain annotation for each model (and alignments):
>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   1.2   7.2e-09   0.00013       3      32 ..       2      40 ..       1      42 [. 0.90

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.2e-09
                              VATC  3 vlrCsiCgesleg.........kvyFekfdfrYCstkCl 32
                                      +++C+ C ++ e           ++ e+ d  +Cst+Cl
  gi|336254667|ref|YP_004597774.1|  2 HRECDNCESESEIaytltthvaSEPNERIDLHFCSTECL 40
                                      799*****9999778999987778**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 371.44
//
Query:       gi|336254668|ref|YP_004597775.1|  [L=325]
Description: transcription initiation factor IIB [Halopiger xanaduensis SH-6]
Scores for 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-40  135.8   0.0    7.7e-19   67.5   0.0    2.2  2  TFIIB           Transcription factor TFIIB repeat
    1.1e-15   56.8   2.6    2.3e-15   55.8   2.6    1.6  1  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.015   15.3   0.5      0.026   14.6   0.5    1.3  1  DZR             Double zinc ribbon
       0.03   14.2   1.7      0.056   13.4   1.3    1.7  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.058   12.9   6.0       0.11   12.1   0.0    3.8  4  Sigma70_r4      Sigma-70, region 4
        0.1   11.6   0.2       0.19   10.7   0.2    1.3  1  YopD            YopD protein
       0.61   10.5   3.7        4.5    7.8   0.2    2.8  3  zf-IS66         zinc-finger binding domain of transposase IS6
        1.2    9.3   5.6        2.7    8.2   0.9    2.4  2  Zn-ribbon_8     Zinc ribbon domain
        1.2    8.7   3.7         10    5.7   3.6    2.1  1  zf-ribbon_3     zinc-ribbon domain
        1.2    9.2   4.0        3.6    7.7   4.0    1.8  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


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 !   66.3   0.0     1e-21   1.8e-18       1      71 []     145     215 ..     145     215 .. 0.98
   2 !   67.5   0.0   4.3e-22   7.7e-19       1      71 []     239     309 ..     239     309 .. 0.99

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 1e-21
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i r+a+al+Lpe V++ A  ++++alee++l Grs +g+  A+ly A+r++++ r++ ei +v++V++ +i
  gi|336254668|ref|YP_004597775.1| 145 IDRMASALGLPENVRETASVIYRRALEEDLLPGRSIEGVSTASLYAAARQAGTPRSLDEIDAVSRVEKDEI 215
                                       789****************************************************************9987 PP

  == domain 2  score: 67.5 bits;  conditional E-value: 4.3e-22
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rfa+ l+Lp++ +++A +l+k+a++ ++++G+sp g+aAA++y ++++ ++k tq ++s+v+++se+ti
  gi|336254668|ref|YP_004597775.1| 239 VPRFASDLDLPDETERRARQLLKTAKDSGIHSGKSPVGLAAAAVYAGALLTNEKVTQNDVSEVANISEVTI 309
                                       689******************************************************************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 !   55.8   2.6   1.3e-18   2.3e-15       2      43 .]      30      70 ..      29      70 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 1.3e-18
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      +CP+Cg++ lv D+e++e+vC dCGlV+++  id gpewr+f
  gi|336254668|ref|YP_004597775.1| 30 QCPECGGR-LVSDAEHAETVCDDCGLVVDEGEIDRGPEWRAF 70
                                      8******9.8******************************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.5   1.4e-05     0.026      11      40 ..      27      58 ..      20      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                               DZR 11 darfCseCgtklkavaa..edrCpsCgekvdp 40
                                      + + C+eCg +l + a+  e++C+ Cg  vd+
  gi|336254668|ref|YP_004597775.1| 27 EREQCPECGGRLVSDAEhaETVCDDCGLVVDE 58
                                      5569*******86555578*******988876 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 ?   13.4   1.3   3.1e-05     0.056      30      57 ..      30      57 ..      13      58 .. 0.91
   2 ?   -4.0   0.0       8.2   1.5e+04      10      24 ..     221     235 ..     218     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfead 57
                                      +C+eCg ++  + ++ + +C++Cg++ d
  gi|336254668|ref|YP_004597775.1| 30 QCPECGGRLVSDAEHAETVCDDCGLVVD 57
                                      8***********************9876 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 8.2
                    OrfB_Zn_ribbon  10 ykakeyGikveevnp 24 
                                       y  +e G +v+ ++p
  gi|336254668|ref|YP_004597775.1| 221 YVIRELGLEVQPADP 235
                                       778899999998887 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.6       1.8   3.3e+03       6      48 ..     111     121 ..     108     123 .. 0.54
   2 ?    0.9   0.0      0.18   3.3e+02      34      46 ..     159     171 ..     149     172 .. 0.89
   3 ?   -0.2   0.0      0.41   7.4e+02      33      44 ..     252     263 ..     250     266 .. 0.82
   4 ?   12.1   0.0     6e-05      0.11      18      46 ..     290     318 ..     281     319 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.8
                                       -HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   6 pererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       +                                +++++ +++L
  gi|336254668|ref|YP_004597775.1| 111 S--------------------------------SRQRQKMQRL 121
                                       4................................4555555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHH CS
                        Sigma70_r4  34 rerVrqiekrAlr 46 
                                       re+++ i +rAl+
  gi|336254668|ref|YP_004597775.1| 159 RETASVIYRRALE 171
                                       89*********97 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.41
                                       -HHHHHHHHHHH CS
                        Sigma70_r4  33 SrerVrqiekrA 44 
                                       ++ r+rq++k A
  gi|336254668|ref|YP_004597775.1| 252 TERRARQLLKTA 263
                                       68899**99988 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 6e-05
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlr 46 
                                        e+ T+ +++e+ +iS+ ++r + ++ l+
  gi|336254668|ref|YP_004597775.1| 290 NEKVTQNDVSEVANISEVTIRNRYHELLE 318
                                       5899********************99876 PP

>> YopD  YopD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00011      0.19     177     230 ..      97     150 ..      87     156 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                              YopD 177 kisdkdreaiGkvWkaeqvadksklkaldkafesrnskaqvlnaviqsleqman 230
                                       +i+ +d++a G+   + q +  ++l++ +  f++r+sk + l+ ++  ++ ma 
  gi|336254668|ref|YP_004597775.1|  97 NIGWQDKDAYGRSLSSRQRQKMQRLRTWNERFRTRDSKERNLKQALGEIDRMAS 150
                                       78889*****************************************99999996 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 ?    7.8   0.2    0.0025       4.5       2      11 ..      29      39 ..      28      45 .. 0.76
   2 ?    2.9   0.1      0.08   1.4e+02       1      10 [.      46      54 ..      46      63 .. 0.73
   3 ?   -3.3   0.0       7.1   1.3e+04      18      30 ..     297     309 ..     291     313 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0025
                           zf-IS66  2 rtCpcCGg.ll 11
                                      ++Cp+CGg l+
  gi|336254668|ref|YP_004597775.1| 29 EQCPECGGrLV 39
                                      59******554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.08
                           zf-IS66  1 prtCpcCGgl 10
                                      +++C++CG l
  gi|336254668|ref|YP_004597775.1| 46 ETVCDDCG-L 54
                                      689*****.4 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 7.1
                           zf-IS66  18 rvreeldipPakf 30 
                                       +v+e+  i ++++
  gi|336254668|ref|YP_004597775.1| 297 DVSEVANISEVTI 309
                                       4888887777665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.9    0.0015       2.7      25      36 ..      26      38 ..      14      42 .. 0.68
   2 ?    3.9   0.2     0.032        58      20      33 ..      40      53 ..      37      58 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                       Zn-ribbon_8 25 plta.CPeCgsev 36
                                       + + CPeCg+++
  gi|336254668|ref|YP_004597775.1| 26 GEREqCPECGGRL 38
                                      34444*****955 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.032
                       Zn-ribbon_8 20 sisdapltaCPeCg 33
                                      s ++ ++t+C +Cg
  gi|336254668|ref|YP_004597775.1| 40 SDAEHAETVCDDCG 53
                                      44478899999998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   3.6    0.0058        10       4      24 ..      30      54 ..      28      56 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0058
                       zf-ribbon_3  4 rCPnCGa.plssd...dnvCpyCGt 24
                                      +CP+CG  ++s+     +vC  CG 
  gi|336254668|ref|YP_004597775.1| 30 QCPECGGrLVSDAehaETVCDDCGL 54
                                      6999999887775222589999997 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 ?    7.7   4.0     0.002       3.6       1      20 [.      30      49 ..      30      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.002
                    DNA_ligase_ZBD  1 hCPvCGsavvReegeaiyRC 20
                                      +CP+CG  +v   + a + C
  gi|336254668|ref|YP_004597775.1| 30 QCPECGGRLVSDAEHAETVC 49
                                      5*********9999888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      694  (0.0387082); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2534.00
//
Query:       gi|336254669|ref|YP_004597776.1|  [L=92]
Description: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C [Halopiger xanaduensis SH-6]
Scores for 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-16   59.2   4.7    3.5e-16   59.2   4.7    1.4  2  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
  ------ inclusion threshold ------
      0.048   13.6   0.7      0.062   13.2   0.7    1.2  1  Ferritin     Ferritin-like domain


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 ?   -2.9   0.0         1   9.1e+03      18      27 ..      12      21 ..       7      21 .. 0.58
   2 !   59.2   4.7   3.9e-20   3.5e-16       1      61 [.      22      87 ..      22      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1
                                      HHHTTCGCS- CS
                       Glu-tRNAGln 18 dyveqLqevd 27
                                       +v +L +vd
  gi|336254669|ref|YP_004597776.1| 12 RHVAELARVD 21
                                      3555666555 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 3.9e-20
                                      --HHHHHHHHHHHHHHHHHHTTCGCS--TT----S....-EB-S--.....HHHHHTT-SSEETTEEE CS
                       Glu-tRNAGln  1 lseeEleklakelnsildyveqLqevdttgveplthp..vlReDev.....reelLknApetedgyfv 61
                                      l+++E++++a+++ +il+y+e+L+ev   + e       v+R+De+     +ee+L+nApetedgyf+
  gi|336254669|ref|YP_004597776.1| 22 LEDDEVDQFARQFADILEYFETLDEVPEVDREA--DLanVMRPDEErdsldTEEALRNAPETEDGYFK 87
                                      689************************324443..33567****98899*9999*************8 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7   6.9e-06     0.062      37      93 ..      23      83 ..      11      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.9e-06
                                      HHHHHHHHHHHHHHHHHHHHHTTS....SHH.HHHHC-SSSS..CS.SHHHHHHHHHHHHH CS
                          Ferritin 37 fdeqaeeerehadklaerilalGgtpvltra.eleeieapke..fg.sveevleaalehek 93
                                       d+++++   ++ +++e+  +l+++p ++r  +l+++  p+e  ++ ++ee+l++a e e+
  gi|336254669|ref|YP_004597776.1| 23 EDDEVDQFARQFADILEYFETLDEVPEVDREaDLANVMRPDEerDSlDTEEALRNAPETED 83
                                      5789999999******************9984566677777778778*******9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 707.66
//
Query:       gi|336254670|ref|YP_004597777.1|  [L=423]
Description: glutamyl-tRNA(Gln) amidotransferase subunit A [Halopiger xanaduensis SH-6]
Scores for complete 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-146  489.1   0.3   1.6e-146  488.8   0.3    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 !  488.8   0.3  9.1e-151  1.6e-146      38     450 ..      10     415 ..       4     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 488.8 bits;  conditional E-value: 9.1e-151
                                       TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS--HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-T CS
                           Amidase  38 krargkekgpLhGvPisvKDnidvkgvpttaGskalenypaekDatvverLkkaGavilgkTnmdefamgsstensv 114
                                       +r +g ++gpL+   ++vKDni+++gv+tt+Gs +le+y++++Datvv+rLk+aGa+i+gk+nmdef+mg++te+s+
  gi|336254670|ref|YP_004597777.1|  10 ERIEGADDGPLADATVAVKDNISTEGVRTTCGSAMLEEYVPPYDATVVSRLKEAGATIVGKANMDEFGMGTTTETSA 86 
                                       4447899********************************************************************** PP

                                       T---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEE CS
                           Amidase 115 fgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsfcglvGlKPtygrvSragvvalessldvvG 191
                                       fg+t NP  + r+pGGSSGGsAAavAag ++la+G+DtGGS+R+PA+fcg+vG+KPtyg+vSr+g+va+++sl+++G
  gi|336254670|ref|YP_004597777.1|  87 FGATDNPAAPGRVPGGSSGGSAAAVAAGEADLALGSDTGGSVRCPAAFCGVVGIKPTYGLVSRYGLVAYANSLEQIG 163
                                       ***************************************************************************** PP

                                       EEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEEEEGGGCSS---CCHHHHHHHHHHHHHC CS
                           Amidase 192 plarsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglriGvvkedgvasldpevqravekalkaLee 268
                                       p+a +ved+a+ll+vi+ged++d t+  +  e e++a+++  + +gl iGv++e+  + +d+ v + + +a++ Le+
  gi|336254670|ref|YP_004597777.1| 164 PFANTVEDAAALLDVIAGEDERDATTREPQLEGESYAAAATADVDGLTIGVPTELL-EGADEGVVETFWDAIADLED 239
                                       ***************************97789999********************9.7******************* PP

                                       TT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS.---SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHC CS
                           Amidase 269 aGhevvevelpsleealslyylilvaeassnlarylgvry.erlsetkvlsellpksraellgeevkrrielgnyal 344
                                        G+e  ev+lps+e+a+++yy i+++eassnlar++gvry +    + +++e ++k r+e++g+evkrri lg+yal
  gi|336254670|ref|YP_004597777.1| 240 RGAEYHEVSLPSVEHAVEAYYVIAMSEASSNLARFDGVRYgNSGGYDGNWNEAFSKARQEGFGDEVKRRILLGTYAL 316
                                       ****************************************999999999**************************** PP

                                       SCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHHHHHGCCTTT...HHHHHTT-- CS
                           Amidase 345 saeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktidsytvlynlldftavvvpvnlaglp 421
                                       sa++ +kyy++aq +r+ ++++f++a+ e Dvl+sPt+p p+++lge     d+++ +y+ ++ t   vpvnla+lp
  gi|336254670|ref|YP_004597777.1| 317 SAGYHDKYYKQAQDARAWVKQDFDEALSEADVLASPTMPVPPFELGESL---DDPLQMYLADANT---VPVNLADLP 387
                                       ***********************************************98...89***********...********* PP

                                       EEEEECCCCT.TECEEEEEEESTT-HHHH CS
                           Amidase 422 alsvpagksedglPvGvqvigkafqeetl 450
                                       a+svpag+++ glPvG+q++g+af ee+l
  gi|336254670|ref|YP_004597777.1| 388 AISVPAGETD-GLPVGLQLVGPAFGEERL 415
                                       ********96.****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3250.90
//
Query:       gi|336254671|ref|YP_004597778.1|  [L=138]
Description: hypothetical protein Halxa_3287 [Halopiger xanaduensis SH-6]
Scores for 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:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 956.41
//
Query:       gi|336254672|ref|YP_004597779.1|  [L=119]
Description: hypothetical protein Halxa_3288 [Halopiger xanaduensis SH-6]
Scores for 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-05   22.7   0.0    9.7e-05   22.2   0.0    1.2  1  MarR            MarR family
    0.00013   21.8   0.0    0.00021   21.1   0.0    1.4  1  MarR_2          MarR family
    0.00084   19.2   0.0     0.0011   18.8   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0012   19.0   0.0     0.0016   18.5   0.0    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
     0.0055   17.2   0.0     0.0073   16.8   0.0    1.2  1  HTH_27          Winged helix DNA-binding domain
  ------ inclusion threshold ------
       0.15   11.9   0.0        0.2   11.5   0.0    1.2  1  DUF1495         Winged helix DNA-binding domain (DUF1495)
       0.16   11.6   0.0       0.27   10.8   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding


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 !   22.2   0.0   3.8e-08   9.7e-05       7      50 ..      19      62 ..      13      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.8e-08
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                        L++++e g++ +s+ +k lgvs+   +r++  L++kGl++R+
  gi|336254672|ref|YP_004597779.1| 19 AGLELVRETGGIHQSDFWKELGVSSRKGSRIVESLVEKGLVDRE 62
                                      67999**************************************7 PP

>> MarR_2  MarR family
   #    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      14      55 ..      24      63 ..      13      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.1e-08
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      ++  +g  + +++  ++lg+s    sri++ Lv++GLv r++
  gi|336254672|ref|YP_004597779.1| 24 VRETGG--IHQSDFWKELGVSSRKGSRIVESLVEKGLVDREE 63
                                      444445..999****************************996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.2e-07    0.0011      16      58 ..      22      65 ..      10      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.2e-07
                                      HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       L+ + g    ++  +elgv+  k  ++++sL++kGlV+re+  
  gi|336254672|ref|YP_004597779.1| 22 ELVrETGGIHQSDFWKELGVSSRKGSRIVESLVEKGLVDREETI 65
                                      5666788888889999************************9865 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 !   18.5   0.0   6.4e-07    0.0016      17      65 ..      28      72 ..      21      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.4e-07
                    B-block_TFIIIC 17 sGitqsdLakeskqdprslfyrlksLekkgLIvkqsiidsatkksists 65
                                       Gi qsd +ke++ ++r+   ++ sL +kgL+ + ++     + +++t+
  gi|336254672|ref|YP_004597779.1| 28 GGIHQSDFWKELGVSSRKGSRIVESLVEKGLVDREET----IYDGHNTY 72
                                      59********************************999....66666665 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 !   16.8   0.0   2.9e-06    0.0073       5      59 ..      17      70 ..      13      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.9e-06
                            HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre 59
                                      +++ L+l+r + ++ +++d  + l v++  +s +++ L+ekGLv r++   d+ +
  gi|336254672|ref|YP_004597779.1| 17 ERAGLELVR-ETGGIHQSDFWKELGVSSRKGSRIVESLVEKGLVDREETIYDGHN 70
                                      566688888.888889999999**********************88876666655 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 ?   11.5   0.0     8e-05       0.2      57      85 ..      51      80 ..      40      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8e-05
                           DUF1495 57 ssLielGLveeeee.seglklYklteeGie 85
                                      +sL+e+GLv +ee   +g ++Y ++++ + 
  gi|336254672|ref|YP_004597779.1| 51 ESLVEKGLVDREETiYDGHNTYYISPTARD 80
                                      7********988877999******998765 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 ?   10.8   0.0   0.00011      0.27       9      47 ..      21      59 ..      21      60 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                            HTH_24  9 LelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      Lel+++ ++i q++  ++lg+S+   +r ++ L+e+Gl+
  gi|336254672|ref|YP_004597779.1| 21 LELVRETGGIHQSDFWKELGVSSRKGSRIVESLVEKGLV 59
                                      89999********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 943.47
//
Query:       gi|336254673|ref|YP_004597780.1|  [L=264]
Description: hypothetical protein Halxa_3289 [Halopiger xanaduensis SH-6]
Scores for 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-24   86.8   0.0    7.2e-24   85.2   0.0    1.7  1  TANGO2    Transport and Golgi organisation 2


Domain annotation for each model (and alignments):
>> TANGO2  Transport and Golgi organisation 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.0     4e-28   7.2e-24       1     159 [.       1     152 [.       1     231 [. 0.76

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 4e-28
                            TANGO2   1 MCIllftveahpkykLiLasNRDEflaRptkeaawweenseilsgrDlerkegGTWlGitkegrlAvLtNlrepsek 77 
                                       MC l ++++  ++ +  +a+NRDE ++R +++ ++ +e++ i+++rD+e+  gGTW+G ++ g +A +tN r ++  
  gi|336254673|ref|YP_004597780.1|   1 MCTLTLAWQVFEDAPVAVAANRDEAVDRDSRPPDVYREEPLIVAPRDAEA--GGTWIGYNEFGVFAGITN-RWTDA- 73 
                                       *************************************************6..******************.55553. PP

                            TANGO2  78 ekkakkarsRGelvldfLtsseksseeyleelak..eakkyggFnLlvgdlkskelayisnrskee.eelspgvhgl 151
                                         + +++rsRG lv+d L+   +s +e +  +a+   a++y gFnL+v+d +  ++++++  ++   ++++pgvh++
  gi|336254673|ref|YP_004597780.1|  74 --ELAGERSRGLLVADVLEA--RSAAEAASIVADatAADEYDGFNLVVADAD--DAYCFQWDGDLVrTDFEPGVHVV 144
                                       ..34689***********74..4444444433334589**************..466666666445588899***** PP

                            TANGO2 152 SNslldsp 159
                                        N ++d +
  gi|336254673|ref|YP_004597780.1| 145 VNVAVDGE 152
                                       **988653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:01.69
# Mc/sec: 472.77
//
Query:       gi|336254674|ref|YP_004597781.1|  [L=532]
Description: O-succinylbenzoate-CoA ligase [Halopiger xanaduensis SH-6]
Scores for complete 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-88  296.9   0.0    2.3e-88  296.6   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    9.6e-17   61.7   2.2    9.1e-16   58.6   0.6    2.4  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 !  296.6   0.0   2.6e-92   2.3e-88       2     422 ..      11     426 ..      10     427 .. 0.87

  Alignments for each domain:
  == domain 1  score: 296.6 bits;  conditional E-value: 2.6e-92
                                       HHHHHHSTTSEEEEE.......CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT CS
                       AMP-binding   2 eeqaaktpdkvalvd.......sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaG 71 
                                       +++aa+tp+++al+d       ++    +TY+++d+rv+r Aa+L+  Gv  +dr +++++++p +  +++a++++G
  gi|336254674|ref|YP_004597781.1|  11 AHRAATTPERTALIDadadagdGDASVEWTYADFDRRVDRTAAALEDEGVV-DDRLGVCMDTRPAFATVFFAAMRLG 86 
                                       6899*****************988999*******************87997.699********************** PP

                                       -EEEEEETTS-HHHHHHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTT CS
                       AMP-binding  72 avvvplnptltaeelayiledseakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseeka 147
                                       ++vvpln + t +ela  +e +e +++i  ++se    +l+ aa+++ ++  v+ +d  e++  +++++e+ + +++
  gi|336254674|ref|YP_004597781.1|  87 LTVVPLNVRETTDELAAKVERTELEAVI--CESETeSTALELAASTDGRRLPVLSVD--EPESGSDADTET-DTDVQ 158
                                       ****************************..888886666655555544444444444..555454444444.33343 PP

                                       ..S.........-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTS CS
                       AMP-binding 148 ..e.........kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplah 213
                                         e           +++++l+ dd+ ++++TSGT G+PK V l+ +nlva++++ ++  r +++++d++l++lp++h
  gi|336254674|ref|YP_004597781.1| 159 flEataggdsgsPSVDPVPLERDDTQLLLFTSGTSGEPKIVRLTVGNLVASATASAF--RLGVDRNDRWLCCLPMYH 233
                                       3415678899995667889********************************999543..3667789*********** PP

                                       CHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEE CS
                       AMP-binding 214 ifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvll 290
                                       + gl + +  + l G tvv+ ++++a++    +++++++ +t + +vP+++++ll+++ +          slr+vll
  gi|336254674|ref|YP_004597781.1| 234 MGGL-APIVRSTLYGTTVVIQREFDARE---TARVMDEYDITGVSLVPTMCKRLLDADWEP-------PESLRFVLL 299
                                       ***9.***************99999866...4789*********************64443.......458****** PP

                                       ESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEE CS
                       AMP-binding 291 ggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGel 367
                                       gg+p s+ell+++ + + + v+ +YG+TEt+  v+++++ + ++  g+vG+pl +++v i+De+ g pvp +e+Gel
  gi|336254674|ref|YP_004597781.1| 300 GGAPASSELLERCLEAGVP-VHPTYGMTETASQVATATPADVREHEGTVGQPLVNTDVTIIDED-GDPVPSDEPGEL 374
                                       ****************875.**************776667777889*****************9.************ PP

                                       EEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 368 lvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       +v+gp+v++gYl   ++t eaf   +r l+TGD+g++d+dG+l+i+ R  d i++
  gi|336254674|ref|YP_004597781.1| 375 VVSGPTVTPGYLDS-DRTDEAFG--DRGLHTGDVGYRDADGRLRILNRRSDRIVT 426
                                       ************76.*******8..579**********************99986 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 ?    2.2   0.0     0.042   3.7e+02      33      63 ..      89     119 ..      78     130 .. 0.76
   2 !   58.6   0.6     1e-19   9.1e-16       4      75 ..     438     511 ..     435     512 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.042
                                       EEE------HHHHHHHHH.HHHT-TTTS-SEE CS
                     AMP-binding_C  33 VvlkdgsealeeeLkahv.rkelgpyavpkkv 63 
                                       Vv+  +++++ +eL a+v r+el+++ + ++ 
  gi|336254674|ref|YP_004597781.1|  89 VVPL-NVRETTDELAAKVeRTELEAVICESET 119
                                       5552.444578*******888***99998765 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 1e-19
                                       HHHHSSTTEEEEEEE-----TTS---EEEEEE---..---HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS CS
                     AMP-binding_C   4 salvshpaVaeaaVvGvpdevkGealvafVvlkdg..sealeeeLkahvrkelgpyavpkkvvfvdelpktrsG 75 
                                       ++l +hpaV++aaVvG  d+ + e+++a+Vv++++  +e+  + L ah+ ++l+ +++pk + f d+lp+t+sG
  gi|336254674|ref|YP_004597781.1| 438 AILREHPAVEDAAVVGLEDPEWSERVAALVVPAADaeVESNVDSLLAHCDEHLAGFKKPKMIAFADSLPRTASG 511
                                       799*****************************7554324478*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3575.65
//
Query:       gi|336254675|ref|YP_004597782.1|  [L=371]
Description: Mandelate racemase/muconate lactonizing protein [Halopiger xanaduensis SH-6]
Scores for 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-37  126.7   8.4    9.7e-37  126.7   8.4    1.7  2  MR_MLE_C  Enolase C-terminal domain-like
    1.2e-07   32.0   0.0    1.1e-06   28.9   0.0    2.4  1  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N


Domain annotation for each model (and alignments):
>> 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 ?   -1.4   0.0      0.16   1.4e+03     128     147 ..      90     109 ..      78     124 .. 0.65
   2 !  126.7   8.4   1.1e-40   9.7e-37       5     215 ..     160     366 ..     156     371 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.16
                                       BHHHHTSHHHHHHHHHHHHH CS
                          MR_MLE_C 128 dvsrvgGitearkvaalaea 147
                                       d+ r+gG++ea++ ++   a
  gi|336254675|ref|YP_004597782.1|  90 DAFRAGGPNEALEAVDRQVA 109
                                       56677777777766654333 PP

  == domain 2  score: 126.7 bits;  conditional E-value: 1.1e-40
                                       HHHHHHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGTESEEESSS CS
                          MR_MLE_C   5 earelvaeqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeldllwlEEPv 81 
                                       ++ + + e+g++ +Klkvg  +v+ed+ervr++r+av  +d v+l+ Dan+aw+ ++A   ++++++l++ ++E+P+
  gi|336254675|ref|YP_004597782.1| 160 AV-REASERGYACCKLKVGLRSVEEDIERVREARDAV--DDAVELRADANEAWTYEDAESALEAFADLGVSLVEQPL 233
                                       34.446789****************************..7788********************************** PP

                                       STTTHHHHHHHHHH.HHSSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSC CS
                          MR_MLE_C  82 ppeddleglaelra.rasipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsg 157
                                       p+   leg+a+lr+ ++++ ia++E l   +++ ++++a+a+d+v ++++  gG++ ar+vaa + + ++  ++ + 
  gi|336254675|ref|YP_004597782.1| 234 PAG-ALEGHADLRRmDTGVDIALDEGLLE-HGVDAICDAEAADAVVLKPMALGGVDVARRVAAWVMEVDIAPIVTTT 308
                                       **6.5********85449********986.89*********************************999999777774 PP

                                       .SSHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTSSSBTSSE CS
                          MR_MLE_C 158 .sgglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtvpdgpGlGve 215
                                        +g +++  ++hlaaaip +      + +  l e+l+ +p+  e+G   vp++ GlG+e
  gi|336254675|ref|YP_004597782.1| 309 iDGVVARTGAVHLAAAIPDVPACGLATAEL-LAEDLGRDPVLLEKGAAVVPQAKGLGIE 366
                                       258***************877777777665.***************************9 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.2e-10   1.1e-06      13     117 .]      35     135 ..      27     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.2e-10
                                       EC.EEEETTEEEEEEEEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHH.TTSBTTHHHHHHHHHHHHCS CS
                          MR_MLE_N  13 lr.PvqlavttvqkqslvlvkietseGvvGigeatsvggraetikaelddhlapll.vgkdaanisdlaqllkravl 87 
                                       l+ P++++ +t++     lv+++ ++GvvG geat+ +g  e++     d+  ++l   +da +  +  +++  av 
  gi|336254675|ref|YP_004597782.1|  35 LAsPLETSNGTIESRDGFLVRLADENGVVGYGEATPLPGWTESR-----DDCRAALeRAQDAFRAGGP-NEALEAVD 105
                                       556***********************************744443.....3333333136777776555.55667888 PP

                                       SCHHHHHHHHHHHHHHHHHHTTSBHHHHTT CS
                          MR_MLE_N  88 gnmsAkaaidmAlwDlkakalnlpladLlG 117
                                        + +A+ a+  Al Dl+  ++ +pl+  lG
  gi|336254675|ref|YP_004597782.1| 106 RQVAARHAVSLALADLQSSRHATPLYRYLG 135
                                       899**********************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2823.94
//
Query:       gi|336254676|ref|YP_004597783.1|  [L=311]
Description: 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-40  138.1  18.0      3e-40  138.1  18.0    1.2  1  UbiA      UbiA prenyltransferase family


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 !  138.1  18.0   1.7e-44     3e-40       3     235 ..      26     279 ..      24     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: 138.1 bits;  conditional E-value: 1.7e-44
                              UbiA   3 ipalvg.lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadme.rt.pnRPlvsGrispkealifaivl 76 
                                        p++vg  ++ + g++++  +ll+++g++l+++++n+ Ndy+D+ ++ad+e r    R   sG+i  ++++++ iv+
  gi|336254676|ref|YP_004597783.1|  26 APVIVGtGLAVSEGVFSPVPALLAFVGAALIQIGTNFANDYYDAIKGADTEdREgFTRVTQSGLIPAEQVKLATIVT 102
                                       689999877777999***********************************98556899999**************** PP

                              UbiA  77 lilgllll...alllnpltallgllalllyvvYt.g.lrlKrrtllgtvvggiafglppllgwaavtgsl....... 141
                                       ++l+++ +   +++ + +++++gl+++l++++Yt g ++l++++l g+ +++++fg+++++g ++v+          
  gi|336254676|ref|YP_004597783.1| 103 FALAIFTGtylVYIGGVPILVIGLVSVLCGWAYTgGpYPLGYHGL-GDPFVFVFFGVVAVMGTFYVQAAAvlaeplt 178
                                       ******999999***********************88********.*******************8888889***** PP

                              UbiA 142 ........sllalllalavflltwaialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllal 210
                                               +l+a++++l+v++ ++ i+++n++rd+e D++ g++tl+v+lG +++r+ +++lla+++la+++++l +
  gi|336254676|ref|YP_004597783.1| 179 taipegtiTLEAFVASLPVGAISTCIIVVNNIRDKETDAETGKRTLAVRLGYRWSRVEYLALLALAYLAPFWFWLEG 255
                                       *********************************************************99999999999944443333 PP

                              UbiA 211 llllylllalllaalallraarlvr 235
                                       ++l + ll l+++++a  +   +++
  gi|336254676|ref|YP_004597783.1| 256 FGLGA-LLPLVSLPYAASVTRTVLT 279
                                       33333.3333333333333333444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2578.72
//
Query:       gi|336254677|ref|YP_004597784.1|  [L=434]
Description: hypothetical protein Halxa_3293 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00072   19.8   0.0     0.0034   17.6   0.0    2.0  2  Iron_transport  Fe2+ transport protein
  ------ inclusion threshold ------
       0.16   11.9   2.4       0.28   11.1   2.4    1.4  1  TAT_signal      TAT (twin-arginine translocation) pathway sig


Domain annotation for each model (and alignments):
>> Iron_transport  Fe2+ transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.8e-07    0.0034      91     122 ..     178     209 ..     155     234 .. 0.74
   2 ?   -1.2   0.0      0.23     2e+03      94     132 ..     379     420 ..     352     425 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.8e-07
                                       ETTEEEEEEEE--T-SEEEEEEEEEE---TTT CS
                    Iron_transport  91 asDgphYganvklkgvgkYkltleieppekke 122
                                       ++ g+h+g+nv l+g g+Y++++++ p ++++
  gi|336254677|ref|YP_004597784.1| 178 QEMGFHFGDNVGLPGDGTYTVEVTLPPISTRK 209
                                       5679********************98877754 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.23
                                       EEEEEEEE--....T-S.EEEEEEEEEE---TTT-EEE-STTTS CS
                    Iron_transport  94 gphYganvkl....kgv.gkYkltleieppekkefgrHvdketg 132
                                       g hYg  +      +gv    ++ +eie+p +  ++rH   et+
  gi|336254677|ref|YP_004597784.1| 379 GLHYGVSLSEigdvSGVeAGDSVAIEIESPPQ--IARHQGYETA 420
                                       56666554321111333322367888888877..7888888876 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.4   3.2e-05      0.28       2      25 ..      11      34 ..      10      35 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.2e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      ++RR+F + ++A++  +al+gc++
  gi|336254677|ref|YP_004597784.1| 11 IDRRTFVRRTGAVTGTLALAGCTS 34
                                      78********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); 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:                         2  (0.000111551); expected 0.2 (1e-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: 3204.78
//
Query:       gi|336254678|ref|YP_004597785.1|  [L=443]
Description: hypothetical protein Halxa_3294 [Halopiger xanaduensis SH-6]
Scores for 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   12.0   0.1       0.15   12.0   0.1    1.8  2  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   8.3e-06      0.15       4      24 ..      11      31 ..       8      32 .. 0.93
   2 ?   -4.4   1.6         1   1.8e+04       4       7 ..     363     366 ..     363     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.3e-06
                        TAT_signal  4 RRdFLKgsAAaaAAaalggca 24
                                      RRd L++  A++  +al +c+
  gi|336254678|ref|YP_004597785.1| 11 RRDYLRALVAVGGTTALSACL 31
                                      *******************96 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 1
                        TAT_signal   4 RRdF 7  
                                       RRdF
  gi|336254678|ref|YP_004597785.1| 363 RRDF 366
                                       9**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 3484.18
//
Query:       gi|336254679|ref|YP_004597786.1|  [L=296]
Description: naphthoate synthase [Halopiger xanaduensis SH-6]
Scores for 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-55  186.9   0.0    4.6e-55  186.6   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    7.1e-14   52.0   0.0    9.8e-14   51.6   0.0    1.3  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.6   0.0   5.2e-59   4.6e-55       4     250 ..      31     291 ..      28     292 .. 0.91

  Alignments for each domain:
  == domain 1  score: 186.6 bits;  conditional E-value: 5.2e-59
                                       TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTS......EEEEEB-HHHHHHHHC...... CS
                             ECH_1   4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdk......aFaaGadlkemaeeek...... 67 
                                       +g + i ++rPe+ Na+ + +++El +ale+++ +  v+ v LtG g+       aF++G+d++ + e ++      
  gi|336254679|ref|YP_004597786.1|  31 SGTVRIAFDRPEVRNAFRPGTVDELYDALEHAKRQTDVGCVFLTGnGPSpkdggwAFCSGGDQTIRGEDGYqydgde 107
                                       56789****************************************87654566669*******99988887555332 PP

                                       .HHHHHHHCCHHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETT.TEEE-GGGGGTS--CTTCHHHHHH CS
                             ECH_1  68 .akqallkeevlelwtklytvpkpviaavnGaaigGGlelalacDiviaadn.asfglnelklGlipgaggtqilar 142
                                        +  ++ + ++le +++++++pk+v+  v G a+gGG+ l+++cD++ a+++ a+f ++   + ++++ +g+ +la+
  gi|336254679|ref|YP_004597786.1| 108 eRASEQGRLHILEVQRLIRHIPKVVVCVVPGWAVGGGHSLHVVCDLTLASEEhAKFLQTDPDVASYDAGFGSAYLAK 184
                                       222333455678999**********************************976377********************** PP

                                       HHHHHHHHHHHHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHH.HHHHHHHH CS
                             ECH_1 143 kvGkskAeeilllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakle.dalaeqle 218
                                       ++G++kA+e+  lgk + a+ea+++G+v++vvp+e+l+e+ale+ e++++ksp+a+r+lk  +n + + +  +++++
  gi|336254679|ref|YP_004597786.1| 185 QIGQKKAREVFFLGKTYDAEEAADMGMVNEVVPHEDLEETALEWGERINSKSPTAMRMLKYGFNMTDDgMIGQQVFA 261
                                       ********************************************************************9******** PP

                                       HHHHHHHHHCTSHHHHHHHHHHHTCSH----- CS
                             ECH_1 219 aeaklfestfskddikeGlqaflEkrkpefed 250
                                        ea+ + +++++++  eG++af+E r+p+f+d
  gi|336254679|ref|YP_004597786.1| 262 GEATRLGYMTDEAK--EGRDAFVEGREPDFDD 291
                                       *********99955..**************86 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   1.1e-17   9.8e-14       3     181 ..      35     225 ..      33     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.1e-17
                                       EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSS......ECE--B--HHHHHHHHCS..-THH.. CS
                             ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagek......afCAGgDvralyeaakeg..kkee.. 69 
                                       +i ++rp+  Na     v++l +al++ +++ +v +v+l+g+g+       afC+GgD     e+  +   ++e+  
  gi|336254679|ref|YP_004597786.1|  35 RIAFDRPEVRNAFRPGTVDELYDALEHAKRQTDVGCVFLTGNGPSpkdggwAFCSGGDQTIRGEDGYQYdgDEERas 111
                                       6889*************************************9877778888*******6655555555433333234 PP

                                       HHHHHHHHHHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-.EEE--GGGGT.----TTHHHHHHCSST CS
                             ECH_2  70 eeffreeYklnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtert.vfAmPEtaIG.lfPDvGgsyfLsrlpg 144
                                       e+   +  +++ li ++pk vv+++ G ++GgG +l v + +  ++e+  +f   +  +  +    G  y+ +++ +
  gi|336254679|ref|YP_004597786.1| 112 EQGRLHILEVQRLIRHIPKVVVCVVPGWAVGGGHSLHVVCDLTLASEEHaKFLQTDPDVAsYDAGFGSAYLAKQIGQ 188
                                       6677778999***********************************98754666666666515567788899999999 PP

                                       THHHHHHHH---B-HHHHHHTTS--EE--GGGHHHHH CS
                             ECH_2 145 elGlylalTGarlkgadalaaglathyvpsekleale 181
                                       + ++ +   G++ ++++a  +g+ + +vp+e+le+ +
  gi|336254679|ref|YP_004597786.1| 189 KKAREVFFLGKTYDAEEAADMGMVNEVVPHEDLEETA 225
                                       999999999***********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2485.67
//
Query:       gi|336254680|ref|YP_004597787.1|  [L=469]
Description: hypothetical protein Halxa_3296 [Halopiger xanaduensis SH-6]
Scores for 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-25   88.9   5.9    2.5e-24   85.9   2.6    2.5  2  Beta_helix  Right handed beta helix region
  ------ inclusion threshold ------
        8.1    6.5  11.7      0.055   13.3   2.7    2.1  2  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.1    0.0065        58       3      41 ..     192     233 ..     186     238 .. 0.77
   2 !   85.9   2.6   2.7e-28   2.5e-24       2     158 .]     240     443 ..     239     443 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0065
                                       EEE-SS-E.EEESEEEES-....SS-SEEE-SSS-.EEES-EE CS
                        Beta_helix   3 isingssnvtiknntisns....ggyGiylrgssnvviennei 41 
                                       i ++g++  t+ n +++       +++i+++++++ vi nn++
  gi|336254680|ref|YP_004597787.1| 192 IRVRGDGA-TVANIEFDADgtqtDNHAIQADDCDGLVIANNRT 233
                                       55666666.8888888777778788999999999999998875 PP

  == domain 2  score: 85.9 bits;  conditional E-value: 2.7e-28
                                       SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-............EEES-EEES-SS-SEEE-TT-S-EEES-EEE-- CS
                        Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssn...........vvienneiannsgsGiyilgssnntisnntisdn 67 
                                       +is++++ nv++ +n++ ++++yGi+ r + +           vv+ +n++a+ ++++i+++++sn+t+++n+++++
  gi|336254680|ref|YP_004597787.1| 240 AISFSRCRNVQVVGNEVLDPNWYGITSRAAPTggdrdlrrsenVVVARNYVAGVTYNNIATYNVSNFTVYGNVVEEG 316
                                       89****************************************99999****************************** PP

                                       -SEEE-TT--S--EEES-EEES-........SS-SEE-TT................-S--EEES-EEESTT...... CS
                        Beta_helix  68 ngggialfgasnnlienneitdn........ggsGiylny................ssnntienNiidnna...... 114
                                       +++ ia++ a++  i +n ++          g++Gi+++y                s+++ti++N++dn+       
  gi|336254680|ref|YP_004597787.1| 317 GHSLIACSPAQQGAIVGNVCRGLeeykpdpgGEAGIEIEYkethvreeiagtdrarSYDITISGNQVDNCPvgilar 393
                                       ***********************66666555555*****99******************************666644 PP

                                       .....--SEE---TT.........---EEES-EEES-SSEEEE-TT-SS--EEES-E. CS
                        Beta_helix 115 .....gsGividdss.........snvtvtnNtitnnkgaGiavvgsssnvtvrnNti 158
                                                    ++         +++tvt+N+i++++ aGi + ++++  +v++Nt+
  gi|336254680|ref|YP_004597787.1| 394 tvpadP-------EDeaareterpHSFTVTGNSINGADAAGIRIRSGAA-GVVATNTV 443
                                       444441.......225566666789*****************8888777.99999985 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.7   6.1e-06     0.055       2      24 ..      18      40 ..      17      42 .. 0.88
   2 ?   -3.8   1.7       1.5   1.4e+04      12      18 ..     433     439 ..     432     440 .. 0.43

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.1e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                       +RR+FL g +A+  ++al g +
  gi|336254680|ref|YP_004597787.1| 18 PTRRSFLSGLGATVGLGALTGSG 40
                                      69***********9999999976 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.5
                        TAT_signal  12 AAaaAAa 18 
                                       +Aa+  a
  gi|336254680|ref|YP_004597787.1| 433 GAAGVVA 439
                                       4444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); 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 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 3694.87
//
Query:       gi|336254681|ref|YP_004597788.1|  [L=101]
Description: hypothetical protein Halxa_3297 [Halopiger xanaduensis SH-6]
Scores for 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  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 801.83
//
Query:       gi|336254682|ref|YP_004597789.1|  [L=294]
Description: hypothetical protein Halxa_3298 [Halopiger xanaduensis SH-6]
Scores for 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-26   90.8  22.1    1.9e-14   54.0  10.8    2.1  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
      0.082   12.2   8.0       0.53    9.6   1.4    2.4  2  TPT       Triose-phosphate Transporter family
        0.1   12.6   0.6        0.1   12.6   0.6    3.6  3  TMEM234   Putative transmembrane family 234


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 !   54.0  10.8   3.2e-18   1.9e-14       4     136 ..       5     140 ..       3     141 .. 0.89
   2 !   42.9   3.5   8.7e-15   5.2e-11       4     136 ..     159     293 ..     156     294 .] 0.90

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 3.2e-18
                              EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl....aklslkd....wllllllgl 72 
                                       + +allaal+w++y+ + k+ + +++p +lt++   ++ +  l++a+ +              +     + +  l +
  gi|336254682|ref|YP_004597789.1|   5 LGVALLAALVWGVYIYVLKRSFDEYPPAALTVLINAFGIAWYLPVAVTQVDGSaaalG-----SfglaEAGVTTLTI 76 
                                       5579***************************999999999999999999988843322.....32444567788888 PP

                              EamA  73 lgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       ++t++af+lf+ a+ ++++s +++i+ ++P+f+l l vl+lg+ lt +++ g+v++ l+v++ +
  gi|336254682|ref|YP_004597789.1|  77 VATAAAFVLFLRAIDEGDVSYVTPINKIVPMFVLPLEVLVLGQVLTPLEVGGVVVATLAVYVAN 140
                                       ************************************************************9976 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 8.7e-15
                              EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagill..liiallkegklaklslkdwllllllgllgtvla 78 
                                       + lall+a+++a++ +  ++ l+++   + + v +l+ g+++  l+ia+ +  + + l l++ l  l ++   ++l+
  gi|336254682|ref|YP_004597789.1| 159 AQLALLSAMCYAVSDLGKRVSLQELAIPERLWVPMLLVGVAVvlLPIAVRNPPTESDLGLRGDLPTLAVAGGMVALG 235
                                       679*****************************99997776653377777777777888888888888888889**** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                         l + ++  ++as+as++++++ +++++l+ +llge+   + l+++vl+++Gv li 
  gi|336254682|ref|YP_004597789.1| 236 EHLTTLSFAVLPASIASPVINTQAIVAVVLGGVLLGERHFRLRLVAAVLAVIGVTLIA 293
                                       *******************************************************996 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.7   0.00082       4.9      75     128 ..      79     132 ..      26     142 .. 0.79
   2 ?    9.6   1.4   8.9e-05      0.53      29     136 ..     184     293 ..     160     294 .] 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00082
                               TPT  75 ktlghvlavvslskvaVSfthtvKasePiFtvilsrlllgeklsllvylsLlpi 128
                                        +++ vl   ++ +  VS+   +  + P+F   l  l+lg++l+ l +  +++ 
  gi|336254682|ref|YP_004597789.1|  79 TAAAFVLFLRAIDEGDVSYVTPINKIVPMFVLPLEVLVLGQVLTPLEVGGVVVA 132
                                       33444556668999999**999999*****999999999999988765554444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 8.9e-05
                               TPT  29 pyPltvsavqllvgsvlilvlwal.glkkrpkisse.flkailplalvktlghvlavvslskvaVSfthtvKasePi 103
                                       ++P  + +  llvg+ ++l+  a+ +     ++  +  l ++ + + + +lg+ l+++s++  + S +  v  ++ i
  gi|336254682|ref|YP_004597789.1| 184 AIPERLWVPMLLVGVAVVLLPIAVrNPPTESDLGLRgDLPTLAVAGGMVALGEHLTTLSFAVLPASIASPVINTQAI 260
                                       55555555555555544444444424555566666667777777777889999************************ PP

                               TPT 104 FtvilsrlllgeklsllvylsLlpivgGvalas 136
                                        +v+l  +llge+   l +++ +  v Gv+l +
  gi|336254682|ref|YP_004597789.1| 261 VAVVLGGVLLGERHFRLRLVAAVLAVIGVTLIA 293
                                       *************99999999999999998865 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   2.3     0.062   3.7e+02      60      83 ..      61      84 ..       8     139 .. 0.55
   2 ?   -1.8   0.0      0.51     3e+03      91     114 ..     179     202 ..     160     204 .. 0.74
   3 ?   12.6   0.6   1.7e-05       0.1      68     115 ..     246     292 ..     233     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.062
                           TMEM234 60 lfflllgkadlslavpiaNslafv 83
                                      l  + l++a +++  ++a + afv
  gi|336254682|ref|YP_004597789.1| 61 LGSFGLAEAGVTTLTIVATAAAFV 84
                                      444444445555555554444444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.51
                           TMEM234  91 llgekvlkkktvlgmllvvvgial 114
                                        l+e  + ++ ++ mllv v+++l
  gi|336254682|ref|YP_004597789.1| 179 SLQELAIPERLWVPMLLVGVAVVL 202
                                       567777778888888888887776 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 1.7e-05
                           TMEM234  68 adlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                        + s+a+p+ N+ a+v+ vl + llge+  + + v+  +l v+g++l+
  gi|336254682|ref|YP_004597789.1| 246 LPASIASPVINTQAIVAVVLGGVLLGERHFRLRLVA-AVLAVIGVTLI 292
                                       5779************************99988766.56777888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2431.11
//
Query:       gi|336254683|ref|YP_004597790.1|  [L=605]
Description: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase [Halopiger xanaduensis SH-6]
Scores for 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-36  124.6   0.1    1.2e-35  122.7   0.0    2.0  2  TPP_enzyme_N    Thiamine pyrophosphate enzyme, N-terminal TPP
    5.9e-09   35.9   0.0    1.3e-08   34.8   0.0    1.6  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
    0.00012   21.8   0.0    0.00026   20.7   0.0    1.6  1  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
    0.00065   19.5   0.0     0.0013   18.5   0.0    1.4  1  TPP_enzyme_M_2  Middle domain of thiamine pyrophosphate


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 !  122.7   0.0   2.6e-39   1.2e-35       4     169 ..      11     182 ..       9     185 .. 0.96
   2 ?   -2.2   0.0      0.59   2.7e+03      75     103 ..     459     487 ..     453     497 .. 0.77

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 2.6e-39
                                       HHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCH CS
                      TPP_enzyme_N   4 aealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnal 80 
                                       +++l++ L+a g e v++ pGsr++pl+ a++e+++++v+ +++E++aa++A g ar+tg+p ++++tsg++a+n  
  gi|336254683|ref|YP_004597790.1|  11 GRVLADELAAGGLEAVCIAPGSRSTPLTVAFAEHPELEVYSHLDERSAAYFALGRARRTGEPTALVCTSGTAAANFH 87 
                                       789************************************************************************** PP

                                       HHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHH.......HHHHHHHSS CS
                      TPP_enzyme_N  81 talaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealr.......rAirtalsg 150
                                       ++++eA+++r+Pllvl++drp +lr+ g+ q ++dq++l+ + + +  ++ +pe+ ++ +r       rA+ ++l  
  gi|336254683|ref|YP_004597790.1|  88 PGVIEANQARVPLLVLTADRPPELRDSGANQ-TIDQVELYGDAVCWYAELPEPEADERKVRslrttaaRALSESLGV 163
                                       *******************************.***********************9999999999999********* PP

                                       S--EEEEEEEHHHCC-EEE CS
                      TPP_enzyme_N 151 rpgPvylelpkdvlleevd 169
                                       +pgPv+l+ p   +le+ +
  gi|336254683|ref|YP_004597790.1| 164 EPGPVHLNCPFKKPLEPLE 182
                                       **********998888876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.59
                                       HHHHCHHHHHHHHHHT--EEEEEEE--CC CS
                      TPP_enzyme_N  75 GatnaltalaeAkvdriPllvlsgdrpts 103
                                       G+ ++  ++ +A  +  Pl++++gd + +
  gi|336254683|ref|YP_004597790.1| 459 GIESTALGAGSATDADEPLVLVTGDLAFY 487
                                       66667778889999999*******97655 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 !   34.8   0.0   2.9e-12   1.3e-08      35     151 ..     462     575 ..     435     577 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.9e-12
                                       HHHHHHHHHST.TSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS-- CS
                      TPP_enzyme_C  35 paAiGaklakp.drevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqepfggkrksgpagkdlkp 110
                                       + A+Ga  a   d++ v ++GD +f++  + l  + r +++ t+v+l+N g g   + +  +++  ++g+  k+ + 
  gi|336254683|ref|YP_004597790.1| 462 STALGAGSATDaDEPLVLVTGDLAFYHDSNGLLAVDRCDVDATIVLLDNDGGGIFHKLPIEEFDPPFTGQF-KTPHG 537
                                       56889988744389********************************************9999998999876.6899* PP

                                       --HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEE CS
                      TPP_enzyme_C 111 vdfaklaealGakgarvekadveeleealkealekkgpali 151
                                       +df+ l e +G +  rve++   e+++a ++ l+++g+ ++
  gi|336254683|ref|YP_004597790.1| 538 IDFESLGETYGLEFERVEPR---EFDDAYRRSLKREGTQVL 575
                                       *************9998777...**********99998776 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 !   20.7   0.0   5.7e-08   0.00026       3      87 ..     223     311 ..     221     353 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.7e-08
                                       HHHHHHHH-SSEEEEE-CH...HCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEE.ESGGGS.CHHHHHH CS
                      TPP_enzyme_M   3 kaaellkaakrpvilvGgg...varsgaseelrelaeklgiPvvttlmgkgvipedhplylg.mlglhg.skaanea 74 
                                        + ++l++akrp+i++G       r+   +++++lae++g+Pv+  +     +  +h +  g ++ + g  ++  +a
  gi|336254683|ref|YP_004597790.1| 223 SLTDALENAKRPLIVAGPAdprNLRELEPDAVVDLAERVGAPVLADPLSGLRFG-SHVRARGdSIRVYGgYDTYIDA 298
                                       57799************751114555699**************66666544454.5666677799888757888899 PP

                                       HHH-SEEEEES-S CS
                      TPP_enzyme_M  75 leeaDlvlalGar 87 
                                       le+ D+vl +Ga 
  gi|336254683|ref|YP_004597790.1| 299 LEDPDVVLRFGAS 311
                                       9********9986 PP

>> TPP_enzyme_M_2  Middle domain of thiamine pyrophosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.8e-07    0.0013      39     153 ..     232     356 ..     226     404 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.8e-07
                                       SSEEEEE-.....B--HHHHHHHHHHHHHHT--EEE-TTT-S......--SSTTHHHHTTSHHHHHHHTT-SEEEEE CS
                    TPP_enzyme_M_2  39 krGvvvaG.....rlsaeegkqvaawaeklGWplltDvqsql......gqalpyaDlwLanpkvkeeLaqadiviqf 104
                                       kr ++vaG      l + e+ +v+ +ae++G p+l+D +s+l       +    + ++   +++ + L++ d+v+ f
  gi|336254683|ref|YP_004597790.1| 232 KRPLIVAGpadprNLRELEPDAVVDLAERVGAPVLADPLSGLrfgshvRARGDSIRVYGGYDTYIDALEDPDVVLRF 308
                                       566677774444347788999*******************9988755444555677888899*************** PP

                                       SB---SHHHHHHHHH---SEEEEEESS-SB--TT--SEEEEES-HHHHH CS
                    TPP_enzyme_M_2 105 GsrlvsKrllqflaelkpeeyWlvdesqgrldpahhrkrrfvakveewl 153
                                       G++ +sK l + l + +  +  +vd+     +++  +   + a++++++
  gi|336254683|ref|YP_004597790.1| 309 GASPTSKPLRHALRDADA-RQFVVDPAGAWREATFTATDLLAATAASVV 356
                                       **********99999999.556899988888887777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); 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 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 4675.22
//
Query:       gi|336254684|ref|YP_004597791.1|  [L=489]
Description: isochorismate synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-74  250.8   0.0    2.2e-74  250.3   0.0    1.2  1  Chorismate_bind  chorismate binding enzyme


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 !  250.3   0.0   1.2e-78   2.2e-74       3     258 .]     228     480 ..     226     480 .. 0.97

  Alignments for each domain:
  == domain 1  score: 250.3 bits;  conditional E-value: 1.2e-78
                                       CHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEE.EETTEEEEEEESSEEEEEE CS
                   Chorismate_bind   3 edYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysfll.eledsellgaSPElllkve 78 
                                       e++++ +e++ e+i++g+l kvvl+++l++ le ++d  a++++lr+++p++y f + + ++ +++ga PE+l+ ++
  gi|336254684|ref|YP_004597791.1| 228 EEWRTGIEAALERIADGRLTKVVLAQALSVALEGPIDVGATLERLRREYPNCYRFRIgREGGVTFFGAPPERLVAKR 304
                                       89*******************************************************64455899************ PP

                                       TTSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEE CS
                   Chorismate_bind  79 ggrrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhl 155
                                       g  r+ te++aG+++rg+tp ed++ +++lle++K r+Eh+++vd+ir++L+++  ++ +++ + ++++++++++hl
  gi|336254684|ref|YP_004597791.1| 305 GP-RVATEALAGSAPRGETPDEDQQHADRLLESDKLRREHELVVDAIRDQLAPL--ARDLEI-DGRTIRKLATIQHL 377
                                       66.***************************************************..799999.889*********** PP

                                       EEEEEEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETT CS
                   Chorismate_bind 156 vstiegelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdk 232
                                        + ie++l+ d ++l++++al+Pt+av+G+P ++a e i+e E+++Rg+Ya++vg++dadg++e+av +R+ +++d+
  gi|336254684|ref|YP_004597791.1| 378 RTPIEATLDGDRHVLEIVEALHPTPAVGGMPPDAAWETIRETEPFDRGWYAAPVGWFDADGDGEFAVGLRSGIATDE 454
                                       ****************************************************************************9 PP

                                       EEEEEEEEEEETT--HHHHHHHHHHH CS
                   Chorismate_bind 233 elrlgaGaGIvadSdpeaEyeEtlaK 258
                                        ++l+aG+GIvadSdp++E+eE++ K
  gi|336254684|ref|YP_004597791.1| 455 AVTLFAGSGIVADSDPDEEWEEVQLK 480
                                       9**********************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.48u 0.19s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 4079.45
//
Query:       gi|336254685|ref|YP_004597792.1|  [L=199]
Description: oxidoreductase molybdopterin binding protein [Halopiger xanaduensis SH-6]
Scores for 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-38  130.1   0.0    7.7e-38  129.8   0.0    1.1  1  Oxidored_molyb  Oxidoreductase molybdopterin binding domain


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.8   0.0   4.3e-42   7.7e-38       3     172 .]      36     181 ..      34     181 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.8 bits;  conditional E-value: 4.3e-42
                                       ----.GCCC-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHH CS
                    Oxidored_molyb   3 avpkvdpekwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlr 79 
                                        +p+ dpe+w+++v+g v+++ls+s+ ++++lp++++  +++C++              +w   + +++e+tGv++ 
  gi|336254685|ref|YP_004597792.1|  36 GTPDWDPETWEFTVTGAVDEELSFSWGEFRDLPSETQRQDFHCVT--------------GW---SKFDCEFTGVPFP 95 
                                       578889***************************************..............8*...9************ PP

                                       HHHHHTTB-ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBT CS
                    Oxidored_molyb  80 dvLekagvkkpearhvvfegadeeleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvK 156
                                       ++ e+agv+ ++a hv+f ++d      +y++ +ple++++d+vl+ +e +gepLp dhG PlR+v p+ ++++ +K
  gi|336254685|ref|YP_004597792.1|  96 ELAERAGVH-DDAVHVMFSALD------GYTTDLPLEDCMRDEVLFIWEFDGEPLPDDHGGPLRVVTPHKYAYKGAK 165
                                       ********7.9**********9......5***********99*********************************** PP

                                       TEEEEEEESS---SHH CS
                    Oxidored_molyb 157 wlkrievsdeesegyw 172
                                       w++ ie+ +e ++gyw
  gi|336254685|ref|YP_004597792.1| 166 WVDGIEFLTESERGYW 181
                                       **************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1543.48
//
Query:       gi|336254686|ref|YP_004597793.1|  [L=99]
Description: hypothetical protein Halxa_3302 [Halopiger xanaduensis SH-6]
Scores for 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:                       465  (0.0259356); 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:                         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: 744.01
//
Query:       gi|336254687|ref|YP_004597794.1|  [L=77]
Description: CopG/Arc/MetJ family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0034   17.3   0.1     0.0045   16.9   0.1    1.2  1  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.019   14.8   0.0    1.1  1  IclR      Bacterial transcriptional regulator


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 !   16.9   0.1     5e-07    0.0045       2      34 ..       4      37 ..       3      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-07
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlr 34
                                      v+i+++e l  ++ ++++r++ ++r e+I+++l 
  gi|336254687|ref|YP_004597794.1|  4 VEITIPEHLEMQIAQMVERGEfVNREEAIEDLLS 37
                                      78*****************************997 PP

>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.1e-06     0.019      50      91 ..       6      47 ..       3      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-06
                                      --SHHHHHHHHHHHHHHTSEEEESSSSTTEEEEEEEEE-TTS CS
                              IclR 50 itdpeeLleeLakvReqGyavdreEeeegvrciAapifdasg 91
                                      it pe+L+ ++a++ e+G  v+reE  e++ + +   +  sg
  gi|336254687|ref|YP_004597794.1|  6 ITIPEHLEMQIAQMVERGEFVNREEAIEDLLSTGIKAYKTSG 47
                                      7889****************************9998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 630.54
//
Query:       gi|336254688|ref|YP_004597795.1|  [L=68]
Description: hypothetical protein Halxa_3304 [Halopiger xanaduensis SH-6]
Scores for 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   14.0   3.4      0.065   13.5   3.4    1.4  1  YjbE      Exopolysaccharide production protein YjbE


Domain annotation for each model (and alignments):
>> YjbE  Exopolysaccharide production protein YjbE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.4   3.6e-06     0.065      33      58 ..      33      58 ..       9      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.6e-06
                              YjbE 33 AsamsaGtseAvgigavaallGvalA 58
                                       + ms+ +s Avg+ga+  ++G a+A
  gi|336254688|ref|YP_004597795.1| 33 TAPMSDYSSRAVGVGALVLAVGAAIA 58
                                      4569********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 518.99
//
Query:       gi|336254689|ref|YP_004597796.1|  [L=229]
Description: hypothetical protein Halxa_3305 [Halopiger xanaduensis SH-6]
Scores for 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  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1783.00
//
Query:       gi|336254690|ref|YP_004597797.1|  [L=456]
Description: hypothetical protein Halxa_3306 [Halopiger xanaduensis SH-6]
Scores for 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   14.3   3.9      0.069   13.0   3.9    1.7  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
      0.029   13.7   0.3       0.11   11.9   0.3    1.9  1  UCR_Fe-S_N    Ubiquitinol-cytochrome C reductase Fe-S subunit
       0.24   10.7   5.4       0.11   11.9   1.8    2.2  2  DUF4407       Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.9   1.1e-05     0.069       4      24 ..      15      34 ..      13      36 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                        TAT_signal  4 RRdFLKgsAAaaAAaalggca 24
                                      RR+FL g AAa  ++a++gca
  gi|336254690|ref|YP_004597797.1| 15 RRQFLAGLAAAS-GVAVAGCA 34
                                      ******777776.66677776 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   1.8e-05      0.11       5      34 ..       9      38 ..       6      40 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
                        UCR_Fe-S_N  5 esdeptRRDFLyiATgavgaVGaaaaawPf 34
                                       +++p+RR FL   ++a g+ +a++a +P+
  gi|336254690|ref|YP_004597797.1|  9 PEVGPRRRQFLAGLAAASGVAVAGCADLPL 38
                                      5789*******9888888888888887776 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.8   1.8e-05      0.11     112     205 ..     107     220 ..      99     279 .. 0.77
   2 ?   -0.8   0.0      0.13   7.7e+02     133     156 ..     431     454 ..     363     456 .] 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
                           DUF4407 112 laeeqqeeakelkeqlaaa.................ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk 171
                                       + e+++e++++ +e  +a+                 ++a l++l a  ++ +a +d++ ++++a + ++++ ldg  
  gi|336254690|ref|YP_004597797.1| 107 IVENREEAVRARDEADRATgrekyhafrgtrdgretARAALTTLLAIEEDTDALVDELADEREAVQSAVRERLDGID 183
                                       55666666666655555556667777777777777788888888888889999999999999999999999999977 PP

                           DUF4407 172 ...gtgttgvaGkgpaakekkaqldaaqaelaelkak 205
                                           +++ g+++   ++++ +++l +aq+ l+ ++a+
  gi|336254690|ref|YP_004597797.1| 184 yrgDDTEDGRRRAALYYQQLESDLVRAQRLLERWSAD 220
                                       9985555689999********************9998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.13
                           DUF4407 133 aelaeleaqiaalqaeidaaearl 156
                                        e+a+l+a++aal  +++a ++rl
  gi|336254690|ref|YP_004597797.1| 431 GEYARLQAELAALPDAVTAFRERL 454
                                       678888888888888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3724.32
//
Query:       gi|336254691|ref|YP_004597798.1|  [L=271]
Description: Imidazole glycerol phosphate synthase subunit hisF [Halopiger xanaduensis SH-6]
Scores for 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  268.8   0.1    3.8e-80  268.6   0.1    1.0  1  His_biosynth  Histidine biosynthesis protein
    9.9e-08   31.4   0.0    6.2e-07   28.8   0.0    1.9  2  Dus           Dihydrouridine synthase (Dus)
    7.3e-06   25.6   1.2    0.00021   20.8   0.1    2.1  2  NMO           Nitronate monooxygenase
    9.8e-05   21.8   0.0     0.0002   20.8   0.0    1.5  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
    0.00028   20.3   0.1     0.0094   15.3   0.0    2.2  2  ThiG          Thiazole biosynthesis protein ThiG
    0.00059   19.1   0.1     0.0014   17.9   0.0    1.5  2  DHO_dh        Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.011   15.1   0.2       0.12   11.7   0.0    2.1  2  TMP-TENI      Thiamine monophosphate synthase
      0.013   15.0   0.1      0.022   14.2   0.1    1.4  1  PcrB          PcrB family
      0.022   13.7   0.0      0.034   13.1   0.0    1.2  1  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.031   13.4   0.1      0.048   12.8   0.1    1.2  1  Glu_synthase  Conserved region in glutamate synthase
      0.043   12.8   0.2      0.094   11.7   0.2    1.5  1  FMN_dh        FMN-dependent dehydrogenase


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 !  268.6   0.1   2.3e-83   3.8e-80       1     228 [.       6     253 ..       6     254 .. 0.96

  Alignments for each domain:
  == domain 1  score: 268.6 bits;  conditional E-value: 2.3e-83
                                       EEEEEEEE...ETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SS CS
                      His_biosynth   1 riipalDl...kdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfi 74 
                                       riip++D+   +dG+   ++ G+ f++l+y gdpve+ak+y+e gade++++D++a++egre++ld+v+ +a+evfi
  gi|336254691|ref|YP_004597798.1|   6 RIIPCIDVdldEDGNPA-VYTGVHFEDLEYTGDPVEMAKAYNESGADEFVFLDITASAEGRETMLDVVRDVADEVFI 81 
                                       8*******998888755.5********************************************************** PP

                                       EEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE.....C............E CS
                      His_biosynth  75 pvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr.....g............y 134
                                       p++vGGGIr+ ed++e l+agadkv+i+t a+++pel++e a++fgsq+iv+++Darr     g            +
  gi|336254691|ref|YP_004597798.1|  82 PLTVGGGIRTTEDIKETLRAGADKVSITTGALERPELVNEGAKAFGSQCIVISVDARRrfdeqGehyvevdgescwF 158
                                       **********************************************************8877626677777899*99 PP

                                       EEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHH CS
                      His_biosynth 135 kvaikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelks 211
                                       +++ kg+re tg+d+ve+a ++e++gage+ +++id+dGt++G+dl+ltk+++e+v+ pvias G+g +ed++++++
  gi|336254691|ref|YP_004597798.1| 159 ECTKKGGREGTGIDVVEWAAEAESRGAGELFVNSIDKDGTKDGYDLPLTKAVSETVDTPVIASSGCGGPEDMYDVFT 235
                                       ****************************************************************************8 PP

                                       TTC.SEEEESHHHHTTSS CS
                      His_biosynth 212 egv.davivgsalyegel 228
                                       e   da +++s++++ge+
  gi|336254691|ref|YP_004597798.1| 236 EADaDAGLAASIFHFGEY 253
                                       8887************97 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   3.8e-10   6.2e-07     169     251 ..      66     148 ..      30     155 .. 0.79
   2 ?    0.3   0.0      0.18   2.9e+02     169     211 ..     201     243 ..     165     246 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3.8e-10
                                       G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHHHHSC------HHHHH CS
                               Dus 169 tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.stavktgeaepapplaeea 244
                                       +  ++ +++v ++v ip+ + G+I+++ed+++ l+  Gad v i  gal++P l++e  +a+  +++  +  +++++
  gi|336254691|ref|YP_004597798.1|  66 ETMLDVVRDVADEVFIPLTVGGGIRTTEDIKETLRA-GADKVSITTGALERPELVNEgAKAFGSQCIVISVDARRRF 141
                                       4567899****************************9.*******************988888777777777777777 PP

                                       HHHHHHH CS
                               Dus 245 eiveehl 251
                                       + + eh+
  gi|336254691|ref|YP_004597798.1| 142 DEQGEHY 148
                                       7777776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.18
                                       G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEE CS
                               Dus 169 tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvm 211
                                         d+   k+v + v +pvia  ++  +ed+ ++  e  ad+ +
  gi|336254691|ref|YP_004597798.1| 201 GYDLPLTKAVSETVDTPVIASSGCGGPEDMYDVFTEADADAGL 243
                                       556666789999999******9999999999999998888876 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.3e-07   0.00021     179     224 ..      66     111 ..      38     120 .. 0.77
   2 ?    3.7   0.1     0.021        34     148     209 ..     176     231 ..     168     247 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.3e-07
                               NMO 179 kglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                       +  + +v  v+d v iP+   GGi + ++++  L++GA  v i t 
  gi|336254691|ref|YP_004597798.1|  66 ETMLDVVRDVADEVFIPLTVGGGIRTTEDIKETLRAGADKVSITTG 111
                                       334556666666666****************************995 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.021
                               NMO 148 earkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgva 209
                                        a ++e+rGa  l v+  ++ G +    +     + L + v + vd PviA  G    +++ 
  gi|336254691|ref|YP_004597798.1| 176 WAAEAESRGAGELFVNSIDKDGTKD--GY----DLPLTKAVSETVDTPVIASSGCGGPEDMY 231
                                       5666777777777777766655554..34....478999************99987666655 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 !   20.8   0.0   1.2e-07    0.0002     127     170 ..      68     111 ..      66     113 .. 0.92
   2 ?   -3.7   0.0       4.2   6.8e+03     132     145 ..     208     221 ..     206     231 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.2e-07
                                       GHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE--H CS
                      G3P_antiterm 127 vpkvikeikkelkipiiaGGLietkedveealkaGaiavstsnk 170
                                       + +v++++ +e+ ip+  GG i+t ed++e l+aGa+ vs ++ 
  gi|336254691|ref|YP_004597798.1|  68 MLDVVRDVADEVFIPLTVGGGIRTTEDIKETLRAGADKVSITTG 111
                                       77899***********************************9976 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.2
                                       CTSTTS...EEEEE CS
                      G3P_antiterm 132 keikkelkipiiaG 145
                                       k++++++++p+ia+
  gi|336254691|ref|YP_004597798.1| 208 KAVSETVDTPVIAS 221
                                       67888999999996 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.7e-06    0.0094     124     209 ..      29     114 ..      23     139 .. 0.80
   2 ?    2.9   0.0     0.035        58     168     200 ..     208     241 ..     196     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.7e-06
                                       -EEEEEE-S-HHHHHHHHHTT-SEBEEBSSSTTS----S-H.HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-S CS
                              ThiG 124 FevlpYvsdDlvlarrleevGcaavmPlaapiGsglGllnk.ealkiiieeakvPvivDAGigspsdaaqamelGad 199
                                       Fe l Y+ d + +a++ +e G+   + l     s++G +++  +++ + +e+ +P+ v  Gi++++d+ +++  Gad
  gi|336254691|ref|YP_004597798.1|  29 FEDLEYTGDPVEMAKAYNESGADEFVFLD-ITASAEGRETMlDVVRDVADEVFIPLTVGGGIRTTEDIKETLRAGAD 104
                                       7889999999999********99888765.4568888877625678999999************************* PP

                                       EEEESHHHHT CS
                              ThiG 200 avllntavae 209
                                        v + t   e
  gi|336254691|ref|YP_004597798.1| 105 KVSITTGALE 114
                                       **99885444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.035
                                       HHHHHH-SS-BEEES---SHHHHHHHH.HTT-SE CS
                              ThiG 168 kiiieeakvPvivDAGigspsdaaqam.elGada 200
                                       k + e+++ Pvi   G g p+d   ++ e  ada
  gi|336254691|ref|YP_004597798.1| 208 KAVSETVDTPVIASSGCGGPEDMYDVFtEADADA 241
                                       6778999**************9987753555555 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   8.4e-07    0.0014     228     276 ..      66     112 ..      62     122 .. 0.90
   2 ?   -2.9   0.0       1.9   3.1e+03      12      32 ..     215     235 ..     207     245 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.4e-07
                                       HHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                            DHO_dh 228 dialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                                       ++ l v+r++++++   ip+   GGi + eD  e ++aGA  v + t+ 
  gi|336254691|ref|YP_004597798.1|  66 ETMLDVVRDVADEVF--IPLTVGGGIRTTEDIKETLRAGADKVSITTGA 112
                                       567899999999999..****************************9986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.9
                                       SSSEEE-TTSSTTSSSHHHHH CS
                            DHO_dh  12 knpiglAaGfdkegeeilkll 32 
                                         p++ ++G+ +  + ++ + 
  gi|336254691|ref|YP_004597798.1| 215 DTPVIASSGCGGPEDMYDVFT 235
                                       456666666665555554444 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.5e-05      0.12     135     178 ..      65     109 ..      35     112 .. 0.74
   2 ?    1.4   0.0       0.1   1.7e+02     121     160 ..     184     225 ..     160     245 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.5e-05
                          TMP-TENI 135 eplgleglkelaealeiPvvaiGGi.tlenvaevleagadgvavv 178
                                       +   l+ ++++a+++ iP+ + GGi t+e+++e l+agad v++ 
  gi|336254691|ref|YP_004597798.1|  65 RETMLDVVRDVADEVFIPLTVGGGIrTTEDIKETLRAGADKVSIT 109
                                       44568999999**************44699***********9986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.1
                          TMP-TENI 121 gvGpifpTdtKkda..eplgleglkelaealeiPvvaiGGit 160
                                       g+G +f  +  kd   +  +l + k+++e++  Pv+a  G  
  gi|336254691|ref|YP_004597798.1| 184 GAGELFVNSIDKDGtkDGYDLPLTKAVSETVDTPVIASSGCG 225
                                       44444443333332245568889999999******9988864 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.4e-05     0.022     165     208 ..      62     109 ..      49     125 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                                       SS-HHHHHHHHHHHSSSE...EEEESS--SHHHHHHHHCC.SSEEEE- CS
                              PcrB 165 ledveevialkkklekar...livGGGirsaEkAkevvea.ADvivvG 208
                                        e  e + ++++ + ++    l vGGGir +E+ ke+++a AD + + 
  gi|336254691|ref|YP_004597798.1|  62 AEGRETMLDVVRDVADEVfipLTVGGGIRTTEDIKETLRAgADKVSIT 109
                                       45556677776666665412267********************87433 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.1e-05     0.034     105     175 ..      38     111 ..      16     113 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHTT-S.EEEEE-STSS..SHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 105 alervkalveagvd.vlvvdsahgh..sekvleavkeikkkveeveviaGnvataegakaLieagadavkvGiG 175
                                         e +ka  e+g+d ++++d++      e++l++v+ + ++v     ++G + t+e +k+ ++agad v +  G
  gi|336254691|ref|YP_004597798.1|  38 PVEMAKAYNESGADeFVFLDITASAegRETMLDVVRDVADEVFIPLTVGGGIRTTEDIKETLRAGADKVSITTG 111
                                       55666677777776344555432221145677777777777754335788888888888888888887777655 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 ?   12.8   0.1   2.9e-05     0.048     275     307 ..      81     113 ..      66     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.9e-05
                                       -EEEEESS--SHHHHHHHHHHT-SEEE-SHHHH CS
                      Glu_synthase 275 vsliadGglktgadvvkalalGAdavgigtaal 307
                                       + l++ Gg++t++d+  +l  GAd+v+i+t+al
  gi|336254691|ref|YP_004597798.1|  81 IPLTVGGGIRTTEDIKETLRAGADKVSITTGAL 113
                                       56899*************************997 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   5.7e-05     0.094     257     299 ..      68     108 ..      58     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                                       HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEE CS
                            FMN_dh 257 tidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavll 299
                                        +dv  +++++v   i++ v gGir+ +D+   l  GAd v +
  gi|336254691|ref|YP_004597798.1|  68 MLDVVRDVADEVF--IPLTVGGGIRTTEDIKETLRAGADKVSI 108
                                       3444444444443..9***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2099.12
//
Query:       gi|336254692|ref|YP_004597799.1|  [L=299]
Description: hypothetical protein Halxa_3308 [Halopiger xanaduensis SH-6]
Scores for 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-08   33.0  18.3    0.00036   20.1   5.0    2.3  2  zinc_ribbon_2   zinc-ribbon domain
    0.00028   21.0   2.7       0.31   11.2   0.2    2.5  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
  ------ inclusion threshold ------
      0.028   14.5   0.4      0.045   13.9   0.4    1.3  1  ARL6IP6         Haemopoietic lineage transmembrane helix
      0.059   13.3   0.2      0.059   13.3   0.2    2.5  3  DUF3797         Domain of unknown function (DUF3797)
        0.1   12.6  13.3       0.37   10.8   2.6    2.2  2  DZR             Double zinc ribbon
       0.22   11.6   6.9        1.5    8.9   0.5    2.3  2  HypA            Hydrogenase/urease nickel incorporation, meta
        1.1    9.7   5.4         26    5.4   0.1    2.3  2  Cytochrom_c3_2  Cytochrome c3
        1.6    9.0   5.1        1.8    8.8   0.2    2.9  2  zf-RING_7       C4-type zinc ribbon domain
        1.8    8.5   8.9         27    4.8   0.1    4.1  4  Nudix_N_2       Nudix N-terminal
        1.9    8.7  12.9        3.5    7.8   2.3    2.9  2  Zn-ribbon_8     Zinc ribbon domain
        2.7    8.0  13.0       0.79    9.7   4.7    2.7  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        3.6    7.6  16.4       0.26   11.2   1.1    3.3  4  HalOD2          Halobacterial output domain 2
        4.9    6.7  18.3        4.2    6.9   0.3    3.7  3  zf-ribbon_3     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 !   18.5   5.4   8.4e-07    0.0012       1      22 [.       4      25 ..       4      25 .. 0.96
   2 !   20.1   5.0   2.6e-07   0.00036       1      22 [.      75      96 ..      75      98 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.4e-07
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGtp 22
                                      +C+ CG+++ +n++ C +CG++
  gi|336254692|ref|YP_004597799.1|  4 RCTWCGKPHAENDPPCDECGHN 25
                                      6*******************95 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 2.6e-07
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGtp 22
                                      +CpnCG+ +  n++ C++CG p
  gi|336254692|ref|YP_004597799.1| 75 RCPNCGRDHVRNNPPCSRCGNP 96
                                      6*******************87 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 !    9.4   0.2   0.00081       1.1      10      46 ..       4      39 ..       2      46 .. 0.81
   2 !   11.2   0.2   0.00022      0.31       5      43 ..      70     107 ..      66     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00081
                      NOB1_Zn_bind 10 rChaCfkvtkdmtkkFCpkCGnktLkrvavsvdenge 46
                                      rC+ C k   +++   C++CG+++ +++ v  de+ +
  gi|336254692|ref|YP_004597799.1|  4 RCTWCGKPHAEND-PPCDECGHNSFEKAVVRADEDSS 39
                                      7888888766655.45**************9999855 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00022
                      NOB1_Zn_bind   5 kswvlrChaCfkvtkdmtkkFCpkCGnktLkrvavsvde 43 
                                        ++v rC  C +     +   C++CGn+ L++++ ++d+
  gi|336254692|ref|YP_004597799.1|  70 TQYVWRCPNCGRDHV-RNNPPCSRCGNPDLEQTEQTYDD 107
                                       5899******98543.44566***********9998876 PP

>> ARL6IP6  Haemopoietic lineage transmembrane helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   3.3e-05     0.045      30      58 ..     129     156 ..     104     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                           ARL6IP6  30 llaGllvaaFsyglvYlDsavPGvsPPsP 58 
                                       +++Gl+va F+ g+v   s+ PG+ PPsP
  gi|336254692|ref|YP_004597799.1| 129 VVVGLVVALFATGIVP-PSVLPGIGPPSP 156
                                       578***********96.8**********9 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       3.5   4.8e+03      16      23 ..      19      26 ..      18      38 .. 0.64
   2 ?   13.3   0.2   4.3e-05     0.059       7      27 ..      66      87 ..      64      89 .. 0.85
   3 ?   -1.5   0.1       1.7   2.4e+03      16      24 ..      90      98 ..      88     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.5
                           DUF3797 16 CPeCgNnk 23
                                      C eCg n 
  gi|336254692|ref|YP_004597799.1| 19 CDECGHNS 26
                                      77888765 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.3e-05
                           DUF3797  7 vkLdekYv.qCPeCgNnkvlNs 27
                                      v+ + +Yv  CP+Cg ++v N+
  gi|336254692|ref|YP_004597799.1| 66 VDTGTQYVwRCPNCGRDHVRNN 87
                                      6678899857***********8 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.7
                           DUF3797 16 CPeCgNnkv 24
                                      C  CgN   
  gi|336254692|ref|YP_004597799.1| 90 CSRCGNPDL 98
                                      999**9765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  13.3    0.0014       1.9       1      49 []       5      94 ..       5      94 .. 0.91
   2 ?   10.8   2.6   0.00027      0.37       1      22 [.      76      98 ..      76     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0014
                               DZR  1 CpqCgeelppdarfCseCgtk...lkavaa..........................................edrCpsC 34
                                      C  Cg+++ +++  C+eCg++        a                                            rCp+C
  gi|336254692|ref|YP_004597799.1|  5 CTWCGKPHAENDPPCDECGHNsfeK----AvvradedsstassdasgdtgtsgapdefdgaapgtvdtgtqyVWRCPNC 79
                                      999*****************95430....235677889*********************************999***** PP

                               DZR 35 gekvdpearfCpeCG 49
                                      g++   +   C  CG
  gi|336254692|ref|YP_004597799.1| 80 GRDHVRNNPPCSRCG 94
                                      ***99999******9 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00027
                               DZR  1 CpqCgeelppdarfCseCgtk.l 22
                                      Cp+Cg+++  ++  Cs+Cg++ l
  gi|336254692|ref|YP_004597799.1| 76 CPNCGRDHVRNNPPCSRCGNPdL 98
                                      9******************9855 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 ?    5.7   1.0      0.01        14      70      98 ..       2      28 ..       1      36 [. 0.81
   2 ?    8.9   0.5    0.0011       1.5      69      99 ..      72     100 ..      67     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.01
                                      EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 70 kvrCreCgkefeleekalrCpkCgsadve 98
                                      k rC+ Cgk   ++  +  C +Cg++++e
  gi|336254692|ref|YP_004597799.1|  2 KWRCTWCGKPHAEN--DPPCDECGHNSFE 28
                                      689*****888866..458*****98765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0011
                                       -EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                              HypA  69 vkvrCreCgkefeleekalrCpkCgsadvei 99 
                                        + rC +Cg++   ++    C +Cg+ d+e 
  gi|336254692|ref|YP_004597799.1|  72 YVWRCPNCGRDHVRNN--PPCSRCGNPDLEQ 100
                                       6789*****8888663..58******99875 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.3      0.02        28      59      78 ..       3      22 ..       1      25 [. 0.90
   2 ?    5.4   0.1     0.019        26      59      78 ..      74      93 ..      48      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.02
                                      S-GGGTS-TTTSBT-GGGGT CS
                    Cytochrom_c3_2 59 leCteCHkeHkksekvCaeC 78
                                       +Ct C k H ++   C+eC
  gi|336254692|ref|YP_004597799.1|  3 WRCTWCGKPHAENDPPCDEC 22
                                      58****************** PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.019
                                      S-GGGTS-TTTSBT-GGGGT CS
                    Cytochrom_c3_2 59 leCteCHkeHkksekvCaeC 78
                                       +C +C + H +++  C++C
  gi|336254692|ref|YP_004597799.1| 74 WRCPNCGRDHVRNNPPCSRC 93
                                      68*****************9 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 ?    0.6   1.0      0.47   6.5e+02      25      30 ..      18      23 ..      13      23 .. 0.86
   2 ?    8.8   0.2    0.0013       1.8      25      31 ..      75      81 ..      65      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.47
                                      E-TTT- CS
                         zf-RING_7 25 tCpeCG 30
                                       C+eCG
  gi|336254692|ref|YP_004597799.1| 18 PCDECG 23
                                      6****9 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0013
                                      E-TTT-- CS
                         zf-RING_7 25 tCpeCGR 31
                                      +Cp+CGR
  gi|336254692|ref|YP_004597799.1| 75 RCPNCGR 81
                                      9*****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 ?    2.1   1.1      0.13   1.8e+02       3      13 ..       5      15 ..       5      24 .. 0.66
   2 ?    2.0   0.1      0.15   2.1e+02       3      14 ..      19      31 ..      18      38 .. 0.67
   3 ?    2.3   0.1      0.12   1.7e+02       3       8 ..      76      81 ..      75      89 .. 0.69
   4 ?    4.8   0.1     0.019        27       3      22 ..      90     110 ..      90     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.13
                                      -TTT--B-EEE CS
                         Nudix_N_2  3 CsqCGtpvelr 13
                                      C+ CG+p +  
  gi|336254692|ref|YP_004597799.1|  5 CTWCGKPHAEN 15
                                      89999886544 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                                      -TTT--B.-EEE- CS
                         Nudix_N_2  3 CsqCGtp.velri 14
                                      C +CG+   e ++
  gi|336254692|ref|YP_004597799.1| 19 CDECGHNsFEKAV 31
                                      8889987555555 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.12
                                      -TTT-- CS
                         Nudix_N_2  3 CsqCGt 8 
                                      C++CG 
  gi|336254692|ref|YP_004597799.1| 76 CPNCGR 81
                                      777775 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.019
                                       -TTT--B.-EEE--TT-SS-E CS
                         Nudix_N_2   3 CsqCGtp.velripdgDnreR 22 
                                       Cs CG+p +e+     D+ eR
  gi|336254692|ref|YP_004597799.1|  90 CSRCGNPdLEQTEQTYDDIER 110
                                       *******88876666666665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   3.1     0.018        24       7      38 ..       4      29 ..       2      31 .. 0.73
   2 ?    7.8   2.3    0.0025       3.5       4      37 ..      72      99 ..      71     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.018
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.evrr 38
                                      rC+ Cg+ + +       ++++C eCg+   ++
  gi|336254692|ref|YP_004597799.1|  4 RCTWCGKPHAE-------NDPPCDECGHnSFEK 29
                                      79999966663.......3566*****977776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0025
                       Zn-ribbon_8  4 YeYrCeeCghefevlqsisdapltaCPeCgs.evr 37
                                      Y  rC +Cg+++   +  +   +++C +Cg  +++
  gi|336254692|ref|YP_004597799.1| 72 YVWRCPNCGRDHV--R--N---NPPCSRCGNpDLE 99
                                      7889*****5544..3..2...5669999997776 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 ?    2.5   1.2       0.1   1.4e+02       4      16 ..       2      11 ..       2      13 .. 0.81
   2 ?    9.7   4.7   0.00057      0.79       2      12 ..      71      81 ..      70     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.1
                    Zn_ribbon_SprT  4 vYrCtgCgreyth 16
                                      ++rCt Cg   + 
  gi|336254692|ref|YP_004597799.1|  2 KWRCTWCG---KP 11
                                      7******9...54 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00057
                    Zn_ribbon_SprT  2 kyvYrCtgCgr 12
                                      +yv+rC++Cgr
  gi|336254692|ref|YP_004597799.1| 71 QYVWRCPNCGR 81
                                      8*********5 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.3     0.014        19      32      45 ..       3      16 ..       1      21 [. 0.81
   2 ?   -2.1   0.1       2.8   3.8e+03      34      39 ..      19      24 ..      18      26 .. 0.77
   3 ?   11.2   1.1   0.00019      0.26      28      39 ..      70      81 ..      56      92 .. 0.73
   4 ?   -1.6   0.1       1.9   2.7e+03      34      39 ..      90      95 ..      89      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.014
                            HalOD2 32 WkCtrCGevqaaAd 45
                                      W+Ct CG+  a  d
  gi|336254692|ref|YP_004597799.1|  3 WRCTWCGKPHAEND 16
                                      *******9776665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                            HalOD2 34 CtrCGe 39
                                      C +CG+
  gi|336254692|ref|YP_004597799.1| 19 CDECGH 24
                                      888887 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00019
                            HalOD2 28 GayvWkCtrCGe 39
                                        yvW+C +CG 
  gi|336254692|ref|YP_004597799.1| 70 TQYVWRCPNCGR 81
                                      469********6 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.9
                            HalOD2 34 CtrCGe 39
                                      C+rCG+
  gi|336254692|ref|YP_004597799.1| 90 CSRCGN 95
                                      889986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   6.2      0.11   1.5e+02       5      24 ..       5      24 ..       3      26 .. 0.84
   2 ?    6.9   0.3     0.003       4.2       4      10 ..      75      81 ..      75      85 .. 0.74
   3 ?    4.2   0.4     0.021        29       5      11 ..      90      96 ..      88     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                       zf-ribbon_3  5 CPnCGa.plssddnvCpyCGt 24
                                      C  CG+ + ++ d+ C  CG+
  gi|336254692|ref|YP_004597799.1|  5 CTWCGKpH-AENDPPCDECGH 24
                                      66699966.999*******97 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.003
                       zf-ribbon_3  4 rCPnCGa 10
                                      rCPnCG 
  gi|336254692|ref|YP_004597799.1| 75 RCPNCGR 81
                                      7999985 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.021
                       zf-ribbon_3  5 CPnCGap 11
                                      C++CG+p
  gi|336254692|ref|YP_004597799.1| 90 CSRCGNP 96
                                      *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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):              13  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2250.92
//
Query:       gi|336254693|ref|YP_004597800.1|  [L=97]
Description: DNA-directed RNA polymerase subunit L [Halopiger xanaduensis SH-6]
Scores for complete 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-17   63.6   0.0    1.3e-17   63.4   0.0    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
    1.7e-07   30.5   0.0    3.4e-07   29.6   0.0    1.5  1  RNA_pol_L    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 !   63.4   0.0   1.4e-21   1.3e-17       1      74 [.      12      88 ..      12      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 1.4e-21
                                      EEEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTT...SEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHHH CS
                       RNA_pol_L_2  1 eltfeingEDhTLgnlLrhlllknpsVefagYkipHPle...pkmnlriqtkssnnpleaLkkalkdlldicdelee 74
                                      el++ei+gEDhT++n+L+ +ll++++V +a+Y+++  ++    +  l+i+t+++ +pleaL++a+ d++++  +++e
  gi|336254693|ref|YP_004597800.1| 12 ELSIEIAGEDHTFMNVLKGALLEHEDVSAATYDVNPEQSggqTEPILTIKTEGGVDPLEALEEAAVDVREKAMSFRE 88
                                      689**********************************6666699************************999887765 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 !   29.6   0.0   3.8e-11   3.4e-07       2      68 ..      15      82 ..      14      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.8e-11
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  2 fllrgvdhtlgNaLRrillsevpgvaiea....pvvkvn..tdkdklilevetdgslkPeealkeAlkiLkek 68
                                       ++ g+dht++N L+  ll e ++v  ++    p    +    +++ il+++t g ++P eal+eA+ + +ek
  gi|336254693|ref|YP_004597800.1| 15 IEIAGEDHTFMNVLKGALL-EHEDVSAATydvnP----EqsGGQTEPILTIKTEGGVDPLEALEEAAVDVREK 82
                                      5799***************.77777766655552....1446667789*******************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 827.83
//
Query:       gi|336254694|ref|YP_004597801.1|  [L=622]
Description: Rhomboid family protein [Halopiger xanaduensis SH-6]
Scores for 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-09   35.9  17.0    7.4e-06   26.0   7.6    2.8  3  Rhomboid  Rhomboid family
  ------ inclusion threshold ------
        4.3    6.9  20.5          1    9.0   0.9    4.2  5  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.59   5.2e+03      78     113 ..      14      56 ..       7      67 .. 0.51
   2 !   15.6   0.2   1.3e-06     0.012       9      43 ..      88     122 ..      79     125 .. 0.88
   3 !   26.0   7.6   8.3e-10   7.4e-06      44     148 ..     146     255 ..     129     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.59
                                       HHHHHHHHHHHHHHCCCCGS----HC..........CCCCCCC CS
                          Rhomboid  78 aifgllgallvlvprnrkllrkliia.......llllllfill 113
                                       a f+l  a++ +  r  +++r + +        + +l++++++
  gi|336254694|ref|YP_004597801.1|  14 ATFALSLATVSRLDRPARRWRDAAGErlvagvpWGTLVVVAFV 56 
                                       4555555555555555555555555564444443333333333 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.3e-06
                                       HHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Rhomboid   9 rlltsmflHagwlHllfNmlallvfGsplerrlGs 43 
                                        l t++f Ha++ Hl++Nm+  +v ++ +e  +G+
  gi|336254694|ref|YP_004597801.1|  88 GLATAAFAHADLGHLVGNMAGTVVAAPIAEYAWGH 122
                                       5899*******************999999988775 PP

  == domain 3  score: 26.0 bits;  conditional E-value: 8.3e-10
                                       HHHHHHHHHHHHHHHHHHHHHH-S...-EESSHHHHHHHHHHHHHHHHCCCCGS----HC...CCCCCCCCCCHHHC CS
                          Rhomboid  44 lrflllyllsglagsllsllfsaesesplvGaSGaifgllgallvlvprnrkllrkliiallllllfillnlvlgll 120
                                       +r l+l+ l++++ +ll+++f      p++G+SG++f+++++++v+ p +   +       +ll ++ +++  +++ 
  gi|336254694|ref|YP_004597801.1| 146 VRALVLFPLAVIGIGLLTSVFALG---PIIGFSGVVFAIVAFAIVHYPIATLIAAIGAQS-ILLTVYRAIQNPVSVH 218
                                       78899999*************999...9**********************9998888877.4444444444333333 PP

                                       TSS.........STTTHHHHHHHHHHHHHHHHHHCCH CS
                          Rhomboid 121 pra.........ggvsnlAHlgGllaGlllgllllrr 148
                                         +         +g++ ++H  G+ +Gl+lg+++l+r
  gi|336254694|ref|YP_004597801.1| 219 VVEqspptapgwAGIAIQGHALGFFIGLVLGAVVLER 255
                                       333469***************************9986 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.0   0.00015       1.3       7      50 ..       5      64 ..       2      75 .. 0.71
   2 ?   -0.8   0.3      0.11     1e+03      27      49 ..     139     161 ..     105     170 .. 0.76
   3 ?   -4.1   4.8       1.2     1e+04      28      50 ..     166     188 ..     140     218 .. 0.51
   4 ?    9.0   0.9   0.00011         1       9      92 ..     239     331 ..     231     355 .. 0.68
   5 ?   -0.0   0.0     0.068   6.1e+02      28      51 ..     397     420 ..     380     449 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00015
                           DUF4131  7 lvllalllllllllllllrr......rprrrv.............llllllllllallgfalr 50
                                      +v+la++l+++++l l          rp rr+             +++l +++++++++++++
  gi|336254694|ref|YP_004597801.1|  5 AVALAAALAATFALSL---AtvsrldRPARRWrdaagerlvagvpWGTLVVVAFVVCVYLFVQ 64
                                      3333333333333333...22335778888889999***********************9886 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.11
                           DUF4131  27 rprrrvllllllllllallgfal 49 
                                       r+r   ++ +l+l+ la++g+ l
  gi|336254694|ref|YP_004597801.1| 139 RWRTNPWVRALVLFPLAVIGIGL 161
                                       78888888888888888888765 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 1.2
                           DUF4131  28 prrrvllllllllllallgfalr 50 
                                            +++++ + +++++++ ++
  gi|336254694|ref|YP_004597801.1| 166 FALGPIIGFSGVVFAIVAFAIVH 188
                                       33333444444444444333333 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.00011
                           DUF4131   9 llalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqlles.gqeviveGvv......... 75 
                                       +l++++ l l +++l rr +r+  l ++l++l++a++  +++ ++ ++   ++++   g  v+v+ v+         
  gi|336254694|ref|YP_004597801.1| 239 ALGFFIGLVLGAVVLERRGRRPNALHVWLAILIFAFSRGLWQIYWYGEG--NSFILFrGPGVVVVTVLalvitiala 313
                                       6889999999999999998888888888888888888888888888773..33333324444433333444455667 PP

                           DUF4131  76 .aslpeltgsgtrfvlev 92 
                                        +++p + ++  rfv++ 
  gi|336254694|ref|YP_004597801.1| 314 gSDEPVVPRRVERFVARL 331
                                       666777776666777764 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 0.068
                           DUF4131  28 prrrvllllllllllallgfalra 51 
                                       +rr  ++l+ ll l++l+g a+++
  gi|336254694|ref|YP_004597801.1| 397 TRRSSAFLVVLLVLAVLAGTAIPV 420
                                       455555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 0.54u 0.20s 00:00:00.74 Elapsed: 00:00:00.36
# Mc/sec: 5215.61
//
Query:       gi|336254695|ref|YP_004597802.1|  [L=272]
Description: phosphonate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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  116.5   0.0    1.6e-33  116.1   0.0    1.2  1  ABC_tran      ABC transporter
    9.9e-07   28.4   0.1    1.7e-06   27.6   0.1    1.3  1  AAA_29        P-loop containing region of AAA domain
    9.7e-06   25.2   0.0    0.00017   21.1   0.0    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00047   20.6   0.2    0.00074   19.9   0.2    1.4  1  AAA_16        AAA ATPase domain
    0.00053   19.9   0.1        1.1    9.0   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0053   16.7   0.3       0.46   10.4   0.1    2.2  2  NTPase_1      NTPase
  ------ inclusion threshold ------
      0.012   15.9   0.1       0.12   12.6   0.1    2.1  1  AAA_22        AAA domain
      0.013   15.3   1.9       0.11   12.2   1.9    2.1  1  AAA_30        AAA domain
      0.018   14.4   0.0      0.027   13.8   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.025   15.1   0.0      0.036   14.6   0.0    1.2  1  AAA_23        AAA domain
      0.036   13.0   0.3      0.059   12.4   0.3    1.3  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.05   14.0   0.0       0.12   12.8   0.0    1.8  1  AAA           ATPase family associated with various cellular 
       0.18   11.6   0.0       0.25   11.0   0.0    1.2  1  PRK           Phosphoribulokinase / Uridine kinase family
       0.25   11.2   0.0       0.34   10.8   0.0    1.2  1  Rad17         Rad17 P-loop domain
       0.29   11.3   1.9        1.4    9.0   1.4    2.2  1  AAA_33        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 !  116.1   0.0   1.3e-36   1.6e-33       1     136 [.      69     217 ..      69     218 .. 0.95

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 1.3e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l++vsl++++ge+v++ G++G+GKSt+l +++gll pt G++++ ++dl++    ++++  r+++g+++q  +l p 
  gi|336254695|ref|YP_004597802.1|  69 LRDVSLSIRPGEIVGLEGPSGSGKSTILHAVTGLLVPTDGTVEVMETDLTSlserERTRMRRRHVGIVFQRFHLLPS 145
                                       689***********************************************999988889999*************** PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       l++r n             +++e++e++l+ +gl + + +     p +LSgG++qrva+aral+++p+++++DEpt
  gi|336254695|ref|YP_004597802.1| 146 LSARANvalplvqvgvpkaTRRERAEELLEGVGLADRASHL----PGELSGGERQRVAIARALATDPDVIVADEPT 217
                                       ****************99888888*********99944444....6*****************************9 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 !   27.6   0.1   1.5e-09   1.7e-06      15      50 ..      72     107 ..      67     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.5e-09
                            AAA_29  15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                        +++i++ +++ l GpsGsGKST+l A++ lLvp+ 
  gi|336254695|ref|YP_004597802.1|  72 VSLSIRPGEIVGLEGPSGSGKSTILHAVTGLLVPTD 107
                                       5677887789999*********************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 !   21.1   0.0   1.4e-07   0.00017      27     212 ..      82     263 ..      64     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.4e-07
                                       EEEEESTTSSHHHHHHHHHHHCTT.TT.TTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAilFvLGersa.kklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrr 102
                                         + Gp GSGKs +l A+  +L  ++   ++ +++l++l    +e+ ++ + +v i+f+     l+  + + ++   
  gi|336254695|ref|YP_004597802.1|  82 VGLEGPSGSGKSTILHAVTGLLVPTDGtVEVMETDLTSLSE--RERTRMRRRHVGIVFQRFHL-LPSLSARANVALP 155
                                       55779*************99998665403555555666554..5889999999***9988766.5888888899999 PP

                                       EETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                       +++ g  + +  ++  +  e   l  +a   + +LSgGe++ va+a  +A+   +p  + + De   +LD +  ++v
  gi|336254695|ref|YP_004597802.1| 156 LVQVGVPKATRRERAEELLEGVGLADRASHLPGELSGGERQRVAIARALAT---DPD-VIVADEPTGELDTATGRNV 228
                                       999998777777777777777777777777788*************99986...455.5688*************** PP

                                       HHHHH..HHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 180 aellk..eksknaQfivislreemlekadklvgvt 212
                                        ell    ++ +  ++v s+++++l+ ad+++ ++
  gi|336254695|ref|YP_004597802.1| 229 LELLTdvGRERDRAVLVASHDDDTLAVADRVISLR 263
                                       ****9443555689****************99876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   6.2e-07   0.00074      23     142 ..      77     214 ..      63     246 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.2e-07
                            AAA_16  23 rp.elvllsGesGvGKsslvrellralekdggif..lrgkcdql.esa.ipy.....salaqalareellrqllde. 88 
                                       rp e+v l G+sG+GKs+++ ++   l  ++g +  ++++ ++l e++ + +     +    ++ r +ll  l ++ 
  gi|336254695|ref|YP_004597802.1|  77 RPgEIVGLEGPSGSGKSTILHAVTGLLVPTDGTVevMETDLTSLsERErT-RmrrrhV--GIVFQRFHLLPSLSARa 150
                                       334899******************99999977776577777777633332.2244333..33333449999999997 PP

                            AAA_16  89 ...........aesaeleawrekleeala......avpelagaea..srllellkrllallsrderplvlvlD 142
                                                  ++++ +e++ e l    +       +++l+g+++  +r + +++r+l   ++  +p v+v D
  gi|336254695|ref|YP_004597802.1| 151 nvalplvqvgvPKATRRERAEELL----EgvgladRASHLPGELSggERQRVAIARAL---AT--DPDVIVAD 214
                                       777777666654443333333333....133357766666666666666666666666...22..22355555 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 !    9.0   0.1   0.00089       1.1       4      22 ..      84     102 ..      81     129 .. 0.82
   2 !    9.0   0.0   0.00095       1.1     187     302 ..     172     253 ..     131     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00089
                            AAA_21   4 liGpNgsGKSnLLdaldll 22 
                                       l Gp gsGKS++L a  +l
  gi|336254695|ref|YP_004597802.1|  84 LEGPSGSGKSTILHAVTGL 102
                                       559************9988 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00095
                            AAA_21 187 rlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllli 263
                                       +l              +eg+ l ++++++                  + elS G ++  a++ al+ ++   ++++ 
  gi|336254695|ref|YP_004597802.1| 172 EL--------------LEGVGLADRASHL------------------PGELSGGERQRVAIARALATDP---DVIVA 213
                                       33..............3444444444444..................3578****99989999999888...9**** PP

                            AAA_21 264 DEpEngLHPkllrrllell.kelsrngaQviltTHSplll 302
                                       DEp   L+ +  r +lell +  ++++  v++++H+   l
  gi|336254695|ref|YP_004597802.1| 214 DEPTGELDTATGRNVLELLtDVGRERDRAVLVASHDDDTL 253
                                       *******************766666**********97655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00038      0.46       3      29 ..      83     109 ..      81     135 .. 0.82
   2 ?    4.3   0.0     0.027        33      89     153 ..     200     268 ..     189     269 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00038
                                       EEE--TTSSHHHHHHHHHHHH...GGG CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvk 29 
                                        + Gp+G+GK+T+++ v+ ll   + +
  gi|336254695|ref|YP_004597802.1|  83 GLEGPSGSGKSTILHAVTGLLVPTDGT 109
                                       678***************999655444 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.027
                                       HHHHH.HHH-EEEE--.-STTGGG-.HHHHHHHHHHHT.TTSEEEEE--SS--SHHHHHHHT-TT-EEE CS
                          NTPase_1  89 lrkal.seadviviDE.iGkmElks.kkfkeaveevLk.sekpvlavihrrkdlalveeirerkdvkvf 153
                                       + +al +++dviv DE  G++   + +++ e +++v + +++ vl+  h  ++la+ +++ + +d++v+
  gi|336254695|ref|YP_004597802.1| 200 IARALaTDPDVIVADEpTGELDTATgRNVLELLTDVGReRDRAVLVASHDDDTLAVADRVISLRDGQVV 268
                                       34444489********78999976427899999999997888888888888899999999999998886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1    0.0001      0.12      10      99 ..      84     215 ..      76     248 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee........................................erpevv..f 44 
                                       + G+sG+GK+t l  ++  l+      +                                        +r+ v+  +
  gi|336254695|ref|YP_004597802.1|  84 LEGPSGSGKSTILHAVTGLLVPT----DgtvevmetdltslserertrmrrrhvgivfqrfhllpslsARANVAlpL 156
                                       77***************999743....12344666666666666666666666666666666666666555554556 PP

                            AAA_22  45 vtlpsst.sskdllrellralglelka.....erlsseellealeqalraravielliiDE 99 
                                       v++ +++ ++++ ++ell+ +gl   a     e    e+ + a+++al +  +  +++ DE
  gi|336254695|ref|YP_004597802.1| 157 VQVGVPKaTRRERAEELLEGVGLADRAshlpgELSGGERQRVAIARALATDPD--VIVADE 215
                                       66666666666666666666666666655444333333333444444444433..666666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.9     9e-05      0.11      19      49 ..      80     110 ..      72     251 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9e-05
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrv 49 
                                        ++ l+Gp G+GK+t+l a++ ++    g+v
  gi|336254695|ref|YP_004597802.1|  80 EIVGLEGPSGSGKSTILHAVTGLLVPTDGTV 110
                                       47889***************98887774333 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.3e-05     0.027      25      71 ..      82     126 ..      65     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeek 71 
                                       + l Gp+GsGK+ + +++++ll p + +  +  + ++s++++++  +
  gi|336254695|ref|YP_004597802.1|  82 VGLEGPSGSGKSTILHAVTGLLVPTDGTVEVMETDLTSLSERER--T 126
                                       5589******************9998776666677888887333..3 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     3e-05     0.036      21      43 ..      81     103 ..      61     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
                            AAA_23  21 ltlItGpNGaGKTTildAiklaL 43 
                                       ++ + Gp G+GK+Til A++  L
  gi|336254695|ref|YP_004597802.1|  81 IVGLEGPSGSGKSTILHAVTGLL 103
                                       66778*************98766 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 ?   12.4   0.3   4.9e-05     0.059      24      69 ..      74     119 ..      59     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.9e-05
                                       GG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                              MeaB  24 akaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPss 69 
                                        +    + vGl G  G+Gkst+++a++  l+     v v+  D +s
  gi|336254695|ref|YP_004597802.1|  74 LSIRPGEIVGLEGPSGSGKSTILHAVTGLLVPTDGTVEVMETDLTS 119
                                       55555678***********************999999999999877 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 ?   12.8   0.0   9.7e-05      0.12       3      51 ..      84     138 ..      82     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.7e-05
                                       EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCS.SSSTTHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel.....gvefleisgsell.skyvgesekkirelfk 51 
                                       l Gp G GK+++ +av   l      ve++e+++++l   +    + +++  +f+
  gi|336254695|ref|YP_004597802.1|  84 LEGPSGSGKSTILHAVTGLLvptdgTVEVMETDLTSLSeRERTRMRRRHVGIVFQ 138
                                       78*****************977665599999999999844444444444444444 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00021      0.25       1      29 [.      81     109 ..      81     140 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                               PRK   1 vIgvagsSGaGkttvarklekifgrekvk 29 
                                       ++g+ g+SG+Gk+t+ ++++ ++  +  +
  gi|336254695|ref|YP_004597802.1|  81 IVGLEGPSGSGKSTILHAVTGLLVPTDGT 109
                                       799***************99998743333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00029      0.34      34      70 ..      68     104 ..      65     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                             Rad17  34 wlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70 
                                       +l+  +L  r+ +i+ + GPsG gkst+++ ++  l+
  gi|336254695|ref|YP_004597802.1|  68 ALRDVSLSIRPGEIVGLEGPSGSGKSTILHAVTGLLV 104
                                       6777789999999***************998876665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.4    0.0012       1.4       4      20 ..      84     100 ..      81     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                            AAA_33   4 lvGlpGsGKstlaerll 20 
                                       l G++GsGKst ++ + 
  gi|336254695|ref|YP_004597802.1|  84 LEGPSGSGKSTILHAVT 100
                                       78*********998774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2217.55
//
Query:       gi|336254696|ref|YP_004597803.1|  [L=449]
Description: hypothetical protein Halxa_3312 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00023   21.6   3.4    0.00023   21.6   3.4    2.8  3  FtsX      FtsX-like permease family
  ------ inclusion threshold ------
        2.8    8.1   5.9        2.3    8.3   0.2    3.3  3  EutK_C    Ethanolamine utilization protein EutK C-terminus


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.029   2.6e+02      27      46 ..      51      71 ..      41      90 .. 0.63
   2 ?   -1.5   0.5       0.4   3.6e+03      30      86 ..     323     332 ..     311     344 .. 0.47
   3 !   21.6   3.4   2.6e-08   0.00023       1      94 [.     349     441 ..     349     443 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.029
                              FtsX 27 litlvalviG.lglgllaaql 46
                                       i++val i+ l++ + +a  
  gi|336254696|ref|YP_004597803.1| 51 TISAVALTIAlLVVVTGVAMG 71
                                      455555555533333333333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.4
                              FtsX  30 lvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagll 86 
                                       l+al+++                                               +++
  gi|336254696|ref|YP_004597803.1| 323 LLALLAS-----------------------------------------------VVI 332
                                       1111111...............................................111 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 2.6e-08
                              FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlll 77 
                                       +r +++l a+G+   + ll++ + +l++t+v++v+G ++g+    ++++v ++ v  + +  ++ ++ v  +++++l
  gi|336254696|ref|YP_004597803.1| 349 RRTLAVLEAVGFPASSRLLVVALSTLVTTVVGAVLGAAIGICGVHAVNAVASATVA-PGAVATVHPLFVPYAVGVAL 424
                                       6889**************************************************88.******************** PP

                              FtsX  78 llallagllsiskilkk 94 
                                       +  l+a+ +++  ++++
  gi|336254696|ref|YP_004597803.1| 425 VSGLVAVPYPLAVASRT 441
                                       ******99998888776 PP

>> EutK_C  Ethanolamine utilization protein EutK C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3     0.093   8.3e+02       6      26 ..      60      80 ..      56      82 .. 0.90
   2 ?   -0.7   0.1      0.16   1.5e+03      21      45 ..     288     316 ..     285     322 .. 0.64
   3 ?    8.3   0.2   0.00026       2.3       3      41 ..     319     355 ..     317     360 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.093
                            EutK_C  6 aLLaLLasvrqGmtaGevaah 26
                                      aLL ++  v  G++ G v +h
  gi|336254696|ref|YP_004597803.1| 60 ALLVVVTGVAMGLADGGVVSH 80
                                      99***************9998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.16
                            EutK_C  21 GevaahfaWP...Lekarq.vLeqLfsdG 45 
                                        e aa  a+P   +e a +  Le Lf dG
  gi|336254696|ref|YP_004597803.1| 288 AEAAAADAYPdaaVESAAElDLESLFDDG 316
                                       56666666663333444431599999999 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00026
                            EutK_C   3 saeaLLaLLasvrqGmtaGevaahfaWPLekarqvLeqL 41 
                                        a +LLaLLasv   + a  va  ++  +++ r+ L  L
  gi|336254696|ref|YP_004597803.1| 319 LATSLLALLASVV--ICASFVATTMGMTVDQDRRTLAVL 355
                                       5779********6..8999*************9988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3533.12
//
Query:       gi|336254697|ref|YP_004597804.1|  [L=410]
Description: hypothetical protein Halxa_3313 [Halopiger xanaduensis SH-6]
Scores for 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   63.9   4.0    2.5e-17   63.9   4.0    2.1  3  MacB_PCD   MacB-like periplasmic core domain
    9.5e-10   38.8   1.1    9.5e-10   38.8   1.1    2.7  3  FtsX       FtsX-like permease family
  ------ inclusion threshold ------
      0.011   14.6   0.8      0.011   14.6   0.8    2.1  2  LptF_LptG  Lipopolysaccharide export system permease LptF/Lpt


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   4.0   4.1e-21   2.5e-17       1     194 [.      28     255 ..      28     256 .. 0.68
   2 ?   -6.8   6.6         3   1.8e+04      45      45 ..     328     328 ..     282     397 .. 0.44
   3 ?   -2.8   0.2       1.1   6.8e+03       7      19 ..     382     394 ..     376     405 .. 0.72

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 4.1e-21
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgk......gsgeslsdpdve..alrrevp.vea 68 
                                       ++ltv+++a++v av+++ slg g+ ++ ++ + ++++ + ++ ++      g+ +++  ++    +l  + + v+ 
  gi|336254697|ref|YP_004597804.1|  28 TALTVIAVAVAVLAVTLLASLGVGVVETGERGLDNADQDIWISSDPvdpaasGTENPIVGSHGIagQLM-QRDdVSY 103
                                       89**********************************998889888777766655555444433112232.3345*** PP

                          MacB_PCD  69 vapvv..tvrgggsg...eeevtvvgvdp.....dyfkvfgl..klaeGrffteadlrg......gpnvvvigeela 127
                                       +ap+    v+ g++    e++  +vgv +     d+++  g+  ++        ++ +g       + ++v++ ++a
  gi|336254697|ref|YP_004597804.1| 104 AAPIGmyDVYVGTDPddlERH-PAVGVREthegfDFQSGGGFetPP--------EAYEGgrteepMTEEIVLDPRVA 171
                                       ***877755666542356333.245555211133444444443222........222221122225668******** PP

                          MacB_PCD 128 erlf.pvGdtirl.........kpftVvGvledppgsgsalgddavylp.....lttl.......qrrsitvrlkdg 182
                                       e++   vGdti +         ++ftVvG  + + +  + lg   v +p     +  +       ++++it+ ++dg
  gi|336254697|ref|YP_004597804.1| 172 EKIGaDVGDTIYVgtsrqtapeYEFTVVGTSSYY-S--QYLGSETVTMPlvdlqA--VagttgtdRATFITADVADG 243
                                       **9999***********9999999******6444.2..2355678****666440..233344445667******** PP

                          MacB_PCD 183 adleaaaaelek 194
                                       ad ea+a el++
  gi|336254697|ref|YP_004597804.1| 244 ADREAVASELDE 255
                                       *********986 PP

  == domain 2  score: -6.8 bits;  conditional E-value: 3
                          MacB_PCD  45 g 45 
                                       g
  gi|336254697|ref|YP_004597804.1| 328 G 328
                                       2 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.1
                          MacB_PCD   7 GiaiGvaaviaiv 19 
                                       ++ai v+ v+a+v
  gi|336254697|ref|YP_004597804.1| 382 AVAIVVGTVVALV 394
                                       6777777777776 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4     0.094   5.6e+02      29      83 ..      31      46 ..       7      56 .. 0.59
   2 ?   -1.8   0.3      0.73   4.3e+03      34      70 ..     286     292 ..     266     307 .. 0.50
   3 !   38.8   1.1   1.6e-13   9.5e-10       1      94 [.     310     402 ..     310     403 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.094
                              FtsX 29 tlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllalla 83
                                      t++a +++                                       +l ++lla
  gi|336254697|ref|YP_004597804.1| 31 TVIAVAVA---------------------------------------VLAVTLLA 46
                                      22222222.......................................22222222 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.73
                              FtsX  34 viGlglgllaaqllsdvllssvfsselkisidlitvl 70 
                                       ++Gl++                              +
  gi|336254697|ref|YP_004597804.1| 286 LVGLAI------------------------------V 292
                                       333222..............................1 PP

  == domain 3  score: 38.8 bits;  conditional E-value: 1.6e-13
                              FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlll 77 
                                       + e++ lra+G++++ +++ + +++l++++v+ ++Gl++  l++  ++ v  s+ + +e  +++++  +++++++++
  gi|336254697|ref|YP_004597804.1| 310 RDELAALRAVGLSRRVLAGTIAVQGLVTGVVGGAVGLVATPLLSSGFNRVAASVAG-FENLLQTPPKVYAAGFAVAI 385
                                       5799********************************99999999999999888766.******************** PP

                              FtsX  78 llallagllsiskilkk 94 
                                       ++ ++++l++ +++ k+
  gi|336254697|ref|YP_004597804.1| 386 VVGTVVALVAGWRAGKY 402
                                       ************99776 PP

>> LptF_LptG  Lipopolysaccharide export system permease LptF/LptG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.4    0.0094        56     287     322 ..      13      49 ..      11      57 .. 0.84
   2 ?   14.6   0.8   1.9e-06     0.011      73     146 ..     305     378 ..     284     390 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0094
                         LptF_LptG 287 liaaplglvkrrggrglrlliaillfvl.yyvllslg 322
                                       ++++++++  r  gr++  +ia++++vl + +l slg
  gi|336254697|ref|YP_004597804.1|  13 VVGLAFAQLRRSPGRTALTVIAVAVAVLaVTLLASLG 49 
                                       7899**************9999999999777777666 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.9e-06
                         LptF_LptG  73 grLaedsEltalrsaGislgrllrpililalllsvlsfllnnyvvPwankkaesllseirqkspsllikpgvfi 146
                                          +++ El+alr+ G+s+  l+  i + +l++ v+  ++ +++ P  +  ++++ ++++  ++ l+ +p+v  
  gi|336254697|ref|YP_004597804.1| 305 VAAQQRDELAALRAVGLSRRVLAGTIAVQGLVTGVVGGAVGLVATPLLSSGFNRVAASVAGFENLLQTPPKVYA 378
                                       5557899*********************************************9999999998888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3234.96
//
Query:       gi|336254698|ref|YP_004597805.1|  [L=205]
Description: methyltransferase small [Halopiger xanaduensis SH-6]
Scores for 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-13   48.6   0.0    9.5e-13   48.0   0.0    1.2  1  MTS              Methyltransferase small domain
      1e-11   44.8   0.2    1.4e-11   44.4   0.2    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    7.2e-10   39.4   0.0    1.3e-09   38.6   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    4.5e-09   36.3   0.0    6.9e-09   35.7   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    7.4e-07   29.7   0.0    1.4e-06   28.8   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    7.7e-07   29.0   0.1    2.8e-06   27.2   0.1    1.9  1  UPF0020          Putative RNA methylase family UPF0020
    0.00048   19.8   0.0    0.00061   19.5   0.0    1.1  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00057   19.7   0.0    0.00086   19.1   0.0    1.2  1  Met_10           Met-10+ like-protein
    0.00082   19.4   0.0      0.001   19.1   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
     0.0014   18.2   0.0     0.0017   18.0   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0015   17.9   0.0     0.0035   16.7   0.0    1.5  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0022   18.7   0.0     0.0043   17.8   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
     0.0043   16.3   0.0      0.006   15.9   0.0    1.2  1  N6_Mtase         N-6 DNA Methylase
     0.0059   15.8   0.0     0.0077   15.4   0.0    1.2  1  Methyltransf_3   O-methyltransferase
     0.0074   16.1   0.0     0.0078   16.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.026   14.3   0.0      0.035   13.9   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.048   13.7   0.0      0.065   13.3   0.0    1.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.14   11.6   0.0       0.28   10.6   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
       0.15   11.7   0.0        0.2   11.3   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F


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 !   48.0   0.0     1e-15   9.5e-13      27     127 ..      45     144 ..      34     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1e-15
                                       CHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEE CS
                               MTS  27 lpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdliv 102
                                       l+ +l++ v+DlG+G+G+l++a+a + ++ +v  +dvd  Al++a+en+++ +++ ++ +  d++     +   +++
  gi|336254698|ref|YP_004597805.1|  45 LEGDLERPVVDLGTGTGMLAIAAALAGSD-RVLGIDVDPDALAVARENAARVGADsIDWILGDATRPPLTRADRTVL 120
                                       67778999**************9998888.8************************************99888889** PP

                                       E---STTTCHCHHHHHHHHHHHHHH CS
                               MTS 103 sNPPfhagkatelavaeeliaeAke 127
                                       sNPPf a++  + ++ ++++++A e
  gi|336254698|ref|YP_004597805.1| 121 SNPPFGAQRG-NRHADRRFLETASE 144
                                       ********99.88899999999986 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.2   1.5e-14   1.4e-11     163     206 ..      51      94 ..      39     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 1.5e-14
                              PrmA 163 eevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNael 206
                                       + v+D+GtG+G+Laiaaa+ g ++v+++D+D+ A+ va+eNa++
  gi|336254698|ref|YP_004597805.1|  51 RPVVDLGTGTGMLAIAAALAGSDRVLGIDVDPDALAVARENAAR 94 
                                       579**************************************987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   1.4e-12   1.3e-09       1      62 [.      53     114 ..      53     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.4e-12
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfed 62 
                                       v+dlG+GtG l++a+a + g+ +v+g+D+++++l+ are+a++ g+ +++++ gda++ p+  
  gi|336254698|ref|YP_004597805.1|  53 VVDLGTGTGMLAIAAALA-GSDRVLGIDVDPDALAVARENAARVGAdSIDWILGDATRPPLTR 114
                                       89*************988.68********************999999*********9987643 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   7.3e-12   6.9e-09       6      65 ..      52     109 ..      48     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 7.3e-12
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee 65 
                                       +v+DlG+GtG l++++a ++g+  +v GiD +++a+ +Arena++ g d +    gd++ 
  gi|336254698|ref|YP_004597805.1|  52 PVVDLGTGTGMLAIAAA-LAGS-DRVLGIDVDPDALAVARENAARVGADSIDWILGDATR 109
                                       699**************.6665.78************************99999999876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.5e-09   1.4e-06       1      58 [.      54     113 ..      54     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.5e-09
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl.kvefvvadaeklpfe 58 
                                       +d+G+GtG la a a +g  rv+g+D+++ +l++a+e+a + g  +++++ +da++ p+ 
  gi|336254698|ref|YP_004597805.1|  54 VDLGTGTGMLAIAAALAGsDRVLGIDVDPDALAVARENAARVGAdSIDWILGDATRPPLT 113
                                       59*************9999************************************98875 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1     3e-09   2.8e-06      32     147 ..      53     141 ..      32     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 3e-09
                                       EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEE CS
                           UPF0020  32 llDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefs 108
                                        +D   G+G ++I aal g++++                          g+D d+ +++ areNa + g  d+i++ 
  gi|336254698|ref|YP_004597805.1|  53 VVDLGTGTGMLAIAAALAGSDRV-------------------------LGIDVDPDALAVARENAARVGA-DSIDWI 103
                                       55555677777777777777777.........................8******************995.79**** PP

                                       E--GGG--STTS---EEEE----------HHHHHHHHHH CS
                           UPF0020 109 qadaakLrlkegevdvivtnpPYGerlgskkalekLYse 147
                                         da+  +  +   +++++npP+G   g+ +a +++ + 
  gi|336254698|ref|YP_004597805.1| 104 LGDATRPP-LTRADRTVLSNPPFGAQRGNRHADRRFLET 141
                                       *****999.5546789********999988887665444 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   6.5e-07   0.00061      42     128 ..      51     130 ..      41     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.5e-07
                                       C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                       +  v+Dl  G+G l++ A+  g ++++ ++ d+ a+++ +en +++++++ ++ +  da++  l++a +      v 
  gi|336254698|ref|YP_004597805.1|  51 RP-VVDLGTGTGMLAIAAALAGSDRVLGIDVDPDALAVARENAARVGADS-IDWILGDATRPPLTRADR-----TVL 120
                                       44.99******************************************886.9*******9998888544.....599 PP

                                       E--SSSTTCH CS
                     Cons_hypoth95 119 lDPPyakell 128
                                        +PP+ ++  
  gi|336254698|ref|YP_004597805.1| 121 SNPPFGAQRG 130
                                       9****98865 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.1e-07   0.00086     103     175 ..      52     121 ..      41     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.1e-07
                                       EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE- CS
                            Met_10 103 vVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmn 175
                                        Vvd+  G G +ai++a  +   rvl+id++P++    +en ++   ++ +  il+D+    + + adr v+ 
  gi|336254698|ref|YP_004597805.1|  52 PVVDLGTGTGMLAIAAAL-AGSDRVLGIDVDPDALAVARENAARVG-ADSIDWILGDATRP-PLTRADRTVLS 121
                                       59***************7.55566*****************99865.45677888887765.36677777765 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.1e-06     0.001      23      75 ..      47      96 ..      33     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                   Methyltransf_32 23 esgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75
                                       + +  vvD+G G g L+ + al     + +v+gid+  +  + a++ a+++g
  gi|336254698|ref|YP_004597805.1| 47 GDLERPVVDLGTGTGMLAIAAAL---AGSDRVLGIDVDPDALAVARENAARVG 96
                                      455778*****************...7788*********************99 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 !   18.0   0.0   1.8e-06    0.0017       4      60 ..      53     109 ..      50     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.8e-06
                   Methyltransf_15   4 ilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60 
                                       ++Dl +G+G  +i+ al   ++v +i+++++ la+a +Na   g +d i+++lgd + 
  gi|336254698|ref|YP_004597805.1|  53 VVDLGTGTGMLAIAAALAgSDRVLGIDVDPDALAVARENAARVG-ADSIDWILGDATR 109
                                       899************999678******************98774.799*******876 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   0.0   3.7e-06    0.0035      50     111 ..      52     111 ..      35     121 .. 0.84
   2 ?   -2.3   0.0       2.4   2.3e+03     113     129 ..     139     155 ..     134     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.7e-06
                                       EEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-T CS
                   Ubie_methyltran  50 kvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLp 111
                                        v+D+ +Gtg la+  + ++  + +v ++D++++ L v+++ + + g  +i+++ ++a + p
  gi|336254698|ref|YP_004597805.1|  52 PVVDLGTGTGMLAI--AAALAGSDRVLGIDVDPDALAVARENAARVGADSIDWILGDATRPP 111
                                       68999999998876..566777889*******************************998755 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                                       S-T-EEEEEEES-GGG- CS
                   Ubie_methyltran 113 eddsfDvvtvsfGlrnv 129
                                        + + ++ tvs+ + n 
  gi|336254698|ref|YP_004597805.1| 139 LETASEIATVSYTIHNE 155
                                       56678899999999985 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.6e-06    0.0043       1      51 [.      54     103 ..      54     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.6e-06
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnv 51 
                                       +++G+GtG l+ a + +    +++g+D++p+a++ a+e  a+ ++++ +++
  gi|336254698|ref|YP_004597805.1|  54 VDLGTGTGMLAIAAALA-GSDRVLGIDVDPDALAVARENAARVGADSIDWI 103
                                       599*****999999888.788999*********999999999988877766 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   6.4e-06     0.006      15     154 ..      17     141 ..      13     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.4e-06
                          N6_Mtase  15 rkfaeeegksgGeffTPrevsklivell..epksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknett 89 
                                        +f+e +++   ++ TP+++   i + +  e   ++ v+D   G+g l + a+         + +  + G ++++ +
  gi|336254698|ref|YP_004597805.1|  17 ADFSEPSASL-EQYLTPSDIAAHICHRAalEGDLERPVVDLGTGTGMLAIAAAL--------AGSDRVLGIDVDPDA 84 
                                       5665555555.79************998778888999*******9866665554........3455789******** PP

                          N6_Mtase  90 yrLakmNlllhgieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqkewkektlekderfrea 154
                                        ++a+ N +  g++   ++  lgd+   p ++ d    +v++Nppf+++     + + d rf e+
  gi|336254698|ref|YP_004597805.1|  85 LAVARENAARVGADS--IDWILGDATRPPLTRAD---RTVLSNPPFGAQ---RGNRHADRRFLET 141
                                       ********9887765..57999**9999999844...469*******99...5666777777665 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   8.1e-06    0.0077      53     109 ..      55     108 ..      17     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.1e-06
                                       EE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HH CS
                    Methyltransf_3  53 eiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdal 109
                                       ++G  tG  +La+a al    ++l id+d++a ++a++   + g +  i+ i gda+
  gi|336254698|ref|YP_004597805.1|  55 DLG--TGTGMLAIAAALAGSDRVLGIDVDPDALAVARENAARVGAD-SIDWILGDAT 108
                                       555..56668999999999***********************9965.69***99997 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.3e-06    0.0078      20      62 ..      47     122 ..       5     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.3e-06
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae................................k 62 
                                        +    v+d+G+GtG l+  ++  g   v g+D +p a + a+                                +
  gi|336254698|ref|YP_004597805.1|  47 GDLERPVVDLGTGTGMLAIAAALAGSdRVLGIDVDPDALAVARenaarvgadsidwilgdatrppltradrtvlsN 122
                                       3444589*******************8899******9999887666666666666666666555555555555550 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 ?   13.9   0.0   3.7e-05     0.035      69     133 ..      45     107 ..       7     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.7e-05
                                       TT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-G CS
                              PCMT  69 lelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDG 133
                                       le +    v+++G+G+G l+ + a l g++  v++i+  ++  + a++n  + +++++  + gD 
  gi|336254698|ref|YP_004597805.1|  45 LEGDLERPVVDLGTGTGMLA-IAAALAGSDR-VLGIDVDPDALAVARENAARVGADSIDWILGDA 107
                                       444556679********986.6677777765.***************************999996 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 ?   13.3   0.0   6.9e-05     0.065      17      55 ..      63     141 ..      58     189 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.9e-05
                                       HHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................... RF
                              CbiA  17 anLaralarrglrVllvDaDpqannlaileglendiep....................................... 54 
                                       +++a+ala    rVl +D+Dp+a + a     en   +                                       
  gi|336254698|ref|YP_004597805.1|  63 LAIAAALAG-SDRVLGIDVDPDALAVAR----ENAA-Rvgadsidwilgdatrppltradrtvlsnppfgaqrgnrh 133
                                       467778887.99**********888772....2211.1344456666666666777777776666666655555555 PP

                                       .......C CS
                                       .......x RF
                              CbiA  55 .......d 55 
                                              +
  gi|336254698|ref|YP_004597805.1| 134 adrrfleT 141
                                       54444440 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0003      0.28       5      61 ..      53     108 ..      50     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                                       EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CC CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdal 61 
                                       v+++G+G G + +a A +     +lGi++  + +a + +++++ ++  +  + gda+
  gi|336254698|ref|YP_004597805.1|  53 VVDLGTGTGMLAIAAALAGS-DRVLGIDVDPDALAVARENAARVGADSIDWILGDAT 108
                                       79********9999888765.579***********************9999999995 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 ?   11.3   0.0   0.00021       0.2      26     114 ..      65     149 ..      46     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                                       HHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEEEE--CCGGGTTT-TCHH CS
                   Methyltr_RsmB-F  26 iaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaPCsgtgvirrdpdvk 102
                                       ia+ ++ + +v+ +d++   l    en  r+g  ++  + +Da++++ + +    Dr  l  P  g    +r+ d +
  gi|336254698|ref|YP_004597805.1|  65 IAAALAGSDRVLGIDVDPDALAVARENAARVGADSIDWILGDATRPPLTRA----DRTVLSNPPFGAQRGNRHADRR 137
                                       5556688899************************************87766....9********************* PP

                                       HH--HHHHHHHH CS
                   Methyltr_RsmB-F 103 lrrkekdiaqla 114
                                       ++ + ++ia+++
  gi|336254698|ref|YP_004597805.1| 138 FLETASEIATVS 149
                                       **9999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); 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:                        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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 1725.76
//
Query:       gi|336254699|ref|YP_004597806.1|  [L=132]
Description: hypothetical protein Halxa_3315 [Halopiger xanaduensis SH-6]
Scores for 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   13.7   0.1      0.039   13.4   0.1    1.1  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 ?   13.4   0.1   2.2e-06     0.039      25     127 ..      32     123 ..      13     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-06
                                       C..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTT CS
                      AP_endonuc_2  25 l..sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlhpGtagagpk 99 
                                           +e+lr+l++ +++ +l  + l+  + f  +     +++    vd+++  +++ + LG+  +++ +        
  gi|336254699|ref|YP_004597806.1|  32 EstAPEYLRDLKREFAAEDLSPVELTVDACFDEDCSLATQEE----VDRIRGYVRAGSFLGVNAVTVAVD------- 97 
                                       144589***************************888766777....**********************65....... PP

                                       SGHHHHHHHHHHHHHHHHHHHHHHTSEE CS
                      AP_endonuc_2 100 gseeeawerlaeslneladyaekegvkl 127
                                         + ++ e+++ +l ++a+ ae+eg  l
  gi|336254699|ref|YP_004597806.1|  98 --DVANDEKVRPALAACAERAEREGLVL 123
                                       ..77899999999999999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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 0.19s 00:00:00.53 Elapsed: 00:00:00.33
# Mc/sec: 1213.73
//
Query:       gi|336254700|ref|YP_004597807.1|  [L=83]
Description: hypothetical protein Halxa_3316 [Halopiger xanaduensis SH-6]
Scores for 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-05   22.3   2.9    8.9e-05   21.7   2.9    1.3  1  zf-TFIIB       Transcription factor zinc-finger
    9.5e-05   22.2   0.7    0.00014   21.6   0.7    1.3  1  zf-FPG_IleRS   Zinc finger found in FPG and IleRS
  ------ inclusion threshold ------
       0.01   14.9   0.5      0.011   14.8   0.5    1.0  1  DUF4776        Domain of unknown function (DUF4776)
      0.017   15.2   2.1       0.62   10.2   0.1    2.4  2  UPF0547        Uncharacterised protein family UPF0547
      0.041   14.0   2.9        1.3    9.2   0.4    2.2  2  TRAF6_Z2       TNF receptor-associated factor 6 zinc finger 2
      0.059   13.5   2.0       0.13   12.4   2.0    1.6  1  Zn-ribbon_8    Zinc ribbon domain
      0.077   13.0   0.7       0.13   12.2   0.7    1.3  1  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi
       0.33   10.7   6.2        1.8    8.4   0.8    2.2  2  Zn_Tnp_IS1     InsA N-terminal domain
       0.33   10.9   4.2        1.9    8.5   0.1    2.2  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
        0.4   10.2   3.5        4.2    6.9   0.6    2.2  2  zf-ribbon_3    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.9   4.9e-08   8.9e-05       2      26 ..       4      28 ..       3      28 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.9e-08
                          zf-TFIIB  2 CPkCqdeleeserggveidyCpqCr 26
                                      CP+Cq +lee+ +g+v    Cp+C+
  gi|336254700|ref|YP_004597807.1|  4 CPRCQGSLEELSLGDVSTVSCPHCE 28
                                      ************************6 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 !   21.6   0.7   7.8e-08   0.00014       4      27 ..       4      27 ..       2      28 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 7.8e-08
                                      -TTT--BBEEEECTTEEEEE-TTT CS
                      zf-FPG_IleRS  4 CpRCwryiervgqagrstyfCprC 27
                                      CpRC + +e+ +++  st+ Cp+C
  gi|336254700|ref|YP_004597807.1|  4 CPRCQGSLEELSLGDVSTVSCPHC 27
                                      ************************ PP

>> DUF4776  Domain of unknown function (DUF4776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.5     6e-06     0.011       9      75 ..       4      74 ..       1      82 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6e-06
                           DUF4776  9 CpvCkedvs..WLPkva..aCPkCGykpvpvveeeekdkkatadqilndllekekselddseedksekakk 75
                                      Cp C+ ++    L +v+  +CP+C y  +pv +e+  +   +  + ln + e++  ++d  ++++++ ak 
  gi|336254700|ref|YP_004597807.1|  4 CPRCQGSLEelSLGDVStvSCPHCEYADIPVEHESVPETPESWRDALNRFYEETVPKVDPVDVESEADAKP 74
                                      88888777622355665337*******************99*****************9999988765554 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3      0.02        36       2       7 ..       3       8 ..       1      11 [. 0.76
   2 ?   10.2   0.1   0.00034      0.62      12      25 ..      19      32 ..      18      33 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.02
                           UPF0547 2 vCPeCe 7
                                     +CP+C+
  gi|336254700|ref|YP_004597807.1| 3 ECPRCQ 8
                                     488886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00034
                           UPF0547 12 vaaqfCphCGyvFq 25
                                      v++++CphC y ++
  gi|336254700|ref|YP_004597807.1| 19 VSTVSCPHCEYADI 32
                                      6899*****99876 PP

>> TRAF6_Z2  TNF receptor-associated factor 6 zinc finger 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4   0.00073       1.3       5      12 ..       3      10 ..       2      12 .. 0.90
   2 ?    5.2   0.1     0.013        23       2      10 ..      20      28 ..      19      30 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00073
                          TRAF6_Z2  5 eCPQCQra 12
                                      eCP CQ+ 
  gi|336254700|ref|YP_004597807.1|  3 ECPRCQGS 10
                                      8*****95 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.013
                          TRAF6_Z2  2 alVeCPQCQ 10
                                      + V CP C 
  gi|336254700|ref|YP_004597807.1| 20 STVSCPHCE 28
                                      78******5 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.0   7.4e-05      0.13       7      33 ..       3      28 ..       3      32 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.4e-05
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCg 33
                                      +C +C+   e+l    d + t+ CP+C 
  gi|336254700|ref|YP_004597807.1|  3 ECPRCQGSLEELS-LGDVS-TVsCPHCE 28
                                      6***********8.55555.555****6 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 ?   12.2   0.7   7.3e-05      0.13      12      37 ..       3      28 ..       2      35 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.3e-05
                                      E-TTTTTTSEETTE......E-TTTT CS
                         Anti-TRAP 12 kCdaCngsGkiepeeprasleCPkCs 37
                                      +C+ C+gs ++ +    +++ CP+C+
  gi|336254700|ref|YP_004597807.1|  3 ECPRCQGSLEELSLGDVSTVSCPHCE 28
                                      7*************999********7 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 ?    5.2   0.5    0.0098        18       8      12 ..       4       8 ..       3      11 .. 0.84
   2 ?    8.4   0.8     0.001       1.8       5      15 ..      21      31 ..      19      38 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0098
                        Zn_Tnp_IS1  8 CPrCs 12
                                      CPrC+
  gi|336254700|ref|YP_004597807.1|  4 CPRCQ 8 
                                      ****9 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.001
                        Zn_Tnp_IS1  5 sihCPrCsstd 15
                                      +++CP C+ +d
  gi|336254700|ref|YP_004597807.1| 21 TVSCPHCEYAD 31
                                      79*****9888 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 ?    5.2   4.8     0.012        21      21      44 ..       4      28 ..       2      29 .. 0.73
   2 ?    8.5   0.1     0.001       1.9      19      27 ..      22      30 ..      11      47 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.012
                     Zn_Tnp_IS1595 21 CPhCgsr.kayriktrglfqCkeCr 44
                                      CP+C+++ +  ++ +     C +C 
  gi|336254700|ref|YP_004597807.1|  4 CPRCQGSlEELSLGDVSTVSCPHCE 28
                                      8888888877777777777787776 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.001
                     Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                      + CPhC+++
  gi|336254700|ref|YP_004597807.1| 22 VSCPHCEYA 30
                                      56****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 ?    4.0   0.1      0.02        36       2       8 ..       1       7 [.       1      12 [. 0.85
   2 ?    6.9   0.6    0.0023       4.2       2       8 ..      21      27 ..      20      29 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.02
                       zf-ribbon_3 2 tvrCPnC 8
                                     + +CP+C
  gi|336254700|ref|YP_004597807.1| 1 MDECPRC 7
                                     6789999 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0023
                       zf-ribbon_3  2 tvrCPnC 8 
                                      tv+CP+C
  gi|336254700|ref|YP_004597807.1| 21 TVSCPHC 27
                                      7778887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 733.17
//
Query:       gi|336254701|ref|YP_004597808.1|  [L=338]
Description: hypothetical protein Halxa_3317 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00075   18.2   0.0       0.32    9.5   0.0    2.2  2  Actin     Actin
  ------ inclusion threshold ------
      0.021   15.2   0.0        0.1   13.0   0.0    1.9  2  FtsA      Cell division protein FtsA


Domain annotation for each model (and alignments):
>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0   0.00023         2      30      76 ..      45      91 ..      30     215 .. 0.83
   2 !    9.5   0.0   3.6e-05      0.32     311     380 ..     253     322 ..     245     327 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00023
                             Actin 30 ipslvgkprgrkveaklyvgdealt..krpelevrspvedGvvedwdav 76
                                       +s v + r+++  + ++vgd+al+  +  + e r+p+++G++ + ++ 
  gi|336254701|ref|YP_004597808.1| 45 SRSEVLHIRKDD--KVYVVGDDALNfaNIFNKETRRPMKHGILSNDEQS 91
                                      555666666664..4899****776658999**************9864 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 3.6e-05
                             Actin 311 aainacd.vdlrpeLlanivvtGGnsllpglteRlekelaqlaskgvkvkiiapeeerkysaWiGGSiLAs 380
                                       + ++++d  d+++ L   +vvtGG+s+  g++e     l++ a   +++  ++  +e+ ys+  GG + A+
  gi|336254701|ref|YP_004597808.1| 253 NIVEEVDeEDVEEGLDVPVVVTGGTSSPSGFEELFRDHLND-ANIPFSISGVTHADEPLYSVARGGLVAAR 322
                                       556677757899999999***************99999999.55556666655555899999888877665 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.19   1.7e+03      70      87 ..      50     106 ..      19     132 .. 0.64
   2 ?   13.0   0.0   1.1e-05       0.1       3     103 .]     171     316 ..     169     316 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.19
                                       H......................................GGGGSTTHHHHHHHHH.T CS
                                       x......................................xxxxxxxxxxxxxxxx.x RF
                              FtsA  70 s......................................ggsalpnleelaeral.s 87 
                                                                              ++sa+p ++ ++e+++ +
  gi|336254701|ref|YP_004597808.1|  50 LhirkddkvyvvgddalnfanifnketrrpmkhgilsndEQSAIPMMKLIIEQVVgE 106
                                       234444444444555555556666666666666777777888888888888888542 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.1e-05
                                       EEE-SSSEEEEEEETTEEEEEEEES-....-HHHHHHHHHHHHT--HHHHHHHHHHH--S--............... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                              FtsA   3 vDiGagktdvavaedgalvhlrvigv....ggngitkdiakalrtaveeAerikikyGsala............... 60 
                                       + +Gag+t+v +       ++ v ++    gg+ +++ +a+a +t+v++  +ik +                     
  gi|336254701|ref|YP_004597808.1| 171 ISFGAGMTNVCLSYY----AVPVMKFsvarGGDWVDEQAARATGTPVDKVTSIKED-----Dfeldfttdvggvega 238
                                       667888887777777....44555556667************************32.....1223344444444445 PP

                                       ................EEEEEHHHHH...........GGGGSTTHHHHHHHHHT-..........HHHT-GGGHHHH CS
                                       ................xxxxxxxxxx...........xxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxx RF
                              FtsA  61 ................ekeigrkels...........ggsalpnleelaeralspk........leevsdpeyasal 102
                                                        +e+++++++           g+s+  ++eel+++ l+          ++++++p y++a 
  gi|336254701|ref|YP_004597808.1| 239 lsiyyenlldyvidniVEEVDEEDVEegldvpvvvtgGTSSPSGFEELFRDHLNDAnipfsisgVTHADEPLYSVAR 315
                                       555666666566555544444444449999**********************8333344466644558889998886 PP

                                       H CS
                                       x RF
                              FtsA 103 g 103
                                       g
  gi|336254701|ref|YP_004597808.1| 316 G 316
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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 0.21s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2842.79
//
Query:       gi|336254702|ref|YP_004597809.1|  [L=301]
Description: permease [Halopiger xanaduensis SH-6]
Scores for 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   13.2   0.2       0.14   12.2   0.2    1.4  1  Aegerolysin  Aegerolysin
      0.077   12.6   0.4       0.13   11.8   0.4    1.3  1  DUF417       Protein of unknown function, DUF417


Domain annotation for each model (and alignments):
>> Aegerolysin  Aegerolysin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   1.6e-05      0.14      19      71 ..     190     242 ..     179     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                                       EEEEEEEESEEEETTEEEEEE-GGGTTT-EE-TT-EEEEEEE--TT-S--EEE CS
                       Aegerolysin  19 irnaklesGkfykendkdkeitaedveelvikpggsrevascGrenaasGteG 71 
                                       +++ +l++G   k ++k+ + ++++ +e+ ++  g+  + s+G +  + G++G
  gi|336254702|ref|YP_004597809.1| 190 MEDVELSWGGVEKTEHKRLNFSEDEFDEVHVSDAGTTTTRSSGVDAQVAGLKG 242
                                       57889*******************************************99998 PP

>> DUF417  Protein of unknown function, DUF417
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   1.5e-05      0.13      88     137 ..      70     121 ..      63     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
                            DUF417  88 nllGii...evivgilvliglrnakvgllggllvlviaivtlSfLittPeawv 137
                                       ++lG++    +i+g+ vl+   ++++g+ ++ ++++   +t+ fL+  P+ w 
  gi|336254702|ref|YP_004597809.1|  70 YALGMLslpAMILGVVVLLPADRKTIGVSTAGAAVT-VAATVGFLFAYPDNWN 121
                                       566655222589***************998887765.568************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); 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):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.35
# Mc/sec: 2559.44
//
Query:       gi|336254703|ref|YP_004597810.1|  [L=349]
Description: universal diphthamide biosynthesis domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-78  264.1   0.0    2.3e-78  263.7   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein
  ------ inclusion threshold ------
      0.067   13.9   0.0        2.5    8.8   0.0    2.4  2  GTP-bdg_N        GTP-binding GTPase N-terminal
       0.25   10.7   0.0       0.41   10.0   0.0    1.2  1  CCB1             Cofactor assembly of complex C subunit B


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 !  263.7   0.0   3.8e-82   2.3e-78       1     295 [.      48     334 ..      48     340 .. 0.93

  Alignments for each domain:
  == domain 1  score: 263.7 bits;  conditional E-value: 3.8e-82
                   Diphthamide_syn   1 fPegllpdsaeiadileef...gaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvdrlpvlYvfveiel 74 
                                       fPegl++  +++ad l+++   +++++++g ++YGaC++d++ +++   d+ vH+Ghs++++  + +v+Yv+  +++
  gi|336254703|ref|YP_004597810.1|  48 FPEGLKRRGPAVADDLRQLaddDVTFMLSGQPCYGACDLDTYLMKR--TDVFVHFGHSPMKN--TDKVIYVPLFSNV 120
                                       9***************999888899*********************..9************9..569********** PP

                   Diphthamide_syn  75 dvehlvetlkknf...kekkk.ivlvstiqyahaleevkeeleeegyevv.kvpqsekplspgevlgctspklkeee 146
                                       +v+ ++e++ +++   +e+ + ++lv+t+q+ + ++e++  lee+gyev  + +++ + +++g+vlgc+++++   +
  gi|336254703|ref|YP_004597810.1| 121 EVTPIMEEALDTLeppEET-EgVGLVTTAQHMNRYDEMSAFLEERGYEVHsRRGDE-RLTHEGQVLGCNYASA---D 192
                                       *************984444.45*********************99**999545555.99**************...5 PP

                   Diphthamide_syn 147 eevdailyigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgr 223
                                         +d++ly+g+g+fh+l+l++++p+++v+ +dp+++ +t    d++k++++Ry a+++a+da+k+G+i++t+ +qgr
  gi|336254703|ref|YP_004597810.1| 193 VPADQVLYVGGGKFHPLGLAMEHPDKHVVIADPVNNVVTVA--DTEKFMKQRYGAVHRAMDAEKWGVIFCTKIGQGR 267
                                       689*********************************88855..6********************************* PP

                   Diphthamide_syn 224 lelverlkkllkeagkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalge 295
                                        e+++ + ++      ++yl++++e++p++L+nf ++dafV+++Cpr+++ddg +F+kP+ltp E+e+a+g+
  gi|336254703|ref|YP_004597810.1| 268 WEIAQDILEDN----DNAYLITMDEVTPDRLRNF-DMDAFVNTGCPRITTDDGPQFHKPMLTPGEYEIAVGN 334
                                       **998876655....589****************.**********************************995 PP

>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.044   2.7e+02      30      58 ..     196     224 ..     178     240 .. 0.84
   2 ?    8.8   0.0   0.00041       2.5      33      70 ..     261     298 ..     245     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.044
                         GTP-bdg_N  30 dpatyiGkGkveeikelveeeeadlvifd 58 
                                       d+  y+G Gk++ +  ++e+ + ++vi d
  gi|336254703|ref|YP_004597810.1| 196 DQVLYVGGGKFHPLGLAMEHPDKHVVIAD 224
                                       6778**************99888888876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00041
                         GTP-bdg_N  33 tyiGkGkveeikelveeeeadlvifddeLspsqqrnLe 70 
                                       t iG+G+ e  ++++e+++  ++i+ de++p   rn  
  gi|336254703|ref|YP_004597810.1| 261 TKIGQGRWEIAQDILEDNDNAYLITMDEVTPDRLRNFD 298
                                       679********************************975 PP

>> CCB1  Cofactor assembly of complex C subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   6.9e-05      0.41      30      74 ..     140     183 ..     136     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.9e-05
                              CCB1  30 eevtleseeseeelleelkeyleqraYrvaevdaeketvtfeGlv 74 
                                       e v l++++++ +  +e++++le+r+Y+v++  +  e++t eG+v
  gi|336254703|ref|YP_004597810.1| 140 EGVGLVTTAQHMNRYDEMSAFLEERGYEVHS-RRGDERLTHEGQV 183
                                       5566777778889999**************9.777799*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); 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:                         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 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2737.86
//
Query:       gi|336254704|ref|YP_004597811.1|  [L=263]
Description: hypothetical protein Halxa_3320 [Halopiger xanaduensis SH-6]
Scores for 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   13.8  10.0        8.6    6.5   2.5    4.3  4  HTH_20    Helix-turn-helix domain
       0.73    9.8   4.2        8.9    6.3   0.2    2.9  4  HTH_5     Bacterial regulatory protein, arsR 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 ?    5.4   0.1    0.0021        19       4      22 ..      18      36 ..      15      59 .. 0.85
   2 ?    3.2   0.0      0.01        90      43      55 ..      77      89 ..      71      92 .. 0.89
   3 ?   -0.7   0.0      0.18   1.6e+03      22      42 ..     110     130 ..     108     135 .. 0.84
   4 ?    6.5   2.5   0.00096       8.6       2      57 ..     131     209 ..     130     212 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0021
                                      HHHHS-HHHHHHHHHHSTC CS
                            HTH_20  4 aeALahPvRrrilraLara 22
                                      ++ La+ +Rr++lr+ +++
  gi|336254704|ref|YP_004597811.1| 18 FRSLADATRRALLRLVHER 36
                                      789***********99443 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.01
                                      HHHHHHHHCTTEE CS
                            HTH_20 43 yHLrvLeeagLve 55
                                       HL +L eagLv 
  gi|336254704|ref|YP_004597811.1| 77 THLPTLLEAGLVA 89
                                      79*9*******97 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.18
                                       CTTB-HHHHHHHHTS-HHHHH CS
                            HTH_20  22 aegltaselaerldlskntls 42 
                                       +e++  + +a rld + ++l+
  gi|336254704|ref|YP_004597811.1| 110 DEPALENVIAGRLDAPAAELD 130
                                       688889999999999998875 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.00096
                                       HHHHHHS-HHHHHHHHHH..............STCTTB-HHHHHHHHT.............S-HHHHHHHHHHHHHC CS
                            HTH_20   2 qiaeALahPvRrrilraL..............araegltaselaerld.............lskntlsyHLrvLeea 51 
                                       ++++A+a+  Rr  l+ L              a a+++ a e     d             +  + ++ HL  Le+a
  gi|336254704|ref|YP_004597811.1| 131 TLFDAVADSRRRLALSVLagnarsdseamdrdALARAVAARET----DagaddiaqehvdaVYSSLVHVHLPLLEDA 203
                                       5677777777777777777777766665333322333333333....233335666666655556699********* PP

                                       TTEEEE CS
                            HTH_20  52 gLvevv 57 
                                       gLv v 
  gi|336254704|ref|YP_004597811.1| 204 GLVAVA 209
                                       ***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 ?   -2.7   0.0      0.63   5.6e+03       1      13 [.      23      35 ..      23      38 .. 0.78
   2 ?    4.2   0.0    0.0044        40      34      45 ..      77      88 ..      76      90 .. 0.90
   3 ?   -3.4   0.0       1.1   9.7e+03       1      13 [.     138     150 ..     138     154 .. 0.77
   4 ?    6.3   0.2   0.00099       8.9      30      45 ..     191     206 ..     189     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.63
                                      SHHHHHHHHHHTT CS
                             HTH_5  1 dptRlkILklLae 13
                                      d tR+ +L+l+ e
  gi|336254704|ref|YP_004597811.1| 23 DATRRALLRLVHE 35
                                      5699999999877 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0044
                                      HHHHHHHHTTSE CS
                             HTH_5 34 hHLkkLreaGLV 45
                                       HL  L eaGLV
  gi|336254704|ref|YP_004597811.1| 77 THLPTLLEAGLV 88
                                      5**********9 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.1
                                       SHHHHHHHHHHTT CS
                             HTH_5   1 dptRlkILklLae 13 
                                       d+ R+  L+ La 
  gi|336254704|ref|YP_004597811.1| 138 DSRRRLALSVLAG 150
                                       6789999999986 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.00099
                                       HHHHHHHHHHHHTTSE CS
                             HTH_5  30 stvShHLkkLreaGLV 45 
                                       s v  HL  L++aGLV
  gi|336254704|ref|YP_004597811.1| 191 SLVHVHLPLLEDAGLV 206
                                       67889**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2123.75
//
Query:       gi|336254705|ref|YP_004597812.1|  [L=276]
Description: Zn-dependent hydrolase-like protein [Halopiger xanaduensis SH-6]
Scores for 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   62.6   0.5    4.8e-17   62.1   0.5    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    9.8e-11   41.8   0.0    1.5e-10   41.2   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0058   16.7   9.6      0.026   14.6   9.6    1.9  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 !   62.1   0.5     8e-21   4.8e-17       1     201 []      40     239 ..      40     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 8e-21
                                       SEEEES--TTHHHH..HTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHHHCCTT CS
                     Lactamase_B_2   1 rriLiDagpdlrqq..alralqPve.lrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvlavlean 73 
                                       + i iD+ ++l  +    r   Pv+ +  +++  daVl th+H DH+ g ++ ++ l+++ +++y+ ++ lav +++
  gi|336254705|ref|YP_004597812.1|  40 TTIYIDPYLGLGNPprTVRM-IPVPfTPGDVETADAVLATHEHTDHVDG-PSQAPiLENTGATFYGADDSLAVAREE 114
                                       5799******9999633333.699999********************66.77777688888****999999999999 PP

                                       CGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---..H CS
                     Lactamase_B_2  74 fvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip..e 148
                                          + ++++ + ++ e+  g+++e+g       a++++   +   d++a+  +++++e +  +v+++gDt+  +  +
  gi|336254705|ref|YP_004597812.1| 115 NWTDEWDVD-GDQFAEVSEGDTLEIG-------AFTVHVEEAY--DPDATHPVSYVVEHEAGTVFHGGDTKPSDefA 181
                                       888888888.9999999999999998.......4555555555..66677*********************888666 PP

                                       HHHHHHCT-SEEEEE...-S-SSTTHHHHHHT---S....TSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 149 eigerlggadlllld...itayeddemirhmgHltp....eeaveaaadlgakrlvliHi 201
                                       +ig++++ +dl +l    +++  d+e   ++    +    ++ veaa+dl  +rl++ H+
  gi|336254705|ref|YP_004597812.1| 182 RIGDEYD-IDLGILAfgtVGMIPDKETL-EPKRTRWyndeNQIVEAADDLALERLLPSHW 239
                                       7776665.88877662123333344433.44444446667*******************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 !   41.2   0.0   2.5e-14   1.5e-10       3     131 ..      25     191 ..      23     238 .. 0.72

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 2.5e-14
                     Lactamase_B_3   3 twlghnsfllet.agarilvDPfkanlgyeppa...............eeaDlvlisqaledHahletlkql..... 58 
                                        +lg n f+l++ +g++i++DP+    g+++p+               e+aD+vl +++++dH + +  +++     
  gi|336254705|ref|YP_004597812.1|  25 WYLGCNGFVLKDsEGTTIYIDPYL---GLGNPPrtvrmipvpftpgdvETADAVLATHEHTDHVDGPSQAPIlentg 98 
                                       69**********559********7...555555668888899999********************999999989999 PP

                     Lactamase_B_3  59 .........................aenvkvleegeslevggleiravatshdavggsergenngflleqdgltiyh 110
                                                                 +++  ++eg+      lei a++   ++  ++     + +++e +  t++h
  gi|336254705|ref|YP_004597812.1|  99 atfygaddslavareenwtdewdvdGDQFAEVSEGD-----TLEIGAFTVHVEEAYDPDATHPVSYVVEHEAGTVFH 170
                                       999998777777555544444444444444444444.....455555555555555555666788************ PP

                     Lactamase_B_3 111 lGhlahelsseelkelgrvDv 131
                                        G++    +++ +    ++D+
  gi|336254705|ref|YP_004597812.1| 171 GGDTKPSDEFARIGDEYDIDL 191
                                       ****98666666655556665 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   9.6   4.3e-06     0.026      44     163 ..      71     192 ..      64     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.3e-06
                                       GEEEEE-SBSSHHHH...TTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECC CS
                       Lactamase_B  44 dvdavilTHlHlDHi...Gglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgna 117
                                         dav+ TH H+DH+   + ++ l ++     ga    a a ++++ d + +        ++ ++ +   + l+++a
  gi|336254705|ref|YP_004597812.1|  71 TADAVLATHEHTDHVdgpSQAPILENTGATFYGADDSLAVAREENWTDEWDVD-------GDQFAEVSEGDTLEIGA 140
                                       569************55555999999999999999999999999999999888.......78999999999****** PP

                                       CTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC....... CS
                       Lactamase_B 118 ggrralyvtggpghghghgvveygggkvlftGDallagetgridl......t 163
                                       + ++  +++   +++++++vve + g+v   GD+ ++ e +ri+        
  gi|336254705|ref|YP_004597812.1| 141 FTVHVEEAYDPDATHPVSYVVEHEAGTVFHGGDTKPSDEFARIGDeydidlG 192
                                       ***************************************9999985544440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2269.36
//
Query:       gi|336254706|ref|YP_004597813.1|  [L=661]
Description: AAA ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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   31.7   7.5     0.0009   19.3   2.4    2.5  2  Laminin_II       Laminin Domain II
    2.4e-07   29.3   6.2    3.6e-07   28.8   6.2    1.3  1  EzrA             Septation ring formation regulator, EzrA
      7e-07   29.1   0.7    3.8e-06   26.7   0.5    2.1  2  Lebercilin       Ciliary protein causing Leber congenital ama
    2.6e-06   26.4   2.3    2.6e-06   26.4   2.3    1.4  1  AAA_13           AAA domain
      4e-06   26.3   1.4    5.8e-05   22.5   0.1    2.5  1  GAS              Growth-arrest specific micro-tubule binding
    6.7e-06   26.2  12.1     0.0026   17.8   2.1    3.4  3  DUF1664          Protein of unknown function (DUF1664)
    1.1e-05   25.8  22.0     0.0027   18.2   6.2    4.2  3  NPV_P10          Nucleopolyhedrovirus P10 protein
    1.2e-05   24.4  13.2    0.00077   18.4   6.9    3.1  2  Spc7             Spc7 kinetochore protein
    1.5e-05   25.1  20.4    2.7e-05   24.2   3.7    2.8  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    2.9e-05   24.3  12.3    0.00067   19.9   0.1    3.4  3  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
    4.9e-05   23.4   7.4      0.003   17.6   2.5    2.5  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      7e-05   23.1  17.3      0.034   14.6   1.0    4.8  4  FlaC_arch        Flagella accessory protein C (FlaC)
    9.1e-05   22.6  17.9     0.0037   17.4   2.3    4.0  3  XhlA             Haemolysin XhlA
     0.0001   22.5   1.5        0.2   11.7   0.1    3.3  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
    0.00011   21.9   7.6      0.064   12.8   0.1    3.7  3  MscS_porin       Mechanosensitive ion channel porin domain
     0.0004   20.5   0.3       0.14   12.3   0.0    2.5  2  ADIP             Afadin- and alpha -actinin-Binding
    0.00058   19.8   9.6     0.0034   17.3   3.8    3.4  3  Prefoldin_2      Prefoldin subunit
    0.00066   20.1   1.2    0.00066   20.1   1.2    2.1  1  HsbA             Hydrophobic surface binding protein A
    0.00069   19.7  13.1      0.068   13.3   1.2    3.3  3  DUF2730          Protein of unknown function (DUF2730)
     0.0014   18.5   8.5      0.095   12.6   0.3    3.0  3  Sec34            Sec34-like family
     0.0021   17.9   1.5       0.13   12.1   0.3    2.3  2  DUF724           Protein of unknown function (DUF724)
     0.0023   18.2  12.8       0.23   11.8   0.9    3.8  3  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0028   17.2   7.5       0.03   13.8   7.4    2.2  1  HMMR_N           Hyaluronan mediated motility receptor N-term
     0.0028   17.0   9.5       0.07   12.4   0.9    3.3  3  DUF3450          Protein of unknown function (DUF3450)
     0.0039   17.7  11.9      0.014   16.0   2.4    3.9  4  APG6_N           Apg6 coiled-coil region
     0.0054   16.6   7.1        2.7    7.9   0.2    4.2  4  Prefoldin        Prefoldin subunit
     0.0075   16.5  14.9      0.011   16.0   5.0    3.2  2  DUF948           Bacterial protein of unknown function (DUF94
     0.0076   16.4   8.9       0.03   14.4   1.7    2.4  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
     0.0079   15.7   5.0       0.13   11.7   0.3    2.6  2  DegS             Sensor protein DegS
      0.009   15.2   5.7      0.026   13.7   0.7    2.4  2  FH2              Formin Homology 2 Domain
     0.0099   15.3   1.1       0.17   11.3   1.9    2.4  1  DUF4618          Domain of unknown function (DUF4618)
  ------ inclusion threshold ------
       0.01   16.3   2.5       0.01   16.3   2.5    3.9  4  Spectrin         Spectrin repeat
      0.011   15.4   2.7      0.019   14.7   2.7    1.3  1  SHE3             SWI5-dependent HO expression protein 3
      0.013   13.8   3.6       0.78    7.9   0.3    2.4  2  COG6             Conserved oligomeric complex COG6
      0.013   15.6   1.3      0.013   15.6   1.3    3.5  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.014   15.5   8.9        1.5    8.9   2.4    3.3  3  COG2             COG (conserved oligomeric Golgi) complex com
      0.014   14.5   0.6        1.8    7.6   0.1    2.7  2  RmuC             RmuC family
      0.015   14.9   6.9      0.044   13.3   1.1    2.4  2  Leu_zip          Leucine zipper
      0.016   15.7   6.6       0.64   10.5   0.6    2.6  2  DUF16            Protein of unknown function DUF16
      0.017   15.7   1.7        6.9    7.4   0.2    3.1  2  YabA             Initiation control protein YabA
      0.018   14.3   0.6       0.83    8.8   0.1    2.1  2  TMPIT            TMPIT-like protein
      0.018   15.4   9.3      0.077   13.4   0.8    3.3  3  TBCC_N           Tubulin-specific chaperone C N-terminal doma
      0.019   14.6  15.2      0.033   13.8  14.0    2.0  2  DUF4795          Domain of unknown function (DUF4795)
       0.02   14.4  22.2      0.045   13.2   1.2    3.6  3  DUF4349          Domain of unknown function (DUF4349)
      0.023   14.8   6.1       0.17   12.0   1.0    2.7  2  Cob_adeno_trans  Cobalamin adenosyltransferase
      0.029   13.5   0.0          3    6.8   0.0    2.1  2  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.031   14.4   2.8       0.49   10.6   0.7    2.5  3  Fib_alpha        Fibrinogen alpha/beta chain family
      0.034   13.7  11.5       0.93    9.0   5.8    2.5  1  Filament         Intermediate filament protein
       0.04   13.6   3.6       0.26   11.0   0.2    2.3  2  Laminin_I        Laminin Domain I
      0.047   13.5   9.4       0.78    9.6   2.4    2.7  2  Nsp1_C           Nsp1-like C-terminal region
       0.05   13.2   1.0        6.5    6.3   1.0    2.7  1  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
      0.055   13.3   7.0        2.4    7.9   0.1    3.4  2  SKA1             Spindle and kinetochore-associated protein 1
      0.056   13.6   0.9       0.44   10.7   0.2    2.3  3  CREPT            Cell-cycle alteration and expression-elevate
      0.059   13.4   0.3       0.13   12.3   0.3    1.6  1  SYCE1            Synaptonemal complex central element protein
      0.071   13.4   6.3       0.64   10.3   6.3    2.9  1  DUF5082          Domain of unknown function (DUF5082)
      0.075   12.8   1.5       0.67    9.7   0.2    2.6  3  DUF4201          Domain of unknown function (DUF4201)
      0.077   12.4   6.4       0.77    9.1   0.8    2.6  2  DUF3552          Domain of unknown function (DUF3552)
      0.082   10.8   0.7       0.13   10.2   0.7    1.2  1  Prominin         Prominin
       0.09   10.9  12.7       0.29    9.2  12.8    1.7  1  HOOK             HOOK protein
       0.11   12.8  13.7        2.8    8.3   0.6    3.9  4  CCDC-167         Coiled-coil domain-containing protein 167
       0.12   12.8   1.9        7.4    7.0   0.1    3.1  2  CENP-H           Centromere protein H (CENP-H)
       0.15   11.8   8.6        1.5    8.6   3.7    2.6  2  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.16   11.6   3.5       0.41   10.2   0.2    2.7  3  Fzo_mitofusin    fzo-like conserved region
       0.19   12.2   1.6         12    6.4   0.1    3.7  2  ZapB             Cell division protein ZapB
       0.23   10.9  12.8       0.43   10.0   3.6    2.3  2  Golgin_A5        Golgin subfamily A member 5
       0.24   11.7  16.9      0.032   14.5   2.0    4.0  3  Rx_N             Rx N-terminal domain
       0.25   11.8   1.2         20    5.7   0.1    3.0  2  Snapin_Pallidin  Snapin/Pallidin
       0.26   11.3   5.4         34    4.5   0.2    4.1  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
       0.28   11.2   6.4       0.29   11.1   0.7    2.4  2  YscO-like        YscO-like protein
        0.3    9.0   3.4        1.8    6.4   2.4    2.2  2  V_ATPase_I       V-type ATPase 116kDa subunit family
        0.3   11.2  28.9      0.036   14.2   7.3    4.0  3  Tropomyosin_1    Tropomyosin like
       0.39   10.8   4.3        3.3    7.9   0.0    3.7  3  Swi5             Swi5
       0.42   11.0   7.7         22    5.5   0.1    4.7  5  CLZ              C-terminal leucine zipper domain of cyclic n
       0.45   10.3   6.1        7.2    6.5   0.6    4.0  3  CdvA             CdvA-like coiled-coil domain
       0.61    9.4   6.0        2.7    7.3   5.5    2.2  1  Cluap1           Clusterin-associated protein-1
       0.62    9.7  11.4        7.9    6.1  11.0    2.6  1  LXG              LXG domain of WXG superfamily
       0.63   10.0   1.7         98    2.8   1.5    3.3  2  Cauli_AT         Aphid transmission protein
       0.63    9.2   3.7        4.2    6.5   3.8    2.2  2  Phage_HK97_TLTM  Tail length tape measure protein
       0.64    8.5   7.3        1.5    7.3   7.3    1.6  1  Zw10             Centromere/kinetochore Zw10
       0.68    9.9   6.9         10    6.2   0.5    3.0  2  Sec2p            GDP/GTP exchange factor Sec2p
       0.68    9.5  10.9       0.37   10.3   0.6    3.3  2  PspA_IM30        PspA/IM30 family
       0.75   10.0   7.1        7.5    6.8   0.2    3.6  2  Cnn_1N           Centrosomin N-terminal motif 1
       0.89    9.3  19.4       0.43   10.4   3.2    3.3  2  Phage_GP20       Phage minor structural protein GP20
          1    7.7  12.2      0.085   11.2   2.6    2.3  2  Sec3_C           Exocyst complex component Sec3
        1.1    8.9   8.9       0.13   11.9   0.6    2.7  2  Phage_tail_NK    Sf6-type phage tail needle knob or tip of so
        1.1    8.3  17.3        7.5    5.5  16.9    2.3  1  AIP3             Actin interacting protein 3
        1.2    9.4   6.4        1.7    8.9   1.9    2.7  2  THOC7            Tho complex subunit 7
        1.2    9.1   7.6          5    7.1   4.0    2.8  2  MIP-T3_C         Microtubule-binding protein MIP-T3 C-termina
        1.5    8.2   6.7        5.5    6.4   4.6    2.4  2  Not3             Not1 N-terminal domain, CCR4-Not complex com
          2    7.9   6.9       0.11   12.0   1.4    1.8  1  CAMP_factor      CAMP factor (Cfa)
        2.5    8.6   7.4         31    5.1   2.3    3.5  2  MtrB             Tetrahydromethanopterin S-methyltransferase 
        2.6    8.5  14.0       0.26   11.7   6.0    2.9  1  Fez1             Fez1
        2.7    8.3  12.5        3.2    8.0   0.5    3.6  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        3.1    8.2  11.8        9.5    6.7   0.4    4.0  4  CC2-LZ           Leucine zipper of domain CC2 of NEMO, NF-kap
        3.6    8.1  26.5       0.14   12.5   1.5    5.1  4  LPP              Lipoprotein leucine-zipper
          4    7.3  13.6       0.68    9.7   0.1    4.5  5  DivIC            Septum formation initiator
        5.1    6.3  14.0        1.9    7.7   4.5    2.5  2  CorA             CorA-like Mg2+ transporter protein
        5.4    6.8   5.7        4.6    7.0   1.4    2.3  3  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
        5.7    7.4  10.2         16    5.9   0.7    3.9  3  Csm1_N           Csm1 N-terminal domain
        5.9    7.4  12.7        2.8    8.4   0.1    4.5  4  DASH_Dad2        DASH complex subunit Dad2
        7.6    7.2  17.3    4.3e+02    1.5   0.4    3.8  2  Syntaxin-6_N     Syntaxin 6, N-terminal
        8.1    6.7  16.8         15    5.8   0.4    4.3  3  JIP_LZII         JNK-interacting protein  leucine zipper II


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 !   15.7   0.4   6.3e-05     0.011      26      95 ..     508     577 ..     487     582 .. 0.89
   2 !   19.3   2.4   5.1e-06    0.0009       6      86 ..     575     655 ..     572     661 .] 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.3e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHH CS
                        Laminin_II  26 lentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdnisei 95 
                                       +e  ++++  ++++++ +++ + d   +++d+++++ +L++   +L+d l+ l++l e   sl d  + +
  gi|336254706|ref|YP_004597813.1| 508 IEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTDDV 577
                                       77889999999*******************************************9999988887766555 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 5.1e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       +++++ ++ v +++ +l++ le +++++++++++v+ ++ +v+d+++ +  +++ v  +e  ++++ + +  +++ +
  gi|336254706|ref|YP_004597813.1| 575 DDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQEWR 651
                                       577888999**********************************************************9999999888 PP

                                       HH.. CS
                        Laminin_II  83 eass 86 
                                       ++ +
  gi|336254706|ref|YP_004597813.1| 652 NQLG 655
                                       7755 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   6.2     2e-09   3.6e-07     288     431 ..     505     645 ..     469     649 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2e-09
                                       HHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-.GGGSSTTTSTTHHHHHHHHHHHHHHHHHH CS
                              EzrA 288 dsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlkq.sYeLseeeleklrelekelkelekdyeel 363
                                       ++L +d++ Ev+   +v+++l+++ ++l  +e+q++++++e+d l + + +L e+el+ l+ l + +++l ++ +++
  gi|336254706|ref|YP_004597813.1| 505 EQLIEDFRSEVA---DVQDELASMDDRLADTESQVDDVETEIDTLTEwTTDL-EDELSDLDHLPETVDSLTDRTDDV 577
                                       789999999995...9*****************************9835566.************************ PP

                                       HHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS CS
                              EzrA 364 eekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkie 431
                                       e+++e+     S l+  le++e+++e++ ++++ +++++++l +d +  ++ ++ ++++l++++ +i 
  gi|336254706|ref|YP_004597813.1| 578 EDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEIT 645
                                       ***************************************************************99885 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.5   2.1e-08   3.8e-06      46     186 ..     492     637 ..     454     644 .. 0.86
   2 ?    2.8   0.0      0.46        80      57     109 ..     604     656 ..     594     661 .] 0.75

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.1e-08
                        Lebercilin  46 kaLskyedteaeLpqllarhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkk.LsedknLaer.e 120
                                       +aL+ + +++    ql++  ++Ev  ++++l  + ++  ++e+++ + e e+  l + +++l++ Ls+  +L+e  +
  gi|336254706|ref|YP_004597813.1| 492 EALETFLGENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDeLSDLDHLPETvD 568
                                       68999999999999***********************************************************9758 PP

                        Lebercilin 121 eLqkkLeeleakleekeekikeLerkleleeksfrr...qlaaekkktkeaqeevkalqeeierlkqkl 186
                                        L+ + +++e+++e+   +++ Le  le  e+  ++    + a +  + ++ e+++a+++ +e+++++l
  gi|336254706|ref|YP_004597813.1| 569 SLTDRTDDVEDEIETVADDVSALETGLETVESDVETvadDVDAVETDVDDLSEDLSAVEDDVESVESDL 637
                                       9************************99998876543111555666666666666666666666666665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.46
                        Lebercilin  57 eLpqllarhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkk 109
                                         ++ ++  + +v  l e+l   ++ ++++e++l +  +e+  +++  ++l +
  gi|336254706|ref|YP_004597813.1| 604 TVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQEWRNQLGS 656
                                       55555667788899999999999999999999999999999988888877765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   2.3   1.5e-08   2.6e-06     285     458 ..     477     649 ..     470     659 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.5e-08
                            AAA_13 285 qerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvk 361
                                        ++L++++e+v+  ++ l + l +  + +++ + f+++++++++e+  ++++L   ++++++  +e+ +   l++ +
  gi|336254706|ref|YP_004597813.1| 477 LDHLQSRVEEVAAYTEALETFLGENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDT---LTEWT 550
                                       456777777777777655555667777788888899999999999999999999988888777777777...45555 PP

                            AAA_13 362 akiesikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkykklekaieklekelkeee 436
                                        ++e   ++++ + e++ +   +++++e+e e++++++ + +  +e +es++++  ++++++e+++ +l ++l++ e
  gi|336254706|ref|YP_004597813.1| 551 TDLEDELSDLDHLPETVDSLTDRTDDVEDEIETVADDVSALEtgLETVESDVETVADDVDAVETDVDDLSEDLSAVE 627
                                       55555556999999************************9998556999***************************** PP

                            AAA_13 437 aelkkleeeikeLekqlrdekp 458
                                       ++++ +e + ++ +++++d+++
  gi|336254706|ref|YP_004597813.1| 628 DDVESVESDLEDVREEITDIQE 649
                                       *****************99986 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 !   22.5   0.1   3.3e-07   5.8e-05      26     167 ..     506     646 ..     506     649 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.3e-07
                               GAS  26 elIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelk 102
                                       +lI+  ++e+++ + + ++++ +l++++++  + + ++ +++e    L+ +l + ++  +  ++l  r  ++e+e++
  gi|336254706|ref|YP_004597813.1| 506 QLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIE 582
                                       58999************************************************************************ PP

                               GAS 103 dlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaqlee 167
                                       ++  +   le  +e+ve++ +++ +  +a+  +v   ++     +e  +++++ +lE   +++++
  gi|336254706|ref|YP_004597813.1| 583 TVADDVSALETGLETVESDVETVADDVDAVETDVDDLSE-DLSAVEDDVESVESDLEDVREEITD 646
                                       *********************999998887777765444.4445677777777777777766665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4     0.016       2.8      62     122 ..     478     541 ..     468     548 .. 0.62
   2 !   17.8   2.1   1.5e-05    0.0026      62     121 ..     561     620 ..     542     627 .. 0.53
   3 !   11.6   1.4    0.0012      0.22      66     114 ..     607     655 ..     603     659 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.016
                           DUF1664  62 rhLssridrvdkkldeqkeiske..ikee.vtevredlseigedvesvkeavegleskleriee 122
                                       +hL+sr+++v +  ++ +    e  + e+ +++ r++++++++++ s+++   + es+++++e+
  gi|336254706|ref|YP_004597813.1| 478 DHLQSRVEEVAAYTEALETFLGEngTGEQlIEDFRSEVADVQDELASMDDRLADTESQVDDVET 541
                                       5777777777766666555433211333314556777777777777777777777777666664 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.5e-05
                           DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       +hL + +d++ ++ d++++ ++ ++++v++++ +l+++++dve+v + v  +e+ +++++
  gi|336254706|ref|YP_004597813.1| 561 DHLPETVDSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLS 620
                                       455555555555555555555555555555555555555555555555555555555443 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.0012
                           DUF1664  66 sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       +++d v++ +d+ +e  ++++++v++v++dl++++e+++ ++e  ++l+
  gi|336254706|ref|YP_004597813.1| 607 DDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQEWRNQLG 655
                                       5788888888888888888999999999999999988888888777665 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1       3.4     6e+02      19      63 ..     476     520 ..     473     524 .. 0.61
   2 !    9.7   6.7    0.0064       1.1      20      63 ..     529     572 ..     506     593 .. 0.57
   3 !   18.2   6.2   1.5e-05    0.0027       8      63 ..     597     649 ..     593     656 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 3.4
                           NPV_P10  19 kVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       k+d lq++v++v++  + ++    +     + ++++ ++v ++qd
  gi|336254706|ref|YP_004597813.1| 476 KLDHLQSRVEEVAAYTEALETFLGENGTGEQLIEDFRSEVADVQD 520
                                       788888888888887766554444433444444555555555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0064
                           NPV_P10  20 VdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       +   ++qvddv++++ ++te ++ L++    L++l ++v++ +d
  gi|336254706|ref|YP_004597813.1| 529 LADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTD 572
                                       44444455555555555555555555554455555554444443 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 1.5e-05
                           NPV_P10   8 vIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                        + +d++ v d Vda+++ vdd++e+l  v+   + +++    L+++ +++++Iq+
  gi|336254706|ref|YP_004597813.1| 597 TVESDVETVADDVDAVETDVDDLSEDLSAVE---DDVESVESDLEDVREEITDIQE 649
                                       6779*********************999955...9*******************97 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   5.8   0.00011     0.019     175     279 ..     476     592 ..     434     594 .. 0.63
   2 !   18.4   6.9   4.4e-06   0.00077     135     273 ..     506     652 ..     505     657 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
                              Spc7 175 ekaeleeeleklqeaaeeles......idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkse 245
                                       + + l++++e+  +  e le+        ++ +e +r+e+a+++ e+++  ++la+ ++q++++e++i++l+e  ++
  gi|336254706|ref|YP_004597813.1| 476 KLDHLQSRVEEVAAYTEALETflgengTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTD 552
                                       33344444444444444444455555456788899999999999999999999999999999999999999999999 PP

                              Spc7 246 leeeiaeaervleeckgws......esevsrlkeevkale 279
                                       le+e++  +++ e   + +      e+e++++ + v+ale
  gi|336254706|ref|YP_004597813.1| 553 LEDELSDLDHLPETVDSLTdrtddvEDEIETVADDVSALE 592
                                       9999998887765544333111111566677777766666 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 4.4e-06
                              Spc7 135 qllegLkegleenlegleedkelLekqeeeldellpeleeeka...eleeeleklqeaaeeles.....id.keeLe 202
                                       ql+e+ ++++ +  ++l + +++L++ e+++d++  e+++  +   +le+el +l    e ++s      d ++e+e
  gi|336254706|ref|YP_004597813.1| 506 QLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEwttDLEDELSDLDHLPETVDSltdrtDDvEDEIE 582
                                       67777777777777777777777777777777777666555444447888887777766655554445433566777 PP

                              Spc7 203 elreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlke 273
                                       ++ +++++l++ +e  + +++++ ++++++e+++++l+e  s +e+++++ e+ le  ++ + ++++++++
  gi|336254706|ref|YP_004597813.1| 583 TVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVRE-EITDIQEWRN 652
                                       777777777777777777777777777777777777777777777777777776665554.4455555555 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 !   12.5   2.9   0.00064      0.11      18     106 ..     476     567 ..     460     570 .. 0.82
   2 !   24.2   3.7   1.5e-07   2.7e-05      20     102 ..     568     650 ..     564     659 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00064
                    CENP-F_leu_zip  18 kadsLkdkvenLerelemsee...nqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqk 91 
                                       k d+L+ +ve+  +  e +e    ++   +   E+ + ev  +++e+  +  +l + e++++++  e ++L++   +
  gi|336254706|ref|YP_004597813.1| 476 KLDHLQSRVEEVAAYTEALETflgENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTD 552
                                       558888888888777776665111333344457999***************************************** PP

                    CENP-F_leu_zip  92 kqervseLeslnssl 106
                                         ++ s+L+ l +++
  gi|336254706|ref|YP_004597813.1| 553 LEDELSDLDHLPETV 567
                                       ********9987665 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1.5e-07
                    CENP-F_leu_zip  20 dsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqerv 96 
                                       dsL d+ +  e e+e++  + +++++  Et    vet+ + ++  ++   +l+ dL+a+  + e++e +l++ +e++
  gi|336254706|ref|YP_004597813.1| 568 DSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEI 644
                                       89999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                    CENP-F_leu_zip  97 seLesl 102
                                        + ++ 
  gi|336254706|ref|YP_004597813.1| 645 TDIQEW 650
                                       887665 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 ?    3.0   0.8      0.67   1.2e+02      13      71 ..     438     496 ..     433     503 .. 0.65
   2 !   19.9   0.1   3.8e-06   0.00067       7      82 ..     501     576 ..     498     579 .. 0.94
   3 ?    7.7   1.1     0.023       4.1      14      79 ..     588     650 ..     578     659 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.67
                       TMF_TATA_bd  13 lverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelek 71 
                                       l erl seir  E++  +l+   ++l++e +  + e++kl +   +++e ++  e le+
  gi|336254706|ref|YP_004597813.1| 438 LAERLASEIRNGEVDEDELEVLRAELATEPELSAPELAKLDHLQSRVEEVAAYTEALET 496
                                       66777888887777777777777777777777777777766666666666555555554 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.8e-06
                       TMF_TATA_bd   7 agpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryet 82 
                                       +g+  ql+e + se+   + Elas+ ++l+  e++ d+++ ei +l++ + +l+++ ++l++l + +++l++r + 
  gi|336254706|ref|YP_004597813.1| 501 NGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTDD 576
                                       566789****************************************************************999875 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.023
                       TMF_TATA_bd  14 verlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqer 79 
                                       v+ l++ +   E++++++ +++  +e+  d+++e++ ++    +++++ +++le++++e++++qe 
  gi|336254706|ref|YP_004597813.1| 588 VSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVE---DDVESVESDLEDVREEITDIQEW 650
                                       4455556666666666666666666666666666655555...44555556666666666666654 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.7     0.004       0.7      29     101 ..     481     557 ..     468     572 .. 0.59
   2 !   17.6   2.5   1.7e-05     0.003      16     106 ..     551     649 ..     547     659 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.004
                      Baculo_PEP_C  29 nvqilaqlatlldaietqL......nalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLls 99 
                                       ++ +  ++a+  +a+et L      ++l ed++s +a+++++l+++ ++L d+  ++  ++++e+++l+   t+L  
  gi|336254706|ref|YP_004597813.1| 481 QSRV-EEVAAYTEALETFLgengtgEQLIEDFRSEVADVQDELASMDDRLADTESQVD-DVETEIDTLTEWTTDLED 555
                                       4444.44555555555555111111457778888888888888888888888888876.566666666665555544 PP

                      Baculo_PEP_C 100 sv 101
                                       ++
  gi|336254706|ref|YP_004597813.1| 556 EL 557
                                       33 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.7e-05
                      Baculo_PEP_C  16 ldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnalq...dtl 83 
                                        dL + L+++  +  ++   l+   d++e +++++++d+++l + l+t       +++ ++++++ +  l+    ++
  gi|336254706|ref|YP_004597813.1| 551 TDLEDELSDLDHLPETV-DSLTDRTDDVEDEIETVADDVSALETGLETvesdveTVADDVDAVETDVDDLSedlSAV 626
                                       68888899998888888.99999999999999999999999999888888866666666666666677776665667 PP

                      Baculo_PEP_C  84 rneLtnlnsiltnLlssvtNins 106
                                       + + ++++s+l +   ++t i++
  gi|336254706|ref|YP_004597813.1| 627 EDDVESVESDLEDVREEITDIQE 649
                                       77888888888888888888865 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 ?    5.0   0.4      0.18        31       3      33 ..     516     546 ..     502     549 .. 0.59
   2 ?    8.9   0.2     0.011       1.9       3      39 ..     551     590 ..     549     591 .. 0.93
   3 !   14.6   1.0   0.00019     0.034       2      40 ..     581     619 ..     573     620 .. 0.86
   4 !   11.4   2.6    0.0019      0.33       3      39 ..     610     646 ..     609     654 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.18
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveel 33 
                                        +++ +l +++ +l+  +++ +++++++++l
  gi|336254706|ref|YP_004597813.1| 516 ADVQDELASMDDRLADTESQVDDVETEIDTL 546
                                       3445555555555555555555555555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.011
                         FlaC_arch   3 delEnklsklst...eletvkkeneelsksveelkenVkd 39 
                                        +lE +ls+l+    +++++ +  +++++++e++ ++V  
  gi|336254706|ref|YP_004597813.1| 551 TDLEDELSDLDHlpeTVDSLTDRTDDVEDEIETVADDVSA 590
                                       589********9999*********************9975 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 0.00019
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       i+++  ++s l+t letv+++ e + ++v+ ++ +V dl
  gi|336254706|ref|YP_004597813.1| 581 IETVADDVSALETGLETVESDVETVADDVDAVETDVDDL 619
                                       456667899999999999999999999999999999887 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.0019
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkd 39 
                                       d +E+++++ls  l+ v+++ e++++++e++ e++ d
  gi|336254706|ref|YP_004597813.1| 610 DAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITD 646
                                       6677777777777777777777777777777777655 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   1.2    0.0039      0.68       1      45 [.     517     561 ..     517     563 .. 0.93
   2 ?    5.9   0.3     0.083        15      12      46 ..     559     593 ..     558     603 .. 0.83
   3 !   17.4   2.3   2.1e-05    0.0037       3      46 ..     606     649 ..     604     651 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0039
                              XhlA   1 eikerlerietkldnleervdkleekaaeaeekiknleedlkkle 45 
                                       +++++l+ ++ +l + e++vd++e   ++  e+   le++l++l 
  gi|336254706|ref|YP_004597813.1| 517 DVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLD 561
                                       58999***********************************99985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.083
                              XhlA  12 kldnleervdkleekaaeaeekiknleedlkkles 46 
                                       +ld l e+vd l ++ + +e +i+ + +d++ le 
  gi|336254706|ref|YP_004597813.1| 559 DLDHLPETVDSLTDRTDDVEDEIETVADDVSALET 593
                                       68888889999999999999999999988888875 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 2.1e-05
                              XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                        +++  +et++d+l+e+++ +e++ + +e+ ++ + e++ ++++
  gi|336254706|ref|YP_004597813.1| 606 ADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQE 649
                                       688999************************************97 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 ?    7.7   0.2      0.02       3.6      17      88 ..     476     547 ..     462     554 .. 0.84
   2 !   11.7   0.1    0.0012       0.2      19      87 ..     558     626 ..     546     661 .] 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.02
                             Mod_r  17 klealvktlpevkqlkeekeellaeneslaeknlsl.epeleelrselqekleelkelekefeekeqeldell 88 
                                       kl+ l + ++ev +++e++e  l en    e+ +++ + e+ ++++el++  + l+  e+++++ e+e d+l 
  gi|336254706|ref|YP_004597813.1| 476 KLDHLQSRVEEVAAYTEALETFLGENGTG-EQLIEDfRSEVADVQDELASMDDRLADTESQVDDVETEIDTLT 547
                                       55555555688999999999999998776.889998899***********999************99999886 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0012
                             Mod_r  19 ealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldel 87 
                                       + l + l ++v++l+++ +++++e+e +a++  +le+ le + s+++   + ++++e+ ++++ ++l+++
  gi|336254706|ref|YP_004597813.1| 558 SDLDH-LpETVDSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAV 626
                                       44433.3255788999999999999999999999999999999999999999999999999988888665 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.19        33     163     207 ..     454     498 ..     449     501 .. 0.92
   2 !   10.3   0.2     0.002      0.36      84     139 ..     505     560 ..     505     563 .. 0.93
   3 !   12.8   0.1   0.00036     0.064      28     132 ..     549     654 ..     547     661 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.19
                        MscS_porin 163 aqieeleqellsnnnrqeLlklqrdllklriqqleqelqaLqell 207
                                       +++e l+ el++ + + +   +++d l+ r+++  ++ +aL++ l
  gi|336254706|ref|YP_004597813.1| 454 DELEVLRAELATEPELSAPELAKLDHLQSRVEEVAAYTEALETFL 498
                                       688999***********************************9876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.002
                        MscS_porin  84 eqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnst 139
                                       eq +++  s+++++q +la+ +++l+ ++++ + + +++ +  + +++++++L+++
  gi|336254706|ref|YP_004597813.1| 505 EQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDL 560
                                       7999999***********************************99999999999776 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00036
                        MscS_porin  28 lLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeila..klsleeLeqrllqtssqlqelqeqla 102
                                       + ++ ++  ++++ l +++d+ + ++++++ e+e+  +++ +a ++ l+  +   e+    +++++ ++ +l+e+l+
  gi|336254706|ref|YP_004597813.1| 549 WTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIETV-ADDVSALETGLEtvESDVETVADDVDAVETDVDDLSEDLS 624
                                       667778888889999999999999999999999999.4444444444441145667888888888888888888888 PP

                        MscS_porin 103 qlnsqlvelqtrperaqqqltearqrlqei 132
                                         ++++ + ++ +e +++++t+ ++  +++
  gi|336254706|ref|YP_004597813.1| 625 AVEDDVESVESDLEDVREEITDIQEWRNQL 654
                                       888888888888888888888877766665 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.085        15      64     110 ..     510     556 ..     480     566 .. 0.57
   2 !   12.3   0.0   0.00078      0.14      56     131 ..     568     643 ..     564     648 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.085
                              ADIP  64 kleaeierlqskierlktqleqlerelalvqakerqlekklktleqk 110
                                       + ++e +  q +  +++++l+++e++++ v+ +  +l+   ++le+ 
  gi|336254706|ref|YP_004597813.1| 510 DFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDE 556
                                       33444444444444444444444444444444444444444443333 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00078
                              ADIP  56 eslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktq 131
                                        sl+++  + e eie    +++ l+t le  e+ +++v  +    e+++ +l++ l    ++++  +++l++++  
  gi|336254706|ref|YP_004597813.1| 568 DSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREE 643
                                       6889999999***********************************************************9999975 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       9.2   1.6e+03       4      31 ..     474     501 ..     472     514 .. 0.79
   2 ?    4.4   0.4      0.19        34      66      95 ..     517     546 ..     502     560 .. 0.56
   3 !   17.3   3.8     2e-05    0.0034       8     101 ..     551     646 ..     545     651 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 9.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   4 inkfqqlqqqlqqlaqqikqletqlkel 31 
                                       ++k+  lq++++++a+  + let l e+
  gi|336254706|ref|YP_004597813.1| 474 LAKLDHLQSRVEEVAAYTEALETFLGEN 501
                                       6888899999999999888888877776 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  66 eLeerketlekeiktlekqleklekeleel 95 
                                       ++++++++++ +++  e+q +++e+e++ l
  gi|336254706|ref|YP_004597813.1| 517 DVQDELASMDDRLADTESQVDDVETEIDTL 546
                                       344444444444444455555544444443 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHH...HHHHHHHHHHHHHHH CS
                       Prefoldin_2   8 qqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkee...Leerketlekeiktl 81 
                                       ++l+++l++l++  ++++   ++ ++v++e+e++++d       G   v+ d+e+v ++   +e++ ++l++ ++++
  gi|336254706|ref|YP_004597813.1| 551 TDLEDELSDLDHLPETVDSLTDRTDDVEDEIETVADD-VSALETGLETVESDVETVADDvdaVETDVDDLSEDLSAV 626
                                       67999999999999***********************.9999**************87622268999********** PP

                                       HHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  82 ekqleklekeleelkeelqk 101
                                       e+  e++e +le+++ee+  
  gi|336254706|ref|YP_004597813.1| 627 EDDVESVESDLEDVREEITD 646
                                       ****************9975 PP

>> HsbA  Hydrophobic surface binding protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.2   3.8e-06   0.00066       2     115 ..     537     655 ..     536     659 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.8e-06
                                       HHHHHHHHHHHHHHHHHHHHHHH--S.H..HHHHHHHHHHHHHHHHHHHHHHHTS--.--HHHH..HHHHHHHHHCH CS
                              HsbA   2 atvisdittistavtaldtavnafnG.gasalpilsasnalvsaikkattdaqasap.ltdeea..lalaqavqtLe 74 
                                       ++v + i+t+++ +t+l + ++  +    ++ ++++ ++++++ i++ ++d++a ++ l   e+  +++a+ v ++e
  gi|336254706|ref|YP_004597813.1| 537 DDVETEIDTLTEWTTDLEDELSDLDHlPETVDSLTDRTDDVEDEIETVADDVSALETgLETVESdvETVADDVDAVE 613
                                       78999*******************9962679***************************9976552279********* PP

                                       HHHHHHHHHHHHTHHHHHHH.T-HHHHHHHHHHHHHHHHHHH CS
                              HsbA  75 pdvkaaldaliaKkpafdka.gltslvlssLqdlkaasdaLs 115
                                       +dv+++ ++l a  ++++++      v+  ++d++   ++L+
  gi|336254706|ref|YP_004597813.1| 614 TDVDDLSEDLSAVEDDVESVeSDLEDVREEITDIQEWRNQLG 655
                                       ******************884447888888888888777776 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   1.6    0.0004     0.071      32      93 ..     512     574 ..     510     577 .. 0.89
   2 !   13.3   1.2   0.00039     0.068      33      96 ..     558     619 ..     555     622 .. 0.93
   3 !   10.3   0.6    0.0032      0.57      36      91 ..     596     649 ..     594     654 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0004
                           DUF2730  32 redleklaekveendkrlteletkvenLPtakd.lekLkllladlrgelkaleaevrqlshqv 93 
                                       r++++ ++++++++d rl+++e++v+++ t+ d l +  ++l+d   +l++l ++v++l  ++
  gi|336254706|ref|YP_004597813.1| 512 RSEVADVQDELASMDDRLADTESQVDDVETEIDtLTEWTTDLEDELSDLDHLPETVDSLTDRT 574
                                       899*************************99976588899999999999999999999998766 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00039
                           DUF2730  33 edleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqvdLL 96 
                                       +dl +l e+v++   r +++e ++e++  a+d+++L++ l+ ++ ++++++ +v+++++ vd L
  gi|336254706|ref|YP_004597813.1| 558 SDLDHLPETVDSLTDRTDDVEDEIETV--ADDVSALETGLETVESDVETVADDVDAVETDVDDL 619
                                       68999********************97..89***************************998855 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0032
                           DUF2730  36 eklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlsh 91 
                                       e+++  ve+    ++++et v++L   +dl++++ +++ ++ +l+++++e++ ++ 
  gi|336254706|ref|YP_004597813.1| 596 ETVESDVETVADDVDAVETDVDDL--SEDLSAVEDDVESVESDLEDVREEITDIQE 649
                                       67788899999999*********9..689*******************99999875 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.7    0.0052      0.92       6      65 ..     509     568 ..     505     578 .. 0.89
   2 !   11.8   0.7   0.00094      0.17      11      70 ..     566     625 ..     549     642 .. 0.56
   3 !   12.6   0.3   0.00054     0.095       5      65 ..     595     655 ..     591     659 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0052
                             Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                       e+ ++e+ ++ +++ ++ + L++ e+++++v+++  +l e + +l +e ++l++l e+++
  gi|336254706|ref|YP_004597813.1| 509 EDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVD 568
                                       5667889999999*********************************99999999988876 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00094
                             Sec34  11 ecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLky 70 
                                       ++d+l ++td++++++e++ +++++ ++  ++++++ e++ ++ + +e+ +++++e+L+ 
  gi|336254706|ref|YP_004597813.1| 566 TVDSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSA 625
                                       555555555555555555555555555555555555555555555555555555555543 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00054
                             Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                       Le+ e+ ++++ +++d++++++++l+e+ ++v+++ +s++++ e++ ee ++++e  +++ 
  gi|336254706|ref|YP_004597813.1| 595 LETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQEWRNQLG 655
                                       77888999999**********************************9999999999887765 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.042       7.3      89     173 ..     479     556 ..     471     562 .. 0.42
   2 !   12.1   0.3   0.00074      0.13      90     179 ..     553     642 ..     536     649 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.042
                            DUF724  89 alqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlks 165
                                       +lqsr++++ +  +  +  l e    e+ ie+ +se + +++e++ ++ + ++ e q        ++ + ei +l  
  gi|336254706|ref|YP_004597813.1| 479 HLQSRVEEVAAYTEALETFLGENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQV-------DDVETEIDTLTE 548
                                       4444444444444444444444444444444444444444444444444444444443.......333333333333 PP

                            DUF724 166 eaekleee 173
                                        + +le+e
  gi|336254706|ref|YP_004597813.1| 549 WTTDLEDE 556
                                       33333333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00074
                            DUF724  90 lqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkse 166
                                       l++ l++L +l +  ++l +++ ++e +ie+ +++ + le+ ++ +e+ + ++    +++ ++ ++ ++++++++ +
  gi|336254706|ref|YP_004597813.1| 553 LEDELSDLDHLPETVDSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDD 629
                                       34445555555555555555555555555555555555555555555555555555555555555555555555555 PP

                            DUF724 167 aekleeeledveq 179
                                       +e++e +ledv++
  gi|336254706|ref|YP_004597813.1| 630 VESVESDLEDVRE 642
                                       5555555555555 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 ?    2.1   0.1       1.4   2.4e+02      58      87 ..     468     497 ..     452     500 .. 0.70
   2 !   11.8   0.9    0.0013      0.23      47      94 ..     509     556 ..     505     558 .. 0.84
   3 ?    8.9   1.3      0.01       1.8      11      91 ..     577     654 ..     568     659 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 1.4
                           BLOC1_2  58 eelqpylqqidqiekqvteLeeavseLDey 87 
                                       e  +p l ++d ++ +v+e  +  ++L+++
  gi|336254706|ref|YP_004597813.1| 468 ELSAPELAKLDHLQSRVEEVAAYTEALETF 497
                                       556677888888888888888877777765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0013
                           BLOC1_2  47 ekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                       e++ +++   ++el+++ +++ + e qv++ e+ ++ L e++++LE+ 
  gi|336254706|ref|YP_004597813.1| 509 EDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDE 556
                                       45556666777899*******************************986 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.01
                           BLOC1_2  11 leaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDey 87 
                                       +e e+e +++d++ Le+  e++++ ++ ++d ++ +e+++++l+e    l+   + ++ +e ++++  e +  + e+
  gi|336254706|ref|YP_004597813.1| 577 VEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSE---DLSAVEDDVESVESDLEDVREEITDIQEW 650
                                       677777777777777777777777777777777777777777777...66666666666666666666666666666 PP

                           BLOC1_2  88 skeL 91 
                                         +L
  gi|336254706|ref|YP_004597813.1| 651 RNQL 654
                                       5555 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   7.4   0.00017      0.03     199     321 ..     516     644 ..     473     655 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00017
                            HMMR_N 199 eeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLeeke 275
                                        + + ++a + ++l ++e +  +  +e++ l+e ++ l+ +   l++  + +++l +  +  +deie++  ++++ e
  gi|336254706|ref|YP_004597813.1| 516 ADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIETVADDVSALE 592
                                       44556666666666666666666666666666666666666666666666666666666666666666666655555 PP

                            HMMR_N 276 qelsk...qvkdlnekcklle...kekeelvreeeekeqtlsaEleelkekl 321
                                       + l++    v+     ++ +e    ++ e ++  e   +++++ le+++e++
  gi|336254706|ref|YP_004597813.1| 593 TGLETvesDVETVADDVDAVEtdvDDLSEDLSAVEDDVESVESDLEDVREEI 644
                                       5444310133334444444442222222223333444444444444444444 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       5.5   9.7e+02      60     100 ..     453     496 ..     439     509 .. 0.52
   2 !   10.6   1.7    0.0014      0.25      16      99 ..     513     596 ..     487     599 .. 0.87
   3 !   12.4   0.9    0.0004      0.07      16     100 ..     572     656 ..     566     660 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5.5
                           DUF3450  60 leslevyneqle...rlvasqeqeiasleeqieeieeierelvp 100
                                        ++lev +++l+   +l a   ++++ l+ + ee+ +  ++l+ 
  gi|336254706|ref|YP_004597813.1| 453 EDELEVLRAELAtepELSAPELAKLDHLQSRVEEVAAYTEALET 496
                                       44444444444411134444444455555555555555555554 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0014
                           DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       ++++++++e ++  +  a++++++d+++ e ++l +  ++l++el++l+   e +++l +  +   +++e+  ++++
  gi|336254706|ref|YP_004597813.1| 513 SEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIETVADDVS 589
                                       67888999999999999999999999999999999999999999999999999999999999999999999999999 PP

                           DUF3450  93 eierelv 99 
                                       ++e++l+
  gi|336254706|ref|YP_004597813.1| 590 ALETGLE 596
                                       9888876 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.0004
                           DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       +  d++++e e   +  ++ ++  + ++ + +++++++ a+++ +++l+   + +e+ v+s+e+++++++e+i++i+
  gi|336254706|ref|YP_004597813.1| 572 DRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQ 648
                                       56778888888888888888888888889999999999999999999999999999999999999999999999999 PP

                           DUF3450  93 eierelvp 100
                                       e +++l  
  gi|336254706|ref|YP_004597813.1| 649 EWRNQLGS 656
                                       99998865 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   2.8       7.6   1.3e+03      72      93 ..     309     330 ..     278     340 .. 0.65
   2 ?   -0.3   1.2       8.2   1.4e+03      43      86 ..     450     493 ..     407     496 .. 0.59
   3 !   16.0   2.4   7.7e-05     0.014      13      98 ..     479     557 ..     474     566 .. 0.59
   4 !   15.6   2.2    0.0001     0.018      11      96 ..     567     649 ..     564     658 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 7.6
                            APG6_N  72 elekereeleaelaaleeelea 93 
                                       e+e+++++le+e a+  ee++a
  gi|336254706|ref|YP_004597813.1| 309 ETEAADADLEDEAADVDEEEAA 330
                                       3444444444444444444443 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 8.2
                            APG6_N  43 ekqdeeleeleeeleklekeeeelleeLkelekereeleaelaa 86 
                                       e +++ele l+ el++  +  +  l++L+ l++  ee++a  +a
  gi|336254706|ref|YP_004597813.1| 450 EVDEDELEVLRAELATEPELSAPELAKLDHLQSRVEEVAAYTEA 493
                                       22444555555555555555555555555555555555555555 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 7.7e-05
                            APG6_N  13 eldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaalee 89 
                                        l    ++  +e  aY+e l+++  e+ + e   + +e+ + e++++++e +++   L+++e++ +++e e+ +l+e
  gi|336254706|ref|YP_004597813.1| 479 HL----QSRVEEVAAYTEALETFLGENGTGE---QLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTE 548
                                       34....4444566666666666665544443...4666666666666666666666666666666666666666666 PP

                            APG6_N  90 elealeeee 98 
                                        + +le+e 
  gi|336254706|ref|YP_004597813.1| 549 WTTDLEDEL 557
                                       666666553 PP

  == domain 4  score: 15.6 bits;  conditional E-value: 0.0001
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaal 87 
                                       ++ l+ + +++e+e+++  +  + l++  ++ e   +++e   ++++++e + ++l e L ++e+  e++e++l++ 
  gi|336254706|ref|YP_004597813.1| 567 VDSLTDRTDDVEDEIETVADDVSALETGLETVE---SDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDV 640
                                       567778888888888888888888887766654...68888888888888888888888888888888888888888 PP

                            APG6_N  88 eeelealee 96 
                                       +ee  +++e
  gi|336254706|ref|YP_004597813.1| 641 REEITDIQE 649
                                       888777665 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       3.1   5.5e+02      10      38 ..     475     503 ..     472     513 .. 0.79
   2 ?    7.9   0.2     0.016       2.7      80     115 ..     523     558 ..     516     562 .. 0.90
   3 ?    4.7   0.1      0.16        27      76     117 ..     564     605 ..     561     608 .. 0.85
   4 ?    4.1   0.2      0.24        42      84     112 ..     621     649 ..     611     659 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHHHHHHHHHHHTT.-TT CS
                         Prefoldin  10 aelaqlkeaieelektletlktlkkedeg 38 
                                       a+l+ l+++ ee+ +  e+l+t+  e+  
  gi|336254706|ref|YP_004597813.1| 475 AKLDHLQSRVEEVAAYTEALETFLGENGT 503
                                       67889999999999999999999885444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  80 ellkkkleelekqlekleeeleklkdqittleanla 115
                                       +  +++l++ e+q++++e e++ l++  t le++l+
  gi|336254706|ref|YP_004597813.1| 523 ASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELS 558
                                       5689****************************9997 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  76 eeAiellkkkleelekqlekleeeleklkdqittleanlaql 117
                                        e ++ l ++ +++e+ +e++ +++  l + ++t+e  ++++
  gi|336254706|ref|YP_004597813.1| 564 PETVDSLTDRTDDVEDEIETVADDVSALETGLETVESDVETV 605
                                       577899999999999999999999999999999999877766 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  84 kkleelekqlekleeeleklkdqittlea 112
                                       + l+ +e+ +e++e +le+ +++it +++
  gi|336254706|ref|YP_004597813.1| 621 EDLSAVEDDVESVESDLEDVREEITDIQE 649
                                       55566666666666666666666666654 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 ?    5.6   1.3      0.11        19      26      82 ..     520     555 ..     477     563 .. 0.53
   2 !   16.0   5.0   6.2e-05     0.011      24      87 ..     563     626 ..     558     628 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.11
                            DUF948  26 ktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlge 82 
                                       + l ++ ++++++e+qvd + +e+++l++ + +                     l +
  gi|336254706|ref|YP_004597813.1| 520 DELASMDDRLADTESQVDDVETEIDTLTEWTTD---------------------LED 555
                                       222333333333333333333333333333333.....................333 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 6.2e-05
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       l +t+d+++++ +++e++++ + ++v +l +  +++ +dv+   ++vd++ + v dl+e +s++
  gi|336254706|ref|YP_004597813.1| 563 LPETVDSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAV 626
                                       6689*******************************************************99987 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 !   14.4   1.7   0.00017      0.03      95     190 ..     450     547 ..     398     550 .. 0.69
   2 ?    6.0   0.9     0.066        12      90     170 ..     566     649 ..     547     660 .. 0.39

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00017
                           UPF0242  95 qeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaek...qellqeyqetieeqrsvlekr 168
                                       + +e+eL+   ++  +e e    e ++L   l+  +e+++++  +le  L e    ++l+++++ ++ + + +l + 
  gi|336254706|ref|YP_004597813.1| 450 EVDEDELEVLRAELATEPELSAPELAKLD-HLQSRVEEVAAYTEALETFLGENgtgEQLIEDFRSEVADVQDELASM 525
                                       44444444443333333333344444444.5555566666666666666665433389******************* PP

                           UPF0242 169 qdqieqLeskVrDlnyEiktLl 190
                                       +d+ ++ es+V D   Ei tL 
  gi|336254706|ref|YP_004597813.1| 526 DDRLADTESQVDDVETEIDTLT 547
                                       ********************95 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.066
                           UPF0242  90 aleelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklele...eqLaekqellqeyqetieeqrs 163
                                       ++  l++++++ ++e++     +  l+   + +++  e +a d++++  +++   e L   +  ++  +  +e+ r+
  gi|336254706|ref|YP_004597813.1| 566 TVDSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDdlsEDLSAVEDDVESVESDLEDVRE 642
                                       44444444444444433333333333333333333333333333333222211113333333333333333333333 PP

                           UPF0242 164 vlekrqd 170
                                       ++   q+
  gi|336254706|ref|YP_004597813.1| 643 EITDIQE 649
                                       3333333 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.6     0.081        14      21      56 ..     507     542 ..     505     547 .. 0.92
   2 !   11.7   0.3   0.00076      0.13       6      90 ..     565     648 ..     562     655 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.081
                              DegS  21 IaEsarkeverlkkeleelkeevsevikevdklekk 56 
                                       + E+ r+ev+++++el+ + ++++++ ++vd++e++
  gi|336254706|ref|YP_004597813.1| 507 LIEDFRSEVADVQDELASMDDRLADTESQVDDVETE 542
                                       67999**************************99976 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00076
                              DegS   6 ktietiekskeeifeIaEsarkeverlkkeleelkeevsevikevdklekkerkarkrLaeVskdFkkyseeeikea 82 
                                       +t++++++  +++ +  E++ ++v+ l++ le+++++v++v ++vd++e++     + L++V+ d ++  e++++++
  gi|336254706|ref|YP_004597813.1| 565 ETVDSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESV-ESDLEDV 640
                                       6788888888888888999*******************************************9998664.5566666 PP

                              DegS  83 Yeeakelq 90 
                                        ee +++q
  gi|336254706|ref|YP_004597813.1| 641 REEITDIQ 648
                                       66655555 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.5      0.21        38     277     346 ..     476     548 ..     436     560 .. 0.62
   2 !   13.7   0.7   0.00015     0.026     277     347 ..     580     650 ..     555     660 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.21
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FH2 277 nleslekevkklekglkklekelessekkeepsdkflevlkef...lkeaeeklkkleeelkeakelvkelve 346
                                       +l++l++ v+++    ++le+ l ++ + e+  + f++ + ++   l++ +++l++ e++ ++++++ ++l+e
  gi|336254706|ref|YP_004597813.1| 476 KLDHLQSRVEEVAAYTEALETFLGENGTGEQLIEDFRSEVADVqdeLASMDDRLADTESQVDDVETEIDTLTE 548
                                       6788888888888888888888888888555555555443333111444555555555555555555555555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00015
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FH2 277 nleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeakelvkelveY 347
                                       ++e+++++v++le+gl+ +e ++e+ + + +  ++ ++ l+e l+  e++++++e++l++++e+ +++ e+
  gi|336254706|ref|YP_004597813.1| 580 EIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQEW 650
                                       45556666666666666666666666665555555566666666666666666666666666665555543 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   1.9   0.00097      0.17     121     230 ..     535     644 ..     505     647 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00097
                           DUF4618 121 qIanlvrqlqqlkd...sqqdeldeleelikevleklskkiqkkkekllkslaektlkatqeaLlqktlenqvlkke 194
                                       q+    ++++ l +   + +del +l++l +    +l ++++  ++++ +    + ++a +++L+    + ++++  
  gi|336254706|ref|YP_004597813.1| 535 QVDDVETEIDTLTEwttDLEDELSDLDHLPE-TVDSLTDRTDDVEDEIETV--ADDVSALETGLETVESDVETVADD 608
                                       5555556666665511145666666666655.5689999999999999764..4778899***************** PP

                           DUF4618 195 iekfrefieeleeeipeLkaeveqLqaqaeeprevi 230
                                       ++ +   +++l e++++ + +ve  + + e++re i
  gi|336254706|ref|YP_004597813.1| 609 VDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEI 644
                                       **********************************98 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       7.8   1.4e+03      45      95 ..     441     490 ..     439     500 .. 0.60
   2 ?    1.3   0.3       2.8   4.9e+02       9      66 ..     483     538 ..     475     545 .. 0.55
   3 ?   16.3   2.5   5.8e-05      0.01       7     104 ..     540     638 ..     534     639 .. 0.83
   4 ?    7.0   0.3     0.044       7.8      36      93 ..     588     648 ..     586     659 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 7.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  45 aleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkel 95 
                                       +l  e+++ +   ++l+ l  +l++e + +++e+ ++l++l++r ee+ + 
  gi|336254706|ref|YP_004597813.1| 441 RLASEIRNGEVDEDELEVLRAELATEPELSAPEL-AKLDHLQSRVEEVAAY 490
                                       5666777777777777777777766644444443.4666666666666544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin   9 dadeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaek 66 
                                       +++e+ +  e  e++l   + g   + +++   +  ++++ela++++r+ + + + ++
  gi|336254706|ref|YP_004597813.1| 483 RVEEVAAYTEALETFL--GENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDD 538
                                       4455555555555555..4444444555555566666666666666666666655554 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 5.8e-05
                                       HHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHTTHTTHHHHHH CS
                          Spectrin   7 aqdadeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkaln...elaeklldeghsaseeiee 80 
                                       + ++d l+eW ++ e +l   dl + +e+v +l ++ +++e+e+++  + v al+   e+ e+ ++   ++ +++e+
  gi|336254706|ref|YP_004597813.1| 540 ETEIDTLTEWTTDLEDEL--SDLDHLPETVDSLTDRTDDVEDEIETVADDVSALEtglETVESDVETVADDVDAVET 614
                                       57899*************..66667******************************6664444444555788899999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  81 rleelnerWeeLkelaaerkqkLe 104
                                        +++l e   ++++ +++ +  Le
  gi|336254706|ref|YP_004597813.1| 615 DVDDLSEDLSAVEDDVESVESDLE 638
                                       999999999999988888887776 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT...HTTHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  36 vqallkkhkaleaelaaqqervkalnelaeklldeg...hsaseeieerleelnerWeeLk 93 
                                       v al++ ++++e ++++  + v+a+++  ++l +     +++ e +e+ le+++e   +++
  gi|336254706|ref|YP_004597813.1| 588 VSALETGLETVESDVETVADDVDAVETDVDDLSEDLsavEDDVESVESDLEDVREEITDIQ 648
                                       5667777778888888888888888866666633331224444555555555554444333 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.7   0.00011     0.019      40     208 ..     487     650 ..     465     657 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH CS
                              SHE3  40 eskflenlaslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenssaseteleeelerlkvq 116
                                        + + e l +   EN     l++     + d+++el+++ ++  + + + + ++++++++++  t+le+el+ l+  
  gi|336254706|ref|YP_004597813.1| 487 VAAYTEALETFLGENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDHL 563
                                       4567788888888999999999999999**********************************************976 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SHE3 117 YdalvdsqkeYkehYqqeieeLkesleklklenekqleelqerissndkdidtkldsynnkkknlesieeeknkkll 193
                                        +  vds     +  ++eie+    + +l++  e ++e   e++ ++  +++t +d++++   ++e+  e+    ++
  gi|336254706|ref|YP_004597813.1| 564 PE-TVDSLTDRTDDVEDEIETVADDVSALETGLE-TVESDVETVADDVDAVETDVDDLSEDLSAVEDDVES----VE 634
                                       55.68***************************99.889999999999999999999999988777655444....44 PP

                                       XXXXXXXXXX.XXXXX CS
                              SHE3 194 kkleslasel.dlesw 208
                                       + le +++e+ d+++w
  gi|336254706|ref|YP_004597813.1| 635 SDLEDVREEItDIQEW 650
                                       4444444443246666 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2     0.015       2.6      30      92 ..     492     554 ..     479     566 .. 0.85
   2 ?    7.9   0.3    0.0044      0.78      37      90 ..     600     653 ..     579     656 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                              COG6  30 kineefleefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkkle 92 
                                       ++ e+fl e ++ ++ ++ ++s+v++ ++   +m ++l  ++++ +d+ +e+++L+e  ++le
  gi|336254706|ref|YP_004597813.1| 492 EALETFLGENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLE 554
                                       566789999999999999999***************************999999998776665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0044
                              COG6  37 eefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkk 90 
                                       ++ ++va+ ++++e+dv++l+e  + +++ ++s +++ +d+ ee+++++e +++
  gi|336254706|ref|YP_004597813.1| 600 SDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQEWRNQ 653
                                       467888999999999999999999999999999999999999999998887776 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.9     0.065        12      44     105 ..     493     557 ..     454     565 .. 0.60
   2 ?    9.9   0.7    0.0043      0.75       2      95 ..     514     603 ..     513     606 .. 0.86
   3 ?   15.6   1.3   7.3e-05     0.013       2     108 ..     535     644 ..     534     656 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.065
                        TPR_MLP1_2  44 kYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesw...eeqkeelekel 105
                                         e+ l ++ +  + ++++r+e++++++e+a++ +++ +++++++  e ++   +e  + le+el
  gi|336254706|ref|YP_004597813.1| 493 ALETFLGENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIdtlTEWTTDLEDEL 557
                                       44555555555556666666777777777666666666666666555544300033344444444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0043
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       e++ +++e++s++++ ++ e+++  +++++ + +e +++ ++    el       +++ +l ++ +++++ei+++ +
  gi|336254706|ref|YP_004597813.1| 514 EVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLED----ELSDLDHLPETVDSLTDRTDDVEDEIETVAD 586
                                       778999****************99999999998888888888....9999999999999999999999999999999 PP

                        TPR_MLP1_2  79 eaesakaeleeseeswe 95 
                                       ++ ++++ le+ e+  e
  gi|336254706|ref|YP_004597813.1| 587 DVSALETGLETVESDVE 603
                                       99999999998888766 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 7.3e-05
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkel....qalreelnelkaeia 74 
                                       +++ +e+ei++l+e  +++e++l+ l   l +  +++++  ++ e e+   a+dv +l    +++ ++++++ +++ 
  gi|336254706|ref|YP_004597813.1| 535 QVDDVETEIDTLTEWTTDLEDELSDLD-HLPETVDSLTDRTDDVEDEIETVADDVSALetglETVESDVETVADDVD 610
                                       677889999999999999999988774.4555566666666666666666666666651111678888888888888 PP

                        TPR_MLP1_2  75 elkaeaesakaeleeseesweeqkeelekelsel 108
                                        +++++++++++l++ e   e+ ++ le+  +e+
  gi|336254706|ref|YP_004597813.1| 611 AVETDVDDLSEDLSAVEDDVESVESDLEDVREEI 644
                                       8888888888888888888888877777655544 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 ?    7.0   0.4     0.034         6      67     113 ..     511     557 ..     503     582 .. 0.54
   2 ?    3.2   0.3      0.51        89      67      96 ..     584     613 ..     553     618 .. 0.58
   3 ?    8.9   2.4    0.0086       1.5      48      90 ..     610     649 ..     595     657 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.034
                              COG2  67 lqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                       +++e+  v+ +la++ +++ ++++++++ e+e++   e  ++le++ 
  gi|336254706|ref|YP_004597813.1| 511 FRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDEL 557
                                       44455555555555555555555555555555555555444444443 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.51
                              COG2  67 lqeeleevesplaaarkkvesvreklsere 96 
                                       + ++++ +e+ l+++ ++ve v + +++ e
  gi|336254706|ref|YP_004597813.1| 584 VADDVSALETGLETVESDVETVADDVDAVE 613
                                       334444444445555555555544444444 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0086
                              COG2  48 elvnedyadFvslSghLvglqeeleevesplaaarkkvesvre 90 
                                       + v++d+ d   lS+ L  +++++e ves+l+ +r+++++++e
  gi|336254706|ref|YP_004597813.1| 610 DAVETDVDD---LSEDLSAVEDDVESVESDLEDVREEITDIQE 649
                                       556666665...8888888888888888888888888888775 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.097        17     232     284 ..     512     563 ..     503     569 .. 0.70
   2 ?    7.6   0.1      0.01       1.8     220     275 ..     573     634 ..     565     656 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.097
                              RmuC 232 aellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaeklkel 284
                                        ++++++ d+++++ ++l +++++++++++++d+  ++ +  +  ++ +l++l
  gi|336254706|ref|YP_004597813.1| 512 RSEVADVQDELASMDDRLADTESQVDDVETEIDT-LTEWTTDLEDELSDLDHL 563
                                       4567778888888888888888888888888888.566666666666666655 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.01
                              RmuC 220 rqeaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle......gnil 275
                                       r++++e++ e +a+ +++l + +e+++ d+e++ + ++ +++++d++ + l+      +++ 
  gi|336254706|ref|YP_004597813.1| 573 RTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSaveddvESVE 634
                                       55666677777777777777777777777777777777777777776666654444443444 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.0      0.14        25     133     218 ..     472     557 ..     409     562 .. 0.63
   2 ?   13.3   1.1   0.00025     0.044     135     218 ..     560     644 ..     553     657 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.14
                           Leu_zip 133 keierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdeke.nskeiskleeklaelkldlektl 208
                                        e+++L+   ++++e     E+ +++ l e+   e+ +++ ++e+ + +de +  + ++++ e+++ +++++++  +
  gi|336254706|ref|YP_004597813.1| 472 PELAKLDHLQSRVEEVAAYTEA-LETFLGENGTGEQLIEDFRSEVADVQDELAsMDDRLADTESQVDDVETEIDTLT 547
                                       4555555555555554444443.334666666666666666665555544433245556666666666666666555 PP

                           Leu_zip 209 eektasaksl 218
                                       e +t+ +++l
  gi|336254706|ref|YP_004597813.1| 548 EWTTDLEDEL 557
                                       5555444444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00025
                           Leu_zip 135 ierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgek.kdekenskeiskleeklaelkldlektlee 210
                                       +++L e  + L +r+ ++E++++++ ++ s+le+ l+ ++++++   +d+ + ++++ +l+e l++++ d+e+  ++
  gi|336254706|ref|YP_004597813.1| 560 LDHLPETVDSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVaDDVDAVETDVDDLSEDLSAVEDDVESVESD 636
                                       56777888889999999999999999999999999999987776652444446777777777777777777766666 PP

                           Leu_zip 211 ktasaksl 218
                                        ++  +++
  gi|336254706|ref|YP_004597813.1| 637 LEDVREEI 644
                                       55555544 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.0     0.038       6.7      35     103 ..     514     578 ..     500     585 .. 0.58
   2 ?   10.5   0.6    0.0036      0.64      35      96 ..     587     648 ..     579     654 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.038
                                       HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC CS
                             DUF16  35 rLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsie 103
                                       ++ ++++++++ + +++  e +v+  + +i+ l++     ++      + l+ + et++++ +R D +e
  gi|336254706|ref|YP_004597813.1| 514 EVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLED----ELSDLDHLPETVDSLTDRTDDVE 578
                                       444555555555555555555555555555555554444444....34455666666666666666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHH CS
                             DUF16  35 rLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkin 96 
                                       ++  +e+ +++ +  ++ +++ v++ +  +++l+++  a ++++++v++ le + e +++i+
  gi|336254706|ref|YP_004597813.1| 587 DVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQ 648
                                       566788999999999*************************************9999999886 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2     0.039       6.9       5      52 ..     517     564 ..     513     596 .. 0.73
   2 ?    6.7   0.2     0.062        11      11      73 ..     582     644 ..     567     659 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.039
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                       ++ d+l++++++l+++ ++++++++e+ +l+e  ++Le e + l ++ 
  gi|336254706|ref|YP_004597813.1| 517 DVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLP 564
                                       6789999******************************99976665443 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.062
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXX CS
                              YabA  11 eeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenL 73 
                                       e++ +++++l + le+++++++++ ++ +++e++ + l e l+  e++ ++ +++l++ +e++
  gi|336254706|ref|YP_004597813.1| 582 ETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEI 644
                                       555555555555555555555555555555555555555555333333333333333333332 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.15        26      16      89 ..     486     557 ..     472     570 .. 0.53
   2 ?    8.8   0.1    0.0047      0.83       6      80 ..     576     649 ..     558     660 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.15
                             TMPIT  16 etakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesll 89 
                                       e a  y++ le+    + +  + i+  + ++ +++++l +++ ++ +++e++v+++++e+++ ++   ++e+ l
  gi|336254706|ref|YP_004597813.1| 486 EVA-AYTEALETFLGENGTGEQLIEDFRSEVADVQDELASMDDRL-ADTESQVDDVETEIDTLTEWTTDLEDEL 557
                                       333.55555555555555555555555555555555555555554.3555555555555555555555544443 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0047
                             TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80 
                                       ++e+e++++ +  + +++ le++++  ++++ +++  + ++ +l+++l+ ++ +v e+ e+ +e+++ee+ ++++
  gi|336254706|ref|YP_004597813.1| 576 DVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDV-ESVESDLEDVREEITDIQE 649
                                       4445555555555555555555555555555555555555555555555555544.2333344444444444333 PP

>> TBCC_N  Tubulin-specific chaperone C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.8   0.00044     0.077       8     108 ..     481     577 ..     473     582 .. 0.80
   2 ?    2.3   0.1       1.2   2.1e+02      31      76 ..     567     620 ..     551     626 .. 0.57
   3 ?    7.1   0.5     0.041       7.2       3      80 ..     570     652 ..     568     658 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00044
                            TBCC_N   8 qerqeqlekrkeereseaveeekvdsFlkaFteekaaieellesveesadksklkqkldeitaeiqeLqkllaessm 84 
                                       q+r e++++ +e+ e    e+ + ++  + F++e a+++++l+s++     ++ ++++d+++ ei++L +++++   
  gi|336254706|ref|YP_004597813.1| 481 QSRVEEVAAYTEALETFLGENGTGEQLIEDFRSEVADVQDELASMD--DRLADTESQVDDVETEIDTLTEWTTDLED 555
                                       567777788888888888888999999*******************..8889999****************999776 PP

                            TBCC_N  85 fLpsYdlrsaqealskLkesleea 108
                                        L+  dl +  e++++L+++ ++ 
  gi|336254706|ref|YP_004597813.1| 556 ELS--DLDHLPETVDSLTDRTDDV 577
                                       666..3445556666666655555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 1.2
                            TBCC_N  31 vdsFlkaFteekaaieellesve........esadksklkqkldeitaeiqeLq 76 
                                       vds +++ ++ +++ie+  ++v+         ++d +++++++d+++ ++++L 
  gi|336254706|ref|YP_004597813.1| 567 VDSLTDRTDDVEDEIETVADDVSaletgletVESDVETVADDVDAVETDVDDLS 620
                                       444444444444444444444445444444444777777777777777777775 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.041
                            TBCC_N   3 LekReqerqeqlekrkeereseaveeekvdsFlkaFteekaaieellesve.....esadksklkqkldeitaeiqe 74 
                                       L+ R  + + ++e    + ++ ++  e+v+s  ++ ++  +a+e+ +++++      + d ++++++l+++ +ei +
  gi|336254706|ref|YP_004597813.1| 570 LTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSedlsaVEDDVESVESDLEDVREEITD 646
                                       66677777777777777777777778888888888888888888888888888877778999999************ PP

                            TBCC_N  75 Lqklla 80 
                                       +q++ +
  gi|336254706|ref|YP_004597813.1| 647 IQEWRN 652
                                       **9976 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       6.2   1.1e+03     127     153 ..     452     488 ..     438     499 .. 0.55
   2 ?   13.8  14.0   0.00019     0.033       6     139 ..     505     645 ..     456     658 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 6.2
                           DUF4795 127 drlelepLkeqle..........erlkelqkelqeam 153
                                       d++ele L+ +l            +l+ lq +++e +
  gi|336254706|ref|YP_004597813.1| 452 DEDELEVLRAELAtepelsapelAKLDHLQSRVEEVA 488
                                       5666666666665555555544444444444444333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00019
                           DUF4795   6 aellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadke.aLatkv 81 
                                       ++l++  ++++ ++q+el++++++ +++e++  d e ++++l++ + +le++  d +++ e ++   d+  +++  +
  gi|336254706|ref|YP_004597813.1| 505 EQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTdDVEDEI 581
                                       45566666777777777777777777777777777777777777777777777777777777777777531455544 PP

                           DUF4795  82 srdq.....fDeakkeLekmleellekleeqeealkkaldtLqeelkekld..rlelepLkeqle 139
                                       +        +++ ++  e  +e + + ++++e +++ + ++L+ +++  ++  + +le+++e++ 
  gi|336254706|ref|YP_004597813.1| 582 ETVAddvsaLETGLETVESDVETVADDVDAVETDVDDLSEDLS-AVEDDVEsvESDLEDVREEIT 645
                                       43336666888888888888899999999*************9.555555555555555555554 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.2   0.00025     0.045      91     147 ..     480     537 ..     477     544 .. 0.94
   2 ?    3.0   9.4      0.34        60      73     148 ..     535     611 ..     532     620 .. 0.89
   3 ?    6.6   1.1     0.027       4.7     116     143 ..     628     655 ..     613     659 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00025
                           DUF4349  91 leaRlkaleasedrllallekaksvedlle.iereLsevqaeieslegqlryLdnqva 147
                                       l++R++   a+ + l+++l ++++ e l+e   +e+++vq e+ s+  +l+  ++qv+
  gi|336254706|ref|YP_004597813.1| 480 LQSRVEEVAAYTEALETFLGENGTGEQLIEdFRSEVADVQDELASMDDRLADTESQVD 537
                                       689**************************769************************98 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.34
                           DUF4349  73 kvtsrstsaeDVTeqyvDleaRlkaleasedrllallekaksvedll.eiereLsevqaeieslegqlryLdnqvay 148
                                       +v++++t+ + +Te  +Dle  l+ l  + + + +l +++++ved + ++ +++s  ++ +e  e+  ++ ++ v+ 
  gi|336254706|ref|YP_004597813.1| 535 QVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIeTVADDVSALETGLETVESDVETVADDVDA 611
                                       68888999999******************************9998662699*******************9999986 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.027
                           DUF4349 116 edlleiereLsevqaeieslegqlryLd 143
                                       +d+ ++e++L++v++ei  ++ ++++L 
  gi|336254706|ref|YP_004597813.1| 628 DDVESVESDLEDVREEITDIQEWRNQLG 655
                                       6788999999999999999999999986 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.0   0.00095      0.17      30     105 ..     475     560 ..     469     566 .. 0.68
   2 ?    4.7   0.4      0.17        30      51     106 ..     575     627 ..     559     657 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00095
                                       HHHHHHHHHHHHHHHHCTTT.............THHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHH CS
                   Cob_adeno_trans  30 GtvDelnsaiglarallaee.............eeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelek 93 
                                       +++D l+s +  ++a++++               e+++++++++q+eL ++   la   ++++  +++ e +++l +
  gi|336254706|ref|YP_004597813.1| 475 AKLDHLQSRVEEVAAYTEALetflgengtgeqlIEDFRSEVADVQDELASMDDRLAD--TESQVDDVETE-IDTLTE 548
                                       567888888887777765557788876777666667777777777777777777773..34444445555.777777 PP

                                       HHHHHHHHS--E CS
                   Cob_adeno_trans  94 eideleaelppl 105
                                       +  +le+el+ l
  gi|336254706|ref|YP_004597813.1| 549 WTTDLEDELSDL 560
                                       777777777665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHHHHHHS--EE CS
                   Cob_adeno_trans  51 eelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelekeideleaelpplk 106
                                       +++++++e + +++  l + l t e  ++ +++ +++v+++e+ +d+l+++l+ ++
  gi|336254706|ref|YP_004597813.1| 575 DDVEDEIETVADDVSALETGLETVE--SDVETV-ADDVDAVETDVDDLSEDLSAVE 627
                                       5566666666666666666665432..222223.3346666666666666665443 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 ?    6.8   0.0     0.017         3      34     107 ..     473     546 ..     446     560 .. 0.86
   2 ?    4.8   0.0      0.07        12      34     125 ..     556     644 ..     544     653 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.017
                             Atg14  34 lksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakl 107
                                        +++ ++l++++e+  + +e+ e+   +  +  + +e+ +s++ad +++l+ + d+l    +++++   ++ +l
  gi|336254706|ref|YP_004597813.1| 473 ELAKLDHLQSRVEEVAAYTEALETFLGENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTL 546
                                       578899***************************************************99999988777666655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.07
                             Atg14  34 lksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdk 110
                                        +s+ ++l + ++ +  +++   + ed+i++ +++++ l +  +  ++ ++++ d+++     +++ ++ l++  d+
  gi|336254706|ref|YP_004597813.1| 556 ELSDLDHLPETVDSLTDRTD---DVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDD 629
                                       44444444444444444444...555555555555555555555555555555555555555555555555555555 PP

                             Atg14 111 lkkRrsdleslqnel 125
                                       +    sdle +++e+
  gi|336254706|ref|YP_004597813.1| 630 VESVESDLEDVREEI 644
                                       555555555444444 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 ?    6.5   0.1     0.049       8.7      44     122 ..     477     561 ..     473     566 .. 0.63
   2 ?   10.6   0.7    0.0028      0.49      32     126 ..     517     617 ..     503     622 .. 0.54
   3 ?    6.4   0.3     0.053       9.2      25     109 ..     569     652 ..     564     659 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.049
                                       CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHH...HHHHCCCHHHHHHHCCHHHHHHHHHHHHHH CS
                         Fib_alpha  44 leeisnstkeaeelvkeikdslrekqkskkdn...dnvikkssk...eleeeilrlketidaqesnirvLqnvlesn 114
                                       l++++++ +e+  +++++++ l e+ + ++      + + ++++   +++++ ++ + ++d+ e++i  L++   ++
  gi|336254706|ref|YP_004597813.1| 477 LDHLQSRVEEVAAYTEALETFLGENGTGEQLIedfRSEVADVQDelaSMDDRLADTESQVDDVETEIDTLTEWTTDL 553
                                       55566666666666666666666665555432112222333332111456699999999999999999999999999 PP

                                       HHHHHHHH CS
                         Fib_alpha 115 eqkiqkLe 122
                                       e ++++L 
  gi|336254706|ref|YP_004597813.1| 554 EDELSDLD 561
                                       99998886 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0028
                                       CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHHHCCCHHHHHHHCCHH CS
                         Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn......dnvikksskeleeeilrlketidaqes 102
                                       dv+++l+++ ++l++ +++  ++e+ + ++++ +++ + + +d          +++ ++++e+ei+++ + ++a e+
  gi|336254706|ref|YP_004597813.1| 517 DVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLdhlpetVDSLTDRTDDVEDEIETVADDVSALET 593
                                       55566666666666666666666666666655555555555543001101333344455555566666666666666 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 103 nirvLqnvlesneqkiqkLeqdid 126
                                        ++   + +e+   ++   e+d+d
  gi|336254706|ref|YP_004597813.1| 594 GLETVESDVETVADDVDAVETDVD 617
                                       666666666666666666666655 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.053
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe 101
                                        l++   dv++++e++ ++++ ++   +++e+ v+++ d + + ++  +d ++ ++ +++++e  ++   e + +++
  gi|336254706|ref|YP_004597813.1| 569 SLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVE-SVESDLEDVREEI 644
                                       566666777777777777777777777777777777777777777777776777777777777.4444445566666 PP

                                       HHHHHHHH CS
                         Fib_alpha 102 snirvLqn 109
                                       + i++ +n
  gi|336254706|ref|YP_004597813.1| 645 TDIQEWRN 652
                                       66666555 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.8    0.0053      0.93     141     277 ..     453     587 ..     437     592 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0053
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HH CS
                          Filament 141 eeEvkelqkqvseqvlvevdaarkld.Lteilkeiraqyeelaeknreeaeewykskleelqeaaeknsealrsake 216
                                       e+E++ l+++++++  ++  +  kld L++ ++e+ a y e  e+   e   + ++ +e+ +++++  +++l s+  
  gi|336254706|ref|YP_004597813.1| 453 EDELEVLRAELATEPELSAPELAKLDhLQSRVEEVAA-YTEALETFLGEN-GTGEQLIEDFRSEVADVQDELASMDD 527
                                       6677777777777777777777777767777777744.444444444443.34467788899999999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 217 eitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeiree 277
                                        ++++  q++  e+e++ l +    le++l++l++ l + +++l +  +++e+e++++ ++
  gi|336254706|ref|YP_004597813.1| 528 RLADTESQVDDVETEIDTLTEWTTDLEDELSDLDH-LPETVDSLTDRTDDVEDEIETVADD 587
                                       99999999999999999999999999999999865.5667888888888888888877665 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.4      0.21        37      22      94 ..     488     560 ..     467     563 .. 0.72
   2 ?   11.0   0.2    0.0015      0.26      14     108 ..     560     654 ..     556     660 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.21
                         Laminin_I  22 edltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkl 94 
                                       +  t+ L+ +l +    +++ie    e+ +++ e  ++  ++  +  +  +v+ e+++ ++ +++L+++  +l
  gi|336254706|ref|YP_004597813.1| 488 AAYTEALETFLGENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDL 560
                                       3445667777777777777888888888888888888888888888888888888888888888887776665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0015
                         Laminin_I  14 pykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaek 90 
                                       + ++ ++++ lt+     + +++  +++++ le  le++++++e+ +  +  v  +  ++ ++ ++     ++ +  
  gi|336254706|ref|YP_004597813.1| 560 LDHLPETVDSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESD 636
                                       567888899999999999999999999************************************************** PP

                         Laminin_I  91 ikkladnikeilekvatl 108
                                        ++++++i+ i e   +l
  gi|336254706|ref|YP_004597813.1| 637 LEDVREEITDIQEWRNQL 654
                                       ****99999998766655 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 ?    6.9   2.0      0.03       5.2      47     105 ..     493     554 ..     475     563 .. 0.73
   2 ?    9.6   2.4    0.0044      0.78      54     109 ..     583     638 ..     544     646 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.03
                            Nsp1_C  47 eWDrvLveng...ekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleell 105
                                       + +  L eng   + I++ +sev +++ e + +d++L   esq d+ e+ +d + + + +l 
  gi|336254706|ref|YP_004597813.1| 493 ALETFLGENGtgeQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLE 554
                                       5555666776332469999*******************999999999988887766555554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0044
                            Nsp1_C  54 engekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellskle 109
                                          + +s+L + ++++e++ + + +  + +e++ d+L++ L   E+++e++ s+le
  gi|336254706|ref|YP_004597813.1| 583 TVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLE 638
                                       45688999***************************************999988765 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.0     0.037       6.5      82     127 ..     514     559 ..     474     659 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.037
                     PI3K_P85_iSH2  82 EieklqenleqlksrlkelhsskekLeedlkqqkeeereleReina 127
                                       E+ ++q+ l+ + +rl   +s+ +++e ++ + +e    le e++ 
  gi|336254706|ref|YP_004597813.1| 514 EVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSD 559
                                       4444445555555555544444444444444444444444444332 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1     0.014       2.4      21      91 ..     504     573 ..     487     593 .. 0.74
   2 ?    7.6   0.1     0.017         3      24      65 ..     608     649 ..     580     660 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.014
                                       ...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  21 lkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaassae 91 
                                        ++ ++++++ev  +++ l+++ ++l++ e++ ++++ ei+   +  + l+  ++ l +hlp+ +++ +  
  gi|336254706|ref|YP_004597813.1| 504 GEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDL-DHLPETVDSLTDR 573
                                       477889999999999999999999999999999999999998887777777666666.5666665555543 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.017
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                              SKA1  24 dlskieaevsaleellnklkkelqeeeeaikklkkeieaslk 65 
                                       d+ ++e++v  l e l+++++ +++ e+ ++++++ei   ++
  gi|336254706|ref|YP_004597813.1| 608 DVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQE 649
                                       444444444444444444444444444444444444433333 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1     0.013       2.2      57     142 ..     484     566 ..     457     571 .. 0.53
   2 ?   10.7   0.2    0.0025      0.44      22     117 ..     506     603 ..     485     620 .. 0.76
   3 ?    1.6   0.1       1.6   2.9e+02      80     116 ..     618     654 ..     574     660 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.013
                             CREPT  57 lellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelkshiqsLPdLt.elpdv 132
                                       +e +a Y++ Le  l e  + ++++edf + +    a+ + +l+++ ++l+ ++s+ +++++ i+ L + t +l d 
  gi|336254706|ref|YP_004597813.1| 484 VEEVAAYTEALETFLGENGTGEQLIEDFRSEV----ADVQDELASMDDRLADTESQVDDVETEIDTLTEWTtDLEDE 556
                                       45566677777766666666666666665443....33333333333333333333333333333333333233344 PP

                             CREPT 133 tgglapLPsa 142
                                        + l++LP +
  gi|336254706|ref|YP_004597813.1| 557 LSDLDHLPET 566
                                       4445555544 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0025
                             CREPT  22 eriaklPpevsdvs.llekikdk.eeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakae 96 
                                       + i  + +ev+dv+  l+++ d+ ++ e+ ++ ve+ +  l+e+++ Le+el++  +l +++++++    +  ++ e
  gi|336254706|ref|YP_004597813.1| 506 QLIEDFRSEVADVQdELASMDDRlADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIE 582
                                       66777788888875379999987356777889999999999999999999999999999999988888877777777 PP

                             CREPT  97 ekleelkeklekvksvrkelk 117
                                       + ++++      +++v+++++
  gi|336254706|ref|YP_004597813.1| 583 TVADDVSALETGLETVESDVE 603
                                       777666666666665555554 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 1.6
                             CREPT  80 mledfleaqkellakaeekleelkeklekvksvrkel 116
                                        l++ l+a+ + ++  e+ le+++e +  +++ r++l
  gi|336254706|ref|YP_004597813.1| 618 DLSEDLSAVEDDVESVESDLEDVREEITDIQEWRNQL 654
                                       2333334444445555555555555555555555555 PP

>> SYCE1  Synaptonemal complex central element protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   0.00073      0.13       4     149 ..     505     654 ..     502     656 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00073
                             SYCE1   4 epqiedLinrineLQqakkksseELgeaqalkealkrElDsLnaEkvhLeevlnkKq...ealriLqlhcqekesea 77 
                                       e  ied  + + ++Q     +++ L ++++  + ++ E+D L +    Le+ l+  +   e++  L  +  + e e 
  gi|336254706|ref|YP_004597813.1| 505 EQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDhlpETVDSLTDRTDDVEDEI 581
                                       677999999******************************************98865433399*************** PP

                             SYCE1  78 qrkqelseeckqrieeltskiqeeklkrrklrlefeeqleelmeqhkdlwefhv.eqrlakeiralesskeqL 149
                                       +      +  +  +e+++s +++       ++ ++++  e+l   + d+ ++++  +   +ei ++++ ++qL
  gi|336254706|ref|YP_004597813.1| 582 ETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESdLEDVREEITDIQEWRNQL 654
                                       **999999**********************************************99*************9998 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   6.3    0.0036      0.64       6     120 ..     516     639 ..     505     657 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0036
                           DUF5082   6 sklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirs......nle 76 
                                       +++q + a++  ++a++e+++   ++  ++l++    l+++ ++l +   + +s++ ++++ +d+i+        le
  gi|336254706|ref|YP_004597813.1| 516 ADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIETvaddvsALE 592
                                       56777777777777777777777777777777777777777777777777777888877777777777777777777 PP

                           DUF5082  77 ssyqtyvdkldel...idaieeEIerLenqiseaqgvldtlqsqlns 120
                                       +  +t++++++++   +da+e+++ +L +++s  + ++++ +s l++
  gi|336254706|ref|YP_004597813.1| 593 TGLETVESDVETVaddVDAVETDVDDLSEDLSAVEDDVESVESDLED 639
                                       77777777777773334567778888888888888777777777765 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       5.6   9.8e+02     109     165 ..     441     495 ..     437     500 .. 0.75
   2 ?    6.4   0.2     0.039       6.8      96     155 ..     511     568 ..     477     604 .. 0.50
   3 ?    9.7   0.2    0.0038      0.67       4     133 ..     511     642 ..     508     656 .. 0.45

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 5.6
                           DUF4201 109 klrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLr 165
                                       +l  e+ + + + d l+  +++l ++ +l ++P+L k  d+ +++vee  +  + L+
  gi|336254706|ref|YP_004597813.1| 441 RLASEIRNGEVDEDELEVLRAELATEPEL-SAPELAK-LDHLQSRVEEVAAYTEALE 495
                                       67778888888888888888888888777.8888888.8888888887666665555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.039
                           DUF4201  96 lkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekve 155
                                        ++e  + +++la+++++l  ++ + d ++++ + l + +++l+  +L  D d+  e v+
  gi|336254706|ref|YP_004597813.1| 511 FRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLE-DEL-SDLDHLPETVD 568
                                       33333333333333333333333333333333333333333322.112.23333333333 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0038
                           DUF4201   4 krnelsklrlklislkhqlakiqeklekkeelgegLtl..idFeqlqienqalnkkIeernkeLkrlkkkttktvha 78 
                                       +r e+++++ +l+s+  +la+++++++ +e+  ++Lt+   d e    +  +l +++++ ++      + + +    
  gi|336254706|ref|YP_004597813.1| 511 FRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEwtTDLEDELSDLDHLPETVDSLTDRTDDVEDEIETVADD 587
                                       55666666666666666666666666666666666653223444444444444444444333333333333333333 PP

                           DUF4201  79 lthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkq 133
                                       ++ l   l ++es +++  ++ +  e++ ++l + l+ v+ + + ++ + e++++
  gi|336254706|ref|YP_004597813.1| 588 VSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVRE 642
                                       3333344444444444444444444444444444444444444444433333333 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.5     0.016       2.8      66     143 ..     508     584 ..     486     586 .. 0.72
   2 ?    9.1   0.8    0.0044      0.77      59     135 ..     567     643 ..     561     650 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.016
                           DUF3552  66 reelekelkerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrqeLer 142
                                        e++ +e+ + ++el+++++Rl + e ++d  e++++   e  ++ e+el+ + ++l e+ ++l++ +   ++e+e 
  gi|336254706|ref|YP_004597813.1| 508 IEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELS-DLDHLPETVDSLTDRTDDVEDEIET 583
                                       57888999*********************9999988877666666666643.3344444455555555555555555 PP

                           DUF3552 143 i 143
                                       +
  gi|336254706|ref|YP_004597813.1| 584 V 584
                                       5 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0044
                           DUF3552  59 keeihklreelekelkerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelvee 135
                                        + + +  +++e+e++   +++++le+ l+  e  ++   ++++  e+++ +  ++l++ e+++e+ e++le++ ee
  gi|336254706|ref|YP_004597813.1| 567 VDSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREE 643
                                       5677788899***********************************************************99987654 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.7   0.00073      0.13     298     413 ..     510     635 ..     458     658 .. 0.41

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00073
                          Prominin 298 kilssleiekldtskcl....dqlpnvdevlealeevlet..nlssivkeglarlneipekvkn......qtaevvp 362
                                       +++s++      ++ +l    d l +++++++++e+ ++t  + +   +++l++l+++pe+v        ++++ ++
  gi|336254706|ref|YP_004597813.1| 510 DFRSEVAD----VQDELasmdDRLADTESQVDDVETEIDTltEWTTDLEDELSDLDHLPETVDSltdrtdDVEDEIE 582
                                       22222222....11111112244444444444444433321122233334444444444444320000001122222 PP

                          Prominin 363 dlkkalakgreqikklakkip..realdavisdlenterssktfddvvekyek 413
                                        +  +++  ++ ++++++++    + +dav  d++++ +++++ +d ve +e+
  gi|336254706|ref|YP_004597813.1| 583 TVADDVSALETGLETVESDVEtvADDVDAVETDVDDLSEDLSAVEDDVESVES 635
                                       22223333333333333333222222333333333333333333333333333 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  12.8    0.0016      0.29     477     643 ..     474     638 ..     429     654 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0016
                              HOOK 477 eekltelqelledanrrkneLet...enrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevq 550
                                         kl +lq+  e+    ++ Let   en + +q i++++++v ++q +l++ + +  d+ +   ++e+ ++ l+e  
  gi|336254706|ref|YP_004597813.1| 474 LAKLDHLQSRVEEVAAYTEALETflgENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWT 550
                                       45777777777777777777765444777777778888888888888887777777777777777777788888888 PP

                              HOOK 551 eelqkkkeqleelepklssnkqkieeleeaLkkkdedlkameerYkkyveKAksViktLdpkqnpaspaevqalknq 627
                                        +l+     l+ l ++++s + +++++e+ ++   +d+ a+e+          +V   +d+ +     ++v  l ++
  gi|336254706|ref|YP_004597813.1| 551 TDLEDELSDLDHLPETVDSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVE-----TDVDDLSED 622
                                       887777777888777777777888888888887777777777655444444444444444443.....455566666 PP

                              HOOK 628 laekdkkieslereve 643
                                       l+  ++ +es+e+++e
  gi|336254706|ref|YP_004597813.1| 623 LSAVEDDVESVESDLE 638
                                       6666666666666554 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 ?    8.3   0.6     0.016       2.8       6      61 ..     508     560 ..     505     564 .. 0.86
   2 ?    7.0   0.6     0.042       7.4       2      59 ..     539     596 ..     539     602 .. 0.91
   3 ?    6.4   3.7     0.063        11       5      63 ..     580     642 ..     569     643 .. 0.55
   4 ?    8.1   0.9     0.019       3.4       2      30 ..     612     640 ..     604     654 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.016
                          CCDC-167   6 IdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeLksL 61 
                                       I++   ++a+++++L +++ rl ++e + +   ++e+E ++l+e  ++ e eL+ L
  gi|336254706|ref|YP_004597813.1| 508 IEDFRSEVADVQDELASMDDRLADTESQVD---DVETEIDTLTEWTTDLEDELSDL 560
                                       888899999999999999999999887665...89999999999999999999887 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.042
                          CCDC-167   2 vaseIdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeLk 59 
                                       v +eId+l e +++++++L +++   +++   +++ +++e+E +++  +++  e  L+
  gi|336254706|ref|YP_004597813.1| 539 VETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIETVADDVSALETGLE 596
                                       5689************************9999999************99999998886 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.063
                          CCDC-167   5 eIdkleeklascrerLeaverrlrkeelseee....ResleeEeaslkeqleenekeLksLrk 63 
                                       eI+++ + +++++  Le+ve+ ++++    ++     ++l e +++++ ++e+ e+ L+  r+
  gi|336254706|ref|YP_004597813.1| 580 EIETVADDVSALETGLETVESDVETVADDVDAvetdVDDLSEDLSAVEDDVESVESDLEDVRE 642
                                       555555555555555555555444433222224444666667777777777777777776665 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.019
                          CCDC-167   2 vaseIdkleeklascrerLeaverrlrke 30 
                                       v +++d+l e l+++++++e+ve+ l+++
  gi|336254706|ref|YP_004597813.1| 612 VETDVDDLSEDLSAVEDDVESVESDLEDV 640
                                       66789999999999999999999999875 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 ?    3.5   0.4      0.52        92      14      62 ..     514     575 ..     506     605 .. 0.52
   2 ?    7.0   0.1     0.042       7.4       8      46 ..     616     654 ..     609     657 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.52
                            CENP-H  14 ellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek.............e 62 
                                       e+++ + el+++ ++l+++e +  +++++  +l++  + l+ e +  +             +
  gi|336254706|ref|YP_004597813.1| 514 EVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDhlpetvdsltdrtD 575
                                       55555555555555555555555555555555555554444444444434322223333332 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.042
                            CENP-H   8 rdelssellklsqelrelqeeltevekenlrlkrknrel 46 
                                        d+ls++l + + ++++++++l++v++e+ ++++  ++l
  gi|336254706|ref|YP_004597813.1| 616 VDDLSEDLSAVEDDVESVESDLEDVREEITDIQEWRNQL 654
                                       799**************************9999877665 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.0     0.018       3.2      92     170 ..     505     586 ..     499     588 .. 0.87
   2 ?    8.6   3.7    0.0085       1.5      81     170 ..     571     635 ..     563     658 .. 0.44

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.018
                                       HHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHH CS
                         MCPsignal  92 ealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeia...aaseeqsasieevnqav 165
                                       e+li++   e+ d+ + l +   r + + ++v++ ++++ +++e +++++d+++++     +++ ++   ++v + +
  gi|336254706|ref|YP_004597813.1| 505 EQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDhlpETVDSLTDRTDDVEDEI 581
                                       689999*********************************************99987622268888999999999988 PP

                                       HHHHH CS
                         MCPsignal 166 eevak 170
                                       e va+
  gi|336254706|ref|YP_004597813.1| 582 ETVAD 586
                                       88875 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0085
                                       HHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  81 Aersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsas 157
                                        +r+ +   ei                         e+ ++ v+  ++ l+++ + v+ vad v+ + + ++++s+ 
  gi|336254706|ref|YP_004597813.1| 571 TDRTDDVEDEI-------------------------ETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSED 622
                                       33333333333.........................33333333333344444444444444444444444444444 PP

                                       HHHHHHHHHHHHH CS
                         MCPsignal 158 ieevnqaveevak 170
                                       ++ v + ve v++
  gi|336254706|ref|YP_004597813.1| 623 LSAVEDDVESVES 635
                                       4444443333332 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0         8   1.4e+03      99     141 ..     456     497 ..     450     516 .. 0.55
   2 ?   10.2   0.2    0.0023      0.41      94     155 ..     517     584 ..     506     588 .. 0.77
   3 ?    0.7   0.1         2   3.5e+02     112     145 ..     611     644 ..     591     658 .. 0.48

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 8
                     Fzo_mitofusin  99 lsstfarlcqqvdetekeleeeikelekeiekleevqkkakll 141
                                       l+   a+l ++ + +  el  ++++l++++e++++ ++ ++++
  gi|336254706|ref|YP_004597813.1| 456 LEVLRAELATEPELSAPELA-KLDHLQSRVEEVAAYTEALETF 497
                                       44444444555555555543.3555555555555555555444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0023
                     Fzo_mitofusin  94 qvqqelsstfarl...cqqvdeteke...leeeikelekeiekleevqkkakllrnkaslleseLekf 155
                                        vq el+s+ +rl   ++qvd +e+e   l+e +++le e++ l+++ ++   l +++  +e e+e+ 
  gi|336254706|ref|YP_004597813.1| 517 DVQDELASMDDRLadtESQVDDVETEidtLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIETV 584
                                       68899999888883334678888776222567788999999999999999999999999999999875 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 2
                     Fzo_mitofusin 112 etekeleeeikelekeiekleevqkkakllrnka 145
                                        +e+++++  ++l++  + +e+v++ ++ +r++ 
  gi|336254706|ref|YP_004597813.1| 611 AVETDVDDLSEDLSAVEDDVESVESDLEDVREEI 644
                                       3333333333333333333333333333333333 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4       2.4   4.2e+02       8      38 ..     479     495 ..     473     560 .. 0.54
   2 ?    6.4   0.1     0.067        12       6      57 ..     560     625 ..     555     657 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 2.4
                              ZapB   8 qLEskiqkaidtitlLqmeieeLkeeneelk 38 
                                       +L+s++              ee+ +  e+l+
  gi|336254706|ref|YP_004597813.1| 479 HLQSRV--------------EEVAAYTEALE 495
                                       333333..............33333333332 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.067
                              ZapB   6 LeqLEskiqkaidtitlLqmeieeLkeeneelkeenrele..............eeneqlkeerea 57 
                                       L++L + ++++ d+ +    eie +  ++++l+   + +e                ++ l e+ +a
  gi|336254706|ref|YP_004597813.1| 560 LDHLPETVDSLTDRTDDVEDEIETVADDVSALETGLETVEsdvetvaddvdaveTDVDDLSEDLSA 625
                                       566666666666666666666666666666666666665522222222222222333333344444 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   4.6     0.039       6.8      49     152 ..     477     585 ..     438     590 .. 0.54
   2 ?   10.0   3.6    0.0024      0.43      49     154 ..     567     653 ..     547     660 .. 0.46

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.039
                         Golgin_A5  49 ldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelry 125
                                       ld+l+++ + + + +++l++ + +  t  ++l + + +e+  ++++l++++++l+  +++  +ve+e+  l+e    
  gi|336254706|ref|YP_004597813.1| 477 LDHLQSRVEEVAAYTEALETFLGENGTG-EQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTD 552
                                       3333333333333333333333333333.334445567777888888888888888888888888888888887777 PP

                         Golgin_A5 126 leeelv......rskatlqsrikdrekeieklr 152
                                       le+el+      ++  +l  r  d e+eie + 
  gi|336254706|ref|YP_004597813.1| 553 LEDELSdldhlpETVDSLTDRTDDVEDEIETVA 585
                                       777765211111334455566666666666655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0024
                         Golgin_A5  49 ldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelry 125
                                       +d+l+++ d +++e++ +   +                  + l+  l+ +e+ +e+      +ve+++  l+e+l++
  gi|336254706|ref|YP_004597813.1| 567 VDSLTDRTDDVEDEIETVADDV------------------SALETGLETVESDVETVADDVDAVETDVDDLSEDLSA 625
                                       3333333333333333333334..................4444444444444444444444455555555555555 PP

                         Golgin_A5 126 leeelvrskatlqsrikdrekeieklrnq 154
                                       +e+++  + ++l+  +++  ++i++ rnq
  gi|336254706|ref|YP_004597813.1| 626 VEDDVESVESDLE-DVREEITDIQEWRNQ 653
                                       5555444433332.344444555555555 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1       2.7   4.7e+02       8      35 ..     437     464 ..     433     465 .. 0.90
   2 ?   14.5   2.0   0.00018     0.032       5      71 ..     490     563 ..     487     573 .. 0.86
   3 ?    1.8   3.1       1.6   2.8e+02      19      45 ..     622     648 ..     563     659 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 2.7
                              Rx_N   8 kLadllaeeakllkgvkeeleklkdeLe 35 
                                       +La+ la+e++  +  ++ele l+ eL 
  gi|336254706|ref|YP_004597813.1| 437 TLAERLASEIRNGEVDEDELEVLRAELA 464
                                       699*******9999999********996 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 0.00018
                              Rx_N   5 llqkLadllaeea...kllkgvkeeleklkdeLesiqavLedaee....rqikdeavkeWlkelrdlaydaeDv 71 
                                         + L+++l e+    +l++++++e+   +deL s++  L+d e      +++ +++ eW  +l d   d++++
  gi|336254706|ref|YP_004597813.1| 490 YTEALETFLGENGtgeQLIEDFRSEVADVQDELASMDDRLADTESqvddVETEIDTLTEWTTDLEDELSDLDHL 563
                                       5678999999999999**************************99965545556699999******999998875 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 1.6
                              Rx_N  19 llkgvkeeleklkdeLesiqavLedae 45 
                                        l  v++++e+ ++ Le ++  + d  
  gi|336254706|ref|YP_004597813.1| 622 DLSAVEDDVESVESDLEDVREEITDIQ 648
                                       334445555555555555544444444 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1       0.3        53      23      85 ..     516     580 ..     502     593 .. 0.49
   2 ?    5.7   0.1      0.11        20      16      89 ..     575     647 ..     560     648 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.3
                   Snapin_Pallidin  23 kelrqsQeeLleqldrlnekLkeleeaqe..aevlpdlkeyakKLvnikkrmsslnerlqklkkR 85 
                                       ++++++   + ++l    ++++++e + +  +e  +dl+  +  L  +   + sl +r+  +++ 
  gi|336254706|ref|YP_004597813.1| 516 ADVQDELASMDDRLADTESQVDDVETEIDtlTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDE 580
                                       44444444444444444444444443333344444444444444555555555544444444443 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.11
                   Snapin_Pallidin  16 deldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaekL 89 
                                       d+++++++ + +  ++L   l++  ++++ ++++ + +v +d++   + L++++ +++s+++ l+ +++ ++ +
  gi|336254706|ref|YP_004597813.1| 575 DDVEDEIETVADDVSALETGLETVESDVETVADDVD-AVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDI 647
                                       566666666666666666667777777776666666.6667777777777777777777777777777777666 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2      0.19        34      36      62 ..     523     549 ..     503     563 .. 0.53
   2 ?    1.6   0.1       1.6   2.8e+02      45      72 ..     563     590 ..     552     592 .. 0.78
   3 ?    4.0   0.3      0.28        49      46      71 ..     613     638 ..     596     649 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.19
                        TMF_DNA_bd  36 kkLrkknkelekeikelkkklekleke 62 
                                        +++  ++++e+++++ + ++++l++ 
  gi|336254706|ref|YP_004597813.1| 523 ASMDDRLADTESQVDDVETEIDTLTEW 549
                                       333444444455555555555555555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 1.6
                        TMF_DNA_bd  45 lekeikelkkkleklekeleeleerlke 72 
                                       l +++++l+++++++e e+e+  +  ++
  gi|336254706|ref|YP_004597813.1| 563 LPETVDSLTDRTDDVEDEIETVADDVSA 590
                                       448999999*********9998877665 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.28
                        TMF_DNA_bd  46 ekeikelkkkleklekeleeleerlk 71 
                                       e+++++l++ l+ +e ++e+ e+ l+
  gi|336254706|ref|YP_004597813.1| 613 ETDVDDLSEDLSAVEDDVESVESDLE 638
                                       56667777777777777777666654 PP

>> YscO-like  YscO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.4      0.45        80      12     109 ..     446     545 ..     441     564 .. 0.71
   2 ?   11.1   0.7    0.0017      0.29      31     129 ..     553     652 ..     545     656 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHH.HH---HHHHHHHHHHHHHHHHH CS
                         YscO-like  12 ikkrrveeAEkvvkdkkkaLekEke..klrkleeerdkvkkhkkaKvaqlreel.dkGttsdkikkmkryikvvkee 85 
                                       i++  v+e E  v  +  a e E    +l+kl + ++ ++++  a  ++l   l ++Gt+ + i+  ++ +  v++e
  gi|336254706|ref|YP_004597813.1| 446 IRNGEVDEDELEVLRAELATEPELSapELAKL-DHLQSRVEEVAAYTEALETFLgENGTGEQLIEDFRSEVADVQDE 521
                                       56666666665555555554444331145554.4566677777788888888884579******************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                         YscO-like  86 lkqeekkvekQkekVkvAerkvEq 109
                                       l+  + ++++ + +V   e +++ 
  gi|336254706|ref|YP_004597813.1| 522 LASMDDRLADTESQVDDVETEIDT 545
                                       *******99999999888777665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHH---.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         YscO-like  31 LekEkeklrkleeerdkvkkhkkaKvaq.lreeldkGtt.sdkikkmkryikvvkeelkqeekkvekQkekVkvAer 105
                                       Le E  +l +l e  d  +    + v++ +  + d+ ++   +++++++ ++ v++++  +e  v++  e  ++ e 
  gi|336254706|ref|YP_004597813.1| 553 LEDELSDLDHLPETVDSLTDR-TDDVEDeIETVADDVSAlETGLETVESDVETVADDVDAVETDVDDLSEDLSAVED 628
                                       666666666666665554433.3333333555555544313467777888889999999999999999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                         YscO-like 106 kvEqareelakkrkeveklekhke 129
                                       +vE  + +l   r e+  +++ ++
  gi|336254706|ref|YP_004597813.1| 629 DVESVESDLEDVREEITDIQEWRN 652
                                       999999999999999998887765 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 ?    2.1   0.2       0.2        35      60     107 ..     504     551 ..     471     573 .. 0.44
   2 ?    6.4   2.4      0.01       1.8      30     104 ..     572     649 ..     498     659 .. 0.47

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.2
                        V_ATPase_I  60 eesleapeekeldeleeelekleeelkelnenleklkkelnelvelka 107
                                        e+l ++ ++e+ ++++el +++++l +++++ +++++e  +l+e++ 
  gi|336254706|ref|YP_004597813.1| 504 GEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTT 551
                                       333333333444444444444444444444444444444444444332 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.01
                        V_ATPase_I  30 rrcdemerklrfleeeieklekavikeeea...eesleapeekeldeleeelekleeelkelnenleklkkelnelv 103
                                        r+d++e +++ + + ++ le+   + e++   +++  ++ e+++d+l+e+l+ +e++++++++ le++++e ++++
  gi|336254706|ref|YP_004597813.1| 572 DRTDDVEDEIETVADDVSALETGLETVESDvetVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQ 648
                                       34444444444444444443332222222222233333334444444444444444444444444444444444444 PP

                        V_ATPase_I 104 e 104
                                       e
  gi|336254706|ref|YP_004597813.1| 649 E 649
                                       4 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.3    0.0065       1.1      43     128 ..     476     561 ..     453     567 .. 0.77
   2 ?   14.2   7.3   0.00021     0.036      15     121 ..     507     613 ..     493     614 .. 0.85
   3 ?   10.8   2.6    0.0023       0.4      17      69 ..     596     648 ..     590     657 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0065
                     Tropomyosin_1  43 knqqleeevekleeklkeakekaeesekkktnnealtrkiqlLEeeleesdkkLkettekLretdvkaeelERkvka 119
                                       k+++l++ ve++ +  +  ++ + e+ + ++  e +   +  + +el + d +L++t  +  +++ + ++l   +++
  gi|336254706|ref|YP_004597813.1| 476 KLDHLQSRVEEVAAYTEALETFLGENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTD 552
                                       77778888888888877778888888888888888888888888888888888888888888888888888888888 PP

                     Tropomyosin_1 120 Leqerdewe 128
                                       Le+e  + +
  gi|336254706|ref|YP_004597813.1| 553 LEDELSDLD 561
                                       887766655 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00021
                     Tropomyosin_1  15 kaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrkiqlLEeelee 91 
                                         e+ +++v + ++e  ++++ +++ + +++ +e e+++l e  ++ ++++++ +++  + ++lt + + +E+e+e 
  gi|336254706|ref|YP_004597813.1| 507 LIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIET 583
                                       56778888888999999999999999999999999999999999999999999999999999**************9 PP

                     Tropomyosin_1  92 sdkkLkettekLretdvkaeelERkvkaLe 121
                                          ++    + L+ ++   e++   v a+e
  gi|336254706|ref|YP_004597813.1| 584 VADDVSALETGLETVESDVETVADDVDAVE 613
                                       999999999999988888888777777666 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0023
                     Tropomyosin_1  17 eeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeese 69 
                                       e +e++v +  ++  + e ++ +L++ ++++e++ve +e++l++++e+  + +
  gi|336254706|ref|YP_004597813.1| 596 ETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQ 648
                                       67788888889999999****************************99887765 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.018       3.3       3      45 ..     506     548 ..     504     550 .. 0.93
   2 ?    0.4   0.0         4   7.1e+02       3      38 ..     579     614 ..     563     621 .. 0.62
   3 ?    1.5   0.0       1.8   3.2e+02       8      45 ..     612     649 ..     598     653 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHH CS
                              Swi5   3 aeikeleeqleelekelaelkeelkekkdpeetvkrhIklLhe 45 
                                       + i++++++++ +++ela+++++l +++   + v++ I+ L e
  gi|336254706|ref|YP_004597813.1| 506 QLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTE 548
                                       668999*********************************9987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 4
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHH CS
                              Swi5   3 aeikeleeqleelekelaelkeelkekkdpeetvkr 38 
                                        ei+++ + +++le+ l+++++  +  +d  + v++
  gi|336254706|ref|YP_004597813.1| 579 DEIETVADDVSALETGLETVESDVETVADDVDAVET 614
                                       455666666666666666666666655555555555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHH CS
                              Swi5   8 leeqleelekelaelkeelkekkdpeetvkrhIklLhe 45 
                                       +e  ++ l ++l+++++  ++ +   e v++ I+ ++e
  gi|336254706|ref|YP_004597813.1| 612 VETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQE 649
                                       44455555555555555555555555666666666665 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 ?   -0.2   0.1       7.5   1.3e+03      38      55 ..     475     492 ..     446     500 .. 0.71
   2 ?    4.4   0.5      0.27        48      21      52 ..     524     555 ..     495     562 .. 0.62
   3 ?    1.2   0.0       2.8     5e+02      31      58 ..     558     585 ..     546     590 .. 0.79
   4 ?    3.5   0.1      0.53        94      23      57 ..     571     605 ..     560     623 .. 0.63
   5 ?    5.5   0.1      0.12        22      19      62 ..     595     638 ..     587     646 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 7.5
                               CLZ  38 ssLeaLqtrlarLlaeye 55 
                                       ++L++Lq r++ + a  e
  gi|336254706|ref|YP_004597813.1| 475 AKLDHLQSRVEEVAAYTE 492
                                       468899999888776555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.27
                               CLZ  21 kagaeqkeleekverLessLeaLqtrlarLla 52 
                                       +  +   ++e++v+ +e+++++L+     L +
  gi|336254706|ref|YP_004597813.1| 524 SMDDRLADTESQVDDVETEIDTLTEWTTDLED 555
                                       33334455666666666666666655555555 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 2.8
                               CLZ  31 ekverLessLeaLqtrlarLlaeyessq 58 
                                       + +++L +++++L++r   + +e e+++
  gi|336254706|ref|YP_004597813.1| 558 SDLDHLPETVDSLTDRTDDVEDEIETVA 585
                                       5678899999***999999999988765 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.53
                               CLZ  23 gaeqkeleekverLessLeaLqtrlarLlaeyess 57 
                                        +  +++e+ +e +   + aL+t l+ + +++e++
  gi|336254706|ref|YP_004597813.1| 571 TDRTDDVEDEIETVADDVSALETGLETVESDVETV 605
                                       44556666666666666666666666655555544 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.12
                               CLZ  19 aakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLk 62 
                                        +  +++ +++ + v+ +e+ ++ L   l  + +++es+++ L+
  gi|336254706|ref|YP_004597813.1| 595 LETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLE 638
                                       56677888999999999999999999999999999999888775 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       3.9   6.8e+02      72     113 ..     448     489 ..     441     497 .. 0.80
   2 ?    6.5   0.6     0.041       7.2       4      67 ..     492     554 ..     490     600 .. 0.80
   3 ?    2.0   0.1      0.97   1.7e+02      85     109 ..     631     655 ..     627     660 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 3.9
                              CdvA  72 sGEidEeaYksaieairellesaleekeeikklleklsklel 113
                                        GE+dE++ +  + ++ ++ e    e++ ++ l+++++++ +
  gi|336254706|ref|YP_004597813.1| 448 NGEVDEDELEVLRAELATEPELSAPELAKLDHLQSRVEEVAA 489
                                       699999999999999999999999999999998888887765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.041
                              CdvA   4 kALeeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanlk 67 
                                        ALe+ + e+   ++  e+++ ++ +  ++l    + l+++ +++++++e +i++l++ +++l+
  gi|336254706|ref|YP_004597813.1| 492 EALETFLGENGTGEQLIEDFRSEVADVQDELASMDDRLADT-ESQVDDVETEIDTLTEWTTDLE 554
                                       58888888888888888888888888888888888888886.8889999999999988888886 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.97
                              CdvA  85 eairellesaleekeeikkllekls 109
                                       e++++ le ++ee+++i+++ ++l 
  gi|336254706|ref|YP_004597813.1| 631 ESVESDLEDVREEITDIQEWRNQLG 655
                                       67788999************99985 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   5.5     0.015       2.7      91     213 ..     529     641 ..     484     654 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.015
                            Cluap1  91 LykalksaeeekeeeekststeldlssklsdlkaarqlaseitekgasLydlLekevelreartkalsrqleleeie 167
                                       L +  ++ ++ ++e +  t+ ++dl+++lsdl +  + + ++t++   + d +e+  +      +al++ le     
  gi|336254706|ref|YP_004597813.1| 529 LADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIETVAD----DVSALETGLE----- 596
                                       3333333333334444444446666666666666666666666665444433333322....2222222222..... PP

                            Cluap1 168 kalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraq 213
                                        ++++ +++v+++++ +++++++l++d +++e+ +e  +++le  +
  gi|336254706|ref|YP_004597813.1| 597 -TVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVR 641
                                       .222222333333333333333333333333333333333333333 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  11.0     0.045       7.9      68     193 ..     506     644 ..     490     659 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.045
                               LXG  68 dlieqyeefLkkikealesvepssngfidedfLeqelenglkkakevteelkdeinkil..............asvs 130
                                       +lie++ ++ ++++ +l s++   +   d +   +++e +++ + e t++l+de+ + l              ++v 
  gi|336254706|ref|YP_004597813.1| 506 QLIEDFRSEVADVQDELASMD---DRLADTESQVDDVETEIDTLTEWTTDLEDELSD-LdhlpetvdsltdrtDDVE 578
                                       788888889999999988844...777777777779999999999999999999988.5366666666666666677 PP

                               LXG 131 divslpelddsevkdslqkakkkvqetiekledfdqe...qksalanlesdlkalktyvseLeemt 193
                                       d ++++  d s+++++l+ +++ v+++ +++++ +++   ++++l+++e+d++++++ +++++e +
  gi|336254706|ref|YP_004597813.1| 579 DEIETVADDVSALETGLETVESDVETVADDVDAVETDvddLSEDLSAVEDDVESVESDLEDVREEI 644
                                       777777777777777777777777777777777776422255667777777777777777776655 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0       0.7   1.2e+02     108     159 ..     472     523 ..     462     525 .. 0.90
   2 ?    2.8   1.5      0.55        98     111     159 ..     579     631 ..     523     649 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.7
                          Cauli_AT 108 klletLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirdslk 159
                                        +l  L + q+r++++   t+ l+  +  +   ++ + d+  ++  ++d+l 
  gi|336254706|ref|YP_004597813.1| 472 PELAKLDHLQSRVEEVAAYTEALETFLGENGTGEQLIEDFRSEVADVQDELA 523
                                       567789999****************************************985 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.55
                          Cauli_AT 111 etLkeaqnrikkleeetkklaekivte....kllkeevkdlderlseirdslk 159
                                       + ++ + + ++ le+  + ++++++t       ++++v dl e ls ++d++ 
  gi|336254706|ref|YP_004597813.1| 579 DEIETVADDVSALETGLETVESDVETVaddvDAVETDVDDLSEDLSAVEDDVE 631
                                       33333444444444444444444444311113466777777777777777765 PP

>> Phage_HK97_TLTM  Tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3     0.065        11      93     168 ..     504     586 ..     473     597 .. 0.63
   2 ?    6.5   3.8     0.024       4.2      69     200 ..     515     653 ..     505     657 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.065
                   Phage_HK97_TLTM  93 aeqkveelkkeldkyq...vsingylvn...kldskeeaik.laeatdklsesqsaleavtkkskeiqsaLtsvead 162
                                        eq +e++++e++  q    s++  l +   ++d  e++i  l+e t++l ++ s l+++ ++++  ++  + ve +
  gi|336254706|ref|YP_004597813.1| 504 GEQLIEDFRSEVADVQdelASMDDRLADtesQVDDVETEIDtLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDE 580
                                       34555555555555555544555555541114566677787789999999999888888888888888777777766 PP

                   Phage_HK97_TLTM 163 rvrlir 168
                                         ++ +
  gi|336254706|ref|YP_004597813.1| 581 IETVAD 586
                                       666655 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.024
                   Phage_HK97_TLTM  69 leevadekdklkeslkeqnklvkeaeqkveelkkeldkyq...vsingy..lvnkldskeeaik..laeatdklses 138
                                       + +v+de   + + l+  + +v++ e++++ l +     +     ++     v+ l+ + +++   +  + d+ s  
  gi|336254706|ref|YP_004597813.1| 515 VADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEdelSDLDHLpeTVDSLTDRTDDVEdeIETVADDVSAL 591
                                       44556666666666666666666666666665554444445542222222246777777777766788888899999 PP

                   Phage_HK97_TLTM 139 qsaleavtkkskeiqsaLtsveadrvrlirqqaaeqnkvkrsllilNeekaesnklldlgNk 200
                                       +  le v+ +++ + + +++ve+d ++l ++ +a +++v+     l + ++e   + +  N+
  gi|336254706|ref|YP_004597813.1| 592 ETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQEWRNQ 653
                                       99999999999999999999999999999999999998888777777777777777777766 PP

>> Zw10  Centromere/kinetochore Zw10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   7.3    0.0087       1.5      11     119 ..     531     638 ..     523     654 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0087
                              Zw10  11 dlekkisklekkveeikeevskmivkkYseflelsssaeellerveslskeidalkkkven..eieqdlkaaveela 85 
                                       d+e+++ ++e+ + ++ +e + +++++ s++  l ++ + l +r++ +++ei+ +   v+     ++++++ ve +a
  gi|336254706|ref|YP_004597813.1| 531 DTESQVDDVETEI-DTLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIETVADDVSAleTGLETVESDVETVA 606
                                       7888888888876.577889999*************************************87678999999999999 PP

                              Zw10  86 elkqqlkekevvlellealkkieealeelkealk 119
                                       + +  ++    v +l+e l  +e  +e +++ l+
  gi|336254706|ref|YP_004597813.1| 607 DDVDAVET--DVDDLSEDLSAVEDDVESVESDLE 638
                                       99999875..467888888888888888887765 PP

>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.5     0.058        10      42      86 ..     512     556 ..     473     562 .. 0.76
   2 ?    5.8   1.2     0.074        13       8      87 ..     573     651 ..     566     655 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.058
                                       HHHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXXXX CS
                             Sec2p  42 rkekealekkneklkeqLkeketlleslqeqLkeLkevlekmeee 86 
                                       r e ++++ +  ++  +L+++e+++++ +++  +L e   ++e+e
  gi|336254706|ref|YP_004597813.1| 512 RSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDE 556
                                       666677777777777777777777777777777777776666665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.074
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXX CS
                             Sec2p   8 kreeaekekkklekEledLtasLFeeANkmVaaarkekealekkneklkeqLkeketlleslqeqLkeLkevlekme 84 
                                       ++ ++e+e +++  ++  L + L e   + V +   + +a+e+  + l e L+  e  +es +++L++ +e + +++
  gi|336254706|ref|YP_004597813.1| 573 RTDDVEDEIETVADDVSALETGL-ETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQ 648
                                       56677777777777787787777.77777888888999999***************************999999988 PP

                                       XXX CS
                             Sec2p  85 ees 87 
                                       e +
  gi|336254706|ref|YP_004597813.1| 649 EWR 651
                                       765 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.6    0.0021      0.37      62     134 ..     476     556 ..     439     562 .. 0.58
   2 ?    9.8   0.5    0.0031      0.55      30     133 ..     506     621 ..     505     654 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0021
                         PspA_IM30  62 eqkeqakklekkA..kaALtkg......eeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealetkiee 130
                                       +      + e+ A  ++AL+         e+L++ +  e ++ +++++  +  la  +s+v++++++++ l    ++
  gi|336254706|ref|YP_004597813.1| 476 KLDHLQSRVEEVAayTEALETFlgengtGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTD 552
                                       44444444444332223444334444666777777777777777777777777777777777777777777666666 PP

                         PspA_IM30 131 lkak 134
                                       l+++
  gi|336254706|ref|YP_004597813.1| 553 LEDE 556
                                       6665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0031
                         PspA_IM30  30 qairdmqselakarqalaqviarqkqlerkleeqkeqakklek...kAkaALtkg................eeeLAr 87 
                                       q i+d +se+a+++++la++  r   +e ++++ + ++  l +     +  L+                        
  gi|336254706|ref|YP_004597813.1| 506 QLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEwttDLEDELSDLdhlpetvdsltdrtddV----- 577
                                       666666666666666666665555555555554444444333300033333333366677766644444443..... PP

                         PspA_IM30  88 ealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelka 133
                                           ei++ ++++ alet l+ ++s ve +   ++a et +++l +
  gi|336254706|ref|YP_004597813.1| 578 --EDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSE 621
                                       ..44555555555555555555555555555555555555544433 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 ?    6.8   0.2     0.043       7.5      35      72 ..     503     542 ..     476     543 .. 0.70
   2 ?    2.0   2.3       1.3   2.3e+02      59      71 ..     588     600 ..     551     649 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.043
                            Cnn_1N  35 e..eqkeellkenielkveveslqkelkekkkllreaeka 72 
                                       +  + +e+  +e  ++++e++s+ + l   + ++++ e++
  gi|336254706|ref|YP_004597813.1| 503 TgeQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETE 542
                                       2446678888888888888888888888888888887765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 1.3
                            Cnn_1N  59 lkekkkllreaek 71 
                                       + +++  l+  e+
  gi|336254706|ref|YP_004597813.1| 588 VSALETGLETVES 600
                                       4444444443332 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 ?   10.4   3.2    0.0024      0.43      16      71 ..     532     587 ..     508     592 .. 0.71
   2 ?    8.2   5.1     0.012         2      13      66 ..     586     638 ..     572     660 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0024
                        Phage_GP20  16 tkakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakae 71 
                                       t++++d+ve+e dtl+e  +d + +L+dL    +++++L+   ++++ ++++  ++
  gi|336254706|ref|YP_004597813.1| 532 TESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIETVADD 587
                                       47777777777777777777777777777777777777777777777777776665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.012
                        Phage_GP20  13 kdit..kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknk 66 
                                       +d++  ++ l++ve++++t+ +++++ +++++dL ++     +++ ++e+++ +++
  gi|336254706|ref|YP_004597813.1| 586 DDVSalETGLETVESDVETVADDVDAVETDVDDLSED---LSAVEDDVESVESDLE 638
                                       3333345555555555555555555555555555332...3333333333333333 PP

>> Sec3_C  Exocyst complex component Sec3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   2.1       0.4        70       6      65 ..     507     562 ..     500     570 .. 0.80
   2 ?   11.2   2.6   0.00048     0.085      23      73 ..     586     636 ..     565     639 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.4
                            Sec3_C   6 leerLsreLskleaanikrllesdkkveelkkdidkalkecdeldalltlysveLstlse 65 
                                       l+e+ ++e+++++     +l + d++ ++  +++d++ +e+d+l+++ t  ++eLs+l +
  gi|336254706|ref|YP_004597813.1| 507 LIEDFRSEVADVQD----ELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDH 562
                                       55555555555554....5889999999***************************99875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00048
                            Sec3_C  23 krllesdkkveelkkdidkalkecdeldalltlysveLstlsedieyIEsq 73 
                                        ++ +++++ e++ +d++++ +++d +++  +  s++Ls++++d+e +Es+
  gi|336254706|ref|YP_004597813.1| 586 DDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVESD 636
                                       5788999******************************************85 PP

>> Phage_tail_NK  Sf6-type phage tail needle knob or tip of some Caudovirales
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   0.00071      0.13       4      36 ..     521     553 ..     518     571 .. 0.88
   2 ?    1.2   0.6       1.4   2.4e+02       3      31 ..     586     614 ..     584     626 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00071
                                       XXXXXXXXXXXXXXXXXXXXXHHHHHHHHTS-- CS
                     Phage_tail_NK   4 dissldtrvqslesqvsdhetridaleyattrk 36 
                                       +++s+d r+   esqv d et id+l   tt  
  gi|336254706|ref|YP_004597813.1| 521 ELASMDDRLADTESQVDDVETEIDTLTEWTTDL 553
                                       689***********************8888765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.4
                                       XXXXXXXXXXXXXXXXXXXXXXHHHHHHH CS
                     Phage_tail_NK   3 sdissldtrvqslesqvsdhetridaley 31 
                                        d+s+l+t ++++es+v      +da+e 
  gi|336254706|ref|YP_004597813.1| 586 DDVSALETGLETVESDVETVADDVDAVET 614
                                       599************99999999999885 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  16.9     0.043       7.5     126     272 ..     489     640 ..     371     650 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.043
                                       X........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXHHH CS
                              AIP3 126 a...............kkelkaqlkevqslrrdLavlrqlysefkseikeslselrekakkvkeaslastkkssnra 187
                                       a               ++  ++  +ev +++ +La++     +   ++++++ +++++++++   +  +t+ + +  
  gi|336254706|ref|YP_004597813.1| 489 AytealetflgengtgEQLIEDFRSEVADVQDELASMD----DRLADTESQVDDVETEIDTLT--EW-TTDLEDEL- 557
                                       14444444444444433444444455555555555543....333344444444444444444..22.11222222. PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 188 yiekgkkkLseesdklvtkvddLqDlvedlrkDV..vqRgvrpskkqlesvakeikkakkelkkleeyiktekpvWk 262
                                          +  ++L e++d+l  + dd++D +e + +DV  ++ g +  ++ +e+va++++++++++++l+e ++ ++    
  gi|336254706|ref|YP_004597813.1| 558 ---SDLDHLPETVDSLTDRTDDVEDEIETVADDVsaLETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVE 631
                                       ...23467899999999****************94446788999999999999999999999999999988776554 PP

                                       HHHHHHHHHH CS
                              AIP3 263 kiWekELqkv 272
                                        + e++L++v
  gi|336254706|ref|YP_004597813.1| 632 SV-ESDLEDV 640
                                       43.5555555 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.1       1.6   2.8e+02      38      84 ..     504     550 ..     437     562 .. 0.58
   2 ?    8.9   1.9    0.0099       1.7      31     105 ..     554     651 ..     528     654 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 1.6
                             THOC7  38 leqlkedllldfaafelsierlqllakanerereryeaekeeiesei 84 
                                        eql ed+  ++a  + +++ ++  ++ +e +++ +e+e +++ + +
  gi|336254706|ref|YP_004597813.1| 504 GEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWT 550
                                       44444444444444444444444444444444444444444444433 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0099
                             THOC7  31 a.......................esteeeleqlkedllldfaafelsierlqllakanerereryeaekeeiesei 84 
                                       +                       e++ e ++ +  +l++ +++ e+ +e +    +a e  ++ + ++ + +e+  
  gi|336254706|ref|YP_004597813.1| 554 EdelsdldhlpetvdsltdrtddvEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDV 630
                                       45555555555555566444444444445555555555555555555555555555555555555555555555555 PP

                             THOC7  85 eavreeieelkaqLeearatr 105
                                       e+v+++ e+ ++++++ ++ r
  gi|336254706|ref|YP_004597813.1| 631 ESVESDLEDVREEITDIQEWR 651
                                       555555555555555555555 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.4      0.92   1.6e+02     111     140 ..     514     543 ..     407     548 .. 0.75
   2 ?    7.1   4.0     0.029         5      50     140 ..     558     644 ..     533     654 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.92
                          MIP-T3_C 111 aleplkaqlaeleeaIkdqkekisnvraki 140
                                       ++ +++++la +++ ++d+++++++v  +i
  gi|336254706|ref|YP_004597813.1| 514 EVADVQDELASMDDRLADTESQVDDVETEI 543
                                       455667777777777777777776665544 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.029
                          MIP-T3_C  50 seiekLresiQkltksvnPLgklldfiqdDidsMqrELemWrseyrqqaeelaeerrateealeplkaqlaeleeaI 126
                                       s++++L e++ +lt         ++ ++dD+ +++  Le   s  +     +a+   a e ++++l + l+ +e+ +
  gi|336254706|ref|YP_004597813.1| 558 SDLDHLPETVDSLTDRTDDVEDEIETVADDVSALETGLETVESDVE----TVADDVDAVETDVDDLSEDLSAVEDDV 630
                                       5666666666666666666666666666666666666665444433....333333444444555555555555555 PP

                          MIP-T3_C 127 kdqkekisnvraki 140
                                       +  ++ +++vr++i
  gi|336254706|ref|YP_004597813.1| 631 ESVESDLEDVREEI 644
                                       55555555555444 PP

>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3       1.5   2.5e+02     163     210 ..     474     526 ..     438     548 .. 0.48
   2 ?    6.4   4.6     0.031       5.5     125     207 ..     560     645 ..     501     658 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.5
                              Not3 163 a.rveeleklierhkfhieklelllrl..leneelep..eevekikedieyyv 210
                                         ++++l++++e+   ++e le++l      ++ +e+  +ev+++++++  + 
  gi|336254706|ref|YP_004597813.1| 474 LaKLDHLQSRVEEVAAYTEALETFLGEngTGEQLIEDfrSEVADVQDELASMD 526
                                       34666666666666666666666554311112222222233444444433333 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.031
                              Not3 125 rewlkdaideLneqvekleaeieklsskkkkkkk..skekarveeleklierhkfhieklelllrlleneelep.ee 198
                                        ++l +++d+L+++++++e eie+++   +  ++  ++ +++ve++ + ++  ++ ++ l++ l ++e++  +  ++
  gi|336254706|ref|YP_004597813.1| 560 LDHLPETVDSLTDRTDDVEDEIETVADDVSALETglETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVESVeSD 636
                                       35566677777777777777777776665444432344444555555555555555555555555555543333345 PP

                              Not3 199 vekikedie 207
                                       +e+++e+i+
  gi|336254706|ref|YP_004597813.1| 637 LEDVREEIT 645
                                       555555554 PP

>> CAMP_factor  CAMP factor (Cfa)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.4   0.00065      0.11       7      92 ..     530     621 ..     513     649 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00065
                       CAMP_factor   7 aeakkelqkvnariaeL....keikkevpkadye.keiekllktakelkealeaiakgkvtl.ydlksIlaRvellv 77 
                                       a+ ++++++v+++i +L     + ++e+++ d   ++++ l +  +++++++e++a    +l   l+++ + ve ++
  gi|336254706|ref|YP_004597813.1| 530 ADTESQVDDVETEIDTLtewtTDLEDELSDLDHLpETVDSLTDRTDDVEDEIETVADDVSALeTGLETVESDVETVA 606
                                       6788999**********7766666888888886538999999************9999888734689********** PP

                       CAMP_factor  78 divdtiktaattLqd 92 
                                       d vd+++t   +L +
  gi|336254706|ref|YP_004597813.1| 607 DDVDAVETDVDDLSE 621
                                       *******99888876 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.43        76      30      56 ..     535     561 ..     527     578 .. 0.84
   2 ?    5.1   2.3      0.18        31       6      60 ..     579     631 ..     574     635 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.43
                              MtrB  30 sldpvleeidkLekiaddlvnsLdpet 56 
                                       ++d+v++eid L + + dl++ L+   
  gi|336254706|ref|YP_004597813.1| 535 QVDDVETEIDTLTEWTTDLEDELSDLD 561
                                       6899****************9998655 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.18
                              MtrB   6 pelnlvldpetgvvaearedvvllsldpvleeidkLekiaddlvnsLdpetalle 60 
                                        e++ v+d ++++  e++ + v  +++ v + +d +e+ +ddl + L+  +  +e
  gi|336254706|ref|YP_004597813.1| 579 DEIETVADDVSAL--ETGLETVESDVETVADDVDAVETDVDDLSEDLSAVEDDVE 631
                                       5666666665554..334457999**********************998766555 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   6.0    0.0015      0.26      23     161 ..     512     640 ..     479     659 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0015
                              Fez1  23 qaevtqklseivalkaqlrelrakleekeeeikeleesleektle...levcenelqrkkseaellrekvekleeel 96 
                                       ++ev+   +e+ ++  +l ++++++++ e+ei++l e +++ ++e   l       ++  ++++ l ++++ +e+e+
  gi|336254706|ref|YP_004597813.1| 512 RSEVADVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDElsdL-------DHLPETVDSLTDRTDDVEDEI 581
                                       4555555555555555555555555555555554444443333332221.......222333334444444444444 PP

                              Fez1  97 kelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFeqE 161
                                       + + +++s+l++  e+  +esd   ++   a+++++ + +v+ l + L+  ++  e+ +s+ e+ 
  gi|336254706|ref|YP_004597813.1| 582 ETVADDVSALETGLET--VESD---VET-VADDVDAVETDVDDLSEDLSAVEDDVESVESDLEDV 640
                                       4444433332221111..1111...111.122333333333333333333333333322222222 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 ?    5.5   0.2      0.11        19      41     102 ..     480     541 ..     473     549 .. 0.72
   2 ?    8.0   0.5     0.018       3.2      26      99 ..     517     590 ..     511     607 .. 0.81
   3 ?    6.5   0.3     0.053       9.2      68     107 ..     608     647 ..     599     648 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Seryl_tRNA_N  41 lqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklll 102
                                       lq+++ee+ a   +l    g+    ++ +e+ + ev+++++el+ ++++l++ e++++++ +
  gi|336254706|ref|YP_004597813.1| 480 LQSRVEEVAAYTEALETFLGENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVET 541
                                       66666666666666666666666666778888888888888888888888888888887654 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  26 advdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelek 99 
                                          del ++d++   ++++++++ +e  +l++    + ++  d ++l + v++l ++++++e+e +++ +++ +
  gi|336254706|ref|YP_004597813.1| 517 DVQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVDSLTDRTDDVEDEIETVADDVSA 590
                                       45588899999999999999999999999999999999988888888888888888888888888888877665 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.053
                                       -TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS--- CS
                      Seryl_tRNA_N  68 daeeliaevkelkeelkaleaelkeleaeleklllaiPNi 107
                                       d +++  +v++l+e+l+a+e++++ +e++le++  +i +i
  gi|336254706|ref|YP_004597813.1| 608 DVDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDI 647
                                       6677778899999999999999999999999988777665 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 ?   -0.4   0.1       8.3   1.5e+03      10      47 ..     450     487 ..     442     497 .. 0.77
   2 ?    6.7   0.4     0.054       9.5      11      52 ..     516     558 ..     502     568 .. 0.57
   3 ?    2.3   0.1       1.2   2.2e+02      14      54 ..     565     605 ..     550     609 .. 0.73
   4 ?    5.0   0.6      0.17        30      13      49 ..     613     649 ..     599     657 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 8.3
                            CC2-LZ  10 kvkkeeieeLkaqlqaaeealaakqeeidelkeeikkk 47 
                                       +v+++e+e L a+l +  e  a +  ++d+l+  +++ 
  gi|336254706|ref|YP_004597813.1| 450 EVDEDELEVLRAELATEPELSAPELAKLDHLQSRVEEV 487
                                       46689999999999999999999999999998887765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.054
                            CC2-LZ  11 vk.keeieeLkaqlqaaeealaakqeeidelkeeikkkeeele 52 
                                        + ++e+ ++  +l + e ++ + + eid l+e  +  e+el 
  gi|336254706|ref|YP_004597813.1| 516 ADvQDELASMDDRLADTESQVDDVETEIDTLTEWTTDLEDELS 558
                                       2334555555555555555555555555555555555555555 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 1.2
                            CC2-LZ  14 eeieeLkaqlqaaeealaakqeeidelkeeikkkeeeleti 54 
                                       e +++L+ + ++ e+ +++  +++  l++ ++  e+++et+
  gi|336254706|ref|YP_004597813.1| 565 ETVDSLTDRTDDVEDEIETVADDVSALETGLETVESDVETV 605
                                       56777777778888888888888888888777777777776 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.17
                            CC2-LZ  13 keeieeLkaqlqaaeealaakqeeidelkeeikkkee 49 
                                       + ++++L++ l+a e+ +++ ++++++++eei+  +e
  gi|336254706|ref|YP_004597813.1| 613 ETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQE 649
                                       4566777777777777777777777777777665544 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3         9   1.6e+03       7      33 ..     513     539 ..     505     544 .. 0.60
   2 ?    4.1   0.1      0.35        62       2      29 ..     560     587 ..     555     589 .. 0.58
   3 ?   11.7   0.3    0.0015      0.27       2      34 ..     581     613 ..     580     615 .. 0.91
   4 ?   12.5   1.5   0.00081      0.14       2      35 ..     616     649 ..     615     649 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 9
                               LPP   7 sqVsqLkskvdqlssdvnsakaaaqaa 33 
                                       s+V + +++ +++ + +++++++++++
  gi|336254706|ref|YP_004597813.1| 513 SEVADVQDELASMDDRLADTESQVDDV 539
                                       556666666666666666666666655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.35
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaa 29 
                                       ld L + V +L +  d ++++++ ++++
  gi|336254706|ref|YP_004597813.1| 560 LDHLPETVDSLTDRTDDVEDEIETVADD 587
                                       4555555666666666666666666665 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.0015
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaak 34 
                                       ++ ++++Vs+L++  + ++sdv+ ++++++a+ 
  gi|336254706|ref|YP_004597813.1| 581 IETVADDVSALETGLETVESDVETVADDVDAVE 613
                                       677899***********************9986 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00081
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaake 35 
                                       +d Ls+++s+ +++v++++sd++++++++ +++e
  gi|336254706|ref|YP_004597813.1| 616 VDDLSEDLSAVEDDVESVESDLEDVREEITDIQE 649
                                       7889999999999999999999999988888876 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.037       6.5      19      52 ..     508     541 ..     493     548 .. 0.82
   2 ?    9.7   0.1    0.0039      0.68      20      58 ..     530     568 ..     527     571 .. 0.89
   3 ?    3.1   0.0      0.47        83      28      58 ..     562     592 ..     558     594 .. 0.85
   4 ?    2.4   0.2      0.75   1.3e+02      27      58 ..     596     627 ..     581     644 .. 0.63
   5 ?    0.6   0.1       2.7   4.7e+02      18      46 ..     622     650 ..     614     656 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                             DivIC  19 ykqlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                       + + ++e+a+ q+ela++ ++ ++ e++v+d + 
  gi|336254706|ref|YP_004597813.1| 508 IEDFRSEVADVQDELASMDDRLADTESQVDDVET 541
                                       568899***********************99864 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0039
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXX CS
                             DivIC  20 kqlkqeiaalqaelaklkaeneeLeaevkdLksdedyie 58 
                                        ++++++++ + e+++l++   +Le+e++dL + ++ ++
  gi|336254706|ref|YP_004597813.1| 530 ADTESQVDDVETEIDTLTEWTTDLEDELSDLDHLPETVD 568
                                       67899**************************87777765 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.47
                                       HHHHHHHHHHHHHHHHHHHHCC-XXXXXXXX CS
                             DivIC  28 alqaelaklkaeneeLeaevkdLksdedyie 58 
                                        l +++++l+++ ++ e+e++   +d +++e
  gi|336254706|ref|YP_004597813.1| 562 HLPETVDSLTDRTDDVEDEIETVADDVSALE 592
                                       5667899**************9998888877 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.75
                                       HHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXX CS
                             DivIC  27 aalqaelaklkaeneeLeaevkdLksdedyie 58 
                                       ++ + +++++ ++ ++ e  v+dL+ d +++e
  gi|336254706|ref|YP_004597813.1| 596 ETVESDVETVADDVDAVETDVDDLSEDLSAVE 627
                                       55555556666666666666666655555554 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC  18 aykqlkqeiaalqaelaklkaeneeLeae 46 
                                       ++++++ +++  + +l+ +++e+ + ++ 
  gi|336254706|ref|YP_004597813.1| 622 DLSAVEDDVESVESDLEDVREEITDIQEW 650
                                       56677888888888888888888877765 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   5.6     0.041       7.2     114     226 ..     478     585 ..     451     600 .. 0.54
   2 ?    7.7   4.5     0.011       1.9     121     220 ..     561     649 ..     560     656 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.041
                              CorA 114 rlldeivdrlfellekleeeldeledel.....edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkl 185
                                         l++ v+++++++e+le+        l      ++  +++++e+a+++ +l+ + + la+++  ++++ +  + ++
  gi|336254706|ref|YP_004597813.1| 478 DHLQSRVEEVAAYTEALETF-------LgengtGEQLIEDFRSEVADVQDELASMDDRLADTESQVDDVET--EIDT 545
                                       33444444444444444444.......43333333334445555555555555555555555555544444..3333 PP

                              CorA 186 lddedkeylrdlldelerllemlealrerleslqdtyssll 226
                                       l++     l+d l++l++l e++++l +r++ + d++ ++ 
  gi|336254706|ref|YP_004597813.1| 546 LTEWT-TDLEDELSDLDHLPETVDSLTDRTDDVEDEIETVA 585
                                       33322.33566666666666666666666666666665544 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.011
                              CorA 121 drlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdl 197
                                       d+l e+++ l +++d++ede+     +  ++++++l++ l ++++ + +  + + + ++ +d + l+++    l+ +
  gi|336254706|ref|YP_004597813.1| 561 DHLPETVDSLTDRTDDVEDEI-----ETVADDVSALETGLETVESDVETVADDV-DAVE-TDVDDLSED----LSAV 626
                                       777899999999999999999.....88999999*********99999999999.8888.788888877....7*** PP

                              CorA 198 ldelerllemlealrerleslqd 220
                                       +d++e+++ +le +re ++ +q+
  gi|336254706|ref|YP_004597813.1| 627 EDDVESVESDLEDVREEITDIQE 649
                                       ********************997 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1         2   3.6e+02     140     174 ..     509     543 ..     473     549 .. 0.68
   2 ?    1.9   0.8      0.97   1.7e+02     103     170 ..     532     598 ..     505     604 .. 0.51
   3 ?    7.0   1.4     0.026       4.6     101     172 ..     582     649 ..     560     653 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 2
                      Bacillus_HBL 140 knFktdvdeltsilagdsgvisqlqneiedlqgki 174
                                       ++F ++v+ ++  la+ +  +++ + ++ d++ +i
  gi|336254706|ref|YP_004597813.1| 509 EDFRSEVADVQDELASMDDRLADTESQVDDVETEI 543
                                       57888888888888888888888888888877776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.97
                      Bacillus_HBL 103 llellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedl 170
                                         +++ + ++ei +  + +++l  eL++l  +l + + +++  +d ++  +++   ++s+l+  +e++
  gi|336254706|ref|YP_004597813.1| 532 TESQVDDVETEIDTLTEWTTDLEDELSDLD-HLPETVDSLTDRTDDVEDEIETVADDVSALETGLETV 598
                                       333344444444444444445555555543.3455555555555555555555555555555555555 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.026
                      Bacillus_HBL 101 aellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqg 172
                                       +++ +++++L++++ + +  v++++ +     ++++ d+ ++++d++ ++  +++ + +++++++ei+d+q+
  gi|336254706|ref|YP_004597813.1| 582 ETVADDVSALETGLETVESDVETVADD----VDAVETDVDDLSEDLSAVEDDVESVESDLEDVREEITDIQE 649
                                       445555555555555555555555444....56778889999999999999999999999999999999986 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1      0.14        25      26      66 ..     498     538 ..     480     548 .. 0.85
   2 ?    5.9   0.7     0.092        16       9      64 ..     568     623 ..     560     629 .. 0.86
   3 ?    1.9   0.2       1.6   2.9e+02      32      65 ..     619     652 ..     617     655 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.14
                            Csm1_N  26 vhENsvLsqkletkdqeiesLkeqlaeleekvkeleerrkk 66 
                                       + EN + +q +e    e+  ++ +la+++ +++++e++ ++
  gi|336254706|ref|YP_004597813.1| 498 LGENGTGEQLIEDFRSEVADVQDELASMDDRLADTESQVDD 538
                                       56899999999999999999999999999999999887654 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.092
                            Csm1_N   9 esVqerldsAdllvsklvhENsvLsqkletkdqeiesLkeqlaeleekvkeleerr 64 
                                       +s+ +r d+ +  ++ +    s L++ let +  +e++   ++++e++v++l e+ 
  gi|336254706|ref|YP_004597813.1| 568 DSLTDRTDDVEDEIETVADDVSALETGLETVESDVETVADDVDAVETDVDDLSEDL 623
                                       68888999999999999999999*************************99998875 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 1.6
                            Csm1_N  32 LsqkletkdqeiesLkeqlaeleekvkeleerrk 65 
                                       Ls++l+  ++ +es++  l+ ++e++ +++e r+
  gi|336254706|ref|YP_004597813.1| 619 LSEDLSAVEDDVESVESDLEDVREEITDIQEWRN 652
                                       6788888889999999999999999988888766 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2       3.9   6.8e+02      10      51 ..     473     514 ..     468     545 .. 0.65
   2 ?   -0.5   0.1       9.4   1.7e+03      25      40 ..     533     548 ..     506     562 .. 0.56
   3 ?    8.4   0.1     0.016       2.8      14      47 ..     567     600 ..     554     605 .. 0.82
   4 ?    3.5   0.1      0.54        95      17      47 ..     605     635 ..     600     648 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 3.9
                         DASH_Dad2  10 ELeaLkqlrdlsdslakqleeLeeklstladgteavasVlan 51 
                                       EL++L +l++  +++a   e+Le+ l++  +g + +++  ++
  gi|336254706|ref|YP_004597813.1| 473 ELAKLDHLQSRVEEVAAYTEALETFLGENGTGEQLIEDFRSE 514
                                       777777777777777777777777777777777666655444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 9.4
                         DASH_Dad2  25 akqleeLeeklstlad 40 
                                       ++q++ +e++++tl++
  gi|336254706|ref|YP_004597813.1| 533 ESQVDDVETEIDTLTE 548
                                       3444444444444443 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.016
                         DASH_Dad2  14 LkqlrdlsdslakqleeLeeklstladgteavas 47 
                                          l+d +d++++++e++++ +s l++g e+v+s
  gi|336254706|ref|YP_004597813.1| 567 VDSLTDRTDDVEDEIETVADDVSALETGLETVES 600
                                       5678899999999999999999999999999976 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.54
                         DASH_Dad2  17 lrdlsdslakqleeLeeklstladgteavas 47 
                                       + d  d++++ ++ L+e ls ++d  e+v+s
  gi|336254706|ref|YP_004597813.1| 605 VADDVDAVETDVDDLSEDLSAVEDDVESVES 635
                                       5556678899999999999999999999986 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 ?    1.5   0.4       2.5   4.3e+02      51      98 ..     478     525 ..     436     540 .. 0.50
   2 ?    0.1  13.8       6.8   1.2e+03      10      98 ..     553     647 ..     511     657 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 2.5
                      Syntaxin-6_N  51 rsiewdledLeetvriveknpskfkidekelsrrrafveevreevkem 98 
                                       + ++  +e+     +++e    + +  e+ ++  r+ v++v++e+ +m
  gi|336254706|ref|YP_004597813.1| 478 DHLQSRVEEVAAYTEALETFLGENGTGEQLIEDFRSEVADVQDELASM 525
                                       222222222222223333344444445555555555555555554444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 6.8
                      Syntaxin-6_N  10 Vqkslnkaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvrivek....npsk.fkidek 79 
                                        +++l+ +  l ++  +l + t++  ++ e + +  + L++ l+++e d+e   + v++ve       s+  +  e+
  gi|336254706|ref|YP_004597813.1| 553 LEDELSDLDHLPETVDSLTDRTDDveDEIETVADDVSALETGLETVESDVETVADDVDAVETdvddL-SEdLSAVED 628
                                       3333333333333333333333322113333334444455555555555555555555554433321.222555555 PP

                      Syntaxin-6_N  80 elsrrrafveevreevkem 98 
                                       ++++ ++ +e+vree+ ++
  gi|336254706|ref|YP_004597813.1| 629 DVESVESDLEDVREEITDI 647
                                       5666666666666665554 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.5      0.33        57      36      69 ..     509     542 ..     506     557 .. 0.77
   2 ?    5.8   0.4     0.086        15      32      69 ..     564     601 ..     558     610 .. 0.67
   3 ?    5.6   1.1       0.1        18      35      68 ..     616     649 ..     610     650 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.33
                          JIP_LZII  36 deLtsereiLreEleslqkakerlesrikelEee 69 
                                       ++  se   +++El s+ + ++  es++ ++E e
  gi|336254706|ref|YP_004597813.1| 509 EDFRSEVADVQDELASMDDRLADTESQVDDVETE 542
                                       5666677777777777777777777777777776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.086
                          JIP_LZII  32 IarvdeLtsereiLreEleslqkakerlesrikelEee 69 
                                        + vd Lt + + +++E+e++ +  ++le+ ++ +E +
  gi|336254706|ref|YP_004597813.1| 564 PETVDSLTDRTDDVEDEIETVADDVSALETGLETVESD 601
                                       55667777777777777777777777777766666655 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.1
                          JIP_LZII  35 vdeLtsereiLreEleslqkakerlesrikelEe 68 
                                       vd+L+++ +++++++es+++ +e ++++i++++e
  gi|336254706|ref|YP_004597813.1| 616 VDDLSEDLSAVEDDVESVESDLEDVREEITDIQE 649
                                       9****************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (661 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1525  (0.0850577); expected 358.6 (0.02)
Passed bias filter:                      765  (0.0426683); expected 358.6 (0.02)
Passed Vit filter:                       245  (0.013665); expected 17.9 (0.001)
Passed Fwd filter:                       156  (0.00870099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             102  [number of targets reported over threshold]
# CPU time: 1.90u 0.34s 00:00:02.23 Elapsed: 00:00:00.54
# Mc/sec: 3685.19
//
Query:       gi|336254707|ref|YP_004597814.1|  [L=315]
Description: hypothetical protein Halxa_3323 [Halopiger xanaduensis SH-6]
Scores for 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   13.0   0.0        0.1   12.5   0.0    1.3  1  HisG         ATP phosphoribosyltransferase
      0.096   12.8   0.3        0.3   11.2   0.1    1.9  2  Lambda_CIII  Lambda Phage CIII


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 ?   12.5   0.0   1.2e-05       0.1     107     152 ..     248     293 ..     126     301 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                                       -SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHHSHHHHH CS
                              HisG 107 aDaIvDlvetGeTLrangLkaietilessavLiankkslkkkekie 152
                                         + v l+ tG+T r++gL   e+++ s++vL  n+++l+k + + 
  gi|336254707|ref|YP_004597814.1| 248 TGLGVYLTVTGSTAREHGLLLGEQLFPSETVLLENTSELRKTDAAA 293
                                       445577999************************9998888544333 PP

>> Lambda_CIII  Lambda Phage CIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   3.3e-05       0.3       8      25 ..      10      27 ..       5      29 .. 0.91
   2 ?   -3.1   0.0      0.96   8.6e+03      18      23 ..     152     157 ..     151     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.3e-05
                       Lambda_CIII  8 pvaGvpqESlLdRitrkl 25
                                      p+ G p ES LdR +r+l
  gi|336254707|ref|YP_004597814.1| 10 PRKGRPLESVLDRLARRL 27
                                      999**************8 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.96
                       Lambda_CIII  18 LdRitr 23 
                                       LdRi++
  gi|336254707|ref|YP_004597814.1| 152 LDRIAD 157
                                       899987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2347.62
//
Query:       gi|336254708|ref|YP_004597815.1|  [L=232]
Description: hypothetical protein Halxa_3324 [Halopiger xanaduensis SH-6]
Scores for 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:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1815.96
//
Query:       gi|336254709|ref|YP_004597816.1|  [L=121]
Description: regulatory protein ArsR [Halopiger xanaduensis SH-6]
Scores for complete 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-11   44.4   0.1    2.5e-11   43.5   0.1    1.5  1  HTH_20        Helix-turn-helix domain
    7.7e-10   38.5   0.0    1.3e-09   37.7   0.0    1.4  1  HTH_5         Bacterial regulatory protein, arsR family
    3.9e-05   23.5   0.0    5.9e-05   22.9   0.0    1.3  1  MarR          MarR family
    0.00016   21.5   0.0    0.00025   20.9   0.0    1.3  1  TrmB          Sugar-specific transcriptional regulator TrmB
    0.00091   19.1   0.0     0.0016   18.3   0.0    1.4  1  MarR_2        MarR family
     0.0029   17.1   0.0     0.0059   16.2   0.0    1.4  1  HTH_24        Winged helix-turn-helix DNA-binding
     0.0031   17.3   0.1     0.0061   16.3   0.1    1.4  1  HTH_IclR      IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.3   0.5      0.026   14.5   0.1    1.6  2  HTH_12        Ribonuclease R winged-helix domain
      0.036   14.1   0.0      0.049   13.7   0.0    1.2  1  Replic_Relax  Replication-relaxation
       0.04   13.8   0.0      0.055   13.3   0.0    1.2  1  TFIIE_alpha   TFIIE alpha subunit
      0.044   12.6   0.0      0.053   12.4   0.0    1.1  1  BBP2_2        Putative beta-barrel porin 2
      0.058   13.9   0.0       0.11   13.0   0.0    1.4  1  HTH_27        Winged helix DNA-binding domain
       0.13   12.5   0.0       0.17   12.1   0.0    1.2  1  HTH_34        Winged helix DNA-binding 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 !   43.5   0.1   1.8e-14   2.5e-11       3      54 ..      35      86 ..      33      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.8e-14
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                       + ++++P+R  il +La+++ l  +ela++ld ++n l++HL++Le+agLv
  gi|336254709|ref|YP_004597816.1| 35 RLQVMGEPTRFTILYLLAEEGRLRSGELADLLDRRQNDLYHHLNTLEDAGLV 86
                                      67899**********************************************8 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 !   37.7   0.0   9.6e-13   1.3e-09       2      45 ..      42      86 ..      41      88 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 9.6e-13
                                      HHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  2 ptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      ptR  IL+lLae g l ++ela+ l+  q  + hHL+ L++aGLV
  gi|336254709|ref|YP_004597816.1| 42 PTRFTILYLLAEeGRLRSGELADLLDRRQNDLYHHLNTLEDAGLV 86
                                      9***********999*****************************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   4.3e-08   5.9e-05       3      52 ..      42      91 ..      41      95 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.3e-08
                                      HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR  3 ltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                      +t+f iL++l+e+g l+  eLa+ l   +  +   l +Le++Gl+ + ++
  gi|336254709|ref|YP_004597816.1| 42 PTRFTILYLLAEEGRLRSGELADLLDRRQNDLYHHLNTLEDAGLVGKFRD 91
                                      699******************************************98887 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   1.8e-07   0.00025      16      66 ..      49     101 ..      45     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.8e-07
                                       HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE-- CS
                              TrmB  16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravd 66 
                                       +Ll ++g+++  e+a  l++ ++  Y  L+ Led+GlV + + g+ ++Y+  +
  gi|336254709|ref|YP_004597816.1|  49 YLLaEEGRLRSGELADLLDRRQNDLYHHLNTLEDAGLVGKFRdGSSRVYELSP 101
                                       45559*********************************998846688998766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.2e-06    0.0016       4      52 ..      41      87 ..      39     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                                      -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +p+ + +L+ L+ +++  l+ gela+ l+  +  +  +l+ L++aGLv 
  gi|336254709|ref|YP_004597816.1| 41 EPTRFTILYLLAEEGR--LRSGELADLLDRRQNDLYHHLNTLEDAGLVG 87
                                      6999**********98..*****************************94 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 !   16.2   0.0   4.2e-06    0.0059       4      47 ..      43      86 ..      41      86 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.2e-06
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      t++ IL lL +++r+   eLA+ l+  ++ +  +l+ Le++Gl+
  gi|336254709|ref|YP_004597816.1| 43 TRFTILYLLAEEGRLRSGELADLLDRRQNDLYHHLNTLEDAGLV 86
                                      8999**************************************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 !   16.3   0.1   4.4e-06    0.0061       6      48 ..      45      86 ..      45      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.4e-06
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      + iL +lae+++ l+  elA+ ++      +++L+tL+  G+v
  gi|336254709|ref|YP_004597816.1| 45 FTILYLLAEEGR-LRSGELADLLDRRQNDLYHHLNTLEDAGLV 86
                                      67999******9.9***************************99 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 ?   -2.5   0.0       3.8   5.3e+03      33      33 ..      32      32 ..      10      42 .. 0.51
   2 ?   14.5   0.1   1.8e-05     0.026       2      54 ..      46      92 ..      45     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.8
                            HTH_12 33 r 33
                                      +
  gi|336254709|ref|YP_004597816.1| 32 E 32
                                      3 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.8e-05
                            HTH_12  2 eILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgya 54
                                       IL +lae+ + + ++e+a+ L  r  d+       +L  le+ gl+ + + +
  gi|336254709|ref|YP_004597816.1| 46 TILYLLAEEGR-LRSGELADLLDRRQNDL-----YHHLNTLEDAGLVGKFRDG 92
                                      69*********.*************9999.....679**********998766 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.6e-05     0.049       1      72 [.      48     110 ..      48     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                      Replic_Relax   1 LrlLaehrvlTtrqiarllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaaq 72 
                                       L lLae + l +  +a ll   ++  ++  L++L++ gl+ ++r           + vY L p+++ ++++ 
  gi|336254709|ref|YP_004597816.1|  48 LYLLAEEGRLRSGELADLLDRRQND-LYHHLNTLEDAGLVGKFRDG---S-----SRVYELSPLAEGFVPQI 110
                                       67899999999*************9.****************9997...3.....45999999998887554 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     4e-05     0.055      14      58 ..      43      87 ..      36      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
                                      HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha 14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                        + +l  L+e+g +   +la +l   +n l + Ln L +a+lv 
  gi|336254709|ref|YP_004597816.1| 43 TRFTILYLLAEEGRLRSGELADLLDRRQNDLYHHLNTLEDAGLVG 87
                                      56899**************************************95 PP

>> BBP2_2  Putative beta-barrel porin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.8e-05     0.053     110     174 ..       5      71 ..       1      77 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.8e-05
                            BBP2_2 110 rsspnsvsagaaeppkyatfgasagveqrfnrlrvslggsvdrttY...qdaeltdGttisqsdRdrt 174
                                        +  n  sa a+e+++ + + +++++e++ nrl+v ++ +     Y   ++ +l++G+ ++  dR ++
  gi|336254709|ref|YP_004597816.1|   5 ETPRNERSA-ARERVESDLLAGTLDLEREANRLQVMGEPTRFTILYllaEEGRLRSGELADLLDRRQN 71 
                                       333334445.89***********************998888888888888888888988888888655 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 ?   13.0   0.0   7.7e-05      0.11       7      66 ..      46     101 ..      40     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.7e-05
                            HTH_27   7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTd 66 
                                        +L l++ +++r +  +l++ l++ +      l+ L+ +GLv   g+ +d+ ++ ++l++
  gi|336254709|ref|YP_004597816.1|  46 TILYLLA-EEGRLRSGELADLLDRRQNDLYHHLNTLEDAGLV---GKFRDGSSRVYELSP 101
                                       5699999.9*********************************...555888888888876 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 ?   12.1   0.0   0.00013      0.17       2      44 ..      44      86 ..      43      95 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                            HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYi 44
                                      R+ +l +La++ +    el + l   +  L+ hl++Le+ag +
  gi|336254709|ref|YP_004597816.1| 44 RFTILYLLAEEGRLRSGELADLLDRRQNDLYHHLNTLEDAGLV 86
                                      9***************************************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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):              13  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 907.04
//
Query:       gi|336254710|ref|YP_004597817.1|  [L=350]
Description: integrase protein [Halopiger xanaduensis SH-6]
Scores for 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-16   58.3   0.0    1.6e-15   57.3   0.0    1.4  1  Phage_integrase  Phage integrase family
    1.7e-08   34.6   0.7    4.3e-08   33.3   0.7    1.7  1  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    1.7e-05   25.2   0.6    4.2e-05   23.9   0.6    1.6  1  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.043   13.7   0.0        0.1   12.5   0.0    1.6  1  Phage_integr_3   Archaeal phage integrase
      0.065   13.8   1.3        2.6    8.6   1.3    2.4  1  SF3A3            Pre-mRNA-splicing factor SF3A3, of SF3a comp


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 !   57.3   0.0   4.5e-19   1.6e-15      22     169 ..     138     332 ..     121     333 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 4.5e-19
                                       HHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEE.............................EEECSSSSEEE CS
                   Phage_integrase  22 rdklllellyetGlRisEllsLrvkdldlengvilvh.............................eregKgskera 69 
                                        +++++ +l++tG+R++El++L++ d +le++  + +                             ++  K+++e++
  gi|336254710|ref|YP_004597817.1| 138 LHRAIVVTLLKTGIRAGELCNLDLIDCHLEHEAQTWQprahiagrpdslfvstehtygeesggerrTASNKRKRETV 214
                                       4799999***********************99998889999***********************999999******* PP

                                       EECTHHHHHHHHHHHHHH........CHCCTTTSBSSBET...TSSB--HHHHHHHHHHHHHHCT-S.......SC- CS
                   Phage_integrase  70 vplseealellkellska........leeaeksellfask...rgkplsrqtvrkafkraveeagie.......kpl 128
                                       +p+ +e+ e+l ++l+++           a  +e lf+ +    g++l+ + v ++++++++e g +       +++
  gi|336254710|ref|YP_004597817.1| 215 IPIDDELKEVLVRWLAVRpdvagdsrTPSAAATEPLFVGTadsWGQRLTPNVVHHVVEQYARERGWYrtgggasENV 291
                                       ******************866655444444455588888888899******************99999999999*** PP

                                       -TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHHHHHCC CS
                   Phage_integrase 129 tpHtlRhsfataLleagvdlrvvqkllGHssisttqiYthv 169
                                       tpH +Rh f t+L  +  d   vq+l G      + +Yth+
  gi|336254710|ref|YP_004597817.1| 292 TPHYFRHFFTTHLRDRTGDRGIVQYLRGDVASDVIDTYTHN 332
                                       ****************************9999999999996 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 !   33.3   0.7   1.2e-11   4.3e-08       4      82 ..      16      93 ..      14      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.2e-11
                                      HHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_1  4 fleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqflvr 82
                                      ++   i+  g+ + T +aY+r L +++ flaer +++  +++ +d+ a++ el++   s++++a + s l +F+++l r
  gi|336254710|ref|YP_004597817.1| 16 YFLQDIEHHGRNERTAAAYQRVLTDYESFLAERFEKAPPEASYRDCMAWIHELRST-HSESTVATYASYLNRFYSYLER 93
                                      445555678889*******************************************6.6******************987 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 !   23.9   0.6   1.2e-08   4.2e-05       4      79 ..      16      92 ..      14      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.2e-08
                   Phage_int_SAM_4  4 rfrealrlaglserTiksYlsaikrflrfl....kkkapeeltkedieaYlnyLanerklsastqknalnalsffykkv 78
                                       f++ ++++g  erT  +Y++ ++++  fl    + kap e + +d +a ++ L+ +++ s st+ ++ + l+ fy+ +
  gi|336254710|ref|YP_004597817.1| 16 YFLQDIEHHGRNERTAAAYQRVLTDYESFLaerfE-KAPPEASYRDCMAWIHELR-STH-SESTVATYASYLNRFYSYL 91
                                      6899**************************44333.6******************.888.****************986 PP

                   Phage_int_SAM_4 79 l 79
                                       
  gi|336254710|ref|YP_004597817.1| 92 E 92
                                      4 PP

>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.8e-05       0.1     103     154 ..     279     341 ..     259     346 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                                       T...........--GHHHHHHHHHHHHHTT--HHHHHHHTTSS-CCTTSCHHCHHHHHHHHHH CS
                    Phage_integr_3 103 k...........vkakyiRkwvatklaelgvpeevidFiqGrkpssvlekhYlnllvlAdeaY 154
                                       +           v+ +y+R++++t l ++  + ++++++ G  +s v  ++  n   +  e+Y
  gi|336254710|ref|YP_004597817.1| 279 GwyrtgggasenVTPHYFRHFFTTHLRDRTGDRGIVQYLRGDVASDVIDTYTHNWGDRVRETY 341
                                       455555666666**********************************99988766655555555 PP

>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.3   0.00071       2.6      30      67 ..      40      93 ..       8     103 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00071
                             SF3A3 30 dYlqYLes.fdkf.............seip..kkqkkskeYkeYlkeLleYLes 67
                                      dY ++L++ f+k              +e+   +++ +   Y +Yl++ ++YLe+
  gi|336254710|ref|YP_004597817.1| 40 DYESFLAErFEKAppeasyrdcmawiHELRstHSESTVATYASYLNRFYSYLER 93
                                      4444442213333555555555555555553345556679***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2551.67
//
Query:       gi|336254711|ref|YP_004597818.1|  [L=136]
Description: hypothetical protein Halxa_3327 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
       0.01   14.3   0.2       0.01   14.3   0.2    1.1  1  Hydantoinase_B  Hydantoinase B/oxoprolinase
  ------ inclusion threshold ------
      0.019   14.8   1.1      0.076   12.8   1.1    1.8  1  DUF2064         Uncharacterized protein conserved in bacteria


Domain annotation for each model (and alignments):
>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2   1.1e-06      0.01     173     230 ..      61     118 ..      16     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-06
                    Hydantoinase_B 173 ednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelpdg 230
                                       +++ +D ++  +a +  ++r+ e++++ G+  +++++d+++d+ e  + aal++l+d+
  gi|336254711|ref|YP_004597818.1|  61 SEMDADAETADSAGDDFADRILEVLQREGVHDWDELVDALIDDVEDDLDAALQQLQDE 118
                                       56667777777899999**************************************994 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 ?   12.8   1.1   8.5e-06     0.076       7     105 ..      41     134 ..      35     136 .] 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.5e-06
                                       TTSSSEEEEEE----TTHHHHHHHH-TTSEEEE--SSSHHHHHHHHHHHHHHTT-SEEEEE-SS-TT--HHHHHHHH CS
                           DUF2064   7 aadaaevvlaldgaldkalaeqlalakglevlpQqggdlgeRlarafdrafeageepvlliGsDcpqltaalleqAf 83 
                                       +a++ + ++  +g+ ++++++  +  ++ e     g+d+ +R+ ++++r   ++ ++ +    D     ++ l++A+
  gi|336254711|ref|YP_004597818.1|  41 QAGRSDFEVPSSGGAADEKQS--EMDADAETADSAGDDFADRILEVLQREGVHDWDELVDALIDD---VEDDLDAAL 112
                                       555555666666665555554..788888888888999999999999888666666655444443...3689***** PP

                                       HHTTT-SEEEEEBTTSSEEEEE CS
                           DUF2064  84 eaLeeadaVlgpaeDGGYyllG 105
                                       ++L++++ V     +GGY+++G
  gi|336254711|ref|YP_004597818.1| 113 QQLQDENKVRYSGREGGYVVVG 134
                                       *********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1079.61
//
Query:       gi|336254712|ref|YP_004597819.1|  [L=77]
Description: hypothetical protein Halxa_3328 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0015   18.4   2.9      0.072   13.0   0.1    2.4  2  zf-C2HC_2    zinc-finger of a C2HC-type
     0.0042   17.5   7.8       0.11   12.9   0.3    3.2  3  zf-C2H2      Zinc finger, C2H2 type
     0.0092   16.0   9.2       0.48   10.5   0.1    2.8  3  zf-C2H2_6    C2H2-type zinc finger
  ------ inclusion threshold ------
      0.027   14.3   3.4       0.66    9.9   0.7    2.3  2  HNH_5        HNH endonuclease
      0.064   13.6   3.7       0.86   10.0   0.5    2.5  2  zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
       0.07   13.3   3.4      0.088   13.0   3.4    1.3  1  FYVE         FYVE zinc finger
      0.088   13.7   7.8          1   10.4   1.1    2.9  3  zf-C2H2_4    C2H2-type zinc finger
       0.11   12.5   7.1          1    9.4   7.1    2.0  1  DZR          Double zinc ribbon
       0.14   11.7   6.0       0.63    9.7   0.2    2.7  3  zf_UBZ       Ubiquitin-Binding Zinc Finger
       0.19   11.8   4.5        2.2    8.4   3.8    2.1  1  Elf1         Transcription elongation factor Elf1 like
       0.24   11.3   4.0        9.2    6.2   0.2    3.1  3  zf-HIT       HIT zinc finger
       0.31   11.5   7.2         10    6.6   7.9    2.1  2  Rhodanese_C  Rhodanase C-terminal
       0.62   10.6   4.3         32    5.2   0.1    3.2  3  zf-H2C2_2    Zinc-finger double domain
        1.5    9.3   3.0        9.4    6.7   0.4    2.2  2  DUF983       Protein of unknown function (DUF983)
        1.5    9.2   9.3       0.12   12.7   2.9    2.0  2  C1_2         C1 domain


Domain annotation for each model (and alignments):
>> 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 !   13.0   0.1     6e-05     0.072       2      25 .]       1      25 [.       1      25 [. 0.93
   2 ?    5.5   0.5     0.014        16       5      14 ..      31      40 ..      28      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6e-05
                         zf-C2HC_2  2 lvpCpkCgRsF.npdrlekHepvCk 25
                                      +  C++C+ sF  + +le H   C+
  gi|336254712|ref|YP_004597819.1|  1 MHTCRNCNQSFqTELALELHLDTCQ 25
                                      578********************96 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.014
                         zf-C2HC_2  5 CpkCgRsFnp 14
                                      C+ Cg +F +
  gi|336254712|ref|YP_004597819.1| 31 CQVCGERFRE 40
                                      ********75 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.3   9.6e-05      0.11       1      20 [.       2      21 ..       2      23 .. 0.92
   2 ?    5.6   0.2     0.021        25       3      11 ..      31      39 ..      29      41 .. 0.90
   3 ?    2.6   0.2      0.18   2.2e+02       1       7 [.      50      58 ..      50      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.6e-05
                                      EEETTTTEEESSHHHHHHHH CS
                           zf-C2H2  1 ykCpdCgksFkrksnLkrHi 20
                                      ++C  C++sF +   L+ H+
  gi|336254712|ref|YP_004597819.1|  2 HTCRNCNQSFQTELALELHL 21
                                      79****************98 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.021
                                      ETTTTEEES CS
                           zf-C2H2  3 CpdCgksFk 11
                                      C +Cg++F+
  gi|336254712|ref|YP_004597819.1| 31 CQVCGERFR 39
                                      *******96 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.18
                                      EEET..TTT CS
                           zf-C2H2  1 ykCp..dCg 7 
                                      y+Cp  dC+
  gi|336254712|ref|YP_004597819.1| 50 YECPneDCD 58
                                      99******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 !   10.1   1.2   0.00051      0.61       2      21 ..       2      21 ..       1      26 [. 0.90
   2 !   10.5   0.1    0.0004      0.48       4      16 ..      31      43 ..      31      43 .. 0.91
   3 ?   -1.5   0.2       2.3   2.8e+03       1       5 [.      49      53 ..      49      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00051
                         zf-C2H2_6  2 heCsvCsksFpslqaLggHk 21
                                      h C  C+ sF++  aL+ H+
  gi|336254712|ref|YP_004597819.1|  2 HTCRNCNQSFQTELALELHL 21
                                      89**************9997 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0004
                         zf-C2H2_6  4 CsvCsksFpslqa 16
                                      C+vC+++F+ ++a
  gi|336254712|ref|YP_004597819.1| 31 CQVCGERFREGDA 43
                                      ********98876 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.3
                         zf-C2H2_6  1 vheCs 5 
                                      ++eC+
  gi|336254712|ref|YP_004597819.1| 49 HYECP 53
                                      79**5 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.7   0.00056      0.66      35      51 ..       3      19 ..       1      27 [. 0.85
   2 ?    5.1   0.1     0.018        21       1      16 [.      31      46 ..      28      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00056
                             HNH_5 35 lCkkCNqkkgqkvdaal 51
                                      +C+ CNq +++++  +l
  gi|336254712|ref|YP_004597819.1|  3 TCRNCNQSFQTELALEL 19
                                      8********99886665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.018
                             HNH_5  1 CiyCgkeiaekelsee 16
                                      C++Cg+++ e +++++
  gi|336254712|ref|YP_004597819.1| 31 CQVCGERFREGDATQD 46
                                      9999999999888876 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5   0.00072      0.86       2      22 ..       2      22 ..       1      27 [. 0.90
   2 ?    4.4   0.2      0.04        48       1      10 [.      28      37 ..      28      40 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00072
                                      CBBTTTTBBBSSHHHHHCCTT CS
                       zf-C2H2_jaz  2 fYCvlCdKyFksenaldnHlk 22
                                      + C  C+  F++e al+ Hl 
  gi|336254712|ref|YP_004597819.1|  2 HTCRNCNQSFQTELALELHLD 22
                                      67999**************96 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.04
                                      ECBBTTTTBB CS
                       zf-C2H2_jaz  1 qfYCvlCdKy 10
                                      q++C++C   
  gi|336254712|ref|YP_004597819.1| 28 QLFCQVCGER 37
                                      79*****755 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.4   7.4e-05     0.088      10      43 ..       2      38 ..       1      65 [. 0.65

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.4e-05
                                      SB-TTT--B-.-SSS--EE-TTT..--EE-STTS-EE CS
                              FYVE 10 kkCeiCakkF.sllrrrhhCrlC..GkvvCekCsskl 43
                                      ++C++C+++F + l    h  +C  G+++C+ C + +
  gi|336254712|ref|YP_004597819.1|  2 HTCRNCNQSFqTELALELHLDTCqkGQLFCQVCGERF 38
                                      79********443444455444444555555555443 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 ?   10.4   1.1   0.00087         1       1      21 [.       2      22 ..       2      25 .. 0.89
   2 ?    6.8   0.1     0.012        15       3      11 ..      31      39 ..      29      44 .. 0.84
   3 ?   -1.1   0.1       4.1   4.9e+03       1       6 [.      50      57 ..      50      64 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00087
                         zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlk 21
                                      ++C+ C++sF +  aL  Hl 
  gi|336254712|ref|YP_004597819.1|  2 HTCRNCNQSFQTELALELHLD 22
                                      68*************999986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.012
                         zf-C2H2_4  3 CpiCgksFs 11
                                      C +Cg++F+
  gi|336254712|ref|YP_004597819.1| 31 CQVCGERFR 39
                                      ********6 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.1
                         zf-C2H2_4  1 fkCpi..C 6 
                                      ++Cp   C
  gi|336254712|ref|YP_004597819.1| 50 YECPNedC 57
                                      67876555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   7.1   0.00086         1       1      33 [.       4      54 ..       4      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00086
                               DZR  1 CpqCgee.............lppdarfCseCgtklkavaa.....edrCps 33
                                      C +C++               ++++ fC+ Cg++ ++  a     ++ Cp+
  gi|336254712|ref|YP_004597819.1|  4 CRNCNQSfqtelalelhldtCQKGQLFCQVCGERFREGDAtqdgwHYECPN 54
                                      99999999999999999888899999********99766699999999986 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00053      0.63       3      22 ..       2      22 ..       1      22 [. 0.89
   2 ?    5.1   0.1     0.014        17       2      14 ..      28      40 ..      27      45 .. 0.81
   3 ?   -2.6   0.2       3.7   4.5e+03       2       6 ..      49      53 ..      48      54 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00053
                            zf_UBZ  3 ylCerCgkeipes.elqEHeD 22
                                      ++C  C+++++++ +l+ H+D
  gi|336254712|ref|YP_004597819.1|  2 HTCRNCNQSFQTElALELHLD 22
                                      79**********988888888 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.014
                            zf_UBZ  2 tylCerCgkeipe 14
                                      + +C+ Cg+++ e
  gi|336254712|ref|YP_004597819.1| 28 QLFCQVCGERFRE 40
                                      579******9976 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.7
                            zf_UBZ  2 tylCe 6 
                                      +y C+
  gi|336254712|ref|YP_004597819.1| 49 HYECP 53
                                      45665 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.8    0.0019       2.2      23      56 ..       3      39 ..       1      46 [. 0.71

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0019
                              Elf1 23 dCpfCnheksvevkldkkek...iaevsCkvCgesfe 56
                                      +C +Cn++   e  l+   +   ++++ C+vCge+f+
  gi|336254712|ref|YP_004597819.1|  3 TCRNCNQSFQTELALELHLDtcqKGQLFCQVCGERFR 39
                                      7999988755554444443344499999****99875 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.029        34      15      21 ..       3       9 ..       2      25 .. 0.85
   2 ?    6.2   0.2    0.0077       9.2       4      11 ..      30      37 ..      27      40 .. 0.81
   3 ?    0.5   0.0      0.49   5.9e+02      13      18 ..      49      54 ..      47      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.029
                                      E-TTT-- CS
                            zf-HIT 15 kCpkCnt 21
                                      +C++Cn+
  gi|336254712|ref|YP_004597819.1|  3 TCRNCNQ 9 
                                      8****97 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0077
                                      B-TTT-SB CS
                            zf-HIT  4 lCgvCgfp 11
                                      +C+vCg+ 
  gi|336254712|ref|YP_004597819.1| 30 FCQVCGER 37
                                      9*****85 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.49
                                      SEE-TT CS
                            zf-HIT 13 kYkCpk 18
                                       Y Cp+
  gi|336254712|ref|YP_004597819.1| 49 HYECPN 54
                                      69**97 PP

>> Rhodanese_C  Rhodanase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   7.9    0.0083        10      20      57 ..       3      40 ..       1      57 [. 0.77
   2 ?    3.8   0.1     0.065        78      33      43 ..      49      59 ..      40      63 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0083
                       Rhodanese_C 20 kCieCgkpvdelrkrnCanedCnelvlvCeeCaeklkg 57
                                      +C  C++++++  + + + ++C++  l C+ C e++++
  gi|336254712|ref|YP_004597819.1|  3 TCRNCNQSFQTELALELHLDTCQKGQLFCQVCGERFRE 40
                                      7********95558899999*************99887 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.065
                       Rhodanese_C 33 krnCanedCne 43
                                      + +C nedC+ 
  gi|336254712|ref|YP_004597819.1| 49 HYECPNEDCDG 59
                                      899******85 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 ?    5.2   0.1     0.027        32      15      24 ..       2      11 ..       1      13 [. 0.90
   2 ?    3.8   0.2     0.071        84      10      24 ..      26      38 ..      16      40 .. 0.70
   3 ?    2.2   0.1      0.23   2.7e+02      15      21 ..      50      58 ..      44      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.027
                         zf-H2C2_2 15 yeCplCdkaF 24
                                      ++C  C+ +F
  gi|336254712|ref|YP_004597819.1|  2 HTCRNCNQSF 11
                                      89*****999 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.071
                         zf-H2C2_2 10 tgekpyeCplCdkaF 24
                                      +g   + C +C+ +F
  gi|336254712|ref|YP_004597819.1| 26 KG--QLFCQVCGERF 38
                                      44..478*****998 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.23
                         zf-H2C2_2 15 yeCp..lCd 21
                                      yeCp   Cd
  gi|336254712|ref|YP_004597819.1| 50 YECPneDCD 58
                                      9***76676 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1       0.1   1.2e+02      10      21 ..       3      14 ..       1      18 [. 0.84
   2 ?    6.7   0.4    0.0078       9.4      11      25 ..      31      46 ..      23      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.1
                            DUF983 10 aCeaCgldlsha 21
                                      +C++C+++++ +
  gi|336254712|ref|YP_004597819.1|  3 TCRNCNQSFQTE 14
                                      7******99865 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0078
                            DUF983 11 CeaCgldlsharad.d 25
                                      C++Cg++++  +a  d
  gi|336254712|ref|YP_004597819.1| 31 CQVCGERFREGDATqD 46
                                      *********9998756 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.4      0.67     8e+02      20      27 ..       3      10 ..       1      18 [. 0.62
   2 ?   12.7   2.9   9.9e-05      0.12       9      39 ..      19      58 ..      12      61 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.67
                              C1_2 20 nCsaCgrk 27
                                      +C+ C ++
  gi|336254712|ref|YP_004597819.1|  3 TCRNCNQS 10
                                      45555544 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 9.9e-05
                              C1_2  9 lskgedssesfnCsaCgrk.......idgffYsCse..Cd 39
                                      l+ +  ++++  C++Cg+         dg +Y+C+   Cd
  gi|336254712|ref|YP_004597819.1| 19 LHLDTCQKGQLFCQVCGERfregdatQDGWHYECPNedCD 58
                                      55556688999********988665444444***877887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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):              15  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 594.59
//
Query:       gi|336254713|ref|YP_004597820.1|  [L=469]
Description: Fumarate hydratase class II [Halopiger xanaduensis SH-6]
Scores for complete 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-110  369.8   0.3   1.7e-110  369.3   0.3    1.2  1  Lyase_1      Lyase
    9.8e-23   80.3   2.8    1.3e-22   80.0   0.5    2.4  2  FumaraseC_C  Fumarase C C-terminus


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 !  369.3   0.3  1.9e-114  1.7e-110       1     312 []      14     343 ..      14     343 .. 0.99

  Alignments for each domain:
  == domain 1  score: 369.3 bits;  conditional E-value: 1.9e-114
                                       CEEEEETCHHHHHHHHHHHHHGGGHHHHHC.....HHHHHHHHHHHTTSST....HHHHHHHHHHHHHHHCHCHHCG CS
                           Lyase_1   1 grftvkadklmgiftersrenfrlseedik.....alaalkkaaakanvdl....keeaaaiikaldevleegkldd 68 
                                       g+++v+ad+++g++t+r+++nf +s+ + +     al+++kkaaa+an dl    + +a+aii+a+dev+e g++dd
  gi|336254713|ref|YP_004597820.1|  14 GEMQVPADAYWGAQTQRAIQNFPISGITFSrrfvrALGVVKKAAAQANRDLdlieEDVAEAIIEAADEVIE-GQHDD 89 
                                       789**********************8887799999*******************999**************.***** PP

                                       GHHHBSSSSSHHHHHHHHHHHHHH....HHTT.....HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHH CS
                           Lyase_1  69 qfvlkviqegsgtavnmnlnevig....ellg.....ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpale 136
                                       qf+++v+q+gsgt++nmn+nevi+    el+g     ++v+pnd+v++gqSsnD++pTa+++a  +a++++++pal+
  gi|336254713|ref|YP_004597820.1|  90 QFPVDVFQTGSGTSSNMNANEVIAnraaELMGseigdRVVHPNDHVNYGQSSNDVIPTAMHVASLEAVEKDVIPALD 166
                                       ***************************9999999999**************************************** PP

                                       HHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCT CS
                           Lyase_1 137 qLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpe 213
                                       +L++al+ek +ef+dvvk GrThlqdAtPvtlgqe+s+y +++e+ + r+ +++ ++l+el+ ggta+gtgln++pe
  gi|336254713|ref|YP_004597820.1| 167 TLREALEEKEEEFDDVVKTGRTHLQDATPVTLGQEFSGYRTQVEKGLARVDKVR-EHLAELALGGTATGTGLNTHPE 242
                                       ******************************************************.********************** PP

                                       HHHHHHHHHHHHHCST.EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSSEEEEGCCTSSC- CS
                           Lyase_1 214 faelvakelakvtglp.vkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssge.aglvelslaesepGS 288
                                       f  + a+ ++k tg++   a+n fea +++Da+ e++gal+++a sL k+a+Dlrll+sg+  gl+e++ +e++pGS
  gi|336254713|ref|YP_004597820.1| 243 FPSRAAEYITKETGVQfREADNHFEAQAAHDAMSEAHGALRTVAGSLNKIANDLRLLASGPrNGLGEIEQPENQPGS 319
                                       ***************************************************************************** PP

                                       TTSTTTEBTHHHHHHHHHHHHHHH CS
                           Lyase_1 289 SiMPgKvNPvqlElltgvagrvvG 312
                                       SiMPgK NPv +E++++v  +vvG
  gi|336254713|ref|YP_004597820.1| 320 SIMPGKINPVVAEAVNQVHKQVVG 343
                                       **********************98 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.34     3e+03      27      48 ..     167     184 ..     162     186 .. 0.70
   2 !   80.0   0.5   1.4e-26   1.3e-22       2      53 ..     410     461 ..     409     462 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.34
                                       -HHHHHHHTT-.-HHHHHHHT- CS
                       FumaraseC_C  27 tlreavlelgllteeeldelld 48 
                                       tlrea  e+    eee+d++++
  gi|336254713|ref|YP_004597820.1| 167 TLREALEEK----EEEFDDVVK 184
                                       566665554....688888875 PP

  == domain 2  score: 80.0 bits;  conditional E-value: 1.4e-26
                                       GGGGHHHHHHHHHHHHHHHHHHHT--HHHHHHHTT-.-HHHHHHHT-HHHHH CS
                       FumaraseC_C   2 VTaLnphIGYekAakIAkeAlkegktlreavlelgllteeeldelldpekMt 53 
                                       +T Ln hIGY+kA+++Ak+Alke+kt+re+vle+g+l+eee de+ldp kMt
  gi|336254713|ref|YP_004597820.1| 410 ATSLNVHIGYDKASEVAKTALKEDKTVREVVLEKGYLDEEEADEVLDPAKMT 461
                                       7**************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3600.72
//
Query:       gi|336254714|ref|YP_004597821.1|  [L=449]
Description: family 1 extracellular solute-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-20   73.6   2.2    2.9e-20   73.2   2.2    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
      0.008   16.0   7.9      0.019   14.8   7.9    1.7  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   2.2   3.2e-24   2.9e-20       2     273 ..      84     389 ..      83     396 .. 0.79

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 3.2e-24
                                       HHHHHHHH-.TEEEEEEE-...-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG....GSTTHHH CS
                         SBP_bac_8   2 lakefekkt.gvkvnvvta...asndleqklkaalaagtapdidvvwanedalatlaeeglladls....dldnldd 70 
                                       l + f++++ + +vn +++   + + l q++ + l+ g+ p+++  w+ +++la++   g+l d++    d+  l+d
  gi|336254714|ref|YP_004597821.1|  84 LFSTFQEQYpDMEVNEQPIgggGNQNLDQTVANRLQGGDPPSSFAGWP-GANLAQYE--GVLGDIEsnvwDEAGLKD 157
                                       66789999999****99985322248999************9985555.67877765..9******87777777777 PP

                                       -HH..HHHTT--TS.----EEEEEEE-EEEEEHHHHHHS.....---BHHHHHHHHHHHHHH-.....SEGG---G. CS
                         SBP_bac_8  71 ltd..alaavgydgklygvPyasetpyvliynkdlleka....edpktwdellaaakklkgkf.....glpdpasg. 135
                                         +  a++a++ d  + +vP+ s +   l+yn +++e+a    ++ +++d+l +a++++   +     +++  ++g 
  gi|336254714|ref|YP_004597821.1| 158 AHAqeAVEACQSDAGFSAVPIGSHRLNDLFYNVEVIEEAgvdpSSLESVDDLISALDTVSSETdatplAFSLAPWGi 234
                                       522359999999999**********999**********9999999**************655555677667777776 PP

                                       ...GGGGGTHHETTEE---H.......HHH.HHHHHHHHHHH.HTT-..EE-.S..--SSTTTTTSBSEEEE-TTHH CS
                         SBP_bac_8 136 ...wlqaallakdgksldddg.....gkdglkealellkklk.dngk..tyd.tgadavsefanGevaftingswdi 200
                                          w+ ++l   +g++   +      ++ ++  ++e+l ++  +++     + + +++++++ +G++af+ +g+w +
  gi|336254714|ref|YP_004597821.1| 235 lqtWGVTMLSE-HGYDAYMNFiegngDESAVRGTFEKLEEILtNYINsdAASiDFTEVNQDIMSGDAAFIHQGNWVA 310
                                       66666666666.554443332355345666677777777766344442222325689******************** PP

                                       HHHH....-TTTSEEEE.--..S--EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTT CS
                         SBP_bac_8 201 aaaq....kagkklgai.vp..kqgsfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnksaal 270
                                        a+     + g ++ a+ +p   + + + +++++ p +++ +++ ++++l+++ s+++q a+ +  g ip+++++a+
  gi|336254714|ref|YP_004597821.1| 311 GAYIteglEYGSDWDAVrFPgtEDLYTLHMDSFIYPGDNPSPEE-TAAWLRYVGSEDAQVAYNQYKGSIPTRTDVAT 386
                                       ****677666779999999954455******************7.*******************************7 PP

                                       HHH CS
                         SBP_bac_8 271 spe 273
                                       +++
  gi|336254714|ref|YP_004597821.1| 387 DEF 389
                                       653 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   7.9   2.2e-06     0.019       3      25 ..      13      37 ..      13      38 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.2e-06
                        TAT_signal  3 SRRdFLKgs..AAaaAAaalggcaa 25
                                      SRR+ LKg+  A+++A++al+gc++
  gi|336254714|ref|YP_004597821.1| 13 SRRTVLKGAglAGTGALTALAGCTG 37
                                      9********8444449999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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 0.20s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3411.46
//
Query:       gi|336254715|ref|YP_004597822.1|  [L=323]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-20   71.3  17.4    8.4e-20   71.3  17.4    2.3  2  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 !    8.1   3.3   0.00012       2.1     108     184 ..      48     130 ..      46     131 .. 0.81
   2 !   71.3  17.4   4.7e-24   8.4e-20       3     177 ..     116     316 ..     115     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00012
                      BPD_transp_1 108 ppiitglilafggllggavlleflgswpGlgtllleailgydyseis.........nggvlalviavlllnlvadil 175
                                       p +++g+++ ++++++g++ l  +    G+g++  + + + +y++ +           +v+ lv+++++++++  +l
  gi|336254715|ref|YP_004597822.1|  48 PFLLMGFFVYAAIVWNGFLSLTSYS---GFGDPDYTDLGIGNYTALLndpqfwsatRNTVVLLVVFTVACLAIGLVL 121
                                       67899*************8776665...8888888888888888888888888888677888888888888888888 PP

                      BPD_transp_1 176 qrlldprvr 184
                                       + lld+++r
  gi|336254715|ref|YP_004597822.1| 122 ALLLDRKIR 130
                                       888888887 PP

  == domain 2  score: 71.3 bits;  conditional E-value: 4.7e-24
                      BPD_transp_1   3 llGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf...................vilsilghlilpvii 58 
                                        +G+++a  l r+ ++ + +r+++ ++++l ++v a ++ ++                     +l+  +    +vi+
  gi|336254715|ref|YP_004597822.1| 116 AIGLVLAllLDRKIRFERSFRTIYLLPFALSFIVTAQFWRWMYnvnngivnqfigifglgpyNWLGNPKLVLGSVIF 192
                                       68999999999***********************8888777777777777778888899996777666666666*** PP

                      BPD_transp_1  59 llllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswp 135
                                       +l++++ +y+++i+ aalrs+p+d++eaar++Gas+++++++v++P++ p +++  +  + ++l+++ +l+ +++  
  gi|336254715|ref|YP_004597822.1| 193 ALVWQFSGYAMVIYLAALRSIPTDQYEAARVDGASTIRMYWRVIIPQLRPAMVSASVTLVLFALKAFDFLYATFG-- 267
                                       **************************************************************************3.. PP

                      BPD_transp_1 136 G....lgtllleailgydyseis.........nggvlalviavlllnlvadilqr 177
                                       G    l         +  + +           +g+++alv++ l l ++a  l++
  gi|336254715|ref|YP_004597822.1| 268 GyrprL------GADILATFMVResfgksewaYGSAIALVLFALSLAVIAPYLYT 316
                                       233442......3333333322234466787789999999999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2349.80
//
Query:       gi|336254716|ref|YP_004597823.1|  [L=309]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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   56.6  15.8    5.2e-15   55.7  15.8    1.5  1  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 !   55.7  15.8   2.9e-19   5.2e-15       3     171 ..     104     298 ..      82     305 .. 0.85

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.9e-19
                      BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf................vilsilghlilp.viil 59 
                                       ++G+ aa   +  n++++ ++  l+i++  +P+ +++++l+  f                  l + +h+ +  +ii+
  gi|336254716|ref|YP_004597823.1| 104 IFGSTAAyglTLVNWRGQVAVFALFIAGIFVPYQAVIVPLFE-FwnqyvqfgerlaflwgLPLLAEHHATILeLIIT 179
                                       57888999999999*********************9999884.459999999999999994455555655556**** PP

                      BPD_transp_1  60 lllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG 136
                                        + + +p+ +l++r+  ++++ + +eaar++Ga+ w+i+r++vlP+++p+++  +i++f+ +++++++ ++++++  
  gi|336254716|ref|YP_004597823.1| 180 HTAYGIPICTLMFRSQYKTMSWEMIEAARLDGATVWRIYRRIVLPLSVPMFAVVFIFQFTQIWNEFLFSLTIIGSVS 256
                                       *************************************************************************7766 PP

                      BPD_transp_1 137 ........lgtllleailgydyseisnggvlalviavlllnlv 171
                                               + + l e+++g dy++ + +g++++++ +l++ ++
  gi|336254716|ref|YP_004597823.1| 257 dsaasatlILSGLGESLQGTDYPLRM-AGAFITALPTLIVYVL 298
                                       89976666566666777777777777.5555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2349.51
//
Query:       gi|336254717|ref|YP_004597824.1|  [L=398]
Description: glycerol-3-phosphate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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  115.2   0.0    5.1e-33  114.5   0.0    1.4  1  ABC_tran         ABC transporter
    9.6e-10   39.2   0.0    4.2e-09   37.1   0.0    2.2  1  OB_MalK          MalK OB fold domain
    7.1e-07   29.3   0.9    2.4e-05   24.4   0.5    3.0  2  TOBE_2           TOBE domain
    7.1e-07   29.3   0.0      0.013   15.4   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00015   21.3   0.3      0.003   17.0   0.3    2.1  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0011   18.9   0.0     0.0018   18.2   0.0    1.3  1  Rad17            Rad17 P-loop domain
     0.0012   19.2   0.0     0.0036   17.6   0.0    1.7  2  AAA_22           AAA domain
     0.0013   18.6   0.0     0.0029   17.5   0.0    1.5  1  RsgA_GTPase      RsgA GTPase
     0.0018   18.8   1.8     0.0069   16.9   0.2    2.9  2  CysA_C_terminal  CysA C-terminal regulatory domain
     0.0035   17.1   0.0      0.009   15.8   0.0    1.6  2  AAA_15           AAA ATPase domain
     0.0038   17.6   0.5       0.01   16.2   0.5    1.8  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.011   16.0   1.3       0.14   12.5   0.4    2.9  1  TOBE             TOBE domain
      0.015   15.0   0.0      0.036   13.8   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
      0.019   15.4   0.0       0.14   12.6   0.0    2.2  2  AAA              ATPase family associated with various cellul
      0.032   14.8   0.1       0.12   12.8   0.0    1.9  2  AAA_23           AAA domain
      0.049   13.3   0.2       0.21   11.3   0.2    1.9  1  Cytidylate_kin   Cytidylate kinase
      0.055   13.5   0.0       0.11   12.5   0.0    1.4  1  MIT_C            Phospholipase D-like domain at C-terminus of
      0.063   12.8   0.1       0.69    9.4   0.0    2.5  2  AAA_25           AAA domain
      0.063   12.7   0.0        3.5    7.0   0.0    2.2  2  PhoH             PhoH-like protein
       0.16   12.1   0.2       0.33   11.1   0.2    1.8  1  AAA_33           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 !  114.5   0.0   5.6e-36   5.1e-33       2     136 ..      25     167 ..      24     168 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 5.6e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++vs++++ ge +++vG++G+GKSt l+++agl++ t Gei+ld++ +++  ++  ++ i++++q   l p++tvre
  gi|336254717|ref|YP_004597824.1|  25 DEVSIDIEDGEFLVLVGPSGCGKSTTLRMIAGLETITDGEIRLDDRVIND--IPAKDRDIAMVFQSYALYPHMTVRE 99 
                                       789**********************************************9..99999******************** PP

                                       H..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n              e ++++e+a++ +g+ el d++      +LSgGq+qrval ra++++p ++l+DEp 
  gi|336254717|ref|YP_004597824.1| 100 NmsfgleestelsddEITDRVEEAAEMMGIGELLDRKP----GELSGGQQQRVALGRAIVREPAVFLMDEPL 167
                                       *******9999988888888999999999999999998....*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   4.7e-12   4.2e-09       1      53 []     241     293 ..     241     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 4.7e-12
                           OB_MalK   1 GSPaMNflpatveedg..vlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                       G P+MNfl++ v+e    +++ g++++ +++++   a + +   +v+lGiRPE+i
  gi|336254717|ref|YP_004597824.1| 241 GEPSMNFLDVDVRETAdgATLVGEHLEYAVSDDI--ADSIEGRSDVVLGIRPEDI 293
                                       99**********9777889999999999999998..******************8 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       8.3   7.4e+03      51      65 ..     196     211 ..     185     213 .. 0.64
   2 !   24.4   0.5   2.7e-08   2.4e-05       1      76 []     286     375 ..     286     375 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.3
                            TOBE_2  51 nadr.dsalapGdtVe 65 
                                       ++++  +a++ Gd+++
  gi|336254717|ref|YP_004597824.1| 196 VTHDqTEAMTMGDRIA 211
                                       3333246889999876 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2.7e-08
                            TOBE_2   1 laiRPEklrla....aagganglsGtVedveylGsstryvvelaggqlvvv.rqpnadr.d..sala......pGdt 63 
                                       l+iRPE++ ++     ++g++ ++++V+ ve  G++  +++ l++ ++    +  ++dr    ++++       Gd+
  gi|336254717|ref|YP_004597824.1| 286 LGIRPEDIDIErdegRQAGGHEVPAQVSVVEPTGDENIVYLVLGNDEFGDDtELLDTDReTiiATIDgmstvnSGDR 362
                                       79*********9774333346*******************9998865543322222222122233334444449999 PP

                            TOBE_2  64 Velswdpddavvl 76 
                                       V  +++ d+++++
  gi|336254717|ref|YP_004597824.1| 363 VVAHIPEDAIHLF 375
                                       9999999999887 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 !   15.4   0.0   1.4e-05     0.013       1      63 [.      36      89 ..      36     122 .. 0.67
   2 !   12.2   0.0   0.00013      0.12     231     298 ..     134     199 ..     103     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie 63
                                      + vl+Gp g+GKS+ L+ + +l          t++++ +   + +++ ++ +d +i+++f+ +
  gi|336254717|ref|YP_004597824.1| 36 FLVLVGPSGCGKSTTLRMIAGLE---------TITDGEIRLDDRVINDIPAKDRDIAMVFQSY 89
                                      579******************93.........4444444455556666666666666666655 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                       ++ + elS G+++  al  a+ r +   +++l DEp ++L+ kl +   + l +l++  ++  + +TH+
  gi|336254717|ref|YP_004597824.1| 134 DRKPGELSGGQQQRVALGRAIVREP---AVFLMDEPLSNLDAKLRAQMRTELQQLQEeLDTATVYVTHD 199
                                       566789999999999*******999...*********************99977777788999999998 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 !   17.0   0.3   3.4e-06     0.003      24     206 ..      34     205 ..      23     218 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-06
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsis 100
                                        +f ++vGp G+GKs  l  i    G ++ +    +  +++i+     +  + a v   +    + ++ e+ ++ ++
  gi|336254717|ref|YP_004597824.1|  34 GEFLVLVGPSGCGKSTTLRMI---AGLETITDGEIRLDDRVIND-IPAKDRDIAMVFQSYALYPHMTVRENMSFGLE 106
                                       468899999999999999888...45544433333333567776.66666777777777666666656666666666 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                        + + +++   +i ++  + +e++ + e  + ++ +LSgG+++ val    Ai  v+  +++l+De  ++LD+k ++
  gi|336254717|ref|YP_004597824.1| 107 ESTELSDD---EITDRVEEAAEMMGIGELLDRKPGELSGGQQQRVALG--RAI--VREPAVFLMDEPLSNLDAKLRA 176
                                       66666555...555555555555555555566788*******977664..444..5677899*************** PP

                                       HHHHHHHHHCTTSEEEEE-SSHHHCCC-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 178 kvaellkeksknaQfivislreemlekad 206
                                       ++ + l++ +++     + ++++++e + 
  gi|336254717|ref|YP_004597824.1| 177 QMRTELQQLQEELDTATVYVTHDQTEAMT 205
                                       ***99999999876666655555555554 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     2e-06    0.0018      45      67 ..      34      56 ..      22      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-06
                             Rad17 45 kriLLisGPsGCgkstvvkvLsk 67
                                       + L++ GPsGCgkst++++++ 
  gi|336254717|ref|YP_004597824.1| 34 GEFLVLVGPSGCGKSTTLRMIAG 56
                                      56899**************9875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     4e-06    0.0036       4      27 ..      33      56 ..      30      89 .. 0.86
   2 ?   -2.3   0.0       5.6   5.1e+03      61     112 ..     179     182 ..     139     206 .. 0.51

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlle 27
                                      +  +lv++G+sG+GK+t+lr+++ 
  gi|336254717|ref|YP_004597824.1| 33 DGEFLVLVGPSGCGKSTTLRMIAG 56
                                      5789****************9875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.6
                            AAA_22  61 lralglelkaerlsseellealeqalraravielliiDEaqhlrseealeeL 112
                                         +                                                L
  gi|336254717|ref|YP_004597824.1| 179 RTE------------------------------------------------L 182
                                       111................................................1 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.3e-06    0.0029      90     132 ..      24      67 ..       6      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.3e-06
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S---- CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelktgevse 132
                                       ++e++  ++d ++ vlvG+SG GKSt + ++++ +++  ge++ 
  gi|336254717|ref|YP_004597824.1|  24 VDEVSIDIEDgEFLVLVGPSGCGKSTTLRMIAGLETITDGEIRL 67 
                                       5667777777799*******************988888888875 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.4   3.9e+03       6      22 ..      59      76 ..      59      82 .. 0.72
   2 !   16.9   0.2   7.6e-06    0.0069       9      43 .]     257     295 ..     246     295 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.4
                   CysA_C_terminal  6 rvedGklriGglalp.vP 22
                                      ++ dG +r+++  +  +P
  gi|336254717|ref|YP_004597824.1| 59 TITDGEIRLDDRVINdIP 76
                                      578999999985555455 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 7.6e-06
                   CysA_C_terminal   9 dGklriGg.lalpvP..elaga.dg.qevvayVRPhDlei 43 
                                       dG   +G+ l+ +v    ++ + +g ++vv+++RP+D++i
  gi|336254717|ref|YP_004597824.1| 257 DGATLVGEhLEYAVSddIAD-SiEGrSDVVLGIRPEDIDI 295
                                       55555566566666654223.245559***********98 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     1e-05     0.009      15      48 ..      25      59 ..      23     134 .. 0.76
   2 ?   -1.6   0.0       1.9   1.7e+03     323     365 ..     157     199 ..     146     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFln 48
                                      ++v+id+++  + vl+G+ ++GKS+ l+++  + +
  gi|336254717|ref|YP_004597824.1| 25 DEVSIDIEDGeFLVLVGPSGCGKSTTLRMIAGLET 59
                                      57999*99999******************965544 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +++++l++EP  +L  ++  ++   l+ l ++ +t +++ TH 
  gi|336254717|ref|YP_004597824.1| 157 EPAVFLMDEPLSNLDAKLRAQMRTELQQLQEELDTATVYVTHD 199
                                       5788899999999999999999999999999999999999996 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.5   1.1e-05      0.01      23      45 ..      33      55 ..      23     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                      ++e ++l+G+sG+GKs+ +r+++
  gi|336254717|ref|YP_004597824.1| 33 DGEFLVLVGPSGCGKSTTLRMIA 55
                                      44899***************997 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   0.00015      0.14       6      64 .]     307     374 ..     303     374 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                              TOBE   6 qlpgtVvvveplgseveVrvdlggga.............tLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                        +p+ V+vvep+g e  V++ lg  +             t++A++++ s ++     G++V+a i   ++hl
  gi|336254717|ref|YP_004597824.1| 307 EVPAQVSVVEPTGDENIVYLVLGNDEfgddtelldtdreTIIATIDGMSTVN----SGDRVVAHIPEDAIHL 374
                                       5899****************9999999999999999999*************....*******997777775 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 ?   13.8   0.0     4e-05     0.036      13      39 ..      25      51 ..      22      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      d+ +i+i+  ++ +l+GpsG GKST l
  gi|336254717|ref|YP_004597824.1| 25 DEVSIDIEDGEFLVLVGPSGCGKSTTL 51
                                      55678887555999***********75 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 ?   12.6   0.0   0.00016      0.14       2      21 ..      38      57 ..      37      93 .. 0.76
   2 ?   -0.2   0.0       1.4   1.2e+03      57      97 ..     155     193 ..     119     210 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                                      EEESSTTSSHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavake 21
                                      +l+Gp G+GK+++ + +a  
  gi|336254717|ref|YP_004597824.1| 38 VLVGPSGCGKSTTLRMIAGL 57
                                      79***************975 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                                       S.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTT CS
                               AAA  57 a.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvk 97 
                                         +p ++++DE  +   ++    + + ++ ++qL +eld  +
  gi|336254717|ref|YP_004597824.1| 155 VrEPAVFLMDEPLSNLDAK---LRAQMRTELQQLQEELDTAT 193
                                       2357888888854444444...33345555666666666554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014      0.12      12      39 ..      26      54 ..      20      87 .. 0.86
   2 ?   -1.0   0.0       2.4   2.1e+03     179     193 ..     176     190 ..      98     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                            AAA_23 12 dqeidFsk.gltlItGpNGaGKTTildAi 39
                                      +++id ++  + +++Gp G+GK+T l+ i
  gi|336254717|ref|YP_004597824.1| 26 EVSIDIEDgEFLVLVGPSGCGKSTTLRMI 54
                                      56789966156689***********9987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.4
                            AAA_23 179 kekekeleeleeele 193
                                        + + el++l+eel 
  gi|336254717|ref|YP_004597824.1| 176 AQMRTELQQLQEELD 190
                                       233445555555554 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00024      0.21       4     154 ..      40     188 ..      37     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                                       E-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHHHTT--TT-HHHHHHHHHT--EEEEEEEEEETTEE-TTGG CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyldtgalYRalalaalrrkvdlldeaalvelakevelsfeaekvllngedveeel 80 
                                        GP+g GKs+  r++a   gl+ +  g++ R    ++ +   +  d+a +++  +        e++ + g + ++el
  gi|336254717|ref|YP_004597824.1|  40 VGPSGCGKSTTLRMIA---GLETITDGEI-RLDDRVINDIPAKDRDIAMVFQSYALYPHMTVRENMSF-GLEESTEL 111
                                       59*********99999...7889999998.66666666666666777777666555444444444444.5556889* PP

                                       GSHHHHHHHHHHTTSHHHHHHHHHHHHTT-B.SSBEEEEESSII...IIISTT-SEEEEEE--HHHHHHHHHHHHHH CS
                    Cytidylate_kin  81 rsdevekavSavaaipavRailvkklrelvk.karvvveGRDig...tvvfpdaelKifldAsveeRakRRlkqlka 153
                                       + de++++v + a +  + + l +k  el   +++ v+ GR i    +v + d +l   ldA+ ++  +  l+ql++
  gi|336254717|ref|YP_004597824.1| 112 SDDEITDRVEEAAEMMGIGELLDRKPGELSGgQQQRVALGRAIVrepAVFLMDEPL-SNLDAKLRAQMRTELQQLQE 187
                                       **************************9999889999999**996222344445554.56888776666666667666 PP

                                       T CS
                    Cytidylate_kin 154 k 154
                                       +
  gi|336254717|ref|YP_004597824.1| 188 E 188
                                       5 PP

>> MIT_C  Phospholipase D-like domain at C-terminus of MIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.11      58     121 ..     171     236 ..     159     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                             MIT_C  58 deeeedeqkenleelkesleklgielevef..sstihdreirldngwiikigrGLdifkkseskfs 121
                                       d++ +++ +++l++l+e+l +  + ++ +     t+ dr  +l++g + ++g  L+ ++++ ++f 
  gi|336254717|ref|YP_004597824.1| 171 DAKLRAQMRTELQQLQEELDTATVYVTHDQteAMTMGDRIAILNDGELQQVGTPLECYHEPANQFV 236
                                       5566788999***********9999999884456889***********************999996 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00077      0.69      30      50 ..      31      51 ..      23      57 .. 0.89
   2 ?   -0.8   0.0       1.1   9.6e+02     164     188 ..     173     198 ..     158     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00077
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +  ge+ +l+G++g+GK+t +
  gi|336254717|ref|YP_004597824.1| 31 IEDGEFLVLVGPSGCGKSTTL 51
                                      56799*************965 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                            AAA_25 164 dv.galvealeriarrtgaavllvhH 188
                                       +  +++ + l++++++++ a++ v H
  gi|336254717|ref|YP_004597824.1| 173 KLrAQMRTELQQLQEELDTATVYVTH 198
                                       33488889999999999988888888 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0039       3.5      16      50 ..      31      66 ..      24      82 .. 0.85
   2 ?    3.3   0.0     0.053        47      50     108 ..     151     213 ..     141     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0039
                                      HHH-SEEEEE--TTSST.THHHHHHHHHHHHTTS-S CS
                              PhoH 16 lkkndivfaiGpaGtGK.tylavalavealkkkkvk 50
                                      +++ ++++ +Gp+G+GK t l + +++e +++++++
  gi|336254717|ref|YP_004597824.1| 31 IEDGEFLVLVGPSGCGKsTTLRMIAGLETITDGEIR 66
                                      56778999*********6689999999999998874 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.053
                                       SEEEEEE-S--T.T----SS---------TTTHHHHHHHTTTS...-TTCHHHHHHTTSEEEE CS
                              PhoH  50 kriiltrpavea.geelGflpgdleekvdpylrplydaLkdll...gaekvekllekgkieva 108
                                        r i+  pav   +e l  l+ +l+ +++  l+ l ++L++ +    ++++e ++  ++i ++
  gi|336254717|ref|YP_004597824.1| 151 GRAIVREPAVFLmDEPLSNLDAKLRAQMRTELQQLQEELDTATvyvTHDQTEAMTMGDRIAIL 213
                                       4778888998445***********************999986544477888888777777765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00037      0.33       2      20 ..      37      55 ..      36     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                            AAA_33  2 vllvGlpGsGKstlaerll 20
                                      ++lvG++G+GKst ++ ++
  gi|336254717|ref|YP_004597824.1| 37 LVLVGPSGCGKSTTLRMIA 55
                                      589**********999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      698  (0.0389313); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.38
# Mc/sec: 3133.94
//
Query:       gi|336254718|ref|YP_004597825.1|  [L=246]
Description: hypothetical protein Halxa_3334 [Halopiger xanaduensis SH-6]
Scores for complete 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   31.4  12.8    1.6e-07   31.4  12.8    2.4  2  DUF4013   Protein of unknown function (DUF4013)


Domain annotation for each model (and alignments):
>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   8.0       0.2   3.6e+03      50      99 ..      38      64 ..       6      79 .. 0.51
   2 !   31.4  12.8   8.7e-12   1.6e-07       8     166 ..      61     203 ..      56     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.2
                           DUF4013 50 afvvslvYl..lipliialltllvalaslaagdsaagallvlallglllall 99
                                      ++vv+l Y+  l+pl++                         +l+ +lla++
  gi|336254718|ref|YP_004597825.1| 38 LLVVGLRYAaaLVPLVV-------------------------GLVPALLAVV 64
                                      33333334444444444.........................1111111111 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 8.7e-12
                           DUF4013   8 iaivlslvllGYlvrvlrdtirgddelPefddwgkllvdGlkafvvslvYllipliialltllvalaslaagdsaag 84 
                                       +a+v++++llG +   l      d +  ++  +++ll+ Gl a+++s+v +l p i      l+al+++  +ds+++
  gi|336254718|ref|YP_004597825.1|  61 LAVVGLVLLLGTTAVLLA-----DPAQRDWPSVRGLLRPGLAALALSIV-GLAPPIG-----LLALSAMQTADSGTL 126
                                       455555556666555555.....3346689899****************.8899999.....778888888888887 PP

                           DUF4013  85 allvlallglllalllvllllllfglllpvalarfartgslsaafnfkeilklikkkigkyiialilllvigivlsl 161
                                        +++++l  +  +ll  l++ll+ ++++pva+a+ + +g+l+aa + + ++ ++++   +y++ +i+ + + ++l+ 
  gi|336254718|ref|YP_004597825.1| 127 EGGAGVLTLVSTTLL--LFALLACAYAYPVAVAASVSNGRLRAAADTDVVMPVLAD--ATYLLRWIVGFSL-VLLGT 198
                                       777777777777666..5566669****************************9966..48*******9997.55555 PP

                           DUF4013 162 laill 166
                                       +++l+
  gi|336254718|ref|YP_004597825.1| 199 WCALM 203
                                       55554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1878.49
//
Query:       gi|336254719|ref|YP_004597826.1|  [L=570]
Description: hypothetical protein Halxa_3335 [Halopiger xanaduensis SH-6]
Scores for complete 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-51  172.8   3.3    1.1e-20   73.6   0.3    3.3  3  bPH_2        Bacterial PH domain
    4.6e-06   26.6   0.0     0.0096   16.0   0.0    3.1  3  bPH_4        Bacterial PH domain
     0.0078   16.5   0.0        4.3    7.8   0.0    2.3  2  bPH_3        Bacterial PH domain
  ------ inclusion threshold ------
      0.014   15.5   0.0        2.9    8.0   0.0    2.6  3  bPH_5        Bacterial PH domain
       0.36   11.4   2.9       0.73   10.4   2.9    1.4  1  NuDC         Nuclear distribution C domain
        1.3    9.0   7.7        2.6    8.0   7.7    1.5  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)


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 !   73.6   0.3   3.6e-24   1.1e-20       1      80 []      65     144 ..      65     144 .. 0.98
   2 !   31.9   0.0   3.8e-11   1.1e-07      11      63 ..     326     385 ..     316     400 .. 0.84
   3 !   66.2   0.5   7.3e-22   2.2e-18       1      76 [.     464     542 ..     464     545 .. 0.88

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 3.6e-24
                             bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeela 77 
                                       y++++y+it+++v v sG++ r+ ++ip+ rIq+v+++q+++qr+lg++ ++ietagg++ e++l  +  ++a++l+
  gi|336254719|ref|YP_004597826.1|  65 YYRFGYQITEDTVDVASGVFARRSREIPYGRIQNVDIRQGVVQRLLGVAVVSIETAGGGTTEATLSVVGEDEADRLQ 141
                                       899*************************************************************************9 PP

                             bPH_2  78 ell 80 
                                       + +
  gi|336254719|ref|YP_004597826.1| 142 AEI 144
                                       865 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 3.8e-11
                             bPH_2  11 rrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsrae.......v 63 
                                       + +v  +G+l+r    ip e++q+v++++++lqr+lg++ + +etag + ++       v
  gi|336254719|ref|YP_004597826.1| 326 DDFVYDRGLLQRYSGSIPAEKVQSVTVTDNPLQRLLGYAGLWVETAGYGPDSdagsqsaV 385
                                       5678899****************************************9976667766444 PP

  == domain 3  score: 66.2 bits;  conditional E-value: 7.3e-22
                             bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsrae.....velplrsvpd 72 
                                       y +++y + d+++v+rsG+++r+t++ip+ rIq+vs+++s++qrrlgl+++v++ta++   +      ++ ++ ++d
  gi|336254719|ref|YP_004597826.1| 464 YTHLGYFVGDDHLVIRSGFWRRRTTVIPYYRIQTVSTRRSIFQRRLGLASLVVDTASSR--SfvwssSTIYDIALED 538
                                       67889****************************************************99..3346667777777777 PP

                             bPH_2  73 aeel 76 
                                       a+++
  gi|336254719|ref|YP_004597826.1| 539 ARDV 542
                                       7765 PP

>> bPH_4  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0037        11       2      32 ..      69     102 ..      68     127 .. 0.80
   2 ?   -0.0   0.0      0.32   9.6e+02      18      37 ..     339     358 ..     327     371 .. 0.85
   3 !   16.0   0.0   3.2e-06    0.0096       2      42 ..     468     510 ..     467     527 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0037
                             bPH_4   2 kYeitegvLliksG.firkk..IpiedIkkirkt 32 
                                        Y+ite++  + sG f r++  Ip+ +I+++   
  gi|336254719|ref|YP_004597826.1|  69 GYQITEDTVDVASGvFARRSreIPYGRIQNVDIR 102
                                       5*************88887677******999755 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.32
                             bPH_4  18 rkkIpiedIkkirktkspls 37 
                                       +++Ip e++++++ t +pl 
  gi|336254719|ref|YP_004597826.1| 339 SGSIPAEKVQSVTVTDNPLQ 358
                                       568**************986 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 3.2e-06
                             bPH_4   2 kYeitegvLliksGfirkk...IpiedIkkirktksplsspals 42 
                                        Y + +++L+i+sGf+r++   Ip+ +I++++  +s++ +  l 
  gi|336254719|ref|YP_004597826.1| 468 GYFVGDDHLVIRSGFWRRRttvIPYYRIQTVSTRRSIFQR-RLG 510
                                       58899***********987789**********99977654.444 PP

>> bPH_3  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0014       4.3      42      75 ..      85     124 ..      79     146 .. 0.68
   2 !    6.3   0.0    0.0042        13      34      67 ..     477     509 ..     468     517 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0014
                             bPH_3  42 gkdfeeipYksIksvdlkkgl.....lgakitlet.sgkt 75 
                                        ++++eipY  I+ vd+ +g+       a +++et +g t
  gi|336254719|ref|YP_004597826.1|  85 ARRSREIPYGRIQNVDIRQGVvqrllGVAVVSIETaGGGT 124
                                       67899***************97777655556777764444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0042
                             bPH_3  34 fldpkmfggkdfeeipYksIksvdlkkgllgaki 67 
                                       +++++ f ++++++ipY  I+ v++ + +++ ++
  gi|336254719|ref|YP_004597826.1| 477 VIRSG-FWRRRTTVIPYYRIQTVSTRRSIFQRRL 509
                                       45566.8899*****************9998775 PP

>> bPH_5  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.011        32       3      44 ..      70     112 ..      68     119 .. 0.78
   2 ?   -3.7   0.0       4.3   1.3e+04      20      34 ..     341     355 ..     338     364 .. 0.78
   3 ?    8.0   0.0   0.00097       2.9       2      34 ..     468     503 ..     467     515 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.011
                             bPH_5   3 yildeeglvIrwifg...keeIplseIeavrvsegvikgvrlfgt 44 
                                       y ++e+++ +++++     +eIp+  I++v   +gv+  +rl g+
  gi|336254719|ref|YP_004597826.1|  70 YQITEDTVDVASGVFarrSREIPYGRIQNVDIRQGVV--QRLLGV 112
                                       77888888885544337789**************997..666665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.3
                             bPH_5  20 eIplseIeavrvseg 34 
                                       +Ip +++++v v ++
  gi|336254719|ref|YP_004597826.1| 341 SIPAEKVQSVTVTDN 355
                                       699999999998776 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00097
                             bPH_5   2 kyildeeglvIrwifg...keeIplseIeavrvseg 34 
                                        y++ +++lvIr++f    + +Ip+  I+ v+   +
  gi|336254719|ref|YP_004597826.1| 468 GYFVGDDHLVIRSGFWrrrTTVIPYYRIQTVSTRRS 503
                                       699********99987788999********987655 PP

>> NuDC  Nuclear distribution C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.9   0.00024      0.73      15      56 ..     135     176 ..     126     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                              NuDC  15 eEAekLQlElDqkKkkeekekqakaesaaekkkdkaeeekse 56 
                                       +EA++LQ+E+ ++    ++  q +++++a ++  +++ e+++
  gi|336254719|ref|YP_004597826.1| 135 DEADRLQAEIRRRTAGVKERRQEQDREHAPESDANVDPESQP 176
                                       7**********9988877777777777777666555533332 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   7.7   0.00087       2.6      69     116 ..     156     203 ..     113     223 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00087
                       Trypan_PARP  69 pepepepepepetepeeepepepepepepepepepepepepepgaatl 116
                                        e + e  pe +++ ++e++p++ep+ +p ++ +  +  e +p a t 
  gi|336254719|ref|YP_004597826.1| 156 QEQDREHAPESDANVDPESQPDAEPDRQPAAGTDGPAGAETDPDAVTA 203
                                       222223333333333333333333333333333333344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 4286.12
//
Query:       gi|336254720|ref|YP_004597827.1|  [L=153]
Description: hypothetical protein Halxa_3336 [Halopiger xanaduensis SH-6]
Scores for 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-14   52.4   0.0    6.4e-14   51.9   0.0    1.2  1  bPH_2            Bacterial PH domain
  ------ inclusion threshold ------
      0.041   13.6   2.7      0.057   13.2   2.1    1.5  2  Mntp             Putative manganese efflux pump
        0.9    9.8   8.9          7    6.9   6.2    2.3  2  Phage_r1t_holin  Putative lactococcus lactis phage r1t holin


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 !   51.9   0.0   1.1e-17   6.4e-14       1      80 []      61     140 ..      61     140 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.1e-17
                             bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeela 77 
                                       y+ ++++++ + +++ +G+++ +++ +p+ r+q+v+++ ++++r +gl ++v++tag   a+v++p++  ++a+el+
  gi|336254720|ref|YP_004597827.1|  61 YQVWKFELQADALYLERGVVTFVETAVPFVRVQHVDTQFGPVERVFGLSSVVVYTAGTRNADVRIPGLTPDRARELQ 137
                                       66788***********************************************************************9 PP

                             bPH_2  78 ell 80 
                                       ++l
  gi|336254720|ref|YP_004597827.1| 138 DTL 140
                                       986 PP

>> Mntp  Putative manganese efflux pump
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.1   9.5e-06     0.057      89     133 ..      20      65 ..      17      73 .. 0.87
   2 ?   -2.3   0.0      0.55   3.3e+03     111     139 ..      78     106 ..      66     116 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.5e-06
                              Mntp  89 AlavGlsLall.kvnillavlliGlvtlvlsllGlllGrklgsllg 133
                                       A++vG++La + ++ + +++++iG v++++ +lG+  + +l ++++
  gi|336254720|ref|YP_004597827.1|  20 AVVVGIGLAAVdQLLVDVPAAAIGGVAALILVLGVAYAVRLYQVWK 65 
                                       899********66677899****************99998888665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.55
                              Mntp 111 GlvtlvlsllGlllGrklgsllgkkaeil 139
                                       G+vt+v +++ ++  +++ + +g    ++
  gi|336254720|ref|YP_004597827.1|  78 GVVTFVETAVPFVRVQHVDTQFGPVERVF 106
                                       77888888777777777777666555555 PP

>> Phage_r1t_holin  Putative lactococcus lactis phage r1t holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.2    0.0012         7      21      54 ..      25      57 ..      17      62 .. 0.88
   2 ?    3.1   0.0     0.019   1.1e+02       9      24 ..      75      90 ..      71      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0012
                   Phage_r1t_holin 21 lgllgagatglldvdwaaaasvaalaAvvSvltS 54
                                      +gl +++++ l+dv +aa+++vaal  v+ v+ +
  gi|336254720|ref|YP_004597827.1| 25 IGLAAVDQL-LVDVPAAAIGGVAALILVLGVAYA 57
                                      78999****.***************999999766 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.019
                   Phage_r1t_holin  9 aERavkTaaqallgll 24
                                       ER v T++++++  +
  gi|336254720|ref|YP_004597827.1| 75 LERGVVTFVETAVPFV 90
                                      59*********99655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1294.22
//
Query:       gi|336254721|ref|YP_004597828.1|  [L=84]
Description: BolA family protein [Halopiger xanaduensis SH-6]
Scores for 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-19   69.5   0.3    2.7e-19   69.2   0.3    1.1  1  BolA      BolA-like protein


Domain annotation for each model (and alignments):
>> BolA  BolA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.3   1.5e-23   2.7e-19      16      76 .]      20      78 ..       6      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.5e-23
                              BolA 16 ShkhaghaeaggetHFkvvivseaFegkslvarhRlvyalLkeelakgiHALslktktpee 76
                                      +  ha+   ++ e H+  ++vs+aFeg++lv++h+ vy++L+++++++iHAL+l+t+tpee
  gi|336254721|ref|YP_004597828.1| 20 TVTHARD--EHDEDHLAATVVSPAFEGLPLVQQHQRVYDALDDHMTTDIHALELSTYTPEE 78
                                      4456666..889***********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 722.02
//
Query:       gi|336254722|ref|YP_004597829.1|  [L=112]
Description: nitrogen-fixing NifU domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-10   41.3   0.0    1.6e-10   41.0   0.0    1.3  1  NifU      NifU-like domain


Domain annotation for each model (and alignments):
>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   8.9e-15   1.6e-10      11      66 ..      31      87 ..      16      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 8.9e-15
                                      GG--GG--EEEE..EEEETTEEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EE CS
                              NifU 11 PaLasdGGdiel..vdvdegvVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeV 66
                                      P+++ +GG+ ++  vd++e++V + l+GaCsgC  s +t+ ++i+++L +e++ + +V
  gi|336254722|ref|YP_004597829.1| 31 PQIELHGGESTIteVDLEERRVGINLTGACSGCGVSPMTT-QAIQRRLPDEIDAIDAV 87
                                      9999****966622666777********************.9**********999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 930.43
//
Query:       gi|336254723|ref|YP_004597830.1|  [L=178]
Description: hypothetical protein Halxa_3339 [Halopiger xanaduensis SH-6]
Scores for 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   10.2   5.1        4.2    8.2   0.1    2.9  3  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00024       4.2      13      41 ..      31      59 ..      28      93 .. 0.77
   2 ?   -0.9   0.1      0.16   2.8e+03      32      43 ..     122     133 ..     116     143 .. 0.66
   3 ?    3.0   0.2    0.0099   1.8e+02      19      36 ..     153     170 ..     147     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00024
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     PSK_trans_fac 13 lareLarltgeskteAvrrAleerlerlr 41
                                       ar La+   e  t+A+ +Al+++ e++ 
  gi|336254723|ref|YP_004597830.1| 31 AARFLAADGLEGDTDAIATALRRYAEEVP 59
                                      678888888899***********999875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.16
                                       XXXXXXXXXXXX CS
                     PSK_trans_fac  32 Aleerlerlrre 43 
                                       Al+++lerl  e
  gi|336254723|ref|YP_004597830.1| 122 ALAAALERLALE 133
                                       777777777644 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.0099
                                       XXXXXXXXXXXXXXXXXX CS
                     PSK_trans_fac  19 rltgeskteAvrrAleer 36 
                                       r+ g++  +Av++Ale  
  gi|336254723|ref|YP_004597830.1| 153 RIEGANAVRAVEAALEGV 170
                                       678999*********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1356.01
//
Query:       gi|336254724|ref|YP_004597831.1|  [L=651]
Description: histidine kinase [Halopiger xanaduensis SH-6]
Scores for complete 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-52  177.4   1.3    5.6e-52  175.8   0.1    2.4  2  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 
    3.7e-26   91.8   0.0    5.8e-26   91.2   0.0    1.3  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    5.6e-11   42.3   2.5    1.1e-10   41.4   0.2    2.6  2  HisKA            His Kinase A (phospho-acceptor) domain
    6.5e-05   22.4   0.0    0.00013   21.4   0.0    1.4  1  ATPase           KaiC
     0.0002   21.6   0.1    0.00083   19.7   0.1    2.1  1  GAF_2            GAF domain
     0.0038   17.6   0.0      0.029   14.7   0.0    2.3  1  GAF_3            GAF domain
     0.0072   16.2   0.0      0.017   15.0   0.0    1.6  1  HATPase_c_5      GHKL domain
  ------ inclusion threshold ------
      0.011   16.3   0.0      0.044   14.4   0.0    2.1  1  GAF              GAF domain
       0.12   12.6   0.9         35    4.6   0.5    3.0  2  PEP-utilisers_N  PEP-utilising enzyme, N-terminal


Domain annotation for each model (and alignments):
>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.8   0.1   2.8e-55   5.6e-52       1     161 []      42     201 ..      42     201 .. 0.99
   2 ?   -1.4   0.0      0.94   1.9e+03      62      95 ..     525     553 ..     456     563 .. 0.61

  Alignments for each domain:
  == domain 1  score: 175.8 bits;  conditional E-value: 2.8e-55
                              MEDS   1 dHvclfyedeeellealvpfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrggg 77 
                                       dH++l+y+ ++++++a+vpf+++gl+rge+++yv++++++d++r alr++g+dv+aa++sg+l + + ++tyl++g+
  gi|336254724|ref|YP_004597831.1|  42 DHFALIYDAPADQFAAVVPFLRQGLERGEQCVYVTDKDSVDAVRTALRDGGIDVEAAVASGSLVVETFQNTYLKNGA 118
                                       8**************************************************************************** PP

                              MEDS  78 fdpermlealrralakaladgyaglrvigemtwalrspaereelleyEallneliadepvtalClYdrrrfsaevla 154
                                       fd ++m++++++++++  a+ y+g+r+++em+w l+s+   ee ++yE+++n+l++de+++a+C+Ydr+rf++ev++
  gi|336254724|ref|YP_004597831.1| 119 FDVDEMISFYADVIDEVNAE-YEGFRLAAEMSWILESDVAIEETMTYESKVNDLFDDEDAVAVCQYDRNRFPPEVIR 194
                                       ****************7766.******************************************************** PP

                              MEDS 155 dvlrtHp 161
                                       dv+r+Hp
  gi|336254724|ref|YP_004597831.1| 195 DVVRVHP 201
                                       ******8 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.94
                              MEDS  62 qleildaeetylrgggfdpermlealrralakal 95 
                                       +l++ d     l+  + dpe+  + +++ l++al
  gi|336254724|ref|YP_004597831.1| 525 DLTVGD-----LPRVTGDPEQLRQLFQNLLDNAL 553
                                       222222.....66667777777777777777776 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 !   91.2   0.0   2.9e-29   5.8e-26       1     110 [.     536     647 ..     536     649 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 2.9e-29
                                       EHHHHHHHHHHHHHHHHHHHHS.TTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSS CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfat.kageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggt 74 
                                       gd+++Lrq+++nl+dNa+ +a+ + ++i+ + ++++  d  +isv+D GiGip+++++++f+ f++  +++ ++ gt
  gi|336254724|ref|YP_004597831.1| 536 GDPEQLRQLFQNLLDNALTYAGdEPPRIDTTAERTSdgDGWTISVRDEGIGIPVAEQDRIFDLFDR-LHSREEYAGT 611
                                       7999****************6667777777777633579***************************.889999**** PP

                                       SHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  75 GlGlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       G+Gl++++++ve++ G i+v+sepg+G tf +tlp 
  gi|336254724|ref|YP_004597831.1| 612 GIGLALCQRIVERHAGAIRVDSEPGEGATFSVTLPA 647
                                       **********************************96 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.2   5.5e-14   1.1e-10       2      66 ..     429     494 ..     428     495 .. 0.95
   2 ?   -0.9   0.1      0.85   1.7e+03      40      60 ..     516     550 ..     504     554 .. 0.64

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 5.5e-14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC...T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre.gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l++f+   +H++  PL  ++ ++++++r+ ++l+ e +eyle ++++a+r++++++ lL++sr ++
  gi|336254724|ref|YP_004597831.1| 429 LEQFAYAASHDMQEPLRMVSSYLQLIERRdEDLSAETREYLEFAVDGAERMRAMIDGLLQYSRVQS 494
                                       789***********************888899******************************9876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.85
                                       HHHHHHHHHH..............HHHHHHHHHHH CS
                             HisKA  40 yletiesear..............rldhlvedlLd 60 
                                       +l+ +e  a+              +l++l ++lLd
  gi|336254724|ref|YP_004597831.1| 516 QLRLAETDADltvgdlprvtgdpeQLRQLFQNLLD 550
                                       45555555555555555556666688888888877 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   6.7e-08   0.00013      39     121 ..      61     138 ..      57     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.7e-08
                            ATPase  39 FlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaeesaeekdkedleelieelaeai 115
                                       Fl +g+e+ ge++v+vt   +  ++r   +  G+d+e+  ++g+l++    +++     +++ +d++e+i+  a++i
  gi|336254724|ref|YP_004597831.1|  61 FLRQGLER-GEQCVYVTDKDSVDAVRTALRDGGIDVEAAVASGSLVVETF-QNTYL---KNGAFDVDEMISFYADVI 132
                                       999**999.**********************************9987655.55444...4789************** PP

                            ATPase 116 keikak 121
                                       +e++a+
  gi|336254724|ref|YP_004597831.1| 133 DEVNAE 138
                                       **9986 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   4.2e-07   0.00083       3     131 ..     268     400 ..     266     404 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.2e-07
                                       HHHHHHHHHHHHHHH.SS..EEEEEEE-.TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EE.ES-GGG CS
                             GAF_2   3 dleelldlvldelve.lgaalgyillvd.ddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvi.lndlee 76 
                                       ++e+ ld++++  +e ++ +lg i+ vd dd++++l++ + + e +   ++ pl+e  ++ a++t ++v  ++d+e+
  gi|336254724|ref|YP_004597831.1| 268 SFEQKLDALFELGCErFDLDLGGIARVDpDDDRFELEYVSDEHEHLEPGAELPLSETFCALAAET-KAVAdVTDPES 343
                                       666667888888877689888888888835555777766666666666665599999********.67777999999 PP

                                       -S-HHHHHHHHHTT--EEEEEE.-T.T.S---EEEEES......--HHHHHHHHHHHH CS
                             GAF_2  77 dpdkkglpaghaglrsflavPl.is.e.grvvGvlnlyankppafdeedlelLeelae 131
                                       +     l+ ++ g+r+ l+  + i+ + +r v++++  ++++++f+e++ e+L+++++
  gi|336254724|ref|YP_004597831.1| 344 EGCDGILACREFGIRAYLGTYVeIDgGpDRSVAFVG-ESTRDEPFSEDECEFLRSIGQ 400
                                       888888889*************99955569999999.9****************9985 PP

>> GAF_3  GAF 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     0.029       2     128 ..     269     407 ..     268     408 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse..sldedsalarralssgevvsepsfaeed 76 
                                        ++ l++l +l+++ ++++ g +  +d+d +++     +d+++ l+   +l+  +  +++a++++ v+ +++ + e 
  gi|336254724|ref|YP_004597831.1| 269 FEQKLDALFELGCERFDLDLGGIARVDPDDDRFELEYVSDEHEHLEPgaELPLSETFCALAAETKAVADVTDPESEG 345
                                       6899***************************998887777777776666999*************995554433333 PP

                             GAF_3  77 g........lpdraa..lavPLvagr.qviGvlalastkprafdaedlelleslArqiataie 128
                                       +           ra+  ++v +  g  +++ ++  +st++++f++++ e+l+s+++++  ++e
  gi|336254724|ref|YP_004597831.1| 346 CdgilacreFGIRAYlgTYVEIDGGPdRSVAFV-GESTRDEPFSEDECEFLRSIGQWVTYELE 407
                                       333544444444777555555555555666554.38889999****************99888 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.5e-06     0.017       4      92 ..     539     636 ..     537     646 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.5e-06
                       HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkks..liisieNsyeg.....ek......kklesskskkeeh 67 
                                         l  ++ nlLdNA+  + + +   + I+ t++++++    +is+  +  g     +       ++l+s  ++    
  gi|336254724|ref|YP_004597831.1| 539 EQLRQLFQNLLDNALTYAGDEP---PRIDTTAERTSDGdgWTISVRDEGIGipvaeQDrifdlfDRLHS-REEYAGT 611
                                       568889*********9988766...89999998766432488998888555666642234544566666.4567899 PP

                       HATPase_c_5  68 GiGlksireivkkykgnlsieaedg 92 
                                       GiGl   ++iv+++ g+++++ e g
  gi|336254724|ref|YP_004597831.1| 612 GIGLALCQRIVERHAGAIRVDSEPG 636
                                       *******************998865 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.2e-05     0.044       6     132 ..     273     405 ..     268     406 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHHHHHTESEEEEEE..EEETT..EEECEEEEECC....EEEETTSHHHHHHHHHSSSEEESTGGTSTTHH CS
                               GAF   6 ldtvveelrellgadrvalyl..pdydG..lhydipqasrw....lfmkngrgicgqvlatgqplvipdstpdprfa 74 
                                       ld + e  +e +++d + + +  pd d   l+y ++++ +      + +  +++c+ +++t+ +  ++d   +++  
  gi|336254724|ref|YP_004597831.1| 273 LDALFELGCERFDLDLGGIARvdPDDDRfeLEY-VSDEHEHlepgAELPLSETFCALAAETKAVADVTDPESEGCDG 348
                                       555666666777777777766543333332455.3333333233333334777999************966666655 PP

                                       TTHHHHHHHHTTESEEEEEEEEE...TTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHH CS
                               GAF  75 qynrrdllenmgirsslvvPlvn...dgelwGllvlhnpsp.pftreelellqvladqvava 132
                                               +++gir++l+  +      ++ ++ +     ++ pf+++e+e+l+++++ v  +
  gi|336254724|ref|YP_004597831.1| 349 I----LACREFGIRAYLGTYVEIdggPDRSVAFVGEST-RDePFSEDECEFLRSIGQWVTYE 405
                                       5....66799***********97344333455444444.4469*************998765 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 ?    4.6   0.0     0.018        35      71      96 ..      76     101 ..      72     115 .. 0.88
   2 ?    4.6   0.5     0.018        35      14      82 ..     401     468 ..     395     479 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.018
                                       T-HHHHHHHHHHHHHHT--HHHHHHH CS
                   PEP-utilisers_N  71 eDpelleeveerIregglnaeaAvee 96 
                                        D++ +++v++++r+gg+++eaAv++
  gi|336254724|ref|YP_004597831.1|  76 TDKDSVDAVRTALRDGGIDVEAAVAS 101
                                       79999*******************86 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.018
                                       EE---.-----G.GGHHHHHHHHHHHHHHHHHHHHHHHHHH..T-HHHHHHHHHHHHHHT..-HHHHHHHHHH CS
                   PEP-utilisers_N  14 aveveveeeeveaedveaelerleeAlekvreelealaeka..lgeeeaaifeahlmlle..Dpelleeveer 82 
                                        v      +e+e+++ e+eler  + le++ e+le+ a  a    +e   +++ +l+l+e  D++l +e++e 
  gi|336254724|ref|YP_004597831.1| 401 WV-----TYELEQHERERELERTVDRLETSNERLEQFAYAAshDMQEPLRMVSSYLQLIErrDEDLSAETREY 468
                                       44.....467788999********************7755555434446688888888754477777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 4165.95
//
Query:       gi|336254725|ref|YP_004597832.1|  [L=878]
Description: PAS/PAC sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for 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-56  188.8  18.1    6.8e-13   48.8   0.3    5.6  5  PAS_4        PAS fold
    4.3e-45  152.2   0.0    3.2e-14   53.1   0.0    5.4  5  PAS_9        PAS domain
    6.9e-41  138.8   1.5    5.2e-14   52.2   0.0    5.8  6  PAS          PAS fold
    5.2e-27   94.6   0.0    1.5e-26   93.1   0.0    1.8  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    4.3e-23   80.8   9.8    9.5e-08   31.9   0.1    5.6  5  PAS_8        PAS domain
    2.5e-17   62.9   1.7    2.6e-06   27.6   0.1    5.8  6  PAS_3        PAS fold
    2.8e-12   46.8   1.6     0.0023   18.1   0.0    6.0  5  PAS_7        PAS fold
    1.5e-10   40.9   2.1    3.6e-10   39.7   0.1    2.8  2  HisKA        His Kinase A (phospho-acceptor) domain
    0.00075   19.4   0.0     0.0014   18.5   0.0    1.4  1  HATPase_c_5  GHKL domain
     0.0015   19.1   0.0        2.4    8.8   0.0    4.0  4  PAS_10       PAS domain
     0.0065   16.4   0.0      0.026   14.5   0.1    2.0  2  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0082   16.2   0.7       0.48   10.5   0.0    2.4  2  ApoLp-III    Apolipophorin-III precursor (apoLp-III)
  ------ inclusion threshold ------
       0.13   12.1   2.6         12    5.8   0.8    2.9  3  Wtap         WTAP/Mum2p family
       0.21   11.7   3.6        1.9    8.6   0.0    3.5  4  MLTR_LBD     MmyB-like transcription regulator ligand binding
        6.6    6.9   8.0        4.1    7.5   4.0    2.5  2  bZIP_2       Basic region leucine zipper


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.3   5.7e-16   6.8e-13       2     109 ..      31     145 ..      30     146 .. 0.94
   2 !   15.3   0.2   1.5e-05     0.018       5     110 .]     161     273 ..     158     273 .. 0.93
   3 !   44.4   0.2   1.3e-14   1.6e-11       7     108 ..     296     399 ..     291     401 .. 0.93
   4 !   46.1   0.5     4e-15   4.7e-12       3     109 ..     416     515 ..     414     516 .. 0.95
   5 !   43.9   0.0     2e-14   2.4e-11       2     109 ..     533     636 ..     532     637 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 5.7e-16
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.... 74 
                                       + + d+l+ ld+ gr++++N a  e  g++++ellG++   ll + d +++er l+++l+g++  e +  l +    
  gi|336254725|ref|YP_004597832.1|  31 ETIDDGLYQLDAAGRFVAVNDAVVETTGYSRDELLGEHISLLLDDTDVEAIERELAAALAGGDEGEAAVALPTfela 107
                                       7789************************************999999**************99988888888778889 PP

                             PAS_4  75 ....pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                           +g+e ++elr++Pl  ++Ge +g+++++rD+ e++
  gi|336254725|ref|YP_004597832.1| 108 irtvDGDEIPCELRVSPL-IADGELQGTIGVARDLAETK 145
                                       ******************.68**************9987 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.5e-05
                             PAS_4   5 pdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee......daarleralrrvlegeepiefleelll. 74 
                                       +++++vld+ + v+++  +aa+ + +++++++G+  + ++ +       + +++ r ++   +++  +++ e++ + 
  gi|336254725|ref|YP_004597832.1| 161 NAGVVVLDDALDVTWVDDTAAAFLDLDRDAVVGRDGRTVVEDTiadrlaAPEPFVRSVTSTYDEGSYLDRYECRATg 237
                                       5799*********************************888888777788899999999999999999999999999* PP

                             PAS_4  75 .pgeerhyelrllPlrdesGe.vigvlvisrDiTerrr 110
                                        +g+ r++e +  P+  esGe + g +++  DiT+r+r
  gi|336254725|ref|YP_004597832.1| 238 dDGQSRWLEYQSKPI--ESGEyAGGRIELYSDITDRKR 273
                                       ***************..99**9**************97 PP

  == domain 3  score: 44.4 bits;  conditional E-value: 1.3e-14
                             PAS_4   7 alavldpdgrvlyaNaaaaelfgappeellGktlaellpee..daarleralrrvlegeepiefleelllpgeerhy 81 
                                       a++ ld+dg+v+ +N+ a ++ g++++e++G+++  ++++e  + +  +++l+ +le + + ++   ++ +g++ + 
  gi|336254725|ref|YP_004597832.1| 296 AIFRLDADGTVISWNQGAKQIKGYDADEIVGEHFSTFYTQEdrADGIPDQNLEIALENGSVEDEGWRVRQDGSRFWA 372
                                       68899**********************************996556667899999****988888888888******* PP

                             PAS_4  82 elrllPlrdesGevigvlvisrDiTer 108
                                       +++++P+rd++G+ +g+l ++rD+T+r
  gi|336254725|ref|YP_004597832.1| 373 NVTITPVRDADGTHRGFLKVTRDMTDR 399
                                       *************************98 PP

  == domain 4  score: 46.1 bits;  conditional E-value: 4e-15
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.daarleralrrvlegeepiefleelllpgee 78 
                                       +++da++++d+++r++++N +aael+ ++ +ellG++l++++p+  d +++ +a   ++e++ p + + ++++   +
  gi|336254725|ref|YP_004597832.1| 416 RVSDAFYAVDDEFRFTHVNDRAAELLERSEDELLGERLWDVFPDLrDFDEVWDAFHTAMETQSPTSYELYYDT--LD 490
                                       5799*****************************************************************9999..** PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerr 109
                                        ++e +l+P         g+ v++rD+Ter+
  gi|336254725|ref|YP_004597832.1| 491 FWVEANLYPSAT------GISVYFRDVTERV 515
                                       *********954......99**********8 PP

  == domain 5  score: 43.9 bits;  conditional E-value: 2e-14
                             PAS_4   2 dslpdalavl.dpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++ p +++ l d+d+ ++ a  ++ + + ++p++l G+ ++++++ee aa+le+al ++lege+   +l +      
  gi|336254725|ref|YP_004597832.1| 533 EHFPNGIVTLfDHDLEYTLAAGQGFDKIPVDPDDLEGENFYDVWSEETAADLEPALLAALEGEQESVELKY-----V 604
                                       67888888888***************************************************855444443.....4 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +r + l ++P+ d++G+v + + +++DiTer+
  gi|336254725|ref|YP_004597832.1| 605 GREWVLYAVPITDSRGDVFAGVTMAHDITERK 636
                                       579****************************8 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   3.8e-14   4.5e-11       3     103 ..      36     142 ..      34     143 .. 0.87
   2 !   12.5   0.0   0.00011      0.13       2     104 .]     162     270 ..     161     270 .. 0.83
   3 !   53.1   0.0   2.6e-17   3.2e-14       4     104 .]     297     398 ..     294     398 .. 0.91
   4 !   26.0   0.0   6.9e-09   8.3e-06       2     104 .]     419     513 ..     418     513 .. 0.85
   5 !   11.0   0.0   0.00033      0.39       2     104 .]     537     634 ..     536     634 .. 0.70

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 3.8e-14
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrk.....kerevevvlirkn 72 
                                       g    +  gr + +N+a+ + +Gys++e+lg +i+ l+   + +  +++l+aal  g++        ++e+ +++ +
  gi|336254725|ref|YP_004597832.1|  36 GLYQLDAAGRFVAVNDAVVETTGYSRDELLGEHISLLLddTDVEAIERELAAALAGGDEgeaavALPTFELAIRTVD 112
                                       566667889*****************************666666666666777777777*****99*********** PP

                             PAS_9  73 getfwvlltaspvkdddgelvgiivilrDit 103
                                       g +++++l++sp++  dgel+g i++ rD+ 
  gi|336254725|ref|YP_004597832.1| 113 GDEIPCELRVSPLIA-DGELQGTIGVARDLA 142
                                       *************85.79***********85 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00011
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrk......kerevevvlirk 71 
                                        g+++ ++   ++++ ++a+ +l  ++++v+g++ ++++ +t +++    + ++++ ++         ++e   + +
  gi|336254725|ref|YP_004597832.1| 162 AGVVVLDDALDVTWVDDTAAAFLDLDRDAVVGRDGRTVVeDTIADRLAAPEPFVRSVTStydegsYLDRYECRATGD 238
                                       578887788889**********************9999985555555555555555555666666999********* PP

                             PAS_9  72 ngetfwvlltaspvkdddgelvg.iivilrDite 104
                                       +g+  w +    p+  ++ge+ g  i +  Dit+
  gi|336254725|ref|YP_004597832.1| 239 DGQSRWLEYQSKPI--ESGEYAGgRIELYSDITD 270
                                       **************..6888998899*****996 PP

  == domain 3  score: 53.1 bits;  conditional E-value: 2.6e-17
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlf....vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       i+  + dg+++++N++a+++ Gy+++e++g ++++++      d   +++l+ ale+g+    e+e   +r +g++f
  gi|336254725|ref|YP_004597832.1| 297 IFRLDADGTVISWNQGAKQIKGYDADEIVGEHFSTFYtqedRADGIPDQNLEIALENGS---VEDEGWRVRQDGSRF 370
                                       554679*******************************8877777777888888888888...*************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       w+++t++pv+d+dg+ +g++ + rD+t+
  gi|336254725|ref|YP_004597832.1| 371 WANVTITPVRDADGTHRGFLKVTRDMTD 398
                                       **************************96 PP

  == domain 4  score: 26.0 bits;  conditional E-value: 6.9e-09
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgrkkerevevvlirknget 75 
                                       d++  +++++r +++N+ a++ll  s++e+lg +++d+f    + +e  + ++ a+e+ +  + ++e+ + + +   
  gi|336254725|ref|YP_004597832.1| 419 DAFYAVDDEFRFTHVNDRAAELLERSEDELLGERLWDVFpdlRDFDEVWDAFHTAMETQS--PTSYELYYDTLD--- 490
                                       5666678********************************777777777788888888888..999999999995... PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                       fwv+++++p        +gi v +rD+te
  gi|336254725|ref|YP_004597832.1| 491 FWVEANLYPS------ATGISVYFRDVTE 513
                                       9********9......3445588999997 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 0.00033
                             PAS_9   2 dgili.dnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       +gi+   ++d + +  a +++ ++   +p+++ g ++ d+   ++e++ +l+ al +    e e+e v+ +  g + 
  gi|336254725|ref|YP_004597832.1| 537 NGIVTlFDHDLEYTlAAGQGFDKIP-VDPDDLEGENFYDVW--SEETAADLEPALLAAL--EGEQESVELKYVG-RE 607
                                       6666444455655557778888884.78*************..6666555555555555..4555555555544.34 PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       wv l a+p+ d+ g +++ +   +Dite
  gi|336254725|ref|YP_004597832.1| 608 WV-LYAVPITDSRGDVFAGVTMAHDITE 634
                                       54.5688*****9999999********8 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   4.3e-17   5.2e-14       2     112 ..      25     140 ..      24     141 .. 0.83
   2 !    9.7   0.0   0.00067       0.8      12      50 ..     162     200 ..     158     259 .. 0.74
   3 !   45.5   0.1   5.2e-15   6.2e-12      13     113 .]     296     396 ..     283     396 .. 0.90
   4 !   19.1   0.0   8.5e-07     0.001       2      71 ..     409     479 ..     408     486 .. 0.86
   5 !    6.0   0.0    0.0097        12      37     103 ..     563     622 ..     526     632 .. 0.73
   6 ?   -2.8   0.0       5.2   6.2e+03      55      74 ..     635     654 ..     627     694 .. 0.75

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 4.3e-17
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r+++e+++d+   +D+ gr++ vN+a  e +G+sr+e+lg++++ l+  +d +   ++l  +l+ g e++a    
  gi|336254725|ref|YP_004597832.1|  25 RFRTLVETIDDGLYQLDAAGRFVAVNDAVVETTGYSRDELLGEHISLLLDDTDVEAIERELAAALAGGDEGEAAVA- 100
                                       89********************************************999777644555555555555555554444. PP

                                       EEC.........TTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  79 fkl.........rdgrpihlevraspvrdaggeilgflgvlrd 112
                                         l         +dg +i++e+r+sp++  g+ + g +gv+rd
  gi|336254725|ref|YP_004597832.1| 101 --LptfelairtVDGDEIPCELRVSPLIADGE-LQGTIGVARD 140
                                       ..344699********************9965.67*****999 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00067
                                       SEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGB CS
                               PAS  12 dpifvvDedgrilyvNaaaeellGlsreevlgkslldli 50 
                                       ++++v+D   ++++v ++a+ +l l+r+ v+g+    ++
  gi|336254725|ref|YP_004597832.1| 162 AGVVVLDDALDVTWVDDTAAAFLDLDRDAVVGRDGRTVV 200
                                       69******************************9866555 PP

  == domain 3  score: 45.5 bits;  conditional E-value: 5.2e-15
                                       EEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEE CS
                               PAS  13 pifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpih 88 
                                       +if +D+dg ++ +N+ a ++ G++++e++g++++ ++  ed+a   +++ ++ ++++ + +++  +++  dg+ ++
  gi|336254725|ref|YP_004597832.1| 296 AIFRLDADGTVISWNQGAKQIKGYDADEIVGEHFSTFYTQEDRAdGIPDQNLEIALENGSVEDEGWRVRQ-DGSRFW 371
                                       7999****************************************98888888888888888887777777.****** PP

                                       EEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  89 levraspvrdaggeilgflgvlrdi 113
                                       + v+ +pvrda+g+++gfl v rd+
  gi|336254725|ref|YP_004597832.1| 372 ANVTITPVRDADGTHRGFLKVTRDM 396
                                       *******************998885 PP

  == domain 4  score: 19.1 bits;  conditional E-value: 8.5e-07
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH..HHHHHHHHHHHHTT- CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda..elaelleqlleqgee 71 
                                       +l++il    d+  +vD   r+++vN+ a+ell  s++e+lg+ l d+++   ++  e+ +++++++e++++
  gi|336254725|ref|YP_004597832.1| 409 ELQQILGRVSDAFYAVDDEFRFTHVNDRAAELLERSEDELLGERLWDVFPDL-RDfdEVWDAFHTAMETQSP 479
                                       567788888999**********************************999754.3368888899998888776 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.0097
                                       THHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEE CS
                               PAS  37 sreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggei 103
                                       +++++ g++++d+++ee    +a+ le +l+++ e++++ + +k+     +++++ a+p++d  g +
  gi|336254725|ref|YP_004597832.1| 563 DPDDLEGENFYDVWSEE----TAADLEPALLAALEGEQESVELKY---VGREWVLYAVPITDSRGDV 622
                                       57999************....555555555555555555554544...5688888888888888775 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 5.2
                                       HHHHHHHHHHHHHHTT-ECC CS
                               PAS  55 daelaelleqlleqgeesra 74 
                                       + + +++le+ ++q ees+ 
  gi|336254725|ref|YP_004597832.1| 635 RKKSQRQLEETIAQLEESNE 654
                                       33678888888888888765 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 !   93.1   0.0   1.3e-29   1.5e-26       1     110 [.     764     873 ..     764     875 .. 0.89

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 1.3e-29
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSS CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtG 75 
                                       gd ++Lrq+++nl++Na+++ + ++  +v+++a+   d+  isv D GiGi+ ++++ +f  f +  ++++++ gtG
  gi|336254725|ref|YP_004597832.1| 764 GDASQLRQVFQNLLSNALEY-SGDEPPRVRVDAERrgDRWLISVADEGIGIDADEQEAVFNVFKR-LHSRDEHPGTG 838
                                       7899****************.54555555555423459*******************99999999.888999***** PP

                                       HHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  76 lGlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                       +Gl++++++ve++gG+iwv+sepg+G tf ftlp 
  gi|336254725|ref|YP_004597832.1| 839 IGLALCQRIVERHGGDIWVDSEPGEGATFSFTLPA 873
                                       *********************************95 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1     8e-11   9.5e-08       1      51 [.      24      75 ..      24      93 .. 0.81
   2 ?    3.5   0.1     0.061        73      12      46 ..     162     197 ..     159     219 .. 0.71
   3 !   14.8   0.0   1.9e-05     0.022       3      45 ..     285     329 ..     283     348 .. 0.85
   4 !   28.1   0.3   1.3e-09   1.5e-06       3      59 ..     410     469 ..     408     477 .. 0.82
   5 ?    4.2   0.0     0.039        46       1      16 [.     526     541 ..     526     552 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 8e-11
                             PAS_8  1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpv 51
                                      +r+r+l+e+++dg+  +d+ +r+v vN+a  e +Gys ++l+ge +  ll++
  gi|336254725|ref|YP_004597832.1| 24 QRFRTLVETIDDGLYQLDAAGRFVAVNDAVVETTGYSrDELLGEHISLLLDD 75
                                      7*****************5556***************999999888544443 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.061
                             PAS_8  12 dgiavvd.lgdrivdvNqaalellGys.adlkgellg 46 
                                        g++v+d + d +++v ++a+ +l ++ + + g + +
  gi|336254725|ref|YP_004597832.1| 162 AGVVVLDdALD-VTWVDDTAAAFLDLDrDAVVGRDGR 197
                                       59999885667.************9775444444443 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 1.9e-05
                             PAS_8   3 lralfesspd.giavvdlgdrivdvNqaalellGys.adlkgell 45 
                                       +++l++++ + +i+ +d++++++ +Nq a ++ Gy+ +++ ge +
  gi|336254725|ref|YP_004597832.1| 285 FESLVDAVEEyAIFRLDADGTVISWNQGAKQIKGYDaDEIVGEHF 329
                                       89***************5555***************999988766 PP

  == domain 4  score: 28.1 bits;  conditional E-value: 1.3e-09
                             PAS_8   3 lralfesspdgiavvdlgd..rivdvNqaalellGys.adlkgellgqllpvlrplle..da 59 
                                       l++++  ++d+   vd  d  r+++vN++a+ell  s ++l+ge l++++p+lr+  e  da
  gi|336254725|ref|YP_004597832.1| 410 LQQILGRVSDAFYAVD--DefRFTHVNDRAAELLERSeDELLGERLWDVFPDLRDFDEvwDA 469
                                       688888999*9**999..4469************9889999999999999999988884444 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.039
                             PAS_8   1 erlralfesspdgiav 16 
                                       +r+r+l e+ p+gi+ 
  gi|336254725|ref|YP_004597832.1| 526 QRYRTLAEHFPNGIVT 541
                                       7*************95 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.2e-07   0.00075       2      89 .]      47     138 ..      46     138 .. 0.81
   2 ?    2.6   0.0      0.14   1.7e+02      54      79 ..     231     254 ..     210     259 .. 0.76
   3 !   27.6   0.1   2.2e-09   2.6e-06       2      88 ..     307     392 ..     306     393 .. 0.88
   4 !    6.4   0.1    0.0091        11       2      55 ..     431     483 ..     430     489 .. 0.87
   5 ?   -3.1   0.0       8.7     1e+04      34      54 ..     765     785 ..     763     786 .. 0.83
   6 ?   -1.8   0.0       3.3   3.9e+03      34      70 ..     817     859 ..     814     860 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.2e-07
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqeal...kkge...py.egeyRirrkdGeyrwvear 71 
                                       + v+++v e++Gys++ellg   ++  l+   D e ++++l++al   ++ge   ++ ++e  ir+ dG+ +  e r
  gi|336254725|ref|YP_004597832.1|  47 VAVNDAVVETTGYSRDELLGE--HISLLLDDTDVEAIERELAAALaggDEGEaavALpTFELAIRTVDGDEIPCELR 121
                                       679******************..5555555667************6663333333346778999**********999 PP

                             PAS_3  72 arvirdengkpvrvigva 89 
                                       ++++   +g+ +  igva
  gi|336254725|ref|YP_004597832.1| 122 VSPL-IADGELQGTIGVA 138
                                       9999.8999999888885 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                             PAS_3  54 geyRirrkdGeyrwveararvirden 79 
                                        e R    dG+ rw+e + ++i  e+
  gi|336254725|ref|YP_004597832.1| 231 YECRATGDDGQSRWLEYQSKPI--ES 254
                                       46777778************99..44 PP

  == domain 3  score: 27.6 bits;  conditional E-value: 2.2e-09
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervr..ealqealkkgepyegeyRirrkdGeyrwveararvir 76 
                                       i++++  ++i Gy+++e+ g   ++  +   eDr+     ++l+ al++g+ +e e  ++r+dG+ +w   +++++r
  gi|336254725|ref|YP_004597832.1| 307 ISWNQGAKQIKGYDADEIVGE--HFSTFYTQEDRADGIpdQNLEIALENGS-VEDEGWRVRQDGSRFWANVTITPVR 380
                                       89*******************..**********887752267778888888.899999999**************** PP

                             PAS_3  77 dengkpvrvigv 88 
                                       d +g    +++v
  gi|336254725|ref|YP_004597832.1| 381 DADGTHRGFLKV 392
                                       ****98877665 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0091
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyege 55 
                                       ++v++r  e+l  s++ellg  + w  +    D ++v++a+++a+++++p + e
  gi|336254725|ref|YP_004597832.1| 431 THVNDRAAELLERSEDELLGE-RLWDVFPDLRDFDEVWDAFHTAMETQSPTSYE 483
                                       689******************.88988888999************999955444 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 8.7
                             PAS_3  34 Drervrealqealkkgepyeg 54 
                                       D +++r+ +q++l++  +y+g
  gi|336254725|ref|YP_004597832.1| 765 DASQLRQVFQNLLSNALEYSG 785
                                       88999*******998777765 PP

  == domain 6  score: -1.8 bits;  conditional E-value: 3.3
                             PAS_3  34 Drervrealqealkkge.pyege.....yRirrkdGeyrwvea 70 
                                       ++e v++ ++++ +++e p +g       Ri+ ++G+ +wv++
  gi|336254725|ref|YP_004597832.1| 817 EQEAVFNVFKRLHSRDEhPGTGIglalcQRIVERHGGDIWVDS 859
                                       5666666666666444433343344444799999999999975 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0017       2.1       1      35 [.      30      64 ..      30      81 .. 0.87
   2 !   18.1   0.0   1.9e-06    0.0023       6     114 ..     162     275 ..     160     276 .. 0.82
   3 !    8.4   0.0    0.0019       2.3       8     114 ..     297     403 ..     294     404 .. 0.72
   4 ?    3.3   0.1     0.074        88       5      38 ..     418     450 ..     414     519 .. 0.50
   5 ?    0.3   0.0      0.63   7.5e+02     101     114 ..     626     639 ..     620     640 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0017
                             PAS_7  1 lenmsqGisvfDadlrLvawNrrylelldlpeelv 35
                                      +e +++G+  +Da++r va+N+ ++e  +++++ +
  gi|336254725|ref|YP_004597832.1| 30 VETIDDGLYQLDAAGRFVAVNDAVVETTGYSRDEL 64
                                      6899**********************999988755 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.9e-06
                             PAS_7   6 qGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsferer 82 
                                        G++v+D +l ++ + +     ldl ++ v vg+  +++++ + +    +++     v+ + ++ +  +++    + 
  gi|336254725|ref|YP_004597832.1| 162 AGVVVLDDALDVTWVDDTAAAFLDLDRDAV-VGRDGRTVVEDTIADRLAAPEPFVRSVTSTYDEGSYLDRYECRATG 237
                                       69****************************.**********999999988666666666666666666677777766 PP

                             PAS_7  83 pdg..rvievrgnpl....pdgGfVttytDiTerrrae 114
                                       +dg  r++e +++p+      gG +  y+DiT+r+r+e
  gi|336254725|ref|YP_004597832.1| 238 DDGqsRWLEYQSKPIesgeYAGGRIELYSDITDRKRSE 275
                                       6663379********4444458**************98 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0019
                             PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaever.rlaaaragkphsfererp 83 
                                       i  +Dad+ ++ wN+   ++ ++ ++ + vg +++++     +   + +++ e ++e+  ++    + ++   r  +
  gi|336254725|ref|YP_004597832.1| 297 IFRLDADGTVISWNQGAKQIKGYDADEI-VGEHFSTFYTQEDRADGIPDQNLEIALENgSVEDEGWRVRQDGSRFWA 372
                                       6679***********************9.9*****999888666666645544444431333333344555555556 PP

                             PAS_7  84 dgrvievrgnplpdgGfVttytDiTerrrae 114
                                       + ++  vr     ++Gf+ +  D T+r + e
  gi|336254725|ref|YP_004597832.1| 373 NVTITPVRDADGTHRGFLKVTRDMTDRWERE 403
                                       6666666666668889999999999988877 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.074
                             PAS_7   5 sqGisvfDadlrLvawNrrylelldlpeelvqvg 38 
                                       s+++  +D + r + +N+r  ell+ +e+ +  g
  gi|336254725|ref|YP_004597832.1| 418 SDAFYAVDDEFRFTHVNDRAAELLERSEDEL-LG 450
                                       5566667777777777777777777666554.33 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 0.63
                             PAS_7 101 VttytDiTerrrae 114
                                       Vt+ +DiTer++++
  gi|336254725|ref|YP_004597832.1| 626 VTMAHDITERKKSQ 639
                                       8999*******987 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.1     3e-13   3.6e-10       2      66 ..     656     722 ..     655     723 .. 0.93
   2 ?   -2.5   0.2       4.6   5.5e+03      39      59 ..     757     777 ..     737     780 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 3e-13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l++f+   +H+L  PL  ++ ++++++ +  + l+e+ +e+le ++++a+r++++++ lL++sr e+
  gi|336254725|ref|YP_004597832.1| 656 LEQFAYAASHDLQEPLRMVSSYLQLIESRyaDTLDEDGEEFLEFAVDGAERMRDMIDGLLEYSRVET 722
                                       789***********************5555*99*******************************987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.6
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  39 eyletiesearrldhlvedlL 59 
                                       e l ++e  a +l+++ ++lL
  gi|336254725|ref|YP_004597832.1| 757 ESLPRVEGDASQLRQVFQNLL 777
                                       467778888889999999986 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.1e-06    0.0014       5      92 ..     768     862 ..     765     871 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                       HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ek......kklesskskkeehGiG 70 
                                        l  ++ nlL NA+e + + +   + +r+ ++++ +  +is+  +  g     ++      k+l+s+  ++   GiG
  gi|336254725|ref|YP_004597832.1| 768 QLRQVFQNLLSNALEYSGDEP---PRVRVDAERRGDRWLISVADEGIGidadeQEavfnvfKRLHSRD-EHPGTGIG 840
                                       57789**********998866...89****************99955555554224554456666655.46689*** PP

                       HATPase_c_5  71 lksireivkkykgnlsieaedg 92 
                                       l   ++iv++++g+++++ e g
  gi|336254725|ref|YP_004597832.1| 841 LALCQRIVERHGGDIWVDSEPG 862
                                       ****************998765 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.97   1.2e+03      11      55 ..     163     208 ..     160     269 .. 0.63
   2 !    8.8   0.0     0.002       2.4      15     106 .]     300     397 ..     291     397 .. 0.70
   3 ?    4.3   0.0     0.049        58      12      67 ..     421     478 ..     410     512 .. 0.79
   4 ?   -1.8   0.0       3.8   4.6e+03      40      99 ..     569     627 ..     560     633 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.97
                            PAS_10  11 eltflDdnlqirrFtpaakklfklipad.vGrpladihpkkavknv 55 
                                       +++ lDd l++++  ++a+ +++l ++  vGr+  +++++ + +++
  gi|336254725|ref|YP_004597832.1| 163 GVVVLDDALDVTWVDDTAAAFLDLDRDAvVGRDGRTVVEDTIADRL 208
                                       6789999999999999999999998765268887777766444433 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.002
                            PAS_10  15 lDdnlqirrFtpaakklfklipad.vGrpladihpk.kavknv..eeviealrtg..ekdevevvvpkngkwvlvry 85 
                                       lD +  ++ +++ ak++  + +++ vG++ +++ ++ ++ + +  +++  al +g  e++  +v ++ +  w  v++
  gi|336254725|ref|YP_004597832.1| 300 LDADGTVISWNQGAKQIKGYDADEiVGEHFSTFYTQeDRADGIpdQNLEIALENGsvEDEGWRVRQDGSRFWANVTI 376
                                       8888999999999888888876543899999996554555555432333334443004444444555777899**** PP

                            PAS_10  86 lpyrdedgeiaGvvetfvDit 106
                                        p+rd dg  +G + +  D+t
  gi|336254725|ref|YP_004597832.1| 377 TPVRDADGTHRGFLKVTRDMT 397
                                       **************9999986 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.049
                            PAS_10  12 ltflDdnlqirrFtpaakklfklipad.vGrpladihpk.kavknveeviealrtgek 67 
                                          +Dd+ +++  +++a++l+++ +++ +G++l d+ p+ +  ++v + +++  ++++
  gi|336254725|ref|YP_004597832.1| 421 FYAVDDEFRFTHVNDRAAELLERSEDElLGERLWDVFPDlRDFDEVWDAFHTAMETQS 478
                                       5669*******************998746*******9998888888887777766665 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.8
                            PAS_10  40 Grpladihpkkavknveeviealrtgekdevevvvpkngkwvlvrylpyrdedge.iaGvv 99 
                                       G++  d+ +++   ++e  + a  +ge++ ve +    g+  +++  p+ d  g+ +aGv 
  gi|336254725|ref|YP_004597832.1| 569 GENFYDVWSEETAADLEPALLAALEGEQESVELK--YVGREWVLYAVPITDSRGDvFAGVT 627
                                       6677777788888888888888888998888755..4466666677888888775256665 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       6.4   7.6e+03      33      65 ..     207     240 ..     199     244 .. 0.80
   2 !   14.5   0.1   2.2e-05     0.026      30     110 ..     767     849 ..     736     864 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.4
                       HATPase_c_2  33 rlaveEactNavehayleap.egpvevrlesdee 65 
                                       rla+ E +++ v+  y+e++  ++ e+r++ d++
  gi|336254725|ref|YP_004597832.1| 207 RLAAPEPFVRSVTSTYDEGSyLDRYECRATGDDG 240
                                       7999999999999999999877877877776665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.2e-05
                       HATPase_c_2  30 deirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep......keslkegGr 100
                                        ++r + + +++Na e+  +e p  +v+v +e+++++  ++vaD+G g d+ +++              ++ +  G+
  gi|336254725|ref|YP_004597832.1| 767 SQLRQVFQNLLSNALEYSGDEPP--RVRVDAERRGDRWLISVADEGIGIDADEQEAVFN--VfkrlhsRDEHPGTGI 839
                                       567777777899******99877..9**********************77765443322..1346677778888899 PP

                       HATPase_c_2 101 GlalikglvD 110
                                       Glal +++v+
  gi|336254725|ref|YP_004597832.1| 840 GLALCQRIVE 849
                                       9999999886 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.058        69      62      99 ..     637     674 ..     629     696 .. 0.85
   2 !   10.5   0.0    0.0004      0.48      54      98 ..     734     779 ..     731     786 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.058
                         ApoLp-III  62 evkkkieetadklseenPevkkkaqelqekvQsgvqsl 99 
                                        ++ ++eet ++l+e+n  +++ a + +  +Q+ ++++
  gi|336254725|ref|YP_004597832.1| 637 KSQRQLEETIAQLEESNERLEQFAYAASHDLQEPLRMV 674
                                       56789999999999999999999999999999987765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0004
                         ApoLp-III  54 deleealkevkkkieetadklse.enPevkkkaqelqekvQsgvqs 98 
                                       + le +l++++ +ieet +++   + P v+  a++l++ +Q+ +++
  gi|336254725|ref|YP_004597832.1| 734 PVLEDVLEDLQLQIEETDAEIAIeSLPRVEGDASQLRQVFQNLLSN 779
                                       56899****************98688***************97766 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       8.2   9.9e+03      19      51 ..     140     171 ..     138     173 .. 0.69
   2 ?    5.8   0.8    0.0098        12     129     154 ..     633     658 ..     629     659 .. 0.91
   3 ?    4.5   0.0     0.026        31      20      70 ..     707     755 ..     683     762 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8.2
                              Wtap  19 elqelksslqelkqslqppsssqlrqvllDPAv 51 
                                        l+e+k+ lq l++ + p++  ++  v+lD A+
  gi|336254725|ref|YP_004597832.1| 140 DLAETKERLQTLESVRAPDG-PNAGVVVLDDAL 171
                                       57788888888888866544.477777777776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0098
                              Wtap 129 eelkkaleeleelleeleeevevlqs 154
                                        e kk++++lee +++lee +e+l++
  gi|336254725|ref|YP_004597832.1| 633 TERKKSQRQLEETIAQLEESNERLEQ 658
                                       6789******************9975 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.026
                              Wtap  20 lqelksslqelkqslqppsssqlrqvllDPAvnlvfsrlrkeleeaenkle 70 
                                       ++++ + l e+++ + +   + l+ ++lDP ++ v++ l+ ++ee++++++
  gi|336254725|ref|YP_004597832.1| 707 MRDMIDGLLEYSRVETQG--APLEPIALDPVLEDVLEDLQLQIEETDAEIA 755
                                       566666666666664443..4799***********************9986 PP

>> MLTR_LBD  MmyB-like transcription regulator ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3      0.24   2.9e+02      16      60 ..     163     209 ..     159     218 .. 0.84
   2 ?    8.6   0.0    0.0016       1.9       2      38 ..     282     318 ..     281     330 .. 0.89
   3 ?   -1.6   0.1       2.2   2.6e+03      19     112 ..     423     470 ..     407     484 .. 0.49
   4 ?   -2.7   0.1       4.7   5.7e+03      84     107 ..     635     658 ..     627     673 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.24
                          MLTR_LBD  16 PAlVldrrwdvlaaNraaraLlgd..paalpeperNllrlvfldpgl 60 
                                        ++Vld+ +dv +  + a+a+l+    a +++++r ++  + +d+ +
  gi|336254725|ref|YP_004597832.1| 163 GVVVLDDALDVTWVDDTAAAFLDLdrDAVVGRDGRTVVEDTIADRLA 209
                                       689*******************9987778888888888888777655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0016
                          MLTR_LBD   2 rpalrrlLdalepvPAlVldrrwdvlaaNraaraLlg 38 
                                       r+a + l+da+e+++ + ld++ +v+ +N+ a++  g
  gi|336254725|ref|YP_004597832.1| 282 REAFESLVDAVEEYAIFRLDADGTVISWNQGAKQIKG 318
                                       788999************************9987655 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.2
                          MLTR_LBD  19 VldrrwdvlaaNraaraLlgdpaalpeperNllrlvfldpglrpliedweevaralvarLraeaarrpddpalaalv 95 
                                        +d+ +     N+ a+ Ll+                                                +d+ l + +
  gi|336254725|ref|YP_004597832.1| 423 AVDDEFRFTHVNDRAAELLER----------------------------------------------SEDELLGERL 453
                                       344444444444444444444..............................................4444444444 PP

                          MLTR_LBD  96 aeLsaaspefarlwarh 112
                                        ++     +f++ w++ 
  gi|336254725|ref|YP_004597832.1| 454 WDVFPDLRDFDEVWDAF 470
                                       44444444444444444 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 4.7
                          MLTR_LBD  84 rrpddpalaalvaeLsaaspefar 107
                                       r   +++l++ +a+L++++++ ++
  gi|336254725|ref|YP_004597832.1| 635 RKKSQRQLEETIAQLEESNERLEQ 658
                                       667789999999999998877665 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.2   1.5e+03      33      47 ..     402     416 ..     396     419 .. 0.63
   2 ?    7.5   4.0    0.0035       4.1      23      46 ..     635     658 ..     634     660 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHH CS
                            bZIP_2  33 rvkeLeeeNaqLrqk 47 
                                       r +eLe+e +q++ +
  gi|336254725|ref|YP_004597832.1| 402 REQELESELQQILGR 416
                                       445666666666555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  23 kkakeeeleervkeLeeeNaqLrq 46 
                                       +k+ +++lee++ +Lee N++L+q
  gi|336254725|ref|YP_004597832.1| 635 RKKSQRQLEETIAQLEESNERLEQ 658
                                       78999*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (878 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.72u 0.26s 00:00:00.98 Elapsed: 00:00:00.42
# Mc/sec: 6245.66
//
Query:       gi|336254726|ref|YP_004597833.1|  [L=498]
Description: cysteinyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-107  357.9   0.1   1.1e-105  353.3   0.1    2.1  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    8.5e-16   58.2   1.6    7.7e-15   55.1   0.4    2.4  2  DALR_2        DALR domain
      3e-11   42.7   0.0    0.00013   20.9   0.0    2.2  2  tRNA-synt_1g  tRNA synthetases class I (M)
    7.8e-10   38.2   0.0    7.5e-06   25.1   0.0    2.3  2  tRNA-synt_1f  tRNA synthetases class I (K)
    0.00061   18.2   0.0      0.004   15.5   0.0    2.2  3  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
     0.0015   17.5   0.1      0.017   14.1   0.0    2.5  3  tRNA-synt_1d  tRNA synthetases class I (R)
  ------ inclusion threshold ------
      0.024   14.4   0.0      0.044   13.6   0.0    1.4  1  FTO_CTD       FTO C-terminal domain
      0.028   14.2   0.4      0.028   14.2   0.4    2.1  2  UVR           UvrB/uvrC motif
      0.057   12.3   0.0       0.15   10.9   0.0    1.7  1  tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic d


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 !  353.3   0.1  5.4e-109  1.1e-105       2     300 ..      16     336 ..      15     337 .. 0.93

  Alignments for each domain:
  == domain 1  score: 353.3 bits;  conditional E-value: 5.4e-109
                                       ---SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHT..TS-HHHHH CS
                      tRNA-synt_1e   2 vkpleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikraree..eksvkela 76 
                                       ++p + ++v lY CG tv d  hlGhaRs v +D+++r+l++lgYdv++v+n+tDi++ki++r  e+  ++s  e+a
  gi|336254726|ref|YP_004597833.1|  16 FEPQDPENVLLYYCGLTVSDPPHLGHARSWVHVDVMHRWLEYLGYDVRHVENFTDINEKIVARVGEDdlGESEPEVA 92 
                                       56778899*******************************************************987622578899** PP

                                       HHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT CS
                      tRNA-synt_1e  77 ekfieefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelg 153
                                       e +ie+  +d+++Ln+l++++ prvse+v+eii+lve+l+ekgyaY+++ g vyfdv+++++Ygkls+q+lee+e++
  gi|336254726|ref|YP_004597833.1|  93 ESYIEHTLADMRSLNLLRAEVYPRVSEHVPEIIDLVETLVEKGYAYESN-GSVYFDVTAFDDYGKLSNQELEEIESQ 168
                                       ***********************************************99.*************************** PP

                                       ----S--S-SSTT-EEEEEE.....--TTS...................--B--TTSSEEE-SSHHHHHHHHHHH-S CS
                      tRNA-synt_1e 154 aegevseekkdkkDfaLWka.....skege...................pswdsPwgkGRPGWhieCsvmaskllgs 206
                                        + +  +ek+++ DfaLWka                              +w+sPwg+GRPGWhieCsvm+++ l +
  gi|336254726|ref|YP_004597833.1| 169 GDPDERSEKRHPADFALWKAggvdaD---AvaehrhegaapaeeacetsQTWESPWGEGRPGWHIECSVMSMTHLDE 242
                                       *99999*************7333320...0223344455666677777779************************** PP

                                       SEEEEEEEGGGTTTHHHHHHHHHHHHSSS--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS CS
                      tRNA-synt_1e 207 eidihsGGiDLafPhhenelaqseaafdkqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsa 283
                                       ++d+h+GG DL+fPhhene+aqseaa+d+q++ky+lh +  ++++ekms sL+nf+t++d++ ++ +++lR +l+  
  gi|336254726|ref|YP_004597833.1| 243 TLDLHVGGRDLVFPHHENEIAQSEAATDRQFAKYWLHCELFQMDDEKMSSSLGNFVTVEDAVDQWGTNVLRTFLTAG 319
                                       ***************************************************************************** PP

                                       -TTS-EEE-HHHHHHHH CS
                      tRNA-synt_1e 284 hyrsqldfkeelleeak 300
                                        y+s+  +++e+++ea+
  gi|336254726|ref|YP_004597833.1| 320 SYNSKQLYSDETIAEAE 336
                                       ************99885 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.4   3.9e-18   7.7e-15       1      58 [.     377     438 ..     377     443 .. 0.88
   2 ?    1.6   0.0       0.2   3.9e+02      20      59 ..     450     486 ..     442     489 .. 0.64

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 3.9e-18
                                       HHHHHHTBT--HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHH...HHHHHHHGGGT-.S-S- CS
                            DALR_2   1 kFeeaMdDDFNTaeAiavlFelakeiNralkeedkaaasalk...allrelaevLGl.lqee 58 
                                       +F eaM+DDFNT eA ++l e+a eiN++ +++d+++ + l+   ++l+el++vLGl +++e
  gi|336254726|ref|YP_004597833.1| 377 AFVEAMNDDFNTREAQSALLEIASEINAHVDDTDEYDYRGLReavDALEELGDVLGLsFTDE 438
                                       59**************************99999999998886445889999******77765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHGGGT-.S-S-H CS
                            DALR_2  20 FelakeiNralkeedkaaasalkallrelaevLGl.lqeep 59 
                                        +l+ e++   +e+d+   ++ ++ lr+  e LG+  q ++
  gi|336254726|ref|YP_004597833.1| 450 VDLVLEVRE--QERDAGNYER-ADELRDELEALGIeVQ-DT 486
                                       577777776..3333333344.4789999999999444.44 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 !   19.7   0.0   1.5e-07    0.0003      10     125 ..      33     149 ..      26     160 .. 0.82
   2 !   20.9   0.0   6.5e-08   0.00013     289     362 ..     250     324 ..     239     337 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-07
                                       -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT..TS-HHHHHHHHHHHHHHHHHHTT-. CS
                      tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke..gvtpeelvekvheeikelfkklni. 83 
                                       +++++HlGh+++ +  D+++R+    g++v +v        +i  +  +   g +  e++e++ e++ +++++ln+ 
  gi|336254726|ref|YP_004597833.1|  33 VSDPPHLGHARSWVHVDVMHRWLEYLGYDVRHVENFTDINEKIVARVGEDdlGESEPEVAESYIEHTLADMRSLNLl 109
                                       5789*****************************98777777777766554116677789999999999*****9972 PP

                                       --SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETT CS
                      tRNA-synt_1g  84 sfdkygrttseehkelvqeifkklkekgliyekeieqlycpk 125
                                         + y r ++  h     +++++l ekg+ ye++ +++++++
  gi|336254726|ref|YP_004597833.1| 110 RAEVYPRVSE--HVPEIIDLVETLVEKGYAYESNGSVYFDVT 149
                                       5667777654..55556689999********99999999875 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 6.5e-08
                                       EGGGH.HHHHTHHHHHHHHTT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS CS
                      tRNA-synt_1g 289 gkdii.kFHtifwPaillgaelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekk 362
                                       g+d + ++H         +++ ++ k     e ++++++K+S+S g++v++++a+++  +++lR +l+a + ++k
  gi|336254726|ref|YP_004597833.1| 250 GRDLVfPHHENEIAQSEAATDRQFAKYWLHCELFQMDDEKMSSSLGNFVTVEDAVDQWGTNVLRTFLTAGSYNSK 324
                                       6664425666666666777788888888888999*********************************98554444 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 !   10.7   0.0   8.8e-05      0.18      22      71 ..      22      71 ..       5     103 .. 0.82
   2 !   25.1   0.0   3.8e-09   7.5e-06     272     343 ..     281     350 ..     271     369 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.8e-05
                      tRNA-synt_1f 22 kdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdm 71
                                      ++  +   G+++S ++H+G +r  + +d++ r l+ +g +vr++    d+
  gi|336254726|ref|YP_004597833.1| 22 ENVLLYYCGLTVSDPPHLGHARSWVHVDVMHRWLEYLGYDVRHVENFTDI 71
                                      44556679***********************************9766665 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 3.8e-09
                      tRNA-synt_1f 272 elillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyfaeq 343
                                       el++++ + kmssS Gn++t+ed+++   ++vlr ++      ++k+l+ d  i ++ + +++ler+y ++ 
  gi|336254726|ref|YP_004597833.1| 281 ELFQMDDE-KMSSSLGNFVTVEDAVDQWGTNVLRTFLTA-GSYNSKQLYSDETIAEAEERWERLERAYETAV 350
                                       77777777.*************************99988.788899**********************8333 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 ?   -0.9   0.0      0.19   3.7e+02      38      66 ..      37      65 ..      32      95 .. 0.90
   2 ?   -2.8   0.0      0.67   1.3e+03     145     184 ..     126     168 ..     117     170 .. 0.76
   3 !   15.5   0.0     2e-06     0.004     546     595 ..     272     321 ..     239     328 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.19
                       tRNA-synt_1 38 lHiGhalaktlkdivirykrmkGkevlyv 66
                                      +H+Gha   +  d++ r+ +  G++v++v
  gi|336254726|ref|YP_004597833.1| 37 PHLGHARSWVHVDVMHRWLEYLGYDVRHV 65
                                      8***********************99876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.67
                       tRNA-synt_1 145 evfvrladkgliyrgkklvnwstkl...ktalselEveykdkk 184
                                            l++kg  y+++  v++++++      ls+ E e  +++
  gi|336254726|ref|YP_004597833.1| 126 DLVETLVEKGYAYESNGSVYFDVTAfddYGKLSNQELEEIESQ 168
                                       5567899**************9976332467888888777766 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 2e-06
                       tRNA-synt_1 546 PfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdv 595
                                        f +  +h  + + +  KmS slgN +  +d +++ g+++lR +l   ++
  gi|336254726|ref|YP_004597833.1| 272 QFAKYWLHCELFQMDDEKMSSSLGNFVTVEDAVDQWGTNVLRTFLTAGSY 321
                                       46666666667777889***************************995554 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 !   14.1   0.0   8.7e-06     0.017       3      66 ..       6      68 ..       4      75 .. 0.82
   2 ?   -1.7   0.0      0.56   1.1e+03     168     198 ..     122     152 ..     106     159 .. 0.82
   3 ?   -0.1   0.1      0.18   3.5e+02      96     150 ..     341     406 ..     289     416 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.7e-06
                                      HHHHCCTTTT.---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE-- CS
                      tRNA-synt_1d  3 ssiLvqkrklqkksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhv 66
                                      ++ L+ +r+   + ++ ++v++ +    ++ + h Gh rs +  d++ r le+lGydv  +   
  gi|336254726|ref|YP_004597833.1|  6 TNTLTGEREP-FEPQDPENVLLYYCGLTVSDPPHLGHARSWVHVDVMHRWLEYLGYDVRHVENF 68
                                      5556555553.5566777899999999*******************************877655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.56
                                       CCHHHHHHHHHCTT-EEECTTCEEEEECCCT CS
                      tRNA-synt_1d 168 eslneivkelkkkglvkesdGalvvfldefg 198
                                       + + ++v+ l +kg++ es+G    +++ f 
  gi|336254726|ref|YP_004597833.1| 122 PEIIDLVETLVEKGYAYESNGSVYFDVTAFD 152
                                       45567788999**********9999998874 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.18
                                       SCCCHHHHHHHHCCCSHC...........CCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1d  96 dLeafykeakkdydeeei...........faerarnyvvkLqsgdedirklwkllvditrtelqkl 150
                                        Le  y+ a   +d  +              + ar+ +v+  ++d ++r++++ l +i+ + + ++
  gi|336254726|ref|YP_004597833.1| 341 RLERAYETAVDALDSPDArtkvedeafraAVDDAREAFVEAMNDDFNTREAQSALLEIASEINAHV 406
                                       455555555444444333444444455545578999999999999999999999999887766555 PP

>> FTO_CTD  FTO C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.2e-05     0.044      53     120 ..     311     385 ..     282     408 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.2e-05
                           FTO_CTD  53 WlRqfwlqGsrhaklhdyWkrkieeLeeawkkmElltrlvLdalrkasetlete........eeildvllelLeer 120
                                        lR f   Gs +++ + y  + i+e ee w+++E  +++++dal + +  ++ e         ++ ++++e++++ 
  gi|336254726|ref|YP_004597833.1| 311 VLRTFLTAGS-YNSKQLYSDETIAEAEERWERLERAYETAVDALDSPDARTKVEdeafraavDDAREAFVEAMNDD 385
                                       5899999886.899999**************************998888777774466444444444444444444 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         3   6.1e+03       6      19 ..     341     354 ..     337     354 .. 0.78
   2 ?   14.2   0.4   1.4e-05     0.028      18      33 ..     464     479 ..     462     482 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3
                               UVR   6 eLeeemeeAaened 19 
                                       +Le++ e A++++d
  gi|336254726|ref|YP_004597833.1| 341 RLERAYETAVDALD 354
                                       67888788999887 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.4e-05
                               UVR  18 edFEkAAklRDqinal 33 
                                        ++E+A +lRD+++al
  gi|336254726|ref|YP_004597833.1| 464 GNYERADELRDELEAL 479
                                       69************98 PP

>> 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 ?   10.9   0.0   7.6e-05      0.15      50      97 ..      93     140 ..      74     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.6e-05
                                       HHHHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE CS
                      tRNA-synt_1c  50 eeaeesiledlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvc 97 
                                       e ++e+ l+d+  l++   e   + s++  e+ +++e L++kG+AY  
  gi|336254726|ref|YP_004597833.1|  93 ESYIEHTLADMRSLNLLRAEVYPRVSEHVPEIIDLVETLVEKGYAYES 140
                                       6689999999*****999777789**********************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); 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: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3420.86
//
Query:       gi|336254727|ref|YP_004597834.1|  [L=323]
Description: hypothetical protein Halxa_3343 [Halopiger xanaduensis SH-6]
Scores for 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-89  298.2  15.4    8.1e-89  297.8  15.4    1.0  1  SPP             Signal-peptide peptidase, presenilin aspartyl
      3e-05   23.7   9.9     0.0014   18.3   5.1    2.6  2  Peptidase_A22B  Signal peptide peptidase
    0.00014   20.7   8.8       0.11   11.2   7.2    2.3  2  Presenilin      Presenilin
  ------ inclusion threshold ------
      0.082   12.4   2.8        2.4    7.7   1.6    2.4  2  DUF1700         Protein of unknown function (DUF1700)


Domain annotation for each model (and alignments):
>> SPP  Signal-peptide peptidase, presenilin aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.8  15.4   1.8e-92   8.1e-89       3     282 ..      18     314 ..      16     315 .. 0.93

  Alignments for each domain:
  == domain 1  score: 297.8 bits;  conditional E-value: 1.8e-92
                               SPP   3 lfvvvqvlalllavplesaelqatedPtqvlnsvvyivlllvftlfvlivikkdkkliiskviyvivvavifyvflv 79 
                                       lf+ +q++al+l +p++++e qa +dP ++ ns+vy  ++lv+t+f+l + k+d +  i+ +i  ++v+ ++yv+  
  gi|336254727|ref|YP_004597834.1|  18 LFLGIQLGALALLEPFYESERQAVDDPANPTNSIVYFGIILVATGFMLAAFKYDLQGLIRAMIVAVSVMLAWYVLSE 94 
                                       78899************************************************************************ PP

                               SPP  80 llsivlvvaglvnlaslvvaialvvllyaypeWyvidlaGvilavGvsalfGislgvlpavvllialavydaisvyk 156
                                        ++ v v++g  n  +   a+++  +ly +peWyvid aGv+++ G++alfGis+g+lpa+ ll++lavydaisvy+
  gi|336254727|ref|YP_004597834.1|  95 FVPPV-VTVGSTNALAAAAAVGVGAALYLHPEWYVIDGAGVLIGAGAAALFGISFGLLPALLLLTVLAVYDAISVYG 170
                                       **999.89999****************************************************************** PP

                               SPP 157 tkhmialaegvvdlklPillvvPetlaysfve.....eafeeaeeaea..........rnvlfiGlGdavlPsilvv 218
                                       t+hm+ laegv+dlk+P++lvvP+tl+ys++e     e++e+++ +ea          r++lfiGlGdav+P+ilv+
  gi|336254727|ref|YP_004597834.1| 171 TEHMLDLAEGVMDLKIPVVLVVPTTLSYSYLEpdsnpETLEDGG-SEAndaddernidRDALFIGLGDAVIPTILVA 246
                                       *****************************998322212222222.34588899*9********************** PP

                               SPP 219 saavfleshil....aglelavllalaGtlvGllvlsilvlrgrpaaGlPllnsGaiaGfligvlaag 282
                                       saa+fle+  +      l++a+l+al+Gtl Gllvl+++vl+gr++aGlPlln+Gai G+lig+la+g
  gi|336254727|ref|YP_004597834.1| 247 SAAFFLEAGTIsvpfIALNWAALGALVGTLAGLLVLMYMVLKGRAHAGLPLLNGGAIGGYLIGALASG 314
                                       ******9866532335899***********************************************98 PP

>> Peptidase_A22B  Signal peptide peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   5.1   3.1e-07    0.0014      44     174 ..      52     194 ..       4     206 .. 0.67
   2 !    7.5   0.2   0.00058       2.6     187     203 ..     232     248 ..     221     288 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.1e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........XXXXXXXXXXXXX------S--XXXXXXX CS
                    Peptidase_A22B  44 ltvlivllgvvalasllsplvtrlflkkvelakvklefla........ielkaaeivalllsiviavlwllkrhwil 112
                                       + + i+l+++  + + +++ ++ l+++ +  ++v l + +        +++ +++ +a+  ++ +    +l+++w +
  gi|336254727|ref|YP_004597834.1|  52 VYFGIILVATGFMLAAFKYDLQGLIRAMIVAVSVMLAWYVlsefvppvVTVGSTNALAAAAAVGVGAALYLHPEWYV 128
                                       44555555555555555555555555555555565555555666666667777777777777777777777777877 PP

                                       XXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXX CS
                    Peptidase_A22B 113 ndilglalailviellrlp.slkvgalLLvglflYDifwVFgtdvmvevAk...eldiPillklPq 174
                                        d  g+ +     +l  +   l  + lLL++l +YD   V+gt+ m+ +A+   +l+iP++l++P+
  gi|336254727|ref|YP_004597834.1| 129 IDGAGVLIGAGAAALFGISfGLLPALLLLTVLAVYDAISVYGTEHMLDLAEgvmDLKIPVVLVVPT 194
                                       7777766655555555554234556799999********************99999*********9 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00058
                                       XXXXXXXXXXXXXXXXX CS
                    Peptidase_A22B 187 iLGlGDivlPGlliall 203
                                        +GlGD v+P +l+a +
  gi|336254727|ref|YP_004597834.1| 232 FIGLGDAVIPTILVASA 248
                                       69************976 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   7.2   2.5e-05      0.11      62     189 ..      48     168 ..       9     175 .. 0.81
   2 !    8.8   0.0   0.00014      0.61     307     355 ..     216     264 ..     195     288 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.5e-05
                        Presenilin  62 lnalililvivvvtfllvlLykyrcykvikgwlilsslllLflvsglllaevlkaynipldyitlllllwnfgvvGv 138
                                       +n+++  ++i+v+t ++++ +ky+ + +i++ ++  s++l  +        vl+++  p+  +  + +l   ++vGv
  gi|336254727|ref|YP_004597834.1|  48 TNSIVYFGIILVATGFMLAAFKYDLQGLIRAMIVAVSVMLAWY--------VLSEFVPPVVTVGSTNALAAAAAVGV 116
                                       699**************************99666666555443........44555555666666677888899999 PP

                        Presenilin 139 iaifw.kgplllqqaYlilisalmAlvfikylpewTtwvlLvvisiyDlvAV 189
                                        a  + +   ++  +  +li+a  A  f   +    + +lL+v+++yD + V
  gi|336254727|ref|YP_004597834.1| 117 GAALYlHPEWYVIDGAGVLIGAGAAALFGISFGLLPALLLLTVLAVYDAISV 168
                                       7766625556799999999999999999999******************998 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00014
                        Presenilin 307 eeeeeeeeseseergvkLGLGDFiFYSvLvgkAalsgdlntvvacfvai 355
                                       e++++++e++ +++++ +GLGD +   +Lv+ Aa   +  t+ + f+a 
  gi|336254727|ref|YP_004597834.1| 216 EANDADDERNIDRDALFIGLGDAVIPTILVASAAFFLEAGTISVPFIAL 264
                                       2233333333355799******************988888887777764 PP

>> DUF1700  Protein of unknown function (DUF1700)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.6   0.00054       2.4     110     170 ..      10      82 ..       7      93 .. 0.77
   2 ?    3.4   0.0     0.011        50      81     137 ..     230     294 ..     205     315 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00054
                           DUF1700 110 llvvalallvsplvllvksllkgfeelsln............vfvsigllglGllllivayylvkilykltvk 170
                                       + v++++ll+ ++ l  + ll+ f e   +            v+++i+l++ G++l+   y l  ++  ++v+
  gi|336254727|ref|YP_004597834.1|  10 VAVGVTVLLFLGIQLGALALLEPFYESERQavddpanptnsiVYFGIILVATGFMLAAFKYDLQGLIRAMIVA 82 
                                       456667777778888888888888877777777888888889*******************999888887775 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.011
                           DUF1700  81 ailavigLsllnlilvlipliviislvlsllvvalal........lvsplvllvksllkgfeels 137
                                       a+++ +g  ++  ilv  +++ + +  +s+  +al          ++++l++l++++lkg  ++ 
  gi|336254727|ref|YP_004597834.1| 230 ALFIGLGDAVIPTILVASAAFFLEAGTISVPFIALNWaalgalvgTLAGLLVLMYMVLKGRAHAG 294
                                       44555555666666666665555444333333332222334444588999999999999977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2401.64
//
Query:       gi|336254728|ref|YP_004597835.1|  [L=84]
Description: hypothetical protein Halxa_3344 [Halopiger xanaduensis SH-6]
Scores for 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-05   23.0   0.0    5.6e-05   22.9   0.0    1.2  1  Gar1      Gar1/Naf1 RNA binding region


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   3.2e-09   5.6e-05      49      88 ..      36      73 ..       2      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.2e-09
                                      TT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHHH CS
                              Gar1 49 fnsilflenktqiGkVdEifGpvnepyysVklnsseeika 88
                                      +++ + + n +++G+V ++fGpv  py +V ++  ++++ 
  gi|336254728|ref|YP_004597835.1| 36 IGTAVLDDNLEEVGRVVDVFGPVGRPYLAVTPD--DDVHL 73
                                      6778888999*********************99..66554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       166  (0.00925874); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); 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: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 622.91
//
Query:       gi|336254729|ref|YP_004597836.1|  [L=93]
Description: Signal recognition particle 19 kDa protein [Halopiger xanaduensis SH-6]
Scores for 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-25   89.0   0.0    3.6e-25   88.7   0.0    1.1  1  SRP19     SRP19 protein
  ------ inclusion threshold ------
       0.12   12.9   0.1         19    5.8   0.0    2.2  2  HMA       Heavy-metal-associated domain


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 !   88.7   0.0     4e-29   3.6e-25       1      92 [.       5      89 ..       5      91 .. 0.94

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 4e-29
                                      EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSS.TTCCEEEEEC-..........SS CS
                             SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrd.wanpGrVrvklkedgkevnekik 78
                                      vi+P+Yld++ +r+eGRrv+++lave+Pt++eia+a++++g+++++e++k+y+r+ wa++GrV v+          + +
  gi|336254729|ref|YP_004597836.1|  5 VIWPAYLDATLSRSEGRRVSQDLAVEEPTVDEIAKAVQQIGYDATIERDKAYSREpWAQRGRVVVRGA--------DDS 75
                                      7*****************************************************************85........457 PP

                                      -CHHHHHHHHHHHH CS
                             SRP19 79 nkkellkkiaellk 92
                                      +k++l++++a+++ 
  gi|336254729|ref|YP_004597836.1| 76 TKNDLIQAVAAYVV 89
                                      89999999998875 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0021        19      44      62 .]      30      47 ..      19      47 .. 0.81
   2 ?    5.2   0.0    0.0033        30      36      57 ..      65      85 ..      62      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0021
                               HMA 44 aestklrkiieaiekagyk 62
                                      +e+ ++ +i +a++++gy+
  gi|336254729|ref|YP_004597836.1| 30 EEP-TVDEIAKAVQQIGYD 47
                                      344.6699**********7 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0033
                               HMA 36 ktvtVegdaestklrkiieaie 57
                                      ++v+V+g ++stk +++i+a+ 
  gi|336254729|ref|YP_004597836.1| 65 GRVVVRGADDSTK-NDLIQAVA 85
                                      68*****999954.99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 767.03
//
Query:       gi|336254730|ref|YP_004597837.1|  [L=406]
Description: ABC transporter periplasmic protein [Halopiger xanaduensis SH-6]
Scores for complete 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   83.4   3.4    1.7e-23   83.4   3.4    1.5  2  Peripla_BP_2  Periplasmic binding protein
     0.0032   17.4   5.4     0.0073   16.2   5.4    1.7  1  PGF-CTERM     PGF-CTERM motif
  ------ inclusion threshold ------
      0.076   13.9   0.1       0.26   12.2   0.1    1.9  1  Pilin_N       Archaeal Type IV pilin, N-terminal
       0.95    8.5  13.4        1.7    7.7  13.4    1.3  1  DUF2457       Protein of unknown function (DUF2457)
        2.1    8.5   8.8        1.5    8.9   5.3    2.4  2  PT-VENN       Pre-toxin domain with VENN motif


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 ?   -3.7   0.0       1.9   6.9e+03      11      39 ..      13      41 ..      11      54 .. 0.63
   2 !   83.4   3.4   4.7e-27   1.7e-23       1     203 [.      76     282 ..      76     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.9
                                      HHHHTT-GGGEEEB-GGG--GGGGGGT.. CS
                      Peripla_BP_2 11 illalGatdkvvgvdtttsdpldadklee 39
                                      +lla+ ++  vvg   +t +++ a+ + +
  gi|336254730|ref|YP_004597837.1| 13 VLLAGAVPAGVVGSPSATAGESTAETAQA 41
                                      56667777777777777777777765543 PP

  == domain 2  score: 83.4 bits;  conditional E-value: 4.7e-27
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                       +++l ps +++l+++Ga+dkvvg   ++++ +    ++   ++ + + ++  E++++  PD+v++ + l+  d ++ 
  gi|336254730|ref|YP_004597837.1|  76 VVALQPSDAQTLYEIGAEDKVVGMPVSPYTDYLNASAD-LDITEDDGVTPVAEEVIDREPDVVLAANALEGDDVIDT 151
                                       89*********************999988888775533.3444455555556*****************99****** PP

                                       HHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE CS
                      Peripla_BP_2  78 llksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvva 154
                                       l+++g  ++++++s+ ++++ e++r +gel+g+ + a +  +++d++l  + +a++ e ++p+++++ +d+   + a
  gi|336254730|ref|YP_004597837.1| 152 LREAGLTVYVFPTSESLDGVAENVRLTGELVGECEGAADTLEWMDERLSVVDEAVPDE-DRPLAYYAMGDG---YTA 224
                                       **********************************************************.********9999...*** PP

                                       -TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH.........H CS
                      Peripla_BP_2 155 gsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr.........a 203
                                       g++++  ++l ++g++n+ a+ + +++++is E ++++dp++i++ ++         a
  gi|336254730|ref|YP_004597837.1| 225 GNGTFQDEILTTAGVDNLGADAGIEGWATISEEVVVEEDPEWIVYGDSaeeppvreaA 282
                                       ******************55555***********************994444443332 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   5.4     2e-06    0.0073       1      22 [.     383     405 ..     383     406 .] 0.93

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2e-06
                         PGF-CTERM   1 tPGFGavlAlaGLLaaa.lLaRR 22 
                                       +PGFGa +A++G La+a lLaRR
  gi|336254730|ref|YP_004597837.1| 383 IPGFGAPVAIVGALAVAvLLARR 405
                                       7****************999999 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 ?   12.2   0.1   7.3e-05      0.26      10      69 ..       6      69 ..       5      80 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.3e-05
                           Pilin_N 10 iLmvaitvIlaAviaafvlgl..asneekapqasievk..idssastgkna.vslehkgGdsidt 69
                                      iL+++ tv+la+ + a v+g   a   e++++++   +   ++ + t +   ++le   G+ i+ 
  gi|336254730|ref|YP_004597837.1|  6 ILLITATVLLAGAVPAGVVGSpsATAGESTAETAQAAQlaQTQADPTCE-YpLTLEDATGEEITI 69
                                      89*********99999888886644444444333323321333333333.269999999998875 PP

>> DUF2457  Protein of unknown function (DUF2457)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  13.4   0.00048       1.7      37     113 ..     310     387 ..     307     389 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00048
                           DUF2457  37 nairkLgeeaeeEaeeeeeee.eddeedeeddddddddedddedddeedededddstvedlseeasdGyetDnEaGF 112
                                       +ai  +++e+  +a ee e++ e d + ++dd++  d+  +d   de d+ ++++s   + ++++++G + D+  GF
  gi|336254730|ref|YP_004597837.1| 310 LAIEEIASEVHPDAYEEAESDlEIDTDVSTDDNETADNGSNDGSADESDDASNEESGDGSADDAEDEGSSGDSIPGF 386
                                       57899999999999998765445555444444444444444444344444444666666678899*******99999 PP

                           DUF2457 113 A 113
                                        
  gi|336254730|ref|YP_004597837.1| 387 G 387
                                       6 PP

>> PT-VENN  Pre-toxin domain with VENN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.3   0.00042       1.5      12      43 ..       9      47 ..       7      48 .. 0.88
   2 ?   -0.8   0.1      0.47   1.7e+03      43      52 .]     294     303 ..     293     303 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00042
                           PT-VENN 12 vsalstlaaGlaGgvvg.......gtladavaGaeagen 43
                                      ++a + la+++ +gvvg       +++a+++++a+ +++
  gi|336254730|ref|YP_004597837.1|  9 ITATVLLAGAVPAGVVGspsatagESTAETAQAAQLAQT 47
                                      677788999999999999999999999999999999986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.47
                           PT-VENN  43 nAVeNNfLsd 52 
                                       +AV  N++s+
  gi|336254730|ref|YP_004597837.1| 294 VAVNDNYMSQ 303
                                       69******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2753.53
//
Query:       gi|336254731|ref|YP_004597838.1|  [L=337]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-94  316.1  30.9    2.5e-94  315.8  30.9    1.0  1  FecCD     FecCD transport family
    0.00029   20.4  17.2    0.00061   19.4  17.2    1.7  1  ABC-3     ABC 3 transport family
  ------ inclusion threshold ------
        5.3    6.4   5.1         11    5.3   5.1    1.5  1  DUF3482   Domain of unknown function (DUF3482)


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 !  315.8  30.9   4.1e-98   2.5e-94       1     312 []      17     331 ..      17     331 .. 0.98

  Alignments for each domain:
  == domain 1  score: 315.8 bits;  conditional E-value: 4.1e-98
                             FecCD   1 llllllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNp 70 
                                       ll+++++ s ++g+v i++ +v +a+l++a       + +++ iv+++rlpr+++a++vG+aLa+aG+++Q+ +rNp
  gi|336254731|ref|YP_004597838.1|  17 LLVVVVVGSAMFGPVRIDAPTVARAILNRAgagpyevSAAHQAIVVDVRLPRIALAAVVGFALAAAGTVMQGFFRNP 93 
                                       689999*********************999******9999999********************************** PP

                             FecCD  71 LadPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsal 147
                                       LadPsi+G+ssgaa+gav+a+++     ++ +l laaf+gal++++lv+++a+ ++++  ++l+LaG+av+a+l+a+
  gi|336254731|ref|YP_004597838.1|  94 LADPSIIGVSSGAAAGAVAAIAFP-ALVPFGSLHLAAFVGALATAFLVYAIATDGGRTPVATLLLAGVAVQAFLGAV 169
                                       ***********************5.999999*********************9************************ PP

                             FecCD 148 tsllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrlll 224
                                       +s++l+  + ++l++++ wl+G l + +w +v ++l+++++++l+l+++ar+l++l lg+e A++lGv+ver++lll
  gi|336254731|ref|YP_004597838.1| 170 ISYMLVH-SGDSLREAVVWLMGHLHNSTWGDVRFALPFAVVGVLALCAFARDLNVLLLGEEDAHHLGVDVERTKLLL 245
                                       *****99.889****************************************************************** PP

                             FecCD 225 lllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtali 301
                                       l+l++++ta+ va++G+igFvGL+vPhi+rllvg+dhr+llp sal+Ga +l+++d+lar    p+e+pvgivta++
  gi|336254731|ref|YP_004597838.1| 246 LALASVVTAAGVAVAGVIGFVGLVVPHIMRLLVGPDHRILLPTSALAGASFLVATDTLARAG--PAEVPVGIVTAAL 320
                                       ************************************************************88..9************ PP

                             FecCD 302 Gapffiylllr 312
                                       Gapff++ll+r
  gi|336254731|ref|YP_004597838.1| 321 GAPFFLFLLVR 331
                                       *********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 !   19.4  17.2     1e-07   0.00061      45     232 ..     109     304 ..      65     332 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1e-07
                             ABC-3  45 Gvalayllgvn.....lllgailvgliaavalellkr...ktklkedtaigivlsvflalglvlvslikk.skvdld 112
                                       G + a+++        l l+a++ +l+ a+ + ++++   +t +++  + g+ +++fl+  +  +   ++ s  +  
  gi|336254731|ref|YP_004597838.1| 109 GAVAAIAFPALvpfgsLHLAAFVGALATAFLVYAIATdggRTPVATLLLAGVAVQAFLGAVISYMLVHSGdSLREAV 185
                                       33333333222224457788888888888888878762224556666778********9776555555545888899 PP

                             ABC-3 113 syLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGv 189
                                        +L+G +   +  d+   +  ++v +l+l+ f ++l ++ + ee A+  g+ v++ kllllal ++  ++ + ++Gv
  gi|336254731|ref|YP_004597838.1| 186 VWLMGHLHNSTWGDVRFALPFAVVGVLALCAFARDLNVLLLGEEDAHHLGVDVERTKLLLLALASVVTAAGVAVAGV 262
                                       9**************************************************************************** PP

                             ABC-3 190 iLvialliiPaatArrltrslesllivAillglvsvvaGlllS 232
                                       i  + l ++P ++ ++++ + + ll +++l g+ ++va  +l 
  gi|336254731|ref|YP_004597838.1| 263 IGFVGL-VVPHIMRLLVGPDHRILLPTSALAGASFLVATDTLA 304
                                       *98885.679999999999999999999888888877765554 PP

>> DUF3482  Domain of unknown function (DUF3482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   5.1    0.0018        11     150     188 ..     102     140 ..      90     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0018
                           DUF3482 150 lgaGaaaGAaaGagiDlavgGltLGaaaaiGalaGglaa 188
                                       + +GaaaGA+a  +  ++v + +L +aa +Gala + + 
  gi|336254731|ref|YP_004597838.1| 102 VSSGAAAGAVAAIAFPALVPFGSLHLAAFVGALATAFLV 140
                                       569******************************977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 2844.24
//
Query:       gi|336254732|ref|YP_004597839.1|  [L=440]
Description: Iron-chelate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-35  120.7   0.0    1.2e-34  119.8   0.0    1.5  1  ABC_tran     ABC transporter
    2.5e-08   34.1   0.7      4e-05   23.6   0.1    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00018   21.1   0.1      0.026   14.0   0.1    2.3  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00022   21.8   0.0     0.0003   21.4   0.0    1.2  1  AAA_23       AAA domain
     0.0007   20.0   1.5     0.0013   19.1   0.5    2.1  2  AAA_16       AAA ATPase domain
     0.0019   17.5   0.0     0.0045   16.3   0.0    1.7  1  Zeta_toxin   Zeta toxin
      0.004   17.6   0.0      0.012   16.0   0.0    1.8  2  AAA          ATPase family associated with various cellular a
     0.0056   16.4   0.1      0.012   15.4   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0061   16.3   0.0      0.017   14.9   0.0    1.7  1  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.015   15.6   0.1      0.051   13.9   0.1    1.9  1  AAA_22       AAA domain
      0.023   14.4   0.0       0.26   10.9   0.0    1.9  2  AAA_15       AAA ATPase domain
      0.034   13.7   0.3       0.11   12.1   0.1    2.0  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.039   13.9   0.0       0.12   12.3   0.0    1.9  2  RsgA_GTPase  RsgA GTPase
       0.05   13.5   0.0       0.15   11.9   0.0    1.8  2  NTPase_1     NTPase
      0.068   13.3   1.2       0.53   10.4   1.2    2.6  1  AAA_33       AAA domain
      0.069   10.7   0.1      0.092   10.3   0.1    1.1  1  DUF3584      Protein of unknown function (DUF3584)
      0.086   12.8   0.0       0.23   11.4   0.0    1.7  1  NACHT        NACHT domain
      0.091   12.8   0.0       0.16   12.0   0.0    1.4  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
       0.11   12.6   0.0       0.25   11.5   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
       0.12   12.0   0.0       0.22   11.1   0.0    1.4  1  AAA_27       AAA domain
       0.12   11.6   0.0       0.19   10.9   0.0    1.2  1  NB-ARC       NB-ARC domain
       0.14   12.2   0.0       0.41   10.7   0.0    1.8  1  AAA_5        AAA domain (dynein-related subfamily)
        0.2   11.4   0.0       0.39   10.4   0.0    1.4  1  AAA_24       AAA domain
       0.22   11.3   0.2        0.8    9.5   0.1    1.9  2  MukB         MukB N-terminal


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 !  119.8   0.0   1.6e-37   1.2e-34       1     137 []      35     184 ..      35     184 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 1.6e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++vsl++ +ge v++vG+nGaGK+tLl++++g l+p++G++++dg+d+++ + + +++ ++v+pq+++l     vr
  gi|336254732|ref|YP_004597839.1|  35 LEDVSLTVDPGEFVGLVGPNGAGKTTLLRTISGALEPDSGTVEIDGTDVHDVSSRASSRLVAVVPQDTTLSFSFDVR 111
                                       689*******************************************************************99999*9 PP

                                       HH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +                  e+++ +e+al++ + +e++d+++     ++SgGq+qrv+lara++++ + lllDEpta
  gi|336254732|ref|YP_004597839.1| 112 DVvemgrhphrsrfvpprpEDQAVVERALERTRTSEFADRPI----DEVSGGQRQRVVLARAIAQATPALLLDEPTA 184
                                       99*9*************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 !   23.6   0.1   5.4e-08     4e-05       1      23 [.      47      69 ..      47     114 .. 0.80
   2 !    8.9   0.0    0.0016       1.2     230     284 ..     149     200 ..     119     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.4e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      + +l+GpNg+GK++LL++++++ 
  gi|336254732|ref|YP_004597839.1| 47 FVGLVGPNGAGKTTLLRTISGAL 69
                                      678****************9985 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellke 284
                                        ++p++e+S G+++    +++  + ++ ++ ll+DEp ++L+   + + lel++e
  gi|336254732|ref|YP_004597839.1| 149 ADRPIDEVSGGQRQR---VVLARAIAQATPALLLDEPTASLDVNHQVETLELVRE 200
                                       578999******999...3333333344499***********9444333333333 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 !   14.0   0.1   3.5e-05     0.026      25     188 ..      46     203 ..      35     218 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTT.TTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSC.EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersak.klrseklsdlihkskekasvkkaeveitfdnedkklkiekee.vsi 99 
                                       +f  +vGpNG+GK+ ll  i+  L  +s + ++  ++++d+ ++      +++  v+++ +++  +++ +  + v++
  gi|336254732|ref|YP_004597839.1|  46 EFVGLVGPNGAGKTTLLRTISGALEPDSGTvEIDGTDVHDVSSR------ASSRLVAVVPQDTTLSFSFDVRDvVEM 116
                                       58889***************988876655213333444443333......333334443333333333333221455 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-S..TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagis..kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                        r+  r+     + +++ v ++ +++   s+  +  +++ SgG+++ v la       ++ +p  llDe  a LD +
  gi|336254732|ref|YP_004597839.1| 117 GRHPHRSRFVPPRPEDQAVVERALERTRTSEFADrpIDEVSGGQRQRVVLA----RAIAQATPALLLDEPTASLDVN 189
                                       555555555444455555555444443333222211468899999865554....4445677788899999999999 PP

                                       HHHHHHHHHHHHCT CS
                                       xxxxxxxxxxxxxx RF
                             SMC_N 175 nvkkvaellkeksk 188
                                       +  +  el++e  +
  gi|336254732|ref|YP_004597839.1| 190 HQVETLELVRELVS 203
                                       88888888887655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0     4e-07    0.0003      21      46 ..      47      72 ..      27     164 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4e-07
                            AAA_23 21 ltlItGpNGaGKTTildAiklaLyge 46
                                      ++ ++GpNGaGKTT+l+ i  aL  +
  gi|336254732|ref|YP_004597839.1| 47 FVGLVGPNGAGKTTLLRTISGALEPD 72
                                      6679***************9999654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.5   1.8e-06    0.0013      24     127 ..      44     170 ..      32     258 .. 0.65
   2 ?   -2.7   0.0       9.1   6.8e+03      99     106 ..     346     353 ..     317     426 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.8e-06
                            AAA_16  24 p.elvllsGesGvGKsslvrellralekdggif.lrgkcdql..esa.......ipysa.laqalareellrqllde 88 
                                       p e v l+G+ G GK++l+r++  ale d g + + g+ ++   ++a       +p ++ l   ++  + + +++++
  gi|336254732|ref|YP_004597839.1|  44 PgEFVGLVGPNGAGKTTLLRTISGALEPDSGTVeIDGTDVHDvsSRAssrlvavVPQDTtLSFSFDV-RDVVEMGRH 119
                                       347899***********************76666666666663322233332222223333333322.333333333 PP

                            AAA_16  89 .......aesaeleawrekleeala..............avpelagaeasrllellkrll 127
                                              +        r + +++++              +++e++g ++   + +l+r++
  gi|336254732|ref|YP_004597839.1| 120 phrsrfvP-------PRPEDQAVVEralertrtsefadrPIDEVSGGQR--QRVVLARAI 170
                                       43332221.......2222222222344455556666665555555544..333333444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.1
                            AAA_16  99 ekleeala 106
                                       + le+a+ 
  gi|336254732|ref|YP_004597839.1| 346 DDLERAVD 353
                                       44433333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.1e-06    0.0045      21      63 ..      50      92 ..      44     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.1e-06
                        Zeta_toxin 21 lgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyee 63
                                      l+G  GAGK++l++ +  +le++++ v++d++d+     ++++
  gi|336254732|ref|YP_004597839.1| 50 LVGPNGAGKTTLLRTISGALEPDSGTVEIDGTDVHDVSSRASS 92
                                      8899****************************99877666555 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 !   16.0   0.0   1.6e-05     0.012       3      50 ..      50      99 ..      48     108 .. 0.82
   2 ?   -2.7   0.0       9.7   7.3e+03      14      66 ..     166     181 ..     146     210 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                                      EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelf 50
                                      l+Gp G GKT+l + +   l+  +  +ei+g+++ +    +s++ ++ + 
  gi|336254732|ref|YP_004597839.1| 50 LVGPNGAGKTTLLRTISGALEpdSGTVEIDGTDVHDVSSRASSRLVAVVP 99
                                      89******************654889*******99777777776666555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.7
                                       HHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                               AAA  14 lakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDE 66 
                                       la+a+a+                                      +  l++DE
  gi|336254732|ref|YP_004597839.1| 166 LARAIAQA-------------------------------------TPALLLDE 181
                                       34444444.....................................34444444 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 !   15.4   0.1   1.6e-05     0.012      15      49 ..      38      72 ..      33      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                       ++++d+ +++ l+Gp+G+GK+Tll  i+  L p+
  gi|336254732|ref|YP_004597839.1| 38 VSLTVDPGEFVGLVGPNGAGKTTLLRTISGALEPD 72
                                      567888888999*************8888777776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.3e-05     0.017      16      49 ..      43      76 ..      37     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrv 49
                                      ++  ++ l+Gp G+GKtt+l+++  a+e + g+v
  gi|336254732|ref|YP_004597839.1| 43 DPGEFVGLVGPNGAGKTTLLRTISGALEPDSGTV 76
                                      55668899****************9999885555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.8e-05     0.051       8      71 ..      48     141 ..      42     213 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee............erpevvfvtlpsst.sskdllrellralglelka. 70 
                                       + ++G+ G+GKTtllr++   l+ ++   e            +++++v v ++  t s +   r++++   +++ + 
  gi|336254732|ref|YP_004597839.1|  48 VGLVGPNGAGKTTLLRTISGALEPDSGTVEidgtdvhdvssrASSRLVAVVPQDTTlSFSFDVRDVVEMGRHPHRSr 124
                                       5689**************99996543333366666666665555555555555555333333555555555555555 PP

                            AAA_22  71 ................e 71 
                                                       e
  gi|336254732|ref|YP_004597839.1| 125 fvpprpedqavveralE 141
                                       55555555555555553 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00035      0.26      15      44 ..      36      66 ..      33      96 .. 0.75
   2 ?    1.2   0.0      0.31   2.3e+02     292     356 ..     151     206 ..     128     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsileald 44
                                      +dv++ +++  +  l+G+N++GK+++l+ + 
  gi|336254732|ref|YP_004597839.1| 36 EDVSLTVDPGeFVGLVGPNGAGKTTLLRTIS 66
                                      56666666656889*************9985 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.31
                            AAA_15 292 lplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnk 356
                                        p+++++ G+++ ++l+  i+ a            ll++EP a+L  ++q +  +l +el+++++
  gi|336254732|ref|YP_004597839.1| 151 RPIDEVSGGQRQRVVLARAIAQATPA---------LLLDEPTASLDVNHQVETLELVRELVSEGR 206
                                       58889999999999998888888888.........9************************99876 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 ?   12.1   0.1   0.00015      0.11       3      21 ..      48      66 ..      46      86 .. 0.86
   2 ?   -2.0   0.0       3.1   2.3e+03      86     124 ..     383     425 ..     355     435 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                                      EEEEESTTCCHHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhll 21
                                      ++l+G+ G+GKTtLl+++ 
  gi|336254732|ref|YP_004597839.1| 48 VGLVGPNGAGKTTLLRTIS 66
                                      6799***********9985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.1
                                       EEEEECTTTTHHHH...HTT.SHHHHHCCCECEEEEEEETTTH CS
                              cobW  86 iliEttGlaePapv...aft.eeelksdltldavvavvDaknl 124
                                       + +Ett ++e  +v   a++  e++++++ + +v  v+Da + 
  gi|336254732|ref|YP_004597839.1| 383 VAVETTPVSERHFVdpaALErYESCRERAAAATVRRVIDAVES 425
                                       4567777777666665433357778888888888888888544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.12      92     129 ..      37      75 ..       7     135 .. 0.82
   2 ?   -1.9   0.0       3.7   2.7e+03      82     124 ..     337     381 ..     319     394 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                       HHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                       +++  ++  +++ lvG+ G+GK+tL+ ++ + le   g 
  gi|336254732|ref|YP_004597839.1|  37 DVSLTVDPgEFVGLVGPNGAGKTTLLRTISGALEPDSGT 75 
                                       5555555557888****************9985544433 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.7
                                       --TTTHTTHHHHHHHCTT.SEEEEECST.TSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  82 vsaktkegleelkellkd.ktsvlvGqS.GvGKStLinallpele 124
                                        sa + ++ ++l+++++  +++vl+  S G G  +++++l + ++
  gi|336254732|ref|YP_004597839.1| 337 FSALSADDRDDLERAVDAsEVTVLADLSiGTGNRAVLEVLEGCER 381
                                       356667888899999988799999987779999999988888643 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.15       3      40 ..      49      88 ..      47     126 .. 0.84
   2 ?   -2.8   0.0       7.2   5.3e+03     116     133 ..     196     213 ..     170     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                                      EEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE-- CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkss..gvkvgGfyteevre 40
                                       + Gp G GKtTl++ ++ +l+ +   v+++G  +++v +
  gi|336254732|ref|YP_004597839.1| 49 GLVGPNGAGKTTLLRTISGALEPDsgTVEIDGTDVHDVSS 88
                                      688******************8553368888888777764 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.2
                                       HHHHHHHTTTSEEEEE-- CS
                          NTPase_1 116 eaveevLksekpvlavih 133
                                       e v+e++++++  +a ih
  gi|336254732|ref|YP_004597839.1| 196 ELVRELVSEGRTAVAAIH 213
                                       455666666666666666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.2   0.00071      0.53       4      24 ..      50      70 ..      47     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00071
                            AAA_33  4 lvGlpGsGKstlaerllkklg 24
                                      lvG++G+GK+tl++ +  +l 
  gi|336254732|ref|YP_004597839.1| 50 LVGPNGAGKTTLLRTISGALE 70
                                      89***********99876665 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00012     0.092      15      37 ..      43      65 ..      38      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                           DUF3584 15 dldghtnieGtNaaGKTtLlrLi 37
                                      d+ + + ++G N+aGKTtLlr+i
  gi|336254732|ref|YP_004597839.1| 43 DPGEFVGLVGPNGAGKTTLLRTI 65
                                      666778899************98 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0003      0.23       4      24 ..      49      69 ..      46      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                                      EEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqklalaw 24
                                       l G++G GKTtLl+ +  a+
  gi|336254732|ref|YP_004597839.1| 49 GLVGPNGAGKTTLLRTISGAL 69
                                      589*************98766 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00022      0.16      18      44 ..      42      70 ..      22      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                                      H..TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrglakalg 44
                                      +  g+++ L G+ GaGKTtl r +  al+
  gi|336254732|ref|YP_004597839.1| 42 VdpGEFVGLVGPNGAGKTTLLRTISGALE 70
                                      14466799***************988875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00033      0.25       2      22 ..      48      68 ..      47      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                                      EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                      v++vG   +GK+tL+++++g+
  gi|336254732|ref|YP_004597839.1| 48 VGLVGPNGAGKTTLLRTISGA 68
                                      89****************996 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00029      0.22      19      47 ..      38      66 ..      27      69 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAis 47
                                      +++  +  ++  ++GpN AGK+t+lr is
  gi|336254732|ref|YP_004597839.1| 38 VSLTVDPGEFVGLVGPNGAGKTTLLRTIS 66
                                      4444457788889*************997 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00025      0.19      17      41 ..      43      66 ..      33      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                                      TSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqil 41
                                      +++  +v+lvG  G GKttl++ i 
  gi|336254732|ref|YP_004597839.1| 43 DPG-EFVGLVGPNGAGKTTLLRTIS 66
                                      666.69***************9885 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   0.00054      0.41       4      24 ..      50      72 ..      48      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00054
                                      EE--SSSSHHHHHHHGGGGB..S CS
                             AAA_5  4 LvGppGtgKselaerlaaal..n 24
                                      LvGp G gK++l + ++ al   
  gi|336254732|ref|YP_004597839.1| 50 LVGPNGAGKTTLLRTISGALepD 72
                                      9****************999532 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   0.00052      0.39       6      43 ..      49      83 ..      47     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00052
                            AAA_24  6 liyGpsgiGKTtlakelgpkplfidtekGlksldadkf 43
                                       ++Gp+g+GKTtl++++   +l    + G+ ++d++++
  gi|336254732|ref|YP_004597839.1| 49 GLVGPNGAGKTTLLRTI-SGAL--EPDSGTVEIDGTDV 83
                                      689*************9.4443..34455555555555 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0011       0.8      30      60 ..      49      79 ..      41      97 .. 0.80
   2 ?   -1.2   0.0         2   1.5e+03     121     155 ..     184     218 ..     155     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                                      HHHS--SHHHHHHHHHHHHHHS--TTT---- CS
                              MukB 30 tlsGgnGaGksttmaafvtaliPdlsllhfr 60
                                       l G nGaGk+t + ++  al Pd   ++  
  gi|336254732|ref|YP_004597839.1| 49 GLVGPNGAGKTTLLRTISGALEPDSGTVEID 79
                                      588*********************9877654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                                       EEES--TT--HHHHHEE--SSS--EE--HHHHHHH CS
                              MukB 121 alqgleedvkltdvlleklddkkarvrelnelkek 155
                                       a  +++++v+  +++ e +++ ++ v ++ +l  +
  gi|336254732|ref|YP_004597839.1| 184 ASLDVNHQVETLELVRELVSEGRTAVAAIHDLDLA 218
                                       45688999999999999999999999999998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3170.78
//
Query:       gi|336254733|ref|YP_004597840.1|  [L=407]
Description: ferrichrome-binding protein [Halopiger xanaduensis SH-6]
Scores for 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   59.8   0.0    6.1e-16   58.7   0.0    1.5  2  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
       0.17   11.8   0.0       0.28   11.1   0.0    1.3  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
       0.32   11.0   2.1       0.51   10.3   2.1    1.3  1  DUF3558       Protein of unknown function (DUF3558)


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 !   58.7   0.0     1e-19   6.1e-16      13     236 ..      99     353 ..      90     355 .. 0.84
   2 ?   -2.6   0.0      0.55   3.3e+03      80     114 ..     367     400 ..     362     403 .. 0.77

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 1e-19
                                       HHTT-GGGEEEB-GGG--GGGGGGT.........TS-BSBESSSB-HHHHHHH--SEEEE-GGG......GGGHHHH CS
                      Peripla_BP_2  13 lalGatdkvvgvdtttsdpldadklee.......aivevgadgeidvEklaalkPDlvilskgl...gltdedeell 79 
                                       +alG++d + +    +s+p++ ++          ++  + ++g++d E   +l++D+ +l++++   ++ +  ee  
  gi|336254733|ref|YP_004597840.1|  99 IALGQLDGLRALVYRDSWPTALYDTIPgvdvsfdEVEQLHGGGSFDQEVFYELDCDVHLLDPNFvslKHDSVSEEDF 175
                                       666666666666666677777776544666667677788889999999****************8886666666666 PP

                                       HHHS-EEE----TTS............HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEE CS
                      Peripla_BP_2  80 ksgiptvivessntg............eslkeqiralgellgledeaeklvaeidsklaaaksaidse.kpkpvlvf 143
                                       +++++ v    +n +            +sl++ ++ +++l+++ d++e + + +d+ +a+++s ++    ++++ ++
  gi|336254733|ref|YP_004597840.1| 176 EEIADDVGPVVGNYIrrhgeewhdypyYSLYDAFEKIAKLFQERDRYEIIKSVHDEFIAELQSQLPPReERPEIGLL 252
                                       6666666666666557889***********************************************99766665555 PP

                                       EETTE......EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH....HHHT-S--HH CS
                      Peripla_BP_2 144 ggade....ggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr....aeadnktgle 212
                                       ++  +    +++ ++  ++++++  ++lgi ++++ +  ++y++ + Eq+l++dpdv++++       +++  ++ e
  gi|336254733|ref|YP_004597840.1| 253 STFSDfeegSFHAYPIGDGNGKKQYRDLGIVDAFEPHIDGSYANWDYEQLLEADPDVLVFAYGlsdvTAEEFEERME 329
                                       55555667999999999999999999***********9********************999999999999999**** PP

                                       HHT-SHHHHTSHHHHTT-EEEE-H CS
                      Peripla_BP_2 213 flkenpllaelpAvkngrVyalds 236
                                       +l ++ +  +l Avkn r y+ + 
  gi|336254733|ref|YP_004597840.1| 330 KLRSHSVGRRLAAVKNDRLYRGGT 353
                                       ********************9875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.55
                                       HHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHH CS
                      Peripla_BP_2  80 ksgiptvivessntgeslkeqiralgellgledea 114
                                       ++  +++ ++++++ +++++ + + ++l+++++ a
  gi|336254733|ref|YP_004597840.1| 367 AAAKQFYPDRFGPW-NGIETLLDEDAQLFDHQRIA 400
                                       55556778888888.99999999999999999866 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.7e-05      0.28       3      24 ..      13      34 ..      11      35 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.7e-05
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggca 24
                                      +RRd  K +++   +++l+gc+
  gi|336254733|ref|YP_004597840.1| 13 TRRDYVKYGGVIVGGGLLAGCT 34
                                      8********************7 PP

>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.1   8.5e-05      0.51       2      41 ..      29      67 ..      28      81 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.5e-05
                           DUF3558  2 llaGCssttdGt.apaasssassssttsssaapavpldtsg 41
                                      llaGC++ ++G  ++a ++++s++++t+++++ +   ++sg
  gi|336254733|ref|YP_004597840.1| 29 LLAGCTDDESGApSAADDAADSEMNSTTDTSSESA--EESG 67
                                      79*********964444444444444444444444..3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3077.20
//
Query:       gi|336254734|ref|YP_004597841.1|  [L=624]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Halopiger xanaduensis SH-6]
Scores for complete 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-64  218.4   0.0    1.9e-64  217.7   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
    1.6e-24   86.5   0.0    3.2e-24   85.5   0.0    1.5  1  GatB_Yqey  GatB domain
    7.9e-16   58.1   0.0    1.5e-15   57.2   0.0    1.5  1  GAD        GAD domain
    0.00067   19.8   0.3     0.0018   18.4   0.3    1.7  1  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 !  217.7   0.0   4.2e-68   1.9e-64       2     268 ..      14     441 ..      13     445 .. 0.95

  Alignments for each domain:
  == domain 1  score: 217.7 bits;  conditional E-value: 4.2e-68
                                       EEEEEEEEEB--SB-SSSSSBSS....SSCE..........STTSS--TTTTTS....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxx....xxxx..........xxxxxxxxxxxxx....................... RF
                            GatB_N   2 viGlEiHaqlktksKlFssaste....eege..........epnsevsevdlal....................... 41 
                                       v GlEiH+ql+t++KlF++++te    e  e           ++se++e+d a+                       
  gi|336254734|ref|YP_004597841.1|  14 VAGLEIHQQLDTATKLFCQCPTElrepE--EaertftrylhPTRSELGEIDEAAleeskverefeylaydttclvee 88 
                                       78*******************8765331..145677778745889999999999*********************** PP

                                       ...TT..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEE CS
                                       ...xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                            GatB_N  42 ...PGtlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrieri 113
                                          P   P+ l+ ea+++++++a  ++++  ++ +++RK+++++++++g+Q++     +a++G++e+ + +v+ie +
  gi|336254734|ref|YP_004597841.1|  89 ddeP---PHeLDDEALDTVLEIAQLMDMSPVDQAHVMRKIVVDGSNTTGFQRST---LMATDGEIETsDGAVGIEDL 159
                                       9998...999*******************************************9...678******97889****** PP

                                       EEEE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 114 hlEeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSv 190
                                        lEe++a+ v e+++ + ++l+R+G+pL+Ei t+pd+++pe+a +++e++++llr++g++++++  G++R+DvNvS+
  gi|336254734|ref|YP_004597841.1| 160 MLEEESAQRVAETDAGVRYSLDRLGIPLVEIGTSPDISTPEQALEAAERIGMLLRSTGKVKRGL--GTIRQDVNVSI 234
                                       ************999*************************************************..*********** PP

                                       CTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................... RF
                            GatB_N 191 reeekgeeegtrvEiKnlnslksiekaieyeierqiell...................................... 229
                                       +e       g+rvEiK+++sl+ i++++++e+ rq++l+                                      
  gi|336254734|ref|YP_004597841.1| 235 AE-------GARVEIKGVQSLDDIDDIVRNEVGRQVALVeianelidrdaevgepedvtdvfedtdsgvirgalnag 304
                                       *4.......59****************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                            GatB_N 230 ............................................................................. 229
                                                                                                                    
  gi|336254734|ref|YP_004597841.1| 305 gsvmgvplygfdglvgreiapdrrlgtefsdhakrhgaggifhtdelpaygvteeevealreavgagpedavaivad 381
                                       ***************************************************************************** PP

                                       ........................-EEEEEETTTTEEEEECC----...-EEE-TTS--EE-- CS
                                       ........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 230 ........................qeTrkfdedkgetvslRskeeaedYryfpepdlppleis 268
                                                               +eTr++++d g+t++lR+ + a   r++pe+d+pp+e +
  gi|336254734|ref|YP_004597841.1| 382 etdvaesaieavveraetalegvpEETRGANDD-GTTRYLRPLPGA--ARMYPETDVPPVEPD 441
                                       ********************************9.**********77..5**********9865 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   0.0   7.1e-28   3.2e-24       2     148 .]     480     620 ..     479     620 .. 0.93

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 7.1e-28
                                       HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHH CS
                         GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspe 77 
                                       +fe vv+ g d+ la + +l+ +l+el++ ++++e+  lt+e+l+ +l+++++g++ ++ + ++l +l+ee +++pe
  gi|336254734|ref|YP_004597841.1| 480 LFEDVVSDGVDPTLA-ATTLESTLTELRRDDVPVEN--LTDEHLTGVLEMVEDGDLPNEGVGDLLTALAEEpDRTPE 553
                                       69******9777665.568899**************..9************************************** PP

                                       HHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  78 eiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       e+ ee+gL  + deee+++++ ev+++n+   +++++  ++a+  l+G++M +++Gkad+ lv++ll+e++
  gi|336254734|ref|YP_004597841.1| 554 EAAEEEGLGGA-DEEEVREAIVEVVERNE---AQVEEEGMQAFSGLMGECMGALRGKADGDLVSQLLREEI 620
                                       ********999.56**************5...55567899****************************986 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   3.4e-19   1.5e-15       1      94 [.     297     389 ..     297     390 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 3.4e-19
                                       HHHHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT-- CS
                               GAD   1 fsealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgae 76 
                                       ++ al+ ggsv ++ + g +++l+++ei + +++++e++++++   + +g ++t++++++ +teeev+ l+eavga 
  gi|336254734|ref|YP_004597841.1| 297 IRGALNAGGSVMGVPLYG-FDGLVGREIAPDRRLGTEFSDHAKRH-GAGGIFHTDELPAYgVTEEEVEALREAVGAG 371
                                       6789**************.8***********************99.******************************* PP

                                       TTEEEEEEEEEHHHHHHH CS
                               GAD  77 egDillfvAdkkktvnka 94 
                                       ++D++ +vAd++++++ a
  gi|336254734|ref|YP_004597841.1| 372 PEDAVAIVADETDVAESA 389
                                       *************99877 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.3     4e-07    0.0018      93     142 ..     566     619 ..     563     620 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4e-07
                                       HHHHHHHHHHHHHHTT--....BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH CS
                              YqeY  93 eeeiealvkeaiaevgae....smkdmGkvmkalkpkvkGkaDgkkvsalvkek 142
                                       eee+++++ e++++ +a+    +m+++  +m+  +  ++GkaDg  vs+l++e+
  gi|336254734|ref|YP_004597841.1| 566 EEEVREAIVEVVERNEAQveeeGMQAFSGLMGECMGALRGKADGDLVSQLLREE 619
                                       7788888887776554443344****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4608.71
//
Query:       gi|336254735|ref|YP_004597842.1|  [L=124]
Description: hypothetical protein Halxa_3351 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0071   16.1   0.0     0.0084   15.9   0.0    1.1  1  PsbQ        Oxygen evolving enhancer protein 3 (PsbQ)
  ------ inclusion threshold ------
      0.055   13.3   0.2        0.1   12.5   0.2    1.5  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
      0.082   13.7   2.3       0.71   10.6   0.4    2.1  2  Big_9       Bacterial Ig domain
       0.16   12.0   0.1       0.23   11.5   0.1    1.3  1  DUF5429     Family of unknown function (DUF5429)


Domain annotation for each model (and alignments):
>> PsbQ  Oxygen evolving enhancer protein 3 (PsbQ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.9e-06    0.0084      28      81 ..       4      59 ..       1      73 [. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-06
                              PsbQ 28 sRRavlglaaaalaagslaaaalaeaaeaikvgpppppng..gvpgidnkteaRdf 81
                                       RR +lg++++a+++++   +++++ a++i v +++++    +++ ++ +++aR +
  gi|336254735|ref|YP_004597842.1|  4 DRRTFLGGLSVAVVGTAGCLSVNSDGATDITVSNERSQTAtaTLRVTRLSDGARLL 59
                                      6***********************************99988899**********87 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   2.3e-05       0.1       2      25 ..       3      24 ..       2      25 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      ++RR+FL   +   A ++++gc++
  gi|336254735|ref|YP_004597842.1|  3 IDRRTFLG--GLSVAVVGTAGCLS 24
                                      89******..88888899999975 PP

>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3   0.00056       2.5      52      86 ..      16      50 ..       4      53 .. 0.85
   2 ?   10.6   0.4   0.00016      0.71       1      71 [.      42     121 ..      42     122 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00056
                             Big_9 52 tapanGtvtinadgtltytpnagfsgtdsftYtvs 86
                                        ++ G +++n+dg    t ++  s t++ t +v+
  gi|336254735|ref|YP_004597842.1| 16 VVGTAGCLSVNSDGATDITVSNERSQTATATLRVT 50
                                      4578899***************9999999999886 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00016
                             Big_9   1 tatvtvtvtpvndaPvavddsvtvtedsv...........landtdp.dgdaltvtsltvtlvta.panGtvtinad 64 
                                       tat+t+ vt   d     +d+++++ed++           ++  + + dg + t   + +++  + +++  v i ad
  gi|336254735|ref|YP_004597842.1|  42 TATATLRVTRLSDGARLLEDTLSLDEDESeaydevvsgarVEVQISVdDGPPET---YEWSDGESdASGLFVDIEAD 115
                                       89***************************6666655555533233330333333...23333333355555555555 PP

                             Big_9  65 gtltytp 71 
                                        ++t++p
  gi|336254735|ref|YP_004597842.1| 116 -SITFSP 121
                                       .898887 PP

>> DUF5429  Family of unknown function (DUF5429)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.1e-05      0.23      10      53 ..       7      51 ..       1      63 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.1e-05
                           DUF5429 10 fflslqhaavsGvavclsvr.rGaGsvPaGnrgkktiiteyrilG 53
                                       fl     av G a clsv   Ga  +   n + +t  +  r++ 
  gi|336254735|ref|YP_004597842.1|  7 TFLGGLSVAVVGTAGCLSVNsDGATDITVSNERSQTATATLRVTR 51
                                      566666789**********7369*99*999999999888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 911.48
//
Query:       gi|336254736|ref|YP_004597843.1|  [L=160]
Description: AsnC family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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   43.1   0.5    5.3e-11   42.3   0.5    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
      4e-07   29.5   0.3    1.1e-06   28.0   0.3    1.8  1  HTH_24          Winged helix-turn-helix DNA-binding
    3.5e-06   26.7   0.0    6.8e-06   25.8   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
    0.00011   22.2   0.0    0.00043   20.3   0.0    1.9  2  HTH_20          Helix-turn-helix domain
    0.00036   20.3   0.0    0.00062   19.6   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0017   18.2   0.2      0.004   17.0   0.0    1.7  2  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.023   14.6   0.0      0.064   13.2   0.0    1.8  2  MarR_2          MarR family
      0.082   13.1   0.0       0.15   12.3   0.0    1.3  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.083   13.4   0.1       0.25   11.9   0.1    1.8  2  HTH_27          Winged helix DNA-binding domain
      0.096   12.5   0.0       0.26   11.2   0.0    1.8  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
       0.11   12.3   0.0       0.62    9.9   0.0    2.1  2  HTH_23          Homeodomain-like domain
       0.12   12.5   0.0       0.18   11.9   0.0    1.4  1  Nfu_N           Scaffold protein Nfu/NifU N terminal


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 !   42.3   0.5   3.6e-14   5.3e-11       1      74 [.      65     137 ..      65     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 3.6e-14
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       vlv++  + + ++eef+++l +++ V+ +y + G+ d+++ ++    e  er++ e + +++gv+rt++++v++
  gi|336254736|ref|YP_004597843.1|  65 VLVQVHADYQGSYEEFADRLLTVEGVTNVYFTMGETDFIVVARLSGSEMVERLIAE-FEQIEGVERTDSTFVIS 137
                                       567777555889********************************************.***************97 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 !   28.0   0.3   7.6e-10   1.1e-06       1      48 []       1      48 [.       1      48 [. 0.96

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 7.6e-10
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +de d+++L+++ +    s  +L e++g+++st+++rl++L eeG+I+
  gi|336254736|ref|YP_004597843.1|  1 MDERDIRLLKAISELETGSPEQLHEETGIPVSTIHYRLNNLREEGVIE 48
                                      7999**********9999*****************************7 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 !   25.8   0.0   4.5e-09   6.8e-06       5      51 ..       5      50 ..       3      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.5e-09
                                      HHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  5 alaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                       +++L+a++e   + +  +l+++tg+p St h  L+ L e+G +e d
  gi|336254736|ref|YP_004597843.1|  5 DIRLLKAISELETG-SPEQLHEETGIPVSTIHYRLNNLREEGVIEND 50
                                      5799*********8.9***************************9987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.9e-07   0.00043      14      57 ..       7      50 ..       5      51 .. 0.89
   2 ?   -2.3   0.0       3.2   4.8e+03      26      37 ..      76      86 ..      73      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.9e-07
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      r+l+a+++ e  ++++l+e+ +++ +t++y+L+ L+e g +e  
  gi|336254736|ref|YP_004597843.1|  7 RLLKAISELETGSPEQLHEETGIPVSTIHYRLNNLREEGVIEND 50
                                      567777777899****************************9965 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.2
                                      -HHHHHHHHTS- CS
                            HTH_20 26 taselaerldls 37
                                      + +e+a+rl l+
  gi|336254736|ref|YP_004597843.1| 76 SYEEFADRL-LT 86
                                      678999998.44 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 !   19.6   0.0   4.2e-07   0.00062       5      46 ..       6      48 ..       2      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.2e-07
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +++Lk+ +e +  +  +l ee+g++ st+ + L+ Lre+G++e
  gi|336254736|ref|YP_004597843.1|  6 IRLLKAISElETGSPEQLHEETGIPVSTIHYRLNNLREEGVIE 48
                                      5789999996669999************************997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.7e-06     0.004       8      55 ..       3      50 ..       1      54 [. 0.93
   2 ?   -3.3   0.1       5.9   8.8e+03      42      54 ..     104     116 ..     104     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.7e-06
                                      HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB  8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      e +++  +a+ +l+  + ++++ee+g+p s++   L++L + G++e  
  gi|336254736|ref|YP_004597843.1|  3 ERDIRLLKAISELETGSPEQLHEETGIPVSTIHYRLNNLREEGVIEND 50
                                      78999999999**********************************975 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.9
                                       HHHHHHHCTSEEE CS
                              TrmB  42 vLrsLedkGlVer 54 
                                       v+ +L+   +Ver
  gi|336254736|ref|YP_004597843.1| 104 VVARLSGSEMVER 116
                                       5778888899987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-05     0.064       8      52 ..       6      48 ..       1      53 [. 0.87
   2 ?   -2.5   0.0       3.2   4.8e+03      42      53 ..     105     116 ..     104     120 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                       r+L a+   + +  ++ +l +++g++ s+++++l+ L + G +e
  gi|336254736|ref|YP_004597843.1|  6 IRLLKAISELETG--SPEQLHEETGIPVSTIHYRLNNLREEGVIE 48
                                      6777788777764..999************************998 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.2
                                       HHHHHHTTSEEE CS
                            MarR_2  42 lkrLvaaGLver 53 
                                       ++rL+   +ver
  gi|336254736|ref|YP_004597843.1| 105 VARLSGSEMVER 116
                                       666666666665 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 ?   12.3   0.0   9.9e-05      0.15      23      51 ..      22      50 ..      20      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.9e-05
                    B-block_TFIIIC 23 dLakeskqdprslfyrlksLekkgLIvkq 51
                                      +L+ e+++ ++ ++yrl+ L + g I+  
  gi|336254736|ref|YP_004597843.1| 22 QLHEETGIPVSTIHYRLNNLREEGVIEND 50
                                      7999*********************9875 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 ?   11.9   0.1   0.00017      0.25       9      52 ..       9      51 ..       2      58 .. 0.82
   2 ?   -1.9   0.0       3.3     5e+03      36      44 ..     111     119 ..     107     141 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                            HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertg 52
                                      L  i  ++++ + ++l++ + +  s+i+y l+ L e G++e  +
  gi|336254736|ref|YP_004597843.1|  9 LKAIS-ELETGSPEQLHEETGIPVSTIHYRLNNLREEGVIENDR 51
                                      55566.777778899*************************5444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.3
                            HTH_27  36 syslkkLte 44 
                                       s+++++L++
  gi|336254736|ref|YP_004597843.1| 111 SEMVERLIA 119
                                       666666665 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 ?   11.2   0.0   0.00017      0.26       1      42 []       1      42 [.       1      42 [. 0.97

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      +De D+++L+a+ e    s ++L e++G+  st++ R++ L+
  gi|336254736|ref|YP_004597843.1|  1 MDERDIRLLKAISELETGSPEQLHEETGIPVSTIHYRLNNLR 42
                                      9*************************************9996 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00042      0.62       9      46 ..       9      46 ..       1      49 [. 0.79
   2 ?   -0.5   0.0      0.81   1.2e+03      34      47 ..     114     128 ..     112     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00042
                            HTH_23  9 r.illllaeGlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      + ++  l  G s+++  +e g++ +T+   l+  reeG+
  gi|336254736|ref|YP_004597843.1|  9 LkAISELETG-SPEQLHEETGIPVSTIHYRLNNLREEGV 46
                                      3366666665.99***************99999999995 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.81
                            HTH_23  34 vyrwlkryre.eGle 47 
                                       v r +  +++ eG+e
  gi|336254736|ref|YP_004597843.1| 114 VERLIAEFEQiEGVE 128
                                       889999998778877 PP

>> Nfu_N  Scaffold protein Nfu/NifU N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.18      36      63 ..      77     107 ..      60     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                             Nfu_N  36 asplakkLfkiegVksVfig...sdFitvtk 63 
                                         ++a +L+++egV++V+++    dFi v +
  gi|336254736|ref|YP_004597843.1|  77 YEEFADRLLTVEGVTNVYFTmgeTDFIVVAR 107
                                       4689**************9744469999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1262.80
//
Query:       gi|336254737|ref|YP_004597844.1|  [L=343]
Description: hypothetical protein Halxa_3353 [Halopiger xanaduensis SH-6]
Scores for complete 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-37  129.1  35.2    3.5e-19   69.3  10.4    2.0  2  EamA      EamA-like transporter family
     0.0088   15.4   2.8      0.014   14.8   2.3    1.6  1  Amj       Alternate to MurJ


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 !   69.3  10.4     4e-23   3.5e-19       5     136 ..      15     147 ..      12     148 .. 0.95
   2 !   66.1  16.8   3.9e-22   3.5e-18       2     135 ..     160     295 ..     159     297 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 4e-23
                              EamA   5 llallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafll 81 
                                       +l+ + al+w+++fv++ i+l++v+pl ++++r+ iag+++l +a++   + +  ++++wl+  + g++ ++l+++l
  gi|336254737|ref|YP_004597844.1|  15 VLFSILALCWGSSFVAIEIGLEYVPPLLFAGFRYAIAGAIVLGYAAVATDQVRPETHTEWLAAGVAGVFVIALYHGL 91 
                                       5677899***********************************99999999997778889****************** PP

                              EamA  82 ffyalkktsasnaslitslePvftlilsvlll.gekltlkqllgivlillGvllil 136
                                       ++ +  +++ ++a+ ++s++P++t+ ++ ++l  e+l    ++g+vl+l+Gv+ ++
  gi|336254737|ref|YP_004597844.1|  92 LYLGELYVPGAVAATVVSTAPILTAAFAGVILpEERLAPAGVVGFVLGLVGVIAVV 147
                                       ********************************9*******************9875 PP

  == domain 2  score: 66.1 bits;  conditional E-value: 3.9e-22
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl..aklslkdwllllllgllgtv 76 
                                       lg+ l++ +a+ +a++ vl++ + ++++  tl ++ +li++ +ll++a++++++     ++ + +l++ +l l+++v
  gi|336254737|ref|YP_004597844.1| 160 LGVALVFGSAIAFALGSVLTRPFKSDLPIETLQAWAMLIGAGVLLAWAAVRGESVssIAYTTETFLSFGYLTLVSGV 236
                                       6999***************************************************888899999************* PP

                              EamA  77 lafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       +af+l+f +l++++a+++ l+++ ePv+++  s+++ g  + +++++g++ il+G ++i
  gi|336254737|ref|YP_004597844.1| 237 FAFFLYFELLERSGATQVILVSYAEPVVAMGASWVVVGYVVDSLTIVGLLTILAGFVII 295
                                       *******************************************************9987 PP

>> Amj  Alternate to MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   2.3   1.5e-06     0.014     154     212 ..     104     160 ..      96     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-06
                               Amj 154 lvtgiytvgvLsalYAgalvpelrttasllsgiingvAtillalfvdPkaalltDqalr 212
                                        +t + t  +L a +Ag+++pe r++ + + g + g+    ++ +v P++a  t +++ 
  gi|336254737|ref|YP_004597844.1| 104 AATVVSTAPILTAAFAGVILPEERLAPAGVVGFVLGLV--GVIAVVQPTSAAFTSEVTL 160
                                       578899****************************9985..556799********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2523.71
//
Query:       gi|336254738|ref|YP_004597845.1|  [L=391]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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-24   87.1  67.8    2.3e-15   56.4  32.2    2.0  2  MFS_1       Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.019   13.8  14.3      0.041   12.8  13.7    1.9  1  MFS_1_like  MFS_1 like family


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 !   56.4  32.2   2.6e-19   2.3e-15       1     233 [.      11     228 ..      11     233 .. 0.81
   2 !   36.0  34.8   4.1e-13   3.7e-09       2     182 ..     208     386 ..     207     391 .] 0.85

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2.6e-19
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       ++l +f  a a+ + gp+l   l+ ++g++++++gl++ + ++g+++a++ +G l+ r+  rr++ +g+++ +++ l
  gi|336254738|ref|YP_004597845.1|  11 IFLFVFGDAVAMQARGPILA-ELGGEFGVTEAALGLVAPAGTAGFVLAVVATGLLAGRLPIRRTVAIGAVGVVVA-L 85 
                                       5788889999999999****.9*****************************************************.4 PP

                             MFS_1  78 lllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                       +++ a++++ ++l + ++qG +ag++  +  a+++++ +  +rgr+++ ++  +++Ga+lgp l +++++ + Wrav
  gi|336254738|ref|YP_004597845.1|  86 AAMAAAPIYlVFLGALLVQGGAAGVFRGLDRAVLSHLHAA-RRGRVYAAYAFVWAVGAVLGPQLVSAVLTVADWRAV 161
                                       44424999999***********888888888888888877.************************************ PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg....l 226
                                       f+++a +++  ++   +  ++e p+   +++  +           a+++ll+++     ++a++l+++ + +    l
  gi|336254738|ref|YP_004597845.1| 162 FVVIACFFVPTIL---VAGRTELPAVDAERSLSR----------AALGELLRRR----SVVAACLGMLLVGAvegiL 221
                                       **********977...444444444444444444..........1366677777....3444444433333334448 PP

                             MFS_1 227 ltllply 233
                                       +t+l  y
  gi|336254738|ref|YP_004597845.1| 222 FTWLAYY 228
                                       8888777 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 4.1e-13
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       +l+ +l+++  +il+++l  ++a ++    ++++lll++y l+++ a l + +++dr+ +  +ll++ l ++ + l+
  gi|336254738|ref|YP_004597845.1| 208 CLGMLLVGAVEGILFTWLA-YYAGTFY-PTATANLLLSAYLLAYIPARLGYTFVIDRVPALALLLVATLPTIPA-LA 281
                                       6899999***********9.9999999.77779*************************8888************.77 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.Wrav 153
                                        +f+ +   +l+++ +++G+g +++fp+  a++++ +p+   g  ++l ++++ +G++++p++ g+la+ +g    +
  gi|336254738|ref|YP_004597845.1| 282 VAFSGTTGpVLFLAVFVAGAGLSSVFPTLSAYAVEAAPE-YSGPLTALTTGATYAGIAIAPAIVGVLAEFAGiG-RA 356
                                       77875555699***************************9.********************************53.44 PP

                             MFS_1 154 fyilaivsllafv.lfllllpeepperkrk 182
                                        ++  ++++ +f  +++ +l++  p+ + +
  gi|336254738|ref|YP_004597845.1| 357 LWLTVALAVALFAtIAGTWLWTGTPSAPSS 386
                                       444444444444447778888877776655 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 ?   12.8  13.7   4.5e-06     0.041     132     359 ..     114     334 ..       7     353 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.5e-06
                        MFS_1_like 132 ldaatlkel.gedrkd.yGrqrlfGsvGyaifafitGilidhysvnllpysallyvlaallvisllvvlilneteke 206
                                       ld a+l +l   +r++ y+      +vG ++   +++++++         +a+++v+a ++v ++lv+   +     
  gi|336254738|ref|YP_004597845.1| 114 LDRAVLSHLhAARRGRvYAAYAFVWAVGAVLGPQLVSAVLTVADW-----RAVFVVIACFFVPTILVAGRTELPAVD 185
                                       566666666322222245554444455555555555555555554.....679999999999999995554444444 PP

                        MFS_1_like 207 sklkvtkslqvllnilknpeviifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaekl 283
                                        +  +   + +l ++l++++v++ +l +l++g++ gi+ ++l  Y     +++ ++  l+    +a ip  +    +
  gi|336254738|ref|YP_004597845.1| 186 AERSLS--RAALGELLRRRSVVAACLGMLLVGAVEGILFTWLAYYA-GTFYPTATANLLLSAYLLAYIPARLGYTFV 259
                                       444444..57899*****************************8776.999*************************** PP

                        MFS_1_like 284 leklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyf 359
                                       ++++ +  ll++a l +i  + +  + +   +++++ +  g+ +  ++ ++  y+ ++ap ++ + + +l +g+++
  gi|336254738|ref|YP_004597845.1| 260 IDRVPALALLLVATLPTIPALAVAFSGTTGPVLFLAVFVAGAGLSSVFPTLSAYAVEAAP-EYSGPLTALTTGATY 334
                                       ******************9998887779999************************98888.577888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2926.82
//
Query:       gi|336254739|ref|YP_004597846.1|  [L=365]
Description: hypothetical protein Halxa_3355 [Halopiger xanaduensis SH-6]
Scores for 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  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2742.20
//
Query:       gi|336254740|ref|YP_004597847.1|  [L=269]
Description: TrmH family RNA methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-28   99.7   0.0    2.1e-28   99.3   0.0    1.2  1  SpoU_methylase  SpoU rRNA Methylase family


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 !   99.3   0.0   1.2e-32   2.1e-28       3     142 .]      25     176 ..      23     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 1.2e-32
                                       EEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEE CS
                    SpoU_methylase   3 ivvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalv 79 
                                        v++v+ ++pgN+G+iaR++k+fg+++l+l++p + d++ +    a++  +++l+ ++  +++e++++ +  g++ v
  gi|336254740|ref|YP_004597847.1|  25 AVAVVDAQSPGNVGTIARAMKNFGFEDLLLIDPPELDPDGEAYGFAGHAREDILPNATEITFDELVENYHTIGCTAV 101
                                       588999******************************999988888888889999988888**********9998888 PP

                                       EESTT-SEGC.....CS.......HHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS
                    SpoU_methylase  80 atslkgksls.....ei.......dlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142
                                       + + + ++++     ++       +++ ++alvfG+E+ Gl+ne+l+++d++++Ip ++e++ LN+ +A+ + ly
  gi|336254740|ref|YP_004597847.1| 102 TNEDDRSHIRfpfstPAdlaerlpTVEAPTALVFGRERVGLTNEELARIDEICSIPGNEEYPVLNLGQAATVTLY 176
                                       888877777764444224444444444*********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2004.36
//
Query:       gi|336254741|ref|YP_004597848.1|  [L=423]
Description: cell division control protein 6-like protein [Halopiger xanaduensis SH-6]
Scores for 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-19   69.1   0.1    5.1e-19   68.0   0.1    1.6  1  Cdc6_C           CDC6, C terminal winged helix domain
    3.2e-13   50.1   0.0    1.1e-12   48.4   0.0    1.8  2  AAA_22           AAA domain
    1.9e-07   31.6   0.1    1.9e-07   31.6   0.1    2.6  2  AAA_16           AAA ATPase domain
    5.4e-05   23.6   0.0    0.00019   21.8   0.0    2.0  1  AAA              ATPase family associated with various cellul
    0.00025   21.1   0.3     0.0024   17.9   0.3    2.4  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00072   19.3   0.2     0.0023   17.7   0.0    1.9  2  Sigma54_activat  Sigma-54 interaction domain
    0.00092   18.1   0.6       0.21   10.4   0.5    2.4  2  AAA_32           AAA domain
     0.0015   17.8   0.0     0.0032   16.6   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
     0.0034   16.9   0.0       0.13   11.7   0.0    2.3  2  PhoH             PhoH-like protein
     0.0038   16.9   0.0     0.0063   16.2   0.0    1.4  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.005   16.3   0.0      0.024   14.1   0.0    2.0  2  TniB             Bacterial TniB protein
     0.0056   15.9   0.1      0.026   13.7   0.0    2.0  2  PIF1             PIF1-like helicase
     0.0096   15.1   0.0      0.018   14.3   0.0    1.5  1  NB-ARC           NB-ARC domain
  ------ inclusion threshold ------
      0.016   15.3   2.4      0.072   13.2   0.0    2.4  2  DUF87            Helicase HerA, central domain
      0.034   14.5   1.5        0.1   13.0   0.7    2.1  2  AAA_assoc_2      AAA C-terminal domain
      0.045   14.0   0.5       0.14   12.4   0.2    2.0  1  PCP_red          Proto-chlorophyllide reductase 57 kD subunit
       0.06   13.1   0.1        1.1    9.0   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
      0.067   13.0   0.7        2.6    7.8   0.1    2.5  2  DEAD             DEAD/DEAH box helicase
      0.082   12.4   0.0       0.14   11.6   0.0    1.3  1  Arf              ADP-ribosylation factor family
      0.098   12.7   0.1       0.24   11.4   0.0    1.8  2  ResIII           Type III restriction enzyme, res subunit
       0.13   11.8   0.0       0.26   10.8   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
       0.18   12.2   0.0       0.67   10.4   0.0    2.0  2  RNA_helicase     RNA helicase


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 !   68.0   0.1   6.3e-22   5.1e-19       1      83 [.     312     394 ..     312     395 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 6.3e-22
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L+al+ll+++s ++e++t+ +y++Yk++++++++d+l++r+v+++l+e+++l ++++e++++Gr++g + k++L  +
  gi|336254741|ref|YP_004597848.1| 312 LYALTLLTENSSEKEFPTKIIYNQYKEIARQLDFDVLSERRVQEILQEQNFLNVIQSEREGRGRGRGAHAKHRLLEN 388
                                       89*************************************************************************** PP

                                       CHHHHH CS
                            Cdc6_C  78 pddvle 83 
                                       p+ v++
  gi|336254741|ref|YP_004597848.1| 389 PSIVKK 394
                                       **9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   1.3e-15   1.1e-12       5     118 ..      58     177 ..      55     192 .. 0.85
   2 ?   -1.6   0.0       3.7     3e+03      62      62 ..     302     302 ..     251     361 .. 0.56

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.3e-15
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......erlss 75 
                                        ++l+++G +GtGK++  r ++++   ea  ++  ++++f+++ ++++ +++ + ++++++++  +      ++l +
  gi|336254741|ref|YP_004597848.1|  58 PNHLFIFGKTGTGKSLISRSVTKRVISEARRDDVTVKYAFIDCGEQNTEASVIKTIAQIVNEPDRSgisvpdRGLGT 134
                                       5799********************854444433555555************************999*********** PP

                            AAA_22  76 eellealeqalraravielliiDEaqhlrs.eealeeLrsllnl 118
                                        +++++l+qa++++ ++ ++i+DE++ l + +e+l++L++  ++
  gi|336254741|ref|YP_004597848.1| 135 GDYYKRLWQAVDHCTDVTIVILDEIDML-EdDEVLRKLSRAGEN 177
                                       ****************************.559999999655443 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.7
                            AAA_22  62 r 62 
                                       +
  gi|336254741|ref|YP_004597848.1| 302 E 302
                                       1 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.1   2.3e-10   1.9e-07       2      63 ..      35     103 ..      34     185 .. 0.61
   2 ?   -0.9   0.9       2.2   1.8e+03     114     114 ..     306     306 ..     199     415 .. 0.62

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.3e-10
                            AAA_16   2 lvGReeeleqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekd....ggif..lrgkcdql 63 
                                        vGR+e+++++++al+ ++  ++p+ +++ G  G+GKs + r++ +++  +    ++ +  +  +c + 
  gi|336254741|ref|YP_004597848.1|  35 IVGRDEQMQRVADALNpAIFGSEPNHLFIFGKTGTGKSLISRSVTKRVISEarrdDVTVkyAFIDCGEQ 103
                                       69**************66666666*********************966655333333332233333333 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.2
                            AAA_16 114 a 114
                                       +
  gi|336254741|ref|YP_004597848.1| 306 Q 306
                                       1 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 !   21.8   0.0   2.4e-07   0.00019       2     117 ..      62     199 ..      61     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.4e-07
                                       EEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS..........................STTHHH CS
                               AAA   2 llyGppGtGKTllakavakel.........gvefleisgsellsk..........................yvgese 43 
                                        ++G  GtGK+l+ ++v k +          v++  i++ e   +                            g+  
  gi|336254741|ref|YP_004597848.1|  62 FIFGKTGTGKSLISRSVTKRVisearrddvTVKYAFIDCGEQNTEasviktiaqivnepdrsgisvpdrglGTGDYY 138
                                       579*****************655544444446677777777664467788888888889999999999988888888 PP

                                       HHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTH CS
                               AAA  44 kkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldp 117
                                       k++ + ++++      +i+++DEid l  ++          v+ +L ++ ++ + ++s + +ig++n++d +d 
  gi|336254741|ref|YP_004597848.1| 139 KRLWQAVDHCTDV---TIVILDEIDMLEDDE----------VLRKLSRAGENRRISDSSIGIIGISNKIDFPDH 199
                                       8888888887544...7**********5555..........***************************765544 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 !   17.9   0.3     3e-06    0.0024       1      95 [.      60     181 ..      60     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3e-06
                                       EEEEE--SSSSHHHHHHHGGGGB.........S--EEEEE--TT--HHHHH--B--..................... CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.........nreveyvqltrdtteedlkgrreik.................ngt 51 
                                       ++++ G++GtgKs +++++ +++         + ++  + + ++ te+ ++  +                     g+
  gi|336254741|ref|YP_004597848.1|  60 HLFIFGKTGTGKSLISRSVTKRVisearrddvTVKYAFIDCGEQNTEASVIKTIAQIvnepdrsgisvpdrglgTGD 136
                                       7899*****************999**999888778888888777777777776664457888666666666655555 PP

                                       .....--------G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE CS
                             AAA_5  52 tslvdsplvraaregeilvlDEverae.sevlnsLlslleerrll 95 
                                       +  +   +v+ ++   i++lDE++++e +evl +L +  e+rr++
  gi|336254741|ref|YP_004597848.1| 137 YYKRLWQAVDHCTDVTIVILDEIDMLEdDEVLRKLSRAGENRRIS 181
                                       5555666666666**************9************99987 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.8e-06    0.0023       1      62 [.      35     104 ..      35     111 .. 0.74
   2 ?   -2.9   0.1       5.9   4.8e+03     126     156 ..     269     299 ..     265     301 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-06
                                       ----SHHHHHHHHHHHHHC..TSSS-EEEECSTTSSHHHHHHHHHH....HSTTTTS...-EEEEETTTS- CS
                   Sigma54_activat   1 ligesealkelleqikkva..ktdlsvlitGesGtGKellaraihe....askrkek...pfvavncaaip 62 
                                       ++g++e+++++ + ++ ++  + + +++i G++GtGK+l++r++ +    +  r++    ++  ++c++ +
  gi|336254741|ref|YP_004597848.1|  35 IVGRDEQMQRVADALNPAIfgSEPNHLFIFGKTGTGKSLISRSVTKrvisE-ARRDDvtvKYAFIDCGEQN 104
                                       689999*******999888445569******************98866532.3332212256666777655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.9
                                       TSSSEEE--EEEEEEESS-HHHHHHTTSS-H CS
                   Sigma54_activat 126 Gsskeikvdvriiaatnedleeaveegkfre 156
                                       G  ++++ d+r+ a   +d +e+ e+++f e
  gi|336254741|ref|YP_004597848.1| 269 GRIAKKQNDTRVTAEHVRDAKEKTEADRFNE 299
                                       6667788899999999999999999999976 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0088       7.2      18      63 ..      47      90 ..      32     106 .. 0.71
   2 !   10.4   0.5   0.00025      0.21     478     511 ..     259     292 ..     253     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0088
                            AAA_32 18 ealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdD 63
                                      +al+ ++   ++  ++f+ G++gtG++ + +++ +++ + e+  dD
  gi|336254741|ref|YP_004597848.1| 47 DALNPAIFG-SEPNHLFIFGKTGTGKSLISRSVTKRVIS-EARRDD 90
                                      555555543.34459***********8877777666544.344444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00025
                            AAA_32 478 seiadllrEAdywakkegaevveaehVekAleek 511
                                       ++ +d+lr A  +akk++++ v+aehV++A e+ 
  gi|336254741|ref|YP_004597848.1| 259 RKAIDILRNAGRIAKKQNDTRVTAEHVRDAKEKT 292
                                       6789**************************8765 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     4e-06    0.0032      27      80 ..      32      85 ..      10     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4e-06
                            DUF815 27 lddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaee 80
                                       d++vg d+q +++ +  +  + g + n+++++G+ GtGKS + +++++++ +e
  gi|336254741|ref|YP_004597848.1| 32 PDRIVGRDEQMQRVADALNPAIFGSEPNHLFIFGKTGTGKSLISRSVTKRVISE 85
                                      57899************************************9999998887665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00015      0.13      10      64 ..      43     103 ..      34     111 .. 0.76
   2 ?    2.8   0.0     0.086        70     121     149 ..     152     180 ..     148     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                                       HHHHHHHH......H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT-- CS
                              PhoH  10 keylealk......kndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveagee 64 
                                       +++++al+      + + +f++G++GtGK++++ ++  +++++ + + + +  + +++ge+
  gi|336254741|ref|YP_004597848.1|  43 QRVADALNpaifgsEPNHLFIFGKTGTGKSLISRSVTKRVISEARRDDVTVKYAFIDCGEQ 103
                                       5555555555555556789**************9999999999888888877777777775 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.086
                                       EEEEE-SGGG--HHHHHHHHTTB-TT-EE CS
                              PhoH 121 afvilDEAQnttkeqmkmfltRlGenskv 149
                                       ++vilDE   ++  ++   l+R Gen ++
  gi|336254741|ref|YP_004597848.1| 152 TIVILDEIDMLEDDEVLRKLSRAGENRRI 180
                                       68***********************9775 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 !   16.2   0.0   7.7e-06    0.0063       2      57 ..      43     108 ..      42     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.7e-06
                                       SHHHHHHS-EBTT-...EEEEEESTTSSHHHHHHHHHHHSSTS......S.EEEEEEESEEHHHHH CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx......x.xxxxxxxxxxxxxxx RF
                       ATP-synt_ab   2 irvlDalfpivqGq...rtlipgafgvGktvisqslskqsnsd......d.aiiyvgiGergneva 57 
                                       +rv Dal p + G     + i+g+ g+Gk+ is+s++k   s+      +    ++ +Ge++ e++
  gi|336254741|ref|YP_004597848.1|  43 QRVADALNPAIFGSepnHLFIFGKTGTGKSLISRSVTKRVISEarrddvTvKYAFIDCGEQNTEAS 108
                                       7999******9996222689*************888888766666764423445889999988764 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.9e-05     0.024      34     132 ..      57     163 ..      38     206 .. 0.79
   2 ?   -1.1   0.0       1.3   1.1e+03     127     151 ..     296     320 ..     293     355 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.9e-05
                              TniB  34 rmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkara.......r 103
                                       ++++l ++G++ +GK+ i ++ +++  +e + d+ +v+   +++ ++ +e+   + i + +++p ++          
  gi|336254741|ref|YP_004597848.1|  57 EPNHLFIFGKTGTGKSLISRSVTKRVISEARRDDVTVKYAFIDCGEQNTEASVIKTIAQIVNEPDRSGIsvpdrglG 133
                                       667899****************************************************9999997655433444444 PP

                              TniB 104 vskleqqvlrllrel.kvrvLiiDEihnll 132
                                       + + +++  +  +++ +v ++i+DEi+ l+
  gi|336254741|ref|YP_004597848.1| 134 TGDYYKRLWQAVDHCtDVTIVILDEIDMLE 163
                                       556777777777766369999999998776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                              TniB 127 EihnllagsarkqreflnalksLgn 151
                                        +++l++gs ++ +++l al  L++
  gi|336254741|ref|YP_004597848.1| 296 RFNELIEGSPQQAKAILYALTLLTE 320
                                       5666666666666666666665544 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   3.2e-05     0.026       6      49 ..      42      85 ..      38      98 .. 0.83
   2 ?   -1.4   0.0       1.2   9.8e+02      98     116 ..     146     164 ..     135     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.2e-05
                                      HHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCT CS
                              PIF1  6 QkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrse 49
                                       ++v+da   a++ ++++ +F+ G  GtgK+ + + ++k + se
  gi|336254741|ref|YP_004597848.1| 42 MQRVADALNPAIFGSEPNHLFIFGKTGTGKSLISRSVTKRVISE 85
                                      36788999899999***********************9998775 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                                       HHHHC-SEEEEECGGGSBH CS
                              PIF1  98 ellkktsliiwDEapmver 116
                                       +  ++++++i+DE+ m+e 
  gi|336254741|ref|YP_004597848.1| 146 DHCTDVTIVILDEIDMLED 164
                                       55667889999***99875 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   2.2e-05     0.018       4      78 ..      41     119 ..      38     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHHHC...TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBT...EEEEEEEESXXHHHHHHHXXHH CS
                            NB-ARC   4 svekviekLle...kdelqslvvalvGmgGvGKttlakqilnksdevegrFd...svawvvvsktdkseeiletilk 74 
                                       ++++v++ L       e++   +++ G+ G GK+ +++++ +   +  +r d    +a++  +++ ++ ++++ti++
  gi|336254741|ref|YP_004597848.1|  41 QMQRVADALNPaifGSEPN--HLFIFGKTGTGKSLISRSVTKRVISEARRDDvtvKYAFIDCGEQNTEASVIKTIAQ 115
                                       5666666665432245666..99********************9888888884344678899*************99 PP

                                       HHHC CS
                            NB-ARC  75 eLsl 78 
                                        +++
  gi|336254741|ref|YP_004597848.1| 116 IVNE 119
                                       8754 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.8e-05     0.072      25      49 ..      60      84 ..      58      93 .. 0.84
   2 ?    0.8   0.9      0.52   4.2e+02     116     206 ..     260     348 ..     241     369 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.8e-05
                             DUF87 25 HlAilgsTGsGKSntvavLleelle 49
                                      Hl i+g+TG+GKS   ++  +++++
  gi|336254741|ref|YP_004597848.1| 60 HLFIFGKTGTGKSLISRSVTKRVIS 84
                                      999***********99999999886 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.52
                             DUF87 116 vqrsvleealdqakakeekeklssdepveklleelk.kekeelrklknqaiarlldkledllrkggsfsnsstdlia 191
                                       +  ++l++a + ak k++++++++++ v   +e+++ ++ +el + + q+++++l +l+ l ++ +++ +++t++i 
  gi|336254741|ref|YP_004597848.1| 260 KAIDILRNAGRIAK-KQNDTRVTAEH-VRDAKEKTEaDRFNELIEGSPQQAKAILYALTLLTENSSEK-EFPTKIIY 333
                                       46678888888887.35555555555.66666666633334666666666677777776666666666.77777776 PP

                             DUF87 192 llleklekegkitii 206
                                       +  +++ ++  + ++
  gi|336254741|ref|YP_004597848.1| 334 NQYKEIARQLDFDVL 348
                                       665555555444444 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 ?   13.0   0.7   0.00012       0.1      13      58 ..     248     292 ..     238     300 .. 0.85
   2 ?   -0.8   0.0       2.4   1.9e+03      12      41 ..     297     343 ..     291     367 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2  13 ealaeladGDaRkaLnlLElaaeaaeakegkieitledleealqrk 58 
                                       +ala+  +GDaRka+ +L  a + a++ ++++++t e++++a +++
  gi|336254741|ref|YP_004597848.1| 248 AALAAQEHGDARKAIDILRNAGRIAKK-QNDTRVTAEHVRDAKEKT 292
                                       57888889***********99999986.99*********9987654 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.4
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX..................X CS
                       AAA_assoc_2  12 lealaeladGDaRkaLnlLElaaeaaeak.................e 41 
                                       ++ l+e +   a+++L +L l+ e++++k                  
  gi|336254741|ref|YP_004597848.1| 297 FNELIEGSPQQAKAILYALTLLTENSSEKefptkiiynqykeiarqL 343
                                       55666667777788888888887777777555555554443333222 PP

>> PCP_red  Proto-chlorophyllide reductase 57 kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00017      0.14      22      45 .]     266     289 ..     263     289 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHT-SEE-HHHHHHHH CS
                           PCP_red  22 raaEklArerGleeVtvevveaAk 45 
                                       r+a + A++++ ++Vt+e+v++Ak
  gi|336254741|ref|YP_004597848.1| 266 RNAGRIAKKQNDTRVTAEHVRDAK 289
                                       78999*****************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 ?    9.0   0.0    0.0014       1.1      32      74 ..      43      85 ..      35     117 .. 0.77
   2 ?    1.1   0.1      0.35   2.9e+02      98     123 ..     140     165 ..     132     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                         IstB_IS21 32 krkvkeLatlsfiekkenivllGpsGvGKshlaialgveavra 74
                                      +r  ++L    f ++ + + ++G +G+GKs ++ ++ ++ + +
  gi|336254741|ref|YP_004597848.1| 43 QRVADALNPAIFGSEPNHLFIFGKTGTGKSLISRSVTKRVISE 85
                                      55556777777778888999************99998876643 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.35
                         IstB_IS21  98 klaralkrllkvdllilDdlgllpld 123
                                       +l +a+++++ v+++ilD++ +l+ d
  gi|336254741|ref|YP_004597848.1| 140 RLWQAVDHCTDVTIVILDEIDMLEDD 165
                                       666788899999*******9988765 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.12     1e+02      15      39 ..      59      82 ..      41      98 .. 0.69
   2 ?    7.8   0.1    0.0032       2.6     118     144 ..     147     173 ..      96     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.12
                                      CEEEEEESTTSSHHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 15 gdvlvaaeTGsGKTlaflipvlqiv 39
                                      +++++ ++TG+GK+l+ +  v ++v
  gi|336254741|ref|YP_004597848.1| 59 NHLFIFGKTGTGKSLI-SRSVTKRV 82
                                      6788999*******98.44444444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0032
                                       HCTTEEEEEEETHHHHHHTTTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 118 nlsqvrflVlDEadrlldqgfsdfinr 144
                                       ++ +v++++lDE+d+l d++  ++++r
  gi|336254741|ref|YP_004597848.1| 147 HCTDVTIVILDEIDMLEDDEVLRKLSR 173
                                       38899************9987777666 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.14      65     141 ..     132     209 ..     102     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                       E-SSGGGGGGGGGGCTTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEE..EEEEE-TTSTTSS-HHHHHHH CS
                               Arf  65 vGGqeklRplWknYfektdavifvvDsadreRleeakeeLkalleeeelkeval..lvlaNKqDlpealseeelrel 139
                                       +G  +  ++lW+   ++td+ i ++D  d    +e  ++L++  e++++++  +  + ++NK+D p+ lse+ ++++
  gi|336254741|ref|YP_004597848.1| 132 LGTGDYYKRLWQAVDHCTDVTIVILDEIDMLEDDEVLRKLSRAGENRRISDSSIgiIGISNKIDFPDHLSER-VKSS 207
                                       566677899********************9999999999999999999986665115578*******99975.5555 PP

                                       TT CS
                               Arf 140 lg 141
                                       l+
  gi|336254741|ref|YP_004597848.1| 208 LS 209
                                       55 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    0.0003      0.24       5      57 ..      38      91 ..      34     159 .. 0.85
   2 ?   -2.2   0.1       4.3   3.5e+03     107     107 ..     316     316 ..     253     367 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                                      -HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-E CS
                            ResIII  5 reyQeeaienll.eklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekf 57
                                      r+ Q++ + + l  ++   + ++++i   TGtGK+l++ ++++r+ ++++++ +
  gi|336254741|ref|YP_004597848.1| 38 RDEQMQRVADALnPAIFGSEPNHLFIFGKTGTGKSLISRSVTKRVISEARRDDV 91
                                      67787777776634555589999*********************9999887755 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.3
                                       E CS
                            ResIII 107 l 107
                                       +
  gi|336254741|ref|YP_004597848.1| 316 T 316
                                       2 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   0.00031      0.26      34      59 ..      59      84 ..      52     128 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldk 59
                                      +++++ G+tGtGK++i ++++k++ +
  gi|336254741|ref|YP_004597848.1| 59 NHLFIFGKTGTGKSLISRSVTKRVIS 84
                                      688999*********99987776543 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00082      0.67       2      26 ..      62      86 ..      61     118 .. 0.83
   2 ?   -2.1   0.0       6.3   5.1e+03      44      64 ..     145     165 ..     142     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00082
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                      +++G++g+GKS+++++++k++ ++ 
  gi|336254741|ref|YP_004597848.1| 62 FIFGKTGTGKSLISRSVTKRVISEA 86
                                      89**************999998665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.3
                      RNA_helicase  44 wdgYtgqevvvidDfgqvkde 64 
                                       +d +t+ ++v+ d++   +d+
  gi|336254741|ref|YP_004597848.1| 145 VDHCTDVTIVILDEIDMLEDD 165
                                       578889999****99998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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):              22  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 3099.77
//
Query:       gi|336254742|ref|YP_004597849.1|  [L=396]
Description: dihydropteroate synthase [Halopiger xanaduensis SH-6]
Scores for 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-41  140.4   0.0      1e-40  140.0   0.0    1.2  1  Pterin_bind  Pterin binding enzyme


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 !  140.0   0.0   5.6e-45     1e-40       1     244 []      20     269 ..      20     269 .. 0.90

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 5.6e-45
                                       EEEEETTTTTCHCCHHCTHHHHHHHHH.HHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHC.TSE CS
                       Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqa.rkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdea.dvp 75 
                                       mg+lNv+++s +d + + d+ +a a + ++++ eGAdi+Dig es++ + e++++eeel+r+   le +++ + d  
  gi|336254742|ref|YP_004597849.1|  20 MGVLNVSEESPYDPSVYDDPGEAAAYVdEDLIGEGADIVDIGLESANKRFEVLSAEEELDRLHIALETIESVSgDAV 96 
                                       9****************9998887776378*****************************************888*** PP

                                       EEEE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESEC...SSTTTHCCCC.CCCSSHHHHH.H CS
                       Pterin_bind  76 isiDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmr...gtpktmqeee.gqyedvveev.e 147
                                        si t  aeva +Al++g d+vNd+ g+  dp+m+ ++ + +aav  m++    ++p  ++e+     ++++    +
  gi|336254742|ref|YP_004597849.1|  97 FSIETRYAEVADEALSRGFDMVNDICGFA-DPAMPTVCEDRDAAVAKMASPpnlERPGAVEETDwAARKSAEWAAeA 172
                                       *****************************.********************977766777777774333443333314 PP

                                       HHHHHHHHHHHHTT--GGGEEEETTTTS...STTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGH CS
                       Pterin_bind 148 aflearveaaeeaGvaperillDpgigf...gkteehnlellrrldelrealevpvllGvSrksflgrllelgkaee 221
                                        ++e+  ea+++ G+ + + ++Dp +g    ++t e++ e  rrl e+ +al+ p+l+++ rk+flg++  + ++ee
  gi|336254742|ref|YP_004597849.1| 173 DYVEKVYEALKQNGLTD-KTIVDPAFGGwseAQTLEDDRETFRRLREF-RALGQPMLVSINRKNFLGEIA-DRETEE 246
                                       5677888999*****88.6678****998999****************.9******************97.45589* PP

                                       HHHHHHHHHHHHHHTT-SEEEES CS
                       Pterin_bind 222 RdagtaaflalaaaaGadivrVh 244
                                       R  +++a++++a+++Ga+++r+h
  gi|336254742|ref|YP_004597849.1| 247 RLPVSLAATSMAVERGAHVIRTH 269
                                       **********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2923.96
//
Query:       gi|336254743|ref|YP_004597850.1|  [L=232]
Description: hypothetical protein Halxa_3359 [Halopiger xanaduensis SH-6]
Scores for 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-21   75.9   0.0    3.6e-21   75.6   0.0    1.1  1  MAF_flag10       Protein of unknown function DUF115
  ------ inclusion threshold ------
      0.015   15.6   0.1      0.054   13.8   0.0    1.9  2  TrkA_N           TrkA-N domain
       0.14   12.1   0.0       0.25   11.3   0.0    1.5  1  Polysacc_deac_1  Polysaccharide deacetylase


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 !   75.6   0.0     6e-25   3.6e-21      22     169 ..      46     186 ..      29     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 6e-25
                        MAF_flag10  22 fkgnkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevfkeaekkgdipl 97 
                                        ++  ++ i gaGPSLe++ el +  r+  v++aa+ta  +L +++I +D +v+ lD+   + + +  ++++g  + 
  gi|336254743|ref|YP_004597850.1|  46 VRD-ATVAIAGAGPSLEDEGEL-ERAREADVVFAASTAADVLRSHDIAVDCMVTdLDK---NPDTVRRLTDRGVPVA 117
                                       444.99************9875.668899*****************************...7888889999977788 PP

                        MAF_flag10  98 vfasgvnpellkkykgpki.flvtgstqalelleeekneilfgGgsvantaldlAvklgfkeIiliGqDlayt 169
                                       v+a+g+n  +++++ +  +  +v ++tqa++      ++++fgG++++++a +lA +lg++e++++G ++  +
  gi|336254743|ref|YP_004597850.1| 118 VHAHGDNVPAVREVVPDCAdAFVLPTTQAAPRD----HVRNFGGFTDGDRAAFLADYLGARELVFVGWNFDDS 186
                                       9***************99999999989874333....449****************************99865 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.3   1.8e+03      38      60 ..      68      90 ..      61      97 .. 0.71
   2 ?   13.8   0.0     9e-06     0.054      21      69 ..      89     142 ..      76     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.3
                                      HHTTSEEEES-TTSHHHHHHTTG CS
                            TrkA_N 38 reeglevvvgdatdeevLeeagi 60
                                      r+++++vv +  t  +vL++ +i
  gi|336254743|ref|YP_004597850.1| 68 RAREADVVFAASTAADVLRSHDI 90
                                      34567788888888888887666 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 9e-06
                                       T.....EEEEEEESSHHHHHHHHHTTSE.EEES-TTSHHHHHHTTGGGESEEEE- CS
                            TrkA_N  21 g.....kdvvvidkdeerveelreegle.vvvgdatdeevLeeagiekadaviaa 69 
                                             + v+  dk++++v++l+++g++ +v++++ +  +++e   + ada++  
  gi|336254743|ref|YP_004597850.1|  89 DiavdcM-VTDLDKNPDTVRRLTDRGVPvAVHAHGDNVPAVREVVPDCADAFVLP 142
                                       3455545.7889**************887999*******************9975 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.2e-05      0.25      23      66 ..      80     121 ..      57     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHCT--EEEEE-HHHHCH-HHHHHHHHHTTEEEEE--S CS
                   Polysacc_deac_1  23 eilpvLkkykvkatffvigglvedypdevremaasGveignHti 66 
                                        + +vL+ +++   + v+    +++pd vr++ ++Gv ++ H +
  gi|336254743|ref|YP_004597850.1|  80 TAADVLRSHDIAVDCMVTD--LDKNPDTVRRLTDRGVPVAVHAH 121
                                       6789999999988888887..89999**********66666643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1754.70
//
Query:       gi|336254744|ref|YP_004597851.1|  [L=70]
Description: hypothetical protein Halxa_3360 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00091   19.9   0.5     0.0011   19.7   0.5    1.2  1  zinc_ribbon_15  zinc-ribbon family
     0.0079   15.9   5.7      0.011   15.5   5.7    1.2  1  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.086   11.6   1.2      0.076   11.8   1.2    1.1  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.13   12.2   4.8       0.14   12.2   4.8    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.46   10.2   6.6       0.72    9.6   0.8    2.2  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
       0.52   10.5   7.1        2.5    8.3   7.2    1.9  2  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.5   3.6e-07    0.0011      64      86 .]      22      60 ..       3      60 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.6e-07
                    zinc_ribbon_15 64 e................kkeCknCgkeveeefkyCpkCg 86
                                      +                 +eC++Cgk++e++ + Cp Cg
  gi|336254744|ref|YP_004597851.1| 22 NavksvlfsrssadattIEECRRCGKTIESREADCPVCG 60
                                      134455566666667779********************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 !   15.5   5.7   3.6e-06     0.011       2      20 ..      42      60 ..      41      62 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCG 20
                                      C +CG++++ ++  Cp CG
  gi|336254744|ref|YP_004597851.1| 42 CRRCGKTIESREADCPVCG 60
                                      ******************9 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.2   2.5e-05     0.076     505     529 ..      37      63 ..       8      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                                       --EEEETT.--..EESSSB-TTT--BE CS
                              NRDD 505 pkidvCnecgy..kgeiekCpkCgsee 529
                                       ++i+ C++cg+  +    +Cp+Cg ++
  gi|336254744|ref|YP_004597851.1|  37 TTIEECRRCGKtiESREADCPVCGCDD 63 
                                       68999******65444588*****655 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 ?   12.2   4.8   4.6e-05      0.14      71      96 ..      40      63 ..       9      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.6e-05
                                      EEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA 71 vrCreCgkefeleekalrCpkCgsad 96
                                       +Cr+Cgk++e++e  + Cp Cg  d
  gi|336254744|ref|YP_004597851.1| 40 EECRRCGKTIESRE--ADCPVCGCDD 63
                                      48*********884..58*****876 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 ?    3.8   0.6     0.015        46      24      29 ..      42      47 ..      42      50 .. 0.80
   2 ?    9.6   0.8   0.00024      0.72       7      13 ..      56      65 ..      55      69 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.015
                           zf-RRN7 24 CrrCht 29
                                      CrrC+ 
  gi|336254744|ref|YP_004597851.1| 42 CRRCGK 47
                                      ****96 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00024
                           zf-RRN7  7 CgvCgc...r 13
                                      C+vCgc   +
  gi|336254744|ref|YP_004597851.1| 56 CPVCGCddiV 65
                                      ******5444 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3    0.0014       4.2      21      36 ..      32      49 ..      26      52 .. 0.66
   2 ?    8.3   7.2   0.00085       2.5       7      34 ..      41      61 ..      40      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                       Zn-ribbon_8 21 is.daplta.CPeCgsev 36
                                      +s da  ++ C +Cg++ 
  gi|336254744|ref|YP_004597851.1| 32 SSaDATTIEeCRRCGKTI 49
                                      444666777788888754 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00085
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs 34
                                      +C++Cg++ e +       + +CP Cg 
  gi|336254744|ref|YP_004597851.1| 41 ECRRCGKTIESR-------EADCPVCGC 61
                                      6*******9944.......455****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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):               6  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 562.80
//
Query:       gi|336254745|ref|YP_004597852.1|  [L=336]
Description: 5,10-methylenetetrahydromethanopterin reductase [Halopiger xanaduensis SH-6]
Scores for 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-79  266.5   8.6    4.5e-79  266.1   8.6    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.1   8.6   2.5e-83   4.5e-79      17     310 ..      11     304 ..       2     308 .. 0.96

  Alignments for each domain:
  == domain 1  score: 266.1 bits;  conditional E-value: 2.5e-83
                    Bac_luciferase  17 aasaslrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatL 93 
                                       aa++sl+ lv+lar+ E+ G++++w++e++g     +da+t+la +a +T+ i+lg +v+++y+r+Pa+l q+aatL
  gi|336254745|ref|YP_004597852.1|  11 AAQPSLEALVDLARLGERRGYEFAWLPETWG-----RDAVTILATIARETDDIGLGPSVVNVYSRSPALLGQTAATL 82 
                                       55689**************************.....***************************************** PP

                    Bac_luciferase  94 dhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvy 170
                                       ++ s+GR+++g+  +gpav+e+++G+++d++++r+rE+++v+r++++ge+v+++G+ fs+ g++l+  p+ +p+P+ 
  gi|336254745|ref|YP_004597852.1|  83 QEASDGRLRMGIAPSGPAVIEGWHGLEFDRPLRRTREYIDVMRAVLSGERVEYDGDIFSLSGFRLRCDPPAEPVPID 159
                                       *********************************************************************9999**** PP

                    Bac_luciferase 171 vaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearaliag 247
                                        a+++p+++ela+r+adg++  +++p+ ++e++e+lr ga   +rdp+d+rv++s+t ++ ++ + Ar+ ar+++a 
  gi|336254745|ref|YP_004597852.1| 160 AAGMGPKAVELAGRFADGWHAILFTPDGLEERLEDLRRGADLGDRDPDDVRVTLSVTACALEDGDRARELARQHLAF 236
                                       ***********************************************************************555554 PP

                    Bac_luciferase 248 ld.....fyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaea 310
                                       +      +y++  +++g+++ea++i  +++++++++a +a+pd+l+  +a+vGtpe ++e+l+ ++++
  gi|336254745|ref|YP_004597852.1| 237 YVgamgtYYRESLARQGYADEAEAIAAAWANGNQEAALEAIPDALLSDLAAVGTPERAREELRKFEQL 304
                                       44556***********************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.19s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2690.38
//
Query:       gi|336254746|ref|YP_004597853.1|  [L=62]
Description: hypothetical protein Halxa_3362 [Halopiger xanaduensis SH-6]
Scores for 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:                       550  (0.0306766); 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:                         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 0.22s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 525.08
//
Query:       gi|336254747|ref|YP_004597854.1|  [L=385]
Description: Tubulin/FtsZ GTPase [Halopiger xanaduensis SH-6]
Scores for 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-27   94.6   0.0    1.6e-26   93.8   0.0    1.4  1  Tubulin    Tubulin/FtsZ family, GTPase domain
  ------ inclusion threshold ------
      0.023   13.9   0.2      0.053   12.7   0.2    1.5  1  Tubulin_2  Tubulin like
       0.14   12.2   0.2       0.39   10.8   0.2    1.7  1  DivIVA     DivIVA 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 !   93.8   0.0   2.6e-30   1.6e-26       3     192 ..       4     172 ..       2     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 2.6e-30
                                       EEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE-- CS
                           Tubulin   3 ivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllg 79 
                                         ig+Gq+G++i++e+      + ++               ++ ++  ++a++  +++l+ ++      ++n++l+g
  gi|336254747|ref|YP_004597854.1|   4 ALIGFGQAGGKIVDEFLA---YDDAV---------------DGGFVEAAIAVNSATTDLKGLEHV---PQENRVLIG 59 
                                       679***************...44455...............578888899999977777777766...677****** PP

                                       CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE...SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEE CS
                           Tubulin  80 kegagnngaggypevgkeaaeeileeirkevekcds..lqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvv 154
                                       +   +++g+g+++e+g+e++ee  +ei+ ++++ +   +++f+i+a++gGGTGSG +pv+++ l++ y   +v++  
  gi|336254747|ref|YP_004597854.1|  60 QARVKGHGVGADNELGAEVTEEDIDEIQGAIDRIQVheIDAFLIVAGMGGGTGSGGAPVLAKHLQRIY-TEPVYGLG 135
                                       ********************************76665599***************************9.778***** PP

                                       EE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHH CS
                           Tubulin 155 vlPsefsevvvepynailalkelieesdavividNdaL 192
                                       +lP ++ e+ ++  na+ + +++++e+d ++v+dNd +
  gi|336254747|ref|YP_004597854.1| 136 ILPGTD-EGGIYTLNAARSFQTFVREVDNLLVFDNDVW 172
                                       ***876.****************************976 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   8.8e-06     0.053     138     220 ..      85     153 ..      75     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.8e-06
                         Tubulin_2 138 alrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllrkilkeekqkvkiiglvllPdvfplnkeggervk 214
                                       +++ ai+r++     +e   + +v ++ GGTGSG +  +a  l+ i+ e       +gl +lP       ++g  + 
  gi|336254747|ref|YP_004597854.1|  85 EIQGAIDRIQV----HEIDAFLIVAGMGGGTGSGGAPVLAKHLQRIYTEPV-----YGLGILPGT-----DEGGIYT 147
                                       34444444444....5667889*************9999999999998765.....678888876.....3456677 PP

                         Tubulin_2 215 aNayaa 220
                                       +Na+++
  gi|336254747|ref|YP_004597854.1| 148 LNAARS 153
                                       777665 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   6.6e-05      0.39      63      90 ..     347     374 ..     344     378 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  63 etLkktlvvaqetaeevkanakkeaeli 90 
                                       ++L++  + aqet+e v+ana++e + +
  gi|336254747|ref|YP_004597854.1| 347 DQLQQVAIEAQETTETVRANAQEEFSSL 374
                                       689********************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 3330.98
//
Query:       gi|336254748|ref|YP_004597855.1|  [L=587]
Description: ABC transporter periplasmic protein [Halopiger xanaduensis SH-6]
Scores for 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-38  131.4   0.0    1.1e-34  120.0   0.0    2.1  2  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   2.5e-05      0.45     296     354 ..      44     102 ..      28     119 .. 0.84
   2 !  120.0   0.0   6.1e-39   1.1e-34       2     287 ..     263     581 ..     262     586 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 2.5e-05
                                       EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEE.CHHHHHHHHHHCTTESEEEEE CS
                         SBP_bac_5 296 klkltlllasgspaekaiaeliqqqlkkiGikvevktv.dwaatylervkdgdfdmillg 354
                                       +l++ +l + +++ +  i+  + ++l+++Gi v+ ++v ++   y +   +g++d+++ +
  gi|336254748|ref|YP_004597855.1|  44 ELTIKTLPTEDDEIAAMIMSQFRENLRRAGIAVSHEPVnEA-DLYRSVLLEGNYDVFIAR 102
                                       567778888899999999999999**************555.999999********9975 PP

  == domain 2  score: 120.0 bits;  conditional E-value: 6.1e-39
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC.....TCTEEEEEEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyasllee.....dqdikkveav 73 
                                       +vp++A+++ +++ D ++ t++LR+g++++D t++ A+Dv+f+++ l d   +       ++     ++ +++veav
  gi|336254748|ref|YP_004597855.1| 263 YVPWVADAITWTESDSLEATVTLRDGLTWHDETAFDADDVAFTYRFLQDTSMGEVEGGVPAPryrdrQTLVETVEAV 339
                                       79****************************************866555444333333333335556789******** PP

                                       ETTEEEEEESSETTTTTTHCHHHHHHHGC........CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-T CS
                         SBP_bac_5  74 ddytvrftlkkpnalfltllaavpasiak........kaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernp 142
                                       dd tvrf ++ ++  + + + avp+ + +        +a ++ ++   + n + +g+G ++l +++  + i+le + 
  gi|336254748|ref|YP_004597855.1| 340 DDGTVRFAFSDTTRSAAARVFAVPILPQHvweprsaiVAEHQPEA-LVTDNVEAMGSGLFQLHAVTD-EGIELEPFA 414
                                       **************9999999999999999999888644444444.5566677799********999.*******99 PP

                                       TST.......TTSCS.......SSSEEEEEE-.SHHHHHHHHHTTSSSEE.ESTTCCTHCHHHHHTTEEEEEEEEEE CS
                         SBP_bac_5 143 dYw.......gggkp.......kldriefkvipdsdaraaalqsGeiddv.aepppsdieqlkeakglkvlyespgg 204
                                       d         +   p       ++d +++++ p++ + +++l++G+id+  + +pps++e ++  + + v  ++ ++
  gi|336254748|ref|YP_004597855.1| 415 DHVlrdettdR---PdvlegfsQFDGLTYQIEPNPGSMIESLRNGDIDITgSPVPPSELEGIRSGEETSV-LTGRTN 487
                                       95566775541...34556666*************************99999999***************.****** PP

                                       EEEEEEETTT.STGGGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH..........S CS
                         SBP_bac_5 205 gvtylafNtk.kppfddkrvRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka..........y 270
                                        +++++fN++ +p + ++++R+ l+  iDre  v+++++g+++pa+ + +     + e++ +++ a           
  gi|336254748|ref|YP_004597855.1| 488 AFYMIGFNSSqHPDLGNPNFRRILARLIDREHAVREFFGGHGEPATEFSSLLGVRNEEWTFDDRAAasifpgsdgkI 564
                                       **********9999**********************************77644444444333332356666666666 PP

                                       HHHHHHHHHHHTT-BCS CS
                         SBP_bac_5 271 dpekAkklLkeaGykdg 287
                                       d +   +l+++ Gy   
  gi|336254748|ref|YP_004597855.1| 565 DADRVHALFEDVGYRYE 581
                                       66666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 4554.20
//
Query:       gi|336254749|ref|YP_004597856.1|  [L=291]
Description: phosphoesterase PA-phosphatase-like protein [Halopiger xanaduensis SH-6]
Scores for 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-21   74.6   9.9    8.2e-21   74.6   9.9    1.8  2  PAP2_3          PAP2 superfamily
    1.1e-11   44.7   5.1    1.1e-11   44.7   5.1    2.3  3  PAP2            PAP2 superfamily
  ------ inclusion threshold ------
       0.14   12.7   4.7       0.12   13.0   1.2    2.5  2  Nucleos_tra2_N  Na+ dependent nucleoside transporter N-termin
        1.2    9.7   8.1       0.12   12.9   2.5    2.3  2  PAP2_C          PAP2 superfamily C-terminal
        2.8    6.1  16.7       0.84    7.9   7.5    2.0  2  DUF2070         Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.8      0.64   2.3e+03      73      82 ..      16      25 ..       3      65 .. 0.58
   2 !   74.6   9.9   2.3e-24   8.2e-21       1     190 []      80     261 ..      80     261 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.64
                            PAP2_3 73 gllvyalfPa 82
                                      ++lv a +  
  gi|336254749|ref|YP_004597856.1| 16 TMLVTASLAI 25
                                      2222222222 PP

  == domain 2  score: 74.6 bits;  conditional E-value: 2.3e-24
                            PAP2_3   1 relialdralgldweaalnklllahpalavilalaYasl.hfqvtllvlvllflrrrerlreflttlllatllgllv 76 
                                       ++l+++dr +g +   al    l++pal+ ++ +aY +   f++++ ++++ +l++++ l  +++++ +  ++gl +
  gi|336254749|ref|YP_004597856.1|  80 QWLFDFDRLFGPGGPVALL-QSLQSPALTSYFVFAYVYGyAFLLLFPFIAYFALEETDDLADLILAFTANYAIGLCC 155
                                       5788888888877666666.5667777776665555444044444445555559*********************** PP

                            PAP2_3  77 yalfPaagPrlleeagfvdtvaaaslagalrdgasravllrgtienglaafPSlHvawallvalalwrlrrkr.llr 152
                                       y+lf a gPr +++  f         +g l d++ r   l+g+++++   fPSlH+ +++ v +++w++r+k   + 
  gi|336254749|ref|YP_004597856.1| 156 YVLFMAYGPRNFDPLLF---------DGLLYDAFPRIRDLTGNVNRPTNVFPSLHTSLSMTVFFFAWQTREKYpTWV 223
                                       *********99943333.........3356667777777788888***************************97888 PP

                            PAP2_3 153 vlalllnvlmivatvatgnHYlvDviaGvalalvaial 190
                                       ++a +l++ +++at+++g H + Dv+aG +la+v++++
  gi|336254749|ref|YP_004597856.1| 224 PVAGVLAISIVFATMYLGIHWFSDVVAGTLLAAVSVYI 261
                                       9999******************************9985 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.0       1.1     4e+03      65     101 ..      15      58 ..      10      62 .. 0.53
   2 ?   -1.0   0.3      0.38   1.4e+03      66      74 ..     121     129 ..     104     163 .. 0.43
   3 !   44.7   5.1     3e-15   1.1e-11      49     126 ..     182     261 ..     139     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                              PAP2  65 falalllalllrrkrkkig.......lvllalillllavlvals 101
                                       ++++++++l +   r+ ++       ++ +++i+ll+++ v + 
  gi|336254749|ref|YP_004597856.1|  15 VTMLVTASLAIVGPRRIVSslgdfrwRLEICFIPLLALASVLIL 58 
                                       44444444444444444445666666555566666665555554 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.38
                              PAP2  66 alalllall 74 
                                       +l++ ++++
  gi|336254749|ref|YP_004597856.1| 121 LLLFPFIAY 129
                                       222222222 PP

  == domain 3  score: 44.7 bits;  conditional E-value: 3e-15
                              PAP2  49 s........keakesfPSgHsafafalalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGl 117
                                       +        +++++ fPS H++ +++++++++ + r+k+++     ++ ++ +la+ + ++ +ylg+H++sDv+aG+
  gi|336254749|ref|YP_004597856.1| 182 RirdltgnvNRPTNVFPSLHTSLSMTVFFFAWQT-REKYPT-----WVPVAGVLAISIVFATMYLGIHWFSDVVAGT 252
                                       144555666889999**********999988875.555555.....68999999*********************** PP

                              PAP2 118 liGialaal 126
                                       l++++ +++
  gi|336254749|ref|YP_004597856.1| 253 LLAAVSVYI 261
                                       ***998875 PP

>> Nucleos_tra2_N  Na+ dependent nucleoside transporter N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       0.8   2.9e+03      20      50 ..      38      68 ..      33      85 .. 0.72
   2 ?   13.0   1.2   3.2e-05      0.12      10      51 ..     210     251 ..     204     261 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.8
                                      --HHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                    Nucleos_tra2_N 20 inwrtVigglllQfvlAlfvlktpagrdvfk 50
                                      ++wr+ i  + l  +  +++l+++   +v++
  gi|336254749|ref|YP_004597856.1| 38 FRWRLEICFIPLLALASVLILRWSTADAVVR 68
                                      5677777777777777788899888877766 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.2e-05
                                       HHHT-S-GGG--HHHHHHHHHHHHHHHHHHHTSHHHHHHHHH CS
                    Nucleos_tra2_N  10 awllSenrkainwrtVigglllQfvlAlfvlktpagrdvfka 51 
                                       +++  +  k   w +V+g l++ +v+A + l + ++ dv+++
  gi|336254749|ref|YP_004597856.1| 210 FFAWQTREKYPTWVPVAGVLAISIVFATMYLGIHWFSDVVAG 251
                                       344445667789**************************9987 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   0.3       2.1   7.5e+03      25      25 ..      27      27 ..      10      59 .. 0.51
   2 ?   12.9   2.5   3.5e-05      0.12       8      67 ..     199     257 ..     194     264 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.1
                            PAP2_C 25 s 25
                                       
  gi|336254749|ref|YP_004597856.1| 27 G 27
                                      2 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.5e-05
                            PAP2_C   8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittl 67 
                                       S Ht   +++++f++++ +k  +    ++ +la++++f  ++   H+  DV+ g +++ +
  gi|336254749|ref|YP_004597856.1| 199 SLHTSLSMTVFFFAWQTREKYPT-WVPVAGVLAISIVFATMYLGIHWFSDVVAGTLLAAV 257
                                       66999999999999999999874.556677899*********************998765 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   7.5   0.00023      0.84      21     148 ..      13     158 ..       2     180 .. 0.74
   2 ?    3.0   2.1    0.0071        26     111     169 ..     203     260 ..     186     274 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00023
                           DUF2070  21 iillalligllaflssk............lfgillfglpalvaflltlpvlrilggrltykrslflalltelivvii 85 
                                       +++++l+++ la ++++              +i ++ l al+++l++ +    +   + ++r +f + +t++++ + 
  gi|336254749|ref|YP_004597856.1|  13 VVVTMLVTASLA-IVGPrrivsslgdfrwRLEICFIPLLALASVLILRWST--ADAVVRLERRVFGNNITQWLFDFD 86 
                                       222222222222.23335777788888854555555566666666664443..5566999999*********99999 PP

                           DUF2070  86 sllaillsall.........qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly 148
                                        l++    + l         ++++++a+v ++a+ + ++++ ++a+ +++ l  +++a++ ++++ l+ +++
  gi|336254749|ref|YP_004597856.1|  87 RLFGPGGPVALlqslqspalTSYFVFAYVYGYAFLLLFPFIAYFALEETDDLADLILAFTANYAIGLCCYVL 158
                                       9998887777678999998899999999**********************************9999988887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0071
                           DUF2070 111 vfalrllvlvavsdesllkavlpaliqpllailllvlyfspesfllllllslifalavy 169
                                       +++++++ +   ++e+++  ++p++  ++++i+++++y++ + f  +++ +l+ a+ vy
  gi|336254749|ref|YP_004597856.1| 203 SLSMTVFFFAWQTREKYP-TWVPVAGVLAISIVFATMYLGIHWFSDVVAGTLLAAVSVY 260
                                       223333333333333333.2334455555555555555555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2180.43
//
Query:       gi|336254750|ref|YP_004597857.1|  [L=476]
Description: Deoxyribodipyrimidine photo-lyase [Halopiger xanaduensis SH-6]
Scores for 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-75  251.7   1.7    5.7e-75  251.2   1.7    1.2  1  FAD_binding_7   FAD binding domain of DNA photolyase
    1.9e-40  138.6   0.6    1.5e-39  135.7   0.1    2.2  2  DNA_photolyase  DNA photolyase


Domain annotation for each model (and alignments):
>> FAD_binding_7  FAD binding domain of DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.2   1.7   6.3e-79   5.7e-75       1     201 [.     274     469 ..     274     470 .. 0.94

  Alignments for each domain:
  == domain 1  score: 251.2 bits;  conditional E-value: 6.3e-79
                                       HHHHHHHHHHHHHHHHCSTTTTTSSTTGCCTT------HH.HHHHHHTT-SS-HHHHHHHHHHHHHS---HHHHHHH CS
                     FAD_binding_7   1 flreLlwrefyyallaaepelaeralkekfdripweeseeekleaWkeGrTGfPlvDAamrqLretGwmhnrlRmiv 77 
                                       f+r+L+++efy+++la +p+l   ++++  + i+w+++ + +l+aWk+GrTG+P+vDA+mrqLr++Gw+hnr+Rmiv
  gi|336254750|ref|YP_004597857.1| 274 FRRQLAFHEFYTHVLAFNPDLVVADFTAYENGIDWRNDPD-ELAAWKAGRTGYPIVDAGMRQLRTEGWVHNRVRMIV 349
                                       889******************99999988888***99877.6*********************************** PP

                                       HHHHCTTT-B-HHHHHHHHHHH-TT--CCHHHHHHHHHCT-STTS-STT----CCCCHHHCSTT-HHHHHH-GGGTT CS
                     FAD_binding_7  78 asFltkdLlidWregeevFeellvDadlasnagnwqwlagtgadaapafrifnpvkqgkkfDpegeyirrwvpeLkk 154
                                       asFlt dLl+dWreg ++++++l D++ a++a++wqw+a+tg da+p+fr+fnp+kqg+++Dp++ey+r++vpeL++
  gi|336254750|ref|YP_004597857.1| 350 ASFLTADLLVDWREGYDWYRQHLADHESANDAAGWQWAASTGPDAQPYFRVFNPMKQGREYDPDAEYVREYVPELAD 426
                                       ***************************************************************************** PP

                                       S-HHHHT-GGGSGCHHHHHHT--TTTSS---SS-HHHHHHHHHHHHH CS
                     FAD_binding_7 155 lpakyihepwkapaeeqkkagvvlgkdYpkpivdhkearkraleayk 201
                                        + ++ih+ w+  +   ++ +++++ dYp+pivdh+e+r+ra++a++
  gi|336254750|ref|YP_004597857.1| 427 ADPDEIHD-WHDLS---ADRRAAVAPDYPAPIVDHAERRERAIAAFE 469
                                       *******7.63332...33468999******************9986 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.7   0.1   1.6e-43   1.5e-39       2     163 ..       3     161 ..       2     164 .. 0.94
   2 ?    0.7   0.1     0.051   4.6e+02      94     128 ..     255     288 ..     226     302 .. 0.65

  Alignments for each domain:
  == domain 1  score: 135.7 bits;  conditional E-value: 1.6e-43
                                       EEEESS---STT-HHHHHHHCTTSEEEEEEEE-HHHHTCGS-CHHHHHHHHHHHHHHHHHHHHTT--EEEEESSHHH CS
                    DNA_photolyase   2 lvWfrrDlRlhDNpALaaAaasgepvipvfvldpekahklrvgaarvdfllesLadLdeeLrelgirLvvrrgdpad 78 
                                       l+W+rrDlR  DN+ALa+Aa+    v+pvfvldp+  +  +++++rv+ +le L++L++ +re+g++Lv+ rg++ +
  gi|336254750|ref|YP_004597857.1|   3 LHWHRRDLRGPDNRALARAATD--AVVPVFVLDPTVLE--YASPIRVACMLEALESLRAWYRERGGDLVIARGEASA 75 
                                       89*****************955..7**********322..479********************************** PP

                                       HHHHHHHHCTECEEEEE---SHHHHHHHHHHHHHHHHCTSEEEEE--SSSS-HHHHHTTTSSSHSSHHHHHHCHHHH CS
                    DNA_photolyase  79 vlpelakelgasavvanreyepdererdeavkealrkagievesfddhtlvepgevktkkgkpykvFtpfrkrwlke 155
                                       v+p+la e+ga+av + ++y+  + erd+av +al+++g+e + + d + +epg++  +kg++y+vF+ f+k+w+++
  gi|336254750|ref|YP_004597857.1|  76 VIPRLADEYGADAVSWAEDYSGLAAERDRAVTAALEDRGLEPRPVRDALHHEPGSITPNKGDHYSVFSYFWKKWRDR 152
                                       ********************************************************99*****************97 PP

                                       HC.S-TTSS CS
                    DNA_photolyase 156 lk.eplpap 163
                                        k +p+ ap
  gi|336254750|ref|YP_004597857.1| 153 EKlDPVDAP 161
                                       666777665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.051
                                       EE---SHHHHHHHHHHHHHHHHCTSEEEEE--SSS CS
                    DNA_photolyase  94 anreyepdererdeavkealrkagievesfddhtl 128
                                       ++r  e++e+e +++  +a+r +++++++f +h+l
  gi|336254750|ref|YP_004597857.1| 255 TERALERAETEAQREDVTAFR-RQLAFHEFYTHVL 288
                                       244455555555555555555.5899999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3868.42
//
Query:       gi|336254751|ref|YP_004597858.1|  [L=101]
Description: hypothetical protein Halxa_3367 [Halopiger xanaduensis SH-6]
Scores for 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-22   79.1   0.8    2.8e-22   78.7   0.8    1.1  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   0.8   1.6e-26   2.8e-22       3      75 .]      14      87 ..      12      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 1.6e-26
                            HalOD1  3 espstaVveavaavegvdptelep.....LydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75
                                       +ps+a+v+ava+ egvd+te+ep     L+ +++p+ALd+Lf++    ++ + ++v+++y+gy +tV++dg++ V++
  gi|336254751|ref|YP_004597858.1| 14 VPPSQAIVAAVADREGVDVTEIEPpeyepLFTVVNPEALDELFDR----PSAGPARVHLEYAGYAITVHGDGRVDVDD 87
                                      58********************888********************....78888*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.33
# Mc/sec: 905.45
//
Query:       gi|336254752|ref|YP_004597859.1|  [L=104]
Description: hypothetical protein Halxa_3368 [Halopiger xanaduensis SH-6]
Scores for 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-07   30.5   0.2    4.4e-07   30.1   0.2    1.2  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    0.00024   21.6   0.0     0.0003   21.3   0.0    1.1  1  DUF4198          Domain of unknown function (DUF4198)
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.076   13.0   0.0    2.2  1  Big_1            Bacterial Ig-like domain (group 1)
      0.094   12.9   0.0       0.12   12.5   0.0    1.1  1  MG4              Macroglobulin domain MG4


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 !   30.1   0.2   9.7e-11   4.4e-07       4      65 ..      24      81 ..      21      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 9.7e-11
                   CarboxypepD_reg  4 GrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatre 65
                                       rV+d  g+pi+ga V++     +  ++ +tda G+  +++ +pg  ++ ++++G + +++ 
  gi|336254752|ref|YP_004597859.1| 24 VRVRDVGGRPIEGAVVEAG----SGAKRKRTDAHGRCEFTFHAPGYWKLIARKAGTDRVAYD 81
                                      59*****************....89999***************************9998874 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   6.6e-08    0.0003     147     210 ..      16      71 ..      10      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 6.6e-08
                           DUF4198 147 lkageelevqvl.ldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGlwlleae 210
                                       + +g +l v+v  + G+P +ga ve+       + a+++   +tda G+ +ft+ ++G+w l a+
  gi|336254752|ref|YP_004597859.1|  16 VAVGTPLAVRVRdVGGRPIEGAVVEA------GSGAKRK---RTDAHGRCEFTFHAPGYWKLIAR 71 
                                       67899999***99************8......4567788...9*****************99775 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 ?   13.0   0.0   1.7e-05     0.076       9      52 ..      22      60 ..      19      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                             Big_1  9 ltatvkDangnpvagatVtfsvsggalsassgtTdanGkatvtl 52
                                      l ++v+D  g p++ga V   +      a   +Tda+G++++t+
  gi|336254752|ref|YP_004597859.1| 22 LAVRVRDVGGRPIEGAVVEAGSG-----AKRKRTDAHGRCEFTF 60
                                      789**************987644.....4567999999999986 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.7e-05      0.12      19      76 ..      23      74 ..      20      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.7e-05
                               MG4 19 kVlvkdpdgspaknvpVkiealkseteekeslttdedGtakfsintpedaksltitvk 76
                                       V+v d  g+p+++  V     +     ++++ td++G+ +f++  p+ +k ++ ++ 
  gi|336254752|ref|YP_004597859.1| 23 AVRVRDVGGRPIEGAVVEAGS-G-----AKRKRTDAHGRCEFTFHAPGYWKLIARKAG 74
                                      79**************99998.5.....678899**********99997776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); 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:                         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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 819.53
//
Query:       gi|336254753|ref|YP_004597860.1|  [L=360]
Description: oxidoreductase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   84.4   0.0    1.6e-23   83.8   0.0    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    1.7e-10   40.9   0.0    3.5e-10   39.9   0.0    1.7  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
    6.5e-05   22.4   0.0    0.00011   21.6   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    0.00014   22.4   0.0    0.00037   21.0   0.0    1.7  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0014   19.3   0.0     0.0027   18.3   0.0    1.5  1  CoA_binding     CoA binding domain
  ------ inclusion threshold ------
       0.01   15.4   0.0      0.017   14.7   0.0    1.3  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.011   15.9   0.0      0.027   14.7   0.0    1.6  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      0.099   12.3   0.0       0.19   11.4   0.0    1.4  1  ox_reductase_C  Putative oxidoreductase C terminal domain


Domain annotation for each model (and alignments):
>> 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 !   83.8   0.0   7.1e-27   1.6e-23       1     120 []       6     121 ..       6     121 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 7.1e-27
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHH CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngthee 77 
                                       +r +iiG+G+ig+ h++ l +      +v+ +d+ +e+  ++ ++++v++y+d++el +   +davi++tpn+ hee
  gi|336254753|ref|YP_004597860.1|   6 IRTGIIGLGNIGQYHAERLVDL--SVPIVGGMDIAEEARTRFGRRYDVDVYEDHQELYD--TVDAVIITTPNKYHEE 78 
                                       689*************999999..889********************************..9*************** PP

                                       HHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  78 lakaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       +a++a+e+  hvllEKPla ++e a++++++a+ ++ ++++g+
  gi|336254753|ref|YP_004597860.1|  79 YAIDAFERDLHVLLEKPLAHSLESARRIADAADDSEGVCMIGF 121
                                       ***********************************99999886 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   1.6e-13   3.5e-10       1      67 [.     133     199 ..     133     263 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.6e-13
                                       HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSH.HCSTSHHHHTCHHHHHHHHHHHTSEEEEEEE CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrk.kksgGvlgdlgiHdiDllqwLfGqppsvvaa 67 
                                       K  Ie g lG+v +v+   +  r+g + + +w  r+   +gG+l+dlg+H iDl+ +L+G p +++++
  gi|336254753|ref|YP_004597860.1| 133 KNRIERGDLGDVIHVE-ANYVRRRGIPGRGSWFTRRqIAGGGALIDLGVHAIDLALYLLGYPEVKEVN 199
                                       678*************.89999999********999999***********************999885 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 !   21.6   0.0   4.9e-08   0.00011      38     111 ..       7      83 ..       2      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.9e-08
                                       EEEEES-SHHHHHHHHHHHHTT-EEEE.ESSSHHHHH...CHHHHTC.EECSHHHHHHH-SEEEE-S--STTTTTSB CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkvia.ydrskkkee...eeeelgv.elvsleellaesDivslhlpltpetrhli 109
                                       + GiiGlG+IGq  a+rl  + + +++ +d  +++++   +  ++ v  +++ +el+ + D v++++p + + +  i
  gi|336254753|ref|YP_004597860.1|   7 RTGIIGLGNIGQYHAERLVDLSVPIVGgMDIAEEARTrfgR--RYDVdVYEDHQELYDTVDAVIITTPNKYHEEYAI 81 
                                       78*********************877526777665556532..33333688*****************998888887 PP

                                       SH CS
                      2-Hacid_dh_C 110 na 111
                                       +a
  gi|336254753|ref|YP_004597860.1|  82 DA 83 
                                       76 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 !   21.0   0.0   1.7e-07   0.00037       2      81 ..       8      83 ..       7      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.7e-07
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlse 80
                                       giiG Gn+g+  a++l+        iv + +  +e ++ + +++ v+v + d++e+ +  d v+++ + +++ee + +
  gi|336254753|ref|YP_004597860.1|  8 TGIIGLGNIGQYHAERLVDLS---VPIVGGMDIAEEARTRFGRRYDVDVYE-DHQELYDTVDAVIITTPNKYHEEYAID 82
                                      59******************9...8899888889999999999999*****.******************999998766 PP

                                      C CS
                     F420_oxidored 81 l 81
                                      +
  gi|336254753|ref|YP_004597860.1| 83 A 83
                                      5 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.2e-06    0.0027       3      85 ..       5      86 ..       3      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                                      TEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TT.TTTCEET...TEEEESCHHHHHHHCTTTEEEEES-HHHHHH CS
                       CoA_binding  3 dtkviviGagglgiaglyhfkeklkygikavfgvnpr.kvgtevl...glpvyksvdeleektevdvavitvPaesaqe 77
                                      d + ++iG g+    g yh ++  + ++++v+g +    + t  +   ++ vy++ +el ++  vd+ +it+P++  +e
  gi|336254753|ref|YP_004597860.1|  5 DIRTGIIGLGNI---GQYHAERLVDLSVPIVGGMDIAeEARTRFGrryDVDVYEDHQELYDT--VDAVIITTPNKYHEE 78
                                      567899999999...88****************998834445555999**************..**********99998 PP

                                      HHHHHHHT CS
                       CoA_binding 78 avdelvea 85
                                       ++++ e 
  gi|336254753|ref|YP_004597860.1| 79 YAIDAFER 86
                                      88888775 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 ?   14.7   0.0   7.7e-06     0.017       7      77 ..       8      80 ..       4     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.7e-06
                                      EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-H.HHHHHHHTT-EEEE.HHHHHHT-SEEEE-S-HHHHHHHH CS
                              IlvN  7 iaviGyGsqGhaqalnlrdsgldvvvglregsk.svkkAkeegfevlt.vaeavkkadvvmiliPDelqkevy 77
                                        +iG G+ G+ +a+ l d  + +v g+   ++  ++  ++  ++v++  +e+ ++ d v+i +P+++++e  
  gi|336254753|ref|YP_004597860.1|  8 TGIIGLGNIGQYHAERLVDLSVPIVGGMDIAEEaRTRFGRRYDVDVYEdHQELYDTVDAVIITTPNKYHEEYA 80
                                      579************************98766527778899999998637899**************999855 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 ?   14.7   0.0   1.2e-05     0.027       2      74 ..       8      82 ..       7     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                      EEEE--SHHHHHHHHHHHHTT-EEE.EE-SSHHHHHHHHHTT.EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHH CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkagykva.vynrtkekveelvaeg.akaaesieelvasldvvitmvkagkavdevie 74
                                       g+iGlG++G+  a++l++    ++ +++  +e+ +++  +  ++++e+ +el +++d+vi+  +++ + +  i+
  gi|336254753|ref|YP_004597860.1|  8 TGIIGLGNIGQYHAERLVDLSVPIVgGMDIAEEARTRFGRRYdVDVYEDHQELYDTVDAVIITTPNKYHEEYAID 82
                                      59*****************999977258888888888887756*******************9999887666665 PP

>> ox_reductase_C  Putative oxidoreductase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.3e-05      0.19       1      72 [.     124     198 ..     124     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.3e-05
                    ox_reductase_C   1 rylkvvqkmkkiikennl.kvvatnaryvsayehaakkawweksis..aGpvveqathfcdlsryfgGdvdldtv 72 
                                       r+ ++v+ +k+ i+  +l +v+  +a yv       +  w+++ +   +G +++ + h  dl+ y+ G  +++ v
  gi|336254753|ref|YP_004597860.1| 124 RFANTVRIVKNRIERGDLgDVIHVEANYVRRRGIPGRGSWFTRRQIagGGALIDLGVHAIDLALYLLGYPEVKEV 198
                                       7899*********9999967999******************9875411578***************998777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2843.02
//
Query:       gi|336254754|ref|YP_004597861.1|  [L=395]
Description: glycerol-3-phosphate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-33  115.1   0.0    5.7e-33  114.3   0.0    1.4  1  ABC_tran         ABC transporter
    1.7e-13   51.1   0.0    4.9e-13   49.7   0.0    1.8  1  OB_MalK          MalK OB fold domain
    1.4e-06   28.3   0.0      0.025   14.4   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      1e-05   26.0   0.6    5.6e-05   23.6   0.2    2.5  2  CysA_C_terminal  CysA C-terminal regulatory domain
    8.2e-05   22.1   0.1    0.00037   20.0   0.1    1.8  1  SMC_N            RecF/RecN/SMC N terminal domain
    0.00014   22.0   0.1     0.0035   17.5   0.1    2.8  1  TOBE_2           TOBE domain
     0.0038   17.2   0.0     0.0056   16.6   0.0    1.3  1  Rad17            Rad17 P-loop domain
      0.004   17.1   0.2      0.015   15.2   0.0    1.8  2  RsgA_GTPase      RsgA GTPase
     0.0049   17.2   0.0      0.013   15.8   0.0    1.7  2  AAA_22           AAA domain
     0.0055   17.1   0.0      0.015   15.7   0.0    1.8  1  AAA_16           AAA ATPase domain
     0.0084   15.8   0.0      0.025   14.3   0.0    1.7  2  AAA_30           AAA domain
  ------ inclusion threshold ------
       0.01   15.6   0.0        1.5    8.5   0.0    2.1  2  AAA_15           AAA ATPase domain
       0.01   16.1   0.0        5.7    7.3   0.0    3.2  2  TOBE             TOBE domain
      0.011   15.4   0.0      0.025   14.3   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
      0.013   14.8   0.1      0.033   13.5   0.0    1.7  2  Zeta_toxin       Zeta toxin
      0.035   14.3   0.4      0.098   12.8   0.4    1.9  1  AAA_33           AAA domain
      0.036   14.1   0.1      0.097   12.7   0.0    1.8  2  AAA_5            AAA domain (dynein-related subfamily)
      0.047   14.1   0.0       0.11   12.9   0.0    1.6  1  RNA_helicase     RNA helicase
      0.068   13.6   0.5       0.16   12.4   0.5    1.8  1  AAA              ATPase family associated with various cellul
       0.13   12.8   0.0       0.27   11.8   0.0    1.7  1  AAA_18           AAA domain
       0.27   10.8   2.7       0.91    9.1   0.3    2.7  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 !  114.3   0.0   6.7e-36   5.7e-33       2     136 ..      20     161 ..      19     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 6.7e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +++sl+++ ge v +vG++G+GKSt ++++agl++pteG++ + ++++++  l   ++ +++++q+  lfp++ v e
  gi|336254754|ref|YP_004597861.1|  20 DDISLEVEDGEFVTLVGPSGCGKSTTMETVAGLTQPTEGKVYIGDDEVTN--LAPKDRGVAMVFQNIALFPHMDVFE 94 
                                       89*********************************************999..999********************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e ++++e+a++ ++l+++ d+      +++SgGq+qrv +ara++++p+++l+DEp 
  gi|336254754|ref|YP_004597861.1|  95 NisfglrlrkyddeEIRRRVEQAADIVQLDGMLDRMP----KEMSGGQQQRVGIARAIVRNPDVFLMDEPL 161
                                       *********9665555555777777777777666666....*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   5.7e-16   4.9e-13       1      52 [.     235     282 ..     235     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 5.7e-16
                           OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEh 52 
                                       GSP+MNf+++t++edg  +e +++t++l++++      ++g++v+lGiRPE+
  gi|336254754|ref|YP_004597861.1| 235 GSPSMNFVEGTLVEDG--LETNNFTVDLDPSR--IPDVTVGDDVTLGIRPED 282
                                       9***************..99999********9..9****************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 !   11.8   0.0   0.00019      0.16       2      66 ..      32     104 ..      31     131 .. 0.66
   2 !   14.4   0.0   2.9e-05     0.025     236     298 ..     133     193 ..     127     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarl........drdvegltdelsggggirkipslldlydpeipfefeieefl 66 
                                         l+Gp g+GKS+ +++  +l +         d++v++l ++++g  +    + l++  d  + + f++++  
  gi|336254754|ref|YP_004597861.1|  32 VTLVGPSGCGKSTTMETVAGLTQPtegkvyigDDEVTNLAPKDRGVAMVFQNIALFPHMDVFENISFGLRLRK 104
                                       679******************8867776666666666655555555555555555555555555555555555 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.9e-05
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                       e+S G+++  +++ a+ r +   +++l DEp ++L+ kl  +  + l +l+r  +a vi +TH+
  gi|336254754|ref|YP_004597861.1| 133 EMSGGQQQRVGIARAIVRNP---DVFLMDEPLANLDAKLRVHMRTELQRLHReLDATVIYVTHD 193
                                       78999998889999999999...9********************999777777**********8 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.8   4.1e+03       9      20 ..      57      68 ..      56      78 .. 0.75
   2 !   23.6   0.2   6.6e-08   5.6e-05       1      43 []     240     285 ..     240     285 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.8
                   CysA_C_terminal  9 dGklriGglalp 20
                                      +Gk+ iG+ ++ 
  gi|336254754|ref|YP_004597861.1| 57 EGKVYIGDDEVT 68
                                      79****997764 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 6.6e-08
                   CysA_C_terminal   1 NlFhGrvedGklriGglalpvP...elagadgqevvayVRPhDlei 43 
                                       N+ +G++ + +l+  ++++++      + + g++v++++RP+D+++
  gi|336254754|ref|YP_004597861.1| 240 NFVEGTLVEDGLETNNFTVDLDpsrIPDVTVGDDVTLGIRPEDVHL 285
                                       9999**96666*********8879766777**************97 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 !   20.0   0.1   4.4e-07   0.00037      24     212 ..      29     205 ..       2     213 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.4e-07
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE...SSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk...lkiekeev 97 
                                        +f  +vGp G+GKs  ++ +    G ++ ++ +    +d +++     + k   v+++f+n        + e+ ++
  gi|336254754|ref|YP_004597861.1|  29 GEFVTLVGPSGCGKSTTMETV---AGLTQPTEGKVYIGDDEVTN----LAPKDRGVAMVFQNIALFphmDVFENISF 98 
                                       46999***************9...45555544455555554444....33444445555555544421133355556 PP

                                       EEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  98 sisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                        ++ r++ ++e    i ++  + +++ +l  + +  ++++SgG+++ v +a       v+   ++l+De  a+LD+k
  gi|336254754|ref|YP_004597861.1|  99 GLRLRKYDDEE----IRRRVEQAADIVQLDGMLDRMPKEMSGGQQQRVGIARA----IVRNPDVFLMDEPLANLDAK 167
                                       66666666666....888889999**********************9988743....45666689************ PP

                                       HHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 175 nvkkvaellkeksknaQfivislreemlekadklvgvt 212
                                        +  + + l++ + +    vi +++++ e +    ++ 
  gi|336254754|ref|YP_004597861.1| 168 LRVHMRTELQRLHRELDATVIYVTHDQAEAMTMSNRIA 205
                                       99999999998888766666555555555554444333 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   4.1e-06    0.0035       1      55 [.     276     336 ..     276     366 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.1e-06
                            TOBE_2   1 laiRPEklrla.....aagganglsGtVedveylGsstryvvelaggqlvvvrqpnadr.d 55 
                                       l+iRPE+++l+      a++ + + ++ + +e +G+++ +++ l + +   ++q++a+   
  gi|336254754|ref|YP_004597861.1| 276 LGIRPEDVHLSqyadsLADPTDPIDARTDVLEPMGDEVFVYLLLSEAAAGSMEQDPATSpN 336
                                       79********988754222235********************9999999999887776432 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.6e-06    0.0056      33      67 ..      17      51 ..      10     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.6e-06
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                      ++++  +Le +  + + + GPsGCgkst+++ ++ 
  gi|336254754|ref|YP_004597861.1| 17 TAVDDISLEVEDGEFVTLVGPSGCGKSTTMETVAG 51
                                      67777889999999999************998775 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-05     0.015      85     122 ..      14      52 ..       2      64 .. 0.81
   2 ?   -1.1   0.1       1.9   1.6e+03       8      65 ..     156     212 ..     149     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                                       TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                        +++++++++ +++d ++++lvG+SG GKSt ++++++ 
  gi|336254754|ref|YP_004597861.1|  14 GEETAVDDISLEVEDgEFVTLVGPSGCGKSTTMETVAGL 52 
                                       56678899999999989**************99988775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                                       ETTTTEES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHH CS
                       RsgA_GTPase   8 lvrpkvaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeel 65 
                                       l++++ aN+d  l v   +e +  ++ ld  ++ + + ++e + + n+i +l++ + l
  gi|336254754|ref|YP_004597861.1| 156 LMDEPLANLDAKLRVHMRTELQRLHRELDATVIYVTHDQAEAMTMSNRIAVLNKGK-L 212
                                       67777888888777777666777777788888888888888877777777777666.4 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   1.5e-05     0.013       4      29 ..      28      53 ..      25     122 .. 0.83
   2 ?   -2.5   0.0       6.6   5.7e+03      82      87 ..     176     181 ..     140     209 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      +  +++++G+sG+GK+t++++++   
  gi|336254754|ref|YP_004597861.1| 28 DGEFVTLVGPSGCGKSTTMETVAGLT 53
                                      567999**************998655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.6
                            AAA_22  82 leqalr 87 
                                       l++  r
  gi|336254754|ref|YP_004597861.1| 176 LQRLHR 181
                                       222222 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.7e-05     0.015      21      51 ..      28      55 ..      16     198 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekd 51
                                      +  +e v l+G+sG+GKs+ +++++  l++ 
  gi|336254754|ref|YP_004597861.1| 28 D--GEFVTLVGPSGCGKSTTMETVA-GLTQP 55
                                      3..3789***************999.45555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0     3e-05     0.025      19      57 ..      30      75 ..      21      95 .. 0.82
   2 ?   -2.5   0.0       4.1   3.5e+03      37      65 ..     175     203 ..     169     211 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g......grviglAptgk 57
                                       +++l+Gp G GK+t++++++ + +   g       +v  lAp+ +
  gi|336254754|ref|YP_004597861.1| 30 EFVTLVGPSGCGKSTTMETVAGLTQPTeGkvyigdDEVTNLAPKDR 75
                                      4899*****************9999885577777777777777665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.1
                            AAA_30  37 alreaweaaggrviglAptgkaAkvLaee 65 
                                       +l++++++   +vi +++ ++ A ++++ 
  gi|336254754|ref|YP_004597861.1| 175 ELQRLHRELDATVIYVTHDQAEAMTMSNR 203
                                       45666666677777777777777777665 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   0.0    0.0017       1.5      16      42 ..      21      48 ..      18      98 .. 0.85
   2 ?    5.1   0.0     0.018        15     322     365 ..     150     193 ..     133     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0017
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsilea 42
                                      d+++++++  + +l+G+ ++GKS+ +e 
  gi|336254754|ref|YP_004597861.1| 21 DISLEVEDGeFVTLVGPSGCGKSTTMET 48
                                      66777777679*************9986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.018
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                        +++++l++EP a+L  ++  ++   l++l ++ +  vi+ TH 
  gi|336254754|ref|YP_004597861.1| 150 RNPDVFLMDEPLANLDAKLRVHMRTELQRLHRELDATVIYVTHD 193
                                       37899**************************************7 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0067       5.7      27      64 .]     251     285 ..     244     285 .. 0.84
   2 ?    4.3   0.0     0.056        48      12      31 ..     304     323 ..     299     365 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0067
                              TOBE  27 lgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                       l+  +  t+ +++ + ++  +++G+ V++ i +++vhl
  gi|336254754|ref|YP_004597861.1| 251 LETNN-FTVDLDPSRIPD--VTVGDDVTLGIRPEDVHL 285
                                       55555.788899999999..*****************7 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.056
                              TOBE  12 vvveplgseveVrvdlggga 31 
                                       +v+ep g ev+V++ l+  a
  gi|336254754|ref|YP_004597861.1| 304 DVLEPMGDEVFVYLLLSEAA 323
                                       78899999999999887654 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 ?   14.3   0.0   2.9e-05     0.025      16      48 ..      23      55 ..      15      61 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.9e-05
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTllDAiqalLvp 48
                                      ++e++  g ++ l+GpsG GKST +  ++ l  p
  gi|336254754|ref|YP_004597861.1| 23 SLEVED-GeFVTLVGPSGCGKSTTMETVAGLTQP 55
                                      455664.35999***********99887776666 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.9e-05     0.033      18      60 ..      31      73 ..      16      82 .. 0.89
   2 ?   -3.0   0.1       4.2   3.6e+03     165     191 ..     171     197 ..     166     204 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-05
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                       + l+G +G+GKs+++e ++  ++++++ v +  D++ +l P+
  gi|336254754|ref|YP_004597861.1| 31 FVTLVGPSGCGKSTTMETVAGLTQPTEGKVYIGDDEVTNLAPK 73
                                      6889*********************************999997 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.2
                        Zeta_toxin 165 glresvealeeekqldrvkikdrdgkt 191
                                       ++r ++++l++e ++  + ++  + ++
  gi|336254754|ref|YP_004597861.1| 171 HMRTELQRLHRELDATVIYVTHDQAEA 197
                                       566777777777766666655544433 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   0.00011     0.098       2      32 ..      32      66 ..      31     205 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                            AAA_33  2 vllvGlpGsGKstlaerllkklg....avllssdt 32
                                      v lvG++G+GKst  e ++  ++     v +  d+
  gi|336254754|ref|YP_004597861.1| 32 VTLVGPSGCGKSTTMETVAGLTQptegKVYIGDDE 66
                                      679*************9964333445444444444 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 ?   12.7   0.0   0.00011     0.097       2      24 ..      32      55 ..      31      69 .. 0.82
   2 ?   -2.9   0.0       7.1   6.1e+03      83     107 ..     168     192 ..     133     216 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                      EEEE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal.n 24
                                      v LvGp+G+gKs+ +e +a ++  
  gi|336254754|ref|YP_004597861.1| 32 VTLVGPSGCGKSTTMETVAGLTqP 55
                                      679****************99963 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.1
                                       HHHHHHHHSSEEE..-SSSEEE--- CS
                             AAA_5  83 nsLlslleerrllleeggelvkakn 107
                                        ++++  e +rl+ e   +++++  
  gi|336254754|ref|YP_004597861.1| 168 LRVHMRTELQRLHRELDATVIYVTH 192
                                       4444444444444444444444444 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   0.00013      0.11       2      36 ..      33      62 ..      32      72 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvys 36
                                       l+Gpsg+GKSt+++++ +     l ++++++vy+
  gi|336254754|ref|YP_004597861.1| 33 TLVGPSGCGKSTTMETV-AG----LTQPTEGKVYI 62
                                      689************93.33....33566666666 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 ?   12.4   0.5   0.00018      0.16       1      22 [.      32      53 ..      32     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                                      EEEESSTTSSHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakel 22
                                      v l+Gp G+GK+++++ va  +
  gi|336254754|ref|YP_004597861.1| 32 VTLVGPSGCGKSTTMETVAGLT 53
                                      579***************9865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00031      0.27       1      68 [.      32     118 ..      32     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf........gvnlrdvakenglllevdpe...........aldeskrldedkld 58 
                                       + l G++G+GK+t  + ++ +++          ++++ +a++++ + +v+++            ++  +rl++  ++
  gi|336254754|ref|YP_004597861.1|  32 VTLVGPSGCGKSTTMETVAGLTQPtegkvyigDDEVTNLAPKDRGVAMVFQNialfphmdvfeNISFGLRLRKYDDE 108
                                       6799**************77752247777999999999999999999999998777777666666666666666666 PP

                            AAA_18  59 klldaleens 68 
                                       ++ + +e+++
  gi|336254754|ref|YP_004597861.1| 109 EIRRRVEQAA 118
                                       6666666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3    0.0011      0.91      32      49 ..      28      45 ..      20     138 .. 0.90
   2 ?    0.7   0.1      0.38   3.2e+02     170     188 ..     174     192 ..     162     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                            AAA_25 32 agelallaGapgtGKttl 49
                                       ge++ l+G++g+GK+t 
  gi|336254754|ref|YP_004597861.1| 28 DGEFVTLVGPSGCGKSTT 45
                                      699*************95 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.38
                            AAA_25 170 ealeriarrtgaavllvhH 188
                                       + l+r+ r+++a+v+ v H
  gi|336254754|ref|YP_004597861.1| 174 TELQRLHRELDATVIYVTH 192
                                       57899*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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 0.23s 00:00:00.74 Elapsed: 00:00:00.36
# Mc/sec: 3290.70
//
Query:       gi|336254755|ref|YP_004597862.1|  [L=360]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-11   42.6  20.9    5.3e-11   42.6  20.9    2.5  2  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 ?   -8.4  14.4         1   1.8e+04      23      67 ..      90     155 ..      75     166 .. 0.53
   2 !   42.6  20.9     3e-15   5.3e-11       1     172 [.     159     345 ..     155     350 .. 0.89

  Alignments for each domain:
  == domain 1  score: -8.4 bits;  conditional E-value: 1
                      BPD_transp_1  23 liivllslPsfvlaillvlvf.....................vilsilghlilpviillllsaapy 67 
                                       ++ ++  +P+++l+++ +                        +    ++++++  ++++l s++ +
  gi|336254755|ref|YP_004597862.1|  90 FFLFTTLFPFYWLLMVALTPEgqleniiftpngfnpgafvevFQVIPFHWYMFNSFVIALGSTIVV 155
                                       445555666666666655444666655555555555555554333344444444444444444433 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 3e-15
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..........vilsilghlilpviillllsaapy 67 
                                       g l+G+  + +  ++++  l+ l+ +++ +P+ +++i+l  +f            ++ l+++ +++++ l   ++p+
  gi|336254755|ref|YP_004597862.1| 159 GSLAGYAFG-RLEFPGRTPLMLLVLIISFFPPAAFFIPLNDLFntsffflepiTGDGTLYNTPFALVTPLSAIFMPL 234
                                       344555555.88899***********************99999999999**9999999******************* PP

                      BPD_transp_1  68 vrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.......l 137
                                       +++i   +  ++p++l+ aar+ G +r   +++v++P+++p ++t  +l+f+++ +++++  +++ +++        
  gi|336254755|ref|YP_004597862.1| 235 AIFILTTFYAQIPDGLEDAARVEGTTRLGALFRVIIPLSAPGVATAGVLTFIAVYNEFFFSFLMTDGQPqnwapilE 311
                                       *********************************************************99988888666688888888 PP

                      BPD_transp_1 138 gtllleailgydyseisnggvlalviavlllnlva 172
                                       g l  + + + +y++++ ++++ +vi v++l+++a
  gi|336254755|ref|YP_004597862.1| 312 GILAYQGQYQVMYHLMA-AASILGVIPVAILVVIA 345
                                       88888888888888777.88888888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2992.01
//
Query:       gi|336254756|ref|YP_004597863.1|  [L=345]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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   58.8  21.4    5.7e-16   58.8  21.4    2.9  3  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        0.2   11.7  12.1      0.087   12.9   5.5    2.5  2  ThiW          Thiamine-precursor transporter protein (ThiW)
        0.3   10.2   3.1        1.3    8.2   0.3    2.2  2  TraP          TraP protein


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 ?    0.8   0.4     0.059   3.5e+02      49      76 ..      39      66 ..      25      69 .. 0.79
   2 ?    1.4   0.9     0.039   2.3e+02     137     172 ..      96     140 ..      77     153 .. 0.54
   3 !   58.8  21.4   9.6e-20   5.7e-16       4     172 ..     140     329 ..     137     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.059
                      BPD_transp_1 49 lghlilpviillllsaapyvrlirraal 76
                                      ++ l lp+++ll+l a+ ++++++ + l
  gi|336254756|ref|YP_004597863.1| 39 AYLLLLPAFALLTLIAFYPMIRTFVMSL 66
                                      5567888999999999999998887665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.039
                      BPD_transp_1 137 lgtllleailgydyseis.........nggvlalviavlllnlva 172
                                       l +++l+++l++ +++            +++la++i+ +++ +++
  gi|336254756|ref|YP_004597863.1|  96 LARQFLDVSLASSFPFVEfgtpffqqaLFVTLAFAIISVVFETLI 140
                                       555555555555555555776664444334444444444433333 PP

  == domain 3  score: 58.8 bits;  conditional E-value: 9.6e-20
                      BPD_transp_1   4 lGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf...................vilsilghlilpviil 59 
                                       +G+  a  l + +++++++r+ ii+++++P+++ +++++l+f                   + l    ++++ ++++
  gi|336254756|ref|YP_004597863.1| 140 IGFGQAyvLDQDFRGRRWVRVAIILPWAVPIVIQGMIFFLLFqptvgfgtdvmqwlgifgaSPLANSRDAFIIILVA 216
                                       556666666778899*******************************************999888889999999**** PP

                      BPD_transp_1  60 lllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG 136
                                        ++ + +++ l++ a+l+s++++l+ +ar+ Gas+wq+f+ ++lP+++p ++  ++++ + ++  + l+e +++ + 
  gi|336254756|ref|YP_004597863.1| 217 DIWKSSAFMALLILAGLQSVDRSLYDVARVAGASPWQRFKLITLPLVMPALLVAMLFRTMDAMRVFGLIEATAGCTT 293
                                       *************************************************************************5555 PP

                      BPD_transp_1 137 lgtllleailgydyseisnggvlalviavlllnlva 172
                                       + +l+  + +++     ++++++a++++++l++ ++
  gi|336254756|ref|YP_004597863.1| 294 VPSLTCLVVEAMFGGTRIYATAAAVAFSTALVIGII 329
                                       444444444444444333333333333333333222 PP

>> ThiW  Thiamine-precursor transporter protein (ThiW)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.5     0.032   1.9e+02      97     142 ..     134     179 ..      89     184 .. 0.79
   2 ?   12.9   5.5   1.5e-05     0.087      74     145 ..     264     336 ..     256     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.032
                              ThiW  97 vlGtgiiGallaypvaklllgkeaallvlvisFilstliGsviall 142
                                       v+   +iG+  ay++ + + g++ + +++++++++  +i ++i +l
  gi|336254756|ref|YP_004597863.1| 134 VVFETLIGFGQAYVLDQDFRGRRWVRVAIILPWAVPIVIQGMIFFL 179
                                       3334579999999999999999999999999999988887776555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.5e-05
                              ThiW  74 iGallagllyrltrklllaalgE.vlGtgiiGallaypvaklllgkeaallvlvisFilstliGsviallvlk 145
                                       + all+++l+r++  + +  l E   G   + +l++++v +++ g++  +++  ++F ++ +iG +i+  vl 
  gi|336254756|ref|YP_004597863.1| 264 MPALLVAMLFRTMDAMRVFGLIEaTAGCTTVPSLTCLVVEAMFGGTRIYATAAAVAFSTALVIGIIIGGYVLL 336
                                       45999999999999987766666267*****************************************998875 PP

>> TraP  TraP protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2     0.013        80      15      59 ..     145     191 ..     135     201 .. 0.73
   2 ?    8.2   0.3   0.00022       1.3      13      52 ..     238     277 ..     228     287 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.013
                              TraP  15 lyavasvLrwliWlvkyaviyPLatmal...lvvlvlrtgdttpGqll 59 
                                        y++ + +r+  W v++a+i+P a+ ++   ++ ++l +    +G  +
  gi|336254756|ref|YP_004597863.1| 145 AYVLDQDFRGRRW-VRVAIILPWAVPIViqgMIFFLLFQPTVGFGTDV 191
                                       5777778899999.79********977723345666666666677655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00022
                              TraP  13 avlyavasvLrwliWlvkyaviyPLatmallvvlvlrtgd 52 
                                         ly va+v     W     + +PL + allv +++rt d
  gi|336254756|ref|YP_004597863.1| 238 RSLYDVARVAGASPWQRFKLITLPLVMPALLVAMLFRTMD 277
                                       57899*****999**9988999***************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2562.59
//
Query:       gi|336254757|ref|YP_004597864.1|  [L=441]
Description: family 1 extracellular solute-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-19   69.4   0.2    6.7e-19   68.8   0.2    1.1  1  SBP_bac_8  Bacterial extracellular solute-binding protein
    4.9e-10   39.9   0.6    1.7e-09   38.1   0.6    1.8  1  SBP_bac_1  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.2   7.4e-23   6.7e-19      11     272 ..      32     366 ..      27     372 .. 0.71

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 7.4e-23
                                       TEEEEEEE-..-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG...GSTTHHH-HH.HHHTT... CS
                         SBP_bac_8  11 gvkvnvvta..asndleqklkaalaagtapdidvvwanedalatlaeeglladls...dldnlddltd.alaav... 78 
                                       +++v+v+t+  +s++ +q++++al+ag ap +d+ ++++++   ++ ++ +++l+    +d l +++d +l+a    
  gi|336254757|ref|YP_004597864.1|  32 DIRVEVQTVvsNSAQRMQTTQSALEAGRAP-PDIHMMDSGWTVPFVLRNQTVNLTenlPEDVLGYVNDnYLEAIlet 107
                                       56666666655999***************9.69**********************9876677888877555555776 PP

                                       ...--TS.----EEEEEEE-EEEEEHHHHHHS.........---BHHHHHHHHHHHHHH-....SEGG---G..... CS
                         SBP_bac_8  79 ...gydgklygvPyasetpyvliynkdlleka........edpktwdellaaakklkgkf....glpdpasg..... 135
                                             g+l ++P+      +  y++d++e+a         dp +w+e+  a++++  ++    g++++a+      
  gi|336254757|ref|YP_004597864.1| 108 arhPETGDLHALPLFPDL-GFTLYREDMIEDAgydtggwgTDPPSWEEFSNAVADARDQAgidyGFTTQAAAyegla 183
                                       687335668999999885.8***********99999*************9988888666644453344333312233 PP

                                       ..GGGGGTHH....................ETTEE---H..HHH.HHHHHHHHHHH..HTT-.....EE........ CS
                         SBP_bac_8 136 ..wlqaalla....................kdgksldddggkdglkealellkklk..dngk.....ty........ 175
                                         +      +                    ++  + + d   + + +a+++++++   +         y        
  gi|336254757|ref|YP_004597864.1| 184 ccT------FnevmtswggayfggvdnlftAGDRPITVD--GERVIDAIRMMRSFIegE--EantldGYaqicpsav 250
                                       332......033333222222333333332122223333..555677777777766431..2222342255566666 PP

                                       ..-S..--SSTTTTTSBSEEEE-TTHHHHHH..-T.TTSEEEE.--..............S--EEEEEEEEEEBTTS CS
                         SBP_bac_8 176 ..dtgadavsefanGevaftingswdiaaaq..ka.gkklgai.vp..............kqgsfaggkglavpkna 232
                                         +t  +  s fa+G++++  n+s +ia+    +a g++lg++  p               +++++gg +lav+  +
  gi|336254757|ref|YP_004597864.1| 251 vqWTEQQSLSPFADGSAVANRNWSYAIAQTGteEAfGENLGVMtRPyavsqeeaeyegtgGTTAALGGWNLAVSPFS 327
                                       779***************98888766665446666699***99536677777766554333449999999******* PP

                                       -HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTHH CS
                         SBP_bac_8 233 knedlaAldFlkwltspenqaalaektgyipvnksaalsp 272
                                       + +++ Al+ l+ ++++e +   ++ +g++p+n ++ + +
  gi|336254757|ref|YP_004597864.1| 328 ERQEE-ALQVLEAFANEEVMLTIFQLGGFLPPNLDLVAEA 366
                                       ****7.***************************9988754 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.6   1.9e-13   1.7e-09      23     312 ..      31     344 ..      14     346 .. 0.75

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.9e-13
                                       TTEEEEEEEECHHHHHH..HHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEEEEHHHH CS
                         SBP_bac_1  23 pgikVeiesvgsgslaq..kltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkdaadklsssv 97 
                                        +i Ve+++v s+s +     + a++aG++p+D+ ++d++w+ +++  ++   l++ + ++    v+d        +
  gi|336254757|ref|YP_004597864.1|  31 EDIRVEVQTVVSNSAQRmqTTQSALEAGRAPPDIHMMDSGWTVPFVLRNQTVNLTENLPEDVLGYVND-------NY 100
                                       48999999996666665559999***********************9977777777777776555554.......47 PP

                                       THHHHCE.EE.....ES.EEEE.EEEEEEEETTTHHCTTGGG......SHBHHHHHHHHHHHHHHCTCT.HCCHCCE CS
                         SBP_bac_1  98 lpkilds.kv.....ly.vPly.aargliYNkdlfekagldp......pwtWdelveaakklkekgkkp.iggargg 159
                                       l++il++ +      l  +Pl        Y+ d  e+ag d       p++W+e+  a   ++++ + + +     +
  gi|336254757|ref|YP_004597864.1| 101 LEAILETaRHpetgdLHaLPLFpDLGFTLYREDMIEDAGYDTggwgtdPPSWEEFSNAVADARDQAGIDyGFTTQAA 177
                                       78888875558888*999****88**********************************9999999888877778888 PP

                                       EHHHHHHHHHHHHHHHHTGGGEECCCT................................HHCSHHHHSHHHHHHHHH CS
                         SBP_bac_1 160 sasgtayyfalalakslggkvfdkdgg................................gldnpegvtaatylvkly 204
                                       +++g a  ++++++ s gg +f++  +                                ++ +++++  + ++v + 
  gi|336254757|ref|YP_004597864.1| 178 AYEGLACCTFNEVMTSWGGAYFGGVDNlftagdrpitvdgervidairmmrsfiegeeaNTLDGYAQICPSAVVQWT 254
                                       8888888899999999999999888889**99999988888877777776655555444444444444555555555 PP

                                       HHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTS CS
                         SBP_bac_1 205 avanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkp 281
                                              e+   ++   ++a a + ++    a+a  g+ +a+  ++    +++a+++e+++          g+gg++
  gi|336254757|ref|YP_004597864.1| 255 -------EQQSLSPFADGSAVANRNWS---YAIAQTGTEEAFGENLGVMTRPYAVSQEEAEY--------EGTGGTT 313
                                       .......33333333333333333333...55566667777777777777788888888876........5555555 PP

                                       EEEEEEEEEEBTTCSTHHHHHHHHHHHTSHH CS
                         SBP_bac_1 282 gilgayglaipkgsknpeaAkkFldfllspe 312
                                       + lg+++la++  s  +e+A ++l+ ++++e
  gi|336254757|ref|YP_004597864.1| 314 AALGGWNLAVSPFSERQEEALQVLEAFANEE 344
                                       55***********************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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 0.21s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 3532.52
//
Query:       gi|336254758|ref|YP_004597865.1|  [L=354]
Description: transcriptional regulator TrmB [Halopiger xanaduensis SH-6]
Scores for 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  224.5   0.7    1.4e-66  224.0   0.4    1.4  2  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    1.2e-20   73.1   0.0    3.1e-20   71.8   0.0    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB
    1.5e-06   27.9   0.1    5.7e-06   26.1   0.1    1.9  1  MarR_2          MarR family
    5.8e-06   26.3   0.3      4e-05   23.6   0.1    2.5  2  HTH_20          Helix-turn-helix domain
    5.2e-05   23.0   0.2    0.00019   21.2   0.1    2.0  2  HTH_IclR        IclR helix-turn-helix domain
    0.00026   20.5   0.1     0.0055   16.2   0.0    2.7  3  HTH_24          Winged helix-turn-helix DNA-binding
    0.00053   19.8   0.0     0.0037   17.1   0.0    2.2  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0022   17.5   0.0     0.0076   15.8   0.0    2.0  1  HTH_CodY        CodY helix-turn-helix domain
     0.0057   17.0   0.0      0.012   15.9   0.0    1.5  1  Rrf2            Transcriptional regulator
  ------ inclusion threshold ------
      0.031   14.4   0.0       0.13   12.4   0.0    1.9  2  DUF2250         Uncharacterized protein conserved in archaea 
      0.062   13.2   0.0       0.15   12.0   0.0    1.6  1  MarR            MarR family
      0.075   13.0   0.0       0.18   11.8   0.0    1.7  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.11   12.6   0.0       0.26   11.4   0.0    1.5  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
       0.13   12.3   0.0        0.4   10.7   0.0    1.8  1  HTH_37          Helix-turn-helix domain
       0.18   11.9   0.4        9.7    6.3   0.0    3.4  4  HTH_29          Winged helix-turn helix


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       4.9   5.9e+03     131     152 ..      37      58 ..      36      72 .. 0.82
   2 !  224.0   0.4   1.2e-69   1.4e-66       1     231 [.     111     345 ..     111     347 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.9
                                       H-EEEEEEES-TT-EEES-HHH CS
                    Regulator_TrmB 131 tseviktdepvekpitfssirl 152
                                       t+++i+  ++ ++p+ + + r 
  gi|336254758|ref|YP_004597865.1|  37 TASEIADRTEIPQPRVYDTVRS 58 
                                       5778888889999999998885 PP

  == domain 2  score: 224.0 bits;  conditional E-value: 1.2e-69
                                       -EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS...----GGGSSSSEEEEE CS
                    Regulator_TrmB   1 avwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliyp...dedleeldleevatev 74 
                                       av++vksr+t+++++ee+I++A++el +sl++ lL ++r el+aa+++gv+V l+++p   ++d++e+d+e+vat +
  gi|336254758|ref|YP_004597865.1| 111 AVSLVKSRSTILRYLEEVITEADYELSLSLTPDLLTRFRAELEAAVQAGVSVDLIVTPaaeAPDPAEFDYESVATSA 187
                                       589************************************************************************** PP

                                       E-S---S..EEEEETTTEEEEE-SSS-EEEE--HHHHHHHHHHHHHH........HHH-EEEEE..EES-TT-EEES CS
                    Regulator_TrmB  75 rvrrsga.pllvivDrkrgvvaprevlrdkeeeyaiifkekelihvlshyFlttlWktsevikt..depvekpitfs 148
                                       r+rr+++ p+++++D++++v+a++++lrd++++y++if++++l +++s++F t+lW+t+e       + + +p++++
  gi|336254758|ref|YP_004597865.1| 188 RARRGITtPVVAVADGNYSVYATQDALRDDQDRYGVIFNRSALGFLVSGFFGTVLWTTAERTLGedGSVRGFPRKYA 264
                                       ************************************************************9998788999******* PP

                                       -HHHHHHHHHHHT.TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTTEEEEEEEETTE.EEEEE-TT--SSSEE CS
                    Regulator_TrmB 149 sirlavedikkllraglkveaeveGrdtetgeevtieGrvveatlnstpgvaslvvetedg.evtVGGlgAvlEDie 224
                                       sir++v+d+     +g +++a++eGrd+e g++++++Gr+ +++++ +++va+l++et dg +vtVGG++A+lED+e
  gi|336254758|ref|YP_004597865.1| 265 SIRRCVKDLID---EGGDFYATIEGRDVEVGGSRVVRGRILDISFEVSEEVAALTLETADGdRVTVGGRVAALEDVE 338
                                       ******99877...*************************************************************** PP

                                       EEEEEEE CS
                    Regulator_TrmB 225 aeeitle 231
                                       a+ei + 
  gi|336254758|ref|YP_004597865.1| 339 AHEIHIG 345
                                       ****996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.0   2.6e-23   3.1e-20       4      67 ..      17      80 ..      15      81 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 2.6e-23
                                      CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                              TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                      ++L eyE+++Yl++l++g++ta+eia ++++p+++vY+++rsL+d+GlVe +++rp++ +a+dp
  gi|336254758|ref|YP_004597865.1| 17 FNLGEYEIDAYLTVLEQGQLTASEIADRTEIPQPRVYDTVRSLSDRGLVELRESRPMKVVALDP 80
                                      89************************************************************99 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   4.7e-09   5.7e-06      18      56 ..      34      70 ..      23      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.7e-09
                                      TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      +   lt++e+a+r+ +++++v  +++ L+++GLve r++
  gi|336254758|ref|YP_004597865.1| 34 G--QLTASEIADRTEIPQPRVYDTVRSLSDRGLVELRES 70
                                      2..29******************************9975 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   3.4e-08     4e-05      22      60 ..      33      71 ..      28      72 .. 0.91
   2 ?   -1.3   0.0         2   2.3e+03      10      24 ..     116     128 ..     107     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.4e-08
                                      CTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 22 aegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                       + ltase+a+r ++++  +++ +r L++ gLve+++++
  gi|336254758|ref|YP_004597865.1| 33 QGQLTASEIADRTEIPQPRVYDTVRSLSDRGLVELRESR 71
                                      5789********************************987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                                       HHHHHHHHHHSTCTT CS
                            HTH_20  10 PvRrrilraLaraeg 24 
                                       ++R  ilr+L  +e 
  gi|336254758|ref|YP_004597865.1| 116 KSRSTILRYL--EEV 128
                                       5789999999..444 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 !   21.2   0.1   1.6e-07   0.00019      17      50 ..      34      67 ..      29      69 .. 0.91
   2 ?   -2.7   0.0       4.3   5.2e+03      31      40 ..     117     126 ..     116     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      + lt se+A+rt +p + v+  +++L  +G+ve 
  gi|336254758|ref|YP_004597865.1| 34 GQLTASEIADRTEIPQPRVYDTVRSLSDRGLVEL 67
                                      459*****************************97 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.3
                                       -HHHHHHHHH CS
                          HTH_IclR  31 pkStvhRlLq 40 
                                       ++St  R+L 
  gi|336254758|ref|YP_004597865.1| 117 SRSTILRYLE 126
                                       6888888885 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 !   16.2   0.0   4.6e-06    0.0055      11      48 .]      29      66 ..      21      66 .. 0.91
   2 ?   -1.4   0.0       1.5   1.8e+03      30      40 ..     117     127 ..     116     129 .. 0.81
   3 ?    0.5   0.0      0.37   4.4e+02      34      45 ..     266     277 ..     264     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.6e-06
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++ +++ ++ +e+A+r+ ++++ v   ++ L + Gl++
  gi|336254758|ref|YP_004597865.1| 29 TVLEQGQLTASEIADRTEIPQPRVYDTVRSLSDRGLVE 66
                                      567899******************************96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                            HTH_24  30 Spstvnrrlkr 40 
                                       S+st++r+l++
  gi|336254758|ref|YP_004597865.1| 117 SRSTILRYLEE 127
                                       88999999875 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.37
                            HTH_24  34 vnrrlkrLeeeG 45 
                                       ++r++k L++eG
  gi|336254758|ref|YP_004597865.1| 266 IRRCVKDLIDEG 277
                                       789*******99 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 !   17.1   0.0   3.1e-06    0.0037       9      46 ..      29      66 ..      28      66 .. 0.93
   2 ?   -0.8   0.0       1.2   1.4e+03       3      12 ..     117     126 ..     114     131 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.1e-06
                                      HHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  9 klLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                        L++g+l+++e+a+ ++++q+ v    + L + GLVe
  gi|336254758|ref|YP_004597865.1| 29 TVLEQGQLTASEIADRTEIPQPRVYDTVRSLSDRGLVE 66
                                      56999******************************996 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                       HHHHHHHHHT CS
                             HTH_5   3 tRlkILklLa 12 
                                        R+ IL++L+
  gi|336254758|ref|YP_004597865.1| 117 SRSTILRYLE 126
                                       4555666665 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 !   15.8   0.0   6.4e-06    0.0076       2      37 ..      33      68 ..      32      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.4e-06
                          HTH_CodY  2 eGrLtaskiaDriGitrsvivnaLrkLesaGiiesr 37
                                       G+Ltas+iaDr  i +  + + +r L   G++e r
  gi|336254758|ref|YP_004597865.1| 33 QGQLTASEIADRTEIPQPRVYDTVRSLSDRGLVELR 68
                                      79*******************************987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     1e-05     0.012      16      57 ..      27      67 ..      22      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                                      HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      yL+  e+++ ++++eia+r++i+++ +   ++ L+  glv+ 
  gi|336254758|ref|YP_004597865.1| 27 YLTVLEQGQ-LTASEIADRTEIPQPRVYDTVRSLSDRGLVEL 67
                                      788888888.******************************85 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 ?   12.4   0.0   0.00011      0.13      25      61 ..      38      74 ..      23      79 .. 0.89
   2 ?   -1.4   0.0       2.2   2.7e+03       9      29 ..     117     139 ..     110     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                           DUF2250 25 aksiakeleipleevrellkkLeelGLlervegktik 61
                                      a  ia+++eip+ +v + +++L + GL+e  e++ +k
  gi|336254758|ref|YP_004597865.1| 38 ASEIADRTEIPQPRVYDTVRSLSDRGLVELRESRPMK 74
                                      5679*************************99887766 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                           DUF2250   9 lalkvlkhlkka..nvdYaksia 29 
                                          ++l++l+++  ++dY +s++
  gi|336254758|ref|YP_004597865.1| 117 SRSTILRYLEEVitEADYELSLS 139
                                       56689999998644788887766 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.15      12      48 ..      30      66 ..      23      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      + eqg+l+ se+a++ ++ ++ v  +++ L ++Gl+e
  gi|336254758|ref|YP_004597865.1| 30 VLEQGQLTASEIADRTEIPQPRVYDTVRSLSDRGLVE 66
                                      5689********************************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 ?   11.8   0.0   0.00015      0.18      21      62 ..      35      80 ..      17      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE...EEES-H CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rgrr...irildl 62
                                      +lt  e+A++  + +  v  + + L+++gl++ r+ r   ++ ld+
  gi|336254758|ref|YP_004597865.1| 35 QLTASEIADRTEIPQPRVYDTVRSLSDRGLVElRESRpmkVVALDP 80
                                      6899****************************76444434666665 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021      0.26      21      57 ..      29      65 ..      25      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                      HHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9 21 tLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                      t l++g lt++e++ +t+++   V +++ +L  ++lV
  gi|336254758|ref|YP_004597865.1| 29 TVLEQGQLTASEIADRTEIPQPRVYDTVRSLSDRGLV 65
                                      6799***********************9999888887 PP

>> HTH_37  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   0.00034       0.4      26      49 ..      30      53 ..      28      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00034
                                      HHHHCT--HHHHHHHHT--HHHHH CS
                            HTH_37 26 liekrelsqseaaqllgiaqPkvs 49
                                      ++e+ +l+ se+a +++i+qP+v 
  gi|336254758|ref|YP_004597865.1| 30 VLEQGQLTASEIADRTEIPQPRVY 53
                                      57899*****************96 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.49   5.8e+02      26      40 ..       7      21 ..       7      29 .. 0.86
   2 ?    6.3   0.0    0.0081       9.7       9      54 ..      32      74 ..      27      82 .. 0.81
   3 ?   -0.9   0.0       1.4   1.7e+03      24      35 ..     116     127 ..     111     131 .. 0.78
   4 ?   -1.6   0.0       2.3   2.7e+03      26      40 ..     263     277 ..     261     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.49
                            HTH_29 26 rrtvyrwlkrfeegG 40
                                      r+tv r+ +rf+ g+
  gi|336254758|ref|YP_004597865.1|  7 RSTVERVGDRFNLGE 21
                                      79**********987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0081
                            HTH_29  9 aeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrpr 54
                                      ++G+ t s+iA ++ +  + vy++++     Gl  l+   +s+  +
  gi|336254758|ref|YP_004597865.1| 32 EQGQLTASEIADRTEIPQPRVYDTVRSLSDRGLVELR---ESRPMK 74
                                      68999***************************76664...455555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.4
                            HTH_29  24 lsrrtvyrwlkr 35 
                                        sr+t+ r+l+ 
  gi|336254758|ref|YP_004597865.1| 116 KSRSTILRYLEE 127
                                       699***999986 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 2.3
                            HTH_29  26 rrtvyrwlkrfeegG 40 
                                       + +++r++k+   +G
  gi|336254758|ref|YP_004597865.1| 263 YASIRRCVKDLIDEG 277
                                       789999999865555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2947.34
//
Query:       gi|336254759|ref|YP_004597866.1|  [L=389]
Description: mechanosensitive ion channel MscS [Halopiger xanaduensis SH-6]
Scores for 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-35  121.5   0.4    4.6e-35  121.0   0.4    1.1  1  MS_channel  Mechanosensitive ion channel
    0.00082   19.3   2.8    0.00082   19.3   2.8    2.0  3  TM_helix    Conserved TM helix
     0.0036   17.6   1.3       0.01   16.1   1.2    1.7  2  EI24        Etoposide-induced protein 2.4 (EI24)
  ------ inclusion threshold ------
      0.068   13.1   5.8       0.11   12.4   5.8    1.2  1  DUF3611     Protein of unknown function (DUF3611)
       0.29   11.1   3.3       0.48   10.4   3.3    1.3  1  IncE        Inclusion membrane protein E


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 !  121.0   0.4   1.3e-38   4.6e-35       4     203 ..     103     311 ..     101     314 .. 0.96

  Alignments for each domain:
  == domain 1  score: 121.0 bits;  conditional E-value: 1.3e-38
                                       HHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS..SEEEEEEE CS
                        MS_channel   4 lkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig..dieGtVed 78 
                                       +++ ++++++ i+ s lgv  + +l ++ +++++++ +l  l+ +l+ G+++l+++p++iGD++e++  +++G Ved
  gi|336254759|ref|YP_004597866.1| 103 VRVSVLLITLGIAASILGVGNTQILLSVTVVSAVIAVVLAPLVGSLINGFFVLADRPYEIGDMIEVAdaEHRGFVED 179
                                       577889999999999****************************************************9999****** PP

                                       E-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-T... CS
                        MS_channel  79 iglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlk... 152
                                       i++r tki t +++ ++iPns++ +  ++N+s e+ ++ri +++++ty+sd   le +++   +a+++  +v++   
  gi|336254759|ref|YP_004597866.1| 180 ITIRYTKIFTLQNTFIVIPNSEIQQRDVVNFSAEDERTRISLQFEITYGSD---LEAARRGAERAARSVDTVISggp 253
                                       ***************************************************...*********************** PP

                                       .........TS-EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT CS
                        MS_channel 153 .........dkellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeeg 203
                                                  +++  ++e+gd+++ +e+ +++k   p +++ v+s++ + i + +   +
  gi|336254759|ref|YP_004597866.1| 254 dirigsaryTAAPMCAINEYGDNGVLLELFFWMKH--PYKQMVVRSAVQQAIRERFADLD 311
                                       ***********************************..*************9999887655 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   2.8   2.3e-07   0.00082      16      44 ..      60      88 ..      58      89 .. 0.92
   2 ?   -5.1   1.4         5   1.8e+04      16      27 ..     111     122 ..     109     122 .. 0.73
   3 ?   -2.8   0.3       1.9   6.7e+03      25      38 ..     136     149 ..     131     152 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.3e-07
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TM_helix 16 nLvgAilILlvGwiiAkfvsrlvtkllak 44
                                      +L++A+++ ++Gw++ k+v rl ++  a+
  gi|336254759|ref|YP_004597866.1| 60 QLILALVVIVIGWYLSKVVVRLAGRTVAR 88
                                      8*********************9998766 PP

  == domain 2  score: -5.1 bits;  conditional E-value: 5
                                       HHHHHHHHHHHH CS
                          TM_helix  16 nLvgAilILlvG 27 
                                        L +A+ IL vG
  gi|336254759|ref|YP_004597866.1| 111 TLGIAASILGVG 122
                                       577788888888 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHH CS
                          TM_helix  25 lvGwiiAkfvsrlv 38 
                                       +++ ++A +v  l+
  gi|336254759|ref|YP_004597866.1| 136 VIAVVLAPLVGSLI 149
                                       45555555555554 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.41   1.5e+03      44      64 ..      61      81 ..      48      92 .. 0.60
   2 !   16.1   1.2   2.8e-06      0.01       7      94 ..      88     192 ..      59     198 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.41
                                      HHHHHHHHHHHHHHHHHHHHH CS
                              EI24 44 sllvllllllplwlfplvall 64
                                      ++l+l ++++ ++l+ +v+ l
  gi|336254759|ref|YP_004597866.1| 61 LILALVVIVIGWYLSKVVVRL 81
                                      555555555555555555444 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.8e-06
                                       HHHTS.TTTHHHHHHHHHHHHHHHHHHHHHHH-......TTHHHHHHHHHHHHHHHHHHHHHHHHHHHH........ CS
                              EI24   7 glllsspkllallllplllnlllfllllvlllw......vllasllvllllllplwlfplvalllaapf........ 69 
                                       + + ++p++ + +l  + +++ll++l++++ +       + l + +++ ++++++ l plv  l++++f        
  gi|336254759|ref|YP_004597866.1|  88 RRI-QRPSVTRTVLRGVRVSVLLITLGIAASILgvgntqI-L-LSVTVVSAVIAVVLAPLVGSLINGFFvladrpye 161
                                       344.448888888888888888888665555524566533.3.34555566666899****************9999 PP

                                       HHHHHHHHHH.HHCCTTSHH......HHHHH CS
                              EI24  70 ygllaekvekrhlglvksla......eslks 94 
                                        g+++e ++++h+g+v++++      ++l++
  gi|336254759|ref|YP_004597866.1| 162 IGDMIEVADAEHRGFVEDITirytkiFTLQN 192
                                       9999999999999999999954444433333 PP

>> DUF3611  Protein of unknown function (DUF3611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   5.8     3e-05      0.11      58     136 ..      62     140 ..      54     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3e-05
                           DUF3611  58 vlglvvllfsifwafrytrlarrLraenpelrpk.kaevlqllklGlivnlvGmllallgaeatvgvLlakalsqpq 133
                                       +l+lvv +++ +++  ++rla r   +++ +rp+    vl+ +++++++  +G+ +++lg++ t  +L + ++s   
  gi|336254759|ref|YP_004597866.1|  62 ILALVVIVIGWYLSKVVVRLAGRTV-ARRIQRPSvTRTVLRGVRVSVLLITLGIAASILGVGNTQILLSVTVVSAVI 137
                                       6788999999999999999998884.44555777467778899999999999************9999999999843 PP

                           DUF3611 134 gva 136
                                       +v 
  gi|336254759|ref|YP_004597866.1| 138 AVV 140
                                       433 PP

>> IncE  Inclusion membrane protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.3   0.00013      0.48      40      82 ..     100     142 ..      68     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              IncE  40 clgvvcsiiclalgiaaaavgvscsgfaiglgviaillgivlf 82 
                                         gv +s++ ++lgiaa+ +gv  + + + + v++ ++ +vl 
  gi|336254759|ref|YP_004597866.1| 100 LRGVRVSVLLITLGIAASILGVGNTQILLSVTVVSAVIAVVLA 142
                                       35999***************************99999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2990.70
//
Query:       gi|336254760|ref|YP_004597867.1|  [L=145]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-32  110.6   1.4    9.4e-32  110.5   1.4    1.0  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 !  110.5   1.4   5.3e-36   9.4e-32       1     141 []       1     140 [.       1     140 [. 0.97

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 5.3e-36
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+ Il+++Dgse+ ++ l ++l  a +++a++++l+v+d+r  +a++++d + e + +++ e++ ++ +  ++a++
  gi|336254760|ref|YP_004597867.1|   1 MYDDILIPTDGSETVDETLAHGLPIATDNDATVHALYVVDSRITAAAGESDADLEPSLEAEGEEAVAEVQ--ERAAD 75 
                                       9******************************************************999999999998885..***** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTT.CSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsr.lllGSvseyvlrhapcpVlvVr 141
                                       +g ++  +v +g pa +ile+a+e+++dliV+G+rg+s  ++   lGSvse+v+ +a++pV vVr
  gi|336254760|ref|YP_004597867.1|  76 AGLETAGEVAQGTPAKTILEYADERGIDLIVIGTRGMSPREKvTSLGSVSERVVDNASIPVFVVR 140
                                       ******************************************555*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1127.52
//
Query:       gi|336254761|ref|YP_004597868.1|  [L=136]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   41.7   1.4    6.3e-09   36.5   1.4    2.1  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
       0.12   12.4   0.1       0.31   11.1   0.1    1.6  2  DUF1803   Domain of unknown function (DUF1803)


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 !   36.5   1.4   7.1e-13   6.3e-09      11     140 ..      12     131 ..       3     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 7.1e-13
                                       SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEE CS
                               Usp  11 gseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvve 87 
                                        +++s++ le+A+e a++r+a+l++lhv   ++ ++v   d +++ e++   ++                ++ vv++
  gi|336254761|ref|YP_004597868.1|  12 LTKHSRRTLERAVEVARERDAALTVLHVDLYQNGKKVTRIDLKEAVERAFGPLE---------------NARYVVRT 73 
                                       57899***********************99999999999999999999988886...............55789999 PP

                                       ESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCS.....SBHHHHHHHHHTSSEEEEE CS
                               Usp  88 egdpaeeilevaeeedadliVvGsrgrsglsrll.....lGSvseyvlrhapcpVlvV 140
                                       +  + e+il+++ +e+ad +V+Gs + s+l+r++       +  +y+ +h +c V+ V
  gi|336254761|ref|YP_004597868.1|  74 GFLVEESILDEVAAEEADVVVIGSQQASRLRRIFrrftdNPDIDRYLRNHLDCEVITV 131
                                       99999*********************99999987675555667788888888888866 PP

>> DUF1803  Domain of unknown function (DUF1803)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.36   3.2e+03      50      65 ..      57      72 ..      39      95 .. 0.60
   2 ?   11.1   0.1   3.5e-05      0.31      27      58 ..     101     132 ..      92     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.36
                           DUF1803 50 idaglikRenkrYkln 65
                                      ++  +   en rY + 
  gi|336254761|ref|YP_004597868.1| 57 VERAFGPLENARYVVR 72
                                      4444444455555443 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.5e-05
                           DUF1803  27 viLRelkkeFadqkkldrlldelidaglikRe 58 
                                         LR++ + F+d++++dr l + +d++ i+ e
  gi|336254761|ref|YP_004597868.1| 101 SRLRRIFRRFTDNPDIDRYLRNHLDCEVITVE 132
                                       569************************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1011.10
//
Query:       gi|336254762|ref|YP_004597869.1|  [L=79]
Description: hypothetical protein Halxa_3378 [Halopiger xanaduensis SH-6]
Scores for 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   12.1   3.7        1.9    8.4   0.5    2.3  2  zf-FPG_IleRS  Zinc finger found in FPG and IleRS
       0.16   11.9   1.0       0.16   11.9   1.0    1.9  2  CLIP1_ZNF     CLIP1 zinc knuckle


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 ?    4.6   0.2    0.0034        31      19      28 ..      39      48 ..      36      49 .. 0.87
   2 ?    8.4   0.5   0.00021       1.9       3      11 ..      61      69 ..      60      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0034
                                      EEEEE-TTTT CS
                      zf-FPG_IleRS 19 rstyfCprCq 28
                                      r+ +fC +C 
  gi|336254762|ref|YP_004597869.1| 39 RYGWFCANCE 48
                                      7899*****6 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00021
                                      B-TTT--BB CS
                      zf-FPG_IleRS  3 pCpRCwryi 11
                                      +C RC++  
  gi|336254762|ref|YP_004597869.1| 61 KCNRCGNFR 69
                                      9*****986 PP

>> CLIP1_ZNF  CLIP1 zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.0   1.8e-05      0.16       3      11 ..      43      51 ..      43      51 .. 0.95
   2 ?   -1.5   0.6      0.28   2.5e+03       4       9 ..      62      67 ..      62      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
                         CLIP1_ZNF  3 YCdnCEvFG 11
                                      +C+nCE F+
  gi|336254762|ref|YP_004597869.1| 43 FCANCESFD 51
                                      7*******8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.28
                         CLIP1_ZNF  4 CdnCEv 9 
                                      C  C+ 
  gi|336254762|ref|YP_004597869.1| 62 CNRCGN 67
                                      999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 635.06
//
Query:       gi|336254763|ref|YP_004597870.1|  [L=107]
Description: hypothetical protein Halxa_3379 [Halopiger xanaduensis SH-6]
Scores for 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:                       272  (0.015171); 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:                         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 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 881.80
//
Query:       gi|336254764|ref|YP_004597871.1|  [L=403]
Description: Serine--pyruvate transaminase [Halopiger xanaduensis SH-6]
Scores for complete 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  116.0   0.0    2.4e-33  115.6   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    0.00069   18.3   0.0    0.00098   17.7   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00092   18.6   0.2     0.0015   17.9   0.2    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


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 !  115.6   0.0   3.9e-37   2.4e-33       3     338 ..      25     347 ..      23     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 3.9e-37
                                       EBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHH.HHHHHH CS
                       Aminotran_5   3 ldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtte.ainlva 78 
                                       l+ ++++ + ++Vl+a++             v+hl   ++++++e++e +++ + +++   +i +sGt++ a+++++
  gi|336254764|ref|YP_004597871.1|  25 LMGPGPSDVNPRVLRAMSTP----------LVGHLDPSFIEIMDEVQELLRYTFRTDN-RWTIPVSGTGSaAMEAAI 90 
                                       78899999999999999988..........679************************7.***********99***** PP

                                       HHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--.TTEEEEEEESBETTTTE CS
                       Aminotran_5  79 lslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldeleklln.ektklvaithvsnvtGt 154
                                        ++   ++pgd+++v ++++ + +  ++ +a+r g +v+ + + ++  l++ ++ ++l+ +++++  + h++++tG+
  gi|336254764|ref|YP_004597871.1|  91 GNV---VEPGDTMLVPTNGYFGGR--MASMARRAGGEVVEVDAPWGEPLEPAAVSDALAeHDPDVFGFVHAETSTGV 162
                                       ***...******************..7888899**********************999769**************** PP

                                       B-.-HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS....SS.S CS
                       Aminotran_5 155 iq.pveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekl..eplllg 227
                                       +q +v e++++a++++alv++D ++++g  ++ v+++++D+++++ +K l  P+G + l  ++e+  k+  +   + 
  gi|336254764|ref|YP_004597871.1| 163 LQpDVSELTAAAHDHDALVIADTVTSLGGVELRVDEWDIDVAYSGPQKcLSCPPGASPLTLSDEAMDKVlsREEDPR 239
                                       6526********************************************9999***********99999864444444 PP

                                       TTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B CS
                       Aminotran_5 228 gemveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdk 304
                                       + +++   le++   +  + +++ T ++ +++++++al++++e g+e+ + +++++a +l++++++++   +    +
  gi|336254764|ref|YP_004597871.1| 240 SWYLDLSLLEGYW--GDERSYHH-TAPITNVYAIREALRLVAEEGIEQRWDRHERMAGALKAGVEAMGLEMN-A-PD 311
                                       4445444445555..44555777.****************************************99987766.4.57 PP

                                       -CTCBSEEEEEE.TTCSHHHHHHHHHHT.TEEEEEE CS
                       Aminotran_5 305 aerrasivsfnf.kgvhaedvatlLdee.gIavrsG 338
                                       +   +s+ ++ + +gv+   v   L ee + ++ sG
  gi|336254764|ref|YP_004597871.1| 312 EYWLPSLNAVRVpDGVDDGAVCDRLIEEyDLEIASG 347
                                       888999999998778887777666666668888887 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 !   17.7   0.0   1.6e-07   0.00098      74     194 ..      80     206 ..      74     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.6e-07
                                       SSHHHHHHHHHHTTS-TTEEEEEESTSS.HHHHHHHHHTHHH..TTCEEEEESTTSHHHHHHHCCT.TEEEE.EEES CS
                   Cys_Met_Meta_PP  74 ssGmaAiaaailallkaGdeivvsddlY.ggtqrllkkvlkk..lgievkfvdtsdleelekaike.ntklv.ylEt 145
                                        +G aA++aai ++++ Gd ++v ++ Y gg  + + + +    +++++ + ++ +++++  a+ e   +++ ++ +
  gi|336254764|ref|YP_004597871.1|  80 GTGSAAMEAAIGNVVEPGDTMLVPTNGYfGGRMASMARRAGGevVEVDAPWGEPLEPAAVSDALAEhDPDVFgFVHA 156
                                       579*****************988777661555444444443312334444555688889999888843444345666 PP

                                       S-TTTT----HHHHHHHHHHTT-EEEEEG.TTTHTTTS-GGGGT-SEEEE CS
                   Cys_Met_Meta_PP 146 ptnpllkvvDiekiaklakkagvlvvvDn.tfaspllqrplklgaDivvh 194
                                        t+  +  +D+ +++++a+++++lv+ D  t + ++  r  ++++D+ + 
  gi|336254764|ref|YP_004597871.1| 157 ETSTGVLQPDVSELTAAAHDHDALVIADTvTSLGGVELRVDEWDIDVAYS 206
                                       666666779*******************8344566888888888998775 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 !   17.9   0.2   2.5e-07    0.0015      46     150 ..      81     190 ..      68     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-07
                                       SHHHHHHHHHHHTTTTTT-EEEEESSS-THH..HHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE.EB- CS
                   DegT_DnrJ_EryC1  46 sGtaAlhlaLralgvgpgdeVIvpsltFvat..anavlelgakpvfvDvdpdtynidpaaieaaitertkaIl.pVh 119
                                       +G+aA++ a+ ++ v+pgd+ +vp++++++   a++++++g ++v vD  p    ++paa+  a+ e    ++  Vh
  gi|336254764|ref|YP_004597871.1|  81 TGSAAMEAAIGNV-VEPGDTMLVPTNGYFGGrmASMARRAGGEVVEVDA-PWGEPLEPAAVSDALAEHDPDVFgFVH 155
                                       6777777777665.889************96448899999999999996.466689***********9955543677 PP

                                       G...GGB--.-HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1 120 l...yGqva.dmdalkaiaakhglkvieDaAhAlG 150
                                       +    G    d+++l+a a++h+  vi D+  +lG
  gi|336254764|ref|YP_004597871.1| 156 AetsTGVLQpDVSELTAAAHDHDALVIADTVTSLG 190
                                       6333677779********************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 3382.71
//
Query:       gi|336254765|ref|YP_004597872.1|  [L=332]
Description: hypothetical protein Halxa_3381 [Halopiger xanaduensis SH-6]
Scores for 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-15   54.4  22.8    9.1e-15   54.4  22.8    2.9  2  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4  22.8   5.1e-19   9.1e-15       3     164 ..       2     222 ..       1     233 [. 0.83
   2 ?    0.1   0.4     0.025   4.4e+02       8      35 ..     241     275 ..     236     280 .. 0.65

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 5.1e-19
                              YdjM   3 gltHallGaalglalaallgaakeavllavavlg..AllPDiDhpsstlgrklgllskklak...........lvgH 66 
                                        l Hal+++a+++++a++ g +   +ll++av+g  A++PDiD+  + +g +   l +   +           +  H
  gi|336254765|ref|YP_004597872.1|   2 FLGHALFAFAVAALVAERRGWDGRRALLVGAVAGafAAIPDIDVAYALVGLADWRLVGG--SlgapaafwdasRAVH 76 
                                       569****************9888788888888889********8888888888777774..245899999999**** PP

                              YdjM  67 RgftHSllf.lallalvlllllrlfgrsa................................................ 94 
                                       R+ tHSll+ ++++++++l+++r   r +                                                
  gi|336254765|ref|YP_004597872.1|  77 RSATHSLLVgAVAAPAFALFVVRDSSRARlvrlagsailvglvalalvvdgsvsafvmalfaasgvfvaavaargts 153
                                       *******9989999999999999999999************************************************ PP

                              YdjM  95 ...lrlglllllgvlsHlllDlltkyGvpllwPfskkkvrlsllfiiidplltllsrrglvalelvllvlylv 164
                                            ++l+ l+g++sH+++Dl+t ++ ++l+P+      l + ++  +p  tl+  + ++ +el++++l+lv
  gi|336254765|ref|YP_004597872.1| 154 lspSAVALAALWGLWSHPWGDLVTGSPPEWLYPLE--SPVLATRVV-LHPDPTLHLLCAFA-IELAAVWLALV 222
                                       *99888999*************************5..333333333.56655666444444.33333333333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.025
                              YdjM   8 llGaalglalaallgaake.......avllavavl 35 
                                         G+a gl+++a ++++          +l+++a++
  gi|336254765|ref|YP_004597872.1| 241 GAGVAYGLVALAATPPTLAvsyhfvfSILVVGALC 275
                                       56777788777777777667785664444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.20s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2589.22
//
Query:       gi|336254766|ref|YP_004597873.1|  [L=223]
Description: hypothetical protein Halxa_3382 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.26   11.1   5.9       0.25   11.1   4.7    1.7  1  DUF2238   Predicted membrane protein (DUF2238)
        1.5    8.5  19.9          3    7.5  19.9    1.4  1  DUF5336   Family of unknown function (DUF5336)
        2.8    6.1  10.7        3.4    5.8  10.7    1.0  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2238  Predicted membrane protein (DUF2238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.7   4.3e-05      0.25      60     116 ..      87     150 ..      44     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.3e-05
                           DUF2238  60 Drl.vHfaqGlllalvvrelllrkkkl......rkwllllavlvvlaisalYEliEwlvalllg 116
                                       Drl +Hfa +l +a v+  l+++ +         +++++++v++++a++ l+ l+ w +a +lg
  gi|336254766|ref|YP_004597873.1|  87 DRLtGHFAAYLSVAAVALVLAVELQSFtsvqmtPSFAVIFVVVATMAAAGLWALLRWSAAQTLG 150
                                       66648******9998888775555554455554558999********************99875 PP

>> DUF5336  Family of unknown function (DUF5336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  19.9    0.0005         3      31     153 ..      16     141 ..       4     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0005
                           DUF5336  31 pskLplyLsiavaaLGliayllgFgplltvsass...adleeasatsgglglavvllLlagLlAgvslLPkqkskta 104
                                       +  L+ +L++a+aa+G+ + l g +  +t  a     a l    + s++++l+  +lLla+L      L   + +  
  gi|336254766|ref|YP_004597873.1|  16 NAALAWVLVAAIAAVGVGELLTGGLLWATFAAVLvalALLPPIAFRSTTAMLPWEVLLLAALPVLGMALGADRLTGH 92 
                                       46799******************9988888888877788899999*****************776667788888999 PP

                           DUF5336 105 vaAvlsvlgfLlvlaevinapegvsiawglwvvlvlallqaaaAvaaLL 153
                                       +aA lsv+++ lvla  ++  + v++   + v+ v++   aaa + aLL
  gi|336254766|ref|YP_004597873.1|  93 FAAYLSVAAVALVLAVELQSFTSVQMTPSFAVIFVVVATMAAAGLWALL 141
                                       **************99999998776666665555555555555555555 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  10.7   0.00057       3.4      18     140 ..      18     150 ..      11     197 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.00057
                           DUF2070  18 llliillalligllaflssklfgillfglpalvaflltlpvlrilggr..ltykrslflalltelivviisllaill 92 
                                        l+++l+a+++++ + +     g+l+ ++ a++ +l++lp + + +++  l+++  l+ al  + +++  + l  ++
  gi|336254766|ref|YP_004597873.1|  18 ALAWVLVAAIAAVGVGELL-TGGLLWATFAAVLVALALLPPIAFRSTTamLPWEVLLLAALPVLGMALGADRLTGHF 93 
                                       5778888888888877777.799999999966666665555555555567999999999999999999999999998 PP

                           DUF2070  93 sall.qalvllalvls........lalvfalrllvlvavsdesllkavlpaliqpll 140
                                       +a+l  a v l l++         ++ +fa+ ++v+ +++ + l+  +  +++q+l 
  gi|336254766|ref|YP_004597873.1|  94 AAYLsVAAVALVLAVElqsftsvqMTPSFAVIFVVVATMAAAGLWALLRWSAAQTLG 150
                                       887765555555555577877777777777777777777777777777666666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1698.14
//
Query:       gi|336254767|ref|YP_004597874.1|  [L=219]
Description: hypothetical protein Halxa_3383 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00059   19.6   1.9     0.0011   18.8   1.9    1.6  1  DUF2238   Predicted membrane protein (DUF2238)


Domain annotation for each model (and alignments):
>> DUF2238  Predicted membrane protein (DUF2238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.9   5.9e-08    0.0011      85     138 ..     131     186 ..      62     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.9e-08
                           DUF2238  85 l...rkwllllavlvvlaisalYEliEwlvalllggeaaeaflGtqGdiWDaqkDml 138
                                       +   rk+++++++l+vla++ l+E++E+++al +++ + +a l ++G + D+  D +
  gi|336254767|ref|YP_004597874.1| 131 IhfpRKFVAVFILLFVLAFGVLWEILEFAIALSADAFGVKAVLTQYG-LGDTMLDFV 186
                                       24558899***************************999999999998.888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); 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:                         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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1719.17
//
Query:       gi|336254768|ref|YP_004597875.1|  [L=66]
Description: hypothetical protein Halxa_3384 [Halopiger xanaduensis SH-6]
Scores for 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-22   77.6   0.1    6.8e-22   77.5   0.1    1.0  1  Dodecin   Dodecin


Domain annotation for each model (and alignments):
>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.1   3.8e-26   6.8e-22       1      64 []       2      65 ..       2      65 .. 0.99

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 3.8e-26
                                      EEEEEEEEEEESS-HHHHHHHHHHHHHHH-SSEEEEEEEEEEEEECTTCCEEEEEEEEEEEE-S CS
                           Dodecin  1 VyKvielvGsSpkSwedAiqnAiaeAsktlrnirwveVketrahvedgkiaeYqvtlkvgFrle 64
                                      V+K+i+l+G+Sp+S+++A+++Ai++A+ tl+ni+wveV e+ ++++  + +eYq+++ v+F+le
  gi|336254768|ref|YP_004597875.1|  2 VFKKITLIGTSPESFDAAADDAIDRAEDTLQNIQWVEVDELGVELATAEDREYQAEVTVAFELE 65
                                      89***********************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 499.88
//
Query:       gi|336254769|ref|YP_004597876.1|  [L=126]
Description: iron-sulfur cluster assembly accessory protein [Halopiger xanaduensis SH-6]
Scores for complete 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-18   67.0   0.0    1.8e-18   66.8   0.0    1.0  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 !   66.8   0.0   9.9e-23   1.8e-18       2     111 .]      18     122 ..      17     122 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 9.9e-23
                                       EEEE-HHHHHHHHHHHHCTTEC.....EEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEEETTEEEEEEG CS
                       Fe-S_biosyn   2 kitlteaAaeklkkllaedkke.....lrLdvddgggpyskggCsiggkyslvlvdeedeeydevlesnggkvyvks 73 
                                       +i++te+Aae+  +ll++++ +     lrL+v++gg       C+ g +y +++ d++ +e+d+  e+++++v+v++
  gi|336254769|ref|YP_004597876.1|  18 EIEVTEDAAEQALSLLDGEGLDadeagLRLFVQQGG-------CA-GLSYGMRFDDSP-DEDDTIYEHHDLRVFVDP 85 
                                       79****************9999999***********.......**.************.****************** PP

                                       GGHHHS.TTEEEEEEEETTEEEEEEETCCEEEEEEEEE CS
                       Fe-S_biosyn  74 yslvfldeglvldfvedlgtlgLksdngilddnvglgk 111
                                        sl ++ eg vld++ +l++ g+  +n+++ +++g+g+
  gi|336254769|ref|YP_004597876.1|  86 ASLKYI-EGSVLDYESGLQAEGFHVENPNVVSECGCGE 122
                                       ******.9****************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1040.40
//
Query:       gi|336254770|ref|YP_004597877.1|  [L=73]
Description: hypothetical protein Halxa_3386 [Halopiger xanaduensis SH-6]
Scores for 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:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.33u 0.19s 00:00:00.52 Elapsed: 00:00:00.33
# Mc/sec: 660.46
//
Query:       gi|336254771|ref|YP_004597878.1|  [L=621]
Description: methyl-accepting chemotaxis sensory transducer with Pas/Pac sensor [Halopiger xanaduensis SH-6]
Scores for complete 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-45  155.0  54.4    1.9e-41  141.8  26.2    3.7  4  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
    4.9e-13   49.1   0.1    1.7e-12   47.3   0.1    1.9  1  PAS              PAS fold
    1.9e-11   44.1   0.4    6.9e-11   42.3   0.0    2.2  1  PAS_9            PAS domain
    2.1e-07   31.1  36.9    0.00066   19.9   4.4    5.4  4  DUF948           Bacterial protein of unknown function (DUF94
      2e-06   27.8  37.9     0.0002   21.4   4.1    4.7  4  Laminin_II       Laminin Domain II
    3.1e-06   27.4   2.6    3.9e-05   23.9   2.6    3.0  1  PAS_4            PAS fold
    5.1e-06   26.5  27.8     0.0003   20.8   3.8    4.9  5  DUF1664          Protein of unknown function (DUF1664)
    5.5e-06   26.6  31.0       0.45   10.8   2.0    5.3  5  BLOC1_2          Biogenesis of lysosome-related organelles co
    3.2e-05   23.8   0.0    0.00014   21.8   0.0    2.1  1  PAS_8            PAS domain
     0.0021   18.2   0.3     0.0021   18.2   0.3    3.3  2  MLTR_LBD         MmyB-like transcription regulator ligand bin
     0.0026   18.3   7.3       0.26   11.9   0.9    3.3  2  ING              Inhibitor of growth proteins N-terminal hist
     0.0027   16.4  30.7      0.008   14.9  13.6    2.1  2  AAA_13           AAA domain
     0.0028   17.4  33.5      0.021   14.5  13.1    3.2  3  YkyA             Putative cell-wall binding lipoprotein
     0.0067   15.3  10.9     0.0067   15.3  10.9    3.1  3  Spc7             Spc7 kinetochore protein
     0.0096   16.5  26.9        0.2   12.2   5.2    4.6  4  Syntaxin-6_N     Syntaxin 6, N-terminal
  ------ inclusion threshold ------
      0.012   15.8  25.6        0.4   10.9   3.2    4.4  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.024   14.5   0.5      0.024   14.5   0.5    3.3  3  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
      0.024   15.1  31.5        0.2   12.1  13.1    2.8  2  T3SSipB          Type III cell invasion protein SipB
      0.027   14.6  21.8       0.47   10.6   2.8    4.7  6  Fib_alpha        Fibrinogen alpha/beta chain family
      0.053   13.7   9.2      0.094   12.9   2.0    3.2  3  Med30            Mediator complex subunit 30
      0.091   13.1   0.2        2.8    8.3   0.2    2.6  1  PAS_3            PAS fold
      0.092   12.8  19.0        2.4    8.2   4.3    3.5  3  Mod_r            Modifier of rudimentary (Mod(r)) protein
      0.097   13.0   2.4         17    5.8   0.1    3.5  2  KxDL             Uncharacterized conserved protein
       0.11   11.5  10.4        3.7    6.6   0.7    3.4  3  FH2              Formin Homology 2 Domain
       0.18   11.7  17.0         12    5.8   0.1    4.5  6  Sec34            Sec34-like family
       0.21   12.0  12.1        4.1    7.8   1.3    4.4  3  Syntaxin_2       Syntaxin-like protein
       0.22   11.6  31.7        1.6    8.8  11.8    4.3  2  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
       0.23   11.6   7.1       0.49   10.6   0.1    4.0  4  PAS_7            PAS fold
       0.32   11.5  27.2        0.7   10.4   8.7    4.0  4  FlgN             FlgN protein
       0.43   10.0  24.6        1.3    8.4   7.6    3.1  3  Not3             Not1 N-terminal domain, CCR4-Not complex com
       0.51    8.1  16.8      0.034   12.0   4.9    2.2  2  Nup88            Nuclear pore component
       0.54   10.0   7.8        0.4   10.5   4.9    2.2  2  Sec5             Exocyst complex component Sec5
       0.64    9.9  16.1       0.12   12.3   3.0    3.3  3  PhaP_Bmeg        Polyhydroxyalkanoic acid inclusion protein (
       0.81    9.9  18.9       0.73   10.0   0.6    3.7  4  Nmad5            Nucleotide modification associated domain 5
       0.88    8.8  33.3          1    8.6   2.8    3.9  5  DUF3450          Protein of unknown function (DUF3450)
        0.9    9.9   8.8        2.1    8.7   0.2    3.3  3  Tup_N            Tup N-terminal
        1.1    6.7  39.4        1.3    6.4  17.2    2.0  2  DUF3584          Protein of unknown function (DUF3584)
        1.1    8.9  36.5       0.65    9.7  10.7    3.5  4  DUF745           Protein of unknown function (DUF745)
        1.2    9.3  25.4        1.8    8.6   1.7    3.9  3  UPF0242          Uncharacterised protein family (UPF0242) N-t
        1.5    9.4  24.9         17    6.0   7.4    5.0  3  DUF16            Protein of unknown function DUF16
        1.5    8.0  15.2        8.5    5.5   2.9    3.1  2  TMPIT            TMPIT-like protein
        1.8    8.7  16.4       0.57   10.4   3.7    3.0  2  CREPT            Cell-cycle alteration and expression-elevate
          2    6.2   9.6       0.64    7.8   0.7    2.2  2  Herpes_U30       Herpes virus tegument protein U30
        2.2    7.3  24.9        2.3    7.2   9.3    2.5  2  AIP3             Actin interacting protein 3
        2.4    8.0   7.7         25    4.8   0.3    4.5  4  DASH_Dam1        DASH complex subunit Dam1
        2.5    7.0  29.2        2.3    7.1  10.1    3.2  3  Kre28            Spindle pole body component
        2.5    7.3  25.6        0.9    8.8   6.0    3.1  3  CorA             CorA-like Mg2+ transporter protein
        2.7    7.5  25.9          1    8.9   6.6    2.5  2  DUF4795          Domain of unknown function (DUF4795)
        3.2    8.3  27.9        2.4    8.7   7.2    5.2  6  Spectrin         Spectrin repeat
        3.4    8.0   7.5        5.1    7.4   1.0    2.8  2  Gp-FAR-1         Nematode fatty acid retinoid binding protein
        3.8    7.8  11.8       0.96    9.7   3.4    2.9  2  BORCS7           BLOC-1-related complex sub-unit 7
          4    7.9  10.4         16    6.0   1.2    3.9  2  Goodbye          fungal STAND N-terminal Goodbye domain
          4    5.9  25.7        3.2    6.2  21.4    2.5  1  FUSC             Fusaric acid resistance protein family
        5.5    6.7   8.7        8.7    6.0   0.2    3.3  3  Hormone_1        Somatotropin hormone family
        5.9    7.1  18.2        1.1    9.5   3.2    4.6  4  IFT20            Intraflagellar transport complex B, subunit 
        6.5    5.8  38.2        1.1    8.4  10.4    3.6  3  APG17            Autophagy protein Apg17
        7.3    6.2  32.9        4.7    6.8   9.2    3.6  3  Laminin_I        Laminin Domain I
        8.3    4.2  13.7         11    3.8   8.7    2.1  2  Prominin         Prominin
        8.7    5.9  27.3       0.18   11.4   5.7    3.4  3  LUC7             LUC7 N_terminus


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1         2   6.2e+02     107     147 ..     255     294 ..     237     303 .. 0.77
   2 !   18.5  17.4   4.7e-06    0.0014      60     164 ..     297     400 ..     258     404 .. 0.88
   3 !  141.8  26.2   6.2e-44   1.9e-41       5     169 ..     405     573 ..     401     576 .. 0.91
   4 ?    0.7   0.1       1.4   4.1e+02     133     168 ..     572     607 ..     568     613 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2
                                       ...HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 107 esleetrqrveegselveetgealkeiveavaevadlvqei 147
                                       esl+ + q v+  +e +++ +ea++++v +v+e  + +++ 
  gi|336254771|ref|YP_004597878.1| 255 ESLQGVIQLVQDNTEVIRR-REAMADLVGEVTETGEAINDG 294
                                       6778888888887777665.788899999988888888775 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 4.7e-06
                                       HHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHH CS
                         MCPsignal  60 AARAGeqGrGFaVVAdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeivea 136
                                       AAR  e+ +   V  ++V ++Ae   + a  +e++i  + +e++d  +   e    ++e+ ++v e +ea++ ive+
  gi|336254771|ref|YP_004597878.1| 297 AARV-EYTDDHDVLDEDVTQIAETINEIAAHVEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEE 372
                                       5554.55666789999************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 137 vaevadlvqeiaaaseeqsasieevnqa 164
                                       +++++++++e+aa+s++ sa++++ + a
  gi|336254771|ref|YP_004597878.1| 373 ISDLSATMEEVAASSDQVSAAAKQAQAA 400
                                       **********************998766 PP

  == domain 3  score: 141.8 bits;  conditional E-value: 6.2e-44
                                       HHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHH CS
                         MCPsignal   5 eeaseeAeeg....gkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEV 77 
                                        eas+eA+e+     +  ++ v+++ ++e++ +ei ++ieVi++iadQTNlLALNA iEAA AGe G+GFaVVA+EV
  gi|336254771|ref|YP_004597878.1| 405 VEASQEAREEmdevLEAADELVETVSQLEDRMDEIDEVIEVINDIADQTNLLALNANIEAAQAGEDGDGFAVVANEV 481
                                       556666666621115556889******************************************************** PP

                                       HHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  78 rkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeq 154
                                       ++LA+++++ +++i++ ++++q  +++++e+ e+t++rve +se ++ +  +l+ei+eav+e a+ ++eia + ++q
  gi|336254771|ref|YP_004597878.1| 482 QSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITEIAETNDDQ 558
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHH CS
                         MCPsignal 155 sasieevnqaveeva 169
                                       +as+eev++  + va
  gi|336254771|ref|YP_004597878.1| 559 AASVEEVASQADGVA 573
                                       *******98876665 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 133 iveavaevadlvqeiaaaseeqsasieevnqaveev 168
                                       +++ ++++++l+ +++  ++ q  +i+e+ + +e+v
  gi|336254771|ref|YP_004597878.1| 572 VADDADRIEELIGDVTERTTAQRDAIDEMVDYLERV 607
                                       455566666666666666666666666665555555 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.1   5.6e-15   1.7e-12       4     109 ..     146     263 ..     145     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 5.6e-15
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisf 79 
                                       +a+l++lp p f+vD  +r++++N++aeel+G +re+vlg+   ++++ + +  +la+++  + ++++++++ e+s 
  gi|336254771|ref|YP_004597878.1| 146 DALLNTLPQPAFIVDTEHRVIGWNREAEELTGVDREDVLGEDAAGSFFRDGRTtTLADEVVDHPRDAHRETDAERSG 222
                                       689**********************************************9999*88888888888888888888888 PP

                                       EC............TTSSEEEEEEEEEEEEETTEEEEEEEEE CS
                               PAS  80 kl............rdgrpihlevraspvrdaggeilgflgv 109
                                       +               g++ h++  a+p++  ++   g++  
  gi|336254771|ref|YP_004597878.1| 223 RDqrayelerelenARGETLHVHSVATPIYQQESLQ-GVIQL 263
                                       888888999999******************998743.66655 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   2.3e-13   6.9e-11       3     104 .]     155     269 ..     153     269 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 2.3e-13
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf.............vtdpeanerlraaleqgrk.kereve 65 
                                       + +i+++++r++ +N+ a++l+G ++e+vlg +    f             v++p++++r+ +a ++gr+  ++e e
  gi|336254771|ref|YP_004597878.1| 155 PAFIVDTEHRVIGWNREAEELTGVDREDVLGEDAAGSFfrdgrtttladevVDHPRDAHRETDAERSGRDqRAYELE 231
                                       567888***************************766666999*********************************** PP

                             PAS_9  66 vvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                        +l +  get++v+  a+p++++ + l+g+i +++D te
  gi|336254771|ref|YP_004597878.1| 232 RELENARGETLHVHSVATPIYQQ-ESLQGVIQLVQDNTE 269
                                       ********************865.58**********997 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 !   10.2   6.1    0.0023       0.7      25      87 ..     317     383 ..     245     385 .. 0.87
   2 ?    7.8   3.8     0.013         4      35      84 ..     408     453 ..     379     458 .. 0.55
   3 !   19.9   4.4   2.2e-06   0.00066      18      86 ..     475     543 ..     474     546 .. 0.94
   4 ?    7.1   1.1     0.022       6.6      22      80 ..     549     607 ..     544     612 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0023
                            DUF948  25 kktldeaaatieele....kqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       ++t++e+aa++e++     ++v+ ++ +++++ + + e  ++v e+ e++ +++e++ dl+++++e+
  gi|336254771|ref|YP_004597878.1| 317 AETINEIAAHVEDVIyglsEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEV 383
                                       455555555555443444499999999999999999999999999****************999887 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.013
                            DUF948  35 ieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                        +e ++++d++l+ +++l+++v +    ++++++++d+++e ++d++++ 
  gi|336254771|ref|YP_004597878.1| 408 SQEAREEMDEVLEAADELVETVSQ----LEDRMDEIDEVIEVINDIADQT 453
                                       223334444444444444444444....6668999999998888888765 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 2.2e-06
                            DUF948  18 ivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       +vv ++++++++e++++ +++ ++v+ + + +e++ + ++++ e v++ +e++d+ ++++++++e+v e
  gi|336254771|ref|YP_004597878.1| 475 AVVANEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDE 543
                                       5788999**********************************9***********************9975 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.022
                            DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadl 80 
                                        ++++t d  aa++ee+ +q+d++ ++++++ + + +++e  + + +++d++++ ++ +
  gi|336254771|ref|YP_004597878.1| 549 TEIAETNDDQAASVEEVASQADGVADDADRIEELIGDVTERTTAQRDAIDEMVDYLERV 607
                                       6788999999******************************************9987766 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   4.1   6.5e-07    0.0002       3      71 ..     315     383 ..     313     399 .. 0.92
   2 !   10.0   7.9    0.0021      0.64       7      97 ..     361     448 ..     358     467 .. 0.83
   3 !   10.1   5.7     0.002      0.61       4      68 ..     477     541 ..     475     543 .. 0.90
   4 ?    7.7   1.7     0.011       3.4       3      70 ..     539     606 ..     533     616 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.5e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       ++a+ +ne+a++v++++ +ls+++e +++++ ei++s+ e + +v + n+air   +++++L  +++++
  gi|336254771|ref|YP_004597878.1| 315 QIAETINEIAAHVEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEV 383
                                       57899*********************************************************9988876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0021
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83 
                                       e ne + ++ e + +ls+ +e++ ++  ++ + +++ ++ ++d  +a ++Ar+++ ++ + a++L++ +++l+ + +
  gi|336254771|ref|YP_004597878.1| 361 EQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQAQAAADDGVEASQEAREEMDEVLEAADELVETVSQLEDRMD 437
                                       6789999999999********************999******************************99888888777 PP

                                       H...HHHHHHHHHH CS
                        Laminin_II  84 assslsdniseike 97 
                                       +   + + i+ i  
  gi|336254771|ref|YP_004597878.1| 438 E---IDEVIEVIND 448
                                       7...4444444433 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.002
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TT CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekla 68 
                                       +a+e+++ a+e++e ++++s ++e ++   +e ++  e+tne v+ a++ i+ A  +  ++ + +
  gi|336254771|ref|YP_004597878.1| 477 VANEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAV 541
                                       68899999*******************************************99988777766655 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTT CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapq 70 
                                       e ++ea   ++e+ e   + ++ +e++ +++ ++++++++++e++ d ++ +   r+++ ++   +++
  gi|336254771|ref|YP_004597878.1| 539 EAVDEAAHGITEIAETNDDQAASVEEVASQADGVADDADRIEELIGDVTERTTAQRDAIDEMVDYLER 606
                                       46788888888888889999999999999999999999999998887666655555554444444333 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   2.6   1.3e-07   3.9e-05       1     108 [.     149     270 ..     149     272 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.3e-07
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla.ellpee...........daarleralrrvlegeep 65 
                                       l+ lp++ +++d++ rv+ +N++a+el g+++e++lG+  a +++ ++           + ++ +r  ++  +g++ 
  gi|336254771|ref|YP_004597878.1| 149 LNTLPQPAFIVDTEHRVIGWNREAEELTGVDREDVLGEDAAgSFFRDGrtttladevvdHPRDAHRETDAERSGRDQ 225
                                       6789*************************************999999888886666555222222222222222222 PP

                             PAS_4  66 iefleelll..........pgeerhyelrllPlrdesGevigvlvisrDiTer 108
                                                           ge+ h+   ++P+   +   +gv+ +++D Te 
  gi|336254771|ref|YP_004597878.1| 226 R-------AyelerelenaRGETLHVHSVATPIYQ-QESLQGVIQLVQDNTEV 270
                                       2.......122223335577888888888899964.55589999999998886 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.2    0.0051       1.6      36     116 ..     274     358 ..     269     361 .. 0.80
   2 !    9.4   3.1    0.0034         1      39     107 ..     323     391 ..     309     409 .. 0.50
   3 ?    5.5   4.6     0.054        16      41     117 ..     378     443 ..     372     454 .. 0.37
   4 !   20.8   3.8   9.8e-07    0.0003      43     122 ..     474     553 ..     471     555 .. 0.94
   5 ?    2.2   0.1      0.57   1.7e+02      71     109 ..     551     589 ..     545     612 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0051
                           DUF1664  36 krslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtev....redlseigedvesvke 108
                                       +  ++d v +v++  e + +   a++ + +++ d +d+ + + +e+++ei+++v++v    +e++++++ d  ++ +
  gi|336254771|ref|YP_004597878.1| 274 REAMADLVGEVTETGEAINDGSLAARVEYTDDHDVLDEDVTQIAETINEIAAHVEDViyglSEEVEDLSADAAEIAD 350
                                       568999999**********99999***************99999999999888876522226777777777777777 PP

                           DUF1664 109 aveglesk 116
                                         ++ +s+
  gi|336254771|ref|YP_004597878.1| 351 SASEADSQ 358
                                       66666665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0034
                           DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                       ++  ve+v   l +  e+l+a   ++++   + d+++ eq+e++++i ee+++++  ++e+   +++v+
  gi|336254771|ref|YP_004597878.1| 323 IAAHVEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQVS 391
                                       222233333333333344444444444444555555555555555555555555555555555555555 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.054
                           DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                         +e+v+ + +qvs++ ++++           +  d+  e+s+e +ee++ev e  +e+ e v+++++ + ++++ +
  gi|336254771|ref|YP_004597878.1| 378 ATMEEVAASSDQVSAAAKQAQ-----------AAADDGVEASQEAREEMDEVLEAADELVETVSQLEDRMDEIDEVI 443
                                       333333333333333333333...........333333333333333333333333333333333333333333333 PP

  == domain 4  score: 20.8 bits;  conditional E-value: 9.8e-07
                           DUF1664  43 vesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                        + v+++++++ ++ ++  +++s+r++ ++++ +e++e++++++e v+ ++e +++   ++e++ eav + ++ +++
  gi|336254771|ref|YP_004597878.1| 474 FAVVANEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITE 550
                                       67899999**************************************************************9999999 PP

                           DUF1664 120 iee 122
                                       i e
  gi|336254771|ref|YP_004597878.1| 551 IAE 553
                                       865 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.57
                           DUF1664  71 vdkkldeqkeiskeikeevtevredlseigedvesvkea 109
                                       + ++ d+q++  +e++++ + v +d ++i+e +  v e 
  gi|336254771|ref|YP_004597878.1| 551 IAETNDDQAASVEEVASQADGVADDADRIEELIGDVTER 589
                                       444444444444444444444444444444444444433 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 !    8.4   0.2    0.0085       2.6      25      87 ..     263     326 ..     253     330 .. 0.87
   2 ?    7.8   1.2     0.013       4.1      34      90 ..     336     389 ..     325     395 .. 0.73
   3 !   10.8   2.0    0.0015      0.45      30      78 ..     409     457 ..     401     461 .. 0.80
   4 !   10.7   3.0    0.0016       0.5      26      87 ..     482     544 ..     477     550 .. 0.85
   5 ?    6.0   0.2     0.049        15      26      82 ..     552     609 ..     548     610 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0085
                           BLOC1_2  25 LeklNeaasekykklkdvaaslekkleklnekye.elqpylqqidqiekqvteLeeavseLDey 87 
                                       L + N++++++ ++++d + +++++ e++n  +  +  +y +  d ++++vt++ e+++e+ + 
  gi|336254771|ref|YP_004597878.1| 263 LVQDNTEVIRRREAMADLVGEVTETGEAINDGSLaARVEYTDDHDVLDEDVTQIAETINEIAAH 326
                                       55669*************************987646679999*****************99765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.013
                           BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyske 90 
                                       e++++l+  aa+++   +  +e + ++ ++ + i +i +++++L ++ +e+ + s +
  gi|336254771|ref|YP_004597878.1| 336 EEVEDLSADAAEIA---DSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQ 389
                                       44445555555555...5555555599999999999999999999999988777665 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0015
                           BLOC1_2  30 eaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78 
                                       ++a e+ +++ ++a++l +++++l+ + +e+++ ++ i++i +q++ L 
  gi|336254771|ref|YP_004597878.1| 409 QEAREEMDEVLEAADELVETVSQLEDRMDEIDEVIEVINDIADQTNLLA 457
                                       5677888888888899999999999999999999999999988887765 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.0016
                           BLOC1_2  26 eklNeaasekykklkdvaaslekkleklnekyeelqpylq.qidqiekqvteLeeavseLDey 87 
                                       + l  ++ e+ ++++d++++l++  e++ e  e+ ++ ++   ++i++ ++ Lee+++++De 
  gi|336254771|ref|YP_004597878.1| 482 QSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEgASERIDAAIANLEEIAEAVDEA 544
                                       556678999999***************999999777766526689****************96 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.049
                           BLOC1_2  26 eklNeaasekykklkdvaaslekkleklnekyeel.qpylqqidqiekqvteLeeavs 82 
                                        + N  +++ +++++++a+++++++++++e+   + +    q d+i++ v+ Le +++
  gi|336254771|ref|YP_004597878.1| 552 AETNDDQAASVEEVASQADGVADDADRIEELIGDVtERTTAQRDAIDEMVDYLERVAD 609
                                       578999************************9996615567899***********9997 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   4.7e-07   0.00014       5      45 ..     147     188 ..     146     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.7e-07
                             PAS_8   5 alfesspdgiavvdlgdrivdvNqaalellGys.adlkgell 45 
                                       al++++p++ ++vd+  r++ +N+ a+el+G++ +d++ge+ 
  gi|336254771|ref|YP_004597878.1| 147 ALLNTLPQPAFIVDTEHRVIGWNREAEELTGVDrEDVLGEDA 188
                                       79************6669*************99988888875 PP

>> MLTR_LBD  MmyB-like transcription regulator ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3     7e-06    0.0021       4     100 ..     144     236 ..     141     249 .. 0.80
   2 ?    1.1   0.4       1.2   3.8e+02      86     114 ..     361     389 ..     334     443 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7e-06
                          MLTR_LBD   4 alrrlLdalepvPAlVldrrwdvlaaNraaraLlgdpaalpeperNllrlvfldpglrpliedweevaralvarLra 80 
                                       ++++lL+ l p PA+++d    v+ +Nr a+ L g  ++    +  ++  +f d + ++l  +  ++ r++ +   a
  gi|336254771|ref|YP_004597878.1| 144 GTDALLNTL-PQPAFIVDTEHRVIGWNREAEELTGV-DREDVLGEDAAGSFFRDGRTTTLADEVVDHPRDAHRETDA 218
                                       568899999.*************************9.6777888899999999998888887777777776655444 PP

                          MLTR_LBD  81 eaarrpddpalaalvaeLsa 100
                                          r  +d+++ +l +eL+ 
  gi|336254771|ref|YP_004597878.1| 219 --ERSGRDQRAYELERELEN 236
                                       ..466668888888888776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.2
                          MLTR_LBD  86 pddpalaalvaeLsaaspefarlwarhdv 114
                                       ++++a++a+v+e+s  s+ +++  a+ d 
  gi|336254771|ref|YP_004597878.1| 361 EQNEAIRAIVEEISDLSATMEEVAASSDQ 389
                                       34788999999999999999888887764 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.0     0.041        12       5      69 ..     302     376 ..     300     439 .. 0.62
   2 !   11.9   0.9   0.00085      0.26       3     101 .]     416     534 ..     414     534 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.041
                                       HHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........TS..S-HHHHHHHHHHHHHHHHHH CS
                               ING   5 yldsvenLPlelqrnltelreiDakvqellkeidskiekfl..........kngslqknekeeelsriqeelkea 69 
                                       y+d+ + L +++++  + + ei a+v++++  +++++e+++          ++ + q  e++e+++ i ee++++
  gi|336254771|ref|YP_004597878.1| 302 YTDDHDVLDEDVTQIAETINEIAAHVEDVIYGLSEEVEDLSadaaeiadsaSEADSQVGEQNEAIRAIVEEISDL 376
                                       778888888888888888888888888888888888888887666666655223333333333333333333332 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00085
                                       HHHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....................TS..S-HHHHHHH CS
                               ING   3 edyldsvenLPlelqrnltelreiDakvqellkeidskiekfl.....................kngslqknekeee 58 
                                       ++ l++ ++L + ++++ +++ eiD +v e++++i ++ + +                      ++ +    e +e+
  gi|336254771|ref|YP_004597878.1| 416 DEVLEAADELVETVSQLEDRMDEID-EVIEVINDIADQTNLLAlnanieaaqagedgdgfavvaNEVQSLASETKEH 491
                                       5677888888889999999999999.47788888877777777899999999*********9974445555667788 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTXXX CS
                               ING  59 lsriqeelkeaqelldeKiqlaqqaldlvdkhlrrLdqdlekl 101
                                       +++i + ++++q   +e  ++++q+ + v+   +r+d+++++l
  gi|336254771|ref|YP_004597878.1| 492 TNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANL 534
                                       99************************************99986 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9  13.6   2.6e-05     0.008     296     466 ..     271     449 ..     231     466 .. 0.67
   2 !    7.2   9.3    0.0056       1.7     357     470 ..     492     607 ..     476     614 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                            AAA_13 296 eskkselleklkavsde........asensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkaki 364
                                        ++++ +++ + +v+++          ++ ++ +d++ l++   +++e+++++   +e+ +  +++  e+e+++a++
  gi|336254771|ref|YP_004597878.1| 271 IRRREAMADLVGEVTETgeaindgsLAARVEYTDDHDVLDEDVTQIAETINEIAAHVEDVIYGLSE--EVEDLSADA 345
                                       333333333333333333333332212234566677777777777777777777777777777777..889999999 PP

                            AAA_13 365 esikklvaeineliakhNekvanleeekeeakkklelhlveeleseld.eykkkykklek...aieklekelkeeea 437
                                        +i ++ +e+  ++ + Ne +  + ee +++   +e   ++   ++++ + k++ +++++   a +++ +e++e  +
  gi|336254771|ref|YP_004597878.1| 346 AEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAAS--SDQVSaAAKQAQAAADDgveASQEAREEMDEVLE 420
                                       99****************************99999995543..4444413344444444400044455556666666 PP

                            AAA_13 438 elkkleeeikeLekqlrdekpaaeeinke 466
                                       ++ +l e +++Le ++ ++ + +e+in++
  gi|336254771|ref|YP_004597878.1| 421 AADELVETVSQLEDRMDEIDEVIEVINDI 449
                                       77778888*******************86 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0056
                            AAA_13 357 lesvkakiesikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkykklekaiekleke 431
                                       ++++++++e ++   +e  e+ ++ Ne+v+   e+  +a  +le     v e+   ++e  ++ ++ ++++e++  +
  gi|336254771|ref|YP_004597878.1| 492 TNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAeaVDEAAHGITEIAETNDDQAASVEEVASQ 568
                                       456666667777777777777777777777777777777777776433367788888888899999999******** PP

                            AAA_13 432 lkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                       ++  ++++  +ee i +  ++++ ++ a++e+ ++L+++
  gi|336254771|ref|YP_004597878.1| 569 ADGVADDADRIEELIGDVTERTTAQRDAIDEMVDYLERV 607
                                       ***********************************9986 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5  13.1     7e-05     0.021      20     163 ..     309     454 ..     301     461 .. 0.91
   2 !    9.3   8.4    0.0027      0.81      16     114 ..     470     559 ..     457     574 .. 0.68
   3 ?    1.1   0.1       0.9   2.7e+02      47      80 ..     574     607 ..     569     615 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7e-05
                              YkyA  20 feeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieei.. 94 
                                       + e   ++ e+ ++   + e++i    +e +++++ ++e  ++++e  +++ +++e+i +  ee++++++++ee+  
  gi|336254771|ref|YP_004597878.1| 309 LDEDVTQIAETINEIAAHVEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVaa 385
                                       56777888999999999999999766666999*******************************************88 PP

                              YkyA  95 edeelkkeaeelieameeryeaydklykaYkealeldkeLYemLkkeeltleeleeqiekiNesyeevk 163
                                         +++   a++ + a ++  ea ++  ++  e+le+  eL e  ++ e  ++e++e ie iN+  ++++
  gi|336254771|ref|YP_004597878.1| 386 SSDQVSAAAKQAQAAADDGVEASQEAREEMDEVLEAADELVETVSQLEDRMDEIDEVIEVINDIADQTN 454
                                       7889**********************************************************9988876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0027
                              YkyA  16 lEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeie 92 
                                       + ++f+  +++ ++l ++ +e+ ++i     d+ +++++  +e  e +e+ +e++e   e i++a  ++e+i e ++
  gi|336254771|ref|YP_004597878.1| 470 DGDGFAVVANEVQSLASETKEHTNQIS----DRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVD 542
                                       347788999999999999999999996....4555577777777777777777777777788888888888888888 PP

                              YkyA  93 ei.....edeelkkeaeelieameery 114
                                       e      e           +e+ +++ 
  gi|336254771|ref|YP_004597878.1| 543 EAahgitE----------IAETNDDQA 559
                                       77333331..........333333333 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.9
                              YkyA  47 defdkikklsdealenveeReellekekesieea 80 
                                       d+ d+i++l+ +++e + ++++ +++  + +e+ 
  gi|336254771|ref|YP_004597878.1| 574 DDADRIEELIGDVTERTTAQRDAIDEMVDYLERV 607
                                       778999***********99999999988887765 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       1.9   5.7e+02     176     239 ..     227     294 ..     213     325 .. 0.68
   2 !   15.3  10.9   2.2e-05    0.0067     136     256 ..     326     449 ..     323     457 .. 0.82
   3 !    8.4  10.4    0.0029      0.88     154     249 ..     470     568 ..     454     609 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.9
                              Spc7 176 kaeleeeleklqeaaeeles.....idkeeLeelreelaelkaeieekkkelaelqeqleeleekieel 239
                                         ele+ele+ + +   + s     +++e+L+ + + +++ ++e+ ++++ +a+l  +++e  e+i++ 
  gi|336254771|ref|YP_004597878.1| 227 AYELERELENARGETLHVHSvatpiYQQESLQGVIQLVQD-NTEVIRRREAMADLVGEVTETGEAINDG 294
                                       5567777777777444444444455667777776544444.4444457777888888887777777665 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.2e-05
                              Spc7 136 llegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelk 212
                                       ++e++  gl+e++e+l +d+++++++ +e+d+ + e +e   ++ ee+ +l +  ee++++  +  ++++++ a+++
  gi|336254771|ref|YP_004597878.1| 326 HVEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQAQAAAD 402
                                       7999999***************************************************9998888899999999999 PP

                              Spc7 213 aeieekkkelaelqeqle...eleekieelkeqkseleeeiaeaerv 256
                                         +e+ ++  +e+ e le   el e++++l+++++e+ e i+  +++
  gi|336254771|ref|YP_004597878.1| 403 DGVEASQEAREEMDEVLEaadELVETVSQLEDRMDEIDEVIEVINDI 449
                                       99998777666666655511156666667777777777766655555 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0029
                              Spc7 154 dkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkkelaelqe 227
                                       d +  +   +e+++l  e++e+ +++++++e+lq++ ee ++    ++e++e + e+++++ a++ee  + ++e   
  gi|336254771|ref|YP_004597878.1| 470 DGDGFAVVANEVQSLASETKEHTNQISDRVEDLQTRTEETAEvteQTNERVEGASERIDAAIANLEEIAEAVDEAAH 546
                                       5555666789999*********************9777666622255777888888888888877777777777777 PP

                              Spc7 228 qleeleekieelkeqkseleee 249
                                        ++e++e+ ++ +++ +e+ ++
  gi|336254771|ref|YP_004597878.1| 547 GITEIAETNDDQAASVEEVASQ 568
                                       7777777666666666666555 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 ?    0.1   0.1         4   1.2e+03      22      22 ..     282     282 ..     210     330 .. 0.58
   2 ?    4.0   4.8      0.25        76      21      80 ..     335     396 ..     269     415 .. 0.75
   3 !    9.9   3.7    0.0034         1       8      70 ..     388     449 ..     381     462 .. 0.73
   4 !   12.2   5.2   0.00065       0.2       1      85 [.     472     569 ..     472     582 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 4
                      Syntaxin-6_N  22 r 22 
                                       +
  gi|336254771|ref|YP_004597878.1| 282 G 282
                                       1 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.25
                      Syntaxin-6_N  21 yrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpskfkideke 80 
                                        ++ e+l  d+ +  ++ +e d++  e ++a+r i ++++dL  t++ v ++ ++++  +k+
  gi|336254771|ref|YP_004597878.1| 335 SEEVEDLSADAAEiaDSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQ 396
                                       33334444444444347889999999999999999999999999998888877775554444 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0034
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvrivekn 70 
                                       ++V  ++++a++  +   +  +++++ + +e+ e+ +eL ++++++e  +++++e++++++  
  gi|336254771|ref|YP_004597878.1| 388 DQVSAAAKQAQAAADDGVEASQEARE-EMDEVLEAADELVETVSQLEDRMDEIDEVIEVINDI 449
                                       45555555555555555444444444.6999**************************999764 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00065
                      Syntaxin-6_N   1 DPFfevkeeVqkslnkaeslyrrwe.rlledtss.s.tseeldetrteLrkalrsiewdledLeetv.......... 64 
                                       D F +v++eVq+ ++++++  ++ + r+ ++++  + t e  ++t++ ++ a + i+  + +Lee            
  gi|336254771|ref|YP_004597878.1| 472 DGFAVVANEVQSLASETKEHTNQISdRVEDLQTRtEeTAEVTEQTNERVEGASERIDAAIANLEEIAeavdeaahgi 548
                                       88****************99999953555554444224455555555677777777776666666661112222333 PP

                      Syntaxin-6_N  65 .riveknpskfkidekelsrrr 85 
                                        +i+e n ++   + +e++++ 
  gi|336254771|ref|YP_004597878.1| 549 tEIAETN-DDQAASVEEVASQA 569
                                       3344444.33444444454444 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 ?    9.0   1.3    0.0052       1.6      41     107 ..     309     376 ..     261     377 .. 0.87
   2 ?    8.6   5.6    0.0071       2.1      32     100 ..     367     439 ..     364     452 .. 0.67
   3 ?   10.9   3.2    0.0013       0.4      40     106 ..     480     550 ..     477     552 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0052
                                       HHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS--- CS
                      Seryl_tRNA_N  41 lqveleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkaleaelkeleaeleklllaiPNi 107
                                       l  ++ ++ +  Ne++++++  +    e+ e+l a+++e+ +  ++++ ++ e ++++ +++ +i ++
  gi|336254771|ref|YP_004597878.1| 309 LDEDVTQIAETINEIAAHVEDVIYGLsEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDL 376
                                       566778888889999999999887558**********************************9999875 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0071
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  32 leldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekl 100
                                        ++ e+   l +++ee+ a + ++s++ ++a ++     e  +e ++e++e+ e  ++l +++++le++++++
  gi|336254771|ref|YP_004597878.1| 367 RAIVEEISDLSATMEEVAASSDQVSAAAKQAQAAAddgvEASQEAREEMDEVLEAADELVETVSQLEDRMDEI 439
                                       5555666666677777777777777777766666666677777777777777777777777777777777665 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS-- CS
                      Seryl_tRNA_N  40 elqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaeleklllaiPN 106
                                       e+q+ + e ++  N++s  ++ +  +     e +e+  ++v+  +e+++a+ a+l+e+ +++++++  i  
  gi|336254771|ref|YP_004597878.1| 480 EVQSLASETKEHTNQISDRVEDLQTRTeetaEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITE 550
                                       567778899999**********999997777777788889999********************99998865 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.5   7.7e-05     0.024      98     175 ..     304     381 ..     290     383 .. 0.89
   2 ?   -0.7   3.3       3.5   1.1e+03     119     154 ..     479     514 ..     392     550 .. 0.63
   3 ?   -1.7   0.1       7.1   2.1e+03     102     137 ..     574     609 ..     553     614 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.7e-05
                      Bacillus_HBL  98 kdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgki 174
                                        d + l e+++++ e+i+++ ++v+++i  L++  ++l +d ++    ++e++s ++ ++  i ++ +ei+dl  ++
  gi|336254771|ref|YP_004597878.1| 304 DDHDVLDEDVTQIAETINEIAAHVEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATM 380
                                       3455566899**************************************************************99887 PP

                      Bacillus_HBL 175 k 175
                                       +
  gi|336254771|ref|YP_004597878.1| 381 E 381
                                       6 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.5
                      Bacillus_HBL 119 kevkqlikeLkklklklakdsknFktdvdeltsila 154
                                       +ev++l+ e k+  +++   +++++t ++e  ++ +
  gi|336254771|ref|YP_004597878.1| 479 NEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTE 514
                                       233333333333333333333333333333333333 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 7.1
                      Bacillus_HBL 102 ellellekLqeeiqqnqkevkqlikeLkklklklak 137
                                       +  +++e+L  ++++   + ++ i e+ ++ +++a 
  gi|336254771|ref|YP_004597878.1| 574 DDADRIEELIGDVTERTTAQRDAIDEMVDYLERVAD 609
                                       456788999999999999999999888888877765 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 ?   12.1  13.1   0.00067       0.2      43     147 ..     333     439 ..     304     446 .. 0.69
   2 ?    8.0  10.4     0.012       3.6      36     145 ..     487     598 ..     477     618 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00067
                                       ---STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH.......H CS
                           T3SSipB  43 klSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaa.....a 114
                                        lS+e++++  +a++++d + +a  ++ + + a+ a  + +++  + ++e+        ++ aa +Qa+aa      
  gi|336254771|ref|YP_004597878.1| 333 GLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEV---AASSDQVSAAAKQAQAAaddgvE 406
                                       467777777777777777777777777777777777777777777777777...33345667777777777423422 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTX CS
                           T3SSipB 115 dalqadealqKkldaasklsekakakekevDdi 147
                                        + +a e ++  l+aa  l e   ++e ++D+i
  gi|336254771|ref|YP_004597878.1| 407 ASQEAREEMDEVLEAADELVETVSQLEDRMDEI 439
                                       244455566999999999999999999999988 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.012
                                       HTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH. CS
                           T3SSipB  36 aqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQaga 112
                                        ++e+  ++Sd ++++   +++ ++  e+  e+++ a   +daa + ++e+ + ++e   ++     +e +  Qa+ 
  gi|336254771|ref|YP_004597878.1| 487 ETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEA--AHGITEIAETNDDQAAS 561
                                       5677888999988777777777777777777777777777777777777777766666..33334444555555554 PP

                                       ..HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHH CS
                           T3SSipB 113 a.adalqadealqKkldaas...klsekakakekevD 145
                                           a qad  ++ +  + +    ++e+  a++  +D
  gi|336254771|ref|YP_004597878.1| 562 VeEVASQADGVADDADRIEEligDVTERTTAQRDAID 598
                                       4333444444333333333300033333344444444 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 ?    1.2   0.1       1.2   3.8e+02      50     112 ..     198     262 ..     194     279 .. 0.69
   2 ?    0.4   0.1       2.1   6.5e+02      21      36 ..     315     330 ..     250     351 .. 0.59
   3 ?    2.3   0.1      0.59   1.8e+02      22      70 ..     316     357 ..     301     375 .. 0.40
   4 ?   10.6   2.8    0.0015      0.47      22     118 ..     348     443 ..     344     457 .. 0.56
   5 ?    9.6   3.3    0.0032      0.98      46     124 ..     480     554 ..     476     567 .. 0.62
   6 ?    0.4   0.0       2.2   6.7e+02      29      68 ..     568     607 ..     562     618 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC.CHHH.HHHHCCHHHHHHHHHHHH CS
                         Fib_alpha  50 stkeaeelvkeikdslrekqkskkdndnvikksskeleeei.lrlk.etidaqesnirvLqnvle 112
                                       +t+ a+e+v + +d +re+ ++ ++ d+   ++++ele+   ++l+ +++ + + + + Lq+v++
  gi|336254771|ref|YP_004597878.1| 198 TTTLADEVVDHPRDAHRETDAERSGRDQRAYELERELENARgETLHvHSVATPIYQQESLQGVIQ 262
                                       56778899999999999999999999999999999998543122221345555555556665554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2.1
                                       HHHHCCCCCCCCCCHH CS
                         Fib_alpha  21 glqdlllkyekdvkkd 36 
                                       ++++++++   +v++ 
  gi|336254771|ref|YP_004597878.1| 315 QIAETINEIAAHVEDV 330
                                       2333333333333333 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.59
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqk 70 
                                       +++++++   +v++ +  l +e+e++s    e+        ds  e+ +
  gi|336254771|ref|YP_004597878.1| 316 IAETINEIAAHVEDVIYGLSEEVEDLSADAAEIA-------DSASEADS 357
                                       3333333333333333333333333333333332.......22222222 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.0015
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvk...eikdslrekqkskkdndnvikksskeleeeilrlke 95 
                                       ++d  ++ +++v ++ e ++  +eeis+ + ++ee+     +++   +++q+ ++d  ++ ++ ++e++ e+l+  +
  gi|336254771|ref|YP_004597878.1| 348 IADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAAssdQVSAAAKQAQAAADDGVEASQEAREEMD-EVLEAAD 423
                                       666677777777777777777777777777777777650004444445555555554556666666666.4444444 PP

                                       HHHCCHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  96 tidaqesnirvLqnvlesneqki 118
                                       ++++++s   +L + +++ ++ i
  gi|336254771|ref|YP_004597878.1| 424 ELVETVS---QLEDRMDEIDEVI 443
                                       4444444...4444444444433 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.0032
                                       CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  46 eisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLe 122
                                       e+++  +e++e++++i+d +++ q+ ++++ +v+++ ++++e       e+ida + n++++ + +++  + i+++ 
  gi|336254771|ref|YP_004597878.1| 480 EVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVE----GASERIDAAIANLEEIAEAVDEAAHGITEIA 552
                                       456666777777777777777777777766666666666666....5555556666666666666666666665555 PP

                                       HH CS
                         Fib_alpha 123 qd 124
                                       + 
  gi|336254771|ref|YP_004597878.1| 553 ET 554
                                       44 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 2.2
                                       CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvkeikdslrek 68 
                                       +   v +d +++e+ + +++++t+  ++ + e+ d+l++ 
  gi|336254771|ref|YP_004597878.1| 568 QADGVADDADRIEELIGDVTERTTAQRDAIDEMVDYLERV 607
                                       6677888889999999999999999999999999998765 PP

>> Med30  Mediator complex subunit 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1      0.08        24     101     144 ..     333     376 ..     253     380 .. 0.68
   2 ?   12.9   2.0   0.00031     0.094      11     143 ..     318     448 ..     312     454 .. 0.50
   3 ?    3.7   0.4      0.21        63      38      93 ..     483     537 ..     475     607 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.08
                             Med30 101 kkseevkqlkeerkelleklkeknkqLkeimdqlrkllWdiNtm 144
                                         seev++l++  +e+ +  +e + q+ e  + +r ++ +i ++
  gi|336254771|ref|YP_004597878.1| 333 GLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDL 376
                                       34899999999999999999999999999999999999999887 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00031
                             Med30  11 etvqdivsrtqelfqllkavql..pngrtqskhqaqdrkkklqeqlrqlkvlfkkLrliYekckencqgleevp.ie 84 
                                       et+ +i+  +++++  l +  +  + + +  + +a+++  ++ eq+++       +r i e++ + ++ +eev  ++
  gi|336254771|ref|YP_004597878.1| 318 ETINEIAAHVEDVIYGLSEEVEdlSADAAEIADSASEADSQVGEQNEA-------IRAIVEEISDLSATMEEVAaSS 387
                                       788888888888887775433200233333445555555555555555.......5555555555555555554444 PP

                             Med30  85 sLipyvdeekskreerkkseevkqlkeerkelle...klkeknkqLkeimdqlrkllWdiNt 143
                                       + +    ++ +++++ +  e ++++ ee++e+le   +l e   qL++ md++ +++  iN+
  gi|336254771|ref|YP_004597878.1| 388 DQVSAAAKQ-AQAAADDGVEASQEAREEMDEVLEaadELVETVSQLEDRMDEIDEVIEVIND 448
                                       444444333.3333333345555555555555554444444555555555555555555554 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.21
                             Med30  38 qskhqaqdrkkklqeqlrqlkvlfkkLrliYekckencqgleevpiesLipyvdee 93 
                                         ++  ++ +++++++++ l+ + ++   + e+++e+++g     i+  i   +e+
  gi|336254771|ref|YP_004597878.1| 483 SLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGAS-ERIDAAIANLEEI 537
                                       444555666777777777777777777777777777775554.2344445444444 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0094       2.8       2      78 ..     166     254 ..     165     263 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0094
                             PAS_3   2 iyvserveeilGyspeellgk......veswldlvhpeD.rervrealqeal.....kkgepyegeyRirrkdGeyr 66 
                                       i ++++ ee++G+++e++lg       +++ +     ++  ++ r+a+ e       +++++ye e  + ++ Ge+ 
  gi|336254771|ref|YP_004597878.1| 166 IGWNREAEELTGVDREDVLGEdaagsfFRDGRTTTLADEvVDHPRDAHRETDaersgRDQRAYELERELENARGETL 242
                                       67888888888888888888733322333333344444433333444432224444356669999999999999999 PP

                             PAS_3  67 wveararvirde 78 
                                       +v++ a++i+++
  gi|336254771|ref|YP_004597878.1| 243 HVHSVATPIYQQ 254
                                       999999999444 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 ?    6.2   0.9     0.034        10      16      90 ..     318     393 ..     304     403 .. 0.78
   2 ?    8.2   4.3     0.008       2.4      18     106 ..     373     464 ..     361     470 .. 0.57
   3 ?    8.0   5.0    0.0096       2.9      18      95 ..     481     559 ..     478     602 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.034
                             Mod_r  16 eklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqk 90 
                                       e +++++  + + +  l ee e+l a   ++a++  +   ++ e+ + + +  ee+  l++++ee  +  d+++  
  gi|336254771|ref|YP_004597878.1| 318 ETINEIAAHVeDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQVSAA 393
                                       5566666666555788999999999999999999999999999999999999999999999999988888887744 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.008
                             Mod_r  18 lealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldell...qkf 91 
                                       ++ l  t++ev +  ++ + + ++ ++ a++  +  +e +e+ +e+ e+ +el e  +++e+   e de++   ++ 
  gi|336254771|ref|YP_004597878.1| 373 ISDLSATMEEVAASSDQVSAAAKQAQAAADDGVEASQEAREEMDEVLEAADELVETVSQLEDRMDEIDEVIeviNDI 449
                                       33333355666666666666666666666666666666666556665555555555555555555556666777666 PP

                             Mod_r  92 spdallarLqtavae 106
                                        ++++l  L++ +++
  gi|336254771|ref|YP_004597878.1| 450 ADQTNLLALNANIEA 464
                                       666766666666655 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0096
                             Mod_r  18 lealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfsp 93 
                                       +++l++++ ++++q+ ++ e+l + +e++ae   + ++++e  ++++ +++ +l+e+ ++++e      e+ +  ++
  gi|336254771|ref|YP_004597878.1| 481 VQSLASETkEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITEIAETNDD 557
                                       67888888688***************************************************998888888766665 PP

                             Mod_r  94 da 95 
                                       +a
  gi|336254771|ref|YP_004597878.1| 558 QA 559
                                       54 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.056        17      24      74 ..     375     425 ..     363     432 .. 0.88
   2 ?    4.9   0.1      0.11        32      37      73 ..     493     529 ..     475     555 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.056
                              KxDL  24 rlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirsl 74 
                                        l ++ +e+ +  +++++  ++++a   +g+++++e +++++ + +  + l
  gi|336254771|ref|YP_004597878.1| 375 DLSATMEEVAASSDQVSAAAKQAQAAADDGVEASQEAREEMDEVLEAADEL 425
                                       58899*************************************987766665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.11
                              KxDL  37 alsqerlaklrarfkqgtkllkevkkdLesifkkirs 73 
                                       ++ + r+++l++r ++ +++  ++++  e   ++i++
  gi|336254771|ref|YP_004597878.1| 493 NQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDA 529
                                       4444444445555555555555544444444444443 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.16        48     177     218 ..     255     296 ..     237     301 .. 0.91
   2 ?    4.6   3.2     0.049        15     281     338 ..     379     437 ..     326     461 .. 0.68
   3 ?    6.6   0.7     0.012       3.7     279     346 ..     482     546 ..     474     604 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHSTCST CS
                               FH2 177 eelkrslealeaaseeLknskkfkklLeliLalGNymNdgtr 218
                                       e+l+  ++ +++ +e +++++ +  l   + ++G   Ndg+ 
  gi|336254771|ref|YP_004597878.1| 255 ESLQGVIQLVQDNTEVIRRREAMADLVGEVTETGEAINDGSL 296
                                       6788899********************************985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.049
                                       HHHHHHHHHHHHHHHHHHHHHCCT.TSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FH2 281 lekevkklekglkklekelessek.keepsdkflevlkeflkeaeeklkkleeelkeak 338
                                         +ev + +++++++ k++++ +    e s++ +e + e+l+ a+e +++++++++++ 
  gi|336254771|ref|YP_004597878.1| 379 TMEEVAASSDQVSAAAKQAQAAADdGVEASQEAREEMDEVLEAADELVETVSQLEDRMD 437
                                       22333333333333333333333334447777777777777777777777777766664 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FH2 279 eslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeakelvkelve 346
                                       +sl++e+k+ + ++++  ++l++  +   +  +++e+++e ++ a+e+++   ++l+e+ e+v+e+++
  gi|336254771|ref|YP_004597878.1| 482 QSLASETKEHTNQISDRVEDLQTRTE---ETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAH 546
                                       44444444444444444444444444...888899999999999999999999999999999998876 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       7.1   2.2e+03      18      57 ..     312     348 ..     301     359 .. 0.48
   2 ?    5.0   0.4      0.07        21       8      63 ..     341     396 ..     334     403 .. 0.72
   3 ?    5.4   2.0     0.053        16       5      64 ..     359     418 ..     355     448 .. 0.68
   4 ?    5.2   0.2     0.059        18       6      45 ..     409     448 ..     404     465 .. 0.70
   5 ?    5.3   3.1     0.055        17       3      67 ..     479     544 ..     472     555 .. 0.75
   6 ?    5.8   0.1     0.038        12       4      68 ..     526     590 ..     523     615 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 7.1
                             Sec34  18 qtdealeqLeeleekfksvsektsslheaceqlleeqkrl 57 
                                       +++++ e+++e+     +v++    l+e+ e+l ++  ++
  gi|336254771|ref|YP_004597878.1| 312 DVTQIAETINEIAA---HVEDVIYGLSEEVEDLSADAAEI 348
                                       33333333333333...33334444555555555554444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.07
                             Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaee 63 
                                        ++   e+ ++++ea +q+ e +e  +++ e+ s+l++++e++ ++ ++++  a++
  gi|336254771|ref|YP_004597878.1| 341 LSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQ 396
                                       55666677777888888888888888888888888888888888877777777665 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.053
                             Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeei 64 
                                       + +++e +++++e+++++  ++ee+  + ++vs+  ++ ++a+++ +e  ++ +e  +e+
  gi|336254771|ref|YP_004597878.1| 359 VGEQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQAQAAADDGVEASQEAREEMDEV 418
                                       566777777788888888888888888888888888887777777776666655544444 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.059
                             Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsektsslhe 45 
                                       ++ +ee+de+le +de+ e++++le+++++++e  + +++
  gi|336254771|ref|YP_004597878.1| 409 QEAREEMDEVLEAADELVETVSQLEDRMDEIDEVIEVIND 448
                                       5667788888888888888888888887777765554444 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.055
                             Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektss.lheaceqlleeqkrleelaeeieek 67 
                                       ++++s  +e++e  +q+++  e+L++ +e+  +v+e+t++ ++ a+e++ +   +lee+ae+++e 
  gi|336254771|ref|YP_004597878.1| 479 NEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNErVEGASERIDAAIANLEEIAEAVDEA 544
                                       456666677777777788888888888888888888887536778888888888888888888775 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.038
                             Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekL 68 
                                       ++++  ++++e+ e +dea   ++e+ e  ++ +++ +++ ++++ + ++ +r+eel  +++e+ 
  gi|336254771|ref|YP_004597878.1| 526 RIDAAIANLEEIAEAVDEAAHGITEIAETNDDQAASVEEVASQADGVADDADRIEELIGDVTERT 590
                                       56677888999999999999999999999999999999999999999999999999999988875 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.46   1.4e+02      27      66 ..     312     351 ..     302     390 .. 0.64
   2 ?    5.4   0.6     0.075        23      24      61 ..     399     441 ..     379     462 .. 0.78
   3 ?    7.8   1.3     0.013       4.1       5      63 ..     481     544 ..     477     564 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.46
                        Syntaxin_2  27 dteelreklhelieeinelikktnellkklsqldnsssds 66 
                                       d +++ e ++e+  ++ ++i   +e +++ls+++    ds
  gi|336254771|ref|YP_004597878.1| 312 DVTQIAETINEIAAHVEDVIYGLSEEVEDLSADAAEIADS 351
                                       6777777777777777777777777777777765554444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.075
                        Syntaxin_2  24 tkkd.....teelreklhelieeinelikktnellkklsqldn 61 
                                        + d     ++e re+++e+ e + el++++++l  +++++d+
  gi|336254771|ref|YP_004597878.1| 399 AAADdgveaSQEAREEMDEVLEAADELVETVSQLEDRMDEIDE 441
                                       3333344559999******************999999999886 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.013
                        Syntaxin_2   5 lqkinsnvstleklvkq....Lgtkk.dteelreklhelieeinelikktnellkklsqldnss 63 
                                       +q+++s +++  +++++    L+t++ +t e+ e+ +e +e ++e i +  ++l+++++  +  
  gi|336254771|ref|YP_004597878.1| 481 VQSLASETKEHTNQISDrvedLQTRTeETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEA 544
                                       5555555555555544444449999746999999999999999999999999999998877655 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  11.8    0.0054       1.6      26     143 ..     315     436 ..     306     439 .. 0.57
   2 ?    4.1  11.0      0.15        44      68     138 ..     478     550 ..     437     610 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0054
                         ApoLp-III  26 tiKensenlvdqlkqvikslqeelkkksd..........eleealkevkkkieetadklseenPevkkkaqelqekv 92 
                                        i e  ++++  +++vi  l+ee+ + s           e+++ + e +++i  +++++s   +++ +++ + +   
  gi|336254771|ref|YP_004597878.1| 315 QIAETINEIAAHVEDVIYGLSEEVEDLSAdaaeiadsasEADSQVGEQNEAIRAIVEEISD-LSATMEEVAASS--- 387
                                       4445555555555555555555555533300000000004444444444455555555544.223333333333... PP

                         ApoLp-III  93 QsgvqslvkesqklaeslkensqeakeklakaikqayddaveaaqklakqL 143
                                        ++v++ +k++q++a +  e+sqea e++ + ++ a d+ ve+ ++l++ +
  gi|336254771|ref|YP_004597878.1| 388 -DQVSAAAKQAQAAADDGVEASQEAREEMDEVLE-AADELVETVSQLEDRM 436
                                       .568999999999999999999999999999886.5699999999988766 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.15
                         ApoLp-III  68 eetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslkensqeakeklaka..ikqayddaveaaqk 138
                                       ++ +++l +e  e + ++++  e +Q++++++++ ++++ e+++ +s+ + + +a++  i +a+d+a+   ++
  gi|336254771|ref|YP_004597878.1| 478 ANEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLeeIAEAVDEAAHGITE 550
                                       4455566666666666666666777777777777777777777777777777777643355556655544443 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0016      0.49       1      95 [.     149     249 ..     149     276 .. 0.61
   2 ?    0.8   0.1       1.7   5.1e+02      27      90 ..     331     393 ..     318     408 .. 0.79
   3 ?   -0.0   0.2       3.1   9.4e+02      42      91 ..     371     422 ..     361     445 .. 0.70
   4 ?    0.8   0.3       1.7   5.2e+02      56      89 ..     488     521 ..     466     567 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0016
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefg...agdveaeverrl.aaarag 73 
                                       l+ ++q   ++D ++r++ wNr+  el ++ +e v       +++r  +++   +   ++ ++a+ e+   ++ r++
  gi|336254771|ref|YP_004597878.1| 149 LNTLPQPAFIVDTEHRVIGWNREAEELTGVDREDVLGEDAAGSFFRDGRTTTLADevvDHPRDAHRETDAeRSGRDQ 225
                                       5677788889********************99988433334444444444433333222334444443331234556 PP

                             PAS_7  74 kphsfererpd..grvievrgnpl 95 
                                       +++ +ere ++  g++++v++ ++
  gi|336254771|ref|YP_004597878.1| 226 RAYELERELENarGETLHVHSVAT 249
                                       666666665542266777777666 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.7
                             PAS_7  27 lldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfererpdgrviev 90 
                                       +++l+ee+    +  +e+ +  +e  +   g+++++++++++++++ +++  e+  ++ +v   
  gi|336254771|ref|YP_004597878.1| 331 IYGLSEEVEDLSADAAEIADSASEADSQV-GEQNEAIRAIVEEISDLSATMEEVAASSDQVSAA 393
                                       67788888888888888888876666655.8999999999999999888888887777777655 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 3.1
                             PAS_7  42 eellrynaergefg..agdveaeverrlaaaragkphsfererpdgrvievr 91 
                                       ee+ +  a+ +e++  +++v+a++++  aaa +g + s e +++  +v+e  
  gi|336254771|ref|YP_004597878.1| 371 EEISDLSATMEEVAasSDQVSAAAKQAQAAADDGVEASQEAREEMDEVLEAA 422
                                       5666666666666644555666677777777777777777777777777665 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 1.7
                             PAS_7  56 agdveaeverrlaaaragkphsfererpdgrvie 89 
                                       +++  +++  r++ ++++++++ e+++++++ +e
  gi|336254771|ref|YP_004597878.1| 488 TKEHTNQISDRVEDLQTRTEETAEVTEQTNERVE 521
                                       4566677788888888888777777766665554 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2      0.45   1.4e+02      36     104 ..     256     324 ..     249     360 .. 0.62
   2 ?   10.4   8.7    0.0023       0.7      27     114 ..     361     450 ..     337     471 .. 0.66
   3 ?    4.3   5.4      0.17        52      36     111 ..     470     542 ..     455     557 .. 0.60
   4 ?    4.5   5.9      0.15        45      26     123 ..     506     606 ..     486     613 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCT.TCCHHHHHHHHHHHHHHHHHH CS
                              FlgN  36 dieaLeelleekqellekleqleqkrakllaelglsaeeatlsellak.eedeelkelwqelkelleelk 104
                                        +++  +l+++ +e++++ e++++   ++++  +   ++ +l + +++ ++++ l e ++++ e+++e+ 
  gi|336254771|ref|YP_004597878.1| 256 SLQGVIQLVQDNTEVIRRREAMADLVGEVTETGEAI-NDGSLAARVEYtDDHDVLDEDVTQIAETINEIA 324
                                       445555555555566655555555555555544444.555555555556666666666666666666554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0023
                                       HHHHHHHTT..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--..SCHHHHHHHHCTTCCHHHHHHHHHHHHH CS
                              FlgN  27 eEteaLkag..dieaLeelleekqellekleqleqkrakllaelgls..aeeatlsellakeedeelkelwqelkel 99 
                                       e+ ea++a   +i+ L +++ee ++  +++++++++ +++ ++  +   + +++++e+l+  +++el e +++l+++
  gi|336254771|ref|YP_004597878.1| 361 EQNEAIRAIveEISDLSATMEEVAASSDQVSAAAKQAQAAADDGVEAsqEAREEMDEVLE--AADELVETVSQLEDR 435
                                       555555554446667777777777777777666666555554443337878888888888..888888888888888 PP

                                       HHHHHHHHHHHHHHH CS
                              FlgN 100 leelkelnelNgrli 114
                                       ++e+ e+ e  + + 
  gi|336254771|ref|YP_004597878.1| 436 MDEIDEVIEVINDIA 450
                                       888888766443333 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--.SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FlgN  36 dieaLeelleekqellekleqleqkrakllaelgls.aeeatlsellakeedeelkelwqelkelleelkelnelNg 111
                                       d +++  +++e q+l+ + +++ ++++  +++l+++ +e+a+++e     ++e+++ + +++++++++l e++e+  
  gi|336254771|ref|YP_004597878.1| 470 DGDGFAVVANEVQSLASETKEHTNQISDRVEDLQTRtEETAEVTEQ----TNERVEGASERIDAAIANLEEIAEAVD 542
                                       5666666777777777777777777777777777774333333333....555555555555555555555554433 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.15
                                       HHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--.....SCHHHHHHHHCTTCCHHHHHHHHHHH CS
                              FlgN  26 eeEteaLkagdieaLeelleekqellekleqleqkrakllaelgls.....aeeatlsellakeedeelkelwqelk 97 
                                        eEt   +++  e+ e+  e++ + +++le+++++ +++ + + +      ++ a+++e+++  +++ +++  ++++
  gi|336254771|ref|YP_004597878.1| 506 TEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITEIaetndDQAASVEEVAS--QADGVADDADRIE 580
                                       46666667777788888888888888888888888888888777776667666777777776..7777777777777 PP

                                       HHHHHHHHHHHHHHHHHHHCCHHHHH CS
                              FlgN  98 elleelkelnelNgrlieqslefnqr 123
                                       el+ ++ e+ ++ + +i    ++++r
  gi|336254771|ref|YP_004597878.1| 581 ELIGDVTERTTAQRDAIDEMVDYLER 606
                                       77777777777777777666666655 PP

>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3      0.25        75     119     168 ..     318     366 ..     298     372 .. 0.74
   2 ?    8.4   7.6    0.0044       1.3     110     211 ..     351     451 ..     335     464 .. 0.77
   3 ?    7.7   6.9     0.007       2.1     130     215 ..     483     567 ..     460     611 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.25
                              Not3 119 kekeearewlkdaideLneqvekleaeieklsskkkkkkkskekarveel 168
                                       ++ +e+ ++++d+i  L+e+ve+l a++ +++ + ++ + s+  ++ e++
  gi|336254771|ref|YP_004597878.1| 318 ETINEIAAHVEDVIYGLSEEVEDLSADAAEIADSASEAD-SQVGEQNEAI 366
                                       556788999999999999999999999999988776655.3333344444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0044
                              Not3 110 aaekldpkekekeearewlkdaideLneqvekleaeieklsskkkkkkkskekarveeleklierhkfhieklelll 186
                                       +a+++d +  e++ea++ + + i++L+  +e++ a+ +++s++ k+ + +++++ ve+ ++  e+    +e  ++l+
  gi|336254771|ref|YP_004597878.1| 351 SASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQAQ-AAADDGVEASQEAREEMDEVLEAADELV 426
                                       34567999999*****************************99888887.4444577777777777777777777777 PP

                              Not3 187 rlleneelepeevekikedieyyve 211
                                       + +++ e + +e++++ e i+ + +
  gi|336254771|ref|YP_004597878.1| 427 ETVSQLEDRMDEIDEVIEVINDIAD 451
                                       7777776666777776666666554 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.007
                              Not3 130 daideLneqvekleaeieklsskkkkkkkskekarveeleklierhkfhieklelllrlleneelepeevekikedi 206
                                       +  +e +e+++++   +e l++++++   + +++  e++e   er    i++le++ +++++ +   +e++++++d 
  gi|336254771|ref|YP_004597878.1| 483 SLASETKEHTNQISDRVEDLQTRTEETA-EVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITEIAETNDDQ 558
                                       4445556666666667777766555544.444457788888888888899999999999999998889999988888 PP

                              Not3 207 eyyvesnqd 215
                                          ve+   
  gi|336254771|ref|YP_004597878.1| 559 AASVEEVAS 567
                                       888866433 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.9   0.00011     0.034     579     703 ..     304     433 ..     243     444 .. 0.82
   2 ?    1.9   4.1      0.12        38     590     668 ..     487     568 ..     475     610 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                             Nup88 579 eerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelekikeklkslknalkqvkkkl 655
                                       ++ ++l e++ ++Ae  +ei  + e+++  +++ +++l + +  + ++  e  +++ + +e+++ + ++++++  ++
  gi|336254771|ref|YP_004597878.1| 304 DDHDVLDEDVTQIAETINEIAAHVEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATM 380
                                       678899**************************************999999999999999999999999999999999 PP

                             Nup88 656 dkqrkqiaks......keeekksslelsekqkktikeiLkeegeeieelikqvk 703
                                       ++++   ++       +++++ + +e s++ ++ + e+L+  ++e+ e ++q++
  gi|336254771|ref|YP_004597878.1| 381 EEVAASSDQVsaaakqAQAAADDGVEASQEAREEMDEVLE-AADELVETVSQLE 433
                                       8876554433111111566677778999999999999995.4555555555554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.12
                             Nup88 590 klAekyeeikdkQeklvrrvk...kvlkrlnsklpvlseaeremkkelekikeklkslknalkqvkkkldkqrkqia 663
                                       +  e+ ++i+d+ e+l  r +   +v +++n+++   se   +   +le+i e++++ ++ + ++ ++ d q+  ++
  gi|336254771|ref|YP_004597878.1| 487 ETKEHTNQISDRVEDLQTRTEetaEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITEIAETNDDQAASVE 563
                                       33344444555555555554411134445555555555444455566666666666666666666666666666666 PP

                             Nup88 664 kskee 668
                                       + +++
  gi|336254771|ref|YP_004597878.1| 564 EVASQ 568
                                       55554 PP

>> Sec5  Exocyst complex component Sec5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       4.1   1.3e+03      57      57 ..     328     328 ..     217     390 .. 0.63
   2 ?   10.5   4.9    0.0013       0.4      21     149 ..     386     524 ..     362     559 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.1
                              Sec5  57 t 57 
                                       +
  gi|336254771|ref|YP_004597878.1| 328 E 328
                                       1 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0013
                              Sec5  21 tldqiykefseskteaqed.....slveeLeeslneairkttllfkpvlenkekadklraalevier...nkflFnL 89 
                                       + dq+  + ++ +             ++e +e+++e+ +++++l++ v + ++++d++  ++evi+       l+ L
  gi|336254771|ref|YP_004597878.1| 386 SSDQVSAAAKQAQA----AaddgvEASQEAREEMDEVLEAADELVETVSQLEDRMDEIDEVIEVINDiadQTNLLAL 458
                                       34444444444444....23345688999***********************************9862115689999 PP

                              Sec5  90 PksLkesiakgdydklindYkkakslfestrqslv......eedkkqvkvfkkvwsevekiieeyr 149
                                         +++ + a +d d +    ++++sl ++t++  +      e+ +++ +   +v ++ ++++e   
  gi|336254771|ref|YP_004597878.1| 459 NANIEAAQAGEDGDGFAVVANEVQSLASETKEHTNqisdrvEDLQTRTEETAEVTEQTNERVEGAS 524
                                       99**99999999999999999999999999666656666664444444444444444444444444 PP

>> PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.0   0.00039      0.12      40     153 ..     318     424 ..     302     441 .. 0.79
   2 ?    2.0   2.2      0.56   1.7e+02      50      99 ..     478     518 ..     441     537 .. 0.69
   3 ?    2.3   0.5      0.46   1.4e+02      38      94 ..     526     583 ..     511     602 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00039
                         PhaP_Bmeg  40 kqqqdlvkeltkalselekeskqltaeledqlqktvenlrskaGnkvednieEwtdkleevsakleklalspsKssl 116
                                       ++ +++  ++ + +  l +e  +l a+   +  +  +++ s+ G + ++ i    + + ++sa +e++a     +s 
  gi|336254771|ref|YP_004597878.1| 318 ETINEIAAHVEDVIYGLSEEVEDLSADA-AEIADSASEADSQVGEQ-NEAIRAIVEEISDLSATMEEVA-----ASS 387
                                       4444555555566666788888888888.67789999999*****9.999***************9987.....567 PP

                         PhaP_Bmeg 117 dllkkaeeqleetvkslieqqkkrReeiqkvleeyve 153
                                       d ++ a +q +   +  +e +++ Ree+  vle+  e
  gi|336254771|ref|YP_004597878.1| 388 DQVSAAAKQAQAAADDGVEASQEAREEMDEVLEAADE 424
                                       889999999999**************99998886433 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.56
                         PhaP_Bmeg  50 tkalselekeskqltaeledqlqktvenlrskaGnkvednieEwtdklee 99 
                                        +++++l  e+k+ t ++     + ve+l+ ++         E t++++e
  gi|336254771|ref|YP_004597878.1| 478 ANEVQSLASETKEHTNQI----SDRVEDLQTRTEET-----AEVTEQTNE 518
                                       567788888888888888....66666665444333.....233333222 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.46
                         PhaP_Bmeg  38 alkqqqdlvkeltkalselekeskqltaeledqlqktvenlrska.Gnk.vednieEwt 94 
                                        ++  +  ++e+ +a++e  +   ++ ae +d +   ve+++s+a G++ ++d ieE+ 
  gi|336254771|ref|YP_004597878.1| 526 RIDAAIANLEEIAEAVDEAAHGITEI-AETNDDQAASVEEVASQAdGVAdDADRIEELI 583
                                       44444445555555666555555544.67777777778887776536552467788775 PP

>> Nmad5  Nucleotide modification associated domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1       1.2   3.7e+02     105     161 ..     276     332 ..     225     335 .. 0.77
   2 ?   10.0   0.6    0.0024      0.73      21      78 ..     334     391 ..     331     404 .. 0.87
   3 ?    5.1   7.3     0.075        23      21     161 ..     393     532 ..     390     554 .. 0.79
   4 ?    5.9   1.7     0.044        13      37     128 ..     479     574 ..     473     609 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.2
                             Nmad5 105 vvlasvdeiaketkslpkvvleadnplvkrfdelekaqeelrekrkaikatVtavln 161
                                       ++ + v e+++ +++    +l a  + ++  d l++++ +++e +++i a V+ v++
  gi|336254771|ref|YP_004597878.1| 276 AMADLVGEVTETGEAINDGSLAARVEYTDDHDVLDEDVTQIAETINEIAAHVEDVIY 332
                                       555556666666666666677777778888889999999999999999999999997 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0024
                             Nmad5  21 iaekekalrkeradlaeevrldalggkkteaalreiikeieklqsklpkeglstnkpk 78 
                                       + e+ ++l ++ a++a+++  +  +  ++ +a+r+i++ei +l++ ++++ +s++++ 
  gi|336254771|ref|YP_004597878.1| 334 LSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQVS 391
                                       678999*****************9999***********************99988743 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.075
                             Nmad5  21 iaekekalrkeradlaeevrldalggkkteaalreiikeieklqsklpkeglstnk..pkstgsvidvnlaGarvel 95 
                                        a++++a+ ++  +  +e+r +     ++ ++l e+++++e+ ++++ ++    n   ++ +  ++++n++ a+   
  gi|336254771|ref|YP_004597878.1| 393 AAKQAQAAADDGVEASQEAREEMDEVLEAADELVETVSQLEDRMDEIDEVIEVINDiaDQTNLLALNANIEAAQAGE 469
                                       5677888888888888999998888999999*******************999988666777777777777554444 PP

                             Nmad5  96 yfngkkletvvlasvdeiaketkslpkvvleadnplvkrfdelekaqeelrekrkaikatVtavln 161
                                         +g     vv  +v+ +a+etk+ +++  ++ ++l+ r +e ++  e+ +e+ + + + ++a++ 
  gi|336254771|ref|YP_004597878.1| 470 DGDG---FAVVANEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIA 532
                                       4444...67777888888888888888888888888888888888888888888888777777765 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.044
                             Nmad5  37 eevrldalggkkteaalreiikeieklqsklpkeglstnk.pkstgsvidvnlaGarvelyfng...kkletvvlas 109
                                        ev   a   k+ ++++ ++++ ++   +++ +++ +tn+ +++ ++ id+ +a++ + +   +   ++ ++    +
  gi|336254771|ref|YP_004597878.1| 479 NEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNErVEGASERIDAAIANLEEIAEAVDeaaHGITEIAETN 555
                                       55555666678889999999**************9999999*************99777777665554444444444 PP

                             Nmad5 110 vdeiaketkslpkvvlead 128
                                        d+ a++++  ++++ +ad
  gi|336254771|ref|YP_004597878.1| 556 DDQAASVEEVASQADGVAD 574
                                       4444444444444444444 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.8    0.0033         1      20      98 ..     312     390 ..     307     392 .. 0.94
   2 ?    7.9   7.8    0.0055       1.7      16      86 ..     378     448 ..     376     471 .. 0.88
   3 ?    5.5   6.7      0.03       9.2      23      91 ..     476     544 ..     452     557 .. 0.45
   4 ?    5.9   9.0     0.022       6.8      14     107 ..     495     588 ..     474     594 .. 0.80
   5 ?    3.9   0.8     0.094        29      41     112 ..     536     607 ..     532     612 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0033
                           DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeier 96 
                                       ++ + ae ++++aa ++  i  l++e ++l+a+  ++ + +++++ +  ++++ +++  +ei++l   +ee+ + ++
  gi|336254771|ref|YP_004597878.1| 312 DVTQIAETINEIAAHVEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSD 388
                                       6889999*****************************************************************99988 PP

                           DUF3450  97 el 98 
                                       ++
  gi|336254771|ref|YP_004597878.1| 389 QV 390
                                       87 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0055
                           DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiaslee 86 
                                       at++++ + + +  aaa+q+q+  d+  + +qe  +e+ ++ e +++l    +qle+ +++ ++ i+ ++ 
  gi|336254771|ref|YP_004597878.1| 378 ATMEEVAASSDQVSAAAKQAQAAADDGVEASQEAREEMDEVLEAADELVETVSQLEDRMDEIDEVIEVIND 448
                                       67889999999999999999999999999999999999999999999999999999999999999987765 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.03
                           DUF3450  23 keaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                        +a++ ++ a+++ +  ++++d  ++l+ + ++  e +e+++   e  ++ ++++ ++++++ e  +e+
  gi|336254771|ref|YP_004597878.1| 476 VVANEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEA 544
                                       333444444444444444444444444444444444444444444444444444444444433333333 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.022
                           DUF3450  14 laatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       +++ +++++  +e++ +  +q++++++  ++  +   a+++++ e +++++    + ++  ++q ++++++  q + 
  gi|336254771|ref|YP_004597878.1| 495 ISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITEIAETNDDQAASVEEVASQADG 571
                                       36778888888888888888888888888888888888888888888888888888888888888888888888888 PP

                           DUF3450  91 ieeierelvpllekmid 107
                                       +   +++++ l+ ++ +
  gi|336254771|ref|YP_004597878.1| 572 VADDADRIEELIGDVTE 588
                                       88888888888777766 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.094
                           DUF3450  41 klddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqf 112
                                       ++++  +e +  ++++ e +++ ++  e+++++ + +  + +++ee i +++e  ++    +++m+d Le++
  gi|336254771|ref|YP_004597878.1| 536 EIAEAVDEAAHGITEIAETNDDQAASVEEVASQADGVADDADRIEELIGDVTERTTAQRDAIDEMVDYLERV 607
                                       556666677777888888889999999999999999999999999999999999999999999999999875 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2    0.0068       2.1       2      58 ..     327     383 ..     326     390 .. 0.90
   2 ?   -1.3   0.2       9.3   2.8e+03      14      59 ..     388     433 ..     379     445 .. 0.60
   3 ?    5.0   0.8       0.1        31      13      59 ..     474     520 ..     472     543 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0068
                             Tup_N   2 lnelLdavkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrki 58 
                                       +++++  + +E + ls +a  +  +  e ++++ +q + + +i +++ +L ++ +++
  gi|336254771|ref|YP_004597878.1| 327 VEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEV 383
                                       5677777889****************************************9987765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 9.3
                             Tup_N  14 dalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkik 59 
                                       d++s  a++ +a  d+     q+  +E++ + ++  eL e+ +++ 
  gi|336254771|ref|YP_004597878.1| 388 DQVSAAAKQAQAAADDGVEASQEAREEMDEVLEAADELVETVSQLE 433
                                       5666666666665555444456666677776666666666555544 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.1
                             Tup_N  13 fdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkik 59 
                                       f  +++e++sl ++++e  ++i+  +++lq+  ++  e  e+ ++  
  gi|336254771|ref|YP_004597878.1| 474 FAVVANEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERV 520
                                       7889**************************99998888888776655 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  17.2    0.0043       1.3     362     533 ..     272     443 ..     206     457 .. 0.74
   2 ?    5.3  15.0    0.0094       2.9     260     392 ..     477     601 ..     441     620 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0043
                           DUF3584 362 eleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrlkaaieealealesqlrkqleaqkee 438
                                          e ++ l +++++  e+ +    ++  e  ++   l+e++ +i e+ ++  a+ e++   l ++ +  l a  +e
  gi|336254771|ref|YP_004597878.1| 272 RRREAMADLVGEVTETGEAINDGSLAARVEYTDDHDVLDEDVTQIAETINEIAAHVEDVIYGLSEEVE-DLSADAAE 347
                                       34455666777777778888889999999999999999999999999999999999999999998888.88999999 PP

                           DUF3584 439 lneeekelesrlselklrldsatat.eEeleqieeadealekaqeelekaeaevealqaeeeqlrkkrdeadealqk 514
                                       +++ + e  s+++e++  +++   + ++++  +ee  +  ++  +++++a+a+  +  ++ +++r++ de +ea  +
  gi|336254771|ref|YP_004597878.1| 348 IADSASEADSQVGEQNEAIRAIVEEiSDLSATMEEVAASSDQVSAAAKQAQAAADDGVEASQEAREEMDEVLEAADE 424
                                       99999999999999988877654332566666666666666666666666666666666666677777777777777 PP

                           DUF3584 515 aerrleqlrqaleeleeql 533
                                         + ++ql ++++e+ e++
  gi|336254771|ref|YP_004597878.1| 425 LVETVSQLEDRMDEIDEVI 443
                                       7777777777777776654 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0094
                           DUF3584 260 lelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeaidelnqelsaakaklaakeselealeeqkk 336
                                       + ++++            la++ +e  ++  +  + l+t ++e +e  +++n++++ a++ ++a+ ++le++ e  +
  gi|336254771|ref|YP_004597878.1| 477 VANEVQ-----------SLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVD 542
                                       444444...........445555555555555556666666666666666666666666666666666666655433 PP

                           DUF3584 337 ..kyedadi.eklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkikeel 392
                                         ++   +i e+   ++  ++++ s+   +  + d+++e + dv+e++ +++ +i+e  
  gi|336254771|ref|YP_004597878.1| 543 eaAHGITEIaETNDDQAASVEEVASQADGVADDADRIEELIGDVTERTTAQRDAIDEMV 601
                                       00344444403333344556777778888888888999999999999998888887654 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       9.8     3e+03     152     162 ..     231     241 ..     217     284 .. 0.51
   2 ?    9.6  10.7    0.0022      0.67      92     178 ..     317     403 ..     301     411 .. 0.91
   3 ?    9.7  10.7    0.0021      0.65      64     174 ..     429     546 ..     418     555 .. 0.76
   4 ?    5.2   5.8     0.051        16      64     147 ..     499     589 ..     497     608 .. 0.51

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.8
                            DUF745 152 kkqlkearkdl 162
                                       +++l++ar + 
  gi|336254771|ref|YP_004597878.1| 231 ERELENARGET 241
                                       33333333222 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0022
                            DUF745  92 akaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektkka 168
                                       a++ +++a++++  +  l++ ++  ++ ++++ + a++a +++ e+++ + a  + +  L+  ++e+ +  +++ +a
  gi|336254771|ref|YP_004597878.1| 317 AETINEIAAHVEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQVSAA 393
                                       77888999999999999************************************************************ PP

                            DUF745 169 AykAacAAqe 178
                                       A++A++AA +
  gi|336254771|ref|YP_004597878.1| 394 AKQAQAAADD 403
                                       ********64 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0021
                            DUF745  64 veqleqelreaeavvqeekkslqsseanakaaakaakqaqqq.......lealkallkaakenlenaeqvaagaqqe 133
                                       v qle+ + e ++v++ +++   +++  a  a+  a+qa +        ++ +++l  ++ke  +++ +  +  q+ 
  gi|336254771|ref|YP_004597878.1| 429 VSQLEDRMDEIDEVIEVINDIADQTNLLALNANIEAAQAGEDgdgfavvANEVQSLASETKEHTNQISDRVEDLQTR 505
                                       78999999999999988887777776555444444444444311111114566666677777777777777889999 PP

                            DUF745 134 laektqlleaAkkRveeLkkqlkearkdlektkkaAykAac 174
                                        +e ++  e+ ++Rve  ++++++a ++le++ +a   Aa 
  gi|336254771|ref|YP_004597878.1| 506 TEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAH 546
                                       9**********************************999986 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.051
                            DUF745  64 veqleqelreaeavvqeekkslqsseanakaa.......akaakqaqqqlealkallkaakenlenaeqvaagaqqe 133
                                       ve l+   +e+ +v ++ ++ ++ +++ ++aa       a+a+++a + ++ + ++ +   +++e++ + a+g++ +
  gi|336254771|ref|YP_004597878.1| 499 VEDLQTRTEETAEVTEQTNERVEGASERIDAAianleeiAEAVDEAAHGITEIAETNDDQAASVEEVASQADGVADD 575
                                       56666666666666666666666666665555111100033444444444444444444444444444444444455 PP

                            DUF745 134 laektqlleaAkkR 147
                                       ++  ++l+ +  +R
  gi|336254771|ref|YP_004597878.1| 576 ADRIEELIGDVTER 589
                                       55555555555555 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 ?    8.6   1.7    0.0059       1.8      95     168 ..     303     383 ..     223     393 .. 0.78
   2 ?    4.3   1.9      0.13        39     124     173 ..     395     444 ..     387     459 .. 0.86
   3 ?    6.3   7.3      0.03       9.2      82     172 ..     472     562 ..     449     608 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0059
                           UPF0242  95 qeeeeeLkeeldakeeelerlkeenq....qLqekleaiae...dfeelkleleeqLaekqellqeyqetieeqrsv 164
                                       +++++ L e + +  e++++     +     L+e+ e+ ++   +++++  e+++q+ e++e +    e+i+++ ++
  gi|336254771|ref|YP_004597878.1| 303 TDDHDVLDEDVTQIAETINEIAAHVEdviyGLSEEVEDLSAdaaEIADSASEADSQVGEQNEAIRAIVEEISDLSAT 379
                                       455666666666666666655554443344566666655555559999***************************** PP

                           UPF0242 165 lekr 168
                                       +e+ 
  gi|336254771|ref|YP_004597878.1| 380 MEEV 383
                                       *985 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.13
                           UPF0242 124 ekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqie 173
                                       ++++a+a d  e ++e+ e+++e  e  +e+ et++++   +++ ++ ie
  gi|336254771|ref|YP_004597878.1| 395 KQAQAAADDGVEASQEAREEMDEVLEAADELVETVSQLEDRMDEIDEVIE 444
                                       68889999999999999999999999999999999999999988887776 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.03
                           UPF0242  82 eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqeti 158
                                       +g+++ +++++ l +e++e  ++++ + e l+ ++ee +++ e++++ +e  +e   ++ ++L+e  e ++e ++ i
  gi|336254771|ref|YP_004597878.1| 472 DGFAVVANEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGI 548
                                       56666666777777777777777777777777777777777766666666333333333333333333333333333 PP

                           UPF0242 159 eeqrsvlekrqdqi 172
                                       +e  ++ + + + +
  gi|336254771|ref|YP_004597878.1| 549 TEIAETNDDQAASV 562
                                       33333333332222 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.6       3.1   9.4e+02      54      76 ..     261     283 ..     212     324 .. 0.49
   2 ?    6.0   7.4     0.055        17      41     103 ..     381     440 ..     297     441 .. 0.73
   3 ?    2.5   5.7      0.66     2e+02      28      82 ..     512     566 ..     470     617 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             DUF16  54 eqkvekqgekikelkveqkaqge 76 
                                        q v+  +e i++ ++  +  ge
  gi|336254771|ref|YP_004597878.1| 261 IQLVQDNTEVIRRREAMADLVGE 283
                                       44444444444333322222222 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.055
                                       HHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC CS
                             DUF16  41 akvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsie 103
                                       ++v++   q+++ +++ ++  +  +  ++ q+a++e +++v e+ + ++et+ ++++R+D+i+
  gi|336254771|ref|YP_004597878.1| 381 EEVAASSDQVSAAAKQAQAAAD--DGVEASQEAREE-MDEVLEAADELVETVSQLEDRMDEID 440
                                       3333333333333333222222..224455555555.889999999**************997 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.66
                                       B-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                             DUF16  28 fkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82 
                                         +++++r++   +++d+   ++++++++v++  + i+e+ ++ + q +++++v 
  gi|336254771|ref|YP_004597878.1| 512 VTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITEIAETNDDQAASVEEVA 566
                                       3445667777777777777777777777777777777777777777777666333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   8.2      0.16        48       2      86 ..     336     430 ..     334     505 .. 0.73
   2 ?    5.5   2.9     0.028       8.5       8      85 ..     489     565 ..     472     610 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.16
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..........eeeeeev 68 
                                       ee+e+l+ ++ e+ ++a+e  +++ e ++ + ++++ei+  +  ++e+ +s +++++++k          e ++e+ 
  gi|336254771|ref|YP_004597878.1| 336 EEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKqaqaaaddgvEASQEAR 412
                                       67777777777777777777777777777777777777777777777777777777665545555555554444444 PP

                             TMPIT  69 eelkeelkerkkvlkeve 86 
                                       ee++e l+ +++ ++ v+
  gi|336254771|ref|YP_004597878.1| 413 EEMDEVLEAADELVETVS 430
                                       444444444444444333 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.028
                             TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlke 84 
                                       ++++++++++ + +++++ee+++  +++ ++++  ++r+ +  ++l+++ ++v +e ++ ++e++e+ +++ ++++e
  gi|336254771|ref|YP_004597878.1| 489 KEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAV-DEAAHGITEIAETNDDQAASVEE 564
                                       44445555555555555555555555555555555555555555555555554.34444455555554444444444 PP

                             TMPIT  85 v 85 
                                       v
  gi|336254771|ref|YP_004597878.1| 565 V 565
                                       4 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.7    0.0019      0.57      24     125 ..     331     434 ..     311     451 .. 0.87
   2 ?    5.1   2.1      0.08        24      45     116 ..     480     551 ..     475     557 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0019
                             CREPT  24 iaklPpevsdvsl.lekik.dkeeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeek 98 
                                       i  l +ev+d+s  +++i  + +ea++ + + +ea++++ e  + L+a +ee    + ++++  ++ ++++++  e 
  gi|336254771|ref|YP_004597878.1| 331 IYGLSEEVEDLSAdAAEIAdSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQAQAAADDGVEA 407
                                       5566778888764378898345688999999********************************************** PP

                             CREPT  99 leelkeklekvksvrkelkshiqsLPd 125
                                        +e +e +++v ++ +el ++++ L d
  gi|336254771|ref|YP_004597878.1| 408 SQEAREEMDEVLEAADELVETVSQLED 434
                                       ******************999998866 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.08
                             CREPT  45 eaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkel 116
                                       e ++l+++ +e  +++++ ++ L+  +ee  +++++ ++ +e   e+++ a ++lee+ e +++  +  +e+
  gi|336254771|ref|YP_004597878.1| 480 EVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITEI 551
                                       556677777777777777777777777777777777777777777777777777777777777766666665 PP

>> Herpes_U30  Herpes virus tegument protein U30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.7    0.0021      0.64     668     804 ..     254     394 ..     242     401 .. 0.82
   2 ?    2.8   1.9     0.068        21     732     805 ..     479     553 ..     472     564 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0021
                        Herpes_U30 668 eelqkavnkflketetlledilrltrlaaklcrtrlnydeetgtvrvpvaegdkivrvdlkafketvkelqellrea 744
                                       +e  + v +++++ + +++    ++ l  ++ +t   ++  ++  rv+  +    ++ d+++  et++e+   ++++
  gi|336254771|ref|YP_004597878.1| 254 QESLQGVIQLVQDNTEVIRRREAMADLVGEVTETGEAINDGSLAARVEYTDDHDVLDEDVTQIAETINEIAAHVEDV 330
                                       5566778888888888999999999999999999999999999999999999999********************** PP

                        Herpes_U30 745 lvtlseslkelqtlyrqllv.ilseseel..anhalkidlse.pdleelketllkalkrlasla 804
                                       + +lse  ++l +  ++++  +++   ++  +n+a+++ + e  dl+++ e++ +   +++  a
  gi|336254771|ref|YP_004597878.1| 331 IYGLSEEVEDLSADAAEIADsASEADSQVgeQNEAIRAIVEEiSDLSATMEEVAASSDQVSAAA 394
                                       *******************989998888844578888877777777777777666555555544 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.068
                        Herpes_U30 732 etvkelqellrealvtlseslkelqtlyrqllv.ilseseelanhalkidlsepdleelketllkalkrlaslas 805
                                       + v+ l ++++e + ++s + ++lqt+  + +    +++e+++  + +id +  +lee+ e + +a + ++++a+
  gi|336254771|ref|YP_004597878.1| 479 NEVQSLASETKEHTNQISDRVEDLQTRTEETAEvTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITEIAE 553
                                       67999*************************9994555678899999999**********9999998887777765 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6  12.0     0.093        28      82     217 ..     310     446 ..     289     466 .. 0.46
   2 ?    7.2   9.3    0.0075       2.3      50     201 ..     438     609 ..     431     614 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.093
                                       XXXXXXXXXXXXXXXXXX...XXXXXX.XXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXX CS
                              AIP3  82 deslaslskelkelkssiesqkaslqe.vserqeeaakekaseslakkelkaqlkevqslrrdLavlrqlysefkse 157
                                       de +++++++++e+ +++e+    l+e v++ +++aa+ + s s a ++  +q + ++++ ++++ l  + +e   +
  gi|336254771|ref|YP_004597878.1| 310 DEDVTQIAETINEIAAHVEDVIYGLSEeVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAAS 386
                                       33344444444444444433322222202222222222222223334445555556666666666665555444433 PP

                                       XXXXXXXXXXXXXXXXXXXX.XXXX.XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 158 ikeslselrekakkvkeaslastkk.ssnrayiekgkkkLseesdklvtkvddLqDlvedl 217
                                        ++++s+  ++a++  +  ++ +++  ++   + ++ ++L e++++l  ++d+++ ++e +
  gi|336254771|ref|YP_004597878.1| 387 -SDQVSAAAKQAQAAADDGVEASQEaREEMDEVLEAADELVETVSQLEDRMDEIDEVIEVI 446
                                       .333444444444444333322222144444455555555555555666666665555544 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0075
                                       XXXXXXXXXXXXXXXX.XXXXX..................XXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXX CS
                              AIP3  50 gvrYeLedlsdvkdrs.vLsLn..................iepldevkkhideslaslskelkelkssiesqkaslq 107
                                       +++   e ++d+ d++ +L Ln                   ++++++ ++ +e+++++s+++++l++++e++++ ++
  gi|336254771|ref|YP_004597878.1| 438 EIDEVIEVINDIADQTnLLALNanieaaqagedgdgfavvANEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTE 514
                                       5555566689999876588999999999999998888876669999999***********************99999 PP

                                       XXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXX.X CS
                              AIP3 108 evserqeeaakekaseslakkelkaqlkevqslrrdLavlrqlysefkseikeslselrekakkvkeaslastkk.s 183
                                       +++er e a+++    +++ +e ++ ++e  +   ++a +   ++++ +e+ ++   + + a++++e+    t+  +
  gi|336254771|ref|YP_004597878.1| 515 QTNERVEGASERIDAAIANLEEIAEAVDEAAHGITEIAETNDDQAASVEEVASQADGVADDADRIEELIGDVTERtT 591
                                       99999999999999888888888888888888888888888888888888889999999999999965443333337 PP

                                       XHHHHHHHHHHHHHHHHH CS
                              AIP3 184 snrayiekgkkkLseesd 201
                                       ++r  i++  + L++ +d
  gi|336254771|ref|YP_004597878.1| 592 AQRDAIDEMVDYLERVAD 609
                                       888888888877777665 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       7.4   2.2e+03       5      19 ..     331     345 ..     316     355 .. 0.70
   2 ?    0.8   0.0       1.4   4.4e+02       3      29 ..     364     390 ..     363     394 .. 0.80
   3 ?    4.8   0.3     0.083        25       2      27 ..     426     451 ..     420     461 .. 0.73
   4 ?    2.7   0.0      0.36   1.1e+02       6      28 ..     493     515 ..     488     524 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 7.4
                         DASH_Dam1   5 faeLaDsletLdknl 19 
                                       +  L++++e+L++  
  gi|336254771|ref|YP_004597878.1| 331 IYGLSEEVEDLSADA 345
                                       445677777776655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.4
                         DASH_Dam1   3 pafaeLaDsletLdknledLqqihesL 29 
                                       +a++ + +++++L++ +e+    ++++
  gi|336254771|ref|YP_004597878.1| 364 EAIRAIVEEISDLSATMEEVAASSDQV 390
                                       578899999999999999887766665 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.083
                         DASH_Dam1   2 epafaeLaDsletLdknledLqqihe 27 
                                       +++ ++L+D ++++d+ +e +++i +
  gi|336254771|ref|YP_004597878.1| 426 VETVSQLEDRMDEIDEVIEVINDIAD 451
                                       45667777777777777777777765 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.36
                         DASH_Dam1   6 aeLaDsletLdknledLqqihes 28 
                                       ++++D +e+L++++e+  +++e+
  gi|336254771|ref|YP_004597878.1| 493 NQISDRVEDLQTRTEETAEVTEQ 515
                                       689**********9998888776 PP

>> Kre28  Spindle pole body component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.2   6.7e+02     112     172 ..     242     298 ..     237     325 .. 0.49
   2 ?    5.6   9.2     0.021       6.4     129     257 ..     323     451 ..     300     467 .. 0.77
   3 ?    7.1  10.1    0.0076       2.3     121     215 ..     473     566 ..     461     615 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.2
                             Kre28 112 lqleSesDpkyvsle.eeVseLedetltekeseieqikgeIkekgkelaekqdqinelyLet 172
                                       l+++S++ p y++ + + V +L +++      e+   ++ + +   e++e  ++in   L +
  gi|336254771|ref|YP_004597878.1| 242 LHVHSVATPIYQQESlQGVIQLVQDN-----TEVIRRREAMADLVGEVTETGEAINDGSLAA 298
                                       66666666666543213355554443.....3333334444444444444444444444444 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.021
                             Kre28 129 VseLedetltekeseieqikgeIkekgkelaekqdqinelyLettneideCwelLnEleelrdrrnkvekqtseekd 205
                                       +    ++++  + +e+e++ ++  e +   +e+  q+ e        ++e  +l   +ee+    ++v   + + + 
  gi|336254771|ref|YP_004597878.1| 323 IAAHVEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQAQA 399
                                       33334566777788888888888888888888888888888777778888888888888888777777777777777 PP

                             Kre28 206 teddlveetYeeWkslqkslqekeelkeeldrLkkekkeleevkkksknkee 257
                                         dd ve   e  +++++ l+   el e  ++L+++++e++ev + ++  ++
  gi|336254771|ref|YP_004597878.1| 400 AADDGVEASQEAREEMDEVLEAADELVETVSQLEDRMDEIDEVIEVINDIAD 451
                                       79***************************************99887766555 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0076
                             Kre28 121 kyvsleeeVseLedetltekeseieqikgeIkekgkelaekqdqinelyLettneideCwelLnEleelrdrrnkve 197
                                        ++ +++eV+ L  et +e+ ++i +  ++++  ++e ae  +q ne   +++  id   + L+E+ e+ d+  +  
  gi|336254771|ref|YP_004597878.1| 473 GFAVVANEVQSLASET-KEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGI 548
                                       58999*******9987.56788999999***************************************9997555555 PP

                             Kre28 198 kqtseekdteddlveetY 215
                                        + +e +d +   vee+ 
  gi|336254771|ref|YP_004597878.1| 549 TEIAETNDDQAASVEEVA 566
                                       555555555666777765 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  11.5     0.016       4.8     114     224 ..     333     445 ..     226     462 .. 0.79
   2 ?    8.8   6.0     0.003       0.9     118     228 ..     420     533 ..     418     536 .. 0.81
   3 ?    4.2   7.5     0.074        22      91     219 ..     458     594 ..     446     615 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.016
                              CorA 114 rlldeivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrlla.kaddklld 187
                                         l e v++l +   ++ +   e+++++  +++  + i++e+++l  ++ ++  +  +  ++ k+  a  +d+ + +
  gi|336254771|ref|YP_004597878.1| 333 G-LSEEVEDLSADAAEIADSASEADSQVgeQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQAQAaADDGVEAS 408
                                       2.344456666666666666666666668777777888888888887777775555555555555555568999999 PP

                              CorA 188 dedkeylrdlldelerllemlealrerleslqdtyss 224
                                       +e++e ++++l+ ++ l+e++++l +r++ + + +  
  gi|336254771|ref|YP_004597878.1| 409 QEAREEMDEVLEAADELVETVSQLEDRMDEIDEVIEV 445
                                       999999*********************9999887654 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.003
                              CorA 118 eivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvkl.....rralapnrevlkrllakaddklldde 189
                                       e +d+l e++++le+++de+++ +e  ++  +   l++l  ++         + +a   + +++l +  ++k+++ +
  gi|336254771|ref|YP_004597878.1| 420 EAADELVETVSQLEDRMDEIDEVIEVINDIADQTNLLALNANIEAAqagedGDGFAVVANEVQSLAS--ETKEHTNQ 494
                                       56899*******************8888888888888888665555555557777777777756666..88888888 PP

                              CorA 190 dkeylrdlldelerllemlealrerleslqdtyssllse 228
                                        +++ +dl+ ++e  +e +e++ er+e  ++ + + +++
  gi|336254771|ref|YP_004597878.1| 495 ISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIAN 533
                                       889999999999999999999999999999888877765 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.074
                              CorA  91 ldevikrlkdeggkpkspgellyrlldeivdrlfellekleeeldeledel.....edstkkeilrelaq.lr.... 157
                                       l++ i++++   g++ + + +++  +++++ +  e + ++++++++l+++            e+ +e ++       
  gi|336254771|ref|YP_004597878.1| 458 LNANIEAAQ--AGEDGDGFAVVANEVQSLASETKEHTNQISDRVEDLQTRTeetaeV----TEQTNERVEgASerid 528
                                       555555555..4778888888888899999999999999999999999999865542....2222222221220011 PP

                              CorA 158 rrlvklrralapnrevlkrlla....kaddkllddedkeylrdlldelerllemlealrerleslq 219
                                         +++l++++ +  e+ + + +    ++d+    +e + + + + d+++r++e +  + er++  +
  gi|336254771|ref|YP_004597878.1| 529 AAIANLEEIAEAVDEAAHGITEiaetNDDQAASVEEVASQADGVADDADRIEELIGDVTERTTAQR 594
                                       223333333333333333222222122222222333333355555555553333333333333333 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7  13.1      0.28        84       9     139 ..     324     463 ..     298     491 .. 0.62
   2 ?    8.9   6.6    0.0034         1       5     119 ..     488     605 ..     477     617 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.28
                           DUF4795   9 lkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdq 85 
                                         ++++ i  l+ee+e+l+  ++e+ ++ ++ ++++    ++i++  ++  d + + ee+a  +d    a+k+ +  
  gi|336254771|ref|YP_004597878.1| 324 AAHVEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQAQAA 400
                                       45555677778888888888888888888888888888888888888888888888777777777777777774444 PP

                           DUF4795  86 .......fDeakkeLekml...eellekleeqeealkkaldtLqeelkekldrlelepLkeqle 139
                                               +ea +e+++ l    el+e +++ e++++++ + ++  ++   d+ +l  L  ++e
  gi|336254771|ref|YP_004597878.1| 401 addgveaSQEAREEMDEVLeaaDELVETVSQLEDRMDEIDEVIE-VINDIADQTNLLALNANIE 463
                                       44443434444444444443334444444444444444333222.4444444555555555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0034
                           DUF4795   5 saellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkea..Lat 79 
                                       ++e  +++ + +e+lq++ e+  e ++++++r e  ++ ++a    +ee  ++ ++  +  +e+ae  d +a  ++ 
  gi|336254771|ref|YP_004597878.1| 488 TKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITEIAETNDDQAasVEE 564
                                       45568899999**********99999999999999999999999999999999999999999998888877544888 PP

                           DUF4795  80 kvsrdq.fDeakkeLekmleellekleeqeealkkaldtLq 119
                                       ++s+ + +   ++++e+ + ++ e+ ++q +a+++++d L+
  gi|336254771|ref|YP_004597878.1| 565 VASQADgVADDADRIEELIGDVTERTTAQRDAIDEMVDYLE 605
                                       888877899999**************************998 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.59   1.8e+02      30      95 ..     254     319 ..     245     329 .. 0.77
   2 ?    4.3   0.8      0.19        57      30      99 ..     310     380 ..     299     382 .. 0.77
   3 ?    8.7   7.2    0.0079       2.4       8     100 ..     343     433 ..     336     438 .. 0.80
   4 ?    2.3   5.6      0.76   2.3e+02      12     103 ..     431     520 ..     427     543 .. 0.67
   5 ?    3.2   5.4      0.41   1.2e+02       2      90 ..     480     570 ..     479     585 .. 0.52
   6 ?    1.7   0.5       1.1   3.5e+02      36      96 ..     548     608 ..     523     612 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.59
                                       SSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  30 gkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkel 95 
                                        ++l++v +l+++ +++ +  +a+ + v +++e++e++ d +  a  e ++  + l+e   ++ e+
  gi|336254771|ref|YP_004597878.1| 254 QESLQGVIQLVQDNTEVIRRREAMADLVGEVTETGEAINDGSLAARVEYTDDHDVLDEDVTQIAET 319
                                       578999999999999999999****************98887666655555555555555555555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.19
                                       SSSHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  30 gkdleevqallkkhkaleaelaa.qqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaer 99 
                                        +d++++ + +++  a+ +++     e+v++l + a +++d+  +a  ++ e+ e+++   ee+++l a++
  gi|336254771|ref|YP_004597878.1| 310 DEDVTQIAETINEIAAHVEDVIYgLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATM 380
                                       56666666666666666666665589999999999999999999999999999999999999998888776 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0079
                                       HHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHH CS
                          Spectrin   8 qdadeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerlee 84 
                                        da+e+ +  +e++ ++   +  + + ++ + + ++ a ++e+aa  ++v a  ++a++ +d g +as+e +e ++e
  gi|336254771|ref|YP_004597878.1| 343 ADAAEIADSASEADSQV--GEQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQAQAAADDGVEASQEAREEMDE 417
                                       56666666666666666..333335666666677999999************************************* PP

                                       HHHHHHHHHHHHHHHH CS
                          Spectrin  85 lnerWeeLkelaaerk 100
                                       + e+ +eL e++ + +
  gi|336254771|ref|YP_004597878.1| 418 VLEAADELVETVSQLE 433
                                       ********99987755 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.76
                                       HHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHH CS
                          Spectrin  12 eleeWieekeellssedlgkdleevqallkkhkaleaelaa.qqervkalnelaeklldeghsaseeieerleelne 87 
                                       +le+ ++e++e +   ++ +d+++  +ll     +ea  a    + +  +    ++l++e ++ + +i++r+e+l++
  gi|336254771|ref|YP_004597878.1| 431 QLEDRMDEIDEVI---EVINDIADQTNLLALNANIEAAQAGeDGDGFAVVANEVQSLASETKEHTNQISDRVEDLQT 504
                                       5666666666666...4556666666666666666655555355566667777777877778888888888888888 PP

                                       HHHHHHHHHHHHHHHH CS
                          Spectrin  88 rWeeLkelaaerkqkL 103
                                       r ee  e ++++ +++
  gi|336254771|ref|YP_004597878.1| 505 RTEETAEVTEQTNERV 520
                                       8777666666665554 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTT.....H CS
                          Spectrin   2 llqqfaqdadeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaekl.ldeg.....h 72 
                                       + q +a++ +e ++ i++  e+l+++    + e+++  +++ +++e   +  +  + +l+e+ae++ ++++      
  gi|336254771|ref|YP_004597878.1| 480 EVQSLASETKEHTNQISDRVEDLQTR----TEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVdEAAHgiteiA 552
                                       56778888888888888888888322....33333333444444444444444444444444444422222122225 PP

                                       TTHHHHHHHHHHHHHHHH CS
                          Spectrin  73 saseeieerleelnerWe 90 
                                       +++++  +++ee+ ++ +
  gi|336254771|ref|YP_004597878.1| 553 ETNDDQAASVEEVASQAD 570
                                       566666666666665555 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  36 vqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkela 96 
                                       + +  ++ ++  a +++   + + + + a+++++  ++ +e+++++ ++++e  + L++ a
  gi|336254771|ref|YP_004597878.1| 548 ITEIAETNDDQAASVEEVASQADGVADDADRIEELIGDVTERTTAQRDAIDEMVDYLERVA 608
                                       3444444445555555555555556666666666666666777777777777666666665 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.8      0.35   1.1e+02      41     124 ..     311     396 ..     298     427 .. 0.75
   2 ?    7.4   1.0     0.017       5.1      63     113 ..     476     528 ..     422     560 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.35
                          Gp-FAR-1  41 ellaalKkkspaLyekaeklqaklkekvdkLspeakeFvkkliakgrkleaqvlagekp..dlselkkvaktifnky 115
                                       e +  + +  +++++++e +   l e+v+ Ls++a e ++  ++   ++ +q  a   +  + s+l +++++++++ 
  gi|336254771|ref|YP_004597878.1| 311 EDVTQIAETINEIAAHVEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIveEISDLSATMEEVAASS 387
                                       55666677778899999999999999999999999999999997777776666555544113456666777777777 PP

                          Gp-FAR-1 116 kslseeaka 124
                                       ++ s++ak+
  gi|336254771|ref|YP_004597878.1| 388 DQVSAAAKQ 396
                                       777777765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.017
                          Gp-FAR-1  63 klkekvdkLspeakeFvkkliakgrkleaqvlagekpd..lselkkvaktifn 113
                                        + ++v++L  e+ke ++++++    l+++  + ++++  ++e+++ a++ + 
  gi|336254771|ref|YP_004597878.1| 476 VVANEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTeqTNERVEGASERID 528
                                       57789****************99999999888777776113344444444444 PP

>> BORCS7  BLOC-1-related complex sub-unit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.4    0.0032      0.96      21     101 ..     363     447 ..     342     454 .. 0.80
   2 ?    2.0   1.2      0.83   2.5e+02      57     101 ..     498     542 ..     476     582 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0032
                            BORCS7  21 tervevivndissvakqvvkgSksseilmkaaksf.aqqedaienteesLkkmsll...ttelnyqveaisksikql 93 
                                       +e ++ iv++is +   +   + ss+ +++aak+  a+ +d +e ++e  ++m  +   ++el ++v+++++ ++++
  gi|336254771|ref|YP_004597878.1| 363 NEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQAqAAADDGVEASQEAREEMDEVleaADELVETVSQLEDRMDEI 439
                                       5677889999999999999*************9753999*******9999999888555567777777777777777 PP

                            BORCS7  94 eevqeqvk 101
                                       +ev e ++
  gi|336254771|ref|YP_004597878.1| 440 DEVIEVIN 447
                                       77666555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.83
                            BORCS7  57 qqedaienteesLkkmsllttelnyqveaisksikqleevqeqvk 101
                                        +ed+  +tee+ + ++++ ++++   e i  +i +lee+ e+v+
  gi|336254771|ref|YP_004597878.1| 498 RVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVD 542
                                       456777777777777777777777777777777777777777776 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   2.1      0.37   1.1e+02      61     115 ..     393     450 ..     317     455 .. 0.55
   2 ?    6.0   1.2     0.053        16      18      74 ..     490     546 ..     481     591 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.37
                           Goodbye  61 piqllggiaaqgasmaFgP...aslcfnAvsyLikaakkvseiydaieeLfeelsdfl 115
                                         ++    a +g++++  +    + ++ A+  L+++  ++++  d+i+e+ e ++d++
  gi|336254771|ref|YP_004597878.1| 393 AAKQAQAAADDGVEASQEAreeMDEVLEAADELVETVSQLEDRMDEIDEVIEVINDIA 450
                                       3333333333333333333222334566666667777777777777777777666665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.053
                           Goodbye  18 dealkelssvedllkqieaekdkfeefrekkeklkealkkilspiqllggiaaqgas 74 
                                       +++++ + +vedl+ + e+ ++ +e+ +e+ e + e +  +++ ++ +++ + ++a 
  gi|336254771|ref|YP_004597878.1| 490 EHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAH 546
                                       344555668999999999999999999999999999999999999999999999886 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  21.4     0.011       3.2     158     330 ..     334     550 ..     328     610 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.011
                              FUSC 158 lrarlrallrdalalaaaalageegaeareaararlaadilalealrsqaayesprirararalrrllsrmlallal 234
                                       l+++++ l +da++ a +a +++++  ++++a ++++++i +l+a  + +a+ s +++a+a++++++  + +++++ 
  gi|336254771|ref|YP_004597878.1| 334 LSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQAQAAADDGVEASQE 410
                                       67889999********************************************************************* PP

                              FUSC 235 lsslarllarlraeeaaavpelaallaelaal............................................e 267
                                       +++  ++  +  +e  ++v +l++ ++e++++                                            e
  gi|336254771|ref|YP_004597878.1| 411 AREEMDEVLEAADELVETVSQLEDRMDEIDEVievindiadqtnllalnanieaaqagedgdgfavvanevqslasE 487
                                       **9988888888899999999***********777666666666666666666666666666666666655555554 PP

                              FUSC 268 aaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslraleaaiaa 330
                                        ++ ++++ ++++ l++r +++ +  e+ +++ + + +r +  +a+l ++ +++++ +++i++
  gi|336254771|ref|YP_004597878.1| 488 TKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITE 550
                                       444555555555555555555555555555555555555555555555555555555555555 PP

>> Hormone_1  Somatotropin hormone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.11        34     107     166 ..     329     387 ..     304     400 .. 0.80
   2 ?   -0.6   0.5         3   9.1e+02     112     147 ..     411     446 ..     406     465 .. 0.74
   3 ?    6.0   0.2     0.029       8.7     123     163 ..     478     518 ..     474     528 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.11
                                       TGGGGGG....GGGSSS------TTTGGGHHHHHHHHHHHHHHHH--------------- CS
                         Hormone_1 107 ePLkhlvtelssmkevsetilskakeieeklkeLlegierilskvevpverkekeekpaw 166
                                         ++ l +e++++ +  ++i  +a+e   +  e  e+i++i++ + +   ++++e   + 
  gi|336254771|ref|YP_004597878.1| 329 DVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISD-LSATMEEVAASS 387
                                       557889999**********************************9996.555555555544 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3
                                       GG....GGGSSS------TTTGGGHHHHHHHHHHHH CS
                         Hormone_1 112 lvtelssmkevsetilskakeieeklkeLlegieri 147
                                        ++e+ ++ e+ +++ +  +++e+ + e+ e+ie i
  gi|336254771|ref|YP_004597878.1| 411 AREEMDEVLEAADELVETVSQLEDRMDEIDEVIEVI 446
                                       567888888888888888888877777777777654 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.029
                                       S------TTTGGGHHHHHHHHHHHHHHHH------------ CS
                         Hormone_1 123 setilskakeieeklkeLlegierilskvevpverkekeek 163
                                        +++ s a+e +e+++++ + +e +++++e+++e +e+ ++
  gi|336254771|ref|YP_004597878.1| 478 ANEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNE 518
                                       6789999***********************99988888765 PP

>> IFT20  Intraflagellar transport complex B, subunit 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.7       1.5   4.4e+02      33      58 ..     304     329 ..     297     396 .. 0.65
   2 ?    0.2   0.4       2.7   8.1e+02      23      58 ..     361     396 ..     334     413 .. 0.63
   3 ?    3.1   0.6      0.34     1e+02      19      57 ..     406     444 ..     393     466 .. 0.66
   4 ?    9.5   3.2    0.0036       1.1      12      63 ..     476     529 ..     472     555 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.5
                             IFT20  33 kkinefqklvkelievleelakkvek 58 
                                       ++ + +++ v+++ e+++e+a +ve+
  gi|336254771|ref|YP_004597878.1| 304 DDHDVLDEDVTQIAETINEIAAHVED 329
                                       55555555566666666666666653 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.7
                             IFT20  23 elkeeckeFvkkinefqklvkelievleelakkvek 58 
                                       e +e  +  v++i++++++++e+    ++++ + ++
  gi|336254771|ref|YP_004597878.1| 361 EQNEAIRAIVEEISDLSATMEEVAASSDQVSAAAKQ 396
                                       334444555566666666666666666666655554 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.34
                             IFT20  19 eeteelkeeckeFvkkinefqklvkelievleelakkve 57 
                                       e ++e +ee +e ++  +e+ ++v++l + ++e+ + +e
  gi|336254771|ref|YP_004597878.1| 406 EASQEAREEMDEVLEAADELVETVSQLEDRMDEIDEVIE 444
                                       556666666666666666666666666666666666555 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0036
                             IFT20  12 vldpevaeeteelkeeckeFvkkinefqklvkelievleelakkve..keKlkA 63 
                                       v+++ev +  +e ke +++ +++++++q+ ++e+ ev+e+  ++ve  +e++ A
  gi|336254771|ref|YP_004597878.1| 476 VVANEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEgaSERIDA 529
                                       67788888888889999999999999*************999999933345544 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  10.4    0.0035       1.1     224     322 ..     300     410 ..     257     413 .. 0.75
   2 ?   -0.3  22.4       1.5   4.5e+02     119     272 ..     311     457 ..     310     501 .. 0.71
   3 ?    4.6  10.3     0.049        15     223     324 ..     478     583 ..     451     620 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0035
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...............HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.. CS
                             APG17 224 eereelleVlekDaaeledVvkelqerleem...............ekakkllsekkeeiekllsalkkaleeleev 285
                                        e+ +  +Vl++D +++ + ++e+ +++e++                ++ ++ se  +++ ++++a+++++ee++++
  gi|336254771|ref|YP_004597878.1| 300 VEYTDDHDVLDEDVTQIAETINEIAAHVEDViyglseevedlsadaAEIADSASEADSQVGEQNEAIRAIVEEISDL 376
                                       344444677777777777777777777777777777777777999888999999999999***************** PP

                                       ..HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHH CS
                             APG17 286 gkklpeylaifkaeeeflerweeekekieekleelee 322
                                       +++++e+ a   +++++ +  ++ ++  ++++e  +e
  gi|336254771|ref|YP_004597878.1| 377 SATMEEVAA---SSDQVSAAAKQAQAAADDGVEASQE 410
                                       *********...7777777777788888888777666 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                                       TTTTHHHHHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHH-------.STCCHHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 119 dsveelkealkesidelqaaqkkldssllefdtdlrelkkelsksksks.essslipellkelesleeemAslLesL 194
                                       ++v ++ e ++e+ ++++++   l+++++ ++ d +e+ ++ s+ +s+  e+++ i+ +++e ++l+  m +   s 
  gi|336254771|ref|YP_004597878.1| 311 EDVTQIAETINEIAAHVEDVIYGLSEEVEDLSADAAEIADSASEADSQVgEQNEAIRAIVEEISDLSATMEEVAAS- 386
                                       5688899999999999999999999999999999999999996555555688888888888888777777555555. PP

                                       HHHHHHHHHH................S-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 195 tnHfDqcvkAvkltegggalrraaaelseeereelleVlekDaaeledVvkelqerleemekakkllsekkeeiekl 271
                                           Dq++ A k+ + ++    + +e s+e ree+ eVle  a el + v +l++r++e+ ++ + +++ +++++ l
  gi|336254771|ref|YP_004597878.1| 387 ---SDQVSAAAKQAQAAA---DDGVEASQEAREEMDEVLEA-ADELVETVSQLEDRMDEIDEVIEVINDIADQTNLL 456
                                       ...699999977666554...455567889999******98.99999999**********99999999988887765 PP

                                       H CS
                             APG17 272 l 272
                                        
  gi|336254771|ref|YP_004597878.1| 457 A 457
                                       4 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.049
                                       CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHH CS
                             APG17 223 eeereelleVlekDaaeledVvkelqerleem....ekakkllsekkeeiekllsalkkaleeleevgkklpeylai 295
                                       ++e + l +  ++ +++++d v++lq+r ee     e+++++++   e+i++++++l ++ e ++e  + + e+ ++
  gi|336254771|ref|YP_004597878.1| 478 ANEVQSLASETKEHTNQISDRVEDLQTRTEETaevtEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITEIAET 554
                                       55666666666666778888888888888888777788888888888888888888888888888888888888887 PP

                                       HHHHHHHHHH...HHHHHHHHHHHHHHHH CS
                             APG17 296 fkaeeeflerweeekekieekleeleeLr 324
                                         ++++ +e+ +++ + ++++ + +eeL+
  gi|336254771|ref|YP_004597878.1| 555 NDDQAASVEEVASQADGVADDADRIEELI 583
                                       77788888887888888888888888775 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2  14.2       0.2        62      66     171 ..     334     440 ..     294     469 .. 0.60
   2 ?    6.8   9.2     0.015       4.7      39     117 ..     482     561 ..     473     572 .. 0.78
   3 ?   -0.6   0.1       2.8   8.5e+02      55      99 ..     561     605 ..     553     609 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.2
                         Laminin_I  66 vlakaqkvnaesertlnnakeLaekikkladnikeilekvatlne..neealpssklseelaeaqrlLeelrsRdft 140
                                        +++ +++ a++ ++  +a+e++ ++ + ++ i +i+e ++ l+   +e a++s + s++ ++aq           +
  gi|336254771|ref|YP_004597878.1| 334 LSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSAtmEEVAASSDQVSAAAKQAQAAADDG-VEASQ 409
                                       35566667777777777777777777777777777777777777767777777777777777777666554.33356 PP

                         Laminin_I 141 kqleeaeaelkaAqkLLsrvqtllqklqeen 171
                                       + +ee +++l+aA +L + v +l  ++ e  
  gi|336254771|ref|YP_004597878.1| 410 EAREEMDEVLEAADELVETVSQLEDRMDEID 440
                                       6666677777777777776666644444444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.015
                         Laminin_I  39 kskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlne.neea 114
                                       +s+++  +++ +++   +e Lq++ +++ + ++++n+++e +++++ ++ ++ +++a+ + e+   + ++ e n+++
  gi|336254771|ref|YP_004597878.1| 482 QSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAEAVDEAAHGITEIAEtNDDQ 558
                                       45566667788889999999999999999999999999999999999888888888888888888888887776665 PP

                         Laminin_I 115 lps 117
                                       ++s
  gi|336254771|ref|YP_004597878.1| 559 AAS 561
                                       554 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.8
                         Laminin_I  55 eteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnik 99 
                                        +ee + +a  v ++a  +++ + + ++++++  ++i +++d ++
  gi|336254771|ref|YP_004597878.1| 561 SVEEVASQADGVADDADRIEELIGDVTERTTAQRDAIDEMVDYLE 605
                                       578889999999999999999999999999999999999887665 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7  10.3      0.16        48     210     412 ..     315     521 ..     306     526 .. 0.49
   2 ?    3.8   8.7     0.037        11     189     338 ..     408     559 ..     387     614 .. 0.41

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.16
                          Prominin 210 hvsddLddagkhlgldladtlesnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvk...rdl 283
                                       ++ ++++++  h+ + +   +e+ v    a+ ++++++ +ea  q  + n+    + ++ s+L++ +++v    +++
  gi|336254771|ref|YP_004597878.1| 315 QIAETINEIAAHVEDVIYGLSEE-VEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAassDQV 390
                                       45555555555554444443333.34444555666666666666666666666666666666665555554111233 PP

                          Prominin 284 nqalsn.lCq....seeCskilssleiekldtskcl.dqlpnvdevlealeevletnlssivkeglarlneipekvk 354
                                       + a+++ +       e  ++++++++   l+   +l ++++++++ +++++ev+e  ++ i+  + ++l +++  ++
  gi|336254771|ref|YP_004597878.1| 391 SAAAKQaQAAaddgVEASQEAREEMDE-VLEAADELvETVSQLEDRMDEIDEVIEV-INDIA--DQTNLLALNANIE 463
                                       333333222233222334444444433.4555444444444444444444444432.22222..3344555555555 PP

                          Prominin 355 nqtaevvpdlkkalakgreqikklakkiprealdavisdle.nterssktfddvvekye 412
                                          a+   d +  +a++ + + +++k+  ++ +++ ++dl+ +te++ +  +++ e++e
  gi|336254771|ref|YP_004597878.1| 464 AAQAGEDGDGFAVVANEVQSLASETKEH-TNQISDRVEDLQtRTEETAEVTEQTNERVE 521
                                       5555555566667776666666666666.666666666666666666666666666654 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.037
                          Prominin 189 lkdvpqhidhvlvq..nyeelekhvsddLddagkhl..gldladtlesnvlpaLaelerllenlkeakeqLeqvnkl 261
                                        ++  +++d+vl+   +  e+  +++d +d++++ +  ++d+ad+ +   l+a  e ++ +e+        ++v++l
  gi|336254771|ref|YP_004597878.1| 408 SQEAREEMDEVLEAadELVETVSQLEDRMDEIDEVIevINDIADQTNLLALNANIEAAQAGEDGDGFAVVANEVQSL 484
                                       33333333333332111223333444444444433222344444444443333334444444444444444444444 PP

                          Prominin 262 ekeLrksgsqLrdglrgvkrdlnqalsn.lCqseeCskilssleiekldtskcldqlpnvdevlealeevletnlss 337
                                        +e ++ ++q++d +++ +++ +++++  + ++e+ + ++++ ++ + ++++     + vde  ++++e+ etn ++
  gi|336254771|ref|YP_004597878.1| 485 ASETKEHTNQISDRVEDLQTRTEETAEVtEQTNERVEGASERIDAAIANLEEIA---EAVDEAAHGITEIAETNDDQ 558
                                       444444444444444444444444444422222222222222222222222222...22333333333333333222 PP

                          Prominin 338 i 338
                                       +
  gi|336254771|ref|YP_004597878.1| 559 A 559
                                       2 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.4      0.56   1.7e+02      81     174 ..     252     362 ..     242     372 .. 0.61
   2 ?   -0.1  11.4         2     6e+02      88     179 ..     326     423 ..     296     466 .. 0.58
   3 ?   11.4   5.7   0.00059      0.18      86     179 ..     478     569 ..     473     616 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.56
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..................XXXXXXXXXXXXXXXXXXX CS
                              LUC7  81 yeeeflrfleklledvdrkiqkgkqrleltqeekeeeeeaka..............kkqeqlkeleekiekllaeae 143
                                       y++e l+ + +l++d  + i++ ++  +l  e +e+ e+ +                 +e++ ++ e+i++  a++e
  gi|336254771|ref|YP_004597878.1| 252 YQQESLQGVIQLVQDNTEVIRRREAMADLVGEVTETGEAINDgslaarveytddhdVLDEDVTQIAETINEIAAHVE 328
                                       78888888888888888888888887777766665555554467788886666555556777777888888777777 PP

                                       XX..XXXXXXXX.XXXXXXXXXXXXXXXXXXXXX CS
                              LUC7 144 el..geeGkVde.aqklmkeveelkeekeeleqq 174
                                           g + +V++ + +  + ++   e  +++ +q
  gi|336254771|ref|YP_004597878.1| 329 DViyGLSEEVEDlSADAAEIADSASEADSQVGEQ 362
                                       6422444444321333333333344434443333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX... CS
                              LUC7  88 fleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekllaeaeelg.eeGkVdeaqklmke... 160
                                       ++e+++  + + ++   +  ++ +++ +e++++  +++e ++ + e+i++l a +ee + ++++V+ a k  +    
  gi|336254771|ref|YP_004597878.1| 326 HVEDVIYGLSEEVEDLSADAAEIADSASEADSQVGEQNEAIRAIVEEISDLSATMEEVAaSSDQVSAAAKQAQAaad 402
                                       33333333344444444444444444444444444888888888888888888888754156677766655543111 PP

                                       ..XXXXXXXXXXXXXXXXXX. CS
                              LUC7 161 ..veelkeekeeleqqyeaaa 179
                                         ve  +e +ee+++  eaa 
  gi|336254771|ref|YP_004597878.1| 403 dgVEASQEAREEMDEVLEAAD 423
                                       123444444555544444433 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00059
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              LUC7  86 lrfleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekllaeaeelgeeGkVdeaqklmkeve 162
                                       ++++++l ++ ++  ++  +r+e+ q+++ee++e +++++e+++  +e+i+  +a+ ee +e   Vdea + ++e+ 
  gi|336254771|ref|YP_004597878.1| 478 ANEVQSLASETKEHTNQISDRVEDLQTRTEETAEVTEQTNERVEGASERIDAAIANLEEIAE--AVDEAAHGITEIA 552
                                       57889999999999*********99999999999999**********************886..6***********9 PP

                                       XXXXXXXXXXXXXXXX. CS
                              LUC7 163 elkeekeeleqqyeaaa 179
                                       e +  +++  +++ ++a
  gi|336254771|ref|YP_004597878.1| 553 ETNDDQAASVEEVASQA 569
                                       99999988887776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2271  (0.126666); expected 358.6 (0.02)
Passed bias filter:                      818  (0.0456244); expected 358.6 (0.02)
Passed Vit filter:                       186  (0.0103743); expected 17.9 (0.001)
Passed Fwd filter:                       133  (0.00741815); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              59  [number of targets reported over threshold]
# CPU time: 1.91u 0.38s 00:00:02.29 Elapsed: 00:00:00.58
# Mc/sec: 3220.72
//
Query:       gi|336254772|ref|YP_004597879.1|  [L=428]
Description: Histidinol dehydrogenase [Halopiger xanaduensis SH-6]
Scores for complete 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-157  525.0   7.3   1.6e-157  524.8   7.3    1.0  1  Histidinol_dh  Histidinol dehydrogenase
  ------ inclusion threshold ------
        3.7    7.8   8.2       0.84    9.9   2.0    3.0  3  GGDEF_2        GGDEF-like domain


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 !  524.8   7.3  1.8e-161  1.6e-157       8     409 .]      26     424 ..      21     424 .. 0.98

  Alignments for each domain:
  == domain 1  score: 524.8 bits;  conditional E-value: 1.8e-161
                                       -HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC-- CS
                     Histidinol_dh   8 seeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaqke 84 
                                        e+v++ v+ei+e+vreeGd a++e+te+FD v+ + +l++++ e+e+a+e+lde+l+ea+e+aa+n+r+fheaq++
  gi|336254772|ref|YP_004597879.1|  26 IEAVRSDVREIVERVREEGDVAVREFTEEFDDVS-VGNLEITD-ECERAYEDLDEDLREAIETAAANVREFHEAQVP 100
                                       678999*************************774.67899998.89******************************9 PP

                                       --EEEEEECTTEEEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SSGG.--HHHHHHHHHCT CS
                     Histidinol_dh  85 seeevketepgvvlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpqdgkvnpavlaaaklag 161
                                       + ++ +  ++g  lg+++rp+ervG+YvPgG aaypS+++m +vpA vAgv++++vvtPp+ +++npa+laa++ ag
  gi|336254772|ref|YP_004597879.1| 101 E-DWREAFDDGRELGRRFRPLERVGVYVPGGAAAYPSSAIMGVVPAVVAGVDHVAVVTPPA-DELNPATLAAIHAAG 175
                                       5.8999******************************************************7.69************* PP

                                       -SEEEE--HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHHHHHH CS
                     Histidinol_dh 162 vdeiykvGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvAaDLl 238
                                       +d++y+vGGaqAia lAyGte+i+ v+kivGPGn++V+aAK  v+g+v+iD++aGPsEvlv+aDetadpe+vAa+L+
  gi|336254772|ref|YP_004597879.1| 176 ADAVYSVGGAQAIAGLAYGTETITCVQKIVGPGNKWVTAAKAEVRGDVEIDFLAGPSEVLVVADETADPELVAAELV 252
                                       ***************************************************************************** PP

                                       HHHTT-TT-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCC.H-EEEE-SSHHHHHHHHHHH--SEEEEES CS
                     Histidinol_dh 239 sqaEHdedaqavlvttseelaeaveeevekqleelprkeiaekslek.qsaiilvedleeaielaneyApEHlelqv 314
                                       +qaEHd++a++v vt++e++a+av+++v++q+++ +r+++++++l++  s ++++++++e+i +a+eyApEHl++ +
  gi|336254772|ref|YP_004597879.1| 253 AQAEHDPNASVVAVTDDEATADAVAAAVDEQANAREREDTIREALANdASGVLVARSMSEVILFAEEYAPEHLSIIA 329
                                       **********************************************98999************************** PP

                                       TTHHHHGGG--S-SEEEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHHHHHHHH CS
                     Histidinol_dh 315 edpeellekiknaGaiflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkelaeavet 391
                                       +d e++le+i++aG++flG+++p+++gDYa+GtnhvLPT+g Ar+++glsve+F+++++vq+ls+++l++l+++++t
  gi|336254772|ref|YP_004597879.1| 330 DDDESILERIDSAGSVFLGPNTPVAAGDYASGTNHVLPTNGGARVTGGLSVETFVRSTTVQRLSSDGLAALGDTITT 406
                                       ***************************************************************************** PP

                                       HHHHTT-HHHHHHHHHHH CS
                     Histidinol_dh 392 lAeaEgLeaHaeavkvRl 409
                                       lAeaEgLeaHae+v+ Rl
  gi|336254772|ref|YP_004597879.1| 407 LAEAEGLEAHAESVRKRL 424
                                       ***************996 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.4   1.3e+04      34      45 ..      77      88 ..      63      95 .. 0.57
   2 ?   -1.1   0.1      0.24   2.1e+03      59      92 ..     151     183 ..     140     196 .. 0.50
   3 ?    9.9   2.0   9.4e-05      0.84      25     100 ..     275     362 ..     228     366 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.4
                           GGDEF_2 34 aerllraleeal 45
                                      +e+l++a+e+a+
  gi|336254772|ref|YP_004597879.1| 77 DEDLREAIETAA 88
                                      233444444444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.24
                           GGDEF_2  59 drlvlllpaedeedaeallerlarrlgglsvriG 92 
                                       d++ ++ p +de +  a l++++++ ++  +++G
  gi|336254772|ref|YP_004597879.1| 151 DHVAVVTPPADELN-PATLAAIHAAGADAVYSVG 183
                                       44445555444422.2444444444444333333 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 9.4e-05
                           GGDEF_2  25 vvvielee..daerllraleealralgpdalvavrgdrlvlllpaedeedae.......allerlarrlgg...lsv 89 
                                       +v++ ++e  +a++  ++++eal++ + ++lva   ++++l+    ++e+++        +ler+ ++ +     + 
  gi|336254772|ref|YP_004597879.1| 275 AVAAAVDEqaNAREREDTIREALANDASGVLVARSMSEVILFAEEYAPEHLSiiadddeSILERIDSAGSVflgPNT 351
                                       3444445545777799*************************999888755555555555999999988777777888 PP

                           GGDEF_2  90 riGiGspvegl 100
                                        +++G++++g 
  gi|336254772|ref|YP_004597879.1| 352 PVAAGDYASGT 362
                                       88888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); 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 0.24s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3255.01
//
Query:       gi|336254773|ref|YP_004597880.1|  [L=73]
Description: hypothetical protein Halxa_3389 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0064   16.8   3.5     0.0072   16.6   3.5    1.1  1  DUF4233       Protein of unknown function (DUF4233)
  ------ inclusion threshold ------
       0.49   10.2   7.6       0.53   10.1   7.6    1.2  1  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr


Domain annotation for each model (and alignments):
>> DUF4233  Protein of unknown function (DUF4233)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   3.5   8.1e-07    0.0072      33      81 ..       9      57 ..       2      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.1e-07
                           DUF4233 33 vlsvggvlavallllagllrrpwglalglvlQvlliaagfvvpamfvvg 81
                                      ++++g++l+va +++ g+ r  +g  l  +lQ++li+agf++ + ++v 
  gi|336254773|ref|YP_004597880.1|  9 LAAIGFALVVASFVVRGVARLVVGRELAELLQAPLIFAGFALLVYLFVR 57
                                      567889************************************9777765 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 ?   10.1   7.6   5.9e-05      0.53      47      73 ..       8      34 ..       3      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.9e-05
                      Trp_oprn_chp 47 alAlvllAaavAvlavrglgrrvvgvl 73
                                       lA ++ A +vA ++vrg++r vvg  
  gi|336254773|ref|YP_004597880.1|  8 KLAAIGFALVVASFVVRGVARLVVGRE 34
                                      5899********************963 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 574.90
//
Query:       gi|336254774|ref|YP_004597881.1|  [L=233]
Description: hypothetical protein Halxa_3390 [Halopiger xanaduensis SH-6]
Scores for 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  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1772.24
//
Query:       gi|336254775|ref|YP_004597882.1|  [L=52]
Description: hypothetical protein Halxa_3391 [Halopiger xanaduensis SH-6]
Scores for 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:                       164  (0.00914719); expected 358.6 (0.02)
Passed bias filter:                      107  (0.00596798); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 429.39
//
Query:       gi|336254776|ref|YP_004597883.1|  [L=103]
Description: hypothetical protein Halxa_3392 [Halopiger xanaduensis SH-6]
Scores for 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   16.8   0.2     0.0062   16.4   0.2    1.2  1  DUF4032   Domain of unknown function (DUF4032)


Domain annotation for each model (and alignments):
>> DUF4032  Domain of unknown function (DUF4032)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   3.4e-07    0.0062      44      98 ..      42      95 ..      25     101 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.4e-07
                           DUF4032 44 dgerlrlrpkvvdaghhrrrLlrLTGldveenQArrlLndlesyraelekeevde 98
                                        +r+rl+++  d+   ++  +++T l+    QAr l  dle+y  + e+ ++d 
  gi|336254776|ref|YP_004597883.1| 42 APDRVRLQVEL-DNATEEHLPKHMTELELTPDQARTLAADLETYAEQVEDGSADG 95
                                      33466666554.44444555589**********************9998776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 905.62
//
Query:       gi|336254777|ref|YP_004597884.1|  [L=164]
Description: hypothetical protein Halxa_3393 [Halopiger xanaduensis SH-6]
Scores for 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-45  152.9  11.4      8e-45  152.7  11.4    1.0  1  DUF892           Domain of unknown function (DUF892)
    0.00092   19.2  13.3     0.0023   17.9  13.2    1.7  1  Ferritin         Ferritin-like domain
  ------ inclusion threshold ------
       0.13   13.0   8.1        2.1    9.1   0.6    3.1  2  Vir_act_alpha_C  Virulence activator alpha C-term
       0.21   12.0   4.8       0.92    9.9   0.4    2.3  2  DUF2383          Domain of unknown function (DUF2383)
       0.28   11.7   6.6        3.8    8.0   0.5    2.4  2  FlgN             FlgN protein


Domain annotation for each model (and alignments):
>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.7  11.4   2.2e-48     8e-45       1     152 [.       5     155 ..       5     161 .. 0.96

  Alignments for each domain:
  == domain 1  score: 152.7 bits;  conditional E-value: 2.2e-48
                                       ..HHHHHHHHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-------.-HHHHTT CS
                            DUF892   1 tleelfvdeLrDlyaaEkqllkalpkmakaaespeLkaaleqHleeTegqierLeqvferlgesasekkcdamegli 77 
                                       t+++lf + L+D+y+aE+qll+al+++ ++ e++e+++a+ +H eeT+gqi+rLe+vfe+ ge +++++c+++egl+
  gi|336254777|ref|YP_004597884.1|   5 TIQDLFEHGLEDIYHAEHQLLDALEDLEENTERDEIASAFSEHREETQGQIDRLEEVFEMFGEPPEKEECEGIEGLL 81 
                                       689************************************************************************** PP

                                       T-----------THHHHHHH...HHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            DUF892  78 aegqelieeaaedeslkdaaliaaaqavehyEiAsYgtLialAeqlgekeaaklLeqtleeekatdekltelaes 152
                                       +e +e+  +    +++ d    aaa + ehyEiA+Yg Li lA+qlg++eaa+lLe++l ee+++ e l+el e+
  gi|336254777|ref|YP_004597884.1|  82 EEYEEFESM-DPSQEVMDYHNMAAAEKTEHYEIAAYGNLIPLADQLGMDEAADLLEENLREEQDALEELKELTEQ 155
                                       *****9888.55566999999***************************************************986 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  13.2   6.4e-07    0.0023      10     140 ..      16     157 ..       7     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.4e-07
                                       HHHHHHHHHHHHHHHHH.STTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH.............. CS
                          Ferritin  10 deltaayqylamawyvk.gpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee.............. 71 
                                       d ++a +q l     ++ +++++++a  f e+ ee ++++d+l e   ++G+     + e ee              
  gi|336254777|ref|YP_004597884.1|  16 DIYHAEHQLLDALEDLEeNTERDEIASAFSEHREETQGQIDRLEEVFEMFGE-----PPEKEEcegieglleeyeef 87 
                                       556666666666666667999******************************9.....66666666666776665555 PP

                                       ..C-SSSSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  72 ..ieapkefgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekle 140
                                          ++ +e+ + ++ ++aa + e + ++++ +li la++ g +  ad+le+ l+e+++ ++el++l e+ e
  gi|336254777|ref|YP_004597884.1|  88 esMDPSQEVMDYHN-MAAAEKTEHYEIAAYGNLIPLADQLGMDEAADLLEENLREEQDALEELKELTEQYE 157
                                       43333333323333.4667777888899*************************************998866 PP

>> Vir_act_alpha_C  Virulence activator alpha C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.3     0.005        18      15      43 ..      35      63 ..      31     114 .. 0.81
   2 ?    9.1   0.6   0.00057       2.1      11      45 ..     122     156 ..     120     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.005
                   Vir_act_alpha_C 15 ldpealieeLerrreeheekLaeyeeiee 43
                                       ++++++  + ++ree + +++++ee  e
  gi|336254777|ref|YP_004597884.1| 35 TERDEIASAFSEHREETQGQIDRLEEVFE 63
                                      678999999*************9997654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00057
                   Vir_act_alpha_C  11 aaavldpealieeLerrreeheekLaeyeeieerl 45 
                                       +a++l+ ++++++Le+ ++e ++ L+e++e+ e++
  gi|336254777|ref|YP_004597884.1| 122 LADQLGMDEAADLLEENLREEQDALEELKELTEQY 156
                                       68999************************999886 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4   0.00026      0.92       6      64 ..      14      72 ..      10      86 .. 0.86
   2 ?    4.1   0.4     0.016        57      80     110 ..     124     154 ..      97     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00026
                                      HHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT------ CS
                           DUF2383  6 LndLietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiralggepedg 64
                                      L+d+  +++   ++ +   e+ +++++++++ ++ ee + ++++L++  + +g+ pe++
  gi|336254777|ref|YP_004597884.1| 14 LEDIYHAEHQLLDALEDLEENTERDEIASAFSEHREETQGQIDRLEEVFEMFGEPPEKE 72
                                      6666777777778888999***************************9999999888875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.016
                                       -------HHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF2383  80 saltsndeeaileeleegEdkaleeyeeale 110
                                       + l+ ++ + +lee  ++E+ alee++e  e
  gi|336254777|ref|YP_004597884.1| 124 DQLGMDEAADLLEENLREEQDALEELKELTE 154
                                       5566666667999999999999999998765 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.0    0.0025       9.1      39      76 ..      13      53 ..       6      90 .. 0.72
   2 ?    8.0   0.5    0.0011       3.8       4      27 ..     132     155 ..      99     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0025
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--...SCHHH CS
                              FlgN 39 aLeelleekqellekleqleqkrakllaelgls...aeeat 76
                                      +Le++ + +++ll++le le++ ++   + + s   +e+++
  gi|336254777|ref|YP_004597884.1| 13 GLEDIYHAEHQLLDALEDLEENTERDEIASAFSehrEETQG 53
                                      6999999***********99988877777777754533333 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0011
                                       HCHHHHHHHHHHHHHHHHHHHHHH CS
                              FlgN   4 leeLielleeelelleeLlellee 27 
                                        + L e+l+ee+++leeL+el+e+
  gi|336254777|ref|YP_004597884.1| 132 ADLLEENLREEQDALEELKELTEQ 155
                                       556778888888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1441  (0.0803726); expected 358.6 (0.02)
Passed bias filter:                      752  (0.0419432); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 1315.66
//
Query:       gi|336254778|ref|YP_004597885.1|  [L=43]
Description: hypothetical protein Halxa_3394 [Halopiger xanaduensis SH-6]
Scores for 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:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); 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):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 379.78
//
Query:       gi|336254779|ref|YP_004597886.1|  [L=159]
Description: ribosomal-protein-alanine acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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   66.7   0.0    2.6e-18   66.3   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.2e-12   46.5   0.0    3.5e-12   46.4   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    6.2e-12   45.8   0.0    9.2e-12   45.2   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.4e-08   34.1   0.0    5.4e-08   33.0   0.0    1.6  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    5.8e-08   32.6   0.0    1.6e-07   31.2   0.0    1.8  2  FR47             FR47-like protein
     0.0022   17.7   0.0     0.0034   17.1   0.0    1.2  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.011   16.4   0.0      0.016   15.9   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
       0.14   11.7   0.0       0.15   11.6   0.0    1.1  1  GNAT_acetyltran  GNAT acetyltransferase
       0.18   11.9   0.0       0.23   11.6   0.0    1.2  1  Acetyltransf_4   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 !   66.3   0.0   1.3e-21   2.6e-18       2     117 .]      24     135 ..      23     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 1.3e-21
                                       HHHHHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHH CS
                    Acetyltransf_1   2 rdlvellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlG 78 
                                       +++v+++++sf  p++ + +e+f      e+++l++ + d e++G++         ++ ++i ++aV+pe+rg G+G
  gi|336254779|ref|YP_004597886.1|  24 LAVVRIENASFAQPWPYDAFERFLG----EPGFLVATKGDTEVVGYVISDVSSTYGRELGHIKDVAVHPEHRGDGVG 96 
                                       5688899999888888888888333....3555555677778*****888888888899****************** PP

                                       HHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  79 saLlealeerareegikkivlaveedndaairlYeklGF 117
                                       saLl   +  + ++g++ i l+v+ +nd+a rlY+++GF
  gi|336254779|ref|YP_004597886.1|  97 SALLSRSIAVLASRGADSIKLEVRRTNDGAKRLYREFGF 135
                                       **********************************66**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   1.7e-15   3.5e-12      20     110 ..      41     141 ..      19     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.7e-15
                   Acetyltransf_10  20 ealrerieegealllvaeeggkivGvi......elrdgs....hisllfVdpeyrgqGigkaLleaveeeaekdgik 86 
                                       +a+++ +  +  +l++ + ++++vG++      ++   +    hi  ++V+pe+rg G+g+aLl + ++ +  +g  
  gi|336254779|ref|YP_004597886.1|  41 DAFERFL-GEPGFLVATKGDTEVVGYVisdvssTY---GrelgHIKDVAVHPEHRGDGVGSALLSRSIAVLASRGAD 113
                                       5555555.6666778888889999**977443222...26677***************************8888888 PP

                   Acetyltransf_10  87 l.eltvnasp.yavpfYeklGFkav..g 110
                                         +l+v+ ++  a+++Y+ +GF+++   
  gi|336254779|ref|YP_004597886.1| 114 SiKLEVRRTNdGAKRLYREFGFEPLrrV 141
                                       89*********************98433 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   4.6e-15   9.2e-12       5      76 .]      52     137 ..      48     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 4.6e-15
                                       EEEEEET.TEEEEEEEEEEES......TCTEEEEE-GGGTTSSHHHHHHH..HTT....SE...EEEEEEEE..THH CS
                    Acetyltransf_7   5 vfVaedd.gkivGfialslld......aeitrlaVdpeyrgkGiGraLle..aae....kg...iileqlel..nae 63 
                                       ++Va ++  ++vG+++  +++      ++i+ +aV+pe+rg G+G+aLl   + +    +g   i+le   +  +++
  gi|336254779|ref|YP_004597886.1|  52 FLVATKGdTEVVGYVISDVSStygrelGHIKDVAVHPEHRGDGVGSALLSrsI-AvlasRGadsIKLE---VrrTND 124
                                       66777766788898887777699877677777*****************8431.13445552223333...222233 PP

                                       HHHHHHHHTTEEE CS
                    Acetyltransf_7  64 kaikfYeklGFee 76 
                                        a ++Y+ +GFe+
  gi|336254779|ref|YP_004597886.1| 125 GAKRLYREFGFEP 137
                                       99*********95 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   2.7e-11   5.4e-08       2     127 ..      15     137 ..      14     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.7e-11
                                       EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEE CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtg 78 
                                       ir+++ +dl +v+++ +++F++  ++      +f++ l+e  +l+a ++++ v  + + +++ + +G+  + + + +
  gi|336254779|ref|YP_004597886.1|  15 IRPAERADLLAVVRIENASFAQPWPY-----DAFERFLGEPGFLVATKGDTEVVGYVISDVSST-YGR--ELGHIKD 83 
                                       8999999*************999999.....478999999999999998887777777777765.454..579**** PP

                                       EEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSH.....HHHHTTT-EE CS
                    Acetyltransf_9  79 VavapehrgrgvlskLlaraleemreegqplsllfPssi.....piYrrfGyei 127
                                       Vav+pehrg gv s+Ll r+++ ++++g+  + l  ++      ++Yr fG+e+
  gi|336254779|ref|YP_004597886.1|  84 VAVHPEHRGDGVGSALLSRSIAVLASRGADSIKLEVRRTndgakRLYREFGFEP 137
                                       ********************************9999554455569******996 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.8   3.5e+03      48      60 ..       3      15 ..       1      32 [. 0.59
   2 !   31.2   0.0   7.8e-11   1.6e-07      19      79 ..      76     137 ..      54     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.8
                                      HHHHHS-S-EEEE CS
                              FR47 48 keiaergktvllv 60
                                        i  rg++++++
  gi|336254779|ref|YP_004597886.1|  3 TSIPDRGDDAFAI 15
                                      5566666666654 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 7.8e-11
                                       -TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EE CS
                              FR47  19 kdggelgalqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfek 79 
                                       ++ g +  + v+pehr+ G gs l +  ++ +a rg +++ l v+ +N+ + rly   Gfe 
  gi|336254779|ref|YP_004597886.1|  76 RELGHIKDVAVHPEHRGDGVGSALLSRSIAVLASRGADSIkLEVRRTNDGAKRLYREFGFEP 137
                                       56799999****************9999999999997765388*****************86 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.7e-06    0.0034      88     143 ..      87     141 ..      81     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-06
                                       SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEE CS
                    Acetyltransf_8  88 eaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekekev 143
                                        +e+rg g+++all++ ++ l ++ +++++ +E + +N  a rl+++ Gfe+ ++v
  gi|336254779|ref|YP_004597886.1|  87 HPEHRGDGVGSALLSRSIAVLASR-GADSIKLEVRRTNDGAKRLYREFGFEPLRRV 141
                                       5899**************988777.**************************98876 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0   7.9e-06     0.016      52     138 .]      50     136 ..      13     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.9e-06
                    Acetyltransf_3  52 egygwaivlkdtgv.iGsvglrdleeedee.aelg.ymlapsfwgkGyateavralleyafeelglerlvavidkeN 125
                                        g  +++ +k++ + +G+v     +   +e +++    ++p+++g G+++  ++  + ++ +  g++ +  ++  +N
  gi|336254779|ref|YP_004597886.1|  50 PG--FLVATKGDTEvVGYVISDVSSTYGRElGHIKdVAVHPEHRGDGVGSALLSRSIAVL-ASRGADSIKLEVRRTN 123
                                       33..777665554449999555444444435677678899********************.5556************ PP

                    Acetyltransf_3 126 eaSirvleklGfe 138
                                        +  r+++  Gfe
  gi|336254779|ref|YP_004597886.1| 124 DGAKRLYREFGFE 136
                                       ************7 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.5e-05      0.15     166     213 ..      64     111 ..      26     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.5e-05
                   GNAT_acetyltran 166 geivsgasSysvyekgieieidTkedyrrkgLAtivaaalileclkrg 213
                                       g ++s +sS+   e g+  +++ ++++r+ g  +++ ++ i     rg
  gi|336254779|ref|YP_004597886.1|  64 GYVISDVSSTYGRELGHIKDVAVHPEHRGDGVGSALLSRSIAVLASRG 111
                                       5689*****************************999999998777776 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.23      79     148 ..      81     149 ..      41     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                    Acetyltransf_4  79 elsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkng 148
                                       +  v + +   +  g+g++l+   + vl+  +  ++  e+  +n+ ++ ++ ++GFe ++++ +++++  
  gi|336254779|ref|YP_004597886.1|  81 IKDVAV-HPEHRGDGVGSALLSRSIAVLASRGADSIKLEVRRTNDGAKRLYREFGFEPLRRVPDYYEDDE 149
                                       445555.466788899999999999***********************************9999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); 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: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1390.86
//
Query:       gi|336254780|ref|YP_004597887.1|  [L=164]
Description: hypothetical protein Halxa_3396 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0025   17.6   0.1     0.0048   16.7   0.1    1.4  1  zf-C2H2_9      C2H2 type zinc-finger (1 copy)
  ------ inclusion threshold ------
        1.2    9.9   5.6       0.45   11.3   2.2    2.0  2  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> zf-C2H2_9  C2H2 type zinc-finger (1 copy)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   5.4e-07    0.0048       4      37 ..       5      38 ..       3      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.4e-07
                                      -TTT--B-SSHHHHHHHHHHHTSSS--HHHHHHH CS
                         zf-C2H2_9  4 CPvCevkfnswkdlseHilsaasksdaeHvmWLN 37
                                      CPvC  +  + k+l++H+ ++as   +eH  WL 
  gi|336254780|ref|YP_004597887.1|  5 CPVCDAEEADAKHLANHLAITASLGRQEHEDWLE 38
                                      ********************************95 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.33   2.9e+03      45      56 ..      45      56 ..      11      78 .. 0.59
   2 ?   11.3   2.2     5e-05      0.45      31      81 ..      90     148 ..      89     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.33
                                      X--HHHHHHHHH CS
                     PSK_trans_fac 45 aepllerllall 56
                                       e++ e+l ++ 
  gi|336254780|ref|YP_004597887.1| 45 PERSPEELGEIV 56
                                      344445555555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5e-05
                                       XXXXXXXXXXXXX........XX--HHHHHHHHHHHHHTS--SS-SSTTSTTTXXXXXX CS
                     PSK_trans_fac  31 rAleerlerlrre........raepllerllallrraaakaekedrspdekllyDeegl 81 
                                        Ale++l+r  r+        +ae +le+ ++l r++++ ++ + +s+ e++  D eg+
  gi|336254780|ref|YP_004597887.1|  90 PALENELARQSRQpgrgsltaEAEGVLEEARELTRQMRESDGGAGESASEAADADGEGG 148
                                       59*********99**************************77777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1307.69
//
Query:       gi|336254781|ref|YP_004597888.1|  [L=158]
Description: hypothetical protein Halxa_3397 [Halopiger xanaduensis SH-6]
Scores for 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   13.2   1.5       0.19   12.3   0.4    1.8  2  Reductase_C  Reductase C-terminal


Domain annotation for each model (and alignments):
>> Reductase_C  Reductase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.14   2.4e+03      19      34 ..      24      39 ..      22      65 .. 0.64
   2 ?   12.3   0.4   1.1e-05      0.19       3      77 ..      78     150 ..      77     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.14
                                      T--EEEEEEETTTTEE CS
                       Reductase_C 19 gadevvvRgdpeeraf 34
                                      +a+++vvR+ +++ +f
  gi|336254781|ref|YP_004597888.1| 24 PAAQTVVREVAKAMSF 39
                                      5678888887764443 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.1e-05
                                       EEEETTEEEEEEE--TT--EEEEEEETTTTEEEEEEEETTEEEEEEEES-HHHHHHHHHHTTTT----HHHHH-T CS
                       Reductase_C   3 WSDqydlklQiaGlatgadevvvRgdpeerafsvfylrdgrlvaveavnrprdlmaarrliaagasvdpaalaDp 77 
                                       W D y   + ++G+ ++ ++vv+   pe+ + ++  +++++  a++++ r++  +++r++++  a+ d++  aD+
  gi|336254781|ref|YP_004597888.1|  78 WRDSYAGDVTTVGHENA-ARVVWHAGPED-EAVAATFQEKEDAAIATLRRQAFGRLYREIVTPDAATDADVDADA 150
                                       999**********8765.569***99995.5555688999999**************************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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 0.19s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1399.16
//
Query:       gi|336254782|ref|YP_004597889.1|  [L=203]
Description: NUDIX hydrolase [Halopiger xanaduensis SH-6]
Scores for complete 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   1.5    2.7e-15   56.6   1.5    1.4  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 !   56.6   1.5   1.5e-19   2.7e-15      12     121 ..      77     183 ..      74     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.5e-19
                                       ETTSEEEEEEESSSSTTT..EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE.EEEEE CS
                             NUDIX  12 nekgevLlvrrskkpfpg..WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd.eheil 85 
                                       ++++++L v++++ + ++   elP+G ve+gE++ +AA REleEEtG+++  + ll+   + a  +g     +h   
  gi|336254782|ref|YP_004597889.1|  77 DPEDRLLFVEQFRPTIREthLELPAGIVEDGESFTAAAERELEEETGFRPTSTALLQ---EYAVATG---VlRHTRG 147
                                       566779****995555555468****************************9999999...2222222...2568888 PP

                                       EEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTH CS
                             NUDIX  86 yvfl.eevegelepndenevsevrwvpleellkekla 121
                                       +v++ + + ge e++ +ne+ ev  vp++e+l+ + +
  gi|336254782|ref|YP_004597889.1| 148 VVYAeGLEPGERELD-SNEFLEVTTVPVDEALERARE 183
                                       888867777777777.***************333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1613.20
//
Query:       gi|336254783|ref|YP_004597890.1|  [L=125]
Description: Rhodanese-like protein [Halopiger xanaduensis SH-6]
Scores for 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-12   46.6   0.0    4.7e-12   46.4   0.0    1.1  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   2.6e-16   4.7e-12       1     105 [.       6      99 ..       6     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.6e-16
                         Rhodanese   1 sakelkell.ekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgg 76 
                                       s++++k+ll ++ +v+++D+R+++ +e++hIpg+ nv             p+ el  ++ e    + +++v++c +g
  gi|336254783|ref|YP_004597890.1|   6 SPDDVKDLLeADADVRIVDIRDENSFEHSHIPGSENV-------------PFHELTSRIDEF--EDADRIVTVCPHG 67 
                                       6899*****6666666*********************.............***********9..************* PP

                         Rhodanese  77 graaaaaallk.k...lGyknvsvldGGfkawk 105
                                       + + +aa+l+  +   +   +v  + GG++++ 
  gi|336254783|ref|YP_004597890.1|  68 KASVQAAQLIGsYegtAD-ATVESMAGGLEKYG 99 
                                       **9999888874444344.77********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1022.49
//
Query:       gi|336254784|ref|YP_004597891.1|  [L=97]
Description: translation initiation factor SUI1 [Halopiger xanaduensis SH-6]
Scores for 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-22   78.6   0.0    4.7e-22   78.3   0.0    1.1  1  SUI1      Translation initiation factor SUI1
     0.0022   18.3   0.0     0.0028   17.9   0.0    1.4  1  Img2      Mitochondrial large subunit ribosomal protein (Img2
     0.0081   15.9   0.4       0.01   15.6   0.4    1.1  1  DTW       DTW domain


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 !   78.3   0.0   7.9e-26   4.7e-22       2      76 ..      24      94 ..      23      95 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 7.9e-26
                              SUI1  2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygv 76
                                      +++++ir+++r+ +K vT+v+g++++++dl++l+++lk+kfac+g+v +dg  +i++QG++  +++e+L ++ g+
  gi|336254784|ref|YP_004597891.1| 24 QQQLNIRIDERRYGKEVTIVEGFDPKDVDLDSLSSDLKSKFACGGTV-EDG--QIELQGNHTGRIEEFLRDR-GF 94
                                      7899******************************************9.999..9****************99.87 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 !   17.9   0.0   4.7e-07    0.0028      36      80 .]      52      94 ..      14      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.7e-07
                              Img2 36 DiaalredLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                      D+  l +dL++ ++  +  + + g+ie++G+++ ++++fL+++gF
  gi|336254784|ref|YP_004597891.1| 52 DLDSLSSDLKSKFA--CGGTVEDGQIELQGNHTGRIEEFLRDRGF 94
                                      66677777777777..7777799*********************9 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   1.7e-06      0.01       2      29 ..       3      31 ..       2      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                               DTW  2 elCerCllpaevclcsslpp.leklpikv 29
                                      e+C +C lp+e+c+c+ + +  ++l+i++
  gi|336254784|ref|YP_004597891.1|  3 EVCSTCGLPEELCVCEDVAKgQQQLNIRI 31
                                      68*****************9666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.33
# Mc/sec: 873.13
//
Query:       gi|336254785|ref|YP_004597892.1|  [L=797]
Description: transglutaminase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-28   99.4   0.0    3.6e-28   98.2   0.0    1.6  1  Transglut_core   Transglutaminase-like superfamily
    6.5e-09   35.9   8.1    6.5e-09   35.9   8.1    2.9  2  DUF4129          Domain of unknown function (DUF4129)
    3.3e-05   23.8   0.2    0.00034   20.5   0.0    2.4  2  Transglut_core3  Transglutaminase-like superfamily
     0.0002   20.4   0.0     0.0002   20.4   0.0    2.8  3  DUF3488          Domain of unknown function (DUF3488)
  ------ inclusion threshold ------
       0.37   10.7   7.7        0.6   10.0   7.7    1.3  1  SPX              SPX domain
       0.45    9.3   3.7       0.62    8.8   3.7    1.1  1  Apt1             Golgi-body localisation protein domain
       0.89    8.7   4.1        1.5    7.9   4.1    1.3  1  SOG2             RAM signalling pathway protein
       0.93    7.7   5.6        1.3    7.2   5.6    1.1  1  CDC45            CDC45-like protein
        1.5    7.5   3.8        2.5    6.8   3.8    1.3  1  Presenilin       Presenilin
        5.9    6.9  14.3         17    5.4  14.3    1.8  1  Trypan_PARP      Procyclic acidic repetitive protein (PARP)
        7.3    6.3   7.9        4.3    7.0   5.8    1.7  2  7tm_3            7 transmembrane sweet-taste receptor of 3 GC


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 !   98.2   0.0   2.2e-31   3.6e-28       3     112 .]     421     533 ..     419     533 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 2.2e-31
                    Transglut_core   3 laeeltagakdplekakaiyewvrknveysaprrtpgsrdaeavle.tgkGncedfaslfvallRalGipaRvvtgy 78 
                                        ++e+ta+a++p+e a+ +++++r++ +ys +   p+++ ae++l     G+c  fa++++ +lR  GipaR+vtgy
  gi|336254785|ref|YP_004597892.1| 421 RTAEITASATTPYETARIVENHLRSSKSYSLDIERPEGDVAESFLLeMDEGYCVYFATAMTQMLRTEGIPARYVTGY 497
                                       5789**************************77777777779999887899*************************** PP

                    Transglut_core  79 lsgeeekeq..svasedaHawvevylegygWvplDp 112
                                       + ge+ +e+   v++ +aHawvevy++g+gWvp+Dp
  gi|336254785|ref|YP_004597892.1| 498 TTGEQVGEDeyLVRGVNAHAWVEVYFPGQGWVPFDP 533
                                       ***998888999***********************9 PP

>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.6   4.2e+03       4      24 ..     479     501 ..     477     518 .. 0.81
   2 !   35.9   8.1     4e-12   6.5e-09       1      66 [.     702     780 ..     702     783 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.6
                           DUF4129   4 allraLaergldrr..pgeTprE 24 
                                       a++++L+  g++ r  +g T++E
  gi|336254785|ref|YP_004597892.1| 479 AMTQMLRTEGIPARyvTGYTTGE 501
                                       78999999999988666666666 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 4e-12
                           DUF4129   1 ayrallraLaergldrrpgeTprEyarrv...riaps........paa.......alaalaelfeearYGgrpasae 59 
                                       a+r+l+r+La+ +++rr+ge+pr+y++++   +   +        + a       + ++++e++e+a Y g+ ++++
  gi|336254785|ref|YP_004597892.1| 702 AFRRLERLLAREYRPRRRGESPRQYLTALaatA---EgeaaggssA-AvplplneRTERVLEWHEQAIY-GGGVDRA 773
                                       69***************************6431...3233444440.15555555**************.899**** PP

                           DUF4129  60 eyrrlve 66 
                                       e++++ e
  gi|336254785|ref|YP_004597892.1| 774 EADEAIE 780
                                       **99987 PP

>> Transglut_core3  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.1e-07   0.00034      57      97 ..     472     521 ..     451     524 .. 0.90
   2 ?   -0.8   0.7      0.83   1.4e+03       7      21 ..     699     712 ..     662     739 .. 0.55

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.1e-07
                   Transglut_core3  57 kCLpralalalllrrrgipatlviGvrkedd.........pfaaHAWvev 97 
                                        C+  a+a+  +lr  gipa+ v+G  + ++          ++aHAWvev
  gi|336254785|ref|YP_004597892.1| 472 YCVYFATAMTQMLRTEGIPARYVTGYTTGEQvgedeylvrGVNAHAWVEV 521
                                       6***************************9989988888877*******96 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.83
                   Transglut_core3   7 frlrlarlglarlra 21 
                                       ++++++rl+++  ++
  gi|336254785|ref|YP_004597892.1| 699 AERAFRRLERLL-AR 712
                                       333344444432.23 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   4.1      0.54   8.9e+02     107     165 ..      36     100 ..      30     112 .. 0.61
   2 ?   -4.0   1.7       3.3   5.3e+03      10      32 ..     172     194 ..     126     234 .. 0.50
   3 !   20.4   0.0   1.2e-07    0.0002     212     275 ..     280     337 ..     266     383 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.54
                           DUF3488 107 latsflfsqsllfalylllalllllaalvalh......asasapslaralrlalkllllalPlal 165
                                       l + +l++ s l +ly +  +++ + +l++l       a++ a++++ +  +a++ll+++l +a 
  gi|336254785|ref|YP_004597892.1|  36 LGCVLLLTASYLSVLYDVTRIVGGTRSLLLLVgtmlvaATVLARTIRPRTATATALLAAGLGFAY 100
                                       34444444445555555555555554444444555554567888888888888888888887765 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.3
                           DUF3488  10 alallplalrlplwvlllaalll 32 
                                       al++l l    ++ v+ll ++++
  gi|336254785|ref|YP_004597892.1| 172 ALLFLVLTGDAETLVTLLGTIAA 194
                                       22333333333333333322222 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 1.2e-07
                           DUF3488 212 fRvefegavppqselYWRglvleefdGrtWaekaraekkaasletsgepakgkavrYevtlePs 275
                                       fRve      +++  YWR+ v++++ G +W +  +++  +  ++ + +p ++++v ++vt+e +
  gi|336254785|ref|YP_004597892.1| 280 FRVE------SEQPSYWRTGVYDRYTGDEWIRTGQNQPLEGGAALDPPPGQHDSVTQTVTAETE 337
                                       4554......45669***************54444445555555558889999*******9964 PP

>> SPX  SPX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   7.7   0.00037       0.6      59     154 ..     543     643 ..     531     732 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                               SPX  59 ksse....rtepstsaaadesgnsaadasssepkdeae..slprrsplsrssrssssygglvssppsansssssdds 129
                                       ++s+    +++p+t+a++de+++s +d+ +++ ++e++  s+p+  p  ++  ++s+ +++++s++++ + + sd+s
  gi|336254785|ref|YP_004597892.1| 543 HQSQleddADAPGTDASTDEESSSTDDEPAQSDDPEQTdeSEPNDGPA-EDPTNDSESESQSTSQSENGTETRSDNS 618
                                       222244456677777777777777777666666666664222222222.2222222222222222222222222222 PP

                               SPX 130 sesnpadssssssssesessssssp 154
                                          + + ++ +++ +e+ +++ ++ 
  gi|336254785|ref|YP_004597892.1| 619 TATSDGGTAAANDTGEAAGNDLDPG 643
                                       2222233333334444444444444 PP

>> Apt1  Golgi-body localisation protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.7   0.00038      0.62     314     389 ..     548     620 ..     520     684 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00038
                              Apt1 314 seeddesdeesessssssssssssassssssssrssslelrlkptsstssssssessssssskkrsseesslessa 389
                                       +++ d   ++ +++++  sss++++ ++s++ ++++++e ++ p +  +++s+ses+s+s s+ + +e++s +s+a
  gi|336254785|ref|YP_004597892.1| 548 EDDADAPGTDASTDEE--SSSTDDEPAQSDDPEQTDESEPNDGPAEDPTNDSESESQSTSQSE-NGTETRSDNSTA 620
                                       2222222222222211..222222222222222222222222222222222222222222111.111111222222 PP

>> SOG2  RAM signalling pathway protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.1   0.00093       1.5     258     346 ..     554     636 ..     514     673 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00093
                              SOG2 258 angaqsetsersasssg.vqssasstPlgegstsppgalsrqslsttgststltsssksrsssrsntnasastprsl 333
                                       + +  s+  e+s+++++ +qs  +    ++++++p    +   +++++++s+ +s+s s+s + ++t++++st  s 
  gi|336254785|ref|YP_004597892.1| 554 PGTDASTDEESSSTDDEpAQSDDPE---QTDESEP----NDGPAEDPTNDSESESQSTSQSENGTETRSDNSTATSD 623
                                       2222233333333333333333322...3333333....34444444555444444444455555557888888888 PP

                              SOG2 334 attpappasaesf 346
                                         t+a++ ++e++
  gi|336254785|ref|YP_004597892.1| 624 GGTAAANDTGEAA 636
                                       8888877777664 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.6   0.00079       1.3     126     195 ..     545     616 ..     534     720 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00079
                             CDC45 126 leeeeesd..eedeeeeeeddddeeeeeeeeedeedeeedeeeskkkrksksdeeee.sddddersrkrrrse 195
                                        + e+++d    d  + +e+++++++e  +++d e+++e+e +++  +  ++d+e+e ++++++++   +rs+
  gi|336254785|ref|YP_004597892.1| 545 SQLEDDADapGTD-ASTDEESSSTDDEPAQSDDPEQTDESEPNDGPAEDPTNDSESEsQSTSQSENGTETRSD 616
                                       3333333322111.11222222222222222222222222233333333222222222222222222222222 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.8    0.0015       2.5     241     307 ..     551     615 ..     531     671 .. 0.43

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0015
                        Presenilin 241 aekkkeeasesskeeeseeesseksaqsseseeeseeesseaessaeesseekeseessesseeeee 307
                                       a++  + as++++++++++e +++ + +++  +ese +  +ae+ ++ s++e++s+++se+ +e+++
  gi|336254785|ref|YP_004597892.1| 551 ADAPGTDASTDEESSSTDDEPAQSDDPEQT--DESEPNDGPAEDPTNDSESESQSTSQSENGTETRS 615
                                       222222222222222222211111111111..11111111111111111111111111111111111 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  14.3      0.01        17      46     108 ..     555     614 ..     539     630 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.01
                       Trypan_PARP  46 gtkvsdd.dtngtdpepepepepepepepepepepetepeeepepepepepepepepepepepe 108
                                       gt  s d ++++td ep + ++pe   e ep+  p  +p +++e e++   + e + e      
  gi|336254785|ref|YP_004597892.1| 555 GTDASTDeESSSTDDEPAQSDDPEQTDESEPNDGPAEDPTNDSESESQSTSQSENGTE----TR 614
                                       5555444145666777777777776555555544444444444444444444444333....33 PP

>> 7tm_3  7 transmembrane sweet-taste receptor of 3 GCPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   5.8    0.0027       4.3      30     121 ..      33     147 ..      26     238 .. 0.74
   2 ?   -3.9   0.0       5.6   9.1e+03      33      58 ..     659     683 ..     655     684 .. 0.47

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0027
                             7tm_3  30 llLlglllcy.ls.lifigkpssvtCilrrwllgvgftlvfsallvKtwrvlrifqs.................... 84 
                                       ll lg++l++  s l ++   + ++  +r +ll vg  lv +++l++t+r + + ++                    
  gi|336254785|ref|YP_004597892.1|  33 LLALGCVLLLtASyLSVLYDVTRIVGGTRSLLLLVGTMLVAATVLARTIRPRTATATallaaglgfayyletsgvgv 109
                                       4566666644333333446779999************************9887766677877888877776655544 PP

                             7tm_3  85 ....rkgrkskslrd...kqllllvlllvlvqviillvwtli.dp 121
                                           +        +d    +++ l+ +l l+q++   vwtl   p
  gi|336254785|ref|YP_004597892.1| 110 gvvtT-------ATDaiiADVVTLATGLELLQMVEAGVWTLGfAP 147
                                       33211.......222344667777777778888888888775444 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.6
                             7tm_3  33 lglllcylslifigkpssvtCilrrw 58 
                                       l ++l+   ++ +++ +++t  +rr+
  gi|336254785|ref|YP_004597892.1| 659 LAAVLLVG-VVAVVHRTDATTRARRT 683
                                       44444222.22344456666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (797 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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):              11  [number of targets reported over threshold]
# CPU time: 0.80u 0.27s 00:00:01.07 Elapsed: 00:00:00.43
# Mc/sec: 5614.53
//
Query:       gi|336254786|ref|YP_004597893.1|  [L=352]
Description: hypothetical protein Halxa_3402 [Halopiger xanaduensis SH-6]
Scores for 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-16   58.4   1.3    4.8e-15   55.6   0.3    2.6  2  DUF58     Protein of unknown function DUF58


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.037   6.7e+02      23      39 ..      46      62 ..      45     120 .. 0.83
   2 !   55.6   0.3   2.7e-19   4.8e-15       2      86 .]     185     267 ..     184     267 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.037
                             DUF58 23 atARtgelyvrefeaer 39
                                      +tAR g++ vr    e+
  gi|336254786|ref|YP_004597893.1| 46 TTARVGRPTVRRHAVEA 62
                                      69999999999877665 PP

  == domain 2  score: 55.6 bits;  conditional E-value: 2.7e-19
                             DUF58   2 ldfaglReYvpgDplrrIdWkatARt..gelyvrefeaera.rtvllvldlspemslgstgdekletavsaaaslar 75 
                                       ++f+ lReY++gD+lr+++Wka A++  ++l+v e+ ++ + r + ++  ++p         +  +++++a+asla+
  gi|336254786|ref|YP_004597893.1| 185 EEFDRLREYRRGDSLRNVHWKAAAKRpdDDLVVAEYATADEaRALSIAAECEPGPGP-----SRSDELATAVASLAT 256
                                       69***********************76588******877774777777777777654.....99************* PP

                             DUF58  76 qlldegdrvgl 86 
                                       ++l++ ++vg+
  gi|336254786|ref|YP_004597893.1| 257 HFLERDRPVGV 267
                                       *********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2727.27
//
Query:       gi|336254787|ref|YP_004597894.1|  [L=343]
Description: ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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-60  203.3   0.1    2.3e-60  202.2   0.1    1.6  2  AAA_3            ATPase family associated with various cellul
    4.9e-18   64.7   3.9    1.4e-17   63.3   3.9    1.8  1  AAA_lid_2        AAA lid domain
    7.2e-14   52.0   0.0    1.3e-13   51.1   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
    3.7e-06   27.4   0.0    8.1e-06   26.3   0.0    1.6  1  AAA              ATPase family associated with various cellul
    4.1e-05   23.4   0.0     0.0012   18.6   0.0    2.1  1  Sigma54_activat  Sigma-54 interaction domain
    0.00026   20.8   0.0     0.0022   17.8   0.0    2.1  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00034   19.8   0.0    0.00083   18.5   0.0    1.6  1  MCM              MCM P-loop domain
      0.002   17.6   0.0      0.029   13.8   0.0    2.1  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
       0.27   11.7   1.1       0.46   10.9   1.1    1.5  1  MCM_lid          MCM AAA-lid domain


Domain annotation for each model (and alignments):
>> 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 !  202.2   0.1   1.2e-63   2.3e-60       1     130 [.      59     188 ..      59     189 .. 1.00
   2 ?   -3.5   0.0       4.5   8.9e+03      76      94 ..     263     281 ..     261     289 .. 0.70

  Alignments for each domain:
  == domain 1  score: 202.2 bits;  conditional E-value: 1.2e-63
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       hvll++vPG++kt+l++++a+++d+ef+r+qftpdllP+d++G++vf++k++efef++Gpvf n++l deinrappk
  gi|336254787|ref|YP_004597894.1|  59 HVLLDDVPGVGKTMLARSIATSVDCEFQRVQFTPDLLPADVTGVNVFNQKTREFEFQPGPVFGNIVLGDEINRAPPK 135
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfl 130
                                       tqsalleamee+qvtv+g+t++lp+pf+v+atqn +e + ty+lp a+ldrf+
  gi|336254787|ref|YP_004597894.1| 136 TQSALLEAMEEEQVTVDGRTRPLPDPFTVIATQNAVEPNQTYELPLAELDRFM 188
                                       ****************************************************8 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.5
                             AAA_3  76 pktqsalleameerqvtve 94 
                                       p+   all a + r v+ +
  gi|336254787|ref|YP_004597894.1| 263 PRGTIALLRAAQARAVAEG 281
                                       6777789999998888654 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   3.9   7.1e-21   1.4e-17       5      72 ..     253     317 ..     249     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 7.1e-21
                         AAA_lid_2   5 ahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegetteeivee 72 
                                       +++ +++gvs+r +++allraA+A+A  egr+yV+p+Dv++ a+ V++HR++ + ++   + +++ve+
  gi|336254787|ref|YP_004597894.1| 253 TRENARIGVSPR-GTIALLRAAQARAVAEGREYVLPDDVQTEARAVMRHRIQTDDRDR--DGDAVVED 317
                                       678899******.**************************************9544443..34777765 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 !   51.1   0.0   6.7e-17   1.3e-13       2     138 .]      60     187 ..      59     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 6.7e-17
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEver 76 
                                       vlL   pG+gK++la+++a  + +e++ vq+t d+ ++d++g   ++   ++ +++++p+      g i++ DE++r
  gi|336254787|ref|YP_004597894.1|  60 VLLDDVPGVGKTMLARSIATSVDCEFQRVQFTPDLLPADVTGVNVFNqkTREFEFQPGPVF-----GNIVLGDEINR 131
                                       666668************************************999996677778999***9.....*********** PP

                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       a+++++++Ll  +ee+++   +g+++   ++      f+viat n ++ ++  el  a ++Rf
  gi|336254787|ref|YP_004597894.1| 132 APPKTQSALLEAMEEEQVT-VDGRTRPLPDP------FTVIATQNAVEpNQTYELPLAELDRF 187
                                       ******************9.66666666777......**********9999988888888887 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 !   26.3   0.0   4.1e-09   8.1e-06       5     130 ..      64     193 ..      60     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.1e-09
                                       SSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SS..STTHHHHHHHHHHHHHHHTS......TSEEEEEETGGGHH CS
                               AAA   5 GppGtGKTllakavakelgvefleisg.sell.sk..yvgesekkirelfkeakeka......kpsilfiDEidala 71 
                                         pG+GKT+la+++a++++ ef +++  ++ll  +   v   ++k+re+       +         i++ DEi +  
  gi|336254787|ref|YP_004597894.1|  64 DVPGVGKTMLARSIATSVDCEFQRVQFtPDLLpADvtGVNVFNQKTREF-------EfqpgpvFGNIVLGDEINRAP 133
                                       57*****************999999862566632244444444444444.......2333343238**********9 PP

                                       HHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS...GGGSTHHHHS.TTSSEEEET CS
                               AAA  72 ksrsgseseeeervvnqLlteldgvkkk........eskvivigatnr...pdkldpallr.gRfdrkiei 130
                                       ++            +++Ll+++++++           ++++vi++ n     ++++ +l   +Rf +k+++
  gi|336254787|ref|YP_004597894.1| 134 PKT-----------QSALLEAMEEEQVTvdgrtrplPDPFTVIATQNAvepNQTYELPLAElDRFMKKLHL 193
                                       999...........*************9********777*****999977545555566666888877765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   5.9e-07    0.0012      14     142 ..      49     169 ..      41     183 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.9e-07
                                       HHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHH CS
                   Sigma54_activat  14 qikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfe 90 
                                       ++  +   + +vl+    G+GK++lar+i ++ + +  + v++    +p+++   ++F  +   F      + G   
  gi|336254787|ref|YP_004597894.1|  49 HVVIALLARGHVLLDDVPGVGKTMLARSIATSVDCE-FQRVQFTPDLLPADVTGVNVFNQKTREFE----FQPG--- 117
                                       555556666788888888888888888887665532.22333333344444444444444433332....2223... PP

                                       HTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEES CS
                   Sigma54_activat  91 kadgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatn 142
                                          g +++ Dei++ p+++Q+ Ll++++e++v+  G +++ +  + +ia+ n
  gi|336254787|ref|YP_004597894.1| 118 PVFGNIVLGDEINRAPPKTQSALLEAMEEEQVTVDGRTRPLPDPFTVIATQN 169
                                       234666777********************************99999998766 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 !   17.8   0.0   1.1e-06    0.0022      34     114 ..      58     150 ..      46     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkit.sgPvlekagdlaallt.nlee...........kdvlfideihrls 97 
                                        hvll   PG+Gkt la+ ia+ ++ +++    +P l  ++d++++ + n ++           +++++ dei r  
  gi|336254787|ref|YP_004597894.1|  58 GHVLLDDVPGVGKTMLARSIATSVDCEFQRVqFTPDLL-PADVTGVNVfNQKTrefefqpgpvfGNIVLGDEINRAP 133
                                       6*************************997551567664.56666653212222111111122223567779999999 PP

                            RuvB_N  98 raveevlysamedfrld 114
                                       ++++  l  ame+ ++ 
  gi|336254787|ref|YP_004597894.1| 134 PKTQSALLEAMEEEQVT 150
                                       99999999999987765 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.1e-07   0.00083      54     153 ..      54     152 ..      22     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.1e-07
                                       BCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSS...SSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEE CS
                               MCM  54 lrgdinvllvgdpgtaKsqlLkyveklapravytsgkgs...saagLtaavvrdeetgefvleaGalvladkGvcci 127
                                       l ++ +vll   pg++K+ l +++++ +    +   + +     a+ t   v +++t+ef ++ G +    + +++ 
  gi|336254787|ref|YP_004597894.1|  54 LLARGHVLLDDVPGVGKTMLARSIATSV-DCEFQRVQFTpdlLPADVTGVNVFNQKTREFEFQPGPVF---GNIVLG 126
                                       556679999999******9999998554.444444444411156899999999************987...569999 PP

                                       ESGGGSTCHHHHHHHHHHHHSEEEEE CS
                               MCM 128 DefdkmkeedrsalhEamEqqtisia 153
                                       De+++   +++sal+EamE++++++ 
  gi|336254787|ref|YP_004597894.1| 127 DEINRAPPKTQSALLEAMEEEQVTVD 152
                                       ***********************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 !   13.8   0.0   1.4e-05     0.029       5      44 ..      40      79 ..      37      89 .. 0.90
   2 ?    1.3   0.0     0.096   1.9e+02     112     158 ..     126     170 ..     119     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                      Mg_chelatase  5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlps 44
                                      ++G+++    + ia   + ++ll   pG GKtmla+ +++
  gi|336254787|ref|YP_004597894.1| 40 IVGHDDVIDHVVIALLARGHVLLDDVPGVGKTMLARSIAT 79
                                      789999999999***********************99865 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.096
                      Mg_chelatase 112 LDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                        DE+     k+  +L e +e+++vt+   ++    p  f+++a+ N 
  gi|336254787|ref|YP_004597894.1| 126 GDEINRAPPKTQSALLEAMEEEQVTVDGRTRP--LPDPFTVIATQNA 170
                                       49999999*****************9866554..4666777777665 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.1   0.00023      0.46      34      83 ..     248     298 ..     224     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                                       HHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHH.HHHHHH CS
                           MCM_lid  34 RkeeedskrksipitvRqLesliRLseAlAklrlsevvteedve.eairll 83 
                                       R  + ++++ +i +++R   +l+R ++A+A  + +e+v ++dv+ ea  ++
  gi|336254787|ref|YP_004597894.1| 248 RLADYTRENARIGVSPRGTIALLRAAQARAVAEGREYVLPDDVQtEARAVM 298
                                       444445568899*******************************83455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2655.74
//
Query:       gi|336254788|ref|YP_004597895.1|  [L=64]
Description: cold-shock DNA-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   75.7   0.3      2e-21   75.6   0.3    1.0  1  CSD       'Cold-shock' DNA-binding domain
     0.0086   16.0   0.7      0.011   15.7   0.7    1.4  1  S1-like   S1-like
  ------ inclusion threshold ------
      0.017   14.8   1.5      0.026   14.2   1.5    1.4  1  OB_RNB    Ribonuclease B OB domain
      0.044   13.7   0.0      0.057   13.4   0.0    1.3  1  CusF_Ec   Copper binding periplasmic protein CusF


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.3   4.5e-25     2e-21       2      65 ..       3      63 ..       2      64 .] 0.97

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 4.5e-25
                                      EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                               CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                      +GtV  fn+  g+GFI++ed d+dvF+H+ ++ g +   L+egqeVeF++++ +kgp+A+nV +
  gi|336254788|ref|YP_004597895.1|  3 KGTVAFFNDTGGYGFIETEDSDEDVFFHMEDVGGPD---LEEGQEVEFDIEQADKGPRATNVER 63
                                      8*******************************9999...***********************75 PP

>> S1-like  S1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.7   2.4e-06     0.011      14      48 ..      14      53 ..       1      63 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-06
                           S1-like 14 tfGfv.....DeevfFqrsvvkGrlpkvgdrVlveAvynp 48
                                       +Gf+     De+vfF+++ v G+  + g  V+++  + +
  gi|336254788|ref|YP_004597895.1| 14 GYGFIetedsDEDVFFHMEDVGGPDLEEGQEVEFDIEQAD 53
                                      599997777789*******************998866655 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.5   5.8e-06     0.026       8      28 ..      13      33 ..       4      36 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.8e-06
                                      SS-EEEEECT.TEEEEE-HHH CS
                            OB_RNB  8 kGFGFlipdegkeDifippeq 28
                                       G+GF+++++ +eD+f + e+
  gi|336254788|ref|YP_004597895.1| 13 GGYGFIETEDSDEDVFFHMED 33
                                      59**************87766 PP

>> CusF_Ec  Copper binding periplasmic protein CusF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.3e-05     0.057      42      67 ..      38      62 ..      25      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                      S-STT-EEEEEEEEETTCEEEEEEEE CS
                           CusF_Ec 42 glkaGdkVrFefekrdggeyvitkie 67
                                      +l++G++V+F++e++d+g ++ t +e
  gi|336254788|ref|YP_004597895.1| 38 DLEEGQEVEFDIEQADKG-PRATNVE 62
                                      799*************99.9998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 520.26
//
Query:       gi|336254789|ref|YP_004597896.1|  [L=101]
Description: hypothetical protein Halxa_3405 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0095   16.0   3.3      0.018   15.2   3.3    1.4  1  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.059   13.3   2.7        0.5   10.4   2.7    2.1  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.087   12.4   3.9        2.9    7.6   0.2    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.12   12.4   4.0       0.27   11.3   0.3    2.3  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.13   12.2   0.7       0.25   11.3   0.7    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.18   11.3   5.0        3.8    7.1   0.2    2.6  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.22   11.3   5.8        4.1    7.2   1.3    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain


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 !   15.2   3.3   6.9e-06     0.018       5      33 ..      73      99 ..      73     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.9e-06
                       Zn-ribbon_8  5 eYrCeeCghefevlqsisdapltaCPeCg 33
                                      eY C +C++e +++ +  d ++ +CP+C+
  gi|336254789|ref|YP_004597896.1| 73 EYVCARCDEESDRVWR--DGDEFVCPDCK 99
                                      8***********6643..666889****6 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.7    0.0002       0.5      10      26 ..      83      99 ..      67     101 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                    PhnA_Zn_Ribbon 10 SeytYedgallvCpeCa 26
                                      S+ +  dg+ +vCp+C+
  gi|336254789|ref|YP_004597896.1| 83 SDRVWRDGDEFVCPDCK 99
                                      666779**********8 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0011       2.9       2      11 ..      73      82 ..      72      85 .. 0.85
   2 ?    5.9   0.5    0.0036       9.3       1      10 [.      91     100 ..      91     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
                            zf_UBZ  2 tylCerCgke 11
                                       y+C+rC++e
  gi|336254789|ref|YP_004597896.1| 73 EYVCARCDEE 82
                                      59*****986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0036
                            zf_UBZ   1 dtylCerCgk 10 
                                       d ++C++C++
  gi|336254789|ref|YP_004597896.1|  91 DEFVCPDCKE 100
                                       679*****85 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 ?    2.2   1.3     0.072   1.9e+02      15      27 ..      71      82 ..      65      88 .. 0.61
   2 ?   11.3   0.3    0.0001      0.27      13      25 ..      85      99 ..      82     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.072
                     Zn_Tnp_IS1595 15 WpngfvCPhCgsr 27
                                      W++ + C +C  +
  gi|336254789|ref|YP_004597896.1| 71 WGEYV-CARCDEE 82
                                      55544.8888765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0001
                     Zn_Tnp_IS1595 13 lrWpng..fvCPhCg 25
                                      ++W++g  fvCP C+
  gi|336254789|ref|YP_004597896.1| 85 RVWRDGdeFVCPDCK 99
                                      68****99******7 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 ?   11.3   0.7   9.6e-05      0.25      31      53 ..      76      99 ..      69     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.6e-05
                    OrfB_Zn_ribbon 31 CseCgsknke.alsgrtfkCpnCg 53
                                      C++C +++++  ++g++f+Cp+C+
  gi|336254789|ref|YP_004597896.1| 76 CARCDEESDRvWRDGDEFVCPDCK 99
                                      **********99***********7 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2    0.0015       3.8      15      25 ..      69      79 ..      61      85 .. 0.83
   2 ?    5.2   5.8    0.0059        15       1      25 [.      74      98 ..      74     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0015
                                      TSTTCEEESSS CS
                      TF_Zn_Ribbon 15 pergelvCtdC 25
                                      ++ ge+vC +C
  gi|336254789|ref|YP_004597896.1| 69 YAWGEYVCARC 79
                                      6669******* PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0059
                                      EEETTTTCEE.CHEETSTTCEEESSS CS
                      TF_Zn_Ribbon  1 ykCPnCgstn.lveDpergelvCtdC 25
                                      y+C  C  ++  v+  +  e+vC+dC
  gi|336254789|ref|YP_004597896.1| 74 YVCARCDEESdRVWR-DGDEFVCPDC 98
                                      799999998855666.668******* PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2    0.0029       7.4       1      13 [.      74      86 ..      74      88 .. 0.87
   2 ?    7.2   1.3    0.0016       4.1      17      23 ..      95     101 .]      94     101 .] 0.94

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0029
                      Rubredoxin_2  1 YvCsqCGfesakw 13
                                      YvC +C  es ++
  gi|336254789|ref|YP_004597896.1| 74 YVCARCDEESDRV 86
                                      9******999775 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0016
                      Rubredoxin_2  17 CpsCgsW 23 
                                       Cp+C++W
  gi|336254789|ref|YP_004597896.1|  95 CPDCKEW 101
                                       ******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 779.86
//
Query:       gi|336254790|ref|YP_004597897.1|  [L=66]
Description: hypothetical protein Halxa_3406 [Halopiger xanaduensis SH-6]
Scores for 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:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 520.30
//
Query:       gi|336254791|ref|YP_004597898.1|  [L=342]
Description: 5,10-methylenetetrahydromethanopterin reductase [Halopiger xanaduensis SH-6]
Scores for 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-63  213.4  11.9    6.6e-63  213.0  11.9    1.1  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
        0.1   12.1   0.0       0.17   11.3   0.0    1.3  1  VitK2_biosynth  Menaquinone biosynthesis


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.0  11.9   7.4e-67   6.6e-63      18     309 ..      24     310 ..       8     314 .. 0.93

  Alignments for each domain:
  == domain 1  score: 213.0 bits;  conditional E-value: 7.4e-67
                    Bac_luciferase  18 asaslrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLd 94 
                                       ++++++++++la +aE+ Gfd ++ + h+++    +d+f++l+ +aaaT+ irlg +v+++y  hP+ lA q at+d
  gi|336254791|ref|YP_004597898.1|  24 PEHPPNRIADLAALAEDEGFDLALSSSHYFN----RDPFVVLSRMAAATDEIRLGPGVVNPYETHPVKLAAQTATID 96 
                                       346899*************************....****************************************** PP

                    Bac_luciferase  95 hlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyv 171
                                       ++s+GR+++g+g+g + +  ++ Gvd+d++++r  E+ +v r lw+ge+v++eG f ++++a l   ++  +iPvyv
  gi|336254791|ref|YP_004597898.1|  97 EVSDGRAVFGVGAGDRSAL-ANLGVDRDRPLRRVLETFDVARDLWAGETVTHEGTF-TARDASLNLDER--EIPVYV 169
                                       ***************9999.999*********************************.777777777663..59**** PP

                    Bac_luciferase 172 aaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraea...rali 245
                                       +a +p +l++ a+hadg+l++ ++p ++++++ +l+ g ae+ +d+++++ ++ ++v+va  e++Ar+ a    a+i
  gi|336254791|ref|YP_004597898.1| 170 GAQGPHMLRMSAKHADGVLINAAHPRDLEWAAGELERGLAERPEDRGAFESLAFASVSVAGAEDDAREAArppVAFI 246
                                       **********************************************************************7777888 PP

                    Bac_luciferase 246 agldfyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayae 309
                                        g+ + +  +++  + ++a + +e+   ++  +a+d v++++++a++++Gt e+vaer++a +e
  gi|336254791|ref|YP_004597898.1| 247 VGGAAEPVLERHDIDRDAAGAVSEALEQGDLGEAFDRVTPAMIDAFCIAGTTETVAERFEAAVE 310
                                       7777888888888888888899*************************************99654 PP

>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.9e-05      0.17      33      97 ..      27      87 ..      12     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.9e-05
                                      EEE-HHHHHHHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEEEESSSSEEEEESS-CCC-SSS CS
                    VitK2_biosynth 33 vledpetlnrallegelDvakiSsaayariaddyalLpdlsisalGrvygvllvskvpleelege 97
                                        + +++l++ ++++ +D+a+ Ss+ + r  d +++L+ ++++ ++  +g+ +v   p+e+   +
  gi|336254791|ref|YP_004597898.1| 27 PPNRIADLAALAEDEGFDLALSSSHYFNR--DPFVVLSRMAAATDEIRLGPGVVN--PYETHPVK 87
                                      56789********************9988..*******9999999999*****99..44444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2474.37
//
Query:       gi|336254792|ref|YP_004597899.1|  [L=270]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-23   81.9   0.1    6.9e-23   81.2   0.1    1.4  1  Methyltransf_25  Methyltransferase domain
    2.5e-21   76.1   0.1      4e-21   75.5   0.1    1.3  1  Methyltransf_11  Methyltransferase domain
    2.8e-17   62.9   0.0    3.7e-17   62.5   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    8.3e-15   54.8   0.0    7.5e-14   51.6   0.0    2.0  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.8e-14   53.6   0.0    4.7e-14   52.9   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
      5e-12   46.0   0.0    6.5e-12   45.6   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      1e-06   27.7   0.0    1.3e-06   27.3   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
    0.00021   21.0   0.0    0.00031   20.4   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
     0.0076   15.6   0.0     0.0098   15.2   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.023   14.7   0.0      0.032   14.2   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.024   14.5   0.2      0.068   13.0   0.2    1.6  1  Methyltransf_8   Hypothetical methyltransferase
      0.026   14.1   0.1      0.041   13.4   0.1    1.2  1  MTS              Methyltransferase small domain
       0.04   13.6   0.6       0.37   10.5   0.6    2.4  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.08   13.1   0.0       0.22   11.7   0.0    1.7  1  Zn-ribbon_8      Zinc ribbon domain
      0.093   12.7   0.0       0.19   11.7   0.0    1.4  1  Thump_like       THUMP domain-like


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 !   81.2   0.1   5.8e-26   6.9e-23       1      97 []     115     206 ..     115     206 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 5.8e-26
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vLd++cGtGr+++ +a++   a+v+g+Dis++mle+a + a+++g++v f +++a+dl f+++ fD  +++ alh+l
  gi|336254792|ref|YP_004597899.1| 115 VLDVACGTGRIARPVAAA---ANVVGIDISAGMLERAMRYAARDGVDVAFARMSADDLWFDANAFDRATCCWALHLL 188
                                       9***************88...8************************************************999**** PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +d+d  ++l+eiarvL+ +G
  gi|336254792|ref|YP_004597899.1| 189 PDPD--AVLEEIARVLRSDG 206
                                       9777..99*********998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.1   3.3e-24     4e-21       1      95 [.     116     209 ..     116     210 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 3.3e-24
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       Ldv+cGtGr+a+++a ++a+vvg+D+s+ ml++a + a ++g+ v f +++a +l f  n fD  ++ ++lh ++dp
  gi|336254792|ref|YP_004597899.1| 116 LDVACGTGRIARPVA-AAANVVGIDISAGMLERAMRYAARDGVDVAFARMSADDLWFDANAFDRATCCWALHLLPDP 191
                                       8**************.557***************99999999999******************************** PP

                                       HHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                       +++l+eiaRvL+ +G++v
  gi|336254792|ref|YP_004597899.1| 192 DAVLEEIARVLRSDGMFV 209
                                       ***************997 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   3.1e-20   3.7e-17       4     110 ..     112     211 ..     109     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 3.1e-20
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       + +vlD++CGtG+++   a      a+vvGiDis+ ++e+A   a++ g+d v F + ++ +l   +  + fD  ++
  gi|336254792|ref|YP_004597899.1| 112 TPTVLDVACGTGRIARPVA----AAANVVGIDISAGMLERAMRYAARDGVD-VAFARMSADDLW--FDANAFDRATC 181
                                       568***************9....4688***********************8.**********99..889******** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggillie 110
                                         +l++l+dpd++leei rvl+++g ++ +
  gi|336254792|ref|YP_004597899.1| 182 CWALHLLPDPDAVLEEIARVLRSDGMFVGT 211
                                       *************************99855 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   6.3e-17   7.5e-14      48     150 ..     112     209 ..     100     221 .. 0.90
   2 ?    0.7   0.0      0.22   2.7e+02     200     222 ..     238     260 ..     233     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 6.3e-17
                                       TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES CS
                   Ubie_methyltran  48 gakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsf 124
                                         +vlDva+Gtg +a    + v +  +vv++Di++ mL+ + + + ++g+ ++ f   +a +L f+ ++fD  t  +
  gi|336254792|ref|YP_004597899.1| 112 TPTVLDVACGTGRIA----RPVAAAANVVGIDISAGMLERAMRYAARDGV-DVAFARMSADDLWFDANAFDRATCCW 183
                                       4589********766....66777789**************999999996.8************************* PP

                                       -GGG-S-HHHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 125 GlrnvtDklkaLkeayrvlkpGGrlv 150
                                        l  ++D + +L+e+ rvl+  G +v
  gi|336254792|ref|YP_004597899.1| 184 ALHLLPDPDAVLEEIARVLRSDGMFV 209
                                       *********************99986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.22
                                       -HHHHHHHHHHTTEEEEEEEEEG CS
                   Ubie_methyltran 200 dqetlkeliedaGfksveyeslt 222
                                       d+ +l+  ++ aGf+sve+++ +
  gi|336254792|ref|YP_004597899.1| 238 DATDLRRRLRTAGFSSVEFDRRG 260
                                       677899999*********98765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0     4e-17   4.7e-14       1      99 []     116     208 ..     116     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 4e-17
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++ cGtG+++r+++++   ++++g+Dis+ ++  ++ + a+r++ ++++ +  a+dl  ++  ++fD  +++ +lh
  gi|336254792|ref|YP_004597899.1| 116 LDVACGTGRIARPVAAA---ANVVGIDISAGML-ERAMRYAARDGVDVAFARMSADDLWFDA--NAFDRATCCWALH 186
                                       8****************...*************.8888888888888888888888766444..6************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        l+d+++vl++i+++L+ +G++
  gi|336254792|ref|YP_004597899.1| 187 LLPDPDAVLEEIARVLRSDGMF 208
                                       ********************86 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   5.4e-15   6.5e-12      25     164 ..     114     255 ..      76     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 5.4e-15
                   Methyltransf_23  25 rvLdiGcGtGillevlrengfsvtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfdlIvlrevlehv 95 
                                        vLd++cGtG+ ++  ++  ++v+g+D+s  + e+a       + + a+  +  +++ +++++ fd +++   l+ +
  gi|336254792|ref|YP_004597899.1| 114 TVLDVACGTGRIARPVAAA-ANVVGIDISAGMLERAMryaardGVDVAFARMS-ADDLWFDANAFDRATCCWALHLL 188
                                       8*********999988665.7*************9988877754444444444.67899999*************** PP

                   Methyltransf_23  96 pdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhi..sffsarslkelleeaGlevve 164
                                       pdp ++l  ia+ l+ +G ++ +    +++ ++l    +  ++a +++    f+a++l++ l+ aG++ ve
  gi|336254792|ref|YP_004597899.1| 189 PDPDAVLEEIARVLRSDGMFVGTALV-EDYVLEL---LPVRATAKGVLdvEPFDATDLRRRLRTAGFSSVE 255
                                       ******************99888874.4576666...5678888888877889**************9876 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 !   27.3   0.0   1.1e-09   1.3e-06     100     218 ..      94     211 ..      77     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.1e-09
                   Methyltransf_29 100 kYidklaelipliaaggkvrtvlDvGCgvasfgayl.lsrdvltlslapkDeheaqvqfaLeRgvpailavlgtkrl 175
                                       k + ++ el +   a+g + tvlDv Cg    +  +    +v+ + ++     e  + +a   gv    a +++  l
  gi|336254792|ref|YP_004597899.1|  94 KTVVEMLELEDIDVADGDTPTVLDVACGTGRIARPVaAAANVVGIDISA-GMLERAMRYAARDGVDVAFARMSADDL 169
                                       4555566666666899*************99987661568999999986.688999********************* PP

                   Methyltransf_29 176 pyPsrsfdlihCsrCridwteedgilllevdRvlRpgGyfvls 218
                                        + +++fd + C    ++   +  ++l e+ RvlR++G fv +
  gi|336254792|ref|YP_004597899.1| 170 WFDANAFDRATCCWA-LHLLPDPDAVLEEIARVLRSDGMFVGT 211
                                       ************865.57777777899*************965 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.6e-07   0.00031      14     103 ..     112     203 ..     100     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.6e-07
                              MetW  14 gsrvldlGcGdGellellkeekqvdgrGleld..eegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqat 88 
                                         +vld+ cG G + + ++   +v g  +     e+++  +   G+ v    +  d   f+ ++fd +    +l  +
  gi|336254792|ref|YP_004597899.1| 112 TPTVLDVACGTGRIARPVAAAANVVGIDISAGmlERAMRYAARDGVDVAFARMSADDLWFDANAFDRATCCWALHLL 188
                                       568***************99888876555432224566666778********************************* PP

                              MetW  89 rnpkevldellrigr 103
                                        +p+ vl+e+ r+ r
  gi|336254792|ref|YP_004597899.1| 189 PDPDAVLEEIARVLR 203
                                       ***********9965 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   8.2e-06    0.0098      55     106 ..     102     153 ..      92     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.2e-06
                                       HTTTT--TT-..EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHH CS
                              CMAS  55 leklelkpGm..tlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvd 106
                                       le +++ +G+  t+Ld+ cG G ++r  ++   ++vvg+ +S+   ++a +  +
  gi|336254792|ref|YP_004597899.1| 102 LEDIDVADGDtpTVLDVACGTGRIARPVAAA--ANVVGIDISAGMLERAMRYAA 153
                                       6777888888446*************99998..9********988877765554 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-05     0.032      22      75 ..     108     156 ..      94     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                   Methyltransf_32  22 kesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75 
                                       ++ +  tv+Dv++G g  ++ +a        +vvgid+++ + e+a++ a++ g
  gi|336254792|ref|YP_004597899.1| 108 ADGDTPTVLDVACGTGRIARPVAA-----AANVVGIDISAGMLERAMRYAARDG 156
                                       4567899****************9.....699****************999876 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   5.7e-05     0.068      74     154 ..     113     208 ..      96     219 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-05
                                       S-EEEES-TT-HHHHH--S-..EEEEESS-..SSTTEE...E...S-T..TS-S--T.....T-EEEEEEES--.-S CS
                    Methyltransf_8  74 lvvadlGcGeakiaeavrekekvrsfdlva..vnervv...a...cdl..akvPled.....esvdvavfclsl.mg 134
                                        +v d+ cG  +ia  v    +v  +d+ a  + er +   a    d+  a++ ++d     ++ d a +c +l + 
  gi|336254792|ref|YP_004597899.1| 113 PTVLDVACGTGRIARPVAAAANVVGIDISAgmL-ERAMryaArdgVDVafARMSADDlwfdaNAFDRATCCWALhLL 188
                                       5799***********************987432.22211112111344336666666333337889999**998446 PP

                                       S-HHHHHHHHHHHEEEEEEE CS
                    Methyltransf_8 135 tnladflkeanrvlkvGGll 154
                                        +    l+e+ rvl+  G++
  gi|336254792|ref|YP_004597899.1| 189 PDPDAVLEEIARVLRSDGMF 208
                                       789999*********99986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.4e-05     0.041      32      88 ..     112     165 ..      97     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-S CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasd 88 
                                       + +vlD++cG+G ++  +a++   a+v+ +d++a  le a + +++ +++v +   +
  gi|336254792|ref|YP_004597899.1| 112 TPTVLDVACGTGRIARPVAAA---ANVVGIDISAGMLERAMRYAARDGVDVAFARMS 165
                                       457***************995...457999999999999999999999996655444 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 ?   10.5   0.6   0.00031      0.37       6      26 ..      12      36 ..      12      40 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                     zf-NADH-PPase  6 CgrCGaptepa....eggwarvCpa 26
                                      CgrCG +        e+g+a+vCp+
  gi|336254792|ref|YP_004597899.1| 12 CGRCGRRLSFRksvdEDGRALVCPN 36
                                      *******9754222289******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 ?   11.7   0.0   0.00019      0.22       6      32 ..      10      37 ..       9      42 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                       Zn-ribbon_8  6 YrCeeCghefevlqsis.dapltaCPeC 32
                                      Y C +Cg++   + s++ d    +CP+ 
  gi|336254792|ref|YP_004597899.1| 10 YACGRCGRRLSFRKSVDeDGRALVCPNG 37
                                      9**********9999995555666**86 PP

>> Thump_like  THUMP domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.19       6      37 ..     231     262 ..     230     264 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                        Thump_like   6 vlevlpfskkklkkllrergigkanikkRgfp 37 
                                       vl+v pf++  l++ lr+ g+ +++  +Rg +
  gi|336254792|ref|YP_004597899.1| 231 VLDVEPFDATDLRRRLRTAGFSSVEFDRRGAA 262
                                       899**************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2020.11
//
Query:       gi|336254793|ref|YP_004597900.1|  [L=258]
Description: F420-0:gamma-glutamyl ligase [Halopiger xanaduensis SH-6]
Scores for complete 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-61  207.7   0.0      2e-61  207.5   0.0    1.0  1  F420_ligase  F420-0:Gamma-glutamyl ligase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.5   0.0   1.1e-65     2e-61       4     243 ..       9     225 ..       7     226 .. 0.98

  Alignments for each domain:
  == domain 1  score: 207.5 bits;  conditional E-value: 1.1e-65
                                       -----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH......TS-H... CS
                       F420_ligase   4 tplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklk.....vidpilS 75 
                                       +p+i++gdd+a++v+e+v++    le gD++ v++++v+kaeg++++led  +s +A+eia+k+      ++dp   
  gi|336254793|ref|YP_004597900.1|   9 LPEIRPGDDIAALVAERVDDD---LEPGDVLTVASTIVSKAEGRTADLEDYPVSGRAQEIADKIGeltdeEKDP--- 79 
                                       79*****************99...****************************************668899****... PP

                                       ...............HHHHHHHHTEEEEEE-..S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHH CS
                       F420_ligase  76 rnrfsliLkalakatrkvevvlsepsdevgn..qlidekytdevlvklGllgsnagidesnveegllkllPedpdks 150
                                                      r+ ++vl+e+++ + +  +l++e+       ++G++++nagid+snv+++ l+llP+ p++s
  gi|336254793|ref|YP_004597900.1|  80 ---------------RFAQAVLEESTELLIDcpFLLTET-------RFGHICVNAGIDRSNVPGHDLLLLPKRPSES 134
                                       ...............****************99******.......******************************* PP

                                       HHHHHHHHHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHH CS
                       F420_ligase 151 aeeikkklkertgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgslad 227
                                       ae+i++ l++r   dv+V++  +D++gr++++++ +vaig++g++a rd+rg++d+dg+el++t+++v+del ++a+
  gi|336254793|ref|YP_004597900.1| 135 AERIRQGLEDRGVEDVAVIV--TDTCGRPFRHGQRGVAIGWAGMPASRDWRGERDRDGHELEVTVQSVVDELSAAAN 209
                                       ********************..******************************************************* PP

                                       HHC-SSSS---EEEEE CS
                       F420_ligase 228 LvsGsadegtPvvlvr 243
                                       Lv+G++  gtP+v+v 
  gi|336254793|ref|YP_004597900.1| 210 LVTGEGAGGTPAVVVS 225
                                       **************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2059.26
//
Query:       gi|336254794|ref|YP_004597901.1|  [L=563]
Description: 5-oxoprolinase [Halopiger xanaduensis SH-6]
Scores for complete 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-209  696.5   5.7   1.9e-209  696.4   5.7    1.0  1  Hydantoinase_B  Hydantoinase B/oxoprolinase


Domain annotation for each model (and alignments):
>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  696.4   5.7  1.1e-213  1.9e-209       1     516 []      20     544 ..      20     544 .. 0.96

  Alignments for each domain:
  == domain 1  score: 696.4 bits;  conditional E-value: 1.1e-213
                    Hydantoinase_B   1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfege 77 
                                       Dp+tlev+rn+l+s+aeemg+tl+r a+Spniker+D+s+alfda+g+++aqa+hipvhlg+m++av+av e   ++
  gi|336254794|ref|YP_004597901.1|  20 DPVTLEVLRNQLESVAEEMGQTLIRGAYSPNIKERRDCSTALFDAEGRMIAQAEHIPVHLGAMPAAVEAVRE---RD 93 
                                       9*******************************************************************9884...45 PP

                    Hydantoinase_B  78 lkpGDvlltNdPyaggtHlpDitvitPvfhege.................lvffvasraHhaDiGGitpGsmppdat 137
                                        +pGDv+++NdP++ggtHlpD+t+++P+   ++                 +v++++sraHhaD+GG+tpGsmp+ a+
  gi|336254794|ref|YP_004597901.1|  94 PQPGDVFVLNDPFTGGTHLPDVTMVSPIAPGHSggesggrggddgddgdeIVGYAVSRAHHADVGGMTPGSMPAGAQ 170
                                       79**************************95443778999999*********************************** PP

                    Hydantoinase_B 138 eifeEGlrippvklveegeleedvlelllanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeild 214
                                       ei++EGlr+pp+klve+g  +edv +l+lanvR+p ++++Dl+Aq aan+++e+rl+el++e+G +tv + +d+++d
  gi|336254794|ref|YP_004597901.1| 171 EIYQEGLRLPPIKLVEGGDVREDVRSLVLANVRNPGERRADLRAQQAANERAEERLEELFAEHGRETVLEGFDAVID 247
                                       ***************************************************************************** PP

                    Hydantoinase_B 215 naeravraalaelpdgtyeaedyl......ddgipikvtvtidgdeatvDftgtspqvkgniNaplavtlsaviyvl 285
                                       ++++++ +++a+lpdgtyea+d+l      dd+i+i+v+vt+dgd++ vDf+gt++qv+gn+Napl+v++sav++v+
  gi|336254794|ref|YP_004597901.1| 248 YSRERISEEIAALPDGTYEATDVLegdgvtDDDIEIAVAVTVDGDRIDVDFAGTAEQVAGNVNAPLSVATSAVYFVV 324
                                       **********************995555544459******************************************* PP

                    Hydantoinase_B 286 rclvdediplNeGclrpievklpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfg 362
                                       rc++d++ip N+Gc++p++v++peg+llnp++paavvggnvetsqrv+dvv++alaqa+p+rv+A++qgtmnnlt+g
  gi|336254794|ref|YP_004597901.1| 325 RCITDPEIPPNHGCYEPVSVRAPEGTLLNPEPPAAVVGGNVETSQRVTDVVFAALAQAAPDRVPAQGQGTMNNLTIG 401
                                       ***************************************************************************** PP

                    Hydantoinase_B 363 gvderggeffgyyetiagGaGArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvv 439
                                           r+g+f +yyeti+gG GArp++dG+++v+v mtnt nt+vE lE++yP++ver++lr++sgG+G+yrGG+G++
  gi|336254794|ref|YP_004597901.1| 402 ---ARDGSF-TYYETIGGGFGARPDRDGMDGVQVGMTNTLNTPVESLETEYPLRVERYALRDGSGGRGRYRGGLGLE 474
                                       ...433555.******************************************************************* PP

                    Hydantoinase_B 440 reieflepevtvsilserrvfapwGlaGGepGargrvvlnllvrgeeenlggkatvelkagdvlvietpGGGGyGdp 516
                                       r++++++p +tvs+l+err++ap G+aGGe+Ga+g+   nll   + e +++k+tv+++ag +++++tpGGGG+Gdp
  gi|336254794|ref|YP_004597901.1| 475 RSVTVEKP-ATVSLLTERRRHAPKGVAGGEDGATGE---NLL---DGEPVPAKTTVDVEAGTTVTVRTPGGGGHGDP 544
                                       *******9.***************************...765...4677789999********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3986.89
//
Query:       gi|336254795|ref|YP_004597902.1|  [L=682]
Description: 5-oxoprolinase [Halopiger xanaduensis SH-6]
Scores for complete 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-99  333.4  11.7    1.4e-99  333.0   5.3    2.5  3  Hydantoinase_A  Hydantoinase/oxoprolinase
    1.7e-50  171.2   2.6    4.1e-50  170.0   0.1    2.5  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.3    0.0038        34      81      98 ..      14      31 ..       8      43 .. 0.82
   2 !  333.0   5.3  1.6e-103   1.4e-99       1     287 [.     208     491 ..     208     495 .. 0.99
   3 ?   -2.6   0.0      0.29   2.6e+03     241     284 ..     535     578 ..     517     580 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0038
                    Hydantoinase_A 81 vItfDmGGTstDvslikd 98
                                       +++D+GGT tDv+l  d
  gi|336254795|ref|YP_004597902.1| 14 QVGVDVGGTFTDVALSVD 31
                                      589**********98665 PP

  == domain 2  score: 333.0 bits;  conditional E-value: 1.6e-103
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       rt+t++v+Ay+ p + +y+ ++ ++  ++g+ ++  +mq++Gg+++ +++r++ v t lSGPaaGvvgaaat + ++
  gi|336254795|ref|YP_004597902.1| 208 RTSTTAVDAYVRPAIDRYVGRLVDRASDEGI-PTPRIMQANGGIADPETVRERAVTTTLSGPAAGVVGAAATVDDED 283
                                       89****************************9.999****************************************** PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpa 154
                                       +  ++tfDmGGTs Dvsl++dg+ e++++ ei g+++r p+++++tvgagGgsi++vd gg+lrvgpes ga+pgp+
  gi|336254795|ref|YP_004597902.1| 284 VAGLVTFDMGGTSSDVSLVRDGRAERTTDAEIDGLPIRTPMVNVNTVGAGGGSIAWVDAGGALRVGPESSGAEPGPV 360
                                       ***************************************************************************** PP

                    Hydantoinase_A 155 cyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlk.veevAegilsvavenmanavr 230
                                       cy+kGgte+tvTDan+vLG++ pe  l   +g++ ldve+ar+a+e la+e +l+ + e+A g+++va+ +m + +r
  gi|336254795|ref|YP_004597902.1| 361 CYGKGGTEPTVTDANVVLGYIGPETAL---GGEMTLDVEAAREALERLADEAGLDgPLEAARGVYRVANATMTRTIR 434
                                       ************************999...***********************998********************* PP

                    Hydantoinase_A 231 klsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdv 287
                                       +++verg+dp+e++lv+fGGaG++haaalae+l v +v+vp+  gvlsa+G+++Ad 
  gi|336254795|ref|YP_004597902.1| 435 SVTVERGHDPREFALVAFGGAGPMHAAALAESLSVDRVVVPRPGGVLSAFGLLAADE 491
                                       *******************************************************96 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.29
                    Hydantoinase_A 241 keltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmal 284
                                       ++++ + ++G +  ++ a+ ++++ + v ++ ++    a+G+a+
  gi|336254795|ref|YP_004597902.1| 535 ERAADCRYAGQSFELTVAVDDAFDASAVAERFHEAHERAYGYAM 578
                                       66777889999999999999999999999999999999999875 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.0   0.1   4.5e-54   4.1e-50       2     177 ..      15     188 ..      14     189 .. 0.97
   2 ?    0.2   0.3     0.059   5.3e+02       3      19 ..     289     305 ..     287     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: 170.0 bits;  conditional E-value: 4.5e-54
                        Hydant_A_N   2 igIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkger 78 
                                       +g+DvGGTfTD+ +  +  ++++++K+++t d +  g++e +e+  + +++++++id   ++ Tv +Naller+g+r
  gi|336254795|ref|YP_004597902.1|  15 VGVDVGGTFTDVALSVD--DRLITAKVPTT-DPQHVGVLEGIEKGCDDAGIDPAEIDGFAHAMTVSVNALLERDGAR 88 
                                       8**********988884..57*********.99999***************************************** PP

                        Hydant_A_N  79 vaLittkgfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevrealkalkaagvesi 153
                                       +aL+tt+gfrd+leigrq rpdl++l+ +  +plv ++ ++evder++a   v +p+de+e+r  ++ l++++ve++
  gi|336254795|ref|YP_004597902.1|  89 TALVTTEGFRDVLEIGRQDRPDLYDLEAEkpDPLVARDLRFEVDERTTA-AGVERPVDESEIRDLAATLRERDVEAV 164
                                       *************************99998999****************.58************************* PP

                        Hydant_A_N 154 avvllhSylnpehElrvaeiarei 177
                                       av+llh+y+ pe+E+ vae +re+
  gi|336254795|ref|YP_004597902.1| 165 AVCLLHAYADPENERVVAETLREE 188
                                       **********************97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.059
                        Hydant_A_N   3 gIDvGGTfTDavaldek 19 
                                         D+GGT  D+ +++++
  gi|336254795|ref|YP_004597902.1| 289 TFDMGGTSSDVSLVRDG 305
                                       56*********999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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 0.23s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 5271.29
//
Query:       gi|336254796|ref|YP_004597903.1|  [L=473]
Description: initiation factor 2B-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-47  162.1   0.2    2.1e-47  161.7   0.2    1.1  1  IF-2B     Initiation factor 2 subunit family
      2e-09   37.6   0.2    4.7e-09   36.4   0.2    1.6  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
        2.3    8.2   8.3       0.15   12.0   1.6    2.6  2  Titin_Z   Titin Z


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 !  161.7   0.2   3.5e-51   2.1e-47       2     282 .]     181     454 ..     180     454 .. 0.91

  Alignments for each domain:
  == domain 1  score: 161.7 bits;  conditional E-value: 3.5e-51
                                       S-SHHHHHHHHHHHHHHHHHHCCCSTHHHH.......HHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSS CS
                             IF-2B   2 vrGspaiaiaalevllevikdaktskvaeL.......keelrkaidlLkkarPtavslgnairrllkeiselksssd 71 
                                       ++G+++++i+alevl++ +     s+ a++       + el++ +++L +arP++  l+n ++r+++e +  + +sd
  gi|336254796|ref|YP_004597903.1| 181 EHGAASLSIRALEVLRDRAGLLV-SERADFgadpegeRDELEELAERLLEARPSMAVLRNRVNRVMAEAAGADADSD 256
                                       5899************9999887.8899999999**9******************************9888888888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHH CS
                             IF-2B  72 vkeakksliekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGr 148
                                       + +a   ++e++ + i+++++ad   ++ aae i  + ++lT ++s+tv e lr+ +     ++V+v+EsrP  +G 
  gi|336254796|ref|YP_004597903.1| 257 DGDAPV-VLEAALDGIDRALAADDEAAATAAESI--DGAVLTLSRSGTVHEALRNGEP----LRVFVAESRPAREGV 326
                                       887775.67888999*******************..779**********998887666....99************* PP

                                       THHHHHHHTT...XEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGG CS
                             IF-2B 149 ltakeLvqag...ipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslk 221
                                        +a+eL+ +g    pv + td+a+a+v+s+ +vd v++GAd+il +Ga++nk+GT+ +A++A + ++p  vva + k
  gi|336254796|ref|YP_004597903.1| 327 AVAEELAADGaleCPVAVHTDAAAAHVLSHeDVDRVVIGADTILPDGALVNKTGTRAVAIAAAREDVPATVVAATDK 403
                                       *******9974447*************************************************************** PP

                                       BESTSSSGGGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 222 fservqldedifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       +s+r    e++  e +d + ++  +        ++v+np+fDvtP++ +t i Te G l+p
  gi|336254796|ref|YP_004597903.1| 404 VSTR----EEVNLESGDRAAVYDGEA------AVDVLNPTFDVTPADCVTEIATERGSLAP 454
                                       **99....555557777777665555......689**********************9987 PP

>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.2   7.8e-13   4.7e-09       8     119 ..      25     141 ..      19     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 7.8e-13
                                       EEEEETTSEEEEEEES..SSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE. CS
                             NUDIX   8 vvllnekgevLlvrrs..kkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd. 80 
                                       + +l+ +g vLl+rrs    + +g W  + G+ e  ++p + +r E++EEtGle +++ ++ + + +++ d+  +  
  gi|336254796|ref|YP_004597903.1|  25 A-FLRHRGNVLLLRRSdaVGTYQGqWGGVSGFAE--DDPDAQVRAEIREETGLEDDDVSFVRSGRPVRFRDDLADGg 98 
                                       3.4445556*******996677777*********..777444666********99*******887777777777669 PP

                                       .EEEEEEEEE...EEECSGCSSTSTTTEEEEEEEEHHHHHHHH CS
                             NUDIX  81 .eheilyvfl...eevegelepndenevsevrwvpleellkek 119
                                        ++++++ +l    ++ +e++ + ++e+++  w p++e++++ 
  gi|336254796|ref|YP_004597903.1|  99 eREWVVHPYLfdvTADADEPAIELSEEHDASAWAPPTEIVAPG 141
                                       88888866665577777777777999999999*******3333 PP

>> Titin_Z  Titin Z
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2      0.88   5.3e+03      30      39 ..     327     335 ..     322     337 .. 0.55
   2 ?   12.0   1.6   2.6e-05      0.15      14      29 ..     395     410 ..     391     413 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.88
                           Titin_Z  30 adtrEEeAae 39 
                                       a   EE Aa 
  gi|336254796|ref|YP_004597903.1| 327 AV-AEELAAD 335
                                       33.5677775 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.6e-05
                           Titin_Z  14 AtVVaAvDkarvrepl 29 
                                       AtVVaA+Dk+  re +
  gi|336254796|ref|YP_004597903.1| 395 ATVVAATDKVSTREEV 410
                                       9************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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 0.22s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3849.33
//
Query:       gi|336254797|ref|YP_004597904.1|  [L=311]
Description: Glyoxylate reductase (NADP(+)) [Halopiger xanaduensis SH-6]
Scores for 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  180.3   0.0    2.6e-53  180.0   0.0    1.1  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    3.8e-06   26.6   0.0    5.3e-06   26.1   0.0    1.3  1  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    1.3e-05   25.4   0.0    2.1e-05   24.7   0.0    1.3  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    6.6e-05   23.4   0.5     0.0029   18.1   0.2    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    7.9e-05   22.8   0.1    0.00073   19.6   0.0    2.1  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
  ------ inclusion threshold ------
      0.013   16.1   0.0      0.029   15.0   0.0    1.6  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.041   13.8   1.7      0.096   12.6   1.7    1.7  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.045   13.7   2.6        5.6    6.9   0.4    2.5  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.05   14.1   0.2        1.1    9.8   0.0    2.3  2  XdhC_C          XdhC Rossmann domain
       0.12   12.5   0.0       0.27   11.3   0.0    1.6  2  DpaA_N          Dipicolinate synthase subunit A N-terminal do
       0.13   11.8   0.0        0.2   11.2   0.0    1.2  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin


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 !  180.0   0.0   1.6e-56   2.6e-53       2     178 .]     104     279 ..     103     279 .. 0.97

  Alignments for each domain:
  == domain 1  score: 180.0 bits;  conditional E-value: 1.6e-56
                                       HHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHH CS
                      2-Hacid_dh_C   2 alllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeel 78 
                                       ++ll+++rr++ a +++++++w++++   g +l g t +++G+G +G+ va++l a+g++v+++ rs ++   ++e 
  gi|336254797|ref|YP_004597904.1| 104 GYLLSFARRIHTAVANQQDRRWDQPDWNDGFTLPGTTACVLGTGTLGSGVAEVLGALGVRVTGVRRSAEPVPGFDE- 179
                                       5799*****************************************************************9997777. PP

                                       TCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--S CS
                      2-Hacid_dh_C  79 gvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfe 155
                                        +  ++l e ++++D+v+++lplt++trhl++ae +++m+++a+++N++RG++vde aL++aL+s  iagaalDvfe
  gi|336254797|ref|YP_004597904.1| 180 VYATEDLLEGVSDADFVIVTLPLTEQTRHLVDAEVFEAMREDAYFVNVGRGPVVDESALIDALESDSIAGAALDVFE 256
                                       455889*********************************************************************** PP

                                       SSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 156 eeplpedspllelpnviltPHia 178
                                       +eplpe+spl+++++vi+tPH+a
  gi|336254797|ref|YP_004597904.1| 257 TEPLPEESPLWDMDEVIVTPHCA 279
                                       *********************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 !   26.1   0.0   3.3e-09   5.3e-06      57     133 ..      57     310 ..      24     311 .] 0.96

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.3e-09
                                       HHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHHHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                        2-Hacid_dh  57 ealpkLkviaragvGvDnvDldaakerGilVtnvpgystesvAElt............................... 102
                                       +a  ++ +++ + +GvD + +d +++ G+++tn  g + + v E++                               
  gi|336254797|ref|YP_004597904.1|  57 DAYLEVDWVHSIQAGVDRFPFDEFEASGVVLTNSTGIHDRWVGETVagyllsfarrihtavanqqdrrwdqpdwndg 133
                                       55567899********************************************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|336254797|ref|YP_004597904.1| 134 ftlpgttacvlgtgtlgsgvaevlgalgvrvtgvrrsaepvpgfdevyatedllegvsdadfvivtlplteqtrhlv 210
                                       ***************************************************************************** PP

                                       .....................................................................T-BHHHHH CS
                                       .....................................................................xxxxxxxx RF
                        2-Hacid_dh 103 .....................................................................aaTeeaqe 110
                                                                                                            a+Te+  +
  gi|336254797|ref|YP_004597904.1| 211 daevfeamredayfvnvgrgpvvdesalidalesdsiagaaldvfeteplpeesplwdmdevivtphcaAFTEDYFR 287
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHTTCCGTTBC CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 111 niaeeaaenlvaflkgespanav 133
                                       ++++++ en+++  +ge+  n+v
  gi|336254797|ref|YP_004597904.1| 288 AVGDIVRENVERLESGEPFHNRV 310
                                       ****************9999988 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 !   24.7   0.0   1.3e-08   2.1e-05       3     106 ..     142     244 ..     140     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.3e-08
                                       EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCC CS
                     NAD_binding_2   3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.lle 78 
                                        ++G+G++Gs  a+ l + g +v+++ r++e v  +   ++ a+e++ e v+++d+vi+ ++ +++++++++  ++e
  gi|336254797|ref|YP_004597904.1| 142 CVLGTGTLGSGVAEVLGALGVRVTGVRRSAEPVPGFD--EVYATEDLLEGVSDADFVIVTLPLTEQTRHLVDAeVFE 216
                                       589*****************************99997..5778999**************************99*** PP

                                       C--TT-EEEE-S---HHHHHHHHHHHHH CS
                     NAD_binding_2  79 alkkgdilidgstsspedtrelakelke 106
                                       a+++++++++++   + d   l ++l++
  gi|336254797|ref|YP_004597904.1| 217 AMREDAYFVNVGRGPVVDESALIDALES 244
                                       **********998877777777776665 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   0.0      0.11   1.7e+02      13      29 ..      22      38 ..      20      57 .. 0.89
   2 !   18.1   0.2   1.8e-06    0.0029       3      41 ..     142     180 ..     140     186 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.11
                                      HHHHHHHHTTSEEEEEE CS
                         Pyr_redox 13 ElAgalaelgkkVtvve 29
                                      ElA++l +l ++Vtvv 
  gi|336254797|ref|YP_004597904.1| 22 ELAAYLDDLPAEVTVVG 38
                                      9**************95 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.8e-06
                                       EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHH CS
                         Pyr_redox   3 vvvGgGyiglElAgalaelgkkVtvversdkllrllDee 41 
                                        v+G G++g  +A++l +lg +Vt v rs ++ +++De 
  gi|336254797|ref|YP_004597904.1| 142 CVLGTGTLGSGVAEVLGALGVRVTGVRRSAEPVPGFDEV 180
                                       69***********************************85 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 ?    0.6   0.0      0.31   5.1e+02      40      73 ..      48      81 ..      33     102 .. 0.67
   2 !   19.6   0.0   4.5e-07   0.00073      21     111 ..     136     229 ..     130     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.31
                                      HHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HH CS
                     AdoHcyase_NAD 40 aslkglGarvivtevdPicalqaameGfevvtle 73
                                      +++ ++  r    evd + ++qa ++ f   ++e
  gi|336254797|ref|YP_004597904.1| 48 DAVVTFEHRDAYLEVDWVHSIQAGVDRFPFDEFE 81
                                      5555566666677999999999999988755443 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 4.5e-07
                                       -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE..-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE....-SSSSSS CS
                     AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivt..evdPicalqaameGfevvtleevvkkadivvt....ttGnkdi 91 
                                       l G +a+v G G +G G a+ l +lG rv+      +P+  +    e +    l e v++ad+v+     t  ++ +
  gi|336254797|ref|YP_004597904.1| 136 LPGTTACVLGTGTLGSGVAEVLGALGVRVTGVrrSAEPVPGF---DEVYATEDLLEGVSDADFVIVtlplTEQTRHL 209
                                       7799**********************9986431145666655...5779999998889999987761333346789* PP

                                       B-HHHHCCS-TTEEEEE-SS CS
                     AdoHcyase_NAD  92 itlehlkkmkddaivcniGh 111
                                       + +e +++m++da   n+G 
  gi|336254797|ref|YP_004597904.1| 210 VDAEVFEAMREDAYFVNVGR 229
                                       ******************96 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 ?   15.0   0.0   1.8e-05     0.029       3      73 ..     142     204 ..     140     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                                       EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHH CS
                     F420_oxidored   3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkped 73 
                                       +++G+G +g+++a+ l a g     ++ + +r+ e +  + e +   +t+ d  e +++ad+v+++++ + 
  gi|336254797|ref|YP_004597904.1| 142 CVLGTGTLGSGVAEVLGALG---VRVT-GVRRSAEPVPGFDEVY---ATE-DLLEGVSDADFVIVTLPLTE 204
                                       689*****************...8899.8788888888887666...788.9**************99865 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   1.7   5.9e-05     0.096       3      34 ..     142     173 ..     140     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
                                       EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseea 34 
                                        v+G+Gt+G+g+a+v+ + g++V+ v +s+e 
  gi|336254797|ref|YP_004597904.1| 142 CVLGTGTLGSGVAEVLGALGVRVTGVRRSAEP 173
                                       69**********************99988765 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 ?   -3.5   0.0       5.5     9e+03      47      74 ..      26      51 ..      22      52 .. 0.69
   2 ?    6.9   0.4    0.0034       5.6       3      32 ..     142     171 ..     140     179 .. 0.86
   3 ?    6.7   0.0    0.0041       6.8      56     105 ..     179     230 ..     174     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.5
                                      TBTT----TTEEEES-HHHHHTT--EEE CS
                    NAD_Gly3P_dh_N 47 yLpgiklpenlvattdlaealkgadiiv 74
                                      yL++  lp++++++ d a+ ++ +d +v
  gi|336254797|ref|YP_004597904.1| 26 YLDD--LPAEVTVVGDDAAEITACDAVV 51
                                      5554..7888888877777777777766 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0034
                                       EEE--SHHHHHHHHHHHTTT--EEEE-S-H CS
                    NAD_Gly3P_dh_N   3 avlGaGswGtalAkvlaenghevrlwvree 32 
                                       +vlG+G  G+ +A vl+  g +v+   r++
  gi|336254797|ref|YP_004597904.1| 142 CVLGTGTLGSGVAEVLGALGVRVTGVRRSA 171
                                       8*******************9998777766 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0041
                                       TEEEES-HHHHHTT--EEEE---HHHHHH..HHHHHCCC--TT-EEEE---S CS
                    NAD_Gly3P_dh_N  56 nlvattdlaealkgadiivlvvPsqalre..vlkklkgllkkkailvsliKG 105
                                       ++ at+dl e +++ad++++ +P    ++  v +++ + ++++a +v++ +G
  gi|336254797|ref|YP_004597904.1| 179 EVYATEDLLEGVSDADFVIVTLPLTEQTRhlVDAEVFEAMREDAYFVNVGRG 230
                                       799*******************964433300334556666777777776666 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.15   2.4e+02      12      35 ..      22      59 ..      20     126 .. 0.64
   2 ?    9.8   0.0   0.00068       1.1       3      68 ..     143     245 ..     141     252 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.15
                                      HHHHHHHHHTEEEEEEES-G.GGG.............- CS
                            XdhC_C 12 alarlaaalgfrvtvvdpre.efa.............t 35
                                      +la+++  l+ +vtvv +++ e++              
  gi|336254797|ref|YP_004597904.1| 22 ELAAYLDDLPAEVTVVGDDAaEITacdavvtfehrdaY 59
                                      68999999999**9999988444444444433333330 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00068
                                       EE--STTHHHHHHHHHHHTEEEEEEES-GGGG..............................-GGG-TT-SE..... CS
                            XdhC_C   3 ifGaghvaqalarlaaalgfrvtvvdpreefa..............................tkerfpeade..... 44 
                                       ++G g  +  +a+++ alg+rvt v+  +e                                +        +     
  gi|336254797|ref|YP_004597904.1| 143 VLGTGTLGSGVAEVLGALGVRVTGVRRSAEPVpgfdevyatedllegvsdadfvivtlplteQ--------Trhlvd 211
                                       89***********************99987446777777666666666555555555555541........044444 PP

                                       ..........-EEEE--S-HHHHHHHHHHHSSS- CS
                            XdhC_C  45 ..........tavvvlthdhklDaealeaalrkk 68 
                                                 +++v + +++  D+ al  al+++
  gi|336254797|ref|YP_004597904.1| 212 aevfeamredAYFVNVGRGPVVDESALIDALESD 245
                                       4456666678999999999999999999999644 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 ?   -3.3   0.0       5.6   9.1e+03      15      30 ..      24      39 ..      22      52 .. 0.55
   2 ?   11.3   0.0   0.00016      0.27      15      69 ..     154     210 ..     152     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.6
                                      HHHHHHTT-EEEEES- CS
                            DpaA_N 15 arkLaekgakvslygl 30
                                      a +L +  a+v+++g 
  gi|336254797|ref|YP_004597904.1| 24 AAYLDDLPAEVTVVGD 39
                                      5566666666666653 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00016
                                       HHHHHHTT-EEEEES-..TSSS-BTTEEEE-GGGS-GGG-SEEE--TT-BETTTEE- CS
                            DpaA_N  15 arkLaekgakvslygl..eleekiegvekaesleealedadviilPvpgtkdggein 69 
                                       a+ L + g +v+ +    e   ++++v  +e+l e ++dad++i+ +p+t++ +++ 
  gi|336254797|ref|YP_004597904.1| 154 AEVLGALGVRVTGVRRsaEPVPGFDEVYATEDLLEGVSDADFVIVTLPLTEQTRHLV 210
                                       666777787777775577889999***************************999875 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 ?   11.2   0.0   0.00012       0.2       3      91 ..     137     224 ..     135     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                       HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-H.HHHHHHHH CS
                              IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPD.elqkevye 78 
                                        g + +v+G G+ G   a+ l   g+ v+ g+r+++       +e + + ++ e v++ad+v++ +P  e+ +++++
  gi|336254797|ref|YP_004597904.1| 137 PGTTACVLGTGTLGSGVAEVLGALGVRVT-GVRRSA-EPVPGFDEVYATEDLLEGVSDADFVIVTLPLtEQTRHLVD 211
                                       567889*****************999986.777766.45567788999999****************6155678999 PP

                                       HHTGGG--TT-EE CS
                              IlvN  79 eeiepnlkegkal 91 
                                       +e+ + ++e+++ 
  gi|336254797|ref|YP_004597904.1| 212 AEVFEAMREDAYF 224
                                       ******9998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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):              11  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2394.98
//
Query:       gi|336254798|ref|YP_004597905.1|  [L=194]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-14   53.9   0.0    2.4e-14   53.4   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.1e-12   48.2   0.0    1.4e-12   47.9   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.6e-10   39.8   0.0    7.4e-10   39.1   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    7.3e-06   25.9   0.0    1.6e-05   24.8   0.0    1.5  1  FR47             FR47-like protein
      5e-05   23.4   0.0     0.0003   20.9   0.0    2.0  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00093   19.4   0.0     0.0038   17.4   0.0    1.8  2  Acetyltransf_4   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 !   53.4   0.0   7.9e-18   2.4e-14      39     120 ..      94     184 ..      91     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 7.9e-18
                   Acetyltransf_10  39 ggkivGvi.......el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFk 107
                                       ++ +vG++       ++ +d+++i  ++V+p++ ++G+g+aLl+++e++a+++g++ +l + as +a++fYe++G++
  gi|336254798|ref|YP_004597905.1|  94 SDDLVGFGlldlepsAYgSDTGRIKSIYVRPDAARTGVGTALLDRLEAAAREAGLE-QLALTASENAIEFYERQGYE 169
                                       5666766644444444556777*****************************99999.******************** PP

                   Acetyltransf_10 108 av..geeqeenGirf 120
                                        +     + e+G+++
  gi|336254798|ref|YP_004597905.1| 170 GIdtRTLEMEDGVTL 184
                                       996566777888754 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   4.6e-16   1.4e-12      41     117 .]      84     168 ..      42     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 4.6e-16
                                       T..........TEEEEEEEEEEEET.TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEH CS
                    Acetyltransf_1  41 d..........geliGfisllkipd.ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveednd 106
                                       +          + l+Gf  l   p     +++ i s++V+p++ + G+G+aLl+ le  are g++ + l + + n 
  gi|336254798|ref|YP_004597905.1|  84 GrddfddrddsDDLVGFGLLDLEPSaYGSDTGRIKSIYVRPDAARTGVGTALLDRLEAAAREAGLEQLAL-TASEN- 158
                                       3334666666678************988899**********************************99999.43445. PP

                                       HHHHHHHHTTE CS
                    Acetyltransf_1 107 aairlYeklGF 117
                                        ai++Ye+ G+
  gi|336254798|ref|YP_004597905.1| 159 -AIEFYERQGY 168
                                       .9********8 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   2.5e-13   7.4e-10       4      75 ..      77     169 ..      74     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 2.5e-13
                                       EEEEEEET..........TEEEEEEEEEEES.......TCTEEEEE-GGGTTSSHHHHHHH.H..TT..SEEEEEEE CS
                    Acetyltransf_7   4 evfVaedd..........gkivGfialslld.......aeitrlaVdpeyrgkGiGraLle.a..ae..kgiileql 58 
                                       +v+Vae +          +  vGf  l l+        + i+ ++V+p++ + G+G+aLl+ +  a+   g+  eql
  gi|336254798|ref|YP_004597905.1|  77 RVLVAEVGrddfddrddsDDLVGFGLLDLEPsaygsdtGRIKSIYVRPDAARTGVGTALLDrLeaAAreAGL--EQL 151
                                       5677777766777777778888888877777888876555555*****************953332244664..333 PP

                                       EE.THHHHHHHHHHTTEE CS
                    Acetyltransf_7  59 el.naekaikfYeklGFe 75 
                                        l ++e+ai+fYe+ G+e
  gi|336254798|ref|YP_004597905.1| 152 ALtASENAIEFYERQGYE 169
                                       44322389*********7 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   5.4e-09   1.6e-05      19      82 ..     112     173 ..     108     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.4e-09
                                       -TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEEE CS
                              FR47  19 kdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekiee 82 
                                       +d g + +++v+p++ r G g+ l   l ++ +e+g + l++++ +N  +i++ye+ G+e i++
  gi|336254798|ref|YP_004597905.1| 112 SDTGRIKSIYVRPDAARTGVGTALLDRLEAAAREAGLEQLALTASEN--AIEFYERQGYEGIDT 173
                                       57899*************************************98876..9*********99866 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     1e-07    0.0003      73     126 ..     114     169 ..      24     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1e-07
                                       EEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--..SSHHHHHTTT-E CS
                    Acetyltransf_9  73 aagvtgVavapehrgrgvlskLlaraleemreegqplsllfP..ssipiYrrfGye 126
                                       ++ + ++ v p+  + gv ++Ll+r+ + +re g +   l++   +i++Y+r Gye
  gi|336254798|ref|YP_004597905.1| 114 TGRIKSIYVRPDAARTGVGTALLDRLEAAAREAGLEQLALTAseNAIEFYERQGYE 169
                                       67899999**********************************55559********8 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.4   1.2e+03       1      50 [.      25      69 ..      25      75 .. 0.64
   2 !   17.4   0.0   1.3e-06    0.0038      56     135 ..      93     169 ..      88     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.4
                    Acetyltransf_4  1 iraateeDakeilaiyaeyvvntaitfeyevssveefekflealdsekey 50
                                      +r at  Da  i +i a   +++   + ++v+   ++e +l+++  +++y
  gi|336254798|ref|YP_004597905.1| 25 VREATAGDAPTIADIHAA-AIRE---RGSNVYDEHQLEAWLANV-HPERY 69
                                      578888899999999886.3322...334455555666677766.55555 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.3e-06
                    Acetyltransf_4  56 esdrivGyaylg.qfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhka 131
                                       +sd++vG   l  ++ + + d   + s+y+ + d+  +g+g +l+d le  ++e ++e+l a +a   en+i+f+++
  gi|336254798|ref|YP_004597905.1|  93 DSDDLVGFGLLDlEPSAYGSDTGRIKSIYV-RPDAARTGVGTALLDRLEAAAREAGLEQL-ALTA--SENAIEFYER 165
                                       58999998888866666688889999****.589*************************9.5556..689******* PP

                    Acetyltransf_4 132 lGFe 135
                                        G+e
  gi|336254798|ref|YP_004597905.1| 166 QGYE 169
                                       ***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1465.20
//
Query:       gi|336254799|ref|YP_004597906.1|  [L=155]
Description: NUDIX hydrolase [Halopiger xanaduensis SH-6]
Scores for 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   42.4   0.1      1e-10   41.8   0.1    1.4  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 !   41.8   0.1   5.6e-15     1e-10      28     116 ..      27     135 ..       4     150 .. 0.63

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 5.6e-15
                                       TTEE.SSEEECBTTSHHHHHHHHHHHHHHSEEEEEE...........EEEEEEEEEEEEEEEEEE............ CS
                             NUDIX  28 pgWe.lPgGkvepgEtpeeAArREleEEtGleaell...........ellgrlhylapydgpygd............ 80 
                                        g +  PgG+v+ +E p eA  RE++EEtGle+ ll           +                +            
  gi|336254799|ref|YP_004597906.1|  27 LGLTlPPGGHVDRDELPHEAGKREVREETGLEPTLLddppaidapdgR--------------SLPkprhhmlydidv 89 
                                       3445489************************99555555555544441..............443443334444444 PP

                                       ......EEEEEEEEEEEECSGCSSTSTTT..EEEEEEEEHHHH..H CS
                             NUDIX  81 ......eheilyvfleevegelepndene..vsevrwvpleel..l 116
                                               +i+ ++ + v ++   ++++e   ++++w+++++l   
  gi|336254799|ref|YP_004597906.1|  90 sdgevgHQHIDQIYYATVPSRDISPADGEvsADAWEWYSPADLrgS 135
                                       44457655555555555555555556888567789********431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1183.71
//
Query:       gi|336254800|ref|YP_004597907.1|  [L=183]
Description: hypothetical protein Halxa_3417 [Halopiger xanaduensis SH-6]
Scores for 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-50  170.0   0.2    4.9e-50  169.8   0.2    1.0  1  GrpB      GrpB protein
  ------ inclusion threshold ------
       0.13   13.2   1.2        2.1    9.4   0.2    2.9  2  TPR_14    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> GrpB  GrpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.8   0.2   5.5e-54   4.9e-50       2     159 ..       9     170 ..       8     171 .. 0.95

  Alignments for each domain:
  == domain 1  score: 169.8 bits;  conditional E-value: 5.5e-54
                                       X--BS--THHHHHHHHHHHHHHHHH...E.EEEEESGGGSTT--B-S-EEEEEEES..-SGGGGGGHHHHHHTT-EE CS
                              GrpB   2 velveydpeWpeqferekarlraal...i.sieHiGSTsvpglaAKpiiDilvvve..dledeeelveaLeaagyel 72 
                                       vel++y++eW+++fe+e++r+r+al   i ++eH+GST+++glaAKpiiD+l+vve   +e+ ++ +++Le+++y++
  gi|336254800|ref|YP_004597907.1|   9 VELEPYNDEWQRAFETEAERVRSALgdrIvALEHVGSTAIEGLAAKPIIDMLLVVEslPDEQRHRWIDRLEDLDYTF 85 
                                       89************************99559*************************55466777899********** PP

                                       .-TTTTSTTEEEEEE-SSS..--EEEEEEETT-HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHTT-SS-HHHH--- CS
                              GrpB  73 lrgepgiperrlfvkgedeeertvhlhvveagspelerhllfrdyLrahpearaeYaalKrelaakaeedidaYtea 149
                                        r ++ +++r +f+kg ++ ert+ l   e+gs+++ +++lfrdyLr+hp+++a+Y++lKrela+++++d+daYte+
  gi|336254800|ref|YP_004597907.1|  86 -RLNDPVADRLFFAKGPER-ERTHYLSATERGSDTHVEQRLFRDYLRQHPTEAAAYEQLKRELASRYPDDRDAYTER 160
                                       .88999*********9777.8******************************************************** PP

                                       -HHHHHHHHH CS
                              GrpB 150 Keefikeilk 159
                                       K++f+++il+
  gi|336254800|ref|YP_004597907.1| 161 KSQFVQRILQ 170
                                       ********97 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00023       2.1      22      41 ..     123     142 ..     107     144 .. 0.90
   2 ?    2.7   0.2     0.032   2.9e+02      20      40 ..     138     159 ..     137     163 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00023
                            TPR_14  22 allrralalaPddaeawlll 41 
                                       +l+r++l+++P++a+a+ +l
  gi|336254800|ref|YP_004597907.1| 123 RLFRDYLRQHPTEAAAYEQL 142
                                       79**************9887 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.032
                            TPR_14  20 Aiallrr.alalaPddaeawll 40 
                                       A + l+r + +++Pdd++a+++
  gi|336254800|ref|YP_004597907.1| 138 AYEQLKReLASRYPDDRDAYTE 159
                                       556666635679*****99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.25s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1469.42
//
Query:       gi|336254801|ref|YP_004597908.1|  [L=127]
Description: DGC domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-33  113.3   0.4      6e-33  113.1   0.4    1.0  1  DGC       DGC domain


Domain annotation for each model (and alignments):
>> DGC  DGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1   0.4   3.3e-37     6e-33       1     105 [.      10     114 ..      10     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 3.3e-37
                               DGC   1 lvvsCsGasnvGqlaneaavklakegeakmiclagvgagveelvelaksarkiiaidGCpleCakkilekagvkpde 77 
                                       lv+sCsG+s+++q+an++av l++e+ a+m+c+agvg++v  lve+a++ r+++aidGCpleCa+++le+++v+p+ 
  gi|336254801|ref|YP_004597908.1|  10 LVYSCSGCSSAAQMANDLAVSLDREKIAEMSCIAGVGGDVAPLVETATADRPVVAIDGCPLECARQCLEQHDVEPEL 86 
                                       69***********************99************************************************** PP

                               DGC  78 hlvvtdlgikkeekldlseeeiekvvea 105
                                       h++++  g+ ke++++++ee++++++e+
  gi|336254801|ref|YP_004597908.1|  87 HYMLAAEGVPKEYHTEYDEEQADELFEE 114
                                       **********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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: 0.39u 0.19s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1073.48
//
Query:       gi|336254802|ref|YP_004597909.1|  [L=205]
Description: GTP-binding protein engB [Halopiger xanaduensis SH-6]
Scores for 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-20   70.8   0.0    1.6e-19   70.1   0.0    1.4  1  MMR_HSR1     50S ribosome-binding GTPase
    1.2e-13   50.9   0.2    2.5e-12   46.6   0.2    2.0  1  FeoB_N       Ferrous iron transport protein B
    8.6e-07   28.7   0.3    2.5e-05   23.9   0.3    2.1  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    7.1e-05   22.8   0.2      0.049   13.5   0.1    2.5  2  RsgA_GTPase  RsgA GTPase
    0.00081   19.5   0.0      0.033   14.3   0.0    2.2  2  Dynamin_N    Dynamin family
    0.00083   19.2   1.1      0.055   13.2   0.1    2.5  2  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0019   18.4   0.1      0.013   15.7   0.0    2.1  2  Roc          Ras of Complex, Roc, domain of DAPkinase
     0.0026   17.6   0.3     0.0059   16.5   0.3    1.5  1  RBD-FIP      FIP domain
     0.0031   18.0   0.0     0.0041   17.6   0.0    1.5  1  ABC_tran     ABC transporter
     0.0047   16.3   0.0     0.0071   15.7   0.0    1.3  1  AIG1         AIG1 family
  ------ inclusion threshold ------
      0.012   14.6   0.3        2.4    7.1   0.0    2.2  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.016   15.8   0.0      0.032   14.8   0.0    1.6  2  AAA_18       AAA domain
      0.044   14.1   0.3       0.61   10.4   0.2    2.7  2  AAA_22       AAA domain
      0.044   13.4   0.0       0.12   11.9   0.0    1.7  2  Ras          Ras family
      0.064   12.7   0.0        3.4    7.1   0.0    2.3  2  Arf          ADP-ribosylation factor family
       0.15   11.8   0.0       0.49   10.1   0.0    1.8  2  AAA_24       AAA domain
       0.15   11.8   0.0       0.29   10.9   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0   1.5e-22   1.6e-19       1     114 []      11     141 ..      11     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.5e-22
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGC..S...SHHHHHH..HHHHHH CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGl..i...egaseek..glgkaf 70 
                                       eva+vGr+NvGKStL++ ltg +  ++ kpg+Tr++n++ ++   ++++++D+pG+  +   +++++e+      ++
  gi|336254802|ref|YP_004597909.1|  11 EVALVGRSNVGKSTLMRELTGHTFDTGGKPGVTRQPNHYDWA--PEDFVITDLPGFgfMsgvDEEHREEikTNIVHY 85 
                                       69***************************************9..678********5431333333444423222233 PP

                                       HH.HHC.TSEEEEEEETT............TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  71 la.lee.adlillvvdas............eeklkpldeeleelleeakkplilvlnk 114
                                       l+   e   +++lvvd +            +e   p d e+  +l++ ++p+++++nk
  gi|336254802|ref|YP_004597909.1|  86 LEdYAEnILVAVLVVDGKsvidiidrhsgpDE--VPYDVEMFHFLRDLDIPVVVAVNK 141
                                       32222335677788884477777666544222..356788999999999999999998 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 !   46.6   0.2   2.3e-15   2.5e-12       2     126 ..      11     153 ..      10     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 2.3e-15
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHH..HHHHHHHHH. CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsaysee..ekvardfll. 75 
                                       +valvG  nvGk+tl+ +ltg + + g  pGvt + +  +++++ +++ i+DlPG   +s + ee  e++ +++++ 
  gi|336254802|ref|YP_004597909.1|  11 EVALVGRSNVGKSTLMRELTGHTFDTGGKPGVTRQPN--HYDWAPEDFVITDLPGFGFMSGVDEEhrEEIKTNIVHy 85 
                                       69******************************96665..566669**********9777655554335566555544 PP

                                       ....CTSSSEEEEEEEGGG....HHH.........HHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE- CS
                            FeoB_N  76 ....eeepdvvvnvvdatn....ler.........nLyLtlqllelgvpvvlalnmideaekkgieid 126
                                            e++ v v vvd ++    ++r         ++ ++  l +l++pvv+a+n++d++++k  +++
  gi|336254802|ref|YP_004597909.1|  86 ledyAENILVAVLVVDGKSvidiIDRhsgpdevpyDVEMFHFLRDLDIPVVVAVNKMDKVDDKDERLN 153
                                       4333344444455566554111123311111112268899999*****************99988775 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 !   23.9   0.3   2.4e-08   2.5e-05       6     141 ..      12     154 ..       8     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.4e-08
                                       EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHH....HHHTSCSSCEEEEEETTCSSEEEEEEEES CS
                          GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeE....rergiTiksaaisleketkkylinliDtP 78 
                                       ++++g  + GK+TL+ +L+ +t ++  k  ++ + +  D+++e+       g+   s + + +   ++ + n++   
  gi|336254802|ref|YP_004597909.1|  12 VALVGRSNVGKSTLMRELTGHTFDTGGKPGVTRQPNHYDWAPEDfvitDLPGFGFMSGVDEEH--REEIKTNIVHY- 85 
                                       667777888888888888877777777777777777788888762211233444444444444..77778888765. PP

                                       SSGGGHHHHHHHHHT-SE..EEEEEETTTBST..HHHHHHHHHHHHTTTEEEEEEESCGST...HHHHHH CS
                          GTP_EFTU  79 GHvdFskevirglrvlDg..avlvvdaveGve..pqteevlrlalkegvpiivfiNKmDrl...kaelke 141
                                         +d+ +++  ++ v+Dg  ++ ++d ++G+   p   e+++ ++++++p++v++NKmD++   +++l+ 
  gi|336254802|ref|YP_004597909.1|  86 -LEDYAENILVAVLVVDGksVIDIIDRHSGPDevPYDVEMFHFLRDLDIPVVVAVNKMDKVddkDERLND 154
                                       .489*************95457789999**76225567899********************555444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   4.6e-05     0.049     102     122 ..      12      32 ..       7      68 .. 0.84
   2 !    6.9   0.0     0.005       5.2      42      75 ..     128     159 ..     122     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.6e-05
                                       EEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpe 122
                                       ++lvG S vGKStL+ +l+++
  gi|336254802|ref|YP_004597909.1|  12 VALVGRSNVGKSTLMRELTGH 32 
                                       789***************997 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.005
                                       HHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHT CS
                       RsgA_GTPase  42 aeekgiepvivlnKiDlleeeeeleelkeeleal 75 
                                       + + +i++v+++nK+D +++++  e+l++   +l
  gi|336254802|ref|YP_004597909.1| 128 LRDLDIPVVVAVNKMDKVDDKD--ERLNDLCDRL 159
                                       567799*************999..4444444444 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.1e-05     0.033       1      36 [.      12      47 ..      12      50 .. 0.94
   2 ?    3.4   0.0     0.068        71      96     137 ..      49     101 ..      47     113 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-E CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrpl 36
                                      +a+vG  + GKS+++  L+g+ +   g+  +Tr p+
  gi|336254802|ref|YP_004597909.1| 12 VALVGRSNVGKSTLMRELTGHTFDTGGKPGVTRQPN 47
                                      799********************9999999***997 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.068
                                       EETTS-SEEEEE---B-SSSGTTS...........HHHHHHHSTTEEEEEEEE CS
                         Dynamin_N  96 lsllvkgltlvDlPGldsvnkrdq...........elvkeyikkadiilavts 137
                                       +++  ++ ++ DlPG+  +   d+           + ++ y+++  + ++v++
  gi|336254802|ref|YP_004597909.1|  49 YDWAPEDFVITDLPGFGFMSGVDEehreeiktnivHYLEDYAENILVAVLVVD 101
                                       677888999******87655444444466666555555555555555555555 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 ?    4.5   0.2     0.025        26       2      25 ..      15      38 ..      14      43 .. 0.84
   2 !   13.2   0.1   5.2e-05     0.055     112     211 ..      80     196 ..      47     203 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.025
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgr 25
                                      vG   +GK+t++++l+ ++ ++g 
  gi|336254802|ref|YP_004597909.1| 15 VGRSNVGKSTLMRELTGHTFDTGG 38
                                      78899***********99988765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.2e-05
                        ATP_bind_1 112 akiveeLes..efalvvvyLvDsqrltdptkfisg...l...lsalsamlrlelPhvvvlnkfDllkeklekeleff 180
                                        +iv+ Le   e  lv+v +vD + + d ++  sg   +   +     +  l++P vv++nk+D +++k+e+  +  
  gi|336254802|ref|YP_004597909.1|  80 TNIVHYLEDyaENILVAVLVVDGKSVIDIIDRHSGpdeVpydVEMFHFLRDLDIPVVVAVNKMDKVDDKDERLNDLC 156
                                       4678888877666778888888888888555555422221112234456689*************998854443333 PP

                        ATP_bind_1 181 edvealslllekee.........ekykklaeaiaelleef 211
                                         +  +   ++ +e         ++ + l+ea++e l e 
  gi|336254802|ref|YP_004597909.1| 157 DRLGLYPPWKQWQEtiapitakkGRIEPLNEAVREHLHEQ 196
                                       3332222222222233355555566666666666666665 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-05     0.013       2      28 ..      12      38 ..      11      52 .. 0.88
   2 ?    0.3   0.1      0.74   7.8e+02     108     119 ..     132     143 ..      75     144 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                                      EEEESSTTSSHHHHHHCHCT-CCC-EE CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfseke 28
                                      v lvG s+vGK++l+++++ ++f++  
  gi|336254802|ref|YP_004597909.1| 12 VALVGRSNVGKSTLMRELTGHTFDTGG 38
                                      789********************9765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.74
                                       SS-EEEEEE-TT CS
                               Roc 108 kspvilvgnkiD 119
                                       ++pv++ +nk+D
  gi|336254802|ref|YP_004597909.1| 132 DIPVVVAVNKMD 143
                                       568888889988 PP

>> RBD-FIP  FIP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   5.5e-06    0.0059      14      31 ..      81      98 ..      73      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.5e-06
                                      HHHHHHHHHHHHHHHHHH CS
                           RBD-FIP 14 eenrrLedYiDnlLlrvm 31
                                      +++++LedY++n+L++v+
  gi|336254802|ref|YP_004597909.1| 81 NIVHYLEDYAENILVAVL 98
                                      68899***********95 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.9e-06    0.0041      12      45 ..      10      43 ..       7     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.9e-06
                                      SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllkpteGeilld 45
                                        va+vG++  GKStL++ l+g++ +t G+  + 
  gi|336254802|ref|YP_004597909.1| 10 AEVALVGRSNVGKSTLMRELTGHTFDTGGKPGVT 43
                                      569********************99999986544 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.7e-06    0.0071       3      92 ..      12     101 ..      10     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.7e-06
                                       EEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SC.CCTTC...CHHCHHHHHHH CS
                              AIG1   3 ivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPgl.fdlsv...sadkiskeivr 75 
                                       + lvG++ +GkS+    + g + F++   + +vt++++++ ++++  + ++ D Pg  f + v   + ++i+ +iv+
  gi|336254802|ref|YP_004597909.1|  12 VALVGRSNVGKSTLMRELTG-HTFDTG-GKPGVTRQPNHYDWAPE--DFVITDLPGFgFMSGVdeeHREEIKTNIVH 84 
                                       679*********88888666.68**99.599****9998876666..56788****764444323468889999999 PP

                                       HHHHCTT-ESEEEEEEE CS
                              AIG1  76 clllseegihalllvls 92 
                                        l+  +e i + +lv++
  gi|336254802|ref|YP_004597909.1|  85 YLEDYAENILVAVLVVD 101
                                       87776776666666665 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 ?    5.4   0.1    0.0074       7.8      28      62 ..       8      42 ..       3      44 .. 0.85
   2 ?    7.1   0.0    0.0022       2.4     167     230 ..     132     194 ..     130     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0074
                                      -SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEE CS
                              MeaB 28 raqvvGltGvPGaGkstlvealglelrrrGkrvav 62
                                      r   v l G   +Gkstl+ +l+ +  + G + +v
  gi|336254802|ref|YP_004597909.1|  8 REAEVALVGRSNVGKSTLMRELTGHTFDTGGKPGV 42
                                      56678999***************999999887665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0022
                                       HH-SEEEEE---HHHH.HHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHHH CS
                              MeaB 167 eiaDiivvnkaDkkea.ekaarelraaleleeekekeWrpkvlktsavegeGidelvdaieehre 230
                                       +i  +++vnk Dk +  ++  ++l   l l  +  k+W+  +  ++a++g+ i+ l +a++eh +
  gi|336254802|ref|YP_004597909.1| 132 DIPVVVAVNKMDKVDDkDERLNDLCDRLGLY-PPWKQWQETIAPITAKKGR-IEPLNEAVREHLH 194
                                       5667899*****6544044445666666654.55789**********9998.**********976 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     3e-05     0.032       1      95 [.      12     125 ..      12     144 .. 0.64
   2 ?   -2.3   0.0       5.7     6e+03      26      43 ..     150     167 ..     135     198 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..........gvnlrdvakenglllevdpe.......aldeskrldedkldkl 60 
                                       ++l G + vGK+tl +eL  ++ f            n+ d a+e + ++++ p        + +  ++++++ +++l
  gi|336254802|ref|YP_004597909.1|  12 VALVGRSNVGKSTLMRELTGHT-FdtggkpgvtrQPNHYDWAPE-DFVITDLPGfgfmsgvDEEHREEIKTNIVHYL 86 
                                       67999*************8885.666889988885566666655.55555555545544222224444555555555 PP

                            AAA_18  61 ldaleenss....aleegknlvidghlaeleseaakdik 95 
                                        d  e++        ++    +id h +  e ++++++ 
  gi|336254802|ref|YP_004597909.1|  87 EDYAENILVavlvVDGKSVIDIIDRHSGPDEVPYDVEMF 125
                                       555555444886655556666888888887777766665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.7
                            AAA_18  26 vnlrdvakenglllevdp 43 
                                       ++l+d++   gl+ ++ +
  gi|336254802|ref|YP_004597909.1| 150 ERLNDLCDRLGLYPPWKQ 167
                                       556666666666666554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00058      0.61       9      28 ..      13      32 ..       7     159 .. 0.71
   2 ?    0.2   0.0      0.81   8.6e+02      70      90 ..     171     197 ..     126     202 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00058
                            AAA_22  9 vvtGesGtGKTtllrrlleq 28
                                      +++G s +GK+tl+r+l+  
  gi|336254802|ref|YP_004597909.1| 13 ALVGRSNVGKSTLMRELTGH 32
                                      799*************9854 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.81
                            AAA_22  70 a......erlsseellealeqalrara 90 
                                       +      + ++ e l ea++++l+++ 
  gi|336254802|ref|YP_004597909.1| 171 TiapitaKKGRIEPLNEAVREHLHEQN 197
                                       033333345566666677777777665 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.12       2      32 ..      12      42 ..      11      54 .. 0.88
   2 ?   -2.2   0.0       2.6   2.8e+03     103     118 ..     131     146 ..     105     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                      EEEEESTTSSHHHHHHHHHHSSCSSSCTTTS CS
                               Ras  2 lvlvGdsavGKtslllrfvkdkFkeeyesTi 32
                                      + lvG s+vGK++l+ + + ++F++  ++ +
  gi|336254802|ref|YP_004597909.1| 12 VALVGRSNVGKSTLMRELTGHTFDTGGKPGV 42
                                      679********************98777655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                                       TTSEEEEEEETTTGGG CS
                               Ras 103 envpivLvGnKvDlee 118
                                        ++p+v+  nK+D  +
  gi|336254802|ref|YP_004597909.1| 131 LDIPVVVAVNKMDKVD 146
                                       4688888899998655 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0032       3.4      12      41 ..       7      36 ..       2      65 .. 0.79
   2 ?    3.4   0.1     0.043        46      76     133 ..      87     150 ..      78     191 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0032
                                      TTEEEEEEEESTTSSHHHHHHHHHHSSCEE CS
                               Arf 12 kkelrilllGLDnaGKtTilkklkleelvt 41
                                      ++e+ + l+G  n GK+T++ +l+ + ++t
  gi|336254802|ref|YP_004597909.1|  7 DREAEVALVGRSNVGKSTLMRELTGHTFDT 36
                                      789999*****************9888776 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.043
                                       GGGCTTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCT......TSEEEEEEE-TTSTTSS-H CS
                               Arf  76 knYfektdavifvvDsadreRleeakeeLkalleeeelk......evallvlaNKqDlpealse 133
                                       ++Y e++ + + vvD      + + ++  +++  + e+       +++++v  NK+D  ++ +e
  gi|336254802|ref|YP_004597909.1|  87 EDYAENILVAVLVVDGKSVIDIIDRHSGPDEVPYDVEMFhflrdlDIPVVVAVNKMDKVDDKDE 150
                                       5566666666666665554444333333333322222222222337899999999999988765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00047      0.49       3      25 ..      10      32 ..       8      45 .. 0.85
   2 ?   -1.4   0.0       1.6   1.7e+03     126     142 ..     135     151 ..     123     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00047
                            AAA_24  3 lkiliyGpsgiGKTtlakelgpk 25
                                      + ++++G s +GK+tl++el+ +
  gi|336254802|ref|YP_004597909.1| 10 AEVALVGRSNVGKSTLMRELTGH 32
                                      6899***************9544 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                            AAA_24 126 ifiahektrkdedpege 142
                                       +++a  k++k++d++++
  gi|336254802|ref|YP_004597909.1| 135 VVVAVNKMDKVDDKDER 151
                                       67777777777777665 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 ?   10.9   0.0   0.00027      0.29      23      39 ..      10      26 ..       2      29 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                            AAA_29 23 gatlltGpsGsGKSTll 39
                                        + l+G+s +GKSTl+
  gi|336254802|ref|YP_004597909.1| 10 AEVALVGRSNVGKSTLM 26
                                      3689***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 1673.87
//
Query:       gi|336254803|ref|YP_004597910.1|  [L=430]
Description: hypothetical protein Halxa_3420 [Halopiger xanaduensis SH-6]
Scores for complete 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  119.2  17.9    1.3e-34  119.2  17.9    2.3  3  DUF389    Domain of unknown function (DUF389)
  ------ inclusion threshold ------
          2    8.6  22.8        1.6    9.0   1.6    2.5  2  HPP       HPP family


Domain annotation for each model (and alignments):
>> DUF389  Domain of unknown function (DUF389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2       1.2   1.1e+04      76      82 ..     123     129 ..     111     143 .. 0.48
   2 !  119.2  17.9   1.5e-38   1.3e-34       1     141 [.     145     288 ..     145     289 .. 0.95
   3 ?    1.7   0.0     0.027   2.4e+02      22      53 ..     313     344 ..     303     364 .. 0.52

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.2
                            DUF389  76 llvAlas 82 
                                       ++ Al++
  gi|336254803|ref|YP_004597910.1| 123 IISALVA 129
                                       2222222 PP

  == domain 2  score: 119.2 bits;  conditional E-value: 1.5e-38
                            DUF389   1 MlisPlmgpilaiafglvigdrkllrrglknlliglllallvgflfglllplk...vlg.eeelptsemlsrtepnl 73 
                                       M+i+Pl+gp+l++++g+vi d +l++++++ +++g++la++ +++f+++++++   + g e ++   e+++r +p+l
  gi|336254803|ref|YP_004597910.1| 145 MVIAPLIGPALGASVGTVIDDEELFKESVLYQAAGIVLAIAAAAVFAFVVRTTnvvPPGlEIDMV-GEISERLTPDL 220
                                       ***********************************************988555576677666665.9********** PP

                            DUF389  74 vdllvAlasGaagalallsgnssslvGvaIaaaLlPPavnaGlglalgewalalgslllllvNivgIv 141
                                       ++l++Al +G+ag++++++g s +lvGv+IaaaL+PPa++aG++la+g+++ a+g+++l++vNi+ ++
  gi|336254803|ref|YP_004597910.1| 221 LSLVIALGAGVAGIISIATGTSVALVGVMIAAALIPPAAAAGVALAWGQPSAAIGATALVMVNILSVN 288
                                       *****************************************************************987 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.027
                            DUF389  22 rkllrrglknlliglllallvgflfglllplk 53 
                                       ++l rr +   +i l++a+++g+++ + + ++
  gi|336254803|ref|YP_004597910.1| 313 QRLRRRIVGLGVIVLVFAVFLGAITYASYSTG 344
                                       44444555555555555555555555333222 PP

>> HPP  HPP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.6   0.00017       1.6      20      74 ..     135     203 ..     122     215 .. 0.70
   2 ?    4.8  13.2    0.0035        31      47     109 ..     231     293 ..     207     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00017
                               HPP  20 laqPrnvvgGhlisalvGvaiaklfgl..............sllwlaaalavalaialmlltrtlhPPa 74 
                                       l +P  vvg+ +i+ l+G a+ + +g               +++ + +a+a a+  a+++ t  + PP+
  gi|336254803|ref|YP_004597910.1| 135 LDSPAVVVGSMVIAPLIGPALGASVGTviddeelfkesvlyQAAGIVLAIAAAAVFAFVVRTTNVVPPG 203
                                       556777888888888888887666666677788888788776665566666666666666677777887 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0035
                               HPP  47 sllwlaaalavalaialmlltrtlhPPagAtaliavlgkeikelgwafllvpvllgslllvlv 109
                                        + ++++a ++++a++ ++++ +l PPa+A ++  + g++++++g + l++  +l++ l  lv
  gi|336254803|ref|YP_004597910.1| 231 VAGIISIATGTSVALVGVMIAAALIPPAAAAGVALAWGQPSAAIGATALVMVNILSVNLAGLV 293
                                       3445799*********************************99999988877433333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.21s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3282.98
//
Query:       gi|336254804|ref|YP_004597911.1|  [L=114]
Description: hypothetical protein Halxa_3421 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        0.6   10.4   5.6       0.47   10.7   3.5    1.8  2  DUF4536   Domain of unknown function (DUF4536)


Domain annotation for each model (and alignments):
>> DUF4536  Domain of unknown function (DUF4536)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.21   3.8e+03      29      41 ..       2      14 ..       1      19 [. 0.62
   2 ?   10.7   3.5   2.6e-05      0.47       6      21 ..      34      49 ..      33      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.21
                           DUF4536 29 klggkfgmltiaq 41
                                      k++g f ml ia+
  gi|336254804|ref|YP_004597911.1|  2 KRLGLFDMLQIAA 14
                                      5666666766663 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 2.6e-05
                           DUF4536  6 RlvSGsGLigaGvYvy 21
                                      Rlv+G+G++++G++++
  gi|336254804|ref|YP_004597911.1| 34 RLVGGVGFLALGAFAL 49
                                      9*************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 960.99
//
Query:       gi|336254805|ref|YP_004597912.1|  [L=331]
Description: small GTP-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-44  151.2   0.2    3.2e-44  150.7   0.2    1.2  1  NOG1_N        NOG1 N-terminal helical domain
    7.2e-22   76.9   0.0    1.5e-21   75.9   0.0    1.6  1  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
    1.2e-18   67.2   0.0    2.2e-18   66.4   0.0    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
    3.1e-09   36.5   0.0    5.6e-09   35.7   0.0    1.4  1  FeoB_N        Ferrous iron transport protein B
     0.0034   17.4   0.0     0.0085   16.1   0.0    1.6  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0065   16.5   1.5        3.8    7.6   0.0    3.0  3  Dynamin_N     Dynamin family
     0.0066   16.4   0.0      0.022   14.7   0.0    1.8  1  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
       0.01   15.6   0.1      0.017   14.9   0.1    1.3  1  APP_E2        E2 domain of amyloid precursor protein
      0.022   14.1   0.0      0.043   13.1   0.0    1.5  1  AIG1          AIG1 family


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 !  150.7   0.2   1.6e-47   3.2e-44       1     160 []       3     156 ..       3     156 .. 0.95

  Alignments for each domain:
  == domain 1  score: 150.7 bits;  conditional E-value: 1.6e-47
                            NOG1_N   1 FekiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnl...delhpFy 74 
                                       Fe +pt+ptseelidka++ra ra+k++     e      +++++++ta+n++sd+Le++v+++P++   d++hpFy
  gi|336254805|ref|YP_004597912.1|   3 FEDLPTTPTSEELIDKAFSRAARAGKAKGGL--E------AQQSMLQTAANIISDNLENVVTAWPDFeyeDDVHPFY 71 
                                       9************************999664..3......5789**********************944458***** PP

                            NOG1_N  75 relldvlvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrk 151
                                       +el+d++vd+d+l++sL++v+wa++++r+i +ey+ +l+k+d +++a++ r++af r+a++++++d++l ++++ r+
  gi|336254805|ref|YP_004597912.1|  72 YELADAIVDVDKLRQSLSEVMWASRKAREIHEEYQPRLRKTD-VDTARKHRKQAFARLADIVEQIDDDLLYINKSRN 147
                                       ***************************************765.599******************************* PP

                            NOG1_N 152 kLrkLpaiD 160
                                       +Lr+Lp+iD
  gi|336254805|ref|YP_004597912.1| 148 DLRDLPDID 156
                                       ********9 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 !   75.9   0.0   7.7e-25   1.5e-21       1      58 []     226     283 ..     226     283 .. 0.99

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 7.7e-25
                              NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                       eIE qA++A++hlad++l ++Dps+ecgy+l +Ql+L+++i  +f++ pv++++nK+D
  gi|336254805|ref|YP_004597912.1| 226 EIESQAVSAIEHLADCMLVMIDPSGECGYPLSSQLELRDSIAGQFEEIPVLTIANKAD 283
                                       6*******************************************************99 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   1.1e-21   2.2e-18       2     114 .]     162     281 ..     161     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 1.1e-21
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHC. CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflalee. 75 
                                       ++++G+pNvGKS+++n  t ++ +++++p+tT+ i  g+++ ++ ++++vDtpGl++   a++++ +++a+ a+e  
  gi|336254805|ref|YP_004597912.1| 162 IVVAGYPNVGKSSFVNGVTSARGETASYPFTTKGIGVGHFERDHIRYQIVDTPGLLDrpPAERNEIESQAVSAIEHl 238
                                       89***************************************888**********98654555666778888888878 PP

                                       TSEEEEEEETT.......TTCSHHHHHHHHHHHHH..TTSEEEEEEES CS
                          MMR_HSR1  76 adlillvvdas.......eeklkpldeeleellee..akkplilvlnk 114
                                       ad +l+++d s       +++l+  d+          +++p++ ++nk
  gi|336254805|ref|YP_004597912.1| 239 ADCMLVMIDPSgecgyplSSQLELRDSIA-----GqfEEIPVLTIANK 281
                                       9********77654444322222222222.....13356777777776 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 !   35.7   0.0   2.8e-12   5.6e-09       2      87 ..     161     247 ..     160     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2.8e-12
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH.CT CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll.ee 77 
                                       t++++G pnvGk++++n +t a+ + + +p +t     g+++ ++ +++ivD PG  +  +  ++e  ++ + + e+
  gi|336254805|ref|YP_004597912.1| 161 TIVVAGYPNVGKSSFVNGVTSARGETASYPFTTKGIGVGHFERDHIRYQIVDTPGLLDRPPAERNEIESQAVSAiEH 237
                                       699***************************************999**********9887666665554444332144 PP

                                       SSSEEEEEEE CS
                            FeoB_N  78 epdvvvnvvd 87 
                                        +d+++ ++d
  gi|336254805|ref|YP_004597912.1| 238 LADCMLVMID 247
                                       4566666555 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 !   16.1   0.0   4.3e-06    0.0085      44     100 ..     261     317 ..     256     322 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.3e-06
                      MMR_HSR1_Xtn  44 dlidviegnrvYipclyvlNKiDlisleeldelarepnsvviSaekelnldeLkeki 100
                                       +l d i+g+ + ip+l++ NK+D+ +  + d l++++    +S+e++ n+++++++ 
  gi|336254805|ref|YP_004597912.1| 261 ELRDSIAGQFEEIPVLTIANKADRRDVWDGDLLEEMDADYTMSVETGENVETVLDAA 317
                                       68899********************************99*************99875 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.33   6.7e+02      32      82 ..      95     145 ..      76     155 .. 0.70
   2 !    5.8   0.1    0.0065        13       1      21 [.     162     182 ..     162     196 .. 0.84
   3 !    7.6   0.0    0.0019       3.8     103     126 ..     208     231 ..     196     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.33
                                       --S-EEEEECCT---CCS...SSEEEET-EB--CHHHHHHHHHHHHHHHTS CS
                         Dynamin_N  32 Trrplelqlgeeeeaseravkeelkekekkledfsevreeieketekiaga 82 
                                       +r+  e++ + +++ +++ v+   k +++ +  + ++ e+i++    i+++
  gi|336254805|ref|YP_004597912.1|  95 SRKAREIHEEYQPRLRKTDVDTARKHRKQAFARLADIVEQIDDDLLYINKS 145
                                       455566666667776666666666677777777777777777777666654 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0065
                                       EEEEEBTTTTHHHHHHHHHTS CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlge 21 
                                       i+v G  + GKSS++n ++ +
  gi|336254805|ref|YP_004597912.1| 162 IVVAGYPNVGKSSFVNGVTSA 182
                                       8999************87765 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0019
                                       EEEEE---B-SSSGTTSHHHHHHH CS
                         Dynamin_N 103 ltlvDlPGldsvnkrdqelvkeyi 126
                                       + +vD+PGl +++  + + +++++
  gi|336254805|ref|YP_004597912.1| 208 YQIVDTPGLLDRPPAERNEIESQA 231
                                       68*******999988886665543 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.1e-05     0.022      53     122 ..     109     182 ..      99     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                                       EE-GGG--HHH....HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  53 lnKiDlleeee....eleelkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       l K+D+ + ++    ++ +l++ +e+++ ++l+++++ +++l++l +   +  t+v++G   vGKS+++n +++ 
  gi|336254805|ref|YP_004597912.1| 109 LRKTDVDTARKhrkqAFARLADIVEQIDDDLLYINKS-RNDLRDLPDIDPEePTIVVAGYPNVGKSSFVNGVTSA 182
                                       556666666555566788999999**********777.7788888776555499****************99886 PP

>> APP_E2  E2 domain of amyloid precursor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   8.5e-06     0.017     116     186 ..      68     138 ..      50     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.5e-06
                            APP_E2 116 ekylqalqeeppnaerilkaLkkllraeqkdrvhtlrhykhllksdpekaeqmkaqvlehLkkidervnqs 186
                                       + +  +l + + + ++++++L + + a +k r+   ++  +l+k+d + a ++++q   +L +i e++++ 
  gi|336254805|ref|YP_004597912.1|  68 HPFYYELADAIVDVDKLRQSLSEVMWASRKAREIHEEYQPRLRKTDVDTARKHRKQAFARLADIVEQIDDD 138
                                       667888999999********************99988889************************9999875 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.2e-05     0.043       2      71 ..     161     229 ..     160     247 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTC.CHHCHHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsv.sadkisk 71 
                                       tiv+ G   +GkS+ +N +   +  + +      tk     + ++d  + +++DTPgl+d    + ++i+ 
  gi|336254805|ref|YP_004597912.1| 161 TIVVAGYPNVGKSSFVNGVTSARGETAS--YPFTTKGIGVGHFERDHIRYQIVDTPGLLDRPPaERNEIES 229
                                       79***************99776653333..4555666667777****************987523444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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 0.20s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 2705.34
//
Query:       gi|336254806|ref|YP_004597913.1|  [L=136]
Description: hypothetical protein Halxa_3423 [Halopiger xanaduensis SH-6]
Scores for complete 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-16   60.4  49.3      2e-16   60.2  49.3    1.0  1  DUF5518    Family of unknown function (DUF5518)
  ------ inclusion threshold ------
       0.65   10.1   5.3       0.43   10.7   1.5    2.5  2  Ldr_toxin  Toxin Ldr, type I toxin-antitoxin system


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2  49.3   2.3e-20     2e-16       1     118 []       4     121 ..       4     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 2.3e-20
                           DUF5518   1 wraaliGavvaivlslllglllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllvlllglva 77 
                                       wra+++G+vva+vl++l+   lp+vg+l+++l+gG+vaGy+agg++++g+++G+laG++g+i++++l++v++ +++ 
  gi|336254806|ref|YP_004597913.1|   4 WRAVFVGFVVATVLGILGL-ALPGVGQLAAGLIGGFVAGYMAGGGIGSGFWHGLLAGALGGIIGGLLIGVAVGVAGL 79 
                                       9******************.********************************************8777777777888 PP

                           DUF5518  78 aigglagfvallvalllvvllllvvllvilg.aiGGaiGgll 118
                                       a+g+++g++ + v++++++++++v l++++  ai+Ga+Gg+l
  gi|336254806|ref|YP_004597913.1|  80 ALGPVGGAISGTVGVGIFAFAVAVSLVMAVEsAIAGAVGGAL 121
                                       88888888888888877777777666666655*******986 PP

>> Ldr_toxin  Toxin Ldr, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2      0.12   1.1e+03      14      25 ..      30      41 ..      28      46 .. 0.78
   2 ?   10.7   1.5   4.8e-05      0.43       7      28 ..      49      70 ..      43      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.12
                                      HHHHHHHHHHHH CS
                         Ldr_toxin 14 LAAPvlAGIlaa 25
                                      LAA ++ G +a 
  gi|336254806|ref|YP_004597913.1| 30 LAAGLIGGFVAG 41
                                      899999888875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4.8e-05
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                         Ldr_toxin  7 aMaFWHDLAAPvlAGIlaaaIV 28
                                      +  FWH L A  l GI+   ++
  gi|336254806|ref|YP_004597913.1| 49 GSGFWHGLLAGALGGIIGGLLI 70
                                      668**************87665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 1136.63
//
Query:       gi|336254807|ref|YP_004597914.1|  [L=115]
Description: hypothetical protein Halxa_3424 [Halopiger xanaduensis SH-6]
Scores for complete 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-09   37.6  47.5    0.00015   21.6   5.2    4.7  4  DUF326         Domain of Unknown Function (DUF326)
  ------ inclusion threshold ------
       0.18   11.7   0.3       0.29   11.1   0.0    1.5  2  Helicase_IV_N  DNA helicase IV / RNA helicase N terminal


Domain annotation for each model (and alignments):
>> DUF326  Domain of Unknown Function (DUF326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5  11.0   0.00022       1.9       2      19 ..      11      35 ..      11      35 .. 0.97
   2 !    8.4   0.9   0.00024       2.1       3      13 ..      40      50 ..      39      53 .. 0.90
   3 !   21.6   5.2   1.7e-08   0.00015       5      21 .]      74      90 ..      70      90 .. 0.92
   4 !   15.9   7.6     1e-06    0.0093       1      20 [.      92     111 ..      92     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00022
                                      HHHHHHH.......HHHHHHHHHHH CS
                            DUF326  2 khckkCA.......kaCrkCAkaCr 19
                                      +h+++C+       + C+ CA+aC+
  gi|336254807|ref|YP_004597914.1| 11 DHMQECIdncleaaQVCEWCADACA 35
                                      7***********************6 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00024
                                      HHHHHHHHHHH CS
                            DUF326  3 hckkCAkaCrk 13
                                      ++ +C++ Cr+
  gi|336254807|ref|YP_004597914.1| 40 DMARCIRLCRD 50
                                      799*******8 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 1.7e-08
                                      HHHHHHHHHHHHHHHHG CS
                            DUF326  5 kkCAkaCrkCAkaCrkc 21
                                      ++CA+ C++CA++C+++
  gi|336254807|ref|YP_004597914.1| 74 ELCADLCEECAEECEQH 90
                                      68************987 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 1e-06
                                       SHHHHHHHHHHHHHHHHHHH CS
                            DUF326   1 hkhckkCAkaCrkCAkaCrk 20 
                                       h+hc++CA+   kCA+ Cr+
  gi|336254807|ref|YP_004597914.1|  92 HEHCQACAEVLPKCAESCRE 111
                                       9*****************98 PP

>> Helicase_IV_N  DNA helicase IV / RNA helicase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.46   4.1e+03      96     110 ..       6      20 ..       2      34 .. 0.48
   2 ?   11.1   0.0   3.2e-05      0.29      77     114 ..      76     113 ..      64     115 .] 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.46
                     Helicase_IV_N  96 vqaladvlqkkeeei 110
                                       ++ ++d++q+  ++ 
  gi|336254807|ref|YP_004597914.1|   6 LEHADDHMQECIDNC 20 
                                       333334444333333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.2e-05
                     Helicase_IV_N  77 tqqfaqtllssyqqWskeqvqaladvlqkkeeeieefv 114
                                       ++ + ++  ++ +q+ +e +qa+a+vl+k  e+ +e++
  gi|336254807|ref|YP_004597914.1|  76 CADLCEECAEECEQHDHEHCQACAEVLPKCAESCREMA 113
                                       88999999*********************999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1063  (0.0592894); 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:                         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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 940.80
//
Query:       gi|336254808|ref|YP_004597915.1|  [L=94]
Description: phosphoribosyl-ATP pyrophosphatase [Halopiger xanaduensis SH-6]
Scores for complete 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   64.0   2.5    1.5e-17   63.8   2.5    1.0  1  PRA-PH    Phosphoribosyl-ATP pyrophosphohydrolase
     0.0001   22.4   3.8    0.00015   21.9   3.8    1.2  1  MazG      MazG nucleotide pyrophosphohydrolase domain
  ------ inclusion threshold ------
      0.076   12.4   0.1      0.076   12.4   0.1    1.1  1  DUF3839   Protein of unknown function (DUF3839)


Domain annotation for each model (and alignments):
>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   2.5   2.4e-21   1.5e-17       2      82 ..       6      93 ..       5      94 .] 0.96

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 2.4e-21
                                      HHHHHHCT----SS----.-HHHHHH......HHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CH CS
                            PRA-PH  2 kefhrligerkpetPeas.taelasl......raaligEEavElleaasegdlaeladelaDllYvtygllvllGidld 73
                                      +++  +i++rk++ Pe s ta+l+++      +++++gEE +El+ aa+++d +e+a+e+aD++Y++++ll  +G+dl+
  gi|336254808|ref|YP_004597915.1|  6 EDLFAVIEDRKETLPEDSyTASLFTHekgenaVLEKLGEETTELVLAAKDDDDEEIAYEAADIVYHLLVLLSMKGMDLE 84
                                      678899************************************************************************* PP

                                      HHHHHHHHH CS
                            PRA-PH 74 avfeevhra 82
                                      ++  e++ +
  gi|336254808|ref|YP_004597915.1| 85 DLEGELESR 93
                                      **9999876 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   3.8   2.5e-08   0.00015       4      57 ..      36      85 ..      33      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.5e-08
                                      HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHH CS
                              MazG  4 etllaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidled 57
                                      +++l+ l eE+ E++ a k +d++e++ E +D+ +++l l  +    +g+dled
  gi|336254808|ref|YP_004597915.1| 36 NAVLEKLGEETTELVLAAKDDDDEEIAYEAADIVYHLLVLLSM----KGMDLED 85
                                      678999************************************9....9999998 PP

>> DUF3839  Protein of unknown function (DUF3839)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.3e-05     0.076      41      72 ..      46      77 ..       7      87 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                           DUF3839 41 qgdldctakdetneeylyemqdiidhlpklpe 72
                                      +++l  +akd+ +ee  ye  di+ hl  l  
  gi|336254808|ref|YP_004597915.1| 46 TTELVLAAKDDDDEEIAYEAADIVYHLLVLLS 77
                                      678999********************987755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 798.05
//
Query:       gi|336254809|ref|YP_004597916.1|  [L=155]
Description: hypothetical protein Halxa_3426 [Halopiger xanaduensis SH-6]
Scores for 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-38  129.8   0.0    5.1e-38  129.6   0.0    1.0  1  DNase-RNase  Bifunctional nuclease


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.6   0.0   2.9e-42   5.1e-38       3     125 ..       6     136 ..       4     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 2.9e-42
                                       EEEEEETTTT..EEEEEEEETTSSEEEEEE--HHHHHHHHHHHCT---SS--HHHHHHHHHHHTTEEEEEEEEEEEE CS
                       DNase-RNase   3 agialdassq..spvvlLreeegrrvlpIwigaaeaqaialalegeeppRPlthDLlasllealgakvervvItdle 77 
                                        +++++ ++q   pvv+L+ +++++v+pI+ig +ea++ia++le e++ RPlthDLl++++e+lg +++rvv++++e
  gi|336254809|ref|YP_004597916.1|   6 DAVRVAGTQQgpVPVVVLSVDDEDDVVPIFIGFNEATSIARGLEAEDIGRPLTHDLLLDVMEELGSRIDRVVVSEIE 82 
                                       56676666644599*********99**************************************************** PP

                                       T......TEEEEEEEEEET---EEEEE-HHHHHHHHHHHT--EEEEHHHHHHH- CS
                       DNase-RNase  78 d......gtfyAelvlrkeeeeleidaRpSDaiaLAlrtgapIyveeevleeas 125
                                       +      gt++A+l+l++ ++ + +daRpSD++aLA+rt+a+I v+eev+e+ +
  gi|336254809|ref|YP_004597916.1|  83 ErdggqgGTYIADLHLETPRGGTVVDARPSDSLALAARTNAEIEVTEEVFENGR 136
                                       9999999**********98556****************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1227.59
//
Query:       gi|336254810|ref|YP_004597917.1|  [L=228]
Description: glutamine amidotransferase subunit pdxT [Halopiger xanaduensis SH-6]
Scores for complete 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-44  152.1   0.0    2.9e-44  151.2   0.0    1.4  1  SNO            SNO glutamine amidotransferase family
      3e-09   36.7   0.0    6.2e-09   35.7   0.0    1.5  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    0.00056   19.6   0.0    0.00081   19.1   0.0    1.2  1  Peptidase_S51  Peptidase family S51
    0.00062   19.6   0.1    0.00094   19.0   0.1    1.2  1  DJ-1_PfpI      DJ-1/PfpI family
     0.0071   15.5   0.0      0.041   13.0   0.0    1.9  2  BPL_N          Biotin-protein ligase, N terminal
  ------ inclusion threshold ------
      0.026   14.3   0.0        5.5    6.7   0.0    2.1  2  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 !  151.2   0.0   9.7e-48   2.9e-44       1     180 [.       7     204 ..       7     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 151.2 bits;  conditional E-value: 9.7e-48
                                       EESSSSSHHHHHHHHHHTTSEE......EEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--E CS
                               SNO   1 vlalqGaveehveaikkclaen......ktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvv 71 
                                       v+a+qG+veeh +ai+++  +       + +++   + ++d l +PGGest++s+l++  g+  ++++ v+ + k++
  gi|336254810|ref|YP_004597917.1|   7 VVAVQGDVEEHADAIERAARARghevtvREIRESGIVPDCDLLAMPGGESTTISRLVHSEGIAAEIRDHVAAG-KPL 82 
                                       79***************988777886656666677789*********************************99.*** PP

                                       EEETHHHHHHCCEETTBSS-SS--CCEEEETTTT-SCCGEEEEEEEETTTC..SEEEEEESS--EEEEE.......- CS
                               SNO  72 lGtCaGlillskelenelvktlellkvkvkrnafGrqvdsfekeldfknli..ekftavfiraPvieei.......l 139
                                       l tCaGli+ s + + + v +l+ll+v v+rnafGrq dsfe+ l++++l   e+++avfiraP +  +       +
  gi|336254810|ref|YP_004597917.1|  83 LATCAGLIVASSDPNDDRVDELGLLDVAVERNAFGRQKDSFEAPLEVEGLAddEPYPAVFIRAPAVADVdigaddnG 159
                                       **************************************************97789***********87633322221 PP

                                       ......TTTCEEEEECTTEEEEEEETTEEEESS-GGGSTTHCHHHH CS
                               SNO 140 d.....deavkvlyeldgeivvakqkkilatsfhPelaeddirvhd 180
                                       d     d + +vl   dg+ v+++q+ +++t+fhPel+ d  r+h 
  gi|336254810|ref|YP_004597917.1| 160 DeggngDANAEVLATWDGRPVAVRQGSVVGTAFHPELTPD-SRIHG 204
                                       12222235678889999*********************98.78775 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 !   35.7   0.0   2.1e-12   6.2e-09      19     118 ..      21     114 ..      14     136 .. 0.77
   2 ?   -3.0   0.0       1.6   4.6e+03     175     188 ..     180     193 ..     162     197 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2.1e-12
                          GATase_3  19 Leaepevrvrfvplkdeslg...edadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeei 92 
                                       +e++++ r++ v++++ +     +d+dl+ +pGg++t+ +  + +++g++ +i+++++ag+p+l+ C+Gl++ ++  
  gi|336254810|ref|YP_004597917.1|  21 IERAARARGHEVTVREIRESgivPDCDLLAMPGGESTTISRLV-HSEGIAAEIRDHVAAGKPLLATCAGLIVASSD- 95 
                                       5555555555555444433344599***********9877655.555***********************997765. PP

                          GATase_3  93 edpegvegeageveglglLdietefe 118
                                         p+       +v+ lglLd+ +e +
  gi|336254810|ref|YP_004597917.1|  96 --PNDD-----RVDELGLLDVAVERN 114
                                       ..5555.....899999999988765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.6
                          GATase_3 175 kksedgnvlGtYlH 188
                                          ++g+v+Gt +H
  gi|336254810|ref|YP_004597917.1| 180 VAVRQGSVVGTAFH 193
                                       44567899999999 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.7e-07   0.00081      80     133 ..      43      96 ..       5     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.7e-07
                                       HHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB- CS
                     Peptidase_S51  80 lleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesi 133
                                       + + d++ + GG+   + +l++++g+++ +r++v++g+++  + AG iva++  
  gi|336254810|ref|YP_004597917.1|  43 VPDCDLLAMPGGESTTISRLVHSEGIAAEIRDHVAAGKPLLATCAGLIVASSDP 96 
                                       446899*******************************************99765 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 !   19.0   0.1   3.2e-07   0.00094      41     106 ..      25      91 ..       6      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.2e-07
                                       EETTSEEEE-SEEGGGCTCCG-SEEEE--BHHH.HHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHH CS
                         DJ-1_PfpI  41 kgsrGlkvtvdaslddvkaaeyDalvlpGGrag.perlrenekvvelvkefaekgklvaaICagpql 106
                                          rG++vtv +  +   + + D+l +pGG++    rl+ +e + + +++++ +gk++ a Cag ++
  gi|336254810|ref|YP_004597917.1|  25 ARARGHEVTVREIRESGIVPDCDLLAMPGGESTtISRLVHSEGIAAEIRDHVAAGKPLLATCAGLIV 91 
                                       567899999988777666779*********98525899**************************665 PP

>> BPL_N  Biotin-protein ligase, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   1.4e-05     0.041      48      97 ..      44      94 ..      30     102 .. 0.85
   2 ?    0.3   0.0     0.094   2.8e+02     206     223 ..     181     198 ..     140     222 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                             BPL_N 48 stcallVlPgGaDlpYvrelngegn.rkikeyVekGGkylGlCAGaYygsk 97
                                        c ll +PgG  +   r +++eg+ ++i+++V +G   l+ CAG   +s+
  gi|336254810|ref|YP_004597917.1| 44 PDCDLLAMPGGESTTISRLVHSEGIaAEIRDHVAAGKPLLATCAGLIVASS 94
                                      68****************9999886269*****************877776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.094
                             BPL_N 206 kvgeGkalLtgvhpEfal 223
                                        v +G+++ t+ hpE ++
  gi|336254810|ref|YP_004597917.1| 181 AVRQGSVVGTAFHPELTP 198
                                       578999999999999887 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0018       5.5      11      82 ..      19      90 ..      14      98 .. 0.82
   2 ?    5.5   0.0    0.0042        13     158     178 ..     183     201 ..     164     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0018
                                      HHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHH CS
                            GATase 11 enlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQ 82
                                       ++++a++++g++v+v++i +s         ++d + ++gG  +        eg  + i+    +++P+L  C G+ 
  gi|336254810|ref|YP_004597917.1| 19 DAIERAARARGHEVTVREIRESGIVP-----DCDLLAMPGGESTTIsrlvhSEGIAAEIRDHVAAGKPLLATCAGLI 90
                                      5899**************99765555.....89********888778888866666666666667********9975 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0042
                                       EEETTTEEEESSBTTSTTSTT CS
                            GATase 158 iekknpfvgvQFHPEststpe 178
                                       ++    +vg+ FHPE t+  +
  gi|336254810|ref|YP_004597917.1| 183 RQG--SVVGTAFHPELTPDSR 201
                                       333..38*********98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1837.17
//
Query:       gi|336254811|ref|YP_004597918.1|  [L=53]
Description: Preprotein translocase subunit secG [Halopiger xanaduensis SH-6]
Scores for 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-17   62.3   0.1    4.2e-17   61.9   0.1    1.2  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 !   61.9   0.1   2.3e-21   4.2e-17       1      41 []      12      53 .]      12      53 .] 0.98

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 2.3e-21
                                      XXXXXXXXXX.----SS-B-THHHHHHHHHHHHHHHHHTSS- CS
                        Sec61_beta  1 SsaGLlryye.edapgikidPkvVlvlsvafiasVilLhila 41
                                      SsaGL+ry++ ed+++iki+Pk+V++ +v+++++V lL ++a
  gi|336254811|ref|YP_004597918.1| 12 SSAGLVRYFDsEDSNAIKINPKTVIATGVLIGVLVQLLTFVA 53
                                      9*************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 424.13
//
Query:       gi|336254812|ref|YP_004597919.1|  [L=100]
Description: Thioredoxin domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-22   77.6   0.0    6.6e-22   77.5   0.0    1.0  1  Thioredoxin    Thioredoxin
    4.3e-08   33.6   0.3    6.4e-07   29.8   0.3    2.0  1  Thioredoxin_2  Thioredoxin-like domain
    3.1e-06   27.4   0.0     0.0046   17.2   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    4.2e-05   23.5   0.0    4.2e-05   23.5   0.0    1.1  1  TraF           F plasmid transfer operon protein
     0.0001   22.3   0.0    0.00012   22.1   0.0    1.2  1  Thioredoxin_3  Thioredoxin domain
    0.00014   21.6   0.0    0.00016   21.5   0.0    1.1  1  Thioredoxin_9  Thioredoxin
    0.00016   22.0   0.1    0.00021   21.6   0.1    1.2  1  DUF836         Glutaredoxin-like domain (DUF836)
     0.0012   18.5   0.3      0.095   12.4   0.1    2.0  2  Redoxin        Redoxin
     0.0013   18.4   0.0     0.0014   18.4   0.0    1.1  1  Thioredoxin_5  Thioredoxin
     0.0017   18.0   0.0     0.0021   17.8   0.0    1.2  1  KaiB           KaiB domain
     0.0024   17.7   0.1      0.027   14.2   0.0    1.9  2  DSBA           DSBA-like thioredoxin domain
      0.003   17.5   0.1     0.0058   16.5   0.1    1.4  1  AhpC-TSA       AhpC/TSA family
     0.0098   16.1   0.1      0.024   14.8   0.0    1.7  2  Glutaredoxin   Glutaredoxin
  ------ inclusion threshold ------
      0.077   13.0   0.0      0.098   12.6   0.0    1.2  1  HyaE           Hydrogenase-1 expression protein HyaE


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 !   77.5   0.0   5.1e-25   6.6e-22      13     102 ..       8      96 ..       2      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 5.1e-25
                                       HHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEE CS
                       Thioredoxin  13 evakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkye 89 
                                       +++   +  l +FyA+wCg+Ck   P le+l e+ ++++ + kv+vde++dla++y+v+++Ptl++ +++  v++++
  gi|336254812|ref|YP_004597919.1|   8 ALNR-MTVTLKDFYADWCGPCKTQDPILEELEEDWEGRFEVEKVNVDEQQDLANEYQVRSLPTLIIENDDGIVERFV 83 
                                       5555.677888*****************************************************9999999****** PP

                                       SS-HHHHHHHHHH CS
                       Thioredoxin  90 garekeklaaflk 102
                                       g  ++e++++ l+
  gi|336254812|ref|YP_004597919.1|  84 GVTQREDIEDALE 96 
                                       ********99886 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.3     5e-10   6.4e-07       9     109 .]      16      95 ..      10      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 5e-10
                     Thioredoxin_2   9 lvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPti 84 
                                       l +f++++C+ Ck     l+el +d++ r         fe + v+++ ++             +la++y+vr++Pt+
  gi|336254812|ref|YP_004597919.1|  16 LKDFYADWCGPCKTQDPILEELeEDWEGR---------FEVEKVNVDEQQ-------------DLANEYQVRSLPTL 70 
                                       55788888888888888777776666555.........555555555444.............578*********** PP

                     Thioredoxin_2  85 vfldgkeivarlpGyvpaeeleall 109
                                       ++ + + iv+r +G +++e++e++l
  gi|336254812|ref|YP_004597919.1|  71 IIENDDGIVERFVGVTQREDIEDAL 95 
                                       *******************999876 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.6e-06    0.0046       3      47 ..      14      56 ..      12      57 .. 0.90
   2 !   11.8   0.0   0.00018      0.23      67      94 ..      51      78 ..      47      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.6e-06
                                      EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-H CS
                     Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkke 47
                                      v+l  f+a+wc pck+  p l el+e+ +   ++e+  v++d+++
  gi|336254812|ref|YP_004597919.1| 14 VTLKDFYADWCGPCKTQDPILEELEEDWE--GRFEVEKVNVDEQQ 56
                                      56668***********************9..99999999999876 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00018
                                      -TT-HHHHTT-S--TT-SEEEEE-TT-B CS
                     Thioredoxin_8 67 ddkkrnklkkkynvkaiPtlvvldknge 94
                                      + ++++ l+++y+v ++Ptl++ + +g 
  gi|336254812|ref|YP_004597919.1| 51 NVDEQQDLANEYQVRSLPTLIIENDDGI 78
                                      557899****************999885 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   3.3e-08   4.2e-05     133     200 ..      16      74 ..       2      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.3e-08
                              TraF 133 LlfFyrgkcpyceaqapilqafadky..glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvd 200
                                       L  Fy+  c+ c+ q pil+++++++   +ev  V+vd++++  l+n         +++v++ P+l++ +
  gi|336254812|ref|YP_004597919.1|  16 LKDFYADWCGPCKTQDPILEELEEDWegRFEVEKVNVDEQQD--LAN---------EYQVRSLPTLIIEN 74 
                                       5559********************99778***********99..999.........9********99865 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   9.2e-08   0.00012      10      75 ..      24      95 ..      12      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.2e-08
                                      STTCHHHHHHHHHHCHCCTCECEEECC..TTHHHH.HHCT-SSSSEEECT...T.CEEEESS---CCHHHHHH CS
                     Thioredoxin_3 10 CakCpklekavkeaaaekgikaevekv..tdfeei.ekygVmsvPalvid...g.kvvvsGkvpseeeirkll 75
                                      C  C++ + +++e+ ++ +  +evekv   + +++ ++y+V+s P+l+i+   g + +++G v ++e+i+  l
  gi|336254812|ref|YP_004597919.1| 24 CGPCKTQDPILEELEEDWEGRFEVEKVnvDEQQDLaNEYQVRSLPTLIIEnddGiVERFVG-VTQREDIEDAL 95
                                      77787555555555555588888888776899999**************866442347999.99999998766 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.2e-07   0.00016      49     108 ..      20      77 ..       7      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.2e-07
                                       --TT-HHHHHHHHHHHHHHH.H-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT- CS
                     Thioredoxin_9  49 tedwCgDaavnvPvlakiae.lnpnievkillrdenlelmdqyltngaraiPtliildeeg 108
                                        +dwCg +    P+l+++ e +  + ev+ +  de+++l ++y+    r+ Ptlii +++g
  gi|336254812|ref|YP_004597919.1|  20 YADWCGPCKTQDPILEELEEdWEGRFEVEKVNVDEQQDLANEYQV---RSLPTLIIENDDG 77 
                                       589***************9636789******************66...********99985 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   1.6e-07   0.00021      10      57 ..      24      74 ..      19      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.6e-07
                                      -HHHHHHHHHHHHHCCCTT..EEEEEEETTT-CCCHCCCCTTT.TEEEECT CS
                            DUF836 10 ChlCeqakekLkelkleeg..leleviDIakdeeleakYglei.pvlaleg 57
                                      C+ C+    +L+el+++ +  +e+e+++++++++l ++Y++++ p l +e+
  gi|336254812|ref|YP_004597919.1| 24 CGPCKTQDPILEELEEDWEgrFEVEKVNVDEQQDLANEYQVRSlPTLIIEN 74
                                      999*********887666689*******************97537777777 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   7.4e-05     0.095      35      71 ..      19      53 ..       8      60 .. 0.81
   2 !    6.0   0.1    0.0071         9      91     145 ..      52      93 ..      47      97 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.4e-05
                                      EESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEES CS
                           Redoxin 35 fvpgafcPtCsaehpyleklaellkekgvdvvavvad 71
                                      f++  +c++C+++ p le+l+e   e+ ++v  v++d
  gi|336254812|ref|YP_004597919.1| 19 FYAD-WCGPCKTQDPILEELEED-WEGRFEVEKVNVD 53
                                      6666.***************998.7777777777666 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0071
                                       E-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHTSTTSHHH CS
                           Redoxin  91 sDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepeteesnaea 145
                                       +D++++++ ++ +r          +p++ +i  d+ +v+++v++  +   +++e+
  gi|336254812|ref|YP_004597919.1|  52 VDEQQDLANEYQVR---------SLPTL-IIENDDGIVERFVGVTQR---EDIED 93 
                                       67788888888866.........56655.555566688999999884...44443 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-06    0.0014     127     167 ..      34      76 ..      14      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                     Thioredoxin_5 127 veefkeDlesklakkafqcD..lklakemgvtevPtlvffnen 167
                                       +ee++eD+e ++ +++ + D  + la+e++v+++Ptl++ n++
  gi|336254812|ref|YP_004597919.1|  34 LEELEEDWEGRFEVEKVNVDeqQDLANEYQVRSLPTLIIENDD 76 
                                       689********9999888775588***************9943 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.6e-06    0.0021      19      56 ..      35      71 ..      28      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                                      HHHCCCHCTTTEEEEEEETTTSHCHHCCTCEESCCCCC CS
                              KaiB 19 kkleeedlgfqyeLqvvdvleqPelaeedrlvatPaLi 56
                                      ++le ed ++++e++ v+v eq +la e+++  +P+Li
  gi|336254812|ref|YP_004597919.1| 35 EELE-EDWEGRFEVEKVNVDEQQDLANEYQVRSLPTLI 71
                                      4554.569*****************************8 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.037        47       4      33 ..      19      48 ..      15      52 .. 0.77
   2 !   14.2   0.0   2.1e-05     0.027     149     192 ..      48      95 ..      35      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.037
                                      EEEBTTBHHHHHHHHHHHHHHHHCCT.EEEE CS
                              DSBA  4 effDvlCPyCylgkerleklaarspd.vkvv 33
                                      ++ D  C+ C++ ++ le+l++ +++ ++v 
  gi|336254812|ref|YP_004597919.1| 19 FYAD-WCGPCKTQDPILEELEEDWEGrFEVE 48
                                      4444.69*****************5556664 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHHHHHTT-SSSSEEEE.TTC....EEEESSSSHHHHHHHH CS
                              DSBA 149 vkeavrentaaaqslgvtGvPtvvv.dgk....rmvfGadrldtladal 192
                                        k  v+e++++a++++v+ +Pt ++ +        ++G+++ + ++dal
  gi|336254812|ref|YP_004597919.1|  48 EKVNVDEQQDLANEYQVRSLPTLIIeN-DdgivERFVGVTQREDIEDAL 95 
                                       56789********************63.335667999*99999999998 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   4.6e-06    0.0058      32     101 ..      19      86 ..       9      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.6e-06
                                       EESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHHTT-E CS
                          AhpC-TSA  32 fypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvakaygvl 101
                                       fy+  wc +C+t+ p l++l e+ +   +ev  v+vd+++++++  +  sl+  ++   +g v +  gv 
  gi|336254812|ref|YP_004597919.1|  19 FYAD-WCGPCKTQDPILEELEEDWE-GRFEVEKVNVDEQQDLANEYQVRSLPTLIIENDDGIVERFVGVT 86 
                                       7777.*******************9.67*************99999999999998888887777766665 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.9e-05     0.024       7      57 ..      22      74 ..      12      79 .. 0.79
   2 ?   -1.3   0.0         2   2.6e+03      27      43 ..      81      97 ..      75      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                                      TSSHHHHHHHHHHHHTT......GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETT CS
                      Glutaredoxin  7 ptCpyCkkakrlLkelg......vkfeeidvdkdeeireelkelsgvrtvPqvfidg 57
                                       +C+ Ck    +L+el       +++e ++vd+ +++  e      vr++P++ i +
  gi|336254812|ref|YP_004597919.1| 22 DWCGPCKTQDPILEELEedwegrFEVEKVNVDEQQDLANEY----QVRSLPTLIIEN 74
                                      79**************9777777779999999965555555....99999*999965 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                                      EEEEGCCSHHHHHHHHH CS
                      Glutaredoxin 27 eeidvdkdeeireelke 43
                                      +++ v++ e+i ++l++
  gi|336254812|ref|YP_004597919.1| 81 RFVGVTQREDIEDALES 97
                                      57789999999999875 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.7e-05     0.098      49      96 ..      33      79 ..      27      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.7e-05
                                      HHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEE CS
                              HyaE 49 vlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeyl 96
                                      +l El + ++ +++   v+  ++++ la++++v+  P+l++  d+ ++
  gi|336254812|ref|YP_004597919.1| 33 ILEELEEDWEGRFEVEKVN-VDEQQDLANEYQVRSLPTLIIENDDGIV 79
                                      7999999****99999999.777889**************98887555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 802.72
//
Query:       gi|336254813|ref|YP_004597920.1|  [L=222]
Description: NADPH-dependent F420 reductase [Halopiger xanaduensis SH-6]
Scores for 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-17   62.3   0.0    8.3e-17   61.6   0.0    1.4  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0018   18.5   0.0     0.0038   17.4   0.0    1.5  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0032   17.9   0.1     0.0047   17.4   0.1    1.5  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
     0.0032   17.1   0.0     0.0049   16.5   0.0    1.3  1  ApbA            Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.033   13.2   0.1      0.057   12.4   0.1    1.3  1  PDH             Prephenate dehydrogenase
      0.034   14.8   0.0       0.12   13.1   0.0    2.0  2  CoA_binding     CoA binding domain
      0.064   13.2   0.0       0.13   12.2   0.0    1.5  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen


Domain annotation for each model (and alignments):
>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   3.2e-20   8.3e-17       1      95 [.       2     103 ..       2     105 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 3.2e-20
                                       EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE CS
                     F420_oxidored   1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvl 67 
                                       +i+++ G+G++ge+la+++ +    +he++v+ sr+pe+a+ + + ++         ++v++  ne + ++adv vl
  gi|336254813|ref|YP_004597920.1|   2 RIALLgGTGDIGEGLALRFGRDT--DHEVLVG-SRDPESARDAVAGYEetleahgaeATVKGFVNEMVTDRADVAVL 75 
                                       79*****************9997..9****88.************************9999999************* PP

                                       -S-HHHHHHHHHHCGHHHHTTSEEEEES CS
                     F420_oxidored  68 avkpedveevlselakdalkgklvisvl 95 
                                       av+p++v ++++++a+++++++++++ +
  gi|336254813|ref|YP_004597920.1|  76 AVPPYHVGDTIESVADALDENTILVTPA 103
                                       ************************9877 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 !   17.4   0.0   1.5e-06    0.0038       6      87 ..       8     100 ..       2     109 .. 0.82
   2 ?   -3.5   0.0       3.9     1e+04     113     124 ..     159     170 ..     157     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                                       --SHHHHHHHHHH.HHTT-EEEEE-SSHHHHHHHHHTT......EEE-SSHHHHHHHC.....SEEEE-SSSHHHHH CS
                     NAD_binding_2   6 GlGvMGsnmalnl.lkagykvavynrtkekveelvaeg......akaaesieelvasl.....dvvitmvkagkavd 70 
                                       G+G +G+ +al++  + +++v v  r++e+++++va          a ++++ +v+++     dv ++ v+   +v 
  gi|336254813|ref|YP_004597920.1|   8 GTGDIGEGLALRFgRDTDHEVLVGSRDPESARDAVAGYeetleaHGAEATVKGFVNEMvtdraDVAVLAVPP-YHVG 83 
                                       79***********7799*****************99867888853334456667777677777888888885.89** PP

                                       HHHHSHCCC--TT-EEE CS
                     NAD_binding_2  71 eviegllealkkgdili 87 
                                       ++ie++++al++++il+
  gi|336254813|ref|YP_004597920.1|  84 DTIESVADALDENTILV 100
                                       **************998 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.9
                                       EEEEESHHHHHH CS
                     NAD_binding_2 113 daPVSGGeegAe 124
                                       d+PV G++  A 
  gi|336254813|ref|YP_004597920.1| 159 DTPVVGTDRDAV 170
                                       788888877764 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 !   17.4   0.1   1.8e-06    0.0047       1      86 [.       2      89 ..       2     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG.GGTTTECEBEEE.GGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk.aleegkdlkved.vdeeelkevdivflalpag 77
                                      ++a++G+tG +G+ l+ +  ++ + e++v +   +sa  ++a + +   ++g++ +v+  v+e  ++++d+++la+p  
  gi|336254813|ref|YP_004597920.1|  2 RIALLGGTGDIGEGLALRFGRDTDHEVLVGSRDPESARDAVAGYEEtLEAHGAEATVKGfVNEMVTDRADVAVLAVPPY 80
                                      69************************9998888889999999998866788999999997777778*********9965 PP

                                      HHHHHHHHH CS
                    Semialdhyde_dh 78 vskelapkl 86
                                         +  +++
  gi|336254813|ref|YP_004597920.1| 81 HVGDTIESV 89
                                      544444433 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.9e-06    0.0049       5      99 ..       8     100 ..       3     103 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-06
                                       S-SHHHHHHHHHHHH.HTHCEEEE-SCHHHHHHHHHCEEEEETT.CEEEEEECEEECCHSCCCCS-ESEEEE-SSGG CS
                              ApbA   5 GaGaiGsllaakLak.agadvtlilrsrrlealkknGlrltseg.geeilrppealsaeekselepidlvivtvKay 79 
                                       G+G iG  la +  + + ++v +  r+++ ++   +G++ t e  g   + ++  +++        +d+ +++v+ y
  gi|336254813|ref|YP_004597920.1|   8 GTGDIGEGLALRFGRdTDHEVLVGSRDPESARDAVAGYEETLEAhG-AEATVKGFVNEM---VTDRADVAVLAVPPY 80 
                                       89***********999999999999999555555555555555522.333333333333...4679*********** PP

                                       GHHHHHHHHGGGECTCEEEE CS
                              ApbA  80 qteealeeikplldpntvvl 99 
                                       ++ + +e+++++ld+nt+ +
  gi|336254813|ref|YP_004597920.1|  81 HVGDTIESVADALDENTILV 100
                                       ****************8876 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.2e-05     0.057      35      76 ..      64     100 ..      36     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                                       EEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEE CS
                               PDH  35 eatddieavkeadivvlavPvevilevlkelaphlkedalit 76 
                                       e  +       ad++vlavP+  + ++++ +a +l e+ +++
  gi|336254813|ref|YP_004597920.1|  64 EMVT-----DRADVAVLAVPPYHVGDTIESVADALDENTILV 100
                                       3333.....589***********************9998875 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.7e-05      0.12      54      86 ..      58      93 ..       2     103 .. 0.79
   2 ?   -1.0   0.0       1.1   2.9e+03      48      59 ..     144     154 ..     113     180 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.7e-05
                                      HHHHHHHC..T.TTEEEEES-HHHHHHHHHHHHHTT CS
                       CoA_binding 54 vdeleekt..e.vdvavitvPaesaqeavdelveag 86
                                      v+  ++++  + +dvav++vP+ ++ ++++ +++a 
  gi|336254813|ref|YP_004597920.1| 58 VKGFVNEMvtDrADVAVLAVPPYHVGDTIESVADAL 93
                                      444444444335******************999985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                                       EEEESCHHHHHH CS
                       CoA_binding  48 lpvyksvdelee 59 
                                       lp+   +++le+
  gi|336254813|ref|YP_004597920.1| 144 LPAA-RLADLEA 154
                                       2222.2333333 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 ?   12.2   0.0   5.1e-05      0.13       2     101 ..       3     101 ..       2     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.1e-05
                                       EEEE-.-SHHHHHHHHHHHTTT.--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE- CS
                    NAD_Gly3P_dh_N   2 iavlG.aGswGtalAkvlaeng.hevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlv 76 
                                       ia+lG +G  G  lA  +++ + hev + +r++e +++  +  e+   L+ +  +++++   + + + ++ad+ vl+
  gi|336254813|ref|YP_004597920.1|   3 IALLGgTGDIGEGLALRFGRDTdHEVLVGSRDPESARDAVAGYEE--TLEAHGAEATVKGFVN-EMVTDRADVAVLA 76 
                                       666642699999999999988879999999999998887776665..4666667788876665.668899******* PP

                                       --HHHHHHHHHHHCCC--TT-EEEE CS
                    NAD_Gly3P_dh_N  77 vPsqalrevlkklkgllkkkailvs 101
                                       vP  ++ ++++++++ l++++ilv 
  gi|336254813|ref|YP_004597920.1|  77 VPPYHVGDTIESVADALDENTILVT 101
                                       *********************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1845.16
//
Query:       gi|336254814|ref|YP_004597921.1|  [L=458]
Description: hypothetical protein Halxa_3431 [Halopiger xanaduensis SH-6]
Scores for 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-05   25.7   0.0      0.027   14.7   0.0    2.6  2  CARDB     CARDB
    0.00059   20.1   1.2        1.8    8.9   0.1    3.4  3  DUF11     Domain of unknown function DUF11
     0.0043   17.3   0.0        6.5    7.1   0.0    3.1  3  DUF4352   Domain of unknown function (DUF4352)


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 !   14.7   0.0   4.6e-06     0.027       1      87 [.      50     138 ..      50     143 .. 0.69
   2 !    8.3   0.0   0.00045       2.7       4      64 ..     362     422 ..     359     450 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.6e-06
                                       S--EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEEEEEEESEE-CTEEEEEE...EEEE-S- CS
                             CARDB   1 tpDLtvtntlnpseafvgeentitvtvkNqGtaa.sgatkvalyldgelvgtvtvpsLaagesttvs...ftwttea 73 
                                       tp+L+v+ + + +++++ge + +tv ++N+Gt a  +++   +  d +  + v+   +++ge++t s   +t++++ 
  gi|336254814|ref|YP_004597921.1|  50 TPNLEVEIIETDAPVHAGEYLGVTVAITNHGTSAiRPDVDFLVGEDPDRFSRVSM-MIEPGETRTTShgfYTYPVP- 124
                                       699*****************************98666666666666665554444.78999998887222333333. PP

                                       S-CEEEEEEEESTT CS
                             CARDB  74 tegevtltvvvDpd 87 
                                          e  ++v +D d
  gi|336254814|ref|YP_004597921.1| 125 RDEEFPVRVETDGD 138
                                       44444455555544 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00045
                                       EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEEEEEEESEE-CTEEEE CS
                             CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaa.sgatkvalyldgelvgtvtvpsLaagestt 64 
                                       L+++  ++ s++ +ge +++ v ++N+G+++  ++ ++ +  d ++ +t++v  +++ge+  
  gi|336254814|ref|YP_004597921.1| 362 LELSIRTTNSPVDAGEYLEVIVDITNTGSETgRQTLELIVGHDPKKLDTQDV-VVEPGETGA 422
                                       55666889999******************99555555666666666688888.566666654 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00075       4.5       8      29 ..      62      83 ..      55      91 .. 0.87
   2 ?   -0.8   0.0      0.33     2e+03      46      84 ..     244     286 ..     236     291 .. 0.79
   3 !    8.9   0.1    0.0003       1.8       6      29 ..     369     392 ..     363     400 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00075
                             DUF11  8 sevrpGdtvtytltvtNtgpas 29
                                      ++v +G+ + +t+  tN g+++
  gi|336254814|ref|YP_004597921.1| 62 APVHAGEYLGVTVAITNHGTSA 83
                                      5799***************987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.33
                             DUF11  46 vsvsasqgtasaltsv.....gsLeagesatlsftvrvtrtaas 84 
                                       v v+as g++s ++ +     g+++  +   ++f++++t  a+s
  gi|336254814|ref|YP_004597921.1| 244 VDVTAS-GIGSPTVEAirpepGTVPMTGNEPVTFELEATDPATS 286
                                       556777.7888887778888899999999999999999877765 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0003
                             DUF11   6 dksevrpGdtvtytltvtNtgpas 29 
                                       ++s+v++G+ +++++  tNtg  +
  gi|336254814|ref|YP_004597921.1| 369 TNSPVDAGEYLEVIVDITNTGSET 392
                                       5678*****************976 PP

>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0011       6.5      29      54 ..      59      84 ..      51      90 .. 0.84
   2 !    6.3   0.0    0.0019        11      28      53 ..     367     392 ..     336     396 .. 0.86
   3 ?   -0.9   0.0      0.32   1.9e+03      85     103 ..     411     429 ..     402     441 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0011
                                      -CEETT-.SEEEEEEEEEEE-SSS-E CS
                           DUF4352 29 eylqpdaggeflivdvtvkNkgkeal 54
                                      e+++p   ge+l v+v+++N+g +a+
  gi|336254814|ref|YP_004597921.1| 59 ETDAPVHAGEYLGVTVAITNHGTSAI 84
                                      556667779*************9987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0019
                                       S-CEETT-.SEEEEEEEEEEE-SSS- CS
                           DUF4352  28 neylqpdaggeflivdvtvkNkgkea 53 
                                       +++++p + ge+l v v ++N+g+e+
  gi|336254814|ref|YP_004597921.1| 367 RTTNSPVDAGEYLEVIVDITNTGSET 392
                                       566777888**************986 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.32
                                       -EEEE-TT-EEEEEEEEEE CS
                           DUF4352  85 flgtlnpGkkvtGklvFdv 103
                                       ++  + pG++  ++l F+ 
  gi|336254814|ref|YP_004597921.1| 411 QDVVVEPGETGAATLGFET 429
                                       556789***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 3799.27
//
Query:       gi|336254815|ref|YP_004597922.1|  [L=108]
Description: hypothetical protein Halxa_3432 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.03   14.2   0.7      0.041   13.8   0.5    1.4  1  DUF3052   Protein of unknown function (DUF3052)
      0.083   12.7   0.3      0.096   12.5   0.3    1.0  1  dCache_1  Cache domain
       0.28    8.3   0.2       0.33    8.0   0.2    1.0  1  Nup192    Nuclear pore complex scaffold, nucleoporins 186/192
       0.68   10.6   4.5          1   10.0   4.5    1.3  1  DUF4404   Domain of unknown function (DUF4404)


Domain annotation for each model (and alignments):
>> DUF3052  Protein of unknown function (DUF3052)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   9.2e-06     0.041      12      48 ..      58      94 ..      48     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.2e-06
                           DUF3052 12 vqelgwDdDvdedlreaiedligeelvdedadevvDv 48
                                       q lg D Dvde+ r+a+e+ +++++ + + +++ D 
  gi|336254815|ref|YP_004597922.1| 58 LQALGNDPDVDEERRQALEERLDQRIREVQNRDAYDS 94
                                      6899***********************9999999986 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   2.1e-05     0.096       3      77 ..      28      96 ..      26     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                          dCache_1  3 ieeqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgv 77
                                      i e++e+ql     + +++  +vl++++  ++ l+++p++    +e +   +a +e+l+++++++++++++ sg+
  gi|336254815|ref|YP_004597922.1| 28 ILEDVERQLNRATDLETEEAVSVLRTAREDLQALGNDPDV----DEER--RQALEERLDQRIREVQNRDAYDSGL 96
                                      7899999*******************************97....3333..58999999999999**999988876 PP

>> Nup192  Nuclear pore complex scaffold, nucleoporins 186/192/205
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2   7.3e-05      0.33      11      58 ..      30      79 ..      26      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 7.3e-05
                                      HHHHHHHTT.XT.THHHHHHHHHHTHHHHHHTTXXXXXXHHHHHCHCC.. CS
                            Nup192 11 nsieaassn.pe.sldelelllkklkqdLknllknppkneksRsqlkkek 58
                                      +++e++ ++ ++ +++e    l+  ++dL++l + p  +e+ R++l++  
  gi|336254815|ref|YP_004597922.1| 30 EDVERQLNRaTDlETEEAVSVLRTAREDLQALGNDPDVDEERRQALEERL 79
                                      556666666555689999999*************************8644 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.5   0.00023         1       5      59 ..      29      85 ..      26      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                           DUF4404  5 LekLheeLeqnesldeet.ralLeslaedieellaeedaaaeeee.laerlneaver 59
                                      Le+ + +L++ ++l++e+  ++L++++ed+++l ++ d  +e ++ l+erl + + +
  gi|336254815|ref|YP_004597922.1| 29 LEDVERQLNRATDLETEEaVSVLRTAREDLQALGNDPDVDEERRQaLEERLDQRIRE 85
                                      7788899998888776551689*********999999999999889****9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 913.86
//
Query:       gi|336254816|ref|YP_004597923.1|  [L=293]
Description: glycerophosphoryl diester phosphodiesterase [Halopiger xanaduensis SH-6]
Scores for complete 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-24   86.9   0.0    2.9e-24   86.2   0.0    1.3  1  GDPD      Glycerophosphoryl diester phosphodiesterase family
  ------ inclusion threshold ------
      0.016   15.6   0.5      0.037   14.5   0.5    1.6  1  GDPD_2    Glycerophosphoryl diester phosphodiesterase family


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.0   3.3e-28   2.9e-24       1     258 [.      14     276 ..      14     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 3.3e-28
                                       TTTTTTTSSTTSHHHHHHHHH.TT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.......BGGGS-HHHHHTS CS
                              GDPD   1 HRGasgnlpEnTlesfakAae.lGadyiEfDvqlTkDgvpVvlHDfnldrttdvagr......ldvkdltleelkrl 70 
                                       HRG+ g  pEnT+++  +Aae +   +iE Dvq    g pVv+HD++l+ t   +gr        v++  leel++ 
  gi|336254816|ref|YP_004597923.1|  14 HRGYAGVAPENTVAAAVRAAErDDTAMIEIDVQPAACGTPVVVHDDRLEGTHPRDGRpltdadGLVRETPLEELQET 90 
                                       *************9887777625789***************************999999999989999999999999 PP

                                       TECCTTCCCCSCCCSSGCCB...BHHHHHHH.HHHCCSEEEEEEECCCCCCCHHHH..HHTCHHHCCCCCSCHHTT. CS
                              GDPD  71 dkiakenkaqlsenrvrlefpfptleevlkk.pqnvglnieikipmlseakeeeel..qivkeilksvdeilkkvlk 144
                                       + +  +      ++      ++ptl+ +l+  p   g+n+e k p +      e l  +  ++   +++ ++++v++
  gi|336254816|ref|YP_004597923.1|  91 R-V-LGT-----DE------TIPTLATLLEAlPDTAGVNVELKNPGTTDLRFGEALapDERDARRDVWKPFVERVVD 154
                                       9.3.222.....34......56*********9*************98877666665576677777777777777666 PP

                                       ...STTCSCEEEESTHHHHHHHHHTCTCTEEEEEEHHHHHHC-E.EECHCCCCCCCT.CCCCHHCCCHCCCE..... CS
                              GDPD 145 k..adkrkvifssfnpdilkllrekqpklpllflteggteaeadssleraakfakad.allgevsavaeglg..... 213
                                          a + ++ fssf   +l +lre++p++  + l+ +  ea   + ++++ +++  + +  + v++++         
  gi|336254816|ref|YP_004597923.1| 155 EcrAFDGDLLFSSFCEGALAALREAAPEYAAAPLVWDDLEAGLTIADRYDCEAIHPPrNAVAGVPLATTEYAglpaa 231
                                       51155689999************************999999999666666666654323333333333333357777 PP

                                       ..B.CHHHHHHHTT-EEEEBSB-THSHHHHHHHHCCC-SEEEES-HH CS
                              GDPD 214 ..dpdlVkraksrglvvhvytvnnedeeemkrlleagvdgvitDfpd 258
                                           d+++ra++ g +v v+tv ++   + ++l  agvdg+i D+p+
  gi|336254816|ref|YP_004597923.1| 232 epELDVLERAHEDGRAVNVWTVETW--GQFDQLAAAGVDGIIADYPG 276
                                       77779********************..******************97 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.5   4.1e-06     0.037       2      29 ..     248     275 ..     247     276 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-06
                            GDPD_2   2 vrfWttddeavwrelvgaGVdgInTDdl 29 
                                       v  Wt+++  ++ +l +aGVdgI+ D++
  gi|336254816|ref|YP_004597923.1| 248 VNVWTVETWGQFDQLAAAGVDGIIADYP 275
                                       678*****99****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2402.96
//
Query:       gi|336254817|ref|YP_004597924.1|  [L=165]
Description: response regulator receiver protein [Halopiger xanaduensis SH-6]
Scores for 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-18   65.7   0.0    4.4e-18   65.5   0.0    1.1  1  Response_reg  Response regulator receiver domain


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 !   65.5   0.0   2.5e-22   4.4e-18       1     111 [.      12     132 ..      12     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 2.5e-22
                                       EEEESSSHHHHHHHHHHHHHTTE.EEEEEESSHHHHHHHHHHHH.......ESEEEEESSCSSSEHHHHHHHHHHCT CS
                      Response_reg   1 vlivdDdplvrellrqlleeegy.eevaeaedgkealellkeek.......vdlillDinmpgmdGlellkeireed 69 
                                       +l+v+ +p  ++l+ + + ++++  +v++++dg++al+ +++++       +dl+llD  +pg++G ++l+e++ ++
  gi|336254817|ref|YP_004597924.1|  12 ILLVEPNPGDARLFDESFADANIaCDVHTVSDGENALDFVHRRNdhverprPDLVLLDFHLPGVSGEDVLTELKSDP 88 
                                       7999999999999999999666534899************77777888899*************************9 PP

                                       ..TTSEEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  70 ..pelpviiltahseeedavealkagaddflsKpfdpeeLlkal 111
                                         + +pvi++t+ ++eed+ + +++ a+ +++Kp++p+e ++ +
  gi|336254817|ref|YP_004597924.1|  89 afRRIPVIVMTSSDAEEDIARSYDLHANAYVQKPIEPDEFVELV 132
                                       9999***********************************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1400.93
//
Query:       gi|336254818|ref|YP_004597925.1|  [L=291]
Description: HAD-superfamily hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-11   43.0   0.7      2e-10   41.3   0.7    1.7  1  Hydrolase       haloacid dehalogenase-like hydrolase
    1.1e-08   35.4   0.0    3.8e-07   30.4   0.0    2.2  2  HAD_2           Haloacid dehalogenase-like hydrolase
    6.6e-07   29.3   0.1    2.1e-06   27.7   0.1    1.9  1  Hydrolase_like  HAD-hyrolase-like
    5.3e-05   23.7   4.3    0.00018   22.0   0.9    2.2  2  HAD             haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.015   15.0   0.0       0.46   10.3   0.0    2.2  2  NIF             NLI interacting factor-like phosphatase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.7   5.5e-14     2e-10       2     209 ..       4     242 ..       3     243 .. 0.62

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 5.5e-14
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrg........... 67 
                                       ++vv+D+dG+L++   s +++iv+                     v +  +r++  +++++f++ g           
  gi|336254818|ref|YP_004597925.1|   4 DAVVLDIDGVLVDVADSYRRAIVES--------------------VDYVYDRTIRKDDIQQFKDAGgfnndweltya 60 
                                       79*************9999999999....................44444444444444444444444444444333 PP

                                       .....................HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH.................... CS
                                       .....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                         Hydrolase  68 .....................ayaigkpewltaldippdlgaaigsaqsqgrtvall.................... 103
                                                            a+a++   + +a+     ++               +                    
  gi|336254818|ref|YP_004597925.1|  61 aalyilatgegydesidaftdAIAENGGGLEAAE---AVVR---------------Drigaratqrvkerwdrerlr 119
                                       3333331111122222222222222222222222...3333...............234444444444444488888 PP

                                       ...................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..GGG CS
                                       ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                         Hydrolase 104 ...................qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG..ddy 159
                                                          + ++  +  i+d+ +v  ea    + L    ++v++ltg  ++ ae a++++G  d+ 
  gi|336254818|ref|YP_004597925.1| 120 dvfqqlylgaelyrgleggEPDIETEGFIHDE-PVLLEADARDRLLE--RYDVGVLTGRPEAEAEIALERVGleDEV 193
                                       88888888888887777662233333333333.48888766666666..689*************99999***6555 PP

                                       E.SEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 160 f.daviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                         ++ ++ d+ + +kp+p+++  +++++ ++   +++VGD++ D+  + +A
  gi|336254818|ref|YP_004597925.1| 194 PlEHRFTMDDWEEGKPHPRALTTLAERFDAER--IVFVGDTLDDVRTANNA 242
                                       556666666666****************6555..***********999877 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.029     1e+02       1      40 [.       6      45 ..       6      96 .. 0.79
   2 !   30.4   0.0   1.1e-10   3.8e-07      94     171 ..     165     242 ..     161     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.029
                             HAD_2  1 iiFDlDgTlldteeliiqafnelleeygls.elseeelrkl 40
                                      ++ D+Dg+l+d  + +  a+ e ++   ++ ++ +++++++
  gi|336254818|ref|YP_004597925.1|  6 VVLDIDGVLVDVADSYRRAIVESVDYV-YDrTIRKDDIQQF 45
                                      578********9987777766666444.3335566655555 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 1.1e-10
                             HAD_2  94 agyklgivTsksreaveekleqlgies..yFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsptDieaa 168
                                       ++y +g+ T + ++++e  le++g+e+   +++  t++d e+ KP+p+ + ++ e++  ++e++++vGD+  D+ +a
  gi|336254818|ref|YP_004597925.1| 165 ERYDVGVLTGRPEAEAEIALERVGLEDevPLEHRFTMDDWEEGKPHPRALTTLAERF--DAERIVFVGDTLDDVRTA 239
                                       5799*********************9733589**********************997..5789************** PP

                             HAD_2 169 kka 171
                                        +a
  gi|336254818|ref|YP_004597925.1| 240 NNA 242
                                       998 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   5.8e-10   2.1e-06       3      74 ..     207     284 ..     206     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 5.8e-10
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT.......-EEEEESSSSS-TTTHHH..HHHHHT---S CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaG.......wksvLVltGvtrpedlee..pehkptyvad 70 
                                       gKP+p ++   +e++  d e+++++GD+  +D++ Anna        ++++ VltG  + e+ ++  +++++++v++
  gi|336254818|ref|YP_004597925.1| 207 GKPHPRALTTLAERF--DAERIVFVGDT-LDDVRTANNAAeadpgreYHGIGVLTGGLTGEEGRRkyEAENAAAVLE 280
                                       9*************7..779********.*********965555566999*****7655444444334478888999 PP

                                       EEES CS
                    Hydrolase_like  71 dlae 74 
                                       ++ e
  gi|336254818|ref|YP_004597925.1| 281 SINE 284
                                       9877 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3     0.026        92       1      50 [.       6      53 ..       6     100 .. 0.59
   2 !   22.0   0.9     5e-08   0.00018      30     187 ..     105     239 ..      71     240 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.026
                               HAD  1 alfDfDgTLldg.dsle.lllrfllrrgaprlwralreklllalfrellrld 50
                                      +++D+Dg L+d  ds+  +    ++++ +    r++r    +++ + ++ ++
  gi|336254818|ref|YP_004597925.1|  6 VVLDIDGVLVDVaDSYRrA----IVESVDYVYDRTIRKDDIQQFKDAGGFNN 53
                                      799*********6666552....33344444455566555555544444443 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 5e-08
                               HAD  30 lwralreklllalfrellrldraglaelleallagls.eelaaelerfvaevirpklldpgalellaahraaGdrvv 105
                                       + + ++e+++  ++r+ +++       l ++l++gl+ +e + e e f+  + +p ll  +a+++l    ++ + v 
  gi|336254818|ref|YP_004597925.1| 105 ATQRVKERWDRERLRDVFQQ-----LYLGAELYRGLEgGEPDIETEGFI--HDEPVLLEADARDRLL---ER-YDVG 170
                                       24444444555555555555.....556666999999999999999999..555667866*******...55.88** PP

                               HAD 106 vvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaaegegidleevvayGDsps 182
                                       v++g ++  +e+ l+++g    l  e+  ++r+t+  + egkp  +     al        e  d e++v++GD+  
  gi|336254818|ref|YP_004597925.1| 171 VLTGRPEAEAEIALERVG----LEDEVPLEHRFTMDDWEEGKPHPR-----ALTT----LAERFDAERIVFVGDTLD 234
                                       ******************....555444444999996666666555.....3333....344668888********* PP

                               HAD 183 Dlpll 187
                                       D+  +
  gi|336254818|ref|YP_004597925.1| 235 DVRTA 239
                                       *9865 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.036   1.3e+02       3      15 ..       6      18 ..       5      46 .. 0.73
   2 ?   10.3   0.0   0.00013      0.46      44     118 ..     161     237 ..     153     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.036
                               NIF  3 LVLDLDetLvhsk 15
                                      +VLD+D++Lv   
  gi|336254818|ref|YP_004597925.1|  6 VVLDIDGVLVDVA 18
                                      8*********665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00013
                               NIF  44 kelsklyevvifTasseeyaeavidildpekkl.lshrlyrescvkkkgeyvKdLsllgr..dlsrvvivDdspdsf 117
                                       ++l + y+v++ T   e  ae  ++ +  e ++ l+hr++ +++  + + + + L++l +  d +r+v+v d+ d +
  gi|336254818|ref|YP_004597925.1| 161 DRLLERYDVGVLTGRPEAEAEIALERVGLEDEVpLEHRFTMDDW-EEGKPHPRALTTLAErfDAERIVFVGDTLDDV 236
                                       67899**********************7777777**********.66889********5558********9988776 PP

                               NIF 118 e 118
                                       +
  gi|336254818|ref|YP_004597925.1| 237 R 237
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); 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 0.20s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2397.41
//
Query:       gi|336254819|ref|YP_004597926.1|  [L=183]
Description: hypothetical protein Halxa_3436 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00042   20.3   0.0    0.00052   20.0   0.0    1.2  1  HD_3      HD domain
    0.00083   19.2   0.0     0.0012   18.6   0.0    1.3  1  HD_2      HD containing hydrolase-like enzyme
  ------ inclusion threshold ------
       0.01   16.0   0.1      0.014   15.7   0.1    1.4  1  HD        HD domain


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 !   20.0   0.0   8.8e-08   0.00052      28      89 ..      52     111 ..      46     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.8e-08
                              HD_3  28 wrvalmalllseelkekvdiarvikmfLiHDlvEiltgDiispdelakeekeeeekeaaeri 89 
                                       + va  ++ +s+el   +d  r+  + L+HD  E+++gD++ p ++  e+ e+ e+++ + +
  gi|336254819|ref|YP_004597926.1|  52 YSVAHHSIHVSRELP--ADSPRLQLLGLLHDAGEAYVGDVPRPLKARFESFERVEERVLDAV 111
                                       8899999*******8..*************************99888888777777776665 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 !   18.6   0.0     2e-07    0.0012      34      85 ..      52     100 ..      44     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2e-07
                              HD_2  34 aliahalalienkkfggkldaerlallalyHDasEiitGDlptpvKyanpei 85 
                                         +ah    ++++      d  rl ll+l+HDa E+ +GD+p p+K + +++
  gi|336254819|ref|YP_004597926.1|  52 YSVAHHSIHVSREL---PADSPRLQLLGLLHDAGEAYVGDVPRPLKARFESF 100
                                       55666666666655...78999************************876554 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.1   2.3e-06     0.014       8      49 ..      54      93 ..      29     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHH CS
                                HD  8 VaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekk 49
                                      Va+ +    ++l  ++d+ +l+l +LlHD G+ ++gd     
  gi|336254819|ref|YP_004597926.1| 54 VAHHSIHVSREL--PADSPRLQLLGLLHDAGEAYVGDVPRPL 93
                                      444444444444..59999*****************955444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1389.17
//
Query:       gi|336254820|ref|YP_004597927.1|  [L=124]
Description: hypothetical protein Halxa_3437 [Halopiger xanaduensis SH-6]
Scores for complete 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-29  102.6   0.2    1.6e-29  102.4   0.2    1.0  1  UPF0146          Uncharacterised protein family (UPF0146)
  ------ inclusion threshold ------
      0.039   13.9   0.0          4    7.4   0.0    2.0  2  Nucleotid_trans  Nucleotide-diphospho-sugar transferase
      0.067   12.5   0.1       0.07   12.5   0.1    1.2  1  HEM4             Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4   0.2   2.6e-33   1.6e-29      14     125 ..       8     118 ..       1     121 [. 0.92

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 2.6e-33
                                       SSEEEEET-TT--HHHHHHHHHS-EEEEE-SS-S....STTEE---SSS--HHHHTTEEEEEEES--TTSHHHHHHH CS
                           UPF0146  14 rgkvvEvGiGrkldvaealakrgvdlvatDikekkakegvrivrDDvtdPnleiYkgadliYslRpPaelqsaildv 90 
                                         + vE+GiGr+++ a+alak gv ++atD+  ++++ gvr+v+DD++dP+ +iY  ad+iY+   P+el++  l+v
  gi|336254820|ref|YP_004597927.1|   8 YDRAVEIGIGRRTELAAALAKAGVSVIATDVYRREVPHGVRFVQDDIVDPDPAIYADADAIYARNLPPELHRPALEV 84 
                                       5799************************************************************************* PP

                                       HHHHT-EEEEE-BTTB-----TT-EEEEETTEEEE CS
                           UPF0146  91 akkvgAaliikpLlgedvvvekelklvnykgalFy 125
                                       a+  +Aa + ++L+g+++ v+++ k     g+l++
  gi|336254820|ref|YP_004597927.1|  85 AREADAAFYFTTLGGDQPAVPVDRKTIE-TGTLYV 118
                                       ******************9999887654.455555 PP

>> Nucleotid_trans  Nucleotide-diphospho-sugar transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00067         4      53      74 ..      17      38 ..       7      40 .. 0.93
   2 ?    4.7   0.0    0.0044        26      70     118 ..      61     118 ..      59     122 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00067
                   Nucleotid_trans 53 wrkvrlllellklGynvllsDv 74
                                       r+++l+ +l+k+G++v+ +Dv
  gi|336254820|ref|YP_004597927.1| 17 GRRTELAAALAKAGVSVIATDV 38
                                      68******************97 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0044
                   Nucleotid_trans  70 llsDvDvvWlrnpfpll........kyedaDvlvss.DsldgttadelknliNsGfff 118
                                       ++ D+D+++ rn  p l        ++ da +++ + ++ ++  + ++k    + +++
  gi|336254820|ref|YP_004597927.1|  61 IYADADAIYARNLPPELhrpalevaREADAAFYFTTlGGDQPAVPVDRKTIETGTLYV 118
                                       789**********999988888765557777777776666666665555444444454 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.2e-05      0.07     126     156 ..      16      46 ..       4      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                                       .S--HHHHHHHHHTTEEEEEE-SEEEEE-HH CS
                              HEM4 126 eiarddlaegLeergaevdevevYetvpaee 156
                                         +r++la++L+++g++v + +vY+++++++
  gi|336254820|ref|YP_004597927.1|  16 IGRRTELAAALAKAGVSVIATDVYRREVPHG 46 
                                       5689**********************77654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1019.29
//
Query:       gi|336254821|ref|YP_004597928.1|  [L=173]
Description: Archemetzincin [Halopiger xanaduensis SH-6]
Scores for 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-22   78.5   0.0    7.9e-22   78.2   0.0    1.2  1  Peptidase_M54  Peptidase family M54
    3.2e-06   26.9   0.0      4e-06   26.6   0.0    1.0  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like
    0.00018   21.5   0.0    0.00024   21.1   0.0    1.2  1  Reprolysin_2   Metallo-peptidase family M12B Reprolysin-like
    0.00038   20.3   0.0    0.00042   20.2   0.0    1.3  1  Peptidase_M10  Matrixin
     0.0011   19.2   0.0     0.0012   19.0   0.0    1.2  1  Reprolysin_5   Metallo-peptidase family M12
     0.0012   19.3   0.0     0.0016   19.0   0.0    1.3  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
     0.0056   15.7   0.0     0.0075   15.3   0.0    1.2  1  Peptidase_M66  Peptidase M66
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.018   14.3   0.0    1.2  1  DUF4953        Met-zincin
      0.081   13.0   0.0       0.13   12.4   0.0    1.3  1  Zincin_1       Zincin-like metallopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0     4e-25   7.9e-22      96     192 ..      68     172 ..      38     173 .] 0.86

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 4e-25
                                       ..EEEESS-EE-TT-S-BSEEE-SSSSEEEEE-T.....--.......SHHHHHHHHHHHHHHHHHHHTT----S-. CS
                     Peptidase_M54  96 ttlplgsrdqyidiykkvlGievsiGnyavlals.....ik.efyte.dkeLflervvkevlhelGhlyGLshCke. 164
                                         ++++ +d +    ++v+G++   G  +v++        +  f ++  +++f +rv ke++he+Gh+yGL hC++ 
  gi|336254821|ref|YP_004597928.1|  68 KNIAITPHDLFYRRRNYVFGLAYLDGSGSVVSTYrlqtsSDgGFSNQsAEDIFEDRVRKEIVHEIGHTYGLEHCDNn 144
                                       5689999****************99**999987654344331466666789***********************998 PP

                                       TSTTS--SSHHHHHHS-SS--HHHHHHH CS
                     Peptidase_M54 165 dCvmnfsndlkdvDrkapkyCksClekl 192
                                        Cvmnfs  +++vD k+ + C sC + +
  gi|336254821|ref|YP_004597928.1| 145 RCVMNFSPTVREVDIKEENLCGSCQRLI 172
                                       9***********************9876 PP

>> Reprolysin_4  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0     2e-09     4e-06      49     158 ..      24     147 ..      16     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2e-09
                      Reprolysin_4  49 elisdqdviytdsetdsfaadisg.edlgnsslatltstrdskdyDlaallrdtrasqqn..vgvawvgalcls..a 120
                                       + + d +v   ds++ +  a +sg ++   +s ++l    +  d+ +a   +d    + n   g+a++ + ++   +
  gi|336254821|ref|YP_004597928.1|  24 RSVYDCEVSINDSQSVPNGAYDSGrNQYSAESFIQLAERVGRGDKNIAITPHDLFYRRRNyvFGLAYLDGSGSVvsT 100
                                       555677888999999999999998355678999**************9999997644444469******99976765 PP

                      Reprolysin_4 121 rq..nkkasgvaas..rdey..di...fAHEiGHtfGaaHdlsdege 158
                                       +   +   +g+++    d +   +   + HEiGHt+G++H  ++ + 
  gi|336254821|ref|YP_004597928.1| 101 YRlqTSSDGGFSNQsaEDIFedRVrkeIVHEIGHTYGLEHCDNNRCV 147
                                       5432444467766545454444445579************9888875 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.2e-07   0.00024      30     145 ..      23     144 ..      14     165 .. 0.59

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                      Reprolysin_2  30 lrneaeieatteasdsgnnycnssttevrr.lnl..lsql..egekdydlahlvllgtfsggvlGLayvg...qicq 98 
                                       lr + ++e+  + s s +n ++ s+ +    + +  l++   +g+k+  ++   l     + v GLay+    ++ +
  gi|336254821|ref|YP_004597928.1|  23 LRSVYDCEVSINDSQSVPNGAYDSGRNQYSaESFiqLAERvgRGDKNIAITPHDLFYRRRNYVFGLAYLDgsgSVVS 99 
                                       5566666666666666666333322222221222002332113444444444444455577899*****65657776 PP

                      Reprolysin_2  99 keassrktntglsttansgsaveetkeidvvaHEvGHaFGatHdndg 145
                                       +   ++++  g+s  +  ++  e ++  + + HE+GH++G  H ++ 
  gi|336254821|ref|YP_004597928.1| 100 TYRLQTSSDGGFS-NQSAEDIFE-DRVRKEIVHEIGHTYGLEHCDNN 144
                                       6665556778899.556666664.66666678***********7763 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.1e-07   0.00042     113     136 ..     128     151 ..      53     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.1e-07
                                       HHHHHHHHTTBESXSSTTSTTSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 113 aaHEiGHalGLeHssdkdalmypl 136
                                        +HEiGH+ GLeH ++++ +m   
  gi|336254821|ref|YP_004597928.1| 128 IVHEIGHTYGLEHCDNNRCVMNFS 151
                                       69****************999744 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     6e-07    0.0012     104     162 ..      82     144 ..      14     168 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6e-07
                      Reprolysin_5 104 fsggvGlAwl.........gqlcnsgsagsvstrveksnsvvvstatevqvvaHElGHnfGavHDcds 162
                                        +++ GlA+l         + l++s+++g  ++++       +  +   + + HE+GH++G +H  ++
  gi|336254821|ref|YP_004597928.1|  82 RNYVFGLAYLdgsgsvvstYRLQTSSDGGFSNQSA----ED-IFEDRVRKEIVHEIGHTYGLEHCDNN 144
                                       33347888886555555555555666666666663....33.44777788899***********5443 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   7.8e-07    0.0016      59     123 ..      65     140 ..      19     141 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.8e-07
                      Reprolysin_3  59 rgqagyDl..vhlftardesgvgGlAyv..gsvcnsskkagvnsgssvlgkvga........dtvaHEiGHnfganH 123
                                       rg +++ +  + lf +r +  v GlAy+  ++   s+++ + +s+ + ++++          + + HEiGH  g++H
  gi|336254821|ref|YP_004597928.1|  65 RGDKNIAItpHDLFYRRRN-YVFGLAYLdgSGSVVSTYRLQTSSDGGFSNQSAEdifedrvrKEIVHEIGHTYGLEH 140
                                       4555555532345666555.99******763333334443333333333333225677788899************* PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.8e-06    0.0075     176     209 ..     109     141 ..      91     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.8e-06
                     Peptidase_M66 176 GGlgggssGivtgdatltgefiHEqGHalGLpHy 209
                                       GG +  s+   + + ++ +e +HE GH +GL H 
  gi|336254821|ref|YP_004597928.1| 109 GGFSNQSAE-DIFEDRVRKEIVHEIGHTYGLEHC 141
                                       666666444.57789999***************4 PP

>> DUF4953  Met-zincin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     9e-06     0.018       3      29 ..     114     140 ..     112     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9e-06
                           DUF4953   3 efpdelmgallrfvvaHEvGhtLGLrh 29 
                                       +  ++++++++r  + HE+Ght GL+h
  gi|336254821|ref|YP_004597928.1| 114 QSAEDIFEDRVRKEIVHEIGHTYGLEH 140
                                       66789999******************9 PP

>> Zincin_1  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.6e-05      0.13      66      87 ..     117     139 ..      98     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                                       --.HHHHHHHHHHHHHHHHHTT- CS
                          Zincin_1  66 ee.leeevretllHEighhfGld 87 
                                       e+ +e+ vr+ ++HEigh  Gl+
  gi|336254821|ref|YP_004597928.1| 117 EDiFEDRVRKEIVHEIGHTYGLE 139
                                       44589****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1412.66
//
Query:       gi|336254822|ref|YP_004597929.1|  [L=230]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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   48.0   0.1    3.1e-12   47.0   0.0    1.6  2  Methyltransf_11  Methyltransferase domain
    6.6e-08   33.1   0.1    3.1e-07   31.0   0.0    2.0  2  Methyltransf_25  Methyltransferase domain
    4.1e-07   30.0   0.0    7.7e-07   29.1   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
      9e-05   23.2   0.0    0.00025   21.7   0.0    1.8  1  Methyltransf_12  Methyltransferase domain
     0.0034   17.2   0.0     0.0058   16.4   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
      0.004   16.5   0.0     0.0077   15.6   0.0    1.5  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0046   16.8   0.0     0.0065   16.4   0.0    1.2  1  Methyltransf_8   Hypothetical methyltransferase
  ------ inclusion threshold ------
      0.067   13.1   0.0       0.73    9.7   0.0    2.2  2  PASTA            PASTA domain
      0.084   12.6   0.0       0.13   12.0   0.0    1.3  1  N6_N4_Mtase      DNA methylase


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 !   47.0   0.0   1.5e-15   3.1e-12       1      96 []      57     142 ..      57     142 .. 0.97
   2 ?   -2.7   0.0       4.9   9.8e+03      25      60 ..     146     183 ..     143     187 .. 0.62

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1.5e-15
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       L+vG+GtGr+a++l+      +g+D++ + l+ a+++++++      v++ ae+lp++d+ +D  +   vl +v+d+
  gi|336254822|ref|YP_004597929.1|  57 LEVGVGTGRFAAPLE----IPIGIDPARTPLTHARDRGVDP------VRGVAESLPVADDAVDRLLFVTVLSFVDDL 123
                                       89*************....789************9999998......9***************************** PP

                                       HHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                       e++l+e++RvL  +G+lv+
  gi|336254822|ref|YP_004597929.1| 124 EATLSEARRVLTDDGTLVV 142
                                       ****************986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.9
                                       ES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT CS
                   Methyltransf_11  25 Dlskemlklakekaseegl..kvefvvadaeklpfedn 60 
                                       D s  + ++ +e++ e+++    ef+ ad     +ed+
  gi|336254822|ref|YP_004597929.1| 146 DRSSPVGQVYQEHKDESPFyaDAEFLTADEAAAALEDA 183
                                       55666666666666666666666677777666666665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.6e-10   3.1e-07       2      97 .]      57     138 ..      56     138 .. 0.94
   2 ?   -0.8   0.0       1.3   2.5e+03      27      65 ..     145     185 ..     141     189 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.6e-10
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhls 78 
                                       L++G GtGr+++ l   ++    +g+D++ + l +ar r       v+ v+g ae+lp +d+ +D  + + +l++++
  gi|336254822|ref|YP_004597929.1|  57 LEVGVGTGRFAAPLE--IP----IGIDPARTPLTHARDRG------VDPVRGVAESLPVADDAVDRLLFVTVLSFVD 121
                                       9*************8..43....8***************9......9**********************98899987 PP

                                       HHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                         dle++l+e++rvL+++G
  gi|336254822|ref|YP_004597929.1| 122 --DLEATLSEARRVLTDDG 138
                                       ..999***********998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                                       EESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTE CS
                   Methyltransf_25  27 vDiseemleaareraeeegl..nvefvqgdaedlpfedgsf 65 
                                       +D s+   +  +e+ +e+ +  ++ef+++d  +  +ed+ f
  gi|336254822|ref|YP_004597929.1| 145 LDRSSPVGQVYQEHKDESPFyaDAEFLTADEAAAALEDAGF 185
                                       66677666777777766555788999999888777777766 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   3.9e-10   7.7e-07      11     162 ..      30     187 ..      18     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.9e-10
                   Methyltransf_23  11 dklerllpklragg...........rvLdiGcGtGillevlrengfsvt.gvDlspeaveiaekakkaqkdqfdeqe 75 
                                       ++ler+lp + a             r L++G GtG+++  l     ++  g+D+ +     a  ++   ++   +++
  gi|336254822|ref|YP_004597929.1|  30 AALERALPDRHALDgsdgnrpltrtRALEVGVGTGRFAAPL-----EIPiGIDPARTPLTHA-RDRGVDPVRGVAES 100
                                       5556666432222245666677777**************77.....4444999987766666.55666666666788 PP

                   Methyltransf_23  76 aaepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslk 152
                                        ++ ++  d      vl  v+d++++l+ +++ l ++G l++ + ++s++  + +++ + + p      f +a++ +
  gi|336254822|ref|YP_004597929.1| 101 LPVADDAVDRLLFVTVLSFVDDLEATLSEARRVLTDDGTLVVAVLDRSSPVGQVYQEHKDESPFYADAEFLTADEAA 177
                                       89999********************************************88888888888877777889******** PP

                   Methyltransf_23 153 elleeaGlev 162
                                        +le+aG++v
  gi|336254822|ref|YP_004597929.1| 178 AALEDAGFTV 187
                                       ********97 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.2e-07   0.00025       1      99 []      57     140 ..      57     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.2e-07
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       Le+G GtG+++++l+        +g+D+ +  +++a+ +        ++ v+  a++l   d+  ++D  +   vl+
  gi|336254822|ref|YP_004597929.1|  57 LEVGVGTGRFAAPLEIP------IGIDPARTPLTHARDRG-------VDPVRGVAESLPVADD--AVDRLLFVTVLS 118
                                       8*************999......9*********4444443.......4455555555555544..9*********** PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        ++d++++l+++r++L+++G l
  gi|336254822|ref|YP_004597929.1| 119 FVDDLEATLSEARRVLTDDGTL 140
                                       ********************86 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.9e-06    0.0058       6     113 ..      55     146 ..      52     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.9e-06
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       r l++G GtG+++  l    +p    +GiD   + +++Ar +    g+d     +g +e+l+  ++d+ +D +l   
  gi|336254822|ref|YP_004597929.1|  55 RALEVGVGTGRFAAPLE---IP----IGIDPARTPLTHARDR----GVD---PVRGVAESLP--VADDAVDRLLFVT 115
                                       66888888888776666...43....8888888888888886....555...55688899**..99*********** PP

                   Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr 113
                                       vl  + d++++l e+ rvl+++g l+++  +
  gi|336254822|ref|YP_004597929.1| 116 VLSFVDDLEATLSEARRVLTDDGTLVVAVLD 146
                                       ***************************9888 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.8e-06    0.0077     100     160 ..      91     153 ..      79     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.8e-06
                                       EEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE..EEE----SH CS
                   Ubie_methyltran 100 ieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv..lefskvelp 160
                                       ++ + + ae Lp  dd+ D +     l  v D + +L ea+rvl   G+lvv  l+ s +  +
  gi|336254822|ref|YP_004597929.1|  91 VDPVRGVAESLPVADDAVDRLLFVTVLSFVDDLEATLSEARRVLTDDGTLVVavLDRSSPVGQ 153
                                       7789999*************999999**********************987522666666555 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.2e-06    0.0065     115     162 ..     100     147 ..      85     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.2e-06
                                       S-S--TT-EEEEEEES--.-SS-HHHHHHHHHHHEEEEEEEEEEEEGGG CS
                    Methyltransf_8 115 kvPledesvdvavfclsl.mgtnladflkeanrvlkvGGllkvaevksr 162
                                        +P++d++vd  +f   l  +++l+  l ea+rvl   G l va +  r
  gi|336254822|ref|YP_004597929.1| 100 SLPVADDAVDRLLFVTVLsFVDDLEATLSEARRVLTDDGTLVVAVLD-R 147
                                       69********777655442589********************99654.3 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.25     5e+02       9      33 ..     125     149 ..     115     160 .. 0.76
   2 ?    9.7   0.0   0.00037      0.73       9      37 ..     171     199 ..     167     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.25
                                       SBHHHHHHHHHHTT--CCCEEEECT CS
                             PASTA   9 msvdeAkatLkalGlkiktveetsd 33 
                                        +++eA++ L++ G  +  v   s+
  gi|336254822|ref|YP_004597929.1| 125 ATLSEARRVLTDDGTLVVAVLDRSS 149
                                       5899999999999876655555444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00037
                                       SBHHHHHHHHHHTT--CCCEEEECTCCGT CS
                             PASTA   9 msvdeAkatLkalGlkiktveetsddvpe 37 
                                       ++ deA a+L+++G+++ +  +t+ d p+
  gi|336254822|ref|YP_004597929.1| 171 LTADEAAAALEDAGFTVEGRLQTVFDEPA 199
                                       689************99988888777765 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.3e-05      0.13      30      71 ..     118     157 ..     113     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-05
                                       HHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHHHH CS
                       N6_N4_Mtase  30 eyleflekvlkevrrvLkddgsifiniddseikkelkalade 71 
                                        +++ le  l+e+rrvL ddg++++ + d+     +  ++ e
  gi|336254822|ref|YP_004597929.1| 118 SFVDDLEATLSEARRVLTDDGTLVVAVLDRSSP--VGQVYQE 157
                                       67888999******************9998764..5555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1756.04
//
Query:       gi|336254823|ref|YP_004597930.1|  [L=604]
Description: ABC transporter-like protein [Halopiger xanaduensis SH-6]
Scores for 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-42  143.3   0.0    1.7e-21   77.2   0.0    2.5  2  ABC_tran      ABC transporter
    5.5e-13   48.9   8.6    8.9e-05   22.0   1.0    4.1  3  SMC_N         RecF/RecN/SMC N terminal domain
    3.8e-12   45.8   1.4    7.6e-12   44.9   1.4    1.5  1  RLI           Possible Fer4-like domain in RNase L inhibitor,
    4.6e-12   46.3   0.4      0.083   12.7   0.0    4.2  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.2e-07   32.3   0.6     0.0098   16.3   0.0    3.3  3  AAA_16        AAA ATPase domain
    2.8e-06   27.7   0.2     0.0073   16.6   0.0    3.0  2  AAA_22        AAA domain
    3.4e-06   27.7   1.7      0.066   13.7   0.0    2.7  2  AAA_23        AAA domain
    1.1e-05   25.8   0.0       0.03   14.8   0.0    2.8  2  AAA           ATPase family associated with various cellular 
    5.9e-05   22.9   0.0      0.069   12.9   0.0    2.4  2  AAA_24        AAA domain
    6.1e-05   23.0   0.0       0.16   11.9   0.0    2.8  3  Rad17         Rad17 P-loop domain
    9.4e-05   22.8   0.0       0.61   10.5   0.0    2.7  2  RNA_helicase  RNA helicase
    0.00018   21.7   0.0       0.39   10.9   0.0    2.8  2  AAA_33        AAA domain
    0.00038   20.4   0.0       0.73    9.7   0.0    2.4  2  RsgA_GTPase   RsgA GTPase
    0.00048   20.2   0.1        2.6    8.1   0.0    3.6  3  AAA_14        AAA domain
    0.00057   19.6   1.6    0.00057   19.6   1.6    2.7  3  Fer4          4Fe-4S binding domain
     0.0017   18.3  12.2     0.0086   16.1   2.1    2.4  2  Fer4_6        4Fe-4S binding domain
     0.0019   17.9   0.4        1.5    8.6   0.1    2.4  2  AAA_29        P-loop containing region of AAA domain
     0.0024   17.7   0.8       0.63    9.7   0.2    2.6  3  AAA_15        AAA ATPase domain
     0.0025   17.7   0.0          3    7.7   0.0    2.7  2  NACHT         NACHT domain
     0.0032   17.2   0.2        1.8    8.3   0.1    3.0  3  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
     0.0046   17.5   0.0        3.2    8.3   0.0    2.8  2  AAA_18        AAA domain
  ------ inclusion threshold ------
      0.012   14.9   0.0        0.9    8.7   0.0    2.4  2  NB-ARC        NB-ARC domain
       0.02   14.5   0.7         13    5.3   0.0    3.5  3  AAA_25        AAA domain
      0.023   15.0   0.2          5    7.3   0.0    3.3  3  AAA_28        AAA domain
      0.043   13.9   0.5       0.93    9.6   0.1    2.8  2  MMR_HSR1      50S ribosome-binding GTPase
      0.045   14.3  11.1      0.099   13.2  11.1    1.6  1  Fer4_7        4Fe-4S dicluster domain
      0.049   13.6   0.1         11    6.0   0.0    2.9  3  AAA_5         AAA domain (dynein-related subfamily)
      0.051   13.7   0.5         18    5.3   0.0    3.3  3  DUF87         Helicase HerA, central domain
      0.081   12.6   0.2        5.8    6.5   0.0    2.5  2  SRP54         SRP54-type protein, GTPase domain
        0.1   12.3   0.2        8.3    6.1   0.0    2.7  3  AAA_30        AAA domain
       0.12   12.2   3.1         14    5.6   0.0    3.3  4  NTPase_1      NTPase
       0.14   12.0   0.0        6.2    6.6   0.0    2.5  2  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
       0.21   11.7  12.2       0.56   10.4   1.6    2.0  2  Fer4_10       4Fe-4S dicluster domain
       0.25   11.0   0.6        2.8    7.6   0.0    2.3  2  IstB_IS21     IstB-like ATP binding protein
       0.63   10.2   8.6        1.1    9.4   8.6    1.4  1  Fer4_21       4Fe-4S dicluster domain
        1.2    9.3  11.1        2.6    8.3  11.1    1.5  1  Fer4_9        4Fe-4S dicluster domain
        1.4    9.1  11.0       0.13   12.4   1.1    2.4  2  Fer4_2        4Fe-4S binding domain
        4.5    8.1   7.1         21    5.9   7.1    2.3  1  Fer4_15       4Fe-4S single cluster 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 !   63.5   0.0   6.2e-20   2.9e-17       9     136 ..     107     250 ..     105     251 .. 0.79
   2 !   77.2   0.0   3.6e-24   1.7e-21       7     137 .]     375     496 ..     372     496 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 6.2e-20
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGG......B-HHHCCHCEEEE-SS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxx......xxxxxxxxxxxxxxxxx RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGei...........lldgkdlke......qeleslrkeigvlpqep 68 
                                       +eg++++i+G+nG GK+t +++lag+l+p+ G+             ++g++l++      + +  + ++ +++ q p
  gi|336254823|ref|YP_004597930.1| 107 QEGQVTGILGPNGIGKTTAVRILAGELEPNLGRHeeeidwddvleAYRGTELQDyiadvrDGEVTVARKPQYVDQIP 183
                                       58***************************655554444888888777777777777666655666666677777777 PP

                                       -S-TTSBHHHH....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  69 qlfpeltvren....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       + f++ t re     +++  +++++++l+++ + ++ +      LSgG+ qrvala++l+++ ++++lDE t
  gi|336254823|ref|YP_004597930.1| 184 ETFDGNT-RELleqtNERGALDQLVERLSIEPVMEQSI----DDLSGGELQRVALAATLARDTDFYFLDEIT 250
                                       7777663.33365334444499********99888888....****************************87 PP

  == domain 2  score: 77.2 bits;  conditional E-value: 3.6e-24
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.HHHH.HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.vren.es 81 
                                       +++e+e+++ivG+nG GKSt++kll+g+l+p+eG+  ld   l+     s++ +  ++ q+ +++  l+ + ++  s
  gi|336254823|ref|YP_004597930.1| 375 QIRENEVLGIVGPNGIGKSTFAKLLTGNLEPDEGDADLD---LD----ISYKPQYVTIDQHMRVDAFLSsITDQfGS 444
                                       6899*******************************9555...22....24456666666666666666545555788 PP

                                       HTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  82 deeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       + + +++++ l+l+ + ++++    s LSgG++qrva+a++l   ++l+llDEp+a
  gi|336254823|ref|YP_004597930.1| 445 SYWNTEIAQPLQLERIMEQNL----SDLSGGERQRVAIAACLSDSADLYLLDEPSA 496
                                       888999999999998888888....*****************************75 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 !   22.0   1.0   1.9e-07   8.9e-05      23     201 ..     108     285 ..     102     301 .. 0.62
   2 !    6.6   0.1    0.0097       4.6      24      41 ..     379     396 ..     360     400 .. 0.82
   3 !   20.3   0.1   6.5e-07   0.00031     121     204 ..     449     533 ..     421     546 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.9e-07
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--......BTTCSSTTEEEEEEEEEETTEESSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk......skekasvkkaeveitfdnedkklkie 93 
                                       + ++t i+GpNG GK+  +  +   L  +  ++  + + +d++ +      ++  a v  +ev++            
  gi|336254823|ref|YP_004597930.1| 108 EGQVTGILGPNGIGKTTAVRILAGELEPNLGRHEEEIDWDDVLEAyrgtelQDYIADVRDGEVTV-----------A 173
                                       56788999999999998777766666655666666667788888743322222223333333333...........3 PP

                                       SSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  94 keevsisrrvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyll 164
                                       ++  ++ +  ++ + ++ ++ +++ ++  + +l+e+  i++        LSgGe + vala  +A    + + +y+l
  gi|336254823|ref|YP_004597930.1| 174 RKPQYVDQIPETFDGNTRELLEQTNERGALDQLVERLSIEPVmeqsidDLSGGELQRVALAATLA----RDTDFYFL 246
                                       3222333222222222333334444445555555555554433333339******9999988876....7899**** PP

                                       CTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                             SMC_N 165 DeidaaLDeknvkkvaellkekskn..aQfivislreem 201
                                       Dei   LD  ++   a+l++e  ++    ++v+ ++  +
  gi|336254823|ref|YP_004597930.1| 247 DEITPYLDIGQRVTAARLIRELAEEenKSMLVVEHDLAI 285
                                       ********************7654322777887776555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0097
                                       SSEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnll 41 
                                       +++  ivGpNG GKs + 
  gi|336254823|ref|YP_004597930.1| 379 NEVLGIVGPNGIGKSTFA 396
                                       45678**********875 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 6.5e-07
                                       HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEE CS
                                       xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                             SMC_N 121 kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQf 192
                                       +e+++ l+ ++i ++    LSgGe++ va+a  +     + a lyllDe  a+LD +++ +  + +++  ++  a +
  gi|336254823|ref|YP_004597930.1| 449 TEIAQPLQLERIMEQnlsDLSGGERQRVAIAACL----SDSADLYLLDEPSAHLDVEQRVQATSAIRRYAEQqdATV 521
                                       566666666666655111579********99886....48899****************999999996554423888 PP

                                       EEE-SSHHHCCC CS
                                       xxxxxxxxxxxx RF
                             SMC_N 193 ivislreemlek 204
                                       +vi ++  m+  
  gi|336254823|ref|YP_004597930.1| 522 MVIDHDIYMIDL 533
                                       888888777765 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 !   44.9   1.4   1.6e-14   7.6e-12       3      35 .]       6      35 ..       5      35 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 1.6e-14
                                      EEEES---------TTHHHHHTTSEEEESS--S CS
                               RLI  3 lAivdadqCdPKKCtgkkcarfcpvrlvrtgkk 35
                                      +A+vd d+C+P++C++ +c+ +cp   +rtgk+
  gi|336254823|ref|YP_004597930.1|  6 IAVVDLDRCQPDRCSY-ECKNYCPP--NRTGKE 35
                                      8***************.********..****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 !   12.7   0.0   0.00018     0.083       1      20 [.     111     130 ..     111     157 .. 0.83
   2 ?    6.9   0.1      0.01       4.8     232     286 ..     218     272 ..     180     287 .. 0.78
   3 !   12.0   0.0   0.00029      0.14       3      20 ..     383     400 ..     381     445 .. 0.83
   4 !   10.0   0.0    0.0012      0.55     232     273 ..     463     501 ..     455     532 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00018
                            AAA_21   1 lnvliGpNgsGKSnLLdald 20 
                                       ++++ GpNg GK++  ++l 
  gi|336254823|ref|YP_004597930.1| 111 VTGILGPNGIGKTTAVRILA 130
                                       699***************94 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHP...kll.rrllellkels 286
                                        ++++lS G ++  al++ l+r+    +++++DE+   L+      + +rl++ l e++
  gi|336254823|ref|YP_004597930.1| 218 QSIDDLSGGELQRVALAATLARDT---DFYFLDEITPYLDIgqrV-TaARLIRELAEEE 272
                                       578999*****999*******988...9************96531.2444444443333 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00029
                            AAA_21   3 vliGpNgsGKSnLLdald 20 
                                       +++GpNg GKS++ ++l 
  gi|336254823|ref|YP_004597930.1| 383 GIVGPNGIGKSTFAKLLT 400
                                       79***********99993 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0012
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPk 273
                                        ++++lS G ++    ++a+l++    +l+l+DEp ++L+ +
  gi|336254823|ref|YP_004597930.1| 463 QNLSDLSGGERQR-VAIAACLSDSA--DLYLLDEPSAHLDVE 501
                                       57899999**999.55555555443..9***********984 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1     0.001      0.47      24      52 ..     109     138 ..      98     240 .. 0.61
   2 ?    1.4   0.0      0.76   3.6e+02      64      93 ..     247     276 ..     227     331 .. 0.66
   3 !   16.3   0.0   2.1e-05    0.0098      25     143 ..     380     526 ..     370     529 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.001
                            AAA_16  24 pelvllsGesGvGKsslvrellralekd.g 52 
                                       ++++ + G+ G+GK++ vr l+ +le + g
  gi|336254823|ref|YP_004597930.1| 109 GQVTGILGPNGIGKTTAVRILAGELEPNlG 138
                                       4677799**************999999842 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.76
                            AAA_16  64 esaipysalaqalareellrqllde.aesae 93 
                                       ++ +py+ + q  ++ +l+r+l++e   ++ 
  gi|336254823|ref|YP_004597930.1| 247 DEITPYLDIGQRVTAARLIRELAEEeN-KSM 276
                                       4569999999999999******99952.332 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 2.1e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekd.......................ggif...lrgkcdqlesaipy..sala 73 
                                       e++ ++G+ G+GKs+ ++ l   le d                       +  +   l+  +dq+  + +y    +a
  gi|336254823|ref|YP_004597930.1| 380 EVLGIVGPNGIGKSTFAKLLTGNLEPDegdadldldisykpqyvtidqhmR--VdafLSSITDQF--GSSYwnTEIA 452
                                       67789**********************555555555555444444443221..122233333333..2223322244 PP

                            AAA_16  74 qalareellrqlldeaesaeleawrekleeala.......................avpelagaea.......srll 120
                                       q l  e++++q l++                                         +        +       ++  
  gi|336254823|ref|YP_004597930.1| 453 QPLQLERIMEQNLSD-----------------LsggerqrvaiaaclsdsadlyllD--------EpsahldvEQRV 504
                                       444444444444444.................0344444443333333555554431........144455566666 PP

                            AAA_16 121 ellkrllallsrderplvlvlDd 143
                                       ++ +++ +++++ ++ +v+v+D+
  gi|336254823|ref|YP_004597930.1| 505 QATSAIRRYAEQ-QDATVMVIDH 526
                                       676777788888.777*****95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.2     0.008       3.8       7      30 ..     111     134 ..     107     279 .. 0.76
   2 !   16.6   0.0   1.5e-05    0.0073       7      91 ..     381     474 ..     376     526 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.008
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqld 30 
                                       ++ + G+ G+GKTt +r l+ +l+
  gi|336254823|ref|YP_004597930.1| 111 VTGILGPNGIGKTTAVRILAGELE 134
                                       56689************9998874 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.5e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee..erpevv..fvtlpsstsskdllrellralglelka....erlss 75 
                                       +l ++G+ G+GK+t ++ l+ +l+ ++  ++   + ++   +vt+ + +  + +l+ +  ++g++  +    ++l++
  gi|336254823|ref|YP_004597930.1| 381 VLGIVGPNGIGKSTFAKLLTGNLEPDEGDADldLDISYKpqYVTIDQHMRVDAFLSSITDQFGSSYWNteiaQPLQL 457
                                       6679*******************877777778744444477999999999999999999999987766888877777 PP

                            AAA_22  76 eell.ealeqalrarav 91 
                                       e+++ + l + +   + 
  gi|336254823|ref|YP_004597930.1| 458 ERIMeQNLSDLSGGERQ 474
                                       77774444444433333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.9   0.00041      0.19      20      39 ..     110     129 ..      93     275 .. 0.81
   2 !   13.7   0.0   0.00014     0.066       8      40 ..     360     400 ..     359     434 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00041
                            AAA_23  20 gltlItGpNGaGKTTildAi 39 
                                        +t I GpNG GKTT ++ +
  gi|336254823|ref|YP_004597930.1| 110 QVTGILGPNGIGKTTAVRIL 129
                                       689************98754 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00014
                            AAA_23   8 rsfrdqeidF........skgltlItGpNGaGKTTildAik 40 
                                       +s++d e+ +        ++ +  I+GpNG GK+T+   ++
  gi|336254823|ref|YP_004597930.1| 360 KSYGDGEFSLeveggqirENEVLGIVGPNGIGKSTFAKLLT 400
                                       58888888777788888888999************987665 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 !   14.8   0.0   6.3e-05      0.03       4      41 ..     115     156 ..     113     210 .. 0.83
   2 !    8.0   0.0    0.0078       3.7       3      22 ..     384     403 ..     382     442 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.3e-05
                                       ESSTTSSHHHHHHHHHHHH....THEEEEEETTTCSSSSTTH CS
                               AAA   4 yGppGtGKTllakavakel....gvefleisgsellskyvge 41 
                                        Gp G+GKT++++ +a el    g++  ei+  ++l+ y g 
  gi|336254823|ref|YP_004597930.1| 115 LGPNGIGKTTAVRILAGELepnlGRHEEEIDWDDVLEAYRGT 156
                                       7*****************844335777778777777776654 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0078
                                       EESSTTSSHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel 22 
                                       ++Gp G+GK+++ak +  +l
  gi|336254823|ref|YP_004597930.1| 384 IVGPNGIGKSTFAKLLTGNL 403
                                       68************998876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0046       2.2       4      22 ..     111     129 ..     108     182 .. 0.87
   2 !   12.9   0.0   0.00015     0.069       4      27 ..     381     401 ..     378     525 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0046
                            AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                          i Gp+giGKTt ++ l
  gi|336254823|ref|YP_004597930.1| 111 VTGILGPNGIGKTTAVRIL 129
                                       5679**********99876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00015
                            AAA_24   4 kiliyGpsgiGKTtlakelgpkpl 27 
                                        + i+Gp+giGK+t+ak l   + 
  gi|336254823|ref|YP_004597930.1| 381 VLGIVGPNGIGKSTFAKLL---TG 401
                                       5789*************99...33 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00033      0.16      46      73 ..     110     137 ..     102     149 .. 0.84
   2 ?   -1.4   0.0       3.9   1.8e+03     128     152 ..     169     193 ..     144     199 .. 0.74
   3 !    7.5   0.0    0.0073       3.5      44      69 ..     378     403 ..     368     409 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00033
                             Rad17  46 riLLisGPsGCgkstvvkvLskelgikl 73 
                                       ++  i GP G gk+t+v++L+ el ++l
  gi|336254823|ref|YP_004597930.1| 110 QVTGILGPNGIGKTTAVRILAGELEPNL 137
                                       566799***************9998876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.9
                             Rad17 128 dlrtdkklilvedlPnkfyrdsdal 152
                                       ++   +k  +v+++P+ f ++++ l
  gi|336254823|ref|YP_004597930.1| 169 EVTVARKPQYVDQIPETFDGNTREL 193
                                       55566677789********999776 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0073
                             Rad17  44 kkriLLisGPsGCgkstvvkvLskel 69 
                                       ++++L i GP G gkst  k L+ +l
  gi|336254823|ref|YP_004597930.1| 378 ENEVLGIVGPNGIGKSTFAKLLTGNL 403
                                       456999**************998665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0     0.003       1.4       3      30 ..     114     141 ..     113     173 .. 0.76
   2 !   10.5   0.0    0.0013      0.61       3      23 ..     384     404 ..     382     432 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.003
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkk 30 
                                       + Gp+g+GK+t+++ La +l+ +l+ ++
  gi|336254823|ref|YP_004597930.1| 114 ILGPNGIGKTTAVRILAGELEPNLGRHE 141
                                       67****************9997773333 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0013
                      RNA_helicase   3 lyGpsgeGKStlakeLakall 23 
                                       ++Gp+g+GKSt+ak L+ +l+
  gi|336254823|ref|YP_004597930.1| 384 IVGPNGIGKSTFAKLLTGNLE 404
                                       78*************988776 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    0.0057       2.7       5      43 ..     115     159 ..     111     211 .. 0.75
   2 !   10.9   0.0   0.00083      0.39       4      25 ..     384     409 ..     381     528 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0057
                            AAA_33   5 vGlpGsGKstlaerllkklg......avllssdtlrrrlfgtdqq 43 
                                        G++G GK+t ++ l+ +l        + ++ d+++++++gt+ q
  gi|336254823|ref|YP_004597930.1| 115 LGPNGIGKTTAVRILAGELEpnlgrhEEEIDWDDVLEAYRGTELQ 159
                                       6**************999987776666667777777777775554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00083
                            AAA_33   4 lvGlpGsGKstlaerllkklg....a 25 
                                       +vG++G GKst+a+ l  +l      
  gi|336254823|ref|YP_004597930.1| 384 IVGPNGIGKSTFAKLLTGNLEpdegD 409
                                       79************998777655543 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0047       2.2      98     128 ..     108     138 ..      95     146 .. 0.84
   2 !    9.7   0.0    0.0016      0.73      99     124 ..     379     404 ..     365     416 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0047
                                       TTSEEEEECSTTSSHHHHHHHHCTT-----S CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktg 128
                                       +++++ ++G+ G+GK+t +  l++ele + g
  gi|336254823|ref|YP_004597930.1| 108 EGQVTGILGPNGIGKTTAVRILAGELEPNLG 138
                                       579999****************999876655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0016
                                       TSEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpele 124
                                       +++  +vG+ G+GKSt+ + l+++le
  gi|336254823|ref|YP_004597930.1| 379 NEVLGIVGPNGIGKSTFAKLLTGNLE 404
                                       578889***************99875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.015         7       3      40 ..     110     148 ..     108     179 .. 0.73
   2 ?    0.9   0.0      0.95   4.5e+02      60      88 ..     237     270 ..     203     280 .. 0.62
   3 !    8.1   0.0    0.0056       2.6       2      29 ..     379     405 ..     378     523 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.015
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell.vkkesilyinldd 40 
                                       ++  i G+  +GKTt ++ l+ el     ++  +i++dd
  gi|336254823|ref|YP_004597930.1| 110 QVTGILGPNGIGKTTAVRILAGELEpNLGRHEEEIDWDD 148
                                       6789*************9999887754444555555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.95
                            AAA_14  60 lkeekktylflDEiqev......pewekalkslvd 88 
                                       l  +++ + flDEi  +       ++ + +++l +
  gi|336254823|ref|YP_004597930.1| 237 LA-RDTDFYFLDEITPYldigqrVTAARLIRELAE 270
                                       33.367899*****988555555455555555555 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0056
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvk 29 
                                       +++l i+G+  +GK+t++k l  +l  +
  gi|336254823|ref|YP_004597930.1| 379 NEVLGIVGPNGIGKSTFAKLLTGNLE-P 405
                                       68999************998886665.4 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   0.0         6   2.8e+03       2       8 ..       8      14 ..       7      15 .. 0.87
   2 ?   -1.1   0.6       4.2     2e+03      13      19 ..      22      28 ..      21      30 .. 0.83
   3 !   19.6   1.6   1.2e-06   0.00057      11      24 .]      64      77 ..      62      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6
                                      EEETTTS CS
                              Fer4  2 videekC 8 
                                      v+d ++C
  gi|336254823|ref|YP_004597930.1|  8 VVDLDRC 14
                                      89***** PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.2
                                      HHHHHST CS
                              Fer4 13 aCvevCP 19
                                      +C + CP
  gi|336254823|ref|YP_004597930.1| 22 ECKNYCP 28
                                      6****** PP

  == domain 3  score: 19.6 bits;  conditional E-value: 1.2e-06
                                      -THHHHHSTTTEEE CS
                              Fer4 11 CGaCvevCPvgAIt 24
                                      CG+Cve CP++AI+
  gi|336254823|ref|YP_004597930.1| 64 CGICVEKCPFDAIE 77
                                      *************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 ?    7.3   2.7     0.011       5.3       1      20 [.       6      28 ..       6      33 .. 0.87
   2 !   16.1   2.1   1.8e-05    0.0086       2      24 .]      52      76 ..      51      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                            Fer4_6  1 vveidpdkCi..gC.gdCvrvCP 20
                                      ++++d d+C    C ++C + CP
  gi|336254823|ref|YP_004597930.1|  6 IAVVDLDRCQpdRCsYECKNYCP 28
                                      689******9767*999****** PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.8e-05
                            Fer4_6  2 veidpdkCig..CgdCvrvCPegai 24
                                      v+i ++ C+g  Cg Cv  CP++ai
  gi|336254823|ref|YP_004597930.1| 52 VRISEEICLGetCGICVEKCPFDAI 76
                                      7899*****999***********98 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 ?    6.8   0.0     0.011       5.4      21      39 ..     107     126 ..      97     130 .. 0.84
   2 !    8.6   0.1    0.0032       1.5      20      38 ..     377     395 ..     368     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                            AAA_29  21 lkg.atlltGpsGsGKSTll 39 
                                       ++g +t + Gp+G GK+T +
  gi|336254823|ref|YP_004597930.1| 107 QEGqVTGILGPNGIGKTTAV 126
                                       4567899**********965 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0032
                            AAA_29  20 dlkgatlltGpsGsGKSTl 38 
                                       +++++  ++Gp+G GKST+
  gi|336254823|ref|YP_004597930.1| 377 RENEVLGIVGPNGIGKSTF 395
                                       44556779**********7 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.034        16      25      43 ..     111     129 ..     105     133 .. 0.89
   2 !    9.7   0.2    0.0013      0.63      25      43 ..     381     399 ..     375     403 .. 0.86
   3 ?   -1.6   0.0       3.7   1.8e+03     324     356 ..     486     518 ..     407     531 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.034
                            AAA_15  25 ltvliGkNnsGKSsileal 43 
                                       +t + G+N++GK++++++l
  gi|336254823|ref|YP_004597930.1| 111 VTGILGPNGIGKTTAVRIL 129
                                       78899**********9988 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                            AAA_15  25 ltvliGkNnsGKSsileal 43 
                                       +  ++G+N++GKS+++++l
  gi|336254823|ref|YP_004597930.1| 381 VLGIVGPNGIGKSTFAKLL 399
                                       7779************998 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.7
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnk 356
                                        +++l++EP ahL  ++  +   ++++ a++ +
  gi|336254823|ref|YP_004597930.1| 486 ADLYLLDEPSAHLDVEQRVQATSAIRRYAEQQD 518
                                       456999999999966666665555555555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0      0.01       4.7       5      24 ..     114     133 ..     110     141 .. 0.85
   2 !    7.7   0.0    0.0064         3       3      22 ..     382     401 ..     380     433 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.01
                                       EEC-TTTCHHHHHHHHHHHH CS
                             NACHT   5 lqGeaGsGKTtLlqklalaw 24 
                                       + G++G+GKTt ++ la ++
  gi|336254823|ref|YP_004597930.1| 114 ILGPNGIGKTTAVRILAGEL 133
                                       89***********9998766 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0064
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       + + G++G+GK+t+++ l  
  gi|336254823|ref|YP_004597930.1| 382 LGIVGPNGIGKSTFAKLLTG 401
                                       5699***********97765 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 !    8.3   0.1    0.0039       1.8      38      61 ..     114     137 ..     109     143 .. 0.90
   2 ?   -1.9   0.0       5.3   2.5e+03      61      93 ..     220     249 ..     212     253 .. 0.66
   3 ?    5.2   0.0     0.033        16      28      58 ..     376     404 ..     354     408 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0039
                            RuvB_N  38 lyGpPGlGkttlakiiakelgvkl 61 
                                       + Gp G+Gktt  +i+a el+ +l
  gi|336254823|ref|YP_004597930.1| 114 ILGPNGIGKTTAVRILAGELEPNL 137
                                       57*****************99776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.3
                            RuvB_N  61 lkitsgPvlekagdlaalltnleekdvlfidei 93 
                                       +   sg  l++   laa l+  +++d  f+dei
  gi|336254823|ref|YP_004597930.1| 220 IDDLSGGELQRV-ALAATLA--RDTDFYFLDEI 249
                                       555566666554.3555554..5789999*999 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.033
                            RuvB_N  28 kreealdhvllyGpPGlGkttlakiiakelg 58 
                                        re+++  + ++Gp G+Gk+t+ak+++ +l+
  gi|336254823|ref|YP_004597930.1| 376 IRENEV--LGIVGPNGIGKSTFAKLLTGNLE 404
                                       555443..3378************9988775 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0068       3.2       3      33 ..     114     163 ..     113     222 .. 0.65
   2 ?    6.3   0.0     0.027        13       3      19 ..     384     400 ..     382     505 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0068
                            AAA_18   3 ltGtpGvGKttlakeLskrl.gf..................gvnlrdvak 33 
                                       + G+ G GKtt  + L+ +l  +                  g++l+d+++
  gi|336254823|ref|YP_004597930.1| 114 ILGPNGIGKTTAVRILAGELePNlgrheeeidwddvleayrGTELQDYIA 163
                                       89**************8777544655555555555555555555555544 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.027
                            AAA_18   3 ltGtpGvGKttlakeLs 19 
                                       + G+ G GK+t+ak L 
  gi|336254823|ref|YP_004597930.1| 384 IVGPNGIGKSTFAKLLT 400
                                       89*************94 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.057        27      19      43 ..     110     132 ..     103     182 .. 0.70
   2 ?    8.7   0.0    0.0019       0.9      21      46 ..     380     405 ..     372     524 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.057
                                       CSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  19 qslvvalvGmgGvGKttlakqilnk 43 
                                       q  v ++ G  G+GKtt ++    +
  gi|336254823|ref|YP_004597930.1| 110 Q--VTGILGPNGIGKTTAVRILAGE 132
                                       4..889***********87765555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0019
                                       EEEEEEESTTSSHHHHHHHHCCSHCC CS
                            NB-ARC  21 lvvalvGmgGvGKttlakqilnksde 46 
                                        v+++vG  G+GK+t ak    +++ 
  gi|336254823|ref|YP_004597930.1| 380 EVLGIVGPNGIGKSTFAKLLTGNLEP 405
                                       499*************9977666555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.39   1.9e+02      32      50 ..     108     126 ..     106     133 .. 0.85
   2 ?    5.3   0.0     0.028        13      28      50 ..     374     396 ..     370     401 .. 0.87
   3 ?    3.5   0.0     0.099        47     128     188 ..     505     526 ..     439     527 .. 0.54

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.39
                            AAA_25  32 agelallaGapgtGKttla 50 
                                       +g ++ + G+ g GKtt++
  gi|336254823|ref|YP_004597930.1| 108 EGQVTGILGPNGIGKTTAV 126
                                       68889999*********86 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.028
                            AAA_25  28 gllpagelallaGapgtGKttla 50 
                                       g ++++e+  ++G+ g GK+t+a
  gi|336254823|ref|YP_004597930.1| 374 GQIRENEVLGIVGPNGIGKSTFA 396
                                       6788999999***********98 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.099
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                       +++ a+++ +e+  ++ + viD                                      H
  gi|336254823|ref|YP_004597930.1| 505 QATSAIRRYAEQ-QDATVMVID--------------------------------------H 526
                                       333445555555.555555555......................................4 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.011         5       4      21 ..     114     134 ..     112     182 .. 0.79
   2 ?    3.0   0.0      0.23   1.1e+02       4      20 ..     384     400 ..     382     409 .. 0.89
   3 ?   -0.4   0.0       2.5   1.2e+03      60      81 ..     506     527 ..     465     544 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                            AAA_28   4 itGgestGKTtlleaLa...a 21 
                                       i+G+ + GKTt ++ La   +
  gi|336254823|ref|YP_004597930.1| 114 ILGPNGIGKTTAVRILAgelE 134
                                       89**************95440 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.23
                            AAA_28   4 itGgestGKTtlleaLa 20 
                                       i+G+ + GK+t ++ L+
  gi|336254823|ref|YP_004597930.1| 384 IVGPNGIGKSTFAKLLT 400
                                       89***********9986 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.5
                            AAA_28  60 leeqleeeaaaaankvlfcDrg 81 
                                          +++++a++++  v+++D +
  gi|336254823|ref|YP_004597930.1| 506 ATSAIRRYAEQQDATVMVIDHD 527
                                       2223444555555555555544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.1   5.3e+02       3      22 ..     113     132 ..     111     142 .. 0.86
   2 ?    9.6   0.1     0.002      0.93       3      55 ..     383     495 ..     381     541 .. 0.48

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.1
                                       EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge 22 
                                       +i+G    GK+t ++ l ge
  gi|336254823|ref|YP_004597930.1| 113 GILGPNGIGKTTAVRILAGE 132
                                       799***********999986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.002
                                       EEEESTTSSHHHHHHHHHT.........S..TEEESSSTTSSSSEEEEEEEETTEE..................... CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltg.........e..kaivsdkpgtTrdinegrvklkgke..................... 47 
                                       +ivG    GKSt+ + ltg         +    i  + + +T+d   + v     +                     
  gi|336254823|ref|YP_004597930.1| 383 GIVGPNGIGKSTFAKLLTGnlepdegdaDldLDISYKPQYVTIDQHMR-V-----Daflssitdqfgssywnteiaq 453
                                       8*****************944333332212112222222333333332.2.....0222223333444444444555 PP

                                       ..................................EEEEECGG CS
                          MMR_HSR1  48 ..................................ielvDtpG 55 
                                                                         ++l+D p 
  gi|336254823|ref|YP_004597930.1| 454 plqlerimeqnlsdlsggerqrvaiaaclsdsadLYLLDEPS 495
                                       555555555444444444444555554444444455555554 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2  11.1   0.00021     0.099       5      52 .]      19      75 ..      13      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00021
                            Fer4_7  5 Cg.aCvaaCp.....vkaieldeeenekgt.ekveidpekClg..CgaCvavCPtga 52
                                      C   C ++Cp      ++i+l+ ee ++g+ e+v+i++e Clg  Cg Cv+ CP++a
  gi|336254823|ref|YP_004597930.1| 19 CSyECKNYCPpnrtgKECITLRGEETDEGQpEQVRISEEICLGetCGICVEKCPFDA 75
                                      6547*****9777777888888776666665899*******9655*********997 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 ?    4.0   0.0     0.095        45       4      22 ..     114     132 ..     113     142 .. 0.86
   2 ?   -1.8   0.0       6.2   2.9e+03      54      75 ..     230     250 ..     180     254 .. 0.65
   3 ?    6.0   0.0     0.024        11       4      23 ..     384     403 ..     382     451 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.095
                                       EE--SSSSHHHHHHHGGGG CS
                             AAA_5   4 LvGppGtgKselaerlaaa 22 
                                       ++Gp G+gK++ ++ la  
  gi|336254823|ref|YP_004597930.1| 114 ILGPNGIGKTTAVRILAGE 132
                                       58***********999865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.2
                                       ...--------G-SEEEEESGG CS
                             AAA_5  54 lvdsplvraaregeilvlDEve 75 
                                       +v  +++  ar  + ++lDE++
  gi|336254823|ref|YP_004597930.1| 230 RVALAAT-LARDTDFYFLDEIT 250
                                       3333333.55688999999996 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.024
                                       EE--SSSSHHHHHHHGGGGB CS
                             AAA_5   4 LvGppGtgKselaerlaaal 23 
                                       +vGp G+gKs++a+ l   l
  gi|336254823|ref|YP_004597930.1| 384 IVGPNGIGKSTFAKLLTGNL 403
                                       69************998666 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0       0.1        48      26      47 ..     112     133 ..     110     138 .. 0.90
   2 ?   -0.4   0.0       2.2     1e+03      39      58 ..     260     279 ..     255     346 .. 0.57
   3 ?    5.3   0.0     0.038        18      26      44 ..     382     400 ..     379     408 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.1
                             DUF87  26 lAilgsTGsGKSntvavLleel 47 
                                       ++ilg  G GK++ v++L  el
  gi|336254823|ref|YP_004597930.1| 112 TGILGPNGIGKTTAVRILAGEL 133
                                       58***************98776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.2
                             DUF87  39 tvavLleellekkgatilil 58 
                                       t+a L++el+e+ + ++l++
  gi|336254823|ref|YP_004597930.1| 260 TAARLIRELAEEENKSMLVV 279
                                       77888888888777766664 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.038
                             DUF87  26 lAilgsTGsGKSntvavLl 44 
                                       l+i+g  G GKS+++++L 
  gi|336254823|ref|YP_004597930.1| 382 LGIVGPNGIGKSTFAKLLT 400
                                       689**************97 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.012       5.8       6      24 ..     114     132 ..     110     140 .. 0.82
   2 ?    3.3   0.0      0.12        54       3      21 ..     381     398 ..     379     406 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.012
                                       EEESTTSSHHHHHHHHHHH CS
                             SRP54   6 lvGlqGaGKTttlaKLaal 24 
                                       ++G++G+GKTt++  La  
  gi|336254823|ref|YP_004597930.1| 114 ILGPNGIGKTTAVRILAGE 132
                                       79**********9988865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.12
                                       EEEEEESTTSSHHHHHHHH CS
                             SRP54   3 villvGlqGaGKTttlaKL 21 
                                       v+ +vG++G+GK t  aKL
  gi|336254823|ref|YP_004597930.1| 381 VLGIVGPNGIGKSTF-AKL 398
                                       5669********985.454 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.017       8.3      18      40 ..     109     131 ..     105     141 .. 0.82
   2 ?    2.8   0.0      0.18        83      18      40 ..     379     401 ..     375     416 .. 0.82
   3 ?   -2.6   0.1       7.8   3.7e+03      90     119 ..     487     521 ..     458     526 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
                            AAA_30  18 drvavltGpAGtGKttalkalre 40 
                                        +v+ + Gp G GKtta++ l+ 
  gi|336254823|ref|YP_004597930.1| 109 GQVTGILGPNGIGKTTAVRILAG 131
                                       56999*************99875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.18
                            AAA_30  18 drvavltGpAGtGKttalkalre 40 
                                       + v  ++Gp G GK+t  k l+ 
  gi|336254823|ref|YP_004597930.1| 379 NEVLGIVGPNGIGKSTFAKLLTG 401
                                       458899**********9988765 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.8
                            AAA_30  90 tllivDEagmv.....dtkqlaallkaaekagakv 119
                                       +l++ DE +         + + a+ + ae+++a+v
  gi|336254823|ref|YP_004597930.1| 487 DLYLLDEPSAHldveqRVQATSAIRRYAEQQDATV 521
                                       55555655543333222333344444444444554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1      0.04        19       4      23 ..     114     133 ..     111     138 .. 0.85
   2 ?   -1.6   0.0       4.8   2.3e+03      93     133 ..     238     281 ..     222     293 .. 0.61
   3 ?    5.6   0.0     0.029        14       3      24 ..     383     404 ..     381     409 .. 0.85
   4 ?   -1.9   0.0       5.7   2.7e+03      85     102 ..     506     525 ..     472     526 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.04
                                       EE--TTSSHHHHHHHHHHHH CS
                          NTPase_1   4 iTGppGvGKtTlvkkvlell 23 
                                       i Gp G+GKtT v+ ++ +l
  gi|336254823|ref|YP_004597930.1| 114 ILGPNGIGKTTAVRILAGEL 133
                                       669**********9988887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.8
                                       HHHH-EEEE---STTGGG-HHH..HHHHHHHHT.TTSEEEEE-- CS
                          NTPase_1  93 lseadviviDEiGkmElkskkf..keaveevLk.sekpvlavih 133
                                        +++d + +DEi +     +++  ++ ++e+ + ++k +l+v h
  gi|336254823|ref|YP_004597930.1| 238 ARDTDFYFLDEITPYLDIGQRVtaARLIRELAEeENKSMLVVEH 281
                                       37788888888887555444441145577777755566655544 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.029
                                       EEE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellk 24 
                                        i Gp G+GK+T+ k ++ +l+
  gi|336254823|ref|YP_004597930.1| 383 GIVGPNGIGKSTFAKLLTGNLE 404
                                       688***********99988875 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 5.7
                                       HHHHHHHHHHHH-..EEEE- CS
                          NTPase_1  85 alealrkalsead..viviD 102
                                       a +a+r+  +++d  v+viD
  gi|336254823|ref|YP_004597930.1| 506 ATSAIRRYAEQQDatVMVID 525
                                       46677777766666788888 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 ?    2.6   0.0      0.22     1e+02       1      18 [.     116     133 ..     116     141 .. 0.91
   2 ?    6.6   0.0     0.013       6.2       1      31 [.     386     415 ..     386     420 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.22
                            CLP1_P   1 GpkdsGKSTlarlLlNya 18 
                                       Gp+  GK+T +r+L+ ++
  gi|336254823|ref|YP_004597930.1| 116 GPNGIGKTTAVRILAGEL 133
                                       8999**********9875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.013
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlD 31 
                                       Gp+  GKST+a+lL  ++ +  +  + +DlD
  gi|336254823|ref|YP_004597930.1| 386 GPNGIGKSTFAKLLTGNL-EPDEGDADLDLD 415
                                       8999**********9985.555555566666 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  13.1    0.0035       1.7       2      56 .]       7      72 ..       6      72 .. 0.86
   2 ?   10.4   1.6    0.0012      0.56       2      27 ..      52      79 ..      51      98 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0035
                           Fer4_10  2 vvidddtC..irCg.kCvkaCPadl......tsvgakgeaseeeavrkkvekCtg..cgaCveaCP 56
                                      +v+d d+C   rC  +C++ CP +       t  g +  + + e+vr+  e C g  cg Cve+CP
  gi|336254823|ref|YP_004597930.1|  7 AVVDLDRCqpDRCSyECKNYCPPNRtgkeciTLRGEETDEGQPEQVRISEEICLGetCGICVEKCP 72
                                      68899***6669999********99***99877788888888888888889998888********9 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0012
                           Fer4_10  2 vvidddtC..irCgkCvkaCPadltsvg 27
                                      v+i ++ C    Cg Cv+ CP+d+ +  
  gi|336254823|ref|YP_004597930.1| 52 VRISEEIClgETCGICVEKCPFDAIEII 79
                                      678899994448*********9763333 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 ?    0.8   0.1      0.76   3.6e+02      51      62 ..     113     124 ..     102     133 .. 0.82
   2 ?    7.6   0.0    0.0059       2.8      44      66 ..     376     398 ..     361     403 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.76
                         IstB_IS21  51 vllGpsGvGKsh 62 
                                        +lGp G+GK+ 
  gi|336254823|ref|YP_004597930.1| 113 GILGPNGIGKTT 124
                                       589*******95 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0059
                         IstB_IS21  44 iekkenivllGpsGvGKshlaia 66 
                                       i+++e + ++Gp G+GKs +a  
  gi|336254823|ref|YP_004597930.1| 376 IRENEVLGIVGPNGIGKSTFAKL 398
                                       88999999**********99975 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   8.6    0.0024       1.1       3      58 ..       9      77 ..       7      78 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0024
                           Fer4_21  3 idedkCi..gCg.kCliaCe..dtshqaieidakt.......vlkvvedeCvG..CnlCssvCPvedcie 58
                                      +d d+C    C  +C   C+   t+ ++i++ +++       ++++ e+ C G  C +C++ CP  d+ie
  gi|336254823|ref|YP_004597930.1|  9 VDLDRCQpdRCSyECKNYCPpnRTGKECITLRGEEtdegqpeQVRISEEICLGetCGICVEKCPF-DAIE 77
                                      55556632234325666664225899***5554432222222457789***9988*********7.9997 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  11.1    0.0056       2.6       4      51 .]      18      76 ..      13      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0056
                            Fer4_9  4 gCga.CveaCpagvvvedaaerkarlraase........eaCig..CgaCveaCpkgai 51
                                      +C + C + Cp + + +++ +   + + +++        e C+g  Cg Cve+Cp +ai
  gi|336254823|ref|YP_004597930.1| 18 RCSYeCKNYCPPNRTGKECITLRGEETDEGQpeqvriseEICLGetCGICVEKCPFDAI 76
                                      47655999999999998888888777766669999***98995445*********9987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   3.0      0.99   4.7e+02       3      21 ..       7      28 ..       5      29 .. 0.80
   2 ?   12.4   1.1   0.00028      0.13       5      21 ..      54      72 ..      50      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.99
                            Fer4_2  3 vvvdtdrC.i.gCg.aCvsaCP 21
                                      +vvd drC   +C+  C + CP
  gi|336254823|ref|YP_004597930.1|  7 AVVDLDRCqPdRCSyECKNYCP 28
                                      6899999984489779989899 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00028
                            Fer4_2  5 vdtdrCig..CgaCvsaCP 21
                                      + +++C+g  Cg+Cv  CP
  gi|336254823|ref|YP_004597930.1| 54 ISEEICLGetCGICVEKCP 72
                                      6689***99********** 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 ?    5.9   7.1     0.045        21       2      66 .]       8      78 ..       7      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.045
                           Fer4_15  2 vvDrdaCigcglCvaeapevfeldedglasvllddgeiaeg...evpddeeeaaqeA....araCPvdAIrv 66
                                      vvD d+C+ + +C  e++++   +  g+  ++l ++e++eg   +v   ee +  e     +++CP dAI++
  gi|336254823|ref|YP_004597930.1|  8 VVDLDRCQPD-RCSYECKNYCPPNRTGKECITLRGEETDEGqpeQVRISEEICLGETcgicVEKCPFDAIEI 78
                                      69******97.7********************9999999989999999999888775333389*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.39
# Mc/sec: 4640.22
//
Query:       gi|336254824|ref|YP_004597931.1|  [L=106]
Description: hypothetical protein Halxa_3441 [Halopiger xanaduensis SH-6]
Scores for 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   12.9   0.5      0.028   12.7   0.5    1.0  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   1.6e-06     0.028      17      88 ..      20      99 ..       7     105 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-06
                           DUF2070 17 sllliillalligllaflssk..........lfgillfglpalvaflltlpvlrilggr.ltykrslflalltelivvi 84
                                      +l++++ +a++++ +a++                  ++ + +lv ++l++ v +i+ +  + +k++l++a++t  +++i
  gi|336254824|ref|YP_004597931.1| 20 ALAALLGVAAALASMAVT--GdlpareaageTLPQAFVVVAILVQLALLN-VTSIYDEDeFGMKHNLYVAFMTFSFWFI 95
                                      333333333333333333..266888876664444555555555555554.444444447******************* PP

                           DUF2070 85 isll 88
                                      +  +
  gi|336254824|ref|YP_004597931.1| 96 TWGI 99
                                      6554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 823.54
//
Query:       gi|336254825|ref|YP_004597932.1|  [L=535]
Description: o-succinylbenzoate--CoA ligase [Halopiger xanaduensis SH-6]
Scores for 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-99  331.5   0.2    7.2e-99  331.2   0.2    1.0  1  AMP-binding    AMP-binding enzyme
      2e-19   70.3   0.1    4.6e-19   69.2   0.1    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 !  331.2   0.2  8.1e-103   7.2e-99       3     422 ..      12     426 ..      10     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: 331.2 bits;  conditional E-value: 8.1e-103
                                       HHHHHST.TSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEE CS
                       AMP-binding   3 eqaaktp.dkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpln 78 
                                       eqa+++  d+ a+v   +g+++TY e+ +rv+r+A++L+++G++kgdrVa+l pn++ ++ a+++++++Ga+++pln
  gi|336254825|ref|YP_004597932.1|  12 EQARRHYgDQEAIVG-TDGERFTYDEFGDRVDRFARALQERGIGKGDRVAVLDPNTHYHLEAAYGAMSIGAIHAPLN 87 
                                       56666555*****99.779********************99************************************ PP

                                       TTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS CS
                       AMP-binding  79 ptltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeee 155
                                        +lt+e+ ay+l+d+e+ ++    d e ++k++++++++  ++++ v+ ++++ + +++++++  e++++ + e++e
  gi|336254825|ref|YP_004597932.1|  88 YRLTSEDYAYMLADAEMDAVY--ADYEYAAKIEAIRDEV--PTETFVTNDADAVEGDWEDFDDVLEAAEP-DYEQPE 159
                                       *********************..6777789999999854..55566666666677777777777776664.456668 PP

                                       -BTTSEEEEEEE--SSSS-EEEEEEH..HHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-E CS
                       AMP-binding 156 lkpddlayiiYTSGTTGkPKGVmlsh..rnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGat 230
                                         +d++++i YTSGTTG PKGV  +h  + l+a + s     +++l+++dv+l++lp++h+ g+   ++++   Ga+
  gi|336254825|ref|YP_004597932.1| 160 MAEDEIITINYTSGTTGDPKGVCRTHrtETLHAYLVS----IYHELTDGDVYLWTLPMFHVNGW-GHIYAVTGLGAK 231
                                       99************************52233344344....4677889****************.************ PP

                                       EEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHC.HHHHCCGTT-SEEEEESS-EBHHHHHHHHH CS
                       AMP-binding 231 vvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalka.akkakdlsslrlvllggeplspellrffra 305
                                        v+ ++ +a   + ++e+i+++ v++++++P+vl++l++  +++ + +++  d + +r++ ++g++++++++r++++
  gi|336254825|ref|YP_004597932.1| 232 HVCTRGVNA---DEVIETIREEDVSFLCAAPTVLNQLIDyYEREGEpEMT-GD-NDVRVT-TAGSAPPEATIRAVEE 302
                                       ***999988...3478*********************8855444332222.22.349984.8*************** PP

                                       HHTCEEEEEEEEGGGSSECEE.....CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSE..EEEEEEETTS- CS
                       AMP-binding 306 lfgeevlegYGlTEttgvvtv.....lpleedkkklgsvGkplpgvevkivDeetgepvpdgee..Gellvrgpgvm 375
                                        fg ++ ++YG TEt++ +t+     l+ +++ ++++++G  + g++v++vDe+ ge vp++ e  Ge++vrg++vm
  gi|336254825|ref|YP_004597932.1| 303 EFGWRLKHLYGATETGPLITIsperlLEADNRFSMKKRQGMGVLGTDVRVVDED-GEDVPRDDEtlGEVVVRGNQVM 378
                                       *******************999999988889999999****************9.88888444448*********** PP

                                       SEBTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 376 kgYlkkpeataeafdse.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                         Y++kpeat+eaf +  +++++TGDl+++de G + i +Rkkd+i++
  gi|336254825|ref|YP_004597932.1| 379 DRYWNKPEATEEAFSERrEGYYHTGDLATVDEHGLIAIRDRKKDIIIS 426
                                       **************953567**************************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 !   69.2   0.1   5.1e-23   4.6e-19       1      76 []     435     514 ..     435     514 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 5.1e-23
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.---...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-T CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.sea...leeeLkahvrkelgpyavpkkvvfvdelpktr 73 
                                       e+E +l  h+aVa+aaV+  p e +Ge+++afVv+++g +e+    ++eL ++ r++l++y+v ++++ v+elpkt+
  gi|336254825|ref|YP_004597932.1| 435 ELEDTLFDHDAVADAAVIPAPSEEWGETPKAFVVPSNGdPEDppvSADELTQFTRDRLASYKVVRRIEYVEELPKTA 511
                                       89*********************************87753335789******************************* PP

                                       TS- CS
                     AMP-binding_C  74 sGK 76 
                                       +GK
  gi|336254825|ref|YP_004597932.1| 512 TGK 514
                                       **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3813.01
//
Query:       gi|336254826|ref|YP_004597933.1|  [L=97]
Description: hypothetical protein Halxa_3443 [Halopiger xanaduensis SH-6]
Scores for 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-06   26.7   0.0    4.1e-06   26.2   0.0    1.2  1  HTH_24        Winged helix-turn-helix DNA-binding
    0.00074   19.4   0.0    0.00085   19.2   0.0    1.2  1  MarR_2        MarR family
    0.00087   19.2   0.0     0.0013   18.7   0.0    1.2  1  HTH_11        HTH domain
     0.0011   18.6   0.1     0.0019   17.8   0.1    1.4  1  GntR          Bacterial regulatory proteins, gntR family
     0.0018   18.1   0.0     0.0024   17.8   0.0    1.2  1  MarR          MarR family
     0.0025   17.7   0.1     0.0033   17.3   0.1    1.2  1  TrmB          Sugar-specific transcriptional regulator TrmB
     0.0032   17.9   0.0     0.0045   17.4   0.0    1.2  1  HTH_27        Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.016   15.0   0.1       0.02   14.8   0.1    1.2  1  TFIIE_alpha   TFIIE alpha subunit
      0.019   15.1   0.0      0.041   14.0   0.0    1.5  1  HTH_28        Helix-turn-helix domain
      0.024   14.6   0.0       0.63   10.0   0.0    2.1  2  HTH_36        Helix-turn-helix domain
      0.024   14.4   0.0      0.054   13.3   0.0    1.5  2  HTH_IclR      IclR helix-turn-helix domain
      0.026   14.6   0.0       0.04   14.0   0.0    1.3  1  HTH_20        Helix-turn-helix domain
      0.035   14.1   0.1       0.09   12.7   0.1    1.7  1  HTH_12        Ribonuclease R winged-helix domain
      0.037   14.2   0.0      0.054   13.7   0.0    1.2  1  PaaX          PaaX-like protein
      0.047   13.6   0.0      0.065   13.1   0.0    1.2  1  HTH_5         Bacterial regulatory protein, arsR family
       0.18   11.8   0.0       0.21   11.6   0.0    1.1  1  Replic_Relax  Replication-relaxation


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 !   26.2   0.0   3.7e-09   4.1e-06      10      47 ..      21      58 ..      17      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.7e-09
                            HTH_24 10 elLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++L+ ++ ++q+++ e++ lS  tv++ l+rLee G++
  gi|336254826|ref|YP_004597933.1| 21 KVLEYDGPLTQKQIVEESMLSARTVRYALERLEEIGIV 58
                                      67889*******************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.6e-07   0.00085       4      53 ..      13      60 ..      10      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.6e-07
                                      -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +p+   v  +L   ++  lt+++++++  ls  +v ++l+rL++ G v +
  gi|336254826|ref|YP_004597933.1| 13 PPSAKLVFKVLEYDGP--LTQKQIVEESMLSARTVRYALERLEEIGIVDE 60
                                      5555555556666666..**************************999865 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.1e-06    0.0013       7      44 ..      20      57 ..      15      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                            HTH_11  7 elLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                        +le +gp++ +++ ee  +S rtvr  +++Lee+g+
  gi|336254826|ref|YP_004597933.1| 20 FKVLEYDGPLTQKQIVEESMLSARTVRYALERLEEIGI 57
                                      44559*******************************93 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.7e-06    0.0019      17      54 ..      22      58 ..      15      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-06
                                      SS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 17 elrpGdkLPsereLaaefgVsrttvReALrrLeaeglv 54
                                      +l+   +L +++++++e   s+ tvR AL rLe+ g+v
  gi|336254826|ref|YP_004597933.1| 22 VLEYDGPL-TQKQIVEESMLSARTVRYALERLEEIGIV 58
                                      67777899.***************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.1e-06    0.0024      12      47 ..      23      58 ..      14      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.1e-06
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      l++ gpl+++++ + +++s  tv  +l rLe+ G +
  gi|336254826|ref|YP_004597933.1| 23 LEYDGPLTQKQIVEESMLSARTVRYALERLEEIGIV 58
                                      7889*****************************998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.9e-06    0.0033      13      54 ..      19      60 ..      15      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.9e-06
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      v+++L   gp+t ++i ee+ ++  +v  +L++Le+ G+V+ 
  gi|336254826|ref|YP_004597933.1| 19 VFKVLEYDGPLTQKQIVEESMLSARTVRYALERLEEIGIVDE 60
                                      56666689*******************************975 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 !   17.4   0.0     4e-06    0.0045      11      64 ..      21      74 ..      13      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4e-06
                            HTH_27 11 lirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrl 64
                                       + + +++ +++++++  ++++ ++ y+l++L+e G v +  + ad r++++rl
  gi|336254826|ref|YP_004597933.1| 21 KVLEYDGPLTQKQIVEESMLSARTVRYALERLEEIGIVDEDIYFADARQSLYRL 74
                                      4556899**********************************9********9997 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.8e-05      0.02      14      58 ..      15      59 ..       7      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha 14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                      +a+lv +vL  +g +t  ++ +e  +    +r +L rL e+++v+
  gi|336254826|ref|YP_004597933.1| 15 SAKLVFKVLEYDGPLTQKQIVEESMLSARTVRYALERLEEIGIVD 59
                                      6899**************************************997 PP

>> HTH_28  Helix-turn-helix 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     0.041      14      41 ..      30      57 ..      21      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-05
                            HTH_28 14 svreaArelgisrrtvyrWikryeegGi 41
                                      +++++ +e  +s rtv+  + r+ee+Gi
  gi|336254826|ref|YP_004597933.1| 30 TQKQIVEESMLSARTVRYALERLEEIGI 57
                                      899************************8 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.12   1.3e+02       3      13 ..      12      22 ..      10      24 .. 0.84
   2 ?   10.0   0.0   0.00056      0.63      27      54 ..      30      57 ..      26      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.12
                            HTH_36  3 Lspsaklllgs 13
                                      L+psakl++  
  gi|336254826|ref|YP_004597933.1| 12 LPPSAKLVFKV 22
                                      99******976 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00056
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGy 54
                                      +q+ + + + ls +Tv+ a+  Le+ G+
  gi|336254826|ref|YP_004597933.1| 30 TQKQIVEESMLSARTVRYALERLEEIGI 57
                                      789999*******************998 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 ?   13.3   0.0   4.9e-05     0.054      14      51 ..      24      61 ..      22      61 .. 0.93
   2 ?   -2.7   0.0       4.8   5.3e+03      11      21 ..      63      74 ..      63      76 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.9e-05
                                      TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      e +++lt +++ +++ l+  tv+  L  L+e G+v  d
  gi|336254826|ref|YP_004597933.1| 24 EYDGPLTQKQIVEESMLSARTVRYALERLEEIGIVDED 61
                                      57899*****************************9876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.8
                                      T-CTTBSS-.BH CS
                          HTH_IclR 11 alaeapqel.tl 21
                                      ++a a+q l +l
  gi|336254826|ref|YP_004597933.1| 63 YFADARQSLyRL 74
                                      588888876555 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.5e-05      0.04      15      55 ..      19      59 ..      14      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      +++ L  +++lt +++ e+  ls  t++y L+ Lee g+v+
  gi|336254826|ref|YP_004597933.1| 19 VFKVLEYDGPLTQKQIVEESMLSARTVRYALERLEEIGIVD 59
                                      6778889999999***99999******************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 ?   12.7   0.1   8.1e-05      0.09      18      49 ..      33      59 ..      18      68 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.1e-05
                            HTH_12 18 eiaeeLkkrgydigeravRyrLrkleergltr 49
                                      +i e     +  +++r+vRy L  lee g++ 
  gi|336254826|ref|YP_004597933.1| 33 QIVE-----ESMLSARTVRYALERLEEIGIVD 59
                                      5444.....35689*************99886 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.8e-05     0.054      31      68 ..      36      76 ..      32      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.8e-05
                              PaaX 31 aelGiseslvRaalsRlakaGwlvre...kegrrsfYrLsd 68
                                      +e  +s+++vR al Rl++ G +++    +++r+s+YrL +
  gi|336254826|ref|YP_004597933.1| 36 EESMLSARTVRYALERLEEIGIVDEDiyfADARQSLYRLEE 76
                                      5556799****************9864447999*****976 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 ?   13.1   0.0   5.8e-05     0.065       8      46 ..      19      59 ..      16      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.8e-05
                                      HHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  8 LklLae..gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++ + e  g+l+  +++ee  ls  tv++ L +L+e G+V+
  gi|336254826|ref|YP_004597933.1| 19 VFKVLEydGPLTQKQIVEESMLSARTVRYALERLEEIGIVD 59
                                      56666667********************************7 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019      0.21       2      46 ..      21      65 ..      20      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                      Replic_Relax  2 rlLaehrvlTtrqiarllfashratarrrLarLrelgllsr.lrkr 46
                                      ++L++ ++lT +qi +    s r+ +r +L rL+e g+++  ++  
  gi|336254826|ref|YP_004597933.1| 21 KVLEYDGPLTQKQIVEESMLSART-VRYALERLEEIGIVDEdIYFA 65
                                      7899999****************9.**************9866665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 754.54
//
Query:       gi|336254827|ref|YP_004597934.1|  [L=137]
Description: hypothetical protein Halxa_3444 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0027   17.3   3.3     0.0034   17.0   3.3    1.0  1  Sulf_transp   Sulphur transport
  ------ inclusion threshold ------
      0.014   15.6   0.2      0.026   14.7   0.2    1.4  1  Babuvirus_MP  Movement and RNA silencing protein
       0.29   11.4   4.6       0.14   12.4   0.5    2.0  2  DUF3093       Protein of unknown function (DUF3093)
        6.4    7.2   8.0         30    5.1   5.3    2.1  2  DUF805        Protein of unknown function (DUF805)


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   3.3   7.5e-07    0.0034     176     272 ..       8     120 ..       2     121 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.5e-07
                       Sulf_transp 176 pwslvlgavllgll.avlawllsaktgrsfgl...gftvpgakilqylvl....gtskflnwg........vvlvlG 236
                                       +w ++l ++ ++ + a +  ++ + +g   ++   ++ + +a +l y+ +     ++ +++++        v++ lG
  gi|336254827|ref|YP_004597934.1|   8 RWGWLLIGLFAASIvAQFLNVVLGRAGLAEEYqvvTVIATMAPVLIYVGVwyddHRQHYWEHSsarivgdiVFVLLG 84 
                                       566666666665552444455556666655550014445555555565442322234455554444444546678** PP

                       Sulf_transp 237 iilGaflaallsgefkleapkarellaallGGllMG 272
                                        i+Ga    ++   f +e+p+  + ++a+ GG+l+ 
  gi|336254827|ref|YP_004597934.1|  85 AIIGATTVIAVLSGFGFEIPRYLQDILAMGGGFLVA 120
                                       ******99999999*******77778899****986 PP

>> Babuvirus_MP  Movement and RNA silencing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   5.7e-06     0.026      15      47 ..      80     112 ..      72     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-06
                      Babuvirus_MP  15 flffgaifiaitilyillvllfevpryikelvr 47 
                                       f+++gai+ a t++ +l  + fe+pry+++++ 
  gi|336254827|ref|YP_004597934.1|  80 FVLLGAIIGATTVIAVLSGFGFEIPRYLQDILA 112
                                       899*************************99875 PP

>> DUF3093  Protein of unknown function (DUF3093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   3.2e-05      0.14       6      49 ..       4      49 ..       2      63 .. 0.74
   2 ?    0.9   0.3      0.11   5.2e+02      18      55 ..      86     128 ..      65     132 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                           DUF3093  6 lwvplwwWllaalvalaaalvaaevglavavlv..aavlvalavva 49
                                       + p+w Wll+ l+a++++  +++v l++a+l+  + v++++a++a
  gi|336254827|ref|YP_004597934.1|  4 ERLPRWGWLLIGLFAASIVAQFLNVVLGRAGLAeeYQVVTVIATMA 49
                                      4679**********9999999999******9999944443333332 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.11
                           DUF3093  18 lvalaaalvaaevglavavlv......aavlvalavvallalsr 55 
                                       ++  a++++a+  g ++++ +      a+    l++++l+++ +
  gi|336254827|ref|YP_004597934.1|  86 II-GATTVIAVLSGFGFEIPRylqdilAMGGGFLVAWLLFWWRN 128
                                       22.22333333333333322233555455556666677777665 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   5.3    0.0066        30      14      71 ..       9      72 ..       3      97 .. 0.66
   2 ?    4.5   0.5      0.01        45      10      47 ..      63      97 ..      60     128 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0066
                            DUF805 14 w.wfvlfllllvivlallaavlaaaavasalsvvlallllvps.lavtv....RRlHDtgrsgw 71
                                      w w ++ l++++iv+++l+ vl  a +a+  +vv +++++ p  + v v     R H   +s  
  gi|336254827|ref|YP_004597934.1|  9 WgWLLIGLFAASIVAQFLNVVLGRAGLAEEYQVVTVIATMAPVlIYVGVwyddHRQHYWEHSSA 72
                                      548888999999*********9999999999999999998888544544444455555555544 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.01
                            DUF805 10 Rsefwwfvlfllllvivlallaavlaaaavasalsvvl 47
                                      R+++w    + ++  iv++ll a++ a++v+   +v+ 
  gi|336254827|ref|YP_004597934.1| 63 RQHYWEHSSARIVGDIVFVLLGAIIGATTVI---AVLS 97
                                      9999966666666667666666666442222...2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1009.84
//
Query:       gi|336254828|ref|YP_004597935.1|  [L=305]
Description: NH(3)-dependent NAD(+) synthetase [Halopiger xanaduensis SH-6]
Scores for 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-72  242.7   0.0    3.5e-72  242.4   0.0    1.0  1  NAD_synthase   NAD synthase
    1.3e-06   27.5   0.0      0.001   18.0   0.0    2.2  2  tRNA_Me_trans  tRNA methyl transferase
    0.00024   20.6   0.0    0.00079   19.0   0.0    1.7  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.042   13.5   0.0      0.065   12.9   0.0    1.2  1  Asn_synthase   Asparagine synthase
       0.15   12.1   0.0       0.24   11.4   0.0    1.3  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami


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 !  242.4   0.0   9.9e-76   3.5e-72       4     242 .]      33     283 ..      30     283 .. 0.96

  Alignments for each domain:
  == domain 1  score: 242.4 bits;  conditional E-value: 9.9e-76
                                       HHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE-- CS
                      NAD_synthase   4 elvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktid 80 
                                       ++v  +++ v++aga+gvv+ +SGG+DS+++ alav+alg+e+vl+l lP ++s++  v +a+++ae lgi++ +i+
  gi|336254828|ref|YP_004597935.1|  33 RIVSEIRSTVADAGAEGVVVAMSGGIDSTVTTALAVEALGNERVLGLGLPCHKSERAGVSEARTIAEGLGIDFREIQ 109
                                       78899************************************************************************ PP

                                       -HHHHHHHHHHHHHHH...........-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT-- CS
                      NAD_synthase  81 ikpivrafeqelkeak...........edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaa 146
                                       ++p +++fe+++++              + a gN+ aR Rm++ y+ an+ ++lvlgT n+sE+++GyfTkyGDgaa
  gi|336254828|ref|YP_004597935.1| 110 LRPLLETFEETATPVLepdadggrpaeRNHALGNVIARFRMVCAYYAANRRSKLVLGTANRSERLLGYFTKYGDGAA 186
                                       **********55443334447788887999*********************************************** PP

                                       SBETTTTS-HHHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--H CS
                      NAD_synthase 147 dlapiaellKtevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpa 222
                                       d  p+++l+Ktev++La ++++P+r+++k+P+A+ ++gqtD +eLg +Yd lD +L+ lv++++s  + ++++e+++
  gi|336254828|ref|YP_004597935.1| 187 DAYPLGDLYKTEVRALAGQIGIPRRIVTKEPTAGFWAGQTDADELGAPYDDLDPFLTrLVDEGQSIADAASGLEIDR 263
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHTGGGGSSS CS
                      NAD_synthase 223 evvekieklvkksehKrklp 242
                                       e+++ i+ l  ++ hKr++p
  gi|336254828|ref|YP_004597935.1| 264 ETARSIAWLCAETTHKRTTP 283
                                       *****************987 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.8e-07     0.001       3      70 ..      50     110 ..      48     126 .. 0.80
   2 !    7.4   0.0   0.00047       1.7     165     186 ..     188     209 ..     185     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.8e-07
                     tRNA_Me_trans   3 vvvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdf 70 
                                       vvva+SgG+DS+v+ al  e+     v g+ l ++++          ++ +++a+ +ae lgi ++ +++
  gi|336254828|ref|YP_004597935.1|  50 VVVAMSGGIDSTVTTALAVEALgnERVLGLGLPCHKS---------ERAGVSEARTIAEGLGIDFREIQL 110
                                       9************999988886235577777777766.........235688999999999999998876 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00047
                     tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagla 186
                                       ++Plg+l K+evr++A ++g++
  gi|336254828|ref|YP_004597935.1| 188 AYPLGDLYKTEVRALAGQIGIP 209
                                       69***************99987 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.2e-07   0.00079       2      68 ..      50     118 ..      49     128 .. 0.84
   2 ?   -1.5   0.0      0.42   1.5e+03     157     177 ..     190     210 ..     188     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-07
                                       EEEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-G.GGGGGS CS
                              QueC   2 avvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildld.llkelg 68 
                                       +vv +SGG+DSt+ +ala ++   ++v  l++  ++ +++ ++ a++ia+ lg+ + + ++l+ ll+++ 
  gi|336254828|ref|YP_004597935.1|  50 VVVAMSGGIDSTVTTALAVEALgnERVLGLGLPCHKSERAGVSEARTIAEGLGI-DFREIQLRpLLETFE 118
                                       6899************999986558899999999*99*****************.777777751445554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.42
                                       TTTT--HHHHHHHHHHTTHHH CS
                              QueC 157 PlidlsKaeivklgkelgvpl 177
                                       Pl dl K+e+ +l+ ++g+p+
  gi|336254828|ref|YP_004597935.1| 190 PLGDLYKTEVRALAGQIGIPR 210
                                       999************999665 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.8e-05     0.065      20      81 ..      50     112 ..      41     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                      Asn_synthase  20 vGalLSGGlDSSliaalaarqsksplktFsigf..eekgsdeakyakevaehlgtehtelvlte 81 
                                       v + +SGG+DS++ +ala + +  + +   +g+  ++ +   ++ a+ +ae lg++ +e++l +
  gi|336254828|ref|YP_004597935.1|  50 VVVAMSGGIDSTVTTALAVEALG-NERVLGLGLpcHKSERAGVSEARTIAEGLGIDFREIQLRP 112
                                       55779***************997.7888888886666888888899999999999998888865 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.8e-05      0.24       2      28 ..      50      76 ..      49      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.8e-05
                                      EEEE--SSCTCHHHHHHHHHHCTTHEE CS
                       PAPS_reduct  2 lvvsvsgGkdslVllhLalkafkpvpv 28
                                      +vv++sgG+ds+V+  La++a+ + +v
  gi|336254828|ref|YP_004597935.1| 50 VVVAMSGGIDSTVTTALAVEALGNERV 76
                                      699*****************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); 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:                         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: 00:00:00.41
# Mc/sec: 2230.73
//
Query:       gi|336254829|ref|YP_004597936.1|  [L=624]
Description: PilT protein domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-12   44.7   0.0    1.4e-11   44.0   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
    0.00036   21.0   0.0    0.00094   19.6   0.0    1.7  1  AAA_16           AAA ATPase domain
    0.00048   19.9   0.1     0.0016   18.2   0.1    1.9  1  KH_1             KH domain
    0.00082   19.1   0.0     0.0019   17.9   0.0    1.6  1  Thymidylate_kin  Thymidylate kinase
     0.0049   16.5   0.1      0.016   14.8   0.0    1.9  2  AAA_25           AAA domain
     0.0074   16.5   0.0      0.075   13.2   0.0    2.3  2  AAA_33           AAA domain
     0.0085   15.9   1.3      0.027   14.3   1.3    1.8  1  KH_2             KH domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.033   14.1   0.0    1.7  1  NTPase_1         NTPase
      0.013   16.1   0.7      0.026   15.1   0.0    1.9  1  AAA_18           AAA domain
      0.014   15.1   0.0      0.038   13.7   0.0    1.7  1  AAA_29           P-loop containing region of AAA domain
      0.016   15.3   0.2      0.043   13.9   0.2    1.7  1  KH_5             NusA-like KH domain
      0.022   14.1   0.0      0.079   12.3   0.0    1.8  2  ATPase           KaiC
      0.025   14.1   0.0      0.042   13.4   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
      0.026   14.2   0.0       0.06   13.1   0.0    1.5  1  AAA_30           AAA domain
       0.03   14.3   0.0      0.067   13.2   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
       0.03   13.6   0.0      0.065   12.5   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.034   14.4   0.0       0.34   11.1   0.0    2.5  2  AAA_28           AAA domain
      0.037   13.7   0.0      0.066   12.9   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.055   13.9   0.0       0.12   12.7   0.0    1.6  1  AAA              ATPase family associated with various cellul
      0.063   13.2   0.0       0.14   12.0   0.0    1.6  1  NACHT            NACHT domain
      0.078   12.7   0.0       0.13   12.0   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.079   12.4   0.0       0.14   11.5   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
      0.083   12.6   0.0       0.18   11.5   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
        0.1   13.1   0.3        2.5    8.6   0.0    3.2  4  AAA_17           AAA domain
       0.11   12.6   0.0       0.22   11.5   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.11   12.6   0.0       0.47   10.6   0.0    2.1  1  ZT_dimer         Dimerisation domain of Zinc Transporter
       0.14   12.7   0.0       0.31   11.6   0.0    1.6  1  ABC_tran         ABC transporter
       0.16   11.7   0.0       0.27   11.0   0.0    1.3  1  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.22   11.9   0.0       0.44   11.0   0.0    1.5  1  RNA_helicase     RNA helicase
       0.22   10.7   0.0        0.4    9.8   0.0    1.3  1  NB-ARC           NB-ARC domain


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 !   44.0   0.0   2.3e-14   1.4e-11      77     246 ..     218     376 ..     182     397 .. 0.77

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.3e-14
                             T2SSE  77 gvrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallke 152
                                        +r+ v  +P + g e  ++R  ++   +++d+    + +e  +++l++       +l+sG+ g GK+t++ a+  +
  gi|336254829|ref|YP_004597936.1| 218 DYRIAVGRPPFSDGiEITAVRPIAQT--DIEDYE---NADELKERLLERQ----RGVLISGAPGAGKSTFAQAVARF 285
                                       56777777788877777777743333..355554...4444455566665....6789******************* PP

                             T2SSE 153 inksderivtvEDpvEiqleganqvqlnakkakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgsls 229
                                       i ++d  + t+E p+ +q+ g++ +q  +   + ++a+   a+L  rPD  +  E+R ++ +e+   +     g ++
  gi|336254829|ref|YP_004597936.1| 286 ISDNDYAVKTMEKPRDLQV-GPEITQYTEL--GGEMANTADALLMVRPDYTIYDEVRKTDDFEVFADMRLAGVGMIG 359
                                       ******************9.3444554444..5568888889999*******************76666655666** PP

                             T2SSE 230 TlHansaagalerLeql 246
                                        +Ha  +++al+rL   
  gi|336254829|ref|YP_004597936.1| 360 VVHATRPIDALQRLVGR 376
                                       *************9754 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.6e-06   0.00094      23      63 ..     261     302 ..     250     378 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.6e-06
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63 
                                       r + vl+sG++G GKs+ +++++r +++++  + + +k ++l
  gi|336254829|ref|YP_004597936.1| 261 RQRGVLISGAPGAGKSTFAQAVARFISDNDYAVkTMEKPRDL 302
                                       3489********************999997444477776666 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.7e-06    0.0016       3      40 ..     493     531 ..     491     543 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.7e-06
                                       EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.STT CS
                              KH_1   3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpk.sed 40 
                                       ++ v  + ++++IGkgG +I +I+++ g  I+v   +e+
  gi|336254829|ref|YP_004597936.1| 493 VVYVEEDDISSVIGKGGGRITDIENRLGIDIDVRThDEN 531
                                       57888999*****************77*****9864444 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.3e-06    0.0019       2      61 ..     268     327 ..     267     341 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.3e-06
                                       EESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHH CS
                   Thymidylate_kin   2 EGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallf 61 
                                        G  GaGK+t+a+++++ ++++ ++v +   p++ ++G  i ++ +   e+++ + all 
  gi|336254829|ref|YP_004597936.1| 268 SGAPGAGKSTFAQAVARFISDNDYAVKTMEKPRDLQVGPEITQYTELGGEMANTADALLM 327
                                       5888*********************999999*************9999999998877776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.2   4.9e+03      99     139 ..      62     100 ..      55     110 .. 0.57
   2 !   14.8   0.0   2.7e-05     0.016      25      66 ..     254     299 ..     240     408 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.2
                            AAA_25  99 ddarllvldlagv.eslpLfakdrggtlltadvdaleaaiee 139
                                       d a++ v++l+ v e+ +   ++ +g++ ++++dal++++ e
  gi|336254829|ref|YP_004597936.1|  62 DLADEGVINLEYVgERPN---AIERGHASEGEIDALIRDLAE 100
                                       555666666666644443...334555556666666666555 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.7e-05
                            AAA_25  25 lvkgllpagelallaGapgtGKttlaldlalavatGkpwlg....p 66 
                                       l ++ll ++  +l+ Gapg+GK+t+a  +a  ++  +   +    p
  gi|336254829|ref|YP_004597936.1| 254 LKERLLERQRGVLISGAPGAGKSTFAQAVARFISDNDYAVKtmekP 299
                                       556788889999*******************999776655534333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.2   7.1e+02      15      39 ..      94     118 ..      93     150 .. 0.81
   2 !   13.2   0.0   0.00013     0.075       2      39 ..     265     298 ..     265     328 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.2
                            AAA_33  15 laerllkklgavllssdtlrrrlfg 39 
                                       l++ l++ lga++l+sd++   +++
  gi|336254829|ref|YP_004597936.1|  94 LIRDLAEDLGATFLTSDIVQAEVAK 118
                                       678899************9887775 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00013
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfg 39 
                                       vl+ G+pG+GKst+a+ ++     ++ + d++ +++++
  gi|336254829|ref|YP_004597936.1| 265 VLISGAPGAGKSTFAQAVA----RFISDNDYAVKTMEK 298
                                       6789************998....344455555555555 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.3   4.4e-05     0.027       5      59 ..     469     524 ..     466     530 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-05
                                       HHHHHT.ECET.EEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                              KH_2   5 slavei.kkag.vskveIertanrviiviresqpgivIGkgGsnikkigkelrkdie 59 
                                        +++ei + a  + +v ++  ++r+++ + e     vIGkgG +i  i+  l+ di+
  gi|336254829|ref|YP_004597936.1| 469 EIEREIrSVARgYVDVQLKG-QDRAVVYVEEDDISSVIGKGGGRITDIENRLGIDID 524
                                       67888844444677888866.68999999999******************9998885 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.5e-05     0.033       2      31 ..     265     294 ..     264     307 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.5e-05
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                       v+i+G pG GK+T+ + v++ ++++++ v+
  gi|336254829|ref|YP_004597936.1| 265 VLISGAPGAGKSTFAQAVARFISDNDYAVK 294
                                       78**********************999987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   4.4e-05     0.026       1      22 [.     265     286 ..     265     326 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.4e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                       +l++G+pG+GK+t+a+++++  
  gi|336254829|ref|YP_004597936.1| 265 VLISGAPGAGKSTFAQAVARFI 286
                                       79***************98743 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 ?   13.7   0.0   6.3e-05     0.038      21      43 ..     262     283 ..     249     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.3e-05
                            AAA_29  21 lkgatlltGpsGsGKSTllDAiq 43 
                                       ++g +l++G+ G+GKST+  A++
  gi|336254829|ref|YP_004597936.1| 262 QRG-VLISGAPGAGKSTFAQAVA 283
                                       345.9************988876 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   7.1e-05     0.043       3      51 ..     490     532 ..     488     534 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.1e-05
                              KH_5   3 ertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDl 51 
                                       +r++v V++++     + +++gk+G ri  +++ L g  idv   +e++
  gi|336254829|ref|YP_004597936.1| 490 DRAVVYVEEDD-----ISSVIGKGGGRITDIENRL-GIDIDVRTHDENP 532
                                       799999**999.....*******************.9999998888876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.3     2e+03     143     178 ..      90     126 ..      83     131 .. 0.77
   2 ?   12.3   0.0   0.00013     0.079       9      37 ..     252     280 ..     243     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.3
                            ATPase 143 ilrqlvrvlkklgvTailvsekss.seeaaggygvee 178
                                       +++ l+r l++    + l+s++ + +  +a+g +ve+
  gi|336254829|ref|YP_004597936.1|  90 EIDALIRDLAEDLGATFLTSDIVQaEVAKAKGLDVEH 126
                                       5778888885555566889998876778999999999 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00013
                            ATPase   9 DeilkgGipegrvvlitGepGtGKtifal 37 
                                       De+ ++ + ++r vli+G pG+GK++fa+
  gi|336254829|ref|YP_004597936.1| 252 DELKERLLERQRGVLISGAPGAGKSTFAQ 280
                                       6676677889999**************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 ?   13.4   0.0     7e-05     0.042      25      67 ..     254     296 ..     244     300 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-05
                             AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkldkekylslti 67 
                                       l e ll++++ vl+ G  G GK++ ++ + + +++++y ++t+
  gi|336254829|ref|YP_004597936.1| 254 LKERLLERQRGVLISGAPGAGKSTFAQAVARFISDNDYAVKTM 296
                                       66889*****************************999999887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001      0.06      14      49 ..     259     293 ..     250     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                            AAA_30  14 ltsgdrvavltGpAGtGKttalkalreaweaaggrv 49 
                                       l +++r +++ G++G+GK+t  +a+++ + ++ + v
  gi|336254829|ref|YP_004597936.1| 259 L-ERQRGVLISGAPGAGKSTFAQAVARFISDNDYAV 293
                                       4.4456899*******************99998877 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   0.00011     0.067       1      34 [.     264     298 ..     264     349 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                       EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--T CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltr 34 
                                       +vl+ G+pG gKs++a+ +a+++  + + ++ + +
  gi|336254829|ref|YP_004597936.1| 264 GVLISGAPGAGKSTFAQAVARFIsDNDYAVKTMEK 298
                                       5899*******************855555444443 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   0.00011     0.065      16      43 ..     262     289 ..     249     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerq 43 
                                          +l++G+pGAGKs+ a+++++ +  +
  gi|336254829|ref|YP_004597936.1| 262 QRGVLISGAPGAGKSTFAQAVARFISDN 289
                                       55699***************99877544 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.1   1.2e+03      25      47 ..     183     205 ..     175     222 .. 0.76
   2 ?   11.1   0.0   0.00057      0.34       2      21 ..     265     284 ..     264     301 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.1
                            AAA_28  25 pvvpEaareileeklakgedalp 47 
                                       +++ E+are+++   ++ e+ l+
  gi|336254829|ref|YP_004597936.1| 183 ETMDEYAREVVDAAKESSEGFLE 205
                                       6789*******999887776665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00057
                            AAA_28   2 ivitGgestGKTtlleaLaa 21 
                                       + i+G++++GK+t ++a a+
  gi|336254829|ref|YP_004597936.1| 265 VLISGAPGAGKSTFAQAVAR 284
                                       78**************9985 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 ?   12.9   0.0   0.00011     0.066      42      79 ..     257     294 ..     236     338 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                         IstB_IS21  42 sfiekkenivllGpsGvGKshlaialgveavraglsvl 79 
                                         +e++ ++++ G +G+GKs +a a+++    ++++v 
  gi|336254829|ref|YP_004597936.1| 257 RLLERQRGVLISGAPGAGKSTFAQAVARFISDNDYAVK 294
                                       5689999********************98888888886 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   0.00021      0.12       1      23 [.     265     287 ..     265     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
                                       EEEESSTTSSHHHHHHHHHHHHT CS
                               AAA   1 vllyGppGtGKTllakavakelg 23 
                                       vl++G pG GK+++a+ava+ ++
  gi|336254829|ref|YP_004597936.1| 265 VLISGAPGAGKSTFAQAVARFIS 287
                                       799****************8764 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   0.00024      0.14       3      28 ..     265     290 ..     263     297 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                                       EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegk 28 
                                       v++ G++G GK+t++q +a+ + +++
  gi|336254829|ref|YP_004597936.1| 265 VLISGAPGAGKSTFAQAVARFISDND 290
                                       89****************98777665 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 ?   12.0   0.0   0.00021      0.13       2      24 ..     266     286 ..     265     339 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsli 24 
                                       +++G+pG+GKSt  + ++r   i
  gi|336254829|ref|YP_004597936.1| 266 LISGAPGAGKSTFAQAVARF--I 286
                                       79****************99..3 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.14       4      36 ..     265     297 ..     264     319 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE- CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvvid 36 
                                       v+++G P +GKst+a+ +a+ +++++++v  ++
  gi|336254829|ref|YP_004597936.1| 265 VLISGAPGAGKSTFAQAVARFISDNDYAVKTME 297
                                       89**********************999998765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00031      0.18      13      47 ..     253     287 ..     243     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                                       HHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  13 eqikkvaktdlsvlitGesGtGKellaraiheask 47 
                                       e  +++ + +  vli G  G+GK+++a+a+ +  +
  gi|336254829|ref|YP_004597936.1| 253 ELKERLLERQRGVLISGAPGAGKSTFAQAVARFIS 287
                                       556778888999****************9987554 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.6   1.6e+03      55     104 ..      58     106 ..      31     123 .. 0.54
   2 ?   -0.9   0.0       3.4     2e+03      13      39 ..      96     122 ..      92     136 .. 0.75
   3 ?   -1.9   0.0       6.9   4.1e+03      34      69 ..     162     196 ..     148     208 .. 0.46
   4 ?    8.6   0.0    0.0041       2.5       2      17 ..     269     284 ..     268     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHHH...HSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SE CS
                            AAA_17  55 kelqkeaaekiaeea...kkkgvlvdghprikeqagfldglpkevleelkpda 104
                                       ++l ++a e + + +   ++ +++  gh++    +g++d l ++  e+l  ++
  gi|336254829|ref|YP_004597936.1|  58 QRLADLADEGVINLEyvgERPNAIERGHAS----EGEIDALIRDLAEDLGATF 106
                                       555555555555544444445566666664....4445555555554442222 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.4
                                       HHHHHHHTEEEEEHHHHHHHHHHTT.TS CS
                            AAA_17  13 eklvekygfthlsaGdllreeakrg.gl 39 
                                       + l+e++g t+l+ +d++ +e+++  gl
  gi|336254829|ref|YP_004597936.1|  96 RDLAEDLGATFLT-SDIVQAEVAKAkGL 122
                                       5689999999998.9***9887766255 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 6.9
                                       HHTTTSHSSHHHHCTSHHHH...HHHHHHHHHHHHHHHH CS
                            AAA_17  34 akrgglakardemrklplee...kkelqkeaaekiaeea 69 
                                       akrg+l    +emr +p+ +   ++e+++e a+++ ++a
  gi|336254829|ref|YP_004597936.1| 162 AKRGEL----GEMRYEPIADeplDEETMDEYAREVVDAA 196
                                       455666....44443222221113333444444443333 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0041
                                       E-TTSSHHHHHHHHHH CS
                            AAA_17   2 GgPGsGKgtqceklve 17 
                                       G PG+GK+t ++ +++
  gi|336254829|ref|YP_004597936.1| 269 GAPGAGKSTFAQAVAR 284
                                       9**********99886 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00037      0.22       6      43 ..     250     286 ..     244     295 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00037
                                       HHHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE   6 etealgkklakalgdvilLeGdLGaGKTtlvrglakal 43 
                                       + ++l ++l +  ++ +l++G  GaGK+t+++++a+ +
  gi|336254829|ref|YP_004597936.1| 250 NADELKERLLE-RQRGVLISGAPGAGKSTFAQAVARFI 286
                                       44555555544.2556******************9976 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 ?   10.6   0.0   0.00079      0.47      29      67 ..     580     618 ..     567     622 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00079
                                       -S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-T CS
                          ZT_dimer  29 ksGskifvdlhievdgdlsvkeaHeiadevekrikeefp 67 
                                       ++G +++   ++   g+++v+++ +iade+e++i ++ p
  gi|336254829|ref|YP_004597936.1| 580 QAGGDYLFTATVSRGGEIQVSRGSAIADELEQAIDRKDP 618
                                       6899999999************************98864 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00051      0.31      10      42 ..     261     293 ..     257     378 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00051
                                       TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGei 42 
                                       + + v i G  GaGKSt+++++a+  +++   +
  gi|336254829|ref|YP_004597936.1| 261 RQRGVLISGAPGAGKSTFAQAVARFISDNDYAV 293
                                       5566899***************99988655555 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   0.00046      0.27       1      29 [.     267     295 ..     267     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvav 29 
                                       + G +G+GK+tf +a++ +++++ + v++
  gi|336254829|ref|YP_004597936.1| 267 ISGAPGAGKSTFAQAVARFISDNDYAVKT 295
                                       579*****************999877765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00074      0.44       1      23 [.     265     287 ..     265     322 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00074
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                       ++++G++g GKSt+a+ +a+ ++
  gi|336254829|ref|YP_004597936.1| 265 VLISGAPGAGKSTFAQAVARFIS 287
                                       679**************888776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00067       0.4       5      42 ..     251     284 ..     248     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00067
                                       HHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC   5 vekviekLlekdelqslvvalvGmgGvGKttlakqiln 42 
                                        ++++e+Ll + + +   v ++G +G GK+t a+ + +
  gi|336254829|ref|YP_004597936.1| 251 ADELKERLL-ERQRG---VLISGAPGAGKSTFAQAVAR 284
                                       689999999.67777...89*************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4360.84
//
Query:       gi|336254830|ref|YP_004597937.1|  [L=277]
Description: hypothetical protein Halxa_3447 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00048   20.1   1.3     0.0055   16.7   0.5    2.4  2  HTH_20         Helix-turn-helix domain
     0.0015   18.4   0.0     0.0033   17.3   0.0    1.5  1  MarR_2         MarR family
     0.0029   17.4   0.1     0.0047   16.8   0.1    1.4  1  HTH_5          Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.037   13.6   0.0      0.072   12.7   0.0    1.5  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.06   13.3   0.0        0.1   12.6   0.0    1.3  1  HTH_11         HTH domain
      0.066   13.0   0.0       0.11   12.3   0.0    1.3  1  HTH_DeoR       DeoR-like helix-turn-helix domain
       0.12   12.5   0.1        2.1    8.6   0.0    2.3  2  DUF1724        Domain of unknown function (DUF1724)
       0.15   11.7   0.0       0.29   10.8   0.0    1.5  1  RP-C           Replication protein C N-terminal domain
       0.18   11.8   0.0       0.29   11.2   0.0    1.3  1  Dimerisation2  Dimerisation domain
        0.2   11.6   0.0       0.46   10.4   0.0    1.5  1  TrmB           Sugar-specific transcriptional regulator TrmB


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 !   16.7   0.5     3e-06    0.0055       7      46 ..      10      48 ..       8      50 .. 0.95
   2 ?    1.3   0.0       0.2   3.6e+02      40      55 ..      78      94 ..      65      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3e-06
                                      HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  7 LahPvRrrilraLaraegltaselaerldlskntlsyHLr 46
                                      +++P R+++lr+L r +++   +l  +l++s+ t+ +HL+
  gi|336254830|ref|YP_004597937.1| 10 FSSPHRLEVLREL-RSAPADTQALTGALSISRVTVQRHLN 48
                                      789**********.************************97 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.2
                                      HHHHHHHHHHH.CTTEE CS
                            HTH_20 40 tlsyHLrvLee.agLve 55
                                      t  ++L+vLe+ a+ ++
  gi|336254830|ref|YP_004597937.1| 78 TYLDRLDVLEShADVID 94
                                      56799******999986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.8e-06    0.0033       5      56 ..      13      61 ..      10      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
                                      HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      p  + vL +L+ +p      ++l+ +l +s+ +v+r+l+r+ + G++ +++g
  gi|336254830|ref|YP_004597937.1| 13 PHRLEVLRELRSAP---ADTQALTGALSISRVTVQRHLNRCCELGWIHKVDG 61
                                      67789*******99...599***************************99854 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 !   16.8   0.1   2.6e-06    0.0047       1      38 [.      12      49 ..      12      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.6e-06
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHH CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkk 38
                                      +p Rl++L+ L++ ++    l+ +l +s+ tv +HL++
  gi|336254830|ref|YP_004597937.1| 12 SPHRLEVLRELRSAPADTQALTGALSISRVTVQRHLNR 49
                                      599*********************************96 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 ?   12.7   0.0     4e-05     0.072       8      47 ..      18      56 ..      12      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4e-05
                            HTH_24  8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +L++L+  +    + L  +l +S+ tv r+l+r++e G+I
  gi|336254830|ref|YP_004597937.1| 18 VLRELRS-APADTQALTGALSISRVTVQRHLNRCCELGWI 56
                                      5555555.5566677888999******************9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.7e-05       0.1       6      44 ..      16      57 ..      14      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-05
                            HTH_11  6 lelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelg..v 44
                                      le L+e r+     + L   L++Sr tv+r++ +  elg   
  gi|336254830|ref|YP_004597937.1| 16 LEVLRELRSApADTQALTGALSISRVTVQRHLNRCCELGwiH 57
                                      567777777778999****************99877777555 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 ?   12.3   0.0   5.9e-05      0.11      16      53 ..      28      65 ..      16      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                          HTH_DeoR 16 sveelvellgvSeaTiRRDLneLeeqglltRthGGavs 53
                                       ++ l+  l +S  T+ R Ln   e g ++++ G++++
  gi|336254830|ref|YP_004597937.1| 28 DTQALTGALSISRVTVQRHLNRCCELGWIHKVDGRYEL 65
                                      68999****************************99875 PP

>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.19   3.4e+02      47      54 ..       4      11 ..       2      12 .. 0.87
   2 ?    8.6   0.0    0.0011       2.1       2      54 ..     189     238 ..     188     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.19
                           DUF1724 47 kWGeeLFe 54
                                       WG++LF+
  gi|336254830|ref|YP_004597937.1|  4 DWGKQLFS 11
                                      6******7 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                           DUF1724   2 klyvydeeikplsltvtDkflslslfdkdgkydhkdlisfdesAlkWGeeLFe 54 
                                        lyv+de++  +++t+tD    ++ +d+ g++    + s++++  +W+ e +e
  gi|336254830|ref|YP_004597937.1| 189 TLYVLDEPL-EFGVTLTDERAFVGCYDD-GTF-VACIESDEPAFREWADEVYE 238
                                       69*******.*********999998765.566.34577799999999999887 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 ?   10.8   0.0   0.00016      0.29      75     105 ..      30      60 ..      10      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                              RP-C  75 aqLsralglsestlrrhlaaLveaGliirrD 105
                                       ++L  al++s+ t++rhl + +e+G+i+  D
  gi|336254830|ref|YP_004597937.1|  30 QALTGALSISRVTVQRHLNRCCELGWIHKVD 60 
                                       4566899********************9877 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00016      0.29       8      81 ..       2      70 ..       1      78 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                     Dimerisation2  8 GFlaSkaLftA.ceLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntelas 81
                                      G+   k Lf++  +L+v   L++ +p +++++  +l++s   ++r l+ c+ Lg  +  k ++    Y+ t+l +
  gi|336254830|ref|YP_004597937.1|  2 GYDWGKQLFSSpHRLEVLRELRS-APADTQALTGALSISRVTVQRHLNRCCELGWIH--KVDG---RYELTPLGD 70
                                      78888999987357999999999.********************************9..4455...599998865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00026      0.46      19      60 ..      23      64 ..      19      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00026
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                      ++ pa+++ +  +l ++r +v++ L++  + G++++++gr+ 
  gi|336254830|ref|YP_004597937.1| 23 RSAPADTQALTGALSISRVTVQRHLNRCCELGWIHKVDGRYE 64
                                      6789999999***************************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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):              10  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2165.76
//
Query:       gi|336254831|ref|YP_004597938.1|  [L=360]
Description: peptidase M20 [Halopiger xanaduensis SH-6]
Scores for complete 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-27   96.5   4.9    2.1e-27   96.2   4.9    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.4e-14   53.9   0.5    1.2e-13   50.9   0.1    2.2  2  M20_dimer      Peptidase dimerisation domain


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 !   96.2   4.9   2.4e-31   2.1e-27       2     205 ..      61     355 ..      60     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 2.4e-31
                                       EEEES-BSS.TTCGGGSSS..TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT CS
                                       xxxxxxxxx.xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVp.eeetdgwtt..pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr 75 
                                       l +H DvV  +e +   +   ++  +e+dG+lyGrG++dmkg v+aa+ a+r  +       g++v++ ++ EE+g+
  gi|336254831|ref|YP_004597938.1|  61 LVGHHDVVEpDESQ--LEAdgEYVVEERDGRLYGRGTADMKGAVAAAMLAFRDAEP-----AGELVFASFVGEEVGG 130
                                       779******54444..5555899999*************************98555.....56***********999 PP

                                       THHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE..................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                     Peptidase_M20  76 gGakallegleerekvdavfelhieepgileagklaigvv..................................... 115
                                        Ga+  ++   e++++d+++   ++e++       ++gv+                                     
  gi|336254831|ref|YP_004597938.1| 131 VGARRAID---EGFAPDYAV---VGEGSTGY---SSPGVTdvavahkgrrastitargtaahaseadagenavyrat 198
                                       ***99999...689999965...66666555...24566666778******************************** PP

                                       ..................................................................EEEEEEEEEES CS
                                       ..................................................................xxxxxxxxxxx RF
                     Peptidase_M20 116 ..................................................................kvevellegga 126
                                                                                                          ve++  ++ +
  gi|336254831|ref|YP_004597938.1| 199 davdvvrdleppavdaagetlagsvvvteieggrawnvvpdrcevtidertvpgeraalerveefeGVEWTVDQDLP 275
                                       ***************************************************************9965888877**** PP

                                       HEEECCHHHHHHHHHHHHHHH.TSCEEEEEESSSBHTHHHH..TTTEEEEEEESSG.GCTTSTTTEEEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 127 pvtlndsplvkalaeaaeelf.gekvelivsgpggtdarff..agiptvmifgpgs.glaHspnEyvdledlekgik 199
                                       p++++d ++++++ eaa+++  g ++el++++  +tda+++  ag+  ++i+g  + g aH+ +E v+++ l ++ +
  gi|336254831|ref|YP_004597938.1| 276 PMRCDDREFAETVLEAADAAQsG-SPELVTKP-HATDAGWLseAGT-ECVICGAAEpGEAHTADESVSIDVLGRCEE 349
                                       *******************9754.79999999.********87777.5668996655*****************999 PP

                                       HHHHHH CS
                                       xxxxxx RF
                     Peptidase_M20 200 vlarll 205
                                       ++ +++
  gi|336254831|ref|YP_004597938.1| 350 TYRKVA 355
                                       998876 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.051   4.6e+02      84     108 ..      15      39 ..       5      40 .. 0.86
   2 !   50.9   0.1   1.3e-17   1.2e-13       1      90 [.     165     255 ..     165     263 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.051
                                       HHHHHHHHHHHHHHHHHHTSCCSTT CS
                         M20_dimer  84 llpgedpeevleeieeilekeaped 108
                                       ++ +ed  +v +eie++l++e ++d
  gi|336254831|ref|YP_004597938.1|  15 VPSHEDETAVGDEIEAWLRRETAAD 39 
                                       678999*************998765 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 1.3e-17
                                       SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.......TCCTCCCCCEECCE-CCCCEESSE CS
                         M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia..eerslprttlnvtgiegGsaknvipde 75 
                                       ++hkG    +it++g+a+H++  +ag+NA++ + ++++  +d+e + a  +   +   ++ vt+iegG+a nv+pd+
  gi|336254831|ref|YP_004597938.1| 165 VAHKGRRASTITARGTAAHASEADAGENAVYRATDAVDVVRDLEPP-AvdAAGETLAGSVVVTEIEGGRAWNVVPDR 240
                                       589***************************************9655.44755555556789**************** PP

                                       EEEEEEEEHHHHHHH CS
                         M20_dimer  76 aeakidiRllpgedp 90 
                                       +e++id R++pge +
  gi|336254831|ref|YP_004597938.1| 241 CEVTIDERTVPGERA 255
                                       ************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); 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 0.20s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2907.41
//
Query:       gi|336254832|ref|YP_004597939.1|  [L=93]
Description: hypothetical protein Halxa_3449 [Halopiger xanaduensis SH-6]
Scores for 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-05   22.4   3.3      0.019   14.8   0.5    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
    0.00022   21.2   0.7    0.00027   21.0   0.7    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
    0.00062   19.6   1.8    0.00098   19.0   1.8    1.3  1  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.001   18.8   0.2     0.0012   18.5   0.2    1.1  1  TackOD1          Thaumarchaeal output domain 1
     0.0011   19.0   4.6     0.0028   17.7   4.6    1.7  1  Zn-ribbon_8      Zinc ribbon domain
     0.0019   18.1   3.2        1.4    9.0   0.1    3.1  3  YhfH             YhfH-like protein
     0.0022   18.0   0.4     0.0036   17.3   0.4    1.3  1  Nop10p           Nucleolar RNA-binding protein, Nop10p family
     0.0051   16.8   1.7     0.0072   16.3   1.7    1.3  1  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.013   15.9   2.5       0.54   10.7   0.1    2.3  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.014   15.4   3.8      0.018   15.1   0.2    2.3  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.017   15.0   0.6      0.024   14.5   0.6    1.2  1  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
      0.027   14.0   1.6        5.7    6.5   0.2    2.6  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.028   14.4   1.5      0.036   14.0   1.5    1.2  1  zinc-ribbons_6   zinc-ribbons
      0.028   13.8   1.3        1.3    8.5   0.1    2.3  2  zf-ribbon_3      zinc-ribbon domain
      0.028   14.7   0.6        9.6    6.6   0.1    2.5  2  zinc_ribbon_9    zinc-ribbon
      0.041   13.6   2.9      0.064   13.0   2.9    1.3  1  Rubredoxin_2     Rubredoxin metal binding domain
      0.059   13.3   1.4          5    7.1   0.2    2.3  2  Nudix_N_2        Nudix N-terminal
      0.069   13.5   1.6       0.74   10.2   1.6    2.0  1  GFA              Glutathione-dependent formaldehyde-activatin
      0.071   13.0   1.4        0.1   12.5   1.4    1.2  1  zf-C3HC4_2       Zinc finger, C3HC4 type (RING finger)
      0.094   12.3   0.2        0.1   12.2   0.2    1.2  1  RE_MamI          MamI restriction endonuclease
      0.099   12.6   1.9        2.4    8.2   0.2    2.2  2  Ogr_Delta        Ogr/Delta-like zinc finger
       0.24   11.0   2.7       0.61    9.7   0.2    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.34   11.0   3.4        2.4    8.3   0.2    2.2  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.45   10.5   3.4        9.9    6.2   0.5    2.2  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.72    9.8   3.7        1.9    8.5   0.8    2.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
        4.8    7.8   4.5        1.1    9.9   0.5    1.9  2  zf-C2H2          Zinc finger, C2H2 type


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 !   14.8   0.5   2.7e-05     0.019      18      38 ..      19      37 ..      12      38 .. 0.87
   2 !    8.2   0.1    0.0033       2.3       2      22 ..      43      61 ..      42      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                           TFIIS_C 18 tRsaDEpmtvfykCtkCghrW 38
                                       R+aDE++t  y Ct+Cg+r+
  gi|336254832|ref|YP_004597939.1| 19 KRAADEEAT--YACTDCGERF 37
                                      69*****99..9*******98 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0033
                           TFIIS_C  2 kCpkCgsreayffqlQtRsaD 22
                                      +Cp Cgs  ++  ++Q  saD
  gi|336254832|ref|YP_004597939.1| 43 ECPACGSAAIV--EQQVSSAD 61
                                      7*****97766..88998888 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 !   21.0   0.7   3.8e-07   0.00027      65      97 ..      22      52 ..       7      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.8e-07
                                      EEE--EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                              HypA 65 eevpvkvrCreCgkefeleekalrCpkCgsadv 97
                                       ++++++ C++Cg++f ++++  +Cp+Cgsa +
  gi|336254832|ref|YP_004597939.1| 22 ADEEATYACTDCGERFYTTQD--ECPACGSAAI 52
                                      5678999**********9877..8******865 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 !   19.0   1.8   1.4e-06   0.00098      14      35 ..      30      51 ..      28      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-06
                           DUF35_N 14 CpdCGtvqfPPravCphCgsdd 35
                                      C+dCG  ++  +  Cp Cgs +
  gi|336254832|ref|YP_004597939.1| 30 CTDCGERFYTTQDECPACGSAA 51
                                      *******99999*******976 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   1.8e-06    0.0012      71     103 ..      25      57 ..      12      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.8e-06
                           TackOD1  71 drirlCpsCksghlnvrevCpkCkSidieeqel 103
                                       + + +C+ C     + +++Cp C+S+ i eq++
  gi|336254832|ref|YP_004597939.1|  25 EATYACTDCGERFYTTQDECPACGSAAIVEQQV 57 
                                       45779***********************99986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   4.6     4e-06    0.0028       6      35 ..      28      51 ..      27      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4e-06
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs.e 35
                                      Y C++Cg++f   q        +CP+Cgs +
  gi|336254832|ref|YP_004597939.1| 28 YACTDCGERFYTTQ-------DECPACGSaA 51
                                      9*********9887.......24*****954 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.17   1.2e+02       6      14 ..       2      10 ..       1      12 [. 0.86
   2 ?    5.5   0.4     0.024        17      16      23 ..      30      37 ..      28      42 .. 0.84
   3 !    9.0   0.1     0.002       1.4      15      29 ..      43      58 ..      40      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.17
                              YhfH  6 eFfrnLPkK 14
                                       Ff+nL+ K
  gi|336254832|ref|YP_004597939.1|  2 GFFENLGRK 10
                                      6******99 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.024
                              YhfH 16 CteCGkei 23
                                      Ct+CG+ +
  gi|336254832|ref|YP_004597939.1| 30 CTDCGERF 37
                                      *****975 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.002
                              YhfH 15 kCteCGke.ieEqaec 29
                                      +C+ CG+  i Eq+ +
  gi|336254832|ref|YP_004597939.1| 43 ECPACGSAaIVEQQVS 58
                                      7******999999876 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 !   17.3   0.4   5.2e-06    0.0036       5      28 ..      30      52 ..      27      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.2e-06
                                      -EE-TTT--EESSSB-TTT-SB-B CS
                            Nop10p  5 lrkcgkcrvYTLkkvcpecggptk 28
                                        +cg+ r YT +++cp cg++++
  gi|336254832|ref|YP_004597939.1| 30 CTDCGE-RFYTTQDECPACGSAAI 52
                                      567999.9************9765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.7     1e-05    0.0072      13      43 ..      28      56 ..      16      60 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                               DZR 13 rfCseCgtklkavaaedrCpsCgekvdpear 43
                                        C +Cg++   ++++d Cp+Cg+++  e++
  gi|336254832|ref|YP_004597939.1| 28 YACTDCGERF--YTTQDECPACGSAAIVEQQ 56
                                      3699999998..4778999999988877665 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 ?    5.7   0.4     0.028        19      21      44 ..      20      40 ..       8      43 .. 0.59
   2 ?   10.7   0.1   0.00078      0.54       5      19 ..      43      57 ..      39      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.028
                   Lar_restr_allev 21 vvaeigqcvyCadCgastpwfkia 44
                                      ++a+ + + +C+dCg     f+++
  gi|336254832|ref|YP_004597939.1| 20 RAADEEATYACTDCGE---RFYTT 40
                                      222333399******8...45444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00078
                   Lar_restr_allev  5 pCPfCggravlersq 19
                                       CP Cg++a++e++ 
  gi|336254832|ref|YP_004597939.1| 43 ECPACGSAAIVEQQV 57
                                      7*********99875 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 ?    1.2   0.5      0.55   3.8e+02      12      21 ..      22      31 ..      12      36 .. 0.78
   2 ?   15.1   0.2   2.6e-05     0.018       1      13 [.      43      55 ..      43      69 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.55
                    DNA_ligase_ZBD 12 eegeaiyRCt 21
                                       ++ea y Ct
  gi|336254832|ref|YP_004597939.1| 22 ADEEATYACT 31
                                      4579999998 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.6e-05
                    DNA_ligase_ZBD  1 hCPvCGsavvRee 13
                                      +CP+CGsa++ e+
  gi|336254832|ref|YP_004597939.1| 43 ECPACGSAAIVEQ 55
                                      5********9777 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 ?   14.5   0.6   3.4e-05     0.024      24      45 ..      28      49 ..      26      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                                      EE-HHHHHHHHHTT-B-TTT-- CS
                        zf-C3HC4_3 24 vlCeeCaekllkrkkkCpiCrr 45
                                      ++C +C e++   +++Cp C +
  gi|336254832|ref|YP_004597939.1| 28 YACTDCGERFYTTQDECPACGS 49
                                      58********99********76 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2    0.0082       5.7      17      27 ..      25      35 ..      21      40 .. 0.83
   2 ?    6.4   0.1    0.0094       6.5       3      12 ..      44      53 ..      43      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0082
                                      TTCEEESSSSB CS
                      TF_Zn_Ribbon 17 rgelvCtdCGl 27
                                      ++++ CtdCG+
  gi|336254832|ref|YP_004597939.1| 25 EATYACTDCGE 35
                                      57899999996 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0094
                                      ETTTTCEECH CS
                      TF_Zn_Ribbon  3 CPnCgstnlv 12
                                      CP Cgs  +v
  gi|336254832|ref|YP_004597939.1| 44 CPACGSAAIV 53
                                      9999998765 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.5   5.3e-05     0.036      12      41 ..      23      53 ..      13      61 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-05
                                      E-SSEEE-TTT--E.EEEEEE-SSS-S---E CS
                    zinc-ribbons_6 12 krgeqyhCeaCqed.lkkealCpeCeqelev 41
                                       ++++y C  C e+ ++ +  Cp C++   v
  gi|336254832|ref|YP_004597939.1| 23 DEEATYACTDCGERfYTTQDECPACGSAAIV 53
                                      45589******9961578899****987655 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   0.1     0.048        33      18      25 ..      29      36 ..      27      37 .. 0.84
   2 ?    8.5   0.1    0.0019       1.3       4      10 ..      43      49 ..      41      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.048
                       zf-ribbon_3 18 vCpyCGtk 25
                                      +C+ CG++
  gi|336254832|ref|YP_004597939.1| 29 ACTDCGER 36
                                      69****87 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0019
                       zf-ribbon_3  4 rCPnCGa 10
                                      +CP+CG+
  gi|336254832|ref|YP_004597939.1| 43 ECPACGS 49
                                      79***98 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1      0.02        14      19      31 ..      23      37 ..      16      37 .. 0.68
   2 ?    6.6   0.1     0.014       9.6      20      33 ..      41      54 ..      38      55 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.02
                     zinc_ribbon_9 19 dsdv..lCPhCgggF 31
                                      d+++  +C +Cg  F
  gi|336254832|ref|YP_004597939.1| 23 DEEAtyACTDCGERF 37
                                      3332258*****998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.014
                     zinc_ribbon_9 20 sdvlCPhCgg.gFVE 33
                                      +d  CP Cg+   VE
  gi|336254832|ref|YP_004597939.1| 41 QDE-CPACGSaAIVE 54
                                      677.****9846666 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.9   9.3e-05     0.064       1      22 [.      28      49 ..      28      49 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.3e-05
                      Rubredoxin_2  1 YvCsqCGfesakwfGrCpsCgs 22
                                      Y C +CG ++ + +  Cp+Cgs
  gi|336254832|ref|YP_004597939.1| 28 YACTDCGERFYTTQDECPACGS 49
                                      99******************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 ?    5.3   0.1     0.026        18      17      30 ..      22      35 ..      12      39 .. 0.73
   2 ?    7.1   0.2    0.0072         5       3      15 ..      44      58 ..      44      65 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.026
                                      T-SS-EEEETTTTE CS
                         Nudix_N_2 17 gDnreRlvCpaCgt 30
                                       D++  + C++Cg 
  gi|336254832|ref|YP_004597939.1| 22 ADEEATYACTDCGE 35
                                      56667788999986 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0072
                                      -TTT--B..-EEE-- CS
                         Nudix_N_2  3 CsqCGtp..velrip 15
                                      C++CG++  ve+++ 
  gi|336254832|ref|YP_004597939.1| 44 CPACGSAaiVEQQVS 58
                                      9****9976667765 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.6    0.0011      0.74      33      66 ..      10      44 ..       3      64 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                               GFA 33 elkeykktadsgnkvtr.sfCpeCgsplyseesaa 66
                                      ++ e++++a++  + +  + C +Cg ++y+++++ 
  gi|336254832|ref|YP_004597939.1| 10 KVGEFTQEAKRAADEEAtYACTDCGERFYTTQDEC 44
                                      67778877555544444499********9887654 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.4   0.00015       0.1      23      40 .]      30      47 ..      28      47 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                        zf-C3HC4_2 23 CqkCilrsLeekneCPlC 40
                                      C +C  r  + ++eCP C
  gi|336254832|ref|YP_004597939.1| 30 CTDCGERFYTTQDECPAC 47
                                      *******99********* PP

>> RE_MamI  MamI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00015       0.1      46      83 ..      18      55 ..      13      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                           RE_MamI 46 vksankldavDkcnatapRvnrlidkgtdastadileq 83
                                       k a   +a   c +++ R+ + +d+++ +++a i+eq
  gi|336254832|ref|YP_004597939.1| 18 AKRAADEEATYACTDCGERFYTTQDECPACGSAAIVEQ 55
                                      5666667777789*********************9987 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 ?    4.1   0.1     0.066        45      23      40 ..      25      40 ..      13      42 .. 0.78
   2 ?    8.2   0.2    0.0034       2.4       1      11 [.      43      53 ..      43      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.066
                         Ogr_Delta 23 eryyqCsnfeCgatfvaa 40
                                      e+ y C++  Cg +f + 
  gi|336254832|ref|YP_004597939.1| 25 EATYACTD--CGERFYTT 40
                                      68999999..99888765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0034
                         Ogr_Delta  1 rCPhCgapaaa 11
                                      +CP Cg++a +
  gi|336254832|ref|YP_004597939.1| 43 ECPACGSAAIV 53
                                      6*******986 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00089      0.61       2      15 ..      27      40 ..      26      43 .. 0.85
   2 ?    2.1   0.2      0.21   1.5e+02       4      10 ..      43      49 ..      40      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00089
                            zf_UBZ  2 tylCerCgkeipes 15
                                      ty C +Cg+++ ++
  gi|336254832|ref|YP_004597939.1| 27 TYACTDCGERFYTT 40
                                      9********99876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.21
                            zf_UBZ  4 lCerCgk 10
                                       C+ Cg+
  gi|336254832|ref|YP_004597939.1| 43 ECPACGS 49
                                      7****97 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 ?    8.3   0.2    0.0035       2.4       9      29 ..      20      40 ..      13      43 .. 0.76
   2 ?    4.5   0.3     0.055        38      18      28 ..      43      53 ..      36      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0035
                          zf-Mss51  9 qtapkhvdfeCpdCGiptycs 29
                                       +a ++ ++ C dCG   y +
  gi|336254832|ref|YP_004597939.1| 20 RAADEEATYACTDCGERFYTT 40
                                      44778999*******877765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.055
                          zf-Mss51 18 eCpdCGiptyc 28
                                      eCp CG    +
  gi|336254832|ref|YP_004597939.1| 43 ECPACGSAAIV 53
                                      9*****87655 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 ?    6.1   0.2     0.015        10      39      55 ..      19      36 ..       9      38 .. 0.80
   2 ?    6.2   0.5     0.014       9.9      25      40 ..      37      53 ..      35      74 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                    OrfB_Zn_ribbon 39 ke.alsgrtfkCpnCgfe 55
                                      k+ a+++ t+ C++Cg +
  gi|336254832|ref|YP_004597939.1| 19 KRaADEEATYACTDCGER 36
                                      34578999********86 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.014
                    OrfB_Zn_ribbon 25 ay.TSktCseCgsknke 40
                                      +y T  +C+ Cgs    
  gi|336254832|ref|YP_004597939.1| 37 FYtTQDECPACGSAAIV 53
                                      5646679*****97655 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 ?    8.5   0.8    0.0028       1.9       4      14 ..      27      37 ..      27      40 .. 0.86
   2 ?    2.1   0.1      0.26   1.8e+02       7      12 ..      44      49 ..      43      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0028
                    Zn_ribbon_SprT  4 vYrCtgCgrey 14
                                      +Y Ct+Cg+++
  gi|336254832|ref|YP_004597939.1| 27 TYACTDCGERF 37
                                      7*******876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.26
                    Zn_ribbon_SprT  7 CtgCgr 12
                                      C+ Cg+
  gi|336254832|ref|YP_004597939.1| 44 CPACGS 49
                                      ****95 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.5    0.0015       1.1       1      12 [.      28      39 ..      28      43 .. 0.83
   2 ?   -0.8   0.3       3.9   2.7e+03       2       7 ..      43      48 ..      42      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0015
                                      EEETTTTEEESS CS
                           zf-C2H2  1 ykCpdCgksFkr 12
                                      y C+dCg++F +
  gi|336254832|ref|YP_004597939.1| 28 YACTDCGERFYT 39
                                      88*****98876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.9
                                      EETTTT CS
                           zf-C2H2  2 kCpdCg 7 
                                      +Cp Cg
  gi|336254832|ref|YP_004597939.1| 43 ECPACG 48
                                      699998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 675.55
//
Query:       gi|336254833|ref|YP_004597940.1|  [L=118]
Description: hypothetical protein Halxa_3450 [Halopiger xanaduensis SH-6]
Scores for 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    8.2  28.3        2.2    8.0  28.3    1.1  1  Yip1      Yip1 domain


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  28.3   0.00012       2.2      66     162 ..       2     115 ..       1     118 [] 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00012
                              Yip1  66 iiggylglllgllllalllhliakllggkgs.....fkqtlsvvgyallPlilgaliaillllllgt.......... 127
                                       +++++++++++ll+ al ++++a++  g  +      + ++ ++++al+ +++g+++++ ++l+l +          
  gi|336254833|ref|YP_004597940.1|   2 VLASAVVFIASLLIGALGIYVGARVIVGAADydhaiVTALIGAIVWALVGFFIGWIPLLGPILALLAyiavinlryp 78 
                                       56788889*******************9999445555559999999999999999999999999999********** PP

                              Yip1 128 ..llllvgllaliWslvllylglkaahnlskkkalla 162
                                           +++++ +++W++vl++l + aa +++  +a+ +
  gi|336254833|ref|YP_004597940.1|  79 agWTAAAMIGLIAWVTVLVVLYVLAALGITGFNAVGV 115
                                       *988888999999999999999999999988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 920.22
//
Query:       gi|336254834|ref|YP_004597941.1|  [L=512]
Description: carboxypeptidase Taq [Halopiger xanaduensis SH-6]
Scores for complete 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-180  601.1   0.0   1.8e-180  600.9   0.0    1.0  1  Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase
  ------ inclusion threshold ------
       0.19   12.2   0.2       0.75   10.3   0.1    2.0  2  DsrC           DsrC like protein


Domain annotation for each model (and alignments):
>> Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.9   0.0    2e-184  1.8e-180       2     488 .]      21     503 ..      20     503 .. 0.98

  Alignments for each domain:
  == domain 1  score: 600.9 bits;  conditional E-value: 2e-184
                     Peptidase_M32   2 lkellkkvsalesasallewDketvmpkkgaearaeqlatLselahelltseevaellekleeekeeldekekavve 78 
                                       ++++++++s++ +a+++l wD+e+vmp +g+ ara+ql+tLs+++hellt++e++elle+le++++++  +++avv+
  gi|336254834|ref|YP_004597941.1|  21 FESRVQRISNVGNAAGILRWDQEVVMPDEGTPARAQQLSTLSSISHELLTADETGELLEELEADELDD--ERAAVVR 95 
                                       68899*********************************************************998866..59***** PP

                     Peptidase_M32  79 elkreykkakkvpaelvealakasakaeaaWreareandfalfepsLeevielkreiaelledlkkspYdaLldeye 155
                                       e++r+y+++++vp+elve++++ +a+a+ +W++a+e++df++f+p Le+++elkr++a+++ d++ +pY++L+ eye
  gi|336254834|ref|YP_004597941.1|  96 EIRRQYDRETSVPQELVEEISETTANAHPKWKQAKEEDDFETFAPVLEKLVELKRDYAHHV-DPDADPYEVLFAEYE 171
                                       *************************************************************.*************** PP

                     Peptidase_M32 156 pgltvekidalFeelkealvpllkkikeskekekkdksflereipeekqrelsrellkalgfdfdrgrldeseHPFt 232
                                       p ++ e+ +++ e+l+++lvpl++++  s+++ ++d   +++e++ ++q++l+r++l+ lg+d+drgrld++ HPF+
  gi|336254834|ref|YP_004597941.1| 172 PYIDLETAERVLENLRDELVPLIEAVDGSDAELTTD--AFAGEFDDDDQEALARDVLDSLGYDWDRGRLDTAPHPFS 246
                                       ******************************976655..78************************************* PP

                     Peptidase_M32 233 tsfsrkDvRittryeednllsslfsvlHEaGHalYeqnlpeelsktplgggvslgihEsqSrlyEniigrskeFwev 309
                                       ++ ++ D+R+ttr+eed+ll s+ s++HE+GHa Y+++lp+e ++tplg++++l++hEsqSrl+En++grs+ Fwe+
  gi|336254834|ref|YP_004597941.1| 247 SG-TQFDARVTTRFEEDDLLGSITSTIHEFGHANYTLGLPDEGYGTPLGEARDLSVHESQSRLWENHVGRSRPFWEH 322
                                       **.88************************************************************************ PP

                     Peptidase_M32 310 llpklkeafpeqlddvsleefyeavnkveps.liRveADEltYslHillRyelEkeliegklsvkdlpeaWnekyke 385
                                       +lp+  e+fpe l+dv+ ee yea+n+v    liRveADEltY+lHi++R+e+E++li+g+l+v+d+pe+Wn+ky+e
  gi|336254834|ref|YP_004597941.1| 323 FLPIAAERFPE-LEDVTPEEAYEAANQVYDDnLIRVEADELTYHLHIVIRFEIERDLISGDLEVEDVPEVWNDKYEE 398
                                       ***********.666*************7766********************************************* PP

                     Peptidase_M32 386 yLgidppddaeGvLQDvHWssgafGYFPtYalGniyaaqlfeamekdlpel..eiakgefseikkWLkenihqkGsl 460
                                       yLg++p++daeG+LQD+HWs+g+fGYFPtY+lG+++aaql+ a+e +l +l  ++++ +f+ ++ WL+en+h++G+ 
  gi|336254834|ref|YP_004597941.1| 399 YLGVRPETDAEGCLQDIHWSHGSFGYFPTYSLGSVLAAQLYAAAEDELGDLddDVREADFDALNGWLRENVHRHGKQ 475
                                       ************************************************9999999********************** PP

                     Peptidase_M32 461 ysseellkkatgeslnaeyyidyLkeky 488
                                       y++++l+++atge+l+a+++++y++eky
  gi|336254834|ref|YP_004597941.1| 476 YETQDLIRRATGEELTADHFLEYVEEKY 503
                                       ***************************9 PP

>> DsrC  DsrC like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   8.4e-05      0.75      27      72 ..      76     119 ..      65     133 .. 0.74
   2 ?   -2.6   0.0      0.89     8e+03       6      21 ..     403     417 ..     398     420 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.4e-05
                              DsrC  27 ealakeegieLteehwevikflreyyeeygvapairklvkalkkel 72 
                                       e l + e  eL++e+  v++ +r++y+++  +p+  +lv+++++++
  gi|336254834|ref|YP_004597941.1|  76 ELLEELEADELDDERAAVVREIRRQYDRETSVPQ--ELVEEISETT 119
                                       556666666********************99996..4555555433 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.89
                              DsrC   6 eieldeegfLkdledw 21 
                                       + e+d+eg L+d+ +w
  gi|336254834|ref|YP_004597941.1| 403 RPETDAEGCLQDI-HW 417
                                       6689999999998.45 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 4093.02
//
Query:       gi|336254835|ref|YP_004597942.1|  [L=89]
Description: hypothetical protein Halxa_3452 [Halopiger xanaduensis SH-6]
Scores for 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:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 722.42
//
Query:       gi|336254836|ref|YP_004597943.1|  [L=248]
Description: 3-oxoacyl-(acyl-carrier-protein) reductase [Halopiger xanaduensis SH-6]
Scores for 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-52  176.3   0.1    6.1e-52  175.9   0.1    1.1  1  adh_short        short chain dehydrogenase
    1.7e-41  142.4   0.4    2.2e-41  142.0   0.4    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.3e-12   48.0   0.0      2e-12   47.4   0.0    1.2  1  KR               KR domain
     0.0006   19.4   0.1     0.0014   18.1   0.1    1.7  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00072   19.5   0.3     0.0029   17.6   0.2    2.1  1  ADH_zinc_N       Zinc-binding dehydrogenase
     0.0069   15.6   0.0      0.012   14.8   0.0    1.4  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
       0.44   10.2   1.2       0.95    9.2   1.2    1.5  1  FeS              Putative Fe-S cluster


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 !  175.9   0.1   2.4e-55   6.1e-52       2     188 ..      11     197 ..      10     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 175.9 bits;  conditional E-value: 2.4e-55
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgk 77 
                                       v +vtGassGIG a+++++a++Ga+vv+++rsee+l+e+a+ l+ e g + l+++++v+++++v+al+++ v+ +g+
  gi|336254836|ref|YP_004597943.1|  11 VTIVTGASSGIGEATCRAFAAAGANVVLASRSEEPLRETAADLETEhGVETLVVPTNVREEDDVDALIDETVDAFGG 87 
                                       689************************************************************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       +dvLvnNAG+++ +++++ls ee+e + e+N+ gvf +tra++p+ +++++G+ ++v+S ag++p    ++Y+AsK+
  gi|336254836|ref|YP_004597943.1|  88 IDVLVNNAGLSRGSDVEDLSTEEYETMQETNVDGVFYATRAAIPH-VRERNGHLIFVGSFAGQYPRSFNPVYAASKW 163
                                       *********************************************.99***************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHH CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmak 188
                                        v+g+++s+a ++ ++g+ v++v+P+ v++++ +
  gi|336254836|ref|YP_004597943.1| 164 WVRGFAKSVAAQVGDEGVGVTVVNPAEVRSEFET 197
                                       ****************************998876 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 !  142.0   0.4   8.4e-45   2.2e-41       1     222 [.      16     233 ..      16     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 142.0 bits;  conditional E-value: 8.4e-45
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE..EEE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae..vlecDVtdeeqvealveevvekfgklDilv 74 
                                       Ga sgIG+a+ +a+a++Ga+vvl+ ++ee  ++++++l++e+g e  v++++V++e++v+al++e+v+ fg++D+lv
  gi|336254836|ref|YP_004597943.1|  16 GASSGIGEATCRAFAAAGANVVLASRSEEPlRETAADLETEHGVEtlVVPTNVREEDDVDALIDETVDAFGGIDVLV 92 
                                       899***************************9************77666***************************** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg.gsivnlssvgaervvpnynaygaaKaalea 150
                                       nnag ++   ++++++s ee+++++++n+ ++f+ ++aa+p+++e+ g ++ + s++++   + + +y+a+K  + +
  gi|336254836|ref|YP_004597943.1|  93 NNAGLSRG--SDVEDLSTEEYETMQETNVDGVFYATRAAIPHVRERnGHLIFVGSFAGQYPRSFNPVYAASKWWVRG 167
                                       ********..*******************************666555***********99999999*********** PP

                                       HHHHHHHHHGGGTEEEEEEEE--BHCTG.GGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT- CS
                      adh_short_C2 151 ltrylAvelgpkgiRvNavspgpikTla.asgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyi 222
                                       +++++A+++g++g+ v +v p  ++ +  +++ + f e+ +e e       + +p eva+a+ f as+  s i
  gi|336254836|ref|YP_004597943.1| 168 FAKSVAAQVGDEGVGVTVVNPAEVRSEFeTTDGSTFAEVFDEDE-------ASDPAEVADAIRFAASQTHSSI 233
                                       *************************8884333344555555554.......4578899999999999887766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   7.7e-16     2e-12       4     166 ..      13     175 ..      11     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 7.7e-16
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       ++tG+  g+G +++r  a+ ga ++vl sRs+++ ++ +a ++  +++g+e  vv+  v ++d+v al++e  + ++
  gi|336254836|ref|YP_004597943.1|  13 IVTGASSGIGEATCRAFAAAGA-NVVLASRSEEPLRETAADLE--TEHGVETLVVPTNVREEDDVDALIDETVDAFG 86 
                                       8*******************98.699*****655555554443..567***************************** PP

                                       ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT...S--SEEEEEEEHHHHH--TT-HHHHHHHH CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled...esldffvlfSSiagllgsagqanYaaaNa 154
                                        i   ++ Ag++r + +e++++e++e++ +  v+G+    ++  +   e+  +++++ S ag +       Yaa   
  gi|336254836|ref|YP_004597943.1|  87 GIDVLVNNAGLSRGSDVEDLSTEEYETMQETNVDGVFYATRAAIPhvrERNGHLIFVGSFAGQYPRSFNPVYAASKW 163
                                       ************************************9998887666888999**********************999 PP

                                       HHHHHHHHHHHH CS
                                KR 155 flDalaeyrrsq 166
                                       ++ ++a++ ++q
  gi|336254836|ref|YP_004597943.1| 164 WVRGFAKSVAAQ 175
                                       999999887665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   5.6e-07    0.0014       2     122 ..      13     153 ..      12     207 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.6e-07
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHH....H.T- CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerlfke....e.qp 65 
                                       +VtGa+  iG a+++a++++g +v+  +r ++   ++  +dl         +v  ++++++++++l++e    + ++
  gi|336254836|ref|YP_004597943.1|  13 IVTGASSGIGEATCRAFAAAGANVVLASRSEE-PLRETAADLetehgvetLVVPTNVREEDDVDALIDEtvdaFgGI 88 
                                       7**********************999888833.33344444478999999667777777777766666522224578 PP

                                       SEEEE--S.---..HHHHHHSHHHHHH.HHTHHHHHHHHHHHHHTCT...EEEEEEE.GGGGTSC CS
                         Epimerase  66 davihlAa.vgg..vaassedpadfie.knlqgtlnlleaarkagvk...rllflsS.sevYGkd 122
                                       d+ ++ A+   g  v++ s++  ++++ +n+ g+     aa  +  +    l+f++S +  Y+++
  gi|336254836|ref|YP_004597943.1|  89 DVLVNNAGlSRGsdVEDLSTEEYETMQeTNVDGVFYATRAAIPHVRErngHLIFVGSfAGQYPRS 153
                                       99999999654411344444444444448998888888887744222334899999966666644 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   1.1e-06    0.0029       1      67 [.      20      96 ..      20     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHHHHHHTT-EEEEEESSHHHH.HHHHHTTESEEEET........TTCHHHHHHHHHT.T.TSSEEEEEESSC CS
                        ADH_zinc_N  1 gvGlaavqlAkalGaeviavdsseekl.elakklGadeviny........keadlverikelt.g.gegvdvvfecvG 67
                                      g+G a++ + +a+Ga+v+ +++see l e a++l  ++ + +        +e d v+++ + t +  +g+dv ++ +G
  gi|336254836|ref|YP_004597943.1| 20 GIGEATCRAFAAAGANVVLASRSEEPLrETAADLETEHGVETlvvptnvrEE-DDVDALIDETvDaFGGIDVLVNNAG 96
                                      89***********************765777778777766666666899633.4344444444323339999999988 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.7e-06     0.012       2      76 ..      13      81 ..      12     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-06
                                      EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.. CS
                   Polysacc_synt_2  2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel 76
                                      +vtGa+  iG++ +r +++   ++++l +r+E  l e + +le+e+       e+++v ++vr+++ ++ +++e+
  gi|336254836|ref|YP_004597943.1| 13 IVTGASSGIGEATCRAFAAAG-ANVVLASRSEEPLRETAADLETEHGV-----ETLVVPTNVREEDDVDALIDET 81
                                      79*************998876.57999*************99655444.....4445668999999999888753 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.2   0.00037      0.95      10      20 ..      22      32 ..      22      35 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00037
                               FeS 10 GypgCmafAea 20
                                      G+++C+afA+a
  gi|336254836|ref|YP_004597943.1| 22 GEATCRAFAAA 32
                                      9********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2005.61
//
Query:       gi|336254837|ref|YP_004597944.1|  [L=204]
Description: hypothetical protein Halxa_3454 [Halopiger xanaduensis SH-6]
Scores for 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  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1718.68
//
Query:       gi|336254838|ref|YP_004597945.1|  [L=64]
Description: cold-shock DNA-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-19   68.8   0.4    2.9e-19   68.7   0.4    1.0  1  CSD              'Cold-shock' DNA-binding domain
     0.0052   16.5   1.7      0.007   16.0   1.7    1.3  1  OB_RNB           Ribonuclease B OB domain
  ------ inclusion threshold ------
      0.066   13.2   0.2      0.096   12.6   0.2    1.3  1  S1-like          S1-like
      0.067   13.1   0.3      0.074   12.9   0.3    1.1  1  Peptidase_M10_C  Peptidase M10 serralysin C terminal
      0.081   12.8   0.0      0.092   12.6   0.0    1.1  1  Rho_RNA_bind     Rho termination factor, RNA-binding domain


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.4   8.1e-23   2.9e-19       2      65 ..       3      63 ..       2      64 .] 0.97

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 8.1e-23
                                      EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                               CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                      +G+V  fn   g+GFI++ed d+dvF+H+ ++ g +   L+egqe+eF++++  kgp+A+nV++
  gi|336254838|ref|YP_004597945.1|  3 NGKVDFFNHTGGYGFISTEDADDDVFFHMEDVGGAD---LEEGQEIEFDIEQAPKGPRATNVVR 63
                                      79******************************9999...***********************85 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.7   1.9e-06     0.007       6      31 ..      11      36 ..       4      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.9e-06
                                      -SSS-EEEEECT.TEEEEE-HHHHTT CS
                            OB_RNB  6 hkkGFGFlipdegkeDifippeqmkk 31
                                      h  G+GF+++++ ++D+f + e++ +
  gi|336254838|ref|YP_004597945.1| 11 HTGGYGFISTEDADDDVFFHMEDVGG 36
                                      889***************98888765 PP

>> S1-like  S1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   2.7e-05     0.096      14      48 ..      14      53 ..      10      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                           S1-like 14 tfGfv.....DeevfFqrsvvkGrlpkvgdrVlveAvynp 48
                                       +Gf+     D++vfF+++ v G   + g  ++++  + p
  gi|336254838|ref|YP_004597945.1| 14 GYGFIstedaDDDVFFHMEDVGGADLEEGQEIEFDIEQAP 53
                                      58888777779************99999988887765555 PP

>> Peptidase_M10_C  Peptidase M10 serralysin C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.1e-05     0.074      11      43 ..       6      38 ..       2      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                                      EEETT--S--GGGBE-STT----EEE---SS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_M10_C 11 vyGfnsntgrdfysaedasdklifsvWdaGGnd 43
                                      v  fn + g  f+s+eda+d + f + d GG d
  gi|336254838|ref|YP_004597945.1|  6 VDFFNHTGGYGFISTEDADDDVFFHMEDVGGAD 38
                                      556999*************************99 PP

>> Rho_RNA_bind  Rho termination factor, RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.6e-05     0.092       3      60 ..       4      60 ..       2      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                                      EEEEE-TT..S-EEEE-GTT---TT-EEE-CCCCCCTT--TT-EEEEEEE---SSS-SEE CS
                      Rho_RNA_bind  3 GiLeilpd..gygFlRtsnylpgpedvYVsasqirkfgLrtGDaveGkvrppkerekyna 60
                                      G ++++++  gygF+ t+     ++dv+ +++ +   +L +G  +e  + ++ ++ + ++
  gi|336254838|ref|YP_004597945.1|  4 GKVDFFNHtgGYGFISTE---DADDDVFFHMEDVGGADLEEGQEIEFDIEQAPKGPRATN 60
                                      66777765559****997...789*********************999888766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); 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:                         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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 511.04
//
Query:       gi|336254839|ref|YP_004597946.1|  [L=323]
Description: ABC transporter periplasmic protein [Halopiger xanaduensis SH-6]
Scores for complete 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-22   80.7   0.6    1.6e-22   80.3   0.6    1.2  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.059   14.0   0.5       0.12   13.0   0.5    1.5  1  DUF883        Bacterial protein of unknown function (DUF883)
       0.34    9.2   0.3       0.46    8.7   0.3    1.1  1  DUF2070       Predicted membrane protein (DUF2070)


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 !   80.3   0.6   2.7e-26   1.6e-22       1     235 [.       3     264 ..       3     266 .. 0.90

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 2.7e-26
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT.........................TS-BSBESSSB-HHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee.......................aivevgadgeidvEk 54 
                                       i+++ ps tei++alG+++  vgv++ + +p da  +++                       a   +++  ++dvE+
  gi|336254839|ref|YP_004597946.1|   3 IVTTLPSATEIVAALGLEP--VGVSHECDYPPDAASAPAitrsqidadgssgeidaqvldatADEGTDGVYDVDVET 77 
                                       89*****************..************999998899877666666655555554444488888889999** PP

                                       HHHH--SEEEE-GGG..........GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                      Peripla_BP_2  55 laalkPDlvilskgl.......gltdedeellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsk 124
                                       l +l PDl++ +           +++++ e+ +++ + ++ ++ ++ +++ e ++ +g ++g+e++a+++ a+++ +
  gi|336254839|ref|YP_004597946.1|  78 LEELEPDLIVTQGICdvcavdeVVVADAVEQISADPEILTTDPHSV-ADVLEDVERIGRATGREERAREVRADLEAR 153
                                       **********9999999*9999999********************8.****************************** PP

                                       HHHHHHTS-TT....-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEE CS
                      Peripla_BP_2 125 laaaksaidse...kpkpvlvfggadeggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvif 198
                                       +++++++++ +    ++ v++f + d+     +  +++  +l++++g+e+ +a+  ++ + +  + +i ++d ++i+
  gi|336254839|ref|YP_004597946.1| 154 IDRVRERTADLedgERPRVAIFDWTDP----AMIAGHWTAELVEWAGGEYGLADV-GERSRPREWVEIREYDLELIV 225
                                       ***********6666666666666666....555678889*************99.99999**************** PP

                                       EEEH..HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 199 vsgr..aeadnktgleflkenpllaelpAvkngrVyald 235
                                       v+++  + +++ ++  +l e++++a+l+Av++grV+a+d
  gi|336254839|ref|YP_004597946.1| 226 VAPCgfDLEQTAANRTDLTEREGWADLTAVEEGRVWAMD 264
                                       ************************************997 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 ?   13.0   0.5   2.1e-05      0.12       7      53 ..     123     167 ..     118     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                            DUF883   7 leslladleellkeaadeageeaeelRerleerlerarerlrdaeea 53 
                                       ++++l+d+e + +++++  +e a+e+R+ le+r++r+rer++d+e+ 
  gi|336254839|ref|YP_004597946.1| 123 VADVLEDVERIGRATGR--EERAREVRADLEARIDRVRERTADLEDG 167
                                       56788888888887775..789*********************9986 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   0.3   7.7e-05      0.46     459     513 ..     103     157 ..      95     169 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 7.7e-05
                           DUF2070 459 realkevdlevevmTTDtHvvngvslgynpvGekvskdelielvlelvekAiadl 513
                                        +a+++++++ e++TTD H+v  v  +   +G ++ ++e ++ v+   e  i+++
  gi|336254839|ref|YP_004597946.1| 103 ADAVEQISADPEILTTDPHSVADVLEDVERIGRATGREERAREVRADLEARIDRV 157
                                       4555554449*************988******99986666666555444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2467.53
//
Query:       gi|336254840|ref|YP_004597947.1|  [L=174]
Description: Mov34/MPN/PAD-1 family protein [Halopiger xanaduensis SH-6]
Scores for 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-20   72.0   0.1    5.1e-20   71.4   0.1    1.3  1  Prok-JAB  Prokaryotic homologs of the JAB domain
      2e-06   27.8   0.0    2.9e-06   27.3   0.0    1.2  1  JAB       JAB1/Mov34/MPN/PAD-1 ubiquitin protease


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 !   71.4   0.1   5.7e-24   5.1e-20       2     116 ..      21     135 ..      20     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 5.7e-24
                          Prok-JAB   2 esvlsalvaharrahpeEtcGlllgke..seseevivvplvnewsn...rfeipdpedslarlkfearerglevvgi 73 
                                       e+v +a +++ar   p E cG+  g+   ++s+++  +p +n+++    r++i +pe++la    ++++rg+e+vg 
  gi|336254840|ref|YP_004597947.1|  21 EAVRDAVLERARDGRPHEICGVFGGDFdpQRSRVRSQYPAENAAETprtRYRI-NPEEQLAIFE-RLEARGEEIVGF 95 
                                       78999**********************664444444445444444499*****.*********9.************ PP

                          Prok-JAB  74 wHSHpggsarPSetDrrdaaalarvkalliivgdkaeelrawr 116
                                       +HSHp g++rPS+tD ++a  +     +++iv+ ++  + +wr
  gi|336254840|ref|YP_004597947.1|  96 YHSHPRGPPRPSATDAAQATWP---DRSYLIVSLEPFAVGSWR 135
                                       *******************987...899999999666667776 PP

>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   3.2e-10   2.9e-06      16     105 ..      27     110 ..      15     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.2e-10
                                       HHHHHHHHHHHTS--EEEEEEEESSSEEEEEEEEEEESEEEES.SECEEEEEHHHHHHHHHHHHHHHCTT.SEEEEE CS
                               JAB  16 ildhalrtekeeeevmGlliGelnddttveitnvfalpfeete.kdvdavsldqeylekksellkklrgr.ervvGW 90 
                                       +l+ a+ ++    e++G+  G ++ + + ++++ +  +   ++  ++  ++++     ++   +++l++r e++vG+
  gi|336254840|ref|YP_004597947.1|  27 VLERARDGRPH--EICGVFGGDFDPQ-RSRVRSQYPAENAAETpRTRYRINPE-----EQLAIFERLEARgEEIVGF 95 
                                       44555555555..*************.99999888776544330333344443.....569**************** PP

                                       EEESSSS-SS--HHH CS
                               JAB  91 Yhshpditvwlsevd 105
                                       Yhshp     +s+ d
  gi|336254840|ref|YP_004597947.1|  96 YHSHPRGPPRPSATD 110
                                       *****9988888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1398.24
//
Query:       gi|336254841|ref|YP_004597948.1|  [L=68]
Description: hypothetical protein Halxa_3458 [Halopiger xanaduensis SH-6]
Scores for 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:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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: 0.30u 0.19s 00:00:00.49 Elapsed: 00:00:00.32
# Mc/sec: 633.41
//
Query:       gi|336254842|ref|YP_004597949.1|  [L=162]
Description: hypothetical protein Halxa_3459 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.048   14.1   1.7        8.3    6.9   0.0    2.1  2  ZapB      Cell division protein ZapB


Domain annotation for each model (and alignments):
>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.4   0.00069        12      28      64 ..      17      52 ..      16      56 .. 0.85
   2 ?    6.9   0.0   0.00046       8.3      22      46 ..     124     155 ..     122     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00069
                              ZapB 28 eeLkeeneelkeenreleeeneqlkeereawqerlkk 64
                                      eeL+ee  e++  +++le  +e+l++e+  ++ rl++
  gi|336254842|ref|YP_004597949.1| 17 EELREEATEYETIADALEDLVEELRDEPLRQT-RLEG 52
                                      799***********************998765.5555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00046
                              ZapB  22 lLqmeieeLkeeneelkeenrele.......e 46 
                                       +Lq ei+e +++ ++  +++++le       e
  gi|336254842|ref|YP_004597949.1| 124 KLQDEIDEFRRRAAKARQRAAALEdgdgtdaE 155
                                       8*****************99999966665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.59 Elapsed: 00:00:00.32
# Mc/sec: 1491.95
//
Query:       gi|336254843|ref|YP_004597950.1|  [L=503]
Description: sulfatase [Halopiger xanaduensis SH-6]
Scores for 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-47  162.0   0.1    2.9e-47  161.5   0.1    1.2  1  Sulfatase     Sulfatase
    3.4e-12   46.5   0.0      6e-12   45.7   0.0    1.4  1  DUF4976       Domain of unknown function (DUF4976)
    4.1e-10   39.8   0.3    0.00011   21.9   0.0    2.3  2  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
  ------ inclusion threshold ------
       0.01   14.5   0.1      0.015   14.0   0.1    1.1  1  DUF229        Protein of unknown function (DUF229)
       0.16   11.0   1.2       0.63    9.0   0.4    2.2  3  DUF1501       Protein of unknown function (DUF1501)


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.5   0.1   8.2e-51   2.9e-47       1     306 [.      10     377 ..      10     380 .. 0.91

  Alignments for each domain:
  == domain 1  score: 161.5 bits;  conditional E-value: 8.2e-51
                                       EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT.. CS
                         Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg.. 75 
                                       pnv+++l+d+ ++ d ++ +g++ +tp++drl  eg+rf ++ +  + c+ +ra+l+tgr ph +g+ +n+  ++  
  gi|336254843|ref|YP_004597950.1|  10 PNVLFVLTDQERY-DCSAPDGPPVETPTMDRLSSEGMRFERATTPISICTSARASLMTGRFPHGHGMLNNSHEADai 85 
                                       9**********99.66677777777**********************************************9999** PP

                                       .HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHCCTTTSEEEETSSSCHHTCCCCCCCCCECTCCC..... CS
                         Sulfatase  76 .gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyknrgfdrflgfptgsaalkdpekseyngevlrv..... 146
                                        ++lp++ +t+ ell e GY+  + gkwh+g +   + ++  gf+++ g+ +  ++++d  ++ey  e++++     
  gi|336254843|ref|YP_004597950.1|  86 qPNLPPELETFSELLAESGYECSYTGKWHVGRD---QTPEDFGFSYLGGSDKHHDDIDD-AFREYREERGVPlgevd 158
                                       *******************************55...44579****99999999998888.778888777777***** PP

                                       .............................TTTTCSHHHHHHHHHHHHH...HCCC.TSSEEEEEEE-TTSSSTCTCG CS
                         Sulfatase 147 .............................ppeggysddrlldealefl...larn.dkpfflylatlapHappeapd 190
                                                                    +++   + +r  d +++      + + d pff    + +pH+p+ +p+
  gi|336254843|ref|YP_004597950.1| 159 leeelytgddprdggegtfaaaktpvdveETRAWFLAERTIDAIERHAageDEGDrDGPFFHRADFYGPHHPYVVPE 235
                                       **********************9998877666666777777777777799966666********************* PP

                                       GHTCCGSTTTTCCCCCCH............................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGG CS
                         Sulfatase 191 eyakkyatffddgseaar............................qlleaylnsveyvDdligrvlaaLeenglld 239
                                       +ya +y   + d +e ++                            ++ ++y+++v+ +Dd+++r+laaLee  l+d
  gi|336254843|ref|YP_004597950.1| 236 PYASMYDPDEIDPPESYAetydgkpqvhenylhyrgadglewdhwaEATAKYWGFVSLIDDQLDRILAALEERALAD 312
                                       *****87776666666668999999999999********************************************** PP

                                       GEEEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHC.EEECSEEEGGGHHHHHHHH CS
                         Sulfatase 240 ntlvvftSDhgasleesngplrggkganayeggtrvPllvwwpgekap.rvseelvshiDlfptildl 306
                                       +t vv  SDhg+ +   +++ + +kg  +y++ +r+Pl ++w g  +p  + e++v++ Dl +t+l+ 
  gi|336254843|ref|YP_004597950.1| 313 ETAVVHASDHGDFV---GNHRQFNKGPLMYDDTYRIPLQIRWLGVTEPgSTCEAPVHLHDLSATFLEM 377
                                       ************99...4577788888**************************************986 PP

>> DUF4976  Domain of unknown function (DUF4976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   1.7e-15     6e-12       2     102 ..     383     484 ..     382     485 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.7e-15
                           DUF4976   2 padmqGksllpllkgkkkk.....ewrkalyYhyyeyPaehavkrhygvrteryklihfykdidewelyDlkkDpke 73 
                                       p+    +sl+pll++  +      +w ++++ +y+    e      + vrteryk +  y+  d+ elyDl++Dp+e
  gi|336254843|ref|YP_004597950.1| 383 PEAFDARSLVPLLENGGDPaaasvDWPDSTFAQYHGD--EFGLYTQRMVRTERYKYV--YNGPDVDELYDLEADPAE 455
                                       6777778888888765432111126778888887765..667778889*******87..999*************** PP

                           DUF4976  74 lknlyddpeyeevvkelkkkleelrkkyk 102
                                       l+nl+d+p+y++v +el+++l +  ++++
  gi|336254843|ref|YP_004597950.1| 456 LQNLIDHPAYADVRRELREQLVDWMERTD 484
                                       *********************99887766 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0     3e-08   0.00011      20      68 ..      33      80 ..      12      94 .. 0.80
   2 !   15.8   0.1   2.2e-06    0.0081     201     233 ..     291     323 ..     266     333 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3e-08
                                      TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSE CS
                      Phosphodiest 20 llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtf 68
                                      ++p +++L +eg +++   ++  ++  ++ asl+TG++P  HG+ +N+ 
  gi|336254843|ref|YP_004597950.1| 33 ETPTMDRLSSEGMRFE-RATTPISICTSARASLMTGRFPHGHGMLNNSH 80
                                      89**************.666667888899*****************985 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.2e-06
                                       HHHHHHHHHHHHHHHHHTTGTTTEEEEEEES-- CS
                      Phosphodiest 201 lrrvDkaigdLlealderglsaetniilvSDHG 233
                                       ++ +D+ ++++l+al+er l++et+++ +SDHG
  gi|336254843|ref|YP_004597950.1| 291 VSLIDDQLDRILAALEERALADETAVVHASDHG 323
                                       6789****************************9 PP

>> DUF229  Protein of unknown function (DUF229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.1e-06     0.015     288     355 ..     268     335 ..     261     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-06
                            DUF229 288 rysnsrlfgffwsnslshdkfnllealDedllkylkklekkgllentlvlllsDHGlrfgklrktsqG 355
                                       +y++     + ++ + + ++  +++ +D++l ++l +le++ l ++t v+  sDHG  +g++r++ +G
  gi|336254843|ref|YP_004597950.1| 268 HYRGADGLEWDHWAEATAKYWGFVSLIDDQLDRILAALEERALADETAVVHASDHGDFVGNHRQFNKG 335
                                       5666666667778888999999*****************************************99887 PP

>> DUF1501  Protein of unknown function (DUF1501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4   0.00018      0.63     256     302 ..     277     323 ..     260     328 .. 0.89
   2 ?   -1.4   0.0      0.26   9.3e+02     347     361 ..     362     376 ..     356     380 .. 0.86
   3 ?   -2.3   0.0       0.5   1.8e+03     352     385 ..     453     486 ..     445     488 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00018
                           DUF1501 256 WDtHsnlekahkklakelDqalaaLlkdLkqrGllddTlVvwagEFG 302
                                       WD+ ++  ++    +  +D+ l+  l++L++r l d+T+Vv a++ G
  gi|336254843|ref|YP_004597950.1| 277 WDHWAEATAKYWGFVSLIDDQLDRILAALEERALADETAVVHASDHG 323
                                       999999999999999999**************************987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.26
                           DUF1501 347 enpvhvrdlhatilh 361
                                       e pvh++dl+at l 
  gi|336254843|ref|YP_004597950.1| 362 EAPVHLHDLSATFLE 376
                                       789*********985 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.5
                           DUF1501 352 vrdlhatilhllgldherltyatlgrpfrltdeg 385
                                       +++l   i+h+   d +r++ + l ++++ td+ 
  gi|336254843|ref|YP_004597950.1| 453 PAELQNLIDHPAYADVRRELREQLVDWMERTDDP 486
                                       667888899********************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); 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:                         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: 00:00:00.38
# Mc/sec: 3946.81
//
Query:       gi|336254844|ref|YP_004597951.1|  [L=79]
Description: hypothetical protein Halxa_3461 [Halopiger xanaduensis SH-6]
Scores for 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:                       607  (0.0338558); 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:                         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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 629.89
//
Query:       gi|336254845|ref|YP_004597952.1|  [L=177]
Description: DoxX family protein [Halopiger xanaduensis SH-6]
Scores for 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-07   31.5  10.6      2e-07   31.5  10.6    1.6  2  DoxX      DoxX
    8.4e-06   25.8   7.9    4.8e-05   23.3   7.9    1.9  1  DoxD      TQO small subunit DoxD


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5  10.6   2.2e-11     2e-07       3      78 ..      29     119 ..      27     123 .. 0.82
   2 ?   -3.0   0.4       1.3   1.2e+04      71      81 ..     138     148 ..     136     152 .. 0.52

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.2e-11
                              DoxX   3 lllRlllgvlfiahGlqkltg..fglegtaasla....alglpp...........pellaylaalvElvgglllllG 62 
                                        l+Rl++g+ f+++G++k+     ++ ++a++la    +++  p            e++ +++ l+E++ gl+l+lG
  gi|336254845|ref|YP_004597952.1|  29 VLIRLVVGYWFLHAGWGKFAFvaGEPFDAAGYLAnaetPIM--PlfefvvgtpwlLEFTNVMIPLGEFLIGLGLILG 103
                                       689*****************777444457777774423333..25589999988889999***************** PP

                              DoxX  63 lltRlaAlalavtllv 78 
                                        l+RlaA++  v+++ 
  gi|336254845|ref|YP_004597952.1| 104 ALVRLAAFFGGVLMVL 119
                                       **********999986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.3
                              DoxX  71 alavtllvatl 81 
                                       +l++++lv ++
  gi|336254845|ref|YP_004597952.1| 138 GLLMFVLVGVF 148
                                       45555555444 PP

>> DoxD  TQO small subunit DoxD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   7.9   5.3e-09   4.8e-05       4     145 ..      30     161 ..      26     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.3e-09
                              DoxD   4 ilRlalgliflsagirkkvlkpakLdP.nsssyvGgkliefLpqa.siikdlleivvlnrsllvtalvlftlvEiiv 78 
                                        +Rl++g  fl+ag+ k     +  +P +++         +L++a ++i +l+e+vv ++ ll  + v++ l E ++
  gi|336254845|ref|YP_004597952.1|  30 LIRLVVGYWFLHAGWGKFAFVAG--EPfDAA--------GYLANAeTPIMPLFEFVVGTPWLLEFTNVMIPLGEFLI 96 
                                       57888888888888877766664..231333........467777699***************************** PP

                              DoxD  79 GlllliGlltRlssl.vafalalgialsayWlgstcedEyqiglllvaaelvliltgsgklslDylll 145
                                       Gl l++G l Rl+++ + + + l ++  a W +   ++   +gll+ +  lv ++ +++ l++D++l 
  gi|336254845|ref|YP_004597952.1|  97 GLGLILGALVRLAAFfGGVLMVLFYLGNADWANG-YVNGDLLGLLMFV--LVGVFAAGRILGVDAYLE 161
                                       *************9736677777787799**999.3444344554443..23356667777***9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1504.06
//
Query:       gi|336254846|ref|YP_004597953.1|  [L=432]
Description: Histidyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-53  181.0   0.1    3.9e-53  180.7   0.1    1.1  1  tRNA-synt_His   Histidyl-tRNA synthetase
    1.1e-13   51.2   1.1      2e-13   50.3   0.2    1.8  2  HGTP_anticodon  Anticodon binding domain
      1e-08   35.4   0.0    1.3e-08   35.1   0.0    1.3  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
     0.0031   17.0   0.0      0.006   16.1   0.0    1.4  1  tRNA-synt_2d    tRNA synthetases class II core domain (F)


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 !  180.7   0.1   8.7e-57   3.9e-53       1     306 [.       7     315 ..       7     319 .. 0.91

  Alignments for each domain:
  == domain 1  score: 180.7 bits;  conditional E-value: 8.7e-57
                                       T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCC.HHHS-EEE-TTSSEEEE-SSSHHHHH CS
                     tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgaged.ldqtfklvDqsgrllglRaDiTpqva 76 
                                       g+rd++p e+++++e   +l d+++++G++++ +P lE+ +  ++++g d  d+++ + Dq gr + l +++Tp va
  gi|336254846|ref|YP_004597953.1|   7 GFRDFYPGEMAARRETIDTLEDTARRYGFREIGTPALERAEMWTDKSGDDiVDELYSFEDQGGRHVTLTPELTPTVA 83 
                                       89************************************************4469*********************** PP

                                       HHHHHHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTS..SSEEEE CS
                     tRNA-synt_His  77 Riaahrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagv..kelrld 150
                                       R++    +  ++p ++ +  + +r ++ ++gr+re++Q+ + ++G++++ead+E+l  +++al   +g+  +++++ 
  gi|336254846|ref|YP_004597953.1|  84 RMVVAKQQeLSKPIKWFSTRPFWRYEQVQQGRQREFYQTNVDIFGSSEPEADAEILAWAANALT-NLGLtgDHFEFR 159
                                       ***999988******************************************************6.99986689999* PP

                                       EEETCHHHHHHHHTT--HHHHHHHHHHHHCT-H..HHHHHHHHCCTTHHHCCHCC...HCCHCCCHHHHCHCCHCTH CS
                     tRNA-synt_His 151 lghvglvralleaaglsesleeallaalarkdl..aelkelaaeaglkealrellkalelygdaevleealealaaa 225
                                       ++h +++  +le+++ + ++e+a++a+ ++ ++  ae+++l+ eagl+ +++e +  l ++gd e+++    ++a+ 
  gi|336254846|ref|YP_004597953.1| 160 VSHRDILGGVLESYDADVDTEAAIRAVDKSDKIsqAEYHDLLVEAGLDYDQAEEFADLIAGGDLEEVK----SFADT 232
                                       ***************8888888887776555542268899999*****99999998886666655444....47899 PP

                                       HHHHHHHHHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT..-SS-SEEEEEECTTTGGG.T---E CS
                     tRNA-synt_His 226 palqaaldeleelaallealakpevrvtlDlaelrgyeYytGlvFaayaeg..vgqaiarGGrYdelgaaf.grarp 299
                                       ++++aa+d+l+++ +++e+++ ++  +++ l   rg++YytG+vF+++ +   v++ i +GGrYd+l+++f g++ p
  gi|336254846|ref|YP_004597953.1| 233 ERVTAAVDNLQNVLEAAEDFG-ARDYCSISLETARGLDYYTGVVFECFDSTgeVSRSIFGGGRYDDLIESFgGQPTP 308
                                       99******************9.6899**********************97544788********************* PP

                                       EEEEEEE CS
                     tRNA-synt_His 300 AtGfsld 306
                                       A+G ++ 
  gi|336254846|ref|YP_004597953.1| 309 AVGVAVG 315
                                       ****986 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       0.9     4e+03      70      92 ..     225     247 ..     223     249 .. 0.84
   2 !   50.3   0.2   4.4e-17     2e-13      15      89 ..     347     421 ..     337     425 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.9
                                       EEEETTTCEEEEEETTHHHHHHH CS
                    HGTP_anticodon  70 tvrdrdtreqervsldelveklk 92 
                                       +v++++++e+++ ++d+l ++l+
  gi|336254846|ref|YP_004597953.1| 225 EVKSFADTERVTAAVDNLQNVLE 247
                                       58899999999999999988876 PP

  == domain 2  score: 50.3 bits;  conditional E-value: 4.4e-17
                                       HHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHH CS
                    HGTP_anticodon  15 eeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelve 89 
                                         +a ++ +eLr+ g  ve d  ++s+g ++++ad ++   +v+vGe++le+++vt++d+++++q +v++de+++
  gi|336254846|ref|YP_004597953.1| 347 RSEAARITRELRERGHVVETDVAGRSFGAQLNYADSINAETVVIVGEQDLENDEVTIKDMESGDQTQVPVDEFPG 421
                                       46899*******************************************************************986 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 !   35.1   0.0   2.8e-12   1.3e-08       1     110 [.      62     195 ..      62     394 .. 0.67

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.8e-12
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskr.LPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasl 76 
                                       Y +ed+ +r  +L P+ ++t+++++  +  +++   P+k + + + +R+E+  ++G  R+reF q +  +f++ +  
  gi|336254846|ref|YP_004597953.1|  62 YSFEDQGGRHVTLTPELTPTVARMVVAK--QQELsKPIKWFSTRPFWRYEQV-QQG--RQREFYQTNVDIFGSSE-- 131
                                       99***********************988..333336****************.9**..***************99.. PP

                                       HHHHHHHHHHHHHHHHHTT.SCEEEEEEGTTSC..............................B CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............................x RF
                      tRNA-synt_2b  77 ddslrdlikaisriferlglefraiielmsaks..............................a 110
                                       ++ +++++  +++ + +lgl   + +   s  +                              a
  gi|336254846|ref|YP_004597953.1| 132 PEADAEILAWAANALTNLGLTGDHFEFRVSHRDilggvlesydadvdteaairavdksdkisqA 195
                                       99****************9987433333222222334443333333333333333333333330 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 !   16.1   0.0   1.3e-06     0.006      11     129 ..      11     124 ..       4     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-06
                                       TSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SST CS
                      tRNA-synt_2d  11 ieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRtht 87 
                                        ++g++ + +++++ ++++ +++gf+e+  p +e+        ++  d++  d+ d +y  +++    ++++L    
  gi|336254846|ref|YP_004597953.1|  11 FYPGEMAARRETIDTLEDTARRYGFREIGTPALERA-------EMWTDKSGDDIVDELYSFEDQG--GRHVTLTPEL 78 
                                       5678888889999999************99999665.......4556778889999999988888..889******* PP

                                       HHHHHHHH....TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEE CS
                      tRNA-synt_2d  88 tavqirtl....ekkkppikiisigrvfRrdavDathlaeFhqveg 129
                                       t++ +r++    ++ ++pik +s    +R ++v + ++ eF+q + 
  gi|336254846|ref|YP_004597953.1|  79 TPTVARMVvakqQELSKPIKWFSTRPFWRYEQVQQGRQREFYQTNV 124
                                       ********986666679**************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3499.60
//
Query:       gi|336254847|ref|YP_004597954.1|  [L=199]
Description: hypothetical protein Halxa_3464 [Halopiger xanaduensis SH-6]
Scores for 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   18.3   0.1     0.0018   18.0   0.1    1.2  1  Asn_synthase  Asparagine synthase


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 !   18.0   0.1     1e-07    0.0018      19      92 ..       2      71 ..       1     106 [. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1e-07
                      Asn_synthase 19 pvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdvi 92
                                      ++G+l S G DS+l a l+ ++   +++ ++ +f    sd+ ++a+e+a++lg e  +l+l+++ + +a++ ++
  gi|336254847|ref|YP_004597954.1|  2 ELGLLYSAGKDSTLAALLLEEFY--DVTLVTGHF--GISDDWQHARETADALGFEFERLELDPDVAREAVDVML 71
                                      689999***************99..799999999..99*****************999**99976655444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1611.56
//
Query:       gi|336254848|ref|YP_004597955.1|  [L=116]
Description: DNA-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-26   92.4  14.2    2.4e-26   92.2  14.2    1.0  1  dsDNA_bind    Double-stranded DNA-binding domain
  ------ inclusion threshold ------
      0.011   16.2   0.1       0.02   15.4   0.1    1.8  1  PCI           PCI domain
       0.12   12.8  10.3      0.057   13.9   7.6    1.6  2  T3SSipB       Type III cell invasion protein SipB
        2.3    9.1   6.5         71    4.3   0.4    3.0  3  VAPB_antitox  Putative antitoxin


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 !   92.2  14.2   5.4e-30   2.4e-26       1     109 [.      13     114 ..      13     116 .] 0.90

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 5.4e-30
                                       XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                        dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaq 77 
                                       +r+++++elq++a+s++g   +++q+++qq+  +e++k+a+L++ L+++Ar+RL++++++kp+  e+ve ++i+la+
  gi|336254848|ref|YP_004597955.1|  13 LREQKMEELQERAESQQG---GEAQEAAQQQ--AEAQKKAVLRKHLTDDARKRLNTVKMSKPQFGEQVERQVITLAR 84 
                                       69**********998876...3455555555..89****************************************** PP

                                       --SS-----HHHHHHHHHHHS---XXXXX..X CS
                        dsDNA_bind  78 sGqlrskvteeqLkeLLeqvaekkketkivis 109
                                       sG++++k++++++k+LL++++ ++k+ +i  +
  gi|336254848|ref|YP_004597955.1|  85 SGRIQGKIDDDKMKQLLKELKPDSKSFDI--Q 114
                                       **********************9998888..4 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1   4.6e-06      0.02      70      97 ..      64      95 ..       9     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.6e-06
                                      HTSSH....HHHHHHHHHHHHTTSSSEEEETT CS
                               PCI 70 ldlsv....devEkilvklIrdgeirakidqe 97
                                      +++s+    ++vE+ +++l r+g+i++kid  
  gi|336254848|ref|YP_004597955.1| 64 VKMSKpqfgEQVERQVITLARSGRIQGKIDDD 95
                                      4555577779********************86 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 ?   13.9   7.6   1.3e-05     0.057      89     142 ..       9      62 ..       5      81 .. 0.88
   2 ?   -0.8   0.0      0.44     2e+03      85      97 ..      96     108 ..      73     113 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                                       HHTT---------CHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           T3SSipB  89 rlkeLaPdePekakleaaeqQagaaadalqadealqKkldaasklsekakakek 142
                                       rl+eL  ++ e  + +a++qQ g+a++a+q+++ +qKk    + l+++a++  +
  gi|336254848|ref|YP_004597955.1|   9 RLEELREQKMEELQERAESQQGGEAQEAAQQQAEAQKKAVLRKHLTDDARKRLN 62 
                                       899999999999999**********************************87554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.44
                                       HHHHHHTT----- CS
                           T3SSipB  85 eaqkrlkeLaPde 97 
                                       + ++ lkeL+Pd+
  gi|336254848|ref|YP_004597955.1|  96 KMKQLLKELKPDS 108
                                       3445677887776 PP

>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.4     0.042   1.9e+02      30      67 ..      10      46 ..       7      48 .. 0.78
   2 ?    3.2   0.0     0.035   1.6e+02       5      29 ..      53      77 ..      52      87 .. 0.85
   3 ?    4.3   0.4     0.016        71       7      24 ..      95     112 ..      91     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.042
                      VAPB_antitox 30 Llekkkkgkkkellelfgilseeeadeiekaskelrke 67
                                      L e+ +++k +el e +++ +  ea+e  ++  e++k+
  gi|336254848|ref|YP_004597955.1| 10 L-EELREQKMEELQERAESQQGGEAQEAAQQQAEAQKK 46
                                      3.4556667789******99999999998888888876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.035
                      VAPB_antitox  5 IsdevYekLkklKregeSFsdvIer 29
                                      ++d++ ++L  +K  +  F + +er
  gi|336254848|ref|YP_004597955.1| 53 LTDDARKRLNTVKMSKPQFGEQVER 77
                                      79***********988777776665 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.016
                      VAPB_antitox   7 devYekLkklKregeSFs 24 
                                       d  ++ Lk+lK + +SF+
  gi|336254848|ref|YP_004597955.1|  95 DKMKQLLKELKPDSKSFD 112
                                       5578899**********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2675  (0.1492); expected 358.6 (0.02)
Passed bias filter:                      865  (0.0482459); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 907.45
//
Query:       gi|336254849|ref|YP_004597956.1|  [L=163]
Description: 30S ribosomal protein S19e [Halopiger xanaduensis SH-6]
Scores for 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-46  156.5   0.0    3.6e-46  156.3   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
  ------ inclusion threshold ------
      0.016   14.8   0.2      0.094   12.4   0.1    2.3  3  GntR            Bacterial regulatory proteins, gntR family
      0.036   14.4   0.0       0.33   11.3   0.0    2.1  2  Rrf2            Transcriptional regulator
       0.13   12.2   1.0       0.67    9.9   0.1    2.4  3  HTH_12          Ribonuclease R winged-helix domain


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 !  156.3   0.0     8e-50   3.6e-46       1     136 [.      15     152 ..      15     153 .. 0.94

  Alignments for each domain:
  == domain 1  score: 156.3 bits;  conditional E-value: 8e-50
                                       TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS CS
                    Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGg 77 
                                       t++dVpa++li+alae L+++  l+ P+wa+++Ktg+ +el+pe+ed++ +RaAs+lRkv+ rgpvGverl+++YGg
  gi|336254849|ref|YP_004597956.1|  15 TMYDVPADALIEALAEDLEER--LDEPDWAQFAKTGVDRELPPEQEDFWATRAASLLRKVADRGPVGVERLATEYGG 89 
                                       78****************998..*****************************************************8 PP

                                       --....-----THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
                    Ribosomal_S19e  78 kk....rrgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                                        k    r  v+p++ +++s+++ir+ilqqLe+ +lv++++++grr+t++Gq+lld +a++v++
  gi|336254849|ref|YP_004597956.1|  90 GKpgsnRYRVAPDKRSDGSRNLIRTILQQLEEEDLVETAEGEGRRVTPEGQSLLDDTAGTVLE 152
                                       7622215677************************************************99975 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.67     3e+03       3      12 ..      26      35 ..      17      41 .. 0.62
   2 ?   -2.4   0.0      0.87   3.9e+03      27      37 ..      80      90 ..      78      92 .. 0.79
   3 ?   12.4   0.1   2.1e-05     0.094      36      64 .]     107     135 ..     103     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.67
                                      HHHHHHHHHH CS
                              GntR  3 eqvyerLred 12
                                      e+++e L+e+
  gi|336254849|ref|YP_004597956.1| 26 EALAEDLEER 35
                                      4444555554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.87
                                      HHHHHHHHTS- CS
                              GntR 27 ereLaaefgVs 37
                                      ++ La+e+g +
  gi|336254849|ref|YP_004597956.1| 80 VERLATEYGGG 90
                                      67899999976 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 2.1e-05
                                       S-HHHHHHHHHHHHHTTSEEEETTCEEEE CS
                              GntR  36 VsrttvReALrrLeaeglverrqgrGtfV 64 
                                        sr+ +R  L++Le+e+lve   g+G +V
  gi|336254849|ref|YP_004597956.1| 107 GSRNLIRTILQQLEEEDLVETAEGEGRRV 135
                                       699**********************9876 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.19   8.7e+02      10      35 ..      62      87 ..      57      91 .. 0.86
   2 ?   11.3   0.0   7.5e-05      0.33      36      62 ..     106     132 ..     102     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.19
                                      HHHHHHHHHHSSTCC-B-HHHHHHHH CS
                              Rrf2 10 alhallyLakeeeeepvsseeiaerq 35
                                      a++a   L k ++++pv +e +a+++
  gi|336254849|ref|YP_004597956.1| 62 ATRAASLLRKVADRGPVGVERLATEY 87
                                      78888899999999999999999876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.5e-05
                                       TS-HHHHHHHHHHHHHTTSEEEETTT- CS
                              Rrf2  36 nispsylekilakLrkaglvksvrGkg 62 
                                       + s++ ++ il++L++++lv++ +G g
  gi|336254849|ref|YP_004597956.1| 106 DGSRNLIRTILQQLEEEDLVETAEGEG 132
                                       66899********************84 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 ?   -0.8   0.1      0.33   1.5e+03      17      28 ..      26      38 ..      21      39 .. 0.83
   2 ?   -2.0   0.0      0.79   3.5e+03      12      22 ..      76      86 ..      68      87 .. 0.76
   3 ?    9.9   0.1   0.00015      0.67      35      66 .]     112     143 ..     102     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.33
                            HTH_12 17 keiaeeLkkr.gy 28
                                      +++ae+L++r ++
  gi|336254849|ref|YP_004597956.1| 26 EALAEDLEERlDE 38
                                      5799999999776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.79
                            HTH_12 12 kpigakeiaee 22
                                       p+g +++a+e
  gi|336254849|ref|YP_004597956.1| 76 GPVGVERLATE 86
                                      48999999986 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00015
                            HTH_12  35 vRyrLrkleergltrrvgyagreltEkGleeL 66 
                                       +R  L+ lee++l++     gr++t  G ++L
  gi|336254849|ref|YP_004597956.1| 112 IRTILQQLEEEDLVETAEGEGRRVTPEGQSLL 143
                                       8999*********************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); 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:                         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 0.21s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1359.12
//
Query:       gi|336254850|ref|YP_004597957.1|  [L=300]
Description: thiamine-monophosphate kinase [Halopiger xanaduensis SH-6]
Scores for 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-19   68.9   1.9      1e-18   67.7   1.9    1.6  1  AIRS      AIR synthase related protein, N-terminal domain
    3.8e-16   59.6   0.7    9.9e-16   58.3   0.1    1.8  2  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 !   67.7   1.9   1.2e-22     1e-18       1      93 [.      19     123 ..      19     124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 1.2e-22
                                       SSSE....EEEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHH CS
                              AIRS   1 dDaa....vvvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp.....wleevvr 60 
                                       dDaa    +vvttd     +l e ++f        +G++av++ lsD+aamGA+ +a++ ++a+p     +l ++vr
  gi|336254850|ref|YP_004597957.1|  19 DDAAavdgLVVTTD-----MLHERTDFpdgttrytAGWRAVGASLSDVAAMGADATAAVAAYAVPefdrdELLAFVR 90 
                                       899977777*****.....********************************************************** PP

                                       HHHHHHHHTT-EEEEEEEEEESSEEEEEEEEEE CS
                              AIRS  61 glaeaaeelgvplvgGdtsfsneptisvtavGl 93 
                                       g +e +e +g++ vgGd+ +++e+t+++ta+G 
  gi|336254850|ref|YP_004597957.1|  91 GAREVCELVGAEYVGGDLDEHEEFTVATTAIGR 123
                                       ********************************6 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 ?   -0.6   0.0      0.14   1.3e+03     110     143 ..      68     100 ..      13     103 .. 0.76
   2 !   58.3   0.1   1.1e-19   9.9e-16       1     150 [.     134     282 ..     134     287 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.14
                                       STTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEE CS
                            AIRS_C 110 ensGrllvavppeeadavlaileeeglpeaavIG 143
                                       ++  +   avp+ ++d++la ++ +++  ++ +G
  gi|336254850|ref|YP_004597957.1|  68 ATAAVAAYAVPEFDRDELLAFVRGARE-VCELVG 100
                                       556666677788888888888888887.477666 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 1.1e-19
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgala 77 
                                       +pGd++ +tg+lG  +ag+ l r+ ++e++     +   d+++ + ++++ ra a    +++a+ D ++ GL+ +l+
  gi|336254850|ref|YP_004597957.1| 134 EPGDLVCVTGTLGRSAAGLELFRRADREDDAS-LRERANDLFRFEPRVRAGRAFAP---HATAMMDSSD-GLARSLH 205
                                       69****************99999998888854.25559*****************9...8*********.8****** PP

                                       HHHHTTTEEEEEECGTHHHHHHHH.......HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEEE CS
                            AIRS_C  78 emapasgvgaeidldkvpifdele.......splemllsensGrllvavppeea.davlaileeeglpeaavIGevt 146
                                       ++a as++g+ i++d+vpi d ++       ++le++ ++ +   lva +pe+a +av+++ +   +   +vIG v+
  gi|336254850|ref|YP_004597957.1| 206 QLAGASNCGFAIESDAVPIADAVRdvadgerEALEYATTFGEDFELVATVPEDAlEAVRSESN---V-AISVIGAVV 278
                                       ******************************************************555555555...4.69******* PP

                                       ESSS CS
                            AIRS_C 147 akee 150
                                       ++++
  gi|336254850|ref|YP_004597957.1| 279 DSDD 282
                                       9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 2515.64
//
Query:       gi|336254851|ref|YP_004597958.1|  [L=384]
Description: peptidase M50 [Halopiger xanaduensis SH-6]
Scores for 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-13   50.1  10.1    6.4e-07   28.9   0.3    2.3  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 !   24.0   4.7   1.1e-09     2e-05       2     109 ..     134     223 ..     133     252 .. 0.86
   2 !   28.9   0.3   3.5e-11   6.4e-07     189     227 ..     262     300 ..     246     312 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.1e-09
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallp....LGGyVkmageepeeelsee 74 
                                       f + ++ ++ +HE+GH+++ + ++v                   +++Y+i++      +G+++km+g  p+++    
  gi|336254851|ref|YP_004597958.1| 134 FTVSILGVLGIHEMGHYVMSRYHNVDA-----------------SLPYFIPIPTligtMGAVIKMKGRIPNRK---- 189
                                       788999999****************99.................789***999999999**********9988.... PP

                                       ....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..........- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........x RF
                     Peptidase_M50  75 eakaflkkspwqrllivlAGplanfilailvfvv..........p 109
                                                  + + i +AGpla+++ +++v vv          p
  gi|336254851|ref|YP_004597958.1| 190 -----------ALFDIGVAGPLAGLVATVIVTVVglhlppvtapP 223
                                       ...........99******************99866666555541 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 3.5e-11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 189 ssflqllalisvnLgilNLlPipvLDGghllfalleair 227
                                        +++ +  ++++ +++lNL+P+ +LDGgh+l+a+  +++
  gi|336254851|ref|YP_004597958.1| 262 VNPVVIGGWVGMFITFLNLIPVGQLDGGHILRAMAGEMQ 300
                                       57888999*************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2900.36
//
Query:       gi|336254852|ref|YP_004597959.1|  [L=81]
Description: hypothetical protein Halxa_3469 [Halopiger xanaduensis SH-6]
Scores for 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  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 661.06
//
Query:       gi|336254853|ref|YP_004597960.1|  [L=39]
Description: hypothetical protein Halxa_3470 [Halopiger xanaduensis SH-6]
Scores for 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:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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: 0.29u 0.22s 00:00:00.51 Elapsed: 00:00:00.34
# Mc/sec: 338.59
//
Query:       gi|336254854|ref|YP_004597961.1|  [L=283]
Description: molybdopterin biosynthesis MoaE protein [Halopiger xanaduensis SH-6]
Scores for complete 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-24   86.1   0.4    3.7e-24   85.2   0.4    1.5  1  MoaE      MoaE protein
  ------ inclusion threshold ------
      0.035   14.2   0.1      0.072   13.2   0.1    1.6  1  DUF3906   Protein of unknown function (DUF3906)


Domain annotation for each model (and alignments):
>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.4   4.1e-28   3.7e-24      10     112 ..     158     262 ..     147     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 4.1e-28
                                       HHHHHH--TT--EEEEEEEE------..TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEEETTS CS
                              MoaE  10 eiealvaspkaGAvvlFvGtvRdsfd..gkkvteLeyeayepmaektleeiaeearerwelervavvHrlGelevge 84 
                                       +++++ + ++ GA+++F+G vR +    +++++ Le+e ye++a + +++i +e++er ++ +v ++Hr+G +e ge
  gi|336254854|ref|YP_004597961.1| 158 DVKRSPKADRSGAIATFTGRVRAKDAadDARTQYLEFEKYEGVADERMAAIESELEERNGVLEVELYHRTGVVEDGE 234
                                       34455557789***********77657799*********************************************** PP

                                       EEEEEEEEESSHHHHHHHHHHHHHHHHH CS
                              MoaE  85 asvvvavssahRkeafeaceylidelKk 112
                                        +v+v+v + hR+eaf+ +e+ i++lK+
  gi|336254854|ref|YP_004597961.1| 235 DIVYVVVLAGHREEAFRTVEDGINRLKD 262
                                       ***************************8 PP

>> DUF3906  Protein of unknown function (DUF3906)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     8e-06     0.072       9      37 ..     231     259 ..     221     276 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8e-06
                           DUF3906   9 eleeetvsvvvvAendeqAFrqleielek 37 
                                       e  e++v vvv+A   e+AFr +e  +++
  gi|336254854|ref|YP_004597961.1| 231 EDGEDIVYVVVLAGHREEAFRTVEDGINR 259
                                       44599*******************98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 2294.95
//
Query:       gi|336254855|ref|YP_004597962.1|  [L=344]
Description: Capsule synthesis protein, CapA [Halopiger xanaduensis SH-6]
Scores for 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-65  220.3   0.0    3.3e-65  220.1   0.0    1.1  1  PGA_cap         Bacterial capsule synthesis protein PGA_cap
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.032   14.2   0.0    1.7  1  Glyco_transf_4  Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> PGA_cap  Bacterial capsule synthesis protein PGA_cap
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.1   0.0   3.7e-69   3.3e-65       2     257 .]      14     266 ..      13     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: 220.1 bits;  conditional E-value: 3.7e-69
                           PGA_cap   2 lafvGDvmlgralkqalkekeydfdpifaevkpllraaDlaivNlEtpvteegeplsgk...plfrappev.laalk 74 
                                       + f+GDvmlgr ++++ +++  + d +++ v++ l+a D  ++NlE++++++g+++++    ++fra+p   ++al+
  gi|336254855|ref|YP_004597962.1|  14 IGFTGDVMLGRLVDDRQQHR--SVDAVWGTVRERLQALDALVINLECVLSTRGRKWRRTrrpFHFRADPTRaVPALE 88 
                                       789************99988..************************************7789*****99876***** PP

                           PGA_cap  75 eagfdvvslAnNHalDygeeGlletlealdeagikhaGagrseaearkpailevkg....irvallaytegtnstae 147
                                       +ag+dv++lAnNH+lDy+e++l++tle+ldeagi+ aGag++ +ea +pa+ +v+g    ++va+++ t  t++ a 
  gi|336254855|ref|YP_004597962.1|  89 AAGVDVCALANNHVLDYEEAALRDTLEHLDEAGIDRAGAGETIDEALEPAVRRVGGeeaaLDVAVVSLTDNTPEYAA 165
                                       ******************************************************66222255666666644433333 PP

                           PGA_cap 148 akagepnseeakeeeagaskerpgvaskdleklladirear.keadlvivslHwgeeyqekpadeqrelaralidaG 223
                                       ++ ++        ++a ++ + +  ++++ e++++ +++ar + +dl+++slHwg +  e+p++  +e+ r+li++G
  gi|336254855|ref|YP_004597962.1| 166 DETAP--------GTARIEIDVD--DAASIERTREGLERARaTDPDLLVASLHWGPNMVEEPPPAFQEFGRWLIEQG 232
                                       32222........2222222222..22457999999*****978********************************* PP

                           PGA_cap 224 advviGhhpHvlqgieiykgklifYSlGNfifdq 257
                                       +d+v+Gh++Hv qgie+++g +i+Y  G+f++d+
  gi|336254855|ref|YP_004597962.1| 233 VDIVHGHSAHVFQGIEVHDGCPILYDTGDFVDDY 266
                                       *******************************996 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.5e-06     0.032      37      84 ..     194     244 ..     139     257 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.5e-06
                    Glyco_transf_4  37 v...elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaal 84 
                                       +    +   +++  +++++     +++++ + r+l ++++D+vH hs++ +
  gi|336254855|ref|YP_004597962.1| 194 RaraTDPDLLVASLHWGPNMVEEPPPAFQEFGRWLIEQGVDIVHGHSAHVF 244
                                       144456667778888999999999***********************7654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 2867.22
//
Query:       gi|336254856|ref|YP_004597963.1|  [L=249]
Description: uridylate kinase [Halopiger xanaduensis SH-6]
Scores for complete 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-26   93.5   5.2    3.2e-26   92.4   5.2    1.5  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.083   12.9   0.0    1.9  2  DUF2844    Protein of unknown function (DUF2844)


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 !   92.4   5.2   3.6e-30   3.2e-26       1     240 [.       1     202 [.       1     203 [. 0.93

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 3.6e-30
                                       TEEEEEE-TTCCC.CTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHH CS
                         AA_kinase   1 krvVvKlGGsslt.dkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagev 76 
                                       ++vVv +GGs+l  +++++++ + a+ i++l+ +g ++  V+Ggg++++++++++++l ++e+++            
  gi|336254856|ref|YP_004597963.1|   1 MKVVVSIGGSVLVpEPGADRVSEHAAVIEDLVADGCRVGAVVGGGGVAREYISAARDLGANEIEL------------ 65 
                                       789*******99955555*********************************************96............ PP

                                       HHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTT CS
                         AA_kinase  77 atrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeeg 153
                                          d+l++  +rl+a+ll a+l + ++ a a d                   e+  e l ++ v +++g +    + 
  gi|336254856|ref|YP_004597963.1|  66 ---DQLGIDVTRLNARLLIAALGSESVAAPAKD------------------YEEASEALRRDDVCIMGGVA----PA 117
                                       ...*******************88777777655..................789999****9*******77....43 PP

                                       EEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHH CS
                         AA_kinase 154 elgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaala 228
                                       +    ++D + a+lAe+++Ad l+++t+V+GVy+adp++++da++++ +s+ e+ +     e+  g+  ++++ a++
  gi|336254856|ref|YP_004597963.1| 118 Q----TTDAVGAALAEYIDADLLVYATSVPGVYSADPNEDDDATKYDSLSATELVDviAGLEMNAGSSAPVDLLAAK 190
                                       3....8***************************************************9999**************** PP

                                       HHHCTT-EEEEE CS
                         AA_kinase 229 aarrggipvvIt 240
                                       +++r+g++++++
  gi|336254856|ref|YP_004597963.1| 191 IIQRSGMRTIVL 202
                                       ********9997 PP

>> DUF2844  Protein of unknown function (DUF2844)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.11   9.7e+02      23      51 ..      28      55 ..       7      58 .. 0.66
   2 ?   12.9   0.0   9.2e-06     0.083       3      66 ..      82     149 ..      81     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.11
                           DUF2844 23 trsasasaytvrettlasgtvvrEYvtaa 51
                                       +  +a++ +v  ++ ++g v rEY++aa
  gi|336254856|ref|YP_004597963.1| 28 IEDLVADGCRVGAVV-GGGGVAREYISAA 55
                                      444455566776666.6677799*99986 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.2e-06
                           DUF2844   3 AaLGgapssvaadaakl.savtrsasas.....aytvrettlasgtvvrEYvtaagtVFAvaWqGptmpd 66 
                                       AaLG+++ +++a++ +  s++ r+   +     +++  +tt+a g  + EY++a+  V+A +  G   +d
  gi|336254856|ref|YP_004597963.1|  82 AALGSESVAAPAKDYEEaSEALRRD--DvcimgGVAPAQTTDAVGAALAEYIDADLLVYATSVPGVYSAD 149
                                       7899987776666543325555555..134677****************************998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 2079.56
//
Query:       gi|336254857|ref|YP_004597964.1|  [L=572]
Description: Lysyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for complete 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-99  333.8   0.0    1.5e-99  333.4   0.0    1.1  1  tRNA-synt_1f  tRNA synthetases class I (K)
    9.4e-09   34.5   0.0    6.4e-07   28.4   0.0    2.2  2  tRNA-synt_1g  tRNA synthetases class I (M)
     0.0011   18.3   0.0      0.013   14.8   0.0    2.3  3  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
       0.04   13.2   0.0        4.8    6.4   0.0    2.2  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)


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 !  333.4   0.0  3.3e-103   1.5e-99       2     348 ..      41     402 ..      40     411 .. 0.93

  Alignments for each domain:
  == domain 1  score: 333.4 bits;  conditional E-value: 3.3e-103
                      tRNA-synt_1f   2 aWadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvp 78 
                                        Wad++a+++ +++       + +v++ GispSG +H+Gn++e++++ +va+ lr+rg evr+++++Dd D+lRk+p
  gi|336254857|ref|YP_004597964.1|  41 FWADVVADRVEAQE-----PDEPIVIKGGISPSGVPHLGNVNEIMRGFYVAEVLRERGYEVRQVFTADDRDPLRKLP 112
                                       59999999999544.....3479****************************************************** PP

                      tRNA-synt_1f  79 e.............nlpekllekylgkpltsiPdpkgkhesyaehfnaelvesLdelgievefisatelYksglyde 142
                                       +             +++  +l ++lg p+t+iPdp+g+++sy++hf+  +++s d+l++ ++ +s+telY++g +++
  gi|336254857|ref|YP_004597964.1| 113 RtlcdlegnlvdlgEVDAGALGRNLGSPYTDIPDPFGCCDSYGDHFSTIIQDSADALDVPIDLVSNTELYENGDLED 189
                                       ********99999999999********************************************************** PP

                      tRNA-synt_1f 143 aikealenrekikeilekyrgeereetyspylpvcekcgrvdt.tevvevdaeeeeieYkc..........eecGee 208
                                        ++ +le++++ +++l ky +++  e y+p++p+ce+cg++ + ++ v+++ ++ ++eY+c          + cG+e
  gi|336254857|ref|YP_004597964.1| 190 VTRFVLEHQDRARDVLSKY-QDKVDEAYVPFNPICEECGKITEtVTSVDLEGDTPTVEYECtdmdagdqtiDGCGHE 265
                                       *******************.778999**************9641466777788999********************* PP

                      tRNA-synt_1f 209 eevdiregngKLqWkvdwamrWaalgVdfEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkggekmss 284
                                       +++++re  gKL+W+ +w+++W+ lgVdfEp+GkDha+  gS   ++++a ++l++e+P+++vYe+++l+g+   ss
  gi|336254857|ref|YP_004597964.1| 266 GTATLRE--GKLPWRFEWPAQWQELGVDFEPFGKDHAE--GSWPSGQDVArNVLEIEPPVPMVYEWFTLEGE-PFSS 337
                                       ******9..7****************************..******************************99.9*** PP

                      tRNA-synt_1f 285 SkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf...aeqeeeee 348
                                       S+Gnv+ ++d+le++epevlr+++++  P+ka +++++  + +lvde+d+le++yf   +++e+e++
  gi|336254857|ref|YP_004597964.1| 338 SEGNVILVSDVLELLEPEVLRYFFAK-DPTKARDFSIE-RLDQLVDEFDRLEAIYFdeiEADEDERA 402
                                       **************************.***********.*****************54333333333 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 !    3.6   0.0    0.0052        23      11      46 ..      68     103 ..      65     106 .. 0.87
   2 !   28.4   0.0   1.4e-10   6.4e-07     316     367 ..     323     374 ..     303     383 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0052
                                       SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE- CS
                      tRNA-synt_1g  11 ngklHlGhllevisaDifaRykrlrgeevlfvcgtD 46 
                                       +g++HlG++ e++ +  +a   r rg+ev  v   D
  gi|336254857|ref|YP_004597964.1|  68 SGVPHLGNVNEIMRGFYVAEVLRERGYEVRQVFTAD 103
                                       699*************************98775444 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.4e-10
                                       EEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE- CS
                      tRNA-synt_1g 316 vaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfs 367
                                       ++ e++t+eg+ +S+S+g+v+ ++++le l++++lRY++a++  + +D++++
  gi|336254857|ref|YP_004597964.1| 323 MVYEWFTLEGEPFSSSEGNVILVSDVLELLEPEVLRYFFAKDPTKARDFSIE 374
                                       5789************************************999999987654 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 ?    0.2   0.0     0.085   3.8e+02      20      52 ..      68     100 ..      59     107 .. 0.83
   2 !   14.8   0.0     3e-06     0.013     245     284 ..     326     365 ..     322     380 .. 0.83
   3 ?   -3.0   0.0       0.8   3.6e+03      66     113 ..     462     509 ..     457     512 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.085
                                       TS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEE CS
                      tRNA-synt_1e  20 ydashlGhaRslvafDilrrilqalgYdvqfvq 52 
                                           hlG++ +++    ++ +l+ +gY+v+ v 
  gi|336254857|ref|YP_004597964.1|  68 SGVPHLGNVNEIMRGFYVAEVLRERGYEVRQVF 100
                                       5678*******999999************9875 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3e-06
                                       --EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS- CS
                      tRNA-synt_1e 245 ghlkiegekmsksLknfitikdvlkkfdprqlRllllsah 284
                                       ++ ++ege  s s +n+i++ dvl+  +p++lR+++++  
  gi|336254857|ref|YP_004597964.1| 326 EWFTLEGEPFSSSEGNVILVSDVLELLEPEVLRYFFAKDP 365
                                       57899******************************98754 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.8
                                       HHTTS-HHHHHHHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHH CS
                      tRNA-synt_1e  66 reeeksvkelaekfieefkkdleaLnvlkptleprvsekvdeiielve 113
                                        ++ +  +++a +  +ef  +l+  ++   ++ +   e ++e+ +++e
  gi|336254857|ref|YP_004597964.1| 462 LARVERARNWARRTGNEFDYELKRSEIPDHDFDADTEEALEELADFIE 509
                                       556677888999999999999999999999999999999999999997 PP

>> 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 ?    6.4   0.0    0.0011       4.8       3      28 ..      56      81 ..      53      99 .. 0.82
   2 ?    4.6   0.0    0.0038        17     146     256 ..     285     391 ..     283     410 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0011
                                      HS--EEEEEEETSSS-BGGGHHHHHH CS
                      tRNA-synt_1b  3 erplrvysGidPTgklHlGylvplkk 28
                                       +p+ ++ Gi P+g +HlG++  ++ 
  gi|336254857|ref|YP_004597964.1| 56 DEPIVIKGGISPSGVPHLGNVNEIMR 81
                                      5789999************9988876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0038
                                       HHHTCHSEEEEEGGG.HHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHH.H CS
                      tRNA-synt_1b 146 illlkadlvpgGsDQ.kqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvk.k 220
                                       ++ l +d++p G+D  ++   +g d+ar + +    ++p++++ +  t l+Ge  +S+S+gn +I  +d  e  + +
  gi|336254857|ref|YP_004597964.1| 285 WQELGVDFEPFGKDHaEGSWPSGQDVARNVLEI---EPPVPMVYEWFT-LEGE-PFSSSEGN-VILVSDVLELLEpE 355
                                       677888999999997367889999999999998...899999999876.6899.9*******.**999998876546 PP

                                       HHHHCHCSTTCSHHHHHHHHHTHHHCHHHHHHHHCC CS
                      tRNA-synt_1b 221 kiqkavtdsdeevekllklktelsnelierleavsg 256
                                       + ++++ ++  + + ++ ++     ++++rlea+  
  gi|336254857|ref|YP_004597964.1| 356 VLRYFFAKDPTKARDFSIERLDQLVDEFDRLEAIYF 391
                                       777777766666666666666666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 4614.63
//
Query:       gi|336254858|ref|YP_004597965.1|  [L=615]
Description: peptidase M50 [Halopiger xanaduensis SH-6]
Scores for complete 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   79.9   0.0    5.3e-22   78.3   0.0    1.8  1  Peptidase_M50  Peptidase family M50
    4.8e-22   78.1   2.9    2.3e-07   31.0   0.1    3.3  3  PDZ_2          PDZ domain
    5.6e-13   48.5  10.3    2.3e-08   33.8   0.6    3.1  4  PDZ_6          PDZ domain
      5e-10   39.6   1.6    3.9e-06   27.1   0.2    2.5  2  PDZ            PDZ domain
    2.1e-08   34.0   3.8     0.0024   17.8   0.2    3.4  3  Tricorn_PDZ    Tricorn protease PDZ domain
     0.0048   17.2   0.0       0.44   10.9   0.0    2.5  2  GRASP55_65     GRASP55/65 PDZ-like domain
  ------ inclusion threshold ------
      0.036   14.3   0.3       0.12   12.6   0.1    1.9  2  Arteri_nsp7a   Arterivirus nonstructural protein 7 alpha


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 !   78.3   0.0   2.1e-25   5.3e-22       3     242 ..     141     591 ..     139     603 .. 0.84

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 2.1e-25
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....X CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   3 illlgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaf 79 
                                       ++ l++ +vvHE GH+l+ + +++ +++++i +               +a++p+G++V+ ++e              
  gi|336254858|ref|YP_004597965.1| 141 VFGLLVGLVVHEGGHGLLCRVEDIDIDSMGIVM---------------LAIVPMGAFVEPDQES------------S 190
                                       77899999*************************...............**************99............3 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX................................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................ RF
                     Peptidase_M50  80 lkkspwqrllivlAGplanfilailvfvv................................................ 108
                                       +++s   r ++++AG  +nf ++i++f++                                                
  gi|336254858|ref|YP_004597965.1| 191 KSASRGGRTRMFAAGVTNNFAITIVAFALlfgpvvgsiglapgaavggvapdspaaaadiepndritaingepvadn 267
                                       578999*********************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M50 109 ............................................................................. 108
                                                                                                                    
  gi|336254858|ref|YP_004597965.1| 268 daleerieaaegnqlavelngertvdversllvtatadssitglqtgdsivavngqevateteflealgedevatlt 344
                                       ***********************************999999999999999999999999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M50 109 ............................................................................. 108
                                                                                                                    
  gi|336254858|ref|YP_004597965.1| 345 vetgdgreerevpigalvtvaedgpladagapagtnfvvtsfdgertatqselnelvgetdpgdqvtvagylqgerv 421
                                       99999999999999999999999999999999999999999999999999999999999999999999999999888 PP

                                       .......................-EEECECTTTSCEE-SEEEC-......XXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                                       .......................xxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                     Peptidase_M50 109 .......................pkkskeseeekrgviGvspkp......vkkegllealkegvektlkvvvltvk. 155
                                                              p   +e++  +++ +G++ +p      v   g +e++    +++l  + + ++ 
  gi|336254858|ref|YP_004597965.1| 422 eyevtlgersettgggtvgylvyP--GSEISGVSTQALGIQLYPadaylsVLGGGSGESFGALSDSFLGKIGIALMl 496
                                       888777776666666666666553..334566666666666666889988777777777777777777666665555 PP

                                       XXXXXXXX.XXXXX.XXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxx.xxxxx.xxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 156 algklitg.klslk.tlggpisiaqlaseaaeagls......sflqllalisvnLgilNLlPipvLDGghllfalle 224
                                        + ++i +   ++    gg   ++q+ +   + g +      + l+++ +i+v+Lg++N +P ++LDGgh+l+   e
  gi|336254858|ref|YP_004597965.1| 497 PIAGVIEAlPYNFAgFAGGIENFYQAQGPLGALGDWplfalaNALFWTGWINVQLGFFNCIPAFPLDGGHILRTSTE 573
                                       788888887777775556666677777554444444566677*********************************** PP

                                       XXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 225 airrkplserkeevanlv 242
                                       a+  +     ++ ++  v
  gi|336254858|ref|YP_004597965.1| 574 AVFSRLPIDATRGMVRVV 591
                                       *99776555555444443 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1     9e-11   2.3e-07      15      61 ..     233     279 ..     223     295 .. 0.83
   2 !   18.6   0.1   6.9e-07    0.0018      21      60 ..     300     339 ..     283     358 .. 0.77
   3 !   27.7   0.1   9.9e-10   2.5e-06      19      82 .]     362     427 ..     341     427 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 9e-11
                                       -EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-T CS
                             PDZ_2  15 gvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkp 61 
                                       g+ v  V +++Paa+a+++++D+i++++g +v + + l++++ +++ 
  gi|336254858|ref|YP_004597965.1| 233 GAAVGGVAPDSPAAAADIEPNDRITAINGEPVADNDALEERIEAAEG 279
                                       788889***********************************985443 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 6.9e-07
                                       E-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS- CS
                             PDZ_2  21 VkeggPaakaglkagDvilkvdgkkvksledlislllkkk 60 
                                       V+    ++  gl++gD i++v+g++v +++++ ++l + +
  gi|336254858|ref|YP_004597965.1| 300 VTATADSSITGLQTGDSIVAVNGQEVATETEFLEALGEDE 339
                                       7788888899**********************99987543 PP

  == domain 3  score: 27.7 bits;  conditional E-value: 9.9e-10
                                       EEE-TTSGGGGT...--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEEEEE- CS
                             PDZ_2  19 vsVkeggPaakag..lkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkktvevkl 82 
                                       v+V e+gP a+ag    ++ v++++dg +  ++++l++l+ +++pGd+V++  + +g++ ++ev+l
  gi|336254858|ref|YP_004597965.1| 362 VTVAEDGPLADAGapAGTNFVVTSFDGERTATQSELNELVGETDPGDQVTVAGYLQGERVEYEVTL 427
                                       67***********44444679*******************************************97 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.6   8.9e-12   2.3e-08       2      47 ..     236     279 ..     236     287 .. 0.82
   2 !   20.8   0.0     1e-07   0.00026      15      55 ..     310     346 ..     304     347 .. 0.91
   3 ?   -3.9   0.6       5.3   1.4e+04       4      15 ..     363     374 ..     362     378 .. 0.78
   4 ?   -2.2   0.0       1.6     4e+03      21      50 ..     382     410 ..     382     413 .. 0.67

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 8.9e-12
                             PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallrgsag 47 
                                       V  V p+sPA+ A ++++D+i+++NG+pv   + + + + +++++g
  gi|336254858|ref|YP_004597965.1| 236 VGGVAPDSPAAAADIEPNDRITAINGEPV--ADNDALEERIEAAEG 279
                                       6789*************************..777777777765555 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1e-07
                             PDZ_6  15 GlrvGDiilsvNGqpveglsladvaallrgsagesvvlvvr 55 
                                       Gl+ GD i++vNGq+v   + +++ ++l   ++e  +l+v+
  gi|336254858|ref|YP_004597965.1| 310 GLQTGDSIVAVNGQEV--ATETEFLEAL--GEDEVATLTVE 346
                                       9***************..**********..59999999886 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 5.3
                             PDZ_6   4 aVdpgsPAdrAG 15 
                                       +V +++P + AG
  gi|336254858|ref|YP_004597965.1| 363 TVAEDGPLADAG 374
                                       588899999998 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.6
                             PDZ_6  21 iilsvNGqpveglsladvaallr.gsagesv 50 
                                       +++s++G+ +   +  ++ +l+  +++g +v
  gi|336254858|ref|YP_004597965.1| 382 VVTSFDGERT--ATQSELNELVGeTDPGDQV 410
                                       5789999998..7777777776555555555 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.2   1.5e-09   3.9e-06      25      64 ..     231     270 ..     221     287 .. 0.75
   2 !   11.2   0.1   0.00015      0.38      43      60 ..     310     327 ..     299     346 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.5e-09
                                       SSSEEEEEECTT.SHHHHHTSSTTEEEEEETTEETTTSHHH CS
                               PDZ  25 dkgifvsevlpg.gaaeadglkvGDkIlsvNgvdvenvshe 64 
                                       ++g+ v  v p+ +aa+ad ++++D+I+++Ng++v++   +
  gi|336254858|ref|YP_004597965.1| 231 APGAAVGGVAPDsPAAAAD-IEPNDRITAINGEPVADNDAL 270
                                       47999*******7777777.***************986443 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00015
                                       TSSTTEEEEEETTEETTT CS
                               PDZ  43 glkvGDkIlsvNgvdven 60 
                                       gl+ GD I++vNg+ v++
  gi|336254858|ref|YP_004597965.1| 310 GLQTGDSIVAVNGQEVAT 327
                                       5************99975 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00023      0.59      41      80 ..     251     290 ..     242     300 .. 0.82
   2 !   17.8   0.2   9.4e-07    0.0024      37      86 ..     310     356 ..     306     358 .. 0.84
   3 !    5.6   0.0    0.0059        15      23      68 ..     360     405 ..     356     421 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00023
                                       .TT-EEEEETTEE-BTTB-HHHHHHTTTTSEEEEEEE-ST CS
                       Tricorn_PDZ  41 reGdlilavdgepvskekgiaelLvgkagkeveLtvkrkd 80 
                                       +  d i+a++gepv  ++ ++e ++ ++g++  ++++ + 
  gi|336254858|ref|YP_004597965.1| 251 EPNDRITAINGEPVADNDALEERIEAAEGNQLAVELNGER 290
                                       56699************************99888888754 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 9.4e-07
                                       S---.TT-EEEEETTEE-BTTB-HHHHHHTTTTSEEEEEEE-STT.-EEEE CS
                       Tricorn_PDZ  37 GvnvreGdlilavdgepvskekgiaelLvgkagkeveLtvkrkdg.karrv 86 
                                       G+  ++Gd i+av+g++v +e+++ e+L + +   ++Ltv+++dg ++r+v
  gi|336254858|ref|YP_004597965.1| 310 GL--QTGDSIVAVNGQEVATETEFLEALGEDE--VATLTVETGDGrEEREV 356
                                       44..49***************99999996644..589*****999788887 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0059
                                       -TTSSS-B-GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTT CS
                       Tricorn_PDZ  23 dswdeearSPLaepGvnvreGdlilavdgepvskekgiaelLvgka 68 
                                       +    ++ +PLa+ G  + +  ++++ dge++ ++++++el  +++
  gi|336254858|ref|YP_004597965.1| 360 ALVTVAEDGPLADAGAPAGTNFVVTSFDGERTATQSELNELVGETD 405
                                       55666789*********99999***********9999998765554 PP

>> GRASP55_65  GRASP55/65 PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00017      0.44      50      97 ..     239     285 ..     233     318 .. 0.84
   2 ?    3.7   0.0     0.028        72      47     126 ..     361     442 ..     349     447 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                                       EBTTSHHHHHT--TTTEEEEEEE.SSSSSTSCSHHHHTTTSSS-EEEE CS
                        GRASP55_65  50 vlegsPaakagLvpksDYiiGldkgllkgeedlselveaheekelkLl 97 
                                       v ++sPaa a++ p +D i +++ + ++++++l e++ea e ++l + 
  gi|336254858|ref|YP_004597965.1| 239 VAPDSPAAAADIEP-NDRITAINGEPVADNDALEERIEAAEGNQLAVE 285
                                       889********988.599***********************9998765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.028
                                       EEEEBTTSHHHHHT--TTTEEEEEEE..SSSSSTSCSHHHHTTTS.SS-EEEEEEETTTTEEEEEEE---TTSSSST CS
                        GRASP55_65  47 vldvlegsPaakagLvpksDYiiGldk.gllkgeedlselveahe.ekelkLlvYnsesdevrevtvkpsrewGgeg 121
                                       +++v e++P a ag  + + +++   + +  + +++l elv ++    ++++  Y + + +  evt+  ++e  g g
  gi|336254858|ref|YP_004597965.1| 361 LVTVAEDGPLADAGAPAGTNFVVTSFDgERTATQSELNELVGETDpGDQVTVAGYLQGERVEYEVTLGERSETTGGG 437
                                       6899******************9865526677999******765426799999999999999999999888888889 PP

                                       TTSEE CS
                        GRASP55_65 122 alGcd 126
                                       ++G  
  gi|336254858|ref|YP_004597965.1| 438 TVGYL 442
                                       88865 PP

>> Arteri_nsp7a  Arterivirus nonstructural protein 7 alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.6e-05      0.12      34      94 ..     268     327 ..     263     348 .. 0.80
   2 ?   -2.1   0.0       1.5     4e+03      77      97 ..     402     421 ..     396     431 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                      Arteri_nsp7a  34 kalkdfiesayakaLraeLasvkavakakralAkLedFaegvskelkpGDvvvll.Gkkpvg 94 
                                        al++ ie+a  ++L  eL   + v+  +++l +  + a++  + l++GD +v++ G++  +
  gi|336254858|ref|YP_004597965.1| 268 DALEERIEAAEGNQLAVELNGERTVDVERSLLVT--ATADSSITGLQTGDSIVAVnGQEVAT 327
                                       689999*************************976..5678899***********98886543 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                      Arteri_nsp7a  77 kelkpGDvvvllGkkpvgelv 97 
                                        e +pGD+v + G  + ge v
  gi|336254858|ref|YP_004597965.1| 402 GETDPGDQVTVAGYLQ-GERV 421
                                       5789*****9999854.6655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); 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:                         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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 4310.94
//
Query:       gi|336254859|ref|YP_004597966.1|  [L=178]
Description: PadR-like family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for complete 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   85.7   0.3    2.4e-24   85.1   0.3    1.3  1  PadR      Transcriptional regulator PadR-like family
     0.0086   16.7   0.1      0.013   16.1   0.1    1.3  1  RTP       Replication terminator protein
  ------ inclusion threshold ------
      0.054   13.8   0.0      0.095   13.0   0.0    1.3  1  CDT1      DNA replication factor CDT1 like
      0.062   13.2   0.0       0.22   11.5   0.0    2.0  1  TrmB      Sugar-specific transcriptional regulator TrmB
       0.15   10.4   0.3       0.19   10.0   0.3    1.1  1  DUF505    Protein of unknown function (DUF505)


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 !   85.1   0.3   6.7e-28   2.4e-24       1      75 []      19      91 ..      19      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 6.7e-28
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrelae 75
                                      +L+llee+p+yGyei ke++e s+g++e+s+Gs+Yp+L ++e++g+ e+ ++e  ++p rky++lT++Gr+el+e
  gi|336254859|ref|YP_004597966.1| 19 VLELLEEKPRYGYEILKEIREISGGHWEPSYGSVYPILYKFEEKGWAERIERE--DEPDRKYFELTEDGRAELEE 91
                                      8***********************************************99887..69***************986 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.7e-06     0.013      12      82 ..      17      82 ..      12     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.7e-06
                                      HHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEB.TSSSSSEEEEEEES CS
                               RTP 12 lylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelk.ekaklqevviYslt 82
                                        +++l+e+k+ yg+++l e+++      ++P+   +y  l  + e+g  +r+++   ++ k     +++lt
  gi|336254859|ref|YP_004597966.1| 17 YLVLELLEEKPRYGYEILKEIRE-ISGGHWEPSYGSVYPILYKFEEKGWAERIEREDePDRK-----YFELT 82
                                      456899**************996.56666********************9998776522333.....34444 PP

>> CDT1  DNA replication factor CDT1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.6e-05     0.095      56     152 ..      51     167 ..      49     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                              CDT1  56 tvyPeayklkqekqlkef.gssgkakaskyelviePnleddl.......................kvsaseaetdkr 108
                                       +vyP  yk++ ek + e  +++++ + +++el+     e ++                        +++++ + +  
  gi|336254859|ref|YP_004597966.1|  51 SVYPILYKFE-EKGWAERiEREDEPDRKYFELTEDGRAELEErreggaekakdfadvilgffhvyAAFSTDDRFEIP 126
                                       69********.8888888799999999999***996444444669**************998766445555555455 PP

                              CDT1 109 kklsaerlleRrkkFrrkLleiVkehHekFLeslnppve.vpdle 152
                                       ++  ++r+    + F+r ++e V +hHe + e+  +++e  p+ e
  gi|336254859|ref|YP_004597966.1| 127 EQDGEWRF---DEEFSRWIVEQVVRHHEHYFETDFERIEeTPE-E 167
                                       55555555...579*****************999988874333.5 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     6e-05      0.22      35      59 ..      48      76 ..      16      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                                      SCHCHHHHHHHHHHCTSEEEESST....T CS
                              TrmB 35 prskvYevLrsLedkGlVerekgr....p 59
                                      ++ +vY +L + e+kG+ er++++    +
  gi|336254859|ref|YP_004597966.1| 48 SYGSVYPILYKFEEKGWAERIEREdepdR 76
                                      7899*****************98877533 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   5.4e-05      0.19     336     406 ..      23      94 ..      14     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5.4e-05
                            DUF505 336 leempkkkeeiakkfeeakdlekWyednfdlreaLysLesfeLiesev..eekgkevyvlTeyGekvledqek 406
                                       lee p+   ei k+  e+    +W  ++ ++   Ly+ e ++  e+ +  +e  +++++lTe G+  le+ ++
  gi|336254859|ref|YP_004597966.1|  23 LEEKPRYGYEILKEIREISGG-HWEPSYGSVYPILYKFEEKGWAERIEreDEPDRKYFELTEDGRAELEERRE 94 
                                       566777777888888888888.6******************9987765437778***********99998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1406.65
//
Query:       gi|336254860|ref|YP_004597967.1|  [L=517]
Description: Chlorite dismutase [Halopiger xanaduensis SH-6]
Scores for 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-64  215.8   0.0    7.1e-64  215.0   0.0    1.4  1  Chlor_dismutase  Chlorite dismutase
    2.8e-07   30.6   0.2    2.8e-07   30.6   0.2    4.0  4  ABM              Antibiotic biosynthesis monooxygenase


Domain annotation for each model (and alignments):
>> Chlor_dismutase  Chlorite dismutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.0   0.0   7.9e-68   7.1e-64       1     193 [.      35     245 ..      35     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: 215.0 bits;  conditional E-value: 7.9e-68
                                       HHHHHHHHHHHHHH......TTSCEEEEEEEETSTTTT-SEEEEEEESSHHHHHHHHHHHHHSTGGGGEEEEEEEEE CS
                   Chlor_dismutase   1 reeaveeleallee......aeegvlralysvlGlradaDlmlwllretleelqeaerelrrtalgkvlepaysyvs 71 
                                       re+a++e  ++l++      aeeg  +a++svlG++  aDl++++lr+tl++++++er++++tal++++e+a sy+s
  gi|336254860|ref|YP_004597967.1|  35 RERAIDEGIEFLSAaervddAEEG-DSAVFSVLGHK--ADLLILHLRPTLSDIDALERSFEHTALAEFTERADSYLS 108
                                       788999999999888888878888.***********..*************************************** PP

                                       EEEEESS..........SSS-GGGHHHCHHHHS----SSSEEEEEEEEE-EE....GGGS-HHHHHHHHHHHHHHHH CS
                   Chlor_dismutase  72 vtelseY..........keedeenkshvearlapelpkkkyvcvYPmsksre....WYllpeeeRrelmaeHgeigr 134
                                       vte+s Y          + ed+++k+++e r++p++p+++++ +YPm+k+r     WY+lp++eR+e++++Hgeig+
  gi|336254860|ref|YP_004597967.1| 109 VTEVSGYmsqeyfeedgEVEDQGMKRYIETRIKPSIPDTDFMSFYPMDKRRGeednWYDLPFDERAEHLSSHGEIGK 185
                                       ****************9999*******************************99************************ PP

                                       GC.TTEEEEEEE-TTTSSSSEEEEEEESSTHHHHHHHHHHCTSHHHHHHEEE-S-EEEEE CS
                   Chlor_dismutase 135 kY.gkVrqiitgsfGldDyEwgvaleaddleefkdlvyelRfdeasakvaeegpfyvGrr 193
                                       +Y g+V+qii+gs+GldD+Ewgv+l+ dd++++kdl+ye+Rfd +++++ae+g+f+ +rr
  gi|336254860|ref|YP_004597967.1| 186 QYaGRVTQIISGSIGLDDFEWGVTLFGDDPTDVKDLLYEMRFDPSTSRYAEFGQFLSARR 245
                                       ********************************************************9987 PP

>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3      0.12   1.1e+03      44      72 ..       6      33 ..       1      37 [. 0.77
   2 ?   -0.4   0.1      0.14   1.2e+03      16      45 ..      97     124 ..      89     130 .. 0.77
   3 ?    1.5   0.2     0.037   3.3e+02      33      63 ..     371     401 ..     340     405 .. 0.73
   4 !   30.6   0.2   3.1e-11   2.8e-07       7      78 .]     432     502 ..     428     502 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.12
                                      EETSTTEEEEEEEESSHHHHHHHHTSHHH CS
                               ABM 44 stedpdevvvieeWeseaaleahlksphf 72
                                      +++ ++ ++v++ ++s++ ++a++++p+ 
  gi|336254860|ref|YP_004597967.1|  6 PPQTEEGWYVLHDFRSID-WDAWRDAPAR 33
                                      566677799999999985.8999999975 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHTSTTEEEEEEEEEE CS
                               ABM  16 eafldafaeavesllaeepGclgyellrst 45 
                                       ++f ++  ++++ ++ e+ G+++ e+++++
  gi|336254860|ref|YP_004597967.1|  97 AEFTERADSYLS-VT-EVSGYMSQEYFEED 124
                                       677888888888.85.9****999999743 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.037
                                       STTEEEEEEEEEETSTTEEEEEEEESSHHHH CS
                               ABM  33 epGclgyellrstedpdevvvieeWeseaal 63 
                                        + +   +++++ ++++e  v++ We+e a 
  gi|336254860|ref|YP_004597967.1| 371 YDTHVKTAVYEPHDGDGEAGVVSLWETERAA 401
                                       44556677888999999999******99886 PP

  == domain 4  score: 30.6 bits;  conditional E-value: 3.1e-11
                                       EEEESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTSHHHHHHHHH CS
                               ABM   7 eirvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahlksphfkaahea 78 
                                        ++vkp+++ +f+  f ++   +l++++G++  +ll ++ed++ +++ ++W+ +++  ++ +s++f +++e+
  gi|336254860|ref|YP_004597967.1| 432 FYTVKPEHRSDFVGTFDDVGA-ILEDMDGHRKTDLLANREDENDMFIASRWDAREDAMQFFRSDEFSETVEW 502
                                       578***************877.88*******************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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 0.20s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 4195.76
//
Query:       gi|336254861|ref|YP_004597968.1|  [L=62]
Description: hypothetical protein Halxa_3478 [Halopiger xanaduensis SH-6]
Scores for 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   1.1        0.1   12.9   1.1    1.1  1  DUF5493   Family of unknown function (DUF5493)
       0.35   10.9   3.8       0.65   10.1   0.4    2.2  2  DUF2933   Protein of unknown function (DUF2933)


Domain annotation for each model (and alignments):
>> DUF5493  Family of unknown function (DUF5493)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.1   1.1e-05       0.1      28      74 ..       6      52 ..       1      58 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                           DUF5493 28 nlmafiigtvaflvfvqgytdiafssstfylgvlplllglvnl.gyff 74
                                       l+a + g + f +fv g++ ++   +  y   + l+lgl  + gyff
  gi|336254861|ref|YP_004597968.1|  6 FLVATLAGHIGFAIFVAGHAFLTDRDA-GYWPYVTLVLGLAGVaGYFF 52
                                      57888899999********98876655.56677899****97648888 PP

>> DUF2933  Protein of unknown function (DUF2933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.4   7.2e-05      0.65       3      29 ..      11      41 ..       4      43 .. 0.86
   2 ?    2.6   0.3     0.015   1.4e+02       1      12 [.      42      53 ..      42      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7.2e-05
                           DUF2933  3 llliaaffLltehrahl....lgllPfllLL 29
                                      l++ ++f++++   a+l    +g++P++ L 
  gi|336254861|ref|YP_004597968.1| 11 LAGHIGFAIFVAGHAFLtdrdAGYWPYVTLV 41
                                      778899***999777777*********9985 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.015
                           DUF2933  1 lvllliaaffLl 12
                                      l+l+++a++f +
  gi|336254861|ref|YP_004597968.1| 42 LGLAGVAGYFFY 53
                                      689*******76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.31u 0.20s 00:00:00.51 Elapsed: 00:00:00.35
# Mc/sec: 535.57
//
Query:       gi|336254862|ref|YP_004597969.1|  [L=129]
Description: hypothetical protein Halxa_3479 [Halopiger xanaduensis SH-6]
Scores for complete 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   0.1    1.4e-30  106.2   0.1    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 !  106.2   0.1   7.7e-35   1.4e-30       1     103 []       1     117 [.       1     117 [. 0.98

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 7.7e-35
                                       -EEE---SSS--SH..HHHHHHHHHHT....-EEEEE.TTEEEE.E.....-TTBS-EEEEE..-SS-EEEEE--.B CS
                           DUF5611   1 mreYkiKrGfkkeee.erlkelleeyfg...geveee.gdllvv.s.....fgaikklevkisskkkklvvdteerd 66 
                                       m+eYk++rG+++ee+ +++++++eeyfg   g++e++ +dl+v+ +     f++i+ ++v++s+kk+kl v+++erd
  gi|336254862|ref|YP_004597969.1|   1 MKEYKMRRGEYLEERiPDMETTIEEYFGpitGTEEYKgSDLFVIgEpdnpvFEKIVVGAVEYSGKKDKLGVEFHERD 77 
                                       9******************************9999999******66******************************* PP

                                       ......-TTS-HHHHHHHHHHHHHHHH---GGGHHHHH-- CS
                           DUF5611  67 aee...eddeaaldtvkkfndFLeeaTGydaKeRkkkakk 103
                                        +e   ++ eaa ++v+ +ndFL eaTG+daK+R++++k+
  gi|336254862|ref|YP_004597969.1|  78 PTElgpDELEAAGEAVDLKNDFLLEATGRDAKARRDSMKR 117
                                       **9**9********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 1100.49
//
Query:       gi|336254863|ref|YP_004597970.1|  [L=357]
Description: hypothetical protein Halxa_3480 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        3.1    8.2   6.3        2.4    8.5   2.7    2.7  3  zinc_ribbon_9  zinc-ribbon


Domain annotation for each model (and alignments):
>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.27   4.8e+03      21      29 ..      36      43 ..      28      46 .. 0.69
   2 ?    1.9   0.8     0.015   2.8e+02      22      28 ..     318     327 ..     309     329 .. 0.64
   3 ?    8.5   2.7   0.00013       2.4       3      32 ..     321     351 ..     319     353 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.27
                     zinc_ribbon_9 21 dvlCPhCgg 29
                                      +  C +Cg 
  gi|336254863|ref|YP_004597970.1| 36 EE-CTRCGE 43
                                      45.999986 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.015
                     zinc_ribbon_9  22 v...lCPhCg 28 
                                       +   +CP+C+
  gi|336254863|ref|YP_004597970.1| 318 PtefYCPRCD 327
                                       23347****7 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00013
                     zinc_ribbon_9   3 yWChqCdrfVsvspdedsd.v..lCPhCgggFV 32 
                                       ++C +Cd fV    +  s  +  +CP+C+ g +
  gi|336254863|ref|YP_004597970.1| 321 FYCPRCD-FVASDDR-ASLrAgdICPDCRKGYL 351
                                       7999999.8885444.33342445******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2735.67
//
Query:       gi|336254864|ref|YP_004597971.1|  [L=99]
Description: hypothetical protein Halxa_3481 [Halopiger xanaduensis SH-6]
Scores for 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   14.6   0.0      0.033   13.9   0.0    1.4  1  GntR          Bacterial regulatory proteins, gntR family
       0.15   12.2   0.1       0.24   11.5   0.1    1.3  1  FANCI_S1-cap  FANCI solenoid 1 cap
       0.22   11.9   1.2       0.62   10.5   0.2    1.9  2  DUF2122       RecB-family nuclease (DUF2122)


Domain annotation for each model (and alignments):
>> 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   5.5e-06     0.033      22      62 ..      27      66 ..      18      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-06
                                      SB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR 22 dkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGt 62
                                      d + ++ eL+a+ +++   + eAL++L+ ++l++++++ G 
  gi|336254864|ref|YP_004597971.1| 27 DGM-TVFELRAAVETDIDDLEEALSTLKDDNLIVVEKNAGE 66
                                      667.8889****************************99885 PP

>> FANCI_S1-cap  FANCI solenoid 1 cap
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1     4e-05      0.24      10      30 ..      38      58 ..      34      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4e-05
                      FANCI_S1-cap 10 aedsteeLqkfLqtLkedeLt 30
                                       e + + L++ L+tLk+d+L+
  gi|336254864|ref|YP_004597971.1| 38 VETDIDDLEEALSTLKDDNLI 58
                                      577899*************97 PP

>> DUF2122  RecB-family nuclease (DUF2122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       0.2   1.2e+03      17      30 ..      10      23 ..       6      30 .. 0.86
   2 ?   10.5   0.2    0.0001      0.62      25      57 ..      42      74 ..      40      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.2
                           DUF2122 17 klgksllvlpdlkD 30
                                      ++g ++ vl++l D
  gi|336254864|ref|YP_004597971.1| 10 REGTEVAVLDELVD 23
                                      6789999***9988 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0001
                           DUF2122 25 lpdlkDalellkpekvlllskeegeelleeeel 57
                                      ++dl++al  lk ++ ++++k+ ge +++ +e+
  gi|336254864|ref|YP_004597971.1| 42 IDDLEEALSTLKDDNLIVVEKNAGETVIKPDER 74
                                      58*******************999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 787.49
//
Query:       gi|336254865|ref|YP_004597972.1|  [L=371]
Description: folate-binding protein YgfZ [Halopiger xanaduensis SH-6]
Scores for 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-40  137.0   0.0    9.3e-40  136.6   0.0    1.1  1  GCV_T     Aminomethyltransferase folate-binding domain
    4.3e-14   52.2   0.0    9.1e-14   51.1   0.0    1.6  1  GCV_T_C   Glycine cleavage T-protein C-terminal barrel domain


Domain annotation for each model (and alignments):
>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.6   0.0     1e-43   9.3e-40       3     247 ..       6     241 ..       4     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 136.6 bits;  conditional E-value: 1e-43
                             GCV_T   3 drhkalgakfvefagwemPvqYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgkat 79 
                                       ++h  +ga+f+e  g  +  ++  + +++ h+avr+++gl +    g + v+G+d++++++++++n++++ + g++ 
  gi|336254865|ref|YP_004597972.1|   6 SVHADHGAEFGERDGRTIVEHF--GRPERTHRAVRNGVGLLEPA-YGVVVVEGEDRLEYVDNVVSNRVPAED-GRGC 78 
                                       68********************..******************98.8***********************776.**** PP

                             GCV_T  80 ytlllnedGgvidDlivarldedefllvvnaankekdl.awlekaaekkdldvevedvteelallalqGPkarevls 155
                                       y+l+l+++Gg++ +++v++ + +++ll ++++++e ++ +w ek      +dv+++ +t+++a++ + GP a+e ++
  gi|336254865|ref|YP_004597972.1|  79 YALVLDPQGGIEVEMYVYNAG-ERLLLFTPPTKAEPLVeDWSEK-VF--IQDVDIRLATDDYAIFGIHGPHATEKIA 151
                                       *********************.5999999999999999677777.77..79***********************888 PP

                             GCV_T 156 kll.gadlselkffsfaevelaggkkvlvsRt.gytGedGfeiyipaeeaeelweaLleagkeegvkpaGlgArdtl 230
                                        +l ga+  + + +sf++ ++  +  v+v Rt   tGe+ +e++++a++ae +++ Ll++g   ++ p+G++++++l
  gi|336254865|ref|YP_004597972.1| 152 SVLnGAPSPD-ERYSFVRGTMG-DAGVTVIRTdALTGEESYEVVCAADDAESVYDILLTQGL--NAAPFGYRTWESL 224
                                       8884555666.9*****99998.9999999994579*********************98776..9************ PP

                             GCV_T 231 RlEaglrlyghdldeet 247
                                       +lEag +l+ ++l+ ++
  gi|336254865|ref|YP_004597972.1| 225 TLEAGSPLFETELEGTI 241
                                       ************98775 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0     1e-17   9.1e-14       1      79 [.     275     358 ..     275     359 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1e-17
                           GCV_T_C   1 Rrlvgleld.....dg..apllrggepilrdgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvp 70 
                                       Rrl+g++l+     d+  a++++ g++++++++ vG++T+++ sp l+  ialA+v+ +l+   ++++v+v g++vp
  gi|336254865|ref|YP_004597972.1| 275 RRLIGVTLEsaadeDDedATVPESGAAVFDGDASVGEITRAGESPLLEDVIALALVDYDLES--DDLTVRVGGEEVP 349
                                       8999999987775522557777*******999*************************99988..9************ PP

                           GCV_T_C  71 aevvkkpfy 79 
                                       a+ ++ pfy
  gi|336254865|ref|YP_004597972.1| 350 ATRTELPFY 358
                                       ********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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: 00:00:00.37
# Mc/sec: 2995.27
//
Query:       gi|336254866|ref|YP_004597973.1|  [L=141]
Description: hypothetical protein Halxa_3483 [Halopiger xanaduensis SH-6]
Scores for 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  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1117.69
//
Query:       gi|336254867|ref|YP_004597974.1|  [L=451]
Description: hypothetical protein Halxa_3484 [Halopiger xanaduensis SH-6]
Scores for complete 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  109.4  17.6    1.5e-31  109.4  17.6    1.9  3  DUF389    Domain of unknown function (DUF389)


Domain annotation for each model (and alignments):
>> DUF389  Domain of unknown function (DUF389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.33   5.9e+03      77      93 ..     120     136 ..     100     144 .. 0.54
   2 !  109.4  17.6   8.1e-36   1.5e-31       1     142 []     145     289 ..     145     289 .. 0.95
   3 ?   -2.3   0.1      0.22     4e+03      33      69 ..     321     350 ..     315     358 .. 0.44

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.33
                            DUF389  77 lvAlasGaagalallsg 93 
                                       ++ l+s ++++  lls+
  gi|336254867|ref|YP_004597974.1| 120 VMLLISAVVATAGLLSD 136
                                       33344444444444444 PP

  == domain 2  score: 109.4 bits;  conditional E-value: 8.1e-36
                            DUF389   1 MlisPlmgpilaiafglvigdrkllrrglknlliglllallvgflfglllplk...vlgeeelptsemlsrtepnlv 74 
                                       M+i+Pl+gp+la+ +g+v+gd +l r+g++ ++ig+  +++ ++++++l++++   ++g + +  +e+++r+ pnl+
  gi|336254867|ref|YP_004597974.1| 145 MVIAPLLGPALAANVGIVTGDDRLKRTGFVYQIIGVTAVVVASIALAALARVAglePAGVDIVVATELEERVAPNLF 221
                                       ***********************************************888555585666777777************ PP

                            DUF389  75 dllvAlasGaagalallsgnssslvGvaIaaaLlPPavnaGlglalgewalalgslllllvNivgIvl 142
                                       +l+vAl +G+ag+l+l++g s+++vGv+IaaaL+PP +++G+++a+g +  a+g+++l++vN++ I+l
  gi|336254867|ref|YP_004597974.1| 222 SLAVALGAGIAGILSLTRGFSEAIVGVMIAAALIPPSAAVGITVAWGMYGAAIGAAALVIVNLLSINL 289
                                       *****************************************************************986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.22
                            DUF389  33 liglllallvgflfglllplkvlgeeelptsemlsrt 69 
                                       ++g++l  l + l+g+       +  +++t+e++s t
  gi|336254867|ref|YP_004597974.1| 321 VFGVALLALAAPLAGV-------TLIDFQTTELESAT 350
                                       3344444444444442.......12234444554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); 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):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3696.04
//
Query:       gi|336254868|ref|YP_004597975.1|  [L=65]
Description: hypothetical protein Halxa_3485 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0019   18.3   6.7     0.0026   17.9   6.7    1.2  1  Bacteriocin_IIc  Bacteriocin class II with double-glycine lea
  ------ inclusion threshold ------
      0.091   12.1   4.0      0.097   12.0   4.0    1.1  1  DUF3482          Domain of unknown function (DUF3482)
        2.1    8.8   6.4        3.9    7.9   2.1    2.1  2  Romo1            Reactive mitochondrial oxygen species modula


Domain annotation for each model (and alignments):
>> 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 !   17.9   6.7   4.3e-07    0.0026      24      57 ..      18      60 ..      15      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.3e-07
                   Bacteriocin_IIc 24 tvggivggalaGaatGaa.........tlgilgaavGavvGav 57
                                      ++++i++g+++G+ tG+a         ++ ++g+a Ga++Ga 
  gi|336254868|ref|YP_004597975.1| 18 NGADIGVGIAIGMSTGVAigtasdnlaLWLPVGVALGAALGAG 60
                                      6778888888888888888888*99888888888888888885 PP

>> DUF3482  Domain of unknown function (DUF3482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.0   1.6e-05     0.097     143     188 ..      19      62 ..       9      65 .] 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                           DUF3482 143 lkelGlslgaGaaaGAaaGagiDlavgGltLGaaaaiGalaGglaa 188
                                         ++G+ ++ G+ +G a+G + D +++ l   ++ a+Ga++G++++
  gi|336254868|ref|YP_004597975.1|  19 GADIGVGIAIGMSTGVAIGTASDNLALWLP--VGVALGAALGAGLN 62 
                                       456677777777777777777777776554..5678*******986 PP

>> Romo1  Reactive mitochondrial oxygen species modulator 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.1   0.00066       3.9      12      27 ..      24      39 ..      19      41 .. 0.85
   2 ?    3.2   0.1      0.02   1.2e+02       8      18 ..      49      59 ..      46      63 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00066
                             Romo1 12 mGaaVGlaiGllfGtf 27
                                      +G a+G+++G+ +Gt+
  gi|336254868|ref|YP_004597975.1| 24 VGIAIGMSTGVAIGTA 39
                                      7999999999999987 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.02
                             Romo1  8 mGalmGaaVGl 18
                                      +G+++Gaa+G+
  gi|336254868|ref|YP_004597975.1| 49 VGVALGAALGA 59
                                      35555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 540.84
//
Query:       gi|336254869|ref|YP_004597976.1|  [L=477]
Description: (R)-6-hydroxynicotine oxidase [Halopiger xanaduensis SH-6]
Scores for complete 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-34  118.7   4.0    2.1e-34  118.2   4.0    1.2  1  FAD_binding_4  FAD binding domain
    5.1e-10   39.3   0.0    9.9e-10   38.4   0.0    1.5  1  BBE            Berberine and berberine like


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 !  118.2   4.0   2.4e-38   2.1e-34       1     138 [.      55     189 ..      55     190 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 2.4e-38
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdl 77 
                                       pa+v+r++ +++v+aa+ +a+e++lp++vrGgG++++g av++g++v+dl+ + + + +d++e+t++ve+G+tlgd+
  gi|336254869|ref|YP_004597976.1|  55 PAIVARCTGVADVVAAVTFAREQELPLTVRGGGHNVAGTAVRDGALVVDLEPMSG-VRVDPDERTVRVEGGATLGDA 130
                                       789**************************************9********88***.89******************* PP

                                       HHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                     FAD_binding_4  78 vealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                       +++++  gl+++   g++++++v+G+++++++G+ s+ yGl+ dn+++++vv+adG+v+++
  gi|336254869|ref|YP_004597976.1| 131 DRETQLFGLATP--LGAVSQTGVAGLTLNGGYGHLSREYGLSLDNLRSVDVVTADGQVRTA 189
                                       ************..99******************************************987 PP

>> BBE  Berberine and berberine like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.1e-13   9.9e-10       2      46 .]     429     473 ..     428     473 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.1e-13
                                       -TTS--GGG-HHHHHHHHGGGHHHHHHHHHHH-TT--S--TT--- CS
                               BBE   2 YvNyrdldlgkewgerYFggNferLvkvKtkyDPdNvFrneqsIp 46 
                                       Y N++ l +  +  ++ Fg+N+erLv vKt+yDP+++F  e s+p
  gi|336254869|ref|YP_004597976.1| 429 YGNFPGLNEEDDPARATFGDNYERLVDVKTEYDPEDLFGTEASVP 473
                                       66777777775566778**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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: 0.46u 0.19s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 4093.85
//
Query:       gi|336254870|ref|YP_004597977.1|  [L=363]
Description: geranylgeranyl reductase [Halopiger xanaduensis SH-6]
Scores for complete 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   41.0   5.3    2.2e-08   33.8   1.9    2.8  2  FAD_binding_3   FAD binding domain
    1.2e-07   31.2   0.2     0.0018   17.4   0.0    2.1  2  Lycopene_cycl   Lycopene cyclase protein
    1.5e-05   24.4   0.7    0.00031   20.1   0.1    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00046   19.9   7.3     0.0012   18.5   0.5    2.8  3  DAO             FAD dependent oxidoreductase
     0.0024   17.3   0.5     0.0033   16.9   0.5    1.1  1  FAD_oxidored    FAD dependent oxidoreductase
     0.0097   15.0   1.1      0.031   13.4   0.2    2.0  2  FAD_binding_2   FAD binding domain
  ------ inclusion threshold ------
      0.026   13.2   0.1       0.12   11.1   0.0    1.8  2  HI0933_like     HI0933-like protein
      0.043   12.6   0.5       0.26   10.1   0.1    2.0  2  Trp_halogenase  Tryptophan halogenase
      0.049   12.9   0.3       0.68    9.1   0.1    2.0  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.075   13.3   1.1        1.2    9.4   0.3    3.0  3  NAD_binding_8   NAD(P)-binding Rossmann-like domain


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 !   33.8   1.9   1.2e-11   2.2e-08       3     175 ..       3     164 ..       1     197 [. 0.76
   2 !    6.8   0.1     0.002       3.6     278     308 ..     247     277 ..     218     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.2e-11
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHH..HHHTT-HHHHHHHSEECCCCEEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmel..lrqlGledrilaegapnelmgealy 77 
                                       d ++VG GpaG+  ++  +e+G +v+ ve+   t+ +p a+  +  t ++  +  +G  d++ ++     + +++++
  gi|336254870|ref|YP_004597977.1|   3 DFVVVGVGPAGARFSRRAAEKGYDVLAVEQG--TIGTPLACSGHVST-DIweFTGAGARDELFQNE--IYGARFHVG 74 
                                       5689***********************9975..56666565555544.440045555555555555..445555555 PP

                                       EECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEE CS
                     FAD_binding_3  78 nelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvr 154
                                       ++     ++ a+     +  +  v+    l+r L+e a+e+g++vr+++ v+ ++++ + v+ ++ +  +g   t +
  gi|336254870|ref|YP_004597977.1|  75 GP-----QSDAYP-FYKREVASNVIDRVGLDRHLAELAREAGADVREEHTVTDVREHHDRVEVVANSP-DGVV-THE 143
                                       55.....333332.355667788899999*******************************99877766.6777.99* PP

                                       EEEEEE--GTT-HHHHHHTGG CS
                     FAD_binding_3 155 akYlvGaDGgrStvrktlgie 175
                                       a+ ++G+DG rS+vr++l ++
  gi|336254870|ref|YP_004597977.1| 144 ARMVAGCDGPRSRVRDELELP 164
                                       *****************9976 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.002
                                       ESSSEETTEEE-GGGTEEE-STTSHHHHHHH CS
                     FAD_binding_3 278 aekyrkgrvflaGDAaHihpPtgGqGlNtai 308
                                       a++ ++ r fl+GDAa  + P +G G+  ++
  gi|336254870|ref|YP_004597977.1| 247 ADRVTSRRGFLIGDAAAQTKPFTGGGILYGM 277
                                       567777899***************9986666 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   9.9e-07    0.0018       1     144 [.       3     155 ..       3     179 .. 0.76
   2 !   11.9   0.0   4.7e-05     0.085     240     313 ..     239     311 ..     229     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.9e-07
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieasp..sllfpnny..vWsdefedlgaleecvehsWsgtivylddgk 73 
                                       D vv+G GpAg +   r   a++g  v+ +e +    +l    +  +   ef+++ga +e+ +    g++ ++ + +
  gi|336254870|ref|YP_004597977.1|   3 DFVVVGVGPAGARFSRRA--AEKGYDVLAVEQGTigTPLACSGHvsTDIWEFTGAGARDELFQNEIYGARFHVGGPQ 77 
                                       89****************..999*******98753234444444345445566666669999999999999998877 PP

                     Lycopene_cycl  74 killg.....raYgrvsskrlkeellerlvengvk.lleakvesveeeea.geslvvleggr.kirarlvvdargla 142
                                       +          a + + +  l ++l+e   e+g+  + e +v+ v+e+++  e+++  ++g+ + +ar+v    g +
  gi|336254870|ref|YP_004597977.1|  78 SDAYPfykreVASNVIDRVGLDRHLAELAREAGADvREEHTVTDVREHHDrVEVVANSPDGVvTHEARMVAGCDG-P 153
                                       77666333345666677788888888877788886255789********97888888889987889999998888.5 PP

                     Lycopene_cycl 143 sl 144
                                       ++
  gi|336254870|ref|YP_004597977.1| 154 RS 155
                                       44 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.7e-05
                     Lycopene_cycl 240 qgviPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres.slsarawatlwprerk 313
                                        g iP+  g+  + +  + + iG aa  ++P TG  +   +  a+  a  i     +  s+++raw++  +re+ 
  gi|336254870|ref|YP_004597977.1| 239 SGAIPI--GPADRVTSRRGFLIGDAAAQTKPFTGGGILYGMTCADHAAREIDPQRPTTlSAYERAWRDDLAREQE 311
                                       799***..9999999999***************************999888654443359999999999888865 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 !   20.1   0.1   1.7e-07   0.00031       1      33 [.       2      34 ..       2      79 .. 0.87
   2 ?    2.7   0.1     0.033        60     186     236 ..      99     152 ..      84     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.7e-07
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                      +d vv+G GpAG ++++++a++g++v+ ve+++
  gi|336254870|ref|YP_004597977.1|  2 YDFVVVGVGPAGARFSRRAAEKGYDVLAVEQGT 34
                                      589**************************6433 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCE...EEESEEEE-S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
                       Pyr_redox_2 186 saaleealekeGvevklgtsvkeidgngeklevvledgee...idadlvvvavG 236
                                        + l+e  ++ G +v+ +++v++++++++++evv ++ +     +a++v  + G
  gi|336254870|ref|YP_004597977.1|  99 DRHLAELAREAGADVREEHTVTDVREHHDRVEVVANSPDGvvtHEARMVAGCDG 152
                                       56677888999******************9998777766534555555555555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.5     0.011        21       1      39 [.       3      44 ..       3      65 .. 0.84
   2 !   18.5   0.5   6.8e-07    0.0012     150     220 ..     100     167 ..      86     285 .. 0.70
   3 ?   -0.4   0.1      0.38   6.9e+02     341     341 ..     275     275 ..     203     335 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.011
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT..SSGGGS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag..sgaSgr 39
                                      d v++G G +G+   + +a++g  V+ +e+g  +g   ++Sg+
  gi|336254870|ref|YP_004597977.1|  3 DFVVVGVGPAGARFSRRAAEKGydVLAVEQG-TIGtpLACSGH 44
                                      89*****************************.66633366666 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 6.8e-07
                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.EEEEEEEE--GGGHHHHHTTCTTTSEEEEE CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttp.gen.daadavVnaaGawsdllgllkeldlpispv 220
                                       + la+ a+++G++++e+++vt+++e+ ++v  v  ++p g + ++a+ v  + G+ s+      el+lp +p 
  gi|336254870|ref|YP_004597977.1| 100 RHLAELAREAGADVREEHTVTDVREHHDRVEVV-ANSPdGVVtHEARMVAGCDGPRSRVR---DELELP-EPD 167
                                       789********************9988888888.77777999777788*******99733...333334.443 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.38
                                       H CS
                               DAO 341 l 341
                                        
  gi|336254870|ref|YP_004597977.1| 275 Y 275
                                       2 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.5   1.8e-06    0.0033       1     140 [.       3     148 ..       3     152 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-06
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrq....rgga 73 
                                       D vVvG gpaG      Aa++G  vl ve+      l+ sg v+tdi   +      g  +e++++       + g 
  gi|336254870|ref|YP_004597977.1|   3 DFVVVGVGPAGARFSRRAAEKGYDVLAVEQGTIGTPLACSGHVSTDIWEFT----GAGARDELFQNEIYgarfHVGG 75 
                                       88***************************988877899999*****99663....3444455444432312112222 PP

                      FAD_oxidored  74 rlkkrskwntfepevakavleeml.........aeagvtvllntrlvevekegkriesvtveskegrktirAkvfi 140
                                       ++++++   +++ eva +v++ +          +eag +v  ++++++v+   +r+e v   s +g  t +A+++ 
  gi|336254870|ref|YP_004597977.1|  76 PQSDAY--PFYKREVASNVIDRVGldrhlaelaREAGADVREEHTVTDVREHHDRVEVVAN-SPDGVVTHEARMVA 148
                                       222222..2455555555555554455555555*****************98767665544.55589999999986 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.2   1.7e-05     0.031       1      40 [.       3      40 ..       3      47 .. 0.85
   2 ?   -0.1   0.0      0.21   3.8e+02     146     176 ..     101     131 ..      62     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggataw 40
                                      D +V+G G AG + + +aae+G +v+ ve++    g+  +
  gi|336254870|ref|YP_004597977.1|  3 DFVVVGVGPAGARFSRRAAEKGYDVLAVEQGTI--GTPLA 40
                                      88****************************985..44444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.21
                                       HHHHHHHTCTEEEEESEEEEEEEECTTEEEE CS
                     FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgrvtG 176
                                        l+e ar+ag d++e++ ++++  + +rv  
  gi|336254870|ref|YP_004597977.1| 101 HLAELAREAGADVREEHTVTDVREHHDRVEV 131
                                       5777888999999999999999776666653 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.6e-05      0.12       2      44 ..       3      44 ..       2      50 .. 0.92
   2 ?   -0.4   0.0       0.2   3.7e+02     115     155 ..     102     142 ..      89     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.6e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCGG CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisGg 44
                                      d +v+G G+AG   + +aa++g +Vl +e++ ++g  ++ sG+
  gi|336254870|ref|YP_004597977.1|  3 DFVVVGVGPAGARFSRRAAEKGYDVLAVEQG-TIGTPLACSGH 44
                                      78***************************99.89999988885 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.2
                                       HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEE CS
                       HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktkseeelea 155
                                       l + ++eag ++r e++v++v++++d++  v+ + ++ ++ 
  gi|336254870|ref|YP_004597977.1| 102 LAELAREAGADVREEHTVTDVREHHDRVEVVANSPDGVVTH 142
                                       66778999*************88888855555455555554 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.12   2.2e+02       2      38 ..       4      37 ..       3      44 .. 0.86
   2 ?   10.1   0.1   0.00015      0.26     151     214 ..      93     158 ..      82     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.12
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS-- CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeigt 38
                                       v+vG G+aG   A   ++a ++ ++v+ ve+ +igt
  gi|336254870|ref|YP_004597977.1|  4 FVVVGVGPAG---ARFSRRAAEKGYDVLAVEQGTIGT 37
                                      699******9...77777888777**********998 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00015
                                       E-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EE..E-SEEEE-SGGG-III CS
                    Trp_halogenase 151 ldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgrev..eadlfiDcsGfrglli 214
                                       +d+  ++++L + a ++G +++e + v+ + ++++rve +  + + +v  ea+++  c G r+++ 
  gi|336254870|ref|YP_004597977.1|  93 IDRVGLDRHLAELAREAGADVREEHTVTDVREHHDRVEVVANSPDGVVthEARMVAGCDGPRSRVR 158
                                       79999*********************9999999******988764443238999999999999875 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 ?    9.1   0.1   0.00038      0.68       1      34 [.       5      37 ..       5      41 .. 0.93
   2 ?    1.8   0.0     0.066   1.2e+02      85     119 ..     100     134 ..      78     152 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00038
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnign 34
                                      +++G GPaG  +   + ++g  d+l +E+g+ig+
  gi|336254870|ref|YP_004597977.1|  5 VVVGVGPAGARFSRRAAEKGY-DVLAVEQGTIGT 37
                                      79*******************.8*********97 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.066
                       Pyr_redox_3  85 eYlrevaksfelpiklfeeVesvkkedegfevets 119
                                       ++l+e+a++   +++++++V++v ++++  ev ++
  gi|336254870|ref|YP_004597977.1| 100 RHLAELAREAGADVREEHTVTDVREHHDRVEVVAN 134
                                       56677777777777777777777776655555443 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 ?    9.4   0.3   0.00067       1.2       1      29 [.       6      34 ..       6      86 .. 0.87
   2 ?   -3.0   0.0         5   8.9e+03      43      66 ..     205     228 ..     199     230 .. 0.74
   3 ?    0.9   0.0      0.31   5.5e+02       4      28 ..     271     301 ..     270     303 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00067
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      +vG G +G+ + +++a++g+dvl +e+++
  gi|336254870|ref|YP_004597977.1|  6 VVGVGPAGARFSRRAAEKGYDVLAVEQGT 34
                                      8*************************984 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5
                                       CEECTS---EEETTHHHHCHHHHC CS
                     NAD_binding_8  43 vrvdygahifhgsgyypnvrrllr 66 
                                         v+yg  +  g++ ++++ +l++
  gi|336254870|ref|YP_004597977.1| 205 AGVEYGLAAPPGVHVNKHFEELID 228
                                       668888888888888888888876 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.31
                                       -S.HHHHHHHHHHHCC.....TEEEEEE-SS CS
                     NAD_binding_8   4 aG.lsGlvaAylLaka.....gfdvlllekr 28 
                                       +G l G+++A ++a++           +e++
  gi|336254870|ref|YP_004597977.1| 271 GGiLYGMTCADHAAREidpqrPTTLSAYERA 301
                                       44158*****999985443223356666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2785.83
//
Query:       gi|336254871|ref|YP_004597978.1|  [L=69]
Description: hypothetical protein Halxa_3488 [Halopiger xanaduensis SH-6]
Scores for 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:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 594.34
//
Query:       gi|336254872|ref|YP_004597979.1|  [L=207]
Description: hypothetical protein Halxa_3489 [Halopiger xanaduensis SH-6]
Scores for 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-41  140.4   0.2    3.1e-41  139.9   0.2    1.2  1  DUF359    Protein of unknown function (DUF359)
  ------ inclusion threshold ------
      0.011   16.2   0.1      0.024   15.0   0.1    1.5  1  DUF2939   Protein of unknown function (DUF2939)


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 !  139.9   0.2   3.5e-45   3.1e-41       1     126 []      71     192 ..      71     192 .. 0.96

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 3.5e-45
                            DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdG 77 
                                       vt++ll+ag+ Pd+a+vD++t+Re+v+e  +e++    + ++++e+ Np+++i+ ++iea+ eal+++e+++ilV G
  gi|336254872|ref|YP_004597979.1|  71 VTYHLLEAGRAPDVALVDERTEREAVNEDVRETI----TAETHLEAVNPPAEISADVIEALLEALSRDEPTTILVAG 143
                                       8***********************9998555555....6799*********************************** PP

                            DUF359  78 EEDLavlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellekfe 126
                                       EEDL++lpai++apeg++vvYGqp+eG+v+v+vt++++e+++ lle+fe
  gi|336254872|ref|YP_004597979.1| 144 EEDLVALPAIVAAPEGASVVYGQPGEGMVHVRVTDDHRERMRALLERFE 192
                                       **********************************************996 PP

>> DUF2939  Protein of unknown function (DUF2939)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   2.7e-06     0.024      16      71 ..      72     130 ..      62     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-06
                           DUF2939  16 lyqlksAararDaaalselVdfpalraslkaqlnael.lraaapdke..ddplgalgaa 71 
                                        y l +A ra D+a ++e+ +++a+ + +++ ++ae  l+a++p++e   d ++al +a
  gi|336254872|ref|YP_004597979.1|  72 TYHLLEAGRAPDVALVDERTEREAVNEDVRETITAEThLEAVNPPAEisADVIEALLEA 130
                                       58899************************************999999854444555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1734.44
//
Query:       gi|336254873|ref|YP_004597980.1|  [L=65]
Description: DNA-directed RNA polymerase subunit E, RpoE2 [Halopiger xanaduensis SH-6]
Scores for 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-13   51.1   0.1    1.3e-13   50.9   0.1    1.1  1  Spt4      Spt4/RpoE2 zinc finger
     0.0019   18.2   0.7     0.0024   17.9   0.7    1.2  1  DZR       Double zinc ribbon
  ------ inclusion threshold ------
      0.061   13.0   3.9        2.2    8.0   0.1    2.2  2  zf-RRN7   Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn


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 !   50.9   0.1   2.1e-17   1.3e-13       3      77 .]       7      65 .]       5      65 .] 0.96

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 2.1e-17
                              Spt4  3 ACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                       C++C++v++ d+   ++C+ C            s++++e++ G+v+i++pe+S++A    ++ ++pg YAlkv+
  gi|336254873|ref|YP_004597980.1|  7 VCRECHRVNEPDN---DTCDAC-----------NSSSLTEDWAGYVVIAHPEDSEIASE--MQITEPGAYALKVR 65
                                      7************...******...........89************************..999*********96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.7     4e-07    0.0024       1      21 [.       8      28 ..       8      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4e-07
                               DZR  1 CpqCgeelppdarfCseCgtk 21
                                      C +C++ ++pd+ +C++C+++
  gi|336254873|ref|YP_004597980.1|  8 CRECHRVNEPDNDTCDACNSS 28
                                      99****************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 ?    6.4   0.7    0.0012       7.4      22      28 ..       6      12 ..       5      14 .. 0.86
   2 ?    8.0   0.1   0.00037       2.2       3      17 ..      18      32 ..      16      38 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0012
                           zf-RRN7 22 yyCrrCh 28
                                       +Cr+Ch
  gi|336254873|ref|YP_004597980.1|  6 LVCRECH 12
                                      79***** PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00037
                           zf-RRN7  3 kgppCgvCgcrsftl 17
                                      ++  C++C++ s t+
  gi|336254873|ref|YP_004597980.1| 18 DNDTCDACNSSSLTE 32
                                      6889******66555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 551.61
//
Query:       gi|336254874|ref|YP_004597981.1|  [L=192]
Description: DNA-directed RNA polymerase [Halopiger xanaduensis SH-6]
Scores for 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-15   56.6   0.0      4e-15   55.9   0.0    1.3  1  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
    6.4e-12   45.7   0.2    1.3e-11   44.6   0.2    1.6  1  S1             S1 RNA binding domain
  ------ inclusion threshold ------
      0.068   13.4   0.0        0.1   12.8   0.0    1.3  1  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25


Domain annotation for each model (and alignments):
>> 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 !   55.9   0.0   6.7e-19     4e-15       1      70 []       8      77 ..       8      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 6.7e-19
                                      EEEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                       SHS2_Rpb7-N  1 edtvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                      +dtv+++P++lg+   d +++ l++k+eg++++++G iv+v+++ ++++g+vl++ ++vy+++ f+a+ F
  gi|336254874|ref|YP_004597981.1|  8 KDTVEVPPEALGDVSPDLVKRLLQDKLEGRMDEEVGSIVSVTEVHDIGQGTVLPNEPGVYYEADFDAVTF 77
                                      69**********9889999999*********************************************998 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.2   2.2e-15   1.3e-11       2      61 ..      79     147 ..      78     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 2.2e-15
                                       STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEE CS
                                S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvl 61 
                                       p+  evv+G+V++v+++GafV +g +v+g++++s++s++           +  ++d+ l v+d ++ ++ 
  gi|336254874|ref|YP_004597981.1|  79 PQMQEVVDGTVVEVVEFGAFVGIG-PVDGLLHVSQISDEylafdgenqrLSSNESDRALGVDDAIRTRIV 147
                                       56679*******************.**************8887777777666677777777777776665 PP

>> RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05       0.1       1      93 [.      79     177 ..      79     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                                       -STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEEEEEEE- CS
                     RNA_pol_Rbc25   1 PfvgevltgkiksstregikvslgffddifvpkelLfepsefdeeeqawvweveeeeelyldvgeeirfrveeeifv 77 
                                       P ++ev+ g++ +  + g +v +g +d ++   +   e+ +fd e+q       +e++  l v+++ir r++ ++  
  gi|336254874|ref|YP_004597981.1|  79 PQMQEVVDGTVVEVVEFGAFVGIGPVDGLLHVSQISDEYLAFDGENQRLS---SNESDRALGVDDAIRTRIVTKSID 152
                                       7899************************999999999********99754...3678899999************** PP

                                       ------HHHHHCHHH.........C CS
                     RNA_pol_Rbc25  78 dvkpkspkeaeleee.........e 93 
                                       +++p+++k   ++++         e
  gi|336254874|ref|YP_004597981.1| 153 ERNPRDSKIGLTAKQpglgkhawlE 177
                                       ****999977776666654432221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1576.25
//
Query:       gi|336254875|ref|YP_004597982.1|  [L=140]
Description: nucleotide binding protein PINc [Halopiger xanaduensis SH-6]
Scores for complete 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  131.9   0.5    1.4e-38  131.7   0.5    1.0  1  PIN_9     PIN like domain
    2.3e-07   30.5   0.1    3.2e-07   30.1   0.1    1.2  1  DUF188    Uncharacterized BCR, YaiI/YqxD family COG1671
  ------ inclusion threshold ------
      0.019   15.7   0.9      0.042   14.6   0.9    1.6  1  PIN_3     PIN domain
      0.082   13.4   0.1       0.28   11.7   0.1    1.7  2  PIN       PIN domain


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 !  131.7   0.5   3.2e-42   1.4e-38       1     116 []      17     132 ..      17     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 3.2e-42
                             PIN_9   1 vilDtnaLmipvqfgvdifeelerllgsvelvvpkavleELerlakagkgkertaakvalsL.aerceiveaeeeka 76 
                                       v+lDt+aLm+pv+++v++f+el+rll++ e   p+av+eEL+rl +++ g+e taa+v+ +L  erc +v++e+++a
  gi|336254875|ref|YP_004597982.1|  17 VALDTSALMMPVELDVRLFDELDRLLEEFEPTAPQAVVEELRRL-AEKGGTEGTAANVGHDLaIERCLVVDTEASYA 92 
                                       79******************************************.777899***********8899*********** PP

                             PIN_9  77 DdailelakeldaavlvTnDreLkkrllekgipvilLRqk 116
                                       Dda++ela+e +++++vTnDr+L++r+le+++pvi LR++
  gi|336254875|ref|YP_004597982.1|  93 DDALVELAREGNVDYVVTNDRPLRDRVLEASVPVIALRGR 132
                                       **************************************98 PP

>> DUF188  Uncharacterized BCR, YaiI/YqxD family COG1671
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1     7e-11   3.2e-07      28      79 ..      79     132 ..      56     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 7e-11
                            DUF188  28 lvetvvVdsgadaaDdaIveraeag..DlvvTqDipLAarvlekgaaalsprGe 79 
                                         + +vVd++a  aDda+ve a++g  D vvT+D pL +rvle+ + ++  rG+
  gi|336254875|ref|YP_004597982.1|  79 IERCLVVDTEASYADDALVELAREGnvDYVVTNDRPLRDRVLEASVPVIALRGR 132
                                       46789******************994456***********************97 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.9   9.4e-06     0.042      37     115 ..      31     113 ..      16     114 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.4e-06
                             PIN_3  37 sprlldElervlarelaypqfklraadkaallakva.ler..kavapdaelrpllkcr...DpdDqkvlelAlaara 107
                                       ++rl+dEl r l  e++ p + +  ++ + +la+   +e   + v  d + + +l +      +D+  +elA +++ 
  gi|336254875|ref|YP_004597982.1|  31 DVRLFDELDRLL--EEFEPTAPQAVVEELRRLAEKGgTEGtaANVGHDLAIERCLVVDteaSYADDALVELAREGNV 105
                                       788999999888..557777777777776666666654445533333333333333334569*************** PP

                             PIN_3 108 dvlVTkdr 115
                                       d++VT dr
  gi|336254875|ref|YP_004597982.1| 106 DYVVTNDR 113
                                       ******97 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   6.3e-05      0.28       2      81 ..      18      95 ..      17     113 .. 0.79
   2 ?    1.0   0.0      0.13   5.7e+02      96     116 ..      95     115 ..      88     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.3e-05
                                      EE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHH CS
                               PIN  2 vlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiae 79
                                       lDTs+l   +  +    +++ +llee  e   +++v++El++ +++   + e  a++v   l  +++ ++++ a+ a+
  gi|336254875|ref|YP_004597982.1| 18 ALDTSALMMPVeLDVRLFDELDRLLEE-FEPTAPQAVVEELRRLAEK--GGTEGTAANVGHDLAIERCLVVDTEASYAD 93
                                      59******9999999999999999999.*******************..777777777777777888888886665555 PP

                                      HH CS
                               PIN 80 ea 81
                                       a
  gi|336254875|ref|YP_004597982.1| 94 DA 95
                                      54 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                                       HHHHHHHHHT-EEE.ESSTHH CS
                               PIN  96 liaAtAkehgikliatfDedf 116
                                        ++ +A+e + + ++t+D+ +
  gi|336254875|ref|YP_004597982.1|  95 ALVELAREGNVDYVVTNDRPL 115
                                       567799******999**9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1174.61
//
Query:       gi|336254876|ref|YP_004597983.1|  [L=410]
Description: translation initiation factor 2 subunit gamma [Halopiger xanaduensis SH-6]
Scores for 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-30  104.3   0.9    3.7e-29  101.7   0.9    1.9  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    1.8e-29  101.8   0.0    3.7e-29  100.8   0.0    1.5  1  eIF2_C        Initiation factor eIF2 gamma, C terminal
      3e-08   34.0   1.2      3e-08   34.0   1.2    2.0  2  GTP_EFTU_D2   Elongation factor Tu domain 2
    7.3e-05   22.7   0.2     0.0067   16.3   0.0    2.2  2  RsgA_GTPase   RsgA GTPase
    0.00012   22.1   0.0    0.00023   21.2   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.043   13.5   0.1       0.25   11.1   0.0    2.1  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.071   12.6   0.5        4.2    6.9   0.0    2.5  2  FeoB_N        Ferrous iron transport protein B
        0.1   12.6   0.0       0.19   11.8   0.0    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
       0.12   11.7   0.0        7.5    5.9   0.0    2.2  2  SRPRB         Signal recognition particle receptor beta subun


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 !  101.7   0.9   1.8e-32   3.7e-29       4     193 ..       9     199 ..       6     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 1.8e-32
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................ CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................ 64 
                                       +nig++ghvDhGKtTL+ +L                 + +D+++eE +rgi+i    +                   
  gi|336254876|ref|YP_004597983.1|   9 VNIGLVGHVDHGKTTLVQALSG---------------SWTDQHSEEMKRGISIRLGYADATfrhcegldepecytve 70 
                                       7******************982...............2478888999999999998888878899999999999999 PP

                                       .......TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESC CS
                          GTP_EFTU  65 .......ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKm 132
                                              +++  ++++++D+PGH+  + ++  g++ +Dgavlv++a+e  ++pqtee+l  +   g+  i+++ NK+
  gi|336254876|ref|YP_004597983.1|  71 eecpdgsESEPMRTVSFVDAPGHETLMATMLSGASLMDGAVLVISANEPvPQPQTEEHLMALDIIGIDnIVIAQNKV 147
                                       99998867999*************************************9679****************9******** PP

                                       GST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                          GTP_EFTU 133 Drl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                       D + +++ ++  ee++ ++      +e  +++   + pvv++Sa +  +++ l++a+ e +p
  gi|336254876|ref|YP_004597983.1| 148 DLVsGDQARQNYEEIQ-EF------VEGTVAE---DAPVVPVSAGQEVNLDLLIQAIEEEIP 199
                                       ***8788888888888.66......4444444...57********************99988 PP

>> 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 !  100.8   0.0   1.9e-32   3.7e-29       2      85 ..     324     407 ..     323     408 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 1.9e-32
                                       EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSE CS
                            eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrW 78 
                                       +++++++ll+r+vg+++ ++v++++++E+Lm+++G+a+t+g vts+++ e++v+Lk+Pv+ae g+kia++Rr+++rW
  gi|336254876|ref|YP_004597983.1| 324 RFTMDVDLLDRVVGAESGETVDEISTGEPLMMTVGTATTVGAVTSAREGECEVNLKRPVAAEPGAKIAINRRIGARW 400
                                       5899************************************************************************* PP

                                       EEEEEEE CS
                            eIF2_C  79 rLiGwGe 85 
                                       rLiG G+
  gi|336254876|ref|YP_004597983.1| 401 RLIGLGT 407
                                       ******8 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 ?   -2.9   0.0       4.8   9.6e+03      30      63 ..     161     194 ..     149     198 .. 0.57
   2 !   34.0   1.2   1.5e-11     3e-08       1      71 [.     231     305 ..     231     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.8
                                       EEEEEEEEEEEETEEESEEETTSEEEEEEEESSC CS
                       GTP_EFTU_D2  30 eivtrissletfhededeavaganaGvivaikgl 63 
                                       ei++ + ++ ++ +++  + ag+ + + ++i  +
  gi|336254876|ref|YP_004597983.1| 161 EIQEFVEGTVAEDAPVVPVSAGQEVNLDLLIQAI 194
                                       4556666666666666666666666555555555 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 1.5e-11
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEE......EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTT CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke......ivtrissletfhededeavaganaGvivaikgledaiivG 70 
                                       G+v +g++++G+l+++de++i++  ++++ +      i t+i+sl++  e++d+a +g+  Gv++++++  +   +G
  gi|336254876|ref|YP_004597983.1| 231 GGVLGGSLVQGELEVDDEIEIRPgREVEEGGqteyvpIETTIRSLQAGGENVDTATPGGLLGVGTGLDPSLT---KG 304
                                       899********************88886665***********************************977654...45 PP

                                       C CS
                       GTP_EFTU_D2  71 d 71 
                                       d
  gi|336254876|ref|YP_004597983.1| 305 D 305
                                       5 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.018        35     104     137 ..      13      43 ..       5      47 .. 0.83
   2 !   16.3   0.0   3.4e-06    0.0067      13     100 ..     104     197 ..      83     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.018
                                       EECSTTSSHHHHHHHHCTT-----S--------- CS
                       RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgevseklgrG 137
                                       lvG+   GK+tL+ al ++    t + se+++rG
  gi|336254876|ref|YP_004597983.1|  13 LVGHVDHGKTTLVQALSGS---WTDQHSEEMKRG 43 
                                       7899999**********98...666677777766 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.4e-06
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE- CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllv 82 
                                       ++ +d +++v+s++ep  +++  +  L+++   gi ++vi+ nK+Dl++ ++      e++e+ e + a + +v+ v
  gi|336254876|ref|YP_004597983.1| 104 ASLMDGAVLVISANEPVPQPQ-TEEHLMALDIIGIdNIVIAQNKVDLVSGDQarqnyeEIQEFVEGTVAEDAPVVPV 179
                                       667899********7777766.577888899999978999*********9998886767777777777889999999 PP

                                       -TTTHTTHHHHHHHCTTS CS
                       RsgA_GTPase  83 saktkegleelkellkdk 100
                                       sa ++ +l+ l ++++++
  gi|336254876|ref|YP_004597983.1| 180 SAGQEVNLDLLIQAIEEE 197
                                       999999999888888765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.1e-07   0.00023       1      95 [.      10     126 ..      10     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.1e-07
                                       EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE.....ETTEE........................ CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk.....lkgke........................ 47 
                                       ++++vG+   GK+tL++al+g+ + + s++    + i+ g  +         e                        
  gi|336254876|ref|YP_004597983.1|  10 NIGLVGHVDHGKTTLVQALSGSwTDQHSEEMKRGISIRLGYADatfrhC---Egldepecytveeecpdgsesepmr 83 
                                       589******************9877777777777777777665333331...1444455666666677777777777 PP

                                       .EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTT.CSHHHHH CS
                          MMR_HSR1  48 .ielvDtpGliegaseekglgkaflalee.adlillvvdasee.klkplde 95 
                                        + +vD pG  e       l  ++l+  + +d ++lv++a+ e   +p+ e
  gi|336254876|ref|YP_004597983.1|  84 tVSFVDAPG-HE------TLMATMLSGASlMDGAVLVISAN-EpVPQPQTE 126
                                       7********.54......7888888877768*******988.312233322 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.25       4      24 ..      11      31 ..       8      41 .. 0.87
   2 ?   -0.2   0.0      0.39   7.7e+02      53     140 ..      96     193 ..      84     196 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                         PduV-EutP  4 illiGkvgsGKttLtqalkge 24
                                      i l+G+v+ GKttL qal+g 
  gi|336254876|ref|YP_004597983.1| 11 IGLVGHVDHGKTTLVQALSGS 31
                                      669***************984 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.39
                         PduV-EutP  53 lysalivtsaeadvialvqdateeesvfppgfasvfnkeviGi....i..tkidla...edeenieaveelLksaGa 120
                                       l+ ++ + +   d  +lv +a+e+    p++  ++++ ++iGi    i   k+dl+   + ++n e  +e+++   a
  gi|336254876|ref|YP_004597983.1|  96 LMATMLSGASLMDGAVLVISANEPV-PQPQTEEHLMALDIIGIdnivIaqNKVDLVsgdQARQNYEEIQEFVEGTVA 171
                                       4555555555555556666665553.457777778888888863332222356655111223344444444444333 PP

                         PduV-EutP 121 ek..ifevsavekegieellky 140
                                       e   +  vsa ++++++ l++ 
  gi|336254876|ref|YP_004597983.1| 172 EDapVVPVSAGQEVNLDLLIQA 193
                                       3311456666666666666655 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 ?    6.9   0.0    0.0021       4.2       2      23 ..      10      31 ..       9      79 .. 0.90
   2 ?    4.0   0.1     0.016        33     107     156 .]     139     194 ..      65     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0021
                                      EEEEEESTTSSHHHHHHHHHTT CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltga 23
                                      ++ lvG  + Gkttl+ al+g+
  gi|336254876|ref|YP_004597983.1| 10 NIGLVGHVDHGKTTLVQALSGS 31
                                      688*****************97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.016
                                       SEEEEEETHHHHHHTTEEE-HHHHHHHHT......S-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N 107 pvvlalnmideaekkgieidlkkLsekLg......vpvvktsakkkegieellkai 156
                                       ++v+a n++d ++ ++ + + ++++e ++       pvv++sa ++ +++ l++ai
  gi|336254876|ref|YP_004597983.1| 139 NIVIAQNKVDLVSGDQARQNYEEIQEFVEgtvaedAPVVPVSAGQEVNLDLLIQAI 194
                                       689999*******9999999999999884333333799999999999999998875 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 ?   11.8   0.0   9.5e-05      0.19      59     102 ..     141     196 ..     137     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.5e-05
                      MMR_HSR1_Xtn  59 lyvlNKiDlisleeldelare............pnsvviSaekelnldeLkekiwe 102
                                       +++ NK+Dl+s ++ ++ ++e              +v++Sa +e+nld L ++i e
  gi|336254876|ref|YP_004597983.1| 141 VIAQNKVDLVSGDQARQNYEEiqefvegtvaedAPVVPVSAGQEVNLDLLIQAIEE 196
                                       6788*****88777766666555667778887668999************999855 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 ?    3.5   0.0     0.021        41       7      26 ..      12      31 ..       5      53 .. 0.80
   2 ?    5.9   0.0    0.0038       7.5      45     125 ..      79     150 ..      63     170 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.021
                                      EEE-STTSSHHHHHHHHHHS CS
                             SRPRB  7 llvGlsdsGKTslftrLttd 26
                                       lvG  d GKT+l + L+  
  gi|336254876|ref|YP_004597983.1| 12 GLVGHVDHGKTTLVQALSGS 31
                                      589***********999865 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0038
                                       ..GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE- CS
                             SRPRB  45 sekgskltliDfPGheklrqklleklkaksslkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnK 121
                                       se   ++ ++D PGhe l   +l      s + g v v+ S+ +p    ++ E l+ + +i +      +i+iA nK
  gi|336254876|ref|YP_004597983.1|  79 SEPMRTVSFVDAPGHETLMATMLSG---ASLMDGAVLVI-SANEPVPQPQTEEHLMALDIIGI-----DNIVIAQNK 146
                                       555667899*********9999887...44466666655.67777777777777776655555.....346667776 PP

                                       TTST CS
                             SRPRB 122 qelf 125
                                        +l+
  gi|336254876|ref|YP_004597983.1| 147 VDLV 150
                                       6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); 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:                         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 0.21s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3278.80
//
Query:       gi|336254877|ref|YP_004597984.1|  [L=344]
Description: hypothetical protein Halxa_3494 [Halopiger xanaduensis SH-6]
Scores for 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:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2636.25
//
Query:       gi|336254878|ref|YP_004597985.1|  [L=78]
Description: hypothetical protein Halxa_3495 [Halopiger xanaduensis SH-6]
Scores for 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-05   24.3   1.2    0.00011   22.5   1.2    1.8  1  DUF2171   Uncharacterized protein conserved in bacteria (DUF2
  ------ inclusion threshold ------
      0.045   13.8   0.8      0.077   13.1   0.8    1.6  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> DUF2171  Uncharacterized protein conserved in bacteria (DUF2171)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.2   1.2e-08   0.00011       3      59 ..       9      77 ..       8      78 .] 0.90

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.2e-08
                           DUF2171  3 ehmeVvgsdGehvGtVDhvegdrikLtkddseeg............gqhhyiplswVasvdddkVhLsk 59
                                      e+ +Vv ++Ge++G V+ veg +  +  d                  + + +++++V+s+ dd+++L++
  gi|336254878|ref|YP_004597985.1|  9 EGKQVVNAEGEQIGIVESVEGGTAHVNPDPGMTDtiksklgwgdtdEETYPLDAENVESISDDEIRLQR 77
                                      7899*****************999999999877799999999998677799***************975 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.8   8.6e-06     0.077      10      28 ..       9      27 ..       6      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.6e-06
                                      TT-EEEETTSSEEEEEEEE CS
                               PRC 10 iGkeVytedGeklGkVkDv 28
                                      +Gk+V++ +Ge++G V+ v
  gi|336254878|ref|YP_004597985.1|  9 EGKQVVNAEGEQIGIVESV 27
                                      69**************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 631.86
//
Query:       gi|336254879|ref|YP_004597986.1|  [L=274]
Description: beta-lactamase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-22   78.2   0.3    7.6e-22   77.8   0.3    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00023   21.2   4.0    0.00037   20.6   4.0    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.23   11.4   0.0    1.2  1  Mur_ligase_M   Mur ligase middle 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 !   77.8   0.3   1.3e-25   7.6e-22       3     200 ..      50     250 ..      48     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.3e-25
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvlavleanfvyla 78 
                                       +L+D +pd+r q+l        rde+p  da ++th H+DHl gl  + + +   +l++ya +++  +  ++    +
  gi|336254879|ref|YP_004597986.1|  50 LLVDFSPDFRYQFL--------RDEVPLPDAAVITHIHFDHLDGLGNVFRvFD--SLEVYAADETDPQTGKSVAETV 116
                                       799*******9944........5679********************9999554..59***99888887777766655 PP

                                       CHTT...TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE..CTTEEEEEESS-S---.HH CS
                     Lactamase_B_2  79 leee...pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie..gggkrvyyigDtgyip.ee 149
                                       ++     ++++v++ ++ e++++   g+++t++p++h            ++Gl+ie  ++g ++  +gDt y   e+
  gi|336254879|ref|YP_004597986.1| 117 RDDYhylDPIDVRPTTPLEPVRIC--GFDVTLVPVEHPPLL--------CYGLAIEdpETGAKLSLSGDTSYGVpER 183
                                       5555688899*************6..789********9999........*******9999***********855499 PP

                                       HHHHHCT-SEEEEE-S-SSTTHHHH..................HHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 150 igerlggadllllditayeddemir..................hmgHltpeeaveaaadlgakrlvliH 200
                                        +e l+++dlll d+ +  + ++ +                  +  H+t e+a+++a+dl+a+r+ l+H
  gi|336254879|ref|YP_004597986.1| 184 SREALADPDLLLADAIV--PARFCEhhpvggrhegpdgvprtfGTKHMTREGALALADDLEAERTRLVH 250
                                       ************99663..333444478999************************************** PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   4.0   6.1e-08   0.00037      13     162 ..      45     187 ..      33     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.1e-08
                                       ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHH CS
                       Lactamase_B  13 gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeadd 89 
                                         g+ +L+D   + +++        l+ +   +da ++TH H+DH  glg + + +d   ++ a+e+   ++  +  
  gi|336254879|ref|YP_004597986.1|  45 RTGESLLVDFSPDFRYQF-------LRDEVPLPDAAVITHIHFDHLDGLGNVFRVFDSLEVYAADETDPQTGKSVAE 114
                                       556677777777777776.......47888889************************99999999999999999955 PP

                                       HHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE.TTCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B  90 aasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey.gggkvlftGDallagetgridl 162
                                           + + +  + +  p +++e+  + ++++ +++v + p+   g ++ +   g+k+ ++GD+++  ++ + + 
  gi|336254879|ref|YP_004597986.1| 115 TVRDDYH-YLDPIDVRPTTPLEPVRICGFDVTLVPVEHPPLLCYGLAIEDPeTGAKLSLSGDTSYGVPERSREA 187
                                       4443333.666667777777777777777777777777777777777777767889999999999887776666 PP

>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.9e-05      0.23      72      95 ..      70      93 ..      62      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.9e-05
                                      ESEEEE---TSTTHHHHSSHHHHH CS
                      Mur_ligase_M 72 pdvavitnispdHldfhgtlenya 95
                                      pd+avit i  dHld +g++ +++
  gi|336254879|ref|YP_004597986.1| 70 PDAAVITHIHFDHLDGLGNVFRVF 93
                                      9***************99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); 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:                         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 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1963.84
//
Query:       gi|336254880|ref|YP_004597987.1|  [L=120]
Description: hypothetical protein Halxa_3497 [Halopiger xanaduensis SH-6]
Scores for 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   12.5   0.1       0.16   12.3   0.1    1.2  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   8.7e-06      0.16       4      90 ..      26     115 ..      23     120 .] 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.7e-06
                                       HHHHHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH.HHHEHHHHHHHHCCCEEECTT.EEEEEECE CS
                      NTP_transf_2   4 lleelkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsre.kkeegleklaeiikfleellg.levdlvtr 76 
                                       ++e+++ +++  + ++v+fG ++rG+     +  +l+vl+ee ++  ++ e l + +  ++ ++  +  l++d v++
  gi|336254880|ref|YP_004597987.1|  26 FAERVRAEHGdaIRDLVVFGDAVRGDRDVHAEAEVLIVLEEEDEEReRQLEALAETVGAEYGVVFSPYvLPADRVEK 102
                                       67889999999999****************************65435444444455544444443332033333344 PP

                                       EECCCCTEEEEEEC CS
                      NTP_transf_2  77 ekledpllvksile 90 
                                        + + pll + ++e
  gi|336254880|ref|YP_004597987.1| 103 REEH-PLLQRAFAE 115
                                       4444.666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 988.31
//
Query:       gi|336254881|ref|YP_004597988.1|  [L=92]
Description: hypothetical protein Halxa_3498 [Halopiger xanaduensis SH-6]
Scores for 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  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 757.43
//
Query:       gi|336254882|ref|YP_004597989.1|  [L=473]
Description: AAA ATPase central domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-38  132.0   0.0      4e-38  130.8   0.0    1.7  1  AAA           ATPase family associated with various cellular 
    9.6e-10   38.1   0.1    2.8e-09   36.6   0.1    1.8  1  AAA_lid_3     AAA+ lid domain
    3.8e-05   23.7   0.0    0.00015   21.8   0.0    2.1  1  AAA_5         AAA domain (dynein-related subfamily)
    0.00016   22.2   0.3     0.0055   17.2   0.0    2.8  2  AAA_18        AAA domain
    0.00026   21.3   1.4       0.13   12.5   0.4    3.2  2  AAA_22        AAA domain
    0.00039   20.9   1.1      0.012   15.9   0.7    3.1  2  AAA_16        AAA ATPase domain
    0.00042   19.9   0.0     0.0011   18.5   0.0    1.7  1  AAA_7         P-loop containing dynein motor region
    0.00049   20.2   0.6     0.0015   18.7   0.0    2.1  2  AAA_2         AAA domain (Cdc48 subfamily)
    0.00098   18.9   0.0     0.0019   17.9   0.0    1.6  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
     0.0016   18.7   0.0     0.0061   16.8   0.0    2.1  1  AAA_28        AAA domain
      0.003   17.2   0.0      0.026   14.1   0.0    2.3  2  AAA_25        AAA domain
     0.0041   17.3   0.4      0.023   14.8   0.0    2.5  2  AAA_33        AAA domain
  ------ inclusion threshold ------
      0.012   14.8   0.0      0.025   13.8   0.0    1.5  1  TIP49         TIP49 P-loop domain
      0.013   15.9   0.2      0.055   13.9   0.0    2.2  2  AAA_17        AAA domain
      0.014   15.1   0.1      0.073   12.8   0.0    2.3  3  IstB_IS21     IstB-like ATP binding protein
      0.022   14.0   0.1      0.041   13.0   0.1    1.5  1  DUF815        Protein of unknown function (DUF815)
      0.025   14.3   0.0      0.047   13.5   0.0    1.4  1  AAA_11        AAA domain
      0.051   14.0   0.0      0.097   13.1   0.0    1.5  1  RNA_helicase  RNA helicase
      0.052   12.9   0.0      0.095   12.1   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.055   12.5   0.0       0.14   11.2   0.0    1.6  1  T2SSE         Type II/IV secretion system protein
       0.06   12.8   0.0        6.4    6.1   0.0    2.4  2  TniB          Bacterial TniB protein
      0.061   13.2   0.3       0.14   12.0   0.0    1.8  2  AAA_3         ATPase family associated with various cellular 
      0.066   13.7   0.0       0.31   11.6   0.0    2.2  2  ABC_tran      ABC transporter
        0.1   12.7   0.0       0.24   11.5   0.0    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
       0.12   12.4   0.0       0.22   11.5   0.0    1.5  1  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 !  130.8   0.0   5.6e-41     4e-38       1     131 [.     232     360 ..     232     361 .. 0.98

  Alignments for each domain:
  == domain 1  score: 130.8 bits;  conditional E-value: 5.6e-41
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       +l++GppGtGKT++a+a+a++++ +f+e+++s ++s+y+ge++k++ ++f+ ak+ + p+ilfiDE+d +ak+r+++
  gi|336254882|ref|YP_004597989.1| 232 LLFVGPPGTGKTSTAQALARDMDLPFVEVKLSMITSQYLGETAKNVDKTFEVAKRLS-PCILFIDEFDFVAKTRRSD 307
                                       69******************************************************9.****************999 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieie 131
                                       e+   +r+vn+Ll+ +d+ +  e++v++igatn+pd+ld+a   +Rfd++i+++
  gi|336254882|ref|YP_004597989.1| 308 EHAALKRAVNTLLKSIDNISLIEDDVLLIGATNHPDQLDDAAW-RRFDEIINFP 360
                                       *******************************************.7******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 !   36.6   0.1   3.9e-12   2.8e-09       3      43 ..     384     424 ..     382     430 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 3.9e-12
                         AAA_lid_3   3 dlkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                                       d + +Ae+TeG +G Dl  + reA+l+Al ++++++t+ed+
  gi|336254882|ref|YP_004597989.1| 384 DPQLIAEATEGLTGSDLRMVLREAVLEALTEDRTTLTQEDL 424
                                       66679***********************************8 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 !   21.8   0.0   2.1e-07   0.00015       2     138 .]     232     353 ..     231     353 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.1e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEvera 77 
                                       +l vGppGtgK++ a+ la+ +  ++++v l+  +t++  +g+      t++ vd+ +  a r +++il++DE++ +
  gi|336254882|ref|YP_004597989.1| 232 LLFVGPPGTGKTSTAQALARDMDLPFVEVKLSM-ITSQ-YLGE------TAKNVDKTFEVAKRlSPCILFIDEFDFV 300
                                       799***************************987.3333.3333......3356677766555579999999999988 PP

                                       -HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5  78 esevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                        +   +  +  l +    l ++   ++  +dd    + +i+++n +d    +l+ a ++Rf
  gi|336254882|ref|YP_004597989.1| 301 AKTRRSDEHAALKRAVNTLLKSIDNISLIEDD----VLLIGATNHPD----QLDDAAWRRF 353
                                       77777777777777777776666666666666....88888888888....7777777777 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.35   2.5e+02      67     104 ..     152     190 ..      94     217 .. 0.71
   2 !   17.2   0.0   7.7e-06    0.0055       3      45 ..     234     302 ..     232     357 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.35
                            AAA_18  67 nssaleegknlvidghlaeleseaakdikk..vvLtaspe 104
                                       +++    ++ + idg+l+e+++++  +     v ++a++e
  gi|336254882|ref|YP_004597989.1| 152 QNR-PIRADRVWIDGLLEEYFDDEEDEDMLdlVEVRAPEE 190
                                       222.345677799999999998877766667888888776 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 7.7e-06
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.....a 45 
                                         G+pG+GKt+ a++L++ + +                     +++  +vak   +++ + +e     +
  gi|336254882|ref|YP_004597989.1| 234 FVGPPGTGKTSTAQALARDMDLpfvevklsmitsqylgetaknVDKTFEVAKRLSPCILFIDEfdfvaK 302
                                       68**************99976677877777788666666666666666666666666666666555542 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.4   0.00018      0.13       8      29 ..     232     253 ..     228     345 .. 0.76
   2 ?    0.9   0.0       0.7     5e+02      55      84 ..     403     430 ..     361     439 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                            AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                       l+ +G++GtGKT +++ l++  
  gi|336254882|ref|YP_004597989.1| 232 LLFVGPPGTGKTSTAQALARDM 253
                                       6789*************99865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.7
                            AAA_22  55 dllrellralglelkaerlsseellealeq 84 
                                        l++++l+al++++ +  l++e+ll+a+e+
  gi|336254882|ref|YP_004597989.1| 403 VLREAVLEALTEDRTT--LTQEDLLNAVEE 430
                                       3577888888877777..999999999887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         6   4.3e+03      70      98 ..     159     186 ..     138     222 .. 0.56
   2 !   15.9   0.7   1.7e-05     0.012      23      51 ..     228     256 ..     204     433 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6
                            AAA_16  70 sa.laqalareellrqlldeaesaeleawr 98 
                                       +  +++ l  ee++ +++de+  +++e  r
  gi|336254882|ref|YP_004597989.1| 159 DRvWIDGL-LEEYFDDEEDEDMLDLVEV-R 186
                                       34477777.4477777777755533332.2 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.7e-05
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekd 51 
                                       + + +l++G++G+GK+s +++l+r +   
  gi|336254882|ref|YP_004597989.1| 228 EIGKLLFVGPPGTGKTSTAQALARDMDLP 256
                                       33779******************977655 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 !   18.5   0.0   1.5e-06    0.0011      24     110 ..     220     298 ..     215     310 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                             AAA_7  24 yllelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggk 100
                                       yl e  l++  ++l+vGp GtGKt++++ l + +d   ++ +++++  +    ++ + +++ +        +++   
  gi|336254882|ref|YP_004597989.1| 220 YLSEIGLREIGKLLFVGPPGTGKTSTAQALARDMD-LPFVEVKLSMITSQYLGETAKNVDKTF-------EVAKRLS 288
                                       5666666777789*********************9.333333333333333333333333333.......3444555 PP

                             AAA_7 101 klvvFvDDln 110
                                        +++F+D+++
  gi|336254882|ref|YP_004597989.1| 289 PCILFIDEFD 298
                                       5666666665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       7.6   5.5e+03      76      82 ..     207     213 ..     172     220 .. 0.82
   2 !   18.7   0.0   2.1e-06    0.0015       1     105 [.     227     325 ..     227     333 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.6
                                       TGGG--- CS
                             AAA_2  76 EidKihp 82 
                                       EidKi++
  gi|336254882|ref|YP_004597989.1| 207 EIDKIAK 213
                                       8888887 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.1e-06
                                       -----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEE CS
                             AAA_2   1 rpiisilllgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllD 75 
                                       r+i+++l++gp g+Gkt +a+ala+ +++    +++ +  s ++     e ++ v++    ++    +    i+++D
  gi|336254882|ref|YP_004597989.1| 227 REIGKLLFVGPPGTGKTSTAQALARDMDL----PFVEVKLSMITSqyLGETAKNVDKTFEVAK----RLSPCILFID 295
                                       57899**********************98....666666666665111123333443333333....33355***** PP

                                       TGGG-------------HHHHHHHHHHHH- CS
                             AAA_2  76 EidKihpkessgadvSregVqrdLLqileg 105
                                       E d ++++++s +    +  ++ LL+ +++
  gi|336254882|ref|YP_004597989.1| 296 EFDFVAKTRRSDEHAALKRAVNTLLKSIDN 325
                                       *******97777777777777888887776 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 !   17.9   0.0   2.7e-06    0.0019      33      95 ..     229     299 ..     195     356 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.7e-06
                            RuvB_N  33 ldhvllyGpPGlGkttlakiiakelg.....vklk.itsgPvlekagdlaalltnle..ekdvlfideihr 95 
                                       +  +l++GpPG Gkt+ a+ +a++++     vkl  its    e a+++   +   +  +  +lfide   
  gi|336254882|ref|YP_004597989.1| 229 IGKLLFVGPPGTGKTSTAQALARDMDlpfveVKLSmITSQYLGETAKNVDKTFEVAKrlSPCILFIDEFDF 299
                                       56789*******************98222113333123333333344433332222200234777777655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.5e-06    0.0061       3      42 ..     233     273 ..     231     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.5e-06
                            AAA_28   3 vitGgestGKTtlleaLaar.gypvvpEaareileeklakg 42 
                                        ++G+++tGKT++++aLa++ + p v+    +i+++ l ++
  gi|336254882|ref|YP_004597989.1| 233 LFVGPPGTGKTSTAQALARDmDLPFVEVKLSMITSQYLGET 273
                                       699***************87688887655555555555444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.7e-05     0.026      10      57 ..     206     253 ..     199     257 .. 0.88
   2 ?   -0.4   0.0      0.98     7e+02     128     172 ..     275     319 ..     251     328 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.7e-05
                            AAA_25  10 vsvadlaapppprrwlvk.gllpagelallaGapgtGKttlaldlalav 57 
                                       ++++++a+++++r++l + gl ++ +  l++G+pgtGKt  a  la ++
  gi|336254882|ref|YP_004597989.1| 206 AEIDKIAKAIEHRDYLSEiGL-REIGKLLFVGPPGTGKTSTAQALARDM 253
                                       56788999**********666.799999****************99876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.98
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galveal 172
                                         vd+  +++++   +  + iD ++++      +++++ +++v+ l
  gi|336254882|ref|YP_004597989.1| 275 KNVDKTFEVAKR-LSPCILFIDEFDFVAKTRRSDEHAAlKRAVNTL 319
                                       456777777777.458999999999999997777776667777765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2         3   2.1e+03      67      93 ..      58      84 ..      55     133 .. 0.52
   2 !   14.8   0.0   3.2e-05     0.023       3      32 ..     233     264 ..     232     361 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3
                            AAA_33 67 lsagrnvildatnlsrrerarflklar 93
                                      ++ag++  l atn ++re   +++ + 
  gi|336254882|ref|YP_004597989.1| 58 RRAGISRPLSATNSTAREATGVDQPWA 84
                                      555666666666666666655554443 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.2e-05
                            AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdt 32 
                                       l+vG+pG+GK+  a+ l++  +  +v +    
  gi|336254882|ref|YP_004597989.1| 233 LFVGPPGTGKTSTAQALARDMDlpFVEVKLSM 264
                                       89***************998766555444444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.5e-05     0.025      53      93 ..     232     270 ..     224     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  53 vLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslev 93 
                                       +L++Gp+gtGkt+ a a+++++   +pfv ++ s + s+ +
  gi|336254882|ref|YP_004597989.1| 232 LLFVGPPGTGKTSTAQALARDMD--LPFVEVKLSMITSQYL 270
                                       799*****************986..9***999998877654 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       7.2   5.2e+03      43      79 ..     177     211 ..     159     224 .. 0.52
   2 ?   13.9   0.0   7.6e-05     0.055       1      25 [.     235     259 ..     235     288 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.2
                                       HHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE- CS
                            AAA_17  43 rdemrklpleekkelqkeaaekiaeeakkkgvlvdgh 79 
                                       +d ++ ++ +  +e++ ++++ +  e+  +++ +d+ 
  gi|336254882|ref|YP_004597989.1| 177 EDMLDLVEVRAPEEVDITLEDLVLTED--QEAEIDKI 211
                                       333334444555555555555554442..23344444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.6e-05
                                       EE-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                       +G+PG GK+  ++ l++++++++++
  gi|336254882|ref|YP_004597989.1| 235 VGPPGTGKTSTAQALARDMDLPFVE 259
                                       7*********************997 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 ?   -2.2   0.0       4.1   2.9e+03     101     137 ..     150     186 ..     146     193 .. 0.84
   2 ?   12.8   0.0    0.0001     0.073      47      70 ..     229     252 ..     186     309 .. 0.71
   3 ?   -1.8   0.0         3   2.2e+03      78     109 ..     291     322 ..     281     336 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.1
                         IstB_IS21 101 ralkrllkvdllilDdlgllpldqaeaellfeviekr 137
                                       r+++r +++d + +D l  + +d++e e++++++e r
  gi|336254882|ref|YP_004597989.1| 150 REQNRPIRADRVWIDGLLEEYFDDEEDEDMLDLVEVR 186
                                       5667778888889999999999*********999977 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.0001
                         IstB_IS21  47 kenivllGpsGvGKshlaialgve 70 
                                          ++++Gp+G+GK+  a al+++
  gi|336254882|ref|YP_004597989.1| 229 IGKLLFVGPPGTGKTSTAQALARD 252
                                       457899***************975 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3
                         IstB_IS21  78 vlfvrvedLveelkrarrdgklaralkrllkv 109
                                       +lf+   d+v++ +r +++  l+ra+++llk+
  gi|336254882|ref|YP_004597989.1| 291 ILFIDEFDFVAKTRRSDEHAALKRAVNTLLKS 322
                                       67788888888888888888888888888775 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.8e-05     0.041      54     123 ..     230     304 ..     171     339 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.8e-05
                            DUF815  54 nnvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvel...lrerperfilfvDDLsFeeeee 123
                                        ++L++G  GtGK s+ +al +++      ++l  ++ + l e  k v++   +++r   +ilf+D   F ++ +
  gi|336254882|ref|YP_004597989.1| 230 GKLLFVGPPGTGKTSTAQALARDMDLPFveVKLSMITSQYLGETAKNVDKtfeVAKRLSPCILFIDEFDFVAKTR 304
                                       46799****************9998876667778888888887777776512245666679******99976543 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.6e-05     0.047      18      42 ..     219     254 ..     200     295 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-05
                            AAA_11  18 e...........itliqGPPGtgKTktivellsqll 42 
                                       +             l+ GPPGtgKT+t  +l + + 
  gi|336254882|ref|YP_004597989.1| 219 DylseiglreigKLLFVGPPGTGKTSTAQALARDMD 254
                                       4444445555558899***********999999885 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00013     0.097       2      24 ..     233     255 ..     232     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallk 24 
                                       +++Gp+g+GK+++a+ La+++  
  gi|336254882|ref|YP_004597989.1| 233 LFVGPPGTGKTSTAQALARDMDL 255
                                       789****************9974 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013     0.095      24      43 ..     231     250 ..     215     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlp 43 
                                       +ll+vGppG+GKt  a++l+
  gi|336254882|ref|YP_004597989.1| 231 KLLFVGPPGTGKTSTAQALA 250
                                       79**************9986 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 ?   11.2   0.0    0.0002      0.14      93     150 ..     183     250 ..     176     262 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                             T2SSE  93 lviRkksakeltlddlgaeealk..........ekiaevlrkavrerglilvsGgTgsGKttllyall 150
                                       + +R +++ ++tl+dl+ +e+++          e+ + + +  +re g +l+ G+ g+GKt ++ al 
  gi|336254882|ref|YP_004597989.1| 183 VEVRAPEEVDITLEDLVLTEDQEaeidkiakaiEHRDYLSEIGLREIGKLLFVGPPGTGKTSTAQALA 250
                                       568999****************977755555543333333334678899*************999876 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.044        31      35      58 ..     229     252 ..     206     259 .. 0.83
   2 ?    6.1   0.0    0.0089       6.4     103     144 ..     272     313 ..     261     338 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.044
                              TniB  35 mpnlllvGdsnnGKtmivekFarl 58 
                                       + +ll+vG++ +GKt+ ++  ar+
  gi|336254882|ref|YP_004597989.1| 229 IGKLLFVGPPGTGKTSTAQALARD 252
                                       5689************99887765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0089
                              TniB 103 rvskleqqvlrllrelkvrvLiiDEihnllagsarkqrefln 144
                                       +++k  +++ ++ ++l++ +L iDE++ + + ++++ +++l 
  gi|336254882|ref|YP_004597989.1| 272 ETAKNVDKTFEVAKRLSPCILFIDEFDFVAKTRRSDEHAALK 313
                                       566777889999****************99988877654432 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 ?   12.0   0.0    0.0002      0.14       2      47 ..     232     275 ..     231     345 .. 0.75
   2 ?   -2.4   0.1       5.6     4e+03      80      96 ..     406     422 ..     403     430 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevf 47 
                                       +l+ g PG++kt +++ala+ +dl f  +++   ++ s  lG +  
  gi|336254882|ref|YP_004597989.1| 232 LLFVGPPGTGKTSTAQALARDMDLPFVEVKLS--MITSQYLGETAK 275
                                       577899*******************9888774..667777776544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.6
                             AAA_3  80 salleameerqvtvege 96 
                                        a+lea+ e + t+++e
  gi|336254882|ref|YP_004597989.1| 406 EAVLEALTEDRTTLTQE 422
                                       58899999998887765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.5   1.8e+03      33      74 ..      92     132 ..      86     216 .. 0.61
   2 ?   11.6   0.0   0.00043      0.31      12      67 ..     230     283 ..     222     411 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.5
                                       TSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  33 gllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpel 74 
                                        + +  +G+i+l ++++ e ++   r+  + l ++p+l ++ 
  gi|336254882|ref|YP_004597989.1|  92 TERDEFSGTITLTQQEMAE-RWFAERADEKRLLENPTLAKHF 132
                                       5556668888888888887.3333333333344444444444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00043
                                       SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                        k+ +vG+ G+GK++ +++la+ ++    e++l +  +++  l ++ k++   ++ 
  gi|336254882|ref|YP_004597989.1| 230 GKLLFVGPPGTGKTSTAQALARDMDLPFVEVKLSMITSQY--LGETAKNVDKTFEV 283
                                       57889*****************999988888888777777..44444554444444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00033      0.24       2      45 ..     232     285 ..     231     355 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                                       EEEEESTTSSHHHHHHHHHT.........S.TEEESSSTTSSSSEEEEEEEETT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg.........e.kaivsdkpgtTrdinegrvklkg 45 
                                        ++vG p +GK++  +al +         +   i+s++ g T + + +++++ +
  gi|336254882|ref|YP_004597989.1| 232 LLFVGPPGTGKTSTAQALARdmdlpfvevKlSMITSQYLGETAKNVDKTFEVAK 285
                                       579****************8777777755456799*******999988888443 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 ?   11.5   0.0   0.00031      0.22       3      47 ..     199     252 ..     197     309 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                                       EE-HHHHHHHHHHT...............TTSEEEEEESTTSTHHHHHHHHHHH CS
                            ResIII   3 elreyQeeaienlleklks.........krdkrglikmaTGtGKTlvaaklier 47 
                                        l e Qe  i+++++++++         ++  ++l++ + GtGKT +a +l++ 
  gi|336254882|ref|YP_004597989.1| 199 VLTEDQEAEIDKIAKAIEHrdylseiglREIGKLLFVGPPGTGKTSTAQALARD 252
                                       578999999*****999967777666655555****************888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3519.98
//
Query:       gi|336254883|ref|YP_004597990.1|  [L=122]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-14   52.1   0.0    2.6e-12   47.4   0.0    2.0  1  Usp        Universal stress protein family
  ------ inclusion threshold ------
      0.041   13.5   0.1       0.11   12.2   0.0    1.6  2  DAGK_cat   Diacylglycerol kinase catalytic domain
      0.049   12.6   0.0      0.055   12.4   0.0    1.0  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
      0.051   13.3   0.0      0.074   12.8   0.0    1.3  1  FMN_red    NADPH-dependent FMN reductase
      0.074   12.5   0.0      0.092   12.2   0.0    1.1  1  Z1         Z1 domain


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 !   47.4   0.0   7.3e-16   2.6e-12       4     141 .]       2     122 .]       1     122 [] 0.82

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 7.3e-16
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       ++l+++ gs+es kAl++ ++  ++ g++l+++   d ++s+ + d++ +++e+ le++                g+
  gi|336254883|ref|YP_004597990.1|   2 NVLLGLGGSDESVKALRQTIDRTREAGDQLTVAVL-DKPESKRSQDEMATEAEDHLEEA----------------GI 61 
                                       79**************************9776643.33333333333333333333333................56 PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       + e+v++egdp+ +++++ae+ + d +V+G   +s   ++ lG  +e vl +ap  V +Vr
  gi|336254883|ref|YP_004597990.1|  62 DAEIVRLEGDPGSALVDYAEQGEFDQLVIGGGTLSPMGKIQLGPITEFVLLNAPTTVKLVR 122
                                       889****************************************************998887 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.083     3e+02      10      45 ..       8      43 ..       6      52 .. 0.74
   2 ?   12.2   0.0     3e-05      0.11      10      64 ..      41      93 ..      32      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.083
                                      CTTTTHHHHHHHCHHHHHHCTCEEEEEE--STTHHH CS
                          DAGK_cat 10 sGkgkgekllrkvrelleeagvelelieteepgdak 45
                                      +G+ ++ k+lr+  +  +eag +l++   ++p++ +
  gi|336254883|ref|YP_004597990.1|  8 GGSDESVKALRQTIDRTREAGDQLTVAVLDKPESKR 43
                                      577778888889999999999999999888877643 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3e-05
                                      CTTTTHHHHHHHCHHHHHHCTCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEES CS
                          DAGK_cat 10 sGkgkgekllrkvrelleeagvelelieteepgdakelakeakeegvdlivvaGG 64
                                      s k++ ++++ +++++leeag+++e+++ e  + + +l+  a++ ++d +v+ GG
  gi|336254883|ref|YP_004597990.1| 41 S-KRSQDEMATEAEDHLEEAGIDAEIVRLE-GDPGSALVDYAEQGEFDQLVIGGG 93
                                      4.677778889******************9.777899****************99 PP

>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.5e-05     0.055     305     367 ..      40     104 ..      15     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                                       TTSHHHHHHHHHHHHHHHHTTEEEEEEEECHH..HHHHHHHHCTTESEEEEEEECTTSTTHHHHH CS
                         SBP_bac_5 305 sgspaekaiaeliqqqlkkiGikvevktvdwa..atylervkdgdfdmillgwgadypdpdnfln 367
                                        ++  ++++a+   + l+++Gi++e+  ++    ++  +++++g+fd  + g g+ +p +  +l 
  gi|336254883|ref|YP_004597990.1|  40 ESKRSQDEMATEAEDHLEEAGIDAEIVRLEGDpgSALVDYAEQGEFDQLVIGGGTLSPMGKIQLG 104
                                       3344555**********************88889899999***********99998888776665 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.1e-05     0.074       9      50 ..      38      78 ..      31      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                                      --STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--...--- CS
                           FMN_red  9 Slrkgsntrklaewaaealkeagaevelidladlilpc.alcd 50
                                       + ++++ + +a +a+++l+eag+++e+++l +   p  al+d
  gi|336254883|ref|YP_004597990.1| 38 KPESKRSQDEMATEAEDHLEEAGIDAEIVRLEGD--PGsALVD 78
                                      5778999************************985..3324444 PP

>> Z1  Z1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.6e-05     0.092      67     141 ..      12      96 ..       8      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.6e-05
                                Z1  67 ellkeleklwekekts............tkseeeelsfeevkeelkealekievvvvNsskkkerldYeeeeeegls 131
                                       e++k l+++ ++++++            +++++++   +e +++l+ea  + e+v + ++  +  +dY e+ e  + 
  gi|336254883|ref|YP_004597990.1|  12 ESVKALRQTIDRTREAgdqltvavldkpESKRSQDEMATEAEDHLEEAGIDAEIVRLEGDPGSALVDYAEQGE--FD 86 
                                       55666666666663335555667777765566677778889999****9*************9999****866..99 PP

                                Z1 132 vIavGGnkLs 141
                                       + ++GG +Ls
  gi|336254883|ref|YP_004597990.1|  87 QLVIGGGTLS 96 
                                       999****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 966.23
//
Query:       gi|336254884|ref|YP_004597991.1|  [L=187]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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    2.5e-19   69.6   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.2e-12   47.9   0.0      2e-12   47.2   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    6.2e-12   45.8   0.0    9.1e-12   45.2   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.2e-08   34.0   0.0      5e-08   33.7   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    5.5e-06   26.3   0.0    8.3e-06   25.7   0.0    1.2  1  FR47             FR47-like protein
    0.00017   21.7   0.0    0.00042   20.4   0.0    1.5  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00031   20.9   0.0    0.00042   20.5   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.43   10.6   0.0    1.9  2  Acetyltransf_13  ESCO1/2 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 !   69.6   0.0   1.1e-22   2.5e-19      19     117 .]      64     170 ..      43     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.1e-22
                                       HHHHHHHHHHHSTTC..EEEEEEETTEEEEEEEEEEEET......TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHH CS
                    Acetyltransf_1  19 aseeefeesfsleae..gllvaeedgeliGfisllkipd......ekggvayieslaVspeyrgkGlGsaLlealee 87 
                                       + ee+ +++++ +a+    +va++ g +iG++ l +++d       + +v +   ++V  +y++ G+G++Lle+l+ 
  gi|336254884|ref|YP_004597991.1|  64 TGEERIRNWLETIADesVNVVARHAGDVIGHAVLVPDTDdpgaieARSDVEWELAIFVLQAYQRAGIGTQLLEHLLG 140
                                       445555566444444347778******************877777555555555*********************** PP

                                       HHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  88 rareegikkivlaveedndaairlYeklGF 117
                                       +a + gi+k++l+ve +n++ai+lYe++GF
  gi|336254884|ref|YP_004597991.1| 141 HASDVGIEKVWLTVERWNQPAIALYERVGF 170
                                       *****************************9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   8.7e-16     2e-12       8     117 ..      67     181 ..      54     185 .. 0.72

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 8.7e-16
                   Acetyltransf_10   8 egietfkefispealreri.eegealllvaeeg.gkivGvielrdgshisll.fVdpeyrgqGigkaLleaveeeae 81 
                                       e i+++ e i++e+++    ++g+++ +++ +  +   G+ie r++ + +l  fV ++y++ Gig++Lle+++ +a+
  gi|336254884|ref|YP_004597991.1|  67 ERIRNWLETIADESVNVVArHAGDVIGHAVLVPdTDDPGAIEARSDVEWELAiFVLQAYQRAGIGTQLLEHLLGHAS 143
                                       44455555555555554443344444333333202223666665555777656************************ PP

                   Acetyltransf_10  82 kdgikl.eltvnasp.yavpfYeklGFkavgeeqeenG 117
                                       + gi++  ltv+  +  a+++Ye++GF+a+g e  e+ 
  gi|336254884|ref|YP_004597991.1| 144 DVGIEKvWLTVERWNqPAIALYERVGFEATGTESFEQE 181
                                       *************999**************88877665 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0     4e-15   9.1e-12       6      75 ..      83     171 ..      73     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 4e-15
                                       EEEEETTEEEEEEEEEEES............TCTEE...EEE-GGGTTSSHHHHHHHH....TT.SEEEEEEEEE.. CS
                    Acetyltransf_7   6 fVaeddgkivGfialslld............aeitr...laVdpeyrgkGiGraLlea....ae.kgiileqlel.. 60 
                                        Va++ g ++G ++l+++             +   +   ++V+++y++ GiG++Lle+    a   gi+  +++l  
  gi|336254884|ref|YP_004597991.1|  83 VVARHAGDVIGHAVLVPDTddpgaiearsdvE---WelaIFVLQAYQRAGIGTQLLEHllghASdVGIE--KVWLtv 154
                                       58999999999999999889998877775433...2456******************855431155544..234432 PP

                                       ..THH.HHHHHHHHTTEE CS
                    Acetyltransf_7  61 ..nae.kaikfYeklGFe 75 
                                           + +ai++Ye+ GFe
  gi|336254884|ref|YP_004597991.1| 155 erW-NqPAIALYERVGFE 171
                                       322.149**********8 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   2.2e-11     5e-08      31     138 .]      63     171 ..      33     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.2e-11
                    Acetyltransf_3  31 pltleeaeewlerawaeeseeegygwaivlkdtg.viGsvglrdleeedee........aelgymlapsfwgkGyat 98 
                                       p+ +e  + wle++     ++e+++ +   ++ g viG + l +  +++++        +el + + +++++ G++t
  gi|336254884|ref|YP_004597991.1|  63 PTGEERIRNWLETI-----ADESVNVVA--RHAGdVIGHAVLVPDTDDPGAiearsdveWELAIFVLQAYQRAGIGT 132
                                       44455556777743.....346666555..555527****99999999888999***99****************** PP

                    Acetyltransf_3  99 eavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                         ++ ll +a ++ g+e+++ +++  N+  i+++e++Gfe
  gi|336254884|ref|YP_004597991.1| 133 QLLEHLLGHA-SDVGIEKVWLTVERWNQPAIALYERVGFE 171
                                       **********.8999************************7 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   3.7e-09   8.3e-06      26      80 ..     118     173 ..     110     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3.7e-09
                                       EEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  26 alqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfeki 80 
                                       a+ vl+  +r G g++l + l  + +  g+ +v l v   N+p+i+lye++Gfe+ 
  gi|336254884|ref|YP_004597991.1| 118 AIFVLQAYQRAGIGTQLLEHLLGHASDVGIeKVWLTVERWNQPAIALYERVGFEAT 173
                                       78899**********************8861577888889*************987 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.9e-07   0.00042      25     126 ..      63     171 ..      51     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.9e-07
                                       --H...HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETT...EEEEEEEEEEEEE-CCGTTS-HHHHHHHH CS
                    Acetyltransf_9  25 esple.eireyfrklleesrvlgaedngelvgqlallplelnvpG...ktlkaagvtgVavapehrgrgvlskLlar 97 
                                       ++  e +ir++++ + +es  ++a+  g+++g++ l+p +   pG   ++ ++ +  ++ v   +++ g+ ++Ll++
  gi|336254884|ref|YP_004597991.1|  63 PTG-EeRIRNWLETIADESVNVVARHAGDVIGHAVLVPDT-DDPGaieARSDVEWELAIFVLQAYQRAGIGTQLLEH 137
                                       333.4489*****************************965.5555333677889999******************** PP

                                       HHHHHHHTT--EEEE--.....SSHHHHHTTT-E CS
                    Acetyltransf_9  98 aleemreegqplsllfP.....ssipiYrrfGye 126
                                       +l+++ + g++ ++l+       +i++Y+r G+e
  gi|336254884|ref|YP_004597991.1| 138 LLGHASDVGIEKVWLTVerwnqPAIALYERVGFE 171
                                       ****************98886655899*****98 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.9e-07   0.00042      74     140 ..     111     176 ..      65     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.9e-07
                    Acetyltransf_4  74 kdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgif 140
                                        d ++el +++  ++ + +g+g +l+++l   ++  +ie+    +   n+++i++++++GFe +g +
  gi|336254884|ref|YP_004597991.1| 111 SDVEWELAIFVL-QAYQRAGIGTQLLEHLLGHASDVGIEKVWLTVERWNQPAIALYERVGFEATGTE 176
                                       466899*****8.89***********************************************99975 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019      0.43       9      32 ..     118     141 ..     117     147 .. 0.91
   2 ?   -0.7   0.1      0.63   1.4e+03       5      13 ..     145     153 ..     141     163 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                   Acetyltransf_13   9 riWvssshRrkgiAtkLldaaren 32 
                                       +i+v ++++r gi t+Ll+++  +
  gi|336254884|ref|YP_004597991.1| 118 AIFVLQAYQRAGIGTQLLEHLLGH 141
                                       59*****************98766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.63
                   Acetyltransf_13   5 cGisriWvs 13 
                                       +Gi+++W  
  gi|336254884|ref|YP_004597991.1| 145 VGIEKVWLT 153
                                       8******65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 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:                         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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1403.32
//
Query:       gi|336254885|ref|YP_004597992.1|  [L=155]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-11   45.0   2.9      4e-11   43.6   2.9    1.7  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 !   43.6   2.9   2.2e-15     4e-11       3     139 ..      10     154 ..       8     155 .] 0.83

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.2e-15
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.....HHHH CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.....akaa 74 
                                       +++l +vDgs+es  A+e+A++ a +++a +++l v+        +++  ++   +++ +   ++        +  +
  gi|336254885|ref|YP_004597992.1|  10 DTVLAPVDGSDESATAVEYAVAVADRYDASVHALFVLGRGVVHGMDAGTVDEDAVAEDTRNFLEDVGTiadeaDVPL 86 
                                       689********************************988777776666665555555555554444444777779999 PP

                                       HHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCC...SSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  75 aeaggvkvevvveegdpaeeilevaeeedadliVvGsrg...rsglsrlllGSvseyvlrhapcpVlv 139
                                           +     +++  +p+ + l++a+e+dad iV+ +      ++ +  +l   +eyvl  a+ pVl 
  gi|336254885|ref|YP_004597992.1|  87 STSIDDGFSQTRKTRHPGNVVLDTADEIDADFIVLPREPvsdATAAEVEVLEKAAEYVLSYASQPVLS 154
                                       999999*******************************9977655555567****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1190.30
//
Query:       gi|336254886|ref|YP_004597993.1|  [L=160]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-35  121.5   6.6    4.6e-35  121.2   6.6    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 !  121.2   6.6   2.6e-39   4.6e-35       1     141 []       1     137 [.       1     137 [. 0.97

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 2.6e-39
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       m+++++Va+Dgse+ k+A++ Al+la++++a++++l v+d+++ +a+++  +e+ + +le  ++++  +     ++ 
  gi|336254886|ref|YP_004597993.1|   1 MFDTVVVATDGSESVKRAVDVALDLAARFDAAVHALSVVDASEVDASPEQLREELRTALETHADAALGT----VEDR 73 
                                       99**********************************************999999999999999988865....7*** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ++ +v++ v+eg pa ei+e+a+e+dadl+ +G+rgr+g  rlllGSv+e+v+r +p pVl Vr
  gi|336254886|ref|YP_004597993.1|  74 ADRDVTTAVREGRPAAEICEYAREIDADLVATGTRGRHGENRLLLGSVAERVVRTSPAPVLTVR 137
                                       *************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1302.75
//
Query:       gi|336254887|ref|YP_004597994.1|  [L=429]
Description: phosphohydrolase (DHH superfamily)-like protein [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0075   16.6   0.0      0.017   15.5   0.0    1.6  1  DrsE            DsrE/DsrF-like family
     0.0096   16.1   0.9      0.019   15.2   0.9    1.5  1  DHH             DHH family
  ------ inclusion threshold ------
      0.014   14.6   0.0       0.02   14.1   0.0    1.2  1  Glyco_hydro_57  Glycosyl hydrolase family 57
      0.015   15.9   0.6      0.083   13.5   0.1    2.5  3  PGM_PMM_II      Phosphoglucomutase/phosphomannomutase, alpha/
      0.021   15.2   0.3      0.077   13.4   0.1    2.2  2  DHHA1           DHHA1 domain
      0.058   13.0   0.0       0.11   12.0   0.0    1.4  1  PrpR_N          Propionate catabolism activator
       0.42   11.1   2.1       0.93   10.0   0.5    2.6  2  CoA_binding_2   CoA binding domain


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.6e-06     0.017      14     100 ..      88     182 ..      82     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.6e-06
                                       BSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS..........---TGGGTS---GGGGGGCGGGT-EEEEEHHH CS
                              DrsE  14 seaarealelalaaaalghevsvffygdGvllllk..........gqtanpadeknlaellkalkeygvklyvCgqa 80 
                                       ++a++ea ++a a+ +++ e +v ++gd v  +l+             a p d ++ +++++++ + g++l+vC  a
  gi|336254887|ref|YP_004597994.1|  88 NDASTEASDAADAVDDAE-EAAVGLTGDEVESPLEepeptphevaLIPASPHDVEDAIARVAEYGDDGIELFVCDLA 163
                                       455778888888888877.99999999999999999999999887666678889999******************** PP

                                       HHHTT--GGGE-T--EEEE- CS
                              DrsE  81 akargldededlgvgvevsg 100
                                        +++ + ede+  +  e ++
  gi|336254887|ref|YP_004597994.1| 164 PDRYEYVEDELE-AALETAS 182
                                       *******88633.3333333 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.9   7.5e-06     0.019       3      94 ..      49     237 ..      47     246 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.5e-06
                                       EEE-ECSSSHHHHHHHHHHHH........................................................ CS
                                       xxxxxxxxxxxxxxxxxxxxx........................................................ RF
                               DHH   3 livghknpDtDsigSaialan........................................................ 23 
                                       ++  + +pD+D+++++ ++++                                                        
  gi|336254887|ref|YP_004597994.1|  49 AV--IADPDADGLACVALIREayddvqnvpepddeaadgdendasteasdaadavddaeeaavgltgdevespleep 123
                                       45..89*********77777757777777777777777777776666666666666666666666666666666666 PP

                                       ......................................CECS--TCGGCGCCHHCCCSEEEEEEE-S---S.....S CS
                                       ......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x RF
                               DHH  24 ......................................llvDhneksqavegeakeeaedviiiDHHrlge.....e 57 
                                                                             l  D  e  +++ ++a e+a  v   DHH+  +      
  gi|336254887|ref|YP_004597994.1| 124 eptphevalipasphdvedaiarvaeygddgielfvcdLAPDRYEYVEDELEAALETASSVAWYDHHQWDDevaqaV 200
                                       66666666666666666666655555555555554433366677777777777***************998888873 PP

                                       ---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  58 fetlapilflnepvgstaeivaelleekkeeiskeia 94 
                                        +   ++++ +++  + a +v++ le++ + + +e+a
  gi|336254887|ref|YP_004597994.1| 201 RDAGVDLVIGDSDEECSADVVYRSLEYDFSPMYEELA 237
                                       3444467888888889999999998887666655555 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 ?   14.1   0.0   7.9e-06      0.02     168     240 ..     178     257 ..     170     295 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.9e-06
                                       HSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS.-EEEE--CHH.......-T CS
                    Glyco_hydro_57 168 fgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllknggiavffRdreL.......sd 237
                                       ++  +++ w     +++e++++++++G + ++ d+ +e ++d   +s+ + + + ++++a + Rd++L       sd
  gi|336254887|ref|YP_004597994.1| 178 LETASSVAWYDHHQWDDEVAQAVRDAGVDLVIGDSDEECSADVVYRSLEYDFSPMYEELAAVTRDHDLwlredprSD 254
                                       66677888999999*****************************999999999999999**********998888866 PP

                                       TTS CS
                    Glyco_hydro_57 238 dig 240
                                       d++
  gi|336254887|ref|YP_004597994.1| 255 DLA 257
                                       654 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 ?   13.5   0.1   3.3e-05     0.083      63      99 ..      27      62 ..      18      67 .. 0.87
   2 ?   -2.8   0.0       3.9   9.9e+03      73      87 ..     195     209 ..     187     243 .. 0.77
   3 ?   -2.9   0.0       4.2   1.1e+04      73      89 ..     326     342 ..     324     347 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                                      ----TT-TTTTHHHHGGGGG-SEEEEE-TTS-BEEEE CS
                        PGM_PMM_II 63 pnpeekealkllielvkkegadlglafDgDaDRlgvv 99
                                      p+  e e+l++ ++++  ega+++++ D+DaD l++v
  gi|336254887|ref|YP_004597994.1| 27 PDTVE-EDLEEEQAAAALEGAEVAVIADPDADGLACV 62
                                      44555.8999999*********************998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.9
                                       THHHHGGGGG-SEEE CS
                        PGM_PMM_II  73 llielvkkegadlgl 87 
                                       +++++v++ g dl++
  gi|336254887|ref|YP_004597994.1| 195 EVAQAVRDAGVDLVI 209
                                       566777777777766 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.2
                                       THHHHGGGGG-SEEEEE CS
                        PGM_PMM_II  73 llielvkkegadlglaf 89 
                                       +++e++++egad+ +++
  gi|336254887|ref|YP_004597994.1| 326 EVAEAMREEGADASVIV 342
                                       56788999999988776 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.2   8.1e+03      78     103 ..      44      68 ..      30      72 .. 0.57
   2 ?   13.4   0.1     3e-05     0.077      83     137 ..     346     392 ..     281     393 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.2
                                       EECTEEEEEEEESSHSS-HHHHHHHH CS
                             DHHA1  78 eegdkvkvsarskkdgvdagelakea 103
                                       e+  +v+v+a   +dg+   +l++ea
  gi|336254887|ref|YP_004597994.1|  44 EGA-EVAVIADPDADGLACVALIREA 68 
                                       222.5677777666677666666665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3e-05
                                       EEEEEEESSHSS-.HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHH CS
                             DHHA1  83 vkvsarskkdgvd.agelakeaaaklgggGGGHdlAaGagipaekleealealeea 137
                                        + s+r ++  +d   e+a +       +GGGH+ AaG + +   ++++l++++++
  gi|336254887|ref|YP_004597994.1| 346 GSASIRGTD-EFDrCHEVAGR------VNGGGHPKAAGCKPD--IYDDMLDFANHW 392
                                       466777776.66535689999......9************97..788999998877 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.4e-05      0.11      49     127 ..     129     212 ..     123     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
                            PrpR_N  49 PVveikvsgyDilralkqakklg.ekialvgfeniikglktlselldldieiytinseee...aeaavkel.kaegv 120
                                        V  i+ s +D+  a++++ ++g + i l+  + +++  + +++ l+  +e+ +   + +    ++ v ++ +++gv
  gi|336254887|ref|YP_004597994.1| 129 EVALIPASPHDVEDAIARVAEYGdDGIELFVCDLAPDRYEYVEDELEAALETASSVAWYDhhqWDDEVAQAvRDAGV 205
                                       5899*******************778*********************9999966555444333999999997889** PP

                            PrpR_N 121 evvvGdg 127
                                       ++v+Gd 
  gi|336254887|ref|YP_004597994.1| 206 DLVIGDS 212
                                       *****95 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       2.1   5.5e+03      89     107 ..      34      52 ..      24      54 .. 0.80
   2 ?   10.0   0.5   0.00036      0.93      56     106 ..     155     208 ..      78     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
                                       ---HHHHHHHHHTT-EEE. CS
                     CoA_binding_2  89 sedeeaaelaeeagirvvg 107
                                        e+e+aa+++e a++ v+ 
  gi|336254887|ref|YP_004597994.1|  34 LEEEQAAAALEGAEVAVIA 52 
                                       5678999999999999886 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00036
                                       --EEEE-S-HHHHGGGHHHHHHH...--SEEEE-TT---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  56 vdlvdvftppeatpeivkealal...gakavwlqpgsedeeaaelaeeagirvv 106
                                       ++l ++ + p++ + + +e++a+      ++w   + +d+e+a+++++ag+++v
  gi|336254887|ref|YP_004597994.1| 155 IELFVCDLAPDRYEYVEDELEAAletASSVAWYDHHQWDDEVAQAVRDAGVDLV 208
                                       555555555555555555553332226999999999***************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); 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 0.20s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 3517.69
//
Query:       gi|336254888|ref|YP_004597995.1|  [L=323]
Description: transcription initiation factor IIB [Halopiger xanaduensis SH-6]
Scores for 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-43  145.1   2.2    8.6e-23   80.2   0.3    2.3  2  TFIIB           Transcription factor TFIIB repeat
      4e-16   58.2   2.7    7.1e-16   57.4   2.7    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
      0.003   17.2   0.7     0.0083   15.8   0.7    1.8  1  A2L_zn_ribbon   A2L zinc ribbon domain
     0.0064   16.2   0.0      0.016   14.9   0.0    1.7  1  Cyclin_N        Cyclin, N-terminal domain
  ------ inclusion threshold ------
       0.02   14.8   2.9      0.041   13.9   2.9    1.5  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.027   14.4   0.1      0.064   13.2   0.1    1.5  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.036   13.6   2.2       0.22   11.1   0.1    3.1  3  Sigma70_r4      Sigma-70, region 4
      0.059   13.1   0.4       0.12   12.1   0.4    1.4  1  Ribosomal_S27e  Ribosomal protein S27
        0.1   12.7   0.3       0.23   11.6   0.3    1.5  1  DUF2318         Predicted membrane protein (DUF2318)
       0.15   12.2   3.0        1.9    8.7   0.6    2.5  2  Zn-ribbon_8     Zinc ribbon domain
       0.15   11.4   0.1       0.27   10.6   0.1    1.3  1  eIF-6           eIF-6 family
       0.31   10.5   1.5          1    8.8   1.5    1.9  1  zf-ribbon_3     zinc-ribbon domain
        4.9    6.9   9.5        1.8    8.3   0.0    3.1  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain


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 !   64.8   0.1   3.8e-21   5.3e-18       1      71 []     145     215 ..     145     215 .. 0.98
   2 !   80.2   0.3   6.2e-26   8.6e-23       1      71 []     239     309 ..     239     309 .. 0.99

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 3.8e-21
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i r+++al++p  V++ A  ++++al+e+++ Grs +g+a  cly Acr+e+  r+++e+++v++V+ k+i
  gi|336254888|ref|YP_004597995.1| 145 IDRMSSALGIPRSVREVASVVYRRALSEDLIRGRSIEGVATGCLYAACRQEGIPRSLEEVAEVSRVERKEI 215
                                       789****************************************************************9997 PP

  == domain 2  score: 80.2 bits;  conditional E-value: 6.2e-26
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rf+++l+L+e+V+ +  e+++ ++e+++l+G+sp+g+aAA++y A++++++k+tq+e+++v+qV+e+ti
  gi|336254888|ref|YP_004597995.1| 239 VPRFCSELDLSEEVTAKTREIIQVTAEKGLLSGKSPTGYAAAAIYAASLLCNEKKTQREVAEVAQVTEVTI 309
                                       689******************************************************************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 !   57.4   2.7   5.2e-19   7.1e-16       2      43 .]      29      70 ..      28      70 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 5.2e-19
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      +CP+C+s++lv+ +++ elvC dCGlV+e+  id gpewr+f
  gi|336254888|ref|YP_004597995.1| 29 VCPECNSDSLVRSEDQRELVCDDCGLVVEESNIDRGPEWRAF 70
                                      8***************************************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 !   15.8   0.7     6e-06    0.0083       3      30 ..      27      55 ..      25      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6e-06
                     A2L_zn_ribbon  3 lkvCsvCggngiln.seqgylvCieCgas 30
                                      ++vC  C+++ ++   +q +lvC +Cg++
  gi|336254888|ref|YP_004597995.1| 27 ERVCPECNSDSLVRsEDQRELVCDDCGLV 55
                                      799**********978899********86 PP

>> Cyclin_N  Cyclin, N-terminal 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      43     125 ..     150     229 ..     118     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                       HHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHH CS
                          Cyclin_N  43 ekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliL 119
                                       + + + +++  +a +++ R ls+  ++ + ++ v+++cL+ A++ e i p +le+++ ++   ++++ei +  r++ 
  gi|336254888|ref|YP_004597995.1| 150 SALGIPRSVREVASVVYRRALSEDLIRGRSIEGVATGCLYAACRQEGI-PRSLEEVAEVS--RVERKEIGRTYRYVA 223
                                       555566667778999******************************999.9******9995..589999998888888 PP

                                       HHTTT- CS
                          Cyclin_N 120 etLnfd 125
                                       ++L  +
  gi|336254888|ref|YP_004597995.1| 224 QELSLE 229
                                       888765 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.9   2.9e-05     0.041       5      26 ..      30      53 ..      29      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-05
                    PhnA_Zn_Ribbon  5 CplCaSeytY..edgallvCpeCa 26
                                      Cp+C+S++    ed   lvC++C+
  gi|336254888|ref|YP_004597995.1| 30 CPECNSDSLVrsEDQRELVCDDCG 53
                                      *******988*************7 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   0.1   4.6e-05     0.064      18      44 ..      27      53 ..      23      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                     Zn_Tnp_IS1595 18 gfvCPhCgsrkayriktrglfqCkeCr 44
                                       +vCP C s+++ r ++ + + C +C+
  gi|336254888|ref|YP_004597995.1| 27 ERVCPECNSDSLVRSEDQRELVCDDCG 53
                                      589***********************7 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.39   5.3e+02      20      29 ..     198     207 ..     191     227 .. 0.78
   2 ?   -3.2   0.0       4.5   6.2e+03       6      14 ..     253     261 ..     250     267 .. 0.77
   3 ?   11.1   0.1   0.00016      0.22      18      42 ..     290     314 ..     281     320 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.39
                                       T--HHHHHHH CS
                        Sigma70_r4  20 glTleEIger 29 
                                       +++leE++e+
  gi|336254888|ref|YP_004597995.1| 198 PRSLEEVAEV 207
                                       6899999986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.5
                                       -HHHHHHHH CS
                        Sigma70_r4   6 pererevle 14 
                                       +++ re+++
  gi|336254888|ref|YP_004597995.1| 253 TAKTREIIQ 261
                                       788999998 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00016
                                       TTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiek 42 
                                        e+ T+ E++e+ ++++ ++r +  
  gi|336254888|ref|YP_004597995.1| 290 NEKKTQREVAEVAQVTEVTIRNRYQ 314
                                       5899*****************9976 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   8.8e-05      0.12      10      36 ..      30      56 ..      28      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.8e-05
                                      -TTTS-EEEEESS-SS-EEESSSTCEE CS
                    Ribosomal_S27e 10 CpdCenetvvFshaatvvkCisCgkvL 36
                                      Cp+C+    v s  ++   C  Cg v+
  gi|336254888|ref|YP_004597995.1| 30 CPECNSDSLVRSEDQRELVCDDCGLVV 56
                                      ************************987 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00017      0.23      26      67 ..      19      62 ..       8      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                           DUF2318 26 sdgklrvaldaCevCekkgYv..qegeelvCknCgvrfaldsig 67
                                      ++++ ++a  +C  C++++ v  +++ elvC  Cg +++ ++i+
  gi|336254888|ref|YP_004597995.1| 19 ENEQDTAAERVCPECNSDSLVrsEDQRELVCDDCGLVVEESNID 62
                                      45556678889****9988885566678*********9999997 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.6    0.0014       1.9      23      38 ..      24      40 ..      11      41 .. 0.70
   2 ?    2.9   0.1     0.089   1.2e+02       5      17 ..      46      58 ..      45      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0014
                       Zn-ribbon_8 23 dapltaCPeCgs.evrr 38
                                       a++ +CPeC+s  + r
  gi|336254888|ref|YP_004597995.1| 24 TAAERVCPECNSdSLVR 40
                                      345666******77766 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.089
                       Zn-ribbon_8  5 eYrCeeCghefev 17
                                      e  C++Cg + e+
  gi|336254888|ref|YP_004597995.1| 46 ELVCDDCGLVVEE 58
                                      5679999988885 PP

>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00019      0.27     113     174 ..     247     309 ..     244     312 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                                       GGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE.-SSEEEE-TT--HHHHHHHHHHHT-SE CS
                             eIF-6 113 dlsketveiiadvLgvevvrgtiagiktvGsaavv.tnkgllvhpkateeeleeleellkvev 174
                                       dls+e+  + +++++v  ++g + g +  G aa++     ll++ k t++e++e++++ +v++
  gi|336254888|ref|YP_004597995.1| 247 DLSEEVTAKTREIIQVTAEKGLLSGKSPTGYAAAAiYAASLLCNEKKTQREVAEVAQVTEVTI 309
                                       79999999**********************877651678899******************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 ?    8.8   1.5   0.00075         1       2      25 ..      27      55 ..      26      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00075
                       zf-ribbon_3  2 tvrCPnCGa.p.lssddn...vCpyCGtk 25
                                      ++ CP+C++   ++s+d+   vC  CG +
  gi|336254888|ref|YP_004597995.1| 27 ERVCPECNSdSlVRSEDQrelVCDDCGLV 55
                                      678*******9899888666699999975 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 ?    4.0   0.6     0.028        39      22      29 ..      28      35 ..      27      38 .. 0.87
   2 ?    8.3   0.0    0.0013       1.8      14      30 ..      39      55 ..      36      56 .. 0.88
   3 ?   -3.4   0.7       5.8     8e+03       4       7 ..     241     244 ..     241     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.028
                     zf-NADH-PPase 22 rvCpaCgl 29
                                      rvCp C+ 
  gi|336254888|ref|YP_004597995.1| 28 RVCPECNS 35
                                      9*****96 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0013
                     zf-NADH-PPase 14 epaeggwarvCpaCgle 30
                                      +++e+++ +vC++Cgl 
  gi|336254888|ref|YP_004597995.1| 39 VRSEDQRELVCDDCGLV 55
                                      6789***********96 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 5.8
                     zf-NADH-PPase   4 rFCg 7  
                                       rFC+
  gi|336254888|ref|YP_004597995.1| 241 RFCS 244
                                       9**8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2546.43
//
Query:       gi|336254889|ref|YP_004597996.1|  [L=233]
Description: hypothetical protein Halxa_3506 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0027   18.1   5.0     0.0027   18.1   5.0    4.2  3  DUF202       Domain of unknown function (DUF202)
  ------ inclusion threshold ------
        1.4    8.1   5.6       0.45    9.7   2.5    1.8  2  Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
        2.4    8.4   4.9         91    3.4   2.2    3.3  2  DPM3         Dolichol-phosphate mannosyltransferase subunit 3


Domain annotation for each model (and alignments):
>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   1.6       0.5     3e+03      36      52 ..      54      69 ..      20      75 .. 0.53
   2 !   18.1   5.0   4.5e-07    0.0027      18      65 ..      97     141 ..      85     144 .. 0.85
   3 ?   -1.5   9.0      0.59   3.5e+03      12      57 ..     146     222 ..     143     233 .] 0.43

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.5
                            DUF202 36 psalgkilglilivlgi 52
                                         ++ ilg+i  +++i
  gi|336254889|ref|YP_004597996.1| 54 FG-TAPILGVIVYGVAI 69
                                      22.24566666666665 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 4.5e-07
                            DUF202  18 lalialglallrffltgepsalgkilglilivlgiltllvglvrylrr 65 
                                       la++++g+++lrf   +  sa   ilg+++iv+++lt+l++ + y r+
  gi|336254889|ref|YP_004597996.1|  97 LAFGIFGAGVLRF--APPDSA-LTILGVTAIVTAVLTALIAGYVYARS 141
                                       899*********8..333333.49********************9986 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.59
                            DUF202  12 aWlRtslalialglallrffl...............................tgepsalg.kilglilivlgiltll 56 
                                        W +++ +++  g+a++++ +                                   +++g + +g+  +v+g+++ +
  gi|336254889|ref|YP_004597996.1| 146 HWGKFANYAFLGGIAVIAIGSfvlsellvvgfvlvflgfllrlgyeiwqvrdN-RDASVGlQTIGVYVAVAGVFVHV 221
                                       56666666666666666653322222222223333333333333334444422.22222235556666666666655 PP

                            DUF202  57 v 57 
                                       +
  gi|336254889|ref|YP_004597996.1| 222 L 222
                                       5 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 ?   -1.2   0.1      0.15   8.9e+02      97     128 ..      38      68 ..      11      78 .. 0.72
   2 ?    9.7   2.5   7.5e-05      0.45     100     140 ..     155     195 ..     123     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.15
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Herpes_LMP1  97 lwnlhgqalylgivlfifgcllvlglwiylle 128
                                       ++ + g  l   i  f+fg   +lg+ +y + 
  gi|336254889|ref|YP_004597996.1|  38 MYAFVGTPL-AAINDFLFGTAPILGVIVYGVA 68 
                                       444444444.4677899999999999888665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 7.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Herpes_LMP1 100 lhgqalylgivlfifgcllvlglwiyllellwrlgatiwql 140
                                       + g    + i  f++  llv+g+ + +l +l rlg  iwq+
  gi|336254889|ref|YP_004597996.1| 155 FLGGIAVIAIGSFVLSELLVVGFVLVFLGFLLRLGYEIWQV 195
                                       4455566788899***************************8 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 ?    3.1   0.0     0.019   1.1e+02       7      51 ..      23      67 ..      18      72 .. 0.87
   2 ?    3.4   2.2     0.015        91      45      75 ..     178     206 ..     113     210 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.019
                              DPM3  7 tlalallllalwlalllrlvslplskvqdevvpvlPlwalvlfGa 51
                                      ++  a+ll+a+ +a+++  v +pl  + d +  ++P++ ++++G+
  gi|336254889|ref|YP_004597996.1| 23 VIGGASLLMAINVAVMYAFVGTPLAAINDFLFGTAPILGVIVYGV 67
                                      666788999999999999999999999999999******999997 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.015
                              DPM3  45 alvlfGayslatlgygvltfndcpeaakeLq 75 
                                       +lv +G   l++lgy++++++d  +a   Lq
  gi|336254889|ref|YP_004597996.1| 178 VLVFLG--FLLRLGYEIWQVRDNRDASVGLQ 206
                                       233333..46789999999999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); 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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1793.14
//
Query:       gi|336254890|ref|YP_004597997.1|  [L=153]
Description: hypothetical protein Halxa_3507 [Halopiger xanaduensis SH-6]
Scores for 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  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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 0.22s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1300.67
//
Query:       gi|336254891|ref|YP_004597998.1|  [L=545]
Description: methyl-accepting chemotaxis sensory transducer [Halopiger xanaduensis SH-6]
Scores for 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-47  158.9  49.7    4.1e-44  150.4  25.2    4.0  4  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
    1.5e-05   25.1  33.1      0.045   14.0   3.5    4.8  4  DUF948          Bacterial protein of unknown function (DUF948
    0.00015   21.8  36.6     0.0055   16.7   6.6    5.1  5  Laminin_II      Laminin Domain II
     0.0013   17.7  35.1     0.0069   15.3   7.4    3.4  4  DUF812          Protein of unknown function (DUF812)
     0.0031   17.5  31.8      0.017   15.1   1.6    5.1  5  DUF1664         Protein of unknown function (DUF1664)
     0.0081   15.5  25.2      0.052   12.9   4.3    3.4  3  CorA            CorA-like Mg2+ transporter protein
  ------ inclusion threshold ------
      0.024   14.7   0.8      0.024   14.7   0.8    3.6  3  Mod_r           Modifier of rudimentary (Mod(r)) protein
       0.03   14.5  19.7       0.24   11.6   0.5    4.3  4  Fib_alpha       Fibrinogen alpha/beta chain family
      0.046   14.1  21.5       0.11   13.0   3.5    4.4  3  DASH_Dad2       DASH complex subunit Dad2
       0.22   12.1   9.1       0.73   10.5   0.5    3.6  4  ING             Inhibitor of growth proteins N-terminal histo
        0.3   10.3  39.3       0.37   10.0  10.1    3.7  3  DUF3450         Protein of unknown function (DUF3450)
        0.5   10.7  33.5        0.4   11.0   0.7    5.1  5  BLOC1_2         Biogenesis of lysosome-related organelles com
        0.6   10.0  16.7        8.1    6.3   3.2    4.7  5  Sec34           Sec34-like family
       0.71   10.5  31.8        3.3    8.3   2.8    5.1  5  Syntaxin-6_N    Syntaxin 6, N-terminal
       0.79    9.5  10.2        8.5    6.2   0.1    4.4  3  DASH_Duo1       DASH complex subunit Duo1
       0.95    9.6  41.6       0.31   11.2  11.3    4.1  4  ATG16           Autophagy protein 16 (ATG16)
       0.95    8.3  39.9        2.2    7.1  15.9    3.5  4  Spc7            Spc7 kinetochore protein
       0.99    9.8   8.4         21    5.6   0.3    4.3  3  Syntaxin_2      Syntaxin-like protein
        1.4    8.4  36.1      0.033   13.7  18.2    3.5  3  MscS_porin      Mechanosensitive ion channel porin domain
        1.4    6.9  30.3       0.52    8.4   9.5    2.7  2  HOOK            HOOK protein
        1.5    9.3  29.7       0.66   10.4   1.5    6.3  5  FlaC_arch       Flagella accessory protein C (FlaC)
        1.6    8.0  20.6          1    8.7  10.4    3.2  3  GAS             Growth-arrest specific micro-tubule binding
        2.4    8.0  12.5        2.9    7.7   7.7    2.5  2  Dynactin_p22    Dynactin subunit p22
        2.4    6.0  13.3       0.79    7.6   9.0    2.0  2  Prominin        Prominin
        2.6    7.8  38.1       0.31   10.7   3.8    4.5  4  DUF745          Protein of unknown function (DUF745)
        2.6    8.5  14.0       0.99    9.8   0.7    4.0  4  DUF3037         Protein of unknown function (DUF3037)
        3.1    7.0  17.4       0.46    9.7   1.2    3.2  3  TMPIT           TMPIT-like protein
        3.2    8.6   8.6         56    4.5   0.1    4.8  5  RecG_N          RecG N-terminal helical domain
        3.6    8.1  14.0         17    5.9   0.5    4.2  5  Goodbye         fungal STAND N-terminal Goodbye domain
        4.3    6.9  21.4       0.35   10.5  11.0    2.6  2  Lebercilin      Ciliary protein causing Leber congenital amau
        5.5    6.0  19.2       0.38    9.8   3.5    3.6  4  FH2             Formin Homology 2 Domain
        5.5    7.5  24.2       0.96   10.0   2.7    4.5  4  Spectrin        Spectrin repeat
        6.1    6.5  29.9        4.5    6.9   5.1    4.3  3  LXG             LXG domain of WXG superfamily
        6.9    5.2  32.5        1.4    7.5  16.6    2.4  2  AAA_13          AAA domain
        7.8    5.3  26.4          2    7.3   4.8    2.6  2  IFT57           Intra-flagellar transport protein 57
        9.1    6.4  42.1        2.3    8.3   9.5    3.8  3  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
        9.2    5.0  26.1      0.034   13.0   6.5    3.0  3  DUF677          Protein of unknown function (DUF677)
        9.5    6.6  25.1       0.19   12.2   7.2    4.1  4  DUF4200         Domain of unknown function (DUF4200)


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   3.8   0.00028      0.13      84     165 ..     210     296 ..     204     297 .. 0.73
   2 !   12.8  10.9   0.00016     0.076      97     161 ..     252     320 ..     225     331 .. 0.52
   3 !  150.4  25.2   8.6e-47   4.1e-44       2     165 ..     329     492 ..     322     499 .. 0.89
   4 ?    4.7   1.7      0.05        24      77     148 ..     488     524 ..     485     534 .. 0.43

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00028
                                       HHHHHHHH.....HHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  84 saqaakei.....ealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqs 155
                                       +  +a+e      ea ++e ++  ++  + +e   +  e  ++  ++ +++l+e++ea+++vad  +ei   ++eqs
  gi|336254891|ref|YP_004597998.1| 210 ARSSAQEAridayEAQLAEYEQRLEEYEAEIEAQDRTREDLADARRSMENTLEEVAEATDDVADGADEIDDLTAEQS 286
                                       44444443111113445566777777777777777777777888888899999************************ PP

                                       HHHHHHHHHH CS
                         MCPsignal 156 asieevnqav 165
                                        s++e+++ +
  gi|336254891|ref|YP_004597998.1| 287 DSMSEIASEI 296
                                       *****99876 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00016
                                       .............HHHHHHHHHHHHHHH....HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  97 eiqkeindsvesleetrqrveegselve....etgealkeiveavaevadlvqeiaaaseeqsasieev 161
                                       +  + +++++e + e++  v+ g+++++    e  ++++ei+++++ ++++v+eia+ +ee sa++e+ 
  gi|336254891|ref|YP_004597998.1| 252 DARRSMENTLEEVAEATDDVADGADEIDdltaEQSDSMSEIASEISGLSATVEEIASNAEEVSATSEQA 320
                                       333444444444444444444444444311112334555555555555555555555555555555553 PP

  == domain 3  score: 150.4 bits;  conditional E-value: 8.6e-47
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHH CS
                         MCPsignal   2 dlaeeaseeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVr 78 
                                       ++aeea ++ e  ++  ++v +++e++++ ++ i +i++Vi++iadQTNlLALNA+iEAA AGe+G+GFaVVA+EV+
  gi|336254891|ref|YP_004597998.1| 329 ETAEEAIDKMEGVQEAADEVTEDVENLREGVQRIDEIVDVINDIADQTNLLALNASIEAATAGEAGDGFAVVANEVK 405
                                       333334344444466677777778888888*********************************************** PP

                                       HHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  79 kLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqs 155
                                       +LAe+s++ a +ie+++ +iq++++++v+sle ++ +++ g+elveet ++l +i eavae ++ ++e+a+a+++q+
  gi|336254891|ref|YP_004597998.1| 406 SLAEESQDEATNIERMVDRIQADTEETVDSLETANAEIDDGVELVEETVDNLGRIEEAVAEASTGIREVATATDDQA 482
                                       ***************************************************************************** PP

                                       HHHHHHHHHH CS
                         MCPsignal 156 asieevnqav 165
                                       as eev++  
  gi|336254891|ref|YP_004597998.1| 483 ASTEEVASMT 492
                                       ******9754 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.05
                                       HHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  77 VrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeia 148
                                       V ++ + ++++++ei++ ++ i++ + d                                    +dlv+ei 
  gi|336254891|ref|YP_004597998.1| 488 VASMTDSAMERSQEIADEVETIVATTAD-----------------------------------ASDLVEEID 524
                                       4444444444444444444444444444...................................444444443 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 !   11.8   2.1   0.00046      0.22      24      85 ..     253     314 ..     241     320 .. 0.66
   2 !    9.2   5.9     0.003       1.4      24      70 ..     313     362 ..     289     380 .. 0.43
   3 !   14.0   3.5   9.5e-05     0.045      18      86 ..     398     466 ..     396     475 .. 0.87
   4 ?    6.9   2.7     0.015       7.3      27      86 ..     463     522 ..     459     531 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00046
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                       +++ ++++ + ++e +++v    +e++dl+a+  + ++++ +++  + + +e++a  +e vs
  gi|336254891|ref|YP_004597998.1| 253 ARRSMENTLEEVAEATDDVADGADEIDDLTAEQSDSMSEIASEISGLSATVEEIASNAEEVS 314
                                       56667777777777777777777777777777777666666666666655555555555554 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.003
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvne...klekv 70 
                                       ++ t ++a++   ++++ +++ ++++e++ + + e++edv++    ++++
  gi|336254891|ref|YP_004597998.1| 313 VSATSEQAESVASDTTETAEEAIDKMEGVQEAADEVTEDVENlreGVQRI 362
                                       22222333333333333333333333333333333333333333344444 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 9.5e-05
                            DUF948  18 ivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       +vv +++k++++e ++  +++e+ vd i  ++e++++  ++  +++ + +e v++ +++++ + e+v+e
  gi|336254891|ref|YP_004597998.1| 398 AVVANEVKSLAEESQDEATNIERMVDRIQADTEETVDSLETANAEIDDGVELVEETVDNLGRIEEAVAE 466
                                       578888999999999999999999999999999999999999999999999999999999999998876 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.015
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                        + ea++ i+e+   +d     +e++ + +   +e  +e  ++v+++++  ad+++ v+e
  gi|336254891|ref|YP_004597998.1| 463 AVAEASTGIREVATATDDQAASTEEVASMTDSAMERSQEIADEVETIVATTADASDLVEE 522
                                       566666666666655555555555555555554445555555555555555555444444 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   7.0      0.11        53      28     103 ..     245     321 ..     210     325 .. 0.52
   2 !   16.7   6.6   1.2e-05    0.0055       7     100 ..     270     360 ..     266     362 .. 0.90
   3 !   14.3   1.3   6.7e-05     0.032       3      56 ..     329     382 ..     327     389 .. 0.90
   4 !   11.8   1.6   0.00038      0.18       1      48 [.     404     451 ..     404     460 .. 0.88
   5 ?    5.0   4.2      0.05        23       3      71 ..     462     530 ..     460     533 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTT.TGGGHHHHHHHHHH...HHHHHHHHHHHHHHHH CS
                        Laminin_II  28 ntkeklseinrsveetnekvkdankairdArrsvkkLeklapq.LldklkelkqleeassslsdniseikelIaqAR 103
                                       +t+e+l  ++rs+e+t e+v +a+  ++d  +++ +L+ +  + + +  +e+  l+   + +  n +e+ +  +qA 
  gi|336254891|ref|YP_004597998.1| 245 RTREDLADARRSMENTLEEVAEATDDVADGADEIDDLTAEQSDsMSEIASEISGLSATVEEIASNAEEVSATSEQAE 321
                                       55566666666666666666666666666666666665433320222223344444333334444444444444444 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83 
                                       ++ + a e+ + +a+ s  ++++ +++s++ ++vee+  ++++ + + ++A++  ++ +++a++ +dk++ +++  +
  gi|336254891|ref|YP_004597998.1| 270 DVADGADEIDDLTAEQSDSMSEIASEISGLSATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKMEGVQEAAD 346
                                       5667788899999999999999999999******************************************9999999 PP

                                       H...HHHHHHHHHHHHH CS
                        Laminin_II  84 assslsdniseikelIa 100
                                       +   + +++++++e ++
  gi|336254891|ref|YP_004597998.1| 347 E---VTEDVENLREGVQ 360
                                       9...9999999999776 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 6.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankaird 56 
                                       e+a+ea ++++ v+e   ++ +++en++e +++i++ v+ +n+ +++ n     
  gi|336254891|ref|YP_004597998.1| 329 ETAEEAIDKMEGVQEAADEVTEDVENLREGVQRIDEIVDVINDIADQTNLLALN 382
                                       89*****************************************99988866555 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00038
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   1 skelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvk 48 
                                       +k+la+e ++ a+++++ +  +++++e+t ++l+++n++++   e+v+
  gi|336254891|ref|YP_004597998.1| 404 VKSLAEESQDEATNIERMVDRIQADTEETVDSLETANAEIDDGVELVE 451
                                       5999**********************************9877666665 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                       e +aea+  + ev   + + ++ +e++ +   ++ +  +e+ ++v+    +++dA++ v +++ ++++L
  gi|336254891|ref|YP_004597998.1| 462 EAVAEASTGIREVATATDDQAASTEEVASMTDSAMERSQEIADEVETIVATTADASDLVEEIDAELDRL 530
                                       6789999999*****************99999999999*************************999998 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       6.2   2.9e+03     299     353 ..       9      67 ..       3      79 .. 0.67
   2 !    9.1   4.5    0.0011      0.54     334     397 ..     207     270 ..     196     273 .. 0.91
   3 !   15.3   7.4   1.5e-05    0.0069     317     413 ..     274     370 ..     268     377 .. 0.87
   4 !    7.8   4.6    0.0028       1.3     342     466 ..     400     524 ..     395     531 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.2
                            DUF812 299 srfthaeklqftkeela....kkaeteeelkkkreeeleelqeqieeleskieeleeei 353
                                       sr++ a ++ ++ ++++    ++a++   l+ + e+ le+++  +++++ ++++ + + 
  gi|336254891|ref|YP_004597998.1|   9 SRLDAAREAVVEPDAVSrddvSRAKDLAGLQSADERRLESMSHLFDAVSDELAAASVDA 67 
                                       55555555555444333444567777788888888999999999888888887766555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0011
                            DUF812 334 elqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeen 397
                                       +l+ + ++ e++i+++e++++++e+++++ e e+e++++++e l++  + ++ tle +++a   
  gi|336254891|ref|YP_004597998.1| 207 ALRARSSAQEARIDAYEAQLAEYEQRLEEYEAEIEAQDRTREDLADARRSMENTLEEVAEATDD 270
                                       6888999999***********************************************9998765 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.5e-05
                            DUF812 317 kaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpd 393
                                        a++ ++l+++++++++e+ ++i+ l++++ee++++ ++++++ +q+e+ +  + e+ ee  ++++  + +++ + +
  gi|336254891|ref|YP_004597998.1| 274 GADEIDDLTAEQSDSMSEIASEISGLSATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKMEGVQEAADEVTE 350
                                       57899*************************************************************99999999999 PP

                            DUF812 394 aeeniekLqalveasaqrlv 413
                                       + en+++  + +++  + + 
  gi|336254891|ref|YP_004597998.1| 351 DVENLREGVQRIDEIVDVIN 370
                                       99998876666666555555 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0028
                            DUF812 342 leskieeleeeikklessikqveeeleeeke.eneelekevklkkktlellpdaeeniekLqalveasaqrlvelak 417
                                       + +++++l+ee ++ +++i+++ + +++  e +   le  ++     +el++++  n+ + +++v +++  + e+a+
  gi|336254891|ref|YP_004597998.1| 400 VANEVKSLAEESQDEATNIERMVDRIQADTEeTVDSLETANAEIDDGVELVEETVDNLGRIEEAVAEASTGIREVAT 476
                                       56789999999999999999999999976550556777778888899999999999999999999999999999999 PP

                            DUF812 418 qWekhRvplieeyrelkesksekekeaerkleeikklrekmkevaeelr 466
                                         +  +++ +ee  +  +s+ e+ +e+ + +e i ++ +   +++ee+ 
  gi|336254891|ref|YP_004597998.1| 477 ATD-DQAASTEEVASMTDSAMERSQEIADEVETIVATTADASDLVEEID 524
                                       865.678999999999999999999999999999999999999888875 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.42     2e+02      65     114 ..     216     258 ..     184     263 .. 0.40
   2 !   15.1   1.6   3.6e-05     0.017      35     112 ..     246     319 ..     244     326 .. 0.80
   3 !   11.3   3.0   0.00055      0.26      39     110 ..     299     373 ..     298     379 .. 0.63
   4 ?    7.1   1.4     0.011       5.3      47     114 ..     415     458 ..     395     477 .. 0.41
   5 ?    5.1   1.8     0.047        22      61     113 ..     478     530 ..     459     533 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.42
                           DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       ++rid  +++l e ++  +e ++e+++  +         e + +a +++e
  gi|336254891|ref|YP_004597998.1| 216 EARIDAYEAQLAEYEQRLEEYEAEIEAQDRT-------REDLADARRSME 258
                                       3344444444443333333333333333222.......222222222222 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.6e-05
                           DUF1664  35 TkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       T+  l+da  s+ + le+v    a++ ++ ++  d++d+   eq++  +ei++e++ ++  ++ei ++ e+v+++ e
  gi|336254891|ref|YP_004597998.1| 246 TREDLADARRSMENTLEEV----AEATDDVADGADEIDDLTAEQSDSMSEIASEISGLSATVEEIASNAEEVSATSE 318
                                       7888888888877777665....556677788888889999999999999999999999999999999999988766 PP

                           DUF1664 112 g 112
                                       +
  gi|336254891|ref|YP_004597998.1| 319 Q 319
                                       6 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00055
                           DUF1664  39 lsdavesvskqleqvseslaatk...rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                       ls  ve+++++ e+vs++ +++     + ++  ++  +k++ ++e++ e++e+v+++re++++i+e v+ ++++ 
  gi|336254891|ref|YP_004597998.1| 299 LSATVEEIASNAEEVSATSEQAEsvaSDTTETAEEAIDKMEGVQEAADEVTEDVENLREGVQRIDEIVDVINDIA 373
                                       566677777777777644444440004444444555556666677777888888888888888888888887765 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.011
                           DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       ++++e++ + ++a                         ++e v++++   +ei++ ve v+e+v +l+
  gi|336254891|ref|YP_004597998.1| 415 ATNIERMVDRIQAD------------------------TEETVDSLETANAEIDDGVELVEETVDNLG 458
                                       33333333333333........................333333333333333333333333333332 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.047
                           DUF1664  61 krhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                        ++ ++  ++v +  d+ +e s+ei++ev+++   +++ ++ ve++++    l
  gi|336254891|ref|YP_004597998.1| 478 TDDQAASTEEVASMTDSAMERSQEIADEVETIVATTADASDLVEEIDAELDRL 530
                                       33333444555555566666666666666666666666666666555555444 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   7.4    0.0016      0.76     119     221 ..     218     316 ..     213     326 .. 0.86
   2 !    8.5   4.5    0.0024       1.1     116     222 ..     257     366 ..     255     381 .. 0.72
   3 !   12.9   4.3   0.00011     0.052      94     219 ..     400     524 ..     392     530 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                              CorA 119 ivdrlfellekleeeldeledeledstkkeilrelaqlrrrlv.klrralapnrevlkrllakaddkllddedkeyl 194
                                        +d ++++l + e++l+e+e e+  + ++  +++la+ rr++  +l++++ ++ +v  +  +  + + l++e+++ +
  gi|336254891|ref|YP_004597998.1| 218 RIDAYEAQLAEYEQRLEEYEAEI--EAQDRTREDLADARRSMEnTLEEVAEATDDVA-DGAD--EIDDLTAEQSDSM 289
                                       58999******************..888889999*******6516799999999999.7776..799999999999* PP

                              CorA 195 rdlldelerllemlealrerleslqdt 221
                                       +++ +e++ l+ ++e +++ +e ++ t
  gi|336254891|ref|YP_004597998.1| 290 SEIASEISGLSATVEEIASNAEEVSAT 316
                                       *********999999998888877655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0024
                              CorA 116 ldeivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrlla.kaddklldde 189
                                       ++  +++++e+++++ +  de++d    ++++  ei++e++ l  ++ ++ + + +  ++ ++  +  +d+ +  +e
  gi|336254891|ref|YP_004597998.1| 257 MENTLEEVAEATDDVADGADEIDDLTaeQSDSMSEIASEISGLSATVEEIASNAEEVSATSEQAESvASDTTETAEE 333
                                       55567778888888888888888888888888899999999999888888665555555555444433455555555 PP

                              CorA 190 dkeylrdlldelerllemlealrerleslqdty 222
                                       + + ++ +++ ++ + e++e+lre ++++ ++ 
  gi|336254891|ref|YP_004597998.1| 334 AIDKMEGVQEAADEVTEDVENLREGVQRIDEIV 366
                                       556688999999999999999999998888775 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00011
                              CorA  94 vikrlkdeggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapn 170
                                       v++++k+  ++ ++ ++ ++r +d+i  + +e+++ le+   e++d +  +  +e ++ l ++++ +++  + +++ 
  gi|336254891|ref|YP_004597998.1| 400 VANEVKSLAEESQDEATNIERMVDRIQADTEETVDSLETANAEIDDGV--ELVEETVDNLGRIEEAVAEASTGIREV 474
                                       66667777789999999*******************************..777888888888888888888888888 PP

                              CorA 171 revlkrlla.kaddkllddedkeylrdlldelerllemlealrerleslq 219
                                        ++ ++  a +++   ++d ++e+ +++ de+e ++ ++   ++++e + 
  gi|336254891|ref|YP_004597998.1| 475 ATATDDQAAsTEEVASMTDSAMERSQEIADEVETIVATTADASDLVEEID 524
                                       8888744444899***************************9999999886 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 ?    4.5   4.8     0.074        35      18      90 ..     215     291 ..     203     297 .. 0.69
   2 ?   14.7   0.8   5.2e-05     0.024      18     104 ..     303     389 ..     295     393 .. 0.93
   3 ?    1.0   3.2      0.91   4.3e+02      19     118 ..     405     506 ..     400     525 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.074
                             Mod_r  18 lealvktl.pevkqlkeekeellaeneslaeknlslep...eleelrselqekleelkelekefeekeqeldellqk 90 
                                        ea+++    ++ ++++++ee +ae+e+  +   +l +   ++e+  +e++e+ + ++   +e +++++e+++ +++
  gi|336254891|ref|YP_004597998.1| 215 QEARIDAYeAQLAEYEQRLEEYEAEIEAQDRTREDLADarrSMENTLEEVAEATDDVADGADEIDDLTAEQSDSMSE 291
                                       45555555456777888888888888776644333333334888888888888888888888888888888777665 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.2e-05
                             Mod_r  18 lealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspd 94 
                                       +e+++++++ev +  e+ e++   + ++ae+ +++ + ++e  +e++e  e+l+e  ++ +e     +++ +++++ 
  gi|336254891|ref|YP_004597998.1| 303 VEEIASNAEEVSATSEQAESVASDTTETAEEAIDKMEGVQEAADEVTEDVENLREGVQRIDEIVDVINDIADQTNLL 379
                                       67888899*******************************************************************99 PP

                             Mod_r  95 allarLqtav 104
                                       al a  ++a+
  gi|336254891|ref|YP_004597998.1| 380 ALNASIEAAT 389
                                       9999888876 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.91
                             Mod_r  19 ealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspd 94 
                                       ++l++++ +e  +++   + + a +e++ ++    + e+++  + ++e+ ++l ++e+++ e  +   e+   ++++
  gi|336254891|ref|YP_004597998.1| 405 KSLAEESqDEATNIERMVDRIQADTEETVDSLETANAEIDDGVELVEETVDNLGRIEEAVAEASTGIREVATATDDQ 481
                                       55666665777888888888888888888866666889999999999999999999999998888888888777766 PP

                             Mod_r  95 allar.LqtavaeaeeeSealaeef 118
                                       a+ +  +   ++ a e S+++a+e+
  gi|336254891|ref|YP_004597998.1| 482 AASTEeVASMTDSAMERSQEIADEV 506
                                       5544325555555566666666554 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 ?    1.0   0.4      0.92   4.4e+02      85     129 ..     201     244 ..     183     250 .. 0.63
   2 ?    7.6   0.6    0.0083       3.9      31      98 ..     248     314 ..     241     318 .. 0.85
   3 ?    8.5   1.9    0.0046       2.2      33     105 ..     299     370 ..     291     387 .. 0.75
   4 ?   11.6   0.5    0.0005      0.24      24     122 ..     434     531 ..     429     534 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.92
                                       HHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  85 eleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqke 129
                                       +++ ++l l+++ +aqe +i +    l + eq++++ e +i+++ 
  gi|336254891|ref|YP_004597998.1| 201 MVD-QQLALRARSSAQEARIDAYEAQLAEYEQRLEEYEAEIEAQD 244
                                       344.66666666666666666666666666666666666666665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0083
                                       CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketid 98 
                                       +d+ +  +++en+lee+++ t ++ +   ei+d ++e+  s ++  + i+ +s ++e ei+   e+++
  gi|336254891|ref|YP_004597998.1| 248 EDLADARRSMENTLEEVAEATDDVADGADEIDDLTAEQSDSMSEIASEISGLSATVE-EIASNAEEVS 314
                                       5555666789******************************99999999999999999.8887777765 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0046
                                       CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHH CS
                         Fib_alpha  33 vkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnir 105
                                       ++ ++e++ ++ ee+s ++++ae++ ++++++ +e+  + ++ +++  ++++++e +  +  ++id+ +  i+
  gi|336254891|ref|YP_004597998.1| 299 LSATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKMEGVQEAADEVTEDVE-NLREGVQRIDEIVDVIN 370
                                       5678999999999999999999999999999999999999988888888888877.55554555555444444 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.0005
                                       HCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCC CS
                         Fib_alpha  24 dlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaq 100
                                       d l++ + ++++ +e +e++++++ + ++ + e ++ i+++ +++  +++ +++v +   + +e + +++ +++ + 
  gi|336254891|ref|YP_004597998.1| 434 DSLETANAEIDDGVELVEETVDNLGRIEEAVAEASTGIREVATATDDQAASTEEVASMTDSAME-RSQEIADEVETI 509
                                       67899999*****************************************999999999999999.999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 101 esnirvLqnvlesneqkiqkLe 122
                                       + +     +++e+ + ++ +Le
  gi|336254891|ref|YP_004597998.1| 510 VATTADASDLVEEIDAELDRLE 531
                                       9999999999999999999998 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   5.5      0.12        58      16      73 ..     249     318 ..     230     346 .. 0.64
   2 ?    3.9   1.0      0.15        71      25      73 ..     342     401 ..     332     427 .. 0.59
   3 ?   13.0   3.5   0.00023      0.11      18      83 ..     423     487 ..     405     510 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.12
                         DASH_Dad2  16 qlrdlsdslakqleeLeeklstladgteavasVlanWqnvlraismaslkllqkaee............e 73 
                                        l d   s+++ lee++e  + +adg++ + +  a+    +  i    ++l ++ ee            e
  gi|336254891|ref|YP_004597998.1| 249 DLADARRSMENTLEEVAEATDDVADGADEIDDLTAEQSDSMSEIASEISGLSATVEEiasnaeevsatsE 318
                                       4667778899999999999999999999999999876666655555555555444442221332222110 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.15
                         DASH_Dad2  25 akqleeLeeklstladgteavasVlanWqnvlraismaslkllqkaee...........e 73 
                                       ++  +e+ e ++ l++g + + ++++  + +    ++  l+   +a++           +
  gi|336254891|ref|YP_004597998.1| 342 QEAADEVTEDVENLREGVQRIDEIVDVINDIADQTNLLALNASIEAATageagdgfavvA 401
                                       455577788888888888888888888888887777665554322222445566666642 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00023
                         DASH_Dad2  18 rdlsdslakqleeLeeklstladgteavasVlanWqnvlraismaslkllqkaeeeaeeeeedeee 83 
                                         + ++ ++ +++Le+  ++++dg e v++ ++n   + +a+  as+++ + a++ ++++++++ee
  gi|336254891|ref|YP_004597998.1| 423 DRIQADTEETVDSLETANAEIDDGVELVEETVDNLGRIEEAVAEASTGIREVATA-TDDQAASTEE 487
                                       4566788999**************************************9854444.3333333333 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       1.9   9.1e+02      30      71 ..     222     266 ..     216     270 .. 0.59
   2 ?   10.5   0.5    0.0015      0.73       2      98 ..     257     359 ..     256     362 .. 0.83
   3 ?    3.7   0.2       0.2        96       4      83 ..     347     439 ..     344     457 .. 0.65
   4 ?    4.6   1.0       0.1        48       5      86 ..     432     516 ..     401     532 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHHTS..S-HHHHHHHHH...HHHHHHHHHHH CS
                               ING  30 vqellkeidskiekflkngslqknekeeels...riqeelkeaqe 71 
                                       ++ +l+e+++++e++ ++ + q+ ++e+      +++++l+e+ e
  gi|336254891|ref|YP_004597998.1| 222 YEAQLAEYEQRLEEYEAEIEAQDRTREDLADarrSMENTLEEVAE 266
                                       677888889999999844344444444333333366666666555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0015
                                       HHHHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......TS..S-HHHHHHHHHHHHHHHHHHHHH CS
                               ING   2 LedyldsvenLPlelqrnltelreiDakvqellkeidskiekfl......kngslqknekeeelsriqeelkeaqel 72 
                                       +e++l+ v +  +++ +  +e+ ++ a+ ++ + ei s+i+ ++      ++++++    +e+ +++ ++  e+ e 
  gi|336254891|ref|YP_004597998.1| 257 MENTLEEVAEATDDVADGADEIDDLTAEQSDSMSEIASEISGLSatveeiASNAEEVSATSEQAESVASDTTETAEE 333
                                       589999999999********************************999998555555555666666777777777777 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               ING  73 ldeKiqlaqqaldlvdkhlrrLdqdl 98 
                                       + +K++ +q+a+d v++ +++L + +
  gi|336254891|ref|YP_004597998.1| 334 AIDKMEGVQEAADEVTEDVENLREGV 359
                                       88899999999999999999987655 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.2
                                       HHHTSGGGHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHH............TS..S-HHHHHHHHHHHHHHHH CS
                               ING   4 dyldsvenLPlelqrnltelrei.Dakvqellkeidskiekfl............kngslqknekeeelsriqeelk 67 
                                       + +++venL + +qr  + +  i D   q++l  ++ +ie               ++ +   +e+++e ++i+++++
  gi|336254891|ref|YP_004597998.1| 347 EVTEDVENLREGVQRIDEIVDVInDIADQTNLLALNASIEAATageagdgfavvaNEVKSLAEESQDEATNIERMVD 423
                                       67788888888888765555544233334445555777777778888888888875555556667777778888888 PP

                                       HHHHHHHHHHHHHHHH CS
                               ING  68 eaqelldeKiqlaqqa 83 
                                       ++q   +e +   ++a
  gi|336254891|ref|YP_004597998.1| 424 RIQADTEETVDSLETA 439
                                       8888777766555555 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.1
                                       HHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.................TS..S-HHHHHHHHHHHHH CS
                               ING   5 yldsvenLPlelqrnltelreiDakvqellkeidskiekfl.................kngslqknekeeelsriqe 64 
                                       ++ds+e   +e+ + ++++ e               ++++                  ++++ q  + ee+ s   +
  gi|336254891|ref|YP_004597998.1| 432 TVDSLETANAEIDDGVELVEE--------------TVDNLGrieeavaeastgirevaTATDDQAASTEEVASMTDS 494
                                       334444444444444444433..............333333333333444455555558889999999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHH CS
                               ING  65 elkeaqelldeKiqlaqqaldl 86 
                                       +++++qe++de  +++ +++d 
  gi|336254891|ref|YP_004597998.1| 495 AMERSQEIADEVETIVATTADA 516
                                       9999999999977777666654 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0  10.1   0.00079      0.37      23     109 ..     203     289 ..     189     295 .. 0.85
   2 ?    5.4   4.4      0.02       9.6       9      75 ..     301     367 ..     293     394 .. 0.70
   3 ?    5.6   9.5     0.018       8.4      14     131 ..     408     530 ..     378     533 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00079
                           DUF3450  23 keaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelv 99 
                                       +++ +  a +++ +++id+++ + +e+++++++ ++e+e+ +  +e l++  +s+e++++++ e  +++   ++e+ 
  gi|336254891|ref|YP_004597998.1| 203 DQQLALRARSSAQEARIDAYEAQLAEYEQRLEEYEAEIEAQDRTREDLADARRSMENTLEEVAEATDDVADGADEID 279
                                       4555666677777889*****************************************************99999999 PP

                           DUF3450 100 pllekmidrL 109
                                        l  +  d++
  gi|336254891|ref|YP_004597998.1| 280 DLTAEQSDSM 289
                                       8877766665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.02
                           DUF3450   9 lasgalaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlva 75 
                                       ++   +a++++++ +++e+a + a+++ +  ++  d+ + +++   +++e +e+l+   ++ +++v+
  gi|336254891|ref|YP_004597998.1| 301 ATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKMEGVQEAADEVTEDVENLREGVQRIDEIVD 367
                                       4444557777777777777777777777777777777777777777777777777776666666655 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.018
                           DUF3450  14 laatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       ++++ d+a + ++   +++a++++ +d+l+   +e+ + ++ ++e +++l   +e +++  +  ++  +  + q ++
  gi|336254891|ref|YP_004597998.1| 408 AEESQDEATNIERMVDRIQADTEETVDSLETANAEIDDGVELVEETVDNLGRIEEAVAEASTGIREVATATDDQAAS 484
                                       3788999999******************************************************************* PP

                           DUF3450  91 ieeierelvpllek...midrLeqfveldlPf..lleeRqarlakL 131
                                        ee+++     +e+   + d+ e++v++      l ee +a+l++L
  gi|336254891|ref|YP_004597998.1| 485 TEEVASMTDSAMERsqeIADEVETIVATTADAsdLVEEIDAELDRL 530
                                       ************8722256788888875433333667777777666 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 ?   -0.0   0.4       2.3   1.1e+03      59      92 ..     225     241 ..     208     258 .. 0.53
   2 ?    7.4   2.8     0.011       5.2      30      92 ..     258     321 ..     237     325 .. 0.78
   3 ?   11.0   0.7   0.00086       0.4      30      78 ..     332     380 ..     325     385 .. 0.82
   4 ?    4.4   2.1     0.095        45      42      93 ..     400     452 ..     394     455 .. 0.82
   5 ?    4.3   2.0      0.11        50      39      92 ..     478     531 ..     471     533 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 2.3
                           BLOC1_2  59 elqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                       +l++y q                 +L+ey  e+E
  gi|336254891|ref|YP_004597998.1| 225 QLAEYEQ-----------------RLEEYEAEIE 241
                                       2222222.................2333322222 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                           BLOC1_2  30 eaasekykklkdvaaslekkleklnekye.elqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                       e++ e++++ +d +a+ ++++++l +++  ++++  ++i  + ++v+e+ ++++e+ + s + E
  gi|336254891|ref|YP_004597998.1| 258 ENTLEEVAEATDDVADGADEIDDLTAEQSdSMSEIASEISGLSATVEEIASNAEEVSATSEQAE 321
                                       6788888888888888888898887766658999999999999999999999988877776655 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00086
                           BLOC1_2  30 eaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78 
                                       e+a+ k + ++++a+++++++e+l+e  + +++ ++ i++i +q++ L 
  gi|336254891|ref|YP_004597998.1| 332 EEAIDKMEGVQEAADEVTEDVENLREGVQRIDEIVDVINDIADQTNLLA 380
                                       6788889999999999999999999999999999999999999988775 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.095
                           BLOC1_2  42 vaaslekkleklnekyeelqpylqqid.qiekqvteLeeavseLDeyskeLEa 93 
                                       va+++++ +e+ + +  +++ ++++i+ + e++v++Le+a +e+D  +   E+
  gi|336254891|ref|YP_004597998.1| 400 VANEVKSLAEESQDEATNIERMVDRIQaDTEETVDSLETANAEIDDGVELVEE 452
                                       678888888888888999999999997579999*****999999987776665 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.11
                           BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                        +d+aas+e+ ++ +++  e  q+  ++++ i +++++  ++v+e+D+   +LE
  gi|336254891|ref|YP_004597998.1| 478 TDDQAASTEEVASMTDSAMERSQEIADEVETIVATTADASDLVEEIDAELDRLE 531
                                       567888889999999999999999999999999999999999999999999998 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3      0.29   1.4e+02      19      66 ..     219     266 ..     216     269 .. 0.88
   2 ?    6.3   3.2     0.017       8.1      30      63 ..     286     319 ..     257     386 .. 0.57
   3 ?   -1.1   0.1       3.3   1.5e+03      30      50 ..     412     432 ..     395     452 .. 0.50
   4 ?    4.8   0.3     0.051        24       3      64 ..     434     495 ..     432     512 .. 0.82
   5 ?    5.3   0.4     0.036        17       9      69 ..     468     528 ..     461     532 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.29
                             Sec34  19 tdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                       +d+ + qL+e e++ ++ +++ ++ +++ e+l + ++++e++ ee+ e
  gi|336254891|ref|YP_004597998.1| 219 IDAYEAQLAEYEQRLEEYEAEIEAQDRTREDLADARRSMENTLEEVAE 266
                                       788889999999999999999999999999999999999999999876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.017
                             Sec34  30 eekfksvsektsslheaceqlleeqkrleelaee 63 
                                       ++++++++++ s l+++ e++ ++ ++++ ++e+
  gi|336254891|ref|YP_004597998.1| 286 SDSMSEIASEISGLSATVEEIASNAEEVSATSEQ 319
                                       5555555555555555555554444444444433 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.3
                             Sec34  30 eekfksvsektsslheaceql 50 
                                       +++ ++++    ++++++e+ 
  gi|336254891|ref|YP_004597998.1| 412 QDEATNIERMVDRIQADTEET 432
                                       333333333333333333333 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.051
                             Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeei 64 
                                       d Le+ ++e+d+ +e ++e+ ++L  +ee + + s+  +++ +a+++  ++++++ +++++ 
  gi|336254891|ref|YP_004597998.1| 434 DSLETANAEIDDGVELVEETVDNLGRIEEAVAEASTGIREVATATDDQAASTEEVASMTDSA 495
                                       77888899999999999999999999999999999999999999999888888888777764 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.036
                             Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                       +  ++e+ + td+   + ee+ +  +s  e+++++ ++ e++++ + + ++l+eei+++L+
  gi|336254891|ref|YP_004597998.1| 468 STGIREVATATDDQAASTEEVASMTDSAMERSQEIADEVETIVATTADASDLVEEIDAELD 528
                                       556778888999999999999999999*****************************99985 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 ?    7.5   2.4     0.012       5.8      14      64 ..     219     268 ..     208     275 .. 0.71
   2 ?    7.6   2.9     0.012       5.7      35      99 .]     274     339 ..     267     339 .. 0.86
   3 ?    1.8   0.1      0.73   3.5e+02       5      33 ..     343     371 ..     341     389 .. 0.70
   4 ?    8.3   2.8    0.0069       3.3       1      67 [.     395     464 ..     395     492 .. 0.62
   5 ?    1.0   0.6       1.4   6.5e+02      34      61 ..     490     517 ..     458     534 .. 0.41

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.012
                      Syntaxin-6_N  14 lnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetv 64 
                                       ++  e+ ++++e+ le+ ++ + e  d+tr++L  a rs+e++le+  e+ 
  gi|336254891|ref|YP_004597998.1| 219 IDAYEAQLAEYEQRLEEYEA-EIEAQDRTREDLADARRSMENTLEEVAEAT 268
                                       66667777777654444443.378888888888888888888888887765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
                      Syntaxin-6_N  35 tseeldetrteLrkalrsiewdledLeetvriveknpsk.fkidekelsrrrafveevreevkemk 99 
                                         +e+d+++ e   ++++i  +++ L  tv+ + +n ++    +e++ s   +  e ++e +++m+
  gi|336254891|ref|YP_004597998.1| 274 GADEIDDLTAEQSDSMSEIASEISGLSATVEEIASNAEEvSATSEQAESVASDTTETAEEAIDKME 339
                                       4789********************************999667777777888888888899999885 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.73
                      Syntaxin-6_N   5 evkeeVqkslnkaeslyrrwerlledtss 33 
                                       e+++eV + ++++++ ++r  ++ ++ ++
  gi|336254891|ref|YP_004597998.1| 343 EAADEVTEDVENLREGVQRIDEIVDVIND 371
                                       67888888888888888888887776555 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0069
                      Syntaxin-6_N   1 DPFfevkeeVqkslnkaeslyrrwerlledtss...stseeldetrteLrkalrsiewdledLeetvriv 67 
                                       D F +v++eV++ +++ +   ++ er+ +  ++   +t ++l+ ++ e+   ++ +e+++++L +  ++v
  gi|336254891|ref|YP_004597998.1| 395 DGFAVVANEVKSLAEESQDEATNIERMVDRIQAdteETVDSLETANAEIDDGVELVEETVDNLGRIEEAV 464
                                       88999*****999999999999997766664331112355555555555555555555555554433333 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 1.4
                      Syntaxin-6_N  34 stseeldetrteLrkalrsiewdledLe 61 
                                       s +++  e ++e+  ++++i  +  d  
  gi|336254891|ref|YP_004597998.1| 490 SMTDSAMERSQEIADEVETIVATTADAS 517
                                       1333333333333333333333222222 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3       0.1        47       7      42 ..     287     322 ..     280     326 .. 0.88
   2 ?    6.2   0.1     0.018       8.5      14      55 ..     336     377 ..     328     380 .. 0.89
   3 ?    3.3   0.1      0.15        69       6      42 ..     433     469 ..     429     471 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.1
                         DASH_Duo1   7 eqLrkinevienviesLkkaksniervketvestnt 42 
                                       +++ +i + i+++ ++ +++ sn e+v+ t e++++
  gi|336254891|ref|YP_004597998.1| 287 DSMSEIASEISGLSATVEEIASNAEEVSATSEQAES 322
                                       677889999***********************9986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.018
                         DASH_Duo1  14 evienviesLkkaksniervketvestntLLdkWirIlsqte 55 
                                       +  e+v+e+ +++++++e++ e v+  ++++d   +I  qt+
  gi|336254891|ref|YP_004597998.1| 336 DKMEGVQEAADEVTEDVENLREGVQRIDEIVDVINDIADQTN 377
                                       5678999999999*******************9999999996 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.15
                         DASH_Duo1   6 leqLrkinevienviesLkkaksniervketvestnt 42 
                                       +++L++ n+ i++ +e  +++ +n+ r++e+v +++t
  gi|336254891|ref|YP_004597998.1| 433 VDSLETANAEIDDGVELVEETVDNLGRIEEAVAEAST 469
                                       67899999************************99986 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2       4.1   1.9e+03     142     162 ..      42      62 ..       5      75 .. 0.56
   2 ?   11.2  11.3   0.00066      0.31      68     158 ..     183     273 ..     137     284 .. 0.63
   3 ?    2.8   8.1      0.26   1.2e+02      70     161 ..     258     349 ..     253     356 .. 0.91
   4 ?    9.7   5.8     0.002      0.94      17     154 ..     362     493 ..     353     533 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.1
                             ATG16 142 reeelrekeklvqdlqDElsa 162
                                        e +l+   +l +++ DEl+a
  gi|336254891|ref|YP_004597998.1|  42 DERRLESMSHLFDAVSDELAA 62 
                                       233444444555555555544 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00066
                             ATG16  68 snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdree 144
                                       + ++++a   +l++ ++++ +++ +l  + +  + r+ + +++l++ e++l+e e+++++  ++r++l +++++ e+
  gi|336254891|ref|YP_004597998.1| 183 ERAVDDALNRALSAVRLSMVDQQLALRARSSAQEARIDAYEAQLAEYEQRLEEYEAEIEAQDRTREDLADARRSMEN 259
                                       33455566666666666666666666666666677888888888888888888888888888888888888888888 PP

                             ATG16 145 elrekeklvqdlqD 158
                                       +l+e +++ +d+ D
  gi|336254891|ref|YP_004597998.1| 260 TLEEVAEATDDVAD 273
                                       88888888877655 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.26
                             ATG16  70 skqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeel 146
                                       +++ +++++ ++ +a   +e  +l  +++++ + + +  + l++  e++ +++e++ + +++ +++     + +ee 
  gi|336254891|ref|YP_004597998.1| 258 ENTLEEVAEATDDVADGADEIDDLTAEQSDSMSEIASEISGLSATVEEIASNAEEVSATSEQAESVASDTTETAEEA 334
                                       56788899999999999999999999999999999999999999********************************* PP

                             ATG16 147 rekeklvqdlqDEls 161
                                        +k + vq+  DE++
  gi|336254891|ref|YP_004597998.1| 335 IDKMEGVQEAADEVT 349
                                       *********999975 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.002
                             ATG16  17 faeliqaynrLldrtsaleaenaklekaaasaks.sksskksakekeasasqsnskqsakiqsleqklaqlreelae 92 
                                         e+++  n+++d+t++l+  na++e+a+a +     +  +++ +++a++sq      ++ ++ e  + +++++ +e
  gi|336254891|ref|YP_004597998.1| 362 IDEIVDVINDIADQTNLLA-LNASIEAATAGEAGdGFAVVANEVKSLAEESQ------DEATNIERMVDRIQADTEE 431
                                       5699************996.56777555555444666666777888888888......7788888888888888888 PP

                             ATG16  93 lyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvq 154
                                       +  s ++ +  + +  e +++  ++l + ee++ae+++ ++++ t+ +d+++  +e + + +
  gi|336254891|ref|YP_004597998.1| 432 TVDSLETANAEIDDGVELVEETVDNLGRIEEAVAEASTGIREVATATDDQAASTEEVASMTD 493
                                       88888888888888888888888888888888888888888888888888888888776665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       7.9   3.7e+03     193     216 ..      38      61 ..       9      80 .. 0.59
   2 ?    7.1  15.9    0.0046       2.2     156     278 ..     217     323 ..     188     338 .. 0.55
   3 ?    5.4   7.1     0.015         7     195     283 ..     283     367 ..     277     387 .. 0.65
   4 ?    6.2   9.4    0.0085         4     159     279 ..     409     531 ..     393     540 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.9
                              Spc7 193 lesidkeeLeelreelaelkaeie 216
                                       l+s d+ +Le++ + +++++ e++
  gi|336254891|ref|YP_004597998.1|  38 LQSADERRLESMSHLFDAVSDELA 61 
                                       344444444444444444444444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0046
                              Spc7 156 elLekqeeeldellpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkaeieekkkelaelqeqle 230
                                       +++              ++++a+l e  ++l+e ++e+e+ d  +e+L+ +r+++++  +e++e  +++a+  ++++
  gi|336254891|ref|YP_004597998.1| 217 ARI--------------DAYEAQLAEYEQRLEEYEAEIEAQDrtREDLADARRSMENTLEEVAEATDDVADGADEID 279
                                       333..............344444444444444444444444433566666666666666666655555555555555 PP

                              Spc7 231 eleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkal 278
                                       +l+++    ++++se+ +ei+    ++ee   ++++evs+  e+ +++
  gi|336254891|ref|YP_004597998.1| 280 DLTAEQ---SDSMSEIASEISGLSATVEEI-ASNAEEVSATSEQAESV 323
                                       555444...444666666666666555543.34455555555555444 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.015
                              Spc7 195 sidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkse.leeeiaeaervleeckgwsesevsr 270
                                       + +++++ e+ +e++ l+a++e    e+a+  e++ + +e+ e++++  +e +ee+i + e v+e+  +++ ++v++
  gi|336254891|ref|YP_004597998.1| 283 AEQSDSMSEIASEISGLSATVE----EIASNAEEVSATSEQAESVASDTTEtAEEAIDKMEGVQEAADEVT-EDVEN 354
                                       5556666666777777777777....666666666666666666655555414556777777777666665.57888 PP

                              Spc7 271 lkeevkaleeltg 283
                                       l+e v++++e+ +
  gi|336254891|ref|YP_004597998.1| 355 LREGVQRIDEIVD 367
                                       8888888877655 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0085
                              Spc7 159 ekqeeeldellpeleeekaeleeeleklqeaaeeles......idkeeLeelreelaelkaeieekkkelaelqeql 229
                                       e++++e++++   +++ +a+ ee++++l++a++e+++       + ++L  + e++ae+++ i+    e+a+ +++ 
  gi|336254891|ref|YP_004597998.1| 409 EESQDEATNIERMVDRIQADTEETVDSLETANAEIDDgvelveETVDNLGRIEEAVAEASTGIR----EVATATDDQ 481
                                       3455666677777777777777777777776666555333322223333333333333333333....444555555 PP

                              Spc7 230 eeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkale 279
                                       ++++e++++++++  e  +eia + +++ ++    ++ v+++ +e+++le
  gi|336254891|ref|YP_004597998.1| 482 AASTEEVASMTDSAMERSQEIADEVETIVATTADASDLVEEIDAELDRLE 531
                                       55566666666666666666666666666666666666666666666665 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       1.5     7e+02      25      71 ..     247     293 ..     231     302 .. 0.70
   2 ?    5.6   0.3     0.044        21       2      57 ..     300     356 ..     286     364 .. 0.71
   3 ?    3.9   2.1      0.15        68      33      63 ..     402     432 ..     348     532 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.5
                        Syntaxin_2  25 kkdteelreklhelieeinelikktnellkklsqldnsssdsqqklq 71 
                                       + d  + r++++++ ee+ e   ++ +   +++ l+  +sds+  ++
  gi|336254891|ref|YP_004597998.1| 247 REDLADARRSMENTLEEVAEATDDVADGADEIDDLTAEQSDSMSEIA 293
                                       45666777777777777777777777777777777777776655444 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.044
                        Syntaxin_2   2 ssnlqkinsnvstleklvkqLgtk.kdteelreklhelieeinelikktnellkkls 57 
                                       s+ + +i+sn  +     +q ++   dt+e+ e++ + +e ++e + +++e++++l 
  gi|336254891|ref|YP_004597998.1| 300 SATVEEIASNAEEVSATSEQAESVaSDTTETAEEAIDKMEGVQEAADEVTEDVENLR 356
                                       455666666666666666666555458888888888888888888888888888876 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.15
                        Syntaxin_2  33 eklhelieeinelikktnellkklsqldnss 63 
                                       +++++l ee ++ ++++++ + +++++++ +
  gi|336254891|ref|YP_004597998.1| 402 NEVKSLAEESQDEATNIERMVDRIQADTEET 432
                                       4445555555555555555554444444433 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7  18.2   7.1e-05     0.033      26     156 ..     206     331 ..     199     339 .. 0.81
   2 ?   -1.1   6.2       2.3   1.1e+03      30     163 ..     329     467 ..     319     477 .. 0.67
   3 ?   -0.1   7.2       1.2   5.5e+02      41     137 ..     410     507 ..     401     536 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-05
                        MscS_porin  26 lnlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqla 102
                                       l+l +   ++++++++++ +++++ ++l+e ++e+ea      + ++e+la    +  e+ l+++ ++  ++     
  gi|336254891|ref|YP_004597998.1| 206 LALRARSSAQEARIDAYEAQLAEYEQRLEEYEAEIEAQ-----DRTREDLADAR-RSMENTLEEVAEATDDVADGAD 276
                                       67777888999999999999999999999999999999.....66666666643.56899999************** PP

                        MscS_porin 103 qlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaage.alsqaqrtalqa 156
                                       +++++ +e++++++++ ++++  +   +ei ++ ++ +a++e a s a  t   a
  gi|336254891|ref|YP_004597998.1| 277 EIDDLTAEQSDSMSEIASEISGLSATVEEIASNAEEVSATSEqAESVASDTTETA 331
                                       ********************************88777666664444444443333 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                        MscS_porin  30 dkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssq.........lqel 97 
                                       +++++  +k+e  q+a d+ ++ +++l++  ++  ++  +  ++i +++ l +L+  ++++ +            e+
  gi|336254891|ref|YP_004597998.1| 329 ETAEEAIDKMEGVQEAADEVTEDVENLREGVQRI-DEIVDVINDIADQTNLLALNASIEAATAGeagdgfavvANEV 404
                                       5666666666666777777777777777777777.666666677777777777777666666532222222224466 PP

                        MscS_porin  98 qeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaalea 163
                                       ++   + ++++++++   +r+q+   e    l++ +++++++    e ++++  ++ ++e+a  ea
  gi|336254891|ref|YP_004597998.1| 405 KSLAEESQDEATNIERMVDRIQADTEETVDSLETANAEIDDG---VELVEETVDNLGRIEEAVAEA 467
                                       666777789999999999999999999999999999988766...346666666666666666665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.2
                        MscS_porin  41 elqkaiddaPkelrelqqelealqkkkeeaskeilaklsl.eeLeqrllqtssqlqelqeqlaqlnsqlvelqtrpe 116
                                       e q+  ++  + ++ +q+++e+  ++ e+a++ei++   l ee    l   +++++e+++ + +  +    +  + e
  gi|336254891|ref|YP_004597998.1| 410 ESQDEATNIERMVDRIQADTEETVDSLETANAEIDDGVELvEETVDNLGRIEEAVAEASTGIREVATATDDQAASTE 486
                                       44455555555555555555555555555555555555543445555555555555555555555555555555555 PP

                        MscS_porin 117 raqqqltearqrlqeirnrLn 137
                                       ++ +   +a++r qei ++ +
  gi|336254891|ref|YP_004597998.1| 487 EVASMTDSAMERSQEIADEVE 507
                                       555555555555555554442 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   9.5    0.0011      0.52     503     585 ..     221     303 ..     189     323 .. 0.79
   2 ?    0.2  16.3      0.32   1.5e+02     372     581 ..     316     527 ..     298     535 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                              HOOK 503 lanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevqeelqkkkeqleelepklssnkqkieelee 579
                                       + + ++ e e+++ee + + ++q+   ed +  ++ +e+ le++ e+ ++++     +++l++++s +++ i++   
  gi|336254891|ref|YP_004597998.1| 221 AYEAQLAEYEQRLEEYEAEIEAQDRTREDLADARRSMENTLEEVAEATDDVADGADEIDDLTAEQSDSMSEIASEIS 297
                                       45678999999******************************************************999987776555 PP

                              HOOK 580 aLkkkd 585
                                        L++  
  gi|336254891|ref|YP_004597998.1| 298 GLSATV 303
                                       555555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.32
                              HOOK 372 klseeskkadklefelkkleeklealqkekerllaerdaLketneELkcaqlqqkelsqadalaskssssgenlaae 448
                                         ++ ++ a  +   + +  +k+e +q + + ++++ ++L+e ++ +    + +      + +a++++  + n++ e
  gi|336254891|ref|YP_004597998.1| 316 TSEQAESVASDTTETAEEAIDKMEGVQEAADEVTEDVENLREGVQRIDE--IVDVI----NDIADQTNLLALNASIE 386
                                       3333223233333334445568888888899999999999988876654..22222....22233333233344444 PP

                              HOOK 449 .llpaevreklirLqhENKmLklkqegseeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqe 524
                                         ++ e  + +  + +E K L ++ + + ++    + +   d ++++++Let n    + ++ +e+ v++l +  ++
  gi|336254891|ref|YP_004597998.1| 387 aATAGEAGDGFAVVANEVKSLAEESQDEATNIERMVDRIQADTEETVDSLETANAEIDDGVELVEETVDNLGRIEEA 463
                                       1556789999***********877777766666666777789999********************999999876665 PP

                              HOOK 525 qgskaed....ssllkkkleehleklkevqeelqkkkeqleelepklssnk...qkieeleeaL 581
                                           +      ++++  +  +  e  +  ++ +++ +e+ +e+e  + +++     +ee+++ L
  gi|336254891|ref|YP_004597998.1| 464 VAEASTGirevATATDDQAASTEEVASMTDSAMERSQEIADEVETIVATTAdasDLVEEIDAEL 527
                                       5444444222123333333333333333455666667777776665544431124455555555 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 ?    3.7   0.7      0.18        85       4      40 ..     228     264 ..     218     280 .. 0.76
   2 ?    5.3   0.4     0.056        27      15      39 ..     288     312 ..     275     319 .. 0.61
   3 ?    6.1   0.9      0.03        14      15      40 ..     337     362 ..     327     377 .. 0.77
   4 ?   10.4   1.5    0.0014      0.66       5      48 ..     418     465 ..     414     469 .. 0.82
   5 ?    0.7   0.6       1.5   6.9e+02      18      35 ..     494     511 ..     478     532 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.18
                         FlaC_arch   4 elEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       e E++l++ + e+e   ++ e+l +    ++ + +++
  gi|336254891|ref|YP_004597998.1| 228 EYEQRLEEYEAEIEAQDRTREDLADARRSMENTLEEV 264
                                       6677788888888877777777777777777776665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.056
                         FlaC_arch  15 eletvkkeneelsksveelkenVkd 39 
                                       +++ + +e++ ls +vee+  n ++
  gi|336254891|ref|YP_004597998.1| 288 SMSEIASEISGLSATVEEIASNAEE 312
                                       5555666666666666666555443 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.03
                         FlaC_arch  15 eletvkkeneelsksveelkenVkdl 40 
                                       ++e v++  +e+ ++ve+l e V+++
  gi|336254891|ref|YP_004597998.1| 337 KMEGVQEAADEVTEDVENLREGVQRI 362
                                       68999999999999999999999664 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0014
                         FlaC_arch   5 lEnklsklst....eletvkkeneelsksveelkenVkdllsLYEvVs 48 
                                       +E  +++++     +++++++ n e+ + ve ++e+V +l  + E V+
  gi|336254891|ref|YP_004597998.1| 418 IERMVDRIQAdteeTVDSLETANAEIDDGVELVEETVDNLGRIEEAVA 465
                                       666677666666669**********************99977777776 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 1.5
                         FlaC_arch  18 tvkkeneelsksveelke 35 
                                       ++ +  +e+ ++ve++  
  gi|336254891|ref|YP_004597998.1| 494 SAMERSQEIADEVETIVA 511
                                       555555666666666543 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 ?    8.7  10.4    0.0022         1      58     190 ..     214     349 ..     202     355 .. 0.77
   2 ?    1.4   5.4      0.36   1.7e+02      29     168 ..     297     439 ..     294     459 .. 0.74
   3 ?    2.3   2.2      0.19        90      30     136 ..     403     506 ..     399     519 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0022
                               GAS  58 rlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiq 134
                                         +  + + e++++e +++l++ye + ++ +++++ l ++ + ++++ +e     + ++   +e+d+l++++ +++ 
  gi|336254891|ref|YP_004597998.1| 214 AQEARIDAYEAQLAEYEQRLEEYEAEIEAQDRTREDLADARRSMENTLEEVAEATDDVADGADEIDDLTAEQSDSMS 290
                                       5566788999******************************************************************* PP

                               GAS 135 evqqktglknllLek...klkalqeelEkkeaqleevlaaanldpaalsavsekleevl 190
                                       e+  +++  +  +e      ++++++ E++e   +++ ++a+   ++++ v+e  +ev 
  gi|336254891|ref|YP_004597998.1| 291 EIASEISGLSATVEEiasNAEEVSATSEQAESVASDTTETAEEAIDKMEGVQEAADEVT 349
                                       *9988776666666411144455555566665555555555555556666666666554 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.36
                               GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlk 105
                                         l   +ee+  ++e+ +   +++++  ++ +e+ ++a  ++e  ++++ +  +d + l++  +r+ e  + ++d+ 
  gi|336254891|ref|YP_004597998.1| 297 SGLSATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKMEGVQEAADEVTEDVENLREGVQRIDEIVDVINDIA 373
                                       55677788888888888888888888888889999999999999999999999999999999999999999999988 PP

                               GAS 106 wehevleqrfekvekerdelykkfeaa...iqevqqktglknllLekklkalqeelEkkeaqleev 168
                                        + + l    +   +   e  + f  +   ++ + ++++ +++ +e++++++q++ E+    le++
  gi|336254891|ref|YP_004597998.1| 374 DQTNLLALNASIEAATAGEAGDGFAVVaneVKSLAEESQDEATNIERMVDRIQADTEETVDSLETA 439
                                       888888777766666777777777666222444557788888888888888888888777766654 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.19
                               GAS  30 slKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                       + K+  ee + +++  e+ ++ i+++ ++ ++ L++a++e++     ++  e+    l ++++ + e+   ++++  
  gi|336254891|ref|YP_004597998.1| 403 EVKSLAEESQDEATNIERMVDRIQADTEETVDSLETANAEID---DGVELVEETVDNLGRIEEAVAEASTGIREVAT 476
                                       566677788888888888888888888888888887776654...45556666666666666666666666666666 PP

                               GAS 107 ehevleqrfekvekerdelykkfeaaiqev 136
                                         +      e+v +  d   ++ ++  +ev
  gi|336254891|ref|YP_004597998.1| 477 ATDDQAASTEEVASMTDSAMERSQEIADEV 506
                                       666666666666666666666666665555 PP

>> Dynactin_p22  Dynactin subunit p22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   7.7    0.0062       2.9       2     146 ..     219     361 ..     218     378 .. 0.83
   2 ?    2.3   0.2      0.28   1.3e+02      28      81 ..     451     508 ..     417     531 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0062
                      Dynactin_p22   2 ldaLEeriaeLEkrvlGeekekekedesiidsLakvqkklssavskr.ekikellkkleelekyLdpeyedsee.lp 76 
                                       +da E+++ae E+r+   e+e e++d    + La++++++++++++  e   ++ +  +e++++      +s++  +
  gi|336254891|ref|YP_004597998.1| 219 IDAYEAQLAEYEQRLEEYEAEIEAQD-RTREDLADARRSMENTLEEVaEATDDVADGADEIDDLTAE---QSDSmSE 291
                                       67889999999999988888888888.8899999999999999776414455666667777666544...3333267 PP

                      Dynactin_p22  77 devKleliLaeedeLkktaalleqlqeLkpvldseeikdvpelkekLekLsqihlkqqeeveelseevkk 146
                                        + ++  + a  +e+ ++a++++  +e  + + s+  + ++e  +k+e +++   + +e+ve+l e v++
  gi|336254891|ref|YP_004597998.1| 292 IASEISGLSATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKMEGVQEAADEVTEDVENLREGVQR 361
                                       78999***********************************************************999986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.28
                      Dynactin_p22  28 esiidsLakvqkklssavskrekikellkkl....eelekyLdpeyedseelpdevKl 81 
                                       e+ +d+L ++++++ +a+++  ++ ++ +      ee+ ++ d+++e+s+e++dev++
  gi|336254891|ref|YP_004597998.1| 451 EETVDNLGRIEEAVAEASTGIREVATATDDQaastEEVASMTDSAMERSQEIADEVET 508
                                       5677888888888888888887777776543344488888888888888877777654 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   9.0    0.0017      0.79     206     406 ..     241     438 ..     230     454 .. 0.77
   2 ?    1.6   2.1      0.11        53     307     408 ..     415     520 ..     403     529 .. 0.42

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0017
                          Prominin 206 elekhvsddLddagkhlgldladtlesnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrd 282
                                       e++++  +dL da +++ ++l++  e++   + +  +++ + + e +++++++ +  + L  + +++ ++ ++v   
  gi|336254891|ref|YP_004597998.1| 241 EAQDRTREDLADARRSMENTLEEVAEAT-DDVADGADEIDDLTAEQSDSMSEIASEISGLSATVEEIASNAEEVSAT 316
                                       67899999******************99.99999999*********************************9999999 PP

                          Prominin 283 lnqalsnlCq.seeCskilssleiekldtskcl.dqlpnvdevlealeevletnlssivkeglarlneipekvknqt 357
                                        +qa s     +e+ +++ +++e    +   ++ + ++n+ e +++++e+++  ++ i+  + ++l +++  ++  t
  gi|336254891|ref|YP_004597998.1| 317 SEQAESVASDtTETAEEAIDKMEG-VQEAADEVtEDVENLREGVQRIDEIVD-VINDIA--DQTNLLALNASIEAAT 389
                                       888888844414777777777776.334444446999999999999999954.344444..4566778888888888 PP

                          Prominin 358 aevvpdlkkalakgreqikklakkiprealdavisdle.nterssktfdd 406
                                       a+   d +  +a++ + + +++++   + ++++++ ++ +te+++++ + 
  gi|336254891|ref|YP_004597998.1| 390 AGEAGDGFAVVANEVKSLAEESQDE-ATNIERMVDRIQaDTEETVDSLET 438
                                       8888888888777777777776666.666666666666666655554443 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.11
                          Prominin 307 kldtskcldql.pnvdevlealeevle..tnlssivkeglarlneipekvknqtaevvp..dlkkalakgreqikkl 378
                                         + ++ +d +  +++e +++le++ +  ++  ++v+e +++l  i+e v++  +++ +    + + a  +e++ ++
  gi|336254891|ref|YP_004597998.1| 415 ATNIERMVDRIqADTEETVDSLETANAeiDDGVELVEETVDNLGRIEEAVAEASTGIREvaTATDDQAASTEEVASM 491
                                       33333344444334444444444443211234445555555555555555555444432112222233333333333 PP

                          Prominin 379 akkiprealdavisdlenterssktfddvv 408
                                       + +   e+ +++++++e++  ++  ++d v
  gi|336254891|ref|YP_004597998.1| 492 TDSA-MERSQEIADEVETIVATTADASDLV 520
                                       3333.4444455555555555555555555 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   9.6      0.62   2.9e+02      62     136 ..     217     291 ..     183     294 .. 0.72
   2 ?   10.7   3.8   0.00066      0.31      99     169 ..     289     359 ..     285     363 .. 0.89
   3 ?    5.3   9.4     0.031        14      65     154 ..     409     505 ..     375     512 .. 0.56
   4 ?    3.9   1.8      0.08        38      68     129 ..     461     522 ..     456     529 .. 0.49

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.62
                            DUF745  62 qlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelae 136
                                       + ++ +e++l+e e+ ++e ++++++  ++ +  a+a++++++ le + ++ + + + +++++++ a+ + +++e
  gi|336254891|ref|YP_004597998.1| 217 ARIDAYEAQLAEYEQRLEEYEAEIEAQDRTREDLADARRSMENTLEEVAEATDDVADGADEIDDLTAEQSDSMSE 291
                                       346778888888888888888888888888888888888888888888888888888888888777777666655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00066
                            DUF745  99 akqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektkkaA 169
                                       ++++ ++++ l+a+++++ +n+e++ +++++a++ +++ t+  e+A  ++e +++  +e+ +d e+ ++  
  gi|336254891|ref|YP_004597998.1| 289 MSEIASEISGLSATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKMEGVQEAADEVTEDVENLREGV 359
                                       5677888999999**************************************************99999865 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.031
                            DUF745  65 eqleqelreaeavvqeekkslqsseanakaaa.......kaakqaqqqlealkallkaakenlenaeqvaagaqqel 134
                                       e+ ++e ++ e++v+++++ ++++  ++++a+       + +++   +l ++++++++a++ ++++ ++ +  +++ 
  gi|336254891|ref|YP_004597998.1| 409 EESQDEATNIERMVDRIQADTEETVDSLETANaeiddgvELVEETVDNLGRIEEAVAEASTGIREVATATDDQAAST 485
                                       44444444444444444433333333333333000000044555555566666666666666666666666666666 PP

                            DUF745 135 aektqlleaAkkRveeLkkq 154
                                       +e +++ ++A +R +e+  +
  gi|336254891|ref|YP_004597998.1| 486 EEVASMTDSAMERSQEIADE 505
                                       66666777777666666655 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.08
                            DUF745  68 eqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaag 129
                                       e+ ++ea++ ++e+ +++    a+ + +a++ ++a +  + + + ++++ ++ ++a ++ ++
  gi|336254891|ref|YP_004597998.1| 461 EEAVAEASTGIREVATATDDQAASTEEVASMTDSAMERSQEIADEVETIVATTADASDLVEE 522
                                       45555555555555555555555555555555555555555555555555555554444444 PP

>> DUF3037  Protein of unknown function (DUF3037)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.2      0.11        52      40      88 ..     209     256 ..     191     285 .. 0.56
   2 ?    0.1   0.3       2.2     1e+03      59     112 ..     277     333 ..     252     338 .. 0.59
   3 ?    0.6   0.5       1.5   7.2e+02      85      85 ..     338     338 ..     281     436 .. 0.65
   4 ?    9.8   0.7    0.0021      0.99      48     113 ..     467     530 ..     437     533 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.11
                           DUF3037  40 Rlralfpeldlealeeelkaleeicegekaagpiakldlaerfrwltap 88 
                                       R r+ ++e+ ++a+e++l++ e+++e+ +a + +a+++++e +    ++
  gi|336254891|ref|YP_004597998.1| 209 RARSSAQEARIDAYEAQLAEYEQRLEEYEA-EIEAQDRTREDLADARRS 256
                                       555666666777777777777777644332.323333333322222222 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.2
                           DUF3037  59 aleeicegeka.agpiak..ldlaerfrwltaprstviqtsevhtgltedpeaeler 112
                                       +++  ++++++  ++ia+    l+  +++++++ + v  tse   ++++d  ++ e+
  gi|336254891|ref|YP_004597998.1| 277 EIDDLTAEQSDsMSEIASeiSGLSATVEEIASNAEEVSATSEQAESVASDTTETAEE 333
                                       444444444444555555556666677777777777777777777777776666665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.5
                           DUF3037  85 l 85 
                                       +
  gi|336254891|ref|YP_004597998.1| 338 M 338
                                       1 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0021
                           DUF3037  48 ldlealeeelkaleeicegekaagpiakldlaerfrwltaprstviqtsevhtgltedpeaelerL 113
                                       +  + ++e  +a++ ++++ ++  +  ++++ er ++++++ +t++ t+     l e+++ael+rL
  gi|336254891|ref|YP_004597998.1| 467 A-STGIREVATATDDQAASTEE-VASMTDSAMERSQEIADEVETIVATTADASDLVEEIDAELDRL 530
                                       2.33444444444444433333.344459999********************************99 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.4      0.12        58      18      71 ..     219     271 ..     200     292 .. 0.49
   2 ?    9.7   1.2   0.00098      0.46       3      88 ..     288     372 ..     286     385 .. 0.86
   3 ?    4.4   1.6     0.039        18       3      86 ..     421     507 ..     401     529 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                             TMPIT  18 akeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveel 71 
                                        + y+++l+e+++  ++   ei+ q +  ++l ++ ++++++++ e +e+++++
  gi|336254891|ref|YP_004597998.1| 219 IDAYEAQLAEYEQRLEEYEAEIEAQDRTREDLADARRSMENTLE-EVAEATDDV 271
                                       34455555555555555555555555555555555555544432.233333333 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00098
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79 
                                       +++e+++e+  l++t +e+ ++ ee+s+  ++  + ++  ++ ++e  ++++ +++++ +e  e ve+l+e +++++
  gi|336254891|ref|YP_004597998.1| 288 SMSEIASEISGLSATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKMEGVQEAA-DEVTEDVENLREGVQRID 363
                                       6789999999********************************************9986.688899999999999998 PP

                             TMPIT  80 kvlkevesl 88 
                                       ++++ ++++
  gi|336254891|ref|YP_004597998.1| 364 EIVDVINDI 372
                                       887765554 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.039
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelke 77 
                                        +++++ +++e  ++ ++ ++++++  +l ++++ ++ + ++ + e ++ ++++ ++++  + + eev++++++ +e
  gi|336254891|ref|YP_004597998.1| 421 MVDRIQADTEETVDSLETANAEIDDGVELVEETVDNLGRIEEAVAEASTGIREVATATDdqAASTEEVASMTDSAME 497
                                       45666777777777777777777777777777777777777777777777777777654444445556666665555 PP

                             TMPIT  78 rkkvlk.eve 86 
                                       r++ ++ eve
  gi|336254891|ref|YP_004597998.1| 498 RSQEIAdEVE 507
                                       5555542454 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.57   2.7e+02       2      42 ..     257     297 ..     256     309 .. 0.84
   2 ?    4.5   0.1      0.12        56       8      64 ..     319     374 ..     316     377 .. 0.87
   3 ?   -0.7   0.1         5   2.4e+03       8      41 ..     403     436 ..     401     448 .. 0.63
   4 ?    0.1   0.0         3   1.4e+03       1      54 [.     449     501 ..     449     510 .. 0.68
   5 ?   -0.1   0.0       3.3   1.5e+03      13      38 ..     506     531 ..     497     534 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHHHTS---TTT........HHHHHHH---GGG CS
                            RecG_N   2 iEeFLeelekllkkvlsgkleteelieeikkkleliddpll 42 
                                       +E+ Lee+ +  ++v +g  e+++l  e  + +++i+ ++ 
  gi|336254891|ref|YP_004597998.1| 257 MENTLEEVAEATDDVADGADEIDDLTAEQSDSMSEIASEIS 297
                                       58889999999999999999999999999999999988765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.12
                                       HHHHHHTS---TTT........HHHHHHH---GGGG-HHHH.HHHHHHHHHHTTSSS CS
                            RecG_N   8 elekllkkvlsgkleteelieeikkkleliddplleneevlkeklskfldYikpias 64 
                                       + e ++ +  ++  e  + +e +++ ++++ +++ +  e+  +++++++d i+ ia+
  gi|336254891|ref|YP_004597998.1| 319 QAESVASDTTETAEEAIDKMEGVQEAADEVTEDVENLREGV-QRIDEIVDVINDIAD 374
                                       67888888889999999999999999999999999999999.99*999999999886 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 5
                                       HHHHHHTS---TTT........HHHHHHH---GG CS
                            RecG_N   8 elekllkkvlsgkleteelieeikkkleliddpl 41 
                                       e+  l+++ +++  ++e +++ i+   e+  d+l
  gi|336254891|ref|YP_004597998.1| 403 EVKSLAEESQDEATNIERMVDRIQADTEETVDSL 436
                                       5666666666666667777777766666655554 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 3
                                       SHHHHHHHHHHHHTS---TTT........HHHHHHH---GGGG-HHHH.HHHHH CS
                            RecG_N   1 liEeFLeelekllkkvlsgkleteelieeikkkleliddplleneevlkeklsk 54 
                                       l+Ee  ++l ++ ++v + +  + e+     +++    +++ +  +++ e+ ++
  gi|336254891|ref|YP_004597998.1| 449 LVEETVDNLGRIEEAVAEASTGIREVATATDDQAAS-TEEVASMTDSAMERSQE 501
                                       789999999999999999999888888777765443.33444444444455555 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 3.3
                                       HTS---TTT........HHHHHHH-- CS
                            RecG_N  13 lkkvlsgkleteelieeikkklelid 38 
                                       ++ ++ +  + ++l+eei  +l+ ++
  gi|336254891|ref|YP_004597998.1| 506 VETIVATTADASDLVEEIDAELDRLE 531
                                       45556667888999***999988775 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.089        42      24      73 ..     230     275 ..     213     278 .. 0.66
   2 ?    5.9   0.5     0.037        17       9      76 ..     243     310 ..     229     317 .. 0.81
   3 ?    5.4   0.5     0.051        24      12      72 ..     316     376 ..     313     385 .. 0.87
   4 ?    3.4   0.3      0.21     1e+02      14      74 ..     405     466 ..     399     470 .. 0.76
   5 ?   -1.1   0.0       5.2   2.5e+03      32      65 ..     476     509 ..     464     525 .. 0.44

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.089
                           Goodbye  24 lssvedllkqieaekdkfeefrekkeklkealkkilspiqllggiaaqga 73 
                                        +++e+ +++iea++      re+   ++++++++l+ +   ++ +a+ga
  gi|336254891|ref|YP_004597998.1| 230 EQRLEEYEAEIEAQDR----TREDLADARRSMENTLEEVAEATDDVADGA 275
                                       3456666666666666....677777788888888887777777666666 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.037
                           Goodbye   9 ekeTgkdlkdealkelssvedllkqieaekdkfeefrekkeklkealkkilspiqllggiaaqgasma 76 
                                       + +T +dl+d++ +  +++e++ +  ++ +d  +e +    +  +++++i s i+ l+  + ++as+a
  gi|336254891|ref|YP_004597998.1| 243 QDRTREDLADARRSMENTLEEVAEATDDVADGADEIDDLTAEQSDSMSEIASEISGLSATVEEIASNA 310
                                       45788888888888888888888888888888888888888888899999999999999888888876 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.051
                           Goodbye  12 Tgkdlkdealkelssvedllkqieaekdkfeefrekkeklkealkkilspiqllggiaaqg 72 
                                       T ++ +  a ++ ++ e+ ++++e  +++ +e +e+ e+l+e +++i + +  + +ia q 
  gi|336254891|ref|YP_004597998.1| 316 TSEQAESVASDTTETAEEAIDKMEGVQEAADEVTEDVENLREGVQRIDEIVDVINDIADQT 376
                                       6777777888999999************99*****************99999999999885 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.21
                           Goodbye  14 kdlkdealkelssvedllkqieaekdkfeefr.ekkeklkealkkilspiqllggiaaqgas 74 
                                       k+l++e+++e++++e+++++i+a+++++ ++  +   ++ + ++ + + + +lg+i   +a+
  gi|336254891|ref|YP_004597998.1| 405 KSLAEESQDEATNIERMVDRIQADTEETVDSLeTANAEIDDGVELVEETVDNLGRIEEAVAE 466
                                       567899999**************999776665355666666677777788888887666665 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 5.2
                           Goodbye  32 kqieaekdkfeefrekkeklkealkkilspiqll 65 
                                          +++++++ee  +  +++ e  ++i   ++++
  gi|336254891|ref|YP_004597998.1| 476 TATDDQAASTEEVASMTDSAMERSQEIADEVETI 509
                                       3333333333333333333333333333333332 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  11.0   0.00075      0.35      36     187 ..     207     360 ..     192     364 .. 0.85
   2 ?    1.3   2.7      0.49   2.3e+02      81     183 ..     431     531 ..     400     533 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00075
                        Lebercilin  36 lLkrlqkrqekaLskyedteaeLpqllarhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkkLse 112
                                       +L++    qe++++ ye + ae  q l++ ++E+++      ++ ++ r++e+ l e  ++   + d  ++ ++L  
  gi|336254891|ref|YP_004597998.1| 207 ALRARSSAQEARIDAYEAQLAEYEQRLEEYEAEIEAQDRTREDLADARRSMENTLEEVAEATDDVADGADEIDDLTA 283
                                       68888899***************************9999999999*****************************987 PP

                        Lebercilin 113 dkn..LaereeLqkkLeeleakleekeekikeLerkleleeksfrrqlaaekkktkeaqeevkalqeeierlkqklk 187
                                       +++  + e +   + L+++ +++ ++ e+++  + ++e   +  +   +    k   +qe  ++++e +e+l++ ++
  gi|336254891|ref|YP_004597998.1| 284 EQSdsMSEIASEISGLSATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKMEGVQEAADEVTEDVENLREGVQ 360
                                       76422666666666677777777788888888888888888888888888889999999999999999999987665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.49
                        Lebercilin  81 ekerelekklkekeaellrlkdklkklkkLsedknLaereeLqkkLeeleakleekeekikeLerkleleeksfrrq 157
                                       e++++le    e ++ ++ +++++++l ++      ae ++  ++++++++   +++e++ ++  ++   +++ + +
  gi|336254891|ref|YP_004597998.1| 431 ETVDSLETANAEIDDGVELVEETVDNLGRIE--EAVAEASTGIREVATATDDQAASTEEVASMTDSAMERSQEIADE 505
                                       3333333333333333444555555555554..45667777777788888888888888888888887777777777 PP

                        Lebercilin 158 laaekkktkeaqeevkalqeeierlk 183
                                       +++    t +a + v++  +e++rl+
  gi|336254891|ref|YP_004597998.1| 506 VETIVATTADASDLVEEIDAELDRLE 531
                                       77777777777777777777777775 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.3    0.0022         1     272     339 ..     213     280 ..     205     287 .. 0.90
   2 ?    9.8   3.5   0.00081      0.38     251     344 ..     262     355 ..     261     359 .. 0.95
   3 ?    1.0   0.2       0.4   1.9e+02     265     311 ..     402     448 ..     359     481 .. 0.52
   4 ?    0.9   0.2      0.41   1.9e+02     282     341 ..     454     513 ..     449     526 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                                       HCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FH2 272 kaakvnleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeake 339
                                       +a++  +++ e+++ ++e++l++ e e+e++++ +e+    + +++  l+e +e  +++ +  +e+ +
  gi|336254891|ref|YP_004597998.1| 213 SAQEARIDAYEAQLAEYEQRLEEYEAEIEAQDRTREDLADARRSMENTLEEVAEATDDVADGADEIDD 280
                                       67888999************************************************999998888766 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00081
                                       HHHHTTSGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHH CS
                               FH2 251 kiireklpevldfsseLknvkkaakvnleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeekl 327
                                       ++++e++++v+d  +e+ +++  ++ ++ ++++e++ l+  ++++  ++e+ +  +e+ + + + ++e  +ea +k+
  gi|336254891|ref|YP_004597998.1| 262 EEVAEATDDVADGADEIDDLTAEQSDSMSEIASEISGLSATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKM 338
                                       57899999**********************************************99********************* PP

                                       HHHHHHHHHHHHHHHHH CS
                               FH2 328 kkleeelkeakelvkel 344
                                       + ++e  +e++e v++l
  gi|336254891|ref|YP_004597998.1| 339 EGVQEAADEVTEDVENL 355
                                       ************99987 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.4
                                       HHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-T CS
                               FH2 265 seLknvkkaakvnleslekevkklekglkklekelessekkeepsdk 311
                                       +e k++ + ++ + +++e  v+ ++ + +++ ++le+ + + ++  +
  gi|336254891|ref|YP_004597998.1| 402 NEVKSLAEESQDEATNIERMVDRIQADTEETVDSLETANAEIDDGVE 448
                                       33333333333333333333333333333333333333333333333 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FH2 282 ekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeakelv 341
                                       ++++  +e+ ++++++ +++ +++ +++ + +e + +++++a e+ +++ +e +++ ++ 
  gi|336254891|ref|YP_004597998.1| 454 VDNLGRIEEAVAEASTGIREVATATDDQAASTEEVASMTDSAMERSQEIADEVETIVATT 513
                                       556666666666666667777776666666777777777777777777777766665544 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.7     0.019         9       7      98 ..     223     284 ..     208     299 .. 0.48
   2 ?   10.0   2.7     0.002      0.96      28      98 ..     284     354 ..     276     361 .. 0.88
   3 ?    1.9   0.5      0.65   3.1e+02      47      92 ..     412     457 ..     398     466 .. 0.59
   4 ?   -0.0   0.2       2.6   1.2e+03      34      61 ..     497     524 ..     463     536 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHH CS
                          Spectrin   7 aqdadeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerle 83 
                                       + +++e e+                          +++++eae++aq++  ++l +  +++++      ee+ e ++
  gi|336254891|ref|YP_004597998.1| 223 EAQLAEYEQ--------------------------RLEEYEAEIEAQDRTREDLADARRSMENT----LEEVAEATD 269
                                       333333333..........................44444444444444444444444444222....233333333 PP

                                       HHHHHHHHHHHHHHH CS
                          Spectrin  84 elnerWeeLkelaae 98 
                                       ++ +  +e+ +l+ae
  gi|336254891|ref|YP_004597998.1| 270 DVADGADEIDDLTAE 284
                                       333333333333333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.002
                                       SCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  28 dlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaae 98 
                                       + + +++e+ + +  + a  +e+a++ e+v a  e+ae++++   +++ee  +++e+++e+ +e+ e ++ 
  gi|336254891|ref|YP_004597998.1| 284 EQSDSMSEIASEISGLSATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKMEGVQEAADEVTEDVEN 354
                                       4457888999999999999*********************9999*****************9999998875 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHH CS
                          Spectrin  47 eaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeL 92 
                                       ++e ++ ++ v+++++  e+ +d+ + a++ei + +e ++e  ++L
  gi|336254891|ref|YP_004597998.1| 412 QDEATNIERMVDRIQADTEETVDSLETANAEIDDGVELVEETVDNL 457
                                       3444455555556666666666666666666666666666666655 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  34 eevqallkkhkaleaelaaqqervkaln 61 
                                       e  q+  ++ +++ a+ a++ + v++++
  gi|336254891|ref|YP_004597998.1| 497 ERSQEIADEVETIVATTADASDLVEEID 524
                                       2222222233333333333333333333 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6  13.8       0.4   1.9e+02      64     182 ..     220     338 ..     212     373 .. 0.47
   2 ?    6.9   5.1    0.0096       4.5      97     179 ..     412     492 ..     399     505 .. 0.78
   3 ?    1.0   1.0      0.62   2.9e+02     101     136 ..     485     520 ..     459     531 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.4
                               LXG  64 tslqdlieqyeefLkkikealesvepssngfidedfLeqelenglkkakevteelkdeinkilasvsdivslpeldd 140
                                       ++++  +++ye++L+++ +++e+ +   ++  d    +++   ++ +a  ++++ +dei++ +a+ sd +s    ++
  gi|336254891|ref|YP_004597998.1| 220 DAYEAQLAEYEQRLEEYEAEIEAQDRTREDLADARRSMENTLEEVAEATDDVADGADEIDDLTAEQSDSMSEIASEI 296
                                       44555556666666666666666554444444444433333344444444444444555554444444333333333 PP

                               LXG 141 sevkdslqkakkkvqetiekledfdqeqksalanlesdlkal 182
                                       s + + +++  ++++e+    e+++  ++  ++++e+ ++++
  gi|336254891|ref|YP_004597998.1| 297 SGLSATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKM 338
                                       333333333333333333333333333333333333333332 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0096
                               LXG  97 edfLeqelenglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksala 173
                                       +d    ++e+++++ +++tee  d+++++ a+++d v+l+e + ++    +++a  ++++ i+ + ++  +q ++++
  gi|336254891|ref|YP_004597998.1| 412 QDEAT-NIERMVDRIQADTEETVDSLETANAEIDDGVELVEETVDN-LGRIEEAVAEASTGIREVATATDDQAASTE 486
                                       55555.89*********************************99998.556777777777777777777666666666 PP

                               LXG 174 nlesdl 179
                                       ++ s  
  gi|336254891|ref|YP_004597998.1| 487 EVASMT 492
                                       666555 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.62
                               LXG 101 eqelenglkkakevteelkdeinkilasvsdivslp 136
                                        +e++ + + a e  +e +de+++i+a++ d  +l+
  gi|336254891|ref|YP_004597998.1| 485 TEEVASMTDSAMERSQEIADEVETIVATTADASDLV 520
                                       445555555555555555555555555555554444 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  16.6    0.0029       1.4     313     465 ..     209     371 ..     179     384 .. 0.47
   2 ?   -1.7  20.0       1.7   8.1e+02     295     468 ..     292     528 ..     286     534 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0029
                            AAA_13 313 asensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanle 389
                                         + sa e  ++ ++a++ + e++L++ + ++ea      ++ +l ++   +e+  ++vae+ + +a+    +++l+
  gi|336254891|ref|YP_004597998.1| 209 RARSSAQEARIDAYEAQLAEYEQRLEEYEAEIEAQD---RTREDLADARRSMENTLEEVAEATDDVADGADEIDDLT 282
                                       222333333344444444444444444444444432...11122333333344444555555555555555555555 PP

                            AAA_13 390 eekeeakkklelhlv.........eeleseldeyk....kkykklekaieklekelkeeeaelkkleeeikeLekql 453
                                       +e+++  +++   +          ++  +e+++      +  +++++++e++ ++++  ++++ ++ e++++L++ +
  gi|336254891|ref|YP_004597998.1| 283 AEQSDSMSEIASEISglsatveeiASNAEEVSATSeqaeSVASDTTETAEEAIDKMEGVQEAADEVTEDVENLREGV 359
                                       55555555555543334444422233334444333111033333344444444444555566666666678888888 PP

                            AAA_13 454 rdekpaaeeink 465
                                       + + +++++in+
  gi|336254891|ref|YP_004597998.1| 360 QRIDEIVDVIND 371
                                       888888888876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                            AAA_13 295 veskkselleklkavsdeasensafeedkeelkaea.ealeeqLkg..........lqraleaKrkepfksvelesv 360
                                       ++s++s l++ +++++  a+e sa+ e+ e + + + e+ ee++++          + + +e+ r+ + +  e+ +v
  gi|336254891|ref|YP_004597998.1| 292 IASEISGLSATVEEIASNAEEVSATSEQAESVASDTtETAEEAIDKmegvqeaadeVTEDVENLREGVQRIDEIVDV 368
                                       44444444444444444444444433332222222213333333330000000000222222222222222222222 PP

                            AAA_13 361 kakie..................................................sikklvaeineliakhNekvan 387
                                        ++i                                                   +i+ + +e  ++ +  N+ +++
  gi|336254891|ref|YP_004597998.1| 369 INDIAdqtnllalnasieaatageagdgfavvanevkslaeesqdeatniermvdRIQADTEETVDSLETANAEIDD 445
                                       22222344455566666677777777777777777777777777766666666666666666666666666666666 PP

                            AAA_13 388 leeekeeakkklelhl..veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaee 462
                                         e +ee  ++l + +  v+e+   + e  ++ ++ +++ e++    + + ++ +++++e++ + +++ d    +ee
  gi|336254891|ref|YP_004597998.1| 446 GVELVEETVDNLGRIEeaVAEASTGIREVATATDDQAASTEEVASMTDSAMERSQEIADEVETIVATTADASDLVEE 522
                                       66666666666665443345666666666666666666666666666777777777777777777777777777777 PP

                            AAA_13 463 inkeLk 468
                                       i  eL 
  gi|336254891|ref|YP_004597998.1| 523 IDAELD 528
                                       777776 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3  13.6     0.068        32     181     323 ..     208     354 ..     144     387 .. 0.80
   2 ?    7.3   4.8    0.0043         2     227     332 ..     402     506 ..     384     533 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.068
                             IFT57 181 e..kekekeeeiieskvdaaeWklEleRvlpqLkv..tikadakdWrahleqmkkhkksieeslpetksqlkklhed 253
                                           ++ +e++i + +   ae+++ le  + ++++  ++++d  d r+++e++ +   + ++++ +   ++++l  +
  gi|336254891|ref|YP_004597998.1| 208 LraRSSAQEARIDAYEAQLAEYEQRLEEYEAEIEAqdRTREDLADARRSMENTLEEVAEATDDVADGADEIDDLTAE 284
                                       14444555555555566666666666666666555447889999*******9999999999999999********** PP

                             IFT57 254 isktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemee 323
                                        s ++++i s  + l   +ee  ++ +e++++ ++++   ++ +e+ +e  ++++ ++e  ++v +++e+
  gi|336254891|ref|YP_004597998.1| 285 QSDSMSEIASEISGLSATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKMEGVQEAADEVTEDVEN 354
                                       ***************************************************************9999986 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0043
                             IFT57 227 eqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsql...eellqeyreaqeelsevkekykqlsegv 300
                                       +++k++ ++ +++ ++++ ++++++ d ++t++ +e+    ++  +   ee+++++   +e ++e++  ++++ +  
  gi|336254891|ref|YP_004597998.1| 402 NEVKSLAEESQDEATNIERMVDRIQADTEETVDSLETANAEIDDGVelvEETVDNLGRIEEAVAEASTGIREVATA- 477
                                       5667777888899999999******************999998765111556666666666666666555555444. PP

                             IFT57 301 seltrelaeiseelekvkqemeergssmtDgs 332
                                          t+++a  +ee+ ++     er+++++D  
  gi|336254891|ref|YP_004597998.1| 478 ---TDDQAASTEEVASMTDSAMERSQEIADEV 506
                                       ...44444455555555555555666655543 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8  13.0      0.24   1.1e+02      23     116 ..     213     307 ..     196     309 .. 0.76
   2 ?    4.3  16.7     0.081        38       3     109 ..     233     339 ..     232     380 .. 0.93
   3 ?    8.3   9.5    0.0049       2.3       5     114 ..     403     515 ..     401     521 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.24
                        TPR_MLP1_2  23 klqklq.edlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqk 98 
                                        +q+++ +  e+q +++++  + Ye e+  +  + ++l+++r  ++++ +e+ae+++++ +   e++  +++ +   
  gi|336254891|ref|YP_004597998.1| 213 SAQEARiDAYEAQLAEYEQRLEEYEAEIEAQDRTREDLADARRSMENTLEEVAEATDDVADGADEIDDLTAEQSDSM 289
                                       33333303345566666666677999999999999999999999999999999999999999999999999999999 PP

                        TPR_MLP1_2  99 eelekelselekriedln 116
                                       +e+ +e+s l + +e++ 
  gi|336254891|ref|YP_004597998.1| 290 SEIASEISGLSATVEEIA 307
                                       999999999999888875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.081
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       l++ e+ei++ +   e+++++ +++++ le+ ae + +  +   +   + ae++++++++ +e++ l a+++e+ ++
  gi|336254891|ref|YP_004597998.1| 233 LEEYEAEIEAQDRTREDLADARRSMENTLEEVAEATDDVADGADEIDDLTAEQSDSMSEIASEISGLSATVEEIASN 309
                                       57889999999******************************9999999***************************** PP

                        TPR_MLP1_2  80 aesakaeleeseesweeqkeelekelsele 109
                                       ae+++a+ e++e+  + + e+ e+ ++++e
  gi|336254891|ref|YP_004597998.1| 310 AEEVSATSEQAESVASDTTETAEEAIDKME 339
                                       ***************999999999999886 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0049
                        TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeae 81 
                                       ++++ +++ ++e+++ e+ +  +q d e+  +++++a+      + + +e+v++l ++ e ++e+ + i+e+ ++ +
  gi|336254891|ref|YP_004597998.1| 403 EVKSLAEESQDEATNIERMVDRIQADTEETVDSLETANAEIDDGVELVEETVDNLGRIEEAVAEASTGIREVATATD 479
                                       5677788999999*************************************************999988888777776 PP

                        TPR_MLP1_2  82 sa...kaeleeseesweeqkeelekelselekried 114
                                       +    ++e++  + s  e+ +e+ +e++ + +   d
  gi|336254891|ref|YP_004597998.1| 480 DQaasTEEVASMTDSAMERSQEIADEVETIVATTAD 515
                                       650115556666778888888888888877666555 PP

>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   2.3     0.077        36     262     329 ..     250     321 ..     210     326 .. 0.60
   2 ?   13.0   6.5   7.2e-05     0.034     248     334 ..     299     382 ..     278     383 .. 0.84
   3 ?   -0.1   7.4      0.71   3.4e+02     223     326 ..     418     521 ..     397     528 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.077
                            DUF677 262 isilverleseiksilktvefAve....keeneaavklaleeikkkvekltekieevgeeaakcskliakar 329
                                       +    +++e   + + ++ ++  +     ++  a+    ++ei  ++  l  ++ee+  +a++ s   ++a 
  gi|336254891|ref|YP_004597998.1| 250 LADARRSMENTLEEVAEATDDVADgadeIDDLTAEQSDSMSEIASEISGLSATVEEIASNAEEVSATSEQAE 321
                                       443334444444444333333222000022223445568999999999999999999999999998877775 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.2e-05
                            DUF677 248 mekgievakkdvenisilverleseiksilktvefAvekeeneaavklaleeikkkvekltekieevgeeaakcskl 324
                                       + + +e    + e++s   e+ es+ +   +t+e+A++k e    v+ a +e++++ve+l+e ++ ++e ++  + +
  gi|336254891|ref|YP_004597998.1| 299 LSATVEEIASNAEEVSATSEQAESVASDTTETAEEAIDKME---GVQEAADEVTEDVENLREGVQRIDEIVDVINDI 372
                                       44555555667788999999999999999**********88...9******************************** PP

                            DUF677 325 iakarlvvLq 334
                                       + ++ l +L+
  gi|336254891|ref|YP_004597998.1| 373 ADQTNLLALN 382
                                       **99999885 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.71
                            DUF677 223 vgkwvasawkkyeealkrqkeivssmekgievakkdvenisilverleseiksilktvefAvekeeneaavklalee 299
                                       + + v+++  + ee++   +++  +++ g+e  +++v+n+    e++    ++i + v  A+++++  ++ +  +++
  gi|336254891|ref|YP_004597998.1| 418 IERMVDRIQADTEETVDSLETANAEIDDGVELVEETVDNLGRIEEAVAEASTGI-REVATATDDQAASTEEVASMTD 493
                                       5566788888999999999***************99999765555555555554.4455666666655555555544 PP

                            DUF677 300 .ikkkvekltekieevgeeaakcsklia 326
                                          +  +++ +++e +   +a+ s l++
  gi|336254891|ref|YP_004597998.1| 494 sAMERSQEIADEVETIVATTADASDLVE 521
                                       1455567788888888777777777776 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   7.2    0.0004      0.19      10     105 ..     223     319 ..     214     323 .. 0.89
   2 ?    2.2   0.4      0.49   2.3e+02      17      54 ..     329     366 ..     316     380 .. 0.62
   3 ?    1.1   0.7       1.1   5.1e+02      37      77 ..     405     445 ..     395     476 .. 0.52
   4 ?    1.8   0.2      0.63     3e+02       6      63 ..     472     529 ..     468     533 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0004
                           DUF4200  10 evqe.aleakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikkl 85 
                                       e+q+ ++e+  ee++   ea+++ +e+l ++++ +e++l+++ +   +  +   +    ++e+++   e ++ei  l
  gi|336254891|ref|YP_004597998.1| 223 EAQLaEYEQRLEEYEAEIEAQDRTREDLADARRSMENTLEEVAEATDDVADGADEIDDLTAEQSDSMSEIASEISGL 299
                                       5554146777899999************************************************************* PP

                           DUF4200  86 kaeietlkseiekleeklee 105
                                        a +e++ s  e+  ++ e+
  gi|336254891|ref|YP_004597998.1| 300 SATVEEIASNAEEVSATSEQ 319
                                       ********999999888776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.49
                           DUF4200  17 akkeeiqrleealkqreeelekkeqeleedllkfdkfl 54 
                                       +  ee   ++e ++++ +e+ +  ++l+e +++ d+ +
  gi|336254891|ref|YP_004597998.1| 329 ETAEEAIDKMEGVQEAADEVTEDVENLREGVQRIDEIV 366
                                       34444555666666666666666666666666666655 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.1
                           DUF4200  37 ekkeqeleedllkfdkflkendakraralkkaeeerklkke 77 
                                       +   +e ++++ + ++++  ++a +++     e+ + ++++
  gi|336254891|ref|YP_004597998.1| 405 KSLAEESQDEATNIERMVDRIQADTEETVDSLETANAEIDD 445
                                       33344445555555555555555555444444444444433 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.63
                           DUF4200   6 remfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakrar 63 
                                       re+  ++  ++a  ee + + +++ +r +e+ ++ + +  + +     ++e+da+  r
  gi|336254891|ref|YP_004597998.1| 472 REVATATDDQAASTEEVASMTDSAMERSQEIADEVETIVATTADASDLVEEIDAELDR 529
                                       6777777788888888888888888888888888888888888888888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2027  (0.113057); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                       150  (0.00836633); expected 17.9 (0.001)
Passed Fwd filter:                       108  (0.00602376); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 1.60u 0.30s 00:00:01.90 Elapsed: 00:00:00.53
# Mc/sec: 3068.52
//
Query:       gi|336254892|ref|YP_004597999.1|  [L=151]
Description: CheW protein [Halopiger xanaduensis SH-6]
Scores for complete 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-25   89.2   0.1    2.1e-25   89.0   0.1    1.0  1  CheW      CheW-like domain


Domain annotation for each model (and alignments):
>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   0.1   1.2e-29   2.1e-25       2     131 ..      21     147 ..      20     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 1.2e-29
                                       EEEEEETTEEEEEEGGGEEEEEECCT.BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTTSTCEEEEEEEET. CS
                              CheW   2 lllfrlgeetyaiplakvreilevppitpipgapgavlgvinlrGevipvidLrellglgpeesrentrvivvelg. 77 
                                       +l f+lge++y++++  v+ei++ +++t +p++p++v+gv++lrGe+  +++Lr+++g + ++s   +r+iv +++ 
  gi|336254892|ref|YP_004597999.1|  21 VLEFSLGENRYCVDIGYVAEIVDTNQLTAVPNTPDHVEGVMDLRGETTKIVNLRRIFGETDDDSAIGNRIIVFKRKr 97 
                                       899**********************************************************************9666 PP

                                       ..TEEEEEEESEEEEEEEEECCGEETTTSSTSSTCCCEEEEEECTTSEEEEEE-CC CS
                              CheW  78 ..nqvvGllVdevkgiqeivikqiepplglssdlagyisGatklgdgrlvliLDve 131
                                         n+++G l dev +++e+ ++ ++       d +g i+G+++  d+++v+++D+ 
  gi|336254892|ref|YP_004597999.1|  98 gsNERIGWLADEVYQVEEVWTDTVDTSV----DGEG-IAGVIRR-DDEFVFWIDPT 147
                                       66***********************994....4589.*******.999******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 1146.29
//
Query:       gi|336254893|ref|YP_004598000.1|  [L=561]
Description: methyl-accepting chemotaxis sensory transducer with Pas/Pac sensor [Halopiger xanaduensis SH-6]
Scores for 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-40  136.6  19.6    7.2e-40  136.6  19.6    3.7  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
    1.2e-12   47.9   0.0    3.7e-12   46.2   0.0    1.9  1  PAS              PAS fold
    6.6e-12   45.6   1.8    1.4e-10   41.4   1.8    3.1  1  PAS_4            PAS fold
    2.1e-08   34.3   0.1    1.6e-07   31.6   0.0    2.5  2  PAS_9            PAS domain
    2.7e-06   27.3   0.1      3e-05   23.9   0.0    2.5  2  PAS_8            PAS domain
    1.4e-05   25.2  36.2    9.2e-05   22.6   4.7    5.0  4  DUF948           Bacterial protein of unknown function (DUF94
    7.3e-05   21.1  18.1     0.0008   17.7  10.6    2.3  2  EzrA             Septation ring formation regulator, EzrA
    0.00044   20.4  13.7       0.23   11.5   0.0    3.3  3  Mod_r            Modifier of rudimentary (Mod(r)) protein
    0.00048   19.5  22.0     0.0016   17.8  10.0    3.4  3  DUF3450          Protein of unknown function (DUF3450)
     0.0016   18.2  30.9       0.25   11.0   4.5    3.3  3  DUF745           Protein of unknown function (DUF745)
     0.0026   17.4  25.5      0.008   15.9   9.8    3.7  3  YkyA             Putative cell-wall binding lipoprotein
     0.0027   17.8  25.4       0.22   11.6   4.9    4.3  4  DUF1664          Protein of unknown function (DUF1664)
     0.0053   16.8  18.4        3.7    7.6   2.0    5.3  5  PilJ             Type IV pili methyl-accepting chemotaxis tra
     0.0086   16.2   0.0     0.0086   16.2   0.0    3.6  3  MLTR_LBD         MmyB-like transcription regulator ligand bin
  ------ inclusion threshold ------
       0.01   15.9  18.9      0.044   13.8   5.5    3.5  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.013   14.4  29.5       0.13   11.1  16.1    3.1  3  Spc7             Spc7 kinetochore protein
      0.014   15.4  30.9      0.021   14.8   4.3    4.7  4  Laminin_II       Laminin Domain II
      0.016   15.6   1.1      0.016   15.6   1.1    4.8  3  HAMP             HAMP domain
      0.017   15.3   4.8      0.017   15.3   4.8    3.7  4  SesA             N-terminal domain on NACHT_NTPase and P-loop
      0.021   15.0   2.9      0.049   13.8   2.4    1.9  1  DUF4047          Domain of unknown function (DUF4047)
      0.024   14.8  19.9      0.082   13.1   0.6    4.4  4  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.031   13.4   2.6      0.045   12.8   2.0    1.5  1  DUF2009          Protein of unknown function (DUF2009)
      0.062   14.0   3.1         73    4.2   0.0    4.7  6  RecG_N           RecG N-terminal helical domain
      0.069   13.4  20.5      0.058   13.6  11.8    2.6  2  ATG16            Autophagy protein 16 (ATG16)
      0.075   12.0  15.6       0.43    9.5  13.2    2.4  4  IFT57            Intra-flagellar transport protein 57
      0.093   12.7   6.2      0.042   13.9   3.5    1.8  2  DUF489           Protein of unknown function (DUF489)
       0.11   11.6  14.6        0.9    8.6   2.3    4.3  5  RmuC             RmuC family
       0.12   12.2  17.8        2.2    8.1   0.4    4.6  4  CdvA             CdvA-like coiled-coil domain
       0.14   12.3  16.0       0.23   11.7   6.5    4.0  5  Fib_alpha        Fibrinogen alpha/beta chain family
       0.16   10.8  18.5       0.17   10.7   3.4    2.9  3  DUF677           Protein of unknown function (DUF677)
        0.2   10.9  11.8        1.1    8.4   5.6    3.1  3  TMPIT            TMPIT-like protein
       0.21   12.2  25.1       0.29   11.7   0.2    4.5  3  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.26   11.4  20.6       0.32   11.1   0.6    4.6  5  COG2             COG (conserved oligomeric Golgi) complex com
       0.27   11.6   2.5        1.9    8.9   0.7    2.7  2  Gp-FAR-1         Nematode fatty acid retinoid binding protein
       0.28   11.3  25.6       0.44   10.6   2.1    4.1  4  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
        0.3   11.3  27.4       0.39   11.0   3.5    6.7  7  WXG100           Proteins of 100 residues with WXG
       0.37    9.4  22.6        1.2    7.7  17.6    2.2  2  AAA_13           AAA domain
       0.52   10.8  39.7        0.1   13.1   0.7    6.0  5  T7SS_ESX_EspC    Excreted virulence factor EspC, type VII ESX
        0.6   10.2   4.1        1.6    8.8   0.1    3.3  3  MCC-bdg_PDZ      PDZ domain of MCC-2 bdg protein for Usher sy
       0.62   10.0  18.9       0.25   11.3   4.8    3.7  3  Ferritin         Ferritin-like domain
       0.86    9.6  10.0         41    4.2   0.0    3.6  3  P4Ha_N           Prolyl 4-Hydroxylase alpha-subunit, N-termin
        0.9    9.9  26.1      0.093   13.1   2.9    4.5  4  Mobilization_B   Mobilization protein B
          1    8.4  25.6      0.098   11.8   4.7    3.3  2  APG17            Autophagy protein Apg17
        1.2    9.5  22.4        2.3    8.6   4.9    4.5  4  BLOC1_2          Biogenesis of lysosome-related organelles co
        1.6    9.2  32.1        5.6    7.4   9.3    3.7  3  T3SSipB          Type III cell invasion protein SipB
        1.7    9.2  20.6          2    8.9   0.9    4.5  4  DUF16            Protein of unknown function DUF16
        1.7    6.5   9.3        4.4    5.1   8.2    2.0  1  Prominin         Prominin
        1.8    9.1  10.2          1    9.8   1.2    3.5  3  Goodbye          fungal STAND N-terminal Goodbye domain
        1.9    8.0  22.1        1.7    8.2  12.2    2.4  2  DUF4795          Domain of unknown function (DUF4795)
        2.1    8.0  21.0        2.2    7.9   8.0    3.2  2  TMP_2            Prophage tail length tape measure protein
        2.4    8.2  31.1        1.6    8.8   4.9    3.3  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        2.5    8.3   6.7          6    7.1   1.5    3.3  4  COG5             Golgi transport complex subunit 5
        2.9    8.0  11.8       0.31   11.2   4.6    2.8  3  Nmad5            Nucleotide modification associated domain 5
        3.6    7.5   9.8        4.4    7.2   0.2    2.7  2  DinB             DinB family
        3.9    5.9  21.3        1.9    6.9   5.2    2.2  2  FUSC             Fusaric acid resistance protein family
        4.2    7.4  17.2        6.4    6.8  11.3    2.7  3  UPF0242          Uncharacterised protein family (UPF0242) N-t
        4.2    7.8  13.3        1.5    9.2   7.3    3.0  3  DUF4200          Domain of unknown function (DUF4200)
        4.5    6.7  19.2        1.2    8.5  12.0    2.6  2  HMMR_N           Hyaluronan mediated motility receptor N-term
        5.1    6.1   7.5         19    4.2   7.5    1.9  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        5.2    7.5  15.7          7    7.1   2.2    4.5  5  Syntaxin_2       Syntaxin-like protein
        7.5    7.3  26.7        9.9    6.9   2.2    4.5  4  DUF2203          Uncharacterized conserved protein (DUF2203)
        7.6    7.2   5.9        7.6    7.2   1.8    2.9  3  DUF4665          Domain of unknown function (DUF4665)
        8.7    5.6  24.1        1.7    7.9   1.2    3.7  3  CorA             CorA-like Mg2+ transporter protein
        9.7    6.4  11.8        3.1    8.0   3.7    3.2  3  CREPT            Cell-cycle alteration and expression-elevate


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       1.3   3.7e+02     132     157 ..     218     243 ..     209     259 .. 0.83
   2 ?    5.8   7.0     0.039        11      74     153 ..     273     352 ..     262     370 .. 0.60
   3 !  136.6  19.6   2.6e-42   7.2e-40       7     169 ..     360     522 ..     354     525 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 132 eiveavaevadlvqeiaaaseeqsas 157
                                       +iv++ +   dlvqei ++++e+s +
  gi|336254893|ref|YP_004598000.1| 218 DIVNERDATVDLVQEIRTTANEISDG 243
                                       57788888888999999999999876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.039
                                       HHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  74 AdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaa 150
                                       Ad   +L  r  ++a e+++++ e +   ++ +  ++e +   e +++++++ +  ++e++++++ev++  +    a
  gi|336254893|ref|YP_004598000.1| 273 ADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGMEEVAAQADEVDSAARTAREA 349
                                       66666677777777777777775555555555555555555555555555555555555555555555555544444 PP

                                       HHH CS
                         MCPsignal 151 see 153
                                       +e+
  gi|336254893|ref|YP_004598000.1| 350 VEQ 352
                                       444 PP

  == domain 3  score: 136.6 bits;  conditional E-value: 2.6e-42
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHH CS
                         MCPsignal   7 aseeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVrkLAer 83 
                                       a+e  e+     ++  + +++++++ +ei d++eVi ++adQTNlLALNA iEAARAGe+G+GFaVVAd V+kLA++
  gi|336254893|ref|YP_004598000.1| 360 AREATEDVVAIGDELRESVDALAEKMNEIGDVVEVISDVADQTNLLALNANIEAARAGESGNGFAVVADQVKKLADE 436
                                       4444444444446677889999******************************************************* PP

                                       HHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  84 saqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasiee 160
                                       +++ ++ei++ + e+q++++d+++++e++++r+e++ e++e   ++l++i+++v+e a+ ++e+a+  ++q+asiee
  gi|336254893|ref|YP_004598000.1| 437 TQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISEVARVIDDQTASIEE 513
                                       ***************************************************************************** PP

                                       HHHHHHHHH CS
                         MCPsignal 161 vnqaveeva 169
                                        ++++e v 
  gi|336254893|ref|YP_004598000.1| 514 LTSTMETVR 522
                                       *99998876 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   1.3e-14   3.7e-12       3     112 ..      92     215 ..      90     216 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.3e-14
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH...HHHHHHHHHHHHTT-ECCCC CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda...elaelleqlleqgeesrage 76 
                                       ++++++ + +p+f++D+dg i+++Naa +el+G +r e++g     + + +d +   +la++++q+ e ++ + ++e
  gi|336254893|ref|YP_004598000.1|  92 YQQLFDGTGVPTFILDADGTIVEWNAALAELTGVDRTEAVGHEHASEHFYPDGRradTLADKVLQAPERAHLEYGVE 168
                                       79999*******************************77777777777777776669********************* PP

                                       EEEEC............TTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  77 isfkl............rdgrpihlevraspvrdaggeilgflgvlrd 112
                                       ++ +             r+g ++h++  a+p++d+++ i g++ v+ d
  gi|336254893|ref|YP_004598000.1| 169 HRDPDrnrygdtstmvdRHGDEKHIDFSATPLYDGDDLI-GVIEVVID 215
                                       *9999*******************************988.99877766 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   1.8   5.1e-13   1.4e-10       1     107 [.      96     218 ..      96     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 5.1e-13
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla..ellpee.daarleralrrvlegeepiefleelll 74 
                                       +d + +++++ld+dg+++ +Naa ael g+++ e++G+  a   ++p++  a+ l++ + ++ e  +  + +e++++
  gi|336254893|ref|YP_004598000.1|  96 FDGTGVPTFILDADGTIVEWNAALAELTGVDRTEAVGHEHAseHFYPDGrRADTLADKVLQAPERAHLEYGVEHRDP 172
                                       677899***********************************855888655444444444444444444445555555 PP

                             PAS_4  75 ..............pgeerhyelrllPlrdesGe.vigvlvisrDiTe 107
                                                      g+e+h++++++Pl d  G+  igv+++++D T+
  gi|336254893|ref|YP_004598000.1| 173 drnrygdtstmvdrHGDEKHIDFSATPLYD--GDdLIGVIEVVIDRTD 218
                                       8888888899999***************88..8889*********997 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   5.6e-10   1.6e-07       3     104 .]     102     218 ..     100     218 .. 0.83
   2 ?   -1.2   0.0       8.5   2.4e+03      27      50 ..     439     469 ..     420     508 .. 0.64

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 5.6e-10
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgks.itdlf.vtdpeanerlraaleqgrk..............kere 63 
                                       +++i + dg+i+ +N a+++l+G ++ e +g+   ++ f  +  +a+   +++l++ ++              + + 
  gi|336254893|ref|YP_004598000.1| 102 PTFILDADGTIVEWNAALAELTGVDRTEAVGHEhASEHFyPDGRRADTLADKVLQAPERahleygvehrdpdrNRYG 178
                                       678988*******************9999998868888854444444444556666666888888889999999999 PP

                             PAS_9  64 vevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                       ++ +++++ g + +++++a+p++d ++ l+g+i +++D t+
  gi|336254893|ref|YP_004598000.1| 179 DTSTMVDRHGDEKHIDFSATPLYD-GDDLIGVIEVVIDRTD 218
                                       99999999999999********87.568**********996 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 8.5
                             PAS_9  27 speevlgksitdlf.......vtdpeanerl 50 
                                        + e + ks+++l+       +  ++++er+
  gi|336254893|ref|YP_004598000.1| 439 EHTEEITKSLDELQaqsedttDAVEQSHERI 469
                                       4667778888888833333222222222222 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.1e-07     3e-05       3      60 ..      92     148 ..      92     155 .. 0.78
   2 ?    0.1   0.1       3.1   8.8e+02      23      57 ..     294     323 ..     262     340 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.1e-07
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGysadlkgellg.qllpvlrplledae 60 
                                       +++lf+   ++ +++d++++iv++N a +el+G++    +++ +    ++++p  ++a+
  gi|336254893|ref|YP_004598000.1|  92 YQQLFDGTGVPTFILDADGTIVEWNAALAELTGVD--RTEAVGHeHASEHFYPDGRRAD 148
                                       89**************5555*************87..7776666666666666666555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 3.1
                             PAS_8  23 ivdvNqaalellGysadlkgellgqllpvlrplle 57 
                                       + ++N+aa e+ G      +e    ll+++ ++++
  gi|336254893|ref|YP_004598000.1| 294 VDEANDAADEIAG----NVTEQH-GLLEDSVDEMQ 323
                                       6679999999999....444444.34444444443 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 ?    3.9   7.1      0.24        66      38      84 ..     258     304 ..     211     352 .. 0.77
   2 ?    5.5   1.4     0.071        20      25      82 ..     343     400 ..     322     406 .. 0.60
   3 !   22.6   4.7   3.3e-07   9.2e-05      19      86 ..     425     492 ..     422     495 .. 0.95
   4 ?    6.7   3.1      0.03       8.4      22      81 ..     498     557 ..     493     559 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.24
                            DUF948  38 lekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                       l +++  +++ v+++ ++ ++l+  v+e+  ++ + +++++d+++ +
  gi|336254893|ref|YP_004598000.1| 258 LDDDLVDVVDAVNGMADNLETLTGRVTEQATEMRSAVDEANDAADEI 304
                                       44777777777777777777777777777777766666666666554 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.071
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlge 82 
                                       ++t++ea ++  + ++++++ +++v ++ ++ +e ++ + ek++++  ++e + d+++
  gi|336254893|ref|YP_004598000.1| 343 ARTAREAVEQGLDAGEDAREATEDVVAIGDELRESVDALAEKMNEIGDVVEVISDVAD 400
                                       3444444444444446666666666666666666666666666666666666666655 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 3.3e-07
                            DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       vv  ++kk++de++++ ee++k +d++  ++ed+++ v++  e +++  e+++++ ++++d+++sv e
  gi|336254893|ref|YP_004598000.1| 425 VVADQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDE 492
                                       677899***********************************************************976 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.03
                            DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlg 81 
                                        ++++++d  +a+ieel++ ++ + + +++  a ++++++   ++ +++++l++ v +l 
  gi|336254893|ref|YP_004598000.1| 498 SEVARVIDDQTASIEELTSTMETVRDRSDESEAAAERIVAATDHQNQTIETLMARVDELQ 557
                                       57899999****************9999999999999999*************9999876 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.8    0.0027      0.77     104     234 ..     256     391 ..     224     410 .. 0.57
   2 !   17.7  10.6   2.9e-06    0.0008      97     217 ..     435     557 ..     424     559 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHHHHHHHHHHHHHTHH....HHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH--- CS
                              EzrA 104 aeleeeldeveekikkileelkel....teseeknreeieklkekYrelrkkllanrfsygealeelekqlenieke 176
                                       ++l+++l +v   ++ + + l+ l    te+ ++ r++++++++  +e+  +++++   ++++++e+++  + +e+ 
  gi|336254893|ref|YP_004598000.1| 256 DALDDDLVDVVDAVNGMADNLETLtgrvTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGMEEV 332
                                       44444444444444444444444411113555555666666666666666666666666666666666666666665 PP

                                       -----------.--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSHHHHHHHHHH CS
                              EzrA 177 fsefeelteng.dyveakeilkkleeeideleevieeiPelleelkkelpkqleelkeg 234
                                        ++ +e+ ++     ea e+  ++ e+  e +e++  i + l+e  + l ++++e+ + 
  gi|336254893|ref|YP_004598000.1| 333 AAQADEVDSAArTAREAVEQGLDAGEDAREATEDVVAIGDELRESVDALAEKMNEIGDV 391
                                       55555555443133455555555555555555555555555555555555555555444 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.9e-06
                                       HHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH CS
                              EzrA  97 kkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleni 173
                                        ++++  +e+++ lde+++++++  +++++  e  e   e+ie++ +  +++ +++ +  +  +e++  +++q + i
  gi|336254893|ref|YP_004598000.1| 435 DETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISEVARVIDDQTASI 511
                                       5788999********************************************************************** PP

                                       ----------------HHH..HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 174 ekefsefeeltengdyvea..keilkkleeeideleevieeiPell 217
                                       e+  s++e++ + +d +ea  ++i+ +++++ + +e+++ ++ el 
  gi|336254893|ref|YP_004598000.1| 512 EELTSTMETVRDRSDESEAaaERIVAATDHQNQTIETLMARVDELQ 557
                                       ************99998752278****************9998875 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 ?    3.3   0.0      0.28        79      22      89 ..     249     316 ..     241     318 .. 0.78
   2 !   11.5   0.0   0.00083      0.23      10     106 ..     313     413 ..     307     417 .. 0.87
   3 ?    6.8   9.7     0.023       6.5      17     120 ..     429     537 ..     426     552 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.28
                             Mod_r  22 vktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellq 89 
                                       ++ ++ +++l++++ +++++   +a++   l  +++e+  e+ ++ +e++ + +e     +e++ ll+
  gi|336254893|ref|YP_004598000.1| 249 AERSDDFDALDDDLVDVVDAVNGMADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLE 316
                                       55556678888888888888888888555558899999999999999999999999999999888775 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00083
                             Mod_r  10 ellede.eklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeld 85 
                                        lled  + +++++  ++ev ++ +e +++  + ++  e+ l+  ++ +e  +++ +  +el+e  +++ ek +e  
  gi|336254893|ref|YP_004598000.1| 313 GLLEDSvDEMQSFAAGMEEVAAQADEVDSAARTAREAVEQGLDAGEDAREATEDVVAIGDELRESVDALAEKMNEIG 389
                                       6899999**************************************99999999999999999999999999999996 PP

                             Mod_r  86 ell...qkfspdallarLqtavae 106
                                       +++   +++ ++++l  L++ +++
  gi|336254893|ref|YP_004598000.1| 390 DVVeviSDVADQTNLLALNANIEA 413
                                       666555888888888888777765 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.023
                             Mod_r  17 klealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldell.... 88 
                                       ++++l++++ +++++++++++el a+ e++ ++  ++++++e+  +++++ l +l+ + ++++e  +  +e+     
  gi|336254893|ref|YP_004598000.1| 429 QVKKLADETqEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISEVArvid 505
                                       667788877688999***************9999999*****************************99999998888 PP

                             Mod_r  89 .qkfspdallarLqtavaeaeeeSealaeefle 120
                                        q  s + l + ++t  +++ +eSea ae+++ 
  gi|336254893|ref|YP_004598000.1| 506 dQTASIEELTSTMETVRDRS-DESEAAAERIVA 537
                                       87778888888887765555.578888888884 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.2    0.0054       1.5      37     113 ..     250     326 ..     224     329 .. 0.88
   2 ?   -0.2   0.3       1.8     5e+02      51      91 ..     348     388 ..     329     406 .. 0.42
   3 !   17.8  10.0   5.7e-06    0.0016      15     105 ..     445     535 ..     437     558 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0054
                           DUF3450  37 kkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfv 113
                                       ++ d+ d   ++l++ + a++  +++le    +++++ +++++ +++ +   +ei    +e   lle+ +d+++ f 
  gi|336254893|ref|YP_004598000.1| 250 ERSDDFDALDDDLVDVVDAVNGMADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFA 326
                                       677888888899999999********************************************************996 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.8
                           DUF3450  51 aeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                       + +++  +  e+++   e + ++ ++++++++ l e+++ei
  gi|336254893|ref|YP_004598000.1| 348 EAVEQGLDAGEDAREATEDVVAIGDELRESVDALAEKMNEI 388
                                       33333333333333333333333333333333333333333 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 5.7e-06
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                        ++ld++++++e +++a +qs+++i++ d++ + +l  ++++ + +++++   ++++r++++q ++i++l+  +e +
  gi|336254893|ref|YP_004598000.1| 445 TKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISEVARVIDDQTASIEELTSTMETV 521
                                       6789***********************************************************************99 PP

                           DUF3450  92 eeierelvpllekm 105
                                       +  ++e +   e++
  gi|336254893|ref|YP_004598000.1| 522 RDRSDESEAAAERI 535
                                       98877766665555 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   4.5   0.00089      0.25      93     177 ..     267     351 ..     263     355 .. 0.92
   2 !   10.5   9.0    0.0013      0.36      64     174 ..     378     495 ..     358     500 .. 0.73
   3 !   10.4   2.7    0.0014      0.39      79     153 ..     484     558 ..     482     559 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00089
                            DUF745  93 kaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektkkaA 169
                                       +a++ +a++ ++   ++++   ++++++++a+++a++ + ++ e++ lle++   +++    ++e+ +  +++ +aA
  gi|336254893|ref|YP_004598000.1| 267 DAVNGMADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGMEEVAAQADEVDSAA 343
                                       5677788899999999999999******************************************************* PP

                            DUF745 170 ykAacAAq 177
                                       + A  A +
  gi|336254893|ref|YP_004598000.1| 344 RTAREAVE 351
                                       **999865 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0013
                            DUF745  64 veqleqelreaeavvqeekkslqsse...anakaaakaakqaqq....qlealkallkaakenlenaeqvaagaqqe 133
                                       v+ l ++++e  +vv+ +++   +++    na++ a+ a +  +     ++++k+l ++++e  e++++  ++ q++
  gi|336254893|ref|YP_004598000.1| 378 VDALAEKMNEIGDVVEVISDVADQTNllaLNANIEAARAGESGNgfavVADQVKKLADETQEHTEEITKSLDELQAQ 454
                                       66677777777666665555555554111333333333333333111145677888888999999999999999999 PP

                            DUF745 134 laektqlleaAkkRveeLkkqlkearkdlektkkaAykAac 174
                                        ++ t+ +e++++R+e+  +q++++ + le++ ++   Aa 
  gi|336254893|ref|YP_004598000.1| 455 SEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAAN 495
                                       9************************9999999999888875 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0014
                            DUF745  79 qeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkk 153
                                       +++ +s+ ++ + ++ +a++ ++ ++++e l++++++++++ +++e++a+   +  + ++q +e+  +Rv+eL++
  gi|336254893|ref|YP_004598000.1| 484 EDIADSVDEAANGISEVARVIDDQTASIEELTSTMETVRDRSDESEAAAERIVAATDHQNQTIETLMARVDELQT 558
                                       677888999999999999******************************************************985 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   3.9     0.011       3.2      48     109 ..     293     356 ..     257     388 .. 0.63
   2 !   15.9   9.8   2.9e-05     0.008      28     122 ..     431     516 ..     406     524 .. 0.68
   3 !    9.8  10.2     0.002      0.56      50     123 ..     442     517 ..     441     558 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.011
                              YkyA  48 efdkikklsdealenveeReellekekesieeakeefekikeeieeiede..elkkeaeeliea 109
                                         d+ ++ +de   nv e+  lle   + +++    +e++ ++ +e++    ++++ +e+  +a
  gi|336254893|ref|YP_004598000.1| 293 AVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGMEEVAAQADEVDSAarTAREAVEQGLDA 356
                                       3566777777777777777777777777777777777777777777732211333333333333 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.9e-05
                              YkyA  28 telekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieeiede..elkke 102
                                       +           ++ + ++++ ++i+k  de+++  e+ ++ +e+  e ie a e++e + +++e+i d+  e+ + 
  gi|336254893|ref|YP_004598000.1| 431 K-----------KLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSvdEAANG 496
                                       4...........44455566666666666666666666666666666666667777777777777774433356777 PP

                              YkyA 103 aeelieameeryeaydklyk 122
                                       ++e++ +++++++++++l++
  gi|336254893|ref|YP_004598000.1| 497 ISEVARVIDDQTASIEELTS 516
                                       88899999999999988876 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.002
                              YkyA  50 dkikklsdealenveeReellekekesieeakeefekikeeieeiede..elkkeaeelieameeryeaydklyka 123
                                       ++i+k  de+++  e+ ++ +e+  e ie a e++e + +++e+i d+  e+ + ++e++ +++++++++++l++ 
  gi|336254893|ref|YP_004598000.1| 442 EEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSvdEAANGISEVARVIDDQTASIEELTST 517
                                       4566666777777777777777777777777777777777777774333356666667777777777777666654 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3     0.038        11      41     108 ..     267     306 ..     226     327 .. 0.59
   2 !   10.5   0.7    0.0017      0.47      37     111 ..     323     400 ..     322     409 .. 0.85
   3 !   11.6   4.9   0.00077      0.22      44     119 ..     424     499 ..     420     502 .. 0.72
   4 ?    3.8   1.7      0.21        58      50     101 ..     497     551 ..     482     559 .. 0.34

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.038
                           DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                       dav+ ++ +le++   ++++  ++ s +d+ ++  de                            +  
  gi|336254893|ref|YP_004598000.1| 267 DAVNGMADNLETLTGRVTEQATEMRSAVDEANDAADE----------------------------IAG 306
                                       4444444444444444444444444444444333333............................222 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0017
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdk...kldeqkeiskeikeevtevredlseigedvesvkeav 110
                                       +s++  +e+v+ q ++v ++ +++++  ++ +d  ++     +++ +i  e++e v+++ e+++eig+ ve ++++ 
  gi|336254893|ref|YP_004598000.1| 323 QSFAAGMEEVAAQADEVDSAARTAREAVEQGLDAGEDareATEDVVAIGDELRESVDALAEKMNEIGDVVEVISDVA 399
                                       57888999************************986651115667778889******************999998876 PP

                           DUF1664 111 e 111
                                        
  gi|336254893|ref|YP_004598000.1| 400 D 400
                                       5 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00077
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       + v+ q++++ ++ ++  +++++ +d+++++ ++++++ ++ +e ++++ e+++++ + +e + + v + ++ +++
  gi|336254893|ref|YP_004598000.1| 424 AVVADQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISE 499
                                       5677777777788888888888888888888888888888888888888888777777777777777776666655 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.21
                           DUF1664  50 leqvseslaatk...rhLssridrvdkkldeqkeiskeikeevtevredlseige 101
                                       + +v   + ++    ++L+s +++v ++ de++++++ i +  ++ ++ ++++  
  gi|336254893|ref|YP_004598000.1| 497 ISEVARVIDDQTasiEELTSTMETVRDRSDESEAAAERIVAATDHQNQTIETLMA 551
                                       2222222222211113344444444444444444443333333333333333333 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.015       4.3       7      22 ..      75      90 ..      72     126 .. 0.89
   2 ?    4.1   0.1      0.16        46      40     101 ..     219     282 ..     209     296 .. 0.80
   3 ?    7.6   2.0     0.013       3.7      21     106 ..     278     361 ..     272     369 .. 0.88
   4 ?    3.7   0.4      0.22        62      53     104 ..     406     457 ..     396     467 .. 0.75
   5 ?    2.9   3.3      0.38   1.1e+02      24     107 ..     456     544 ..     450     550 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.015
                              PilJ  7 egdaaaINvAGslRMq 22
                                      e daaa+N+AG lR  
  gi|336254893|ref|YP_004598000.1| 75 EPDAAAVNDAGTLRRA 90
                                      569***********75 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.16
                              PilJ  40 aaearaqlretiaqfdrtlaalrlgdpapgllvpae..avraqleaveqlWqelkkpaeaalaq 101
                                       +  +r++  + ++++++t ++ ++gd++ +    ++  a  ++l +v +  + + +++e+++  
  gi|336254893|ref|YP_004598000.1| 219 IVNERDATVDLVQEIRTTANEISDGDLTARAERSDDfdALDDDLVDVVDAVNGMADNLETLTGR 282
                                       556778888999****************98888888**9***************9999655443 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.013
                              PilJ  21 MqsqRlakeallaaagaydaaearaqlretiaqfdrtlaalrlgdpapgllvpae.avraqleaveqlWqelkkpae 96 
                                        ++ R++ +a+++  +    +ea ++++e ++   +++  l+++ ++++ ++    +v aq ++v++  + +++++e
  gi|336254893|ref|YP_004598000.1| 278 TLTGRVTEQATEMRSAV---DEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGMeEVAAQADEVDSAARTAREAVE 351
                                       57779999999999999...99999999****************999999998769********************* PP

                              PilJ  97 aalaqqddaa 106
                                       + l +++da 
  gi|336254893|ref|YP_004598000.1| 352 QGLDAGEDAR 361
                                       *999998854 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.22
                              PilJ  53 qfdrtlaalrlgdpapgllvpaeavraqleaveqlWqelkkpaeaalaqqdd 104
                                       +++++++a r g++  g++v a++v++  ++ +++ +e  k+++ + aq +d
  gi|336254893|ref|YP_004598000.1| 406 ALNANIEAARAGESGNGFAVVADQVKKLADETQEHTEEITKSLDELQAQSED 457
                                       5778899999999999999999999999999999999999999544444433 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.38
                              PilJ  24 qRlakeallaaagaydaaearaqlretiaqfdrtlaalrlg.dpapgllvpae....avraqleaveqlWqelkkpa 95 
                                          +  + +   +++ a+e+ +++  +++++++++++ ++g ++  ++ + ++    + ++ +e v+++ +e + +a
  gi|336254893|ref|YP_004598000.1| 456 EDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGiSEVARVIDDQTasieELTSTMETVRDRSDESEAAA 532
                                       55554444444444677788888888899999999999999444444444444999999999************999 PP

                              PilJ  96 eaalaqqddaay 107
                                       e++ a+ d +++
  gi|336254893|ref|YP_004598000.1| 533 ERIVAATDHQNQ 544
                                       999999998776 PP

>> MLTR_LBD  MmyB-like transcription regulator ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.1e-05    0.0086       2      52 ..      89     137 ..      89     175 .. 0.79
   2 ?   -1.3   0.3       7.2     2e+03      65     129 ..     253     315 ..     241     348 .. 0.66
   3 ?    1.2   0.2       1.2   3.4e+02      70     113 ..     425     466 ..     399     487 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.1e-05
                          MLTR_LBD   2 rpalrrlLdalepvPAlVldrrwdvlaaNraaraLlgdpaalpeperNllr 52 
                                       r++ ++l d+   vP ++ld++ +++ +N+a + L g  ++ ++ ++  + 
  gi|336254893|ref|YP_004598000.1|  89 RAGYQQLFDGT-GVPTFILDADGTIVEWNAALAELTGV-DRTEAVGHEHAS 137
                                       56778888888.9**********************998.344444444444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 7.2
                          MLTR_LBD  65 edweevaralvarLraeaarrpddpalaalvaeLsaaspefarlwa.rhdvaarrsgrkrlrhpev 129
                                        d ++  ++lv+ + a  +     + l+ l ++++++  e++   + ++d+a+  +g ++ +h  +
  gi|336254893|ref|YP_004598000.1| 253 DDFDALDDDLVDVVDAVNGMA---DNLETLTGRVTEQATEMRSAVDeANDAADEIAGNVTEQHGLL 315
                                       556666666666666665555...677777777777777777654404466666666666666555 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.2
                          MLTR_LBD  70 varalvarLraeaarrpddpalaalvaeLsaaspefarlwarhd 113
                                       v ++ v +L  e++++   +++++ ++eL+a+s++     ++ +
  gi|336254893|ref|YP_004598000.1| 425 VVADQVKKLADETQEH--TEEITKSLDELQAQSEDTTDAVEQSH 466
                                       5667788888888877..999999*******9999877655544 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.6     0.048        13      37      86 ..     252     304 ..     226     329 .. 0.64
   2 ?    4.7   0.8      0.11        30      26      89 ..     333     397 ..     300     417 .. 0.50
   3 ?   13.8   5.5   0.00016     0.044       4     122 ..     430     560 ..     426     561 .] 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.048
                      Baculo_PEP_C  37 atlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrne 86 
                                       + ++da++  L ++ ++++ +  +l+t   r+++++t++ +a+ + +d+ ++ 
  gi|336254893|ref|YP_004598000.1| 252 SDDFDALDDDLVDVVDAVNGMADNLETltgRVTEQATEMRSAVDEANDAADEI 304
                                       45667777777777777777666666666666666666666666666544433 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.11
                      Baculo_PEP_C  26 rlqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtn 89 
                                        +q  ++ ++  t+ +a+e+ L+a  ed +++ +++ +   +l +++++L +++n++ d ++  +  
  gi|336254893|ref|YP_004598000.1| 333 AAQADEVDSAARTAREAVEQGLDA-GEDAREATEDVVAigdELRESVDALAEKMNEIGDVVE-VISD 397
                                       334444444444444444444444.3333333333333555666666666666666664442.3333 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 0.00016
                      Baculo_PEP_C   4 vqqLnggggnqfldLtnvLnairlqnvqilaqlatlldaie...tqLnalsedlksllaeldt......rldtlltn 71 
                                       v++L   +  ++ ++t+ L+ +++q+  ++ ++++  + ie   +q++a+ ++l++   ++d+      +++ +++ 
  gi|336254893|ref|YP_004598000.1| 430 VKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEhadEQIEAVLTSLEDIADSVDEaangisEVARVIDD 506
                                       56665555566779********************9988876222688888888888888888888866666666666 PP

                      Baculo_PEP_C  72 Ltdalnalq...dtlrneLtnlnsiltnLlssvtNinstLnnllqalnnldlga 122
                                        t+++ +l+   +t+r + +  ++    +++     n+t++ l++ ++ l+++ 
  gi|336254893|ref|YP_004598000.1| 507 QTASIEELTstmETVRDRSDESEAAAERIVAATDHQNQTIETLMARVDELQTDD 560
                                       666666666888899999888888888888888888888888888888887765 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1       0.3        83     180     257 ..     227     301 ..     212     312 .. 0.49
   2 ?    6.4   5.2     0.012       3.5     144     225 ..     315     398 ..     275     421 .. 0.58
   3 ?   11.1  16.1   0.00047      0.13     163     279 ..     428     557 ..     418     560 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.3
                              Spc7 180 eeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaerv 256
                                        + ++++++ a+e+++ d +  +e  +++++l+ ++    + ++ + ++le+l+ ++   +eq +e+++++ ea++ 
  gi|336254893|ref|YP_004598000.1| 227 VDLVQEIRTTANEISDGDLTARAERSDDFDALDDDLVDVVDAVNGMADNLETLTGRV---TEQATEMRSAVDEANDA 300
                                       444455555555555555555555555555555555544444444444444444444...33344444444444433 PP

                              Spc7 257 l 257
                                        
  gi|336254893|ref|YP_004598000.1| 301 A 301
                                       3 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.012
                              Spc7 144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkaeieek 218
                                       le+ ++++++ ++ +e+  +++de+  + ++ ++++e+ l+  ++a+e  e++    +eL+e  ++lae ++ei   
  gi|336254893|ref|YP_004598000.1| 315 LEDSVDEMQSFAAGMEEVAAQADEVDSAARTAREAVEQGLDAGEDAREATEDVVaiGDELRESVDALAEKMNEIGDV 391
                                       45556666666666666666666666666666666666666666655555553324555555555555555555555 PP

                              Spc7 219 kkelael 225
                                        + ++++
  gi|336254893|ref|YP_004598000.1| 392 VEVISDV 398
                                       5555554 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00047
                              Spc7 163 eeldellpeleeekaeleeeleklqeaaeeles..........idkeeLeelreelaelkaeieekkkelaelqeql 229
                                       +++++l +e++e+ +e+++ l++lq+++e+ ++             e++e++  +l+++   ++e  + ++e+ + +
  gi|336254893|ref|YP_004598000.1| 428 DQVKKLADETQEHTEEITKSLDELQAQSEDTTDaveqsherieHADEQIEAVLTSLEDIADSVDEAANGISEVARVI 504
                                       45666666666666666666666666443333333323334333467777777777888888888888888888888 PP

                              Spc7 230 eeleekieelkeqkseleeeiaeaervle...eckgwsesevsrlkeevkale 279
                                       ++++++ieel++ +++++++  e+e   e   +  +++++ +++l+++v++l+
  gi|336254893|ref|YP_004598000.1| 505 DDQTASIEELTSTMETVRDRSDESEAAAErivAATDHQNQTIETLMARVDELQ 557
                                       88888888888888777766665555444111367788888888888888888 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.1     0.016       4.4       4      68 ..     272     336 ..     255     341 .. 0.77
   2 ?    4.6   0.5      0.11        31       6      57 ..     358     409 ..     354     416 .. 0.84
   3 ?    6.5   2.3     0.029       8.1      13      55 ..     428     470 ..     424     472 .. 0.56
   4 ?   14.8   4.3   7.6e-05     0.021       2      74 ..     466     538 ..     465     558 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.016
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TT CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekla 68 
                                       +a++ +  +  v eq +++   +++ ++ + ei+++v e + +++d+   +++    + ++  +a
  gi|336254893|ref|YP_004598000.1| 272 MADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGMEEVAAQA 336
                                       66666777778899999999999999999999999999988888888777776666666666655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.11
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdA 57 
                                       ++a e ++ v ++  +l + ++ + ek++ei + ve + +++++ n     A
  gi|336254893|ref|YP_004598000.1| 358 EDAREATEDVVAIGDELRESVDALAEKMNEIGDVVEVISDVADQTNLLALNA 409
                                       5789999999999999999999999999999999999999888877655555 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.029
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  13 kevleqlaplsqnlentkeklseinrsveetnekvkdankair 55 
                                        +v++   + ++ +e++ ++l e++++ e t++ v+++ + i+
  gi|336254893|ref|YP_004598000.1| 428 DQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIE 470
                                       4555555566666666666666666666666666666655554 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 7.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGG CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldk 74 
                                        e ++ a+e++++vl  l++++  +++  + +se++r ++  ++ +++++ +++ +r+ + + e  a+++++ 
  gi|336254893|ref|YP_004598000.1| 466 HERIEHADEQIEAVLTSLEDIADSVDEAANGISEVARVIDDQTASIEELTSTMETVRDRSDESEAAAERIVAA 538
                                       67899***************************************************************99976 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   1.1   5.7e-05     0.016      11      52 ..     231     277 ..     227     278 .. 0.91
   2 ?    0.6   0.2       2.8   7.7e+02      14      37 ..     298     322 ..     292     338 .. 0.79
   3 ?    1.7   0.0       1.2   3.4e+02       7      21 ..     508     522 ..     478     534 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.7e-05
                                       HHHHHHHHHHTTTBTSST....CCT.TSSSHHHHHHHHHHHHHHHHH CS
                              HAMP  11 rrLaraarriaaGdldtr....lpv.sgrDEiGeLarafNaMldrLr 52 
                                       ++++++a++i++Gdl++r     +    +D + +++ a+N M+d+L+
  gi|336254893|ref|YP_004598000.1| 231 QEIRTTANEISDGDLTARaersDDFdALDDDLVDVVDAVNGMADNLE 277
                                       789******************9555589*****************98 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 2.8
                                       HHHHHHHTTTBTSST..CCTTSSSHH CS
                              HAMP  14 araarriaaGdldtr..lpvsgrDEi 37 
                                        +aa++ia G+++++  l +++ DE+
  gi|336254893|ref|YP_004598000.1| 298 NDAADEIA-GNVTEQhgLLEDSVDEM 322
                                       68999999.58888878888999997 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHT CS
                              HAMP   7 lrPLrrLaraarria 21 
                                       ++++++L+++++ ++
  gi|336254893|ref|YP_004598000.1| 508 TASIEELTSTMETVR 522
                                       456666666666666 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3      0.28        79       3      76 ..     225     304 ..     224     311 .. 0.78
   2 ?    2.0   0.2      0.78   2.2e+02      30      83 ..     331     395 ..     307     406 .. 0.62
   3 ?    1.9   1.0      0.86   2.4e+02      28      98 ..     385     461 ..     364     471 .. 0.47
   4 ?   15.3   4.8   5.9e-05     0.017      13     115 ..     454     553 ..     441     557 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.28
                              SesA   3 stiaiveaaiklydaikd.....ikglpeaFrevgkrLplvqetLedaksqlesskldedtesa.ikpvlesckeka 73 
                                       +t+ +v+ + ++ ++i+d       +    F++  + L  v ++ +   ++le+ +   +++++ +++++++ +++a
  gi|336254893|ref|YP_004598000.1| 225 ATVDLVQEIRTTANEISDgdltaRAERSDDFDALDDDLVDVVDAVNGMADNLETLTGRVTEQATeMRSAVDEANDAA 301
                                       67888888888888888888877777788888999999999999999999988877766666556888888888888 PP

                              SesA  74 tkl 76 
                                       +++
  gi|336254893|ref|YP_004598000.1| 302 DEI 304
                                       876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.78
                              SesA  30 evgkrLplvqetLedaksqlesskldedtesa...........ikpvlesckekatkleeifekv 83 
                                       ev+++   v  + ++a++++e++ +  ++  +           +++++++  ek++++ ++ e +
  gi|336254893|ref|YP_004598000.1| 331 EVAAQADEVDSAARTAREAVEQGLDAGEDAREatedvvaigdeLRESVDALAEKMNEIGDVVEVI 395
                                       55555555555555555555554333333222244566677779999999999999998888776 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.86
                              SesA  28 FrevgkrLplvqetLedaksqlesskldedtesa....ikpvlesckekatkleeifekvapapad.srl.eryrka 98 
                                        +e+g+ +++++++ ++++  + +++++ +   +    +  v++++k+ a++ +e  e+++++ ++ +   e ++ a
  gi|336254893|ref|YP_004598000.1| 385 MNEIGDVVEVISDVADQTNLLALNANIEAARAGEsgngFAVVADQVKKLADETQEHTEEITKSLDElQAQsEDTTDA 461
                                       44444444444444333333333333333222224444555555555555555555555544444442222444444 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 5.9e-05
                              SesA  13 klydaikdikglpeaFrevgkrLplvqetLedaksqlesskldedtesaikpvlesckekatkleeifekvapapad 89 
                                       +  d+ + +++  e ++++ ++++ v   Led+ ++++++ +  +   ++  v+++  + +++l + +e+v++  ++
  gi|336254893|ref|YP_004598000.1| 454 QSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGIS---EVARVIDDQTASIEELTSTMETVRDRSDE 527
                                       455666668899999999999999999999999999999998875...389********************666666 PP

                              SesA  90 srl..eryrkavrslgkgskVEtLmkgi 115
                                       s+   er+++a  +  +++++EtLm  +
  gi|336254893|ref|YP_004598000.1| 528 SEAaaERIVAA--TDHQNQTIETLMARV 553
                                       44425777777..567*********875 PP

>> DUF4047  Domain of unknown function (DUF4047)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.4   0.00018     0.049      24     107 ..     425     507 ..     408     521 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00018
                           DUF4047  24 ifPktvdtlveqakqhkelilheyeemksklkvdsveeieqalsvwkqgrekikaerealqkvyteieepynqvqee 100
                                       +    v++l ++++ h e i +  +e++++ + d+++ +eq  +  ++  e+i a   +l ++  +++e  n + e 
  gi|336254893|ref|YP_004598000.1| 425 VVADQVKKLADETQEHTEEITKSLDELQAQSE-DTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISEV 500
                                       5567899********************99876.7899***************************************9 PP

                           DUF4047 101 lkvnkse 107
                                        +v +++
  gi|336254893|ref|YP_004598000.1| 501 ARVIDDQ 507
                                       9997665 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 ?    0.1   0.0       3.3   9.2e+02      42      92 ..     227     285 ..     216     295 .. 0.46
   2 ?   13.1   0.6   0.00029     0.082      25     107 ..     316     398 ..     301     399 .. 0.93
   3 ?    6.0   4.0     0.049        14      43     101 ..     432     487 ..     426     497 .. 0.58
   4 ?    2.9   0.4      0.45   1.3e+02      57     101 ..     502     546 ..     487     551 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHHHHHHH..CCCCCCTT......S-TCCCCCCCHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  42 qveleelqaerNelske..Igkakkkk......edaeeliaevkelkeelkaleaelke 92 
                                          ++e+++  Ne+s     ++a +++      +d  ++++ v+ + ++l++l+ +++e
  gi|336254893|ref|YP_004598000.1| 227 VDLVQEIRTTANEISDGdlTARAERSDdfdaldDDLVDVVDAVNGMADNLETLTGRVTE 285
                                       55566666666666653102222222233322233333344444444444444444444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00029
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  25 kadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                       +  vde+ +  + ++e+ ++++e+ +   ++ +++++  +++eda e  ++v ++++el +  ++l+e  +e+ +++
  gi|336254893|ref|YP_004598000.1| 316 EDSVDEMQSFAAGMEEVAAQADEVDSAARTAREAVEQGLDAGEDAREATEDVVAIGDELRESVDALAEKMNEIGDVV 392
                                       56799999999999*************************************************************99 PP

                                       CTS--- CS
                      Seryl_tRNA_N 102 laiPNi 107
                                        +i ++
  gi|336254893|ref|YP_004598000.1| 393 EVISDV 398
                                       999875 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.049
                                       HHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  43 veleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                       + ++e q+   e++k+  ++ ++ ed++   + v++  e++++++++ +++ + le+++
  gi|336254893|ref|YP_004598000.1| 432 KLADETQEHTEEITKSLDELQAQSEDTT---DAVEQSHERIEHADEQIEAVLTSLEDIA 487
                                       4456666666666666666666654433...4445555566666666666666665554 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.45
                                       HHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  57 keIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                       + I    ++ e+ ++ ++ v++ ++e +a+ ++  ++++ +++ +
  gi|336254893|ref|YP_004598000.1| 502 RVIDDQTASIEELTSTMETVRDRSDESEAAAERIVAATDHQNQTI 546
                                       333333333355566666666666666666666666666655554 PP

>> DUF2009  Protein of unknown function (DUF2009)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.0   0.00016     0.045     141     233 ..     418     510 ..     384     528 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                           DUF2009 141 eekealelledklielataeisaekksreeiqkeikekeeaieklakkysskklskeeieqvlysiednnafleanr 217
                                       e+ +  +++ d+  +la ++ +++++  +++++   + e +++++++ +++ ++ +e+ie+vl+s+ed    + ++ 
  gi|336254893|ref|YP_004598000.1| 418 ESGNGFAVVADQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAA 494
                                       556667788888777777777778888889999999999************************************** PP

                           DUF2009 218 epvekllkllekffep 233
                                       + ++++ ++++++   
  gi|336254893|ref|YP_004598000.1| 495 NGISEVARVIDDQTAS 510
                                       ***9999999876654 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0       1.2   3.3e+02      15      46 ..     218     249 ..     210     265 .. 0.81
   2 ?    4.2   0.0      0.26        73       7      64 ..     274     331 ..     269     339 .. 0.91
   3 ?   -0.2   0.0       6.1   1.7e+03      28      64 ..     361     397 ..     337     410 .. 0.63
   4 ?    1.3   0.6       2.2     6e+02       6      35 ..     441     470 ..     422     489 .. 0.51
   5 ?    2.2   0.1       1.1     3e+02       6      46 ..     459     499 ..     454     520 .. 0.63
   6 ?    1.1   0.1       2.4   6.8e+02       2      46 ..     476     513 ..     469     549 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 1.2
                                       S---TTT........HHHHHHH---GGGG-HH CS
                            RecG_N  15 kvlsgkleteelieeikkkleliddpllenee 46 
                                       ++++++  t +l++ei+ ++++i d  l +  
  gi|336254893|ref|YP_004598000.1| 218 DIVNERDATVDLVQEIRTTANEISDGDLTARA 249
                                       6788999999*************998776654 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.26
                                       HHHHHHHTS---TTT........HHHHHHH---GGGG-HHHH.HHHHHHHHHHTTSSS CS
                            RecG_N   7 eelekllkkvlsgkleteelieeikkkleliddplleneevlkeklskfldYikpias 64 
                                       ++le+l   v ++  e+   ++e ++ +++i+ ++ e++ +l++ ++++ +++  +++
  gi|336254893|ref|YP_004598000.1| 274 DNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGMEE 331
                                       78999999999999*******************************9999999887776 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 6.1
                                       ..HHHHHHH---GGGG-HHHH.HHHHHHHHHHTTSSS CS
                            RecG_N  28 eeikkkleliddplleneevlkeklskfldYikpias 64 
                                       +e  + + +i d+l e  + l ek++++ d ++ i +
  gi|336254893|ref|YP_004598000.1| 361 REATEDVVAIGDELRESVDALAEKMNEIGDVVEVISD 397
                                       4455555666677777777777777776666555554 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 2.2
                                       HHHHHHHHTS---TTT........HHHHHH CS
                            RecG_N   6 Leelekllkkvlsgkleteelieeikkkle 35 
                                        ee+ k+l++ + ++ +t + +e  ++++e
  gi|336254893|ref|YP_004598000.1| 441 TEEITKSLDELQAQSEDTTDAVEQSHERIE 470
                                       233334444444444433333333333333 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 1.1
                                       HHHHHHHHTS---TTT........HHHHHHH---GGGG-HH CS
                            RecG_N   6 Leelekllkkvlsgkleteelieeikkkleliddpllenee 46 
                                        + +e++ + +++   ++e ++  +++ ++ +d+     +e
  gi|336254893|ref|YP_004598000.1| 459 TDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISE 499
                                       56677777777777776666666666666666554444333 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHHTS---TTT........HHHHHHH---GGGG-HH CS
                            RecG_N   2 iEeFLeelekllkkvlsgkleteelieeikkkleliddpllenee 46 
                                       iE  L  le ++++v +    ++e+ + i ++   i+       e
  gi|336254893|ref|YP_004598000.1| 476 IEAVLTSLEDIADSVDEAANGISEVARVIDDQTASIE-------E 513
                                       4444555555555555555555555555555444443.......3 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.2     0.062        17      19     114 ..     264     363 ..     244     397 .. 0.55
   2 ?   13.6  11.8   0.00021     0.058      10     159 ..     379     524 ..     369     552 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.062
                             ATG16  19 eliqaynrLldrtsaleaenaklekaaasaks..sksskksakekeasasq....snskqsakiqsleqklaqlree 89 
                                       ++++a n ++d+ ++l  +  +  +++ sa    +   +     + +++      ++ ++ ++ ++  +++a++ +e
  gi|336254893|ref|YP_004598000.1| 264 DVVDAVNGMADNLETLTGRVTEQATEMRSAVDeaN-DAADEIAGNVTEQ-HglleDSVDEMQSFAAGMEEVAAQADE 338
                                       66777777777777777776666555555544321.1111112222222.135555555556666666666666666 PP

                             ATG16  90 laelyksrgelaqrllelneelqkl 114
                                       +  + ++  e  ++ l++ e  ++ 
  gi|336254893|ref|YP_004598000.1| 339 VDSAARTAREAVEQGLDAGEDAREA 363
                                       6666666555555544444444444 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00021
                             ATG16  10 darqekafa..eliqaynrLldrtsaleaenaklekaaasaks.sksskksakekeasasqsnskqsakiqsleqkl 83 
                                       da  ek+++  ++++  ++ +d+t++l+  na++e+a a ++    +  +++ +k+a ++q   + +++i+++ ++l
  gi|336254893|ref|YP_004598000.1| 379 DALAEKMNEigDVVEVISDVADQTNLLAL-NANIEAARAGESGnGFAVVADQVKKLADETQ---EHTEEITKSLDEL 451
                                       5555677777789999999*****99965.5666444443333555556677777777777...4445555555555 PP

                             ATG16  84 aqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDE 159
                                       +++ e+ +++    +++ +r+  + e++++  ++l+  + +++e+ + ++++ + ++d+++ ++e++ ++++++D 
  gi|336254893|ref|YP_004598000.1| 452 QAQSEDTTDA---VEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISEVARVIDDQTASIEELTSTMETVRDR 524
                                       5555555555...678889999999999999999999999999999999999999999999999999999999985 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.3   3.7e+02     285     332 ..     254     301 ..     219     309 .. 0.68
   2 ?    1.3   0.1      0.47   1.3e+02     257     314 ..     265     322 ..     246     346 .. 0.46
   3 ?    1.5   0.7      0.42   1.2e+02     214     320 ..     282     387 ..     269     419 .. 0.49
   4 ?    9.5  13.2    0.0015      0.43     225     325 ..     426     529 ..     330     555 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                             IFT57 285 elsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDgs 332
                                        ++++ +++ ++ + v+ + ++l++++ ++++  +em +  ++++D++
  gi|336254893|ref|YP_004598000.1| 254 DFDALDDDLVDVVDAVNGMADNLETLTGRVTEQATEMRSAVDEANDAA 301
                                       455555555556666666666666666666666666666666666654 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.47
                             IFT57 257 tlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseel 314
                                       +++ ++    +l++     +++  e++  ++e+++  +++ ++v+e+   l++  +e+
  gi|336254893|ref|YP_004598000.1| 265 VVDAVNGMADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEM 322
                                       3333333333333333333333333333444444444444444444444444444444 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.42
                             IFT57 214 tikadakdWrahleqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevk 290
                                       ++ ++a + r+ +++ ++  ++i+ +++e +  l++  ++++     +e+   +   ++++  +  rea e+  ++ 
  gi|336254893|ref|YP_004598000.1| 282 RVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGMEEVAAQA-DEVDSAARTAREAVEQGLDAG 357
                                       4555555666666666666666666666666666666666555444443333322.223333333333333333344 PP

                             IFT57 291 ekykqlsegvseltrelaeiseelekvkqe 320
                                       e+ ++++e v +  +el+e  + l +  +e
  gi|336254893|ref|YP_004598000.1| 358 EDAREATEDVVAIGDELRESVDALAEKMNE 387
                                       444444444444444333333333333333 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0015
                             IFT57 225 hleqmkkhkksieeslpetksqlkklhedisktlekiesrEkyl...nsqleellqeyreaqeelsevkekykqlse 298
                                         +q+kk+ ++ +e+++e++++l++l+ + + t + +e+  +++   ++q+e  l+ +++  ++++e+ + ++++ +
  gi|336254893|ref|YP_004598000.1| 426 VADQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIehaDEQIEAVLTSLEDIADSVDEAANGISEVAR 502
                                       55778888888888888888888888888888888887777766444678888888888888888888888888888 PP

                             IFT57 299 gvseltrelaeiseelekvkqemeerg 325
                                        + ++t   +e++  +e+v  + +e +
  gi|336254893|ref|YP_004598000.1| 503 VIDDQTASIEELTSTMETVRDRSDESE 529
                                       888888888888888887776655544 PP

>> DUF489  Protein of unknown function (DUF489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       8.7   2.4e+03      13      21 ..     333     341 ..     264     408 .. 0.61
   2 ?   13.9   3.5   0.00015     0.042      11     138 ..     425     550 ..     421     554 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 8.7
                                       HHHHHHHHH CS
                            DUF489  13 aklvqqlAr 21 
                                       a++ +++ +
  gi|336254893|ref|YP_004598000.1| 333 AAQADEVDS 341
                                       222222222 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHS---HHHHHHHHHHHH--S-SSHHHHTTSGGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHH CS
                            DUF489  11 qaaklvqqlArtGqadeealetllkslletdpestedvygglanlklGletlleqlekekkkkdaeltryalsllal 87 
                                         a++v++lA + q ++e+++++l+ l ++++++t++v +++++++++ e+++++l++ ++    ++   a ++ ++
  gi|336254893|ref|YP_004598000.1| 425 VVADQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLED-IADSVDEAANGISEV 500
                                       5689************************9999999999999*****************998.6778899999999** PP

                                       HHHHHHSTTHHHHHHHHHHTTHHHHTTS-TTSHHHHHHHHHHHHHHTGGGS CS
                            DUF489  88 erkLsknkealaklgerieqierqlehfdllhenvlanlasiYsdtiSklg 138
                                       +r +  +++ +++l++ +e+++ ++++ +   e+++a+  +  ++ti +l 
  gi|336254893|ref|YP_004598000.1| 501 ARVIDDQTASIEELTSTMETVRDRSDESEAAAERIVAATDH-QNQTIETLM 550
                                       **************************999999999987543.345555555 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.028       7.9     229     278 ..     263     312 ..     254     324 .. 0.81
   2 ?    4.9   0.2     0.043        12       2      57 ..     275     330 ..     274     345 .. 0.66
   3 ?    1.4   0.0      0.51   1.4e+02     224     265 ..     360     401 ..     348     421 .. 0.75
   4 ?    8.6   2.3    0.0032       0.9     223     271 ..     436     484 ..     398     501 .. 0.63
   5 ?    2.8   0.5      0.19        52      20     266 ..     482     535 ..     472     560 .. 0.42

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.028
                              RmuC 229 eeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrka 278
                                        +++++++ + d++e+++ ++++  +++++a+++ ++a+++ +gn++++ 
  gi|336254893|ref|YP_004598000.1| 263 VDVVDAVNGMADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQH 312
                                       56888889999999999999999999999999999999999999988765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.043
                              RmuC   2 qleellkplkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLt 57 
                                       +le+l+ +++e+ ++++ +v+e +++  e  ++++eq + l++   ++++ a+ ++
  gi|336254893|ref|YP_004598000.1| 275 NLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGME 330
                                       68888888999999999998888855555555555555555555555555444443 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.51
                              RmuC 224 qeknaeeiaellgelydkfekfgedleklgkklekaqksydk 265
                                        ++ +e+++  + el + +  ++e+++++g+ +e +++  d+
  gi|336254893|ref|YP_004598000.1| 360 AREATEDVVAIGDELRESVDALAEKMNEIGDVVEVISDVADQ 401
                                       456677788888888888888888888888888777777666 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0032
                              RmuC 223 aqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle 271
                                       + ++++eei + l el  + e  ++ +e+  +++e+a ++++ + ++le
  gi|336254893|ref|YP_004598000.1| 436 ETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLE 484
                                       3455555555555555555555555555555555555555555555554 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.19
                              RmuC  20 kveeeskeeaeeleslkeqlkelqelneqlgdeaenLtkaLknsktrGnwGEvqLerilessgleegeeyetqvslk 96 
                                       ++e+  +++ e+ + +                                                             
  gi|336254893|ref|YP_004598000.1| 482 SLEDIADSVDEAANGI------------------------------------------------------------- 497
                                       3333333333333333............................................................. PP

                              RmuC  97 deegelrpDvvvklpggkklviDsKvpleaYerlveaeddeereealkahaksvkkhikeLseKdYeelesldyvlm 173
                                                                                                                    
  gi|336254893|ref|YP_004598000.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                              RmuC 174 FiPiEsayaealeadpeLleealrkkVvlasPttLlalLrtvamlwrqeaqeknaeeiaellgelydkfekfgedle 250
                                                                                              +e+a+ + +    +e+++ ++e
  gi|336254893|ref|YP_004598000.1| 498 -------------------------------------------------------SEVARVIDDQTASIEELTSTME 519
                                       .......................................................3344444444444444444444 PP

                              RmuC 251 klgkklekaqksydka 266
                                       +++++ ++++ + +++
  gi|336254893|ref|YP_004598000.1| 520 TVRDRSDESEAAAERI 535
                                       4444444444444433 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4    0.0079       2.2      22     105 ..     285     368 ..     266     376 .. 0.80
   2 ?    7.4   3.8     0.013       3.6      18     121 ..     365     464 ..     358     466 .. 0.76
   3 ?    3.5   0.4      0.21        59      16      63 ..     465     515 ..     460     522 .. 0.68
   4 ?    1.6   0.3      0.84   2.3e+02       6      52 ..     511     556 ..     507     559 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0079
                              CdvA  22 eikekleealkklkekakelkeklkkrlkeledqikslekalanlk.isyasGEidEeaYksaieairellesalee 97 
                                       e   ++++a+++ ++ a+e++ +++++ + led +++++++ a ++ +   + E+d +a ++a+ea++++l+  ++ 
  gi|336254893|ref|YP_004598000.1| 285 EQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGMEeVAAQADEVD-SAARTAREAVEQGLDAGEDA 360
                                       55678999*********************************999862555555554.55588888888888887777 PP

                              CdvA  98 keeikkll 105
                                       +e+++ ++
  gi|336254893|ref|YP_004598000.1| 361 REATEDVV 368
                                       77776665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.013
                              CdvA  18 styeeikekleealkklkekakelkeklkkrlkeledqikslekalanlkisyasGEidEeaYksaieairellesa 94 
                                       +++  i  +l+e++++l ek++e+ + ++  ++++ dq   ++ + +n+ i+ a    + + +  + +++++l + +
  gi|336254893|ref|YP_004598000.1| 365 EDVVAIGDELRESVDALAEKMNEIGDVVE-VISDVADQ---TNLLALNANIEAARAGESGNGFAVVADQVKKLADET 437
                                       55566777888888888888888887663.56666665...555566777776655558999*************** PP

                              CdvA  95 leekeeikklleklskleleeeeveet 121
                                       +e  eei k l++l++ +++++++ e+
  gi|336254893|ref|YP_004598000.1| 438 QEHTEEITKSLDELQAQSEDTTDAVEQ 464
                                       **************8777777766665 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.21
                              CdvA  16 pkstyeeikekleealkklkekakelkek...lkkrlkeledqikslekal 63 
                                       ++++ e+  e++e  l+ l++ a+ + e    +++  + ++dq +s+e+++
  gi|336254893|ref|YP_004598000.1| 465 SHERIEHADEQIEAVLTSLEDIADSVDEAangISEVARVIDDQTASIEELT 515
                                       667778888888888777777776665542226677777888888877765 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.84
                              CdvA   6 LeeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkel 52 
                                       +eeL s+ +  +++ +e  e   e + +  +++++ +e+l +r++el
  gi|336254893|ref|YP_004598000.1| 511 IEELTSTMETVRDRSDES-EAAAERIVAATDHQNQTIETLMARVDEL 556
                                       455555555555555553.4444556666677777777777777776 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 ?    0.4   0.0       2.4   6.8e+02      84     119 ..     256     291 ..     218     299 .. 0.67
   2 ?    2.3   0.1      0.61   1.7e+02      22      61 ..     272     311 ..     255     393 .. 0.58
   3 ?    0.4   0.0       2.3   6.6e+02      38      68 ..     372     402 ..     360     412 .. 0.81
   4 ?   11.7   6.5    0.0008      0.23      23     114 ..     427     521 ..     425     524 .. 0.66
   5 ?    8.7   1.5    0.0066       1.8      34     115 ..     473     557 ..     470     559 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.4
                                       HHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  84 keleeeilrlketidaqesnirvLqnvlesneqkiq 119
                                       + l+++ +++ + ++    n++ L++ + ++  ++ 
  gi|336254893|ref|YP_004598000.1| 256 DALDDDLVDVVDAVNGMADNLETLTGRVTEQATEMR 291
                                       567777777778888888888888888888887775 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.61
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkei 61 
                                       ++d l++    v+++ +++++ ++e+++   e+   v+e 
  gi|336254893|ref|YP_004598000.1| 272 MADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQ 311
                                       4444444444444444444444444444444443333332 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 2.3
                                       CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  38 ekleneleeisnstkeaeelvkeikdslrek 68 
                                       ++l+++++ ++++ +e+ ++v+ i+d+  ++
  gi|336254893|ref|YP_004598000.1| 372 DELRESVDALAEKMNEIGDVVEVISDVADQT 402
                                       6889999999999999999999999887665 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.0008
                                       HHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...CCCHHHHH CS
                         Fib_alpha  23 qdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskelee...eilrlket 96 
                                       +d ++k   +++++ e+++++l+e++ +++++ + v++ ++ ++++ ++ +   + +++++++++e    i+++ + 
  gi|336254893|ref|YP_004598000.1| 427 ADQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEaanGISEVARV 503
                                       56667777777788888888888888888888888888888877777777765444444444444311156667777 PP

                                       HHCCHHHHHHHHHHHHHH CS
                         Fib_alpha  97 idaqesnirvLqnvlesn 114
                                       id+q  +i++L++++e+ 
  gi|336254893|ref|YP_004598000.1| 504 IDDQTASIEELTSTMETV 521
                                       778888888887777665 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0066
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrlketidaqesnirvL 107
                                       ++++e +  +le+i++s  ea + ++e+  ++ ++ +s ++     +++++ s+e e   +r+ +  d+q ++i+ L
  gi|336254893|ref|YP_004598000.1| 473 DEQIEAVLTSLEDIADSVDEAANGISEVARVIDDQTASIEELtstMETVRDRSDESEAAAERIVAATDHQNQTIETL 549
                                       45566666666666666666666666666666666666555511144555555666666667777777888999999 PP

                                       HHHHHHHH CS
                         Fib_alpha 108 qnvlesne 115
                                          +++++
  gi|336254893|ref|YP_004598000.1| 550 MARVDELQ 557
                                       98888765 PP

>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.7     0.067        19     258     332 ..     275     350 ..     269     354 .. 0.81
   2 ?   10.7   3.4    0.0006      0.17     256     334 ..     326     408 ..     308     410 .. 0.68
   3 ?    6.1   4.6     0.015       4.3     224     320 ..     431     527 ..     413     539 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.067
                            DUF677 258 dvenisilverleseiksilktvefAvekeenea.avklaleeikkkvekltekieevgeeaakcskliakarlvv 332
                                       ++e++   v +  +e++s +  +++A ++ + ++ + +  le+  ++++ +   +eev  +a++  + +++ar  v
  gi|336254893|ref|YP_004598000.1| 275 NLETLTGRVTEQATEMRSAVDEANDAADEIAGNVtEQHGLLEDSVDEMQSFAAGMEEVAAQADEVDSAARTAREAV 350
                                       567778888888899999999999999887755414455678888999*******************999999876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0006
                            DUF677 256 kkdvenisilverleseiksilktvefAvekeen....eaavklaleeikkkvekltekieevgeeaakcskliaka 328
                                          +e++  + ++++s  +   ++ve+  + +e+     ++v+   +e+++ v+ l ek++e+g+ ++  s ++ ++
  gi|336254893|ref|YP_004598000.1| 326 AAGMEEVAAQADEVDSAARTAREAVEQGLDAGEDareaTEDVVAIGDELRESVDALAEKMNEIGDVVEVISDVADQT 402
                                       34455666666666666666666665555443321100235666669*****************************9 PP

                            DUF677 329 rlvvLq 334
                                        l +L+
  gi|336254893|ref|YP_004598000.1| 403 NLLALN 408
                                       999885 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.015
                            DUF677 224 gkwvasawkkyeealkrqkeivssmekgievakkdvenisilverleseiksilktvefAvekeen.eaavklalee 299
                                        k +++  ++ ee  k   e+  + e  + + ++  e+i+   e++e + +s+   ++  v++ +n   +v  ++++
  gi|336254893|ref|YP_004598000.1| 431 KKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIAD-SVDEAANgISEVARVIDD 506
                                       4555566666666667777777777776666666666666666666666666554444.344444413589999999 PP

                            DUF677 300 ikkkvekltekieevgeeaak 320
                                        +  +e+lt+++e v ++ ++
  gi|336254893|ref|YP_004598000.1| 507 QTASIEELTSTMETVRDRSDE 527
                                       999999999999999887766 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.23        63       8      80 ..     277     348 ..     252     407 .. 0.70
   2 ?    8.4   5.6    0.0039       1.1       7      86 ..     430     515 ..     424     520 .. 0.62
   3 ?    4.4   0.3     0.065        18       6      58 ..     506     558 ..     501     560 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.23
                             TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80 
                                       e+ + ++ e+a+e+++ ++e +   ++++ ++++q+  l++  ++++++ + + ee + +++e+++  +++++
  gi|336254893|ref|YP_004598000.1| 277 ETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGM-EEVAAQADEVDSAARTARE 348
                                       44455566666666666666666666666666666666666666666666664.3444555555544444444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0039
                             TMPIT   7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkeelke 77 
                                       ++k ++e +e+ +e++++l+el+++ ++++ ++++ ++r+++ +++++ + +s++      +e ++ ++e+++ +++
  gi|336254893|ref|YP_004598000.1| 430 VKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEdiadsvDEAANGISEVARVIDD 506
                                       55556666677777777777777777777777777777777777777777766543333334555566666666666 PP

                             TMPIT  78 rkkvlkeve 86 
                                       ++++++e+ 
  gi|336254893|ref|YP_004598000.1| 507 QTASIEELT 515
                                       666666555 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.065
                             TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkk 58 
                                       + + +++el +t ++++ +++e ++  ++++ ++++q++ ++ l +++++l++
  gi|336254893|ref|YP_004598000.1| 506 DQTASIEELTSTMETVRDRSDESEAAAERIVAATDHQNQTIETLMARVDELQT 558
                                       55678899999999*****************************9999999886 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 ?    3.4   0.3      0.41   1.2e+02       5      48 ..     264     303 ..     218     335 .. 0.57
   2 ?   11.7   0.2     0.001      0.29       7      73 ..     336     401 ..     325     416 .. 0.83
   3 ?   -0.6  13.9       7.2     2e+03       3      91 ..     423     514 ..     421     559 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.41
                      Syntaxin-6_N   5 evkeeVqkslnkaeslyrrwerlledtssstseeldetrteLrk 48 
                                       +v + V+  ++++e+l +r ++  ++     ++ +de+++   +
  gi|336254893|ref|YP_004598000.1| 264 DVVDAVNGMADNLETLTGRVTEQATE----MRSAVDEANDAADE 303
                                       34444444455555555555432222....22233333333333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.001
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpsk 73 
                                       ++eV +++++a++ +++  +  ed++++ +e++    +eLr++++ + ++++++ ++v++++   ++
  gi|336254893|ref|YP_004598000.1| 336 ADEVDSAARTAREAVEQGLDAGEDAREA-TEDVVAIGDELRESVDALAEKMNEIGDVVEVISDVADQ 401
                                       5788888888888888887777777665.9*****************************99875544 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 7.2
                      Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrwe.rlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpskfki 76 
                                       F +v+++V+k ++++++  ++ + +l e++ +  +t++ +++ ++ ++ a ++ie  l  Le+  + v +  +  + 
  gi|336254893|ref|YP_004598000.1| 423 FAVVADQVKKLADETQEHTEEITkSLDELQAQseDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISE 499
                                       67778888888887777777774233333333223677777777777777777777666666666555554444444 PP

                      Syntaxin-6_N  77 dekelsrrrafveev 91 
                                        ++ ++ + a +ee+
  gi|336254893|ref|YP_004598000.1| 500 VARVIDDQTASIEEL 514
                                       444555555555555 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 ?   11.1   0.6    0.0011      0.32      56     114 ..     261     321 ..     256     343 .. 0.77
   2 ?    2.4   0.3      0.55   1.5e+02      69     113 ..     320     364 ..     312     389 .. 0.52
   3 ?    3.3   0.2      0.28        79      69     119 ..     358     408 ..     350     415 .. 0.81
   4 ?    5.2   2.9     0.077        21      72     123 ..     431     484 ..     421     494 .. 0.46
   5 ?    3.8   1.1      0.21        59      69     119 ..     474     524 ..     471     558 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0011
                              COG2  56 dFvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr..e 114
                                       d v++ ++  g+ ++le+++  +++  ++++s++++ +++  e+ +++ e+  l e +  e
  gi|336254893|ref|YP_004598000.1| 261 DLVDVVDAVNGMADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSvdE 321
                                       479999999***************************************9998665544432 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.55
                              COG2  69 eeleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                       +e++ +   ++++  + ++v ++   ++e+ve+ l++ ++++e+ 
  gi|336254893|ref|YP_004598000.1| 320 DEMQSFAAGMEEVAAQADEVDSAARTAREAVEQGLDAGEDAREAT 364
                                       334444444445555555555555556666666666666666555 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.28
                              COG2  69 eeleevesplaaarkkvesvreklsereeeveskleeakeleekrellkll 119
                                       e+ +e + ++ a+ +++++ +++l+e+++e+ + +e  ++++++ +ll l 
  gi|336254893|ref|YP_004598000.1| 358 EDAREATEDVVAIGDELRESVDALAEKMNEIGDVVEVISDVADQTNLLALN 408
                                       556777788889999999999999999999999999999998888887665 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.077
                              COG2  72 eevesplaaarkkvesvreklsereeeveskleeakeleekr..ellklllkld 123
                                       +++  + ++ ++++++  ++l++++e+ ++ +e+  e  e+   ++  +l +l+
  gi|336254893|ref|YP_004598000.1| 431 KKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHAdeQIEAVLTSLE 484
                                       444445555555555555555555555555554444433333332222222222 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.21
                              COG2  69 eeleevesplaaarkkvesvreklsereeeveskleeakeleekrellkll 119
                                       e++e v ++l+ + + v+++ + +se  + ++++ +  +el+++ e +++ 
  gi|336254893|ref|YP_004598000.1| 474 EQIEAVLTSLEDIADSVDEAANGISEVARVIDDQTASIEELTSTMETVRDR 524
                                       566666666666666666666666666666666666555555555444433 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       2.1   5.8e+02      41      98 ..     267     323 ..     231     354 .. 0.71
   2 ?    8.9   0.7    0.0067       1.9      64      98 ..     426     460 ..     423     508 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 2.1
                          Gp-FAR-1  41 ellaalKkkspaLyekaeklqaklkekvdkLspeakeFvkkliakgrkleaqvlagek 98 
                                       ++++ + +  ++L +++ +  ++++  vd+ +++a e + ++ ++   le+  +++++
  gi|336254893|ref|YP_004598000.1| 267 DAVNGMADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDS-VDEMQ 323
                                       5666777777889999999999999999999999999999976555444444.44444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0067
                          Gp-FAR-1  64 lkekvdkLspeakeFvkkliakgrkleaqvlagek 98 
                                       + ++v+kL +e++e ++++ +   +l+aq+ +   
  gi|336254893|ref|YP_004598000.1| 426 VADQVKKLADETQEHTEEITKSLDELQAQSEDTTD 460
                                       678*****************999999999765433 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.1    0.0016      0.44      30     121 ..     268     354 ..     255     370 .. 0.71
   2 ?    1.6   4.8      0.96   2.7e+02     121     144 ..     426     449 ..     355     463 .. 0.57
   3 ?    8.4   8.0    0.0077       2.2      41     119 ..     429     506 ..     417     524 .. 0.80
   4 ?    0.2   0.3       2.5     7e+02     100     127 ..     525     552 ..     509     559 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0016
                         ApoLp-III  30 nsenlvdqlkqvikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqkl 106
                                        +++++d+l+++ + ++e+++    e+ +a++e++++  e+a +++e++  ++ +++e+q ++ +g ++++ +++++
  gi|336254893|ref|YP_004598000.1| 268 AVNGMADNLETLTGRVTEQAT----EMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQ-SFAAGMEEVAAQADEV 339
                                       456666666666666666665....556999999***********************997.5777777666666665 PP

                         ApoLp-III 107 aeslkensqeakekl 121
                                       +++   + ++++++l
  gi|336254893|ref|YP_004598000.1| 340 DSAARTAREAVEQGL 354
                                       555555544444444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.96
                         ApoLp-III 121 lakaikqayddaveaaqklakqLk 144
                                       +a+ +k++ d+++e +++++k+L 
  gi|336254893|ref|YP_004598000.1| 426 VADQVKKLADETQEHTEEITKSLD 449
                                       455555555555555555555554 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0077
                         ApoLp-III  41 vikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslkensqea 117
                                         k+l +e +++++e++++l+e++++ e t+d +++ + e  + a+e  e v ++++ ++ +++++a+ ++e ++ +
  gi|336254893|ref|YP_004598000.1| 429 QVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQ-SHERIEHADEQIEAVLTSLEDIADSVDEAANGISEVARVI 504
                                       45667777888999999****************999.5677788999999999999999999999999999987766 PP

                         ApoLp-III 118 ke 119
                                        +
  gi|336254893|ref|YP_004598000.1| 505 DD 506
                                       54 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 2.5
                         ApoLp-III 100 vkesqklaeslkensqeakeklakaikq 127
                                         es+++ae++ +++   ++ +++++  
  gi|336254893|ref|YP_004598000.1| 525 SDESEAAAERIVAATDHQNQTIETLMAR 552
                                       4688888888888888888888877755 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 ?    3.0   0.1      0.44   1.2e+02      47      83 ..     256     292 ..     221     294 .. 0.74
   2 ?    4.2   0.2      0.19        52      51      61 ..     285     295 ..     250     318 .. 0.57
   3 ?    1.9   4.3      0.97   2.7e+02      14      81 ..     281     350 ..     273     353 .. 0.54
   4 ?    1.7   0.6       1.1     3e+02      54      71 ..     372     389 ..     328     403 .. 0.60
   5 ?    6.2   1.2     0.043        12      38      80 ..     412     454 ..     374     458 .. 0.68
   6 ?   11.0   3.5    0.0014      0.39      12      82 ..     426     498 ..     422     502 .. 0.76
   7 ?    3.2   0.9      0.36     1e+02       7      39 ..     526     558 ..     520     560 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  47 dafqaefeewkqaaqklvdaLeeisealkqaanafed 83 
                                       da ++ +  +  a++ ++d+Le+++  +++ a+++++
  gi|336254893|ref|YP_004598000.1| 256 DALDDDLVDVVDAVNGMADNLETLTGRVTEQATEMRS 292
                                       4445555555666777777777777777777777776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHH CS
                            WXG100  51 aefeewkqaaq 61 
                                       ++ +e++ a++
  gi|336254893|ref|YP_004598000.1| 285 EQATEMRSAVD 295
                                       23334444444 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.97
                                       HHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHC..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  14 arfqkqaeeledelqrlkaevdalqsgWsGaaa..dafqaefeewkqaaqklvdaLeeisealkqaanaf 81 
                                        r+ +qa+e+++++++ +   d+++++   + +  +   +e++ + +++++++++ +e+ +a ++a +a+
  gi|336254893|ref|YP_004598000.1| 281 GRVTEQATEMRSAVDEANDAADEIAGNVTEQHGllEDSVDEMQSFAAGMEEVAAQADEVDSAARTAREAV 350
                                       5555555555555555555555555554444443345556666666666666666666666666665555 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHH CS
                            WXG100  54 eewkqaaqklvdaLeeis 71 
                                       +e++++++ l+++++ei+
  gi|336254893|ref|YP_004598000.1| 372 DELRESVDALAEKMNEIG 389
                                       244444444444444444 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.043
                                       GCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  38 qsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaana 80 
                                       +++  G++++ f+ + +++k+ a++ ++  eei+++l++  ++
  gi|336254893|ref|YP_004598000.1| 412 EAARAGESGNGFAVVADQVKKLADETQEHTEEITKSLDELQAQ 454
                                       5555677777777777777777777777777777777766555 PP

  == domain 6  score: 11.0 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCGCGCT..HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  12 aaarfqkqaeeledelqrlkaevdalqsgWs..GaaadafqaefeewkqaaqklvdaLeeisealkqaanafe 82 
                                       +a +++k a+e ++  +++ +++d+lq++ +   +a ++ ++ +e  +++++ + + Le+i++++++aan  +
  gi|336254893|ref|YP_004598000.1| 426 VADQVKKLADETQEHTEEITKSLDELQAQSEdtTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGIS 498
                                       46666666666666666666666666666552246899999999999999****************9999765 PP

  == domain 7  score: 3.2 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGC CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdalqs 39 
                                       +e ++aa r+ ++ ++  + +++l+a vd+lq 
  gi|336254893|ref|YP_004598000.1| 526 DESEAAAERIVAATDHQNQTIETLMARVDELQT 558
                                       566899************************965 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  17.6    0.0043       1.2     281     468 ..     325     519 ..     249     523 .. 0.73
   2 ?    6.2  14.0     0.012       3.5     320     451 ..     427     558 ..     393     559 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0043
                            AAA_13 281 feekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksve. 356
                                       f++ +e+    +++v+s+ + + e ++++ d+        ed  e+++   a+ ++L++  +al +K +e+   ve 
  gi|336254893|ref|YP_004598000.1| 325 FAAGMEEVAAQADEVDSAARTAREAVEQGLDA-------GEDAREATEDVVAIGDELRESVDALAEKMNEIGDVVEv 394
                                       23333333333344444433333333333333.......23344444444555555666666666666666666663 PP

                            AAA_13 357 lesvkakie..............sikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkyk 419
                                       +++v+++++              +  +  a + ++++k    +++++ee ++  ++l++   e+ ++++++ ++ ++
  gi|336254893|ref|YP_004598000.1| 395 ISDVADQTNllalnanieaaragESGNGFAVVADQVKKLADETQEHTEEITKSLDELQA-QSEDTTDAVEQSHERIE 470
                                       46666666566666666688777556667788899999999999999999999999998.66778899999999999 PP

                            AAA_13 420 klekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLk 468
                                        ++++ie + ++l+++++ + ++++ i+e  + + d++ ++ee+++ ++
  gi|336254893|ref|YP_004598000.1| 471 HADEQIEAVLTSLEDIADSVDEAANGISEVARVIDDQTASIEELTSTME 519
                                       9999999999999999999999999999999999999999999998876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.012
                            AAA_13 320 eedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeak 396
                                       ++++++l +e+++++e++++  ++l+a  ++      +e++ ++ie++ ++++++ ++ ++    v++ ++  +e++
  gi|336254893|ref|YP_004598000.1| 427 ADQVKKLADETQEHTEEITKSLDELQAQSEDTTD--AVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISEVA 501
                                       5667888888888888888888888888888777..45566677777777777777777777777777777666666 PP

                            AAA_13 397 kklelhl..veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLek 451
                                         +  +   +eel+s +++  +  ++ e+a+e   ++ + +++ +++l +++ eL++
  gi|336254893|ref|YP_004598000.1| 502 RVIDDQTasIEELTSTMETVRDRSDESEAAAERIVAATDHQNQTIETLMARVDELQT 558
                                       666555433688999999999999999999999999999999999999999999996 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1       2.3   6.5e+02      35      69 ..      61      95 ..      50     100 .. 0.72
   2 ?   13.1   0.7   0.00037       0.1       1      46 [.     272     314 ..     272     319 .. 0.91
   3 ?    7.7   4.2     0.018       4.9      10      81 ..     320     386 ..     315     394 .. 0.77
   4 ?    7.7   4.3     0.017       4.9       6      84 ..     410     494 ..     406     500 .. 0.80
   5 ?    2.2   0.6      0.91   2.5e+02       2      36 ..     511     545 ..     510     553 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 2.3
                     T7SS_ESX_EspC 35 gasaavldshGpicaatndavaaaeaarraageal 69
                                      +a+ +  +  G+ + + ++av++a ++rra +++l
  gi|336254893|ref|YP_004598000.1| 61 PATGEGDEEVGTDGEPDAAAVNDAGTLRRAGYQQL 95
                                      4444444556667789999**********999987 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00037
                     T7SS_ESX_EspC   1 mtdnLsVdpdhlrelaakhdevaaeiasavaaaagasaavldshGp 46 
                                       m+dnL+  ++++ e a++++++++e+++a++     + +v+++hG 
  gi|336254893|ref|YP_004598000.1| 272 MADNLETLTGRVTEQATEMRSAVDEANDAADEI---AGNVTEQHGL 314
                                       99*************************999999...7788888886 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.018
                     T7SS_ESX_EspC  10 dhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteLadkLr 81 
                                       d+++++aa ++evaa+++ + +aa +++++ +++    +++   + ++a ++  a g++l+++ + La+k++
  gi|336254893|ref|YP_004598000.1| 320 DEMQSFAAGMEEVAAQADEVDSAA-RTAREAVEQ----GLDAGEDAREATEDVVAIGDELRESVDALAEKMN 386
                                       799****************99999.666666666....5677777777777777777777777777777654 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.017
                     T7SS_ESX_EspC   6 sVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarr......aagealaaasteL 76 
                                       ++++++  e +  +  va++++++++ +++ ++++++s   + a++ d+ +a+e++++      +++ea+ ++++++
  gi|336254893|ref|YP_004598000.1| 410 NIEAARAGESGNGFAVVADQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHEriehadEQIEAVLTSLEDI 486
                                       56677777888999999999999999999999999999999999999999999887642222226888888899999 PP

                     T7SS_ESX_EspC  77 adkLraAA 84 
                                       ad +++AA
  gi|336254893|ref|YP_004598000.1| 487 ADSVDEAA 494
                                       99999998 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.91
                     T7SS_ESX_EspC   2 tdnLsVdpdhlrelaakhdevaaeiasavaaaaga 36 
                                       +++L+ + + +r  +++ +++a++i +a++  +++
  gi|336254893|ref|YP_004598000.1| 511 IEELTSTMETVRDRSDESEAAAERIVAATDHQNQT 545
                                       578999999*******************9988544 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 ?    0.3   0.3       2.5   7.1e+02      14      28 ..     442     456 ..     429     471 .. 0.67
   2 ?   -0.9   0.0       5.9   1.7e+03       3      21 ..     466     484 ..     464     489 .. 0.84
   3 ?    8.8   0.1    0.0058       1.6       4      33 ..     509     538 ..     508     557 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2.5
                       MCC-bdg_PDZ  14 elLsltleerkqqse 28 
                                       e ++++l+e ++qse
  gi|336254893|ref|YP_004598000.1| 442 EEITKSLDELQAQSE 456
                                       556666666666665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 5.9
                       MCC-bdg_PDZ   3 ksrIeeLkaqnelLsltle 21 
                                       ++rIe+   q e +  +le
  gi|336254893|ref|YP_004598000.1| 466 HERIEHADEQIEAVLTSLE 484
                                       6899999999999998887 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0058
                       MCC-bdg_PDZ   4 srIeeLkaqnelLsltleerkqqseeLsld 33 
                                       ++IeeL++++e ++  ++e+ + +e+++  
  gi|336254893|ref|YP_004598000.1| 509 ASIEELTSTMETVRDRSDESEAAAERIVAA 538
                                       69************************9976 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   4.7      0.41   1.1e+02      34     118 ..     287     381 ..     272     405 .. 0.71
   2 ?    3.4   0.0      0.23        65      42      67 ..     372     392 ..     370     416 .. 0.80
   3 ?   11.3   4.8    0.0009      0.25      27     103 ..     420     494 ..     402     527 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH...........C-SSSSCS.SHHHHHHHHHHHHHHHHHH CS
                          Ferritin  34 aeffdeqaeeerehadklaerilalGgtpvltraelee...........ieapkefg.sveevleaalehekkvtes 98 
                                       a +++  ++e  + ad++a  + +  g    +  e +             +++++ + +++e++e+ l++ +++ e+
  gi|336254893|ref|YP_004598000.1| 287 ATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSfaagmeevaaqADEVDSAArTAREAVEQGLDAGEDAREA 363
                                       56778888888888888888888888866666555555777777766565555554449999999999999999999 PP

                                       HHHHHHHHHHTT-HHHHHHH CS
                          Ferritin  99 lrelielaeeegDpatadfl 118
                                        ++++++ +e     ++d l
  gi|336254893|ref|YP_004598000.1| 364 TEDVVAIGDEL--RESVDAL 381
                                       99998888876..4444444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHTTS....SHH CS
                          Ferritin  42 eeerehadklaerilalGgtpvltra 67 
                                       +e re  d+lae+++++G       +
  gi|336254893|ref|YP_004598000.1| 372 DELRESVDALAEKMNEIGD-----VV 392
                                       799***************8.....33 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0009
                                       STTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS.CSSHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  27 gpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke.fgsveevleaalehekkvteslrel 102
                                       g g+  +a   ++ a+e +eh +++ + + +l ++   t+  +e+     e  + ++e++ea+l++ +++ +s+ e+
  gi|336254893|ref|YP_004598000.1| 420 GNGFAVVADQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQ---SHErIEHADEQIEAVLTSLEDIADSVDEA 493
                                       889999****************************33333333333...22224455555555555555555555544 PP

                                       H CS
                          Ferritin 103 i 103
                                       +
  gi|336254893|ref|YP_004598000.1| 494 A 494
                                       3 PP

>> P4Ha_N  Prolyl 4-Hydroxylase alpha-subunit, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.14        41      15     114 ..     265     367 ..     260     372 .. 0.63
   2 ?    4.1   2.8      0.15        43       4      54 ..     429     479 ..     426     482 .. 0.69
   3 ?    3.7   0.1       0.2        56       1      55 [.     482     536 ..     482     555 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.14
                            P4Ha_N  15 lveeLesyieeeekkleklkrfleeleeehesakedkeeylsnPlnaFklikRltsdWeeleklleesese.elieq 90 
                                       +v++++  ++++e  + ++ + ++e++++ ++a++ ++e ++n   +  l+   + + + +   +ee  ++ ++ ++
  gi|336254893|ref|YP_004598000.1| 265 VVDAVNGMADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGMEEVAAQaDEVDS 341
                                       55666666777777777777777777777777777778888888888888888888877777777653333122222 PP

                            P4Ha_N  91 l.ealkkrkes.lPteeDlegaakal 114
                                         ++ ++  e+ l   eD ++a++ +
  gi|336254893|ref|YP_004598000.1| 342 AaRTAREAVEQgLDAGEDAREATEDV 367
                                       22455555566666777777776655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.15
                            P4Ha_N   4 dlekLlklErelveeLesyieeeekkleklkrfleeleeehesakedkeey 54 
                                       +++kL +  +e+ ee+++ ++e++++ e+   ++e+  e+ e a+e+ e +
  gi|336254893|ref|YP_004598000.1| 429 QVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAV 479
                                       667777777777777777777777777777777777777666666666655 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.2
                            P4Ha_N   1 SladlekLlklErelveeLesyieeeekkleklkrfleeleeehesakedkeeyl 55 
                                       Sl+d+ + ++   + ++e+ + i+++++ +e+l + +e+++++++++++ +e  +
  gi|336254893|ref|YP_004598000.1| 482 SLEDIADSVDEAANGISEVARVIDDQTASIEELTSTMETVRDRSDESEAAAERIV 536
                                       677888888888899999999********************99988776666655 PP

>> Mobilization_B  Mobilization protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0       1.2   3.3e+02      62      86 ..     225     249 ..     218     253 .. 0.87
   2 ?   13.1   2.9   0.00033     0.093      10      88 ..     266     350 ..     257     355 .. 0.75
   3 ?    1.2   3.2       1.6   4.4e+02      14      81 ..     424     487 ..     407     496 .. 0.48
   4 ?    4.6   5.2      0.14        38       5      81 ..     460     539 ..     457     548 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.2
                    Mobilization_B  62 awvelakelrevaaelakaaqsars 86 
                                       a v+l +e+r +a e+++   +ar+
  gi|336254893|ref|YP_004598000.1| 225 ATVDLVQEIRTTANEISDGDLTARA 249
                                       778999************9999996 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00033
                    Mobilization_B  10 srginelaeeieplaqsmatladearqviaevqqaseeqaaewlkaq...rqagaawvela...kelrevaaelaka 80 
                                          +n +a+++e l+  ++  a e r  + e+++a++e a + +++    ++++   +  a    e+ + a e+ +a
  gi|336254893|ref|YP_004598000.1| 266 VDAVNGMADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHgllEDSVDEMQSFAagmEEVAAQADEVDSA 342
                                       56799***********************************9999886222334444444450005555556689999 PP

                    Mobilization_B  81 aqsarsaa 88 
                                       a++ar a 
  gi|336254893|ref|YP_004598000.1| 343 ARTAREAV 350
                                       99999885 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.6
                    Mobilization_B  14 nelaeeieplaqsmatladearqviaevqqaseeqaaewlkaqrqagaawvelakelrevaaelakaa 81 
                                         +a++++ la+     ++e  + + e q  se+     ++a +q+     ++  ++ +v + l + a
  gi|336254893|ref|YP_004598000.1| 424 AVVADQVKKLADETQEHTEEITKSLDELQAQSEDT----TDAVEQSHERIEHADEQIEAVLTSLEDIA 487
                                       34444444444444444444444444444444433....33334444444444444444444444444 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.14
                    Mobilization_B   5 drvkksrg.inelaeeieplaqsmatla...dearqviaevqqaseeqaaewlkaqrqagaawvelakelrevaael 77 
                                       d v +s   i+   e+ie +  s+  +a   dea + i+ev +  ++q+a+  ++   ++ + ++ + e  ++a  +
  gi|336254893|ref|YP_004598000.1| 460 DAVEQSHErIEHADEQIEAVLTSLEDIAdsvDEAANGISEVARVIDDQTASI-EELTSTMETVRDRSDESEAAAERI 535
                                       66777664166666899*99999876662227999**************996.566789999999988887777777 PP

                    Mobilization_B  78 akaa 81 
                                         a+
  gi|336254893|ref|YP_004598000.1| 536 VAAT 539
                                       6665 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   7.8   0.00045      0.13     239     325 ..     440     523 ..     426     526 .. 0.86
   2 ?   11.8   4.7   0.00035     0.098     237     324 ..     473     557 ..     469     559 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHH CS
                             APG17 239 eledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekiee 315
                                       + e++ k+l+e  ++ e++++++++ +e+ie++ +++ ++l+ le++ + ++e  +    ++e+ +  +++ ++iee
  gi|336254893|ref|YP_004598000.1| 440 HTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAAN---GISEVARVIDDQTASIEE 513
                                       4567777777777777****************************************...888888888889999999 PP

                                       HHHHHHHHHH CS
                             APG17 316 kleeleeLre 325
                                        ++++e +r+
  gi|336254893|ref|YP_004598000.1| 514 LTSTMETVRD 523
                                       9999998775 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00035
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHH CS
                             APG17 237 aaeledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekeki 313
                                       ++++e+V+++l+++++++ +a + +se ++ i+ +++++ ++ +++e+v+++ +e  a   a+e++++ +++++++i
  gi|336254893|ref|YP_004598000.1| 473 DEQIEAVLTSLEDIADSVDEAANGISEVARVIDDQTASIEELTSTMETVRDRSDESEA---AAERIVAATDHQNQTI 546
                                       5799******************************************************...9999999999999999 PP

                                       HHHHHHHHHHH CS
                             APG17 314 eekleeleeLr 324
                                       e+ ++ ++eL 
  gi|336254893|ref|YP_004598000.1| 547 ETLMARVDELQ 557
                                       99999999986 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 ?    5.0   0.3      0.11        31      23      86 ..     274     338 ..     250     344 .. 0.65
   2 ?    4.6   0.2      0.15        41      42      79 ..     370     407 ..     358     411 .. 0.82
   3 ?    8.6   4.9    0.0082       2.3      26      87 ..     431     493 ..     425     500 .. 0.87
   4 ?    2.0   0.5       0.9   2.5e+02       9      56 ..     502     549 ..     495     559 .. 0.42

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.11
                           BLOC1_2  23 klLeklNeaasekykklkdvaaslekkleklnekye.elqpylqqidqiekqvteLeeavseLDe 86 
                                       + Le+l  +++e+ ++++++++++++ ++++      +   + +++d+++   + +ee++++ De
  gi|336254893|ref|YP_004598000.1| 274 DNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTeQHGLLEDSVDEMQSFAAGMEEVAAQADE 338
                                       45666666677777777777777777777776654414444445666666666666666666555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.15
                           BLOC1_2  42 vaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                       + ++l++++++l ek +e+   ++ i ++ +q++ L  
  gi|336254893|ref|YP_004598000.1| 370 IGDELRESVDALAEKMNEIGDVVEVISDVADQTNLLAL 407
                                       5578999999999*******999999999999987765 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0082
                           BLOC1_2  26 eklNeaasekykklkdvaaslekkleklnekyeelqpylqqid.qiekqvteLeeavseLDey 87 
                                       +kl  +++e+ +++++++++l++++e++    e+ ++ +++ d qie+ +t+Le++++ +De 
  gi|336254893|ref|YP_004598000.1| 431 KKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADeQIEAVLTSLEDIADSVDEA 493
                                       678889999999*************9999999988888888864799999**********996 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.9
                           BLOC1_2   9 kyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnek 56 
                                       ++++ ++++  e  +++e++  ++ e  ++ ++++a +  + + ++ +
  gi|336254893|ref|YP_004598000.1| 502 RVIDDQTASIEELTSTMETVRDRSDESEAAAERIVAATDHQNQTIETL 549
                                       444444444444444444444444444444444433333333333333 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 ?    7.4   9.3      0.02       5.6      44     151 ..     258     385 ..     246     388 .. 0.68
   2 ?    7.3   6.1     0.021       5.9      35      91 ..     435     491 ..     388     502 .. 0.60
   3 ?    4.8   1.4      0.13        35      48      97 ..     511     560 ..     507     561 .] 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.02
                                       --STHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHH...........HHTT---------CHHH CS
                           T3SSipB  44 lSdelqtalseakgatddlea....aiekadqaksaadaatkkvdeaqk...........rlkeLaPdePekaklea 105
                                       l d l +++++ +g++d+le       e+a ++ sa+d+a+ ++de+             +++e+   +   a +e+
  gi|336254893|ref|YP_004598000.1| 258 LDDDLVDVVDAVNGMADNLETltgrVTEQATEMRSAVDEANDAADEIAGnvteqhglledSVDEM---QSFAAGMEE 331
                                       55556666666666666666411113455556666777777777776666666666777788888...444566666 PP

                                       HHHHHH...HHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHTXXXXX CS
                           T3SSipB 106 aeqQagaa.adalqadealqKkldaasklseka.......kakekevDdisakv 151
                                          Qa +    a  a ea++  lda + ++e          ++++ vD+++ k+
  gi|336254893|ref|YP_004598000.1| 332 VAAQADEVdSAARTAREAVEQGLDAGEDAREATedvvaigDELRESVDALAEKM 385
                                       667777554556678888899999999999888888899999999999999987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.021
                                       HHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                           T3SSipB  35 kaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlk 91 
                                         +qe+ +++ + l ++  + ++ td++e++ e++++a+ +++a+   ++++  +++
  gi|336254893|ref|YP_004598000.1| 435 DETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVD 491
                                       334445555555555555555555555555555555555555554444444444444 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----- CS
                           T3SSipB  48 lqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPde 97 
                                       +++++s ++ + d  +++ ++a+ + +a d  ++ ++   +r++eL+ d+
  gi|336254893|ref|YP_004598000.1| 511 IEELTSTMETVRDRSDESEAAAERIVAATDHQNQTIETLMARVDELQTDD 560
                                       77899999999999999999999999999999999999999999998775 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1       1.1   3.2e+02      32      95 ..     258     322 ..     248     333 .. 0.75
   2 ?    1.8   0.1       1.2   3.2e+02      61      91 ..     371     398 ..     330     405 .. 0.68
   3 ?    8.4   5.4     0.011         3      45     101 ..     425     492 ..     400     494 .. 0.79
   4 ?    8.9   0.9    0.0072         2      35     101 ..     482     555 ..     479     559 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 1.1
                                       BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH........HHHHHHHHHHHH CS
                             DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln.kvdetleliletLqki 95 
                                        + +L ++ + v+    +++ l+  v++q  +++    e +   +e+  +v e   l+ ++++++
  gi|336254893|ref|YP_004598000.1| 258 LDDDLVDVVDAVNGMADNLETLTGRVTEQATEMRSAVDEANDAADEIAgNVTEQHGLLEDSVDEM 322
                                       56788888888888888999999999999988888877777766667666666666666666655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHH.......HHHHHHHH CS
                             DUF16  61 gekikelkveqkaqgeelnkvdetlelilet 91 
                                       g   +el++ ++a  e++n++++ +e+i + 
  gi|336254893|ref|YP_004598000.1| 371 G---DELRESVDALAEKMNEIGDVVEVISDV 398
                                       3...456778888888888887777777655 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.011
                                       ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..................HHHHHHHHHHHHHHHHHH CS
                             DUF16  45 klgeqinkleqkvekqgekikelkveqkaqgeeln...........kvdetleliletLqkinkRlDs 101
                                       +   q++kl+++ ++ +e+i++   e +aq+e+             + de +e +l +L++i + +D+
  gi|336254893|ref|YP_004598000.1| 425 VVADQVKKLADETQEHTEEITKSLDELQAQSEDTTdaveqsherieHADEQIEAVLTSLEDIADSVDE 492
                                       56678888888888888888888888888888777778888887778999999999999999988875 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0072
                                       HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHH CS
                             DUF16  35 rLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln.......kvdetleliletLqkinkRlDs 101
                                        L++i + vd   + i++++  ++ q++ i+el+ ++++ +++ +       ++  + +   +t++++  R+D+
  gi|336254893|ref|YP_004598000.1| 482 SLEDIADSVDEAANGISEVARVIDDQTASIEELTSTMETVRDRSDeseaaaeRIVAATDHQNQTIETLMARVDE 555
                                       68999999*******************************99988844444443333333334555555555555 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   8.2     0.016       4.4     241     404 ..     350     521 ..     287     558 .. 0.43

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.016
                          Prominin 241 lerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcl... 314
                                       +e+ l++ ++a+e+ e v +   eLr+s + L + ++++ + + +++s++  +++   ++ + e+ +   s +    
  gi|336254893|ref|YP_004598000.1| 350 VEQGLDAGEDAREATEDVVAIGDELRESVDALAEKMNEIGD-VVEVISDVADQTNLLALNANIEAARAGESGNGfav 425
                                       44444444444444444444444444444444444444432.22233332333333333333333333333222233 PP

                          Prominin 315 ..dqlpnvdevlealeevletnlssivkeglarlneipekvk..nqtaevvpdlkkalakgreqikklakkip..re 385
                                         dq++++ ++ ++ +e + ++l+++  ++ ++ +++++  +  ++ +e ++ +  +l+++ + +++ a+ i    +
  gi|336254893|ref|YP_004598000.1| 426 vaDQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHEriEHADEQIEAVLTSLEDIADSVDEAANGISevAR 502
                                       33444333333333333333333333333333333333222111223333333333333333333333333321112 PP

                          Prominin 386 aldavisdlenterssktf 404
                                       ++d+ + ++e++ ++++t 
  gi|336254893|ref|YP_004598000.1| 503 VIDDQTASIEELTSTMETV 521
                                       2222222222222222222 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.56   1.6e+02      27     116 ..     287     379 ..     272     397 .. 0.68
   2 ?    9.8   1.2    0.0037         1      18      74 ..     439     495 ..     427     504 .. 0.81
   3 ?    0.2   0.1       3.4   9.6e+02      24      48 ..     508     532 ..     496     556 .. 0.45

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.56
                           Goodbye  27 vedllkqieaekdkfeefr....ekkeklkealkkilspiqllggiaaqgasmaFgPaslcfnAvsyLikaakkvse 99 
                                         ++++ +++++d+ +e      e++  l++++ ++ s+   + ++aaq+   +  +a +   Av   ++a+++ +e
  gi|336254893|ref|YP_004598000.1| 287 ATEMRSAVDEANDAADEIAgnvtEQHGLLEDSVDEMQSFAAGMEEVAAQA-DEVDSAARTAREAVEQGLDAGEDARE 362
                                       55666666666666666554455666777777777777777777777774.44447788888888888888888888 PP

                           Goodbye 100 iydaieeLfeelsdfle 116
                                       + +++ ++ +el++++ 
  gi|336254893|ref|YP_004598000.1| 363 ATEDVVAIGDELRESVD 379
                                       88887777776666554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0037
                           Goodbye  18 dealkelssvedllkqieaekdkfeefrekkeklkealkkilspiqllggiaaqgas 74 
                                       +++ +  +s+++l++q e+ +d+ e+++e+ e++ e ++ +l+ ++ +++ + ++a+
  gi|336254893|ref|YP_004598000.1| 439 EHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAAN 495
                                       3335556789999999999999999999*******************9999998886 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 3.4
                           Goodbye  24 lssvedllkqieaekdkfeefrekk 48 
                                        +s+e+l++ +e  +d+ +e+++  
  gi|336254893|ref|YP_004598000.1| 508 TASIEELTSTMETVRDRSDESEAAA 532
                                       2333333333333333333333222 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.2     0.053        15      47     150 ..     272     386 ..     229     409 .. 0.58
   2 ?    8.2  12.2     0.006       1.7       4     120 ..     429     547 ..     425     561 .] 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.053
                           DUF4795  47 lkkqieelekvk.adkeeveeelaekadkea.Latkvsrdq..fDeakkeLekmleellekleeqeealkkaldtLq 119
                                       + + +e l  +  +  +e+  +++e+ d  + +a  v +++  ++ +++e++  +  + e + +q +++++a  t +
  gi|336254893|ref|YP_004598000.1| 272 MADNLETLTGRVtEQATEMRSAVDEANDAADeIAGNVTEQHglLEDSVDEMQSFAAGM-EEVAAQADEVDSAARTAR 347
                                       4444444433221444455555555555432245555444455555555555444443.445566666666666666 PP

                           DUF4795 120 eelkekld........rlelepLkeqleerlkelqkelq 150
                                       e++++ ld          ++  + ++l e +++l+++++
  gi|336254893|ref|YP_004598000.1| 348 EAVEQGLDagedareaTEDVVAIGDELRESVDALAEKMN 386
                                       777777776666655544455555555555555554444 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.006
                           DUF4795   4 nsaellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekad.keaLat 79 
                                       ++++l ++ qe+ e++ ++l++l+ + +++ +  e+ ++ +e+  +qie+  ++ +d   +++ ++e+a+  + +a+
  gi|336254893|ref|YP_004598000.1| 429 QVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLED---IADSVDEAANgISEVAR 502
                                       5678899999*********************************************99...9*****99963789*** PP

                           DUF4795  80 kvsrdqfDeakkeLekmleellekleeqeealkkaldtLq......e 120
                                       ++++++  ++++eL+  +e ++++++e e+a ++++          e
  gi|336254893|ref|YP_004598000.1| 503 VIDDQT--ASIEELTSTMETVRDRSDESEAAAERIVAATDhqnqtiE 547
                                       **6665..899999**********99999998888766555554444 PP

>> TMP_2  Prophage tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   8.0    0.0079       2.2      86     197 ..     293     406 ..     265     412 .. 0.70
   2 ?    4.1   4.0      0.11        32      90     195 ..     437     520 ..     429     555 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0079
                             TMP_2  86 AyykgakearefnkaliltGnaaGlTasqLeamaesiaeagg...tqaaaaealaalastGkiggeqlervakaaae 159
                                       A+ ++++ a+e+   ++   +    +++++++ a+ ++e++     + +aa ++ + ++ G  +ge+ +++++ +++
  gi|336254893|ref|YP_004598000.1| 293 AVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGMEEVAAqadEVDSAARTAREAVEQGLDAGEDAREATEDVVA 369
                                       55556666666666666666666667777777666554443311245566666666666666666777777777777 PP

                             TMP_2 160 lekatGqsvdetakelaklakdPvkaaeklneqlhfLt 197
                                       + + + +svd++a+++++++ d v+ ++++++q ++L 
  gi|336254893|ref|YP_004598000.1| 370 IGDELRESVDALAEKMNEIG-DVVEVISDVADQTNLLA 406
                                       77777889*******99997.78999999999999885 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.11
                             TMP_2  90 gakearefnkaliltGnaaGlTasqLeamaesiaeaggtqaaaaealaalastGkiggeqlervakaaaelekatGq 166
                                        ++ ++e++k+l  +  ++  T++ +e+  e+i+ a ++++a+ ++l  +a++   +++ +++va++          
  gi|336254893|ref|YP_004598000.1| 437 TQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISEVARVI--------- 504
                                       45556666666666666666666666666666666666666666666666666666666555555543......... PP

                             TMP_2 167 svdetakelaklakdPvkaaeklneqlhf 195
                                                    +d +  +e+l++++++
  gi|336254893|ref|YP_004598000.1| 505 -------------DDQTASIEELTSTMET 520
                                       .............3333333333333333 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.9    0.0057       1.6      10     103 ..     273     366 ..     266     388 .. 0.83
   2 ?    5.0   9.2     0.086        24      53     112 ..     427     487 ..     387     493 .. 0.81
   3 ?    3.8  17.4       0.2        56       8     121 ..     428     545 ..     423     556 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0057
                        TPR_MLP1_2  10 ikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakae 86 
                                       +++l++   + +++++++++ + +  + a e   +  ++  + ++ v+e+q++ + ++e+ a++ e+ ++a +a+++
  gi|336254893|ref|YP_004598000.1| 273 ADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAAGMEEVAAQADEVDSAARTAREA 349
                                       5566777778889999999999999999999999999999999********************************** PP

                        TPR_MLP1_2  87 leeseesweeqkeelek 103
                                       +e+   + e  +e+ e+
  gi|336254893|ref|YP_004598000.1| 350 VEQGLDAGEDAREATED 366
                                       **988888887777665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.086
                        TPR_MLP1_2  53 aedvkelqalreel.nelkaeiaelkaeaesakaeleeseesweeqkeelekelselekri 112
                                       a++vk+l++  +e+ +e+++ + el+a+ e+++ ++e+s e +e   e++e  l++le   
  gi|336254893|ref|YP_004598000.1| 427 ADQVKKLADETQEHtEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIA 487
                                       6677777765555548888889999999999999999999999999999998888887655 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.2
                        TPR_MLP1_2   8 eeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaed.....vkelqalreelnelkaeiaelkae 79 
                                       +++k+l +e +e++++++k  ++l++q+e +++a +  ++e ++ha++     +++l+++ + ++e+ + i+e+   
  gi|336254893|ref|YP_004598000.1| 428 DQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVE-QSHERIEHADEqieavLTSLEDIADSVDEAANGISEVARV 503
                                       577888999999999999999999999999988866.356666666432222267788888888999********** PP

                        TPR_MLP1_2  80 aesakaeleeseesweeqkeelekelselekriedlneqNkl 121
                                        ++ +a++ee ++ +e+ +++ ++  + +e+ +   ++qN++
  gi|336254893|ref|YP_004598000.1| 504 IDDQTASIEELTSTMETVRDRSDESEAAAERIVAATDHQNQT 545
                                       ****************************************86 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       5.3   1.5e+03      73      93 ..     304     324 ..     267     384 .. 0.55
   2 ?   -0.5   0.0       4.6   1.3e+03      72      91 ..     368     388 ..     314     406 .. 0.58
   3 ?    7.1   1.5     0.021         6      63     116 ..     429     483 ..     425     490 .. 0.86
   4 ?    1.4   0.1       1.2   3.4e+02      33     120 ..     488     522 ..     481     558 .. 0.49

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 5.3
                                       XXXXXXXXXXXXXXXXXXXX- CS
                              COG5  73 vlselksslesLsasyerlks 93 
                                       +  +++++   L+ s++ ++s
  gi|336254893|ref|YP_004598000.1| 304 IAGNVTEQHGLLEDSVDEMQS 324
                                       444444444444444444333 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 4.6
                                       X.XXXXXXXXXXXXXXXXXXX CS
                              COG5  72 s.vlselksslesLsasyerl 91 
                                         + +el++s+++L + ++ +
  gi|336254893|ref|YP_004598000.1| 368 VaIGDELRESVDALAEKMNEI 388
                                       236677777777777766665 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.021
                                       XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHHHH CS
                              COG5  63 hlskskslss.vlselksslesLsasyerlkskvlepyeeaeklqsalkrlhqtl 116
                                       +++k + + + +++e+++sl++L+a  e  +  v + +e++e+  ++++ + ++l
  gi|336254893|ref|YP_004598000.1| 429 QVKKLADETQeHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSL 483
                                       56666666666**********************************9999987765 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 1.2
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHH CS
                              COG5  33 tplkrlnydiqeldkrlrqlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeaeklqsal 109
                                        ++     +i+e+ + ++++                                                     ++++
  gi|336254893|ref|YP_004598000.1| 488 DSVDEAANGISEVARVIDDQ-----------------------------------------------------TASI 511
                                       33344444444444444444.....................................................3333 PP

                                       HHHHHHHHHHH CS
                              COG5 110 krlhqtldLlr 120
                                       + l +t+++ r
  gi|336254893|ref|YP_004598000.1| 512 EELTSTMETVR 522
                                       33333333322 PP

>> Nmad5  Nucleotide modification associated domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2       2.5     7e+02     122     151 ..     316     345 ..     220     356 .. 0.60
   2 ?   11.2   4.6    0.0011      0.31      31     162 ..     352     482 ..     339     487 .. 0.82
   3 ?   -1.3   0.1       7.5   2.1e+03     129     160 ..     519     550 ..     489     558 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2.5
                             Nmad5 122 kvvleadnplvkrfdelekaqeelrekrka 151
                                       + +++  + +++ ++e++++++e+++++ +
  gi|336254893|ref|YP_004598000.1| 316 EDSVDEMQSFAAGMEEVAAQADEVDSAART 345
                                       233333344444444444444555554444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0011
                             Nmad5  31 eradlaeevrldalggkkteaalreiikeieklqsklpkeglstnk..pkstgsvidvnlaGarvelyfngkkletv 105
                                       +  d +e++r +        ++lre + ++ ++++++ +++       ++ +  ++++n++ ar   + ng     v
  gi|336254893|ref|YP_004598000.1| 352 QGLDAGEDAREATEDVVAIGDELRESVDALAEKMNEIGDVVEVISDvaDQTNLLALNANIEAARAGESGNG---FAV 425
                                       5555555555555555556699****************997665555577778888889998899999999...888 PP

                             Nmad5 106 vlasvdeiaketkslpkvvleadnplvkrfdelekaqeelrekrkaikatVtavlns 162
                                       v ++v+++a et++ ++  ++  ++l+++ ++ ++a+e+  e+++++ ++++avl s
  gi|336254893|ref|YP_004598000.1| 426 VADQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTS 482
                                       9999999999999999999999*********************************88 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 7.5
                             Nmad5 129 nplvkrfdelekaqeelrekrkaikatVtavl 160
                                       +++++r de e+a+e + ++ ++  +t++ ++
  gi|336254893|ref|YP_004598000.1| 519 ETVRDRSDESEAAAERIVAATDHQNQTIETLM 550
                                       33344444444444444444444444444443 PP

>> DinB  DinB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2     0.016       4.4      20     103 ..     232     317 ..     227     345 .. 0.83
   2 ?    3.6   3.2       0.2        57      35     104 ..     417     486 ..     390     501 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.016
                                       HHHHHHCT--CCCTT..--SSTTS--HHHHHHHHHHHHHHHHHHHHH..SSSGGGT---------HHHHHHHHHHHH CS
                              DinB  20 rtldaiaaLpdeelk..aengegfqsvkqtlnHvldveelwlsrlegeegapavddqterkeleeldalrealderl 94 
                                        +++ +++++d++l+  ae++  f ++ + l+ v+d+  +  ++le   g+ + +  + r+++ e++++  +    +
  gi|336254893|ref|YP_004598000.1| 232 EIRTTANEISDGDLTarAERSDDFDALDDDLVDVVDAVNGMADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNV 308
                                       5788899********999*****************************888888888888888888888777666555 PP

                                       HHHHCT--H CS
                              DinB  95 iafldqltd 103
                                        ++   l+d
  gi|336254893|ref|YP_004598000.1| 309 TEQHGLLED 317
                                       555555555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.2
                                       --SSTTS--HHHHHHHHHHHHHHHHHHHHH..SSSGGGT---------HHHHHHHHHHHHHHHHCT--HH CS
                              DinB  35 aengegfqsvkqtlnHvldveelwlsrlegeegapavddqterkeleeldalrealderliafldqltdl 104
                                        e g gf+ v+++++ ++d  ++ +++++   ++ + + ++ ++++e+  +  e +de++ a+l++l+d 
  gi|336254893|ref|YP_004598000.1| 417 GESGNGFAVVADQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDI 486
                                       588999************************9999********************************9994 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.2    0.0067       1.9     217     306 ..     251     369 ..     222     417 .. 0.52
   2 ?    4.6   8.2     0.034       9.4     238     346 ..     426     544 ..     422     553 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0067
                              FUSC 217 raralrrllsrmlallallsslarllarlraeeaaavpelaallaelaal........................... 266
                                       r++   +l  ++++++  ++++a++l++l  + ++++ e++  ++e+ ++                           
  gi|336254893|ref|YP_004598000.1| 251 RSDDFDALDDDLVDVVDAVNGMADNLETLTGRVTEQATEMRSAVDEANDAadeiagnvteqhglledsvdemqsfaa 327
                                       55555666666666666666666666666666666666666666666664444444444332222222222221133 PP

                              FUSC 267 ...eaaaaaealeaalaalrarlralrraleadadtaalllar 306
                                          e aa+a++ + a+++ r+++++   a e da  a + + +
  gi|336254893|ref|YP_004598000.1| 328 gmeEVAAQADEVDSAARTAREAVEQGLDAGE-DAREATEDVVA 369
                                       3332223333333333333333322222222.22222222222 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.034
                              FUSC 238 larllarlraeeaaavpelaallaelaal..eaaaaaealeaalaalrarlralrraleadadtaalllarlaella 312
                                       +a++ + l +e +++++e+ + l+el+a   + ++a e+ ++++++ +++++a+ ++le+ ad  ++++    e+ +
  gi|336254893|ref|YP_004598000.1| 426 VADQVKKLADETQEHTEEITKSLDELQAQseDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISEVAR 502
                                       78899999999999999999999999998885556666667777777777777777777444444444444444444 PP

                              FUSC 313 elaqllaslraleaaiaa........arraerlarhrdhlaa 346
                                          +  as+++l++  ++        +++aer++  +dh+  
  gi|336254893|ref|YP_004598000.1| 503 VIDDQTASIEELTSTMETvrdrsdesEAAAERIVAATDHQNQ 544
                                       444444444444444444444555577888888888888765 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 ?    2.6   0.1      0.46   1.3e+02     120     172 ..     270     322 ..     217     339 .. 0.69
   2 ?    0.5  12.8       2.1   5.7e+02      80     181 ..     384     485 ..     272     487 .. 0.81
   3 ?    6.8  11.3     0.023       6.4      73     162 ..     430     522 ..     401     558 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.46
                           UPF0242 120 qqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqi 172
                                       + +   le     + e+  e+ ++++e +   +e + +++eq+  le   d+ 
  gi|336254893|ref|YP_004598000.1| 270 NGMADNLETLTGRVTEQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEM 322
                                       55555566666667777778888888888888888888888888887665554 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.1
                           UPF0242  80 ldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqe 156
                                       + +++    e + ++ ++++ L+ + +       +  +  + +  + ++ a + +e+  e+ + L+e q + ++   
  gi|336254893|ref|YP_004598000.1| 384 KMNEIGDVVEVISDVADQTNLLALNANIEAARAGESGNGFAVVADQVKKLADETQEHTEEITKSLDELQAQSEDTTD 460
                                       33444444456667777777777666666666666666666777788888889999999999999999999999999 PP

                           UPF0242 157 tieeqrsvlekrqdqieqLeskVrD 181
                                        +e+ ++ +e  ++qie   +  +D
  gi|336254893|ref|YP_004598000.1| 461 AVEQSHERIEHADEQIEAVLTSLED 485
                                       9999999999999999876665555 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.023
                           UPF0242  73 keaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae...dfeelkleleeqLae 146
                                        +++  e++e+ +++ ++l elq++ e+  + +++ +e +e+  e+ + +   le+ia    + ++   e+   ++ 
  gi|336254893|ref|YP_004598000.1| 430 VKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADsvdEAANGISEVARVIDD 506
                                       34445566688888888899999998888888888888888888777776667776655333222223333344444 PP

                           UPF0242 147 kqellqeyqetieeqr 162
                                       ++  ++e+  t+e  r
  gi|336254893|ref|YP_004598000.1| 507 QTASIEELTSTMETVR 522
                                       4444444444444444 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       4.7   1.3e+03      80     116 ..     295     332 ..     258     337 .. 0.57
   2 ?    0.2   0.2       3.4   9.5e+02      99     116 ..     315     332 ..     281     390 .. 0.50
   3 ?    9.2   7.3    0.0055       1.5       5     104 ..     438     533 ..     433     558 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 4.7
                           DUF4200  80 aeikklkaei.etlkseiekleekleeykkYeefLekv 116
                                        e +++ +ei  ++ +++  le+ ++e++++ + +e+v
  gi|336254893|ref|YP_004598000.1| 295 DEANDAADEIaGNVTEQHGLLEDSVDEMQSFAAGMEEV 332
                                       22222222220334455556666666666666655555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 3.4
                           DUF4200  99 leekleeykkYeefLekv 116
                                       le+ ++e++++ + +e+v
  gi|336254893|ref|YP_004598000.1| 315 LEDSVDEMQSFAAGMEEV 332
                                       333333333333333332 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0055
                           DUF4200   5 kremfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeae 81 
                                       +   +e++++l++ +++ + + +a++q  e +e +++++e  l      l+++ +   +a   + e ++ +++ +a 
  gi|336254893|ref|YP_004598000.1| 438 QEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVL----TSLEDIADSVDEAANGISEVARVIDDQTAS 510
                                       4455666666666666666666666666666666666666666....88889999999999**************** PP

                           DUF4200  82 ikklkaeietlkseiekleekle 104
                                       i++l++ +et++ + ++ e++ e
  gi|336254893|ref|YP_004598000.1| 511 IEELTSTMETVRDRSDESEAAAE 533
                                       ************99998887766 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.7      0.72     2e+02     248     290 ..     285     327 ..     250     388 .. 0.49
   2 ?    8.5  12.0    0.0045       1.2     211     315 ..     429     529 ..     406     552 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.72
                            HMMR_N 248 ldiaqleellkekndeiesLkssLeekeqelskqvkdlnekck 290
                                       ++ +++++ ++e+nd   ++  ++ e++  l+  v+++++   
  gi|336254893|ref|YP_004598000.1| 285 EQATEMRSAVDEANDAADEIAGNVTEQHGLLEDSVDEMQSFAA 327
                                       2223333333333333333333333333333333333332222 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0045
                            HMMR_N 211 klvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdlne 287
                                       +   ++k+  e++++te+ ++  +el++ se        ++q++e +++++++ie + +sLe+ ++ +++ ++  +e
  gi|336254893|ref|YP_004598000.1| 429 Q---VKKLADETQEHTEEITKSLDELQAQSEDT---TDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISE 499
                                       4...45666779999*************99999...999***************************99999999999 PP

                            HMMR_N 288 kckllekeke..elvreeeekeqtlsaEle 315
                                         ++++ ++   e+++   e  + +s E e
  gi|336254893|ref|YP_004598000.1| 500 VARVIDDQTAsiEELTSTMETVRDRSDESE 529
                                       999999665411133344444444444444 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 ?    4.2   7.5     0.067        19      31     131 ..     430     531 ..     423     559 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.067
                             Atg14  31 laklksekeslkkkiekalegke.eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklak 106
                                       ++kl  e ++  ++i+k l + + ++e+++d+++++++++e    +i+     l+ + d++++    i e  + +  
  gi|336254893|ref|YP_004598000.1| 430 VKKLADETQEHTEEITKSLDELQaQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVDEAANGISEVARVIDD 506
                                       55666666666667776666666555566666666666666666666666666666666666666666666666666 PP

                             Atg14 107 lsdklkkRrsdleslqneleerrkk 131
                                       + +++ + +s++e ++++  e++++
  gi|336254893|ref|YP_004598000.1| 507 QTASIEELTSTMETVRDRSDESEAA 531
                                       6666665555555555555444433 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       2.9   8.2e+02      26      51 ..     217     242 ..     213     254 .. 0.85
   2 ?   -0.6   0.0       6.4   1.8e+03      41      61 ..     275     295 ..     245     335 .. 0.49
   3 ?   -0.5   0.0       5.6   1.6e+03      29      51 ..     372     390 ..     352     411 .. 0.61
   4 ?    7.1   2.2     0.025         7       9      61 ..     438     491 ..     426     506 .. 0.72
   5 ?    4.5   1.0      0.16        44       8      58 ..     504     558 ..     497     561 .] 0.66

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.9
                        Syntaxin_2  26 kdteelreklhelieeinelikktne 51 
                                       +d  + r+   +l++ei+++++++++
  gi|336254893|ref|YP_004598000.1| 217 TDIVNERDATVDLVQEIRTTANEISD 242
                                       577778999999********999976 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 6.4
                        Syntaxin_2  41 einelikktnellkklsqldn 61 
                                       ++ +l  +++e+  ++ +  +
  gi|336254893|ref|YP_004598000.1| 275 NLETLTGRVTEQATEMRSAVD 295
                                       222333333333333333333 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 5.6
                        Syntaxin_2  29 eelreklhelieeinelikktne 51 
                                       +elre+++ l e++n    ++ +
  gi|336254893|ref|YP_004598000.1| 372 DELRESVDALAEKMN----EIGD 390
                                       344444444444444....4444 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.025
                        Syntaxin_2   9 nsnvstleklvkqLgtkk.dteelreklhelieeinelikktnellkklsqldn 61 
                                       ++++ ++ k ++ L+ +  dt++  e+ he ie++ e i+++  +l++++   +
  gi|336254893|ref|YP_004598000.1| 438 QEHTEEITKSLDELQAQSeDTTDAVEQSHERIEHADEQIEAVLTSLEDIADSVD 491
                                       456667777777787774488888888888888888888888888877776655 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.16
                        Syntaxin_2   8 insnvstleklvkqLgtkkd....teelreklhelieeinelikktnellkklsq 58 
                                       i  ++ ++e+l+++ +t +d    +e   e++   +++ n++i++  +++ +l++
  gi|336254893|ref|YP_004598000.1| 504 IDDQTASIEELTSTMETVRDrsdeSEAAAERIVAATDHQNQTIETLMARVDELQT 558
                                       778899************9984444444455555555555555555555555554 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3      0.41   1.2e+02      25      73 ..     265     312 ..     211     331 .. 0.64
   2 ?    4.2   0.8      0.24        67      16      79 ..     330     391 ..     313     406 .. 0.47
   3 ?    6.9   3.9     0.037        10      14      71 ..     429     485 ..     424     490 .. 0.85
   4 ?    6.9   2.2     0.035       9.9       5      72 ..     490     556 ..     488     559 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.41
                           DUF2203  25 lrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelG 73 
                                       + + ++ ++++le+ + + + ++a+e++++++e+++ ++e+  +++e  
  gi|336254893|ref|YP_004598000.1| 265 VVDAVNGMADNLETLTGRVT-EQATEMRSAVDEANDAADEIAGNVTEQH 312
                                       33333333344444444432.2255566666666666666665555544 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.24
                           DUF2203  16 kelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelGvevkdl 79 
                                       +e+ +++ ++ + +++++e++e+  ++    +  a+e+ +++ ++ +e++e v+ + e   e+ d+
  gi|336254893|ref|YP_004598000.1| 330 EEVAAQADEVDSAARTAREAVEQGLDA----GedAREATEDVVAIGDELRESVDALAEKMNEIGDV 391
                                       222222223333333333333333333....13355555555555566666655555554444444 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.037
                           DUF2203  14 llkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeiee 71 
                                       ++k+l +e ++ ++e+++  +el++++++++ ++ ++ ++++e+++++ie++++ +e+
  gi|336254893|ref|YP_004598000.1| 429 QVKKLADETQEHTEEITKSLDELQAQSEDTT-DAVEQSHERIEHADEQIEAVLTSLED 485
                                       7899999999999999999999999998864.45899999999999***999999886 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.035
                           DUF2203   5 leeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieel 72 
                                       ++eA + + ++ +++++  a  +el++++e +++ ++e+e+  a++  a+ ++ ++ ie l+++++el
  gi|336254893|ref|YP_004598000.1| 490 VDEAANGISEVARVIDDQTASIEELTSTMETVRDRSDESEAA-AERIVAATDHQNQTIETLMARVDEL 556
                                       7999999************99999999999999999997655.5555555666666666666665554 PP

>> DUF4665  Domain of unknown function (DUF4665)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       6.7   1.9e+03      46      96 ..     254     301 ..     246     305 .. 0.66
   2 ?    7.2   1.8     0.027       7.6      32      90 ..     426     484 ..     423     500 .. 0.78
   3 ?    2.0   0.1       1.2   3.3e+02      43      97 ..     465     519 ..     459     522 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 6.7
                           DUF4665  46 kvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvnvdeaaell 96 
                                           ld  lvd+   +++++ +l++ t +    +++  + + +vdea++ +
  gi|336254893|ref|YP_004598000.1| 254 DFDALDDDLVDVVDAVNGMADNLETLTGRV---TEQATEMRSAVDEANDAA 301
                                       556789999999999999999665554443...455555566666666654 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.027
                           DUF4665  32 VttnLKkinavkkekvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvnvd 90 
                                       V  + Kk+   ++e +e++ k+l ++q++ + ++  +++ +++ e++ ++ e   ++++
  gi|336254893|ref|YP_004598000.1| 426 VADQVKKLADETQEHTEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLE 484
                                       66789************************999999877777666666666555554444 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 1.2
                           DUF4665  43 kkekvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvnvdeaaella 97 
                                        +e++e+ d++++ +  +l+ ++ +++  ++  ++v +  ++++++++e + +++
  gi|336254893|ref|YP_004598000.1| 465 SHERIEHADEQIEAVLTSLEDIADSVDEAANGISEVARVIDDQTASIEELTSTME 519
                                       6799999999999999999999999999999888888888888888888888776 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.3      0.23        64     177     220 ..     240     281 ..     210     291 .. 0.60
   2 ?    7.9   1.2     0.006       1.7     116     232 ..     294     409 ..     281     413 .. 0.69
   3 ?    1.7  11.6      0.45   1.3e+02     107     226 ..     421     553 ..     401     559 .. 0.44

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.23
                              CorA 177 llakaddkllddedkeylrdlldelerllemlealrerleslqd 220
                                       +   + d +  +e+++ ++ l d+l  +++ ++ +++ le l  
  gi|336254893|ref|YP_004598000.1| 240 IS--DGDLTARAERSDDFDALDDDLVDVVDAVNGMADNLETLTG 281
                                       22..2333344444556888888888888888888888877765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.006
                              CorA 116 ldeivdrlfellekleeeldeledel.edstkkeilrelaqlrrrlvklrralapnrevlkrlla.kaddklldded 190
                                       +de +d  +e+  ++ e+   led + e ++ +  ++e+a    ++ ++ +a+++ re++++ l+  +d+ + +++ 
  gi|336254893|ref|YP_004598000.1| 294 VDEANDAADEIAGNVTEQHGLLEDSVdEMQSFAAGMEEVA---AQADEVDSAARTAREAVEQGLDaGEDAREATEDV 367
                                       5566666666666666666666666643333333333333...589999************9999556666666666 PP

                              CorA 191 keylrdlldelerllemlealrerleslqdtyssllserlNr 232
                                           ++l++ ++ l+e+++ + +++e+++d   ++    lN 
  gi|336254893|ref|YP_004598000.1| 368 VAIGDELRESVDALAEKMNEIGDVVEVISDVADQTNLLALNA 409
                                       6667888999999**************999887766666665 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.45
                              CorA 107 spgellyrlldeivdrlfellekleeeldeledel............edstkkeilre.laqlrrrlvklrralapn 170
                                       + + +++  + +++d+  e +e++ + ldel+ +             + +  +e+++  l+ l+  +  + +a++  
  gi|336254893|ref|YP_004598000.1| 421 NGFAVVADQVKKLADETQEHTEEITKSLDELQAQSedttdaveqsheRIEHADEQIEAvLTSLEDIADSVDEAANGI 497
                                       55556666666666666666666666666666666443333332222111111111110111222222223333333 PP

                              CorA 171 revlkrlla..kaddkllddedkeylrdlldelerllemlealrerleslqdtyssll 226
                                        ev  r+++  +a  ++l++++ e  rd +de e ++e + a  +  ++  +t+++++
  gi|336254893|ref|YP_004598000.1| 498 SEVA-RVIDdqTASIEELTSTM-ETVRDRSDESEAAAERIVAATDHQNQTIETLMARV 553
                                       3333.33333333444444443.44444444444444444444444444444444444 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1       1.6   4.5e+02      46     122 ..     301     380 ..     271     400 .. 0.59
   2 ?    8.0   3.7     0.011       3.1      56     121 ..     422     488 ..     373     494 .. 0.70
   3 ?    2.0   0.2      0.75   2.1e+02      48     114 ..     485     551 ..     482     558 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.6
                             CREPT  46 aekllkqveealellaeYn...krLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelksh 119
                                       a++ + +v e   ll++ +   ++ +a +ee    a  +++  +  +e++++     e+ +e  e v +  +el++ 
  gi|336254893|ref|YP_004598000.1| 301 ADEIAGNVTEQHGLLEDSVdemQSFAAGMEEVAAQADEVDSAARTAREAVEQGLDAGEDAREATEDVVAIGDELRES 377
                                       44444444444444444330002334455555555555555555666666666666666666666666666666655 PP

                             CREPT 120 iqs 122
                                       ++ 
  gi|336254893|ref|YP_004598000.1| 378 VDA 380
                                       555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.011
                             CREPT  56 alellaeYnkrLeaeleeR.kklakmledfleaqkellakaeekleelkeklekvksvrkelkshiq 121
                                       + +++a+ +k+L++e++e  ++++k l++++++  ++ +  e+  e++++  e++++v ++l++  +
  gi|336254893|ref|YP_004598000.1| 422 GFAVVADQVKKLADETQEHtEEITKSLDELQAQSEDTTDAVEQSHERIEHADEQIEAVLTSLEDIAD 488
                                       3578999999999999775267888888888888888888888888888888888888888876655 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.75
                             CREPT  48 kllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrk 114
                                         +++v+ea + ++e    +++++   ++l++++e+      e+ a ae+ ++ + ++ +++++  +
  gi|336254893|ref|YP_004598000.1| 485 DIADSVDEAANGISEVARVIDDQTASIEELTSTMETVRDRSDESEAAAERIVAATDHQNQTIETLMA 551
                                       5667788888888888888888888877777777777777777766666666666666666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1902  (0.106085); expected 358.6 (0.02)
Passed bias filter:                      822  (0.0458475); expected 358.6 (0.02)
Passed Vit filter:                       198  (0.0110436); expected 17.9 (0.001)
Passed Fwd filter:                       130  (0.00725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              64  [number of targets reported over threshold]
# CPU time: 1.47u 0.30s 00:00:01.77 Elapsed: 00:00:00.51
# Mc/sec: 3337.93
//
Query:       gi|336254894|ref|YP_004598001.1|  [L=402]
Description: CheW protein [Halopiger xanaduensis SH-6]
Scores for 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-23   82.0   0.2    4.7e-23   81.4   0.2    1.3  1  CheW      CheW-like domain


Domain annotation for each model (and alignments):
>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.2   2.6e-27   4.7e-23       1     136 [.     246     389 ..     246     391 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 2.6e-27
                                       EEEEEEETTEEEEEEGGGEEEEEECCT.BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTTSTCEEEEEEE.. CS
                              CheW   1 qlllfrlgeetyaiplakvreilevppitpipgapgavlgvinlrGevipvidLrellglgpeesrentrvivve.. 75 
                                       q+l f l++++yai++  v  i+e+++it+ p+ p a+ gv +lrGe+  v+d   +l ++++e++e+++++v+e  
  gi|336254894|ref|YP_004598001.1| 246 QMLEFYLNDNRYAIEIGRVSAIVEMKDITRFPRGPKAIDGVTDLRGEITGVLDPTVMLDVERSEPSEDHYIVVIErd 322
                                       799**************************************************************999999999954 PP

                                       ETTEEEEEEESEEEEEEEEECCGEETT...TSSTSSTCCCEEEEEEC..TTS.EEEEEE-CCCHHHH CS
                              CheW  76 lgnqvvGllVdevkgiqeivikqiepp...lglssdlagyisGatkl..gdg.rlvliLDveallrs 136
                                        ++q++G+ V+ v++ ++++++qi++      +++ + +++ G++k+  +dg  lv +LD++ l++ 
  gi|336254894|ref|YP_004598001.1| 323 GDKQKLGIRVTDVSQAVTYRESQIDETgtvMDGTDAQHEFVEGIIKKnvDDGtALVAWLDIDSLIET 389
                                       55*************************9996778899**********8878845**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 3012.39
//
Query:       gi|336254895|ref|YP_004598002.1|  [L=264]
Description: cobyrinic acid a,c-diamide synthase [Halopiger xanaduensis SH-6]
Scores for 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-39  134.6   0.0    4.9e-39  134.1   0.0    1.1  1  AAA_31           AAA domain
    1.3e-21   77.0   0.0    7.6e-16   58.3   0.0    2.2  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    7.8e-10   38.6   0.1    1.7e-09   37.5   0.1    1.8  1  ParA             NUBPL iron-transfer P-loop NTPase
    3.6e-09   36.3   0.5    1.4e-05   24.5   0.1    2.3  2  MipZ             ATPase MipZ
    4.4e-07   29.6   0.1    1.3e-06   28.1   0.0    1.7  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
    4.6e-07   29.3   0.1    1.5e-06   27.7   0.1    1.8  1  ArsA_ATPase      Anion-transporting ATPase
    1.4e-05   24.7   0.0    9.6e-05   22.0   0.0    2.0  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
    8.1e-05   22.5   0.2      0.083   12.7   0.0    2.3  2  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0014   18.4   0.0     0.0033   17.2   0.0    1.5  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
     0.0026   17.1   0.1      0.037   13.3   0.0    2.2  2  YcaO             YcaO cyclodehydratase, ATP-ad Mg2+-binding
  ------ inclusion threshold ------
      0.033   13.9   0.2          2    8.1   0.0    2.2  2  Thymidylate_kin  Thymidylate kinase
       0.05   13.3   0.0        1.1    9.0   0.0    2.4  2  AAA_24           AAA domain
      0.053   12.8   0.1       0.19   11.0   0.0    1.8  2  VirC1            VirC1 protein
      0.063   12.8   0.4       0.73    9.4   0.4    2.3  1  AAA_25           AAA domain
       0.12   11.5   0.1       0.44    9.6   0.1    1.8  2  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
       0.13   11.9   0.1       0.49   10.0   0.0    1.8  2  SRP54            SRP54-type protein, GTPase domain
       0.14   11.1   0.1       0.25   10.3   0.1    1.4  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 


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 !  134.1   0.0   4.7e-42   4.9e-39       5     172 ..       8     179 ..       5     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 4.7e-42
                            AAA_31   5 aianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgi.ekne.iektlyevli..eeknikeaiiktk 77 
                                       +++nqKGGvGKTT ++nla al ++g  vL vDlDpQ+nat glg  +  +    tl+++l+  + + ++e+++  +
  gi|336254895|ref|YP_004598002.1|   8 CVTNQKGGVGKTTVAINLAGALNERGRDVLFVDLDPQGNATEGLGQlDAYDaEPPTLLDALVdpSGVPLEEIVY--D 82 
                                       799****************************************9974444424469999997556678888888..6 PP

                            AAA_31  78 venldlipssidLaeaeielvelekkeeilkellekvkde..YDyiiiDcpPsLglltenaLvasdsviipvqaeay 152
                                       + ++d++ s++d+ +a+  l+e  + e++l+ ll++++ e  YD++++DcpP+Lgl+t+naL+a   ++ip  ae  
  gi|336254895|ref|YP_004598002.1|  83 HPEMDVLASNVDMNAAQSTLAEQPDGEDRLDALLTALEREggYDVVVVDCPPQLGLITDNALCATKNLVIPALAEST 159
                                       7799*********************************99999*********************************** PP

                            AAA_31 153 aleGleqllktieevkkkln 172
                                       + + le l++++ +++ ++ 
  gi|336254895|ref|YP_004598002.1| 160 SKRSLELLFDYVGSLQMDYD 179
                                       ************99987755 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 !   58.3   0.0   7.2e-19   7.6e-16       1      45 [.       7      51 ..       7     108 .. 0.84
   2 !   16.9   0.0   4.7e-06    0.0049      19     126 ..     115     231 ..     112     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 7.2e-19
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlail 45
                                      ++++++kGGvGKTt+a+nLa al++rg++Vl vD+Dpq+n+++ l
  gi|336254895|ref|YP_004598002.1|  7 LCVTNQKGGVGKTTVAINLAGALNERGRDVLFVDLDPQGNATEGL 51
                                      689**************************************9933 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.7e-06
                                       HHHHHHH.TT--EEEEEEEESSCCCCHHTTEB-HHHH..................CCHCCCHHHHHHCHCHHHH..E CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  19 Laralar.rglrVllvDaDpqannlaileglendiep..................dlkrllellealgkkkalllki 76 
                                       L++al r +g++V++vD+ pq        gl  d +                   +l+ l   + +l+  + +++++
  gi|336254895|ref|YP_004598002.1| 115 LLTALEReGGYDVVVVDCPPQL-------GLITDNALcatknlvipalaestskrSLELLFDYVGSLQMDYDVEIEP 184
                                       677777768************4.......444455556666688899999*99999999999999999999999*** PP

                                       EEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  77 agvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparge 126
                                         +v+nrv+  n+  ++ e ++e +    vp++ ++++++a+ +a + g 
  gi|336254895|ref|YP_004598002.1| 185 RALVANRVEYTNQADEMLEWFDEALP--DVPLF-EVRKRVALQRAFEAGT 231
                                       *********99888888888888765..77777.7888888888877665 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 !   37.5   0.1   1.6e-12   1.7e-09       6     133 ..       7     149 ..       4     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.6e-12
                              ParA   6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee...ekpeqs....ekkliPvea..... 70 
                                       ++v+  KGGVGK+tva+nlA aL+++g +v  +D+D  G     l +++    e p+      + + +P+e      
  gi|336254895|ref|YP_004598002.1|   7 LCVTNQKGGVGKTTVAINLAGALNERGRDVLFVDLDPQGNATEGLGQLDAydaEPPTLLdalvDPSGVPLEEivydh 83 
                                       679999**********************************9999887776444222222222333456666666665 PP

                              ParA  71 kgikvmSigfllesedeavvwrGpmkskaikqllkdvew.gelDyLiiDlPPGtg...Deqltvaqk 133
                                        ++ v+  ++ ++   ++ +   p  +  ++ ll+  e  g  D++++D+PP  g   D +l  +++
  gi|336254895|ref|YP_004598002.1|  84 PEMDVLASNVDMN-AAQSTLAEQPDGEDRLDALLTALEReGGYDVVVVDCPPQLGlitDNALCATKN 149
                                       6788888887777.7888999999999*******999874789*********865333666655555 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   1.3e-08   1.4e-05       3      40 ..       7      44 ..       5      50 .. 0.91
   2 !    9.9   0.0   0.00039      0.41      69     128 ..      94     153 ..      78     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.3e-08
                                      EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TT CS
                              MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlr 40
                                      + ++n+kGG Gk+t+a+ +a aL ++G  v  +dld +
  gi|336254895|ref|YP_004598002.1|  7 LCVTNQKGGVGKTTVAINLAGALNERGRDVLFVDLDPQ 44
                                      5799********************************65 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00039
                                       -SSS-HHHHTTS-HHHHHHHHHHHHHHHHHH..-SEEEEE--SS--HHHHHHHHT-SEEEEE CS
                              MipZ  69 alseaeeaeveeeeeaevaeleelvadleae..ldfividtPGsdsalsrlahsladtlvtP 128
                                        ++ a+++ +e+++ ++  +l++l+++le+e  +d++v+d+P +   ++  a      lv P
  gi|336254895|ref|YP_004598002.1|  94 DMNAAQSTLAEQPDGED--RLDALLTALEREggYDVVVVDCPPQLGLITDNALCATKNLVIP 153
                                       44444444445555444..999999998876559*********9999999999999888887 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.2e-09   1.3e-06       4     143 ..       7     152 ..       5     167 .. 0.77
   2 ?   -3.3   0.0       4.8   5.1e+03     176     200 ..     195     220 ..     178     238 .. 0.58

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.2e-09
                          CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspd.nlLrlhFnvdi..eqregwaraeldga..pwrqaaley 75 
                                       l+++  +GGvG+t+++  La al+e g  vl +Dl p+ n  +   ++d   ++  ++  a++d    p+++ +++ 
  gi|336254895|ref|YP_004598002.1|   7 LCVTNQKGGVGKTTVAINLAGALNERGRDVLFVDLDPQgNATEGLGQLDAydAEPPTLLDALVDPSgvPLEEIVYD- 82 
                                       5677779****************************997344433333333115667999***99661155555544. PP

                          CBP_BcsQ  76 apgldllPfGelnveekenlqqlaekaeallaalkelk..eqyrwillDlpagasaltrellaladlvll 143
                                        p++d+l      ++ +++l++  + +++l a l++l+  + y+ +++D+p +   +t ++l  +   + 
  gi|336254895|ref|YP_004598002.1|  83 HPEMDVLASNVDMNAAQSTLAEQPDGEDRLDALLTALEreGGYDVVVVDCPPQLGLITDNALCATKNLVI 152
                                       699****98888888888899999999**********98889*************999998885544443 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.8
                          CBP_BcsQ 176 qlqqDllqlWlqslrrllPl.vihrD 200
                                       + q D ++ W +++   +Pl  +++ 
  gi|336254895|ref|YP_004598002.1| 195 TNQADEMLEWFDEALPDVPLfEVRKR 220
                                       33455555555555555554344444 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   1.4e-09   1.5e-06       7     134 ..      11     134 ..       5     140 .. 0.66

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.4e-09
                                       EESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS..--BSS-EEET.SSEEEEE--HH.HHHHHHHCC CS
                       ArsA_ATPase   7 gGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdq..klgkeptkvk.eNLsavEidpe.veleeakqe 79 
                                         KGGVGKttv+  +a  l e g++vl + +DP  +    + q           +   L  + +dp+ v lee   +
  gi|336254895|ref|YP_004598002.1|  11 NQKGGVGKTTVAINLAGALNERGRDVLFVDLDPQGNATEGLGQldA-----YDAEpPTLLDALVDPSgVPLEEIVYD 82 
                                       56**********************************9999998322.....22233556666688886444444333 PP

                                       HHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHH.HHHHCSSSSEEEEESBS CS
                       ArsA_ATPase  80 vqkeeeallgleeledvlaeelaslPGideilsfeell.kyvkeeeydvvvlDtaP 134
                                           e ++l ++   ++ +++la  P  ++   +++ll  + +e  ydvvv+D +P
  gi|336254895|ref|YP_004598002.1|  83 HP--EMDVLASNVDMNAAQSTLAEQPDGEDR--LDALLtALEREGGYDVVVVDCPP 134
                                       22..233344444444444444444544554..34444044558999999999988 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 !   22.0   0.0   9.1e-08   9.6e-05       7      46 ..      12      51 ..       6      89 .. 0.79
   2 ?    0.2   0.0      0.39   4.1e+02     179     246 ..     187     255 ..     179     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 9.1e-08
                         Fer4_NifH  7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrll 46
                                       kGG+Gk+t + nl+ al e+g+ vl v  DP+ ++t  l
  gi|336254895|ref|YP_004598002.1| 12 QKGGVGKTTVAINLAGALNERGRDVLFVDLDPQGNATEGL 51
                                      69*******************************9999644 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.39
                         Fer4_NifH 179 liinsrk.vddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkile 246
                                       l+ n  + +++ +e++e f e+l+   l  v +   +++a  +   ++e +++ ++   ++ +a+ + e
  gi|336254895|ref|YP_004598002.1| 187 LVANRVEyTNQADEMLEWFDEALPDVPLFEVRKRVALQRAFEAGTSIFEVEEDVDMEAVFESMAETLDE 255
                                       56664331456678888899999888788888999999999999999*******999999999998766 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 !   12.7   0.0   7.8e-05     0.083       6      35 ..      15      44 ..      13      50 .. 0.93
   2 !    8.0   0.1    0.0021       2.2      75     182 ..     108     207 ..      77     257 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.8e-05
                        ATP_bind_1  6 GsGKttfvgalseilelrgrsvavvNLDPA 35
                                      G+GKtt   +l+  l++rgr+v  v LDP 
  gi|336254895|ref|YP_004598002.1| 15 GVGKTTVAINLAGALNERGRDVLFVDLDPQ 44
                                      9****************************5 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0021
                        ATP_bind_1  75 lresldwldeeleke.eddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsals 150
                                       ++++ld l  +le+e   d +++D+P Q+ l t  +  a        + +lv+  L++s+  ++  +++   + +l+
  gi|336254895|ref|YP_004598002.1| 108 GEDRLDALLTALEREgGYDVVVVDCPPQLGLITDNALCA--------TKNLVIPALAESTSKRS-LELLFDYVGSLQ 175
                                       68899*******888666***********9998777666........56666666666654444.555555566677 PP

                        ATP_bind_1 151 amlrlel.PhvvvlnkfDllkeklekeleffed 182
                                       + + +e+ P   v n+++  + ++++ le+f +
  gi|336254895|ref|YP_004598002.1| 176 MDYDVEIePRALVANRVEYTN-QADEMLEWFDE 207
                                       777777656777777777733.56666666664 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 !   17.2   0.0   3.2e-06    0.0033       4      33 ..      15      44 ..      13      48 .. 0.92
   2 ?   -3.3   0.0       6.2   6.6e+03      22      38 ..     124     140 ..     115     176 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.2e-06
                            CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                       +GK+T+a +L+  + ++gr +++vDlD+ 
  gi|336254895|ref|YP_004598002.1| 15 GVGKTTVAINLAGALNERGRDVLFVDLDPQ 44
                                      59**************************95 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.2
                            CLP1_P  22 grkpvyvDlDvGqseis 38 
                                       g+ +v+vD+ +  + i+
  gi|336254895|ref|YP_004598002.1| 124 GYDVVVVDCPPQLGLIT 140
                                       45677777766555444 PP

>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.13   1.4e+02     288     307 ..      24      43 ..      19      55 .. 0.86
   2 !   13.3   0.0   3.5e-05     0.037     261     312 ..      84     138 ..      46     151 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.13
                              YcaO 288 tllerlkaagldvlvvdltr 307
                                       +l  +l+++g dvl+vdl++
  gi|336254895|ref|YP_004598002.1|  24 NLAGALNERGRDVLFVDLDP 43 
                                       577899************96 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.5e-05
                              YcaO 261 peaaakrldfll...faewassgdleedletllerlkaagld.vlvvdltrpdlgl 312
                                       pe+   +   ++   +++ a+++d e++l++ll++l+++g   v+vvd+ + +lgl
  gi|336254895|ref|YP_004598002.1|  84 PEMDVLASNVDMnaaQSTLAEQPDGEDRLDALLTALEREGGYdVVVVDCPP-QLGL 138
                                       444443333333333334566789************8887655*****996.7775 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0019         2       6      30 ..      15      39 ..      14      51 .. 0.83
   2 ?    3.6   0.1     0.045        48     103     161 ..     197     255 ..     189     262 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0019
                                      TSSHHHHHHHHHHHHHHTTE.EEEE CS
                   Thymidylate_kin  6 GaGKttqaellkerlkeegikvvlt 30
                                      G+GKtt+a +l+ +l+e+g+ v++ 
  gi|336254895|ref|YP_004598002.1| 15 GVGKTTVAINLAGALNERGRDVLFV 39
                                      89*****************996663 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.045
                                       TCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSS...TTTSHHHHHHHHHHHHHHHHH CS
                   Thymidylate_kin 103 dldlvlslnedvllkPdltflldvdpevalkRlakrde...ldeeeeeqldflrkvreryle 161
                                        +d +l++ +++   Pd+ ++    ++val+R+ + ++   + ee+   + +++++ e ++e
  gi|336254895|ref|YP_004598002.1| 197 QADEMLEWFDEA--LPDVPLFEV-RKRVALQRAFEAGTsifEVEEDVDMEAVFESMAETLDE 255
                                       566777777777..599998876.*********99999555556666666677777776655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0     0.001       1.1      11      33 ..      14      43 ..       5     150 .. 0.67
   2 ?    2.0   0.0      0.14   1.4e+02     150     188 ..     154     198 ..     139     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.001
                            AAA_24 11 sgiGKTtlakel.......gpkplfidtek 33
                                       g+GKTt+a +l       g ++lf+d++ 
  gi|336254895|ref|YP_004598002.1| 14 GGVGKTTVAINLagalnerGRDVLFVDLDP 43
                                      69************************9985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.14
                            AAA_24 150 pklgkktanelkeevDlvlranlkred......kvgervlktsks 188
                                          ++ +++ l+  +D+v+ ++++  +       v  rv +t+++
  gi|336254895|ref|YP_004598002.1| 154 ALAESTSKRSLELLFDYVGSLQMDYDVeiepraLVANRVEYTNQA 198
                                       4456677999********999987444677777666677777665 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.19       6      39 ..       9      42 ..       5      49 .. 0.86
   2 ?   -0.8   0.0      0.73   7.7e+02      83     150 ..     124     192 ..     110     246 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                             VirC1  6 fcslkGGaGkttalmglcsalasdgkrvalfead 39
                                      ++  kGG Gktt  + l +al  +g+ v + + d
  gi|336254895|ref|YP_004598002.1|  9 VTNQKGGVGKTTVAINLAGALNERGRDVLFVDLD 42
                                      5678**********************99777766 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.73
                             VirC1  83 GfdyaladtrgGsselnntiiassdllliPtmltpldidealatyryvielllaeelai.pvailrqrv 150
                                       G+d++++d       + +  + +++ l+iP++       +    + yv  l +  +++i p a++ +rv
  gi|336254895|ref|YP_004598002.1| 124 GYDVVVVDCPPQLGLITDNALCATKNLVIPALAESTSKRSLELLFDYVGSLQMDYDVEIePRALVANRV 192
                                       677777776655555544444444445667644433333333345555555555555552344444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.4   0.00069      0.73      41      66 ..      13      40 ..       5     133 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00069
                            AAA_25 41 apgtGKttlaldlalava.tGkpwlg.p 66
                                       +g+GKtt+a++la a+  +G+ +l  +
  gi|336254895|ref|YP_004598002.1| 13 KGGVGKTTVAINLAGALNeRGRDVLFvD 40
                                      68************99988777666543 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00042      0.44      45      71 ..      13      39 ..       7      40 .. 0.87
   2 ?   -1.0   0.0       0.7   7.3e+02     113     135 ..     108     131 ..     107     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00042
                                      SS-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK 45 vGGtGKTPlvialvkllqarglkvgvl 71
                                       GG GKT ++i l+ +l++rg  v ++
  gi|336254895|ref|YP_004598002.1| 13 KGGVGKTTVAINLAGALNERGRDVLFV 39
                                      5********************999775 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.7
                                       ESSHHHHHHHHHHHC-.-SEEEEE CS
                              LpxK 113 gsdRvaaarallakae.ldviilD 135
                                       g+dR +a+ ++l++++  dv+++D
  gi|336254895|ref|YP_004598002.1| 108 GEDRLDALLTALEREGgYDVVVVD 131
                                       579999*9999999999*****99 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   0.0   0.00046      0.49      11      39 ..      15      43 ..      10      59 .. 0.88
   2 ?   -1.2   0.0       1.3   1.4e+03      61      90 ..     104     131 ..      86     136 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
                                      TSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54 11 GaGKTttlaKLaallkkegkkvllvaaDt 39
                                      G+GKTt +  La  l+++g++vl+v +D 
  gi|336254895|ref|YP_004598002.1| 15 GVGKTTVAINLAGALNERGRDVLFVDLDP 43
                                      9************************9996 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                                       ESSTTSCHHHHHHHHHHHHHHTTSSEEEEE CS
                             SRP54  61 kkkeeadpaavakeavekakeekidvvlvD 90 
                                       ++  ++d  + +  a+e+  e ++dvv+vD
  gi|336254895|ref|YP_004598002.1| 104 EQPDGEDRLDALLTALER--EGGYDVVVVD 131
                                       355555555555555554..4459999999 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 ?   10.3   0.1   0.00024      0.25      31      74 ..       6      50 ..       1      54 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
                                      EEEEEE.-TTSSHHHHHHHHHHHHHCTT--EEEEEE--------- CS
                              MeaB 31 vvGltG.vPGaGkstlvealglelrrrGkrvavlavDPsspftGG 74
                                      ++ +t    G+Gk t+  +l+  l +rG+ v  + +DP  + t G
  gi|336254895|ref|YP_004598002.1|  6 RLCVTNqKGGVGKTTVAINLAGALNERGRDVLFVDLDPQGNATEG 50
                                      5556651468****************************9888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1958.02
//
Query:       gi|336254896|ref|YP_004598003.1|  [L=156]
Description: hypothetical protein Halxa_3513 [Halopiger xanaduensis SH-6]
Scores for 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:                       171  (0.00953762); expected 358.6 (0.02)
Passed bias filter:                      134  (0.00747392); 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 0.20s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1261.37
//
Query:       gi|336254897|ref|YP_004598004.1|  [L=360]
Description: response regulator receiver modulated CheB methylesterase [Halopiger xanaduensis SH-6]
Scores for 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-52  176.9   0.4    4.9e-52  176.1   0.4    1.4  1  CheB_methylest  CheB methylesterase
    8.3e-23   80.7   0.2      2e-22   79.4   0.2    1.7  1  Response_reg    Response regulator receiver domain
  ------ inclusion threshold ------
      0.021   14.9   0.0        1.3    9.2   0.0    2.2  2  DUF2023         Protein of unknown function (DUF2023)


Domain annotation for each model (and alignments):
>> CheB_methylest  CheB methylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.1   0.4   8.2e-56   4.9e-52       2     168 ..     172     349 ..     171     351 .. 0.92

  Alignments for each domain:
  == domain 1  score: 176.1 bits;  conditional E-value: 8.2e-56
                                       EEEE-TTHHHHHTTTGGGS-TT-SS-EEEEE---TT-HHHHHHHHHHH-SSEEEE--TT-B--TTEEEE--TTSEEE CS
                    CheB_methylest   2 vigaStGGlealkellaalpedfpaavvvvqhmppsftsslaelLnresslkVkeaedgeelepgrvyvapgdkhll 78 
                                       vigaStGG++ ++++l++lpe+ ++ ++vvqhm  ++t+++a++Ln+++++ ++ea+ ++ + pg++++a+g+kh+ 
  gi|336254897|ref|YP_004598004.1| 172 VIGASTGGPRVVEQVLSELPERAGLRILVVQHMADHYTERFAKRLNDRTAYDIREATGSDTIGPGEAVLAKGGKHMA 248
                                       9**************************************************************************** PP

                                       EE...........E...E.-.-SS-HHHHHHHHHHHH.GGEEEEE-SBSS-TTHHHHHHHHHTT-EEEEE-GGG-SS CS
                    CheB_methylest  79 ie......lals.a...k.kgerpsiDvlfesaaeaygeraigviLtGmgsDGaeGlkaikeaggltiaqdpesavv 144
                                       ++      ++++ +   k ++ +p+iDv++e+aae++++++ gvi+tGmg+DGaeGl aik+agg++i+qd++++ v
  gi|336254897|ref|YP_004598004.1| 249 VTgwrngrVTVEhDdgpKrHNVKPAIDVTMETAAETVRGNLAGVIMTGMGADGAEGLGAIKAAGGKAIVQDEATSRV 325
                                       **99996632333134333445******************************************************* PP

                                       BSHHHHHHHTT--SEEE-GGGHHH CS
                    CheB_methylest 145 pgmPkaaieagavdevlpleeiae 168
                                       +gmPk a+e++ vd vlp  ++ae
  gi|336254897|ref|YP_004598004.1| 326 YGMPKVAAEQVDVDMVLPKGRLAE 349
                                       ***********999****988876 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.2   3.4e-26     2e-22       2     104 ..       5     108 ..       4     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 3.4e-26
                                       EEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEE CS
                      Response_reg   2 livdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviilt 78 
                                       +i+dD+ ++re l ++le+ g+e+v+ a++g+ea++++ + ++d+ ++Di+mpg++G+e+++++ +++p++  +i +
  gi|336254897|ref|YP_004598004.1|   5 VIADDSAVMRETLGKILEDGGVEVVGRAKNGTEAVAMIGRLEPDVATIDIQMPGLTGHEVIERVMADNPTPMLVISS 81 
                                       69**************************************************************9999666666666 PP

                                       .SSTSHHHHHHHHHCTESEEEESSG-H CS
                      Response_reg  79 .ahseeedavealkagaddflsKpfdp 104
                                        ++++ + + +al+aga+df++Kp   
  gi|336254897|ref|YP_004598004.1|  82 qTTKNADATFDALEAGAVDFIAKPSGD 108
                                       45555788899*************865 PP

>> DUF2023  Protein of unknown function (DUF2023)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00022       1.3      17      77 ..      77     137 ..      74     141 .. 0.91
   2 ?    3.5   0.0     0.013        75      11      44 ..     193     225 ..     181     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00022
                                       EEEEEEEGGGHHHHHHHHHHTT--EEEEE-TSSEEEEEEE-HHHHHHHHHHHTS-GGG--H CS
                           DUF2023  17 lvlltlkkkeeelvvkrLekkeieylvqevseekvnlffGkkecievvrslvkkplneltp 77 
                                       lv+   ++k+++++ + Le   ++++ ++ +++ v+++  ++e++e v+ +++ ++++ t+
  gi|336254897|ref|YP_004598004.1|  77 LVISSQTTKNADATFDALEAGAVDFIAKPSGDNSVDIWSKQDEIVEQVEAVASADVSKATE 137
                                       6778888999999**************************************9999888775 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.013
                                       HCTS-SEEEEEEEGGGHHHHHHHHHHTT--EEEE CS
                           DUF2023  11 kkgvRklvlltlkkkeeelvvkrLekkeieylvq 44 
                                       + g+R lv+  ++++++e + krL++++ +y ++
  gi|336254897|ref|YP_004598004.1| 193 RAGLRILVVQHMADHYTERFAKRLNDRT-AYDIR 225
                                       469*********************9764.45555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2794.56
//
Query:       gi|336254898|ref|YP_004598005.1|  [L=668]
Description: signal transduction histidine kinase CheA [Halopiger xanaduensis SH-6]
Scores for complete 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   70.5   0.7    2.8e-19   69.1   0.7    1.8  1  CheW          CheW-like domain
    4.7e-19   69.0   0.3    4.7e-19   69.0   0.3    2.5  3  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
      2e-18   66.4   1.0    2.6e-17   62.8   0.0    2.7  2  Hpt           Hpt domain
    9.2e-08   32.4   3.4    2.7e-07   30.9   3.4    1.9  1  H-kinase_dim  Signal transducing histidine kinase, homodimeri
     0.0024   17.7   0.4     0.0069   16.2   0.0    1.9  2  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
      0.003   17.6   0.1      0.024   14.7   0.0    2.7  2  P2            P2 response regulator binding domain
  ------ inclusion threshold ------
       0.06   13.3   2.2       0.15   12.0   0.1    2.8  2  HATPase_c_2   Histidine kinase-like ATPase domain
        7.7    6.7   6.4       0.75   10.0   0.8    2.3  2  DUF4530       Domain of unknown function (DUF4530)
        9.6    6.0  21.2        0.1   12.4   2.2    3.1  3  Sigma70_ner   Sigma-70, non-essential region


Domain annotation for each model (and alignments):
>> CheW  CheW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.7   1.4e-22   2.8e-19       2     133 ..     544     668 .]     543     668 .] 0.97

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.4e-22
                                       EEEEEETTEEEEEEGGGEEEEEECCT.BTTTTSSTTEEEEEEETTEEEEEEEHHHHCTSSSSTTSTCEEEEEEEETT CS
                              CheW   2 lllfrlgeetyaiplakvreilevppitpipgapgavlgvinlrGevipvidLrellglgpeesrentrvivvelgn 78 
                                       +l +++g+e+y++p+ ++ ei e+++   ++ ++g     i++ ++v+p+++Lr  l +++  ++e++ vi +++  
  gi|336254898|ref|YP_004598005.1| 544 VLFVTVGDEQYGVPIKNIDEISEFED-VTVESVEGR--PAITHDDRVYPLLSLRDHLDVPEAAPSEDDMVIRIKDTV 617
                                       799***********************.789999999..99************************************* PP

                                       EEEEEEESEEEEEEEEECCGEETTTSSTSSTCCCEEEEEECTTSEEEEEE-CCCH CS
                              CheW  79 qvvGllVdevkgiqeivikqiepplglssdlagyisGatklgdgrlvliLDveal 133
                                       + v l  + v+g++e+vik++e  l+   + +g isGa++lg+g++v+iLDve l
  gi|336254898|ref|YP_004598005.1| 618 RQVYLRCSDVVGQEEVVIKPFEGLLS---GAPG-ISGASVLGEGEVVMILDVETL 668
                                       ************************99...8899.******************986 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 ?   -1.7   0.1         2     4e+03      11      68 ..     309     371 ..     299     385 .. 0.58
   2 !   69.0   0.3   2.4e-22   4.7e-19       3     110 ..     398     537 ..     396     539 .. 0.89
   3 ?   -3.7   0.0       8.6   1.7e+04      34      46 ..     605     617 ..     584     620 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2
                                       HHHHHHHHHHHS.TTTEEEEEEEEEE....TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTC CS
                         HATPase_c  11 snlvdNavkfat.kageieveikase....ddlvisveDnGiGipkedlkklfekfsq.ddstk 68 
                                        ++v+  +k  +  +++  ve +  e    ++++ s +D+   i    lkk+ ++f +  ++ +
  gi|336254898|ref|YP_004598005.1| 309 EEMVTSRIKLRKiIEEHDLVEAED-EleehGKITSSLQDTVLQIRLVPLKKIVGNFPRvVRDIS 371
                                       555555555422333344444442.234345666678888888888888888888877633333 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 2.4e-22
                                       HHHHHHHHHHHHHHHHHH......HSTTTEEEEEEEEEE...TEEEEEEEESSSSSTTHHHT............... CS
                         HATPase_c   3 ekrLrqiisnlvdNavkf......atkageieveikase...ddlvisveDnGiGipkedlk............... 55 
                                       ++ L+++i+n+vd+ ++       ++k  e+++++   e   d+++i+veD+G G+++e +                
  gi|336254898|ref|YP_004598005.1| 398 SDPLMHLIRNAVDHGIESpeerekKGKPREGSIKLVG-ErerDRVSITVEDDGAGLDVERIRekavekgikteeevk 473
                                       689**************98887663333355555553.12469********************************** PP

                                       .........GTCS.TTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  56 .........klfe.kfsqddstkrggggtGlGlsivkklvelmgGeiwvesepgrGttftftlpl 110
                                                ++f   fs+  ++ ++ +g+G+G+ +v+++v+ ++G+i+vesep++Gt +t+tlp 
  gi|336254898|ref|YP_004598005.1| 474 vlddsevfdLIFHpGFST-TEEVTEVSGRGVGMDVVNQVVRGVDGSINVESEPDEGTAITLTLPV 537
                                       ************99****.999999****************9*********************97 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 8.6
                                       EETEEEEEEEESS CS
                         HATPase_c  34 seddlvisveDnG 46 
                                       sedd vi+++D+ 
  gi|336254898|ref|YP_004598005.1| 605 SEDDMVIRIKDTV 617
                                       4589999999985 PP

>> Hpt  Hpt domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.0   1.3e-20   2.6e-17       4      82 ..       6     101 ..       3     104 .. 0.91
   2 ?    1.1   0.2      0.24   4.9e+02      14      32 ..     159     177 ..     138     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 1.3e-20
                                       HHHHHHHHHHHHHHHHHH........SCCHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHH..HCTSCHHHHH CS
                               Hpt   4 elfleeaeelleqleqal........dqedlqelaraaHtLKGsagmlGltelaelahelEdlld..ragelelepe 70 
                                        +f++e++e++ +l++al        ++++++ ++r+aH LKG  g +G+t+ + +ah++Edlld  r+gel+++pe
  gi|336254898|ref|YP_004598005.1|   6 STFVQESQEDIRKLNNALldleddpeSSDAIETVFRVAHNLKGNFGVMGYTKASNMAHAIEDLLDciRDGELAVTPE 82 
                                       58*******************99877777************************************************ PP

                                       HHH.......HHHHHHHHH CS
                               Hpt  71 lle.......alkalleal 82 
                                        ++       +l+a+++++
  gi|336254898|ref|YP_004598005.1|  83 RMDlifegvdHLEAMVNEI 101
                                       ***8887777777777776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.24
                                       HHHHHHHHSCCHHHHHHHH CS
                               Hpt  14 leqleqaldqedlqelara 32 
                                       le+l++a+d ed +el+ra
  gi|336254898|ref|YP_004598005.1| 159 LEELAEAVDLEDDEELFRA 177
                                       899**************97 PP

>> H-kinase_dim  Signal transducing histidine kinase, homodimeric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   3.4   1.3e-10   2.7e-07       2      69 .]     292     351 ..     291     351 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.3e-10
                      H-kinase_dim   2 stlRVdakrlDyLlnlvGElVitkarLnqsleefrfenglkasvtelksslqnlgrisgeLQegvmki 69 
                                       +++RVd++ +D+L n+v E+V ++ +L++++ee            e +++l++ g+i++ LQ+ v++i
  gi|336254898|ref|YP_004598005.1| 292 ESIRVDVEQIDQLYNQVEEMVTSRIKLRKIIEEHD--------LVEAEDELEEHGKITSSLQDTVLQI 351
                                       58*********************************........7888999999************987 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 ?   -3.4   0.1       3.9   7.8e+03      95     124 ..     288     316 ..     285     326 .. 0.61
   2 !   16.2   0.0   3.4e-06    0.0069       7      56 ..     401     464 ..     396     507 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.9
                       HATPase_c_3  95 egesstltldvdkidkenekvleeltveei 124
                                       ++e + +++dv++id+   +++ee+ +++i
  gi|336254898|ref|YP_004598005.1| 288 SQEVESIRVDVEQIDQLY-NQVEEMVTSRI 316
                                       455567888888888644.44555555444 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.4e-06
                       HATPase_c_3   7 laelvdNsldAdaen..............vkievnknrgktgeivieDdGkGmseeelkn.alrl 56 
                                       l+ l++N++d   e+              +k++ +++r +  +i++eDdG+G++ e +++ a + 
  gi|336254898|ref|YP_004598005.1| 401 LMHLIRNAVDHGIESpeerekkgkpregsIKLVGERER-DRVSITVEDDGAGLDVERIREkAVEK 464
                                       889*******999999999********99999999987.799**************999866654 PP

>> P2  P2 response regulator binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.024       2      57 ..     175     229 ..     174     249 .. 0.90
   2 ?   -3.0   0.1         4   8.1e+03      65      79 ..     558     572 ..     543     573 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                       EEEEEE--TT-SSHHHHHHHHHHHHHHTTEEEEEES-HHHHHTT-SSSEEEEEEEE CS
                                P2   2 ykikvkldedclmksvRaflvfkaLeelgeiiksiPsvedieeekfdegfevvllt 57 
                                       +++ v++d d + + v a+ v+ a e+  ++++++P+ + +e+e+f++ ++ +l t
  gi|336254898|ref|YP_004598005.1| 175 FRASVSIDND-DSPHVDAMFVLDATEDEYDVVRMVPEDDVLESEEFGGVLDAYLRT 229
                                       6788899988.899********************************9999999866 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4
                                       HHHHHTSSS-SEEEE CS
                                P2  65 kealasiseiesvev 79 
                                        + + +ise e+v+v
  gi|336254898|ref|YP_004598005.1| 558 IKNIDEISEFEDVTV 572
                                       455556666666666 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.87   1.7e+03      67      86 ..      97     117 ..      78     171 .. 0.70
   2 ?   12.0   0.1   7.7e-05      0.15      50     112 ..     423     515 ..     404     535 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.87
                       HATPase_c_2  67 ltvevaDsGpg.fdpetlpdp 86 
                                       ++ e++D+G+   +pe+  ++
  gi|336254898|ref|YP_004598005.1|  97 MVNEISDDGEThTNPEATIEE 117
                                       455667777766666654443 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.7e-05
                       HATPase_c_2  50 eap.egpvevrlesdeealtvevaDsGpgfdpetlpdpteeep.............................keslk 96 
                                       ++p eg++++  e++ +++ ++v+D+G+g d+e ++++++e+                               ++  
  gi|336254898|ref|YP_004598005.1| 423 GKPrEGSIKLVGERERDRVSITVEDDGAGLDVERIREKAVEKGikteeevkvlddsevfdlifhpgfstteeVTEVS 499
                                       3444588889999********************99999887778999999999998888888888888885544444 PP

                       HATPase_c_2  97 egGrGlalikglvDev 112
                                        +G+G+ +++++v  v
  gi|336254898|ref|YP_004598005.1| 500 GRGVGMDVVNQVVRGV 515
                                       5555555566666666 PP

>> DUF4530  Domain of unknown function (DUF4530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.6       5.3   1.1e+04      82     107 ..     114     139 ..     111     144 .. 0.66
   2 ?   10.0   0.8   0.00038      0.75      57     104 ..     290     336 ..     268     344 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.3
                           DUF4530  82 lreelvtileeeeeeeeeeeeeeeee 107
                                         ee+ + le  ++e+e+  + + +e
  gi|336254898|ref|YP_004598005.1| 114 TIEEIRASLEAGANESEDAADADADE 139
                                       55788888888777777766655554 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00038
                           DUF4530  57 elgnlrrvdvqllgqlcslglemgalreelvtileeeeeeeeeeeeee 104
                                       e++ + rvdv  ++ql +   em + r +l  i+ee +  e e+e ee
  gi|336254898|ref|YP_004598005.1| 290 EVESI-RVDVEQIDQLYNQVEEMVTSRIKLRKIIEEHDLVEAEDELEE 336
                                       55555.6*****************************998887777553 PP

>> Sigma70_ner  Sigma-70, non-essential region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.6   1.2e+03     182     204 .]       5      27 ..       2      27 .. 0.89
   2 ?   -0.2   8.7      0.38   7.6e+02       5      73 ..      98     163 ..      64     192 .. 0.56
   3 ?   12.4   2.2   5.2e-05       0.1      23     119 ..     235     355 ..     223     379 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.6
                       Sigma70_ner 182 wsekleeveeeiqelqqklaeie 204
                                        s +++e +e+i++l + l ++e
  gi|336254898|ref|YP_004598005.1|   5 TSTFVQESQEDIRKLNNALLDLE 27 
                                       68899*************99987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.38
                       Sigma70_ner   5 iaellelydrveageirLrdiidGflDeeeeeeeeeeeedeeeeeeeedddeeeseseaadeeelkeea 73 
                                       ++e+ +  +   + e  +++i    l++ ++e+e+++  d++++e++ dd++++++ ++a   +l+e a
  gi|336254898|ref|YP_004598005.1|  98 VNEISDDGETHTNPEATIEEIRA-SLEAGANESEDAA--DADADESASDDGDANADVADAHDVPLEELA 163
                                       44555555555555555555444.4442223333222..223333323333223333333333333322 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 5.2e-05
                       Sigma70_ner  23 rdiidGflD..............eeeeeeeeeeeedeeeeeeeeddd..eeeseseaadeeelkeealekfeelreq 83 
                                       +d + Gf D              +    + +++++++++++++eddd      +      ++  e ++  +e++ ++
  gi|336254898|ref|YP_004598005.1| 235 SDDVAGFYDenryvgdvavealgD----DLAADADSDADDTASEDDDsgR---STGGSHGSQEVESIRVDVEQIDQL 304
                                       677899999999999988754332....2222222222222223444232...233333333344444444444444 PP

                       Sigma70_ner  84 yeklrk..........alkkkgr.kskkyekareel....seefkefrLtp 119
                                       y+++++          ++++++  + ++  +++ ++     + + ++rL+p
  gi|336254898|ref|YP_004598005.1| 305 YNQVEEmvtsriklrkIIEEHDLvEAEDELEEHGKItsslQDTVLQIRLVP 355
                                       444444444666666677776443444444444333333378888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); 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):               9  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.41
# Mc/sec: 4881.87
//
Query:       gi|336254899|ref|YP_004598006.1|  [L=118]
Description: response regulator receiver protein [Halopiger xanaduensis SH-6]
Scores for 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-29  101.3   1.2    3.8e-29  101.1   1.2    1.0  1  Response_reg  Response regulator receiver domain


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 !  101.1   1.2   2.1e-33   3.8e-29       1     111 [.       3     112 ..       3     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 2.1e-33
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       vli dD+  +r+llr++lee++   v+eae+g ea+el++ee++d++++Di mp  dG+e+++ei + dp+ +v+++
  gi|336254899|ref|YP_004598006.1|   3 VLITDDSGFMRDLLREILEEDHN-IVGEAENGVEAVELYQEESPDIVFMDIVMPIKDGIEATDEITDMDPDAKVVMC 78 
                                       89*****************7777.9**************************************************** PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlkal 111
                                       t+ ++ e++++ +kaga+++++Kpf++e +l+ l
  gi|336254899|ref|YP_004598006.1|  79 TSVEQAEQMKDSIKAGAEGYITKPFQKESVLEEL 112
                                       **************************99988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 954.57
//
Query:       gi|336254900|ref|YP_004598007.1|  [L=404]
Description: inhibitor of MCP methylation CheC [Halopiger xanaduensis SH-6]
Scores for 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-21   73.5   0.4    2.4e-09   36.9   0.0    3.5  3  CheC      CheC-like family
    3.3e-15   56.0   0.1    1.1e-06   28.7   0.0    2.4  2  CheX      Chemotaxis phosphatase CheX


Domain annotation for each model (and alignments):
>> CheC  CheC-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.04   3.6e+02      16      26 ..      21      31 ..      19      34 .. 0.90
   2 !   31.2   0.0   1.6e-11   1.5e-07       4      35 ..     100     131 ..      98     134 .. 0.92
   3 !   36.9   0.0   2.7e-13   2.4e-09       1      37 [.     293     329 ..     293     330 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.04
                                      HHHHHHHTCCT CS
                              CheC 16 saatalatlln 26
                                      saa++la+l++
  gi|336254900|ref|YP_004598007.1| 21 SAADSLAQLTG 31
                                      89******997 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 1.6e-11
                                       HHHHHHHHHHHHHHHHHHHTCCTS-EEE---E CS
                              CheC   4 SAlgEigNIlaGsaatalatllnfkidisPPt 35 
                                       S ++E+gNI+++++++++a+ ln ki  sPP+
  gi|336254900|ref|YP_004598007.1| 100 SSIKEVGNIMSSGFVDGWANYLNAKIKNSPPD 131
                                       558****************************8 PP

  == domain 3  score: 36.9 bits;  conditional E-value: 2.7e-13
                                       HHHHHHHHHHHHHHHHHHHHHHTCCTS-EEE---EEE CS
                              CheC   1 melSAlgEigNIlaGsaatalatllnfkidisPPtvv 37 
                                       me+ Al+E+gNI+++++++++a+ l+ +i + PP++v
  gi|336254900|ref|YP_004598007.1| 293 MEQEALKELGNIMTSGFIDGWANVLDAEIKHKPPEFV 329
                                       8899******************************986 PP

>> CheX  Chemotaxis phosphatase CheX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.1e-09   1.8e-05       3      83 ..      61     143 ..      59     152 .. 0.87
   2 !   28.7   0.0   1.2e-10   1.1e-06       4      83 ..     254     339 ..     251     353 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.1e-09
                              CheX   3 giiglaGdisGliilsadeelalkiasal.gedeeeieedvndavgEltNmiaGnak....sklgeevklspPlvis 74 
                                       + i+l+G+isG ++l++de+  ++i+ +l   d++e     ++ + E+ N+++ ++     + l++++k spP  i+
  gi|336254900|ref|YP_004598007.1|  61 VNIDLSGEISGEVVLAFDERGRRAITDELvPADDPE---KKKSSIKEVGNIMSSGFVdgwaNYLNAKIKNSPPDYIE 134
                                       6799************************76777777...6899**************999666699*********** PP

                              CheX  75 gkeltisep 83 
                                       g++  +  +
  gi|336254900|ref|YP_004598007.1| 135 GTGVDVLPK 143
                                       **9887554 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 1.2e-10
                              CheX   4 iiglaGdisGliilsadeelalkiasal..gedeeeieedvndavgEltNmiaGnak....sklgeevklspPlvis 74 
                                       +++++G++ G++++ +d+ + ++++ +l  +e++e+   + ++a+ El N+++ ++     + l++e+k  pP++++
  gi|336254900|ref|YP_004598007.1| 254 VMEFEGKLGGYLVILFDQPSGRAVVDSLvpMETDEQWGSMEQEALKELGNIMTSGFIdgwaNVLDAEIKHKPPEFVA 330
                                       789***********************9669******9********************888455599*********** PP

                              CheX  75 gkeltisep 83 
                                       +++ +i  p
  gi|336254900|ref|YP_004598007.1| 331 DTGSSIMSP 339
                                       **9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 3267.08
//
Query:       gi|336254901|ref|YP_004598008.1|  [L=302]
Description: hypothetical protein Halxa_3518 [Halopiger xanaduensis SH-6]
Scores for 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-67  228.1   1.9    2.5e-67  226.8   0.9    1.9  3  CheF-arch  Chemotaxis signal transduction system protein F fr
  ------ inclusion threshold ------
      0.054   13.5   0.0       0.11   12.5   0.0    1.5  1  HTH_45     Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> CheF-arch  Chemotaxis signal transduction system protein F from archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.8   0.9   2.8e-71   2.5e-67       1     216 [.       5     212 ..       5     213 .. 0.99
   2 ?   -2.4   0.0      0.37   3.3e+03     175     212 ..     225     263 ..     218     267 .. 0.74
   3 ?   -0.9   0.0      0.13   1.1e+03      11      34 ..     266     287 ..     257     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 226.8 bits;  conditional E-value: 2.8e-71
                         CheF-arch   1 kiadfkGkfllvvkkgrkkkdvkWekgrilLsnkrlvlasedkkitiplssvedvg.gevPrklkdifddtvtdakv 76 
                                       ++adf+G+f+ +  +++++++    +gri+ ++kr+vl++ed+k+tipls+v+dv+ g+vP++++++fddtvt    
  gi|336254901|ref|YP_004598008.1|   5 VVADFTGRFFFNRGGTGDGTPF---TGRIITTEKRVVLVTEDEKKTIPLSRVVDVNvGTVPSHVRQFFDDTVT---- 74 
                                       69********************...************************************************.... PP

                         CheF-arch  77 sgyialktkdgenvllieaedesiekFetkLfkalLngkevlvkhpAvvGGvvqdtewekgklkvekkaielatkkg 153
                                          i +kt++g+++++ie+++es+e+F++ Lf++lL+g++++v+hpA+vGG+v+dt++ +gk+ +++++ie+++k+g
  gi|336254901|ref|YP_004598008.1|  75 ---IGYKTDEGTRSAVIESRGESVEEFVSLLFRCLLDGRKAAVRHPARVGGRVKDTSVVPGKIGIDDRRIEVRSKAG 148
                                       ...************************************************************************** PP

                         CheF-arch 154 sfveielsdvgdvereektvdgeerpvleveht..edgesvttylagkdkrkvslLerylreeye 216
                                       +f+ +++++v++++r++k  ++++r +l+v+h+   +g + t+++a++++++v+lL+r+lr+e++
  gi|336254901|ref|YP_004598008.1| 149 TFS-FDVETVMEIDRTNKIGESDDRVTLVVKHIdrGSGLTQTSLIAPSKSQYVNLLARFLRLEFD 212
                                       **9.*****************************888899**********************9987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.37
                         CheF-arch 175 geerpvleveht.edgesvttylagkdkrkvslLerylr 212
                                       + e++vl+  h+  ++ + t +l g+ +  +++L+++ +
  gi|336254901|ref|YP_004598008.1| 225 NPEKRVLVGIHAtGGDIDFTNMLDGDPTYVTNVLNSVQK 263
                                       456666666666588999999999999888888887765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.13
                         CheF-arch  11 lvvkkgrkkkdvkWekgrilLsnk 34 
                                       l+v++g++++ +   kgri++s++
  gi|336254901|ref|YP_004598008.1| 266 LIVENGNEMSLT--AKGRIIVSER 287
                                       678999999999..9*****9986 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.2e-05      0.11      38      68 ..     256     286 ..     252     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                            HTH_45  38 kYLdmLvekglikkskekYvlTekGlellek 68 
                                       + L+  ++kgli +++++ +lT+kG+ ++++
  gi|336254901|ref|YP_004598008.1| 256 NVLNSVQKKGLIVENGNEMSLTAKGRIIVSE 286
                                       679999*******************998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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 0.20s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2454.39
//
Query:       gi|336254902|ref|YP_004598009.1|  [L=557]
Description: type II secretion system protein E [Halopiger xanaduensis SH-6]
Scores for complete 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  145.4   0.0    2.5e-42  144.8   0.0    1.2  1  T2SSE        Type II/IV secretion system protein
    2.8e-05   24.6   0.1     0.0011   19.3   0.0    2.3  2  AAA_16       AAA ATPase domain
    0.00081   19.2   0.1       0.59    9.8   0.0    2.2  2  AAA_15       AAA ATPase domain
     0.0056   17.2   0.0      0.041   14.4   0.0    2.3  2  ABC_tran     ABC transporter
     0.0094   15.5   0.0      0.016   14.7   0.0    1.3  1  AAA_7        P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.033   13.9   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.032   14.3   0.0      0.077   13.1   0.0    1.6  1  Dynamin_N    Dynamin family
      0.068   13.4   0.0       0.19   12.0   0.0    1.7  1  AAA_22       AAA domain
      0.085   12.2   0.0       0.24   10.7   0.0    1.8  1  AIG1         AIG1 family
       0.14   12.1   0.0       0.39   10.6   0.0    1.7  1  Microtub_bd  Microtubule binding
       0.51   10.8   2.1        3.3    8.1   0.0    2.3  2  AAA_23       AAA domain


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 !  144.8   0.0   1.5e-45   2.5e-42       3     243 ..     172     417 ..     170     432 .. 0.95

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 1.5e-45
                             T2SSE   3 illeallddekvsdihvekpervkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvr 79 
                                        +le++++d++  dihv  p+++ v   v g++   v + +++a  r +s++    ++ + + +p++d +lp +g r
  gi|336254902|ref|YP_004598009.1| 172 GPLEPIMRDPENEDIHVIGPNECYVDHGVFGMVETSVDFGTREAFDRWLSNMGERIGNPMTDAEPIVDSTLP-DGSR 247
                                       57899********************9999999****************************************.**** PP

                             T2SSE  80 lrvvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkein 154
                                       l+v+    v    ++l+iR+ ++  l++ ++   ++l++++a+ l   +++++++ v G T sGKtt+l++++++i+
  gi|336254902|ref|YP_004598009.1| 248 LNVIYSDDVSVkgPSLTIRQGDEVPLSVTQITNWGTLSPELAAYLWLCLENEQTVFVVGETASGKTTTLNSIMSFIP 324
                                       **999864433359*************************************************************** PP

                             T2SSE 155 ksderivtvEDpvEiqleganqvqlnak......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHl 225
                                        +  +i t+ED++E+ + ++   ql ++      +++v++ +l++aaLR rP  i+vGE+R++e   + +A++TGH+
  gi|336254902|ref|YP_004598009.1| 325 RD-SKIYTAEDTAEVLPPHNTWQQLLTResqsedSVDVDMFKLVEAALRSRPEYIVVGEVRGEEGRMAFQAAQTGHP 400
                                       *9.**********************999999999999**************************************** PP

                             T2SSE 226 gslsTlHansaagalerL 243
                                       + + T Ha + ++ ++r 
  gi|336254902|ref|YP_004598009.1| 401 V-MLTFHASDIVSMIQRF 417
                                       *.*************997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.089   1.4e+02      73     124 ..      92     142 ..      72     152 .. 0.86
   2 !   19.3   0.0     7e-07    0.0011      25     116 ..     300     388 ..     288     419 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.089
                            AAA_16  73 aqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellk 124
                                        +   +++llr  +++++  + +++++++ee l+++ +++g+e   lle+lk
  gi|336254902|ref|YP_004598009.1|  92 FESV-KDSLLRRSATKKAPEKDAEYDDRIEELLQETTHIKGEETDNLLEELK 142
                                       5566.669999999999999********************999988888875 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 7e-07
                            AAA_16  25 elvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                       + v+++Ge ++GK++ +++++  + +d  +++++ +++ l    p  ++ q+l+re+  ++  d +  +++ea+ + 
  gi|336254902|ref|YP_004598009.1| 300 QTVFVVGETASGKTTTLNSIMSFIPRDSkIYTAEDTAEVL---PPHNTWQQLLTRESQSEDSVDVDMFKLVEAALRS 373
                                       789*********************9996599999999999...7777799999999999999999888777777666 PP

                            AAA_16 101 leealaavpelagaea 116
                                        +e +  v+e++g+e 
  gi|336254902|ref|YP_004598009.1| 374 RPEYIV-VGEVRGEEG 388
                                       665555.666666654 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.2    0.0024         4     209     266 ..      83     140 ..      74     186 .. 0.79
   2 !    9.8   0.0   0.00036      0.59      24      52 ..     299     328 ..     292     370 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0024
                            AAA_15 209 edsekkssllgklkekileealqekleeelteklkeiqeklkeidkklaeelkkilkk 266
                                       ++se+++++++++k+++l+ ++ +k+ e++ e  ++i+e l+e+  + +ee+ + l++
  gi|336254902|ref|YP_004598009.1|  83 TLSEEEQEVFESVKDSLLRRSATKKAPEKDAEYDDRIEELLQETTHIKGEETDNLLEE 140
                                       6789999*************99999988899999999999999888888888754433 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00036
                            AAA_15  24 e.ltvliGkNnsGKSsilealdlFlnnkek 52 
                                       e + +++G+ +sGK++ l+ +  F+ +++k
  gi|336254902|ref|YP_004598009.1| 299 EqTVFVVGETASGKTTTLNSIMSFIPRDSK 328
                                       337899*****************9987633 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2   1.9e+03      61      90 ..      75     124 ..      19     142 .. 0.59
   2 !   14.4   0.0   2.5e-05     0.041       6      42 ..     294     329 ..     291     373 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                                       EEEE-SS--S-TTSB.HHHH...................HHHTCHHHHHH CS
                                       xxxxxxxxxxxxxxx.xxxx...................xxxxxxxxxxx RF
                          ABC_tran  61 igvlpqepqlfpelt.vren...................esdeeiekals 90 
                                       ++++  ep+l +e + v e+                   e+d++ie++l+
  gi|336254902|ref|YP_004598009.1|  75 MQYFAVEPTLSEEEQeVFESvkdsllrrsatkkapekdaEYDDRIEELLQ 124
                                       33333333333333323333444555555555555555555555555555 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.5e-05
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGei 42 
                                       l l++ ++v +vGe+ +GK+t l+ ++        +i
  gi|336254902|ref|YP_004598009.1| 294 LCLENEQTVFVVGETASGKTTTLNSIMSFIP-RDSKI 329
                                       678999********************98864.44444 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 !   14.7   0.0     1e-05     0.016      26      61 ..     292     327 ..     283     347 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                             AAA_7  26 lelllknkkpvllvGptGtGKtviikdllkkldkek 61 
                                       l l+l+n++ v++vG+t +GKt++++++++ +++++
  gi|336254902|ref|YP_004598009.1| 292 LWLCLENEQTVFVVGETASGKTTTLNSIMSFIPRDS 327
                                       66899***********************99888654 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 ?   13.9   0.0     2e-05     0.033       3      44 ..     275     321 ..     273     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                            AAA_29   3 rlqlvNWgtfdghtie.....idlkgatlltGpsGsGKSTllDAiqa 44 
                                         q+ NWgt++ + +      ++ +++++++G++ sGK+T l +i+ 
  gi|336254902|ref|YP_004598009.1| 275 VTQITNWGTLSPELAAylwlcLENEQTVFVVGETASGKTTTLNSIMS 321
                                       57999****9985533111114444499************9988875 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.7e-05     0.077       1      34 [.     302     333 ..     302     384 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.7e-05
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34 
                                       + vvG++ sGK++ ln+++   + pr++ + T+ 
  gi|336254902|ref|YP_004598009.1| 302 VFVVGETASGKTTTLNSIMS--FIPRDSKIYTAE 333
                                       68****************97..55***9999986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.19       5      56 ..     299     348 ..     296     383 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl 56 
                                       ++ ++v+Ge+ +GKTt+l+ +++  ++++k+ +   ++++v +p+ t +++l
  gi|336254902|ref|YP_004598009.1| 299 EQTVFVVGETASGKTTTLNSIMSFIPRDSKIYT-AEDTAEVLPPHNT-WQQL 348
                                       67789******************9986444333.3333444444444.4444 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00015      0.24       2      22 ..     301     321 ..     300     347 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                                       EEEEESSTTSSHHHHHHHHHT CS
                              AIG1   2 tivlvGktgnGkSaTgNsilg 22 
                                       t+ +vG t +Gk +T Nsi+ 
  gi|336254902|ref|YP_004598009.1| 301 TVFVVGETASGKTTTLNSIMS 321
                                       789****************85 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00024      0.39      69     102 ..     286     318 ..     275     337 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                                       CCCHHHHHHHHTT--EEEEEEES........... CS
                       Microtub_bd  69 eeisqlvqsaldgynvcifaygqTGsGKtyTmeg 102
                                        e+++++  +l++   ++f +g+T sGKt T+++
  gi|336254902|ref|YP_004598009.1| 286 PELAAYLWLCLENE-QTVFVVGETASGKTTTLNS 318
                                       57888888899765.579*************987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.9      0.27   4.4e+02     143     176 ..     100     133 ..      69     165 .. 0.56
   2 ?    8.1   0.0     0.002       3.3      22      39 ..     302     319 ..     282     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.27
                            AAA_23 143 feefelkdkkerleelekeleeledekkllekle 176
                                         + ++k+ +e+ +e+ + +eel +e   ++ +e
  gi|336254902|ref|YP_004598009.1| 100 LRRSATKKAPEKDAEYDDRIEELLQETTHIKGEE 133
                                       2223335555566666666666665555554442 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.002
                            AAA_23  22 tlItGpNGaGKTTildAi 39 
                                       + ++G++ +GKTT l+ i
  gi|336254902|ref|YP_004598009.1| 302 VFVVGETASGKTTTLNSI 319
                                       6789***********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 4254.18
//
Query:       gi|336254903|ref|YP_004598010.1|  [L=252]
Description: AAA ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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-15   56.8   0.2    2.9e-15   56.2   0.2    1.2  1  ATPase       KaiC
      8e-05   22.3   0.1    0.00021   20.9   0.1    1.7  1  AAA_25       AAA domain
    0.00018   20.9   0.8     0.0012   18.2   0.8    2.0  1  Rad51        Rad51
     0.0008   19.4   0.1     0.0071   16.3   0.0    2.1  2  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
     0.0014   18.6   0.2     0.0097   15.8   0.2    2.1  1  NACHT        NACHT domain
     0.0064   15.7   0.0        1.9    7.6   0.0    2.1  2  PAXNEB       PAXNEB protein
  ------ inclusion threshold ------
      0.011   14.9   0.0          2    7.5   0.0    2.2  2  TIP49        TIP49 P-loop domain
      0.016   15.5   0.1      0.032   14.5   0.1    1.5  1  AAA_22       AAA domain
      0.043   13.4   0.1       0.49   10.0   0.1    2.2  1  SRP54        SRP54-type protein, GTPase domain
      0.049   13.4   0.1       0.13   12.0   0.0    1.5  1  IstB_IS21    IstB-like ATP binding protein
      0.061   13.7   0.1       0.12   12.8   0.1    1.5  1  AAA_16       AAA ATPase domain
      0.069   13.1   0.2       0.23   11.3   0.0    1.9  2  APS_kinase   Adenylylsulphate kinase
      0.074   13.5   0.3       0.19   12.1   0.3    1.8  1  AAA          ATPase family associated with various cellular a
      0.094   12.0   0.0       0.16   11.2   0.0    1.4  1  MipZ         ATPase MipZ
       0.11   11.6   0.0       0.16   11.1   0.0    1.4  1  ArsA_ATPase  Anion-transporting ATPase
       0.17   12.1   0.1       0.36   11.0   0.1    1.5  1  FF           FF domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.2   2.6e-18   2.9e-15       9     209 ..      19     227 ..      10     250 .. 0.72

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 2.6e-18
                            ATPase   9 DeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlek.leeegkla 84 
                                        + l gGip g++vl+ G++G+GK+ ++++F++  +++ g+ + f ++e + + ++ ++ sl  ++e+ l  e++l+
  gi|336254903|ref|YP_004598010.1|  19 NKELGGGIPTGSIVLMEGDYGAGKSAISQRFAYGLCQT-GKSVTFLSTELEVQGFIDQMDSLNYNVEEhLLFENMLF 94 
                                       44567****************************99999.***************************98433444444 PP

                            ATPase  85 i.idasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl..ayeekeava.....Reilrqlvrvlkk 153
                                       +  d+ + +   ++ +++++ + l+++l+e      a  v+iD+ +++  +  + ea++     R+   +++++l++
  gi|336254903|ref|YP_004598010.1|  95 LhGDLDSGGVL-SSTTEEDNRQDLLTDLMEEETLWSADIVIIDTFDAIlrNDPKFEALVrqneeRQAALEIISFLRD 170
                                       40455555555.55699999*************************99952222333334111115556666666643 PP

                            ATPase 154 ...lgvTailvsekss.seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtk 209
                                           g + +l+ + s+ +eea+g +     i+d  i L+  e+ ++++R l i    g +
  gi|336254903|ref|YP_004598010.1| 171 iisQGKVVVLTVDPSTvGEEAIGPF--RS-IADVFIELEMIEVGNDIRRQLFIKRFAGMG 227
                                       1113445555555333344444444..34.89********************98766555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   1.9e-07   0.00021      23     164 ..      19     151 ..       8     182 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.9e-07
                            AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal. 97 
                                       ++ ++g +p g+++l  G+ g+GK+++    a+ ++ tGk            V ++s+E   +++   +  +  ++ 
  gi|336254903|ref|YP_004598010.1|  19 NKELGGGIPTGSIVLMEGDYGAGKSAISQRFAYGLCqTGK-----------SVTFLSTELEVQGFIDQMDSLNYNVe 84 
                                       45566778****************************8888...........79999999999999999998887764 PP

                            AAA_25  98 ...rddarllvldlagv.eslpLfakdrggtlltadvdaleaaieeveg...vrlvviDplsralggdensnsd 164
                                           +   l++   +g  +s  ++++++++  ++  + +l+++    e    ++ v+iD+++++l++d++ ++ 
  gi|336254903|ref|YP_004598010.1|  85 ehlLFENMLFL---HGDlDSGGVLSSTTEEDNRQDLLTDLMEE----ETlwsADIVIIDTFDAILRNDPKFEAL 151
                                       33222222222...22323333333333332222222223333....224459**************9875555 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.8   1.1e-06    0.0012      12      80 ..       3      66 ..       1     186 [. 0.61

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.1e-06
                                      HHHSS-EE--S-H.HHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHH.HTTS-TTTS--SSEEEEEESS CS
                             Rad51 12 krsellqlttGsk.klDelLgGGietgsiteifGefrsGktqlchtlcv.tvqlplelgGgegkavyidte 80
                                      kr+++ ++   ++ +l++ LgGGi+tgsi  + G++++Gk+ +++ ++   +q         + + +++te
  gi|336254903|ref|YP_004598010.1|  3 KRNNIFSIGLDDRdRLNKELGGGIPTGSIVLMEGDYGAGKSAISQRFAYgLCQTG-------KSVTFLSTE 66
                                      566666666555426999*************************999886345544.......344455554 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.3e-06    0.0071      10      53 ..      18      62 ..      12      71 .. 0.80
   2 ?    0.3   0.0      0.58   6.5e+02       7      31 ..      76     102 ..      73     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.3e-06
                                      HHHHHHHCH..TEEEEEEESTTSSHHHHHHHHHHHTT------TTT CS
                              TsaE 10 lgkklakal..gdvilLeGdLGaGKTtlvrglakalgveevkSPTF 53
                                      l k+l+  +  g+++l+eGd GaGK+++++ +a +l +++ kS TF
  gi|336254903|ref|YP_004598010.1| 18 LNKELGGGIptGSIVLMEGDYGAGKSAISQRFAYGL-CQTGKSVTF 62
                                      55555555566889********************99.557788887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHCH..TEEEEEEESTTSS CS
                              TsaE   7 tealgkklakal..gdvilLeGdLGaG 31 
                                       +++l  ++ ++l  +++++L+GdL +G
  gi|336254903|ref|YP_004598010.1|  76 MDSLNYNVEEHLlfENMLFLHGDLDSG 102
                                       55666666666667889*******988 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   8.6e-06    0.0097       2     161 ..      31     221 ..      30     225 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.6e-06
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-......-HCHHHCCCCTS--SSS-C.... CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna...rsladllfsqlpepaapvse.... 71 
                                       +v+++G+ G GK++  q++a  + +      +  l+  l+++ + ++ ++        llf++++ + ++ +     
  gi|336254903|ref|YP_004598010.1|  31 IVLMEGDYGAGKSAISQRFAYGLCQTGKSV-T-FLSTELEVQGFIDQMDSlnyNVEEHLLFENMLFLHGDLDSggvl 105
                                       6899******************99888333.2.34444555555555555774455668899999999999888865 PP

                                       ....CHHHHCCSCCCEE..............EEEE-STT-SS-TCH.................HHHHHCTTTTT--E CS
                             NACHT  72 ....vwavllelperlL..............lilDglDelvtdlgq........kekqpvrtlLselirkkllpeas 122
                                                  +++ lL               i+D +D + + +++        +e+q++ + + + +r  + ++  
  gi|336254903|ref|YP_004598010.1| 106 ssttE----EDNRQDLLtdlmeeetlwsadiVIIDTFDAILRNDPKfealvrqnEERQAALEII-SFLRDIISQGKV 177
                                       33330....3344445577778888899************9988889******66666666666.999999999*** PP

                                       EEEEEECCCHHH.....HCTTSSCE......EEEE--TCCHHHHHHHH CS
                             NACHT 123 llltvrpralrd.....leeqleea....ivlevegfsesrrkqlvrk 161
                                       ++ltv p+++ +          +      i le+ + + + r+ql+ k
  gi|336254903|ref|YP_004598010.1| 178 VVLTVDPSTVGEeaigpF---RS-IadvfIELEMIEVGNDIRRQLFIK 221
                                       ********9977542221...11.134456666666666666666655 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0017       1.9      25      45 ..      17      37 ..       3      79 .. 0.71
   2 !    6.2   0.0    0.0043       4.8     227     286 ..     154     210 ..     141     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0017
                            PAXNEB 25 sLDklLgGGLplGsillieEd 45
                                       L k LgGG+p Gsi+l+e d
  gi|336254903|ref|YP_004598010.1| 17 RLNKELGGGIPTGSIVLMEGD 37
                                      36667*************977 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0043
                            PAXNEB 227 eeskpedllkFLhsLrallrssnlvalitlplsliarssslvrkieqlvDtvieLesfag 286
                                       ++++ ++ l+ +  Lr ++++ ++v+l   p+++    ++ +  +++++D  ieLe ++ 
  gi|336254903|ref|YP_004598010.1| 154 QNEERQAALEIISFLRDIISQGKVVVLTVDPSTVG---EEAIGPFRSIADVFIELEMIEV 210
                                       57888999************999999888888877...899999***********98877 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1    0.0086       9.7      50      75 ..      29      54 ..      24      70 .. 0.76
   2 ?    7.5   0.0    0.0018         2      17      66 ..     142     192 ..     114     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0086
                                      XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 50 GravLlaGpsgtGktalaiaiskelg 75
                                      G  vL+ G+ g+Gk+a++   +  l 
  gi|336254903|ref|YP_004598010.1| 29 GSIVLMEGDYGAGKSAISQRFAYGLC 54
                                      889*************9877766654 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXX CS
                             TIP49  17 geaekeeeglvGqkkareaagvivelikekklaGravLlaGpsgt.Gktal 66 
                                       ++ + + e+lv q++ r+aa  i++++++    G++v+l+ +++t G  a+
  gi|336254903|ref|YP_004598010.1| 142 LRNDPKFEALVRQNEERQAALEIISFLRDIISQGKVVVLTVDPSTvGEEAI 192
                                       556667789*********************999**9998877665376665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.9e-05     0.032       6     115 ..      30     154 ..      27     184 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............ 70 
                                       +i++  G  G+GK+   +r+++ l++  k    ++++++ +l +++   d +  l  ++++ l              
  gi|336254903|ref|YP_004598010.1|  30 SIVLMEGDYGAGKSAISQRFAYGLCQTGK----SVTFLSTELEVQG-FIDQMDSLNYNVEEHLLFenmlflhgdlds 101
                                       6778889*****************97654....4444444444444.333334444444444444444555555555 PP

                            AAA_22  71 ........erlsseell.ealeqalraravielliiDEaqh.lrseealeeLrsl 115
                                               e++++++ll +++e+     a+  ++iiD ++  lr++  +e L++ 
  gi|336254903|ref|YP_004598010.1| 102 ggvlssttEEDNRQDLLtDLMEEETLWSAD--IVIIDTFDAiLRNDPKFEALVRQ 154
                                       799988888888888887777777777777..*********77534444444332 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   0.1   0.00044      0.49       3      91 ..      31     137 ..      29     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00044
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE.................. CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvik.................. 61 
                                       ++l+ G  GaGK     + a  l + gk+v + ++     + ++Q+  l  +++ +++                   
  gi|336254903|ref|YP_004598010.1|  31 IVLMEGDYGAGKSAISQRFAYGLCQTGKSVTFLSTELEVQGFIDQMDSLNYNVEEHLLFenmlflhgdldsggvlss 107
                                       78999****************************************99988776644332244444456666666653 PP

                                       SSTTSCHHHHHHHHHHHHHHTTSSEEEEEE CS
                             SRP54  62 kkeeadpaavakeavekakeekidvvlvDT 91 
                                       ++ee++  +++ + +e++   ++d+v++DT
  gi|336254903|ref|YP_004598010.1| 108 TTEEDNRQDLLTDLMEEETLWSADIVIIDT 137
                                       334445666677777777777777777777 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 ?   12.0   0.0   0.00011      0.13      49      84 ..      31      66 ..      24      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                         IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlfvrve 84
                                       +++ G  G+GKs ++  +++  +++g+sv+f+++e
  gi|336254903|ref|YP_004598010.1| 31 IVLMEGDYGAGKSAISQRFAYGLCQTGKSVTFLSTE 66
                                      46778***************************9986 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    0.0001      0.12      22     142 ..      27     183 ..      13     185 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdql.esaipysalaqalareellrqllde......... 88 
                                       +++++vl  G+ G GKs++ ++++  l+++      gk + + +++++ + ++++ +  +l   ++++         
  gi|336254903|ref|YP_004598010.1|  27 PTGSIVLMEGDYGAGKSAISQRFAYGLCQT------GKSVTFlSTELEVQGFIDQMD--SLNYNVEEHllfenmlfl 95 
                                       33499*******************766666......444444333333335666662..333333333334444444 PP

                            AAA_16  89 ..........aesaeleawrekleeala........................avpelagaea.......srllellk 124
                                                 +++   e+ r+ l++ l                                  a       ++ + ++ 
  gi|336254903|ref|YP_004598010.1|  96 hgdldsggvlSST-TEEDNRQDLLTDLMeeetlwsadiviidtfdailrndpKFE------AlvrqneeRQAALEII 165
                                       4444455553222.33333333333333355555555555555555444333111......1223333455555666 PP

                            AAA_16 125 rll.allsrderplvlvlD 142
                                       ++l + +s+ ++ +vl++D
  gi|336254903|ref|YP_004598010.1| 166 SFLrDIISQ-GKVVVLTVD 183
                                       666555555.443666655 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0002      0.23       2      37 ..      29      64 ..      28      73 .. 0.93
   2 ?   -1.4   0.0       1.7   1.9e+03      50      79 ..     152     181 ..     145     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                      -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                        APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvylLd 37
                                      g +v++ G  g+GKs+i+++++  L ++g+sv+ L 
  gi|336254903|ref|YP_004598010.1| 29 GSIVLMEGDYGAGKSAISQRFAYGLCQTGKSVTFLS 64
                                      7899***************************99986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
                                       -SSHHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                        APS_kinase  50 gfseedRkenirrvaevaklladaglivlv 79 
                                         ++e+R+  +  ++++   +++  ++vl+
  gi|336254903|ref|YP_004598010.1| 152 VRQNEERQAALEIISFLRDIISQGKVVVLT 181
                                       557788888888888888777777777765 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 ?   12.1   0.3   0.00017      0.19       2     106 ..      33     180 ..      32     203 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                                       EEESSTTSSHHHHHHHHHHHH.....THEE..EEEETTTCSSS..............................STTH CS
                               AAA   2 llyGppGtGKTllakavakel.....gvef..leisgsellsk..............................yvge 41 
                                       l+ G  G GK+++ +  a  l     +v+f   e+++  ++++                                  
  gi|336254903|ref|YP_004598010.1|  33 LMEGDYGAGKSAISQRFAYGLcqtgkSVTFlsTELEVQGFIDQmdslnynveehllfenmlflhgdldsggvlSSTT 109
                                       56666777777776666666544433233322344444555335666666666666666777777777777764444 PP

                                       HHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHH....TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEE CS
                               AAA  42 sekkirelfkeakeka...kpsilfiDEidalaksr....sgseseeeervvnqLlteldgvkkkeskvivi 106
                                        e++ ++l++++ e++   +  i++iD +da+ +++        ++ee++++ +++++l +  ++ +kv+v+
  gi|336254903|ref|YP_004598010.1| 110 EEDNRQDLLTDLMEEEtlwSADIVIIDTFDAILRNDpkfeALVRQNEERQAALEIISFLRDIISQ-GKVVVL 180
                                       555556666665444458888***************99875567778888888888888888774.546655 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.16       3     107 ..      31     137 ..      29     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                       EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT-.-----EEE-SSS-HHHHT CS
                              MipZ   3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkgl.sLplpealalseaeeaev 78 
                                       ivl     G+Gks+++   a  L ++G++v+ +  +l  + +   ++     +e++ l +  l  +  l+++ + + 
  gi|336254903|ref|YP_004598010.1|  31 IVLMEGDYGAGKSAISQRFAYGLCQTGKSVTFLSTELEVQGFIDQMDSLNYNVEEHLLfENMLFLHGDLDSGGVLSS 107
                                       78888888****************************99999998888766555544431333445556777777777 PP

                                       TS-HHHHHHHHHHHHHH.HHHH-SEEEEE- CS
                              MipZ  79 eeeeeaevaeleelvad.leaeldfividt 107
                                       + ee++++  l++l+++ +  ++d+++idt
  gi|336254903|ref|YP_004598010.1| 108 TTEEDNRQDLLTDLMEEeTLWSADIVIIDT 137
                                       77777776777777765155789*****98 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.16       3      38 ..      31      66 ..      29     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      ++l+ G  G GK+++s  +a+ l ++gk+v  +st 
  gi|336254903|ref|YP_004598010.1| 31 IVLMEGDYGAGKSAISQRFAYGLCQTGKSVTFLSTE 66
                                      7999******************************96 PP

>> FF  FF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00032      0.36      27      48 ..     140     162 ..     123     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                                       HHCTTSCCCHHG.TSHHHHHHHH CS
                                FF  27 kilenDpRYlal.ldkseReelF 48 
                                        il+nDp + al +  +eR+++ 
  gi|336254903|ref|YP_004598010.1| 140 AILRNDPKFEALvRQNEERQAAL 162
                                       699***************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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):              16  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 1972.84
//
Query:       gi|336254904|ref|YP_004598011.1|  [L=753]
Description: flagella accessory C family protein [Halopiger xanaduensis SH-6]
Scores for complete 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-24   85.7   0.0    2.8e-24   84.8   0.0    1.5  1  Arch_fla_DE     Archaeal flagella protein
    1.2e-20   73.7   4.9    2.1e-20   72.8   4.9    1.5  1  FlaC_arch       Flagella accessory protein C (FlaC)
     0.0022   17.9   0.0     0.0035   17.2   0.0    1.2  1  Sec34           Sec34-like family
  ------ inclusion threshold ------
      0.021   14.7   0.5      0.033   14.1   0.5    1.2  1  Dynactin_p22    Dynactin subunit p22
      0.046   13.0   0.0      0.081   12.2   0.0    1.3  1  CcmH            Cytochrome C biogenesis protein
      0.059   13.4   0.8        0.1   12.6   0.8    1.3  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
      0.078   13.4   1.5       0.14   12.7   1.5    1.3  1  ZapB            Cell division protein ZapB
        0.1   11.5   0.0       0.17   10.7   0.0    1.3  1  Fmp27_WPPW      RNA pol II promoter Fmp27 protein domain
       0.18   12.0   2.6       0.53   10.5   2.6    1.8  1  XhlA            Haemolysin XhlA
       0.52   10.8   3.1       0.59   10.6   0.4    2.6  2  LPP             Lipoprotein leucine-zipper
       0.72   10.0   1.4        1.6    8.9   0.5    1.7  2  bZIP_1          bZIP transcription factor


Domain annotation for each model (and alignments):
>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.8   0.0   1.7e-27   2.8e-24       2      94 ..     389     480 ..     388     481 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 1.7e-27
                       Arch_fla_DE   2 ekpyLeelpedyaaelvvleWlefLvervgvenaaealdyYeeigWiseevreeLlkylkgikle.deekeelkkse 77 
                                       ++pyLe++p++y++++vv++Wl++Lv+++g ++aa+++++Ye+i W+s+ v+++L+++l+g++   d e+ e+ +s+
  gi|336254904|ref|YP_004598011.1| 389 GRPYLESIPSEYDTQFVVMDWLDYLVSEAGLNGAARTIKFYESIRWVSSPVEAHLQTTLNGFGGGpDVEDPEP-RSA 464
                                       589***********************************************************97345554455.688 PP

                       Arch_fla_DE  78 ltvedHvkSllyiekla 94 
                                       l v +H++Sl+ i++++
  gi|336254904|ref|YP_004598011.1| 465 LGV-NHKRSLWRISQIK 480
                                       988.9*********997 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 !   72.8   4.9   1.3e-23   2.1e-20       1      55 []     121     175 ..     121     175 .. 0.99

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 1.3e-23
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdllsLYEvVsnqvNPFv 55 
                                       r++e+En +++ls++++tv++ene++s+s+ee++e++++ll++YE+V+++vNPFv
  gi|336254904|ref|YP_004598011.1| 121 RVEEIENNVGSLSSTVNTVQSENEKISDSLEEIEEDIRKLLEVYEMVTQGVNPFV 175
                                       8*****************************************************8 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.1e-06    0.0035      14      83 ..     117     186 ..     113     191 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-06
                             Sec34  14 elleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpitrkLns 83 
                                       el ++++e+++++ +l++ +++v+++ ++++++ e++ e+ ++l e++e +++ ++ F e d+++ ++++
  gi|336254904|ref|YP_004598011.1| 117 ELESRVEEIENNVGSLSSTVNTVQSENEKISDSLEEIEEDIRKLLEVYEMVTQGVNPFVEGDSLSDSFEH 186
                                       677899*********************************************************9999887 PP

>> Dynactin_p22  Dynactin subunit p22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5     2e-05     0.033       4      53 ..     117     169 ..     115     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                      Dynactin_p22   4 aLEeriaeLEkrvlGeekekeked...esiidsLakvqkklssavskrekike 53 
                                        LE+r++e+E+ v + +++ ++ +   e+i dsL+++++ ++++++ +e +++
  gi|336254904|ref|YP_004598011.1| 117 ELESRVEEIENNVGSLSSTVNTVQsenEKISDSLEEIEEDIRKLLEVYEMVTQ 169
                                       69999999999998877776655556699999999999999999999998886 PP

>> CcmH  Cytochrome C biogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.9e-05     0.081      23      68 ..     123     170 ..     113     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.9e-05
                                       HHHHHHHHHHHHHEE-TTSSS-BTTT--SHHHHHHHH..HHHHHHHHT CS
                              CcmH  23 paqeararalseeLRClvCqnqsiadSnaelAkdlrr..evremlkaG 68 
                                       ++ e+++ +ls+++  ++  n++i+dS  e+ +d+r+  ev+em+++G
  gi|336254904|ref|YP_004598011.1| 123 EEIENNVGSLSSTVNTVQSENEKISDSLEEIEEDIRKllEVYEMVTQG 170
                                       566889999***************************75589*****99 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 ?   12.6   0.8   6.2e-05       0.1      55     100 ..     116     161 ..     113     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.2e-05
                    CENP-F_leu_zip  55 etlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLe 100
                                       ++l++ +ee++++   l++ +++++se+e++  +l++  e +  L 
  gi|336254904|ref|YP_004598011.1| 116 SELESRVEEIENNVGSLSSTVNTVQSENEKISDSLEEIEEDIRKLL 161
                                       5899***********************************9999874 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.5   8.3e-05      0.14      22      67 ..     117     162 ..     115     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                              ZapB  22 lLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLLg 67 
                                       +L  ++ee +  + +l++  + +++ene+  +  e+++e ++kLL+
  gi|336254904|ref|YP_004598011.1| 117 ELESRVEEIENNVGSLSSTVNTVQSENEKISDSLEEIEEDIRKLLE 162
                                       788999**************************************97 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.17     176     245 ..     118     201 ..     111     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                        Fmp27_WPPW 176 leeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesse........ 244
                                       le+R+ee+e+++ +l+++++++++++ek    +++ +ee+e++i++l e +e++++ ++ + e ++ s+        
  gi|336254904|ref|YP_004598011.1| 118 LESRVEEIENNVGSLSSTVNTVQSENEK----ISDSLEEIEEDIRKLLEVYEMVTQGVNPFVEGDSLSDsfehgsgg 190
                                       6788888888888888888888888888....9***********************999998888776666666666 PP

                        Fmp27_WPPW 245 ..........e 245
                                                 +
  gi|336254904|ref|YP_004598011.1| 191 ggaqgtgnfgD 201
                                       66666655541 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.6   0.00032      0.53       2      44 ..     118     160 ..     117     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00032
                              XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleedlkkl 44 
                                       ++ r+e+ie+++ +l+++v++++  +++   +++++eed+ kl
  gi|336254904|ref|YP_004598011.1| 118 LESRVEEIENNVGSLSSTVNTVQSENEKISDSLEEIEEDIRKL 160
                                       688**************************************98 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   0.00036      0.59       2      36 ..     122     156 ..     121     158 .. 0.93
   2 ?   -3.0   0.1       6.4     1e+04       4      35 ..     517     542 ..     516     548 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00036
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaakeE 36 
                                       ++e+ ++V +L+s v+ ++s+ +++++ ++++ e+
  gi|336254904|ref|YP_004598011.1| 122 VEEIENNVGSLSSTVNTVQSENEKISDSLEEIEED 156
                                       899************************99999886 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.4
                               LPP   4 eLssqVsqLkskvdqlssdvnsakaaaqaake 35 
                                       eLs +++  ++  d l+ d ++ ++      +
  gi|336254904|ref|YP_004598011.1| 517 ELSIDIEGPEDATDDLETDGADDAD------D 542
                                       6666666666666666655333333......3 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.5     0.001       1.6      29      60 ..     116     147 ..     115     151 .. 0.91
   2 ?    7.1   0.2    0.0034       5.6      30      60 ..     131     161 ..     127     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  29 eeLerrvkaLekeNksLkseleelkkevekLk 60 
                                       +eLe+rv+++e+   sL+s++++ + e+ek  
  gi|336254904|ref|YP_004598011.1| 116 SELESRVEEIENNVGSLSSTVNTVQSENEKIS 147
                                       59*************************99875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0034
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  30 eLerrvkaLekeNksLkseleelkkevekLk 60 
                                        L++ v + ++eN++ ++ lee+++++ kL+
  gi|336254904|ref|YP_004598011.1| 131 SLSSTVNTVQSENEKISDSLEEIEEDIRKLL 161
                                       6889999*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (753 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                       172  (0.0095934); 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):              11  [number of targets reported over threshold]
# CPU time: 1.04u 0.28s 00:00:01.32 Elapsed: 00:00:00.45
# Mc/sec: 4980.46
//
Query:       gi|336254905|ref|YP_004598012.1|  [L=231]
Description: flagella cluster protein [Halopiger xanaduensis SH-6]
Scores for 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  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1902.91
//
Query:       gi|336254906|ref|YP_004598013.1|  [L=44]
Description: hypothetical protein Halxa_3523 [Halopiger xanaduensis SH-6]
Scores for 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  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); 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: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 360.07
//
Query:       gi|336254907|ref|YP_004598014.1|  [L=573]
Description: type II secretion system F domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-16   60.2   2.4    4.6e-12   46.0   0.7    3.6  4  T2SSF     Type II secretion system (T2SS), protein F
     0.0013   18.2   2.8     0.0049   16.3   2.8    1.9  1  DUF599    Protein of unknown function, DUF599
  ------ inclusion threshold ------
      0.048   12.5   0.2      0.074   11.8   0.2    1.2  1  AAA_32    AAA domain


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 ?   -2.7   0.9      0.88   5.3e+03     103     119 ..      36      52 ..      16      53 .. 0.66
   2 !   46.0   0.7   7.6e-16   4.6e-12       1     122 [.      96     222 ..      96     228 .. 0.94
   3 ?   -2.8   0.9      0.97   5.8e+03     108     123 ..     287     302 ..     274     307 .. 0.52
   4 !   22.1   0.0   1.8e-08   0.00011      16     122 ..     369     478 ..     353     481 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.88
                                       HTTXXXXXXXXXXXXXX CS
                             T2SSF 103 lepllllvvallvllil 119
                                       l p++l++++ +v++++
  gi|336254907|ref|YP_004598014.1|  36 LLPAVLIFLGTIVAAVV 52 
                                       33555555555555544 PP

  == domain 2  score: 46.0 bits;  conditional E-value: 7.6e-16
                                       HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHH CS
                             T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqlirage 72 
                                       f+ ++ +l+ + +   e+L+ la+e e+g+la+e++ri++ ++ ++ sl++a +      ps+  ++l+ ++  + +
  gi|336254907|ref|YP_004598014.1|  96 FVIHMTVLSTTNIDRMEVLRQLAQEEEYGELADEMQRIVDLVDVWHlSLDDACRrrakAVPSESVADLLERMAYTLS 172
                                       678999************************************************88877777888************ PP

                                       HHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXX CS
                             T2SSF  73 eggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillai 122
                                       +g+ Lae+L++ ++ l e++ + ++  ++ l +l  l++ l+++  + ++
  gi|336254907|ref|YP_004598014.1| 173 AGQGLAEFLQQEQDVLVEKYSTVYRQSLSNLDVLKDLYLSLIISTTFALV 222
                                       ******************************************99887766 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.97
                                       XXXXXXXXXXXXXXXX CS
                             T2SSF 108 llvvallvllillail 123
                                       + v ++++++ +++++
  gi|336254907|ref|YP_004598014.1| 287 VGVGGSVLVVGVMLFM 302
                                       3444444444444443 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 1.8e-08
                                       HHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS.-HHHHHHHHHHHHHT-HHHHHHHHHHH CS
                             T2SSF  16 veaLellaeeaengplaeelkriarrlraGgslseale....rtpssef.pelvvqlirageeggnLaevLerlaey 87 
                                        e+L++l +++ +gpl+e +++++rrl++  s +++++       +s +  ++  +++   e gg      e ++++
  gi|336254907|ref|YP_004598014.1| 369 SEVLSTLRDQD-FGPLTENIDDLYRRLNMRLSTEKSWRyftgD-AHSFLvQKFSEMYLIGREMGGGPKRLGELISQN 443
                                       68999******.**************************99852.445777*************************** PP

                                       HHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXX CS
                             T2SSF  88 leeerelrrkllaallepllllvvallvllillai 122
                                       +    +lr +++ +++  + +++ + + +++ ++i
  gi|336254907|ref|YP_004598014.1| 444 MSVIINLREERKQQTTTLVGVIYGITAAASFAFFI 478
                                       **999999999999999999999998888888776 PP

>> DUF599  Protein of unknown function, DUF599
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.8   8.2e-07    0.0049      46     124 ..     449     528 ..     443     531 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.2e-07
                            DUF599  46 derknrilavqtlrnlimastllAstaillisglaallsstd.klsdllkslpvfgatsealfelKlllllliflvA 121
                                       + r++r  +++tl  +i + t  As a ++   laa+lss d ++++ + s +++++ + ++  l++l+ll++ + A
  gi|336254907|ref|YP_004598014.1| 449 NLREERKQQTTTLVGVIYGITAAASFAFFIGLELAAMLSSFDiDMQSQIMSGSLIHTDQYNIHVLRYLILLVLIFNA 525
                                       66888899999*******************************9888888888998999999999************* PP

                            DUF599 122 Flk 124
                                       F++
  gi|336254907|ref|YP_004598014.1| 526 FIS 528
                                       *97 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   1.2e-05     0.074     162     259 ..     101     198 ..      86     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.2e-05
                            AAA_32 162 kplseeefealpeeerkeleekseeleeeleeilrelrelekeakeklkelerevakeaveplleelkekykdlekv 238
                                        +ls  ++++++  ++ + ee++ el +e+++i++ +  +  +++++ ++  + v +e v +lle++  + ++ + +
  gi|336254907|ref|YP_004598014.1| 101 TVLSTTNIDRMEVLRQLAQEEEYGELADEMQRIVDLVDVWHLSLDDACRRRAKAVPSESVADLLERMAYTLSAGQGL 177
                                       566777777777778888899******************************************************** PP

                            AAA_32 239 leyLeaveedilenlelflee 259
                                       +e+L++ ++ ++e+++ + ++
  gi|336254907|ref|YP_004598014.1| 178 AEFLQQEQDVLVEKYSTVYRQ 198
                                       ************999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       957  (0.0533772); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 4347.99
//
Query:       gi|336254908|ref|YP_004598015.1|  [L=386]
Description: flagella protein [Halopiger xanaduensis SH-6]
Scores for complete 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-27   95.0   0.0    3.5e-27   94.1   0.0    1.5  1  Arch_fla_DE  Archaeal flagella protein
    3.1e-20   72.3   1.4    6.6e-20   71.3   1.4    1.6  1  FlaC_arch    Flagella accessory protein C (FlaC)
  ------ inclusion threshold ------
      0.056   12.3   0.0      0.081   11.8   0.0    1.2  1  Fmp27_WPPW   RNA pol II promoter Fmp27 protein domain
      0.062   13.4   0.1       0.11   12.6   0.1    1.3  1  bZIP_1       bZIP transcription factor
       0.13   12.2   2.2       0.63   10.0   0.1    2.2  2  Prefoldin    Prefoldin subunit
       0.21   10.4   0.2       0.32    9.8   0.2    1.1  1  DUF812       Protein of unknown function (DUF812)
         10    6.4   6.6        0.6   10.4   1.0    1.9  2  XhlA         Haemolysin XhlA


Domain annotation for each model (and alignments):
>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.0   1.4e-30   3.5e-27       2      94 ..     269     362 ..     268     363 .. 0.91

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 1.4e-30
                       Arch_fla_DE   2 ekpyLeelpedyaaelvvleWlefLvervgvenaaealdyYeeigWiseevreeLlkylkgikle..deekeelk.k 75 
                                       e pyL + p++++aelv++eWl++L+e++g+++aa++++yYe+i+Wis+ v+++L+++l+g++ +  +  ++e++ +
  gi|336254908|ref|YP_004598015.1| 269 EPPYLVRHPSRTDAELVTIEWLQYLIETAGMDGAARTIAYYESIDWISDPVETYLQSLLNGFTDApvA--DDEIEpR 343
                                       679***********************************************************854443..3566668 PP

                       Arch_fla_DE  76 seltvedHvkSllyiekla 94 
                                       s lt+++H++Sl+yi+++a
  gi|336254908|ref|YP_004598015.1| 344 SVLTTDEHKRSLQYIANIA 362
                                       ****************997 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 !   71.3   1.4   2.6e-23   6.6e-20       1      55 []      50     104 ..      50     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 2.6e-23
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdllsLYEvVsnqvNPFv 55 
                                       r+de+E+++++l+ ++etv+ ene++s+s++++++nV +l+++YE+V++++NPFv
  gi|336254908|ref|YP_004598015.1|  50 RLDEIEKEIDSLEGKVETVRGENEKISDSIQTVERNVDRLVDMYEIVTQGINPFV 104
                                       89****************************************************8 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.2e-05     0.081     174     244 ..      45     111 ..      34     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                        Fmp27_WPPW 174 elleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesse 244
                                       e l+ Rl+e+e++i++le k+e++  ++ek    +++ i+++e+++++l + +e++++ ++ +  ++e  +
  gi|336254908|ref|YP_004598015.1|  45 EELSYRLDEIEKEIDSLEGKVETVRGENEK----ISDSIQTVERNVDRLVDMYEIVTQGINPFVGDQEIGD 111
                                       56788*******************999999....9**********************99998877766554 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.4e-05      0.11      26      59 ..      56      89 ..      54      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 26 aeieeLerrvkaLekeNksLkseleelkkevekL 59
                                      +ei+ Le +v++  +eN++ ++ +++ + +v+ L
  gi|336254908|ref|YP_004598015.1| 56 KEIDSLEGKVETVRGENEKISDSIQTVERNVDRL 89
                                      89************************99999876 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00025      0.63      82     117 ..      54      89 ..      51      91 .. 0.92
   2 ?    1.6   0.2     0.097   2.5e+02      76      94 ..     139     157 ..     135     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanlaql 117
                                       ++k++++le  +e++  e ek++d i+t+e+n+++l
  gi|336254908|ref|YP_004598015.1|  54 IEKEIDSLEGKVETVRGENEKISDSIQTVERNVDRL 89 
                                       6899****************************9987 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.097
                                       HHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  76 eeAiellkkkleelekqle 94 
                                        eA+++l++ lee+++  +
  gi|336254908|ref|YP_004598015.1| 139 AEAEDFLDDDLEEVDEDED 157
                                       69***********998665 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00012      0.32     330     369 ..      49      88 ..      35      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00012
                            DUF812 330 eeleelqeqieeleskieeleeeikklessikqveeelee 369
                                         l+e++++i++le k+e+++ e +k+++si+ ve ++++
  gi|336254908|ref|YP_004598015.1|  49 YRLDEIEKEIDSLEGKVETVRGENEKISDSIQTVERNVDR 88 
                                       4578888888888888888888888888888888887764 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.0   0.00023       0.6       5      47 ..      50      92 ..      46      94 .. 0.92
   2 ?   -3.0   0.4       3.3   8.5e+03      16      24 ..     145     153 ..     130     160 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                              XhlA  5 rlerietkldnleervdkleekaaeaeekiknleedlkklesn 47
                                      rl +ie+++d+le +v+++   +++   +i+ +e ++++l ++
  gi|336254908|ref|YP_004598015.1| 50 RLDEIEKEIDSLEGKVETVRGENEKISDSIQTVERNVDRLVDM 92
                                      899***********************************99876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.3
                              XhlA  16 leervdkle 24 
                                       l++++++++
  gi|336254908|ref|YP_004598015.1| 145 LDDDLEEVD 153
                                       333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                       180  (0.0100396); 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):               7  [number of targets reported over threshold]
# CPU time: 0.74u 0.27s 00:00:01.01 Elapsed: 00:00:00.39
# Mc/sec: 2989.50
//
Query:       gi|336254909|ref|YP_004598016.1|  [L=154]
Description: flagellin [Halopiger xanaduensis SH-6]
Scores for 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   50.1  11.7    4.1e-13   49.8  11.7    1.0  1  Arch_flagellin   Archaebacterial flagellin
  ------ inclusion threshold ------
      0.027   14.6   0.2      0.032   14.3   0.2    1.3  1  F420H2_quin_red  F420H(2)-dependent quinone reductase


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8  11.7   4.6e-17   4.1e-13       2     157 ..       3     144 ..       2     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 4.6e-17
                                       --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE..EEE-SSSSSEEEEEEE-- CS
                    Arch_flagellin   2 fvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg..dsatngtineitiyvkln 76 
                                       +v++ +lI+fI  +++A+++ag++i  ++++++++++ g+   e+++++++i++d    d   n+t+++ t+ vk n
  gi|336254909|ref|YP_004598016.1|   3 SVTATHLIMFIGSLVIASAVAGTVIMEVDQVSNSIETRGSAVAEEIETDIAIISDESqsDAIINQTNETATVLVK-N 78 
                                       57799**************************************************99665566777888******.* PP

                                       TTS--EEGGG-EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE CS
                    Arch_flagellin  77 aGsspidlnkttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevv 153
                                        G+ ++      ++v++dg          ++  +++ +   t++ + + +g +ve++    +d+++ +++e++v v 
  gi|336254909|ref|YP_004598016.1|  79 IGDRDVPAHPNYVDVLVDG----------SYDPVTSVERVDTDS-NRWAPGGVVEVTASY-GDQNVQNDTEITVIV- 142
                                       *******************..........566666666655555.99**********998.677788888888844. PP

                                       -SSS CS
                    Arch_flagellin 154 penG 157
                                         nG
  gi|336254909|ref|YP_004598016.1| 143 --NG 144
                                       ..44 PP

>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   3.6e-06     0.032      71     128 ..      84     143 ..      37     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.6e-06
                                       HHH--E.EEEEETTEEEEEEEEE--HHHHHHHHH.HHHHH-THHHHHHHHHSSTS-EEEE CS
                   F420H2_quin_red  71 lkanPr.vevqvgakkldvtAreveddekarlwk.lvvenspsYadyqsktdreipvvVl 128
                                       + a+P+ v v v ++  +vt  e  d + +r+    vve+ +sY d   + d+ei+v+V 
  gi|336254909|ref|YP_004598016.1|  84 VPAHPNyVDVLVDGSYDPVTSVERVDTDSNRWAPgGVVEVTASYGDQNVQNDTEITVIVN 143
                                       668886699***********************97268999999***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1204.92
//
Query:       gi|336254910|ref|YP_004598017.1|  [L=162]
Description: flagellin [Halopiger xanaduensis SH-6]
Scores for 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-09   36.2   9.9    7.6e-09   36.0   9.9    1.1  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   9.9   4.3e-13   7.6e-09       1     163 [.       2     157 ..       2     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 4.3e-13
                                       X--HHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE-- CS
                    Arch_flagellin   1 GfvgigtlIv.fIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvkln 76 
                                       Gf++ g++Iv +I ++++ ++ + ++ n + ++ ++ +++ ++  eq++s++ i +   +s+ +       + v+ n
  gi|336254910|ref|YP_004598017.1|   2 GFSTSGAIIViLIGVLVAFSAIVPTVFNITSTTGDAFSAKNDQFREQANSEIVIESFETESTVD-----AVVNVT-N 72 
                                       788888988736888888889999***************************9887765544444.....689***.* PP

                                       TTS--EEGGG-EEEEEESS--EE--E.......................T-EE-TT-EEEEEEE--..TTT---TT- CS
                    Arch_flagellin  77 aGsspidlnkttisvtddgqetlltadefgivvisdtdgsltng.....devlekgekvelevnvn..eddgitagd 146
                                       +G+ ++ +++t++  +++g+     +    +++ +++++ +tn+     ++v+ +g ++++e++++  e+d+  +gd
  gi|336254910|ref|YP_004598017.1|  73 DGARSLSVERTDV--VVNGEY----Y---PTNDSDAETAIITNDstrssSDVWLPGTVLQIEIDNSklESDSEITGD 140
                                       **99666666555..566611....2...2333333333333335555599*************99**999999999 PP

                                       EEEEEEE-SSS--EEEE CS
                    Arch_flagellin 147 evsvevvpenGasttie 163
                                         +v++++e G ++t e
  gi|336254910|ref|YP_004598017.1| 141 GDRVKITTERGIAATAE 157
                                       99*********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.24s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1327.45
//
Query:       gi|336254911|ref|YP_004598018.1|  [L=208]
Description: flagellin domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-42  144.7   7.2    3.1e-42  144.5   7.2    1.0  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.5   7.2   1.8e-46   3.1e-42       1     163 [.      10     192 ..      10     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 144.5 bits;  conditional E-value: 1.8e-46
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE...EEE-SSSSSEEEEEEE CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg...dsatngtineitiyvk 74 
                                       G+vgigtlIvfIAmVlVAA+aagvlintag+lq++a++tgeest+ vs+++++t+ vg   d+ + +++++i+i+v+
  gi|336254911|ref|YP_004598018.1|  10 GQVGIGTLIVFIAMVLVAAIAAGVLINTAGMLQTQAEATGEESTDLVSERIDVTSEVGiveDEENPSNLSSINITVT 86 
                                       89********************************************************9999999999999****** PP

                                       --TTS--EEGGG-EEEEEESS.--EE--E.........................T-EE-TT-EEEEEEE--...... CS
                    Arch_flagellin  75 lnaGsspidlnkttisvtddg.qetlltad.......efgivvisdtdgsltngdevlekgekvelevnvn...... 137
                                        +aG+ +idln+t+++ ++++ qetl+ a+       e g ++ +d dg ++++ +++  +e+ + ++ +n      
  gi|336254911|ref|YP_004598018.1|  87 GAAGAGEIDLNETIVQAVGPNgQETLTLANvsnvsdlERGEFAAKDDDGFVDWN-NAVLSDENSDFTLIFNpangpf 162
                                       *********************999999998777776655555566655555555.889999999999999999**** PP

                                       ....TTT---TT-EEEEEEE-SSS--EEEE CS
                    Arch_flagellin 138 ....eddgitagdevsvevvpenGasttie 163
                                             +++++gde s+ +v+++Ga+t++e
  gi|336254911|ref|YP_004598018.1| 163 gdsdAGTEFGEGDESSLSIVSPSGATTEVE 192
                                       ***99999*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1685.14
//
Query:       gi|336254912|ref|YP_004598019.1|  [L=193]
Description: flagellin domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-43  147.6  12.7    4.2e-43  147.4  12.7    1.0  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.067   13.6   0.4       0.15   12.4   0.4    1.7  1  DUF296          Plants and Prokaryotes Conserved (PCC) domain
        2.5    9.1   9.3       0.35   11.8   3.0    2.6  3  Pilin_N         Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4  12.7     7e-47   4.2e-43       1     163 [.      10     177 ..      10     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 7e-47
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--T CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklna 77 
                                       G+vgigtlIvfIAmVlVAA+aagvlintag+lq++a++tgeest+qvs +lei+++ g+ ++++++++i ++++ ++
  gi|336254912|ref|YP_004598019.1|  10 GQVGIGTLIVFIAMVLVAAIAAGVLINTAGMLQTQAEATGEESTSQVSDRLEIVSVSGNVSDSNNVTDIDFVLAMAP 86 
                                       89*************************************************************************** PP

                                       TS--EEGGG-EEEEEESS.--EE--E....................T-EE-TT-EEEEEEE--..TTT---TT-EEE CS
                    Arch_flagellin  78 Gsspidlnkttisvtddg.qetlltadefgivvisdtdgsltng..devlekgekvelevnvn..eddgitagdevs 149
                                       Gsspidlnktt ++++++ +et +t ++++ v+i++ +g +  g    + e +++++l+v +n  +  ++ +gd+++
  gi|336254912|ref|YP_004598019.1|  87 GSSPIDLNKTTAQFIGSEgEETFTTENDTSGVSITNIQGVTEGGdnPVLTESSDRLKLNVGLNdvGYAELAEGDRMT 163
                                       ******************8888888886666666666665555543378899************999********** PP

                                       EEEE-SSS--EEEE CS
                    Arch_flagellin 150 vevvpenGasttie 163
                                       v+++++ Ga+t  e
  gi|336254912|ref|YP_004598019.1| 164 VTFTTDAGATTQTE 177
                                       **********9876 PP

>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   2.5e-05      0.15      24      68 ..      28      73 ..      15      91 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                                      HT-SSEEEEEEEEEEEEEEEEECTTT...EE-S-EEEEEEEEEEEETT CS
                            DUF296 24 rgiraacvlsaiGavsnvtrladgee...kllgrfeilslsGtilpdg 68
                                        i a+++++  G+++     a+gee   ++ +r+ei+s+sG+++ ++
  gi|336254912|ref|YP_004598019.1| 28 A-IAAGVLINTAGMLQTQA-EATGEEstsQVSDRLEIVSVSGNVSDSN 73
                                      4.67777778888887655.2333336788889***********9843 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 ?   -3.5   0.0         3   1.8e+04      59      65 ..       2       8 ..       1       9 [. 0.87
   2 ?   11.8   3.0   5.9e-05      0.35      11      72 ..      17      75 ..      12      86 .. 0.75
   3 ?    0.8   0.1      0.16   9.3e+02      51      69 ..     158     176 ..      80     187 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3
                           Pilin_N 59 lehkgGd 65
                                      +eh +Gd
  gi|336254912|ref|YP_004598019.1|  2 FEHTDGD 8 
                                      99****9 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.9e-05
                           Pilin_N 11 LmvaitvIlaAviaafvlgl.asneekapqasievkidssastgknavslehkgGdsidtkdl 72
                                      L+v i ++l+A iaa vl   a+  +++++a+ e+++++ ++     +++   +G++ d +++
  gi|336254912|ref|YP_004598019.1| 17 LIVFIAMVLVAAIAAGVLINtAGMLQTQAEATGEESTSQVSDR----LEIVSVSGNVSDSNNV 75
                                      8999999999999999998856666666666665554444444....9999999999988766 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.16
                           Pilin_N  51 stgknavslehkgGdsidt 69 
                                       + +  +v+++ + G +++t
  gi|336254912|ref|YP_004598019.1| 158 EGDRMTVTFTTDAGATTQT 176
                                       2233336677766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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: 0.43u 0.19s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1625.27
//
Query:       gi|336254913|ref|YP_004598020.1|  [L=64]
Description: hypothetical protein Halxa_3530 [Halopiger xanaduensis SH-6]
Scores for 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   18.1   0.4      0.003   17.8   0.4    1.1  1  DUF2197         Uncharacterized protein conserved in bacteria
  ------ inclusion threshold ------
      0.015   15.1   0.1        1.5    8.7   0.0    2.1  2  zinc_ribbon_12  Probable zinc-ribbon domain
      0.051   13.2   1.1       0.52    9.9   0.1    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> DUF2197  Uncharacterized protein conserved in bacteria (DUF2197)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.4     5e-07     0.003       2      39 ..       8      44 ..       7      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5e-07
                           DUF2197  2 rvkCvlCdkveeiddesllaKrLrNrpihtYmCkeCee 39
                                      +v C+ Cd++ ++dd ++l K   N+     +C++C +
  gi|336254913|ref|YP_004598020.1|  8 KVECSRCDELISLDDANVLGKT-HNKSYAKPLCDDCLQ 44
                                      79*****************996.9************76 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 ?    8.7   0.0   0.00025       1.5      31      43 ..       8      20 ..       5      32 .. 0.72
   2 ?    5.0   0.0    0.0036        22       9      22 ..      39      52 ..      37      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00025
                    zinc_ribbon_12 31 klrCGaCsevlsf 43
                                      k+ C++C e++s+
  gi|336254913|ref|YP_004598020.1|  8 KVECSRCDELISL 20
                                      6677777777765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0036
                    zinc_ribbon_12  9 CsnCfelLqlPkkf 22
                                      C+ C++ + +Pk  
  gi|336254913|ref|YP_004598020.1| 39 CDDCLQNVGVPKGY 52
                                      ***********865 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   8.7e-05      0.52       3      16 ..       9      22 ..       7      24 .. 0.85
   2 ?    2.3   0.1     0.022   1.3e+02       4      12 ..      38      46 ..      36      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 8.7e-05
                            zf_UBZ  3 ylCerCgkeipese 16
                                      + C+rC++ i+ ++
  gi|336254913|ref|YP_004598020.1|  9 VECSRCDELISLDD 22
                                      68********9886 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.022
                            zf_UBZ  4 lCerCgkei 12
                                      lC++C +++
  gi|336254913|ref|YP_004598020.1| 38 LCDDCLQNV 46
                                      6****7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.31u 0.22s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 564.20
//
Query:       gi|336254914|ref|YP_004598021.1|  [L=287]
Description: hypothetical protein Halxa_3531 [Halopiger xanaduensis SH-6]
Scores for 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-71  238.1   2.7    1.2e-70  237.7   2.7    1.2  1  CheF-arch       Chemotaxis signal transduction system protein
  ------ inclusion threshold ------
      0.016   15.4   0.0      0.049   13.8   0.0    1.8  1  Vps36_ESCRT-II  Vacuolar protein sorting protein 36 Vps36
      0.027   14.4   2.4       0.55   10.2   0.0    3.8  4  DUF903          Bacterial protein of unknown function (DUF903
      0.051   13.7   0.1       0.13   12.3   0.1    1.8  1  bPH_4           Bacterial PH domain


Domain annotation for each model (and alignments):
>> CheF-arch  Chemotaxis signal transduction system protein F from archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.7   2.7   2.6e-74   1.2e-70       1     216 [.       7     209 ..       7     210 .. 0.99

  Alignments for each domain:
  == domain 1  score: 237.7 bits;  conditional E-value: 2.6e-74
                         CheF-arch   1 kiadfkGkfllvvkkgrkkkdvkWekgrilLsnkrlvlasedkkitiplssvedvggevPrklkdifddtvtdakvs 77 
                                       k+ad++Gkf++v ++grk++d++W++gri+Lsnkrlv+as+d+k+t pls++        +++k+++d+++t+akvs
  gi|336254914|ref|YP_004598021.1|   7 KLADVTGKFTQVMRDGRKMSDTNWSNGRIVLSNKRLVIASNDGKKTMPLSEI--------KSIKGRYDVNQTVAKVS 75 
                                       69**************************************************........***************** PP

                         CheF-arch  78 gyialktkdgenvllieaedesiekFetkLfkalLngkevlvkhpAvvGGvvqdtewekgklkvekkaielatkkgs 154
                                       +yi+++t  g +v li++++  +++Fe ++ ka+L+g+ vl+khpAv+GGvvqdt+w+k+++kv+ +  ++a+++gs
  gi|336254914|ref|YP_004598021.1|  76 DYISINT--GADVHLISMAE--VNEFELQIQKAILDGEIVLIKHPAVKGGVVQDTSWSKARVKVDTGVANFAVENGS 148
                                       *******..***********..******************************************************* PP

                         CheF-arch 155 fveielsdvgdvereektvdgeerpvlevehtedgesvttylagkdkrkvslLerylreeye 216
                                       fv+ie++dvg+ve ee+t+ ++erpv+e ehtedg sv+tyl+g   +++ +L+++l +++e
  gi|336254914|ref|YP_004598021.1| 149 FVQIEVDDVGTVESEERTILSKERPVIEAEHTEDGSSVQTYLSGGP-QNCAVLKSVLDKGAE 209
                                       **********************************************.**********99987 PP

>> Vps36_ESCRT-II  Vacuolar protein sorting protein 36 Vps36
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.1e-05     0.049      33      72 ..      28      64 ..      20      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                    Vps36_ESCRT-II 33 lnrqnGrlyLTthriiyvdsadpkkeslslelklvesvs.e 72
                                      +n++nGr++L+++r++ + s+d kk   +++l++++s++ +
  gi|336254914|ref|YP_004598021.1| 28 TNWSNGRIVLSNKRLVIA-SNDGKK---TMPLSEIKSIKgR 64
                                      69**************86.778887...6899999998544 PP

>> DUF903  Bacterial protein of unknown function (DUF903)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.1   4.9e+03       6      12 ..      46      52 ..      43      62 .. 0.53
   2 ?   10.2   0.0   0.00012      0.55      17      48 ..     130     161 ..     124     162 .. 0.90
   3 ?   -2.1   0.1      0.81   3.6e+03       5      14 ..     179     188 ..     179     189 .. 0.84
   4 ?    1.4   0.1     0.066     3e+02      39      49 .]     243     253 ..     241     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                                      ETTS-EE CS
                            DUF903  6 tkDGqti 12
                                       +DG++ 
  gi|336254914|ref|YP_004598021.1| 46 SNDGKKT 52
                                      5555543 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00012
                                       --EE-TTTSCEEEEBTTS-EEEEEGGGEEEEE CS
                            DUF903  17 kPelDkdtGmyeYeDeeGkevqInkddVkqik 48 
                                       k ++  dtG   +  e+G  vqI+ ddV +++
  gi|336254914|ref|YP_004598021.1| 130 KARVKVDTGVANFAVENGSFVQIEVDDVGTVE 161
                                       667899**********************9885 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.81
                                       EETTS-EEEE CS
                            DUF903   5 ttkDGqtivt 14 
                                       +t DG+ ++t
  gi|336254914|ref|YP_004598021.1| 179 HTEDGSSVQT 188
                                       6999999988 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.066
                                       EEGGGEEEEEE CS
                            DUF903  39 InkddVkqike 49 
                                       In+d+V +i e
  gi|336254914|ref|YP_004598021.1| 243 INTDEVEEIYE 253
                                       9*******976 PP

>> bPH_4  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1     3e-05      0.13       5      72 ..      37     103 ..      27     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                             bPH_4   5 itegvLliksGfirkkIpiedIkkirktksplsspalsldrleIkygkydtilisPkkkeeFieeLkk 72 
                                       + +++L+i s   +k+ p+++Ik+i+   ++    a ++d++ I++g  d  lis  + +eF  +++k
  gi|336254914|ref|YP_004598021.1|  37 LSNKRLVIASNDGKKTMPLSEIKSIKGRYDVNQTVAKVSDYISINTG-ADVHLISMAEVNEFELQIQK 103
                                       5789999999999**********************************.66678887777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2247.17
//
Query:       gi|336254915|ref|YP_004598022.1|  [L=420]
Description: PBS lyase HEAT domain-containing protein repeat-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-54  180.7  27.0    3.9e-15   56.0   0.5    5.6  6  HEAT_2      HEAT repeats
    1.4e-24   84.1  10.7     0.0032   17.6   0.0    9.6 10  HEAT        HEAT repeat
    2.3e-21   75.9  17.3    0.00057   20.3   0.0    7.5  8  HEAT_EZ     HEAT-like repeat
      5e-21   73.2  28.7     0.0023   18.4   0.8   10.3 10  HEAT_PBS    PBS lyase HEAT-like repeat
    1.6e-15   56.5   2.7    0.00058   19.8   0.0    7.8 10  Arm         Armadillo/beta-catenin-like repeat
    1.3e-08   33.9   0.0    0.00015   20.5   0.1    4.2  4  Adaptin_N   Adaptin N terminal region
    1.2e-07   31.9   4.6       0.09   12.8   0.0    5.3  6  Cnd1        non-SMC mitotic condensation complex subunit 1
    0.00045   20.6   0.4        5.4    7.5   0.0    4.5  5  RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N 
  ------ inclusion threshold ------
      0.014   14.8   0.6      0.014   14.8   0.6    1.9  3  DUF3458_C   Domain of unknown function (DUF3458_C) ARM repeat
      0.096   12.2   0.1         25    4.3   0.0    3.2  3  CLASP_N     CLASP N terminal
        2.4    8.2  12.1        2.3    8.2   1.9    4.2  4  ALF         Short repeats of unknown function
          5    7.6   7.6        8.2    6.9   0.1    3.7  4  HTH_31      Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.1   6.2e-12   9.3e-09       2      62 ..      13      83 ..      12     100 .. 0.83
   2 !   56.0   0.5   2.6e-18   3.9e-15       4      78 ..     108     181 ..     105     182 .. 0.91
   3 !   54.9   3.2   5.9e-18   8.9e-15      15      82 ..     180     247 ..     178     252 .. 0.95
   4 !   32.9   2.7   4.4e-11   6.5e-08       4      83 ..     254     338 ..     250     342 .. 0.81
   5 !   31.5   2.2   1.2e-10   1.7e-07       1      74 [.     283     360 ..     283     364 .. 0.88
   6 !   15.1   0.0   1.5e-05     0.023      12      62 ..     362     413 ..     350     416 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 6.2e-12
                            HEAT_2  2 daLlqalendpdpevrraairaLg.........rignpealpaLvell.ededpavRraaaeaLgaigdpe 62
                                      ++L++ le +++ ++rr+ ++ Lg         r+  +e+++aLv++  +d+  +vR+aa++aL ++g ++
  gi|336254915|ref|YP_004598022.1| 13 EQLIEHLEGSSNSNIRRRSAEILGsleseaggnRYPRDEVIDALVDASqTDDADEVRAAAIDALDQYGQDA 83
                                      689*********************66655555555555**********5556689***********99764 PP

  == domain 2  score: 56.0 bits;  conditional E-value: 2.6e-18
                            HEAT_2   4 LlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddv 78 
                                       L   l +   pe+r aa+  Lgrig++ +++aLv+ l+d+dp+vR+ +a+aLg+i +pe +paL ++l++d+  v
  gi|336254915|ref|YP_004598022.1| 108 LARGL-QADRPELRMAAATGLGRIGEDNVVRALVNQLDDPDPRVRKRIARALGRIESPEPVPALSKRLHEDQYGV 181
                                       55567.56779*********************************************************9988765 PP

  == domain 3  score: 54.9 bits;  conditional E-value: 5.9e-18
                            HEAT_2  15 evrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvRea 82 
                                        vr +++ aL++ig++ al+ Lv++++ded+ vRr a++aLg++g+ ea+++L+ +l+dd+d+v+R+a
  gi|336254915|ref|YP_004598022.1| 180 GVRVEIAYALADIGTDNALRELVDVADDEDETVRRIAVDALGRLGSVEAVEILAGALRDDSDSVRRTA 247
                                       59*************************************************************99986 PP

  == domain 4  score: 32.9 bits;  conditional E-value: 4.4e-11
                            HEAT_2   4 LlqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaig....dpealpaLkelldddd 75 
                                       Ll+ +  +++++vr +++ +L + +  ea++ L+e+l +++++a Rr+aa+ Lg+i+    +++a +aL + l+d+d
  gi|336254915|ref|YP_004598022.1| 254 LLSEAPASASHKVREKIVGELEQANASEAIEPLIEILdRSSETAQRRNAAWLLGRIAneeyRQAAQDALIDTLADED 330
                                       44444459999**************************888999*************8433347799*****999988 PP

                            HEAT_2  76 ddvvReaA 83 
                                       +   + aA
  gi|336254915|ref|YP_004598022.1| 331 EMTSKFAA 338
                                       76656654 PP

  == domain 5  score: 31.5 bits;  conditional E-value: 1.2e-10
                            HEAT_2   1 ldaLlqalendpdpevrraairaLgrignp....ealpaLvellededpavRraaaeaLgaigdpealpaLkelldd 73 
                                       +++L+++l ++++++ rr+a++ Lgri+n+     a++aL++ l ded+++ + aa++L+ +   +  + L++l+ d
  gi|336254915|ref|YP_004598022.1| 283 IEPLIEILDRSSETAQRRNAAWLLGRIANEeyrqAAQDALIDTLADEDEMTSKFAATSLSLLEGGDLEQRLLDLVED 359
                                       689*****99******************99566567************************99877777777777766 PP

                            HEAT_2  74 d 74 
                                       d
  gi|336254915|ref|YP_004598022.1| 360 D 360
                                       5 PP

  == domain 6  score: 15.1 bits;  conditional E-value: 1.5e-05
                            HEAT_2  12 pdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpe 62 
                                        d+e r +a+ +Lg+ig +++++ L +++ ++e+ + R+    aL+++g   
  gi|336254915|ref|YP_004598022.1| 362 RDEEMRVKALFVLGKIGGEQSRNRLSSFVdRTESDRLRKRGFSALSKLGGAG 413
                                       4667888888888888888888888888877788888888888888887665 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.069     1e+02       4      27 ..      14      38 ..      12      40 .. 0.86
   2 !    9.9   0.1   0.00064      0.95       2      26 ..      53      78 ..      52      82 .. 0.82
   3 !   11.5   0.0    0.0002       0.3       5      29 ..     108     132 ..     106     133 .. 0.90
   4 !   17.6   0.0   2.1e-06    0.0032       2      27 ..     136     161 ..     135     163 .. 0.91
   5 ?    1.5   0.0      0.32   4.8e+02       2      27 ..     167     192 ..     167     194 .. 0.87
   6 !   12.6   0.1   8.9e-05      0.13       9      29 ..     205     225 ..     198     226 .. 0.85
   7 !   12.8   0.1   7.5e-05      0.11       3      29 ..     230     256 ..     228     258 .. 0.90
   8 !   10.3   0.0   0.00047       0.7       4      28 ..     285     310 ..     282     312 .. 0.84
   9 ?   -1.6   0.0       3.1   4.7e+03       4      24 ..     321     341 ..     313     344 .. 0.68
  10 ?   -0.2   0.0       1.1   1.7e+03       6      27 ..     354     377 ..     351     378 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.069
                                      HHHHHH.T-SSHHHHHHHHHHHHHH CS
                              HEAT  4 lllkll.sDpspeVReaAakaLgal 27
                                       l++ l  ++++++R+ +a+ Lg l
  gi|336254915|ref|YP_004598022.1| 14 QLIEHLeGSSNSNIRRRSAEILGSL 38
                                      567777799*************987 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00064
                                      HHHHHHHH.T-SSHHHHHHHHHHHHH CS
                              HEAT  2 lPlllkll.sDpspeVReaAakaLga 26
                                      +++l+ +  +D++ eVR+aA+ aL +
  gi|336254915|ref|YP_004598022.1| 53 IDALVDASqTDDADEVRAAAIDALDQ 78
                                      5667777779*************976 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.0002
                                       HHHHHT-SSHHHHHHHHHHHHHHHH CS
                              HEAT   5 llkllsDpspeVReaAakaLgalae 29 
                                       l + l+ + pe R+aAa  Lg++ e
  gi|336254915|ref|YP_004598022.1| 108 LARGLQADRPELRMAAATGLGRIGE 132
                                       78899*****************976 PP

  == domain 4  score: 17.6 bits;  conditional E-value: 2.1e-06
                                       HHHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsDpspeVReaAakaLgal 27 
                                       + +l++ l Dp+p+VR+  a+aLg++
  gi|336254915|ref|YP_004598022.1| 136 VRALVNQLDDPDPRVRKRIARALGRI 161
                                       5679999*****************98 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.32
                                       HHHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsDpspeVReaAakaLgal 27 
                                       +P+l k l+ +   VR   a+aL+++
  gi|336254915|ref|YP_004598022.1| 167 VPALSKRLHEDQYGVRVEIAYALADI 192
                                       58999999888888*********998 PP

  == domain 6  score: 12.6 bits;  conditional E-value: 8.9e-05
                                       HT-SSHHHHHHHHHHHHHHHH CS
                              HEAT   9 lsDpspeVReaAakaLgalae 29 
                                         D++  VR+ A+ aLg+l +
  gi|336254915|ref|YP_004598022.1| 205 ADDEDETVRRIAVDALGRLGS 225
                                       589***************987 PP

  == domain 7  score: 12.8 bits;  conditional E-value: 7.5e-05
                                       HHHHHHHT-SSHHHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgalae 29 
                                        +l  +l+D+s +VR++A  +L++l++
  gi|336254915|ref|YP_004598022.1| 230 EILAGALRDDSDSVRRTAMFSLVQLLS 256
                                       578899******************986 PP

  == domain 8  score: 10.3 bits;  conditional E-value: 0.00047
                                       HHHHHH.T-SSHHHHHHHHHHHHHHH CS
                              HEAT   4 lllkll.sDpspeVReaAakaLgala 28 
                                       +l++ l ++++  +R++Aa+ Lg++a
  gi|336254915|ref|YP_004598022.1| 285 PLIEILdRSSETAQRRNAAWLLGRIA 310
                                       5666677999***************8 PP

  == domain 9  score: -1.6 bits;  conditional E-value: 3.1
                                       HHHHHHT-SSHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaL 24 
                                       +l+  l D++    + Aa +L
  gi|336254915|ref|YP_004598022.1| 321 ALIDTLADEDEMTSKFAATSL 341
                                       456667777777766676666 PP

  == domain 10  score: -0.2 bits;  conditional E-value: 1.1
                                       HHHHT-..SSHHHHHHHHHHHHHH CS
                              HEAT   6 lkllsD..pspeVReaAakaLgal 27 
                                       l l +D   + e R  A+  Lg++
  gi|336254915|ref|YP_004598022.1| 354 LDLVEDdiRDEEMRVKALFVLGKI 377
                                       555544466777788888888877 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   7.5e-06     0.011       2      52 ..      26      76 ..      25      79 .. 0.83
   2 ?    6.2   0.1      0.01        15      32      55 .]     107     130 ..     105     130 .. 0.91
   3 !   20.3   0.0   3.8e-07   0.00057      28      55 .]     134     161 ..     132     161 .. 0.94
   4 !   10.2   0.1   0.00055      0.82      29      55 .]     197     223 ..     181     223 .. 0.85
   5 !   10.1   0.1    0.0006      0.89      28      52 ..     227     251 ..     225     254 .. 0.85
   6 !   13.7   0.1   4.5e-05     0.067      20      55 .]     273     309 ..     268     309 .. 0.81
   7 !   19.1   0.2   9.2e-07    0.0014       2      52 ..     297     341 ..     296     344 .. 0.84
   8 ?   -1.6   0.0       2.7   4.1e+03      41      55 .]     363     377 ..     349     377 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.5e-06
                           HEAT_EZ  2 rvRraAawaLGrlaggepellqplvpeilpaLlalL.nddsdeVRaaAagaL 52
                                      ++Rr  a  LG+l+  e+   +   +e+++aL+ +  +dd deVRaaA+ aL
  gi|336254915|ref|YP_004598022.1| 26 NIRRRSAEILGSLE-SEAGGNRYPRDEVIDALVDASqTDDADEVRAAAIDAL 76
                                      58999999999977.77777777889*******999555666*******999 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.01
                           HEAT_EZ  32 aLlalLnddsdeVRaaAagaLgnl 55 
                                        L+++L+ d +e R aAa  Lg++
  gi|336254915|ref|YP_004598022.1| 107 VLARGLQADRPELRMAAATGLGRI 130
                                       68999999**************97 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 3.8e-07
                           HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaLgnl 55 
                                        +++aL++ L d++++VR+  a+aLg++
  gi|336254915|ref|YP_004598022.1| 134 NVVRALVNQLDDPDPRVRKRIARALGRI 161
                                       689***********************97 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00055
                           HEAT_EZ  29 ilpaLlalLnddsdeVRaaAagaLgnl 55 
                                       +l++L+    d++ +VR  A+ aLg+l
  gi|336254915|ref|YP_004598022.1| 197 ALRELVDVADDEDETVRRIAVDALGRL 223
                                       5677777778888899*********97 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.0006
                           HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaL 52 
                                       e++  L+ +L+ddsd+VR +A   L
  gi|336254915|ref|YP_004598022.1| 227 EAVEILAGALRDDSDSVRRTAMFSL 251
                                       57788999************98877 PP

  == domain 6  score: 13.7 bits;  conditional E-value: 4.5e-05
                           HEAT_EZ  20 ellqplvpeilpaLlalL.nddsdeVRaaAagaLgnl 55 
                                       el q + +e++ +L+  L ++++ + R +Aa+ Lg++
  gi|336254915|ref|YP_004598022.1| 273 ELEQANASEAIEPLIEILdRSSETAQRRNAAWLLGRI 309
                                       566778899*********55555577*********97 PP

  == domain 7  score: 19.1 bits;  conditional E-value: 9.2e-07
                           HEAT_EZ   2 rvRraAawaLGrlaggepellqplvpeilpaLlalLnddsdeV.RaaAagaL 52 
                                       ++Rr+Aaw LGr+a  + e+ q +++++++ L+     d+de   + Aa  L
  gi|336254915|ref|YP_004598022.1| 297 AQRRNAAWLLGRIA--NEEYRQAAQDALIDTLA-----DEDEMtSKFAATSL 341
                                       68************..99***************.....**954366666655 PP

  == domain 8  score: -1.6 bits;  conditional E-value: 2.7
                           HEAT_EZ  41 sdeVRaaAagaLgnl 55 
                                       + e R +A+  Lg++
  gi|336254915|ref|YP_004598022.1| 363 DEEMRVKALFVLGKI 377
                                       457899999999986 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0018       2.7       1      26 [.      27      61 ..      27      62 .. 0.95
   2 ?    4.4   0.1     0.054        80       1      19 [.      68      85 ..      68      88 .. 0.86
   3 !   11.4   0.1   0.00029      0.43       1      27 []     119     145 ..     119     145 .. 0.91
   4 !    8.6   0.0    0.0023       3.4       1      22 [.     150     171 ..     150     175 .. 0.87
   5 !   10.3   0.1   0.00064      0.96       1      27 []     181     207 ..     181     207 .. 0.93
   6 !   18.4   0.8   1.6e-06    0.0023       1      27 []     212     238 ..     212     238 .. 0.95
   7 ?    0.9   0.0      0.67     1e+03       1      12 [.     243     254 ..     243     260 .. 0.92
   8 ?    5.6   0.0     0.021        32       7      26 ..     272     291 ..     266     292 .. 0.75
   9 !   11.6   1.5   0.00024      0.36       2      27 .]     299     328 ..     298     328 .. 0.92
  10 ?    4.2   0.0     0.059        88       2      21 ..     367     386 ..     366     391 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
                                      HHHHHHHHHHHCTS.........GGGHHHHHHHCT CS
                          HEAT_PBS  1 vRraAakaLgqlgd.........eeaipaLleaLq 26
                                      +Rr+ a+ Lg l +         +e+i+aL+ a q
  gi|336254915|ref|YP_004598022.1| 27 IRRRSAEILGSLESeaggnryprDEVIDALVDASQ 61
                                      69*****************************9987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.054
                                      HHHHHHHHHHHCTSGGGHH CS
                          HEAT_PBS  1 vRraAakaLgqlgdeeaip 19
                                      vR+aA+ aL q g  +a++
  gi|336254915|ref|YP_004598022.1| 68 VRAAAIDALDQYGQ-DALE 85
                                      9*********9999.7766 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00029
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       +R aAa +Lg++g + ++ aL++ L+d
  gi|336254915|ref|YP_004598022.1| 119 LRMAAATGLGRIGEDNVVRALVNQLDD 145
                                       599************999999988876 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHHHCTSGGGHHHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLl 22 
                                       vR + a+aLg++ ++e +paL 
  gi|336254915|ref|YP_004598022.1| 150 VRKRIARALGRIESPEPVPALS 171
                                       899***********99888875 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00064
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR + a+aL+ +g++ a+  L+ + +d
  gi|336254915|ref|YP_004598022.1| 181 VRVEIAYALADIGTDNALRELVDVADD 207
                                       8*****************999998876 PP

  == domain 6  score: 18.4 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vRr A+ aLg+lg+ ea+++L  aL d
  gi|336254915|ref|YP_004598022.1| 212 VRRIAVDALGRLGSVEAVEILAGALRD 238
                                       9********************999976 PP

  == domain 7  score: 0.9 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHHC CS
                          HEAT_PBS   1 vRraAakaLgql 12 
                                       vRr A+++L ql
  gi|336254915|ref|YP_004598022.1| 243 VRRTAMFSLVQL 254
                                       9********886 PP

  == domain 8  score: 5.6 bits;  conditional E-value: 0.021
                                       HHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   7 kaLgqlgdeeaipaLleaLq 26 
                                         L q ++ eai++L+e L+
  gi|336254915|ref|YP_004598022.1| 272 GELEQANASEAIEPLIEILD 291
                                       446666779********997 PP

  == domain 9  score: 11.6 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHCTS....GGGHHHHHHHCTC CS
                          HEAT_PBS   2 RraAakaLgqlgd....eeaipaLleaLqd 27 
                                       Rr+Aa+ Lg++      ++a +aL+  L+d
  gi|336254915|ref|YP_004598022.1| 299 RRNAAWLLGRIANeeyrQAAQDALIDTLAD 328
                                       9***************99999999988776 PP

  == domain 10  score: 4.2 bits;  conditional E-value: 0.059
                                       HHHHHHHHHHCTSGGGHHHH CS
                          HEAT_PBS   2 RraAakaLgqlgdeeaipaL 21 
                                       R  A++ Lg++g e++  +L
  gi|336254915|ref|YP_004598022.1| 367 RVKALFVLGKIGGEQSRNRL 386
                                       7889*********9988776 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.74   1.1e+03      16      37 ..      14      36 ..      12      38 .. 0.84
   2 ?    0.8   0.0      0.39   5.8e+02      13      36 ..      52      76 ..      49      76 .. 0.84
   3 ?   -1.1   0.0       1.5   2.2e+03      21      38 ..     112     129 ..     110     131 .. 0.85
   4 !   19.8   0.0   3.9e-07   0.00058       8      38 ..     130     160 ..     128     161 .. 0.92
   5 ?   -0.7   0.0       1.1   1.7e+03      14      37 ..     167     190 ..     167     194 .. 0.91
   6 !   11.0   0.0   0.00023      0.35      11      39 ..     195     223 ..     190     225 .. 0.91
   7 ?   -0.1   0.0      0.73   1.1e+03      13      32 ..     228     247 ..     224     247 .. 0.87
   8 ?   -1.8   0.0       2.4   3.6e+03      17      30 ..     251     268 ..     251     272 .. 0.71
   9 !   13.5   0.0   3.8e-05     0.056      12      40 ..     281     310 ..     278     311 .. 0.93
  10 ?   -1.2   0.0       1.6   2.4e+03      16      37 ..     321     342 ..     320     344 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.74
                                      HHHHHTT.TSSHHHHHHHHHHHH CS
                               Arm 16 pLvrLLs.sedeevqeeAawALs 37
                                      +L++ L+ s + ++++ +a  L+
  gi|336254915|ref|YP_004598022.1| 14 QLIEHLEgSSNSNIRRRSAEILG 36
                                      7999999********99987776 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.39
                                      HHHHHHHHTT.TSSHHHHHHHHHHH CS
                               Arm 13 avppLvrLLs.sedeevqeeAawAL 36
                                      ++++Lv+  + ++ +ev+ +A  AL
  gi|336254915|ref|YP_004598022.1| 52 VIDALVDASQtDDADEVRAAAIDAL 76
                                      7999999999999999999988887 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.5
                                       TTTSSHHHHHHHHHHHHH CS
                               Arm  21 LssedeevqeeAawALsN 38 
                                       L+ + +e++ +Aa+ L+ 
  gi|336254915|ref|YP_004598022.1| 112 LQADRPELRMAAATGLGR 129
                                       6678899*******9986 PP

  == domain 4  score: 19.8 bits;  conditional E-value: 3.9e-07
                                       HHHTTHHHHHHHHTTTSSHHHHHHHHHHHHH CS
                               Arm   8 vieaGavppLvrLLssedeevqeeAawALsN 38 
                                       + e ++v++Lv+ L+++d++v++ +a+AL+ 
  gi|336254915|ref|YP_004598022.1| 130 IGEDNVVRALVNQLDDPDPRVRKRIARALGR 160
                                       56889************************96 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 1.1
                                       HHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  14 vppLvrLLssedeevqeeAawALs 37 
                                       vp+L + L+ +  +v+ e+a AL+
  gi|336254915|ref|YP_004598022.1| 167 VPALSKRLHEDQYGVRVEIAYALA 190
                                       8999999************99996 PP

  == domain 6  score: 11.0 bits;  conditional E-value: 0.00023
                                       TTHHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                               Arm  11 aGavppLvrLLssedeevqeeAawALsNL 39 
                                        +a++ Lv+  ++ede+v++ A+ AL+ L
  gi|336254915|ref|YP_004598022.1| 195 DNALRELVDVADDEDETVRRIAVDALGRL 223
                                       5899**********************977 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 0.73
                                       HHHHHHHHTTTSSHHHHHHH CS
                               Arm  13 avppLvrLLssedeevqeeA 32 
                                       av++L   L++++++v++ A
  gi|336254915|ref|YP_004598022.1| 228 AVEILAGALRDDSDSVRRTA 247
                                       799999999*9***999987 PP

  == domain 8  score: -1.8 bits;  conditional E-value: 2.4
                                       HHHHTT....TSSHHHHH CS
                               Arm  17 LvrLLs....sedeevqe 30 
                                       Lv+LLs    s + +v+e
  gi|336254915|ref|YP_004598022.1| 251 LVQLLSeapaSASHKVRE 268
                                       89***9776666666665 PP

  == domain 9  score: 13.5 bits;  conditional E-value: 3.8e-05
                                       THHHHHHHHTT.TSSHHHHHHHHHHHHHHT CS
                               Arm  12 GavppLvrLLs.sedeevqeeAawALsNLa 40 
                                        a++pL++ L+ s  +  +++Aaw L+ +a
  gi|336254915|ref|YP_004598022.1| 281 EAIEPLIEILDrSSETAQRRNAAWLLGRIA 310
                                       58************************9886 PP

  == domain 10  score: -1.2 bits;  conditional E-value: 1.6
                                       HHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  16 pLvrLLssedeevqeeAawALs 37 
                                       +L++ L +ede++ + Aa+ Ls
  gi|336254915|ref|YP_004598022.1| 321 ALIDTLADEDEMTSKFAATSLS 342
                                       8999999999999887777776 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       0.9   1.3e+03     497     518 ..      15      36 ..       7      77 .. 0.61
   2 !    5.1   0.0    0.0046       6.9      84     140 ..     108     160 ..     105     204 .. 0.79
   3 !   20.5   0.1     1e-07   0.00015     341     448 ..     198     315 ..     182     342 .. 0.82
   4 ?    1.4   0.0     0.062        92     417     448 ..     351     383 ..     347     398 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.9
                                       HHHHHHHXXSHHHHHHHHHHHH CS
                         Adaptin_N 497 lvlslatssdlevrdRaveylq 518
                                       l+++l  ss+  +r R+ e+l 
  gi|336254915|ref|YP_004598022.1|  15 LIEHLEGSSNSNIRRRSAEILG 36 
                                       3333333444444444444333 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0046
                                       HHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHH CS
                         Adaptin_N  84 lqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailk 140
                                       l + l+   + +r+ A ++L++i++++++++l+++    l d++p vrk  a a+ +
  gi|336254915|ref|YP_004598022.1| 108 LARGLQADRPELRMAAATGLGRIGEDNVVRALVNQ----LDDPDPRVRKRIARALGR 160
                                       567788899999**************999988776....689999999987776655 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 1e-07
                                       HHHHHHHTTSSXXHHHHHHHHHHHHHHHHHS.............CCHHHHHHHHHHHHHTTXXHHHHHHHHHHHHHH CS
                         Adaptin_N 341 vkeLkkyvkevadedfksklvkaIgrlaekf.............atdaewvldvllellslsgesvkdeivevirdl 404
                                       ++eL   + +  de +++ +v+a+grl++                ++ ++ +  l++lls +  s+++++ e i   
  gi|336254915|ref|YP_004598022.1| 198 LRELVDVA-DDEDETVRRIAVDALGRLGSVEaveilagalrddsDSVRRTAMFSLVQLLSEAPASASHKVREKIVGE 273
                                       56666666.555777999999999999887677889999999988999999***********9*******9999988 PP

                                       HHHSTTTSTTCHHHHCCTCCGXXSHHHHHHHHHHHHHTTTTXTT CS
                         Adaptin_N 405 iqkvpelheeiiekLaellekieseearaaaiWllGeygelvsn 448
                                       +++  ++  e+ie L+e l+  ++++ r++a+WllG ++++  +
  gi|336254915|ref|YP_004598022.1| 274 LEQANAS--EAIEPLIEILDRSSETAQRRNAAWLLGRIANEEYR 315
                                       8887777..78**************************9998776 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.062
                                       HHHCCTCCG.XXSHHHHHHHHHHHHHTTTTXTT CS
                         Adaptin_N 417 ekLaellek.ieseearaaaiWllGeygelvsn 448
                                       ++L++l+e+ i+ ee+r +a+++lG++g + s+
  gi|336254915|ref|YP_004598022.1| 351 QRLLDLVEDdIRDEEMRVKALFVLGKIGGEQSR 383
                                       5899999999****************9977665 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       0.4     6e+02      60     120 ..      53     108 ..      12     110 .. 0.65
   2 !    8.3   0.1    0.0015       2.2      20      49 ..     133     162 ..     119     192 .. 0.84
   3 ?    3.4   0.1     0.046        68      60      83 ..     198     221 ..     164     231 .. 0.55
   4 !   12.8   0.0   6.1e-05      0.09      23      53 ..     229     259 ..     225     280 .. 0.80
   5 ?    3.4   0.0     0.047        70      37      83 ..     298     342 ..     265     359 .. 0.73
   6 ?    3.7   0.0     0.038        56       3      76 ..     299     370 ..     297     392 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.4
                              Cnd1  60 lselakll.eDenprVvanalaalteiseksenaiynllpdiisklsdalnecsewgqitil 120
                                       ++ l ++  +D+ ++V+a a+ al ++ + +    +++++  is    +l+e+ ew+  ++l
  gi|336254915|ref|YP_004598022.1|  53 IDALVDASqTDDADEVRAAAIDALDQYGQDA----LEQFIGEISGQ--DLDEIAEWKKAKVL 108
                                       4555544446777777777777777666554....34444434433..35678888877776 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0015
                              Cnd1  20 eylvepLrkrLkDedpyVRktaaivvakLi 49 
                                       +++v  L ++L D+dp VRk  a ++ ++ 
  gi|336254915|ref|YP_004598022.1| 133 DNVVRALVNQLDDPDPRVRKRIARALGRIE 162
                                       456778889999*******99998877664 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.046
                              Cnd1  60 lselaklleDenprVvanalaalt 83 
                                       l el +  +De+++V+  a+ al 
  gi|336254915|ref|YP_004598022.1| 198 LRELVDVADDEDETVRRIAVDALG 221
                                       344444455555555555554443 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 6.1e-05
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndm 53 
                                       ve L  +L+D++  VR+ta++ + +L+++  
  gi|336254915|ref|YP_004598022.1| 229 VEILAGALRDDSDSVRRTAMFSLVQLLSEAP 259
                                       6678899*******************88764 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.047
                              Cnd1  37 VRktaaivvakLilndmvkekgflselaklleDenprVvanalaalt 83 
                                        R++aa ++ ++ ++++ +  +  + l + l De+++ ++ a ++l+
  gi|336254915|ref|YP_004598022.1| 298 QRRNAAWLLGRIANEEYRQAAQ--DALIDTLADEDEMTSKFAATSLS 342
                                       4888888888888888877777..88888888888888888887776 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.038
                              Cnd1   3 RalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVva 76 
                                       R +a   lg i  ++  ++  + L  +L Ded++  k aa  ++ L   d   e+ +l+ +++ ++De+ rV a
  gi|336254915|ref|YP_004598022.1| 299 RRNAAWLLGRIANEEYRQAAQDALIDTLADEDEMTSKFAATSLSLLEGGD--LEQRLLDLVEDDIRDEEMRVKA 370
                                       55666666666667777777777777777777777777776666543333..3455666666666666666655 PP

>> RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.018        26      15      43 ..      62      88 ..      52     115 .. 0.71
   2 !    7.5   0.0    0.0036       5.4       4      32 ..     133     161 ..     131     177 .. 0.86
   3 ?   -0.1   0.0      0.84   1.2e+03      16      32 ..     207     223 ..     195     256 .. 0.55
   4 ?    1.2   0.0      0.32   4.8e+02       7      41 ..     229     264 ..     225     297 .. 0.72
   5 ?   -0.9   0.0       1.4   2.2e+03      19      57 ..     312     351 ..     305     357 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.018
                        RasGEF_N_2 15 ydqsrevvaaaleiLeeacddkeslevlv 43
                                       d+++ev+aaa+++L+++ +d   le+++
  gi|336254915|ref|YP_004598022.1| 62 TDDADEVRAAAIDALDQYGQDA--LEQFI 88
                                      68999*************7764..55554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0036
                        RasGEF_N_2   4 kWgiellvnqLydqsrevvaaaleiLeea 32 
                                       + +++ lvnqL d+++ v++ ++++L ++
  gi|336254915|ref|YP_004598022.1| 133 DNVVRALVNQLDDPDPRVRKRIARALGRI 161
                                       678999***************99999765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.84
                        RasGEF_N_2  16 dqsrevvaaaleiLeea 32 
                                       d+++ v++ a+++L + 
  gi|336254915|ref|YP_004598022.1| 207 DEDETVRRIAVDALGRL 223
                                       55555555555555433 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.32
                        RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLeeacddk.eslev 41 
                                       +e+l   L d+s++v+++a+  L + +++  +s+ +
  gi|336254915|ref|YP_004598022.1| 229 VEILAGALRDDSDSVRRTAMFSLVQLLSEApASASH 264
                                       678888899999999999877766665544344444 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 1.4
                        RasGEF_N_2  19 revvaaaleiLeeacddk.eslevlvelkpslqhlgeigs 57 
                                       +e ++aa ++L + + d+ e++ +++ +  sl + g+ ++
  gi|336254915|ref|YP_004598022.1| 312 EEYRQAAQDALIDTLADEdEMTSKFAATSLSLLEGGDLEQ 351
                                       6677788888777755554888888886656544455444 PP

>> DUF3458_C  Domain of unknown function (DUF3458_C) ARM repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.4   2.1e+03      90     112 ..      70      92 ..      46     155 .. 0.47
   2 ?   -3.5   0.0       3.6   5.3e+03     260     282 ..     139     161 ..     134     163 .. 0.73
   3 ?   14.8   0.6   9.5e-06     0.014      75     199 ..     253     372 ..     225     388 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHTHHHHHHHHHHHH CS
                         DUF3458_C  90 ealrkalaealedellalyeala 112
                                        a   al +  +d+l++ + +++
  gi|336254915|ref|YP_004598022.1|  70 AAAIDALDQYGQDALEQFIGEIS 92 
                                       33333333333333333333322 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.6
                                       HHHHHHTT-HHHHHHHGGGGTTG CS
                         DUF3458_C 260 qvleldaiNpqvAaRlvtaltrw 282
                                        v +ld+  p v  R+++al r 
  gi|336254915|ref|YP_004598022.1| 139 LVNQLDDPDPRVRKRIARALGRI 161
                                       56778888888888888888765 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 9.5e-06
                                       TT-SSB-HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHC--SHHHHHHHHHHHHHHHHHHHHHCTTTHHHHHHH. CS
                         DUF3458_C  75 eqlkevdpdaihaarealrkalaealedellalyealaaegayspdaaaagrRaLknlaLsylaaaddeeaaelav. 150
                                       + l+e+   a h++re++  +l +a ++e  + + +      +   + ++++R+ +  +L+ +a+ + ++aa++a+ 
  gi|336254915|ref|YP_004598022.1| 253 QLLSEAPASASHKVREKIVGELEQANASEAIEPLIE------ILDRSSETAQRRNAAWLLGRIANEEYRQAAQDALi 323
                                       444455555666666666666666555444333333......23356678899999999999999988888888777 PP

                                       HHHHHSSSHHHHHHHHHHHTTSSSHHHHHHHHHHHHHCTTSHHHHHHHH CS
                         DUF3458_C 151 aqfkaadnmTdrlaALaalvnsdlpereealadfyqrwkdealvldkWf 199
                                       + +++ d mT ++aA ++     ++ ++++l+ ++++ +de++ ++  f
  gi|336254915|ref|YP_004598022.1| 324 DTLADEDEMTSKFAATSLSLLEGGDLEQRLLDLVEDDIRDEEMRVKALF 372
                                       ******************999999***************9998777666 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.26   3.8e+02       4      42 ..      11      50 ..       9     102 .. 0.78
   2 ?    3.1   0.0      0.04        60     175     195 ..     133     153 ..     119     166 .. 0.86
   3 ?    4.3   0.0     0.017        25     176     213 ..     227     264 ..     206     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.26
                           CLASP_N  4 kaeellaafegketelnwdaReknil.klrslikgn.vped 42
                                      ++e+l++++eg  ++ n++ R ++il +l s   gn  p+d
  gi|336254915|ref|YP_004598022.1| 11 EFEQLIEHLEG-SSNSNIRRRSAEILgSLESEAGGNrYPRD 50
                                      68999999955.79999****99998457777777765554 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.04
                           CLASP_N 175 dliekslkkgleDanptVRet 195
                                       d ++ +l+  l D++p VR+ 
  gi|336254915|ref|YP_004598022.1| 133 DNVVRALVNQLDDPDPRVRKR 153
                                       778999*************85 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.017
                           CLASP_N 176 liekslkkgleDanptVRetaRstfweffkvwPsrAks 213
                                       +++++l  +l D + +VR+ta   ++++ + +P+ A +
  gi|336254915|ref|YP_004598022.1| 227 EAVEILAGALRDDSDSVRRTAMFSLVQLLSEAPASASH 264
                                       57889999*************************99975 PP

>> ALF  Short repeats of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.9    0.0016       2.3      13      35 ..      66      88 ..      54      90 .. 0.89
   2 ?   -2.5   0.1       3.6   5.3e+03      13      23 ..     148     158 ..     137     159 .. 0.66
   3 ?    0.1   0.1      0.55   8.2e+02      20      33 ..     186     200 ..     180     204 .. 0.76
   4 ?    3.8   0.1     0.038        58      14      23 ..     313     322 ..     299     336 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0016
                               ALF 13 paVraAAqaALdaGtpaalraFL 35
                                       +VraAA  ALd    +al++F+
  gi|336254915|ref|YP_004598022.1| 66 DEVRAAAIDALDQYGQDALEQFI 88
                                      58********************7 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.6
                               ALF  13 paVraAAqaAL 23 
                                       p Vr+  ++AL
  gi|336254915|ref|YP_004598022.1| 148 PRVRKRIARAL 158
                                       77888888887 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.55
                               ALF  20 qaAL.daGtpaalra 33 
                                       + AL d Gt+ alr+
  gi|336254915|ref|YP_004598022.1| 186 AYALaDIGTDNALRE 200
                                       567877799999997 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.038
                               ALF  14 aVraAAqaAL 23 
                                       + r+AAq AL
  gi|336254915|ref|YP_004598022.1| 313 EYRQAAQDAL 322
                                       679******* PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0055       8.2      36      62 ..      40      69 ..      15      71 .. 0.79
   2 ?   -1.1   0.0       1.6   2.4e+03      46      61 ..     104     119 ..      97     123 .. 0.77
   3 ?    2.8   0.4       0.1   1.5e+02      15      55 ..     119     159 ..     109     170 .. 0.74
   4 ?   -1.6   0.2       2.4   3.5e+03      43      59 ..     225     241 ..     208     247 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0055
                            HTH_31 36 q...Grrgrpspavlealaralgldpa.era 62
                                      +   G r  p+ +v++al++a ++d+a e++
  gi|336254915|ref|YP_004598022.1| 40 SeagGNRY-PRDEVIDALVDASQTDDAdEVR 69
                                      44446665.***************7552665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                            HTH_31  46 vlealaralgldpaer 61 
                                           lar+l++d+ e+
  gi|336254915|ref|YP_004598022.1| 104 KAKVLARGLQADRPEL 119
                                       56679******97765 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.1
                            HTH_31  15 LsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55 
                                       L+ +++ ++ ++ e+ + r    + + p p+v  ++aralg
  gi|336254915|ref|YP_004598022.1| 119 LRMAAATGLGRIGEDNVVRALVNQLDDPDPRVRKRIARALG 159
                                       556666666666666666666666667*************9 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 2.4
                            HTH_31  43 spavlealaralgldpa 59 
                                       s +++e la al+ d +
  gi|336254915|ref|YP_004598022.1| 225 SVEAVEILAGALRDDSD 241
                                       78888888888886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.39
# Mc/sec: 3244.78
//
Query:       gi|336254916|ref|YP_004598023.1|  [L=202]
Description: hypothetical protein Halxa_3533 [Halopiger xanaduensis SH-6]
Scores for 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   13.1   5.1       0.18   12.5   5.1    1.4  1  IMUP      Immortalisation up-regulated protein


Domain annotation for each model (and alignments):
>> IMUP  Immortalisation up-regulated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   5.1   9.8e-06      0.18      26      70 ..     156     199 ..     130     202 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.8e-06
                              IMUP  26 khsPkkvqGaseagaaekprhghgkssssdsssssssssdsdaea 70 
                                           + + G+s++ a++  r++  ++s+sd+ sss+s  dsd+ a
  gi|336254916|ref|YP_004598023.1| 156 SANETNASGTSNETATTTDRNAS-DESESDAESSSGSENDSDETA 199
                                       44456789******999999888.99***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1060  (0.0591221); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 1720.78
//
Query:       gi|336254917|ref|YP_004598024.1|  [L=910]
Description: hypothetical protein Halxa_3534 [Halopiger xanaduensis SH-6]
Scores for complete 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   31.6  18.7    0.00094   19.4   1.0    5.4  6  CARDB     CARDB


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 ?   -2.2   0.0      0.27   4.9e+03      37      48 ..     284     295 ..     243     341 .. 0.54
   2 !    8.9   0.4   9.9e-05       1.8      15      82 ..     359     428 ..     341     437 .. 0.74
   3 ?   -1.4   0.0      0.15   2.8e+03      37      73 ..     423     462 ..     418     472 .. 0.65
   4 !    5.3   0.1    0.0013        23      35      72 ..     483     519 ..     480     539 .. 0.79
   5 !    7.5   0.3   0.00027       4.8      13      72 ..     554     617 ..     545     647 .. 0.71
   6 !   19.4   1.0   5.2e-08   0.00094       9      88 ..     652     728 ..     645     734 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.27
                                       EEEEEEEETTEE CS
                             CARDB  37 atkvalyldgel 48 
                                       +++v+l  +g+ 
  gi|336254917|ref|YP_004598024.1| 284 DVTVRLLDSGSP 295
                                       333333333333 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 9.9e-05
                                       EETTSEEEEEEEEEE-SSS-..EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S.-S-CEEEEEE CS
                             CARDB  15 afvgeentitvtvkNqGtaa..sgatkvalyldgelvgtvtvpsLaagesttvsftwtte.ategevtltv 82 
                                       +++g+++++t+++   Gt     ++  ++l ++g+ v  ++v  La++++tt++ft+ ++     +v+++v
  gi|336254917|ref|YP_004598024.1| 359 TVEGDALEVTAELDRFGTVPegKQDYPITLSINGTDVR-TNVVTLAPDATTTETFTYEADrDDVPQVDVRV 428
                                       5666666666677767765522455668999*****88.66779*************99955556666665 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.15
                                       EEEEEEEETTEEE.EEEEE.SEE-CTEEEEEEEEEE-S.- CS
                             CARDB  37 atkvalyldgelv.gtvtv.psLaagesttvsftwtte.a 73 
                                       ++ v++    +++ +tv+v + L+ + ++  ++t+tt+  
  gi|336254917|ref|YP_004598024.1| 423 QVDVRVSSPTDSAsTTVPVlSRLEHDHNIRTEVTDTTIgG 462
                                       5555555555554344454799999999999999998843 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.0013
                                       EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S CS
                             CARDB  35 sgatkvalyldgelvgtvtvpsLaagesttvsftwtte 72 
                                       +++++++l++dg++v+++++  L+ ++ ++ +ft+  +
  gi|336254917|ref|YP_004598024.1| 483 ETQFTANLTADGTVVDQQDI-TLSGSSAANATFTHELS 519
                                       5799****************.79999999999988766 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.00027
                                       SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEE.SEE-CTEEEEEEEEEE-S CS
                             CARDB  13 seafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtv.psLaagesttvsftwtte 72 
                                       ++a  + ++t tvtv+NqG+   ++t +    +   v   gt t  ++L+++es t+++t+ ++
  gi|336254917|ref|YP_004598024.1| 554 DPAARNGQLTATVTVENQGETPGTETLTIEPRNPYAVesdGTYTAsAPLEPSESFTETVTFDVT 617
                                       567788899**********998666655555555555554444446899999999999887665 PP

  == domain 6  score: 19.4 bits;  conditional E-value: 5.2e-08
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEES CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltvvvD 85 
                                       ++++++  +g++  +t+t++N+G  a+g+  ++l+ d+e+ +t +v sL+++e++t s  + ++ ++g++ + v++D
  gi|336254917|ref|YP_004598024.1| 652 NVSVDAGADGTNPVVTATIRNTGG-AAGTQDATLTFDDESIATESV-SLEPDEKRTLSGAVEPA-ETGTYSYGVTTD 725
                                       56777888999999********96.67888999*************.9***************9.************ PP

                                       TT- CS
                             CARDB  86 pdn 88 
                                        d+
  gi|336254917|ref|YP_004598024.1| 726 DDS 728
                                       875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (910 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.22s 00:00:00.88 Elapsed: 00:00:00.36
# Mc/sec: 7667.73
//
Query:       gi|336254918|ref|YP_004598025.1|  [L=81]
Description: hypothetical protein Halxa_3535 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.92    9.3   3.3         14    5.5   3.3    2.2  1  YacG      DNA gyrase inhibitor YacG


Domain annotation for each model (and alignments):
>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   3.3    0.0008        14       2      25 ..      38      71 ..      37      74 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0008
                              YacG  2 kCPtCkkev..........ewseenpfrPFCSeR 25
                                      +CP C++++             e+ p rPFC  R
  gi|336254918|ref|YP_004598025.1| 38 RCPACNRAFdrlfvseretATFETAPDRPFCLAR 71
                                      6888877541111111100223467899999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 633.01
//
Query:       gi|336254919|ref|YP_004598026.1|  [L=175]
Description: transcriptional regulator PadR family protein [Halopiger xanaduensis SH-6]
Scores for complete 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-08   34.9   0.1    2.1e-08   34.0   0.1    1.4  1  PadR      Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
       0.11   13.2   0.1       0.23   12.1   0.1    1.6  2  RTP       Replication terminator protein
        0.2   11.4   0.6       0.31   10.8   0.6    1.6  1  DUF3708   Phosphate ATP-binding cassette transporter


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 !   34.0   0.1   3.4e-12   2.1e-08       2      65 ..      87     144 ..      86     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 3.4e-12
                                       HHHHCC.S-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEE CS
                              PadR   2 Lallee.qpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrl 65 
                                       L+l++  ++++G e+ ++l++l++   +ls+G++YpaL++L++e++++ + +      ++k Y +
  gi|336254919|ref|YP_004598026.1|  87 LMLIALrEETHGKELLSDLTHLFDA--TLSPGTVYPALHDLKEEDVLAMHTKV-----RTKEYSI 144
                                       6677544999************987..9*******************999886.....5677766 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.4   8.3e+03      82     105 ..      41      64 ..      13      68 .. 0.64
   2 ?   12.1   0.1   3.8e-05      0.23      16      70 ..      89     140 ..      76     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.4
                                       SS..HHHHHHHHHHHHHHHHHHHH CS
                               RTP  82 tdeGkekaklykkqvkidldrckk 105
                                       +d+G+++ +   +++   l++ ++
  gi|336254919|ref|YP_004598026.1|  41 ADAGTDAGNSVERELDSLLEQVQG 64 
                                       456666666666666666666655 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.8e-05
                                       HHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTS CS
                               RTP  16 tlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkek 70 
                                        ++ +++++g +ll +l + F       ++ ++y alh+l e+ +l  + ++++k
  gi|336254919|ref|YP_004598026.1|  89 LIALREETHGKELLSDLTHLFDAT-L--SPGTVYPALHDLKEEDVLAMHTKVRTK 140
                                       333445567999999999999763.4..4579**************988888744 PP

>> DUF3708  Phosphate ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.6   5.2e-05      0.31      65     130 ..       8      69 ..       1     171 [. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.2e-05
                           DUF3708  65 eslvaaelpeavlalsegqrqllledvrniaegldaLsaaeaealkatadeirallaavgvalgte 130
                                        ++v +el++a  +++  + +  +e +r  a+g+da   +  ++++    e+ +ll++v  al+t+
  gi|336254919|ref|YP_004598026.1|   8 TRSVFDELSNAAANKQSESESESYETIRGTATGADA-GTDAGNSVE---RELDSLLEQVQGALATD 69 
                                       67889999998888888999****************.444444554...58888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1362.57
//
Query:       gi|336254920|ref|YP_004598027.1|  [L=145]
Description: hypothetical protein Halxa_3537 [Halopiger xanaduensis SH-6]
Scores for 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:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1131.85
//
Query:       gi|336254921|ref|YP_004598028.1|  [L=132]
Description: 30S ribosomal protein S6e [Halopiger xanaduensis SH-6]
Scores for complete 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-41  141.1   0.0    1.9e-41  140.9   0.0    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 !  140.9   0.0   1.1e-45   1.9e-41       2     124 ..       5     125 ..       4     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 140.9 bits;  conditional E-value: 1.1e-45
                                       EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEET CS
                     Ribosomal_S6e   2 klnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlsk 78 
                                        +++ dp++g+++++e+++++++++igk+igeevdg+a+G  l+gy+l+itggsd++G+p++++v++++ +++L+++
  gi|336254921|ref|YP_004598028.1|   5 TVVVGDPDSGSSYQLEAEDQDANRFIGKSIGEEVDGGAVG--LDGYTLEITGGSDDAGRPLNPNVPGANLTEVLMEG 79 
                                       689*************************************..*********************************** PP

                                       TSSSS-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--SS--TTTS CS
                     Ribosomal_S6e  79 ggvgyrprrkGerkrksvrGcivsadisqlnlvivkkgekdieglt 124
                                       +++gy+p r+Ger+r++vrG++vs++++q+n+ iv +g+ d+++l+
  gi|336254921|ref|YP_004598028.1|  80 RQTGYKPSRDGERRRVTVRGSEVSDAVAQINASIVDRGSADVDELL 125
                                       ********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1103.99
//
Query:       gi|336254922|ref|YP_004598029.1|  [L=92]
Description: hypothetical protein Halxa_3539 [Halopiger xanaduensis SH-6]
Scores for 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  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 733.50
//
Query:       gi|336254923|ref|YP_004598030.1|  [L=241]
Description: regulatory protein TetR [Halopiger xanaduensis SH-6]
Scores for 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-14   52.3   3.4      6e-14   52.3   3.4    1.8  2  TetR_C_6   BetI-type transcriptional repressor, C-terminal
    5.1e-10   39.0   0.0    1.4e-09   37.6   0.0    1.8  2  TetR_N     Bacterial regulatory proteins, tetR family
      4e-06   27.0   5.9      4e-06   27.0   5.9    2.2  2  TetR_C_31  Tetracyclin repressor-like, C-terminal domain
    1.1e-05   25.7   0.3    2.9e-05   24.3   0.3    1.9  1  TetR_C_24  Tetracyclin repressor-like, C-terminal domain
    5.9e-05   23.1   0.1    0.00013   22.0   0.1    1.6  1  TetR_C_27  Tetracyclin repressor-like, C-terminal domain
    0.00017   21.6   0.0    0.00044   20.3   0.0    1.6  1  TetR_C_17  Tetracyclin repressor-like, C-terminal domain
    0.00035   20.7   0.0    0.00057   20.1   0.0    1.3  1  TetR_C_5   QacR-like protein, C-terminal region
     0.0075   16.6   1.6     0.0075   16.6   1.6    3.1  3  TetR_C_11  Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.067   13.2   0.3       0.16   12.0   0.3    1.6  1  TetR_C_7   AefR-like transcriptional repressor, C-terminal do
      0.091   12.7   0.0       0.15   12.0   0.0    1.5  1  TetR_C_13  Tetracyclin repressor-like, C-terminal domain
      0.091   13.4   0.0       0.18   12.4   0.0    1.5  1  TetR_C_37  Tetracyclin repressor-like, C-terminal domain
       0.13   12.4   0.0       0.25   11.5   0.0    1.4  1  TetR_C_29  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.5   6.8e+03       5      21 ..      56      72 ..      52      75 .. 0.64
   2 !   52.3   3.4     4e-17     6e-14       1     114 [.      76     193 ..      76     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.5
                                      HHHHHHCCSTHSHHHHH CS
                          TetR_C_6  5 lraileallpldqerra 21
                                      l a+l+++++   e+ +
  gi|336254923|ref|YP_004598030.1| 56 LLAYLREQFDEGIETTR 72
                                      66777777776666655 PP

  == domain 2  score: 52.3 bits;  conditional E-value: 4e-17
                                       HHHHHHHHHHCCS...THSHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSTHHH CS
                          TetR_C_6   1 prerlraileall...pldqerraelavwlafwaeaardpelaelqrenyarlrsnlrallaelaegglradadaea 74 
                                       p  rl  +++++l   ++++err + ++ l++  +a+++++++e++++++++lr++l ++l+++ ++g++ d d+++
  gi|336254923|ref|YP_004598030.1|  76 PTTRLAMFIDWYLygsSGEDERRSFHTALLELRTQAPHNERYREQLQRSDEQLRTTLEEILQDGIDAGEFVDHDTAE 152
                                       567888889999844347899999***************************************************** PP

                                       HHHHHHHHHHHHHHHHHHTCTTCHHHHHH.HHHHHHHHHHT CS
                          TetR_C_6  75 aAerlaAlidGLwlraalapeeldaerar.alvrrhldall 114
                                        A+ l A +dG  +r +  +++    ++r  ++++ +d+ll
  gi|336254923|ref|YP_004598030.1| 153 TAALLLAALDGARTRQLAFNRDEYLGQVRsGVITQVIDDLL 193
                                       ************99877666444444444356666666665 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 !   37.6   0.0   9.3e-13   1.4e-09       1      46 [.      10      55 ..      10      56 .. 0.97
   2 ?   -2.5   0.0       3.1   4.6e+03       3      15 ..     129     141 ..     128     143 .. 0.56

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 9.3e-13
                                      HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                            TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                      I++a+ e + e+Gy  +t ++IA+r   sk++l+++++sK++L++ 
  gi|336254923|ref|YP_004598030.1| 10 IMEATYEALCEHGYTDLTAQDIADRTDKSKSLLFYHYDSKDDLVAD 55
                                      89*****************************************975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHTT CS
                            TetR_N   3 daArelfaerGyd 15 
                                        +++e + + G+d
  gi|336254923|ref|YP_004598030.1| 129 RTTLEEILQDGID 141
                                       4555566666665 PP

>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.73   1.1e+03       4      26 ..      51      75 ..      48      85 .. 0.69
   2 !   27.0   5.9   2.7e-09     4e-06      20     101 ..      97     189 ..      75     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.73
                                      CHHHHHHHHHCCCCCT..THHHHHH CS
                         TetR_C_31  4 eeladlladlldrala..drertlA 26
                                      + +adlla l +++ +  + +rtlA
  gi|336254923|ref|YP_004598030.1| 51 DLVADLLAYLREQFDEgiETTRTLA 75
                                      5667777766666655678888887 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 2.7e-09
                                       THHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHHH...HHCS...S-HHHHHHHHHHHHHHHHHHHHHSGT CS
                         TetR_C_31  20 drertlAryelfleaarrPeLraalarlrralrealaalla...alGl...pdpeeaarllvaaldGllldrLagpa 90 
                                       +r+ + A++el+ +a ++++ r+ l+r+ ++lr  l+++l+   ++G    +d +e+a+ll+aaldG+  ++La   
  gi|336254923|ref|YP_004598030.1|  97 RRSFHTALLELRTQAPHNERYREQLQRSDEQLRTTLEEILQdgiDAGEfvdHDTAETAALLLAALDGARTRQLAFN- 172
                                       89999************************************888677663235558******************97. PP

                                       S-H......HHHHHHHH CS
                         TetR_C_31  91 adp......raevrell 101
                                       +d+        ++++++
  gi|336254923|ref|YP_004598030.1| 173 RDEylgqvrSGVITQVI 189
                                       34444333334444444 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.3   1.9e-08   2.9e-05      34      85 ..     111     162 ..      73     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.9e-08
                                       GGS-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB-SS-HHHHHHHHHHHHH CS
                         TetR_C_24  34 raLspehreeiralrreyerllrdlieeGvaagefedldpklaalailgmln 85 
                                          ++ +re++++  ++++++l++++++G++agef d+d++ +a ++l +l 
  gi|336254923|ref|YP_004598030.1| 111 APHNERYREQLQRSDEQLRTTLEEILQDGIDAGEFVDHDTAETAALLLAALD 162
                                       4446778999999999*******************************99986 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 !   22.0   0.1   8.6e-08   0.00013      36      82 ..     116     162 ..     100     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.6e-08
                                       H-HHHHHHHHHHHHHHHHHHHHHHHHCT-STT--HHHHHHHHHHHSG CS
                         TetR_C_27  36 eelevvekhieeleeqlaeIireGvaaGeFkaadpeaaaravfdata 82 
                                       +++e  ++  e+l+  l+eI+++G++aGeF   d +++a ++++a+ 
  gi|336254923|ref|YP_004598030.1| 116 RYREQLQRSDEQLRTTLEEILQDGIDAGEFVDHDTAETAALLLAALD 162
                                       6667777777999*****************************99985 PP

>> TetR_C_17  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.9e-07   0.00044      18      95 ..      98     174 ..      89     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.9e-07
                                       GSSHHHHHHHHHGGGG-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS---SS-HHHHHHHHHHHHHHHHHHHHHS-H CS
                         TetR_C_17  18 eslllakyEyfltsyreeerrayleeRyerlvealkellqeGvergEfkPqlplesiakylisfldGliletlalge 94 
                                       +s+ +a +E   ++ ++e  r+ l++  e+l ++l+e+lq+G++ gEf  +  +e+ a +l++ ldG  +++la++ 
  gi|336254923|ref|YP_004598030.1|  98 RSFHTALLELRTQAPHNERYREQLQRSDEQLRTTLEEILQDGIDAGEFVDHDTAET-AALLLAALDGARTRQLAFNR 173
                                       5667777777777778888899999999********************98776666.55677899**9999988876 PP

                                       H CS
                         TetR_C_17  95 e 95 
                                       +
  gi|336254923|ref|YP_004598030.1| 174 D 174
                                       6 PP

>> TetR_C_5  QacR-like protein, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.8e-07   0.00057      37     110 ..      99     172 ..      87     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.8e-07
                          TetR_C_5  37 PlsnaieelaseqvksksilekllkLerkslkayekileeGiqsGefrienvedvskivasllsGlvvlihele 110
                                        ++ a  el ++   ++   e+l+  +++   + e il++Gi  Gef+  ++ + + ++ ++l+G  +    ++
  gi|336254923|ref|YP_004598030.1|  99 SFHTALLELRTQAPHNERYREQLQRSDEQLRTTLEEILQDGIDAGEFVDHDTAETAALLLAALDGARTRQLAFN 172
                                       5678999****************************************************999999766555555 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.23   3.4e+02       5      21 ..      50      66 ..      47      83 .. 0.75
   2 !   16.6   1.6     5e-06    0.0075      27      89 ..     100     160 ..      90     166 .. 0.82
   3 ?   -0.4   0.1      0.92   1.4e+03      58      78 ..     206     226 ..     173     229 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.23
                         TetR_C_11  5 GslrgDLrallralaea 21
                                      ++l +DL+a+lr+  ++
  gi|336254923|ref|YP_004598030.1| 50 DDLVADLLAYLREQFDE 66
                                      68999*****9986654 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5e-06
                         TetR_C_11  27 agallrallaeaqrdpelaealrerlleprraalravlrrAvarGelradadvelvldlllgp 89 
                                        + +l  l ++a ++++ +e+l++   e+ r++l+++l+ +++ Ge     d++  ++lll++
  gi|336254923|ref|YP_004598030.1| 100 FHTALLELRTQAPHNERYREQLQR-SDEQLRTTLEEILQDGIDAGEFVD-HDTAETAALLLAA 160
                                       566788888999999999****99.99999*****************97.5666666666554 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.92
                         TetR_C_11  58 aalravlrrAvarGelradad 78 
                                       + +    + A+a Ge +ada+
  gi|336254923|ref|YP_004598030.1| 206 ELFGSGPEDAQADGEPSADAN 226
                                       444444466778888777775 PP

>> TetR_C_7  AefR-like transcriptional repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3    0.0001      0.16      35      94 ..     115     174 ..     106     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                       HHHCCHHHT.T----HHHHHHHHHHHHTTSB-SS-HHHHHHHHHHHHHHHHTHHHHHH-- CS
                          TetR_C_7  35 elarafyeagpgrveealaayLeaavaaGrLridDpelAAeqflgllkgelfwprlfgve 94 
                                       e  r+ +++  ++++++l+++L++  +aG+   +D++ +A+ +l+ l g    ++ f+ +
  gi|336254923|ref|YP_004598030.1| 115 ERYREQLQRSDEQLRTTLEEILQDGIDAGEFVDHDTAETAALLLAALDGARTRQLAFNRD 174
                                       56677888889**********************************999887777666654 PP

>> TetR_C_13  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001      0.15      38      94 ..     113     168 ..      75     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                       S-TTHHHHHHHHHHHHHHHHHHHHHHHHCTTSS-TTS-HHHHHHHHHHHHHHHHHHH CS
                         TetR_C_13  38 lpesfrerleevledwqkrvaacleeaqeageiaadadaeelaeffwigWeGAvlRa 94 
                                        +e++re+l++  e+ ++ ++++l++  +age   d+d++e a++++ + +GA +R 
  gi|336254923|ref|YP_004598030.1| 113 HNERYREQLQRSDEQLRTTLEEILQDGIDAGEF-VDHDTAETAALLLAALDGARTRQ 168
                                       5799****************************9.899****************8885 PP

>> TetR_C_37  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012      0.18      37      87 ..     114     164 ..     106     182 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                       -GGGHHHHHHHHHHHHHHHHHHHHTT--TTTBSS.-HHHHHHHHHHHHHHH CS
                         TetR_C_37  37 ekeikekykkildsLrevLksklkelneekkiklknkeetaelIfvlvdga 87 
                                       +++ +e+ ++  ++Lr++L+++l++  + +++  ++++eta l ++ +dga
  gi|336254923|ref|YP_004598030.1| 114 NERYREQLQRSDEQLRTTLEEILQDGIDAGEFVDHDTAETAALLLAALDGA 164
                                       677789999999*************************************98 PP

>> TetR_C_29  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.25      40      83 ..     118     161 ..     106     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                                       S--SS-.THHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHHHH CS
                         TetR_C_29  40 sesirelnspliekleeilerGqaagvFrpgvdaldlyllissl 83 
                                       +e++++  ++l  +leeil+ G +ag F +   a+   ll ++l
  gi|336254923|ref|YP_004598030.1| 118 REQLQRSDEQLRTTLEEILQDGIDAGEFVDHDTAETAALLLAAL 161
                                       46667778899*****************9977777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1857.92
//
Query:       gi|336254924|ref|YP_004598031.1|  [L=350]
Description: hypothetical protein Halxa_3541 [Halopiger xanaduensis SH-6]
Scores for 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  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 2856.80
//
Query:       gi|336254925|ref|YP_004598032.1|  [L=112]
Description: hypothetical protein Halxa_3542 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.039   14.3   1.3      0.039   14.3   1.3    1.6  2  TM2       TM2 domain


Domain annotation for each model (and alignments):
>> TM2  TM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.3   2.2e-06     0.039       8      42 ..      11      42 ..       4      47 .. 0.79
   2 ?   -2.6   0.2      0.42   7.6e+03       8      15 ..      81      88 ..      79      95 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-06
                               TM2  8 aylLwffLGglGvHRFYlGktgsGvlqlltfvGgl 42
                                      ay L+ f  + G+ + YlG+++ G+ ++ ++ G++
  gi|336254925|ref|YP_004598032.1| 11 AYPLSAF--VAGLGHCYLGRWKRGLTWFGLY-GLA 42
                                      5666666..6788999**************9.775 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.42
                               TM2  8 aylLwffL 15
                                      a+lL ++L
  gi|336254925|ref|YP_004598032.1| 81 AVLLVCLL 88
                                      55555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 937.58
//
Query:       gi|336254926|ref|YP_004598033.1|  [L=141]
Description: hypothetical protein Halxa_3543 [Halopiger xanaduensis SH-6]
Scores for 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   27.0   0.2    4.1e-06   26.4   0.2    1.4  1  SHOCT            Short C-terminal domain
     0.0089   16.1   0.3      0.018   15.1   0.3    1.5  1  DUF1707          Domain of unknown function (DUF1707)
  ------ inclusion threshold ------
      0.024   14.0   1.5      0.059   12.7   0.0    1.9  2  CCB1             Cofactor assembly of complex C subunit B
      0.057   14.4   1.8        1.3   10.0   1.8    2.2  1  DUF4834          Domain of unknown function (DUF4834)
      0.065   13.2   5.9       0.24   11.4   0.1    3.0  3  DUF4083          Domain of unknown function (DUF4083)
      0.066   13.6   0.1       0.16   12.3   0.1    1.8  1  FtsH_ext         FtsH Extracellular
      0.067   13.2   0.2        0.1   12.6   0.2    1.2  1  GvpG             Gas vesicle protein G
       0.15   12.0   0.0       0.18   11.8   0.0    1.2  1  Halogen_Hydrol   5-bromo-4-chloroindolyl phosphate hydrolysis
       0.21   10.3   0.0       0.21   10.3   0.0    1.2  1  DUF2207          Predicted membrane protein (DUF2207)
        0.3   10.9   3.0       0.46   10.3   1.3    1.8  2  Trp_oprn_chp     Tryptophan-associated transmembrane protein 
       0.72   10.2   7.1          1    9.7   7.1    1.2  1  IncF             Inclusion membrane protein F
       0.75    9.9  10.6          1    9.4  10.6    1.2  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.2   2.7e-09   4.1e-06       5      28 .]      89     112 ..      85     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.7e-09
                             SHOCT   5 kLkeLyarGeIteEEFeakKakLL 28 
                                       +L+e+y +Ge++e+EFe+  ++ L
  gi|336254926|ref|YP_004598033.1|  89 QLQERYVAGELSEAEFERELDRVL 112
                                       8*****************999876 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   1.2e-05     0.018      14      38 ..      89     113 ..      79     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                           DUF1707  14 lLrealaeGrLtldEfdeRleaala 38 
                                       +L+e + +G L+ +Ef++ l+++l+
  gi|336254926|ref|YP_004598033.1|  89 QLQERYVAGELSEAEFERELDRVLE 113
                                       8**********************97 PP

>> CCB1  Cofactor assembly of complex C subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.8      0.18   2.7e+02      85     118 ..      15      48 ..       8      50 .. 0.83
   2 ?   12.7   0.0   3.9e-05     0.059       4      47 ..      46      90 ..      43     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.18
                              CCB1  85 tllaalgllclaLVlsilvpelgnlflllvllsP 118
                                        +la+++l  +a ++ il+  +  ++ llv+++ 
  gi|336254926|ref|YP_004598033.1|  15 LVLAFIALSVIATIVGILFSVVATIVSLLVTVAV 48 
                                       4788999999999999999999999988888775 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.9e-05
                              CCB1  4 sstLlLtlLllvGLfffira.svKdrteevtleseeseeelleel 47
                                      ++ L+L +L +vGLf+++r  s+ + t + ++es+   ++  ++l
  gi|336254926|ref|YP_004598033.1| 46 VAVLGLLVLGAVGLFSMLRDgSSDSSTGTYEYESADRTHDPKSQL 90
                                      6789***************62667778899999985554444444 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.8   0.00087       1.3       3      60 ..      35      93 ..       7     137 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00087
                           DUF4834  3 fLlfilifiiailviglsilsvi.lrtvfglgsrkkssksaqkqfgnstnsnqqksqsr 60
                                      +++ i+ ++++++v+gl +l+++ l +++  gs  +s+ +++ +++ +t++++++ q+r
  gi|336254926|ref|YP_004598033.1| 35 VVATIVSLLVTVAVLGLLVLGAVgLFSMLRDGSSDSSTGTYEYESADRTHDPKSQLQER 93
                                      34444444445555555555443122223355555555444444444444444433322 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   5.1       1.9   2.8e+03       8      26 ..      21      39 ..      14      44 .. 0.77
   2 ?   11.4   0.1   0.00016      0.24       4      35 ..      41      72 ..      38      81 .. 0.89
   3 ?    1.4   0.0      0.21   3.1e+02      34      52 ..      95     113 ..      89     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.9
                           DUF4083  8 liivivLilllvfsftlfi 26
                                       + vi  i++++fs++  i
  gi|336254926|ref|YP_004598033.1| 21 ALSVIATIVGILFSVVATI 39
                                      5668889999999998766 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00016
                           DUF4083  4 dliyliivivLilllvfsftlfiRrvvsrsaa 35
                                       l+ +++v++L++l+ +++  ++R  +s s++
  gi|336254926|ref|YP_004598033.1| 41 SLLVTVAVLGLLVLGAVGLFSMLRDGSSDSST 72
                                      6899*********************9999986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.21
                           DUF4083  34 aakkkkskeleqKLDkiIe 52 
                                       +a + ++ e e+ LD++ e
  gi|336254926|ref|YP_004598033.1|  95 VAGELSEAEFERELDRVLE 113
                                       6667788999******976 PP

>> FtsH_ext  FtsH Extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00011      0.16       6      90 ..      48     137 ..      14     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                          FtsH_ext   6 llallllllllslfg......gsgtg.......stkeisyseFledleqgnvekvvvqestisalirrptgdgvstt 69 
                                       +l+ll+l+++ ++++       s+tg       ++   + s+++e + +g+ +++++++  ++        +++s++
  gi|336254926|ref|YP_004598033.1|  48 VLGLLVLGAVGLFSMlrdgssDSSTGtyeyesaDRTHDPKSQLQERYVAGELSEAEFERELDR--------VLESDD 116
                                       4444444444444447665543333345555555555555999***************77666........789999 PP

                          FtsH_ext  70 kkgnstttystptlgsvesle 90 
                                        +g++  t + p+++++ +++
  gi|336254926|ref|YP_004598033.1| 117 GRGTGGRTRTEPDRSRTRDFD 137
                                       999999999999999988876 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   6.7e-05       0.1      30      63 ..      80     113 ..      71     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.7e-05
                              GvpG  30 qenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLd 63 
                                        +  +   ++Lq +  aGe +e+eF+r+ +++L+
  gi|336254926|ref|YP_004598033.1|  80 ADRTHDPKSQLQERYVAGELSEAEFERELDRVLE 113
                                       5555566689******************999996 PP

>> 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 ?   11.8   0.0   0.00012      0.18       5      73 ..      20     102 ..      16     114 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                    Halogen_Hydrol   5 llsiliavival.vsffllgfsffla...llia..ilggilvyvasr.............knkkkkhlkksglsrke 62 
                                       +  ++ia+iv++ +s++++ +s++++   l  +  +lg++ +++  r             + ++++h  ks+l+++ 
  gi|336254926|ref|YP_004598033.1|  20 IALSVIATIVGIlFSVVATIVSLLVTvavL--GllVLGAVGLFSMLRdgssdsstgtyeyESADRTHDPKSQLQER- 93 
                                       444444444444044444444444444222..23477777777777799999999999998888888888887765. PP

                    Halogen_Hydrol  63 lkyiretlkea 73 
                                         y++  l+ea
  gi|336254926|ref|YP_004598033.1|  94 --YVAGELSEA 102
                                       ..345555555 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00014      0.21     383     429 ..      19      61 ..       6     118 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                           DUF2207 383 lsalglgliilglilillallllvlllvfllilllillliaiivlll 429
                                       ++al+++++i+g++++++a ++    + +  + +l+ll+++++ l+ 
  gi|336254926|ref|YP_004598033.1|  19 FIALSVIATIVGILFSVVATIV----SLLVTVAVLGLLVLGAVGLFS 61 
                                       2333333333333333333222....444444444444444444433 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 ?    2.1   2.2     0.096   1.4e+02      52      86 ..      15      49 ..       4      52 .. 0.53
   2 ?   10.3   1.3    0.0003      0.46     115     164 ..      40      92 ..      20     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.096
                      Trp_oprn_chp 52 llAaavAvlavrglgrrvvgvllalagagaavaal 86
                                      l+ a++A+ +   ++ ++++v++ +++++++va+l
  gi|336254926|ref|YP_004598033.1| 15 LVLAFIALSVIATIVGILFSVVATIVSLLVTVAVL 49
                                      33344455555555555555555555555555554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0003
                      Trp_oprn_chp 115 ltawpvlalaggvllllagvllllrarswpamssrYerpaarraeaeae...d 164
                                       ++  + +a++g ++l + g++ +lr +s  ++ + Ye ++a+r+++++    +
  gi|336254926|ref|YP_004598033.1|  40 VSLLVTVAVLGLLVLGAVGLFSMLRDGSSDSSTGTYEYESADRTHDPKSqlqE 92 
                                       4447889999*******************************999887665540 PP

>> IncF  Inclusion membrane protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   7.1    0.0007         1      43      88 ..       4      49 ..       2      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0007
                              IncF 43 laalvlnga.lcvlslvalcvgatpvgplavlvattlasflcaacvl 88
                                      l +l+l+g+ + vl+++al v at vg l  +vat + s+l++ +vl
  gi|336254926|ref|YP_004598033.1|  4 LGSLMLKGTgVLVLAFIALSVIATIVGILFSVVATIV-SLLVTVAVL 49
                                      5678888863789****************99998765.666666555 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 ?    9.4  10.6    0.0007         1      32      93 ..       3      65 ..       1      77 [. 0.59

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0007
                   Phage_holin_3_6 32 ragsgagllgaagvlallalllllvalalala.alwlaalivaavllvlagvlalvglkklkk 93
                                      r+gs+++   + +vla++al ++   + ++++ ++ +  l+v++++l l ++ a+   + l++
  gi|336254926|ref|YP_004598033.1|  3 RLGSLMLKGTGVLVLAFIALSVIATIVGILFSvVATIVSLLVTVAVLGLLVLGAVGLFSMLRD 65
                                      455555555555666666655555555455554466666666666666666666655555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1298  (0.0723967); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 1185.87
//
Query:       gi|336254927|ref|YP_004598034.1|  [L=412]
Description: RNA-metabolising metallo-beta-lactamase [Halopiger xanaduensis SH-6]
Scores for 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    1.4e-12   47.9   0.0    1.5  1  Beta-Casp      Beta-Casp domain
    8.7e-11   41.6   0.0    3.5e-10   39.7   0.0    1.9  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    2.8e-09   37.3   9.1    3.4e-09   37.0   7.2    2.0  2  Lactamase_B    Metallo-beta-lactamase superfamily
    1.5e-07   31.2   1.0      5e-07   29.4   0.3    2.0  2  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0011   18.4   0.0      0.002   17.6   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.028   14.3   0.0      0.093   12.6   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 !   47.9   0.0   4.7e-16   1.4e-12      22     110 .]     235     334 ..     223     334 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 4.7e-16
                                       -EEEEE-HHHHHHHHHGGGGGG...................E-SHH....HHHH..HHHS-SSEEEEES-TTSSSSH CS
                         Beta-Casp  22 lpiyldsplaskatevYkeyae...................veakslewmeskkeelnsskgpkvilassgmlegGr 79 
                                       l+ y+d+ +++++te++ + ++                   v+ ++     ++ e++   ++  vi+++sgml+gG+
  gi|336254927|ref|YP_004598034.1| 235 LECYVDG-MGKRVTELFLREPNrgflrdpdllrrakgnarfVDGRD----GQR-ERI--AEQNTVIVTTSGMLHGGP 303
                                       4679999.*********99999***999999977655544444333....222.234..45889************* PP

                                       HHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  80 srellkklledprntvilvgyqaegTlgrkl 110
                                       +  ++ ++ ++p n + ++gyq+egT+gr+l
  gi|336254927|ref|YP_004598034.1| 304 AMTYVPAVRSHPTNKIAMTGYQVEGTPGREL 334
                                       *****************************86 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 ?   -1.5   0.0       0.8   2.4e+03      30      43 ..      43      56 ..      40      67 .. 0.78
   2 !   39.7   0.0   1.2e-13   3.5e-10       3      62 .]     348     404 ..     346     404 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.8
                             RMMBL 30 kprnvilvHGeeea 43
                                       p+ v++ HG+ ++
  gi|336254927|ref|YP_004598034.1| 43 DPEAVVVSHGHLDH 56
                                      578899****8766 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 1.2e-13
                             RMMBL   3 pvkarieeidfSgHadknellelirklkprnvilvHGeeeatsalarllkeeegidvfiP 62 
                                       +v ar e++dfS+Had+++lle+++  +   v ++HG++  ++a+a+ l +  g d+ +P
  gi|336254927|ref|YP_004598034.1| 348 RVSARTEQYDFSAHADREGLLEFLEAYRGCEVLVNHGDR--CAAFAEEL-RSDGFDARAP 404
                                       799************************************..********.7777777665 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   7.2   1.1e-12   3.4e-09       6     160 ..      14     167 ..       9     182 .. 0.87
   2 ?   -2.8   0.0       1.8   5.4e+03      96     149 ..     263     323 ..     246     323 .. 0.57

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.1e-12
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                        +++li   ++++L D G+++ ++  +       +++ d++av+++H+HlDH+G  + l +    p+++    ++ l
  gi|336254927|ref|YP_004598034.1|  14 RSAVLI---DETLLLDYGMDSGNPPSF------PVGDADPEAVVVSHGHLDHVGSIPSLLSGDSRPSIHWTPPTYDL 81 
                                       566666...699999999999999985......8******************************************* PP

                                       HCHHHHHHHHHCCHH.....TTCHCGCCEEEEETTTEECCCTEEEEEHE...CTTSTSCCEEEEEETTCCEEEECTT CS
                       Lactamase_B  83 fmeeaddaasrkgll.....lagvsadkpdvdeeeldgnaggrralyvt...ggpghghghgvveygggkvlftGDa 151
                                       +m  a d    +g+       +++ a+  +v e  +  + +++ ++++t    g+++g+ h+ v++g+ ++l+tGD+
  gi|336254927|ref|YP_004598034.1|  82 TMVLARDTLKLHGGTydcpfTEAELARVTQVSETHGYREPFEVAGYEITffdAGHVPGSAHVLVDDGDTRLLYTGDF 158
                                       *****9999999999***99888888888888888888888888877776668***********************9 PP

                                       TSSHHCCCC CS
                       Lactamase_B 152 llagetgri 160
                                         +g +++ 
  gi|336254927|ref|YP_004598034.1| 159 HTEGQRLLS 167
                                       887766665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.8
                                       HH.......TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEEC CS
                       Lactamase_B  96 ll.......lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftG 149
                                       +l       +++v+ ++ ++ +  ++ ++    ++  +ggp+ + +++v + +  k++ tG
  gi|336254927|ref|YP_004598034.1| 263 DLlrrakgnARFVDGRDGQRERIAEQNTVIVTTSGMLHGGPAMTYVPAVRSHPTNKIAMTG 323
                                       3345444545555556666666666666666666666677777777776666666666665 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 !   29.4   0.3   1.7e-10     5e-07      24     173 ..      38     191 ..      22     209 .. 0.67
   2 ?   -0.5   0.0      0.25   7.4e+02     102     149 ..     302     345 ..     266     358 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.7e-10
                                       SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH..........HCCTTCGHHHCHTT........ CS
                     Lactamase_B_2  24 lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla..........vleanfvylaleee........ 82 
                                       ++ + ++ +aV+++h+H DH+  +++l  +  +   ++ ++ +++          +l           +        
  gi|336254927|ref|YP_004598034.1|  38 PVGD-ADPEAVVVSHGHLDHVGSIPSLLSGDSRP-SIHWTPPTYDltmvlardtlKL-----------Hggtydcpf 101
                                       3444.5889********************54432.3444444444334333333322...........222223333 PP

                                       ......TTEEEEEE-.TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HH..H CS
                     Lactamase_B_2  83 ......pavnvheld.wgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipee..i 150
                                               ++v e +   e+fe++  g eit++ a h  g          + +++++g+ r++y+gD  +  ++   
  gi|336254927|ref|YP_004598034.1| 102 teaelaRVTQVSETHgYREPFEVA--GYEITFFDAGHVPGS---------AHVLVDDGDTRLLYTGDFHTEGQRllS 167
                                       333344333333333699999*99..899********9999.........999***************966655333 PP

                                       HHHHCT.-SEEEEE-S-SSTTHHH CS
                     Lactamase_B_2 151 gerlgg.adllllditayeddemi 173
                                       g+  ++ ad+++ + t+ +  ++ 
  gi|336254927|ref|YP_004598034.1| 168 GTTARPdADVVITESTYADTTRPP 191
                                       455555699999999988877655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.25
                                       TEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HH CS
                     Lactamase_B_2 102 gleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipee 149
                                       g  +t +pa  ++++    n+  + G+ +eg+  r +  +++++i+++
  gi|336254927|ref|YP_004598034.1| 302 GPAMTYVPAVRSHPT----NKIAMTGYQVEGTPGRELLETGSAEIDGR 345
                                       335889999999999....88899999999666666666666666654 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 !   17.6   0.0   6.8e-07     0.002      36     175 ..      44     171 ..      19     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.8e-07
                     Lactamase_B_6  36 vdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslldlyaskgllgpedseeleledideafdk 112
                                        +++++sh  l+h+G+ + l+        ++  +  t p++ L +v+  d+ + +g   ++d+  ++  + +++ + 
  gi|336254927|ref|YP_004598034.1|  44 PEAVVVSHGHLDHVGSIPSLLS-----GDSRPSIHWTPPTYDLTMVLARDTLKLHGG--TYDC-PFTEAELARVTQV 112
                                       5799***********9888875.....46899******************9886644..4554.5778899999999 PP

                     Lactamase_B_6 113 iktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYavdwnhakeshLngaal 175
                                        +t  Y  ++e+     g  it + aGh++G +   + ++  +++Y  d++ +  ++L+g++ 
  gi|336254927|ref|YP_004598034.1| 113 SETHGYREPFEVA----GYEITFFDAGHVPGSAHVLVDDGDTRLLYTGDFHTEGQRLLSGTTA 171
                                       99999****9887....578999***********************************99865 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 ?   12.6   0.0   3.1e-05     0.093      17     134 ..      21     180 ..      12     183 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.1e-05
                     Lactamase_B_3  17 arilvDPfkanlgyeppa......eeaDlvlisqaledHahletlkql............................. 58 
                                        ++l+D++    + ++p+       ++++v++s+++ dH     +++l                             
  gi|336254927|ref|YP_004598034.1|  21 ETLLLDYGM---DSGNPPsfpvgdADPEAVVVSHGHLDHVG--SIPSLlsgdsrpsihwtpptydltmvlardtlkl 92 
                                       567777774...333333455555999***********974..5666667788888888888755555553333333 PP

                     Lactamase_B_3  59 ...aenvkvleeges....levggleiravatsh.......davggser...........genngflleq.dgltiy 109
                                                          +e++ +++++v++ h                           ++++ +l + ++ +++
  gi|336254927|ref|YP_004598034.1|  93 hggT----------YdcpfTEAELARVTQVSETHgyrepfeV------AgyeitffdaghVPGSAHVLVDdGDTRLL 153
                                       3330..........1333333333344444444433333220......02222333333355666655553799999 PP

                     Lactamase_B_3 110 hlGhlahelsseel..kelgrvDvvlt 134
                                       + G+ ++e +       +  ++Dvv+t
  gi|336254927|ref|YP_004598034.1| 154 YTGDFHTEGQRLLSgtTARPDADVVIT 180
                                       999999875554442244445677775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.50u 0.20s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3288.19
//
Query:       gi|336254928|ref|YP_004598035.1|  [L=140]
Description: hypothetical protein Halxa_3545 [Halopiger xanaduensis SH-6]
Scores for 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  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 1186.64
//
Query:       gi|336254929|ref|YP_004598036.1|  [L=148]
Description: hypothetical protein Halxa_3546 [Halopiger xanaduensis SH-6]
Scores for 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  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1222.84
//
Query:       gi|336254930|ref|YP_004598037.1|  [L=377]
Description: Sarcosine oxidase [Halopiger xanaduensis SH-6]
Scores for 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-43  148.9   2.4      3e-43  148.8   2.4    1.0  1  DAO            FAD dependent oxidoreductase
    0.00025   20.5   0.0    0.00038   19.9   0.0    1.2  1  Amino_oxidase  Flavin containing amine oxidoreductase
     0.0039   15.9   0.2      0.014   14.1   0.0    1.8  2  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
       0.05   12.8   0.0       0.81    8.9   0.0    2.5  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
       0.18   11.0   0.3       0.45    9.7   0.3    1.6  2  FAD_binding_3  FAD binding domain
       0.19   10.9   0.0       0.37   10.0   0.0    1.4  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
       0.21   11.6   0.1       0.21   11.6   0.1    3.0  3  NAD_binding_9  FAD-NAD(P)-binding
        1.4    9.2   5.1        1.3    9.3   0.6    2.6  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.8   2.4   1.3e-46     3e-43       1     352 []       6     359 ..       6     359 .. 0.83

  Alignments for each domain:
  == domain 1  score: 148.8 bits;  conditional E-value: 1.3e-46
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags.gaSgrnsgllhsglrylpeaselarlslealeelreleee 74 
                                       d ++ G G +G++t  +La+rg  V+ le+ d +   g+S + ++ ++ + ++ p   + ++l+++a e++++le++
  gi|336254930|ref|YP_004598037.1|   6 DAIVLGVGGTGSATVAHLAERGvdVLGLERYDVPRGyGSSRGIARSFRLADAEEP---ASVPLVRRAEELWADLEAD 79 
                                       789****************************888855888888888888665333...678**************** PP

                                       HSSTTSEEEEEEEEEES.SHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT..STTTSEEEEETTEEEEEHHHH CS
                               DAO  75 lgididyrrtGllslaa.deeelealdkllallleagldaelldaeevrelepa..lpgllgalfypdtgqvdpakl 148
                                       ++ ++ yr tG++  +  d    + +d  +++ +e++l++e l+++ + e++pa  lp+   a++ pd+g + p++ 
  gi|336254930|ref|YP_004598037.1|  80 HDRQLLYR-TGSIDAGPpD---DPLVDGAARAFEEHDLEYERLSSAALSERYPAyqLPDDYEAIYQPDGGYLVPEEC 152
                                       *9999998.******8532...4555555555578*****9999999******9886677889************** PP

                                       HHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HHHTTCTTTSEEEEEEEE CS
                               DAO 149 taalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.llgllkeldlpispvrgq 223
                                       + a  ++a ++G++i+ +++v++ +  ++++++v  +t+  +  +ad +V++aGaw+  ++   ++l   ++p r  
  gi|336254930|ref|YP_004598037.1| 153 LVAHVNRAHQAGATIRARERVVDWRPLEDGGVRV--ETDrDT-YEADRLVVTAGAWTArFV---EPLADVLVPEREV 223
                                       ***********************96644455777..555343.35699*********9777...6664456****** PP

                                       EEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTS..EEEEEESSE......EETTCSSTSCSHHHHHHHHHHH CS
                               DAO 224 vlvlkplseklvspaailpvpetdddgrgvyvtprkdg..rvlvGgtad......eesgdddpevdeedidelleal 292
                                         +++p + ++ +p   +pv     +++ +y +p   g  ++ vG  ++      +++++++ e++++d + l++ +
  gi|336254930|ref|YP_004598037.1| 224 LARFQPEEPAHFEP-DRFPVWSLQVPEGRFYGFPVH-GvpGFTVGRYHHhreeavDPDAFER-EPTQADERLLRDFA 297
                                       ****9987776666.677776688888888999962.4224999998889876555555666.888888888***** PP

                                       HHHSGGG.CGEEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 293 rklfPql.gdvlrkwaGlrp.lpdglpligetpgvkglylatGhsghGltlapatGkllael 352
                                       +++fP++ g+  r  ++l + +pd+ ++++ +p ++ +++ +G+sghG+t+ap++G++la+l
  gi|336254930|ref|YP_004598037.1| 298 ERYFPAVaGPTMRLETCLFAnTPDERFVLDTHPDHPQVVVGAGFSGHGFTFAPVVGEILADL 359
                                       ******64778899999999559********99***************************97 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.7e-07   0.00038     156     276 ..      72     215 ..      53     234 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.7e-07
                                       HHHHHHHHHHHHHHHHHHHCHTSTT..TTCBHHHHTCCCCHHHHHTSCCCEE...................TTHTHH CS
                     Amino_oxidase 156 vwdrliepelfaklefasglfagdp..selsaklalpllwelegfggslllp...................rgGlsq 211
                                       +w  l  ++ ++ l   + + ag p  ++    +  +++ +le ++ s   +                   +gG+  
  gi|336254930|ref|YP_004598037.1|  72 LWADLEADHDRQLLYRTGSIDAGPPddPLVDGAARAFEEHDLEYERLSSAALserypayqlpddyeaiyqpDGGYLV 148
                                       55555555555555555555555554322222222333333333333333335666666666666666776778777 PP

                                       HHHHHHH.....TTTTEEEETSEEEEEEEE.ETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEESCCSH CS
                     Amino_oxidase 212 lpealae.....elrgldirlntrVkeikr.egdgvtvtledgevveaDaVvvTvplgvlkailfsPplpd 276
                                       + e l +     ++ g +ir ++rV + +  e++gv+v++ d +++eaD+ vvT+  ++++   f+ pl d
  gi|336254930|ref|YP_004598037.1| 149 PEECLVAhvnraHQAGATIRARERVVDWRPlEDGGVRVET-DRDTYEADRLVVTAGAWTAR---FVEPLAD 215
                                       77777777776889999999999999888899999***96.9999***************9...7777744 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.27     6e+02       2      30 ..       6      34 ..       5      38 .. 0.88
   2 !   14.1   0.0   6.2e-06     0.014     114     164 ..     155     204 ..     149     207 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.27
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE- CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllle 30
                                      d iv+G G  G  + +++a+rg +Vl le
  gi|336254930|ref|YP_004598037.1|  6 DAIVLGVGGTGSATVAHLAERGVDVLGLE 34
                                      89*********999999999999998776 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.2e-06
                                       HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       a ++++++ag ++r +++v +++  edg +rv+t +++++ead+lv++ G 
  gi|336254930|ref|YP_004598037.1| 155 AHVNRAHQAGATIRARERVVDWRPLEDGGVRVET-DRDTYEADRLVVTAGA 204
                                       5678999***************************.9************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 ?    8.9   0.0   0.00036      0.81       2     114 ..       6     209 ..       5     222 .. 0.71
   2 ?    0.4   0.0      0.14   3.1e+02     146     155 ..     335     344 ..     308     360 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00036
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias................. 57 
                                       d +v+G G  G a+  +la+ g++v+ +e     +g+   +g+  s  l+ ++e+a++ +                 
  gi|336254930|ref|YP_004598037.1|   6 DAIVLGVGGTGSATVAHLAERGVDVLGLErydvPRGYGSSRGIARSFRLADAEEPASVPLvrraeelwadleadhdr 82 
                                       56777777777777777777777777776666666666666666666666666666655577777777777777777 PP

                                       ........................................................................HHHHC CS
                                       ........................................................................xxxxx RF
                       Pyr_redox_2  58 ........................................................................evvkk 62 
                                                                                                                +v++
  gi|336254930|ref|YP_004598037.1|  83 qllyrtgsidagppddplvdgaarafeehdleyerlssaalserypayqlpddyeaiyqpdggylvpeeclvAHVNR 159
                                       77777777777777777777777777777788888888888888888888888888888888888888888866666 PP

                                       HHHH.CCCCHCCTCEEEEESC.EEEEETEEECTCEEEEEESEEEE---EEE-BC CS
                                       xxxx.xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  63 lnqg.ielllgeevvkidpgk.kkvklekkkegdeekiaydklvlAtGssprdl 114
                                         q   + +++e vv+  p + + v +e+++     ++++d+lv+  G+++ ++
  gi|336254930|ref|YP_004598037.1| 160 AHQAgATIRARERVVDWRPLEdGGVRVETDR----DTYEADRLVVTAGAWTARF 209
                                       6555477777766888886554777775444....4899999999999988876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.14
                                       EEES-SHHHH CS
                                       xxxxxxxxxx RF
                       Pyr_redox_2 146 vvvGgGyiGv 155
                                       vvvG+G+ G 
  gi|336254930|ref|YP_004598037.1| 335 VVVGAGFSGH 344
                                       5666666554 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3    0.0002      0.45       2      42 ..       5      45 ..       4      55 .. 0.85
   2 ?   -2.6   0.0       1.1   2.6e+03     173     204 ..     183     216 ..     180     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0002
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS- CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpra 42
                                      +d ++ G G +G  +   L+e+Gv+v+ +e+++    ++ +
  gi|336254930|ref|YP_004598037.1|  5 YDAIVLGVGGTGSATVAHLAERGVDVLGLERYDVPRGYGSS 45
                                      68899**************************9877666544 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                                       TGGEEEEEEEEEEEEEEEEEEC-SCCCTTC..CE CS
                     FAD_binding_3 173 giefegeetvyeagvldvlfdadlsdivep..lv 204
                                       g+++e+ +++yea+ l v++ a+++++vep   v
  gi|336254930|ref|YP_004598037.1| 183 GVRVETDRDTYEADRLVVTAGAWTARFVEPlaDV 216
                                       6777788888888888888888888888875433 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 ?   10.0   0.0   0.00016      0.37      96     135 ..     165     205 ..     151     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00016
                       Pyr_redox_3  96 lpiklfeeVesvkk.edegfevetsketyeAkkviiAtGef 135
                                         i++ e+V +  + ed+g +vet+++tyeA+++++ +G +
  gi|336254930|ref|YP_004598037.1| 165 ATIRARERVVDWRPlEDGGVRVETDRDTYEADRLVVTAGAW 205
                                       5688888998888878999*******************986 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 ?   -0.3   0.3      0.41   9.2e+02       2      19 ..       9      26 ..       7      43 .. 0.85
   2 ?   11.6   0.1   9.3e-05      0.21     107     154 ..     156     203 ..     146     204 .. 0.81
   3 ?   -0.0   0.4      0.34   7.6e+02       1      11 [.     335     345 ..     335     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.41
                     NAD_binding_9  2 ivGaGprGlavlerLlar 19
                                      + G G +G a++++L++r
  gi|336254930|ref|YP_004598037.1|  9 VLGVGGTGSATVAHLAER 26
                                      56*************998 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 9.3e-05
                     NAD_binding_9 107 llarl.pegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                        ++r+ ++g t++  r++vvd ++ +dg   +++d ++++ad++v++ G
  gi|336254930|ref|YP_004598037.1| 156 HVNRAhQAGATIR-ARERVVDWRPLEDGGVRVETDRDTYEADRLVVTAG 203
                                       4555525555555.69************9999**************998 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.34
                     NAD_binding_9   1 aivGaGprGla 11 
                                       ++vGaG++G  
  gi|336254930|ref|YP_004598037.1| 335 VVVGAGFSGHG 345
                                       69******975 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 ?    9.3   0.6   0.00058       1.3       1      38 [.       9      46 ..       9      59 .. 0.88
   2 ?    1.2   0.4       0.2   4.4e+02       1       8 [.     336     343 ..     336     349 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00058
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                      ++G G +G+++ ++La++g+dvl le+ d + G  +s+
  gi|336254930|ref|YP_004598037.1|  9 VLGVGGTGSATVAHLAERGVDVLGLERYDVPRGYGSSR 46
                                      6788999********************99999988886 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.2
                                       EE--SHHH CS
                     NAD_binding_8   1 IvGaGlsG 8  
                                       +vGaG+sG
  gi|336254930|ref|YP_004598037.1| 336 VVGAGFSG 343
                                       8******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2886.96
//
Query:       gi|336254931|ref|YP_004598038.1|  [L=495]
Description: hypothetical protein Halxa_3548 [Halopiger xanaduensis SH-6]
Scores for 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-51  174.3   0.0    7.8e-51  172.6   0.0    1.8  2  DUF5305   Family of unknown function (DUF5305)


Domain annotation for each model (and alignments):
>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0     0.065   1.2e+03     115     135 ..      35      58 ..       8      75 .. 0.48
   2 !  172.6   0.0   4.3e-55   7.8e-51       1     219 []     154     369 ..     154     369 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.065
                           DUF5305 115 e...gilliilgllaliglvvlir 135
                                            ++l+++g++ +++l    +
  gi|336254931|ref|YP_004598038.1|  35 LfaeYGVLLLVGFVLVAALGGWLT 58 
                                       133345555555555555555544 PP

  == domain 2  score: 172.6 bits;  conditional E-value: 4.3e-55
                           DUF5305   1 Wekeeplasettqeveskeltisesvsinlseyndrieeieeelglsvgtseltvvlevnvegeidgesieesktsr 77 
                                       W+++e la ++++ v+++e ++ +++s+n+s++++ri+eie++lg+s+g++e+ ++++ ++eg++dge++++s+  r
  gi|336254931|ref|YP_004598038.1| 154 WSERERLAAASEDGVAPGE-SVAAPFSLNVSAIDARIAEIESDLGTSPGETEIALEVRREIEGTVDGEHRTASDRFR 229
                                       *******************.********************************************************* PP

                           DUF5305  78 lpiplteqtyeikkdetdeengeitetvtvkespslae..gilliilgllaliglvvlirriiftsskaekyelele 152
                                       +p+++++ ty+i++  t +e++e++etvtv  ++  ++  g++l++lgl+++i+++v+++r + ++++ae+++l+++
  gi|336254931|ref|YP_004598038.1| 230 IPVTHDGATYRIETADTYDEQYETYETVTVAGDDPDPPlaGLGLLALGLAGTIAAAVAAVR-VPEPTAAEREWLAYR 305
                                       ******************************9888877779*********************.*************** PP

                           DUF5305 153 kilkeYdewIvkgslppdlgdekvievdsledLvdvaielnepvlydeeedeegkFvvvddevvYvY 219
                                       +++ +++e+I+++ lp+++ + ++ +vd+l+dL ++ i+++ep+++d++++   ++vv +++vvYv+
  gi|336254931|ref|YP_004598038.1| 306 DDRAQFEEVIASIALPESELEGERASVDTLADLAEFGIDVDEPIVFDRRTG---RYVVRREGVVYVF 369
                                       ***************************************************...***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); 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:                         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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3749.93
//
Query:       gi|336254932|ref|YP_004598039.1|  [L=392]
Description: peptidase S26B, signal peptidase [Halopiger xanaduensis SH-6]
Scores for 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   30.4   0.0    7.3e-07   29.1   0.0    1.7  1  Peptidase_S24  Peptidase S24-like


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 !   29.1   0.0     4e-11   7.3e-07       2      59 ..      36      98 ..      35     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 4e-11
                                      XXSSTTCCTXXTTXEEEEECTS...---TTSEEEEEETTCE..-EEEEEEEEETTEEEEE.SS CS
                     Peptidase_S24  2 vpGdSMeptlldGdlilVdkfs...epkrGdivvfrlpgee..eayiKrviglpgdrvllasn 59
                                      v+ +SMept++ Gd  +  + +   ep+++d+vvf+ ++     ++ +r+++++++ + ++ +
  gi|336254932|ref|YP_004598039.1| 36 VETGSMEPTIETGDGFVAVPAAltgEPEPDDVVVFQAQELHggGLTTHRIVEETDRGYVTRGD 98
                                      899***********99999999999**********766666667************9997755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2946.87
//
Query:       gi|336254933|ref|YP_004598040.1|  [L=453]
Description: hypothetical protein Halxa_3550 [Halopiger xanaduensis SH-6]
Scores for 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  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3596.68
//
Query:       gi|336254934|ref|YP_004598041.1|  [L=133]
Description: hypothetical protein Halxa_3551 [Halopiger xanaduensis SH-6]
Scores for 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  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 987.89
//
Query:       gi|336254935|ref|YP_004598042.1|  [L=188]
Description: hypothetical protein Halxa_3552 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00016   21.9   1.5    0.00023   21.4   1.5    1.3  1  DUF1102   Protein of unknown function (DUF1102)
  ------ inclusion threshold ------
       0.07   12.8   1.7       0.41   10.4   0.0    2.2  2  Cupin_3   Protein of unknown function (DUF861)


Domain annotation for each model (and alignments):
>> DUF1102  Protein of unknown function (DUF1102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   1.5   2.5e-08   0.00023       4      87 ..      42     135 ..      39     184 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.5e-08
                           DUF1102   4 DdnelidLtpvqpYayi.dnGkLvidisennpnypgyGdGlspnseYvFdevfevsndlwenees...pivveikse 76 
                                       D    + L++ +  + +  nG+L i +  n     g G+G+  nseY Fd vfev n+  ++ +     +   ++ +
  gi|336254935|ref|YP_004598042.1|  42 DADAYLALESSSSHSEVdPNGRLKI-FDINGITNDGGGHGVGGNSEYHFDGVFEVTNQGTDTVHFyvgGLGTFVNGN 117
                                       66677899999999999779***98.66677778889********************98887775333223334444 PP

                           DUF1102  77 nssvklyage.......v 87 
                                       ++  ++y  e        
  gi|336254935|ref|YP_004598042.1| 118 DELANVYVYEdgardtpL 135
                                       444444444422444442 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 ?    1.4   0.4     0.029   2.6e+02      33      57 ..      90     114 ..      73     123 .. 0.80
   2 ?   10.4   0.0   4.5e-05      0.41      16      48 ..     139     172 ..     128     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.029
                                       ECEEEEEETTTEEEEEETTEEEEE- CS
                           Cupin_3  33 eGevkvtpeggetvelraGDlvvlp 57 
                                        G  +vt +g  tv++  G+l ++ 
  gi|336254935|ref|YP_004598042.1|  90 DGVFEVTNQGTDTVHFYVGGLGTFV 114
                                       7999999999999*99999987775 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 4.5e-05
                                       CEEEEECESSEEEE..EEEECEEEEEETTTEEEEE CS
                           Cupin_3  16 pGkfrltyeedEfc..yileGevkvtpeggetvel 48 
                                       +G ++ + +++E +  y+  G v+v+p+ g+t   
  gi|336254935|ref|YP_004598042.1| 139 AGALQIDSGTTESIgvYVETGDVDVEPD-GSTTNS 172
                                       7888999999998888***********5.555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1420.96
//
Query:       gi|336254936|ref|YP_004598043.1|  [L=146]
Description: hypothetical protein Halxa_3553 [Halopiger xanaduensis SH-6]
Scores for 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   13.4   2.6      0.052   13.4   0.3    1.9  2  DUF4906    Domain of unknown function (DUF4906)
      0.065   13.4   1.1       0.11   12.7   1.1    1.4  1  ASH        Abnormal spindle-like microcephaly-assoc'd, ASPM-S
       0.89    9.6   5.6       0.82    9.7   0.3    2.3  2  POC3_POC4  20S proteasome chaperone assembly proteins 3 and 4
        1.1    8.5   2.8        1.2    8.3   2.8    1.1  1  SLAIN      SLAIN motif-containing family
        7.2    7.0  14.4         18    5.7   5.5    3.7  4  Gp5_C      Gp5 C-terminal repeat (3 copies)


Domain annotation for each model (and alignments):
>> DUF4906  Domain of unknown function (DUF4906)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   1.5e-05     0.052     142     187 ..      17      63 ..       5      68 .. 0.84
   2 ?   -0.3   0.1      0.23   8.2e+02      51      74 ..      79     106 ..      63     122 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                           DUF4906 142 ageeknegtapekatyvqiegdirekaggstevvyriyLGe.nnvdd 187
                                       a   ++  ta +  +y+ i+gd ++++++s++   +i+LG+ +n +d
  gi|336254936|ref|YP_004598043.1|  17 ADRTVQVSTAGDADAYLGITGDGEYVTDDSSDSELTIDLGGpTNSND 63 
                                       44567778899999**************************9877665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.23
                           DUF4906  51 viva..gtttva..vpltRlvakvdfrv 74 
                                       v+++  gt +v+  ++ t +++ vdf+ 
  gi|336254936|ref|YP_004598043.1|  79 VTITnqGTENVTvsINETDVQSAVDFEL 106
                                       3333334443331144455555555554 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.1   3.1e-05      0.11      24      73 ..      74     123 ..      67     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                                       EEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX.XXXXXXXXXXXXXX CS
                               ASH  24 saerlLtveNpseepaevkvskvpaaekgfsveete.levqpgesvtltvt 73 
                                         ++ +t++N + e+++v +  +   + ++  e ++  e++pg+svtl+vt
  gi|336254936|ref|YP_004598043.1|  74 EVSDVVTITNQGTENVTVSINETD-VQSAVDFELSHsDELEPGDSVTLDVT 123
                                       56889**********999999999.8888999988889************8 PP

>> POC3_POC4  20S proteasome chaperone assembly proteins 3 and 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00023      0.82      45      90 ..      16      59 ..      14      65 .. 0.84
   2 ?    2.2   0.7     0.045   1.6e+02      19      57 ..     100     139 ..      71     146 .] 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00023
                                      B--EEEEEEEE...EEEEEEEEESHHHHHHHH---EEEEEEES-TT CS
                         POC3_POC4 45 emdstyevsskglllinyvyaidleeesvsdklsdvevvvllgnss 90
                                      e+d t++v  +++ +++++ +i ++ e v+d++sd e +++lg   
  gi|336254936|ref|YP_004598043.1| 16 EADRTVQV--STAGDADAYLGITGDGEYVTDDSSDSELTIDLGGPT 59
                                      56777777..67778*******99******************9544 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.045
                                       --EEEEEEEE.CCESSSSCEEEEEECCB--EEEEEEEE.. CS
                         POC3_POC4  19 ssedvevaih.alhfsnkiplqiringemdstyevsskgl 57 
                                       s++d e++ +  l+  +++ l +++++ +d+  e  s++l
  gi|336254936|ref|YP_004598043.1| 100 SAVDFELSHSdELEPGDSVTLDVTVDDLNDDVDENASETL 139
                                       3444444444778888899999999999999888888877 PP

>> SLAIN  SLAIN motif-containing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.8   0.00035       1.2      70     136 ..      60     129 ..      44     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00035
                             SLAIN  70 assvssglnspsalkstn.kqlllkgssgylsrssalSpqsSvDSelstS.Ele.dDSismgYKLqDltD 136
                                       +s   +g+n++++++ ++  +   +g+++++ + +    qs vD els S Ele  DS+ ++   +Dl D
  gi|336254936|ref|YP_004598043.1|  60 NSNDGEGFNENAVTEVSDvVTITNQGTENVTVSINETDVQSAVDFELSHSdELEpGDSVTLDVTVDDLND 129
                                       566678888888776666345555667777777799999*********99678756******99999987 PP

>> Gp5_C  Gp5 C-terminal repeat (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0074        26       6      15 ..      14      23 ..      11      25 .. 0.86
   2 ?    5.7   5.5    0.0051        18       3      20 ..      79      96 ..      79      98 .. 0.92
   3 ?   -1.2   0.2      0.82     3e+03      10      17 ..     117     124 ..     115     132 .. 0.63
   4 ?   -1.3   0.0      0.86   3.1e+03       2      10 ..     136     144 ..     135     146 .] 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0074
                                      EESS-EEEEE CS
                             Gp5_C  6 tVkGNrTvtV 15
                                       V+++rTv+V
  gi|336254936|ref|YP_004598043.1| 14 SVEADRTVQV 23
                                      799******9 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0051
                                      EEEEESS-EEEEESS-EE CS
                             Gp5_C  3 etetVkGNrTvtVgGNqT 20
                                      +t+t +G+++vtV  N+T
  gi|336254936|ref|YP_004598043.1| 79 VTITNQGTENVTVSINET 96
                                      599**************9 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.82
                                       -EEEEESS CS
                             Gp5_C  10 NrTvtVgG 17 
                                       ++T++V  
  gi|336254936|ref|YP_004598043.1| 117 SVTLDVTV 124
                                       56777765 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.86
                                       -EEEEESS- CS
                             Gp5_C   2 netetVkGN 10 
                                       +et+++++N
  gi|336254936|ref|YP_004598043.1| 136 SETLVIEAN 144
                                       699999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1163.27
//
Query:       gi|336254937|ref|YP_004598044.1|  [L=237]
Description: hypothetical protein Halxa_3554 [Halopiger xanaduensis SH-6]
Scores for 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   0.2       0.42   10.7   0.2    2.0  1  HTH_20    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 ?   10.7   0.2   2.3e-05      0.42       1      24 [.      51      73 ..      51     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.3e-05
                                      HHHHHHHS-HHHHHHHHHHSTCTT CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraeg 24
                                      d+++e+L+++ Rr il +L  +eg
  gi|336254937|ref|YP_004598044.1| 51 DELFEILSNRRRRHILHEL-MREG 73
                                      689****************.3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.41u 0.19s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 2083.93
//
Query:       gi|336254938|ref|YP_004598045.1|  [L=350]
Description: hypothetical protein Halxa_3555 [Halopiger xanaduensis SH-6]
Scores for 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  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 2936.89
//
Query:       gi|336254939|ref|YP_004598046.1|  [L=308]
Description: luciferase-type oxidoreductase [Halopiger xanaduensis SH-6]
Scores for complete 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   6.3    1.8e-43  149.2   6.3    1.1  1  Bac_luciferase  Luciferase-like monooxygenase
     0.0049   17.3   0.1        4.2    7.7   0.0    2.3  2  Radical_SAM     Radical SAM superfamily
  ------ inclusion threshold ------
      0.096   12.9   0.1       0.28   11.4   0.0    1.8  2  TetR_C_16       Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2   6.3     3e-47   1.8e-43      16     256 ..      32     283 ..      20     305 .. 0.82

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 3e-47
                    Bac_luciferase  16 gaasaslrylvelaraaEelGfdavwvaehhggpgga......ldaftllaalaaaTerirlgtavtplytrhPavl 86 
                                       ++++++++  v+la++aEelGf ++w+ +  + + +       +d++ +l+++aa+T+ + lgt+ ++l++rhP+++
  gi|336254939|ref|YP_004598046.1|  32 NRSTPDVNGEVHLAKRAEELGFAGLWARDVPTYWPQFgdagqtFDTWPWLSHVAAHTDEVALGTSSVVLTLRHPIHV 108
                                       2333689999*******************9999888788************************************** PP

                    Bac_luciferase  87 AqqaatLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsv.kgalllprp 162
                                       A++aat+d+ls+GR++lg+ +g + +e+ +f vd+++r + +rE  e++r lwr+e +d eGe+ s+  ++ ++p+p
  gi|336254939|ref|YP_004598046.1| 109 AKSAATVDRLSDGRLVLGVASGDRDPEYPAFDVDREARGEVFRERFEAVRTLWREEFPDLEGEWGSLdGQLEVVPKP 185
                                       *****************************************************77777******99989999***** PP

                    Bac_luciferase 163 gqgpiPvyvaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAra 239
                                         + iP++  +   +++e+ a+h+dg+l+   p+  ++ ++e++ra    ag        ++++   +ad++++  +
  gi|336254939|ref|YP_004598046.1| 186 TTETIPMLPTGNARQTREWIAEHGDGWLFYHLPERTLEGYLEDWRA---DAGD----KPYAMAVRAELADDPAAQPE 255
                                       9999*****************************************8...6666....33455555555555555555 PP

                    Bac_luciferase 240 ea....raliagld.......fyaldse 256
                                       ++    ra ++++         y  d++
  gi|336254939|ref|YP_004598046.1| 256 QLhlgyRAGVEWFRdyfrrleEYGVDHV 283
                                       5545554444444444333334444444 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0007       4.2      78     143 ..      89     166 ..      12     207 .. 0.78
   2 !    7.5   0.0   0.00082       4.9      76     120 ..     255     298 ..     232     305 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0007
                                       EEEEEEECSSCHG.......HHHHHHHHHTT-SEEEEEEBSSSHH......HHHHHHTCTSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpd.......eeklerllelgvdrvslgleaadde......kvlklmnrghtfeevlealeklreag 141
                                        ++++ t+ ++++        + +++ ++l   r+ lg+ ++d +      +v +   rg+ f e+ ea+++l +  
  gi|336254939|ref|YP_004598046.1|  89 DEVALGTSSVVLTlrhpihvAKSAATVDRLSDGRLVLGVASGDRDpeypafDVDREA-RGEVFRERFEAVRTLWREE 164
                                       566666666666677766677777788888889************************.999**9999****997766 PP

                                       SE CS
                                       xx RF
                       Radical_SAM 142 ik 143
                                       ++
  gi|336254939|ref|YP_004598046.1| 165 FP 166
                                       66 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00082
                                       CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlkl 120
                                       + +++ + +   +  +++ +rl e+gvd+v +gle  d+e+ l++
  gi|336254939|ref|YP_004598046.1| 255 EQLHLGYRAGVEWF-RDYFRRLEEYGVDHVIVGLENEDSERALER 298
                                       45555555555556.8999***************99888865555 PP

>> TetR_C_16  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.7e-05      0.28       3      38 ..     217     253 ..     216     259 .. 0.93
   2 ?   -3.2   0.0       1.7   9.9e+03      33      50 ..     289     305 ..     283     307 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.7e-05
                                       HHHHHHHHHHHHHH.HHT-HHHHHHHHH--------H CS
                         TetR_C_16   3 lGerlvravlevwe.pearepllallrsalsseeaae 38 
                                       l+er ++ +le+w+ +++++p+++++r+ l+++ aa+
  gi|336254939|ref|YP_004598046.1| 217 LPERTLEGYLEDWRaDAGDKPYAMAVRAELADDPAAQ 253
                                       799**************************99999886 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.7
                                       -----HHHHHHHHHHHHH CS
                         TetR_C_16  33 seeaaellrefleeqvla 50 
                                       +e+++++l++f   +v++
  gi|336254939|ref|YP_004598046.1| 289 NEDSERALERFAD-EVVE 305
                                       4444445544444.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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 0.20s 00:00:00.61 Elapsed: 00:00:00.33
# Mc/sec: 2756.13
//
Query:       gi|336254940|ref|YP_004598047.1|  [L=352]
Description: cellulase [Halopiger xanaduensis SH-6]
Scores for 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-80  268.8   0.1    5.1e-80  268.6   0.1    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
  ------ inclusion threshold ------
       0.12   11.1   0.0        4.6    5.9   0.0    2.1  2  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.6   0.1   5.7e-84   5.1e-80       1     291 [.      46     333 ..      46     334 .. 0.97

  Alignments for each domain:
  == domain 1  score: 268.6 bits;  conditional E-value: 5.7e-84
                                       S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGC CS
                     Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHll 77 
                                       Gn ia+ +g++++p++++++H DeiGf+V++I+e+Gf+r  ++GG dp++  gq+v+i+  +g ++Gv+g++++Hl+
  gi|336254940|ref|YP_004598047.1|  46 GNAIAVHEGEADAPEIALTGHADEIGFIVRSIDENGFVRPGPIGGSDPSISRGQHVTIHAADGPVDGVVGQTAIHLR 122
                                       9**************************************************************************** PP

                                       HHHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS- CS
                     Peptidase_M42  78 keeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeeel 154
                                       +++   +++e+++l+iDiga+s+eea e   ++Gd+++f+++++ l++ +++++ +D+r+g ++++e +++  e   
  gi|336254940|ref|YP_004598047.1| 123 EDD---DEPEVSDLWIDIGAESEEEASER-LEIGDPITFSSTVSWLSETRLAARGIDNRVGTWAAAEGFRAAVEAGA 195
                                       964...456699****************9.*********************************************** PP

                                       SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS...TTS-CEEEEEETTCCSHHHHHHH CS
                     Peptidase_M42 155 eatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak...lgkGpvirvkDasgiyhpklrkk 228
                                       eatvy+v tvqEEvG++Ga+++ ++++pd+a++vDv++a d p++++ +++   lg+Gp++      +  hp l + 
  gi|336254940|ref|YP_004598047.1| 196 EATVYAVSTVQEEVGVKGAQMVGFDLQPDAAVVVDVGHAVDYPSAPSGKTSqmgLGEGPALGRG---SSNHPVLFDA 269
                                       ********************************************9998877889*******988...999******* PP

                                       HHHHHHHTT--EEEE.EESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHH CS
                     Peptidase_M42 229 llelAkknnipyqle.vlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvk 291
                                       l+ +A++ +i++q+e + +g+gtDA+ + ++ +g+p+ ++s+p ry+H+pve+++ ddle ++ 
  gi|336254940|ref|YP_004598047.1| 270 LRSVADDRGIDVQVEaLGRGTGTDADGFFTAAGGIPSQVVSVPNRYMHTPVELIDTDDLEGVAA 333
                                       ***************888999**************************************98776 PP

>> Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0   0.00051       4.6     221     278 ..     161     215 ..     136     221 .. 0.78
   2 ?    3.1   0.0    0.0036        32     358     431 ..     267     338 ..     226     339 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.00051
                                       EETTTT-EEEESSHHHHHHHHHHHHHHCCCCHT-TTTS-SEEEEEEESSCCGTS-STT CS
                     Peptidase_M18 221 ivGiekeflfaprlDnkvscfaaleallesaedsleeedkvrivalfDnEEvGStsaq 278
                                       +  + +  l+a ++Dn+v+++aa e++ ++ e     e  +  +++  +EEvG ++aq
  gi|336254940|ref|YP_004598047.1| 161 VSWLSETRLAARGIDNRVGTWAAAEGFRAAVEA--GAE-ATVYAVSTVQEEVGVKGAQ 215
                                       5556677799*****************999888..333.444555556899*998876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHHHC-EEEEEEE-TTS----HCHHHHHHHHT-EEEEEE-EEBSTTSSSEEEECCHHHHHHHHHHHC CS
                     Peptidase_M18 358 aallkevaqkanvklQelvvrndspcGstigpilaaktGirtiDlGaaqlsmHSireltgskdveeavklfkaF 431
                                       + +l++va   ++ +Q+  +     +G+     ++a  Gi    +  +   mH + el+++ d+e   +l+ +F
  gi|336254940|ref|YP_004598047.1| 267 FDALRSVADDRGIDVQVEALGR--GTGTDADGFFTAAGGIPSQVVSVPNRYMHTPVELIDTDDLEGVAALLGGF 338
                                       5678889999999999887764..5799999999******************************9999888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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: 0.44u 0.18s 00:00:00.62 Elapsed: 00:00:00.34
# Mc/sec: 3072.47
//
Query:       gi|336254941|ref|YP_004598048.1|  [L=658]
Description: aconitate hydratase [Halopiger xanaduensis SH-6]
Scores for complete 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-108  364.0   0.2   7.4e-107  358.2   0.2    2.2  1  Aconitase    Aconitase family (aconitate hydratase)
      4e-20   72.5   0.0      8e-20   71.5   0.0    1.5  1  Aconitase_C  Aconitase C-terminal domain
     0.0023   16.7   0.0     0.0035   16.1   0.0    1.2  1  DUF521       Protein of unknown function (DUF521)


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 !  358.2   0.2  1.2e-110  7.4e-107       1     461 []       7     407 ..       7     407 .. 0.91

  Alignments for each domain:
  == domain 1  score: 358.2 bits;  conditional E-value: 1.2e-110
                         Aconitase   1 ekiwdahlvee.....egiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeeal 72 
                                       ek++d+hlv+      e+i    d+vl+qd+tg ++  +++a++ +          +++ + ++  +dh+      +
  gi|336254941|ref|YP_004598048.1|   7 EKVLDDHLVDGeletgEEIGIEIDQVLTQDTTGTMVWLQFEAMGLDE---------VQTEIAAQ-YCDHQT-----Y 68 
                                       79999999944344333354448*********************999.........67777777.788888.....4 PP

                         Aconitase  73 eknledefernkeryefLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgie 149
                                       + +++     n+   +fL+saa ++g  +  pg+GI+H v  E+ +a pgkt++g+DSHT++ gglG laiG Ggi+
  gi|336254941|ref|YP_004598048.1|  69 QFDFK-----NTDDHRFLRSAAGKYGAYFSRPGNGICHNVHREN-FAAPGKTLLGSDSHTPTPGGLGQLAIGAGGID 139
                                       44454.....355679****************************.******************************** PP

                         Aconitase 150 aeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaE 226
                                       +  ++ g p+++++p++v+v+l+G+l+e++takD++l++ ++l +kg+vgk++E++G+gvesL++ +r+Ti+NM++E
  gi|336254941|ref|YP_004598048.1| 140 VTVAMGGAPYYIEMPEIVNVRLEGELPEWATAKDVILELLRRLSVKGGVGKILEYTGPGVESLTAPERMTITNMGTE 216
                                       ***************************************************************************** PP

                         Aconitase 227 vGAttglfpvdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavpl 303
                                       +GAt+++fp+de+t +YL+  +r   a   ++++      e++ dedaeyd+++ +dls+lep +a p  P+++vp+
  gi|336254941|ref|YP_004598048.1| 217 LGATSSIFPTDEQTKDYLERLDR---A---DDFE------EIQPDEDAEYDDEIVVDLSDLEPLIAQPSMPDNVVPV 281
                                       *******************4444...3...3333......36679******************************** PP

                         Aconitase 304 selvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsv 380
                                       se +                              +vd++++gSCTN+ +ed+   a++l+     g++v ++ +++v
  gi|336254941|ref|YP_004598048.1| 282 SEVA----------------------------GQDVDQVIVGSCTNGGYEDILPGAKMLE-----GREVDKKTDMIV 325
                                       4443............................23599***********************.....************ PP

                         Aconitase 381 aPGSevvkayleaeGlleiLekaGfevvgagCstCignsdrleegeaivsssNRNFegRqgpntra.yLaSPelvva 456
                                       aPGS++ ++ l ++G    +++aG+++ +a C+ Cig     +++++++ ++NRNFegR g +  + yL+SPe+++a
  gi|336254941|ref|YP_004598048.1| 326 APGSKQASEMLARQGWVAEMMAAGVNFSEATCGACIGIGHVPASDSVSLRTFNRNFEGRSGIEDDNvYLCSPEVATA 402
                                       *************************************888878999***************555555********** PP

                         Aconitase 457 aAlaG 461
                                       aA++G
  gi|336254941|ref|YP_004598048.1| 403 AAIKG 407
                                       ***98 PP

>> Aconitase_C  Aconitase C-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     8e-20      66     130 ..     517     580 ..     477     581 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1.3e-23
                                       HHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEEST CS
                       Aconitase_C  66 aerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefke 130
                                       aer k+++  ++v++ +n+G+GSSRehAA+ +  lGi+ v+a+SF+rI++ nl++ g++pl+++e
  gi|336254941|ref|YP_004598048.1| 517 AERAKNADGGFLVAG-ENYGQGSSREHAAMCPMYLGIEGVLAQSFARIHRANLFNFGIVPLTIDE 580
                                       456666677777777.*********************************************9976 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.9e-07    0.0035     206     358 ..     188     358 ..     183     373 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.9e-07
                            DUF521 206 vGkkvgeriPvlkglekpsedelKalgAalaasgavalfhiegvTPe.......aetleealg.ekek.aekititk 273
                                       vGk+++   P ++ l  p++ ++ ++g  l+a+++  +f  ++ T +       a+++ee +  e ++ +++i ++ 
  gi|336254941|ref|YP_004598048.1| 188 VGKILEYTGPGVESLTAPERMTITNMGTELGATSS--IFPTDEQTKDylerldrADDFEEIQPdEDAEyDDEIVVDL 262
                                       67777777777888888888888888888888776..5778888888888887777777776644455678999999 PP

                            DUF521 274 edleevleel.........skakeekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvtt.srevkeeaerl 339
                                       +dle ++++          s+   ++vd v++G c    +e++   a++l+g+++++k++++v   s++  e++ r 
  gi|336254941|ref|YP_004598048.1| 263 SDLEPLIAQPsmpdnvvpvSEVAGQDVDQVIVGsCTNGGYEDILPGAKMLEGREVDKKTDMIVAPgSKQASEMLARQ 339
                                       9999988876556666777778889999999986788899**********************99725669999**** PP

                            DUF521 340 glveklekaGvkvlsdtCm 358
                                       g+v+++ +aGv++ + tC 
  gi|336254941|ref|YP_004598048.1| 340 GWVAEMMAAGVNFSEATCG 358
                                       ******************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (658 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 4807.89
//
Query:       gi|336254942|ref|YP_004598049.1|  [L=160]
Description: dUTP diphosphatase [Halopiger xanaduensis SH-6]
Scores for complete 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   44.6   0.0    1.6e-11   44.0   0.0    1.3  1  dUTPase   dUTPase
     0.0069   15.2   0.0     0.0086   14.9   0.0    1.3  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


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 !   44.0   0.0   1.7e-15   1.6e-11      26     106 ..      68     146 ..      58     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.7e-15
                                       EETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEEEEE CS
                           dUTPase  26 vkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiAqLifa 102
                                         p++ ++   +  i++p+g+ +++ pRS+l ++  +  + v+d+ y+G  +  l ++ +  v+i +g+RiAqL++a
  gi|336254942|ref|YP_004598049.1|  68 YLPKGAYVARYGERIEIPEGHIGFVYPRSSLMRNSCMLNTAVWDAGYEGRGEGLLQVHHD--VEIARGARIAQLVLA 142
                                       4457888899999************************************88888888876..*************** PP

                                       EBEC CS
                           dUTPase 103 rilt 106
                                       ++++
  gi|336254942|ref|YP_004598049.1| 143 EADH 146
                                       9999 PP

>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   9.5e-07    0.0086      22     112 ..      12     102 ..       1     150 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.5e-07
                               DCD  22 eepleeeqiqPaslDLrLgkkayrvrasFlpgkgekvaeklee.lklheldLtegavlekgcvYivplleslaLpad 97 
                                        +p+++eq+qP+ +DL L  +  ++    +  +g+++ +++++ l+  e +  +  +l kg+ Y++   e++++p+ 
  gi|336254942|ref|YP_004598049.1|  12 VSPTTDEQVQPNGVDLTLDIVFEQLEPGRIGRDGKQIGDRVARpLEELEQKDPDTYYLPKGA-YVARYGERIEIPEG 87 
                                       468899**********************************9875666666667899999996.************** PP

                               DCD  98 lsaaanpksstGRlD 112
                                         + + p+ss  R  
  gi|336254942|ref|YP_004598049.1|  88 HIGFVYPRSSLMRNS 102
                                       **********88855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1194.80
//
Query:       gi|336254943|ref|YP_004598050.1|  [L=186]
Description: hypothetical protein Halxa_3560 [Halopiger xanaduensis SH-6]
Scores for 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   10.6  21.1        9.6    5.5  20.9    2.6  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  20.9   0.00054       9.6       1     114 [.       1      95 [.       1     175 [. 0.67

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.00054
                              YdjM   1 MdgltHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllf.. 75 
                                       M+  tH+  ++al + +a   +    + l a+avlg+l+PD+D         l+l         +HR  +H  l   
  gi|336254943|ref|YP_004598050.1|   1 MMATTHVFAALALLAPVAYAVPGF-ATPLAAGAVLGGLAPDFD---------LPL---------EHRRTFHFPLLgl 58 
                                       99*****************99875.57****************.........333.........3677777655523 PP

                              YdjM  76 lallalvlllllrlfgrsalrlgll.lllgvlsHlllDll 114
                                       ++++++++l++++   ++   ++l+ +++++++H + D++
  gi|336254943|ref|YP_004598050.1|  59 AVAVPTAALAIVAPSTTI---VALAaFAVAAWLHAASDAI 95 
                                       444455555555555544...4454499999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 1520.85
//
Query:       gi|336254944|ref|YP_004598051.1|  [L=154]
Description: hypothetical protein Halxa_3561 [Halopiger xanaduensis SH-6]
Scores for 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-05   24.0   8.5      4e-05   24.0   8.5    1.9  2  CopD      Copper resistance protein D
  ------ inclusion threshold ------
       0.66    9.8   7.5       0.13   12.1   2.9    2.1  3  IncD      Inclusion membrane protein D


Domain annotation for each model (and alignments):
>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3      0.37   3.3e+03      85      98 ..      16      29 ..       5      35 .. 0.54
   2 !   24.0   8.5   4.4e-09     4e-05       9     104 ..      53     145 ..      45     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.37
                              CopD 85 rrsaalelvlalvv 98
                                      + +a+ ++ +a+vv
  gi|336254944|ref|YP_004598051.1| 16 ALWAGSVFYVAFVV 29
                                      33444445555554 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 4.4e-09
                              CopD   9 rlalaavavvlvtGvvnallrvglagllttayGrlllaKlalllvllalaalnrfrlvprleaatgaggqalrhrlr 85 
                                       ++  ++  ++l++G  +a + +++++l++t+ Grl+l++++l+lvl++l  +   rl   l   +g++ ++++  + 
  gi|336254944|ref|YP_004598051.1|  53 TISRVSSLALLLSGGHLAGRGYTFESLVGTTNGRLVLVMVGLWLVLTGLVEVGSKRLESGL---NGKKLREPAANVL 126
                                       667788899*********99999**************************************...5666667777788 PP

                              CopD  86 rsaalelvlalvvlllaaa 104
                                        + ++ +v++++ l++a++
  gi|336254944|ref|YP_004598051.1| 127 GLYRVAAVVGIALLVVAGV 145
                                       8888888888888887765 PP

>> IncD  Inclusion membrane protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.13   1.2e+03      96      96 ..      79      79 ..      46     107 .. 0.55
   2 ?   -1.5   0.1      0.23     2e+03      33      54 ..      83     104 ..      70     118 .. 0.71
   3 ?   12.1   2.9   1.4e-05      0.13      32      64 ..     121     153 ..     107     154 .] 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.13
                              IncD 96 v 96
                                      +
  gi|336254944|ref|YP_004598051.1| 79 L 79
                                      2 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.23
                              IncD  33 takrlvavavatilavallvva 54 
                                       t  rlv v v   l ++ lv  
  gi|336254944|ref|YP_004598051.1|  83 TNGRLVLVMVGLWLVLTGLVEV 104
                                       5567777777766666655544 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 1.4e-05
                              IncD  32 ptakrlvavavatilavallvvagllfsgvlcs 64 
                                       p+a+ l    va+++ +allvvag++ sgv +s
  gi|336254944|ref|YP_004598051.1| 121 PAANVLGLYRVAAVVGIALLVVAGVITSGVAAS 153
                                       7788888889*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 1325.15
//
Query:       gi|336254945|ref|YP_004598052.1|  [L=145]
Description: hypothetical protein Halxa_3562 [Halopiger xanaduensis SH-6]
Scores for 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:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1163.03
//
Query:       gi|336254946|ref|YP_004598053.1|  [L=299]
Description: 6-phosphogluconate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-38  132.0   0.0      3e-38  131.5   0.0    1.2  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    4.3e-24   85.4   0.0    6.4e-24   84.8   0.0    1.3  1  6PGD            6-phosphogluconate dehydrogenase, C-terminal 
      3e-06   27.7   0.0    4.6e-06   27.1   0.0    1.3  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    2.4e-05   24.5   0.1     0.0049   17.1   0.0    3.1  3  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut
    0.00028   20.8   0.1    0.00038   20.4   0.1    1.2  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    0.00037   20.7   0.2    0.00074   19.8   0.0    1.6  2  TrkA_N          TrkA-N domain
    0.00096   18.5   0.0     0.0013   18.1   0.0    1.2  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
      0.022   14.3   0.0      0.061   12.9   0.1    1.7  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.34   11.0   1.2       0.83    9.8   1.2    1.7  1  DapB_N          Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> 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 !  131.5   0.0   1.5e-41     3e-38       1     151 [.       2     151 ..       2     168 .. 0.96

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 1.5e-41
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHC...SEEEE-SSSHHHHHHHHH CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasl...dvvitmvkagkavdevie 74 
                                       ++g+iGlG MG+  + + l+ag++v+++++++e+v +++++ga++aes+e+lv++l   + +++mv+ag+avd+++e
  gi|336254946|ref|YP_004598053.1|   2 QLGVIGLGRMGQIVVDRTLEAGHDVVAFDLDAEAVATAADAGADPAESMEDLVDRLgdgKRIWLMVPAGEAVDATLE 78 
                                       58*************************************************************************** PP

                                       SHCCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEE CS
                     NAD_binding_2  75 gllealkkgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaiga 151
                                       +l ++l+++d+++dg++s +ed+ ++a+ +    + +ld++ SGG +gAe G  s+mvGG+e a+e+++pv++a+++
  gi|336254946|ref|YP_004598053.1|  79 ELEPHLDADDVVVDGGNSYFEDSVRRAESCP---AAYLDCGTSGGPAGAELGF-SLMVGGPEWAYEELAPVFDAVAT 151
                                       *************************998865...679****************.********************997 PP

>> 6PGD  6-phosphogluconate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.8   0.0   3.2e-27   6.4e-24       1     120 [.     165     278 ..     165     291 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 3.2e-27
                              6PGD   1 GhyVKmvHNGieygdmqliaEaydllkkvlglsneeiaevFeeWnkgel.esyLieitakilrkkdeedgkplvdki 76 
                                       GhyVKm+HNG+ey+ mq+ +E ++ll+++      ++++v + Wn+g + +s+L+e +++ +r++ ++     +  +
  gi|336254946|ref|YP_004598053.1| 165 GHYVKMIHNGVEYALMQAYGEGFELLHEG--RYDLDLESVASVWNNGAViRSWLLELCEEAFREEGND-----LGTV 234
                                       9**************************96..566778888889****555*************99975.....6799 PP

                              6PGD  77 lDkagqkGTgkwtvqealelgvpvptiaeavfaRllSslkeerv 120
                                       +D+ +   Tg+wtvqeale +vp+p+i +a++ R+ S + + r 
  gi|336254946|ref|YP_004598053.1| 235 ADRVEGGSTGTWTVQEALEQEVPLPLIYTALAERFGSRADDGRF 278
                                       9999*********************************9998875 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 !   27.1   0.0   2.3e-09   4.6e-06       2      94 ..       3      93 ..       2      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.3e-09
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH...H-SEEEE-S-H.HHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae...eadvvvlavkp.edvee 76
                                      +g+iG G+mg+ ++ + l+ag   h++v a + + e ++ +a+++g++  + + e++++   + + + l v+  e+v++
  gi|336254946|ref|YP_004598053.1|  3 LGVIGLGRMGQIVVDRTLEAG---HDVV-AFDLDAEAVA-TAADAGADPAE-SMEDLVDrlgDGKRIWLMVPAgEAVDA 75
                                      89*******************...****.8788888665.55555777777.7888887777999******98467899 PP

                                      HHHHCGHHHHTTSEEEEE CS
                     F420_oxidored 77 vlselakdalkgklvisv 94
                                      +l+el ++++++ +v++ 
  gi|336254946|ref|YP_004598053.1| 76 TLEELEPHLDADDVVVDG 93
                                      9***************95 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.059   1.2e+02      22      41 ..      33      52 ..      19      73 .. 0.84
   2 !   17.1   0.0   2.5e-06    0.0049       1      52 [.     163     217 ..     163     227 .. 0.85
   3 ?    0.6   0.0      0.32   6.3e+02      32      59 ..     228     255 ..     219     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.059
                    NAD_binding_11 22 sEalvlaekaGldpekvlev 41
                                      +Ea+++a+ aG dp++ +e 
  gi|336254946|ref|YP_004598053.1| 33 AEAVATAADAGADPAESMED 52
                                      79***********9987765 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.5e-06
                    NAD_binding_11   1 GaGqavKlvnnlllainlaaasEalvlae..kaGldpekvlevinassg.rsnal 52 
                                       G+G+ vK+++n +  + + a +E++ l++  +++ld+e v  v n+++  rs+ l
  gi|336254946|ref|YP_004598053.1| 163 GSGHYVKMIHNGVEYALMQAYGEGFELLHegRYDLDLESVASVWNNGAViRSWLL 217
                                       9************************9997446***********999874255554 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.32
                    NAD_binding_11  32 Gldpekvlevinassgrsnalenklpqr 59 
                                       G d+ +v + ++++s + +++++ l+q 
  gi|336254946|ref|YP_004598053.1| 228 GNDLGTVADRVEGGSTGTWTVQEALEQE 255
                                       7789999999999999999988887775 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 !   20.4   0.1   1.9e-07   0.00038       2      44 ..       3      45 ..       2      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.9e-07
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44
                                      ++viG G mG+ +   +++ag++Vv +d ++ea+++a+++ ++
  gi|336254946|ref|YP_004598053.1|  3 LGVIGLGRMGQIVVDRTLEAGHDVVAFDLDAEAVATAADAGAD 45
                                      79*******************************9999887666 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.7e-07   0.00074       3      42 ..       5      44 ..       3      49 .. 0.90
   2 ?   -3.6   0.0       6.8   1.3e+04       7      18 ..     276     287 ..     276     289 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.7e-07
                                      EES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTS CS
                            TrkA_N  3 iiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreegl 42
                                      +iGlGr+G+ ++++  e g+ dvv+ d d e+v+++++ g+
  gi|336254946|ref|YP_004598053.1|  5 VIGLGRMGQIVVDRTLEaGH-DVVAFDLDAEAVATAADAGA 44
                                      9*************999555.8**************99885 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.8
                                       SHHHHHHHHHHH CS
                            TrkA_N   7 GrvGrslaeeLs 18 
                                       Gr+ r+la++L+
  gi|336254946|ref|YP_004598053.1| 276 GRFSRRLANRLR 287
                                       8999****9997 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 !   18.1   0.0   6.8e-07    0.0013      38      89 ..       2      54 ..       1      73 [. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.8e-07
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC.EECSHHHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv.elvsleell 89
                                      ++G+iGlGr+Gq v +r  + g +v+a+d   ++ +++++ g+   +s+e+l+
  gi|336254946|ref|YP_004598053.1|  2 QLGVIGLGRMGQIVVDRTLEAGHDVVAFDLDAEAVATAADAGAdPAESMEDLV 54
                                      79*****************************9988888888884444777776 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 ?   12.9   0.1   3.1e-05     0.061       1      39 [.       1      39 [.       1      55 [. 0.92
   2 ?   -2.1   0.0       1.2   2.5e+03      99     118 ..      72      91 ..      70      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdkl 39
                                      m++ viGlG +G +      e+gh+v+  D d+e+v++ 
  gi|336254946|ref|YP_004598053.1|  1 MQLGVIGLGRMGQIVVDRTLEAGHDVVAFDLDAEAVATA 39
                                      7889*******************************9875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHCEEEEE CS
                    UDPG_MGDP_dh_N  99 yvesaarsiaealkkgkvvv 118
                                       +v +++++++++l+ ++vvv
  gi|336254946|ref|YP_004598053.1|  72 AVDATLEELEPHLDADDVVV 91 
                                       57889999**********98 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.2   0.00042      0.83       1      45 [.       1      43 [.       1     102 [. 0.65

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00042
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHH CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdag 45
                                      ++++v+G  GrmG+ vv+   e +++ +va     e  + + dag
  gi|336254946|ref|YP_004598053.1|  1 MQLGVIGL-GRMGQIVVDRTLE-AGHDVVAFDLDAEAVATAADAG 43
                                      7899***9.*********9999.5666655443334455666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2379.58
//
Query:       gi|336254947|ref|YP_004598054.1|  [L=408]
Description: cell division control protein 6-like protein [Halopiger xanaduensis SH-6]
Scores for 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-21   75.0   0.6    1.3e-20   73.1   0.1    2.4  1  Cdc6_C         CDC6, C terminal winged helix domain
    1.2e-11   45.1   0.0    2.7e-11   43.9   0.0    1.6  1  AAA_22         AAA domain
      8e-10   39.4   0.0    2.7e-08   34.4   0.0    2.9  2  AAA_16         AAA ATPase domain
    1.1e-06   29.1   0.0      3e-06   27.7   0.0    1.8  1  AAA            ATPase family associated with various cellular
    0.00082   18.8   0.0     0.0014   18.1   0.0    1.3  1  TniB           Bacterial TniB protein
    0.00091   19.2   0.0     0.0018   18.3   0.0    1.5  1  ATPase_2       ATPase domain predominantly from Archaea
     0.0019   18.2   0.0     0.0036   17.2   0.0    1.5  1  NACHT          NACHT domain
     0.0059   16.6   0.0      0.041   13.9   0.0    2.2  2  AAA_5          AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.012   14.8   0.0       0.02   14.1   0.0    1.3  1  DUF815         Protein of unknown function (DUF815)
      0.015   14.5   0.0        0.1   11.8   0.0    2.2  3  NB-ARC         NB-ARC domain
      0.019   15.5   0.2       0.32   11.5   0.0    2.5  2  AAA_18         AAA domain
      0.044   13.4   0.1       0.47   10.0   0.0    2.4  2  AAA_25         AAA domain
      0.048   14.1   0.0      0.094   13.1   0.0    1.5  1  RNA_helicase   RNA helicase
      0.048   12.9   0.0        1.4    8.0   0.0    2.2  2  KAP_NTPase     KAP family P-loop domain
       0.05   12.5   0.0        0.2   10.5   0.0    1.8  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.071   12.6   0.0       0.13   11.8   0.0    1.3  1  AAA_7          P-loop containing dynein motor region
      0.094   12.8   0.0       0.24   11.5   0.0    1.7  1  AAA_2          AAA domain (Cdc48 subfamily)
      0.095   11.5   0.1          7    5.3   0.0    2.2  2  AAA_32         AAA domain
       0.14   12.1   0.0       0.35   10.9   0.0    1.5  1  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
       0.15   11.7   0.1       0.32   10.7   0.1    1.5  1  AAA_24         AAA domain
       0.16   11.9   0.0        0.7    9.8   0.0    2.0  2  RsgA_GTPase    RsgA GTPase


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 !   73.1   0.1   1.6e-23   1.3e-20       1      81 [.     303     381 ..     303     384 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 1.6e-23
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L+a+v+ +  +++++++t+e+y++Y+slCes g d l qr+v+++ls+L mlgil++++++ G+r g+++ ++L+v+
  gi|336254947|ref|YP_004598054.1| 303 LLAVVSKAA-KESTPCRTRELYQEYESLCESSGTDSLAQRSVHNHLSDLRMLGILSAKENRSGSR-GNYYSYELDVP 377
                                       899999999.******************************************************7.**********9 PP

                                       CHHH CS
                            Cdc6_C  78 pddv 81 
                                        +  
  gi|336254947|ref|YP_004598054.1| 378 FSSA 381
                                       8765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   3.2e-14   2.7e-11       7     126 ..      51     178 ..      48     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 3.2e-14
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdllrellralglelka...erlssee 77 
                                        ++++G +G+GKT + + ll+ l+e+   +e    + +v++v+++ ++ss +++ el++ l  ++ +    +  ++ 
  gi|336254947|ref|YP_004598054.1|  51 NIFLYGNTGVGKTAVTEYLLDVLQED--VTEyddVDLSVLSVNCKTLNSSYQVAIELVNTLRPDGAEistTGYPQQT 125
                                       689*******************9654..444568888999**********************99999*988888999 PP

                            AAA_22  78 llealeqalraravielliiDEaqhlr.seealeeL.rsllnl..srkgvqli 126
                                       ++++l+  l+a + ++++++DE++ +  ++e+l eL r ++n   ++++v li
  gi|336254947|ref|YP_004598054.1| 126 VFKKLYSELEALGGTVVIVLDEIDSIGdRDELLYELpRARSNGylESTKVGLI 178
                                       99************************767*******99999976655555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   3.2e-11   2.7e-08       5     164 ..      29     167 ..      27     175 .. 0.68
   2 ?   -0.3   0.2       1.5   1.2e+03     119     135 ..     251     268 ..     188     324 .. 0.53

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3.2e-11
                            AAA_16   5 ReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalare 79 
                                       R+ee+e+  +al+++ +g + ++++l+G+ GvGK+++ + ll+ l++d    +++  d     ++ +    ++l   
  gi|336254947|ref|YP_004598054.1|  29 RDEEIEAYMDALQPIIDGWEpNNIFLYGNTGVGKTAVTEYLLDVLQED----VTEYDDVD---LSVLSvNCKTL--- 95 
                                       9*****************888*********************999999....66666655...22211133333... PP

                            AAA_16  80 ellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslqlla 156
                                           q++ e+ ++++++ +e  ++ +                ++k+l + l+  + ++v+vlD+++ + +   +ll+
  gi|336254947|ref|YP_004598054.1|  96 NSSYQVAIELVNTLRPDGAEISTTGYP------------QQTVFKKLYSELEALGGTVVIVLDEIDSIGD-RDELLY 159
                                       333333333334444444444444444............4555556665555656669999999998888.445667 PP

                            AAA_16 157 aLlrlles 164
                                       +L r++++
  gi|336254947|ref|YP_004598054.1| 160 ELPRARSN 167
                                       77777665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                            AAA_16 119 llellkrll.allsrder 135
                                        +  l rl+ + ++++++
  gi|336254947|ref|YP_004598054.1| 251 QALDLLRLAgEVAENNDD 268
                                       222222222233333222 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 !   27.7   0.0   3.5e-09     3e-06       2     129 ..      53     204 ..      52     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.5e-09
                                       EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS................STTHHHHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavakel..........gvefleisgsellsk................yvgesekkirelfke 52 
                                        lyG+ G+GKT++ + +   l          + ++l++++++l s+                 ++ +    + +fk+
  gi|336254947|ref|YP_004598054.1|  53 FLYGNTGVGKTAVTEYLLDVLqedvteyddvDLSVLSVNCKTLNSSyqvaielvntlrpdgaEISTTGYPQQTVFKK 129
                                       79****************99844444433334779******999889*************99666666666666666 PP

                                       HHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS....SSTEEEEEEESS...GGGSTHH CS
                               AAA  53 akeka....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk....eskvivigatnr...pdkldpa 118
                                       + ++     +++++++DEid+++ ++             +Ll el + +++    + kv +ig++n+    ++ldp 
  gi|336254947|ref|YP_004598054.1| 130 LYSELealgGTVVIVLDEIDSIGDRD-------------ELLYELPRARSNgyleSTKVGLIGISNDfkfREQLDPR 193
                                       54444467677***********7666.............66666666666666668889999999997777788877 PP

                                       HHSTTSSEEEE CS
                               AAA 119 llrgRfdrkie 129
                                       +    ++r+++
  gi|336254947|ref|YP_004598054.1| 194 VQDTLCERELQ 204
                                       76555666555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.7e-06    0.0014      15     131 ..      29     151 ..      21     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-06
                              TniB  15 rakeilerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppe.kdedaekvpvlvvqappkpdekrlyaai 90 
                                       r +ei + +++L    +  +++n+ l+G++ +GKt++ e   +  +++ ++ d+  + vl v++ +  +  +   ++
  gi|336254947|ref|YP_004598054.1|  29 RDEEIEAYMDALQPIIDGWEPNNIFLYGNTGVGKTAVTEYLLDVLQEDvTEYDDVDLSVLSVNCKTLNSSYQVAIEL 105
                                       567788888888888889999******************99976665526788889********************* PP

                              TniB  91 Lealgaplkararvs....kleqqvlrllrelk.vrvLiiDEihnl 131
                                       +++l+ + ++  ++     +  ++ ++ l++l+ + v+++DEi+++
  gi|336254947|ref|YP_004598054.1| 106 VNTLRPDGAEISTTGypqqTVFKKLYSELEALGgTVVIVLDEIDSI 151
                                       ****977655554441001344455556677652667899**9986 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 !   18.3   0.0   2.1e-06    0.0018      10     147 ..      39     163 ..      28     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.1e-06
                          ATPase_2  10 eleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiav 86 
                                        l+ i++  + + +f+YG  g+GKta+   ++  l++   +v  y+++  + +s   ++    +++ +++  l +++
  gi|336254947|ref|YP_004598054.1|  39 ALQPIIDGWEPNNIFLYGNTGVGKTAVTEYLLDVLQE---DVTEYDDVDLSVLSVNCKT---LNSSYQVAIELVNTL 109
                                       56667777777889********************955...5666666665555544444...455555566666666 PP

                          ATPase_2  87 pkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLln 147
                                       + + + ei+ +   + +  +++l+ +++  g  ++i++De+  ++        +l++eL +
  gi|336254947|ref|YP_004598054.1| 110 RPDGA-EISTTGYPQ-QTVFKKLYSELEALGGTVVIVLDEIDSIG-----DRDELLYELPR 163
                                       66666.565544444.77788899999999999**********99.....35577777755 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.2e-06    0.0036       3      98 ..      52     156 ..      50     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.2e-06
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC.-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C....... CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqga.fklvFflslrelsrsgnarsladllfsqlpepaapvse....... 71 
                                       ++l G  G+GKT+  + l + ++e+  + +     v+ +++++l+ s ++   a  l+  l + +a++s+       
  gi|336254947|ref|YP_004598054.1|  52 IFLYGNTGVGKTAVTEYLLDVLQEDVTEYDDvDLSVLSVNCKTLNSSYQV---AIELVNTLRPDGAEISTtgypqqt 125
                                       789**********************9999885667999********9654...555555555555555555666888 PP

                                       ....CHHHHCCSCCCEEEEEE-STT-SS-TC CS
                             NACHT  72 ....vwavllelperlLlilDglDelvtdlg 98 
                                             ++l +l   ++++lD +D + + ++
  gi|336254947|ref|YP_004598054.1| 126 vfkkLYSELEALGGTVVIVLDEIDSIGDRDE 156
                                       88888889999999999*******9997554 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 !   13.9   0.0   4.8e-05     0.041       1      29 [.      51      79 ..      51      81 .. 0.88
   2 ?   -0.6   0.0       1.4   1.2e+03      67      78 ..     141     152 ..     122     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                                      EEEEE--SSSSHHHHHHHGGGGBS--EEE CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaalnrevey 29
                                      +++L G++G+gK+ ++e+l+ +l+  v++
  gi|336254947|ref|YP_004598054.1| 51 NIFLYGNTGVGKTAVTEYLLDVLQEDVTE 79
                                      689*******************9777654 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                                       SEEEEESGGG-- CS
                             AAA_5  67 eilvlDEverae 78 
                                        ++vlDE++ + 
  gi|336254947|ref|YP_004598054.1| 141 VVIVLDEIDSIG 152
                                       589999999765 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.3e-05      0.02      28      93 ..      24      96 ..      12     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                            DUF815 28 ddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg.......Lrlievekedlk 93
                                      +++ + d++ ea ++  +  ++g + nn++L+G+ G+GK ++   ll  ++e+        L ++ v+ ++l+
  gi|336254947|ref|YP_004598054.1| 24 ERIEERDEEIEAYMDALQPIIDGWEPNNIFLYGNTGVGKTAVTEYLLDVLQEDVteyddvdLSVLSVNCKTLN 96
                                      66777888999999999999*********************99999888777655555555666666655555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012       0.1      17     117 ..      48     153 ..      30     169 .. 0.67
   2 ?   -0.6   0.0      0.73   6.2e+02      92     132 ..     209     248 ..     180     249 .. 0.77
   3 ?   -3.3   0.0       4.8   4.1e+03      58     106 ..     306     353 ..     302     356 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                       TSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEE....SXXHHHHHHHXXHHHHHCCCTTSSSS-ST CS
                            NB-ARC  17 elqslvvalvGmgGvGKttlakqilnksdevegrFdsvawvvvs....ktdkseeiletilkeLslseddleekeev 89 
                                       e++   ++l+G  GvGKt + +  l  ++e   ++d v   v+s       +s+++  ++++ L       e+ +++
  gi|336254947|ref|YP_004598054.1|  48 EPN--NIFLYGNTGVGKTAVTEYLLDVLQEDVTEYDDVDLSVLSvnckTLNSSYQVAIELVNTLRPDG--AEISTTG 120
                                       555..79******************9999999999965444444111144566777777777775554..4444444 PP

                                       TS...HHHHHHHHCCCT..TEEEEEEEE-SHHH CS
                            NB-ARC  90 es...lkrklvrlLltk..rfllvlDDVweeed 117
                                       ++     +kl+  L+     +++vlD +    d
  gi|336254947|ref|YP_004598054.1| 121 YPqqtVFKKLYSELEALggTVVIVLDEIDSIGD 153
                                       444457788888887656688899998765555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.73
                                       HHHHHHHHCCCTTEEEEEEEE-SHHHH.....HHHHCHTTS CS
                            NB-ARC  92 lkrklvrlLltkrfllvlDDVweeedwdkigvvlparenrl 132
                                        +++l ++L+++  + +  D  e+ ++ +++++l ar++++
  gi|336254947|ref|YP_004598054.1| 209 EADELTNILESRAEVAIAEDACETGVL-NLCAALAARDSGS 248
                                       5899********************999.9999999998875 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.8
                                       EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS.HHHHHHHHCCCTTEE CS
                            NB-ARC  58 vvsktdkseeiletilkeLslseddleekeeves.lkrklvrlLltkrfl 106
                                       vvsk  k+++  +   +eL+++ + l e +  +s ++r +++ L + r+l
  gi|336254947|ref|YP_004598054.1| 306 VVSKAAKESTPCR--TRELYQEYESLCESSGTDSlAQRSVHNHLSDLRML 353
                                       5666666666666..67777666665555555555677788887777776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00037      0.32       1      31 [.      52      80 ..      52     150 .. 0.74
   2 ?    1.2   0.0      0.61   5.2e+02      13      69 ..     236     288 ..     230     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00037
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdv 31
                                      I+l G  GvGKt ++++L + l   + ++++
  gi|336254947|ref|YP_004598054.1| 52 IFLYGNTGVGKTAVTEYLLDVL--QEDVTEY 80
                                      89****************4443..3333333 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.61
                            AAA_18  13 tlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss 69 
                                        l+ +L+ r   +   r+ +   +l  ev ++  ++   ++ed +d++ ++le+ + 
  gi|336254947|ref|YP_004598054.1| 236 NLCAALAARD--SGSARQALDLLRLAGEVAEN--NDDPTIREDHVDQARSKLEQERV 288
                                       5788888888..88999999999999999999..99999999999999999999754 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00055      0.47      10      51 ..      28      67 ..      20     157 .. 0.72
   2 ?   -3.0   0.1       5.2   4.4e+03      99     139 ..     249     285 ..     233     290 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00055
                            AAA_25 10 vsvadlaapppprrwlvkgllpagelallaGapgtGKttlal 51
                                       ++++++a +  ++ +++g+      + l+G +g+GKt+++ 
  gi|336254947|ref|YP_004598054.1| 28 ERDEEIEAYMDALQPIIDGWE--PNNIFLYGNTGVGKTAVTE 67
                                      3568899999999*******5..58899**********9863 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.2
                            AAA_25  99 ddarllvldlagveslpLfakdrggtl.ltadvdaleaaiee 139
                                       +++ l++l lag+     +a+ +++++ ++  vd+ + ++e+
  gi|336254947|ref|YP_004598054.1| 249 ARQALDLLRLAGE-----VAENNDDPTiREDHVDQARSKLEQ 285
                                       4455666666665.....334444444255556666666666 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.094       1      27 [.      52      78 ..      52     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklk 27
                                      i+lyG++g+GK+ ++++L + l++++ 
  gi|336254947|ref|YP_004598054.1| 52 IFLYGNTGVGKTAVTEYLLDVLQEDVT 78
                                      79****************999998773 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 ?    2.4   0.0     0.087        75      20      47 ..      49      76 ..      33     109 .. 0.82
   2 ?    8.0   0.0    0.0017       1.4     158     185 ..     124     151 ..     109     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.087
                        KAP_NTPase 20 pivvgLygkWGsGKssllnkledelkef 47
                                      p  + Lyg+ G+GK+++ + l d l+e 
  gi|336254947|ref|YP_004598054.1| 49 PNNIFLYGNTGVGKTAVTEYLLDVLQED 76
                                      55689***********999988877766 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0017
                        KAP_NTPase 158 eelladmektLdalqkrlVvviDdLDrc 185
                                       +++++++ ++L+al  ++V+v+D++D++
  gi|336254947|ref|YP_004598054.1| 124 QTVFKKLYSELEALGGTVVIVLDEIDSI 151
                                       678999********************97 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 ?   10.5   0.0   0.00023       0.2       8      41 ..      42      75 ..      35      80 .. 0.87
   2 ?   -1.2   0.0      0.86   7.4e+02     247     272 ..     143     168 ..     139     170 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00023
                     TrwB_AAD_bind  8 plpkeretqhilivGttGsGKtqalekllraira 41
                                      p+    e + i++ G tG GKt ++e ll+ +++
  gi|336254947|ref|YP_004598054.1| 42 PIIDGWEPNNIFLYGNTGVGKTAVTEYLLDVLQE 75
                                      788888999********************98876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.86
                     TrwB_AAD_bind 247 fflDElpaLgrleelksllaegRkfG 272
                                        +lDE++++g  +el   l ++R+ G
  gi|336254947|ref|YP_004598054.1| 143 IVLDEIDSIGDRDELLYELPRARSNG 168
                                       689********************998 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 ?   11.8   0.0   0.00015      0.13      35      70 ..      51      86 ..      48     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                             AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfs 70
                                      +++l+G+tG+GKt++++ ll+ l+++ + +  + +s
  gi|336254947|ref|YP_004598054.1| 51 NIFLYGNTGVGKTAVTEYLLDVLQEDVTEYDDVDLS 86
                                      789*****************9999877766666555 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.24       5      82 ..      51     153 ..      48     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS........... CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG........... 70 
                                       +i l g+tgvGkt +++ l ++l+ ++  +   +d s l    + ++l s+ ++a +  +    +G           
  gi|336254947|ref|YP_004598054.1|  51 NIFLYGNTGVGKTAVTEYLLDVLQ-EDVTEYDDVDLSVLSV--NCKTLNSSYQVAIELVNTLRPDGaeisttgypqq 124
                                       78899*********9999999999.6777777777777777..6666666666666666666666666666778888 PP

                                       .................EEEEETGGG--- CS
                             AAA_2  71 .................ivllDEidKihp 82 
                                                        ++ lDEid i  
  gi|336254947|ref|YP_004598054.1| 125 tvfkklyselealggtvVIVLDEIDSIGD 153
                                       89***********************8866 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0082         7      32      63 ..      51      82 ..      47      84 .. 0.84
   2 ?    3.8   0.1     0.023        19     476     510 ..     248     282 ..     234     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0082
                            AAA_32 32 NifvlGesgtGrttlvkrlleeiakkeptpdD 63
                                      Nif+ G++g+G+t +++ ll+  +++    dD
  gi|336254947|ref|YP_004598054.1| 51 NIFLYGNTGVGKTAVTEYLLDVLQEDVTEYDD 82
                                      9*************999999887777666665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.023
                            AAA_32 476 rfseiadllrEAdywakkegaevveaehVekAlee 510
                                       + ++  dllr A  +a+++++ +++++hV++A ++
  gi|336254947|ref|YP_004598054.1| 248 SARQALDLLRLAGEVAENNDDPTIREDHVDQARSK 282
                                       567889**************************765 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   0.00041      0.35       6      44 ..      32      74 ..      26      80 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
                                      HHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  6 etealgkklakal....gdvilLeGdLGaGKTtlvrglakalg 44
                                      e+ea   +l+  +     + i+L+G+ G+GKT+ +  l+  l+
  gi|336254947|ref|YP_004598054.1| 32 EIEAYMDALQPIIdgwePNNIFLYGNTGVGKTAVTEYLLDVLQ 74
                                      55566666655555544456****************9998875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00037      0.32       3      75 ..      50     149 ..      48     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00037
                            AAA_24   3 lkiliyGpsgiGKTtlakel.....gpkplfidtekGlksldadkfpdieswedfldevvel............... 59 
                                       ++i++yG  g+GKT +   l     ++ + + d++ ++ s++ + ++  +s++  ++ v++l               
  gi|336254947|ref|YP_004598054.1|  50 NNIFLYGNTGVGKTAVTEYLldvlqEDVTEYDDVDLSVLSVNCKTLN--SSYQVAIELVNTLrpdgaeisttgypqq 124
                                       789*************9999777744444455788888888888877..6888888888888666666666666555 PP

                            AAA_24  60 .........aaeladyktlviDtid 75 
                                                 ++l +  ++v+D id
  gi|336254947|ref|YP_004598054.1| 125 tvfkklyseLEALGGTVVIVLDEID 149
                                       5555555554445555566666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00081       0.7      89     129 ..      39      79 ..      11      85 .. 0.77
   2 ?   -1.5   0.0       2.5   2.1e+03      37      66 ..     129     158 ..     118     173 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00081
                                       THHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  89 gleelkellkdktsvlvGqSGvGKStLinallpelelktge 129
                                       +l+ + + ++ + ++l G++GvGK+++ + ll  l+  + e
  gi|336254947|ref|YP_004598054.1|  39 ALQPIIDGWEPNNIFLYGNTGVGKTAVTEYLLDVLQEDVTE 79 
                                       344444555668899*************9999887777765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                                       HHHHHHHHTT-EEEEEEE-GGG--HHHHHH CS
                       RsgA_GTPase  37 rfLvlaeekgiepvivlnKiDlleeeeele 66 
                                       ++  ++e+ g ++vivl  iD + +++el 
  gi|336254947|ref|YP_004598054.1| 129 KLYSELEALGGTVVIVLDEIDSIGDRDELL 158
                                       445567888889999999999998887554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.39
# Mc/sec: 3103.69
//
Query:       gi|336254948|ref|YP_004598055.1|  [L=478]
Description: restriction endonuclease-like protein [Halopiger xanaduensis SH-6]
Scores for 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   39.5   0.1    9.7e-10   38.4   0.1    1.6  1  HNH_2        HNH endonuclease
    0.00098   19.6   0.0      0.082   13.4   0.0    2.5  2  AAA_assoc_C  C-terminal AAA-associated domain
     0.0016   18.5   0.4      0.011   15.8   0.1    2.3  2  HemN_C       HemN C-terminal domain
  ------ inclusion threshold ------
      0.037   14.2   0.1         21    5.3   0.0    3.4  3  Mrr_N        Mrr N-terminal domain
      0.075   12.7   0.0       0.16   11.6   0.0    1.5  1  DUF4423      Domain of unknown function (DUF4423)
      0.085   13.0   0.2       0.16   12.2   0.2    1.4  1  HNH          HNH endonuclease
       0.16   12.0   0.0        3.8    7.6   0.0    2.3  2  HTH_45       Winged helix-turn-helix
       0.19   11.8   0.0       0.43   10.6   0.0    1.6  2  FokI_C       Restriction endonuclease FokI, catalytic domain


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 !   38.4   0.1   4.3e-13   9.7e-10       1      71 [.     372     425 ..     372     426 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 4.3e-13
                             HNH_2   1 Cvitgiddp....s.lleaAHIiPwslssffndlilnrfeigrillekgstidspsNgllLspdiHklFdqflfaf 71 
                                       C+i+g  ++    +  +eaAHI+P           ++++             d  +Ngl L++ +H++Fd++++a+
  gi|336254948|ref|YP_004598055.1| 372 CAICGAARKapdgTrDIEAAHIYP----------KRENG------------RDTIRNGLALCRLHHWAFDAGWLAI 425
                                       9****443356775599*******..........56666............8**********************98 PP

>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   3.7e-05     0.082      18      77 ..      60     116 ..      47     135 .. 0.72
   2 ?    3.4   0.0     0.049   1.1e+02      21      49 ..     148     176 ..     146     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.7e-05
                       AAA_assoc_C  18 veaaelLglveveegdielTelGrkfveadikerKeifreqllklvplaaairrvLdere 77 
                                       +  +e +gl+e+e+g i+lT+ G +++  +      ++ e l ++v+ +++i ++L + +
  gi|336254948|ref|YP_004598055.1|  60 LAFLERIGLLEIESGRIRLTQRGMEWLSETDP---AVLYELLAEHVRGFDTILEALLDGP 116
                                       667899*******************9865433...3455555555555666666655555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.049
                       AAA_assoc_C  21 aelLglveveegdielTelGrkfveadik 49 
                                       +++Lg ve ++g   lT+ Gr++++  ++
  gi|336254948|ref|YP_004598055.1| 148 LQSLGYVERSDGVNSLTDPGRELARRRTS 176
                                       689*******************9988765 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   4.7e-06     0.011      41      65 ..      59      83 ..      41      84 .. 0.90
   2 ?   -0.4   0.0      0.54   1.2e+03      44      65 ..     147     168 ..     144     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.7e-06
                            HemN_C 41 aleklqeqGLLeldggrlrltprGr 65
                                       l+ l++ GLLe++ gr+rlt+rG+
  gi|336254948|ref|YP_004598055.1| 59 RLAFLERIGLLEIESGRIRLTQRGM 83
                                      58899*******************7 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.54
                            HemN_C  44 klqeqGLLeldggrlrltprGr 65 
                                       +lq  G++e ++g  +lt+ Gr
  gi|336254948|ref|YP_004598055.1| 147 WLQSLGYVERSDGVNSLTDPGR 168
                                       5899*********999999998 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0093        21      61      86 ..      63      87 ..      37      88 .. 0.89
   2 ?   -0.0   0.0      0.44   9.8e+02       6      30 ..     106     129 ..     103     139 .. 0.86
   3 ?    4.0   0.0     0.024        54      61      86 ..     148     172 ..     144     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0093
                             Mrr_N 61 LkkagllespkrgvwkiTekGrevlk 86
                                      L + glle +  g +++T++G e+l+
  gi|336254948|ref|YP_004598055.1| 63 LERIGLLEIE-SGRIRLTQRGMEWLS 87
                                      6778888887.9************97 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.44
                             Mrr_N   6 lplLealadgsehrlkeirervaer 30 
                                         +Leal dg  +  +e+ ++++++
  gi|336254948|ref|YP_004598055.1| 106 DTILEALLDGPKTD-AELGDAIESE 129
                                       679**********9.**99999875 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.024
                             Mrr_N  61 LkkagllespkrgvwkiTekGrevlk 86 
                                       L+  g++e++  gv ++T+ Gre+ +
  gi|336254948|ref|YP_004598055.1| 148 LQSLGYVERS-DGVNSLTDPGRELAR 172
                                       5677999998.9**********9976 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.3e-05      0.16      29      93 ..      31      93 ..      26     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.3e-05
                           DUF4423 29 llplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevksea 93
                                      l++ + ++a ++++   +r + s + +++ l fL+++gll+ +  g++r t++ ++  se+ +++
  gi|336254948|ref|YP_004598055.1| 31 LADSPSEAAAIDWIRSNTR-ATSDDGIRRRLAFLERIGLLEIES-GRIRLTQRGMEWLSETDPAV 93
                                      7788888999*********.999999****************99.7*****99988777776665 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   7.1e-05      0.16       1      38 [.     372     412 ..     372     415 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.1e-05
                               HNH   1 CeyCgrkfhks....ealevdHiipisqggaddieNlqllCk 38 
                                       C +Cg   +       ++e  Hi p+ ++g+d+i N  +lC+
  gi|336254948|ref|YP_004598055.1| 372 CAICGAARK-ApdgtRDIEAAHIYPKRENGRDTIRNGLALCR 412
                                       666665532.23556788999********************7 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0017       3.8      39      69 ..      59      89 ..      54      92 .. 0.90
   2 ?    1.7   0.0      0.12   2.6e+02      43      67 ..     148     172 ..     146     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0017
                            HTH_45 39 YLdmLvekglikkskekYvlTekGlellekl 69
                                       L +L   gl++ +++  +lT++G+e l++ 
  gi|336254948|ref|YP_004598055.1| 59 RLAFLERIGLLEIESGRIRLTQRGMEWLSET 89
                                      5899**********************99875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.12
                            HTH_45  43 LvekglikkskekYvlTekGlelle 67 
                                       L++ g+++ s++  +lT+ G+el +
  gi|336254948|ref|YP_004598055.1| 148 LQSLGYVERSDGVNSLTDPGRELAR 172
                                       78899****************9976 PP

>> FokI_C  Restriction endonuclease FokI, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019      0.43      55     104 ..      29      79 ..       5     100 .. 0.74
   2 ?   -3.8   0.0       5.5   1.2e+04      86      97 ..     146     157 ..     145     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                            FokI_C  55 qglaea.eeekekkklksdtegssDkYvrmiaswLkklglvkkeakvvtvd 104
                                       + la++ +e+   + ++s+t ++sD  +r    +L+++gl+++e+  +  +
  gi|336254948|ref|YP_004598055.1|  29 HVLADSpSEAAAIDWIRSNTRATSDDGIRRRLAFLERIGLLEIESGRIRLT 79 
                                       4444441333445589***************************99888755 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.5
                            FokI_C  86 swLkklglvkke 97 
                                       +wL+ lg+v+++
  gi|336254948|ref|YP_004598055.1| 146 GWLQSLGYVERS 157
                                       699999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3647.56
//
Query:       gi|336254949|ref|YP_004598056.1|  [L=413]
Description: hypothetical protein Halxa_3566 [Halopiger xanaduensis SH-6]
Scores for 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   11.9   0.0       0.48   10.5   0.0    1.7  2  VRR_NUC   VRR-NUC domain


Domain annotation for each model (and alignments):
>> VRR_NUC  VRR-NUC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   2.7e-05      0.48      51      81 ..      64     104 ..      19     128 .. 0.81
   2 ?   -2.9   0.0      0.39   6.9e+03       4      29 ..     267     293 ..     265     307 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.7e-05
                                       HHSSTS-SEEEEETTTTE............EEEEEEE-TT- CS
                           VRR_NUC  51 glrsGvPDLilwieeqkry..........vflliEvKgpgd 81 
                                       + ++G+PDL+ +++ +++           +  +iE Kg+++
  gi|336254949|ref|YP_004598056.1|  64 EIGGGFPDLVGVRDLESELvavervgdepPLIAIEAKGETS 104
                                       6789********9999876889999999999*******985 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.39
                                       TCHHHHHHHHHH.HTTCBBTTB-TTTS CS
                           VRR_NUC   4 esaqvaiadkle.klgllapvvnwgel 29 
                                       esa + + +++  +++++   ++wg+l
  gi|336254949|ref|YP_004598056.1| 267 ESALAEFEEWFRsRKRFVDLAPQWGQL 293
                                       566677778888666678888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 3306.51
//
Query:       gi|336254950|ref|YP_004598057.1|  [L=92]
Description: hypothetical protein Halxa_3567 [Halopiger xanaduensis SH-6]
Scores for 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   12.5   0.0        7.8    6.6   0.0    2.3  2  Cuticle_1  Crustacean cuticle protein repeat


Domain annotation for each model (and alignments):
>> Cuticle_1  Crustacean cuticle protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0   0.00043       7.8      26      37 ..      21      32 ..      20      35 .. 0.75
   2 ?    3.8   0.0    0.0034        60      15      38 ..      59      83 ..      51      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00043
                         Cuticle_1 26 GpSGaVlsdGkn 37
                                      G+SG V++dG+ 
  gi|336254950|ref|YP_004598057.1| 21 GESGDVTADGER 32
                                      788888888875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0034
                         Cuticle_1 15 fthgva.nivliGpSGaVlsdGknv 38
                                      f +++  + v++ +SG ++  G+ v
  gi|336254950|ref|YP_004598057.1| 59 FEQDEPvDLVVDHESGSLTVEGDDV 83
                                      888888899**********999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 812.82
//
Query:       gi|336254951|ref|YP_004598058.1|  [L=62]
Description: hypothetical protein Halxa_3568 [Halopiger xanaduensis SH-6]
Scores for 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   13.1   2.4      0.057   13.0   2.4    1.1  1  DUF4225   Protein of unknown function (DUF4225)


Domain annotation for each model (and alignments):
>> DUF4225  Protein of unknown function (DUF4225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.4   3.2e-06     0.057      46      86 ..       8      48 ..       5      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-06
                           DUF4225 46 vVagglqivaGvalvskasetvvgavaGalLilhGannvve 86
                                      +V+ggl++vaG+ l+   +++  + +aG+ L l Ga +v  
  gi|336254951|ref|YP_004598058.1|  8 IVVGGLALVAGLWLAALFARGSTVWIAGVGLALLGAASVFA 48
                                      89*************9999999999**********999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.19s 00:00:00.52 Elapsed: 00:00:00.32
# Mc/sec: 573.37
//
Query:       gi|336254952|ref|YP_004598059.1|  [L=141]
Description: hypothetical protein Halxa_3569 [Halopiger xanaduensis SH-6]
Scores for complete 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   42.4   0.1    1.8e-10   42.2   0.1    1.1  1  DUF393    Protein of unknown function, DUF393


Domain annotation for each model (and alignments):
>> DUF393  Protein of unknown function, DUF393
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.1   9.9e-15   1.8e-10       1     112 [.      10     117 ..      10     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 9.9e-15
                            DUF393   1 vlyDgeCplCnravqflerrdrkgrirfadlqsasgkallkelgidaeqldslllvieagrvysgsdAaleiaralp 77 
                                       ++yD++C +C+++++++ +r   +++r++ + s+ + +l ++l   +e +++l+    ++ vys+ + ++e +++++
  gi|336254952|ref|YP_004598059.1|  10 LVYDDDCGFCTWWAEYFDDRT--NDVRIVGF-SDLTPELRERLPEHYEACSHLMT---DEGVYSCGASIEETLARVE 80 
                                       68***************9995..57888888.66666655444444455554444...666**********977777 PP

                            DUF393  78 g..lwrllalllvlprlkklrdalYrliarnRyrlfg 112
                                       g     ++ +l+ +  + +lr+ +Yr++a+nR  + +
  gi|336254952|ref|YP_004598059.1|  81 GggVRDVVDFLRNFEDYGRLRETGYRWVADNRDLWGR 117
                                       6567789999999*******************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1104.54
//
Query:       gi|336254953|ref|YP_004598060.1|  [L=315]
Description: hypothetical protein Halxa_3570 [Halopiger xanaduensis SH-6]
Scores for 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  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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):               0  [number of targets reported over threshold]
# CPU time: 0.80u 0.23s 00:00:01.03 Elapsed: 00:00:00.40
# Mc/sec: 2362.20
//
Query:       gi|336254954|ref|YP_004598061.1|  [L=494]
Description: hypothetical protein Halxa_3571 [Halopiger xanaduensis SH-6]
Scores for 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-126  422.4  15.3    4.5e-67  227.1   0.3    2.7  3  LMF1      Lipase maturation factor
  ------ inclusion threshold ------
       0.01   15.6   0.3      0.018   14.8   0.3    1.3  1  Nrap_D5   Nrap protein PAP/OAS1-like domain 5


Domain annotation for each model (and alignments):
>> LMF1  Lipase maturation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.5      0.13   1.1e+03      15      54 ..      83     121 ..      80     123 .. 0.81
   2 !  204.2   2.9   4.2e-64   3.8e-60       1     164 [.     125     278 ..     125     291 .. 0.96
   3 !  227.1   0.3     5e-71   4.5e-67     258     440 ..     299     482 ..     290     483 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.13
                              LMF1  15 laillapfkllsklpkslplpslvvwlvrwLlfRlmfgsG 54 
                                       l+++ ap ++  +   +  + s+v+w+  w l+   + +G
  gi|336254954|ref|YP_004598061.1|  83 LTLFAAPYWSVVPDAYA-TPVSMVLWAAMWALYLSFVNAG 121
                                       78999999999888766.7778999*****9997777777 PP

  == domain 2  score: 204.2 bits;  conditional E-value: 4.2e-64
                              LMF1   1 lsFqwdslLLEvGflaillapfkllsklpkslplpslvvwlvrwLlfRlmfgsGlvKlrsgdptWwdLtaldyhyet 77 
                                       ++++w+s+LLE+Gflai+l             ++p +v++lv+w+lfR mfg+Gl+Klr gd++W+dL+++d+hyet
  gi|336254954|ref|YP_004598061.1| 125 YGYGWESMLLETGFLAIFLGAGSA--------APPVVVLVLVQWVLFRNMFGAGLIKLR-GDECWRDLSCMDHHYET 192
                                       79*****************86555........89*************************.***************** PP

                              LMF1  78 qplPtplawyahqlpswlhkletvvtlvvelvvpfllllPirklrlfggviqvllqlliilsGNynflnlltivlal 154
                                       qp+P+p++w+ah+lp+ +h++et++++ vel++pfl+++P +++  ++g++ + ++ +++l+GN+++ln ltivla+
  gi|336254954|ref|YP_004598061.1| 193 QPIPNPASWFAHHLPDRFHRVETFGNHAVELLIPFLYFAP-QPWSSLAGAATIGFMGWLMLTGNFAWLNALTIVLAI 268
                                       ****************************************.************************************ PP

                              LMF1 155 slldDqflsa 164
                                       +++ D +l+a
  gi|336254954|ref|YP_004598061.1| 269 ATFSDGALEA 278
                                       *****88765 PP

  == domain 3  score: 227.1 bits;  conditional E-value: 5e-71
                              LMF1 258 llvllllavlvftlslvpksklasvrnllskrqlmnsslnpfrlvnsYglfrrvtkeRpeviiegtndse....tkW 330
                                        ++ +llav+v++ls+ p +      n+ls+ q+mn++++p++lvn+Yg+f+++t++R+e++iegt+d+e    t+W
  gi|336254954|ref|YP_004598061.1| 299 QALSILLAVFVLALSVRPAR------NMLSRSQTMNTAFDPLHLVNTYGAFGSITRDRYEIVIEGTTDEEitenTEW 369
                                       56678888899999998855......9************************************************** PP

                              LMF1 331 keyeFkykPgdvsrrprlvaPyqprLDwqmwfaalgky.eqnpWllsLlyrLLqnskevlkLlaenPfekk..ppky 404
                                       +ey Fk kP+d++rrp++vaPy+ rLDwq+wfaa+++  +++pW+l+Ll + L+++++v +Llae+Pf ++   p+ 
  gi|336254954|ref|YP_004598061.1| 370 HEYRFKGKPTDPERRPPQVAPYHLRLDWQLWFAAMSPSpRRHPWFLRLLEKVLEGDDAVRGLLAEDPFADAgeTPEH 446
                                       ********************************************************************55336**** PP

                              LMF1 405 vRaelYkYrftkkeesrargawWtRelvgeyvPpls 440
                                       vRa +Y+Yr+t+ +e++++g+wW+Re+vg yv p+s
  gi|336254954|ref|YP_004598061.1| 447 VRAIRYRYRYTTPAERAETGRWWRRERVGTYVSPVS 482
                                       ************9999999*************9986 PP

>> Nrap_D5  Nrap protein PAP/OAS1-like domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3     2e-06     0.018      14      73 ..     201     265 ..     199     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-06
                                       HHHHTT-T.....TTS-HHHHHHHHHHHHHS-TTS--.--SHHHHHHHHHHHHHH--TTT--EE- CS
                           Nrap_D5  14 WlashlLl....eghvseelvELlvakvFlqpapysv.PssaetGFlrvLelLarwdWkeepLiv 73 
                                       W+a hl       + + +++vELl+  ++  p+p+s+ ++ a+ GF+ +L l  ++ W +   iv
  gi|336254954|ref|YP_004598061.1| 201 WFAHHLPDrfhrVETFGNHAVELLIPFLYFAPQPWSSlAGAATIGFMGWLMLTGNFAWLNALTIV 265
                                       7777775422233567889****************98799******************6655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3567.05
//
Query:       gi|336254955|ref|YP_004598062.1|  [L=263]
Description: HpcH/HpaI aldolase [Halopiger xanaduensis SH-6]
Scores for 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-28   97.7   0.0    6.9e-28   97.3   0.0    1.1  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.0   3.9e-32   6.9e-28      10     216 ..      29     246 ..      22     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 3.9e-32
                                       SHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHHGGHHHTTSS CS
                         HpcH_HpaI  10 naalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqdlevldlgaq 86 
                                       +++l+e     g D v iDlE+a      d   ++++e+l+  d+ +   +e+ VR+++ d+++i++   +ld+ga 
  gi|336254955|ref|YP_004598062.1|  29 SPTLVEFYGELGLDFVWIDLEHAG-PSPFD--GERLEELLRAADV-SG--TELLVRLPEPDPGMIRK---ALDAGAR 96 
                                       67888888999***********98.33333..3556777777777.44..5****************...******* PP

                                       EEEESS--SHHHHHHHHHHTSHTTTS---.....................HCCC-EEEEEE-SHHHHHTHHHHHTST CS
                         HpcH_HpaI  87 vvlvPkvetaeealevvsalrepekgirg.....................anketrllaqiEsaegvknaeeIaave 142
                                       +v v  +etae+++++v+a r  ++g+ g                     +++e+++ + iE  ++v+n+e+I+av+
  gi|336254955|ref|YP_004598062.1|  97 NVFVSRIETAEDVRQAVEAARFTYDGEPGkrgfanprasrwgttddyaatEDEEIVVGVTIENPTAVENLEDILAVP 173
                                       *************************9999999********************************************* PP

                                       TEEEEEE-HHHHHHHTT-TTSTTSHHHHHHHHHHHHTTHCEEEEEEE.E-SSHHHHHHHHHTTHCEEEEEEHHH CS
                         HpcH_HpaI 143 gldgvflGaeDlsadlgtkrspegtevldareriltaaraagiaaldtvasdiddaegflaegalfvalGfdgk 216
                                       +l  vf G+ Dl+++ g+ ++p+++ev +   +i   a  ag+  l+++ +++dd+++  ++g+++ +lG+++ 
  gi|336254955|ref|YP_004598062.1| 174 ELGFVFAGPLDLAVSTGHPGEPSHEEVAEHVGEIEERALEAGV-PLGGLGFGMDDVNEKAEAGYQILNLGSTTG 246
                                       ****************************999999999999999.9999**********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 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:                        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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2156.49
//
Query:       gi|336254956|ref|YP_004598063.1|  [L=471]
Description: hypothetical protein Halxa_3573 [Halopiger xanaduensis SH-6]
Scores for 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  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 3929.41
//
Query:       gi|336254957|ref|YP_004598064.1|  [L=95]
Description: hypothetical protein Halxa_3574 [Halopiger xanaduensis SH-6]
Scores for 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:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 752.44
//
Query:       gi|336254958|ref|YP_004598065.1|  [L=498]
Description: sulfatase [Halopiger xanaduensis SH-6]
Scores for complete 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-44  152.6   0.0    1.9e-44  152.3   0.0    1.1  1  Sulfatase        Sulfatase
    2.2e-17   63.7   3.5    5.2e-17   62.5   0.8    2.4  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
     0.0015   17.7   0.0     0.0041   16.2   0.0    1.7  2  DUF1501          Protein of unknown function (DUF1501)
  ------ inclusion threshold ------
      0.032   13.4   0.2       0.17   11.1   0.1    1.9  2  Phosphoesterase  Phosphoesterase family
      0.061   13.3   0.0        0.2   11.6   0.0    1.9  1  DUF4994          Domain of unknown function
        0.3    9.6   0.0       0.37    9.4   0.0    1.1  1  DUF229           Protein of unknown function (DUF229)


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.3   0.0   6.5e-48   1.9e-44       1     309 []      16     356 ..      16     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 6.5e-48
                                       EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHH CS
                         Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgggg 77 
                                       +nvvl+++d+++a++        +ttp l+rla+eg+ f n+++aap + ps a+++tg yp ++g   ++++    
  gi|336254958|ref|YP_004598065.1|  16 RNVVLVVLDTARAKS-----IDKRTTPSLSRLAAEGTAFDNAFAAAPWTLPSHASMFTGTYPSEHGT--HGDH--LF 83 
                                       69*********7754.....44578*****************************************4..3333..57 PP

                                       CTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHCCTTTSEEEETSSSCHHTCCCCCCCCCECTCCC........ CS
                         Sulfatase  78 lpqteatLpellkeaGYntaaigkwhlgwssrqsvyknrgfdrflgfptgsaalkdpekseyngevlrv........ 146
                                       l  +  tLpe + e+G++t  +g  +++w+ ++ ++  rgfd++ +++ + + ++d +++    +   +        
  gi|336254958|ref|YP_004598065.1|  84 LEDDLRTLPEAFAENGVQT--VGVSNNTWITEEFGF-DRGFDELRKGWQYVQSDADMGAVVRGEDLREKlvatrerl 157
                                       899****************..999999999777643.68999999999999999998877665545444999***** PP

                                       ..................TTTTCSHHHHHHHHHHHHHHCCCTSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCC CS
                         Sulfatase 147 ..................ppeggysddrlldealefllarndkpfflylatlapHappeapdeyakkyatffddgse 205
                                                         +p+g   +dr +  + ++l++r d+pffl+  +++pH  +  p+eya+++     +   
  gi|336254958|ref|YP_004598065.1| 158 fdgnpvvnaanilysevvQPAGDDGSDRSTTWIRNWLAERGDDPFFLFCNFIEPHVEYDPPREYAAEFLPDGASY-- 232
                                       ******************88888888888889****76666**************97766777766643333333.. PP

                                       CCH.........................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHH CS
                         Sulfatase 206 aar.........................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesn 257
                                         +                          l++ y + ++yvDd+i+ +  +Lee+g++++tl+v+ +Dhg+++  + 
  gi|336254958|ref|YP_004598065.1| 233 --EeaasirqdpraydcedydisgrefaMLRGFYRAELAYVDDQIAALRSTLEEAGEWEDTLFVVCGDHGEHV--GE 305
                                       ..23445788899999***********8888889999************************************..55 PP

                                       TTSSSCTTCSSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHHHTTE CS
                         Sulfatase 258 gplrggkganayeggtrvPllvwwpgekaprvseelvshiDlfptildlagi 309
                                       + + g+++ n y+  ++vPl++++      +++ elv +iDl  t+l+ agi
  gi|336254958|ref|YP_004598065.1| 306 HGFFGHQY-NLYDTLINVPLVLHGGPFTDGGTRRELVQLIDLPDTLLETAGI 356
                                       99999999.****************99999********************97 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.8   1.7e-20   5.2e-17       1     235 [.      18     302 ..      18     322 .. 0.73
   2 ?   -2.3   0.1      0.88   2.6e+03     272     272 ..     438     438 ..     357     494 .. 0.60

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.7e-20
                                       EEEEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEE CS
                      Phosphodiest   1 vlvislDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgeyv 77 
                                       v++++lD +ra+ +d+  +++p+l++La eg+ ++n  + +P  T p+has+ TG+yP+eHG  g++ + +++ + +
  gi|336254958|ref|YP_004598065.1|  18 VVLVVLDTARAKSIDK--RTTPSLSRLAAEGTAFDNAFAAAP-WTLPSHASMFTGTYPSEHGTHGDHLFLEDDLRTL 91 
                                       79**************..*****************9888887.69************************66666655 PP

                                       EEETTTTGG......GGGCTTS-HHHHHHHTHTTCEEEESE..TTTTSEBTTCT.SC.......TBHHSBTCT...C CS
                      Phosphodiest  78 vfvtededa......prwwqgepiwdtaakarglkaaalfw..pgsevdystyyylvs......etppryled..df 138
                                       +   +++ +      ++ w +e++ ++     g+     +w    s++d+    + +        t++r ++    +
  gi|336254958|ref|YP_004598065.1|  92 PEAFAENGVqtvgvsNNTWITEEFGFDR----GFDELRKGWqyVQSDADMGAVVRGEDlreklvATRERLFDGnpVV 164
                                       5555555533334444444444444444....555444445444455555433332225555668888888557655 PP

                                       STTS............CHHHHHHHHHHHHHHHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TTSHH....... CS
                      Phosphodiest 139 nakv............pledkvdkavlqtwldaafakvvlekelekpdlllvyleetDtvgHkfGpdspe....... 196
                                       na++            +  d+ +++++ +wl++           ++p +l++++ e+        p           
  gi|336254958|ref|YP_004598065.1| 165 NAANilysevvqpagdDGSDRSTTWIR-NWLAERG---------DDPFFLFCNFIEPHVE-YDP-P---Reyaaefl 226
                                       555588888889877666667777666.8877666.........8999999999998321.111.2...12223455 PP

                                       .....................................HHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---E CS
                      Phosphodiest 197 .....................................vedalrrvDkaigdLlealderglsaetniilvSDHGma 235
                                                                             +++l++vD+ i+ L++ l+e g +++t +++ +DHG  
  gi|336254958|ref|YP_004598065.1| 227 pdgasyeeaasirqdpraydcedydisgrefamlrgfYRAELAYVDDQIAALRSTLEEAGEWEDTLFVVCGDHGEH 302
                                       55555667889999999999999999999999****9*************************************65 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.88
                                       E CS
                      Phosphodiest 272 n 272
                                        
  gi|336254958|ref|YP_004598065.1| 438 E 438
                                       2 PP

>> DUF1501  Protein of unknown function (DUF1501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.4e-06    0.0041     269     302 ..     267     300 ..     260     313 .. 0.88
   2 ?   -2.9   0.0       0.9   2.7e+03     349     378 ..     340     369 ..     332     378 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-06
                           DUF1501 269 lakelDqalaaLlkdLkqrGllddTlVvwagEFG 302
                                        ++ +D+ +aaL + L++ G ++dTl v++g+ G
  gi|336254958|ref|YP_004598065.1| 267 ELAYVDDQIAALRSTLEEAGEWEDTLFVVCGDHG 300
                                       56789***************************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.9
                           DUF1501 349 pvhvrdlhatilhllgldherltyatlgrp 378
                                        v++ dl  t+l + g+d+ +l  + +gr 
  gi|336254958|ref|YP_004598065.1| 340 LVQLIDLPDTLLETAGIDDPKLREQSAGRS 369
                                       577889999999999999999988888876 PP

>> Phosphoesterase  Phosphoesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   5.6e-05      0.17     103     164 ..      32      93 ..      24     123 .. 0.82
   2 ?   -0.2   0.0      0.15   4.6e+02     262     290 ..     272     300 ..     265     317 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.6e-05
                   Phosphoesterase 103 kredipvlwelaqeftlcDryFssvlggtepNrlflisgts.dpsGteggpsladpkktvlkg 164
                                       +++++p l +la e t +D+ F ++   t p +  +++gt+ +++Gt+g+  + +++ ++l++
  gi|336254958|ref|YP_004598065.1|  32 DKRTTPSLSRLAAEGTAFDNAF-AAAPWTLPSHASMFTGTYpSEHGTHGDHLFLEDDLRTLPE 93 
                                       6789999***************.55668************97789****99888776555554 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.15
                   Phosphoesterase 262 dklikevlealtsspqwaktllivtyDEn 290
                                       d+ i+ + ++l++  +w++tl++v  D  
  gi|336254958|ref|YP_004598065.1| 272 DDQIAALRSTLEEAGEWEDTLFVVCGDHG 300
                                       5667777788999999********87754 PP

>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.5e-05       0.2      62      97 ..     426     461 ..     414     462 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.5e-05
                           DUF4994  62 lGnskepqLydlkkdegekenvaekhpekvkelkel 97 
                                        G +  ++L++l++d+ e+++v + +p++v+++++ 
  gi|336254958|ref|YP_004598065.1| 426 RGDDGFERLHHLETDPRERTDVSDAQPDVVERMRDH 461
                                       5777789*************************9875 PP

>> DUF229  Protein of unknown function (DUF229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00012      0.37     312     349 ..     269     306 ..     255     403 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00012
                            DUF229 312 ealDedllkylkklekkgllentlvlllsDHGlrfgkl 349
                                         +D++++++ ++le+ g  e+tl ++ +DHG  +g++
  gi|336254958|ref|YP_004598065.1| 269 AYVDDQIAALRSTLEEAGEWEDTLFVVCGDHGEHVGEH 306
                                       56799999999*********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3792.47
//
Query:       gi|336254959|ref|YP_004598066.1|  [L=458]
Description: N-sulfoglucosamine sulfohydrolase [Halopiger xanaduensis SH-6]
Scores for 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-47  161.4   0.0    4.3e-47  161.0   0.0    1.2  1  Sulfatase     Sulfatase
    1.2e-08   34.9   0.3     0.0038   16.9   0.2    2.4  2  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
    7.8e-07   29.3   1.1      0.025   14.8   0.4    2.4  2  DUF4976       Domain of unknown function (DUF4976)
     0.0017   17.5   0.7      0.003   16.7   0.3    1.5  2  DUF1501       Protein of unknown function (DUF1501)
  ------ inclusion threshold ------
      0.015   16.0   0.0      0.037   14.7   0.0    1.6  1  Sulfatase_C   C-terminal region of aryl-sulfatase
      0.019   14.8   0.6       0.67    9.9   0.6    2.3  1  DUF4994       Domain of unknown function
       0.23   10.0   0.0       0.32    9.6   0.0    1.2  1  DUF229        Protein of unknown function (DUF229)


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.0   0.0   1.7e-50   4.3e-47       1     309 []       8     300 ..       8     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 161.0 bits;  conditional E-value: 1.7e-50
                                       EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHH CS
                         Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgggg 77 
                                       pn+vl+   dlg  +lg+yg  +  tp++d+ a+ g+rf +++++ap cspsr++l+tgr ph++g+     +g ++
  gi|336254959|ref|YP_004598066.1|   8 PNIVLVHCHDLGT-YLGCYGAAVD-TPRIDAFAADGVRFDRHFVTAPQCSPSRSSLMTGRHPHQNGMLGLAHAG-WE 81 
                                       8**********77.*********9.9******************************************999999.** PP

                                       CTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHCCTTTSEEEETSSSCHHTCCCCCCCCCECTCCCTTTTCSHH CS
                         Sulfatase  78 lpqteatLpellkeaGYntaaigkwhlgwssrqsvyknrgfdrflgfptgsaalkdpekseyngevlrvppeggysd 154
                                       + ++e+ Lpell +aGY+t+++g  h + ++     ++ g+dr+ +  ++s + ++p++++                
  gi|336254959|ref|YP_004598066.1|  82 IDEDEQLLPELLGAAGYETHLFGLQHITEYP-----DRLGYDRIHS--ENSLTADGPPSVHESA----------RAR 141
                                       ***********************99999883.....478***9999..6677777777666553..........455 PP

                                       HHHHHHHHHHHHCCC.TSSEEEEEEE-TTSS.....ST.CTCGGHTCCGSTTTTCCCCCCH.........HHHHHHH CS
                         Sulfatase 155 drlldealefllarn.dkpfflylatlapHa.....pp.eapdeyakkyatffddgseaar.........qlleayl 215
                                       ++ +d a  + +a   ++pff+ + + ++H      ++ +a+d+y++ + +  d++    +         + +++  
  gi|336254959|ref|YP_004598066.1| 142 EVAADFADAL-AAGGlGEPFFASVGFFEVHRmeetdGFgFADDRYETPSPDDVDPL----EflpddpgirSDIAEIQ 213
                                       5555555555.66666**************94444411577777777765555554....2555699999******* PP

                                       HHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHC.EEEC CS
                         Sulfatase 216 nsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkganayeggtrvPllvwwpgekap.rvse 291
                                       ++ve  Dd++g vl+aLe++gl d+tlvvft  hg ++          kg ++ + g++  + v++p ++   rv++
  gi|336254959|ref|YP_004598066.1| 214 GMVEALDDGVGTVLDALEDAGLTDETLVVFTTEHGLAM-------PRAKG-TCFDPGIEAAFAVRYPAGFDGeRVED 282
                                       **************************************.......57888.9************************* PP

                                       SEEEGGGHHHHHHHHTTE CS
                         Sulfatase 292 elvshiDlfptildlagi 309
                                       +lvs++D+f+t+l+ a++
  gi|336254959|ref|YP_004598066.1| 283 ALVSNVDVFATLLEIADA 300
                                       **************9985 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.1e-06     0.008      20      65 ..      30      74 ..      20      86 .. 0.90
   2 !   16.9   0.2   1.5e-06    0.0038     196     235 ..     211     250 ..     186     357 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.1e-06
                                      TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--S CS
                      Phosphodiest 20 llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivg 65
                                      ++p ++a+a  gv+++  + v  ++  p+ +sl+TG++P ++G+ g
  gi|336254959|ref|YP_004598066.1| 30 DTPRIDAFAADGVRFD-RHFVTAPQCSPSRSSLMTGRHPHQNGMLG 74
                                      89**************.7788888899****************987 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---E CS
                      Phosphodiest 196 evedalrrvDkaigdLlealderglsaetniilvSDHGma 235
                                       e++  ++ +D+ +g  l+al++ gl++et ++ + +HG a
  gi|336254959|ref|YP_004598066.1| 211 EIQGMVEALDDGVGTVLDALEDAGLTDETLVVFTTEHGLA 250
                                       59999*********************************86 PP

>> DUF4976  Domain of unknown function (DUF4976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   3.7e-05     0.095       3      66 ..     305     366 ..     303     383 .. 0.82
   2 !   14.8   0.4   9.7e-06     0.025      55      95 ..     380     426 ..     376     434 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                           DUF4976   3 admqGksllpllkgkkkkewrkalyYhyyeyPaehavkrhygvrteryklih.fykdidewelyD 66 
                                       +++ G+s++ ll+++ + e r+ ++     +  ++  ++ +++rt+r+k i+ f++  d++   D
  gi|336254959|ref|YP_004598066.1| 305 KEIAGESFASLLREDGTYEPRDRIFAGM-TW--HDRYNPVRAIRTDRWKYIRnFWNLPDVYLTND 366
                                       6899*******************98653.33..5678999*********9975888888775555 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 9.7e-06
                           DUF4976  55 fykdid.ewelyDlkkDpkelknly.....ddpeyeevvkelkkkle 95 
                                       fy+++  + elyDl++Dp e +nl+     dd+e ++v ++l+++l 
  gi|336254959|ref|YP_004598066.1| 380 FYDEQRsHEELYDLEDDPLERENLLaedvpDDSEIADVHDRLRTELG 426
                                       7766551568*************983222245666677777777665 PP

>> DUF1501  Protein of unknown function (DUF1501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.1   5.4e+03     117     145 ..      58      86 ..      16      97 .. 0.59
   2 !   16.7   0.3   1.2e-06     0.003     268     302 ..     214     248 ..     208     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.1
                           DUF1501 117 rgaagagsanwgsGflgralqgltlrssa 145
                                       r +   g++ +++G lg a+ g ++++++
  gi|336254959|ref|YP_004598066.1|  58 RSSLMTGRHPHQNGMLGLAHAGWEIDEDE 86 
                                       44445556666677777777777765555 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.2e-06
                           DUF1501 268 klakelDqalaaLlkdLkqrGllddTlVvwagEFG 302
                                         ++ lD+++ + l++L++ Gl d+TlVv+++E G
  gi|336254959|ref|YP_004598066.1| 214 GMVEALDDGVGTVLDALEDAGLTDETLVVFTTEHG 248
                                       56689****************************88 PP

>> Sulfatase_C  C-terminal region of aryl-sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.5e-05     0.037      10      85 ..     337     423 ..     327     436 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                       ETTEECEEEETTEEEE..CEE.--GCGTT-GGGTTTS......SSTT-EEECCEEEEETTT-TT--S-TTSTT.... CS
                       Sulfatase_C  10 cgaelhAvRlgkyKah..fvt.psfdpegaegcygse......cvekvtehdpPllFdlerDpsEkyplsaes.... 73 
                                       + + + A+R  ++K    f+  p+++   ++++y s+      ++   ++     l+dle+Dp E+ +l ae+    
  gi|336254959|ref|YP_004598066.1| 337 RYNPVRAIRTDRWKYIrnFWNlPDVYL--TNDIYRSDagrevrDEFYDEQRSHEELYDLEDDPLERENLLAEDvpdd 411
                                       556689999999995322444333322..44444444444443222344444567***************9998545 PP

                                       CCHHHHHHHHHH CS
                       Sulfatase_C  74 peykevlkeikk 85 
                                       +e ++v+++++ 
  gi|336254959|ref|YP_004598066.1| 412 SEIADVHDRLRT 423
                                       555555555544 PP

>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.6   0.00026      0.67      64      86 ..     384     406 ..     335     418 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00026
                           DUF4994  64 nskepqLydlkkdegekenvaek 86 
                                       +++++ Lydl++d+ e+en+ ++
  gi|336254959|ref|YP_004598066.1| 384 QRSHEELYDLEDDPLERENLLAE 406
                                       35678899999999999997544 PP

>> DUF229  Protein of unknown function (DUF229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00012      0.32     310     350 ..     215     255 ..     209     344 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00012
                            DUF229 310 llealDedllkylkklekkgllentlvlllsDHGlrfgklr 350
                                       ++ealD+ +  +l +le+ gl ++tlv++  +HGl + +++
  gi|336254959|ref|YP_004598066.1| 215 MVEALDDGVGTVLDALEDAGLTDETLVVFTTEHGLAMPRAK 255
                                       7899******************************8766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 3704.08
//
Query:       gi|336254960|ref|YP_004598067.1|  [L=98]
Description: hypothetical protein Halxa_3577 [Halopiger xanaduensis SH-6]
Scores for 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:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 867.67
//
Query:       gi|336254961|ref|YP_004598068.1|  [L=326]
Description: Inosine/uridine-preferring nucleoside hydrolase [Halopiger xanaduensis SH-6]
Scores for complete 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-78  264.5   0.7    1.7e-78  264.3   0.7    1.0  1  IU_nuc_hydro  Inosine-uridine preferring nucleoside hydrolase


Domain annotation for each model (and alignments):
>> IU_nuc_hydro  Inosine-uridine preferring nucleoside hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.3   0.7   9.2e-83   1.7e-78       1     304 [.       4     306 ..       4     307 .. 0.91

  Alignments for each domain:
  == domain 1  score: 264.3 bits;  conditional E-value: 9.2e-83
                                       EEEEEEE--SHHHHHHHHHHHCTHTTEEEEEEEE-SSSS-HHHHHHHHHHHHHHHCTTT.S-EEEE-SS-SSSS.S- CS
                      IU_nuc_hydro   1 rkvilDtDpGiDDalAlllalaespeiellgittvaGnvsleqatrnalrvlealggrddipvyaGaekpllre.ka 76 
                                       r+v++DtDpG DDa+Alllal++ p++e++g+ttv+Gn++++++trna+++le++ +r+ +p++aGa++pl    ++
  gi|336254961|ref|YP_004598068.1|   4 RPVVIDTDPGCDDAVALLLALEN-PALEVVGLTTVHGNAPVADTTRNARAILESV-DRTGVPIAAGADRPLNVLlET 78 
                                       68********************7.****************************666.5888**********7555789 PP

                                       SHHHHTTTSS.TSS-.--SSHCSCSSHHHHHHHHHHHHCHHTTTTEEEEECS-SHHHHHHHHHTCCHHHHEEEEEEE CS
                      IU_nuc_hydro  77 aaeihGedGl.gdvllpeperkaesesavdalidaveaareypgevtlvatGplTNiAlalrldpelakkvkrlviM 152
                                       a+eihGe G+ g+  +p+p++++++ +a++++++++   r++ g++ l a+GplTN+Ala +l+pel++++ +l++M
  gi|336254961|ref|YP_004598068.1|  79 AEEIHGEGGIrGELPEPTPATQPADVHAARFIVEQA---RAHDGDLALAAIGPLTNVALAHALEPELPDLLDELIVM 152
                                       999*******8887888889999999***9998777...999878******************************** PP

                                       ---SSS--SSSSSS-HHHHHSHHHHHHHHHTS-E.EEEE-HHHHTTSCHEECHHHHHHHHCST.....CBHHH...H CS
                      IU_nuc_hydro 153 GGaftarGNvtpvaEfNifvDPeAAkiVlesapvkitlvpldvthkvqalltseeveelaale.....kglga...f 221
                                       GGa +a+GN tp+aE+N++ DP+AA++V++ ++   tlv+ldvt+  qa ++++++e+l++ e     +   a    
  gi|336254961|ref|YP_004598068.1| 153 GGAAFAQGNATPLAEANFHSDPHAARRVVRDCE--PTLVGLDVTT--QATVPPARLESLSEDEgrdrdD---AlahS 222
                                       *****************************8644..4*********..7778999999976665544433...14458 PP

                                       HHHHHHHHHHHHHHHHHSSEEE-HHHHHHHHHH-GGGEEEEEEEEEEESSSSTTTTEEEEETSTT.TTS--EEEEEE CS
                      IU_nuc_hydro 222 ladllefyikaykeaegsdgaplhDplavavaldpelvttkrlavdveleggltrGrtvvdlrrl.kkaknvkvate 297
                                       +++ l++y +a  e+ g++ a lhD+lava ++d ++++t++++++v ++g+l+rG+ v+d+++  ++++n  va e
  gi|336254961|ref|YP_004598068.1| 223 IREWLTYYDAARLERYGIESAALHDALAVAGLVDGNVLETESYPLEVGTDGDLARGALVADRNGVtGDEPNGDVALE 299
                                       89999****99999999*******************************************999999*********** PP

                                       E-HHHHH CS
                      IU_nuc_hydro 298 vdverfl 304
                                        d erf 
  gi|336254961|ref|YP_004598068.1| 300 ADYERFR 306
                                       *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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 0.18s 00:00:00.58 Elapsed: 00:00:00.34
# Mc/sec: 2906.23
//
Query:       gi|336254962|ref|YP_004598069.1|  [L=118]
Description: carboxymuconolactone decarboxylase [Halopiger xanaduensis SH-6]
Scores for 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   49.4   0.2    5.1e-13   48.9   0.2    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 !   48.9   0.2   2.8e-17   5.1e-13       1      84 [.      24     106 ..      24     107 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2.8e-17
                                       HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHH CS
                               CMD   1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaar 77 
                                       p++ +a+++l+ea+ +  g +d  ++ L++l++++a + e  v++H+r+Ale   ++e +++v+    ++ag+p+a+
  gi|336254962|ref|YP_004598069.1|  24 PDVWDAYADLGEAAAE-AGPIDDETKRLVKLGMAVAVQSEGAVHSHVRRALEEDISPETLKQVAVLSIPTAGFPQAM 99 
                                       788899*********9.999*********************99********************************** PP

                                       HHHHHHH CS
                               CMD  78 aAlaaae 84 
                                       aAl + +
  gi|336254962|ref|YP_004598069.1| 100 AALSWIA 106
                                       ***9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.33
# Mc/sec: 1076.10
//
Query:       gi|336254963|ref|YP_004598070.1|  [L=281]
Description: tRNA pseudouridine synthase A [Halopiger xanaduensis SH-6]
Scores for 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-15   55.3   0.0    4.4e-11   43.2   0.0    2.4  2  PseudoU_synth_1  tRNA pseudouridine synthase


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 !    9.6   0.0   6.6e-05       1.2       4      89 ..      10      89 ..       9     106 .. 0.69
   2 !   43.2   0.0   2.4e-15   4.4e-11       1     107 [.     132     231 ..     132     232 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 6.6e-05
                   PseudoU_synth_1  4 elvGthdfgsfckqkqekkntvrtileaaieevsgeekell.vvtvkgsgFldhqVRamvgvlfavgqgklspedv.ke 80
                                      +++Gt ++g f  q+q++  tv      a++ ++  +++        ++g++d++V a+ ++++      ++p+++ ++
  gi|336254963|ref|YP_004598070.1| 10 AYDGTDYYG-F--QRQPDVPTVEDAVFDALRSLEVLDQDADkPDGYAAAGRTDRGVSALAQTIAF-----EAPDWLePR 80
                                      599999999.9..788888888887777777666555444424557899**************33.....556665236 PP

                   PseudoU_synth_1 81 llnakkrkk 89
                                      +lna+++++
  gi|336254963|ref|YP_004598070.1| 81 ALNAELPAD 89
                                      777777666 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 2.4e-15
                   PseudoU_synth_1   1 AakelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklsped 77 
                                       A+ +l G hdf ++   +++++nt+r  +  a +     ++++lv+tv++ gF    VR++v ++  vg g+ s e 
  gi|336254963|ref|YP_004598070.1| 132 ACDALSGPHDFHNL---TPDEHNTERAPTLEATR-----DGDYLVLTVTAGGFARELVRRLVSLARRVGTGDASLEA 200
                                       7899********88...67777888877766666.....56789********************************* PP

                   PseudoU_synth_1  78 vkellnakk.rkkiavetapavglvlfhvrY 107
                                       v+++l+ +  + +  ++ ap+++lvl  v+Y
  gi|336254963|ref|YP_004598070.1| 201 VDRALAPEPlPGHEGIPPAPPEPLVLTGVDY 231
                                       *******9999999***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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: 0.39u 0.19s 00:00:00.58 Elapsed: 00:00:00.33
# Mc/sec: 2524.39
//
Query:       gi|336254964|ref|YP_004598071.1|  [L=80]
Description: hypothetical protein Halxa_3582 [Halopiger xanaduensis SH-6]
Scores for 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   13.6   0.3      0.068   13.6   0.3    2.0  2  DUF4212   Domain of unknown function (DUF4212)


Domain annotation for each model (and alignments):
>> DUF4212  Domain of unknown function (DUF4212)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   3.8e-06     0.068       3      31 ..      10      37 ..       8      49 .. 0.85
   2 ?    1.4   0.5     0.023   4.2e+02      11      28 ..      51      68 ..      43      78 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-06
                           DUF4212  3 aYwrenlrlililLviWfvvsfglgilla 31
                                      aYwr+ +r+ + lLvi ++ ++  + l+a
  gi|336254964|ref|YP_004598071.1| 10 AYWRASIRIAAGLLVIALARTIT-APLFA 37
                                      8****************999999.66776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.023
                           DUF4212 11 lililLviWfvvsfglgi 28
                                       +l++L+  fv++ gl+ 
  gi|336254964|ref|YP_004598071.1| 51 FVLLVLAGTFVATLGLAR 68
                                      456677777777777544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.18s 00:00:00.54 Elapsed: 00:00:00.32
# Mc/sec: 739.58
//
Query:       gi|336254965|ref|YP_004598072.1|  [L=500]
Description: hypothetical protein Halxa_3583 [Halopiger xanaduensis SH-6]
Scores for complete 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-32  112.7   2.0    1.5e-18   67.7   0.3    3.5  3  DUF4397     Domain of unknown function (DUF4397)
  ------ inclusion threshold ------
      0.037   13.9   0.3      0.067   13.1   0.3    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> DUF4397  Domain of unknown function (DUF4397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.3   1.7e-22   1.5e-18       2      85 ..      50     128 ..      49     150 .. 0.87
   2 !   37.0   0.1   5.4e-13   4.9e-09       2      53 ..     226     278 ..     225     310 .. 0.87
   3 !    5.6   0.0     0.003        27      57      85 ..     327     355 ..     316     373 .. 0.83

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 1.7e-22
                           DUF4397   2 tvrvvhaspdapsvDvyvngkkvlknvaygdvtgylqvpaGqytielnpagnkikagttvallnvditleagteytv 78 
                                        +rv+h spdap vDvyvn++++l++vay+dv++yl++ +G+yt+++++ag+     +++++ +++i++ +g +yt+
  gi|336254965|ref|YP_004598072.1|  50 AIRVAHFSPDAPEVDVYVNDQQILTEVAYDDVSPYLEIVPGTYTLTITAAGD-----EEAVVYEQQINVGSG-YYTA 120
                                       59*********************************************88887.....234467777******.5*** PP

                           DUF4397  79 aavgsa.a 85 
                                       aa+g++ a
  gi|336254965|ref|YP_004598072.1| 121 AAIGELeA 128
                                       ****9852 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 5.4e-13
                           DUF4397   2 tvrvvhaspdapsvDvyvngkkv.lknvaygdvtgylqvpaGqytielnpagn 53 
                                       +vr+vhaspdap+v v v++ +v +++vay++ +gy+ v aG+ t++++ a +
  gi|336254965|ref|YP_004598072.1| 226 QVRLVHASPDAPNVAVAVDSGQVlFEDVAYTEPSGYVGVSAGDVTLDIYDAAD 278
                                       8******************66665************************65554 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.003
                           DUF4397  57 agttvallnvditleagteytvaavgsaa 85 
                                       ++++  +++vd+++  g+ yt++a+g ++
  gi|336254965|ref|YP_004598072.1| 327 TEEPEPVASVDVEVDRGQGYTIYAIGYLE 355
                                       56677789******************884 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   7.5e-06     0.067       2      24 ..       3      25 ..       2      27 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.5e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      lSRR+ +K+ ++++A+ al + +
  gi|336254965|ref|YP_004598072.1|  3 LSRRSTIKTIGVVGAGSALSNSV 25
                                      8******************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.26s 00:00:00.97 Elapsed: 00:00:00.41
# Mc/sec: 3622.34
//
Query:       gi|336254966|ref|YP_004598073.1|  [L=91]
Description: transcriptional regulator PadR family protein [Halopiger xanaduensis SH-6]
Scores for 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-13   50.1   0.2    2.4e-13   49.8   0.2    1.1  1  PadR             Transcriptional regulator PadR-like family
    9.6e-05   22.8   0.0    0.00012   22.5   0.0    1.2  1  HTH_27           Winged helix DNA-binding domain
    0.00015   21.7   0.0     0.0019   18.1   0.0    2.0  2  HTH_45           Winged helix-turn-helix
     0.0045   16.8   0.0     0.0048   16.7   0.0    1.3  1  DUF4364          Domain of unknown function (DUF4364)
     0.0047   16.7   0.0      0.007   16.2   0.0    1.2  1  DUF1495          Winged helix DNA-binding domain (DUF1495)
     0.0086   16.2   0.0      0.012   15.8   0.0    1.2  1  HTH_34           Winged helix DNA-binding domain
     0.0086   14.5   0.0     0.0096   14.3   0.0    1.1  1  DUF505           Protein of unknown function (DUF505)
  ------ inclusion threshold ------
      0.012   15.6   0.1      0.015   15.4   0.1    1.1  1  Replic_Relax     Replication-relaxation
      0.027   14.3   0.0      0.032   14.1   0.0    1.2  1  HxlR             HxlR-like helix-turn-helix
      0.071   13.5   0.0      0.071   13.5   0.0    1.2  1  Penicillinase_R  Penicillinase repressor


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 !   49.8   0.2   1.4e-16   2.4e-13       2      74 ..      12      79 ..      11      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 1.4e-16
                                      HHHH.CC.S-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  2 Lall.ee.qpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      L+++ ++ +p  G ei ++++++++    + +G+lYp+L++L +++lve+ + +    ++++yY+lT++Grr l+
  gi|336254966|ref|YP_004598073.1| 12 LYVIaGKdRP-SGQEILDDINRYIDQ--PVTHGRLYPNLDTLVEKELVEKGQLD----RRTNYYALTPKGRRVLE 79
                                      7777433255.8***********986..9**********************998....7*************998 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 !   22.5   0.0   6.8e-08   0.00012       4      68 .]       7      74 ..       4      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.8e-08
                            HTH_27  4 qqalvLhlir...hrrrrkkladlcgrlnvedshis.y.slkkLtekGLvertgdeadrrekrvrlTdkG 68
                                       q+ +L +i+   ++ ++ +l d+ ++ +   +h+  y +l+ L+ek+Lv  ++   drr+  ++lT+kG
  gi|336254966|ref|YP_004598073.1|  7 FQRDLLYVIAgkdRPSGQEILDDINRYIDQPVTHGRlYpNLDTLVEKELV--EKGQLDRRTNYYALTPKG 74
                                      566678889878788888888*************998549**********..444469***********9 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.15   2.8e+02      62      74 ..      23      35 ..       8      37 .. 0.79
   2 !   18.1   0.0   1.1e-06    0.0019      40      71 ..      47      83 ..      39      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.15
                            HTH_45 62 Glelleklkelee 74
                                      G+e+l++++++++
  gi|336254966|ref|YP_004598073.1| 23 GQEILDDINRYID 35
                                      9999999999865 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.1e-06
                            HTH_45 40 LdmLvekgli.....kkskekYvlTekGlelleklke 71
                                      Ld+Lvek+l+     + +++ Y lT kG+++le+ +e
  gi|336254966|ref|YP_004598073.1| 47 LDTLVEKELVekgqlDRRTNYYALTPKGRRVLEQRQE 83
                                      8899999998777768899*************99776 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.7e-06    0.0048      39      75 ..      46      83 ..      11      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.7e-06
                           DUF4364 39 alseLvesglieee.ekenktlykiTekGketlelfen 75
                                       l+ Lve++l+e+   ++ +++y++T+kG+++le+ ++
  gi|336254966|ref|YP_004598073.1| 46 NLDTLVEKELVEKGqLDRRTNYYALTPKGRRVLEQRQE 83
                                      5899********99667999*************98665 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 !   16.2   0.0   3.9e-06     0.007      52      88 ..      43      79 ..      38      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.9e-06
                           DUF1495 52 rynsessLielGLveeeeeseglklYklteeGieive 88
                                       y + + L+e+ Lve+ + ++ +++Y lt++G+++ e
  gi|336254966|ref|YP_004598073.1| 43 LYPNLDTLVEKELVEKGQLDRRTNYYALTPKGRRVLE 79
                                      5777789********9999***************987 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 !   15.8   0.0   6.5e-06     0.012      26      80 .]      38      89 ..      29      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.5e-06
                            HTH_34 26 atdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLksll 80
                                      +t g+L+ +l++L +++ +  +k+  ++ +   + +Tp+Gr   ++  +++++++
  gi|336254966|ref|YP_004598073.1| 38 VTHGRLYPNLDTLVEKELV--EKGQLDR-RTNYYALTPKGRRVLEQRQEWVDQYV 89
                                      699*************976..5887777.8889******************9986 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   5.3e-06    0.0096     368     405 ..      45      82 ..      22      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.3e-06
                            DUF505 368 eaLysLesfeLieseveekgkevyvlTeyGekvledqe 405
                                        +L +L  +eL+e+   +  +++y lT++G++vle+ +
  gi|336254966|ref|YP_004598073.1|  45 PNLDTLVEKELVEKGQLDRRTNYYALTPKGRRVLEQRQ 82 
                                       467888889999999877889**************765 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1   8.2e-06     0.015      16      73 ..      31      81 ..      27      90 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.2e-06
                      Replic_Relax 16 arllfashra.tarrrLarLrelgllsr..lrkrvggarggsepyvYaLtpkGarllaaqr 73
                                       r++ + ++  +++  L +L e++l+++  l++r    ++      YaLtpkG+r+l +qr
  gi|336254966|ref|YP_004598073.1| 31 NRYIDQPVTHgRLYPNLDTLVEKELVEKgqLDRR----TN-----YYALTPKGRRVL-EQR 81
                                      5666666666679999************433333....44.....6***********.343 PP

>> HxlR  HxlR-like helix-turn-helix
   #    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      21      88 ..      27      90 ..      12      91 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHSTT.S-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHHHHHHHHH CS
                              HxlR 21 fselkralpk.isqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkkwgeeyle 88
                                        +++r + + +++  L  +L  L +++l+e+  +++  +   Y lt+kGr    vl++ ++w+++y++
  gi|336254966|ref|YP_004598073.1| 27 LDDINRYIDQpVTHGRLYPNLDTLVEKELVEKGQLDRRTN--YYALTPKGRR---VLEQRQEWVDQYVD 90
                                      5677777764489999999*************99999887..8*******97...68899999999976 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     4e-05     0.071      42      84 ..      47      89 ..      11      91 .] 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                                      HHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXXXXXXXXX CS
                   Penicillinase_R 42 lrrLvkKgllsrekegrafiYsplvseeeavasavkqlldklf 84
                                      l  Lv+K+l+++ +  r++ Y++l+ + + v ++ ++ +d+++
  gi|336254966|ref|YP_004598073.1| 47 LDTLVEKELVEKGQLDRRTNYYALTPKGRRVLEQRQEWVDQYV 89
                                      778**********************999998888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 763.32
//
Query:       gi|336254967|ref|YP_004598074.1|  [L=184]
Description: NUDIX hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-11   43.0   0.5      6e-11   42.5   0.5    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 !   42.5   0.5   3.4e-15     6e-11       5     115 ..      47     156 ..      44     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 3.4e-15
                                       EEEEEEEETTSEEEEEEES....SSSTTTEESSEEECBTTS.HHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   5 avgvvllnekgevLlvrrs....kkpfpgWelPgGkvepgE.tpeeAArREleEEtGleaellellgrlhylapydg 76 
                                       +v+v+ + ++g v+ +++     ++  +  +lP G+ ep + ++e+AArREl+EEtG eae+le l    ++ p +g
  gi|336254967|ref|YP_004598074.1|  47 SVSVLPFTPDGDVVCIEEWrqavDRVNR--SLPVGGTEPEDdDLEAAARRELREETGHEAEELEPLV---TVEPANG 118
                                       799**************88444333333..599999999999***************9998888888...3444444 PP

                                       EEEEEEEEEEEEE...EEECSGCSSTSTTTEEEEEEEEHHHH CS
                             NUDIX  77 pygdeheilyvfl...eevegelepndenevsevrwvpleel 115
                                       +    ++++++f+   ++++ +++++  ne   v  + +++l
  gi|336254967|ref|YP_004598074.1| 119 I---ADSVVHFFVargCRPTADQQLD-HNESIRVTPLAFDDL 156
                                       4...5556666666688888888887.777555556666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1491.41
//
Query:       gi|336254968|ref|YP_004598075.1|  [L=378]
Description: hypothetical protein Halxa_3586 [Halopiger xanaduensis SH-6]
Scores for 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   17.2   0.2      0.024   14.8   0.0    2.3  2  Pentapeptide_4  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
       0.39   11.3   4.8        3.8    8.1   0.1    3.0  2  DUF5629         Family of unknown function (DUF5629)


Domain annotation for each model (and alignments):
>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.7e-06     0.024       2      71 ..      35     128 ..      33     133 .. 0.84
   2 ?   -2.6   0.0       0.7   6.3e+03      22      45 ..     239     262 ..     225     264 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-06
                    Pentapeptide_4   2 eftrcsfnncklsnvnFsearlrdcnFtecrl.......................snvnFdecnlsdvdfaevdlkr 55 
                                       ++++++     l+nv+ ++a++++ n ++ ++                         +n ++++ ++v ++++++  
  gi|336254968|ref|YP_004598075.1|  35 TLENVQVDVLELENVTVENATIEELNVEQLNAdaeqlqqelnasdnetaganetnATANETNATGESVTLSGIEIEQ 111
                                       66777777778888999999999999999999999999999999988888866544455****************** PP

                    Pentapeptide_4  56 asFsgcnlknvnfsd.k 71 
                                       ++F+++ +++ +f++ +
  gi|336254968|ref|YP_004598075.1| 112 LAFENVSFEELEFDGgE 128
                                       *************8655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.7
                    Pentapeptide_4  22 rlrdcnFtecrlsnvnFdecnlsd 45 
                                       ++ + ++++ + ++v+ d+ ++++
  gi|336254968|ref|YP_004598075.1| 239 EIDELTIEQFDVDEVVIDQMSIQS 262
                                       444555555555555555555554 PP

>> DUF5629  Family of unknown function (DUF5629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.6      0.01        93      13      47 ..      55      89 ..      41      99 .. 0.82
   2 ?    8.1   0.1   0.00043       3.8      13      45 ..     239     272 ..     233     277 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.01
                                      EETTEEESEEEE-HHHHHHHHHHHTTT------SE CS
                           DUF5629 13 eidglhawqfeldeelldqadaaaeadepfaseev 47
                                       i++l   q++ d e+l+q  +a++ + + a+e+ 
  gi|336254968|ref|YP_004598075.1| 55 TIEELNVEQLNADAEQLQQELNASDNETAGANETN 89
                                      68999999999999999999999999998888764 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00043
                                       EETTEEESEEEE-HHHHHHHHHHH.TTT------ CS
                           DUF5629  13 eidglhawqfeldeelldqadaaa.eadepfase 45 
                                       eid+l   qf++de ++dq++  + + +ep a+e
  gi|336254968|ref|YP_004598075.1| 239 EIDELTIEQFDVDEVVIDQMSIQSlQEGEPAANE 272
                                       8******************986541455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1422  (0.0793128); 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:                         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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2953.80
//
Query:       gi|336254969|ref|YP_004598076.1|  [L=432]
Description: hypothetical protein Halxa_3587 [Halopiger xanaduensis SH-6]
Scores for 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  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1379  (0.0769145); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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):               0  [number of targets reported over threshold]
# CPU time: 1.14u 0.34s 00:00:01.48 Elapsed: 00:00:00.45
# Mc/sec: 2912.95
//
Query:       gi|336254970|ref|YP_004598077.1|  [L=491]
Description: 7-cyano-7-deazaguanine tRNA-ribosyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-78  263.4   0.0    4.4e-78  262.9   0.0    1.2  1  TGT       Queuine tRNA-ribosyltransferase
     0.0006   20.1   0.2      0.049   14.0   0.0    2.5  2  TGT_C1    C1 domain of tRNA-guanine transglycosylase dimerisa


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 !  262.9   0.0   4.9e-82   4.4e-78       2     349 ..      13     340 ..      10     341 .. 0.95

  Alignments for each domain:
  == domain 1  score: 262.9 bits;  conditional E-value: 4.9e-82
                                       TEEEEEEEETTE..EEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S CS
                               TGT   2 gaRlGklelphg..tietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdk 76 
                                       g+R+G+l++p++  t+etPa++pv  ++++ +++p+ ++ee+ga+i+++n+y+++ +   +  a + glh++l++++
  gi|336254970|ref|YP_004598077.1|  13 GGRIGELTVPRAdvTVETPALLPV-INPNLDTISPRRMAEEFGAEILITNSYIIHGTDDVRERALEDGLHEVLDFPG 88 
                                       58*******995357*********.999***************************888888888899********** PP

                                       -EEEE-SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHH CS
                               TGT  77 piltdsggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlr 153
                                       +i+tdsg+fq   l           s++ G+ + +t ee++e+q+++gsDi +++d ++p++ +++r+e ++ +T +
  gi|336254970|ref|YP_004598077.1|  89 AIMTDSGSFQ---L-----------SEY-GE-IDVTTEEILEFQHRIGSDIGTPVDIPTPPDVDRERAEDELATTKE 149
                                       **********...4...........557.99.********************************************* PP

                                       HHHHHHHHH..SE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-E CS
                               TGT 154 wldrcleah..qa.lfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkpr 224
                                       +l+ +      ++ + ++vqG++y+dlree+ +++  + +d++++g+ +++++  +++++++vv+a+++ l +d p+
  gi|336254970|ref|YP_004598077.1| 150 RLEVAETVDtgDMlVTAPVQGSTYPDLREEAGRHADGTSLDVFPVGAvVPLMNdyRYDDMVDVVAAAKRGLGADAPV 226
                                       **999865578777*********************************7788887899******************** PP

                                       EETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHH CS
                               TGT 225 ylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhl 301
                                       +l+G+g+P++++ +va+G+D+fd+++++++ar++r+lt +g+ +l++ +y     p    CsC++C+++++  l+ l
  gi|336254970|ref|YP_004598077.1| 227 HLFGAGHPMMFALGVAMGCDLFDSAAYALYARDDRYLTVRGTRQLEDLEYL----P----CSCPVCTEHSPDDLRAL 295
                                       ***********************************************9999....9....***************** PP

                                       HHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                               TGT 302 lktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                           +      l+ HNlh+++e+++r+++aI++g++ e+ve++ar+++
  gi|336254970|ref|YP_004598077.1| 296 PDRAR---EEELAAHNLHVTFEEIRRVKQAIRAGNLLELVEQRARAHP 340
                                       98888...8999********************************9986 PP

>> TGT_C1  C1 domain of tRNA-guanine transglycosylase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   5.4e-06     0.049       5      31 ..     364     390 ..     361     396 .. 0.89
   2 ?    3.5   0.1      0.01        92      42      58 ..     417     433 ..     411     437 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-06
                            TGT_C1   5 ksaffkvseealkwpiverakeraekv 31 
                                       k aff vs e+ + p v r +er e++
  gi|336254970|ref|YP_004598077.1| 364 KGAFFHVSHESARRPEVLRHHERLERL 390
                                       68***********************96 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.01
                            TGT_C1  42 pifGeipkylslsypfa 58 
                                       p fG  p+ ls syp++
  gi|336254970|ref|YP_004598077.1| 417 PPFGPFPRALSKSYPLT 433
                                       88*************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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 0.22s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3956.17
//
Query:       gi|336254971|ref|YP_004598078.1|  [L=112]
Description: hypothetical protein Halxa_3589 [Halopiger xanaduensis SH-6]
Scores for complete 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   85.9   0.0    2.6e-24   85.3   0.0    1.3  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.0   1.5e-28   2.6e-24       2      73 ..      14      84 ..      14      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 1.5e-28
                            HalOD1  2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieV 73
                                      ees+s++V++avaa +gv+ptel+pLy++iDpdALd+Lf+++++g + + g+vsF y+g++++V  d   e+
  gi|336254971|ref|YP_004598078.1| 14 EESVSISVITAVAARRGVEPTELPPLYEWIDPDALDSLFEPTRTG-GPRGGRVSFVYDGHDIVVAFDEGLEI 84
                                      689**************************************5555.67789*************87765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 931.35
//
Query:       gi|336254972|ref|YP_004598079.1|  [L=157]
Description: AsnC family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-14   51.9   0.1    1.6e-13   50.0   0.1    1.8  2  HTH_24          Winged helix-turn-helix DNA-binding
      1e-13   50.9   3.2    1.5e-13   50.4   2.0    1.9  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    2.8e-07   30.5   0.1    1.3e-06   28.4   0.0    2.0  2  HTH_20          Helix-turn-helix domain
    4.2e-06   26.6   0.0    7.9e-06   25.7   0.0    1.4  1  HTH_11          HTH domain
    2.3e-05   24.2   0.1    0.00037   20.3   0.0    2.2  2  MarR_2          MarR family
    4.6e-05   23.5   0.1    0.00011   22.3   0.1    1.6  1  HTH_28          Helix-turn-helix domain
    4.7e-05   22.8   0.3    0.00013   21.5   0.3    1.7  1  HTH_CodY        CodY helix-turn-helix domain
    0.00031   21.2   0.2     0.0011   19.5   0.1    1.9  2  HTH_27          Winged helix DNA-binding domain
     0.0007   19.5   0.0     0.0038   17.2   0.0    2.0  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.001   18.8   0.1     0.0019   18.0   0.1    1.4  1  HTH_23          Homeodomain-like domain
     0.0026   17.5   0.1     0.0047   16.7   0.1    1.4  1  HTH_10          HTH DNA binding domain
     0.0037   16.7   0.2     0.0081   15.6   0.2    1.6  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
     0.0081   15.9   0.1      0.018   14.7   0.1    1.6  1  HTH_DeoR        DeoR-like helix-turn-helix domain
     0.0098   15.7   0.2      0.032   14.0   0.2    1.9  1  HTH_30          PucR C-terminal helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.037   13.9   0.0    1.8  2  MarR            MarR family
      0.012   15.3   0.1      0.031   14.0   0.1    1.6  1  Sigma70_r4_2    Sigma-70, region 4
      0.018   15.4   0.0      0.062   13.7   0.0    1.8  1  Rrf2            Transcriptional regulator
      0.023   14.9   0.0      0.066   13.4   0.0    1.7  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.023   14.6   0.0      0.039   13.9   0.0    1.4  1  HTH_36          Helix-turn-helix domain
       0.03   14.4   0.0        5.5    7.2   0.0    2.3  2  TxDE            Toxoflavin-degrading enzyme
      0.033   13.8   1.9      0.057   13.1   0.1    2.2  3  GntR            Bacterial regulatory proteins, gntR family
       0.04   13.8   0.0      0.072   13.0   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
       0.05   13.8   0.1        0.9    9.8   0.1    2.2  2  PaaX            PaaX-like protein
       0.05   13.5   0.0       0.13   12.1   0.0    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.053   13.6   0.1       0.98    9.6   0.0    2.1  2  Nkap_C          NF-kappa-B-activating protein C-terminal doma
      0.074   12.6   0.1        1.3    8.6   0.0    2.2  2  HTH_47          winged helix-turn-helix
      0.098   12.4   0.0       0.19   11.5   0.0    1.5  1  LexA_DNA_bind   LexA DNA binding domain
       0.11   12.3   0.1       0.26   11.1   0.1    1.6  1  HTH_IclR        IclR helix-turn-helix domain
       0.13   12.0   0.2          5    6.9   0.0    2.9  3  Get5_C          Get5 C-terminal domain
       0.17   11.4   0.0       0.29   10.7   0.0    1.3  1  DDRGK           DDRGK domain


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 !   50.0   0.1   2.6e-16   1.6e-13       1      47 [.       5      52 ..       5      53 .. 0.99
   2 ?   -0.8   0.0       1.9   1.1e+03      35      46 ..     120     131 ..     119     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 2.6e-16
                            HTH_24  1 ldetdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ld++dr IL  Lq+++r ++ +++A ++g++ +tv+ r++rLee+G+I
  gi|336254972|ref|YP_004598079.1|  5 LDDIDRGILHRLQDDARhTTAADIAGEVGVTANTVRNRIRRLEEAGVI 52
                                      79*********************************************9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.9
                            HTH_24  35 nrrlkrLeeeGl 46 
                                       ++ + rL+++G+
  gi|336254972|ref|YP_004598079.1| 120 TAIVSRLQRAGI 131
                                       67899***9997 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 !   50.4   2.0   2.4e-16   1.5e-13       1      42 []       5      47 ..       5      47 .. 0.94
   2 ?   -2.2   0.0       6.3   3.7e+03       7      15 ..     121     129 ..     120     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2.4e-16
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaR.isyaeLAervGlSestvlrRvrrLe 42
                                      LD+iDr IL+ Lq daR ++ a++A +vG++++tv++R+rrLe
  gi|336254972|ref|YP_004598079.1|  5 LDDIDRGILHRLQDDARhTTAADIAGEVGVTANTVRNRIRRLE 47
                                      8**************99456789*******************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.3
                     HTH_AsnC-type   7 kILeaLqed 15 
                                       +I++ Lq+ 
  gi|336254972|ref|YP_004598079.1| 121 AIVSRLQRA 129
                                       688888886 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   2.2e-09   1.3e-06      13      56 ..      10      54 ..       5      57 .. 0.92
   2 ?   -0.8   0.0       2.7   1.6e+03      21      35 ..      82      96 ..      70     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.2e-09
                                      HHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 13 rrilraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      r+il  L  +a+  ta+++a +++++ nt+++++r Leeag + +
  gi|336254972|ref|YP_004598079.1| 10 RGILHRLqDDARHTTAADIAGEVGVTANTVRNRIRRLEEAGVIAG 54
                                      89*****8889999***************************9975 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.7
                                      TCTTB-HHHHHHHHT CS
                            HTH_20 21 raegltaselaerld 35
                                      +++++ta e++  ++
  gi|336254972|ref|YP_004598079.1| 82 GEAAATALEIDGVVG 96
                                      688999999986665 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.3e-08   7.9e-06       5      44 ..      12      51 ..      10      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.3e-08
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      il++L +   + +++++A e +v+  tvr++I++Lee+gv
  gi|336254972|ref|YP_004598079.1| 12 ILHRLQDDARHTTAADIAGEVGVTANTVRNRIRRLEEAGV 51
                                      89999777777****************************4 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   6.2e-07   0.00037       8      51 ..      10      52 ..       3      69 .. 0.83
   2 ?    1.6   0.0      0.42   2.5e+02      38      49 ..     119     130 ..     115     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.2e-07
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      + +L+ L +  +   t++++a + g++  +v ++++rL++aG +
  gi|336254972|ref|YP_004598079.1| 10 RGILHRLQDDARH-TTAADIAGEVGVTANTVRNRIRRLEEAGVI 52
                                      6678888888864.5***************************99 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHTT CS
                            MarR_2  38 vsrilkrLvaaG 49 
                                       ++ i+ rL++aG
  gi|336254972|ref|YP_004598079.1| 119 ITAIVSRLQRAG 130
                                       899********9 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   1.8e-07   0.00011      11      46 ..      21      57 ..      12      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.8e-07
                            HTH_28 11 aGhsvreaArelgisrrtvyrWikryeegG.iagLvp 46
                                      ++ +++++A e+g++  tv+  i+r+ee G iag vp
  gi|336254972|ref|YP_004598079.1| 21 RHTTAADIAGEVGVTANTVRNRIRRLEEAGvIAGYVP 57
                                      4569**************************7799988 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 !   21.5   0.3   2.2e-07   0.00013       6      34 ..      24      52 ..      20      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.2e-07
                          HTH_CodY  6 taskiaDriGitrsvivnaLrkLesaGii 34
                                      ta+ ia ++G+t   + n +r+Le aG+i
  gi|336254972|ref|YP_004598079.1| 24 TAADIAGEVGVTANTVRNRIRRLEEAGVI 52
                                      89**************************9 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 !   19.5   0.1   1.8e-06    0.0011       5      48 ..       9      52 ..       5      68 .. 0.88
   2 ?   -1.1   0.0       4.7   2.8e+03      17      30 ..     115     128 ..     109     135 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.8e-06
                            HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                      ++ +Lh ++   r  ++ad++g + v++ ++ + +++L+e+G++
  gi|336254972|ref|YP_004598079.1|  9 DRGILHRLQDDARHTTAADIAGEVGVTANTVRNRIRRLEEAGVI 52
                                      7789*****66666666************************988 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.7
                            HTH_27  17 rrkkladlcgrlnv 30 
                                       +++++++++ rl++
  gi|336254972|ref|YP_004598079.1| 115 DTDEITAIVSRLQR 128
                                       45566666666554 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   6.4e-06    0.0038      21      52 ..      22      53 ..      10      63 .. 0.82
   2 ?   -0.3   0.0       1.8   1.1e+03      37      50 ..     118     131 ..     110     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.4e-06
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis 52
                                      + t +++A  +G+t  tv   +++L+++g+i 
  gi|336254972|ref|YP_004598079.1| 22 HTTAADIAGEVGVTANTVRNRIRRLEEAGVIA 53
                                      57899**************************8 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHTTS CS
                         HTH_Crp_2  37 tvsrilseLkregl 50 
                                        ++ i s+L+r+g+
  gi|336254972|ref|YP_004598079.1| 118 EITAIVSRLQRAGI 131
                                       57889999**9997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   3.1e-06    0.0019      18      46 ..      23      51 ..      11      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.1e-06
                            HTH_23 18 lsvreIAreLgvsrrTvyrwlkryreeGl 46
                                       + ++IA e gv+ +Tv++ ++r +e G+
  gi|336254972|ref|YP_004598079.1| 23 TTAADIAGEVGVTANTVRNRIRRLEEAGV 51
                                      57899******************999994 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   7.9e-06    0.0047      19      49 ..      18      48 ..      17      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.9e-06
                            HTH_10 19 dyPRrvtlkeLAkelGIskstlsehLrkaes 49
                                      d  R +t++++A e G++++t+ +++r+ e+
  gi|336254972|ref|YP_004598079.1| 18 DDARHTTAADIAGEVGVTANTVRNRIRRLEE 48
                                      6789***********************9875 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 !   15.6   0.2   1.4e-05    0.0081      27      51 ..      19      46 ..       7      47 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                      HTH_Tnp_ISL3 27 s...rsvkavArqlgvSwtTVwrildry 51
                                      +    + +++A ++gv+++TV+++++r+
  gi|336254972|ref|YP_004598079.1| 19 DarhTTAADIAGEVGVTANTVRNRIRRL 46
                                      4444599******************996 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 !   14.7   0.1   3.1e-05     0.018       5      44 ..      12      52 ..       9      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                          HTH_DeoR  5 ilellkqq.gklsveelvellgvSeaTiRRDLneLeeqgll 44
                                      il+ l+++ ++ +  +++ + gv+ +T+R+ ++ Lee+g++
  gi|336254972|ref|YP_004598079.1| 12 ILHRLQDDaRHTTAADIAGEVGVTANTVRNRIRRLEEAGVI 52
                                      8888887525667789***********************97 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 !   14.0   0.2   5.4e-05     0.032      16      38 ..      26      48 ..      20      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-05
                                      HHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_30 16 satAkaLhvHrnTlryRLrriee 38
                                      ++ A + +v  nT+r+R+rr+ee
  gi|336254972|ref|YP_004598079.1| 26 ADIAGEVGVTANTVRNRIRRLEE 48
                                      678899999*************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.3e-05     0.037       8      47 ..      12      52 ..       9      54 .. 0.84
   2 ?   -2.4   0.0         8   4.8e+03      34      45 ..     119     130 ..     118     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.3e-05
                                      HHHHHHHSTTEEHH.HHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  8 iLrilyeqgplsvs.eLakklgvskstvtrvldrLekkGli 47
                                      iL+ l +   ++ + ++a  +gv+  tv + ++rLe++G i
  gi|336254972|ref|YP_004598079.1| 12 ILHRLQDDARHTTAaDIAGEVGVTANTVRNRIRRLEEAGVI 52
                                      566666666666556************************88 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8
                                       HHHHHHHHHHTT CS
                              MarR  34 vtrvldrLekkG 45 
                                       +t ++ rL ++G
  gi|336254972|ref|YP_004598079.1| 119 ITAIVSRLQRAG 130
                                       688888888887 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 ?   14.0   0.1   5.1e-05     0.031      28      49 ..      24      45 ..      21      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.1e-05
                                      -HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 28 sykEIAellgisegtVksrlsR 49
                                      + ++IA + g++ +tV++r++R
  gi|336254972|ref|YP_004598079.1| 24 TAADIAGEVGVTANTVRNRIRR 45
                                      669*****************99 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0    0.0001     0.062      20      56 ..      17      53 ..      12      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.0001
                                      SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      +++ ++ ++++ia ++++ ++ ++  +++L++ag++ 
  gi|336254972|ref|YP_004598079.1| 17 QDDARHTTAADIAGEVGVTANTVRNRIRRLEEAGVIA 53
                                      5666779***************************996 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 ?   13.4   0.0   0.00011     0.066      15      51 ..      15      51 ..      12      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                                      HHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress 15 tlseekkvvktkdlaerLnvspssVsemlkkLekdGy 51
                                      +l+++    + +d+a + +v + +V   +++Le++G 
  gi|336254972|ref|YP_004598079.1| 15 RLQDDARHTTAADIAGEVGVTANTVRNRIRRLEEAGV 51
                                      78899999999***********************995 PP

>> HTH_36  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   6.5e-05     0.039      27      55 .]      24      52 ..      11      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      + +++a   g+  nTv++ i+ Le++G i
  gi|336254972|ref|YP_004598079.1| 24 TAADIAGEVGVTANTVRNRIRRLEEAGVI 52
                                      5789**********************976 PP

>> TxDE  Toxoflavin-degrading enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0092       5.5       2      23 ..      30      51 ..      29      58 .. 0.94
   2 ?    5.0   0.0     0.044        26       8      32 ..     116     140 ..     112     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0092
                              TxDE  2 SEiglttedvksvgeqLeeigI 23
                                      +E+g+t + v +  ++Lee+g+
  gi|336254972|ref|YP_004598079.1| 30 GEVGVTANTVRNRIRRLEEAGV 51
                                      7*******************98 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.044
                              TxDE   8 tedvksvgeqLeeigIplrdneeie 32 
                                       t+++++++ +L+ +gI + ++e ++
  gi|336254972|ref|YP_004598079.1| 116 TDEITAIVSRLQRAGIDVGEEELLK 140
                                       8999************999888775 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.5e-05     0.057      29      54 ..      27      52 ..      24      53 .. 0.92
   2 ?   -1.9   0.0       4.4   2.6e+03      44      57 ..      85      98 ..      84      99 .. 0.79
   3 ?   -2.2   0.0       5.6   3.3e+03      52      63 ..     121     132 ..     118     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.5e-05
                                      HHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 29 eLaaefgVsrttvReALrrLeaeglv 54
                                      ++a e gV+++tvR  +rrLe++g++
  gi|336254972|ref|YP_004598079.1| 27 DIAGEVGVTANTVRNRIRRLEEAGVI 52
                                      6999*******************987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.4
                                      HHHHHHHTTSEEEE CS
                              GntR 44 ALrrLeaeglverr 57
                                      A   Le +g+v +r
  gi|336254972|ref|YP_004598079.1| 85 AATALEIDGVVGVR 98
                                      55789999999886 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.6
                                       TSEEEETTCEEE CS
                              GntR  52 glverrqgrGtf 63 
                                        +v r q+ G+ 
  gi|336254972|ref|YP_004598079.1| 121 AIVSRLQRAGID 132
                                       578888888875 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 ?   13.0   0.0   0.00012     0.072       7      45 ..      12      52 ..      10      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                      HHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  7 ILklLae..gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      IL+ L++  + +++ ++a e+g++  tv+   ++L+eaG++
  gi|336254972|ref|YP_004598079.1| 12 ILHRLQDdaRHTTAADIAGEVGVTANTVRNRIRRLEEAGVI 52
                                      788888887889***************************97 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0015       0.9      29      54 ..      28      53 ..      18      56 .. 0.89
   2 ?    1.7   0.0      0.49   2.9e+02      41      64 ..     120     143 ..     111     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0015
                              PaaX 29 llaelGiseslvRaalsRlakaGwlv 54
                                      +  e+G+ +++vR  + Rl++aG ++
  gi|336254972|ref|YP_004598079.1| 28 IAGEVGVTANTVRNRIRRLEEAGVIA 53
                                      6679*******************986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.49
                              PaaX  41 RaalsRlakaGwlvrekegrrsfY 64 
                                        a +sRl++aG  v+e+e  ++ Y
  gi|336254972|ref|YP_004598079.1| 120 TAIVSRLQRAGIDVGEEELLKAEY 143
                                       5679*******8777777667766 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022      0.13      23      52 ..      23      52 ..      16      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                                      CHHCHHCCCTTSSCHCHHHHHHHHHHCTSE CS
                              TrmB 23 atadeiaeelgvprskvYevLrsLedkGlV 52
                                       ta +ia e+gv  ++v + +r+Le++G++
  gi|336254972|ref|YP_004598079.1| 23 TTAADIAGEVGVTANTVRNRIRRLEEAGVI 52
                                      69**************************97 PP

>> Nkap_C  NF-kappa-B-activating protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.39   2.3e+02      30      48 ..      30      52 ..      26      58 .. 0.71
   2 ?    9.6   0.0    0.0016      0.98      15      63 ..      67     115 ..      62     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.39
                            Nkap_C 30 GevGltse....eiekfekaGyv 48
                                      GevG+t++     i+++e+aG +
  gi|336254972|ref|YP_004598079.1| 30 GEVGVTANtvrnRIRRLEEAGVI 52
                                      99999986222257788888854 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0016
                            Nkap_C  15 alaqyvqegkRiPrRGevGltseeiekfekaGyvmsGsrhkrmnavrlr 63 
                                       ++   vq    i  RGe   t+ ei+ +  +  +m+G r+ r++ v   
  gi|336254972|ref|YP_004598079.1|  67 SMHMVVQCTVPIHERGEAAATALEIDGVVGVRELMTGDRNLRIDLVAAD 115
                                       6778888899999******************************988754 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0022       1.3      51      77 ..      27      53 ..      19      54 .. 0.93
   2 ?    1.7   0.0      0.31   1.9e+02      57      75 ..     113     131 ..     108     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0022
                                      HHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 51 diAeriglpfdrvaaiaraLaeaglla 77
                                      diA ++g+ +++v + +r+L+eag++a
  gi|336254972|ref|YP_004598079.1| 27 DIAGEVGVTANTVRNRIRRLEEAGVIA 53
                                      9************************96 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.31
                                       T--HHHHHHHHHHHHHTT- CS
                            HTH_47  57 glpfdrvaaiaraLaeagl 75 
                                        ++ d+++ai+ +L++ag+
  gi|336254972|ref|YP_004598079.1| 113 AADTDEITAIVSRLQRAGI 131
                                       57899***********997 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 ?   11.5   0.0   0.00032      0.19      27      56 ..      24      52 ..      11      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                                      -HHHHHHHHTS-.HHHHHHHHHHHHHTTSE CS
                     LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyi 56
                                      + ++ia ++g++ +++v ++ ++Le  G+i
  gi|336254972|ref|YP_004598079.1| 24 TAADIAGEVGVT-ANTVRNRIRRLEEAGVI 52
                                      7899********.***************99 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 ?   11.1   0.1   0.00044      0.26       8      47 ..      12      51 ..      10      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00044
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGy 47
                                      iL  l   ++  t +++A + g++  tv++ ++ L+e G 
  gi|336254972|ref|YP_004598079.1| 12 ILHRLQDDARHTTAADIAGEVGVTANTVRNRIRRLEEAGV 51
                                      788888999999*************************996 PP

>> Get5_C  Get5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.6   1.6e+03      25      31 ..      11      17 ..       6      18 .. 0.85
   2 ?    6.9   0.0    0.0084         5      20      32 ..     115     128 ..     110     129 .. 0.86
   3 ?    1.0   0.0      0.59   3.5e+02      10      20 ..     136     146 ..     136     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.6
                            Get5_C 25 avleRLq 31
                                       +l RLq
  gi|336254972|ref|YP_004598079.1| 11 GILHRLQ 17
                                      599***9 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0084
                            Get5_C  20 d.aearavleRLqK 32 
                                       d  e++a++ RLq+
  gi|336254972|ref|YP_004598079.1| 115 DtDEITAIVSRLQR 128
                                       5589*********8 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.59
                            Get5_C  10 eaLLknkfknd 20 
                                       e LLk+++  +
  gi|336254972|ref|YP_004598079.1| 136 EELLKAEYRQP 146
                                       78*****9875 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00048      0.29     115     145 ..      24      54 ..      18      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00048
                                       -HHHHHHHH-S-HHHHHHHHHHHHHHSSS-E CS
                             DDRGK 115 lleelavkfklktqevierikeLeeqgsltG 145
                                       +  ++a + +++++ v++ri+ Lee g + G
  gi|336254972|ref|YP_004598079.1|  24 TAADIAGEVGVTANTVRNRIRRLEEAGVIAG 54 
                                       56799************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1134.57
//
Query:       gi|336254973|ref|YP_004598080.1|  [L=119]
Description: hypothetical protein Halxa_3591 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.046   13.9   1.5      0.069   13.3   1.5    1.2  1  HemY_N    HemY protein N-terminus
      0.092   13.1   2.6       0.82   10.1   2.6    2.1  1  NfeD      NfeD-like C-terminal, partner-binding


Domain annotation for each model (and alignments):
>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.5   7.7e-06     0.069      23      62 ..       3      42 ..       1      47 [. 0.49

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.7e-06
                            HemY_N 23 lvllfvllylllrllrlllrlparvrrwrrrrrerkarea 62
                                      l ++++++ l+++l+ +++ l +   rw +rr+ ++ ++ 
  gi|336254973|ref|YP_004598080.1|  3 LGVVAAVVALVVSLVVATWLLLRIGGRWADRRKSERRHRE 42
                                      4455555555555555555555555555555555444443 PP

>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.6   9.2e-05      0.82       2      83 ..      11      85 ..       6      86 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.2e-05
                                      XXXXXX.XXXXXXXXXS---SSS--S.S---GGTTSEEEEEE-BS-EEEEETTEEEEEE-..SSB-TT-EEEEEEE-SS CS
                              NfeD  2 favvsv.lllvllrplllkklkkkekktnaealiGkegvvledigtGrvkvdGeeWsarse.geiekgerVrVveveGl 78
                                      ++vvs+ ++++ll ++  +  ++++  ++      +e++  e+     v++++e+  a+ e  e  +g+r  V ++eG 
  gi|336254973|ref|YP_004598080.1| 11 ALVVSLvVATWLLLRIGGRWADRRK--SE---RRHREAQEREP----PVEIGDERAVAVQEfTEHHSGKRHAVCKIEGF 80
                                      3333333444444444444332211..22...22455555554....48999999999998455999999999999999 PP

                                      SEEEE CS
                              NfeD 79 tliVe 83
                                       ++Ve
  gi|336254973|ref|YP_004598080.1| 81 VVFVE 85
                                      99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1056  (0.058899); expected 358.6 (0.02)
Passed bias filter:                      815  (0.0454571); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 979.15
//
Query:       gi|336254974|ref|YP_004598081.1|  [L=583]
Description: tRNA-guanine transglycosylase [Halopiger xanaduensis SH-6]
Scores for 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-60  202.8   0.6    3.8e-60  202.2   0.6    1.3  1  DUF5591   Domain of unknown function (DUF5591)
    1.2e-22   79.8   0.0    3.7e-22   78.2   0.0    1.9  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    1.8e-13   50.4   0.1      5e-13   48.9   0.1    1.8  2  TGT       Queuine tRNA-ribosyltransferase
    2.6e-12   46.5   0.8    7.4e-12   45.1   0.6    1.8  2  PUA       PUA domain


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 !  202.2   0.6   8.4e-64   3.8e-60       1     154 []     283     432 ..     283     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 202.2 bits;  conditional E-value: 8.4e-64
                                       X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT------- CS
                           DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqY 77 
                                       ++rf++rv++rY++++ +++lvL+Pcsa+kPyses+shr+f++ i++r   +h v++tsP+GvvP+ele++YPa++Y
  gi|336254974|ref|YP_004598081.1| 283 IQRFADRVTTRYRNRF-DNPLVLVPCSATKPYSESQSHRQFHDVIQWR---AHLVSMTSPIGVVPQELETTYPAQHY 355
                                       89*************9.*******************************...9************************* PP

                                       ---------HHHHHHHHHHHHHHHHHHT-SEEEE---TH.HHHHHHHHHTT-SSEEEE--.SS-TTSHHHHHHHHHH CS
                           DUF5591  78 diavtgewseeeiefvaellakylektkyekviahleee.yreiveevaeelgleiiytvvedkptskeslknLkea 153
                                       d++vtg+wse+e++fv+e+l++yle+++y+++iah+++e yr+ive+v++el+l+i+ytv  ++pt++esl+nL+ea
  gi|336254974|ref|YP_004598081.1| 356 DTVVTGRWSEDEKQFVSEVLRRYLERNEYPEIIAHVPDEgYRDIVERVEDELELDITYTV-AEHPTDDESLANLSEA 431
                                       *************************************999********************.99************99 PP

                                       H CS
                           DUF5591 154 L 154
                                       L
  gi|336254974|ref|YP_004598081.1| 432 L 432
                                       7 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 !   78.2   0.0   8.3e-26   3.7e-22       1      70 [.     446     513 ..     446     513 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 8.3e-26
                            TGT_C2   1 nrlraiadYqFGagagdaLfpedvtitrsatgrirqvlv...dgerlatlraqdgrltLsleGarrlheslpp 70 
                                       n++raiadY++G+gagd+Lf+   +i+  +t r+++++v   ++++lat+++q+g+l+++leGarr+ es++p
  gi|336254974|ref|YP_004598081.1| 446 NTVRAIADYLLGDGAGDDLFE---NIQ--TTSRYPKIQVrdsEDTQLATMVPQYGTLSFTLEGARRWLESDAP 513
                                       79******************5...599..**********9989***************************875 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       0.8   3.6e+03       2      20 ..      13      30 ..      11      31 .. 0.82
   2 !   48.9   0.1   1.1e-16     5e-13     181     343 ..      92     236 ..      84     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.8
                                      TEEEEEEEETTEEEEESEE CS
                               TGT  2 gaRlGklelphgtietPaf 20
                                      +aR+G+l+l+++  +tPa+
  gi|336254974|ref|YP_004598081.1| 13 AARVGELRLAES-HTTPAL 30
                                      39*******985.899987 PP

  == domain 2  score: 48.9 bits;  conditional E-value: 1.1e-16
                                       HHHHHHHH--SEEEE-SSS.SSSHHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHH CS
                               TGT 181 saeelakrdfdgyaigGls.vgeekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtar 256
                                       s +++ + ++d ya++ ++  +   + l+e v +v+e++p+d   ++ Gv tP +++ +  +GvD+fd +++   + 
  gi|336254974|ref|YP_004598081.1|  92 SSDHVEDHGTDAYAVSDVQsAMGHGAALVEAVVNVREEIPTDTALLFSGVTTPRNVALLAYAGVDLFDATAAVVKGT 168
                                       67889999999****9976455578999************************************************* PP

                                       TTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               TGT 257 ngraltsegelnlknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiHNlhyylelfkriReaIk 333
                                       +gr+lt++  + l++     d  p    CsC++C++      ++ +  +       +++HN   +  +++ +R+ I+
  gi|336254974|ref|YP_004598081.1| 169 EGRYLTTDEAYFLED----LDELP----CSCPACQK-----PREEFTRE------DCAEHNRNALESELAIVRRRIR 226
                                       ******999888873....34457....******92.....22223222......4788****************** PP

                                       TT-HHHHHHH CS
                               TGT 334 egtfeefvee 343
                                       +g++ ++ve 
  gi|336254974|ref|YP_004598081.1| 227 DGRLRDYVEG 236
                                       ***9999985 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.6   1.2e+04      22      38 ..     192     208 ..     191     225 .. 0.68
   2 !   45.1   0.6   1.7e-15   7.4e-12      18      73 ..     527     580 ..     516     580 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.6
                                       GGEEEEETT--TTSEEE CS
                               PUA  22 pGvvevegdfeegdvVa 38 
                                       p   + +++f + d+ +
  gi|336254974|ref|YP_004598081.1| 192 PACQKPREEFTREDCAE 208
                                       55567889999999865 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 1.7e-15
                                       EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA  18 sLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                       s+lapGvv++++d++ gd+V++  +  ++ a+G+a++ + e+a+ ++g+++e+++v
  gi|336254974|ref|YP_004598081.1| 527 SVLAPGVVDADEDIRVGDEVVVEGP--KAFAIGRAEMFGREMAESTRGVAAEVRHV 580
                                       9*********************999..***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 4384.20
//
Query:       gi|336254975|ref|YP_004598082.1|  [L=67]
Description: hypothetical protein Halxa_3593 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.16   11.8   0.0       0.17   11.8   0.0    1.1  1  PRP21_like_P  Pre-mRNA splicing factor PRP21 like protein


Domain annotation for each model (and alignments):
>> PRP21_like_P  Pre-mRNA splicing factor PRP21 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.2e-06      0.17     149     175 ..      34      60 ..       4      63 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.2e-06
                      PRP21_like_P 149 katkekkka....kcpitgeliPedeleeHm 175
                                       ++++         +c ++g  +P+ ++ eH+
  gi|336254975|ref|YP_004598082.1|  34 SRQE----GqgrrECDVCGADVPAASYHEHL 60 
                                       2222....133559****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 555.85
//
Query:       gi|336254976|ref|YP_004598083.1|  [L=136]
Description: DtxR family iron (metal) dependent repressor [Halopiger xanaduensis SH-6]
Scores for 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   49.9   0.1    7.1e-13   48.6   0.0    1.7  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    6.4e-07   29.2   0.0    1.4e-06   28.1   0.0    1.6  1  MarR_2          MarR family
    9.1e-05   22.5   0.2    0.00014   21.8   0.2    1.3  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
     0.0012   18.6   0.1     0.0028   17.4   0.1    1.6  1  HTH_IclR        IclR helix-turn-helix domain
     0.0026   17.6   0.0     0.0048   16.8   0.0    1.4  1  MarR            MarR family
  ------ inclusion threshold ------
      0.012   15.6   0.6        0.2   11.6   0.1    2.5  2  HTH_12          Ribonuclease R winged-helix domain
      0.023   15.2   0.0      0.043   14.3   0.0    1.5  1  HTH_27          Winged helix DNA-binding domain
      0.033   14.1   0.2       0.16   11.9   0.0    2.3  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.034   13.7   0.0      0.078   12.6   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.047   13.7   0.0        1.1    9.3   0.0    2.2  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.058   13.2   0.0        0.1   12.4   0.0    1.4  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 !   48.6   0.0   4.3e-16   7.1e-13       8      60 .]       6      59 ..       1      59 [. 0.95
   2 ?   -2.6   0.0       4.1   6.8e+03      19      32 ..     102     115 ..      97     118 .. 0.67

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 4.3e-16
                                      HHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  8 dYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      +YL ++Y++s   +++v++ ++a +L+ sp+  +eml++Le  G++eye+y g+
  gi|336254976|ref|YP_004598083.1|  6 QYLLVVYRASRnAGEPVSPGRVADELDRSPAATTEMLQRLETRGLLEYEPYEGA 59
                                      7**********9****************************************97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
                                       HHSSB-HHHHHHHH CS
                    Fe_dep_repress  19 ekkvvktkdlaerL 32 
                                       + ++  t ++ae L
  gi|336254976|ref|YP_004598083.1| 102 SVSPLVTERVAETL 115
                                       55666677777766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   8.5e-10   1.4e-06      15      56 ..      15      56 ..       2      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 8.5e-10
                                      HCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 15 grrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                       r+ g+++++g +a++l+ s++a++ +l+rL+ +GL+e++p 
  gi|336254976|ref|YP_004598083.1| 15 SRNAGEPVSPGRVADELDRSPAATTEMLQRLETRGLLEYEPY 56
                                      34455589******************************9985 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 !   21.8   0.2   8.8e-08   0.00014       1      56 [.      62     115 ..      62     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.8e-08
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHC CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldell 56 
                                       T +Gre A +l++ + +l +f+ +vl++  e+ + eA +l   +s+ + er+ e l
  gi|336254976|ref|YP_004598083.1|  62 TAEGRETAAELYETYVVLSQFFREVLDL--EDPEAEALELAGSVSPLVTERVAETL 115
                                       99***********************998..66667899************999876 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 !   17.4   0.1   1.7e-06    0.0028      15      52 .]      18      55 ..      16      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.7e-06
                                      TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                      a+++++   +A++++ +++++  +Lq L+ +G++e+++
  gi|336254976|ref|YP_004598083.1| 18 AGEPVSPGRVADELDRSPAATTEMLQRLETRGLLEYEP 55
                                      67889999***************************975 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     3e-06    0.0048      23      48 ..      27      52 ..      17      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3e-06
                                      HHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 23 LakklgvskstvtrvldrLekkGlie 48
                                       a+ l  s++++t++l rLe +Gl+e
  gi|336254976|ref|YP_004598083.1| 27 VADELDRSPAATTEMLQRLETRGLLE 52
                                      588999******************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 ?   11.6   0.1   0.00012       0.2      10      63 ..      18      66 ..      13      68 .. 0.83
   2 ?    1.0   0.0      0.25   4.1e+02       8      33 ..     100     127 ..      98     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                            HTH_12 10 sdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGl 63
                                      + +p++ +++a+eL     +         L+ le rgl +   y g++lt  G 
  gi|336254976|ref|YP_004598083.1| 18 AGEPVSPGRVADELDRSPAAT-----TEMLQRLETRGLLEYEPYEGATLTAEGR 66
                                      678999999999997765444.....4579********************9986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.25
                            HTH_12   8 aesdkpigakeiaeeLkkr..gydiger 33 
                                       a s  p+  +++ae L +r   + i  +
  gi|336254976|ref|YP_004598083.1| 100 AGSVSPLVTERVAETLLERdaAESIDGE 127
                                       55668999999**999999444556555 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 ?   14.3   0.0   2.7e-05     0.043       9      54 ..       8      57 ..       2      69 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                            HTH_27  9 Lhlir....hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                                      L +++      +++++  ++++ l+++ +++ ++l +L+ +GL+e +++e
  gi|336254976|ref|YP_004598083.1|  8 LLVVYrasrNAGEPVSPGRVADELDRSPAATTEMLQRLETRGLLEYEPYE 57
                                      5555555534455555599*************************988776 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   9.9e-05      0.16      23      56 ..      22      55 ..      17      79 .. 0.86
   2 ?   -1.2   0.0       1.1   1.9e+03      26      26 ..     109     109 ..      84     134 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.9e-05
                                      CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerek 56
                                       +   +a el+++ +   e+L++Le +Gl e e+
  gi|336254976|ref|YP_004598083.1| 22 VSPGRVADELDRSPAATTEMLQRLETRGLLEYEP 55
                                      556689***********************99876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                                       C CS
                              TrmB  26 d 26 
                                       +
  gi|336254976|ref|YP_004598083.1| 109 E 109
                                       2 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 ?   12.6   0.0   4.8e-05     0.078      19      47 ..      23      51 ..      18      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.8e-05
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      s   +A++l+ Sp+++++ l+rLe  Gl+
  gi|336254976|ref|YP_004598083.1| 23 SPGRVADELDRSPAATTEMLQRLETRGLL 51
                                      66679**********************97 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 ?    9.3   0.0   0.00068       1.1      21      53 ..      21      53 ..       6      63 .. 0.79
   2 ?    2.2   0.0      0.11   1.8e+02       1      13 [.     109     121 ..     109     135 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00068
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisr 53
                                      p++    A+ l  ++  ++ +l++L+ +gl++ 
  gi|336254976|ref|YP_004598083.1| 21 PVSPGRVADELDRSPAATTEMLQRLETRGLLEY 53
                                      7788889999********************994 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHCT CS
                         HTH_Crp_2   1 qRlArfLlrlaer 13 
                                       +R+A +Ll+ ++ 
  gi|336254976|ref|YP_004598083.1| 109 ERVAETLLERDAA 121
                                       7******986332 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 ?   12.4   0.0   6.2e-05       0.1      31      60 ..      27      55 ..       7      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.2e-05
                                      HHHHHTS-.HHHHHHHHHHHHHTTSEE-GG CS
                     LexA_DNA_bind 31 iaralglkSpsaveehLkaLerKGyierdp 60
                                      +a++l  +Sp+a  e L++Le++G++e +p
  gi|336254976|ref|YP_004598083.1| 27 VADELD-RSPAATTEMLQRLETRGLLEYEP 55
                                      555665.89******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1036.26
//
Query:       gi|336254977|ref|YP_004598084.1|  [L=181]
Description: Ferritin Dps family protein [Halopiger xanaduensis SH-6]
Scores for 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-34  117.0   8.5      7e-34  116.8   8.5    1.1  1  Ferritin  Ferritin-like domain
  ------ inclusion threshold ------
      0.088   12.1   2.6        0.1   11.9   2.0    1.3  1  CorA      CorA-like Mg2+ transporter protein
      0.094   12.7   7.4      0.096   12.7   1.3    2.5  2  DUF1451   Zinc-ribbon containing domain
       0.34   11.2   8.7       0.34   11.2   0.1    3.1  3  Osmo_CC   Osmosensory transporter coiled coil


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.8   8.5   1.6e-37     7e-34       1     139 [.      30     172 ..      30     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 1.6e-37
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH...C-S CS
                          Ferritin   1 ikaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee...iea 74 
                                       i+aLn+ lad +++++q ++++w+v+g ++ +++ f++e +e+  e ad++aer++alGg+p ++  +l+e   +e+
  gi|336254977|ref|YP_004598084.1|  30 IEALNRDLADAYVLYHQLHKHHWNVEGAEFLDVHVFLQEVYEDVEEAADDVAERLQALGGVPHASMTTLAEkatVEP 106
                                       79***************************************************************999999888777 PP

                                       SSS.CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  75 pke.fgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                       ++e + +++  l+++le+  +++es+re ielae  gD+ata++l + le+ eeh +++e++le+ 
  gi|336254977|ref|YP_004598084.1| 107 EDEdVYDIRTSLANDLEMIGDIIESYREHIELAEGLGDHATAQMLREQLETIEEHTHHIEHYLEDD 172
                                       777545*********************************************************986 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.0   2.3e-05       0.1     112     214 ..      62     171 ..      57     181 .] 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                              CorA 112 lyrlldeivdrlfellekleeeldeledel........edstkkeilrelaqlr....rrlvklrralapnrevlkr 176
                                       ++ +l+e+ ++++e+ +++ e+l+ l            e+ t +++ ++++++r     +l  + +++   re + +
  gi|336254977|ref|YP_004598084.1|  62 VHVFLQEVYEDVEEAADDVAERLQALGGVPhasmttlaEKATVEPEDEDVYDIRtslaNDLEMIGDIIESYREHI-E 137
                                       57899**********************999888899999999999999999999333333444477777777777.7 PP

                              CorA 177 llakaddkllddedkeylrdlldelerllemlealrer 214
                                       l + +++++ ++++   lr+ l+ +e    ++e++ e 
  gi|336254977|ref|YP_004598084.1| 138 LAE-GLGDHATAQM---LREQLETIEEHTHHIEHYLED 171
                                       777.8888888887...555555555555555555543 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.3   2.2e-05     0.096      19      88 ..       9      81 ..       2      96 .. 0.79
   2 ?    2.9   0.5     0.023     1e+02      32      89 ..     107     164 ..      94     175 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
                           DUF1451 19 ekakeklseaeeltkeelelvaeylkrDleeaarsleeske...eleewlsldlelieesllealasiaDktq 88
                                      ++a + +++a +l+ e++e++ e+l+rDl++a+  +++ ++   ++e  + ld+++  ++++e   + aD   
  gi|336254977|ref|YP_004598084.1|  9 QEAGTVEENALRLEPEKAEQIIEALNRDLADAYVLYHQLHKhhwNVEGAEFLDVHVFLQEVYEDVEEAADDVA 81
                                      456666777889999*****************99998888866677888888888888888888888888655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.023
                           DUF1451  32 tkeelelvaeylkrDleeaarsleeskeeleewlsldlelieesllealasiaDktqv 89 
                                       ++e++  ++  l +Dle +++ +e+ +e++e  + l  ++  + l e+l  i + t+ 
  gi|336254977|ref|YP_004598084.1| 107 EDEDVYDIRTSLANDLEMIGDIIESYREHIELAEGLGDHATAQMLREQLETIEEHTHH 164
                                       5667777777788888888888887777777777777777777777777777666654 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.6   7.2e+03      18      29 ..      27      38 ..      24      42 .. 0.71
   2 ?   11.2   0.1   7.6e-05      0.34       9      31 ..      65      87 ..      63      89 .. 0.93
   3 ?    3.2   1.8     0.025   1.1e+02       9      28 ..     150     169 ..     144     171 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                                      HHHHHHHHHHHH CS
                           Osmo_CC 18 EqkvedideeIa 29
                                      Eq +e ++ ++a
  gi|336254977|ref|YP_004598084.1| 27 EQIIEALNRDLA 38
                                      777887776665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 7.6e-05
                                      XXXXXXTHHHHHHHHHHHHHHHH CS
                           Osmo_CC  9 lLqehYdnIEqkvedideeIaaL 31
                                       Lqe Y+++E+  +d+ e ++aL
  gi|336254977|ref|YP_004598084.1| 65 FLQEVYEDVEEAADDVAERLQAL 87
                                      59*****************9998 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.025
                                       XXXXXXTHHHHHHHHHHHHH CS
                           Osmo_CC   9 lLqehYdnIEqkvedideeI 28 
                                       +L+e+ + IE+   +i++ +
  gi|336254977|ref|YP_004598084.1| 150 MLREQLETIEEHTHHIEHYL 169
                                       78889999998888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1090  (0.0607954); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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: 00:00:00.39
# Mc/sec: 1392.15
//
Query:       gi|336254978|ref|YP_004598085.1|  [L=201]
Description: hypothetical protein Halxa_3597 [Halopiger xanaduensis SH-6]
Scores for complete 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   63.9  36.6    4.9e-08   33.2   8.9    3.1  3  DUF308    Short repeat of unknown function (DUF308)
  ------ inclusion threshold ------
       0.14   11.9   8.5          1    9.2   0.2    3.6  3  DUF4538   Domain of unknown function (DUF4538)
        7.5    4.7   8.6        1.7    6.8   5.5    1.4  1  DUF2070   Predicted membrane protein (DUF2070)


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 !   33.2   8.9   8.3e-12   4.9e-08       1      58 [.      27      82 ..      27      86 .. 0.88
   2 !   31.8  11.6   2.1e-11   1.3e-07       2      71 ..      84     151 ..      83     153 .. 0.93
   3 !   13.5   7.5   1.2e-05     0.069       2      48 ..     140     187 ..     139     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 8.3e-12
                            DUF308  1 llGillivlGilalllPvaallalvllfGilllvsGivqiiaafaarkknrggrwlgl 58
                                      + G +  +lG+la+++P+a++l l++ fG+ll++sG+v+ ++a++ar+ +rg++w + 
  gi|336254978|ref|YP_004598085.1| 27 IAGAVVGLLGLLAMAFPLATGLSLTIGFGALLVLSGVVHGAHAVTARG-WRGRTW-QA 82
                                      5789999*************************************9999.777776.43 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 2.1e-11
                            DUF308   2 lGillivlGilalllPvaallalvllfGilllvsGivqiiaafaarkknrggrwlglllGilyliaGlll 71 
                                       l++++i++G++a+++P++ l++l+l++  +ll+ Gi++ + ++++ ++ ++  +  +++G+++l++++ll
  gi|336254978|ref|YP_004598085.1|  84 LAVVAIIAGLVAFVNPAIGLVTLTLVLVGYLLADGIAETWMGLRMAGQPGRTSI--VASGVVSLVLAALL 151
                                       79*****************************************88888887776..99*********997 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 1.2e-05
                            DUF308   2 lGillivlGilall.lPvaallalvllfGilllvsGivqiiaafaark 48 
                                       +G++++vl++l+ + +P++a+ a+ ll+G+ l++ G+   i a++ar+
  gi|336254978|ref|YP_004598085.1| 140 SGVVSLVLAALLWAgFPATASWAIGLLVGVSLFMTGLSMGIVAISARR 187
                                       799*99999888655*************************99998887 PP

>> DUF4538  Domain of unknown function (DUF4538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2   0.00017         1       2      19 ..      20      37 ..      19      43 .. 0.91
   2 ?    2.2   0.4     0.025   1.5e+02       6      17 ..      86      97 ..      77     108 .. 0.68
   3 ?    3.8   0.1    0.0079        47       5      21 ..     134     150 ..     131     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00017
                           DUF4538  2 rglkyvllvggvvgligl 19
                                       g+++ ++ g+vvgl+gl
  gi|336254978|ref|YP_004598085.1| 20 HGWRTLAIAGAVVGLLGL 37
                                      69*************997 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.025
                           DUF4538  6 yvllvggvvgli 17
                                      +v++++g+v+++
  gi|336254978|ref|YP_004598085.1| 86 VVAIIAGLVAFV 97
                                      456666777666 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.0079
                           DUF4538   5 kyvllvggvvgliglal 21 
                                       ++ ++ +gvv+l+ +al
  gi|336254978|ref|YP_004598085.1| 134 RTSIVASGVVSLVLAAL 150
                                       8999*********9997 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.5   0.00029       1.7      13     134 ..      79     195 ..      65     198 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00029
                           DUF2070  13 swkvsllliillalligllaflssklfgillfglpalvaflltlpvlrilggr...ltykrslflalltelivviis 86 
                                        w+ +l++++++a l+++++  ++ l ++ l+++ +l+a  +   ++   g r    + + s++ + +  l++++++
  gi|336254978|ref|YP_004598085.1|  79 TWQAALAVVAIIAGLVAFVNPAIG-LVTLTLVLVGYLLADGIAETWM---GLRmagQPGRTSIVASGVVSLVLAALL 151
                                       455555555555555555554444.4555555555555555555555...444221333344444444444444433 PP

                           DUF2070  87 llaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpa 134
                                       +++  +    +a+    l+++++l +    + +va+s +++  ++ pa
  gi|336254978|ref|YP_004598085.1| 152 WAGFPA----TASWAIGLLVGVSLFMTGLSMGIVAISARRVDESTPPA 195
                                       333333....46677889999999999999999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 1514.69
//
Query:       gi|336254979|ref|YP_004598086.1|  [L=339]
Description: luciferase oxidoreductase, group 1 [Halopiger xanaduensis SH-6]
Scores for 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-40  138.0   5.5      6e-40  137.6   5.4    1.3  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
        4.3    7.9   5.3         10    6.7   5.3    1.6  1  EF-1_beta_acid  Eukaryotic elongation factor 1 beta central a


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.6   5.4   6.7e-44     6e-40       4     248 ..       4     253 ..       1     313 [. 0.81

  Alignments for each domain:
  == domain 1  score: 137.6 bits;  conditional E-value: 6.7e-44
                    Bac_luciferase   4 gvflptrqggalgaasaslrylvelaraaEelGfdavwvaehhggpgga..ldaftllaalaaaTerirlgtavtpl 78 
                                       +++ ++ ++ + +a+  +++++v+lar aEe G++++wvaehhg++++     + tl+a+laa+T+ ir+g++++ l
  gi|336254979|ref|YP_004598086.1|   4 SIVDLAPIPQDGSATD-AYANTVDLARSAEEFGYERFWVAEHHGMADHIasTTPETLIAHLAAETDEIRIGSGTVLL 79 
                                       5555555555555555.9***************************99999*99************************ PP

                    Bac_luciferase  79 ytrhPavlAqqaatLdhlsgGRfglglgt..ggpaveerrfGv..dhderyarlrEfvevlrrlwrgeev.dfeGef 150
                                         ++P+ +A+++a+Ld +++GR++lglg+  g pav+++  G   +++ + +  +E +e+    ++++ + d+    
  gi|336254979|ref|YP_004598086.1|  80 NHYQPFKVAETFASLDAMAPGRVDLGLGRatGIPAVDQAL-GTdrHKQNPDEDHAEKIEATVSHLYDGFPeDHPYAD 155
                                       ****************************985777777555.66577788999999**99988888675555763333 PP

                    Bac_luciferase 151 fsvkgalllprpgqgpiP.vyvaaaspaglelaarhadglllag.eppeeaaelierlragaae..agrdpadirvg 223
                                              +lpr++++ +P v+v ++sp ++e+a++ +  + +a   +p  a++++e++r+  +    g++p+d++ +
  gi|336254979|ref|YP_004598086.1| 156 ------ISLPRSADD-VPeVWVLGSSPSSAEIAGKLGLRYCFAAfIRPNLAERAFETYREHFESsdVGAGPDDPEGM 225
                                       ......679999999.999***********************9999**************888745778888***** PP

                    Bac_luciferase 224 isltvivadteeeAraea...raliagl 248
                                       +++ v++a+t+eeA + +   +a ++++
  gi|336254979|ref|YP_004598086.1| 226 LAINVACAETDEEAARLRataEAAYKRM 253
                                       **************99996655555332 PP

>> EF-1_beta_acid  Eukaryotic elongation factor 1 beta central acidic region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   5.3    0.0012        10       8      25 ..     234     251 ..     234     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0012
                    EF-1_beta_acid   8 EEDeEaerlreeRLaaYa 25 
                                       E DeEa+rlr+   aaY+
  gi|336254979|ref|YP_004598086.1| 234 ETDEEAARLRATAEAAYK 251
                                       459**************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.47u 0.18s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2924.41
//
Query:       gi|336254980|ref|YP_004598087.1|  [L=587]
Description: response regulator receiver modulated GAF sensor protein [Halopiger xanaduensis SH-6]
Scores for 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-38  130.1  11.4    6.1e-38  130.1  11.4    2.7  3  BAT           GAF and HTH_10 associated domain
    1.2e-21   77.5   0.9    2.9e-21   76.2   0.2    2.1  2  GAF_2         GAF domain
    9.3e-21   73.4   0.0    2.4e-20   72.1   0.0    1.8  1  HTH_10        HTH DNA binding domain
    1.7e-17   63.6   0.2    3.7e-16   59.3   0.2    2.8  2  Response_reg  Response regulator receiver domain
    6.8e-10   39.7   0.0    1.7e-09   38.4   0.0    1.7  1  GAF           GAF domain
    2.4e-05   24.7   0.0    0.00012   22.5   0.0    2.2  2  GAF_3         GAF domain
      0.001   18.7   0.1      0.024   14.3   0.0    3.0  2  Sigma70_r4_2  Sigma-70, region 4
     0.0066   16.0   0.0      0.015   14.8   0.0    1.7  1  HTH_24        Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.076   12.6   0.0       0.16   11.5   0.0    1.5  1  GerE          Bacterial regulatory proteins, luxR family


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       2.7   5.4e+03     107     135 ..      41      69 ..      26      88 .. 0.68
   2 ?    0.3   1.1      0.29   5.9e+02      93     144 ..     139     190 ..     111     193 .. 0.74
   3 !  130.1  11.4   3.1e-41   6.1e-38       1     150 [.     369     518 ..     369     523 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.7
                               BAT 107 dgrarlvvevPpgadvRsvvealeerypd 135
                                       d++ r+ +   +  d+R + e+l+++ + 
  gi|336254980|ref|YP_004598087.1|  41 DETLRILLIEDNPGDARLIEEMLKDTEEL 69 
                                       45555666666777777777777776654 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.29
                               BAT  93 laehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrer 144
                                       ++++ + v++++    ++ +  ev ++  vR++  a+e++ ++ e +++re+
  gi|336254980|ref|YP_004598087.1| 139 VSDQQVGVEAIQRGAQDFLVKDEVTSELLVRTIHHAIERARQESERRRQREQ 190
                                       5555555555555566666666777788899999999999999999888886 PP

  == domain 3  score: 130.1 bits;  conditional E-value: 3.1e-41
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       DavveLe+++++ ++ lval+a+  c++e+e+lv+ +d+++lv+++++g++++e+++ + ++++++++r+++++ d+
  gi|336254980|ref|YP_004598087.1| 369 DAVVELEFRVEEMAEELVALSATESCTIEIEQLVQ-GDETLLVYGSATGVSQDEFEESVVETEGIDELRILAARRDE 444
                                       99********************************9.999************************************** PP

                               BAT  78 tllelt.vsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrt 150
                                         +el   +  sl++t+a+hGg+v+sa+++dg++r+vve+P+g+d+R+++e ++++ pdv+++a+r++er++ +
  gi|336254980|ref|YP_004598087.1| 445 FEFELVaPTAISLFETIATHGGRVESATITDGEFRFVVELPRGRDTRQMIELIKDERPDVTYLAQRTTERSEPS 518
                                       ****99778889999*******************************************************9876 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.2   1.5e-24   2.9e-21       3     137 ..     213     357 ..     211     358 .. 0.83
   2 ?   -2.7   0.0       3.4   6.8e+03       9      65 ..     509     575 ..     503     583 .. 0.50

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 1.5e-24
                                       HHHHHHHHHHHHHHHSS...EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B--......-TTHHHHHHHHTS-EEE CS
                             GAF_2   3 dleelldlvldelvelg.aalgyillvdddgg.lrlaawgeaeeefgaaldrpl......geglvgealrtgrpvil 71 
                                       +  el ++v+d+lve +  ++++i+ v+++ + ++  a+++ e++  + ++ ++      g+g++g+a+rtg+  i 
  gi|336254980|ref|YP_004598087.1| 213 TRAELEQRVCDRLVESDaYRFAWIGGVNPGSDeIVPKAAAGVEDGYLETVEISVneddpsGKGPAGRAIRTGEVKIT 289
                                       6789***********98799******9965553444444444444444333322222335*************9999 PP

                                       S-GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  72 ndleedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       +d+++d+   +++  a+++g+rs++a+P+++e+ v+Gvln+ya+ p+af++ ++e+L+ +++ ia ai
  gi|336254980|ref|YP_004598087.1| 290 DDIQTDAEFEPWReaARERGYRSSAAIPVVHEDLVYGVLNVYAESPRAFTAPEQEILSRIGDIIAHAI 357
                                       99***9999999999****************99**********************************9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.4
                                       HHHHHHHHHSS..EEEEEEE-..TTS-..EEEE......EEEES-TTSTT-S-B---TT.H.HHHHHHH CS
                             GAF_2   9 dlvldelvelgaalgyillvd..ddgg..lrla......awgeaeeefgaaldrplgeg.l.vgealrt 65 
                                       ++++++ +  ga+ + +l+ d  ++++  l  +      ++  ++e+ g+++ ++lg +   + + lrt
  gi|336254980|ref|YP_004598087.1| 509 QRTTERSEPSGASSASVLEEDltEKQRaaL--EtayfagYFDWPRESTGEEIADRLGIApAtFNQHLRT 575
                                       555555555555555555545433333222..1334455555666666666666664442224566666 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.0   1.2e-23   2.4e-20       1      52 [.     530     581 ..     530     582 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 1.2e-23
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT+kq+++l +Ay +GYFd+PR+ t +e+A++lGI+++t+ +hLr ae+k +
  gi|336254980|ref|YP_004598087.1| 530 LTEKQRAALETAYFAGYFDWPRESTGEEIADRLGIAPATFNQHLRTAERKFF 581
                                       9************************************************965 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.2   1.8e-19   3.7e-16       1     108 [.      46     167 ..      46     171 .. 0.74
   2 ?   -2.6   0.0         3   5.9e+03      31      47 ..     489     505 ..     484     507 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 1.8e-19
                                       EEEESSSHHHHHHHHHHHH..HTTE............EEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHH CS
                      Response_reg   1 vlivdDdplvrellrqlle..eegy............eevaeaedgkealellkeekvdlillDinmpgmdGlellk 63 
                                       +l+++D+p  ++l++++l+  ee               e++  +  ++ le l++e  d++llD+n+p+  Gle+l+
  gi|336254980|ref|YP_004598087.1|  46 ILLIEDNPGDARLIEEMLKdtEELAqrvspdeaagrtPEITRETRLEDGLETLESEPTDVVLLDLNLPDSAGLETLE 122
                                       567777777777777777753222211111111111112333345667788888888******************** PP

                                       HHHHCTTTSEEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHH CS
                      Response_reg  64 eireedpelpviiltahseeedavealkagaddflsKpfdpeeLl 108
                                        ++ee++++p+++lt+ s++++ vea++ ga+dfl+K+   +eLl
  gi|336254980|ref|YP_004598087.1| 123 AVHEESETTPIVVLTGVSDQQVGVEAIQRGAQDFLVKDEVTSELL 167
                                       *************************************99888876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3
                                       SHHHHHHHHHHHHESEE CS
                      Response_reg  31 dgkealellkeekvdli 47 
                                       d ++++el+k e++d+ 
  gi|336254980|ref|YP_004598087.1| 489 DTRQMIELIKDERPDVT 505
                                       67899999999999986 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   8.6e-13   1.7e-09      43     133 .]     268     357 ..     219     357 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 8.6e-13
                                       EEEETTSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHH CS
                               GAF  43 lfmkngrgicgqvlatgqplvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftree 118
                                         ++ g+g +g++++tg++ + +d+++d  f +  +r+ +++ g+rss+++P+v+++ ++G+l ++ +sp  ft  e
  gi|336254980|ref|YP_004598087.1| 268 EDDPSGKGPAGRAIRTGEVKITDDIQTDAEFEP--WREAARERGYRSSAAIPVVHEDLVYGVLNVYAESPrAFTAPE 342
                                       45566889999********99999*********..99******************************88888***** PP

                                       HHHHHHHHHHHHHHH CS
                               GAF 119 lellqvladqvaval 133
                                        e+l  ++d +a a+
  gi|336254980|ref|YP_004598087.1| 343 QEILSRIGDIIAHAI 357
                                       *********999886 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.9   3.7e+03      78     127 ..     128     175 ..     113     177 .. 0.66
   2 !   22.5   0.0   5.9e-08   0.00012      57     127 ..     277     357 ..     223     359 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.9
                             GAF_3  78 lpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                       +++++++++   + +q +Gv a+++   ++f+ +d+   e l r i  ai
  gi|336254980|ref|YP_004598087.1| 128 SETTPIVVL-TGVSDQQVGVEAIQRGA-QDFLVKDEVTSELLVRTIHHAI 175
                                       456666665.33446999999999855.7788777766666665555555 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 5.9e-08
                             GAF_3  57 arralssgevvse......psfaeedglpd.......raalavPLvagrqviGvlalastkprafdaedlelleslA 120
                                       a ra+ +gev ++      +   e + ++        r+  a+P+v+++ v+Gvl ++  +praf+a ++e l+ ++
  gi|336254980|ref|YP_004598087.1| 277 AGRAIRTGEVKITddiqtdA---EFEPWREaarergyRSSAAIPVVHEDLVYGVLNVYAESPRAFTAPEQEILSRIG 350
                                       56888888888884553321...2222222333333477799*********************************** PP

                             GAF_3 121 rqiatai 127
                                       + ia ai
  gi|336254980|ref|YP_004598087.1| 351 DIIAHAI 357
                                       ****999 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 ?   -1.7   0.1       1.2   2.5e+03      40      52 ..     168     180 ..     166     181 .. 0.89
   2 !   14.3   0.0   1.2e-05     0.024      11      53 ..     530     579 ..     528     580 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHH CS
                      Sigma70_r4_2  40 egtVksrlsRArk 52 
                                       ++t+ +++ RAr+
  gi|336254980|ref|YP_004598087.1| 168 VRTIHHAIERARQ 180
                                       68999******97 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.2e-05
                                       S-HHHHHHHHHHHTS--.......-HHHHHHHHT--HHHHHHHHHHHHHH CS
                      Sigma70_r4_2  11 Lperqreifllrylegl.......sykEIAellgisegtVksrlsRArkk 53 
                                       L+e+qr++++  y+ g+       + +EIA +lgi ++t +++l+ A +k
  gi|336254980|ref|YP_004598087.1| 530 LTEKQRAALETAYFAGYfdwpresTGEEIADRLGIAPATFNQHLRTAERK 579
                                       78888888888888874444444499******************988776 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 !   14.8   0.0   7.5e-06     0.015      21      43 ..     556     578 ..     550     579 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.5e-06
                            HTH_24  21 reLAerlglSpstvnrrlkrLee 43 
                                        e+A+rlg+ p+t n++l+  e+
  gi|336254980|ref|YP_004598087.1| 556 EEIADRLGIAPATFNQHLRTAER 578
                                       69****************98876 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.1e-05      0.16      21      45 ..     556     580 ..     553     581 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.1e-05
                                       HHHHHHHTS-HHHHHHHHHHHHHHH CS
                              GerE  21 keIAeelniSekTVkvhksnimkKL 45 
                                       +eIA++l+i++ T + h++ + +K+
  gi|336254980|ref|YP_004598087.1| 556 EEIADRLGIAPATFNQHLRTAERKF 580
                                       89*****************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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 0.27s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 4397.07
//
Query:       gi|336254981|ref|YP_004598088.1|  [L=153]
Description: response regulator receiver protein [Halopiger xanaduensis SH-6]
Scores for 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-22   78.7   0.0      4e-22   78.5   0.0    1.1  1  Response_reg  Response regulator receiver domain


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 !   78.5   0.0   2.3e-26     4e-22       1     111 [.      14     134 ..      14     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 2.3e-26
                                       EEEESSSHHHHHHHHHHHHHTTE.EEEEEESSHHHHHHHHHHHH.......ESEEEEESSCSSSEHHHHHHHHHHCT CS
                      Response_reg   1 vlivdDdplvrellrqlleeegy.eevaeaedgkealellkeek.......vdlillDinmpgmdGlellkeireed 69 
                                       +l+v+D+p  ++l+++++++  + ++ ++++dg+eale lk++        +dlillD+n+p+ dG e+l+e+++++
  gi|336254981|ref|YP_004598088.1|  14 ILLVEDNPGDVRLTEEAFKQGRIeNDLHVVSDGTEALEFLKQRGefvdaprPDLILLDLNLPRTDGEEVLEELKNDP 90 
                                       89*****************888834566************88888888999*************************9 PP

                                       ..TTSEEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  70 ..pelpviiltahseeedavealkagaddflsKpfdpeeLlkal 111
                                         +++pvi+lt+  ++ed+ + +++ a+ +l+Kp+dp+e ++ +
  gi|336254981|ref|YP_004598088.1|  91 elRSIPVIVLTSSRANEDIARSYELHANAYLTKPVDPDEFIETV 134
                                       9999***********************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1275.64
//
Query:       gi|336254982|ref|YP_004598089.1|  [L=1350]
Description: multi-sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for complete 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  240.9  30.2    2.5e-13   50.2   0.8    7.6  8  PAS_4        PAS fold
    1.4e-58  195.8   0.6    5.5e-13   48.9   0.0    7.0  7  PAS          PAS fold
    4.6e-49  165.0   0.0      2e-11   44.0   0.0    7.5  7  PAS_9        PAS domain
    6.6e-34  115.4   7.4    8.7e-10   38.4   0.0    7.0  6  PAS_8        PAS domain
    5.4e-27   94.5   0.1    6.5e-26   91.0   0.0    2.5  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.5e-21   75.8   1.4    0.00041   20.6   0.0    6.6  6  PAS_3        PAS fold
    1.8e-19   70.0   6.1    3.2e-06   27.3   0.0    8.9  7  PAS_7        PAS fold
    3.8e-17   62.8   0.0    1.5e-06   28.6   0.1    3.9  3  GAF_3        GAF domain
    5.3e-12   46.2  10.6    3.2e-09   37.2   1.2    4.9  4  GAF_2        GAF domain
    1.5e-10   41.8   0.5    7.8e-05   23.3   0.2    3.4  3  GAF          GAF domain
    8.7e-10   38.5   0.1    8.7e-10   38.5   0.1    4.0  4  HisKA        His Kinase A (phospho-acceptor) domain
    0.00031   20.8   0.6        1.4    9.0   0.0    3.5  4  sCache_like  Single Cache-like
    0.00059   19.7   0.0     0.0014   18.5   0.0    1.6  1  HATPase_c_5  GHKL domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.032   14.0   0.0    1.5  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
      0.076   13.2   0.2       0.47   10.6   0.1    2.4  1  GCN5L1       GCN5-like protein 1 (GCN5L1)


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       6.8   8.1e+03      50      95 ..      32      74 ..      17      82 .. 0.60
   2 !   50.2   0.8   2.1e-16   2.5e-13       1     110 []     187     302 ..     187     302 .. 0.86
   3 !   45.2   0.2   7.8e-15   9.4e-12       2     110 .]     315     419 ..     314     419 .. 0.89
   4 !   36.2   0.2   4.9e-12   5.9e-09       1      93 [.     435     535 ..     435     539 .. 0.89
   5 ?   -0.5   0.1       1.2   1.4e+03      92     110 .]     556     574 ..     550     574 .. 0.80
   6 !   41.6   0.0     1e-13   1.2e-10       2     110 .]     584     684 ..     583     684 .. 0.95
   7 !   37.7   0.2   1.6e-12   1.9e-09       2     109 ..     867     970 ..     866     971 .. 0.91
   8 !   48.1   0.1   9.8e-16   1.2e-12       1     110 []     994    1105 ..     994    1105 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.8
                             PAS_4 50 arleralrrvlegeepiefleelllpgeerhyelrllPlrdesGev 95
                                      ++++r lr +++g    ++le  ++ g  ++ + + l+lr esG+ 
  gi|336254982|ref|YP_004598089.1| 32 GDVDRLLRDAVDGV--RTQLEAAHC-GVFEVADAETLRLRSESGRE 74
                                      55666666666662..222332333.55577777778888888874 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 2.1e-16
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla.ellpeedaarler....alrrvlegeepiefleel 72 
                                       ++ +p++++v d dg+v++aN++a+++ g+++ el++++la e+ p +da++ ++    ++ rvle++ep++++e+ 
  gi|336254982|ref|YP_004598089.1| 187 VETSPVGIVVTDVDGTVRFANERAEAITGRDRSELVDRPLAaEWDPVDDAGEPMShcqlPVSRVLETGEPVWDVEFG 263
                                       5889*************************************665555566665551222689*************** PP

                             PAS_4  73 ll..pgeerhyelrllPlrdesGe.vigvlvisrDiTerrr 110
                                        +  +g+++++  ++ P+  + G+   gv+ ++ D+T++rr
  gi|336254982|ref|YP_004598089.1| 264 IRtpGGDRVWVAANAAPM--TAGDeYTGVVTTFEDVTDERR 302
                                       *9*8999999999*****..557779************997 PP

  == domain 3  score: 45.2 bits;  conditional E-value: 7.8e-15
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       +  ++++  ld+d r++y+N+a+ae++g++pee++G+++  l+pe++a++  + +++ l++  +++ +++ l+ +++
  gi|336254982|ref|YP_004598089.1| 315 ETASEGISLLDEDDRFTYVNQAYAEMYGYEPEEMIGEHWGILYPEGAAEDANAEIEAELAETGTWSGETIGLRRDGT 391
                                       667889999************************************************999999**********6666 PP

                             PAS_4  79 rhyelrl.lPlrdesGevigvlvisrDiTerrr 110
                                       +++e ++  ++ d      g++++++D+T++rr
  gi|336254982|ref|YP_004598089.1| 392 EFVEDHYlARVGD-----GGLVCVVQDVTDERR 419
                                       6666666366655.....88**********997 PP

  == domain 4  score: 36.2 bits;  conditional E-value: 4.9e-12
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla....ellpee....daarleralrrvlegeepiefl 69 
                                       ++ +p++++v+d+dg  ++aN +aae++ +++e++ G +      e+   +    +  + er+ +rv++++e+++++
  gi|336254982|ref|YP_004598089.1| 435 VETSPVGITVIDTDGDLRFANDRAAEILECDREAIAGLSSDdsdwEVR--DadgrLLSAAERPFDRVISSGEALFDV 509
                                       5889***********************************996533343..255888889999*************** PP

                             PAS_4  70 eelll..pgeerhyelrllPlrdesG 93 
                                       e +l+  + +er+++++  Plr+++ 
  gi|336254982|ref|YP_004598089.1| 510 ELRLRhpDARERWLSINGAPLRADET 535
                                       *99999***************99775 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 1.2
                             PAS_4  92 sGevigvlvisrDiTerrr 110
                                         ev g ++++ D+Te++r
  gi|336254982|ref|YP_004598089.1| 556 ADEVTGGIFTIEDVTEQKR 574
                                       4469999*********986 PP

  == domain 6  score: 41.6 bits;  conditional E-value: 1e-13
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       ++++da++ ld++ +++yaN +a+ l+ a++e ++G+ l   +p+ d+ ++e+ lr +++ +ep + +e++     e
  gi|336254982|ref|YP_004598089.1| 584 SRISDAFIGLDSNWTITYANDRAETLIDAAGEGIVGRDLSAAFPTADGSEFETELRGAMDRQEPTSIEEYVPA--LE 658
                                       678999***************************************************************8877..** PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        ++e++++P         g+ v++rD+Ter++
  gi|336254982|ref|YP_004598089.1| 659 TWFEIHVYPSPT------GLSVYFRDVTERKE 684
                                       *********965......************85 PP

  == domain 7  score: 37.7 bits;  conditional E-value: 1.6e-12
                             PAS_4   2 dslpdalavl.dpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++ p +l++l d+d+r++    +a e + ++ ee++G+t+ e +  e  +++e++ r++l+ge++ ++ e l+    
  gi|336254982|ref|YP_004598089.1| 867 EQFPNGLVALfDEDLRYTLGGGQALEEIDLSVEEFVGQTVTERYEGETLEQFESNFRAALAGEQRSFEFE-LHS--- 939
                                       67777777777***************9***********************************87776666.555... PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                        r ++  ++P++d++Gev + +++++DiTer+
  gi|336254982|ref|YP_004598089.1| 940 -REWLAYAVPVEDSRGEVFAGMLMVQDITERV 970
                                       .7*****************************7 PP

  == domain 8  score: 48.1 bits;  conditional E-value: 9.8e-16
                             PAS_4    1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll. 74  
                                        ld++ d+++v+d++g ++++N++ ++l g++++el G    e++  e  + +++a+++v e++ +  ++e+  + 
  gi|336254982|ref|YP_004598089.1|  994 LDAIDDVFYVIDENGDFQRWNESLRALTGLSDDELEGINALEFFEGETEETVAAAIDEVFETGSARLEAEVEPDp 1068
                                        799**********************************************************99665544444445 PP

                             PAS_4   75 ..pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110 
                                          +ge+++ye+ ++ l+d+sGe   + +i+rDi+err+
  gi|336254982|ref|YP_004598089.1| 1069 dpGGETVPYEFVASALEDPSGE-PVLTGIGRDISERRE 1105
                                        *9********************.77899********96 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.5   6.6e+03       4      21 ..      46      63 ..      45      76 .. 0.76
   2 !   48.9   0.0   4.6e-16   5.5e-13       4     113 .]     184     297 ..     181     297 .. 0.95
   3 !   43.4   0.0   2.3e-14   2.8e-11       3     113 .]     310     414 ..     308     414 .. 0.95
   4 !   28.7   0.0   8.5e-10     1e-06       3      99 ..     431     533 ..     429     536 .. 0.95
   5 !   21.4   0.0   1.6e-07   0.00019       2      78 ..     578     654 ..     574     671 .. 0.88
   6 ?    3.9   0.0     0.043        52       2     110 ..     861     963 ..     860     966 .. 0.66
   7 !   40.4   0.0     2e-13   2.4e-10       6     113 .]     993    1100 ..     989    1100 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.5
                                      HHHHHHSSSEEEEEETTS CS
                               PAS  4 raileslpdpifvvDedg 21
                                      r++le++++++f v    
  gi|336254982|ref|YP_004598089.1| 46 RTQLEAAHCGVFEVADAE 63
                                      7899********997655 PP

  == domain 2  score: 48.9 bits;  conditional E-value: 4.6e-16
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.....HHHHHHHHHHHHTT-ECCC CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.....elaelleqlleqgeesrag 75 
                                       ++i+e++p++i+v+D dg + ++N+ ae ++G +r+e++ ++l  ++ + dda       +  ++++le+ge+  ++
  gi|336254982|ref|YP_004598089.1| 184 DRIVETSPVGIVVTDVDGTVRFANERAEAITGRDRSELVDRPLAAEWDPVDDAgepmsHCQLPVSRVLETGEPVWDV 260
                                       79***************************************************99988888899************* PP

                                       CEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  76 eisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       e  ++++ g  +++  +a+p++ +++  +g++ ++ d+
  gi|336254982|ref|YP_004598089.1| 261 EFGIRTPGGDRVWVAANAAPMTAGDE-YTGVVTTFEDV 297
                                       **********************9975.67*****9997 PP

  == domain 3  score: 43.4 bits;  conditional E-value: 2.3e-14
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       + + le++ ++i ++Ded r++yvN+a++e+ G+++ee++g++  +l++e   ++ ++++e  l+++  ++++ i +
  gi|336254982|ref|YP_004598089.1| 310 IYRALETASEGISLLDEDDRFTYVNQAYAEMYGYEPEEMIGEHWGILYPEGAAEDANAEIEAELAETGTWSGETIGL 386
                                       6789***********************************************888*********************** PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++ dg+++  +   + v+d+     g+++v++d+
  gi|336254982|ref|YP_004598089.1| 387 RR-DGTEFVEDHYLARVGDG-----GLVCVVQDV 414
                                       **.****9999999999999.....999999997 PP

  == domain 4  score: 28.7 bits;  conditional E-value: 8.5e-10
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH......HHHHHHHHHHHHTT-EC CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda......elaelleqlleqgeesr 73 
                                        ++i+e++p++i v+D dg+  ++N+ a+e+l  +re + g s  d+ +e  da         + + +++++ge   
  gi|336254982|ref|YP_004598089.1| 431 KEQIVETSPVGITVIDTDGDLRFANDRAAEILECDREAIAGLSSDDSDWEVRDAdgrllsAAERPFDRVISSGEALF 507
                                       589*******************************************99998888999**99**************** PP

                                       CCCEEEECTTSSEEEEEEEEEEEEET CS
                               PAS  74 ageisfklrdgrpihlevraspvrda 99 
                                       ++e +++ +d r+++l ++ +p+r  
  gi|336254982|ref|YP_004598089.1| 508 DVELRLRHPDARERWLSINGAPLRAD 533
                                       **********************9865 PP

  == domain 5  score: 21.4 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +l+a ++ + d+ +++D +  i+y+N+ ae+l   + e ++g+ l+  +++ d +e+  +l+ ++  +e+ +++e  
  gi|336254982|ref|YP_004598089.1| 578 ELEATFSRISDAFIGLDSNWTITYANDRAETLIDAAGEGIVGRDLSAAFPTADGSEFETELRGAMDRQEPTSIEEYV 654
                                       5666677799*********************************************************9999998875 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.043
                                       HHHHHHHHSSSEEEEE.ETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   2 dlraileslpdpifvv.DedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       ++r+++e+ p++ +++ Ded r ++    a e   ls ee +g+++ + +  e    + e++e + +++  +++   
  gi|336254982|ref|YP_004598089.1| 861 RYRTLVEQFPNGLVALfDEDLRYTLGGGQALEEIDLSVEEFVGQTVTERYEGE----TLEQFESNFRAALAGEQRSF 933
                                       56667777776666553577777777777777777999**************9....55555555555544444444 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEE CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvl 110
                                        f+l     ++++  a+pv d  ge+   ++++
  gi|336254982|ref|YP_004598089.1| 934 EFEL---HSREWLAYAVPVEDSRGEVFAGMLMV 963
                                       4444...56888888888888888865555555 PP

  == domain 7  score: 40.4 bits;  conditional E-value: 2e-13
                                        HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS    6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80  
                                        +l++++d   v+De+g++  +N++ + l+Gls +e+ g + l+++  e+++++a+++ ++ e+g+ +   e+  +
  gi|336254982|ref|YP_004598089.1|  993 VLDAIDDVFYVIDENGDFQRWNESLRALTGLSDDELEGINALEFFEGETEETVAAAIDEVFETGSARLEAEVEPD 1067
                                        7899*********************************************************************99 PP

                                        C.TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS   81 l.rdgrpihlevraspvrdaggeilgflgvlrdi 113 
                                          + g++++ e  as + d++ge+  + g++rdi
  gi|336254982|ref|YP_004598089.1| 1068 PdPGGETVPYEFVASALEDPSGEP-VLTGIGRDI 1100
                                        9***********************.*******98 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   1.7e-14     2e-11       1     104 []     191     299 ..     191     299 .. 0.93
   2 !   39.8   0.0   3.5e-13   4.2e-10       2     104 .]     319     416 ..     318     416 .. 0.86
   3 !   14.0   0.0   3.7e-05     0.044       1      89 [.     439     534 ..     439     539 .. 0.78
   4 ?    0.9   0.2      0.46   5.5e+02      87     104 .]     554     571 ..     546     571 .. 0.86
   5 !   12.5   0.0   0.00011      0.13       2     104 .]     588     681 ..     587     681 .. 0.70
   6 !    9.8   0.0   0.00075       0.9      19     104 .]     889     968 ..     870     968 .. 0.73
   7 !   33.2   0.0   4.1e-11   4.9e-08       3     104 .]    1000    1102 ..     998    1102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.7e-14
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgks...itdlf....vtdpeanerlraaleqgrkkerevevvlir 70 
                                       p+gi++++ dg++ +aNe a+ ++G ++ e++ ++    +d +    ++ ++ +  ++++le+g+ ++++ve  +++
  gi|336254982|ref|YP_004598089.1| 191 PVGIVVTDVDGTVRFANERAEAITGRDRSELVDRPlaaEWDPVddagEPMSHCQLPVSRVLETGE-PVWDVEFGIRT 266
                                       78****99***999*********************666566669999******************.*********** PP

                             PAS_9  71 kngetfwvlltaspvkdddgelvgiivilrDite 104
                                       + g ++wv ++a+p+  +++e++g++ +++D+t+
  gi|336254982|ref|YP_004598089.1| 267 PGGDRVWVAANAAPMT-AGDEYTGVVTTFEDVTD 299
                                       ***************5.589************96 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 3.5e-13
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       +gi + ++d r +y+N+a ++++Gy pee++g ++  l+    +++an +++a l +     +++e++  r++g++f
  gi|336254982|ref|YP_004598089.1| 319 EGISLLDEDDRFTYVNQAYAEMYGYEPEEMIGEHWGILYpeGAAEDANAEIEAELAETG--TWSGETIGLRRDGTEF 393
                                       7999999********************************88666666666666666666..8*************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                         +  +++v  +dg+   ++++++D+t+
  gi|336254982|ref|YP_004598089.1| 394 VEDHYLARV--GDGG---LVCVVQDVTD 416
                                       *********..4444...44******96 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3.7e-05
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlf........vtdpeanerlraaleqgrkkerevevvli 69 
                                       p+gi ++++dg + +aN+ a+++l  ++e++ g s +d             + a++ +++++ +g+   ++ve+ l+
  gi|336254982|ref|YP_004598089.1| 439 PVGITVIDTDGDLRFANDRAAEILECDREAIAGLSSDDSDwevrdadgRLLSAAERPFDRVISSGE-ALFDVELRLR 514
                                       68999999***999*******************994444343333333333556666666666666.99******** PP

                             PAS_9  70 rkngetfwvlltaspvkddd 89 
                                       +++ ++ w  ++ +p++ d+
  gi|336254982|ref|YP_004598089.1| 515 HPDARERWLSINGAPLRADE 534
                                       ****************9885 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.46
                             PAS_9  87 dddgelvgiivilrDite 104
                                       +d +e++g i++++D+te
  gi|336254982|ref|YP_004598089.1| 554 EDADEVTGGIFTIEDVTE 571
                                       56899************8 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 0.00011
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       d+++  +++ +i+yaN+ a++l+    e ++g++++  f  ++ +e + +lr a+++ +       ++++ +   + 
  gi|336254982|ref|YP_004598089.1| 588 DAFIGLDSNWTITYANDRAETLIDAAGEGIVGRDLSAAFptADGSEFETELRGAMDRQE----PTSIEEYVPAL-ET 659
                                       6677677888999**********9999************55555555555555555555....44444444432.56 PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       w++++++p        +g+ v +rD+te
  gi|336254982|ref|YP_004598089.1| 660 WFEIHVYPSP------TGLSVYFRDVTE 681
                                       8889998884......334577888876 PP

  == domain 6  score: 9.8 bits;  conditional E-value: 0.00075
                             PAS_9  19 aalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk....kerevevvlirkngetfwvlltaspvkdddge 91 
                                       +al+ +  s ee++g+ +t+ +     + e+l+++  + r     ++r++e +l  ++    w l+ a+pv d+ ge
  gi|336254982|ref|YP_004598089.1| 889 QALEEIDLSVEEFVGQTVTERY-----EGETLEQFESNFRAalagEQRSFEFELHSRE----W-LAYAVPVEDSRGE 955
                                       5666667788899999988888.....3333333333333344346699999999994....6.999********** PP

                             PAS_9  92 lvgiivilrDite 104
                                       +++  + ++Dite
  gi|336254982|ref|YP_004598089.1| 956 VFAGMLMVQDITE 968
                                       ************8 PP

  == domain 7  score: 33.2 bits;  conditional E-value: 4.1e-11
                             PAS_9    3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkng.. 73  
                                         + +++++g   ++Ne+++ l+G s +e+ g +  ++f  +t++  +  +++++e+g+  +r +  v+ +++   
  gi|336254982|ref|YP_004598089.1| 1000 VFYVIDENGDFQRWNESLRALTGLSDDELEGINALEFFegETEETVAAAIDEVFETGS--ARLEAEVEPDPDPgg 1072
                                        556667********************************77667777777777777777..555555554444234 PP

                             PAS_9   74 etfwvlltaspvkdddgelvgiivilrDite 104 
                                        et+++++ as++ d +ge v + +i rDi+e
  gi|336254982|ref|YP_004598089.1| 1073 ETVPYEFVASALEDPSGEPV-LTGIGRDISE 1102
                                        ***************99999.59******98 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   7.3e-09   8.8e-06       6      45 ..     186     226 ..     181     244 .. 0.76
   2 !   38.4   0.0   7.3e-13   8.7e-10       2      57 ..     309     365 ..     308     377 .. 0.84
   3 !   24.1   0.0   2.1e-08   2.6e-05       4      43 ..     432     471 ..     429     499 .. 0.71
   4 !    7.0   0.0    0.0051       6.1       9      46 ..     585     623 ..     578     646 .. 0.70
   5 ?    4.8   0.0     0.024        29       1      24 [.     860     884 ..     860     934 .. 0.60
   6 !   12.6   0.1   8.9e-05      0.11       5      57 ..     992    1042 ..     981    1055 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 7.3e-09
                             PAS_8   6 lfesspdgiavvd.lgdrivdvNqaalellGys.adlkgell 45 
                                       ++e+sp+gi+v+d +g+ ++++N++a+ ++G +  +l + +l
  gi|336254982|ref|YP_004598089.1| 186 IVETSPVGIVVTDvDGT-VRFANERAEAITGRDrSELVDRPL 226
                                       89*********999999.*************44444444444 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 7.3e-13
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrplle 57 
                                       r+  ++e++++gi ++d++dr+++vNqa++e++Gy+ ++++ge  g+l p+   + +
  gi|336254982|ref|YP_004598089.1| 309 RIYRALETASEGISLLDEDDRFTYVNQAYAEMYGYEpEEMIGEHWGILYPEGAAEDA 365
                                       778899***********8889*********************999977777666655 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 2.1e-08
                             PAS_8   4 ralfesspdgiavvd.lgdrivdvNqaalellGysadlkge 43 
                                       ++++e+sp+gi v+d +gd ++++N++a+e+l  + + ++ 
  gi|336254982|ref|YP_004598089.1| 432 EQIVETSPVGITVIDtDGD-LRFANDRAAEILECDREAIAG 471
                                       799************9999.************855222222 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0051
                             PAS_8   9 sspdgiavvdlgdrivdvNqaalellGys.adlkgellg 46 
                                        ++d+ + +d +++i+++N++a+ l     +++ g +l 
  gi|336254982|ref|YP_004598089.1| 585 RISDAFIGLDSNWTITYANDRAETLIDAAgEGIVGRDLS 623
                                       57899999997779***********96545667777776 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.024
                             PAS_8   1 erlralfesspdgiav.vdlgdriv 24 
                                       +r+r+l+e+ p+g++  +d++ r +
  gi|336254982|ref|YP_004598089.1| 860 RRYRTLVEQFPNGLVAlFDEDLRYT 884
                                       59**********9996467555543 PP

  == domain 6  score: 12.6 bits;  conditional E-value: 8.9e-05
                             PAS_8    5 alfesspdgiavvd.lgdrivdvNqaalellGysadlkgellgqllpvlrplle 57  
                                         ++++++d   v+d +gd +  +N++   l+G+s  +++ +  + l+ ++++ e
  gi|336254982|ref|YP_004598089.1|  992 DVLDAIDDVFYVIDeNGD-FQRWNESLRALTGLS--DDELEGINALEFFEGETE 1042
                                        389***************.*************99..444444577777777666 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 ?    0.4   0.0      0.76     9e+02      29      55 ..    1198    1228 ..    1170    1231 .. 0.63
   2 !   91.0   0.0   5.5e-29   6.5e-26       1     110 [.    1232    1341 ..    1232    1343 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.76
                                        EEEEEEE......TEEEEEEEESSSSSTTHHHT CS
                         HATPase_c   29 veikase......ddlvisveDnGiGipkedlk 55  
                                        v ++  e       dl++++e +G  i++ dl+
  gi|336254982|ref|YP_004598089.1| 1198 VDVD--EvvadvcTDLEMRIEETGAEIDVGDLP 1228
                                        3333..333345679**************9998 PP

  == domain 2  score: 91.0 bits;  conditional E-value: 5.5e-29
                                        EHHHHHHHHHHHHHHHHHHHHS.TTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSS CS
                         HATPase_c    1 gdekrLrqiisnlvdNavkfat.kageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggt 74  
                                        gd+ +Lrq+++nl+dNa+ +++ ++++i+v  +++e + visv D GiGi+++d++++f  f++  ++  ++ gt
  gi|336254982|ref|YP_004598089.1| 1232 GDPGQLRQLFQNLIDNAITYSGeETPRISVFAEKREATWVISVCDQGIGIDPDDVDRIFRVFDR-LHSVEEYDGT 1305
                                        7999****************66677899999997779***************************.889999**** PP

                                        SHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c   75 GlGlsivkklvelmgGeiwvesepgrGttftftlpl 110 
                                        G+Gl+++++++e+++G+i+v+sepg+G+tf ++lp 
  gi|336254982|ref|YP_004598089.1| 1306 GIGLALCQRIAERHDGTIRVDSEPGEGSTFSVHLPT 1341
                                        **********************************97 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.6e-06    0.0043       3      75 ..     205     281 ..     203     292 .. 0.78
   2 !   20.6   0.0   3.4e-07   0.00041       2      74 ..     331     400 ..     330     412 .. 0.79
   3 !   13.3   0.0   6.6e-05     0.079      36      79 ..     490     534 ..     453     539 .. 0.86
   4 ?   -1.8   0.0       3.4   4.1e+03       2      55 ..     600     651 ..     599     653 .. 0.87
   5 !    6.7   0.1    0.0075       8.9      11      55 ..     894     936 ..     888     942 .. 0.84
   6 !    9.9   0.0   0.00072      0.86       3      82 ..    1012    1091 ..    1010    1096 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.6e-06
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeD.....rervrealqealkkge.pyegeyRirrkdGeyrwvearar 73 
                                       +++er e i+G +++el ++   ++    p D      ++++  + ++l++ge ++++e+ ir++ G+ +wv a a 
  gi|336254982|ref|YP_004598089.1| 205 FANERAEAITGRDRSELVDR--PLAAEWDPVDdagepMSHCQLPVSRVLETGEpVWDVEFGIRTPGGDRVWVAANAA 279
                                       7999****************..666666665543223344444455999****999********************9 PP

                             PAS_3  74 vi 75 
                                       ++
  gi|336254982|ref|YP_004598089.1| 280 PM 281
                                       98 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.4e-07
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwveararv 74 
                                       +yv++++ e++Gy+pee++g   +w  +++pe   e +++++++ l++ + ++ge   +r+dG+   ve+++ +
  gi|336254982|ref|YP_004598089.1| 331 TYVNQAYAEMYGYEPEEMIGE--HWG-ILYPEGaAEDANAEIEAELAETGTWSGETIGLRRDGTE-FVEDHYLA 400
                                       79*******************..665.55555559999****988888888****9999999998.56666655 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 6.6e-05
                             PAS_3  36 ervrealqealkkge.pyegeyRirrkdGeyrwveararvirden 79 
                                       + +++ +++++++ge  +++e R+r++d   rw++  + ++r ++
  gi|336254982|ref|YP_004598089.1| 490 SAAERPFDRVISSGEaLFDVELRLRHPDARERWLSINGAPLRADE 534
                                       566777999******788**********************95544 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.4
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyege 55 
                                       +y+++r e +++   e + g+  ++  +    D ++++++l  a++++ep ++e
  gi|336254982|ref|YP_004598089.1| 600 TYANDRAETLIDAAGEGIVGR--DLSAAFPTADGSEFETELRGAMDRQEPTSIE 651
                                       799999999999999999999..9999999999999999999999888877665 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.0075
                             PAS_3  11 ilGyspeellgkveswldlvhpeDrervrealqealkkge.pyege 55 
                                       i ++s ee+ g+  ++ ++   e +e++++++ +al++ + ++e+e
  gi|336254982|ref|YP_004598089.1| 894 I-DLSVEEFVGQ--TVTERYEGETLEQFESNFRAALAGEQrSFEFE 936
                                       4.8899******..**********************8888666655 PP

  == domain 6  score: 9.9 bits;  conditional E-value: 0.00072
                             PAS_3    3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrk.dGeyrwveararvi 75  
                                         ++e+ + ++G+s++el+g   + l++   e  e v +a++e++++g+ ++e e+       Ge++  e  a+++
  gi|336254982|ref|YP_004598089.1| 1012 RWNESLRALTGLSDDELEGI--NALEFFEGETEETVAAAIDEVFETGSaRLEAEVEPDPDpGGETVPYEFVASAL 1084
                                        59******************..*************************9888888654333355555555555555 PP

                             PAS_3   76 rdengkp 82  
                                         d +g+p
  gi|336254982|ref|YP_004598089.1| 1085 EDPSGEP 1091
                                        5555555 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.2e-05     0.038       5     113 ..     191     303 ..     187     305 .. 0.82
   2 !   27.3   0.0   2.7e-09   3.2e-06       1     114 [.     314     421 ..     314     422 .. 0.76
   3 !   10.6   0.0    0.0004      0.48       5      37 ..     439     470 ..     435     531 .. 0.88
   4 ?    0.9   0.1       0.4   4.8e+02      99     114 ..     561     576 ..     550     577 .. 0.86
   5 ?    3.0   0.0      0.09   1.1e+02      69     114 ..     641     686 ..     586     687 .. 0.78
   6 ?    1.5   0.1      0.27   3.2e+02      57     114 ..     912     973 ..     889     974 .. 0.69
   7 ?    4.6   0.0      0.03        36       1      38 [.     994    1030 ..     994    1064 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                             PAS_7   5 sqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfere 81 
                                       + Gi+v D d+ +++ N+r   + +  ++ + v +pl++  +   + ge   +  +  v r+l+  +      f  +
  gi|336254982|ref|YP_004598089.1| 191 PVGIVVTDVDGTVRFANERAEAITGRDRSEL-VDRPLAAEWDPVDDAGEPM-SHCQLPVSRVLETGEPVWDVEFGIR 265
                                       6699999999999999999999999999999.9999999999999999999.7788889999999999888899888 PP

                             PAS_7  82 rpdgr..vievrgnpl....pdgGfVttytDiTerrra 113
                                       +p g   ++  ++ p+    +  G+Vtt++D+T++rr+
  gi|336254982|ref|YP_004598089.1| 266 TPGGDrvWVAANAAPMtagdEYTGVVTTFEDVTDERRH 303
                                       88776225666677775554457************996 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2.7e-09
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphs 77 
                                       le  s+Gis++D+d+r + +N+ y e++++ +e + +g +      ++  +g+ +  d++ae+e+ la+  + + ++
  gi|336254982|ref|YP_004598089.1| 314 LETASEGISLLDEDDRFTYVNQAYAEMYGYEPEEM-IGEHWG----ILYPEGAAE--DANAEIEAELAETGTWSGET 383
                                       68889*************************88888.455544....444444444..66677777777777766666 PP

                             PAS_7  78 fererpdgrvie.vrgnplpdgGfVttytDiTerrrae 114
                                       +  +r+  +++e     ++ dgG+V + +D+T++rr e
  gi|336254982|ref|YP_004598089.1| 384 IGLRRDGTEFVEdHYLARVGDGGLVCVVQDVTDERRIE 421
                                       66666666666614567899***************987 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0004
                             PAS_7   5 sqGisvfDadlrLvawNrrylelldlpeelvqv 37 
                                       + Gi+v+D d+ L++ N+r  e+l+  +e + +
  gi|336254982|ref|YP_004598089.1| 439 PVGITVIDTDGDLRFANDRAAEILECDREAI-A 470
                                       67**********************9998887.4 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.4
                             PAS_7  99 GfVttytDiTerrrae 114
                                       G + t +D+Te++r e
  gi|336254982|ref|YP_004598089.1| 561 GGIFTIEDVTEQKRLE 576
                                       7799********9976 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.09
                             PAS_7  69 aaragkphsfererpd.grvievrgnplpdgGfVttytDiTerrrae 114
                                       a+ +++p+s+e   p+ +++ e++  p p g + + + D+Ter++ e
  gi|336254982|ref|YP_004598089.1| 641 AMDRQEPTSIEEYVPAlETWFEIHVYPSPTG-LSVYFRDVTERKEME 686
                                       4555666666655544278899999999975.5668********987 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.27
                             PAS_7  57 gdveaeverrlaaaragkphsfererpdgrvievrgnplpdgGfV....ttytDiTerrrae 114
                                       g++ +++e  ++aa ag++ sfe e ++ +++       + +G V     + +DiTer+++e
  gi|336254982|ref|YP_004598089.1| 912 GETLEQFESNFRAALAGEQRSFEFELHSREWLAYAVPVEDSRGEVfagmLMVQDITERVETE 973
                                       56666677777777778888888888888877765544455554422216799******998 PP

  == domain 7  score: 4.6 bits;  conditional E-value: 0.03
                             PAS_7    1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvg 38  
                                        l+ +++ + v+D+++    wN+  + l +l+++ +  g
  gi|336254982|ref|YP_004598089.1|  994 LDAIDDVFYVIDENGDFQRWNESLRALTGLSDDEL-EG 1030
                                        567888899*********************99977.45 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   1.2e-09   1.5e-06       1     129 []      33     169 ..      33     169 .. 0.81
   2 ?    3.6   0.0     0.065        78      37      99 ..     227     292 ..     208     323 .. 0.74
   3 !   26.0   0.0   8.1e-09   9.7e-06       2     129 .]     710     848 ..     709     848 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.2e-09
                             GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagw.dgkpalsesld.edsalarralssgevvsepsfaee 75 
                                       ++d ll ++++ +   l a  + ++++  d ++l+ ++ +  +  a+  + + e+++l  ral  + +++e +  e+
  gi|336254982|ref|YP_004598089.1|  33 DVDRLLRDAVDGVRTQLEAAHCGVFEVA-DAETLRLRSESgRETLAVGATAPaEPDSLLGRALVDEDPIVEHAPGEA 108
                                       578899999999**************88.778999999884555555545568999999999999999988554332 PP

                             GAF_3  76 dg........lpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                                 ++ +  lav + +++ + Gvl++++t+ r+f  +++e+++s+A+++a+aie+
  gi|336254982|ref|YP_004598089.1| 109 -EigvvacpeSDIETGLAVAVGSREDPWGVLGVYTTERRDFATDTREFVKSVAAVLASAIEN 169
                                       .213333222556666*******99************************************8 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.065
                             GAF_3  37 aagwdgkpalsesldedsalarralssgevvsepsfaeedglpd...raalavPLvagrqviGvla 99 
                                       aa wd+ ++  e +  +++  +r+l++ge+v   +f  ++   d    aa a+P++ag++  Gv+ 
  gi|336254982|ref|YP_004598089.1| 227 AAEWDPVDDAGEPMSHCQLPVSRVLETGEPVWDVEFGIRTPGGDrvwVAANAAPMTAGDEYTGVVT 292
                                       5778**************************998877332222223456777789999888888876 PP

  == domain 3  score: 26.0 bits;  conditional E-value: 8.1e-09
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalse....sldedsalarralssgevvsepsf.. 72 
                                        de +++ll l+ + lg+e g+l   d++ +++ v+++ +  p+l+     sl+  +  +r++++s++ +++++   
  gi|336254982|ref|YP_004598089.1| 710 FDEKVDELLALGRERLGLETGFLAAIDPENERFEVTHADGDDPRLQPgstsSLV--ETYCRTTIESDGLLAFTDQpt 784
                                       7999**********************************9788888667545555..77779*******999955522 PP

                             GAF_3  73 .....aeedglpdraalavPLvagr.qviGvlalastkpra..fdaedlelleslArqiataier 129
                                            ++ +++++ ++l   +++ +   +G+l++  ++pr+  f++++++++e ++++++ ++er
  gi|336254982|ref|YP_004598089.1| 785 ehvdeRAYETWELDCYLGGQITV-DgDRYGTLCFVDDEPRSrpFTQTEKSFVELVTQWVSYELER 848
                                       2222233588********99999.66********999999888******************9997 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   1.2   2.7e-12   3.2e-09       3     138 .]      33     168 ..      31     168 .. 0.83
   2 ?    2.7   0.1      0.12   1.4e+02      43     110 ..     232     293 ..     181     324 .. 0.64
   3 ?    0.6   0.1      0.55   6.6e+02      20     101 ..     438     533 ..     428     539 .. 0.55
   4 !    8.0   0.0    0.0028       3.4       2     130 ..     708     839 ..     707     844 .. 0.69

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 2.7e-12
                                       HHHHHHHHHHHHHHH.SS...EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG- CS
                             GAF_2   3 dleelldlvldelve.lg.aalgyillvdddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndleed 77 
                                       d++ ll+ ++d +++ l  a++g++ + d ++ lrl++ +++e    +a+ ++  ++l+g+al +  p++ ++ + +
  gi|336254982|ref|YP_004598089.1|  33 DVDRLLRDAVDGVRTqLEaAHCGVFEVAD-AETLRLRSESGRETLAVGATAPAEPDSLLGRALVDEDPIV-EHAPGE 107
                                       899**********7779747777777766.5668988666666666666644556779*******99999.777777 PP

                                       S-HHHHHHHHHTT--EEEEEE.-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  78 pdkkglpaghaglrsflavPl.isegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       +     +  + ++ ++lav +  +e+ + Gvl++y++++++f  + +e+++++a+ +a aie
  gi|336254982|ref|YP_004598089.1| 108 AEIGVVACPESDIETGLAVAVgSRED-PWGVLGVYTTERRDFATDTREFVKSVAAVLASAIE 168
                                       78878888999**********66665.**********************************8 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                                       -TTSTT-S-B---TT.HHHHHHHHTS-EEES-GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEE CS
                             GAF_2  43 eeefgaaldrplgeg.lvgealrtgrpvilndleedpdkkglpaghaglrsflavPlisegrvvGvlnl 110
                                       +  + +++  +  +  +v ++l+tg+pv+          ++ p g++ + +  a P++++++  Gv++ 
  gi|336254982|ref|YP_004598089.1| 232 PVDDAGEP--MSHCQlPVSRVLETGEPVWDVE-----FGIRTPGGDRVWVAANAAPMTAGDEYTGVVTT 293
                                       33333333..4456656************433.....45566778888888888888887788888875 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.55
                                       ..EEEEEEE-TTS-EEEE.......................EEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES- CS
                             GAF_2  20 aalgyillvdddgglrla.......................awgeaeeefgaaldrplgeglvgealrtgrpvilnd 73 
                                       + +g+ + +d dg+lr a                        w e ++ +g  l  + +e ++ +++ +g++++   
  gi|336254982|ref|YP_004598089.1| 438 SPVGITV-IDTDGDLRFAndraaeilecdreaiaglssddsDW-EVRDADGRLL--SAAERPFDRVISSGEALFDVE 510
                                       5666543.45567766555555555555555444422221111.2333333333..336669999999999999433 PP

                                       GGG-S-HHHHHHHHHTT--EEEEEE-TT CS
                             GAF_2  74 leedpdkkglpaghaglrsflavPlise 101
                                             + ++p +++++ s+ + Pl+++
  gi|336254982|ref|YP_004598089.1| 511 -----LRLRHPDARERWLSINGAPLRAD 533
                                       .....35567777777777777777774 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHHHHHHH.SS..EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG CS
                             GAF_2   2 adleelldlvldelve.lgaalgyillvdddgg.lrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndlee 76 
                                       ++++e +d++l   +e lg + g+++ +d++++ +++ ++ ++++++     ++l e  + + +++   + ++d ++
  gi|336254982|ref|YP_004598089.1| 708 RSFDEKVDELLALGRErLGLETGFLAAIDPENErFEVTHADGDDPRLQPGSTSSLVETYCRTTIESDGLLAFTDQPT 784
                                       678888999999998889***********666646666555565555555545555556666666666666666333 PP

                                       -S-HHHHHHHHHTT--E.....EEEEE-TTS---EEEEES........--HHHHHHHHHHH CS
                             GAF_2  77 dpdkkglpaghaglrsf.....lavPlisegrvvGvlnlyankppa..fdeedlelLeela 130
                                             ++ +++++ ++     l+  ++ +g  +G l+++ ++p++  f++++ +++e++ 
  gi|336254982|ref|YP_004598089.1| 785 ------EHVDERAYETWeldcyLGGQITVDGDRYGTLCFVDDEPRSrpFTQTEKSFVELVT 839
                                       ......3333333333345556999**99999******9766655588********99876 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.2   6.5e-08   7.8e-05       1     133 []      33     167 ..      33     167 .. 0.73
   2 ?   -3.1   0.0       9.4   1.1e+04      13      63 ..     458     507 ..     456     528 .. 0.57
   3 !   15.0   0.0   2.5e-05      0.03       6     132 ..     714     845 ..     709     846 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.5e-08
                                       SHHHHHHHHHHHHHHHHTESEEEEEE.........EEETTEEECEEEEECC.....EEEETTSHHHHHHHHHSSSEE CS
                               GAF   1 dleelldtvveelrellgadrvalyl.........pdydGlhydipqasrw.....lfmkngrgicgqvlatgqplv 63 
                                       d+++ll+ +v+ +r  l+a ++ ++           +++G        ++      + + +++++ g++l   +p+v
  gi|336254982|ref|YP_004598089.1|  33 DVDRLLRDAVDGVRTQLEAAHCGVFEvadaetlrlRSESG--------RETlavgaTAPAEPDSLLGRALVDEDPIV 101
                                       7899********************9964433333322233........22234433555556677788899888888 PP

                                       ESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE..SSSCSHHHHHHHHHHHHHHHHHHH CS
                               GAF  64 ipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhn..psppftreelellqvladqvaval 133
                                        +   + +            +  i + l+v++ ++++ wG+l ++   ++  f ++ +e+++++a+ +a a+
  gi|336254982|ref|YP_004598089.1| 102 EH---APGEAEIG--VVACPESDIETGLAVAVGSREDPWGVLGVYTteRR-DFATDTREFVKSVAAVLASAI 167
                                       88...44443332..2233568888*********************6444.6**************999887 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.4
                                       HHHHHTESEEEE.EEEEETTEEECEEEEECCEEEETTSHHHHHHHHHSSSEE CS
                               GAF  13 lrellgadrval.ylpdydGlhydipqasrwlfmkngrgicgqvlatgqplv 63 
                                       ++e+l++dr a+  l ++d++++++ +a+  l     r+ +++v+++g++l 
  gi|336254982|ref|YP_004598089.1| 458 AAEILECDREAIaGL-SSDDSDWEVRDADGRLLSAAERP-FDRVISSGEALF 507
                                       678899999777223.22222222444444455555566.667777777665 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHTESEEEEEE..EEETTEEECEEEEECC.......EEEETTSHHHHHHHHHSSSEEESTGGTSTTH CS
                               GAF   6 ldtvveelrellgadrvalyl..pdydGlhydipqasrw.......lfmkngrgicgqvlatgqplvipdstpdprf 73 
                                       +d++++  re lg++ + l    p  +  ++++++a+         +  + +++ c ++++++  l ++d  +   +
  gi|336254982|ref|YP_004598089.1| 714 VDELLALGRERLGLETGFLAAidP--ENERFEVTHADGDdprlqpgSTSSLVETYCRTTIESDGLLAFTD--QPTEH 786
                                       566777777777777766643222..22222233333333322222222225556889999999999998..44445 PP

                                       HTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS...CSHHHHHHHHHHHHHHHHHH CS
                               GAF  74 aqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp...pftreelellqvladqvava 132
                                        +    +  e ++   +l+  +++dg+ +G+l++++  p   pft+ e  +++ + + v+ +
  gi|336254982|ref|YP_004598089.1| 787 VD---ERAYETWELDCYLGGQITVDGDRYGTLCFVDDEPrsrPFTQTEKSFVELVTQWVSYE 845
                                       55...3677899999*********************4444579************9999876 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.38   4.5e+02      23      58 ..     834     869 ..     832     870 .. 0.87
   2 ?   -3.3   0.4       8.4     1e+04      35      60 ..     970     995 ..     959     999 .. 0.65
   3 ?    0.3   0.1      0.63   7.6e+02      46      60 ..    1105    1118 ..    1081    1123 .. 0.83
   4 !   38.5   0.1   7.3e-13   8.7e-10       2      66 ..    1124    1190 ..    1123    1191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.38
                                       HHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  23 naeaLkregklteelkeyletiesearrldhlvedl 58 
                                       ++e+   ++++  e ++  +++e+++rr + lve++
  gi|336254982|ref|YP_004598089.1| 834 FVELVTQWVSYELERRRHQRDLEESERRYRTLVEQF 869
                                       67888888888899999****************985 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.4
                                       SSCHHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  35 eelkeyletiesearrldhlvedlLd 60 
                                        e +++l+  e+  ++  +  +d+Ld
  gi|336254982|ref|YP_004598089.1| 970 VETERQLRERERRLEQFKRYTDDVLD 995
                                       55566666666666666667777665 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.63
                                        HHHHHHHHHHHHHHH CS
                             HisKA   46 searrldhlvedlLd 60  
                                        +++rrl++lv+dl +
  gi|336254982|ref|YP_004598089.1| 1105 EHERRLEALVDDL-E 1118
                                        6789********9.3 PP

  == domain 4  score: 38.5 bits;  conditional E-value: 7.3e-13
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA    2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66  
                                        l++f+   +H+L  PL  ++ ++ +L+r+  ++l+++  e++e ++++a+r++++++ lL++sr ++
  gi|336254982|ref|YP_004598089.1| 1124 LEQFAYAASHDLQEPLRMVSSYLTLLERRyeDDLDDDAHEFIEFAVDGADRMQEMIDGLLQYSRVDT 1190
                                        789***********************7777*999******************************986 PP

>> sCache_like  Single Cache-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0012       1.4      15      62 ..     160     209 ..     149     224 .. 0.83
   2 ?   -3.5   0.0       9.1   1.1e+04      36      58 ..     310     332 ..     299     337 .. 0.69
   3 !    7.6   0.0    0.0033         4      35      81 ..     430     477 ..     414     486 .. 0.80
   4 ?   -1.5   0.0       2.1   2.5e+03      73     108 ..     922     956 ..     905     964 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                                       HHHHHHHS-GGG-SSHHHHH.HHHH.HHHHHT-EEEEEETTS-EEEETTS CS
                       sCache_like  15 akllasllenenlkaaenkk.vlee.asekldaritivdadgkvlydtgq 62 
                                       a++las +en   ++++ ++ +l++ + e +++ i++ d dg+v++  + 
  gi|336254982|ref|YP_004598089.1| 160 AAVLASAIENARTERQLREEaALNDrIVETSPVGIVVTDVDGTVRFANER 209
                                       889*************99987776559*******************9877 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.1
                                       HHHHHHHHT-EEEEEETTS-EEE CS
                       sCache_like  36 leeasekldaritivdadgkvly 58 
                                       +  a e  ++ i+++d+d++  y
  gi|336254982|ref|YP_004598089.1| 310 IYRALETASEGISLLDEDDRFTY 332
                                       55556667788999999887665 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0033
                                       HHHHHHHHHT-EEEEEETTS-EEEETTS....S---HHHHHHHHTT-- CS
                       sCache_like  35 vleeasekldaritivdadgkvlydtgq.eieeaeseavikellskee 81 
                                       + e++ e +++ it++d+dg  ++         + +++ i  l+s + 
  gi|336254982|ref|YP_004598089.1| 430 LKEQIVETSPVGITVIDTDGDLRFANDRaAEILECDREAIAGLSSDDS 477
                                       45899*******************998876777777888877777665 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 2.1
                                       HHHHHTT--.....EE-----S-EEEEEEEEE.TTEE CS
                       sCache_like  73 ikellskeerskevviteeeedlyyyavpikk.egeq 108
                                        +++l +e+    +  + +  + + yavp+ +  ge 
  gi|336254982|ref|YP_004598089.1| 922 FRAALAGEQ--RSFEFELHSREWLAYAVPVEDsRGEV 956
                                       455566666..34444556678899*****9977775 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.2e-06    0.0014       5      92 ..    1236    1330 ..    1233    1339 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                       HATPase_c_5    5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.......ek....kklesskskkeehG 68  
                                         l  ++ nl+dNAi  + +   e++ I++ +++++ + +is+  +  g       ++    ++l+s  ++ +  G
  gi|336254982|ref|YP_004598089.1| 1236 QLRQLFQNLIDNAITYSGE---ETPRISVFAEKREATWVISVCDQGIGidpddvdRIfrvfDRLHS-VEEYDGTG 1306
                                        57789*********98766...3689**************99998666666655411433466666.567999** PP

                       HATPase_c_5   69 iGlksireivkkykgnlsieaedg 92  
                                        iGl   ++i+++++g+++++ e g
  gi|336254982|ref|YP_004598089.1| 1307 IGLALCQRIAERHDGTIRVDSEPG 1330
                                        ******************998865 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 ?   14.0   0.0   2.7e-05     0.032       9      58 ..    1243    1294 ..    1239    1315 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-05
                       HATPase_c_3    9 elvdNsldAdaen...vkievnknrgktgeivieDdGkGmseeelknalrlat 58  
                                         l+dN+++ + e+   +++ ++k++ +t  i++ D G G++++++++ +r+  
  gi|336254982|ref|YP_004598089.1| 1243 NLIDNAITYSGEEtprISVFAEKRE-ATWVISVCDQGIGIDPDDVDRIFRVFD 1294
                                        699***9955554466999888875.89*******************998644 PP

>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00039      0.47      52      97 ..     972    1017 ..     962    1021 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                            GCN5L1   52 lekeakalqanvakfakqtdqWlalvesfnsalkeiGDvenWakti 97  
                                         e ++++ ++++++f++ td  l +++++   ++e GD++ W +++
  gi|336254982|ref|YP_004598089.1|  972 TERQLRERERRLEQFKRYTDDVLDAIDDVFYVIDENGDFQRWNESL 1017
                                        4778999999********************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.88u 0.27s 00:00:01.14 Elapsed: 00:00:00.42
# Mc/sec: 9580.06
//
Query:       gi|336254983|ref|YP_004598090.1|  [L=414]
Description: Extracellular ligand-binding receptor [Halopiger xanaduensis SH-6]
Scores for 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-29  101.1  10.5    1.2e-28  100.7  10.5    1.1  1  Peripla_BP_6  Periplasmic binding protein
    4.1e-19   68.9   0.0    5.4e-19   68.5   0.0    1.1  1  ANF_receptor  Receptor family ligand binding region


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7  10.5   1.4e-32   1.2e-28       5     312 ..      45     344 ..      41     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 1.4e-32
                                       EEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETTEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-BSHHH CS
                      Peripla_BP_6   5 GlltplsGpyassgksllagaqaafeeiNaaGGinGrkielverDdaydpdraaeaarrlvdqdgvdalvgplssav 81 
                                       G++ plsG + s+g +l +ga + ++e+ aa   + ++++ +++D + +p+ a++aa +l d +   a+vg+ +s+v
  gi|336254983|ref|YP_004598090.1|  45 GAVLPLSGELESFGGALTNGAALPAAELEAAD--LEVEVDHTVADSETSPTAAVDAAAELAD-ESYPAIVGAAGSDV 118
                                       999*************************9985..89**************************.************** PP

                                       HHHHHHHHHH.HT-EEEESS-HHCC....TTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHHHHHH CS
                      Peripla_BP_6  82 aaavaevlak.dgvpvigpagltge....kcspyvfslgpsysaqasalveylakelggkkvalvyadyafgregia 153
                                       ++++++ ++    v+  +pa++t++    +  +y f+++p++s qa  +++ ++ e+++ ++a++ya+  +gr++  
  gi|336254983|ref|YP_004598090.1| 119 TLQMTQQATIpSEVVSCSPASTTPTmsilNDRGYSFRTAPDDSLQAVIAARLAVIEHDADSAATLYAAGDYGRQLSG 195
                                       ****99888846677777999998667779*********************************************** PP

                                       HHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC.-CH CS
                      Peripla_BP_6 154 alkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakrillvsws.gse 229
                                       a+ a++    ge+  ++ ++ +++++++ + ++ +  +d+++l+ ++++ + ll ++ +       il+vs +  +e
  gi|336254983|ref|YP_004598090.1| 196 AFSASFD---GEIQHQVSFT-PGESYAEPLSEALSDDPDILFLICYPESGIPLLEEYYAEHAGD-EILFVSDGlQDE 267
                                       ******9...8986566666.5589********************************5554443.599999886888 PP

                                       HHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCTHCCHHHHHH CS
                      Peripla_BP_6 230 edlkalggeaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaagsltreavra 306
                                       + l+++gg +++ +++++p     ++p  +af+  y++ y+++  p +faa++y+aa+ +l a  aag+++++a++ 
  gi|336254983|ref|YP_004598090.1| 268 AVLEGVGG-SMDDAYGTAP---RSNGPGRDAFASLYRDEYDAD--PGLFAANCYDAAATILLANAAAGANDGAAIAG 338
                                       88999999.9*******77...55799***************8..******************************** PP

                                       HHHHS- CS
                      Peripla_BP_6 307 aleslg 312
                                       ++++++
  gi|336254983|ref|YP_004598090.1| 339 RMREVT 344
                                       ***998 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 !   68.5   0.0     6e-23   5.4e-19      25     346 ..      77     392 ..      70     400 .. 0.81

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 6e-23
                                       EEEEE....EE-TT-HHHHHHHHHHHCCCCEEEEEE-SSHHHHHHHHHHHCC.TT-EEEESS---GGGG-TTTTTTE CS
                      ANF_receptor  25 lgyei....idtccdfslaleaaldflkgkvvaviGpssssvsdavaslanl.fkiPvisygstspelsdknryptf 96 
                                       l++e+     d++ ++++a+ aa ++   +  a++G+++s+v+ ++ + a+   ++   s++st+p++s +n   + 
  gi|336254983|ref|YP_004598090.1|  77 LEVEVdhtvADSETSPTAAVDAAAELADESYPAIVGAAGSDVTLQMTQQATIpSEVVSCSPASTTPTMSILNDRGYS 153
                                       4555544569******************99**********9998887777753789999****************** PP

                                       EESS--CHHHHHHHHHHHH.HTT--EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEESTCHHHCHHHHHHHHH CS
                      ANF_receptor  97 lrtvpsdtsqaqAivdilk.hfgWkkvaliysdddygesglqaleeeleergicvalkekipessnddevvrkllke 172
                                       +rt+p+d+ qa   +++   +   +++a++y+ +dyg+ +  a++ +++    +++++ +++     ++ +++l + 
  gi|336254983|ref|YP_004598090.1| 154 FRTAPDDSLQAVIAARLAViEHDADSAATLYAAGDYGRQLSGAFSASFDG---EIQHQVSFT---PGESYAEPLSEA 224
                                       **********9988888777889***********************7776...9********...566777777766 PP

                                       HTTT--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC..HHHHHTT-EEEEE--B-HHHHHH CS
                      ANF_receptor 173 ikskarvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpeltgleaaegvlgfrlkdpnspkfse 249
                                       +++++++ +l c++e+   ll++ + +   +e   ++ sd+++++ vl          ++ + g +  ++n p+ + 
  gi|336254983|ref|YP_004598090.1| 225 LSDDPDILFLICYPESGIPLLEEYYAEHAGDE-ILFV-SDGLQDEAVLEGVG----GSMDDAYGTAP-RSNGPGRDA 294
                                       799************************99995.8888.99988888888553....34566666665.999999999 PP

                                       HHHST--CCCSSSTCCGSTTCCHHHHH...HHHH..HHHHHHHHHHHCHH........SSSHCCB-HHHH....... CS
                      ANF_receptor 250 fldkreklsdekqnyenegkeqisyqaalmYdaV..yllaeAlnkllrkk........kpgralscntlk....... 309
                                       f           + y++e    +  +aa  Yda    lla+A+  ++  +          ++++     +       
  gi|336254983|ref|YP_004598090.1| 295 FA----------SLYRDEYDADPGLFAANCYDAAatILLANAAAGAN--DgaaiagrmREVTSG-----Egedvlpg 354
                                       99..........566666666666677777*9861156666666665..656866555333333.....14445578 PP

                                       CCHHHHHHHHHHHT-EEEETTSCEEB-TTSBBE.-EEE CS
                      ANF_receptor 310 pweggqkllrylrnvnfeGltGdvkfdengdrv.ptyd 346
                                       ++  g     + + v+++G +G+++fdengd     y+
  gi|336254983|ref|YP_004598090.1| 355 DLAAGIERAAAGEPVRYRGAAGEIEFDENGDGGsVEYE 392
                                       899999999999*******************9888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 3411.71
//
Query:       gi|336254984|ref|YP_004598091.1|  [L=825]
Description: methyl-accepting chemotaxis sensory transducer [Halopiger xanaduensis SH-6]
Scores for complete 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-37  129.2  25.2    1.4e-37  129.2  25.2    4.7  4  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
    2.1e-13   50.4   1.6    2.1e-13   50.4   1.6    5.2  5  HAMP            HAMP domain
    4.5e-09   36.5   0.3    4.5e-09   36.5   0.3    3.9  2  dCache_1        Cache domain
    2.7e-06   27.5  53.3    0.00018   21.7   3.4    7.4  7  DUF948          Bacterial protein of unknown function (DUF948
  ------ inclusion threshold ------
      0.082   12.9  49.4       0.98    9.4   8.0    5.7  5  Laminin_II      Laminin Domain II
       0.11    9.9  56.2       0.21    9.0  30.5    2.2  2  DUF3584         Protein of unknown function (DUF3584)
       0.17   12.2   1.2        6.4    7.1   0.1    3.5  2  Retrotrans_gag  Retrotransposon gag protein
       0.21   12.0  45.9       0.41   11.1  10.4    3.6  3  Fez1            Fez1
       0.22   11.6  39.5      0.071   13.2   2.9    6.5  5  DUF1664         Protein of unknown function (DUF1664)
       0.47   10.8  34.2      0.081   13.2   4.0    6.0  5  BLOC1_2         Biogenesis of lysosome-related organelles com
       0.77    9.9   5.2         13    5.9   0.3    3.3  2  MbeD_MobD       MbeD/MobD like
       0.92    9.9  12.7         16    6.0   2.1    5.0  5  Syntaxin_2      Syntaxin-like protein
        1.7    6.9  43.1      0.047   12.1  10.7    2.4  2  MAD             Mitotic checkpoint protein
        3.1    7.7  13.8        5.2    7.0   0.6    4.8  5  DUF1759         Protein of unknown function (DUF1759)
        3.5    8.4  45.7       0.26   12.0   2.0    5.8  5  DUF2203         Uncharacterized conserved protein (DUF2203)
        3.5    7.6  28.3      0.085   12.9   4.9    4.9  5  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
        5.6    6.8  12.1        3.4    7.6   4.1    3.8  3  STAT_alpha      STAT protein, all-alpha domain
        7.4    7.1  25.4         13    6.3   4.0    5.8  5  NPV_P10         Nucleopolyhedrovirus P10 protein
        7.6    5.9  14.1       0.44    9.9   2.9    3.0  3  Mce4_CUP1       Cholesterol uptake porter CUP1 of Mce4, putat
          8    5.4  37.5        1.8    7.6   8.0    3.3  3  AIP3            Actin interacting protein 3
        9.5    5.0  21.6      0.092   11.6   7.4    2.4  2  LMBR1           LMBR1-like membrane protein


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0  10.3       3.2   2.8e+03      74     153 ..     414     494 ..     372     495 .. 0.72
   2 !   13.4  17.2   5.9e-05     0.051      75     167 ..     479     571 ..     475     576 .. 0.90
   3 !  129.2  25.2   1.6e-40   1.4e-37       2     170 ..     581     749 ..     574     751 .. 0.93
   4 ?    3.3   2.6     0.076        65     133     169 ..     747     783 ..     745     798 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHH.HHHHHHHHHHHH CS
                         MCPsignal  74 AdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveav.aevadlvqeiaa 149
                                       A+  ++ Ae+++  a+  ++ i+e+++e +++++   et + ++ g   v+ t ++ +e   a+ +e ++++ ei +
  gi|336254984|ref|YP_004598091.1| 414 AERAQADAEEAKADAEAERERIAEVTEELERTADRYGETMRAAADGDLSVRATVDTDNEQMRAIgEEFNAMLAEIER 490
                                       55555567777777777777788888888888888888888888888888888777666666662456777888888 PP

                                       HHHH CS
                         MCPsignal 150 asee 153
                                       a+ee
  gi|336254984|ref|YP_004598091.1| 491 AVEE 494
                                       8776 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.9e-05
                                       HHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  75 dEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaas 151
                                       +E  ++ ++   a +e+++  +++ ++++++++s e++r+  e+ +e v++  e+ ++ + + + +++++++++a++
  gi|336254984|ref|YP_004598091.1| 479 EEFNAMLAEIERAVEEVKQFAVDVAAQSEEVTASSEQVRTASEQVAESVQQISEVAETQSVRLQTIESEMSDLSAST 555
                                       556666667788999*****99******************************************************* PP

                                       HHHHHHHHHHHHHHHH CS
                         MCPsignal 152 eeqsasieevnqavee 167
                                       ee+++++++v++  e+
  gi|336254984|ref|YP_004598091.1| 556 EEIASTATDVATVAER 571
                                       **********998776 PP

  == domain 3  score: 129.2 bits;  conditional E-value: 1.6e-40
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHH CS
                         MCPsignal   2 dlaeeaseeAeeggkevanvvkqmeeieksskeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVAdEVr 78 
                                       ++ae a +e +  +   + +v++++++e +++++ ++++ i eiadQT lLALNA+iEAA AG+ G+GFaVVA+EV+
  gi|336254984|ref|YP_004598091.1| 581 EAAERAIDEMTAVESDAEYAVETIRSLEAEVEQVDELVDAIAEIADQTSLLALNASIEAADAGGDGDGFAVVANEVK 657
                                       34444444444556666779999****************************************************** PP

                                       HHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  79 kLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqs 155
                                       +L + +++aa eie+ i+ i + +++sv+++eet +rv++g+e+v+ + e+l+ei+e ++e ++ vqei+aa+e+q+
  gi|336254984|ref|YP_004598091.1| 658 SLSADAKEAAAEIEDRIETIRERTDQSVNVVEETSERVQQGTETVRPAVESLEEIAEYAEETNEGVQEISAATEDQA 734
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHH CS
                         MCPsignal 156 asieevnqaveevak 170
                                        s  +v +av+ va+
  gi|336254984|ref|YP_004598091.1| 735 DSTAQVVTAVDDVAS 749
                                       **********99986 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.076
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 133 iveavaevadlvqeiaaaseeqsasieevnqaveeva 169
                                       ++++ +e a++ + ++aa+eeq+as+++v+++v  +a
  gi|336254984|ref|YP_004598091.1| 747 VASSSEESASEAESVSAAAEEQTASLTQVSESVGDLA 783
                                       5566677778888899999999999999999987654 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   1.6   2.5e-16   2.1e-13       1      52 [.     343     394 ..     343     395 .. 0.97
   2 !   13.0   1.7   0.00012     0.099      15      52 ..     451     489 ..     440     490 .. 0.88
   3 ?   -1.5   0.1       4.1   3.5e+03      10      22 ..     614     626 ..     611     641 .. 0.76
   4 ?   -1.1   0.1       3.1   2.6e+03      10      36 ..     685     711 ..     683     714 .. 0.77
   5 ?   -0.3   0.1       1.7   1.4e+03       7      28 ..     776     806 ..     772     818 .. 0.59

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2.5e-16
                                       HHHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHHH CS
                              HAMP   1 llarrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrLr 52 
                                       +lar+++ PL+ L+  a+r+ +Gdld++l++++ DE+G+L raf++M++ L 
  gi|336254984|ref|YP_004598091.1| 343 VLARQTVTPLQDLRNRAERMEEGDLDVDLETDRIDEVGRLYRAFDEMRTTLT 394
                                       69**********************************************9985 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                                       HHHHHHTTTBTSSTCCTTSSSH.HHHHHHHHHHHHHHHH CS
                              HAMP  15 raarriaaGdldtrlpvsgrDE.iGeLarafNaMldrLr 52 
                                       +++r+ a+Gdl++r +v++++E ++++++ fNaMl +++
  gi|336254984|ref|YP_004598091.1| 451 ETMRAAADGDLSVRATVDTDNEqMRAIGEEFNAMLAEIE 489
                                       58999999*********666666************9987 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHHTT CS
                              HAMP  10 LrrLaraarriaa 22 
                                       + +L++a+++ia+
  gi|336254984|ref|YP_004598091.1| 614 VDELVDAIAEIAD 626
                                       578999*****96 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHTTTBTSSTCCTTSSSH CS
                              HAMP  10 LrrLaraarriaaGdldtrlpvsgrDE 36 
                                       ++ ++++ +r+++G  ++r+ v++  E
  gi|336254984|ref|YP_004598091.1| 685 VNVVEETSERVQQGTETVRPAVESLEE 711
                                       566789999*****9999988876555 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHTTT.........BTSST CS
                              HAMP   7 lrPLrrLaraarriaaG.........dldtr 28 
                                       + ++  La++a+++++          ++dt+
  gi|336254984|ref|YP_004598091.1| 776 SESVGDLAEQAAALSSRldrfetsdgNVDTD 806
                                       5667889999999998333333333344433 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.3   5.3e-12   4.5e-09       2     248 ..      85     308 ..      84     309 .. 0.77
   2 ?    1.1   1.6      0.33   2.8e+02       9      82 ..     657     731 ..     650     757 .. 0.66

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 5.3e-12
                          dCache_1   2 aieeqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvy 78 
                                       ++e++ae+ql++++ + a++i+++  s+e+ ++ l+s p+l++          + +   ++ ++s ++   d++++ 
  gi|336254984|ref|YP_004598091.1|  85 TVERDAEQQLTSTVDMHADSINEWTISMESHTRSLSSAPELAGT---------DAETTEAHVIQSQAALPVDVRAIH 152
                                       6899***********************************99874.........34445567777777777799**** PP

                          dCache_1  79 lvdadGq.viassdpssppnlegtddpadrdw..ykealaggg.gkpvisdp.yvdqtggkpvitiavpiyddsgkf 150
                                       +vd +++ v++s++ +  ++       +d++w  +   ++    ++++ sd+ y+d t ++ vi++a+p+  d    
  gi|336254984|ref|YP_004598091.1| 153 VVDTNNDrVLTSTNGELRGQS---LGSVDEPWteIEPGVDLTAaNDVWQSDTaYRDGTLDDQVISFASPVEGD-EAR 225
                                       **9777715555544444333...4555788877444444444668889999679988999**********97.788 PP

                          dCache_1 151 iGvlaadldldnlqdllsniklgetgyvfivdsdG.niiahpdkdllgknlrdelkaqealekalakiesgvssvkl 226
                                       i v+++ +      d l++++++  ++++ivd +G +++a+++ +       d +    a+  ++ ++    +++++
  gi|336254984|ref|YP_004598091.1| 226 IAVVVGTIEYR--VDGLRQLHED--QETMIVDTEGrTVLASSELEG------DAD----AEIVEQLGTVRDGTRFER 288
                                       99999999877..8999*99955..69*****99967777887444......222....34566678999999999* PP

                          dCache_1 227 ngeeylvayapiptglgWylvv 248
                                       +g+    aya+   +++W  v 
  gi|336254984|ref|YP_004598091.1| 289 DGDLV-TAYAATA-DNDWVAVT 308
                                       99887.8899998.6***9885 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.33
                          dCache_1   9 eqllglaeqlanniedvldsle....nlaetlasnps.lqdlleepnraneasreslqallksilksnpdisgvylv 80 
                                       ++l++ a+++a++ied +++++    ++++ + ++++ +q++ e          esl+++ +   ++n+++++++ +
  gi|336254984|ref|YP_004598091.1| 657 KSLSADAKEAAAEIEDRIETIRertdQSVNVVEETSErVQQGTETV----RPAVESLEEIAEYAEETNEGVQEISAA 729
                                       6788889999999999998877555566666655554466654432....234444444444444446666666655 PP

                          dCache_1  81 da 82 
                                       ++
  gi|336254984|ref|YP_004598091.1| 730 TE 731
                                       54 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 ?   -0.3   0.0       1.5   1.3e+03      10      52 ..      60     104 ..      59     122 .. 0.62
   2 ?    2.7   3.0      0.18   1.5e+02      21      80 ..     386     445 ..     327     451 .. 0.76
   3 !   21.7   3.4   2.1e-07   0.00018      23      86 ..     462     525 ..     460     528 .. 0.96
   4 !    6.9   3.8    0.0085       7.3      32      87 ..     513     568 ..     510     570 .. 0.93
   5 ?    4.2   5.7     0.059        50      25      85 ..     570     629 ..     536     632 .. 0.62
   6 !   15.9   2.0   1.3e-05     0.011      19      87 ..     651     719 ..     649     721 .. 0.92
   7 ?    4.1   5.1     0.065        55      28      87 ..     723     782 ..     716     791 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                            DUF948  10 FvvLviflivvllkl..kktldeaaatieelekqvdpilkevedl 52 
                                       Fv+ ++ +ivvl  +  +  +d+ ++  ++ e+q++++++  +d 
  gi|336254984|ref|YP_004598091.1|  60 FVISIVAIIVVLSAVgaAGYVDAERTVERDAEQQLTSTVDMHADS 104
                                       777777888888777654445555555555666666555544444 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.18
                            DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadl 80 
                                       + +++ tl++  +  +e +++++    e+e++ a ++e  +d + + e++ ++te+++ +
  gi|336254984|ref|YP_004598091.1| 386 FDEMRTTLTAQITEAREAKEEAETAQAEAERAQADAEEAKADAEAERERIAEVTEELERT 445
                                       333444555555555555567777777777777777777777777888888887776655 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 2.1e-07
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       +++ t+d  +++++ ++++ +++l e+e+++++v++ + dv  ++e+v +  e+v++++e+v+e
  gi|336254984|ref|YP_004598091.1| 462 SVRATVDTDNEQMRAIGEEFNAMLAEIERAVEEVKQFAVDVAAQSEEVTASSEQVRTASEQVAE 525
                                       6899********************************************************9975 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0085
                            DUF948  32 aatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       ++++++  +qv + ++++ ++ ++  + l+ +++++ ++ + te++a +++ v+++
  gi|336254984|ref|YP_004598091.1| 513 SEQVRTASEQVAESVQQISEVAETQSVRLQTIESEMSDLSASTEEIASTATDVATV 568
                                       6899999********************************************99987 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.059
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvne.........lledvneklekvdplteavadlgesvs 85 
                                       ++t++e ++  e  e+ +d+++           +         +   ++ ++e+vd+l++a+a+++++ s
  gi|336254984|ref|YP_004598091.1| 570 ERTVEESRRGSEAAERAIDEMTA----------VesdaeyaveTIRSLEAEVEQVDELVDAIAEIADQTS 629
                                       34444444444444444443333..........02222222224666888***************99876 PP

  == domain 6  score: 15.9 bits;  conditional E-value: 1.3e-05
                            DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       vv +++k++   a+++ +e+e++++ i + +++ ++ v+e+ e v++ +e+v p +e++++++e  +e 
  gi|336254984|ref|YP_004598091.1| 651 VVANEVKSLSADAKEAAAEIEDRIETIRERTDQSVNVVEETSERVQQGTETVRPAVESLEEIAEYAEET 719
                                       778889999999**************************************************9877665 PP

  == domain 7  score: 4.1 bits;  conditional E-value: 0.065
                            DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       ++e++a+ e+  + + ++++ v+d+ + ++e +++ ++ +++ ++ t+++ +++esv +l
  gi|336254984|ref|YP_004598091.1| 723 VQEISAATEDQADSTAQVVTAVDDVASSSEESASEAESVSAAAEEQTASLTQVSESVGDL 782
                                       455555555555666666666666666666666666665555555555555555555554 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   3.5     0.048        41       1      62 [.     403     464 ..     403     466 .. 0.93
   2 ?    9.4   8.0    0.0011      0.98       3      95 ..     465     558 ..     463     558 .. 0.69
   3 ?    6.7   5.6    0.0079       6.7       9      95 ..     538     624 ..     527     634 .. 0.86
   4 ?    5.9   3.0     0.014        12       5      69 ..     653     717 ..     651     721 .. 0.83
   5 ?    8.9   5.8    0.0017       1.4       2      84 ..     720     802 ..     707     809 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.048
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   1 skelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvk 62 
                                       +ke a+ a+  a+  +++ ++ +++ e ++e + e+ +++e+t +   + ++a +d   sv+
  gi|336254984|ref|YP_004598091.1| 403 AKEEAETAQAEAERAQADAEEAKADAEAERERIAEVTEELERTADRYGETMRAAADGDLSVR 464
                                       7999*****************************************99999999998887776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXX--TTTTTGGGH CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdAr....rsvkkLeklapqLldkl 75 
                                       ++++  ne++ ++ e  +++ +++e+  e++++++ +v+   e+v ++++++r A+    +sv+++ ++a+    +l
  gi|336254984|ref|YP_004598091.1| 465 ATVDTDNEQMRAIGEEFNAMLAEIERAVEEVKQFAVDVAAQSEEVTASSEQVRTASeqvaESVQQISEVAETQSVRL 541
                                       66666777777777777777777777777777777777777777766666666655111167889999999999999 PP

                                       HHHHHHHHH...HHHHHHHH CS
                        Laminin_II  76 kelkqleeassslsdnisei 95 
                                       ++++   +    ls++ +ei
  gi|336254984|ref|YP_004598091.1| 542 QTIESEMSD---LSASTEEI 558
                                       999988888...88777766 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0079
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH. CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeas 85 
                                       +  ++ +++ + +ls+ +e++ + +  +++ +e+t e+ +  ++a + A +++  +e  a+  ++ +++l+   e+ 
  gi|336254984|ref|YP_004598091.1| 538 SVRLQTIESEMSDLSASTEEIASTATDVATVAERTVEESRRGSEAAERAIDEMTAVESDAEYAVETIRSLEAEVEQV 614
                                       45678899999999****************999999999999***************************99999996 PP

                                       ..HHHHHHHH CS
                        Laminin_II  86 sslsdnisei 95 
                                         l d i ei
  gi|336254984|ref|YP_004598091.1| 615 DELVDAIAEI 624
                                       6677777766 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTT CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklap 69 
                                       a+e+++  +  +e  a+++ ++e ++e   +  + veet e v++ ++++r A +s  ++ + a+
  gi|336254984|ref|YP_004598091.1| 653 ANEVKSLSADAKEAAAEIEDRIETIRERTDQSVNVVEETSERVQQGTETVRPAVESLEEIAEYAE 717
                                       56667777778888999999999999999999999999999999999999999888888777665 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0017
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                       +e ++e++  ++   + +a++ + ++ + ++ +e ++++e + + +++ +  + ++++sv +L ++a  L ++l + 
  gi|336254984|ref|YP_004598091.1| 720 NEGVQEISAATEDQADSTAQVVTAVDDVASSSEESASEAESVSAAAEEQTASLTQVSESVGDLAEQAAALSSRLDRF 796
                                       45566677777777777788888888888888888888888888899999999999999999999999999999888 PP

                                       HHHHHH CS
                        Laminin_II  79 kqleea 84 
                                       ++   +
  gi|336254984|ref|YP_004598091.1| 797 ETSDGN 802
                                       876655 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  22.7    0.0025       2.2     603     753 ..     381     529 ..     366     533 .. 0.77
   2 ?    9.0  30.5   0.00025      0.21     602     895 ..     521     815 ..     511     823 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0025
                           DUF3584 603 eLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklekaiaerk 679
                                        L ++ + + ++l ++  ++ +a ee+++++ae+e a++ ++ea++ ++ +r+++  +++e e+ +d+  + + ++ 
  gi|336254984|ref|YP_004598091.1| 381 RLYRAFDEMRTTLTAQITEAREAKEEAETAQAEAERAQADAEEAKADAEAERERIAEVTEELERTADRYGETMRAAA 457
                                       677889999********************************************************999876665554 PP

                           DUF3584 680 q...qaeeqlqkldaqlkqleeqqkaaleelkedlseerlekkakwqevvgeldeqlaelkkaieaartqakarlke 753
                                       +   ++++ +++ ++q+ ++ e+ +a+l+e+++ ++e +     + ++ v++ +e++++ ++++  a +q ++ +++
  gi|336254984|ref|YP_004598091.1| 458 DgdlSVRATVDTDNEQMRAIGEEFNAMLAEIERAVEEVK-----QFAVDVAAQSEEVTASSEQVRTASEQVAESVQQ 529
                                       4222788999999999***************99998877.....444444444444444444444444444444443 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00025
                           DUF3584 602 eeLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklekaiaer 678
                                       e++ e +q+++e  ++++ + + +e+e+++l+a  ee    +++ at ++ + ++ +r +++ e++ d+++ a+++ 
  gi|336254984|ref|YP_004598091.1| 521 EQVAESVQQISEVAETQSVRLQTIESEMSDLSASTEEIASTATDVATVAERTVEESRRGSEAAERAIDEMT-AVESD 596
                                       5888999***********************************************************99997.67888 PP

                           DUF3584 679 kqqaeeqlqkldaqlkqleeqqkaaleelkedlseerlekkakwqevvgeld......eqlaelkkaieaartqaka 749
                                        + a e +++l+a+ +q++e   +a++e++++ s   l+ + + ++  g+ d      +++++l++ +++a ++ + 
  gi|336254984|ref|YP_004598091.1| 597 AEYAVETIRSLEAEVEQVDE-LVDAIAEIADQTSLLALNASIEAADAGGDGDgfavvaNEVKSLSADAKEAAAEIED 672
                                       899999***********997.56778899999999888888888887776553333337778888888888888888 PP

                           DUF3584 750 rlkeleeaykreLkskdvDpetvkelkrkieeLekkieriekrreevreYraflqetwlkvdslaeerpalkeqvee 826
                                       r++++ e  ++++    v +et +++++ +e+    +e  e+ +e + e ++ +qe  ++ ++ a+  ++ ++ v +
  gi|336254984|ref|YP_004598091.1| 673 RIETIRERTDQSV---NVVEETSERVQQGTETVRPAVESLEEIAEYAEETNEGVQEISAATEDQADSTAQVVTAVDD 746
                                       8888888877766...466777778888888888888888888888888888899999999999999999******* PP

                           DUF3584 827 lesaaeeleqeltrliedtklerkklekerkalekqldqldenlrklrdllsklaelkldadaeqaege 895
                                       + s+ ee+  e +  +++++ + + l + +++  ++++q+ ++ ++l+ +    +++  d d ++a+ +
  gi|336254984|ref|YP_004598091.1| 747 VASSSEESASEAESVSAAAEEQTASLTQVSESVGDLAEQAAALSSRLDRFETSDGNVDTDVDRDSADRT 815
                                       *****************************************9999987766666888888888777754 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0075       6.4      54      83 ..     693     720 ..     666     741 .. 0.81
   2 ?    1.4   0.0      0.46   3.9e+02      44      79 ..     760     795 ..     753     806 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0075
                    Retrotrans_gag  54 sslrQgtesvreYvtrfktladqldevlte 83 
                                        +++Qgte+vr +v+ ++++a +++e  t+
  gi|336254984|ref|YP_004598091.1| 693 ERVQQGTETVRPAVESLEEIAEYAEE--TN 720
                                       57899*******************96..32 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.46
                    Retrotrans_gag  44 erkdqleeelsslrQgtesvreYvtrfktladqlde 79 
                                       ++++++ee+  sl+Q +esv + +++   l ++ld+
  gi|336254984|ref|YP_004598091.1| 760 SVSAAAEEQTASLTQVSESVGDLAEQAAALSSRLDR 795
                                       5788999999**********9999999999999997 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  10.4   0.00048      0.41      27     139 ..     373     490 ..     366     500 .. 0.73
   2 ?    5.3  13.6     0.028        24      19     142 ..     495     616 ..     486     634 .. 0.74
   3 ?    6.5   7.8     0.012        11      30     136 ..     653     785 ..     649     816 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00048
                              Fez1  27 tqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreel 103
                                       t +++e+  l   + e+r++l+++ +e++e++e++e+ ++e e+ +++ +++k++ae  re++ ++ eel+++ +++
  gi|336254984|ref|YP_004598091.1| 373 TDRIDEVGRLYRAFDEMRTTLTAQITEAREAKEEAETAQAEAERAQADAEEAKADAEAERERIAEVTEELERTADRY 449
                                       67899999999999***********************************************************9998 PP

                              Fez1 104 selsleeeeaa......lesdeakaqrqe.aeeleelkrever 139
                                        e+ + +++        +  d+ ++q ++  ee +++ +e+er
  gi|336254984|ref|YP_004598091.1| 450 GETMRAAADGDlsvratV--DTDNEQMRAiGEEFNAMLAEIER 490
                                       887776666553333221..22122211122222222233333 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.028
                              Fez1  19 Lkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkse.aellrekveklee 94 
                                        k+   +v+++ +e+ a   q+r +++++ e+ ++i+e+ e+ + + + +e   ++l+ +++e a++  + ++ +e+
  gi|336254984|ref|YP_004598091.1| 495 VKQFAVDVAAQSEEVTASSEQVRTASEQVAESVQQISEVAETQSVRLQTIESEMSDLSASTEEiASTATDVATVAER 571
                                       5777789***************************************9999999999998866626677788888999 PP

                              Fez1  95 elkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlra 142
                                        ++e r+  +++++  +e+++  ++a+    + e++++l++eve++ +
  gi|336254984|ref|YP_004598091.1| 572 TVEESRRGSEAAERAIDEMTAVESDAEY---AVETIRSLEAEVEQVDE 616
                                       9999999766655554444433333333...34455566665555443 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.012
                              Fez1  30 lseivalkaqlrelrakleekeeeikeleesl.eektlelevcenelqrkkseaellrekvekleeelkelreelse 105
                                       ++e+ +l a+ +e+ a++e++ e+i+e  +++ +  ++  e++++  +  +  +e l+e +e +ee  ++++e +s+
  gi|336254984|ref|YP_004598091.1| 653 ANEVKSLSADAKEAAAEIEDRIETIRERTDQSvNVVEETSERVQQGTETVRPAVESLEEIAEYAEETNEGVQE-ISA 728
                                       5788889999999999988887777765554404444555667777776677777777766666666666655.333 PP

                              Fez1 106 lsleeeeaa....................lesdeakaqrqe................aeeleelkre 136
                                       +++++++++                    +          e                +e++++l ++
  gi|336254984|ref|YP_004598091.1| 729 ATEDQADSTaqvvtavddvassseesaseA----------EsvsaaaeeqtasltqvSESVGDLAEQ 785
                                       333333333466777776655444433331..........112222211112233333333333333 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.2      0.12   1.1e+02      52     116 ..     381     445 ..     373     453 .. 0.76
   2 ?    5.4   6.8     0.021        18      48     121 ..     472     545 ..     451     561 .. 0.51
   3 ?    2.8   2.0      0.14   1.2e+02      55     120 ..     556     621 ..     541     630 .. 0.55
   4 ?   13.2   2.9   8.3e-05     0.071      42     121 ..     648     727 ..     646     730 .. 0.91
   5 ?    4.1   0.6     0.052        44      55     105 ..     745     795 ..     729     809 .. 0.51

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.12
                           DUF1664  52 qvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                       +++ +  + +  L+++i +  +  +e + +++e ++  ++++e  ++ + + e + e+ e+le +
  gi|336254984|ref|YP_004598091.1| 381 RLYRAFDEMRTTLTAQITEAREAKEEAETAQAEAERAQADAEEAKADAEAERERIAEVTEELERT 445
                                       45677778888888888888888888888888888888888888888888888888888888765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.021
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       +q+  + e+ +a   ++++ +++v +   ++++ s+e+++  ++vr   +++ e v++++e+ e+   +l++ie
  gi|336254984|ref|YP_004598091.1| 472 EQMRAIGEEFNAMLAEIERAVEEVKQFAVDVAAQSEEVTASSEQVRTASEQVAESVQQISEVAETQSVRLQTIE 545
                                       33444444444444444444444444444444444444444444444444444444444444444444444444 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.14
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       e++a+t  + +   +r  ++    +e+++   +e+t+v++d +   e ++s+++ ve++++ ++ i
  gi|336254984|ref|YP_004598091.1| 556 EEIASTATDVATVAERTVEESRRGSEAAERAIDEMTAVESDAEYAVETIRSLEAEVEQVDELVDAI 621
                                       455555555555555555555555555555555566666666666666666666666666555544 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 8.3e-05
                           DUF1664  42 avesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                         + v+++++++s++ +++  ++++ri+++ ++ d++ ++ +e++e v++  e ++   e +e++ e  e+ ++ ++
  gi|336254984|ref|YP_004598091.1| 648 GFAVVANEVKSLSADAKEAAAEIEDRIETIRERTDQSVNVVEETSERVQQGTETVRPAVESLEEIAEYAEETNEGVQ 724
                                       567899******************************************99999999999999999999998888888 PP

                           DUF1664 119 rie 121
                                       +i+
  gi|336254984|ref|YP_004598091.1| 725 EIS 727
                                       876 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.052
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedves 105
                                       +++a+  ++ +s+ ++v +  +eq++  ++++e v ++ e+ +++++ ++ 
  gi|336254984|ref|YP_004598091.1| 745 DDVASSSEESASEAESVSAAAEEQTASLTQVSESVGDLAEQAAALSSRLDR 795
                                       334444444444444444444444444444444444444444444444333 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   1.0       2.5   2.1e+03      32      80 ..     396     445 ..     383     458 .. 0.49
   2 ?    4.7   1.7     0.043        36      39      78 ..     488     527 ..     463     539 .. 0.48
   3 ?    6.8   2.7    0.0099       8.5      14      88 ..     550     625 ..     542     632 .. 0.77
   4 ?    6.0   1.1     0.017        15      13      84 ..     672     744 ..     660     748 .. 0.64
   5 ?   13.2   4.0   9.5e-05     0.081       4      92 ..     709     797 ..     707     799 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.5
                           BLOC1_2  32 asekykklkdvaaslekkleklnekyeelqpyl.qqidqiekqvteLeea 80 
                                       ++++  + k++a+ +++++e+ ++  ee +     + ++i + ++eLe +
  gi|336254984|ref|YP_004598091.1| 396 QITEAREAKEEAETAQAEAERAQADAEEAKADAeAERERIAEVTEELERT 445
                                       34444444444444444444444444433322202233344444444444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.043
                           BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78 
                                       ++++++++++++ ++ +++ee+    +q+    +qv+e  
  gi|336254984|ref|YP_004598091.1| 488 IERAVEEVKQFAVDVAAQSEEVTASSEQVRTASEQVAESV 527
                                       3334444444444444444444444444433333333222 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0099
                           BLOC1_2  14 eleatvedy.klLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                       +l+a++e++ ++ + + ++a++ +++ ++  + +e+ ++++ + +   +  ++ i  +e++v++  e+v+++ e+ 
  gi|336254984|ref|YP_004598091.1| 550 DLSASTEEIaSTATDVATVAERTVEESRRGSEAAERAIDEMTAVESDAEYAVETIRSLEAEVEQVDELVDAIAEIA 625
                                       5666666652455667777888888888888899999999999999999999999999999999988888887765 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.017
                           BLOC1_2  13 aeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidq.iekqvteLeeavseL 84 
                                         +e  +e  +   ++ e++se++++ ++ +  + ++le++ e  ee ++ +q+i +  e+q ++  ++v ++
  gi|336254984|ref|YP_004598091.1| 672 DRIETIRERTDQSVNVVEETSERVQQGTETVRPAVESLEEIAEYAEETNEGVQEISAaTEDQADSTAQVVTAV 744
                                       5555666666666677777777777777777777777777777777777777777531455555555555555 PP

  == domain 5  score: 13.2 bits;  conditional E-value: 9.5e-05
                           BLOC1_2   4 fekvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                       +e++++y e++ e+++e     e    ++++ +++++dva+s e+++++ ++ +++ +++  ++ q+ ++v +L e 
  gi|336254984|ref|YP_004598091.1| 709 LEEIAEYAEETNEGVQEISAATEDQADSTAQVVTAVDDVASSSEESASEAESVSAAAEEQTASLTQVSESVGDLAEQ 785
                                       5788999999999999999999******************************************************* PP

                           BLOC1_2  81 vseLDeyskeLE 92 
                                       +++L +   + E
  gi|336254984|ref|YP_004598091.1| 786 AAALSSRLDRFE 797
                                       ****99888777 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.7      0.05        43      43      66 ..     501     524 ..     479     534 .. 0.76
   2 ?    5.9   0.3     0.016        13      40      68 ..     768     796 ..     750     798 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.05
                         MbeD_MobD  43 enaaLseqvtgLsqQVesLseqvr 66 
                                       + aa se vt  s QV   seqv+
  gi|336254984|ref|YP_004598091.1| 501 DVAAQSEEVTASSEQVRTASEQVA 524
                                       567888999999999999888885 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.016
                         MbeD_MobD  40 tqrenaaLseqvtgLsqQVesLseqvrRl 68 
                                       +   +++ se v +L+ Q   Ls +++R+
  gi|336254984|ref|YP_004598091.1| 768 QTASLTQVSESVGDLAEQAAALSSRLDRF 796
                                       333344899*****************997 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.6   2.2e+03      25      49 ..     425     449 ..     375     462 .. 0.72
   2 ?    5.1   1.4     0.034        29       8      71 ..     481     545 ..     479     637 .. 0.85
   3 ?    1.4   0.2      0.48   4.1e+02      28      58 ..     667     697 ..     601     705 .. 0.63
   4 ?    6.0   2.1     0.018        16      29      85 ..     699     757 ..     670     771 .. 0.71
   5 ?   -2.0   0.0       5.7   4.9e+03      34      61 ..     771     798 ..     762     803 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.6
                        Syntaxin_2  25 kkdteelreklhelieeinelikkt 49 
                                       k d e  re++ e++ee+ +++ + 
  gi|336254984|ref|YP_004598091.1| 425 KADAEAERERIAEVTEELERTADRY 449
                                       3466666777777777777666555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.034
                        Syntaxin_2   8 insnvstleklvkqLgtkk.dteelreklhelieeinelikktnellkklsqldnsssdsqqklq 71 
                                       +n  + ++e+ v+ ++    d     e++  + e++++ ++++ e+++++s++++++s + q ++
  gi|336254984|ref|YP_004598091.1| 481 FNAMLAEIERAVEEVKQFAvDVAAQSEEVTASSEQVRTASEQVAESVQQISEVAETQSVRLQTIE 545
                                       66677777888888777755888888888889999999999999999999998888876655554 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.48
                        Syntaxin_2  28 teelreklhelieeinelikktnellkklsq 58 
                                         e+ +++++++e++ + ++ ++e  ++++q
  gi|336254984|ref|YP_004598091.1| 667 AAEIEDRIETIRERTDQSVNVVEETSERVQQ 697
                                       4455555555555555555555555555544 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.018
                        Syntaxin_2  29 eelreklhelieeinelikktnellkklsqldnsssds..qqklqkekLkkdfkealqe 85 
                                       +e+ + + e+ eei e +++tne ++++s+ ++ + ds  q  ++ +  +++ +e+ +e
  gi|336254984|ref|YP_004598091.1| 699 TETVRPAVESLEEIAEYAEETNEGVQEISAATEDQADStaQVVTAVDDVASSSEESASE 757
                                       45555567999**********************99998844444666666666666555 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 5.7
                        Syntaxin_2  34 klhelieeinelikktnellkklsqldn 61 
                                       +l ++ e++ +l+++  +l ++l++ + 
  gi|336254984|ref|YP_004598091.1| 771 SLTQVSESVGDLAEQAAALSSRLDRFET 798
                                       5667777777777777777777776665 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3  26.1       0.6   5.2e+02      55     252 ..     395     595 ..     354     606 .. 0.66
   2 ?   12.1  10.7   5.5e-05     0.047      38     243 ..     602     799 ..     585     811 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.6
                               MAD  55 krikllekreeekeealreqiElarlkkknlealnkkekekesklaearevisalknelaelkrqiekqelelsek. 130
                                       ++i++ +   e+keea  +q+E +r++   +ea   +e e+e   ae+ e  +   ++  e  r + + +l ++++ 
  gi|336254984|ref|YP_004598091.1| 395 AQITEAR---EAKEEAETAQAEAERAQADAEEAKADAEAERERI-AEVTEELERTADRYGETMRAAADGDLSVRATv 467
                                       3443333...3344444455555553355555555555554443.44444444556777777888888888888763 PP

                               MAD 131 eseleelqerldllkkklseleqli.......qqlekkqkelaeaeqrikeLefeiqsqeddslivknskselarip 200
                                       ++++e+++   ++ ++ l+e+e+ +        +  ++++e +++ +++++ + ++++  ++  +v +   + +r+ 
  gi|336254984|ref|YP_004598091.1| 468 DTDNEQMRAIGEEFNAMLAEIERAVeevkqfaVDVAAQSEEVTASSEQVRTASEQVAESVQQISEVAET--QSVRLQ 542
                                       566677766666666666666666644433336667788888888888888888777666655555544..448899 PP

                               MAD 201 elekelerlreenkklnelkenkelLkEe.vedlkkkLereEkareelvkLel 252
                                       ++e+e+  l +  +++ ++  ++  + E  ve+ ++  e  E+a +e+ ++e 
  gi|336254984|ref|YP_004598091.1| 543 TIESEMSDLSASTEEIASTATDVATVAERtVEESRRGSEAAERAIDEMTAVES 595
                                       99999999999999999999999998886245566666777777777776665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.5e-05
                               MAD  38 alkrqleeesdrnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekesklaearevisalknela 114
                                       +  r le e+++  el + i ++ ++ +    al++ iE a       +     ++e +s  a+a+e   +++++++
  gi|336254984|ref|YP_004598091.1| 602 ETIRSLEAEVEQVDELVDAIAEIADQTS--LLALNASIEAAD-AGGDGDGFAVVANEVKSLSADAKEAAAEIEDRIE 675
                                       4456777788888888887777776654..356677777776.5567778888888888888888888888888887 PP

                               MAD 115 elkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqsqeddslivkn 191
                                         +   e++++ ++  e+  e++q+  +  +         +++le+  +  +e ++ ++e++   + q+d+ + v +
  gi|336254984|ref|YP_004598091.1| 676 TIR---ERTDQSVNVVEETSERVQQGTETVRP-------AVESLEEIAEYAEETNEGVQEISAATEDQADSTAQVVT 742
                                       655...45666666555555666666555444.......44677777777888999999999999999888765554 PP

                               MAD 192 sksel.....aripelekelerlreenkklnelkenkelLkEevedlkkkLereEka 243
                                       + + +     ++ +e e+  ++ +e+ + l +++e ++ L E+++ l ++L+r+E  
  gi|336254984|ref|YP_004598091.1| 743 AVDDVassseESASEAESVSAAAEEQTASLTQVSESVGDLAEQAAALSSRLDRFETS 799
                                       4444311113678889999999*********************************76 PP

>> DUF1759  Protein of unknown function (DUF1759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.043        37      62     119 ..     441     498 ..     432     505 .. 0.80
   2 ?   -0.7   0.1       1.5   1.2e+03      90     116 ..     511     537 ..     501     555 .. 0.74
   3 ?    0.9   0.2      0.45   3.9e+02      76     119 ..     585     628 ..     559     637 .. 0.78
   4 ?    7.0   0.6    0.0061       5.2      56     118 ..     670     732 ..     652     754 .. 0.80
   5 ?   -0.1   0.0      0.96   8.2e+02      77     117 ..     740     780 ..     733     790 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.043
                           DUF1759  62 aLkkrYdnkrkiirellnelmklpslkeedasqlrrivdavneivralealgeeadky 119
                                        L++  d+  + +r+  +   +++ +   d++q+r+i ++ n ++  +e++ ee++++
  gi|336254984|ref|YP_004598091.1| 441 ELERTADRYGETMRAAADGDLSVRATVDTDNEQMRAIGEEFNAMLAEIERAVEEVKQF 498
                                       5555555555566666667778999999***********************9999876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                           DUF1759  90 edasqlrrivdavneivralealgeea 116
                                        + +q+r+ +++v e+v+++ +++e++
  gi|336254984|ref|YP_004598091.1| 511 ASSEQVRTASEQVAESVQQISEVAETQ 537
                                       567778888888888888887777765 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.45
                           DUF1759  76 ellnelmklpslkeedasqlrrivdavneivralealgeeadky 119
                                         ++e++ ++s  e  ++++r++  +v+++   ++a++e ad+ 
  gi|336254984|ref|YP_004598091.1| 585 RAIDEMTAVESDAEYAVETIRSLEAEVEQVDELVDAIAEIADQT 628
                                       56788888888888888899998888888888888888888854 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0061
                           DUF1759  56 YeaaveaLkkrYdnkrkiirellnelmklpslkeedasqlrrivdavneivralealgeeadk 118
                                        e  +e++++r d++ ++++e  +++++  ++ +  ++ l++i + ++e+  ++++++  +++
  gi|336254984|ref|YP_004598091.1| 670 IEDRIETIRERTDQSVNVVEETSERVQQGTETVRPAVESLEEIAEYAEETNEGVQEISAATED 732
                                       5667999************************99999999999988888887777777655543 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.96
                           DUF1759  77 llnelmklpslkeedasqlrrivdavneivralealgeead 117
                                        ++++ ++ s +ee+as+ ++++ a++e    l +++e + 
  gi|336254984|ref|YP_004598091.1| 740 VVTAVDDVASSSEESASEAESVSAAAEEQTASLTQVSESVG 780
                                       5677888999999*****************99999988765 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.9    0.0056       4.8      15      72 ..     393     445 ..     346     459 .. 0.70
   2 ?    7.8   4.5    0.0063       5.4       6      79 ..     479     551 ..     477     553 .. 0.83
   3 ?   12.0   2.0   0.00031      0.26      10      97 ..     546     631 ..     540     634 .. 0.79
   4 ?    4.7   3.4     0.057        49       8      71 ..     663     728 ..     652     730 .. 0.64
   5 ?    2.7   3.5      0.24     2e+02       6      76 ..     717     779 ..     701     798 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0056
                           DUF2203  15 lkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieel 72 
                                       l+ +++e+r++++e+e++++e e+     ++ +a+e++a+ e+ +++i e++ee+e++
  gi|336254984|ref|YP_004598091.1| 393 LTAQITEAREAKEEAETAQAEAER-----AQADAEEAKADAEAERERIAEVTEELERT 445
                                       333333333344443333333333.....33337777777788888888888887764 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0063
                           DUF2203   6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdl 79 
                                       ee na+L ++++ +ee+++ + +++  +ee+++++++ ++ + ++ +++++++++ +e    +++ +  e+ dl
  gi|336254984|ref|YP_004598091.1| 479 EEFNAMLAEIERAVEEVKQFAVDVAAQSEEVTASSEQVRT-ASEQVAESVQQISEVAETQSVRLQTIESEMSDL 551
                                       67899*********************99999999999754.477888888888888888888888777776665 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00031
                           DUF2203  10 alLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleaglvDF 86 
                                       + +  l+  +ee++++++++++++e+  e++++ + ++a+++  e++++e+ +e +ve+i++l +ev +++  lvD 
  gi|336254984|ref|YP_004598091.1| 546 SEMSDLSASTEEIASTATDVATVAERTVEESRRGS-EAAERAIDEMTAVESDAEYAVETIRSLEAEVEQVD-ELVDA 620
                                       45666777778888888888887777766666654.348899999*************************7.89**9 PP

                           DUF2203  87 pakldgeevll 97 
                                        a++ +++ ll
  gi|336254984|ref|YP_004598091.1| 621 IAEIADQTSLL 631
                                       99999887766 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.057
                           DUF2203   8 AnalLpllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeiee 71 
                                       A++   ++++++e +r+ +++  +++ee +e  ++ +++   a e  +e++e+++e +e v+ei++
  gi|336254984|ref|YP_004598091.1| 663 AKEAAAEIEDRIETIRERTDQSVNVVEETSERVQQGTETVrpAVESLEEIAEYAEETNEGVQEISA 728
                                       555555666666666655555555555554444444333344888888999999999999999875 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.24
                           DUF2203   6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvev 76 
                                       ee n+ +++++  +e+ ++ ++++ +++++++++++e++        +e e+++a +ee ++ ++++   v
  gi|336254984|ref|YP_004598091.1| 717 EETNEGVQEISAATEDQADSTAQVVTAVDDVASSSEESA--------SEAESVSAAAEEQTASLTQVSESV 779
                                       445555555555555555555555555555555554443........333333333333333333333333 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1         4   3.4e+03      30      62 ..     391     422 ..     376     456 .. 0.52
   2 ?   12.9   4.9   9.9e-05     0.085      21     111 ..     473     565 ..     463     593 .. 0.79
   3 ?    0.5   0.2      0.67   5.7e+02      22      47 ..     601     624 ..     595     642 .. 0.69
   4 ?    5.9   2.0     0.015        12      42     118 ..     651     729 ..     647     747 .. 0.71
   5 ?    0.9   1.4      0.49   4.2e+02      59      77 ..     763     787 ..     719     821 .. 0.47

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4
                      Baculo_PEP_C  30 vqilaqlatlldaietqLnalsedlksllaeld 62 
                                       ++++aq++++ +a e+  ++ +++ +++ a+ +
  gi|336254984|ref|YP_004598091.1| 391 TTLTAQITEAREAKEE-AETAQAEAERAQADAE 422
                                       4555555555554333.3444444444444444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.9e-05
                      Baculo_PEP_C  21 vLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsil 94 
                                       ++ ai      +la+++++++++++   +++++ ++ +++ ++++ t+++++ +++++++   +t + +L++++s++
  gi|336254984|ref|YP_004598091.1| 473 QMRAIGEEFNAMLAEIERAVEEVKQFAVDVAAQSEE-VTASSEQVRTASEQVAESVQQISevaETQSVRLQTIESEM 548
                                       555665555566677777777777777776666666.5556669*************999888899999******** PP

                      Baculo_PEP_C  95 tnLlssvtNinstLnnl 111
                                       ++L +s   i st + +
  gi|336254984|ref|YP_004598091.1| 549 SDLSASTEEIASTATDV 565
                                       ******99999997665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.67
                      Baculo_PEP_C  22 LnairlqnvqilaqlatlldaietqL 47 
                                       +++ir++++++  q+ +l+dai++ +
  gi|336254984|ref|YP_004598091.1| 601 VETIRSLEAEV-EQVDELVDAIAE-I 624
                                       67889999999.899999888876.3 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.015
                      Baculo_PEP_C  42 aietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstLnnllqal 115
                                        +++++++ls+d k++ ae+++r++t  ++ ++++n ++   + +++  +++   + +L  +++   +  n  +q +
  gi|336254984|ref|YP_004598091.1| 651 VVANEVKSLSADAKEAAAEIEDRIETIRERTDQSVNVVEetsERVQQGTETVRPAVESLE-EIAEYAEETNEGVQEI 726
                                       578899999999999999999999999999999999999666566666666666666665.5555555555555555 PP

                      Baculo_PEP_C 116 nnl 118
                                        + 
  gi|336254984|ref|YP_004598091.1| 727 SAA 729
                                       555 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.49
                      Baculo_PEP_C  59 aeldt......rldtlltnLtdaln 77 
                                       a+ ++      ++++++  L ++ +
  gi|336254984|ref|YP_004598091.1| 763 AAAEEqtasltQVSESVGDLAEQAA 787
                                       2222211222222222222222222 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   4.1    0.0039       3.4      43     166 ..     406     532 ..     346     538 .. 0.69
   2 ?    4.7   0.9     0.029        25       3      67 ..     508     571 ..     506     628 .. 0.72
   3 ?    1.7   0.4      0.25   2.1e+02      14      14 ..     701     701 ..     585     798 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0039
                        STAT_alpha  43 eqeraesekkelkkqkellqqmlnaLdqkRkelvdklkellnlleslqeklldeeLieW....KrrQqlagiGapfn 115
                                       e+e+a+ e ++ +   e+ ++ ++a  ++ +e+ ++l+++ +++ + +    d  L         + q+  iG  fn
  gi|336254984|ref|YP_004598091.1| 406 EAETAQAEAERAQADAEEAKADAEAERERIAEVTEELERTADRYGETMRAAADGDLSVRatvdTDNEQMRAIGEEFN 482
                                       22333333333333333333344445556678888999999999999999999988876222245788999****** PP

                        STAT_alpha 116 esLDqlqkwfealaeliwqlrqqlkkleelrqkltyeedpeltdqlpqlne 166
                                       + L ++++ +e + ++ + + +q +++   +++++  +++ ++++++q +e
  gi|336254984|ref|YP_004598091.1| 483 AMLAEIERAVEEVKQFAVDVAAQSEEVTASSEQVRTASEQ-VAESVQQISE 532
                                       **********************************776555.8888888776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.029
                        STAT_alpha   3 eieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkleqeraesekkelkkqkellqqmlna 67 
                                       e++++ e++r   +++ ++++++ ++ e+ +++ q+++++  +  + +++e++   + ++  +++
  gi|336254984|ref|YP_004598091.1| 508 EVTASSEQVRTASEQVAESVQQISEVAETQSVRLQTIESE-MSDLSASTEEIASTATDVATVAER 571
                                       6777889999999**************************9.333334444455555554444433 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.25
                        STAT_alpha  14 k 14 
                                       +
  gi|336254984|ref|YP_004598091.1| 701 T 701
                                       1 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       4.5   3.8e+03      46      62 ..     480     496 ..     463     499 .. 0.64
   2 ?    6.3   4.0     0.015        13      12      61 ..     501     551 ..     495     568 .. 0.79
   3 ?    3.2   0.3      0.14   1.2e+02      20      41 ..     604     625 ..     583     641 .. 0.51
   4 ?    3.9   2.5      0.09        77      15      63 ..     680     728 ..     650     747 .. 0.88
   5 ?    3.5   0.8      0.12     1e+02      18      61 ..     739     782 ..     728     790 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.5
                           NPV_P10  46 aqsaqLaeletkvenIq 62 
                                       + +a Lae+e +ve+++
  gi|336254984|ref|YP_004598091.1| 480 EFNAMLAEIERAVEEVK 496
                                       45667777777777765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.015
                           NPV_P10  12 dikavddkVdalqqqvddvqenl.pdvtelnekLdaqsaqLaeletkvenI 61 
                                       d++a ++ V+a ++qv   +e++ + v++++e  + qs  L+++e+++++ 
  gi|336254984|ref|YP_004598091.1| 501 DVAAQSEEVTASSEQVRTASEQVaESVQQISEVAETQSVRLQTIESEMSDL 551
                                       89999999********87777752458888888899999999998876654 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.14
                           NPV_P10  20 Vdalqqqvddvqenlpdvteln 41 
                                       + +l+++v++v+e +  + e+ 
  gi|336254984|ref|YP_004598091.1| 604 IRSLEAEVEQVDELVDAIAEIA 625
                                       2333333333333333333333 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.09
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                        +d+ V+++++  ++vq+  ++v    e L+++++  +e ++ v++I+ 
  gi|336254984|ref|YP_004598091.1| 680 RTDQSVNVVEETSERVQQGTETVRPAVESLEEIAEYAEETNEGVQEISA 728
                                       4788899999999999999999999999999999999999999999975 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.12
                           NPV_P10  18 dkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                       + V+a+++   + +e   + + +++  ++q+a+L++++++v + 
  gi|336254984|ref|YP_004598091.1| 739 QVVTAVDDVASSSEESASEAESVSAAAEEQTASLTQVSESVGDL 782
                                       4566777666777777788899999*************999765 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 ?    9.9   2.9   0.00052      0.44      33     121 ..     488     576 ..     465     592 .. 0.87
   2 ?   -1.6   0.0       1.7   1.5e+03      82     110 ..     600     628 ..     595     636 .. 0.82
   3 ?    1.6   1.7      0.18   1.6e+02      38     104 ..     703     769 ..     662     795 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00052
                         Mce4_CUP1  33 lGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsnt 109
                                       + ++++++ ++  ++ ++ +++++  +++ ++++  a++ +++ ++ +  ++  +Ti+++ ++L+a   ++++++++
  gi|336254984|ref|YP_004598091.1| 488 IERAVEEVKQFAVDVAAQSEEVTASSEQVRTASEQVAESVQQISEVAETQSVRLQTIESEMSDLSASTEEIASTATD 564
                                       55788899999999*************************************************************** PP

                         Mce4_CUP1 110 gadllerngdnL 121
                                       +a++ er  ++ 
  gi|336254984|ref|YP_004598091.1| 565 VATVAERTVEES 576
                                       **9998876665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
                         Mce4_CUP1  82 avttsrTiveqqaeLdalllaavglsntg 110
                                       av t r+++++ +++d+l+ a++++++++
  gi|336254984|ref|YP_004598091.1| 600 AVETIRSLEAEVEQVDELVDAIAEIADQT 628
                                       67899999999999999999999998875 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.18
                         Mce4_CUP1  38 tdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaav 104
                                         + e L+e+ +  ++ +e ++e+ ++++  ad+  ++++a+d+++  s+  ++++++++a+  + +
  gi|336254984|ref|YP_004598091.1| 703 RPAVESLEEIAEYAEETNEGVQEISAATEDQADSTAQVVTAVDDVASSSEESASEAESVSAAAEEQT 769
                                       5556778888888888888888888888888888888888888888888877777777776654433 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   3.0     0.038        32      73     145 ..     378     443 ..     352     459 .. 0.62
   2 ?    5.0  11.5     0.013        11      71     192 ..     471     583 ..     459     614 .. 0.65
   3 ?    7.6   8.0    0.0021       1.8      54     209 ..     616     795 ..     603     810 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.038
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXX CS
                              AIP3  73 pldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrdLa 145
                                       ++  + + +de+ ++l+++++e +++ e+ +++++e++   + +a+e++       + +a+ + + ++ ++L+
  gi|336254984|ref|YP_004598091.1| 378 EVGRLYRAFDEMRTTLTAQITEAREAKEEAETAQAEAERA-QADAEEAKA------DAEAERERIAEVTEELE 443
                                       3344445888888888888888887777777766663333.333333333......34445555555555554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXX CS
                              AIP3  71 iepldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrdLavl 147
                                        e++  + ++++ +la++++ ++e+k+   + +a+++e        ++++++  +a+++ ++++++++++ +  +v 
  gi|336254984|ref|YP_004598091.1| 471 NEQMRAIGEEFNAMLAEIERAVEEVKQFAVDVAAQSEE-------VTASSEQVRTASEQVAESVQQISEVAETQSVR 540
                                       45566666666666666666666666555444444444.......33333333344566778888888888888888 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXHHHHHHHH CS
                              AIP3 148 rqlysefkseikeslselrekakkvkeaslastkkssnrayiekg 192
                                        q+ ++ +s++++s +e+ ++a++v   ++a+ +++++r   e++
  gi|336254984|ref|YP_004598091.1| 541 LQTIESEMSDLSASTEEIASTATDVA--TVAERTVEESRRGSEAA 583
                                       89999999999999999999999999..55555555555544444 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0021
                                       XXXX.XXXXXXX.XXXXXX..................XXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXX CS
                              AIP3  54 eLed.lsdvkdr.svLsLn..................iepldevkkhideslaslskelkelkssiesqkaslqevs 110
                                       eL d + ++ d+ s+L Ln                   +++++++   +e  a+++++++ ++++++++ +  +e+s
  gi|336254984|ref|YP_004598091.1| 616 ELVDaIAEIADQtSLLALNasieaadaggdgdgfavvANEVKSLSADAKEAAAEIEDRIETIRERTDQSVNVVEETS 692
                                       56666888877537999999999999999988888765577777777778888888888888887777777777777 PP

                                       XXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXX.XXXXX CS
                              AIP3 111 erqeeaakekaseslakkelkaqlkevqslrrdLavlrqlysefkseikeslselrekakkvk....easlastkks 183
                                       er ++ +++    + + +e ++  +e ++  +++++  + +++++ ++ + + ++ +  ++      ++s a  +++
  gi|336254984|ref|YP_004598091.1| 693 ERVQQGTETVRPAVESLEEIAEYAEETNEGVQEISAATEDQADSTAQVVTAVDDVASSSEESAseaeSVSAAAEEQT 769
                                       77777766666666665555555555555555555555555555555555555554444333323325556667778 PP

                                       XHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 184 snrayiekgkkkLseesdklvtkvdd 209
                                       ++ + ++++   L e++ +l +++d 
  gi|336254984|ref|YP_004598091.1| 770 ASLTQVSESVGDLAEQAAALSSRLDR 795
                                       88888888888999988888888875 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   7.4   0.00011     0.092     163     314 ..     315     551 ..     292     632 .. 0.63
   2 ?   -4.5   9.9       8.5   7.3e+03     212     323 ..     659     763 ..     571     796 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                             LMBR1 163 lislantwGlvllilllGyGlvelPrslwr............................................... 192
                                       + ++++ +G  ll + +G Glv+l ++                                                  
  gi|336254984|ref|YP_004598091.1| 315 AFAASSAVGKSLLAI-IGTGLVALLLGGLVlarqtvtplqdlrnraermeegdldvdletdridevgrlyrafdemr 390
                                       566666666666654.567777772222224556666999************************************* PP

                             LMBR1 193 .......eiksdldeelkklyfeaaklntekeeaereledllkevkklrksisesd..........plrkyleeilk 252
                                              +++++ +ee + +++ea++ + + eea+ + e   ++++++++++++++                    +
  gi|336254984|ref|YP_004598091.1| 391 ttltaqiTEAREAKEEAETAQAEAERAQADAEEAKADAEAERERIAEVTEELERTAdrygetmraaA---------D 458
                                       *******999999999************999999977777777777777777777633333333330.........2 PP

                             LMBR1 253 .....................kvPeeiaeklks...................nenkteeslaklekqlikalqkrer 289
                                                            +                              +  ++ e+++ + +q+ +a+++ ++
  gi|336254984|ref|YP_004598091.1| 459 gdlsvratvdtdneqmraigeE----------FnamlaeieraveevkqfavDVAAQSEEVTASSEQVRTASEQVAE 525
                                       4433333333333233322221..........011122122233334444443333444444444555555555555 PP

                             LMBR1 290 tekqwkrlleka.lelediiknkssk 314
                                       + +q ++  e + ++l++i +++s+ 
  gi|336254984|ref|YP_004598091.1| 526 SVQQISEVAETQsVRLQTIESEMSDL 551
                                       55555555555534444444433333 PP

  == domain 2  score: -4.5 bits;  conditional E-value: 8.5
                             LMBR1 212 lntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklks......nenkteeslaklekqlik 282
                                       l+   ++a++   ++ ++++++r+++ +s            +v ee +e++++         +++e++a+  +++ +
  gi|336254984|ref|YP_004598091.1| 659 LS---ADAKEAAAEIEDRIETIRERTDQSV-----------NVVEETSERVQQgtetvrPAVESLEEIAEYAEETNE 721
                                       22...2222222223333333333333333...........222222223333333333222233333333333333 PP

                             LMBR1 283 alqk.rertekqwkrllekalelediiknksskekefksses 323
                                        +q+ ++ te+q +   + + ++ d++++++++  e +s + 
  gi|336254984|ref|YP_004598091.1| 722 GVQEiSAATEDQADSTAQVVTAVDDVASSSEESASEAESVSA 763
                                       333312223333333333333335555555544444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (825 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3131  (0.174633); expected 358.6 (0.02)
Passed bias filter:                      929  (0.0518155); expected 358.6 (0.02)
Passed Vit filter:                       179  (0.00998383); expected 17.9 (0.001)
Passed Fwd filter:                       114  (0.00635841); 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: 2.14u 0.37s 00:00:02.51 Elapsed: 00:00:00.58
# Mc/sec: 4273.93
//
Query:       gi|336254985|ref|YP_004598092.1|  [L=128]
Description: hypothetical protein Halxa_3604 [Halopiger xanaduensis SH-6]
Scores for 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   15.4   0.7      0.014   15.4   0.7    1.8  2  DHR10     Designed helical repeat protein 10 domain
      0.032   14.0   0.5        4.5    7.1   0.0    2.4  2  GPW_gp25  Gene 25-like lysozyme
        1.5    7.3   3.8        1.8    7.0   3.8    1.1  1  FUSC      Fusaric acid resistance protein family


Domain annotation for each model (and alignments):
>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.7   2.4e-06     0.014      81     114 ..      25      58 ..      19      61 .. 0.88
   2 ?   -1.2   0.1      0.33     2e+03      66      72 ..     107     113 ..      94     123 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.4e-06
                             DHR10  81 erlqrqlenaeeklerlreqaeekreaakarlee 114
                                       + +q+ ++++eekl+r+ e+a++ reaa + le+
  gi|336254985|ref|YP_004598092.1|  25 ADMQQAVASWEEKLNRAIEEADDDREAAGRVLEA 58 
                                       56899***********************998887 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.33
                             DHR10  66 leekeie 72 
                                        e++e+e
  gi|336254985|ref|YP_004598092.1| 107 AEHLERE 113
                                       2222222 PP

>> GPW_gp25  Gene 25-like lysozyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0   0.00075       4.5      34      64 ..      12      40 ..       3      42 .. 0.77
   2 ?    4.8   0.2    0.0039        24      42      61 ..      46      65 ..      40      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00075
                                      HHHHCS--CHHHHHHHHHHHHHHHH-TTEEE CS
                          GPW_gp25 34 allfaslsedreriareireailrfEpRirl 64
                                       l + ++  d e++a+++++a++ +E ++++
  gi|336254985|ref|YP_004598092.1| 12 LLERLPD--DDEAAAADMQQAVASWEEKLNR 40
                                      4445554..79999************99976 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0039
                                      CHHHHHHHHHHHHHHHH-TT CS
                          GPW_gp25 42 edreriareireailrfEpR 61
                                      +d +++a ++ eai rfE R
  gi|336254985|ref|YP_004598092.1| 46 DDDREAAGRVLEAIDRFEER 65
                                      5777889999*********9 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.8    0.0003       1.8     242     307 ..      13      87 ..       4     121 .. 0.43

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0003
                              FUSC 242 larlraeeaaavpelaallaelaal............eaaaaaealeaalaalrarlralrraleadadtaalllar 306
                                       l+rl++ ++aa    a++ +++a++            ++++aa +  +a++++++r +  ++  ++ +++++  +++
  gi|336254985|ref|YP_004598092.1|  13 LERLPDDDEAA---AADMQQAVASWeeklnraieeadDDREAAGRVLEAIDRFEERYETYDELVPELRAWGQSPIYA 86 
                                       33333333333...333333333333334444444443444444444444444444444444444444444444444 PP

                              FUSC 307 l 307
                                       l
  gi|336254985|ref|YP_004598092.1|  87 L 87 
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1167  (0.0650901); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1013.66
//
Query:       gi|336254986|ref|YP_004598093.1|  [L=131]
Description: F420-dependent protein [Halopiger xanaduensis SH-6]
Scores for 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-17   63.1   0.0    2.6e-17   62.8   0.0    1.1  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
    2.8e-06   27.4   0.0    3.8e-06   26.9   0.0    1.1  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    4.4e-05   23.1   0.0    4.8e-05   23.0   0.0    1.0  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like


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 !   62.8   0.0   4.3e-21   2.6e-17       2      85 ..       5      89 ..       4      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 4.3e-21
                                      HHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT.GSEEEEEEE CS
                    Putative_PNPOx  2 deelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde.lgrgvrieG 79
                                      +ee+r++++++ ++++AT +e+G P+v+pv+  ++ ++++i++ t + ++k+rn+++np v+l+ +d++  ++ ++i G
  gi|336254986|ref|YP_004598093.1|  5 PEEFRDLFEKETFAHVATLTEKGLPHVTPVWIDYDADDNRILVNTERGRQKVRNVQANPGVGLSMVDPDnPYQHLSIIG 83
                                      79*******************************************************************9999****** PP

                                      EEEEES CS
                    Putative_PNPOx 80 taelvs 85
                                      ++  ++
  gi|336254986|ref|YP_004598093.1| 84 EVDEIT 89
                                      998877 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   6.4e-10   3.8e-06       3     137 ..       6     128 ..       5     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 6.4e-10
                                       HHHHHHHHC-SEEEEEEEETTE.EEEEEEEEEEE..TTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGG CS
                      Pyridox_ox_2   3 eeilalLdegevgrlafvddge.pvilPvnyvvd..gdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfn 75 
                                       ee  +l +++ ++++a+ +++  p+++Pv   +d  ++++++ +++g ++++  +++p v  +  + d+        
  gi|336254986|ref|YP_004598093.1|   6 EEFRDLFEKETFAHVATLTEKGlPHVTPVWIDYDadDNRILVNTERGRQKVRNVQANPgVGLSMVDPDN-----P-- 75 
                                       678899999*********96666******9999955666****************99999999999888.....4.. PP

                                       EEEEEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTT.GGCSB---CCCCCTEEEEEEEEEEE CS
                      Pyridox_ox_2  76 slnyrSVvvrGraeevtdeeekaealellvekivpgr.wenlrpptrkelkatsvlrlkieev 137
                                          y+   + G++ e+t+e  +++++e l+++++ +  +      ++ e +   +lr++++++
  gi|336254986|ref|YP_004598093.1|  76 ---YQHLSIIGEVDEITTEGAREHIDE-LAQRYMGEDdYP-----NPIETER-VILRIRPDQI 128
                                       ...888999*******77777777666.567886654444.....4445544.999**99986 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 !   23.0   0.0     8e-09   4.8e-05       4     107 ..       6     107 ..       3     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8e-09
                     Pyrid_ox_like   4 kklkelvkdiktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsdesk.kkyvsvs 79 
                                       +++++l ++  +a ++t +++g  ++ P  +  +++d+++   t++  +kv+++++++ v l ++d+++  +++s+ 
  gi|336254986|ref|YP_004598093.1|   6 EEFRDLFEKETFAHVATLTEKGLPHVTPVWIDYDADDNRILVNTERGRQKVRNVQANPGVGLSMVDPDNpYQHLSII 82 
                                       6789999***********************************************************9873579**** PP

                     Pyrid_ox_like  80 GtaevvedrakieelWspvvkawfpegk 107
                                       G+++  + +  ++e+ +++++ ++  g+
  gi|336254986|ref|YP_004598093.1|  83 GEVDEITTE-GAREHIDELAQRYM--GE 107
                                       *99755533.34566666666666..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1080.94
//
Query:       gi|336254987|ref|YP_004598094.1|  [L=217]
Description: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase [Halopiger xanaduensis SH-6]
Scores for complete 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-44  151.8   2.0    1.8e-44  151.5   2.0    1.0  1  Aldolase        KDPG and KHG aldolase
  ------ inclusion threshold ------
       0.01   15.1   0.8      0.056   12.6   0.1    2.1  2  PEP_hydrolase   Phosphoenolpyruvate hydrolase-like
        5.8    6.2   6.5        2.8    7.3   0.4    3.0  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family


Domain annotation for each model (and alignments):
>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.5   2.0     3e-48   1.8e-44       3     194 ..       9     201 ..       7     203 .. 0.96

  Alignments for each domain:
  == domain 1  score: 151.5 bits;  conditional E-value: 3e-48
                                       HHHHCHSEEEEE--SSGGGHHHHHHHHHHTT--EEEEETTSTTHHHHHHHHHHH-T..TSEEEEES--SHHHHHHHH CS
                          Aldolase   3 silkeakvvpvivikdkedalplaeaLvagGlrvlevtlrteaaldairvlrkerp..dllvgaGtvlnaeqlaeak 77 
                                       +++  + vv+v++  d+++++++a a+ + G+ +levt   + a++ i ++ +e    d++vgaGtvl+a  ++ + 
  gi|336254987|ref|YP_004598094.1|   9 ERIVDSGVVAVLRGIDEDQITDVATAIHEAGVTALEVTADGKRASEKIAAIDRELAdtDAVVGAGTVLDAPTAQSVI 85 
                                       56677889*******************************************999752279***************** PP

                                       HCT-SEEEESS--HHHHHHHHHTTS-EEEEESSHHHHHHHHHTT--EEEETTTTTTTHHHHHHHHCTTTTT-EEEEB CS
                          Aldolase  78 eaGaqfvvsPGltadllkaavdlkipllPGvstpseimlaldlGlkrlklfPaeasGGvkalkalagpfaqvrfiPt 154
                                       +aGa+fv++P  +++++++++ + +  +PGv tp+e   a++ G + lk+fPa ++G    + al gp ++v ++Pt
  gi|336254987|ref|YP_004598094.1|  86 DAGAEFVLAPDCNPEMIELCNRQGVVSIPGVMTPTEAVTAMEAGADMLKMFPATTVG-PGHIGALQGPLGDVDVMPT 161
                                       ********************************************************9.789**************** PP

                                       SS--TTTHHHHHTSTTBS-EEESCCC-HHHHHTT-HHHHH CS
                          Aldolase 155 GGispanvrdylalpsvlvvgGswlveaslikkedldkit 194
                                       GG+sp nv d++ +++++v +Gs +v+ ++i+++d+d++ 
  gi|336254987|ref|YP_004598094.1| 162 GGVSPDNVDDFFDAGAIAVGAGSAIVDYDAIEAGDMDQVR 201
                                       *************************************996 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0     0.066   3.9e+02       6      40 ..      59      94 ..      54      98 .. 0.71
   2 ?   12.6   0.1   9.4e-06     0.056     140     186 ..     100     147 ..      95     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.066
                     PEP_hydrolase  6 lrkkikkgkpiigagaGtGl.sakaaeaggaDlili 40
                                      + +++++ ++++gag+     +a+++ ++ga+++l+
  gi|336254987|ref|YP_004598094.1| 59 IDRELADTDAVVGAGTVLDApTAQSVIDAGAEFVLA 94
                                      667777777888887776543778888888888765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.4e-06
                     PEP_hydrolase 140 elikkAheldllttayvfneeearamaeaGadvivahlGlttg.gsig 186
                                       e+i+  +++++++++ v++++ea + +eaGad++ +    t g g+ig
  gi|336254987|ref|YP_004598094.1| 100 EMIELCNRQGVVSIPGVMTPTEAVTAMEAGADMLKMFPATTVGpGHIG 147
                                       89*******************************988766665535555 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 ?    0.8   0.8     0.046   2.8e+02     175     175 ..      76      76 ..      24     139 .. 0.59
   2 ?    7.3   0.4   0.00047       2.8     167     197 ..     156     186 ..     146     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.046
                                       - CS
                    Ribul_P_3_epim 175 v 175
                                       +
  gi|336254987|ref|YP_004598094.1|  76 L 76 
                                       1 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00047
                                       -EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 167 lkievDGGvkldnieqiaeagadvlVagsav 197
                                       + +   GGv+ dn++   +aga ++ agsa+
  gi|336254987|ref|YP_004598094.1| 156 VDVMPTGGVSPDNVDDFFDAGAIAVGAGSAI 186
                                       556667***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1675.02
//
Query:       gi|336254988|ref|YP_004598095.1|  [L=321]
Description: PfkB domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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  175.5   0.2    1.8e-51  175.2   0.2    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 !  175.2   0.2     1e-55   1.8e-51       1     291 [.       1     295 [.       1     304 [. 0.95

  Alignments for each domain:
  == domain 1  score: 175.2 bits;  conditional E-value: 1e-55
                                       EEEEEEEEEEEEEEEEECSSHTTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTE CS
                              PfkB   1 mtkvvviGealidliavseklegelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegv 77 
                                       m +++ +Ge++  l+++  +    l +++++ ++ +Ga  NvA a+++lg ++++ +++ d+++G+++ +e +++gv
  gi|336254988|ref|YP_004598095.1|   1 MSSLLTFGETMLRLSPTPGN---RLETARQLDFRTAGAESNVAIAASNLGLEATWASKLPDSPLGRRVTREVRSHGV 74 
                                       568899***********988...999*************************************************** PP

                                       EETTEEEESSSEEEEEEEEETTT.SEEEEEEEEGGGGGHHHHHHH.HHHHHHGCTSEEEEES...EECTTSHHHHHH CS
                              PfkB  78 dtdyvkidedtrtglalivvded.gertivfnrgaaadltkeele.ededlleeadllyisg...llsselpeavle 149
                                       +t  v ++++ r+g ++i+  ++   ++++++r +aa  t ++ e  d  +le +d ly sg   +ls+ l  ++ +
  gi|336254988|ref|YP_004598095.1|  75 ET-NVAWTDEGRQGAYFIEQGGEpRGTNVIYDRADAAVRTATPDElTDGIDLETVDALYTSGitpALSDRLEATTAT 150
                                       **.66667778*************99*************************************************** PP

                                       HHHHHHHHTTE..EEEEECESSSHH..HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTS.S CS
                              PfkB 150 elaeaaknggt..fdpnlldplgaq..fkeallellaladllkpneeElealtgekledieealaalhklkakga.k 221
                                       +l+ a ++g t  fd+n++++l++   ++ +++ell+ +d+  + +++++ +++ ++ d+e a + + +    +  +
  gi|336254988|ref|YP_004598095.1| 151 LLERAQEAGATtvFDLNYRSKLWSPaeARACCEELLESVDIPVVAARDARSVLDLSGSDEEIAREIATT----YDaD 223
                                       ***********************99*******************************9999999999877....444* PP

                                       EEEEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHT..THHHHHHHHHHHHHHHHHHT CS
                              PfkB 222 tvvvtlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaalle..gksleealrfanavAalvvq 291
                                       +vvvt+G+eGal+ e+dg+++ +++++ +  D++G+GD+fvggfla++l+    +++ al++++a+Aal  +
  gi|336254988|ref|YP_004598095.1| 224 VVVVTQGAEGALALEGDGTVHDQPAFPAETTDPIGTGDAFVGGFLASYLAgeDRDVAGALEYGSATAALKRT 295
                                       **************************************************666789************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2656.72
//
Query:       gi|336254989|ref|YP_004598096.1|  [L=393]
Description: Galactonate dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-66  223.2   0.3    3.9e-66  222.8   0.3    1.2  1  MR_MLE_C  Enolase C-terminal domain-like
      1e-25   90.2   0.0    1.9e-25   89.4   0.0    1.4  1  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N


Domain annotation for each model (and alignments):
>> 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 !  222.8   0.3   4.4e-70   3.9e-66       3     220 .]     140     367 ..     138     367 .. 0.95

  Alignments for each domain:
  == domain 1  score: 222.8 bits;  conditional E-value: 4.4e-70
                                       HHHHHHHHHHHT-SEEEEETSSS........HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGG CS
                          MR_MLE_C   3 aeearelvaeqgfravKlkvggd........dvaedvervravreavgpgddvdlmvDanqawdlatAirvarelee 71 
                                        e+a+e+v++ gf+a+K++ +++         v+   er+++vr+av  gd+vd+ vD++++++ ++A r++++le+
  gi|336254989|ref|YP_004598096.1| 140 GEAAAEKVDA-GFTALKMNATPElrridnpaAVEAAQERLAEVRDAV--GDEVDIGVDFHGRVSKSMAKRLVEALEP 213
                                       6777777776.********8888************************..5577**********************99 PP

                                       GTESEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHH CS
                          MR_MLE_C  72 ldllwlEEPvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaea 147
                                       ++++++EEPv pe+  ++l e++ ++ +ipia+gE+++sr+df+ l+e+g+vd +qpd+s++gGite++k+a +aea
  gi|336254989|ref|YP_004598096.1| 214 YEPFFVEEPVLPEH-NDALPEIA-QHtTIPIATGERMFSRWDFKSLFEQGVVDLIQPDLSHAGGITEVKKIASMAEA 288
                                       ************76.999*****.5559************************************************* PP

                                       TT-EEEEBSCSSHHHHHHHHHHHHTTTTBEEEEEEGGGGH......TSGCSBSSSSEEETTEEECTSSSBTSSEB-H CS
                          MR_MLE_C 148 fgvpvapHsgsgglglaaslhlaaaipnllileyfldael......leeelleeplevedGrvtvpdgpGlGvelde 218
                                       ++v +apH++ g+++la ++++ a++pn+li+e++ld ++      l++   ++ +e+edG+v++pd pGlG+e+de
  gi|336254989|ref|YP_004598096.1| 289 YDVAIAPHCPLGPIALASCIQVDACTPNTLIQEQSLDIHYnetsdvLDYLADPSVFEYEDGYVDLPDDPGLGIEVDE 365
                                       *********889*********************************99999999***********************9 PP

                                       HH CS
                          MR_MLE_C 219 ea 220
                                       ++
  gi|336254989|ref|YP_004598096.1| 366 DV 367
                                       85 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.0   2.1e-29   1.9e-25      29     117 .]      26     118 ..      23     118 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 2.1e-29
                                       EEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSS.....CHHHHHHHHHHH CS
                          MR_MLE_N  29 vlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlg.....nmsAkaaidmAl 100
                                        ++k++t++G vG+ge++ +g ra+t+ a++++ + ++l+gkd+++i++ +q l+r  ++      msA+a+id+Al
  gi|336254989|ref|YP_004598096.1|  26 LFLKVTTADGTVGWGEPVVEG-RAKTVRAAVEELMENYLLGKDPSRIEHHWQRLYRGGFYrggpvLMSAIAGIDQAL 101
                                       689******************.*************************************99**************** PP

                                       HHHHHHHTTSBHHHHTT CS
                          MR_MLE_N 101 wDlkakalnlpladLlG 117
                                       wD+k+k+ +lp+++LlG
  gi|336254989|ref|YP_004598096.1| 102 WDIKGKQYGLPVYELLG 118
                                       ****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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 0.20s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3138.32
//
Query:       gi|336254990|ref|YP_004598097.1|  [L=435]
Description: alpha-galactosidase [Halopiger xanaduensis SH-6]
Scores for complete 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-65  221.6   0.0    2.3e-65  220.6   0.0    1.5  2  Glyco_hydro_4C  Family 4 glycosyl hydrolase C-terminal domain
    1.3e-63  213.8   0.0    2.2e-63  213.1   0.0    1.3  1  Glyco_hydro_4   Family 4 glycosyl hydrolase
  ------ inclusion threshold ------
      0.051   13.7   0.1        6.8    6.8   0.0    2.6  3  Ldh_1_N         lactate/malate dehydrogenase, NAD binding dom
       0.16   12.1   0.0       0.36   10.9   0.0    1.5  1  OTCace          Aspartate/ornithine carbamoyltransferase, Asp


Domain annotation for each model (and alignments):
>> Glyco_hydro_4C  Family 4 glycosyl hydrolase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.3   5.9e+03     107     127 ..      38      58 ..      24      64 .. 0.71
   2 !  220.6   0.0   5.2e-69   2.3e-65       1     208 []     193     407 ..     193     407 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                                       SSCHTS-SHHHHHHHHHHTS- CS
                    Glyco_hydro_4C 107 lekrsgeyavdiieaivtdkp 127
                                       +++   e+ v+i+ea+v + +
  gi|336254990|ref|YP_004598097.1|  38 IDEHRLEQTVEIAEAMVDNGR 58 
                                       556677889999999998865 PP

  == domain 2  score: 220.6 bits;  conditional E-value: 5.2e-69
                                       EEEETTEEEEEEEECTTEEHHHHHHHHHHHHHHHHHCTGGGTSHHHHHHHHHHSSEEECGGHHCTTSS..HCHHHHS CS
                    Glyco_hydro_4C   1 vaGlNHlaWllkledkGeDlypelrelveedewleeiaekkaervridllrrlgllpteysrhyaEYvp.ylkreap 76 
                                       vaG+NH+aW+l+ e++G+D+yp l++++e+d    ei e  ++ vr++ll+++g+++te+s+h++EY p ++++  p
  gi|336254990|ref|YP_004598097.1| 193 VAGINHMAWFLECEWRGQDVYPMLEDAMEDD----EIYE--KDTVRFELLKHFGAFVTESSQHNSEYHPyFRTD--P 261
                                       79************99**********99998....4444..469*************************55555..9 PP

                                       HHHHHHHHHHHHHHHHHHTTTTTHHHHHHH.............SSCHTS-SHHHHHHHHHHTS-EEEEEEEE-T.TS CS
                    Glyco_hydro_4C  77 eliekektraevvkevekelfeelekekle.............lekrsgeyavdiieaivtdkprrlvvnvpNn.gl 139
                                       +lie+ + +  +++   + ++e +++++ e               +rs+eya+++i++i+td+prrl++nvpN  g 
  gi|336254990|ref|YP_004598097.1| 262 DLIEELTGTSYAERMPTATYLEGWKARSAErddaladvdpgevEIERSEEYASRLIHSIETDTPRRLNLNVPNGpGH 338
                                       99998663333333345667777777333344444555577774559**************************659* PP

                                       STTS-TTSEEEEEEEEETTEEEEB--CS-HHHHHHCHHHHHHHHHHHHHHHHHTBHHHHHHHHHCSTT- CS
                    Glyco_hydro_4C 140 IpnLpddavVEvpclvdkngirpvavgelpeqlaallrtniaveeltveAalegdrelalqallldplv 208
                                       I+nL++da+VEvpclvd++g++p++vg+lp+qlaal+rtn++v++l+v+ al+gdre++ qa+ ldpl+
  gi|336254990|ref|YP_004598097.1| 339 IQNLENDACVEVPCLVDGTGVHPCSVGKLPPQLAALNRTNVNVQRLAVKGALKGDREAVHQAVKLDPLT 407
                                       *******************************************************************97 PP

>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.1   0.0   4.9e-67   2.2e-63       1     182 [.       3     183 ..       3     184 .. 0.98

  Alignments for each domain:
  == domain 1  score: 213.1 bits;  conditional E-value: 4.9e-67
                                       EEEEETTTSSSHHHHHHHHHHTTTTCTEEEEEEE-SSHHHHHHHHHHHHHHHHHCTTTCEEEEESSHHHHHTT-SEE CS
                     Glyco_hydro_4   1 kiviiGgGStifaklllgdlkkteelsvselaLvDideerldaiqtlakklveeagadlkieattdrkealkdadfV 77 
                                       ki++iG+GS +fak+l+gd+   e+ls s++ L+Dide+rl++  ++a+ +v++  +d  ieattdr+eal+ ad+V
  gi|336254990|ref|YP_004598097.1|   3 KIAFIGAGSMVFAKNLVGDILSFEALSDSTISLMDIDEHRLEQTVEIAEAMVDNGRVDATIEATTDRREALEGADYV 79 
                                       8**************************************************************************** PP

                                       EE---TTHHHHHHHHHHCCHTTTTT-CTTSSSHHHHHHHHHHHHHHHHHHHHHHHHH-TTSEEEE-SSSHHHHHHHH CS
                     Glyco_hydro_4  78 itairvGlekareidekiplryGieqtiqdtvgpggifrglrtipvlleIakdieelcPdawvlnytNPaavvteal 154
                                       ++ i vG  +  e + +ip+ryG+eq i dt+gpggifrglrtip+lleIa d+eelcPda +lnytNP+a+v +al
  gi|336254990|ref|YP_004598097.1|  80 LNMINVGGTEPFENEIRIPERYGVEQAIGDTLGPGGIFRGLRTIPTLLEIAADMEELCPDALLLNYTNPMAIVCWAL 156
                                       *******99999***************************************************************** PP

                                       HHHSTTSEEEEE-SHHHHHHHHHHHHHC CS
                     Glyco_hydro_4 155 lrlvpnikavglChsvigvkeelakllt 182
                                       +  +  i +vglChsv  ++e +a+ ++
  gi|336254990|ref|YP_004598097.1| 157 YEATD-IETVGLCHSVPHTAEAIAEYVD 183
                                       *6665.***************9999875 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 ?    3.9   0.2     0.012        52       2      74 ..       3      80 ..       2      86 .. 0.64
   2 ?    6.8   0.0    0.0015       6.8     100     133 ..     128     161 ..     121     167 .. 0.88
   3 ?   -2.9   0.0       1.5   6.8e+03      32      57 ..     182     207 ..     176     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.012
                                      EEEEETTTSHH.HHHHHHHHHHT.TSSSE.EEEE-SSHHHHHHHHHHHHHCHC...CSTS-EEEEESSGGGGTTESEEE CS
                           Ldh_1_N  2 kvavvGaaGgi.Gqslalllank.klade.laLlDiakekleGvaldlshist...flsvkvkvsekeeealkdadvvv 74
                                      k+a +Ga+ ++ +++l   +++   l d  + L+Di++++le  ++++ ++ +    + + ++++ +  eal++ad+v+
  gi|336254990|ref|YP_004598097.1|  3 KIAFIGAGSMVfAKNLVGDILSFeALSDStISLMDIDEHRLEQ-TVEIAEAMVdngRVDATIEATTDRREALEGADYVL 80
                                      89999995555344555555555244443799*****997764.44444443311145556666779999999999996 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHT CS
                           Ldh_1_N 100 eiveaiakvapnaivlvvsNPvdiltevlkkasg 133
                                       ei++ +++ +p+a++l  +NP+ i++ +l++a++
  gi|336254990|ref|YP_004598097.1| 128 EIAADMEELCPDALLLNYTNPMAIVCWALYEATD 161
                                       789999********************99998776 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.5
                                       E-SSHHHHHHHHHHHHHCHCCSTS-E CS
                           Ldh_1_N  32 lDiakekleGvaldlshistflsvkv 57 
                                       +D+++e+le  ++ ++h++ fl+++ 
  gi|336254990|ref|YP_004598097.1| 182 VDVPQEELEYWVAGINHMAWFLECEW 207
                                       79999999999999999999997654 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 ?   10.9   0.0     8e-05      0.36       4     105 ..       3     107 ..       2     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8e-05
                                       EEEEES....STTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT..-EEEEESSCHHHHTT-SE CS
                            OTCace   4 kiafvG....dkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksg..gsititedleeavkgaDv 74 
                                       kiaf+G       +n + + + + a  + +++l+  ++++  ++++e a++ +++    ++i+ t+d  ea++gaD 
  gi|336254990|ref|YP_004598097.1|   3 KIAFIGagsmVFAKNLVGDILSFEALSDSTISLMDIDEHRL-EQTVEIAEAMVDNGRvdATIEATTDRREALEGADY 78 
                                       89999955442235788888888899999999999999777.4455566666555535599***************8 PP

                                       EEE--SSETTCCGGHHHHHHHHCCCSB-HHH CS
                            OTCace  75 vytdvwvsmgeekereerlkklkdyqvteel 105
                                       v    ++ +g  +  e++++  + y v +++
  gi|336254990|ref|YP_004598097.1|  79 VLN--MINVGGTEPFENEIRIPERYGVEQAI 107
                                       864..44446656666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3442.74
//
Query:       gi|336254991|ref|YP_004598098.1|  [L=241]
Description: hypothetical protein Halxa_3610 [Halopiger xanaduensis SH-6]
Scores for 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  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1995.40
//
Query:       gi|336254992|ref|YP_004598099.1|  [L=200]
Description: hypothetical protein Halxa_3611 [Halopiger xanaduensis SH-6]
Scores for complete 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-54  184.6   0.0    1.8e-54  184.5   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 !  184.5   0.0     1e-58   1.8e-54       1     196 [.       1     195 [.       1     197 [. 0.98

  Alignments for each domain:
  == domain 1  score: 184.5 bits;  conditional E-value: 1e-58
                                       -EEEEEEESSEESSSHHHCCCTTTTTTSHHHHHHHHHHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S-- CS
                   Methyltrn_RNA_2   1 mrefvvlankapTdsdiplddlpGaagrldvlarcvsaalfvshgiRedvvvylvLegtpdpprtikieasevkkvs 77 
                                       mr+fv+l+++ pT++d++lddl+  agrld l+r++ a++ +shgiRedv  +l+      ++ ti++++se+++ +
  gi|336254992|ref|YP_004598099.1|   1 MRQFVLLGHEVPTEPDFSLDDLASGAGRLDALCRSITASFVTSHGIREDVRTHLIAR----DELTITFDGSELRRLN 73 
                                       9**********************99*****************************988....9*************** PP

                                       SSHHHHHHHHHHHHCHCC.TGCCSEEEEETTEEEE---HHHHHHHHHCTSEEEEESTTSEEGGGS---S..SEEEEE CS
                   Methyltrn_RNA_2  78 pderniailikkalkave.eikkqekkvrpgltVrkegfealleelsekksiillkekGedisnakiel..nPvFil 151
                                       pder+ a l++kal+ ++ +i+   ++ +pg+ V ++gfea lee+++  +i+ l+e+G+ + +++     + +F+l
  gi|336254992|ref|YP_004598099.1|  74 PDERSTAALVRKALEHRDeAIGALPAEPSPGIEVYRRGFEATLEEIADDGPIVQLHEDGDAVTDVDAAAlaDGIFVL 150
                                       ***************998799999*****************************************998889****** PP

                                       E-TT-SHHHHHHHHHCTTSEEEES-SS---HHHHHHHHHHHHHHH CS
                   Methyltrn_RNA_2 152 gdHidlpeeeekllerlkakrvslgPlsLhadhcvtlihneldkk 196
                                       +dH+d+++eee lle++ ++r++lgP  Lhad+++t++h+ ld++
  gi|336254992|ref|YP_004598099.1| 151 SDHRDFTDEEEGLLEDAVDQRLRLGPELLHADQAITIAHHYLDTE 195
                                       ******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1585.04
//
Query:       gi|336254993|ref|YP_004598100.1|  [L=186]
Description: hypothetical protein Halxa_3612 [Halopiger xanaduensis SH-6]
Scores for 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   48.8   4.1    5.6e-13   48.6   4.1    1.2  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   4.1   3.1e-17   5.6e-13       4     126 ..       4     123 ..       1     163 [. 0.88

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 3.1e-17
                              YdjM   4 ltHallGaalglalaallgaake.avllavavlgAllPD.iDhpsstlgrklgllskklaklvgHRgftHSllflal 78 
                                         H++++ ++  a+a +   ++  a   +++++g+ +PD iD     ++ ++  l +        R++tHSllf a+
  gi|336254993|ref|YP_004598100.1|   4 WGHLAVAYLCYTAYAHRQFDRPPlALPALALAVGSQFPDlID---KPFAWNFDVLPG-------GRTLTHSLLFGAA 70 
                                       58*************9998887777777778888*****99*...888888999889.......************* PP

                              YdjM  79 lalvlllllrlfgrsalrlglllllgvlsHlllDlltk......yGvpl.lwPfs 126
                                       l++++l+++ +fgr+   +g+++l+g  sHl++D+  +      +G++  lwP+ 
  gi|336254993|ref|YP_004598100.1|  71 LSALVLVAADRFGRR--DVGVGFLVGHYSHLVADVPPSvlrgdlSGTEYfLWPVL 123
                                       **************9..99***************988888888888876578876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); 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: 0.42u 0.18s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1541.04
//
Query:       gi|336254994|ref|YP_004598101.1|  [L=59]
Description: hypothetical protein Halxa_3613 [Halopiger xanaduensis SH-6]
Scores for complete 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   31.1   0.9    2.4e-07   30.6   0.9    1.2  1  Prok-RING_1      Prokaryotic RING finger family 1
    5.5e-05   22.4   2.4      0.092   12.2   0.3    2.3  2  zf-ribbon_3      zinc-ribbon domain
      0.002   18.2   9.0      0.065   13.4   3.8    2.1  2  Zn-ribbon_8      Zinc ribbon domain
     0.0025   17.5   2.2        0.4   10.5   0.2    2.2  2  zinc_ribbon_2    zinc-ribbon domain
      0.004   17.5   1.0     0.0055   17.0   1.0    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.004   16.6   2.8     0.0057   16.1   2.8    1.2  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0051   16.8   1.4      0.038   14.0   1.7    1.7  2  DZR              Double zinc ribbon
     0.0078   16.1   2.6      0.044   13.7   2.6    2.0  2  Nudix_N_2        Nudix N-terminal
  ------ inclusion threshold ------
      0.011   15.4   1.6      0.041   13.6   1.6    1.8  1  A2L_zn_ribbon    A2L zinc ribbon domain
      0.013   15.5   2.2      0.066   13.2   2.2    1.9  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.013   15.4   0.2      0.018   14.9   0.2    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.026   14.6   3.3       0.86    9.7   0.1    2.2  2  UPF0547          Uncharacterised protein family UPF0547
      0.028   13.8   1.6       0.04   13.3   1.6    1.4  1  zf_Rg            Reverse gyrase zinc finger
      0.031   14.3   0.5      0.031   14.3   0.5    2.7  3  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.041   13.9   1.9       0.11   12.5   1.6    1.7  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.052   13.8   0.5          4    7.8   0.0    2.2  2  zinc_ribbon_9    zinc-ribbon
      0.058   13.8   1.9       0.98    9.9   0.2    2.2  2  zf-IS66          zinc-finger binding domain of transposase IS
      0.061   13.3   0.3      0.067   13.2   0.3    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.07   13.3   1.7       0.16   12.1   1.4    1.7  2  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
      0.072   12.8   3.1        3.4    7.4   0.3    2.3  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.12   12.2   2.1       0.23   11.3   0.1    2.0  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
        0.2   11.4   0.1       0.24   11.1   0.1    1.1  1  FlhC             Flagellar transcriptional activator (FlhC)
       0.27   11.3   0.3       0.27   11.3   0.3    2.0  2  DUF1272          Protein of unknown function (DUF1272)
       0.39   10.8   1.8        3.7    7.7   0.1    2.1  2  DUF2752          Protein of unknown function (DUF2752)
       0.83    9.3   4.8        4.2    7.1   0.4    2.2  2  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
        3.1    7.9   5.9        9.1    6.4   0.5    2.2  2  YhfH             YhfH-like protein


Domain annotation for each model (and alignments):
>> 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 !   30.6   0.9   3.4e-10   2.4e-07       4      29 ..      22      51 ..      20      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.4e-10
                       Prok-RING_1  4 gkkCpvCgkelkee....dDiVvCpeCgtp 29
                                      g +Cp Cg el+ +    +D+VvC eCgtp
  gi|336254994|ref|YP_004598101.1| 22 GRSCPSCGGELERDvykdKDAVVCAECGTP 51
                                      789********98888889**********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 !   10.4   0.1    0.0005      0.35       4      25 ..      24      31 ..      21      36 .. 0.62
   2 !   12.2   0.3   0.00013     0.092      13      25 ..      39      51 ..      38      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0005
                       zf-ribbon_3  4 rCPnCGaplssddnvCpyCGtk 25
                                      +              Cp+CG++
  gi|336254994|ref|YP_004598101.1| 24 S--------------CPSCGGE 31
                                      4..............5555554 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                       zf-ribbon_3 13 ssddnvCpyCGtk 25
                                      ++d++vC+ CGt+
  gi|336254994|ref|YP_004598101.1| 39 DKDAVVCAECGTP 51
                                      789********96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.2   0.00013     0.092      28      39 ..      24      35 ..       5      36 .. 0.85
   2 !   13.4   3.8   9.4e-05     0.065       8      36 ..      25      53 ..      24      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                       Zn-ribbon_8 28 aCPeCgsevrrv 39
                                       CP+Cg+e++r 
  gi|336254994|ref|YP_004598101.1| 24 SCPSCGGELERD 35
                                      4*********96 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9.4e-05
                       Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCgs.ev 36
                                      C +Cg e e+ +  +d++ ++C eCg  ++
  gi|336254994|ref|YP_004598101.1| 25 CPSCGGELERDV-YKDKDAVVCAECGTpRA 53
                                      *********777.55677777*****9555 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0073         5       2       6 ..      25      29 ..      23      36 .. 0.66
   2 !   10.5   0.2   0.00059       0.4      11      22 ..      40      51 ..      37      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0073
                     zinc_ribbon_2  2 CpnCG 6 
                                      Cp+CG
  gi|336254994|ref|YP_004598101.1| 25 CPSCG 29
                                      66665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00059
                     zinc_ribbon_2 11 dnakFCpyCGtp 22
                                      ++a+ C +CGtp
  gi|336254994|ref|YP_004598101.1| 40 KDAVVCAECGTP 51
                                      68999******8 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 !   17.0   1.0     8e-06    0.0055       5      36 ..      24      50 ..      21      59 .] 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8e-06
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga 36
                                       CP Cgg+ +    ++++      v Ca+Cg 
  gi|336254994|ref|YP_004598101.1| 24 SCPSCGGELERDVYKDKD-----AVVCAECGT 50
                                      7******99999998888.....6*******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 !   16.1   2.8   8.2e-06    0.0057       2      27 ..      24      50 ..      23      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.2e-06
                                      EETTTTCEECHEE.TSTTCE.EESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveD.pergel.vCtdCGl 27
                                       CP Cg++ l++D ++  +  vC +CG+
  gi|336254994|ref|YP_004598101.1| 24 SCPSCGGE-LERDvYKDKDAvVCAECGT 50
                                      5******8.8****9999999*****95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   1.3   0.00034      0.24      14      35 ..      24      49 ..       7      49 .. 0.67
   2 !   14.0   1.7   5.6e-05     0.038       1      21 [.      25      51 ..      25      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00034
                               DZR 14 fCseCgtklkavaa....edrCpsCg 35
                                       C+ Cg +l++       + +C +Cg
  gi|336254994|ref|YP_004598101.1| 24 SCPSCGGELERDVYkdkdAVVCAECG 49
                                      56666666653222556666666665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.6e-05
                               DZR  1 CpqCgee......lppdarfCseCgtk 21
                                      Cp+Cg e       ++da +C eCgt+
  gi|336254994|ref|YP_004598101.1| 25 CPSCGGElerdvyKDKDAVVCAECGTP 51
                                      888888888887778888889999887 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   2.6   6.4e-05     0.044       3      30 ..      25      50 ..      23      52 .. 0.87
   2 ?    5.0   0.5     0.034        23       3       9 ..      45      51 ..      44      56 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.4e-05
                                      -TTT--B-EEE--TT-SS-EEEETTTTE CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgt 30
                                      C++CG+++e+ + ++ +    vC+ Cgt
  gi|336254994|ref|YP_004598101.1| 25 CPSCGGELERDVYKDKDA--VVCAECGT 50
                                      ************866555..6*****97 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.034
                                      -TTT--B CS
                         Nudix_N_2  3 CsqCGtp 9 
                                      C +CGtp
  gi|336254994|ref|YP_004598101.1| 45 CAECGTP 51
                                      7777776 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 ?   13.6   1.6   5.9e-05     0.041       6      29 ..      25      50 ..      21      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-05
                     A2L_zn_ribbon  6 CsvCggng..ilnseqgylvCieCga 29
                                      C  Cgg+   +++++++  vC eCg+
  gi|336254994|ref|YP_004598101.1| 25 CPSCGGELerDVYKDKDAVVCAECGT 50
                                      7779998733599***********95 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.2   9.6e-05     0.066       5      26 ..      25      49 ..      24      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.6e-05
                    PhnA_Zn_Ribbon  5 CplCaSeyt...YedgallvCpeCa 26
                                      Cp C+ e +   Y d++  vC eC+
  gi|336254994|ref|YP_004598101.1| 25 CPSCGGELErdvYKDKDAVVCAECG 49
                                      *******743339***********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 ?   14.9   0.2   2.7e-05     0.018      29      54 ..      23      50 ..      12      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-05
                    OrfB_Zn_ribbon 29 ktCseCgsknke..alsgrtfkCpnCgf 54
                                       +C+ Cg ++++   ++++ ++C +Cg+
  gi|336254994|ref|YP_004598101.1| 23 RSCPSCGGELERdvYKDKDAVVCAECGT 50
                                      68**********9999999*******96 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4     0.025        17      16      21 ..      24      29 ..      23      32 .. 0.56
   2 ?    9.7   0.1    0.0012      0.86      13      22 ..      41      50 ..      40      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.025
                           UPF0547 16 fCphCG 21
                                      +Cp CG
  gi|336254994|ref|YP_004598101.1| 24 SCPSCG 29
                                      455555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                           UPF0547 13 aaqfCphCGy 22
                                      +a++C++CG+
  gi|336254994|ref|YP_004598101.1| 41 DAVVCAECGT 50
                                      699******8 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.6   5.8e-05      0.04       5      20 ..      19      35 ..      15      52 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.8e-05
                             zf_Rg  5 vfe.klCPNCgGdisde 20
                                      ++e ++CP CgG+++ +
  gi|336254994|ref|YP_004598101.1| 19 ILEgRSCPSCGGELERD 35
                                      555379********965 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 ?    0.5   0.0      0.93   6.4e+02       7      18 ..       6      17 ..       5      17 .. 0.83
   2 ?   14.3   0.5   4.6e-05     0.031       2      12 ..      25      35 ..      24      47 .. 0.85
   3 ?    0.1   0.2       1.2   8.5e+02       4       8 ..      47      51 ..      44      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.93
                    DNA_ligase_ZBD  7 savvReegeaiy 18
                                      s +++ +g+a++
  gi|336254994|ref|YP_004598101.1|  6 STAEQQDGGAVL 17
                                      78999999*985 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.6e-05
                    DNA_ligase_ZBD  2 CPvCGsavvRe 12
                                      CP+CG +++R 
  gi|336254994|ref|YP_004598101.1| 25 CPSCGGELERD 35
                                      *********96 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.2
                    DNA_ligase_ZBD  4 vCGsa 8 
                                      +CG++
  gi|336254994|ref|YP_004598101.1| 47 ECGTP 51
                                      8*997 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 ?   12.5   1.6   0.00016      0.11      17      44 ..      21      49 ..      18      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                     Zn_Tnp_IS1595 17 ngfvCPhCgsr.kayriktrglfqCkeCr 44
                                      +g+ CP Cg++ +   +k+     C+eC+
  gi|336254994|ref|YP_004598101.1| 21 EGRSCPSCGGElERDVYKDKDAVVCAECG 49
                                      5789*******9777777777999***98 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0058         4      23      29 ..      24      30 ..       5      32 .. 0.79
   2 ?    4.9   0.1     0.047        32      18      28 ..      40      49 ..      33      52 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0058
                     zinc_ribbon_9 23 lCPhCgg 29
                                      +CP+Cgg
  gi|336254994|ref|YP_004598101.1| 24 SCPSCGG 30
                                      4*****9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.047
                     zinc_ribbon_9 18 edsdvlCPhCg 28
                                      + ++v+C +Cg
  gi|336254994|ref|YP_004598101.1| 40 K-DAVVCAECG 49
                                      3.3346****8 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 ?    9.9   0.2    0.0014      0.98       2      12 ..      23      33 ..      22      41 .. 0.76
   2 ?    3.7   0.1      0.12        81       3      10 ..      44      51 ..      43      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0014
                           zf-IS66  2 rtCpcCGgllk 12
                                      r+Cp CGg+l 
  gi|336254994|ref|YP_004598101.1| 23 RSCPSCGGELE 33
                                      68******643 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.12
                           zf-IS66  3 tCpcCGgl 10
                                      +C++CG++
  gi|336254994|ref|YP_004598101.1| 44 VCAECGTP 51
                                      69***984 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   0.3   9.7e-05     0.067      72      99 ..      24      55 ..       3      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.7e-05
                                      EETTTS-EEECHH..H..HHS-TTTSSS-EEE CS
                              HypA 72 rCreCgkefelee..k..alrCpkCgsadvei 99
                                       C +Cg e e +   +  a+ C +Cg+ + ++
  gi|336254994|ref|YP_004598101.1| 24 SCPSCGGELERDVykDkdAVVCAECGTPRAQV 55
                                      6*****999977654246779*****998876 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 ?   12.1   1.4   0.00023      0.16      15      40 .]      22      49 ..      18      49 .. 0.86
   2 ?    5.7   0.2     0.024        16      17      25 ..      44      52 ..      41      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                     Auto_anti-p27 15 aetCpvCgvPLmrdr..kggkvyCvaCd 40
                                      + +Cp Cg  L rd   ++  v+C+ C+
  gi|336254994|ref|YP_004598101.1| 22 GRSCPSCGGELERDVykDKDAVVCAECG 49
                                      789**********999767889*****6 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.024
                     Auto_anti-p27 17 tCpvCgvPL 25
                                      +C +Cg+P 
  gi|336254994|ref|YP_004598101.1| 44 VCAECGTPR 52
                                      7******96 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 ?    7.4   0.3    0.0049       3.4      22      28 ..      23      29 ..      22      35 .. 0.61
   2 ?    5.9   0.1     0.015        10       6      12 ..      45      51 ..      41      55 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0049
                     zf-NADH-PPase 22 rvCpaCg 28
                                      r Cp+Cg
  gi|336254994|ref|YP_004598101.1| 23 RSCPSCG 29
                                      5566665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.015
                     zf-NADH-PPase  6 CgrCGap 12
                                      C+ CG+p
  gi|336254994|ref|YP_004598101.1| 45 CAECGTP 51
                                      6666665 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 ?   11.3   0.1   0.00033      0.23       2      11 ..      23      32 ..      22      40 .. 0.87
   2 ?    0.7   0.2      0.68   4.7e+02       3       9 ..      44      50 ..      42      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                                      EE-SSS--EE CS
                    zf-C4_Topoisom  2 ekCPkCggdL 11
                                      + CP+Cgg+L
  gi|336254994|ref|YP_004598101.1| 23 RSCPSCGGEL 32
                                      79******98 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.68
                                      E-SSS-- CS
                    zf-C4_Topoisom  3 kCPkCgg 9 
                                       C +Cg 
  gi|336254994|ref|YP_004598101.1| 44 VCAECGT 50
                                      799**95 PP

>> FlhC  Flagellar transcriptional activator (FlhC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00035      0.24     131     164 ..      19      52 ..      15      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00035
                              FlhC 131 llqlasCkrCkgefvthaedlesefvCglCqlps 164
                                       +l+  sC +C+ge     +++++++vC+ C  p 
  gi|336254994|ref|YP_004598101.1|  19 ILEGRSCPSCGGELERDVYKDKDAVVCAECGTPR 52 
                                       577889************************9885 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00039      0.27      42      52 ..      23      33 ..      15      38 .. 0.82
   2 ?    1.4   0.2      0.51   3.5e+02      17      29 ..      38      48 ..      33      52 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                           DUF1272 42 nvCPncgGelv 52
                                        CP cgGel 
  gi|336254994|ref|YP_004598101.1| 23 RSCPSCGGELE 33
                                      57*******96 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.51
                           DUF1272 17 pdseearicsyEc 29
                                      +d+ +a++c+ Ec
  gi|336254994|ref|YP_004598101.1| 38 KDK-DAVVCA-EC 48
                                      444.666665.44 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0053       3.7       8      16 ..      22      30 ..      15      31 .. 0.82
   2 ?    2.9   0.1      0.17   1.1e+02      11      21 ..      45      55 ..      42      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0053
                           DUF2752  8 GipCPGCGl 16
                                      G +CP CG+
  gi|336254994|ref|YP_004598101.1| 22 GRSCPSCGG 30
                                      889*****7 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.17
                           DUF2752 11 CPGCGltRavh 21
                                      C  CG+ Ra +
  gi|336254994|ref|YP_004598101.1| 45 CAECGTPRAQV 55
                                      99****99965 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 ?    7.1   0.4    0.0061       4.2      11      17 ..      23      29 ..      19      31 .. 0.89
   2 ?    4.1   0.5      0.05        35      13      18 ..      45      50 ..      44      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0061
                           zf-tcix 11 rkCpkCG 17
                                      r Cp+CG
  gi|336254994|ref|YP_004598101.1| 23 RSCPSCG 29
                                      89***** PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.05
                           zf-tcix 13 CpkCGt 18
                                      C++CGt
  gi|336254994|ref|YP_004598101.1| 45 CAECGT 50
                                      *****9 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.5     0.013       9.1      14      24 ..      23      33 ..      19      40 .. 0.83
   2 ?    4.5   0.7      0.05        34      15      21 ..      44      50 ..      34      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.013
                              YhfH 14 KkCteCGkeie 24
                                        C++CG e+e
  gi|336254994|ref|YP_004598101.1| 23 RSCPSCGGELE 33
                                      68*****9987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.05
                              YhfH 15 kCteCGk 21
                                      +C+eCG 
  gi|336254994|ref|YP_004598101.1| 44 VCAECGT 50
                                      6*****5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 472.51
//
Query:       gi|336254995|ref|YP_004598102.1|  [L=68]
Description: hypothetical protein Halxa_3614 [Halopiger xanaduensis SH-6]
Scores for 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   2.2        0.3   11.1   2.2    1.5  1  PsbL      PsbL protein


Domain annotation for each model (and alignments):
>> PsbL  PsbL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.2   1.7e-05       0.3      14      29 ..      37      52 ..      36      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.7e-05
                              PsbL 14 RtSLYlGLLLvfvlal 29
                                      R SL+lGL+ + vlal
  gi|336254995|ref|YP_004598102.1| 37 RLSLFLGLVTINVLAL 52
                                      88************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 554.17
//
Query:       gi|336254996|ref|YP_004598103.1|  [L=76]
Description: hypothetical protein Halxa_3615 [Halopiger xanaduensis SH-6]
Scores for 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:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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 0.22s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 639.82
//
Query:       gi|336254997|ref|YP_004598104.1|  [L=371]
Description: peptidase S1 and S6 chymotrypsin/Hap [Halopiger xanaduensis SH-6]
Scores for complete 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-28  100.6   2.7    2.3e-28  100.0   2.7    1.3  1  Trypsin_2      Trypsin-like peptidase domain
    1.7e-13   50.9   0.2    1.3e-12   48.0   0.2    1.9  1  Trypsin        Trypsin
    1.3e-08   35.0   0.0    2.6e-08   34.0   0.0    1.5  1  PDZ_2          PDZ domain
    0.00012   22.4   0.0      0.042   14.2   0.0    2.6  2  PDZ            PDZ domain
     0.0011   18.7   0.1        0.2   11.5   0.0    2.9  2  PDZ_6          PDZ domain
  ------ inclusion threshold ------
      0.027   13.7   0.8       0.91    8.6   0.2    2.1  2  Peptidase_S32  Equine arteritis virus serine endopeptidase S3
      0.088   12.8   0.0       0.63   10.0   0.0    2.3  2  Tricorn_PDZ    Tricorn protease PDZ domain


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 !  100.0   2.7   9.1e-32   2.3e-28       1     150 []      86     222 ..      86     222 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 9.1e-32
                         Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgp 77 
                                       GsGfl+++++ ++Tn Hvv++ + a              +g +  +++v++d  +DlA+l+v ++ ++   pl l++
  gi|336254997|ref|YP_004598104.1|  86 GSGFLYDENH-VITNEHVVAGGEAADL---------QYINGDWTGTRLVGTDYFSDLAVLEV-DHVPDVATPLSLAD 151
                                       9*********.****************.........999*************666*******.************** PP

                         Trypsin_2  78 sealkggepvyvvGyplggeksgsvssGivsgvve.sesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                        ++++g+ +v ++G+p g e+  s+s+Givsgv++   s ++++ ++++qtdaa++pG+SGGpl+d dG+vvG+
  gi|336254997|ref|YP_004598104.1| 152 ARPAVGQ-QVLAIGNPYGLEG--SMSQGIVSGVERtLDSGREFSFPDVVQTDAALNPGNSGGPLVDLDGNVVGV 222
                                       9877777.*************..9***********999***********************************8 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.2   5.1e-16   1.3e-12      27     214 ..      86     239 ..      77     245 .. 0.74

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 5.1e-16
                                       EEEEEEETTEEEEEGGGTTT..GGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSB CS
                           Trypsin  27 CgGslisenwvlTAaHCvsn..asdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklg 101
                                        +G+l++en v+T+ H+v +  a d++ + g+             +  +      ++ + +  D+a+l+++      
  gi|336254997|ref|YP_004598104.1|  86 GSGFLYDENHVITNEHVVAGgeAADLQYINGD------------WTGTRL-----VGTD-YFSDLAVLEVDHV---P 141
                                       47*****************9444444444443............333332.....2222.345********98...9 PP

                                       SSBHCCBBCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHH.HHHHHTTTTSTTTEEEEESTTSSSBCT CS
                           Trypsin 102 dtvrpiclpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsre.tcksaykgkvtenmlcagakeggkdac 177
                                       d   p++l++a++  +vg+++l++G ++    +   ++ ++ v+ v+r  +  +++     ++ ++++a     + +
  gi|336254997|ref|YP_004598104.1| 142 DVATPLSLADARP--AVGQQVLAIGNPYG--LE--GSMSQGIVSGVERTlDSGREF---SFPDVVQTDA-----ALN 204
                                       **********666..99977766666664..44..579999****99963333322...4588899999.....9** PP

                                       TTTTTSEEEETTTEEEEEEEEESSSSCTTSEEEEEEG CS
                           Trypsin 178 qGDSGGPlvcsdgelvGivswgkgcakgnrpgvytkv 214
                                       +G+SGGPlv  dg +vG+v +g + a++  +g+++  
  gi|336254997|ref|YP_004598104.1| 205 PGNSGGPLVDLDGNVVGVVNAGVNGADN--IGFAISA 239
                                       *********************9555554..6877765 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0     1e-11   2.6e-08       2      76 ..     259     358 ..     258     364 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1e-11
                                       ...XX------............-EEEEEE-TTSGGGGT.--T...............T-EEEEETTB--SSHHHHH CS
                             PDZ_2   2 ylGvsvsdeed..........tggvlvvsVkeggPaakaglka...............gDvilkvdgkkvksledli 53 
                                       y+G+ ++++++          ++g++v  V +ggPa++  l+                gDvi + dg+++ ++  l 
  gi|336254997|ref|YP_004598104.1| 259 YMGIGLRSVDRlvaeenrleeATGIIVSRVVDGGPADGV-LEEadrtvrrrgepipvgGDVIFEMDGQPIPDRHALS 334
                                       78888998888899999999999************9999.7778********************************* PP

                                       HHHH.TS-TT-EEEEEEEETTEEE CS
                             PDZ_2  54 slll.kkkpGdtVkltvlRdgkkk 76 
                                       + l+ +++pG+t++l++ R+g + 
  gi|336254997|ref|YP_004598104.1| 335 RFLAlETSPGQTIELRLWRNGAET 358
                                       ********************9876 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.6e-05     0.042       9      49 ..     257     303 ..     249     306 .. 0.81
   2 !    5.5   0.0    0.0085        22      47      79 ..     316     349 ..     307     352 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                                       TSESSEEEEEETTSS.......SSSSEEEEEECTTSHHHHHTSSTTEE CS
                               PDZ   9 rgglGfslkggsdqr.......gdkgifvsevlpggaaeadglkvGDk 49 
                                       ++++G+ l++ +          +++gi+vs+v+ gg+a+   l++ D+
  gi|336254997|ref|YP_004598104.1| 257 HSYMGIGLRSVDRLVaeenrleEATGIIVSRVVDGGPADGV-LEEADR 303
                                       6677777777666667778889****************998.999887 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0085
                                       TEEEEEETTEETTTSHHHHHHHHHHTTTS.EEEE CS
                               PDZ  47 GDkIlsvNgvdvenvsheeavqaikgskg.kvtL 79 
                                       GD+I +++g+++ +   +   +a++ s g ++ L
  gi|336254997|ref|YP_004598104.1| 316 GDVIFEMDGQPIPDRHALSRFLALETSPGqTIEL 349
                                       9***********9988888888877777665555 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2      0.02        50       1      17 [.     284     299 ..     284     303 .. 0.78
   2 !   11.5   0.0   7.8e-05       0.2      19      56 .]     316     353 ..     315     353 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.02
                             PDZ_6   1 vVtaVdpgsPAdrAG.lr 17 
                                       +V+ V+ g+PAd  G l+
  gi|336254997|ref|YP_004598104.1| 284 IVSRVVDGGPAD--GvLE 299
                                       599********9..6555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.8e-05
                             PDZ_6  19 GDiilsvNGqpveglsladvaallr..gsagesvvlvvrr 56 
                                       GD+i + +Gqp+   + + +++ l+  +s+g+ ++l+++r
  gi|336254997|ref|YP_004598104.1| 316 GDVIFEMDGQPI--PDRHALSRFLAleTSPGQTIELRLWR 353
                                       9***********..88888888877658888888888776 PP

>> Peptidase_S32  Equine arteritis virus serine endopeptidase S32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.013        33     110     150 ..      82     120 ..      68     171 .. 0.64
   2 ?    8.6   0.2   0.00036      0.91     206     225 ..     204     223 ..     186     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.013
                                       SSSEEEEEEEECTTEEEEEEEHHHH-.TSEEEEEETTEEEEE CS
                     Peptidase_S32 110 GsslGsGgvftidgevvvvtashvlg.dnkarvsivgasqtl 150
                                       G   GsG ++  d+   v+t  hv++ ++ a +++ +   t 
  gi|336254997|ref|YP_004598104.1|  82 GRGQGSGFLY--DE-NHVITNEHVVAgGEAADLQYINGDWTG 120
                                       4455565555..43.4689*****995666777775544443 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00036
                                       -GGGTT-EEEETTE.EEEEE CS
                     Peptidase_S32 206 kcGDsGspvvdedgelvGvh 225
                                       ++G+sG p+vd dg++vGv 
  gi|336254997|ref|YP_004598104.1| 204 NPGNSGGPLVDLDGNVVGVV 223
                                       79****************84 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.58   1.5e+03       4      27 ..     108     131 ..     105     134 .. 0.86
   2 ?   10.0   0.0   0.00025      0.63      42      85 ..     315     360 ..     284     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.58
                                       SEEEEEETTEEEEEEE-BS-TTSS CS
                       Tricorn_PDZ   4 GadleldkgayriakilpGdswde 27 
                                       +adl++ +g ++ ++++  d++++
  gi|336254997|ref|YP_004598104.1| 108 AADLQYINGDWTGTRLVGTDYFSD 131
                                       79*************999998765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00025
                                       TT-EEEEETTEE-BTTB-HHHHHH..TTTTSEEEEEEE-STT-EEE CS
                       Tricorn_PDZ  42 eGdlilavdgepvskekgiaelLv..gkagkeveLtvkrkdgkarr 85 
                                        Gd+i + dg+p+  ++ +++ L+     g+++eL++ r+++++r+
  gi|336254997|ref|YP_004598104.1| 315 GGDVIFEMDGQPIPDRHALSRFLAleTSPGQTIELRLWRNGAETRE 360
                                       59******************9886214557*******998887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2864.11
//
Query:       gi|336254998|ref|YP_004598105.1|  [L=451]
Description: hypothetical protein Halxa_3617 [Halopiger xanaduensis SH-6]
Scores for 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    5.5e-08   33.0   0.0    2.0  2  THUMP          THUMP domain
     0.0016   18.7   2.1     0.0016   18.7   2.1    2.5  3  DnaJ_CXXCXGXG  DnaJ central domain
  ------ inclusion threshold ------
      0.091   13.1   0.0       0.56   10.6   0.0    2.3  1  SpaA           Prealbumin-like fold domain
       0.48   10.4   7.2      0.082   12.9   1.9    2.4  2  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi


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 !   33.0   0.0   1.2e-11   5.5e-08      56     133 ..      62     153 ..      53     156 .. 0.94
   2 ?   -0.8   0.0      0.33   1.5e+03      81     110 ..     265     292 ..     257     294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.2e-11
                                       EEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS.................SSHHHHHHHHHHHHHHCC CS
                             THUMP  56 vcevceadledileaakeivkkkfeeeketFaVrvkrrgkhf.................eftsreinrevGkaivek 115
                                       vce+ +a+++ + + ++++ +   +e   t++V+++++   +                 e  +re+nrevG+++  k
  gi|336254998|ref|YP_004598105.1|  62 VCEGYCATFDAVADTIVAALEGVDFE---TYQVGTRVPPLAEenerllredaglepdvgESLKRELNREVGRRVGAK 135
                                       4899999****************999...*********9988999******************************** PP

                                       TT-EE-SSS-SEEEEEEE CS
                             THUMP 116 tglkVdlenPdivvrvei 133
                                       tg++Vd+++Pd++  +++
  gi|336254998|ref|YP_004598105.1| 136 TGAEVDFDRPDVLAVIDL 153
                                       *************99987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.33
                                       HCT-EEEEEEEESSSTSSSHHHHHHHHHHH CS
                             THUMP  81 eeketFaVrvkrrgkhfeftsreinrevGk 110
                                       e+   F  +vkr++ + + +  e++re+ +
  gi|336254998|ref|YP_004598105.1| 265 EG-RPFVLEVKRPKTR-DPDPAELEREINA 292
                                       33.38999********.*********9965 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.1   5.2e+03      17      22 ..      16      21 ..      11      28 .. 0.65
   2 ?   -0.2   0.0       0.3   1.4e+03      13      24 ..      56      67 ..      48      80 .. 0.70
   3 !   18.7   2.1   3.7e-07    0.0016       1      49 [.     199     252 ..     199     258 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                     DnaJ_CXXCXGXG 17 CktCkG 22
                                      C++C G
  gi|336254998|ref|YP_004598105.1| 16 CDSCLG 21
                                      444444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.3
                     DnaJ_CXXCXGXG 13 kkktCktCkGsG 24
                                      ++ +C  C+G  
  gi|336254998|ref|YP_004598105.1| 56 DPADCWVCEGYC 67
                                      466777777765 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 3.7e-07
                     DnaJ_CXXCXGXG   1 CkkCkGsgakkgk..kktCktCkGsG.vvreeqkt.lgp.fvqqsqstCpeCeG 49 
                                       C++C Gsg + g+  ++ C+ C+GsG +  ++ ++ + p +v+++  +  + +G
  gi|336254998|ref|YP_004598105.1| 199 CRECGGSGVQLGEtgEEPCDYCGGSGyMYDTSVEQvVRPhVVEAMDGEEGTFHG 252
                                       9*******9875557888********5433333234666566655555555555 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00012      0.56       6      60 ..      81     312 ..      78     329 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                                       -TS-EEEEEET.................................................................. CS
                              SpaA   6 LaGaeFtlykv.................................................................. 16 
                                       L+G+ F+ y+v                                                                  
  gi|336254998|ref|YP_004598105.1|  81 LEGVDFETYQVgtrvpplaeenerllredaglepdvgeslkrelnrevgrrvgaktgaevdfdrpdvlavidleafd 157
                                       55555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                                       ............................................................................. CS
                              SpaA  17 ............................................................................. 16 
                                                                                                                    
  gi|336254998|ref|YP_004598105.1| 158 pldleadesvtshavdvqinpafvygryrklerdipqtewpcrecggsgvqlgetgeepcdycggsgymydtsveqv 234
                                       55555555555555555555555555555555555555555555555555555555555555544444444444444 PP

                                       ........................TTSCCCHCHHTT.....................TTCCEESEEE-BTTSEEEEE CS
                              SpaA  17 ........................dtttdgkdalea....................kktgtevttlttdenGkatfe 49 
                                                               d          a                     + ++   ++   ++G +++e
  gi|336254998|ref|YP_004598105.1| 235 vrphvveamdgeegtfhgagredvD----------ArmldegrpfvlevkrpktrdPDPAELEREINAAADGSVEVE 301
                                       4444444444333333332222220..........12222223333333333333344455668888999******* PP

                                       EEESEEEEEEE CS
                              SpaA  50 gLplGtYllvE 60 
                                       gL l tY +vE
  gi|336254998|ref|YP_004598105.1| 302 GLRLATYEMVE 312
                                       ********998 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 ?   -1.5   0.3      0.57   2.5e+03      12      18 ..      59      65 ..      51      70 .. 0.82
   2 ?   12.9   1.9   1.8e-05     0.082       6      42 ..     192     226 ..     188     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.57
                                      E-TTTTT CS
                         Anti-TRAP 12 kCdaCng 18
                                       C+ C+g
  gi|336254998|ref|YP_004598105.1| 59 DCWVCEG 65
                                      6999987 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.8e-05
                                       HHHCEEE-TTTTTTSEETTE......E-TTTTTSSEE CS
                         Anti-TRAP   6 lpeLEtkCdaCngsGkiepeeprasleCPkCsGkgli 42 
                                       +p+ E +C +C gsG   +e   +  +C  C+G g +
  gi|336254998|ref|YP_004598105.1| 192 IPQTEWPCRECGGSGVQLGE--TGEEPCDYCGGSGYM 226
                                       68889**************9..9999*******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 3550.40
//
Query:       gi|336254999|ref|YP_004598106.1|  [L=741]
Description: dipeptidyl aminopeptidase/acylaminoacyl peptidase [Halopiger xanaduensis SH-6]
Scores for 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-48  162.5   0.0    1.3e-47  162.0   0.0    1.2  1  Peptidase_S9    Prolyl oligopeptidase family
      1e-09   38.4   0.3      1e-05   25.3   0.5    2.3  2  Peptidase_S15   X-Pro dipeptidyl-peptidase (S15 family)
    9.5e-09   35.1   0.0    1.7e-08   34.3   0.0    1.3  1  DLH             Dienelactone hydrolase family
    2.4e-08   33.5   0.2    0.00027   20.3   0.0    2.2  2  Hydrolase_4     Serine aminopeptidase, S33
    0.00012   21.8   0.4       0.45   10.1   0.0    2.3  2  Abhydrolase_1   alpha/beta hydrolase fold
    0.00062   19.5   0.0     0.0011   18.7   0.0    1.3  1  FSH1            Serine hydrolase (FSH1)
     0.0022   16.9   0.0      0.028   13.2   0.0    2.1  2  Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propel
     0.0023   17.7  10.3       0.45   10.2   1.4    4.2  3  Gmad1           Lipoprotein LpqB beta-propeller domain
     0.0055   16.2   0.0      0.012   15.1   0.0    1.5  1  Esterase_phd    Esterase PHB depolymerase
  ------ inclusion threshold ------
       0.15   12.3   0.0         28    5.1   0.0    3.8  4  ANAPC4_WD40     Anaphase-promoting complex subunit 4 WD40 dom
        8.3    4.3  14.1         11    3.9  14.1    1.1  1  AF-4            AF-4 proto-oncoprotein


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.0   0.0   7.9e-51   1.3e-47       3     207 ..     498     699 ..     496     701 .. 0.96

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 7.9e-51
                                       --HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHH CS
                      Peptidase_S9   3 fsselqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltg 79 
                                       f++  + l++rGy+v+ +n+rG++ +G+af++++++++g++e++D++a+++ala++g++ds+r++ +G SyGG   g
  gi|336254999|ref|YP_004598106.1| 498 FRFAHAALTSRGYAVFRPNYRGGASRGRAFAEELYGRWGTVEVEDIVAGVDALADRGWADSDRVFGYGFSYGGIAQG 574
                                       565556678******************************************************************** PP

                                       HHHHH-GGG-SEEEEESE---CCCHHCSTTS..THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT- CS
                      Peptidase_S9  80 aalnqrpdlFkaavaevpvvdvlrydsdtdl..lteeymewgnpeeneegykelspyspldnvkaypplLlihGlaD 154
                                        +++ ++dl  aav e +++d++++  ++d+  + e  +e+g p+en+e y+e+s++  +d+  +++plL++ G +D
  gi|336254999|ref|YP_004598106.1| 575 YLVT-QTDLLTAAVPEHGIYDLRSSFGSDDAhvWME--TEFGLPWENPETYDEASSILEADA--IDTPLLIMAGGED 646
                                       ****.**********************999977666..78899*******************..************* PP

                                       SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHH CS
                      Peptidase_S9 155 drvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlke 207
                                        r+pp+++++l+ a +k++ +++l+++pde H +g+p++ +++l+r+l++++ 
  gi|336254999|ref|YP_004598106.1| 647 WRCPPSQSEQLYVAARKQDIDAKLVVYPDEHHNIGDPDRAIDRLERILEWYEA 699
                                       **************************************************976 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.5   6.1e-09     1e-05      49     151 ..     501     607 ..     463     620 .. 0.86
   2 !   10.3   0.0   0.00023      0.37     219     268 ..     627     678 ..     616     679 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 6.1e-09
                                       GGHHHHHTT-EEEEEE-TTSTTS-S---TT......TTTHHHHHHHHHHHHHHC.TTEEEEEEEEEECHHHHHHHHH CS
                     Peptidase_S15  49 qdkvfvarGYavVvqdvrGtggSeGeftvg......dsdeaedgadvidWlakq.pwsnGkVgmtGiSYlGttqlla 118
                                       +++++ +rGYav   + rG g+S G    +      ++ e+ed ++ +d la   +  +++V  +G+SY+G+ q ++
  gi|336254999|ref|YP_004598106.1| 501 AHAALTSRGYAVFRPNYRG-GASRGRAFAEelygrwGTVEVEDIVAGVDALADRgWADSDRVFGYGFSYGGIAQGYL 576
                                       4555899************.799**9999999**9999****************9999****************999 PP

                                       CTT--TTEEEEEEECE-S-TCCCCSECTTEEBC CS
                     Peptidase_S15 119 aatgvpalkaivpeaaisdlyddyyregGlvra 151
                                        + +++ l a+vpe +i dl   ++ +  ++++
  gi|336254999|ref|YP_004598106.1| 577 VT-QTDLLTAAVPEHGIYDLRS-SFGSDDAHVW 607
                                       98.9***************998.6666666655 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00023
                                       -HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-..EEEEECECTT CS
                     Peptidase_S15 219 nlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv..klilgpwtHv 268
                                       ++  +ad++++p+l++ G  Dw     ++ +ly a++++++  kl++ p +H 
  gi|336254999|ref|YP_004598106.1| 627 SIL-EADAIDTPLLIMAGGEDWRCPpSQSEQLYVAARKQDIdaKLVVYPDEHH 678
                                       444.579*********************************9********9996 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0     1e-11   1.7e-08      35     188 ..     504     679 ..     479     699 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1e-11
                               DLH  35 rlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavaylksvpevstkkvgvvGfCmGGal 111
                                        l + GY+++ P+ Y+++a  +  +a a++++ +++  v   +v d++ a v++l+ ++ +++++v   Gf  GG  
  gi|336254999|ref|YP_004598106.1| 504 ALTSRGYAVFRPN-YRGGA--SRGRAFAEELY-GRWGTV---EVEDIV-AGVDALADRGWADSDRVFGYGFSYGGIA 572
                                       67899*******9.77766..67777777777.555555...566666.9999************************ PP

                               DLH 112 alllaaevpevdaavafYG..............................lspekeleeaakikapilalfgeeDefi 158
                                         +l ++ + + aav+ +G                                  + + ea+ i +p+l+++g+eD   
  gi|336254999|ref|YP_004598106.1| 573 QGYLVTQTDLLTAAVPEHGiydlrssfgsddahvwmetefglpwenpetYDEASSILEADAIDTPLLIMAGGEDWRC 649
                                       99999999************************************9998877888999******************** PP

                               DLH 159 padevekleealkaanvdlelkvYpgagHa 188
                                       p ++ e+l  a +++ +d++l+vYp+  H 
  gi|336254999|ref|YP_004598106.1| 650 PPSQSEQLYVAARKQDIDAKLVVYPDEHHN 679
                                       **************************9995 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00011      0.17       2      94 ..     478     576 ..     477     589 .. 0.64
   2 !   20.3   0.0   1.7e-07   0.00027     186     234 ..     630     680 ..     621     683 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                       Hydrolase_4   2 epkavvvlvHGlaehsgr..yaelaeaLaaqGfavyalDhrGhGrse......gkrghvpsfddyvdDlaafvekvk 70 
                                       +pk +vv +HG    ++   +    +aL+ +G+av+  ++rG G s           + +  +  v+D+ a v++++
  gi|336254999|ref|YP_004598106.1| 478 DPKPLVVAIHGGPLAYDEpvFRFAHAALTSRGYAVFRPNYRG-GASRgrafaeE--LYGRWGTVEVEDIVAGVDALA 551
                                       689999999996544442113334467***************.55553666552..222222333777777777777 PP

                       Hydrolase_4  71 .eehpel.plfllGhSmGGliallyl 94 
                                        + + ++ ++f +G S GG+ a+ yl
  gi|336254999|ref|YP_004598106.1| 552 dRGWADSdRVFGYGFSYGGI-AQGYL 576
                                       3444554799********95.44444 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.7e-07
                       Hydrolase_4 186 raakitlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyHel 234
                                       +a++i++Pll++ G++D+ ++p++s++ly +++++  d +l +yp   H +
  gi|336254999|ref|YP_004598106.1| 630 EADAIDTPLLIMAGGEDWRCPPSQSEQLYVAARKQdiDAKLVVYPDEHHNI 680
                                       57899****************************9988899999*9999976 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00039      0.63       1      84 [.     481     570 ..     481     572 .. 0.77
   2 !   10.1   0.0   0.00028      0.45     189     252 ..     616     680 ..     594     682 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00039
                                       SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB..CHHSHHHHHHHHH...HH..HHHCT CS
                     Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacin.ddygtasvaddld...ri..ldalg 71 
                                       p++v +hG+p   d +  r+   aL  +g+ v+ ++ rG ++  +a a+    ++gt+ v+d++    ++  +   +
  gi|336254999|ref|YP_004598106.1| 481 PLVVAIHGGPLAYDEPVFRFAHAALTSRGYAVFRPNYRGGASRGRAFAEELyGRWGTVEVEDIVAgvdALadRGWAD 557
                                       689************99999*******************98887777764467778888888777653334444455 PP

                                       TSSEEEEEETHHH CS
                     Abhydrolase_1  72 ddkltlvGhSmGG 84 
                                        d++   G+S+GG
  gi|336254999|ref|YP_004598106.1| 558 SDRVFGYGFSYGG 570
                                       5666666667776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00028
                                       HHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS....EEEEEEETCSSSH CS
                     Abhydrolase_1 189 ieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpk....krlvvisdagHla 252
                                       +e ++t+d+a+++l+ +    +  p l+++g +D+  pp+++e+l  + +k    ++lvv++d+ H++
  gi|336254999|ref|YP_004598106.1| 616 WENPETYDEASSILEADA---IDTPLLIMAGGEDWRCPPSQSEQLYVAARKqdidAKLVVYPDEHHNI 680
                                       778899999999999776...999***************77666655533336777999999999976 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   6.4e-07    0.0011     107     201 ..     564     678 ..     532     679 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.4e-07
                              FSH1 107 iGFSqGaalaallaslleellkeashpslkfailvsGfkleepk................yeeyy...eedkiqtpt 164
                                        GFS G++  ++l+++++ l      p+  +  l s+f +++ +                y+e+    e d i tp 
  gi|336254999|ref|YP_004598106.1| 564 YGFSYGGIAQGYLVTQTDLLTA--AVPEHGIYDLRSSFGSDDAHvwmetefglpwenpetYDEASsilEADAIDTPL 638
                                       59**************998887..89*99***********999999999999999999996664455799******* PP

                              FSH1 165 LhvlGelDtvvdeerseaLaeafkns...skvlkHpggHf 201
                                       L + G +D   ++++se+L+ a +++   +k++ +p  H+
  gi|336254999|ref|YP_004598106.1| 639 LIMAGGEDWRCPPSQSEQLYVAARKQdidAKLVVYPDEHH 678
                                       ***********************99999999**9999996 PP

>> Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.08   1.3e+02     124     186 ..      15      81 ..      10      94 .. 0.82
   2 !   13.2   0.0   1.7e-05     0.028     119     224 ..     383     500 ..     377     512 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.08
                                       EEEEEEEE-TTSSEEEEE...EEETTSSEEEEEEEETTTTEEEEEEEEEEESEE.EEECTTSSEEEE CS
                    Peptidase_S9_N 124 valgefavsedgkllAys...lsksGsdwytirvkdietgedlpdeledvkfsg.ivWaadekgffY 186
                                       ++++++avs++g+ +A+    +++  +d++t  ++  ++g + p +l+ v +++  +W + ++ + +
  gi|336254999|ref|YP_004598106.1|  15 TRITDLAVSPSGDRVAFTateYDQDEDDAVTSLFVVPTDGSREPHRLTTVAGASsPAWSPSGEELAF 81 
                                       678899***********63337888889999999999999999999999999888999988776655 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.7e-05
                                       TTS-.EEEEEEEE-TTSSE..EEEEEEETTSSEEEEEEEETTTTE.............EEEEEEEEEESEEEEECTT CS
                    Peptidase_S9_N 119 edgtfvalgefavsedgkl..lAyslsksGsdwytirvkdietge.............dlpdeledvkfsgivWaad 180
                                       ++++  a+ +f++s dg+   lA+s  + G+d y ++v d+e ++             dl+de   +    ++W  d
  gi|336254999|ref|YP_004598106.1| 383 QGDD-RAIAAFDISADGSTaaLAFSDPREGQDIYAVAVDDLEATDrpgslrrlsrvnaDLTDEYPMPAVRRVEWESD 458
                                       5556.7999*******975337888889****************99******************************* PP

                                       SSEE...EEEESS-SSS-TSTSB-S-BEEEEEETTS-GGG-EEEES- CS
                    Peptidase_S9_N 181 ekgf...fYtrydkedersdtdtnlnqkvyrhkLGtaqseDelvfee 224
                                       ++++   +Y + d  d   d    +   v  h  G +   De vf++
  gi|336254999|ref|YP_004598106.1| 459 GWTIdgvLYHDPD-VDLEAD--DPKPLVVAIH--GGPLAYDEPVFRF 500
                                       9876111444433.222222..2334444444..6666666666665 PP

>> Gmad1  Lipoprotein LpqB beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.3    0.0033       5.3      24      76 ..      16      76 ..       6     115 .. 0.75
   2 ?   -0.8   0.1      0.66   1.1e+03     161     191 ..     154     185 ..     143     229 .. 0.74
   3 !   10.2   1.4   0.00028      0.45      74     158 ..     349     436 ..     252     458 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0033
                             Gmad1 24 dlrsaAvSrdgqqvaavt......apdggrtLvvgsygg..easevleggsltrpSwdrdg 76
                                      +++ +AvS++g++va+ +      ++d  ++L v++++g  e+  +++    ++p w++ g
  gi|336254999|ref|YP_004598106.1| 16 RITDLAVSPSGDRVAFTAteydqdEDDAVTSLFVVPTDGsrEPHRLTTVAGASSPAWSPSG 76
                                      688999*********9999999887888889999877762245555566677777777764 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.66
                             Gmad1 161 tglleeavsvsWr.sedtLvVlrsseggpvqa 191
                                       t+ +e +++ +W  ++d++v++++++++  q+
  gi|336254999|ref|YP_004598106.1| 154 TDREEGVSAFDWGpDGDRFVIAARDPTDEEQE 185
                                       66788899999964678899988888877666 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00028
                             Gmad1  74 rdgalWvvedgaevvravrddaegevavveVdasalragpvtelrvSrDGtRaAvivekdgggk.vyvavVvrdadG 149
                                       +d++l++ + ++  +r+vr ++e e++v ++   + +++ + ++ +S DG  aA+  ++  +g+ +y  +V   + +
  gi|336254999|ref|YP_004598106.1| 349 ADDDLYALVGDESRTRLVRASDEDEGTVERTFEAQGDDRAIAAFDISADGSTAALAFSDPREGQdIYAVAVDDLEAT 425
                                       35677777777777777776666777788888888888****************99877655441444444433333 PP

                             Gmad1 150 ..qksltapva 158
                                         + sl+   +
  gi|336254999|ref|YP_004598106.1| 426 drPGSLRRLSR 436
                                       44555555555 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.3e-06     0.012      16     197 ..     480     663 ..     465     669 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.3e-06
                      Esterase_phd  16 mplvvmlhGctqsveefaaGtrmnlladklGvvvlypeqslranaqkcwnwyk.dtdraGrGeaavvvalvdalvde 91 
                                        plvv +hG     +e        +l+   G++v+ p+   r  a +   + +    r G  e + +va vdal+d 
  gi|336254999|ref|YP_004598106.1| 480 KPLVVAIHGGPLAYDEPVFRFAHAALT-SRGYAVFRPN--YRGGASRGRAFAEeLYGRWGTVEVEDIVAGVDALADR 553
                                       599999999999999987766666665.579****997..5777777777777467899****************** PP

                      Esterase_phd  92 hrvdaarvyvaGlsaGaaladllalhypdvfaavalhsGlalGeaadvisa...ldvmrrGlrqapaaavdalveag 165
                                          d+ rv+  G+s G+     l        aav  h    l  +  +  a   +++    + ++p +  +a +   
  gi|336254999|ref|YP_004598106.1| 554 GWADSDRVFGYGFSYGGIAQGYLVTQTDLLTAAVPEHGIYDLRSSFGSDDAhvwMETEFGLPWENPETYDEASSILE 630
                                       **************998766666666666678898888766655443333300144444456688988888776543 PP

                      Esterase_phd 166 a.ypglpalvvqGdadtvvavknaeslvvalrr 197
                                       a     p l++ G  d    + ++e+l va r+
  gi|336254999|ref|YP_004598106.1| 631 AdAIDTPLLIMAGGEDWRCPPSQSEQLYVAARK 663
                                       313468999999999999999999999988776 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.017        28      28      59 ..     138     178 ..     136     213 .. 0.80
   2 ?   -0.7   0.0       1.1   1.9e+03      39      53 ..     292     306 ..     271     316 .. 0.80
   3 ?    1.7   0.0      0.19   3.1e+02       7      59 ..     351     407 ..     346     417 .. 0.83
   4 ?   -3.1   0.0       6.3     1e+04      40      51 ..     449     460 ..     433     472 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.017
                       ANAPC4_WD40  28 rvwtl.........eedkedsevrsLaWkpdgklLavaysd 59 
                                       +vwt+         +e+++++ v+++ W pdg  +++a  d
  gi|336254999|ref|YP_004598106.1| 138 QVWTFdlvrggdarQETDREEGVSAFDWGPDGDRFVIAARD 178
                                       5777777888887778889999**************99887 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                       ANAPC4_WD40  39 sevrsLaWkpdgklL 53 
                                          ++L+W+ dg l 
  gi|336254999|ref|YP_004598106.1| 292 LLCTDLSWRGDGALG 306
                                       45689******9875 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.19
                       ANAPC4_WD40   7 mDLiAlatedgellvfRlng......qrvwtleedkedsevrsLaWkpdgklLavaysd 59 
                                        DL Al+ ++++ ++ R +       +r +++  +++d+ + ++  + dg+  a a+sd
  gi|336254999|ref|YP_004598106.1| 351 DDLYALVGDESRTRLVRASDedegtvERTFEA--QGDDRAIAAFDISADGSTAALAFSD 407
                                       59***************988555555555555..8999999999999999999999887 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 6.3
                       ANAPC4_WD40  40 evrsLaWkpdgk 51 
                                        vr ++W+ dg 
  gi|336254999|ref|YP_004598106.1| 449 AVRRVEWESDGW 460
                                       689999999985 PP

>> AF-4  AF-4 proto-oncoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  14.1    0.0067        11     463     489 ..     711     737 ..     697     741 .] 0.71

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0067
                              AF-4 463 esahsssaeSeSsSeSeSSSeSDSesE 489
                                       +  +  s+eS S S+SeS SeS+SesE
  gi|336254999|ref|YP_004598106.1| 711 AGTEDASTESDSESDSESESESESESE 737
                                       555667778887777777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (741 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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):              11  [number of targets reported over threshold]
# CPU time: 0.70u 0.25s 00:00:00.95 Elapsed: 00:00:00.40
# Mc/sec: 5496.44
//
Query:       gi|336255000|ref|YP_004598107.1|  [L=233]
Description: ribonuclease HII [Halopiger xanaduensis SH-6]
Scores for 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   0.0    5.3e-35  121.1   0.0    1.6  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 !  121.1   0.0   2.9e-39   5.3e-35       2     198 .]       4     218 ..       3     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: 121.1 bits;  conditional E-value: 2.9e-39
                                       EEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHH....SEEEEEEE-HHHHH.HHTTT CS
                         RNase_HII   2 GiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklik....kkiekrklvaeeikyasene 74 
                                       G+DEaG+GpvlG++++aav +e+   + l   g++DSK L++ +reeLa  i+      +  +++  e i+     e
  gi|336255000|ref|YP_004598107.1|   4 GVDEAGKGPVLGSMFAAAVHLEDPSLDALP-EGIADSKRLAPARREELAATIRaddrIGVGVAEITPELID---DPE 76 
                                       9*************************9776.6*********************986644555555555555...567 PP

                                       S-HHHHHHHHHHHHHHHHHHT.CEECCEC..CCE--SS...............HHHHHHHHHHHHCCEEEEETTGGG CS
                         RNase_HII  75 inlneikaaltlavikllekl.gvkvdei..lvdgvtt...............peslkkkleqiikikvtvekkade 133
                                        + n++ +++++++i +  ++ ++  d+i  l d+++t               +  l++  e+  ++++ + + ad 
  gi|336255000|ref|YP_004598107.1|  77 TDMNSLTVQAHAEAIAAAVPDvAAPADKItgLCDACDTdadrfarrvtdacaaALGLEHDCETDAPLEIDARHGADD 153
                                       77777777777777775555514444455335777777755554444433322333334444444599********* PP

                                       T-HHHHHHHHHHHHHHHHHHHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHHH CS
                         RNase_HII 134 kyllvaaASiiAkverdeelellkrkpgtldkgsGyasdektrallkkgats..klpdivrlsfktv 198
                                        + lv aASi+Akverd  +e + +++g  + gsGy+sd+ tr +l++++++  +lp ++r s+ t+
  gi|336255000|ref|YP_004598107.1| 154 DSTLVGAASIVAKVERDAHIEAIGEEYG--NVGSGYPSDPTTRDFLESYVDEhgELPPFARESWSTC 218
                                       **************************98..**********************9***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1908.31
//
Query:       gi|336255001|ref|YP_004598108.1|  [L=537]
Description: SecD/SecF/SecDF export membrane protein [Halopiger xanaduensis SH-6]
Scores for 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   49.6   3.3      3e-13   49.6   3.3    1.7  2  SecD_SecF       Protein export membrane protein
     0.0055   15.7  11.2      0.012   14.6  11.2    1.4  1  MMPL            MMPL family
  ------ inclusion threshold ------
       0.01   15.7   1.4      0.018   14.8   1.4    1.3  1  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2      0.63   3.7e+03     103     129 ..     143     169 ..     143     171 .. 0.83
   2 !   49.6   3.3     5e-17     3e-13      12     173 ..     362     520 ..     357     524 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.63
                                       HHHHHHHHHHHH--SS-HHHHHHHHHH CS
                         SecD_SecF 103 vvfdrvrenlrkkkratlkeiinlsln 129
                                       v  d +r+ +++++r++l + i++ +n
  gi|336255001|ref|YP_004598108.1| 143 VTADDIRNGVTEQTRNDLVQTIQDKIN 169
                                       567899999999999999999988776 PP

  == domain 2  score: 49.6 bits;  conditional E-value: 5e-17
                                       -EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HH.HHHHHHHHHHHHHHHHHHHHHHTT----HHHH CS
                         SecD_SecF  12 daekisvetvgpsvskelaekavlallialvliliyvalrFewr.valaaiialvhDviitvgvlsllgievdlatv 87 
                                       d+++ +v +  ps+ ++++  +++  l++++++  +v+lr++++ va   i+++   v i++g+++++++++dl+ v
  gi|336255001|ref|YP_004598108.1| 362 DFSQEQVYSLQPSLADQFKLYSLFIGLLSVLAVSGVVFLRYRDPnVAAPMILTATAEVAILLGFVAAIRMPIDLSHV 438
                                       5677888999999999*9999999999999***********985388889999************************ PP

                                       HHHHHHTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHH CS
                         SecD_SecF  88 aalLtiiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalal 164
                                       a+ + +iG  v+d v++ d v ++       + +++++    + +    ++ +tt++++  l +l  + l++fa++ 
  gi|336255001|ref|YP_004598108.1| 439 AGFIAVIGTGVDDLVIIADEVMDEGDV----SSQRVFESRFRKAFWVIGAAAATTIIALSPLAVLSLGDLRGFAIIT 511
                                       *********************999555....555555556666666555788889999999**************** PP

                                       HHHTSTTTT CS
                         SecD_SecF 165 lvGlivgty 173
                                       ++G+++g++
  gi|336255001|ref|YP_004598108.1| 512 ILGVLIGVL 520
                                       *******97 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6  11.2   1.9e-06     0.012     145     292 ..     383     523 ..     372     525 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-06
                              MMPL 145 lklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYall 221
                                       + +i++++++ +  + ++ yr +  a+ ++lt+  ++++ lg+  + a    ++ls ++    ++ +i++G+D  ++
  gi|336255001|ref|YP_004598108.1| 383 SLFIGLLSVLAVSGVVFLRYRDPNVAAPMILTATAEVAILLGF--VAAIRMPIDLSHVAG---FIAVIGTGVDDLVI 454
                                       56788999999999*****************************..456666677877775...66679*****9999 PP

                              MMPL 222 LvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivl 292
                                       +     +e +  ++r   +   ++++  v+ aa++t +ia+  L+v++l+ l+++++   lGvl+ vli++
  gi|336255001|ref|YP_004598108.1| 455 IADEVMDEGDVSSQR--VFESRFRKAFWVIGAAAATTIIALSPLAVLSLGDLRGFAIITILGVLIGVLITR 523
                                       999888888888888..99999**********************************************987 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 ?   14.8   1.4   3.1e-06     0.018       9     122 ..     408     519 ..     405     531 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-06
                                       HHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHH.HHHHCHHCCHHCHHHHHHHHTTTCHHHHH.HHHHHHHCC CS
                    Sterol-sensing   9 glagviivllsvasslgllaylgltltliilevlPfl.vlavgvdnifvlvkavqrtsrsldeseri.aealgevgp 83 
                                       ++ +++++++ va  lg++a++ +++ l ++  + f+ v+  gvd+  ++  +v +   + + s+r+    ++++ +
  gi|336255001|ref|YP_004598108.1| 408 AAPMILTATAEVAILLGFVAAIRMPIDLSHV--AGFIaVIGTGVDDLVIIADEVMDE-GDVS-SQRVfESRFRKAFW 480
                                       666889999999999*****99999998776..78874789*****99999998654.4444.45551456888889 PP

                                       CCHHCCCHHHHHHH.HHHHCCHHHHHHHHHHHHHHHHHHH CS
                    Sterol-sensing  84 silltsltellall.lgaltdvpavqeFclfaavavlvdF 122
                                        i + ++t ++al  l+ + ++  ++ F++ ++++vl+  
  gi|336255001|ref|YP_004598108.1| 481 VIGAAAATTIIALSpLA-VLSLGDLRGFAIITILGVLIGV 519
                                       99999999999999777.77899************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); 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: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3855.40
//
Query:       gi|336255002|ref|YP_004598109.1|  [L=292]
Description: SecD/SecF/SecDF export membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-29  101.1  12.3    7.7e-29  100.4  12.3    1.3  1  SecD_SecF  Protein export membrane protein
    0.00022   20.6   0.0    0.00066   19.1   0.0    1.9  1  Sec_GG     SecD/SecF GG Motif
     0.0027   15.5   7.7     0.0034   15.1   7.7    1.2  1  ACR_tran   AcrB/AcrD/AcrF family
  ------ inclusion threshold ------
        0.2    9.7  12.4       0.42    8.6  12.4    1.5  1  Patched    Patched family


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4  12.3   1.7e-32   7.7e-29      12     187 ..     115     286 ..     103     288 .. 0.93

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 1.7e-32
                                       -EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHH.HHHHHHHHHHHHHHTT----HHHH CS
                         SecD_SecF  12 daekisvetvgpsvskelaekavlallialvliliyvalrFewrvalaaiia.lvhDviitvgvlsllgievdlatv 87 
                                        + + + +tv+ps+ ++ +++a+l l++a+v++    +l F+  v++ ai+  +++D++i ++++s+ gi ++l tv
  gi|336255002|ref|YP_004598109.1| 115 GMDVLQQSTVSPSFADQAQQTALLGLAVAFVGMSALAFLLFRTFVPSIAIVIsAFSDLVIPLAFMSIAGISLSLGTV 191
                                       5778899**************************************99887655************************ PP

                                       HHHHHHTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHH CS
                         SecD_SecF  88 aalLtiiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalal 164
                                       a+lL++iGYSv++++++ + +  +     + ++ e + ++ ++ +t+ti+ +  +l+++va  l+g + l+++ ++l
  gi|336255002|ref|YP_004598109.1| 192 AGLLMLIGYSVDSDILLNNHILRR-----QGDFYESTLRATKTGVTMTITSMTAMLVMAVAASLFGVELLRSIGIIL 263
                                       ******************999877.....789*****************99999*********************** PP

                                       HHHTSTTTTTHHHHHHHHHHHHH CS
                         SecD_SecF 165 lvGlivgtyssifiasplllllk 187
                                       +vGl+++ +++  ++  ll ++k
  gi|336255002|ref|YP_004598109.1| 264 FVGLAADLMNTYMLNLSLLRWYK 286
                                       *******************9997 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.5e-07   0.00066       6      25 ..      43      62 ..      38      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-07
                                      C--EE-TTTS-EEEEEEEE- CS
                            Sec_GG  6 kGlNLGlDFtGGthielqfd 25
                                       +++LG DF+GG ++++q+ 
  gi|336255002|ref|YP_004598109.1| 43 TPVQLGMDFAGGAELTVQTT 62
                                      699***************86 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   7.7   7.5e-07    0.0034     837    1003 ..     119     268 ..      40     278 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.5e-07
                                        CTT..SSTTEEEEEEHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHTSSSTCHHHHTTHHHHHHHHHHHHHHTT CS
                          ACR_tran  837 akkvklpegvtiewtgqaeqeqeasnsllilvalalllvflvLaalyeslsepllilltvPlalvGallalllrg 911 
                                         ++    ++v+ +++ q      a++++l+ +a+a++ +  + ++l+  ++  ++i+++    lv  l  ++++g
  gi|336255002|ref|YP_004598109.1|  119 LQQ----STVSPSFADQ------AQQTALLGLAVAFVGMSALAFLLFRTFVPSIAIVISAFSDLVIPLAFMSIAG 183 
                                        333....3333333333......3334444444444444444455555555555555555555555555567888 PP

                                        --BSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCT-S. CS
                          ACR_tran  912 lelsviaqvGlilliGlavkNaillvefakelrekegksleeaileaakeRLrPiLMTalaailGvlPLalstg. 985 
                                        ++ls+ +  Gl++liG +v   ill + +      +g +  e +l+a k+    + MT ++++  +l +a++ + 
  gi|336255002|ref|YP_004598109.1|  184 ISLSLGTVAGLLMLIGYSVDSDILLNNHILRR---QG-DFYESTLRATKTG---VTMT-ITSMTAMLVMAVAASl 250 
                                        88888888888888888888888875554433...33.4678888888874...5565.5666667777777663 PP

                                        TTHHHHHHHHHHHHHHHH CS
                          ACR_tran  986 aGselqqplgivvlgGlv 1003
                                         G el + +gi ++ Gl 
  gi|336255002|ref|YP_004598109.1|  251 FGVELLRSIGIILFVGLA 268 
                                        588888888888888875 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  12.4   9.5e-05      0.42     658     769 ..     135     253 ..     106     265 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 9.5e-05
                           Patched 658 stiqnivlallcmfvvallfipelitvlvitlsivsidigviGflslWgvdLDpismitiimsiGfsvd....lsaH 730
                                       +++  +++a++ m++ a+l+   ++ +++i++s  s  +  + f+s+ g+ L   +++ ++m iG+svd    l  H
  gi|336255002|ref|YP_004598109.1| 135 TALLGLAVAFVGMSALAFLLFRTFVPSIAIVISAFSDLVIPLAFMSIAGISLSLGTVAGLLMLIGYSVDsdilLNNH 211
                                       45566789****************************99999****************************44444556 PP

                           Patched 731 iaya...fvrsekddakeRvvealealgwPvvqgalSTilgv 769
                                       i  +   f++s    +k  v++++  +   +v +    + gv
  gi|336255002|ref|YP_004598109.1| 212 ILRRqgdFYESTLRATKTGVTMTITSMTAMLVMAVAASLFGV 253
                                       643222255555556666677777766665555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2242.61
//
Query:       gi|336255003|ref|YP_004598110.1|  [L=135]
Description: hypothetical protein Halxa_3622 [Halopiger xanaduensis SH-6]
Scores for 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  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1105.90
//
Query:       gi|336255004|ref|YP_004598111.1|  [L=157]
Description: hypothetical protein Halxa_3623 [Halopiger xanaduensis SH-6]
Scores for 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:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1354.50
//
Query:       gi|336255005|ref|YP_004598112.1|  [L=433]
Description: glucose-6-phosphate isomerase [Halopiger xanaduensis SH-6]
Scores for 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-29  101.8   0.0    5.2e-25   88.0   0.0    2.1  2  PGI       Phosphoglucose isomerase


Domain annotation for each model (and alignments):
>> PGI  Phosphoglucose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.0   2.9e-29   5.2e-25      97     309 ..      72     278 ..      65     299 .. 0.90
   2 !   11.7   0.0   3.8e-06     0.068     410     461 ..     356     407 ..     340     423 .. 0.91

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 2.9e-29
                                       -EEEEE--GGGTHHHHHHHHHTGGG-TT-EEEEE--SSHHHHHHHHTT--GGGEEEEEE-SSS--HHHHHHHHHHHH CS
                               PGI  97 tdvvniGiGGsdlGPvlvtealkkeserlkvafvsnvdgthiaevlkkldpettlfivasktfttaetllnaesake 173
                                       + +v +GiGGs+lG   +t+al  es++    f+ nvd+  + + l++l  e+t + v+s+  ttaetl n   ++e
  gi|336255005|ref|YP_004598112.1|  72 EALVTVGIGGSALGAATITNALADESDTE-TVFLDNVDPEWVTQRLESLPLEETAINVVSRSGTTAETLANFLVVRE 147
                                       5689*******************999876.789******************************************** PP

                                       HHHHHH--GGGGGGTEEEESS-HHHHHHHT--GG..GEEE--TTS-GGG-TTSGGGHHHHHHH-HHHHHHHHHHHHH CS
                               PGI 174 wllkalkedsavakhfvalstnaekveefGidek..nmfefwdwvGGryslwsaiGlsvalsiGfenfeelleGaaa 248
                                       ++ +a ++ +   ++ +  +  +   +++  d +    ++  d v Gr+s  sa+G+ +a   G++ +e+lleGaaa
  gi|336255005|ref|YP_004598112.1| 148 AFESAGVDWT---ERTIVTTGESGPLRNLA-DRHdlPSLKVPDGVPGRFSALSAVGMVAAAVCGHD-LEALLEGAAA 219
                                       ****999644...67777777777788775.44401569999***************999999987.8********* PP

                                       HHHHHHHS-GGG-HHHHHHHHHHHHHHTS---EEEEEES-GGGTTHHHHHHHHHHHHH--- CS
                               PGI 249 idkhfleaplekniPvllalvgvwyvnflgaeteailpydqylerlaaylqqldmesnGks 309
                                         + ++ + +e   P  +  +  +  + +ga  +a++py + le  a ++ ql  es Gk 
  gi|336255005|ref|YP_004598112.1| 220 ERETLAGSLFE--CPAYAYGATTYALDARGAGINAVMPYAESLETQAEWFAQLWAESLGKD 278
                                       99999999998..5777777899************************************95 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.8e-06
                                       ----EEEEEEEE--HHHHHHHHHHHHHHHHHHHHHHTB-TT--GGGHHHHHH CS
                               PGI 410 GnrPsnsillekltpaelGalialyehkilvqGviwginsfdqwGvelGkel 461
                                         rP   + ++++ ++elG l+   e   +  G ++g+n+f+q  ve  k+ 
  gi|336255005|ref|YP_004598112.1| 356 AGRPNVRVEIDRVDAYELGGLLYGMEAACVLAGELYGVNTFEQPAVEWAKKA 407
                                       5799999****************************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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 0.20s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3547.77
//
Query:       gi|336255006|ref|YP_004598113.1|  [L=377]
Description: abortive infection protein [Halopiger xanaduensis SH-6]
Scores for 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-14   51.6   1.4    8.9e-14   51.6   1.4    3.0  3  CPBP      CPBP intramembrane metalloprotease


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 ?   -5.0   6.8         1   1.8e+04      40      56 ..      51      73 ..      20     209 .. 0.70
   2 ?   -2.9   0.1      0.51   9.1e+03      43      54 ..     232     243 ..     215     252 .. 0.59
   3 !   51.6   1.4     5e-18   8.9e-14       5      92 .]     271     367 ..     265     367 .. 0.86

  Alignments for each domain:
  == domain 1  score: -5.0 bits;  conditional E-value: 1
                                      HHHHHHHHHHHCSGGG......H CS
                              CPBP 40 ailissilFglaHlpn......g 56
                                      a++++++l  la  +       +
  gi|336255006|ref|YP_004598113.1| 51 AFAVAAVLAFLARRHGvadrriA 73
                                      44444444444433333333321 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.51
                                       HHHHHHHHCSGG CS
                              CPBP  43 issilFglaHlp 54 
                                          ++Fg++ ++
  gi|336255006|ref|YP_004598113.1| 232 GVVVIFGAIMAI 243
                                       344444444333 PP

  == domain 3  score: 51.6 bits;  conditional E-value: 5e-18
                                       HHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG.........HHHHHHHHHHHHHHHHH CS
                              CPBP   5 llvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn.........gpsvllaalaGlvlgyl 72 
                                       l+++ + +l+ + +EEll+R ++++ l   +s+  a+++ s++F+++H            + s+ +++ +++vlg +
  gi|336255006|ref|YP_004598113.1| 271 LVLIPASILVIGPFEELLYRNVIQKSLYGTFSRYGAVVVGSVIFAIIHTQAywtagpgqvAASLGTVFGLSIVLGTV 347
                                       4555667888899*****************9999***************9977776665444459999999****** PP

                                       HHHTT-HHHHHHHHHHHHHH CS
                              CPBP  73 ylktgsllaaillHallnll 92 
                                       y++t +l++++l+H+++n++
  gi|336255006|ref|YP_004598113.1| 348 YERTDNLVVPALVHGIYNAV 367
                                       ******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.21s 00:00:00.75 Elapsed: 00:00:00.36
# Mc/sec: 3103.09
//
Query:       gi|336255007|ref|YP_004598114.1|  [L=152]
Description: nucleic acid-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-13   50.6   0.1      6e-13   49.1   0.1    1.6  2  PIN_6           PIN domain of ribonuclease
     0.0021   17.5   0.8     0.0034   16.8   0.4    1.6  2  PIN_5           PINc domain ribonuclease
     0.0022   18.1   3.0      0.006   16.7   3.0    1.7  1  Zn-ribbon_8     Zinc ribbon domain
     0.0027   17.7   1.5      0.037   14.0   0.2    2.5  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
     0.0051   16.8   1.9     0.0072   16.3   1.9    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0054   16.6   1.3      0.008   16.0   1.3    1.2  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
     0.0076   16.2   0.1      0.071   13.0   0.0    2.1  2  DUF4411         Domain of unknown function (DUF4411)
     0.0077   16.2   0.7      0.012   15.5   0.7    1.3  1  zinc-ribbons_6  zinc-ribbons
     0.0093   15.8   0.5      0.036   13.9   1.1    1.6  2  Prok-RING_4     Prokaryotic RING finger family 4
  ------ inclusion threshold ------
      0.012   15.4   2.2      0.021   14.6   2.2    1.4  1  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
      0.013   15.5   0.3       0.02   14.9   0.3    1.3  1  DZR             Double zinc ribbon
      0.017   15.1   0.0      0.047   13.7   0.0    1.8  1  DUF3663         Peptidase
      0.021   14.7   2.0       0.27   11.1   1.1    2.4  2  Rad50_zn_hook   Rad50 zinc hook motif
      0.024   15.4   0.1      0.035   14.9   0.1    1.3  1  zinc_ribbon_15  zinc-ribbon family
       0.04   13.9   0.6       0.06   13.3   0.6    1.3  1  zf-RING_5       zinc-RING finger domain
      0.047   14.1   0.5       0.18   12.3   0.1    1.9  2  DUF2710         Protein of unknown function (DUF2710)
      0.048   14.0   0.1      0.093   13.1   0.1    1.5  1  C1_2            C1 domain
      0.054   13.6   0.4       0.11   12.7   0.4    1.5  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.057   13.6   0.6      0.092   12.9   0.6    1.3  1  Ribosomal_L37e  Ribosomal protein L37e
       0.11   12.4   3.2       0.24   11.3   3.2    1.5  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.21   11.5   3.8        3.1    7.8   3.8    2.2  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.31   11.0   0.4       0.31   11.0   0.4    2.3  2  zf-C2HC_2       zinc-finger of a C2HC-type


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 !   49.1   0.1   7.3e-16     6e-13       2      89 .]       3      85 ..       2      85 .. 0.94
   2 ?   -1.2   0.0       3.8   3.1e+03      15      31 ..      95     111 ..      87     136 .. 0.68

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 7.3e-16
                             PIN_6  2 VlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellplelevrePspesvkkvtefakktGDlsvLSktDi 80
                                      VlD++a+i++      ++ e+  t+p V +E+ d++a +  ++   ++++  P+++  +kv+++a++ GDl+vLS+tD+
  gi|336255007|ref|YP_004598114.1|  3 VLDSSAFIHD-----FHTSEQTATIPLVREELEDESAYRYDAMEGSGMHIHIPNDDTTEKVQRAARESGDLEVLSETDV 76
                                      9*******99.....45789999*************9998888889********************************* PP

                             PIN_6 81 evlALtyeL 89
                                      +++A ++eL
  gi|336255007|ref|YP_004598114.1| 77 RLIAASFEL 85
                                      ****99887 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.8
                             PIN_6  15 slqnlaeklyttpeVva 31 
                                        +qn+aekl +  eV+a
  gi|336255007|ref|YP_004598114.1|  95 AMQNVAEKLNVAVEVIA 111
                                       56777777777776664 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.2   9.5e+02       2      12 ..       2      12 ..       1      70 [. 0.68
   2 !   16.8   0.4   4.2e-06    0.0034     151     190 ..      65     106 ..      25     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                             PIN_5  2 fvlDTsaltdp 12
                                      +vlD sa++  
  gi|336255007|ref|YP_004598114.1|  2 YVLDSSAFIHD 12
                                      78888888753 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.2e-06
                             PIN_5 151 kGilD..saeDldvllLAkELdaavvssDeGikkwaeklGlr 190
                                       +G l+  s+ D+ ++    ELd+++v++D  ++++aekl + 
  gi|336255007|ref|YP_004598114.1|  65 SGDLEvlSETDVRLIAASFELDGTLVTDDYAMQNVAEKLNVA 106
                                       4666611445555555557*******************9885 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   3.0   7.4e-06     0.006       7      38 ..     124     148 ..     122     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.4e-06
                       Zn-ribbon_8   7 rCeeCghefevlqsisdaplta.CPeCgsevrr 38 
                                       +C+ Cg+ef++         ++ CP Cgse+ r
  gi|336255007|ref|YP_004598114.1| 124 QCQGCGREFDEE--------KDrCPICGSELAR 148
                                       7*********43........344******7776 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 ?    2.0   0.1      0.26   2.1e+02       8      19 ..      23      36 ..      23      36 .. 0.84
   2 !   14.0   0.2   4.6e-05     0.037       1      12 [.     138     149 ..     138     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.26
                    DNA_ligase_ZBD  8 avvRee..geaiyR 19
                                      ++vRee  +e++yR
  gi|336255007|ref|YP_004598114.1| 23 PLVREEleDESAYR 36
                                      68998877999999 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.6e-05
                    DNA_ligase_ZBD   1 hCPvCGsavvRe 12 
                                       +CP+CGs++ R+
  gi|336255007|ref|YP_004598114.1| 138 RCPICGSELARK 149
                                       5********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 !   16.3   1.9   8.8e-06    0.0072      65      95 ..     117     145 ..      48     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.8e-06
                                       EEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  65 eevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       e+ + + +C+ Cg+ef++e++  rCp Cgs+
  gi|336255007|ref|YP_004598114.1| 117 EQRHWHWQCQGCGREFDEEKD--RCPICGSE 145
                                       5677899**********9977..9*****97 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 !   16.0   1.3   9.8e-06     0.008      22      47 ..     122     146 ..     120     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.8e-06
                                       EEEE-HHHHHHHHHTT-B-TTT--B- CS
                        zf-C3HC4_3  22 HlvlCeeCaekllkrkkkCpiCrrpi 47 
                                       H+  C+ C +++ ++k++CpiC ++ 
  gi|336255007|ref|YP_004598114.1| 122 HW-QCQGCGREFDEEKDRCPICGSEL 146
                                       66.8********99********9876 PP

>> DUF4411  Domain of unknown function (DUF4411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.3   2.4e+02       1      11 [.       2      12 ..       2      32 .. 0.84
   2 !   13.0   0.0   8.7e-05     0.071      90     137 ..      59     105 ..      17     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.3
                           DUF4411  1 YllDtnvfiea 11
                                      Y+lD+++fi+ 
  gi|336255007|ref|YP_004598114.1|  2 YVLDSSAFIHD 12
                                      9*******975 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.7e-05
                           DUF4411  90 sekyskaakkeflsvaDpfliAaAlaknatvVTkEvkkpnkkknkvkI 137
                                       +++ +++ + e ls+ D +liAa  + + t+VT + + +n  + k  +
  gi|336255007|ref|YP_004598114.1|  59 QRAARESGDLEVLSETDVRLIAASFELDGTLVTDDYAMQNVAE-KLNV 105
                                       2333333488999**********************99666555.4444 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.7   1.5e-05     0.012      12      40 ..     118     147 ..     108     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                                       E-SSEEE-TTT--EEEEE.EE-SSS-S--- CS
                    zinc-ribbons_6  12 krgeqyhCeaCqedlkke.alCpeCeqele 40 
                                       +r+ + +C+ C +++++e   Cp C++el 
  gi|336255007|ref|YP_004598114.1| 118 QRHWHWQCQGCGREFDEEkDRCPICGSELA 147
                                       5667899********976268******996 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 ?   -2.6   0.0       6.4   5.2e+03      28      45 ..      17      34 ..      14      35 .. 0.71
   2 !   13.9   1.1   4.5e-05     0.036      18      45 ..     122     151 ..     121     152 .] 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.4
                       Prok-RING_4 28 kdlssCPlCqrrisksdp 45
                                      ++ ++ Pl +++++++++
  gi|336255007|ref|YP_004598114.1| 17 EQTATIPLVREELEDESA 34
                                      566677888888887765 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.5e-05
                       Prok-RING_4  18 HlvCkeCfdskdls..sCPlCqrrisksdp 45 
                                       H  C+ C  + d +  +CP+C +++++++p
  gi|336255007|ref|YP_004598114.1| 122 HWQCQGCGREFDEEkdRCPICGSELARKNP 151
                                       66799998887666669*******999876 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.2   2.6e-05     0.021      19      40 .]     121     142 ..     113     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                        zf-C3HC4_2  19 gHvfCqkCilrsLeekneCPlC 40 
                                       +H  Cq C ++  eek++CP+C
  gi|336255007|ref|YP_004598114.1| 121 WHWQCQGCGREFDEEKDRCPIC 142
                                       89*********867777***** PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.3   2.4e-05      0.02       1      22 [.     125     146 ..     104     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                               DZR   1 CpqCgeelppdarfCseCgtkl 22 
                                       C+ Cg+e ++++  C+ Cg++l
  gi|336255007|ref|YP_004598114.1| 125 CQGCGREFDEEKDRCPICGSEL 146
                                       6666666666666666666665 PP

>> DUF3663  Peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.8e-05     0.047      23      46 ..      41      64 ..      37      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.8e-05
                                      -SS-EEEE--SS-HHHHHHHHHHH CS
                           DUF3663 23 neegatihllekdelraiqrAaRk 46
                                      + +g++ih+ ++d+ +++qrAaR+
  gi|336255007|ref|YP_004598114.1| 41 EGSGMHIHIPNDDTTEKVQRAARE 64
                                      6789*******************6 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 ?    6.5   1.1    0.0093       7.6      25      34 ..     128     138 ..     125     139 .. 0.91
   2 ?   11.1   1.1   0.00033      0.27      16      30 ..     133     147 ..     131     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0093
                                       T--EE-HHH.H CS
                     Rad50_zn_hook  25 CgReldeeh.r 34 
                                       CgRe+dee+ r
  gi|336255007|ref|YP_004598114.1| 128 CGREFDEEKdR 138
                                       ********977 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00033
                                       TT-SEE-TTT--EE- CS
                     Rad50_zn_hook  16 keakgcCPlCgReld 30 
                                        e+k++CP Cg+el 
  gi|336255007|ref|YP_004598114.1| 133 DEEKDRCPICGSELA 147
                                       58899*******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 ?   14.9   0.1   4.2e-05     0.035      64      86 .]     116     143 ..      82     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.2e-05
                    zinc_ribbon_15  64 e.....kkeCknCgkeveeefkyCpkCg 86 
                                       +       +C+ Cg+e +ee + Cp Cg
  gi|336255007|ref|YP_004598114.1| 116 DeqrhwHWQCQGCGREFDEEKDRCPICG 143
                                       144556889******************9 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   7.3e-05      0.06      22      43 ..     122     143 ..     121     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.3e-05
                         zf-RING_5  22 HifCekClkkllekeavCpiCr 43 
                                       H  C+ C ++  e++++CpiC+
  gi|336255007|ref|YP_004598114.1| 122 HWQCQGCGREFDEEKDRCPICG 143
                                       888******************7 PP

>> DUF2710  Protein of unknown function (DUF2710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.7   1.4e+03      86     103 ..      21      38 ..       6      42 .. 0.71
   2 ?   12.3   0.1   0.00022      0.18      47      94 ..      64     114 ..      52     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.7
                           DUF2710  86 vitalreeveaefearyg 103
                                       +i  +ree e e   ry 
  gi|336255007|ref|YP_004598114.1|  21 TIPLVREELEDESAYRYD 38 
                                       455678888888888885 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00022
                           DUF2710  47 dlgdvravansdgrllelt..lhpgvvs.dyayselaerlnlvitalreev 94 
                                       + gd+  ++++d rl+  +  l  ++v+ dya  ++ae+ln+++  +  e 
  gi|336255007|ref|YP_004598114.1|  64 ESGDLEVLSETDVRLIAASfeLDGTLVTdDYAMQNVAEKLNVAVEVIAREG 114
                                       56999999999***9975411666666537*************98876554 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00011     0.093      11      39 ..     115     143 ..      99     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                              C1_2  11 kgedssesfnCsaCgrkidgffYsCseCd 39 
                                       ++e+++  ++C++Cgr+ d+++ +C++C 
  gi|336255007|ref|YP_004598114.1| 115 IDEQRHWHWQCQGCGREFDEEKDRCPICG 143
                                       56889999*********888889**9995 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 ?   12.7   0.4   0.00014      0.11       1      32 [.     115     145 ..     115     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                      NOB1_Zn_bind   1 ikrvkswvlrChaCfkvtkdmtkkFCpkCGnk 32 
                                       i + ++w  +C++C + + d +k  Cp CG++
  gi|336255007|ref|YP_004598114.1| 115 IDEQRHWHWQCQGCGREF-DEEKDRCPICGSE 145
                                       67889*********9976.678889*****86 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   0.00011     0.092      11      44 ..     117     149 ..     112     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                    Ribosomal_L37e  11 qkkktHilCrrCgkrsyhvqkktCascGypsakl 44 
                                       ++++ H  C+ Cg++ +  +k +C  cG   a++
  gi|336255007|ref|YP_004598114.1| 117 EQRHWHWQCQGCGRE-FDEEKDRCPICGSELARK 149
                                       56779********87.************877765 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 ?   11.3   3.2    0.0003      0.24       6      28 ..     124     144 ..     120     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                       Prok-RING_1   6 kCpvCgkelkeedDiVvCpeCgt 28 
                                       +C+ Cg+e++ee+D   Cp Cg+
  gi|336255007|ref|YP_004598114.1| 124 QCQGCGREFDEEKD--RCPICGS 144
                                       7*************..7****97 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 ?    7.8   3.8    0.0038       3.1       2      34 ..     120     146 ..     119     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0038
                    Zn_ribbon_SprT   2 kyvYrCtgCgreythhlsirrhnYrCrrCkgtL 34 
                                        + ++C gCgr       ++ ++ rC++C+++L
  gi|336255007|ref|YP_004598114.1| 120 HWHWQCQGCGR------EFDEEKDRCPICGSEL 146
                                       69********5......4555555588888776 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 ?   11.0   0.4   0.00038      0.31       4      14 ..     124     134 ..     124     136 .. 0.87
   2 ?    2.4   1.3      0.19   1.5e+02       5       9 ..     139     143 ..     138     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00038
                         zf-C2HC_2   4 pCpkCgRsFnp 14 
                                       +C++CgR F +
  gi|336255007|ref|YP_004598114.1| 124 QCQGCGREFDE 134
                                       8********65 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.19
                         zf-C2HC_2   5 CpkCg 9  
                                       Cp+Cg
  gi|336255007|ref|YP_004598114.1| 139 CPICG 143
                                       ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); 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):              22  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1233.21
//
Query:       gi|336255008|ref|YP_004598115.1|  [L=81]
Description: PRC-barrel domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   42.2   0.1    7.6e-11   42.0   0.1    1.1  1  PRC       PRC-barrel domain
  ------ inclusion threshold ------
       0.19   11.7   0.0       0.24   11.4   0.0    1.1  1  RalF_SCD  RalF C-terminal Sec-7 capping domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.1   8.4e-15   7.6e-11       3      73 ..       3      80 ..       1      81 [] 0.94

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 8.4e-15
                                      ECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.............-EEEEEGG.CEECCCTEEEET CS
                               PRC  3 efrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi........gekevliPfdlavkigkdriivd 73
                                       + a +l Gk+V+ +dG++lG ++++ +d k+g+++ lv++  + l          ++ ++l+P+  +v ++kd+i+v+
  gi|336255008|ref|YP_004598115.1|  3 DILAENLSGKSVMGSDGTELGLLYNITMDLKSGELHDLVIEPDEELPTrsvdfninEDGRFLVPVS-RVQAVKDYIVVQ 80
                                      57899*************************************998654******************.**********96 PP

>> RalF_SCD  RalF C-terminal Sec-7 capping domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.6e-05      0.24      88     133 ..      31      77 ..      24      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.6e-05
                          RalF_SCD  88 kllfGeqprviiqpigqn.kasidlaakvaadfelpvksvkatydye 133
                                        l  Ge + ++i+p  +    s+d+      +f +pv++v+a  dy 
  gi|336255008|ref|YP_004598115.1|  31 DLKSGELHDLVIEPDEELpTRSVDFNINEDGRFLVPVSRVQAVKDYI 77 
                                       5667999*******6655689*************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 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:                        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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 681.14
//
Query:       gi|336255009|ref|YP_004598116.1|  [L=607]
Description: translation initiation factor aIF-2 [Halopiger xanaduensis SH-6]
Scores for 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-31  108.0   0.0    3.9e-30  104.9   0.0    2.4  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    5.7e-25   87.0   2.6    1.3e-24   85.9   0.1    2.7  3  GTP_EFTU_D4  Elongation factor Tu domain 4
    3.2e-23   81.8   1.2    9.1e-23   80.4   0.5    2.2  2  IF-2         Translation-initiation factor 2
    6.6e-14   52.1   8.0    7.8e-10   39.0   0.1    3.1  3  GTP_EFTU_D2  Elongation factor Tu domain 2
      2e-08   34.3   0.0    7.3e-08   32.5   0.0    2.0  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0018   18.3   0.1       0.22   11.5   0.0    2.6  2  Dynamin_N    Dynamin family
      0.009   15.8   0.0      0.034   13.9   0.0    2.0  2  ATP_bind_1   Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
       0.09   13.0   0.0       0.39   10.9   0.0    2.1  2  Roc          Ras of Complex, Roc, domain of DAPkinase
       0.25   10.7   0.9       0.91    8.9   0.9    2.0  1  Delta_lysin  Delta lysin family


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 !  104.9   0.0   1.9e-33   3.9e-30       4     189 ..      23     228 ..      20     233 .. 0.81
   2 ?   -3.0   0.0       2.2   4.5e+03     161     161 ..     474     474 ..     441     517 .. 0.56

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 1.9e-33
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSS CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGH 80 
                                         ++++ghvDhGKt+L+d++  ++ +  ++g+ ++    +  ++       Ti    +  + + +   + +iDtPGH
  gi|336255009|ref|YP_004598116.1|  23 PIVAVLGHVDHGKTSLLDKIRGSAVIEGEAGAITQ---HIGATAVPLDIISTIAGDLVDPD-DFDLPGLLFIDTPGH 95 
                                       5789*****************99888888666554...35555555556677888888887.8999*********** PP

                                       GGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHH CS
                          GTP_EFTU  81 vdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeiveev 146
                                        +F+   +rg + +D+a+lvvd+++G +pqt e l ++++ ++p+iv+ NK+D +           +++++ + + v
  gi|336255009|ref|YP_004598116.1|  96 HSFTTLRSRGGALADIAILVVDVNDGFQPQTLEALDILKRSETPFIVAANKIDTVpgwnenedspiNDTYESQSDRV 172
                                       *********************************************************99888777766666666666 PP

                                       HHHHHHH...............HHHHHHHHHTTT........TTEEEEEEBTTTTBTHHHHHHHHH CS
                          GTP_EFTU 147 kqklsrk...............eeklekygekge........kevpvvfgSalkgegvktllealv 189
                                       +++l+++               +                   ++v vv++Sa++gegv +ll +++
  gi|336255009|ref|YP_004598116.1| 173 RSRLDEQlyeiignlsdegfsaD----------LywrvqnfqRNVGVVPVSAMTGEGVPDLLAVMM 228
                                       66665556666555555555433..........05555555568*****************99886 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.2
                                       H CS
                          GTP_EFTU 161 g 161
                                        
  gi|336255009|ref|YP_004598116.1| 474 I 474
                                       0 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 ?   -2.8   0.1         3     6e+03      38      53 ..     242     257 ..     235     259 .. 0.78
   2 ?   -0.3   0.0      0.52     1e+03      42      68 ..     314     340 ..     303     349 .. 0.86
   3 !   85.9   0.1   6.4e-28   1.3e-24       1      85 [.     476     563 ..     476     564 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3
                                       ETTE.EEEEEEEEEET CS
                       GTP_EFTU_D4  38 kedGrevGeilqiqdk 53 
                                       + +G  vG++l+++d+
  gi|336255009|ref|YP_004598116.1| 242 DVQGPGVGTVLEVKDE 257
                                       5578889999999987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.52
                                       .EEEEEEEEEETTEEESEEETT-EEEE CS
                       GTP_EFTU_D4  42 revGeilqiqdkgkkleeakaGqevai 68 
                                        evG  + i+    +l+ea aG+ v +
  gi|336255009|ref|YP_004598116.1| 314 DEVGAAAGIKVAAPELDEAMAGAPVRV 340
                                       68999999999999*******998866 PP

  == domain 3  score: 85.9 bits;  conditional E-value: 6.4e-28
                                       S-CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE....EEEEEEEEEETTEEESEEETT-EEEEEEESS- CS
                       GTP_EFTU_D4   1 rPgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGr...evGeilqiqdkgkkleeakaGqevaisiegki 74 
                                       rP++++ilp+  fr+ dpa+vGvev +G+++ + +++k +G+   +vG+i+ iq++g+ ++ea+aG++v+++i+g++
  gi|336255009|ref|YP_004598116.1| 476 RPARFRILPDHTFRQNDPAVVGVEVNSGTVQNNANVVKFEGNepdRVGQIKGIQEQGEDVDEARAGDRVSVAIDGPT 552
                                       7***************************************973336******************************* PP

                                       TTTS--TT-EE CS
                       GTP_EFTU_D4  75 vGrqikegdil 85 
                                       vGrqi+e+d+l
  gi|336255009|ref|YP_004598116.1| 553 VGRQIEEDDEL 563
                                       *********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 ?   -3.0   0.0         4   8.1e+03      38      55 ..     235     252 ..     225     254 .. 0.74
   2 !   80.4   0.5   4.6e-26   9.1e-23       7     105 .]     359     456 ..     351     456 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4
                                       T.SSTEEEECEEEESSB- CS
                              IF-2  38 eseevkvkvihsgvGait 55 
                                        +ee++++v   gvG++ 
  gi|336255009|ref|YP_004598116.1| 235 MKEEMEIDVQGPGVGTVL 252
                                       348999999999999985 PP

  == domain 2  score: 80.4 bits;  conditional E-value: 4.6e-26
                                       CCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHH....STEEEEEESSSCTHH CS
                              IF-2   7 eikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasa....snaiiigFnvkvskk 79 
                                       +i+ ++ e +v++kaD+ GsleA+++aL++      +v++++++vG++  +Dv+ as+    ++ +i+gFnv++ ++
  gi|336255009|ref|YP_004598116.1| 359 DIAVDTGEEGVVVKADTLGSLEAMADALDEA-----EVPIVRAEVGDVAPRDVSVASTaddpKQRVILGFNVDTLSD 430
                                       5555667889*******************98.....5********************9555555************* PP

                                       HHHCCCCCTSEEEEESSHHHHHHHHH CS
                              IF-2  80 akklaekegvkirlynvIYkliddvk 105
                                       a++ ae ++v+i++ +vIY+li++++
  gi|336255009|ref|YP_004598116.1| 431 AERRAEADDVTIFTDEVIYQLIEEYE 456
                                       ***********************985 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 !   39.0   0.1   3.9e-13   7.8e-10       1      73 [.     261     338 ..     261     339 .. 0.91
   2 ?   -2.2   0.0       2.9   5.8e+03      34      49 ..     375     393 ..     356     402 .. 0.62
   3 !   15.8   1.5   6.8e-06     0.013       3      62 ..     495     552 ..     494     558 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.9e-13
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEE.........ETTSEEEEEEEESSCCSGS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededea.........vaganaGvivaikgledai 67 
                                       Gt+++ ++y+Gt++ +d+++++g n+    +ivt++++l+ +++  ++          ++ga+aG++va+++l++a 
  gi|336255009|ref|YP_004598116.1| 261 GTTIDTVLYDGTIRADDQLVVGGqNE----PIVTDVRALLQPRPLAEIRtesrfekvdEVGAAAGIKVAAPELDEA- 332
                                       89*******************99665....9***********875555599************************8. PP

                                       STTCEE CS
                       GTP_EFTU_D2  68 ivGdtl 73 
                                       ++G+++
  gi|336255009|ref|YP_004598116.1| 333 MAGAPV 338
                                       **9975 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                                       EEEEEEEETEEESEE...E CS
                       GTP_EFTU_D2  34 rissletfhededea...v 49 
                                       + +sle++   +dea   +
  gi|336255009|ref|YP_004598116.1| 375 TLGSLEAMADALDEAevpI 393
                                       5667777777777775554 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 6.8e-06
                                       EEEEEEEESEEETTEEEEEEC.TCTTSEE.EEEEEEEEEEETEEESEEETTSEEEEEEEESS CS
                       GTP_EFTU_D2   3 valgrvysGtlkkGdevrilg.ndtskke.ivtrissletfhededeavaganaGvivaikg 62 
                                       v+++ v sGt++ + +v+    n+    +  v++i++++   ed+dea+ag+++ v + ++ 
  gi|336255009|ref|YP_004598116.1| 495 VVGVEVNSGTVQNNANVVKFEgNE----PdRVGQIKGIQEQGEDVDEARAGDRVSVAIDGPT 552
                                       8999*************9955443....3589**********************99997765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   3.7e-11   7.3e-08       2     114 .]      25     146 ..      24     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.7e-11
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE................EEEEECGGCSSHHHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke................ielvDtpGliegase 62 
                                       va++G+   GK++L+ ++ g+++i ++    T++i    v l+  +                + ++DtpG  +    
  gi|336255009|ref|YP_004598116.1|  25 VAVLGHVDHGKTSLLDKIRGSAVIEGEAGAITQHIGATAVPLDIIStiagdlvdpddfdlpgLLFIDTPG-HH---- 96 
                                       89******************988888888888888777777441112233334444555555999*****.44.... PP

                                       HHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  63 ekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                       +   +    +    ad+++lvvd++ ++++p+  e  ++l++++ p+i+++nk
  gi|336255009|ref|YP_004598116.1|  97 SF--TTLRSRGGAlADIAILVVDVN-DGFQPQTLEALDILKRSETPFIVAANK 146
                                       22..22222222247********87.88***********************98 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00011      0.22       1      33 [.      25      57 ..      25      62 .. 0.91
   2 ?    4.0   0.0     0.023        45      95     118 ..      79     102 ..      72     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS--- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTr 33
                                      +av+G++ +GK+S+l+++ g+++   +++ +T+
  gi|336255009|ref|YP_004598116.1| 25 VAVLGHVDHGKTSLLDKIRGSAVIEGEAGAITQ 57
                                      79********************99888888886 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.023
                                       EEETTS-SEEEEE---B-SSSGTT CS
                         Dynamin_N  95 ilsllvkgltlvDlPGldsvnkrd 118
                                       + +++ +gl ++D+PG +s  + +
  gi|336255009|ref|YP_004598116.1|  79 PDDFDLPGLLFIDTPGHHSFTTLR 102
                                       66788999********99965544 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 !   13.9   0.0   1.7e-05     0.034      66     232 ..      60     224 ..      49     232 .. 0.59
   2 ?   -2.3   0.0       1.6   3.2e+03     173     219 ..     436     484 ..     417     491 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                        ATP_bind_1  66 galvvaleflresl.dwldeelekeed....dyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltd 137
                                       ga+ v l+++++   d +     + +d     +l +DtPG   + t+++ +           a +++ +vD++    
  gi|336255009|ref|YP_004598116.1|  60 GATAVPLDIISTIAgDLV-----DPDDfdlpGLLFIDTPGHHSFTTLRSRGG--------ALADIAILVVDVND--- 120
                                       666666665555553333.....2222212368999***********99999........55567777888764... PP

                        ATP_bind_1 138 ptkfisgllsalsamlrlelPhvvvlnkfDllkeklekeleffedvealslllekee................ekyk 198
                                          f  ++l al ++ r e+P++v+ nk+D +   +e e   ++d+ +      + +                   +
  gi|336255009|ref|YP_004598116.1| 121 --GFQPQTLEALDILKRSETPFIVAANKIDTVPGWNENEDSPINDTYES-----QSDrvrsrldeqlyeiignLSDE 190
                                       ..4666778889******************9874433333333332221.....11201111222345555332222 PP

                        ATP_bind_1 199 klaeaiaelleefalvlrflplssekeesiedll 232
                                          +++   +++f+++  ++p+s+ ++e++ dll
  gi|336255009|ref|YP_004598116.1| 191 GFSADLYWRVQNFQRNVGVVPVSAMTGEGVPDLL 224
                                       3344455555555555556666666666665555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.6
                        ATP_bind_1 173 lekeleffedvealslllekee...ekykklaeaiaelleefalvlrflp 219
                                       +  ++  f+d   ++l++e ee   e  + ++++i e ++ +a+  r+lp
  gi|336255009|ref|YP_004598116.1| 436 EADDVTIFTDEVIYQLIEEYEEfveEMEQAQQSTILENISRPARF-RILP 484
                                       444555666655555555555566555555555666666666665.5555 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0002      0.39       2     119 ..      25     148 ..      24     149 .. 0.73
   2 ?   -2.1   0.0       2.2   4.3e+03      21      44 ..     485     508 ..     481     516 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                       EEEESSTTSSHHHHHHCHCT-CCC-EE....ETTTTEEEEEEECG.GSG.GCTTBTTTTCEEEEEEEE-SGGCTTTT CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfseke....kstigvdfltkevt.kik.gvendkkvkkvklniWDtaGqerfrsl 72 
                                       v ++G    GKtsll+++  + + e e    ++ ig++ +  ++  +i   + + ++ +   l + Dt G+  f +l
  gi|336255009|ref|YP_004598116.1|  25 VAVLGHVDHGKTSLLDKIRGSAVIEGEagaiTQHIGATAVPLDIIsTIAgDLVDPDDFDLPGLLFIDTPGHHSFTTL 101
                                       5789**************999886554222267788888776654134423345566666778999*********** PP

                                       -HHHHCTSCEEEEEEEGHHHHCHHHHHHHHHHH.CSSS-EEEEEE-TT CS
                               Roc  73 hplylreaalailvydsrssenlkeWlkelkkv.agkspvilvgnkiD 119
                                       ++     a++ailv+d ++  +  + l+ l+   ++++p+i+ +nkiD
  gi|336255009|ref|YP_004598116.1| 102 RSRGGALADIAILVVDVNDGFQ-PQTLEALDILkRSETPFIVAANKID 148
                                       ****************765433.234555555414577999999**99 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                                       T-CCC-EEETTTTEEEEEEECGGS CS
                               Roc  21 edkfsekekstigvdfltkevtki 44 
                                       +++f+++  + +gv++ + +v++ 
  gi|336255009|ref|YP_004598116.1| 485 DHTFRQNDPAVVGVEVNSGTVQNN 508
                                       5789999999*****999877543 PP

>> Delta_lysin  Delta lysin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.9   0.00046      0.91       4      13 ..      67      77 ..      65      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00046
                       Delta_lysin  4 DIISTI.GDLV 13
                                      DIISTI GDLV
  gi|336255009|ref|YP_004598116.1| 67 DIISTIaGDLV 77
                                      9*****9***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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: 0.58u 0.22s 00:00:00.80 Elapsed: 00:00:00.37
# Mc/sec: 4980.66
//
Query:       gi|336255010|ref|YP_004598117.1|  [L=67]
Description: hypothetical protein Halxa_3629 [Halopiger xanaduensis SH-6]
Scores for 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   14.4   1.5      0.045   14.1   1.5    1.1  1  DUF4133   Domain of unknown function (DUF4133)
      0.068   13.3   0.6      0.088   12.9   0.6    1.2  1  SPC12     Microsomal signal peptidase 12 kDa subunit (SPC12)
       0.61    9.4   2.3       0.63    9.3   2.3    1.0  1  DUF4191   Domain of unknown function (DUF4191)


Domain annotation for each model (and alignments):
>> DUF4133  Domain of unknown function (DUF4133)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.5   7.5e-06     0.045      11      47 ..      12      49 ..       8      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.5e-06
                           DUF4133 11 fkGLkaqylfilagglvallllv.vilyiiGvsqlicl 47
                                      + GL a  ++ la+g+  l++l+ ++l +++v+q+++l
  gi|336255010|ref|YP_004598117.1| 12 YVGLAAGLFYCLAIGATDLFVLLaAVLLVLAVPQWLIL 49
                                      569****************9987689*********987 PP

>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   1.5e-05     0.088      16      62 ..       6      52 ..       2      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                             SPC12 16 ilvlsaviafivGyitqdlkltlyillagvvltllvvvPpWpfYnrn 62
                                       ++++a +++++G ++     +  ++++ +++ l++ vP+W +  r 
  gi|336255010|ref|YP_004598117.1|  6 WVLVAAYVGLAAGLFYCLAIGATDLFVLLAAVLLVLAVPQWLILSRR 52
                                      577888999999988888888888999999999********998665 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.3   0.00011      0.63      24      75 ..       3      55 ..       1      64 [. 0.69

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00011
                           DUF4191 24 kllwlllaaflvvvvvfvvlglllgslilllilgillgllv.alivltrraek 75
                                      +l+w+l+aa ++ ++ ++ +  +  + +++l+ ++ll l v   ++l+rr  +
  gi|336255010|ref|YP_004598117.1|  3 RLVWVLVAAYVGLAAGLFYCLAIGATDLFVLLAAVLLVLAVpQWLILSRRNGR 55
                                      68899999998888777776666445677777777665555156788888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 514.05
//
Query:       gi|336255011|ref|YP_004598118.1|  [L=126]
Description: hypothetical protein Halxa_3630 [Halopiger xanaduensis SH-6]
Scores for 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-27   94.0   0.0    5.8e-27   93.9   0.0    1.0  1  Cyclophil_like   Cyclophilin-like
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.017   15.1   0.0    1.2  1  Cyclophil_like2  Cyclophilin-like family
      0.079   12.7   0.1       0.11   12.1   0.0    1.3  1  DUF3830          Protein of unknown function (DUF3830)


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 !   93.9   0.0   9.8e-31   5.8e-27       3     103 ..       4     106 ..       2     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 9.8e-31
                                       EEEEETTEEEEEEEETT..HHHHHHHHC-SEEEEEEECTTEEEEE-S-----SSSEESSB-TTEEEEECCCTEEEEE CS
                    Cyclophil_like   3 ikidiesseveveLddt..etaraikealPiesrvntWgeEiYfstpvklekeenakevveagdiaywppGkalclf 77 
                                       + i+++  e+e+  +d+  et ra+++alP+++++ +Wg+E+Y ++ +++   e+ +evv++g i+ywp G+ lclf
  gi|336255011|ref|YP_004598118.1|   4 LTISVDDLELEATWTDEapETRRALENALPVAGDAVRWGDELYIDAALDAP-LESEREVVPEGAITYWPAGNKLCLF 79 
                                       789999**********999*******************************9.889999******************* PP

                                       SS--TT-.TTSB--SSSEEEEEEEEC- CS
                    Cyclophil_like  78 fGktPis.ddeirpaspvnviGrived 103
                                       +G+tP+s +de+r+a pv v+ r+++ 
  gi|336255011|ref|YP_004598118.1|  80 WGPTPASvEDEPRAAAPVSVVARVTDV 106
                                       ***********************9864 PP

>> Cyclophil_like2  Cyclophilin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.8e-06     0.017       2      80 ..       7      84 ..       6      90 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.8e-06
                   Cyclophil_like2  2 tiggqtftatLedn..aaaralleklPltltmedyngnEkiay..lpeklptddapegssikaGdlayyapwgnlvlfy 76
                                      ++++ +++at+ d   ++ ral + lP+  +  + ++ E + +  l+ +l+++ +     + +G ++y++ +++l+lf+
  gi|336255011|ref|YP_004598118.1|  7 SVDDLELEATWTDEapETRRALENALPVAGDAVRWGD-ELYIDaaLDAPLESERE----VVPEGAITYWPAGNKLCLFW 80
                                      6677777777766522467888888888888777774.44444247777777666....7889**************** PP

                   Cyclophil_like2 77 kdfe 80
                                      + + 
  gi|336255011|ref|YP_004598118.1| 81 GPTP 84
                                      9874 PP

>> DUF3830  Protein of unknown function (DUF3830)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.9e-05      0.11       3      75 ..       6      79 ..       4      90 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
                                      ETTTTEEEEEEE-TTTSHHHHHHHHHH--EEEE-EE-SSSSSEEEE......EEE--SSS---S-SEESS--TTEEEEE CS
                           DUF3830  3 lekrgvsataeLledkAPetcaavwealplssdviHakyagneiyv......llpefaatelpaENaTvtPipGdvvlf 75
                                      +++++++ +a    d+APet  a+ +alp+++d++  ++ g e y+      +l++   + +p+   T  P    ++lf
  gi|336255011|ref|YP_004598118.1|  6 ISVDDLELEAT-WTDEAPETRRALENALPVAGDAV--RW-GDELYIdaaldaPLESER-EVVPEGAITYWPAGNKLCLF 79
                                      56666666665.4689*****************96..44.334443110000333333.34444445666665566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1024.90
//
Query:       gi|336255012|ref|YP_004598119.1|  [L=337]
Description: hypothetical protein Halxa_3631 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.002   18.2   0.3     0.0063   16.6   0.3    1.9  1  bPH_6     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_6  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3   3.5e-07    0.0063      19      71 ..     240     290 ..     226     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.5e-07
                             bPH_6  19 trrlpWsaiagvrfpegrrlarldlrdgelvplpavqlgddpelvadalrrlr 71 
                                       ++++pW +ia+vr+++    ++l+ +  +  +  a+ + ddpe+v++  +r+r
  gi|336255012|ref|YP_004598119.1| 240 RKFVPWKQIADVRLTDDE--LVLERDGYGFDIRCARSAIDDPEAVLEGIERAR 290
                                       89****************..9999999999999999999********999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 0.46u 0.19s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2823.32
//
Query:       gi|336255013|ref|YP_004598120.1|  [L=140]
Description: hypothetical protein Halxa_3632 [Halopiger xanaduensis SH-6]
Scores for 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  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); 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:                         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 0.19s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 1189.81
//
Query:       gi|336255014|ref|YP_004598121.1|  [L=566]
Description: CTP synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-125  417.9   0.2   1.8e-125  417.6   0.2    1.1  1  CTP_synth_N    CTP synthase N-terminus
    3.2e-54  183.6   0.0    5.5e-54  182.8   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    3.3e-07   30.3   0.0    7.8e-06   25.8   0.0    2.3  1  Peptidase_C26  Peptidase C26
     0.0019   18.2   0.0     0.0032   17.5   0.0    1.7  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.067   12.8   0.0       0.13   11.9   0.0    1.4  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.6   0.2  5.1e-129  1.8e-125       1     265 []      16     277 ..      16     277 .. 0.99

  Alignments for each domain:
  == domain 1  score: 417.6 bits;  conditional E-value: 5.1e-129
                                       EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHH CS
                       CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfl 77 
                                       k+i+vtGGv+SglGkGi+aas+g+llk+ g++vt++kiDPYlnvdagt++p++hGEv+vl+dG+e+DlDlGnYeRfl
  gi|336255014|ref|YP_004598121.1|  16 KFIFVTGGVMSGLGKGITAASTGRLLKNAGFDVTAVKIDPYLNVDAGTMNPYQHGEVYVLKDGGEVDLDLGNYERFL 92 
                                       8**************************************************************************** PP

                                       T----GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHH CS
                       CTP_synth_N  78 dikltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfle 154
                                       d+++t+++nittGk y++vieker GdylGktvq+iph+td+ik+ri+++a+   +dv+ive+gGtvgdie++p+le
  gi|336255014|ref|YP_004598121.1|  93 DVDMTSDHNITTGKTYQHVIEKERAGDYLGKTVQIIPHITDDIKRRIREAAE--GTDVCIVEVGGTVGDIEGMPYLE 167
                                       ***************************************************8..8********************** PP

                                       HHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--G CS
                       CTP_synth_N 155 airqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvek 231
                                       a+rq+++e  +envl+ hvtlvp+ k +ge+ktkptqhsvke+rs+G+qpdiiv r+e++le ++kekialfc++++
  gi|336255014|ref|YP_004598121.1| 168 ALRQFAHEEPEENVLFTHVTLVPYSK-NGEQKTKPTQHSVKEVRSIGLQPDIIVGRCEDRLEPKTKEKIALFCDIPT 243
                                       ************************95.9************************************************* PP

                                       GGEEEEE--S-GGGHHHHHHHCTHHHHHHHHTT- CS
                       CTP_synth_N 232 eavisvkdvesiyevpllleeqglaelileklkl 265
                                       eav+s++dve++y+vpl++ee+gl++++le++ l
  gi|336255014|ref|YP_004598121.1| 244 EAVFSNPDVEDVYHVPLMVEEEGLDQYVLEHFGL 277
                                       *****************************99875 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.8   0.0   1.5e-57   5.5e-54       2     189 ..     313     534 ..     312     535 .. 0.93

  Alignments for each domain:
  == domain 1  score: 182.8 bits;  conditional E-value: 1.5e-57
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH..THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile..llknpdgilvsgGpgspgvegkieaikearenkiPiLG 76 
                                       l D+y s++e+l+ha+ elgv+v+v++++a+        +l+++dgi+v+gG+g +g+egki+a+++aren++P+LG
  gi|336255014|ref|YP_004598121.1| 313 LEDAYMSIHESLKHAGFELGVDVNVHWVHADGMADAYddQLEDVDGIIVPGGFGMRGTEGKIRAVQYARENDVPFLG 389
                                       67***************************98777744567************************************* PP

                                       ETHHHHHHHHHTTTEEE.......................EEECEEEEEEEEEEEETTT........CGGTTTTSEE CS
                            GATase  77 ICLGmQllaiefgrkvv.......................kekekehhggtmrlgddet........allyglknev 122
                                        CLG+Q+++ e++r+v                        ++ e e++ggtmrlg++ t         +lyg+  + 
  gi|336255014|ref|YP_004598121.1| 390 LCLGFQMAVVEYARNVLgledahsaemdeetphpvidilpEQYEVEDMGGTMRLGEHTTviepetlaYELYGD-TSC 465
                                       **************9999999999999999999999***98999************888********99***9.888 PP

                                       EEEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHH CS
                            GATase 123 ierhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflik 189
                                        erhrHryevnp+   ++e++ l+++++      +mei e+++ p f+g+QFHPE++s+p++p+++f +l++
  gi|336255014|ref|YP_004598121.1| 466 SERHRHRYEVNPEyfdQFEDEPLTFSGTAG---NRMEILEHEDhPfFFGTQFHPEYKSRPGQPSPPFVGLVE 534
                                       ***************9*********99993...57999999999***********************99875 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.2e-09   7.8e-06      97     216 .]     376     517 ..     332     517 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.2e-09
                     Peptidase_C26  97 LiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe..............q....saashavkvek 155
                                        ++ a e++vP lg C+G+q+  v +  ++    +++s+++d   ++                      +h+  +e+
  gi|336255014|ref|YP_004598121.1| 376 AVQYARENDVPFLGLCLGFQMAVVEYARNVLGLEDAHSAEMDEETPHpvidilpeqyevedMggtmRLGEHTTVIEP 452
                                       56788999************99998877765433333444444444468888888776665055568889******* PP

                     Peptidase_C26 156 gsllaellgseeievnslHhqaike.....laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       ++l +el+g+++ +    H+  ++       ++e    + ++ + +E +e+e+++ f++g Q+HPE
  gi|336255014|ref|YP_004598121.1| 453 ETLAYELYGDTSCSERHRHRYEVNPeyfdqFEDEPLTFSGTAGNRMEILEHEDHP-FFFGTQFHPE 517
                                       *********999999*****9998777777555555555566789********88.*********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 !   17.5   0.0     9e-07    0.0032       7      55 ..      25     124 ..      18     440 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9e-07
                                       STTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
                              CbiA   7 kGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................. 54 
                                        +G GK  +aa+ +r+l+++g++V +v+ Dp  n +a   g+ n  +                              
  gi|336255014|ref|YP_004598121.1|  25 MSGLGKGITAASTGRLLKNAGFDVTAVKIDPYLNVDA---GTMNPYQHgevyvlkdggevdldlgnyerfldvdmts 98 
                                       69******************************99988...6655555556666666666666666666666666655 PP

                                       .........................C CS
                                       .........................x RF
                              CbiA  55 .........................d 55 
                                                                +
  gi|336255014|ref|YP_004598121.1|  99 dhnittgktyqhviekeragdylgkT 124
                                       55555555555555555555555551 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 ?   11.9   0.0   3.5e-05      0.13      34     112 ..     350     429 ..     329     491 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
                          GATase_3  34 deslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeei.edpegveg.......ea 102
                                       d++l ed+d +i+pGg+  +        +g  +a++ a e+++p lg C G+qm   e+ ++  g e+       e+
  gi|336255014|ref|YP_004598121.1| 350 DDQL-EDVDGIIVPGGFGMRG------TEGKIRAVQYARENDVPFLGLCLGFQMAVVEYaRNVLGLEDahsaemdEE 419
                                       5666.67*********98776......4678889********************77766566677766554444333 PP

                          GATase_3 103 geveglglLd 112
                                       + ++ +++L+
  gi|336255014|ref|YP_004598121.1| 420 TPHPVIDILP 429
                                       3555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 4180.12
//
Query:       gi|336255015|ref|YP_004598122.1|  [L=305]
Description: GMP synthase subunit B [Halopiger xanaduensis SH-6]
Scores for 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-29   99.6   0.4    5.8e-28   96.8   0.2    2.1  2  GMP_synt_C     GMP synthase C terminal domain
    1.5e-08   34.1   0.0    3.8e-05   22.9   0.0    2.2  2  NAD_synthase   NAD synthase
      3e-05   23.0   0.0     0.0017   17.2   0.0    2.2  2  tRNA_Me_trans  tRNA methyl transferase
     0.0036   17.4   0.0     0.0066   16.5   0.0    1.5  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.034   13.7   0.0    1.8  2  QueC           Queuosine biosynthesis protein QueC
      0.021   14.4   0.0       0.14   11.8   0.0    2.1  1  ThiI           Thiamine biosynthesis protein (ThiI)
      0.029   14.1   0.0      0.051   13.2   0.0    1.5  1  Asn_synthase   Asparagine 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 ?    0.2   0.0      0.31   7.8e+02      33      48 ..      70      85 ..      58      93 .. 0.85
   2 !   96.8   0.2   2.3e-31   5.8e-28      10      92 .]     223     304 ..     214     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.31
                                      --EEEEEEEEE----- CS
                        GMP_synt_C 33 tyeyvvalRaveseDa 48
                                      t++y+  lR+ve++D 
  gi|336255015|ref|YP_004598122.1| 70 TFDYMESLRIVEAQDR 85
                                      799999******9995 PP

  == domain 2  score: 96.8 bits;  conditional E-value: 2.3e-31
                                       GGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---TT CS
                        GMP_synt_C  10 kkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditskP 86 
                                        + wQa a+++  k++Gv+gd+R +++vv +R+ves+D+mta+++e+++e+L++i+sri+   ++v+rvvyd+t+kP
  gi|336255015|ref|YP_004598122.1| 223 YEPWQALAAVIG-KATGVKGDNRVHGWVVSVRSVESRDGMTARAQEIDWETLQRIQSRITGTNENVARVVYDVTHKP 298
                                       567******998.9*************************************************************** PP

                                       TS-S-- CS
                        GMP_synt_C  87 patiEw 92 
                                       patiE+
  gi|336255015|ref|YP_004598122.1| 299 PATIEY 304
                                       *****7 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.5e-08   3.8e-05      15      46 ..      18      48 ..       4      92 .. 0.80
   2 !    9.0   0.0   0.00027      0.69     148     177 ..     158     187 ..     153     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-08
                                      HCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGE CS
                      NAD_synthase 15 kagakgvvlGlSGGvDSslvaalavkalgken 46
                                      + g +++v+ lSGGvDSs++aala +a+g+ +
  gi|336255015|ref|YP_004598122.1| 18 EIGDENAVIALSGGVDSSVAAALAYEAIGD-R 48
                                      5677899*********************75.3 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00027
                                       BETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                      NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpP 177
                                       ++p+ +l+K ev+e a++l+  e v ++ P
  gi|336255015|ref|YP_004598122.1| 158 VEPVRDLYKDEVREVARHLGLEEIVAERMP 187
                                       78*******************999999988 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.7e-07    0.0017       3      34 ..      24      56 ..      22     113 .. 0.74
   2 !    3.8   0.0    0.0081        21     164     188 ..     157     183 ..     152     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.7e-07
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeq.gyevigvflkl 34
                                       v+alSgGVDSsvaaal  e+ g  ++ v++ +
  gi|336255015|ref|YP_004598122.1| 24 AVIALSGGVDSSVAAALAYEAiGDRLTPVYVDT 56
                                      689************998776245566666655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0081
                     tRNA_Me_trans 164 llfPlgeltKeevrkiAkeagla..va 188
                                       ++ P+ +l K+evr++A++ gl+  va
  gi|336255015|ref|YP_004598122.1| 157 IVEPVRDLYKDEVREVARHLGLEeiVA 183
                                       5679****************9986555 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.6e-06    0.0066       2      73 ..      24      95 ..      23     127 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.6e-06
                                      EEEE--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB-H.HHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH- CS
                       PAPS_reduct  2 lvvsvsgGkdslVllhLalkafkpv.pvvfvdtghefp.etiefvdeleeryglrlkvyepeeevaekinaekh 73
                                       v++ sgG ds+V   La +a  ++ + v+vdtg   + et + ++ +       l ++e ++++ e+++  + 
  gi|336255015|ref|YP_004598122.1| 24 AVIALSGGVDSSVAAALAYEAIGDRlTPVYVDTGLMRKgETDQIRETFDYME--SLRIVEAQDRFLEALEGVTD 95
                                      6899********************7589******865524444444333222..24455555555555555555 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.3e-05     0.034       2      53 ..      24      76 ..      23     114 .. 0.77
   2 ?   -1.4   0.0      0.52   1.3e+03     154     175 ..     157     178 ..     125     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                                      EEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT-- CS
                              QueC  2 avvllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgv 53
                                      av+ lSGG+DS++++ala +++ ++++ + +d g  +k e++  ++ ++ ++ 
  gi|336255015|ref|YP_004598122.1| 24 AVIALSGGVDSSVAAALAYEAIgDRLTPVYVDTGLMRKGETDQIRETFDYMES 76
                                      89***************988743899999999998888888888877776664 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.52
                                       EE-TTTT--HHHHHHHHHHTTH CS
                              QueC 154 ieaPlidlsKaeivklgkelgv 175
                                       i+ P+ dl K e+ +++ +lg+
  gi|336255015|ref|YP_004598122.1| 157 IVEPVRDLYKDEVREVARHLGL 178
                                       7889999999999999999986 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.3e-05      0.14       4     164 ..      22     181 ..      20     188 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.3e-05
                              ThiI   4 gkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkei 79 
                                       ++++  lSgG+DS Vaa l+ +  G r   v+++  ++ + e+ +    + e +   +      l++v+ ++   e 
  gi|336255015|ref|YP_004598122.1|  22 ENAVIALSGGVDSSVAAALAYEAiGDRLTPVYVDTGLMRKGETDQ----IRETFDYME-----SLRIVEAQDRFLEA 89 
                                       5778889**********9988644889999998755554444433....333333333.....25555555555555 PP

                              ThiI  80 lekv.kekltivllkrkmlriAekvaeeegakalvtGesLg.qVaS....qtleNlrvisavvnl.lilrPLigldK 149
                                       le v +++ +  ++  +++r  e+ a+  +a+ lv+G      + S    +  +N+  +  vv+   i++P+  l K
  gi|336255015|ref|YP_004598122.1|  90 LEGVtDPEEKREIIGEQFIREFEREAKDADADYLVQGTIYPdRIESeggiKSHHNVGGLPDVVEFeGIVEPVRDLYK 166
                                       55443223333344556666666677777777777764332122221111233555555555544136666666666 PP

                              ThiI 150 eeiiklAkeigtyei 164
                                       +e+ ++A+++g +ei
  gi|336255015|ref|YP_004598122.1| 167 DEVREVARHLGLEEI 181
                                       666666666666655 PP

>> Asn_synthase  Asparagine synthase
   #    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      17      40 ..      21      44 ..      11     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                      Asn_synthase 17 dvpvGalLSGGlDSSliaalaarq 40
                                      d    + LSGG+DSS+ aala + 
  gi|336255015|ref|YP_004598122.1| 21 DENAVIALSGGVDSSVAAALAYEA 44
                                      6667789*************9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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 0.21s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2489.56
//
Query:       gi|336255016|ref|YP_004598123.1|  [L=113]
Description: CTP/GMP synthase operon protein [Halopiger xanaduensis SH-6]
Scores for 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:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 911.20
//
Query:       gi|336255017|ref|YP_004598124.1|  [L=238]
Description: 5-formyltetrahydrofolate cyclo-ligase [Halopiger xanaduensis SH-6]
Scores for 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-29  102.7   0.0    2.6e-29  102.4   0.0    1.1  1  5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family


Domain annotation for each model (and alignments):
>> 5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4   0.0   1.5e-33   2.6e-29       1     187 []       3     197 ..       3     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 1.5e-33
                                       HHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHTSHHHHH-.SEE........EE----TTS---HHHHHHHHHTTEE CS
                    5-FTHF_cyc-lig   1 KqelRkqllaalralseeevaaesealsqrieslkesqea.krv........alyvsvkgeidtkelikklleegke 68 
                                       Kq+lR++   ++++l++ + a+ + + ++ri+++ +++ea  r+        a +v+ +++ ++ ++++ +l++gk 
  gi|336255017|ref|YP_004598124.1|   3 KQALRER---IWDELEDGGEARFPFPPHGRIPNFAGADEAaDRLqetdawqeADVVKANPDAPQLPVRRAALRQGKT 76 
                                       8999*99...9*****************************99*********************************** PP

                                       EEEEEECSSCTEECEEEEEECCCCCCCCCHCTS....SCE--TTECCBCGGGG-SEEEE--SEEETTS-EE-SSTTH CS
                    5-FTHF_cyc-lig  69 vllPrvrlesgslkvvrlttlkeedslesgkyg....lkePeeeeerelalekldlvlvPgvAfdkeGaRlGkGkGy 141
                                       v++ ++rl++++   +rl++ + +d   ++++g       P+ +e     +e +dl++ ++vA+ ++GaR+GkG+Gy
  gi|336255017|ref|YP_004598124.1|  77 VYMAVPRLRDEQ-CFLRLDPDDVDDIDHATTVGgsseAGVPVHPED----VEPIDLIVSGSVAVTEDGARIGKGEGY 148
                                       ***999999932.333333333333333333331111334444333....348************************ PP

                                       HHHHHHHHTS.T-SS--EEEEE--GGGEES..-----ST----SEEE-S CS
                    5-FTHF_cyc-lig 142 yDrflarlkg.gagdkpltvglaldeqlve..rlPleehDvpvdevvte 187
                                        D ++a l +    d+++  +++++e +v    +Pl++hDvp+d +vt+
  gi|336255017|ref|YP_004598124.1| 149 SDLEFAILGEfDLVDDSTVTATTVHELQVVdeAVPLSSHDVPMDLIVTP 197
                                       **********88888999999****99988789**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1938.10
//
Query:       gi|336255018|ref|YP_004598125.1|  [L=203]
Description: molybdenum cofactor synthesis domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-22   78.2   0.3    6.5e-22   77.7   0.3    1.2  1  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.3   3.6e-26   6.5e-22      15     141 ..      40     168 ..      24     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 3.6e-26
                                       GBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHH..HHHHHTS..SEEEEESS-SSSTT--HHHHHHHHHSEE-H CS
                     MoCF_biosynth  15 eDtngpllaellkelgvevskytvvpDdeeeikeal..laaleea..dviittGGtGptpdDvtpealaklfekele 87 
                                       +D  g  + e+l+ + ++++ +++++   +++++++  +  +e+   d+++t GGt++ pdDv+ ea++ l++kel+
  gi|336255018|ref|YP_004598125.1|  40 DDPAGTAVEEALEGADFDLATREHIAPSHDRVQSTIlrM--IERDdvDLVVTAGGTSVEPDDVVIEAVETLLDKELT 114
                                       6788999999**************************554..444445****************************** PP

                                       HHHHHHHHHHHHHCCTTSHGGGGGGE.EE.....TTEEEEE-SSHHHHHHHHHHHHHGG CS
                     MoCF_biosynth  88 gfeeafrrvslkpgkpvgvapgailsrav.....gktiigLPGspkavkealeeillpa 141
                                        f+e+f  +++++     v++ +i  r+      gk++++LPG+  a++ a eei+lp+
  gi|336255018|ref|YP_004598125.1| 115 AFSEVFTSLAYEE-----VGTRVIAARTLagvaeGKPVFCLPGNAEAARLATEEIILPE 168
                                       ************9.....5555555555566676889******************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1458.57
//
Query:       gi|336255019|ref|YP_004598126.1|  [L=346]
Description: NADPH:quinone reductase [Halopiger xanaduensis SH-6]
Scores for complete 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-34  118.7   0.0      3e-34  117.8   0.0    1.5  1  ADH_zinc_N      Zinc-binding dehydrogenase
    1.2e-26   92.7   0.1    2.1e-26   91.9   0.1    1.4  1  ADH_N           Alcohol dehydrogenase GroES-like domain
    4.3e-21   76.4   0.0    7.1e-21   75.7   0.0    1.4  1  ADH_zinc_N_2    Zinc-binding dehydrogenase
     0.0084   15.4   0.3     0.0084   15.4   0.3    1.6  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0087   16.5   0.1      0.017   15.5   0.1    1.5  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
  ------ inclusion threshold ------
      0.021   14.3   0.3      0.037   13.5   0.3    1.5  1  adh_short       short chain dehydrogenase
        0.2   11.7   0.5       0.38   10.9   0.5    1.4  1  NADH_4Fe-4S     NADH-ubiquinone oxidoreductase-F iron-sulfur 


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 !  117.8   0.0   1.2e-37     3e-34       1     128 [.     178     304 ..     178     306 .. 0.94

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 1.2e-37
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       gvG+aa+q+A  +Gaev+a+ s++ekle+a+  Gad+v+ny+e ++ ++i+e tg++gvdvv++++G   t+++++k
  gi|336255019|ref|YP_004598126.1| 178 GVGHAALQIADYAGAEVYATGSTDEKLEYARAHGADHVVNYEERNFADWIREETGKRGVDVVVDYIG-AGTWRDSIK 253
                                       9****************************************555***********************.********* PP

                                       CEEEEEEEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                        ADH_zinc_N  78 llkpgGrlvvvGg.gkgeeefdlrnlllkeksilGsllgslreefkealdll 128
                                       +l+ +Grlv++Gg  +g+ e d+ +++ ++++i+Gs++gs + ++ ++++l+
  gi|336255019|ref|YP_004598126.1| 254 SLANNGRLVTCGGtAGGNPETDIPRIFWNQLHIIGSTMGS-PGQVDDVMELV 304
                                       *************7444444********************.99999999887 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.1   8.3e-30   2.1e-26       2     109 .]      28     135 ..      27     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 8.3e-30
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-G CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegee 78 
                                       +evl++vka ++++ D+++ +g   l+ ++p ++G +++G+veevg +v++++ GdrV+v + +scgeC+ C++g++
  gi|336255019|ref|YP_004598126.1|  28 DEVLVDVKAGALNHLDVWVRRGLPTLSLEMPHVPGSDAAGVVEEVGADVSRFEPGDRVAVTAGVSCGECEFCRDGDP 104
                                       89********************999**************************************************** PP

                                       GG-TTBEETTTSS-SSSBSEEEECGGGEEEE CS
                             ADH_N  79 nlCeeakllgvsldGgfaeyvvvpekklvkl 109
                                       +lC + +llg ++ G ++ey  v+e++l+++
  gi|336255019|ref|YP_004598126.1| 105 TLCVNFHLLGEHVTGVHSEYAAVSEDNLIPV 135
                                       ****************************986 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0   2.8e-24   7.1e-21       2     133 .]     211     340 ..     210     340 .. 0.83

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 2.8e-24
                                       T-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----..S-EEE-CHHHCTTT-EE CS
                      ADH_zinc_N_2   2 GAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsiggpp.lsaallkpakkrkgrsv 73 
                                       GAd+v++y++ +f+    ++tg++gvDvv+d +g  ++ ++s+k l+++Grlv+ gg+     ++         +++
  gi|336255019|ref|YP_004598126.1| 211 GADHVVNYEERNFAdwirEETGKRGVDVVVDYIGAGTW-RDSIKSLANNGRLVTCGGTAgGNPETDI-------PRI 279
                                       9*************999999999***********999*.*******999*******74332222222.......333 PP

                                       EE--GGG...-....-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  74 kyeflfsmkas...aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                        ++ l  +  s    + +  +++++l+ +G+++p + +v+p++e+a+Ah+ +e++  +GK+V+
  gi|336255019|ref|YP_004598126.1| 280 FWNQLH-IIGStmgSPGQ-VDDVMELVWDGTFEPAIREVLPMSETARAHEIIEQREGFGKVVV 340
                                       333333.22222444778.99*****************************************8 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 ?   -2.9   0.1       1.3   3.4e+03      39      58 ..      61      80 ..      60      92 .. 0.81
   2 !   15.4   0.3   3.3e-06    0.0084      30      89 ..     169     227 ..     143     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                                      HHHHHHHHHHHTT-EEEEEE CS
                       AlaDh_PNT_C 39 aGlqAiatakglgakVtvlD 58
                                       G  A+ +  ++ga+V  ++
  gi|336255019|ref|YP_004598126.1| 61 PGSDAAGVVEEVGADVSRFE 80
                                      68899999999999998776 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 3.3e-06
                                       EEEEEST.SHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHH CS
                       AlaDh_PNT_C  30 kvlviGg.GvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeav 89 
                                        vlv+G+ G +G +A+++a   ga+V+++    ++le+ ++ ga   +v++ +e+++a+ +
  gi|336255019|ref|YP_004598126.1| 169 SVLVLGAsGGVGHAALQIADYAGAEVYATGSTDEKLEYARAHGAD--HVVNYEERNFADWI 227
                                       69****8799*******************************9999..66666666666655 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 !   15.5   0.1   6.8e-06     0.017       2      91 ..     170     260 ..     169     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.8e-06
                                       EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG..GGTTTECEBEEEGGGGGC..TT-SEEEE-S CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk..aleegkdlkvedvdeeel..kevdivflal 74 
                                       v ++Ga+G vG + l++ +      +v++++s+  +  ++a+a++  ++ ++++ ++ d   ee+  ++vd+v+   
  gi|336255019|ref|YP_004598126.1| 170 VLVLGASGGVGHAALQIADY--AGAEVYATGSTD-EKLEYARAHGadHVVNYEERNFADWIREETgkRGVDVVVDYI 243
                                       88*************98766..335566677776.789999999999************555555579********* PP

                                       CHHHHHHHHHHHHHTTS CS
                    Semialdhyde_dh  75 pagvskelapklaeagv 91 
                                       +ag+ ++  ++la++g 
  gi|336255019|ref|YP_004598126.1| 244 GAGTWRDSIKSLANNGR 260
                                       *********99999985 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   1.4e-05     0.037       3      43 ..     170     210 ..     168     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHH CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevake 43 
                                       vlv Gas+G+G+a  +    +Ga+v+++++++ekle + ++
  gi|336255019|ref|YP_004598126.1| 170 VLVLGASGGVGHAALQIADYAGAEVYATGSTDEKLEYARAH 210
                                       9**********************************766554 PP

>> NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   0.00015      0.38       9      28 ..      87     106 ..      83     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                                       HHHHH--S--HHHHIIIIHH CS
                       NADH_4Fe-4S   9 fyaaesCGkCtpCreGtkrl 28 
                                       ++a  sCG+C  Cr G + l
  gi|336255019|ref|YP_004598126.1|  87 VTAGVSCGECEFCRDGDPTL 106
                                       67888***********8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2788.04
//
Query:       gi|336255020|ref|YP_004598127.1|  [L=105]
Description: hypothetical protein Halxa_3640 [Halopiger xanaduensis SH-6]
Scores for 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:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 843.54
//
Query:       gi|336255021|ref|YP_004598128.1|  [L=187]
Description: Isopentenyl-diphosphate delta-isomerase [Halopiger xanaduensis SH-6]
Scores for 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   59.3   0.7    5.1e-16   58.9   0.7    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 !   58.9   0.7   2.8e-20   5.1e-16       2     130 ..      42     176 ..      41     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 2.8e-20
                                       EEEEEEEEEEETTSEEEEEEES..SSSTTT.EE.SSEEECBTTSHHHHHHHHHHHHHHSEEEEEE...EEEEEEEEE CS
                             NUDIX   2 lrravgvvllnekgevLlvrrs..kkpfpg.We.lPgGkvepgEtpeeAArREleEEtGleaell...ellgrlhyl 71 
                                       ++ra+  ++++++g +Ll++r+  k+ +   W+ +++ +  +g++ eeA r +leEE+G+++++    +l++r++y+
  gi|336255021|ref|YP_004598128.1|  42 RHRAFTSLVFDGEGNILLAQRApdKRLWCTyWDgTVASHPVEGQSQEEATRQRLEEELGITPDQYddlRLTDRFEYK 118
                                       79********************86666666887799************************77666222666655554 PP

                                       EEEEEEEEE...EEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHHH CS
                             NUDIX  72 apydgpygd...eheilyvfl.eevegelepndenevsevrwvpleellkeklaaesrkllpw 130
                                       + ++    +   ehe++ v+    ++ +l pn e+ev+++ wvp+e l   + + ++ +l pw
  gi|336255021|ref|YP_004598128.1| 119 RYFE----NegvEHEVCAVLKvTLNDRTLDPN-EDEVAGLMWVPYERLHSNPEWYRQLRLCPW 176
                                       4444....3455*********66666666666.***************666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1534.45
//
Query:       gi|336255022|ref|YP_004598129.1|  [L=328]
Description: hypothetical protein Halxa_3642 [Halopiger xanaduensis SH-6]
Scores for complete 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-22   79.2   0.7    4.5e-22   78.0   0.6    1.7  2  DAGK_cat  Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.6   2.5e-26   4.5e-22       3     124 ..      19     134 ..      17     136 .. 0.90
   2 ?   -2.8   0.0      0.26   4.7e+03      54      67 ..     300     313 ..     276     315 .. 0.69

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 2.5e-26
                                       EEEE-TTCTTTTHHHHHHHCHHHHHHCTCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCT.H CS
                          DAGK_cat   3 lvivNpksGkgkgekllrkvrelleeagvelelieteepgdakelakeakeegvdlivvaGGDGtvsevlnglle.e 78 
                                       ++++Np sG+g+    ++ v el +++g+  e+++tee+gdak++a++a+  +++l+ +aGGDGtv+ v+ng++  +
  gi|336255022|ref|YP_004598129.1|  19 VLVLNPVSGSGD---HVDDVVELAANRGF--EIRRTEEAGDAKRFARDAAP-DASLVAAAGGDGTVNGVANGIAAaD 89 
                                       6899*****664...56778889888886..********************.69*********************99 PP

                                       HCTTSEEEEEE-SS--HHHHHCT--SSHHHHHHCHHCTBEEEEEEE CS
                          DAGK_cat  79 latkpplgiiPlGtgNdlaralgigkdieealesiikgetrkvdvg 124
                                       + +++ lg++P+GtgN++a ++gi+  +e+++  i +g++r++d+g
  gi|336255022|ref|YP_004598129.1|  90 ELETTTLGVVPAGTGNNFASNIGIE-GLEHSFAVIDEGRRREIDLG 134
                                       9999********************9.67777888889999999986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.26
                                       CC-SEEEEEESHHH CS
                          DAGK_cat  54 egvdlivvaGGDGt 67 
                                       ++ +++ va GDG 
  gi|336255022|ref|YP_004598129.1| 300 TDPNALTVAVGDGY 313
                                       34478888999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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: 0.43u 0.17s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 2852.06
//
Query:       gi|336255023|ref|YP_004598130.1|  [L=241]
Description: PHP domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   64.1   0.4    2.3e-17   62.5   0.0    2.1  2  PHP_C      PHP-associated
  ------ inclusion threshold ------
      0.088   13.0   0.0          3    8.0   0.0    2.4  3  RraA-like  Aldolase/RraA


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 ?   -2.6   0.1      0.54   4.9e+03       8      20 ..      34      46 ..      31      46 .. 0.77
   2 !   62.5   0.0   2.6e-21   2.3e-17       6      56 .]     143     195 ..     138     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.54
                             PHP_C  8 rrfAeklglpgtg 20
                                      +++A+++gl g++
  gi|336255023|ref|YP_004598130.1| 34 AEAAARRGLDGVA 46
                                      5789999998775 PP

  == domain 2  score: 62.5 bits;  conditional E-value: 2.6e-21
                             PHP_C   6 rArrfAeklglpgtgGSDAHrleeVGrayTefeepia..tpdelleairegrt 56 
                                        ++++A++++lp +gGSDAH++ eVGrayT++e++ +  tp ++++air gr+
  gi|336255023|ref|YP_004598130.1| 143 LVEELAAERDLPLVGGSDAHYPFEVGRAYTVLETDADrlTPSAVVDAIRDGRV 195
                                       6789****************************5555555************96 PP

>> RraA-like  Aldolase/RraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.48   4.3e+03      73      86 ..      32      45 ..      28      49 .. 0.85
   2 ?    2.3   0.0     0.019   1.7e+02      50      89 ..      73     113 ..      58     158 .. 0.75
   3 ?    8.0   0.0   0.00033         3      25      55 ..     166     196 ..     143     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.48
                                      HHHHHHHHTTBSEE CS
                         RraA-like 73 llataakangvaGv 86
                                      lla+aa+++g+ Gv
  gi|336255023|ref|YP_004598130.1| 32 LLAEAAARRGLDGV 45
                                      78999*****9998 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.019
                                       -TTEEEEE..ESTT.SSSSSECE-HHHHHHHHHTTBSEEEEE CS
                         RraA-like  50 gpgdvlVv..dgggdeslraallGgllataakangvaGvvvd 89 
                                        +g+vlV+  d   ++ +  al  +  +++a+++++a++v++
  gi|336255023|ref|YP_004598130.1|  73 DRGHVLVIgpDPPRET-KPGALSPEEAVALAHDRDCAAIVAH 113
                                       6799999966333333.46777799999*********99985 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00033
                                       EEEEEEEEEESS.BGHHHHHHHTS--TTEEE CS
                         RraA-like  25 fvGpavTvkvveadnslvkealeeagpgdvl 55 
                                        vG+a+Tv  ++ad  +  ++++++++g+v 
  gi|336255023|ref|YP_004598130.1| 166 EVGRAYTVLETDADRLTPSAVVDAIRDGRVS 196
                                       46**************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 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:                        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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1886.06
//
Query:       gi|336255024|ref|YP_004598131.1|  [L=137]
Description: AsnC family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for complete 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   69.7   2.1    1.2e-17   63.4   1.1    2.3  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    7.9e-16   57.4   0.1    5.8e-15   54.6   0.1    2.1  2  HTH_24          Winged helix-turn-helix DNA-binding
    4.9e-11   42.4   0.6    4.9e-11   42.4   0.6    1.6  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    4.1e-05   23.2   0.0    0.00011   21.8   0.0    1.7  1  Sigma70_r4_2    Sigma-70, region 4
    0.00027   20.4   0.0    0.00051   19.5   0.0    1.5  1  Sigma70_r4      Sigma-70, region 4
     0.0004   20.4   0.0    0.00073   19.6   0.0    1.4  1  HTH_20          Helix-turn-helix domain
     0.0043   17.0   0.1      0.011   15.6   0.0    1.7  1  HTH_11          HTH domain
     0.0044   17.0   0.5     0.0098   15.9   0.5    1.5  1  NapD            NapD protein
     0.0051   16.6   0.0     0.0081   15.9   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
     0.0054   16.1   0.1      0.012   15.0   0.0    1.7  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
     0.0066   16.0   0.0      0.026   14.1   0.0    2.0  2  GerE            Bacterial regulatory proteins, luxR family
     0.0067   16.3   0.0      0.012   15.5   0.0    1.5  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.015   15.1   0.1      0.026   14.3   0.1    1.5  1  HTH_23          Homeodomain-like domain
      0.022   14.5   0.1      0.033   14.0   0.1    1.3  1  HTH_38          Helix-turn-helix domain
      0.022   14.4   0.0      0.048   13.3   0.0    1.6  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
      0.023   14.4   0.2       0.12   12.1   0.1    2.1  2  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.025   14.5   1.1      0.093   12.7   0.3    2.1  2  GYD             GYD domain
      0.027   14.4   0.0      0.044   13.7   0.0    1.3  1  MarR            MarR family
      0.054   13.3   0.1       0.37   10.6   0.0    2.1  2  DUF746          Domain of Unknown Function (DUF746)
      0.084   12.9   0.0       0.13   12.3   0.0    1.3  1  HTH_Mga         M protein trans-acting positive regulator (MG


Domain annotation for each model (and alignments):
>> 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 !   63.4   1.1   1.3e-20   1.2e-17       1      41 [.       1      41 [.       1      42 [. 0.99
   2 ?    5.1   0.0     0.023        21      20      39 ..      62      81 ..      60      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 1.3e-20
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      +D++Dr+IL++L++daR++y+e+A+++G Se tv++Rv+r+
  gi|336255024|ref|YP_004598131.1|  1 MDDLDRQILDILRRDARTPYTEIADEIGTSEGTVRNRVERM 41
                                      9***************************************9 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.023
                     HTH_AsnC-type 20 yaeLAervGlSestvlrRvr 39
                                      + e++ +v +++ +v+ R++
  gi|336255024|ref|YP_004598131.1| 62 MLEISVEVDVDTKAVADRMA 81
                                      679***************96 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 !   54.6   0.1   6.5e-18   5.8e-15       1      48 []       1      48 [.       1      48 [. 0.98
   2 ?    0.2   0.0      0.64   5.8e+02      20      39 ..      62      81 ..      60      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 6.5e-18
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +d++dr+IL +L++++r++++e+A+++g S +tv+ r++r++++ +I+
  gi|336255024|ref|YP_004598131.1|  1 MDDLDRQILDILRRDARTPYTEIADEIGTSEGTVRNRVERMMDDDVIE 48
                                      89********************************************97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.64
                            HTH_24 20 qreLAerlglSpstvnrrlk 39
                                      + e++ ++++   +v  r+ 
  gi|336255024|ref|YP_004598131.1| 62 MLEISVEVDVDTKAVADRMA 81
                                      579999*********99986 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 ?   -2.9   0.1       7.8     7e+03      47      59 ..       1      13 [.       1      16 [. 0.76
   2 !   42.4   0.6   5.5e-14   4.9e-11       4      75 .]      66     134 ..      63     134 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.8
                                      HHHHHHHHHHTTT CS
                    AsnC_trans_reg 47 lealerflrekla 59
                                      +++l+r + + l+
  gi|336255024|ref|YP_004598131.1|  1 MDDLDRQILDILR 13
                                      7889999888766 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 5.5e-14
                                       EE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg   4 slepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                       s+e +   +++++++++ae++e+  +++v+G+ d++l v ++d++  ++++ +  ++ ++v +t+t ++le+
  gi|336255024|ref|YP_004598131.1|  66 SVEVDV--DTKAVADRMAEWDEIDFVWMVSGEQDIVLVVDAADTRGVNDLITK-ARNQDEVMSTKTRLILEE 134
                                       444334..5899**************************************999.****************96 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 !   21.8   0.0   1.2e-07   0.00011      21      49 ..      12      40 ..       3      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.2e-07
                                      HHHTS---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 21 lryleglsykEIAellgisegtVksrlsR 49
                                      lr+    +y EIA ++g+segtV++r+ R
  gi|336255024|ref|YP_004598131.1| 12 LRRDARTPYTEIADEIGTSEGTVRNRVER 40
                                      56666679******************987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.7e-07   0.00051       8      45 ..       4      42 ..       1      44 [. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.7e-07
                                      HHHHHHH.HHHTTT--HHHHHHHHTS-HHHHHHHHHHHH CS
                        Sigma70_r4  8 rerevle.lrfgeglTleEIgerlgiSrerVrqiekrAl 45
                                       +r++l  lr++   ++ EI+++ g S+++Vr +  r +
  gi|336255024|ref|YP_004598131.1|  4 LDRQILDiLRRDARTPYTEIADEIGTSEGTVRNRVERMM 42
                                      567777437889999*******************98876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   8.1e-07   0.00073      13      56 ..       6      49 ..       2      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.1e-07
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      r il+ L+r++    +e+a+++++s  t++++++ + + + +e+
  gi|336255024|ref|YP_004598131.1|  6 RQILDILRRDARTPYTEIADEIGTSEGTVRNRVERMMDDDVIER 49
                                      89********************************9999999986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.3e-05     0.011       3      38 ..       6      40 ..       5      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIka 38
                                      +qil +L+  +   +  e+A+e++ S+ tvr+++++
  gi|336255024|ref|YP_004598131.1|  6 RQILDILR-RDARTPYTEIADEIGTSEGTVRNRVER 40
                                      69999994.44459*******************987 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.5   1.1e-05    0.0098      15      68 ..      73     127 ..      68     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                              NapD  15 laavkaalaalpgvE.vhasdeegklVvviEaesedeladtieaiealpgVlsas 68 
                                       ++av++++a+ ++++ v  +++e+ +V+v++a++++ + d i++ ++ + V+s++
  gi|336255024|ref|YP_004598131.1|  73 TKAVADRMAEWDEIDfVWMVSGEQDIVLVVDAADTRGVNDLITKARNQDEVMSTK 127
                                       67888999999999944567888*****************************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 !   15.9   0.0   9.1e-06    0.0081       7      44 ..       7      43 ..       6      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.1e-06
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHH CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLve 44
                                      +iLd+l++ ++    +e+A+++g +  tv++ +  ++ 
  gi|336255024|ref|YP_004598131.1|  7 QILDILRRDART-PYTEIADEIGTSEGTVRNRVERMMD 43
                                      8**********8.9****************98887765 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 !   15.0   0.0   1.4e-05     0.012      15      50 ..       3      40 ..       2      42 .. 0.90
   2 ?   -3.1   0.0       6.2   5.6e+03      31      36 ..      74      79 ..      62      81 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                      HTH_Tnp_ISL3 15 rleayilellles..rsvkavArqlgvSwtTVwrildr 50
                                      +l+++il  l+++   + +++A++ g+S+ TV++++ r
  gi|336255024|ref|YP_004598131.1|  3 DLDRQILDILRRDarTPYTEIADEIGTSEGTVRNRVER 40
                                      6888999999999999******************9876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.2
                      HTH_Tnp_ISL3 31 kavArq 36
                                      kavA++
  gi|336255024|ref|YP_004598131.1| 74 KAVADR 79
                                      566665 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.9e-05     0.026      21      42 ..      21      42 ..       6      43 .. 0.94
   2 ?   -1.0   0.0       1.4   1.3e+03      33      46 ..      51      64 ..      47      80 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.9e-05
                                      HHHHHHHTS-HHHHHHHHHHHH CS
                              GerE 21 keIAeelniSekTVkvhksnim 42
                                      +eIA+e + Se TV++ ++++m
  gi|336255024|ref|YP_004598131.1| 21 TEIADEIGTSEGTVRNRVERMM 42
                                      69*******************9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                      HHHHHHHHHHHHHT CS
                              GerE 33 TVkvhksnimkKLn 46
                                      T+++  +n++  L+
  gi|336255024|ref|YP_004598131.1| 51 TISTRTGNVQAMLE 64
                                      55555555555444 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.3e-05     0.012       7      53 ..       5      49 ..       1      57 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      ++++L  L+r  +     +e+a++ g s ++v ++++r+ +   +er
  gi|336255024|ref|YP_004598131.1|  5 DRQILDILRRDAR--TPYTEIADEIGTSEGTVRNRVERMMDDDVIER 49
                                      5789999988887..899***********************999998 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.9e-05     0.026      13      40 ..      13      40 ..       6      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.9e-05
                            HTH_23 13 llaeGlsvreIAreLgvsrrTvyrwlkr 40
                                        + + +++eIA+e g s+ Tv++ ++r
  gi|336255024|ref|YP_004598131.1| 13 RRDARTPYTEIADEIGTSEGTVRNRVER 40
                                      4444889****************88776 PP

>> HTH_38  Helix-turn-helix 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     0.033       9      43 ..       5      40 ..       1      41 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                            HTH_38  9 eReeIerll.aeGlslreIArrLgrspsTIsRElkR 43
                                      +R+ + +l+ ++   + eIA ++g s +T+ + + R
  gi|336255024|ref|YP_004598131.1|  5 DRQILDILRrDARTPYTEIADEIGTSEGTVRNRVER 40
                                      78888999625778888*************998877 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 ?   13.3   0.0   5.3e-05     0.048      27      46 ..      21      40 ..       5      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.3e-05
                      HrcA_DNA-bdg 27 eeiAevlkrneGtvRNqlqs 46
                                      +eiA+ ++  eGtvRN ++ 
  gi|336255024|ref|YP_004598131.1| 21 TEIADEIGTSEGTVRNRVER 40
                                      79**************9865 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 ?   12.1   0.1   0.00014      0.12       3      46 ..       6      49 ..       5      51 .. 0.86
   2 ?    1.1   0.0      0.37   3.3e+02      18      30 ..      44      56 ..      38      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                          HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                       qil+ l+++     +e++++ g+Se T+R+  + +  +++++R
  gi|336255024|ref|YP_004598131.1|  6 RQILDILRRDARTPYTEIADEIGTSEGTVRNRVERMMDDDVIER 49
                                      59****************************97777666666666 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.37
                          HTH_DeoR 18 eelvellgvSeaT 30
                                      ++++e++ +S+ T
  gi|336255024|ref|YP_004598131.1| 44 DDVIERFTISTRT 56
                                      5899******998 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.96   8.6e+02      70      88 ..      30      48 ..      26      51 .. 0.82
   2 ?   12.7   0.3    0.0001     0.093      40      85 ..      89     134 ..      60     137 .] 0.81

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.96
                               GYD 70 asGtvrtetlrafteeefd 88
                                      + Gtvr+++ r+++ + ++
  gi|336255024|ref|YP_004598131.1| 30 SEGTVRNRVERMMDDDVIE 48
                                      789****999999987665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0001
                               GYD  40 lyatlGeyDvvvivEapDdetaaalslalaasGtvrtetlraftee 85 
                                       ++++ Ge+D+v +v+a D + +  l  + + +  v ++ +r++ ee
  gi|336255024|ref|YP_004598131.1|  89 VWMVSGEQDIVLVVDAADTRGVNDLITKARNQDEVMSTKTRLILEE 134
                                       7999****************99999999998888888777776665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.9e-05     0.044       8      50 ..       8      50 ..       6      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.9e-05
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      iL il++      +e+a+ +g+s +tv + + r+ +++ ieR 
  gi|336255024|ref|YP_004598131.1|  8 ILDILRRDARTPYTEIADEIGTSEGTVRNRVERMMDDDVIERF 50
                                      7899999999999****************************96 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00042      0.37      15      35 ..      20      40 ..      17      43 .. 0.88
   2 ?   -0.5   0.1       1.2   1.1e+03      17      37 ..      64      84 ..      61      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00042
                            DUF746 15 laeaadllgtdegiiakwvre 35
                                       +e+ad +gt+eg+++++v++
  gi|336255024|ref|YP_004598131.1| 20 YTEIADEIGTSEGTVRNRVER 40
                                      589***************986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                            DUF746 17 eaadllgtdegiiakwvreFr 37
                                      e++  +++d + +a +++e+ 
  gi|336255024|ref|YP_004598131.1| 64 EISVEVDVDTKAVADRMAEWD 84
                                      777889999999999999885 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 ?   12.3   0.0   0.00014      0.13       9      54 ..       7      52 ..       3      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                           HTH_Mga  9 kLlelLteneksltldelakeLglseltlqsdiseLnel.Fpeelsi 54
                                      ++l++L   + +++++e+a e g+se t++++++ + +  ++e ++i
  gi|336255024|ref|YP_004598131.1|  7 QILDILRR-DARTPYTEIADEIGTSEGTVRNRVERMMDDdVIERFTI 52
                                      79999999.9**********************998765555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 1157.09
//
Query:       gi|336255025|ref|YP_004598132.1|  [L=359]
Description: carbamoyl-phosphate synthase, small subunit [Halopiger xanaduensis SH-6]
Scores for 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-36  122.6   0.1    1.6e-34  118.5   0.0    2.4  2  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    9.9e-36  123.3   0.0    1.8e-35  122.4   0.0    1.4  2  GATase           Glutamine amidotransferase class-I
    1.3e-06   28.3   0.2     0.0024   17.7   0.0    2.2  2  Peptidase_C26    Peptidase C26
    5.5e-06   26.3   0.1    9.2e-06   25.6   0.1    1.5  1  DJ-1_PfpI        DJ-1/PfpI family


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 !  118.5   0.0   3.6e-38   1.6e-34       2     128 .]       4     121 ..       3     121 .. 0.96
   2 ?    1.5   0.1     0.057   2.5e+02      22      36 ..     275     289 ..     254     298 .. 0.77

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 3.6e-38
                   CPSase_sm_chain   2 avLvLedGtvfeGksfgakeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedvesekikvaglvv 78 
                                       a+++Le G+v+eG++ + ++a GE+vf+T+ tGY+e+ltDpsY++q+l+++ypliGnyGv+ee++e+++++ +++++
  gi|336255025|ref|YP_004598132.1|   4 AYVALEGGHVIEGRGRAPGTARGELVFTTAYTGYEESLTDPSYEEQVLTFSYPLIGNYGVREERFEDDRVHPRAVLA 80 
                                       799************999*********************************************************** PP

                   CPSase_sm_chain  79 relseepsnwraeesLsewlkeekipgisgvDTRaLtkklrekgamkgvi 128
                                       +el+          +++ewl++e++p++ ++DTR++++ +r++gamk+ i
  gi|336255025|ref|YP_004598132.1|  81 KELTA---------DVAEWLESEGVPAVDHLDTREVVTDIRDEGAMKCGI 121
                                       *9985.........5789****************************9866 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.057
                   CPSase_sm_chain  22 avGEvvfnTgmtGYq 36 
                                       ++G vv++T   GY+
  gi|336255025|ref|YP_004598132.1| 275 ESGQVVMTTQNHGYT 289
                                       489***********6 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.3   5.7e+03     115     150 ..     133     165 ..     106     169 .. 0.51
   2 !  122.4   0.0   4.1e-39   1.8e-35       2     189 ..     171     344 ..     170     345 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
                                       GTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEET CS
                            GATase 115 lyglknevierhrHryevnpkelepaglevtaksed 150
                                       l++l ++ +++  H +   +  +  +++ev++++++
  gi|336255025|ref|YP_004598132.1| 133 LEQL-EQCKAMSEHTDIGAQ--VSVDEVEVYGEDNN 165
                                       3333.333444444444443..44455555555555 PP

  == domain 2  score: 122.4 bits;  conditional E-value: 4.1e-39
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGI 77 
                                       l+D++   + ++v++l++++++v+v+p+das      ++ +pd +++s+Gpg+p+ +e++i++++e+ e ++P+ GI
  gi|336255025|ref|YP_004598132.1| 171 LVDCG--AKDSIVDSLLARDAEVHVLPYDASVADV--EAVDPDVLFISNGPGDPAnYEQAISLVEEFVE-DTPVAGI 242
                                       79999..***********************99999..489*****************************.******* PP

                                       THHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEE CS
                            GATase  78 CLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeel 154
                                       CLG Q++a+++g++++k++ ++h+g ++++ d       +++++v ++++H+y+v +     + levt  + +d++ 
  gi|336255025|ref|YP_004598132.1| 243 CLGQQIVAEALGGTTEKMT-FGHRGVNQPVLD------LESGQVVMTTQNHGYTVAD---PGEHLEVTQINVNDDTP 309
                                       *******************.************......7788**************9...7888************* PP

                                       EEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHHH CS
                            GATase 155 meiiekknpfvgvQFHPEststpegpellfnflik 189
                                       ++i   ++ ++  Q+HPE+ ++pe++  +f+++++
  gi|336255025|ref|YP_004598132.1| 310 EGIDGIEYDVITRQYHPEANPGPEDTLDFFDSVLE 344
                                       *************************9999988765 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.3e-07    0.0024      93     128 ..     225     259 ..     211     270 .. 0.79
   2 !    8.5   0.0   0.00034       1.5     169     216 .]     281     327 ..     270     327 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.3e-07
                     Peptidase_C26  93 lelaLiraalergvPilgiCrGlqllnvalGGtlyq 128
                                         + L+++ + +++P+ giC+G q+++ alGGt+ +
  gi|336255025|ref|YP_004598132.1| 225 QAISLVEEFV-EDTPVAGICLGQQIVAEALGGTTEK 259
                                       5566666655.689******************9865 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00034
                     Peptidase_C26 169 evnslHhqaikelaeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                       +++  H  ++ + +e+l+v+ +   D++ E i  +e +  v+  Q+HPE
  gi|336255025|ref|YP_004598132.1| 281 MTTQNHGYTVADPGEHLEVTQINVnDDTPEGIDGIEYD--VITRQYHPE 327
                                       56778****************9988***********66..9*******9 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 !   25.6   0.1   2.1e-09   9.2e-06      46     126 ..     192     269 ..     130     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.1e-09
                                       EEEE-SEEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE-.-S CS
                         DJ-1_PfpI  46 lkvtvdaslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvT.sy 121
                                       + ++ das+ dv+a + D+l +  G   p + ++ e++++lv ef+e +++va IC g+q+ a+a   + +++T ++
  gi|336255025|ref|YP_004598132.1| 192 HVLPYDASVADVEAVDPDVLFISNG---PGDPANYEQAISLVEEFVE-DTPVAGICLGQQIVAEALGGTTEKMTfGH 264
                                       45678*****************988...558888889********97.68***************999999999566 PP

                                       GGGHH CS
                         DJ-1_PfpI 122 pavkd 126
                                        +v++
  gi|336255025|ref|YP_004598132.1| 265 RGVNQ 269
                                       66664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2722.41
//
Query:       gi|336255026|ref|YP_004598133.1|  [L=146]
Description: hypothetical protein Halxa_3646 [Halopiger xanaduensis SH-6]
Scores for 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-22   77.7  13.8    8.5e-22   77.5  13.8    1.0  1  DUF5518   Family of unknown function (DUF5518)


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5  13.8   4.7e-26   8.5e-22       1     118 []      16     132 ..      16     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 4.7e-26
                           DUF5518   1 wraaliGavvaivlslllglllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipv.lvlllvlllglv 76 
                                       wr+al+G+++a+++ + +++ ++ +++l +++v+Gl++Gy+ +g++++  ++G ++G++ga+pv l++++ ++  l+
  gi|336255026|ref|YP_004598133.1|  16 WRYALVGGLLALPFAARSYWRTGTTLELEAIFVAGLLVGYFFRGTADEVSRVGSRTGFVGALPVlLWMVSDVVYFLF 92 
                                       9***************************************************************99***999999** PP

                           DUF5518  77 aaigglagfvallvalllvvllllvvllvilgaiGGaiGgll 118
                                       ++    ++f+ +++++llv  ++  ++++++gaiG++iG +l
  gi|336255026|ref|YP_004598133.1|  93 ETESSYTLFAPIVGGVLLV--TIGSLFAALVGAIGARIGDWL 132
                                       ***********99999999..999*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.53
# Mc/sec: 824.81
//
Query:       gi|336255027|ref|YP_004598134.1|  [L=348]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-07   29.0   0.5    2.6e-05   23.6   0.1    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    8.5e-06   25.2   2.2    0.00079   18.8   0.2    2.5  3  FAD_binding_3   FAD binding domain
    0.00018   21.0   1.2     0.0014   18.1   0.8    2.1  2  FAD_oxidored    FAD dependent oxidoreductase
    0.00027   20.2   0.8    0.00036   19.7   0.1    1.5  2  GIDA            Glucose inhibited division protein A
    0.00052   19.2   3.5     0.0017   17.6   0.4    2.4  2  FAD_binding_2   FAD binding domain
    0.00065   19.9   0.0     0.0016   18.6   0.0    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0021   16.9   0.1      0.006   15.3   0.1    1.7  2  HI0933_like     HI0933-like protein
     0.0023   17.3   0.1      0.044   13.0   0.0    2.4  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0048   16.0   0.2       0.11   11.5   0.2    2.1  2  Lycopene_cycl   Lycopene cyclase protein
  ------ inclusion threshold ------
      0.019   15.5   0.0       0.05   14.2   0.0    1.7  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.023   14.0   0.0      0.035   13.4   0.0    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.054   13.5   0.7      0.098   12.7   0.7    1.4  1  NUDIX           NUDIX domain
       0.09   11.6   2.0       0.34    9.7   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
       0.13   11.8  10.5        0.1   12.2   0.5    3.3  4  DAO             FAD dependent oxidoreductase
       0.22   11.4   0.9        0.4   10.6   0.9    1.4  1  ACAS_N          Acetyl-coenzyme A synthetase N-terminus


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 !   23.6   0.1   2.2e-08   2.6e-05       2      58 ..      51     120 ..      50     157 .. 0.65
   2 !    5.5   0.0    0.0073       8.7     187     294 .]     108     223 ..     103     224 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.2e-08
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..............H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............x RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias..............e 58 
                                        v+viGgGpAG+aa  + a++g++++++ ++g   +++c   + +lg++   ei++              +
  gi|336255027|ref|YP_004598134.1|  51 AVAVIGGGPAGCAAGVFTARYGLETIIF-DRGPSSLRRCASLENYLGFPCGIEIETflelaqdhaeqagcQ 120
                                       69**************************.888888888888777777776666666777766444333342 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0073
                                       HHHHHHHHHTTEEEEESCEEEEEEETTE..EEEEEETTSCEEEESEEEE-S-EEES-HHCS....HCCT-EEEETTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx RF
                       Pyr_redox_2 187 aaleealekeGvevklgtsvkeidgnge..klevvledgeeidadlvvvavGvrpstelle....eklgleldergg 257
                                       + ++++ e+ G +++ +  v+ + + ++    +++ ++ge++ a+ vv a  +  s  l++    e++ ++ +++gg
  gi|336255027|ref|YP_004598134.1| 108 ELAQDHAEQAGCQLR-NDLVESVSRLEDgeGFRLEPQEGESVTARFVVAASKYDGSY-LRGldddESMFVTQEHDGG 182
                                       567888888888888.77777777777766777888999999999988888666553.2223367777777777777 PP

                                       E.......E--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       x.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 258 i.......vvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                                 d+ + t v+g+y++G  a   g+ ++a  A  +G
  gi|336255027|ref|YP_004598134.1| 183 TaerfdrdYPDDDGTTPVDGLYVAGPLA---GSGDQAIIAAGHG 223
                                       76655554567777899********999...7777776666655 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   6.6e-07   0.00079       2      34 ..      50      82 ..      49      93 .. 0.90
   2 !    5.8   0.0    0.0056       6.7     100     161 ..      99     156 ..      85     162 .. 0.72
   3 ?   -2.8   0.0       2.3   2.8e+03      94     116 ..     287     309 ..     243     320 .. 0.54

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.6e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                        V+++G+GpaG  ++ + +++G ++++ ++  
  gi|336255027|ref|YP_004598134.1| 50 FAVAVIGGGPAGCAAGVFTARYGLETIIFDRGP 82
                                      579*************************99965 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0056
                                       EE--HHHHHHHHHHHHHHHTEEETCS.EEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE- CS
                     FAD_binding_3 100 tvypqteleriLvehaeerglqvrfk.tevesleqdeegvtaevrdketgeeetvrakYlvGa 161
                                       + +  + ++ +  +hae++g+q+r +  e +s ++d+eg     ++ +  e e v+a+++v+a
  gi|336255027|ref|YP_004598134.1|  99 CGIEIETFLELAQDHAEQAGCQLRNDlVESVSRLEDGEG---FRLEPQ--EGESVTARFVVAA 156
                                       55555666677789********99762466666666666...333343..4456********8 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.3
                                       HCST-CEE--HHHHHHHHHHHHH CS
                     FAD_binding_3  94 sspervtvypqteleriLvehae 116
                                          ++   y+ +++e++++++++
  gi|336255027|ref|YP_004598134.1| 287 LAETYADEYGSDYVEPDVAAQRA 309
                                       33344444555555555555555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.8   1.2e-06    0.0014       2      32 ..      52      82 ..      51      83 .. 0.94
   2 ?    0.9   0.0       0.2   2.3e+02      54      97 ..     225     275 ..     203     320 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-06
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveerg 32
                                      v V+GGgpaG+aA +  ar G ++++ ++ +
  gi|336255027|ref|YP_004598134.1| 52 VAVIGGGPAGCAAGVFTARYGLETIIFDRGP 82
                                      89************************99875 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.2
                      FAD_oxidored  54 qvvtgiareflerlrqrgga......rlkkrskwn.......tfepevakavleeml 97 
                                        v++ ++re++e+    g++      r+      +        ++pe + +++ee  
  gi|336255027|ref|YP_004598134.1| 225 TVARTLIRELREEAGFWGKYaghydwRR------KvenrreeWVDPERWVELFEESA 275
                                       5666677777777766555534333211......12234455899999999999877 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   3.1e-07   0.00036       2      29 ..      52      82 ..      51     110 .. 0.80
   2 ?   -2.6   0.1       1.9   2.2e+03     355     381 ..     200     227 ..     197     237 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.1e-07
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE...E CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi...t 29
                                      v ViGgG AGc+A + +ar G++++++    
  gi|336255027|ref|YP_004598134.1| 52 VAVIGGGPAGCAAGVFTARYGLETIIFdrgP 82
                                      89***********************995552 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                                       SBTEEE-CGGGTB.-SHHHHHHHHHHHH CS
                              GIDA 355 vkgLflAGqinGt.eGYeEaaaqGllAG 381
                                       v+gL++AG + G     + aa+ G   +
  gi|336255027|ref|YP_004598134.1| 200 VDGLYVAGPLAGSgDQAIIAAGHGATVA 227
                                       7899999999996222233444555544 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.4   1.4e-06    0.0017       2      33 ..      52      83 ..      51      90 .. 0.93
   2 ?    1.8   0.1     0.084     1e+02     385     405 ..     193     213 ..     186     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      v ViG+G AG+aA++  a+ Gl++++ + +++
  gi|336255027|ref|YP_004598134.1| 52 VAVIGGGPAGCAAGVFTARYGLETIIFDRGPS 83
                                      89*************************99986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.084
                                       STTEEESSBTEEE-STCEESS CS
                     FAD_binding_2 385 ldadgqpipGLYAaGevaagg 405
                                       +d++ +p++GLY aG  a++g
  gi|336255027|ref|YP_004598134.1| 193 DDDGTTPVDGLYVAGPLAGSG 213
                                       567788*********999665 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 !   18.6   0.0   1.3e-06    0.0016       1      38 [.      54      91 ..      54     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                      ++G+G +G++a  + a++g++  +++++++   r+as 
  gi|336255027|ref|YP_004598134.1| 54 VIGGGPAGCAAGVFTARYGLETIIFDRGPSSLRRCASL 91
                                      8**************************99865666665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1     5e-06     0.006       2      37 ..      51      86 ..      50      90 .. 0.91
   2 ?   -1.5   0.0      0.65   7.8e+02     110     161 ..     105     156 ..      97     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37
                                       v+viGgG+AG  a +  a+ g ++++++++++ +r
  gi|336255027|ref|YP_004598134.1| 51 AVAVIGGGPAGCAAGVFTARYGLETIIFDRGPSSLR 86
                                      699***************************998877 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHHHT-EEE-S--EEEEEC.ETTE.EEEEE.TTEEEEESEEEE- CS
                       HI0933_like 110 divdallkelkeagvklrletevksvek.eedgkfrvktkseeeleadklvlA 161
                                       + +++ + ++++ag++lr +  v+sv++ e+++ fr++ +++e+++a+ +v A
  gi|336255027|ref|YP_004598134.1| 105 TFLELAQDHAEQAGCQLRNDL-VESVSRlEDGEGFRLEPQEGESVTARFVVAA 156
                                       556666777888888887653.4444331556669999977777777777665 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 !   13.0   0.0   3.7e-05     0.044       2      30 ..      54      81 ..      53      94 .. 0.89
   2 ?    0.8   0.0       0.2   2.4e+02     103     139 ..     125     163 ..     120     181 .. 0.72
   3 ?   -1.8   0.0       1.2   1.4e+03     289     305 .]     191     207 ..     182     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg 30
                                      +iG+GPaG aa++   + gle  +i ++g
  gi|336255027|ref|YP_004598134.1| 54 VIGGGPAGCAAGVFTARYGLE-TIIFDRG 81
                                      8*******************5.7899998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.2
                       Pyr_redox_3 103 eVesvkk..edegfevetsketyeAkkviiAtGefdkPn 139
                                        Vesv++  ++egf++e ++++  + + ++A+ ++d  +
  gi|336255027|ref|YP_004598134.1| 125 LVESVSRleDGEGFRLEPQEGESVTARFVVAASKYDGSY 163
                                       5899999645678****9998655555556666776555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.2
                       Pyr_redox_3 289 lteeteetnvpglflaG 305
                                       + +++  t v+gl++aG
  gi|336255027|ref|YP_004598134.1| 191 YPDDDGTTPVDGLYVAG 207
                                       66788899********9 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.2   9.6e-05      0.11       2      38 ..      52      86 ..      51      90 .. 0.87
   2 ?    2.4   0.0     0.056        67      92     140 ..     108     158 ..     103     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.6e-05
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieaspsllf 38
                                      v+viG+GpAg++  a +  a++gl+ ++ + +ps+l+
  gi|336255027|ref|YP_004598134.1| 52 VAVIGGGPAGCA--AGVFTARYGLETIIFDRGPSSLR 86
                                      89*********5..56667**************9876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.056
                     Lycopene_cycl  92 ellerlv.engvklleakvesveeeeage.slvvleggrkirarlvvdarg 140
                                       el+++ + ++g +l++  vesv   e+ge  +   ++g+ + ar+vv a+ 
  gi|336255027|ref|YP_004598134.1| 108 ELAQDHAeQAGCQLRNDLVESVSRLEDGEgFRLEPQEGESVTARFVVAASK 158
                                       5677777688999***********999662578889999********9985 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.2e-05      0.05       2      35 ..      52      85 ..      51      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v+v+GgG  g+ ++ + a++g ++ +++r++  l
  gi|336255027|ref|YP_004598134.1| 52 VAVIGGGPAGCAAGVFTARYGLETIIFDRGPSSL 85
                                      89**********99999************99887 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   2.9e-05     0.035      28      72 ..      49      93 ..      27     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-05
                                      --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTT CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslga 72
                                         v viGgG aG +A    ++ g ++ ++D  p+ l++  sl++
  gi|336255027|ref|YP_004598134.1| 49 DFAVAVIGGGPAGCAAGVFTARYGLETIIFDRGPSSLRRCASLEN 93
                                      5579*********************************99998765 PP

>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   8.2e-05     0.098      40     124 ..     223     313 ..     207     320 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.2e-05
                                       TSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE.EEEEEEEEE..EEECSGCSST...STTTEEEE..E CS
                             NUDIX  40 gEtpeeAArREleEEtGleaellellgrlhylapydgpygd.eheilyvfl..eevegelepn...denevsev..r 108
                                       g t++ +++REl+EE+G+  +    ++  +++   ++ + d e+++  +f+  ++++ ++ +    +e   +e+   
  gi|336255027|ref|YP_004598134.1| 223 GATVARTLIRELREEAGFWGKYAGHYDWRRKVENRREEWVDpERWVE-LFEesAPDDYDPITVrrlAETYADEYgsD 298
                                       668999***********866333333333334444444444566666.55534333333333356666666666433 PP

                                       EEEHHHHHHHHTHCTH CS
                             NUDIX 109 wvpleellkeklaaes 124
                                       +v+++ + +++++ ++
  gi|336255027|ref|YP_004598134.1| 299 YVEPDVA-AQRAERGQ 313
                                       7777777.55555555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   1.1      0.21   2.5e+02       2      21 ..      52      71 ..      51      78 .. 0.81
   2 ?    9.7   0.0   0.00028      0.34     153     209 ..     103     159 ..      84     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.21
                                      EEEE--SHHHHHHHHHHHHH CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalaka 21
                                      + ++GGG+aG  a    a++
  gi|336255027|ref|YP_004598134.1| 52 VAVIGGGPAGCAAGVFTARY 71
                                      89********9887776665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00028
                                       HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGG CS
                    Trp_halogenase 153 aalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGf 209
                                        + + ++ +++ae++G + +++ v++v   edg+  +l+ ++g++v a++++ +s +
  gi|336255027|ref|YP_004598134.1| 103 IETFLELAQDHAEQAGCQLRNDLVESVSRLEDGEGFRLEPQEGESVTARFVVAASKY 159
                                       5667788899******************************************99955 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   8.3e-05       0.1       2      30 ..      52      82 ..      51      91 .. 0.92
   2 ?    4.6   0.0     0.017        21     151     199 ..     109     156 ..      98     179 .. 0.74
   3 ?   -2.2   0.0         2   2.4e+03     325     347 ..     200     222 ..     190     230 .. 0.48
   4 ?   -1.0   1.1      0.83     1e+03      66      91 ..     265     289 ..     212     345 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgd 30
                                      v++iGGG +G+++  + ar g  ++++++g+
  gi|336255027|ref|YP_004598134.1| 52 VAVIGGGPAGCAAGVFTARYGleTIIFDRGP 82
                                      89**************************994 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.017
                                       HHHHHHHHTT-EEEESECEEEEEE.EETCEEEEEEECT.EEEEEEEEEEE- CS
                               DAO 151 alaraaealGveilegtevtglee.edgkvwgverttp.gendaadavVna 199
                                         ++ ae++G+++++   v+++++ edg + ++  + + ge ++a+ vV a
  gi|336255027|ref|YP_004598134.1| 109 LAQDHAEQAGCQLRND-LVESVSRlEDGEGFRL--EPQeGESVTARFVVAA 156
                                       44556**********9.9999966578899999..6665775443445554 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2
                                       EEEEEEEEECTTTHHHHHHHHHH CS
                               DAO 325 vkglylatGhsghGltlapatGk 347
                                       v+gly+a    g+G +  +a+G+
  gi|336255027|ref|YP_004598134.1| 200 VDGLYVAGPLAGSGDQAIIAAGH 222
                                       33444444333333333333332 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.83
                                       HHHHHHHHHHSSTTSEEEEEEEEEES CS
                               DAO  66 eelreleeelgididyrrtGllslaa 91 
                                       e++ el ee ++d dy++ ++  la+
  gi|336255027|ref|YP_004598134.1| 265 ERWVELFEESAPD-DYDPITVRRLAE 289
                                       4555555555554.666666666664 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.9   0.00034       0.4       9      34 ..     234     259 ..     228     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                                       HH-HHHHHHHHHCCS--SB--S-SEC CS
                            ACAS_N   9 iedpeaFWaeqakeldWekpfdkvld 34 
                                       +++ ++FW++ a + dW ++ ++  +
  gi|336255027|ref|YP_004598134.1| 234 LREEAGFWGKYAGHYDWRRKVENRRE 259
                                       56789**************9987554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2441.21
//
Query:       gi|336255028|ref|YP_004598135.1|  [L=413]
Description: Fe3+-hydroxamate ABC transporter periplasmic component-like protein [Halopiger xanaduensis SH-6]
Scores for 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-20   72.3   0.0    5.9e-20   71.9   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.012   15.4   1.2      0.024   14.5   1.2    1.5  1  TAT_signal    TAT (twin-arginine translocation) pathway signa


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 !   71.9   0.0   6.6e-24   5.9e-20       3     235 ..      87     353 ..      86     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 6.6e-24
                                       E-SHHHHHHHHHTT-GG...GEEEB-GGG--GGGGGGT........TS-BSBESSSB-HHHHHHH--SEEEE-GGG. CS
                      Peripla_BP_2   3 slspsvteillalGatd...kvvgvdtttsdpldadklee......aivevgadgeidvEklaalkPDlvilskglg 70 
                                       +++p ++++ +alG+ +    +++++ +  ++++ ++ +e      +       + ++ E+l +l+ D+ +l++++ 
  gi|336255028|ref|YP_004598135.1|  87 VTYPQYADMAVALGHGEgvnTLFSTEMAGTTMNKFYEHLEgvsfdwEGLPNPLEDGLTKEQLYELDSDVHFLDPSY- 162
                                       68999999999997665111467777777777777777744555555555555555555*****************. PP

                                       ..GGGHHHHHHHS-EEE----TTS.....................HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                      Peripla_BP_2  71 ltdedeellksgiptvivessntg.....................eslkeqiralgellgledeaeklvaeidskla 126
                                       +++++++ ++s+i+ ++   ++++                     + l e+++ ++ ++++ +++e+l a +d+ +a
  gi|336255028|ref|YP_004598135.1| 163 PVKHNDDWDESDIDEIASALGPWFgnfhsgvhsepadayaddyeyYTLWEMFERVAAVFQERERYEELKAIHDDLIA 239
                                       *******************************************999999**************************** PP

                                       HHHHTS-TT..-EEEEEEEETTE..EEEE-TTS.TTTHHHHTS--EESTTT--.STT-EEE-HHHHHHH--SEEEEE CS
                      Peripla_BP_2 127 aaksaidse.kpkpvlvfggadeggyvvagsns.yigdlldalgieniaaesk.kseyeeisaEqilasdpdvifvs 200
                                       +++s ++ e  +++++ +  +d++++++  + + ++++ ++ lg+++++ ++  ++++++i+ E++l++dpdvi+  
  gi|336255028|ref|YP_004598135.1| 240 RIESNLPPEeERPTAARVTLGDGQFFTYHLNTPgFWQAETRPLGADDALTDHDwSGDWGTIDYETMLEEDPDVILHL 316
                                       *********888888888889999988877665267888888*********************************** PP

                                       EH..HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 201 gr..aeadnktgleflkenpllaelpAvkngrVyald 235
                                       +      + + + e l+ +p+ ++l+Av+n rV+a +
  gi|336255028|ref|YP_004598135.1| 317 WGitSRYSIDNVRETLADHPVGSDLTAVQNDRVVAGG 353
                                       *9777788999**********************9875 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.2   2.6e-06     0.024       2      24 ..       9      30 ..       8      32 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                       SRR+F  ++ A++ A+ l+gca
  gi|336255028|ref|YP_004598135.1|  9 PSRRQFVATGIALGGAT-LAGCA 30
                                      69************666.66776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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 0.21s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3269.53
//
Query:       gi|336255029|ref|YP_004598136.1|  [L=256]
Description: hypothetical protein Halxa_3649 [Halopiger xanaduensis SH-6]
Scores for 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-37  128.8   4.1    4.3e-37  128.5   4.1    1.1  1  SIMPL       Protein of unknown function (DUF541)
    0.00048   19.9   4.5     0.0012   18.6   4.5    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
  ------ inclusion threshold ------
      0.063   13.8   2.1       0.45   11.0   0.1    2.4  2  OsmC        OsmC-like protein


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 !  128.5   4.1   7.2e-41   4.3e-37       1     200 []      49     250 ..      49     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 128.5 bits;  conditional E-value: 7.2e-41
                             SIMPL   1 ItVtGsaevevapDqatltlsvesegkdaaeakaevaekmnavlealkklgikekdiqtsslslkpeysyengknki 77 
                                       ItV++s+eve +pD+at++++ve++g++a+++++e+a+ +++++ a+  lgi+e++++ ++++++pe   +++  + 
  gi|336255029|ref|YP_004598136.1|  49 ITVSASGEVESEPDRATVSVGVEARGETAEDVTDELATGAEQLRRAFDDLGIPEENVEEGRYRVRPEPGPDGESEV- 124
                                       9***********************************************99**************877766666666. PP

                             SIMPL  78 tgyeasqsltvkfrdldklgevldaavka.aneingvsfslsde..delrdeareeAvkdArakAealAkalgvklg 151
                                          + ++s++v+++d +++gev+daav+a a++i+ v+fsl++e  d lr++a++eA+ +A + A  +A++ +v+l 
  gi|336255029|ref|YP_004598136.1| 125 --IRGTHSFEVTLEDVERVGEVIDAAVEAgADNIGRVNFSLQEEtrDRLRKDAIDEALTNADDEAGYIADNREVELA 199
                                       ..8999************************************6668999*********************9999999 PP

                             SIMPL 152 kvvsise......sgsnpyappapamaaaaaaaasaatpfepgeievtasVtvvf 200
                                       + +s++       +     + +   + +aa  +a+++t++ ++ ++v+asVtv++
  gi|336255029|ref|YP_004598136.1| 200 GTKSVTTgdvrvhA----VSHDVGYSGGAAEDSAAPPTEIDAEPVTVSASVTVTY 250
                                       88888775433221....222222233334448999*****************98 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   4.5   1.9e-07    0.0012       3      25 ..       4      26 ..       3      27 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-07
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggcaa 25
                                      +RR+FL +s+++ AAa++g +++
  gi|336255029|ref|YP_004598136.1|  4 NRRQFLAASGVGIAAAMAGCASS 26
                                      8***************9987765 PP

>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   7.5e-05      0.45      12      83 ..      16      90 ..      12      91 .. 0.79
   2 ?    1.8   0.2     0.057   3.4e+02      52      83 ..     146     185 ..     124     195 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.5e-05
                                      HHHHHHHHHHHHHHHHTCCCT---SCE.......EEEEEEEEECCECTCEEEEEEEEEEE-SS-H..HHHHHHHHHHHH CS
                              OsmC 12 llaalasCfaitlravakkkgikledl.......eveveaerdpegakgiteirlkvevkipgadseeklkkllekaek 83
                                      ++aa+a+C++++    a ++  + ++        +v++++e + e     ++++++v v++ g++ e+  ++l++ ae+
  gi|336255029|ref|YP_004598136.1| 16 IAAAMAGCASSASTDEAGAQSGDENSStggdreiTVSASGEVESE----PDRATVSVGVEARGETAEDVTDELATGAEQ 90
                                      68******************6655333566664466666777777....888999999999999999999998887765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.057
                                       T........CEEEEEEEEEEE-SS-H..HHHHHHHHHHHH CS
                              OsmC  52 k........giteirlkvevkipgadseeklkkllekaek 83 
                                       +         i +++++++ ++ +  +++ ++++l++a++
  gi|336255029|ref|YP_004598136.1| 146 DaaveagadNIGRVNFSLQEETRDRLRKDAIDEALTNADD 185
                                       0222222335889999999999999999999999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2102.35
//
Query:       gi|336255030|ref|YP_004598137.1|  [L=323]
Description: cysteine synthase A [Halopiger xanaduensis SH-6]
Scores for complete 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-56  192.1   6.3    1.5e-56  191.9   6.3    1.0  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 !  191.9   6.3   8.6e-61   1.5e-56       3     294 .]      23     303 ..      21     303 .. 0.91

  Alignments for each domain:
  == domain 1  score: 191.9 bits;  conditional E-value: 8.6e-61
                                       GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHH CS
                              PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaal 76 
                                         ig TPl+rl++++     +lf K E  np  S+KdR a  ++a+++++   +++ tvve++sGN+g++lAa++a+
  gi|336255030|ref|YP_004598137.1|  23 ELIGTTPLLRLDAFA----DNLFGKVEAANP-YSVKDRIAREMIAAAERAgalEPGGTVVESTSGNTGIGLAAVCAA 94 
                                       6799*********98....569*********.7*************99999************************** PP

                                       HT-EEEEEEETTS-HHHHHHHHHTT-EEEEE..CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHH CS
                              PALP  77 lGlkvtivvpadaspekvallrllGaevvev..ggdydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEi 150
                                        G+++++ +p+++s e+++ll +lGae++++  +++   a ++a+el ae ++a+l+ qf+n+++ +   +t+g+Ei
  gi|336255030|ref|YP_004598137.1|  95 RGYDCVLTMPESMSIERRQLLSALGAELELTpaEDGMGGANERAEELVAERDDAILARQFENEANPAVhRETTGPEI 171
                                       **************************9999977777***************************************** PP

                                       HHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT..-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.C CS
                              PALP 151 leqlggkpdavvvpvGgGgliaGiaaglkerrpd..vrvigvepegsdalarslragrrvtvpvsdtiadglavg.s 224
                                       ++ ++g +davv++vG+Gg+i+G++ ++ke+r+d   + ++vep++s++l +              + ++g++ g +
  gi|336255030|ref|YP_004598137.1| 172 WAATDGGVDAVVAGVGTGGTITGVSEYVKEERGDtaFTSVAVEPAESPTLSELSSD---------GHDIQGIGPGfV 239
                                       ******************************99996788889*************33.........344666666644 PP

                                       GTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 225 pselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       p +l      +l+de+ +v  ++a +a+r+l  +eg++v+ s++aal a+ +  a+e +e+  vv++l++
  gi|336255030|ref|YP_004598137.1| 240 PDVLR----TELIDEVRAVEAADAKAAARTLGLTEGLLVGISAGAALSAA-ADYAAEHPEE-LVVTVLPD 303
                                       44444....566677778********************************.9999999999.99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2755.10
//
Query:       gi|336255031|ref|YP_004598138.1|  [L=543]
Description: phosphoribosylglycinamide formyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-86  289.3   0.0    4.5e-86  289.0   0.0    1.1  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
    1.5e-35  122.5   0.0    2.9e-34  118.4   0.0    2.4  1  Formyl_trans_N   Formyl transferase
     0.0087   16.5   0.2        1.4    9.4   0.0    3.1  3  CoA_binding_2    CoA binding domain
  ------ inclusion threshold ------
       0.14   12.1   0.2       0.36   10.8   0.2    1.7  1  Toxin_25         Hefutoxin family


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 !  289.0   0.0     1e-89   4.5e-86      64     296 .]     226     471 ..     186     471 .. 0.92

  Alignments for each domain:
  == domain 1  score: 289.0 bits;  conditional E-value: 1e-89
                                       ..EEEEEEEEESSSSSTTS-EEEEE-TT..STTHHH-EEEE..SS---HHHHHHHHHHHHHHCTS..EEEEEEETTE CS
                   AICARFT_IMPCHas  64 lklslekkqkLrYGeNphQkaalyeeee..eeglakaeqlq..GkelsynNllDadaalelvkef..aavaivKHan 134
                                         +s +++ +LrYGeNphQ+aa+y++ +  e+++++a+ql+   k+lsynN++Dad al+l+kef   a+a++KH+n
  gi|336255031|ref|YP_004598138.1| 226 RLVSSDRADTLRYGENPHQDAAVYADYTcdEASVVHADQLNegAKALSYNNYNDADGALNLIKEFdePAAAVIKHTN 302
                                       456678899***************988798999******95546*********************764788****** PP

                                       EEEEEEESSHHHHHHHHHCCSHHHHTTEEEEECCEE-HHHHHHHTTS-ECEEEECEE-CCHHHCCTTSSS-EEEE-S CS
                   AICARFT_IMPCHas 135 pcGvAvgetlaeAyekAlaaDpvSaFGgiialnrevdaetaeeikkefleviiApsfeeealeilkkkknlrvlelk 211
                                       p+G+A++++la+AyekAl++Dp+SaFGgi+alnre+da+tae+i + f ev++Ap+++++ale+l +k+nlrvl++ 
  gi|336255031|ref|YP_004598138.1| 303 PAGCATADSLADAYEKALSTDPMSAFGGIVALNRECDAATAEQIVDSFKEVVVAPGYTDDALEVLFEKENLRVLDVG 379
                                       ****************************************************************************9 PP

                                       S..-.....EEEEETTEEEEEE--G..TTCCCSEEECSC---HHHHHHHHHHHHHCCCS-SS-EEEEETTEEEEEE- CS
                   AICARFT_IMPCHas 212 e..e.....elrsvsgglLvqerdeakieeeelkvvtkkkpteeeledllfawkvvkhvkSNaivlakdgqtvgiGa 281
                                       e  e     + + + gg Lvqerd ++i+ ++l++vt+++pteeele + faw+++khvkSN i++a+ ++tvgiG+
  gi|336255031|ref|YP_004598138.1| 380 ElgErterfTEKPLVGGRLVQERDLQSISVDDLEIVTEREPTEEELETMVFAWQTLKHVKSNGILFADGTETVGIGM 456
                                       965156766777899************************************************************** PP

                                       SSSSHHHHHHHHHHH CS
                   AICARFT_IMPCHas 282 GqmsRvdsarlAvek 296
                                       Gq+sRvd++rlA+ k
  gi|336255031|ref|YP_004598138.1| 457 GQVSRVDAVRLAAMK 471
                                       ************976 PP

>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4   0.0   6.6e-38   2.9e-34      15     181 .]      13     190 ..       3     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 6.6e-38
                                       HHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCTT-SEEEEES--S- CS
                    Formyl_trans_N  15 qalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkelkadlivlagymkl 91 
                                       ++ll+ +  +   a+ ++v++n ++a  le a++ +ipt+++  ++  +r+++ee++ e+l  +  dl++l gym++
  gi|336255031|ref|YP_004598138.1|  13 RNLLNIADRRPGRAELAVVLTNDEDAPVLEAAAERGIPTEIVPLEDGMSRREHEEAVLEALSDYDFDLVCLDGYMRI 89 
                                       455666666777799************************************************************** PP

                                       --HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--S...........SSSTS-EEEEEEEE-- CS
                    Formyl_trans_N  92 lpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvde...........elDtGailaqkkveii 157
                                       l+++++++ +   ln+Hp+LLP+f+G++a   aleaG+ +tG+t+h+v++           e+D G+i+ q+ +++ 
  gi|336255031|ref|YP_004598138.1|  90 LSDTFLEEAPT-TLNVHPALLPSFPGMDAWGDALEAGVSVTGCTVHVVTDatddeggvvesEVDAGPIVTQEPIPVY 165
                                       ******99999.9*********************************98764555555555579************** PP

                                       TT--HHHHHHHHHHHHH.HHHHHHH CS
                    Formyl_trans_N 158 aedtkeeleqrvadaeh.kalveal 181
                                       + d++e+l++rv  +++ +a+++a+
  gi|336255031|ref|YP_004598138.1| 166 EGDDEETLKERVLYEGEfRAYPRAV 190
                                       ************9776669999886 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.073   3.3e+02      50     101 ..      19      76 ..      11      84 .. 0.69
   2 ?    0.7   0.0      0.16   7.1e+02      72     106 ..     343     376 ..     331     379 .. 0.77
   3 !    9.4   0.0   0.00031       1.4      70     106 ..     496     533 ..     493     536 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.073
                                       T.....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT......---HHHHHHHHHT CS
                     CoA_binding_2  50 ae.dpepvdlvdvftppeatpeivkealalgakavwlqpg......sedeeaaelaeea 101
                                       a+  p+  +l++v+t+ e++p ++++a+++g+++ ++ ++      + +e+++e++ ++
  gi|336255031|ref|YP_004598138.1|  19 ADrRPGRAELAVVLTNDEDAP-VLEAAAERGIPTEIVPLEdgmsrrEHEEAVLEALSDY 76 
                                       543378888999999999876.7888888887776666665677665666666666555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                                       HHHHHHH--SEEEE-TT---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  72 vkealalgakavwlqpgsedeeaaelaeeagirvv 106
                                       +++++    k v++ pg  d+++  l e++++rv+
  gi|336255031|ref|YP_004598138.1| 343 AEQIV-DSFKEVVVAPGYTDDALEVLFEKENLRVL 376
                                       34443.34899********************9998 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00031
                                       GGHHHHHHH--SEEEE-TT..---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  70 eivkealalgakavwlqpg..sedeeaaelaeeagirvv 106
                                       + ++ea+++g++av+ qpg  + de+++e+a+e+g+ +v
  gi|336255031|ref|YP_004598138.1| 496 DGIEEAAEVGIEAVI-QPGgsVNDEDVIEAADEHGMAMV 533
                                       56899******9987.5555778899**********987 PP

>> Toxin_25  Hefutoxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2     8e-05      0.36      11      21 ..     166     176 ..     165     177 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8e-05
                          Toxin_25  11 EGNDEETCKER 21 
                                       EG DEET KER
  gi|336255031|ref|YP_004598138.1| 166 EGDDEETLKER 176
                                       9*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3971.50
//
Query:       gi|336255032|ref|YP_004598139.1|  [L=465]
Description: adenylosuccinate lyase [Halopiger xanaduensis SH-6]
Scores for 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  174.6   0.0    4.2e-51  174.2   0.0    1.1  1  Lyase_1   Lyase
    6.2e-42  142.3   0.0    1.1e-41  141.6   0.0    1.4  1  ASL_C     Adenylosuccinate lyase C-terminal
  ------ inclusion threshold ------
        0.2   11.6   1.5         25    4.9   0.0    2.9  2  DUF3944   Domain of unknown function (DUF3944)


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 !  174.2   0.0     7e-55   4.2e-51       2     307 ..      16     320 ..      15     324 .. 0.89

  Alignments for each domain:
  == domain 1  score: 174.2 bits;  conditional E-value: 7e-55
                                       EEEEETCHHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSS CS
                           Lyase_1   2 rftvkadklmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqeg 78 
                                       r++  + +l    +e +++++r+      +++ +  a+a +++ + e+  +  + l+ + e + ++d++ +k+ +++
  gi|336255032|ref|YP_004598139.1|  16 RYSSRTAPLSPYASEAALMRARVR-----VEVEYLLALADLEATPLEIDTDEREHLRGLYEHFAQKDAQLIKKLETE 87 
                                       666666666666677777777777.....67778888899999988999999999********************** PP

                                       HHHHHHHHHHHHHH..HHTT.....HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHH CS
                           Lyase_1  79 sgtavnmnlnevig..ellg.....ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekake 148
                                        +  +++ +n  ++  e+       e  +++ ++h+g +s+D++++a+rl+++ a++e+Llpal + +dal e a+ 
  gi|336255032|ref|YP_004598139.1|  88 GHAGFEA-TNHDVKavEYFVrhrlpEGSDASAWIHFGLTSEDVNNLAHRLLVRGAIDEVLLPALYDVRDALAEMARD 163
                                       ******9.55555536554478888999************************************************* PP

                                       TTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHH.. CS
                           Lyase_1 149 fkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakela.. 223
                                       ++dv+++ rTh+q+AtP+t+g+e++ ya  l r   r+++++   l ++lgg++++++++ a+++   + ++ +a  
  gi|336255032|ref|YP_004598139.1| 164 YRDVPMLARTHGQPATPTTFGKEMAVYASRLGRATGRIRRAT-DALSGKLGGASGTYAAHVAAYP--DVDWQAFAee 237
                                       ******************************************.9****************99997..7777777765 PP

                                       .HHHCSTEESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHH CS
                           Lyase_1 224 .kvtglpvkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvq 299
                                          +gl+   ++ +++v+++D+++ +++a +  +  + +++ D++l+ s   ++  ++  e+e GSS+MP+KvNP++
  gi|336255032|ref|YP_004598139.1| 238 fVTEGLGLEFEPLTTQVNPCDDLAAVFDAFRGANNVILDLDLDVWLYVS--DRYLGQEAVEGETGSSTMPHKVNPID 312
                                       336788899999999**********************************..8899999999999************* PP

                                       HHHHHHHH CS
                           Lyase_1 300 lElltgva 307
                                       +E+  g +
  gi|336255032|ref|YP_004598139.1| 313 FENSEGNL 320
                                       **987755 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6   0.0   1.8e-45   1.1e-41       1     115 []     337     451 ..     337     451 .. 0.99

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 1.8e-45
                                       -STT--TCHHHHHTTCHHHHHHHHHHHHHHHHHHCCEEE-HHHHHHHHHT-GGGGHHHHHHHHHHTT-TTHHHHHHH CS
                             ASL_C   1 SrlQRDLtdStvlRnlgvalahslialksllkglsklevneealaedLdenwevlaEaiqtvlrregiekpYeklke 77 
                                       SrlQRDL+dStv+Rn+g+a+ah+li++ +++ gl+k+  ne++++edL++++e+++Ea+qt+lrreg e++Ye++k+
  gi|336255032|ref|YP_004598139.1| 337 SRLQRDLSDSTVKRNIGAAFAHCLIGYGKTQAGLEKVVPNEKVMREDLESTPEIIGEAVQTILRREGQEDAYEQVKA 413
                                       9**************************************************************************** PP

                                       HHTTS---HHHHHHHHHCS-S-HHHHHHHHC--CCC-- CS
                             ASL_C  78 ltrgkkitkeslkefieslevseeakeeLkaltpatYi 115
                                       ltrgk++t +++++++++l v+e+++eeL++ltpa Y+
  gi|336255032|ref|YP_004598139.1| 414 LTRGKDVTLADFRDLFDDLVVDEDVREELRNLTPAGYT 451
                                       ************************************97 PP

>> DUF3944  Domain of unknown function (DUF3944)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0041        25      15      26 ..     324     335 ..     321     338 .. 0.82
   2 ?    4.3   0.6    0.0062        37      16      30 ..     423     437 ..     418     439 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0041
                           DUF3944  15 sedLedLfdiLt 26 
                                       ++dLe L+d++t
  gi|336255032|ref|YP_004598139.1| 324 NSDLEFLADYIT 335
                                       788888988888 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0062
                           DUF3944  16 edLedLfdiLthdkd 30 
                                       +d +dLfd L+ d+d
  gi|336255032|ref|YP_004598139.1| 423 ADFRDLFDDLVVDED 437
                                       799**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); 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:                         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 0.23s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3664.56
//
Query:       gi|336255033|ref|YP_004598140.1|  [L=140]
Description: hypothetical protein Halxa_3653 [Halopiger xanaduensis SH-6]
Scores for 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-10   39.9  15.4    4.6e-10   39.8  15.4    1.0  1  EamA             EamA-like transporter family
     0.0045   16.4   2.7     0.0056   16.0   2.5    1.4  1  Sugar_transport  Sugar transport protein
  ------ inclusion threshold ------
      0.058   12.5   3.2      0.069   12.3   2.6    1.3  1  Mg_trans_NIPA    Magnesium transporter NIPA
        5.1    6.0   5.1          2    7.3   0.4    1.9  2  Chloroplast_duf  Petal formation-expressed


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 !   39.8  15.4     1e-13   4.6e-10       4     135 ..       4     135 ..       1     137 [. 0.94

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1e-13
                              EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80 
                                       +l++++a l+++++++l+  + ++v+p  ++f++++i   + + ++l+++   +    ++ + +++++ l    + l
  gi|336255033|ref|YP_004598140.1|   4 LLWVVVAFLTYGLMAPLTSSVTEDVPPAVALFLSTVIFLCATSGVLLVTGTGTPADAASPAAGYVYVAGLFLSTGIL 80 
                                       689***********************************************99945555558888999999999**** PP

                              EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       ++++al+ +++s++++i  l  v + + ++++lge lt +  +gi+++ l+++l 
  gi|336255033|ref|YP_004598140.1|  81 AYYQALEIGPVSTVVPIYGLFIVGSSLVGIAFLGEELTATRAAGIGVAALAIYLA 135
                                       ****************************************************986 PP

>> Sugar_transport  Sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   2.5   1.3e-06    0.0056      58     124 ..      68     134 ..       8     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-06
                   Sugar_transport  58 slisGllWaigqllqfkalklvgvskamPistglqLvgasLigvlvlgeW.stsiqvilGllaliliv 124
                                         ++Gl+ + g l  ++al++  vs   Pi  gl +vg+sL+g+ +lge  + + +  +G++al++ +
  gi|336255033|ref|YP_004598140.1|  68 VYVAGLFLSTGILAYYQALEIGPVSTVVPIY-GLFIVGSSLVGIAFLGEElTATRAAGIGVAALAIYL 134
                                       5699**************************5.999*********999875155566779**9998754 PP

>> Mg_trans_NIPA  Magnesium transporter NIPA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.6   1.5e-05     0.069      51     112 ..      68     128 ..      59     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                     Mg_trans_NIPA  51 lWwaGlltmavGeaanfaayafaPatLvtPLGalsvivsavlasllLkekLkllgllGclla 112
                                       ++ aGl  +++G  a + a  + P++ v P+  l ++ s+++   +L e+L ++   G+ +a
  gi|336255033|ref|YP_004598140.1|  68 VYVAGLF-LSTGILAYYQALEIGPVSTVVPIYGLFIVGSSLVGIAFLGEELTATRAAGIGVA 128
                                       5677865.57899**************************************99988887655 PP

>> Chloroplast_duf  Petal formation-expressed
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4   0.00045         2      37      81 ..      10      55 ..       3      63 .. 0.81
   2 ?    0.9   0.5      0.04   1.8e+02     214     251 ..      94     131 ..      83     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00045
                   Chloroplast_duf 37 itltaavmaglaaasss.gapllalklsstlllaaatgllavvnki 81
                                        lt + ma l+++ ++   p +al ls+ ++l+a++g+l+v    
  gi|336255033|ref|YP_004598140.1| 10 AFLTYGLMAPLTSSVTEdVPPAVALFLSTVIFLCATSGVLLVTGTG 55
                                      5689999****999888567899****9999999999999987665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.04
                   Chloroplast_duf 214 ilaiagPlltgiaavgsafvgsaengswaaivavlaga 251
                                       ++ i g ++ g + vg af+g++ +++ aa ++v+a a
  gi|336255033|ref|YP_004598140.1|  94 VVPIYGLFIVGSSLVGIAFLGEELTATRAAGIGVAALA 131
                                       55677778888888999999988877777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); 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:                         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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1163.15
//
Query:       gi|336255034|ref|YP_004598141.1|  [L=138]
Description: hypothetical protein Halxa_3654 [Halopiger xanaduensis SH-6]
Scores for 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-08   33.8  13.5    5.2e-08   33.1  13.5    1.3  1  EamA             EamA-like transporter family
    0.00087   18.7   4.1     0.0011   18.4   4.1    1.1  1  Sugar_transport  Sugar transport protein
  ------ inclusion threshold ------
       0.23   12.1   9.3       0.51   11.0   3.1    2.2  2  Multi_Drug_Res   Small Multidrug Resistance protein
          1    9.2  14.6        2.7    7.8   3.3    2.0  2  7TMR-DISM_7TM    7TM diverse intracellular signalling


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 !   33.1  13.5   1.2e-11   5.2e-08       5     136 ..       6     137 ..       2     138 .] 0.91

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.2e-11
                              EamA   5 llallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvlafl 80 
                                        l ++a+l +++ ++l  i+++++++  ++f++  +  +++ +++++++ +  + l++     l+ +g+l +v + l
  gi|336255034|ref|YP_004598141.1|   6 SLSIVACLAYSLVAPLLSIAMTDLPSTVAVFLSNSVMLVVVGLVIVYRGLPVrRYLRHPRTPHLVAMGVLLSV-GLL 81 
                                       6789***************************999999999999999999999666677778888888877665.559 PP

                              EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        ++ al+ +++s++++i  l  v++ + +++ + e++t +++++i+l++++++l++
  gi|336255034|ref|YP_004598141.1|  82 TYYRALELGPVSVVVPIYGLFIVVSSLVGIVAFDETVTPRKVAAIGLSVVAIALMS 137
                                       ******************************************************97 PP

>> Sugar_transport  Sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   4.1   2.4e-07    0.0011     153     272 ..       6     134 ..       2     138 .] 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.4e-07
                   Sugar_transport 153 llstigyviyvvlaqlvkv......dgleailpqaiGmvivalilalakkk...alvekvslkniisGllwaignlf 220
                                        ls +  ++y+ +a l+++      ++++++l  ++ +v+v+l++ +        l++ ++ + +  G+l ++g l+
  gi|336255034|ref|YP_004598141.1|   6 SLSIVACLAYSLVAPLLSIamtdlpSTVAVFLSNSVMLVVVGLVIVYRGLPvrrYLRHPRTPHLVAMGVLLSVGLLT 82 
                                       5566666666666666644222223578899***********9999988766645667778888889********** PP

                   Sugar_transport 221 lllsaqkvGvatafslsqlsvvistlggillLkekktkkelvlviiGivlil 272
                                       +  + +   v++   +  l +v+s l gi+ + e+ t +++ ++   +v i 
  gi|336255034|ref|YP_004598141.1|  83 YYRALELGPVSVVVPIYGLFIVVSSLVGIVAFDETVTPRKVAAIGLSVVAIA 134
                                       ******999*******************************999988888775 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 ?    3.8   2.1     0.021        94      29      59 ..       5      35 ..       1      58 [. 0.74
   2 ?   11.0   3.1   0.00011      0.51      35      92 ..      70     128 ..      40     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.021
                                      -----HHHHHHHHHHHHHHHHH-------HH CS
                    Multi_Drug_Res 29 ltpsllvivgygisfllLskalkslpvsvAY 59
                                      l +s+++ ++y++   lLs a+  lp  vA 
  gi|336255034|ref|YP_004598141.1|  5 LSLSIVACLAYSLVAPLLSIAMTDLPSTVAV 35
                                      4567777778999999**********99974 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHH..HH-------HHHHHHHHHHHHHHHHHHHHH--------HHHHHH CS
                    Multi_Drug_Res  35 vivgygisfllLsk..alkslpvsvAYavwsGiGtvlivlvgillfgeslslkkliglal 92 
                                       v +g+++s+ lL++  al+  pvsv+ +++ G+ +v+ +lvgi+ f+e++   k++ ++l
  gi|336255034|ref|YP_004598141.1|  70 VAMGVLLSVGLLTYyrALELGPVSVVVPIY-GLFIVVSSLVGIVAFDETVTPRKVAAIGL 128
                                       34467777777764339999*********8.899********************999876 PP

>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8  14.6      0.01        46      95     195 ..       3     109 ..       1     114 [. 0.73
   2 ?    7.8   3.3    0.0006       2.7     100     166 ..      69     135 ..      57     138 .] 0.67

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.01
                     7TMR-DISM_7TM  95 rllklllllavllsllllllpllpyteslslaqllallvillllligikawrkgnkparyf.......liawlllli 164
                                       r+l l ++ ++++sl++ ll++ +++  +++  ++ l+ +++l+++g++++++g +  ry+       l+a+ +ll 
  gi|336255034|ref|YP_004598141.1|   3 RYLSLSIVACLAYSLVAPLLSIAMTDLPSTV--AVFLSNSVMLVVVGLVIVYRGLPVRRYLrhprtphLVAMGVLLS 77 
                                       5677788888888888888555555544444..68888888999999999999988888876666666899999999 PP

                     7TMR-DISM_7TM 165 gvlidilsllgllpsn.ffteyllqigvllev 195
                                        +l++ +++l l p++ +++ y+l i v   v
  gi|336255034|ref|YP_004598141.1|  78 VGLLTYYRALELGPVSvVVPIYGLFIVVSSLV 109
                                       99999999999999996666688877555544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0006
                     7TMR-DISM_7TM 100 llllavllsllllllpllpyteslslaqllallvillllligikawrkgnkparyfliawlllligv 166
                                       l+++ vlls+ ll+    ++   +s++  ++ l+i+++ l+gi+a+ +   p +  +i++++++i+ 
  gi|336255034|ref|YP_004598141.1|  69 LVAMGVLLSVGLLTYYRALELGPVSVVVPIYGLFIVVSSLVGIVAFDETVTPRKVAAIGLSVVAIAL 135
                                       22333333333333333356666666779999999999******99999999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1133.48
//
Query:       gi|336255035|ref|YP_004598142.1|  [L=378]
Description: peptidase M20 [Halopiger xanaduensis SH-6]
Scores for complete 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-24   86.9   0.0    4.1e-24   85.5   0.0    1.8  2  Peptidase_M20  Peptidase family M20/M25/M40
    8.9e-18   64.2   0.0    1.6e-17   63.4   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain


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 ?   -2.4   0.0      0.35   3.2e+03     125     154 ..      20      48 ..      12      58 .. 0.71
   2 !   85.5   0.0   4.5e-28   4.1e-24       2     206 ..      77     374 ..      76     375 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.35
                                       ESHEEECCHHHHHHHHHHHHHHHTSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 125 gapvtlndsplvkalaeaaeelfgekveli 154
                                       g p + + s++++++ e+++++ g+++e+ 
  gi|336255035|ref|YP_004598142.1|  20 GTPSHEDVSEMRELVCETLRDA-GLEPEVD 48 
                                       5566666889999999999997.9876665 PP

  == domain 2  score: 85.5 bits;  conditional E-value: 4.5e-28
                                       EEEES-BSSTTCGGGSSSTTSEEETTT.EEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVpeeetdgwttpfslteedG.klyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgG 77 
                                       l+ H+D+V          p+ + e+dG ++ GrGa+d kg ++a+l+a+ +++ +     g ++l++++dEE+ + G
  gi|336255035|ref|YP_004598142.1|  77 LNTHMDTVA---------PHVPYERDGdVVRGRGACDAKGPLAALLAAFLRVEPT----AGRVTLAITYDEETLMTG 140
                                       899******.........7777777788*********************887777....89***********87789 PP

                                       HHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE....................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................... RF
                     Peptidase_M20  78 akallegleerekvdavfelhieepgileagklaigvv....................................... 115
                                       a+ l e l     +d+++   ++ep++l+       v+                                       
  gi|336255035|ref|YP_004598142.1| 141 AAGLQETLA--PSADGFV---VGEPTNLD-------VCiaargqcegtvtirgegghaaqvpaernavfglasvlea 205
                                       988888443..5677755...********.......444588899******************************** PP

                                       ..........................................................................EEE CS
                                       ..........................................................................xxx RF
                     Peptidase_M20 116 ..........................................................................kve 118
                                                                                                                 +v+
  gi|336255035|ref|YP_004598142.1| 206 lrryddesgpdedevlgapkltatmleggeapnrvpeactvtfdrrsvppetadsfradleaylkaqdrvpdglEVS 282
                                       *************************************************************************9788 PP

                                       EEEE....EEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH.TTTEEEEEEESS...G...GCTT CS
                                       xxxx....xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx...x...xxxx RF
                     Peptidase_M20 119 vell....eggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff.agiptvmifgpg...s...glaH 183
                                       v+l+       +p++++ d++lv++l++a     g   ++ + g ++t+a+ff a  ptv +fgpg   +   g aH
  gi|336255035|ref|YP_004598142.1| 283 VDLIrpdtPFPKPFVTDaDDRLVRTLRDAS----G--GDVRPFG-AATEAGFFaADAPTV-VFGPGvleDdegGVAH 351
                                       887754545555778889999999999993....6..3566789.********6666999.588887642789**** PP

                                       STTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 184 spnEyvdledlekgikvlarlle 206
                                       s+ Eyv+l+d+++++++l+++l 
  gi|336255035|ref|YP_004598142.1| 352 SEREYVRLPDVRAAADALEKTLV 374
                                       ******************99885 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   1.8e-21   1.6e-17       2     104 ..     168     272 ..     167     275 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 1.8e-21
                                       EB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.......TCCTCCCCCEECCE-CCCCEESSEE CS
                         M20_dimer   2 ghkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia..eerslprttlnvtgiegGsaknvipdea 76 
                                       + +G ++g++t++g++gH++   a +NA+  la +l++l+  +++ +  e++ l+ + l+ t++egG a+n +p+ +
  gi|336255035|ref|YP_004598142.1| 168 AARGQCEGTVTIRGEGGHAAQVPAERNAVFGLASVLEALRRYDDESGpdEDEVLGAPKLTATMLEGGEAPNRVPEAC 244
                                       789*****************999999****************99888****************************** PP

                                       EEEEEEEHHHHHHHHHHHHHHHHHHTSC CS
                         M20_dimer  77 eakidiRllpgedpeevleeieeileke 104
                                       ++++d+R +p e++++ ++++e++l+++
  gi|336255035|ref|YP_004598142.1| 245 TVTFDRRSVPPETADSFRADLEAYLKAQ 272
                                       *************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 3098.81
//
Query:       gi|336255036|ref|YP_004598143.1|  [L=417]
Description: diaminopimelate decarboxylase [Halopiger xanaduensis SH-6]
Scores for 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-41  140.9   0.0    5.3e-41  140.6   0.0    1.1  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    9.1e-21   73.9   0.0      1e-20   73.7   0.0    1.3  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina
    2.1e-07   30.8   0.0    3.4e-07   30.1   0.0    1.4  1  Ala_racemase_N   Alanine racemase, N-terminal domain


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 !  140.6   0.0   8.9e-45   5.3e-41       2     247 .]      38     279 ..      37     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: 140.6 bits;  conditional E-value: 8.9e-45
                                       HHHHHHHHHHHHHCTCCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHHH CS
                     Orn_Arg_deC_N   2 asierklkrwkkalprikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqreelry 78 
                                       ++++++++r+  a+p+++v+Ya Ka++ +avle + e G  ++ca  +El++++ ag++p++  +++ +    +l y
  gi|336255036|ref|YP_004598143.1|  38 DRVKENYSRFSAAFPDAHVMYAAKAHTGKAVLEAVLEAGGTIECAAWGELQRAIDAGADPNELQYTAVNPPDHDLDY 114
                                       7899************************************************************************* PP

                                       HHHCTHT....EEEESSHHHHHHHHHHHCCEEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHHHTT CS
                     Orn_Arg_deC_N  79 alekgvk....vvtvdnveeleklaklapeakvllRiktdvsaatcelistggessKFGaaleeavealleaakeen 151
                                       a++   +     +t++  + l++la+   + ++ +Ri++++ ++++e ++tg  + KFG+ + e v+ + +  + e+
  gi|336255036|ref|YP_004598143.1| 115 AADLATEhpglTITIGATDTLDRLAERGYDGRIAIRINPGIGTGHHEKVATGA-DAKFGIPY-ERVPDVADRVR-EE 188
                                       **9999988889************************************88886.79******.88888888776.56 PP

                                       EEEEEEE---BSSC-SCHHHHHHHHHHHHHHHHHHHHT-.--SEEE--S-BS-HCSTTSSSSTHHHHHHHHHHHHHH CS
                     Orn_Arg_deC_N 152 lqlvGvsfHvGSgvsdleafvkavekalklfdelaelGv.klkiLdvGGGfgveyeeeeeplkleeiaekirealee 227
                                        +lvG++ H GSgv  + ++ ++ + + ++ d+++ +G  +l+++dvGGG+gv y+e+e pl+le+    +rea+++
  gi|336255036|ref|YP_004598143.1| 189 FDLVGIHAHAGSGVL-TDDLEDHCRAISRVGDMARRVGDaDLEFVDVGGGYGVPYREDEAPLDLEKTSDMVREAVGD 264
                                       89************9.999999999999*******999659**********************************77 PP

                                       HHHTSSS-EEEE--SHHHHG CS
                     Orn_Arg_deC_N 228 afpgdkevtiiaEpGRalva 247
                                       +     + ++ +EpGR++va
  gi|336255036|ref|YP_004598143.1| 265 L-----DAQLKLEPGRYIVA 279
                                       6.....67899*******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 !   73.7   0.0   1.8e-24     1e-20       5      98 .]     203     368 ..      32     368 .. 0.66

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.8e-24
                                       E............................................................................ CS
                                       x............................................................................ RF
                   Orn_DAP_Arg_deC   5 d............................................................................ 5  
                                                                                                                    
  gi|336255036|ref|YP_004598143.1| 203 Ltddledhcraisrvgdmarrvgdadlefvdvgggygvpyredeapldlektsdmvreavgdldaqlklepgryiva 279
                                       05555555555555555555555555555555555555555555555555555566666666666666666666666 PP

                                       GGEEEEEEEEEEEEETCEEEEEES--TTTS-HHHHCTT-S-E.ESBTT-SCEEC.EEEEEEEE-SSSSTT-EEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC   6 eagvLvtrViavkesekkkfvivdaGmndllrpalygsfhei.pvkeeeaekeeeeeeevdvvGptCesgDvlakdr 81 
                                       +ag+++++V+++ke  ++++v +da++++l+rpa++gs+h++ +v++++     +e +ev+v Gp+C+s+Dv+a+dr
  gi|336255036|ref|YP_004598143.1| 280 DAGLILSEVNTIKEAPDTTVVGIDASLATLIRPAMFGSYHPMlNVSSPD-----REPREVTVGGPVCTSADVFAHDR 351
                                       9***************99************************8886433.....34567****************** PP

                                       EEEE--TT-EEEESS-S CS
                                       xxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC  82 elpelevGdllafedaG 98 
                                        + ++e+ d++a+ +aG
  gi|336255036|ref|YP_004598143.1| 352 PIARPEREDVIAIGNAG 368
                                       ***************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 !   30.1   0.0   5.7e-11   3.4e-07       2     161 ..      36     206 ..      35     259 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 5.7e-11
                                       EHHHHHHHHHHHHHHSCTTSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTSCSEEEEESCST CS
                    Ala_racemase_N   2 dldalrhNlrrlralagpgaklmavvKanayghgavevaralaeggadgfgvatleEalelreagitapilvlegfs 78 
                                       dld++++N++r++a++ p+a++m   Ka + g  ++e++  +  g +++ +   l+ a+   +   + +   +++ +
  gi|336255036|ref|YP_004598143.1|  36 DLDRVKENYSRFSAAF-PDAHVMYAAKA-HTGKAVLEAVLEAG-GTIECAAWGELQRAIDAGADPNELQYTAVNP-P 108
                                       9***************.9999*******.55555555555344.6688888888888885555533444444444.4 PP

                                       GGGHHHHHH....T.TEEEEESSHHHHHHHHHHHHHTTS-EEEEEEBESSSS.........SSSBSCHHHHHHHHHH CS
                    Ala_racemase_N  79 peelaalae....y.dltvtvdsleqlealaaaareagkplrvhlkidtgmg.........RlGftpeeleelleal 141
                                         +l+ +a+    + +lt+t+   + l++la+   + +  +r+   i tg +         + G++ e ++++++++
  gi|336255036|ref|YP_004598143.1| 109 DHDLDYAADlateHpGLTITIGATDTLDRLAERGYDGRIAIRINPGIGTGHHekvatgadaKFGIPYERVPDVADRV 185
                                       444444444444667******************998666666655555665577766777***************** PP

                                       HHTTTEEEEEEE-S-SST...TS CS
                    Ala_racemase_N 142 aalpglrleglmtHfasa...de 161
                                       ++  +++l+g+  H +s    d+
  gi|336255036|ref|YP_004598143.1| 186 RE--EFDLVGIHAHAGSGvltDD 206
                                       97..69********999744433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.34
# Mc/sec: 3662.92
//
Query:       gi|336255037|ref|YP_004598144.1|  [L=146]
Description: hypothetical protein Halxa_3657 [Halopiger xanaduensis SH-6]
Scores for 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:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1119.27
//
Query:       gi|336255038|ref|YP_004598145.1|  [L=278]
Description: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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   86.0   1.5    2.4e-24   85.3   1.5    1.3  1  THDPS_N_2  Tetrahydrodipicolinate N-succinyltransferase N-ter
      2e-12   46.3   5.8      6e-05   22.6   0.4    3.4  3  Hexapep    Bacterial transferase hexapeptide (six repeats)
    4.5e-07   29.5  11.0      4e-06   26.5   1.0    3.2  3  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> THDPS_N_2  Tetrahydrodipicolinate N-succinyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   1.5     4e-28   2.4e-24       2      67 .]       4      71 ..       3      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 4e-28
                                      HHHHHHHHHHTGGG--.S.SS--HHHHHHHHHHHHHHHTTSS-SEEEETTEEEE-HHHHHHHHHHHHH CS
                         THDPS_N_2  2 LesdIeaawerrdele.p.etagaearaaveevleaLdaGelRvAekkdgeWevneWvKkAiLLsFrl 67
                                      Les++ ++w+r+++ + + e+ag++++a+++++leaL++Ge+R+Aek++geWe+neWvK++iLL+F+l
  gi|336255038|ref|YP_004598145.1|  4 LESEVSELWDRYQNDDvDaESAGEDEYATIDAFLEALEDGEVRAAEKRNGEWEANEWVKQGILLNFGL 71
                                      89***********99986799*********************************************97 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0039        23       6      21 ..     106     121 ..     103     123 .. 0.83
   2 !   19.6   0.8   9.2e-08   0.00055       2      36 .]     132     166 ..     131     166 .. 0.91
   3 !   22.6   0.4     1e-08     6e-05       2      35 ..     176     209 ..     175     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0039
                                       TTEEE-TTEEEETTEE CS
                           Hexapep   6 snvlIgpfaviggnVk 21 
                                       ++++I+ +a++g++++
  gi|336255038|ref|YP_004598145.1| 106 DGTTIRRGAYLGSDCI 121
                                       7889999999999986 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 9.2e-08
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       + +G+++l+++  ++g+ ++IG+nvk+ga++ igg
  gi|336255038|ref|YP_004598145.1| 132 AYVGDGTLVDSCDTVGSCAQIGENVKLGANTLIGG 166
                                       7899999999999999***************9997 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 1e-08
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       ++I++nv +g+++ + ++ ++G+n+++g+++ ++
  gi|336255038|ref|YP_004598145.1| 176 VIIEDNVSLGAGCRVTSGFVVGENSVVGENTLLT 209
                                       79****************************9876 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 ?   -0.3   0.1      0.15     9e+02      11      15 ..     117     121 ..     107     142 .. 0.56
   2 !    8.3   0.4   0.00032       1.9       4      17 ..     152     165 ..     147     168 .. 0.73
   3 !   26.5   1.0   6.7e-10     4e-06       1      33 [.     175     209 ..     175     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                                       -TT-E CS
                         Hexapep_2  11 Ganag 15 
                                       G++++
  gi|336255038|ref|YP_004598145.1| 117 GSDCI 121
                                       33333 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00032
                                       E-TT-EE-TT-EES CS
                         Hexapep_2   4 IGdnCliGanagiG 17 
                                       IG+n+ +Gan  iG
  gi|336255038|ref|YP_004598145.1| 152 IGENVKLGANTLIG 165
                                       77777777777773 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 6.7e-10
                                       .EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
                         Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvgaGvvit 33 
                                       pviI+dn+ +Ga + +  G  +G+n+vvg +  +t
  gi|336255038|ref|YP_004598145.1| 175 PVIIEDNVSLGAGCRVtsGFVVGENSVVGENTLLT 209
                                       8**************88************999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2162.33
//
Query:       gi|336255039|ref|YP_004598146.1|  [L=255]
Description: dihydrodipicolinate reductase [Halopiger xanaduensis SH-6]
Scores for complete 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  125.4   0.0    1.6e-36  124.9   0.0    1.2  1  DapB_C           Dihydrodipicolinate reductase, C-terminus
    2.5e-30  105.1   0.0    7.5e-30  103.6   0.0    1.7  2  DapB_N           Dihydrodipicolinate reductase, N-terminus
    1.9e-06   28.1   0.3    1.6e-05   25.2   0.1    2.5  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      5e-05   23.9   0.1    9.8e-05   23.0   0.1    1.4  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    0.00048   20.9   0.0    0.00086   20.1   0.0    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    0.00086   19.7   0.0     0.0014   19.1   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    0.00089   18.8   0.1     0.0033   16.9   0.0    1.9  2  Epimerase        NAD dependent epimerase/dehydratase family
     0.0011   19.7   0.1     0.0025   18.4   0.1    1.6  1  CoA_binding      CoA binding domain
     0.0025   18.3   0.1     0.0045   17.5   0.1    1.5  1  CoA_binding_2    CoA binding domain
     0.0036   16.5   0.0     0.0074   15.4   0.0    1.4  1  RmlD_sub_bind    RmlD substrate binding domain
      0.004   16.7   0.0     0.0085   15.7   0.0    1.6  1  NmrA             NmrA-like family
     0.0083   16.1   0.2      0.015   15.3   0.2    1.6  1  ADH_zinc_N       Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.022   14.7   0.9      0.044   13.7   0.3    1.9  2  NAD_binding_10   NAD(P)H-binding
       0.14   12.5   0.4       0.46   10.8   0.0    2.0  2  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA


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 !  124.9   0.0   1.3e-39   1.6e-36       1     121 []     122     253 ..     122     253 .. 0.93

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 1.3e-39
                                       HHHHHHHHHHHHCCCSTTT-EEEEEEEESTT--SSS-HHHHHHHHHHH..................-S-ETTCCCEE CS
                            DapB_C   1 GvnlllklveeaakllkeaydveiiEkHhnkKaDaPSGTAlalaeaia.........egke.....arkkkeigihs 63 
                                       Gv+ l+++v +a + l++ ydve++E+Hhn K DaPSGTA +l+e+i+         +        +r+++eig+h 
  gi|336255039|ref|YP_004598146.1| 122 GVQALVNVVGDAVQSLEG-YDVELVETHHNGKRDAPSGTANRLLEEIEangdfkdrkH--GregfdPREEGEIGVHV 195
                                       8999************99.*****************************8888776552..0557769********** PP

                                       EETTT--CCCCEEEECTTEEEEEEEEEESCHHHHHHHHHHHHHH.HCTSSEESHHHHH CS
                            DapB_C  64 vRgggvvgehevlfagegevieikhealsreiFaeGallaaewlakkkkglysmedvL 121
                                       +R+g+++gehe+++ag++e ++++h+a++r +Fa Ga++aa wla++++g y++ dv+
  gi|336255039|ref|YP_004598146.1| 196 LRAGDITGEHEIVIAGNHEEVRLTHRAEDRGVFAAGAVDAAVWLAEREPGSYDFADVI 253
                                       ********************************************************95 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.6   0.0   5.8e-33   7.5e-30       2     124 .]       4     119 ..       3     119 .. 0.92
   2 ?   -1.8   0.0       2.4   3.1e+03      10      36 ..     189     215 ..     188     249 .. 0.69

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 5.8e-33
                                       EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH..-SEEEE-S- CS
                            DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek..advliDFTt 76 
                                       +++v+Ga+GrmG+ev+ av e+ed+e++ av+r++      d  ++     ++v+  +++++++++   d +iDFT 
  gi|336255039|ref|YP_004598146.1|   4 RIGVTGATGRMGREVIAAVAEREDCEVAFAVNRDP------DDDNV---AGVDVQPAAEFDALVADrePDAVIDFTG 71 
                                       8*********************************9......22223...3468888899999999989********* PP

                                       HHHHHHHHHHHHHTT-EEEE--SS--HHHHHHHHHHTTTSEEEE-S-- CS
                            DapB_N  77 peavlenlklalekgvklViGTTGlseeelaeleelakkigvviapNf 124
                                       pe++le++++++e+gv++V GTTG++++++++l++++++i+v+ apNf
  gi|336255039|ref|YP_004598146.1|  72 PESALEYVRACAEAGVPFVTGTTGFDDDQRETLQAASDEIPVLHAPNF 119
                                       ***********************************************9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.4
                                       SHHHHHHHHHHHHSTTEEEEEEEETTC CS
                            DapB_N  10 GrmGkevvkaveeaedlelvaavdrke 36 
                                       G +G +v++a + + ++e+v a +++e
  gi|336255039|ref|YP_004598146.1| 189 GEIGVHVLRAGDITGEHEIVIAGNHEE 215
                                       777888888877777777777766665 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 !   25.2   0.1   1.3e-08   1.6e-05       3     119 ..       7     115 ..       5     126 .. 0.74
   2 ?   -1.2   0.0       1.8   2.2e+03      19      36 ..     197     216 ..     189     236 .. 0.61

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.3e-08
                                       EE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS..SEEEE- CS
                   Sacchrp_dh_NADP   3 iiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg..dlvvnl 76 
                                       + Ga G++G+ v+  +a+++d   e++ a   +   +++           + +d++  ++  +al++++  d+v++ 
  gi|336255039|ref|YP_004598146.1|   7 VTGAtGRMGREVIAAVAEREDC--EVAFAVNRDPDDDNV-----------AGVDVQPAAE-FDALVADRepDAVIDF 69 
                                       6678888888888888888887..555554444443444...........3688888888.9999999999****** PP

                                       SSGGGHHHHHHHHHHHT-EEEE..SS-.BCGCCSCHCCSHHHHHTH CS
                   Sacchrp_dh_NADP  77 sppissldvlkaCietgvhyvd..tsi.skeertnyalreavlklk 119
                                       ++p s+l+ ++aC+e+gv +v+  t + + +++t+ a ++++  l+
  gi|336255039|ref|YP_004598146.1|  70 TGPESALEYVRACAEAGVPFVTgtTGFdDDQRETLQAASDEIPVLH 115
                                       **********************877777666677776666665555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                                       CTCCT-G..EEEEEESSHHH CS
                   Sacchrp_dh_NADP  19 rhfdvda..eitvadrskek 36 
                                       r +d+++  ei++a+ ++e 
  gi|336255039|ref|YP_004598146.1| 197 RAGDITGehEIVIAGNHEEV 216
                                       55556556689999888876 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 !   23.0   0.1   7.7e-08   9.8e-05       3      92 ..      12      95 ..      10     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 7.7e-08
                                      SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHHH CS
                     NAD_binding_3  3 GaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvlkaLk 81
                                      G  G++v++++++ +   ++e+++ ++rd    +d      + +  +++d+l+a+ +pd v++ +++e++ e+v ++ +
  gi|336255039|ref|YP_004598146.1| 12 GRMGREVIAAVAERE---DCEVAFAVNRD---PDDDNVAGVDVQPAAEFDALVADREPDAVIDFTGPESALEYVRACAE 84
                                      889999999999999...59*********...44444455667778899*****99*********************** PP

                                      TTEEEE-S--C CS
                     NAD_binding_3 82 agkdvvtankg 92
                                      ag+  vt   g
  gi|336255039|ref|YP_004598146.1| 85 AGVPFVTGTTG 95
                                      ****9997655 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 !   20.1   0.0   6.7e-07   0.00086       2      87 ..       4      87 ..       3      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.7e-07
                                      EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHH CS
                      GFO_IDH_MocA  2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheela 79
                                      r+++ Ga G++g++ ++++ e+ ++ ev+ ++++d+       +  +v+  +++++l+ad e+davi  t +++  e++
  gi|336255039|ref|YP_004598146.1|  4 RIGVTGAtGRMGREVIAAVAER-EDCEVAFAVNRDPDDDNV--AGVDVQPAAEFDALVADREPDAVIDFTGPESALEYV 79
                                      89**************777777.888999999999987774..58889999**************************** PP

                                      HHHHHTT- CS
                      GFO_IDH_MocA 80 kaaleagk 87
                                      +a++eag+
  gi|336255039|ref|YP_004598146.1| 80 RACAEAGV 87
                                      *****997 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 !   19.1   0.0   1.1e-06    0.0014       1      94 [.       4      90 ..       4     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvs 79
                                      ++++ GatG +G+e++  ++e  ++e+++++ ++  +  ++a +  +++ + d  v d      +e d v+  ++ + +
  gi|336255039|ref|YP_004598146.1|  4 RIGVTGATGRMGREVIAAVAEREDCEVAFAVNRDP-DDDNVAGVDVQPAAEFDALVAD------REPDAVIDFTGPESA 75
                                      699*******************************9.8888888866667777777777......788999999999999 PP

                                      HHHHHHHHHTTSEEE CS
                    Semialdhyde_dh 80 kelapklaeagvkvi 94
                                       e+++++aeagv  +
  gi|336255039|ref|YP_004598146.1| 76 LEYVRACAEAGVPFV 90
                                      999999999999876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.5e-06    0.0033       2      74 ..       6      73 ..       5      85 .. 0.82
   2 ?   -1.4   0.0         1   1.3e+03      26      73 ..     209     241 ..     187     247 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.5e-06
                                      EEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.- CS
                         Epimerase  2 lVtGatGfiGsalvkallekg.yevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.v 74
                                       VtGatG +G+ ++ a++e+   ev    ++         +d ++  +d+  ++++++l+++ +pdavi + + +
  gi|336255039|ref|YP_004598146.1|  6 GVTGATGRMGREVIAAVAEREdCEVAFAVNR-------DPDDDNVAGVDVQPAAEFDALVADREPDAVIDFTGpE 73
                                      59**************999998886666655.......233346779**********************996644 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1
                                       EEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                         Epimerase  26 igldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa 73 
                                       i+                +  e+ lt+r++ + +f+  ++da + lA 
  gi|336255039|ref|YP_004598146.1| 209 IAG---------------NHEEVRLTHRAEDRGVFAAGAVDAAVWLAE 241
                                       222...............345888888888888888888888888876 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1     2e-06    0.0025       3      90 ..       2      90 ..       1      94 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2e-06
                                      TEEEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHC...TTTEEEEES-HHHHHH CS
                       CoA_binding  3 dtkviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevlglpvyksvdeleekt...evdvavitvPaesaqe 77
                                      +t+++v Ga+g+ + ++   ++e+ ++++  ++  +p+   ++v g+ v+   +e  + +   e+d+ + ++ +esa e
  gi|336255039|ref|YP_004598146.1|  2 TTRIGVTGATGRMGREViAAVAEREDCEVAFAVNRDPD--DDNVAGVDVQ-PAAEFDALVadrEPDAVIDFTGPESALE 77
                                      699********988888788888888777666666666..9********9.5555555555226*************** PP

                                      HHHHHHHTT-SEE CS
                       CoA_binding 78 avdelveagikgi 90
                                       v +++eag++ +
  gi|336255039|ref|YP_004598146.1| 78 YVRACAEAGVPFV 90
                                      *********9865 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.5e-06    0.0045       7      99 ..       6     108 ..       3     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.5e-06
                                       T--S-TTSHHHHHHHHHHH.HT--E.EEES..SS-SEETTEES----T........T--EEEE-S-HHHHGGGHHHH CS
                     CoA_binding_2   7 Gasdnpgkfgykvlrylle.hglpv.vpVn..pkeeeilgekvyaslaed....pepvdlvdvftppeatpeivkea 75 
                                       G+   +g+ g+ v++ + e ++++v ++Vn  p  + + g++v +  + d    + ++d+v  ft pe ++e+v+++
  gi|336255039|ref|YP_004598146.1|   6 GVTGATGRMGREVIAAVAErEDCEVaFAVNrdPDDDNVAGVDVQPAAEFDalvaDREPDAVIDFTGPESALEYVRAC 82 
                                       55557788888988888884446662567622555999998865555522244579********************* PP

                                       HHH--SEEEE-TT..---HHHHHHHH CS
                     CoA_binding_2  76 lalgakavwlqpg..sedeeaaelae 99 
                                       +++g++ v    g    ++e++++a 
  gi|336255039|ref|YP_004598146.1|  83 AEAGVPFVTGTTGfdDDQRETLQAAS 108
                                       ********999995544444444443 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 !   15.4   0.0   5.7e-06    0.0074       2      57 ..       4      68 ..       3      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.7e-06
                                      EEEEESTTSHHHHHHHHHCTTTS.EEE.EEE-TT.......T--TTSHHHHHHHHHHH--SEEEE CS
                     RmlD_sub_bind  2 kilvtGanGqlGseLakqlaeeg.lev.laltre.......eldltdaeavaellkeakpdvvvn 57
                                      +i vtGa+G +G+e+++++ae++ +ev  a++r+        +d++ a++ ++l+++ +pd+v++
  gi|336255039|ref|YP_004598146.1|  4 RIGVTGATGRMGREVIAAVAEREdCEVaFAVNRDpdddnvaGVDVQPAAEFDALVADREPDAVID 68
                                      6889*************999965144413556669****999*********************97 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.6e-06    0.0085       1      45 [.       5      51 ..       5      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.6e-06
                                      EEESSTTSHHHHHHHHHHHH.HT-EE.EEEES-S-SHHHHHHHHSTT CS
                              NmrA  1 IlviGaTGrqGksvvrallk.aghkv.ralvRdtkselakslkeaGv 45
                                      I v+GaTGr+G+ v++a+++ ++ +v +a+ Rd++ ++++ +  +++
  gi|336255039|ref|YP_004598146.1|  5 IGVTGATGRMGREVIAAVAErEDCEVaFAVNRDPDDDNVAGVDVQPA 51
                                      679****************976777758999***9999888777665 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.1e-05     0.015      45      96 ..      49     100 ..       5     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC.TSSEEE CS
                        ADH_zinc_N  45 dlverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGg.gkgeee 96 
                                       ++ ++  +l  ++ +d+v++++G +++  ++++++++ G  +v G+ g+++++
  gi|336255039|ref|YP_004598146.1|  49 QPAAEFDALVADREPDAVIDFTG-PESALEYVRACAEAGVPFVTGTtGFDDDQ 100
                                       5788888999999**********.*********************98776665 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 ?   13.7   0.3   3.4e-05     0.044       1      90 [.       9      87 ..       9     121 .. 0.71
   2 ?   -1.4   0.0       1.4   1.8e+03      43      88 ..     122     170 ..     105     171 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-05
                                      TTTSHHHHHHHHHHHHC-T-EEEEEE.TTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-..SEEEES---TCCHHH CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalv.Rnpeklaeleaeeglevvegdvtdvedlaealkga..daVvsalggggkdee 76
                                      GAtG+ Gr++++  ++r++ ev   v R+p++          +v  +dv+ +++  + +++   daV+  +g+++    
  gi|336255039|ref|YP_004598146.1|  9 GATGRMGREVIAAVAEREDCEVAFAVnRDPDDD---------NVAGVDVQPAAEFDALVADRepDAVIDFTGPES---- 74
                                      9****************9999854442455543.........356677777788888887663368888888654.... PP

                                      HHHHHHHHHHHCT- CS
                    NAD_binding_10 77 gaknivdaakeagv 90
                                       a   v+a+ eagv
  gi|336255039|ref|YP_004598146.1| 75 -ALEYVRACAEAGV 87
                                      .5566777777777 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                                       EEE--TT-CCHHHHHHTT-SE.EEES---TCCHHHH..HHHHHHHHHHC CS
                    NAD_binding_10  43 vvegdvtdvedlaealkgada.Vvsalggggkdeeg..aknivdaakea 88 
                                        v++ v+ v d  + l+g+d+  v ++ +g++d+ +  a+++++  +++
  gi|336255039|ref|YP_004598146.1| 122 GVQALVNVVGDAVQSLEGYDVeLVETHHNGKRDAPSgtANRLLEEIEAN 170
                                       5677777788888899999984444444444433334477777766665 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 ?   10.8   0.0   0.00036      0.46       2      32 ..       4      36 ..       3      46 .. 0.80
   2 ?   -2.4   0.0       4.8   6.1e+03       9      28 ..     189     208 ..     189     224 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                                      EEEEES.TSHHHHHHHHHHHHHTTCEEE.EEE- CS
                           Gp_dh_N  2 kvainG.fGRIGrlvlralleekelevv.aind 32
                                      ++++ G  GR+Gr v+ a++e++++ev  a+n+
  gi|336255039|ref|YP_004598146.1|  4 RIGVTGaTGRMGREVIAAVAEREDCEVAfAVNR 36
                                      78888856***************9999635665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.8
                                       SHHHHHHHHHHHHHTTCEEE CS
                           Gp_dh_N   9 GRIGrlvlralleekelevv 28 
                                       G IG  vlra   + e e+v
  gi|336255039|ref|YP_004598146.1| 189 GEIGVHVLRAGDITGEHEIV 208
                                       55666666665544444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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):              14  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1975.86
//
Query:       gi|336255040|ref|YP_004598147.1|  [L=309]
Description: dihydrodipicolinate synthase [Halopiger xanaduensis SH-6]
Scores for complete 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-93  313.2   0.0    1.2e-93  313.0   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
      0.019   14.3   0.0      0.031   13.6   0.0    1.2  1  ThiG      Thiazole biosynthesis protein ThiG


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 !  313.0   0.0   1.4e-97   1.2e-93       2     287 ..       7     291 ..       6     293 .. 0.97

  Alignments for each domain:
  == domain 1  score: 313.0 bits;  conditional E-value: 1.4e-97
                                       -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE-- CS
                             DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvG 78 
                                       ++g+++a+ tpfd d ++d+e l++ ++ l ++gvdglv +G+tGEsatl ++e++ +ve + ea+++ +pviag+G
  gi|336255040|ref|YP_004598147.1|   7 LEGVFPAMCTPFDDDERIDFETLQEDAQRLEAAGVDGLVPVGSTGESATLTHDEHVRVVEAVIEAVDD-VPVIAGTG 82 
                                       689*********************************************************99999975.******** PP

                                       -SSHHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTST CS
                             DHDPS  79 snstseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaele 155
                                       sn+t+ea++l+++a++aGadg+l++ PYYnkp+q+gl +h+++i+ a dlp+i+Ynvpsrtg +++p+t  +La  e
  gi|336255040|ref|YP_004598147.1|  83 SNNTREALELSERAADAGADGLLLISPYYNKPEQRGLVDHYRTIADAVDLPQIVYNVPSRTGRNIEPDTAVELASHE 159
                                       ***************************************************************************** PP

                                       TEEEEEE-SS-CTHHHHHHCCCS.TTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHH CS
                             DHDPS 156 nivgvKeavgdleevikikkevg.kdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaae 231
                                       ni+g K+a+gdl ++ +++++++ +d++++sGdd+l+l++ls+Ga+G+isv++ni +er  +++ a+ +Gd a a++
  gi|336255040|ref|YP_004598147.1| 160 NIAGYKAASGDLGQIGEVVERTRdEDFAVLSGDDALTLPMLSVGATGAISVAANIEPERTCAMVGAALDGDYARARA 236
                                       ****************9999886268*************************************************** PP

                                       HHHHHHHHHHHCCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHH CS
                             DHDPS 232 lnekllplikilfaepnvilvktalellGlvveatlrkPltpleeeekeeleallk 287
                                       l+++l pl+ +lf+e+n+i+vk+a+++ G      lr+Plt l+ee++e l+a+l 
  gi|336255040|ref|YP_004598147.1| 237 LHHELGPLFRELFVETNPIPVKEAMQIRGYGPAR-LRSPLTRLSEEYREDLAAVLA 291
                                       ******************************9999.****************99875 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.5e-06     0.031     137     203 ..      33     106 ..      28     113 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-06
                                       HHHHHHTT-SEBEEBSSSTTS----S-HH...HHHHHHHH-.SS-BEEES---SHHHHHH....HHHTT-SEEEE CS
                              ThiG 137 arrleevGcaavmPlaapiGsglGllnke...alkiiieea.kvPvivDAGigspsdaaq....amelGadavll 203
                                       a+rle +G+  ++P+++   s+  l++ e   +++ +ie + +vPvi   G  ++ +a +    a + Gad++ll
  gi|336255040|ref|YP_004598147.1|  33 AQRLEAAGVDGLVPVGSTGESAT-LTHDEhvrVVEAVIEAVdDVPVIAGTGSNNTREALElserAADAGADGLLL 106
                                       89**************9855554.5544401156778999999****9999988888875222255567777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2424.27
//
Query:       gi|336255041|ref|YP_004598148.1|  [L=277]
Description: peptidase M48 Ste24p [Halopiger xanaduensis SH-6]
Scores for 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-37  128.4   0.0    3.4e-37  128.1   0.0    1.1  1  Peptidase_M48    Peptidase family M48
    2.2e-07   30.4   0.1    2.1e-06   27.2   0.0    2.1  2  Peptidase_M56    BlaR1 peptidase M56
     0.0028   16.3   0.1     0.0028   16.3   0.1    2.0  2  MFS_2            MFS/sugar transport protein
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.017   14.9   0.0    1.2  1  SprT-like        SprT-like family
       0.23   10.2   3.9          2    7.1   0.2    2.0  2  DUF2207          Predicted membrane protein (DUF2207)
       0.25   11.0   5.6        1.3    8.6   1.8    2.6  2  RhodobacterPufX  Intrinsic membrane protein PufX
       0.35   10.5   5.5        1.3    8.7   0.6    2.2  2  Orai-1           Mediator of CRAC channel activity
        3.4    6.4   7.0        3.6    6.3   2.6    2.1  2  LptF_LptG        Lipopolysaccharide export system permease Lp


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 !  128.1   0.0   1.5e-40   3.4e-37       5     193 ..      75     276 ..      71     277 .] 0.83

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 1.5e-40
                                       SHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   5 aelkevveelakeaglpkpltkvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsv 81 
                                       ++++e+ e+l + +++   +++++v+++   NAFa+g+     +v++++L+ +ll+e+el++V++HEl+H+k+r++v
  gi|336255041|ref|YP_004598148.1|  75 RRVHEMTESLCRDMNM--DKPRLMVADMGVPNAFATGRKGAGIVVVSSELM-RLLDEDELEGVIAHELAHLKNRDTV 148
                                       79**************..9999999999999********999*********.************************* PP

                                       HHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S--..-HHHHHHHHHHTTHHHHHHHHHHHHHHHHTTT.HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  82 vslivsllasillllglallisraeedaagafldal..avliglliillflalSRkrEyqADeagvellkrakdlvr 156
                                       ++++ +++a+++ + +++l+ +  +e+  g+f+ a+   +++ +l ++ ++a+SR+rEy AD  + +++   + l+r
  gi|336255041|ref|YP_004598148.1| 149 IMVLGQSIATVVSYAVFFLVQALGDENP-GGFIIAWiaSIIANFLVMIFVMAISRYREYVADDTARQYIGSGDPLAR 224
                                       ************9999976666655554.4444433014444555666666************************** PP

                                       HHHHHHHHTT-.........-S---HHHH.............HHS-SS--HHHHHHHHH CS
                                       xxxxxxxxxxx.........xxxxxxxxx.............xxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 157 aliklakdler.........qdvsaslrs.............ellstHPplleRiqalk 193
                                       al k+++++e+         +       +              ++stHPp+++Ri++l+
  gi|336255041|ref|YP_004598148.1| 225 ALEKISAGAEGreprvedsgV-------NalcifnadrsmlqRIFSTHPPTEKRIEKLR 276
                                       *********996655555550.......255555555555559**************98 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   9.2e-10   2.1e-06     151     223 ..      85     158 ..      22     168 .. 0.74
   2 ?    1.0   0.1     0.089     2e+02     107     134 ..     181     209 ..     177     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 9.2e-10
                     Peptidase_M56 151 keemqlkrnikirlsssidsPavlgll.kprIvlPadflkklsdeeleyillHElaHlkrkDllvnllvavlqc 223
                                        ++m++ ++  ++    + + + +g     ++v+++++++ l+++ele +++HElaHlk++D+++ +l + +  
  gi|336255041|ref|YP_004598148.1|  85 CRDMNMDKPRLMVADMGVPNAFATGRKgAGIVVVSSELMRLLDEDELEGVIAHELAHLKNRDTVIMVLGQSIAT 158
                                       456666666655555555555555544145788999*****************************998766555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.089
                     Peptidase_M56 107 liWivgalilllyliaallvlkkr.fvrk 134
                                       ++Wi+ +++ +l +i+++ + + r +v  
  gi|336255041|ref|YP_004598148.1| 181 IAWIASIIANFLVMIFVMAISRYReYVAD 209
                                       78999999999999998888887766654 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.6     0.097   2.2e+02     413     425 ..      18      30 ..       2      60 .. 0.60
   2 !   16.3   0.1   1.3e-06    0.0028     138     208 ..     145     213 ..     136     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.097
                             MFS_2 413 llvallllvrypl 425
                                       + + l+  +++++
  gi|336255041|ref|YP_004598148.1|  18 FGLYLAAAWFFSI 30 
                                       4444444444433 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.3e-06
                             MFS_2 138 vrsflsvlggvlaailafllvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqk 208
                                          +++vlg  +a+++ +++++  ++l++e+ g +i+a+i +++++++v+i v++  + +e+    +++++
  gi|336255041|ref|YP_004598148.1| 145 RDTVIMVLGQSIATVVSYAVFFLVQALGDENPGGFIIAWIASIIANFLVMIFVMAISRYREY--VADDTAR 213
                                       5668899**************************************98888777776666665..3344444 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   7.7e-06     0.017      43      77 ..     110     144 ..      49     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.7e-06
                         SprT-like  43 vrhhasIeLseklldsrsedrllntLaHElcHlal 77 
                                       +++   +  s++l++  +ed+l+ ++aHEl+Hl +
  gi|336255041|ref|YP_004598148.1| 110 RKGAGIVVVSSELMRLLDEDELEGVIAHELAHLKN 144
                                       344445678999********************966 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.6    0.0061        14     388     437 ..      15      57 ..       2      74 .. 0.53
   2 ?    7.1   0.2   0.00087         2     384     446 ..     151     212 ..     129     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0061
                           DUF2207 388 lgliilglilillallllvlllvfllilllillliaiivlllfsrllgrr 437
                                        +l+ l+l+++ ++       ++++++ ++i+l+ +i++l   ++ lg++
  gi|336255041|ref|YP_004598148.1|  15 SILFGLYLAAAWFF-------SILFGVSFVIVLIPSIVLLPAGQYKLGKW 57 
                                       22222222222222.......55555555555666655555555555555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00087
                           DUF2207 384 salglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrteeGaella 446
                                        +   +++++++++++l+ +l    + + +i+++i  +ia +++++f + ++r+ e+ a+  a
  gi|336255041|ref|YP_004598148.1| 151 VLGQSIATVVSYAVFFLVQALGDE-NPGGFIIAWIASIIANFLVMIFVMAISRYREYVADDTA 212
                                       444556666666666666666666.**************999999999*****9998887665 PP

>> RhodobacterPufX  Intrinsic membrane protein PufX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.8    0.0006       1.3      14      46 ..       6      38 ..       1      48 [. 0.88
   2 ?    3.2   0.1     0.029        65      21      44 ..     147     170 ..     136     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0006
                   RhodobacterPufX 14 srLradvlllMlkGAgyAavfvlvllfllvala 46
                                       +Lr+ v++  l G  +Aa  ++ +lf++ ++ 
  gi|336255041|ref|YP_004598148.1|  6 LQLRMAVAGSILFGLYLAAAWFFSILFGVSFVI 38
                                      689************************998765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.029
                   RhodobacterPufX  21 lllMlkGAgyAavfvlvllfllva 44 
                                       ++ M+ G   A v+  +++fl+ a
  gi|336255041|ref|YP_004598148.1| 147 TVIMVLGQSIATVVSYAVFFLVQA 170
                                       789*****************9977 PP

>> Orai-1  Mediator of CRAC channel activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.4     0.015        33     104     127 ..      18      41 ..      11      51 .. 0.83
   2 ?    8.7   0.6   0.00056       1.3     130     172 ..     160     210 ..     149     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.015
                            Orai-1 104 leeyiekaWlfatalGillFLvev 127
                                       +  y+  aW+f+  +G+++ +v +
  gi|336255041|ref|YP_004598148.1|  18 FGLYLAAAWFFSILFGVSFVIVLI 41 
                                       5679999*********99877765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00056
                            Orai-1 130 lswvkFlavss.........aaalvvtailvpvlilfvvfavhfyrklvkkk 172
                                       +s+  F+ v++           a+++++i+ + +++fv +a+++yr++v  +
  gi|336255041|ref|YP_004598148.1| 160 VSYAVFFLVQAlgdenpggfIIAWIASIIANFLVMIFV-MAISRYREYVADD 210
                                       56666666666777777877889**************9.999******9875 PP

>> LptF_LptG  Lipopolysaccharide export system permease LptF/LptG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.029        66      95     128 ..      25      58 ..       3      77 .. 0.71
   2 ?    6.3   2.6    0.0016       3.6     288     352 ..     135     201 ..     133     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.029
                         LptF_LptG  95 lrpililalllsvlsfllnnyvvPwankkaesll 128
                                       ++ + il  + +v++++ + +++P +++k+ ++l
  gi|336255041|ref|YP_004598148.1|  25 AWFFSILFGVSFVIVLIPSIVLLPAGQYKLGKWL 58 
                                       4455566666667777777778888888877766 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0016
                         LptF_LptG 288 iaaplglvkrrggrglrlliaillfvlyyvllslgkalaen...gvlppilaawlpnilflllglfll 352
                                       ia  l+  k+r+  ++ l  +i+ +v+y  +++l +al+ +   g + +++a +++n+l++++ +++ 
  gi|336255041|ref|YP_004598148.1| 135 IAHELAHLKNRDTVIMVLGQSIATVVSYA-VFFLVQALGDEnpgGFIIAWIASIIANFLVMIFVMAIS 201
                                       66667788888888886666666666655.56677888877687999999999999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2171.35
//
Query:       gi|336255042|ref|YP_004598149.1|  [L=165]
Description: hypothetical protein Halxa_3662 [Halopiger xanaduensis SH-6]
Scores for 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-38  133.1   0.3    1.2e-38  132.9   0.3    1.0  1  NYN       NYN domain


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   0.3   6.7e-43   1.2e-38       1     147 []       9     157 ..       9     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 6.7e-43
                               NYN   1 rvavfiDgenlpvpak...gkevdyrklleeirskgelvraraygn.wedeeqnkfqdalsstgikvkhkplkkrg. 72 
                                       rvav++D++nl+++a+   ++++dy++lle++++ ++l+ra ay+   +++e ++f +al ++g++ k k+ k+++ 
  gi|336255042|ref|YP_004598149.1|   9 RVAVLVDAQNLYHSAQslySRNIDYSSLLEKAVQDRQLTRAIAYVIrADAPEEESFFEALVDIGFEPKIKDIKTFAd 85 
                                       89*************9998888************************65555679999***************99999 PP

                               NYN  73 gsgkkavDvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaadefisle 147
                                       gs+k ++Dv++ +da++la  n++dtivL++gDgDF++l+++lr++g+rVev+++e +st++eL +aad f++l+
  gi|336255042|ref|YP_004598149.1|  86 GSKKADWDVGMSLDAVTLA--NHVDTIVLCTGDGDFSRLCSHLRHEGVRVEVMAFE-SSTADELVDAADSFLDLD 157
                                       9999***************..99*******************************88.8*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1359.09
//
Query:       gi|336255043|ref|YP_004598150.1|  [L=54]
Description: hypothetical protein Halxa_3663 [Halopiger xanaduensis SH-6]
Scores for 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:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      117  (0.00652574); 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: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 436.66
//
Query:       gi|336255044|ref|YP_004598151.1|  [L=164]
Description: PUA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   89.0   0.1    3.3e-25   88.0   0.1    1.5  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    1.2e-18   66.8   0.3    1.9e-18   66.2   0.3    1.3  1  PUA       PUA domain
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.021   15.1   0.0    1.5  1  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> 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 !   88.0   0.1   5.5e-29   3.3e-25       2      71 .]      13      85 ..      12      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 5.5e-29
                            TGT_C2  2 rlraiadYqFGagagdaLfped....vtitrsatgrirqvlvdgerlatlraqdgrltLsleGarrlheslppP 71
                                      +lr+iadYqFGagag aLfp      ++itr+++gr+rqv++d  r++++ ++dgr+tL+leG+rrl  +l++P
  gi|336255044|ref|YP_004598151.1| 13 TLRTIADYQFGAGAGTALFPPTetdsLEITRTSSGRPRQVHADAGRIVSF-GTDGRFTLGLEGGRRLDAALEHP 85
                                      79*****************6533446***********************9.********************998 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.3   3.1e-22   1.9e-18       2      72 ..      88     158 ..      87     160 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 3.1e-22
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                       rvvvdd++  ++++ ++++a++v+e++ ++++gd+V +v e gel+avG+a+++++ +a+++ g++v++++
  gi|336255044|ref|YP_004598151.1|  88 RVVVDDESEPFVREEKNVFAKFVLEAGPEIRPGDEVLVVHERGELLAVGRAELDAAAIADFDTGMAVNVRE 158
                                       8*******************************************************************997 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.5e-06     0.021      16      55 ..     103     142 ..      88     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.5e-06
                           UPF0113  16 rdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt 55 
                                       ++v+ + +l+  ++++ ++ v+V+ e+ge+l++G++  d 
  gi|336255044|ref|YP_004598151.1| 103 KNVFAKFVLEAGPEIRPGDEVLVVHERGELLAVGRAELDA 142
                                       89*********************************97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.38u 0.19s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1369.57
//
Query:       gi|336255045|ref|YP_004598152.1|  [L=102]
Description: hypothetical protein Halxa_3665 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.37   10.3   2.4       0.42   10.1   2.4    1.1  1  DUF1700    Protein of unknown function (DUF1700)


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 ?   10.1   2.4   2.3e-05      0.42     103     161 ..      22      82 ..      16      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 2.3e-05
                           DUF1700 103 iislvlsllvvalallvsplvllvksllkgfeelsln..vfvsigllglGllllivayylv 161
                                       ++ +++s  ++++a+++s++++++ + + gf        v v++++l+ G+l++ v+   +
  gi|336255045|ref|YP_004598152.1|  22 LVDVLASSAIIGTAVTTSGAAVVGIVYVAGFPASEWFrnVTVTVAALAAGFLFVTVCAVAA 82 
                                       567889999********************99655433339999*********998876544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 793.06
//
Query:       gi|336255046|ref|YP_004598153.1|  [L=130]
Description: Nascent polypeptide-associated complex protein [Halopiger xanaduensis SH-6]
Scores for complete 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   60.4   0.1    1.7e-16   59.9   0.1    1.2  1  NAC          NAC domain
     0.0034   17.2   0.6     0.0077   16.0   0.6    1.5  1  UBA_4        UBA-like domain
  ------ inclusion threshold ------
       0.02   14.6   0.1       0.02   14.6   0.1    2.0  2  CUE          CUE domain
      0.093   12.7   0.0          1    9.3   0.0    2.3  2  TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa s
       0.19   11.3   0.0       0.43   10.1   0.0    1.5  2  LptC         Lipopolysaccharide-assembly, LptC-related


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 !   59.9   0.1   4.7e-20   1.7e-16       1      56 [.      11      68 ..      11      69 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 4.7e-20
                               NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeaee 56
                                      ++K+ +++ ++g+   +i ++eeV+ir+++ + lvf++P+V+  ++ g++ty+++G++ee
  gi|336255046|ref|YP_004598153.1| 11 PRKMEQMMEQMGIdvDDI-DAEEVIIRTDE-HDLVFSDPEVTkmDARGQETYQIIGSPEE 68
                                      79************9999.9**********.***********888899**********98 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.6   2.1e-06    0.0077      12      34 ..     105     127 ..     101     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-06
                             UBA_4  12 GadeekArqlLeannWdLerAis 34 
                                       G++e+ Ar  Le n++dL +A++
  gi|336255046|ref|YP_004598153.1| 105 GVSEDDARAALEENDGDLAAAVE 127
                                       89*******************97 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3      0.61   2.2e+03      13      21 ..      90      98 ..      90     100 .. 0.84
   2 ?   14.6   0.1   5.5e-06      0.02      15      38 ..     106     129 ..     105     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.61
                                      TTS-HHHHH CS
                               CUE 13 PdldeevIr 21
                                      P++++e+++
  gi|336255046|ref|YP_004598153.1| 90 PSIPDEDVE 98
                                      999999997 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.5e-06
                                       S-HHHHHHHHHHCTTTHHHHHHHH CS
                               CUE  15 ldeevIravLrasngnvEatinaL 38 
                                       ++e++ ra+L++++g++ a+++ L
  gi|336255046|ref|YP_004598153.1| 106 VSEDDARAALEENDGDLAAAVEDL 129
                                       689******************987 PP

>> 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 ?    0.7   0.0      0.14     5e+02      10      23 ..      16      29 ..      14      53 .. 0.65
   2 ?    9.3   0.0   0.00029         1       1      23 [.      90     112 ..      90     117 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.14
                       TFIID_30kDa 10 yyLekaGletsDpr 23
                                      +++e+ G++ +D  
  gi|336255046|ref|YP_004598153.1| 16 QMMEQMGIDVDDID 29
                                      67888888876654 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00029
                       TFIID_30kDa   1 PiIPDavtayyLekaGletsDpr 23 
                                       P IPD+ ++ + ++aG+  +D+r
  gi|336255046|ref|YP_004598153.1|  90 PSIPDEDVELVATRAGVSEDDAR 112
                                       89*******************98 PP

>> LptC  Lipopolysaccharide-assembly, LptC-related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00012      0.43      23      58 ..      30      65 ..      20      72 .. 0.87
   2 ?   -2.1   0.0      0.68   2.4e+03      84     107 ..      95     118 ..      86     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                                      ....XXXXXXXXXXXXXXXXXXXXXXXXX-EEEEEE CS
                              LptC 23 ekqlkkkksepdyvaenfettqydedGklqyrltad 58
                                       ++++ +++e+d+v  + e t++d  G+ +y+++++
  gi|336255046|ref|YP_004598153.1| 30 AEEVIIRTDEHDLVFSDPEVTKMDARGQETYQIIGS 65
                                      578999***************************987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.68
                                       EEEEEE-SEEEE-T.TSEEEEEEE CS
                              LptC  84 qswkvtAkkAkltkkgqeleLegn 107
                                       +++++ A +A +++++ +  Le+n
  gi|336255046|ref|YP_004598153.1|  95 EDVELVATRAGVSEDDARAALEEN 118
                                       567889999999999988888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1039.06
//
Query:       gi|336255047|ref|YP_004598154.1|  [L=268]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-18   65.3   0.1      2e-14   53.9   0.0    2.1  2  GCD14            tRNA methyltransferase complex GCD14 subunit
    3.2e-09   36.8   0.0    4.1e-09   36.4   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.9e-08   34.9   0.6    3.9e-08   33.9   0.6    1.5  1  Methyltransf_25  Methyltransferase domain
    1.4e-07   32.0   0.4    2.5e-07   31.2   0.4    1.5  1  Methyltransf_11  Methyltransferase domain
    2.3e-07   30.5   0.5    2.9e-07   30.2   0.5    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.8e-06   28.9   0.4      4e-06   27.8   0.4    1.6  1  Methyltransf_24  Methyltransferase domain
    2.1e-06   27.4   0.2    4.9e-06   26.2   0.2    1.6  1  MTS              Methyltransferase small domain
    3.2e-05   23.8   0.1    4.1e-05   23.4   0.1    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      7e-05   22.7   0.0    0.00013   21.9   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    0.00015   21.0   0.0    0.00019   20.7   0.0    1.1  1  Methyltransf_3   O-methyltransferase
    0.00034   19.8   0.0    0.00045   19.4   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00067   19.3   0.0    0.00089   18.9   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0014   19.3   0.2     0.0029   18.3   0.2    1.5  1  Methyltransf_12  Methyltransferase domain
     0.0023   17.5   0.0     0.0032   17.0   0.0    1.1  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.005   16.8   0.5     0.0071   16.3   0.5    1.2  1  ADH_zinc_N       Zinc-binding dehydrogenase
     0.0052   17.8   1.2       0.02   16.0   0.2    2.0  2  ADH_zinc_N_2     Zinc-binding dehydrogenase
     0.0097   15.5   0.2      0.015   14.9   0.2    1.2  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
      0.014   15.2   0.0       0.02   14.7   0.0    1.2  1  Met_10           Met-10+ like-protein
       0.02   14.2   0.0      0.025   13.9   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.025   14.5   0.1      0.041   13.8   0.1    1.3  1  Methyltransf_18  Methyltransferase domain


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 !   53.9   0.0   2.2e-17     2e-14      27     178 ..      97     243 ..      88     249 .. 0.93
   2 !    9.8   0.1   0.00066       0.6     229     246 ..     249     266 ..     243     267 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 2.2e-17
                             GCD14  27 aDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvck 103
                                        Di l+i +  +  G +v+++GtG+g l+ ++ar+ a    + t+e   + a+ are++   +++++v v++ Dvc+
  gi|336255047|ref|YP_004598154.1|  97 RDIGLVIGETGIARGDRVLDAGTGTGVLAASMARAGA---DVVTYEQDPDFADVARENMALGGVDDVVDVRTGDVCE 170
                                       69********************************966...689*********************************9 PP

                             GCD14 104 eGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevllrtye 178
                                       e   +  s++ D + LD     + + ha + l  +gg +  +sP ie  ++ +e+ re +  +++t e  +r+ e
  gi|336255047|ref|YP_004598154.1| 171 ELE-TLESSSFDVITLDTADAADVVAHAPELL-VDGGFVAVYSPFIESTREVAETAREADLANVRTRETIQREME 243
                                       855.4445899********************9.9**********************************9999865 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00066
                             GCD14 229 lkPvselkghtgyLtfat 246
                                       ++P +  +ghtgyLtfa+
  gi|336255047|ref|YP_004598154.1| 249 SRPSTAPVGHTGYLTFAR 266
                                       7999999**********8 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   4.6e-12   4.1e-09       3     113 ..     110     213 ..     108     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 4.6e-12
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDl 77 
                                       +g rvlD+G+GtG l+  +a +   +a+vv  + +++   +Aren +  g+d  v ++ gd+ e le+ le ++fD+
  gi|336255047|ref|YP_004598154.1| 110 RGDRVLDAGTGTGVLAASMA-R--AGADVVTYEQDPDFADVARENMALGGVDdVVDVRTGDVCEeLET-LESSSFDV 182
                                       5789****************.4..579*************************8999******998998.6889**** PP

                   Methyltransf_31  78 ilsnevlnaladpdkileeiervlkpggilliedpr 113
                                       i+ +     +ad +++   ++++l +gg +++ +p 
  gi|336255047|ref|YP_004598154.1| 183 ITLD-----TADAADVVAHAPELLVDGGFVAVYSPF 213
                                       *995.....899999999999999988888887776 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.6   4.4e-11   3.9e-08       1      71 [.     114     186 ..     114     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 4.4e-11
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBC.CGBS.SSTTTEEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgda.edlp.fedgsfDlvvss 71 
                                       vLd+G+GtG l++ +a+++  a+v+  + ++++ + are+++  g+   v++++gd+ e+l+ +e++sfD++++ 
  gi|336255047|ref|YP_004598154.1| 114 VLDAGTGTGVLAASMARAG--ADVVTYEQDPDFADVARENMALGGVddVVDVRTGDVcEELEtLESSSFDVITLD 186
                                       9*****************5..********************99999999********7889846999*****983 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.4   2.8e-10   2.5e-07       1      68 [.     115     186 ..     115     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.8e-10
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC.T.SS-TT-EEEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaek.l.pfednsfDlvvss 68 
                                       Ld+G+GtG la+ +a++ga+vv+ + ++ + ++a+e+    g+   v+++ +d+ + l  +e++sfD++++ 
  gi|336255047|ref|YP_004598154.1| 115 LDAGTGTGVLAASMARAGADVVTYEQDPDFADVARENMALGGVddVVDVRTGDVCEeLeTLESSSFDVITLD 186
                                       8*************************************999999999******9965978*********975 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.5   3.2e-10   2.9e-07     158     231 ..     107     184 ..      99     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.2e-10
                              PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleval.....seellkeekadv 229
                                        + +g++vlD GtG+G+La   a+ ga +vv +  D+   +va+eN++l +v++ ++v +     + e l+++++dv
  gi|336255047|ref|YP_004598154.1| 107 GIARGDRVLDAGTGTGVLAASMARAGA-DVVTYEQDPDFADVARENMALGGVDDVVDVRTgdvceELETLESSSFDV 182
                                       567899*************99999998.5899**********************99994322211333334788999 PP

                              PrmA 230 iv 231
                                       i 
  gi|336255047|ref|YP_004598154.1| 183 IT 184
                                       85 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.4   4.5e-09     4e-06       7     101 ..     117     207 ..     115     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 4.5e-09
                   Methyltransf_24   7 sGvstlwllralrrngagrlvavdhdpgaeeaaalare....aglddrvrlikadseealaslaagsiDllfiDggh 79 
                                       +G  t +l++ + r+ga  +v+ + dp   ++a +are     g+dd+v+++ +d  e+l++l+++s+D++ +D   
  gi|336255047|ref|YP_004598154.1| 117 AGTGTGVLAASMARAGA-DVVTYEQDP---DFADVAREnmalGGVDDVVDVRTGDVCEELETLESSSFDVITLDTA- 188
                                       57788889999999998.899******...888888888888********************************76. PP

                   Methyltransf_24  80 aaeavledleallprlapggvv 101
                                          ++++ + ++ ++l +gg+v
  gi|336255047|ref|YP_004598154.1| 189 ---DAADVVAHAPELLVDGGFV 207
                                       ...3333344566666777766 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   5.5e-09   4.9e-06      32     102 ..     111     184 ..     103     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.5e-09
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST...TS-EEEEE CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve...ekkfdliv 102
                                        ++vlD G+G+Gvl+a++a++  +  v+ +++d    ++a+en++  +++  v+v++ dv ee+e     +fd+i 
  gi|336255047|ref|YP_004598154.1| 111 GDRVLDAGTGTGVLAASMARAGAD--VVTYEQDPDFADVARENMALGGVDdvVDVRTGDVCEELEtleSSSFDVIT 184
                                       568*****************9888..99********************************9887633367888875 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 !   23.4   0.1   4.6e-08   4.1e-05      71     170 ..     108     208 ..      95     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.6e-08
                                       --TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTG..GG-SEE CS
                              PCMT  71 lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkGye..ekaPYd 144
                                       + +g+rvL+ G+G+G l+a +ar   + + vv+ e+ +++++ a++n+   +++  v v++gD  +  e  e + +d
  gi|336255047|ref|YP_004598154.1| 108 IARGDRVLDAGTGTGVLAASMAR---AGADVVTYEQDPDFADVARENMALGGVDdVVDVRTGDVCEELEtlESSSFD 181
                                       7899**************99887...456789********************99567899***98777633789999 PP

                                       EEEE.SSBBSS--HHHHHTEEEEEEEE CS
                              PCMT 145 aihv.gaaapeiPealidQLkeGGrlv 170
                                       +i + +a a ++     + L +GG + 
  gi|336255047|ref|YP_004598154.1| 182 VITLdTADAADVVAHAPELLVDGGFVA 208
                                       998735556777777777777777654 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.4e-07   0.00013      21      87 ..     109     184 ..      84     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.4e-07
                   Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...........kakkaqkdqfdeqeaaepqgkfdlI 86 
                                        +g rvLd G+GtG l+ ++++ g++v+ ++++p   + a+                +   + e+ ++ ++ +fd+I
  gi|336255047|ref|YP_004598154.1| 109 ARGDRVLDAGTGTGVLAASMARAGADVVTYEQDPDFADVARenmalggvddvV--DVRTGDVCEELETLESSSFDVI 183
                                       4677***************************9998777666666666665330..2222222233333344455555 PP

                   Methyltransf_23  87 v 87 
                                       +
  gi|336255047|ref|YP_004598154.1| 184 T 184
                                       5 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.1e-07   0.00019      48     154 ..     111     208 ..      97     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.1e-07
                                       --EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSSS---E CS
                    Methyltransf_3  48 akrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLeelvkdkklpef 124
                                         rvl+ G+ tG  + ++a a      +++ ++d++ +++a++ +   gv++ +++++gd  + Le l + +    f
  gi|336255047|ref|YP_004598154.1| 111 GDRVLDAGTGTGVLAASMARA---GADVVTYEQDPDFADVARENMALGGVDDVVDVRTGDVCEELETLESSS----F 180
                                       568999999999988888887...4569**************************************998776....* PP

                                       EEEEE-S-GGGHHHHHHHHHHTEEEEEEEE CS
                    Methyltransf_3 125 DfifvDaDkssyvnyyeklleLvkvGglia 154
                                       D+i +D    + v  +  + eL+  Gg++a
  gi|336255047|ref|YP_004598154.1| 181 DVITLDTADAADVVAH--APELLVDGGFVA 208
                                       ***9995444333333..345555566555 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     5e-07   0.00045      28      73 ..     108     153 ..     100     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5e-07
                                       GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT CS
                            RrnaAD  28 leekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls 73 
                                       +   + vl+ g+G+G+l +++a     vv +E+d+++a + ++++ 
  gi|336255047|ref|YP_004598154.1| 108 IARGDRVLDAGTGTGVLAASMARAGADVVTYEQDPDFADVARENMA 153
                                       556799****************999***************999876 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.9e-07   0.00089      41     120 ..     110     186 ..     102     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.9e-07
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                       +g rvLD   G+G+l+   + R  + +v  e+d+  + + +en++  ++++ +++   d  e+l++l  ++++fd++
  gi|336255047|ref|YP_004598154.1| 110 RGDRVLDAGTGTGVLAA-SMARAGADVVTYEQDPDFADVARENMALGGVDDVVDVRTGDVCEELETL--ESSSFDVI 183
                                       6789*********9987.68899999************************999999********999..7789**** PP

                                       EE- CS
                     Cons_hypoth95 118 flD 120
                                        lD
  gi|336255047|ref|YP_004598154.1| 184 TLD 186
                                       999 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   3.3e-06    0.0029       1      95 [.     115     203 ..     115     207 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.3e-06
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg...ssfDlvvasn 74 
                                       L+ G+GtG l++ ++++  +++++ ++ +p++ + a+e +a  + +  ++v++++ d+ ++ +    ssfD++++  
  gi|336255047|ref|YP_004598154.1| 115 LDAGTGTGVLAASMARA--GADVVTYEQDPDFADVARENMALGGVD--DVVDVRTGDVCEELETlesSSFDVITLD- 186
                                       89***************..**************7777776665544..4666666666655555666******842. PP

                   Methyltransf_12  75 vlhhlkdirevldnirklLkp 95 
                                           ++d ++v++++ +lL++
  gi|336255047|ref|YP_004598154.1| 187 ----TADAADVVAHAPELLVD 203
                                       ....24455555555555555 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 !   17.0   0.0   3.6e-06    0.0032       3      75 ..     113     183 ..     111     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.6e-06
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlv 75 
                                        +lD+ +G+G  +  +a+ +  v++ e +++   +a +N  + gv+d +++ +gdv e l++l++++   d++
  gi|336255047|ref|YP_004598154.1| 113 RVLDAGTGTGVLAASMARAGADVVTYEQDPDFADVARENMALGGVDDVVDVRTGDVCEELETLESSSF--DVI 183
                                       689*******************************************************9999888776..766 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.5   7.9e-06    0.0071       1      89 [.     120     211 ..     120     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.9e-06
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHT....TESEEEETTTC.HHHHHHHHHTTTSSEEE.EEESSCSHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakkl....Gadevinykea.dlverikeltggegvdv.vfecvGsgat 71 
                                       g G++a  +A+a Ga v++   +++ ++ a+++    G+d v++  ++ d+ e+++ l     +dv  ++++ + ++
  gi|336255047|ref|YP_004598154.1| 120 GTGVLAASMARA-GADVVTYEQDPDFADVARENmalgGVDDVVDV-RTgDVCEELETLE-SSSFDViTLDTADAADV 193
                                       679999999986.9******************779988*******.888**********.779**94589999999* PP

                                       HHHHHHCEEEEEEEEECS CS
                        ADH_zinc_N  72 leaalkllkpgGrlvvvG 89 
                                       +  a +ll  gG ++v+ 
  gi|336255047|ref|YP_004598154.1| 194 VAHAPELLVDGGFVAVYS 211
                                       ***********9999886 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.4   1.3e+03      24      59 ..     112     145 ..      99     154 .. 0.61
   2 !   16.0   0.2   2.2e-05      0.02       2      75 ..     156     234 ..     155     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.4
                                       EEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-E CS
                      ADH_zinc_N_2  24 DvvldtvggealleaslkvlpggGrlvsiggpplsa 59 
                                       D vld+  g+  l+as+   + g+++v++ ++p +a
  gi|336255047|ref|YP_004598154.1| 112 DRVLDAGTGTGVLAASM--ARAGADVVTYEQDPDFA 145
                                       77777755555656776..34446677777655333 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.2e-05
                                       T-SEEEETTSTTHH...HHH-TT-EEEE.EES-HHHHH.HHHHHHEEEEEEEEE----...S-EEE-CHHHCTTT-E CS
                      ADH_zinc_N_2   2 GAdevidyrtedfe...aatggegvDvv.ldtvggealleaslkvlpggGrlvsiggpp..lsaallkpakkrkgrs 72 
                                       G+d v+d rt d++   + +++ ++Dv+ ldt++ ++ ++++ ++l + G +v + +p+   ++++++ a+++  ++
  gi|336255047|ref|YP_004598154.1| 156 GVDDVVDVRTGDVCeelETLESSSFDVItLDTADAADVVAHAPELLVD-GGFVAVYSPFieSTREVAETAREADLAN 231
                                       89************999888999****989****99999*******77.9**9999987774445555555444444 PP

                                       EEE CS
                      ADH_zinc_N_2  73 vky 75 
                                       v++
  gi|336255047|ref|YP_004598154.1| 232 VRT 234
                                       444 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   1.7e-05     0.015      11      83 ..     108     187 ..     101     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                              MetW  11 ikpgsrvldlGcGdGellell.keekqvdgrGleldeegvae.cvakG.....lsviqgdldkdlenfedksfdyvv 80 
                                       i  g rvld G+G G l   + +   +v ++  + d + va+  +a G     + v  gd+ ++le+ e++sfd++ 
  gi|336255047|ref|YP_004598154.1| 108 IARGDRVLDAGTGTGVLAASMaRAGADVVTYEQDPDFADVAReNMALGgvddvVDVRTGDVCEELETLESSSFDVIT 184
                                       67899************8766155678888888877777754245544344438999******************99 PP

                              MetW  81 lsq 83 
                                       l  
  gi|336255047|ref|YP_004598154.1| 185 LDT 187
                                       864 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.2e-05      0.02      99     163 ..     109     171 ..     104     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                                       -TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG- CS
                            Met_10  99 eegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrev 163
                                         g++V+d   G G +a ++a+   +  v++ + +P+     +en++l  v++vv + ++D+ e 
  gi|336255047|ref|YP_004598154.1| 109 ARGDRVLDAGTGTGVLAASMAR--AGADVVTYEQDPDFADVARENMALGGVDDVVDVRTGDVCEE 171
                                       5799*****************9..677799**************************999998654 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.8e-05     0.025      53     123 ..     101     170 ..      96     243 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                                       HHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG CS
                              CMAS  53 lileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyed 123
                                       l+++  ++  G+++Ld G+G G l+  +++  +++vv      + a +a+++++  ++++ v+v+  d  +
  gi|336255047|ref|YP_004598154.1| 101 LVIGETGIARGDRVLDAGTGTGVLAASMARA-GADVVTYEQDPDFADVARENMALGGVDDVVDVRTGDVCE 170
                                       5667788999****************99999.******999999999*****9999999999999877533 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.6e-05     0.041      12      81 ..     108     175 ..     105     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                   Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkee 81 
                                       + +g+rv+D Gt  g+l++ +++ g    v+  +  +   + a+en++  g++d ++vr +d  e+l++ 
  gi|336255047|ref|YP_004598154.1| 108 IARGDRVLDAGTGTGVLAASMARAGA--DVVTYEQDPDFADVARENMALGGVDDVVDVRTGDVCEELETL 175
                                       66799*****************8775..699999*****************************9998743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1810.94
//
Query:       gi|336255048|ref|YP_004598155.1|  [L=102]
Description: transcription termination factor Tfs [Halopiger xanaduensis SH-6]
Scores for 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-19   68.7   5.0    2.8e-19   68.7   5.0    3.0  3  TFIIS_C          Transcription factor S-II (TFIIS)
    1.9e-08   34.0   1.3    1.9e-08   34.0   1.3    3.1  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    2.8e-06   27.2   4.3     0.0015   18.4   0.3    2.4  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    2.2e-05   23.8   7.2      0.001   18.6   0.3    3.5  3  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00019   21.4   9.3      0.011   15.8   0.5    2.8  2  DZR              Double zinc ribbon
    0.00034   19.9  10.3       0.16   11.5   2.6    3.3  3  zf-ribbon_3      zinc-ribbon domain
    0.00049   20.0  10.6      0.027   14.4   0.8    2.6  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    0.00091   19.1   1.2    0.00091   19.1   1.2    3.2  3  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
     0.0034   17.3   1.5     0.0049   16.8   0.1    1.8  2  FdhE             Protein involved in formate dehydrogenase fo
  ------ inclusion threshold ------
      0.063   13.2   0.2      0.063   13.2   0.2    2.6  3  DUF3797          Domain of unknown function (DUF3797)
      0.066   13.3   0.3      0.066   13.3   0.3    2.6  2  Ribosomal_L37ae  Ribosomal L37ae protein family
      0.091   12.7  12.3       0.18   11.7   0.2    3.9  4  HalOD2           Halobacterial output domain 2
        0.1   12.7   0.3        0.1   12.7   0.3    2.1  2  ArfGap           Putative GTPase activating protein for Arf
        0.1   12.5  12.4        2.3    8.2   3.0    3.8  3  Nudix_N_2        Nudix N-terminal
       0.12   12.7   0.6       0.12   12.7   0.6    2.1  2  DUF3268          zinc-finger-containing domain
       0.14   11.8   6.3        2.5    7.8   6.3    2.5  1  TackOD1          Thaumarchaeal output domain 1
       0.18   12.2   4.6        1.8    8.9   0.3    2.4  2  zf-UBP           Zn-finger in ubiquitin-hydrolases and other 
       0.22   11.2  12.8        8.9    6.1   0.1    4.1  3  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.26   11.5   7.6        3.9    7.7   2.6    2.4  2  DUF2387          Probable metal-binding protein (DUF2387)
       0.31   11.0   9.2        2.9    8.0   0.4    2.7  2  zinc-ribbons_6   zinc-ribbons
       0.43   11.0   6.9        9.2    6.8   0.0    3.9  4  zf-IS66          zinc-finger binding domain of transposase IS
       0.49   10.4  10.1         94    3.1   0.3    3.0  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.61   10.3  12.1        1.1    9.5   0.2    3.9  3  Zn-ribbon_8      Zinc ribbon domain
       0.65   10.1   4.9        3.3    7.8   4.9    1.9  1  zf-RRPl_C4       Putative ribonucleoprotein zinc-finger pf C4
       0.74    9.6  15.4       0.79    9.5   0.2    3.9  4  zinc_ribbon_2    zinc-ribbon domain
        1.3    9.2  15.2        4.2    7.5   0.3    4.1  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
        1.4    8.9   8.8        1.5    8.8   0.7    3.0  3  Prok-RING_1      Prokaryotic RING finger family 1
        2.1    8.6  13.9        5.7    7.2   1.1    4.0  4  zf-RING_7        C4-type zinc ribbon domain
        2.4    8.0  17.6        6.8    6.5   1.7    4.0  4  Rubredoxin_2     Rubredoxin metal binding domain
        2.4    7.9  12.9         28    4.6   0.7    4.1  4  A2L_zn_ribbon    A2L zinc ribbon domain
        2.5    8.4   7.3        5.1    7.3   3.0    2.5  2  Ribosomal_S27    Ribosomal protein S27a
        2.8    7.6  12.1        1.3    8.7   0.1    3.8  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
        4.8    7.2   8.8        3.2    7.8   1.2    2.8  3  zf-RING_5        zinc-RING finger domain
          5    7.7  10.3         39    4.9   0.1    3.6  3  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
        5.3    7.3   5.5         39    4.5   0.0    3.3  4  Rdx              Rdx family
        7.8    6.3  11.7         38    4.1   0.1    3.9  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
          9    7.1  11.3    2.8e+03   -0.8  11.3    3.1  1  zinc_ribbon_15   zinc-ribbon family
        9.4    6.2   8.1         14    5.7   0.5    3.0  3  Zn_ribbon_SprT   SprT-like 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 ?    1.0   0.1      0.86   4.1e+02       3       8 ..       4       9 ..       3      13 .. 0.72
   2 ?    2.0   0.3       0.4   1.9e+02       2       9 ..      19      26 ..      18      27 .. 0.64
   3 !   68.7   5.0     6e-22   2.8e-19       2      39 .]      61      98 ..      60      98 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.86
                           TFIIS_C 3 CpkCgs 8
                                     C +Cgs
  gi|336255048|ref|YP_004598155.1| 4 CDECGS 9
                                     777776 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.4
                           TFIIS_C  2 kCpkCgsr 9 
                                      kC +Cg +
  gi|336255048|ref|YP_004598155.1| 19 KCGSCGYT 26
                                      57777755 PP

  == domain 3  score: 68.7 bits;  conditional E-value: 6e-22
                           TFIIS_C  2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39
                                       Cp+Cg+++ay++++Q+RsaDE++t+f+ Ct+C+h+Wr
  gi|336255048|ref|YP_004598155.1| 61 HCPECGNDRAYWYMQQIRSADESETRFFICTECEHKWR 98
                                      7************************************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 !   34.0   1.3     4e-11   1.9e-08       1      35 [.       1      31 [.       1      32 [. 0.96
   2 ?    4.6   1.3     0.065        31       4       9 ..      62      67 ..      61      68 .. 0.96
   3 ?    1.5   0.1       0.6   2.8e+02      16      28 ..      81      94 ..      77      97 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 4e-11
                                      EEBESTTTSBEEEEECSCCCEEEESSSS-EEESSC CS
                    RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepadq 35
                                      ++FC +Cg+++  +++ ++    C +CgY ep+++
  gi|336255048|ref|YP_004598155.1|  1 MEFCDECGSMMKADDGLWK----CGSCGYTEPKGD 31
                                      99*****************....*********975 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.065
                                      ESTTTS CS
                    RNA_POL_M_15KD  4 CpkCgN 9 
                                      Cp+CgN
  gi|336255048|ref|YP_004598155.1| 62 CPECGN 67
                                      *****9 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.6
                                      CSCCCE.EEESSSS CS
                    RNA_POL_M_15KD 16 dkegkn.feCrqCg 28
                                      d++ ++ f C  C 
  gi|336255048|ref|YP_004598155.1| 81 DESETRfFICTECE 94
                                      55556679999996 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 !   10.2   0.4    0.0012      0.56      21      46 .]       4      26 ..       2      26 .. 0.79
   2 !   18.4   0.3   3.2e-06    0.0015      19      45 ..      60      95 ..      42      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                     Zn_Tnp_IS1595 21 CPhCgsrkayriktrglfqCkeCrkq 46
                                      C  Cg  +  +  + gl++C +C+++
  gi|336255048|ref|YP_004598155.1|  4 CDECG--SMMKADD-GLWKCGSCGYT 26
                                      77788..6677777.********985 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.2e-06
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayrikt.........rglfqCkeCrk 45
                                       +CP Cg+++ay + +          + f C eC +
  gi|336255048|ref|YP_004598155.1| 60 AHCPECGNDRAYWYMQqirsadeseTRFFICTECEH 95
                                      67*******77766666999**************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 ?    5.5   0.2     0.025        12      21      32 ..       3      14 ..       2      16 .. 0.83
   2 ?    2.4   0.1      0.24   1.1e+02      22      29 ..      20      27 ..      19      40 .. 0.79
   3 !   18.6   0.3   2.1e-06     0.001       3      33 ..      62     101 ..      60     102 .] 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.025
                                      EESSSSBEEEEC CS
                      TF_Zn_Ribbon 21 vCtdCGlVledn 32
                                      +C +CG+++  +
  gi|336255048|ref|YP_004598155.1|  3 FCDECGSMMKAD 14
                                      5******99866 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.24
                                      ESSSSBEE CS
                      TF_Zn_Ribbon 22 CtdCGlVl 29
                                      C++CG+  
  gi|336255048|ref|YP_004598155.1| 20 CGSCGYTE 27
                                      99**9865 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 2.1e-06
                                       ETTTTCEE.C........HEETSTTCEEESSSSBEEEECC CS
                      TF_Zn_Ribbon   3 CPnCgstn.l........veDpergelvCtdCGlVledns 33 
                                       CP+Cg+++ +          + e+  ++Ct+C+  + +++
  gi|336255048|ref|YP_004598155.1|  62 CPECGNDRaYwymqqirsADESETRFFICTECEHKWREDD 101
                                       ******9977*****995555777777******9998886 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   2.3e-05     0.011      13      38 ..       2      27 ..       1      32 [. 0.84
   2 !    8.3   2.7    0.0049       2.3       7      40 ..      54      99 ..      51     102 .] 0.65

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.3e-05
                               DZR 13 rfCseCgtklkavaaedrCpsCgekv 38
                                      +fC+eCg+ +ka     +C sCg+  
  gi|336255048|ref|YP_004598155.1|  2 EFCDECGSMMKADDGLWKCGSCGYTE 27
                                      69********98888999****9875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0049
                               DZR  7 elppdarfCseCgtk.....lkavaa...........edrCpsCgekvdp 40
                                       lp+ +  C+eCg++     +    +              C +C++k  +
  gi|336255048|ref|YP_004598155.1| 54 SLPETDAHCPECGNDraywyM----QqirsadesetrFFICTECEHKWRE 99
                                      567888899999988554442....1344567777776778888877655 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   2.6   0.00033      0.16       2      24 ..       1      25 [.       1      26 [. 0.90
   2 !   11.1   0.2   0.00043       0.2      13      24 ..      56      67 ..      52      68 .. 0.76
   3 ?    0.9   0.0      0.71   3.3e+02      18      25 ..      89      96 ..      88     102 .] 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                       zf-ribbon_3  2 tvrCPnCGa.p.lssddnvCpyCGt 24
                                      + +C +CG+   ++++  +C +CG+
  gi|336255048|ref|YP_004598155.1|  1 MEFCDECGSmMkADDGLWKCGSCGY 25
                                      679******977999999******7 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00043
                       zf-ribbon_3 13 ssddnvCpyCGt 24
                                       + d +Cp CG 
  gi|336255048|ref|YP_004598155.1| 56 PETDAHCPECGN 67
                                      678889999996 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.71
                       zf-ribbon_3 18 vCpyCGtk 25
                                      +C+ C +k
  gi|336255048|ref|YP_004598155.1| 89 ICTECEHK 96
                                      58888765 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   0.8   5.8e-05     0.027      31      55 ..       4      26 ..       2      35 .. 0.89
   2 !    9.8   3.1    0.0016      0.76      29      59 ..      60     100 ..      45     102 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.8e-05
                    OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfe 55
                                      C eCgs +k   ++ ++kC +Cg++
  gi|336255048|ref|YP_004598155.1|  4 CDECGSMMKA--DDGLWKCGSCGYT 26
                                      **********..***********97 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0016
                    OrfB_Zn_ribbon  29 ktCseCgsknke..........alsgrtfkCpnCgfeadrD 59 
                                         C+eCg    +          + ++r f C++C +++  D
  gi|336255048|ref|YP_004598155.1|  60 AHCPECGNDRAYwymqqirsadESETRFFICTECEHKWRED 100
                                       68*****9999999999999999999**********99777 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.4      0.29   1.3e+02      22      27 ..       4       9 ..       3       9 .. 0.84
   2 ?    1.7   0.1      0.53   2.5e+02      15      27 ..      13      25 ..      13      25 .. 0.84
   3 !   19.1   1.2   1.9e-06   0.00091       4      29 ..      61      97 ..      54      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.29
                    PhnA_Zn_Ribbon 22 CpeCah 27
                                      C+eC++
  gi|336255048|ref|YP_004598155.1|  4 CDECGS 9 
                                      999986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.53
                    PhnA_Zn_Ribbon 15 edgallvCpeCah 27
                                      +d+ l+ C  C++
  gi|336255048|ref|YP_004598155.1| 13 ADDGLWKCGSCGY 25
                                      5899999999986 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 1.9e-06
                    PhnA_Zn_Ribbon  4 kCplCaSeytY...........edgallvCpeCahEw 29
                                      +Cp+C+ + +Y            ++  ++C eC h w
  gi|336255048|ref|YP_004598155.1| 61 HCPECGNDRAYwymqqirsadeSETRFFICTECEHKW 97
                                      8********************999***********99 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       2.1     1e+03     235     245 ..       2      12 ..       1      15 [. 0.83
   2 !   16.8   0.1     1e-05    0.0049     153     205 ..      43      98 ..      34     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.1
                                       EEETTTTEEEE CS
                              FdhE 235 esCdeChsYlk 245
                                       e CdeC s +k
  gi|336255048|ref|YP_004598155.1|   2 EFCDECGSMMK 12 
                                       78999999887 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1e-05
                                       HHT-.-TTSSS-.-TT-SS-TTT---EEE...EEEE-------EEEEEETTT--EEE CS
                              FdhE 153 aaal.dakalaelaeekglCPvCgsaPva...svvriggeaeglRylhCslCeteWh 205
                                       a+++ + ++ ++l e+ ++CP Cg          +r  + ++ +R+  C+ Ce++W+
  gi|336255048|ref|YP_004598155.1|  43 ASEIiESSEETSLPETDAHCPECGNDRAYwymQQIRSAD-ESETRFFICTECEHKWR 98 
                                       444415556667888999******987651114455555.789*************7 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   1.7         9   4.2e+03      35      45 ..      14      24 ..       4      26 .. 0.56
   2 ?   13.2   0.2   0.00013     0.063      11      23 ..      57      69 ..      45      91 .. 0.82
   3 ?   -1.1   0.0       3.7   1.8e+03      10      20 ..      84      94 ..      74      96 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 9
                           DUF3797 35 ddtfyreCkCg 45
                                      dd   +  +Cg
  gi|336255048|ref|YP_004598155.1| 14 DDGLWKCGSCG 24
                                      44444444555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00013
                           DUF3797 11 ekYvqCPeCgNnk 23
                                      e  + CPeCgN++
  gi|336255048|ref|YP_004598155.1| 57 ETDAHCPECGNDR 69
                                      55689*******9 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.7
                           DUF3797 10 dekYvqCPeCg 20
                                      + ++  C eC 
  gi|336255048|ref|YP_004598155.1| 84 ETRFFICTECE 94
                                      45588899996 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   0.00014     0.066      38      68 ..       3      35 ..       1      52 [. 0.69
   2 ?    2.3   0.9      0.38   1.8e+02      35      54 ..      61      80 ..      41      98 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00014
                                      SSSSS.EEEEEETTEEEETTTTEEEE.-BSSSS CS
                   Ribosomal_L37ae 38 fcgkt.kvkRkavgiwkCkkcgktva.GgAytp 68
                                      fc++  ++ +   g+wkC++cg+t   G A ++
  gi|336255048|ref|YP_004598155.1|  3 FCDECgSMMKADDGLWKCGSCGYTEPkGDADQY 35
                                      5666557899999*********98543555555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.38
                                      EESSSSSSEEEEEETTEEEE CS
                   Ribosomal_L37ae 35 tCpfcgktkvkRkavgiwkC 54
                                      +Cp+cg+++  +    i + 
  gi|336255048|ref|YP_004598155.1| 61 HCPECGNDRAYWYMQQIRSA 80
                                      58888887766666666554 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       1.2   5.8e+02      34      43 ..       4      13 ..       3      17 .. 0.75
   2 ?   11.7   0.2   0.00039      0.18      31      51 ..      17      37 ..      11      38 .. 0.85
   3 ?    2.5   0.2      0.29   1.4e+02       4      12 ..      61      69 ..      57      75 .. 0.78
   4 ?    4.3   0.5      0.08        38       5      12 ..      90      97 ..      88     102 .] 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.2
                            HalOD2 34 CtrCGevqaa 43
                                      C +CG +++a
  gi|336255048|ref|YP_004598155.1|  4 CDECGSMMKA 13
                                      8899987765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00039
                            HalOD2 31 vWkCtrCGevqaaAdpShqrV 51
                                       WkC+ CG +    d+  + V
  gi|336255048|ref|YP_004598155.1| 17 LWKCGSCGYTEPKGDADQYIV 37
                                      6********998888887766 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.29
                            HalOD2  4 kCseCsldW 12
                                      +C+eC+ d 
  gi|336255048|ref|YP_004598155.1| 61 HCPECGNDR 69
                                      699999885 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.08
                            HalOD2  5 CseCsldW 12
                                      C+eC+ +W
  gi|336255048|ref|YP_004598155.1| 90 CTECEHKW 97
                                      ******** PP

>> ArfGap  Putative GTPase activating protein for Arf
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.3       3.1   1.5e+03      11      25 ..      15      29 ..       5      31 .. 0.72
   2 ?   12.7   0.3   0.00021       0.1      11      45 ..      57      99 ..      44     102 .] 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.1
                                      CCCCB-TTT-SBS-- CS
                            ArfGap 11 penkvCaDCgakept 25
                                      ++  +C  Cg +ep+
  gi|336255048|ref|YP_004598155.1| 15 DGLWKCGSCGYTEPK 29
                                      455589999998885 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00021
                                      CCCCB-TTT-SBS--EEETTTT........EEE-HHHHHHHCC CS
                            ArfGap 11 penkvCaDCgakeptWaslnlg........vflCieCsgvHrs 45
                                      + +++C +Cg+ ++ W + ++          f+C+eC    r+
  gi|336255048|ref|YP_004598155.1| 57 ETDAHCPECGNDRAYWYMQQIRsadesetrFFICTECEHKWRE 99
                                      35569************9998888888988*******998886 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.018       8.3       2      11 ..       3      12 ..       2      14 .. 0.84
   2 ?    2.1   0.3       0.4   1.9e+02      25      31 ..      20      26 ..      19      27 .. 0.83
   3 ?    8.2   3.0    0.0049       2.3       2      30 ..      61      95 ..      60      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.018
                                      B-TTT--B-E CS
                         Nudix_N_2  2 FCsqCGtpve 11
                                      FC +CG+ ++
  gi|336255048|ref|YP_004598155.1|  3 FCDECGSMMK 12
                                      9*****9765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.4
                                      ETTTTEE CS
                         Nudix_N_2 25 CpaCgti 31
                                      C +Cg++
  gi|336255048|ref|YP_004598155.1| 20 CGSCGYT 26
                                      9999986 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0049
                                      B-TTT--B-E....EE--.TT-SS-EE.EETTTTE CS
                         Nudix_N_2  2 FCsqCGtpve....lrip.dgDnreRl.vCpaCgt 30
                                      +C++CG+  +    ++i  ++++++R+ +C+ C++
  gi|336255048|ref|YP_004598155.1| 61 HCPECGNDRAywymQQIRsADESETRFfICTECEH 95
                                      8******9766777677757888899548****86 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.8       3.4   1.6e+03      33      42 ..       4      13 ..       1      35 [. 0.60
   2 ?   12.7   0.6   0.00025      0.12       3      38 ..      60      95 ..      58     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.4
                           DUF3268 33 CpkCdayvgv 42
                                      C +C++ +++
  gi|336255048|ref|YP_004598155.1|  4 CDECGSMMKA 13
                                      4444443333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00025
                           DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkCda 38
                                       +Cp CG+  ++   ++i ++ + ++ +++C++C+ 
  gi|336255048|ref|YP_004598155.1| 60 AHCPECGNDRAYWYMQQIRSADESETRFFICTECEH 95
                                      58********************************85 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.3    0.0052       2.5      88     154 ..       2      67 ..       1     101 [. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0052
                           TackOD1  88 evCpkCkSidieeqelihhftCgnvgpeeeflkegkleCpkCktkLrhiGvDYdrplevykCnsCks 154
                                       e C +C+S+    + l ++ +Cg+++p+ +  +   ++ ++ ++++ +   + + p+++ +C +C++
  gi|336255048|ref|YP_004598155.1|   2 EFCDECGSMMKADDGLWKCGSCGYTEPKGDADQYI-VTDSQEASEIIESSEETSLPETDAHCPECGN 67 
                                       78************************998765544.4445555666667777777777777777764 PP

>> zf-UBP  Zn-finger in ubiquitin-hydrolases and other protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3    0.0039       1.8       1      20 [.       4      26 ..       4      46 .. 0.81
   2 ?    4.9   0.6     0.071        34       1      19 [.      62      95 ..      60      99 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0039
                                      -TTTH..--..SSEEEETTT--E CS
                            zf-UBP  1 CseCn..se.nknlWlCLkCghv 20
                                      C eC+   + ++ lW C +Cg+ 
  gi|336255048|ref|YP_004598155.1|  4 CDECGsmMKaDDGLWKCGSCGYT 26
                                      9999955233567********86 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.071
                                      -TTTH................--.SSEEEETTT-- CS
                            zf-UBP  1 CseCn................senknlWlCLkCgh 19
                                      C eC+                s +++ ++C +C h
  gi|336255048|ref|YP_004598155.1| 62 CPECGndraywymqqirsadeS-ETRFFICTECEH 95
                                      6667766666666666666433.4889******87 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 ?    3.4   3.7      0.13        61       6      28 ..       3      24 ..       1      24 [. 0.69
   2 ?    6.1   0.1     0.019       8.9       7      13 ..      62      69 ..      60      75 .. 0.75
   3 ?    4.4   0.1     0.064        30      21      27 ..      87      93 ..      87     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
                           zf-RRN7  6 pCgvCgcrsftl.ddGfyyCrrCh 28
                                       C++Cg+      ddG++ C +C+
  gi|336255048|ref|YP_004598155.1|  3 FCDECGS--MMKaDDGLWKCGSCG 24
                                      5778887..555588888888776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.019
                           zf-RRN7  7 CgvCgc.r 13
                                      C++Cg+ r
  gi|336255048|ref|YP_004598155.1| 62 CPECGNdR 69
                                      ******63 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.064
                           zf-RRN7 21 fyyCrrC 27
                                      f++C++C
  gi|336255048|ref|YP_004598155.1| 87 FFICTEC 93
                                      8999999 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2     0.017       7.8      29      55 ..      16      42 ..       3      57 .. 0.74
   2 ?    7.7   2.6    0.0082       3.9       9      39 ..      60      96 ..      58     102 .] 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.017
                           DUF2387 29 eyrECvsCgftdelsekgqsvakelkt 55
                                          C sCg+t+ + +++q + ++ ++
  gi|336255048|ref|YP_004598155.1| 16 GLWKCGSCGYTEPKGDADQYIVTDSQE 42
                                      5567********999988777666554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0082
                           DUF2387  9 avCPrCsemD......kirmweedeveyrECvsCgft 39
                                      a CP C +        +ir  +e e+++  C++C++ 
  gi|336255048|ref|YP_004598155.1| 60 AHCPECGNDRaywymqQIRSADESETRFFICTECEHK 96
                                      78****87334444449999999999*********96 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4    0.0061       2.9       3      50 ..       4      25 ..       1      36 [. 0.62
   2 ?    6.3   3.0     0.019       9.2       2      38 ..      61      96 ..      41     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0061
                                      -SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S---EEEETTEEEE CS
                    zinc-ribbons_6  3 CpeCqqelekrgeqyhCeaCqedlkkealCpeCeqelevlkaCgavdy 50
                                      C eC + ++ ++   +C +C                          +y
  gi|336255048|ref|YP_004598155.1|  4 CDECGSMMKADDGLWKCGSC--------------------------GY 25
                                      55555555555555555555..........................44 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.019
                                      --SSS-S--E.E-SSEEE-TTT--EEEEEEE-SSS-S- CS
                    zinc-ribbons_6  2 kCpeCqqele.krgeqyhCeaCqedlkkealCpeCeqe 38
                                      +CpeC +    +  +q++  + +e+ ++  +C eCe++
  gi|336255048|ref|YP_004598155.1| 61 HCPECGNDRAyWYMQQIR--SADESETRFFICTECEHK 96
                                      799998888878885554..345556666677777654 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 ?    4.2   0.1      0.13        60       3      12 ..       3      12 ..       2      15 .. 0.80
   2 ?    0.7   0.1       1.5   7.2e+02       4       8 ..      20      24 ..      17      39 .. 0.73
   3 ?    6.8   0.0      0.02       9.2       3      10 ..      61      68 ..      59      85 .. 0.70
   4 ?    0.1   0.1       2.3   1.1e+03       4       9 ..      90      95 ..      89     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.13
                           zf-IS66  3 tCpcCGgllk 12
                                       C++CG+ +k
  gi|336255048|ref|YP_004598155.1|  3 FCDECGSMMK 12
                                      6*****9764 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.5
                           zf-IS66  4 CpcCG 8 
                                      C  CG
  gi|336255048|ref|YP_004598155.1| 20 CGSCG 24
                                      55555 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.02
                           zf-IS66  3 tCpcCGgl 10
                                      +Cp+CG +
  gi|336255048|ref|YP_004598155.1| 61 HCPECGND 68
                                      8*****84 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 2.3
                           zf-IS66  4 CpcCGg 9 
                                      C +C +
  gi|336255048|ref|YP_004598155.1| 90 CTECEH 95
                                      888887 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 ?    1.4   9.6      0.68   3.2e+02      69      94 ..      16      67 ..       2      93 .. 0.63
   2 ?    3.1   0.3       0.2        94      68      83 ..      85     100 ..      74     102 .] 0.77

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.68
                                      -EEEETTTS-EEECHHH.HH.........................S-TTTSS CS
                              HypA 69 vkvrCreCgkefeleek.al.........................rCpkCgs 94
                                         +C +Cg++  + ++ ++                         +Cp+Cg+
  gi|336255048|ref|YP_004598155.1| 16 GLWKCGSCGYTEPKGDAdQYivtdsqeaseiiesseetslpetdaHCPECGN 67
                                      3445666665444332212255666666666666666666666666777766 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.2
                                       --EEEETTTS-EEECH CS
                              HypA  68 pvkvrCreCgkefele 83 
                                          + C+eC+++++++
  gi|336255048|ref|YP_004598155.1|  85 TRFFICTECEHKWRED 100
                                       55578*****999865 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   3.4      0.73   3.4e+02       8      33 ..       4      24 ..       3      29 .. 0.59
   2 ?    9.5   0.2    0.0023       1.1      25      34 ..      54      67 ..      37      70 .. 0.62
   3 ?    2.5   0.1      0.34   1.6e+02       6      14 ..      88      96 ..      77      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.73
                       Zn-ribbon_8  8 CeeCghefevlqsis.dapltaCPeCg 33
                                      C+eCg     ++  + d+ l +C +Cg
  gi|336255048|ref|YP_004598155.1|  4 CDECG----SMM--KaDDGLWKCGSCG 24
                                      77777....333..2244555677776 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0023
                       Zn-ribbon_8 25 p....ltaCPeCgs 34
                                      +    + +CPeCg 
  gi|336255048|ref|YP_004598155.1| 54 SlpetDAHCPECGN 67
                                      23332555****97 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.34
                       Zn-ribbon_8  6 YrCeeCghe 14
                                      + C+eC h+
  gi|336255048|ref|YP_004598155.1| 88 FICTECEHK 96
                                      569999886 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.9    0.0071       3.3      27      89 ..      34      96 ..       1     100 [. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0071
                        zf-RRPl_C4 27 yfkvknekqkvelvpikelekislrdkLCtkCkeknekeke..ircetfeeylkklklCkeCker 89
                                       + v+++++  e ++++e + + ++d  C +C +      +  ir+   +e  ++  +C+eC ++
  gi|336255048|ref|YP_004598155.1| 34 QYIVTDSQEASEIIESSEETSLPETDAHCPECGNDRAYWYMqqIRSA--DESETRFFICTECEHK 96
                                      46678888899999999999************887665433127666..999999*******875 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.059        28      15      21 ..       3       9 ..       2      11 .. 0.80
   2 ?    1.9   1.6      0.41   1.9e+02       1       7 [.      19      25 ..      19      26 .. 0.67
   3 ?    9.5   0.2    0.0017      0.79       9      21 ..      55      67 ..      53      68 .. 0.76
   4 ?    1.2   0.1       0.7   3.3e+02       2       7 ..      90      95 ..      86     102 .] 0.77

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.059
                     zinc_ribbon_2 15 FCpyCGt 21
                                      FC +CG+
  gi|336255048|ref|YP_004598155.1|  3 FCDECGS 9 
                                      8999986 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.41
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +C +CG+
  gi|336255048|ref|YP_004598155.1| 19 KCGSCGY 25
                                      6777775 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0017
                     zinc_ribbon_2  9 lqdnakFCpyCGt 21
                                      l++++  Cp+CG 
  gi|336255048|ref|YP_004598155.1| 55 LPETDAHCPECGN 67
                                      7888888999885 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.7
                     zinc_ribbon_2  2 CpnCGa 7 
                                      C++C +
  gi|336255048|ref|YP_004598155.1| 90 CTECEH 95
                                      888865 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 ?    7.5   0.3    0.0088       4.2       4      14 ..       4      14 ..       4      15 .. 0.87
   2 ?    4.1   0.3      0.11        50       2       8 ..      18      24 ..      18      26 .. 0.89
   3 ?    2.7   1.3       0.3   1.4e+02       4       9 ..      62      67 ..      61      67 .. 0.81
   4 ?    3.1   0.0      0.22   1.1e+02      19      26 .]      86      93 ..      81      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0088
                            zf-ACC  4 CpsCgemlykk 14
                                      C++Cg+m+ + 
  gi|336255048|ref|YP_004598155.1|  4 CDECGSMMKAD 14
                                      *******9876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.11
                            zf-ACC  2 tKCpsCg 8 
                                      +KC sCg
  gi|336255048|ref|YP_004598155.1| 18 WKCGSCG 24
                                      6*****9 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.3
                            zf-ACC  4 CpsCge 9 
                                      Cp+Cg+
  gi|336255048|ref|YP_004598155.1| 62 CPECGN 67
                                      999985 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.22
                            zf-ACC 19 nlyVCPkC 26
                                       +++C++C
  gi|336255048|ref|YP_004598155.1| 86 RFFICTEC 93
                                      57899999 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 ?    8.8   0.7    0.0032       1.5       6      27 ..       3      24 ..       1      28 [. 0.92
   2 ?    2.9   0.2      0.22     1e+02      23      27 ..      62      66 ..      56      70 .. 0.76
   3 ?    1.2   0.1      0.77   3.6e+02       6      17 ..      89     100 ..      84     102 .] 0.67

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0032
                       Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCg 27
                                       C  Cg  +k +d +  C  Cg
  gi|336255048|ref|YP_004598155.1|  3 FCDECGSMMKADDGLWKCGSCG 24
                                      5********************9 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.22
                       Prok-RING_1 23 CpeCg 27
                                      CpeCg
  gi|336255048|ref|YP_004598155.1| 62 CPECG 66
                                      88887 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.77
                       Prok-RING_1   6 kCpvCgkelkee 17 
                                       +C+ C+++ +e+
  gi|336255048|ref|YP_004598155.1|  89 ICTECEHKWRED 100
                                       466676666665 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 ?    7.1   0.1     0.013       6.1      25      32 ..       3      10 ..       1      11 [. 0.83
   2 ?   -0.2   0.4       2.5   1.2e+03       1       6 [.      19      24 ..      16      26 .. 0.83
   3 ?    7.2   1.1     0.012       5.7      10      30 ..      39      66 ..      35      66 .. 0.64
   4 ?    1.0   0.1         1   4.9e+02      16      29 ..      76      93 ..      74      94 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                                      E-TTT--E CS
                         zf-RING_7 25 tCpeCGRI 32
                                      +C+eCG +
  gi|336255048|ref|YP_004598155.1|  3 FCDECGSM 10
                                      9*****87 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.5
                                      EETTT- CS
                         zf-RING_7  1 tCgGCh 6 
                                      +Cg C+
  gi|336255048|ref|YP_004598155.1| 19 KCGSCG 24
                                      688886 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.012
                                      -CCHHHHHCCS.TB..-....EE-TTT- CS
                         zf-RING_7 10 ppqvlselrag.de..v....vtCpeCG 30
                                      ++q+ se+    +e  +    ++CpeCG
  gi|336255048|ref|YP_004598155.1| 39 DSQEASEIIESsEEtsLpetdAHCPECG 66
                                      6788888866642233234459*****9 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 1
                                      HHCCSTB....-EE-TTT CS
                         zf-RING_7 16 elragde....vvtCpeC 29
                                      ++r +de     + C eC
  gi|336255048|ref|YP_004598155.1| 76 QIRSADEsetrFFICTEC 93
                                      577776655557999999 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   7.0     0.075        35       3      21 ..       4      24 ..       3      25 .. 0.80
   2 ?    6.5   1.7     0.014       6.8       1      11 [.      18      28 ..      18      29 .. 0.77
   3 ?    5.7   0.4     0.027        13       3       8 ..      62      67 ..      61      73 .. 0.51
   4 ?    1.7   0.2      0.46   2.2e+02       1       8 [.      88      95 ..      88      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.075
                      Rubredoxin_2  3 CsqCGfe..sakwfGrCpsCg 21
                                      C++CG+   +   +++C sCg
  gi|336255048|ref|YP_004598155.1|  4 CDECGSMmkADDGLWKCGSCG 24
                                      9999986226678*******8 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                      Rubredoxin_2  1 YvCsqCGfesa 11
                                      + C +CG++ +
  gi|336255048|ref|YP_004598155.1| 18 WKCGSCGYTEP 28
                                      67999999877 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.027
                      Rubredoxin_2  3 CsqCGf 8 
                                      C +CG+
  gi|336255048|ref|YP_004598155.1| 62 CPECGN 67
                                      555555 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.46
                      Rubredoxin_2  1 YvCsqCGf 8 
                                      ++C +C +
  gi|336255048|ref|YP_004598155.1| 88 FICTECEH 95
                                      78988865 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 ?    4.6   0.7      0.06        28      22      29 ..       2       9 ..       1      13 [. 0.89
   2 ?    3.3   3.0      0.15        73      17      33 .]      13      29 ..       4      29 .. 0.73
   3 ?    4.2   0.0     0.079        37      24      29 ..      62      67 ..      59      75 .. 0.84
   4 ?    0.3   0.5       1.3     6e+02       6      10 ..      90      94 ..      88      96 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.06
                     A2L_zn_ribbon 22 lvCieCga 29
                                      ++C eCg+
  gi|336255048|ref|YP_004598155.1|  2 EFCDECGS 9 
                                      8******8 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.15
                     A2L_zn_ribbon 17 seqgylvCieCgasfpy 33
                                      +++g   C  Cg+++p+
  gi|336255048|ref|YP_004598155.1| 13 ADDGLWKCGSCGYTEPK 29
                                      57777789999999985 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.079
                     A2L_zn_ribbon 24 CieCga 29
                                      C+eCg+
  gi|336255048|ref|YP_004598155.1| 62 CPECGN 67
                                      999986 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 1.3
                     A2L_zn_ribbon  6 CsvCg 10
                                      C+ C 
  gi|336255048|ref|YP_004598155.1| 90 CTECE 94
                                      55554 PP

>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.0     0.011       5.1      20      45 .]       4      26 ..       2      26 .. 0.87
   2 ?    2.5   0.1      0.34   1.6e+02      18      26 ..      60      67 ..      51      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                                      -SS-S-TTSBEEECTTEEEESSTTTE CS
                     Ribosomal_S27 20 CpreCGaGvfMAehkdRkyCGkCglT 45
                                      C + C  G  M    + + CG+Cg+T
  gi|336255048|ref|YP_004598155.1|  4 CDE-C--GSMMKADDGLWKCGSCGYT 26
                                      888.9..8999888889********9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.34
                                      -B-SS-S-T CS
                     Ribosomal_S27 18 keCpreCGa 26
                                       +Cp+ CG+
  gi|336255048|ref|YP_004598155.1| 60 AHCPE-CGN 67
                                      58***.*97 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0027       1.3       4      15 ..       3      14 ..       1      15 [. 0.84
   2 ?   -1.2   0.1       3.3   1.5e+03       3       9 ..      18      24 ..      16      28 .. 0.82
   3 ?    2.4   0.3      0.25   1.2e+02       5       9 ..      62      66 ..      58      69 .. 0.87
   4 ?    2.9   0.2      0.18        85       3      11 ..      88      96 ..      86     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0027
                            zf_UBZ  4 lCerCgkeipes 15
                                      +C++Cg+++  +
  gi|336255048|ref|YP_004598155.1|  3 FCDECGSMMKAD 14
                                      8*******9876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.3
                            zf_UBZ  3 ylCerCg 9 
                                      + C  Cg
  gi|336255048|ref|YP_004598155.1| 18 WKCGSCG 24
                                      7899998 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.25
                            zf_UBZ  5 CerCg 9 
                                      C++Cg
  gi|336255048|ref|YP_004598155.1| 62 CPECG 66
                                      ****9 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.18
                            zf_UBZ  3 ylCerCgke 11
                                      ++C +C ++
  gi|336255048|ref|YP_004598155.1| 88 FICTECEHK 96
                                      89****876 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.4      0.27   1.3e+02      24      42 ..       3      23 ..       2      35 .. 0.76
   2 ?    2.8   0.1      0.25   1.2e+02      34      43 ..      57      66 ..      44      67 .. 0.75
   3 ?    7.8   1.2    0.0068       3.2       1      22 [.      61      95 ..      61      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.27
                         zf-RING_5 24 fCekClkkll..ekeavCpiC 42
                                      fC++C +  +      +C  C
  gi|336255048|ref|YP_004598155.1|  3 FCDECGSMMKadDGLWKCGSC 23
                                      899999988855444455555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.25
                         zf-RING_5 34 ekeavCpiCr 43
                                      e +a Cp C+
  gi|336255048|ref|YP_004598155.1| 57 ETDAHCPECG 66
                                      5678999997 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0068
                         zf-RING_5  1 hCnkCfekl.............skeekfyltsCgH 22
                                      hC+ C +               s+++ f+ t+C H
  gi|336255048|ref|YP_004598155.1| 61 HCPECGNDRaywymqqirsadeSETRFFICTECEH 95
                                      9*****99999***9999998888888*******9 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 ?    4.6   0.2       0.1        48       7      16 ..       3      12 ..       1      14 [. 0.89
   2 ?    4.9   0.1     0.082        39       4      13 ..      16      25 ..      15      38 .. 0.91
   3 ?    2.1   1.8      0.58   2.7e+02       8      30 ..      62      91 ..      60      99 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.1
                   Zn_ribbon_recom  7 rCgeCGspmt 16
                                      +C eCGs m+
  gi|336255048|ref|YP_004598155.1|  3 FCDECGSMMK 12
                                      8******997 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.082
                   Zn_ribbon_recom  4 GllrCgeCGs 13
                                      Gl +Cg CG 
  gi|336255048|ref|YP_004598155.1| 16 GLWKCGSCGY 25
                                      8899*****7 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.58
                   Zn_ribbon_recom  8 CgeCGsp.....mtrrkrk..gkrhyYrCs 30
                                      C eCG+      m + ++   ++++ ++C 
  gi|336255048|ref|YP_004598155.1| 62 CPECGNDraywyMQQIRSAdeSETRFFICT 91
                                      888887655443333332234444444444 PP

>> Rdx  Rdx family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.082        39       5      17 ..       2      14 ..       1      16 [. 0.87
   2 ?   -0.3   0.0       2.6   1.2e+03       7      24 ..      20      37 ..      19      57 .. 0.68
   3 ?    3.2   0.2      0.21     1e+02       6      25 ..      61      79 ..      60      88 .. 0.75
   4 ?   -1.1   0.2       4.6   2.2e+03       5      13 ..      88      96 ..      84      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.082
                                      EEETTTTTHHHHH CS
                               Rdx  5 eYCtqCkwmlraa 17
                                      e+C++C+ m +a 
  gi|336255048|ref|YP_004598155.1|  2 EFCDECGSMMKAD 14
                                      8*******99885 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.6
                                      ETTTTTHHHHHHHHHHHH CS
                               Rdx  7 CtqCkwmlraaelaqell 24
                                      C +C++ +   +  q + 
  gi|336255048|ref|YP_004598155.1| 20 CGSCGYTEPKGDADQYIV 37
                                      899999876555555554 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.21
                                      EETTTTTHHHHHHHHHHHHH CS
                               Rdx  6 YCtqCkwmlraaelaqells 25
                                       C +C+   ra ++ q++ s
  gi|336255048|ref|YP_004598155.1| 61 HCPECGN-DRAYWYMQQIRS 79
                                      5999996.577777777765 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 4.6
                                      EEETTTTTH CS
                               Rdx  5 eYCtqCkwm 13
                                        Ct+C+ +
  gi|336255048|ref|YP_004598155.1| 88 FICTECEHK 96
                                      57****865 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 ?    0.7   4.6       0.9   4.3e+02       3      25 ..       4      25 ..       3      26 .. 0.69
   2 ?    3.3   0.1      0.14        66      19      24 ..      61      66 ..      50      69 .. 0.73
   3 ?    4.1   0.1     0.081        38       2      10 ..      89      97 ..      88     102 .] 0.76

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.9
                                      -SSS--B----SSS----SSS-- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCGh 25
                                      C eCg+ ++ + g   +C  CG+
  gi|336255048|ref|YP_004598155.1|  4 CDECGSMMKADDG-LWKCGSCGY 25
                                      6777777776666.667777776 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                                      --SSS- CS
                    DNA_RNApol_7kD 19 RCkeCG 24
                                       C eCG
  gi|336255048|ref|YP_004598155.1| 61 HCPECG 66
                                      699998 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.081
                                      B-SSS--B- CS
                    DNA_RNApol_7kD  2 iCgeCgaev 10
                                      iC eC+++ 
  gi|336255048|ref|YP_004598155.1| 89 ICTECEHKW 97
                                      899998876 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8  11.3       5.8   2.8e+03      37      86 .]      17      66 ..       2     102 .] 0.64

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 5.8
                    zinc_ribbon_15 37 ylacskCkslleaskelgkeiekkessekkeCknCgkeveeefkyCpkCg 86
                                      + +c +C+++ ++ +  +  +++++++++ + ++ ++++ e  ++Cp+Cg
  gi|336255048|ref|YP_004598155.1| 17 LWKCGSCGYTEPKGDADQYIVTDSQEASEIIESSEETSLPETDAHCPECG 66
                                      56677777766666644444444444443333333444455555555555 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 ?    5.7   0.5     0.029        14       5      12 ..      18      25 ..      17      28 .. 0.83
   2 ?    4.1   0.2     0.092        43       5      13 ..      60      68 ..      59      71 .. 0.78
   3 ?   -1.1   0.1       3.8   1.8e+03       7      10 ..      90      93 ..      88      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.029
                    Zn_ribbon_SprT  5 YrCtgCgr 12
                                      ++C++Cg 
  gi|336255048|ref|YP_004598155.1| 18 WKCGSCGY 25
                                      9******4 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.092
                    Zn_ribbon_SprT  5 YrCtgCgre 13
                                      ++C+ Cg+ 
  gi|336255048|ref|YP_004598155.1| 60 AHCPECGND 68
                                      68*****65 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.8
                    Zn_ribbon_SprT  7 CtgC 10
                                      Ct C
  gi|336255048|ref|YP_004598155.1| 90 CTEC 93
                                      9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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):              38  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 743.84
//
Query:       gi|336255049|ref|YP_004598156.1|  [L=458]
Description: hypothetical protein Halxa_3669 [Halopiger xanaduensis SH-6]
Scores for 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   13.2   0.0       0.38   11.5   0.0    1.9  2  FliD_N        Flagellar hook-associated protein 2 N-terminus
        8.5    6.7  13.9        1.5    9.1   0.8    4.2  5  ABC_tran_CTD  ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> 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 ?   -2.1   0.0      0.71   6.3e+03      21      49 ..      88     116 ..      81     139 .. 0.58
   2 ?   11.5   0.0   4.3e-05      0.38      20      87 ..     170     243 ..     151     253 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.71
                                       XXXXXXXXXXXXXHHHHHHHHHHHHHHHH CS
                            FliD_N  21 dkleqkktklewkqsayrelnsklsnlks 49 
                                       +++e +++ le   +++++    l+++ +
  gi|336255049|ref|YP_004598156.1|  88 KRVEHAESRLEDAAAELEAADDRLDAFGT 116
                                       55555555555555555555555555544 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.3e-05
                                       XXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHH....HHHXX.GGGG.GXEEEEECSTTTEEEEEETTS-SEEEE CS
                            FliD_N  20 ldkleqkktklewkqsayrelnsklsnlksal....salsk.sstf.sakkatssdesvvtatassgaaagsys 87 
                                        d l+ + t+l+   +ay+el   l++++ ++     +l++  st  s+  at+s+++++ a as  a++   +
  gi|336255049|ref|YP_004598156.1| 170 ADDLTYRATELSRAVAAYGELDERLEDVRLTIragrRSLEStGSTGqSNADATVSTDDMMLARASMRASDAAAE 243
                                       56789999**********************99765426644222221234788888888777777666665555 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 ?    9.1   0.8   0.00017       1.5      15      62 ..      61     109 ..      57     113 .. 0.91
   2 ?   -0.7   0.0      0.19   1.7e+03      19      58 ..     161     195 ..     150     199 .. 0.60
   3 ?   -1.7   0.1      0.39   3.5e+03      33      59 ..     220     246 ..     217     257 .. 0.70
   4 ?    0.7   0.1     0.073   6.6e+02      28      60 ..     251     283 ..     242     286 .. 0.68
   5 ?    2.6   0.5     0.018   1.6e+02      24      62 ..     377     416 ..     371     417 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00017
                      ABC_tran_CTD  15 aeIeaLEeeiaeleaeladpelysdp.eklaelsaeleeleaeLeelye 62 
                                       a ++ LE ++++ + +  d ++  dp +++  +  +le++ aeLe++ +
  gi|336255049|ref|YP_004598156.1|  61 AALDDLERRLTDAQRAWDDFDVEDDPrKRVEHAESRLEDAAAELEAADD 109
                                       56789*****************9999999****************9865 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.19
                      ABC_tran_CTD  19 aLEeeiaeleaeladpelysdpeklaelsaeleeleaeLe 58 
                                       aLE e  ++ + l   +     ++l+++ a + el++ Le
  gi|336255049|ref|YP_004598156.1| 161 ALEDEYGAVADDLTYRA-----TELSRAVAAYGELDERLE 195
                                       55555555555555443.....566666666666666666 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.39
                      ABC_tran_CTD  33 dpelysdpeklaelsaeleeleaeLee 59 
                                       d+++ +d+  la++s +  ++ aeLe 
  gi|336255049|ref|YP_004598156.1| 220 DATVSTDDMMLARASMRASDAAAELED 246
                                       556666667777777777777777775 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.073
                      ABC_tran_CTD  28 eaeladpelysdpeklaelsaeleeleaeLeel 60 
                                        ++lad++    +     l a++e+l+ e+e+ 
  gi|336255049|ref|YP_004598156.1| 251 ADRLADEAGADADVVDDVLDARYETLNGEIEAT 283
                                       557777776544455666788899998888875 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.018
                      ABC_tran_CTD  24 iaeleaeladpelysdp.ek..laelsaeleeleaeLeelye 62 
                                         elea+l +++   dp  +   ael a le  +  Le+++e
  gi|336255049|ref|YP_004598156.1| 377 VDELEARLDAEG--DDPlVRylCAELAADLESHDGRLERALE 416
                                       568999999888..8888556699**************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3450.02
//
Query:       gi|336255050|ref|YP_004598157.1|  [L=88]
Description: hypothetical protein Halxa_3670 [Halopiger xanaduensis SH-6]
Scores for 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:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 751.82
//
Query:       gi|336255051|ref|YP_004598158.1|  [L=430]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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-48  164.2  52.1      4e-25   88.5  25.9    2.1  2  MFS_1       Major Facilitator Superfamily
    3.9e-10   39.2  27.5    3.8e-08   32.6   4.5    3.1  3  Sugar_tr    Sugar (and other) transporter
    1.4e-06   27.5  10.7    6.3e-06   25.3  10.7    2.0  1  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
      0.015   14.1   0.0      0.024   13.5   0.0    1.2  1  ALMT        Aluminium activated malate transporter


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 !   88.5  25.9   8.9e-29     4e-25       2     198 ..      22     239 ..      21     261 .. 0.78
   2 !   77.1  24.9   2.6e-25   1.2e-21       4     172 ..     246     410 ..     240     424 .. 0.84

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 8.9e-29
                             MFS_1   2 llaaflsalarsilgpalplalaed......lgispse.igllltlyalgaavaslplGrlsdrfGrrr.vlllgll 70 
                                       ++a +  +++ s+l++++pl++++       +g+++s  igl+l+l++++ + +++++Grlsdr Grr+ ++l+gl+
  gi|336255051|ref|YP_004598158.1|  22 AFARMADGIGNSFLIIVIPLYVSSGlvggptFGLAESMlIGLILSLFGFLNSSFQPLTGRLSDRTGRRKpFILIGLA 98 
                                       7888999999*********88866644444477666668************************************** PP

                             MFS_1  71 lfalg.lllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllas 146
                                       ++a++ l++ l a ++ +l+v r lqG+  ++++pa++al+ ++++ e+rg  +g+++++  +G+  gp+++g+++ 
  gi|336255051|ref|YP_004598158.1|  99 GLAVTnLAYVL-AETYAALVVIRGLQGVSVSFIIPASVALVNELATTEDRGGNMGVYNTFRLVGFGAGPVAAGAVV- 173
                                       *****444444.57766***********************************************************. PP

                             MFS_1 147 slg...........Wravfyilaivsllafvlfllllpeepperkrkspkeee.....kgtgpaplvp 198
                                       +lg           + a+fy++ai + ++ +l+ +l+++++++ ++     ++      + gp  l p
  gi|336255051|ref|YP_004598158.1| 174 NLGpyrlggltlsgFDAAFYVAAITATISYLLVTVLITDPESTQANA--GADLsidvlDRSGPNLLDP 239
                                       7778*************************999666665555555544..3332133333333333333 PP

  == domain 2  score: 77.1 bits;  conditional E-value: 2.6e-25
                             MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                       a +++a+a+++++++ p  ++  l    + +gl ++++ ++++v++ p+Gr  dr+Grr+++l g+++++ + +l  
  gi|336255051|ref|YP_004598158.1| 246 ASLFMAAAIALFATIQP-QVNARLEQGSTWFGLQFAAFIVAQIVLQTPIGRACDRYGRRPFILGGMIVLIPS-TLVQ 320
                                       33444444444444445.666666666666******************************************.5555 PP

                             MFS_1  81 .fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyi 156
                                        f+ ++ +++++r+ qG++++++f+ ++al+ d++ + e g+ +++l+++f++G+++gp ++g+l+  +g+ a+f++
  gi|336255051|ref|YP_004598158.1| 321 gFVLTSEAMFLARLAQGIAGAMVFAPSLALAGDLAGEGESGSKLSVLTMAFGFGIAVGPFASGALV-GYGFAAPFVF 396
                                       57656669**********************************************************.999******* PP

                             MFS_1 157 laivsllafvlfllll 172
                                        ++++ l+++l  ++ 
  gi|336255051|ref|YP_004598158.1| 397 GTVLASLGAIL--VYT 410
                                       ********996..443 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0     0.083   3.7e+02     100     128 ..      16      44 ..       8      46 .. 0.85
   2 !   32.6   4.5   8.5e-12   3.8e-08      45     191 ..      58     209 ..      51     239 .. 0.78
   3 !   11.5  14.6   2.1e-05     0.096      10     189 ..     184     409 ..     179     415 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.083
                                       SS-TGGGGGHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 100 nsvevlivgRvlvGigvGlasvlvPmyis 128
                                       + v +l+++R+  Gig  +  +++P+y+s
  gi|336255051|ref|YP_004598158.1|  16 RRVLALAFARMADGIGNSFLIIVIPLYVS 44 
                                       567889999******************97 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 8.5e-12
                                       ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHH.HHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslli.aavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                       s+l+gli+s+f +     + ++g l+dr GR+k ++  + + + + ++  ++a+   ++ +l+v R l G++v ++ 
  gi|336255051|ref|YP_004598158.1|  58 SMLIGLILSLFGFLNSSFQPLTGRLSDRTGRRKPFILiGLAGLAVTNLAYVLAE---TYAALVVIRGLQGVSVSFII 131
                                       6788888888888888888899*********99988747778999999999999...9******************* PP

                                       HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHH...HHHHHHHHHHHTSS-....TTHHHHHHHCCHHHHHHHHHHGGG CS
                          Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGi...lvaaifglglnktsn....adgwrillglqlvpallllilllf 190
                                         +  +++E+A+++ Rg  +++y+++  +G+    vaa+  ++l  ++      +g+   ++++++ a +  +l+++
  gi|336255051|ref|YP_004598158.1| 132 PASVALVNELATTEDRGGNMGVYNTFRLVGFgagPVAAGAVVNLGPYRLggltLSGFDAAFYVAAITATISYLLVTV 208
                                       ****************9999999998888863335666666665444446688778888888888887665555544 PP

                                       S CS
                          Sugar_tr 191 l 191
                                       l
  gi|336255051|ref|YP_004598158.1| 209 L 209
                                       4 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHC.GGGTHHHHHHHHTSTT--SHHHHHH.......................................... CS
                          Sugar_tr  10 llfgYdtgv.igafltllkfaknfglsksksskee.......................................... 43 
                                       +l g+d ++ ++a+++ ++++    l +  +s+++                                          
  gi|336255051|ref|YP_004598158.1| 184 TLSGFDAAFyVAAITATISYLLVTVLITDPESTQAnagadlsidvldrsgpnlldpiftlgvaslfmaaaialfati 260
                                       56666655413444444555555555444444444556666666666666666666666666666666666666666 PP

                                       .............HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHH CS
                          Sugar_tr  44 ..........ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRv 110
                                                  s++ gl +++f+v +i+ +  +g + dr+GR++ +l + ++++ ++++q++     + e+++++R+
  gi|336255051|ref|YP_004598158.1| 261 qpqvnarleqGSTWFGLQFAAFIVAQIVLQTPIGRACDRYGRRPFILGGMIVLIPSTLVQGFVL---TSEAMFLARL 334
                                       6666666666889***************************************************...89******** PP

                                       HHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHH CS
                          Sugar_tr 111 lvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllil 187
                                         Gi+  ++ + +  +++ +A +   g   s+  +a  fGi v+ +   +l  +++  g+  ++ +  v+a l +il
  gi|336255051|ref|YP_004598158.1| 335 AQGIAGAMVFAPSLALAGDLAGEGESGSKLSVLTMAFGFGIAVGPFASGAL--VGY--GFAAPFVFGTVLASLGAIL 407
                                       ****9888888888899999*999999999988888888888887665544..333..4457888888888777777 PP

                                       GG CS
                          Sugar_tr 188 ll 189
                                       ++
  gi|336255051|ref|YP_004598158.1| 408 VY 409
                                       65 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 !   25.3  10.7   1.4e-09   6.3e-06      35     379 ..      60     392 ..      53     397 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.4e-09
                        MFS_1_like  35 eigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsvaqdvdaektf 111
                                        ig+i+++  +++   +p++g l+Dr+g+rk+ ++++l   av+ l+ +                         +t+
  gi|336255051|ref|YP_004598158.1|  60 LIGLILSLFGFLNSSFQPLTGRLSDRTGRRKPFILIGLAGLAVTNLAYV-----------------------LAETY 113
                                       68999999999999999***************************99777.......................45677 PP

                        MFS_1_like 112 wilfllvvl....asfflaailvlldaatlkelgedrkdyGrqrlfGsvGyaifafitGilidhysvnllp.....y 179
                                       ++l++++ l     sf+++a+++l++ +   +++++ ++ G    f  vG++   ++ G++++     l +     +
  gi|336255051|ref|YP_004598158.1| 114 AALVVIRGLqgvsVSFIIPASVALVNEL--ATTEDRGGNMGVYNTFRLVGFGAGPVAAGAVVNLGPYRLGGltlsgF 188
                                       7777776652222578888888888765..456778888888888999***************98887755889999 PP

                        MFS_1_like 180 sallyvlaallvisllvvlilnetekesklkvtksl.........qvllnilknpeviifllvalilgmswgiienF 247
                                        a++yv+a+  +is l+v +l  +   ++ +  + l          +ll  +    v+ ++++a+i   +++ i+  
  gi|336255051|ref|YP_004598158.1| 189 DAAFYVAAITATISYLLVTVLITDPESTQANAGADLsidvldrsgPNLLDPIFTLGVASLFMAAAIA--LFATIQPQ 263
                                       99************99998888877777777776555666653332233333333333333333332..23334444 PP

                        MFS_1_like 248 lflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhg 324
                                       ++     l+  +t  G   a   va+i+l     +  +++G +  ++ ++++ i   l+ +++     ++++ + +g
  gi|336255051|ref|YP_004598158.1| 264 VNA---RLEQGSTWFGLQFAAFIVAQIVLQTPIGRACDRYGRRPFILGGMIVLIPSTLVQGFVLTSEAMFLARLAQG 337
                                       444...4566789999999999*****************************************999999******** PP

                        MFS_1_like 325 isfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllw.dlksa 379
                                       i+ ++++a     + ++a+++  +   ++l+++ fg+G a+G +++G+l    + a
  gi|336255051|ref|YP_004598158.1| 338 IAGAMVFAPSLALAGDLAGEGESGSKLSVLTMA-FGFGIAVGPFASGALVgYGFAA 392
                                       ******************************998.*************998333444 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.4e-06     0.024      97     169 ..     245     319 ..     223     321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.4e-06
                              ALMT  97 gvsvFiiaalatflrliPaikarYdYgvlvflLTFclvvvsgyrtdevielAvkRflt..iaiGaliclivsifv 169
                                       ++s F++aa+a f+ + P++ ar + g + f L F+  +v++   ++ i  A +R      ++G++i+li s +v
  gi|336255051|ref|YP_004598158.1| 245 VASLFMAAAIALFATIQPQVNARLEQGSTWFGLQFAAFIVAQIVLQTPIGRACDRYGRrpFILGGMIVLIPSTLV 319
                                       6799***************************************************85433889999999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); 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):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3222.67
//
Query:       gi|336255052|ref|YP_004598159.1|  [L=169]
Description: hypothetical protein Halxa_3672 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.02   15.2   0.1      0.059   13.7   0.1    1.9  1  PqqD      Coenzyme PQQ synthesis protein D (PqqD)
      0.021   15.5   0.3        6.3    7.5   0.0    2.4  2  HTH_32    Homeodomain-like domain


Domain annotation for each model (and alignments):
>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.6e-06     0.059      31      67 .]     106     142 ..      90     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.6e-06
                                       -..HHHHHHHHHHHCT--HHHHHHHHHHHHHHHHCTT-- CS
                              PqqD  31 s..veeivaalaeeydvdeeeaeadvlafldqLrekgli 67 
                                       s  v  + ++l++e+dvd+   ++dv++ l+ Lr+k+++
  gi|336255052|ref|YP_004598159.1| 106 SesVVSVLHKLRDEFDVDP--DAEDVRSGLQSLRRKDVV 142
                                       1359999***********9..99************9876 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0007       6.3      29      58 ..       3      42 ..       2      50 .. 0.84
   2 ?    5.9   0.1    0.0023        20      16      65 ..      72     125 ..      58     149 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0007
                            HTH_32 29 lsdevrariiallreep........rW...sprqlaarlae 58
                                      ls+e r+r+ ++++ +p        rW   s ++++++l e
  gi|336255052|ref|YP_004598159.1|  3 LSEEARDRLADVVELQPtknselqdRWgmeSGSEVHQYL-E 42
                                      89***********8799999*******777777799999.3 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0023
                            HTH_32  16 gLk.drprrgrprk.lsdevrariiallreep...rWsprqlaarlaeregvkvS 65 
                                       g++ d +  g+p++   +e++a+i+++l   p     s   + ++l++++ v++ 
  gi|336255052|ref|YP_004598159.1|  72 GIEsDPEAEGAPSRiRVPELQAQIVQVL-AGPdeeSESVVSVLHKLRDEFDVDPD 125
                                       5552334458998537899*********.77744433444555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1335.43
//
Query:       gi|336255053|ref|YP_004598160.1|  [L=326]
Description: alpha/beta hydrolase fold protein [Halopiger xanaduensis SH-6]
Scores for complete 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   94.6   4.5    1.8e-26   94.1   4.5    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family
      2e-12   47.3   0.0    2.2e-10   40.7   0.0    2.1  1  Abhydrolase_1  alpha/beta hydrolase fold
    5.4e-09   35.7   0.0    8.9e-09   35.0   0.0    1.4  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.029   14.8   0.0       0.04   14.3   0.0    1.2  1  DUF4198        Domain of unknown function (DUF4198)


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   4.5   4.1e-30   1.8e-26       2     219 ..      63     305 ..      62     306 .. 0.74

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 4.1e-30
                                       EEE--..GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT...TTSEEEEEETCH CS
                     Abhydrolase_6   2 lllHG..agssassWlvapLaallaagvhvlapDlpGhGrsdpppldledladlaalldelaa.gggpvvlvGHSlG 75 
                                       ll+HG  +g+s++ +   p+++ la+++hv+a+DlpG+Grs++ppl +++   +a++++++aa +++++++v+ Sl 
  gi|336255053|ref|YP_004598160.1|  63 LLCHGiyTGASSHEFE--PVVEQLAEDYHVIAVDLPGFGRSERPPLVYSP-TLYAEFIRDFAAdVTDEPIVVASSLT 136
                                       9****66666677776..999999************************99.88888888888888999********* PP

                                       HHHHHHHHHCC........EE.EEES-..----TTTS----TTHHHHHHTT-C.CCCHCCH......S-HSCCCCHH CS
                     Abhydrolase_6  76 Galalaaapla......lvvg.vlldppptalpagllaaalelllallallrl.lawlsre......plprlflade 138
                                       Gala     +a      + +  vl++p   ++ +g ++++l+ ll+ + + ++ + +l+ +      ++++++++ +
  gi|336255053|ref|YP_004598160.1| 137 GALAVD---GAgeqeseF-EHlVLICP---TDETGGQRPWLRTLLRTPIVGTTlYNLLASKpsiryfYDRDGYYDSD 206
                                       ******...888888853.446*****...99999988888888888886665322222222333433444777744 PP

                                       H....C.CCCHCHCCCGHHHHCC......HHC.......HTTCCHHTT-TTGCEEECTT-C.HHHHCHHCCCH...S CS
                     Abhydrolase_6 139 d....a.daawrarlarlaalla......glg.......llpaaawadlpvpllvlggeDp.lvprllerlla...q 193
                                            a ++aw  +++++a++++      +         +   +++a+l +p+ +++g+D+ lvp  l++      +
  gi|336255053|ref|YP_004598160.1| 207 RideeAvRYAWDSAHQPGARYATasfaagM-LdpdadseFDLKTELAALETPTTLVWGRDAeLVP--LREGRDlaeA 280
                                       443322588888888888877774444431.0233333233477999999999777*****7666..5544446578 PP

                                       TTEEETCE...SSS-HHHHSHHHHHH CS
                     Abhydrolase_6 194 agarlpvvlpgaGHlphleepdevae 219
                                       a+ +l vv+ +a +lph e+pd+++e
  gi|336255053|ref|YP_004598160.1| 281 ADTDL-VVIDYATQLPHAEHPDKFVE 305
                                       88888.*****************997 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   4.8e-14   2.2e-10       3     238 ..      62     282 ..      60     306 .. 0.69

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 4.8e-14
                                       EEEE-STTT..CGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEE CS
                     Abhydrolase_1   3 lvilhGlpg..ssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltl 77 
                                       ++++hG+    ss+ +    +++ La+ +++vi++Dl+G+g+S+++p    +  +t  +a++++ + +   d+++ +
  gi|336255053|ref|YP_004598160.1|  62 MLLCHGIYTgaSSHEFEP--VVEQLAE-DYHVIAVDLPGFGRSERPPL---VYSPTL-YAEFIRDFAADVTDEPI-V 130
                                       69*****99999******..*******.*******************9...444666.****************9.* PP

                                       EEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHH CS
                     Abhydrolase_1  78 vGhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqr 154
                                       v+ S+ G++a   a e  +   +lvl+++ ++     + +++ + + p    + ++  a +p+ +++ d+ + +++ 
  gi|336255053|ref|YP_004598160.1| 131 VASSLTGALAVDGAGEQESEFEHLVLICP-TDETGGQRPWLRTLLRTPIVGTTLYNLLASKPSIRYFYDRDGYYDSD 206
                                       *****************************.66666666666666666666666666666666666666655555554 PP

                                       HHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHC...........THHHHSEEEEEEET CS
                     Abhydrolase_1 155 hrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlre...........lknvlaptlvisgt 220
                                                          ++d +    ++++ +  ++ +   +   ++l+            l +   pt +++g+
  gi|336255053|ref|YP_004598160.1| 207 -------------------RIDEEAVRYAWDSAHQPGARYATASFAAGMLDPdadsefdlkteLAALETPTTLVWGR 264
                                       ...................3333333333333333333333333333333333333333222244444499999999 PP

                                       TCSSSCHHHHHHHHHCHT CS
                     Abhydrolase_1 221 sDplvppkaledlaqllp 238
                                       +  lvp ++++dla++  
  gi|336255053|ref|YP_004598160.1| 265 DAELVPLREGRDLAEAAD 282
                                       999999999999998833 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0     2e-12   8.9e-09       7     232 ..      62     296 ..      56     302 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2e-12
                       Hydrolase_4   7 vvlvHGl..aehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfll 81 
                                       ++l+HG+  + +s  ++ ++e+La ++++v+a+D  G+Grse     v s + y + ++ f   v     ++p +++
  gi|336255053|ref|YP_004598160.1|  62 MLLCHGIytGASSHEFEPVVEQLA-EDYHVIAVDLPGFGRSERPPL-VYSPTLYAEFIRDFAADVT----DEP-IVV 131
                                       689999744789999********8.58**************84444.5555566555555544444....555.889 PP

                       Hydrolase_4  82 GhSmGGliallyllrypdkvaglilsaPalkikaklkappllkl..llkllgkllpklqv..........snnlkad 146
                                       + S+ G++a+  + +++++++ l+l++P  +   +   +p+l+      ++g++l +l             ++   +
  gi|336255053|ref|YP_004598160.1| 132 ASSLTGALAVDGAGEQESEFEHLVLICPTDETGGQ---RPWLRTllRTPIVGTTLYNLLAskpsiryfydRDGYYDS 205
                                       99**99*******999999**********777754...666665222356777777777778888889884444444 PP

                       Hydrolase_4 147 slsrdpevvaayeadplv.hgkitvrlllelldamk....rleeraakitlPllllhGeaDkvvdpeasrelyerlg 218
                                       +  ++++v+ a ++ +    +  t+++++++ld  +    +l+++ a++++P+ l+ G + ++v+ ++ r+l+e++ 
  gi|336255053|ref|YP_004598160.1| 206 DRIDEEAVRYAWDSAHQPgARYATASFAAGMLDPDAdsefDLKTELAALETPTTLVWGRDAELVPLREGRDLAEAAD 282
                                       44555555555555555558888999999998755422226788899999*************************99 PP

                       Hydrolase_4 219 skdktlklypglyH 232
                                        + + + +  +l H
  gi|336255053|ref|YP_004598160.1| 283 TDLVVIDYATQLPH 296
                                       87666666666666 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.9e-06      0.04     109     167 ..     222     280 ..     171     310 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.9e-06
                           DUF4198 109 vkysqyaktfvtvgkpsetwdkpvglglEivPlthpydlkageelevqvlldGkPlaga 167
                                           +ya + + +g  + ++d++  l++E+ +l+ p++l+ g ++e++ l +G+ la+a
  gi|336255053|ref|YP_004598160.1| 222 QPGARYATASFAAGMLDPDADSEFDLKTELAALETPTTLVWGRDAELVPLREGRDLAEA 280
                                       66679999999***9999*********************99*************88874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2479.52
//
Query:       gi|336255054|ref|YP_004598161.1|  [L=107]
Description: hypothetical protein Halxa_3674 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0075   16.5   0.0     0.0093   16.2   0.0    1.2  1  CBM_35    Carbohydrate binding module (family 35)


Domain annotation for each model (and alignments):
>> CBM_35  Carbohydrate binding module (family 35)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.2e-07    0.0093      27      59 ..      50      82 ..      25      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.2e-07
                            CBM_35 27 yvgefegagdavslnVnvekaGeynlnvtfsap 59
                                       ++ f+ +++ ++ +V+ +++G+y+l + f+ +
  gi|336255054|ref|YP_004598161.1| 50 AIDRFDADTNTLTCEVTGPQGGDYSLRIDFANK 82
                                      5899*************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 798.72
//
Query:       gi|336255055|ref|YP_004598162.1|  [L=359]
Description: hypothetical protein Halxa_3675 [Halopiger xanaduensis SH-6]
Scores for complete 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   25.4   1.4    0.00044   20.6   0.8    3.0  2  HEAT_2    HEAT repeats
  ------ inclusion threshold ------
       0.04   14.4   0.3       0.13   12.8   0.0    1.9  2  HEAT_EZ   HEAT-like repeat


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.042   3.7e+02      15      35 ..       9      29 ..       6      48 .. 0.78
   2 !   20.6   0.8   4.9e-08   0.00044      22      87 ..     282     352 ..     255     353 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.042
                            HEAT_2 15 evrraairaLgrignpealpa 35
                                      +  ++a ++Lgri+n e+l a
  gi|336255055|ref|YP_004598162.1|  9 NDEQRATEELGRIHNGEILTA 29
                                      56789**********998765 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 4.9e-08
                            HEAT_2  22 raLgrignpealpaLvellededpavRraaaeaLgai......gdpealpaLkellddddddvvReaAaeaL 87 
                                       r+L++ +++ +++a++++l+++d+ +Rr a e++ +i       + ea ++ + lld ddd+++R+ Aa aL
  gi|336255055|ref|YP_004598162.1| 282 RVLADADPDAVFEAVRPYLSSPDRTTRRDATETATRIfmladcSLGEARELFEPLLD-DDDEEIRTYAADAL 352
                                       57888899999*********************9998866644345779999999886.566777999**998 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.61   5.5e+03      20      34 ..     286     300 ..     267     312 .. 0.53
   2 ?   12.8   0.0   1.4e-05      0.13      32      54 ..     332     354 ..     331     355 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.61
                           HEAT_EZ  20 ellqplvpeilpaLl 34 
                                       ++++++v e++++ l
  gi|336255055|ref|YP_004598162.1| 286 DADPDAVFEAVRPYL 300
                                       344455555555555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.4e-05
                           HEAT_EZ  32 aLlalLnddsdeVRaaAagaLgn 54 
                                       ++ +lL dd+ e+R++Aa aL+ 
  gi|336255055|ref|YP_004598162.1| 332 LFEPLLDDDDEEIRTYAADALEL 354
                                       5899*****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2738.34
//
Query:       gi|336255056|ref|YP_004598163.1|  [L=389]
Description: LAO/AO transport system ATPase [Halopiger xanaduensis SH-6]
Scores for 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-88  294.9   4.2      5e-88  294.6   4.2    1.1  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
    9.2e-07   28.6   1.3    9.4e-06   25.3   1.3    2.3  1  cobW            CobW/HypB/UreG, nucleotide-binding domain
    1.7e-05   24.5   0.3    5.9e-05   22.8   0.3    1.8  1  SRP54           SRP54-type protein, GTPase domain
      6e-05   22.9   0.0    0.00018   21.4   0.0    1.7  2  ATP_bind_1      Conserved hypothetical ATP binding protein
    9.4e-05   22.2   0.0    0.00025   20.8   0.0    1.6  1  AAA_30          AAA domain
    0.00013   22.0   0.1    0.00036   20.5   0.1    1.8  1  NTPase_1        NTPase
     0.0002   20.9   0.0       0.45   10.0   0.0    2.3  2  GTP_EFTU        Elongation factor Tu GTP binding domain
    0.00043   20.8   0.1    0.00083   19.9   0.1    1.5  1  ABC_tran        ABC transporter
    0.00053   20.4   0.4     0.0032   17.9   0.1    2.5  2  AAA_16          AAA ATPase domain
     0.0019   18.5   0.0     0.0077   16.5   0.0    2.0  2  AAA_22          AAA domain
      0.002   18.7   0.3      0.012   16.1   0.1    2.3  3  AAA_18          AAA domain
     0.0035   17.0   0.1     0.0079   15.9   0.1    1.5  1  AAA_29          P-loop containing region of AAA domain
     0.0055   16.0   0.0      0.015   14.6   0.0    1.7  1  Zeta_toxin      Zeta toxin
     0.0087   16.0   0.1      0.031   14.2   0.1    2.1  1  MobB            Molybdopterin guanine dinucleotide synthesis 
  ------ inclusion threshold ------
      0.011   15.9   0.2       0.22   11.7   0.0    2.2  2  AAA_33          AAA domain
      0.012   14.6   0.0      0.035   13.0   0.0    1.7  2  TrwB_AAD_bind   Type IV secretion-system coupling protein DNA
      0.013   15.7   1.5      0.019   15.2   0.1    1.9  2  AAA_28          AAA domain
      0.016   14.5   0.0      0.026   13.8   0.0    1.3  1  KAP_NTPase      KAP family P-loop domain
      0.026   14.6   0.3      0.059   13.5   0.1    2.0  1  MMR_HSR1        50S ribosome-binding GTPase
      0.036   13.8   0.1      0.077   12.7   0.1    1.5  1  PRK             Phosphoribulokinase / Uridine kinase family
      0.043   13.3   0.0      0.074   12.5   0.0    1.3  1  KTI12           Chromatin associated protein KTI12
      0.048   13.6   0.1       0.12   12.3   0.0    1.8  1  RsgA_GTPase     RsgA GTPase
      0.065   13.2   0.0       0.14   12.0   0.0    1.6  1  NACHT           NACHT domain
      0.082   12.1   0.0       0.13   11.4   0.0    1.2  1  NB-ARC          NB-ARC domain
      0.083   12.8   0.0       0.16   11.9   0.0    1.4  1  Ploopntkinase3  P-loop Nucleotide Kinase3
      0.084   13.3   0.0      0.084   13.3   0.0    2.3  1  AAA_17          AAA domain
      0.088   13.1   0.1        0.3   11.4   0.0    1.9  1  AAA_19          AAA domain
      0.097   12.7   0.0       0.18   11.8   0.0    1.4  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
       0.19   11.1   1.9       0.74    9.2   0.2    2.1  2  ParA            NUBPL iron-transfer P-loop NTPase
        0.2   10.8   0.0       0.33   10.1   0.0    1.2  1  DUF815          Protein of unknown function (DUF815)
          6    7.4   9.1        6.7    7.3   1.6    3.2  2  Rnk_N           Rnk N-terminus


Domain annotation for each model (and alignments):
>> 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 !  294.6   4.2   8.6e-91     5e-88       1     264 [.      39     332 ..      39     335 .. 0.98

  Alignments for each domain:
  == domain 1  score: 294.6 bits;  conditional E-value: 8.6e-91
                                       HHHHHHHHH--SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------ CS
                              MeaB   1 LaraitlveserpeakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsil 77 
                                       Lar+i  +e + p  ++l+++l a++G+a v+G+tG+PGaGkstlv++l++++r+rG+ v+++a+DPsspf+GG++l
  gi|336255056|ref|YP_004598163.1|  39 LARVISKIEDRSPGYRALVSELYAHTGEADVIGITGSPGAGKSTLVDKLAETYRDRGETVGIIAIDPSSPFSGGAVL 115
                                       89*************************************************************************** PP

                                       ------HCCCTSTTEEEEEE-----HHHHHHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESST CS
                              MeaB  78 GDklRleelavdegvfiRslpsrGalGGlaaktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpea 154
                                       GD++R+++   d +vf+Rs+++rG+lGGl+++t ++v+ ++a+G D+++ietvG+Gq e+d+++ +dt+ vl+ p++
  gi|336255056|ref|YP_004598163.1| 116 GDRIRMASTVGDMDVFVRSMSARGTLGGLSTATADAVKAMDAFGKDKIIIETVGAGQNEIDIVRTADTVAVLVPPGS 192
                                       ***************************************************************************** PP

                                       TTTTTT--CCCHHH-SEEEEE---HHHHHHHHHHHHHHHHHCST..............................TBT CS
                              MeaB 155 GDelqgikkGileiaDiivvnkaDkkeaekaarelraaleleee..............................kek 201
                                       GD++q++k+GileiaD++vvnkaD+ +++++ +elr +++l e                               +++
  gi|336255056|ref|YP_004598163.1| 193 GDDVQTLKAGILEIADVFVVNKADRDGSDRTVQELREMINLGEGggpgagagaghhgvgaanhgersedadgngEDD 269
                                       *******************************************9***************************99889* PP

                                       TB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                              MeaB 202 eWrpkvlktsavegeGidelvdaieehrevlkktGllekrrrerakeelrelvedellkrvka 264
                                       +Wrp++++t+a++g+G++ +vd++  hr++l ++G+l+ + r+r +ee+r+  ++++ + + a
  gi|336255056|ref|YP_004598163.1| 270 SWRPPIVETVATTGDGVEAFVDELAAHRDYLVDSGTLADNARQRYAEEIRTHLREDVHALLEA 332
                                       ********************************************************9887665 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 !   25.3   1.3   1.6e-08   9.4e-06       2     166 ..      69     231 ..      68     235 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.6e-08
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCC....HCCCT...........EEEETT.TTE CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaell....retgve..........ivelen.Gci 61 
                                       v+++tG++G+GK+tL+ +l    + +g+ + +i  + ++    +++l    r    +          + +++  G +
  gi|336255056|ref|YP_004598163.1|  69 VIGITGSPGAGKSTLVDKLAetYRDRGETVGIIAIDPSSPFSGGAVLgdriR----MastvgdmdvfVRSMSArGTL 141
                                       789*****************87778899******998865555555533332....223345668885556542433 PP

                                       C..CHCTT-HHHHHHHHHHHHTT-SEEEEEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHH CS
                              cobW  62 C..ctlredllkelealeereerldviliEttGlaePapvafteeelksdltldavvavvDaknleaeeekieekae 136
                                           t   d++k+++a+ +++     i+iEt+G  +               t+d+v ++v       ++++ +++  
  gi|336255056|ref|YP_004598163.1| 142 GglSTATADAVKAMDAFGKDK-----IIIETVGAGQNEID--------IVRTADTVAVLVPP----GSGDDVQTLKA 201
                                       300234666777776666655.....*******7765444........24555665555666....78999999999 PP

                                       HHHHTSSEEEEE-HHHHCHC..HHHHHHHH CS
                              cobW 137 dqlaaadllvlnKtDlldeeallekleerl 166
                                         l+ ad++v+nK+D   +++++++l+e++
  gi|336255056|ref|YP_004598163.1| 202 GILEIADVFVVNKADRDGSDRTVQELREMI 231
                                       99*************999998888887765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.3     1e-07   5.9e-05       3     105 ..      69     181 ..      67     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1e-07
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST...SSTTHH..HHHHHHHHHTTEEEEE...SSTTS..CHH CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt...fRaaAv..eQLktlaeklgvpvik...kkeea..dpa 69 
                                       vi + G  GaGK t + KLa+ ++++g++v ++a D    f  +Av  + +++  +  +++v+    + +++     
  gi|336255056|ref|YP_004598163.1|  69 VIGITGSPGAGKSTLVDKLAETYRDRGETVGIIAIDPsspFSGGAVlgDRIRMASTVGDMDVFVrsmSARGTlgGLS 145
                                       6778999*****************************64447788986677777777666666653342222233567 PP

                                       HHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHH CS
                             SRP54  70 avakeavekakeekidvvlvDTaGrlqndkelmeel 105
                                       + +++av+++++ + d +++ T G  qn+ ++++  
  gi|336255056|ref|YP_004598163.1| 146 TATADAVKAMDAFGKDKIIIETVGAGQNEIDIVRTA 181
                                       788899999999999999999999988887776655 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 !   21.4   0.0     3e-07   0.00018       1      36 [.      72     107 ..      72     110 .. 0.95
   2 ?   -2.8   0.0       7.6   4.4e+03     194     235 ..     308     347 ..     288     350 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3e-07
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAa 36 
                                       ++G +G+GK+t+v +l+e++++rg +v ++ +DP +
  gi|336255056|ref|YP_004598163.1|  72 ITGSPGAGKSTLVDKLAETYRDRGETVGIIAIDPSS 107
                                       68********************************75 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.6
                        ATP_bind_1 194 eekykklaeaiaelleefalvlrflplssekeesiedllsli 235
                                       ++++++ ae+i+  l e  +   +l ++ e+  +++dl +++
  gi|336255056|ref|YP_004598163.1| 308 DNARQRYAEEIRTHLREDVHA--LLEAELERAGGVDDLAEAV 347
                                       355566666666666665555..6666667777777776666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   4.3e-07   0.00025      14      53 ..      63     102 ..      54     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.3e-07
                            AAA_30  14 ltsgdrvavltGpAGtGKttalkalreaweaaggrviglA 53 
                                       +t+++ v  +tG +G+GK+t++ +l+e+++++g++v ++A
  gi|336255056|ref|YP_004598163.1|  63 HTGEADVIGITGSPGAGKSTLVDKLAETYRDRGETVGIIA 102
                                       566777999************************9998888 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   6.1e-07   0.00036       2      31 ..      70      99 ..      69     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.1e-07
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                      + iTG+pG GK+Tlv+k++e+ +++g +vg
  gi|336255056|ref|YP_004598163.1| 70 IGITGSPGAGKSTLVDKLAETYRDRGETVG 99
                                      78********************99997774 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 !    8.6   0.0    0.0021       1.2       6      26 ..      70      90 ..      66      99 .. 0.85
   2 !   10.0   0.0   0.00079      0.45      92     191 ..     179     296 ..     164     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0021
                                      EEEEESTTSSHHHHHHHHHHH CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlyk 26
                                      igi g   +GK+TL+d+L ++
  gi|336255056|ref|YP_004598163.1| 70 IGITGSPGAGKSTLVDKLAET 90
                                      899***************865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00079
                                       HT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST..HHHHHHHHHHHHHHHHHH............. CS
                          GTP_EFTU  92 rvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl..kaelkeiveevkqklsrk............. 153
                                       r++D + ++v   +G  +qt      a  +++  ++++NK+Dr   + +++e+ e+++  l +              
  gi|336255056|ref|YP_004598163.1| 179 RTADTVAVLVPPGSGDDVQTL----KAGILEIADVFVVNKADRDgsDRTVQELREMIN--LGEGggpgagagaghhg 249
                                       556666666666666666664....3556678889********987777777777777..64558999******999 PP

                                       .........HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 154 .........eeklekygekgekevpvvfgSalkgegvktllealvel 191
                                                 e+ +  ge+++   p+v + a +g+gv+++++ l  +
  gi|336255056|ref|YP_004598163.1| 250 vgaanhgerSEDADGNGEDDSWRPPIVETVATTGDGVEAFVDELAAH 296
                                       99999988877788888888789999************999998765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.4e-06   0.00083      12      45 ..      68     104 ..      59     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.4e-06
                                       SEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkp...teGeilld 45 
                                        +++i+G+ GaGKStL+  la+ +++   t G i +d
  gi|336255056|ref|YP_004598163.1|  68 DVIGITGSPGAGKSTLVDKLAETYRDrgeTVGIIAID 104
                                       689*********************9955555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   5.6e-06    0.0032      19      52 ..      62      95 ..      49     239 .. 0.78
   2 ?   -0.2   0.0         2   1.2e+03     111     127 ..     306     322 ..     258     372 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.6e-06
                            AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekdg 52
                                      +++g+  ++ ++G +G GKs+lv++l++ ++++g
  gi|336255056|ref|YP_004598163.1| 62 AHTGEADVIGITGSPGAGKSTLVDKLAETYRDRG 95
                                      4677778999*****************9999883 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2
                            AAA_16 111 lagaeasrllellkrll 127
                                       la+ +++r +e+++ +l
  gi|336255056|ref|YP_004598163.1| 306 LADNARQRYAEEIRTHL 322
                                       22222222222222222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.3e-05    0.0077       5      51 ..      67     109 ..      62     156 .. 0.83
   2 ?   -2.1   0.0       7.4   4.3e+03      90     117 ..     207     232 ..     183     239 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsst 51 
                                       a ++ +tG +G+GK+tl+ +l+e++       + e ++++ ++++s+ 
  gi|336255056|ref|YP_004598163.1|  67 ADVIGITGSPGAGKSTLVDKLAETYRD-----RgETVGIIAIDPSSPF 109
                                       667889******************943.....2356666677777765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.4
                            AAA_22  90 avielliiDEaqhlrseealeeLrslln 117
                                       a   ++++  a++  s++ ++eLr++ n
  gi|336255056|ref|YP_004598163.1| 207 A--DVFVVNKADRDGSDRTVQELREMIN 232
                                       3..3788888888646888888887777 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   2.1e-05     0.012       1      21 [.      70      90 ..      70     120 .. 0.85
   2 ?   -2.2   0.0       9.8   5.7e+03      46      68 ..     209     231 ..     146     238 .. 0.61
   3 ?   -1.2   0.0       4.8   2.8e+03      28      70 ..     296     346 ..     286     367 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.1e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                      I++tG pG+GK+tl + L++ 
  gi|336255056|ref|YP_004598163.1| 70 IGITGSPGAGKSTLVDKLAET 90
                                      89****************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9.8
                            AAA_18  46 ldeskrldedkldklldaleens 68 
                                       +   +++d+d  d+ +++l+e +
  gi|336255056|ref|YP_004598163.1| 209 VFVVNKADRDGSDRTVQELREMI 231
                                       44456666666666666666665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.8
                            AAA_18  28 lrdvakenglllevdpealdeskrldedkldklldaleenss..........a 70 
                                       +rd++ ++g+l ++  +  +  ++++++ ++ ++ +le+  +          a
  gi|336255056|ref|YP_004598163.1| 296 HRDYLVDSGTLADNARQ--RYAEEIRTHLREDVHALLEAELEraggvddlaeA 346
                                       46777777777777777..7777777777777777777655544445444442 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 !   15.9   0.1   1.4e-05    0.0079      24      41 ..      69      86 ..      59      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-05
                            AAA_29 24 atlltGpsGsGKSTllDA 41
                                      ++ +tG  G+GKSTl+D 
  gi|336255056|ref|YP_004598163.1| 69 VIGITGSPGAGKSTLVDK 86
                                      5569*************5 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   2.6e-05     0.015      17      49 ..      68     100 ..      57     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                        Zeta_toxin  17 klillgGqpGAGKselaellkdelerqgnvvrl 49 
                                       ++i + G+pGAGKs+l ++l++  + +g+ v +
  gi|336255056|ref|YP_004598163.1|  68 DVIGITGSPGAGKSTLVDKLAETYRDRGETVGI 100
                                       567789****************99988777765 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 !   14.2   0.1   5.4e-05     0.031       1      33 [.      69     101 ..      69     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-05
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvgti 33 
                                       v+gi+g  g+GK tL+ kl ++ ++rg +vg+i
  gi|336255056|ref|YP_004598163.1|  69 VIGITGSPGAGKSTLVDKLAETYRDRGETVGII 101
                                       799****************************98 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00037      0.22       4      21 ..      72      89 ..      69      99 .. 0.83
   2 ?    1.9   0.0       0.4   2.3e+02      67      94 ..     293     320 ..     264     337 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00037
                            AAA_33  4 lvGlpGsGKstlaerllk 21
                                      + G pG+GKstl+++l++
  gi|336255056|ref|YP_004598163.1| 72 ITGSPGAGKSTLVDKLAE 89
                                      68*************996 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.4
                            AAA_33  67 lsagrnvildatnlsrrerarflklarr 94 
                                       l+a r++++d++ l  ++r+r+ +  r 
  gi|336255056|ref|YP_004598163.1| 293 LAAHRDYLVDSGTLADNARQRYAEEIRT 320
                                       6677777777777777777776655544 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 ?   13.0   0.0     6e-05     0.035      12      51 ..      64     105 ..      60     111 .. 0.81
   2 ?   -2.7   0.0       3.5     2e+03     158     182 ..     305     329 ..     290     336 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6e-05
                     TrwB_AAD_bind  12 eretqhilivGttGsGKtqalekllrairargdra..ivlDl 51 
                                         e+  i i+G+ G+GK++ + kl ++ r rg+++  i +D+
  gi|336255056|ref|YP_004598163.1|  64 TGEADVIGITGSPGAGKSTLVDKLAETYRDRGETVgiIAIDP 105
                                       56788899************************8752144565 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.5
                     TrwB_AAD_bind 158 alvaeeaertaasiratlatnlevl 182
                                       +l ++  +r+a++ir+ l + +++l
  gi|336255056|ref|YP_004598163.1| 305 TLADNARQRYAEEIRTHLREDVHAL 329
                                       4555677788888888888877665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   3.2e-05     0.019       2      22 ..      70      90 ..      69     102 .. 0.83
   2 ?   -2.1   0.1       6.7   3.9e+03     129     147 ..     318     336 ..     290     339 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar 22
                                      i itG +++GK+tl+ +La++
  gi|336255056|ref|YP_004598163.1| 70 IGITGSPGAGKSTLVDKLAET 90
                                      569****************86 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.7
                            AAA_28 129 edleereaiderlrealre 147
                                        + + re+++++l++ l++
  gi|336255056|ref|YP_004598163.1| 318 IRTHLREDVHALLEAELER 336
                                       2445566666666666655 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 ?   13.8   0.0   4.4e-05     0.026      18      62 ..      65     107 ..      49     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-05
                        KAP_NTPase  18 atpivvgLygkWGsGKssllnkledelkefakpvrflfaefnaws 62 
                                       ++  v+g++g  G+GKs+l+ kl + ++++   +++ ++ +++ s
  gi|336255056|ref|YP_004598163.1|  65 GEADVIGITGSPGAGKSTLVDKLAETYRDR--GETVGIIAIDPSS 107
                                       66779***********************99..7888887777765 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   0.1    0.0001     0.059       2      22 ..      70      90 ..      69     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0001
                                      EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                      ++i G p +GKStL+ +l ++
  gi|336255056|ref|YP_004598163.1| 70 IGITGSPGAGKSTLVDKLAET 90
                                      89**************99874 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00013     0.077       1      25 [.      69      93 ..      69     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                               PRK  1 vIgvagsSGaGkttvarklekifgr 25
                                      vIg++gs GaGk+t+  kl +  + 
  gi|336255056|ref|YP_004598163.1| 69 VIGITGSPGAGKSTLVDKLAETYRD 93
                                      8******************998875 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013     0.074       5      36 ..      71     102 ..      68     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                       EEE--TTSSHHHHHHHHHHHHHHTT--EEEE- CS
                             KTI12   5 vltGlPssGKstrakeLakaleeekrsvvvid 36 
                                        +tG P +GKst++++La++ ++++ +v +i 
  gi|336255056|ref|YP_004598163.1|  71 GITGSPGAGKSTLVDKLAETYRDRGETVGIIA 102
                                       59***********************9999886 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00021      0.12      99     122 ..      66      90 ..      35     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                                       T.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallpe 122
                                       + +++ + G+ G+GKStL+++l+++
  gi|336255056|ref|YP_004598163.1|  66 EaDVIGITGSPGAGKSTLVDKLAET 90 
                                       44778899**************986 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   0.00025      0.14       2      26 ..      69      93 ..      68      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                                      CEEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                      ++ ++G +G GK+tL+ kla++ ++
  gi|336255056|ref|YP_004598163.1| 69 VIGITGSPGAGKSTLVDKLAETYRD 93
                                      6779****************98765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.13      11      42 ..      59      89 ..      52      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                      HHHC.TTTSCSEEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 11 kLle.kdelqslvvalvGmgGvGKttlakqiln 42
                                      +L    +e +  v+++ G +G GK+tl+ +  +
  gi|336255056|ref|YP_004598163.1| 59 ELYAhTGEAD--VIGITGSPGAGKSTLVDKLAE 89
                                      5553245555..***************998765 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00028      0.16       5      28 ..      69      92 ..      66     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                    Ploopntkinase3  5 liylvGqPGaGkstlmaeltkgfd 28
                                      +i + G+PGaGkstl+ +l++++ 
  gi|336255056|ref|YP_004598163.1| 69 VIGITGSPGAGKSTLVDKLAETYR 92
                                      67799***************9995 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00015     0.084       1      19 [.      73      91 ..      73     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00015
                                      EE-TTSSHHHHHHHHHHHH CS
                            AAA_17  1 lGgPGsGKgtqceklveky 19
                                      +G PG+GK+t+++kl+e y
  gi|336255056|ref|YP_004598163.1| 73 TGSPGAGKSTLVDKLAETY 91
                                      699**************99 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00052       0.3       9      40 ..      66      97 ..      59     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00052
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggv 40
                                      +++v+ +t+ pG GK++++ +  + + ++g+ 
  gi|336255056|ref|YP_004598163.1| 66 EADVIGITGSPGAGKSTLVDKLAETYRDRGET 97
                                      678999**************999999888754 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 ?   11.8   0.0   0.00031      0.18       6      55 ..      74     176 ..      69     239 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                                       SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx........................... RF
                              CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep........................... 54 
                                       ++ G+GK+tl+ +La    +rg  V  +  Dp ++ +   + g++++ +                            
  gi|336255056|ref|YP_004598163.1|  74 GSPGAGKSTLVDKLAETYRDRGETVGIIAIDPSSPFSGGaVLGDRIRMAStvgdmdvfvrsmsargtlgglstatad 150
                                       5569*****************************99887444444444444777777777777666666666666666 PP

                                       .........................C CS
                                       .........................x RF
                              CbiA  55 .........................d 55 
                                                                d
  gi|336255056|ref|YP_004598163.1| 151 avkamdafgkdkiiietvgagqneiD 176
                                       66666666666555555555555553 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 ?    9.2   0.2    0.0013      0.74      11      41 ..      74     104 ..      67     116 .. 0.89
   2 ?    1.1   0.1       0.4   2.3e+02     113     143 ..     182     213 ..     176     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                              ParA  11 gKGGVGKStvavnlAlaLakkglkvgllDaD 41 
                                       g  G GKSt+  +lA + +++g +vg++ +D
  gi|336255056|ref|YP_004598163.1|  74 GSPGAGKSTLVDKLAETYRDRGETVGIIAID 104
                                       6679***********************9998 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.4
                              ParA 113 DyLiiDlPPGtgDeqltvaqkl.plagaviVt 143
                                       D + + +PPG gD   t+   + ++a++ +V 
  gi|336255056|ref|YP_004598163.1| 182 DTVAVLVPPGSGDDVQTLKAGIlEIADVFVVN 213
                                       6667779******9988877665777777775 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00057      0.33      50      88 ..      64     104 ..      54     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00057
                            DUF815  50 glpannvLLwGarGtGKSslvkallneyaeeg..Lrlieve 88 
                                         +a  + ++G+ G+GKS+lv  l ++y+++g  + +i ++
  gi|336255056|ref|YP_004598163.1|  64 TGEADVIGITGSPGAGKSTLVDKLAETYRDRGetVGIIAID 104
                                       5566677799******************9998777778776 PP

>> Rnk_N  Rnk N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.0      0.28   1.6e+02       4      22 ..      19      37 ..      19      61 .. 0.69
   2 ?    7.3   1.6     0.012       6.7      16      38 ..     306     337 ..     304     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.28
                                      EEEHHHHHHHHHHHHCTTT CS
                             Rnk_N  4 yitelDleRLeaLldslad 22
                                      ++te D + Le+Ll++ ++
  gi|336255056|ref|YP_004598163.1| 19 TLTEDDRALLEDLLAGKHR 37
                                      6899**********96532 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.012
                                       HHHCTTTTSSTTHHH.........HHHHHHCS CS
                             Rnk_N  16 Lldsladrdppaaea.........LeaELdRA 38 
                                       L+d++++r+++ ++          LeaEL+RA
  gi|336255056|ref|YP_004598163.1| 306 LADNARQRYAEEIRThlredvhalLEAELERA 337
                                       788777777777777888899999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); 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):              31  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 2886.02
//
Query:       gi|336255057|ref|YP_004598164.1|  [L=138]
Description: methylmalonyl-CoA mutase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-23   82.0   0.9    3.8e-23   81.8   0.9    1.0  1  B12-binding   B12 binding domain
     0.0074   16.0   0.2       0.33   10.8   0.0    2.4  2  Staph_haemo   Staphylococcus haemolytic protein
  ------ inclusion threshold ------
      0.028   14.6   0.2          1    9.6   0.1    2.6  2  DUF1611_N     Domain of unknown function (DUF1611_N) Rossmann
      0.096   12.2   0.0       0.15   11.5   0.0    1.3  1  BcrAD_BadFG   BadF/BadG/BcrA/BcrD ATPase family
       0.11   12.2   0.0       0.21   11.2   0.0    1.5  1  Peripla_BP_6  Periplasmic binding protein


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 !   81.8   0.9   1.1e-26   3.8e-23       2     119 ..      11     127 ..      10     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 1.1e-26
                       B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lk 76 
                                       + l+a+vg d h++G+ v+ +a+rdagfeV++ g+  ++e+iv+a+ +e++dv+g+S+l++++ + v ++++   + 
  gi|336255057|ref|YP_004598164.1|  11 RCLVAKVGLDGHDRGAHVVSRAFRDAGFEVIYSGLHKSPEEIVQAAVQEDVDVLGISILSGAHDTLVPKVMDGleEY 87 
                                       789**********************************************************************8877 PP

                       B12-binding  77 rirprvkvvvGGahpsldpeetleaklgiddvvvgegedalea 119
                                       ++++++ v+vGG++p+ d  e le+  g + +++g g++ +e 
  gi|336255057|ref|YP_004598164.1|  88 GAKDDTLVLVGGVIPEEDRPE-LEE-AG-VAAIFGPGTSIAET 127
                                       8888*****************.555.99.888******98876 PP

>> Staph_haemo  Staphylococcus haemolytic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   9.1e-05      0.33       4      27 ..      45      68 ..      43      71 .. 0.84
   2 ?    2.7   0.0     0.031   1.1e+02      24      32 ..     121     129 ..     121     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.1e-05
                       Staph_haemo  4 LfeAikntVeAaikqDwveLGtsI 27
                                      L  +   +V+Aa+++D   LG sI
  gi|336255057|ref|YP_004598164.1| 45 LHKSPEEIVQAAVQEDVDVLGISI 68
                                      5556678****************9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.031
                       Staph_haemo  24 GtsIvdIVa 32 
                                       GtsI+ +V+
  gi|336255057|ref|YP_004598164.1| 121 GTSIAETVE 129
                                       89******8 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 ?    9.6   0.1   0.00029         1      28      76 ..      35      79 ..      16      90 .. 0.69
   2 ?    2.5   0.0     0.049   1.8e+02      41      56 ..      97     112 ..      79     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00029
                         DUF1611_N 28 aagaevlviGiapeggklpeswreavkeAle.aGldvvsGlHerLsddpe 76
                                      +ag ev++ G+  + + +   +++av+e ++ +G+++ sG+H+ L   p+
  gi|336255057|ref|YP_004598164.1| 35 DAGFEVIYSGLHKSPEEI---VQAAVQEDVDvLGISILSGAHDTLV--PK 79
                                      467777777777777777...777777777547**********986..55 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.049
                         DUF1611_N  41 eggklpeswreavkeA 56 
                                        gg++pe+ r++++eA
  gi|336255057|ref|YP_004598164.1|  97 VGGVIPEEDRPELEEA 112
                                       59***********999 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 ?   11.5   0.0   4.2e-05      0.15     187     230 ..      61     104 ..      48     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.2e-05
                                       TT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG-H CS
                       BcrAD_BadFG 187 ggekaedIlaglhraialrvialisrsggvtdevtltGGvakne 230
                                        +   ++Il g+h  +   v+   ++ g+ +d+++l+GGv  +e
  gi|336255057|ref|YP_004598164.1|  61 VDVLGISILSGAHDTLVPKVMDGLEEYGAKDDTLVLVGGVIPEE 104
                                       5667789*********************************9875 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     6e-05      0.21     151     246 ..      25     120 ..      11     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6e-05
                                       HHHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SE....EEEESSHHHHHHHHHHHHHTT-SSSCEEEE CS
                      Peripla_BP_6 151 giaalkaaakaaGgevvgeepvplgttdfsaqvlqikaagada....vllagtgadlaallkaaaeaGldakrillv 223
                                       g+  + +a++ aG+ev+ +  +     +++++v+++ ++ +d+    +l ++  + +++++  ++e G + + + lv
  gi|336255057|ref|YP_004598164.1|  25 GAHVVSRAFRDAGFEVIYSGLH----KSPEEIVQAAVQEDVDVlgisILSGAHDTLVPKVMDGLEEYGAKDDTLVLV 97 
                                       5667899*********944444....5889************998777777777788999**********9988888 PP

                                       CCC-CHHHHHHHHHHHHTTEEEE CS
                      Peripla_BP_6 224 swsgseedlkalggeaaegvlav 246
                                       +  + eed   l++++ + ++++
  gi|336255057|ref|YP_004598164.1|  98 GGVIPEEDRPELEEAGVAAIFGP 120
                                       88898888888887665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1025.76
//
Query:       gi|336255058|ref|YP_004598165.1|  [L=223]
Description: metal dependent phosphohydrolase [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.8   1.0    2.1e-15   57.0   1.0    1.4  1  HD        HD domain
  ------ inclusion threshold ------
      0.017   14.9   0.1      0.037   13.8   0.1    1.5  1  HD_4      HD domain
      0.041   12.8   0.1        1.4    7.7   0.1    2.3  2  TraI_2    Putative helicase


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 !   57.0   1.0   3.6e-19   2.1e-15       1     120 [.      50     150 ..      50     151 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 3.6e-19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld 77 
                                       r++H+l+V  l+ ++ae +g  +d++++++aaL+HD++k  + +            + H++ ga+++re+++++ ++
  gi|336255058|ref|YP_004598165.1|  50 RFNHILNVVDLSTEIAEGEG--ADVDVTRVAALFHDVAKLETDQ------------ELHAEAGARVAREYLESRVDY 112
                                       79******************..*******************664............68***************9777 PP

                                       ....HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHH CS
                                HD  78 ....ledvaklirehheswegkkrprglaerqlslearivklaDrla 120
                                           +  v+++i++h+ + + +         +l le +++  aD l+
  gi|336255058|ref|YP_004598165.1| 113 pesfITQVCRAIEHHSYQGDLT---------DLALETQCLIEADMLD 150
                                       *******************988.........9999999999999776 PP

>> HD_4  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.1e-06     0.037      16      69 ..      46     103 ..      38     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.1e-06
                              HD_4  16 tgepllahalevAailael....gldae.tviAalLhdvvedalsleeirerfGeevar 69 
                                       + e  ++h l v+ +  e+    g d + t++Aal hdv + +++++e+ ++ G++var
  gi|336255058|ref|YP_004598165.1|  46 SAEYRFNHILNVVDLSTEIaegeGADVDvTRVAALFHDVAK-LETDQELHAEAGARVAR 103
                                       566678899999998888844323554469**********8.6899***********97 PP

>> TraI_2  Putative helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00024       1.4      78     131 ..      46      99 ..      42     106 .. 0.83
   2 ?    2.7   0.0    0.0082        49      58      76 ..     124     142 ..     121     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00024
                            TraI_2  78 alklrqghilpaneepeeraaqeerWrvaailaaLlhdlgkivtdleitdrdgs 131
                                       +++ r +hil+      e a+ e +   ++ +aaL+hd++k+ td e + + g 
  gi|336255058|ref|YP_004598165.1|  46 SAEYRFNHILNVVDLSTEIAEGEGADVDVTRVAALFHDVAKLETDQELHAEAGA 99 
                                       56667778888888888888888888889999*************999988775 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0082
                            TraI_2  58 shhhskaGGLLdhglevaa 76 
                                        +hhs++G L d++le+ +
  gi|336255058|ref|YP_004598165.1| 124 IEHHSYQGDLTDLALETQC 142
                                       57**************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1827.23
//
Query:       gi|336255059|ref|YP_004598166.1|  [L=232]
Description: lysine exporter LysE/YggA [Halopiger xanaduensis SH-6]
Scores for complete 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   3.1    1.1e-23   83.7   3.1    2.1  2  LysE      LysE type translocator


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   3.1   6.2e-28   1.1e-23       2     127 ..      16     146 ..      15     153 .. 0.94
   2 !    3.9   2.4    0.0018        32     118     190 ..     152     224 ..     147     227 .. 0.70

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 6.2e-28
                              LysE   2 slllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlal 78 
                                       +l+++pGp n+++ ++++ rg+++g++++lg++++da++++l l G+ ++++++p+v   l l+Gg+  l+++v a+
  gi|336255059|ref|YP_004598166.1|  16 ALAAPPGPMNAIIAEESVVRGWAAGFWAGLGAMLADALFFVLTLAGVVAVIDRYPFVRPALYLAGGLLMLYFAVGAI 92 
                                       7899************************************************************************9 PP

                              LysE  79 rdakekkveaeksve.....aslvkpflkglllslsNPkailfwlsvisallak 127
                                        +a    + +++ ++     a+ v+ f+k ++lsl+NP+ i fwl v+ +ll+ 
  gi|336255059|ref|YP_004598166.1|  93 EEARAAASFTAEGDRdvaaaAAKVRGFRKTFVLSLTNPYQIGFWLTVGVGLLET 146
                                       99999998888888888899999**************************99984 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0018
                              LysE 118 lsvisallaka..eqygdagrlilaaglvvasliwfsllaflaarlsrrlsskkvlriinvvvgvlligfavkll 190
                                       +s ++a++++       ++g  +l +g++ ++ iw++ +    +   +r+ +     ++ +  +++l+gf++ +l
  gi|336255059|ref|YP_004598166.1| 152 FSHVPAVGEQLagTLLVQTGSPALLVGFFGGIAIWIVTYPAALSSAGKRVDALA--PAVAAGSAAVLVGFGLLFL 224
                                       555555555433245567888899999999999999988666655555555543..4789999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1787.37
//
Query:       gi|336255060|ref|YP_004598167.1|  [L=371]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for complete 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  67.4    4.1e-16   58.9  41.2    2.1  2  MFS_1     Major Facilitator Superfamily
    1.6e-07   31.0  44.0      2e-07   30.6  44.0    1.0  1  MFS_4     Uncharacterised MFS-type transporter YbfB


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 !   58.9  41.2   4.6e-20   4.1e-16      18     269 ..      13     253 ..       1     254 [. 0.80
   2 !   45.7  31.8   4.6e-16   4.1e-12       2     173 ..     198     364 ..     197     369 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 4.6e-20
                             MFS_1  18 alplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.sslwlllvlrv 93 
                                       ++ +  ae++ +s  ++++++++  ++++++s ++G+ls r+++r vll++++++a+ +  l  +  s+ +l+++ +
  gi|336255060|ref|YP_004598167.1|  13 IFREPFAETFAVSTVAMSTVFSVMLFTFFIGSGLVGVLSARVSARAVLLACAAASAVLAPSLY-VvDSYGALMLVFA 88 
                                       455567899*************************************99999999999934444.426666******* PP

                             MFS_1  94 lqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfll 170
                                       + G++ g++f + a+++ +wf + +rg a+gl+ +g++lG  + p++    +s +g r  f+ +  +++ afv++++
  gi|336255060|ref|YP_004598167.1|  89 VLGIALGTVFVLTASIVPRWFDE-RRGAATGLIFVGNGLGLTVLPPIWQGAISTFGVRRGFLYIMSITAAAFVVAGV 164
                                       **********************9.********************999999999*******99999999999995444 PP

                             MFS_1 171 llpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg.lltllplylqevlgls.glll 245
                                        + ++p   + +++ +     +  ++v   ++  ++ +  +l++++ l+f ++++ l ++   +    +gl+ ++ +
  gi|336255060|ref|YP_004598167.1| 165 -VCRRPAWAEQSATSTG----ELLGWVR--RLAGTRTFQ-LLFVGMSLAF-AWYQlLAAYAVDF-FAARGLTdAAAS 231
                                       .4455555555555555....6677777..444444433.3666666665.6666255555556.999999975566 PP

                             MFS_1 246 aglllallalvgailallagrlsd 269
                                       ++  ++l++ v++i+++ +g+++d
  gi|336255060|ref|YP_004598167.1| 232 TA--FGLIGGVSIISRIGGGYVAD 253
                                       66..*****************987 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 4.6e-16
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       l++++  a+a++ l++a+      + g++ ++++++++l + +++++ + +G+++d +G+rr +l++l++ +lg + 
  gi|336255060|ref|YP_004598167.1| 198 LFVGMSLAFAWYQLLAAYAVDFFAARGLTDAAASTAFGLIGGVSIISRIGGGYVADVVGSRRAFLASLACAGLG-VG 273
                                       67778888888888888888555667999*********************************************.55 PP

                             MFS_1  79 llfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                       ll+++++ +l+++ ++ Glg g+++++ + l+ +++ +e+ + +ig++++++++Ga+  p+lg + +++ g   v +
  gi|336255060|ref|YP_004598167.1| 274 LLVVPQFAMLALGVFFVGLGLGGSATLYIPLLMEIYDPEKDTAVIGVFNVAAGIGALAMPPLGTASVTYTGSYTVAI 350
                                       55349999***********************************************************7766444444 PP

                             MFS_1 156 ilaivsllafvlfllllp 173
                                       +l++v +l++    ++l+
  gi|336255060|ref|YP_004598167.1| 351 LLTLVVVLGA----FWLV 364
                                       4444444442....3332 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 !   30.6  44.0   2.2e-11     2e-07      26     355 ..      25     357 ..      18     367 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.2e-11
                             MFS_4  26 slsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaaflliRflaGvasAvvlvfg 102
                                       s  +++ + ++ +  +++G+ l  +  ++  +R +lla + a+++l+    +++s  a++l+  ++G+a ++v+v++
  gi|336255060|ref|YP_004598167.1|  25 STVAMSTVFSVMLFTFFIGSGLVGVLSARVSARAVLLACAAASAVLAPSLYVVDSYGALMLVFAVLGIALGTVFVLT 101
                                       555666677777778889998888888999*********************************************** PP

                             MFS_4 103 sslvlahaaaarrervgallfaGvGlGiavsgllvlll.lqlglsasslWlalavlsavllll.valllpraalrea 177
                                       +s+v +   + rr++  +l+f G GlG  v   +   +  ++g+   +l+ ++++ +a+ +++ v+  +p+ a++ a
  gi|336255060|ref|YP_004598167.1| 102 ASIVPRW-FDERRGAATGLIFVGNGLGLTVLPPIWQGAiSTFGVRRGFLY-IMSITAAAFVVAgVVCRRPAWAEQSA 176
                                       **99777.78899**************98866666555055566666555.55555555444415555555555555 PP

                             MFS_4 178 saaaeaa...kaeqkslpllalllaYglaGfGYiitatFlvaiardgaggalleallWllvGlaaivgvlvwlrvak 251
                                        +  e     + ++ ++    l +   la + Y + a + v++ ++++   ++++ +  l+G  +i++      va+
  gi|336255060|ref|YP_004598167.1| 177 TSTGELLgwvRRLAGTRTFQLLFVGMSLAFAWYQLLAAYAVDFFAARGLTDAAASTAFGLIGGVSIISRIGGGYVAD 253
                                       55555531113444444444555556666666999*******999999999999999999988889999******** PP

                             MFS_4 252 rsglrralaaallieavgvllsllspsplglivssvllGltflaitalvlqlarelappat.rrllglmTasfgigQ 327
                                         g rra+ a l+  ++gv l ++ p  ++l++++  +Gl   +   l ++l  e++ p++  +++g+  ++ gig 
  gi|336255060|ref|YP_004598167.1| 254 VVGSRRAFLASLACAGLGVGLLVV-PQFAMLALGVFFVGLGLGGSATLYIPLLMEIYDPEKdTAVIGVFNVAAGIGA 329
                                       *********************888.9999************************999987776899************ PP

                             MFS_4 328 ilGpllasllaeatgslalallvaaaal 355
                                       ++ p l  ++  +tgs++ a+l+  +++
  gi|336255060|ref|YP_004598167.1| 330 LAMPPLGTASVTYTGSYTVAILLTLVVV 357
                                       *******************998864443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 2837.29
//
Query:       gi|336255061|ref|YP_004598168.1|  [L=213]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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   56.8   0.1    4.6e-15   56.1   0.1    1.3  1  Methyltransf_25  Methyltransferase domain
    1.7e-12   47.8   0.1    2.9e-12   47.1   0.1    1.3  1  Methyltransf_11  Methyltransferase domain
    6.9e-11   41.9   0.0      9e-11   41.5   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    7.2e-11   42.2   0.0    9.4e-11   41.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.3e-09   37.2   0.0    2.9e-09   36.9   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    3.8e-09   37.2   0.1    6.1e-09   36.5   0.1    1.3  1  Methyltransf_12  Methyltransferase domain
    5.3e-09   35.8   0.0    6.9e-09   35.4   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    3.5e-05   23.4   0.0    3.5e-05   23.4   0.0    1.1  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    5.6e-05   22.8   0.0    8.9e-05   22.1   0.0    1.2  1  MTS              Methyltransferase small domain
    0.00068   19.4   0.0    0.00088   19.0   0.0    1.2  1  TPMT             Thiopurine S-methyltransferase (TPMT)
     0.0012   18.6   0.0     0.0016   18.1   0.0    1.3  1  NodS             Nodulation protein S (NodS)
     0.0016   17.8   0.0     0.0023   17.3   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.045   13.7   0.0      0.062   13.2   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
      0.048   13.4   0.0      0.076   12.8   0.0    1.3  1  DUF938           Protein of unknown function (DUF938)
       0.06   14.4   0.2       0.12   13.4   0.2    1.5  1  Methyltransf_24  Methyltransferase domain
      0.066   13.1   0.1       0.12   12.2   0.0    1.4  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.067   12.9   0.0      0.096   12.4   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
      0.086   12.6   0.0       0.12   12.1   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


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 !   56.1   0.1   4.6e-18   4.6e-15       2      86 ..      43     127 ..      42     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 4.6e-18
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEE.EST.G CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvs.sga.l 74 
                                       Ld+++GtGr++  la+++  ++v +vD+s+e+le+a++ra+e+g+  +v+++++d+ +++fe+g +D++++ ++a l
  gi|336255061|ref|YP_004598168.1|  43 LDVATGTGRNAVFLAANG--YDVDAVDVSDEALERAQQRADERGVddSVDWIRADLAEYEFESGAYDVITIgFFAaL 117
                                       9***************95..*************************************************99766679 PP

                                       GGSSHHHHHHHH CS
                   Methyltransf_25  75 hhlsdedlekal 86 
                                       +hl+  d+++al
  gi|336255061|ref|YP_004598168.1| 118 EHLP--DIKEAL 127
                                       9987..666665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.1   2.9e-15   2.9e-12       1      82 [.      43     128 ..      43     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.9e-15
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES..-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvsse..vlhh 73 
                                       Ldv++GtGr+a  la +g++v +vD+s+e+l++a+++a e+g+  +v++++ad+ +  fe++ +D++++ +  +l+h
  gi|336255061|ref|YP_004598168.1|  43 LDVATGTGRNAVFLAANGYDVDAVDVSDEALERAQQRADERGVddSVDWIRADLAEYEFESGAYDVITIGFfaALEH 119
                                       8*******************************************************************998889*** PP

                                       -CCHHHHHH CS
                   Methyltransf_11  74 vedpekalk 82 
                                       ++d ++al+
  gi|336255061|ref|YP_004598168.1| 120 LPDIKEALA 128
                                       ***999986 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   9.1e-14     9e-11      47     136 ..      38     127 ..       9     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 9.1e-14
                                       -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEEE CS
                   Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvtv 122
                                       +  ++lDva+Gtg  a+ l+    + ++v+ +D++++ L+ +++++ e+g+  +++++ a+  e +fe +++Dv+t+
  gi|336255061|ref|YP_004598168.1|  38 PEGRALDVATGTGRNAVFLAA---NGYDVDAVDVSDEALERAQQRADERGVDdSVDWIRADLAEYEFESGAYDVITI 111
                                       44589*********9998864...5679***********************989*********************** PP

                                       ES..-GGG-S-HHHHH CS
                   Ubie_methyltran 123 sf..GlrnvtDklkaL 136
                                       +f   l  ++D+++aL
  gi|336255061|ref|YP_004598168.1| 112 GFfaALEHLPDIKEAL 127
                                       *966688899998887 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   9.4e-14   9.4e-11      20     125 ..      36     154 ..      15     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 9.4e-14
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..........kakkaqkdqfdeq........eaae 78 
                                         + gr Ld+++GtG+++  l++ng++v++vD s+ea e+a+          +                    e ++
  gi|336255061|ref|YP_004598168.1|  36 TLPEGRALDVATGTGRNAVFLAANGYDVDAVDVSDEALERAQqradergvddS-----------VdwiradlaEYEF 101
                                       45679**********************************98555444442221...........1222332225566 PP

                   Methyltransf_23  79 pqgkfdlIv..lrevlehvpdppellrqiatllkpgGylllseplasl...........k 125
                                       ++g +d+I+   +  leh+pd       i++ l+p G+l+ + +l+s+           +
  gi|336255061|ref|YP_004598168.1| 102 ESGAYDVITigFFAALEHLPD-------IKEALAPSGVLVYEHHLRSSdpidvgpsgdrY 154
                                       999***986337999******.......78889999999999998887666665554440 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   2.9e-12   2.9e-09       6     110 ..      41     136 ..      38     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.9e-12
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsn 81 
                                       r lD+++GtG+ +  la +   + +v  +D s ea+e+A+++a++ g+d  v   ++d  e e  +e   +D+i+  
  gi|336255061|ref|YP_004598168.1|  41 RALDVATGTGRNAVFLAAN---GYDVDAVDVSDEALERAQQRADERGVDdSVDWIRADLAEYE--FESGAYDVITI- 111
                                       68***************55...45588**********************99************..99******887. PP

                   Methyltransf_31  82 evlnaladpdkileeiervlkpggillie 110
                                       ++++al +++     i+++l p g+l+ e
  gi|336255061|ref|YP_004598168.1| 112 GFFAALEHLP----DIKEALAPSGVLVYE 136
                                       4444444433....344556666666555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.1   6.1e-12   6.1e-09       1      87 [.      43     128 ..      43     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 6.1e-12
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvas..n 74 
                                       L++ +GtG+++  l+++  + ++ +vD+s +a+e+a+++  +r+ +  + v++   dl++ + + +++D++++    
  gi|336255061|ref|YP_004598168.1|  43 LDVATGTGRNAVFLAAN--GYDVDAVDVSDEALERAQQRADERGVD--DSVDWIRADLAEYEFEsGAYDVITIGffA 115
                                       89***************..**************9999998888865..478888777777766679******76448 PP

                   Methyltransf_12  75 vlhhlkdirevld 87 
                                       +l+hl+di+e+l+
  gi|336255061|ref|YP_004598168.1| 116 ALEHLPDIKEALA 128
                                       9********9985 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0     7e-12   6.9e-09      26      99 ..      34     109 ..       9     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 7e-12
                                       CCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-T.TEEEEE--GGG----S.-EEEE CS
                              TehB  26 vkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlk.nistalydineaklde.rydfi 99 
                                        +++  g++ld+  g grn+++l+++gydv+a+d  +++++  ++ ++   ++ +++    d+ e +++   yd i
  gi|336255061|ref|YP_004598168.1|  34 LETLPEGRALDVATGTGRNAVFLAANGYDVDAVDVSDEALERAQQRADERGVDdSVDWIRADLAEYEFESgAYDVI 109
                                       5678889**********************************99999888777515666777888888765357766 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 !   23.4   0.0   3.5e-08   3.5e-05       4      61 ..      42     110 ..      39     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.5e-08
                   Methyltransf_15   4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe...........l 61 
                                        lD+ +G+G n++ +a ++  v a++++ e l+ aq+ a   gv+d ++++ +d+ e           +
  gi|336255061|ref|YP_004598168.1|  42 ALDVATGTGRNAVFLAANGYDVDAVDVSDEALERAQQRADERGVDDSVDWIRADLAEyefesgaydviT 110
                                       79****************99**********************************988555555555540 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   8.9e-08   8.9e-05      26     101 ..      33     109 ..      28     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.9e-08
                                       HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTT.TSTTS-EE CS
                               MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvle.eveekkfd 99 
                                        l++  +g++lD+++G+G  ++ la++  +  v++vdv+ +Ale a++ + + +++  v+ +  d+ e e+e + +d
  gi|336255061|ref|YP_004598168.1|  33 RLETLPEGRALDVATGTGRNAVFLAANGYD--VDAVDVSDEALERAQQRADERGVDdsVDWIRADLAEyEFESGAYD 107
                                       566667899****************98777..9***********************999999999887456778888 PP

                                       EE CS
                               MTS 100 li 101
                                       +i
  gi|336255061|ref|YP_004598168.1| 108 VI 109
                                       87 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   8.8e-07   0.00088       3      81 ..       8      82 ..       6     122 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.8e-07
                                      HHHHHHHHHTT--TT--SS--HHHHHHHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTT CS
                              TPMT  3 edfWekrweeeqipfhqeevnpllkkfldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanl 81
                                       ++W++++++   +    +  p l + l++    +++r+l    G + ++v lA++g++v +v++s+ A+e++ + a++
  gi|336255061|ref|YP_004598168.1|  8 RERWNEKYNDADFELPG-DPIPVLERRLET---LPEGRALDVATGTGRNAVFLAANGYDVDAVDVSDEALERAQQRADE 82
                                      56788887766544443.344677777777...7888999999****************************98665554 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.6e-06    0.0016      45     112 ..      40     111 ..      26     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-06
                              NodS  45 adalevGcaaGalterlapyckrltvvdvveeaiararervkes...shiswivsdvqqfstde.kfdlivv 112
                                       + al+v   +G  ++ la     +  vdv +ea++ra++r +e      + wi +d+ +++ +   +d+i +
  gi|336255061|ref|YP_004598168.1|  40 GRALDVATGTGRNAVFLAANGYDVDAVDVSDEALERAQQRADERgvdDSVDWIRADLAEYEFESgAYDVITI 111
                                       67999999********************************9986332579*********9976537999876 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.3e-06    0.0023      63     140 ..      39     117 ..      28     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-06
                                       T-EEEEES-TTSHHHHH.HHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EE...EEES-GGG-----SEEEEES CS
                              CMAS  63 GmtlLdiGcGWGslvrr.averydvkvvglTlSkeqaklakkrvdeldlerkve...vklldyedldekvdrvvsvg 135
                                         + Ld+ +G G  ++  a++ ydv+  ++ +S+e  ++a++r de++++++v+    +l++ye  ++ +d v+++g
  gi|336255061|ref|YP_004598168.1|  39 EGRALDVATGTGRNAVFlAANGYDVD--AVDVSDEALERAQQRADERGVDDSVDwirADLAEYEFESGAYD-VITIG 112
                                       45679*******98776155566666..6678******************998622255666654444666.77888 PP

                                       -GGGT CS
                              CMAS 136 afehv 140
                                        f ++
  gi|336255061|ref|YP_004598168.1| 113 FFAAL 117
                                       87665 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.3e-05     0.062      16      75 ..      40      97 ..      30     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.3e-05
                   Methyltransf_18 16 srvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGl 75
                                       r +D+ t  g  +++l+ +g    v a+D+++++le+a++ +++ g++d+++ + +d  
  gi|336255061|ref|YP_004598168.1| 40 GRALDVATGTGRNAVFLAANGYD--VDAVDVSDEALERAQQRADERGVDDSVDWIRADLA 97
                                      47899999999999999999875..999************************99887743 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.6e-05     0.076      17      46 ..      29      59 ..      24     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.6e-05
                            DUF938 17 vLksylaktte.rvLEiasGtGqHAvffApa 46
                                      vL++ l++  e r L++a+GtG+ Avf+A++
  gi|336255061|ref|YP_004598168.1| 29 VLERRLETLPEgRALDVATGTGRNAVFLAAN 59
                                      67777777666689***************97 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   0.00012      0.12       7     102 ..      49     134 ..      45     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                   Methyltransf_24   7 sGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiDgghaae 82 
                                        G+ +++l+    +ng   + avd   +  e+a++ a+e g+dd v+ i+ad+ e+  ++++g +D++ i +     
  gi|336255061|ref|YP_004598168.1|  49 TGRNAVFLA----ANGY-DVDAVDVSDEaLERAQQRADERGVDDSVDWIRADLAEY--EFESGAYDVITIGFF---- 114
                                       666666666....5554.666777755436778999999*****************..99999*******987.... PP

                   Methyltransf_24  83 avledleallprlapggvvl 102
                                       a+le l+ + + lap gv++
  gi|336255061|ref|YP_004598168.1| 115 AALEHLPDIKEALAPSGVLV 134
                                       78889999999999999998 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 ?   12.2   0.0   0.00013      0.12      15      44 ..      53      82 ..      47     101 .. 0.83
   2 ?   -3.6   0.0         9     9e+03      24      49 ..     169     194 ..     164     201 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                      HHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N 15 aavfasagleVvlvdiseealekalekiek 44
                                      a  +a++g++V  vd+s+eale+a++++ +
  gi|336255061|ref|YP_004598168.1| 53 AVFLAANGYDVDAVDVSDEALERAQQRADE 82
                                      5566777*******************9876 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9
                                       EEEEE-S-HHHHHHHHHHHHHHHHCC CS
                           3HCDH_N  24 eVvlvdiseealekalekiekslekl 49 
                                       +V  ++ ++++++++++++++ +++ 
  gi|336255061|ref|YP_004598168.1| 169 TVLSYEERRRTVNDGTAAVATIVARS 194
                                       56666666666666666666655554 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.7e-05     0.096      76     125 ..      60     109 ..      38     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.7e-05
                                       H--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EE CS
                           UPF0020  76 elklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvi 125
                                        + + ++D   +++++a++ a + gv+d++++  ad a+ + ++g +dvi
  gi|336255061|ref|YP_004598168.1|  60 GYDVDAVDVSDEALERAQQRADERGVDDSVDWIRADLAEYEFESGAYDVI 109
                                       5667899*******************************999888899988 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 ?   12.1   0.0   0.00012      0.12      73     168 ..      38     132 ..      29     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                       TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTGGG-SEEEEEE CS
                              PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkGyeekaPYdaihv 148
                                       +  r+L+v +G+G +++ la        v +++ + e  e+a+++  + +++ +v  + +D  +   e   Yd+i +
  gi|336255061|ref|YP_004598168.1|  38 PEGRALDVATGTGRNAVFLAANGY---DVDAVDVSDEALERAQQRADERGVDdSVDWIRADLAEYEFESGAYDVITI 111
                                       6679*********99988876433...34588999999********99999889*******8776667788***999 PP

                                       S..SBBSS--HHHHHTEEEEEE CS
                              PCMT 149 g..aaapeiPealidQLkeGGr 168
                                       g  aa +++P+ + + L++ G 
  gi|336255061|ref|YP_004598168.1| 112 GffAALEHLPD-IKEALAPSGV 132
                                       85566677774.4455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 0.42u 0.18s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1836.06
//
Query:       gi|336255062|ref|YP_004598169.1|  [L=196]
Description: alkyl hydroperoxide reductase/thiol specific antioxidant/Mal allergen [Halopiger xanaduensis SH-6]
Scores for 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-05   24.0   0.0    3.9e-05   23.6   0.0    1.3  1  AhpC-TSA       AhpC/TSA family
    0.00047   20.4   0.0    0.00065   20.0   0.0    1.2  1  Thioredoxin_8  Thioredoxin-like
     0.0011   18.7   0.0     0.0014   18.4   0.0    1.1  1  Redoxin        Redoxin
     0.0023   17.9   0.0      0.013   15.4   0.0    1.9  2  Thioredoxin    Thioredoxin
  ------ inclusion threshold ------
      0.066   13.7   0.0      0.089   13.2   0.0    1.2  1  Thioredoxin_2  Thioredoxin-like domain


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 !   23.6   0.0   1.1e-08   3.9e-05      32     121 ..      79     164 ..      50     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.1e-08
                                       EESTST-CCHHHHHHHHHHCHHHCCCT...TEEEEEEES.SSCHHHHHHHHH-H.SSEEEE-TTSHHHHHTT-EETT CS
                          AhpC-TSA  32 fypkdwcpvCttelpalaklyeefker...gvevigvsv.dspeshkkfiekeslnfpllsDeegkvakaygvlkee 104
                                       f p   c  C++ +p+l+++ ee+++     ++v+ v++ ++p++++++ ++++ ++ l +D+++ + ++y+v+   
  gi|336255062|ref|YP_004598169.1|  79 FSP--VCSRCRALMPELEAAREELRADygdALTVLSVTAeQTPDRLRDWWAENDGEWVLGYDPDRRLGERYDVV--- 150
                                       333..5*******************7644467899999988899******************************... PP

                                       TTECSCEEEEE-TTSBE CS
                          AhpC-TSA 105 kglalratfvidkegki 121
                                            +    id+ g +
  gi|336255062|ref|YP_004598169.1| 151 ---GHPMLLAIDDAGEL 164
                                       ...77777777777765 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.8e-07   0.00065       3      94 ..      73     163 ..      71     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-07
                                       EEEEEE--SSSHHHHHHHHHHHHHHHHHHH..TTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT- CS
                     Thioredoxin_8   3 vvlLyfgaswcppckaftpklkelyeklkk..kkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkkk 77 
                                       v+l ++++  c+ c+a +p+l +  e+l++  ++ + +++v   ++ +  ++  ++n  +w+   +d      l ++
  gi|336255062|ref|YP_004598169.1|  73 VTLAMIFSPVCSRCRALMPELEAAREELRAdyGDALTVLSVTAEQTPDRLRDWWAENDGEWVL-GYD--PDRRLGER 146
                                       567789999********************999*************************889988.555..4579**** PP

                                       S--TT-SEEEEE-TT-B CS
                     Thioredoxin_8  78 ynvkaiPtlvvldknge 94 
                                       y+v + P+l+ +d  ge
  gi|336255062|ref|YP_004598169.1| 147 YDVVGHPMLLAIDDAGE 163
                                       ************98886 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.9e-07    0.0014      40     135 ..      82     172 ..      59     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.9e-07
                                       T-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH....HHHHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG CS
                           Redoxin  40 fcPtCsaehpyleklaellkekgvdvvavvadndaf....vkefwgkeglkfpvlsDgsaaftkalGlrleedaseg 112
                                        c  C+a +p+le   e+l++   d + v +++ ++     +++w++++  +++ +D++  + + +++         
  gi|336255062|ref|YP_004598169.1|  82 VCSRCRALMPELEAAREELRADYGDALTVLSVTAEQtpdrLRDWWAENDGEWVLGYDPDRRLGERYDVV-------- 150
                                       3666889999*****666666655555666666666689****************************88........ PP

                                       EEE-EEEEEEETTEEEEEEESSS CS
                           Redoxin 113 lrtpryavidedgkvvylevepe 135
                                        + p + +id+ g + + +++  
  gi|336255062|ref|YP_004598169.1| 151 -GHPMLLAIDDAGELHWDNRGRL 172
                                       .99**********9998887765 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.7e-06     0.013      19      63 ..      72     120 ..      65     127 .. 0.81
   2 ?   -0.2   0.0      0.27   9.6e+02      61      99 ..     140     179 ..     135     182 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.7e-06
                                       SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT....TSEEEEEETTTSHH CS
                       Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkd....kvklakvdvdened 63 
                                          l   ++p C  C+al Pele++ eel++     ++++ v +++ +d
  gi|336255062|ref|YP_004598169.1|  72 GVTLAMIFSPVCSRCRALMPELEAAREELRAdygdALTVLSVTAEQTPD 120
                                       556777899****************999988777788888888877766 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.27
                                       SHHHHHHTT-SSSSEEEEEETTE.EEEEEESS-HHHHHHH CS
                       Thioredoxin  61 nedlakkyevegiPtlklfkngk.evkkyegarekeklaa 99 
                                        + l ++y+v g P l+ + +      +  g  e+ ++++
  gi|336255062|ref|YP_004598169.1| 140 DRRLGERYDVVGHPMLLAIDDAGeLHWDNRGRLEAGQIVE 179
                                       5678899*******99776654325666666666666655 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.5e-05     0.089       7      90 ..      73     161 ..      68     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                     Thioredoxin_2   7 pvlvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkd.........ieenvela 73 
                                        +l+++ +p C  C++l+ el+   ++++       ++++    +v   +++++ +++ +         ++  + l+
  gi|336255062|ref|YP_004598169.1|  73 VTLAMIFSPVCSRCRALMPELEAArEELRAD-----YGDALTVLSVTAEQTPDRLRDWWAendgewvlgYDPDRRLG 144
                                       6899999*****************8888888.....999999999999999999888777899999999******** PP

                     Thioredoxin_2  74 rkygvrgtPtivfldgk 90 
                                       ++y+v g P ++ +d  
  gi|336255062|ref|YP_004598169.1| 145 ERYDVVGHPMLLAIDDA 161
                                       **********8866654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1535.40
//
Query:       gi|336255063|ref|YP_004598170.1|  [L=826]
Description: DNA topoisomerase [Halopiger xanaduensis SH-6]
Scores for 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-123  412.3   0.0   2.7e-123  412.0   0.0    1.1  1  Topoisom_bac     DNA topoisomerase
    7.8e-20   70.4  14.4    2.4e-13   49.6   1.0    3.6  4  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
    1.3e-16   60.7   0.1    2.6e-16   59.7   0.1    1.5  1  Toprim           Toprim domain
    1.4e-08   35.2   2.1    1.8e-08   34.9   0.2    2.3  1  HHH_5            Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.028   14.7   0.0      0.079   13.2   0.0    1.8  1  Cdd1             Pathogenicity locus
      0.042   13.7   0.0       0.16   11.9   0.0    2.0  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
       0.17   12.2   0.0       0.38   11.0   0.0    1.6  1  DUF4332          Domain of unknown function (DUF4332)
       0.23   11.2   3.1         18    5.2   0.1    2.9  2  zinc_ribbon_2    zinc-ribbon domain
       0.72    9.6   2.2         30    4.4   0.2    2.7  2  Rubredoxin_2     Rubredoxin metal binding domain
        1.4    8.5   8.9       0.81    9.2   0.1    3.9  3  TF_Zn_Ribbon     TFIIB zinc-binding
        5.6    7.0   6.3        2.3    8.2   0.0    3.1  3  Ogr_Delta        Ogr/Delta-like zinc finger


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 !  412.0   0.0  1.7e-126  2.7e-123       2     412 ..     150     562 ..     149     563 .. 0.95

  Alignments for each domain:
  == domain 1  score: 412.0 bits;  conditional E-value: 1.7e-126
                      Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkg..kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkke 76 
                                       ++++l++a+eaR+++D+++G++l+r+l++++ +  ++++s+GRVq+ptL+liv+Rerei++F pe+ywe+ a+l+k+
  gi|336255063|ref|YP_004598170.1| 150 LDFDLAAAGEARQIIDLVWGAALTRFLSLSAGQlgNDFISVGRVQSPTLKLIVDREREIQAFDPEDYWELFADLAKD 226
                                       6899*************************6555669**************************************666 PP

                      Topoisom_bac  77 kkeke......kkkkkkkerikdkeeaeaileklkkk.eakvesvekkekkkppplpfdtttLqkeasrklglsakk 146
                                       ++++e      ++   + er++++ +ae+++ +l++  +a+v++v++++++++pp+pf+tt++ ++a   lg+sa++
  gi|336255063|ref|YP_004598170.1| 227 DTTFEsqyfyrDEDDNEAERVWEEAAAEEVYDTLSQRdSATVVDVNRRTRTDAPPTPFNTTQFIRAAGA-LGYSAQR 302
                                       6666669**998899999****************99669**************************9988.7****** PP

                      Topoisom_bac 147 tlsiaqkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPt 223
                                       ++sia++LY+  g+itYpRTd+t+++++ + +++l+ +  +  +++ e+ae+ll+  + + + +++++++H++I+Pt
  gi|336255063|ref|YP_004598170.1| 303 AMSIAEDLYTA-GYITYPRTDNTVYPDDLDPEELLDDFVGH--PTLGESAEDLLEADEIQPTEGDEETTDHPPIHPT 376
                                       **********5.****************668********97..7799999999987776658889999********* PP

                      Topoisom_bac 224 eelpklkelsddekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelp 300
                                       +e+p + + sdde++++el+vrrf a+++++a++e+ +v  eve++++ka+gk+++e+G++ vy++ ++ e+   +p
  gi|336255063|ref|YP_004598170.1| 377 GEIPARGDVSDDEWEIFELVVRRFYATVAEAAVWEHLKVVSEVEDYRLKANGKRLVEPGYHDVYPYFSTAENY--VP 451
                                       ****8899**********************************************************9999886..** PP

                      Topoisom_bac 301 elkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalve 377
                                       +++egee+ + +veleek+T+pp ry +++Li++me+ giGt++Tr++++ekl++rgY+e++    +pt+l++a+v+
  gi|336255063|ref|YP_004598170.1| 452 DVEEGEELALSDVELEEKQTQPPRRYGQSRLIETMEDMGIGTKSTRHNTLEKLYDRGYIESDP--PRPTKLAMAVVD 526
                                       *************************************************************76..89********** PP

                      Topoisom_bac 378 llekf.kdlvspelTaeleekLdeIaegkadakevl 412
                                       + e++ +++vs+e+Ta+le ++d+Ia+g+a  ++v 
  gi|336255063|ref|YP_004598170.1| 527 AAENYaDRVVSEEMTAQLEADMDAIASGEAGLEDVT 562
                                       **9999************************999986 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 !   49.6   1.0   1.4e-16   2.4e-13       4      38 ..     600     635 ..     598     636 .. 0.95
   2 ?   -2.1   0.3       2.1   3.4e+03       4       9 ..     667     672 ..     664     673 .. 0.78
   3 !   28.7   0.2   5.2e-10   8.5e-07       2      38 ..     682     723 ..     681     724 .. 0.87
   4 ?   -0.3   0.0      0.58   9.5e+02       4      19 ..     755     771 ..     754     772 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.4e-16
                                       -SSS--EEEEEE-SSS.EEEEESST.T----EEB-G CS
                    zf-C4_Topoisom   4 CPkCggdLvlkrgkkG.kFvGCsnYPeCkftkklkk 38 
                                       CP+Cg+dL++++++ G  F+GC+ YP+C++t +l++
  gi|336255063|ref|YP_004598170.1| 600 CPECGEDLLVRNSRHGsYFIGCDGYPDCENTLPLPS 635
                                       ********************************9986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.1
                                       -SSS-- CS
                    zf-C4_Topoisom   4 CPkCgg 9  
                                       CP C++
  gi|336255063|ref|YP_004598170.1| 667 CPLCKA 672
                                       ****86 PP

  == domain 3  score: 28.7 bits;  conditional E-value: 5.2e-10
                                       EE-SSS-.-...EEEEEE-SSS.EEEEESST.T----EEB-G CS
                    zf-C4_Topoisom   2 ekCPkCg.g...dLvlkrgkkG.kFvGCsnYPeCkftkklkk 38 
                                       ++CP Cg +   dL +k+   G + vGC++YP+C++  +l++
  gi|336255063|ref|YP_004598170.1| 682 GECPDCGeEhdgDLAVKTLQSGsRLVGCTRYPDCEYSLPLPR 723
                                       68****9533337************************99986 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.58
                                       -SSS-.-EEEEEE-SSS CS
                    zf-C4_Topoisom   4 CPkCg.gdLvlkrgkkG 19 
                                       CP C+ ++ + +++  G
  gi|336255063|ref|YP_004598170.1| 755 CPICNyQEFQARESDSG 771
                                       *****999998888665 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.1   1.6e-19   2.6e-16       1     103 []       2     135 ..       2     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.6e-19
                                       EEEEESSHHHHHHHHHTHT................STEEEEEEESSSSEEEHS..............TTEEEEEECT CS
                            Toprim   1 elvivEgpsdaktiakalg................sgfqavtaslGhildlet..............efkpvyeeie 47 
                                       el+i E++++a+ ia +l+                 g+++++ ++Gh++ +++               +++  e+  
  gi|336255063|ref|YP_004598170.1|   2 ELIITEKDNAARRIADILSggtydssrengvnvyeWGGKRCVGLSGHVVGVDFpdeysdwrdvepaeLIDADVEKTA 78 
                                       69********************************9999***************888887777666666666666*** PP

                                       TTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTT.TEEEEEESSS CS
                            Toprim  48 dkkkvlkalkelakradeiilatDpDreGeaiawellevlkellen.kigrvefsei 103
                                       +k++++++l+  a++a  + +atD DreGe i++e++e +++ +e+  i+rv+fs+i
  gi|336255063|ref|YP_004598170.1|  79 TKENIVATLRIFARKATSVTIATDYDREGELIGKEAYEIVRDVNEDvPIRRVRFSSI 135
                                       ******************************************************987 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.2   1.1e-11   1.8e-08       3      55 ..     773     826 .]     772     826 .] 0.95

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.1e-11
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHT.STTS-HHHHHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLak.ipGiGkktAeriilel 55 
                                       +L  ++G+G+kt+ +l++aGies++dl +ad++++a+ + G+++++ +++  e+
  gi|336255063|ref|YP_004598170.1| 773 DLEALDGLGAKTVEKLADAGIESIDDLTEADPDAVAEdVDGVSADRIRNWQAEA 826
                                       7999******************************9999***********99886 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.8e-05     0.079       6      47 ..     772     813 ..     767     820 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.8e-05
                              Cdd1   6 kelqdiPniGkalaedlvelGirsveelkgedpeelyeklek 47 
                                       ++l+ + + G ++ e+l + Gi+s+++l++ dp+++ e++  
  gi|336255063|ref|YP_004598170.1| 772 SDLEALDGLGAKTVEKLADAGIESIDDLTEADPDAVAEDVDG 813
                                       68999*****************************99887665 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 ?   -3.6   0.0       6.4     1e+04      13      22 ..     306     315 ..     305     317 .. 0.83
   2 ?   11.9   0.0   9.6e-05      0.16       8      30 ..     779     801 ..     778     811 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.4
                   DNA_pol_lambd_f  13 tAkkwyakGi 22 
                                       +A+++y +G+
  gi|336255063|ref|YP_004598170.1| 306 IAEDLYTAGY 315
                                       69*****998 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.6e-05
                   DNA_pol_lambd_f   8 GVGpktAkkwyakGirtledlra 30 
                                       G G+kt +k+ ++Gi +++dl +
  gi|336255063|ref|YP_004598170.1| 779 GLGAKTVEKLADAGIESIDDLTE 801
                                       78*******************88 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023      0.38       2      52 ..     779     825 ..     778     826 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                           DUF4332   2 gigkeeaekLkkaGikttedLlelgktekgrkalaeklgisernvlklanl 52 
                                       g+g++  ekL+ aGi++ +dL+e+ ++  ++    +  g+s+ +++++++ 
  gi|336255063|ref|YP_004598170.1| 779 GLGAKTVEKLADAGIESIDDLTEADPDAVAE----DVDGVSADRIRNWQAE 825
                                       6788999*****************9999999....8889999999999986 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.011        18      16      23 .]     600     607 ..     589     607 .. 0.71
   2 ?    5.1   0.6     0.012        19       2      10 ..     684     692 ..     683     694 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.011
                     zinc_ribbon_2  16 CpyCGtpl 23 
                                       Cp+CG+ l
  gi|336255063|ref|YP_004598170.1| 600 CPECGEDL 607
                                       88888765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.012
                     zinc_ribbon_2   2 CpnCGaelq 10 
                                       Cp CG+e++
  gi|336255063|ref|YP_004598170.1| 684 CPDCGEEHD 692
                                       9****9986 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.027        44      13      22 ..     596     605 ..     593     605 .. 0.84
   2 ?    4.4   0.2     0.018        30      13      22 ..     680     689 ..     675     689 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.027
                      Rubredoxin_2  13 wfGrCpsCgs 22 
                                        +G Cp+Cg+
  gi|336255063|ref|YP_004598170.1| 596 RLGPCPECGE 605
                                       6899****96 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.018
                      Rubredoxin_2  13 wfGrCpsCgs 22 
                                       ++G Cp+Cg+
  gi|336255063|ref|YP_004598170.1| 680 VLGECPDCGE 689
                                       589*****96 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0005      0.81       3      20 ..     600     617 ..     598     619 .. 0.90
   2 ?    1.1   0.6      0.17   2.8e+02       3       9 ..     684     690 ..     682     696 .. 0.76
   3 ?   -0.1   0.1      0.41   6.6e+02       3      13 ..     755     766 ..     753     772 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0005
                                       ETTTTCEECHEETSTTCE CS
                      TF_Zn_Ribbon   3 CPnCgstnlveDpergel 20 
                                       CP+Cg + lv++  +g +
  gi|336255063|ref|YP_004598170.1| 600 CPECGEDLLVRNSRHGSY 617
                                       *****999*****99987 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.17
                                       ETTTTCE CS
                      TF_Zn_Ribbon   3 CPnCgst 9  
                                       CP+Cg +
  gi|336255063|ref|YP_004598170.1| 684 CPDCGEE 690
                                       8888865 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.41
                                       ETTTTCEE.CHE CS
                      TF_Zn_Ribbon   3 CPnCgstn.lve 13 
                                       CP+C+  + + +
  gi|336255063|ref|YP_004598170.1| 755 CPICNYQEfQAR 766
                                       ****97543555 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 ?    8.2   0.0    0.0014       2.3       2      16 ..     600     614 ..     599     619 .. 0.90
   2 ?   -1.1   0.3       1.2   1.9e+03       2       7 ..     667     672 ..     666     675 .. 0.88
   3 ?    0.0   0.5      0.54   8.7e+02       1       8 [.     683     690 ..     683     718 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0014
                         Ogr_Delta   2 CPhCgapaaartsrn 16 
                                       CP+Cg+   +r+sr 
  gi|336255063|ref|YP_004598170.1| 600 CPECGEDLLVRNSRH 614
                                       *************95 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                         Ogr_Delta   2 CPhCga 7  
                                       CP+C+a
  gi|336255063|ref|YP_004598170.1| 667 CPLCKA 672
                                       ****98 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.54
                         Ogr_Delta   1 rCPhCgap 8  
                                       +CP Cg++
  gi|336255063|ref|YP_004598170.1| 683 ECPDCGEE 690
                                       6****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (826 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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):              11  [number of targets reported over threshold]
# CPU time: 0.70u 0.25s 00:00:00.95 Elapsed: 00:00:00.42
# Mc/sec: 5937.72
//
Query:       gi|336255064|ref|YP_004598171.1|  [L=38]
Description: hypothetical protein Halxa_3684 [Halopiger xanaduensis SH-6]
Scores for 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:                       154  (0.00858944); expected 358.6 (0.02)
Passed bias filter:                      112  (0.00624686); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 305.98
//
Query:       gi|336255065|ref|YP_004598172.1|  [L=1274]
Description: hypothetical protein Halxa_3685 [Halopiger xanaduensis SH-6]
Scores for 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-90  301.5   0.0    8.2e-90  300.9   0.0    1.2  1  Glyco_hydro_97  Glycoside hydrolase 97
    9.1e-62  208.6   0.0    2.1e-61  207.4   0.0    1.6  2  GH97_N          Glycosyl-hydrolase 97 N-terminal
    3.1e-56  190.4   0.0    8.2e-56  189.0   0.0    1.7  1  Glucodextran_C  C-terminal binding-module, SLH-like, of gluco
    5.9e-30  103.4   0.0    1.5e-29  102.0   0.0    1.8  1  GH97_C          Glycosyl-hydrolase 97 C-terminal, oligomerisa
  ------ inclusion threshold ------
      0.022   15.0   0.0      0.079   13.2   0.0    1.8  1  CBM_35          Carbohydrate binding module (family 35)


Domain annotation for each model (and alignments):
>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.9   0.0   2.3e-93   8.2e-90       1     270 [.     345     645 ..     345     654 .. 0.97

  Alignments for each domain:
  == domain 1  score: 300.9 bits;  conditional E-value: 2.3e-93
                    Glyco_hydro_97   1 DtsWikpgkyvwdWwemiagke..............tlkedfkhgantetvkryiDfAaengleyvlvegwdegWee 63 
                                       Dt Wi+p kyv++Ww+miag++              +  +++ hga+te++kry+ fAaeng+++vlvegw++gW++
  gi|336255065|ref|YP_004598172.1| 345 DTGWIEPRKYVGIWWTMIAGSAnweyksddeisvegNDPASYVHGARTERMKRYMSFAAENGIDSVLVEGWNQGWDT 421
                                       899*****************99*************99999************************************* PP

                    Glyco_hydro_97  64 ..kkkkekefdftkpypdfdleelvaYakekgvgvelwlhsetsgnvanlekq.l.dkafklyeklGvkgvKvdfvg 136
                                         ++ ++ +f + ++ypdfd++e+++++++ + +ve+++h+et+g++ ++e+q l d++f++ye++G++++K ++v+
  gi|336255065|ref|YP_004598172.1| 422 ypGDGTGLRFGVDDSYPDFDVREVTDFGRSLESDVEMTIHNETAGALPHYEEQiLeDDIFQQYEDVGIRSIKNGYVS 498
                                       9988999**********************************************7699******************** PP

                    Glyco_hydro_97 137 r................ddqemvnhyekvlekAakyklmvdfHgavkptGleRtYPnlitrEgvrgqEynaws.esk 196
                                       +                ++q +vnh++ v+e+Aa  + ++++H+ +kptG  RtYPn+++rE v++qEy+ ++  s+
  gi|336255065|ref|YP_004598172.1| 499 DaglgiegdgsdpthnqHNQLAVNHHRLVIEAAAADRQLLEIHEGIKPTGEIRTYPNVANREVVKAQEYDGFGqLSS 575
                                       *********************************************************************98885789 PP

                    Glyco_hydro_97 197 dnepehtvtlpFtRmlaGpmDytpgifdnatkkfkedkeesrvqtTrakqLAlyvvlesplqmladlpenyeke 270
                                       +++p+h+vtlpFtR+laGp+ ++pgifd+++     d+++ ++qtTr+kqLA+y ++ s+lqm+ad++e+y +e
  gi|336255065|ref|YP_004598172.1| 576 NVDPDHHVTLPFTRNLAGPVSFQPGIFDITFT----DDRGGQIQTTRTKQLAMYPTYLSGLQMAADRIEAYVDE 645
                                       99*****************************9....889********************************776 PP

>> GH97_N  Glycosyl-hydrolase 97 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.4   0.0   5.9e-65   2.1e-61       1     230 [.      54     329 ..      54     330 .. 0.92
   2 ?   -4.1   0.3       2.6   9.2e+03      94     108 ..    1092    1106 ..    1084    1110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 207.4 bits;  conditional E-value: 5.9e-65
                                       EE-TTSSEEEEE.T.SCS.EEEEEEETTEEEEEEEEEEEEET.........CCECC.S-EEEEEEEEEEEEEEEEST CS
                            GH97_N   1 lsSPdgklkvtvslsekgelsYsvsykgkeviepsrLglelk.........dgdfs.nlkvkkvkrssvdetwkpvw 67 
                                       + SPdg++ vt ++ ++g+++Y v  +g++ +eps+Lg++++         dg+   nl+v++++r+s +e+w+pvw
  gi|336255065|ref|YP_004598172.1|  54 VRSPDGSIAVTADV-SSGTPTYAVAIDGTTYLEPSPLGFDFRnqpsfgaagDGSSGpNLTVTGSERRSETEEWEPVW 129
                                       68**********64.5889*********************99666665544334455******************** PP

                                       TTSSEEEEEEEEEEEEEETTT.....EEEEEEEETTEEEEEEEE.S...BT...EEEEEEEEEEE-STTEEEEE-BH CS
                            GH97_N  68 gerseirnhyneltltlkkekk....lnlefrvyddGvAfRYefpe...lt...fvikeElteFafpgdttawlipg 134
                                       g ++e++  yn l++ l+++++     nle+rv+ddG++fR +f e   ++    v ++E+t+Faf++d+taw+i +
  gi|336255065|ref|YP_004598172.1| 130 GAYDEVTADYNALVVGLEETEGpgrtANLELRVFDDGLGFRVVFDEsfaSNagkAVLESENTAFAFADDYTAWWIRN 206
                                       *****************999889***********************87622688999******************** PP

                                       HHHS-SS----EEEECCGS.SSTTS...........B-SSEEEEEECT.EEEEEEEE-STTS--EEEESS....... CS
                            GH97_N 135 ekdydsyeeeytesklseirekkek...........vqtPllvktddg.lyvlihEAaledYpgmkLkld....... 192
                                       e +++++e+ey+e++lsei++ +++           ++tPl+v+++dg  y+++hEA ledY++ +L+ +       
  gi|336255065|ref|YP_004598172.1| 207 EVTNPRFEQEYEETPLSEIPGGRREtrptgtpmqtgAHTPLTVEAGDGdAYLSVHEAGLEDYAAATLAPRvdegdte 283
                                       *******************987766*******************77666******************9999999999 PP

                                       ........SSSBTCTEEEEE---EEEEEEESSCHHHHH--HHHHTS CS
                            GH97_N 193 ........aegakgklqaafatPWRviivgddlkdlvestlvlnLn 230
                                                +g+k +l+++ atPWR+i++g++++dl+es+lv  L+
  gi|336255065|ref|YP_004598172.1| 284 ftteltplPDGTKVSLEVPNATPWRTIQIGRRPGDLIESQLVPLLS 329
                                       999999998998999999999********************98775 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 2.6
                                        EEEETTEEEEEEEE. CS
                            GH97_N   94 frvyddGvAfRYefp 108 
                                        f vy+ + A+R++f 
  gi|336255065|ref|YP_004598172.1| 1092 FAVYEADDAYRFVFE 1106
                                        88999*******975 PP

>> Glucodextran_C  C-terminal binding-module, SLH-like, of glucodextranase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.0   0.0   2.3e-59   8.2e-56       1     226 [.    1058    1269 ..    1058    1271 .. 0.94

  Alignments for each domain:
  == domain 1  score: 189.0 bits;  conditional E-value: 2.3e-59
                    Glucodextran_C    1 ifelkDPvgDDkGpGeytYPtdevfkpgvfDlvkfkvlekgdkvvfevkfaelgenpwngpngFslqlvqiYidd 75  
                                        ++e++DP+gDD+GpGeytYPt+++f++g+fDl++f+v+e++d+++f ++++el +++++g  +Fs +++ +Y++d
  gi|336255065|ref|YP_004598172.1| 1058 VAEFDDPQGDDHGPGEYTYPTSDDFRDGAFDLRSFAVYEADDAYRFVFEVEEL-YDTFGG--EFSPHYFVVYLRD 1129
                                        689**************************************************.******..9************ PP

                    Glucodextran_C   76 tkeggstrtdtpGlnvtlaeespWdkavlisgwesagklvvqeeaketedsvkveadqvkntivvevpkslLdge 150 
                                         +++g ++t+  +l+vt++  +pW++ v +sg+   g++vv++++++     + ++d  + t +++vpk+ L + 
  gi|336255065|ref|YP_004598172.1| 1130 PDRDGGRTTELGDLEVTAEFGDPWHYRVAASGF---GSSVVDADGSNLGA-PETTVDFESGTAILSVPKDAL-EL 1199
                                        *********************************...89*****9999864.3333334499***********.99 PP

                    Glucodextran_C  151 niakwgyvvlvgsqdgygpdkiRkvseeagewrfgggsaidagvaPkviDllapegetQeevLssydvsakklAt 225 
                                        ++a+++++ +vgs+d+    ++R+v++ea++++fgg+++++a++aP+viDll+p+g +Q+e+L++   +a++lAt
  gi|336255065|ref|YP_004598172.1| 1200 DVANAEVLPVVGSEDRG---TFRNVAVEAAAYTFGGAKEGAAENAPRVIDLLTPSGVDQSEALAY---DANELAT 1268
                                        ***************99...9*******************************************9...7777887 PP

                    Glucodextran_C  226 l 226 
                                        l
  gi|336255065|ref|YP_004598172.1| 1269 L 1269
                                        5 PP

>> GH97_C  Glycosyl-hydrolase 97 C-terminal, oligomerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.0   4.2e-33   1.5e-29       2      96 ..     833     943 ..     832     944 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 4.2e-33
                            GH97_C   2 wdetkvlegeigeyvvvARrkgnkWyvgaltnekareleldlsflekgk.............kytaeiyaDgknad. 64 
                                       wdet+++++eig+y+v+ARrkg++Wyvga+t+e  r+++++lsfl++g+             ky aeiy+Dg+ ad 
  gi|336255065|ref|YP_004598172.1| 833 WDETRIVDAEIGDYTVTARRKGEEWYVGAMTDEGGRAVDVPLSFLAPGNsagkgngngprgpKYVAEIYSDGIGADy 909
                                       **********************************************9999999999999999*************** PP

                            GH97_C  65 ..nptdykietkkvtskktlkvklapgGGfairl 96 
                                         +p+ ++i++++v++++tl  ++a++GG+a+rl
  gi|336255065|ref|YP_004598172.1| 910 esDPDPVRIDEAVVDPSTTLLASMARSGGTAVRL 943
                                       ********************************98 PP

>> CBM_35  Carbohydrate binding module (family 35)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.2e-05     0.079      35     106 ..     688     770 ..     683     776 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                            CBM_35  35 gdavslnVnvekaGeynlnvtfsapygsKentlvvnGtavatvafaesde...........vkqttvitvkLkAGan 100
                                       g+ vs+ V+ + aG+y+l ++++a        +v  G   at  +++s+            + +  +++v+L+ G+n
  gi|336255065|ref|YP_004598172.1| 688 GSSVSFTVKDADAGTYELHLRYAAAPEDNAQRVVDAGRTQATLRVNDSTRtitpaftdywdQWEVFTTEVELEDGDN 764
                                       899*********************99988888888898888888888874111111111112234566788888888 PP

                            CBM_35 101 tikidr 106
                                       +i+i+ 
  gi|336255065|ref|YP_004598172.1| 765 EIAIEL 770
                                       888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); 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:                         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 0.27s 00:00:01.00 Elapsed: 00:00:00.42
# Mc/sec: 9070.06
//
Query:       gi|336255066|ref|YP_004598173.1|  [L=506]
Description: polysaccharide biosynthesis protein [Halopiger xanaduensis SH-6]
Scores for 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-28   97.3  16.8    1.9e-27   96.2  16.8    1.5  1  Polysacc_synt_3  Polysaccharide biosynthesis protein
    2.3e-24   86.2  41.0    9.5e-24   84.2  25.0    2.0  2  Polysacc_synt    Polysaccharide biosynthesis protein
    1.4e-11   44.6  11.5    1.4e-11   44.6  11.5    4.4  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2  16.8   3.2e-31   1.9e-27       1     291 [.      39     342 ..      39     344 .. 0.89

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 3.2e-31
                   Polysacc_synt_3   1 vLARLLspedFGvvaialvvislanlfvdmGlssal....iqkedltee.....dlstvftfnlvlgllialvlfll 68 
                                       +++R++sp+ +G+  + + vi +a++f ++Gl  a+     q  d+ e+      + +v  + lv++ l+a++l++ 
  gi|336255066|ref|YP_004598173.1|  39 LMTRFVSPSVYGLWVLSTSVILFAQVFGNLGLPLAIdyfvPQYLDDGERgkakgVILQVTATVLVTSSLVAFALAAG 115
                                       699****************************98776443145556655566566778899999************** PP

                   Polysacc_synt_3  69 apliasfynqpelvtvlrvlalvlilsglssvq.eallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvi 144
                                       ++++ +f+++p +   l +l++++ + ++++v  +++++++  + ++++++lv  +v ++v+  l l g+g+  L+ 
  gi|336255066|ref|YP_004598173.1| 116 SRVVGDFFQEPAMRIALLLLSVTIPMLAIYNVLlTSYYSIKKLQYRVVMRDLVRPTVRFAVTAGLLLSGFGLLGLIG 192
                                       ************************99999887525566666666677789*************************** PP

                   Polysacc_synt_3 145 gtllssllslvllwlaskwr....prlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsva 217
                                       g ++  ++ +++ +    ++    + ++ +l ++k+l+ +++ l +++++ +l+ ++d++++G++l+s ++G+Y v+
  gi|336255066|ref|YP_004598173.1| 193 GYVVGLFVAIAVGTALFVYKawdlLTTTTELVAAKPLVTYSVPLAMTSVVFVLMGQVDYFVVGYFLNSDDVGIYRVG 269
                                       *******9998877776666666889999************************************************ PP

                   Polysacc_synt_3 218 krlaslpvaeitsviakVlfPalSrlqddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWlea 291
                                       + l s ++ +i +++++V+ P +++ +++ + +++ ++ + r i  i+lPia++l + a+  + vl++ q+  a
  gi|336255066|ref|YP_004598173.1| 270 YMLGSGLM-IIFNSLSPVFKPLIAETRENVDLVEQRFRIMARWIVGITLPIAIVLSLGADSYLAVLYTPQYAAA 342
                                       *9988877.566679*******************************************************9876 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2  25.0   1.6e-27   9.5e-24       2     272 ..      16     293 ..      15     295 .. 0.83
   2 !    8.3   8.2   0.00022       1.3      80     235 ..     312     466 ..     291     480 .. 0.76

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 1.6e-27
                     Polysacc_synt   2 lkgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek.......k 71 
                                       +k  ++++++++i+  ++f ++ +++r+++p  +Gl  l ++++ +++++ +lGl++a+  ++ +y ++        
  gi|336255066|ref|YP_004598173.1|  16 AKQGSITFVGNVINGAFGFAIVMLMTRFVSPSVYGLWVLSTSVILFAQVFGNLGLPLAIDYFVPQYLDDgergkakG 92 
                                       6778899**************************************************************99544444 PP

                     Polysacc_synt  72 elvslillnvllvllvlvllfllllliaaflglpelavlylilalmll.llvgvasfrrglfqglermkyaavsqvv 147
                                        + +++   +++++lv+++l++ + ++ +f+++p+ ++ +l+l+++++ l+++++++ + +   +   + ++ + v 
  gi|336255066|ref|YP_004598173.1|  93 VILQVTATVLVTSSLVAFALAAGSRVVGDFFQEPAMRIALLLLSVTIPmLAIYNVLLTSYYSIKKLQYRVVMRDLVR 169
                                       44444444444445555555555555555*******************88888888877777777777777777777 PP

                     Polysacc_synt 148 eqlsrvilvliavflfldivaavlgavlaalvggivslav.lrkkfrprfvilslklvrellsfsapltisslaill 223
                                         ++++++ ++++ +f+ ++++++g+v++ +v++ v+ a+ ++k++   +++ +l   + l+++s+pl ++s++  l
  gi|336255066|ref|YP_004598173.1| 170 PTVRFAVTAGLLLSGFG-LLGLIGGYVVGLFVAIAVGTALfVYKAWDLLTTTTELVAAKPLVTYSVPLAMTSVVFVL 245
                                       77777777777777888.***********9999888876516666766666666*********************** PP

                     Polysacc_synt 224 ytyidsillglllgaeavGiYnaayqllvaisgllapivtaalfPvfse 272
                                         ++d+++ g++l++++vGiY+++y+l + + +++++    +  P+++e
  gi|336255066|ref|YP_004598173.1| 246 MGQVDYFVVGYFLNSDDVGIYRVGYMLGSGLMIIFNSLSP-VFKPLIAE 293
                                       ***************************9999888888877.88888877 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00022
                     Polysacc_synt  80 nvllvllvlvllfllllliaaflglpelavlylilalmll...llvgvasfrrglfqglermkyaavsqvveqlsrv 153
                                        v ++l ++++l l ++   a+l+ p++a   l+ +l      + v++    ++l+qg+   + ++ +++v + + +
  gi|336255066|ref|YP_004598173.1| 312 IVGITLPIAIVLSLGADSYLAVLYTPQYAAASLVVILLCGaflFNVTFGGPDGSLLQGMGYSRFVFANTLVLFGANF 388
                                       455666677777777776666666666655444444444401155555555789********999999998666666 PP

                     Polysacc_synt 154 ilvliavflfldivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyidsi 230
                                         ++++v l++ i +a++g + a ++ g +sla ++  +    + + ++++ + +  ++p t+  + i ++  +d +
  gi|336255066|ref|YP_004598173.1| 389 LVSAALVPLVG-IEGAAIGSATALVLVGCLSLAEIY--YLDGIHPF-TRDFAKVVAAGVPATVAGAPIVVFLESDAL 461
                                       66666666666.************************..98888888.99**************************** PP

                     Polysacc_synt 231 llgll 235
                                       + gll
  gi|336255066|ref|YP_004598173.1| 462 IVGLL 466
                                       *9987 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 ?   -2.5   4.1      0.81   4.8e+03      57      92 ..      25      59 ..      13     114 .. 0.55
   2 !    6.9   7.7     0.001       6.2      70     136 ..     147     211 ..     135     218 .. 0.79
   3 !   44.6  11.5   2.4e-15   1.4e-11       3     141 ..     347     481 ..     344     483 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.81
                   Polysacc_synt_C 57 Gaaiatvlallvvavlnlyalrrllgiklellrrll 92
                                      G +i  ++++++v+++  +     +g+ + l ++++
  gi|336255066|ref|YP_004598173.1| 25 GNVINGAFGFAIVMLMTRFVSPSVYGLWV-LSTSVI 59
                                      44444445555555555555555555544.222222 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.001
                   Polysacc_synt_C  70 avlnlyalrrllgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYll 136
                                        +l  y+  ++l++++ + r+l++p +  +v +++++     llgl+ +  + l++a++vg +++++
  gi|336255066|ref|YP_004598173.1| 147 VLLTSYYSIKKLQYRV-VMRDLVRPTVRFAVTAGLLL-SGFGLLGLIGGYVVGLFVAIAVGTALFVY 211
                                       45558999999*****.79****************55.55666666666656999999999999987 PP

  == domain 3  score: 44.6 bits;  conditional E-value: 2.4e-15
                   Polysacc_synt_C   3 ailalsiiflsls.tvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalr 78 
                                        +l+ +++f + +  + +s+Lqg+g+ ++++ ++++ + ++++++  l+pl gi Gaai+++ al++v +l l  ++
  gi|336255066|ref|YP_004598173.1| 347 ILLCGAFLFNVTFgGPDGSLLQGMGYSRFVFANTLVLFGANFLVSAALVPLVGIEGAAIGSATALVLVGCLSLAEIY 423
                                       456667777777789************************************************************** PP

                   Polysacc_synt_C  79 rllgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllll 141
                                        l gi++ + r++ k+++a++   ++    + +++ l ++a l+++l  ++ +  Yl+ l+++
  gi|336255066|ref|YP_004598173.1| 424 YLDGIHP-FTRDFAKVVAAGVPATVA---GAPIVVFLESDA-LIVGLLPVAVIGTYLGTLIAT 481
                                       *******.89***9988888888888...555555555544.444444448889999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.21s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 3956.38
//
Query:       gi|336255067|ref|YP_004598174.1|  [L=131]
Description: hypothetical protein Halxa_3687 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00021   21.5   0.0    0.00039   20.6   0.0    1.5  1  DUF3426   Protein of unknown function (DUF3426)
  ------ inclusion threshold ------
      0.066   13.2   0.0       0.08   12.9   0.0    1.1  1  DUF2393   Protein of unknown function (DUF2393)


Domain annotation for each model (and alignments):
>> DUF3426  Protein of unknown function (DUF3426)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   4.4e-08   0.00039      37     102 ..      22      90 ..       4     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.4e-08
                           DUF3426  37 aplgcelppprdielisiessslr.ekagean..lvlegtlrNradkpqalpaleltLtDaqgqvvarr 102
                                       + ++ + +  +d  ++ +  s+l   ++g  +  + + g++rN  d++  +++l++t++Da g+ + + 
  gi|336255067|ref|YP_004598174.1|  22 EFVENDGEEITDPGDVEVVWSDLVrDDPGTEDerVTVWGIVRNVGDRTLSYVELRATFFDAEGEELESV 90 
                                       55556667778889999999*99988899888*******************************988764 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     9e-06      0.08      61      96 ..      54      88 ..      50     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9e-06
                           DUF2393 61 eafvvdgtitNeGkftikeCkleiklvnkshnkksk 96
                                      e + v g ++N G++t+ ++ l++++++++ ++  +
  gi|336255067|ref|YP_004598174.1| 54 ERVTVWGIVRNVGDRTLSYVELRATFFDAEGEE-LE 88
                                      678899**********************99988.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1061.26
//
Query:       gi|336255068|ref|YP_004598175.1|  [L=261]
Description: hypothetical protein Halxa_3688 [Halopiger xanaduensis SH-6]
Scores for complete 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-39  133.8   0.2    2.9e-39  133.0   0.2    1.4  1  DUF2103   Predicted metal-binding protein (DUF2103)


Domain annotation for each model (and alignments):
>> DUF2103  Predicted metal-binding protein (DUF2103)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.0   0.2   1.6e-43   2.9e-39       2      97 ..     157     252 ..     156     253 .. 0.98

  Alignments for each domain:
  == domain 1  score: 133.0 bits;  conditional E-value: 1.6e-43
                           DUF2103   2 pkeklggsHstiiggreGkkllekiakhpevkkviPgvikakgsssggglrvkvtraderGnlrlllrdgssvQevf 78 
                                       p ek+ggsHst+iggr+G+++++ +a hp+vkkviPg+i+a+g+ s++glr+kvtrad+ Gn+r+llrdgssvQe++
  gi|336255068|ref|YP_004598175.1| 157 PIEKIGGSHSTLIGGRTGMEAIRAVAGHPHVKKVIPGPIDAGGKGSQSGLRAKVTRADDGGNVRMLLRDGSSVQENR 233
                                       669************************************************************************** PP

                           DUF2103  79 ivttakdreegeriaeeLn 97 
                                       +vtta+dre geri+e+Ln
  gi|336255068|ref|YP_004598175.1| 234 VVTTARDREMGERIREDLN 252
                                       ******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 2092.49
//
Query:       gi|336255069|ref|YP_004598176.1|  [L=66]
Description: hypothetical protein Halxa_3689 [Halopiger xanaduensis SH-6]
Scores for 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:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      155  (0.00864521); 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: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 563.29
//
Query:       gi|336255070|ref|YP_004598177.1|  [L=86]
Description: ribosomal L37ae protein [Halopiger xanaduensis SH-6]
Scores for 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   79.0   0.1    2.5e-22   78.8   0.1    1.1  1  Ribosomal_L37ae  Ribosomal L37ae protein family


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 !   78.8   0.1   1.4e-26   2.5e-22       4      83 ..       6      81 ..       3      83 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 1.4e-26
                                      XXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH-XXX CS
                   Ribosomal_L37ae  4 kvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsaktvksairr 82
                                       vg+aG++g+rYG+ +r+rv +ie ++++    ++++ ++v R ++giwk +++g++++GgAy pet++++tv+++ir 
  gi|336255070|ref|YP_004598177.1|  6 SVGSAGRFGARYGRVARRRVSEIEDDMEN----AQVDGDDVTRIGTGIWKNEETGEVFTGGAYRPETPAGRTVTRSIRA 80
                                      79*************************99....589*****************************************97 PP

                                      X CS
                   Ribosomal_L37ae 83 l 83
                                      +
  gi|336255070|ref|YP_004598177.1| 81 A 81
                                      5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 713.11
//
Query:       gi|336255071|ref|YP_004598178.1|  [L=44]
Description: DNA-directed RNA polymerase subunit P [Halopiger xanaduensis SH-6]
Scores for complete 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-10   40.2   6.8    2.3e-10   39.9   6.8    1.1  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
    5.9e-05   22.3   0.2     0.0044   16.4   0.0    2.1  2  zf-ribbon_3      zinc-ribbon domain
    0.00072   19.6   0.5    0.00074   19.5   0.5    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
    0.00094   18.7   1.7       0.21   11.2   0.4    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
     0.0036   17.3   4.6      0.077   13.0   0.1    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0037   17.3   0.5     0.0065   16.5   0.5    1.4  1  zf-CHCC          Zinc-finger domain
     0.0057   16.3   2.2       0.17   11.6   0.3    2.1  2  zinc_ribbon_2    zinc-ribbon domain
     0.0067   16.4   1.1      0.014   15.4   1.1    1.6  1  DZR              Double zinc ribbon
     0.0078   15.9   1.0        0.7    9.7   2.3    2.1  2  A2L_zn_ribbon    A2L zinc ribbon domain
  ------ inclusion threshold ------
      0.012   15.3   0.2       0.33   10.7   0.0    2.0  2  YacG             DNA gyrase inhibitor YacG
      0.014   15.4   0.3      0.015   15.3   0.3    1.1  1  RNHCP            RNHCP domain
      0.017   14.7   2.2       0.84    9.2   0.3    2.2  2  Sgf11            Sgf11 (transcriptional regulation protein)
      0.023   14.6   0.2      0.092   12.7   0.0    2.0  2  Cys_rich_CPXG    Cysteine-rich CPXCG
       0.03   14.7   0.7      0.081   13.3   0.0    1.8  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.036   14.0   0.8      0.056   13.4   0.8    1.3  1  zinc-ribbons_6   zinc-ribbons
      0.043   13.8   0.1      0.049   13.6   0.1    1.2  1  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
      0.051   13.5   0.5          3    7.8   0.1    2.1  2  DUF951           Bacterial protein of unknown function (DUF95
      0.059   13.7   0.1       0.48   10.8   0.0    2.0  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
       0.06   13.5   0.7       0.15   12.2   0.1    1.8  2  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
      0.092   13.1   1.1       0.39   11.1   0.1    1.9  2  DUF3268          zinc-finger-containing domain
       0.12   12.4   3.3       0.19   11.7   2.9    1.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.12   11.9   3.4       0.81    9.3   3.9    1.8  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.17   12.0   1.2       0.43   10.6   0.2    1.8  2  CpXC             CpXC protein
       0.22   11.7   4.2       0.52   10.5   4.2    1.7  1  Zn-ribbon_8      Zinc ribbon domain
        0.4   10.6   5.7         17    5.4   5.7    2.2  1  zinc_ribbon_4    zinc-ribbon domain
       0.58   10.3   1.8       0.68   10.1   0.0    1.8  2  Thioredoxin_4    Thioredoxin


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 !   39.9   6.8   3.4e-13   2.3e-10       1      32 []       3      34 ..       3      34 .. 0.99

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 3.4e-13
                                      -B-SSS--B----SSS----SSS-----B--- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevslkkgdpiRCkeCGhRilYKkR 32
                                      Y+C +C+ +v+l++   +RC +CGhR+l K+R
  gi|336255071|ref|YP_004598178.1|  3 YKCSRCKRDVQLDEYGGVRCPYCGHRVLLKER 34
                                      9******************************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 ?    4.8   0.0     0.029        20       3      10 ..       3      10 ..       1      16 [. 0.78
   2 !   16.4   0.0   6.4e-06    0.0044       3      14 ..      20      33 ..      18      36 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.029
                       zf-ribbon_3  3 vrCPnCGa 10
                                      ++C++C+ 
  gi|336255071|ref|YP_004598178.1|  3 YKCSRCKR 10
                                      68****85 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6.4e-06
                       zf-ribbon_3  3 vrCPnCGa.p.lss 14
                                      vrCP+CG+ + l++
  gi|336255071|ref|YP_004598178.1| 20 VRCPYCGHrVlLKE 33
                                      89******986665 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 !   19.5   0.5   1.1e-06   0.00074      70      98 ..       2      31 ..       1      44 [] 0.76

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
                                      EEEETTTS-EEECHHH.HHS-TTTSSS-EE CS
                              HypA 70 kvrCreCgkefeleek.alrCpkCgsadve 98
                                      +++C++C+++++l+e+  +rCp Cg++ + 
  gi|336255071|ref|YP_004598178.1|  2 SYKCSRCKRDVQLDEYgGVRCPYCGHRVLL 31
                                      689*********9997789******97543 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   0.4   0.00031      0.21       2      16 ..       2      16 ..       1      18 [. 0.86
   2 !    7.4   0.0    0.0046       3.2       3      17 ..      20      34 ..      18      35 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                            zf_UBZ  2 tylCerCgkeipese 16
                                      +y C+rC++ ++ +e
  gi|336255071|ref|YP_004598178.1|  2 SYKCSRCKRDVQLDE 16
                                      69******9998877 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0046
                            zf_UBZ  3 ylCerCgkeipesel 17
                                      + C+ Cg++++  e+
  gi|336255071|ref|YP_004598178.1| 20 VRCPYCGHRVLLKER 34
                                      67*******998775 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 ?    6.3   0.9     0.014       9.5      38      45 ..       3      10 ..       1      11 [. 0.87
   2 !   13.0   0.1   0.00011     0.077      18      31 ..      19      32 ..      17      39 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                     Zn_Tnp_IS1595 38 fqCkeCrk 45
                                      ++C++C++
  gi|336255071|ref|YP_004598178.1|  3 YKCSRCKR 10
                                      9*****97 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00011
                     Zn_Tnp_IS1595 18 gfvCPhCgsrkayr 31
                                      g++CP+Cg+r + +
  gi|336255071|ref|YP_004598178.1| 19 GVRCPYCGHRVLLK 32
                                      789*****996654 PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.5   9.4e-06    0.0065      21      36 ..      13      28 ..      12      28 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.4e-06
                                      E--TTSEEEETTTTEE CS
                           zf-CHCC 21 eldkkgpvdCgYCglr 36
                                      +ld+ g v+C+YCg r
  gi|336255071|ref|YP_004598178.1| 13 QLDEYGGVRCPYCGHR 28
                                      799***********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 ?    4.7   0.1     0.037        26       1      10 [.       4      13 ..       4      17 .. 0.79
   2 !   11.6   0.3   0.00025      0.17      16      22 ..      22      28 ..      20      29 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.037
                     zinc_ribbon_2  1 fCpnCGaelq 10
                                      +C++C + +q
  gi|336255071|ref|YP_004598178.1|  4 KCSRCKRDVQ 13
                                      7999988877 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00025
                     zinc_ribbon_2 16 CpyCGtp 22
                                      CpyCG+ 
  gi|336255071|ref|YP_004598178.1| 22 CPYCGHR 28
                                      9999996 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.1   2.1e-05     0.014      15      38 ..       5      29 ..       1      36 [. 0.56

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-05
                               DZR 15 CseCgtklkavaa..edrCpsCgekv 38
                                      Cs+C+ +++   +    rCp Cg+ v
  gi|336255071|ref|YP_004598178.1|  5 CSRCKRDVQLD-EygGVRCPYCGHRV 29
                                      66666665522.23566666666665 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 !    9.7   2.3     0.001       0.7       4      28 ..       3      26 ..       2      26 .. 0.96
   2 !    8.9   0.0    0.0017       1.2       6      20 ..      22      35 ..      19      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.001
                     A2L_zn_ribbon  4 kvCsvCggngilnseqgylvCieCg 28
                                      ++Cs C++++ l  e g+  C+ Cg
  gi|336255071|ref|YP_004598178.1|  3 YKCSRCKRDVQL-DEYGGVRCPYCG 26
                                      89**********.***********8 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0017
                     A2L_zn_ribbon  6 CsvCggngilnseqg 20
                                      C +Cg+ ++l +e++
  gi|336255071|ref|YP_004598178.1| 22 CPYCGHRVLL-KERS 35
                                      99********.9987 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.11        76       2      13 ..       4      15 ..       3      18 .. 0.80
   2 ?   10.7   0.0   0.00048      0.33       1      16 [.      20      35 ..      20      38 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.11
                              YacG  2 kCPtCkkevews 13
                                      kC  Ck++v+ +
  gi|336255071|ref|YP_004598178.1|  4 KCSRCKRDVQLD 15
                                      799999999876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00048
                              YacG  1 vkCPtCkkevewseen 16
                                      v+CP C+++v  +e++
  gi|336255071|ref|YP_004598178.1| 20 VRCPYCGHRVLLKERS 35
                                      89********999876 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   2.2e-05     0.015       3      40 ..       2      36 ..       1      41 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                             RNHCP  3 sftCeeCgkeveklaagsakrnHCpsCLlskHvdeepg 40
                                      s++C++C+++v+ +++g      Cp+C +   ++e+  
  gi|336255071|ref|YP_004598178.1|  2 SYKCSRCKRDVQLDEYGG---VRCPYCGHRVLLKERSR 36
                                      689**************9...67****87766666555 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3    0.0012      0.84       5      15 ..       3      13 ..       1      14 [. 0.88
   2 ?    5.3   0.1      0.02        14       5      13 ..      20      28 ..      18      30 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                                      EE-TTTSSEEE CS
                             Sgf11  5 vtCpnCgRqia 15
                                      ++C  C+R+++
  gi|336255071|ref|YP_004598178.1|  3 YKCSRCKRDVQ 13
                                      79*******97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.02
                                      EE-TTTSSE CS
                             Sgf11  5 vtCpnCgRq 13
                                      v+Cp+Cg  
  gi|336255071|ref|YP_004598178.1| 20 VRCPYCGHR 28
                                      79****965 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1         1   7.1e+02       3      10 ..       5      12 ..       3      18 .. 0.53
   2 ?   12.7   0.0   0.00013     0.092       1      10 [.      20      29 ..      20      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1
                     Cys_rich_CPXG  3 CPyCgeei 10
                                      C  C   +
  gi|336255071|ref|YP_004598178.1|  5 CSRCKRDV 12
                                      55554443 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00013
                     Cys_rich_CPXG  1 iqCPyCgeei 10
                                      + CPyCg+++
  gi|336255071|ref|YP_004598178.1| 20 VRCPYCGHRV 29
                                      68******86 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 ?    0.4   0.1       1.3   8.8e+02       4      17 ..       3      16 ..       2      21 .. 0.62
   2 ?   13.3   0.0   0.00012     0.081       5      24 ..      21      40 ..      18      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.3
                   Lar_restr_allev  4 kpCPfCggravler 17
                                      + C  C+ +  l +
  gi|336255071|ref|YP_004598178.1|  3 YKCSRCKRDVQLDE 16
                                      56777776666555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00012
                   Lar_restr_allev  5 pCPfCggravlersqrvvae 24
                                       CP Cg+r  l+++ r v+e
  gi|336255071|ref|YP_004598178.1| 21 RCPYCGHRVLLKERSRDVKE 40
                                      5************9998876 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.8   8.1e-05     0.056      17      39 ..       3      29 ..       1      35 [. 0.60

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.1e-05
                                      EE-TTT--EEEEEEE....-SSS-S-- CS
                    zinc-ribbons_6 17 yhCeaCqedlkkeal....CpeCeqel 39
                                      y+C+ C++d++   +    Cp C++++
  gi|336255071|ref|YP_004598178.1|  3 YKCSRCKRDVQLDEYggvrCPYCGHRV 29
                                      677777776666543333377776654 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 ?   13.6   0.1   7.1e-05     0.049      12      45 ..       4      33 ..       1      40 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.1e-05
                                      E-TTTTTTSEETTE......E-TTTTTSSEEE-H CS
                         Anti-TRAP 12 kCdaCngsGkiepeeprasleCPkCsGkglipTa 45
                                      kC  C++  + +     +++ CP C G+ +++ +
  gi|336255071|ref|YP_004598178.1|  4 KCSRCKRDVQLDE---YGGVRCPYC-GHRVLLKE 33
                                      6888887666655...5********.78888766 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 ?    4.6   0.1     0.044        31      32      43 ..       4      15 ..       1      17 [. 0.85
   2 ?    7.8   0.1    0.0043         3      31      44 ..      20      33 ..      18      41 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.044
                            DUF951 32 kClgcgrevmlp 43
                                      kC++c+r v l+
  gi|336255071|ref|YP_004598178.1|  4 KCSRCKRDVQLD 15
                                      9******99875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0043
                            DUF951 31 lkClgcgrevmlpR 44
                                      ++C  cg+ v+l+ 
  gi|336255071|ref|YP_004598178.1| 20 VRCPYCGHRVLLKE 33
                                      69*********864 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 ?    1.5   0.0      0.55   3.8e+02       3      42 ..       3      13 ..       1      18 [. 0.53
   2 ?   10.8   0.0    0.0007      0.48       4      14 ..      21      31 ..      19      41 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.55
                           zf-Di19  3 ftCPyCgkeltvkeLveHvedeHrveskevvCPvCaekvt 42
                                      ++C  C+++                             v+
  gi|336255071|ref|YP_004598178.1|  3 YKCSRCKRD-----------------------------VQ 13
                                      455555554.............................43 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0007
                           zf-Di19  4 tCPyCgkeltv 14
                                       CPyCg+ +  
  gi|336255071|ref|YP_004598178.1| 21 RCPYCGHRVLL 31
                                      7*****97554 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 ?    0.0   0.4       1.4   9.7e+02       1       6 [.       4       9 ..       4      11 .. 0.66
   2 ?   12.2   0.1   0.00022      0.15      27      57 ..      11      41 ..       6      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.4
                    zinc_ribbon_13 1 kCpKCg 6
                                     kC++C+
  gi|336255071|ref|YP_004598178.1| 4 KCSRCK 9
                                     577776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00022
                    zinc_ribbon_13 27 dvqnkkfitvsCknCgYtelYkaetsegkni 57
                                      dvq  ++  v C  Cg+  l k+++ + k++
  gi|336255071|ref|YP_004598178.1| 11 DVQLDEYGGVRCPYCGHRVLLKERSRDVKEV 41
                                      9*****************9999998887765 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.49   3.4e+02      29      42 ..       1      14 [.       1      20 [. 0.78
   2 ?   11.1   0.1   0.00056      0.39       3      18 ..      20      35 ..      18      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.49
                           DUF3268 29 llylCpkCdayvgv 42
                                      + y C +C   v++
  gi|336255071|ref|YP_004598178.1|  1 MSYKCSRCKRDVQL 14
                                      67999999988876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00056
                           DUF3268  3 trCpyCGekvilvsas 18
                                      +rCpyCG++v l++ s
  gi|336255071|ref|YP_004598178.1| 20 VRCPYCGHRVLLKERS 35
                                      69********998765 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 ?   11.7   2.9   0.00027      0.19      28      55 ..       2      28 ..       1      38 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                    OrfB_Zn_ribbon 28 SktCseCgsknkealsgrtfkCpnCgfe 55
                                      S +Cs+C + ++  ++   ++Cp Cg++
  gi|336255071|ref|YP_004598178.1|  2 SYKCSRCKRDVQL-DEYGGVRCPYCGHR 28
                                      7789999999999.99999999999986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.9    0.0012      0.81       1      27 [.       3      27 ..       3      29 .. 0.78
   2 ?    9.0   0.3    0.0014      0.98       2      11 ..      21      30 ..      20      38 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                                      EEETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGl 27
                                      ykC  C+ + + +D e g ++C+ CG 
  gi|336255071|ref|YP_004598178.1|  3 YKCSRCKRD-VQLD-EYGGVRCPYCGH 27
                                      89*****75.4455.457*******95 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                                      EETTTTCEEC CS
                      TF_Zn_Ribbon  2 kCPnCgstnl 11
                                      +CP+Cg++ l
  gi|336255071|ref|YP_004598178.1| 21 RCPYCGHRVL 30
                                      7*****9755 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.19   1.3e+02      37      50 ..       2      15 ..       1      17 [. 0.80
   2 ?   10.6   0.2   0.00063      0.43      28      50 ..      10      32 ..       6      40 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.19
                              CpXC 37 eatCpkCgatakle 50
                                      +++C +C ++++l+
  gi|336255071|ref|YP_004598178.1|  2 SYKCSRCKRDVQLD 15
                                      68999999988875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00063
                              CpXC 28 eklldgslfeatCpkCgatakle 50
                                       ++  +++  ++Cp+Cg+++ l+
  gi|336255071|ref|YP_004598178.1| 10 RDVQLDEYGGVRCPYCGHRVLLK 32
                                      56667778889*******99886 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.2   0.00076      0.52       6      36 ..       3      29 ..       2      37 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00076
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgsev 36
                                      Y+C +C+++   l   ++   + CP Cg++v
  gi|336255071|ref|YP_004598178.1|  3 YKCSRCKRDVQ-L---DEYGGVRCPYCGHRV 29
                                      *******8777.3...3444788*****955 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   5.7     0.025        17       4      33 ..       4      27 ..       1      29 [. 0.69

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.025
                     zinc_ribbon_4  4 tCpsCkakyeiddeklpakgvkvrCskCgh 33
                                       C +Ck   ++d+       + vrC+ Cgh
  gi|336255071|ref|YP_004598178.1|  4 KCSRCKRDVQLDE------YGGVRCPYCGH 27
                                      5666666666666......4679*****99 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4         1     7e+02      21      30 ..       1      10 [.       1      10 [. 0.86
   2 ?   10.1   0.0   0.00098      0.68      15      29 ..      12      26 ..       9      44 .] 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1
                                      E-TT-HHHHH CS
                     Thioredoxin_4 21 edlrCphCak 30
                                      ++++C+ C++
  gi|336255071|ref|YP_004598178.1|  1 MSYKCSRCKR 10
                                      589*****85 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00098
                                      EEEEEEE-TT-HHHH CS
                     Thioredoxin_4 15 vtvieyedlrCphCa 29
                                      v ++ey  +rCp+C 
  gi|336255071|ref|YP_004598178.1| 12 VQLDEYGGVRCPYCG 26
                                      7899**********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 328.73
//
Query:       gi|336255072|ref|YP_004598179.1|  [L=84]
Description: hypothetical protein Halxa_3692 [Halopiger xanaduensis SH-6]
Scores for 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-11   43.3   0.7    3.2e-11   43.2   0.7    1.0  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 !   43.2   0.7   1.8e-15   3.2e-11       2      72 ..       6      77 ..       5      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 1.8e-15
                                      EEEEEE-SSHHHHHHHHHHHHHHCHC-TTE.CEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHH CS
                              Pcc1  2 ltisvpfpterlAsialrtLqvDkelspla.vkrslslegnvLqveykAttnrmLRvavngfleslglvlet 72
                                      +t+++ +++++ A+++ ++++ +    +++ ++ +l+ +g ++q+ + A +  +LR+a+n+++++++++ +t
  gi|336255072|ref|YP_004598179.1|  6 ATLEFDYESAARARTVAESVAREIGEIDDDrSQTTLERDGATVQIAIDAADVVALRAALNTWFSLVDVAERT 77
                                      699********************77777777**************************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 703.73
//
Query:       gi|336255073|ref|YP_004598180.1|  [L=454]
Description: beta-lactamase [Halopiger xanaduensis SH-6]
Scores for 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-68  230.8   0.5    3.1e-68  230.4   0.5    1.1  1  Beta-lactamase  Beta-lactamase
    9.6e-08   32.0   0.0      2e-07   31.0   0.0    1.5  1  Pab87_oct       Pab87 octamerisation domain
  ------ inclusion threshold ------
        9.6    6.9  10.2        6.5    7.4   1.6    3.3  3  MDMPI_N         Mycothiol maleylpyruvate isomerase N-terminal


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.4   0.5   5.2e-72   3.1e-68       1     318 [.      16     339 ..      16     349 .. 0.91

  Alignments for each domain:
  == domain 1  score: 230.4 bits;  conditional E-value: 5.2e-72
                                       HHHHHHHHHHHTTESEEEEEEEETTEEEEEEEEEEEETTTTEEESTTSBEEEGGGHHHHHHHHHHHHHHTTSSCTTS CS
                    Beta-lactamase   1 ldrlvrelmaqggipGvavavvrdgkvvldkggGvadleggrpvtadtlfriaSvtKtftaaavlqlveeGkldLdd 77 
                                       +++lv+e m++ +ipG++v+v++++ + +++g+Gv+d+e+++p+t+dtl+++aS+tK++ta+avlqlve+G +dL d
  gi|336255073|ref|YP_004598180.1|  16 IEALVEEWMESESIPGASVVVADRDGIRYANGFGVRDVESEAPATPDTLYAVASLTKSVTAIAVLQLVERGDIDLED 92 
                                       578999*********************************************************************** PP

                                       BGGGTSTTCTTGGGTTEBHHHHHTTHSSCSSSS.TSTTCTSHHHTH..HHHHHHHHHSBSSSSTTSCEE-SHHHHHH CS
                    Beta-lactamase  78 pVskylPefagpgkgkiTlrdLltHtsGlpdlf.asdlleeaaada..aellralatlppkyapGtkwgYsntgygl 151
                                        + +y+  +  + + +iT+r+Ll H+sG+p +f a++ ++++ ++    e ++  a  ++++    +++Y n gy +
  gi|336255073|ref|YP_004598180.1|  93 ELREYVAVLNEAPGPPITVRELLAHSSGMPQDFvARRPAIDDGRNLdlFEHVDGAADRRLVD--DDRYMYYNGGYFV 167
                                       *******9999999****************88724555666666669999999999999997..99999******** PP

                                       HHHHHHHHHTSHHHHHHHHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHCTTTBEEEEHHHH CS
                    Beta-lactamase 152 lgellekvtgrsleqllreeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeaegagglistardl 228
                                       lgel+e+v+gr++e+++r+ei++pLgm+  ++ p++ +++ da + ++++++  ++p+  + +a++agglis ar l
  gi|336255073|ref|YP_004598180.1| 168 LGELVEAVDGRPYEEYVRTEIFEPLGMTRSTYDPDALARADDAMTGYTRADG-ELSPDAYDGGAGPAGGLISPAREL 243
                                       *********************************************9665555.555555556667************ PP

                                       HHHH.....HHHHHCCSSSSHHHHHHHHHHHTSEEEECTTEEEECECSSEEEEECCHTEEEEEEE..STEEEEEEEE CS
                    Beta-lactamase 229 arfl.....glalegglllsaetlaqltaklssgttrpagiraglglGwvladktgapgtfghtG..ggygtyvfvd 298
                                       a +l     ++  +g+++l++   +++  ++s +   ++g+ +g+g+Gw + d  + +++++h G  g  g+y++  
  gi|336255073|ref|YP_004598180.1| 244 ATVLrcvlnDGTVDGTRILEPDLVEAMCGRQSPSLPTVDGTYRGYGYGWEVRDFLD-ETLVSHLGgiGVSGAYMGCL 319
                                       ****999997778999999999999999************************9988.8******************* PP

                                       CGGTEEEEEEESBCSSHHHH CS
                    Beta-lactamase 299 peanlvvavltnrdppneda 318
                                       +e++++va+ +n+ +p   a
  gi|336255073|ref|YP_004598180.1| 320 REHDVAVALAFNTHGPSVTA 339
                                       *************9985544 PP

>> Pab87_oct  Pab87 octamerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   3.3e-11     2e-07       3      86 ..     356     437 ..     353     449 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3.3e-11
                         Pab87_oct   3 elpflalerkleeLeGeYesYrGiveasverk.ggtLalkvggkieeeeslpLvPedlegdyaeFytltangerlpv 78 
                                       ++++l ++++++  +G+YesYrG  +a+ve + +gt++++v    e +  ++  P+ +e+  + F + t +g r  +
  gi|336255073|ref|YP_004598180.1| 356 AVRALRVREAIDAVAGTYESYRGALTATVEPAaAGTIRIRVP---ERDVAFTASPDAVERSPYSFSAGTGSGVRWTA 429
                                       799**************************9652688888888...478999************************** PP

                         Pab87_oct  79 efeikgdd 86 
                                       ef   + +
  gi|336255073|ref|YP_004598180.1| 430 EFRDRETE 437
                                       **844433 PP

>> MDMPI_N  Mycothiol maleylpyruvate isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.45   2.7e+03      60      88 ..      39      66 ..       5     106 .. 0.67
   2 ?    3.3   0.5      0.02   1.2e+02      30     118 ..     110     235 ..      92     253 .. 0.59
   3 ?    7.4   1.6    0.0011       6.5      28     132 ..     291     411 ..     290     412 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.45
                           MDMPI_N 60 rdaaaalvtaadaeavdlaaslapealla 88
                                      rd+  + + +   ++v+ +a+++p+ l a
  gi|336255073|ref|YP_004598180.1| 39 RDGIRYANGFG-VRDVESEAPATPDTLYA 66
                                      33333333344.66677777777766643 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.02
                           MDMPI_N  30 tvadlvaHlarsaralaaalaaegaesalardaaaalvtaad................................... 71 
                                       tv++l+aH  +  + + a  +a   ++++  d  +++  aad                                   
  gi|336255073|ref|YP_004598180.1| 110 TVRELLAHSSGMPQDFVARRPA--IDDGRNLDLFEHVDGAADrrlvdddrymyynggyfvlgelveavdgrpyeeyv 184
                                       8888888866666666666333..33334444444444444433333444444444444555555555555555555 PP

                           MDMPI_N  72 .....aeavdlaaslapeallaafraavtrlaaalaalppdaiadrlgipgg 118
                                            +     + ++ +++ la+ ++a t+  +a  +l pda     g++gg
  gi|336255073|ref|YP_004598180.1| 185 rteifEPLGMTRSTY-DPDALARADDAMTGYTRADGELSPDAYDGGAGPAGG 235
                                       554433333333344.444477778888888888888888877666655555 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0011
                           MDMPI_N  28 GWtvadlvaHlarsaralaaa.......laaegaesalardaaaalvtaad.........aeavdlaaslapealla 88 
                                       GW v+d +  +  s++   ++       l++++ ++ala+++  + vta+          ++ +d+ ++l   + ++
  gi|336255073|ref|YP_004598180.1| 291 GWEVRDFLDETLVSHLGGIGVsgaymgcLREHDVAVALAFNTHGPSVTAVGagilaalcgERPEDAVRALRVREAID 367
                                       788877666655555555555444555578888888888888888888887999999999***************** PP

                           MDMPI_N  89 afraavtrlaaalaalppdaiadrlgipggprslgeflrtrlvE 132
                                       a+++++++ + al a+ + a a ++ i+  +r++++++   +vE
  gi|336255073|ref|YP_004598180.1| 368 AVAGTYESYRGALTATVEPAAAGTIRIRVPERDVAFTASPDAVE 411
                                       *************************9999999988877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3756.69
//
Query:       gi|336255074|ref|YP_004598181.1|  [L=135]
Description: hypothetical protein Halxa_3695 [Halopiger xanaduensis SH-6]
Scores for 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  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); 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: 0.34u 0.19s 00:00:00.53 Elapsed: 00:00:00.33
# Mc/sec: 1209.83
//
Query:       gi|336255075|ref|YP_004598182.1|  [L=55]
Description: hypothetical protein Halxa_3696 [Halopiger xanaduensis SH-6]
Scores for 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:                       343  (0.019131); 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:                         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 0.20s 00:00:00.52 Elapsed: 00:00:00.33
# Mc/sec: 503.72
//
Query:       gi|336255076|ref|YP_004598183.1|  [L=101]
Description: multi-sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.35   10.3   4.6       0.87    9.1   4.6    1.7  1  VEGFR-2_TMD  VEGFR-2 Transmembrane domain


Domain annotation for each model (and alignments):
>> VEGFR-2_TMD  VEGFR-2 Transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   4.6   4.9e-05      0.87      10      25 ..      86     101 .]      84     101 .] 0.93

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 4.9e-05
                       VEGFR-2_TMD  10 ligtgViAvFFWlLLv 25 
                                       l+g +++A F+W+ L+
  gi|336255076|ref|YP_004598183.1|  86 LVGGAIAALFLWVVLI 101
                                       9************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.19s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 810.74
//
Query:       gi|336255077|ref|YP_004598184.1|  [L=253]
Description: hypothetical protein Halxa_3698 [Halopiger xanaduensis SH-6]
Scores for complete 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  107.2   8.9    1.1e-28  100.8   8.9    2.2  1  DUF2797   Protein of unknown function (DUF2797)
  ------ inclusion threshold ------
      0.064   13.4   0.0       0.21   11.7   0.0    1.7  2  SoxG      Sarcosine oxidase, gamma subunit family


Domain annotation for each model (and alignments):
>> DUF2797  Protein of unknown function (DUF2797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   8.9   1.2e-32   1.1e-28       3     231 .]      34     236 ..      32     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 1.2e-32
                           DUF2797   3 elaltltgerrCvnCgrktkksfsqgvCakCfkklaeadecimkpekchahlgtclrdpeweekaclqphvVYLa.. 77 
                                        l++ l gerrC++   + ++      C +     + ++    +   c   +gtcl+d    e++c+++h VY+a  
  gi|336255077|ref|YP_004598184.1|  34 ALSYAL-GERRCAGTIDDGEH----VACDRP--AAPYCEYH-TSTWVCARCTGTCLKD----EMDCYEEHAVYIAaf 98 
                                       556666.77777775444222....233333..23333333.3333677889******....*************99 PP

                           DUF2797  78 nssevKVGiTrkeqvptRwidQGAvqaiplaevanRrlaglvevalketvaDktnwrkmlksevedvdlsaeaeela 154
                                       +++++KVG+T++ +++tR+ +QGA+ a ++ +v+n+r+a+++e++++++++D+++   + +s ++ vd +a++++l+
  gi|336255077|ref|YP_004598184.1|  99 APDTFKVGVTKSRRLETRLREQGADRAAHVHTVSNGRIAREIEAEIARRLTDRVRTGPKIASLAATVDQAAWERTLE 175
                                       9***************************************************************************9 PP

                           DUF2797 155 eliaeeselgaeaiesleaeeeveikypveeypekikslnlekeaeveGtllGikGqylildtgt...vlnirkleG 228
                                       +l+++       +i+++      +++y++e         +   e+  +Gt++G+kG++l+l++g+   ++++r+l G
  gi|336255077|ref|YP_004598184.1| 176 SLKTD-------VIDRF------SFDYGLELRG------RPVRETIASGTVVGVKGRLLVLENGGttyAVDMRDLVG 233
                                       99998.......77777......6778887433......345677899****************9999********* PP

                           DUF2797 229 yev 231
                                       ye+
  gi|336255077|ref|YP_004598184.1| 234 YEL 236
                                       *85 PP

>> SoxG  Sarcosine oxidase, gamma subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.3e-05      0.21      33      86 ..      94     148 ..      72     154 .. 0.85
   2 ?   -1.4   0.0      0.26   2.3e+03      73      92 ..     188     207 ..     158     213 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                              SoxG  33 svlwlaPdeflvidqegkaalaalaealaela.svvdlShgrvlisisGakaeav 86 
                                        + ++aPd f v + + +  + +l+e  a++a  v  +S gr++ +i+   a+++
  gi|336255077|ref|YP_004598184.1|  94 YIAAFAPDTFKVGVTKSRRLETRLREQGADRAaHVHTVSNGRIAREIEAEIARRL 148
                                       5679********99999999**********66367789********999888876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.26
                              SoxG  73 rvlisisGakaeavlaklta 92 
                                          +++ G+ +++++a++t 
  gi|336255077|ref|YP_004598184.1| 188 DYGLELRGRPVRETIASGTV 207
                                       55678899999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2060.77
//
Query:       gi|336255078|ref|YP_004598185.1|  [L=119]
Description: hypothetical protein Halxa_3699 [Halopiger xanaduensis SH-6]
Scores for 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-33  113.5   0.1    4.2e-33  113.4   0.1    1.1  1  BsuPI            Intracellular proteinase inhibitor
  ------ inclusion threshold ------
      0.029   14.4   0.1      0.055   13.5   0.1    1.5  1  CPT_N            Carnitine O-palmitoyltransferase N-terminus
      0.036   14.4   0.0      0.052   13.9   0.0    1.4  1  DUF11            Domain of unknown function DUF11
      0.055   13.6   0.1      0.086   13.0   0.1    1.4  1  DUF4232          Protein of unknown function (DUF4232)
      0.084   12.3   0.0       0.09   12.2   0.0    1.1  1  Glyco_hydr_116N  beta-glucosidase 2, glycosyl-hydrolase famil
        0.2   11.6   0.0       0.24   11.3   0.0    1.2  1  DUF5067          Domain of unknown function (DUF5067)


Domain annotation for each model (and alignments):
>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.4   0.1   1.4e-36   4.2e-33      12      99 ..      14     106 ..       3     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 1.4e-36
                                       S.......-EEEEEEEEE-SSS-EEEEESSS--EEEEEE-TT--EEEETTTT-------EEEEE-TT-EEEEEEEE. CS
                             BsuPI  12 e.......avelaltvtNesdeavtlqFssgqkydlvvkdeegeevwrysegrmFtqalssetlepgesatyeetwd 81 
                                       +       av++++tvtN++ e+ +lqFs++ k+++vv ++e++evwr++egr+F+q+ls e+l+p+es+ty+ +w 
  gi|336255078|ref|YP_004598185.1|  14 DgdgtgspAVAFRFTVTNTGAEPLELQFSDAAKAEFVV-QDEDREVWRFTEGRAFMQMLSAERLAPEESTTYDGEW- 88 
                                       333456679*****************************.9************************************. PP

                                       S---SEEEEEEEEE--EE CS
                             BsuPI  82 edlepGeYtleaelvaee 99 
                                       e+++pGeYt++ael+a+e
  gi|336255078|ref|YP_004598185.1|  89 ERPRPGEYTAVAELRAQE 106
                                       9***************97 PP

>> CPT_N  Carnitine O-palmitoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.8e-05     0.055       7      20 ..      22      35 ..      20      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                             CPT_N  7 AVAFqftvtpdGid 20
                                      AVAF+ftvt  G++
  gi|336255078|ref|YP_004598185.1| 22 AVAFRFTVTNTGAE 35
                                      9*********9985 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.7e-05     0.052      15      72 ..      22      84 ..       6     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                             DUF11 15 tvtytltvtNtgpasangvvvtDtlPaglayvsvsas.......qgtasaltsv.gsLeagesatl 72
                                      +v +  tvtNtg+ ++ +++ +D   a  ++v            +g a +++ + ++L++ es+t 
  gi|336255078|ref|YP_004598185.1| 22 AVAFRFTVTNTGAEPL-ELQFSD--AAKAEFVVQDEDrevwrftEGRAFMQMLSaERLAPEESTTY 84
                                      68899***********.******..56666665555567999888888888888899999999886 PP

>> DUF4232  Protein of unknown function (DUF4232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.9e-05     0.086       6      83 ..       7      92 ..       4     114 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
                           DUF4232  6 lkvta.aaega..agsryvtltltNtgsrtCtldGy..PgVsll..dadgqqvgaaaeregpaavp.vtLapGesAyag 76
                                      l++++ + +++   +  +++ t+tNtg ++ +l+    +  +++  d+d++ +  ++ r+  +  +  +Lap es++ +
  gi|336255078|ref|YP_004598185.1|  7 LEARVsTDGDGtgSPAVAFRFTVTNTGAEPLELQFSdaAKAEFVvqDEDREVWRFTEGRAFMQMLSaERLAPEESTTYD 85
                                      55555333333479999**************997433366777665555544443333333333323457777777766 PP

                           DUF4232 77 lrwtnag 83
                                       +w +++
  gi|336255078|ref|YP_004598185.1| 86 GEWERPR 92
                                      6666665 PP

>> Glyco_hydr_116N  beta-glucosidase 2, glycosyl-hydrolase family 116 N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     3e-05      0.09     113     145 ..      14      46 ..      11     116 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                   Glyco_hydr_116N 113 dykeSslPvavfewtveNtgkeevevsillswe 145
                                       d + ++ P++ f++tv+Ntg e++e++     +
  gi|336255078|ref|YP_004598185.1|  14 DGDGTGSPAVAFRFTVTNTGAEPLELQFSDAAK 46 
                                       6678999***************99876554444 PP

>> DUF5067  Domain of unknown function (DUF5067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     8e-05      0.24      34      72 ..      10      52 ..       7      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8e-05
                                      EEEEECC..CTCEEEEEEEEEE-SS-TTB..CHHHHHHHEEEE CS
                           DUF5067 34 evikdye..gkpvlvvyyeftNnsdeeis..pssavsvylkAy 72
                                      +v++d +  g+p++++ +++tN++ e+    +s+a++  + + 
  gi|336255078|ref|YP_004598185.1| 10 RVSTDGDgtGSPAVAFRFTVTNTGAEPLElqFSDAAKAEFVVQ 52
                                      566555555****************987655788877755444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); 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:                         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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 985.67
//
Query:       gi|336255079|ref|YP_004598186.1|  [L=127]
Description: hypothetical protein Halxa_3700 [Halopiger xanaduensis SH-6]
Scores for 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:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1065.98
//
Query:       gi|336255080|ref|YP_004598187.1|  [L=160]
Description: hypothetical protein Halxa_3701 [Halopiger xanaduensis SH-6]
Scores for 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  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1260.84
//
Query:       gi|336255081|ref|YP_004598188.1|  [L=310]
Description: cobalamin (vitamin B12) biosynthesis CbiX protein [Halopiger xanaduensis SH-6]
Scores for 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-44  149.4   0.6    6.8e-22   77.8   0.1    2.2  2  CbiX      CbiX
    3.1e-08   33.3   0.1    0.00019   20.8   0.2    2.1  2  CbiK      Cobalt chelatase (CbiK)
  ------ inclusion threshold ------
      0.011   15.5   0.5       0.13   12.0   0.0    2.0  2  LTV       Low temperature viability protein


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 !   77.8   0.1   1.1e-25   6.8e-22       1     107 []       9     130 ..       9     130 .. 0.95
   2 !   70.2   0.1   2.6e-23   1.6e-19       1     106 [.     152     262 ..     152     263 .. 0.89

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.1e-25
                                       -STSS.CCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHC CS
                              CbiX   1 HGSrd.pesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeel 76 
                                       HGS++ p+++++ +++a+++re g+f++v+ +f + eep ++e++r+l   + ++++vvPlf+++G++++++Ip+el
  gi|336255081|ref|YP_004598188.1|   9 HGSHLnPDASDPTYAHADRVRETGAFDEVREAF-WKEEPHFREVIRTL---ESDEVFVVPLFISEGYFTEQVIPREL 81 
                                       9**776***************************.99************...99************************ PP

                                       T--SSSS-..................TTEEEEE---CCCSCCHHHHHHH CS
                              CbiX  77 eeaeeahp..................kdveieytepLGthplvaevlke 107
                                       +++e +++                   d +++y+ p+Gth+++++v+++
  gi|336255081|ref|YP_004598188.1|  82 RLEEWHPEkwdsdgtsasqvtleatdVDKTVHYCGPVGTHDAMTDVIVQ 130
                                       9977777799**************999999****************975 PP

  == domain 2  score: 70.2 bits;  conditional E-value: 2.6e-23
                                       -ST.SSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHC CS
                              CbiX   1 HGS.rdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeel 76 
                                       HG+ r+++s ++ve ++e++re+++f++ve  f++ eep+++++ + +   + ++ivvvPlf+++G+h++eDIpe +
  gi|336255081|ref|YP_004598188.1| 152 HGTeRNENSAKAVEYHTERIRERDRFDEVEALFMD-EEPEVDDVTEYF---ESEDIVVVPLFIADGYHTQEDIPEDM 224
                                       9**899*****************************.*********999...99**********************66 PP

                                       T--SSSS-........TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  77 eeaeeahp........kdveieytepLGthplvaevlk 106
                                       ++ e+           ++++i+y+ ++Gt+ l+a+v+ 
  gi|336255081|ref|YP_004598188.1| 225 GLTEDYRLgwdvpaevDGHRIWYAGAVGTEGLMADVIL 262
                                       64333222344777777******************996 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   4.6e-05      0.27     142     210 ..       2      70 ..       1     106 [. 0.83
   2 !   20.8   0.2   3.2e-08   0.00019     140     220 ..     143     223 ..     109     232 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.6e-05
                                       EEEEEEE---SC...HHHHHHHHHHHHHHHCT-S.EEEEETTSSS-HHHHHHHHHHHT--EEEEEE-SSS-- CS
                              CbiK 142 ealvfvgHGteh...esnavyaeldkvlkekdfkqvvvgtvegyPeveevieelkkkgikevkliPlmlvAG 210
                                       +alv  +HG++    +s  +ya+ d+v +   f++v  +  +  P++ evi++l+ ++   v ++Pl++  G
  gi|336255081|ref|YP_004598188.1|   2 QALVIAAHGSHLnpdASDPTYAHADRVRETGAFDEVREAFWKEEPHFREVIRTLESDE---VFVVPLFISEG 70 
                                       589999***98622257779*********************************99865...66777777666 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 3.2e-08
                                       TTEEEEEEE---SCHHHHH...HHHHHHHHHHCT-S.EEEEETTSSS-HHHHHHHHHHHT--EEEEEE-SSS--HHH CS
                              CbiK 140 kdealvfvgHGtehesnav...yaeldkvlkekdfkqvvvgtvegyPeveevieelkkkgikevkliPlmlvAGdHa 213
                                       +   l  vgHGte + n++     +++++ +  +f++v    ++  Pev++v e+ + ++i    ++Pl++  G H 
  gi|336255081|ref|YP_004598188.1| 143 EGVGLAVVGHGTERNENSAkavEYHTERIRERDRFDEVEALFMDEEPEVDDVTEYFESEDI---VVVPLFIADGYHT 216
                                       55567789***9876554411144678888889***********************99875...688********** PP

                                       HCCCCSS CS
                              CbiK 214 knDmasd 220
                                       ++D+ +d
  gi|336255081|ref|YP_004598188.1| 217 QEDIPED 223
                                       ***9876 PP

>> LTV  Low temperature viability protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.1e-05      0.13     155     216 ..      45     102 ..      35     173 .. 0.80
   2 ?    1.5   0.5     0.033     2e+02     300     332 ..     175     204 ..     168     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                               LTV 155 DPrLRevleaLedeayvddeeeeedDiFaelakdgeevdeeefeeeeddewdsdatekadeq 216
                                       +P+ Rev+  Le ++ +  +    +  F e++   e ++ ee++ e   +wdsd+t+ ++ +
  gi|336255081|ref|YP_004598188.1|  45 EPHFREVIRTLESDEVFVVPLFISEGYFTEQVIPRE-LRLEEWHPE---KWDSDGTSASQVT 102
                                       69**********9988888999***********986.688899865...8999988887322 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.033
                               LTV 300 drFekleekYdddeeeeedeeeleeevdmksvv 332
                                       drF+++e+ + d+e e +d +   e ++++++v
  gi|336255081|ref|YP_004598188.1| 175 DRFDEVEALFMDEEPEVDDVT---EYFESEDIV 204
                                       8*********88876555444...477776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2409.41
//
Query:       gi|336255082|ref|YP_004598189.1|  [L=389]
Description: hypothetical protein Halxa_3703 [Halopiger xanaduensis SH-6]
Scores for 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-46  154.6   0.4    7.4e-46  154.6   0.4    2.3  2  DR2241    DR2241 stabilising domain
    3.3e-31  107.6   0.4    6.6e-31  106.6   0.4    1.5  1  Fer4_23   4Fe-4S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> DR2241  DR2241 stabilising domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.6   0.4   8.2e-50   7.4e-46       1     110 [.     116     229 ..     116     230 .. 0.98
   2 ?    1.8   0.6     0.024   2.1e+02      26      70 ..     317     364 ..     306     372 .. 0.74

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 8.2e-50
                                       HHHHHHHHHHHHHH-ETTEEEEEE.......TT..EEEEEEGGGTT--GGGSEEE-SHHHHHHHTSB-TTS-B-SST CS
                            DR2241   1 vaeryaalaegaerelgellvtaeldd....agervyelrhaddegadeeeletyddpedaRelvrldeegryRPlk 73 
                                       v+ery+al++g++re+g+l +ta++ d    +gervy+l+h+dd+gad ++le+yddp+daRel++ de+gryRPlk
  gi|336255082|ref|YP_004598189.1| 116 VPERYEALRDGIDREWGQLSITARFVDvanpDGERVYDLWHVDDAGADLADLEVYDDPRDARELATDDEDGRYRPLK 192
                                       689**********************9999999********************************************* PP

                                       TBS---SSEE.EEE-TTTHHHHHHHHSTTHHHHHHHH CS
                            DR2241  74 taptlprGWrfavldeadlveavellYPAtvenwyre 110
                                       taptl +GW+f+ l++a+lveave++YPAtv+nw+re
  gi|336255082|ref|YP_004598189.1| 193 TAPTLLSGWAFTGLSGAELVEAVEFFYPATVANWHRE 229
                                       ***********************************97 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.024
                                       ..TT..EEEEEEGGGTT--GGGSEEE...-SHHHHHHHTSB-TTS-B- CS
                            DR2241  26 ddagervyelrhaddegadeeelety...ddpedaRelvrldeegryR 70 
                                       + ++er+yel  +  e  + eel      d   ++Re    d + ryR
  gi|336255082|ref|YP_004598189.1| 317 ESEQERTYELELTPSERNQLEELIDAvaeDRTDEIREADVADGANRYR 364
                                       3467799*9999988888887774321114567899999999999998 PP

>> Fer4_23  4Fe-4S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.4   7.4e-35   6.6e-31       1      82 []     231     312 ..     231     312 .. 0.99

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 7.4e-35
                           Fer4_23   1 rgrlvvtslretaeRQtGiYavvkkltdeqaervvealCadsvClkrrlWavekgeklevegaagelPCaEaCslfv 77 
                                       rg+l+v+++retaeRQtGiY+v  +l++e++++v+ea+C+ds+Cl+rr W++e g+ le  g++g +PC+E+Csl+v
  gi|336255082|ref|YP_004598189.1| 231 RGNLDVDHWRETAERQTGIYDVLDELPREAVDWVAEACCVDSQCLRRRKWEYEAGDDLEPPGGDGPFPCREPCSLVV 307
                                       69*************************************************************************** PP

                           Fer4_23  78 aaaRk 82 
                                       aaaR+
  gi|336255082|ref|YP_004598189.1| 308 AAARQ 312
                                       ****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3051.74
//
Query:       gi|336255083|ref|YP_004598190.1|  [L=203]
Description: hypothetical protein Halxa_3704 [Halopiger xanaduensis SH-6]
Scores for 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:                      1062  (0.0592336); 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:                         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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 1729.64
//
Query:       gi|336255084|ref|YP_004598191.1|  [L=66]
Description: hypothetical protein Halxa_3705 [Halopiger xanaduensis SH-6]
Scores for 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-09   37.8   1.0    4.8e-09   36.7   1.0    1.6  1  Trm112p   Trm112p-like protein
  ------ inclusion threshold ------
      0.012   15.6   0.1      0.014   15.4   0.1    1.1  1  DUF1451   Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   1.0   5.4e-13   4.8e-09       1      68 []       2      51 ..       2      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 5.4e-13
                                      BTGGCCC-B-TTTHHC--HHHHHHHHHTT---S-SS----S......CHHTTEECCCCEEEETTTTEEEEEETT CS
                           Trm112p  1 kllllniLaCpackgpLdwealvevaalglnelpkekpedy......ellleldieegeLvCpncgraYpIkdG 68
                                      k+ ll+iL Cp++k++L                     ed+      e     +++ g LvC++cg  Yp++dG
  gi|336255084|ref|YP_004598191.1|  2 KESLLDILRCPLDKHEL-------------------ELEDAeygddgE-----EVVGGDLVCTECGERYPVDDG 51
                                      678************99...................222223344456.....8888****************9 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1   1.6e-06     0.014      91     124 ..      13      46 ..       3      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-06
                           DUF1451  91 laelaedlehagvyqsGevvglGtlvCekCgkel 124
                                       l + + +le+a++   Ge v  G lvC++Cg++ 
  gi|336255084|ref|YP_004598191.1|  13 LDKHELELEDAEYGDDGEEVVGGDLVCTECGERY 46 
                                       5566677888889999***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); 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: 0.33u 0.18s 00:00:00.51 Elapsed: 00:00:00.33
# Mc/sec: 605.88
//
Query:       gi|336255085|ref|YP_004598192.1|  [L=454]
Description: adenylosuccinate synthetase [Halopiger xanaduensis SH-6]
Scores for 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-154  514.2   0.1   2.9e-154  514.0   0.1    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 !  514.0   0.1  1.6e-158  2.9e-154       2     419 .]       4     447 ..       3     447 .. 0.96

  Alignments for each domain:
  == domain 1  score: 514.0 bits;  conditional E-value: 1.6e-158
                                       EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHH CS
                   Adenylsucc_synt   2 vvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealle 78 
                                       ++vG+q GDEGKG +vDl  + advv+R+qGG+nAGHtvv+dg++ykl+l+pSG+++ g++ v+Gng+vv+pe+l+ 
  gi|336255085|ref|YP_004598192.1|   4 TIVGSQLGDEGKGGVVDLYGDAADVVARYQGGDNAGHTVVHDGETYKLSLVPSGAVR-GKIGVLGNGCVVNPETLFG 79 
                                       79******************************************************6.9999*************** PP

                                       HHTTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGSHHHH CS
                   Adenylsucc_synt  79 EieeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlldeeel 155
                                       Ei++l+++g++    ++++++rah++lpyh+alD++ee++k++ + GtT++GiGp+y+dk+ rrg+rvgdlld+++l
  gi|336255085|ref|YP_004598192.1|  80 EIDTLRERGLKP---DVRVAERAHVILPYHRALDGIEENEKEDLAAGTTGRGIGPTYEDKAGRRGVRVGDLLDPDTL 153
                                       **********77...9************************9999********************************* PP

                                       HHHHHHHHHHTHHHHHHT.......T-----HHHHHHHHHHHHGG..GEE-HHHHHHHHHHTT--EEEE--S-GGG- CS
                   Adenylsucc_synt 156 eeklekllelknkllekldk....eeleveelleellkyaerlkp..yvvdtvallnealkegkkvLfEGaqgtllD 226
                                       +e+le ++ +k++l+e++      ee++v++l+e++++y erl++  + vd+ ++l+e +++g++v++EGaqgt +D
  gi|336255085|ref|YP_004598192.1| 154 RERLEYVVPQKKALAEDVFGketgEEFDVDHLFETYREYGERLAEenMTVDCGTFLQERIDAGDNVMLEGAQGTSID 230
                                       **************99997778999******************9876899*************************** PP

                                       TTTSSTTSS-SS--SHHHHHHHTT--GGGEE..EEEEEEESSEEESSSS--TTB--S...................H CS
                   Adenylsucc_synt 227 idhGtYPfvTsSnttaggaltglglapkkid..evlgvvKAyttrvGeGpfptelkd...................e 282
                                       idhG YP+vTsSn+tagga +g+gl+p+ ++  ev+g+vKAy +rvG+Gp+ptel +                   e
  gi|336255085|ref|YP_004598192.1| 231 IDHGIYPYVTSSNPTAGGASVGTGLGPTVVGdgEVIGIVKAYLSRVGTGPLPTELGGvegqtpdydadegagdeeeE 307
                                       ******************************556*********************96477788888888888888889 PP

                                       HHHHHHHHTT-B-TTT--B-EEE-EEHHHHHHHHHHHT-SEEEEE-GGGGTT-SEEEEEEEEEETTEEESS--S... CS
                   Adenylsucc_synt 283 vgeklrekGkEfgtttgrpRrcGwlDlvllryavrvngvtelaltklDvldgldeikvcvaYkldgkeldefpasle 359
                                        ++++r++G+E+gt+tgrpRr+GwlD+++lr+a+r+ng+t+la++++Dvl+glde+kv+ +Y+ldg+e+ ++p ++e
  gi|336255085|ref|YP_004598192.1| 308 LATYIRDEGGEYGTVTGRPRRVGWLDMPMLRHAARANGFTGLAINHIDVLAGLDEVKVGHSYELDGEEVFTMPPTTE 384
                                       99*************************************************************************** PP

                                       ..-GEEEEEEEEE--..S--TT-..--GGGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-EE CS
                   Adenylsucc_synt 360 elekvepvyeelpgWk.edisgv..rsfedlpenakkyvefieellgvpvkiisvGpereqti 419
                                       ++ ++e  +++++gW+  d+++v  + ++++pena++y+e+++++l++p+  ++vGp+re+t+
  gi|336255085|ref|YP_004598192.1| 385 KWGDCEATLRTFDGWDeVDWEAVaeDGYDAIPENARTYLEYVSDELDAPIYAVGVGPGREETV 447
                                       ***************846799998889*********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); 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: 0.44u 0.19s 00:00:00.63 Elapsed: 00:00:00.34
# Mc/sec: 4021.31
//
Query:       gi|336255086|ref|YP_004598193.1|  [L=101]
Description: hypothetical protein Halxa_3707 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.009   15.9   0.1      0.017   15.1   0.0    1.6  1  HTH_12           Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
      0.012   15.2   0.4      0.021   14.4   0.0    1.6  2  HTH_24           Winged helix-turn-helix DNA-binding
      0.026   14.4   0.1      0.056   13.3   0.1    1.5  1  HTH_5            Bacterial regulatory protein, arsR family
      0.029   14.3   0.3      0.044   13.7   0.1    1.4  2  TrmB             Sugar-specific transcriptional regulator Trm
      0.031   14.2   0.0      0.035   14.1   0.0    1.1  1  DUF977           Bacterial protein of unknown function (DUF97
      0.049   13.6   0.0      0.092   12.7   0.0    1.5  1  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_


Domain annotation for each model (and alignments):
>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   5.7e-06     0.017      24      61 ..      35      69 ..      16      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.7e-06
                            HTH_12 24 kkrgydigeravRyrLrkleergltrrvgyagreltEk 61
                                      +++gy      vRy Lr+lee++l++  + + +  tE+
  gi|336255086|ref|YP_004598193.1| 35 NETGYPH--HKVRYSLRVLEEENLIEPSSQG-AIKTER 69
                                      4556666..88**************987776.666666 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 ?   -2.7   0.1       1.5   4.6e+03      38      44 ..       2       8 ..       1       8 [. 0.81
   2 ?   14.4   0.0   6.9e-06     0.021       3      48 .]      13      58 ..      11      58 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.5
                            HTH_24 38 lkrLeee 44
                                      ++rLe+e
  gi|336255086|ref|YP_004598193.1|  2 IDRLEKE 8 
                                      7899996 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.9e-06
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      e ++++L+ + +n  i +   + ++g +   v++ l+ Leee lI+
  gi|336255086|ref|YP_004598193.1| 13 ERHLQVLKMVIENEPIGIVKMSNETGYPHHKVRYSLRVLEEENLIE 58
                                      7899****************************************96 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 ?   13.3   0.1   1.9e-05     0.056       5      46 ..      16      58 ..      13      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      l++Lk++ e ++  +   ++e+g +  +v++ L++L+e++L+e
  gi|336255086|ref|YP_004598193.1| 16 LQVLKMVIEnEPIGIVKMSNETGYPHHKVRYSLRVLEEENLIE 58
                                      789999999666999999***********************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.5e-05     0.044       5      56 ..      10      61 ..       5      74 .. 0.87
   2 ?   -3.5   0.0       3.4     1e+04      21      30 ..      89      98 ..      87      99 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                                      HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB  5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      ++ e   +v + +++++p  + + ++e+g p+ kv  +Lr Le+  l+e + 
  gi|336255086|ref|YP_004598193.1| 10 DMLERHLQVLKMVIENEPIGIVKMSNETGYPHHKVRYSLRVLEEENLIEPSS 61
                                      55667789999999**********************************9875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.4
                                      CCCHHCHHCC CS
                              TrmB 21 gpatadeiae 30
                                      + ++++++ae
  gi|336255086|ref|YP_004598193.1| 89 DGMKIEDVAE 98
                                      5678888887 PP

>> DUF977  Bacterial protein of unknown function (DUF977)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.2e-05     0.035      16      82 ..      17      82 ..       5      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                            DUF977 16 riiGlvkkneritisdleritGvgrtsvrkylvdvlerGdlirpGkyGvfrdervvrvwrkaaekat 82
                                      +++ +v +ne i i ++ + tG  ++ vr  l+ vle  +li p   G  + er v    +  +k  
  gi|336255086|ref|YP_004598193.1| 17 QVLKMVIENEPIGIVKMSNETGYPHHKVRYSLR-VLEEENLIEPSSQGAIKTERTVEFVDELDDKLD 82
                                      4677899********************987776.89******************9986655555544 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.1e-05     0.092      58     101 ..      32      75 ..      19      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                   Phage_rep_org_N  58 mlalifnreletvrlaLkvlkdlelieisedkvikiknwekhqn 101
                                       +++ ++  + ++vr  L+vl++ +lie s++++ik + + +++ 
  gi|336255086|ref|YP_004598193.1|  32 KMSNETGYPHHKVRYSLRVLEEENLIEPSSQGAIKTERTVEFVD 75 
                                       6788899999*************************999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      718  (0.0400469); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 888.98
//
Query:       gi|336255087|ref|YP_004598194.1|  [L=867]
Description: hypothetical protein Halxa_3708 [Halopiger xanaduensis SH-6]
Scores for 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-05   22.3   4.0    0.00014   21.2   4.0    1.5  1  DUF3450         Protein of unknown function (DUF3450)
    0.00052   19.5   9.3    0.00098   18.6   9.3    1.4  1  DUF3552         Domain of unknown function (DUF3552)
     0.0011   19.2   2.1     0.0033   17.6   2.1    1.8  1  CENP-Q          CENP-Q, a CENPA-CAD centromere complex subuni
     0.0014   18.2   7.6     0.0023   17.4   7.6    1.2  1  HMMR_N          Hyaluronan mediated motility receptor N-termi
     0.0019   18.1   3.1     0.0019   18.1   3.1    2.3  1  FlxA            FlxA-like protein
     0.0021   17.0   9.0     0.0029   16.6   9.0    1.1  1  DUF812          Protein of unknown function (DUF812)
     0.0032   16.3   3.1     0.0032   16.3   3.1    1.8  2  Tektin          Tektin family
     0.0033   17.3   0.0      0.006   16.5   0.0    1.3  1  Spc29           Spindle Pole Component 29
     0.0034   16.3   0.5     0.0054   15.6   0.5    1.2  1  Fmp27_WPPW      RNA pol II promoter Fmp27 protein domain
     0.0043   17.1  11.2     0.0081   16.2  11.2    1.4  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
     0.0065   16.3   0.6     0.0065   16.3   0.6    2.5  1  Pox_A_type_inc  Viral A-type inclusion protein repeat
     0.0073   16.4   6.8      0.013   15.5   6.8    1.4  1  Rootletin       Ciliary rootlet component, centrosome cohesio
     0.0086   16.1   2.1      0.017   15.2   2.1    1.4  1  DUF1664         Protein of unknown function (DUF1664)
     0.0097   16.0  15.1       0.02   15.0  15.1    1.5  1  Cep57_CLD_2     Centrosome localisation domain of PPC89
  ------ inclusion threshold ------
       0.01   16.1  10.1       0.02   15.1  10.1    1.4  1  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding
      0.014   14.0   0.2       0.02   13.5   0.2    1.1  1  FapA            Flagellar Assembly Protein A
      0.014   14.5   7.6      0.027   13.5   7.6    1.4  1  Atg14           Vacuolar sorting 38 and autophagy-related sub
      0.016   15.7   1.9      0.026   15.0   1.9    1.4  1  AAA_23          AAA domain
      0.017   15.5   2.7      0.035   14.5   2.7    1.5  1  DUF4094         Domain of unknown function (DUF4094)
      0.019   15.1  10.3       0.19   11.8   4.9    2.4  2  bZIP_1          bZIP transcription factor
       0.02   15.4  13.5       0.02   15.4  13.5    2.2  1  ZapB            Cell division protein ZapB
      0.023   15.0   6.5      0.059   13.7   6.5    1.7  1  BLOC1_2         Biogenesis of lysosome-related organelles com
      0.024   15.2   1.5       0.78   10.3   1.8    2.6  2  Syntaxin-6_N    Syntaxin 6, N-terminal
      0.028   14.6  10.4      0.072   13.3  10.4    1.6  1  Tropomyosin_1   Tropomyosin like
       0.03   13.8   0.7       0.05   13.1   0.7    1.3  1  DUF2884         Protein of unknown function (DUF2884)
      0.032   14.6   1.3      0.059   13.8   1.3    1.3  1  Syntaxin_2      Syntaxin-like protein
       0.04   14.2  14.9        0.4   11.0  14.8    2.6  1  ABC_tran_CTD    ABC transporter C-terminal domain
      0.044   12.3   2.2      0.084   11.4   2.2    1.4  1  Herpes_UL25     Herpesvirus UL25 family
      0.054   12.8   4.4      0.081   12.3   4.4    1.1  1  FAM76           FAM76 protein
      0.072   13.5   9.8       0.16   12.4   9.8    1.5  1  CENP-H          Centromere protein H (CENP-H)
      0.081   12.9  13.9       0.23   11.5  13.9    1.7  1  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
       0.09   10.9   6.5       0.13   10.4   6.5    1.1  1  HOOK            HOOK protein
      0.091   12.0   0.5       0.13   11.5   0.5    1.1  1  TMPIT           TMPIT-like protein
       0.11   12.2   9.9       0.19   11.3   9.9    1.4  1  DUF2968         Protein of unknown function (DUF2968)
       0.11   11.3   8.3       0.19   10.6   8.3    1.3  1  Spc7            Spc7 kinetochore protein
       0.12   12.0   9.3      0.043   13.4   4.1    2.5  2  PspA_IM30       PspA/IM30 family
       0.12   13.1   5.1       0.69   10.6   4.9    2.2  1  YabA            Initiation control protein YabA
       0.12   11.6   2.7       0.22   10.8   2.7    1.3  1  HemX            HemX, putative uroporphyrinogen-III C-methylt
       0.17   10.4  10.2       0.24    9.9  10.2    1.1  1  Macoilin        Macoilin family
       0.18    9.7   0.1       0.29    9.0   0.1    1.2  1  V_ATPase_I      V-type ATPase 116kDa subunit family
       0.22   11.5  12.7        1.5    8.8   6.6    2.4  2  Prefoldin_2     Prefoldin subunit
       0.23   11.5  11.9       0.84    9.7  11.9    1.8  1  ADIP            Afadin- and alpha -actinin-Binding
       0.24   11.9   2.9       0.49   10.9   2.9    1.4  1  DUF16           Protein of unknown function DUF16
       0.25   11.5   3.7       0.49   10.5   3.7    1.4  1  Nup54           Nucleoporin complex subunit 54
       0.39   10.7   4.4          1    9.4   4.4    1.6  1  Laminin_II      Laminin Domain II
       0.41   10.0   8.1       0.91    8.8   8.1    1.5  1  GAS             Growth-arrest specific micro-tubule binding
       0.42   10.4   4.4       0.82    9.5   4.4    1.3  1  DUF724          Protein of unknown function (DUF724)
       0.42    9.7   9.5       0.67    9.0   9.5    1.3  1  Tmemb_cc2       Predicted transmembrane and coiled-coil 2 pro
       0.44   10.1   4.4       0.75    9.4   4.4    1.3  1  DUF4795         Domain of unknown function (DUF4795)
       0.45   10.6   7.6       0.89    9.6   7.6    1.4  1  Mod_r           Modifier of rudimentary (Mod(r)) protein
       0.51   10.5  10.7          2    8.7  10.7    1.9  1  JIP_LZII        JNK-interacting protein  leucine zipper II
       0.58    9.0  15.5        1.6    7.6  15.5    1.7  1  DUF3375         Protein of unknown function (DUF3375)
       0.65    9.8   3.9        1.4    8.7   3.9    1.5  1  Nsp1_C          Nsp1-like C-terminal region
       0.71    9.9   6.6        1.6    8.8   6.6    1.5  1  CtIP_N          Tumour-suppressor protein CtIP N-terminal dom
       0.82    9.7   6.9        1.5    8.9   6.9    1.3  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
       0.85    7.7   7.2        1.2    7.2   7.2    1.1  1  EzrA            Septation ring formation regulator, EzrA
       0.91    9.3   2.5        1.4    8.6   2.0    1.5  1  DUF3287         Protein of unknown function (DUF3287)
        1.1    8.9   7.0          2    8.1   7.0    1.3  1  SHE3            SWI5-dependent HO expression protein 3
        1.2    9.0   3.5        2.1    8.2   3.5    1.3  1  Sec34           Sec34-like family
        1.2    8.9  13.7       0.59    9.9   5.2    2.4  2  DivIC           Septum formation initiator
        1.3    8.9  11.9      0.041   13.8   4.7    2.1  1  JAKMIP_CC3      JAKMIP CC3 domain
        1.6    8.7   5.5        2.6    8.0   0.5    2.5  2  HSBP1           Heat shock factor binding protein 1
        1.7    8.8   8.3        3.9    7.7   8.3    1.6  1  Cnn_1N          Centrosomin N-terminal motif 1
        2.6    8.0   5.3        3.4    7.6   0.4    2.3  2  Shugoshin_N     Shugoshin N-terminal coiled-coil region
        2.7    5.4  12.6        3.7    4.9  12.6    1.1  1  DUF3584         Protein of unknown function (DUF3584)
        2.8    8.5  16.6      0.032   14.7   8.7    1.8  1  APG6_N          Apg6 coiled-coil region
        3.7    7.3  17.2       0.19   11.5  11.5    1.6  1  ERM             Ezrin/radixin/moesin family
        3.7    7.5   7.8        4.2    7.3   4.1    2.2  2  Prefoldin       Prefoldin subunit
        3.8    7.7  14.7          2    8.6   4.6    2.5  2  bZIP_2          Basic region leucine zipper
        4.6    6.0   4.7        6.6    5.5   4.7    1.1  1  FemAB           FemAB family
        4.8    5.6   4.5        7.2    5.0   4.5    1.2  1  FUSC            Fusaric acid resistance protein family
        6.4    5.3   5.9        9.8    4.7   5.9    1.1  1  AAA_13          AAA domain
        6.6    7.3   8.4        1.8    9.1   4.7    2.0  1  UPF0449         Uncharacterised protein family UPF0449
        6.6    6.8   7.3        3.4    7.8   3.6    2.1  2  DUF4337         Domain of unknown function (DUF4337)
        7.8    6.2  11.6       0.55    9.9   3.6    2.5  2  DUF2312         Uncharacterized protein conserved in bacteria
        8.3    7.1   8.7         37    5.0   6.7    2.8  2  SlyX            SlyX
        9.2    6.4   6.4         14    5.8   0.8    2.4  2  Swi5            Swi5


Domain annotation for each model (and alignments):
>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   4.0   6.1e-07   0.00014      33      92 ..     551     610 ..     526     613 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.1e-07
                           DUF3450  33 aqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       ++ + +i++l+++++ l+++ ++l +e ++l+ +n+ql++ ++ +e++i++le ++e ++
  gi|336255087|ref|YP_004598194.1| 551 ERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEAAR 610
                                       456789************************************************998765 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   9.3   4.2e-06   0.00098      69     141 ..     536     607 ..     486     610 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.2e-06
                           DUF3552  69 lekelkerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrqeLe 141
                                       + +  +  rn+ +r+e Rl ++ e+L+++ e+le+k+++l +++++l++k+q+l+e+ ++le+ +ee ++eLe
  gi|336255087|ref|YP_004598194.1| 536 APSGATADRNQSERIE-RLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELE 607
                                       5555566666667766.9**************************************************99998 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 !   17.6   2.1   1.4e-05    0.0033      19      89 ..     542     613 ..     531     713 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-05
                            CENP-Q  19 ggkekeldfeklldekaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknakaeare.rkeklkk 89 
                                         + ++  +e+l+d++ +le q ++++ + ++L ae++++ ++ ++  e++ +Le  ++ +++e +  ++  
  gi|336255087|ref|YP_004598194.1| 542 ADRNQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESElEAARAGD 613
                                       556677789******************************************************966556554 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   7.6     1e-05    0.0023     234     298 ..     548     608 ..     540     613 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1e-05
                            HMMR_N 234 eelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekckllekekee 298
                                       e+++ +s+++    +++++ +e l++kn++++  + +L+ek+q+ls++++ l++++++le+e+e 
  gi|336255087|ref|YP_004598194.1| 548 ERIERLSDRI----ERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEA 608
                                       3344444444....444677889***************************************994 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   3.1   8.3e-06    0.0019       7      73 ..     538     607 ..     532     614 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.3e-06
                              FlxA   7 sssssssgsasqiasLqkQiknlqkqLkelses.del..tkeekkkqqqliqaQIqqlqaQIaqlqqqqa 73 
                                       s ++ + + +++i++L   i++l++q + l ++ ++l    ++ +++ q++++ I+ l++ I+ l+++ +
  gi|336255087|ref|YP_004598194.1| 538 SGATADRNQSERIERLSDRIERLEEQREALESKnKDLvaERDQLREKNQQLSETIDRLESRIEELESELE 607
                                       445566677788999999999999999999988644411456677********************99865 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   9.0   1.2e-05    0.0029     224     383 ..     451     608 ..     410     611 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
                            DUF812 224 eeeaneqglasrlteeeykkrkkeklqkrlaeqlrkaalkseeaessasksksdlaellsef........seksetd 292
                                       ee++ e ++                                    +s  ++k + + + s++        s++++++
  gi|336255087|ref|YP_004598194.1| 451 EEQWRETRRI-----------------------------------PSIDPEKTTADGSTSAVsgsgaasgSQSASQS 492
                                       2233222221...................................22222222222222222111111111111111 PP

                            DUF812 293 slktkgsrfthaekl.qftke......................ela...kkaeteeelkkkreeeleelqeqieele 343
                                       + k+ g+r++ + ++ + t++                      + +   ++ +++ e+ ++ ++ +e l+eq e+le
  gi|336255087|ref|YP_004598194.1| 493 TRKEAGARTEAQRSTgSATQDsasgtrgsgqadgaagsgtrttA-PsgaTADRNQSERIERLSDRIERLEEQREALE 568
                                       11111111111111111122233333333333344444433321.23445667788888888999999999999999 PP

                            DUF812 344 skieeleeeikklessikqveeeleeekeeneelekevkl 383
                                       sk + l +e ++l+++ +q++e+++++++  eele+e++ 
  gi|336255087|ref|YP_004598194.1| 569 SKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEA 608
                                       9999999999999999999999999999999999998875 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.1   7.3e+02      37      60 ..     433     456 ..     422     458 .. 0.84
   2 !   16.3   3.1   1.4e-05    0.0032      28      94 ..     533     599 ..     512     611 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.1
                            Tektin  37 tkktqadsnkrLeeRiediefwke 60 
                                       +  ++ad +++LeeR e+ e+w+e
  gi|336255087|ref|YP_004598194.1| 433 AADADADGENQLEERFEEEEQWRE 456
                                       566788999*************98 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.4e-05
                            Tektin  28 rlideteektkktqadsnkrLeeRiediefwkeeLekeleelkeeieaLeeekrrlekalealeepl 94 
                                       r+     ++++++q++  +rL++Rie +e  +e Le + ++l++e ++L e  ++l ++++ le  +
  gi|336255087|ref|YP_004598194.1| 533 RTTAPSGATADRNQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRI 599
                                       56666678999***********************************************999998765 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.6e-05     0.006      97     166 ..     535     604 ..     526     646 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.6e-05
                             Spc29  97 sspglapsdesrldsiyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrlaa 166
                                        +p+ a +d+++ ++i +  ++i++le + +  + + k L  e +q r  n++L e +++le+++++l++
  gi|336255087|ref|YP_004598194.1| 535 TAPSGATADRNQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELES 604
                                       5677888*********************999999999****************************99886 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.5   2.3e-05    0.0054     177     244 ..     547     610 ..     536     679 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-05
                        Fmp27_WPPW 177 eeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesse 244
                                       +eR+e+l+++ie+lee+ e le+k++     l +e ++l+++ ++l e ++ le+ +e+l+++ e+++
  gi|336255087|ref|YP_004598194.1| 547 SERIERLSDRIERLEEQREALESKNKD----LVAERDQLREKNQQLSETIDRLESRIEELESELEAAR 610
                                       689999999999999999999888888....6666666666666666666666666666666665443 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 !   16.2  11.2   3.5e-05    0.0081      20      79 ..     551     610 ..     544     613 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.5e-05
                    CENP-F_leu_zip  20 dsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr 79 
                                       + L d++e+Le + e +e+++ +++ e ++ +++ ++l e i++l+++ +ele++L+a r
  gi|336255087|ref|YP_004598194.1| 551 ERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEAAR 610
                                       6799****************************************************9877 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   2.8e-05    0.0065       3      21 ..     592     610 ..     590     612 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.8e-05
                    Pox_A_type_inc   3 msrlRsRIsDLErqLseCr 21 
                                       ++rl sRI++LE++L+++r
  gi|336255087|ref|YP_004598194.1| 592 IDRLESRIEELESELEAAR 610
                                       89**************998 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   6.8   5.7e-05     0.013      55     127 ..     521     608 ..     441     611 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.7e-05
                         Rootletin  55 l..................ssareleeeesadleealakLeeErqrseklaqvnslLreqleearqaneaLtedlqk 113
                                       +                   +a++ ++e+++ l   +++Lee r+    l++ n+ L  + ++ r++n++L+e +++
  gi|336255087|ref|YP_004598194.1| 521 SgqadgaagsgtrttapsgATADRNQSERIERLSDRIERLEEQREA---LESKNKDLVAERDQLREKNQQLSETIDR 594
                                       0444444444444445444455777788888888888888887754...556************************* PP

                         Rootletin 114 ltkdwerlreeleq 127
                                       l++ +e+l+ ele 
  gi|336255087|ref|YP_004598194.1| 595 LESRIEELESELEA 608
                                       *********99986 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.1   7.3e-05     0.017      62     122 ..     544     604 ..     537     606 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.3e-05
                           DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       r+ s+ri+r+ ++++  +e  ++++++ +++  + ++++e+ ++++e++  les++e++e+
  gi|336255087|ref|YP_004598194.1| 544 RNQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELES 604
                                       66789*****************************************************997 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0  15.1   8.4e-05      0.02       5      65 ..     550     610 ..     547     612 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.4e-05
                       Cep57_CLD_2   5 vktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkELkeqr 65 
                                       +++L +r ++l+++ ++ e+ +k+L +ERd    + ++  e+++ L ++ e l+ EL+  r
  gi|336255087|ref|YP_004598194.1| 550 IERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEAAR 610
                                       789******************************************************9876 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 ?   15.1  10.1   8.6e-05      0.02       7      75 ..     543     608 ..     538     611 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.6e-05
                       TMF_TATA_bd   7 agpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekelee 75 
                                         ++++ +erls +i rlE + ++l+++++ l aerd++re   +l+   e+ ++l++++eele+ele+
  gi|336255087|ref|YP_004598194.1| 543 DRNQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLS---ETIDRLESRIEELESELEA 608
                                       5678899**********************************999998...6667777889999999886 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   8.5e-05      0.02     333     411 ..     544     609 ..     501     630 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.5e-05
                              FapA 333 pelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeele 409
                                        +  e++++l +++e+lee+ e l++k k l               + ++l+e+ ++l+e +  le +++el++ele
  gi|336255087|ref|YP_004598194.1| 544 RNQSERIERLSDRIERLEEQREALESKNKDL-------------VAERDQLREKNQQLSETIDRLESRIEELESELE 607
                                       5555666777777777777777777774444.............456777888888888888888888888888887 PP

                              FapA 410 sk 411
                                         
  gi|336255087|ref|YP_004598194.1| 608 AA 609
                                       65 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 ?   13.5   7.6   0.00012     0.027      18      85 ..     544     608 ..     533     612 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                             Atg14  18 rngperlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqe 85 
                                       rn++er+++l  r+ +l +++e+l++k ++++++++   ql++k +++++ +++l s+i++l+++l+ 
  gi|336255087|ref|YP_004598194.1| 544 RNQSERIERLSDRIERLEEQREALESKNKDLVAERD---QLREKNQQLSETIDRLESRIEELESELEA 608
                                       556666666666666666666666666666666666...66666666666666666666666666554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.9   0.00011     0.026     149     200 .]     544     607 ..     427     607 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 0.00011
                            AAA_23 149 kdkkerleelekeleeledekkllekl............eqekekekeleeleeeleeilkele 200
                                        +++er+e l++ +e le++++ le +            e+ ++  ++++ le+++ee+++ele
  gi|336255087|ref|YP_004598194.1| 544 RNQSERIERLSDRIERLEEQREALESKnkdlvaerdqlrEKNQQLSETIDRLESRIEELESELE 607
                                       4555566666666666666666666666666665655555556667788888888888888775 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.7   0.00015     0.035      42      87 ..     564     611 ..     533     612 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00015
                           DUF4094  42 sedcdskdaesr....skdilg.evskthkaiqtLdktissLemeLaaara 87 
                                       +e  +s   +++    ++d l+ + ++ ++ i +L+ +i +Le eL+aara
  gi|336255087|ref|YP_004598194.1| 564 REALES---KNKdlvaERDQLReKNQQLSETIDRLESRIEELESELEAARA 611
                                       222222...11123345677776888999999999***************7 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   4.9   0.00083      0.19      26      63 ..     548     585 ..     544     586 .. 0.84
   2 ?   11.1   2.4    0.0014      0.32      31      63 ..     574     606 ..     572     607 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00083
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                       ++ie+L++r + Le++ ++L s+++ l  e+++L++k+
  gi|336255087|ref|YP_004598194.1| 548 ERIERLSDRIERLEEQREALESKNKDLVAERDQLREKN 585
                                       78999999999999999999999999999999999887 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  31 LerrvkaLekeNksLkseleelkkevekLkskv 63 
                                       L  + ++L ++N++L++++++l+  +e+L+s++
  gi|336255087|ref|YP_004598194.1| 574 LVAERDQLREKNQQLSETIDRLESRIEELESEL 606
                                       5567799**********************9987 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4  13.5   8.4e-05      0.02      12      64 ..     549     601 ..     547     608 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.4e-05
                              ZapB  12 kiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64 
                                       +i+ + d+i++L ++ e+L+ +n+ l  e ++l+e+n+ql e+   +++r++ 
  gi|336255087|ref|YP_004598194.1| 549 RIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEE 601
                                       44455555555555555555555555555555555555555555555555555 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 ?   13.7   6.5   0.00025     0.059      30      95 ..     544     606 ..     540     607 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00025
                           BLOC1_2  30 eaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                       +++se+++ l+d+++ le++ e+l++k++ l       dq+ ++ ++L e++++L++ + eLE+ +
  gi|336255087|ref|YP_004598194.1| 544 RNQSERIERLSDRIERLEEQREALESKNKDLVAER---DQLREKNQQLSETIDRLESRIEELESEL 606
                                       7999**********************887776666...566778888999************9976 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 ?   10.3   1.8    0.0033      0.78      17      65 ..     550     607 ..     544     621 .. 0.58
   2 ?    1.2   0.0       2.3   5.4e+02      35      82 ..     778     822 ..     762     832 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0033
                      Syntaxin-6_N  17 aeslyrrwerlledtss..s.......tseeldetrteLrkalrsiewdledLeetvr 65 
                                       +e l +r erl e+ ++  s       ++++l+e +++L ++++ +e  +e+Le   +
  gi|336255087|ref|YP_004598194.1| 550 IERLSDRIERLEEQREAleSknkdlvaERDQLREKNQQLSETIDRLESRIEELESELE 607
                                       4444444444444333332222333346777777777777777777777777776554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 2.3
                      Syntaxin-6_N  35 tseeldetrteLrkalrsiewdledLeetvriveknpskfkidekels 82 
                                       +++ +++t   L++a + ++ +  dL  ++++ +   s f+  + e++
  gi|336255087|ref|YP_004598194.1| 778 RKPLSEDTLAGLEEAASAVKANYPDLAAAIAVTS---SYFESGAHEVT 822
                                       566678888999******************5544...35666555555 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  10.4   0.00031     0.072      10      68 ..     551     609 ..     543     613 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00031
                     Tropomyosin_1  10 eeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaees 68 
                                       e   ++ e lee+  +le++n++   e  +L +knqql e +++le++++e ++++e++
  gi|336255087|ref|YP_004598194.1| 551 ERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEAA 609
                                       45567888888888888888888888888888888888888888888888888777765 PP

>> DUF2884  Protein of unknown function (DUF2884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.7   0.00021      0.05     169     223 ..     543     596 ..     496     603 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00021
                           DUF2884 169 leafeqrmeklgekieeeveeqakalekkaealCeslkeldaleqqLqkkipeLk 223
                                        ++ ++r+e+l+++ie ++eeq +ale k ++l  + ++l+++ qqL ++i  L+
  gi|336255087|ref|YP_004598194.1| 543 DRNQSERIERLSDRIE-RLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLE 596
                                       5666889999999997.58999999999999999999999999999999998875 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.3   0.00025     0.059       2      57 ..     547     607 ..     547     614 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00025
                        Syntaxin_2   2 ssnlqkinsnvstleklvkqLgtk.kd....teelreklhelieeinelikktnellkkls 57 
                                       s+ + +++  +  le++++ L++k kd     ++lrek ++l e i +l ++++el ++l+
  gi|336255087|ref|YP_004598194.1| 547 SERIERLSDRIERLEEQREALESKnKDlvaeRDQLREKNQQLSETIDRLESRIEELESELE 607
                                       5789999*****************5476666667777777777777777777777666665 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 ?   11.0  14.8    0.0017       0.4       5      63 ..     545     605 ..     542     608 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0017
                      ABC_tran_CTD   5 keqreleeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLeelyer 63 
                                       ++  ++e+l ++Ie+LEe+ ++le +  d     d+  ek ++ls+ +++le+ +eel+++
  gi|336255087|ref|YP_004598194.1| 545 NQSERIERLSDRIERLEEQREALESKNKDLVAERDQlrEKNQQLSETIDRLESRIEELESE 605
                                       566789*******************988776556667788888888888888888888776 PP

>> Herpes_UL25  Herpesvirus UL25 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.2   0.00036     0.084      32     114 ..     553     638 ..     540     667 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXX..XXXXXXXXXXXXXX CS
                       Herpes_UL25  32 lreealeasreevevlevkkralraeLdnlaqkavalaeeier...rlkevEellekiael..eaaaaaeeaaaarp 103
                                       l ++++e+ +e+ e+le k++ l ae d+l++k+++l+e i+r   r++e+E+ le +a +   a a a+ +aaa  
  gi|336255087|ref|YP_004598194.1| 553 L-SDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRlesRIEELESELE-AARAgdGAGAGAGAGAAAGT 627
                                       3.455666799***************************999763337777777777.33333444444444444445 PP

                                       XXXXXXXXXXX CS
                       Herpes_UL25 104 plspssasplt 114
                                       +lsp  a ++t
  gi|336255087|ref|YP_004598194.1| 628 ELSPDRALAGT 638
                                       56665555444 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.4   0.00035     0.081     156     276 ..     486     608 ..     456     611 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00035
                             FAM76 156 skkskkskekskekkaskkkskkhkkrssrlevskleeeklaeekesnetskk.....sldsnssdhlvavtqLkee 227
                                       s++ ++s+   ke+ a ++ ++++ ++++ + +     +++a+ +++++t+++     ++d n+s+++  +++  e+
  gi|336255087|ref|YP_004598194.1| 486 SQSASQST--RKEAGARTEAQRSTGSATQDSASGTRG-SGQADGAAGSGTRTTapsgaTADRNQSERIERLSDRIER 559
                                       22222222..112222222222222222222222222.222333333333333344559999999999999999999 PP

                             FAM76 228 iaslkkqleqkdqellekdkkitelkaellekekelreklkelekeake 276
                                       +++ +  le+k+++l++   ++ e   +l e+  +l+++++ele+e ++
  gi|336255087|ref|YP_004598194.1| 560 LEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEA 608
                                       9999999**********************************99999875 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 ?   12.4   9.8    0.0007      0.16      17      79 ..     545     610 ..     540     612 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0007
                            CENP-H  17 klsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkksr 79 
                                       ++s+ ++ l ++++++e+++ +l+ kn+ l+ae  +l++++++ +   ++l++++e+le+el+++r
  gi|336255087|ref|YP_004598194.1| 545 NQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSetiDRLESRIEELESELEAAR 610
                                       677888888899999999999999999999999877777777777778888899999999998887 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  13.9   0.00098      0.23      12      66 ..     555     609 ..     545     611 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00098
                        TMF_DNA_bd  12 eqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleel 66 
                                       ++I+ L e  e+L++k+ +l +  ++Lr+kn++l ++i++l++++e+le+ele  
  gi|336255087|ref|YP_004598194.1| 555 DRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEAA 609
                                       5799999999999999999999999999999999999999999999999999975 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   6.5   0.00056      0.13     500     567 ..     542     606 ..     536     612 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00056
                              HOOK 500 enrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevqeelqkkkeqleelepkl 567
                                         r + +ri+ L+ ++e l+++ ++ +sk++d ++ + +l e+ ++l+e  + l++    +eele++l
  gi|336255087|ref|YP_004598194.1| 542 ADRNQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLES---RIEELESEL 606
                                       56778888888888888888888888888888666666666666666655555444...555555554 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   0.00055      0.13       3      56 ..     556     609 ..     547     620 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00055
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkkl 56 
                                       ++e+le++ ++le+++k + ++ ++l + ++++s++i++ + r++el+s+l+  
  gi|336255087|ref|YP_004598194.1| 556 RIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEAA 609
                                       456666666677777777777777777777777777777777777777666654 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   9.9   0.00083      0.19     117     179 ..     545     607 ..     540     608 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00083
                           DUF2968 117 asearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaqqe 179
                                       ++++r+erL+  +++ ++Q++a++++ k++ +e ++L+++++++ + +++l+ +i++L+ + e
  gi|336255087|ref|YP_004598194.1| 545 NQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELE 607
                                       5789*******************************************************9876 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   8.3   0.00083      0.19     142     200 ..     551     605 ..     543     612 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00083
                              Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkee 200
                                       e+l++++e lee++e Le++++ l +  ++l+e+ ++l+e++++l+++ eeles    e
  gi|336255087|ref|YP_004598194.1| 551 ERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELES----E 605
                                       567777777777777777777777777777777777777777777777777766....3 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   4.1   0.00019     0.043      91     137 ..     562     608 ..     539     614 .. 0.70
   2 ?   -0.1   0.2       2.5   5.7e+02      72     107 ..     790     825 ..     781     829 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00019
                         PspA_IM30  91 aeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkel 137
                                       ++++ le++ ++l ++ +q+r+  +ql + +++le +ieel+++ e+
  gi|336255087|ref|YP_004598194.1| 562 EQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEA 608
                                       45666777777777777777777777777777777777777776654 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.5
                         PspA_IM30  72 kkAkaALtkgeeeLArealaeikslekqaealetql 107
                                       ++A +A ++++++LA++++    + e+ a +  +++
  gi|336255087|ref|YP_004598194.1| 790 EEAASAVKANYPDLAAAIAVTSSYFESGAHEVTEEA 825
                                       5688999***********999999998888777765 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   4.9     0.003      0.69       8      66 ..     548     599 ..     542     613 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXX CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkel 66 
                                       +++e+l++++e+l e+ e+l+++ ++l+ e ++L+  n++l e+++       + ++++
  gi|336255087|ref|YP_004598194.1| 548 ERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETID-------RLESRI 599
                                       4455555555555555555555555555555555555555555553.......333333 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 ?   10.8   2.7   0.00094      0.22      33      98 ..     546     608 ..     527     614 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00094
                              HemX  33 ltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlsk 98 
                                       ++ ++++l+++++ le+q ++   +++++++l ++ +ql ek ++l+++++ l++++eel+++l++
  gi|336255087|ref|YP_004598194.1| 546 QSERIERLSDRIERLEEQREA---LESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEA 608
                                       333445555555566555555...455555555555666666666666666666666666655554 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  10.2     0.001      0.24     277     444 ..     442     610 ..     354     614 .. 0.41

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
                          Macoilin 277 esvdsklqekeymenkskskrlsksessgsesellveesvkskssssssssnknskkasagsagssnssskkhsess 353
                                       ++++++ +e+e   +  +++r+ + + ++++ +  ++  + s+++s s+s +++s +++ag+ + ++ s+ +  + s
  gi|336255087|ref|YP_004598194.1| 442 NQLEERFEEEE---QWRETRRIPSIDPEKTTADGSTSAVSGSGAASGSQS-ASQSTRKEAGARTEAQRSTGSATQDS 514
                                       22222222111...111122222222211111111111111111111111.11111111112222222222222222 PP

                          Macoilin 354 ksvtsss.....ssknskkqklpaGkssaalkdaaenslpnnqlskkdalvrLeadikkLkaeLqasrqteqelrsk 425
                                        s t +s     ++ +  +  +p+G ++ +++ +  + l++     +++ + Le++ k L ae ++ r+++q+l + 
  gi|336255087|ref|YP_004598194.1| 515 ASGTRGSgqadgAAGSGTRTTAPSGATADRNQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSET 591
                                       22222221122223333444555555555444444444444444445555577777777777777777777777777 PP

                          Macoilin 426 issltseerslkselqqlk 444
                                       i+ l s+  +l sel++ +
  gi|336255087|ref|YP_004598194.1| 592 IDRLESRIEELESELEAAR 610
                                       7777777777777776655 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 ?    9.0   0.1    0.0012      0.29      21      86 ..     542     607 ..     522     620 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                        V_ATPase_I  21 fqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelk 86 
                                        +r+  +++ r+ +  ++l+  +e +e+++k  + e+++ ++++++ ++++d+le+++e+le+el+
  gi|336255087|ref|YP_004598194.1| 542 ADRNQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELE 607
                                       344444444444444444444444444444444444444555555555555555555555555554 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   6.6    0.0065       1.5      59     101 ..     545     587 ..     538     588 .. 0.90
   2 ?    8.2   4.1      0.01       2.3      63      96 ..     577     610 ..     571     612 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0065
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  59 dkeevkeeLeerketlekeiktlekqleklekeleelkeelqk 101
                                       ++ e +e+L +r+e+le++ ++le++ ++l +e ++l+e++q+
  gi|336255087|ref|YP_004598194.1| 545 NQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQ 587
                                       67788999*******************************9997 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  63 vkeeLeerketlekeiktlekqleklekeleelk 96 
                                        +++L e+  +l++ i++le+++e+le ele  +
  gi|336255087|ref|YP_004598194.1| 577 ERDQLREKNQQLSETIDRLESRIEELESELEAAR 610
                                       5789999999999999999999999999999876 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  11.9    0.0036      0.84      64     125 ..     545     606 ..     535     612 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0036
                              ADIP  64 kleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknal 125
                                       + +  ierl+ +ierl++q e+le++++ + a+  ql+ k+++l++++ ++   ++ l++ l
  gi|336255087|ref|YP_004598194.1| 545 NQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESEL 606
                                       44445677777777777777777777776666666777777777777666666665555555 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.9    0.0021      0.49      45     104 .]     545     604 ..     535     608 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0021
                                       ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC- CS
                             DUF16  45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsieg 104
                                        + e+i++l + +e+++e+ + l+ + k   +e +++ e  + + et+++++ R+ ++e+
  gi|336255087|ref|YP_004598194.1| 545 NQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELES 604
                                       57899999999999999999999999999999999********************99996 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.7    0.0021      0.49      65     125 ..     548     608 ..     539     616 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHHHHHHHHHS- CS
                             Nup54  65 khqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelrarletleaqlnd 125
                                       ++  ++s r+e++  +  +l+++   l++  + lr ++++l++  ++l++r+e+le++l++
  gi|336255087|ref|YP_004598194.1| 548 ERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEA 608
                                       5556788999999999999999999999999999999999999999999999999999985 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.4    0.0043         1      23      84 ..     547     608 ..     541     612 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0043
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II  23 sqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                       s+++e++++ +++++++ e  + k kd+    ++ r++ ++L +++++L+++++el+   ea
  gi|336255087|ref|YP_004598194.1| 547 SERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEA 608
                                       678999***********888899999999999999*********************987766 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 ?    8.8   8.1    0.0039      0.91      92     135 ..     548     591 ..     541     611 .. 0.45

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0039
                               GAS  92 arlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqe 135
                                       +r+++l + +++l+++ e le + + + +erd+l++k ++  ++
  gi|336255087|ref|YP_004598194.1| 548 ERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSET 591
                                       44444555555555555555555555555555555444443222 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.4    0.0035      0.82     119     177 ..     551     609 ..     539     615 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0035
                            DUF724 119 eeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledv 177
                                       e  +++ ++lee+ + le+k ++l  ++++l+ek+++ ++ i rl+s  e+le ele++
  gi|336255087|ref|YP_004598194.1| 551 ERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEAA 609
                                       33444444555555555555555555555555555555555555555555555555544 PP

>> Tmemb_cc2  Predicted transmembrane and coiled-coil 2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   9.5    0.0029      0.67     156     273 ..     487     606 ..     434     609 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0029
                         Tmemb_cc2 156 eseeesgskslssstallvskskytsddesssssvesssadsnsnseestasasksaesesqeklekileelqeike 232
                                       +s ++s++k+++ + +  ++++  + +d++s ++ ++++ +++++ + +ta+++ +a+++++e++e + + ++ ++e
  gi|336255087|ref|YP_004598194.1| 487 QSASQSTRKEAGAR-TEAQRSTGSATQDSASGTRGSGQADGAAGSGTRTTAPSGATADRNQSERIERLSDRIERLEE 562
                                       11111222222222.11222222333344444443345555555555555555667777777777777777777777 PP

                         Tmemb_cc2 233 eqerleeelerl...keqlkkelkllkqaLqeeryryerLEeql 273
                                       + e le++  +l   ++ql++  + l+++++    r+e+LE  l
  gi|336255087|ref|YP_004598194.1| 563 QREALESKNKDLvaeRDQLREKNQQLSETIDRLESRIEELESEL 606
                                       7777766666552226899999999*******9*******9877 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.4    0.0032      0.75       3      57 ..     544     598 ..     542     611 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0032
                           DUF4795   3 vnsaellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekv 57 
                                       +n++e ++ l + ie l+e+ e le+k k+l  +  ++++k + l + i++le++
  gi|336255087|ref|YP_004598194.1| 544 RNQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESR 598
                                       688999999****************************************999976 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 ?    9.6   7.6    0.0038      0.89      25      86 ..     547     608 ..     541     613 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0038
                             Mod_r  25 lpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqelde 86 
                                       ++++++l ++ e l+++ e+l +kn +l  e ++lr++ q+  e++++le++ ee+e+el++
  gi|336255087|ref|YP_004598194.1| 547 SERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEA 608
                                       57788999999999999999999999999999999999999999999999999999999986 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  10.7    0.0085         2      26      70 ..     562     606 ..     547     607 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0085
                          JIP_LZII  26 vvkddLIarvdeLtsereiLreEleslqkakerlesrikelEeel 70 
                                        +++ L ++  +L  er+ Lre +++l ++ +rlesri+elE el
  gi|336255087|ref|YP_004598194.1| 562 EQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESEL 606
                                       4455555555667789999999999999999***********998 PP

>> DUF3375  Protein of unknown function (DUF3375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  15.5    0.0067       1.6     132     198 ..     542     609 ..     539     612 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0067
                           DUF3375 132 tepDpeeRlaeLeaeiaeidaeidrlra.geveelddeqvlerireilnlareLpaDFrrVeeefrel 198
                                       ++ +++eR+++L  +i+++++++++l++ ++  + +++q++e+ ++++ ++ +L + + ++e e++++
  gi|336255087|ref|YP_004598194.1| 542 ADRNQSERIERLSDRIERLEEQREALESkNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEAA 609
                                       68899***********************99999999********************999999999876 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 ?    8.7   3.9     0.006       1.4      56     112 ..     554     610 ..     549     614 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.006
                            Nsp1_C  56 gekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellsklesqk 112
                                       +++I++L ++ ++ e++++ +  e + + ++ ++L++ +d++E+++eel s+le ++
  gi|336255087|ref|YP_004598194.1| 554 SDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEAAR 610
                                       589***********************************************9988766 PP

>> CtIP_N  Tumour-suppressor protein CtIP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   6.6     0.007       1.6      14      65 ..     548     599 ..     544     605 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.007
                            CtIP_N  14 kevqglqekvlelkkercldaqrleelfsknqqlreqqkalkenikvlenrL 65 
                                       + ++ l ++++ l+++r    ++ ++l++  +qlre+++ l+e+i +le+r+
  gi|336255087|ref|YP_004598194.1| 548 ERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRI 599
                                       56889999***********99****************************997 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 ?    8.9   6.9    0.0063       1.5      72     128 ..     548     608 ..     532     613 .. 0.44

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0063
                           UPF0242  72 ekeaklteldeglktkeeale....elqeeeeeLkeeldakeeelerlkeenqqLqeklea 128
                                       e+++ l++  e l++++eale    +l +e ++L+e+ ++ +e++ rl+ + ++L+++lea
  gi|336255087|ref|YP_004598194.1| 548 ERIERLSDRIERLEEQREALEsknkDLVAERDQLREKNQQLSETIDRLESRIEELESELEA 608
                                       2222222222222222222220000333444555555555555555555555555555544 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   7.2    0.0052       1.2      90     156 ..     544     610 ..     540     612 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0052
                                       -S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTT CS
                              EzrA  90 lldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanr 156
                                        +++ ++ ++  +++ lee+ + +e+k k++ +e ++l+e++++ +e i+ l+++ +el+ +l+a r
  gi|336255087|ref|YP_004598194.1| 544 RNQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEAAR 610
                                       5677788888888888888888888888888888888888888888888888888888888888765 PP

>> DUF3287  Protein of unknown function (DUF3287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.0    0.0062       1.4      59      99 ..     566     606 ..     558     610 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0062
                           DUF3287  59 kvvekHrrlcderqklgkkrqtleaRiarveRklrelesep 99 
                                       ++  k + l  er +l+ k q+l   i r+e ++ elese+
  gi|336255087|ref|YP_004598194.1| 566 ALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESEL 606
                                       67788899999****************************98 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.0    0.0086         2      21      77 ..     552     608 ..     545     612 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0086
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  21 qLtqqsqeLleklelaqkkeskflenlaslkhENdnLsslLkRKerrlkdlekelse 77 
                                       +L    + L e+ e  ++k++ ++ +  +l++ N++Ls  ++R e r+ +le+el+ 
  gi|336255087|ref|YP_004598194.1| 552 RLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEA 608
                                       455566678888888888888999999999999999999999999999999988865 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.5     0.009       2.1      18      68 ..     549     599 ..     544     610 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.009
                             Sec34  18 qtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekL 68 
                                       +++++ + +e lee+ ++ ++k ++l ++ +ql e++++l+e+ + +e+++
  gi|336255087|ref|YP_004598194.1| 549 RIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRI 599
                                       456666677777777777777777777777777777777777777666655 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   3.0      0.21        50      31      56 ..     548     574 ..     541     578 .. 0.51
   2 ?    9.9   5.2    0.0025      0.59      20      53 ..     572     605 ..     569     611 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHHCC-XX.XXXX CS
                             DivIC  31 aelaklkaeneeLeaevkdLks.dedy 56 
                                       + +++l++++e+Le++ + L+s ++d 
  gi|336255087|ref|YP_004598194.1| 548 ERIERLSDRIERLEEQREALESkNKDL 574
                                       345555555555555555554344444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                             DivIC  20 kqlkqeiaalqaelaklkaeneeLeaevkdLksd 53 
                                       k+l +e+++l +++++l++++++Le+++++L+s+
  gi|336255087|ref|YP_004598194.1| 572 KDLVAERDQLREKNQQLSETIDRLESRIEELESE 605
                                       67779999*********************99755 PP

>> JAKMIP_CC3  JAKMIP CC3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   4.7   0.00018     0.041     114     176 ..     547     610 ..     529     613 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00018
                        JAKMIP_CC3 114 eselrktkskikdLee...aLaqkGqdskwveekQalikrnqeLvekikkleeeeskLkqeiqdlr 176
                                        + +++   +i+ Lee   aL+ k +d   v e+ +l  +nq+L e i++le++   L++e++++r
  gi|336255087|ref|YP_004598194.1| 547 SERIERLSDRIERLEEqreALESKNKD--LVAERDQLREKNQQLSETIDRLESRIEELESELEAAR 610
                                       344677788888888611145554444..4677777***************************998 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 ?    2.3   0.5      0.65   1.5e+02      27      42 ..     548     563 ..     545     572 .. 0.83
   2 ?    8.0   0.5     0.011       2.6      23      44 ..     586     607 ..     579     613 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.65
                             HSBP1  27 sriDdMssriDdLEks 42 
                                       +ri+ +s ri+ LE++
  gi|336255087|ref|YP_004598194.1| 548 ERIERLSDRIERLEEQ 563
                                       6999**********87 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.011
                             HSBP1  23 dqilsriDdMssriDdLEksia 44 
                                       +q+ + iD ++sri++LE  ++
  gi|336255087|ref|YP_004598194.1| 586 QQLSETIDRLESRIEELESELE 607
                                       46667789999*****998775 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 ?    7.7   8.3     0.017       3.9      22      72 ..     549     598 ..     548     606 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.017
                            Cnn_1N  22 riyfLeerleklseeqkeellkenielkveveslqkelkekkkllreaeka 72 
                                       ri  L +r+e+l+e q+e+l+++n +l  e+ +l+ +++++ + ++++e++
  gi|336255087|ref|YP_004598194.1| 549 RIERLSDRIERLEE-QREALESKNKDLVAERDQLREKNQQLSETIDRLESR 598
                                       67778888888877.777777777777777777777777777777777654 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.4     0.015       3.4      26      44 ..     567     585 ..     565     586 .. 0.93
   2 ?    4.3   1.2      0.16        38      15      36 ..     584     605 ..     584     608 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.015
                       Shugoshin_N  26 lekevseLlsENlnLReli 44 
                                       le+++ +L++E ++LRe++
  gi|336255087|ref|YP_004598194.1| 567 LESKNKDLVAERDQLREKN 585
                                       9****************98 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.16
                       Shugoshin_N  15 sNsalslkirelekevseLlsE 36 
                                       +N++ls +i  le++++eL sE
  gi|336255087|ref|YP_004598194.1| 584 KNQQLSETIDRLESRIEELESE 605
                                       699*****************99 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  12.6     0.016       3.7     414     529 ..     494     609 ..     441     613 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.016
                           DUF3584 414 kaaieealealesqlrkqleaqkeelneeekelesrlselklrldsatateEeleqieeadealekaqeelekaeae 490
                                       ++++ +  ea++s   + ++ +   +   +++ +   +   +    ata  +++e+ie   +++e+ +e+ e+ e +
  gi|336255087|ref|YP_004598194.1| 494 RKEAGARTEAQRSTGSATQDSASGTRGSGQADGAAGSGTRTTAPSGATADRNQSERIERLSDRIERLEEQREALESK 570
                                       55556666666666666666666666666667677777777777889999999999********************* PP

                           DUF3584 491 vealqaeeeqlrkkrdeadealqkaerrleqlrqaleel 529
                                       +++l ae+ qlr+k  + +e+  + e r+e+l ++le++
  gi|336255087|ref|YP_004598194.1| 571 NKDLVAERDQLREKNQQLSETIDRLESRIEELESELEAA 609
                                       ******************************999999875 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   8.7   0.00014     0.032      44      99 ..     552     607 ..     521     611 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00014
                            APG6_N  44 kqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeee 99 
                                       +  + +e+lee+ e+le++ ++l++e ++l +++++l + +  le+  e+le e e
  gi|336255087|ref|YP_004598194.1| 552 RLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELE 607
                                       24566777777777777777777777777777777777777777777777777765 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  11.5   0.00081      0.19      29      93 ..     544     608 ..     537     613 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00081
                               ERM  29 reseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaar 93 
                                       r++ e++e+L  + +r+ee++e Le k++++ +e ++l+e++++  e+ ++le +++e e+e++ 
  gi|336255087|ref|YP_004598194.1| 544 RNQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEA 608
                                       78999999999999999999999999999999999999999999999999999999999998765 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.1     0.018       4.2      78     118 ..     549     589 ..     539     591 .. 0.89
   2 ?    2.1   0.5      0.74   1.7e+02       8      27 ..     588     607 ..     584     613 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  78 Aiellkkkleelekqlekleeeleklkdqittleanlaqly 118
                                        ie l +++e le+q+e le + ++l ++ ++l+++ +ql+
  gi|336255087|ref|YP_004598194.1| 549 RIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLS 589
                                       5899****************************999999876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.74
                                       HHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin   8 lqaelaqlkeaieelektle 27 
                                       l +++++l+++ieele+ le
  gi|336255087|ref|YP_004598194.1| 588 LSETIDRLESRIEELESELE 607
                                       34444444444444444333 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   2.8      0.28        65      26      47 ..     549     570 ..     543     577 .. 0.54
   2 ?    8.6   4.6    0.0086         2      20      51 ..     578     609 ..     577     611 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  26 keeeleervkeLeeeNaqLrqk 47 
                                       + e l +r+++Lee+ ++L+ k
  gi|336255087|ref|YP_004598194.1| 549 RIERLSDRIERLEEQREALESK 570
                                       3444555555555555555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0086
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  20 RekkkakeeeleervkeLeeeNaqLrqkveqL 51 
                                       R+  ++k+++l e++ +Le+++++L+ ++e+ 
  gi|336255087|ref|YP_004598194.1| 578 RDQLREKNQQLSETIDRLESRIEELESELEAA 609
                                       77779999999999999999999999999986 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   4.7     0.029       6.6     239     298 ..     545     606 ..     540     614 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.029
                             FemAB 239 nlaeylkelqekleklekklakleekleknpe..kkkkkklkelekqlaslekelkeaeefi 298
                                       n +e++++l  ++e le++++ le+k++      ++  +k+++l++++++le +++e+e+  
  gi|336255087|ref|YP_004598194.1| 545 NQSERIERLSDRIERLEEQREALESKNKDLVAerDQLREKNQQLSETIDRLESRIEELESEL 606
                                       6778888999999999999888888766555466888999*****************99755 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   4.5     0.031       7.2     269     331 ..     540     608 ..     477     663 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.031
                              FUSC 269 aaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslraleaaiaa......a 331
                                       a a   + +++++l +r+++l++++ea  + +  l+a+ ++l ++ +ql +++++le++i++      a
  gi|336255087|ref|YP_004598194.1| 540 ATADRNQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEEleseleA 608
                                       333444445555555555555555555555555555555555555555555555555555542222220 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   5.9     0.042       9.8     409     468 ..     548     607 ..     540     613 .. 0.47

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.042
                            AAA_13 409 seldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLk 468
                                       + ++++ + +++le++ e le + k+  ae  +l+e+ ++L +++   +  +ee+++eL+
  gi|336255087|ref|YP_004598194.1| 548 ERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELE 607
                                       334444444444444444444444444444444444444444444444444444444444 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   4.7    0.0078       1.8      46      96 ..     553     603 ..     532     608 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0078
                           UPF0449  46 ssseeedleaeveelYeqvrtylelnerLeeakeeLkqkceeLktageeLe 96 
                                        s + e le+++e l  + + +++  ++L+e++++L +  ++L++  eeLe
  gi|336255087|ref|YP_004598194.1| 553 LSDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELE 603
                                       223444555555555556666666666666666666666666666666655 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.6     0.015       3.4      68     116 ..     539     587 ..     527     589 .. 0.87
   2 ?    1.0   0.5       1.8   4.2e+02      73     123 ..     586     683 ..     582     685 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.015
                           DUF4337  68 aeelaaavdkkiakykkkiarykkekkeikkkAkeleaerdeaneasdk 116
                                        ++++++ +++i++++++i+r ++++++++ k k+l aerd++ e++++
  gi|336255087|ref|YP_004598194.1| 539 GATADRNQSERIERLSDRIERLEEQREALESKNKDLVAERDQLREKNQQ 587
                                       55667788899*********************************99886 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.8
                           DUF4337  73 aavdkkiakykkkiarykkekkeikk...............................................kAke 102
                                       ++ +++i++++ +i++ ++e ++ ++                                               +A++
  gi|336255087|ref|YP_004598194.1| 586 QQLSETIDRLESRIEELESELEAARAgdgagagagagaaagtelspdralagtnlfvryrsksqptletahggDADR 662
                                       33444455555555555555555555999999999998888888888888888888888888888888888888999 PP

                           DUF4337 103 leaerdeaneasdkfdlasal 123
                                        e +++ + e++ +fd ++++
  gi|336255087|ref|YP_004598194.1| 663 DEVASNLQLEHHTEFDASDVA 683
                                       999999999999999998876 PP

>> DUF2312  Uncharacterized protein conserved in bacteria (DUF2312)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.6    0.0024      0.55       3      32 ..     548     577 ..     546     580 .. 0.90
   2 ?    0.1   1.0       2.7   6.3e+02       3      18 ..     586     601 ..     584     610 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0024
                           DUF2312   3 dqLrqfieRiErleeEkkaiaedikdvyae 32 
                                       +++ ++ +RiErlee ++a++ + kd+ ae
  gi|336255087|ref|YP_004598194.1| 548 ERIERLSDRIERLEEQREALESKNKDLVAE 577
                                       67888889*******************998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.7
                           DUF2312   3 dqLrqfieRiErleeE 18 
                                       +qL ++i+R+E   eE
  gi|336255087|ref|YP_004598194.1| 586 QQLSETIDRLESRIEE 601
                                       6788888877643333 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.9      0.24        56      29      56 ..     546     573 ..     543     580 .. 0.80
   2 ?    5.0   6.7      0.16        37       2      59 ..     554     611 ..     553     620 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                              SlyX  29 qqqqidrlqrqlrllaerlkeleessga 56 
                                       q ++i+rl  ++++l+e+ ++le+++++
  gi|336255087|ref|YP_004598194.1| 546 QSERIERLSDRIERLEEQREALESKNKD 573
                                       8888999999999999999999988764 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXX CS
                              SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgasea 59 
                                        +r+e+LE++   +e   ++L ++  + +++ ++l + +++l+ r++ele++ +a++a
  gi|336255087|ref|YP_004598194.1| 554 SDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLESRIEELESELEAARA 611
                                       6899999999999999999999999999999999999999999999999999887665 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   3.8     0.075        18       2      44 ..     554     596 ..     547     600 .. 0.91
   2 ?    5.8   0.8     0.062        14       3      28 ..     583     608 ..     581     617 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.075
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHH CS
                              Swi5   2 eaeikeleeqleelekelaelkeelkekkdpeetvkrhIklLh 44 
                                       + +i++leeq e+le++ ++l +e ++  ++++ +++ I++L 
  gi|336255087|ref|YP_004598194.1| 554 SDRIERLEEQREALESKNKDLVAERDQLREKNQQLSETIDRLE 596
                                       578999****************99999999**********997 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.062
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Swi5   3 aeikeleeqleelekelaelkeelke 28 
                                       +++++l e++++le+ ++el++el++
  gi|336255087|ref|YP_004598194.1| 583 EKNQQLSETIDRLESRIEELESELEA 608
                                       66777777777777777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (867 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1436  (0.0800937); expected 358.6 (0.02)
Passed bias filter:                      809  (0.0451224); expected 358.6 (0.02)
Passed Vit filter:                       308  (0.0171789); expected 17.9 (0.001)
Passed Fwd filter:                       111  (0.00619109); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              77  [number of targets reported over threshold]
# CPU time: 1.22u 0.31s 00:00:01.53 Elapsed: 00:00:00.46
# Mc/sec: 5608.02
//
Query:       gi|336255088|ref|YP_004598195.1|  [L=92]
Description: hypothetical protein Halxa_3709 [Halopiger xanaduensis SH-6]
Scores for complete 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-34  118.5   1.0    1.3e-34  118.3   1.0    1.0  1  UPF0058   Uncharacterised protein family UPF0058
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.011   15.9   0.0    1.1  1  Ada3      Histone acetyltransferases subunit 3


Domain annotation for each model (and alignments):
>> UPF0058  Uncharacterised protein family UPF0058
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   1.0   1.4e-38   1.3e-34       1      86 [.       1      87 [.       1      88 [. 0.98

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 1.4e-38
                                      --HHHHHHHHHHHHHHHHHH.TSTT--TTTTHHHHHH---TT-TTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH CS
                           UPF0058  1 MhKdeLieLHqllvevkkel.eeeevekeefkeYeeLdisPhhihrsKaehkaAifvLgnaiakalsekeessaervsk 78
                                      MhKdeL+eLH+ lv++++++ ++eev++e f+ Y++Ld++P+h+h+sK+ehk+A+fvLgna+ak +se+e+ssa+r+ k
  gi|336255088|ref|YP_004598195.1|  1 MHKDELLELHEELVTIMEYFaQREEVDEELFEPYRQLDVDPSHVHKSKSEHKHAVFVLGNALAKGMSEDEFSSAGRIGK 79
                                      ********************8899******************************************************* PP

                                      HHHHHHHH CS
                           UPF0058 79 rlkelaek 86
                                      r+kelae+
  gi|336255088|ref|YP_004598195.1| 80 RMKELAED 87
                                      *****996 PP

>> Ada3  Histone acetyltransferases subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0   1.2e-06     0.011      58     122 ..       2      71 ..       1      87 [. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-06
                              Ada3  58 rkarLlelvkermayqeyqtiledlDkqvqqaYlKrtrtlkkkkkkkrsga.....aaaaaaagaarpgi 122
                                        k +Llel +e +   ey    e++D+++ + Y++    +++  k k++++      ++a a+g+++ + 
  gi|336255088|ref|YP_004598195.1|   2 HKDELLELHEELVTIMEYFAQREEVDEELFEPYRQLDVDPSHVHKSKSEHKhavfvLGNALAKGMSEDEF 71 
                                       5899*******************************77766666666544445567744444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 729.54
//
Query:       gi|336255089|ref|YP_004598196.1|  [L=222]
Description: hypothetical protein Halxa_3710 [Halopiger xanaduensis SH-6]
Scores for 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-14   51.9  37.4    8.6e-14   51.6  36.6    1.5  2  DUF998    Protein of unknown function (DUF998)
  ------ inclusion threshold ------
      0.027   14.0   0.5      0.065   12.8   0.5    1.8  1  Frag1     Frag1/DRAM/Sfk1 family


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 !    3.3   0.8    0.0059        53     128     156 ..       9      37 ..       3      47 .. 0.51
   2 !   51.6  36.6   9.6e-18   8.6e-14       3     184 ..      26     210 ..      24     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0059
                            DUF998 128 rrrawallrlvggvallllvaalvwllaa 156
                                       r r   ++r+++  +l+++v++l+++++a
  gi|336255089|ref|YP_004598196.1|   9 RPRSSTATRVATHCGLAAAVVGLGAIVLA 37 
                                       44444444445555555555555555554 PP

  == domain 2  score: 51.6 bits;  conditional E-value: 9.6e-18
                            DUF998   3 aallalav.ilaaallrpgy.dplrhaiSeLgaeggpggwlfnaglvllgllvlalavgllraargragragrllla 77 
                                       aa++ l + +la  ++ p+   + + a+S+ g +++ +  lfn+glvl+gll + +++ l+ra+++ ++r+g++ll+
  gi|336255089|ref|YP_004598196.1|  26 AAVVGLGAiVLATLVASPETfTWRSAALSDMGRYETRTFPLFNGGLVLSGLLGVPFGWRLWRASETILERIGVALLV 102
                                       5555555534444444455559******************************************************* PP

                            DUF998  78 vaglglvlagvfptdpgggspslsglvHglasavaflalavavllla...saarrrawallrlvggvallllvaalv 151
                                       va +gl+++gvf ++ +  +  l+   Hg a+++ f+a ++a l+++     a+r +++l++++ g++  l+ ++++
  gi|336255089|ref|YP_004598196.1| 103 VATVGLIGVGVFFLGHADWY--LERSFHGPAALTYFAAAPLAQLIYGtgaVLAGRLRRGLVSIWLGIVHPLAWLGWL 177
                                       ************99988776..6999******************6666666669*********************** PP

                            DUF998 152 wllaaaldgslllGlaerllvlaitawllalal 184
                                       ++l+a++d +++++++e+++++a+ aw+  la+
  gi|336255089|ref|YP_004598196.1| 178 LVLVAGGDAGAWFAVPEFVAAVAFGAWIGFLAV 210
                                       ****************************99997 PP

>> Frag1  Frag1/DRAM/Sfk1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   7.2e-06     0.065      83     217 ..      86     213 ..      12     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.2e-06
                             Frag1  83 atksernlnfaalvlgligalglllvsif.....staeyhsvHlvgavvffvfgflyvllqtalyykmgrhyvwnks 154
                                        + se+ l ++ + l +++++gl++v++f     +     s+H  +a+ +f++  l  l+        gr    ++ 
  gi|336255089|ref|YP_004598196.1|  86 WRASETILERIGVALLVVATVGLIGVGVFflghaDWYLERSFHGPAALTYFAAAPLAQLIYGTGAVLAGRL---RRG 159
                                       34455557777777777777777777777666444444557777777777777777777766666666665...777 PP

                             Frag1 155 tisfrlkvvllilavvlailfgvffvrhkkkcgygayslsAifEWllafwfiiffltfsvDFy 217
                                        +s++l +v  ++++ +++++++ ++            ++A+ E++ a++f++ ++ ++vD++
  gi|336255089|ref|YP_004598196.1| 160 LVSIWLGIVHPLAWLGWLLVLVAGGDA---------GAWFAVPEFVAAVAFGAWIGFLAVDLE 213
                                       777777777777777777777777776.........589**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1639.30
//
Query:       gi|336255090|ref|YP_004598197.1|  [L=392]
Description: Fe(3+)-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-33  113.9   0.0    1.3e-32  113.2   0.0    1.4  1  ABC_tran     ABC transporter
    4.1e-09   36.5   0.7    4.1e-09   36.5   0.7    2.2  3  TOBE_2       TOBE domain
      8e-05   22.6   0.2       0.33   10.7   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00093   19.6   0.1     0.0021   18.5   0.1    1.7  1  AAA_16       AAA ATPase domain
      0.001   19.0   0.0     0.0016   18.4   0.0    1.2  1  Rad17        Rad17 P-loop domain
     0.0018   18.5   0.0      0.004   17.3   0.0    1.6  1  AAA_33       AAA domain
     0.0081   16.4   0.6      0.026   14.8   0.6    1.9  1  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.014   15.8   0.1      0.061   13.8   0.1    2.0  1  AAA          ATPase family associated with various cellular a
      0.072   13.3   0.4       0.41   10.9   0.4    2.1  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.073   13.0   0.0       0.15   11.9   0.0    1.4  1  RsgA_GTPase  RsgA GTPase


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 !  113.2   0.0   7.1e-36   1.3e-32       3     136 ..      49     193 ..      47     194 .. 0.94

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 7.1e-36
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpelt 75 
                                       ++sl+++ ge++ ++G++G+GK+t l+l+agl++p++G+++l+++++      +  +  ++ +g+++qe  lfp+lt
  gi|336255090|ref|YP_004598197.1|  49 DLSLSVRDGEILTLLGPSGCGKTTTLRLIAGLETPDAGRVRLQDDPVAVaeegRFVPPENRGVGIVFQEFALFPHLT 125
                                       799****************************************999998877777788899**************** PP

                                       HHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +ren           e++++++++l+ +gl+   d+       +LSgGq+qrvalar+l+ +p++lllDEp+
  gi|336255090|ref|YP_004598197.1| 126 ARENiafglqdwseaEREARVDELLELVGLEAHGDDYP----DELSGGQQQRVALARSLAPEPEMLLLDEPF 193
                                       ***********998888888999999999999777776....*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       8.3   1.5e+04      39      52 ..     166     179 ..     165     184 .. 0.64
   2 ?   -3.8   0.0       8.3   1.5e+04      48      65 ..     219     237 ..     214     238 .. 0.60
   3 !   36.5   0.7   2.3e-12   4.1e-09       1      74 [.     307     377 ..     307     379 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8.3
                            TOBE_2  39 laggqlvvvrqpna 52 
                                       l ggq+++v+ + +
  gi|336255090|ref|YP_004598197.1| 166 LSGGQQQRVALARS 179
                                       67777777776654 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.3
                            TOBE_2  48 rqpnadr.dsalapGdtVe 65 
                                       +++++++ ++al + d+V+
  gi|336255090|ref|YP_004598197.1| 219 AVSVTHDqEEALSISDRVA 237
                                       4455555456777777776 PP

  == domain 3  score: 36.5 bits;  conditional E-value: 2.3e-12
                            TOBE_2   1 laiRPEklrla.aagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddav 74 
                                       l +RP+++    a + a   +G+V+ + ylG +++y+vel++g+ v++  +++d   +++ +++V++++ +d+ +
  gi|336255090|ref|YP_004598197.1| 307 LLVRPDDVVAVpA-DEAAEPNGRVVYRRYLGPTVLYRVELDSGETVECMHNHSD---RIDLDERVGVRVVADHEL 377
                                       679*****99522.223477*********************************9...9*************9976 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 !    9.8   0.0   0.00036      0.65       3      22 ..      61      80 ..      59     106 .. 0.85
   2 !   10.7   0.0   0.00018      0.33     234     293 ..     163     220 ..     136     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00036
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                       l Gp g+GK++ L+++ +l
  gi|336255090|ref|YP_004598197.1| 61 TLLGPSGCGKTTTLRLIAGL 80
                                      699**************998 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00018
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkelsrngaQvi 293
                                       ++elS G+++  al+ +l+  +     ll+DEp ++L+     ++ +++ +++ke+   g+  +
  gi|336255090|ref|YP_004598197.1| 163 PDELSGGQQQRVALARSLAPEP---EMLLLDEPFSNLDVdlrvEMREEVRRIIKEA---GVTAV 220
                                       6789999999989999998877...9*************44443335555555544...45555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   1.2e-06    0.0021      20      52 ..      55     110 ..      48     255 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekd..........................g 52 
                                       r+g  e++ l G+sG+GK++ +r ++  le+                           g
  gi|336255090|ref|YP_004598197.1|  55 RDG--EILTLLGPSGCGKTTTLRLIAG-LETPdagrvrlqddpvavaeegrfvppenrG 110
                                       455..89******************95.5555355555555544444433333333331 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.8e-07    0.0016      40      67 ..      52      79 ..      44     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.8e-07
                             Rad17 40 LesrkkriLLisGPsGCgkstvvkvLsk 67
                                      L  r  +iL + GPsGCgk+t+++ ++ 
  gi|336255090|ref|YP_004598197.1| 52 LSVRDGEILTLLGPSGCGKTTTLRLIAG 79
                                      6667778****************99875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.2e-06     0.004       3     140 ..      61     261 ..      59     263 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.2e-06
                            AAA_33   3 llvGlpGsGKstlaerllkklg....avllssdt........................................... 32 
                                        l G++G+GK+t ++ ++  ++     v+l  d                                            
  gi|336255090|ref|YP_004598197.1|  61 TLLGPSGCGKTTTLRLIAGLETpdagRVRLQDDPvavaeegrfvppenrgvgivfqefalfphltareniafglqdw 137
                                       578************99766667866666666669******************999999999999888888888888 PP

                            AAA_33  33 ..........lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnls......rrerarflklar 93 
                                                 ++  l+g + + + ++ +++    q++ +lar+ + +   ++ld ++ +       + r++++++ +
  gi|336255090|ref|YP_004598197.1| 138 seaerearvdELLELVGLEAHGDDYPDELSGGQQQRV-ALARSLAPEPEMLLLDEPFSNldvdlrVEMREEVRRIIK 213
                                       8886666666555555566665556666777777777.9*****************77777777457789******* PP

                            AAA_33  94 rlgvpvrivvvetdeet.lkeRlakRaangddrsevpeealdrqkarf 140
                                       ++gv    v+ +  e++ + +R+a+ ++   +++ +pe+++++ k+rf
  gi|336255090|ref|YP_004598197.1| 214 EAGVTAVSVTHDQEEALsISDRVAVMNEGDIEQIGAPERVFQQPKSRF 261
                                       ***887777777777763567888877755588999999999988887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.6   1.5e-05     0.026       4      29 ..      56      81 ..      54     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      +  il++ G+sG+GKTt+lr ++   
  gi|336255090|ref|YP_004598197.1| 56 DGEILTLLGPSGCGKTTTLRLIAGLE 81
                                      56799**************9987654 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 ?   13.8   0.1   3.4e-05     0.061       2      20 ..      61      79 ..      60     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-05
                                      EEESSTTSSHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavak 20
                                       l Gp G+GKT++ + +a 
  gi|336255090|ref|YP_004598197.1| 61 TLLGPSGCGKTTTLRLIAG 79
                                      589**************97 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 ?   10.9   0.4   0.00023      0.41      61      83 ..     181     203 ..     160     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                           SbcCD_C  61 epalrlvfLDEAFsklDeesiat 83 
                                        p +++++LDE Fs+lD + + +
  gi|336255090|ref|YP_004598197.1| 181 APEPEMLLLDEPFSNLDVDLRVE 203
                                       5789*************987655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.4e-05      0.15      89     129 ..      46      87 ..      30      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.4e-05
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                        + +l+  ++d ++ +l+G+SG GK+t +  +++ ++   g 
  gi|336255090|ref|YP_004598197.1|  46 VIPDLSLSVRDgEILTLLGPSGCGKTTTLRLIAGLETPDAGR 87 
                                       5667777777779**************999998866655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 2933.03
//
Query:       gi|336255091|ref|YP_004598198.1|  [L=158]
Description: hypothetical protein Halxa_3712 [Halopiger xanaduensis SH-6]
Scores for 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  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); 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:                         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: 1187.29
//
Query:       gi|336255092|ref|YP_004598199.1|  [L=633]
Description: type II secretion system protein E [Halopiger xanaduensis SH-6]
Scores for 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  170.4   0.0    5.9e-50  169.8   0.0    1.2  1  T2SSE     Type II/IV secretion system protein
      0.006   15.9   0.1      0.051   12.9   0.0    2.3  2  HEM4      Uroporphyrinogen-III synthase HemD
  ------ inclusion threshold ------
      0.048   13.4   0.0      0.097   12.4   0.0    1.4  1  AAA_29    P-loop containing region of AAA domain
       0.13   11.8   0.0       0.23   11.0   0.0    1.3  1  AAA_7     P-loop containing dynein motor region


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 !  169.8   0.0   1.3e-53   5.9e-50       5     269 ..     198     466 ..     195     470 .. 0.92

  Alignments for each domain:
  == domain 1  score: 169.8 bits;  conditional E-value: 1.3e-53
                             T2SSE   5 leallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrl 80 
                                       le++++d++v d+    ++  ++v    + +++++  +  +++l  ++ r+a++++++is  +p+++ +lp +g r 
  gi|336255092|ref|YP_004598199.1| 198 LEPIMHDPHVEDVSCDGYDLpIFV-YHDEYTDVETTVSFGADELDGFVVRLAQHSGRHISIGEPMVETTLP-DGSRA 272
                                       678999**************9***.6666689***************************************.88888 PP

                             T2SSE  81 rvvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeink 155
                                       +++l   v     a++iRk +++ +t  dl   ++++ ++ + l  a+++++++l++GgT sGKtt+++a+  +i+ 
  gi|336255092|ref|YP_004598199.1| 273 ELALGKEVTPrgSAFTIRKYASEPFTPVDLLEYGTFSVEQMAYLWLAIEHNKSLLFAGGTASGKTTSMNAISMFIPP 349
                                       88876544433699*************************************************************** PP

                             T2SSE 156 sderivtvEDpvEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgs 227
                                       +  +++t+ED++E++l ++n ++ +++      ++vt+ dllr+aLR+rP  i+vGE+R++e++++ +A+nTGH   
  gi|336255092|ref|YP_004598199.1| 350 R-AKVLTIEDTRELELYHDNWLSSVTRervheGKDVTMYDLLRSALRHRPEYIVVGEVRGEEAITLFQAMNTGHTT- 424
                                       *.******************999998889998899*****************************************. PP

                             T2SSE 228 lsTlHansaagalerLeqlgaeveaaelkssilavvdivvrl 269
                                        sT+Ha+s++ a++rLe+   +v++ +++s  ++ v+++ rl
  gi|336255092|ref|YP_004598199.1| 425 YSTMHADSVQTAINRLENEPINVPRSMVQSLDILSVQTLTRL 466
                                       *****************9988899988888777765666555 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   1.1e-05     0.051      86     151 ..     115     184 ..      54     195 .. 0.86
   2 ?    0.0   0.0     0.099   4.4e+02     102     141 ..     507     546 ..     504     572 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                                       HHHHTT---SEE-..SSSHHHHGGGS-.---EEEEEE-SS.S-.......-HHHHHHHHHTTEEEEEE-SEEE CS
                              HEM4  86 aLeelglrvdlvpseegtaegLaeelaeslagkrvlllrgeia.......rddlaegLeergaevdevevYet 151
                                       ++ ++++rv+  p+ ++  + L+e+l e++++   ll r+++a       r+++ e+Le+ gaevd+++ Y+ 
  gi|336255092|ref|YP_004598199.1| 115 SASQHRYRVV-EPQLTEEERVLLETLFEDVRD--PLLYRADDAedvegllRETIHEYLERYGAEVDMATFYRL 184
                                       4555566774.8999999999***99999999..9999999999999999*********************97 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.099
                                       SSHHHHGGGS-.---E.EEEEE-SS.S--HHHHHHHHHTTE CS
                              HEM4 102 gtaegLaeelaeslag.krvlllrgeiarddlaegLeerga 141
                                       gt+  ++ee++ + +g +r  ll +   r+++ e+L+ + +
  gi|336255092|ref|YP_004598199.1| 507 GTGSRVLEEIR-DEQGwSRTELLTELRNRERFLEYLRDNDI 546
                                       7899999****.77777*******************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 ?   12.4   0.0   2.2e-05     0.097      18      50 ..     319     351 ..     298     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                            AAA_29  18 eidlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                        i+ + + l++G + sGK+T + Ai++ + p+ 
  gi|336255092|ref|YP_004598199.1| 319 AIEHNKSLLFAGGTASGKTTSMNAISMFIPPRA 351
                                       45555589*****************99877765 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 ?   11.0   0.0   5.1e-05      0.23      22      55 ..     312     345 ..     307     357 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.1e-05
                             AAA_7  22 ysyllelllknkkpvllvGptGtGKtviikdllk 55 
                                       +   l l ++++k++l+ G t +GKt+ ++ +  
  gi|336255092|ref|YP_004598199.1| 312 QMAYLWLAIEHNKSLLFAGGTASGKTTSMNAISM 345
                                       555667889*******************998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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 0.24s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4604.26
//
Query:       gi|336255093|ref|YP_004598200.1|  [L=710]
Description: type II secretion system F domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-37  128.4  15.3    2.4e-21   76.0   2.5    3.4  3  T2SSF     Type II secretion system (T2SS), protein F
    0.00034   19.5   3.3        0.3    9.8   0.0    3.2  3  DUF2207   Predicted membrane protein (DUF2207)
  ------ inclusion threshold ------
       0.18   12.1  12.9        1.7    8.9   0.2    4.2  4  DUF4064   Protein of unknown function (DUF4064)


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 ?   -1.6   0.9      0.41   2.4e+03     100     120 ..      73      93 ..      68      99 .. 0.72
   2 !   60.6   0.2   2.4e-20   1.4e-16       4     124 ..     180     306 ..     177     307 .. 0.95
   3 !   76.0   2.5   3.9e-25   2.4e-21       2     123 ..     494     618 ..     493     620 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.41
                                       HHHHTTXXXXXXXXXXXXXXX CS
                             T2SSF 100 aallepllllvvallvllill 120
                                       + +l+ +l++v +++v++ ++
  gi|336255093|ref|YP_004598200.1|  73 TTMLYAMLFAVAGSIVGIYVV 93 
                                       567888888777777777665 PP

  == domain 2  score: 60.6 bits;  conditional E-value: 2.4e-20
                                       HHHHHHHTT--HHHHHHHHHHHHS.SHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHH CS
                             T2SSF   4 qlatllsaGvplveaLellaeeae.ngplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageeg 74 
                                        ++ l+++G+ + +++++la++ + +g+ a e+  ++r+++  g ++ +al+    r+ps++f+++v +l+++ ++g
  gi|336255093|ref|YP_004598200.1| 180 FMYALSRSGMEFPKIVRILARHEDtYGEAAAEFGVAVRNMDTFGmDVITALQttgrRSPSPKFADFVENLVSVLQSG 256
                                       6999*******************9*****************988777888888888********************* PP

                                       T-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  75 gnLaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                        +L+ +Le   ++++ee e+++++  +ll++l++++v++lv+++l++i++
  gi|336255093|ref|YP_004598200.1| 257 NSLSTFLETQYRDFQEESESQQESTIELLGTLAEAYVTVLVAGPLFLITI 306
                                       **********************************************9986 PP

  == domain 3  score: 76.0 bits;  conditional E-value: 3.9e-25
                                       HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC...T-TT.TS.-HHHHHHHHHHHHH CS
                             T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale...rtpssef.pelvvqlirageeg 74 
                                       l+ la+   aG+plv a++ +  ++  g l+ el+ri +++++G +l +ale   r+ ++   +++v+ +++a  ++
  gi|336255093|ref|YP_004598200.1| 494 LERLASVNDAGMPLVSAIDQVRGSD-LGTLGAELDRIWADVQWGADLQTALErfgRRVRTRAtSRVVTLVTEAMNAS 569
                                       7889*********************.**************************77733346666************** PP

                                       T-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  75 gnLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                       gnLa vL  +a++  ++r+l+r+++ a+ e+l+++++a++v+l+++++l
  gi|336255093|ref|YP_004598200.1| 570 GNLATVLTIAARQAAADRRLKRERKQAMVEYLVVVYIAFFVFLFIITVL 618
                                       *********************************************9987 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.4    0.0033        20     372     442 ..      67     166 ..      45     172 .. 0.75
   2 !    9.8   0.0     5e-05       0.3     338     443 ..     248     353 ..     210     356 .. 0.70
   3 !    5.0   0.1    0.0014       8.7     367     409 ..     585     662 ..     536     710 .] 0.64

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0033
                           DUF2207 372 fdkkgkkklkklsalglgliilglilillallllvll.............................lvfllilllil 419
                                       +++ g + + +  ++++++ i+g++++ ++l++l++                              + ++++ +l +
  gi|336255093|ref|YP_004598200.1|  67 YREYGATTMLYAMLFAVAGSIVGIYVVWGLLFVLAVDpaamrealpgtlaflanlggvpslsptelFGLFALSCLTI 143
                                       45555555555555555555555555555555444448899**********************99999999999999 PP

                           DUF2207 420 lliaiivlllfsrllgrrteeGa 442
                                       + +a + ++++++  + + ++G+
  gi|336255093|ref|YP_004598200.1| 144 GTVAGFGAYWLRWWYPSYVADGR 166
                                       99999999999999999988887 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 5e-05
                           DUF2207 338 eikkyakkskkkakkfkkalkkwksavkkkergyfdkkgkkklkklsalglgliilglilillallllvlllvflli 414
                                       ++ + +++ +++ + + +++++++++ +++++  ++  g    +++ +l  g ++l++il+++++ + +++  + ++
  gi|336255093|ref|YP_004598200.1| 248 NLVSVLQSGNSLSTFLETQYRDFQEESESQQESTIELLGTLAEAYVTVLVAGPLFLITILVVIGISVGNTFDPLRAL 324
                                       44444555555677778889999999999777777777666666666666666666666666666666666999*** PP

                           DUF2207 415 lllillliaiivlllfsrllgrrteeGae 443
                                       + lil+l ++++++++s++++  t+ G +
  gi|336255093|ref|YP_004598200.1| 325 IYLILPLGNVAFIVYLSMVTDTITPGGVA 353
                                       ******************99999999865 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0014
                           DUF2207 367 kergyfdkkgkkklkklsalglgliilglilillallllvll................................... 408
                                       + r++ ++++++   +l +++++++++++i+++la++ll  l                                   
  gi|336255093|ref|YP_004598200.1| 585 ADRRLKRERKQAMVEYLVVVYIAFFVFLFIITVLAAFLLPNLptegieaasggsggggggggidglgglsqnaaaqy 661
                                       45666677777777777788888888888877777777665566666666666666666666666666666666665 PP

                           DUF2207 409 l 409
                                       +
  gi|336255093|ref|YP_004598200.1| 662 N 662
                                       1 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2   0.00029       1.7      19      79 ..      37      93 ..      32      99 .. 0.87
   2 ?   -2.9   0.2       1.4   8.3e+03       8      29 ..     133     154 ..     130     159 .. 0.72
   3 ?    2.2   0.3     0.037   2.2e+02      42      78 ..     266     311 ..     246     334 .. 0.46
   4 ?    7.5   0.2   0.00083         5      52      82 ..     593     623 ..     556     631 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00029
                           DUF4064 19 lglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgivga 79
                                      +gl++++++ + ++ +++q+ +     ++++a+++ e+  t++++++++a+  +++gi  +
  gi|336255093|ref|YP_004598200.1| 37 IGLFGGYVAEFKGEHPNRQSALR----AAHFATTYREYGATTMLYAMLFAVAGSIVGIYVV 93
                                      78999999999999999988765....789999999*********************9765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                           DUF4064   8 LglIGgilgillglllllflfl 29 
                                       +gl + ++  +++++++++++l
  gi|336255093|ref|YP_004598200.1| 133 FGLFALSCLTIGTVAGFGAYWL 154
                                       5677777777777777777665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.037
                           DUF4064  42 e....qalsgedasavleflstllivlgvi.....aliaivlgivg 78 
                                       +    q+ s++ ++++ e l+tl  ++ ++     ++++++l ++g
  gi|336255093|ref|YP_004598200.1| 266 QyrdfQEESESQQESTIELLGTLAEAYVTVlvagpLFLITILVVIG 311
                                       2444533334444444433333332222221112222333333333 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.00083
                           DUF4064  52 avleflstllivlgvialiaivlgivgalll 82 
                                          ++++ l++v++ ++++++++++++a+ll
  gi|336255093|ref|YP_004598200.1| 593 RKQAMVEYLVVVYIAFFVFLFIITVLAAFLL 623
                                       4457889999999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (710 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.41
# Mc/sec: 5148.86
//
Query:       gi|336255094|ref|YP_004598201.1|  [L=243]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-20   72.0   0.1    8.1e-20   71.3   0.1    1.4  1  Methyltransf_11  Methyltransferase domain
    2.4e-19   69.8   0.1      6e-19   68.6   0.1    1.6  2  Methyltransf_25  Methyltransferase domain
    1.3e-12   47.8   0.0    1.8e-12   47.3   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    3.8e-09   37.2   0.0    7.1e-09   36.3   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    7.2e-06   25.5   0.0    9.4e-06   25.1   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00034   20.5   0.0    0.00051   19.9   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0021   17.9   0.2     0.0073   16.2   0.2    1.7  1  Methyltransf_8   Hypothetical methyltransferase
  ------ inclusion threshold ------
      0.059   13.0   0.0      0.081   12.5   0.0    1.1  1  NodS             Nodulation protein S (NodS)


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 !   71.3   0.1   3.6e-23   8.1e-20       1      95 [.      70     167 ..      70     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 3.6e-23
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-... CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv... 74 
                                       Ld+GcG+ r+ae la  +++vvg+D s  +l++ +e+++e+g+ v++ ++da++lp++ + +D+ v   +lhh+   
  gi|336255094|ref|YP_004598201.1|  70 LDLGCGNCRHAELLAADCETVVGLDASRGLLETGRERGRERGFDVTLCQGDASSLPLAADCVDIAVYVATLHHLptr 146
                                       8*************************************************************************998 PP

                                       CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                       e +++ l+e+aRvL p+G+ +
  gi|336255094|ref|YP_004598201.1| 147 EVRRASLNELARVLSPDGRAL 167
                                       89999*************976 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       6.6   1.5e+04      80      94 ..      41      55 ..      23      63 .. 0.56
   2 !   68.6   0.1   2.7e-22     6e-19       2      97 .]      70     164 ..      70     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.6
                                      HHHHHHHHHHHHHEE CS
                   Methyltransf_25 80 edlekalkeiarvLk 94
                                      +++e +++e a +L+
  gi|336255094|ref|YP_004598201.1| 41 PEVESFVDERAAALE 55
                                      455555555555544 PP

  == domain 2  score: 68.6 bits;  conditional E-value: 2.7e-22
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhls 78 
                                       LdlGcG+ r+++ la+ +  ++v+g+D s ++le+ rer +e+g++v++ qgda++lp++++ +D+ v + +lhhl+
  gi|336255094|ref|YP_004598201.1|  70 LDLGCGNCRHAELLAADC--ETVVGLDASRGLLETGRERGRERGFDVTLCQGDASSLPLAADCVDIAVYVATLHHLP 144
                                       8****************9..9************************************************988***87 PP

                                       HHHH.HHHHHHHHHHEEEEE CS
                   Methyltransf_25  79 dedl.ekalkeiarvLkpgG 97 
                                        +++ ++ l+e+arvL p+G
  gi|336255094|ref|YP_004598201.1| 145 TREVrRASLNELARVLSPDG 164
                                       76651677**********99 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   8.1e-16   1.8e-12       8     113 ..      70     172 ..      66     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 8.1e-16
                   Methyltransf_31   8 lDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                       lDlGCG+ + +  la     ++e vvG+D s   +e  re+ ++ g+d v+++qgd+ +l+  l+ +++D+ +  ++
  gi|336255094|ref|YP_004598201.1|  70 LDLGCGNCRHAELLA-A---DCEtVVGLDASRGLLETGRERGRERGFD-VTLCQGDASSLP--LAADCVDIAVYVAT 139
                                       9******99999999.3...3444***********************8.************..889*********** PP

                   Methyltransf_31  84 lnaladp...dkileeiervlkpggilliedpr 113
                                       l++l+      + l+e+ rvl+p+g+ l++  +
  gi|336255094|ref|YP_004598201.1| 140 LHHLPTRevrRASLNELARVLSPDGRALVSAWS 172
                                       *999986222699*************9998766 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   3.2e-12   7.1e-09       1      98 [.      70     165 ..      70     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 3.2e-12
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       L++GcG+ + ++ l+++    +++g+D s+  +e  +e+ ++r+      v+l + d+++l+   + +D+ v   +l
  gi|336255094|ref|YP_004598201.1|  70 LDLGCGNCRHAELLAAD--CETVVGLDASRGLLETGRERGRERGF----DVTLCQGDASSLPLAaDCVDIAVYVATL 140
                                       8***************9..88899*********888888777775....555555555555555579********** PP

                   Methyltransf_12  77 hhl...kdirevldnirklLkpgGr 98 
                                       hhl   + +r++l++++++L+p+Gr
  gi|336255094|ref|YP_004598201.1| 141 HHLptrEVRRASLNELARVLSPDGR 165
                                       *****88888**************7 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   4.2e-09   9.4e-06      49     154 ..      67     171 ..      19     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.2e-09
                                       TEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES- CS
                   Ubie_methyltran  49 akvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfG 125
                                       a  lD+ +G    a  l+       +vv+lD +  +L++g+++ +e+g+ ++ + q++a  Lp   d  D+      
  gi|336255094|ref|YP_004598201.1|  67 AVGLDLGCGNCRHAELLAADC---ETVVGLDASRGLLETGRERGRERGF-DVTLCQGDASSLPLAADCVDIAVYVAT 139
                                       366899999888877666554...489********************97.8*******************9888888 PP

                                       GGG-S-H...HHHHHHHHHHEEEEEEEEEEEE CS
                   Ubie_methyltran 126 lrnvtDk...lkaLkeayrvlkpGGrlvvlef 154
                                       l  ++ +     +L+e+ rvl p Gr +v   
  gi|336255094|ref|YP_004598201.1| 140 LHHLPTRevrRASLNELARVLSPDGRALVSAW 171
                                       8887765111579************9887655 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.3e-07   0.00051      21     160 ..      64     223 ..      32     228 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.3e-07
                   Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaae....pqgkfd 84 
                                        +++  Ld+GcG  + +e+l++   +v+g D+s+ + e  +          + ++ +               ++  d
  gi|336255094|ref|YP_004598201.1|  64 AEPAVGLDLGCGNCRHAELLAADCETVVGLDASRGLLETGRergrergfdVTLCQGDA--------SslplAADCVD 132
                                       467799**************99988********9776665565553333222222222........1233366799* PP

                   Methyltransf_23  85 lIvlrevlehvpd...ppellrqiatllkpgGylllseplasl.......kedrllld.........wlylvpag.. 140
                                       ++v   +l+h+p      + l+ +a+ l+p+G++l+s +   +       +                w+++  +   
  gi|336255094|ref|YP_004598201.1| 133 IAVYVATLHHLPTrevRRASLNELARVLSPDGRALVSAWSTAHdrfdadpE------AaggfdttveWTLPGGEAvd 203
                                       ************63335589*****************99655444433331......02233334444443222222 PP

                   Methyltransf_23 141 rhisffsarslkelleeaGl 160
                                       r  + +   +++ +l +++l
  gi|336255094|ref|YP_004598201.1| 204 RFYHIYAPAEFEADLAASDL 223
                                       44555555566555555555 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   3.3e-06    0.0073      75     156 ..      68     168 ..      40     180 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.3e-06
                                       -EEEES-TT-HHHHH.--S-..EEEEE....SS-SST........TEEES..-TTS-S--TT-EEEEEEES---S.. CS
                    Methyltransf_8  75 vvadlGcGeakiaea.vrekekvrsfd....lvavne........rvvac..dlakvPledesvdvavfclslmg.. 134
                                       v  dlGcG+++ ae    + e v  +d    l   +         +v+ c  d + +Pl+ + vd+av+  +l    
  gi|336255094|ref|YP_004598201.1|  68 VGLDLGCGNCRHAELlAADCETVVGLDasrgLLETGRergrergfDVTLCqgDASSLPLAADCVDIAVYVATLHHlp 144
                                       557**********65156778999999444422222112222233689886678***************98875411 PP

                                       .S-H.HHHHHHHHHHEEEEEEEEE CS
                    Methyltransf_8 135 .tnl.adflkeanrvlkvGGllkv 156
                                         ++ +  l+e  rvl + G   v
  gi|336255094|ref|YP_004598201.1| 145 tREVrRASLNELARVLSPDGRALV 168
                                       133314679999999999887665 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.6e-05     0.081      46     143 ..      68     167 ..      43     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
                              NodS  46 dalevGcaaGalterlapyckrltvvdvveeaiararervkess.hiswivsdvqqfstde.kfdlivvaevlyyie 120
                                         l++Gc     +e la  c+ +  +d     ++  rer +e   +++  + d   + + +   d+ v    l+++ 
  gi|336255094|ref|YP_004598201.1|  68 VGLDLGCGNCRHAELLAADCETVVGLDASRGLLETGRERGRERGfDVTLCQGDASSLPLAAdCVDIAVYVATLHHLP 144
                                       4699*********************************99988644999********9976516899999******** PP

                              NodS 121 dvaelraavrnlvsllapdgqlv 143
                                         +  ra++++l ++l+pdg+ +
  gi|336255094|ref|YP_004598201.1| 145 TREVRRASLNELARVLSPDGRAL 167
                                       *******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1895.95
//
Query:       gi|336255095|ref|YP_004598202.1|  [L=316]
Description: hypothetical protein Halxa_3716 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0015   17.9  10.3       0.04   13.2   0.5    3.7  4  PSII_BNR    Photosynthesis system II assembly factor YCF48
  ------ inclusion threshold ------
       0.14   12.1   0.8       0.52   10.3   0.1    2.1  2  DUF4314     Domain of unknown function (DUF4314)


Domain annotation for each model (and alignments):
>> PSII_BNR  Photosynthesis system II assembly factor YCF48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.2    0.0019        17       4      79 ..      30     104 ..      27     109 .. 0.67
   2 !   13.2   0.5   4.4e-06      0.04     199     299 ..      98     198 ..      88     202 .. 0.75
   3 !    2.2   0.2    0.0099        89     228     299 ..     211     276 ..     200     278 .. 0.65
   4 !    4.7   0.2    0.0017        15      19      53 ..     256     287 ..     245     303 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0019
                                       -SS--EEEEE-S-SS-EEEEEESSSS-EEEEETTTEEEEESSTTSS-EE-----S--.--EEEEEEEETTEE..EEE CS
                          PSII_BNR   4 assspWevvelptestllDiaftdekhGflvGtkatlletlDGGktWeersldleeevnyrlesvsfkgdeg..wiv 78 
                                       ++ s+W v e p++st+ D+  t +++ + v +  +++e +D G  We             l  v+ ++d g  wiv
  gi|336255095|ref|YP_004598202.1|  30 EEESTWTVAESPIDSTVHDVIHT-ATNAHAVASGGLVIERTDAG--WEVVLQGGPTGNGNDLYGVDTTDDGGrlWIV 103
                                       67899**************9877.34456788899999*99998..5544433333334445555555444333666 PP

                                       E CS
                          PSII_BNR  79 G 79 
                                       G
  gi|336255095|ref|YP_004598202.1| 104 G 104
                                       6 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.4e-06
                                       S-EEEEETTTEEEEEE.TTEEEEE---B-TTSS--S-EEEEEES...SSS-EEEEESTT-EEEESSTTSS-EE-GGG CS
                          PSII_BNR 199 gelWllarGgelqfsdeeedeeefsealapiksngyglldlayr...dekeiwvaGGsgtllvskDgGktwkkdksa 272
                                       g+lW++   g++   d   ++ +  +  ap    + ++ d+a +    + +++va  sg++ +s ++G++ + d ++
  gi|336255095|ref|YP_004598202.1|  98 GRLWIVGASGAIGEYD--VTTGNLVDRSAPN-DFTANFNDVAVTgpaGDADVYVADDSGSIHYSFENGEEGTWDYEV 171
                                       5677776665555444..3444444444443.4455666766651114689************************** PP

                                       TTSSS---EEEEEETTEEEEE-STTEE CS
                          PSII_BNR 273 ekvpsnlykikfleedkgfvlGerGvl 299
                                           s + +++f ++  g+v+  +G +
  gi|336255095|ref|YP_004598202.1| 172 PGSGSGFNAVEFYDDRAGHVIDTNGKV 198
                                       **********************99986 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.0099
                                       TTSS--S-EEEEEESSSS-EEEEESTT-EEEESSTTSS-EE-GGGTTSSS---EEEEEETTEEEEE-STTEE CS
                          PSII_BNR 228 piksngyglldlayrdekeiwvaGGsgtllvskDgGktwkkdksaekvpsnlykikfleedkgfvlGerGvl 299
                                        i+ +g+ +  l  +  +++ v+GG+++++    +G  w  ++  +   ++l++++  e+  g+++G  Gv+
  gi|336255095|ref|YP_004598202.1| 211 GIEDAGVTFYGLDSDAADDVVVSGGNASVFE--YDGSRWVPESLGD---ADLLDVEI-EDGDGYAVGGGGVI 276
                                       4556777788888888888999999988874..5677787766654...56666664.44556666666665 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.0017
                                       -EEEEEESSSS-EEEEETTTEEEEESSTTSS-EE- CS
                          PSII_BNR  19 tllDiaftdekhGflvGtkatlletlDGGktWeer 53 
                                        llD++ + + +G+ vG   +++e +DG  +W++ 
  gi|336255095|ref|YP_004598202.1| 256 DLLDVEIE-DGDGYAVGGGGVIFEQTDG--EWSQV 287
                                       45666654.4557777777777777777..35444 PP

>> DUF4314  Domain of unknown function (DUF4314)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   5.8e-05      0.52      38      55 ..     146     163 ..     133     166 .. 0.87
   2 ?   -1.0   0.1      0.19   1.7e+03      25      44 ..     185     204 ..     175     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.8e-05
                           DUF4314  38 VkgVDDiGtihvkWdnGs 55 
                                       V   DD G+ih +++nG 
  gi|336255095|ref|YP_004598202.1| 146 VYVADDSGSIHYSFENGE 163
                                       7788*************7 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.19
                           DUF4314  25 deqaplppGtkGtVkgVDDi 44 
                                       d+ a    +t+G+V + DD 
  gi|336255095|ref|YP_004598202.1| 185 DDRAGHVIDTNGKVFATDDG 204
                                       44455567899999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2549.11
//
Query:       gi|336255096|ref|YP_004598203.1|  [L=142]
Description: hypothetical protein Halxa_3717 [Halopiger xanaduensis SH-6]
Scores for 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:                       464  (0.0258799); 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:                         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 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1119.26
//
Query:       gi|336255097|ref|YP_004598204.1|  [L=770]
Description: multi-sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for complete 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  131.7   9.9    1.5e-12   47.7   0.3    3.9  4  PAS_4        PAS fold
    5.2e-29  101.0   0.0    1.5e-27   96.3   0.0    2.5  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    3.8e-18   65.7   0.0    9.5e-08   32.2   0.0    3.7  3  PAS_9        PAS domain
    2.3e-12   47.4   3.0      5e-12   46.3   1.5    2.4  2  GAF_2        GAF domain
    2.4e-11   44.4   0.1    6.3e-11   43.0   0.1    1.8  1  GAF          GAF domain
    4.7e-10   39.9   0.0    8.2e-10   39.1   0.0    1.4  1  GAF_3        GAF domain
    1.9e-09   37.4   1.5    3.2e-08   33.5   0.1    3.3  2  HisKA        His Kinase A (phospho-acceptor) domain
    1.8e-05   24.7   0.1       0.19   11.8   0.0    4.0  4  PAS          PAS fold
    4.2e-05   23.4   0.0    0.00011   22.1   0.0    1.7  2  HATPase_c_5  GHKL domain
    0.00013   21.9   0.5     0.0004   20.4   0.1    2.0  2  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.011   16.0   2.0        1.5    9.1   0.0    4.1  5  PAS_3        PAS fold
      0.026   14.3   0.0      0.058   13.2   0.0    1.5  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like


Domain annotation for each model (and alignments):
>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.2   1.1e-15   1.7e-12       2     109 ..     185     285 ..     184     286 .. 0.96
   2 !   47.7   0.3     1e-15   1.5e-12       7     110 .]     308     415 ..     302     415 .. 0.93
   3 !   41.0   0.2   1.2e-13   1.8e-10       6     110 .]     436     536 ..     431     536 .. 0.91
   4 ?   -3.1   0.0       6.1   9.1e+03      73      98 ..     706     733 ..     698     738 .. 0.74

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.1e-15
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       d++ da++ l++d  ++y+N +aael+ +++e l+G+t ++++ +++   l++ ++r+le++e+ +f+ ++   + e
  gi|336255097|ref|YP_004598204.1| 185 DRITDAFYSLNADWEFTYLNDRAAELIDFTGEGLRGETIWDVFEWGADSTLREEYERALETQESTSFEFYYPE-PLE 260
                                       678899*************************************************************998888.999 PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTerr 109
                                        ++e++++P +       g+ v++rD+Ter+
  gi|336255097|ref|YP_004598204.1| 261 TWFEVHAYPSET------GLSVYFRDVTERV 285
                                       *********966......************8 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 1e-15
                             PAS_4   7 alavldpdgrvlyaNaaaaelfgappeellGktlae..llpee..daarleralrrvlegeepiefleelllpgeer 79 
                                       ++  l pdg+v+++N +a++++ a+ e+++G++++e  ++ e+  +++++++  +r+++ge + ++++ ++++g + 
  gi|336255097|ref|YP_004598204.1| 308 LVGLLEPDGTVIDINGTAMAYIDADLEAVRGEPFWEtpWWGEGddVGDDVREWTERAAAGEYVEFEADLTRPDGNRY 384
                                       677889*****************************76699998999**************999999999999***** PP

                             PAS_4  80 hyelrllPlrdesGevigvlvisrDiTerrr 110
                                       ++e +++P+ d++G+v+ ++v  rD++er+r
  gi|336255097|ref|YP_004598204.1| 385 TLEGTFRPVTDDDGDVVSIIVSDRDVSERKR 415
                                       *****************************97 PP

  == domain 3  score: 41.0 bits;  conditional E-value: 1.2e-13
                             PAS_4   6 dalavl.dpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhy 81 
                                        +++   d++ r++ a  ++ + + ++p ++ G  + +++p+++ ++le+a +++l+ge+++++ e      ++r +
  gi|336255097|ref|YP_004598204.1| 436 NGIVTMfDEERRYTLAAGRMFDELPVSPSDVEGAYVGDVWPDHVSEPLEEAFEAALAGERRATEFE-----YAGREW 507
                                       5555444************8888************************************9999999.....5778** PP

                             PAS_4  82 elrllPlrdesGevigvlvisrDiTerrr 110
                                        +r++P+ d++G+v   + i++DiTer++
  gi|336255097|ref|YP_004598204.1| 508 IVRAVPITDDNGDVFSGITIAQDITERKE 536
                                       ***************************85 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 6.1
                             PAS_4  73 llpgeerhyelrl..lPlrdesGevigv 98 
                                       +++ ++r++e++   +   d++G+ ig+
  gi|336255097|ref|YP_004598204.1| 706 DPDEADRVFEVFQrlHSHSDHQGTGIGL 733
                                       5578899999987668888888886665 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 ?    1.8   0.0      0.22   3.3e+02      29      55 ..     622     652 ..     595     655 .. 0.62
   2 !   96.3   0.0     1e-30   1.5e-27       1     109 [.     656     764 ..     656     766 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.22
                                       EEEEE..EE..TEEEEEEEESSSSSTTHHHT CS
                         HATPase_c  29 veika..se..ddlvisveDnGiGipkedlk 55 
                                       + ++a   +  ddl++++eD+   i+ + l+
  gi|336255097|ref|YP_004598204.1| 622 IDLNAvlADvlDDLRLQIEDTDAEIDADALP 652
                                       3444333225689*************99987 PP

  == domain 2  score: 96.3 bits;  conditional E-value: 1e-30
                                       EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSS CS
                         HATPase_c   1 gdekrLrqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtG 75 
                                       gd ++Lrq+++nl++Na+++ + ++  +v+i+a+   d+ vi+v D GiG+++++ +++fe f++  ++ ++++gtG
  gi|336255097|ref|YP_004598204.1| 656 GDASQLRQVFQNLLSNALEY-SGDEPPRVRIDAERrgDRWVITVADEGIGMDPDEADRVFEVFQR-LHSHSDHQGTG 730
                                       7899****************.55556677777533459***************************.8889999**** PP

                                       HHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  76 lGlsivkklvelmgGeiwvesepgrGttftftlp 109
                                       +Gl++++++ve++gG+iwv+sep++G tf ftlp
  gi|336255097|ref|YP_004598204.1| 731 IGLALCERIVERHGGDIWVDSEPDEGATFSFTLP 764
                                       ********************************99 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-05     0.017       6     104 .]     193     283 ..     188     283 .. 0.77
   2 !   32.2   0.0   6.4e-11   9.5e-08       6     104 .]     311     412 ..     305     412 .. 0.91
   3 !   13.9   0.0   3.3e-05      0.05      15     104 .]     451     533 ..     435     533 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                             PAS_9   6 idnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvllta 82 
                                         n d + +y N+ a++l+ ++ e + g  i+d+f +   +    +++ ++++ ++++   ++++++  + w++++a
  gi|336255097|ref|YP_004598204.1| 193 SLNADWEFTYLNDRAAELIDFTGEGLRGETIWDVF-EWGADSTLREEYERALE-TQESTSFEFYYPEPLETWFEVHA 267
                                       456777889**************************.44444444445555555.6778888888888899******* PP

                             PAS_9  83 spvkdddgelvgiivilrDite 104
                                       +p        +g+ v +rD+te
  gi|336255097|ref|YP_004598204.1| 268 YPSE------TGLSVYFRDVTE 283
                                       **93......445599999997 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 6.4e-11
                             PAS_9   6 idnpdgrilyaNeaalrllGyspeevlgksitdlf.....vtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       +  pdg+++++N +a+  +  + e+v g +++++      ++  ++ ++  +   +g+    e+e +l+r++g+++ 
  gi|336255097|ref|YP_004598204.1| 311 LLEPDGTVIDINGTAMAYIDADLEAVRGEPFWETPwwgegDDVGDDVREWTERAAAGE--YVEFEADLTRPDGNRYT 385
                                       367*********************************9988888888888888888888..9**************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                        + t++pv dddg +v+iiv  rD++e
  gi|336255097|ref|YP_004598204.1| 386 LEGTFRPVTDDDGDVVSIIVSDRDVSE 412
                                       ********************9999997 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 3.3e-05
                             PAS_9  15 yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvkdddge 91 
                                        a +++ +l   sp +v g ++ d+   +++  e l++a+e+    + e+  ++    g++    ++a+p+ dd+g 
  gi|336255097|ref|YP_004598204.1| 451 AAGRMFDEL-PVSPSDVEGAYVGDVW--PDHVSEPLEEAFEAAL--AGERRATEFEYAGREWI--VRAVPITDDNGD 520
                                       444444444.27899***********..8888888888888888..55555555555554444..8*********** PP

                             PAS_9  92 lvgiivilrDite 104
                                       +++ i i +Dite
  gi|336255097|ref|YP_004598204.1| 521 VFSGITIAQDITE 533
                                       ************8 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   1.5   3.4e-15     5e-12       2     138 .]      32     172 ..      31     172 .. 0.84
   2 ?   -1.6   0.0       2.1   3.1e+03      15      44 ..     430     458 ..     426     496 .. 0.65

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 3.4e-15
                                       HHHHHHHHHHHHHHHH.SS..EEEEEEE-TTS-..EEEE..EEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES- CS
                             GAF_2   2 adleelldlvldelve.lgaalgyillvdddgg..lrla..awgeaeeefgaaldrplgeglvgealrtgrpvilnd 73 
                                        dle+ll  + +++++ lg ++g +  +d+d++  l  +    g  ++++gaa+ ++ +++  g+al++  pvi++d
  gi|336255097|ref|YP_004598204.1|  32 NDLEQLLADAASTIADtLGNEYGAVFDLDPDDEraL--LrrGVGWSDDRVGAATVPAASDCQPGRALEESDPVIVAD 106
                                       699*************6699***9999997766232..2566667777777777557788867************** PP

                                       GGG-S-HHHHH.HHHHTT--EEEEEE.-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  74 leedpdkkglp.aghaglrsflavPl.isegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                        ++d++ +++   +++g+ s+++  +  +++ + Gvl+ ya++p+a +e d  +++++a+ +a+aie
  gi|336255097|ref|YP_004598204.1| 107 RRTDDRFDAADlFADHGVVSGVSARIgSADD-PWGVLGTYATEPQAVSEHDANFVQSIANVLATAIE 172
                                       777777777777**************55565.**********************************8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.1
                                       HHHSS..EEEEEEE-TTS-EEEEEEEES-T CS
                             GAF_2  15 lvelgaalgyillvdddgglrlaawgeaee 44 
                                       l+e ++  g++ + d++++++laa ++ +e
  gi|336255097|ref|YP_004598204.1| 430 LAE-NFPNGIVTMFDEERRYTLAAGRMFDE 458
                                       455.67789999999998887775554333 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.1   4.2e-14   6.3e-11       1     133 []      33     171 ..      33     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 4.2e-14
                                       SHHHHHHHHHHHHHHHHTESEEEEEEEEETTE.EECEEEEECCEEEETTSHHHH........HHHHHSSSEEESTGG CS
                               GAF   1 dleelldtvveelrellgadrvalylpdydGl.hydipqasrwlfmkngrgicg........qvlatgqplvipdst 68 
                                       dle+ll+ ++++++++lg +++a++  d d+     +  +  w+ +++g   +         ++l++ +p++++d +
  gi|336255097|ref|YP_004598204.1|  33 DLEQLLADAASTIADTLGNEYGAVFDLDPDDErAL-LRRGVGWSDDRVGAATVPaasdcqpgRALEESDPVIVADRR 108
                                       89***********************9445553244.77777775555533311123334455*************99 PP

                                       TSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHHH CS
                               GAF  69 pdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvaval 133
                                       +d+rf +    dl++ +g++s +++ + + ++ wG+l  + + p   ++++ +++q++a+ +a a+
  gi|336255097|ref|YP_004598204.1| 109 TDDRFDA---ADLFADHGVVSGVSARIGSADDPWGVLGTYATEPqAVSEHDANFVQSIANVLATAI 171
                                       *******...89*****************************999667****************997 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   5.5e-13   8.2e-10       1     129 []      33     173 ..      33     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 5.5e-13
                             GAF_3   1 sldellekllkllvkllgaevgalllldedgnklqvaagw.dgkpalse..sld.edsalarralssgevvse.... 69 
                                       +l++ll+++++ ++++lg e+ga++ ld+d +++  ++g     +++    +++ + ++   ral++  +v++    
  gi|336255097|ref|YP_004598204.1|  33 DLEQLLADAASTIADTLGNEYGAVFDLDPDDERALLRRGVgWSDDRV-GaaTVPaASDCQPGRALEESDPVIVadrr 108
                                       799****************************9887777663244444.43466644445455**********98888 PP

                             GAF_3  70 ..psfaeedglpdraala.vPLvagr..qviGvlalastkprafdaedlelleslArqiataier 129
                                          +f+++d   d+ ++  v+ ++g+   + Gvl+ + t+p+a ++ d+ +++s+A+++ataie+
  gi|336255097|ref|YP_004598204.1| 109 tdDRFDAADLFADHGVVSgVSARIGSadDPWGVLGTYATEPQAVSEHDANFVQSIANVLATAIEN 173
                                       8777788999999***999******999************************************8 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1   2.2e-11   3.2e-08       2      66 ..     548     614 ..     533     615 .. 0.95
   2 ?    1.0   0.1      0.31   4.6e+02      31      59 ..     641     669 ..     621     675 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.2e-11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l++f+   +H+L  PL  ++ ++ ++  +  ++ + + +e+l+ ++++a+r++++++ lL++srie+
  gi|336255097|ref|YP_004598204.1| 548 LEQFAYAASHDLQEPLRMVSSYLRLIDTQygDAFDADGEEFLAFAVDGADRMREMIDGLLEYSRIET 614
                                       7899**********************5556989999*****************************97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.31
                                       .T-HSSCHHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  31 gklteelkeyletiesearrldhlvedlL 59 
                                       +   e  +++l t+e  a +l+++ ++lL
  gi|336255097|ref|YP_004598204.1| 641 DTDAEIDADALPTVEGDASQLRQVFQNLL 669
                                       345688889999999*********99997 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00012      0.19       3      71 ..     180     248 ..     175     253 .. 0.89
   2 ?   -0.1   0.0      0.59   8.8e+02      64     100 ..     287     332 ..     276     338 .. 0.67
   3 !    6.8   0.0    0.0043       6.4      54     112 ..     351     409 ..     296     410 .. 0.75
   4 ?    0.0   0.0      0.56   8.3e+02      39     104 ..     464     522 ..     426     531 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT- CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgee 71 
                                       l+++ + ++d+   +++d +++y N+ a+el  ++ e + g+++ d++    d++l+e++e++le++e+
  gi|336255097|ref|YP_004598204.1| 180 LETLHDRITDAFYSLNADWEFTYLNDRAAELIDFTGEGLRGETIWDVFEWGADSTLREEYERALETQES 248
                                       555556699***************************************999999999999999999886 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.59
                                       HHHHHTT-ECCCCEEEEC.............TTSSEEEEEEEEEEEEETT CS
                               PAS  64 qlleqgeesrageisfkl.............rdgrpihlevraspvrdag 100
                                       +  e  + +r +e                  +dg++i +  +a  ++da+
  gi|336255097|ref|YP_004598204.1| 287 REHELEQTERRFE----AifedpnilvgllePDGTVIDINGTAMAYIDAD 332
                                       3333333333334....344448888899999*******99999999986 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0043
                                       HHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                               PAS  54 ddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeilgflgvlrd 112
                                       dd  +  + ++ ++++ e   +e +++++dg  + le + +pv+d +g +  +++  rd
  gi|336255097|ref|YP_004598204.1| 351 DDVGDDVREWTERAAAGEYVEFEADLTRPDGNRYTLEGTFRPVTDDDGDVVSIIVSDRD 409
                                       5556666777888888999999999999*********************9988886555 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.56
                                       HHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTEEEE CS
                               PAS  39 eevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdaggeil 104
                                       ++v g  + d+++   +  + e le++ e++  ++   + f++     +++ vra+p++d  g + 
  gi|336255097|ref|YP_004598204.1| 464 SDVEGAYVGDVWPD--H--VSEPLEEAFEAALAGERRATEFEY---AGREWIVRAVPITDDNGDVF 522
                                       55555555555542..2..555555555555555554444555...77999999999999998764 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       8.3   1.2e+04       5      21 ..     158     174 ..     155     182 .. 0.67
   2 !   22.1   0.0   7.3e-08   0.00011       5      91 ..     660     753 ..     657     763 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8.3
                       HATPase_c_5   5 dlcvilgnlLdNAieac 21 
                                       +++  + n+L  Aie  
  gi|336255097|ref|YP_004598204.1| 158 NFVQSIANVLATAIENR 174
                                       56666778888888765 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 7.3e-08
                       HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg..........ek.kklesskskkeehGiG 70 
                                        l  ++ nlL NA+e + + +   + +r+ ++++ +  +i++  +  g          e  ++l+s  s+++  GiG
  gi|336255097|ref|YP_004598204.1| 660 QLRQVFQNLLSNALEYSGDEP---PRVRIDAERRGDRWVITVADEGIGmdpdeadrvfEVfQRLHS-HSDHQGTGIG 732
                                       57789**********998866...89****************999666566655444322566666.66899***** PP

                       HATPase_c_5  71 lksireivkkykgnlsieaed 91 
                                       l   ++iv++++g+++++ e 
  gi|336255097|ref|YP_004598204.1| 733 LALCERIVERHGGDIWVDSEP 753
                                       ****************99875 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       6.3   9.4e+03      17      44 ..     485     512 ..     478     523 .. 0.76
   2 !   20.4   0.1   2.7e-07    0.0004      28     110 ..     657     741 ..     627     756 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.3
                       HATPase_c_2  17 avlrraglseelldeirlaveEactNav 44 
                                       ++ ++a   e+++ e + a  E +++av
  gi|336255097|ref|YP_004598204.1| 485 EAFEAALAGERRATEFEYAGREWIVRAV 512
                                       4445677788888899999999999998 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 2.7e-07
                       HATPase_c_2  28 lldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep....keslkegGr 100
                                       ++ ++r + + +++Na e+  +e p  +v++ +e+++++ +++vaD+G g dp ++++  e  +      + +  G+
  gi|336255097|ref|YP_004598204.1| 657 DASQLRQVFQNLLSNALEYSGDEPP--RVRIDAERRGDRWVITVADEGIGMDPDEADRVFEVFQrlhsHSDHQGTGI 731
                                       5557777788889*******99877..9**********************9999876655444488988999999** PP

                       HATPase_c_2 101 GlalikglvD 110
                                       Glal +++v+
  gi|336255097|ref|YP_004598204.1| 732 GLALCERIVE 741
                                       *****99987 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.091   1.4e+02       2      57 ..     201     254 ..     200     273 .. 0.83
   2 ?    9.1   0.0     0.001       1.5      40      86 ..     358     404 ..     350     406 .. 0.85
   3 ?   -1.8   0.0       2.5   3.8e+03      36      56 ..     481     502 ..     472     527 .. 0.59
   4 ?   -2.1   0.0       3.3   4.9e+03      34      55 ..     657     678 ..     655     698 .. 0.78
   5 ?   -1.5   0.0       2.1   3.1e+03      32      69 ..     707     750 ..     705     752 .. 0.54

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.091
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyR 57 
                                       +y+++r  e+++++ e l+g   ++ d+      + +re++++al+++e+ ++e+ 
  gi|336255097|ref|YP_004598204.1| 201 TYLNDRAAELIDFTGEGLRGE--TIWDVFEWGADSTLREEYERALETQESTSFEFY 254
                                       6999*****************..99999999999***********99997777763 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.001
                             PAS_3  40 ealqealkkgepyegeyRirrkdGeyrwveararvirdengkpvrvi 86 
                                       +++ e ++ ge +e+e  + r+dG  + +e + r++ d++g +v +i
  gi|336255097|ref|YP_004598204.1| 358 REWTERAAAGEYVEFEADLTRPDGNRYTLEGTFRPVTDDDGDVVSII 404
                                       5556666788888******************************9987 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.5
                             PAS_3  36 ervrealqealkkge.pyegey 56 
                                       e ++ea+++al++ + + e+ey
  gi|336255097|ref|YP_004598204.1| 481 EPLEEAFEAALAGERrATEFEY 502
                                       5667777777766664446665 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.3
                             PAS_3  34 Drervrealqealkkgepyege 55 
                                       D +++r+ +q++l++  +y+g+
  gi|336255097|ref|YP_004598204.1| 657 DASQLRQVFQNLLSNALEYSGD 678
                                       889999*****99988888765 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 2.1
                             PAS_3  32 peDrervrealqeal....kkge..pyegeyRirrkdGeyrwve 69 
                                       p++ +rv+e +q++      +g+   +    Ri+ ++G+ +wv+
  gi|336255097|ref|YP_004598204.1| 707 PDEADRVFEVFQRLHshsdHQGTgiGLALCERIVERHGGDIWVD 750
                                       77788888888866533221121112233357777777777776 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 ?   13.2   0.0   3.9e-05     0.058      21      66 ..     682     725 ..     657     738 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-05
                       HATPase_c_3  21 nvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakrk 66 
                                       +v i +++ rg+   i++ D+G Gm+++e ++++++ +  +++ ++
  gi|336255097|ref|YP_004598204.1| 682 RVRIDAER-RGDRWVITVADEGIGMDPDEADRVFEVFQRLHSH-SD 725
                                       37777777.47899******************99865554442.22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (770 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); 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:                        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: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.40
# Mc/sec: 5713.56
//
Query:       gi|336255098|ref|YP_004598205.1|  [L=86]
Description: hypothetical protein Halxa_3719 [Halopiger xanaduensis SH-6]
Scores for 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  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.32u 0.19s 00:00:00.51 Elapsed: 00:00:00.32
# Mc/sec: 792.02
//
Query:       gi|336255099|ref|YP_004598206.1|  [L=135]
Description: hypothetical protein Halxa_3720 [Halopiger xanaduensis SH-6]
Scores for 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  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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: 0.36u 0.17s 00:00:00.53 Elapsed: 00:00:00.32
# Mc/sec: 1264.28
//
Query:       gi|336255100|ref|YP_004598207.1|  [L=192]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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   32.4   0.0    1.8e-07   31.4   0.0    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.021   14.8   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
       0.03   14.5   0.0      0.055   13.6   0.0    1.5  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
       0.17   12.4   0.0       0.27   11.7   0.0    1.4  1  Acetyltransf_7   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 !   31.4   0.0     4e-11   1.8e-07      28     117 .]      28     122 ..       2     122 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4e-11
                                       HHSTTCEEEEEEET........TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESE CS
                    Acetyltransf_1  28 fsleaegllvaeed........geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikk 96 
                                       f  ++ g  va+e+        ge+++ + ++ +   + ++ +++ + V++++rg G+G  L + +  ra+e+g+++
  gi|336255100|ref|YP_004598207.1|  28 FVMTNTGKAVAREGesdgededGEIVAAVAFNEDRT-DADTLWLRYVTVARDRRGEGVGPDLCRLVRNRALERGYDR 103
                                       444444334433333335555599*****9999999.99************************************** PP

                                       EEEEEETTEHHH.HHHHHHTTE CS
                    Acetyltransf_1  97 ivlaveedndaa.irlYeklGF 117
                                       + +av  +n  a  +lY ++GF
  gi|336255100|ref|YP_004598207.1| 104 LRIAV--NNPFAyEALY-RCGF 122
                                       99988..5555516666.***9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.7e-06     0.021      37     112 ..      47     128 ..      41     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-06
                   Acetyltransf_10  37 eeggkivGviel.rdgs.....hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnaspyavpfYeklGF 106
                                       +e+g+iv +++  +d+       +  + V+++ rg G+g  L   v+++a ++g+   ++ vn   + +++Y ++GF
  gi|336255100|ref|YP_004598207.1|  47 DEDGEIVAAVAFnEDRTdadtlWLRYVTVARDRRGEGVGPDLCRLVRNRALERGYDRlRIAVNNPFAYEALY-RCGF 122
                                       5788999999886666677777777889*********************99*****7788887655555555.7999 PP

                   Acetyltransf_10 107 kavgee 112
                                         +ge 
  gi|336255100|ref|YP_004598207.1| 123 AYTGET 128
                                       988775 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 ?   13.6   0.0   1.2e-05     0.055       7      58 ..      48     101 ..      42     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                   Acetyltransf_CG   7 degeevafleYe..vrkegvldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                       ++ge va + +   +++ ++l +  + V    rG+G++  L++ + + a e+g+
  gi|336255100|ref|YP_004598207.1|  48 EDGEIVAAVAFNedRTDADTLWLRYVTVARDRRGEGVGPDLCRLVRNRALERGY 101
                                       3688999999963355556******************************99986 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     6e-05      0.27      10      54 ..      48     102 ..      28     124 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6e-05
                                       ETTEEEEEEEEEEES.....TCTEEEEE-GGGTTSSHHHHHHHH...TT..SEEE CS
                    Acetyltransf_7  10 ddgkivGfialslld.....aeitrlaVdpeyrgkGiGraLlea...ae..kgii 54 
                                       +dg+iv  +a+ ++       ++ ++ V+ + rg G+G  L ++   ++  +g+ 
  gi|336255100|ref|YP_004598207.1|  48 EDGEIVAAVAFNEDRtdadtLWLRYVTVARDRRGEGVGPDLCRLvrnRAleRGYD 102
                                       348888877777777886544444499**************99744311444532 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1497.59
//
Query:       gi|336255101|ref|YP_004598208.1|  [L=292]
Description: hypothetical protein Halxa_3722 [Halopiger xanaduensis SH-6]
Scores for 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  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2286.83
//
Query:       gi|336255102|ref|YP_004598209.1|  [L=479]
Description: hypothetical protein Halxa_3723 [Halopiger xanaduensis SH-6]
Scores for 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-20   73.2  11.0    3.4e-10   39.9   4.6    2.9  2  PQQ_2     PQQ-like domain
    3.1e-07   30.0   7.2        1.6    8.8   0.1    6.2  6  PQQ       PQQ enzyme repeat
    0.00039   20.8  29.4       0.08   13.5   0.4    7.8  8  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.3   1.7e-12     1e-08      58     219 ..      78     305 ..      73     324 .. 0.71
   2 !   39.9   4.6   5.7e-14   3.4e-10       5     137 ..     331     478 ..     329     479 .] 0.78

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.7e-12
                             PQQ_2  58 vlWettlegpvvgaplvaegrvvvvasdg.qlialdaedGkr................................... 98 
                                       v We+++++    +p va+g v+++  +g  ++ +++ dGk+                                   
  gi|336255102|ref|YP_004598209.1|  78 VAWERSVSADGWLPPVVANGTVYCQYTNGlFVLDVESGDGKEvrtyggfgrgagpmafasttlyrdgallvpygrav 154
                                       67888888888888888888888886444444445555555588888888888888888888888888888888888 PP

                             PQQ_2  99 ......................lWstqqrs......eepae...lrssaspavagdtvvvgessgklvaldpkdGkv 144
                                                              W ++ ++      +        + sa+p+v+++ v+  +++g ++a++p+dG +
  gi|336255102|ref|YP_004598209.1| 155 agyaaapdgwpdevsgrgkrraRWWFDGDRadsrppG---GhspPSWSATPVVHDGAVITLHPRGIVAAVSPDDGTP 228
                                       8888888888899999999999999898885544431...12334567888888*********************** PP

                             PQQ_2 145 lWerelaaprgtsels......rvgdisgrpvvaegtVyassgqgrllaldlatgrrlwske.issinglpildgdl 214
                                       +W ++ a++ + + l        v+d+++++vv+ g+V       +l+ ldl+tg+ +w ++  +s+ +    d+++
  gi|336255102|ref|YP_004598209.1| 229 RWRYAFADADRDD-LRsfdpfeYVVDPASATVVVYGRVGWTP---TLVGLDLTTGSLEWLDAaNGSPEA-ESTDHGV 300
                                       ******7766444.4335666666666666666656666555...58999******88*8884555554.5555554 PP

                             PQQ_2 215 lyvvs 219
                                         +  
  gi|336255102|ref|YP_004598209.1| 301 PELRL 305
                                       44433 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 5.7e-14
                             PQQ_2   5 vsaldaatGaelWrvdlarplgggvsravlsggtlfva........tgggrlvaldaatGkvlWettl.egpvvga. 71 
                                       ++ ++aa+G   W+ +l+r++  g+  av +g t++          ++++ ++a+d+++G+v+We+ l + p  g  
  gi|336255102|ref|YP_004598209.1| 331 LREVNAASGDDSWSRSLERESHVGL--AV-DGTTVYHLgtvetddrGERAAVAAVDREDGTVRWEVVLdDDPGGGVw 404
                                       5678999**********99999999..99.999999996555544449999*****************644444447 PP

                             PQQ_2  72 ......plvaegrvvvvasdgqlialdaedGkrlWstqqrseepae....lrssaspavagdtvvvgessgklval 137
                                             p+va+++++v  +++ l al+ ++G+rlW+ + ++ ++a      r   +pav+++  +v ++ ++l++l
  gi|336255102|ref|YP_004598209.1| 405 atnqpsPTVAGDQLLVP-AGKGLHALERTSGERLWT-FTETVPTAGgsedERAGITPAVVSNDRIVLGATLRLYGL 478
                                       789999********555.7999**************.555547777666677777888885555555557777665 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.1    0.0055        33       1      21 [.      97     116 ..      97     125 .. 0.84
   2 ?    0.4   0.0      0.12   7.3e+02      18      26 ..     224     232 ..     209     239 .. 0.82
   3 !    5.1   0.1    0.0038        23       9      24 ..     268     283 ..     259     293 .. 0.81
   4 ?   -1.1   0.0      0.36   2.1e+03      11      25 ..     330     344 ..     330     348 .. 0.80
   5 !    8.8   0.1   0.00027       1.6      12      29 ..     379     396 ..     378     403 .. 0.81
   6 !    8.0   0.0   0.00047       2.8       8      28 ..     422     442 ..     418     450 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0055
                                       TEEEEEETTSEEEEEETTTCC CS
                               PQQ   1 gvvylgsadGylyAlDadTGk 21 
                                       g+vy+  + + l+ lD+++G+
  gi|336255102|ref|YP_004598209.1|  97 GTVYCQ-YTNGLFVLDVESGD 116
                                       566776.9999********97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.12
                                       TTCCEEEEE CS
                               PQQ  18 dTGkvlWrf 26 
                                       d+G+ +Wr+
  gi|336255102|ref|YP_004598209.1| 224 DDGTPRWRY 232
                                       89*****99 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0038
                                       TSEEEEEETTTCCEEE CS
                               PQQ   9 dGylyAlDadTGkvlW 24 
                                         +l+ lD++TG + W
  gi|336255102|ref|YP_004598209.1| 268 TPTLVGLDLTTGSLEW 283
                                       568999*********9 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.36
                                       EEEEEETTTCCEEEE CS
                               PQQ  11 ylyAlDadTGkvlWr 25 
                                       +l+ ++a++G+  W+
  gi|336255102|ref|YP_004598209.1| 330 RLREVNAASGDDSWS 344
                                       577899999999887 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.00027
                                       EEEEETTTCCEEEEEESS CS
                               PQQ  12 lyAlDadTGkvlWrfktg 29 
                                       + A+D+++G+v+W++ ++
  gi|336255102|ref|YP_004598209.1| 379 VAAVDREDGTVRWEVVLD 396
                                       67***********98555 PP

  == domain 6  score: 8.0 bits;  conditional E-value: 0.00047
                                       TTSEEEEEETTTCCEEEEEES CS
                               PQQ   8 adGylyAlDadTGkvlWrfkt 28 
                                       a+  l Al +++G+ lW+f +
  gi|336255102|ref|YP_004598209.1| 422 AGKGLHALERTSGERLWTFTE 442
                                       556799************986 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.4   1.3e-05      0.08       2      39 ..      77     113 ..      76     114 .. 0.87
   2 ?   -3.6   0.0         3   1.8e+04      24      30 ..     134     143 ..     126     149 .. 0.47
   3 ?    2.4   0.1      0.04   2.4e+02      14      39 ..     198     224 ..     180     225 .. 0.79
   4 ?    0.4   0.9      0.17     1e+03       1       8 [.     226     238 ..     226     278 .. 0.47
   5 ?    2.1   0.0     0.049   2.9e+02      16      29 ..     310     323 ..     284     326 .. 0.75
   6 ?    2.6   0.1     0.034     2e+02       5      27 ..     343     365 ..     339     386 .. 0.72
   7 !   11.7   0.6   4.9e-05      0.29       1      39 [.     387     432 ..     387     433 .. 0.79
   8 ?    3.8   0.1     0.015        87       1      28 [.     434     471 ..     434     479 .] 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                             PQQ_3   2 evlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       +v W++++ ++++ +p+v++g+vy+  + ++l+ lD e
  gi|336255102|ref|YP_004598209.1|  77 DVAWERSVSADGWLPPVVANGTVYCQYT-NGLFVLDVE 113
                                       589*********************9776.777777776 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3
                             PQQ_3  24 vyvgtg...d 30 
                                        +++t+   d
  gi|336255102|ref|YP_004598209.1| 134 AFASTTlyrD 143
                                       3333333333 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.04
                             PQQ_3  14 n.sspavdgglvyvgtgdGtlyAlDae 39 
                                       + ++p+v +g v +  + G + A+ ++
  gi|336255102|ref|YP_004598209.1| 198 WsATPVVHDGAVITLHPRGIVAAVSPD 224
                                       32566********99999999998876 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.17
                             PQQ_3   1 GevlWsv.....q 8  
                                       G+++W++     +
  gi|336255102|ref|YP_004598209.1| 226 GTPRWRYafadaD 238
                                       8899999444431 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.049
                             PQQ_3  16 spavdgglvyvgtg 29 
                                        +a++++ vyv+++
  gi|336255102|ref|YP_004598209.1| 310 RLAAADRSVYVTDW 323
                                       3599*******987 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.034
                             PQQ_3   5 Wsvqlpgpvnsspavdgglvyvg 27 
                                       Ws++l  + + ++avdg +vy  
  gi|336255102|ref|YP_004598209.1| 343 WSRSLERESHVGLAVDGTTVYHL 365
                                       8887777777789*******955 PP

  == domain 7  score: 11.7 bits;  conditional E-value: 4.9e-05
                             PQQ_3   1 GevlWsvqlpgpvnssp........avdgglvyvgtgdGtlyAlDae 39 
                                       G+v+W+v l+++ ++++        +v+g+ + v +g  +l+Al+ +
  gi|336255102|ref|YP_004598209.1| 387 GTVRWEVVLDDDPGGGVwatnqpspTVAGDQLLVPAG-KGLHALERT 432
                                       99*****665544455555666688***********9.*****9976 PP

  == domain 8  score: 3.8 bits;  conditional E-value: 0.015
                             PQQ_3   1 GevlWsv.......qlpg.....pvnsspavdgglvyvgt 28 
                                       Ge+lW++       +  g     ++ ++++v++++++ g+
  gi|336255102|ref|YP_004598209.1| 434 GERLWTFtetvptaG--GsederAGITPAVVSNDRIVLGA 471
                                       999****88775330..23433222244488888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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 0.22s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3874.76
//
Query:       gi|336255103|ref|YP_004598210.1|  [L=325]
Description: Flap structure-specific endonuclease [Halopiger xanaduensis SH-6]
Scores for 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-22   77.2   0.0    1.8e-21   76.3   0.0    1.5  1  XPG_I            XPG I-region
    1.3e-10   41.6   0.0    2.3e-10   40.9   0.0    1.4  1  XPG_N            XPG N-terminal domain
    4.1e-05   24.1   0.0    0.00011   22.7   0.0    1.8  1  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold
     0.0086   16.0   0.0      0.032   14.1   0.0    1.9  2  5_3_exonuc_N     5'-3' exonuclease, N-terminal resolvase-like
  ------ inclusion threshold ------
       0.19   10.4   1.0       0.24   10.1   0.2    1.5  2  Chorismate_synt  Chorismate synthase
        2.7    8.7   6.0          2    9.1   0.2    2.7  3  SlyX             SlyX


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 !   76.3   0.0   5.9e-25   1.8e-21       2      94 .]     142     224 ..     141     224 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 5.9e-25
                                       HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT.ECECTT..EEECEEEEEEHHHHHHHHT CS
                             XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnlskkkskkkkekekkkvevidlekvlkelg 78 
                                       l+ +p+v+Ap E+EAq+a+++++g++d+v seD+D+llFGap +lr+l+  + k         +e +dle +l +++
  gi|336255103|ref|YP_004598210.1| 142 LLDVPIVEAPAEGEAQAAHIVRRGDADYVGSEDYDALLFGAPLTLRQLT--S-KGD-------PELMDLEATLAHHD 208
                                       789*********************************************8..3.333.......79************ PP

                                       --HHHHHHHHHHHCET CS
                             XPG_I  79 ltreqlidlaillgcD 94 
                                       lt eqlid ail+g+D
  gi|336255103|ref|YP_004598210.1| 209 LTLEQLIDAAILIGTD 224
                                       **************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 !   40.9   0.0   7.6e-14   2.3e-10      27      99 ..      22     100 ..       3     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 7.6e-14
                                       EEEEEEHHHHHHHHHHHSE..ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE--S--GGGHHHHHHHHHH CS
                             XPG_N  27 kklaiDaslwlyrfliavre.qlgnalen.....tshlmglfsrllrlldfgikPifVFdgkapdlkkeelekrser 97 
                                        ++a+Da  wlyr l++  +  +   +++        l+g+++ l ++ ++ ++P++VFdg++ +lk++e+e r+++
  gi|336255103|ref|YP_004598210.1|  22 GVVAVDAHNWLYRYLTTTVKwTDSSVYTTadgteVANLVGIVQGLPKFFENDVTPVMVFDGGPSELKEDEIESRRDQ 98 
                                       489***********9876651455555558887667899********************************999988 PP

                                       HH CS
                             XPG_N  98 rq 99 
                                       r 
  gi|336255103|ref|YP_004598210.1|  99 RR 100
                                       75 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 !   22.7   0.0   3.7e-08   0.00011       4      48 ..     212     254 ..     209     279 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.7e-08
                        5_3_exonuc   4 eqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenl 48 
                                       eq+id + L+G   D  +Gv+giG+ktA+k ++e+g+l ++le+ 
  gi|336255103|ref|YP_004598210.1| 212 EQLIDAAILIGT--DFNEGVSGIGPKTAIKEITEHGDLWSVLEAR 254
                                       799999****96..5668*********************999954 PP

>> 5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.1e-05     0.032       2      82 ..      23     109 ..      22     178 .. 0.80
   2 ?   -1.0   0.0      0.49   1.5e+03      74      96 ..     300     322 ..     273     325 .] 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                      5_3_exonuc_N   2 llLiDgsslifRayyal........lttsdgeptnavygflnmllklleeekpthlavvfDakkktfRhelypeYKa 70 
                                       ++ +D+++ ++R    +        +tt+dg++++ ++g+++ l k+ e+    + ++vfD ++++ +++ +++ + 
  gi|336255103|ref|YP_004598210.1|  23 VVAVDAHNWLYRYLTTTvkwtdssvYTTADGTEVANLVGIVQGLPKFFENDV--TPVMVFDGGPSELKEDEIESRRD 97 
                                       5779********88876799999988999*******************9754..5799***9888999999999999 PP

                      5_3_exonuc_N  71 nReetpeelkeq 82 
                                       +R   +e+l+  
  gi|336255103|ref|YP_004598210.1|  98 QRRTYEEQLETA 109
                                       995555554433 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.49
                      5_3_exonuc_N  74 etpeelkeqlplikevlealgik 96 
                                        +p+e+++ ++ ike +++ g+ 
  gi|336255103|ref|YP_004598210.1| 300 VAPDEVERGFERIKESVTQTGLD 322
                                       57999999999999999998876 PP

>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   8.1e-05      0.24      17      59 ..      79     119 ..      75     130 .. 0.88
   2 ?   -3.3   0.0      0.93   2.8e+03      89     106 ..     158     175 ..     152     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.1e-05
                                       EEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEE CS
                   Chorismate_synt  17 vidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveil 59 
                                       v dg p+  el+e++i+++ d+Rr+ +++l+t+r+E Dev i 
  gi|336255103|ref|YP_004598210.1|  79 VFDGGPS--ELKEDEIESRRDQRRTYEEQLETAREEGDEVAIA 119
                                       5666665..678**************99************985 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.93
                                       STSBE-TTSTCHHHHHHC CS
                   Chorismate_synt  89 ikevpRpgHADltyalkY 106
                                        ++++R g AD+++++ Y
  gi|336255103|ref|YP_004598210.1| 158 AAHIVRRGDADYVGSEDY 175
                                       5678999*****999888 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.3     4e+03      31      53 ..      90     112 ..      88     117 .. 0.71
   2 ?    1.7   0.2      0.13     4e+02       5      28 ..     118     141 ..     114     144 .. 0.77
   3 ?    9.1   0.2   0.00066         2       5      25 ..     197     217 ..     194     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX  31 qqidrlqrqlrllaerlkelees 53 
                                       ++i+  + q r  +e+l++++e+
  gi|336255103|ref|YP_004598210.1|  90 DEIESRRDQRRTYEEQLETAREE 112
                                       57777788888888888777766 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   5 leeLEiklafqedtieeLndvvae 28 
                                       + +LE++   +  ti+e ++++ +
  gi|336255103|ref|YP_004598210.1| 118 IAQLESRTQRLTPTIQETSRELLR 141
                                       778888888888888888877765 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00066
                                       HHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   5 leeLEiklafqedtieeLndv 25 
                                       l++LE  la+++ t+e+L d+
  gi|336255103|ref|YP_004598210.1| 197 LMDLEATLAHHDLTLEQLIDA 217
                                       89****************776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2616.97
//
Query:       gi|336255104|ref|YP_004598211.1|  [L=340]
Description: alcohol dehydrogenase zinc-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-25   87.1   0.1    1.9e-24   86.1   0.1    1.5  1  ADH_zinc_N    Zinc-binding dehydrogenase
    1.5e-14   55.1   0.0    4.5e-14   53.6   0.0    1.8  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    3.7e-10   39.6   0.0    1.7e-09   37.5   0.0    2.0  1  ADH_N         Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
      0.012   14.9   0.1      0.023   14.0   0.1    1.3  1  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-terminal domain
      0.093   12.7   0.3        0.3   11.0   0.1    2.0  2  UBA           UBA/TS-N domain


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 !   86.1   0.1   5.2e-28   1.9e-24       1     125 [.     173     296 ..     173     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 5.2e-28
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvGsgatleaal 76 
                                       gv ++a+q+A + Ga v++++ss+ kle a++lGa+ ++ny+e+ ++ ++++e  g  gvd v+e+ G + tl++++
  gi|336255104|ref|YP_004598211.1| 173 GVSTFALQFATMQGADVFVTSSSDAKLERARELGATWTLNYEETpEWGDAVQEEVG--GVDHVIEVGG-PGTLQQSI 246
                                       899****************************************************4..9*********.******** PP

                                       HCEEEEEEEEECSCTSSEEE.EEHHHHHHTT-EEEEE-SSCHHHHHHHHH CS
                        ADH_zinc_N  77 kllkpgGrlvvvGggkgeee.fdlrnlllkeksilGsllgslreefkeal 125
                                       ++++ +G + ++G+++g+e  + ++++l k ++++Gs++ + r  f +++
  gi|336255104|ref|YP_004598211.1| 247 EAATFDGYVHLIGVLSGPEGqVHPGPILQKALTVKGSMGVGSRAMFDRMN 296
                                       **************5555555******************99666665555 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   1.3e-17   4.5e-14       1     133 []     205     337 ..     205     337 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.3e-17
                                       TT-SEEEETT.STTHH...HHH-T..T-EEEEEES-HHHHH.HHHHHHE..EEEEEEEE--.--.S-EEE-CHHHCT CS
                      ADH_zinc_N_2   1 lGAdevidyr.tedfe...aatgg..egvDvvldtvggealleaslkvl..pggGrlvsig.gpplsaallkpakkr 68 
                                       lGA+  ++y+ t+++    +   +  +gvD+v++  gg+ +l++s+++   +g+ +l+ ++ gp   +  + p + +
  gi|336255104|ref|YP_004598211.1| 205 LGATWTLNYEeTPEWGdavQ---EevGGVDHVIEV-GGPGTLQQSIEAAtfDGYVHLIGVLsGP-EGQVHPGPIL-Q 275
                                       78999999999999985442...33489******6.666666****888777777788888443.3333333333.5 PP

                                       TT-EEEE--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGG..HHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  69 kgrsvkyeflfsmkasaqadileelaalieeGklrpvvdrvfplee..aaeAhrylesgrarGKiVl 133
                                       k  +vk ++ +    s +a+ ++++   ie+ +l+pv+dr+f++ee  ++eA+ry+ +g++ GK+V+
  gi|336255104|ref|YP_004598211.1| 276 KALTVKGSMGVG---S-RAM-FDRMNSAIEAAALEPVIDRTFGFEEdeVREAYRYVDEGAHQGKVVI 337
                                       556666666663...4.777.************************999******************7 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   4.7e-13   1.7e-09       2     107 ..      29     129 ..      28     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 4.7e-13
                                       TEEEEEEEEEEE-HHHHHHHTTS.TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT- CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkgg.kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkege 77 
                                       +e+l++++aa+i+  Dl i++++   + ++lp+++  + +Gev++vg++v++l+ GdrV+ ++      ++++ +g 
  gi|336255104|ref|YP_004598211.1|  29 NEALVEMRAASINYRDLAIAHEDlVYPGAELPVVPLCDGAGEVVAVGDDVERLSEGDRVATPF------APDWVDGP 99 
                                       799****************999878899********************************955......57888898 PP

                                       GGG-TTBEETTTSS-SSSBSEEEECGGGEE CS
                             ADH_N  78 enlCeeakllgvsldGgfaeyvvvpekklv 107
                                        +  + a+++g ++dG++aey ++p+++l+
  gi|336255104|ref|YP_004598211.1| 100 VTPEKVARTTGGNVDGTLAEYATFPADSLA 129
                                       888899999999999999999999998876 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 ?   14.0   0.1   6.3e-06     0.023      29      94 ..     164     232 ..     153     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.3e-06
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHH....HHHHHHHHH-SE CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqe....ellaeavkeadv 94 
                                        +vl +G G + + A++ a+  ga+V v+  + a+le+ ++lga+  ++ +++     ++++e+v  +d 
  gi|336255104|ref|YP_004598211.1| 164 ETVLALGTGGVSTFALQFATMQGADVFVTSSSDAKLERARELGAT-WTLNYEETpewgDAVQEEVGGVDH 232
                                       57999**************************************99.444333330111345555555555 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.1   1.1e+04      24      31 ..     107     114 ..     106     115 .. 0.83
   2 ?   11.0   0.1   8.3e-05       0.3      12      25 ..     312     325 ..     310     327 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.1
                                       HHTTTSHH CS
                               UBA  24 ratgnNeE 31 
                                       r tg+N++
  gi|336255104|ref|YP_004598211.1| 107 RTTGGNVD 114
                                       6799**97 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.3e-05
                                       TTS-HHHHHHHHHH CS
                               UBA  12 MGFdreevveALra 25 
                                        GF+++ev+eA+r+
  gi|336255104|ref|YP_004598211.1| 312 FGFEEDEVREAYRY 325
                                       6***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2723.16
//
Query:       gi|336255105|ref|YP_004598212.1|  [L=395]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Halopiger xanaduensis SH-6]
Scores for complete 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  106.5   0.3    1.9e-30  106.1   0.3    1.2  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    3.9e-12   46.6   1.0    8.6e-09   35.8   0.1    2.4  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    8.9e-05   22.8   0.2     0.0011   19.3   0.0    2.4  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00056   19.6   7.7       0.73    9.4   0.1    3.6  4  DAO              FAD dependent oxidoreductase
    0.00061   19.8   4.1        4.4    7.3   0.2    4.0  4  NAD_binding_9    FAD-NAD(P)-binding
     0.0093   16.2   0.2        1.9    8.8   0.0    2.7  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.072   13.4   0.3       0.62   10.3   0.1    2.3  2  TrkA_N           TrkA-N domain
      0.091   12.6   0.0       0.31   10.9   0.0    2.0  1  PapC_C           PapC C-terminal domain
       0.11   11.7   0.2        2.2    7.5   0.0    2.2  2  Thi4             Thi4 family


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 !  106.1   0.3   9.6e-34   1.9e-30       2     294 .]       2     296 ..       1     296 [. 0.87

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 9.6e-34
                                       SEEEE--SHHHHHHHHHHHH...HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.......HHHHCHHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq...agakvtlvelegtclnggcllskallgvaedaeias.......evvkklnqgie 68 
                                       +vvv+G+G AGl++ + l +     a++t+v++   +     l++++l++v +++e as       ev+++ +  + 
  gi|336255105|ref|YP_004598212.1|   2 HVVVLGAGYAGLTLTRLLEEklpEAADITIVNESPDH-----LVQHELHRVVRRPELASaitvslpEVLERATVRVA 73 
                                       8*******************77779******444433.....45577888888888888777777755444443333 PP

                                       CCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       Pyr_redox_2  69 lllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp... 142
                                             v +id++++ v l+   +    +++yd   ++ G+++   +++Gv e+   l + l +a ++++  l+   
  gi|336255105|ref|YP_004598212.1|  74 -----RVEGIDREERVVDLS---S---GRLEYDVAAICLGARTAYYDLEGVREHSMPL-KRLSHALQIRSRALEvlq 138
                                       .....3677*****777772...2...37**************************999.99**************** PP

                                       ........SEEEEES-SHHHHHHHHHHHHHT-........EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEES CS
                                       ........xxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 ........krivvvGgGyiGvElAaalaklgk........evtlveardrllraldkelsaaleealekeGvevklg 203
                                                rivv G+G+ G+ +A++la l++         +tl+e++d + +++++++++a++ ale++G+ev+++
  gi|336255105|ref|YP_004598212.1| 139 drsardgdGRIVVGGAGLSGIQVAGELAALADeergtatvTITLLEQLDSVAPTFPENFQRAVRSALEEQGIEVRTR 215
                                       ******************************9999999998899********************************** PP

                                       CEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       Pyr_redox_2 204 tsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.. 278
                                       + v ++dg +    v+le+gee+++d  v+  G+  s++l+          + + +v + lr  ++  +a+GD +  
  gi|336255105|ref|YP_004598212.1| 216 SAVRRADGTH----VHLESGEELPYDQFVWTGGIAGSDALA----------GERPLVESDLRL-DERTFALGDAVra 277
                                       ***9999887....8***********************997..........455667777766.8888*****99** PP

                                       ...TECCSS--HHHHHHHH CS
                                       ...xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 279 ...ggkggpelaqaAvqqG 294
                                          +g+ +p++aqaAv+++
  gi|336255105|ref|YP_004598212.1| 278 tdaDGEPVPASAQAAVREA 296
                                       ***99***********997 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1   0.00089       1.8       1      47 [.       2      49 ..       2      82 .. 0.71
   2 !   35.8   0.1   4.3e-12   8.6e-09       1      70 [.     148     225 ..     148     231 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00089
                                      EEEEECSSHHHHHHHHHHHH.TT..SEEEEEESSSSSSTTSSHHHHHHHH CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalae.lg..kkVtvversdkllrllDeeaskilq 47
                                      +vvv+G+Gy gl l   l e l   +++t+v  s+  l    +e+ ++++
  gi|336255105|ref|YP_004598212.1|  2 HVVVLGAGYAGLTLTRLLEEkLPeaADITIVNESPDHL--VQHELHRVVR 49
                                      89***************966332448999999998888..5555555555 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 4.3e-12
                                       EEEEECSSHHHHHHHHHHHHTT........SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelg........kkVtvversdkllrllDeeaskilqeklekngievllntkveeiegs 69 
                                       ++vv G+G++g+ +Ag+la+l+          +t++e  d + + ++e ++++++  le++giev++ + v + +g+
  gi|336255105|ref|YP_004598212.1| 148 RIVVGGAGLSGIQVAGELAALAdeergtatVTITLLEQLDSVAPTFPENFQRAVRSALEEQGIEVRTRSAVRRADGT 224
                                       699***************999988888877789**************************************999976 PP

                                       T CS
                         Pyr_redox  70 e 70 
                                        
  gi|336255105|ref|YP_004598212.1| 225 H 225
                                       5 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 !   19.3   0.0   5.3e-07    0.0011       1     101 [.       3     112 ..       3     139 .. 0.74
   2 ?    0.7   0.0       0.3   5.9e+02       1      41 [.     149     190 ..     149     217 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.3e-07
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.........TTTCEEEEE--TTTHHHHHHHHHT CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.........lgvrfeaialdaenyeavLaallk 68 
                                       v+++GaG+ G  +++ll+++ +  a+it++  s ++l +   +          + +   ++ l ++ ++   ++ + 
  gi|336255105|ref|YP_004598212.1|   3 VVVLGAGYAGLTLTRLLEEKLPEAADITIVNESPDHLVQHELHRvvrrpelasAITVSLPEVLERATVRVARVEGID 79 
                                       89********************988**********965555444798776554222223344444444444455566 PP

                                       TSSEEEE-SSGGGHHHHHHHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  69 egdlvvnlsppissldvlkaCietgvhyvdtsi 101
                                         + vv+ls   +  dv+++C+ ++++y d + 
  gi|336255105|ref|YP_004598212.1|  80 REERVVDLSSGRLEYDVAAICLGARTAYYDLEG 112
                                       66****************************443 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.3
                                       EEEE--SHHHHHHHHHHHCTCCT-G.EEEEEESSHHHHHHHH CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvda.eitvadrskekleala 41 
                                       +++ GaG  G  va +la+  d ++ + tv    +e+l+ +a
  gi|336255105|ref|YP_004598212.1| 149 IVVGGAGLSGIQVAGELAALADEERgTATVTITLLEQLDSVA 190
                                       556677************999998886666666666665554 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00075       1.5       1      28 [.       2      34 ..       2      38 .. 0.82
   2 ?    0.1   0.1      0.24   4.7e+02     167     238 ..      73     131 ..      63     153 .. 0.54
   3 ?    2.7   1.8     0.039        77       2      29 ..     149     186 ..     148     192 .. 0.78
   4 !    9.4   0.1   0.00036      0.73     145     207 ..     194     252 ..     190     348 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00075
                                      EEEEECTSHHHHHHHHHHHHT.T....EEEEES CS
                               DAO  1 dvviiGGGiiGlstAyeLarr.g....Vtllek 28
                                      +vv+ G+G++Gl+  + L ++ +    +t++  
  gi|336255105|ref|YP_004598212.1|  2 HVVVLGAGYAGLTLTRLLEEKlPeaadITIVNE 34
                                      79****************766546788998865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.24
                                       ECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTTCTTTSEEEEEEEEEEEEEECCTHSTGSG CS
                               DAO 167 tevtgleeedgkvwgverttp.gendaadavVnaaGawsdllgllkeldlpispvrgqvlvlkplseklvspa 238
                                       ++v+g+++e ++v+ +    + g+  ++d   ++ Ga +            +++vr +++ lk+ls +l+ + 
  gi|336255105|ref|YP_004598212.1|  73 ARVEGIDRE-ERVVDL----SsGRL-EYDVAAICLGARTAYY--------DLEGVREHSMPLKRLSHALQIRS 131
                                       378888553.455666....22544.5799999999997522........33777777777777666443332 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.039
                                       EEEECTSHHHHHHHHHHHH.....TT.....EEEEESS CS
                               DAO   2 vviiGGGiiGlstAyeLar.....rg.....Vtllekg 29 
                                       +v+ G+G  G+ +A eLa+     rg     +tlle+ 
  gi|336255105|ref|YP_004598212.1| 149 IVVGGAGLSGIQVAGELAAladeeRGtatvtITLLEQL 186
                                       78889************763333356999999999985 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH..HH CS
                               DAO 145 pakltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd..ll 207
                                       p+ + +a+++a+e++G+e+++++ v++    d  +++v + ++ge+  +d+ V + G+  +  l+
  gi|336255105|ref|YP_004598212.1| 194 PENFQRAVRSALEEQGIEVRTRSAVRRA---D--GTHV-HLESGEELPYDQFVWTGGIAGSdaLA 252
                                       778999****************999987...3..6777.4444777567********65433443 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 !    5.8   0.0    0.0062        12       1      35 [.       4      36 ..       4      53 .. 0.81
   2 ?   -0.5   0.0      0.54   1.1e+03     118     154 ..      66     102 ..      51     104 .. 0.73
   3 !    7.3   0.2    0.0022       4.4       4      33 ..     153     185 ..     149     194 .. 0.81
   4 ?    5.1   0.0      0.01        20     104     154 ..     197     244 ..     193     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0062
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpse 35
                                      ++ GaG +Gl++ +rLl+++  ++  +it++++s+
  gi|336255105|ref|YP_004598212.1|  4 VVLGAGYAGLTL-TRLLEEK-LPEAADITIVNESP 36
                                      578******976.6777774.7999*****99875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.54
                     NAD_binding_9 118 evhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                       e  + +v ++e  +++ +v+  +  +l++d   ++lG
  gi|336255105|ref|YP_004598212.1|  66 ERATVRVARVEGIDREERVVDLSSGRLEYDVAAICLG 102
                                       4445567777777777788888899999999999999 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0022
                     NAD_binding_9   4 GaGprGlavlerLlara...kkkspleitlfdp 33 
                                       GaG +G+ v+ +L+a a   + ++ ++itl ++
  gi|336255105|ref|YP_004598212.1| 153 GAGLSGIQVAGELAALAdeeRGTATVTITLLEQ 185
                                       89**************98655567799999887 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.01
                     NAD_binding_9 104 feellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                       f+++++++ e+  +ev +    +  +radg +v+l++g++l +d+ v + G
  gi|336255105|ref|YP_004598212.1| 197 FQRAVRSALEEQGIEVRT---RSAVRRADGTHVHLESGEELPYDQFVWTGG 244
                                       677777775555566544...4555789999*************9987765 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 !    8.8   0.0   0.00096       1.9       1      25 [.       5      32 ..       5      38 .. 0.80
   2 ?    4.5   0.2      0.02        40       3      30 ..     153     188 ..     150     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00096
                                      EE--SHHHHHHHHHHHCC...TEEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka...gfdvlll 25
                                      ++GaG +Gl++ +lL ++    +d++++
  gi|336255105|ref|YP_004598212.1|  5 VLGAGYAGLTLTRLLEEKlpeAADITIV 32
                                      89*************9865546677776 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.02
                                       --SHHHHHHHHHHHC.....C...TEEEEEE-SSSS CS
                     NAD_binding_8   3 GaGlsGlvaAylLak.....a...gfdvlllekrdr 30 
                                       GaGlsG   A +La      +    + ++lle+ d+
  gi|336255105|ref|YP_004598212.1| 153 GAGLSGIQVAGELAAladeeRgtaTVTITLLEQLDS 188
                                       78********99985433332333678999998765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00031      0.62       1      63 [.       3      73 ..       3      79 .. 0.80
   2 ?    0.5   0.0      0.34   6.7e+02       1      22 [.     149     178 ..     149     208 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                                      EEEES-SHHHHHHHHHHHHTT...EEEEEEESSHHHHHHHHHTT.SE....EEES-TTSHHHHHHTTGGGE CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLsegg...kdvvvidkdeerveelreeg.le....vvvgdatdeevLeeagieka 63
                                      ++++G+G  G +l++ L+e+     d++++  +++++ +++ +  ++    +    ++ +evLe+a +  a
  gi|336255105|ref|YP_004598212.1|  3 VVVLGAGYAGLTLTRLLEEKLpeaADITIVNESPDHLVQHELHRvVRrpelASAITVSLPEVLERATVRVA 73
                                      79****************97678978*********988877555333556677778888888888877666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.34
                                       EEEES-SHHHHHHHHHHHH.TT.......E CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.gg.......k 22 
                                       i++ G+G  G ++a eL + +         
  gi|336255105|ref|YP_004598212.1| 149 IVVGGAGLSGIQVAGELAAlADeergtatV 178
                                       789999********9999855455555442 PP

>> PapC_C  PapC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016      0.31       2      46 ..     275     324 ..     274     328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                                       EEEEETTTEE--TT-EEEETTSSS....-.EEB-CCCEEEEECE-SEEEE CS
                            PapC_C   2 ltltradGkplPfGAevtdeengk....v.giVgqgGqvylrglpdqgtL 46 
                                       ++ t+adG+p+P  A+++  e       v    g+g ++ l+g   +g++
  gi|336255105|ref|YP_004598212.1| 275 VRATDADGEPVPASAQAAVREARTvaenVsRLAGDGDETALEGGTTHGEV 324
                                       5789*************999877788884489999999999888888776 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0011       2.2      19      41 ..       2      25 ..       1      35 [. 0.81
   2 ?    2.0   0.1     0.052     1e+02      20      38 ..     149     167 ..     129     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0011
                                      EEEEE--SHHHHHHHHHHHHC.TT CS
                              Thi4 19 DvvivGaGssGLtaayylakk.pd 41
                                       vv+ GaG +GLt ++ l +k p+
  gi|336255105|ref|YP_004598212.1|  2 HVVVLGAGYAGLTLTRLLEEKlPE 25
                                      69****************999876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.052
                                       EEEE--SHHHHHHHHHHHH CS
                              Thi4  20 vvivGaGssGLtaayylak 38 
                                       +v+ GaG sG+  a  la 
  gi|336255105|ref|YP_004598212.1| 149 IVVGGAGLSGIQVAGELAA 167
                                       89**********9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 0.51u 0.21s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 3212.13
//
Query:       gi|336255106|ref|YP_004598213.1|  [L=53]
Description: hypothetical protein Halxa_3727 [Halopiger xanaduensis SH-6]
Scores for 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  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); 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 0.20s 00:00:00.51 Elapsed: 00:00:00.34
# Mc/sec: 473.43
//
Query:       gi|336255107|ref|YP_004598214.1|  [L=565]
Description: NAD(P)H-quinone oxidoreductase subunit H [Halopiger xanaduensis SH-6]
Scores for 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-84  281.8   0.1      1e-82  277.3   0.1    2.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    5.9e-36  123.8   0.1    1.1e-35  122.8   0.1    1.5  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
  ------ inclusion threshold ------
      0.045   13.2   0.0      0.094   12.2   0.0    1.6  1  Autoind_bind    Autoinducer binding domain


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 !  277.3   0.1   1.7e-86     1e-82       5     271 .]     315     565 .]     311     565 .] 0.92

  Alignments for each domain:
  == domain 1  score: 277.3 bits;  conditional E-value: 1.7e-86
                                       HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---T...THHHHHHHHHHHHHHHHHHHHHHHHSSSSHHH CS
                    Complex1_49kDa   5 ltvflyafreRekildlleevtGaRltasyiriGGvarDlpe...gllekikeflkelekkldeleklltknrifkk 78 
                                       +++f yafr+Re + d+le++tG+R++  y+r+GGva+Dlp+   +++ek+++fl+el++k+de+++l+++n+if++
  gi|336255107|ref|YP_004598214.1| 315 TAIFQYAFRDREVVQDILEDLTGQRMMFYYFRLGGVAWDLPRpreEFIEKCRDFLDELPAKVDEYHDLIVTNEIFRM 391
                                       35799***********************************988889******************************* PP

                                       HHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  79 RtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqa 155
                                       Rt++ g+l+ e a ++g+tGpv+R+sG++yDlR+++pY  Y++l++dv++++ +D  +R+l+r+eE+++S+kIieq+
  gi|336255107|ref|YP_004598214.1| 392 RTVDTGILEPEVAKDYGCTGPVARGSGIDYDLRRDDPYGYYENLEWDVVTRDGCDNHARVLCRIEEVEESAKIIEQC 468
                                       ***************************************************************************** PP

                                       HHT--.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----S.EEEEEEEEETTEEEEEEEEEESSSS-SEEE CS
                    Complex1_49kDa 156 leklpegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpk.gevyaavEapkGelgvylvsdgsskpyrlk 231
                                       l+ l++ p   +        ++ev++++ ++           k  +  e+y+avE +kGelgvy+ sdg+++p r+k
  gi|336255107|ref|YP_004598214.1| 469 LDLLEDWP--ED--------EREVQSNVPRTL----------KPDAgKETYRAVEIAKGELGVYIRSDGTNSPARFK 525
                                       ****8654..33........333344443332..........3444269**************************** PP

                                       EE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 232 irapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       ir+p+f nl+al+e+++ge++ D+va lgsldivlg vDR
  gi|336255107|ref|YP_004598214.1| 526 IRSPCFHNLSALPEMSEGEYVPDLVASLGSLDIVLGSVDR 565
                                       ***************************************9 PP

>> 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 !  122.8   0.1   1.9e-39   1.1e-35       2     120 ..      50     166 ..      49     168 .. 0.95

  Alignments for each domain:
  == domain 1  score: 122.8 bits;  conditional E-value: 1.9e-39
                                       E--HHHHHHHHHHHHH...TT--EEEEEEEEETTSSSEEEEEEEE--.S-.-EEEEEE....-S-BEE--TTT-STH CS
                    Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDekeerfevvyhllsl.eknerirvkvevdeeepevpSvtdlfpga 77 
                                       v++p+d++ev+ +l+d  e gfd+ls+lta ++ e+r+e + hl+++ e+++++++ v++++ +p+ +S+ ++f++a
  gi|336255107|ref|YP_004598214.1|  50 VIRPDDVQEVLGLLRD--EAGFDHLSCLTAQEY-EDRYESILHLTKYdERQHEVSLVVQLPQGDPVAQSAEPVFRTA 123
                                       789*************..599***********9.7************666699*****9**9*************** PP

                                       HHHHHHHHHHSHHBCTTSSTSS-SSSSTTSSS-TTSTTS---- CS
                    Complex1_30kDa  78 dwyEREayDmfGivfeghpdlrrillpedfeghPLRkdfplsg 120
                                       dw+EREayD++Gi++eghpd+rrillp+ ++ghPL  d++ ++
  gi|336255107|ref|YP_004598214.1| 124 DWHEREAYDLVGIEYEGHPDPRRILLPDSWQGHPLSLDYDQEK 166
                                       ***************************************9876 PP

>> Autoind_bind  Autoinducer binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.6e-05     0.094       2      79 ..      53     130 ..      52     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHHHTTCSEEEEEEEETTSCESCEEEEEESS-HHHHHHHHHTTGGGT-HHHHHHHHCSSEEEEECGG CS
                      Autoind_bind   2 eeelfdlltrlaaalGfdrfaygarapskdsaedvlllsnyPaeWlerYveegylaiDPvvreaarssspfvWsddl 78 
                                       ++++ ++l  l+++ Gfd+++++     +d+ e++l l+ y +  +e  +  ++ + DPv + a   ++  +W++ +
  gi|336255107|ref|YP_004598214.1|  53 PDDVQEVLGLLRDEAGFDHLSCLTAQEYEDRYESILHLTKYDERQHEVSLVVQLPQGDPVAQSAEPVFRTADWHERE 129
                                       58999******************8899999999999999*************************9999999999976 PP

                                       C CS
                      Autoind_bind  79 l 79 
                                        
  gi|336255107|ref|YP_004598214.1| 130 A 130
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 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:                        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: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 4258.25
//
Query:       gi|336255108|ref|YP_004598215.1|  [L=385]
Description: Tryptophan synthase subunit beta [Halopiger xanaduensis SH-6]
Scores for 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-45  154.5   0.8    4.7e-45  154.3   0.8    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 !  154.3   0.8   2.6e-49   4.7e-45       4     294 .]      52     370 ..      49     370 .. 0.78

  Alignments for each domain:
  == domain 1  score: 154.3 bits;  conditional E-value: 2.6e-49
                                       CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                              PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlk 80 
                                       + +pTPl  +++ls+++g++++lK+E+l ++g++K++      + +k++ + + ++e+++G+hg a+A+++allGl+
  gi|336255108|ref|YP_004598215.1|  52 AGRPTPLYYARNLSERYGADIYLKREDLLHGGAHKINNCLGQALLAKRAGRERLIAETGAGQHGTATAMVGALLGLD 128
                                       689***********************************9966666666659999999999***************** PP

                                       EEEEEETTS-...HHHHHHHHHTT-EEEEE...CCHHHHHHHH.HHHHHHH..STTCEE--TTT.SHH...HHHHHH CS
                              PALP  81 vtivvpadas...pekvallrllGaevvev...ggdydeavaa.aaelaae..gegaylvsqfd.npt...viegyg 144
                                        +i++ +++    + +v ++rl+Gaev ev   +++  +av+a  +++aa+  ++++++ s  + +p    v + ++
  gi|336255108|ref|YP_004598215.1| 129 TEIYMGKKDAerqEMNVFRMRLMGAEVNEVtrgNEGLADAVDAaLEDFAANvdDTHYLVGSVVGpDPFprmVRDFQS 205
                                       *********95555****************877444666666637788888754555555555575557756666** PP

                                       THHHHHH....HHTTTTEEEEEEE-SSSHHHHHHHHHHHH............HSTT.-EEEEEEECTTCGGTTCCS. CS
                              PALP 145 tiglEil....eqlggkpdavvvpvGgGgliaGiaaglke............rrpd.vrvigvepegsdalarslra 204
                                        ig E      e++gg pda v++vGgG+++ G+ +++++            ++pd  r  +  ++g d + ++   
  gi|336255108|ref|YP_004598215.1| 206 VIGEEAReqfrERTGGLPDAAVACVGGGSNAIGLFHAFRDddvdfygtegggEGPDsSRHAAPLSSGTDDVIHG--- 279
                                       ******955556666************************94444444443333333333334444455555555... PP

                                       .S.SS..B............SSS.CCSTCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHH CS
                              PALP 205 grrvtvpvs...........dtiadglavg..spselafelldrlvdeivtvsdeealeamrllarregivvepssa 268
                                               +           ++   gl+ +   p+   f+++ r+     +v+deeal+a r+l ++egi++   s 
  gi|336255108|ref|YP_004598215.1| 280 --------MktrvlendvdvHSVSAGLDYPgvGPEHAMFRAVGRCEY--TGVTDEEALAAFRELSETEGIIPALESS 346
                                       ........34445555555699999**99999999999999999988..99***********************999 PP

                                       HHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 269 aalaalklreagelkegdrvvviltg 294
                                       +a+a +  + a++ + + +++v l+g
  gi|336255108|ref|YP_004598215.1| 347 HAVARA-IELAEDGEHE-TILVNLSG 370
                                       999999.4555555555.88888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 3170.49
//
Query:       gi|336255109|ref|YP_004598216.1|  [L=57]
Description: hypothetical protein Halxa_3730 [Halopiger xanaduensis SH-6]
Scores for 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:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 489.14
//
Query:       gi|336255110|ref|YP_004598217.1|  [L=132]
Description: hypothetical protein Halxa_3731 [Halopiger xanaduensis SH-6]
Scores for 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:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1070.80
//
Query:       gi|336255111|ref|YP_004598218.1|  [L=345]
Description: hypothetical protein Halxa_3733 [Halopiger xanaduensis SH-6]
Scores for 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-19   69.2  14.4    3.2e-19   69.2  14.4    2.0  2  Ni_hydr_CYTB  Prokaryotic cytochrome b561
     0.0056   16.4   2.1     0.0056   16.4   2.1    3.1  3  PepSY_TM      PepSY-associated TM region
  ------ inclusion threshold ------
       0.07   13.3   0.0       0.26   11.4   0.0    1.9  2  DUF2371       Uncharacterised conserved protein (DUF2371)
      0.074   13.0   0.2      0.074   13.0   0.2    3.2  3  DctQ          Tripartite ATP-independent periplasmic transpor
       0.31   11.5   1.8         28    5.2   0.0    2.4  2  SIT           SHP2-interacting transmembrane adaptor protein,
        8.2    6.4   8.5        5.4    6.9   0.2    3.4  3  COX14         Cytochrome oxidase c assembly
          9    6.4   9.0        9.9    6.2   0.9    3.0  3  DUF4227       Protein of unknown function (DUF4227)


Domain annotation for each model (and alignments):
>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2  14.4   1.2e-22   3.2e-19       2     181 ..       9     213 ..       8     214 .. 0.92
   2 ?    0.3   0.3      0.18   4.6e+02      41      64 ..     275     305 ..     230     332 .. 0.50

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.2e-22
                                       ----TTHHHHHHHHHHHHHHHHHHHHHS------S-GGG-....HHHHHHHHHHHHHHHHHHHHHHH.......... CS
                      Ni_hydr_CYTB   2 yslvarllHWlnallvvllllsgllianlhprlywgdsgk....aralHklaGlvllalllfrllwl.......... 64 
                                       +s+v+ ++H l+al+v+ l+++g+ ia+  + +++ ++++    ++++H++aG++l++l++f++l++          
  gi|336255111|ref|YP_004598218.1|   9 FSRVTTIFHSLLALTVFFLFFTGYSIAFNAELWWLVELMGgnewVLTIHRVAGFALMLLTVFWVLYMllrpssrsnl 85 
                                       899************************************988888888***************************** PP

                                       ..------------STTTSSSSS----------------TT...........THHHHHHHHHHHHHHHHHHHT.HHH CS
                      Ni_hydr_CYTB  65 ..kkakkpspriifrqikrdltlllrgrkpeagknnplqkl...........vhlllyvllvvliltGlllsf.aat 127
                                           +  +++ ++f+q  +   ++  +r+p+a++    ++            v++++ v lv+l+++Gll++  +  
  gi|336255111|ref|YP_004598218.1|  86 gdVIPDIKQDTAAFVQDVKFALGYAEERHPHAKQFAGYKADevpllsyvgkgVIAIFAVELVLLMISGLLIWQkT-- 160
                                       *88888888999999999999******************99******************************9853.. PP

                                       HHHHH......HTS-THHHHHHH.HHHHHHHHHHHHHHHHHHHHHH---XXXXXXXX CS
                      Ni_hydr_CYTB 128 agfpll...lddkggaqlarelHellaaallafvvlHiaaallhgpvkkdtlrrMit 181
                                           +l    ++   a+ +   H+ll++++++ v+ H + +  h ++    ++++++
  gi|336255111|ref|YP_004598218.1| 161 ----WLidfYNTQSVAMGFVAFHGLLGIIMFMGVMFHTFEHACHPAFYPVEMKAFLP 213
                                       ....333455699****************************9999998668888765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.18
                                       -.......HHHHHHHHHHHHHHHHHHHHHHH CS
                      Ni_hydr_CYTB  41 k.......aralHklaGlvllalllfrllwl 64 
                                               +r++ + +G+++l++ l+  +++
  gi|336255111|ref|YP_004598218.1| 275 LafnegniFRTIAINVGVLVLFIGLALSMYG 305
                                       1333333333333444555555555555554 PP

>> PepSY_TM  PepSY-associated TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   8.9      0.53   1.3e+03     126     186 ..      15      72 ..       6      76 .. 0.82
   2 !   16.4   2.1   2.2e-06    0.0056     121     185 ..     132     193 ..     112     195 .. 0.87
   3 ?   -0.5   0.0       0.3   7.6e+02      17      53 ..     293     329 ..     285     344 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.53
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          PepSY_TM 126 llvglaallllvllvsGlilwwprrkkkrfftfrpkkgrrfwldlHnvlGvwllpflllla 186
                                       ++  l al  ++l ++G  +    ++   ++ +   +g  + l +H+v+G+ l+++ ++ +
  gi|336255111|ref|YP_004598218.1|  15 IFHSLLALTVFFLFFTGYSIA---FNAELWWLVELMGGNEWVLTIHRVAGFALMLLTVFWV 72 
                                       666889999999999999999...4444688888888899999********9999998865 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.2e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          PepSY_TM 121 kpvGrllvglaallllvllvsGlilwwprrkkkrfftfrpkkg.rrfwldlHnvlGvwllpfllll 185
                                         vG+ ++ + a+ l++l++sGl++w   +k++ +++f ++++    +  +H +lG+++++++++ 
  gi|336255111|ref|YP_004598218.1| 132 SYVGKGVIAIFAVELVLLMISGLLIW---QKTW-LIDFYNTQSvAMGFVAFHGLLGIIMFMGVMFH 193
                                       456***********************...4454.999999999999999**********9998875 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.3
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          PepSY_TM  17 vlalTGallvfkpeieawlnpellvvapaaaaallaa 53 
                                       ++ + G++l+++  i ++ ++ +++++ +++++++++
  gi|336255111|ref|YP_004598218.1| 293 LVLFIGLALSMYGNILRVRYQRQREAQTQREREAEQS 329
                                       5556677777777777777777777777666665432 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.6     4e+03      40      59 ..     173     194 ..     169     218 .. 0.68
   2 ?   11.4   0.0    0.0001      0.26      41      85 ..     285     329 ..     282     339 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
                           DUF2371  40 sglvlllGll..vllvGiamav 59 
                                        g+v++ Gll  ++++G+ + +
  gi|336255111|ref|YP_004598218.1| 173 MGFVAFHGLLgiIMFMGVMFHT 194
                                       4666666663225566666554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0001
                           DUF2371  41 glvlllGllvllvGiamavlgywpkkaklaseekssssstaesss 85 
                                       ++ + +G+lvl++G+a+++ g   + + ++++e +++++ + ++s
  gi|336255111|ref|YP_004598218.1| 285 TIAINVGVLVLFIGLALSMYGNILRVRYQRQREAQTQREREAEQS 329
                                       67789****************988874444433333333222222 PP

>> DctQ  Tripartite ATP-independent periplasmic transporters, DctQ component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   5.3    0.0049        12      59     129 ..       7      76 ..       1      79 [. 0.82
   2 ?    0.6   2.5       0.2     5e+02      67     101 ..     142     174 ..     130     200 .. 0.56
   3 ?   13.0   0.2   2.9e-05     0.074      56     125 ..     236     309 ..     231     316 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0049
                              DctQ  59 prvrrlleliadllall.faavliwagwlevaaalfeettpvlglplwwvylvlpigaallalvalarllrl 129
                                        ++ r++ ++  llal  f+++++ +++  +++a  +     +g   w+  +  + g+al++l   + l+ l
  gi|336255111|ref|YP_004598218.1|   7 GKFSRVTTIFHSLLALTvFFLFFTGYSI--AFNAELWWLVELMGGNEWVLTIHRVAGFALMLLTVFWVLYML 76 
                                       6788999999999888735556666666..999999999***********************9888777665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.2
                              DctQ  67 liadllallfaavliwagwlevaaalfeettpvlg 101
                                       +++ l++l+++++liw+        ++++++ ++g
  gi|336255111|ref|YP_004598218.1| 142 FAVELVLLMISGLLIWQKT--WLIDFYNTQSVAMG 174
                                       3345567777778888876..44444444444444 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 2.9e-05
                              DctQ  56 rlpprvrrlleliadllallfaa....vliwagw..levaaalfeettpvlglplwwvylvlpigaallalvalar 125
                                       rl+p+++++++l+++++++ +a+     +++ g+   e+ a++ ++   ++++ +++    l+ig+al +   + r
  gi|336255111|ref|YP_004598218.1| 236 RLKPTWKWATNLFGAMVIIGIAGvlagSMTYGGYpiPETLAFNEGNIFRTIAINVGVLV--LFIGLALSMYGNILR 309
                                       899*************9999555344488888889999999999999999999999997..999998887765555 PP

>> SIT  SHP2-interacting transmembrane adaptor protein, SIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.0     0.021        53       3      24 ..     138     159 ..     137     161 .. 0.90
   2 ?    5.2   0.0     0.011        28       5      38 ..     293     326 ..     290     339 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.021
                               SIT   3 lllilallLlllviasllawrm 24 
                                       +++i+a+ L+ll+i  ll w +
  gi|336255111|ref|YP_004598218.1| 138 VIAIFAVELVLLMISGLLIWQK 159
                                       679*****************76 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                               SIT   5 lilallLlllviasllawrmkkrqkkaaeysseq 38 
                                       l+l + L l++  ++l  r +++++ +++ + e 
  gi|336255111|ref|YP_004598218.1| 293 LVLFIGLALSMYGNILRVRYQRQREAQTQREREA 326
                                       5566888899999999988887776655543333 PP

>> COX14  Cytochrome oxidase c assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.14   3.5e+02       8      34 ..      11      32 ..       8      38 .. 0.57
   2 ?    1.3   0.3      0.12   3.1e+02      12      27 ..      55      70 ..      47      78 .. 0.82
   3 ?    6.9   0.2    0.0021       5.4      27      57 ..     294     320 ..     290     328 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.14
                             COX14  8 rlaDkaHrltVltLiGvTlyaggllvy 34
                                      r+++++H l +lt     ++    ++y
  gi|336255111|ref|YP_004598218.1| 11 RVTTIFHSLLALT-----VFFLFFTGY 32
                                      6777777666666.....333333333 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.12
                             COX14 12 kaHrltVltLiGvTly 27
                                      ++Hr+  ++L+ +T++
  gi|336255111|ref|YP_004598218.1| 55 TIHRVAGFALMLLTVF 70
                                      78************96 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0021
                             COX14  27 yaggllvytvysygkynrkqkaeliereklk 57 
                                       +   +l+ ++y ++ ++r q++    re+++
  gi|336255111|ref|YP_004598218.1| 294 VLFIGLALSMYGNILRVRYQRQ----REAQT 320
                                       66789999**********9999....33332 PP

>> DUF4227  Protein of unknown function (DUF4227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.9    0.0039       9.9       4      30 ..      20      46 ..      17      52 .. 0.85
   2 ?   -3.1   0.6       3.2   8.2e+03       9      30 ..     138     161 ..     137     166 .. 0.54
   3 ?    4.7   0.0     0.012        30       3      26 ..     286     309 ..     284     317 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0039
                           DUF4227  4 lerlkvflLFtvltllfyyallwlnee 30
                                      l    +fl Ft+ ++ f   l wl e 
  gi|336255111|ref|YP_004598218.1| 20 LALTVFFLFFTGYSIAFNAELWWLVEL 46
                                      556679999**************9875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.2
                           DUF4227   9 vflLFtvltllfyya..llwlnee 30 
                                       v+ +F v  +l+  +  l+w +++
  gi|336255111|ref|YP_004598218.1| 138 VIAIFAVELVLLMISglLIWQKTW 161
                                       566777655554443115555555 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.012
                           DUF4227   3 llerlkvflLFtvltllfyyallw 26 
                                       +   + v++LF++l+l +y  +l 
  gi|336255111|ref|YP_004598218.1| 286 IAINVGVLVLFIGLALSMYGNILR 309
                                       5556789************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 2638.79
//
Query:       gi|336255112|ref|YP_004598219.1|  [L=165]
Description: hypothetical protein Halxa_3734 [Halopiger xanaduensis SH-6]
Scores for 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  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); 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:                         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 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1292.33
//
Query:       gi|336255113|ref|YP_004598220.1|  [L=226]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   59.6  12.1    2.5e-16   59.6  12.1    2.1  2  Fer4_11   4Fe-4S dicluster domain
    1.8e-15   57.2  24.9    1.8e-07   31.6   7.3    2.5  2  Fer4_7    4Fe-4S dicluster domain
    4.3e-13   49.2  24.0      5e-06   26.6   8.3    3.2  3  Fer4_9    4Fe-4S dicluster domain
    6.2e-11   41.6  31.9    8.2e-06   25.4   1.0    5.3  5  Fer4      4Fe-4S binding domain
    3.7e-08   33.4  30.6    3.7e-05   23.7   9.7    3.2  4  Fer4_10   4Fe-4S dicluster domain
    2.4e-07   30.7  31.7      0.056   14.0   2.3    4.4  4  Fer4_4    4Fe-4S binding domain
    2.5e-07   30.4  32.8     0.0024   17.9   0.8    4.3  4  Fer4_2    4Fe-4S binding domain
    4.2e-07   30.8  20.1      0.088   13.8   0.7    4.6  4  Fer4_16   4Fe-4S double cluster binding domain
    6.7e-07   29.1  38.0    0.00086   19.3   1.2    5.1  4  Fer4_6    4Fe-4S binding domain
    8.6e-07   29.0  26.4    1.3e-05   25.2   7.8    3.5  3  Fer4_21   4Fe-4S dicluster domain
    4.8e-06   26.9  21.6    0.00052   20.4   4.5    2.8  2  Fer4_8    4Fe-4S dicluster domain
    0.00027   21.7  41.8      0.049   14.6   5.1    4.3  4  Fer4_3    4Fe-4S binding domain
     0.0053   17.3  28.2      0.059   13.9   0.5    4.5  5  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.039   14.5   0.4      0.039   14.5   0.4    3.9  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.78   10.5  16.2        4.9    8.0   0.3    3.7  3  Fer4_15   4Fe-4S single cluster domain
          3    8.1  22.7        3.9    7.7   2.1    3.5  3  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3       9.4   1.1e+04      13      20 ..      35      40 ..      26      51 .. 0.54
   2 !   59.6  12.1   2.2e-19   2.5e-16       6      98 ..      89     189 ..      87     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.4
                           Fer4_11 13 CleppCva 20
                                      C    Cv 
  gi|336255113|ref|YP_004598220.1| 35 CG--GCVV 40
                                      32..2332 PP

  == domain 2  score: 59.6 bits;  conditional E-value: 2.2e-19
                           Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneet..........gkvekCd 72 
                                       +p qC hC+++pCv+++p++a+ k + +G V l+e+ +  +++ + +acP+ +++  +e           g++ekC+
  gi|336255113|ref|YP_004598220.1|  89 VPMQCFHCENAPCVSVCPTDALQKSD-DGFVDLKESLCV-GCQYCLSACPFGAPQFPNEDegsaeivgtgGTMEKCT 163
                                       699****************9998887.***********7.***********9987643321122222222689**** PP

                           Fer4_11  73 mcldrveaGllpacvescptgalnfg 98 
                                       +c +r+ a + pacv+ c+t+al +g
  gi|336255113|ref|YP_004598220.1| 164 GCKERQMADQGPACVDECATNALLVG 189
                                       *********************99887 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   7.3   1.6e-10   1.8e-07       1      52 []      31     109 ..      31     109 .. 0.67
   2 !   31.3   9.6     2e-10   2.3e-07       2      52 .]     125     185 ..     124     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.6e-10
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek..................gtekv..........eidpekClgCga..Cvav 47 
                                       +Ci Cg Cv+aC+  +   +++e+ +                      +          + +p++C +C++  Cv+v
  gi|336255113|ref|YP_004598220.1|  31 ACIDCGGCVVACKRTWDVGPDRERIDivnmlegqeadegyngrqS---AaladganpgeTNVPMQCFHCENapCVSV 104
                                       5***********766666665555545555544444444454430...14444444444888********99***** PP

                            Fer4_7  48 CPtga 52 
                                       CPt+a
  gi|336255113|ref|YP_004598220.1| 105 CPTDA 109
                                       ***97 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 2e-10
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgt.ekveidpekClgCg.........aCvavCPtga 52 
                                       C+gC++C +aCp +a ++++e++ +     + + +ekC+gC+         aCv++C t+a
  gi|336255113|ref|YP_004598220.1| 125 CVGCQYCLSACPFGAPQFPNEDEGSAEiVGTGGTMEKCTGCKerqmadqgpACVDECATNA 185
                                       ******************9875554431334567*******65555555558*****9997 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.9   2.4e-06    0.0027      33      49 ..      17      45 ..       1      48 [. 0.69
   2 !   23.3   9.7   4.6e-08   5.2e-05       1      50 [.      31     109 ..      31     110 .. 0.92
   3 !   26.6   8.3   4.5e-09     5e-06       2      50 ..     125     185 ..     124     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.4e-06
                            Fer4_9 33 e............eaCigCgaCveaCpkg 49
                                      +            eaCi+Cg Cv aC+++
  gi|336255113|ref|YP_004598220.1| 17 MstgegmrlfpdvEACIDCGGCVVACKRT 45
                                      255566677777889***********985 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 4.6e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase...........................eaCigCga..CveaCpk 48 
                                       +C++Cg Cv aC+ +  v+ + er++ +++ +                             +C++C+   Cv +Cp+
  gi|336255113|ref|YP_004598220.1|  31 ACIDCGGCVVACKRTWDVGPDRERIDIVNMLEGqeadegyngrqsaaladganpgetnvpMQCFHCENapCVSVCPT 107
                                       6***********99999999999999988877789999999999****************99*************** PP

                            Fer4_9  49 ga 50 
                                       +a
  gi|336255113|ref|YP_004598220.1| 108 DA 109
                                       97 PP

  == domain 3  score: 26.6 bits;  conditional E-value: 4.5e-09
                            Fer4_9   2 CtgCgaCveaCpagvvveda.aerkarlraase..eaCigCga.........CveaCpkga 50 
                                       C+gC++C +aCp+g+ +  +  e+ a++  ++   e+C+gC++         Cv+ C ++a
  gi|336255113|ref|YP_004598220.1| 125 CVGCQYCLSACPFGAPQFPNeDEGSAEIVGTGGtmEKCTGCKErqmadqgpaCVDECATNA 185
                                       **************9964440344444444444779*********************9986 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   4.3   2.2e-05     0.024       4      18 ..      28      42 ..      25      44 .. 0.92
   2 !   12.6   0.5   8.4e-05     0.094      14      23 ..     101     110 ..     100     111 .. 0.93
   3 !   25.4   1.0   7.3e-09   8.2e-06       5      23 ..     122     140 ..     118     141 .. 0.91
   4 ?    5.4   0.6     0.015        17       5      12 ..     159     166 ..     158     167 .. 0.86
   5 ?    2.3   0.3      0.15   1.7e+02      13      23 ..     176     186 ..     176     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                                      ETTTSSS-THHHHHS CS
                              Fer4  4 deekCigCGaCvevC 18
                                      d e Ci CG Cv +C
  gi|336255113|ref|YP_004598220.1| 28 DVEACIDCGGCVVAC 42
                                      889************ PP

  == domain 2  score: 12.6 bits;  conditional E-value: 8.4e-05
                                       HHHHSTTTEE CS
                              Fer4  14 CvevCPvgAI 23 
                                       Cv+vCP++A+
  gi|336255113|ref|YP_004598220.1| 101 CVSVCPTDAL 110
                                       *********8 PP

  == domain 3  score: 25.4 bits;  conditional E-value: 7.3e-09
                                       TTTSSS-THHHHHSTTTEE CS
                              Fer4   5 eekCigCGaCvevCPvgAI 23 
                                       e++C+gC +C ++CP+gA 
  gi|336255113|ref|YP_004598220.1| 122 ESLCVGCQYCLSACPFGAP 140
                                       799**************96 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.015
                                       TTTSSS-T CS
                              Fer4   5 eekCigCG 12 
                                       +ekC+gC+
  gi|336255113|ref|YP_004598220.1| 159 MEKCTGCK 166
                                       59*****7 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.15
                                       HHHHHSTTTEE CS
                              Fer4  13 aCvevCPvgAI 23 
                                       aCv+ C ++A+
  gi|336255113|ref|YP_004598220.1| 176 ACVDECATNAL 186
                                       7*****88885 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   3.1   0.00047      0.52      41      55 ..      28      42 ..      12      43 .. 0.75
   2 !   10.2  13.8   0.00056      0.62       5      56 .]      28     106 ..      23     106 .. 0.87
   3 !   10.3   2.5   0.00054      0.61       7      23 ..      91     109 ..      86     120 .. 0.77
   4 !   23.7   9.7   3.3e-08   3.7e-05       5      55 ..     121     181 ..     117     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00047
                           Fer4_10 41 kvekCtgcgaCveaC 55
                                      +ve+C++cg Cv aC
  gi|336255113|ref|YP_004598220.1| 28 DVEACIDCGGCVVAC 42
                                      678888888888888 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00056
                           Fer4_10   5 dddtCirCgkCvkaCPadl..........................tsvgakgeaseeeavrk.kvekCtgcg..aCv 52 
                                       d + Ci Cg Cv aC  +                           ++ +  + a++ ++ ++ ++ +C +c+   Cv
  gi|336255113|ref|YP_004598220.1|  28 DVEACIDCGGCVVAC--KRtwdvgpdreridivnmlegqeadegyNGRQSAALADGANPGETnVPMQCFHCEnaPCV 102
                                       6789***********..6667*********************999666666777777777776899999997669** PP

                           Fer4_10  53 eaCP 56 
                                       ++CP
  gi|336255113|ref|YP_004598220.1| 103 SVCP 106
                                       ***9 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00054
                           Fer4_10   7 dtCirCg..kCvkaCPadl 23 
                                        +C +C+   Cv++CP+d+
  gi|336255113|ref|YP_004598220.1|  91 MQCFHCEnaPCVSVCPTDA 109
                                       58****9889******944 PP

  == domain 4  score: 23.7 bits;  conditional E-value: 3.3e-08
                           Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgc........g.aCveaC 55 
                                        ++ C++C+ C +aCP+ + +  +++e s e +  +  +ekCtgc        g aCv++C
  gi|336255113|ref|YP_004598220.1| 121 KESLCVGCQYCLSACPFGAPQFPNEDEGSAEIVGTGgTMEKCTGCkerqmadqGpACVDEC 181
                                       5788*************999999999999999999989*******6666655538****** PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   2.3     5e-05     0.056       2      15 ..      30      43 ..      30      53 .. 0.91
   2 !   11.5   1.8   0.00031      0.35       4      16 ..      93     107 ..      86     112 .. 0.91
   3 !   13.3   2.7     8e-05      0.09       3      17 .]     124     138 ..     121     138 .. 0.89
   4 !    8.8   2.3    0.0022       2.5       2      15 ..     160     182 ..     159     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-05
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      e Ci+Cg Cv aC+
  gi|336255113|ref|YP_004598220.1| 30 EACIDCGGCVVACK 43
                                      68***********7 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00031
                            Fer4_4   4 CigCgs..CvaaCPq 16 
                                       C++C    Cv++CP+
  gi|336255113|ref|YP_004598220.1|  93 CFHCENapCVSVCPT 107
                                       *****889******7 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 8e-05
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                        C+gC  C +aCP+g
  gi|336255113|ref|YP_004598220.1| 124 LCVGCQYCLSACPFG 138
                                       5************86 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0022
                            Fer4_4   2 erCigCgs.........CvaaCP 15 
                                       e+C+gC+          Cv+ C 
  gi|336255113|ref|YP_004598220.1| 160 EKCTGCKErqmadqgpaCVDECA 182
                                       89*****5556666777***995 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   2.8   4.5e-05     0.051       6      20 ..      28      42 ..      24      44 .. 0.90
   2 !    9.6   4.8   0.00094       1.1      10      22 .]      93     107 ..      88     107 .. 0.89
   3 !   17.9   0.8   2.1e-06    0.0024       7      21 ..     122     136 ..     117     137 .. 0.87
   4 ?    6.0   2.1     0.013        14       8      20 ..     160     181 ..     159     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                            Fer4_2  6 dtdrCigCgaCvsaC 20
                                      d ++Ci Cg Cv aC
  gi|336255113|ref|YP_004598220.1| 28 DVEACIDCGGCVVAC 42
                                      889************ PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00094
                            Fer4_2  10 CigCg..aCvsaCPa 22 
                                       C +C+  +Cvs+CP+
  gi|336255113|ref|YP_004598220.1|  93 CFHCEnaPCVSVCPT 107
                                       99**889*******7 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 2.1e-06
                            Fer4_2   7 tdrCigCgaCvsaCP 21 
                                       +  C+gC  C+saCP
  gi|336255113|ref|YP_004598220.1| 122 ESLCVGCQYCLSACP 136
                                       568************ PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.013
                            Fer4_2   8 drCigCg.........aCvsaC 20 
                                       ++C+gC+         aCv+ C
  gi|336255113|ref|YP_004598220.1| 160 EKCTGCKerqmadqgpACVDEC 181
                                       89****7677888889999999 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 !    7.8   0.2    0.0058       6.6       2      14 ..      32      44 ..      31      78 .. 0.83
   2 !   13.8   0.7   7.8e-05     0.088       1      22 [.      92     115 ..      92     123 .. 0.81
   3 !   12.8   4.6   0.00016      0.18       2      24 ..     125     147 ..     124     174 .. 0.76
   4 ?    4.6   1.1     0.057        63       7      26 ..     176     195 ..     161     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0058
                           Fer4_16  2 CgtCgkCaevCPt 14
                                      C++Cg C+ +C  
  gi|336255113|ref|YP_004598220.1| 32 CIDCGGCVVACKR 44
                                      ***********65 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.8e-05
                           Fer4_16   1 rCgtCgk..CaevCPtnaikekke 22 
                                       +C  C++  C++vCPt+a+++  +
  gi|336255113|ref|YP_004598220.1|  92 QCFHCENapCVSVCPTDALQKSDD 115
                                       599999889**********98855 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00016
                           Fer4_16   2 CgtCgkCaevCPtnaikekkeke 24 
                                       C++C+ C+++CP +a + ++e e
  gi|336255113|ref|YP_004598220.1| 125 CVGCQYCLSACPFGAPQFPNEDE 147
                                       **************988886554 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.057
                           Fer4_16   7 kCaevCPtnaikekkekeie 26 
                                       +C++ C tna+   ++ ei+
  gi|336255113|ref|YP_004598220.1| 176 ACVDECATNALLVGTAGEIA 195
                                       7*********9988555543 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   5.3   5.5e-05     0.061       5      19 ..      28      42 ..      28      45 .. 0.91
   2 !    9.8   3.3   0.00076      0.86      11      24 .]      95     110 ..      92     110 .. 0.81
   3 !   19.3   1.2   7.7e-07   0.00086       6      23 ..     122     139 ..     118     140 .. 0.93
   4 ?    2.5   5.3      0.15   1.7e+02       7      24 .]     160     186 ..     159     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.5e-05
                            Fer4_6  5 dpdkCigCgdCvrvC 19
                                      d ++Ci+Cg Cv++C
  gi|336255113|ref|YP_004598220.1| 28 DVEACIDCGGCVVAC 42
                                      6689*********** PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00076
                            Fer4_6  11 gCgd..CvrvCPegai 24 
                                       +C++  Cv+vCP++a+
  gi|336255113|ref|YP_004598220.1|  95 HCENapCVSVCPTDAL 110
                                       676667*******997 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 7.7e-07
                            Fer4_6   6 pdkCigCgdCvrvCPega 23 
                                       +++C+gC  C ++CP+ga
  gi|336255113|ref|YP_004598220.1| 122 ESLCVGCQYCLSACPFGA 139
                                       79**************99 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.15
                            Fer4_6   7 dkCigCgd.........CvrvCPegai 24 
                                       +kC+gC +         Cv+ C ++a+
  gi|336255113|ref|YP_004598220.1| 160 EKCTGCKErqmadqgpaCVDECATNAL 186
                                       79999977799999999*****99996 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.2   3.2e-05     0.036       5      20 ..      29      44 ..      27      49 .. 0.87
   2 !   25.2   7.8   1.1e-08   1.3e-05       7      53 ..      92     137 ..      88     140 .. 0.91
   3 ?    0.1   2.5      0.82   9.2e+02      38      45 ..     159     166 ..     149     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-05
                           Fer4_21  5 edkCigCgkCliaCed 20
                                       + Ci+Cg C++aC+ 
  gi|336255113|ref|YP_004598220.1| 29 VEACIDCGGCVVACKR 44
                                      589***********96 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.1e-08
                           Fer4_21   7 kCigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                       +C +C++  C+ +C+   ++a++++++  + + e+ CvGC+ C+s CP 
  gi|336255113|ref|YP_004598220.1|  92 QCFHCENapCVSVCP---TDALQKSDDGFVDLKESLCVGCQYCLSACPF 137
                                       8****8666******...6*****************************5 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.82
                           Fer4_21  38 edeCvGCn 45 
                                        ++C+GC+
  gi|336255113|ref|YP_004598220.1| 159 MEKCTGCK 166
                                       58999996 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   4.5   4.6e-07   0.00052       2      64 ..      29     108 ..      28     109 .. 0.60
   2 !   11.6   9.2   0.00026      0.29       5      63 ..     125     183 ..     122     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.6e-07
                            Fer4_8   2 lekCieCgaCqsaCp.............vlrrtk.khlldargeaaedvqeeqvlee..............eealws 50 
                                       +e+Ci Cg C  aC              +++    ++  + ++             +               +   +
  gi|336255113|ref|YP_004598220.1|  29 VEACIDCGGCVVACKrtwdvgpdreridIVNMLEgQEADEGYN-------------GrqsaaladganpgeTNVPMQ 92 
                                       789***********64444333444444333222222222222.............1222333334445668999** PP

                            Fer4_8  51 Cttcga..CtevCpvg 64 
                                       C +c++  C++vCp++
  gi|336255113|ref|YP_004598220.1|  93 CFHCENapCVSVCPTD 108
                                       **************85 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00026
                            Fer4_8   5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga.........CtevCpv 63 
                                       C++C++C saCp+   +  ++++ +g a+  v +         +++Ct+c++         C+++C +
  gi|336255113|ref|YP_004598220.1| 125 CVGCQYCLSACPFGAPQ--FPNEDEGSAEI-VGTGGT------MEKCTGCKErqmadqgpaCVDECAT 183
                                       ************87765..88888888777.666665......9*******98888888889998876 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   4.8     0.031        34       1      11 [.      32      42 ..      32      44 .. 0.93
   2 !   14.6   5.1   4.4e-05     0.049       1      15 []      93     109 ..      93     109 .. 0.91
   3 !   13.2   5.2   0.00012      0.14       1      15 []     125     139 ..     125     139 .. 0.97
   4 ?    6.9   3.0     0.013        14       1      15 []     162     185 ..     162     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.031
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+ Cg Cv++C
  gi|336255113|ref|YP_004598220.1| 32 CIDCGGCVVAC 42
                                      9********** PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.4e-05
                            Fer4_3   1 CtgCg..aCvevCPvgA 15 
                                       C +C+  +Cv vCP++A
  gi|336255113|ref|YP_004598220.1|  93 CFHCEnaPCVSVCPTDA 109
                                       9***8778*******98 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00012
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gC+ C+ +CP gA
  gi|336255113|ref|YP_004598220.1| 125 CVGCQYCLSACPFGA 139
                                       *************98 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.013
                            Fer4_3   1 CtgCg.........aCvevCPvgA 15 
                                       CtgC          aCv+ C ++A
  gi|336255113|ref|YP_004598220.1| 162 CTGCKerqmadqgpACVDECATNA 185
                                       ****66889999999*****9988 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.5   5.2e-05     0.059      30      57 ..      16      43 ..       1      47 [. 0.64
   2 !   11.3   9.4   0.00036       0.4       1      59 [.      31     108 ..      31     110 .. 0.58
   3 !   10.8   2.7    0.0005      0.56       2      14 ..     125     137 ..     119     140 .. 0.60
   4 ?    2.0  13.0      0.28   3.1e+02       2      20 ..     125     144 ..     124     184 .. 0.65
   5 ?   -1.2   2.7       2.8   3.1e+03       2      15 ..     162     184 ..     161     205 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-05
                           Fer4_17 30 klglleeaekeekaslCieCgeCerkCP 57
                                      +++  e++   + ++ Ci Cg+C+ +C 
  gi|336255113|ref|YP_004598220.1| 16 NMSTGEGMRLFPDVEACIDCGGCVVACK 43
                                      34555555555899*************6 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00036
                           Fer4_17   1 rCiqCgyClpeCpsyea..............ydnepk...kllraaklglleeaekeekaslCieCge..CerkCPq 58 
                                       +Ci Cg C+ +C + ++               ++e +   + ++ a+l++  +  + ++  +C +C++  C+++CP 
  gi|336255113|ref|YP_004598220.1|  31 ACIDCGGCVVACKRTWDvgpdreridivnmlEGQEADegyNGRQSAALADGANPGETNVPMQCFHCENapCVSVCPT 107
                                       6*************8885544333333322211111111122233233333333334799******8777******8 PP

                           Fer4_17  59 g 59 
                                       +
  gi|336255113|ref|YP_004598220.1| 108 D 108
                                       6 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0005
                           Fer4_17   2 CiqCgyClpeCps 14 
                                       C +C+yCl +Cp+
  gi|336255113|ref|YP_004598220.1| 125 CVGCQYCLSACPF 137
                                       5555555555554 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.28
                           Fer4_17   2 CiqCgyClpeCpsyea.ydn 20 
                                       C +C+yCl +Cp+++   +n
  gi|336255113|ref|YP_004598220.1| 125 CVGCQYCLSACPFGAPqFPN 144
                                       99999999999987653333 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 2.8
                           Fer4_17   2 CiqCgy.........ClpeCpsy 15 
                                       C++C+          C++eC ++
  gi|336255113|ref|YP_004598220.1| 162 CTGCKErqmadqgpaCVDECATN 184
                                       66665222233334477777765 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 ?   14.5   0.4   3.5e-05     0.039       3      33 ..      29      59 ..      28      79 .. 0.79
   2 ?   -0.5   1.9       1.7   1.9e+03       6      17 ..      93     106 ..      90     112 .. 0.68
   3 ?    3.1   8.3      0.12   1.4e+02       4      37 ..     123     159 ..     118     187 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-05
                           Fer4_13  3 rdtCiacgaCvelaPdvFeeddeggasvvae 33
                                       + Ci+cg Cv ++  + +  ++ ++  +++
  gi|336255113|ref|YP_004598220.1| 29 VEACIDCGGCVVACKRTWDVGPDRERIDIVN 59
                                      589****************999988776665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                           Fer4_13   6 Ciacga..CvelaP 17 
                                       C  c++  Cv+++P
  gi|336255113|ref|YP_004598220.1|  93 CFHCENapCVSVCP 106
                                       66665444888887 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.12
                           Fer4_13   4 dtCiacgaCvelaP...dvFeeddeggasvvaeqpts 37 
                                       + C++c+ C +++P     F  +deg+a +v  + t 
  gi|336255113|ref|YP_004598220.1| 123 SLCVGCQYCLSACPfgaPQFPNEDEGSAEIVGTGGTM 159
                                       67************44446888888888877665444 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   0.3    0.0044       4.9       4      21 ..      28      45 ..      26      87 .. 0.81
   2 ?    0.5   0.1      0.96   1.1e+03      57      64 ..     103     110 ..      99     112 .. 0.82
   3 ?    7.9   5.1    0.0046       5.2       5      41 ..     122     161 ..     117     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0044
                           Fer4_15  4 DrdaCigcglCvaeapev 21
                                      D +aCi cg Cv ++++ 
  gi|336255113|ref|YP_004598220.1| 28 DVEACIDCGGCVVACKRT 45
                                      779************754 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.96
                           Fer4_15  57 raCPvdAI 64 
                                       ++CP+dA+
  gi|336255113|ref|YP_004598220.1| 103 SVCPTDAL 110
                                       68999997 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0046
                           Fer4_15   5 rdaCigcglCvaea....pevfeldedglasvllddgeiae 41 
                                       +++C gc  C+ ++    p  f ++++g a++++++g+ ++
  gi|336255113|ref|YP_004598220.1| 122 ESLCVGCQYCLSACpfgaP-QFPNEDEGSAEIVGTGGTMEK 161
                                       689***********88754.788888*******87666443 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   2.1    0.0035       3.9      59      76 ..      30      47 ..       4      68 .. 0.73
   2 ?    6.9   8.8    0.0063         7      54      95 ..      86     135 ..      56     136 .. 0.68
   3 ?   -2.3   0.2       4.4   4.9e+03      90      95 ..     176     181 ..     155     190 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0035
                           Fer4_18 59 gdcidcescvkvcPtgid 76
                                        cidc+ cv  c    d
  gi|336255113|ref|YP_004598220.1| 30 EACIDCGGCVVACKRTWD 47
                                      557777777777766555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0063
                           Fer4_18  54 kekgagdcidces..cvkvcPtgidir..kGl.qle...ciscllcidac 95 
                                       +++   +c +ce   cv+vcPt+   +  +G+  l+   c+ c+ c+ ac
  gi|336255113|ref|YP_004598220.1|  86 ETNVPMQCFHCENapCVSVCPTDALQKsdDGFvDLKeslCVGCQYCLSAC 135
                                       4556679****9666*******86333125643232334**********9 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.4
                           Fer4_18  90 lcidac 95 
                                        c+d c
  gi|336255113|ref|YP_004598220.1| 176 ACVDEC 181
                                       344544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1763.38
//
Query:       gi|336255114|ref|YP_004598221.1|  [L=1077]
Description: Nitrate reductase [Halopiger xanaduensis SH-6]
Scores for 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-52  176.7   2.0    1.2e-51  176.0   2.0    1.4  1  Molybdopterin    Molybdopterin oxidoreductase
    1.8e-19   69.8   0.1    1.1e-18   67.3   0.1    2.3  2  Molydop_binding  Molydopterin dinucleotide binding domain
    1.1e-12   47.8   0.2      2e-12   46.9   0.2    1.5  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
     0.0034   17.2   1.9     0.0071   16.1   1.9    1.5  1  TAT_signal       TAT (twin-arginine translocation) pathway si
  ------ inclusion threshold ------
        0.8   10.0   5.8        1.3    9.3   0.7    3.3  3  Rieske_3         Rieske 3Fe-4S


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.0   2.0   3.4e-55   1.2e-51       1     431 [.     107     606 ..     107     607 .. 0.91

  Alignments for each domain:
  == domain 1  score: 176.0 bits;  conditional E-value: 3.4e-55
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rlk+P+++   + +G++++++W eA+++ia+  +++ ++ygpd+ ++++s    s+e+ ++++kl++ +g    +++
  gi|336255114|ref|YP_004598221.1| 107 RLKHPLKK---E-NGEWRKITWNEAYDEIAETWQEVTEEYGPDSTMMVGSAHH-SNEEAYAFRKLAAFMGT---NNV 175
                                       9*******...6.9********************************9777555.59****9***9998888...899 PP

                                       ECCGGGTTHHHH...CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB CS
                     Molybdopterin  78 dwyadlppasaq...qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpry 151
                                       d++a+ +++ ++      ++      +++n+++d  n dl i++G N++e +pi+  +i+  + +++  +++i+pry
  gi|336255114|ref|YP_004598221.1| 176 DHQARICHSPTVaglANTWGF----GAMTNTINDYRNFDLNIIIGQNPAEAHPIAMQHILEGQARGG-TIVSIDPRY 247
                                       999999998775555333332....35788999**********************999999999975.5******** PP

                                       -HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHH CS
                     Molybdopterin 152 aellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarela 228
                                       ++++ +ad +   +pgtd+a+++++ +++ ++   d+e l  + +g e     l+ +  e +++++   ++   e  
  gi|336255114|ref|YP_004598221.1| 248 TKTSAHADHYYRMRPGTDVAIMMGLLYYLDEQDELDEEMLSDRVNGWEDAYAELDRYDLETAAEISWLSVEDLEEIG 324
                                       **99********************99999999999****************************************** PP

                                       HHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCT CS
                     Molybdopterin 229 rnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslk 305
                                       + +++++++  i + +g +++++g++++r  + L l+ g   ++gGg + ++G  +++ga        +l+ ++s+ 
  gi|336255114|ref|YP_004598221.1| 325 DMIIENKPNVQIEWAMGGTQHNNGTQNIRSYALLSLASGSAARSGGGLQVMRGHANVQGATDLGVDADILPGYYSVS 401
                                       *****************************************************999999777666666777777777 PP

                                       T............................................................................ CS
                     Molybdopterin 306 e............................................................................ 306
                                       +                                                                            
  gi|336255114|ref|YP_004598221.1| 402 Spgswahwtnvwdrspwtsgstdfndmygrfdmlpedlmeelgeteetvttaqvdtevedslggdeyrpnevttrsm 478
                                       799999999999999999999999999999999999999999999999999999999999999***********999 PP

                                       ...HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH..HHHHSTTSCCCHCHHHCSSEEEEEESCSSHH CS
                     Molybdopterin 307 ...ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgn.npevdhadenevekalekldlvvvldgrltst 379
                                            + +a + +  l++   ++    snl + + +k+l+l g+  ++++  d++++  a e ldl+vv+d++ +  
  gi|336255114|ref|YP_004598221.1| 479 mfqSGLTVARWYEAALPQ---EERLHESNLYQPNPLKMLFLWGHsANSINEMDKMKR--AMEALDLLVVVDVFPAVA 550
                                       997667777777776666...4444578999************97789999999999..***************999 PP

                                       HHTSS....EEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                     Molybdopterin 380 alyaD....iiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                          +D    i+LPa++ yE+    tn+ +++q  ++a +p+ ++k+d +I+++La+
  gi|336255114|ref|YP_004598221.1| 551 GTLSDednvILLPASSQYEHYRSLTNTHRSVQWSEPAGKPAHNSKPDLQIMQELAD 606
                                       9999999*99********************************************97 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.76   2.7e+03      47      73 ..     238     264 ..     232     274 .. 0.85
   2 !   67.3   0.1     3e-22   1.1e-18       2     108 ..     903    1029 ..     902    1032 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.76
                                       T-EEEEEETTEEEEEEEEEESSB-TTE CS
                   Molydop_binding  47 GdlVevesrrGsvevrakvtervrpGv 73 
                                       G +V +  r+ ++ + a   +r+rpG+
  gi|336255114|ref|YP_004598221.1| 238 GTIVSIDPRYTKTSAHADHYYRMRPGT 264
                                       88899999999**************98 PP

  == domain 2  score: 67.3 bits;  conditional E-value: 3e-22
                                        EEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTE...EEEEEEEEESSB-TT CS
                   Molydop_binding    2 rLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrG...svevrakvtervrpG 72  
                                        +L++gr++++   + +tr+ +  a+++p +++ei+p+ A+++Gi+ Gd+V v+s++    ++ v+akv++r +p+
  gi|336255114|ref|YP_004598221.1|  903 ILTSGRQVEHQGGGSETRNNEMTADRQPhMYAEIHPDRAEEMGISGGDEVIVHSAHDaksAILVKAKVDYRPHPD 977 
                                        79*****99999999999999999999999*************************999999************** PP

                                        EEEEESSHCC.....................S-GHCTS--SCSTTT--CSTT CS
                   Molydop_binding   73 vvfmpfgwwe................agekggnaNaltddatdplsgtpefk 108 
                                         vf+p++w+                 +   g ++N +t+ ++d  +++ e k
  gi|336255114|ref|YP_004598221.1|  978 EVFLPYHWGGvfggkdksddwpegtkPLAIGDSVNIVTAHGFDAETQMQETK 1029
                                        **************************9999*************999998877 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.2   5.5e-16     2e-12       3      52 ..      52     101 ..      50     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 5.5e-16
                                       EEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHC CS
                    Molybdop_Fe4S4   3 vvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtller 52 
                                       ++k +C yC+vgCg++++ +++ +v  e+++++p+n+g lC KG+++le+
  gi|336255114|ref|YP_004598221.1|  52 TAKVICNYCSVGCGFKAVKEGDSFVGQEPWKENPINNGSLCSKGASILET 101
                                       67889*****************************************9987 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.9     2e-06    0.0071       2      22 ..      10      30 ..       9      33 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalgg 22
                                      l+RR+F+K+sA a+A  +  g
  gi|336255114|ref|YP_004598221.1| 10 LDRRSFMKASALAGATILGSG 30
                                      79************9876555 PP

>> Rieske_3  Rieske 3Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.7   0.00037       1.3       1      14 [.      57      70 ..      57      87 .. 0.86
   2 ?   -1.1   0.0      0.65   2.3e+03      67      93 ..      80     106 ..      71     108 .. 0.86
   3 ?    0.7   0.1      0.17   6.2e+02      25      61 ..     873     910 ..     865     913 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00037
                                      -SSBTT--EEEEEE CS
                          Rieske_3  1 CdyCivgCgYkvYk 14
                                      C+yC vgCg+k+ k
  gi|336255114|ref|YP_004598221.1| 57 CNYCSVGCGFKAVK 70
                                      **********9865 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.65
                                       E-TT-TTTTT---TTGGGTTTTS-BTT CS
                          Rieske_3  67 pdkdcvvnkGdssirGgrlaeklysee 93 
                                       p k+  +n+G    +G+ + e+ +s++
  gi|336255114|ref|YP_004598221.1|  80 PWKENPINNGSLCSKGASILETEHSPT 106
                                       779999***********9998888765 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.17
                                       GGGSTT-S-TTS.---TT-SS---GGGEEEEEETTEEE CS
                          Rieske_3  25 aeenalgvDlsk.qqkalseawvapsmynvvkkdgkdv 61 
                                        ++n + +D ++ q+++++++ v ++ ++v+   g++v
  gi|336255114|ref|YP_004598221.1| 873 HQQNVYRLDQNNgQTQQQATEAVHEKGFEVILTSGRQV 910
                                       4789999998762455566688999999***9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1077 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:                        41  (0.0022868); 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 0.26s 00:00:00.99 Elapsed: 00:00:00.42
# Mc/sec: 7618.05
//
Query:       gi|336255115|ref|YP_004598222.1|  [L=719]
Description: methyl-viologen-reducing hydrogenase subunit delta [Halopiger xanaduensis SH-6]
Scores for 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-26   90.4   0.0    3.8e-25   88.3   0.0    2.2  2  FlpD            Methyl-viologen-reducing hydrogenase, delta s
    2.5e-17   63.2  25.1    1.4e-07   32.0   9.3    5.6  5  Fer4_7          4Fe-4S dicluster domain
    1.9e-14   52.8  42.9    5.8e-06   25.9   1.1    7.3  7  Fer4            4Fe-4S binding domain
    2.9e-12   47.3  25.8     0.0013   19.6   0.5    6.7  6  Fer4_16         4Fe-4S double cluster binding domain
    1.7e-11   44.1  33.2    2.6e-06   27.5   9.0    5.0  5  Fer4_9          4Fe-4S dicluster domain
    2.1e-07   30.9  34.5    4.1e-05   23.6   6.4    5.3  5  Fer4_21         4Fe-4S dicluster domain
    3.3e-07   30.7  25.7      0.078   13.4   1.6    5.8  5  Fer4_8          4Fe-4S dicluster domain
    3.9e-07   30.1  41.0    4.4e-06   26.7  10.0    4.8  5  Fer4_10         4Fe-4S dicluster domain
    4.9e-07   29.5  51.2    1.9e-05   24.5   0.8    7.0  6  Fer4_6          4Fe-4S binding domain
    2.2e-06   28.1  25.9      0.035   14.7   0.1    6.0  6  Fer4_17         4Fe-4S dicluster domain
    0.00016   21.6   2.7    0.00016   21.6   2.7    6.8  6  Fer4_2          4Fe-4S binding domain
     0.0057   17.1   3.5     0.0057   17.1   3.5    6.4  6  Fer4_4          4Fe-4S binding domain
  ------ inclusion threshold ------
      0.022   15.0  25.9      0.027   14.7   1.4    4.4  4  Fer4_18         4Fe-4S dicluster domain


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 ?   -3.0   0.0         5   6.9e+03      53      64 ..     132     143 ..     114     182 .. 0.60
   2 !   88.3   0.0   2.8e-28   3.8e-25       1     120 [.     395     516 ..     395     517 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5
                              FlpD  53 dgVlvlgChpgd 64 
                                       d+V+v+g+ +  
  gi|336255115|ref|YP_004598222.1| 132 DAVAVVGDAETA 143
                                       556666655433 PP

  == domain 2  score: 88.3 bits;  conditional E-value: 2.8e-28
                              FlpD   1 ilaFlCnwcayaaadlag......vsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGn 71 
                                       ++aF+C++ a +a+ ++g       ++++ypp + +++v+C+++v ++++++al++GadgV+++gC+ gdC + +G+
  gi|336255115|ref|YP_004598222.1| 395 VVAFVCSERAADALAEYGrlaasgRADVEYPP-ILPVQVNCTDTVGEAHVMHALAAGADGVAIVGCG-GDCLH-SGP 468
                                       79***********99998888888999*****.**********************************.*****.*** PP

                              FlpD  72 ekaerrveklkelleelgiepeRvrleevsaaegekfaevikefvekik 120
                                       + +++ v++l  ++++lg++ +Rv++++ +++e+e+f+e +++fv  ++
  gi|336255115|ref|YP_004598222.1| 469 DPKADLVRRLDVATDDLGLG-KRVEFFAPDPNEPEAFVEDVSTFVVGLE 516
                                       ********************.***********************97765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0046       6.3       2      15 ..     200     213 ..     173     229 .. 0.73
   2 ?    1.0   0.0      0.47   6.5e+02      11      25 ..     234     248 ..     232     304 .. 0.83
   3 !   32.0   9.3     1e-10   1.4e-07       3      52 .]     311     354 ..     309     354 .. 0.93
   4 !    9.3   0.0    0.0013       1.7      33      52 .]     575     594 ..     537     594 .. 0.79
   5 !   19.6   1.4   7.4e-07     0.001       1      42 [.     608     668 ..     608     672 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0046
                            Fer4_7   2 CigCgaCvaaCpvk 15 
                                       Ci C +Cv+  p +
  gi|336255115|ref|YP_004598222.1| 200 CISCMKCVREAPEG 213
                                       55555555555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.47
                            Fer4_7  11 aCpvkaieldeeene 25 
                                        Cp++aield +e+ 
  gi|336255115|ref|YP_004598222.1| 234 CCPTDAIELDGVERT 248
                                       6*******9977554 PP

  == domain 3  score: 32.0 bits;  conditional E-value: 1e-10
                            Fer4_7   3 igCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +gC+ Cv+aCp++a+e         +++ve++ e C++CgaC + CPtga
  gi|336255115|ref|YP_004598222.1| 311 VGCNECVEACPHDAVERSS------IDEVEFNTELCQNCGACTSSCPTGA 354
                                       79**************966......577********************98 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0013
                            Fer4_7  33 idpekClgCgaCvavCPtga 52 
                                        + + C+ +  C + CPt+a
  gi|336255115|ref|YP_004598222.1| 575 EVDDACTLTPTCSTLCPTDA 594
                                       34689*************97 PP

  == domain 5  score: 19.6 bits;  conditional E-value: 7.4e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaielde.................eenekgt.......ekveidpekClgCg 42 
                                       rC++Cg C++ C  +ai+++e                 e             +  e+++ +C +Cg
  gi|336255115|ref|YP_004598222.1| 608 RCVNCGLCEDGCVENAITVEEgldlsllpenreddvadE-----EdadpawtQVFEGSMLECKNCG 668
                                       8*****************995444444443333222111.....1222223355688888899997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   1.5    0.0017       2.3       5      16 ..     197     208 ..     195     209 .. 0.88
   2 ?    2.7   0.1     0.089   1.2e+02      18      24 .]     235     241 ..     235     241 .. 0.94
   3 !   18.3   2.7     1e-06    0.0014       9      23 ..     311     325 ..     311     326 .. 0.93
   4 !   25.9   1.1   4.2e-09   5.8e-06       1      22 [.     333     354 ..     333     355 .. 0.95
   5 !    5.7   0.0    0.0098        13      14      24 .]     586     596 ..     585     596 .. 0.88
   6 !   17.3   1.9   2.2e-06     0.003       2      23 ..     603     624 ..     602     625 .. 0.87
   7 ?   -2.0   0.5       2.6   3.6e+03       7      12 ..     663     668 ..     662     669 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0017
                                       TTTSSS-THHHH CS
                              Fer4   5 eekCigCGaCve 16 
                                       +e+Ci C++Cv 
  gi|336255115|ref|YP_004598222.1| 197 TEDCISCMKCVR 208
                                       699*******96 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.089
                                       STTTEEE CS
                              Fer4  18 CPvgAIt 24 
                                       CP++AI+
  gi|336255115|ref|YP_004598222.1| 235 CPTDAIE 241
                                       ******6 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1e-06
                                       SS-THHHHHSTTTEE CS
                              Fer4   9 igCGaCvevCPvgAI 23 
                                       +gC++Cve+CP++A 
  gi|336255115|ref|YP_004598222.1| 311 VGCNECVEACPHDAV 325
                                       79************7 PP

  == domain 4  score: 25.9 bits;  conditional E-value: 4.2e-09
                                       EEEETTTSSS-THHHHHSTTTE CS
                              Fer4   1 vvideekCigCGaCvevCPvgA 22 
                                       v++++e+C +CGaC + CP+gA
  gi|336255115|ref|YP_004598222.1| 333 VEFNTELCQNCGACTSSCPTGA 354
                                       579******************9 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.0098
                                       HHHHSTTTEEE CS
                              Fer4  14 CvevCPvgAIt 24 
                                       C   CP++A++
  gi|336255115|ref|YP_004598222.1| 586 CSTLCPTDALR 596
                                       99*******85 PP

  == domain 6  score: 17.3 bits;  conditional E-value: 2.2e-06
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       +++ e+C++CG+C++ C  +AI
  gi|336255115|ref|YP_004598222.1| 603 EFNHERCVNCGLCEDGCVENAI 624
                                       6899************977777 PP

  == domain 7  score: -2.0 bits;  conditional E-value: 2.6
                                       TSSS-T CS
                              Fer4   7 kCigCG 12 
                                        C +CG
  gi|336255115|ref|YP_004598222.1| 663 ECKNCG 668
                                       599999 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 ?    4.1   0.2     0.064        88       2      19 ..     200     217 ..     199     229 .. 0.82
   2 ?    3.0   0.0      0.15     2e+02      10      25 ..     233     249 ..     232     266 .. 0.75
   3 !   15.0   0.4   2.6e-05     0.036       4      26 ..     312     334 ..     311     338 .. 0.82
   4 !   19.6   0.5   9.2e-07    0.0013       2      27 ..     340     365 ..     339     382 .. 0.73
   5 ?    4.3   0.2     0.057        78       2      20 ..     580     598 ..     579     606 .. 0.80
   6 !   14.9   1.0   2.9e-05     0.039       1      60 [.     608     667 ..     608     669 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.064
                           Fer4_16   2 CgtCgkCaevCPtnaike 19 
                                       C++C kC+   P++ ++ 
  gi|336255115|ref|YP_004598222.1| 200 CISCMKCVREAPEGTVTR 217
                                       ********9999887765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.15
                           Fer4_16  10 evCPtnaikek.kekei 25 
                                       e CPt+ai+ +  e+++
  gi|336255115|ref|YP_004598222.1| 233 ECCPTDAIELDgVERTL 249
                                       78*******88544444 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2.6e-05
                           Fer4_16   4 tCgkCaevCPtnaikekkekeie 26 
                                       +C++C+e+CP++a++  +  e+e
  gi|336255115|ref|YP_004598222.1| 312 GCNECVEACPHDAVERSSIDEVE 334
                                       7*************998666665 PP

  == domain 4  score: 19.6 bits;  conditional E-value: 9.2e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiea 27 
                                       C++Cg+C+++CPt+a + ++  + ++
  gi|336255115|ref|YP_004598222.1| 340 CQNCGACTSSCPTGATQLREPSNERI 365
                                       ***************88764333333 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.057
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C+    C   CPt+a++ +
  gi|336255115|ref|YP_004598222.1| 580 CTLTPTCSTLCPTDALRRT 598
                                       555667**********977 PP

  == domain 6  score: 14.9 bits;  conditional E-value: 2.9e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisy.ntaekkdlaedeekckkqeaitgCdiC 60 
                                       rC++Cg C + C +nai+ ++   +    +  +  +a+++d+ +   +   ++ +  C++C
  gi|336255115|ref|YP_004598222.1| 608 RCVNCGLCEDGCVENAITVEEGLDLSLLPENREdDVADEEDADPAWTQVF-EGSMLECKNC 667
                                       6*****************99555554433333325555555555555554.6667888888 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1    0.0003      0.41      26      48 ..     190     212 ..     169     215 .. 0.69
   2 ?   -0.6   0.0       1.1   1.6e+03      11      28 ..     234     251 ..     232     254 .. 0.72
   3 !   27.5   9.0   1.9e-09   2.6e-06       3      50 ..     311     354 ..     311     355 .. 0.91
   4 !   16.1   6.4   6.9e-06    0.0095       2      51 .]     580     624 ..     578     624 .. 0.87
   5 ?   -2.2   0.0       3.5   4.9e+03      35      40 ..     663     668 ..     642     670 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                            Fer4_9  26 arlraaseeaCigCgaCveaCpk 48 
                                       + +ra+  e+Ci+C++Cv   p+
  gi|336255115|ref|YP_004598222.1| 190 VTVRARVTEDCISCMKCVREAPE 212
                                       3333333367********87665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                            Fer4_9  11 aCpagvvvedaaerkarl 28 
                                        Cp+++++ d +er+ ++
  gi|336255115|ref|YP_004598222.1| 234 CCPTDAIELDGVERTLEV 251
                                       588888888888877665 PP

  == domain 3  score: 27.5 bits;  conditional E-value: 1.9e-09
                            Fer4_9   3 tgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       +gC++CveaCp+++v++++  +   +++     C  CgaC+  Cp+ga
  gi|336255115|ref|YP_004598222.1| 311 VGCNECVEACPHDAVERSSIDEVEFNTE----LCQNCGACTSSCPTGA 354
                                       59***************99999988765....6************996 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 6.9e-06
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       Ct   +C + Cp+++ ++ + + + +++     +C+ Cg C++ C ++ai
  gi|336255115|ref|YP_004598222.1| 580 CTLTPTCSTLCPTDALRRTQTGLEFNHE-----RCVNCGLCEDGCVENAI 624
                                       444457****************999985.....5***********99887 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 3.5
                            Fer4_9  35 aCigCg 40 
                                       +C  Cg
  gi|336255115|ref|YP_004598222.1| 663 ECKNCG 668
                                       455554 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   1.1    0.0046       6.4      37      52 ..     196     211 ..     180     217 .. 0.65
   2 ?    4.7   3.4     0.024        33       6      23 ..     198     215 ..     194     242 .. 0.72
   3 !   23.6   6.4   2.9e-08   4.1e-05       9      55 ..     311     353 ..     305     357 .. 0.91
   4 !    6.4   0.5    0.0071       9.9      35      56 ..     574     594 ..     550     597 .. 0.79
   5 !    9.1   2.8   0.00099       1.4       4      23 ..     605     624 ..     603     631 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0046
                           Fer4_21  37 vedeCvGCnlCssvCP 52 
                                       v+++C+ C  C+   P
  gi|336255115|ref|YP_004598222.1| 196 VTEDCISCMKCVREAP 211
                                       4555555555555444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                           Fer4_21   6 dkCigCgkCliaCedtsh 23 
                                       ++Ci+C kC+   +++++
  gi|336255115|ref|YP_004598222.1| 198 EDCISCMKCVREAPEGTV 215
                                       678888888877666554 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 2.9e-08
                           Fer4_21   9 igCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPved 55 
                                       +gC++C+ aC+   h+a+e ++   ++  ++ C  C  C+s CP+ +
  gi|336255115|ref|YP_004598222.1| 311 VGCNECVEACP---HDAVERSSIDEVEFNTELCQNCGACTSSCPT-G 353
                                       89*********...9****9999999******************6.4 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0071
                           Fer4_21  35 kvvedeCvGCnlCssvCPvedc 56 
                                         v+d C+    Cs+ CP+ d+
  gi|336255115|ref|YP_004598222.1| 574 VEVDDACTLTPTCSTLCPT-DA 594
                                       34799*************7.65 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.00099
                           Fer4_21   4 dedkCigCgkCliaCedtsh 23 
                                       ++++C++Cg+C   C ++++
  gi|336255115|ref|YP_004598222.1| 605 NHERCVNCGLCEDGCVENAI 624
                                       66788888888888877554 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   0.0    0.0074        10      44      62 ..     189     211 ..     145     214 .. 0.69
   2 ?    2.7   2.0      0.13   1.8e+02      53      63 ..     312     322 ..     309     324 .. 0.78
   3 !   13.0   2.7   7.5e-05       0.1       4      29 ..     339     364 ..     336     382 .. 0.70
   4 ?    5.4   0.0     0.019        26      48      64 ..     577     593 ..     533     594 .. 0.83
   5 !   13.4   1.6   5.6e-05     0.078       3      55 ..     607     668 ..     605     669 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0074
                            Fer4_8  44 e....eealwsCttcgaCtevCp 62 
                                       e    ++  + C +c++C+++ p
  gi|336255115|ref|YP_004598222.1| 189 EvtvrARVTEDCISCMKCVREAP 211
                                       24445677899999999998655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.13
                            Fer4_8  53 tcgaCtevCpv 63 
                                       +c++C+e+Cp 
  gi|336255115|ref|YP_004598222.1| 312 GCNECVEACPH 322
                                       68888888886 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 7.5e-05
                            Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldar 29 
                                        C +CgaC+s+Cp+  ++ +++ + r
  gi|336255115|ref|YP_004598222.1| 339 LCQNCGACTSSCPTGATQLREPSNER 364
                                       47778888888887777666655555 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.019
                            Fer4_8  48 lwsCttcgaCtevCpvg 64 
                                        ++Ct +  C++ Cp++
  gi|336255115|ref|YP_004598222.1| 577 DDACTLTPTCSTLCPTD 593
                                       579************85 PP

  == domain 5  score: 13.4 bits;  conditional E-value: 5.6e-05
                            Fer4_8   3 ekCieCgaCqsaCp....vlrrtkkhlldargeaaedvqeeqvlee......eealwsCttcg 55 
                                       e+C++Cg+C++ C     ++++  + +l ++++  + v +e+  +       e ++ +C +cg
  gi|336255115|ref|YP_004598222.1| 607 ERCVNCGLCEDGCVenaiTVEEGLDLSLLPENREDD-VADEEDADPawtqvfEGSMLECKNCG 668
                                       79***********54444444444566666665555.33333222246667788899999987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.4      0.02        28      36      53 ..     191     208 ..     179     211 .. 0.65
   2 ?    3.9   3.3     0.042        58       7      25 ..     198     214 ..     193     250 .. 0.70
   3 !   26.7  10.0   3.2e-09   4.4e-06      10      56 .]     311     351 ..     298     351 .. 0.91
   4 !   11.6   8.4   0.00016      0.23       5      55 ..     576     619 ..     573     621 .. 0.80
   5 ?    5.7   5.1     0.011        16       4      49 ..     604     668 ..     602     670 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.02
                           Fer4_10  36 eavrkkvekCtgcgaCve 53 
                                        +   + e+C+ c +Cv+
  gi|336255115|ref|YP_004598222.1| 191 TVRARVTEDCISCMKCVR 208
                                       555557778888888875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.042
                           Fer4_10   7 dtCirCgkCvkaCPadlts 25 
                                       + Ci C kCv+  P    +
  gi|336255115|ref|YP_004598222.1| 198 EDCISCMKCVREAPE--GT 214
                                       679999999988887..33 PP

  == domain 3  score: 26.7 bits;  conditional E-value: 3.2e-09
                           Fer4_10  10 irCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       ++C++Cv+aCP          e+s +++v+ + e C++cgaC+++CP
  gi|336255115|ref|YP_004598222.1| 311 VGCNECVEACPH------DAVERSSIDEVEFNTELCQNCGACTSSCP 351
                                       69**********......9999************************9 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00016
                           Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                        dd C+   +C + CP+        + +  +   + + e+C +cg C + C
  gi|336255115|ref|YP_004598222.1| 576 VDDACTLTPTCSTLCPT-------DALRRTQTGLEFNHERCVNCGLCEDGC 619
                                       5799*************.......555555555666788999999999988 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.011
                           Fer4_10   4 idddtCirCgkCvkaCPadl..................tsvgakgease..eeavrkkvekCtgcg 49 
                                       ++ ++C++Cg C + C + +                  + v  ++ a++   ++ ++ + +C +cg
  gi|336255115|ref|YP_004598222.1| 604 FNHERCVNCGLCEDGC-VENaitveegldlsllpenreDDVADEEDADPawTQVFEGSMLECKNCG 668
                                       67899***********.4336777777777777777652222222222211233444666666665 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   1.9    0.0035       4.8       9      17 ..     200     208 ..     197     209 .. 0.88
   2 ?   -1.5   0.6       2.2   3.1e+03      18      24 .]     234     240 ..     232     240 .. 0.84
   3 !   12.7   3.4   7.2e-05       0.1      10      23 ..     311     324 ..     301     325 .. 0.90
   4 !   24.5   0.8   1.4e-08   1.9e-05       2      23 ..     333     354 ..     332     355 .. 0.96
   5 ?    0.9   0.3      0.41   5.6e+02      15      24 .]     586     595 ..     577     595 .. 0.78
   6 !   16.5   1.9   4.8e-06    0.0066       3      24 .]     603     624 ..     602     624 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0035
                            Fer4_6   9 CigCgdCvr 17 
                                       Ci+C++Cvr
  gi|336255115|ref|YP_004598222.1| 200 CISCMKCVR 208
                                       ********8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                            Fer4_6  18 vCPegai 24 
                                        CP++ai
  gi|336255115|ref|YP_004598222.1| 234 CCPTDAI 240
                                       5****98 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 7.2e-05
                            Fer4_6  10 igCgdCvrvCPega 23 
                                       +gC++Cv +CP++a
  gi|336255115|ref|YP_004598222.1| 311 VGCNECVEACPHDA 324
                                       59**********98 PP

  == domain 4  score: 24.5 bits;  conditional E-value: 1.4e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       ve++ ++C  Cg+C++ CP+ga
  gi|336255115|ref|YP_004598222.1| 333 VEFNTELCQNCGACTSSCPTGA 354
                                       89******************98 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.41
                            Fer4_6  15 CvrvCPegai 24 
                                       C + CP++a+
  gi|336255115|ref|YP_004598222.1| 586 CSTLCPTDAL 595
                                       9999***996 PP

  == domain 6  score: 16.5 bits;  conditional E-value: 4.8e-06
                            Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                       e++ ++C+ Cg C++ C e+ai
  gi|336255115|ref|YP_004598222.1| 603 EFNHERCVNCGLCEDGCVENAI 624
                                       799****************998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0013       1.7      32      58 ..     186     212 ..     165     214 .. 0.77
   2 !    7.3   0.7    0.0049       6.8      47      59 ..     311     323 ..     306     324 .. 0.91
   3 !   14.7   0.1   2.5e-05     0.035       2      23 ..     340     361 ..     328     390 .. 0.74
   4 ?    1.6   0.4      0.29     4e+02      44      59 ..     578     593 ..     552     595 .. 0.83
   5 !    8.2   2.7    0.0027       3.7      42      59 ..     605     622 ..     594     624 .. 0.79
   6 ?    3.6   6.2     0.071        98       1      18 [.     608     625 ..     608     669 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                           Fer4_17  32 glleeaekeekaslCieCgeCerkCPq 58 
                                       g++e + + ++ ++Ci+C +C+r+ P+
  gi|336255115|ref|YP_004598222.1| 186 GEFEVTVRARVTEDCISCMKCVREAPE 212
                                       455555667899**********98776 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0049
                           Fer4_17  47 ieCgeCerkCPqg 59 
                                       ++C+eC+++CP++
  gi|336255115|ref|YP_004598222.1| 311 VGCNECVEACPHD 323
                                       58*********97 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 2.5e-05
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepk 23 
                                       C++Cg+C+ +Cp+++    ep 
  gi|336255115|ref|YP_004598222.1| 340 CQNCGACTSSCPTGATQLREPS 361
                                       7777777777777766666554 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.29
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                       + C+    C++ CP +
  gi|336255115|ref|YP_004598222.1| 578 DACTLTPTCSTLCPTD 593
                                       6899999999999976 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.0027
                           Fer4_17  42 kaslCieCgeCerkCPqg 59 
                                       + ++C++Cg+Ce  C ++
  gi|336255115|ref|YP_004598222.1| 605 NHERCVNCGLCEDGCVEN 622
                                       668999999999999765 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.071
                           Fer4_17   1 rCiqCgyClpeCpsyeay 18 
                                       rC +Cg C++ C  ++++
  gi|336255115|ref|YP_004598222.1| 608 RCVNCGLCEDGCVENAIT 625
                                       577777777777776664 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   1.2    0.0094        13       7      17 ..     197     207 ..     193     210 .. 0.84
   2 !    7.8   2.5    0.0029       3.9      11      22 .]     311     322 ..     300     322 .. 0.92
   3 !   21.6   2.7   1.2e-07   0.00016       3      22 .]     333     352 ..     331     352 .. 0.93
   4 ?    0.7   1.7      0.49   6.7e+02      13      22 .]     580     592 ..     573     592 .. 0.72
   5 !   12.4   2.2   9.5e-05      0.13       4      20 ..     603     619 ..     601     621 .. 0.90
   6 ?   -1.5   0.5       2.6   3.6e+03      10      14 ..     664     668 ..     662     669 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0094
                            Fer4_2   7 tdrCigCgaCv 17 
                                       t+ Ci+C +Cv
  gi|336255115|ref|YP_004598222.1| 197 TEDCISCMKCV 207
                                       778*******8 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0029
                            Fer4_2  11 igCgaCvsaCPa 22 
                                       +gC+ Cv aCP+
  gi|336255115|ref|YP_004598222.1| 311 VGCNECVEACPH 322
                                       58*********7 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 1.2e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       v+++t+ C +CgaC+s+CP+
  gi|336255115|ref|YP_004598222.1| 333 VEFNTELCQNCGACTSSCPT 352
                                       789****************7 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.49
                            Fer4_2  13 Cg...aCvsaCPa 22 
                                       C    +C + CP+
  gi|336255115|ref|YP_004598222.1| 580 CTltpTCSTLCPT 592
                                       433349******7 PP

  == domain 5  score: 12.4 bits;  conditional E-value: 9.5e-05
                            Fer4_2   4 vvdtdrCigCgaCvsaC 20 
                                       +++ +rC++Cg C + C
  gi|336255115|ref|YP_004598222.1| 603 EFNHERCVNCGLCEDGC 619
                                       5899*********9999 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 2.6
                            Fer4_2  10 CigCg 14 
                                       C +Cg
  gi|336255115|ref|YP_004598222.1| 664 CKNCG 668
                                       88998 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.9     0.012        17       2      12 ..     198     208 ..     197     209 .. 0.87
   2 !    7.9   1.0    0.0035       4.9       4      15 ..     303     321 ..     300     332 .. 0.78
   3 !   17.1   3.5   4.1e-06    0.0057       2      17 .]     338     353 ..     337     354 .. 0.92
   4 ?   -0.6   0.5         2   2.7e+03       2      16 ..     578     592 ..     578     593 .. 0.82
   5 !   10.4   4.3   0.00056      0.77       2      14 ..     607     619 ..     606     620 .. 0.96
   6 ?   -2.4   0.4       7.4     1e+04       7      11 ..     703     707 ..     701     708 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                            Fer4_4   2 erCigCgsCva 12 
                                       e Ci C++Cv+
  gi|336255115|ref|YP_004598222.1| 198 EDCISCMKCVR 208
                                       67*******96 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0035
                            Fer4_4   4 C.......igCgsCvaaCP 15 
                                       C       +gC  Cv aCP
  gi|336255115|ref|YP_004598222.1| 303 CaagdssrVGCNECVEACP 321
                                       555555557*********9 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 4.1e-06
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       e C++Cg+C+++CP+g
  gi|336255115|ref|YP_004598222.1| 338 ELCQNCGACTSSCPTG 353
                                       78************86 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + C+  + C   CP+
  gi|336255115|ref|YP_004598222.1| 578 DACTLTPTCSTLCPT 592
                                       579989999999997 PP

  == domain 5  score: 10.4 bits;  conditional E-value: 0.00056
                            Fer4_4   2 erCigCgsCvaaC 14 
                                       erC++Cg C++ C
  gi|336255115|ref|YP_004598222.1| 607 ERCVNCGLCEDGC 619
                                       8************ PP

  == domain 6  score: -2.4 bits;  conditional E-value: 7.4
                            Fer4_4   7 CgsCv 11 
                                       C+ C+
  gi|336255115|ref|YP_004598222.1| 703 CPECR 707
                                       66665 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.7    0.0056       7.8      54      75 ..     193     214 ..     171     235 .. 0.79
   2 ?    2.8   8.4     0.096   1.3e+02      57     101 ..     306     356 ..     291     362 .. 0.68
   3 ?   14.7   1.4   1.9e-05     0.027      53      97 ..     572     621 ..     552     635 .. 0.75
   4 ?   -3.2   0.0         7   9.6e+03      77      89 ..     656     668 ..     651     670 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0056
                           Fer4_18  54 kekgagdcidcescvkvcPtgi 75 
                                       +++ + dci+c +cv+  P g 
  gi|336255115|ref|YP_004598222.1| 193 RARVTEDCISCMKCVREAPEGT 214
                                       4556778888888888888765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.096
                           Fer4_18  57 gagdcidcescvkvcPtgidirkGlq.le.....ciscllcidacdkvmek 101
                                       g++  + c+ cv+ cP +   r  +  +e     c +c+ c  +c +   +
  gi|336255115|ref|YP_004598222.1| 306 GDSSRVGCNECVEACPHDAVERSSIDeVEfntelCQNCGACTSSCPTGATQ 356
                                       5566789********987655554421112233499999999999765555 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 1.9e-05
                           Fer4_18  53 rkekgagdcidcescvkvcPtgidir..kGlqle...ciscllcidacdk 97 
                                        + + +  c+   +c ++cPt+   r   Gl ++   c++c+lc d c +
  gi|336255115|ref|YP_004598222.1| 572 GRVEVDDACTLTPTCSTLCPTDALRRtqTGLEFNherCVNCGLCEDGCVE 621
                                       45666778*************9876622577663555***********54 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 7
                           Fer4_18  77 irkGlqleciscl 89 
                                       + +G  lec +c+
  gi|336255115|ref|YP_004598222.1| 656 VFEGSMLECKNCG 668
                                       5678888999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (719 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); 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):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.23s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 5160.28
//
Query:       gi|336255116|ref|YP_004598223.1|  [L=210]
Description: anaerobic dehydrogenase-like protein [Halopiger xanaduensis SH-6]
Scores for 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-27   94.4   0.1      1e-26   93.6   0.1    1.4  1  Nitrate_red_del  Nitrate reductase delta subunit


Domain annotation for each model (and alignments):
>> Nitrate_red_del  Nitrate reductase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.1   5.7e-31     1e-26       3     136 ..      50     176 ..      45     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 5.7e-31
                   Nitrate_red_del   3 alsaeveealaelaeal..aa...ededllelaaeYtrLFlgpgrrsasPyesvYlsekkgllfgestlevrefyrq 74 
                                       +l+++++     l++++  +     ++ ++el+ eYtrLF+g +r++++P+e++Y++++  +  ge+  +v++ y +
  gi|336255116|ref|YP_004598223.1|  50 DLDTGFDL----LEQFIeqNRgrsLEDVADELEVEYTRLFVG-PRPPVLPHETYYREDT--EYLGEGLPKVEASYGA 119
                                       45555555....8888876224458999*************8.9*************55..59************** PP

                   Nitrate_red_del  75 aglevaeefneppDHlaveLeflahLaereaeaeeaeeaealleaqkafleehllpWlpefa 136
                                       ag++ +e+++e +DH+aveL+fl +L++++ +       e++l  q+ f eehl+ W++++a
  gi|336255116|ref|YP_004598223.1| 120 AGWSPPEDYPEENDHVAVELAFLRYLVRSQYQG-----REETLGYQRVFHEEHLSHWIDDCA 176
                                       ***************************999975.....6789*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.80
# Mc/sec: 788.43
//
Query:       gi|336255117|ref|YP_004598224.1|  [L=60]
Description: hypothetical protein Halxa_3739 [Halopiger xanaduensis SH-6]
Scores for 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  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 474.10
//
Query:       gi|336255118|ref|YP_004598225.1|  [L=112]
Description: hypothetical protein Halxa_3740 [Halopiger xanaduensis SH-6]
Scores for 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  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 00:00:00.37
# Mc/sec: 897.20
//
Query:       gi|336255119|ref|YP_004598226.1|  [L=88]
Description: hypothetical protein Halxa_3741 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.057   13.5   4.3      0.076   13.1   4.3    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
       0.15   12.3   1.5       0.22   11.8   1.5    1.2  1  DPM3             Dolichol-phosphate mannosyltransferase subun
       0.41   10.6   9.4       0.76    9.8   0.3    2.2  2  OppC_N           N-terminal TM domain of oligopeptide transpo


Domain annotation for each model (and alignments):
>> 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 ?   13.1   4.3   1.3e-05     0.076      41     100 ..      13      81 ..       7      82 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                   Phage_holin_3_6  41 gaagvlallalllllvala.......lala.a.lwlaalivaavllvlagvlalvglkklkkakplper 100
                                       ++ g+la+ a+++l++  +       +  + + +     +v+++ lv+ g+la+v + +l + +plpe+
  gi|336255119|ref|YP_004598226.1|  13 VLIGLLAFGAWVFLTIQNVaasmgsvVYGDwVgQSGVVGLVGLAALVAIGLLAVVVYGELGETEPLPEE 81 
                                       3444444444444444443122222122222244444455899999999999*9999999999999985 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 ?   11.8   1.5   3.6e-05      0.22       3      55 ..       8      67 ..       7      72 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                              DPM3  3 raqktlalallllalwlalllrlvslpl.skvqdev......vpvlPlwalvlfGaysla 55
                                      r +k+++++ll++++w++l+++ v  ++ s v+ ++      v ++ l alv++G+ +++
  gi|336255119|ref|YP_004598226.1|  8 RQHKLVLIGLLAFGAWVFLTIQNVAASMgSVVYGDWvgqsgvVGLVGLAALVAIGLLAVV 67
                                      7899********************888655555554444444777777777777776665 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   0.00013      0.76       9      31 ..       6      28 ..       3      48 .. 0.77
   2 ?    4.9   3.7    0.0045        27      17      36 ..      49      68 ..      46      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00013
                            OppC_N  9 rFkrNklAvvglvilllllliai 31
                                       F+++kl ++gl  + + +++ i
  gi|336255119|ref|YP_004598226.1|  6 AFRQHKLVLIGLLAFGAWVFLTI 28
                                      6**************99998853 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0045
                            OppC_N 17 vvglvilllllliaifaPli 36
                                      vvglv l++l++i ++a ++
  gi|336255119|ref|YP_004598226.1| 49 VVGLVGLAALVAIGLLAVVV 68
                                      89999999999998877555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 712.70
//
Query:       gi|336255120|ref|YP_004598227.1|  [L=257]
Description: hypothetical protein Halxa_3742 [Halopiger xanaduensis SH-6]
Scores for 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  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2042.64
//
Query:       gi|336255121|ref|YP_004598228.1|  [L=597]
Description: aldehyde ferredoxin oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-99  332.4   0.0    4.9e-99  331.9   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    3.6e-64  216.3   0.1      5e-64  215.8   0.1    1.2  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.9   0.0  5.5e-103   4.9e-99      12     382 .]     222     578 ..     212     578 .. 0.93

  Alignments for each domain:
  == domain 1  score: 331.9 bits;  conditional E-value: 5.5e-103
                                       HSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHH.TEEEE.E-TT-SS--EEEEE..... CS
                            AFOR_C  12 sspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeek.ylvknegCfsCpiaCgrevkveegk 87 
                                       +++ +  ++++  T e+v++ane g+lpt+ +q+g+f++a++++ ea++e  y+ ++   +  p+  g +v+ ++g+
  gi|336255121|ref|YP_004598228.1| 222 DDE-TGRWHAASETVETVDFANEVGVLPTRGWQKGRFDGADSVGIEAVREAaYERER---ADDPVPGGFRVESDDGD 294
                                       333.4449999***************************************5344444...568*********88887 PP

                                       .ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS----TT-THH CS
                            AFOR_C  88 kvkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglelefgdaea 164
                                           ++p+  t+ alGs lgidd++a+++l  +cd+l +D+is Gn++a+am+++e+G l++      +l+fgd+++
  gi|336255121|ref|YP_004598228.1| 295 ----TVPRGSTPIALGSGLGIDDFDAVATLGSVCDRLAVDVISSGNAVAWAMRASEEGHLDR------DLSFGDEDD 361
                                       ....589*****************************************************99......99******* PP

                                       HHHHHHHHHTT-T.THHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SGGG-THHHH CS
                            AFOR_C 165 llellekiAkreg.igdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacHlrayliale 240
                                       ++ l+e+ A+r++ +gd lA+Gv+++a ++ga el  +vkG+elp ydprg+ +malaYats+rGacH ra ++++e
  gi|336255121|ref|YP_004598228.1| 362 ARTLIEELATRSSsLGDALADGVEAAADAYGADELIPSVKGMELPSYDPRGSAAMALAYATSDRGACHRRARPVETE 438
                                       ***************************************************************************** PP

                                       S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT-..---HHHHHHHHHHHHHHHH CS
                            AFOR_C 241 ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGi..dvteeellkaGeRiynleR 315
                                             +  +++  v+  qd++a+++sl++ +f     e l+++l a++l a  +   d+ ++el ++GeRi++l R
  gi|336255121|ref|YP_004598228.1| 439 AIEGDWTIAERVVTVAAEQDRRAVLWSLIADDFFG---EALTPDLGAEWLAA-SDRaaDYAPDELQRVGERIWTLVR 511
                                       6666776799*************************...8899*******998.554459****************** PP

                                       HHHHHHT--HHHS---HHHHHS---SSTTTT---...-HHHHHHHHHHHHT--TTS---HHHHHHCT- CS
                            AFOR_C 316 lfnlreGltrkddtlperlleeplkegpakgkvl.edeleemldeyYelrGWdetGvPtketlkrLgL 382
                                       lfn+reG++r+dd+lp+ l+ epl+ gp++g+ +  + +eeml++yYe rGWde+G+Pt etl+rLgL
  gi|336255121|ref|YP_004598228.1| 512 LFNVREGFSRADDELPAQLT-EPLEGGPNDGSAVaAEAFEEMLERYYEYRGWDEQGRPTTETLERLGL 578
                                       *******************9.9**********996777*****************************8 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.8   0.1   5.6e-68     5e-64       2     197 ..       6     200 ..       5     201 .. 0.97

  Alignments for each domain:
  == domain 1  score: 215.8 bits;  conditional E-value: 5.6e-68
                                       EEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE- CS
                            AFOR_N   2 kilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaks 78 
                                        i+rvdL+t++++ e++pee+ +ky+Gg+gl+a++l++e+++g++pl+ en l+f tGpltg  +pg +r+vvv+ks
  gi|336255121|ref|YP_004598228.1|   6 SIVRVDLTTESVTNEPVPEEWRRKYVGGKGLGARYLYEELEAGAEPLGGENALLFLTGPLTGH-LPGEQRYVVVTKS 81 
                                       589***********************************************************9.************* PP

                                       TTTSSEEEEEEETCHHHHHHHCT-S..EEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTSEEE CS
                            AFOR_N  79 PltgtlgesnaGgrfgaelkraGyd..aivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgdkva 153
                                       Pltg + +s+aGg+++ +l+ +  d  +i ++G a++pv l++ d++v+ie+a+d wgld+ e++e++ +     va
  gi|336255121|ref|YP_004598228.1|  82 PLTGAFLDSYAGGSMADRLAGSLGDhvGILVTGCADEPVALEVADGEVSIEPADDWWGLDAREVDERVPDA---AVA 155
                                       *********************999867899**************************************996...899 PP

                                       EE-HHHHTT-TTB-E.EE.TTEEE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 154 viGpaGenlvrfAsisvd.dgraagrgGlGavmgsKnlkaivvrg 197
                                       +iGpaGen v++A+i+ d  +++agrgG GavmgsK+lka+v+r+
  gi|336255121|ref|YP_004598228.1| 156 CIGPAGENVVSYATIASDgGDHHAGRGGAGAVMGSKRLKAVVARD 200
                                       ***************88887789*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 4868.65
//
Query:       gi|336255122|ref|YP_004598229.1|  [L=353]
Description: group 1 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for 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   68.9   1.3    8.4e-19   68.2   0.3    1.8  2  Glyco_transf_4   Glycosyltransferase Family 4
    3.4e-17   63.3   5.4    3.4e-17   63.3   5.4    2.7  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.3e-11   44.3   0.0      2e-11   43.7   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.1e-10   42.1   0.0    5.8e-10   39.7   0.0    2.0  2  Glyco_trans_1_4  Glycosyl transferases group 1
    0.00059   19.9   0.0     0.0016   18.5   0.0    1.7  2  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
       0.16   12.2   0.0       0.28   11.4   0.0    1.3  1  Tctex-1          Tctex-1 family


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.3   2.8e-22   8.4e-19       5     170 .]      19     169 ..      18     169 .. 0.84
   2 ?   -1.2   0.0      0.59   1.8e+03      68      68 ..     247     247 ..     200     329 .. 0.53

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 2.8e-22
                    Glyco_transf_4   5 erhvleLaraLarrGheVtvvtpg.ddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahs 80 
                                       +r + ++++ L ++Gh+V+v++ + +dg+++       r    ++ l + +  + af++rl  +l   kpD+vHa  
  gi|336255122|ref|YP_004598229.1|  19 NRRLQTICELLEEAGHDVHVFCAQfWDGEHDTF----EREDVTYHGLVGEPDARSAFALRLPTALAGAKPDIVHASA 91 
                                       57788999*************666155555544....556666666667777788999****************998 PP

                    Glyco_transf_4  81 paalgaallalrr.rlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvpp 156
                                        +++ ++++   +   ++p+Vl   g                ++ ++ r+++ radr+ ++Se +a +lre +gv +
  gi|336255122|ref|YP_004598229.1|  92 NPPGQVVAASVGAtLARAPMVLEWYGDG------------GVRNDRWRRWAAGRADRIHVPSELVATWLRE-LGVGE 155
                                       777755444444479*************............78999999***********************.***** PP

                    Glyco_transf_4 157 ekitVipnGvDler 170
                                       + ++++pn++Dler
  gi|336255122|ref|YP_004598229.1| 156 DALETVPNPIDLER 169
                                       ************98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.59
                    Glyco_transf_4  68 l 68 
                                       +
  gi|336255122|ref|YP_004598229.1| 247 I 247
                                       2 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 !   63.3   5.4   1.1e-20   3.4e-17       4     160 .]      19     164 ..      18     164 .. 0.81
   2 ?    2.7   0.4     0.053   1.6e+02      12      43 ..     201     232 ..     199     317 .. 0.70

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 1.1e-20
                   Glyco_trans_4_4   4 gryvaelaraLaarGheVtvltpa.papgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvha 79 
                                       +r+ + +++ L+++Gh+V+v++++ ++++ +  e++ v++h+l   +     a+ a++ +l  +l  +  +pd+vha
  gi|336255122|ref|YP_004598229.1|  19 NRRLQTICELLEEAGHDVHVFCAQfWDGEHDTFEREDVTYHGLVGEPD----ARSAFALRLPTAL--AGAKPDIVHA 89 
                                       588999****************77356666679999*****9755444....5778999999999..********** PP

                   Glyco_trans_4_4  80 hs.ptaglaarla.rrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelralgvpadrv 154
                                          p++  +a+   +  +++p v++++g+ ++r         +++ r+++ rad+++v+se +a  lr+lgv  d +
  gi|336255122|ref|YP_004598229.1|  90 SAnPPGQVVAASVgATLARAPMVLEWYGDGGVRN--------DRWRRWAAGRADRIHVPSELVATWLRELGVGEDAL 158
                                       995554444433314578**********865544........45567889*************************** PP

                   Glyco_trans_4_4 155 vvvpng 160
                                       ++vpn+
  gi|336255122|ref|YP_004598229.1| 159 ETVPNP 164
                                       ****95 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.053
                   Glyco_trans_4_4  12 raLaarGheVtvltpapapgapeleedgvrvh 43 
                                       ++L++r ++ tv+ ++p ++++e+ +  +r+ 
  gi|336255122|ref|YP_004598229.1| 201 AELRDRDWSATVVGDGPERERYEQLASDLRID 232
                                       68999999999999999999888777766665 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   6.6e-15     2e-11       3     154 ..     166     314 ..     164     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 6.6e-15
                                       HHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEE CS
                   Glycos_transf_1   3 ekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflg 79 
                                       + +r ++++++++  +++  rl++  +++ l+  +a+l+   + ++  +++G+g+e++++++la  l + d+++f g
  gi|336255122|ref|YP_004598229.1| 166 DLERVRSVEPDDRVDVVYARRLDEGANLESLLLGLAELR---DRDWSATVVGDGPERERYEQLASDLRIDDRITFAG 239
                                       5678889999****************************7...67********************************* PP

                                       CCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET..TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHH CS
                   Glycos_transf_1  80 evsredleellknadifvlpsisEgfGivllEAmaaglpviasn..aggpaevvkdgetGllvkpnnaealaeairk 154
                                         s e+ ++ ++ a++f+++++   f++  l A+a+g+  i+     + + e+v+ ++ G+   ++  ++la+ai  
  gi|336255122|ref|YP_004598229.1| 240 DCSLEERIAAYRGAHVFAQTAEHCVFPTEMLWALASGCVGIVEYhaDSSAHELVEGWDRGFRTTSE--DELADAIVA 314
                                       ***999*******************************99887433488899999999999988877..888888755 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 ?   -0.6   0.0      0.56   1.7e+03      27      72 ..     106     150 ..      94     160 .. 0.73
   2 !   39.7   0.0   1.9e-13   5.8e-10       3     129 ..     180     313 ..     178     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.56
                                       HH.HHEEEEEES---...HHHHHHHTT-T.TEEEE---THHHHHHHH CS
                   Glyco_trans_1_4  27 lrkkdvrlvivGdgp.rpeeleelaagleerveftGfvedlaellaa 72 
                                       l+++++ l  +Gdg  r+++ ++ aag ++r+++  ++  +a +l++
  gi|336255122|ref|YP_004598229.1| 106 LARAPMVLEWYGDGGvRNDRWRRWAAGRADRIHVPSEL--VATWLRE 150
                                       44335788899999988889987777777899998866..6666655 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 1.9e-13
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprpeeleelaa..gleerveftGfv..edlaellaaadv 75 
                                       ++++  rl+ +  +++ ll  +++lr++d+  ++vGdgp++e++e+la+  ++++r++f+G    e+  ++++ a+v
  gi|336255122|ref|YP_004598229.1| 180 DVVYARRLD-EGANLESLLLGLAELRDRDWSATVVGDGPERERYEQLASdlRIDDRITFAGDCslEERIAAYRGAHV 255
                                       688999995.44899***********99***********556999888668899********99999********** PP

                                       EEE---..--SHHHHHHHHTT-EEEE-TGG..GTTT--.T.TSSEE--TT-HHHHHHHHH CS
                   Glyco_trans_1_4  76 fvaPse..gfglkllEamaaglpvVatdvg..giaevv.g.engllvppgdpealaeail 129
                                       f  + e   f+  +l a+a+g+  ++   +   + e+v g + g+     ++++la+ai+
  gi|336255122|ref|YP_004598229.1| 256 FAQTAEhcVFPTEMLWALASGCVGIVEYHAdsSAHELVeGwDRGFRTT--SEDELADAIV 313
                                       *****86679*************9999663224799999756678777..899****997 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 !   18.5   0.0   5.2e-07    0.0016      15     105 ..      24     114 ..       2     123 .. 0.70
   2 ?   -2.9   0.0       2.2   6.4e+03      19      41 ..     202     224 ..     199     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.2e-07
                   Glyco_trans_4_2  15 rlakeLakrgyeVhvitp..kkgakdeleaegihvhrlkvdrkgpleylkafklkklikkikPDvvhahyakpy.gl 88 
                                        +++ L ++g++Vhv++    +g+ d  e+e+++ h l    +  +  + a++l   ++  kPD+vha   +p  ++
  gi|336255122|ref|YP_004598229.1|  24 TICELLEEAGHDVHVFCAqfWDGEHDTFEREDVTYHGLV--GEPDARSAFALRLPTALAGAKPDIVHASANPPGqVV 98 
                                       34888************9642333333447889999985..22344444477999999**********987777577 PP

                   Glyco_trans_4_2  89 lgslaarlsgvipvvls 105
                                       ++s  a l++  p+vl 
  gi|336255122|ref|YP_004598229.1|  99 AASVGATLAR-APMVLE 114
                                       7777777777.888876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.2
                   Glyco_trans_4_2  19 eLakrgyeVhvitpkkgakdele 41 
                                       eL++r++  +v+  +++++++++
  gi|336255122|ref|YP_004598229.1| 202 ELRDRDWSATVVGDGPERERYEQ 224
                                       899****9999999988888776 PP

>> Tctex-1  Tctex-1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.3e-05      0.28      51      83 ..      19      51 ..       6      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.3e-05
                                      SCEEEEEEEEEETTTS-EEEEEEEES-TTT-EE CS
                           Tctex-1 51 ryKfivnvtivqkkgqgmhsasgaywdektDgm 83
                                      + ++ + + +++++g+ +h+ ++ +wd ++D++
  gi|336255122|ref|YP_004598229.1| 19 NRRLQTICELLEEAGHDVHVFCAQFWDGEHDTF 51
                                      5677788999*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 3006.94
//
Query:       gi|336255123|ref|YP_004598230.1|  [L=299]
Description: ATPase [Halopiger xanaduensis SH-6]
Scores for 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  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1333  (0.0743488); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                       226  (0.0126053); expected 17.9 (0.001)
Passed Fwd filter:                       135  (0.0075297); 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: 2.07u 0.36s 00:00:02.42 Elapsed: 00:00:00.57
# Mc/sec: 1592.63
//
Query:       gi|336255124|ref|YP_004598231.1|  [L=628]
Description: peptidase S9 prolyl oligopeptidase active site domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-45  154.9   0.0    3.2e-45  154.2   0.0    1.4  1  Peptidase_S9    Prolyl oligopeptidase family
    4.9e-13   49.1   0.1    1.4e-12   47.7   0.1    1.6  1  DLH             Dienelactone hydrolase family
    2.2e-11   43.9   0.0    1.8e-08   34.3   0.1    2.2  2  Peptidase_S15   X-Pro dipeptidyl-peptidase (S15 family)
    6.6e-11   42.3   0.1    2.2e-05   24.2   0.1    2.2  2  Abhydrolase_1   alpha/beta hydrolase fold
    2.2e-08   33.6   0.2    0.00085   18.7   0.1    2.5  3  Hydrolase_4     Serine aminopeptidase, S33
    2.9e-06   27.0   5.5     0.0059   16.5   0.0    5.5  5  PD40            WD40-like Beta Propeller Repeat
    0.00014   20.8   0.0    0.00023   20.1   0.0    1.3  1  Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propel
    0.00027   19.7   0.0     0.0097   14.6   0.0    2.1  1  AXE1            Acetyl xylan esterase (AXE1)
    0.00091   19.1   0.0      0.032   14.1   0.0    2.2  1  Abhydrolase_3   alpha/beta hydrolase fold
    0.00096   19.1   0.0      0.016   15.2   0.0    2.1  1  BAAT_C          BAAT / Acyl-CoA thioester hydrolase C termina
     0.0017   18.3   0.1       0.22   11.5   0.0    2.6  2  PepSY_2         Peptidase propeptide and YPEB domain
  ------ inclusion threshold ------
      0.012   15.5   0.0        3.6    7.3   0.0    2.2  2  Abhydrolase_2   Phospholipase/Carboxylesterase
      0.042   13.5   0.0       0.19   11.3   0.0    2.1  2  Esterase        Putative esterase
      0.046   13.8   0.0       0.12   12.5   0.0    1.6  1  Abhydrolase_4   TAP-like protein
       0.22   11.4   0.0       0.39   10.6   0.0    1.3  1  DUF829          Eukaryotic protein of unknown function (DUF82


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.2   0.0   2.7e-48   3.2e-45       1     208 [.     420     627 ..     420     628 .] 0.95

  Alignments for each domain:
  == domain 1  score: 154.2 bits;  conditional E-value: 2.7e-48
                                       ----HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHH CS
                      Peptidase_S9   1 psfsselqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyl 77 
                                       psfss+ q++ drGy+++ +n+rGs+gyG +++   + ++   +++D+ a++e+l ++  vd++r+a+ GgSyGG++
  gi|336255124|ref|YP_004598231.1| 420 PSFSSVKQYFLDRGYAYFEPNVRGSAGYGADYAALDDVEKRMDSVADIEACVEWLQDHPAVDPDRIAAKGGSYGGFM 496
                                       68998888888***********************999999************************************* PP

                                       HHHHHHH-GGG-SEEEEESE---CCCHHCSTTS.THH.HCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEET CS
                      Peptidase_S9  78 tgaalnqrpdlFkaavaevpvvdvlrydsdtdl.lte.eymewgnpeeneegykelspyspldnvkaypplLlihGl 152
                                       ++aal++ pdl++a+v +v++++ +++  +t     e +  e+g   e++e  +e+sp ++ ++  +++pl+++hG+
  gi|336255124|ref|YP_004598231.1| 497 VLAALTEYPDLWAAGVDVVGIANFVTFLENTGDwRRElREAEYGSLAEDREFLEEISPTNNIEH--IEAPLFVLHGE 571
                                       *****************************99876556788999999999999999999999999..*********** PP

                                       T-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHHH CS
                      Peptidase_S9 153 aDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlkea 208
                                       +D rvp+ ea++++++ + +g++v+  if degHg++k ++++e +  +++Fl+e+
  gi|336255124|ref|YP_004598231.1| 572 NDPRVPVGEAEQIAEKAEAQGVPVRKFIFDDEGHGFSKLENRIEAYSAIADFLDEH 627
                                       *****************************************************998 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.1   1.1e-15   1.4e-12      15     198 ..     403     618 ..     392     625 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.1e-15
                               DLH  15 vvvviqeifGvn.....dnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaav 86 
                                       +v vi +i G         +  +++ +++ GY+ + P++    +     +  + +ald + +     + ++d++a v
  gi|336255124|ref|YP_004598231.1| 403 GVPVIVDIHGGPesqrrPSFSSVKQYFLDRGYAYFEPNVRGSAG-----YGADYAALDDVEKRM---DSVADIEACV 471
                                       555666666655455566777899999***********976666.....666667776665555...5667778*** PP

                               DLH  87 aylksvpevstkkvgvvGfCmGGalalllaaev.pevdaavafYG................................ 130
                                       ++l+  p v+++++++ G   GG ++l+  +e  +  +a v   G                                
  gi|336255124|ref|YP_004598231.1| 472 EWLQDHPAVDPDRIAAKGGSYGGFMVLAALTEYpDLWAAGVDVVGianfvtflentgdwrrelreaeygslaedref 548
                                       ***************************999999677889999*********************************99 PP

                               DLH 131 lspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsre..syn 198
                                       l+  ++ +++++i+ap+++l+ge+D+ +p +e+e+++e+ +a++v+++  ++++ gH+F + +++   y+
  gi|336255124|ref|YP_004598231.1| 549 LEEISPTNNIEHIEAPLFVLHGENDPRVPVGEAEQIAEKAEAQGVPVRKFIFDDEGHGFSKLENRieAYS 618
                                       9999*******************************************************99887744454 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   1.5e-11   1.8e-08      44     140 ..     420     522 ..     389     533 .. 0.84
   2 !    7.2   0.0    0.0028       3.4     207     263 ..     541     601 ..     526     606 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.5e-11
                                       HCCHGGGHHHHHTT-EEEEEE-TTSTTS-S---TT.....TTTHHHHHHHHHHHHHHC.TTEEEEEEEEEECHHHHH CS
                     Peptidase_S15  44 eelelqdkvfvarGYavVvqdvrGtggSeGeftvg.....dsdeaedgadvidWlakq.pwsnGkVgmtGiSYlGtt 114
                                       ++ +  ++ f++rGYa    +vrG++g   ++          d ++d  ++++Wl+ +     +++++ G SY+G++
  gi|336255124|ref|YP_004598231.1| 420 PSFSSVKQYFLDRGYAYFEPNVRGSAGYGADYAALddvekRMDSVADIEACVEWLQDHpAVDPDRIAAKGGSYGGFM 496
                                       333344455*****************999999998999989999**************89999************** PP

                                       HHHHCTT--TTEEEEEEECE-S-TCC CS
                     Peptidase_S15 115 qllaaatgvpalkaivpeaaisdlyd 140
                                        l+a+++ ++  +a v +++i+++++
  gi|336255124|ref|YP_004598231.1| 497 VLAALTEYPDLWAAGVDVVGIANFVT 522
                                       ******98888888888888877766 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0028
                                       C--SSSHHHHTT-HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-...EEEEE CS
                     Peptidase_S15 207 etgdydafWkdrnlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv...klilg 263
                                       +  + ++f +++++ ++++ ++ap+++++G nD  v   +a ++ e+++a+gv   k i+ 
  gi|336255124|ref|YP_004598231.1| 541 SLAEDREFLEEISPTNNIEHIEAPLFVLHGENDPRVPvGEAEQIAEKAEAQGVpvrKFIFD 601
                                       56678899999**********************8888888999999988888777666665 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   1.8e-08   2.2e-05       1     101 [.     405     511 ..     405     537 .. 0.78
   2 !   16.2   0.0     5e-06     0.006     196     250 ..     534     605 ..     521     611 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.8e-08
                                       SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTS.TTSSSTTTGB.CHH.....SHHHHHHHHHHH..HHH CS
                     Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGv.gySspapacinddy.....gtasvaddldri..lda 69 
                                       pv+v +hG+p+s   +   ++ +++ ++g+ ++ +++rG+ gy+    a   dd      + a+++++++++    a
  gi|336255124|ref|YP_004598231.1| 405 PVIVDIHGGPESQRRPSFSSVKQYFLDRGYAYFEPNVRGSaGYGADYAAL--DDVekrmdSVADIEACVEWLqdHPA 479
                                       78999******777766666******************973445444444..333444467888999999**66668 PP

                                       CTTSSEEEEEETHHHHHHHHHHHHHGGGEEEE CS
                     Abhydrolase_1  70 lgddkltlvGhSmGGmialayaaeyperVkal 101
                                        + d+++  G+S+GG+++la++ eyp+  +a 
  gi|336255124|ref|YP_004598231.1| 480 VDPDRIAAKGGSYGGFMVLAALTEYPDLWAAG 511
                                       9*************************976655 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 5e-06
                                       CHHHHHHHHHC.............THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS....EEEEEEETCSS CS
                     Abhydrolase_1 196 dsaklllrlre.............lknvlaptlvisgtsDplvppkaledlaqllpk....krlvvisdagH 250
                                       ++ + +++l e             +  + ap +v++g++Dp vp ++ e++a++       +r+++++d+gH
  gi|336255124|ref|YP_004598231.1| 534 LREAEYGSLAEdrefleeisptnnIEHIEAPLFVLHGENDPRVPVGEAEQIAEKAEAqgvpVRKFIFDDEGH 605
                                       444444444446667777776666777777************************66667888********** PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   7.1e-07   0.00085       6     103 ..     406     510 ..     403     521 .. 0.83
   2 !   12.2   0.0   6.7e-05      0.08     185     220 ..     556     591 ..     548     608 .. 0.88
   3 ?   -2.1   0.0       1.6   1.9e+03      35      47 ..     598     611 ..     592     625 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.1e-07
                       Hydrolase_4   6 vvvlvHGlaehsgr..yaelaeaLaaqGfavyalDhrGhGrse...gkrghvpsfddyvdDlaafvekvkeehpel. 76 
                                       v+v +HG  e+ +r  ++ + +++ ++G+a +  + rG    +    +  +v++  d v+D++a ve ++ +hp   
  gi|336255124|ref|YP_004598231.1| 406 VIVDIHGGPESQRRpsFSSVKQYFLDRGYAYFEPNVRGSAGYGadyAALDDVEKRMDSVADIEACVEWLQ-DHPAVd 481
                                       677789999998875578899****************98666634466668888899*********9988.666666 PP

                       Hydrolase_4  77 ..plfllGhSmGGliallyllrypdkvag 103
                                         ++   G S GG+++l++l++ypd +a+
  gi|336255124|ref|YP_004598231.1| 482 pdRIAAKGGSYGGFMVLAALTEYPDLWAA 510
                                       888999*******************8874 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.7e-05
                       Hydrolase_4 185 eraakitlPllllhGeaDkvvdpeasrelyerlgsk 220
                                       ++ ++i++Pl++lhGe+D+ v+ +++++++e++ ++
  gi|336255124|ref|YP_004598231.1| 556 NNIEHIEAPLFVLHGENDPRVPVGEAEQIAEKAEAQ 591
                                       5778999************************99876 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.6
                       Hydrolase_4  35 yalDhrGhGrse.g 47 
                                       +++D  GhG s+  
  gi|336255124|ref|YP_004598231.1| 598 FIFDDEGHGFSKlE 611
                                       789******99642 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.058        69      11      37 ..      14      39 ..       6      40 .. 0.85
   2 !   16.5   0.0   4.9e-06    0.0059      14      38 .]     108     133 ..     103     133 .. 0.93
   3 ?    0.5   0.2      0.51   6.1e+02      16      23 ..     158     165 ..     154     168 .. 0.86
   4 ?    3.0   0.0     0.086     1e+02       3      21 ..     192     212 ..     190     227 .. 0.76
   5 ?   -0.7   0.0       1.2   1.5e+03      22      36 ..     260     273 ..     259     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.058
                                      EEEEEE-TTSSEEEEEEECT.TCEEEE CS
                              PD40 11 egaPsfSPDGkrlaFsSdRgsGkpdIy 37
                                       ++ sf PDG rl F  + + G+ +++
  gi|336255124|ref|YP_004598231.1| 14 AYGASFGPDGERLSFLMNTT-GTAQVW 39
                                      57889********9999999.999998 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 4.9e-06
                                       EEE-TTSSEEEEEEECT..TCEEEEE CS
                              PD40  14 PsfSPDGkrlaFsSdRg.sGkpdIyv 38 
                                         +S DG r aF+S+R  +  +dIyv
  gi|336255124|ref|YP_004598231.1| 108 GGWSHDGDRCAFASNRRdEAVFDIYV 133
                                       57***********************8 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.51
                                       E-TTSSEE CS
                              PD40  16 fSPDGkrl 23 
                                       +SPD +rl
  gi|336255124|ref|YP_004598231.1| 158 WSPDDSRL 165
                                       ****9998 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.086
                                       E--SSSS...EEEEEE-TTSS CS
                              PD40   3 rltntpg..negaPsfSPDGk 21 
                                        lt+++g   + + s+ PDG 
  gi|336255124|ref|YP_004598231.1| 192 HLTPHEGdvRYQSASWAPDGE 212
                                       57777777778889******6 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 1.2
                                       EEEEEEECT.TCEEE CS
                              PD40  22 rlaFsSdRgsGkpdI 36 
                                       r+++s++ + G++d+
  gi|336255124|ref|YP_004598231.1| 260 RFVYSRNVE-GYTDL 273
                                       678888888.**996 PP

>> Peptidase_S9_N  Prolyl oligopeptidase, N-terminal beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.9e-07   0.00023     114     312 ..      44     237 ..      28     339 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.9e-07
                                       GGGGSTTS-.EE..EEEEEE-TTSSEEEEEEEETTSSEEEEEEEETTTTE.EEEEEEEEEESEEEEECTTSSEEEEE CS
                    Peptidase_S9_N 114 pNtlsedgtfva..lgefavsedgkllAyslsksGsdwytirvkdietge.dlpdeledvkfsgivWaadekgffYt 187
                                       p +++e+ tf++  +   + s++   l ++++++G+++ ++   d++tge +    + d+k     W +d++   + 
  gi|336255124|ref|YP_004598231.1|  44 PQEWPEQRTFYDetVSFASWSPERPELIFGMDEGGNERAQLYRLDAATGEiENLTAMPDAKHRWGGWSHDGDRCAFA 120
                                       5567777777752233344899999************************83334567777877799*******9999 PP

                                       ESS-SSS-TSTSB-S-BEEEEEETTS-GGG-EEEES-TTGTTBEEEEEE-TTSSEEEE.EEESSSS--EEEEEEGGG CS
                    Peptidase_S9_N 188 rydkedersdtdtnlnqkvyrhkLGtaqseDelvfeeeeepkwllgaersedgkylfi.ssasgtdtnelyvldlek 263
                                       + ++++ + d        +y  + ++  +++elv+e    + wl     s d++ l++ +++s+  +++lyvldle 
  gi|336255124|ref|YP_004598231.1| 121 SNRRDEAVFD--------IYVQSRDETGDDAELVYE---GDGWLSLSGWSPDDSRLLVsQAYSNF-DQDLYVLDLEA 185
                                       9999999999........999999************...56666666666666555550566666.*********** PP

                                       TSS--EEEEESSSSS-EEEEEE..ETTEEEEEE-.TT-TT-EEEEEETTSSS CS
                    Peptidase_S9_N 264 eskkvlklvdnrfdaeysvehn..egdrfliltn.dgapnfrlvsvdlndps 312
                                       ++ + + l + + d +y+   +  +g+  ++ t+  +a    l   dl++++
  gi|336255124|ref|YP_004598231.1| 186 DDPDLEHLTPHEGDVRYQSASWapDGEGIYLVTDeGDADTLYLAYLDLETKE 237
                                       *999999999988889999999888899999998666766666666666554 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.1e-06    0.0097     156     191 ..     465     500 ..     377     521 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.1e-06
                                       HHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHH CS
                              AXE1 156 lDavrlveivaslpevDeeRvavlGasqGGalalav 191
                                        D+   ve ++++p vD++R+a+ G+s GG + la+
  gi|336255124|ref|YP_004598231.1| 465 ADIEACVEWLQDHPAVDPDRIAAKGGSYGGFMVLAA 500
                                       58888999**********************999886 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.6e-05     0.032      49     209 ..     464     607 ..     458     609 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                                       HHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---..EEEEEEESE-SSTSSTTSHHHHHC CS
                     Abhydrolase_3  49 vedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepk..vagqvliyPvtdlertesesikka 123
                                       v d+ a ++wl+++    ++dp+ri+  G S GG +++a++ +  d    +  v+g++ +   +  e+t   ++++ 
  gi|336255124|ref|YP_004598231.1| 464 VADIEACVEWLQDHP---AVDPDRIAAKGGSYGGFMVLAALTEYPDLWAAGvdVVGIANFVTFL--ENTGDWRRELR 535
                                       67889999*****95...8*********************999888632222255555555544..55644444222 PP

                                       HHTTTSSSSCHHHHHHHHHHHSSGGGGGSTTTSGGGC.S-SST---EEEEEETT-TTHH..HHHHHHHHHHHTT--E CS
                     Abhydrolase_3 124 eeladgplltraaldlfwrlylpeadrddplasplla.edlsglpptlvvvaefDplrd..egeayaerlraagvev 197
                                           ++   + a+ ++f              +sp  + e ++  +p +v+ +e+Dp     e+e+ ae+ +a+gv+v
  gi|336255124|ref|YP_004598231.1| 536 ----EAEYGSLAEDREF-----------LEEISPTNNiEHIE--APLFVLHGENDPRVPvgEAEQIAEKAEAQGVPV 595
                                       ....2112122222222...........33456664423344..689999999999765337888999999999999 PP

                                       EEEEETTEETTG CS
                     Abhydrolase_3 198 elieyegmvHgf 209
                                       +   ++++ Hgf
  gi|336255124|ref|YP_004598231.1| 596 RKFIFDDEGHGF 607
                                       999999999999 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.3e-05     0.016       7      49 ..     468     510 ..     467     609 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSSSEEEE CS
                            BAAT_C   7 eeainyllrhpkvkkdkigllGiSkGgelalllasflkkisav 49 
                                       e  +++l++hp v  d+i+  G S Gg ++l+  + +++  a+
  gi|336255124|ref|YP_004598231.1| 468 EACVEWLQDHPAVDPDRIAAKGGSYGGFMVLAALTEYPDLWAA 510
                                       6679****************************99999976554 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.045        53      33      54 ..     236     257 ..     231     269 .. 0.83
   2 !   11.5   0.0   0.00019      0.22      32      72 ..     581     617 ..     567     622 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.045
                           PepSY_2  33 eklvakleaqGykvkkievddg 54 
                                       ++l++ + ++G++v+ i +dd+
  gi|336255124|ref|YP_004598231.1| 236 KELETVADGEGWNVDGIALDDE 257
                                       678889999**********886 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00019
                           PepSY_2  32 reklvakleaqGykvkkievddggcyEvegldkdGkkveik 72 
                                       +e++ +k+eaqG  v+k+ + d+   E +g+ k  +++e++
  gi|336255124|ref|YP_004598231.1| 581 AEQIAEKAEAQGVPVRKFIF-DD---EGHGFSKLENRIEAY 617
                                       69******************.55...569999999999998 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0085        10      82     129 ..     459     507 ..     447     530 .. 0.83
   2 ?    7.3   0.0     0.003       3.6     153     199 ..     561     605 ..     546     625 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0085
                                       HHHHHHHHHHHHHHHHHHTT.--GGGEEEEEETHHHHHHHHHHHT-SS- CS
                     Abhydrolase_2  82 gikksaekleelidaelkkg.ipssriiigGFSqGaalalylaltlpkk 129
                                       + ++s+  +e+ ++  ++++ ++ +ri+  G S G+ ++l++   +p  
  gi|336255124|ref|YP_004598231.1| 459 KRMDSVADIEACVEWLQDHPaVDPDRIAAKGGSYGGFMVLAALTEYPDL 507
                                       557888899999999999999********************99998874 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.003
                                       GGGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--S CS
                     Abhydrolase_2 153 vtkklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaH 199
                                       +  + p + +Hge Dp vp+  +++ +e  ++    v + ++ + +H
  gi|336255124|ref|YP_004598231.1| 561 I--EAPLFVLHGENDPRVPVGEAEQIAEKAEAQGVPVRKFIFDDEGH 605
                                       3..5899******************9999888877777777777777 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.8   2.2e+03      10      35 ..     385     414 ..     380     434 .. 0.75
   2 ?   11.3   0.0   0.00016      0.19     103     140 ..     471     508 ..     467     546 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.8
                                       EEEEE.CC......GGTTTEEEEEEE--TTH CS
                          Esterase  10 vqvyLPedy.....spgrkypvvylldGltg 35 
                                        ++ LP+dy     ++g + pv++  +G   
  gi|336255124|ref|YP_004598231.1| 385 GFLTLPDDYeegdaNDGDGVPVIVDIHG-GP 414
                                       56789****9999999999999999888.55 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00016
                                       HHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTC CS
                          Esterase 103 lplldanfrtapdgravaGqSmGGlgALilalkhpdrF 140
                                       + +l+++  ++pd+ a+ G S GG++ L + +++pd++
  gi|336255124|ref|YP_004598231.1| 471 VEWLQDHPAVDPDRIAAKGGSYGGFMVLAALTEYPDLW 508
                                       579*********************************87 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0001      0.12      33      91 ..     561     624 ..     547     626 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                     Abhydrolase_4  33 gaapvLllqnerDpaTPyegakklakalgg.a...vlvtvegeGHgala.agntCvdkavdaYL 91 
                                        +ap  +l +e+Dp +P   a+++a++ +  +   + ++ ++eGHg+++ ++   + +a++++L
  gi|336255124|ref|YP_004598231.1| 561 IEAPLFVLHGENDPRVPVGEAEQIAEKAEAqGvpvRKFIFDDEGHGFSKlENRIEAYSAIADFL 624
                                       35899*********************9996556667778899****998444334556666665 PP

>> DUF829  Eukaryotic protein of unknown function (DUF829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00032      0.39     175     223 ..     558     606 ..     545     609 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                            DUF829 175 tkplrcpqlylySkaDeviswrdveshaeeaeqrgvkvtakkfedspHv 223
                                        ++ ++p + l  ++D+ ++  + e+ ae+ae +gv+v++  f+d+ H+
  gi|336255124|ref|YP_004598231.1| 558 IEHIEAPLFVLHGENDPRVPVGEAEQIAEKAEAQGVPVRKFIFDDEGHG 606
                                       45667899999*************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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 0.24s 00:00:00.86 Elapsed: 00:00:00.39
# Mc/sec: 4829.93
//
Query:       gi|336255125|ref|YP_004598232.1|  [L=326]
Description: ABC transporter-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-27   96.4   0.0    3.2e-27   95.7   0.0    1.4  1  ABC_tran     ABC transporter
    1.5e-11   44.6   0.0    7.5e-08   32.5   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0014   18.4   0.0      0.003   17.3   0.0    1.5  1  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.021   14.7   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
      0.014   15.9   0.0      0.025   15.1   0.0    1.3  1  AAA_23       AAA domain
      0.035   14.5   0.0      0.097   13.1   0.0    1.8  2  AAA_16       AAA ATPase domain
      0.082   12.7   0.0       0.17   11.6   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
       0.18   11.4   0.0        1.2    8.7   0.0    2.0  2  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 !   95.7   0.0   1.4e-30   3.2e-27       2     136 ..      21     159 ..      20     160 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 1.4e-30
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++++l ++ ge+ +++G+nGaGKSt +++l+  ++pt G+ ++ g+d +e e  + r++igvlp+ ++l ++lt re
  gi|336255125|ref|YP_004598232.1|  21 DDLELVVEDGEIFGFLGPNGAGKSTTINMLLDFVRPTTGRATVLGHDAQE-EADVIRERIGVLPEGATLYDRLTGRE 96 
                                       789999********************************************.9************************* PP

                                       H........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +         +de+++++l+++gl+  + ++    +  +S+G++qr+  a+al+ +p+ll+lDEp+
  gi|336255125|ref|YP_004598232.1|  97 HlewvidtkGADEDPDALLERVGLEPEDGDRS---AGGYSKGMQQRLGFAMALVGDPDLLILDEPS 159
                                       ******99989999**********99666664...7*****************************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 !    9.9   0.2   0.00026      0.59       2      19 ..      33      50 ..      32     110 .. 0.81
   2 !   32.5   0.0   3.4e-11   7.5e-08     226     297 ..     121     189 ..     101     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00026
                            AAA_21  2 nvliGpNgsGKSnLLdal 19
                                       ++ GpNg+GKS+ +  l
  gi|336255125|ref|YP_004598232.1| 33 FGFLGPNGAGKSTTINML 50
                                      6789*********98766 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 3.4e-11
                            AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       ++ +++++a   S G+++ l+++ al  ++   +ll++DEp +gL+P  +    e++ +++++g+ v++++H
  gi|336255125|ref|YP_004598232.1| 121 EPEDGDRSAGGYSKGMQQRLGFAMALVGDP---DLLILDEPSSGLDPTGMQGMREIIAAEADRGTTVFFSSH 189
                                       46788999999*****************99...9***********************99999********** PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.3e-06     0.003      20     119 ..      32     184 ..      22     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                            AAA_30  20 vavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaeelgi..eastiakllkrlk............ 81 
                                       +    Gp G+GK+t+++ l + ++   g+  ++    ++ A+v++e +g+  e++t+   l+  +            
  gi|336255125|ref|YP_004598232.1|  32 IFGFLGPNGAGKSTTINMLLDFVRPTtGRATVLGHDAQEEADVIRERIGVlpEGATLYDRLTGREhlewvidtkgad 108
                                       67788**************9999999677766667778899********9997777765554444599999999999 PP

                            AAA_30  82 ..................................grarlepgtllivDEagmv....dtkqlaallkaaekagakv 119
                                                                         ++a + + +lli DE +      +++ ++++++a +++g++v
  gi|336255125|ref|YP_004598232.1| 109 edpdallervglepedgdrsaggyskgmqqrlgfAMALVGDPDLLILDEPSSGldptGMQGMREIIAAEADRGTTV 184
                                       9999999999999999999999999999999998666777779999999876555557777777777766667666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   9.3e-06     0.021      90     122 ..      20      53 ..       5      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.3e-06
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       +++l+ +++d ++  ++G+ G+GKSt in+ll  
  gi|336255125|ref|YP_004598232.1|  20 VDDLELVVEDgEIFGFLGPNGAGKSTTINMLLDF 53 
                                       678888888889999***************9875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.1e-05     0.025      19      39 ..      30      50 ..      19      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                            AAA_23 19 kgltlItGpNGaGKTTildAi 39
                                        ++ + GpNGaGK+T ++ +
  gi|336255125|ref|YP_004598232.1| 30 GEIFGFLGPNGAGKSTTINML 50
                                      56999***********99865 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   4.3e-05     0.097      25     114 ..      31     127 ..      19     180 .. 0.61
   2 ?   -1.4   0.0       1.2   2.6e+03      94      94 ..     252     252 ..     188     318 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekd.ggiflrgkcdqlesa........ipysa.laqalareellrqlldeaes 91 
                                       e+  + G+ G GKs+ +++ll+ ++ + g  ++ g+  q e++        +p  a l + l+ +e l+ + d    
  gi|336255125|ref|YP_004598232.1|  31 EIFGFLGPNGAGKSTTINMLLDFVRPTtGRATVLGHDAQEEADvirerigvLPEGAtLYDRLTGREHLEWVIDT--- 104
                                       566789***************87777742333555555554443322222222222244444444444444333... PP

                            AAA_16  92 aeleawrekleealaavpelaga 114
                                       + +++++++l+e+++  pe+ + 
  gi|336255125|ref|YP_004598232.1| 105 KGADEDPDALLERVGLEPEDGDR 127
                                       55566666666666644444444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                            AAA_16  94 l 94 
                                       +
  gi|336255125|ref|YP_004598232.1| 252 V 252
                                       2 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   0.0   7.7e-05      0.17      23      39 ..      30      47 ..      20      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.7e-05
                            AAA_29 23 g.atlltGpsGsGKSTll 39
                                      g ++ + Gp+G+GKST +
  gi|336255125|ref|YP_004598232.1| 30 GeIFGFLGPNGAGKSTTI 47
                                      4477799*********87 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00055       1.2      31      49 ..      35      53 ..      11      61 .. 0.81
   2 ?   -0.1   0.0      0.26   5.9e+02     132     164 ..     168     200 ..     161     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00055
                            AAA_27 31 iyGpNEAGKstalrAisdl 49
                                       +GpN AGKst+++ + d+
  gi|336255125|ref|YP_004598232.1| 35 FLGPNGAGKSTTINMLLDF 53
                                      57**********9988886 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.26
                            AAA_27 132 eGGealleaegelgqlLfeasaGlaslrevlea 164
                                       +G +++++ae + g+++f +s  l +++++ ++
  gi|336255125|ref|YP_004598232.1| 168 QGMREIIAAEADRGTTVFFSSHILGEVEAICDR 200
                                       7999**************999988888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2476.26
//
Query:       gi|336255126|ref|YP_004598233.1|  [L=276]
Description: ABC-2 type transporter [Halopiger xanaduensis SH-6]
Scores for 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-40  138.4  14.5    2.5e-39  135.3  14.5    1.9  1  ABC2_membrane_2  ABC-2 family transporter protein
    1.2e-11   44.9   3.6    1.2e-11   44.9   3.6    1.4  2  ABC2_membrane_4  ABC-2 family transporter protein
    1.3e-10   41.2   6.1    3.9e-10   39.6   6.2    1.7  1  ABC2_membrane_5  ABC-2 family transporter protein
      8e-09   35.0  12.0      8e-09   35.0  12.0    1.3  1  ABC2_membrane_3  ABC-2 family transporter protein
    1.3e-05   24.7  13.6    2.3e-05   23.9  13.6    1.4  1  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
       0.22   11.7   2.7       0.52   10.5   2.7    1.6  1  DUF872           Eukaryotic protein of unknown function (DUF8
       0.97    9.7   4.1          2    8.6   0.3    2.4  2  DUF4293          Domain of unknown function (DUF4293)


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 !  135.3  14.5   9.7e-43   2.5e-39       2     288 .]       5     275 ..       4     275 .. 0.92

  Alignments for each domain:
  == domain 1  score: 135.3 bits;  conditional E-value: 9.7e-43
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                        +akk+f d +rs++++ +++l+ l+ v   y+ + g s+++  ++++++++                         
  gi|336255126|ref|YP_004598233.1|   5 SVAKKDFLDVRRSKTVWTVGALYTLFAVLFFYFGQTGVSEPNVINQLFSLAS------------------------- 56 
                                       69************************77777778888888888888887765......................... PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgiv 155
                                        i +++ip+ia+++++ aiagE+e+g++k lLs+P++R++++lgK +++ a+   +  a++ ++ ++ +++l +  +
  gi|336255126|ref|YP_004598233.1|  57 -IGSLFIPLIALVAAYLAIAGERESGSIKYLLSLPNTRRDVVLGKYLSRGAV---VGAAIGFAFAVGAVLTLLWYPS 129
                                       .699************************************************...********************** PP

                   ABC2_membrane_2 156 laledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp...... 226
                                       l+++ + ++v++++l+ l  +++a+++++S+ + s+++a+  a+g+++v ++l++  ++ +   ++++ +       
  gi|336255126|ref|YP_004598233.1| 130 LEAATFARVVALTLLFTL--AYVAVAIGISAATSSRSRAMGGAVGFYFVGNLLMIFPGLSIVGVFQYALNGrlgldi 204
                                       **************8888..89***************************9999999998888888888888999999 PP

                   ABC2_membrane_2 227 .qeindflsllsptsayntllneilagsdlna........lgstatnllilllllavllvlgyvlFkrkDl 288
                                        ++   f++ lspt+ay+ +    +  +++          ++     ll+l+++l+v+++lg++ F+r Dl
  gi|336255126|ref|YP_004598233.1| 205 sEHAFEFVRRLSPTVAYESAMPLAIPDDEITLtgttdvpaYLEPEVALLVLVAWLVVPVALGLWHFDRVDL 275
                                       9*****************9999888888777699999**7777777888999****************997 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 !   44.9   3.6   4.8e-15   1.2e-11       6     160 ..      11     161 ..       8     184 .. 0.68
   2 ?   -4.3   0.3       5.8   1.5e+04      20      60 ..     256     261 ..     250     269 .. 0.38

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 4.8e-15
                   ABC2_membrane_4   6 flKlkrskivwllvlaallvpllallyfnllgktgldp....aefyslsvfgftlllllplilgiiasylifrEeqn 78 
                                       fl ++rsk vw + ++  l+++l ++yf   g+tg+++    ++++sl+++g    l++pli  + a   i  E+++
  gi|336255126|ref|YP_004598233.1|  11 FLDVRRSKTVWTVGALYTLFAVL-FFYF---GQTGVSEpnviNQLFSLASIG---SLFIPLIALVAAYLAIAGERES 80 
                                       6668*******977666666543.4555...556654411134444444444...4678888877777789****** PP

                   ABC2_membrane_4  79 dtlknLltiPvsrtklllaKlivllllsv.llmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlp 154
                                       + +k+Ll +P +r+ ++l+K++    ++  ++ +++++ +vl   l+ +++++++++++++  +l+++l  +++ + 
  gi|336255126|ref|YP_004598233.1|  81 GSIKYLLSLPNTRRDVVLGKYLSRGAVVGaAIGFAFAVGAVL--TLLWYPSLEAATFARVVALTLLFTLAYVAVAIG 155
                                       *********************987655440444444444444..48899*******999999888888766655555 PP

                   ABC2_membrane_4 155 iialvl 160
                                       i a ++
  gi|336255126|ref|YP_004598233.1| 156 ISAATS 161
                                       555433 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 5.8
                   ABC2_membrane_4  20 laallvpllallyfnllgktgldpaefyslsvfgftlllll 60 
                                       +a                                   +l++
  gi|336255126|ref|YP_004598233.1| 256 VA-----------------------------------WLVV 261
                                       12...................................2222 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 !   39.6   6.2   1.5e-13   3.9e-10       4     159 ..       8     177 ..       6     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.5e-13
                   ABC2_membrane_5   4 lkDlylikk..likillivllllaiiilifl..........ndsvl..lifsilslvisiililttlsyDekskwnk 66 
                                       +kD++ +++  +++++  +++l+a+++++f+          n+ ++   i+s+++++i+ + +  +++ ++ s++ k
  gi|336255126|ref|YP_004598233.1|   8 KKDFLDVRRskTVWTVGALYTLFAVLFFYFGqtgvsepnviNQLFSlaSIGSLFIPLIALVAAYLAIAGERESGSIK 84 
                                       57888666656788888899999999999996666666555444432345788888888888889999********* PP

                   ABC2_membrane_5  67 ylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgn.vtisevllsiliglvialiflaivlPlyfkfg 142
                                       yll+LP tr+++V  KYl+   ++ +ai + ++++++ +l+  + +   ++  ++++ l+++l+++a+ + +   ++
  gi|336255126|ref|YP_004598233.1|  85 YLLSLPNTRRDVVLGKYLSRGAVVGAAIGFAFAVGAVLTLLWYPsLEAATFARVVALTLLFTLAYVAVAIGISAATS 161
                                       *******************999999999999999998777666658999999999***************9999998 PP

                   ABC2_membrane_5 143 vekgrivliiiifgiif 159
                                        +++r +  ++ f +++
  gi|336255126|ref|YP_004598233.1| 162 -SRSRAMGGAVGFYFVG 177
                                       .5666433333333222 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 !   35.0  12.0   3.1e-12     8e-09     155     313 ..      43     225 ..      36     268 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 3.1e-12
                   ABC2_membrane_3 155 elsnvasflvgliliilifitasfiav...siveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll. 227
                                       +++nv ++l++l+ i ++fi+++ +++   +i+ E+es+ ++ +l+ + ++   +l+k+l+ ++v    + +++++ 
  gi|336255126|ref|YP_004598233.1|  43 SEPNVINQLFSLASIGSLFIPLIALVAaylAIAGERESGSIKYLLSLPNTRRDVVLGKYLSRGAVVGAAIGFAFAVg 119
                                       567888999998888888888776666444679**********************************9999999965 PP

                   ABC2_membrane_3 228 .afgl....gipfgnlglllllfllfglayialgyllsslfknsetaqilifivil...llsgffgglfp...ledl 293
                                        ++ l    +++   +  ++ l llf lay+a++  +s+++++ + a++ ++ + +   ll++f g++++     +l
  gi|336255126|ref|YP_004598233.1| 120 aVLTLlwypSLEAATFARVVALTLLFTLAYVAVAIGISAATSSRSRAMGGAVGFYFvgnLLMIFPGLSIVgvfQYAL 196
                                       56666766788888**************************9999998876555555466555555544434332233 PP

                   ABC2_membrane_3 294 p.........salkwifsiiPffapglgl 313
                                       +         +a+  + ++ P++a+  ++
  gi|336255126|ref|YP_004598233.1| 197 NgrlgldiseHAFEFVRRLSPTVAYESAM 225
                                       35555555557777788888888876665 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9  13.6   9.1e-09   2.3e-05       5     175 ..       5     180 ..       2     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 9.1e-09
                     ABC2_membrane   5 allkreflqrwrdpslgllwrliqplllalvfgtvfgnlg.nsedglnr....pgllffsvlflafsaltsvapvfe 76 
                                        + k++fl   r+++    w +     l+ v+ + fg++g ++ +++n     + +   ++  +a + ++ +a+  e
  gi|336255126|ref|YP_004598233.1|   5 SVAKKDFLDVRRSKTV---WTVGALYTLFAVLFFYFGQTGvSEPNVINQlfslASIGSLFIPLIA-LVAAYLAIAGE 77 
                                       5778999999999954...5555555555555555666665333333223443444444444444.5577778999* PP

                     ABC2_membrane  77 rergvlerelvsplyslsayvlakvlve.lpvsllqalifllivyflvgldls....rfflflllllltalaasslg 148
                                       re g+++ +l+ p  ++ ++vl+k+l+  ++v+++++++f + +++++ +++s     f+ +++l+ll++la ++++
  gi|336255126|ref|YP_004598233.1|  78 RESGSIKYLLSLPN-TRRDVVLGKYLSRgAVVGAAIGFAFAVGAVLTLLWYPSleaaTFARVVALTLLFTLAYVAVA 153
                                       **************.**********99988888999999988777777888888887889999*************9 PP

                     ABC2_membrane 149 llisalapsfedasqlaslvllpllll 175
                                       + isa ++s   a+  a  ++++ +ll
  gi|336255126|ref|YP_004598233.1| 154 IGISAATSSRSRAMGGAVGFYFVGNLL 180
                                       999999999999999998888876666 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 ?   10.5   2.7    0.0002      0.52      44     108 ..     137     203 ..     114     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0002
                            DUF872  44 kvvlaallLlllGlvLlllgvvilvep...seGvssavflvlGlllfiPGvYhvvyiylavrGakGyk 108
                                       + v+a +lL +l  v +++g+  +++      G     ++v  ll++ PG+  v +  +a+ G+ G +
  gi|336255126|ref|YP_004598233.1| 137 R-VVALTLLFTLAYVAVAIGISAATSSrsrAMGGAVGFYFVGNLLMIFPGLSIVGVFQYALNGRLGLD 203
                                       4.4455677788889999999888776444456666667888899999****************9975 PP

>> DUF4293  Domain of unknown function (DUF4293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.3   0.00079         2      91     139 ..      26      75 ..      16      78 .. 0.65
   2 ?    1.9   0.4     0.095   2.4e+02      82     115 ..     136     166 ..      99     195 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00079
                           DUF4293  91 llvllyvllal..lllvnkanaaaeslgesslkig.lilplialilnlLAir 139
                                       l +l++vl+++   + v++ n  ++ +  s ++ig l++plial++ +LAi 
  gi|336255126|ref|YP_004598233.1|  26 LYTLFAVLFFYfgQTGVSEPNVINQLF--SLASIGsLFIPLIALVAAYLAIA 75 
                                       444555555553455566666666666..4445554889***********96 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.095
                           DUF4293  82 lrlclinllllvllyvllallllvnkanaaaesl 115
                                       +r+++++ll++++++++++    +++a+++ +  
  gi|336255126|ref|YP_004598233.1| 136 ARVVALTLLFTLAYVAVAIG---ISAATSSRSRA 166
                                       45566666666666655555...33333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2173.81
//
Query:       gi|336255127|ref|YP_004598234.1|  [L=86]
Description: hypothetical protein Halxa_3749 [Halopiger xanaduensis SH-6]
Scores for 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  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 724.54
//
Query:       gi|336255128|ref|YP_004598235.1|  [L=117]
Description: hypothetical protein Halxa_3750 [Halopiger xanaduensis SH-6]
Scores for 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:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 929.55
//
Query:       gi|336255129|ref|YP_004598236.1|  [L=65]
Description: hypothetical protein Halxa_3751 [Halopiger xanaduensis SH-6]
Scores for 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:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 508.36
//
Query:       gi|336255130|ref|YP_004598237.1|  [L=210]
Description: anaerobic dehydrogenase-like protein [Halopiger xanaduensis SH-6]
Scores for 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-28   99.1   0.1    2.7e-28   98.7   0.1    1.2  1  Nitrate_red_del  Nitrate reductase delta subunit


Domain annotation for each model (and alignments):
>> Nitrate_red_del  Nitrate reductase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.1   1.5e-32   2.7e-28       7     136 ..      50     176 ..      44     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 1.5e-32
                   Nitrate_red_del   7 eveealaelaeal....aa.ededllelaaeYtrLFlgpgrrsasPyesvYlsekkgllfgestlevrefyrqagle 78 
                                        +++  + l++++    +   d+ +++l++e+trLF+g +r++++P+e++Y++++  +++g + +ev++ y +ag++
  gi|336255130|ref|YP_004598237.1|  50 RLDRGFERLDSFIaeneNRdPDAVQEDLEREFTRLFVG-PRPPILPHETYYREDT--DFRGAGLAEVEASYGAAGWS 123
                                       444444559999988643389****************8.9*************54..6******************* PP

                   Nitrate_red_del  79 vaeefneppDHlaveLeflahLaereaeaeeaeeaealleaqkafleehllpWlpefa 136
                                        +e+++e +D++aveL+fl +L++r++e      +e++   q+ f eehl++W+ +fa
  gi|336255130|ref|YP_004598237.1| 124 PPEDYPEENDYVAVELAFLRNLIRRQRE-----GYEETFGYQRVFHEEHLSEWIADFA 176
                                       **************************97.....68999*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1727.06
//
Query:       gi|336255131|ref|YP_004598238.1|  [L=736]
Description: methyl-viologen-reducing hydrogenase subunit delta [Halopiger xanaduensis SH-6]
Scores for 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   87.8   0.0    1.6e-24   86.2   0.0    1.9  1  FlpD      Methyl-viologen-reducing hydrogenase, delta subunit
    3.1e-13   48.9  51.2    1.3e-05   24.7   2.4    7.7  8  Fer4      4Fe-4S binding domain
    3.5e-13   49.9  44.0      2e-07   31.5  11.6    6.5  7  Fer4_7    4Fe-4S dicluster domain
    7.1e-12   46.1  30.2     0.0003   21.6   0.3    7.4  7  Fer4_16   4Fe-4S double cluster binding domain
    2.7e-11   43.5  42.0    3.6e-06   27.0  10.4    5.5  6  Fer4_9    4Fe-4S dicluster domain
    6.5e-09   35.8  32.3    0.00022   21.3   8.0    5.3  5  Fer4_21   4Fe-4S dicluster domain
    3.6e-07   30.5  21.8     0.0053   17.2   0.4    5.9  5  Fer4_8    4Fe-4S dicluster domain
    4.1e-07   30.0  45.0      2e-05   24.6  11.3    5.2  4  Fer4_10   4Fe-4S dicluster domain
    2.2e-06   27.5  11.6    1.2e-05   25.2   2.2    7.9  7  Fer4_6    4Fe-4S binding domain
    0.00056   19.8   3.3    0.00056   19.8   3.3    7.7  8  Fer4_2    4Fe-4S binding domain
     0.0044   17.5  33.6      0.016   15.7   0.3    5.9  6  Fer4_17   4Fe-4S dicluster domain
     0.0044   17.4   4.7     0.0044   17.4   4.7    6.4  4  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.014   15.6  21.3       0.11   12.7   3.8    4.4  4  Fer4_18   4Fe-4S dicluster domain
      0.067   13.1   0.6       0.33   10.8   0.3    2.1  2  YidD      Putative membrane protein insertion efficiency fact
       0.38   10.9  19.2       0.34   11.1   1.8    3.7  3  Fer4_11   4Fe-4S dicluster domain


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 !   86.2   0.0   1.4e-27   1.6e-24       1     121 [.     395     517 ..     395     518 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 1.4e-27
                              FlpD   1 ilaFlCnwcayaaadlag......vsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGn 71 
                                       i+aF+C++ a++a+ ++g       ++++ypp + ++ v+C+++v +++ ++al+ GadgV+++gC+ gdC + +G+
  gi|336255131|ref|YP_004598238.1| 395 IVAFVCSEEADDALREYGrlaaagKAEVEYPP-ILPVHVNCTDTVGEAHAMHALACGADGVAIVGCG-GDCLH-SGP 468
                                       8*********99997777766666********.**********************************.*****.*** PP

                              FlpD  72 ekaerrveklkelleelgiepeRvrleevsaaegekfaevikefvekike 121
                                       + +++ v++l+++ ++l+++ eR+++++ +++e+ +f+e+i++f+ +++e
  gi|336255131|ref|YP_004598238.1| 469 DPKADLVDRLNRASRDLELG-ERFEFFAPDPDEPGAFVEAISTFAVELEE 517
                                       ********************.***********************999875 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   1.5    0.0036       4.3       5      15 ..     197     207 ..     196     209 .. 0.89
   2 !    6.9   0.1    0.0049       5.9      16      24 .]     233     241 ..     232     241 .. 0.89
   3 !   17.0   2.8   3.2e-06    0.0038      10      23 ..     312     325 ..     311     326 .. 0.93
   4 !   24.7   2.4   1.1e-08   1.3e-05       2      22 ..     334     354 ..     333     355 .. 0.93
   5 !    7.6   0.1    0.0029       3.5      14      24 .]     586     596 ..     585     596 .. 0.90
   6 !   16.6   2.5   4.1e-06    0.0049       2      23 ..     605     626 ..     604     627 .. 0.86
   7 ?   -3.4   0.6       8.9   1.1e+04       8      12 ..     660     664 ..     659     665 .. 0.72
   8 ?   -1.8   0.1       2.7   3.2e+03       6      12 ..     697     703 ..     695     704 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0036
                                       TTTSSS-THHH CS
                              Fer4   5 eekCigCGaCv 15 
                                       +e+Ci C++Cv
  gi|336255131|ref|YP_004598238.1| 197 TEDCISCMKCV 207
                                       699*******9 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0049
                                       HHSTTTEEE CS
                              Fer4  16 evCPvgAIt 24 
                                       evCP++AI+
  gi|336255131|ref|YP_004598238.1| 233 EVCPTDAID 241
                                       8******95 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 3.2e-06
                                       S-THHHHHSTTTEE CS
                              Fer4  10 gCGaCvevCPvgAI 23 
                                       gC++CvevCP++A 
  gi|336255131|ref|YP_004598238.1| 312 GCNECVEVCPHDAV 325
                                       9************7 PP

  == domain 4  score: 24.7 bits;  conditional E-value: 1.1e-08
                                       EEETTTSSS-THHHHHSTTTE CS
                              Fer4   2 videekCigCGaCvevCPvgA 22 
                                       +++++ C +CGaC ++CP+gA
  gi|336255131|ref|YP_004598238.1| 334 EFHKDACQNCGACTSACPTGA 354
                                       6889****************9 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.0029
                                       HHHHSTTTEEE CS
                              Fer4  14 CvevCPvgAIt 24 
                                       C   CP++AI+
  gi|336255131|ref|YP_004598238.1| 586 CSTLCPTDAIR 596
                                       99********6 PP

  == domain 6  score: 16.6 bits;  conditional E-value: 4.1e-06
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       +++ e+C++CG+C+e C  +AI
  gi|336255131|ref|YP_004598238.1| 605 EFNHERCVNCGTCEEGCVEDAI 626
                                       6899***********9977777 PP

  == domain 7  score: -3.4 bits;  conditional E-value: 8.9
                                       SSS-T CS
                              Fer4   8 CigCG 12 
                                       C +CG
  gi|336255131|ref|YP_004598238.1| 660 CRNCG 664
                                       88888 PP

  == domain 8  score: -1.8 bits;  conditional E-value: 2.7
                                       TTSSS-T CS
                              Fer4   6 ekCigCG 12 
                                       + C +C 
  gi|336255131|ref|YP_004598238.1| 697 DYCDNCR 703
                                       7899996 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       5.2   6.2e+03      22      22 ..      30      30 ..       9      85 .. 0.53
   2 !    6.6   0.1      0.01        12      35      49 ..     197     211 ..     164     225 .. 0.76
   3 !   16.8   2.4   6.4e-06    0.0077      10      52 .]     233     324 ..     229     324 .. 0.60
   4 !   31.5  11.6   1.7e-10     2e-07       4      52 .]     312     354 ..     311     354 .. 0.94
   5 !    9.4   0.5    0.0014       1.6      34      52 .]     576     594 ..     534     594 .. 0.81
   6 !   19.8   9.8   7.6e-07   0.00091       2      51 ..     580     624 ..     578     625 .. 0.89
   7 !   17.6   4.5   3.6e-06    0.0043       1      43 [.     610     665 ..     610     669 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.2
                            Fer4_7 22 e 22
                                      +
  gi|336255131|ref|YP_004598238.1| 30 V 30
                                      0 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                            Fer4_7  35 pekClgCgaCvavCP 49 
                                        e+C++C +Cv + P
  gi|336255131|ref|YP_004598238.1| 197 TEDCISCMKCVHEGP 211
                                       566777777776544 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 6.4e-06
                            Fer4_7  10 aaCpvkaieldeeenek..........................................gtekveidpekCl..... 39 
                                       ++Cp++ai+l+ +e+                                            + ++++++++ C      
  gi|336255131|ref|YP_004598238.1| 233 EVCPTDAIDLEGVERTLevdqvvypaanrqtrggrigfytapidaatiaavkrhvggleKPDHLDLEMDVCAagdss 309
                                       6899999998854333233334444444445555555555555554444444444333222556999****967766 PP

                            Fer4_7  40 ..gCgaCvavCPtga 52 
                                         gC++Cv+vCP++a
  gi|336255131|ref|YP_004598238.1| 310 qpGCNECVEVCPHDA 324
                                       666*********987 PP

  == domain 4  score: 31.5 bits;  conditional E-value: 1.7e-10
                            Fer4_7   4 gCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       gC+ Cv++Cp++a+e ++       ++ve++ + C++CgaC ++CPtga
  gi|336255131|ref|YP_004598238.1| 312 GCNECVEVCPHDAVERTKI------DEVEFHKDACQNCGACTSACPTGA 354
                                       8**************9884......779*******************98 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.0014
                            Fer4_7  34 dpekClgCgaCvavCPtga 52 
                                       + + C+++  C + CPt+a
  gi|336255131|ref|YP_004598238.1| 576 VDDGCTFTPTCSTLCPTDA 594
                                       4689*************97 PP

  == domain 6  score: 19.8 bits;  conditional E-value: 7.6e-07
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       C+ +  C   Cp++ai+ dee      + +e+++e+C++Cg C++ C  +
  gi|336255131|ref|YP_004598238.1| 580 CTFTPTCSTLCPTDAIRRDEE-----GAVLEFNHERCVNCGTCEEGCVED 624
                                       777789************997.....4899*****************765 PP

  == domain 7  score: 17.6 bits;  conditional E-value: 3.6e-06
                            Fer4_7   1 rCigCgaCvaaCpvkaield.........eeenekgtekv....eidpekClgCga 43 
                                       rC++Cg C++ C  +ai+++         e+ +++  + +    ++++++C +Cg+
  gi|336255131|ref|YP_004598238.1| 610 RCVNCGTCEEGCVEDAITMHdglhlsllpERRDDASEPAWvtvhDGEMRECRNCGE 665
                                       8*****************99555555554222222222333333778899999985 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 ?   -2.6   0.0       9.3   1.1e+04      11      29 ..      60      78 ..      58     107 .. 0.60
   2 ?    5.1   0.2     0.038        45       2      20 ..     200     218 ..     199     227 .. 0.84
   3 ?    4.6   0.0     0.053        63       9      25 ..     232     249 ..     229     266 .. 0.76
   4 !   15.2   0.5   2.5e-05      0.03       4      26 ..     312     334 ..     311     338 .. 0.83
   5 !   21.6   0.3   2.5e-07    0.0003       2      33 ..     340     371 ..     339     401 .. 0.74
   6 !    7.0   0.1    0.0094        11       7      23 ..     585     601 ..     579     608 .. 0.80
   7 !    9.4   1.6    0.0017         2       1      20 [.     610     629 ..     610     665 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 9.3
                           Fer4_16 11 vCPtnaikekkekeieare 29
                                      +CP++ ++ k ++++e+r 
  gi|336255131|ref|YP_004598238.1| 60 TCPEERVQRKLRRVAEQRS 78
                                      6888888877555555444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.038
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++C kC+   P +a++  
  gi|336255131|ref|YP_004598238.1| 200 CISCMKCVHEGPDGAVTRY 218
                                       *********9999998765 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.053
                           Fer4_16   9 aevCPtnaikek.kekei 25 
                                       +evCPt+ai+ +  e+++
  gi|336255131|ref|YP_004598238.1| 232 TEVCPTDAIDLEgVERTL 249
                                       58*******987455554 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 2.5e-05
                           Fer4_16   4 tCgkCaevCPtnaikekkekeie 26 
                                       +C++C+evCP++a++ +k  e+e
  gi|336255131|ref|YP_004598238.1| 312 GCNECVEVCPHDAVERTKIDEVE 334
                                       6*************999777666 PP

  == domain 5  score: 21.6 bits;  conditional E-value: 2.5e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy 33 
                                       C++Cg+C+++CPt+a + ++  + ++ +++++
  gi|336255131|ref|YP_004598238.1| 340 CQNCGACTSACPTGATRLREPSNERIAREVEA 371
                                       ***************88774444445555444 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.0094
                           Fer4_16   7 kCaevCPtnaikekkek 23 
                                        C   CPt+ai+ ++e 
  gi|336255131|ref|YP_004598238.1| 585 TCSTLCPTDAIRRDEEG 601
                                       6***********99654 PP

  == domain 7  score: 9.4 bits;  conditional E-value: 0.0017
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       rC++Cg C e C ++ai++ 
  gi|336255131|ref|YP_004598238.1| 610 RCVNCGTCEEGCVEDAITMH 629
                                       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 !   10.9   0.1   0.00034       0.4      33      50 ..     193     214 ..     157     215 .. 0.75
   2 ?    0.2   0.0      0.73   8.7e+02      10      28 ..     233     251 ..     231     255 .. 0.72
   3 !   27.0  10.4     3e-09   3.6e-06       4      50 ..     312     354 ..     311     355 .. 0.91
   4 !   21.9   6.5   1.2e-07   0.00014       6      51 .]     584     626 ..     578     626 .. 0.86
   5 ?   -2.0   0.1       3.5   4.2e+03      35      40 ..     659     664 ..     641     666 .. 0.65
   6 ?   -3.4   0.1       9.5   1.1e+04       2       6 ..     699     703 ..     692     704 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                            Fer4_9  33 e....eaCigCgaCveaCpkga 50 
                                       e    e+Ci+C++Cv+  p ga
  gi|336255131|ref|YP_004598238.1| 193 EacvtEDCISCMKCVHEGPDGA 214
                                       1444578********9877765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.73
                            Fer4_9  10 eaCpagvvvedaaerkarl 28 
                                       e+Cp++++  + +er+ ++
  gi|336255131|ref|YP_004598238.1| 233 EVCPTDAIDLEGVERTLEV 251
                                       6788888887777777665 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 3e-09
                            Fer4_9   4 gCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       gC++Cve+Cp+++v++ +  +   ++     aC  CgaC+ aCp+ga
  gi|336255131|ref|YP_004598238.1| 312 GCNECVEVCPHDAVERTKIDEVEFHKD----ACQNCGACTSACPTGA 354
                                       8**************999999988765....6************996 PP

  == domain 4  score: 21.9 bits;  conditional E-value: 1.2e-07
                            Fer4_9   6 gaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                        +C + Cp++++++d+ +   + +++   +C+ Cg+C+e C ++ai
  gi|336255131|ref|YP_004598238.1| 584 PTCSTLCPTDAIRRDEEGAVLEFNHE---RCVNCGTCEEGCVEDAI 626
                                       47*******************99774...8***********99987 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 3.5
                            Fer4_9  35 aCigCg 40 
                                       +C  Cg
  gi|336255131|ref|YP_004598238.1| 659 ECRNCG 664
                                       466665 PP

  == domain 6  score: -3.4 bits;  conditional E-value: 9.5
                            Fer4_9   2 CtgCg 6  
                                       C +C+
  gi|336255131|ref|YP_004598238.1| 699 CDNCR 703
                                       55554 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.8    0.0021       2.6       6      23 ..     198     215 ..     189     226 .. 0.65
   2 ?   -1.5   0.0       2.4   2.8e+03      49      58 ..     233     241 ..     230     242 .. 0.80
   3 !   21.3   8.0   1.8e-07   0.00022      10      55 ..     312     353 ..     307     357 .. 0.92
   4 !    7.3   0.2    0.0042         5      34      58 ..     573     596 ..     553     597 .. 0.80
   5 !   14.2   7.8     3e-05     0.036       7      59 .]     579     628 ..     573     628 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0021
                           Fer4_21   6 dkCigCgkCliaCedtsh 23 
                                       ++Ci+C kC+   +d+++
  gi|336255131|ref|YP_004598238.1| 198 EDCISCMKCVHEGPDGAV 215
                                       456666666655555444 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                           Fer4_21  49 svCPvedcie 58 
                                       +vCP+ d+i+
  gi|336255131|ref|YP_004598238.1| 233 EVCPT-DAID 241
                                       79**6.8886 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 1.8e-07
                           Fer4_21  10 gCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPved 55 
                                       gC++C+ +C+   h+a+e ++   ++  +d C  C  C+s CP+ +
  gi|336255131|ref|YP_004598238.1| 312 GCNECVEVCP---HDAVERTKIDEVEFHKDACQNCGACTSACPT-G 353
                                       7*********...89999999999999****************6.4 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0042
                           Fer4_21  34 lkvvedeCvGCnlCssvCPvedcie 58 
                                          v+d C+    Cs+ CP+ d+i+
  gi|336255131|ref|YP_004598238.1| 573 RMAVDDGCTFTPTCSTLCPT-DAIR 596
                                       4568999************7.8885 PP

  == domain 5  score: 14.2 bits;  conditional E-value: 3e-05
                           Fer4_21   7 kCigCgkCliaCedtshqaieidak.tvlkvvedeCvGCnlCssvCPvedciem 59 
                                        C     C + C+   ++ai+ d++ +vl+  +++Cv C  C + C ved+i+m
  gi|336255131|ref|YP_004598238.1| 579 GCTFTPTCSTLCP---TDAIRRDEEgAVLEFNHERCVNCGTCEEGC-VEDAITM 628
                                       5666678******...6***998763678999**************.59***99 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.044        52      49      59 ..     198     208 ..     158     239 .. 0.83
   2 ?    4.4   0.9     0.042        51      53      63 ..     312     322 ..     295     324 .. 0.91
   3 !   17.2   0.4   4.4e-06    0.0053       3      33 ..     338     368 ..     336     403 .. 0.77
   4 ?    3.1   0.0      0.11   1.3e+02      49      64 ..     578     593 ..     526     594 .. 0.85
   5 !   11.0   2.5   0.00037      0.45       3      55 ..     609     664 ..     607     667 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.044
                            Fer4_8  49 wsCttcgaCte 59 
                                       + C +c++C+ 
  gi|336255131|ref|YP_004598238.1| 198 EDCISCMKCVH 208
                                       55666666654 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.042
                            Fer4_8  53 tcgaCtevCpv 63 
                                       +c++C+evCp 
  gi|336255131|ref|YP_004598238.1| 312 GCNECVEVCPH 322
                                       5999*****97 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 4.4e-06
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaa 33 
                                       ++C +CgaC+saCp+  ++ +++ + r  ++
  gi|336255131|ref|YP_004598238.1| 338 DACQNCGACTSACPTGATRLREPSNERIARE 368
                                       5899999999999988887777766665544 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.11
                            Fer4_8  49 wsCttcgaCtevCpvg 64 
                                       + Ct +  C++ Cp++
  gi|336255131|ref|YP_004598238.1| 578 DGCTFTPTCSTLCPTD 593
                                       67************85 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 0.00037
                            Fer4_8   3 ekCieCgaCqsaCp....vlrrtkkhlldargeaae....dvqeeqvleeeealwsCttcg 55 
                                       e+C++Cg C++ C     ++++  + +l ++ +  +          v+  +  + +C +cg
  gi|336255131|ref|YP_004598238.1| 609 ERCVNCGTCEEGCVedaiTMHDGLHLSLLPERRDDAsepaW-----VTVHDGEMRECRNCG 664
                                       69***********4444344444444444444433323221.....112256688999887 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   2.9      0.12   1.4e+02       7      20 ..     198     211 ..     193     264 .. 0.77
   2 !   24.6  11.3   1.7e-08     2e-05      11      56 .]     312     351 ..     298     352 .. 0.93
   3 !   18.8   7.1   1.1e-06    0.0013       6      55 ..     577     621 ..     574     622 .. 0.95
   4 ?   -1.0   0.1       1.6   1.9e+03      40      49 ..     655     664 ..     649     669 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.12
                           Fer4_10   7 dtCirCgkCvkaCP 20 
                                       + Ci C kCv   P
  gi|336255131|ref|YP_004598238.1| 198 EDCISCMKCVHEGP 211
                                       56888888877544 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.7e-08
                           Fer4_10  11 rCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +C++Cv++CP          e++++++v+   ++C++cgaC++aCP
  gi|336255131|ref|YP_004598238.1| 312 GCNECVEVCPH------DAVERTKIDEVEFHKDACQNCGACTSACP 351
                                       7**********......888999999999999*************9 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 1.1e-06
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       dd C+   +C + CP+     +a+  ++e+++ + + e+C +cg C e C
  gi|336255131|ref|YP_004598238.1| 577 DDGCTFTPTCSTLCPT-----DAIRRDEEGAVLEFNHERCVNCGTCEEGC 621
                                       689*************.....9**************************99 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.6
                           Fer4_10  40 kkvekCtgcg 49 
                                       + + +C +cg
  gi|336255131|ref|YP_004598238.1| 655 GEMRECRNCG 664
                                       5677888887 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   4.4     0.066        78       9      16 ..     200     207 ..     195     209 .. 0.88
   2 ?    1.6   0.1      0.28   3.3e+02      17      24 .]     233     240 ..     232     240 .. 0.88
   3 !   12.9   3.3   7.7e-05     0.091      11      23 ..     312     324 ..     301     325 .. 0.88
   4 !   25.2   2.2     1e-08   1.2e-05       2      23 ..     333     354 ..     332     355 .. 0.95
   5 ?    2.1   0.4       0.2   2.4e+02      12      24 .]     580     595 ..     578     595 .. 0.75
   6 !   16.3   2.2   6.5e-06    0.0077       2      24 .]     604     626 ..     603     626 .. 0.92
   7 ?   -2.1   0.7         4   4.8e+03       7      13 ..     697     703 ..     697     704 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.066
                            Fer4_6   9 CigCgdCv 16 
                                       Ci+C++Cv
  gi|336255131|ref|YP_004598238.1| 200 CISCMKCV 207
                                       *******9 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.28
                            Fer4_6  17 rvCPegai 24 
                                        vCP++ai
  gi|336255131|ref|YP_004598238.1| 233 EVCPTDAI 240
                                       69****98 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 7.7e-05
                            Fer4_6  11 gCgdCvrvCPega 23 
                                       gC++Cv vCP++a
  gi|336255131|ref|YP_004598238.1| 312 GCNECVEVCPHDA 324
                                       9**********98 PP

  == domain 4  score: 25.2 bits;  conditional E-value: 1e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       ve+ +d+C  Cg+C+++CP+ga
  gi|336255131|ref|YP_004598238.1| 333 VEFHKDACQNCGACTSACPTGA 354
                                       89******************98 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.2
                            Fer4_6  12 Cgd...CvrvCPegai 24 
                                       C     C + CP++ai
  gi|336255131|ref|YP_004598238.1| 580 CTFtptCSTLCPTDAI 595
                                       5555569999****98 PP

  == domain 6  score: 16.3 bits;  conditional E-value: 6.5e-06
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                        e++ ++C+ Cg C+  C e+ai
  gi|336255131|ref|YP_004598238.1| 604 LEFNHERCVNCGTCEEGCVEDAI 626
                                       589***************99997 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 4
                            Fer4_6   7 dkCigCg 13 
                                       d C+ C+
  gi|336255131|ref|YP_004598238.1| 697 DYCDNCR 703
                                       5699998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   3.9      0.11   1.3e+02       7      18 ..     197     208 ..     195     209 .. 0.85
   2 ?   -2.5   0.2       6.2   7.4e+03      17      22 .]     232     237 ..     232     237 .. 0.80
   3 !    7.7   1.8    0.0033         4      12      22 .]     312     322 ..     297     322 .. 0.86
   4 !   19.8   3.3   4.7e-07   0.00056       3      22 .]     333     352 ..     331     352 .. 0.89
   5 ?   -0.2   2.7       1.1   1.4e+03      12      22 .]     579     592 ..     578     592 .. 0.80
   6 !   13.0   3.0     7e-05     0.083       3      20 ..     604     621 ..     602     622 .. 0.88
   7 ?   -1.9   0.7         4   4.7e+03      10      14 ..     660     664 ..     657     665 .. 0.75
   8 ?   -1.5   0.1       2.8   3.4e+03      10      14 ..     699     703 ..     695     704 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                            Fer4_2   7 tdrCigCgaCvs 18 
                                       t+ Ci+C +Cv+
  gi|336255131|ref|YP_004598238.1| 197 TEDCISCMKCVH 208
                                       677*******95 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.2
                            Fer4_2  17 vsaCPa 22 
                                       + +CP+
  gi|336255131|ref|YP_004598238.1| 232 TEVCPT 237
                                       579**7 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0033
                            Fer4_2  12 gCgaCvsaCPa 22 
                                       gC+ Cv +CP+
  gi|336255131|ref|YP_004598238.1| 312 GCNECVEVCPH 322
                                       6*********7 PP

  == domain 4  score: 19.8 bits;  conditional E-value: 4.7e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       v++  d+C +CgaC+saCP+
  gi|336255131|ref|YP_004598238.1| 333 VEFHKDACQNCGACTSACPT 352
                                       567889*************7 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 1.1
                            Fer4_2  12 gCg...aCvsaCPa 22 
                                       gC    +C + CP+
  gi|336255131|ref|YP_004598238.1| 579 GCTftpTCSTLCPT 592
                                       6766669******7 PP

  == domain 6  score: 13.0 bits;  conditional E-value: 7e-05
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                        +++ +rC++Cg+C   C
  gi|336255131|ref|YP_004598238.1| 604 LEFNHERCVNCGTCEEGC 621
                                       67999*********9888 PP

  == domain 7  score: -1.9 bits;  conditional E-value: 4
                            Fer4_2  10 CigCg 14 
                                       C +Cg
  gi|336255131|ref|YP_004598238.1| 660 CRNCG 664
                                       88887 PP

  == domain 8  score: -1.5 bits;  conditional E-value: 2.8
                            Fer4_2  10 CigCg 14 
                                       C +C+
  gi|336255131|ref|YP_004598238.1| 699 CDNCR 703
                                       88887 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.2    0.0064       7.7      39      57 ..     193     211 ..     174     214 .. 0.80
   2 ?    5.9   1.1     0.016        20      48      59 ..     312     323 ..     308     325 .. 0.91
   3 !   15.7   0.3   1.4e-05     0.016       1      31 [.     339     371 ..     339     402 .. 0.74
   4 ?   -0.1   0.3       1.2   1.4e+03      44      59 ..     578     593 ..     561     595 .. 0.79
   5 ?    1.5  10.1      0.37   4.4e+02      41      58 ..     606     623 ..     578     625 .. 0.79
   6 ?   -3.0   0.2       9.2   1.1e+04      45      50 ..     659     664 ..     652     665 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0064
                           Fer4_17  39 keekaslCieCgeCerkCP 57 
                                       + ++ ++Ci+C +C+++ P
  gi|336255131|ref|YP_004598238.1| 193 EACVTEDCISCMKCVHEGP 211
                                       457899********98766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.016
                           Fer4_17  48 eCgeCerkCPqg 59 
                                       +C+eC+++CP++
  gi|336255131|ref|YP_004598238.1| 312 GCNECVEVCPHD 323
                                       6*********97 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.4e-05
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepk..kllraakl 31 
                                       +C++Cg+C+ +Cp+++ +  ep   +++r++++
  gi|336255131|ref|YP_004598238.1| 339 ACQNCGACTSACPTGATRLREPSneRIAREVEA 371
                                       5*************9998888763357777666 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.2
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                       + C+    C++ CP +
  gi|336255131|ref|YP_004598238.1| 578 DGCTFTPTCSTLCPTD 593
                                       5688888899999975 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.37
                           Fer4_17  41 ekaslCieCgeCerkCPq 58 
                                        + ++C++Cg Ce+ C +
  gi|336255131|ref|YP_004598238.1| 606 FNHERCVNCGTCEEGCVE 623
                                       57799***********76 PP

  == domain 6  score: -3.0 bits;  conditional E-value: 9.2
                           Fer4_17  45 lCieCg 50 
                                       +C +Cg
  gi|336255131|ref|YP_004598238.1| 659 ECRNCG 664
                                       555554 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.8    0.0099        12       2      11 ..     198     207 ..     197     213 .. 0.81
   2 ?    4.9   1.6     0.039        46       6      15 ..     312     321 ..     300     329 .. 0.81
   3 !   17.4   4.7   3.7e-06    0.0044       1      17 []     337     353 ..     337     353 .. 0.93
   4 !    7.3   5.8    0.0064       7.7       2      14 ..     609     621 ..     608     621 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0099
                            Fer4_4   2 erCigCgsCv 11 
                                       e Ci C++Cv
  gi|336255131|ref|YP_004598238.1| 198 EDCISCMKCV 207
                                       67*******9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.039
                            Fer4_4   6 gCgsCvaaCP 15 
                                       gC  Cv +CP
  gi|336255131|ref|YP_004598238.1| 312 GCNECVEVCP 321
                                       9********9 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 3.7e-06
                            Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                       ++ C++Cg+C++aCP+g
  gi|336255131|ref|YP_004598238.1| 337 KDACQNCGACTSACPTG 353
                                       689************86 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0064
                            Fer4_4   2 erCigCgsCvaaC 14 
                                       erC++Cg C+  C
  gi|336255131|ref|YP_004598238.1| 609 ERCVNCGTCEEGC 621
                                       8*********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 ?    4.2   0.7     0.039        47      58      74 ..     197     213 ..     188     223 .. 0.73
   2 ?   12.7   3.8   9.2e-05      0.11      63     103 ..     312     358 ..     289     363 .. 0.78
   3 ?    7.9   1.5    0.0029       3.4      55      96 ..     574     622 ..     553     636 .. 0.73
   4 ?   -2.8   0.0       5.9     7e+03      72      90 ..     647     665 ..     646     668 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.039
                           Fer4_18  58 agdcidcescvkvcPtg 74 
                                       + dci+c +cv+  P g
  gi|336255131|ref|YP_004598238.1| 197 TEDCISCMKCVHEGPDG 213
                                       56888888888777655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 9.2e-05
                           Fer4_18  63 dcescvkvcP......tgidirkGlqleciscllcidacdkvmeklg 103
                                        c+ cv+vcP      t+id  +  +  c +c+ c  ac +   +l+
  gi|336255131|ref|YP_004598238.1| 312 GCNECVEVCPhdaverTKIDEVEFHKDACQNCGACTSACPTGATRLR 358
                                       6*********555555578888888899***********87666655 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0029
                           Fer4_18  55 ekgagdcidcescvkvcPtgidirk..Glqle.....ciscllcidacd 96 
                                        + +  c+   +c ++cPt+   r+  G  le     c++c+ c + c 
  gi|336255131|ref|YP_004598238.1| 574 MAVDDGCTFTPTCSTLCPTDAIRRDeeGAVLEfnherCVNCGTCEEGCV 622
                                       45566799999********986665346555344445*******99995 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 5.9
                           Fer4_18  72 PtgidirkGlqleciscll 90 
                                       P  + + +G   ec +c++
  gi|336255131|ref|YP_004598238.1| 647 PAWVTVHDGEMRECRNCGE 665
                                       5667888999999999986 PP

>> YidD  Putative membrane protein insertion efficiency factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.2   1.4e+03      28      44 ..     400     416 ..     398     420 .. 0.87
   2 ?   10.8   0.3   0.00028      0.33      20      58 ..     578     617 ..     562     624 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                              YidD  28 CSeYaleaiekyGllkG 44 
                                       CSe a +a+++yG l++
  gi|336255131|ref|YP_004598238.1| 400 CSEEADDALREYGRLAA 416
                                       *************8876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00028
                              YidD  20 ksCrfyptCSeYa.leaiekyGllkGlllalkRilrCnpl 58 
                                         C f+ptCS+ +  +ai++    + l    +R + C  +
  gi|336255131|ref|YP_004598238.1| 578 DGCTFTPTCSTLCpTDAIRRDEEGAVLEFNHERCVNCGTC 617
                                       68********997457888877666666666777777665 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3       1.9   2.3e+03      15      36 ..     197     215 ..     190     244 .. 0.56
   2 ?   11.1   1.8   0.00028      0.34      17      62 ..     315     358 ..     308     369 .. 0.84
   3 ?   10.9   1.2   0.00031      0.37      15      54 ..     583     621 ..     578     633 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                           Fer4_11  15 eppCvasapseaivkdeetGaV 36 
                                       +  C++ ++    v++  +GaV
  gi|336255131|ref|YP_004598238.1| 197 TEDCISCMK---CVHEGPDGAV 215
                                       333333322...2233334443 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00028
                           Fer4_11  17 pCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkn 62 
                                        Cv+++p++a+ + +    V +++++++ ++ ++++acP  ++r  
  gi|336255131|ref|YP_004598238.1| 315 ECVEVCPHDAVERTK-IDEVEFHKDACQ-NCGACTSACPTGATRLR 358
                                       6999***99987766.7799*******8.**********8887765 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00031
                           Fer4_11  15 eppCvasapseaivkdeetGaVlldektkkeevrevveac 54 
                                       +p C + +p++ai +dee  +  ++++++  ++ ++ e+c
  gi|336255131|ref|YP_004598238.1| 583 TPTCSTLCPTDAIRRDEEGAVLEFNHERCV-NCGTCEEGC 621
                                       699**********99996666678999996.999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (736 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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):              15  [number of targets reported over threshold]
# CPU time: 0.60u 0.23s 00:00:00.83 Elapsed: 00:00:00.38
# Mc/sec: 5747.07
//
Query:       gi|336255132|ref|YP_004598239.1|  [L=1124]
Description: Nitrate reductase [Halopiger xanaduensis SH-6]
Scores for complete 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-48  165.7   2.7    8.7e-48  163.3   2.7    1.9  1  Molybdopterin    Molybdopterin oxidoreductase
    2.9e-16   59.5   0.0    8.5e-16   58.0   0.0    1.8  2  Molydop_binding  Molydopterin dinucleotide binding domain
    2.2e-10   40.4   0.2    4.5e-10   39.4   0.2    1.6  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
  ------ inclusion threshold ------
      0.069   13.0   1.9       0.17   11.8   1.9    1.7  1  TAT_signal       TAT (twin-arginine translocation) pathway si
      0.083   13.2   1.3        0.9    9.8   0.2    2.8  2  Rieske_3         Rieske 3Fe-4S
       0.44   11.0  13.9        1.8    9.1  13.9    2.0  1  Prothymosin      Prothymosin/parathymosin family


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.3   2.7   2.9e-51   8.7e-48       1     431 [.     111     642 ..     111     643 .. 0.82

  Alignments for each domain:
  == domain 1  score: 163.3 bits;  conditional E-value: 2.9e-51
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rlk+Pm +   + +G+++rv+Wd+A+ +ia+  ++ti++y  ++v++ +s    s+e+ ++ +k+++ +g    +++
  gi|336255132|ref|YP_004598239.1| 111 RLKHPMRK---E-DGEWRRVTWDDAFREIADTWEQTIEEYSRESVMFLGSA-HHSNEAAYASRKFAAFMGT---NNV 179
                                       9*****99...6.9********************************86664.5558999988888877776...899 PP

                                       ECCGGGTTHHHH...CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB CS
                     Molybdopterin  78 dwyadlppasaq...qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpry 151
                                       d++a+ +++ ++      ++      +++n+++d  n dl i+ G N++e +pi+  +i+  + +++  +++i+pry
  gi|336255132|ref|YP_004598239.1| 180 DHQARICHSPTVtglANTWG----FGAMTNTINDYRNFDLLIILGQNPAESHPIAMQHILEGQARGG-TIVSIDPRY 251
                                       *******9877655433333....346888999**********************999999999975.5******** PP

                                       -HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHH CS
                     Molybdopterin 152 aellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarela 228
                                       ++++ +ad    ++pgtd+al++++ ++i ++   d efl+ +  g   +++ l+++  e ++ ++ +      e  
  gi|336255132|ref|YP_004598239.1| 252 TKTSAHADYFYRLRPGTDVALVMGLLNYINEQDELDDEFLAGRVMGWPDVESELEQYDLETVSDITWIDQGDLEEIG 328
                                       **99************************************************************************* PP

                                       HHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCT CS
                     Molybdopterin 229 rnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslk 305
                                       + +++++++  + + +g +++++g++++r  + + l++g   ++gGg + ++G  +++ga       ++l+ ++ + 
  gi|336255132|ref|YP_004598239.1| 329 DLIIENKPQIQVEWAMGGTQHNNGTQNIRSYAIFSLATGSAARSGGGLQVMRGHANVQGATDLGVDASILPGYYGVD 405
                                       ********999******************************************666666555555555555555555 PP

                                       T............................................................................ CS
                     Molybdopterin 306 e............................................................................ 306
                                                                                                                    
  gi|336255132|ref|YP_004598239.1| 406 Apgswehwadvwdrspwtsgstsfeelyekfellpedvwegtqtpaeveaggagvdveeeaageggegeadvqgede 482
                                       56666666666666666666666666666666666666666666666666666666666666666666666777777 PP

                                       ...................................HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH. CS
                     Molybdopterin 307 ...................................ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgn. 347
                                                                            + +a + +  l +  + ++   snl +   +k+ ++ g+ 
  gi|336255132|ref|YP_004598239.1| 483 eaegdedagdeeeeeeglqaeapiddveersmmfqIGLTVARWYEAALEQ--GDRLL-ESNLYQPDPLKMAFFWGHs 556
                                       77777777777777777777777777777888754444445555545444..77776.599**************76 PP

                                       .HHHHSTTSCCCHCHHHCSSEEEEEESCS..SHHH.HTSSEE.EEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-B CS
                     Molybdopterin 348 npevdhadenevekalekldlvvvldgrl..tsta.lyaDii.LPaatwyEkedlytndegrfqhlkqavsppgeak 420
                                        ++++  d+++   a e+ldl+vv+d++   ++t    aD++ LPa++ yE+  ++tn+ +++q  +++ +p+ ++k
  gi|336255132|ref|YP_004598239.1| 557 ANSISEMDKMKQ--AMENLDLLVVVDVFPavAGTLpDDADVLlLPASSQYEHVRTVTNSHRSVQWSEAVAEPAHNSK 631
                                       677777777777..**************9533333257998537********************************* PP

                                       EHHHHHHHHHH CS
                     Molybdopterin 421 sdwkIlkaLak 431
                                       +d +I+++La+
  gi|336255132|ref|YP_004598239.1| 632 PDLQIMQELAQ 642
                                       *********96 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.5   1.1e+04      47      73 ..     242     268 ..     239     271 .. 0.87
   2 !   58.0   0.0   2.8e-19   8.5e-16       2     109 ..     948    1074 ..     947    1076 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.5
                                       T-EEEEEETTEEEEEEEEEESSB-TTE CS
                   Molydop_binding  47 GdlVevesrrGsvevrakvtervrpGv 73 
                                       G +V +  r+ ++ + a   +r+rpG+
  gi|336255132|ref|YP_004598239.1| 242 GTIVSIDPRYTKTSAHADYFYRLRPGT 268
                                       7788999999999999*999***9997 PP

  == domain 2  score: 58.0 bits;  conditional E-value: 2.8e-19
                                        EEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT.-EEEEEE.TTEEEEEEEEEESSB-TTE CS
                   Molydop_binding    2 rLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdG.dlVeves.rrGsvevrakvtervrpGv 73  
                                        +L++gr++++   +++tr+ ++ a+++p +++ei+p+ A+al++  G d V ves ++G++ v+akvt+rv+   
  gi|336255132|ref|YP_004598239.1|  948 ILTSGRQVEHQGGGAETRNNEYTADRQPhMYAEISPALAEALDVVGGdDHVIVESaDKGAILVKAKVTNRVNDEE 1022
                                        79*****************************************8887258***994589**************** PP

                                        EEEESSHCC.....................S-GHCTS--SCSTTT--CSTT- CS
                   Molydop_binding   74 vfmpfgwwe................agekggnaNaltddatdplsgtpefks 109 
                                        +f+p++w+                 +   g++aN +t++++d  +++ e ks
  gi|336255132|ref|YP_004598239.1| 1023 IFLPYHWGGvfhgedltpnwpdgtePLAIGESANIITPSGFDAETQMQETKS 1074
                                        *************************9*****************999998875 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.2   1.5e-13   4.5e-10       3      52 ..      56     105 ..      54     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.5e-13
                                       EEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHC CS
                    Molybdop_Fe4S4   3 vvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtller 52 
                                       + k +C yC vgCg++++  ++ +v  e++ ++p+n+g lC KG+ +le+
  gi|336255132|ref|YP_004598239.1|  56 TSKVICNYCAVGCGFKAVKDGNSFVGQEPWFENPINNGSLCSKGAGILET 105
                                       56779****************************************99886 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.9   5.6e-05      0.17       2      24 ..      12      34 ..      11      36 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      l+RR+F K+sA a+   + gg+a
  gi|336255132|ref|YP_004598239.1| 12 LDRRSFVKASALAGGVFLGGGAA 34
                                      79********9999555444544 PP

>> Rieske_3  Rieske 3Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2    0.0003       0.9       1      14 [.      61      74 ..      61     109 .. 0.91
   2 ?    0.8   0.1       0.2   5.9e+02      19      72 ..     958    1008 ..     953    1019 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0003
                                      -SSBTT--EEEEEE CS
                          Rieske_3  1 CdyCivgCgYkvYk 14
                                      C+yC vgCg+k+ k
  gi|336255132|ref|YP_004598239.1| 61 CNYCAVGCGFKAVK 74
                                      **********9865 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.2
                                        ----SSGGGSTT-S-TTS---TT-SS---GGGEEEEEETTEEEEEEE.EE-TT-T CS
                          Rieske_3   19 keGGlkaeenalgvDlskqqkalseawvapsmynvvkkdgkdvnvvi.vpdkdcv 72  
                                        + GG+++ +n +  D + +      a ++p+  + +   g d +v++  +dk ++
  gi|336255132|ref|YP_004598239.1|  958 QGGGAETRNNEYTADRQPH----MYAEISPALAEALDVVGGDDHVIVeSADKGAI 1008
                                        4678889999999887333....33456777766666445444544414566554 PP

>> Prothymosin  Prothymosin/parathymosin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  13.9   0.00059       1.8       8      95 ..     424     508 ..     418     514 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00059
                       Prothymosin   8 tsevtakdLKeKKev.veeaekgkdapangnaneengeeeadeeveeeeeeeeeee.eeeeeeeeegeeeegeeeee 82 
                                       +  +++++L eK e+  e+  +g+++pa+ +a    g    d e+e++ e  e e+  + e+ee eg+e+ g+ eee
  gi|336255132|ref|YP_004598239.1| 424 SGSTSFEELYEKFELlPEDVWEGTQTPAEVEA----GGAGVDVEEEAAGEGGEGEAdVQGEDEEAEGDEDAGD-EEE 495
                                       44789999999999945667788899987775....4444455555556666655545666667777777777.555 PP

                       Prothymosin  83 eaegatvkraAed 95 
                                       e+eg     + +d
  gi|336255132|ref|YP_004598239.1| 496 EEEGLQAEAPIDD 508
                                       6666655555454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.26s 00:00:01.00 Elapsed: 00:00:00.42
# Mc/sec: 7981.65
//
Query:       gi|336255133|ref|YP_004598240.1|  [L=218]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   66.1  11.4    2.4e-18   66.1  11.4    2.2  2  Fer4_11   4Fe-4S dicluster domain
    1.6e-15   57.4  22.1    9.4e-08   32.5   6.5    2.4  2  Fer4_7    4Fe-4S dicluster domain
    7.4e-13   48.4  55.2    3.1e-06   27.3   8.8    3.2  4  Fer4_9    4Fe-4S dicluster domain
    1.6e-08   34.0  40.4    2.8e-05   23.7   1.6    5.5  6  Fer4      4Fe-4S binding domain
      4e-08   33.3  26.1    5.5e-06   26.4   8.2    3.7  4  Fer4_21   4Fe-4S dicluster domain
    8.3e-08   32.0  39.0    0.00036   20.5   1.1    5.4  4  Fer4_6    4Fe-4S binding domain
    7.6e-07   29.2  30.1    0.00077   19.5   9.0    3.3  3  Fer4_10   4Fe-4S dicluster domain
    7.7e-07   28.8  33.2     0.0038   17.2   1.1    4.3  4  Fer4_2    4Fe-4S binding domain
      9e-06   26.5  22.2      0.017   16.0   1.0    4.6  4  Fer4_16   4Fe-4S double cluster binding domain
    1.6e-05   25.2  22.0    0.00097   19.5   6.0    2.7  2  Fer4_8    4Fe-4S dicluster domain
    0.00026   21.3  31.2      0.048   14.2   2.2    4.5  4  Fer4_4    4Fe-4S binding domain
      0.007   17.2  41.9      0.056   14.4   5.9    4.3  4  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.058   13.9  27.8      0.069   13.7   8.5    4.0  5  Fer4_17   4Fe-4S dicluster domain
       0.13   12.8   0.5       0.13   12.8   0.5    4.5  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
          2    8.7  20.3        7.3    6.8   1.7    3.3  3  Fer4_18   4Fe-4S dicluster domain
        3.6    8.4  22.5        3.8    8.3   0.5    4.3  3  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3       5.7   6.4e+03      18      22 ..      27      31 ..      14      44 .. 0.54
   2 !   66.1  11.4   2.2e-21   2.4e-18       6      98 ..      78     178 ..      75     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.7
                           Fer4_11 18 Cvasa 22
                                      Cv ++
  gi|336255133|ref|YP_004598240.1| 27 CVVAC 31
                                      32222 PP

  == domain 2  score: 66.1 bits;  conditional E-value: 2.2e-21
                           Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneet..........gkvekCd 72 
                                       lp qC hC+++pCv+++p++a+ kd+ +G V ++e+ +  +++ + ++cP+ +++  ++           g + kC+
  gi|336255133|ref|YP_004598240.1|  78 LPMQCYHCENAPCVSVCPTNALQKDD-DGFVAVHEDLCV-GCQYCLSGCPFGAPQFPDSDdgsaqivgtgGIMDKCT 152
                                       799*******************9999.***********7.***********99986443211122222226799*** PP

                           Fer4_11  73 mcldrveaGllpacvescptgalnfg 98 
                                       +c +r+eaG+ pac e c+t a+ +g
  gi|336255133|ref|YP_004598240.1| 153 GCRERQEAGKGPACAEECATDAILVG 178
                                       ********************998776 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   6.5   8.4e-11   9.4e-08       1      52 []      20      98 ..      20      98 .. 0.60
   2 !   30.6   7.6   3.5e-10   3.9e-07       2      52 .]     114     174 ..     113     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 8.4e-11
                            Fer4_7  1 rCigCgaCvaaC.................pvkaieldeeenek....................gtekveidpekClgCg 42
                                      +Ci Cg Cv+aC                 +            +                    +++  +  p++C++C+
  gi|336255133|ref|YP_004598240.1| 20 ACIDCGGCVVACkrtwdreiqnqridittM------------AegvagpqgenadktgrleagENPGETSLPMQCYHCE 86
                                      5***********555555553333333331............022222222222233333332334458889******* PP

                            Fer4_7 43 a..CvavCPtga 52
                                      +  Cv+vCPt+a
  gi|336255133|ref|YP_004598240.1| 87 NapCVSVCPTNA 98
                                      99********97 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 3.5e-10
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekvei.dpekClgCg.........aCvavCPtga 52 
                                       C+gC++C + Cp +a +++++++ + +   ++  ++kC+gC+         aC+++C t+a
  gi|336255133|ref|YP_004598240.1| 114 CVGCQYCLSGCPFGAPQFPDSDDGSAQIVGTGgIMDKCTGCRerqeagkgpACAEECATDA 174
                                       *******************9977776555554269******65555555558*****9987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.0   1.5e-05     0.016      34      49 ..      19      34 ..       2      36 .. 0.71
   2 !   19.5  12.6   7.3e-07   0.00081       1      50 [.      20      98 ..      20      99 .. 0.90
   3 !   27.3   8.8   2.7e-09   3.1e-06       1      49 [.      81     127 ..      81     129 .. 0.92
   4 !   24.7   8.2   1.8e-08     2e-05       2      51 .]     114     175 ..     113     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                            Fer4_9 34 eaCigCgaCveaCpkg 49
                                      eaCi+Cg Cv aC+++
  gi|336255133|ref|YP_004598240.1| 19 EACIDCGGCVVACKRT 34
                                      68***********985 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 7.3e-07
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase...........................eaCigCga..CveaCpkga 50
                                      +C++Cg Cv aC+ +  +e +++r++  ++a+                             +C++C+   Cv +Cp++a
  gi|336255133|ref|YP_004598240.1| 20 ACIDCGGCVVACKRTWDREIQNQRIDITTMAEGvagpqgenadktgrleagenpgetslpMQCYHCENapCVSVCPTNA 98
                                      6***********88888888888888888777688999999999999999**********9****************97 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 2.7e-09
                            Fer4_9   1 kCtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       +C+ C +  Cv++Cp+++ ++d+ +  a ++      C+gC+ C+  Cp g
  gi|336255133|ref|YP_004598240.1|  81 QCYHCENapCVSVCPTNALQKDDDGFVAVHED----LCVGCQYCLSGCPFG 127
                                       6****9888****************9999876....6************87 PP

  == domain 4  score: 24.7 bits;  conditional E-value: 1.8e-08
                            Fer4_9   2 CtgCgaCveaCpagvvv.edaaerkarlraase..eaCigCga.........CveaCpkgai 51 
                                       C+gC++C + Cp+g+ + +d+  + a++  ++   ++C+gC++         C+e C ++ai
  gi|336255133|ref|YP_004598240.1| 114 CVGCQYCLSGCPFGAPQfPDSDDGSAQIVGTGGimDKCTGCRErqeagkgpaCAEECATDAI 175
                                       ****************72455555555555555999***********************987 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   5.3   3.4e-05     0.038       4      18 ..      17      31 ..      14      33 .. 0.90
   2 ?   -2.5   0.2       4.7   5.3e+03      10      16 ..      81      87 ..      80      88 .. 0.65
   3 !   12.9   0.5   6.7e-05     0.075      14      23 ..      90      99 ..      89     100 .. 0.93
   4 !   23.7   1.6   2.5e-08   2.8e-05       2      23 ..     108     129 ..     107     130 .. 0.92
   5 ?    5.7   0.6     0.012        14       5      12 ..     148     155 ..     147     156 .. 0.85
   6 ?    2.5   0.7      0.12   1.4e+02      13      23 ..     165     175 ..     165     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-05
                                      ETTTSSS-THHHHHS CS
                              Fer4  4 deekCigCGaCvevC 18
                                      d e Ci CG Cv +C
  gi|336255133|ref|YP_004598240.1| 17 DVEACIDCGGCVVAC 31
                                      89************* PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
                                      S-THHHH CS
                              Fer4 10 gCGaCve 16
                                       C  C++
  gi|336255133|ref|YP_004598240.1| 81 QCYHCEN 87
                                      5777776 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 6.7e-05
                                      HHHHSTTTEE CS
                              Fer4 14 CvevCPvgAI 23
                                      Cv+vCP++A+
  gi|336255133|ref|YP_004598240.1| 90 CVSVCPTNAL 99
                                      *********8 PP

  == domain 4  score: 23.7 bits;  conditional E-value: 2.5e-08
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                        ++e++C+gC +C + CP+gA 
  gi|336255133|ref|YP_004598240.1| 108 AVHEDLCVGCQYCLSGCPFGAP 129
                                       589*****************96 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.012
                                       TTTSSS-T CS
                              Fer4   5 eekCigCG 12 
                                       ++kC+gC 
  gi|336255133|ref|YP_004598240.1| 148 MDKCTGCR 155
                                       69*****6 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.12
                                       HHHHHSTTTEE CS
                              Fer4  13 aCvevCPvgAI 23 
                                       aC+e C ++AI
  gi|336255133|ref|YP_004598240.1| 165 ACAEECATDAI 175
                                       7*****99998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.8   6.5e-06    0.0073       5      27 ..      18      40 ..      15      54 .. 0.77
   2 !   26.4   8.2   4.9e-09   5.5e-06       7      53 ..      81     126 ..      78     129 .. 0.91
   3 ?    0.2   2.8      0.74   8.3e+02      38      45 ..     148     155 ..     137     176 .. 0.84
   4 ?   -0.7   2.7       1.4   1.6e+03      39      45 ..     149     155 ..     148     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.5e-06
                           Fer4_21  5 edkCigCgkCliaCedtshqaie 27
                                       + Ci+Cg C++aC+ t    i+
  gi|336255133|ref|YP_004598240.1| 18 VEACIDCGGCVVACKRTWDREIQ 40
                                      589***********987666664 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 4.9e-09
                           Fer4_21   7 kCigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                       +C +C++  C+ +C+   ++a+++d++  ++v ed CvGC+ C+s CP 
  gi|336255133|ref|YP_004598240.1|  81 QCYHCENapCVSVCP---TNALQKDDDGFVAVHEDLCVGCQYCLSGCPF 126
                                       799998556******...6999**************************5 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.74
                           Fer4_21  38 edeCvGCn 45 
                                        d+C+GC 
  gi|336255133|ref|YP_004598240.1| 148 MDKCTGCR 155
                                       68999996 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.4
                           Fer4_21  39 deCvGCn 45 
                                       d+C+GC 
  gi|336255133|ref|YP_004598240.1| 149 DKCTGCR 155
                                       7888885 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.4   1.3e-05     0.014       5      19 ..      17      31 ..      17      38 .. 0.91
   2 !    9.6   4.7   0.00086      0.96       9      24 .]      82      99 ..      80      99 .. 0.82
   3 !   20.5   1.1   3.2e-07   0.00036       1      23 [.     106     128 ..     106     129 .. 0.94
   4 ?    1.8   6.9      0.25   2.8e+02       6      24 .]     148     175 ..     147     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                            Fer4_6  5 dpdkCigCgdCvrvC 19
                                      d ++Ci+Cg Cv++C
  gi|336255133|ref|YP_004598240.1| 17 DVEACIDCGGCVVAC 31
                                      6689*********** PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00086
                            Fer4_6  9 CigCgd..CvrvCPegai 24
                                      C +C++  Cv+vCP++a+
  gi|336255133|ref|YP_004598240.1| 82 CYHCENapCVSVCPTNAL 99
                                      55786668********97 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 3.2e-07
                            Fer4_6   1 vveidpdkCigCgdCvrvCPega 23 
                                       +v++ +d+C+gC  C + CP+ga
  gi|336255133|ref|YP_004598240.1| 106 FVAVHEDLCVGCQYCLSGCPFGA 128
                                       6899*****************99 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.25
                            Fer4_6   6 pdkCigCgd.........CvrvCPegai 24 
                                        dkC+gC++         C+  C ++ai
  gi|336255133|ref|YP_004598240.1| 148 MDKCTGCRErqeagkgpaCAEECATDAI 175
                                       59*****988888888899999998887 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9  13.8   0.00034      0.39       5      56 .]      17      95 ..      13      95 .. 0.86
   2 !   14.1  12.1   3.5e-05      0.04       8      56 .]      81     125 ..      75     125 .. 0.90
   3 !   19.5   9.0   6.9e-07   0.00077       4      55 ..     109     170 ..     106     171 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                           Fer4_10  5 dddtCirCgkCvkaCPadl..........................tsvgakgeaseeeavrk.kvekCtgcg..aCvea 54
                                      d + Ci Cg Cv aC  +                           +++++   + +e++ ++  + +C +c+   Cv++
  gi|336255133|ref|YP_004598240.1| 17 DVEACIDCGGCVVAC--KRtwdreiqnqridittmaegvagpqgeNADKTGRLEAGENPGETsLPMQCYHCEnaPCVSV 93
                                      7899***********..6667***********************9666666667777777777999*****7669**** PP

                           Fer4_10 55 CP 56
                                      CP
  gi|336255133|ref|YP_004598240.1| 94 CP 95
                                      *9 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.5e-05
                           Fer4_10   8 tCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +C +C+   Cv++CP+      +  ++++++ v +  + C gc +C + CP
  gi|336255133|ref|YP_004598240.1|  81 QCYHCEnaPCVSVCPT------NALQKDDDGFVAVHEDLCVGCQYCLSGCP 125
                                       7****9889*******......88888888888888999***********9 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 6.9e-07
                           Fer4_10   4 idddtCirCgkCvkaCPadl....tsvgakgeaseeeavrk.kvekCtgc......g...aCveaC 55 
                                       + +d C++C+ C + CP+ +    +    ++  s + +  +  ++kCtgc      g   aC+e+C
  gi|336255133|ref|YP_004598240.1| 109 VHEDLCVGCQYCLSGCPFGApqfpD----SDDGSAQIVGTGgIMDKCTGCrerqeaGkgpACAEEC 170
                                       67899*************9954444....4444444444444677777775555552568****** PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   2.7   2.6e-05     0.029       4      20 ..      15      31 ..      12      33 .. 0.87
   2 !    9.5   4.7     0.001       1.1      10      22 .]      82      96 ..      78      96 .. 0.89
   3 !   17.2   1.1   3.4e-06    0.0038       3      21 ..     107     125 ..     105     126 .. 0.89
   4 ?    5.0   2.3     0.026        29       8      20 ..     149     170 ..     147     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
                            Fer4_2  4 vvdtdrCigCgaCvsaC 20
                                      + d ++Ci Cg Cv aC
  gi|336255133|ref|YP_004598240.1| 15 FPDVEACIDCGGCVVAC 31
                                      56899************ PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.001
                            Fer4_2 10 CigCg..aCvsaCPa 22
                                      C +C+  +Cvs+CP+
  gi|336255133|ref|YP_004598240.1| 82 CYHCEnaPCVSVCPT 96
                                      9999889*******7 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 3.4e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       v+v +d C+gC  C+s CP
  gi|336255133|ref|YP_004598240.1| 107 VAVHEDLCVGCQYCLSGCP 125
                                       56789************** PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.026
                            Fer4_2   8 drCigCg.........aCvsaC 20 
                                       d+C+gC+         aC   C
  gi|336255133|ref|YP_004598240.1| 149 DKCTGCRerqeagkgpACAEEC 170
                                       8*****7666666778887777 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   0.3    0.0052       5.8       2      14 ..      21      33 ..      20      70 .. 0.80
   2 !   16.0   1.0   1.5e-05     0.017       1      21 [.      81     103 ..      81     112 .. 0.86
   3 !   11.7   0.9   0.00034      0.38       2      18 ..     114     130 ..     113     144 .. 0.85
   4 ?    3.9   1.4     0.093     1e+02       7      22 ..     165     180 ..     149     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0052
                           Fer4_16  2 CgtCgkCaevCPt 14
                                      C++Cg C+ +C  
  gi|336255133|ref|YP_004598240.1| 21 CIDCGGCVVACKR 33
                                      ***********65 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.5e-05
                           Fer4_16   1 rCgtCgk..CaevCPtnaikekk 21 
                                       +C  C++  C++vCPtna++++ 
  gi|336255133|ref|YP_004598240.1|  81 QCYHCENapCVSVCPTNALQKDD 103
                                       5999*9999**********9984 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00034
                           Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                       C++C+ C++ CP +a +
  gi|336255133|ref|YP_004598240.1| 114 CVGCQYCLSGCPFGAPQ 130
                                       ************99865 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.093
                           Fer4_16   7 kCaevCPtnaikekke 22 
                                       +Cae C t+ai    +
  gi|336255133|ref|YP_004598240.1| 165 ACAEECATDAILVGGA 180
                                       7**********87733 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   6.0   8.6e-07   0.00097       2      64 ..      18      97 ..      17      98 .. 0.61
   2 !   10.7   8.1   0.00049      0.55       5      63 ..     114     172 ..     112     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.6e-07
                            Fer4_8  2 lekCieCgaCqsaCp.vlrrtk.khlldargeaae.......dvqeeqvlee..............eealwsCttcga. 56
                                      +e+Ci Cg C  aC  ++ r+  + + d   +a++                +                   +C +c++ 
  gi|336255133|ref|YP_004598240.1| 18 VEACIDCGGCVVACKrTWDREIqNQRIDITTMAEGvagpqgeN--------AdktgrleagenpgeTSLPMQCYHCENa 88
                                      789***********63222222233333333333333333331........12233444556677788899******99 PP

                            Fer4_8 57 .CtevCpvg 64
                                       C++vCp++
  gi|336255133|ref|YP_004598240.1| 89 pCVSVCPTN 97
                                      *******97 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00049
                            Fer4_8   5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga.........CtevCpv 63 
                                       C++C++C s Cp+   +  ++ +  g a+  v +  +     ++++Ct+c++         C+e+C +
  gi|336255133|ref|YP_004598240.1| 114 CVGCQYCLSGCPFGAPQ--FPDSDDGSAQI-VGTG-G-----IMDKCTGCRErqeagkgpaCAEECAT 172
                                       ************88776..66666666555.5554.4.....5*******999999999999999965 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   2.2   4.3e-05     0.048       2      15 ..      19      32 ..      19      43 .. 0.90
   2 ?    6.4   2.1     0.013        15       4      17 .]      82      97 ..      78     100 .. 0.85
   3 !   12.9   2.2   0.00011      0.12       2      17 .]     112     127 ..     111     128 .. 0.92
   4 ?    4.4   2.1     0.057        64       1       9 [.     148     156 ..     148     173 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-05
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      e Ci+Cg Cv aC+
  gi|336255133|ref|YP_004598240.1| 19 EACIDCGGCVVACK 32
                                      68***********8 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                            Fer4_4  4 CigCgs..CvaaCPqg 17
                                      C +C    Cv++CP++
  gi|336255133|ref|YP_004598240.1| 82 CYHCENapCVSVCPTN 97
                                      66888668******85 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00011
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       + C+gC  C + CP+g
  gi|336255133|ref|YP_004598240.1| 112 DLCVGCQYCLSGCPFG 127
                                       78************86 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.057
                            Fer4_4   1 qerCigCgs 9  
                                       +++C+gC+ 
  gi|336255133|ref|YP_004598240.1| 148 MDKCTGCRE 156
                                       599****94 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   4.8     0.029        33       1      11 [.      21      31 ..      21      33 .. 0.93
   2 !   14.4   5.9     5e-05     0.056       1      15 []      82      98 ..      82      98 .. 0.91
   3 !    9.8   5.0    0.0014       1.6       1      15 []     114     128 ..     114     128 .. 0.97
   4 ?    5.8   2.6     0.027        31       1      15 []     151     174 ..     151     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.029
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+ Cg Cv++C
  gi|336255133|ref|YP_004598240.1| 21 CIDCGGCVVAC 31
                                      9********** PP

  == domain 2  score: 14.4 bits;  conditional E-value: 5e-05
                            Fer4_3  1 CtgCg..aCvevCPvgA 15
                                      C +C+  +Cv vCP++A
  gi|336255133|ref|YP_004598240.1| 82 CYHCEnaPCVSVCPTNA 98
                                      99**8778*******98 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0014
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gC+ C+  CP gA
  gi|336255133|ref|YP_004598240.1| 114 CVGCQYCLSGCPFGA 128
                                       *************98 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.027
                            Fer4_3   1 CtgCg.........aCvevCPvgA 15 
                                       CtgC+         aC e C ++A
  gi|336255133|ref|YP_004598240.1| 151 CTGCRerqeagkgpACAEECATDA 174
                                       ****88999999999*****8887 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   8.5   6.1e-05     0.069       1      59 [.      20      97 ..      20      99 .. 0.71
   2 ?    4.7   2.6      0.04        45       1      19 [.      81     101 ..      81     111 .. 0.79
   3 ?   10.2   1.9   0.00078      0.88       2      14 ..     114     126 ..      97     129 .. 0.71
   4 ?    0.7  12.1       0.7   7.9e+02       2      16 ..     114     128 ..     113     174 .. 0.72
   5 ?   -2.3   2.9       5.9   6.6e+03       2       7 ..     151     156 ..     150     189 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-05
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraakl..............glleeaeke..........ekaslCieCge..Ce 53
                                      +Ci Cg C+ +C + ++++ +++++   +++              g       +          +   +C +C++  C+
  gi|336255133|ref|YP_004598240.1| 20 ACIDCGGCVVACKRTWDREIQNQRIDITTMAegvagpqgenadktG-------RleagenpgetSLPMQCYHCENapCV 91
                                      6****************88888865555444556666655554432.......03334555665688******8777** PP

                           Fer4_17 54 rkCPqg 59
                                      ++CP +
  gi|336255133|ref|YP_004598240.1| 92 SVCPTN 97
                                      ****86 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.04
                           Fer4_17   1 rCiqCgy..ClpeCpsyeayd 19 
                                       +C +C+   C+ +Cp+++  +
  gi|336255133|ref|YP_004598240.1|  81 QCYHCENapCVSVCPTNALQK 101
                                       599999777999999887654 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00078
                           Fer4_17   2 CiqCgyClpeCps 14 
                                       C +C+yCl  Cp+
  gi|336255133|ref|YP_004598240.1| 114 CVGCQYCLSGCPF 126
                                       5555555555554 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.7
                           Fer4_17   2 CiqCgyClpeCpsye 16 
                                       C +C+yCl  Cp+++
  gi|336255133|ref|YP_004598240.1| 114 CVGCQYCLSGCPFGA 128
                                       899999999999765 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 5.9
                           Fer4_17   2 CiqCgy 7  
                                       C++C+ 
  gi|336255133|ref|YP_004598240.1| 151 CTGCRE 156
                                       555552 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 ?   12.8   0.5   0.00011      0.13       3      25 ..      18      40 ..      17      65 .. 0.81
   2 ?    2.2   2.6      0.25   2.8e+02       5      33 ..      81     111 ..      79     112 .. 0.76
   3 ?   -2.9  11.5       9.5   1.1e+04       3      17 ..     111     125 ..     109     177 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                           Fer4_13  3 rdtCiacgaCvelaPdvFeedde 25
                                       + Ci+cg Cv ++  + +++ +
  gi|336255133|ref|YP_004598240.1| 18 VEACIDCGGCVVACKRTWDREIQ 40
                                      589***********999998765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.25
                           Fer4_13   5 tCiacga..CvelaPdvFeeddeggasvvae 33 
                                       +C  c++  Cv+++P     +d++g ++v+e
  gi|336255133|ref|YP_004598240.1|  81 QCYHCENapCVSVCPTNALQKDDDGFVAVHE 111
                                       688886555******9877777778877765 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 9.5
                           Fer4_13   3 rdtCiacgaCvelaP 17 
                                       +d C++c+ C + +P
  gi|336255133|ref|YP_004598240.1| 111 EDLCVGCQYCLSGCP 125
                                       689***********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 ?    6.7   2.6    0.0071       7.9      84     100 ..      20      36 ..       6      48 .. 0.74
   2 ?    6.8   1.7    0.0065       7.3      51      74 ..      72      97 ..      39     104 .. 0.70
   3 ?    6.1   1.9     0.011        12      57      74 ..     110     127 ..      97     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0071
                           Fer4_18  84 eciscllcidacdkvme 100
                                        ci c+ c+ ac++  +
  gi|336255133|ref|YP_004598240.1|  20 ACIDCGGCVVACKRTWD 36 
                                       47777777777766544 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0065
                           Fer4_18 51 eerkekgagdcidces..cvkvcPtg 74
                                      +  +++   +c +ce   cv+vcPt+
  gi|336255133|ref|YP_004598240.1| 72 NPGETSLPMQCYHCENapCVSVCPTN 97
                                      444455567899998666******96 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.011
                           Fer4_18  57 gagdcidcescvkvcPtg 74 
                                        +  c+ c++c++ cP g
  gi|336255133|ref|YP_004598240.1| 110 HEDLCVGCQYCLSGCPFG 127
                                       4556************87 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 ?    8.3   0.5    0.0034       3.8       4      21 ..      17      34 ..      14      66 .. 0.80
   2 ?    1.9   0.4      0.34   3.8e+02      13      29 ..      89     106 ..      81     110 .. 0.67
   3 ?    5.4   9.8     0.027        31       1      65 [.     107     176 ..     107     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0034
                           Fer4_15  4 DrdaCigcglCvaeapev 21
                                      D +aCi cg Cv ++++ 
  gi|336255133|ref|YP_004598240.1| 17 DVEACIDCGGCVVACKRT 34
                                      889************865 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.34
                           Fer4_15  13 lCvaea.pevfeldedgl 29 
                                        Cv ++ ++  ++d+dg+
  gi|336255133|ref|YP_004598240.1|  89 PCVSVCpTNALQKDDDGF 106
                                       699999335667777776 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.027
                           Fer4_15   1 VvvDrdaCigcglCvaea....pevfeldedglasvllddgeiaegevpddeeeaaqe...AaraCPvdAIr 65 
                                       V v +d+C gc  C+  +    p  f   +dg a+++++ g i ++  +  e+++a +    a++C +dAI 
  gi|336255133|ref|YP_004598240.1| 107 VAVHEDLCVGCQYCLSGCpfgaP-QFPDSDDGSAQIVGT-GGIMDKCTGCRERQEAGKgpaCAEECATDAIL 176
                                       67889*************87754.788899*******65.34444422222222222211146667777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); 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):              16  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1609.48
//
Query:       gi|336255134|ref|YP_004598241.1|  [L=281]
Description: hypothetical protein Halxa_3756 [Halopiger xanaduensis SH-6]
Scores for 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   1.4      0.012   15.5   1.4    1.3  1  SPX       SPX domain


Domain annotation for each model (and alignments):
>> SPX  SPX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   1.4   6.9e-07     0.012      62     136 ..      29     125 ..       2     277 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.9e-07
                               SPX  62 e.............rtepstsaaadesgnsaadasssepkdeae..........................slprrsp 99 
                                       +             r ++st                       +                           +p+ s+
  gi|336255134|ref|YP_004598241.1|  29 TdtdssssaptddgRVDEST-----------------------AddapgaadsgepsetrrstsdprsegGSPSDSH 82 
                                       01111112222222111111.......................1223333333333333334444445566666666 PP

                               SPX 100 lsrssrssssygglvssppsansssssddssesnpa......d 136
                                         r ++ +  y++  ++p+++++ s  ++  e+ p+       
  gi|336255134|ref|YP_004598241.1|  83 EGRHEQADGGYSEERTPPEQRDRESPPESGTEPGPEepgepaG 125
                                       6677777778887777777777777777777777443333330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1972.84
//
Query:       gi|336255135|ref|YP_004598242.1|  [L=345]
Description: hypothetical protein Halxa_3757 [Halopiger xanaduensis SH-6]
Scores for 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-20   70.9  16.0      2e-19   69.9  11.9    2.0  2  Ni_hydr_CYTB  Prokaryotic cytochrome b561
  ------ inclusion threshold ------
       0.03   14.0   0.0      0.094   12.5   0.0    1.9  1  DUF3094       Protein of unknown function (DUF3094)
        3.7    7.1  20.8         97    2.5  18.0    3.5  3  PepSY_TM      PepSY-associated TM region


Domain annotation for each model (and alignments):
>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9  11.9   3.3e-23     2e-19       2     181 ..       9     212 ..       8     213 .. 0.93
   2 ?    3.0   0.1     0.012        70      12      64 ..     246     304 ..     239     334 .. 0.70

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 3.3e-23
                                       ----TTHHHHHHHHHHHHHHHHHHHHHS------S-GGG-....HHHHHHHHHHHHHHHHHHHHHHH.......... CS
                      Ni_hydr_CYTB   2 yslvarllHWlnallvvllllsgllianlhprlywgdsgk....aralHklaGlvllalllfrllwl.......... 64 
                                       +s+ + ++H l+al+v++l+++g++ia+  + +++ ++++    ++ +H+ aG++l+al+ f++ +           
  gi|336255135|ref|YP_004598242.1|   9 FSRATTMFHSLLALTVFVLFFTGYAIAFNTELWWLVELMGgnegVLSIHRAAGFALIALTGFWVPYVllrsssrsnf 85 
                                       789999********************************99********************99999988********9 PP

                                       .------------STTTSSSSS----------------TT...........THHHHHHHHHHHHHHHHHHHT.HHHH CS
                      Ni_hydr_CYTB  65 .kkakkpspriifrqikrdltlllrgrkpeagknnplqkl...........vhlllyvllvvliltGlllsf.aata 128
                                         + ++p++  +f+q  +   +   +r+p+a++    ++            v++++ v l++l+++Gll++  +   
  gi|336255135|ref|YP_004598242.1|  86 rSVLPSPDDARAFIQDVKFALGRADERHPSARQFAGFKADevpllsyvgkgVIWIFTVELILLMISGLLIWQkT--- 159
                                       999999****************************************************************9853... PP

                                       HHHH......HTS-THHHHHHH.HHHHHHHHHHHHHHHHHHHHHH---XXXXXXXX CS
                      Ni_hydr_CYTB 129 gfpll...lddkggaqlarelHellaaallafvvlHiaaallhgpvkkdtlrrMit 181
                                          +l    ++   a+++   H+ll++++l+ v+ H + + +h ++    ++++++
  gi|336255135|ref|YP_004598242.1| 160 ---WLidfYNSQSVAMAFVAFHGLLGIIMLMGVMFHTFEHGFHPAFYPVEMKAFLP 212
                                       ...333455699********************************998668888876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHS------S-GGG-.......HHHHHHHHHHHHHHHHHHHHHHH CS
                      Ni_hydr_CYTB  12 lnallvvllllsgllianlhprlywgdsgk.......aralHklaGlvllalllfrllwl 64 
                                       ++a+lvv+ ++s + +a+l+   y  +++        +r++ + aG+++l+l l+  +++
  gi|336255135|ref|YP_004598242.1| 246 VVAVLVVVGIVSVM-MASLEYGGYPVPDTLafgegsvLRTIGINAGIFVLLLGLLLSMYG 304
                                       46777777777766.566666666555544688999888888899999999988888888 PP

>> DUF3094  Protein of unknown function (DUF3094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.6e-05     0.094      13      54 ..     224     263 ..     215     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                           DUF3094  13 dqYLsaPqHqvERqPFrpWlllvvvlavvigLGllsRlLsrL 54 
                                       d+Y  +      R+P   W+ ++ v+av +++G++s +++ L
  gi|336255135|ref|YP_004598242.1| 224 DEYDTTGIERLRRKP--SWRWATNVVAVLVVVGIVSVMMASL 263
                                       556566666666777..69999**************999877 PP

>> PepSY_TM  PepSY-associated TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5  18.0     0.016        97      11     185 ..      20     192 ..      17     194 .. 0.62
   2 ?   -1.6   0.0      0.29   1.7e+03     122     141 ..     238     257 ..     220     263 .. 0.82
   3 ?   -2.3   0.0      0.48   2.9e+03      11      20 ..     289     298 ..     283     340 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.016
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                          PepSY_TM  11 vglfllvlalTGallvfkpeieawlnpellvvapaaaaallaaeaaaaaaaaaaaaaaaaatavvrtaa..gekrsv 85 
                                       ++l ++vl++TG +++f  e+  wl  el+  ++   +  +    aa  a  a    + + +   +  +  +++rsv
  gi|336255135|ref|YP_004598242.1|  20 LALTVFVLFFTGYAIAFNTELW-WLV-ELMGGNEGVLSIHR----AAGFALIALTGFWVPYVLLRS--SsrSNFRSV 88 
                                       6777889999999999999883.333.34444444444432....223333333333333333332..134777777 PP

                                       xxxxxxxx........xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          PepSY_TM  86 fvdpytge........vlgersgesasafaeflrrlHr.glllgkpvGrllvglaallllvllvsGlilwwprrkkk 153
                                          p  ++         lg+ ++++  + a+ +  +   ++ l   vG+ ++ + ++ l++l++sGl++w   +k++
  gi|336255135|ref|YP_004598242.1|  89 LPSPDDARafiqdvkfALGRADERH--PSARQFAGFKAdEVPLLSYVGKGVIWIFTVELILLMISGLLIW---QKTW 160
                                       7777776555444444455432222..11212222222333355677***********************...4454 PP

                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          PepSY_TM 154 rfftfrpkkg.rrfwldlHnvlGvwllpfllll 185
                                        +++f + ++    +  +H +lG+++l+++++ 
  gi|336255135|ref|YP_004598242.1| 161 -LIDFYNSQSvAMAFVAFHGLLGIIMLMGVMFH 192
                                       .999999999999999***********999885 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.29
                                       xxxxxxxxxxxxxxxxxxxx RF
                          PepSY_TM 122 pvGrllvglaallllvllvs 141
                                       p  r+ + ++a+l +v +vs
  gi|336255135|ref|YP_004598242.1| 238 PSWRWATNVVAVLVVVGIVS 257
                                       45688888888888888886 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.48
                                       xxxxxxxxxx RF
                          PepSY_TM  11 vglfllvlal 20 
                                       +g+f+l+l+l
  gi|336255135|ref|YP_004598242.1| 289 AGIFVLLLGL 298
                                       3333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2684.75
//
Query:       gi|336255136|ref|YP_004598243.1|  [L=61]
Description: hypothetical protein Halxa_3758 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        2.7    8.2   4.4        1.8    8.8   2.8    1.5  2  Metal_resist   Heavy-metal resistance
        4.4    7.6   9.1       0.18   12.0   3.5    1.5  2  YjbE           Exopolysaccharide production protein YjbE


Domain annotation for each model (and alignments):
>> Metal_resist  Heavy-metal resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.8    0.0002       1.8       3      31 ..      11      39 ..       9      51 .. 0.82
   2 ?   -0.8   0.1      0.19   1.7e+03       2      15 ..      44      57 ..      43      60 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0002
                                      .XXXXXXXXXXXXXXXXXXXXXXXTTHHB CS
                      Metal_resist  3 LalNlfllGalvgaalrgpggpppggpar 31
                                      +a+ ++++G+lvg+a++ p+g++ +g++ 
  gi|336255136|ref|YP_004598243.1| 11 VAVLVVAVGGLVGVAFGTPSGGGTAGRNY 39
                                      89999******************998754 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.19
                                      ..XXXXXXXXXXXX CS
                      Metal_resist  2 sLalNlfllGalvg 15
                                      ++++++++++al++
  gi|336255136|ref|YP_004598243.1| 44 LVIVAALFIAALIA 57
                                      46666666666665 PP

>> YjbE  Exopolysaccharide production protein YjbE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.5     2e-05      0.18      43      66 ..      12      35 ..       8      40 .. 0.83
   2 ?   -2.3   0.3      0.62   5.5e+03       9      11 ..      48      50 ..      42      57 .. 0.42

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                              YjbE 43 AvgigavaallGvalAasGGGdGa 66
                                      Av + av+ l+Gva  +  GG+ a
  gi|336255136|ref|YP_004598243.1| 12 AVLVVAVGGLVGVAFGTPSGGGTA 35
                                      88999************9888765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.62
                              YjbE  9 ail 11
                                      a+l
  gi|336255136|ref|YP_004598243.1| 48 AAL 50
                                      222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 507.66
//
Query:       gi|336255137|ref|YP_004598244.1|  [L=353]
Description: 3-dehydroquinate synthase [Halopiger xanaduensis SH-6]
Scores for 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  207.6   2.0    3.1e-61  207.3   2.0    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    2.2e-21   76.1   6.2    7.1e-21   74.4   6.2    1.6  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    1.4e-07   30.9   0.1    3.8e-07   29.5   0.1    1.6  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 !  207.3   2.0   5.2e-65   3.1e-61       2     250 .]      16     273 ..      15     273 .. 0.92

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 5.2e-65
                          Fe-ADH_2   2 igegaleklgellkelelk.kvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketd 77 
                                       +g+g+ +++ e++ +l+l+ + llv++ +  ++a++ v+ +++ agi++++v+   e+a++++ve+++e ++++e+ 
  gi|336255137|ref|YP_004598244.1|  16 VGHGVRSSVVEVVDDLHLQgRPLLVTSPTPREVAADPVAADFEAAGIDPAIVT--IETATFDSVERVIETAEAEEVS 90 
                                       789999999*******987799****************************996..689******************* PP

                          Fe-ADH_2  78 lvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrll 154
                                        +v+vGgG++iDiak++s +l++ ++svpTaaS+DG+ s   s+ +   + +v  a+ Plav+aD+++laeAP +l+
  gi|336255137|ref|YP_004598244.1|  91 YLVGVGGGKAIDIAKMASDHLEMGFLSVPTAASHDGIVSNRGSVPEGDTRHSV-AAEPPLAVVADTEILAEAPWELT 166
                                       ***********************************************999999.9********************** PP

                          Fe-ADH_2 155 asGvGDllgkytaladwklan........evseplaklsaamvqeaaeklve..dkketealeellea.lalsgigi 220
                                       ++G++D++++yta++dw+la+        e+++ l++++a++++++a+ +    ++    ++++l+++ +a+s++ +
  gi|336255137|ref|YP_004598244.1| 167 TAGCADIISNYTAVMDWRLATrlkdveysEYAAALSEMTAEILVDNADLIRPglEESAWVVTKALMSSgVAMSIADS 243
                                       *********************9999988888889*************999873233334444555554359999999 PP

                          Fe-ADH_2 221 srpaSGsEHliSHaldmlalkqalHGeqVG 250
                                       srpaSG+EHl+SH ld+l+++ alHG qVG
  gi|336255137|ref|YP_004598244.1| 244 SRPASGAEHLFSHQLDRLEPNGALHGHQVG 273
                                       *****************************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 !   74.4   6.2   1.2e-24   7.1e-21       1     337 [.      11     314 ..      11     328 .. 0.84

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 1.2e-24
                                       -SEEEEETTGGGGHHHHHTTT-...EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTT CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkklgak.ralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaal 76 
                                       P+++v g g+ +++ e +++l ++ r+l+vt++     + ++d v + +e+agi+ ++++   +  t ++ve++++ 
  gi|336255137|ref|YP_004598244.1|  11 PRNVVVGHGVRSSVVEVVDDLHLQgRPLLVTSPTPR--EVAADPVAADFEAAGIDPAIVT--IETATFDSVERVIET 83 
                                       899******************9777*********54..669****************855..6889*********** PP

                                       S-TT.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEE CS
                            Fe-ADH  77 areegadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegek 153
                                       a++e++ ++++vGGG++iD+AK+++  l+                  + +  +PT a+ +  v++   +  e + ++
  gi|336255137|ref|YP_004598244.1|  84 AEAEEVSYLVGVGGGKAIDIAKMASDHLE------------------MGFLSVPTAASHDGIVSNRGSVP-EGD-TR 140
                                       *****************************..................89*********999998887777.344.45 PP

                                       EEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSS.B--HHHHHHHHHHHHHHHHHHH CS
                            Fe-ADH 154 lsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsda.laleairliaknleravadged 229
                                        s++     P +++ D+e+++ +P ++t a+ +D+++ +   +  + a+ l d+ ++++a+ l     e +v++++ 
  gi|336255137|ref|YP_004598244.1| 141 HSVA--AEPPLAVVADTEILAEAPWELTTAGCADIISNYTAVMDWRLATRLKDVeYSEYAAALSEMTAEILVDNAD- 214
                                       5666..34577899************************9999888********88999999999999999999975. PP

                                       H.....HHHHHHHHHHHH.HHHHHHSS---.....HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHH CS
                            Fe-ADH 230 l.....eareqmllastl.aglafsnaglg.....avHalahalgalfgiphglanaillpavlrfnaeaaperlaq 295
                                       l     e  + ++  +++ +g+a+s a  +     a H ++h+l  l   p+g++++  +  +              
  gi|336255137|ref|YP_004598244.1| 215 LirpglEESAWVVTKALMsSGVAMSIADSSrpasgAEHLFSHQLDRL--EPNGALHGHQVGVGS------------- 276
                                       44556688888888888888888887777777778999999999992..568888888887777............. PP

                                       HHHT.......T--HHHHHHHHHHHHHTT---SHHHHT-TT- CS
                            Fe-ADH 296 laralggesdeeaaeeliealrellkelglptsLselgvdee 337
                                       +  a      + + + + + +r+ l+++++pt+ +elg+d+e
  gi|336255137|ref|YP_004598244.1| 277 IMTAY----LHGGEDGVWRDIRDALASIDAPTTAAELGIDDE 314
                                       22221....236888999999999999999999999999985 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   6.3e-11   3.8e-07      14     254 ..      72     319 ..      68     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 6.3e-11
                                       HHHHHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEE CS
                      DHQ_synthase  14 etlekildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliG 90 
                                       +t+ ++ +++ +a++e  s+l+ +GGG   D+a  ++  +  G  f+ vPt+  a  D  v  + ++     +  + 
  gi|336255137|ref|YP_004598244.1|  72 ATFDSVERVIETAEAEEVSYLVGVGGGKAIDIAKMASDHLEMG--FLSVPTA--ASHDGIVSNRGSVPEGDTRHSVA 144
                                       566778888888999999****************999999876..99***97..999******************96 PP

                                       EE---SEEEEEGGGGGGS-HHHHHHHHHHHH.HHHHHT-HHHHHHHHHHHHHHHC.......TTTHHHHHHHHHHHH CS
                      DHQ_synthase  91 afaqPkavlidlevLktLperelraGlaEvi.Kyalikdeelfelleenaeallk.......eeeeealeeliarsi 159
                                       a   P av++d+e+L+  p + ++aG+a++i  y++++d +l ++l++ + +  +       +e   + ++li+  +
  gi|336255137|ref|YP_004598244.1| 145 A-EPPLAVVADTEILAEAPWELTTAGCADIIsNYTAVMDWRLATRLKDVEYSEYAaalsemtAEILVDNADLIRPGL 220
                                       5.99*************************9956999***********998888775566555222333344556666 PP

                                       HHHHHHHHHCCTTTTGGGG........GGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHH CS
                      DHQ_synthase 160 evkaevveeDekekglral........LnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeever 228
                                       e  a vv++    +g+ +             H ++H++++l      lHG+ V +G +++a+l        +   ++
  gi|336255137|ref|YP_004598244.1| 221 EESAWVVTKALMSSGVAMSiadssrpaSGAEHLFSHQLDRLEPN-GALHGHQVGVGSIMTAYLHGGE----DGVWRD 292
                                       6666666666666665544222222226678********99887.99************99998443....344678 PP

                                       HHHHHHHTT---STTTT..-HHHHHHH CS
                      DHQ_synthase 229 llkllkklglpvslkel.leveellea 254
                                       +++ l++++ p++  el ++ e+++ea
  gi|336255137|ref|YP_004598244.1| 293 IRDALASIDAPTTAAELgIDDETVIEA 319
                                       889999999998887765555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2571.51
//
Query:       gi|336255138|ref|YP_004598245.1|  [L=255]
Description: 3-oxoacyl-(acyl-carrier-protein) reductase [Halopiger xanaduensis SH-6]
Scores for 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  212.7   2.2    6.5e-63  212.4   2.2    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    7.6e-49  165.8   0.6      1e-48  165.4   0.6    1.1  1  adh_short        short chain dehydrogenase
      3e-15   56.6   0.7      4e-15   56.2   0.7    1.1  1  KR               KR domain
     0.0067   15.8   0.1       0.01   15.2   0.1    1.2  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0072   16.9   2.3      0.049   14.2   1.3    2.6  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.025   14.8   0.2      0.039   14.2   0.2    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.027   14.0   0.7      0.038   13.6   0.7    1.2  1  NmrA             NmrA-like family
      0.071   12.2   0.2        0.1   11.7   0.2    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
       0.11   12.5   1.4        3.4    7.7   0.3    2.3  2  Pam16            Pam16
       0.14   11.5   0.1       0.73    9.1   0.0    1.9  2  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
       0.15   12.0   0.5       0.25   11.2   0.5    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


Domain annotation for each model (and alignments):
>> 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 !  212.4   2.2     4e-66   6.5e-63       3     233 ..      21     250 ..      18     251 .. 0.95

  Alignments for each domain:
  == domain 1  score: 212.4 bits;  conditional E-value: 4e-66
                                       TTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.E.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                      adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.v.lecDVtdeeqvealveevvekfgklDilvnn 76 
                                        sgIG +i +a+a++Ga+v+++ ++e++ +++++el + lgae + + c+V+d e+v++l +e+++ +g++D+lvn+
  gi|336255138|ref|YP_004598245.1|  21 TSGIGLEIGRAFARNGADVIASSRSEDSvADAAAELRD-LGAEtAeVTCNVRDLESVRNLKDEAEAALGGIDVLVNS 96 
                                       59**************************7777777766.6666379******************************* PP

                                       ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHH CS
                      adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtr 153
                                       ag + +  +p++e++++e+ + +dv l ++f+ +k +  +m e gsi+n+ss++ae++ ++ + y  aKa+l++ltr
  gi|336255138|ref|YP_004598245.1|  97 AGSVAA--APVTEMTEKEWYQDIDVCLSGVFRATKVFGDAMDE-GSIINISSMSAEQSREERAGYVSAKAGLNGLTR 170
                                       ******..*********************************75.8******************************** PP

                                       HHHHHHGGGTEEEEEEEE--BHCTG.GGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEE CS
                      adh_short_C2 154 ylAvelgpkgiRvNavspgpikTla.asgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvv 229
                                       + A++l+p  iRvNa++pg++kT++   ++++ +e++e +++r+p++r++tp+e+  aal+Lasd+as++tG+++ +
  gi|336255138|ref|YP_004598245.1| 171 ATAADLAP-DIRVNAIAPGFVKTELaGPKLEDGSEFREGVDERTPMERVATPDEISGAALYLASDAASFTTGEIITI 246
                                       ********.9*************995678999********************************************* PP

                                       STTG CS
                      adh_short_C2 230 DgGl 233
                                       DgG+
  gi|336255138|ref|YP_004598245.1| 247 DGGY 250
                                       ***9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4   0.6   6.1e-52     1e-48       1     190 [.      13     198 ..      13     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 6.1e-52
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       k v+++G++sGIG++i +++a++Ga+v++ +rse+ ++ +a+el+++ga+   ++++v+d e+v++l ++a++ lg+
  gi|336255138|ref|YP_004598245.1|  13 KNVVIIGGTSGIGLEIGRAFARNGADVIASSRSEDSVADAAAELRDLGAETAEVTCNVRDLESVRNLKDEAEAALGG 89 
                                       789************************************************************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       +dvLvn AG    +p+ e++e+ew + i+v l gvf +t+ + +am+   +G+I+n+sS+ ++++ ++ a Y ++Ka
  gi|336255138|ref|YP_004598245.1|  90 IDVLVNSAGSVAAAPVTEMTEKEWYQDIDVCLSGVFRATKVFGDAMD---EGSIINISSMSAEQSREERAGYVSAKA 163
                                       *********************************************99...9************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakel 190
                                       +++gltr+ a +lap+ irvna+aPG+v+T++a ++
  gi|336255138|ref|YP_004598245.1| 164 GLNGLTRATAADLAPD-IRVNAIAPGFVKTELAGPK 198
                                       ***************8.**************98776 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.7   2.4e-18     4e-15       3     166 ..      15     175 ..      14     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 2.4e-18
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                       ++i+GG+ g+Gle+ r  a++ga  ++  sRs   +++ ++  ael++lgae   v + v d ++v++l +e++a  
  gi|336255138|ref|YP_004598245.1|  15 VVIIGGTSGIGLEIGRAFARNGAD-VIASSRS---EDSVADAAAELRDLGAETAEVTCNVRDLESVRNLKDEAEAAL 87 
                                       58********************96.6678999...455566789********************************* PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT.S--SEEEEEEEHHHHH--TT-HHHHHHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled.esldffvlfSSiagllgsagqanYaaaNaf 155
                                       + i   +++Ag ++ ++++emt++++ q +   ++G+    +++ d  +   ++ +SS+++     ++a Y +a a 
  gi|336255138|ref|YP_004598245.1|  88 GGIDVLVNSAGSVAAAPVTEMTEKEWYQDIDVCLSGVFRATKVFGDaMDEGSIINISSMSAEQSREERAGYVSAKAG 164
                                       ********************************************996777799************************ PP

                                       HHHHHHHHHHH CS
                                KR 156 lDalaeyrrsq 166
                                       l++l +  ++ 
  gi|336255138|ref|YP_004598245.1| 165 LNGLTRATAAD 175
                                       **999877665 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 !   15.2   0.1   6.3e-06      0.01      33     113 ..       9      84 ..       2      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.3e-06
                                       -GTTSEEEEE.S-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTS CS
                      2-Hacid_dh_C  33 elsgktvGii.GlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhl 108
                                       ++ gk v ii G+  IG ++ + ++  g++via +rs+++ +   +     ++l +l ae+  v++++   ++ r+l
  gi|336255138|ref|YP_004598245.1|   9 SVDGKNVVIIgGTSGIGLEIGRAFARNGADVIASSRSEDSVA---D---AAAELRDLGAETAEVTCNVRDLESVRNL 79 
                                       678999988835999**********************77333...3...3568999999999999998888888887 PP

                                       BSHHH CS
                      2-Hacid_dh_C 109 inaee 113
                                        +++e
  gi|336255138|ref|YP_004598245.1|  80 KDEAE 84 
                                       77665 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 !   14.2   1.3     3e-05     0.049       2      48 ..      15      66 ..      14     127 .. 0.81
   2 ?   -2.0   0.0       3.4   5.5e+03      33      47 ..     150     164 ..     130     192 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                                      EEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC........- CS
                     F420_oxidored  2 igii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg........v 48
                                      + ii G+  +g  + + ++++g    +++ a+sr++++++ +a+el         v
  gi|336255138|ref|YP_004598245.1| 15 VVIIgGTSGIGLEIGRAFARNG---ADVI-ASSRSEDSVADAAAELRdlgaetaeV 66
                                      689999999*************...****.99************998655544441 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.4
                                       ESSCCCHHHHHHHHC CS
                     F420_oxidored  33 srnpekaeelaeelg 47 
                                       ++ +e+a +  +++g
  gi|336255138|ref|YP_004598245.1| 150 QSREERAGYVSAKAG 164
                                       444555555555554 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 ?   14.2   0.2   2.4e-05     0.039       1      89 [.      15     109 ..      15     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                                       EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.....TTTCEEEEE--...TTTHHHHHHHHHT CS
                   Sacchrp_dh_NADP   1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka.....lgvrfeaiald...aenyeavLaallk 68 
                                       v+iiG+  ++G  + +  ar++    +++  +rs+++++ +aa++        ++++   d   + n ++  +a+l 
  gi|336255138|ref|YP_004598245.1|  15 VVIIGGtSGIGLEIGRAFARNGA---DVIASSRSEDSVADAAAELrdlgaETAEVTCNVRDlesVRNLKDEAEAALG 88 
                                       799999999***********997...59999*******999999967444222222222221123444555666666 PP

                                       TSSEEEE-SSGGGHHHHHHHH CS
                   Sacchrp_dh_NADP  69 egdlvvnlsppissldvlkaC 89 
                                       + d++vn ++++ +++v ++ 
  gi|336255138|ref|YP_004598245.1|  89 GIDVLVNSAGSVAAAPVTEMT 109
                                       66*************999876 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   2.3e-05     0.038       1      67 [.      15      85 ..      15     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S..-SHHHHHHHHSTTEEE..ES-TT-HHHHHHHHTT-SE CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdt..kselakslkeaGvelv..kgdlddkeslvealkgvdv 67
                                      +++iG+T  +G  + ra++++g +v a  R +    ++a++l + G+e+     ++ d es++++ +++++
  gi|336255138|ref|YP_004598245.1| 15 VVIIGGTSGIGLEIGRAFARNGADVIASSRSEdsVADAAAELRDLGAETAevTCNVRDLESVRNLKDEAEA 85
                                      689***************************99446689**********98334556677777777666655 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 ?   11.7   0.2   6.3e-05       0.1       2      47 ..      14      80 ..      13     112 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.3e-05
                                      EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.....................T--TTSHHHHHHHH CS
                     RmlD_sub_bind  2 kilvtGanGqlGseLakqlaeeglevlaltre.....................eldltdaeavaell 47
                                      +++++G++  +G e+ +++a++g++v+a +r+                     +++++d e+v++l 
  gi|336255138|ref|YP_004598245.1| 14 NVVIIGGTSGIGLEIGRAFARNGADVIASSRSedsvadaaaelrdlgaetaevTCNVRDLESVRNLK 80
                                      6899**************************9945555555555555555444444444444444444 PP

>> Pam16  Pam16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3    0.0021       3.4      17      51 ..      28      63 ..      13      85 .. 0.77
   2 ?    3.5   0.0     0.042        69      10      56 ..     124     169 ..     112     178 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0021
                                      XXXXXXXXXXXXX.XXXXXXXX.XXXXX.XXXXXXX CS
                             Pam16 17 vgkalaralrqeiaaaraaadartsase.reaaksn 51
                                      +g+a+ar   + ia++r + +  + a+e r+ ++  
  gi|336255138|ref|YP_004598245.1| 28 IGRAFARNGADVIASSRSEDSVADAAAElRDLGAET 63
                                      79*****************99999999888877654 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.042
                                       XXXXXXXXXXXXXXXXXXXX.XXXXXXXX.XXXXXXXXXXXXXXXX- CS
                             Pam16  10 ivagtqvvgkalaralrqeiaaaraaadartsasereaaksnlkGis 56 
                                       +  +t+v+g a+ +    +i++ +a+++ +++a+   +ak+ l+G++
  gi|336255138|ref|YP_004598245.1| 124 VFRATKVFGDAMDEGSIINISSMSAEQSREERAGYV-SAKAGLNGLT 169
                                       345677778888777777888888888887777764.4566667766 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 ?    9.1   0.0   0.00045      0.73      31      72 ..       7      48 ..       4      57 .. 0.83
   2 ?   -0.2   0.1      0.33   5.3e+02      84     121 ..     100     134 ..      62     147 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00045
                                      T---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCC CS
                     THF_DHG_CYH_C 31 gielegkkvvvvGrsnivgkplallLleknatVtvchsktkd 72
                                       i+++gk+vv++G  + +g  +   +++++a V    ++ ++
  gi|336255138|ref|YP_004598245.1|  7 AISVDGKNVVIIGGTSGIGLEIGRAFARNGADVIASSRSEDS 48
                                      5899*************************9999776555444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.33
                                       EE-SS-TT-B-GGGS-TT-EEEE---EEC.-TTEEE-SB CS
                     THF_DHG_CYH_C  84 vvavGkpelikaemvkegavviDvGinrv.ekgklvGDv 121
                                       v+a+ + e+ ++e+ +     iDv ++ v + +k+ GD 
  gi|336255138|ref|YP_004598245.1| 100 VAAAPVTEMTEKEWYQ----DIDVCLSGVfRATKVFGDA 134
                                       2233333333333333....3666666655666677765 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 ?   11.2   0.5   0.00016      0.25       2      49 ..      15      63 ..      14     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                                      EEEE--.SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCC CS
                           3HCDH_N  2 vaviGa.GtmGagiaavfasagleVvlvdiseealekalekiekslekl 49
                                      v +iG    +G +i  +fa++g +V    +se+++++a++++++  ++ 
  gi|336255138|ref|YP_004598245.1| 15 VVIIGGtSGIGLEIGRAFARNGADVIASSRSEDSVADAAAELRDLGAET 63
                                      56666435699******************************99833332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2115.18
//
Query:       gi|336255139|ref|YP_004598246.1|  [L=484]
Description: MATE efflux family protein [Halopiger xanaduensis SH-6]
Scores for 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-44  150.4  25.4    4.7e-25   88.1   7.4    2.7  3  MatE             MatE
    2.3e-10   40.7   4.6    2.3e-10   40.7   4.6    4.3  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    2.7e-10   39.4   6.9    1.5e-08   33.7   2.0    2.8  2  MurJ             Lipid II flippase MurJ


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 !   88.1   7.4   7.8e-29   4.7e-25       4     160 ..      45     202 ..      42     203 .. 0.96
   2 ?   -2.3   0.7      0.51     3e+03      28      51 ..     212     235 ..     211     244 .. 0.59
   3 !   74.5   2.8   1.2e-24   7.3e-21       1     161 []     270     433 ..     270     433 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 7.8e-29
                              MatE   4 lenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglill 79 
                                       ++ l+ ++ +++d+ +vg   g+ a+A+v++a + + l f+++ g++ ++ +lv+q++Ga+  ++++ a+r +++l+
  gi|336255139|ref|YP_004598246.1|  45 VTGLARMSKGAVDVAMVGVAvGTAAVAGVGVAGPYWGLAFALGGGVAGGTIALVSQRFGAEAHDELALAVRSSTLLV 121
                                       56666677789*******999******************************************************** PP

                              MatE  80 lllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllni 156
                                       +++s++++++ +lf+  ++  + ++e  +e++++ylr+++lgip+ +l+lv s++l ga ++ +++ + + +++ ni
  gi|336255139|ref|YP_004598246.1| 122 VAISVPVSVVFWLFPYELVTPIASSERAIEYGATYLRVVGLGIPFAGLNLVGSRTLVGADDAYTAMQVRAGGAVANI 198
                                       ***************************************************************************** PP

                              MatE 157 plny 160
                                        ln 
  gi|336255139|ref|YP_004598246.1| 199 ALNA 202
                                       *997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.51
                              MatE  28 lAavsialsilsllfvfllglsta 51 
                                       +A++++++ ++++ ++ ++++++a
  gi|336255139|ref|YP_004598246.1| 212 VAGAALGTVLSNVAVTAVFAVGIA 235
                                       566666666666666555555544 PP

  == domain 3  score: 74.5 bits;  conditional E-value: 1.2e-24
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       Pi   nl+ ++  + +  +++ +g+  lAa  ia +i+ ++ ++++g++ a+++lvgq+lG+++ ++a+ + r ++ 
  gi|336255139|ref|YP_004598246.1| 270 PIGARNLVWTVAEFPMLTVLAIFGEPTLAAFVIARRIWGIMNTPGWGFGLAASSLVGQSLGKNDERGAEAYGRDIVR 346
                                       77777888888888888888888****************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdee..vlelakrylrililgipalalqlvlsgilrgagktkvplyislisl 152
                                       ++l+ ++++a+l+ lf++ i+ lf  d++   +++a +++ ++++ ++++++  +++g l++ g+t++p+   ++++
  gi|336255139|ref|YP_004598246.1| 347 FSLATYVLFAVLIALFADRIVVLFAEDPTspEIPIAVNLVYAACVAVLFQGVGGAAAGPLDASGDTRIPFLSQALGV 423
                                       ***************************************************************************** PP

                              MatE 153 .llniplnyl 161
                                           ipl+yl
  gi|336255139|ref|YP_004598246.1| 424 fFGAIPLAYL 433
                                       8888999996 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 ?   -4.8   7.2         3   1.8e+04      97     137 ..      61      98 ..      43     136 .. 0.61
   2 !   40.7   4.6   3.8e-14   2.3e-10       1      76 [.     156     233 ..     156     238 .. 0.94
   3 ?   -2.0   0.0      0.59   3.5e+03      16      25 ..     352     361 ..     340     382 .. 0.57
   4 !   11.1   1.3   5.2e-05      0.31       5      78 ..     389     464 ..     385     470 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.8 bits;  conditional E-value: 3
                   Polysacc_synt_C  97 aalvmgivvylllllllgllllaalalllavlvgalvYlll 137
                                       +++++g +  +++ + +  + +  la++l+++v++   +l+
  gi|336255139|ref|YP_004598246.1|  61 VGVAVGTA--AVAGVGVAGPYWG-LAFALGGGVAGGTIALV 98 
                                       22222222..3333333333333.44445554554444444 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 3.8e-14
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli..plfgivGaaiatvlallvvavlnly 75 
                                       +L+++ l+i+f++l+ v+s  L g + + +a+ + + ga+++++ln ++i   ++g+ Gaa++tvl+ ++v+++  +
  gi|336255139|ref|YP_004598246.1| 156 YLRVVGLGIPFAGLNLVGSRTLVGADDAYTAMQVRAGGAVANIALNAVFIfgLEWGVAGAALGTVLSNVAVTAVFAV 232
                                       58999*********************************************888******************998766 PP

                   Polysacc_synt_C  76 a 76 
                                        
  gi|336255139|ref|YP_004598246.1| 233 G 233
                                       5 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.59
                   Polysacc_synt_C  16 tvlssiLqgl 25 
                                        vl ++L++l
  gi|336255139|ref|YP_004598246.1| 352 YVLFAVLIAL 361
                                       2222222222 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 5.2e-05
                   Polysacc_synt_C   5 lalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli..plfgivGaaiatvlallvvavlnlyalr 78 
                                        +++++f+++    ++ L + g ++i++++ ++g+++  i   +l    ++g+ G  +a ++   v a++n+++ r
  gi|336255139|ref|YP_004598246.1| 389 ACVAVLFQGVGGAAAGPLDASGDTRIPFLSQALGVFFGAIPLAYLGatTSLGYWGLYLAFLAEASVPAAINYWRFR 464
                                       6899********************************877665555547899*********************9876 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   2.0   2.5e-12   1.5e-08     260     402 ..      96     236 ..      43     249 .. 0.92
   2 !    6.6   0.0   0.00043       2.6      47     122 ..     332     407 ..     322     421 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.5e-12
                              MurJ 260 PrlSrsakekdedevrdllsqairltllllipvsfgllvlskpivsllferGnFseedveataevLaayalgLipya 336
                                       + +S+ + ++ +de+   ++ ++ l++++++pvs+++ ++  ++v+ +     +se ++e+ a+ L++ +lg+++  
  gi|336255139|ref|YP_004598246.1|  96 ALVSQRFGAEAHDELALAVRSSTLLVVAISVPVSVVFWLFPYELVTPIA----SSERAIEYGATYLRVVGLGIPFAG 168
                                       45899999999***********************************997....9*********************** PP

                              MurJ 337 lvklllrvfYAredtktPvkislislvlnills..llllpplgvvglalatslsaliglvllyvllrk 402
                                       l+ + +r++    d+ t++ +    +v ni+l+  +++   +gv+g al+t+ls+++ ++++ v +++
  gi|336255139|ref|YP_004598246.1| 169 LNLVGSRTLVGADDAYTAMQVRAGGAVANIALNavFIFGLEWGVAGAALGTVLSNVAVTAVFAVGIAR 236
                                       *********************************9999999*******************999887766 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00043
                              MurJ  47 kdeekaaefvrkvltllilvlllvtligilaapllirllatgfdeetlelavsllrillpylllvslsavfgavLn 122
                                       +de +a++  r ++++  ++ +l++++  l+a  ++ l+a + +  +  +av+l++     +l+ ++ + + + L 
  gi|336255139|ref|YP_004598246.1| 332 NDERGAEAYGRDIVRFSLATYVLFAVLIALFADRIVVLFAEDPTSPEIPIAVNLVYAACVAVLFQGVGGAAAGPLD 407
                                       578899999999999999999999999999*********9999999999999999998888888777666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3801.09
//
Query:       gi|336255140|ref|YP_004598247.1|  [L=121]
Description: hypothetical protein Halxa_3762 [Halopiger xanaduensis SH-6]
Scores for 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   11.6   0.2       0.49    9.5   0.1    1.8  2  Regulator_TrmB  Archaeal transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   2.7e-05      0.49     197     231 ..      11      45 ..       3      47 .. 0.85
   2 ?    0.3   0.0     0.018   3.2e+02     101     158 ..      58     116 ..      48     121 .] 0.64

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 2.7e-05
                                       TTEEEEEEEETTEEEEEE-TT--SSSEEEEEEEEE CS
                    Regulator_TrmB 197 pgvaslvvetedgevtVGGlgAvlEDieaeeitle 231
                                        +  +l++e +d ++++G ++Av+E i +e+ tle
  gi|336255140|ref|YP_004598247.1|  11 LENGTLYLEDDDARIEIGPMDAVVELIGGETYTLE 45 
                                       567899*******************9999988875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.018
                                       EEEE--HHHHHHHHHHHHHH........HHH-EEEEE.EES-TT-EE.ES-HHHHHHHHH CS
                    Regulator_TrmB 101 rdkeeeyaiifkekelihvlshyFlttlWktsevikt.depvekpit.fssirlavedik 158
                                       +d++++  i ++++ l + ++  F t+   +s   +t d+  +  ++ f+++ ++++d k
  gi|336255140|ref|YP_004598247.1|  58 TDDDNTITIDVRDSVLDWAYTEDFTTN-VGNSPLEQTgDSGYPIRTEvFADMVTSIWDSK 116
                                       677788888899999999999999888.56666666444433333323566666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1011.82
//
Query:       gi|336255141|ref|YP_004598248.1|  [L=411]
Description: Galactonate dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-60  205.1   1.4    1.4e-60  204.6   1.4    1.2  1  MR_MLE_C  Enolase C-terminal domain-like
    5.5e-16   58.8   0.0      1e-15   58.0   0.0    1.4  1  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N


Domain annotation for each model (and alignments):
>> 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 !  204.6   1.4   1.5e-64   1.4e-60       4     219 ..     168     396 ..     165     397 .. 0.95

  Alignments for each domain:
  == domain 1  score: 204.6 bits;  conditional E-value: 1.5e-64
                                       HHHHHHHHHHT-SEEEEETSSS...............HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHH CS
                          MR_MLE_C   4 eearelvaeqgfravKlkvggd...............dvaedvervravreavgpgddvdlmvDanqawdlatAirv 65 
                                       +e ++ v+e g++a+K+++  +               ++++ v+ v++v e+v  gd++d+++D+++a+++  A r+
  gi|336255141|ref|YP_004598248.1| 168 DEGERVVEELGYDAIKFDLDVPsghevdranrhlrdpEIDHKVQIVKEVTERV--GDRADVAFDCHWAFTAGSAHRL 242
                                       5667779999********99999************9999**************..5577****************** PP

                                       HHHHGGGTESEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHH CS
                          MR_MLE_C  66 areleeldllwlEEPvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkv 141
                                       a elee+d++wlE+Pvppe+  +  +e++ ++ ++pia+gE++y+ ++ r+lle++avdi+ pd+ rvgGi e++k+
  gi|336255141|ref|YP_004598248.1| 243 ADELEEYDVWWLEDPVPPEN-HDVQREVT-QHtTTPIATGENVYRTHGQRRLLEEQAVDIIAPDLPRVGGIRETVKI 317
                                       ******************76.999*****.5559******************************************* PP

                                       HHHHHHTT-EEEEBSCSSHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTSSSBTSSEB-. CS
                          MR_MLE_C 142 aalaeafgvpvapHsgsgglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtvpdgpGlGveld. 217
                                       a+la+ + +pva+H++s+++g++as++ aaaipn+l ley+ ++  + e+l+ee+  +edGr++vp++pGlG++ld 
  gi|336255141|ref|YP_004598248.1| 318 ANLADLYYIPVAMHNVSSPIGTMASAQAAAAIPNSLALEYHSYQLGWWEDLVEEDNLIEDGRMEVPEKPGLGLTLDf 394
                                       ***************989**********************************************************6 PP

                                       HH CS
                          MR_MLE_C 218 ee 219
                                       ++
  gi|336255141|ref|YP_004598248.1| 395 DA 396
                                       65 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   1.1e-19     1e-15      25     117 .]      48     142 ..      29     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.1e-19
                                       EEEEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSS.......CHHHHH CS
                          MR_MLE_N  25 kqslvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlg.......nmsAka 94 
                                       + + +lv+++t++G+vG ge+   g       a++++ +ap ++g+++  i  l + + +++ g       + sA++
  gi|336255141|ref|YP_004598248.1|  48 NYPWILVRVYTDAGIVGNGECYWGG----GDDAIIQR-MAPFIIGENPLDIDRLYEHMIQKMSGegsisgkTISAIS 119
                                       45789******************99....45666666.*************************99************ PP

                                       HHHHHHHHHHHHHTTSBHHHHTT CS
                          MR_MLE_N  95 aidmAlwDlkakalnlpladLlG 117
                                       +i++Al+D+++k l++p ++L+G
  gi|336255141|ref|YP_004598248.1| 120 GIEIALHDIAGKILDVPAYQLVG 142
                                       *********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 00:00:00.39
# Mc/sec: 3195.11
//
Query:       gi|336255142|ref|YP_004598249.1|  [L=482]
Description: aldehyde dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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   2.1   6.5e-164  545.8   2.1    1.0  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 !  545.8   2.1  3.6e-168  6.5e-164       1     462 []      13     478 ..      13     478 .. 0.98

  Alignments for each domain:
  == domain 1  score: 545.8 bits;  conditional E-value: 3.6e-168
                                       EET-SS.SEEEEEETT.TCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHH CS
                            Aldedh   1 wveses.etievinPa.tgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaele 75 
                                       w++se+ et+e+ +Pa   e +a++++++aed++aav+aA++a ++wa++pa+eR++iLr+a ++l++rkeel+el+
  gi|336255142|ref|YP_004598249.1|  13 WTDSETgETFETEDPAaPAEAVAEYQQSGAEDANAAVEAAAAAEDEWATTPAPERGAILREAGSILADRKEELTELL 89 
                                       999999788*******99*********************************************************** PP

                                       HHHH---HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEEC.TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHH CS
                            Aldedh  76 tletGkplaearaeveeaidvlryyaelaeklegevlpss.egklalvrrePlGvvgaItPWNfPlllaawklapal 151
                                       t+e Gk+ aea +ev++aid++ yyae  ++l g+v + s ++++ +++ eP+Gv ++ItPWN+P++++awk+apal
  gi|336255142|ref|YP_004598249.1|  90 TREEGKTHAEAGGEVQRAIDIFYYYAEKTRDLGGDVKSASgPRTNLYTVDEPVGVAALITPWNYPIAIPAWKIAPAL 166
                                       ***********************************9888559*********************************** PP

                                       HTT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCT CS
                            Aldedh 152 aaGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaakn 228
                                       a+GNt+vl Pa+ +p +al ++++++eag+P+g+ nvvtg+gs+vg+a+++h+evd+vsftGs+evg+ ++ +a+++
  gi|336255142|ref|YP_004598249.1| 167 ATGNTIVLNPASVAPGVALEIFKALDEAGIPDGAANVVTGPGSTVGDAIMTHDEVDAVSFTGSSEVGEMVYDKATDD 243
                                       ***************************************************************************** PP

                                       TSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT CS
                            Aldedh 229 lkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdplded 305
                                        krv+ ElGGknp++v+++aD+d+a+e +++gafg +GQ C+a+sr++v+ ++ydefv+++ve+a+++++g +  ++
  gi|336255142|ref|YP_004598249.1| 244 GKRVQTELGGKNPTVVTDSADVDEAAEIVANGAFGVTGQACTACSRAIVHTDVYDEFVDAVVEQAESIEIGPG--DE 318
                                       ************************************************************************9..47 PP

                                       -SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEES CS
                            Aldedh 306 tdvGPliseaqlekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfk 381
                                        d+GP+++e++le   +y+e a++ega+l +Gg   e ++  +gy+vePtv+++v++d riaqeE+FGPVl+vi+++
  gi|336255142|ref|YP_004598249.1| 319 YDMGPQVTESELEGTLDYIEIAENEGATLATGGGqPEGDRFGDGYYVEPTVFTDVDNDYRIAQEEVFGPVLAVIEVE 395
                                       *******************************8877889999************************************ PP

                                       SHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES..-BSHHHHHHHT CS
                            Aldedh 382 deeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglG..reggkegleey 456
                                       d+e+ +e aNd +yGL+a+++t+d ++aer+++++eaG   +Nd+ttg + ++pfgG+k+S+    re+g +g+++y
  gi|336255142|ref|YP_004598249.1| 396 DFEDGLETANDVQYGLSASIVTDDHTEAERFVREVEAGVAKVNDKTTGLELHVPFGGFKRSSSEtwREQGDAGIDFY 472
                                       **************************************************99**********9999*********** PP

                                       EEEEEE CS
                            Aldedh 457 tevktv 462
                                       t  ktv
  gi|336255142|ref|YP_004598249.1| 473 TIEKTV 478
                                       *99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3595.59
//
Query:       gi|336255143|ref|YP_004598250.1|  [L=296]
Description: fumarylacetoacetate (FAA) hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-24   84.3   0.1    2.1e-22   79.9   0.1    2.4  2  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.017     3e+02     108     161 ..      50     116 ..      39     118 .. 0.69
   2 !   79.9   0.1   1.2e-26   2.1e-22      13     218 .]     101     294 ..      87     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.017
                                       HHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEE.............TTEEEEEEEGGGTTTSHH CS
                     FAA_hydrolase 108 gwflgksfdtftpiGpwivtpdeledpedlelrlrv.............ngeevqdsntkdmifspa 161
                                       + ++ +  d++++++p +  +d  +d+++++  ++              +++++ +s+++dm+ +++
  gi|336255143|ref|YP_004598250.1|  50 DRVAERLLDGAAVLSPDVLDADGDGDDGAVSAPISSgevwaagvtyrisEEARKAESSMEDMYIDVY 116
                                       6667778899999999998888888877444444445555555555556666677788899998876 PP

  == domain 2  score: 79.9 bits;  conditional E-value: 1.2e-26
                                       HHHHTTT.....-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHHHHTTE CS
                     FAA_hydrolase  13 vreagka....aeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsveeAedai 85 
                                       +r+a++       ++ d+++p+  vff +++s  vgp++++ ++a se    E EL+vv+++  +e          i
  gi|336255143|ref|YP_004598250.1| 101 ARKAESSmedmYIDVYDSERPE--VFFKATPSRTVGPDERVGIRADSEWDVPEPELGVVLSD--GE----------I 163
                                       4444333444455666655555..999999****************887667********97..34..........5 PP

                                       EEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEE..TTEEEEEEEG..GGTTT CS
                     FAA_hydrolase  86 aGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrv..ngeevqdsnt..kdmif 158
                                       +Gyt++nD+s R +  ++   l   ++k +d+ ++iGp++ ++d+++dp+dle+++++  +ge++ d +t   +m+ 
  gi|336255143|ref|YP_004598250.1| 164 VGYTIGNDMSSRSIEGRNP--LYLPQAKVYDRCCSIGPCVRSADSVDDPHDLEMWMTIsrDGEVLYDDSTntGKMVR 238
                                       8*************87775..88889****************************9999999999877655449**** PP

                                       SHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE. CS
                     FAA_hydrolase 159 spaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrVa 218
                                       s++el+   ++   ++  +++ltGT        + +  l++gD +e+ +e++G+l n+V+
  gi|336255143|ref|YP_004598250.1| 239 SVEELVDCYTSHNAVPEVSVLLTGTSLV----PDDDFTLREGDLIEIGVEDIGTLSNTVV 294
                                       ********99999************944....67899*********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2290.22
//
Query:       gi|336255144|ref|YP_004598251.1|  [L=608]
Description: ABC transporter periplasmic protein [Halopiger xanaduensis SH-6]
Scores for 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   88.9   1.4    2.2e-24   86.1   1.4    2.1  1  SBP_bac_5   Bacterial extracellular solute-binding proteins, 
  ------ inclusion threshold ------
        1.2    9.1   7.0        1.8    8.5   7.0    1.3  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   1.4   2.5e-28   2.2e-24       1     353 [.     110     476 ..     110     500 .. 0.76

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 2.5e-28
                                       SEEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTE CS
                         SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddyt 77 
                                       e+vp++Ae+ w+v +D++ +++ L ++  ++DG+++tAeD+++ ++       ++g  +++   + +++v avddyt
  gi|336255144|ref|YP_004598251.1| 110 EYVPRVAED-WTVGEDNL-VEVQLSEDYGWHDGSDITAEDFAARIRMDC--YMQMGLEQYI---DPDEGVRAVDDYT 179
                                       69*******.7*******.************************555433..3444444444...479********** PP

                                       EEEEESSETT.............TTTTHCHHHHHHHGC..CHTCTCTTTTTGTTTSE-BSSS.EEEEEEETTTEEEE CS
                         SBP_bac_5  78 vrftlkkpna.............lfltllaavpasiak..kaaekeddkdkdtnekpvgtGP.Yklkefkpgqkivl 138
                                       ++++    +a             ++l++ a++  ++ +  +  + ++++  +  e+++g  P +  ++f+       
  gi|336255144|ref|YP_004598251.1| 180 LEIEPRDDYAnleqglweaqwaeTLLSVSAEQYGDFLEqfE-EASSEEEQQTVQEEVIGFEPeWNQVKFSG-PLFYA 254
                                       ****9999999988888887665444444444444444643.344555588899999**999455555544.58889 PP

                                       EE-TTS..TTTSCSSSSEEEEEE-...SHHHHHHHHHTTSSSEE.ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEE CS
                         SBP_bac_5 139 ernpdY..wgggkpkldriefkvip..dsdaraaalqsGeiddv.aepppsdieqlkeakglkvlyespgggvtyla 210
                                       e+n++Y  ++++++++    + +++     +  a +qsG++d++ ++p+++ ++  ++++ + +     +g++  + 
  gi|336255144|ref|YP_004598251.1| 255 EANEQYgdRVPNQNHPIAKDWDFYQrcGYYTGEAGMQSGDADWIhNDPTLEGLPDKYDSPPVSY-----SGQSLAII 326
                                       99****433455556666677777543677778888*****98866677777777777777777.....88888888 PP

                                       ETTT.STGGGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH..........SHHHHHH CS
                         SBP_bac_5 211 fNtk.kppfddkrvRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka..........ydpekAk 276
                                       f  +  ++ d+++vR+A++yA+D e + ++     +tp + + + + +g+ e++ ++  +           d + A 
  gi|336255144|ref|YP_004598251.1| 327 FGAEdEYIRDNPEVRKAIAYAVDMENVTEVT--APGTPVDEYSGGIDSGYIENFVSE--DvldampnyapQDTDRAA 399
                                       88884556688********************..455666666666666666666654..2346777777789***** PP

                                       HHHHHTT-BCSSTSCEETCEEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEE CS
                         SBP_bac_5 277 klLkeaGykdgdggglrekklkltlllasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmill 353
                                       +lL+e G+  +++++ +++   + +l  + +   ++  e++ ++l++ Gi+v+  + +  +++ ++++d  +d+ ++
  gi|336255144|ref|YP_004598251.1| 400 ELLEEVGFSRNGDDMWETPDGDTWTLNFPVGDWFEDHSEMVYNNLAEFGIDVDWYVEEMPTWQSDTQNDLAYDLTIH 476
                                       ***************99997777777888889999******************888865466667788888888876 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.0    0.0002       1.8       2      24 ..      11      33 ..      11      35 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0002
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      lSRR  L  ++A++AA+++g  +
  gi|336255144|ref|YP_004598251.1| 11 LSRRKMLALTGATGAATLAGCSG 33
                                      6*************999766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4492.48
//
Query:       gi|336255145|ref|YP_004598252.1|  [L=357]
Description: glucose-fructose oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-20   72.7   0.3    9.9e-20   71.6   0.3    1.6  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    0.00011   22.2   0.0    0.00028   20.9   0.0    1.7  2  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
      0.006   17.0   0.1      0.012   16.1   0.1    1.4  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
  ------ inclusion threshold ------
       0.16   12.1   0.1        0.4   10.7   0.0    1.7  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> 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 !   71.6   0.3   2.2e-23   9.9e-20       1     111 [.      28     142 ..      28     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 2.2e-23
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH.HHHTTHE...EESSHHHHHTCTTESEEEE-S-GG CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeav.aesfgve...aysdleelladpeidavivatpng 73 
                                       +r+a++G+G+ +++ + p  e++ + e + +++++ae+a++v ae+  ve   + +++ + +a ++ dav+v+tpn 
  gi|336255145|ref|YP_004598252.1|  28 VRFALVGLGWWTKERAMPAIENSTFCETTVVVSRSAEKAQRVaAEHDAVEaglSSEEFHDGAAADAYDAVYVCTPNA 104
                                       589********888888888888999****************766677776655555666666678*********** PP

                                       GHHHHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHH CS
                      GFO_IDH_MocA  74 theelakaaleagkhvllEKPlattveeakelvelaek 111
                                        h e+++ a+++gk+vl+EKP+ +t+e a++l+++a+ 
  gi|336255145|ref|YP_004598252.1| 105 RHLEFVESAAARGKAVLCEKPMEATLERAERLADAAAD 142
                                       ***********************************986 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   6.3e-08   0.00028       1     104 [.     161     262 ..     161     269 .. 0.73
   2 ?   -3.3   0.0       1.9   8.7e+03      67      84 ..     302     318 ..     296     335 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.3e-08
                                       HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSH..HCSTSHHHHTCHHHHHHHHHHHTSEEEEEE..EEE.SEE CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrk..kksgGvlgdlgiHdiDllqwLfGqppsvva..algrmrq 73 
                                       +el+++g++G++v+v++    ++ + + + +w+ ++  +++g +++dlgi+ ++ +++ + ++p+ v+  +  +  +
  gi|336255145|ref|YP_004598252.1| 161 RELVREGAIGDPVHVHG-NMSQSITGWGPDQWRLDPdlAGPGTSVTDLGIYPLNTTRFVLESDPVAVQsmMDSSHEY 236
                                       79**************5.555667889999999999*******************************9743333333 PP

                                       ESCTCCSCSEEEEEEEEEEETTEEEEEEEEC CS
                    GFO_IDH_MocA_C  74 naeaaededaavmsvlnlekgsgevitlesg 104
                                         + +++  a+    +++e+g++++   +++
  gi|336255145|ref|YP_004598252.1| 237 FEDVPDEVAAF---NVTFEDGTLASC--TAS 262
                                       33333333333...355555555544..444 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.9
                                       EEE.SEEESCTCCSCSEE CS
                    GFO_IDH_MocA_C  67 algrmrqnaeaaededaa 84 
                                       +++ + q++ ++e++d++
  gi|336255145|ref|YP_004598252.1| 302 DIE-TPQVDQMEEEFDYF 318
                                       553.67888888999988 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 !   16.1   0.1   2.6e-06     0.012      17      93 ..      45     120 ..      30     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.6e-06
                                       HHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEE.GGGGGCTT-SEEEE-SCHHHHHHHHHHHHHTTSE CS
                    Semialdhyde_dh  17 rlLeehpevelvvllsssrsaGkklaeavkaleegkdlkved.vdeeelkevdivflalpagvskelapklaeagvk 92 
                                         +e++  +e +v++s+s ++ +++a+ +   + ++ l+ e+  d ++ ++ d v  ++p+  + e+++++a++g  
  gi|336255145|ref|YP_004598252.1|  45 PAIENSTFCETTVVVSRSAEKAQRVAAEHD--AVEAGLSSEEfHDGAAADAYDAVYVCTPNARHLEFVESAAARGKA 119
                                       567888889999999999999999999988..66677777776778888*************************998 PP

                                       E CS
                    Semialdhyde_dh  93 v 93 
                                       v
  gi|336255145|ref|YP_004598252.1| 120 V 120
                                       7 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     9e-05       0.4      16      83 ..      31     101 ..      22     120 .. 0.69
   2 ?   -3.6   0.0       2.3     1e+04      45      58 ..     129     142 ..     126     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9e-05
                                       EEES-SHHH.HHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHH..HHHHT-SEEEE-S CS
                      Shikimate_DH  16 lliGaGema.elvakhLlak.gvkkvvvaNRtlerakelaeelkgeeiealkleelk..ellaeadvvisat 83 
                                        l+G G    e+++ ++ ++  ++  vv+ R+ e+a+++a e++++e+     ee +  ++ +++d v ++t
  gi|336255145|ref|YP_004598252.1|  31 ALVGLGWWTkERAMPAIENStFCETTVVVSRSAEKAQRVAAEHDAVEAGLS-SEEFHdgAAADAYDAVYVCT 101
                                       5677776441455666666535788899***************98865433.23333112455667776666 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.3
                                       SHHHHHHHHHHHT. CS
                      Shikimate_DH  45 tlerakelaeelkg 58 
                                       tlera++la+   +
  gi|336255145|ref|YP_004598252.1| 129 TLERAERLADAAAD 142
                                       78999999987755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2807.17
//
Query:       gi|336255146|ref|YP_004598253.1|  [L=353]
Description: oligopeptide/dipeptide ABC transporter ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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-23   83.5   0.0    2.6e-23   83.1   0.0    1.2  1  ABC_tran   ABC transporter
    6.3e-18   65.1   0.1    1.2e-17   64.1   0.1    1.5  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    3.2e-09   37.0   0.2    5.8e-07   29.6   0.2    2.2  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    1.4e-05   24.6   0.3      0.032   13.7   0.0    2.2  2  SMC_N      RecF/RecN/SMC N terminal domain
    0.00013   22.3   0.2       0.29   11.4   0.0    2.2  2  AAA_22     AAA domain
    0.00093   18.9   0.1      0.002   17.8   0.1    1.5  1  AAA_29     P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.026   14.9   0.0      0.058   13.8   0.0    1.5  1  AAA_16     AAA ATPase domain
      0.032   13.7   0.1        1.1    8.6   0.0    2.3  2  TniB       Bacterial TniB protein
      0.033   13.8   0.0       0.22   11.1   0.0    2.0  2  AAA_25     AAA domain
      0.049   13.4   0.0       0.56    9.9   0.0    2.1  2  IstB_IS21  IstB-like ATP binding protein
      0.073   13.2   0.0       0.15   12.1   0.0    1.5  1  DUF87      Helicase HerA, central domain
       0.11   12.4   0.0       0.18   11.7   0.0    1.3  1  NACHT      NACHT domain
       0.23   10.8   0.0        1.7    7.9   0.0    2.0  2  ATPase     KaiC


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 !   83.1   0.0   1.9e-26   2.6e-23       1     137 []      40     201 ..      40     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 1.9e-26
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG.........B-HHHCCHCEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx.........xxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke.........qeleslrkeigvlp 65 
                                       l++vs+++++ge++++vGe+G+GKS ++ +l+  + +     Gei++  kd +          + +e   ++i++++
  gi|336255146|ref|YP_004598253.1|  40 LNDVSMDIHRGETLGVVGESGSGKSMFADALLDAVVDpgiLTGEITFYPKDGEPidvlnlepwELRELRWEKISMVF 116
                                       799**************************9998776558889999887666665666888886666777799***** PP

                                       SS..--S-TTSBHHHH..........HHHTCHHHHHHHSTTGGTTCBG.ESTTSGGS-HHHHHHHHHHHHHHHTSSE CS
                                       xx..xxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  66 qe..pqlfpeltvren..........esdeeiekalsklglkelkdtv.vksspssLSgGqkqrvalarallkkpkl 129
                                       q   + ++p+++++e+          +++e +e+a++ +++ +l+ ++ ++s p++LSgGqkqr  +a +l+ +p++
  gi|336255146|ref|YP_004598253.1| 117 QGamSAFNPTMSIGEHfeetldahnwDKEEGLERARELFSDLHLEPDRmMSSYPHELSGGQKQRALIALSLILEPEV 193
                                       **99999**************999865555589999988888876555055666*********************** PP

                                       EEEESTTT CS
                                       xxxxxxxx RF
                          ABC_tran 130 lllDEpta 137
                                       l++DEpta
  gi|336255146|ref|YP_004598253.1| 194 LVMDEPTA 201
                                       ******97 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.1     9e-21   1.2e-17       1      65 []     252     316 ..     252     316 .. 0.99

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 9e-21
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE g++++++ ++ HPYT+aLl+s+p ld   d+++ i+ge p++  +++GC ++pRCp   e C
  gi|336255146|ref|YP_004598253.1| 252 VEVGEANEILGNSVHPYTRALLKSTPNLDISLDEMRPIEGESPDPVSHPQGCSYHPRCPLGDERC 316
                                       8***********************************************************99999 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 !    5.4   0.0    0.0097        13       3      22 ..      54      73 ..      53     113 .. 0.73
   2 !   29.6   0.2   4.2e-10   5.8e-07     234     299 ..     170     233 ..     133     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0097
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                      +++G  gsGKS + dal  +
  gi|336255146|ref|YP_004598253.1| 54 GVVGESGSGKSMFADALLDA 73
                                      589**************443 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 4.2e-10
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                                       ++elS G+k+ + ++++l+  +    +l+ DEp + L+  ++r++l ll +++ + ++ +++ +H+ 
  gi|336255146|ref|YP_004598253.1| 170 PHELSGGQKQRALIALSLILEP---EVLVMDEPTAALDLLMQRSILNLLyDIKDKYNVTLVFISHDL 233
                                       6899*******77777777777...9***********************75565588********94 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 !    9.1   0.1   0.00059      0.81      20      44 ..      45      70 ..      34      73 .. 0.78
   2 !   13.7   0.0   2.3e-05     0.032     135     201 ..     163     235 ..     106     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00059
                                      EETTSSEE.EEEESTTSSHHHHHHHH CS
                                      xxxxxxxx.xxxxxxxxxxxxxxxxx RF
                             SMC_N 20 lpfsksft.aivGpNGSGKsnlldAi 44
                                      ++++++ t  +vG+ GSGKs + dA+
  gi|336255146|ref|YP_004598253.1| 45 MDIHRGETlGVVGESGSGKSMFADAL 70
                                      55555544269**************8 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.3e-05
                                       T........CS-HHHH..HHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSH CS
                                       x........xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                             SMC_N 135 e........lLSgGek..tLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislre 199
                                       +        +LSgG+k  +L+al+L+      +p+   ++De  aaLD    + + +ll   +++  + ++ is++ 
  gi|336255146|ref|YP_004598253.1| 163 DrmmssyphELSGGQKqrALIALSLI-----LEPEV-LVMDEPTAALDLLMQRSILNLLYDIKDKynVTLVFISHDL 233
                                       3555555559****983357888888.....46765.58***********999999999855544115566666665 PP

                                       HH CS
                                       xx RF
                             SMC_N 200 em 201
                                        +
  gi|336255146|ref|YP_004598253.1| 234 PI 235
                                       55 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00021      0.29      10      29 ..      55      74 ..      47      97 .. 0.86
   2 !    8.7   0.1    0.0014       1.9      58     128 ..     152     229 ..     136     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                            AAA_22 10 vtGesGtGKTtllrrlleql 29
                                      v+GesG+GK++ +  ll+  
  gi|336255146|ref|YP_004598253.1| 55 VVGESGSGKSMFADALLDAV 74
                                      89***********9999865 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0014
                            AAA_22  58 rellralglelka.erlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLrsllnlsrkgvql 125
                                       rel+++l+le ++      +el   + ++al a +    +e+l+ DE    l+   +  +l+ L ++ +  +++v+l
  gi|336255146|ref|YP_004598253.1| 152 RELFSDLHLEPDRmMSSYPHELSgGQKQRALIALSLilePEVLVMDEPTAaLDllmQRSILNLLYDIKD--KYNVTL 226
                                       6677777777777634444555558888888888889999*******8887878778************..****** PP

                            AAA_22 126 iLv 128
                                       +++
  gi|336255146|ref|YP_004598253.1| 227 VFI 229
                                       *98 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 !   17.8   0.1   1.5e-06     0.002      13      43 ..      41      71 ..      38      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiq 43
                                      ++ +++i++ ++  ++G+sGsGKS + DA+ 
  gi|336255146|ref|YP_004598253.1| 41 NDVSMDIHRGETLGVVGESGSGKSMFADALL 71
                                      55788999777778**************986 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   4.2e-05     0.058      22      55 ..      48      81 ..      37      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekdggif 55
                                      +r+e + ++GesG+GKs  +++ll+a+ + g+++
  gi|336255146|ref|YP_004598253.1| 48 HRGETLGVVGESGSGKSMFADALLDAVVDPGILT 81
                                      45588999****************9998886544 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.062        85      33      52 ..      48      67 ..      38      73 .. 0.84
   2 ?    8.6   0.0   0.00079       1.1     105     160 ..     176     229 ..     163     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.062
                              TniB 33 krmpnlllvGdsnnGKtmiv 52
                                      +r + l +vG+s  GK+m +
  gi|336255146|ref|YP_004598253.1| 48 HRGETLGVVGESGSGKSMFA 67
                                      6778899**********976 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00079
                              TniB 105 skleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                        +++++ ++l   l+++vL++DE   +l      qr +ln+l  +++++++++v +
  gi|336255146|ref|YP_004598253.1| 176 GQKQRALIALSLILEPEVLVMDEPTAAL--DLLMQRSILNLLYDIKDKYNVTLVFI 229
                                       5666677777777899********9999..8999*******************975 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   0.00016      0.22      17      61 ..      35      83 ..      19     109 .. 0.73
   2 ?    0.1   0.0      0.38   5.3e+02     166     188 ..     209     231 ..     195     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                            AAA_25 17 apppprrwlvkgllpagelallaGapgtGKttlaldlalava.....tGk 61
                                       +   ++++ +++  +ge+  ++G +g+GK+++a  l  av+     tG+
  gi|336255146|ref|YP_004598253.1| 35 GTSNVLNDVSMDI-HRGETLGVVGESGSGKSMFADALLDAVVdpgilTGE 83
                                      5555566666666.6899999****************9999854444444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.38
                            AAA_25 166 galvealeriarrtgaavllvhH 188
                                       +++++ l +i+++++++++++ H
  gi|336255146|ref|YP_004598253.1| 209 RSILNLLYDIKDKYNVTLVFISH 231
                                       678888999************99 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 ?    9.9   0.0    0.0004      0.56      44      75 ..      47      78 ..      23      86 .. 0.85
   2 ?    1.0   0.0      0.23   3.1e+02     100     151 ..     182     235 ..     160     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0004
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialgveavrag 75
                                      i++ e + ++G sG GKs +a al  + v  g
  gi|336255146|ref|YP_004598253.1| 47 IHRGETLGVVGESGSGKSMFADALLDAVVDPG 78
                                      7889999****************987777655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.23
                         IstB_IS21 100 aralkrllkvdllilDd..lgllpldqaeaellfeviekryerrsiiitsnlpf 151
                                         al+ +l++++l++D+   +l  l q +  +l+  i+++y+ + + i+ +lp+
  gi|336255146|ref|YP_004598253.1| 182 LIALSLILEPEVLVMDEptAALDLLMQRSILNLLYDIKDKYNVTLVFISHDLPI 235
                                       44567788999*****94345556667777777777899999999999888875 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   0.0   0.00011      0.15      26      51 ..      53      77 ..      37      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                             DUF87 26 lAilgsTGsGKSntvavLleellekk 51
                                      l+++g++GsGKS ++  Ll+ ++ ++
  gi|336255146|ref|YP_004598253.1| 53 LGVVGESGSGKSMFADALLDAVV-DP 77
                                      79*****************9888.65 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   0.00013      0.18       2      24 ..      52      74 ..      51      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                      CEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                      ++ + Ge+GsGK++++  l +a 
  gi|336255146|ref|YP_004598253.1| 52 TLGVVGESGSGKSMFADALLDAV 74
                                      56699************999876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0012       1.7      16      37 ..      47      68 ..      37      75 .. 0.89
   2 ?    0.2   0.0      0.29   3.9e+02     138     163 ..     206     231 ..     185     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0012
                            ATPase 16 ipegrvvlitGepGtGKtifal 37
                                      i +g++  ++Ge+G+GK++fa 
  gi|336255146|ref|YP_004598253.1| 47 IHRGETLGVVGESGSGKSMFAD 68
                                      7799999*************96 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.29
                            ATPase 138 avaReilrqlvrvlkklgvTailvse 163
                                        + R+il  l+ +  k++vT +++s 
  gi|336255146|ref|YP_004598253.1| 206 LMQRSILNLLYDIKDKYNVTLVFISH 231
                                       5678888888888899*******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 2930.19
//
Query:       gi|336255147|ref|YP_004598254.1|  [L=386]
Description: oligopeptide/dipeptide ABC transporter ATPase [Halopiger xanaduensis SH-6]
Scores for 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-28   98.7   0.0    5.5e-28   98.2   0.0    1.2  1  ABC_tran     ABC transporter
    1.1e-15   57.9   0.5    2.2e-15   56.9   0.5    1.5  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    7.4e-05   22.7   2.0      0.072   12.9   0.2    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00036   20.8   0.2     0.0019   18.5   0.2    2.1  1  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.017   14.9   0.2      0.034   13.9   0.2    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.084   12.8   0.0       0.14   12.0   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
       0.11   12.3   0.0       0.15   11.8   0.0    1.2  1  AAA_24       AAA domain
       0.11   12.5   0.0        0.2   11.7   0.0    1.3  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
       0.12   11.5   0.0       0.18   11.0   0.0    1.2  1  NB-ARC       NB-ARC 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 !   98.2   0.0   2.8e-31   5.5e-28       2     136 ..      48     206 ..      47     207 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 2.8e-31
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG........B-HHHCCHCEEEE-SS..- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxx..x RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke........qeleslrkeigvlpqe..p 68 
                                       +++sl+l e+ ++a+vGe+G+GK+tL k++ gl++pt+G+++++g+d+ +        ++ e+ r+++++++q+  +
  gi|336255147|ref|YP_004598254.1|  48 DDISLDLGENDVLALVGESGSGKTTLGKTMVGLTRPTSGSVEYRGHDIWDvregeddeITFEEIRRSLQIIHQDpgS 124
                                       89***********************************************99*****99999*************999 PP

                                       -S-TTSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEE CS
                                       xxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  69 qlfpeltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkll 130
                                        l+p  +v en               e++ +i k+l++ g++  +++ +++  ++LSgG++qrval rall +p+++
  gi|336255147|ref|YP_004598254.1| 125 ALNPYRSVLENlevplkrwhpelnyaERRGRILKLLERTGISP-PEDYAERYVHQLSGGEQQRVALIRALLVEPEVI 200
                                       9**********************97777777999999999998.888899999************************ PP

                                       EEESTT CS
                                       xxxxxx RF
                          ABC_tran 131 llDEpt 136
                                       l+DE+ 
  gi|336255147|ref|YP_004598254.1| 201 LADEAV 206
                                       ****96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.5   1.1e-18   2.2e-15       1      65 []     262     332 ..     262     332 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 1.1e-18
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerlde........GCpFapRCpfaleeC 65 
                                       vE g++++++++p+HPYTk L  ++p+ld+e+   e++  e p ++++d         GC+F++RCp a+e+C
  gi|336255147|ref|YP_004598254.1| 262 VELGTAEEIIQNPKHPYTKVLQWATPELDPEQA--EQAMRESPPVRKIDIpdatnppsGCRFHTRCPKAREAC 332
                                       8********************************..44444444333333333445555*************** 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 !    9.9   0.1    0.0003       0.6       3      24 ..      61      82 ..      59     100 .. 0.77
   2 !   12.9   0.2   3.6e-05     0.072     166     299 ..      96     239 ..      81     240 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0003
                            AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                      +l+G  gsGK++L +++ +l r
  gi|336255147|ref|YP_004598254.1| 61 ALVGESGSGKTTLGKTMVGLTR 82
                                      89**************999965 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.6e-05
                            AAA_21 166 igllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer............gvvflengdgq 230
                                       +++ +  +d+++f +++r lq     +  + ++++  +e  e + ++ ++++ +             + +  ++d+ 
  gi|336255147|ref|YP_004598254.1|  96 WDVREGEDDEITFEEIRRSLQIIHQDPGSALNPYRSVLENLEVPLKRWHPELNYaerrgrilklleRTGISPPEDYA 172
                                       5555666777777888888888888888888888888777777777777777778888888888889999999**** PP

                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                       e+ +++lS G ++  al+ all  +    ++l DE  + L+ +l   +++l+ e ++  ++ +++ +H+ 
  gi|336255147|ref|YP_004598254.1| 173 ERYVHQLSGGEQQRVALIRALLVEP---EVILADEAVSALDVSLRIGVMDLFLEMQEiFDTSFVFISHDL 239
                                       **************9*******999...9***********************5555559*********85 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   9.4e-07    0.0019       6     104 ..      58     210 ..      54     240 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.4e-07
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee........................erpevvfvtlpsstsskdllr 58 
                                        +l+++GesG+GKTtl ++++                                   e ++ + +  + ++s  + +r
  gi|336255147|ref|YP_004598254.1|  58 DVLALVGESGSGKTTLGKTMVGLTRPT----SgsveyrghdiwdvregeddeitfeEIRRSLQIIHQDPGSALNPYR 130
                                       5799**************999876322....1335579999999999987777776555666888888888899999 PP

                            AAA_22  59 ellralglelka.............................erlsseellealeqalrarav........ielliiD 98 
                                        +l++l+++lk+                             +    e+++++l    ++r +        +e+++ D
  gi|336255147|ref|YP_004598254.1| 131 SVLENLEVPLKRwhpelnyaerrgrilkllertgisppedyA----ERYVHQLSGGEQQRVAlirallvePEVILAD 203
                                       999999999999997777777777777776666555532221....2222222222222222444556677777777 PP

                            AAA_22  99 Eaqh.lr 104
                                       Ea   l+
  gi|336255147|ref|YP_004598254.1| 204 EAVSaLD 210
                                       7766565 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 ?   13.9   0.2   1.7e-05     0.034      15      38 ..      50      73 ..      43      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTl 38
                                       ++++ ++++  l+G+sGsGK+Tl
  gi|336255147|ref|YP_004598254.1| 50 ISLDLGENDVLALVGESGSGKTTL 73
                                      445556666999***********8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.1e-05      0.14      88     122 ..      45      80 ..       9      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       +++++++  l + ++ +lvG+SG GK+tL +++++ 
  gi|336255147|ref|YP_004598254.1|  45 HAVDDISLDLGEnDVLALVGESGSGKTTLGKTMVGL 80 
                                       566777777766699**************9888765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.6e-05      0.15       4      23 ..      59      80 ..      56     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.6e-05
                            AAA_24  4 kiliyGpsgiGKTtlakel..g 23
                                       ++++G+sg+GKTtl k++   
  gi|336255147|ref|YP_004598254.1| 59 VLALVGESGSGKTTLGKTMvgL 80
                                      5799*************99553 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.9e-05       0.2       9      40 ..      49      78 ..      40      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.9e-05
                                      HHHHHHHHCHTEEEEEEESTTSSHHHHHHHHH CS
                              TsaE  9 algkklakalgdvilLeGdLGaGKTtlvrgla 40
                                      ++  +l++  +dv++L G+ G+GKTtl + ++
  gi|336255147|ref|YP_004598254.1| 49 DISLDLGE--NDVLALVGESGSGKTTLGKTMV 78
                                      45555555..899**************99876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     9e-05      0.18      17      40 ..      56      77 ..      43     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9e-05
                                      TSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqi 40
                                      e +  v+alvG  G+GKttl k +
  gi|336255147|ref|YP_004598254.1| 56 END--VLALVGESGSGKTTLGKTM 77
                                      455..9**************8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 3088.99
//
Query:       gi|336255148|ref|YP_004598255.1|  [L=54]
Description: hypothetical protein Halxa_3770 [Halopiger xanaduensis SH-6]
Scores for 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:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 463.55
//
Query:       gi|336255149|ref|YP_004598256.1|  [L=82]
Description: hypothetical protein Halxa_3771 [Halopiger xanaduensis SH-6]
Scores for 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   12.8   6.9       0.11   12.5   6.9    1.1  1  Sensor    Putative sensor
        0.3   11.1   8.0        3.7    7.6   3.4    2.1  2  DUF3561   Protein of unknown function (DUF3561)
       0.35    9.6   5.8        0.4    9.4   5.8    1.0  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> Sensor  Putative sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   6.9   1.9e-05      0.11      93     154 ..      13      75 ..       9      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                            Sensor  93 ylllhfplglvlfvvavvllalalalltaPl.wtlpeallvavlGlllllvllwvvrglarlq 154
                                       yll+  p++ vlf++avv  +l++ + +  l +  +++l+ +v+G +++ + ++ + +l +++
  gi|336255149|ref|YP_004598256.1|  13 YLLALVPIACVLFTFAVVASVLGANTWAGFLaLYTMAVLIICVIGHVAVYTIAYSTEVLRQWR 75 
                                       899999999999999999866666666544433458899999999999999999999998776 PP

>> DUF3561  Protein of unknown function (DUF3561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.9    0.0019        11      56      71 ..       9      24 ..       3      37 .. 0.72
   2 ?    7.6   3.4   0.00062       3.7      56      87 ..      37      68 ..      24      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0019
                           DUF3561 56 ytWPfflallPvsvlv 71
                                      +  P++lal+P++ ++
  gi|336255149|ref|YP_004598256.1|  9 FEHPYLLALVPIACVL 24
                                      668********98664 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00062
                           DUF3561 56 ytWPfflallPvsvlvGvalsvllrgkllysi 87
                                       tW  flal  ++vl+  ++  +    + ys+
  gi|336255149|ref|YP_004598256.1| 37 NTWAGFLALYTMAVLIICVIGHVAVYTIAYST 68
                                      59************998888888888888876 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   5.8   6.7e-05       0.4     383     434 ..      14      65 ..       8      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 6.7e-05
                           DUF2207 383 lsalglgliilglilillallllvlllvfllilllillliaiivlllfsrll 434
                                       l al  ++++l+++++++++l+++++  fl+++++++l+i++i  +  +++ 
  gi|336255149|ref|YP_004598256.1|  14 LLALVPIACVLFTFAVVASVLGANTWAGFLALYTMAVLIICVIGHVAVYTIA 65 
                                       7788899999999999999999999999999999999999999988886644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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 0.21s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 696.50
//
Query:       gi|336255150|ref|YP_004598257.1|  [L=691]
Description: alpha-glucuronidase [Halopiger xanaduensis SH-6]
Scores for 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-134  446.5   0.0   6.1e-134  446.2   0.0    1.1  1  Glyco_hydro_67M  Glycosyl hydrolase family 67 middle domain
    1.2e-83  280.1   0.0    1.8e-83  279.5   0.0    1.3  1  Glyco_hydro_67C  Glycosyl hydrolase family 67 C-terminus
    1.1e-26   93.5   0.0    1.7e-26   92.9   0.0    1.3  1  Glyco_hydro_67N  Glycosyl hydrolase family 67 N-terminus
  ------ inclusion threshold ------
       0.19   11.1   0.0       0.31   10.4   0.0    1.2  1  DUF4838          Domain of unknown function (DUF4838)


Domain annotation for each model (and alignments):
>> Glyco_hydro_67M  Glycosyl hydrolase family 67 middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.2   0.0  1.4e-137  6.1e-134       3     325 .]     136     464 ..     134     464 .. 0.96

  Alignments for each domain:
  == domain 1  score: 446.2 bits;  conditional E-value: 1.4e-137
                                       HTT---TT-EEEE--SSSEEEEE--B-TT.S-BTT--S-S-S.--CCCTTT---HHHHHHHHHHTTT--EEE-S-SS CS
                   Glyco_hydro_67M   3 qtgksleeleiaekPkaklRllnhWdnld.gsvERgyaGesiffeeeklaedldrvkdyarllasvgingvvlnnvn 78 
                                       + g+++++l+++e+P+++ R++nhWdn   +svERgyaG+si f++e+l++  +r+ dyarllasvgingvv nnvn
  gi|336255150|ref|YP_004598257.1| 136 ALGEPIDDLDVVEEPANNSRIINHWDNPFrRSVERGYAGQSI-FDWERLPDVRERYYDYARLLASVGINGVVPNNVN 211
                                       5688999********************86589**********.********************************** PP

                                       -.............-GG....GGSHHHHHHHHHHHHHHGGGT-EEEEEE-TTHHHHTTS-S---TTSHHHHHHHHHH CS
                   Glyco_hydro_67M  79 a.............kak....lltkeylekvaaladvlrpygikvylsvnfaapielggletadPldeevkkwWkek 138
                                       +             + +    ll++++lek++ala+v+r+ygi++ylsvn+aapi+lggletadP d+ev++wW++k
  gi|336255150|ref|YP_004598257.1| 212 TgipsrptandavsE-RagwqLLERDNLEKLEALASVFRRYGIRIYLSVNYAAPIKLGGLETADPHDSEVRQWWQDK 287
                                       *99999999887761.14566******************************************************** PP

                                       HHHHHHH-TT--EEEE--SBTTB--GGGGT--HHHHHHHHHHHHGGGT-EEEEE-----.....TTSS-GGGHHHHH CS
                   Glyco_hydro_67M 139 vkeiyeaipdfgGflvkAdsEgqpGPltygrthadganmlaealkpyggiviwRaFvYnaqdwrdkkedRakaayee 215
                                       v+eiye+ipdfgGflvkAdsEgqpGP++y+r+ha+gan+l+ea++ ++g v+wRaFvY++      ++dRa +aye 
  gi|336255150|ref|YP_004598257.1| 288 VDEIYEIIPDFGGFLVKADSEGQPGPYDYDRSHAEGANVLGEAFEGHDGRVWWRAFVYSE------HDDRAVQAYEA 358
                                       **********************************************************98......99********* PP

                                       HGGGTT-S-TTEEEEEESSSSSS-SS----THHHH-SSSEEEEEEE-S-TTTTTTTS----HHHHHHHHT-B--TTS CS
                   Glyco_hydro_67M 216 FkpldgkfkdnvilqiknGpiDfqvrEpvsplfgalektnlalElqitqEylGqqthlvylaplwkevldfdtyakg 292
                                       F+++dg+f+d+v++qiknGpiDfq rEpvs+lfga+++tnl +Elq+t Ey+Gq  h + ++p+wkevl+fdtya+g
  gi|336255150|ref|YP_004598257.1| 359 FEHIDGEFHDKVTVQIKNGPIDFQQREPVSTLFGAMPETNLGCELQLTGEYTGQGVHATSHIPMWKEVLEFDTYADG 435
                                       ***************************************************************************** PP

                                       TT-BHHHHHTTTTTT-S-EEEEEE----SSTTS CS
                   Glyco_hydro_67M 293 egstvkkvvdgklfkkkltgiagvanvGedenW 325
                                       eg+ vk+v+++    ++ +giagv  vGed +W
  gi|336255150|ref|YP_004598257.1| 436 EGTPVKDVLAE----RDGQGIAGVGIVGEDPSW 464
                                       ********865....6689************99 PP

>> Glyco_hydro_67C  Glycosyl hydrolase family 67 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.5   0.0   4.1e-87   1.8e-83       1     222 [.     465     687 ..     465     688 .. 0.96

  Alignments for each domain:
  == domain 1  score: 279.5 bits;  conditional E-value: 4.1e-87
                                       SSSTTHHHHHHHHHHHHH-TT--HHHHHHHHHHHHT---HHHHHHHHHHHHHHHHHHHHT.T--TT----B-T.... CS
                   Glyco_hydro_67C   1 tGhplaqanlYafGrlawdpelsseeiaeeWirltfskdeevvetvkellleSreayvnY.taplGlhhlvka.... 72 
                                       tG++l q+nlY+f+rl+wdp+l+se+i+eeW+r+tf++deevv+tv+e+ll+S++a+++Y t  lGl h++ +    
  gi|336255150|ref|YP_004598257.1| 465 TGNHLLQSNLYGFARLCWDPDLESETIIEEWARQTFGRDEEVVDTVSEILLDSWQACIDYhTGGLGLMHMMYNgeea 541
                                       89**********************************************************7789*******884433 PP

                                       .TT-SSB-T--SSSGGGSSHH---SSEEE---STTTT-GGGGS-HHHHHHHHSTTTS-GGGGGGT-EEETT-B-TTS CS
                   Glyco_hydro_67C  73 .ghHygpepdkaersdwgtyhradkkgiGvdRtatGtgavaqYaeelaeeyedletcpeelLLwfHhvpythklksG 148
                                        ++Hy+p+p+     +w +y  a+++giGvdRt++G+g++aqY+++++e+y+d+etcpeelLL+fHh+p++++l++G
  gi|336255150|ref|YP_004598257.1| 542 lENHYDPGPE-----EWPEYIGATADGIGVDRTSEGSGYAAQYRDPITERYDDPETCPEELLLFFHHLPWEYELEDG 613
                                       3459999998.....9************************************************************* PP

                                       -BHHHHHHHHHHHHHHHHHHHHHHHHCCCCCS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----TTS CS
                   Glyco_hydro_67C 149 ktliqelydayfegveeveelqktweslegkideerfeevkerleiqaeeakeWrdailtYfqrfskipdekgr 222
                                       +t+iq+lyd+ ++gveev+el+++wesleg +de+r+++v+er+++++ +a++Wrd +++Yf+++s++pdekgr
  gi|336255150|ref|YP_004598257.1| 614 RTVIQTLYDNCYAGVEEVRELRAKWESLEGVVDERRHRHVAERFDEHVLQARRWRDRLCEYFYEHSGVPDEKGR 687
                                       ***********************************************************************987 PP

>> Glyco_hydro_67N  Glycosyl hydrolase family 67 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.0   3.8e-30   1.7e-26       1     122 []       9     131 ..       9     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 3.8e-30
                                       TT------S-HHHHHHHHHH-SEEEE---SHHHHHHHHHHHHHHHHHHTS---EE-SS--SSE..EEEE-TTT-HHH CS
                   Glyco_hydro_67N   1 lWLrYapiedaalkekykalpsaivvlnatstievakqELkeglkgilgkelkvsseekkess..ilvgtleelaei 75 
                                       +WLrY++++d++l   y++ +s+ +v + ++++ ++++EL++gl+g+lg+el++ ++ +++    +++g  ee++ i
  gi|336255150|ref|YP_004598257.1|   9 CWLRYERVDDSKL-APYRERLSHAYVSEGAPELGAVRAELRRGLEGMLGRELHLWQHPPRSVDsfLVIGHPEEMRPI 84 
                                       8************.799************************************777777765558************ PP

                                       HHT--THHHHTTTTT-EEEEEEEETTEEEEEEEESSHHHHHHHHHHH CS
                   Glyco_hydro_67N  76 eslalpeeleelgeeGfllktveveekksvvivgqterGvLYGaFey 122
                                       +++  p+e+ +l+e+G++++tve+e+++ +v+++ ++rG++YG+F++
  gi|336255150|ref|YP_004598257.1|  85 HQTIDPDEVWDLHEDGYVIRTVEWEGHECTVVTAPSDRGLVYGTFHL 131
                                       *********************************************97 PP

>> DUF4838  Domain of unknown function (DUF4838)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0     7e-05      0.31     220     257 ..     467     504 ..     450     511 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7e-05
                           DUF4838 220 sdfaelraYllakllwdpsldvdallddfldayYgaAa 257
                                       ++  + + Y +a+l wdp+l+ +++++++ ++ +g   
  gi|336255150|ref|YP_004598257.1| 467 NHLLQSNLYGFARLCWDPDLESETIIEEWARQTFGRDE 504
                                       5555566799************************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (691 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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: 0.57u 0.21s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 5297.31
//
Query:       gi|336255151|ref|YP_004598258.1|  [L=553]
Description: glycoside hydrolase 10 [Halopiger xanaduensis SH-6]
Scores for 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-35  122.3   0.7    2.2e-35  122.3   0.7    1.5  2  Glyco_hydro_10   Glycosyl hydrolase family 10
    0.00052   20.2   1.1       0.62   10.4   0.4    2.5  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0018   18.5   3.8       0.13   12.6   0.9    2.8  2  Big_3            Bacterial Ig-like domain (group 3)
     0.0099   16.2   1.6        0.3   11.4   0.0    2.6  2  Invasin_D3       Invasin, domain 3
  ------ inclusion threshold ------
       0.15   12.1   0.0       0.15   12.1   0.0    3.0  3  Big_1            Bacterial Ig-like domain (group 1)
       0.17   12.1   0.1       0.17   12.1   0.1    2.7  3  bMG6             Bacterial macroglobulin domain 6
        4.8    7.8   7.3        1.8    9.1   0.3    2.8  3  TipAS            TipAS antibiotic-recognition domain
        5.8    7.3   9.9        5.2    7.4   7.2    2.4  2  Cytomega_UL20A   Cytomegalovirus UL20A protein


Domain annotation for each model (and alignments):
>> Glyco_hydro_10  Glycosyl hydrolase family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.84   1.9e+03     216     258 ..      56      98 ..      47     108 .. 0.74
   2 !  122.3   0.7   9.9e-39   2.2e-35      23     311 ..     129     429 ..     119     434 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.84
                                       HHHHHHHHHHHTTTSEEEEEEEEEECETTSSHHHHHHHHHHHH CS
                    Glyco_hydro_10 216 seieaalkklaalglevaitELDirvkkssseeealeaqakry 258
                                       ++ e+ +++  +  leva+t  D +  +  + e ++++ a+++
  gi|336255151|ref|YP_004598258.1|  56 TAAEERIQEHRTANLEVAVTDADGNELDGAEVEVTMQEHAYDF 98 
                                       5678889999999999999999988777666566666666655 PP

  == domain 2  score: 122.3 bits;  conditional E-value: 9.9e-39
                                       CTTHHHHHHHHH-SEEEESSTTSHHHHCSBTTBEE-HHHHHHHHHHHHTT-EEEEEEEEESS....S--HHHHTS.C CS
                    Glyco_hydro_10  23 geskekellkkefnsltaeNemKwealepsegnftfekadklvdfakennmkvrGHtLvWhs....qlPdwvkke.n 94 
                                       ++++++e++++ fn ++ eN  Kw++ e+++     e ad+ vd+a e++m+vrGH ++W +     +P+ v +   
  gi|336255151|ref|YP_004598258.1| 129 DQQRYRETVDELFNTVVLENLHKWNQWEDNQ-----EIADNAVDWAVERGMNVRGHVCLWGNvdawAIPADVVEAmG 200
                                       44599***********************766.....58***********************9777767776666663 PP

                                       CCHHH..........HHHHHHHHHHHHHHHHHTTTTESEEEEEES-B-TTS......CSBE-SHHHHHHTTHHHHHH CS
                    Glyco_hydro_10  95 gskae..........eallkrlenhiktvverykgkiyawDVVNEavddng......gslresvwyqilGedyiekA 155
                                       +++++          e + +r ++hi++++++y +++++w V NE+++ ++      g+  + +  +ilG d+ ekA
  gi|336255151|ref|YP_004598258.1| 201 IEWEAggatdpdhdpEYVVERANEHIEEIISHYGDDVAEWEVKNEVLHATAmieaveGEDVDPATAEILG-DWYEKA 276
                                       3444455667889999*********************************997754432223355556666.677888 PP

                                       HHHHHHH-TTSEEEEEESSTTST.SHHHHHHH.HHHHHH.HHTT----EEEE--EEETTSC.HHHHHHHHHHHHHTT CS
                    Glyco_hydro_10 156 FeaAreadpdakLyyNDYnieea.nakrkavv.elvkel.kekgvpidgvGiQsHlsvdsp.siseieaalkklaal 228
                                         +A e+d  + + +NDYn  e  +  ++a + + +  l +e+gv +dg+G+Q+H+ +d++ +++e+ a l+++   
  gi|336255151|ref|YP_004598258.1| 277 EAVADEYD--VDIAVNDYNALEGgYDDTQAEYeRQIDYLvNERGVDLDGIGFQCHFANDETlEPDELLADLERYEGY 351
                                       88888886..56789****988855567766635566653789**************999889************** PP

                                       TSEEEEEEEEEECETTSSHHHHHHHHHHHHHHHHHHHHHCTTTEEEEEESSSBGGGSTTHHHSTTEC--SSB-TTS- CS
                    Glyco_hydro_10 229 glevaitELDirvkkssseeealeaqakrykelvkallevkekitgvtvWgvtDkysWlsglkkkeeapllfdsnyq 305
                                       g     tE+D  + +++    + e+q +  ++++k+  +++  +++ +vWg  D   W +++       +lfd + +
  gi|336255151|ref|YP_004598258.1| 352 GAGFRATEFDTFQGNWE----SPEEQGEYLRTFLKTWFSHP-DTDSFLVWGHWDGVHWAPDFDGSDPDGVLFDLDWN 423
                                       **********9998876....68999999************.*******************999999********** PP

                                       B-HHHH CS
                    Glyco_hydro_10 306 pkpaye 311
                                       pkpa +
  gi|336255151|ref|YP_004598258.1| 424 PKPAHD 429
                                       ****76 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0016       3.5       4      24 ..      72      92 ..      69     104 .. 0.83
   2 !   10.4   0.4   0.00028      0.62      38      75 ..     450     484 ..     440     490 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                   CarboxypepD_reg  4 GrVtdasgapiagatVtvtna 24
                                        Vtda+g+ + ga+V+vt +
  gi|336255151|ref|YP_004598258.1| 72 VAVTDADGNELDGAEVEVTMQ 92
                                      57****************954 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00028
                   CarboxypepD_reg  38 GafrlrglppgtysvtvsapGyatatreevtltagqtt 75 
                                       G +  r    g+y++tv+++G +t+t    t+++g++t
  gi|336255151|ref|YP_004598258.1| 450 GVYETR-AFKGEYEITVRYDGAETTTT--ATVSDGGET 484
                                       556644.556****************6..588877654 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 !    5.6   0.1    0.0088        20      18      44 ..      69      97 ..      65     101 .. 0.84
   2 !   12.6   0.9   5.8e-05      0.13      48      68 .]     458     478 ..     443     478 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0088
                             Big_3 18 dlfvsatykdGdaevpfddvevsg...svd 44
                                       l v++t++dG++ ++ ++vev+    ++d
  gi|336255151|ref|YP_004598258.1| 69 NLEVAVTDADGNE-LDGAEVEVTMqehAYD 97
                                      689*********9.********99666666 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 5.8e-05
                             Big_3  48 aGeytvtvtykgvsatftVtV 68 
                                       +Gey++tv+y+g+++t t tV
  gi|336255151|ref|YP_004598258.1| 458 KGEYEITVRYDGAETTTTATV 478
                                       7************99999998 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00014       0.3      19      47 ..      65      93 ..      55     111 .. 0.83
   2 ?    3.1   0.4     0.053   1.2e+02      71      92 ..     458     479 ..     441     503 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                        Invasin_D3 19 kststltvtlkDangnpvsgltvtfstts 47
                                      + t+ l+v ++Da+gn + g++v++++++
  gi|336255151|ref|YP_004598258.1| 65 HRTANLEVAVTDADGNELDGAEVEVTMQE 93
                                      78999*****************9999873 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.053
                        Invasin_D3  71 agtatitptvnGvaiaatatvt 92 
                                       +g++ it+ ++G+++++tatv+
  gi|336255151|ref|YP_004598258.1| 458 KGEYEITVRYDGAETTTTATVS 479
                                       6899999999998888888885 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 ?   12.1   0.0   6.5e-05      0.15       6      31 ..      67      92 ..      65      97 .. 0.89
   2 ?   -2.0   0.0       1.7   3.7e+03      17      33 ..     157     173 ..     156     177 .. 0.82
   3 ?   -1.1   3.4       0.9     2e+03       6      46 ..     471     506 ..     468     507 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.5e-05
                             Big_1  6 tntltatvkDangnpvagatVtfsvs 31
                                      t+ l + v+Da+gn + ga+V +++ 
  gi|336255151|ref|YP_004598258.1| 67 TANLEVAVTDADGNELDGAEVEVTMQ 92
                                      67899****************99975 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                             Big_1  17 ngnpvagatVtfsvsgg 33 
                                       +++ +a+ +V + v  g
  gi|336255151|ref|YP_004598258.1| 157 DNQEIADNAVDWAVERG 173
                                       578899******99875 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.9
                             Big_1   6 tntltatvkDangnpvagatVtfsvsggals.assgtTdanG 46 
                                       ++t tatv D       g tV + ++gg+ s  ss   d++G
  gi|336255151|ref|YP_004598258.1| 471 ETTTTATVSD------GGETVELAIDGGSSSgDSSDDGDDDG 506
                                       4577888888......48899999999888877777777766 PP

>> bMG6  Bacterial macroglobulin domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.4e-05      0.17       8      47 ..      59      98 ..      49     101 .. 0.89
   2 ?   -2.4   0.2       2.3   5.2e+03      58      90 ..     151     184 ..     147     185 .. 0.76
   3 ?    0.5   0.1       0.3   6.6e+02      86     109 ..     455     478 ..     441     481 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.4e-05
                              bMG6  8 dgeveegseaefeivavdadgkkvatkelkvklyreerdy 47
                                      +++++e+++a++e++ +dadg++++  e++v++ +  +d+
  gi|336255151|ref|YP_004598258.1| 59 EERIQEHRTANLEVAVTDADGNELDGAEVEVTMQEHAYDF 98
                                      5899*********************999999999887765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
                              bMG6  58 ryestekdkpvasgtvdlsaegkaklslpv.dwG 90 
                                       ++++ e ++++a++ vd + e+  +++  v  wG
  gi|336255151|ref|YP_004598258.1| 151 KWNQWEDNQEIADNAVDWAVERGMNVRGHVcLWG 184
                                       6788888888899888888888888887777777 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.3
                              bMG6  86 pvdwGrYrleVedeesgaatsvrf 109
                                       +   G+Y+++V+  +++++t  ++
  gi|336255151|ref|YP_004598258.1| 455 RAFKGEYEITVRYDGAETTTTATV 478
                                       55569*******999988777665 PP

>> TipAS  TipAS antibiotic-recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.6         3   6.7e+03      25      66 ..      54      94 ..      41      96 .. 0.58
   2 ?    1.9   0.0      0.14   3.2e+02      24      70 ..     124     169 ..     113     183 .. 0.84
   3 ?    9.1   0.3   0.00079       1.8      34     100 ..     219     284 ..     212     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3
                                      XXXXXXXXXXX.XXXXXXXXXXXX..XXXXXXXXXXXXXXXXX CS
                             TipAS 25 lskedweelka.elkelfaklaaalaagkdpdseeaqelaeeh 66
                                      ++++  e++++ ++++l  ++++a  +g + d +e+   ++eh
  gi|336255151|ref|YP_004598258.1| 54 WETAAEERIQEhRTANLEVAVTDA--DGNELDGAEVEVTMQEH 94
                                      344444444440444444444544..78888888888887777 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.14
                                       XXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXX CS
                             TipAS  24 klskedweelkaelkelfaklaaalaagkdpdseeaqelaeehrali 70 
                                       +++++d++++ + ++elf+ +    + +k  + e+ qe+a++ ++++
  gi|336255151|ref|YP_004598258.1| 124 PFDEDDQQRYRETVDELFNTVVLE-NLHKWNQWEDNQEIADNAVDWA 169
                                       6889**************999877.4577788899999999988886 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00079
                                       XXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TipAS  34 kaelkelfaklaaalaagkdpdseeaqelaeehralieefwg.ecskeilaglgqmYvadprftenyd 100
                                        ++++e ++++ +++  g+d++  e+++ +   +a+ie+  g +++++    lg++Y+  +  +++yd
  gi|336255151|ref|YP_004598258.1| 219 VERANEHIEEIISHY--GDDVAEWEVKNEVLHATAMIEAVEGeDVDPATAEILGDWYEKAEAVADEYD 284
                                       577888888899997..*********************988866********************9999 PP

>> Cytomega_UL20A  Cytomegalovirus UL20A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.3   2.9e+03      68      82 ..      67      81 ..      23      95 .. 0.76
   2 ?    7.4   7.2    0.0023       5.2      32      72 ..     470     512 ..     452     524 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                    Cytomega_UL20A 68 ggdydvlitdtdggn 82
                                        + +v +td+dg +
  gi|336255151|ref|YP_004598258.1| 67 TANLEVAVTDADGNE 81
                                      456677777777754 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0023
                    Cytomega_UL20A  32 veqpststnsdgnttpsknv..tlsqggsttdgdedysggdyd 72 
                                        e  +t+t sdg  t    +    s g s+ dgd+d sggd d
  gi|336255151|ref|YP_004598258.1| 470 AETTTTATVSDGGETVELAIdgGSSSGDSSDDGDDDGSGGDED 512
                                       5788999****99998766622579999*************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); 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:                         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: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 4090.49
//
Query:       gi|336255152|ref|YP_004598259.1|  [L=324]
Description: endo-1,4-beta-xylanase [Halopiger xanaduensis SH-6]
Scores for complete 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-99  333.3   0.0    1.5e-99  333.2   0.0    1.0  1  Glyco_hydro_10  Glycosyl hydrolase family 10
     0.0023   17.4   0.6       0.17   11.3   0.4    2.4  2  Cellulase       Cellulase (glycosyl hydrolase family 5)
     0.0051   16.3   0.0      0.013   14.9   0.0    1.7  2  AP_endonuc_2    Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.064   13.1   0.4       0.16   11.8   0.4    1.7  1  Choline_sulf_C  Choline sulfatase enzyme C terminal


Domain annotation for each model (and alignments):
>> Glyco_hydro_10  Glycosyl hydrolase family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.2   0.0  3.3e-103   1.5e-99       7     315 ..      13     319 ..       6     320 .. 0.96

  Alignments for each domain:
  == domain 1  score: 333.2 bits;  conditional E-value: 3.3e-103
                                       HHTTEEEEEESCHGHHCTTHHHHHHHHH-SEEEESSTTSHHHHCSBTTBEE-HHHHHHHHHHHHTT-EEEEEEEEES CS
                    Glyco_hydro_10   7 kakfkvgtavsaselegeskekellkkefnsltaeNemKwealepsegnftfekadklvdfakennmkvrGHtLvWh 83 
                                       +++f++g+a+++  l  + ++ +++k+efn++t+eN++K+  l+ps+ +++f++ad++v+f  e++m vrGHtLvWh
  gi|336255152|ref|YP_004598259.1|  13 SNEFRIGAALDPDALRVDPSYWKTAKNEFNAVTPENALKMGPLRPSRHTYDFADADAIVNFGVEHDMYVRGHTLVWH 89 
                                       4678***********9999********************************************************** PP

                                       SS--HHHHTSCCCHHHHHHHHHHHHHHHHHHHHTTTTESEEEEEES-B-TTSCSBE-SHHHHHHTTHHHHHHHHHHH CS
                    Glyco_hydro_10  84 sqlPdwvkkengskaeeallkrlenhiktvverykgkiyawDVVNEavddnggslresvwyqilGedyiekAFeaAr 160
                                       +q P w++ ++++ ++  l++ l++hi+tv++ry+ ki awDVVNEav+d+g slre+vw+++lGedy+  AF++A 
  gi|336255152|ref|YP_004598259.1|  90 NQKPGWFQAWDYTPDQ--LRTFLRDHIHTVAGRYRAKIDAWDVVNEAVADDG-SLRETVWSDALGEDYLADAFRWAD 163
                                       *********9998888..*********************************7.9*********************** PP

                                       HH-TTSEEEEEESSTTSTSHHHHHHHHHHHHHHHTT----EEEE--EEETTSCHHHHHHHHHHHHHTTTSEEEEEEE CS
                    Glyco_hydro_10 161 eadpdakLyyNDYnieeanakrkavvelvkelkekgvpidgvGiQsHlsvdspsiseieaalkklaalglevaitEL 237
                                       e+  da LyyNDY  +e n+k++a+++l+++l + gvpidgvG+Q H   d+p++++i ++++++ +lgl+v+itE+
  gi|336255152|ref|YP_004598259.1| 164 EVT-DADLYYNDYGADEVNQKSDAIYDLLEDLLADGVPIDGVGLQLHALGDHPDPESIAENIERFRDLGLDVQITEM 239
                                       997.69*********************************************************************** PP

                                       EEECETTSSHHHHHHHHHHHHHHHHHHHHHCTTTEEEEEESSSBGGGSTTHHHST....TEC--SSB-TTS-B-HHH CS
                    Glyco_hydro_10 238 DirvkkssseeealeaqakrykelvkallevkekitgvtvWgvtDkysWlsglkk....keeapllfdsnyqpkpay 310
                                       D++ +  ++ + a+e qa+ y+e+v+a+ ++   ++++++Wgv+D  sWl+++k      ++ pllfd+ y++kpay
  gi|336255152|ref|YP_004598259.1| 240 DVAFHAGEAPADADEVQADYYREVVEACRDAG--CDTLVTWGVHDGSSWLRSFKDfgerYTGDPLLFDDRYDEKPAY 314
                                       *****99999********************98..******************8879887899*************** PP

                                       HHHHH CS
                    Glyco_hydro_10 311 eavvd 315
                                       +av +
  gi|336255152|ref|YP_004598259.1| 315 DAVKA 319
                                       **975 PP

>> Cellulase  Cellulase (glycosyl hydrolase family 5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.4   3.8e-05      0.17      47     140 ..      55     146 ..      25     168 .. 0.74
   2 ?    3.2   0.0     0.011        50     223     270 ..     218     272 ..     210     284 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.8e-05
                                       GTTSSTTTGCTHHHHHHHHHHHHHHHHTT-EE...EEEEESS.TTTCSSSSTTTTHHHHHHHHHHHHHHHHHHHTTT CS
                         Cellulase  47 lvenapdykvdenslerveevvkyakenglyv...ildiHse.egwltkadgnssedtaeeffkklwtqiAerykkn 119
                                       l ++  +y      +++ +++v+   e+++yv    l +H++ +gw++  d+  + d+ + f+ + +  +A ry   
  gi|336255152|ref|YP_004598259.1|  55 LRPSRHTY-----DFADADAIVNFGVEHDMYVrghTLVWHNQkPGWFQAWDY--TPDQLRTFLRDHIHTVAGRY--R 122
                                       44444555.....788999*************9999******9999666655..55667799************..7 PP

                                       TTTEEEESSSS--STTCT...CCT CS
                         Cellulase 120 devvifelmNEPhgnntg...aew 140
                                        ++ +++++NE    + +   + w
  gi|336255152|ref|YP_004598259.1| 123 AKIDAWDVVNEAVADDGSlreTVW 146
                                       78889******9884444655555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHTTSEEEEEEEESS.TTSSH.......HHHHHHHHHHHHHHHTTT CS
                         Cellulase 223 qrledaakylvekgipviigEfGgs.nadgd.......lakeeaekwldylkekgi 270
                                       ++++++++++++ g+ v i+E+ +  +  g+       ++ ++  +++++ ++ g+
  gi|336255152|ref|YP_004598259.1| 218 ESIAENIERFRDLGLDVQITEMDVAfH-AGEapadadeVQADYYREVVEACRDAGC 272
                                       667888999999999999999998852.3332333333444555555666665554 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 ?   -2.4   0.0      0.59   2.6e+03     120     148 ..      74     110 ..      66     119 .. 0.61
   2 !   14.9   0.0     3e-06     0.013      22     105 ..     209     289 ..     188     313 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.59
                                       HHHHTSEEEEE--TTTTSSSTC........HHHHHHH CS
                      AP_endonuc_2 120 aekegvklalEtlagsgvelgd........eelarll 148
                                       + ++++ +  +tl ++++ +g+        ++l+ +l
  gi|336255152|ref|YP_004598259.1|  74 GVEHDMYVRGHTLVWHNQKPGWfqawdytpDQLRTFL 110
                                       5555666666777777777777655555555555555 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3e-06
                                       HHHC...HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGB CS
                      AP_endonuc_2  22 vsel...sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlhpGtag 95 
                                        +     ++e ++e  +++++lgl +   ++   f++ +    +a+ e + d++++ +e++++ G+++lv++     
  gi|336255152|ref|YP_004598259.1| 209 HALGdhpDPESIAENIERFRDLGLDVQITEMDVAFHAGEA-PADAD-EVQADYYREVVEACRDAGCDTLVTWG---- 279
                                       3333444678899999999******999999999999444.45555.889**********************4.... PP

                                       CTTTSGHHHH CS
                      AP_endonuc_2  96 agpkgseeea 105
                                        ++++s+   
  gi|336255152|ref|YP_004598259.1| 280 VHDGSSWLRS 289
                                       4555555444 PP

>> Choline_sulf_C  Choline sulfatase enzyme C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   3.6e-05      0.16      12      42 ..      86     114 ..      78     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                    Choline_sulf_C  12 lvysalkkGkitsWDyqplddasekYiRnhi 42 
                                       lv+   k G +++WDy+p +     + R hi
  gi|336255152|ref|YP_004598259.1|  86 LVWHNQKPGWFQAWDYTPDQ--LRTFLRDHI 114
                                       89999*************54..566777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2598.76
//
Query:       gi|336255153|ref|YP_004598260.1|  [L=80]
Description: hypothetical protein Halxa_3775 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0044   16.8   0.1      0.016   15.0   0.0    1.8  2  LapA_dom  Lipopolysaccharide assembly protein A domain
  ------ inclusion threshold ------
       0.22   12.0   2.6       0.56   10.7   2.6    1.6  1  DUF202    Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.13   1.2e+03      26      32 ..      18      24 ..      11      32 .. 0.61
   2 !   15.0   0.0   1.7e-06     0.016      28      54 ..      36      62 ..      33      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.13
                          LapA_dom 26 afgiGal 32
                                      ++++Gal
  gi|336255153|ref|YP_004598260.1| 18 SVLVGAL 24
                                      4555554 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.7e-06
                          LapA_dom 28 giGallgwllslwsylrlrrelrrlkk 54
                                      + G+++g l+++ sy+ ++r++r l++
  gi|336255153|ref|YP_004598260.1| 36 VTGVVVGALFGVGSYWEYKRRMRDLDR 62
                                      68*********************9987 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.6   6.3e-05      0.56       7      66 ..       7      57 ..       6      59 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.3e-05
                            DUF202  7 ERTfLaW.lRtslalialglallrffltgepsalgkilglilivlgiltllvglvrylrrq 66
                                      +RT   W +R s++ +algl+ +    +ge  + g       +v+g+l+ + +++ y rr 
  gi|336255153|ref|YP_004598260.1|  7 QRTVAKWgMRLSVLVGALGLVYFTT--RGELVT-G-------VVVGALFGVGSYWEYKRRM 57
                                      69*****889999999999999984..333333.3.......6666666667777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 579.37
//
Query:       gi|336255154|ref|YP_004598261.1|  [L=360]
Description: 5,10-methylenetetrahydromethanopterin reductase [Halopiger xanaduensis SH-6]
Scores for 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-66  223.4   5.5    5.4e-66  223.1   5.5    1.0  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
       0.12   12.8   1.2       0.74   10.2   0.7    2.4  2  Radical_SAM     Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.1   5.5   6.1e-70   5.4e-66      15     313 ..      15     332 ..       6     333 .. 0.89

  Alignments for each domain:
  == domain 1  score: 223.1 bits;  conditional E-value: 6.1e-70
                    Bac_luciferase  15 lgaasaslrylvelaraaEelGfdavwvaehhggpgga........ldaftllaalaaaTerirlgtavtplytrhP 83 
                                         +++ ++  +ve+a++aEe+Gfd + +++h++ p g+         +aft+l+a+a++T+r  ++ +vt   +rhP
  gi|336255154|ref|YP_004598261.1|  15 VVTYG-DVTGTVEQAQRAEEAGFDVLTLPDHLFHPTGSdeflvdppWEAFTVLGAIAQHTDRATIMPGVTDSVRRHP 90 
                                       55566.78899**************************9********9****************************** PP

                    Bac_luciferase  84 avlAqqaatLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrg..eev.dfeGeffsvkgal 157
                                       + lA + +tLd++++GR+ lg+g+g++ + + +  +++d++  ++ E+v+v+ +lw++  +++ +f+G+f+ +++a+
  gi|336255154|ref|YP_004598261.1|  91 TELAHSTVTLDRMTDGRAALGIGAGEAFNFTPMTDIEWDDPFSQFVEAVKVIDGLWNSqaDDPfSFDGDFYGLEDAH 167
                                       ******************************888888********************66776666*********9999 PP

                    Bac_luciferase 158 llprpgqgpiP.vyvaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadt 233
                                          +p+q+p+P ++v++++p ++ +a+ +adg++++  +p+++a+ +er+ ++a+ +grdp++i+ ++++++ v+d+
  gi|336255154|ref|YP_004598261.1| 168 MGLKPVQDPRPpIWVGGYGPSMRGFAGAVADGWFPWIHSPDQYAADLERVLSAAEDRGRDPEEIDRAVMVPTTVTDD 244
                                       999999999555***************************************************************** PP

                    Bac_luciferase 234 eeeAraea...raliagldfyaldsegagreaeaa.......eiqeeedanlwagaadavpdelvaatalvGtpeqv 300
                                       ++eAr+ a   ++ +  l   +   +++g+e+ a+         + +e+ ++  +aa+ +p+e v++ ++ G+pe +
  gi|336255154|ref|YP_004598261.1| 245 ADEAREIAverNRTT--LALRPPLLAEMGYEEIAEetpimrdMAFTDEQEEQLLSAAERIPAEAVDEVTISGDPERA 319
                                       ********8663333..23334444444444444433444336788889999999999******************* PP

                    Bac_luciferase 301 aerlaayaeagvd 313
                                       +er++a+a+agvd
  gi|336255154|ref|YP_004598261.1| 320 IERIEAFADAGVD 332
                                       ************8 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.12   1.1e+03      92     158 ..      26      85 ..      10      89 .. 0.55
   2 ?   10.2   0.7   8.2e-05      0.74     115     162 ..     301     351 ..     200     353 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.12
                                       HHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  92 eklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                                       e+++r  e+g+d+++l+ + +++    + +     ++  +ea+  l +   +  +dr +++pG++d+
  gi|336255154|ref|YP_004598261.1|  26 EQAQRAEEAGFDVLTLPDHLFHPT-GSDEF----LVDPPWEAFTVLGAIAQH--TDRATIMPGVTDS 85 
                                       555566666655555554444444.22222....123334444444444444..7788888888875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 8.2e-05
                                       H....HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHH CS
                                       x....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 115 e....kvlklmnrghtfeevlealeklreagikrvvdrivglpGendeelee 162
                                       +     v + +   +++e+ +e +e++++ag+++ v + vg   e+ +++e+
  gi|336255154|ref|YP_004598261.1| 301 RipaeAVDEVT-ISGDPERAIERIEAFADAGVDNLVLIPVGDFDETLRHYED 351
                                       24444688889.889******************8888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2676.46
//
Query:       gi|336255155|ref|YP_004598262.1|  [L=454]
Description: Uronate isomerase [Halopiger xanaduensis SH-6]
Scores for 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-146  488.2   0.0   2.8e-146  488.1   0.0    1.0  1  UxaC      Glucuronate isomerase


Domain annotation for each model (and alignments):
>> UxaC  Glucuronate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.1   0.0  1.5e-150  2.8e-146       3     463 ..       2     451 ..       1     452 [. 0.97

  Alignments for each domain:
  == domain 1  score: 488.1 bits;  conditional E-value: 1.5e-150
                              UxaC   3 kfleedfllsnetakklyheyakklPiiDyhchlspkeiaenkkfenltevwlegDhYkWramRanGveeklitGda 79 
                                       +fl+ed+ll++ +a++ly+  a +lPi+D h+h +++ei+en  +++++ev+ ++DhY W +mR  Gv+e+litGda
  gi|336255155|ref|YP_004598262.1|   2 SFLDEDYLLETAAARELYDAIA-DLPIVDPHTHADVAEIVENDGWDDIWEVEAATDHYVWALMRNCGVDEELITGDA 77 
                                       49*****************966.9***************************************************** PP

                              UxaC  80 sdkekflawaktvpktignPlyhWthleLkrvFgidellseksaeeiwekanelLaeeefkarelleksnvevvctt 156
                                       +++ek++a+a+++p+++gnP+y+W+hl+Lkr Fgi++ +s ++a+eiwe+++++La ++++++ell+++nvevv+ t
  gi|336255155|ref|YP_004598262.1|  78 DNREKWTALAEVFPQFAGNPTYEWVHLDLKRRFGIEKPISAETADEIWEETKTQLAADDMRPQELLAEMNVEVVGST 154
                                       ***************************************************************************** PP

                              UxaC 157 DdPidsLeyhkklaedeefkvkvlPtfRPDkalkiekeefadyvkkLeevseieiksfddllkalekrlefFeelGc 233
                                       DdP+d+Leyh++  e e   v ++Pt+R D+a+kie+ e++d+v++Le+++e+  ++fd +l+ale  +++F+e Gc
  gi|336255155|ref|YP_004598262.1| 155 DDPTDDLEYHERAVE-EVEGVDIVPTWRADRAVKIERPEWTDFVAELEAATELGTDDFDGFLAALEASHDYFAERGC 230
                                       ************984.4566********************************************************* PP

                              UxaC 234 rvsDhaleevvfaetkeeeleaifkkalegeelseeelekfktalllalaklyaekgwvmqlhlgalRnnnskllek 310
                                       r+ D ++e+ v   +++e +++i+++ ++g +lse+e+e+f+++l + +++l+a+kgwv+qlh+g +Rn++  l+e+
  gi|336255155|ref|YP_004598262.1| 231 RACDLGIEQPVSRPVSDERAREIYQRGIAGGSLSEREVEDFQAYLTEYIGELNAAKGWVTQLHIGPVRNYRDSLFER 307
                                       ***************************************************************************** PP

                              UxaC 311 lGadtGfDsi.gdeeiakelaklldkldkkdelpktilyslnprdnevlatiigsFqdegvkgklqlGaaWWFnDtk 386
                                       lG+ +G D+  +d ++ak+l+++l+++d +    +++ y+++p++  ++ati++ F       ++ +G aWWFnD+ 
  gi|336255155|ref|YP_004598262.1| 308 LGPAAGGDIStQDVDLAKPLEHFLNRFDDEM---NIVCYTIDPTHYPTIATIARVFP------NVTVGPAWWFNDSP 375
                                       ********7615666*************998...78********************8......7999********** PP

                              UxaC 387 dgmekqlkalanvgllskFvGmltDsRsflsy.tRheyFRrilcdligewveegevpedeellgelvkdicynnake 462
                                        g+e ql+++  v+lls+  Gm++DsR++lsy +R e+FRr l++++g++v++g+vp+d +   +lv+ ++y++ ke
  gi|336255155|ref|YP_004598262.1| 376 FGIEGQLEYVGTVELLSQHAGMVSDSRKLLSYgSRFEMFRRSLANVVGNQVDRGQVPTDVAH--DLVERLAYDRPKE 450
                                       ********************************99************************9987..9*******99987 PP

                              UxaC 463 y 463
                                        
  gi|336255155|ref|YP_004598262.1| 451 L 451
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3393.29
//
Query:       gi|336255156|ref|YP_004598263.1|  [L=435]
Description: endo-1,4-beta-xylanase [Halopiger xanaduensis SH-6]
Scores for 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-76  253.8  13.6    7.2e-76  253.8  13.6    2.3  2  Glyco_hydro_11   Glycosyl hydrolases family 11
    2.4e-39  133.9  21.5    3.9e-25   88.4   6.3    3.9  4  RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
    3.5e-20   72.5   2.1    9.5e-14   51.7   0.1    2.5  2  Ricin_B_lectin   Ricin-type beta-trefoil lectin domain
  ------ inclusion threshold ------
      0.091   12.6   0.2      0.091   12.6   0.2    1.9  2  TAT_signal       TAT (twin-arginine translocation) pathway si


Domain annotation for each model (and alignments):
>> Glyco_hydro_11  Glycosyl hydrolases family 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.8  13.6   1.6e-79   7.2e-76       1     178 []      87     262 ..      87     262 .. 0.98
   2 ?   -1.2   2.5       0.3   1.4e+03       4      37 ..     324     357 ..     321     389 .. 0.77

  Alignments for each domain:
  == domain 1  score: 253.8 bits;  conditional E-value: 1.6e-79
                                       ----EEEEEECCCSEEEEEC-TTTEEEEEEECSSEEEEEEEESS-TT-EEEEEEEEEECCEEEEEEEEEECTTTEEE CS
                    Glyco_hydro_11   1 nngyyyslwkdgggsvtytngaggsysvswsnagnfvvgkGwnpgskrtikYsgtyspsgnsylavYGWtrnplvEY 77 
                                       ++gyyys+w+d++g+vt+t ++gg ysv+w+++gnfv+gkGw++g++r+++Ys++++  +n+yl++YGWt++plvEY
  gi|336255156|ref|YP_004598263.1|  87 HEGYYYSFWTDSEGTVTMTLESGGDYSVEWNDTGNFVCGKGWETGARRQVDYSASFNGGSNGYLCLYGWTTDPLVEY 163
                                       579******************************************************888***************** PP

                                       EEEEEESSS-HHHHSEEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEESS--SCEEEEHHHHHHHHHHCT- CS
                    Glyco_hydro_11  78 YivenwgsynpssgatkkgtvtsdgatYdiykstrvnqpsieGtatfqqywSvrqskrtsgtitvanhfkaWaslGl 154
                                       Yi+en+gsy+p  ++++kgtvtsdg+tYdiy+s r n+psieG+atf qywSvrqs+r+sgtit  nhf+aW+s+G+
  gi|336255156|ref|YP_004598263.1| 164 YIIENHGSYRP--EHDYKGTVTSDGGTYDIYESLRENAPSIEGEATFPQYWSVRQSTRSSGTITAGNHFDAWESNGM 238
                                       ***********..79************************************************************** PP

                                       --SEECEEEEEEEEEEEEEEEEEE CS
                    Glyco_hydro_11 155 klgklnyqvlavEgyqssGsasit 178
                                       ++g+++yq+la+Egy+ssGs+s+t
  gi|336255156|ref|YP_004598263.1| 239 DMGSHDYQILATEGYESSGSSSVT 262
                                       ********************9986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.3
                                       -EEEEEECCCSEEEEEC-TTTEEEEEEECSSEEE CS
                    Glyco_hydro_11   4 yyyslwkdgggsvtytngaggsysvswsnagnfv 37 
                                         y++w  ++ + +++ + gg+y+++  n+g+++
  gi|336255156|ref|YP_004598263.1| 324 QQYEYWGGENQQWNVEDTGGGEYRIENVNSGKVL 357
                                       67999*999999999999*****99987777765 PP

>> RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.48   2.1e+03      11      43 ..     108     140 ..     101     174 .. 0.62
   2 ?   -3.1   0.0       3.2   1.4e+04      50      62 ..     210     222 ..     201     234 .. 0.61
   3 !   88.4   6.3   8.7e-29   3.9e-25      10      89 .]     294     373 ..     290     373 .. 0.96
   4 !   54.7   0.6   2.8e-18   1.3e-14       1      55 [.     379     433 ..     379     435 .] 0.95

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.48
                                       TTTEEEEECTSSSEEEECGCCTBCTTEEEEEE- CS
                   RicinB_lectin_2  11 gdgyytiknvasgkvLdvaggstanganvqqwt 43 
                                       ++g y+++   +g+++  +g  t +  +v++++
  gi|336255156|ref|YP_004598263.1| 108 SGGDYSVEWNDTGNFVCGKGWETGARRQVDYSA 140
                                       456788888888888877777777555555544 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.2
                                       CEEEEECCESSEE CS
                   RicinB_lectin_2  50 qqWrledtgdgty 62 
                                       q W +++ + ++ 
  gi|336255156|ref|YP_004598263.1| 210 QYWSVRQSTRSSG 222
                                       4444444333333 PP

  == domain 3  score: 88.4 bits;  conditional E-value: 8.7e-29
                                       TTTTEEEEECTSSSEEEECGCCTBCTTEEEEEE-TTT-GGCEEEEECCESSEEEEEETTTTEEEEECGCS-STTEEE CS
                   RicinB_lectin_2  10 ggdgyytiknvasgkvLdvaggstanganvqqwtcsgaanqqWrledtgdgtyrivnkasgkvLdvaggstanGtnv 86 
                                        +dg+y+i+nv sgk Ldva+ st++ganvqq+++ g++nqqW +edtg+g yri+n++sgkvLdv+++st++G+nv
  gi|336255156|ref|YP_004598263.1| 294 LADGTYSIQNVDSGKGLDVADESTDDGANVQQYEYWGGENQQWNVEDTGGGEYRIENVNSGKVLDVESSSTDDGANV 370
                                       5689*********************************************99****************8899****** PP

                                       EEE CS
                   RicinB_lectin_2  87 qqw 89 
                                       qq+
  gi|336255156|ref|YP_004598263.1| 371 QQY 373
                                       **8 PP

  == domain 4  score: 54.7 bits;  conditional E-value: 2.8e-18
                                       CCGEEEECETTTTEEEEECTSSSEEEECGCCTBCTTEEEEEE-TTT-GGCEEEEE CS
                   RicinB_lectin_2   1 anQqWtlgsggdgyytiknvasgkvLdvaggstanganvqqwtcsgaanqqWrle 55 
                                       +nQ+++l+++gdg y+i+ v+sgk+Ldv+++st++ganvqq+t++g a+q+W+++
  gi|336255156|ref|YP_004598263.1| 379 DNQRFYLSDQGDGEYRIEPVHSGKALDVSDASTEDGANVQQYTWNGEAHQRWTFD 433
                                       69*****88999****************************************985 PP

>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   1.3e-07   0.00057       3      46 ..     299     342 ..     297     346 .. 0.90
   2 !   51.7   0.1   2.1e-17   9.5e-14       3      86 ..     346     433 ..     344     435 .] 0.94

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.3e-07
                                       EEEEETTTGEEEEETTCTTS.TEBEEEEE-TSCCGGGEEEEETTS CS
                    Ricin_B_lectin   3 geirnvasgkCLdvegeska.gapvglydChgskgkQlwtltkdg 46 
                                       + i+nv+sgk Ldv +es++ ga+v++y+  g+++ Q+w+++++g
  gi|336255156|ref|YP_004598263.1| 299 YSIQNVDSGKGLDVADESTDdGANVQQYEYWGGEN-QQWNVEDTG 342
                                       689****************9**********99977.***999765 PP

  == domain 2  score: 51.7 bits;  conditional E-value: 2.1e-17
                                       EEEEETTTGEEEEETTCTTS.TEBEEEEE-TSCCGGGEEEEE..TTSEEEETT..TTEEEEES..SSSTTSBEEEEE CS
                    Ricin_B_lectin   3 geirnvasgkCLdvegeska.gapvglydChgskgkQlwtlt..kdgeirska.qselCldvs..staegakvvlak 73 
                                       ++i nv+sgk Ldve++s++ ga+v++y+  g+++ Q+++l+  +dge+r++  +s++ ldvs  st++ga+v++++
  gi|336255156|ref|YP_004598263.1| 346 YRIENVNSGKVLDVESSSTDdGANVQQYSDGGGDN-QRFYLSdqGDGEYRIEPvHSGKALDVSdaSTEDGANVQQYT 421
                                       68****************************99988.******8888999998899********************** PP

                                       TTTTSGGGCEEEE CS
                    Ricin_B_lectin  74 ChkgkgnqrWefd 86 
                                       ++ g+++qrW+fd
  gi|336255156|ref|YP_004598263.1| 422 WN-GEAHQRWTFD 433
                                       *9.*********8 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2     2e-05     0.091       2      22 ..      47      67 ..      46      71 .. 0.62
   2 ?   -7.3   5.3         4   1.8e+04      14      17 ..     271     274 ..     267     278 .. 0.34

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                        TAT_signal  2 lSRRdFLKgsAAaa.AAaalg.g 22
                                      ++RRd +K+    a AAa+lg g
  gi|336255156|ref|YP_004598263.1| 47 FDRRDYMKAV--SAtAAAGLGiG 67
                                      89******55..44444445534 PP

  == domain 2  score: -7.3 bits;  conditional E-value: 4
                        TAT_signal  14 aaAA 17 
                                       ++ +
  gi|336255156|ref|YP_004598263.1| 271 GGGG 274
                                       2221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3166.68
//
Query:       gi|336255157|ref|YP_004598264.1|  [L=774]
Description: beta-glucosidase [Halopiger xanaduensis SH-6]
Scores for 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-78  262.4   0.0    8.2e-78  262.0   0.0    1.2  1  Glyco_hydro_3    Glycosyl hydrolase family 3 N terminal domai
    8.5e-54  182.6   0.2    1.9e-53  181.4   0.2    1.6  2  Glyco_hydro_3_C  Glycosyl hydrolase family 3 C-terminal domai
    4.4e-18   65.1   0.0    1.9e-17   63.1   0.0    2.2  2  Fn3-like         Fibronectin type III-like domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_3  Glycosyl hydrolase family 3 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.0   0.0   1.4e-81   8.2e-78       1     318 [.      29     353 ..      29     354 .. 0.96

  Alignments for each domain:
  == domain 1  score: 262.0 bits;  conditional E-value: 1.4e-81
                                       -HHHHHHHTEE-B-SE......-S--HHHHHHHHHH--SEEE--GG..GTSSHHHHHHHHHHHHHH-SS....S--E CS
                     Glyco_hydro_3   1 tldekigqLlvvevse......ekkseeaaellkkyqvGgiilfae..nledtkqleelieaarqaseksrlgiPll 69 
                                       t++ek +qL +v++        e + ++++e+l++  +G  +  ++  +l + ++++  +e +    e++rlgiP++
  gi|336255157|ref|YP_004598264.1|  29 TVEEKAAQLGSVNADRlldedgEIDWDAVDEWLAH-GIGHFTRLGGegSLAPSEAARVTNELQTYLREETRLGIPAI 104
                                       79*********999889999999999999999987.589988877778999999999999999999*********** PP

                                       EEE---BTTB---SSS---S-HHHHHHHT-HHHHHHHHHHHHHHHHHHT--EE---B-----STTSSSGGGSS-SSH CS
                     Glyco_hydro_3  70 lavDqegGlvqrlgegtlfPsalalaatssldlikelgriiakelralgididfaPvvdvnrdprngigvrsFsedp 146
                                        + ++++G++    e+t fP++l++a++++++l++++++ i+ el  +g    ++Pv+dv+rd r+g+ +++F+edp
  gi|336255157|ref|YP_004598264.1| 105 PHEECLSGYM--GPEATTFPQMLGMASSWNPELLQTVTETIRGELEGIGTVHALSPVLDVARDLRWGRVEETFGEDP 179
                                       **********..5555************************************************************* PP

                                       HHHHHHHHHHHHHHHHT....T-EEEEEEETTGTT-SSETTTSEEB----HHHHHHTTHHHHHHHH.HTT-SEEEE- CS
                     Glyco_hydro_3 147 elvaalaaamvkGlqga....gvaatvKHFpghGdgavdshkelptvdhseeelrevdlvpfqaai.eagvdsVMta 218
                                       ++va +a+a+v Glqg     g+ at+KHF gh  ga+d++k++   +   +elre +l+p++a i ea+++sVM+a
  gi|336255157|ref|YP_004598264.1| 180 YMVAEMARAYVSGLQGDgradGISATLKHFVGH--GATDGGKNRSSLNVGPRELRETHLFPYEAVIsEANAESVMNA 254
                                       ****************9999*************..99**************************************** PP

                                       --B-TTT---BGGG-HHHHIIIIIIIS---SEEEES-TTSHHHHCCS-....HHHHHHHHHHHT-SBEES-S---SG CS
                     Glyco_hydro_3 219 HvqfpaldgtpatgskklltdvLRkelGFdGvvvsDalamkeiadrgg....keeavvlaLkAGvDilLvpeertse 291
                                          + +ldg+p++ s++llt+vLR e GFdG+vvsD+ ++ ++ + +     k ea+v+aL+AG+D++L  +e++  
  gi|336255157|ref|YP_004598264.1| 255 ---YHDLDGVPCANSEWLLTEVLRGEFGFDGTVVSDYYSVRHLVTEHEtastKPEAAVQALEAGIDVELPYTEYY-- 326
                                       ...***************************************9999887888899******************98.. PP

                                       HHHHHHHHHTTSS-HHHHHHHHHHHHH CS
                     Glyco_hydro_3 292 ikalkkavkeGeltearidesvrrvlr 318
                                        + l++av+eG+l+e+ ++esvrr+lr
  gi|336255157|ref|YP_004598264.1| 327 GEHLVEAVEEGDLAEETLNESVRRILR 353
                                       89***********************97 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 ?   -2.2   0.0      0.56   3.4e+03      37      59 ..     128     212 ..     113     354 .. 0.56
   2 !  181.4   0.2   3.2e-57   1.9e-53       1     204 []     392     635 ..     392     635 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.56
                                       SS----S---HHHHHHHHHHH........................................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxx....................................................... RF
                   Glyco_hydro_3_C  37 sgtvtvsylvsplegirerles....................................................... 58 
                                        ++++++ l+++ e+ir +le                                                        
  gi|336255157|ref|YP_004598264.1| 128 ASSWNPELLQTVTETIRGELEGigtvhalspvldvardlrwgrveetfgedpymvaemarayvsglqgdgradgisa 204
                                       44456666666666666666445555555555555555555555444444444444444444444444444444444 PP

                                       ........ CS
                                       .......x RF
                   Glyco_hydro_3_C  59 .......e 59 
                                               
  gi|336255157|ref|YP_004598264.1| 205 tlkhfvgH 212
                                       44444440 PP

  == domain 2  score: 181.4 bits;  conditional E-value: 3.2e-57
                                       -EEEEEGSS--S-S-STEEEEEESGGGS.SS-SS-BSSS--......--S---HHHHHHHHHHH............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx......xxxxxxxxxxxxxxxxxx............ RF
                   Glyco_hydro_3_C   1 iVLLkNennlLPLkkklkkiaviGpnad.etlklGggsgtv......tvsylvsplegirerles............ 58 
                                       ++LLkNe++lLPL  ++  +av+Gp+ad  +  +G++  ++          +v+ple++++r +             
  gi|336255157|ref|YP_004598264.1| 392 MTLLKNEDDLLPL--DVDDVAVVGPKADnPKELMGDYAYAAhypeeeYEADAVTPLEALEARDGLdvtyeqgctisg 466
                                       79***********..5559*********777889999999988876633355699****99886699********** PP

                                       ...-HHHHHHHHHHHTSEEEEEEEES....................SB-TTSCSGHHSSTTHHHHHHHHHHTTSSEE CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Glyco_hydro_3_C  59 ..eegideaveaakeaDvavvvvgedpei.................egEgvDrtdlalpeaqdelikavaaanknvv 116
                                         ++g+d+a++aa++aDva+++vg+ + +                 +gEg+D t+l lp+ q+el++++ ++ ++vv
  gi|336255157|ref|YP_004598264.1| 467 psTDGFDAAADAAADADVALAFVGARSAVdfsdveaekeekpsvptSGEGCDVTHLGLPGVQEELVAELLETDTPVV 543
                                       **99**********************888************************************************ PP

                                       EEEEESSGG--TTTGTTTEEEEEE-S--GCCHHHHHHHHHTTSS---B--SS-EESSSGGG................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx....x RF
                   Glyco_hydro_3_C 117 vvlqsggpvavepwkeenvkAilaawlpGqegGtaiadvLfGdvnPsGkLpvtfpksledlpddyyeek.dt....y 188
                                       vvl+sg+p a+e++  ++++Ail+awlpG egGtaia+ LfG+ nP+GkLpv+ pks+++lp+ yy++k +t    y
  gi|336255157|ref|YP_004598264.1| 544 VVLVSGKPHAIEDI-AAEAPAILYAWLPGDEGGTAIAETLFGENNPAGKLPVSLPKSVGQLPV-YYNRKeNTankdY 618
                                       ***********999.77*********************************************9.8888862255678 PP

                                       S.-----SETTTT-BCH CS
                                       x.xxxxxxxxxxxxxxx RF
                   Glyco_hydro_3_C 189 k.fegtplYpeGlglsY 204
                                         ++++p+Yp+G+g sY
  gi|336255157|ref|YP_004598264.1| 619 VyTDSEPVYPFGHGESY 635
                                       8899**********998 PP

>> Fn3-like  Fibronectin type III-like domain
   #    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      29      42 ..      77      90 ..      76      92 .. 0.84
   2 !   63.1   0.0   3.3e-21   1.9e-17       1      70 [.     672     740 ..     672     741 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.7
                                      E-TT-EEEEEEEEE CS
                          Fn3-like 29 LapGesktvtftld 42
                                      Lap e ++vt +l+
  gi|336255157|ref|YP_004598264.1| 77 LAPSEAARVTNELQ 90
                                      99*******98876 PP

  == domain 2  score: 63.1 bits;  conditional E-value: 3.3e-21
                                       EEEEEEEEESS-STTSBS-EEEEEEEEEE-TT-EEEEEEEEECGGG-EEETTTTEEE--SCEEEEEEESS CS
                          Fn3-like   1 evvqlYvsdpessverpvkeLkgFekveLapGesktvtftldrkdlsvwdeekqkwvvepGeytvlvgts 70 
                                       e+vq Y ++ ++s  rpv+eL gFe+v+L+pGesk+v f+l++++l++ d   ++  ve+G y++ +g+s
  gi|336255157|ref|YP_004598264.1| 672 EIVQCYGRATNASQARPVQELLGFERVSLEPGESKRVAFDLSATQLAFHDLS-MNLAVEEGPYEIRIGRS 740
                                       89**************************************************.79*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (774 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.61u 0.22s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 5832.22
//
Query:       gi|336255158|ref|YP_004598265.1|  [L=685]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for complete 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-54  184.2  33.4      1e-30  106.9  10.1    3.3  3  BPD_transp_1  Binding-protein-dependent transport system inne
     0.0048   16.8   2.6       0.31   11.1   0.1    3.9  3  OppC_N        N-terminal TM domain of oligopeptide transport 
  ------ inclusion threshold ------
      0.024   15.1   0.0      0.079   13.5   0.0    1.8  2  TPR_19        Tetratricopeptide repeat
       0.11   12.3   0.1       0.19   11.6   0.1    1.4  1  Gp37          Gp37 protein


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 !  106.9  10.1   2.2e-34     1e-30       2     184 ..     122     326 ..     121     327 .. 0.97
   2 ?    0.3   0.9      0.11     5e+02      37      70 ..     417     484 ..     409     487 .. 0.73
   3 !   88.0   7.7   1.4e-28   6.1e-25       1     184 [.     485     672 ..     485     673 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 2.2e-34
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf........................vilsilghlil 54 
                                       i lG+++a++ ++k+d +++++  v +s+P++v+a+l+ +vf                        +++++l+h++l
  gi|336255158|ref|YP_004598265.1| 122 ICLGAIMAYYEGSKFDTAMTVVAVVESSTPYYVVALLMSFVFayqlgwfptnsrypgaaeiglngeFVFGALHHAAL 198
                                       789************************************************************************** PP

                      BPD_transp_1  55 pviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllefl 131
                                       p++ l++++aa+  + +r + +++l  d++++ar++G+++ +i  ++v++na+ p+ tgl+l +g+++gg+++le +
  gi|336255158|ref|YP_004598265.1| 199 PILSLIVTGAAA-SLSMRGNSISVLGADHIRVARLRGLPPTRIALRYVMRNAILPLYTGLLLLLGFMIGGSIILEDI 274
                                       *99988777665.689************************************************************* PP

                      BPD_transp_1 132 gswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       +++ G+g  + e  +++dy+++  gg+ ++ i v++++++ad+ +  ldpr +
  gi|336255158|ref|YP_004598265.1| 275 FQYRGMGWYMYEGVQNRDYPLMV-GGFMVICITVVIMMFIADLTYSRLDPRAK 326
                                       ***********************.**************************976 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.11
                      BPD_transp_1  37 illvlvf..................................vilsilghlilpviillllsaapyvrl 70 
                                       ++l+++f                                   +ls   h+  pv+i+++++a+++v+l
  gi|336255158|ref|YP_004598265.1| 417 FVLIALFgerfvpsptatfdrwvspldfnpahplgttnggqDLLSLMVHGTSPVLIMITVGAFATVTL 484
                                       4555555666666666666666677777777777777777777888899999********99999886 PP

  == domain 3  score: 88.0 bits;  conditional E-value: 1.4e-28
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       g+ +G+ a+ +r++ +d+ll++l +++ s+P + l+i++ ++        h ++ +++l++  ++++ r ir+++l+
  gi|336255158|ref|YP_004598265.1| 485 GVSIGATAG-FRGGNTDRLLMTLCDIIVSVPGLPLIIVIAAI----VEPRHPAMVGLVLSVAAWGGLGRSIRSEVLK 556
                                       7899*****.************************99999964....78899************************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                       ++++++vea+ra+G++++ i+ k +lPn+ p+i+  l++++ +++  +v l+flg      +++ + ++g  +++++
  gi|336255158|ref|YP_004598265.1| 557 VRSQEYVEASRAMGVNTFSIILKDILPNIWPYILINLANNARNIIFSSVGLYFLG-----FLPRSTRNWGVVLDAAQ 628
                                       *******************************************************.....***************** PP

                      BPD_transp_1 155 ..............nggvlalviavlllnlvadilqrlldprvr 184
                                                     ++++++++++ + l+lv+  l r+ +pr+r
  gi|336255158|ref|YP_004598265.1| 629 snnalysvgqihyiAVPAVFIIALSMGLILVSQSLDRISNPRIR 672
                                       ******************************************98 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.026   1.2e+02      20      39 ..     301     318 ..     292     328 .. 0.72
   2 !   11.1   0.1   6.8e-05      0.31      15      41 ..     406     432 ..     400     449 .. 0.83
   3 ?   -1.7   0.0      0.65   2.9e+03      15      22 ..     531     538 ..     529     541 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.026
                            OppC_N  20 lvilllllliaifaPliaPy 39 
                                       +vi ++++++ ++a+l   y
  gi|336255158|ref|YP_004598265.1| 301 MVICITVVIMMFIADLT--Y 318
                                       56666677788999887..4 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.8e-05
                            OppC_N  15 lAvvglvilllllliaifaPliaPydp 41 
                                       + ++g +il+ ++lia+f++ ++P + 
  gi|336255158|ref|YP_004598265.1| 406 RGLLGTAILAGFVLIALFGERFVPSPT 432
                                       67899*****************98654 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.65
                            OppC_N  15 lAvvglvi 22 
                                        A+vglv+
  gi|336255158|ref|YP_004598265.1| 531 PAMVGLVL 538
                                       69****96 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.8e-05     0.079      13      37 ..      38      62 ..      36      64 .. 0.90
   2 ?   -2.5   0.0       1.7   7.4e+03      28      57 ..     123     152 ..     121     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                            TPR_19 13 lleqalqedpknaearllLAealla 37
                                      + +q+l+e+p+n++a+ +L+e++++
  gi|336255158|ref|YP_004598265.1| 38 MVAQMLSENPNNPAAARRLVEIYIN 62
                                      6789*******************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                            TPR_19  28 rllLAeallalgqldeAealLdalpeedpd 57 
                                        l+ + a+++   +d A+ +++ +  ++p 
  gi|336255158|ref|YP_004598265.1| 123 CLGAIMAYYEGSKFDTAMTVVAVVESSTPY 152
                                       577788999999999999999998888775 PP

>> Gp37  Gp37 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.2e-05      0.19      23      65 ..     117     159 ..      95     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                                       -TTT---SSSEEEEEEEEEE----SSSS-EEEEEEEEEEEEEE CS
                              Gp37  23 eyrlnhpvGavLvsyagskfaepedtdavvqtrtlqleltvll 65 
                                       ++  ++  Ga++ +y+gskf++++++ avv++ t    +++l+
  gi|336255158|ref|YP_004598265.1| 117 TFTTSICLGAIMAYYEGSKFDTAMTVVAVVESSTPYYVVALLM 159
                                       57778889***********************999888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.39
# Mc/sec: 5267.61
//
Query:       gi|336255159|ref|YP_004598266.1|  [L=489]
Description: alpha-galactosidase [Halopiger xanaduensis SH-6]
Scores for 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-42  143.4   0.0    8.1e-42  142.8   0.0    1.2  1  Glyco_hydro_4   Family 4 glycosyl hydrolase
    2.7e-41  142.0   0.0    3.9e-41  141.4   0.0    1.3  1  Glyco_hydro_4C  Family 4 glycosyl hydrolase C-terminal domain
     0.0084   16.5   0.1       0.03   14.8   0.0    1.9  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
  ------ inclusion threshold ------
      0.021   14.3   0.1        5.2    6.4   0.0    2.2  2  Ribonuc_red_sm  Ribonucleotide reductase, small chain
      0.044   13.9   0.0       0.78    9.8   0.0    2.5  3  Ldh_1_N         lactate/malate dehydrogenase, NAD binding dom


Domain annotation for each model (and alignments):
>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.8   0.0   2.3e-45   8.1e-42       2     180 ..      21     201 ..      20     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 142.8 bits;  conditional E-value: 2.3e-45
                                       EEEETTTSSSHHHHHHHHHHTTTTCTEEEEEEE-SSH..HHHHHHHHH..HHHHHHHCTTTCEEEEESSHHHHHTT- CS
                     Glyco_hydro_4   2 iviiGgGStifaklllgdlkkteelsvselaLvDide..erldaiqtl..akklveeagadlkieattdrkealkda 74 
                                       i++iGgGS  +a +l+ dl +  +l++ ++ L+D      +l+a + +   ++   e  ad+ +ea+ d++ al+ a
  gi|336255159|ref|YP_004598266.1|  21 IAYIGGGSRQWAPNLIRDLAQS-DLHG-QVRLYDEYYesAQLNAEFGNwvHDEADVEPSADWSYEAVEDLETALSGA 95 
                                       99*****************875.6999.9*****765226666655541134444566789**************** PP

                                       SEEEE---TTHHHHHHHHHHCCHTTTTT-CTTSSSHHHHHHHHHHHHHHHHHHHHHHHHH-TTSEEEE-SSSHHHHH CS
                     Glyco_hydro_4  75 dfVitairvGlekareidekiplryGieqtiqdtvgpggifrglrtipvlleIakdieelcPdawvlnytNPaavvt 151
                                       d+Vi + +    ++ + d  ip++yGi++ ++ t+gpggifr++rt+p     a +i+e cPdawv nytNP+  vt
  gi|336255159|ref|YP_004598266.1|  96 DIVILSTQYDPAETFVHDLDIPKEYGIYGAVAATIGPGGIFRAMRTVPLYRKFAAAIREHCPDAWVFNYTNPVHFVT 172
                                       ***************************************************************************** PP

                                       HHHHHHSTTSEEEEE-SHHHHHHHHHHHH CS
                     Glyco_hydro_4 152 eallrlvpnikavglChsvigvkeelakl 180
                                       +al+  +p i a+glCh+v+g++++la+ 
  gi|336255159|ref|YP_004598266.1| 173 RALYDEYPDINALGLCHEVLGTRHRLARY 201
                                       *************************9986 PP

>> Glyco_hydro_4C  Family 4 glycosyl hydrolase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.0   1.1e-44   3.9e-41       1     207 [.     219     445 ..     219     446 .. 0.82

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 1.1e-44
                                       EEEETTEEEEEEEECTTEEHHHHHHHHHHHHHHHHHCTGGG.........TSHHHHHHHHHHSSEEECGGHHCTTSS CS
                    Glyco_hydro_4C   1 vaGlNHlaWllkledkGeDlypelrelveedewleeiaekk.........aervridllrrlgllpteysrhyaEYv 68 
                                       v G+NH++W+++++ kG Dl+p l++lve+d++ +e+  ++         + +v+++l+rr+++lp++++rh+ EY 
  gi|336255159|ref|YP_004598266.1| 219 VKGINHFTWIDEARCKGVDLWPVLEDLVESDHAHQEFSWEDledesvfvdNWQVTWELFRRFDVLPAAGDRHLVEYA 295
                                       57************99*************965655554444667778999999************************ PP

                                       ..HCHHHH............SHHHHHHHHHHHHHHHHHHTTTTTHHH.....HHHHSSCHTS-SHHHHHHHHHHTS- CS
                    Glyco_hydro_4C  69 p.ylkrea............peliekektraevvkevekelfeelek.....eklelekrsgeyavdiieaivtdkp 127
                                         ++++               ++  k++t a      e++ ++++e+     +++el+ +s+e  vdi +a+v+ ++
  gi|336255159|ref|YP_004598266.1| 296 TsFIQNGQeglnrwgvkrtgSDYRSKHWTPA------ESDQTTDVEAwldgeKEFELT-ESHEVFVDILRALVGRDT 365
                                       *977765544443333222333333333333......333333333333345566677.6***************** PP

                                       EEEEEEEE-TTSSTTS-TTSEEEEEEEEETTEEEEB--CS-HHHHHHCHHHHHHHHHHHHHHHHHTBHHHHHHHHHC CS
                    Glyco_hydro_4C 128 rrlvvnvpNnglIpnLpddavVEvpclvdkngirpvavgelpeqlaallrtniaveeltveAalegdrelalqalll 204
                                       +++++n pN g++++L+d+avVE++++v +n ++p+a+g +p+ +++l+r +++  e+++eA   gd ++a+q +l+
  gi|336255159|ref|YP_004598266.1| 366 YVTNINLPNVGQVSDLQDGAVVETNAVVRNNEVKPTAAGGFPRPVRSLIRGHVDTIETVIEASRDGDVDAAFQGFLI 442
                                       ***************************************************************************** PP

                                       STT CS
                    Glyco_hydro_4C 205 dpl 207
                                       d+ 
  gi|336255159|ref|YP_004598266.1| 443 DQQ 445
                                       975 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 !   14.8   0.0   8.2e-06      0.03      22      77 ..      35     105 ..      32     116 .. 0.86
   2 ?   -2.5   0.0         2   7.1e+03      50      65 ..     330     361 ..     304     393 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.2e-06
                                       HHHHHHHCTS..EEEEE-SSTHHCCCCHHGG.............BTCCEEES-CHHHHTT-SEEEE-S--G CS
                    UDPG_MGDP_dh_C  22 iieeLleega..evkiyDPkvkeeaveaele.............ekgvevvdsleealkgadaiviltehd 77 
                                       +i++L++ +   +v+ yD + ++++ +ae               ++++e v++le+al+gad++++ t+ d
  gi|336255159|ref|YP_004598266.1|  35 LIRDLAQSDLhgQVRLYDEYYESAQLNAEFGnwvhdeadvepsaDWSYEAVEDLETALSGADIVILSTQYD 105
                                       6777777754337************9997779************889********************9876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                                       G................BTCCEEES-CHHHHT CS
                    UDPG_MGDP_dh_C  50 e................ekgvevvdsleealk 65 
                                       +                 ++ ev  ++ +al 
  gi|336255159|ref|YP_004598266.1| 330 QttdveawldgekefelTESHEVFVDILRALV 361
                                       33444444444333333223333334444444 PP

>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0014       5.2      20      67 ..     319     370 ..     312     393 .. 0.76
   2 ?    5.6   0.0    0.0027       9.7     188     238 ..     428     472 ..     406     484 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0014
                                       HCT---GGGS-GHHHHHHHHS.....TS-HHHHHHHHHHHHHHHHHHHHHHHC CS
                    Ribonuc_red_sm  20 eanfWtpeevdlskDlkdwke.....kLsedekefikkvlaflalldtivnen 67 
                                        + +Wtp e d + D++ w +     +L+e  +e++  +l+ l+  dt+v++ 
  gi|336255159|ref|YP_004598266.1| 319 RSKHWTPAESDQTTDVEAWLDgekefELTES-HEVFVDILRALVGRDTYVTNI 370
                                       678****************764444556654.456667888888888888775 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Ribonuc_red_sm 188 lrDeglHtdfagllfkelkeenelenkeleeeveelikeavelEkefitda 238
                                       +rD  + + f g l+ +  +         +ee +el+ e+v  E+e+++d 
  gi|336255159|ref|YP_004598266.1| 428 SRDGDVDAAFQGFLIDQQIRT------LQTEEARELFAELVAAEEEYLQDW 472
                                       688888888888888877555......7899*****************653 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 ?    0.6   0.0      0.15   5.4e+02      43      76 ..      68     101 ..      26     105 .. 0.69
   2 ?    9.8   0.0   0.00022      0.78      95     130 ..     142     177 ..     138     184 .. 0.88
   3 ?   -2.6   0.0       1.4   5.2e+03      40      55 ..     375     390 ..     361     401 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.15
                                       HHHHHHCHCCSTS-EEEEESSGGGGTTESEEEE- CS
                           Ldh_1_N  43 aldlshistflsvkvkvsekeeealkdadvvvit 76 
                                       + d  +++  +  + ++ e+ e al++ad+v++ 
  gi|336255159|ref|YP_004598266.1|  68 VHDEADVEPSADWSYEAVEDLETALSGADIVILS 101
                                       4566677777777888888999*********986 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00022
                                       HHHHHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHH CS
                           Ldh_1_N  95 akIvkeiveaiakvapnaivlvvsNPvdiltevlkk 130
                                       + ++++ ++ai +++p+a v   +NPv  +t++l++
  gi|336255159|ref|YP_004598266.1| 142 VPLYRKFAAAIREHCPDAWVFNYTNPVHFVTRALYD 177
                                       66789999********************99998876 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.4
                                       HHHHHHHHHCHCCSTS CS
                           Ldh_1_N  40 eGvaldlshistflsv 55 
                                        G++ dl+++++  + 
  gi|336255159|ref|YP_004598266.1| 375 VGQVSDLQDGAVVETN 390
                                       5899999999887633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.35
# Mc/sec: 4191.08
//
Query:       gi|336255160|ref|YP_004598267.1|  [L=152]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-12   48.8   0.3    2.9e-12   47.3   0.3    1.6  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.015   14.5   0.0      0.015   14.4   0.0    1.2  1  DUF1464   Protein of unknown function (DUF1464)


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 !   47.3   0.3   3.2e-16   2.9e-12       3     132 ..       2     142 ..       1     149 [. 0.93

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 3.2e-16
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH......... CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada......... 70 
                                       +r lV+v  se +k++++ A ela+  +ael ll   d +++++  + +++ +  e  +     +++          
  gi|336255160|ref|YP_004598267.1|   2 DRALVVVESSEFAKRLIREAGELAAGVDAELKLLATMDKDEYEQDVETMSTIANVEGTSYSPDDVRESgrqfaadla 78 
                                       789****************************************999999999999888888888888888999*999 PP

                                       ..HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHH CS
                               Usp  71 ..akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrh 132
                                         + + ++   +   +v+ +g+ a+ei+ +ae++d+d i ++ r+rs   ++l+G+ ++ v+ +
  gi|336255160|ref|YP_004598267.1|  79 ksQLEDLDVDYEPLCIVIDDGPEAQEIVATAEKHDCDHIFIAGRKRSPTGKALFGDRTQGVILN 142
                                       888888888999999*****************************************99999876 PP

>> DUF1464  Protein of unknown function (DUF1464)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.7e-06     0.015     194     272 ..       4      84 ..       1     142 [. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-06
                           DUF1464 194 AyllgkvakiekslifsgGvasiagea.elekklsee..aferlkevvksvaellsskykleeiivSGrlkrikelg 267
                                       A ++ + +++ k+li ++G +  ag+  el+  +++    +e+ +e + ++a+++ + y ++++  SGr++ ++  +
  gi|336255160|ref|YP_004598267.1|   4 ALVVVESSEFAKRLIREAG-ELAAGVDaELKLLATMDkdEYEQDVETMSTIANVEGTSYSPDDVRESGRQFAADLAK 79 
                                       56667789***********.66666556666555444459******************************9766555 PP

                           DUF1464 268 kkles 272
                                       ++le+
  gi|336255160|ref|YP_004598267.1|  80 SQLED 84 
                                       55554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1187.54
//
Query:       gi|336255161|ref|YP_004598268.1|  [L=303]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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   77.5  17.8      1e-21   77.5  17.8    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        1.3    8.6   5.8        1.9    8.0   0.0    2.9  3  DUF2208       Predicted membrane protein (DUF2208)


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 ?    2.2   5.0     0.014   1.3e+02      13      59 ..      33     115 ..      29     126 .. 0.69
   2 !   77.5  17.8   1.1e-25     1e-21      11     183 ..     124     296 ..     116     298 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.014
                      BPD_transp_1  13 nkkldkllrpliivllslPsfvlaillvlvf....................................vilsilghli 53 
                                       ++++ ++l++  i++  +P+f+++i+ v                                       ++l ++g +i
  gi|336255161|ref|YP_004598268.1|  33 KRIGFHALLWSLIAIVLFPVFWMFIVSVNQTsfeafvgdplgwaananlegyrdvwfgsdfrywfrnSLLVSIGATI 109
                                       56667778888899999999999999888778888899999999999999999986666444444444444444444 PP

                      BPD_transp_1  54 lpviil 59 
                                       l+++++
  gi|336255161|ref|YP_004598268.1| 110 LSIAVC 115
                                       443333 PP

  == domain 2  score: 77.5 bits;  conditional E-value: 1.1e-25
                      BPD_transp_1  11 nrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaa 87 
                                       + + +++k++ ++  +++++P +++ai+l+lvf  + +l ++ ++++i+++ +++p+++++ r++ ++lp++l+eaa
  gi|336255161|ref|YP_004598268.1| 124 RLRYRGRKAVATFLLITQMFPAILIAIPLFLVFRDI-GLFNTLTGLVIAYVAFTLPFAIWMLRGFYENLPESLEEAA 199
                                       55668999**********************986444.56778999******************************** PP

                      BPD_transp_1  88 ralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtlll.eailgydyseisnggvlalvi 163
                                        ++G +r+  +++v+lP+++p i+t++i++++ +++++v++++l++++  +tl    +++  +y++    +++ ++ 
  gi|336255161|ref|YP_004598268.1| 200 MIDGSTRFGAVVRVILPLSAPAIATTAIFTWVQAWNEFVFALILINDSQTQTLPPgMSQWVGQYALQWDMLMAGALG 276
                                       ***********************************************996655541555556666555558888888 PP

                      BPD_transp_1 164 avlllnlvadilqrlldprv 183
                                       a+l++++v+++lq ++ + +
  gi|336255161|ref|YP_004598268.1| 277 ATLPMLIVFFLLQSYIVKGL 296
                                       88999999999999988765 PP

>> DUF2208  Predicted membrane protein (DUF2208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00021       1.9      84     122 ..      29      68 ..      23      76 .. 0.77
   2 ?   -1.2   1.2      0.14   1.3e+03      85     110 ..     132     159 ..     125     190 .. 0.63
   3 ?    2.0   0.1     0.015   1.4e+02      83     113 ..     263     294 ..     240     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00021
                           DUF2208  84 keqlkasmitlll.lliviilffllyryiiplassllgev 122
                                       ++q+k   +  ll +li i+lf++++ +i+++ +++++ +
  gi|336255161|ref|YP_004598268.1|  29 TAQAKRIGFHALLwSLIAIVLFPVFWMFIVSVNQTSFEAF 68 
                                       56666665544444*****************999988776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.14
                           DUF2208  85 eqlkasmitlll..lliviilffllyry 110
                                       +++++++it ++  +li i lf++++++
  gi|336255161|ref|YP_004598268.1| 132 AVATFLLITQMFpaILIAIPLFLVFRDI 159
                                       5667777777775566666666666543 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.015
                           DUF2208  83 lkeqlkasmitlll.lliviilffllyryiip 113
                                       +  q  ++m   l  +l ++i+ffll++yi++
  gi|336255161|ref|YP_004598268.1| 263 YALQWDMLMAGALGaTLPMLIVFFLLQSYIVK 294
                                       5566667777666647779999*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2348.87
//
Query:       gi|336255162|ref|YP_004598269.1|  [L=309]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for complete 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-17   64.3  19.1    1.1e-17   64.3  19.1    2.5  2  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 ?   -0.3   4.0     0.043   7.7e+02      56     111 ..      36      97 ..      18     107 .. 0.51
   2 !   64.3  19.1   6.3e-22   1.1e-17       4     180 ..     102     302 ..      99     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.043
                      BPD_transp_1  56 viillllsaapyvrlirraalr...slpk...dlveaaralGasrwqifrkvvlPnalppii 111
                                       +++l+l+s  p++r i+ ++++   + +    +l+ +ar+ G++++ ++ + +l  a+  ++
  gi|336255162|ref|YP_004598269.1|  36 LFALGLVSVYPLFRGIYLSFFEydgIGDPewvGLEHYARIVGWTEFWVVMRNTLVWAFAAVV 97 
                                       56666666666666666666552211122111355677777777777555544443333333 PP

  == domain 2  score: 64.3 bits;  conditional E-value: 6.3e-22
                      BPD_transp_1   4 lGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf....................vilsilghlilpvii 58 
                                       +G+  a  lnr + ++ + ++l  +++++P++ +a+ + l+                      +l +  ++ +++++
  gi|336255162|ref|YP_004598269.1| 102 IGLGFAtlLNREFYGRSIATTLLLLPWAIPFISIAFNWRLMYdyelgainglfrtvgltdgiQWLASSRYALFSIML 178
                                       6666777799***************************999999******************9999999999999*** PP

                      BPD_transp_1  59 llllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgs.w 134
                                       + ++ ++p+++l++ a+++ +p dl+eaar++G +r  +fr+++lP + p+++   +l + + l++++l++ +++ +
  gi|336255162|ref|YP_004598269.1| 179 AWVWRNFPFFMLTFLAGMKGIPGDLYEAARVDGSTRLDTFRHITLPFLQPVAVVMTLLMSLWTLNHFTLIYVMTGgG 255
                                       **********************************************************************9766505 PP

                      BPD_transp_1 135 pGlgtllleailgydyseis.nggvlalviavlllnlvadilqrlld 180
                                       pG ++++l ++++++    + +g++ a+++++ll++l + +++  l+
  gi|336255162|ref|YP_004598269.1| 256 PGNSSMVLPVYIYRQAFHLQnMGLASAIAVVMLLVMLTYGLIYLRLY 302
                                       55666666666666655555799999999999999998888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); 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:                         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: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2518.74
//
Query:       gi|336255163|ref|YP_004598270.1|  [L=520]
Description: family 1 extracellular solute-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-23   82.4   7.5    4.8e-23   82.4   7.5    1.5  2  SBP_bac_8   Bacterial extracellular solute-binding protein
    8.9e-19   68.6   5.3    1.6e-18   67.8   5.3    1.4  1  SBP_bac_1   Bacterial extracellular solute-binding protein
     0.0001   22.0   2.2     0.0002   21.1   2.2    1.5  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   7.5     8e-27   4.8e-23       3     278 ..      87     404 ..      85     407 .. 0.76
   2 ?   -3.3   0.2         1   6.1e+03      54      79 ..     477     508 ..     462     514 .. 0.60

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 8e-27
                                       HHHHHH..H-TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGS.TTHHH-HHHHH CS
                         SBP_bac_8   3 akefek..ktgvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdl.dnlddltdala 76 
                                       a+efe   +  v+++ + + ++++ +   +a++  ++p +  ++ane a++ +  +g++ + ++l  ++dd+ d+  
  gi|336255163|ref|YP_004598270.1|  87 AAEFENwsDEEVNLTTEVITWDQVFESWASAIQGQNTPNVS-EMANEHAVD-YGSRGVVRPNTELfNEYDDWYDTPS 161
                                       6777763233577777778*******************975.888776666.8889*******9999*****99888 PP

                                       TT.--TS.----EEEEEEE-EEEEEHHHHHHS....---BHHHHHHHHHHH...HHH-SE...GG---G...GGGGG CS
                         SBP_bac_8  77 av.gydgklygvPyasetpyvliynkdlleka...edpktwdellaaakkl...kgkfgl...pdpasg...wlqaa 140
                                       ++  ydg++ g+P+ +e    ++ n+d+le+a   + p+tw+el+++a ++   + k+g+     +++g   +l+ a
  gi|336255163|ref|YP_004598270.1| 162 YWgNYDGEVWGFPWFVEV-RNFYANTDILEDAghdSIPETWEELVDTATDVeseTDKTGFvsaGSQSTGtgqVLYGA 237
                                       88899************7.8***********9999**************9977668888844312334433444555 PP

                                       THHETTEE---H..........HHH.HHHHHHHHHHH.HTT-...EE.-.S..--SSTTTTTSBSEEEE-TTHHHHH CS
                         SBP_bac_8 141 llakdgksldddg........gkdglkealellkklk.dngk...ty.d.tgadavsefanGevaftingswdiaaa 203
                                       +++ +g ++ ++         ++++   a  ++++++ +       + + +g+da++++++Ge+af+in+  ++++ 
  gi|336255163|ref|YP_004598270.1| 238 AVQ-AGGEFYGYEddqwtvelDSPTSLFAHLWMASMQeEWEIgpgGWaGmDGTDAEQLYREGEAAFMINSGDAANNM 313
                                       555.5555555522234444456666777779999994334444533443679************************ PP

                                       H-TTTSEEEE.....--.....S--EEEEEEEEEE....BTTS-HHHHHHHHHHHHHTTSHHHHHHHH..HH---BS CS
                         SBP_bac_8 204 qkagkklgai.....vp.....kqgsfaggkglav....pknaknedlaAldFlkwltspenqaalae..ktgyipv 264
                                        ++g+ ++       +p      +++f gg+ l +    +++ + ed  ++ F++++tsp+ ++ ++   + +++pv
  gi|336255163|ref|YP_004598270.1| 314 IDEGDAVADStslelIPegpmgTNTAFMGGSCLSAfesdFTQHNVEDGLSMSFIEYMTSPDTMEGYYPdaTPNFLPV 390
                                       *999977765322323466566677*********956554444444447******************9866677899 PP

                                       -S-TTTHHHHHH-H CS
                         SBP_bac_8 265 nksaalspevkkdp 278
                                       + + ++ p ++++p
  gi|336255163|ref|YP_004598270.1| 391 REAQEELPPFTENP 404
                                       99888888888886 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1
                                       HHTTSB-.-GG..GS.TTHHH-HHHHHTT..- CS
                         SBP_bac_8  54 aeeglla.dls..dl.dnlddltdalaav..g 79 
                                        e++++  +l+  d+ + ldd +d l+++  g
  gi|336255163|ref|YP_004598270.1| 477 SESDAVDyELEqsDEqPSLDDAPDELQDWidG 508
                                       44444444555554448888888888887433 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   5.3   2.6e-22   1.6e-18      14     261 ..      87     326 ..      75     377 .. 0.82

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 2.6e-22
                                       HHHHHHH.HHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCCT CS
                         SBP_bac_1  14 vakafek.ehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkda 89 
                                       + ++fe      ++ + e + ++++ +  + ai++ + p  v  ++n +  ++ + g++ p ++++++y    ++ +
  gi|336255163|ref|YP_004598270.1|  87 A-AEFENwSDEEVNLTTEVITWDQVFESWASAIQGQNTP-NVSEMANEHAVDYGSRGVVRPNTELFNEYD---DWYD 158
                                       4.666554444588889999*****************88.*****************************3...4444 PP

                                       EEEEHHHHTHHHHCEEEESEEEE.EEEEEEEETTTHHCTTGGG.SHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHH CS
                         SBP_bac_1  90 adklsssvlpkildskvlyvPly.aargliYNkdlfekagldp.pwtWdelveaakklkekgkkpiggarggsasgt 164
                                       + ++++ +++ +++     +P+  ++r ++ N+d++e+ag d  p+tW+elv+ a  +   + k+ g +  gs+s+ 
  gi|336255163|ref|YP_004598270.1| 159 TPSYWGNYDGEVWG-----FPWFvEVRNFYANTDILEDAGHDSiPETWEELVDTATDVESETDKT-GFVSAGSQSTG 229
                                       56666666555555.....****55****************************************.55555555555 PP

                                       HHHHHHHHHHHHTGGGEECCCT....HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSE CS
                         SBP_bac_1 165 ayyfalalakslggkvfdkdgg....gldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaam 237
                                       +++ ++  a ++gg++++ +       ld+p+   a  ++  ++ ++    e ++ g ++ dg++a +l  +Geaa+
  gi|336255163|ref|YP_004598270.1| 230 TGQVLYGAAVQAGGEFYGYEDDqwtvELDSPTSLFAHLWMASMQEEW----EIGPGGWAGMDGTDAEQLYREGEAAF 302
                                       55555566666666666666666777999999999999999999888....8************************* PP

                                       EEEEHHHHHHHHCEEEEECHHCHH CS
                         SBP_bac_1 238 aivglwaalaamkvapkvafaadk 261
                                       +i+++ aa+++ +++ +va+ ++ 
  gi|336255163|ref|YP_004598270.1| 303 MINSGDAANNMIDEGDAVADSTSL 326
                                       **********99999998877665 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   2.2   3.3e-08    0.0002       2      26 .]      29      53 ..      28      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.3e-08
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaaa 26
                                       SRR F+ +++A +AA+a++g+a++
  gi|336255163|ref|YP_004598270.1| 29 YSRRGFMETAGAMGAAGATAGLAGC 53
                                      6*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.53u 0.21s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3934.56
//
Query:       gi|336255164|ref|YP_004598271.1|  [L=51]
Description: hypothetical protein Halxa_3786 [Halopiger xanaduensis SH-6]
Scores for 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:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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: 0.34u 0.19s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 448.06
//
Query:       gi|336255165|ref|YP_004598272.1|  [L=561]
Description: chaperonin Cpn60/TCP-1 [Halopiger xanaduensis SH-6]
Scores for 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-89  298.3   0.0      1e-88  298.2   0.0    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


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 !  298.2   0.0   5.7e-93     1e-88       3     489 ..      34     536 ..      32     538 .. 0.88

  Alignments for each domain:
  == domain 1  score: 298.2 bits;  conditional E-value: 5.7e-93
                                       HHHHCCSSTTXXEEEEEETTSE....EEEEXSHHHHHHCSX..XXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHH CS
                        Cpn60_TCP1   3 divkttlGPkGmdKmlvnkggk....vvvTnDGatilkele..iehPaakllveaaesqdeevGDGTttvviLageL 73 
                                       ++v++tlGP G dKm+v ++++     +vTnDG++il+e e   +hP+a+  + +ae++++e+GDGTtt+++La+ L
  gi|336255165|ref|YP_004598272.1|  34 ELVRSTLGPLGVDKMIVRRMQDdrlrGFVTNDGVAILEEFEgeTDHPIANQFIGLAETHEDEIGDGTTTTTLLASDL 110
                                       78***************97765222268***********973369******************************** PP

                                       HHHHHHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCST.........T.HHHHHHHHHHCTTSSXXST.HH CS
                        Cpn60_TCP1  74 leeaekliaagvhpttiiegyekalekaleaLkeiaveisseek.........dreeLlkvartslsskltske.ae 140
                                       l  + +li++gv p++++eg+   ++++le  + +   i++ +          d+++L ++a++ +++    ++  e
  gi|336255165|ref|YP_004598272.1| 111 LATGIDLIEDGVPPVAVVEGFSIGAQRTLEVWDDV--GIPVANTgqpttraafDESRLERIATCGMTNGRAGSWpLE 185
                                       ********************************999..5555533345677888***********9888755554379 PP

                                       HHHHHHHHHH.HCHCCCSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HH CS
                        Cpn60_TCP1 141 elsklvvdAv.klieenekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiekt 216
                                       +l++ vvdAv ++ e +++++ lg + ++ i gg+  dsel++G +   ++  +   +   +  vl++d sLe+ + 
  gi|336255165|ref|YP_004598272.1| 186 RLGDDVVDAVlRAWEPRRGTVHLGYVSIEAIPGGDAADSELIRGTLAPSEPMVE--GTLPVDGGVLVVDGSLEPREI 260
                                       **********99999999*****************************9998877..2333889***********987 PP

                                       CC.HHHCCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHH CS
                        Cpn60_TCP1 217 et.kttvvlsdaeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlaka 292
                                        + ++t++ ++a e++ l    e++  ++  +i++++   v++++++ + + + la ++i + r+vk +d+e l+++
  gi|336255165|ref|YP_004598272.1| 261 RAsSVTIDGDSAGEIAGL----ENEAARIAAAIARADPAAVFVAGDVTHDVGTELAHRDIACFRNVKDSDVEVLSRV 333
                                       442667777777777766....556889************************************************* PP

                                       HT--EBSCGGGGGCGC-EEEEE..EEECCE.TTCCEEEEE..CESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1 293 tGatavssledltpeelGtakk..veeeki.gsekttiie..evksgkiatillrgatdtvldeieraiedAlnvvk 364
                                       tGat+   +    p ++ ++++  v+ ++  g+++++ ++  + ++++++ +++rg t+  +de+ r+i+ +ln+v+
  gi|336255165|ref|YP_004598272.1| 334 TGATIRGPVTPTAPASVAECGRgaVRLREAqGDTTWLEVTapDGADPRSVGLVVRGGTESAADEARRRIKVGLNAVR 410
                                       ****99999777776655554411344444045555556688779******************************** PP

                                       HHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTT CS
                        Cpn60_TCP1 365 naiedekvvpGGGatelelakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgeke 441
                                       +a++ + ++pGGGa+ele+a+++++ a + +g+eqla++afa+ Le+ip+tLa+Na  dpi+ +++lra+h++g+  
  gi|336255165|ref|YP_004598272.1| 411 AAVKRPVALPGGGAAELEAARAVRDLAPKFDGREQLAVDAFADVLESIPRTLARNAARDPIDAVTELRARHDAGHAR 487
                                       ***************************************************************************** PP

                                       EEEETTTTCEEECCCCT.XEEEHHHHHHHHHHHHHHHHHHHCEEEEEXX CS
                        Cpn60_TCP1 442 lgidvesgeiidlveag.vvDplkvkrqalksAteaastiLrideiika 489
                                       +gid++ + + d+v+ag  +D   v +++l  ++e a+++Lrid ++++
  gi|336255165|ref|YP_004598272.1| 488 AGIDANGDLVDDVVAAGgALDAQLVRTSSLARSVEFANSLLRIDGVVRN 536
                                       ****98888999888877****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 4241.90
//
Query:       gi|336255166|ref|YP_004598273.1|  [L=230]
Description: hypothetical protein Halxa_3788 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.067   13.3   1.1      0.067   13.3   1.1    2.1  3  PT-VENN   Pre-toxin domain with VENN motif


Domain annotation for each model (and alignments):
>> PT-VENN  Pre-toxin domain with VENN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.19   3.5e+03      21      28 ..     100     107 ..      98     116 .. 0.62
   2 ?   13.3   1.1   3.7e-06     0.067      20      47 ..     138     165 ..     134     168 .. 0.84
   3 ?   -3.7   0.0      0.74   1.3e+04       8      14 ..     209     215 ..     208     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.19
                           PT-VENN  21 GlaGgvvg 28 
                                       Gl+G+++g
  gi|336255166|ref|YP_004598273.1| 100 GLVGAIAG 107
                                       44455444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.7e-06
                           PT-VENN  20 aGlaGgvvggtladavaGaeagenAVeN 47 
                                       a+++  ++    a+a+ Ga++ge AVe+
  gi|336255166|ref|YP_004598273.1| 138 AAVIVTITVPEGATAAMGAQTGEEAVEF 165
                                       6666677777889**************8 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 0.74
                           PT-VENN   8 EKqtvsa 14 
                                       EKq v++
  gi|336255166|ref|YP_004598273.1| 209 EKQSVLS 215
                                       9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1831.83
//
Query:       gi|336255167|ref|YP_004598274.1|  [L=402]
Description: glycerol-3-phosphate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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  105.9   0.0    5.4e-30  104.7   0.0    1.6  2  ABC_tran         ABC transporter
    8.7e-10   39.3   0.1    3.1e-09   37.5   0.1    2.0  1  OB_MalK          MalK OB fold domain
    4.2e-08   33.4   0.3     0.0063   16.4   0.0    2.9  3  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      5e-06   26.6   0.5    9.6e-05   22.5   0.5    2.7  1  TOBE_2           TOBE domain
    0.00077   19.7   0.1      0.002   18.4   0.0    1.8  2  AAA_22           AAA domain
    0.00081   18.9   0.1       0.62    9.5   0.0    2.2  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00089   19.0   0.0     0.0022   17.7   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
     0.0016   19.0   0.3      0.088   13.4   0.1    2.7  2  CysA_C_terminal  CysA C-terminal regulatory domain
     0.0019   18.6   0.3     0.0053   17.2   0.3    1.8  1  AAA_16           AAA ATPase domain
     0.0033   17.3   0.0     0.0064   16.4   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
  ------ inclusion threshold ------
      0.028   14.6   0.2       0.12   12.6   0.1    1.9  2  AAA_33           AAA domain
      0.031   14.0   0.2          2    8.0   0.0    2.1  2  AAA_15           AAA ATPase domain
       0.06   13.1   0.0       0.11   12.2   0.0    1.4  1  AAA_30           AAA domain
      0.075   12.8   0.1       0.64    9.7   0.0    2.1  2  Cytidylate_kin   Cytidylate kinase
       0.11   12.1   0.1       0.55    9.8   0.1    2.0  2  AAA_25           AAA domain
       0.12   12.8   0.1       0.41   11.1   0.0    1.8  2  AAA_23           AAA domain
       0.25   10.5   0.4       0.45    9.7   0.0    1.5  2  NB-ARC           NB-ARC 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 !  104.7   0.0   5.1e-33   5.4e-30       2     136 ..      21     163 ..      20     164 .. 0.97
   2 ?   -2.6   0.0       6.7   7.1e+03      55      79 ..     172     193 ..     166     228 .. 0.52

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 5.1e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++ +l+++ ge + +vG++G+GKStLl+++agl++ t G+i + g+ ++   l+  ++ i++++q   l p+l+vre
  gi|336255167|ref|YP_004598274.1|  21 EDFNLTIESGEFLTLVGPSGSGKSTLLRMVAGLEDITDGTISIGGERVNL--LPPRHRDIAMVFQSYALYPHLSVRE 95 
                                       6899**********************************************..9************************ PP

                                       H..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n              e  e++e+a++ +g++el d++     ++LSgGq+qrva  ra++++p ++l+DEp 
  gi|336255167|ref|YP_004598274.1|  96 NmafglkrstslpeeEIYERVEDAAELMGIPELLDDRP----KQLSGGQQQRVATGRAIVREPAVFLFDEPL 163
                                       *********99998888889************999998....*****************************7 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.7
                                       HHCCHCEEEE-SS--S-TTSBHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  55 eslrkeigvlpqepqlfpeltvren 79 
                                       +++r e++ ++qe    +++t++ +
  gi|336255167|ref|YP_004598274.1| 172 KHMRTELQRIQQE---LDTTTIYVT 193
                                       5555555556555...222222222 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.1   2.9e-12   3.1e-09       1      53 []     237     290 ..     237     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2.9e-12
                           OB_MalK   1 GSPaMNflpatveedg.vlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                       GSP+MN++++++e  +    + g+v++pl++e++ + + +   ++ lG+RPEhi
  gi|336255167|ref|YP_004598274.1| 237 GSPSMNIFNVRYEPAEnGGRLTGDVDIPLDPEHAEQIETAGSTDLKLGVRPEHI 290
                                       9***********955555899999*****999934555555599*********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 !   16.4   0.0     6e-06    0.0063       3      49 ..      34      71 ..      32     120 .. 0.67
   2 !   13.4   0.0   4.6e-05     0.049     250     298 ..     149     195 ..     109     199 .. 0.80
   3 ?   -0.3   0.0      0.72   7.6e+02     165     215 ..     237     287 ..     218     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsll 49
                                       l+Gp gsGKS+LL+   +l +        td    ++  ++  +ll
  gi|336255167|ref|YP_004598274.1| 34 TLVGPSGSGKSTLLRMVAGLED-------ITDGT--ISIGGERVNLL 71
                                      69***************99944.......33333..22333333444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.6e-05
                            AAA_21 250 allralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                       a+ r +   +++l+DEp ++L+ kl ++  + l ++ ++ ++  i +TH+
  gi|336255167|ref|YP_004598274.1| 149 AIVREP---AVFLFDEPLSNLDAKLRKHMRTELqRIQQELDTTTIYVTHD 195
                                       455544...9********************99966666699********8 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.72
                            AAA_21 165 rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvder 215
                                        ++  nif+  + +a+++++l++ v+ ++++e   + +++g+ + ++  ++
  gi|336255167|ref|YP_004598274.1| 237 GSPSMNIFNVRYEPAENGGRLTGDVDIPLDPEHAEQIETAGSTDLKLGVRP 287
                                       677789999999999999999999999999999999999888777766555 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.5   9.1e-08   9.6e-05       1      54 [.     283     336 ..     283     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.1e-08
                            TOBE_2   1 laiRPEklrlaaagg.anglsGtVedveylGsstryvvelaggqlvvvrqpnadr 54 
                                       l++RPE+++++ ++g a+ +++ V+ +e lG+  +++ el+g+ + +++  +a++
  gi|336255167|ref|YP_004598274.1| 283 LGVRPEHITVS-RTGdAGDIAASVDIIEPLGARDLLYFELEGEGDDTLVSGDAAA 336
                                       79********5.444356************************7664444444443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.9e-06     0.002       4      30 ..      29      55 ..      26     161 .. 0.84
   2 ?   -2.0   0.0       3.9   4.1e+03      84      89 ..     176     181 ..     140     225 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqld 30
                                      +  +l+++G+sG+GK+tllr+++   d
  gi|336255167|ref|YP_004598274.1| 29 SGEFLTLVGPSGSGKSTLLRMVAGLED 55
                                      6789*****************987765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.9
                            AAA_22  84 qalrar 89 
                                         l++ 
  gi|336255167|ref|YP_004598274.1| 176 TELQRI 181
                                       222222 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 !    7.2   0.0    0.0029       3.1      25      41 ..      31      47 ..      21      52 .. 0.84
   2 !    9.5   0.0   0.00059      0.62     134     210 ..     133     207 ..      68     215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0029
                                      SEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnll 41
                                      +f  +vGp GSGKs ll
  gi|336255167|ref|YP_004598274.1| 31 EFLTLVGPSGSGKSTLL 47
                                      68899*********987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00059
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadkl 208
                                       +++LSgG+++ va     A   v+  +++l+De  ++LD+k +k + + l++ +++  +  i +++++e    ++  
  gi|336255167|ref|YP_004598274.1| 133 PKQLSGGQQQRVATGR--A--IVREPAVFLFDEPLSNLDAKLRKHMRTELQRIQQEldTTTIYVTHDQEEAMTMSDR 205
                                       4599999998777643..3..35677899************999999888865555336778888877766666554 PP

                                       EE CS
                                       xx RF
                             SMC_N 209 vg 210
                                       + 
  gi|336255167|ref|YP_004598274.1| 206 IA 207
                                       44 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 !   17.7   0.0   2.1e-06    0.0022      18      39 ..      26      47 ..      19      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                            AAA_29 18 eidlkgatlltGpsGsGKSTll 39
                                      +i+  ++  l+GpsGsGKSTll
  gi|336255167|ref|YP_004598274.1| 26 TIESGEFLTLVGPSGSGKSTLL 47
                                      566444889************8 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.16   1.6e+02       7      22 ..      56      72 ..      55      81 .. 0.80
   2 !   13.4   0.1   8.4e-05     0.088       8      43 .]     252     292 ..     242     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.16
                   CysA_C_terminal  7 vedGklriGglalp.vP 22
                                      + dG++ iGg ++  +P
  gi|336255167|ref|YP_004598274.1| 56 ITDGTISIGGERVNlLP 72
                                      679********999777 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.4e-05
                   CysA_C_terminal   8 edGklriGglalpvP.elaga...dg.qevvayVRPhDlei 43 
                                       e+G+   G++++p+  e+a+    +g  +  ++VRP+++++
  gi|336255167|ref|YP_004598274.1| 252 ENGGRLTGDVDIPLDpEHAEQietAGsTDLKLGVRPEHITV 292
                                       67777789*****766555555554449***********87 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3     5e-06    0.0053      23      46 ..      29      52 ..      20     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellr 46
                                      ++e + l+G+sG+GKs+l+r+++ 
  gi|336255167|ref|YP_004598274.1| 29 SGEFLTLVGPSGSGKSTLLRMVAG 52
                                      347899**************9983 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   6.1e-06    0.0064      98     131 ..      28      62 ..       8      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.1e-06
                                       TT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  98 kd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       ++ ++ +lvG+SG GKStL+ ++++ +++  g +s
  gi|336255167|ref|YP_004598274.1|  28 ESgEFLTLVGPSGSGKSTLLRMVAGLEDITDGTIS 62 
                                       5448899***************9998888777776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00011      0.12       4      20 ..      35      51 ..      33      68 .. 0.88
   2 ?   -1.1   0.0       1.8   1.9e+03      72     107 ..     156     195 ..     105     207 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                            AAA_33  4 lvGlpGsGKstlaerll 20
                                      lvG++GsGKstl++ ++
  gi|336255167|ref|YP_004598274.1| 35 LVGPSGSGKSTLLRMVA 51
                                      89**********99776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                            AAA_33  72 nvildat..nls....rrerarflklarrlgvpvrivvvetd 107
                                        +++d +  nl+    ++ r ++ ++ ++l+   + ++v+ d
  gi|336255167|ref|YP_004598274.1| 156 VFLFDEPlsNLDaklrKHMRTELQRIQQELD--TTTIYVTHD 195
                                       3444555443332221344444444444444..334444444 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    0.0019         2      19      42 ..      25      49 ..      19      54 .. 0.79
   2 ?    3.9   0.1     0.033        35     323     365 ..     153     195 ..     141     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0019
                            AAA_15 19 idlsee.ltvliGkNnsGKSsilea 42
                                      + +++  + +l+G+ +sGKS++l++
  gi|336255167|ref|YP_004598274.1| 25 LTIESGeFLTLVGPSGSGKSTLLRM 49
                                      444444499*************986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.033
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +++++l++EP  +L  ++ k++   l+++ ++ +t +i+ TH 
  gi|336255167|ref|YP_004598274.1| 153 EPAVFLFDEPLSNLDAKLRKHMRTELQRIQQELDTTTIYVTHD 195
                                       67899*************************************7 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   0.00011      0.11      15      41 ..      28      53 ..      21      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalrea 41
                                      +sg  + +l+Gp G+GK+t+l+ ++ +
  gi|336255167|ref|YP_004598274.1| 28 ESG-EFLTLVGPSGSGKSTLLRMVAGL 53
                                      455.4999**************99865 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00061      0.64       2      19 ..      34      51 ..      33      57 .. 0.88
   2 ?    0.7   0.0      0.35   3.7e+02      76     122 ..     103     150 ..      77     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00061
                                      EEE-STTSSHHHHHHHHH CS
                    Cytidylate_kin  2 aiDGPagsGKssvarala 19
                                      ++ GP+gsGKs++ r++a
  gi|336255167|ref|YP_004598274.1| 34 TLVGPSGSGKSTLLRMVA 51
                                      677************998 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.35
                                       -TTGGGSHHHHHHHHHHTTSHHHHHHHHHHHHTT-B.SSBEEEEESSI CS
                    Cytidylate_kin  76 veeelrsdevekavSavaaipavRailvkklrelvk.karvvveGRDi 122
                                        +++l  +e+ ++v   a    + + l ++ ++l   +++ v+ GR i
  gi|336255167|ref|YP_004598274.1| 103 RSTSLPEEEIYERVEDAAELMGIPELLDDRPKQLSGgQQQRVATGRAI 150
                                       566788999999999999999999999999999998889999999987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00052      0.55      30      50 ..      27      47 ..      23      52 .. 0.88
   2 ?   -1.0   0.0       1.1   1.1e+03     166     188 ..     172     194 ..     157     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00052
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +  ge+  l+G++g+GK+tl+
  gi|336255167|ref|YP_004598274.1| 27 IESGEFLTLVGPSGSGKSTLL 47
                                      56799**************97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                            AAA_25 166 galvealeriarrtgaavllvhH 188
                                       +++ + l+ri+++++ +++ v H
  gi|336255167|ref|YP_004598274.1| 172 KHMRTELQRIQQELDTTTIYVTH 194
                                       67778999***********9999 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00039      0.41      20      37 ..      31      48 ..      16      51 .. 0.73
   2 ?   -1.8   0.0       3.5   3.7e+03     118     193 ..     171     186 ..     125     210 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                            AAA_23 20 gltlItGpNGaGKTTild 37
                                       +  ++Gp G+GK+T+l+
  gi|336255167|ref|YP_004598274.1| 31 EFLTLVGPSGSGKSTLLR 48
                                      445689**********97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.5
                            AAA_23 118 eqfisellgskkiilnlilflgqerfeefelkdkkerleelekeleeledekkllekleqekekekeleeleeele 193
                                       ++ ++++l+                                                             +++el 
  gi|336255167|ref|YP_004598274.1| 171 RKHMRTELQ------------------------------------------------------------RIQQELD 186
                                       222222333............................................................2322222 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00043      0.45      21      40 ..      31      50 ..      20      59 .. 0.85
   2 ?   -3.3   0.1       3.7   3.9e+03     210     231 ..     171     192 ..     167     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00043
                                      EEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqi 40
                                       +++lvG  G+GK+tl++ +
  gi|336255167|ref|YP_004598274.1| 31 EFLTLVGPSGSGKSTLLRMV 50
                                      489*************9876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.7
                                       -TCSCCHHHHHHHHHHCTGCCT CS
                            NB-ARC 210 tkktveewkkvlekleskllev 231
                                        k++  e+++++++l++  + v
  gi|336255167|ref|YP_004598274.1| 171 RKHMRTELQRIQQELDTTTIYV 192
                                       5678888888888888777663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); 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: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 2915.27
//
Query:       gi|336255168|ref|YP_004598275.1|  [L=322]
Description: xylose isomerase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-34  118.2   0.7    4.5e-34  117.7   0.7    1.2  1  AP_endonuc_2    Xylose isomerase-like TIM barrel
    2.3e-20   72.1   0.1    4.9e-20   71.0   0.1    1.6  1  AP_endonuc_2_N  AP endonuclease family 2 C terminus


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 !  117.7   0.7     5e-38   4.5e-34       2     194 ..      20     237 ..      19     263 .. 0.90

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 5e-38
                                       HHHHHCT-SEEEEECCTCSHHHHC.......HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvsel.......sdeelrelrkaldelglriaslslftrfgypdederearreesvda 71 
                                       + +a +G+++vEl + +     +l       ++++  e+ +a+++++++i++l +++++ +pd++  +++     ++
  gi|336255168|ref|YP_004598275.1|  20 EYLAGIGVEAVELGCGGFTGDGHLstdthldDEDARVEVLEAVEKYDMEISALATHNNPLHPDDERAAED----DQQ 92 
                                       678999********999999999999999*9999999***************************988888....*** PP

                                       HHHHHHHHHHHTBSEEEEEBCC................GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE-- CS
                      AP_endonuc_2  72 lkraielaaaLGapllvlhpGt................agagpkgseeeawerlaeslneladyaekegvklalEtl 132
                                       l++aiela +LG++ +++++G                 +++ + +  e +w+ +++ + e+ d a++++v +++E +
  gi|336255168|ref|YP_004598275.1|  93 LRDAIELAGQLGVDAITCFSGLpggspndetpnwitapWPSEHLEALEYQWDVAIDYWSEINDLADEHDVDIGIEMH 169
                                       *********************9*************9766666666666***************************** PP

                                       TTTTSSSTCHHHHHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGG..EEEEEE.EESS......T CS
                      AP_endonuc_2 133 agsgvelgdeelarlldavdspnvgvclDtgHlliaeedvddalraladr..ikhvHikDakg......d 194
                                       ++  v+   + +++l ++++ + +g ++D++Hl++++ dv +a+r l++   i+h+H+kD+k+      +
  gi|336255168|ref|YP_004598275.1| 170 PNMLVYEP-QGMLKLREETGER-IGANFDPSHLYWQGIDVTEAIRLLGEEdaIHHFHAKDTKVydanarE 237
                                       *****999.***********65.****************************************6544430 PP

>> AP_endonuc_2_N  AP endonuclease family 2 C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.1   5.4e-24   4.9e-20       1      56 []     267     321 ..     267     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 5.4e-24
                    AP_endonuc_2_N   1 dwkdifsaLrqiGYdgplSiEwEDslmsreeGareAvaflkdkllieeseaafdwa 56 
                                       +wkd++s+Lr+++Ydg+lSiE+EDsl+s +eG+++Av++l + +++e+s+++++wa
  gi|336255168|ref|YP_004598275.1| 267 HWKDVVSTLRMVDYDGALSIEHEDSLTSGREGLEKAVDVLSR-AVFETSPGEAYWA 321
                                       6****************************************6.88**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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 0.21s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2579.12
//
Query:       gi|336255169|ref|YP_004598276.1|  [L=362]
Description: oxidoreductase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-18   68.0   0.3    2.3e-18   67.1   0.1    1.5  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    3.8e-05   23.7   0.0    6.9e-05   22.8   0.0    1.5  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
  ------ inclusion threshold ------
      0.025   14.1   0.0      0.041   13.4   0.0    1.3  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin


Domain annotation for each model (and alignments):
>> 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 !   67.1   0.1   3.9e-22   2.3e-18       6     119 ..       8     127 ..       4     128 .. 0.90
   2 ?   -3.5   0.0         3   1.8e+04      94     109 ..     319     334 ..     318     342 .. 0.68

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 3.9e-22
                                       ETTSHHHHHHHHHHHHTTTTE....EEEEEECSSHHHHHHHHHHTTHE...EESSHHHHHTCTTESEEEE-S-GGGH CS
                      GFO_IDH_MocA   6 iGaGkigskhlrplnesqrle....evvalldpdaeraeavaesfgve...aysdleelladpeidavivatpngth 75 
                                       +G+G  g+++ +++  + + e    +vva++d+++++ e++ + +g++   +y+d +  +a  ++d+++v++p++ h
  gi|336255169|ref|YP_004598276.1|   8 VGTGGQGERWCKQYLPP-NVEdgliDVVAAVDTNEAALENAKDGLGLSgeqCYTDAATAFAVHDADCCTVVVPPQYH 83 
                                       89999999886555444.3334556**********************9***************************** PP

                                       HHHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE CS
                      GFO_IDH_MocA  76 eelakaaleagkhvllEKPlattveeakelvelaekkgklvsvg 119
                                       e+++ +al++  h+l EKP+a+t+++  +++e++++++k+++v+
  gi|336255169|ref|YP_004598276.1|  84 EDVVDEALAHDLHILSEKPIADTLDASVRIAEKVDRADKKMGVT 127
                                       ****************************************9997 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3
                                       SS-SSHHHHHHHHHHH CS
                      GFO_IDH_MocA  94 Plattveeakelvela 109
                                       P+at+v+e  + ++l+
  gi|336255169|ref|YP_004598276.1| 319 PMATNVRENLQSMALV 334
                                       8888888765555544 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.2e-08   6.9e-05      14      98 ..     153     233 ..     140     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.2e-08
                                       EEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCTCCSCSEEEEEEEE CS
                    GFO_IDH_MocA_C  14 svdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaeaaededaavmsvln 90 
                                       +  + +  +++++ ++   +++     ++l++ g+H++D+l  L+ + +++ +a +++ +++e+++d +a   + l+
  gi|336255169|ref|YP_004598276.1| 153 YLMLRFTCNCRSYGSWGAFRHD--IEDPLLIEGGVHHLDILADLADARCETLYAQTWLPEWGEYGGDAQAL--INLT 225
                                       5544566666666666666666..5789**********************************999999999..7788 PP

                                       EEETTEEE CS
                    GFO_IDH_MocA_C  91 lekgsgev 98 
                                       +e+g+ +v
  gi|336255169|ref|YP_004598276.1| 226 FEDGTRAV 233
                                       88777765 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 ?   13.4   0.0   6.9e-06     0.041       8      86 ..       6      96 ..       2     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.9e-06
                                      EEES-SHHHHHHHH.....HHHHTT--EEEEE-TT-HHHHHHHH.......TT-EEEEHHHHHHT-SEEEE-S-HHHHH CS
                              IlvN  8 aviGyGsqGhaqal.....nlrdsgldvvvglregsksvkkAke.......egfevltvaeavkkadvvmiliPDelqk 74
                                        +G G qG+ + +     n+ d  +dvv ++ ++++ +++Ak+       + ++ + +a av++ad  ++++P ++++
  gi|336255169|ref|YP_004598276.1|  6 IQVGTGGQGERWCKqylppNVEDGLIDVVAAVDTNEAALENAKDglglsgeQCYTDAATAFAVHDADCCTVVVPPQYHE 84
                                      55899999999876444558899999**********9999998633331114455556777899*************** PP

                                      HHHHHHTGGG-- CS
                              IlvN 75 evyeeeiepnlk 86
                                      +v++e++++ l+
  gi|336255169|ref|YP_004598276.1| 85 DVVDEALAHDLH 96
                                      *****9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 3198.21
//
Query:       gi|336255170|ref|YP_004598277.1|  [L=482]
Description: aldehyde dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-164  545.8   4.4   7.3e-164  545.6   4.4    1.0  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 !  545.6   4.4  4.1e-168  7.3e-164       1     462 []      13     478 ..      13     478 .. 0.98

  Alignments for each domain:
  == domain 1  score: 545.6 bits;  conditional E-value: 4.1e-168
                                       EET-SS.SEEEEEETT.TCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHH CS
                            Aldedh   1 wveses.etievinPa.tgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaele 75 
                                       w+ese+ et+e++nPa   +v+a++++++a+d+daav+aA++a+++wa++pa++R++iLr++a++le rk+el++l+
  gi|336255170|ref|YP_004598277.1|  13 WTESETgETFETTNPAaPTDVVAEYERSSAADADAAVEAAAAAQDEWANTPAPDRGAILRETASILEGRKQELTTLL 89 
                                       899999788*******99*********************************************************** PP

                                       HHHH---HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEEC.TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHH CS
                            Aldedh  76 tletGkplaearaeveeaidvlryyaelaeklegevlpss.egklalvrrePlGvvgaItPWNfPlllaawklapal 151
                                       t+e Gk  aea++ev++aid++ yyae  ++l g+v + s ++++ +++r P+Gv g+ItPWN+P++++awk+apal
  gi|336255170|ref|YP_004598277.1|  90 TREEGKAHAEASGEVQRAIDIFYYYAEKTRDLGGTVKSASgPQTTLYTVRGPVGVAGLITPWNYPIAIPAWKIAPAL 166
                                       **********************************9988855************************************ PP

                                       HTT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCT CS
                            Aldedh 152 aaGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaakn 228
                                       a+GNt vlKPae +p++al l+e+++eag+P+gv nvvtg g+++g+a+v+h++vd+vsftGs +vg+ ++ +a+++
  gi|336255170|ref|YP_004598277.1| 167 ATGNTLVLKPAEVAPAVALELFEALDEAGIPDGVANVVTGFGATAGNAVVAHDDVDAVSFTGSGQVGQLVYDQATDD 243
                                       ***************************************************************************** PP

                                       TSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT CS
                            Aldedh 229 lkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdplded 305
                                        krv+ ElGGknp++v ++aD++ a+e ++ gafg++GQ C+a+sr++v+ ++ydefv+++v++a+++++g +  ++
  gi|336255170|ref|YP_004598277.1| 244 AKRVQTELGGKNPTVVSDSADVETAAEIVAGGAFGTTGQSCTACSRAVVHTDVYDEFVDAVVAEAEAIEIGPG--DE 318
                                       ************************************************************************9..47 PP

                                       -SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEES CS
                            Aldedh 306 tdvGPliseaqlekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfk 381
                                        d+GP++se++le   +y+e a++ega+l +Gg   e ++  +g+fvePtv+++v++d riaqeE+FGPVl+v++++
  gi|336255170|ref|YP_004598277.1| 319 YDMGPQVSEDELEGTLDYIEIAENEGATLETGGGqPEGDRFGDGHFVEPTVFTGVENDYRIAQEEVFGPVLTVLEVE 395
                                       *******************************8877889999************************************ PP

                                       SHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES..-BSHHHHHHHT CS
                            Aldedh 382 deeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglG..reggkegleey 456
                                       +++ea+++aNd +yGL+a+++t+d ++aer+++++eaG   +N++t g + ++pfgGvk+S+    re+g +g+++y
  gi|336255170|ref|YP_004598277.1| 396 EFDEALAVANDVQYGLSASIVTDDHSEAERFVREIEAGVAKVNEKTSGLELHVPFGGVKNSSSEtwREQGDAGIDFY 472
                                       *********************************************9999999**********9999*********** PP

                                       EEEEEE CS
                            Aldedh 457 tevktv 462
                                       t  ktv
  gi|336255170|ref|YP_004598277.1| 473 TIEKTV 478
                                       *99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.35
# Mc/sec: 4070.52
//
Query:       gi|336255171|ref|YP_004598278.1|  [L=596]
Description: ABC transporter periplasmic protein [Halopiger xanaduensis SH-6]
Scores for complete 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-21   76.4   6.4    2.4e-20   72.9   6.4    2.2  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
      0.061   13.2   0.0       0.11   12.4   0.0    1.3  1  Baseplate  Baseplate protein


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   6.4   2.6e-24   2.4e-20       2     374 ..      97     486 ..      96     488 .. 0.73

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 2.6e-24
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       + p++A++ w+++dD +  ++ L ++  +s G+++tA+D+v +++    ++ +++   ++      +++ a ddyt+
  gi|336255171|ref|YP_004598278.1|  97 YLPRIADD-WSIDDDTLRTEVSLSEEYAWSTGEDITAHDFVTAYKLDGYMGLGMQDFVDI-----EEGIYAEDDYTL 167
                                       679*****.7********************************998887777777777776.....7*********** PP

                                       EEEESSETT.............TTTTHCHHHHHHHGC...................CHTCTCTTTTTGTTTSE-BSS CS
                         SBP_bac_5  79 rftlkkpna.............lfltllaavpasiak...................kaaekeddkdkdtnekpvgtG 123
                                       +++  + ++             ++lt+         +                   +   ++  + + + ++++++G
  gi|336255171|ref|YP_004598278.1| 168 VIEPREEYSdmeeelwmtewaeTNLTVS--------EaqyghfvedfedattedetQRVQESLINYEVSWDEVMYSG 236
                                       *******999987766666443333333........1444446669*********9999999999************ PP

                                       SEEEEEEETTTEEEEEE-TTSTTTSCSSSSEEEEEE-..SHHHHHHHH.HTTSSSEE..ESTTCCTHCHHHHHTTEE CS
                         SBP_bac_5 124 PYklkefkpgqkivlernpdYwgggkpkldriefkvip.dsdaraaal.qsGeiddv..aepppsdieqlkeakglk 196
                                       P++++e +  q +    np+       ++    +++++ +     ++  qsGe+ d+    p ++d++  + +  l+
  gi|336255171|ref|YP_004598278.1| 237 PWVFVEANE-QFADQIPNPE-------HPIAQDWEFFQrTGMYVDEEGiQSGEV-DWgdDTPEIQDVPDKYGKGPLP 304
                                       *****9666.5555555555.......3344456666323334444445*****.6624444445555555555555 PP

                                       EEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSS.STTTSTTCCSCHCCCSHH... CS
                         SBP_bac_5 197 vlyespgggvtylafNtkkppfddkrvRqAlsyAiDreeivkavlegyatpansl.lppsspgadeeykpayka... 269
                                       +     g+++  ++ N++ ++ d ++vR+A++yA+D   + +     ++t  + +  +  s +  ++ + +  +   
  gi|336255171|ref|YP_004598278.1| 305 Y----DGQSFAIIFGNSDEYIRDHPEVRKAITYAVDVPYLTESTA-TDGTEYDEYsAGIDSLYVEDYVDADVLDamp 376
                                       5....6777777777777888888********************4.4444444441444444444444444433899 PP

                                       ....SHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEE..EEEE.CHHHHH CS
                         SBP_bac_5 270 ....ydpekAkklLkeaGykdgdggglrekklkltlllasgspaekaiaeliqqqlkkiGikve..vktv.dwaaty 339
                                            d + A +lL++ G++ ++g++ ++++ ++tl + s ++  +    +i ++l++ Gi+v+  v+ +  w ++ 
  gi|336255171|ref|YP_004598278.1| 377 nyapQDTDRAAELLESVGFERSNGTWQTPEGDTWTLNF-SVGNWFESHSKVISNNLQEFGIDVDhyVEEMpTW-QAT 451
                                       98889*******************99988877766655.5667888999**************9445555444.444 PP

                                       HHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTC CS
                         SBP_bac_5 340 lervkdgdfdmillgwgadypdpdnflnpflsssg 374
                                       + ++ d d+ ++l    a + +p++ ++ ++++++
  gi|336255171|ref|YP_004598278.1| 452 TRANLDFDVTVHLNYGQARNYHPYSDFDGIFNDTN 486
                                       34455555555555677778999988888887765 PP

>> Baseplate  Baseplate protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.2e-05      0.11      24     115 ..     424     509 ..     418     528 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                         Baseplate  24 tglavlnpsgLGvdiendldqyqasqivknRtltlpnfevnveiGlnysaetnrqiykdlvrflnkspytLeyeden 100
                                       +++   n ++ G+d++  ++++ + q       t  n++++v + lny +  n+  y d+  ++n +   L  e  +
  gi|336255171|ref|YP_004598278.1| 424 SKVISNNLQEFGIDVDHYVEEMPTWQA-----TTRANLDFDVTVHLNYGQARNYHPYSDFDGIFNDTNLGLFTE-RT 494
                                       567777778888888888888888874.....35568889999999************************9776.58 PP

                         Baseplate 101 giyyrdvelkdmtlt 115
                                       gi+ +dve+ ++   
  gi|336255171|ref|YP_004598278.1| 495 GIVEEDVEVPEVGNP 509
                                       99*****99888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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: 0.56u 0.20s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 4672.40
//
Query:       gi|336255172|ref|YP_004598279.1|  [L=289]
Description: fumarylacetoacetate (FAA) hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-23   83.2   0.1      3e-22   79.4   0.1    2.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.1   1.7e-26     3e-22      13     218 .]      94     287 ..      80     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 1.7e-26
                                       HHHHTTT.....-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHHHHTTE CS
                     FAA_hydrolase  13 vreagka....aeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsveeAedai 85 
                                       +r+a++       ++ d+++p+  vff +++s  vgp++++ ++a se    E EL+vv+++  +e          i
  gi|336255172|ref|YP_004598279.1|  94 ARKAESSmedmYIDVYDSERPE--VFFKATPSRTVGPDERVGIRADSEWDVPEPELGVVLSD--GE----------I 156
                                       4444333444455666655555..999999****************887667********97..34..........5 PP

                                       EEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEE..TTEEEEEEEG..GGTTT CS
                     FAA_hydrolase  86 aGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrv..ngeevqdsnt..kdmif 158
                                       +Gyt++nD+s R +  ++   l   ++k +d+ +++Gp++ ++++l+dp+dle+++++  +ge++ d +t   +m+ 
  gi|336255172|ref|YP_004598279.1| 157 VGYTIGNDMSSRSIEGRNP--LYLPQAKVYDRCCSLGPCVRSAESLDDPHDLEMWMTIsrDGEVLYDDSTntGKMVR 231
                                       8*************87775..88889****************************9999999999877655449**** PP

                                       SHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE. CS
                     FAA_hydrolase 159 spaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrVa 218
                                       s++el+   ++   ++  +++ltGT        + +  l++gD +e+ +e++G+l n+V+
  gi|336255172|ref|YP_004598279.1| 232 SVEELVDCYTSHNAVPEVSVLLTGTSLV----PDDDFTLREGDLIEIGVEDIGTLSNTVV 287
                                       ********99999************944....67899*********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2313.78
//
Query:       gi|336255173|ref|YP_004598280.1|  [L=253]
Description: IclR family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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  132.7   0.0    9.9e-39  132.1   0.0    1.3  1  IclR            Bacterial transcriptional regulator
    9.9e-13   47.7   0.0    3.2e-12   46.0   0.0    1.9  2  HTH_IclR        IclR helix-turn-helix domain
    1.3e-05   24.7   0.0    2.3e-05   23.9   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    3.9e-05   23.5   0.0    6.8e-05   22.7   0.0    1.4  1  MarR            MarR family
    0.00012   22.5   0.0    0.00027   21.4   0.0    1.5  1  HTH_27          Winged helix DNA-binding domain
     0.0016   18.3   0.0     0.0029   17.5   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0033   17.5   0.0      0.007   16.4   0.0    1.5  1  HTH_20          Helix-turn-helix domain
     0.0042   17.0   0.1      0.011   15.6   0.0    1.7  2  HTH_45          Winged helix-turn-helix
     0.0052   16.6   0.0      0.017   15.0   0.0    1.8  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.022   14.6   0.0    1.4  1  MarR_2          MarR family
      0.012   15.8   0.0      0.039   14.1   0.0    1.8  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.067   13.0   0.0       0.13   12.0   0.0    1.5  1  LexA_DNA_bind   LexA DNA binding domain
      0.075   13.5   0.2        0.2   12.2   0.1    1.7  2  HTH_40          Helix-turn-helix domain
      0.084   12.8   0.0       0.17   11.9   0.0    1.5  1  HTH_11          HTH domain
      0.098   12.9   0.0       0.25   11.6   0.0    1.6  1  UPF0122         Putative helix-turn-helix protein, YlxM / p13
        0.1   12.4   0.0       0.25   11.2   0.0    1.7  1  HTH_10          HTH DNA binding domain


Domain annotation for each model (and alignments):
>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.1   0.0   8.9e-42   9.9e-39       5     127 ..     125     247 ..     121     249 .. 0.97

  Alignments for each domain:
  == domain 1  score: 132.1 bits;  conditional E-value: 8.9e-42
                                       ETTSTT-EEEGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTEEE CS
                              IclR   5 avsaiGtrlplyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegvrc 81 
                                       + ++ G+r+pl++t++GKa+La+ ++ee++++l + +l ++te+Titd+e++ eeL++vReq yavdreE  +g+rc
  gi|336255173|ref|YP_004598280.1| 125 LDTHEGKRVPLHCTGLGKAILAFRPQEEVDEILDANGLPKVTEHTITDRETFSEELENVREQRYAVDREERLNGLRC 201
                                       67899************************************************************************ PP

                                       EEEEEE-TTSSEEEEEEEEEETTTSHHHHHHHHHHHHHHHHHHHHH CS
                              IclR  82 iAapifdasgevvaAvsvsgptarlteeelkeellalvreaArkis 127
                                       iAapi d++ + +aAvsvs+p+ r+ +e++ ++l ++v  +A+ i+
  gi|336255173|ref|YP_004598280.1| 202 IAAPITDDKDRSIAAVSVSCPVHRVGDERFYQDLPEAVLGTANVIE 247
                                       ******************************************9987 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 !   46.0   0.0   2.9e-15   3.2e-12       1      52 []      10      60 ..      10      60 .. 0.97
   2 ?   -2.5   0.0         4   4.5e+03      16      32 ..     149     164 ..     144     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 2.9e-15
                                      HHHHHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR  1 sldRalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                      ++dR+++iL+++ e +++ ++se+A+r ++ kS+vh++L tL ++ yv +dg
  gi|336255173|ref|YP_004598280.1| 10 TVDRTFEILEIIQELDGA-GISEIAERVDIGKSAVHNHLTTLANREYVDKDG 60
                                      69***************8.9*****************************996 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4
                                       BSS-BHHHHHHHHTS-H CS
                          HTH_IclR  16 pqeltlselArrtglpk 32 
                                       pqe  + e+ ++ glpk
  gi|336255173|ref|YP_004598280.1| 149 PQE-EVDEILDANGLPK 164
                                       555.5789999999998 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 !   23.9   0.0     2e-08   2.3e-05       5      47 ..      14      56 ..      12      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2e-08
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +++ILe++q+  +  ++e+Aer+++ +s+v+ +l  L + +++
  gi|336255173|ref|YP_004598280.1| 14 TFEILEIIQELDGAGISEIAERVDIGKSAVHNHLTTLANREYV 56
                                      799***********************************99998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   6.1e-08   6.8e-05       6      49 ..      15      58 ..      12      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.1e-08
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      f+iL+i+ e +++ +se+a+++ + ks+v + l++L  ++++++
  gi|336255173|ref|YP_004598280.1| 15 FEILEIIQELDGAGISEIAERVDIGKSAVHNHLTTLANREYVDK 58
                                      99**************************************9986 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 !   21.4   0.0   2.4e-07   0.00027       6      54 ..      15      62 ..      12      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.4e-07
                            HTH_27  6 alvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                                        +L+ i+ +++++ ++++++r+++++s++++ l  L ++++v + gde
  gi|336255173|ref|YP_004598280.1| 15 FEILEIIQ-ELDGAGISEIAERVDIGKSAVHNHLTTLANREYVDKDGDE 62
                                      5799****.**********************************988887 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 !   17.5   0.0   2.6e-06    0.0029       6      47 .]      16      58 ..      15      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.6e-06
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      +IL + +e   + ++e+ae +++ +s+v  HL  L +  +V+k
  gi|336255173|ref|YP_004598280.1| 16 EILEIIQElDGAGISEIAERVDIGKSAVHNHLTTLANREYVDK 58
                                      56777777666779***********************999986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.3e-06     0.007      14      55 ..      19      57 ..      16      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.3e-06
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      +i ++L   +g+  se+aer+d+ k+ +++HL +L+  ++v+
  gi|336255173|ref|YP_004598280.1| 19 EIIQEL---DGAGISEIAERVDIGKSAVHNHLTTLANREYVD 57
                                      688888...99999*********************9887776 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     1e-05     0.011       8      58 ..      14      65 ..      10      70 .. 0.94
   2 ?   -2.7   0.1       5.3   5.9e+03      48      64 ..     100     121 ..      83     125 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                            HTH_45  8 iadILeais.egeakkTkimykanLsykllnkYLdmLvekglikkskekYvl 58
                                      +++ILe+i+  ++a  ++i  ++++  + +++ L +L ++++++k++++Y +
  gi|336255173|ref|YP_004598280.1| 14 TFEILEIIQeLDGAGISEIAERVDIGKSAVHNHLTTLANREYVDKDGDEYHI 65
                                      589*****97799*************************************87 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.3
                            HTH_45  48 li.....kkskekYvlTekGle 64 
                                       l+     k+  + Y   +kG++
  gi|336255173|ref|YP_004598280.1| 100 LVnllveKNGMGIYLYQAKGEN 121
                                       3333344555666666666665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.5e-05     0.017      19      60 ..      23      64 ..      15      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                      +l+ a ++eiae++++ +s v + L  L ++ +V++   +++
  gi|336255173|ref|YP_004598280.1| 23 ELDGAGISEIAERVDIGKSAVHNHLTTLANREYVDKDGDEYH 64
                                      5677889***************************99877665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     2e-05     0.022      10      53 ..      17      58 ..      13      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +L  +   +g    ++e+a+r ++ ksav+++l  L  + +v +
  gi|336255173|ref|YP_004598280.1| 17 ILEIIQELDG--AGISEIAERVDIGKSAVHNHLTTLANREYVDK 58
                                      6666777777..679**************************986 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 ?   14.1   0.0   3.5e-05     0.039      13      55 ..      17      59 ..      15      62 .. 0.89
   2 ?   -3.2   0.0       9.4     1e+04      38      48 ..      85      95 ..      85      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-05
                                      HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                      I+++  e + ++ +++aer ++ +s V   l  L++ +yv+  
  gi|336255173|ref|YP_004598280.1| 17 ILEIIQELDGAGISEIAERVDIGKSAVHNHLTTLANREYVDKD 59
                                      6677778889999***************************965 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.4
                                      HHHHHHHHHHH CS
                    Fe_dep_repress 38 sVsemlkkLek 48
                                      ++++ + kL++
  gi|336255173|ref|YP_004598280.1| 85 TAQKEVDKLAD 95
                                      79999999987 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 ?   12.0   0.0   0.00012      0.13      28      59 ..      29      59 ..      13      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                      HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                     LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyierd 59
                                      i eia+++ +   sav++hL +L+++ y++ d
  gi|336255173|ref|YP_004598280.1| 29 ISEIAERVDIG-KSAVHNHLTTLANREYVDKD 59
                                      78********9.9*************999875 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00017       0.2      11      43 ..      25      56 ..      16      69 .. 0.88
   2 ?   -2.7   0.0       7.8   8.7e+03      53      60 ..     152     159 ..     143     186 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                            HTH_40 11 eglsieeIAkerglkesTIegHLaelieegeei 43
                                      +g  i eIA++  + +s + +HL+ l++ ++ +
  gi|336255173|ref|YP_004598280.1| 25 DGAGISEIAERVDIGKSAVHNHLTTLANREY-V 56
                                      67889********************999865.4 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.8
                            HTH_40  53 eekeIeea 60 
                                       e +eI +a
  gi|336255173|ref|YP_004598280.1| 152 EVDEILDA 159
                                       44444444 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00015      0.17       1      39 [.      13      50 ..      13      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                            HTH_11  1 RllqilelLleargpisgeeLAeeLnvSrrtvrrdIkaL 39
                                      R++ ile++ e +g   ++e+Ae+ ++ +++v++++ +L
  gi|336255173|ref|YP_004598280.1| 13 RTFEILEIIQELDG-AGISEIAERVDIGKSAVHNHLTTL 50
                                      78899999988888.7899*****************998 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00022      0.25      35      56 ..      28      49 ..      12      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                           UPF0122 35 SlsEiAeefnvsrqavydnikr 56
                                       +sEiAe+ ++ ++av++++ +
  gi|336255173|ref|YP_004598280.1| 28 GISEIAERVDIGKSAVHNHLTT 49
                                      589***************9976 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   0.00023      0.25      24      45 ..      27      48 ..      26      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                            HTH_10 24 vtlkeLAkelGIskstlsehLr 45
                                      + ++e+A++ +I ks++++hL 
  gi|336255173|ref|YP_004598280.1| 27 AGISEIAERVDIGKSAVHNHLT 48
                                      5789****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2062.34
//
Query:       gi|336255174|ref|YP_004598281.1|  [L=389]
Description: hypothetical protein Halxa_3796 [Halopiger xanaduensis SH-6]
Scores for complete 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   3.1    1.8e-44  152.3   3.1    1.1  1  Peripla_BP_4  Periplasmic binding protein domain
    8.2e-09   35.3   0.1    1.1e-08   34.9   0.1    1.1  1  Peripla_BP_1  Periplasmic binding proteins and sugar binding 
  ------ inclusion threshold ------
      0.026   14.3   0.1      0.054   13.4   0.1    1.5  1  TAT_signal    TAT (twin-arginine translocation) pathway signa


Domain annotation for each model (and alignments):
>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.3   3.1     3e-48   1.8e-44       1     255 [.      87     351 ..      87     354 .. 0.92

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 3e-48
                                       EEEEES-SSTCHHHHHHHHHHHHHHHTTCEEEEE.ECSTT-HHHHHHHHHHHHHTT-SEEEE--SSHHHHHHHHHHH CS
                      Peripla_BP_4   1 igvvvkdksnpffsaaregleeaakelgaevtvv.gdaendaaeQvaqiedaiakgvdgiivapvdstalapalkka 76 
                                       i +v +++ ++f+++a  gl +aa +lg++ t++   ++ +++eQ++++e+++a+ +d+i+ ++ d++a ++++++a
  gi|336255174|ref|YP_004598281.1|  87 ITMVCHNAAISFWDPAIGGLHDAASQLGWNATFTgPSGGFSVEEQINILENVVASEPDAIVTTVSDTEAYNSVIQDA 163
                                       6788999999************************55566666*********************************** PP

                                       HHTT-EEEEESTTGCTTT-CEE..........EEEC-HHHHHHHHHHHHHHHCTTH.EEEEEETSCCCHHHHHHHHH CS
                      Peripla_BP_4  77 kaaGIpVvafdsddapsgerla..........yvgfdneaaGelqaeylaeklggkkgkvvilaGspgdpnaeerie 143
                                        ++ I V +f++    ++ r +          +vg+d++ +G++ + +l++kl+++  kv i  ++p ++ +++r+ 
  gi|336255174|ref|YP_004598281.1| 164 LDNDIAVLTFNTNSLREEGRQHmreefgqalpFVGQDQYSSGYANGMALLDKLPDDASKVTIGLADPAHSGQAARAS 240
                                       *************5555555556888888899************************777777789************ PP

                                       HHHHHHHH-TTCEECCEEESTTTCHHHHHHHHHHHHHTTT.ECEEEESSCCHHHCHHHHHHHTTTTSTEEEEEES-H CS
                      Peripla_BP_4 144 gfrkvlkeypgikivaevaganwdaekaqqalealltanp.ldgilaandgmaegalealeaaglagkvvvtgqDat 219
                                       g+++++++ ++i+i + v++  +d +++ +++++ l+anp ldg+ + ++   + + +a e++g+a ++v+ g+D++
  gi|336255174|ref|YP_004598281.1| 241 GAEDAIRQNSDIEITDRVNY-TDDSNEGVSRIANHLAANPeLDGMAGSDAYSWF-IGQAAEEEGMAEDMVIGGFDLD 315
                                       ********88******8788.799999************77****888777777.*************99******* PP

                                       HHHHHHHHTTSSEEEEE--HHHHHHHHHHHHHHHHT CS
                      Peripla_BP_4 220 pealeaikdGtidatvaqdpyelgyaavelavallk 255
                                       + +l++i++G ++ t +qdpy +gy  v  a a+l+
  gi|336255174|ref|YP_004598281.1| 316 QNTLDYIQQGVMNYTTGQDPYSQGYLPVHQAFAYLE 351
                                       ********************************9986 PP

>> Peripla_BP_1  Periplasmic binding proteins and sugar binding domain of LacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   1.9e-12   1.1e-08       4     203 ..      87     302 ..      84     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.9e-12
                                       EEEEES-TTSHHHHHHHHHHHHHHHHHTEEEEEEE-SSHHHHH...HHHHHHHHTT-SEEEEE-S-GG.HHHHHHHH CS
                      Peripla_BP_1   4 lglvlpqldePffldlvkgitkaakehgvdvlllaageeedla...kaidllkakgidgliiatsdts.fdditaka 76 
                                       + +v  +   +f++  + g+  aa+++g++ +     ++  ++   + ++ + a+ +d+++ + sdt+ ++++ + a
  gi|336255174|ref|YP_004598281.1|  87 ITMVCHNAAISFWDPAIGGLHDAASQLGWNATFTGPSGGFSVEeqiNILENVVASEPDAIVTTVSDTEaYNSVIQDA 163
                                       56677777889*******************999876555444423388888889*********66666666666666 PP

                                       HH.T-EEEEESS--B-T...........TTS-EEEE-HHHHHHHHHHHHHHHHHHHT..GEEEEEE-TTSHHHHHHH CS
                      Peripla_BP_1  77 es.gipvialedaidap...........dgvPcvipddtqageestqkLiaeghkrp..iallegpesaltakervq 139
                                          +i v+  +  +              +++P v  d++  g+  +  L+ +       + +  ++  ++++++r+ 
  gi|336255174|ref|YP_004598281.1| 164 LDnDIAVLTFNTNSLREegrqhmreefgQALPFVGQDQYSSGYANGMALLDKLPDDAskVTIGLADPAHSGQAARAS 240
                                       666********9999889********************************99888777899999999999******* PP

                                       HHHHHHHHTT-GGGEEEEE-SSSSHHHHHHHHHHHHTT-TT-SEEE-SSHHHHHHHHHHHHHTT CS
                      Peripla_BP_1 140 GflaalaeaGlevkdvhvalgsndiedaaealnelleshPeidaivaindeaalGavlalkkeG 203
                                       G ++a+++   ++++ +    ++d +++ + + ++l  +Pe+d ++a++d     + +a++ eG
  gi|336255174|ref|YP_004598281.1| 241 GAEDAIRQN-SDIEITDRVNYTDDSNEGVSRIANHLAANPELD-GMAGSDAYSWFIGQAAEEEG 302
                                       *******99.569****************************98.66777777777778888888 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   9.1e-06     0.054       2      24 ..      16      38 ..      15      39 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.1e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      +SRR+ ++  +A aA ++l+gc+
  gi|336255174|ref|YP_004598281.1| 16 ISRRQVMQQLGAIAAVGGLAGCL 38
                                      8*********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3182.28
//
Query:       gi|336255175|ref|YP_004598282.1|  [L=274]
Description: Monosaccharide-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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  118.1   0.0    6.1e-34  117.5   0.0    1.3  1  ABC_tran     ABC transporter
    2.8e-11   43.8   0.2    5.5e-06   26.4   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.6e-05   24.4   0.1     0.0018   17.7   0.1    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00025   20.0   2.5      0.039   12.7   0.5    3.0  2  ABC_ATPase   Predicted ATPase of the ABC class
    0.00066   19.4   0.0     0.0015   18.3   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0012   18.8   0.0     0.0021   18.0   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
     0.0017   18.9   0.0     0.0033   18.0   0.0    1.3  1  AAA_23       AAA domain
     0.0017   18.1   0.0     0.0044   16.8   0.0    1.6  1  AAA_30       AAA domain
     0.0048   17.2   0.3      0.051   13.8   0.3    2.1  1  AAA_22       AAA domain
      0.006   16.3   0.0      0.016   15.0   0.0    1.6  2  AAA_15       AAA ATPase domain
     0.0066   16.9   0.1        1.2    9.6   0.0    2.4  2  AAA          ATPase family associated with various cellular a
     0.0094   16.0   0.1      0.022   14.7   0.1    1.6  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
  ------ inclusion threshold ------
      0.018   14.4   0.1        2.2    7.7   0.1    2.2  2  TniB         Bacterial TniB protein
      0.027   13.4   0.3        1.1    8.1   0.0    2.2  2  AAA_10       AAA-like domain
      0.029   14.5   0.0      0.094   12.8   0.0    1.9  2  MMR_HSR1     50S ribosome-binding GTPase
       0.03   13.9   0.3       0.83    9.2   0.0    2.3  2  AAA_25       AAA domain
      0.039   14.0   0.0      0.068   13.2   0.0    1.4  1  Dynamin_N    Dynamin family
      0.044   13.1   0.0      0.087   12.1   0.0    1.5  1  Zeta_toxin   Zeta toxin
      0.069   12.9   0.0       0.29   10.8   0.0    1.9  2  AAA_24       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 !  117.5   0.0   6.5e-37   6.1e-34       2     137 .]      24     179 ..      23     179 .. 0.94

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 6.5e-37
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       + v+++l+ege++a+vG+nGaGKSt++k+l+g ++pt+Gei++dg+++   +     +  i+++ q+  l ++ tv+
  gi|336255175|ref|YP_004598282.1|  24 EGVDFSLREGEIMALVGDNGAGKSTFIKMLCGVHEPTSGEIHVDGEQVAFeDYSDAREMGIETVYQDLALAEQQTVA 100
                                       679*********************************************994445566679***************** PP

                                       HH.......................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEE CS
                                       xx.......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.......................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpklll 131
                                        n                       ++++++ + l++++++ ++d +v    s LSgGq+q va+aral ++p++l+
  gi|336255175|ref|YP_004598282.1| 101 ANvflgqepvrsdplgrflgvvdkqAMRDRARESLNRVQIPVDPDAKV----SDLSGGQQQAVAVARALQSDPDILI 173
                                       **********************99888899999999999999999999....************************* PP

                                       EESTTT CS
                                       xxxxxx RF
                          ABC_tran 132 lDEpta 137
                                       lDEpt+
  gi|336255175|ref|YP_004598282.1| 174 LDEPTS 179
                                       ****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 !   15.2   0.0   1.5e-05     0.014       1      19 [.      35      53 ..      35      80 .. 0.85
   2 !   26.4   0.0   5.8e-09   5.5e-06     187     298 ..     121     209 ..     101     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdal 19
                                      +++l+G+Ng+GKS++++ l
  gi|336255175|ref|YP_004598282.1| 35 IMALVGDNGAGKSTFIKML 53
                                      689*************987 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 5.8e-09
                            AAA_21 187 rlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllli 263
                                          ++  +++++ s+++++++                       +  +++lS G++++ a++ al +++   ++l++
  gi|336255175|ref|YP_004598282.1| 121 VVDKQAMRDRARESLNRVQIPVDP--------------------DAKVSDLSGGQQQAVAVARALQSDP---DILIL 174
                                       444444555555555444443333....................3345699*******99999999888...***** PP

                            AAA_21 264 DEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       DEp + L  +  r +l+++++l+++g  +il +H+
  gi|336255175|ref|YP_004598282.1| 175 DEPTSALSIEGARNVLRVIDDLRNEGLSIILISHN 209
                                       **********************************8 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 !   17.7   0.1   1.9e-06    0.0018      25     208 ..      34     220 ..      24     229 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsis 100
                                       ++ a+vG NG+GKs ++  ++ v   +s  ++  +  +++ ++  + + + +  +e ++++   + +++ + +v + 
  gi|336255175|ref|YP_004598282.1|  34 EIMALVGDNGAGKSTFIKMLCGVHEPTSG-EIHVDG-EQVAFE--DYSDAREMGIETVYQDLALAeQQTVAANVFLG 106
                                       57789999999999999999666554444.666554.555554..56666677777777655443245566778888 PP

                                       EEEETTSE..EEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTT CS
                                       xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkge..seykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeida 169
                                       ++ +r++       + +k++ +   +e l++++i  +       LSgG+++ va+a    +q  +p  + +lDe  +
  gi|336255175|ref|YP_004598282.1| 107 QEPVRSDPlgRFLGVVDKQAMRDRARESLNRVQIPVDpdakvsDLSGGQQQAVAVARA--LQ-SDPD-ILILDEPTS 179
                                       88887776333333456677777888999999998778888889******98888754..43.4554.789****** PP

                                       TS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHC.CC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx.xxxxxx RF
                             SMC_N 170 aLDeknvkkvaellkekskn.aQfivislreeml.ekadkl 208
                                       aL  +  ++v ++++  +++   +i is++ +++ + ad++
  gi|336255175|ref|YP_004598282.1| 180 ALSIEGARNVLRVIDDLRNEgLSIILISHNIRQVlTLADRV 220
                                       ***************98887699999**9965540444544 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 ?    3.0   0.1     0.037        35     241     264 ..      29      53 ..       9      64 .. 0.81
   2 !   12.7   0.5   4.1e-05     0.039     320     412 ..     148     224 ..     139     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.037
                                       EE-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAl 264
                                        +++G ++++vG +  GKsT ++ l
  gi|336255175|ref|YP_004598282.1|  29 SLREGeIMALVGDNGAGKSTFIKML 53 
                                       688999**************99876 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.1e-05
                                       ESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEES CS
                        ABC_ATPase 320 tedASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvg 396
                                        +d SG   qA+++++al+ + ++l++DE tsA  +               e+ + ++  + +l ++ g+s+il++ 
  gi|336255175|ref|YP_004598282.1| 148 VSDLSGGQQQAVAVARALQSDPDILILDEPTSALSI---------------EGARNVLRVIDDL-RNEGLSIILISH 208
                                       5788****************************9532...............3333344444444.666777777777 PP

                                       S-GCCTTT-SEEEEEE CS
                        ABC_ATPase 397 gsgdyldvAdtvilme 412
                                        + + l++Ad+v ++ 
  gi|336255175|ref|YP_004598282.1| 209 NIRQVLTLADRVSVLA 224
                                       7777777777776665 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 !   18.3   0.0   1.5e-06    0.0015      15      39 ..      26      50 ..      18      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                       ++++++ +++ l+G++G+GKST++
  gi|336255175|ref|YP_004598282.1| 26 VDFSLREGEIMALVGDNGAGKSTFI 50
                                      566676555**************98 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.2e-06    0.0021      90     130 ..      23      64 ..       4     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       +e +   l++ ++++lvG  G+GKSt+i++l + +e   ge+
  gi|336255175|ref|YP_004598282.1|  23 VEGVDFSLREgEIMALVGDNGAGKSTFIKMLCGVHEPTSGEI 64 
                                       556677777779*******************99866655555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.5e-06    0.0033      15      40 ..      26      54 ..      15      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.5e-06
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAik 40
                                      +dF   +  + +++G+NGaGK+T++  ++
  gi|336255175|ref|YP_004598282.1| 26 VDFslrEGEIMALVGDNGAGKSTFIKMLC 54
                                      45555777899**************9988 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.6e-06    0.0044      17     122 ..      33     206 ..      26     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.6e-06
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaa.g.........................grviglAptgkaAkv..Laee 65 
                                       g  +++l+G  G+GK+t +k l  ++e   g                         ++ ++lA ++++A++  L+ +
  gi|336255175|ref|YP_004598282.1|  33 G-EIMALVGDNGAGKSTFIKMLCGVHEPTsGeihvdgeqvafedysdaremgietvYQDLALAEQQTVAANvfLG-Q 107
                                       3.4899*********************99779*******************998887777888877776664444.4 PP

                            AAA_30  66 lgieastiakllkrlk.....................................grarlepg.tllivDEagmv.... 100
                                         ++++ + ++l   +                                      + +l+++ ++li DE   +    
  gi|336255175|ref|YP_004598282.1| 108 EPVRSDPLGRFLGVVDkqamrdrareslnrvqipvdpdakvsdlsggqqqavaVARALQSDpDILILDEPTSAlsie 184
                                       4788888888887777888888888999999999999999999999****999445677777*******76665555 PP

                            AAA_30 101 dtkqlaallkaaekagakvilv 122
                                       +++++ ++++ ++++g ++il+
  gi|336255175|ref|YP_004598282.1| 185 GARNVLRVIDDLRNEGLSIILI 206
                                       6666666666666677888776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.3   5.4e-05     0.051       5     128 ..      33     206 ..      30     214 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.4e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee.....erpevv..fvtlpsstsskdllrellralglelka.... 70 
                                         i++++G  G+GK+t +++l   ++  +   e     e  +v+   +  + +++ ++++++l+ a ++   a    
  gi|336255175|ref|YP_004598282.1|  33 GEIMALVGDNGAGKSTFIKMLCGVHEPTSG--EihvdgE--QVAfeDYSDAREMGIETVYQDLALAEQQTVAAnvfl 105
                                       6799****************9888753333..2456342..333224444444467777777777766666667777 PP

                            AAA_22  71 ......................................erlsseell.ealeqalrarav....ielliiDEaqh.l 103
                                                                             + ++ ++l   + +  + ar +    + +li+DE    l
  gi|336255175|ref|YP_004598282.1| 106 gqepvrsdplgrflgvvdkqamrdrareslnrvqipvdPDAKVSDLSgGQQQAVAVAR-AlqsdPDILILDEPTSaL 181
                                       7777777788888888888888888888888888888644444444422222222222.246777788888888878 PP

                            AAA_22 104 rs.eealeeLrsllnlsrkgvqliLv 128
                                        s e a + Lr + +l+  g+++iL+
  gi|336255175|ref|YP_004598282.1| 182 -SiEGARNVLRVIDDLRNEGLSIILI 206
                                       .7555555555555556688888887 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   1.7e-05     0.016      23      43 ..      34      53 ..      24     109 .. 0.81
   2 ?   -1.4   0.0       1.5   1.5e+03     321     361 ..     166     205 ..     119     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                            AAA_15 23 eeltvliGkNnsGKSsileal 43
                                      e ++ l+G N++GKS+++++l
  gi|336255175|ref|YP_004598282.1| 34 E-IMALVGDNGAGKSTFIKML 53
                                      3.99***************99 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                            AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQvii 361
                                       +++++il+++EP   L ++  + + + + +l n++   +i+
  gi|336255175|ref|YP_004598282.1| 166 QSDPDILILDEPTSALSIEGARNVLRVIDDLRNEGL-SIIL 205
                                       567899999999877777777777777777766664.5555 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 !    9.6   0.0    0.0013       1.2       1      53 [.      36      91 ..      36     105 .. 0.82
   2 ?    5.2   0.0     0.029        28      48     114 ..     157     212 ..     134     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                                      EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCS.SSSTTHHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakelg..vefleisgsell.skyvgesekkirelfkea 53
                                      + l+G  G GK++++k ++   +  +  + ++g ++  ++y  ++e+ i+ + +++
  gi|336255175|ref|YP_004598282.1| 36 MALVGDNGAGKSTFIKMLCGVHEptSGEIHVDGEQVAfEDYSDAREMGIETVYQDL 91
                                      679****************9975335569999999998999999999999999874 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.029
                                       HHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGG CS
                               AAA  48 elfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdk 114
                                       + ++ a++ + +p il++DE  +  + +           +   l+++d+++++   + +i++++++++
  gi|336255175|ref|YP_004598282.1| 157 QAVAVARALQsDPDILILDEPTSALSIE----------GARNVLRVIDDLRNE--GLSIILISHNIRQ 212
                                       44445555556799******99998888..........678888999999884..4777777777655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   2.4e-05     0.022       9      40 ..      12      54 ..       5      66 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                                      HHHHHHHHCH...........TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE  9 algkklakal...........gdvilLeGdLGaGKTtlvrgla 40
                                      +l k++++++           g++++L Gd GaGK+t+++ l+
  gi|336255175|ref|YP_004598282.1| 12 ELTKHFGNVVavegvdfslreGEIMALVGDNGAGKSTFIKMLC 54
                                      444444443333345555555677****************997 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.02        19      38      63 ..      36      61 ..      29      75 .. 0.84
   2 ?    7.7   0.1    0.0023       2.2      91     152 ..     135     199 ..     123     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.02
                              TniB 38 lllvGdsnnGKtmivekFarlhppek 63
                                      + lvGd   GK++ ++  +  h+p++
  gi|336255175|ref|YP_004598282.1| 36 MALVGDNGAGKSTFIKMLCGVHEPTS 61
                                      789*************9998888775 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
                              TniB  91 Lealgaplkararvskl...eqqvlrllrelk..vrvLiiDEihnllagsarkqreflnalksLgne 152
                                       L++++ p+ ++a+vs+l   +qq++++ r+l+  + +Li+DE  ++l  s +  r++l ++  L ne
  gi|336255175|ref|YP_004598282.1| 135 LNRVQIPVDPDAKVSDLsggQQQAVAVARALQsdPDILILDEPTSAL--SIEGARNVLRVIDDLRNE 199
                                       677888888888777663336888888887653379*********99..888899999999999998 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0012       1.1      22      42 ..      34      54 ..      17      64 .. 0.81
   2 ?    3.5   0.0      0.03        28     154     196 ..     183     224 ..     153     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0012
                            AAA_10 22 sasliiGdlGnGKSvlakllv 42
                                        ++++Gd G+GKS ++k+l 
  gi|336255175|ref|YP_004598282.1| 34 EIMALVGDNGAGKSTFIKMLC 54
                                      4569**************985 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.03
                            AAA_10 154 ekvareiarhlesvvkkslaklvfsdgsveeaislekkvtvle 196
                                        + ar++ r ++ +++++l  +++s++ + ++++l  +v vl+
  gi|336255175|ref|YP_004598282.1| 183 IEGARNVLRVIDDLRNEGLSIILISHN-IRQVLTLADRVSVLA 224
                                       566899999999999999999999999.689999999999997 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0    0.0001     0.094       2      22 ..      36      56 ..      35      90 .. 0.86
   2 ?   -1.2   0.0       2.2   2.1e+03      83      83 ..     193     193 ..     125     257 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                                      EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                      +a+vG   +GKSt+i+ l+g 
  gi|336255175|ref|YP_004598282.1| 36 MALVGDNGAGKSTFIKMLCGV 56
                                      589***************984 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.2
                                       E CS
                          MMR_HSR1  83 v 83 
                                       +
  gi|336255175|ref|YP_004598282.1| 193 I 193
                                       2 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00088      0.83      30      50 ..      30      50 ..      25      62 .. 0.90
   2 ?    2.6   0.1      0.09        85     127     159 ..     155     185 ..      91     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00088
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      l++ge+ +l+G+ g+GK+t+ 
  gi|336255175|ref|YP_004598282.1| 30 LREGEIMALVGDNGAGKSTFI 50
                                      679****************96 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.09
                            AAA_25 127 tadvdaleaaieevegvrlvviDplsralggde 159
                                       +++  a+++a+++  +++ +++D  ++al+ + 
  gi|336255175|ref|YP_004598282.1| 155 QQQAVAVARALQS--DPDILILDEPTSALSIEG 185
                                       3444567888888..79******9999887754 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.2e-05     0.068       2      27 ..      37      61 ..      36      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.2e-05
                                      EEEEBTTTTHHHHHHHHHTS--S--- CS
                         Dynamin_N  2 avvGsqSsGKSSvlnaLlgedilprg 27
                                      a+vG+  +GKS+++  L+g +  p++
  gi|336255175|ref|YP_004598282.1| 37 ALVGDNGAGKSTFIKMLCGVH-EPTS 61
                                      79*****************99.4443 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.3e-05     0.087      19      53 ..      36      70 ..      31      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.3e-05
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDd 53
                                      + l+G  GAGKs+ +++l   +e++++ +++d+ +
  gi|336255175|ref|YP_004598282.1| 36 MALVGDNGAGKSTFIKMLCGVHEPTSGEIHVDGEQ 70
                                      6799***************************9876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00031      0.29       5      23 ..      36      58 ..      32     104 .. 0.79
   2 ?   -0.5   0.0      0.93   8.8e+02     108     131 ..     186     209 ..     165     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                            AAA_24  5 iliyGpsgiGKTtlakel....g 23
                                      ++++G++g+GK+t++k+l    +
  gi|336255175|ref|YP_004598282.1| 36 MALVGDNGAGKSTFIKMLcgvhE 58
                                      799*************9966553 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.93
                            AAA_24 108 aeefrrllkklqelrknvifiahe 131
                                       a+ + r++++l++ +  +i+i+h 
  gi|336255175|ref|YP_004598282.1| 186 ARNVLRVIDDLRNEGLSIILISHN 209
                                       456677777777777799999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 2177.05
//
Query:       gi|336255176|ref|YP_004598283.1|  [L=340]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-49  166.7  39.1    7.7e-49  166.3  39.1    1.1  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
      0.067   13.1   2.8      0.077   12.9   0.4    2.4  2  DUF1467       Protein of unknown function (DUF1467)


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.3  39.1   8.6e-53   7.7e-49       2     267 ..      62     331 ..      61     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: 166.3 bits;  conditional E-value: 8.6e-53
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvl 78 
                                       +++ll++aa+++i+++G++ ++ i+G+++l++g+++++++ ++a+ll+ +   +++all+ l++gaavgl++g+ v+
  gi|336255176|ref|YP_004598283.1|  62 LSRLLRQAAPYVIIGIGMTYLM-IGGEFDLSVGSMYGVAGLSFAMLLTDYRLTVPAALLAVLVIGAAVGLANGVVVT 137
                                       6789******************.****************************************************** PP

                      BPD_transp_2  79 rlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv...llalllvlavllllrrt 152
                                       ++++++li+t++++s+l+g++++l  g+++++       +ll+ +g +++ ++  i+   ++++ l++++ l+l++t
  gi|336255176|ref|YP_004598283.1| 138 KVGIPSLITTIGMMSILRGVAYMLTAGGSQQTP---DDLALLELFGGSITVAGVEITymvFWMFGLLIVFGLVLQKT 211
                                       **********************66665555554...555555555555555555555565***************** PP

                      BPD_transp_2 153 rfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGga.... 225
                                       rfG++++a+g++++aa+ +Gi+++r+k++ fvi+g++A++aG++ ++++gs   ++g g+++ +iaavv+Gg+    
  gi|336255176|ref|YP_004598283.1| 212 RFGHHVYATGDDQSAADRSGIDTDRIKIANFVITGIVAAFAGVVAIAYYGSMFGSAGRGFELLIIAAVVIGGTnlfg 288
                                       ***************************************************************************** PP

                      BPD_transp_2 226 ..gsllgtviGaliigvvksllltllgiptelarvllgallilv 267
                                         gs+ g ++G+l+i+v+   ll l  ++ + +  l+ga++i +
  gi|336255176|ref|YP_004598283.1| 289 geGSISGMFLGSLVIAVIPV-LLVLNNMSVDIQETLTGAVIIGA 331
                                       ********************.89999999***********9987 PP

>> DUF1467  Protein of unknown function (DUF1467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   8.5e-06     0.077       6      67 ..     188     255 ..     183     266 .. 0.67
   2 ?   -2.8   0.1      0.67     6e+03      56      70 ..     320     334 ..     315     337 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.5e-06
                           DUF1467   6 alaiYfviWwvvlFavLPfgvrtqdeegevkvpGtdasAParprllr......kvlitTivaavvfal 67 
                                       + + Y+v+W++ l++v  + +++    ++v  +G d+sA  r  +         ++it ivaa+  ++
  gi|336255176|ref|YP_004598283.1| 188 VEITYMVFWMFGLLIVFGLVLQKTRFGHHVYATGDDQSAADRSGIDTdrikiaNFVITGIVAAFAGVV 255
                                       5578****************99999999999********99876643111111234444444433222 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.67
                           DUF1467  56 itTivaavvfalvll 70 
                                         T+  av++++v++
  gi|336255176|ref|YP_004598283.1| 320 QETLTGAVIIGAVMV 334
                                       568889999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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 0.20s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2941.23
//
Query:       gi|336255177|ref|YP_004598284.1|  [L=292]
Description: SMP-30/gluconolaconase/LRE-like region-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-72  242.9   0.0    4.4e-72  242.6   0.0    1.1  1  SGL           SMP-30/Gluconolactonase/LRE-like region
  ------ inclusion threshold ------
       0.21   11.8   0.0       0.41   10.9   0.0    1.4  1  Arylesterase  Arylesterase


Domain annotation for each model (and alignments):
>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.6   0.0   4.9e-76   4.4e-72       2     245 ..      15     255 ..      14     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: 242.6 bits;  conditional E-value: 4.9e-76
                               SGL   2 gEGpvwdeeegaLlwvDilgqrihrldpatgketvldtpe.....svGaiaprkdgrlvvasksglalldlasgele 73 
                                       gEGp+w++ee+ L+wvDi++++++++dpat+++  +   e       G++++ +dg l++  ++++ ++++ s e e
  gi|336255177|ref|YP_004598284.1|  15 GEGPLWHPEEELLYWVDIPAGKLYAYDPATDEYDLAYETEgddepLGGYTIE-ADGALLLFTHGTVSRWEPGSDEAE 90 
                                       9*********************************954444599988999999.************************ PP

                               SGL  74 tladeeedekpllrfNDgvvdpdGrlwfGtmgdeeakgeevgalyrldpdgklervlddltipNGlawspdgktlYl 150
                                       ++a+   d  +++rfND+ +dp+Gr+++Gtm  e +     g lyrl++dg+++ v++d+ ipNG+++++d +t+Y+
  gi|336255177|ref|YP_004598284.1|  91 PVAEI--DG-AETRFNDVIADPEGRVFCGTMPGEGD--L--GDLYRLETDGTVTPVVEDVDIPNGMGFTEDLETFYF 160
                                       ****9..67.89*******************88774..3..77********************************** PP

                               SGL 151 aDsltrkiwaydvdaeggklsnrrvfadlkkgegepDGlavDaeGnvwvAvwgggkvvrfdpdGklieeiklpakrv 227
                                       ++s ++ i+ay++d+e+g +snrr+f++++ ++g+pDG++vD+eG vw+A+w+gg+vvr+d dG+ ++ei+lpa++v
  gi|336255177|ref|YP_004598284.1| 161 TESEEHVIYAYEYDRETGAISNRRPFVEVPSDDGVPDGMTVDEEGSVWSARWNGGRVVRYDRDGEPVDEIELPARKV 237
                                       ***************************************************************************** PP

                               SGL 228 tscaFgGpdlrtLyitsa 245
                                       +s++FgGpd+++Ly+t+a
  gi|336255177|ref|YP_004598284.1| 238 SSVTFGGPDYEDLYLTTA 255
                                       *****************8 PP

>> Arylesterase  Arylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.6e-05      0.41      46      83 ..     136     173 ..     132     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.6e-05
                      Arylesterase  46 vkvvasglssanGInidadkkyiyvadilresihvmkk 83 
                                       v  v++ ++ +nG+++  d    y +++ ++ i++++ 
  gi|336255177|ref|YP_004598284.1| 136 VTPVVEDVDIPNGMGFTEDLETFYFTESEEHVIYAYEY 173
                                       677999******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2310.18
//
Query:       gi|336255178|ref|YP_004598285.1|  [L=329]
Description: NAD-dependent epimerase/dehydratase [Halopiger xanaduensis SH-6]
Scores for complete 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-34  119.3   0.2    1.4e-18   67.2   0.0    2.1  2  Epimerase       NAD dependent epimerase/dehydratase family
    2.4e-11   43.1   0.0    1.7e-09   37.1   0.0    2.1  1  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase
    3.4e-10   39.8   0.1    4.5e-05   23.0   0.0    2.2  2  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase
    7.5e-10   39.0   0.0    1.3e-09   38.2   0.0    1.5  1  NAD_binding_10  NAD(P)H-binding
    1.7e-07   30.7   0.0     0.0013   17.9   0.0    2.2  2  NAD_binding_4   Male sterility protein
      9e-07   28.3   0.1      0.027   13.6   0.0    2.1  2  RmlD_sub_bind   RmlD substrate binding domain
  ------ inclusion threshold ------
      0.016   15.5   0.0      0.033   14.5   0.0    1.5  1  TrkA_N          TrkA-N domain
      0.057   13.0   0.0       0.12   11.9   0.0    1.5  2  NmrA            NmrA-like family
       0.07   12.6   0.0       0.15   11.5   0.0    1.6  1  adh_short       short chain dehydrogenase


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 !   50.5   0.0   9.1e-17   1.8e-13       1      74 [.       4      78 ..       4      88 .. 0.93
   2 !   67.2   0.0   7.2e-22   1.4e-18     106     241 .]      91     224 ..      81     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 9.1e-17
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.- CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.v 74
                                      +lV+G+t fiG++lv++ll++ y+v+ ++r ++++++a +++++ ve+d t++sale++  +++pdav+ + a +
  gi|336255178|ref|YP_004598285.1|  4 ALVIGGTRFIGRHLVEELLAHEYDVTIFNRGNHENPFADDDRVDHVEGDRTNESALEAAAMTVDPDAVFDCVAyQ 78
                                      59*********************************************************************7744 PP

  == domain 2  score: 67.2 bits;  conditional E-value: 7.2e-22
                                       TCTEEEEEEEGGGGTSCSSSS.BSTCSTTS--.......--SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEES CS
                         Epimerase 106 gvkrllflsSsevYGkdaeqp.keettltgpl.......kpnspYaaaKlageklveayaaqyglnaiilrlfnlyG 174
                                       +++ ++++sS + YG+ +  p +e++t  +p+        +++ Y+  K+ g++ v a+a+++ +na+++r+  +yG
  gi|336255178|ref|YP_004598285.1|  91 DCDAYVYISSGAAYGREDI-PkREDETPLEPCtadqatdDSQETYGNRKAEGDRAVFAAAEEG-VNAMAVRPPIVYG 165
                                       56689**********7776.7677777677777666668899***************986666.9************ PP

                                       TTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
                         Epimerase 175 prngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                                       p+    + +  +  +i +++e    v++ gdgt+++  +yveDva a+  v+e+   g++ge+yn+G
  gi|336255178|ref|YP_004598285.1| 166 PH----DYTERLDFWIDRVNEYD-RVIVPGDGTNVWHRVYVEDVASALRIVAER---GESGEAYNVG 224
                                       **....999999*********99.******************************...9999*****9 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 !   37.1   0.0   8.7e-13   1.7e-09       1     230 [.       5     214 ..       5     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 8.7e-13
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +v+Gg+ F+Gr+lv+eL+  e   +v ++   ++++    +   ++ + +egD t+++ le+a   vd      ++ 
  gi|336255178|ref|YP_004598285.1|   5 LVIGGTRFIGRHLVEELLAHE--YDVTIFNRGNHENP---FADDDRVDHVEGDRTNESALEAAAMTVD----PDAVF 72 
                                       69*****************99..59999998777777...44555555789****9998887776665....56667 PP

                         3Beta_HSD  78 dvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyesl........hqday 146
                                       d    + +d      v+   ++ + c      + vY Ss  + g     e+i + ++e+++e++         q++y
  gi|336255178|ref|YP_004598285.1|  73 DCVAYQPRD------VRAATTIFADC-----DAYVYISSGAAYGR----EDIPKREDETPLEPCtadqatddSQETY 134
                                       777877788......66677788777.....578*****999888....666666666666666555556667899* PP

                         3Beta_HSD 147 pesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegd.kllvpllkqlaklglalfkigdeevlsdrvYvgNva 222
                                        + Ka  +++v +a +    +g  ++  a+Rp ++yG+ d ++ + +    ++    ++  gd  ++  rvYv+ va
  gi|336255178|ref|YP_004598285.1| 135 GNRKAEGDRAVFAAAE----EG--VNAMAVRPPIVYGPHDyTERLDFWIDRVNEYDRVIVPGDGTNVWHRVYVEDVA 205
                                       **************99....66..8899**********9844556676677777779******************** PP

                         3Beta_HSD 223 wa.hilAar 230
                                        a  i+A r
  gi|336255178|ref|YP_004598285.1| 206 SAlRIVAER 214
                                       983466655 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 !   23.0   0.0   2.3e-08   4.5e-05       1      81 [.       5      73 ..       5      85 .. 0.83
   2 !   15.0   0.0   6.1e-06     0.012     124     286 ..      95     262 ..      80     296 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.3e-08
                                      EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEE CS
                     GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdev 79
                                      L+ G++ fiG +l+e Ll+ +y+v+++       n g+ e+   d     ++++  ++gD t++s+le +   v+pd+v
  gi|336255178|ref|YP_004598285.1|  5 LVIGGTRFIGRHLVEELLAHEYDVTIF-------NRGNHENPFAD-----DDRVDHVEGDRTNESALEAAAMTVDPDAV 71
                                      899*********************874.......44444444433.....4577889********************99 PP

                                      EE CS
                     GDP_Man_Dehyd 80 yn 81
                                      + 
  gi|336255178|ref|YP_004598285.1| 72 FD 73
                                      75 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 6.1e-06
                                       EEEEEEGGGG-S-SSSSB-TTS----..........-SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-T CS
                     GDP_Man_Dehyd 124 fyqaStsEvYGkvqevpqtEttpfyP..........rsPYaaaKlyadwivvnyreayglfavngilfnhesprrge 190
                                       ++ +S+   YG+ +  + +++tp++P          +  Y+  K+  d  v +  e  g+ a+  +    ++p+   
  gi|336255178|ref|YP_004598285.1|  95 YVYISSGAAYGREDIPKREDETPLEPctadqatddsQETYGNRKAEGDRAVFAAAE-EGVNAMAVRPPIVYGPHD-- 168
                                       56789999999987666677899999888888888899999999999999998877.799999999999999994.. PP

                                       TSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS-.--EEE-TT-EEECHHCHHCCHHCC CS
                     GDP_Man_Dehyd 191 tfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkp.edyviatgethsvrefvelaflel 266
                                        + +r +   + r+++    v++ G++ ++    +v+D+++a++ + +++++ e y++++ + ++++e+vel + +l
  gi|336255178|ref|YP_004598285.1| 169 -YTER-LDFWIDRVNEYD-RVIVPGDGTNVWHRVYVEDVASALRIVAERGESgEAYNVGDRRIVTLEEMVELIADAL 242
                                       .4444.445777877755.78889***********************997763889***************999988 PP

                                       CHHHHHH............T CS
                     GDP_Man_Dehyd 267 gktiewegkgeeevgrakes 286
                                         +++    g +e ++a+ s
  gi|336255178|ref|YP_004598285.1| 243 ETSVDIVHAGPRELEAADLS 262
                                       88877777777776655444 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 !   38.2   0.0   6.8e-13   1.3e-09       1     103 [.       8     105 ..       8     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 6.8e-13
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-S..EEEES---TCCHH CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgad..aVvsalggggkde 75 
                                       G+t  +Gr+lv+ella+ +++vt++ R  ++ + ++++++++ vegd t++++l++a   +d  aV+ +++ + +d 
  gi|336255178|ref|YP_004598285.1|   8 GGTRFIGRHLVEELLAH-EYDVTIFNRGNHENP-FADDDRVDHVEGDRTNESALEAAAMTVDpdAVFDCVAYQPRDV 82 
                                       99***************.5********999999.8999******************99877555***********99 PP

                                       HHHHHHHHHHHHCT--EEEEEEETTTTS CS
                    NAD_binding_10  76 egaknivdaakeagvkRfvlvsaigvgd 103
                                       ++a +i + +++     +v++s+  ++ 
  gi|336255178|ref|YP_004598285.1|  83 RAATTIFADCDA-----YVYISSGAAYG 105
                                       999999988876.....66666666653 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0    0.0001      0.21       3      26 ..       8      31 ..       6      67 .. 0.78
   2 !   17.9   0.0   6.6e-07    0.0013     130     210 ..      94     172 ..      82     203 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0001
                                      -TTSHHHHHHHHHHHHHS-.TEEE CS
                     NAD_binding_4  3 GaTGFLGkvLlekLLrttpevkiy 26
                                      G+T F+G++L+e+LL  + +v+i+
  gi|336255178|ref|YP_004598285.1|  8 GGTRFIGRHLVEELLAHEYDVTIF 31
                                      9****************9987776 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 6.6e-07
                                       -EEEEEE..GGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE- CS
                     NAD_binding_4 130 vllhvST..ayvngeregeveekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRps 204
                                       +++++S+  ay +++  ++ +e++         +  ++ +  ++ ++tY + Ka++++ v +a+++ g++++ vRp+
  gi|336255178|ref|YP_004598285.1|  94 AYVYISSgaAYGREDIPKREDETP--------LEPCTADQATDDSQETYGNRKAEGDRAVFAAAEE-GVNAMAVRPP 161
                                       678999954455555454433333........345556666677889*****************77.********** PP

                                       EEE-.....-S CS
                     NAD_binding_4 205 iitg.....es 210
                                       i++g     e 
  gi|336255178|ref|YP_004598285.1| 162 IVYGphdytER 172
                                       ***95444433 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 !   13.6   0.0   1.3e-05     0.027       4      65 ..       5      81 ..       2      87 .. 0.94
   2 !   12.6   0.0   2.6e-05     0.052     122     282 ..     131     299 ..     119     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                                      EEESTTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHHHHH--SEEEE------HH CS
                     RmlD_sub_bind  4 lvtGanGqlGseLakqlaeeglevlaltre...............eldltdaeavaellkeakpdvvvnaAAytavD 65
                                      lv+G++  +G++L+++l +++++v+ ++r                e d t+++a++++   ++pd+v ++ Ay+  D
  gi|336255178|ref|YP_004598285.1|  5 LVIGGTRFIGRHLVEELLAHEYDVTIFNRGnhenpfadddrvdhvEGDRTNESALEAAAMTVDPDAVFDCVAYQPRD 81
                                      899************************9999******************************************8655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.6e-05
                                       SSHHHHHHHHHHHHHHH...H-SSEEEEEE-SEESSSS.S-HHHHHHHHHHH-SEEEEESS-EE..--EEHHHHHHH CS
                     RmlD_sub_bind 122 lnvYGrtKlaGEqavla...agkkalivRtswvygekg.knfvktmlrlakereelkvvaDqlg..sPTsardlAev 192
                                       + +YG+ K++G +av a   +g +a+ vR + vyg ++  + +   +++++e +++ v  D +      +++d+A++
  gi|336255178|ref|YP_004598285.1| 131 QETYGNRKAEGDRAVFAaaeEGVNAMAVRPPIVYGPHDyTERLDFWIDRVNEYDRVIVPGDGTNvwHRVYVEDVASA 207
                                       579************9844456699*********986526778888999999****999996551156788999999 PP

                                       HHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTT.......SEEEEE-CCCS--SS---SBE-B--HH CS
                     RmlD_sub_bind 193 llqllekaaeekelagvyHlanegetswlefArailkeagads.......eevkpistaeyptpAkRPanSvLdtek 262
                                       l  ++e+  +     + y ++ ++ ++  e+ + i+++++++        +e+++ + +       R    vL+t+k
  gi|336255178|ref|YP_004598285.1| 208 LRIVAERGES----GEAYNVGDRRIVTLEEMVELIADALETSVdivhagpRELEAADLSLDDYVLYRDYPHVLSTAK 280
                                       9999998887....888999999999999999999999998876666666555554444444445555556677777 PP

                                       HHHCCT----BHHHHHHHHH CS
                     RmlD_sub_bind 263 leatfgiklrewrealkevl 282
                                       l+a  g++ ++ +ea+++++
  gi|336255178|ref|YP_004598285.1| 281 LAAL-GWESTPLEEAMERSV 299
                                       6666.666666666666655 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.6e-05     0.033       3      59 ..       6      63 ..       4      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                                      EES-SH.HHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTT CS
                            TrkA_N  3 iiGlGr.vGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeag 59
                                      +iG  r +Gr+l+eeL + ++ dv++  +       + ++ ++ v gd t+e++Le+a 
  gi|336255178|ref|YP_004598285.1|  6 VIGGTRfIGRHLVEELLAhEY-DVTIFNRGNHENPFADDDRVDHVEGDRTNESALEAAA 63
                                      66666637**********666.7999999877777777888***************996 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.1e-05      0.12       2      75 ..       5      78 ..       4      91 .. 0.80
   2 ?   -3.4   0.0       2.9   5.9e+03     182     226 ..     200     243 ..     180     247 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.1e-05
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-S..EEEE---GG CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvd..vvfsvtgfy 75
                                      lviG+T  +G+++v+ ll+++++v +  R  +++  +   +  v  v+gd  +++ l++a  +vd  +vf  ++++
  gi|336255178|ref|YP_004598285.1|  5 LVIGGTRFIGRHLVEELLAHEYDVTIFNRGNHENPFA--DDDRVDHVEGDRTNESALEAAAMTVDpdAVFDCVAYQ 78
                                      7***************************988666554..4778999999999999999999888533676666655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHT CS
                              NmrA 182 aeeDiGafvikilkdprklkgkriklagntlsgneivelfekkig 226
                                        +eD++++   i+ ++ +    +      +++++e+vel+  +++
  gi|336255178|ref|YP_004598285.1| 200 YVEDVASAL-RIVAERGESGEAYNVGDRRIVTLEEMVELIADALE 243
                                       566666553.34444444444444445566777777777766655 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.6e-05      0.15       3      67 ..       4      62 ..       2      69 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.6e-05
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreeveal 67
                                      +lv+G+++ IGr +++el++  ++v++++r + +         ++ +++ ++++D t+++++ea+
  gi|336255178|ref|YP_004598285.1|  4 ALVIGGTRFIGRHLVEELLAHEYDVTIFNRGNHEN------PFADDDRVDHVEGDRTNESALEAA 62
                                      89*************************99886643......222234566677776666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); 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:                         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 0.24s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 2583.50
//
Query:       gi|336255179|ref|YP_004598286.1|  [L=337]
Description: TRASH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   59.8   0.0    4.7e-16   58.8   0.0    1.4  1  ATPase      KaiC
     0.0044   16.6   0.5      0.018   14.7   0.5    1.9  1  AAA_25      AAA domain
  ------ inclusion threshold ------
      0.049   13.6   1.8       0.15   12.1   1.8    1.8  1  zf-FCS      MYM-type Zinc finger with FCS sequence motif
       0.22   11.0   0.0       0.37   10.3   0.0    1.3  1  Elong_Iki1  Elongator subunit Iki1


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   1.1e-19   4.7e-16       2     212 ..      63     297 ..      62     310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.1e-19
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                        tgIe lD +l +Gip ++ vl++G+ Gt  + +  + +++ +e+ gep v v+   p+++  e++ + Gw++    
  gi|336255179|ref|YP_004598286.1|  63 VTGIEPLDSLLPNGIPADAFVLLSGDEGTRRSELLTELVWRALER-GEPAVVVSYANPPTATLERFFQNGWNVLPAL 138
                                       69****************************************999.***************************9999 PP

                            ATPase  79 eegklaiidasesaeesaee.......................kdkedleelieelaeaikeika...krvviDsit 129
                                       e ++l++id ++++ e+  +                       +d +dl +++++l++++++ +      v iDs++
  gi|336255179|ref|YP_004598286.1| 139 EDDRLTVIDCFTHRLEDRDRfletqtewtnfvgeaaadalvevEDPSDLAAVASRLQDVLDDREMsetGIVTIDSLD 215
                                       999**********998777699999***********************************99988322345567777 PP

                            ATPase 130 glayeekeavaReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeiee..elvRtleivk 204
                                        l+   +e+ + + ++ +  ++ k + + i       +  ++  y  +e++ dg++ L+l+ +++   + + l ++k
  gi|336255179|ref|YP_004598286.1| 216 ELDSLLREESVHNFVKDVRATVCKGRFVPIVAGA---TTAGTDPYPEAEYVFDGIVDLRLTDEMTpnARLKQLGVRK 289
                                       7766666666666666666666555555554444...5566777888999********9998888778888888888 PP

                            ATPase 205 mRgtkhsk 212
                                       + g++  +
  gi|336255179|ref|YP_004598286.1| 290 LIGAQFLP 297
                                       76666555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.5   3.9e-06     0.018      15      66 ..      62     123 ..      49     237 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.9e-06
                            AAA_25  15 laapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlg.........p 66 
                                       + + ++p++ l+++ +pa++++ll G++gt  + l+++l+   + +G+p             
  gi|336255179|ref|YP_004598286.1|  62 VVTGIEPLDSLLPNGIPADAFVLLSGDEGTRRSELLTELVWRALeRGEPAVVvsyanpptaT 123
                                       556799***********************************999899976544444333330 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 ?   12.1   1.8   3.3e-05      0.15       2      38 ..      13      44 ..      12      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.3e-05
                            zf-FCS  2 vkkrCwfCkkyikgkpeftyvlendgvvgqFCStsCl 38
                                      v +rC++C+  i+g  e       d+  g+FCSt C+
  gi|336255179|ref|YP_004598286.1| 13 VPFRCDHCHYPIPGEAE-----RADDGDGHFCSTACK 44
                                      6789****999999886.....99999*********7 PP

>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   8.2e-05      0.37      29     120 ..      96     234 ..      79     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.2e-05
                        Elong_Iki1  29 lleelirrakssktkvifvsfe.....tlkk.............................................p 55 
                                       ll el+ ra  +    ++vs++     tl++                                              
  gi|336255179|ref|YP_004598286.1|  96 LLTELVWRALERGEPAVVVSYAnpptaTLERffqngwnvlpaleddrltvidcfthrledrdrfletqtewtnfvgE 172
                                       66777777777888888888876665555557777888888888888888888888888888888888888888888 PP

                        Elong_Iki1  56 kgvdvfieaterskklkelakeiksalspkssekkkkalviiDslnplaslikeeslaaflssll 120
                                       + +d ++e+++ s +l+++a++++  l   +++  +  +v iDsl  l sl +ees+ +f++ + 
  gi|336255179|ref|YP_004598286.1| 173 AAADALVEVEDPS-DLAAVASRLQDVLDDREMS--ETGIVTIDSLDELDSLLREESVHNFVKDVR 234
                                       8999999996665.8**********99776665..799**********99999*******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2442.75
//
Query:       gi|336255180|ref|YP_004598287.1|  [L=581]
Description: hypothetical protein Halxa_3802 [Halopiger xanaduensis SH-6]
Scores for 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  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1111  (0.0619666); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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):               0  [number of targets reported over threshold]
# CPU time: 1.40u 0.32s 00:00:01.72 Elapsed: 00:00:00.48
# Mc/sec: 3655.69
//
Query:       gi|336255181|ref|YP_004598288.1|  [L=236]
Description: hypothetical protein Halxa_3803 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00012   22.5   0.9    0.00024   21.5   0.1    1.9  2  DUF123    Domain of unknown function DUF123


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 !   21.5   0.1   1.3e-08   0.00024       2      31 ..      37      65 ..      36      81 .. 0.88
   2 ?   -2.4   0.1       0.4   7.2e+03      24      37 ..     171     184 ..     161     188 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.3e-08
                            DUF123  2 elkkgvylYvGsalgsgglasRvkrHasls 31
                                      e++ g+y+YvGsa+g+gg+ +Rv+r +s+ 
  gi|336255181|ref|YP_004598288.1| 37 EFAVGAYAYVGSAFGPGGF-ARVDRRRSVL 65
                                      6889***************.9****87765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.4
                            DUF123  24 vkrHaslskkkekk 37 
                                        +rH+s++++++ k
  gi|336255181|ref|YP_004598288.1| 171 ANRHVSVKNETRAK 184
                                       47888888776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1929.00
//
Query:       gi|336255182|ref|YP_004598289.1|  [L=1519]
Description: glutamate synthase (ferredoxin) [Halopiger xanaduensis SH-6]
Scores for 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-157  522.1   0.0   1.2e-156  521.7   0.0    1.2  1  GATase_2         Glutamine amidotransferases class-II
   1.9e-151  504.4   0.1   6.7e-150  499.3   0.0    2.1  2  Glu_synthase     Conserved region in glutamate synthase
   2.4e-116  388.1   0.0   4.5e-116  387.2   0.0    1.5  1  Glu_syn_central  Glutamate synthase central domain
    1.6e-80  269.2   6.2    2.7e-80  268.5   6.2    1.4  1  GXGXG            GXGXG motif
    9.5e-05   21.9   0.9    0.00018   21.0   0.9    1.3  1  NMO              Nitronate monooxygenase
     0.0046   16.0   2.9     0.0046   16.0   2.9    2.5  3  FMN_dh           FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.7   0.0  4.1e-160  1.2e-156       1     420 []      26     442 ..      26     442 .. 0.97

  Alignments for each domain:
  == domain 1  score: 521.7 bits;  conditional E-value: 4.1e-160
                                       -EEEEEE-SSS--BSHHHHHHHHHHHHGGGGS-B-TTSSSBSEEEEEEE--HHHHHHHHHHTT-----GGG-EEEEE CS
                          GATase_2   1 CGvgfiaelkgkkshkivekalealenleHRGavgadektGDGaGillqiPdeflrkeakekgielpeageyavgml 77 
                                       CGvg++++l+g++ h++v ++le+l nleHRG++ga+++tGDGaGi+lq P++f+++++   +++lp+  +yavg +
  gi|336255182|ref|YP_004598289.1|  26 CGVGVVMDLDGDRGHDVVADGLELLVNLEHRGTTGAEKDTGDGAGIMLQTPHTFFESVL---KTNLPD--TYAVGSI 97 
                                       *********************************************************99...567876..9****** PP

                                       EE-SSHHHHHHHHHHHHHHHHHTT-EEEEEEE--B-GGGS-HHHHHH--EEEEEEEE-TT-.--HHHHHHHHHHHHH CS
                          GATase_2  78 flpkdeekaeeakkileeiveeeglevlgwRevpvdksvlgeaakesePsieqvfvekked.lseeelerklyviRk 153
                                       f+p+d++++ee  +  e+++++ +levl wR+vp++++ lg++a +seP + qv+v+ + + ls+e+++r+lyv+R+
  gi|336255182|ref|YP_004598289.1|  98 FFPQDTAAREELVALAEDTFATYDLEVLEWRDVPTNNEDLGKTAVDSEPDVWQVVVAPEDEgLSQEDFDRRLYVARR 174
                                       ********************************************************988777*************** PP

                                       HHGGG.......-BTTBEEEEEESSEEEEEESS-GGGHHHHBHGGGSTT--BSEEEEEE---SSSS--GGGSSS-SS CS
                          GATase_2 154 riekeiakkk..aekefYicslssrtivYkglltseqlkefykdlkdeelesalalvHsRfstntfPsWelaqPlRl 228
                                         e++++  +  ++++fY++sl s+tivYkgll+  q+ ++y+dl+de+++s++++vH+Rfstnt+  W+la+P+R 
  gi|336255182|ref|YP_004598289.1| 175 ALENAVEDAAieNKERFYVVSLDSKTIVYKGLLKGVQVPSYYPDLTDERIDSNFVMVHERFSTNTLGAWHLAHPYRN 251
                                       ****998777768999************************************************************* PP

                                       EEEEE--TTHHHHHHHHHHHCTT--BT-HH.HHHTC--S--.TTS-HHHHHHHHHHHHHHTT--HHHHHHHHS---- CS
                          GATase_2 229 laHnGEintlrGnknwmkareaelksellgdelekllPivn.eegsDsasldnvlellvlsgrslaealmlliPeaw 304
                                       + HnGE nt++Gn+nwm+are+ l+se+l+ +le ++Pi++  ++sD+as+dn+lell++ gr+la+al++l+Peaw
  gi|336255182|ref|YP_004598289.1| 252 IIHNGEFNTIQGNINWMRARETDLESEVLE-DLEAVKPIIDdPDQSDTASVDNALELLMQDGRDLAHALRMLVPEAW 327
                                       ****************************97.9*******973699******************************** PP

                                       TT-GGGTHHHHHHHHHHTTT-----SSEEEEEE-SSEEEEEE-TT--S--EEEEETT--EEEESSTTSS---GGGEE CS
                          GATase_2 305 ennksldkekkafyeyasalmepWDGPalivftdGkvvgavLDRnGLRPaRylvtkddlvvlasEvGvldleeeevv 381
                                       + ++ +d+++k++y+++++l+epWDGPal++ tdG+ vgavLDRnGLRP+Ry vt+d+++++asE+G l+ e+e++ 
  gi|336255182|ref|YP_004598289.1| 328 RGDEGMDEDRKDWYDFHASLVEPWDGPALVAATDGERVGAVLDRNGLRPCRYDVTTDNRLIMASEAGALETEPENIE 404
                                       ***************************************************************************** PP

                                       EEEE--TT-EEEEETTTTEEEEHHHHHHHHHTTS-HHHH CS
                          GATase_2 382 ekgrlqPGrmllvdleegriledeeikkkiaskkpykew 420
                                       e+grlqPG+++l d eegr++ dee+ ++++++  y+ew
  gi|336255182|ref|YP_004598289.1| 405 ERGRLQPGQLFLADPEEGRVIPDEEVFEDLTDE-RYGEW 442
                                       **************************9998764.58887 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 ?    2.9   0.0     0.017        50     249     280 ..     639     670 ..     624     691 .. 0.89
   2 !  499.3   0.0  2.2e-153  6.7e-150       3     367 ..     815    1177 ..     813    1178 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.017
                                       HHB---HHHHHHHHHHHHHHTT-GGG-EEEEE CS
                      Glu_synthase 249 khaGlPlelalaevdqtlkeeglrdrvsliad 280
                                       + + +P +la   v++ l+++glr++v l ++
  gi|336255182|ref|YP_004598289.1| 639 DRVAIPSLLATGGVHHHLVRNGLRNHVGLVVE 670
                                       7789***********************99875 PP

  == domain 2  score: 499.3 bits;  conditional E-value: 2.2e-153
                                        S-HHHHHHHHHHHHH---HHHHHHHHHHHTS..-S-SGGGGEEE--SS--.--GGGS--HHHHHTTEE---B-TT CS
                      Glu_synthase    3 neievikllqkavqveskesidkyrekleer.evlkakrdlleldaaeealikleevepalkikkriltsamSyG 76  
                                         ++++   lq+av+++++e++++++e+++++ ++l+++r lle+d+++++ ++le+vep++ i++r+ t+amS+G
  gi|336255182|ref|YP_004598289.1|  815 WNPNTVGALQQAVRSNDYERYQEFAEQINDQqQNLQTLRGLLEFDSDRDP-VPLEDVEPIKDIVERFSTAAMSLG 888 
                                        57788889******************99876157899*************.8*********************** PP

                                        TS-HHHHHHHHHHHHHHT-B-EETTS---GGGGS-----SEEEE-TT-TT--HHHHHH-SEEEEE---TTSTTS- CS
                      Glu_synthase   77 alseeahealakamnrlgtksntGEGGedeerlktakdvaikQvasgrFGvteeyLnnakaleikiaQGakpgeG 151 
                                        +ls eahe  ++amnrlg+ksn+GEGGe++er+ t+++  +kQvasgrFGvt++yL+na++l+ik+aQG+kpgeG
  gi|336255182|ref|YP_004598289.1|  889 SLSPEAHENNSIAMNRLGGKSNSGEGGEPPERFDTERECNVKQVASGRFGVTSTYLSNAEELQIKMAQGSKPGEG 963 
                                        *************************************************************************** PP

                                        -EE-GGG--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-TTSEEEEEEE-STTHHHHHHHHHHT CS
                      Glu_synthase  152 gqlpgeKvseeiakiRkikpgvdliSPaphhdiysiedlaqliedLkevnkeakvsvKlvaeagvetiaagvaka 226 
                                        g+lpg+Kv e+ia++Rk++pgv+liSP+p hdiysiedl+qli+dLk +n+ea + vKlv+eag++t+aagvaka
  gi|336255182|ref|YP_004598289.1|  964 GHLPGSKVNEMIAHVRKSTPGVGLISPPPLHDIYSIEDLKQLIFDLKAANEEADINVKLVSEAGIGTVAAGVAKA 1038
                                        *************************************************************************** PP

                                        T-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE CS
                      Glu_synthase  227 nadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavg 301 
                                        nad++ i+G++GGTGAspk+sik aGlP+el+lae++q+l++++lrdr+++ adGg+ktg+dv++a++lGA+++ 
  gi|336255182|ref|YP_004598289.1| 1039 NADVVHISGHDGGTGASPKTSIKSAGLPWELGLAEANQMLCATELRDRIRVSADGGMKTGRDVAVAALLGAEEYV 1113
                                        *************************************************************************** PP

                                        -SHHHHHHTT--S---GGGT--TTSSS---HHHH..TT----HHHHHHHHHHHHHHHHHHHHHHT- CS
                      Glu_synthase  302 igtaalialgCimarvChtntCpvGvatqdpeLrkrlkveekaervvnyikalaeevrellaalgi 367 
                                        +gta+l++ gC+mar+Ch ntCpvGvatq+++Lr  +++ +++e+v+ny++++a+e+rel+a+lg+
  gi|336255182|ref|YP_004598289.1| 1114 FGTASLVTSGCVMARQCHKNTCPVGVATQREDLR--KRFPGEPEHVINYMTFIAQELRELMAELGF 1177
                                        **********************************..99**************************98 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 !  387.2   0.0  1.5e-119  4.5e-116       2     279 .]     471     754 ..     470     754 .. 0.95

  Alignments for each domain:
  == domain 1  score: 387.2 bits;  conditional E-value: 1.5e-119
                                       HHHHTT--HHHHHHTHHHHHHHSS--EE-S---S--TTT-SS---GGGGEEE----SSS----TTTTGGG-B--EEE CS
                   Glu_syn_central   2 rqkafgyteedlelllepmakegkeaigsmGdDtplavLsekprllydYFkqlfAqVTNPpiDpiREelvmsletll 78 
                                        q+afgyt+++l++l+epm ++gk+++gsmGdDtpl+vL + +r+l++YFkqlfAqVTNPp+D+iREelv+s+e++l
  gi|336255182|ref|YP_004598289.1| 471 YQAAFGYTHDELDNLIEPMTQKGKDPVGSMGDDTPLSVLADFNRPLFSYFKQLFAQVTNPPLDYIREELVTSMESRL 547
                                       589************************************************************************** PP

                                       S----SSS--GGGG-EEEESSSB--HHHHHHH....HHSSS-EEEEESEE.........SHHHHHHHHHHHHHHHHH CS
                   Glu_syn_central  79 GkegnlleeeeeqakrlklesPiLteeeleklkklkekkefkaktlditfeae......aleealerlceeaeeavr 149
                                       G ++nll+e++e+a++l+l+sPiLt +ele++++++++ +++a+t+dit+e e      +le+a+er++e++ +a++
  gi|336255182|ref|YP_004598289.1| 548 GFQRNLLDESPEHARQLVLDSPILTGAELESIRDCSAN-DITAATIDITYEPEsdelgaDLEAAIERVREDVVDAIE 623
                                       ***********************************655.9**********8887766655***************** PP

                                       TT-SEEEEESS--STTEEE--HHHHHHHHHHHHHHTT-GGG-EEEEEESS--SHHHHHHHHHTT-SEEEEHHHHHHH CS
                   Glu_syn_central 150 egaeilvLsDrkvseervpipslLavgavhhhLvrkglrtkvslvvesgearevhhfavllgyGadavnPylaleti 226
                                       +g++++vLsDr+v+e+rv+ipslLa+g vhhhLvr+glr++v+lvves+++r+vhhfa+l+gyGa a+nPyla++ti
  gi|336255182|ref|YP_004598289.1| 624 DGHDVIVLSDRTVDEDRVAIPSLLATGGVHHHLVRNGLRNHVGLVVESADPRTVHHFATLVGYGAGAINPYLAYQTI 700
                                       ***************************************************************************** PP

                                       HHHHTTTS-.----HHHHHHHHHHHHHHHHHHHTT--BHHHHHHS--EEESSB- CS
                   Glu_syn_central 227 eklveegal.aeeeleknyrkavekGllKimskmGistlqSYkgaqifeavGls 279
                                       e++++  +  ++e++ ++y+ ave+GllKim+kmGist++SY+gaqifeavGl+
  gi|336255182|ref|YP_004598289.1| 701 EDITAGPDGaDTETAIDAYVGAVEDGLLKIMAKMGISTVESYQGAQIFEAVGLD 754
                                       9998776662445555************************************95 PP

>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.5   6.2     9e-84   2.7e-80       2     187 ..    1255    1441 ..    1254    1444 .. 0.96

  Alignments for each domain:
  == domain 1  score: 268.5 bits;  conditional E-value: 9e-84
                                        EE-TT--STTHHHHHHHHHHHTTT---.-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE CS
                             GXGXG    2 eirnldrsvgtilsneiakrygeeglpedtikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivik 76  
                                        e++n+dr+vg++lsn+i++ryge glpedti+++l+G+aGqs+gafla+G++++l+G andyvGkglsgGk+ i+
  gi|336255182|ref|YP_004598289.1| 1255 EVTNVDRTVGAMLSNRITSRYGEPGLPEDTITVDLEGTAGQSFGAFLASGVSMHLNGSANDYVGKGLSGGKVAIR 1329
                                        799************************************************************************ PP

                                        --TT-SS-GGGSB-S-SSTTTT--SEEEEESSB--SSTTTT-SS-EEEESEB-SSTTTT-EEEEEEE-S-B-SSB CS
                             GXGXG   77 pskeskfkaeeniivGnvvlygatgGklfirgkageRfavrnsgatavvegvgdhgceYmtGGvvvvLgktgrnf 151 
                                        ++++++++++eni +Gnv+lygat+G+l+++g ageRfavrnsga+avvegvgdhgceYmtGGvv vLg+tg+nf
  gi|336255182|ref|YP_004598289.1| 1330 TPETANYDPSENIAIGNVALYGATDGQLYVNGVAGERFAVRNSGAKAVVEGVGDHGCEYMTGGVVAVLGETGKNF 1404
                                        *************************************************************************** PP

                                        TTT--EEEEEEE-SSSTHHHHB-TTT-EEEE.S-SHH CS
                             GXGXG  152 aaGmsgGiayvldedekfekklnkelvelek.vedee 187 
                                        aaGmsgG+ayv+d d++f++k n+ +v+l++ +ed++
  gi|336255182|ref|YP_004598289.1| 1405 AAGMSGGVAYVYDPDDEFAAKANTGMVSLHDeLEDKD 1441
                                        ***************************9975144444 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.9     6e-08   0.00018     143     262 ..    1028    1157 ..    1004    1193 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6e-08
                               NMO  143 issvkearkvearGaDalivqGpeaG.GhqGtpevgd.....kglfaLvpqvldavd....iPviAaGGiidrrg 207 
                                        i++v  a  v+++ aD++ + G ++G G  ++ +++      +  +a  +q+l a +    i v A GG+ ++r+
  gi|336255182|ref|YP_004598289.1| 1028 IGTV--AAGVAKANADVVHISGHDGGtGASPKTSIKSaglpwELGLAEANQMLCATElrdrIRVSADGGMKTGRD 1100
                                        3333..55688888*********9996777755555433653333444689999999999*************** PP

                               NMO  208 vaaaLalGAsgvqigtrfLltkesd.akdahkkk.lleaklddteltsavsGrpaRa 262 
                                        va a  lGA+    gt+ L+t+ +  a++ hk+  ++    ++  l +++ G p  +
  gi|336255182|ref|YP_004598289.1| 1101 VAVAALLGAEEYVFGTASLVTSGCVmARQCHKNTcPVGVATQREDLRKRFPGEPEHV 1157
                                        ***********************9526677775413444445555566666655555 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.82   2.5e+03     228     245 ..     616     633 ..     613     651 .. 0.82
   2 !   16.0   2.9   1.5e-06    0.0046     233     304 ..    1035    1119 ..    1027    1127 .. 0.74
   3 ?   -1.2   0.0      0.26   7.8e+02     315     341 ..    1157    1183 ..    1152    1187 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.82
                                       HHHHHHHHTTESEEEE-- CS
                            FMN_dh 228 edakraveaGvdgivvSN 245
                                       ed+  a+e G d iv+S+
  gi|336255182|ref|YP_004598289.1| 616 EDVVDAIEDGHDVIVLSD 633
                                       89**************97 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.5e-06
                                        HHHTTESEEEE--GGGTSSTT---HHHCH........HHH.....HHHH..SS-EEEESS--SHHHHHHHHHTT- CS
                            FMN_dh  233 aveaGvdgivvSNHGGRqldgapatidvL........pei.....veavggrievlvDgGirrGsDvlkAlalGA 294 
                                        +++a +d + +S H G    +  ++i+           e      + ++++ri v +DgG ++G Dv+ A  lGA
  gi|336255182|ref|YP_004598289.1| 1035 VAKANADVVHISGHDGGTGASPKTSIKSAglpwelglAEAnqmlcATELRDRIRVSADGGMKTGRDVAVAALLGA 1109
                                        567888888888888866666666665544444434422233444778899************************ PP

                                        SEEEESHHHH CS
                            FMN_dh  295 davllGRpfl 304 
                                        +  ++G + l
  gi|336255182|ref|YP_004598289.1| 1110 EEYVFGTASL 1119
                                        9988887665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.26
                                        HHHHHHHHHHHHHHHHHHHT-SBHHHH CS
                            FMN_dh  315 vervleilraelertmallGvksvael 341 
                                        v +++  + +el++ ma lG+++++e+
  gi|336255182|ref|YP_004598289.1| 1157 VINYMTFIAQELRELMAELGFETLDEM 1183
                                        667788999**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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: 0.90u 0.25s 00:00:01.14 Elapsed: 00:00:00.43
# Mc/sec: 10710.04
//
Query:       gi|336255183|ref|YP_004598290.1|  [L=493]
Description: Prolyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for 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-23   82.9   0.0      5e-23   82.0   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    2.3e-21   75.7   0.7    5.4e-21   74.6   0.7    1.7  1  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
    1.4e-20   73.2   0.2    2.9e-20   72.2   0.2    1.5  1  HGTP_anticodon  Anticodon binding domain
  ------ inclusion threshold ------
       0.15   12.7   0.1        4.6    7.9   0.0    2.8  3  TIR_2           TIR domain


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 !   82.0   0.0   1.1e-26     5e-23       6     176 ..     105     275 ..      98     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 1.1e-26
                                       TTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                      tRNA-synt_2b   6 rndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddsl 80 
                                       + +++++++Pt+e  ++  + d+ +rs ++LPl+l q +++ R E+ ++++ +R +eF +++g+  ha  ++++ ++
  gi|336255183|ref|YP_004598290.1| 105 ELEERLAVRPTSESIITPFMADW-VRShRDLPLRLNQWCSVVRWEATETKPFFRTKEFMWQEGHTAHAsSEDAWKEV 180
                                       56899*****************9.***556****************99********************8899***** PP

                                       HHHHHHHHHHHHHTT.SCEEEEEE..GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  81 rdlikaisriferlglefraiiel..msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennr 155
                                          + +++r++e+++    ++++    ++k + ++ ++ +ea+++  +k ++ gt + lg++++e++++t++de+++
  gi|336255183|ref|YP_004598290.1| 181 WTRLGQYERVYEDVLA-IPVLRGKkpEHDKFPGADTTTTVEALMP-DGKSVQGGTSHHLGQSFAEAFDITFVDEDEE 255
                                       *************973.3456666667777799999*********.9****************************** PP

                                       EEEEEEEEEEEEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 156 eksvimicaaigveRllsail 176
                                       e++ +++  +++  R l+a++
  gi|336255183|ref|YP_004598290.1| 256 ERTAYTTSWGLS-WRALGALV 275
                                       ********9999.78888876 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 !   74.6   0.7   1.2e-24   5.4e-21       2      69 .]     417     493 .]     416     493 .] 0.94

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.2e-24
                                       HHHHHHHHTT-.EEEEEESSGHHHHHHHHHHHS-EEEEEESSB........-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                         ProRS-C_1   2 eefkealekkg.fvlapWcgeeecEekIkeetgakslcipfdq........epseegtkCivcgkpakkwvlfgrsY 69 
                                       ee++ ++ k+g +v++pWcg+e+cEe Ike+++a++++ p+++         p++e+++C vcg+pa+++++f++sY
  gi|336255183|ref|YP_004598290.1| 417 EEIMGTIGKHGgYVKTPWCGDEACEEAIKEKVAAEIVMQPLEDeggetageVPEPEEDECGVCGEPADEIAYFAKSY 493
                                       899*****9999*****************************96667778888999********************** PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.2   6.4e-24   2.9e-20       1      92 [.     294     388 ..     294     390 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 6.4e-24
                                       SEEEEESSSS..HHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET CS
                    HGTP_anticodon   1 qvvviplnek..aeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrdr 74 
                                       qvv++p+ ++  +++++ey + +a+eL++ag+rveldd +++++g+k++e++l g+p+++++G++e+e+++vt+ +r
  gi|336255183|ref|YP_004598290.1| 294 QVVIVPIWQEdtKDDVLEYSENIADELEEAGFRVELDDrDERNPGFKFNEHELNGVPLRLEIGPNEVEDEEVTLVHR 370
                                       8******99999788************************************************************** PP

                                       TTCEEEEEETTHHHHHHH CS
                    HGTP_anticodon  75 dtreqervsldelveklk 92 
                                        + eq   ++de+v+ + 
  gi|336255183|ref|YP_004598290.1| 371 PDNEQSVGDRDEIVDTVD 388
                                       **************9886 PP

>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.9   8.4e+03      70     107 ..     104     145 ..      97     153 .. 0.61
   2 ?    7.9   0.0     0.001       4.6      11      40 ..     311     341 ..     304     349 .. 0.77
   3 ?    1.4   0.0      0.11   4.7e+02      11      77 ..     382     445 ..     375     462 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.9
                             TIR_2  70 eeleaaleaaeegkkrlipvlle...p.ekpplaslqyidls 107
                                       eele  l+ ++++++ + p++ +   +  + pl+  q+  + 
  gi|336255183|ref|YP_004598290.1| 104 EELEERLAVRPTSESIITPFMADwvrShRDLPLRLNQWCSVV 145
                                       566666666677777788888886531222235666666655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.001
                             TIR_2  11 ewaeklaeaLeaagirvwldrwdl.kpgedw 40 
                                       e+ e++a++Le+ag+rv ld +d   pg ++
  gi|336255183|ref|YP_004598290.1| 311 EYSENIADELEEAGFRVELDDRDErNPGFKF 341
                                       67799************88887743666555 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.11
                             TIR_2  11 ewaeklaeaLeaagirvwldrwdlkpgedweeeieeaiessdvvlvvlspa..ylesewcree.leaale 77 
                                       e+++ + ++Le+  ++ +++     + e++ee+i+ea    + ++  ++++  y++ +wc +e  e a++
  gi|336255183|ref|YP_004598290.1| 382 EIVDTVDAHLEEI-YDKLYE----TAEENLEENIREAHSPEE-IMGTIGKHggYVKTPWCGDEaCEEAIK 445
                                       5666777777766.443333....346788888876666666.666666666899999999973555654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); 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):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.37
# Mc/sec: 3995.60
//
Query:       gi|336255184|ref|YP_004598291.1|  [L=177]
Description: NUDIX hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-16   59.4   2.7    4.9e-16   59.0   2.7    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 !   59.0   2.7   2.7e-20   4.9e-16      14     129 ..      26     137 ..      21     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 2.7e-20
                                       TSEEEEEEESSSSTTTEE.SSEEECBTTSHHHHHHHHHHHHHHS..EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX  14 kgevLlvrrskkpfpgWe.lPgGkvepgEtpeeAArREleEEtG..leaellellgrlhylapydgpygdeheilyv 87 
                                        +evLl++ ++    gW   PgGk+e +Etp+e+A+RE++EE+G  +++ +le  g+l+ l+ +     +eh +++v
  gi|336255184|ref|YP_004598291.1|  26 ANEVLLIEKRRGLGEGWYnGPGGKLEGDETPRECAVRETREEVGleIDPADLEKAGELRFLLDG-----EEHTFCHV 97 
                                       4579999977455555955*******999***************66688899999977665544.....59****** PP

                                       EE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHH CS
                             NUDIX  88 fl.eevegelepndenevsevrwvpleellkeklaaesrkllp 129
                                       fl  +++ge++    +e +  +wv+++e+  e++++++r +lp
  gi|336255184|ref|YP_004598291.1|  98 FLtTAFDGEPTAS--DE-ARPEWVDIDEVPYEQMWEDDRLWLP 137
                                       **9******8877..44.3356*******99999888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       176  (0.0098165); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); 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: 0.38u 0.19s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1456.74
//
Query:       gi|336255185|ref|YP_004598292.1|  [L=1253]
Description: UvrD/REP helicase [Halopiger xanaduensis SH-6]
Scores for 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-49  168.4   0.0    8.6e-49  166.7   0.0    1.8  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
    3.5e-28   99.0   0.0    1.3e-13   51.1   0.0    3.0  3  UvrD_C           UvrD-like helicase C-terminal domain
    1.9e-26   93.2   0.0    1.2e-25   90.5   0.0    2.5  2  AAA_19           AAA domain
    1.9e-18   67.3   1.8    5.1e-18   65.9   0.0    2.7  3  PDDEXK_1         PD-(D/E)XK nuclease superfamily
    9.7e-09   34.9   0.2    0.00032   20.5   0.0    3.3  3  UvrD_C_2         UvrD-like helicase C-terminal domain
    3.3e-07   30.1   0.0    0.00025   20.7   0.0    2.8  3  AAA_12           AAA domain
    0.00029   20.6   0.0    0.00083   19.1   0.0    1.7  1  AAA_30           AAA domain
     0.0021   17.9   0.1      0.066   12.9   0.0    2.8  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase


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 !  166.7   0.0   3.8e-52   8.6e-49       4     314 ..      21     426 ..      19     427 .. 0.81

  Alignments for each domain:
  == domain 1  score: 166.7 bits;  conditional E-value: 3.8e-52
                                       HHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-H CS
                     UvrD-helicase   4 eqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdde 80 
                                       +qr+ i s    i v A+AG+GKT+++  ri + i+++ ++pd++lv+TF n Aa  ++  ++e+l  +        
  gi|336255185|ref|YP_004598292.1|  21 NQRAVIDSDAACISVDAGAGTGKTTTMLMRIEHAIENGDVDPDDVLVLTFANEAAGSIRDAVAERLDPE-------- 89 
                                       5888889999999****************************************************9987........ PP

                                       HHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTTTHHHHHHHHH CS
                     UvrD-helicase  81 rlrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqellkelleksaddslnldkkklekl 157
                                              ++  ++++T Hsfc+++++++a+++g+ p+f+i +e++   +  + l  ++   +a  + n + ++l   
  gi|336255185|ref|YP_004598292.1|  90 -------TAAAIDVYTYHSFCYRLVREYAYSLGYSPEFEIVTEHTRRRIVGRLLATNDYGFAASPERNGPRSDLTDA 159
                                       .......589***********************************77444443334444334444445555555555 PP

                                       HHHHHCCCCCH.................................................................. CS
                     UvrD-helicase 158 ikelsksrnik.................................................................. 168
                                       + ++++    +                                                                  
  gi|336255185|ref|YP_004598292.1| 160 VDDFIRTMSQEdvtperlraglpdvrtielcnefvlwlerragrnlsfdneglryfnrdehletareslvgygklve 236
                                       5555554444466677777888888888888888888999999999999999999999999999999********** PP

                                       ....................................HHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS...... CS
                     UvrD-helicase 169 ....................................keelslskskaeelrelvskakekqlspkelkkaf...... 203
                                                                           +e+lsl++   ++l  ++   +   +++++ ++ +      
  gi|336255185|ref|YP_004598292.1| 237 ycrekiaespepfreddvvqdvdrylrvlqtcvtetIEALSLEEPTTKQLPRALFGNEIWRQKTERIEQSPfgrlkh 313
                                       *************9999999999888888888888844444444333333333322222222222222222556665 PP

                                       .TSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHH CS
                     UvrD-helicase 204 .ekasdlqkkiaeflkeyqeqkkeenalDfsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkll 279
                                         +   l +  a+++ +y+e++ ee+alDf++l+  ++ell++ e +a+++  +++ + +DE+QDT+++Q+ +++ l
  gi|336255185|ref|YP_004598292.1| 314 yVEFLRLARHYADVYADYHETLAEERALDFDELVRTATELLDD-EAIADEITGQWEQVYCDEFQDTDETQFGLITEL 389
                                       45556778899****************************9997.9******************************** PP

                                       HTTTTT..EEEEE-GGG--GGGGTB-THHHHHHHHHS CS
                     UvrD-helicase 280 asghee..lfmvGDpkQsIYgFRgAdielflkkkkdf 314
                                       + g++   l+ +GD++Q+IYg+Rg d e + +  +++
  gi|336255185|ref|YP_004598292.1| 390 TGGPDRpnLLAIGDKDQAIYGWRGTDREGLDRLADEY 426
                                       ***98788*****************999888777766 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 ?   -0.7   0.0      0.33   7.4e+02     162     226 ..     246     340 ..     220     365 .. 0.71
   2 !   44.0   0.0     8e-15   1.8e-11       1     138 [.     432     584 ..     432     614 .. 0.81
   3 !   51.1   0.0   5.9e-17   1.3e-13     276     345 ..     706     800 ..     624     804 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.33
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxx............... RF
                            UvrD_C 162 ltDfikedtleygeeFieliraleeknl....................elllkkiektaeer............... 203
                                       +  f ++d ++ ++++++ ++    +++                    e     i ++++er               
  gi|336255185|ref|YP_004598292.1| 246 PEPFREDDVVQDVDRYLRVLQTCVTETIealsleepttkqlpralfgnE-----IWRQKTERieqspfgrlkhyvef 317
                                       5567778888889999999998888888777777777777775444431.....44444444555555557777777 PP

                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 204 qalvskyadlfkelaeklaelke 226
                                        +l ++yad ++ + e lae ++
  gi|336255185|ref|YP_004598292.1| 318 LRLARHYADVYADYHETLAEERA 340
                                       77777777777777777776554 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 8e-15
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx.......xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            UvrD_C   1 ivLekNyRStksLlkaankflenilnrrale..kek.......ktvekge.kivvleaeteeeEaekiaatikall. 66 
                                       i Le N+RS +++l+++n +     ++++l+             t+e+ +  ++v +a+  e+ a+++a t+ +ll 
  gi|336255185|ref|YP_004598292.1| 432 IELELNFRSRQEILDLTNYCDYGLQSSKTLRevD-RdrgenadDTAEPVDrVVKVESADIPESTADQVATTVSRLLn 507
                                       689***************8865444443333332.23566555555555545667777777899999********9* PP

                                       .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  67 .....ekneklediavLvRsnkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkllankqdkialkrilkr 138
                                              +  led+av+vR+n+ a+ ++++L++ +ip+ + ++ +    + i+++l yl+ l+ ++ ++ l+r+l  
  gi|336255185|ref|YP_004598292.1| 508 geaetVPQRSLEDVAVIVRTNRHAQAVADELRERRIPYEISGSPRGEISPGIRTVLSYLRALVDPDADVHLRRVLLY 584
                                       9998888999********************************999999*************************7643 PP

  == domain 3  score: 51.1 bits;  conditional E-value: 5.9e-17
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxx....................xxx RF
                            UvrD_C 276 seleeskkkekipiiTiHqAKGlEFdvVflagleegtfP.........syrskk....................ekr 323
                                       +  ++ ++ ++i ++T+HqAKGlEFd+V +  l++++           +    +                     ++
  gi|336255185|ref|YP_004598292.1| 706 ERTRGTQSSDSIDVMTVHQAKGLEFDTVLVPYLSDEEWCvesdyaqraQ----ErllaatlddevdsplladlaAET 778
                                       334455555****************************997766654440....156666666777777788888889 PP

                                       xxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 324 leEEkRlfYVaiTRAkkrLfis 345
                                       ++EE R++ Va+TRA + Lf+ 
  gi|336255185|ref|YP_004598292.1| 779 VAEEWRVLHVALTRAENHLFVF 800
                                       ********************95 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.0   5.4e-29   1.2e-25       2     144 ..      22     410 ..      21     412 .. 0.97
   2 ?   -3.3   0.0       4.5     1e+04      67      84 ..     892     909 ..     862     962 .. 0.76

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 5.4e-29
                            AAA_19   2 reavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.......atT 71 
                                       ++av ++ + ++ v aG+GtGKT+++ +++++++e+g+v+p+++l+++f++ Aa  +r+++a+ + +        +T
  gi|336255185|ref|YP_004598292.1|  22 QRAVIDSDAACISVDAGAGTGKTTTMLMRIEHAIENGDVDPDDVLVLTFANEAAGSIRDAVAERLDPetaaaidVYT 98 
                                       56777999***************************************************99666666899999999* PP

                            AAA_19  72 iHrlal....................................................................... 77 
                                       +H++                                                                         
  gi|336255185|ref|YP_004598292.1|  99 YHSFCYrlvreyayslgyspefeivtehtrrrivgrllatndygfaasperngprsdltdavddfirtmsqedvtpe 175
                                       **9987*********************************************************************** PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|336255185|ref|YP_004598292.1| 176 rlraglpdvrtielcnefvlwlerragrnlsfdneglryfnrdehletareslvgygklveycrekiaespepfred 252
                                       ***************************************************************************** PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|336255185|ref|YP_004598292.1| 253 dvvqdvdrylrvlqtcvtetiealsleepttkqlpralfgneiwrqkterieqspfgrlkhyveflrlarhyadvya 329
                                       ***************************************************************************** PP

                            AAA_19  78 ...........ldfddlltealelleeaeeekklqeee.llivDEfqdvdelqyrLlkallgekkk..lllvGDpdQ 140
                                                  ldfd+l+ +a ell++++  ++++ ++  +  DEfqd+de+q+ L+ +l+g  ++  ll++GD+dQ
  gi|336255185|ref|YP_004598292.1| 330 dyhetlaeeraLDFDELVRTATELLDDEAIADEITGQWeQVYCDEFQDTDETQFGLITELTGGPDRpnLLAIGDKDQ 406
                                       **************************9999999999************************96444344********* PP

                            AAA_19 141 liyv 144
                                       +iy 
  gi|336255185|ref|YP_004598292.1| 407 AIYG 410
                                       **96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.5
                            AAA_19  67 aeatTiHrlalldfddll 84 
                                       ++++T+H+l+ l  d++l
  gi|336255185|ref|YP_004598292.1| 892 EAIETVHQLGRLLRDGTL 909
                                       458999999885444444 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 ?   -2.1   0.1       1.3   2.9e+03      28      79 ..     300     363 ..     277     383 .. 0.59
   2 ?   -2.9   0.1       2.2   4.9e+03      35     106 ..     603     677 ..     583     695 .. 0.56
   3 !   65.9   0.0   2.3e-21   5.1e-18       3     252 ..     963    1227 ..     961    1228 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                          PDDEXK_1  28 eeeleapdlGtlvHaa....leefye.........wkkldke...dleelleeaveelwpellleeei 79 
                                       +e++e++ +G+l H +    l+   +          ++l +e   d++el+ + ++el+++++ ++ei
  gi|336255185|ref|YP_004598292.1| 300 TERIEQSPFGRLKHYVeflrLA---RhyadvyadyHETLAEEralDFDELV-RTATELLDDEAIADEI 363
                                       5566666666666644322222...12335666653334444456777777.5555566665555554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.2
                          PDDEXK_1  35 dlGtlvHaaleefye....wkkldke.dleelleeaveelwpellleeeilessarlrylaeklkevleklverlae 106
                                         G+l+ a+++   +     ++l+ + d+ e l + ++++ p  ++ ++ + + +rl+++  +++++  + ++r+ e
  gi|336255185|ref|YP_004598292.1| 603 REGSLYDAVFDIDPDdlenPGRLETArDHLEEL-ATLRDVYPLSGFVRR-FRDLTRLEWFLTDEERAELDHLDRFVE 677
                                       557777777753333444433333334333333.345566666666664.578888888888887777777776666 PP

  == domain 3  score: 65.9 bits;  conditional E-value: 2.3e-21
                          PDDEXK_1    3 SvsrletfleCplrfflryllgl..re...........eeelea..pdlGtlvHaaleefyewkkldkedleell 62  
                                        S+s++et  +Cp++++l+++      +           +   ++  + +Gt++H+++ee +     d e ++e +
  gi|336255185|ref|YP_004598292.1|  963 SYSAMETHDTCPRKHYLEHVVTAidDPlplgtvdspdeN--AASgsRIVGTVFHDVAEEAFY---RDYETRAEWR 1032
                                        9**********************8722577778876433..333536**********97655...2556888888 PP

                          PDDEXK_1   63 eeaveelwpellleeeilessarlrylaeklkevleklverlaeeleakrgfrpvalelefg............. 124 
                                        e+av++l +++lle++     + l+ + +  +++++++ + +ae       ++p+a e+ f+             
  gi|336255185|ref|YP_004598292.1| 1033 EAAVRHLTARDLLEHRE----PVLACIDRYFEATAAAFGRPVAE-------WEPLAAEVPFSlssvdgvagdvig 1096
                                        88899999998888865....44555555555555555555555.......445555544444444444444555 PP

                          PDDEXK_1  125 ..gekvrLkGriDrvd..................dkegelriiDyKtgsappkskelaelkeglQlllYllalae 179 
                                          +           +                   ++ g+l ++DyKt++   ++ +       +Ql+lY+ a+++
  gi|336255185|ref|YP_004598292.1| 1097 yvD----------SIRrlpaevtadanagltrtqERAGDLAVLDYKTTA---ERID---PDSAVQLALYARACER 1155
                                        551..........44444444433322233333355559**********...5555...33567*********** PP

                          PDDEXK_1  180 geelkeegepagalylrlee.pkvkdeevvkkmalteeeleallqeleelaeeilag.efparpskkCeyCpyks 252 
                                          +   + +++g +y++  e    + +++ +    ++++l  + + ++e++e++ ++   + +p+++C+yCp +s
  gi|336255185|ref|YP_004598292.1| 1156 RFDD--PIGAVGYVYVGDLEgADANTANEPRVELFDPDDLPPWSS-VRETLEAVDDPsYLETTPGEHCQYCPHRS 1227
                                        *443..333555555555343444444444444668999988865.56667******999************997 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 ?   -3.3   0.0       3.8   8.6e+03      12      26 ..     605     619 ..     605     627 .. 0.79
   2 !   20.5   0.0   1.4e-07   0.00032       3      27 ..     718     740 ..     716     744 .. 0.87
   3 !   10.7   0.1   0.00016      0.37      25      51 ..     774     799 ..     770     800 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.8
                          UvrD_C_2  12 GsefpaVivfdpdla 26 
                                       Gs ++aV+ +dpd  
  gi|336255185|ref|YP_004598292.1| 605 GSLYDAVFDIDPDDL 619
                                       8889****9999854 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.4e-07
                          UvrD_C_2   3 yaltihkaQGsefpaVivfdpdlaa 27 
                                        ++t+h+a+G+ef++V v  p+l++
  gi|336255185|ref|YP_004598292.1| 718 DVMTVHQAKGLEFDTVLV--PYLSD 740
                                       68****************..88765 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00016
                          UvrD_C_2  25 laaarmgelrrrlLYtavTRAreklil 51 
                                       laa+   ++  r L++a+TRA  +l++
  gi|336255185|ref|YP_004598292.1| 774 LAAET-VAEEWRVLHVALTRAENHLFV 799
                                       55555.44589*************987 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.89     2e+03      98     151 ..      50     102 ..      43     102 .. 0.82
   2 !    5.9   0.0    0.0038       8.5       7      96 ..     420     514 ..     415     545 .. 0.66
   3 !   20.7   0.0   1.1e-07   0.00025     133     197 ..     707     802 ..     661     804 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.89
                            AAA_12  98 lvekllkkgseeerkkigvitpYraqvellkkklkekeeeksekeievntvdgf 151
                                        +e+ +++g  +  +++ v+t+ ++ +  ++++++e+ + +++ +i+v t  +f
  gi|336255185|ref|YP_004598292.1|  50 RIEHAIENGDVD-PDDVLVLTFANEAAGSIRDAVAERLDPETAAAIDVYTYHSF 102
                                       556666677776.89**********************99999999999997665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0038
                            AAA_12   7 erllkke.kekvvlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkrele...aqealeepleplvfidvekseeek 79 
                                       +rl +++ +++++ L+ ++R+++eI+++ +   Y+  L++++++++ + +     +++ ep  ++v ++  +  e++
  gi|336255185|ref|YP_004598292.1| 420 DRLADEYdDHESIELELNFRSRQEILDLTNYCDYG--LQSSKTLREVDRDrgeNADDTAEPVDRVVKVESADIPEST 494
                                       67777777889999********************9..5566655544444222555666666666666555555555 PP

                            AAA_12  80 ekke...ksyiNeeEaelvv 96 
                                        ++     s   + Eae+v 
  gi|336255185|ref|YP_004598292.1| 495 ADQVattVSRLLNGEAETVP 514
                                       44333334444455555554 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 1.1e-07
                            AAA_12 133 ekeeeksekeievntvdgfQGrekdviilslVRsn....ekk............................eigflkd 177
                                       +++ ++s+ +i+v tv +  G e d +++     +    e +                                 ++
  gi|336255185|ref|YP_004598292.1| 707 RTRGTQSSDSIDVMTVHQAKGLEFDTVLVPYLSDEewcvE-SdyaqraqerllaatlddevdsplladlaAETVAEE 782
                                       3444455566******************998877644441.134455677899999999999999999876679*** PP

                            AAA_12 178 errlNValTRAkskliivGn 197
                                       +r l ValTRA ++l+++G 
  gi|336255185|ref|YP_004598292.1| 783 WRVLHVALTRAENHLFVFGA 802
                                       ******************96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.7e-07   0.00083      11      81 ..      23     107 ..      19     132 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.7e-07
                            AAA_30  11 ealltsgdrvavltGpAGtGKttalkalreaweaag....grviglAptgkaAkvLae..........elgieasti 73 
                                       +a++ s++ +  + ++AGtGKtt++    e++ ++g     +v++l+  ++aA  +++          ++ i+ +t 
  gi|336255185|ref|YP_004598292.1|  23 RAVIDSDAACISVDAGAGTGKTTTMLMRIEHAIENGdvdpDDVLVLTFANEAAGSIRDavaerldpetAAAIDVYTY 99 
                                       5667788889999********99887765555556559999***************963333333322555788888 PP

                            AAA_30  74 akllkrlk 81 
                                       +++ +rl 
  gi|336255185|ref|YP_004598292.1| 100 HSFCYRLV 107
                                       88887765 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 ?    1.1   0.0      0.12   2.7e+02       2      21 ..      34      53 ..      33      85 .. 0.82
   2 !   12.9   0.0     3e-05     0.066     172     214 ..     707     751 ..     668     761 .. 0.80
   3 ?   -1.5   0.0      0.76   1.7e+03     216     232 ..     783     799 ..     771     801 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.12
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrt 21
                                       v++ +G GK+t     +++
  gi|336255185|ref|YP_004598292.1| 34 SVDAGAGTGKTTTMLMRIEH 53
                                      699*********87766655 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3e-05
                   Viral_helicase1 172 ftqalkealgvrevttvhevqGltfdkVtlvllketdlelis...e 214
                                        t+ + ++ + + v+tvh++ Gl+fd+V + +l++ + ++ s   +
  gi|336255185|ref|YP_004598292.1| 707 RTRGTQSSDSID-VMTVHQAKGLEFDTVLVPYLSDEEWCVESdyaQ 751
                                       455566666677.********************9999997775553 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.76
                   Viral_helicase1 216 renllvAlTRhrkslvi 232
                                         +l vAlTR+ + l +
  gi|336255185|ref|YP_004598292.1| 783 WRVLHVALTRAENHLFV 799
                                       56788******998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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):               8  [number of targets reported over threshold]
# CPU time: 0.78u 0.26s 00:00:01.04 Elapsed: 00:00:00.43
# Mc/sec: 8716.26
//
Query:       gi|336255186|ref|YP_004598293.1|  [L=373]
Description: hypothetical protein Halxa_3808 [Halopiger xanaduensis SH-6]
Scores for 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-06   26.1   0.1     0.0026   17.7   0.0    2.3  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.018   14.4   0.9      0.031   13.7   0.9    1.3  1  CobT      Cobalamin biosynthesis protein CobT


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 !   17.7   0.0   2.9e-07    0.0026       2     109 ..      18     138 ..      17     168 .. 0.77
   2 !    6.6   0.0    0.0007       6.3     213     254 ..     313     361 ..     222     362 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.9e-07
                          PDDEXK_1   2 lSvsrletfleCplrfflryllgl..reeeelea.pdlGtlvHaaleefye..........wkkldkedleelleea 65 
                                       lS+  ++t+l+Cp+r+ + ++  +   e+ + +a +d+  l+ +al    e           + ++++++++l + a
  gi|336255186|ref|YP_004598293.1|  18 LSADGIRTYLRCPRRYEFAHVHEFdgDEDDAAAAtADRIDLLRRALCTALErveiddggdsGSGTNDDAADALEDVA 94 
                                       79999*******************87443333331477777777777666677789999974445555777777777 PP

                          PDDEXK_1  66 veelwpellleeeilessarlrylaeklkevleklverlaeele 109
                                       +++l+  + + +e+++s ++ r+ ++ l+++++++ve++ + ++
  gi|336255186|ref|YP_004598293.1|  95 LDRLATLWNEHDERFHSREQRRHERRVLEATVTAYVEAVGADHA 138
                                       78888888889999999999999999999999999997776555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0007
                          PDDEXK_1 213 lteeel.eallqeleelaeeilagefparpskk......CeyCpyksvC 254
                                        t+e++ e + ++l +++ +i ag f++++  +      C  C+y  +C
  gi|336255186|ref|YP_004598293.1| 313 RTHEHRnETVDNRLASVVGRIVAGGFDPSDRWEqvaehaCPDCAYTVCC 361
                                       45566678899999999**************889999************ PP

>> CobT  Cobalamin biosynthesis protein CobT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.9   3.5e-06     0.031      61     111 ..      95     143 ..      94     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-06
                              CobT  61 aDslALrlrhHDakvharlapegkaAravydAlEqaRvEalGarrmaGvaa 111
                                       +D lA     HD++ h+r + +    r+v +A  +a vEa+Ga + aGv +
  gi|336255186|ref|YP_004598293.1|  95 LDRLATLWNEHDERFHSREQRRH--ERRVLEATVTAYVEAVGADHAAGVGQ 143
                                       6889999999******9866555..79*********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 3005.50
//
Query:       gi|336255187|ref|YP_004598294.1|  [L=767]
Description: hypothetical protein Halxa_3809 [Halopiger xanaduensis SH-6]
Scores for 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   13.0   3.5        5.7    6.9   0.1    4.0  3  HlyD_D4   Long alpha hairpin domain of cation efflux system p


Domain annotation for each model (and alignments):
>> HlyD_D4  Long alpha hairpin domain of cation efflux system protein, CusB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1   0.00032       5.7      28      46 ..     141     159 ..     134     164 .. 0.81
   2 ?    2.9   0.0    0.0057     1e+02      32      46 ..     388     402 ..     383     405 .. 0.90
   3 ?    0.6   0.2     0.029   5.2e+02       8      24 ..     494     510 ..     493     517 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHHHCT--HHHH CS
                           HlyD_D4  28 lldaareRlrLaGMpdadI 46 
                                       ll+a r+RlrLa + +  +
  gi|336255187|ref|YP_004598294.1| 141 LLEATRQRLRLADLDERAV 159
                                       799*********8877766 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0057
                                       HHHHHHHCT--HHHH CS
                           HlyD_D4  32 areRlrLaGMpdadI 46 
                                        r+Rlr aG p a+I
  gi|336255187|ref|YP_004598294.1| 388 TRRRLREAGVPTATI 402
                                       589**********99 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.029
                                       THHHHHHHHHHHHHTT- CS
                           HlyD_D4   8 eWvaaQeEYLalkelgd 24 
                                       +Wv+a e Y  ++++ +
  gi|336255187|ref|YP_004598294.1| 494 DWVDAREQYASVRRVLE 510
                                       8*********9999855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (767 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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 0.24s 00:00:00.80 Elapsed: 00:00:00.38
# Mc/sec: 6061.38
//
Query:       gi|336255188|ref|YP_004598295.1|  [L=136]
Description: signal transduction protein with CBS domains [Halopiger xanaduensis SH-6]
Scores for 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-27   95.4   3.9    1.1e-15   57.8   0.2    2.1  2  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 !   39.0   0.5   4.4e-14   7.9e-10       1      54 [.       6      59 ..       6      62 .. 0.93
   2 !   57.8   0.2   6.1e-20   1.1e-15       1      56 [.      71     126 ..      71     127 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 4.4e-14
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54
                                      V+ +m++ ++tv  dt +e+a + m e++++++ VV e ++l Gi+t +D ++ 
  gi|336255188|ref|YP_004598295.1|  6 VARVMSTSLHTVGRDTLVEDAGQVMLENNIGSVVVVGEHNELEGILTSTDFVDI 59
                                      7889*****************************8899999**********9865 PP

  == domain 2  score: 57.8 bits;  conditional E-value: 6.1e-20
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+ +mt+dvvt++ ++++++a+++m+e+g+ +lPVVded+ ++G+v+ +Dl+++l+
  gi|336255188|ref|YP_004598295.1|  71 VERYMTEDVVTASAQDSIRDAADTMIEHGFKHLPVVDEDEGVIGMVSTTDLASYLS 126
                                       7789********************************99999************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1194.19
//
Query:       gi|336255189|ref|YP_004598296.1|  [L=138]
Description: hypothetical protein Halxa_3811 [Halopiger xanaduensis SH-6]
Scores for 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:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.33
# Mc/sec: 1238.70
//
Query:       gi|336255190|ref|YP_004598297.1|  [L=110]
Description: hypothetical protein Halxa_3812 [Halopiger xanaduensis SH-6]
Scores for 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   16.7   0.1      0.057   13.1   0.0    2.2  2  HTH_33    Winged helix-turn helix


Domain annotation for each model (and alignments):
>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   3.2e-06     0.057       2      34 ..      23      55 ..      22      57 .. 0.90
   2 ?    1.1   0.1     0.017     3e+02       8      19 ..      93     104 ..      91     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-06
                            HTH_33  2 fgrWtlarlaqlieerfgvsysvsgvyrlLkrl 34
                                       ++ t+a+la+ +e+ +gvs+++s++ +lL +l
  gi|336255190|ref|YP_004598297.1| 23 RVLATTAQLARTVEDALGVSLEPSTLEDLLLEL 55
                                      5688************************99665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.017
                            HTH_33   8 arlaqlieerfg 19 
                                       ar+ ++i+e+++
  gi|336255190|ref|YP_004598297.1|  93 ARIDEWIAEQTD 104
                                       8999****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 879.79
//
Query:       gi|336255191|ref|YP_004598298.1|  [L=209]
Description: DSBA oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-32  112.5   0.0    2.3e-32  112.3   0.0    1.0  1  DSBA           DSBA-like thioredoxin domain
    8.1e-13   48.9   0.1      1e-10   42.0   0.0    2.2  2  Thioredoxin_4  Thioredoxin
     0.0024   18.3   0.4      0.062   13.8   0.1    2.3  2  Thioredoxin_2  Thioredoxin-like domain


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 !  112.3   0.0   3.9e-36   2.3e-32       2     192 ..       9     206 ..       8     207 .. 0.94

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 3.9e-36
                                       EEEEEBTTBHHHHHHHHHHHHHHHHCCT.EEEEEEE-SSSCHHHHCT.S.GGG.......SHHHHHHHHHHHHHHHH CS
                              DSBA   2 vdeffDvlCPyCylgkerleklaarspd.vkvvlrpfelagakkasgnvgpse.......lpeklkylledlkrlae 70 
                                       v ++ D++CP+C+lg e l+ ++ ++++ ++v ++pf+l+++++   + g  +        +e +++ +++ +rla+
  gi|336255191|ref|YP_004598298.1|   9 VLVYADYVCPFCFLGYESLDLYRDQRDEpLTVDWHPFDLRAQQRG--PDGEIDhdvdngkDDEYYEQAKQNVERLAD 83 
                                       789***********************889*************774..44444466999999999999********** PP

                                       HHT....GGSSHHHHHHHHHHHHHHHHHHH..GHHHHHHHHHHHHHTSSS-TSSHHHHHHHHHHTTS.HHHHHHHHT CS
                              DSBA  71 aegiplrfpkdklknstraarlllaagaeg..laekvvrelfealwsegqaitddqellevaekaGldaeeldeale 145
                                       +++++l    ++  +s +a+r++  a+ ++    e++ r +f+ lw eg++i+++++l e+a +aGl    + e l+
  gi|336255191|ref|YP_004598298.1|  84 RYDVELAQYLKRDVDSYDAQRVARRAADAHpgAFEDFHRGVFDTLWREGRDIGEQDVLEELAAEAGLPDGFVTETLS 160
                                       ******99999877****************9999*********************************9999****** PP

                                       SHHHHHHHHHHHHHHHHTT-SSSSEEEETTCEEEESSSSHHHHHHHH CS
                              DSBA 146 seavkeavrentaaaqslgvtGvPtvvvdgkrmvfGadrldtladal 192
                                       +e+ +++++   a aq+ g+tGvPt++ + + ++ Ga ++++l++ +
  gi|336255191|ref|YP_004598298.1| 161 DEESADELEAAFADAQQTGITGVPTFISGEH-AARGAVPPEQLERLI 206
                                       ***************************9999.***********9987 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.1    0.0043        26      15      28 ..       7      20 ..       2      32 .. 0.84
   2 !   42.0   0.0   1.7e-14     1e-10      57     165 ..      93     207 ..      67     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0043
                                      EEEEEEE-TT-HHH CS
                     Thioredoxin_4 15 vtvieyedlrCphC 28
                                        v +y+d+ Cp C
  gi|336255191|ref|YP_004598298.1|  7 DAVLVYADYVCPFC 20
                                      44789********* PP

  == domain 2  score: 42.0 bits;  conditional E-value: 1.7e-14
                                       .---STTTHHHHHHHTT--TTHHHHHHHHHHHHTHHHHTTS-........HHHHH.....HHHHHTS-------HHH CS
                     Thioredoxin_4  57 ldkekeslkaamaarcageespeaflaikallysqqeewaes........lkelaaealdkdekfeacleeekldal 125
                                       l+++  s++a  +ar+a++ +p af+++++  +++   w+e         l+elaaea+  d  + + l++e+  ++
  gi|336255191|ref|YP_004598298.1|  93 LKRDVDSYDAQRVARRAADAHPGAFEDFHRGVFDT--LWREGrdigeqdvLEELAAEAGLPDGFVTETLSDEESADE 167
                                       33333699*********************955554..55554446666788889999******************** PP

                                       HHHHHHHHHHHT--SS-EEEETTEEE-TT--HHHHHHHHT CS
                     Thioredoxin_4 126 veaeskeakkagiestPtfiingekveepqtyeelkalid 165
                                       +ea+ ++a+++gi+++Ptfi +++   ++ ++e+l++li+
  gi|336255191|ref|YP_004598298.1| 168 LEAAFADAQQTGITGVPTFISGEHAARGAVPPEQLERLIE 207
                                       **************************************97 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.024   1.5e+02       6      33 ..       6      33 ..       2      54 .. 0.79
   2 !   13.8   0.1     1e-05     0.062      65     108 ..     160     205 ..      62     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.024
                     Thioredoxin_2  6 kpvlvvftdpdCpyCkklkkelkelddv 33
                                         ++v++d  Cp+C + ++ l+ ++d 
  gi|336255191|ref|YP_004598298.1|  6 ADAVLVYADYVCPFCFLGYESLDLYRDQ 33
                                      5679999********8877777777655 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1e-05
                     Thioredoxin_2  65 d.......ieenvelarkygvrgtPtivfldgkeivarlpGyvpaeeleal 108
                                               +e+ ++ a++ g++g+Pt++  +        +G+vp+e+le l
  gi|336255191|ref|YP_004598298.1| 160 SdeesadeLEAAFADAQQTGITGVPTFISGEHA-----ARGAVPPEQLERL 205
                                       0444444467777779999*********99999.....79********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1615.97
//
Query:       gi|336255192|ref|YP_004598299.1|  [L=54]
Description: hypothetical protein Halxa_3814 [Halopiger xanaduensis SH-6]
Scores for 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:                       545  (0.0303977); 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:                         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 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 418.34
//
Query:       gi|336255193|ref|YP_004598300.1|  [L=42]
Description: hypothetical protein Halxa_3815 [Halopiger xanaduensis SH-6]
Scores for 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   20.4   1.4       0.13   12.2   0.0    2.1  2  zinc_ribbon_4   zinc-ribbon domain
     0.0026   17.8   0.3       0.24   11.5   0.0    2.1  2  Zn-ribbon_8     Zinc ribbon domain
     0.0032   17.5   5.1      0.022   14.8   0.8    2.1  2  UPF0547         Uncharacterised protein family UPF0547
     0.0064   16.3   1.9      0.049   13.5   0.1    2.0  2  TFIIS_C         Transcription factor S-II (TFIIS)
     0.0069   16.7   0.5      0.031   14.7   0.0    1.9  2  DUF4379         Probable Zinc-ribbon domain
     0.0093   15.3   2.8       0.17   11.3   0.5    2.2  2  zf-ribbon_3     zinc-ribbon domain
       0.01   15.8   6.2      0.021   14.8   1.9    2.1  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
  ------ inclusion threshold ------
      0.012   15.6   1.7      0.012   15.6   1.7    2.3  2  DUF1610         Domain of unknown function (DUF1610)
      0.019   14.9   0.3       0.37   10.8   0.0    2.0  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.024   15.1   1.3       0.85   10.2   0.1    2.1  2  zf-H2C2_2       Zinc-finger double domain
      0.026   14.3   2.5       0.43   10.4   0.5    2.1  2  zinc_ribbon_5   zinc-ribbon domain
      0.033   13.9   3.8      0.087   12.6   0.1    2.4  2  zinc_ribbon_2   zinc-ribbon domain
      0.033   13.6   0.5       0.49    9.8   0.1    2.1  2  zf_Rg           Reverse gyrase zinc finger
       0.04   14.0   2.4      0.081   13.0   2.4    1.6  1  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
      0.042   14.1   0.1      0.047   13.9   0.1    1.1  1  IBR             IBR domain, a half RING-finger domain
      0.044   13.4   0.9       0.19   11.3   0.1    2.0  2  Sgf11           Sgf11 (transcriptional regulation protein)
      0.045   13.8   0.5        1.9    8.6   0.1    2.1  2  DUF1272         Protein of unknown function (DUF1272)
      0.057   13.1   0.1      0.066   12.8   0.1    1.0  1  DpnI            Dam-replacing family
      0.073   13.3   2.3        3.1    8.1   0.1    2.1  2  zf-RING_7       C4-type zinc ribbon domain
      0.093   12.8   2.1        0.3   11.1   0.1    2.0  2  CpXC            CpXC protein
        0.1   12.5   2.7        2.9    7.8   0.2    2.1  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.13   12.3   2.9        1.9    8.6   0.3    2.1  2  Rubredoxin      Rubredoxin
       0.18   11.9   0.5        0.3   11.1   0.5    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.18   11.9   1.1       0.27   11.3   0.1    1.8  2  Elf1            Transcription elongation factor Elf1 like
       0.23   11.4   1.2       0.43   10.5   1.2    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.37   10.5   4.7        1.7    8.4   0.5    2.3  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        1.2    8.9   6.3        2.7    7.8   0.6    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain


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 !    7.6   0.4    0.0053       3.5       1       8 [.       1       8 [.       1      10 [. 0.89
   2 !   12.2   0.0   0.00019      0.13      22      35 ..      25      38 ..      20      39 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0053
                     zinc_ribbon_4 1 MkitCpsC 8
                                     M+ +Cp C
  gi|336255193|ref|YP_004598300.1| 1 MIARCPDC 8
                                     999***99 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00019
                     zinc_ribbon_4 22 kgvkvrCskCghvF 35
                                      ++v   C++Cgh +
  gi|336255193|ref|YP_004598300.1| 25 TIVDFECPNCGHEW 38
                                      567889******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 ?    5.0   0.1     0.041        27      28      33 ..       3       9 ..       1      16 [. 0.74
   2 !   11.5   0.0   0.00036      0.24       5      15 ..      28      38 ..      26      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.041
                       Zn-ribbon_8 28 a.CPeCg 33
                                      a CP+C 
  gi|336255193|ref|YP_004598300.1|  3 ArCPDCD 9 
                                      5599995 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00036
                       Zn-ribbon_8  5 eYrCeeCghef 15
                                      +++C +Cghe 
  gi|336255193|ref|YP_004598300.1| 28 DFECPNCGHEW 38
                                      799*****985 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2      0.04        27       2       7 ..       4       9 ..       4      12 .. 0.80
   2 !   14.8   0.8   3.3e-05     0.022      16      25 ..      30      39 ..      29      40 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.04
                           UPF0547 2 vCPeCe 7
                                     +CP C+
  gi|336255193|ref|YP_004598300.1| 4 RCPDCD 9
                                     599998 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.3e-05
                           UPF0547 16 fCphCGyvFq 25
                                      +Cp CG++++
  gi|336255193|ref|YP_004598300.1| 30 ECPNCGHEWS 39
                                      7********7 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 ?    2.6   0.2      0.18   1.2e+02       2       7 ..       4       9 ..       3      11 .. 0.75
   2 !   13.5   0.1   7.4e-05     0.049      26      38 ..      26      38 ..      23      39 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.18
                           TFIIS_C 2 kCpkCg 7
                                     +Cp C+
  gi|336255193|ref|YP_004598300.1| 4 RCPDCD 9
                                     699996 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.4e-05
                           TFIIS_C 26 tvfykCtkCghrW 38
                                      +v ++C +Cgh+W
  gi|336255193|ref|YP_004598300.1| 26 IVDFECPNCGHEW 38
                                      56699*******9 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2         1   6.9e+02      53      56 .]       5       8 ..       2      10 .. 0.78
   2 !   14.7   0.0   4.6e-05     0.031      23      40 ..      22      39 ..      12      42 .] 0.77

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1
                           DUF4379 53 CpkC 56
                                      Cp+C
  gi|336255193|ref|YP_004598300.1|  5 CPDC 8 
                                      8888 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.6e-05
                           DUF4379 23 gskkkvwWkCakCgheWe 40
                                      g ++ v   C++CgheW+
  gi|336255193|ref|YP_004598300.1| 22 GGETIVDFECPNCGHEWS 39
                                      556667889********8 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.041        27       4       9 ..       4       9 ..       2      15 .. 0.81
   2 !   11.3   0.5   0.00026      0.17       4      10 ..      30      36 ..      29      39 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.041
                       zf-ribbon_3 4 rCPnCG 9
                                     rCP C+
  gi|336255193|ref|YP_004598300.1| 4 RCPDCD 9
                                     799886 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00026
                       zf-ribbon_3  4 rCPnCGa 10
                                      +CPnCG+
  gi|336255193|ref|YP_004598300.1| 30 ECPNCGH 36
                                      6888887 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.11        71       5       8 ..       5       8 ..       1      10 [. 0.66
   2 !   14.8   1.9   3.1e-05     0.021      22      30 .]      31      39 ..      29      39 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.11
                    PhnA_Zn_Ribbon 5 CplC 8
                                     Cp C
  gi|336255193|ref|YP_004598300.1| 5 CPDC 8
                                     6665 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.1e-05
                    PhnA_Zn_Ribbon 22 CpeCahEwe 30
                                      Cp+C+hEw+
  gi|336255193|ref|YP_004598300.1| 31 CPNCGHEWS 39
                                      ********7 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.1      0.57   3.8e+02      19      22 ..       5       8 ..       4       8 .. 0.93
   2 ?   15.6   1.7   1.7e-05     0.012      12      23 ..      24      35 ..      20      36 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.57
                           DUF1610 19 CPNC 22
                                      CP C
  gi|336255193|ref|YP_004598300.1|  5 CPDC 8 
                                      **** PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.7e-05
                           DUF1610 12 EravvFpCPNCG 23
                                      E  v F CPNCG
  gi|336255193|ref|YP_004598300.1| 24 ETIVDFECPNCG 35
                                      55689******* 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 ?    2.9   0.1      0.17   1.1e+02      20      25 ..       4       9 ..       3      15 .. 0.86
   2 ?   10.8   0.0   0.00056      0.37      19      27 ..      29      37 ..      20      42 .] 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.17
                     Zn_Tnp_IS1595 20 vCPhCg 25
                                      +CP C 
  gi|336255193|ref|YP_004598300.1|  4 RCPDCD 9 
                                      7****6 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00056
                     Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                      f CP+Cg++
  gi|336255193|ref|YP_004598300.1| 29 FECPNCGHE 37
                                      89*****87 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 ?    4.3   0.1     0.089        59      16      22 ..       4      10 ..       2      12 .. 0.86
   2 ?   10.2   0.1    0.0013      0.85      11      21 ..      23      35 ..      18      37 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.089
                         zf-H2C2_2 16 eCplCdk 22
                                       Cp Cd+
  gi|336255193|ref|YP_004598300.1|  4 RCPDCDD 10
                                      6****97 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0013
                         zf-H2C2_2 11 gekp..yeCplCd 21
                                      ge++  +eCp C+
  gi|336255193|ref|YP_004598300.1| 23 GETIvdFECPNCG 35
                                      7888779*****7 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5   0.00065      0.43       1       9 [.       1       9 [.       1      11 [. 0.93
   2 ?    4.1   0.1     0.058        39       4      10 ..      30      36 ..      28      41 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00065
                     zinc_ribbon_5 1 LiirCpdCd 9
                                     +i rCpdCd
  gi|336255193|ref|YP_004598300.1| 1 MIARCPDCD 9
                                     99******8 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.058
                     zinc_ribbon_5  4 rCpdCdt 10
                                       Cp+C+ 
  gi|336255193|ref|YP_004598300.1| 30 ECPNCGH 36
                                      6999985 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.6      0.16   1.1e+02       1       5 [.       4       8 ..       4      20 .. 0.84
   2 ?   12.6   0.1   0.00013     0.087      16      22 ..      31      37 ..      23      38 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.16
                     zinc_ribbon_2 1 fCpnC 5
                                     +Cp C
  gi|336255193|ref|YP_004598300.1| 4 RCPDC 8
                                     58888 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00013
                     zinc_ribbon_2 16 CpyCGtp 22
                                      Cp+CG++
  gi|336255193|ref|YP_004598300.1| 31 CPNCGHE 37
                                      7777765 PP

>> zf_Rg  Reverse gyrase 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        80       9      14 ..       4       9 ..       1      18 [. 0.77
   2 ?    9.8   0.1   0.00074      0.49       4      14 ..      25      35 ..      23      40 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.12
                             zf_Rg  9 lCPNCg 14
                                       CP C+
  gi|336255193|ref|YP_004598300.1|  4 RCPDCD 9 
                                      6****7 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00074
                             zf_Rg  4 avfeklCPNCg 14
                                       ++   CPNCg
  gi|336255193|ref|YP_004598300.1| 25 TIVDFECPNCG 35
                                      578889****9 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 ?   13.0   2.4   0.00012     0.081       2      24 ..       5      36 ..       4      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                          zf-Mss51  2 CPvpkhkqt.........apkhvdfeCpdCGi 24
                                      CP +++  +          +  vdfeCp+CG 
  gi|336255193|ref|YP_004598300.1|  5 CPDCDDGLGeqldkyvsgGETIVDFECPNCGH 36
                                      8888776668888888888889*********6 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     7e-05     0.047      19      48 ..       3      38 ..       1      41 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7e-05
                               IBR 19 kwCprpdCeaiieksegcks.........vtCskCgfef 48
                                        Cp  dC+  + ++ + k+          +C++Cg+e+
  gi|336255193|ref|YP_004598300.1|  3 ARCP--DCDDGLGEQLD-KYvsggetivdFECPNCGHEW 38
                                      68*9..***99966666.2234556677788******97 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.52   3.4e+02       6      10 ..       4       8 ..       1       9 [. 0.78
   2 ?   11.3   0.1   0.00029      0.19       3      11 ..      27      35 ..      25      39 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.52
                                      E-TTT CS
                             Sgf11  6 tCpnC 10
                                      +Cp C
  gi|336255193|ref|YP_004598300.1|  4 RCPDC 8 
                                      79999 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00029
                                      -EEE-TTTS CS
                             Sgf11  3 eyvtCpnCg 11
                                      ++++CpnCg
  gi|336255193|ref|YP_004598300.1| 27 VDFECPNCG 35
                                      78******9 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.063        42      43      51 ..       4      12 ..       1      18 [. 0.72
   2 ?    8.6   0.1    0.0029       1.9      37      50 ..      24      37 ..      19      40 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.063
                           DUF1272 43 vCPncgGel 51
                                      +CP+c  +l
  gi|336255193|ref|YP_004598300.1|  4 RCPDCDDGL 12
                                      688887665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0029
                           DUF1272 37 eevlenvCPncgGe 50
                                      e++++  CPncg e
  gi|336255193|ref|YP_004598300.1| 24 ETIVDFECPNCGHE 37
                                      5666778****976 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1    0.0001     0.066      34      65 ..       5      40 ..       2      41 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                                      -TTT--...SS-EE---.-----EEE-TTT--EEEE CS
                              DpnI 34 CpkCgs...kklsefen.nkpvaDfyCesckeefeL 65
                                      Cp C++   ++l+++ +  + ++Df C +c  e+ L
  gi|336255193|ref|YP_004598300.1|  5 CPDCDDglgEQLDKYVSgGETIVDFECPNCGHEWSL 40
                                      999*864446799997626789*********99987 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   0.3     0.028        19      23      29 ..       2       8 ..       2       9 .. 0.89
   2 ?    8.1   0.1    0.0047       3.1      24      30 ..      29      35 ..      15      35 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.028
                                      -EE-TTT CS
                         zf-RING_7 23 vvtCpeC 29
                                      +++Cp C
  gi|336255193|ref|YP_004598300.1|  2 IARCPDC 8 
                                      79***** PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0047
                                      EE-TTT- CS
                         zf-RING_7 24 vtCpeCG 30
                                      + Cp+CG
  gi|336255193|ref|YP_004598300.1| 29 FECPNCG 35
                                      68****9 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4      0.24   1.6e+02      38      45 ..       3      10 ..       1      17 [. 0.80
   2 ?   11.1   0.1   0.00046       0.3      34      49 ..      25      40 ..      12      42 .] 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.24
                              CpXC 38 atCpkCga 45
                                      a+Cp+C+ 
  gi|336255193|ref|YP_004598300.1|  3 ARCPDCDD 10
                                      57999975 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00046
                              CpXC 34 slfeatCpkCgatakl 49
                                      ++ +++Cp+Cg++ +l
  gi|336255193|ref|YP_004598300.1| 25 TIVDFECPNCGHEWSL 40
                                      67899******98776 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 ?    7.8   0.2    0.0044       2.9      10      18 ..       1       9 [.       1       9 [. 0.87
   2 ?    5.2   0.2      0.03        20      14      19 ..      31      36 ..      30      40 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0044
                           DUF35_N 10 vgqrCpdCG 18
                                      ++ rCpdC+
  gi|336255193|ref|YP_004598300.1|  1 MIARCPDCD 9 
                                      689*****7 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.03
                           DUF35_N 14 CpdCGt 19
                                      Cp+CG+
  gi|336255193|ref|YP_004598300.1| 31 CPNCGH 36
                                      555554 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.057        38      36      41 ..       4       9 ..       3      15 .. 0.84
   2 ?    8.6   0.3    0.0029       1.9      34      42 ..      28      36 ..      26      39 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.057
                                      BBTTTB CS
                        Rubredoxin 36 vCPdCg 41
                                      +CPdC+
  gi|336255193|ref|YP_004598300.1|  4 RCPDCD 9 
                                      6****7 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0029
                                      T-BBTTTB- CS
                        Rubredoxin 34 dWvCPdCgv 42
                                      d++CP+Cg 
  gi|336255193|ref|YP_004598300.1| 28 DFECPNCGH 36
                                      899****96 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 ?   11.1   0.5   0.00045       0.3      71      95 ..       3      37 ..       1      42 [] 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00045
                                      EEETTTS-EEECHHHHH..........S-TTTSSS CS
                              HypA 71 vrCreCgkefeleekal..........rCpkCgsa 95
                                      +rC +C+    ++ +++          +Cp+Cg++
  gi|336255193|ref|YP_004598300.1|  3 ARCPDCDDGLGEQLDKYvsggetivdfECPNCGHE 37
                                      68999987766554333567777888899999875 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       1.5     1e+03      23      28 ..       4       9 ..       2      20 .. 0.67
   2 ?   11.3   0.1    0.0004      0.27      21      33 ..      28      40 ..      14      42 .] 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.5
                              Elf1 23 dCpfCn 28
                                      +Cp C+
  gi|336255193|ref|YP_004598300.1|  4 RCPDCD 9 
                                      355554 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0004
                              Elf1 21 kFdCpfCnheksv 33
                                       F+Cp+C+he s+
  gi|336255193|ref|YP_004598300.1| 28 DFECPNCGHEWSL 40
                                      7********9776 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 ?   10.5   1.2   0.00065      0.43      31      56 ..       5      38 ..       3      39 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00065
                    OrfB_Zn_ribbon 31 CseCgsknke........alsgrtfkCpnCgfea 56
                                      C+ C   + e          +   f+CpnCg+e+
  gi|336255193|ref|YP_004598300.1|  5 CPDCDDGLGEqldkyvsgGETIVDFECPNCGHEW 38
                                      7777666666666677666777789******987 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 ?    4.1   0.3     0.057        38      22      28 ..       3       9 ..       1      10 [. 0.84
   2 ?    8.4   0.5    0.0025       1.7      24      30 ..      31      37 ..      30      38 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.057
                     zf-NADH-PPase 22 rvCpaCg 28
                                       +Cp+C+
  gi|336255193|ref|YP_004598300.1|  3 ARCPDCD 9 
                                      59****6 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0025
                     zf-NADH-PPase 24 CpaCgle 30
                                      Cp+Cg+e
  gi|336255193|ref|YP_004598300.1| 31 CPNCGHE 37
                                      9999997 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.6     0.051        34      16      21 ..       4       9 ..       4      10 .. 0.86
   2 ?    7.8   0.6    0.0041       2.7       1       8 [.      29      36 ..      29      39 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.051
                      Rubredoxin_2 16 rCpsCg 21
                                      rCp+C 
  gi|336255193|ref|YP_004598300.1|  4 RCPDCD 9 
                                      8****6 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0041
                      Rubredoxin_2  1 YvCsqCGf 8 
                                      ++C +CG+
  gi|336255193|ref|YP_004598300.1| 29 FECPNCGH 36
                                      56777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 337.40
//
Query:       gi|336255194|ref|YP_004598301.1|  [L=80]
Description: hypothetical protein Halxa_3816 [Halopiger xanaduensis SH-6]
Scores for 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:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 634.03
//
Query:       gi|336255195|ref|YP_004598302.1|  [L=178]
Description: retinitis pigmentosa GTPase regulator-like protein [Halopiger xanaduensis SH-6]
Scores for 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-06   26.7   3.2    1.1e-05   25.4   3.1    1.7  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
  ------ inclusion threshold ------
      0.025   15.1   3.3       0.89   10.2   0.8    2.4  2  DUF883           Bacterial protein of unknown function (DUF88
      0.031   14.3   3.5       0.19   11.7   1.0    2.1  2  Chlorosome_CsmC  Chlorosome envelope protein C
       0.11   13.0  16.7       0.64   10.6   4.2    3.1  2  YtxH             YtxH-like protein
       0.74    9.3   6.3        0.9    9.1   6.3    1.4  1  SseC             Secretion system effector C (SseC) like fami
        3.7    7.6   6.5       0.46   10.6   1.9    1.7  2  ATP-synt_B       ATP synthase B/B' CF(0)


Domain annotation for each model (and alignments):
>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   3.1   3.7e-09   1.1e-05      25     183 ..       7     165 ..       1     170 [. 0.93

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.7e-09
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHC CS
                    Apolipoprotein  25 qelrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavya 101
                                       +e+ + +++  ++  + +++  ee+ + +e+      e+++++ ee  + +++  ++ +e +++  +e+  +l++  
  gi|336255195|ref|YP_004598302.1|   7 EEAGEMVEESGKKTAETVEESGEEAGEMVEESGKKTAETVEESGEEAGEMIEEGGKKAAETVEEGGDEVGGTLREGD 83 
                                       5677888899999999999********************************************************** PP

                                       HHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..-----SSSHHHHHHHTS-TTSHHHHHS--XXX CS
                    Apolipoprotein 102 eelrerlerhvealkarlapyveelrqklaerleelkeslaphaeeveerlssrveelrekleeqaeelrerleanl 178
                                       ee  e  e++ +++  ++ +  ee+ ++++e  +e++ ++++  ee +e++++  ee ++  e++ e++r+   +++
  gi|336255195|ref|YP_004598302.1|  84 EETGEMPEEGGDEVGGTFREGDEETGEMVEEDGDEVGGTFREGDEETGEMFEDGGEEGEDDDEDTREKMRDGGKEIA 160
                                       ************************************************************************99999 PP

                                       XXXXX CS
                    Apolipoprotein 179 eelka 183
                                       e+ ++
  gi|336255195|ref|YP_004598302.1| 161 EKTEE 165
                                       99887 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 ?   10.2   0.8    0.0003      0.89       8      67 ..      11      70 ..       3      89 .. 0.78
   2 ?    5.5   0.1    0.0089        27      25      60 ..     130     165 ..      95     177 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0003
                            DUF883  8 eslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67
                                      e++ ++ ++ +++ +++++e  e + e  ++++e++ e+ ++a e ++e  k+aae++++
  gi|336255195|ref|YP_004598302.1| 11 EMVEESGKKTAETVEESGEEAGEMVEESGKKTAETVEESGEEAGEMIEEGGKKAAETVEE 70
                                      455666667777777777777778888888888888888888888888888888887765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0089
                            DUF883  25 ageeaeelRerleerlerarerlrdaeeavaerake 60 
                                       +ge  e+  e+ e+  e++re++rd  +++ae+++e
  gi|336255195|ref|YP_004598302.1| 130 TGEMFEDGGEEGEDDDEDTREKMRDGGKEIAEKTEE 165
                                       333333333444444444444444444444444433 PP

>> Chlorosome_CsmC  Chlorosome envelope protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.0   6.5e-05      0.19      70     127 ..       9      70 ..       2      82 .. 0.83
   2 ?    3.1   0.1     0.029        86      69     123 ..     107     161 ..     101     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.5e-05
                   Chlorosome_CsmC  70 tsgvvgetidrvaitvkdvsraaGelysd....avknvenvtdnaakavGdvgvsasevvkn 127
                                       ++++v e+ ++ a tv + +  aGe+ ++    ++++ve+  ++a + + + g +a+e+v +
  gi|336255195|ref|YP_004598302.1|   9 AGEMVEESGKKTAETVEESGEEAGEMVEEsgkkTAETVEESGEEAGEMIEEGGKKAAETVEE 70 
                                       677888999999*************987622225778999999***************9974 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.029
                   Chlorosome_CsmC  69 stsgvvgetidrvaitvkdvsraaGelysdavknvenvtdnaakavGdvgvsase 123
                                       +t+++v e  d v  t ++    +Ge+++d  ++ e+  ++  + + d g + +e
  gi|336255195|ref|YP_004598302.1| 107 ETGEMVEEDGDEVGGTFREGDEETGEMFEDGGEEGEDDDEDTREKMRDGGKEIAE 161
                                       6889999999**********************99999999998888888877666 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   4.2   0.00022      0.64      21      72 ..       4      55 ..       2      58 .. 0.82
   2 ?    3.7  16.0     0.031        91      21      74 ..      15      68 ..      14     173 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00022
                              YtxH 21 ksGketRkdlkekaddlkekakelleeakekakekaedlkekvkekadelke 72
                                      +sG+e  + + e+ ++++e ++e  eea e ++e++++ +e+v+e  +e+ e
  gi|336255195|ref|YP_004598302.1|  4 ESGEEAGEMVEESGKKTAETVEESGEEAGEMVEESGKKTAETVEESGEEAGE 55
                                      6888888999999999999998888888888899999999999888887655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.031
                              YtxH 21 ksGketRkdlkekaddlkekakelleeakekakekaedlkekvkekadelkekv 74
                                      +sGk+t + + e+ +++ e ++e  ++++e+++e++e++ e ++e+ ++++e+v
  gi|336255195|ref|YP_004598302.1| 15 ESGKKTAETVEESGEEAGEMVEESGKKTAETVEESGEEAGEMIEEGGKKAAETV 68
                                      69*******************999999999999999999999999888888766 PP

>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   6.3    0.0003       0.9     151     217 ..      12      72 ..       2     176 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0003
                              SseC 151 avgsaakgaaaavksgaaklaeavaeaigkaikkaaekagkevaeqvskqvlnelakkatkvakavk 217
                                       +v +++k++a  v++++++++e+v+e  +k+++ ++e++g+e++e     +++e +kka+++ ++ +
  gi|336255195|ref|YP_004598302.1|  12 MVEESGKKTAETVEESGEEAGEMVEESGKKTAE-TVEESGEEAGE-----MIEEGGKKAAETVEEGG 72 
                                       567788889999999899999988888887775.56669999884.....66666666665553222 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 ?   10.6   1.9   0.00015      0.46      54     119 ..       7      72 ..       2      81 .. 0.76
   2 ?   -1.4   0.2      0.75   2.2e+03      89      98 ..     156     165 ..     128     175 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                        ATP-synt_B  54 aeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqekdralaeLreqv 119
                                       +ea +  +e+ ++ ae +++  +ea +  ee  +++++ +e   e+A + Ie   ++a + ++e  
  gi|336255195|ref|YP_004598302.1|   7 EEAGEMVEESGKKTAETVEESGEEAGEMVEESGKKTAETVEESGEEAGEMIEEGGKKAAETVEEGG 72 
                                       566666777778888888888888888888888888888888888888888888888888887755 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.75
                        ATP-synt_B  89 aeaeaerlke 98 
                                        ++ ae+++e
  gi|336255195|ref|YP_004598302.1| 156 GKEIAEKTEE 165
                                       2222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 1347.25
//
Query:       gi|336255196|ref|YP_004598303.1|  [L=216]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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    3.7e-16   58.6   0.0    1.3  1  HTH_10         HTH DNA binding domain
      1e-08   35.2   0.0    1.6e-08   34.6   0.0    1.2  1  BAT            GAF and HTH_10 associated domain
    1.1e-08   34.4   0.0    2.5e-08   33.3   0.0    1.4  1  Sigma70_r4     Sigma-70, region 4
    3.1e-05   23.6   0.0    0.00011   21.9   0.0    1.8  2  Sigma70_r4_2   Sigma-70, region 4
    0.00023   21.0   0.9    0.00069   19.5   0.9    1.9  1  MarR_2         MarR family
    0.00057   19.4   0.0     0.0011   18.5   0.0    1.5  1  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.025   14.4   0.1      0.044   13.6   0.1    1.3  1  HTH_23         Homeodomain-like domain
      0.026   14.5   0.5      0.059   13.3   0.0    1.8  2  HTH_11         HTH domain
      0.026   14.3   0.1      0.055   13.3   0.1    1.5  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.037   14.1   0.1        1.3    9.1   0.0    2.4  2  AgrD           Staphylococcal AgrD protein
      0.042   13.4   0.0       0.07   12.7   0.0    1.3  1  GerE           Bacterial regulatory proteins, luxR family


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 !   58.6   0.0   2.3e-19   3.7e-16       1      52 [.     156     207 ..     156     208 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2.3e-19
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LTd q+++l lAy  GYFd PR++t +++A+el+Is++++s +L++  ++l+
  gi|336255196|ref|YP_004598303.1| 156 LTDGQRSALVLAYSRGYFDSPRKATQDDIADELDISRQAVSSRLQRGLRRLV 207
                                       9*********************************************999987 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   9.6e-12   1.6e-08       4     143 ..       3     144 ..       2     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 9.6e-12
                               BAT   4 veLeleirdeddvlvalaael.dcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtl 79 
                                       +e  +++  ++++l+++ ++l d+++el++++p +d+  + +f+++ + + ++++ ++   +v++  v++e ++++l
  gi|336255196|ref|YP_004598303.1|   3 IEASFTVPQPEFPLNTVFEQLpDATIELDRIIP-TDDAIIPYFWIHAENVGDLTADLSGDKGVDEFKVIDELEEEML 78 
                                       57778899999999976655439**********.5667*************************************99 PP

                               BAT  80 lelt..vsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarre 143
                                       ++++  ++ +s++ ++++ + t+ s   e++++++ v+  ++  + ++ ++++e+   +eL++ + 
  gi|336255196|ref|YP_004598303.1|  79 VRIKwnLDHESILIAIVNTDITLVSGLGEQENWTFEVRSGDQKSLSEFQSYCRENDIPIELTQLHA 144
                                       999855779*********************************************999999887665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   1.5e-11   2.5e-08       5      48 ..     156     206 ..     155     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.5e-11
                                       S-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   5 Lpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       L++ +r  l+l +        ++ T+ +I+++l+iSr +V++++ r+lr+L
  gi|336255196|ref|YP_004598303.1| 156 LTDGQRSALVLAYsrgyfdsPRKATQDDIADELDISRQAVSSRLQRGLRRL 206
                                       999**************99999***************************98 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 ?   -2.1   0.0       1.9   3.1e+03      11      23 ..     156     168 ..     156     171 .. 0.83
   2 !   21.9   0.0   6.5e-08   0.00011      28      54 .]     180     206 ..     179     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.9
                                       S-HHHHHHHHHHH CS
                      Sigma70_r4_2  11 Lperqreifllry 23 
                                       L+  qr +++l y
  gi|336255196|ref|YP_004598303.1| 156 LTDGQRSALVLAY 168
                                       6678999*99987 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 6.5e-08
                                       -HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsRArkkL 54 
                                       ++++IA +l+is ++V srl+R++++L
  gi|336255196|ref|YP_004598303.1| 180 TQDDIADELDISRQAVSSRLQRGLRRL 206
                                       679**********************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.9   4.2e-07   0.00069      18      44 ..     176     201 ..     155     216 .] 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.2e-07
                                       TTSEEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2  18 pgrdltvgelarrlglsksavsrilkr 44 
                                       p r+ t+ ++a++l++s++avs +l+r
  gi|336255196|ref|YP_004598303.1| 176 P-RKATQDDIADELDISRQAVSSRLQR 201
                                       3.378*****************99876 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 !   18.5   0.0   6.8e-07    0.0011      17      40 ..     177     201 ..     174     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.8e-07
                            HTH_24  17 r.isqreLAerlglSpstvnrrlkr 40 
                                       r  +q ++A++l++S+++v+ rl+r
  gi|336255196|ref|YP_004598303.1| 177 RkATQDDIADELDISRQAVSSRLQR 201
                                       448********************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.7e-05     0.044      16      40 ..     175     201 ..     157     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                            HTH_23  16 e..GlsvreIAreLgvsrrTvyrwlkr 40 
                                          ++++ +IA+eL++sr+ v+  l+r
  gi|336255196|ref|YP_004598303.1| 175 SprKATQDDIADELDISRQAVSSRLQR 201
                                       155899***************955544 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         4   6.5e+03      35      46 ..      69      81 ..      68      82 .. 0.64
   2 ?   13.3   0.0   3.6e-05     0.059      16      37 ..     179     200 ..     173     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4
                            HTH_11 35 dIkaLeelg.vpI 46
                                       I++Lee + v+I
  gi|336255196|ref|YP_004598303.1| 69 VIDELEEEMlVRI 81
                                      5889966554776 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.6e-05
                            HTH_11  16 isgeeLAeeLnvSrrtvrrdIk 37 
                                        + +++A+eL++Sr++v  +++
  gi|336255196|ref|YP_004598303.1| 179 ATQDDIADELDISRQAVSSRLQ 200
                                       6889*************98776 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 ?   13.3   0.1   3.4e-05     0.055      18      40 ..     179     201 ..     177     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                     HTH_AsnC-type  18 isyaeLAervGlSestvlrRvrr 40 
                                       ++  ++A+++ +S+++v  R++r
  gi|336255196|ref|YP_004598303.1| 179 ATQDDIADELDISRQAVSSRLQR 201
                                       67789****************98 PP

>> AgrD  Staphylococcal AgrD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.094   1.5e+02      16      40 ..      49      73 ..      41      75 .. 0.91
   2 ?    9.1   0.0   0.00082       1.3      28      44 ..     127     143 ..     121     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.094
                              AgrD 16 kfIGtvAadSvCdsifDEvEVPkEL 40
                                      +++G + ad   d  +DE  V +EL
  gi|336255196|ref|YP_004598303.1| 49 ENVGDLTADLSGDKGVDEFKVIDEL 73
                                      89******************99998 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00082
                              AgrD  28 dsifDEvEVPkELTkLy 44 
                                       +s+  E ++P ELT+L+
  gi|336255196|ref|YP_004598303.1| 127 QSYCRENDIPIELTQLH 143
                                       68999***********9 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.3e-05      0.07      21      48 ..     182     209 ..     179     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-05
                                       HHHHHHHTS-HHHHHHHHHHHHHHHT-S CS
                              GerE  21 keIAeelniSekTVkvhksnimkKLnvk 48 
                                        +IA+el+iS + V++ +++ +++L + 
  gi|336255196|ref|YP_004598303.1| 182 DDIADELDISRQAVSSRLQRGLRRLVAS 209
                                       68******************99999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1722.94
//
Query:       gi|336255197|ref|YP_004598304.1|  [L=84]
Description: hypothetical protein Halxa_3819 [Halopiger xanaduensis SH-6]
Scores for 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:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 701.66
//
Query:       gi|336255198|ref|YP_004598305.1|  [L=372]
Description: peptidase M48 Ste24p [Halopiger xanaduensis SH-6]
Scores for 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   80.9   0.0    4.8e-22   78.7   0.0    1.9  1  Peptidase_M48  Peptidase family M48
    8.7e-05   21.9   0.0    0.00015   21.1   0.0    1.5  1  Peptidase_M56  BlaR1 peptidase M56
     0.0014   18.4   0.0     0.0021   17.9   0.0    1.2  1  SprT-like      SprT-like family
  ------ inclusion threshold ------
      0.077   12.6   0.0       0.12   11.9   0.0    1.2  1  DUF2268        Predicted Zn-dependent protease (DUF2268)


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 !   78.7   0.0   1.1e-25   4.8e-22       4     195 ..     169     369 ..     166     370 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 1.1e-25
                                       SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   4 eaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhs 80 
                                       ++el+++v++la+ a +  p ++vyv ++++   F+lg g++  iv+++gL  + l ++el+aVl+HE++H+++ +s
  gi|336255198|ref|YP_004598305.1| 169 DPELEATVRRLAQFASV--PAPEVYVTDADRPESFTLGSGASAVIVVSTGLC-ERLADDELEAVLAHEVSHLANFDS 242
                                       689**************..*********************999*********.************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTTHHHHHHHHHHHHHHHHTTT.HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  81 vvslivsllasillllglallisraeedaagafldalavliglliillflalSRkrEyqADeagvellkrakdlvra 157
                                        + +  + ++ ++    + +  s  ++   +a+  al  +    +++ +++lS  rE  AD+ ++ l++ +++l++a
  gi|336255198|ref|YP_004598305.1| 243 -RIVAAAIVPVVIADDWIDPDASDPGDLLWNAVFRALKRY----GQFGVAVLSQGREWHADAGAAALAS-PAALASA 313
                                       .335555556666666666666666666666666666665....677788*******************.******* PP

                                       HHHHHH..HTT--S---HHHH................HHS-SS--HHHHHHHHHH- CS
                                       xxxxxx..xxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 158 liklak..dlerqdvsaslrs................ellstHPplleRiqalkel 195
                                       l +la+  +  ++d  +++rs                  ++tHP+++ Ri++l++l
  gi|336255198|ref|YP_004598305.1| 314 LETLADarRVPETDLREWERSvvaldilppaleeqgsGPFRTHPSTAARIRRLRRL 369
                                       *99986113445677777777************999999**************975 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.4e-08   0.00015     179     220 ..     209     250 ..     139     261 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.4e-08
                     Peptidase_M56 179 prIvlPadflkklsdeeleyillHElaHlkrkDllvnllvav 220
                                        +Iv+++ + ++l+d+ele +l+HE +Hl++ D  + + ++v
  gi|336255198|ref|YP_004598305.1| 209 AVIVVSTGLCERLADDELEAVLAHEVSHLANFDSRIVAAAIV 250
                                       58*******************************987766555 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   4.8e-07    0.0021      44      78 ..     206     240 ..     152     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.8e-07
                         SprT-like  44 rhhasIeLseklldsrsedrllntLaHElcHlalf 78 
                                       + +a I  s+ l++   +d+l+ +LaHE+ Hla+f
  gi|336255198|ref|YP_004598305.1| 206 GASAVIVVSTGLCERLADDELEAVLAHEVSHLANF 240
                                       56788999**************************8 PP

>> DUF2268  Predicted Zn-dependent protease (DUF2268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.7e-05      0.12      34      80 ..     195     241 ..     171     245 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                           DUF2268  34 klieekgykgglaipdkiflflleneyskerlaallaHEyhHvvrlk 80 
                                       ++++e+ + g +a++  ++ + l +   +++l+a+laHE+ H+  ++
  gi|336255198|ref|YP_004598305.1| 195 ADRPESFTLGSGASAVIVVSTGLCERLADDELEAVLAHEVSHLANFD 241
                                       556777777778877777777799999***************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2860.73
//
Query:       gi|336255199|ref|YP_004598306.1|  [L=233]
Description: Rhomboid family protein [Halopiger xanaduensis SH-6]
Scores for complete 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   87.0  16.5    1.2e-24   87.0  16.5    1.8  2  Rhomboid  Rhomboid family
     0.0018   18.8  10.4     0.0021   18.6   0.9    2.5  3  DUF1751   Eukaryotic integral membrane protein (DUF1751)


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.12   1.1e+03      74     101 ..      25      52 ..      13      62 .. 0.51
   2 !   87.0  16.5   1.3e-28   1.2e-24       6     145 ..      68     219 ..      63     223 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.12
                                       SSHHHHHHHHHHHHHHHHCCCCGS---- CS
                          Rhomboid  74 GaSGaifgllgallvlvprnrkllrkli 101
                                       G S  i  llg++++ +  +  ++   +
  gi|336255199|ref|YP_004598306.1|  25 GSSSPIIELLGIFVLVFALQTVTALIGV 52 
                                       5555555555554444444443333333 PP

  == domain 2  score: 87.0 bits;  conditional E-value: 1.3e-28
                                       -TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S..............- CS
                          Rhomboid   6 elwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaeses...........p 71 
                                         w+++ts+  H+++ Hl+ N++al+vfG p++r   +lrf ++++++g ++++ ++++s+               p
  gi|336255199|ref|YP_004598306.1|  68 NPWTIVTSVYAHGSVGHLVSNSVALVVFGWPVARATTRLRFHAFFAVTGAIAGVSQIVLSRVFAGlpfvgnwfavhP 144
                                       68************************************************************9779*********** PP

                                       EESSHHHHHHHHHHHHHHHHCCCCGS----HC....CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHHHHHHHHHH CS
                          Rhomboid  72 lvGaSGaifgllgallvlvprnrkllrkliia.llllllfillnlvlgllpraggvsnlAHlgGllaGlllglll 145
                                       ++GaSGa+f+llg+l++    +  l+ ++ ++ +++ l+f+ l +++ l + a+gv+ lAH++G+l+Gll+g+l 
  gi|336255199|ref|YP_004598306.1| 145 VLGASGAVFALLGYLIASNRLSTGLASFVDVPnWVSALVFLGLAIAVTLATAAPGVALLAHFSGFLVGLLAGRLR 219
                                       *****************9999999888887777*************************************99886 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3         1   9.3e+03      56      59 ..      45      48 ..      31      62 .. 0.45
   2 !   18.6   0.9   2.4e-07    0.0021       6      89 ..      67     151 ..      63     161 .. 0.82
   3 !    7.4   0.3   0.00074       6.6      34      92 ..     156     212 ..     146     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1
                           DUF1751 56 vitn 59
                                      ++t+
  gi|336255199|ref|YP_004598306.1| 45 TVTA 48
                                      2222 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.4e-07
                           DUF1751   6 pypwtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvlltlllylvtkseelll.v 81 
                                         pwt++t+ +   +v +++ + ++l+++g  + r+  +  +  F++v++ i+++  ++l  +++ +    ++    
  gi|336255199|ref|YP_004598306.1|  67 TNPWTIVTSVYAHGSVGHLVSNSVALVVFGWPVARATTRLRFHAFFAVTGAIAGVSQIVLSRVFAGLPFVGNWFAvH 143
                                       58*****************************************************9988887776655555554435 PP

                           DUF1751  82 pisGlagi 89 
                                       p+ G+ g 
  gi|336255199|ref|YP_004598306.1| 144 PVLGASGA 151
                                       55555555 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00074
                           DUF1751  34 ggkylErlWgskEllkFilvvnvitnllvvlltlllylvtkseelll.vpisGlagilag 92 
                                       +g ++ ++  s+ l+ F+ v n +++l+ + l++++ l+t+   + l +++sG+   l+g
  gi|336255199|ref|YP_004598306.1| 156 LGYLIASNRLSTGLASFVDVPNWVSALVFLGLAIAVTLATAAPGVALlAHFSGF---LVG 212
                                       56666666668899****************************998444888885...333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1913.02
//
Query:       gi|336255200|ref|YP_004598307.1|  [L=102]
Description: 30S ribosomal protein S10 [Halopiger xanaduensis SH-6]
Scores for complete 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   89.4   0.0    1.5e-25   89.3   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e


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 !   89.3   0.0   8.2e-30   1.5e-25       1      97 [.       5      98 ..       5      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 8.2e-30
                                      EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHH CS
                     Ribosomal_S10  1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketi 78
                                      r+rl ++++ +L+++++++ ++a+++g++++gp+plPtk+++v+++ksp ++ + ++e++e+r+hkRlid+ da+++ +
  gi|336255200|ref|YP_004598307.1|  5 RVRLAGTSPDDLDDICDDVREIANNTGVNLSGPIPLPTKTLEVPTRKSPDGEgTATWEHWEMRVHKRLIDL-DADERAL 82
                                      799********************************************************************.8****** PP

                                      HHHS-...S---SS-EEEE CS
                     Ribosomal_S10 79 dtllkllqlnlpegVsvev 97
                                      ++l++   +++p  Vs+e+
  gi|336255200|ref|YP_004598307.1| 83 RQLMR---IQVPNDVSIEI 98
                                      *****...*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 807.30
//
Query:       gi|336255201|ref|YP_004598308.1|  [L=420]
Description: translation elongation factor EF-1 subunit alpha [Halopiger xanaduensis SH-6]
Scores for 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-57  192.8   0.0    5.1e-57  192.6   0.0    1.1  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    3.1e-37  127.3   0.0    7.8e-37  126.0   0.0    1.7  2  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
      5e-15   55.7   3.8    1.5e-14   54.1   1.2    2.5  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    3.7e-07   30.2   0.1    2.8e-06   27.4   0.1    2.3  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0009   19.2   1.2      0.068   13.1   0.2    2.3  2  RsgA_GTPase  RsgA GTPase
     0.0026   17.1   0.1      0.068   12.5   0.0    2.2  2  Gtr1_RagA    Gtr1/RagA G protein conserved region
     0.0073   16.4   0.0        1.4    8.9   0.0    2.4  1  Dynamin_N    Dynamin family
  ------ inclusion threshold ------
      0.011   15.2   0.0       0.41   10.1   0.0    2.2  1  SRPRB        Signal recognition particle receptor beta subuni
      0.016   15.1   0.6      0.057   13.3   0.6    1.9  1  GTP_EFTU_D4  Elongation factor Tu domain 4
      0.018   14.6   0.1       0.33   10.5   0.1    2.5  2  FeoB_N       Ferrous iron transport protein B
       0.12   11.7   0.0       0.28   10.4   0.0    1.5  1  Septin       Septin


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 !  192.6   0.0   3.1e-60   5.1e-57       2     183 ..       4     203 ..       3     277 .. 0.90

  Alignments for each domain:
  == domain 1  score: 192.6 bits;  conditional E-value: 3.1e-60
                                       CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH..HHHST.............HCHSHHHHHHTSCSSCEEEEE CS
                          GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgeka..eeerv.............lDtlkeErergiTiksaaisl 63 
                                       r+ n++iighvDhGK+TL++rLly+tg + ++  ++  e  ++             +D+l+eErerg+Ti++a+ ++
  gi|336255201|ref|YP_004598308.1|   4 RHQNLAIIGHVDHGKSTLVGRLLYETGSVPEHVIEQhrE--EAeekgkggfefayvMDNLAEERERGVTIDIAHQEF 78 
                                       899*************************99988777431..224568999*************************** PP

                                       ETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST...H CS
                          GTP_EFTU  64 eketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl...k 136
                                       +  t++y ++++D+PGH+dF+k++i+g++++D avlvv+a++Gv pqt+e++ la+++g+  +i+ iNKmD +   +
  gi|336255201|ref|YP_004598308.1|  79 S--TDEYDFTIVDCPGHRDFVKNMITGASQADNAVLVVAADDGVAPQTQEHVFLARTLGIDeLIIGINKMDVVdyeE 153
                                       *..**********************************************************************9999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH...........H CS
                          GTP_EFTU 137 aelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk...........t 183
                                       ++++e+veev+q l       ++++++++ + +++++Sa++g+++            +
  gi|336255201|ref|YP_004598308.1| 154 STYNEVVEEVNQLL-------QQVQFNTD-DASFIPISAFEGDNIAeesdntpwydgE 203
                                       99*********777.......77778874.899**********998555555555552 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 ?   -2.9   0.0       5.2   8.6e+03      53      74 ..     273     289 ..     257     292 .. 0.58
   2 !  126.0   0.0   4.8e-40   7.8e-37       4     111 ..     312     417 ..     309     418 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.2
                                       TSB-BSS-SSCCSTT-CEEEEE CS
                       GTP_EFTU_D3  53 tekvsekkpefvkpGdnvivev 74 
                                       +     ++   + pGdnv ++v
  gi|336255201|ref|YP_004598308.1| 273 H-----EEVPKAEPGDNVGFNV 289
                                       2.....3335578888887776 PP

  == domain 2  score: 126.0 bits;  conditional E-value: 4.8e-40
                                       EECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEE CS
                       GTP_EFTU_D3   4 phtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpi 80 
                                        +++f+Aq++++++  ++ itagY+pv++++ta+v+++++++ +k+d+++++v+e++p+f+++Gd+++v+++++kp+
  gi|336255201|ref|YP_004598308.1| 312 VAETFQAQIVVMQH--PSVITAGYTPVFHAHTAQVACTIESIDKKMDPSSGEVAEENPDFIQSGDAAVVTIRPQKPL 386
                                       6899**********..************************************************************* PP

                                       EE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  81 alekgseypqlGrFaiReggrTvaaGvvtei 111
                                        +e  se+p+lG FaiR++g+T+aaG+v e+
  gi|336255201|ref|YP_004598308.1| 387 SIEPSSEIPELGSFAIRDMGQTIAAGKVLEV 417
                                       ****************************998 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 ?    1.3   0.1      0.29   4.7e+02      15      53 ..       4      40 ..       3      48 .. 0.87
   2 !   54.1   1.2   9.1e-18   1.5e-14       1      73 [.     237     303 ..     237     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.29
                                      TTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSE CS
                       GTP_EFTU_D2 15 kGdevrilg.ndtskkeivtrissletfhededeavagan 53
                                      + +++ i+g +d +k+   t +++l+ + + + e v +++
  gi|336255201|ref|YP_004598308.1|  4 RHQNLAIIGhVDHGKS---TLVGRLLYETGSVPEHVIEQH 40
                                      5688899999999999...**********99999987765 PP

  == domain 2  score: 54.1 bits;  conditional E-value: 9.1e-18
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       Gtv  gr+++G++++Gd v +  ++++     ++++ +e++he++  a++g+n+G++v+++g +d i++Gd+ 
  gi|336255201|ref|YP_004598308.1| 237 GTVPVGRIETGVMNTGDDVSF--QPSDVG---GEVKTIEMHHEEVPKAEPGDNVGFNVRGIGKDD-IRRGDVC 303
                                       99*******************..666667...89*******************************.*****95 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   1.7e-09   2.8e-06       2      97 ..       8     127 ..       7     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.7e-09
                                       EEEEESTTSSHHHHHHHHH....................T...........STEEESSSTTSSSSEEEEEEEETTEE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinalt....................g...........ekaivsdkpgtTrdinegrvklkgke 47 
                                        ai+G+   GKStL+ +l+                    +           ++   +++ g+T+di + ++++++ +
  gi|336255201|ref|YP_004598308.1|   8 LAIIGHVDHGKSTLVGRLLyetgsvpehvieqhreeaeeKgkggfefayvmDNLAEERERGVTIDIAHQEFSTDEYD 84 
                                       69****************977777777776666665555056666665554466778888************999** PP

                                       EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHH CS
                          MMR_HSR1  48 ielvDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldeel 97 
                                       +++vD+pG  +    +  +++ +    +ad ++lvv a  ++++p+ +e 
  gi|336255201|ref|YP_004598308.1|  85 FTIVDCPG--H----RDFVKNMITGASQADNAVLVVAAD-DGVAPQTQEH 127
                                       ********..3....223555555566688888888765.5576665554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.017        28     100     123 ..       6      37 ..       2      99 .. 0.68
   2 !   13.1   0.2   4.2e-05     0.068      13      79 ..     104     170 ..      96     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.017
                                       SEEEEECSTTSSHHHHHHHHCTT........- CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpe........l 123
                                       +  +++G+   GKStL+ +ll e         
  gi|336255201|ref|YP_004598308.1|   6 QNLAIIGHVDHGKSTLVGRLLYEtgsvpehvI 37 
                                       567899************99987444444440 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.2e-05
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH.HHHHHHHHHHHTTSEE CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee.eleelkeelealgyev 79 
                                       ++  d++++vv+++ + + +++ +  ++la + gi e++i +nK+D+++ ee +++e+ ee+++l  +v
  gi|336255201|ref|YP_004598308.1| 104 ASQADNAVLVVAAD-DGVAPQTQEH-VFLARTLGIdELIIGINKMDVVDYEEsTYNEVVEEVNQLLQQV 170
                                       6789*********9.6777766555.566778888689999********99977777777777774444 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 !   12.5   0.0   4.2e-05     0.068      30      67 ..      66     102 ..      56     116 .. 0.83
   2 ?    2.2   0.0     0.057        94     118     154 ..     143     179 ..     133     188 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                         Gtr1_RagA  30 rlgatidveksevrflgnltlnlwDcgGqeafveeyls 67 
                                       + g+tid+ ++e+  +++ ++ ++Dc+G ++fv+++++
  gi|336255201|ref|YP_004598308.1|  66 ERGVTIDIAHQEF-STDEYDFTIVDCPGHRDFVKNMIT 102
                                       5589*********.7999*****************765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.057
                         Gtr1_RagA 118 ihKmDliqedereeifeerkeeireeiekleke..eiqf 154
                                       i+KmD +  d +e++++e  ee+++ +++++++  + +f
  gi|336255201|ref|YP_004598308.1| 143 INKMDVV--DYEESTYNEVVEEVNQLLQQVQFNtdDASF 179
                                       8999999..777788888888888888877655444444 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00087       1.4      52     135 ..      41     114 ..       8     147 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00087
                                       .SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHST CS
                         Dynamin_N  52 keelkekekkledfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikk 128
                                       +ee +ek k   +f  v +++ +e+e+         ++ i ++ +s ++ + t+vD PG  +  k   ++++ + + 
  gi|336255201|ref|YP_004598308.1|  41 REEAEEKGKGGFEFAYVMDNLAEERERGV-------TIDIAHQEFSTDEYDFTIVDCPGHRDFVK---NMITGASQA 107
                                       23333344444444444444444444444.......44677777788888888888888766332...355555554 PP

                                       TEEEEEE CS
                         Dynamin_N 129 adiilav 135
                                        +++l+v
  gi|336255201|ref|YP_004598308.1| 108 DNAVLVV 114
                                       4455444 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 ?   10.1   0.0   0.00025      0.41      42      80 ..      76     113 ..       3     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                                       TG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEE CS
                             SRPRB  42 kvksekgskltliDfPGheklrqklleklkaksslkglv 80 
                                       +  s+++  +t++D PGh  + +++++   + +++  lv
  gi|336255201|ref|YP_004598308.1|  76 QEFSTDEYDFTIVDCPGHRDFVKNMITGASQADNA-VLV 113
                                       334788999*************9999994444433.333 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 ?   13.3   0.6   3.5e-05     0.057      21      83 ..     241     301 ..     230     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.5e-05
                                       EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTT.S--TT- CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGr.qikegd 83 
                                       vG ++ +Gv+++g ++  +     Ge++ i+ +++++ +a+ G++v+  ++g  +G+ +i  gd
  gi|336255201|ref|YP_004598308.1| 241 VG-RIETGVMNTGDDVSFQPSDVGGEVKTIEMHHEEVPKAEPGDNVGFNVRG--IGKdDIRRGD 301
                                       77.89999999999997777766789**********************9998..3442466665 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 ?    0.9   0.0      0.18   2.9e+02       2      21 ..       7      26 ..       6      44 .. 0.85
   2 ?   10.5   0.1    0.0002      0.33      32      60 ..      68      96 ..      66     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.18
                                      EEEEEESTTSSHHHHHHHHH CS
                            FeoB_N  2 tvalvGnpnvGkttlfnalt 21
                                      ++a++G  + Gk+tl+ +l 
  gi|336255201|ref|YP_004598308.1|  7 NLAIIGHVDHGKSTLVGRLL 26
                                      5799***********98875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0002
                                      TSSSEEEEEEEEETTEEEEEEE----SSS CS
                            FeoB_N 32 GvtvekkegklklkgkeveivDlPGiYsl 60
                                      Gvt++ ++ ++++++++++ivD PG  ++
  gi|336255201|ref|YP_004598308.1| 68 GVTIDIAHQEFSTDEYDFTIVDCPGHRDF 96
                                      9************************8655 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00017      0.28       6      78 ..       7      99 ..       3     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                                      EEEEEEBTTSSCCCCCCTTS.SSS----.....................--------------S-EEEEEEEEETTCEE CS
                            Septin  6 tlmvvGesglGkttlintlf.etdliee.....................ekleeasekkkktveikkkkvvieedgvkl 62
                                      +l ++G+   Gk+tl+  l+ et  ++e                       +++ +e+ ++ v+i+ ++++   d  + 
  gi|336255201|ref|YP_004598308.1|  7 NLAIIGHVDHGKSTLVGRLLyETGSVPEhvieqhreeaeekgkggfefaYVMDNLAEERERGVTIDIAHQEFSTD--EY 83
                                      8999************88761555566578888999999999999999866777788888889999888888888..56 PP

                                      EEEEEE---BSSSSSH CS
                            Septin 63 nltviDtpgfGdavdn 78
                                       +t++D pg+ d+v n
  gi|336255201|ref|YP_004598308.1| 84 DFTIVDCPGHRDFVKN 99
                                      889*********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.69
# Mc/sec: 1844.35
//
Query:       gi|336255202|ref|YP_004598309.1|  [L=317]
Description: Homoserine dehydrogenase [Halopiger xanaduensis SH-6]
Scores for complete 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-48  165.3   0.1    1.9e-48  164.6   0.1    1.3  1  Homoserine_dh  Homoserine dehydrogenase
    5.7e-08   32.8   0.1    1.1e-07   31.9   0.1    1.5  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
    5.2e-07   30.3   0.1    1.2e-06   29.2   0.1    1.6  1  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
     0.0032   17.4   0.0      0.005   16.8   0.0    1.3  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.004   16.5   0.0     0.0063   15.9   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
     0.0081   16.8   0.0      0.017   15.8   0.0    1.7  1  PglD_N         PglD N-terminal domain
     0.0083   16.6   0.1      0.017   15.7   0.1    1.6  1  XdhC_C         XdhC Rossmann domain
      0.009   16.6   0.1      0.058   14.0   0.0    2.3  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.015   14.9   0.0    1.3  1  ApbA           Ketopantoate reductase PanE/ApbA
      0.021   15.6   0.0       0.04   14.8   0.0    1.4  1  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
      0.072   13.3   0.1       0.67   10.2   0.0    2.4  2  TrkA_N         TrkA-N domain


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 !  164.6   0.1   1.2e-51   1.9e-48       1     172 [.     140     311 ..     140     311 .. 0.96

  Alignments for each domain:
  == domain 1  score: 164.6 bits;  conditional E-value: 1.2e-51
                                       --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHH CS
                     Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarla 77 
                                       P+++t+++  + + +t+++G+lngt n+ilt+m++eg ++++vl+eaq+lG+aeaDpt+Dv+G+Daa K +ila+++
  gi|336255202|ref|YP_004598309.1| 140 PVLSTVED-ETPQAVTAVRGVLNGTANFILTRMAAEGLDYEHVLAEAQDLGVAEADPTFDVDGTDAALKFVILANVL 215
                                       77777743.68899*************************************************************** PP

                                       CTTT--GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEE..CEEEEEEEEEETTSGGGHSSST-EEEEEEESSSEEE CS
                     Homoserine_dh  78 fgleveledvevegiskltaedikeakeegkvlklvasa..vearVkpelvpkshplasvkgsenavlvetdrlgel 152
                                        +  + led +v+gi++++   ++ a+e+g++++l+++a    +rV+p+lvp++ pla v+g+ n+v++et+++g+l
  gi|336255202|ref|YP_004598309.1| 216 ADGGFALEDADVTGIQNIPGSALDLAAEDGRTIRLIGEAtrEGVRVAPRLVPENGPLA-VTGTRNIVQIETKNAGSL 291
                                       **************************************955479**************.****************** PP

                                       EEEES-SSHHHHHHHHHHHH CS
                     Homoserine_dh 153 viqGpgaGaepTAsavlsDl 172
                                         +G+gaG+ +TA avlsD+
  gi|336255202|ref|YP_004598309.1| 292 HSSGRGAGGPETATAVLSDV 311
                                       *******************7 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 !   31.9   0.1   6.6e-11   1.1e-07      32      89 ..       2      59 ..       1      85 [. 0.87

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 6.6e-11
                                      TEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSS CS
                     ELFV_dehydrog 32 gkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldieellelkeerksv 89
                                      g+++ai G G+vg  +a l+ e g++vva+ Dss + +dp+G+d+e+ le k   +sv
  gi|336255202|ref|YP_004598309.1|  2 GRKLAILGAGDVGRSVADLAGEYGHEVVALADSSSAAVDPDGIDVESTLERKVGGESV 59
                                      6799******************************************999888766665 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 !   29.2   0.1   7.3e-10   1.2e-06       1     116 [.       9     131 ..       9     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 7.3e-10
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TT.......HHHHHT--CB---HHHHHHHHS-EEEEE-S-- CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrd.sllskd.......rkallasealtldlddliahldpdvvVEcass 69 
                                       G+G +G++v+++  +       e+va+ad++  +++ d        +++++ e + +d ++ + + d dv+VE+++ 
  gi|336255202|ref|YP_004598309.1|   9 GAGDVGRSVADLAGEYG----HEVVALADSSsAAVDPDgidvestLERKVGGESVGTDDPEAVFETDYDVLVEATPT 81 
                                       78888888887655554....58********5555555******98999999998887777777799*******997 PP

                                       HHHH.....TTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE- CS
                     NAD_binding_3  70 eava.....elvlkaLkagkdvvtankgaladealyeeLreaaeangakiyv 116
                                       +        ++v++aL+a+ +vv ankg +a  ++yeeL ++   +   +++
  gi|336255202|ref|YP_004598309.1|  82 TLGDaepgfSHVERALEADRHVVLANKGPVA--ERYEELQALEADSAGSVRF 131
                                       6543223338*********************..9999999887766665555 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 !   16.8   0.0     3e-06     0.005       1      64 [.       4      68 ..       4      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3e-06
                                      EEEEE--SCCHHHHHHHHHHTT-EEE.EE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVv.lvdiseealekalekieksleklvekgklkeeeveaal 64
                                      k+a++GaG +G+++a ++ + g+eVv l d s++a++     +e++le+ v  +++ +++ ea++
  gi|336255202|ref|YP_004598309.1|  4 KLAILGAGDVGRSVADLAGEYGHEVVaLADSSSAAVDPDGIDVESTLERKVGGESVGTDDPEAVF 68
                                      579*********************87367889999999999999999999999988888887766 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 !   15.9   0.0   3.9e-06    0.0063      36      71 ..       2      37 ..       1      52 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.9e-06
                                      TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHH CS
                      2-Hacid_dh_C 36 gktvGiiGlGrIGqavakrlkafgmkviaydrskkk 71
                                      g++++i+G+G++G++va+++ + g +v+a   s ++
  gi|336255202|ref|YP_004598309.1|  2 GRKLAILGAGDVGRSVADLAGEYGHEVVALADSSSA 37
                                      789*************************99888664 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     1e-05     0.017       1      35 [.       4      37 ..       4      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                            PglD_N  1 kivIiGaGGhgkvvadiieangeyeiigflDdnkk 35
                                      k++I+GaG  g+ vad++   g +e++++ D++++
  gi|336255202|ref|YP_004598309.1|  4 KLAILGAGDVGRSVADLAGEYG-HEVVALADSSSA 37
                                      79******************99.899999998874 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1     1e-05     0.017       1     108 [.       5     138 ..       5     155 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG..............-GGG-TT-SE..................- CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefa..............tkerfpeade..................t 45 
                                       l+i+Gag+v++++a+la + g +v+ + + +++a              +                           +
  gi|336255202|ref|YP_004598309.1|   5 LAILGAGDVGRSVADLAGEYGHEVVALADSSSAAvdpdgidvestlerK--------VggesvgtddpeavfetdyD 73 
                                       78***********************999999766666666555544440........04555555556666666665 PP

                                       EEEE--S-HHHHHH....HHHHHSSS--SEEEESS-HHHHHHHCTTS.--.......TTEESS-S-- CS
                            XdhC_C  46 avvvlthdhklDae....aleaalrkkaayigllGSrkkaarrlerlraaglseeelarlhaPiGld 108
                                       ++v +t     Dae     +e+al  +a    +l+ +   a+r+e+l+a + +++   r+ a +G +
  gi|336255202|ref|YP_004598309.1|  74 VLVEATPTTLGDAEpgfsHVERAL--EADRHVVLANKGPVAERYEELQALEADSAGSVRFEATVGGA 138
                                       555555555555432222778888..77788889999999999999988888888888888888865 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 !   14.0   0.0   3.6e-05     0.058       1      31 [.       4      30 ..       4      55 .. 0.84
   2 ?   -1.2   0.0       1.9   3.1e+03      12      34 ..      90     109 ..      83     146 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-05
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEE CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivva 31
                                      k++i+GaG++g+++a  + + g   he+v a
  gi|336255202|ref|YP_004598309.1|  4 KLAILGAGDVGRSVADLAGEYG---HEVV-A 30
                                      78********************...***9.5 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                                       HHHHHHHHHTTS-GGCEEEEEES CS
                     F420_oxidored  12 ealasgllaagaqpheivvansr 34 
                                       ++ ++++l+a+   +++v+an+ 
  gi|336255202|ref|YP_004598309.1|  90 FSHVERALEAD---RHVVLANKG 109
                                       55566777777...777767432 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   9.4e-06     0.015       2     105 ..       6     112 ..       5     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.4e-06
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSG CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrppealsaeekselepidlvivtvKa 78 
                                       ailGaG +G+ +a    + g++v+ ++ s   +a+  +G++++s  + ++  +++ ++++e    +++d+++ ++++
  gi|336255202|ref|YP_004598309.1|   6 AILGAGDVGRSVADLAGEYGHEVVALADSS-SAAVDPDGIDVESTLERKVGGESVGTDDPEAVFETDYDVLVEATPT 81 
                                       8**********9876677************.99*************555555555555557888899*****99999 PP

                                       G..GHHHHHHHHGGGECTCEEEEEESSS..S CS
                              ApbA  79 y..qteealeeikplldpntvvlllqNG..l 105
                                       +  ++e   + ++++l+ + +v+l   G   
  gi|336255202|ref|YP_004598309.1|  82 TlgDAEPGFSHVERALEADRHVVLANKGpvA 112
                                       6447778899999999999999988777544 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 ?   14.8   0.0   2.4e-05      0.04       2     105 ..       4     121 ..       3     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH........HHHTTHE..EESSHHHHHTCTTESEEEE CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeav........aesfgve..aysdleelladpeidaviv 68 
                                       + ai GaG +g+  +  l  +  ++evval d+++++ +           ++ g e    +d e++++ ++ d+++ 
  gi|336255202|ref|YP_004598309.1|   4 KLAILGAGDVGRSVA-DLAGE-YGHEVVALADSSSAAVDPDgidvestlERKVGGEsvGTDDPEAVFE-TDYDVLVE 77 
                                       6799******99998.66666.7889999999988877754455444454444444444444777777.88****** PP

                                       -S-G.....GGHHHHHHHHHHTT-EEEE.ES.SS-SSHHHHHHH CS
                      GFO_IDH_MocA  69 atpn.....gtheelakaaleagkhvll.EK.Plattveeakel 105
                                       atp+     + ++ ++++alea  hv+l  K P+a  +ee+++l
  gi|336255202|ref|YP_004598309.1|  78 ATPTtlgdaEPGFSHVERALEADRHVVLaNKgPVAERYEELQAL 121
                                       ****7777666*************98762447999999998876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00041      0.67       2      31 ..       6      35 ..       5      44 .. 0.81
   2 ?   -0.3   0.0      0.78   1.3e+03      72      98 ..     161     187 ..     141     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00041
                                      EEES-SHHHHHHHHHHHH.TTEEEEEEESSH CS
                            TrkA_N  2 iiiGlGrvGrslaeeLse.ggkdvvvidkde 31
                                      +i+G+G+vGrs+a+   e g+ +vv+  ++ 
  gi|336255202|ref|YP_004598309.1|  6 AILGAGDVGRSVADLAGEyGH-EVVALADSS 35
                                      79****************666.588776655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.78
                                       SHHHHHHHHHHHHHHTSSSEEEEEESS CS
                            TrkA_N  72 ddeanilavllakelnpkkkiiaraqd 98 
                                       + +an +++ +a e  +  ++ a+aqd
  gi|336255202|ref|YP_004598309.1| 161 NGTANFILTRMAAEGLDYEHVLAEAQD 187
                                       668999999999988888999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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):              11  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2352.58
//
Query:       gi|336255203|ref|YP_004598310.1|  [L=203]
Description: amino acid-binding ACT domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-06   27.0   0.5    0.00095   18.9   0.0    3.1  3  ACT            ACT domain
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.22   11.3   0.0    1.3  1  Arg_repressor  Arginine repressor, DNA binding domain
       0.22   11.6   0.0       0.22   11.6   0.0    2.1  2  Sigma70_r1_1   Sigma-70 factor, region 1.1


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 !   18.9   0.0   1.6e-07   0.00095       1      35 [.      38      72 ..      38      92 .. 0.90
   2 !    4.6   0.1    0.0046        27      16      31 ..      96     111 ..      83     142 .. 0.83
   3 ?   -0.5   0.0      0.18   1.1e+03      47      65 ..     168     186 ..     154     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.6e-07
                                      EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEE CS
                               ACT  1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrs 35
                                      +++r+++ D+PG L r ++ +a++g N+ si++ +
  gi|336255203|ref|YP_004598310.1| 38 YTVRLELVDEPGELLRALSPIAENGGNLLSIHHER 72
                                      7899***************************9876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0046
                                       HHHHHHHHTTSEEEEE CS
                               ACT  16 rvfgaladrgiNidsi 31 
                                       ++  al d+g+N++ +
  gi|336255203|ref|YP_004598310.1|  96 DIVEALRDAGVNVIQA 111
                                       78999********876 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.18
                                       EEEEEHHHHHHHHHHHHTT CS
                               ACT  47 vivvdeedleevlealkkl 65 
                                        + +d  d++++le+++++
  gi|336255203|ref|YP_004598310.1| 168 RLAIDSGDADDTLETIRSI 186
                                       5567888888888888876 PP

>> Arg_repressor  Arginine repressor, DNA binding domain
   #    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      23      51 ..      95     123 ..      93     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.7e-05
                                       HHHHHHHHTTT----HHHHHHHHHHHT-E CS
                     Arg_repressor  23 kelvelLkeeGidvtQatvSRdLkelglv 51 
                                       +++ve+L+++G++v Qa   R  +e+++v
  gi|336255203|ref|YP_004598310.1|  95 EDIVEALRDAGVNVIQAGADRYGEEINVV 123
                                       579**************999999999887 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 ?   -3.3   0.4       1.7     1e+04      61      63 ..      21      23 ..      12      32 .. 0.42
   2 ?   11.6   0.0   3.6e-05      0.22      36      57 ..      91     112 ..      81     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.7
                                      ... CS
                      Sigma70_r1_1 61 del 63
                                      de+
  gi|336255203|ref|YP_004598310.1| 21 DEE 23
                                      111 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHHHHHCCT-EEE-SS CS
                      Sigma70_r1_1  36 seqiediiemLedmgIdvveea 57 
                                       ++ +edi+e L d+g++v++  
  gi|336255203|ref|YP_004598310.1|  91 PDRFEDIVEALRDAGVNVIQAG 112
                                       89****************9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1675.34
//
Query:       gi|336255204|ref|YP_004598311.1|  [L=125]
Description: nitrogen-fixing NifU domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-09   36.5   0.3    6.8e-09   35.8   0.3    1.4  1  NifU      NifU-like domain


Domain annotation for each model (and alignments):
>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.3   3.8e-13   6.8e-09      10      66 ..      26      82 ..      18      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 3.8e-13
                                      GGG--GG--EEEEEEEETT..EEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EE CS
                              NifU 10 rPaLasdGGdielvdvdeg..vVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeV 66
                                       P ++++GG   + + d +  +V ++l G+C+gC+ s+vt+   ie+ L +  pe+ eV
  gi|336255204|ref|YP_004598311.1| 26 MPIIQMHGGTSAVRKADPEsgEVIIELGGGCKGCSVSDVTT-GNIEAELIK-WPEIDEV 82
                                      599*******99988877777********************.999999985.5666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 960.27
//
Query:       gi|336255205|ref|YP_004598312.1|  [L=207]
Description: hypothetical protein Halxa_3828 [Halopiger xanaduensis SH-6]
Scores for 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  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); 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:                         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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1557.52
//
Query:       gi|336255206|ref|YP_004598313.1|  [L=187]
Description: hypothetical protein Halxa_3829 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.085   12.7   1.9       0.14   12.0   1.9    1.4  1  DAGK_prokar  Prokaryotic diacylglycerol kinase
       0.22   11.8  12.2       0.98    9.6  12.5    1.9  1  EI24         Etoposide-induced protein 2.4 (EI24)
        1.1    9.6   4.2        6.1    7.2   3.7    2.4  2  DUF948       Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> DAGK_prokar  Prokaryotic diacylglycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.9   2.4e-05      0.14      31      98 ..      44     111 ..      18     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                       DAGK_prokar  31 alllklsalewlllilaillvlvaEllNtaiEavvDlvspeyhelakraKDiaaaavlvaailavvvg 98 
                                         l+  +++ +++++ +i+ v v+ ll     a++Dlv ++++  a  + D+a+   l+++++av+v+
  gi|336255206|ref|YP_004598313.1|  44 DRLVPGTPITFAAIASVIATVTVVGLLLFLAPALADLVRSTFDGPASVVDDVASIVHLFVVLVAVLVA 111
                                       44556789999*****************************************************9986 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  12.5   0.00016      0.98      21      90 ..      21     121 ..      14     162 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHHHHHHH..........-......TTHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHH CS
                              EI24  21 lplllnlllfllllvlll..........w......vllasllvllllllplwlfplvalllaapf......ygllae 75 
                                         lll+ l +++ll+l++                 +++++++++ ++ l+l+l p++a l+ ++f      ++++a 
  gi|336255206|ref|YP_004598313.1|  21 SKLLLATLSLIGLLYLASllpgidrlvpGtpitfaAIASVIATVTVVGLLLFLAPALADLVRSTFdgpasvVDDVAS 97 
                                       567888888888888888888777765515667789999**************************998888888888 PP

                                       HHHH.HH...........CCTTSHHH CS
                              EI24  76 kvekrhl...........glvkslae 90 
                                       +v+   +           gl  ++  
  gi|336255206|ref|YP_004598313.1|  98 IVHL--FvvlvavlvahrGLAPAIVP 121
                                       8853..11222222222222222222 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 ?    7.2   3.7     0.001       6.1       1      40 [.      57      97 ..      57     113 .. 0.85
   2 ?   -0.4   0.0      0.24   1.4e+03       5      28 ..     134     157 ..     122     178 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.001
                            DUF948  1 IAglIaAiAFvvLviflivvllkl.kktldeaaatieelek 40
                                      IA +Ia +++v L +fl+++l  l ++t+d  a+ ++++ +
  gi|336255206|ref|YP_004598313.1| 57 IASVIATVTVVGLLLFLAPALADLvRSTFDGPASVVDDVAS 97
                                      899********************988888888888887765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.24
                            DUF948   5 IaAiAFvvLviflivvllklkktl 28 
                                        +A+A+  L i+ +++ ++l  ++
  gi|336255206|ref|YP_004598313.1| 134 FLALALPPLGILAARLYVSLDPIA 157
                                       344444445555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1390.13
//
Query:       gi|336255207|ref|YP_004598314.1|  [L=142]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Halopiger xanaduensis SH-6]
Scores for 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-30  103.8   1.4    8.2e-30  103.5   1.4    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
       0.19   11.6   0.1       0.31   11.0   0.1    1.3  1  Rubredoxin_C   Rubredoxin NAD+ reductase C-terminal domain
       0.32   11.7   7.0          2    9.1   7.0    2.2  1  Cadherin_4     Bacterial cadherin-like domain


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 !  103.5   1.4   1.4e-33   8.2e-30       4     137 ..       4     130 ..       2     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 1.4e-33
                                       EEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHH CS
                     DMRL_synthase   4 iaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfe 80 
                                       +++Vva+fn+ +t+++ e+al+++++ag+  e +++v+VPGa++ plaa++la++ +++dav ++G++i G+t+h++
  gi|336255207|ref|YP_004598314.1|   4 LGLVVAEFNRPVTEQMEEAALEAASDAGA--EVYETVHVPGAYDAPLAADRLARR-AEVDAVAVVGAIITGDTDHDQ 77 
                                       689*************************7..5**********************4.457****************** PP

                                       HHHHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHHHHHH CS
                     DMRL_synthase  81 yvaeavskglmrvsldtgvPvifgvltvd.teeqaleraggkagnkGeeaaeaalema 137
                                       ++ +a+++ l +v l++++Pv+ gv  +  + ++a+er+     + ++ a+++al+++
  gi|336255207|ref|YP_004598314.1|  78 VIGDAIAQRLSDVTLERDTPVTLGVTGPGmSAAEARERV-----ENAATAVDSALDLV 130
                                       ****************************98999999999.....67777888887765 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 ?   11.0   0.1   5.2e-05      0.31      46      69 ..      63      86 ..      55      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.2e-05
                                      EEEEEEEES-HHHHHHHHHHHHTT CS
                      Rubredoxin_C 46 klvGAiliGDtkesaklkkliekk 69
                                       +vGAi+ GDt+  + + ++i ++
  gi|336255207|ref|YP_004598314.1| 63 AVVGAIITGDTDHDQVIGDAIAQR 86
                                      68******************9875 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.0   0.00033         2       4      47 ..      37      82 ..      36     142 .] 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00033
                        Cadherin_4  4 titvtgvndaPvavddsatvtedtpltitagnvlandtDvd...gdd 47
                                      t++v g+ daP a+d  a  +e +++ +  g +++ dtD d   gd+
  gi|336255207|ref|YP_004598314.1| 37 TVHVPGAYDAPLAADRLARRAEVDAVAV-VGAIITGDTDHDqviGDA 82
                                      899***************9999888887.49********99665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1159.30
//
Query:       gi|336255208|ref|YP_004598315.1|  [L=382]
Description: aspartate transaminase [Halopiger xanaduensis SH-6]
Scores for 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-65  219.6   0.0    7.6e-65  219.4   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    0.00013   20.6   0.0    0.00021   19.9   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00095   18.2   0.1     0.0035   16.4   0.0    1.8  2  Aminotran_5      Aminotransferase class-V
     0.0075   15.6   0.2      0.013   14.8   0.2    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.017   13.9   0.1      0.023   13.5   0.1    1.2  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
       0.11   11.1   0.0        0.2   10.3   0.0    1.4  1  Aminotran_3      Aminotransferase class-III
       0.13   11.5   0.1       0.32   10.2   0.0    1.6  2  Beta_elim_lyase  Beta-eliminating lyase
       0.13   12.2   0.1       0.41   10.6   0.1    1.8  1  Cucumopine_C     Cucumopine synthase C-terminal helical bundl


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 !  219.4   0.0   3.4e-68   7.6e-65       2     363 .]      33     376 ..      32     376 .. 0.93

  Alignments for each domain:
  == domain 1  score: 219.4 bits;  conditional E-value: 3.4e-68
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       d+++L+++e+++     t++++++a k+  ++  + + y+++ g  el+ea+ + l    +l+++++ +v+v++Ga+
  gi|336255208|ref|YP_004598315.1|  33 DIVDLSVGEPDFP----TPENIVEAGKD--AMDAGHTGYTTSAGILELREAIVDKLA-ADGLEHTTD-EVIVTPGAK 101
                                       789*********9....***********..8888999*******************9.99*******.********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEET.TTTEE-HHHHHHHHTTHHCTTETEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyse.edfhldlealeealkeapegnkktkvilv 154
                                       +++  + + l +  gde+++ dp + sy+ +++++gg + r+ l+++  + +  l++l +a+++      +t +++v
  gi|336255208|ref|YP_004598315.1| 102 QALYEIVQSL-VGEGDEVVLLDPAWVSYEAMVKMAGGDLTRVDLSDSdFQLEPALDDLADAVSD------ETELLIV 171
                                       **********.9*******************************885533445568888888888......89***** PP

                                       ESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-E CS
                     Aminotran_1_2 155 esphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRv 230
                                       +sp+NPtG+v++ e le + dla ++ + +++De+Y +  +g  ++++ + +++   + +++v+++sKa++++G+R+
  gi|336255208|ref|YP_004598315.1| 172 NSPSNPTGAVYSDEALEGVRDLAVEHDVTVISDEIYKEITYG-VEPTS-LGTFDGMADrTITVNGFSKAYSMTGWRL 246
                                       ******************************************.44444.55555555569***************** PP

                                       EEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCS CS
                     Aminotran_1_2 231 Gyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsg 305
                                       Gy++g +++++q+ kl+++  s   + +q+a  +al++++     +e+m++ +++rr+ + d L++ g++v ++q++
  gi|336255208|ref|YP_004598315.1| 247 GYFAGPEELIDQAGKLHSHSVSsaVNFVQHAGIEALENTDT---AVEQMVEAFEERRDLVIDLLDDHGVDVAEPQGA 320
                                       **********************78889***********997...9******************************** PP

                                       SEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 306 mflltdlsaetakelskkLleevgvyvtpgtsftvpgrlRitvAglteeeleelveal 363
                                       ++++  ++   ++e ++  +e  +v+ +pg+ f++pg  Ri++ + +ee lee +e+l
  gi|336255208|ref|YP_004598315.1| 321 FYMMLPVDDD-DQEWCEGAIEDAHVATVPGSAFGTPGYARISY-AASEERLEEGIERL 376
                                       ********99.9999999*************************.99********9997 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 !   19.9   0.0   9.5e-08   0.00021      64     176 ..      87     207 ..      63     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.5e-08
                                       HHT-SEEEEESSH.HHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHT...HHHTTCE.EEEESTTSHHHHHHHCC CS
                   Cys_Met_Meta_PP  64 LeggeaalavssG.maAiaaailallkaGdeivvsddlYggtqrllkkv...lkklgie.vkfvdtsdleelekaik 135
                                       Le+++  ++v+ G   A+  ++++l+ +Gde+v+ d ++ + ++++k     l+++ ++ ++f     l++l+ a++
  gi|336255208|ref|YP_004598315.1|  87 LEHTTDEVIVTPGaKQALYEIVQSLVGEGDEVVLLDPAWVSYEAMVKMAggdLTRVDLSdSDFQLEPALDDLADAVS 163
                                       7777555555555168999*****************9988777777766212455444312333335789******* PP

                                       TTEEEEEEESS-TTTT---.-..HHHHHHHHHHTT-EEEEEGTT CS
                   Cys_Met_Meta_PP 136 entklvylEtptnpllkvv.D..iekiaklakkagvlvvvDntf 176
                                       ++t+l+ + +p+np+  v  D  +e + +la +++v+v+ D  +
  gi|336255208|ref|YP_004598315.1| 164 DETELLIVNSPSNPTGAVYsDeaLEGVRDLAVEHDVTVISDEIY 207
                                       ***************99863345889999999999999999766 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.6e-06    0.0035      60     173 ..      90     202 ..      54     207 .. 0.78
   2 ?   -0.9   0.0      0.28   6.3e+02      12      57 ..     252     294 ..     251     304 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-06
                                       TGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH- CS
                       Aminotran_5  60 seeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekll 136
                                       +++e+i+t G+ +a+  +++sl   + +gde+v+ +    +   +++++a     +v+    d + e  ld+l++++
  gi|336255208|ref|YP_004598315.1|  90 TTDEVIVTPGAKQALYEIVQSL---VGEGDEVVLLDPAWVSYE-AMVKMAGGDLTRVDLSDSDFQLEPALDDLADAV 162
                                       459*******************...*********998777777.6666665666778888888888999******** PP

                                       -TTEEEEEEESBETTTTEB...--HHHHHHHHHHTT-EEE CS
                       Aminotran_5 137 nektklvaithvsnvtGti...qpveeigklakkkgalvl 173
                                       +++t+l++++  sn tG +   + +e + +la ++++ v+
  gi|336255208|ref|YP_004598315.1| 163 SDETELLIVNSPSNPTGAVysdEALEGVRDLAVEHDVTVI 202
                                       *****************97222235556666666666655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.28
                                       -HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT CS
                       Aminotran_5  12 pqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelin 57 
                                       p+e +d++ + ++++ +++ + v+h+g ea +      + v ++++
  gi|336255208|ref|YP_004598315.1| 252 PEELIDQAGKLHSHSVSSAVNFVQHAGIEALENT---DTAVEQMVE 294
                                       6778888888888777777777777777554444...444444444 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 !   14.8   0.2   5.9e-06     0.013      59     144 ..     111     204 ..      81     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.9e-06
                                       TTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GG..GCGGG--TTEEEEE...EB-GGGB--...-H CS
                   DegT_DnrJ_EryC1  59 gvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpa..aieaaitertkaIl...pVhlyGqva...dm 127
                                        vg+gdeV+     +v+  ++v  +g +   vD    +++++pa  +++ a+  +t   +   p +  G+v     +
  gi|336255208|ref|YP_004598315.1| 111 LVGEGDEVVLLDPAWVSYEAMVKMAGGDLTRVDLSDSDFQLEPAldDLADAVSDETELLIvnsPSNPTGAVYsdeAL 187
                                       4899*************************************9963379********876523456677887655569 PP

                                       HHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 128 dalkaiaakhglkvieD 144
                                       + ++++a +h++ vi+D
  gi|336255208|ref|YP_004598315.1| 188 EGVRDLAVEHDVTVISD 204
                                       99*************99 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1     1e-05     0.023     135     278 ..     126     264 ..     109     348 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHT-EEEEEEEETTEE-HH.HHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT---SSTT-EE CS
                    Aminotran_MocR 135 drhfllleelGielltvdlqddGpdvd.aveklvaedasvkGilavpkysnptGetiseevarrlaalkaaapdfri 210
                                         + ++++  G +l  vdl d   +++ a++ l+   +    +l v   snptG ++s e    +  l a   d ++
  gi|336255208|ref|YP_004598315.1| 126 VSYEAMVKMAGGDLTRVDLSDSDFQLEpALDDLADAVSDETELLIVNSPSNPTGAVYSDEALEGVRDL-AVEHDVTV 201
                                       5566788888999999999988777654677787777777889****************987776666.457899** PP

                                       EEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTT.S-TTSS-EEEEE-HHHHHHHHHHHH CS
                    Aminotran_MocR 211 faddayavhdlvaeedkdanivalardaGhpdrafvlastski.tfaGaGvafvassedniawlkkylG 278
                                         d+ y+     +e        +l    G  dr++ +   sk  +++G  ++++a  e+ i +++k   
  gi|336255208|ref|YP_004598315.1| 202 ISDEIYKEITYGVEPT------SLGTFDGMADRTITVNGFSKAySMTGWRLGYFAGPEELIDQAGKLHS 264
                                       ***9998766644443......45556788889998888888537888889999988888888888544 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0     9e-05       0.2     208     234 ..     180     206 ..     127     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9e-05
                                       EB--CCHHHHHHHHHHHHT-EEEEE-T CS
                       Aminotran_3 208 vvaspeflaklrelckkhdvllivDEv 234
                                        v+s+e l+++r+l+ +hdv +i DE+
  gi|336255208|ref|YP_004598315.1| 180 AVYSDEALEGVRDLAVEHDVTVISDEI 206
                                       4689999*******************9 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00014      0.32      20     167 ..      57     204 ..      44     205 .. 0.67
   2 ?   -2.7   0.0       1.2   2.7e+03     230     260 ..     259     293 ..     256     303 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00014
                                       CS----CCCT--HHHHHHHHHHHH.......HTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTH CS
                   Beta_elim_lyase  20 aamlGdesYgedktvnrLedavae.......lfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetga 89 
                                       a+ +G+  Y ++ ++ +L +a+ +          ++ ++ +p   +A    ++ l+  g+ev++ +pa +      a
  gi|336255208|ref|YP_004598315.1|  57 AMDAGHTGYTTSAGILELREAIVDklaadglEHTTDEVIVTPGAKQALYEIVQSLVGEGDEVVLLDPAWVS---YEA 130
                                       55566666666666666666666644444432223334444444445444556667777777777777554...357 PP

                                       HHHCC--EEEEE-EBTTTBE-HH.HHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEE CS
                   Beta_elim_lyase  90 iaelagvklrdlknkeaGkmdle.kleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplh 165
                                       ++ +ag  l+ ++ ++  +++le +l ++ ++v+   ++++l+++    n   G v+s e l+ v+++a +++++++
  gi|336255208|ref|YP_004598315.1| 131 MVKMAGGDLTRVDLSD-SDFQLEpALDDLADAVS---DETELLIVNSPSNP-TGAVYSDEALEGVRDLAVEHDVTVI 202
                                       8889999999999999.88988833444555544...58888888887774.7**********************99 PP

                                       EE CS
                   Beta_elim_lyase 166 lD 167
                                        D
  gi|336255208|ref|YP_004598315.1| 203 SD 204
                                       88 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                                       T---SSTHHHHH......HHHHHHHHSSTTHHHHH CS
                   Beta_elim_lyase 230 ggglrqagvlaa....leagiraleeglaslerdh 260
                                       +g+l ++ v +a    ++agi ale+ +  +e+  
  gi|336255208|ref|YP_004598315.1| 259 AGKLHSHSVSSAvnfvQHAGIEALENTDTAVEQMV 293
                                       56666666666666667888888888877666654 PP

>> Cucumopine_C  Cucumopine synthase C-terminal helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00018      0.41      19     121 ..     202     303 ..     192     306 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                      Cucumopine_C  19 epeeik.alhkGevpsgaGskgqylstlvfangelRtlgyevldgliklAekaevdlksLvelakellkvkaeflgy 94 
                                       +++ei+ ++  G  p++ G+++      + +ng   +++++  + l  +A  +e  +++  +l  + +++ ++f+++
  gi|336255208|ref|YP_004598315.1| 202 ISDEIYkEITYGVEPTSLGTFDGMADRTITVNGFSKAYSMT-GWRLGYFAGPEE-LIDQAGKLHSHSVSSAVNFVQH 276
                                       66777425777777777888888888888888887777764.456666666643.3566677888889999****** PP

                      Cucumopine_C  95 vGlekladllkeleelideletredfl 121
                                        G+e l+++   +e+++++ e r d++
  gi|336255208|ref|YP_004598315.1| 277 AGIEALENTDTAVEQMVEAFEERRDLV 303
                                       ***********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2962.11
//
Query:       gi|336255209|ref|YP_004598316.1|  [L=244]
Description: HNH endonuclease [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00099   19.1  21.4      0.048   13.7   4.2    4.3  3  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.013   15.5   0.9      0.013   15.5   0.9    4.2  4  zf-C2H2_6        C2H2-type zinc finger
      0.019   15.1   1.2      0.019   15.1   1.2    4.4  3  FYVE             FYVE zinc finger
      0.028   14.3  18.5      0.049   13.5   0.3    5.0  5  C1_1             Phorbol esters/diacylglycerol binding domain
      0.057   13.5  10.7       0.61   10.2   0.1    4.5  3  zf-MYND          MYND finger
      0.063   13.4  24.2       0.22   11.7   0.5    5.6  5  Zn-ribbon_8      Zinc ribbon domain
       0.12   12.4   6.2        0.3   11.2   0.3    3.0  3  Opiods_neuropep  Vertebrate endogenous opioids neuropeptide
       0.23   11.4  24.0        2.1    8.4   0.8    5.2  5  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
        1.1    9.3  20.5         15    5.7   5.1    4.4  4  zinc-ribbons_6   zinc-ribbons
        1.6    8.8   6.4         12    6.0   0.2    3.5  4  Kp4              Kp4
          2    8.7   8.2       0.17   12.1   0.5    2.7  3  FYVE_2           FYVE-type zinc finger
          2    8.4  18.7        1.4    8.9   0.6    4.2  3  HypA             Hydrogenase/urease nickel incorporation, met
        2.3    8.6   7.5        9.1    6.6   0.1    2.9  2  FpoO             F420H2 dehydrogenase subunit FpoO
        2.5    7.6  27.9        3.4    7.2   0.3    6.3  6  zf-ribbon_3      zinc-ribbon domain
        3.3    8.1  11.0       0.08   13.2   1.8    2.9  3  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
        3.8    7.9   0.0        3.8    7.9   0.0    3.2  2  zf-C2H2_jaz      Zinc-finger double-stranded RNA-binding
        6.9    6.7  25.1       0.51   10.3   1.5    6.5  6  Nudix_N_2        Nudix N-terminal


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 !   13.7   4.2   4.6e-05     0.048      15      48 ..       3      53 ..       2      54 .. 0.91
   2 ?   -2.4  15.0       4.7     5e+03       1      37 [.      73     124 ..      50     197 .. 0.77
   3 ?    2.8   0.2      0.11   1.2e+02      10      23 ..     183     196 ..     178     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.6e-05
                               DZR 15 CseCgtklkavaa..............edrCpsCgek.vdpearf..CpeC 48
                                      C++Cg++l+ ++               +++C+ Cg+   dp+ar   C+ C
  gi|336255209|ref|YP_004598316.1|  3 CPTCGKSLQTEQGmrqhhtkvhgeplpNRVCSGCGSVfYDPKARResCDDC 53
                                      ********966669***********************99999987779999 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.7
                               DZR   1 CpqCgee.....lppdarfCseCgtk....lkavaa..........edrCpsCgek 37 
                                       C +Cge       ++d  +C++C ++    l                  C sCg+ 
  gi|336255209|ref|YP_004598316.1|  73 CDSCGETfsyypSDKDGVYCPDCVEDaiglL----PenpsekgarvTVECGSCGSN 124
                                       5555555555444555556666666644443....123346677777777777765 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.11
                               DZR  10 pdarfCseCgtklk 23 
                                        d   C++Cg+ ++
  gi|336255209|ref|YP_004598316.1| 183 RDGYECQHCGAGPD 196
                                       55566888887665 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 ?   15.5   0.9   1.2e-05     0.013       4      23 ..       3      22 ..       2      26 .. 0.87
   2 ?   -1.3   0.2       2.2   2.3e+03       3      11 ..      32      40 ..      31      40 .. 0.86
   3 ?    8.8   1.1    0.0016       1.7       4      14 ..      73      83 ..      70      85 .. 0.90
   4 ?    1.8   0.3      0.24   2.5e+02       2       9 ..     186     193 ..     186     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                         zf-C2H2_6  4 CsvCsksFpslqaLggHkks 23
                                      C++C+ks+++ q ++ H   
  gi|336255209|ref|YP_004598316.1|  3 CPTCGKSLQTEQGMRQHHTK 22
                                      *****************755 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                         zf-C2H2_6  3 eCsvCsksF 11
                                      +Cs C+ +F
  gi|336255209|ref|YP_004598316.1| 32 VCSGCGSVF 40
                                      6999*9988 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0016
                         zf-C2H2_6  4 CsvCsksFpsl 14
                                      C+ C+++F+++
  gi|336255209|ref|YP_004598316.1| 73 CDSCGETFSYY 83
                                      *********99 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.24
                         zf-C2H2_6   2 heCsvCsk 9  
                                       +eC+ C++
  gi|336255209|ref|YP_004598316.1| 186 YECQHCGA 193
                                       9*****97 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   4.4     0.054        57      12      44 ..       3      41 ..       1      57 [. 0.60
   2 ?   15.1   1.2   1.8e-05     0.019       2      63 ..      63     119 ..      62     126 .. 0.87
   3 ?   -1.4   0.2       2.6   2.7e+03      27      32 ..     187     192 ..     180     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.054
                                      -TTT--B--SS..S--EE-TTT-....-EE-STTS-EEE CS
                              FYVE 12 CeiCakkFsll..rrrhhCrlCG....kvvCekCssklv 44
                                      C+ C k+ ++   +r+hh ++ G    + vC+ C s ++
  gi|336255209|ref|YP_004598316.1|  3 CPTCGKSLQTEqgMRQHHTKVHGeplpNRVCSGCGSVFY 41
                                      888888885544588888888883333356777776666 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.8e-05
                                       ---...--SB-TTT--B--SSS--EE-TTT--EE-STTS-EEE.EEGGGTEEEEEEE-HHHH CS
                              FYVE   2 kwkddsevkkCeiCakkFsllrrrhhCrlCGkvvCekCssklvallekeaeeksvrvCkeCl 63 
                                       +wkd +e+++C++C ++Fs+    +       v+C +C +  + ll+++ +ek  rv  eC 
  gi|336255209|ref|YP_004598316.1|  63 NWKDATETTSCDSCGETFSYYPSDK-----DGVYCPDCVEDAIGLLPENPSEKGARVTVECG 119
                                       7*****************9874444.....47999***********9*********988885 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.6
                                       E-TTT- CS
                              FYVE  27 hCrlCG 32 
                                        C++CG
  gi|336255209|ref|YP_004598316.1| 187 ECQHCG 192
                                       577777 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 ?    1.3   0.1       0.3   3.2e+02      14      29 ..       3      16 ..       1      26 [. 0.76
   2 ?    5.1   0.5      0.02        21      12      35 ..      31      54 ..      19      58 .. 0.83
   3 ?   13.5   0.3   4.6e-05     0.049       3      34 ..      64      95 ..      60      98 .. 0.85
   4 ?    1.4   0.6      0.28     3e+02      11      32 ..     115     142 ..     108     145 .. 0.75
   5 ?    2.7   0.1      0.11   1.2e+02      24      35 ..     181     192 ..     175     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.3
                                      -TTT-SB--SSSS-EE CS
                              C1_1 14 CkhCgeflwgkekqgl 29
                                      C +Cg++l  +  qg+
  gi|336255209|ref|YP_004598316.1|  3 CPTCGKSL--QTEQGM 16
                                      999***99..444444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.02
                                      -B-TTT-SB--SSSS-EEEETTT- CS
                              C1_1 12 tfCkhCgeflwgkekqglkCswCk 35
                                        C+ Cg+ ++    +  +C++C+
  gi|336255209|ref|YP_004598316.1| 31 RVCSGCGSVFYDPKARRESCDDCN 54
                                      67********999999999****7 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 4.6e-05
                                      EEEE--SS--B-TTT-SB-..-SSSS-EEEETTT CS
                              C1_1  3 wvhrnfkqptfCkhCgefl..wgkekqglkCswC 34
                                      w++ +  ++t C+ Cge +  +   k g+ C +C
  gi|336255209|ref|YP_004598316.1| 64 WKDAT--ETTSCDSCGETFsyYPSDKDGVYCPDC 95
                                      66666..9***********85559********** PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.28
                                       --B-TTT-SB-.....-S.SSS-EEEET CS
                              C1_1  11 ptfCkhCgefl.....wg.kekqglkCs 32 
                                       +  C  Cg+ l     ++    +g+ C+
  gi|336255209|ref|YP_004598316.1| 115 TVECGSCGSNLevrpaKFeTQERGFFCT 142
                                       6789999999988888444778888885 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.11
                                       SSS-EEEETTT- CS
                              C1_1  24 kekqglkCswCk 35 
                                       +e+ g+ C+ C+
  gi|336255209|ref|YP_004598316.1| 181 LERDGYECQHCG 192
                                       567888999996 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00058      0.61       1      21 [.       3      41 ..       3      45 .. 0.79
   2 ?    2.6   3.1      0.14   1.5e+02       1       7 [.      73      85 ..      44     152 .. 0.60
   3 ?    0.1   0.1      0.86   9.1e+02       1       6 [.     188     193 ..     187     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00058
                                      -TTT--.................B-SC..E-TTTS-SEE CS
                           zf-MYND  1 CavCgk................aealk..kCagCksvfY 21
                                      C  Cgk                 e+l    C+gC svfY
  gi|336255209|ref|YP_004598316.1|  3 CPTCGKslqteqgmrqhhtkvhGEPLPnrVCSGCGSVFY 41
                                      88888888888888888877763333356*********9 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                                      -TTT--....... CS
                           zf-MYND  1 CavCgk......a 7 
                                      C +Cg+      +
  gi|336255209|ref|YP_004598316.1| 73 CDSCGEtfsyypS 85
                                      3333333333321 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.86
                                       -TTT-- CS
                           zf-MYND   1 CavCgk 6  
                                       C++Cg 
  gi|336255209|ref|YP_004598316.1| 188 CQHCGA 193
                                       999987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.5     0.052        55      29      36 ..       3      10 ..       1      16 [. 0.79
   2 ?    0.6   2.9      0.61   6.4e+02       8      33 ..      33      54 ..      31      59 .. 0.64
   3 ?   11.7   0.5   0.00021      0.22       8      33 ..      73      96 ..      64     100 .. 0.82
   4 ?    4.3   0.1     0.042        44       7      16 ..     117     126 ..     109     136 .. 0.67
   5 ?    4.8   0.1     0.028        30       6      13 ..     186     193 ..     176     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.052
                       Zn-ribbon_8 29 CPeCgsev 36
                                      CP+Cg+ +
  gi|336255209|ref|YP_004598316.1|  3 CPTCGKSL 10
                                      99999865 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.61
                       Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCg 33
                                      C  Cg++f        a  + C +C+
  gi|336255209|ref|YP_004598316.1| 33 CSGCGSVFYDPK----ARRESCDDCN 54
                                      999999997322....1133477775 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00021
                       Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCg 33
                                      C++Cg++f      sd++ + CP+C 
  gi|336255209|ref|YP_004598316.1| 73 CDSCGETFSYYP--SDKDGVYCPDCV 96
                                      *********775..4666778****5 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.042
                       Zn-ribbon_8   7 rCeeCghefe 16 
                                       +C +Cg+  e
  gi|336255209|ref|YP_004598316.1| 117 ECGSCGSNLE 126
                                       4555555555 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.028
                       Zn-ribbon_8   6 YrCeeCgh 13 
                                       Y+C+ Cg 
  gi|336255209|ref|YP_004598316.1| 186 YECQHCGA 193
                                       88888886 PP

>> Opiods_neuropep  Vertebrate endogenous opioids neuropeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.074        78       5      17 ..       2      14 ..       1      19 [. 0.86
   2 ?   -3.3   0.1       9.6     1e+04       5      11 ..      72      78 ..      70      86 .. 0.72
   3 ?   11.2   0.3   0.00029       0.3       5      35 ..     117     151 ..     115     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.074
                   Opiods_neuropep  5 dCllCayklqdqq 17
                                      dC +C+++lq  q
  gi|336255209|ref|YP_004598316.1|  2 DCPTCGKSLQTEQ 14
                                      9********9854 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.6
                   Opiods_neuropep  5 dCllCay 11
                                       C +C++
  gi|336255209|ref|YP_004598316.1| 72 SCDSCGE 78
                                      6888876 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00029
                   Opiods_neuropep   5 dCllCayklqdqqksfntlv....ClleCegklss 35 
                                       +C +C+  l  ++ +f t      C+leC g+  s
  gi|336255209|ref|YP_004598316.1| 117 ECGSCGSNLEVRPAKFETQErgffCTLECYGEWLS 151
                                       8****************9755556*****998766 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 ?    2.6   0.2      0.12   1.3e+02      30      41 ..       2      13 ..       1      25 [. 0.71
   2 ?    5.3   1.6     0.017        18      30      53 ..      32      54 ..      30      58 .. 0.91
   3 ?    8.4   0.8    0.0019       2.1      29      54 ..      71      97 ..      65      99 .. 0.89
   4 ?    4.5   0.4      0.03        32      30      50 ..     117     142 ..     112     150 .. 0.85
   5 ?    4.4   0.1     0.033        35      38      54 ..     177     193 ..     169     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.12
                    OrfB_Zn_ribbon 30 tCseCgsknkea 41
                                      +C+ Cg+ ++++
  gi|336255209|ref|YP_004598316.1|  2 DCPTCGKSLQTE 13
                                      699999988883 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.017
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCg 53
                                       Cs Cgs+ ++ ++ r+  C++C+
  gi|336255209|ref|YP_004598316.1| 32 VCSGCGSVFYD-PKARRESCDDCN 54
                                      6**********.999999*****6 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0019
                    OrfB_Zn_ribbon 29 ktCseCgsknke.alsgrtfkCpnCgf 54
                                      ++C  Cg++ ++ + +++ ++Cp+C  
  gi|336255209|ref|YP_004598316.1| 71 TSCDSCGETFSYyPSDKDGVYCPDCVE 97
                                      57**********99***********75 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.03
                    OrfB_Zn_ribbon  30 tCseCgsknke.....alsgrtfkCp 50 
                                       +C  Cgs+++      + ++r f C+
  gi|336255209|ref|YP_004598316.1| 117 ECGSCGSNLEVrpakfETQERGFFCT 142
                                       8*******999899999999999998 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.033
                    OrfB_Zn_ribbon  38 nkealsgrtfkCpnCgf 54 
                                        ++al+++ ++C++Cg+
  gi|336255209|ref|YP_004598316.1| 177 RRRALERDGYECQHCGA 193
                                       3448999********97 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   5.1     0.014        15       2      37 ..       2      55 ..       1      62 [. 0.82
   2 ?    4.4   7.3     0.035        37       2      37 ..      49      97 ..      31     103 .. 0.75
   3 ?    2.6   0.3      0.13   1.4e+02      29      43 ..     115     129 ..     106     148 .. 0.68
   4 ?    1.5   0.0      0.28   2.9e+02      15      24 ..     184     193 ..     171     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.014
                                      --SSS-S--EE-S..............SEEE-TTT--....EEEEEEE-SSS-S CS
                    zinc-ribbons_6  2 kCpeCqqelekrg..............eqyhCeaCqe....dlkkealCpeCeq 37
                                       Cp+C + l++++               +  C+ C +       +   C++C+ 
  gi|336255209|ref|YP_004598316.1|  2 DCPTCGKSLQTEQgmrqhhtkvhgeplPNRVCSGCGSvfydPKARRESCDDCNP 55
                                      6*********55559999999999999899999999976655567889999975 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.035
                                      --SSS-S--EE-S.......SEEE-TTT--......EEEEEEE-SSS-S CS
                    zinc-ribbons_6  2 kCpeCqqelekrg.......eqyhCeaCqe......dlkkealCpeCeq 37
                                      +C +C+ +  +++       e+++C++C e      + k   +Cp+C +
  gi|336255209|ref|YP_004598316.1| 49 SCDDCNPNAGEHNgnwkdatETTSCDSCGEtfsyypSDKDGVYCPDCVE 97
                                      5888887776444477778889999999995555544455678999976 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.13
                                       EEE-SSS-S---EEE CS
                    zinc-ribbons_6  29 ealCpeCeqelevlk 43 
                                       +  C  C+++lev  
  gi|336255209|ref|YP_004598316.1| 115 TVECGSCGSNLEVRP 129
                                       566888888887754 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.28
                                       SEEE-TTT-- CS
                    zinc-ribbons_6  15 eqyhCeaCqe 24 
                                       + y+C++C +
  gi|336255209|ref|YP_004598316.1| 184 DGYECQHCGA 193
                                       4688888876 PP

>> Kp4  Kp4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.011        12      74     105 ..      10      41 ..       3      66 .. 0.83
   2 ?    2.4   0.2      0.15   1.6e+02      95     114 ..      71      90 ..      54      92 .. 0.86
   3 ?   -2.6   0.0       5.3   5.6e+03      96     102 ..     117     123 ..     114     136 .. 0.82
   4 ?    1.8   0.0      0.22   2.4e+02      94     110 ..     185     201 ..     169     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                               Kp4  74 lqktggvsgatiksllqelvdhgCkvCGsvPl 105
                                       lq+++g++ ++ k   + l +  C+ CGsv +
  gi|336255209|ref|YP_004598316.1|  10 LQTEQGMRQHHTKVHGEPLPNRVCSGCGSVFY 41 
                                       688888999999999999***********965 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.15
                               Kp4  95 hgCkvCGsvPllyakgnndv 114
                                        +C  CG    +y+++++ v
  gi|336255209|ref|YP_004598316.1|  71 TSCDSCGETFSYYPSDKDGV 90 
                                       58************999865 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.3
                               Kp4  96 gCkvCGs 102
                                        C+ CGs
  gi|336255209|ref|YP_004598316.1| 117 ECGSCGS 123
                                       5999998 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.22
                               Kp4  94 dhgCkvCGsvPllyakg 110
                                        + C+ CG+ P  ++++
  gi|336255209|ref|YP_004598316.1| 185 GYECQHCGAGPDELGQN 201
                                       589******99877654 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5   0.00016      0.17      46     102 ..      24      78 ..       5      84 .. 0.83
   2 ?    2.9   0.8      0.11   1.2e+02      53      78 ..      69      96 ..      63     132 .. 0.82
   3 ?    0.3   0.5      0.71   7.5e+02      72      98 ..     116     142 ..      90     148 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                            FYVE_2  46 lgnqaklgethCilCleefkllvnskrqCldCklnvCkkCsvenkkekvwlCkiCse 102
                                        g  + l ++ C  C + f   ++ ++ C+dC+ n  ++ ++ +   ++  C+ C e
  gi|336255209|ref|YP_004598316.1|  24 HG--EPLPNRVCSGCGSVFYDPKARRESCDDCNPNAGEHNGNWKDATETTSCDSCGE 78 
                                       33..378899*********************************9999999*****76 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                            FYVE_2 53 gethCilCleefkllvnsk..rqCldCk 78
                                      ++t C  C e+f +  + k  + C dC 
  gi|336255209|ref|YP_004598316.1| 69 ETTSCDSCGETFSYYPSDKdgVYCPDCV 96
                                      5688999*****9999888778999996 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.71
                            FYVE_2  72 rqCldCklnvCkkCsvenkkekvwlCk 98 
                                       ++C  C  n+  + ++ + +e+++ C+
  gi|336255209|ref|YP_004598316.1| 116 VECGSCGSNLEVRPAKFETQERGFFCT 142
                                       456666666655555669999999997 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 ?    1.2   5.2      0.33   3.5e+02      70      93 ..      30      54 ..       1      63 [. 0.50
   2 ?    8.9   0.6    0.0014       1.4      69      96 ..      69      99 ..      63     104 .. 0.74
   3 ?    4.8   0.5     0.026        28      68      94 ..     113     193 ..     108     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.33
                                      EEEETTTS-EEECHHH.HHS-TTTS CS
                              HypA 70 kvrCreCgkefeleek.alrCpkCg 93
                                      +  C+ Cg+ f   ++ +++C +C+
  gi|336255209|ref|YP_004598316.1| 30 NRVCSGCGSVFYDPKArRESCDDCN 54
                                      2346666666664332255677775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0014
                                      -EEEETTTS-EEECHH..H.HHS-TTTSSS- CS
                              HypA 69 vkvrCreCgkefelee..k.alrCpkCgsad 96
                                       ++ C++Cg++f+     k  + Cp+C +  
  gi|336255209|ref|YP_004598316.1| 69 ETTSCDSCGETFSYYPsdKdGVYCPDCVEDA 99
                                      5689********94443335678****8765 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.026
                                       --EEEETTTS-EEECHHHHH......................................................S-T CS
                              HypA  68 pvkvrCreCgkefeleekal......................................................rCp 90 
                                       +v+v+C +Cg++ e++ +++                                                      +C+
  gi|336255209|ref|YP_004598316.1| 113 RVTVECGSCGSNLEVRPAKFetqergffctlecygewlstnvvgpdhhqweggtieygrewwrirrralerdgyECQ 189
                                       67899999999998765323346677877777777777777777777777777777777777777777777777888 PP

                                       TTSS CS
                              HypA  91 kCgs 94 
                                       +Cg+
  gi|336255209|ref|YP_004598316.1| 190 HCGA 193
                                       8876 PP

>> FpoO  F420H2 dehydrogenase subunit FpoO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   3.4      0.12   1.2e+02       3      74 ..       2      84 ..       1      89 [. 0.63
   2 ?    6.6   0.1    0.0086       9.1      35      76 ..      90     131 ..      81     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.12
                              FpoO  3 dcdlcgvsiPtviPvrvfkPrle.lsyPeGvwkGlc..........ekclkaakktydelskeeasgtaGkcdlcgkkt 70
                                      dc  cg+s+ t   +r ++ +++ +  P+ v+ G            e+c ++  ++ +++ + + ++ +  cd cg++ 
  gi|336255209|ref|YP_004598316.1|  2 DCPTCGKSLQTEQGMRQHHTKVHgEPLPNRVCSGCGsvfydpkarrESCDDCNPNAGEHNGNWKDATETTSCDSCGETF 80
                                      8999999999999999988887635688988888531111111111344444444445555555566666899999888 PP

                              FpoO 71 rlyd 74
                                        y+
  gi|336255209|ref|YP_004598316.1| 81 SYYP 84
                                      7776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0086
                              FpoO  35 GlcekclkaakktydelskeeasgtaGkcdlcgkktrlydve 76 
                                         c++c++ a     e+ +e+ + ++ +c  cg++ ++ + +
  gi|336255209|ref|YP_004598316.1|  90 VYCPDCVEDAIGLLPENPSEKGARVTVECGSCGSNLEVRPAK 131
                                       46***************999999999********99887765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.3    0.0032       3.4       5      15 ..       3      13 ..       2      15 .. 0.83
   2 ?    0.2   3.0      0.51   5.4e+02       3      11 ..      31      40 ..      29      54 .. 0.64
   3 ?    5.7   0.1    0.0096        10       1      10 [.      69      78 ..      69      81 .. 0.80
   4 ?    0.6   0.2      0.38     4e+02       3       8 ..      90      95 ..      88      95 .. 0.78
   5 ?    5.1   0.1     0.015        16       2      13 ..     115     126 ..     114     128 .. 0.78
   6 ?    3.4   0.2      0.05        52       4      11 ..     187     195 ..     185     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0032
                       zf-ribbon_3  5 CPnCGaplssd 15
                                      CP CG+ l+++
  gi|336255209|ref|YP_004598316.1|  3 CPTCGKSLQTE 13
                                      ******77876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.51
                       zf-ribbon_3  3 vrCPnCGa.p 11
                                      + C+ CG+  
  gi|336255209|ref|YP_004598316.1| 31 RVCSGCGSvF 40
                                      4577777744 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0096
                       zf-ribbon_3  1 stvrCPnCGa 10
                                      +t++C +CG+
  gi|336255209|ref|YP_004598316.1| 69 ETTSCDSCGE 78
                                      5889999997 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.38
                       zf-ribbon_3  3 vrCPnC 8 
                                      v+CP C
  gi|336255209|ref|YP_004598316.1| 90 VYCPDC 95
                                      688888 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.015
                       zf-ribbon_3   2 tvrCPnCGapls 13 
                                       tv+C +CG++l+
  gi|336255209|ref|YP_004598316.1| 115 TVECGSCGSNLE 126
                                       789999999765 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.05
                       zf-ribbon_3   4 rCPnCGa.p 11 
                                       +C +CGa p
  gi|336255209|ref|YP_004598316.1| 187 ECQHCGAgP 195
                                       677888766 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 ?   13.2   1.8   7.6e-05      0.08       4      38 ..       2      37 ..       1      52 [. 0.88
   2 ?   -0.4   0.3       1.4   1.5e+03      28      39 ..      86      97 ..      70     105 .. 0.77
   3 ?   -1.9   0.1       4.1   4.3e+03       3      11 ..     186     194 ..     184     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.6e-05
                           zf-Di19  4 tCPyCgke.ltvkeLveHvedeHrveskevvCPvCa 38
                                       CP Cgk+  t++ + +H ++ H +   + vC+ C 
  gi|336255209|ref|YP_004598316.1|  2 DCPTCGKSlQTEQGMRQHHTKVHGEPLPNRVCSGCG 37
                                      6******648999********************996 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                           zf-Di19 28 eskevvCPvCae 39
                                      ++  v CP C e
  gi|336255209|ref|YP_004598316.1| 86 DKDGVYCPDCVE 97
                                      555677777754 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.1
                           zf-Di19   3 ftCPyCgke 11 
                                       + C +Cg +
  gi|336255209|ref|YP_004598316.1| 186 YECQHCGAG 194
                                       788899875 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0036       3.8       4      20 ..       3      19 ..       2      19 .. 0.97
   2 ?    1.4   0.2       0.4   4.2e+02       2       7 ..     186     191 ..     185     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0036
                                      BTTTTBBBSSHHHHHCC CS
                       zf-C2H2_jaz  4 CvlCdKyFksenaldnH 20
                                      C++C K  ++e+ +++H
  gi|336255209|ref|YP_004598316.1|  3 CPTCGKSLQTEQGMRQH 19
                                      ****************9 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.4
                                       CBBTTT CS
                       zf-C2H2_jaz   2 fYCvlC 7  
                                       ++C++C
  gi|336255209|ref|YP_004598316.1| 186 YECQHC 191
                                       89**** PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.5   0.00048      0.51       3      33 ..       3      41 ..       3      42 .. 0.80
   2 ?   -0.8   0.5       1.4   1.5e+03      22      29 ..      47      54 ..      44      54 .. 0.83
   3 ?    1.7   0.1      0.23   2.5e+02       3       9 ..      73      79 ..      71      88 .. 0.68
   4 ?   -0.2   0.0       0.9   9.5e+02       2       6 ..      91      95 ..      90     105 .. 0.81
   5 ?    3.8   0.7     0.051        54       3      22 ..     118     137 ..     118     145 .. 0.85
   6 ?    1.8   0.1      0.23   2.4e+02       3       8 ..     188     193 ..     186     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00048
                                      -TTT--B-E........EE--TT-SS-EEEETTTTEEE- CS
                         Nudix_N_2  3 CsqCGtpve........lripdgDnreRlvCpaCgtihY 33
                                      C+ CG+ ++        +   +g+  +  vC+ Cg ++Y
  gi|336255209|ref|YP_004598316.1|  3 CPTCGKSLQteqgmrqhHTKVHGEPLPNRVCSGCGSVFY 41
                                      9999999887777766433448999999*********** PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.4
                                      EEEETTTT CS
                         Nudix_N_2 22 RlvCpaCg 29
                                      R  C++C+
  gi|336255209|ref|YP_004598316.1| 47 RESCDDCN 54
                                      899****6 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.23
                                      -TTT--B CS
                         Nudix_N_2  3 CsqCGtp 9 
                                      C +CG++
  gi|336255209|ref|YP_004598316.1| 73 CDSCGET 79
                                      5555554 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.9
                                      B-TTT CS
                         Nudix_N_2  2 FCsqC 6 
                                      +C+ C
  gi|336255209|ref|YP_004598316.1| 91 YCPDC 95
                                      88888 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.051
                                       -TTT--B-EEE--TT-SS-E CS
                         Nudix_N_2   3 CsqCGtpvelripdgDnreR 22 
                                       C +CG+ +e r  + +++eR
  gi|336255209|ref|YP_004598316.1| 118 CGSCGSNLEVRPAKFETQER 137
                                       999******99888888888 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.23
                                       -TTT-- CS
                         Nudix_N_2   3 CsqCGt 8  
                                       C++CG+
  gi|336255209|ref|YP_004598316.1| 188 CQHCGA 193
                                       777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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):              17  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 1714.42
//
Query:       gi|336255210|ref|YP_004598317.1|  [L=373]
Description: GMP reductase [Halopiger xanaduensis SH-6]
Scores for 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-122  408.4   4.8   2.6e-122  408.1   4.8    1.0  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    8.2e-09   35.3  11.4    0.00015   21.3   8.5    2.5  2  NMO           Nitronate monooxygenase
    4.6e-07   29.2  10.4    1.5e-06   27.5  10.4    1.8  1  FMN_dh        FMN-dependent dehydrogenase
    2.6e-06   27.1   1.2    0.00029   20.4   0.1    2.3  2  His_biosynth  Histidine biosynthesis protein
    0.00065   18.9   2.5    0.00065   18.9   2.5    2.1  2  Glu_synthase  Conserved region in glutamate synthase
     0.0095   15.2   0.7      0.016   14.4   0.7    1.3  1  DHO_dh        Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.021   14.2   5.4      0.037   13.4   5.1    1.5  1  TMP-TENI      Thiamine monophosphate synthase
      0.077   12.4   4.4       0.15   11.5   0.9    2.4  3  Aldolase      KDPG and KHG aldolase


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.1   4.8  1.2e-125  2.6e-122       1     345 []       7     340 ..       7     340 .. 0.96

  Alignments for each domain:
  == domain 1  score: 408.1 bits;  conditional E-value: 1.2e-125
                                       E--GGGEEEE---B-S-GG.GSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH   1 gltfddvllvpaksevlpk.evdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeev 76 
                                       gl++ dvllvp++s v ++ +vdl+t++t +++l +Plvsaamdtvte+e+Ai+l+r+Ggigv+h+ l++eeqa++v
  gi|336255210|ref|YP_004598317.1|   7 GLSYGDVLLVPKRSPVDSRsNVDLETNFTPNLELGTPLVSAAMDTVTETELAIELSRNGGIGVLHRFLTPEEQANQV 83 
                                       699**************998********************************************************* PP

                                       HHHHTSTTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  77 kkvkrspnaakdekgrllvgaavgvkedalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnv 153
                                       ++vk       d+    +v+aavg++ed+  r +alveagvd+lvvd+ahgh e++leav+ei++++++ +++aGnv
  gi|336255210|ref|YP_004598317.1|  84 EEVK-------DAG--ERVAAAVGINEDHVGRSAALVEAGVDALVVDVAHGHLERTLEAVAEIHEEFPDTDLVAGNV 151
                                       ****.......433..469********************************************************** PP

                                       -SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 154 ataegakaLieagadavkvGiGpGsiCttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGa 230
                                       at +g+++L++agad+vkvGiGpGs Cttr vag+GvpqltAv ++a+aa++ +v+++aDGGi++sgd vkAl aGa
  gi|336255210|ref|YP_004598317.1| 152 ATPAGVEDLAAAGADCVKVGIGPGSHCTTRKVAGAGVPQLTAVDDCADAAEDLDVTICADGGIRTSGDAVKALMAGA 228
                                       ***************************************************************************** PP

                                       SEEEESCCCTTBTTSSSEEEEETTEEEEEEEETTSHHHHHH-SS-TTS-..--SS-SBEEEEEE--B-HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 231 davmlGsllagteEspgeviliegrkyKeyrGmgslgamkkgskdryfqkkeklvpeGvegrvpykgsvkevveqlv 307
                                       d+vm+Gsl+agteE+pg v+ +eg+kyK  rGm++++a ++ ++d+   +++    eGve+ +pykg+v++vv++++
  gi|336255210|ref|YP_004598317.1| 229 DTVMMGSLFAGTEEAPGAVVEVEGTKYKRSRGMATTTAAEN-RDDKD--EANVRADEGVEALTPYKGPVADVVKEFC 302
                                       **************************************943.33333..235889********************** PP

                                       HHHHHHHHHHT-SSHHHHHHH-EEEEE-HHHHHHHS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 308 gglrsgmgylGaktieelkekakfvritaaglkeshvH 345
                                       +g++sg++y+G +ti + +eka+f+r++ ++ +  + H
  gi|336255210|ref|YP_004598317.1| 303 AGIQSGLSYCGGHTIPAAREKAEFIRVADSAKEREGYH 340
                                       ****************************9998776666 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   1.4e-05     0.032      12      60 ..      42      89 ..      33     100 .. 0.90
   2 !   21.3   8.5   6.5e-08   0.00015     143     238 ..     151     250 ..     138     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                               NMO 12 ppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvkal 60
                                       p+v + m  +++ +La   s +Gg+Gvl    lt+ + a+++++vk +
  gi|336255210|ref|YP_004598317.1| 42 TPLVSAAMDTVTETELAIELSRNGGIGVLH-RFLTPEEQANQVEEVKDA 89
                                      689999************************.9***********999976 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 6.5e-08
                               NMO 143 issvkearkvearGaDalivqGpeaGGhqGtpevgd..kglfaLvpqvldavd...iPviAaGGiidrrgvaaaLal 214
                                       +++   +  ++a+GaD + v G   G h  t++v++  + +++ v+  +da +   + + A GGi +  +   aL +
  gi|336255210|ref|YP_004598317.1| 151 VATPAGVEDLAAAGADCVKV-GIGPGSHCTTRKVAGagVPQLTAVDDCADAAEdldVTICADGGIRTSGDAVKALMA 226
                                       556666778999****8655.9999*****99999956666777899999988899**************999**** PP

                               NMO 215 GAsgvqigtrfLltkesdakdahk 238
                                       GA  v +g+ f +t+e++  ++  
  gi|336255210|ref|YP_004598317.1| 227 GADTVMMGSLFAGTEEAPGAVVEV 250
                                       ****************98776654 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5  10.4   6.7e-10   1.5e-06     203     303 ..     129     237 ..      19     247 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 6.7e-10
                                       --HHHHHHHHHHHS.SEEEEEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT-.--HHHCHHHHHHHH...S CS
                            FMN_dh 203 ltwddikwlreqtk.lplvvKGvltaedakraveaGvdgivvSNHGG.....Rqldga.patidvLpeiveavgg.r 271
                                        t + ++++ e+ +   lv   v t++ ++ +++aG+d + v    G     R++ ga ++ + +  ++++a+++ +
  gi|336255210|ref|YP_004598317.1| 129 RTLEAVAEIHEEFPdTDLVAGNVATPAGVEDLAAAGADCVKVGIGPGshcttRKVAGAgVPQLTAVDDCADAAEDlD 205
                                       36778888888877467888889999999999999999999965555555557776652556777788899999889 PP

                                       S-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 272 ievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                       +++ +DgGir+  D++kAl  GAd v++G  f
  gi|336255210|ref|YP_004598317.1| 206 VTICADGGIRTSGDAVKALMAGADTVMMGSLF 237
                                       *****************************876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.1    0.0048        11      30     102 ..     102     171 ..      84     175 .. 0.85
   2 !   20.4   0.1   1.3e-07   0.00029      65     105 ..     197     237 ..     183     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0048
                                       SHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEES CS
                      His_biosynth  30 dpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviig 102
                                       d v    ++ e+g+d l vvD+  a+ + e+ l++v+ei ee+  +  v G + +   ve+l  agad v +g
  gi|336255210|ref|YP_004598317.1| 102 DHVGRSAALVEAGVDAL-VVDV--AHGHLERTLEAVAEIHEEFPDTDLVAGNVATPAGVEDLAAAGADCVKVG 171
                                       55555666778888887.5788..889999************9999999999****************87665 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 1.3e-07
                                       HHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHH CS
                      His_biosynth  65 veeiaeevfipvqvGGGIrsledveelleagadkviigtaa 105
                                        +  ae ++++++ +GGIr+  d+ ++l agad v++g+  
  gi|336255210|ref|YP_004598317.1| 197 CADAAEDLDVTICADGGIRTSGDAVKALMAGADTVMMGSLF 237
                                       56789999******************************975 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 ?   -0.1   0.1      0.18     4e+02     182     238 ..      71     125 ..      69     127 .. 0.80
   2 !   18.9   2.5   2.9e-07   0.00065     223     304 ..     160     235 ..     131     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.18
                                       TT-SSHHHHHHHHHHHHHH-TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEEE-TT- CS
                      Glu_synthase 182 hdiysiedlaqliedLkevnkeakvsvKlvaeagvetiaagvakanadiilidGleG 238
                                       h +  +e+ a+ +e+ k++++++   v +   ++    a  +++a++d++++d  +G
  gi|336255210|ref|YP_004598317.1|  71 HRFLTPEEQANQVEEVKDAGERVAAAVGINEDHVGRSAA--LVEAGVDALVVDVAHG 125
                                       566788999999********9999999988777655544..5999999999996665 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.9e-07
                                       HHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SE CS
                      Glu_synthase 223 vakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAda 299
                                       +a a+ad++++ G+  G   +    +  aG+P ++a+     +  +      v++ adGg++t+ d vkal+ GAd+
  gi|336255210|ref|YP_004598317.1| 160 LAAAGADCVKV-GIGPGSHCTTR-KVAGAGVPQLTAVDDCADAAED----LDVTICADGGIRTSGDAVKALMAGADT 230
                                       56778888877.55555444433.3456889998888877665443....3699*********************** PP

                                       EE-SH CS
                      Glu_synthase 300 vgigt 304
                                       v +g+
  gi|336255210|ref|YP_004598317.1| 231 VMMGS 235
                                       **997 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.7   7.1e-06     0.016     244     276 ..     205     237 ..     183     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.1e-06
                                       .S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                            DHO_dh 244 eipiIgvGGiesgeDalekieaGAslvqvytal 276
                                       ++ i + GGi ++ Da+  ++aGA  v +++ +
  gi|336255210|ref|YP_004598317.1| 205 DVTICADGGIRTSGDAVKALMAGADTVMMGSLF 237
                                       599************************999865 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   5.1   1.6e-05     0.037      39     178 ..      76     234 ..      57     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                          TMP-TENI  39 arellelaeklaalcrkygvpliindrvdlala...........vgadgvHlgqddlpvaearellgpdliiGlSvh 104
                                       ++e ++++e+++++ ++  +++ in++     a           v++   Hl  +  +vae+ e +++  ++   v 
  gi|336255210|ref|YP_004598317.1|  76 PEEQANQVEEVKDAGERVAAAVGINEDHVGRSAalveagvdalvVDVAHGHLERTLEAVAEIHEEFPDTDLVAGNVA 152
                                       67788899999999999999999997543333335556777777888999*************************** PP

                          TMP-TENI 105 sleeaeeaealgadYi..gvGpifpTdtKkda..eplgleglkelaeale...iPvvaiGGitle.nvaevleagad 173
                                       +++ +e ++a+gad +  g+Gp  + +t+k a   +  l+ + ++a+a+e   + ++a GGi+++ ++ ++l agad
  gi|336255210|ref|YP_004598317.1| 153 TPAGVEDLAAAGADCVkvGIGPGSHCTTRKVAgaGVPQLTAVDDCADAAEdldVTICADGGIRTSgDAVKALMAGAD 229
                                       *************98622666777766666654445555555555555557779********875478888899999 PP

                          TMP-TENI 174 gvavv 178
                                        v + 
  gi|336255210|ref|YP_004598317.1| 230 TVMMG 234
                                       99875 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.62   1.4e+03      70      92 ..      80     102 ..      79     107 .. 0.88
   2 ?   11.5   0.9   6.5e-05      0.15      20      84 ..     101     168 ..      92     196 .. 0.81
   3 ?    1.1   0.1       0.1   2.3e+02      43      79 ..     207     243 ..     192     253 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.62
                                       HHHHHHHHHCT-SEEEESS--HH CS
                          Aldolase  70 aeqlaeakeaGaqfvvsPGltad 92 
                                       a+q++e+k+aG   + + G+++d
  gi|336255210|ref|YP_004598317.1|  80 ANQVEEVKDAGERVAAAVGINED 102
                                       789*********99999999998 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.5e-05
                                       GGHHHHHHHHHHTT--EEEEETTS...TTHHHHHHHHHHH-TTSEEEEES--SHHHHHHHHHCT-SEE CS
                          Aldolase  20 edalplaeaLvagGlrvlevtlrt...eaaldairvlrkerpdllvgaGtvlnaeqlaeakeaGaqfv 84 
                                       ed +    aLv+ G+ +l v +     e +l+a+  + +e pd  + aG v ++  +++ ++aGa+ v
  gi|336255210|ref|YP_004598317.1| 101 EDHVGRSAALVEAGVDALVVDVAHghlERTLEAVAEIHEEFPDTDLVAGNVATPAGVEDLAAAGADCV 168
                                       566677789******9877766542237899****9*****************************976 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.1
                                       STTHHHHHHHHHHH-TTSEEEEES--SHHHHHHHHHC CS
                          Aldolase  43 teaaldairvlrkerpdllvgaGtvlnaeqlaeakea 79 
                                       t +a   ir +   ++ l+ ga tv+  + +a  +ea
  gi|336255210|ref|YP_004598317.1| 207 TICADGGIRTSGDAVKALMAGADTVMMGSLFAGTEEA 243
                                       3344555666666666666666666666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2878.35
//
Query:       gi|336255211|ref|YP_004598318.1|  [L=388]
Description: phosphoribosylaminoimidazole carboxylase, ATPase subunit [Halopiger xanaduensis SH-6]
Scores for 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-52  176.3   0.0    6.2e-52  175.6   0.0    1.3  1  ATP-grasp        ATP-grasp domain
    7.6e-20   70.4   0.1    1.8e-19   69.2   0.1    1.6  1  PurK_C           Phosphoribosylaminoimidazole carboxylase C-t
    2.2e-08   33.9   0.1    2.9e-07   30.2   0.1    2.4  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    6.1e-08   32.9   0.0    9.2e-08   32.3   0.0    1.3  1  ATP-grasp_3      ATP-grasp domain
    3.4e-06   26.5   0.0    6.4e-06   25.6   0.0    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00046   19.7   0.1    0.00074   19.1   0.1    1.4  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
     0.0012   19.3   0.2      0.004   17.6   0.0    1.9  2  XdhC_C           XdhC Rossmann domain
     0.0018   18.2   0.2     0.0042   17.0   0.0    1.8  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
  ------ inclusion threshold ------
      0.014   14.8   0.0      0.039   13.4   0.0    1.8  2  ATP-grasp_5      ATP-grasp domain
      0.023   15.2   0.5       0.14   12.8   0.0    2.7  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.036   13.5   0.1       0.22   10.9   0.0    2.2  2  PALP             Pyridoxal-phosphate dependent enzyme
       0.04   13.7   0.0      0.066   13.0   0.0    1.4  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
       0.16   12.1   0.0       0.54   10.4   0.0    1.9  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
       0.18   11.7   0.1        5.3    6.9   0.0    2.6  2  RRM_1            RNA recognition motif. (a.k.a. RRM, RBD, or 


Domain annotation for each model (and alignments):
>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.6   0.0   4.8e-55   6.2e-52       2     171 .]     117     284 ..     116     284 .. 0.98

  Alignments for each domain:
  == domain 1  score: 175.6 bits;  conditional E-value: 4.8e-55
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE----SEEE CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqalealkeekvivEefvpfekEl 78 
                                       e++g+pvp+f  ve++++++ea+++ g+pv++Kar++gydG+G+  v+s++++e+ale + +++ +vE fv+fe+E+
  gi|336255211|ref|YP_004598318.1| 117 EAAGVPVPPFREVEDADDIREAIDDYGAPVMLKARTGGYDGRGNVPVESKDEAEEALESV-AGPAMVEAFVEFEREV 192
                                       6899********************************************************.9*************** PP

                                       EEEEEEETTC-EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEE CS
                         ATP-grasp  79 svlvvrsaeGetafypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnE 155
                                       sv++v   +  ta++p+ e+v+ d+ilr+ ++pa+ s++ +++a+e+a++++e ++g Gv+++ElF+++dge+l+nE
  gi|336255211|ref|YP_004598318.1| 193 SVIAVEGYDE-TAAFPIGENVHVDEILRETIVPARSSDAVAERAREVAEDVLEVMDGRGVYGIELFETTDGEILLNE 268
                                       *****99996.****************************************************************** PP

                                       EESS--GGGGGHHHHB CS
                         ATP-grasp 156 lapRpHnsGhvtldaa 171
                                       +apRpHnsGh+t+++a
  gi|336255211|ref|YP_004598318.1| 269 IAPRPHNSGHWTIEGA 284
                                       *************985 PP

>> PurK_C  Phosphoribosylaminoimidazole carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.1   1.4e-22   1.8e-19       1      51 [.     310     366 ..     310     371 .. 0.85

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.4e-22
                            PurK_C   1 avMvNlLGedae......ekleellaipgahlHlYgKeearpgRKmGHitvvgdsae 51 
                                       +vM NlLG+ +e      ++ e+++++p ahlH+YgK+earp RKmGH+tv++ ++e
  gi|336255211|ref|YP_004598318.1| 310 TVMTNLLGDVEEnqkaalRGVEKIHETPAAHLHWYGKREARPLRKMGHVTVCARDDE 366
                                       79*********755555555555******************************8876 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 ?   -1.8   0.0       1.5   1.9e+03      20      45 ..      77     102 ..      62     103 .. 0.84
   2 !   30.2   0.1   2.3e-10   2.9e-07       3     176 ..     117     273 ..     116     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
                                       HCH-H-HHHHHHHHHC-SSEEEEESS CS
                   Dala_Dala_lig_C  20 akeekkellekveeelgypvfVKpar 45 
                                       ++ +++++le+v e  g pv  Kpa 
  gi|336255211|ref|YP_004598318.1|  77 IELADQDVLERVSEDSGTPVHPKPAT 102
                                       5667789999**********999996 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 2.3e-10
                                       HHTT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSST.TTTEEEESSGGGHHHHHHHHHTT-SCEEEE CS
                   Dala_Dala_lig_C   3 kaaGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGS.SvGvskveseeelkeaieeafkydekvlvE 78 
                                       +aaG+pv+p+  +e ++  +e        ++  g pv+ K+   G    G   ves++e +ea+e+ +      +vE
  gi|336255211|ref|YP_004598318.1| 117 EAAGVPVPPFREVEDADDIREA-------IDDYGAPVMLKARTGGYdGRGNVPVESKDEAEEALESVA---GPAMVE 183
                                       6899999999999999888777.......899********98888526799999*******9999765...689*** PP

                                       E--.ESEEEEE.EEEETSSCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--S CS
                   Dala_Dala_lig_C  79 eai.egreiev.avlgneklevsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrG 153
                                       +++   re+ v av g +++ ++++ge v  +++            +  vpa+ +++v+e+ +e+a ++ +++d+rG
  gi|336255211|ref|YP_004598318.1| 184 AFVeFEREVSViAVEGYDETAAFPIGENVHVDEIL----------RETIVPARSSDAVAERAREVAEDVLEVMDGRG 250
                                       ***55688875477778999999999998887775..........4678**************************** PP

                                       EEEEEEEEETTTEEEEEEEESS- CS
                   Dala_Dala_lig_C 154 laRvDfflteegeivlnEvNtlP 176
                                       +  + +f t++gei+lnE+ + P
  gi|336255211|ref|YP_004598318.1| 251 VYGIELFETTDGEILLNEIAPRP 273
                                       *******************8877 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   7.1e-11   9.2e-08       2     159 ..     107     274 ..     106     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 7.1e-11
                                       TSHHHHHHHHTTT.S---...........-EESS--....SSSEEEEESS-.------B--SS--TTE......... CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvP.......tkleaeeleee....ekklvvKprdG.aggesvrvveekeeaeaaieeve.. 64 
                                        dKl   ++L++agv+vP            + ++e+      ++ +K r+G  +g +++ ve k+eae+a+e+v+  
  gi|336255211|ref|YP_004598318.1| 107 HDKLVQKRELEAAGVPVPpfrevedA----DDIREAiddyGAPVMLKARTGgYDGRGNVPVESKDEAEEALESVAgp 179
                                       79****************88644322....2233325555999****9986269*******************9999 PP

                                       .EEEE---.SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H..HHHHHHHHHHHHTTSTT--EE CS
                       ATP-grasp_3  65 .lvqefie.GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietel..keevvelaeevvekleglaGy 137
                                        +v +f+e  +++Sv ++    +   + + +++       ++ +  ++p++ ++  +e+++e+ae+v+e + + +G+
  gi|336255211|ref|YP_004598318.1| 180 aMVEAFVEfEREVSVIAVEGYDETAAFPIGENVHVD----EILRETIVPARSSDavAERAREVAEDVLEVM-DGRGV 251
                                       9*******4579*******99999999999998755....78888999999888889**************.99*** PP

                                       EEEEEE.ESS.SEEEEEEESS-- CS
                       ATP-grasp_3 138 vGvDlv.lkdeepyviEvNPRlt 159
                                        G++l   +d+e+ + E+ PR+ 
  gi|336255211|ref|YP_004598318.1| 252 YGIELFeTTDGEILLNEIAPRPH 274
                                       *****96778999999*****86 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 !   25.6   0.0     5e-09   6.4e-06      35     103 ..       7      81 ..       1      84 [. 0.78

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 5e-09
                                       TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.....CHHHHTC.EECSHHHHHHH-SEEEE-S--ST CS
                      2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.....eeeelgv.elvsleellaesDivslhlpltp 103
                                        g t+G++G G++G+ +a+ ++++g++v++ d++++  +     ++    + + + + el a++D+++  + l +
  gi|336255211|ref|YP_004598318.1|   7 PGPTLGVVGGGQLGRMLAEAAAPLGVEVVVLDPTPDCPAapvarDQIVADFdDEAGIRELAARADVLTFEIELAD 81 
                                       5789******************************994444443322222232556899**********9998876 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 !   19.1   0.1   5.8e-07   0.00074       1      74 [.     108     180 ..     108     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.8e-07
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCC.TTTTEEEESSHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafgl.GGkGmrvarneeelaelvkkalaea 74 
                                       Dk   k+ l++++vpv p  ++  e++++  ++ +++g Pv++ka  g+  G+G   +++++e +e++++    a
  gi|336255211|ref|YP_004598318.1| 108 DKLVQKRELEAAGVPVPPFREV--EDADDIREAIDDYGAPVMLKARTGGyDGRGNVPVESKDEAEEALESVAGPA 180
                                       777889999*******999999..********************9765438**********99999988765555 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.1e-06     0.004       2      64 ..      12      88 ..      11      97 .. 0.68
   2 ?   -1.9   0.0       3.6   4.6e+03      44      59 ..     340     370 ..     284     380 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.1e-06
                                      EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG.....-GGG-TT-SE.................-EEEE--S-HHHHH CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefa.....tkerfpeade.................tavvvlthdhklDa 58
                                       ++G+g+ ++ la+ aa lg++v+v+dp ++       +        +                  a v+  +    D+
  gi|336255211|ref|YP_004598318.1| 12 GVVGGGQLGRMLAEAAAPLGVEVVVLDPTPDCPaapvaR--------DqivadfddeagirelaaRADVLTFEIELADQ 82
                                      69***************************9754333331........12334444455566666555555555555666 PP

                                      HHHHHH CS
                            XdhC_C 59 ealeaa 64
                                      ++le++
  gi|336255211|ref|YP_004598318.1| 83 DVLERV 88
                                      666665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
                                       E...............-EEEE--S-HHHHHH CS
                            XdhC_C  44 e...............tavvvlthdhklDae 59 
                                       +                +v v+ +d ++D e
  gi|336255211|ref|YP_004598318.1| 340 HlhwygkrearplrkmGHVTVCARDDETDVE 370
                                       0344444444445555666666666666655 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 !   17.0   0.0   3.3e-06    0.0042       2      37 ..      11      46 ..      10     113 .. 0.81
   2 ?   -3.4   0.1       5.9   7.6e+03     153     169 ..     225     241 ..     216     247 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.3e-06
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealek 37
                                      ++v+G G++G+ +a+++a  g+eVv++d +++  ++
  gi|336255211|ref|YP_004598318.1| 11 LGVVGGGQLGRMLAEAAAPLGVEVVVLDPTPDCPAA 46
                                      79***************************9886554 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.9
                                       TT--HHHHHHHHHHHHH CS
                           3HCDH_N 153 ekTseetvatvvelakk 169
                                       +++s+++ ++++e+a++
  gi|336255211|ref|YP_004598318.1| 225 ARSSDAVAERAREVAED 241
                                       44455555555554443 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.1e-05     0.039      18      54 ..     115     151 ..     104     178 .. 0.91
   2 ?   -2.8   0.0       2.7   3.5e+03     154     183 ..     303     332 ..     301     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
                       ATP-grasp_5  18 lleaygipvvetrlassaeeaveaaeeigypvvlKiv 54 
                                        lea g+pv+++r +++a++  ea++  g+pv lK +
  gi|336255211|ref|YP_004598318.1| 115 ELEAAGVPVPPFREVEDADDIREAIDDYGAPVMLKAR 151
                                       589********************************87 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                       ATP-grasp_5 154 areliertkaskllkgvrgekkadlaalee 183
                                       a +l ++t +++ll +v++++ka l+ +e+
  gi|336255211|ref|YP_004598318.1| 303 ATDLRSSTVMTNLLGDVEENQKAALRGVEK 332
                                       566677888899999999998999888876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011      0.14       3      30 ..      12      39 ..      10      62 .. 0.91
   2 ?   -2.9   0.0       8.3   1.1e+04      18      33 ..     352     366 ..     348     371 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                      EEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvver 30
                                       vvGgG +g +lA+a+a lg +V v++ 
  gi|336255211|ref|YP_004598318.1| 12 GVVGGGQLGRMLAEAAAPLGVEVVVLDP 39
                                      69*********************99875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.3
                                       HHHTTSEEEEEESSSS CS
                         Pyr_redox  18 laelgkkVtvversdk 33 
                                       l+++g +Vtv+ r d+
  gi|336255211|ref|YP_004598318.1| 352 LRKMG-HVTVCARDDE 366
                                       66666.8999999886 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00017      0.22      54      90 ..       7      43 ..       2      88 .. 0.84
   2 ?   -0.9   0.0       0.7   8.9e+02     109     151 ..     226     265 ..     208     274 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                                      TTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS- CS
                              PALP 54 gaktvveassGNhgralAaaaallGlkvtivvpadas 90
                                      ++ t+ + ++G+ gr lA aaa lG++v+++ p  + 
  gi|336255211|ref|YP_004598318.1|  7 PGPTLGVVGGGQLGRMLAEAAAPLGVEVVVLDPTPDC 43
                                      5667888899********************9665544 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.7
                                       CHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHH CS
                              PALP 109 gdydeavaaaaelaaegegaylvsqfdnptviegygtiglEil 151
                                       ++ d+ +++a+e+a++   ++ v ++  +++ie  +t+  Eil
  gi|336255211|ref|YP_004598318.1| 226 RSSDAVAERAREVAED---VLEVMDGRGVYGIELFETTDGEIL 265
                                       3345555557888887...777777777777777777777775 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 ?   13.0   0.0   5.1e-05     0.066       3      98 ..     109     196 ..     107     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.1e-05
                                       HHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEE.SC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCC CS
                            GARS_A   3 KsfakdllkkagiptaeyeaftdpeeakeyieeatakalVvKa.dglaagKgvivakseeealkavkeilekkkfGe 78 
                                       K   k+ l++ag+p + +++++d+++++e i++ +a++  +Ka  g   g+g + ++s++ea +a++++      G 
  gi|336255211|ref|YP_004598318.1| 109 KLVQKRELEAAGVPVPPFREVEDADDIREAIDDYGAPV-MLKArTGGYDGRGNVPVESKDEAEEALESVA-----G- 178
                                       667788899*****************************.7776357889999999999999999998875.....3. PP

                                       CCSSEEEEE---S.EEEEEEE CS
                            GARS_A  79 agekvviEelleG.eEvslla 98 
                                            ++E ++e   Evs++a
  gi|336255211|ref|YP_004598318.1| 179 ---PAMVEAFVEFeREVSVIA 196
                                       ...334444444313555555 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 ?   10.4   0.0   0.00042      0.54       2      58 ..      11      72 ..      10      93 .. 0.76
   2 ?   -2.0   0.0       2.8   3.6e+03      34      57 ..     213     236 ..     176     248 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00042
                                      EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.....EEE-SSHHHHHHHCSE CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.....akaaesieelvasldv 58
                                      +g++G G++G+ +a+  +  g +v+v + t++   + va+      ++  + i+el+a++dv
  gi|336255211|ref|YP_004598318.1| 11 LGVVGGGQLGRMLAEAAAPLGVEVVVLDPTPDCPAAPVARDqivadFDDEAGIRELAARADV 72
                                      79****************************98777777665444444444455555555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                                       HHHHHHHTTEEE-SSHHHHHHHCS CS
                     NAD_binding_2  34 kveelvaegakaaesieelvasld 57 
                                       +v+e++ e +++a s  +++++++
  gi|336255211|ref|YP_004598318.1| 213 HVDEILRETIVPARSSDAVAERAR 236
                                       345555555555555555555553 PP

>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0042       5.3      13      61 ..     133     178 ..     130     183 .. 0.80
   2 ?    2.3   0.1      0.12   1.5e+02      38      52 ..     180     194 ..     176     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0042
                                       HHHHHHHHTTSCEEEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTT CS
                             RRM_1  13 eeLkelFskfGpiksiklvrd.etgkskgfafVeFeskedAekAlealng 61 
                                       ++++e   ++G      ++ + +tg  +g + V  esk++Ae+Ale++ g
  gi|336255211|ref|YP_004598318.1| 133 DDIREAIDDYGAP----VMLKaRTGGYDGRGNVPVESKDEAEEALESVAG 178
                                       6677777777777....4444489999*******************9876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.12
                                       EEEEEEEEESSHHHH CS
                             RRM_1  38 skgfafVeFeskedA 52 
                                       ++  afVeFe + + 
  gi|336255211|ref|YP_004598318.1| 180 AMVEAFVEFEREVSV 194
                                       5667******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 2983.27
//
Query:       gi|336255212|ref|YP_004598319.1|  [L=212]
Description: phosphoribosylaminoimidazole carboxylase, catalytic subunit [Halopiger xanaduensis SH-6]
Scores for complete 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-48  164.2   0.0    1.8e-48  163.9   0.0    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 !  163.9   0.0     1e-52   1.8e-48       1     146 [.      27     189 ..      27     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 163.9 bits;  conditional E-value: 1e-52
                                       EEEEEESSGGGHHHH......HHHHHH.HHHTT-..............EEEEEE--TTTSHHHHHHHHHHCHTTTEE CS
                              AIRC   1 kVgiimGSdsDlevm......kkaaei.lkelgv..............eyevrvvSahrtpeelleyaeeaeerglk 56 
                                       +Vgi+mGSdsDle+m      ++a+++ ++elg+              ++e++v+Sahrtp+ +++yae+aeergl+
  gi|336255212|ref|YP_004598319.1|  27 DVGIVMGSDSDLETMmtggrrRGAYDAfVDELGFaeqtdyenppaerfTFETYVTSAHRTPDLMTAYAETAEERGLE 103
                                       69*************9999986676651577999******************************************* PP

                                       EEEEEEES.S--HHHHHHHHS.SS-EEEEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT- CS
                              AIRC  57 viIagAGg.aahLpgvvaslt.tlPVigvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkd 131
                                       viIagAGg +a+Lp+++as++ +lPVigvPv++      +s+ S++ mP+g+p+++v++gk+ nAal+Aaqila+++
  gi|336255212|ref|YP_004598319.1| 104 VIIAGAGGkSADLPNMTASIAyPLPVIGVPVQE------KSVDSVIGMPTGAPLVAVDAGKSFNAALSAAQILARQH 174
                                       *******99***********99***********......9************************************* PP

                                       HHHHHHHHHHHHHHH CS
                              AIRC 132 eelaekleeyreelk 146
                                       +e++++l +y+e+l+
  gi|336255212|ref|YP_004598319.1| 175 DEVRDRLVSYHEDLR 189
                                       ***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 1832.93
//
Query:       gi|336255213|ref|YP_004598320.1|  [L=137]
Description: NADH-ubiquinone/plastoquinone oxidoreductase chain 3 [Halopiger xanaduensis SH-6]
Scores for 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-31  107.3   0.4    4.1e-31  107.1   0.4    1.1  1  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch
  ------ inclusion threshold ------
      0.041   14.1   3.2       0.35   11.1   0.2    2.3  2  TrbC         TrbC/VIRB2 family


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 !  107.1   0.4   4.6e-35   4.1e-31       3      99 .]      20     123 ..      18     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 4.6e-35
                                       HHHHHHCHSS-----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST.......HHHH. CS
                       Oxidored_q4   3 lllllsallgpkkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkel.....glfg. 73 
                                        ++++s+ll+p+ p+++k+++YE+G  p+g +r+rf++++y+vallFl+FD+e+v+lfpwav+++e+        + 
  gi|336255213|ref|YP_004598320.1|  20 GMMAVSYLLRPTVPETSKRATYESGEVPTGGTRVRFNIQYYMVALLFLVFDIETVLLFPWAVVYREAvesdaV--Sl 94 
                                       6899************************************************************988765430..23 PP

                                       ...HHHHHHHHHHHHHHHHHHHHH-S-XX CS
                       Oxidored_q4  74 ...liemllFllillvglvYewkkgaLeW 99 
                                          l  m+ F++illvgl+++w++ga++W
  gi|336255213|ref|YP_004598320.1|  95 leiLGPMVAFVAILLVGLAWAWRNGAVQW 123
                                       445789**********************9 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3     0.011        98      56      78 ..       4      26 ..       3      31 .. 0.85
   2 ?   11.1   0.2   3.9e-05      0.35      46      78 ..      92     123 ..      84     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.011
                              TrbC 56 viatiaiivaGimlafgrlswrt 78
                                      +ia+ a++ +G+ + fg + +  
  gi|336255213|ref|YP_004598320.1|  4 WIAIGALALVGLLIPFGMMAVSY 26
                                      599*************9988665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.9e-05
                              TrbC  46 vdfltgplakviatiaiivaGimlafgrlswrt 78 
                                       v+ l+  l++ +a +ai+ +G+++a++   +++
  gi|336255213|ref|YP_004598320.1|  92 VSLLEI-LGPMVAFVAILLVGLAWAWRNGAVQW 123
                                       566777.9******************9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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: 0.36u 0.19s 00:00:00.55 Elapsed: 00:00:00.33
# Mc/sec: 1237.37
//
Query:       gi|336255214|ref|YP_004598321.1|  [L=235]
Description: NADH-quinone oxidoreductase subunit B [Halopiger xanaduensis SH-6]
Scores for 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-21   75.3   0.1    5.6e-21   74.7   0.1    1.2  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 !   74.7   0.1   3.1e-25   5.6e-21       8     131 .]      77     182 ..      70     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 3.1e-25
                                       HT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHH CS
                       Oxidored_q6   8 llaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGtCAa 84 
                                       +++++    dl      ry+  +   ++     a+ ++adv++v G++++k  +++++++++++++k+v+ +G+C +
  gi|336255214|ref|YP_004598321.1|  77 MMHTYAIKHDL-----DRYGAGV---PR-----ASPRQADVMIVPGTIVSKFGPRMKRVYDQMPEPKFVVGMGSCTI 140
                                       54444444444.....4444433...12.....22349*************************************** PP

                                       H-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHHH CS
                       Oxidored_q6  85 fGGipaaannpsvgeevgellevvpvdinipGCPphpeailetllal 131
                                       +GG ++ +     +  v++++e +pvdi++pGCPp+pea+l+++l+l
  gi|336255214|ref|YP_004598321.1| 141 SGGPFQKGY---NV--VKGAEEIIPVDIHVPGCPPRPEALLYGVLKL 182
                                       *****5555...33..56999********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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: 0.39u 0.18s 00:00:00.57 Elapsed: 00:00:00.32
# Mc/sec: 2189.76
//
Query:       gi|336255215|ref|YP_004598322.1|  [L=550]
Description: NAD(P)H-quinone oxidoreductase subunit H [Halopiger xanaduensis SH-6]
Scores for complete 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-87  292.8   0.2    4.6e-86  288.3   0.2    2.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    1.6e-33  115.9   0.2      3e-33  115.1   0.2    1.5  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
  ------ inclusion threshold ------
      0.045   12.6   0.0        2.8    6.7   0.0    2.4  3  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 !  288.3   0.2   7.6e-90   4.6e-86       5     271 .]     300     550 .]     296     550 .] 0.93

  Alignments for each domain:
  == domain 1  score: 288.3 bits;  conditional E-value: 7.6e-90
                                       HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---T...THHHHHHHHHHHHHHHHHHHHHHHHSSSSHHH CS
                    Complex1_49kDa   5 ltvflyafreRekildlleevtGaRltasyiriGGvarDlpe...gllekikeflkelekkldeleklltknrifkk 78 
                                       +++f+y+fr+Re + d+le++tG+R++ +y+r+GGva+Dlpe   +++ek+++fl+el++k+de+++++t+n+if++
  gi|336255215|ref|YP_004598322.1| 300 TAIFMYTFRDREVVQDILEDLTGQRMMFNYFRVGGVAWDLPEpreEFIEKTRDFLDELPAKVDEYHDMVTSNEIFQT 376
                                       4589*************************************98889******************************* PP

                                       HHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  79 RtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqa 155
                                       R+ + gv++ e a ++g+tGpv+RasG++yDlR+++pY  Y++l++dv+++e +D y+R+l r+eE+++S+kIieq+
  gi|336255215|ref|YP_004598322.1| 377 RCIDTGVIEPEVAKDYGCTGPVARASGIDYDLRRDDPYGYYENLEWDVVTREGCDNYARVLARMEEVEESAKIIEQC 453
                                       ***************************************************************************** PP

                                       HHT--.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEE CS
                    Complex1_49kDa 156 leklpegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlki 232
                                       l+ l++ p   ++++v    +++v ++++               ++ e+y+avEa+kGelg+y+ sdg++kp r+ki
  gi|336255215|ref|YP_004598322.1| 454 LDLLEDWP--EDEREV----QANVPRTLKP-------------DADAETYRAVEAAKGELGIYMRSDGTDKPARFKI 511
                                       ****8655..333333....2334443332.............34689***************************** PP

                                       E-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 233 rapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       r+p+f nlq+l+e+++ge++ D++a lgsldivlgevDR
  gi|336255215|ref|YP_004598322.1| 512 RSPCFSNLQVLPEMSEGEYVPDLIASLGSLDIVLGEVDR 550
                                       **************************************9 PP

>> 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 !  115.1   0.2     5e-37     3e-33       2     120 ..      38     154 ..      37     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 5e-37
                                       E--HHHHHHHHHHHHH...TT--EEEEEEEEETTSSSEEEEEEEE--...S-.-EEEEEE....-S-BEE--TTT-S CS
                    Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDekeerfevvyhllsl...eknerirvkvevdeeepevpSvtdlfp 75 
                                       v++p+++++v++ l++  + g+d+ls++ta  + ++r+e +yhl ++   +++++i+v +   +++p+ +S+ ++f+
  gi|336255215|ref|YP_004598322.1|  38 VINPDEVQSVLSDLRE--RAGYDHLSCVTAQQY-DDRYESIYHLKKYsdpTDEVSIVVPT--TRNDPVSESAEPVFR 109
                                       789************9..599***********9.5***********96443345555555..899************ PP

                                       THHHHHHHHHHHSHHBCTTSSTSS-SSSSTTSSS-TTSTTS---- CS
                    Complex1_30kDa  76 gadwyEREayDmfGivfeghpdlrrillpedfeghPLRkdfplsg 120
                                       +adw+EREayD++Gi++ +hpdlrrillpe+++ghPL  d++ ++
  gi|336255215|ref|YP_004598322.1| 110 TADWHEREAYDLVGIEYADHPDLRRILLPETWQGHPLSDDYDQTK 154
                                       *****************************************9876 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0   0.00048       2.8      33      68 ..     251     286 ..     246     297 .. 0.89
   2 ?   -3.7   0.0      0.66   3.9e+03     173     213 ..     323     363 ..     308     376 .. 0.73
   3 ?    3.1   0.0    0.0058        35     372     440 ..     433     499 ..     418     508 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00048
                                       HHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases  33 asvravedAlgikipknarlirnliaaalllhdhiv 68 
                                       a +ra+ed  +i++p+ a++ir++ a    + +h++
  gi|336255215|ref|YP_004598322.1| 251 AYARAIEDMADIEVPEYAQVIRTMGAELCRIASHML 286
                                       6689********************999999999886 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.66
                                       SSSS--.EBTTBESSGBGSBSHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases 173 knPhpqslvvGGvtcaidllnaerlaevkslikevkefvee 213
                                       +    + + vGGv+  +  +++e +++ +++++e+ + v+e
  gi|336255215|ref|YP_004598322.1| 323 QRMMFNYFRVGGVAWDLPEPREEFIEKTRDFLDELPAKVDE 363
                                       55555668899999998888888888888888877665554 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.0058
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTB---B--TT-SGGGS-SEEEEEEEEEETTEEEEEEEE CS
                      NiFeSe_Hases 372 lGRtaaRaleakliaellkewldelvenikkgdtetaneekldkkevpkeakGvglveapRGaLsHwik 440
                                        +R +aR+ e +  a+ +++ ld l++  +    + ++ +  ++ + +++a+ +  vea++G L+ +++
  gi|336255215|ref|YP_004598322.1| 433 YARVLARMEEVEESAKIIEQCLDLLEDWPEDE--REVQANVPRTLKPDADAETYRAVEAAKGELGIYMR 499
                                       689***********999999988777665554..33333333444445799*************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 4136.60
//
Query:       gi|336255216|ref|YP_004598323.1|  [L=364]
Description: NAD(P)H-quinone oxidoreductase subunit 1 [Halopiger xanaduensis SH-6]
Scores for 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-94  315.8  12.7    3.3e-94  315.6  12.7    1.0  1  NADHdh    NADH dehydrogenase


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 !  315.6  12.7   1.8e-98   3.3e-94       9     298 ..      48     356 ..      38     357 .. 0.95

  Alignments for each domain:
  == domain 1  score: 315.6 bits;  conditional E-value: 1.8e-98
                                       HHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTT CS
                            NADHdh   9 vlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallafav 85 
                                       +l+++ +   +++Rk++A++ dR+  n++Gp G+l  +aDa++ll Ke i+p++ad+  + lapv++  +all fav
  gi|336255216|ref|YP_004598323.1|  48 MLAMTGVAGPWAKRKITAAFTDRIAVNHLGPGGVLIIVADAVRLLSKELIVPENADRPAYDLAPVVIAGSALLGFAV 124
                                       2333334788******************************************************************* PP

                                       S-SSS..SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-HH CS
                            NADHdh  86 iPfge..vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagslsls 160
                                       iP+g+   lad +vgl +++a++ ++ +g+++aG+as +kY+llG+lR++aq ++yE++l+++ ++vvl++gsl +s
  gi|336255216|ref|YP_004598323.1| 125 IPMGSgvHLADPEVGLAYVFAIAGIASIGLVMAGYASDNKYSLLGGLRAVAQNVAYEIPLVVTGMSVVLFSGSLRMS 201
                                       ****77899******************************************************************** PP

                                       HHHHCCCTT..............-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHH CS
                            NADHdh 161 eiveaqeei..............wfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalffla 223
                                       eiv+ q+++              wf+l++++af++flia +ae++r PFD+pea +ELvaG++tEYs++ f+l++l+
  gi|336255216|ref|YP_004598323.1| 202 EIVAVQNQTtlftipglewgipaWFALVNPFAFVLFLIANFAEVGRNPFDMPEAPAELVAGYQTEYSSVYFVLVYLG 278
                                       ***99988889*******9999999999************************************************* PP

                                       HHHHHHHHHHHHHHHCT.SS-HCCS...HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHH CS
                            NADHdh 224 eyanmvlvsalavllFlgGwllpfs...gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlll 297
                                       e+++++l  a+++++FlgG ++p +   g++wf++K+++ ++l+ w+r+++pR+R+dql+++gwk ll l++anl l
  gi|336255216|ref|YP_004598323.1| 279 EFLHIFLGGAIIATIFLGGPAGPGPeglGIVWFIIKIWAAFLLTQWLRSAIPRVRIDQLIEIGWKGLLVLSFANLGL 355
                                       ********************9999899***********************************************998 PP

                                       H CS
                            NADHdh 298 t 298
                                       t
  gi|336255216|ref|YP_004598323.1| 356 T 356
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 3068.65
//
Query:       gi|336255217|ref|YP_004598324.1|  [L=153]
Description: NADH-quinone oxidoreductase subunit I [Halopiger xanaduensis SH-6]
Scores for complete 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   46.7   8.9    1.9e-06   27.5   2.3    2.2  2  Fer4      4Fe-4S binding domain
      8e-12   45.6  10.6    1.2e-11   44.9  10.6    1.3  1  Fer4_7    4Fe-4S dicluster domain
    1.6e-10   41.7   3.2    1.8e-05   25.6   0.1    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    3.3e-09   36.8  22.8    4.7e-07   29.9  12.2    1.9  2  Fer4_9    4Fe-4S dicluster domain
    4.3e-09   36.4   8.0    6.8e-09   35.7   8.0    1.3  1  Fer4_21   4Fe-4S dicluster domain
    5.6e-06   26.4  10.7    4.7e-05   23.4  11.9    1.8  2  Fer4_10   4Fe-4S dicluster domain
    6.6e-06   26.0  12.8     0.0053   16.8   1.5    2.2  2  Fer4_6    4Fe-4S binding domain
    1.5e-05   25.4  12.7     0.0057   17.2   1.8    2.2  2  Fer4_17   4Fe-4S dicluster domain
    5.1e-05   23.6  11.1    0.00084   19.7  12.2    2.0  2  Fer4_8    4Fe-4S dicluster domain
    0.00011   22.1  12.8     0.0044   17.0   1.8    2.3  2  Fer4_2    4Fe-4S binding domain
    0.00036   20.8  14.3     0.0034   17.8   3.8    2.3  2  Fer4_4    4Fe-4S binding domain
      0.001   19.8  15.2      0.018   16.0   3.6    2.3  2  Fer4_3    4Fe-4S binding domain
     0.0018   18.4   9.7       0.09   13.0   1.8    2.2  2  Fer4_18   4Fe-4S dicluster domain
     0.0029   18.4   4.2       0.73   10.7   0.3    2.2  2  Fer4_22   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.07   13.3   7.7       0.22   11.7   7.7    1.7  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
       0.16   12.4   7.5        2.5    8.6   1.2    2.5  2  TNFR_c6   TNFR/NGFR cysteine-rich region
        1.1    9.8  13.1        2.2    8.9   3.2    2.6  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


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 !   23.3   0.6   3.6e-08   3.8e-05       2      23 ..      41      62 ..      40      63 .. 0.92
   2 !   27.5   2.3   1.8e-09   1.9e-06       7      23 ..      81      97 ..      78      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.6e-08
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      ++ +e+Ci C +C++vCP++ I
  gi|336255217|ref|YP_004598324.1| 41 KWSQERCIWCRQCENVCPNDTI 62
                                      6889****************98 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 1.8e-09
                                      TSSS-THHHHHSTTTEE CS
                              Fer4  7 kCigCGaCvevCPvgAI 23
                                       C++C +C+evCP++AI
  gi|336255217|ref|YP_004598324.1| 81 QCVYCRLCEEVCPTDAI 97
                                      5***************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9  10.6   1.2e-14   1.2e-11       1      52 []      46      96 ..      46      96 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 1.2e-14
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      rCi C++C+++Cp+++i++  +++ +g e+++++  +C++C+ C++vCPt+a
  gi|336255217|ref|YP_004598324.1| 46 RCIWCRQCENVCPNDTIQIVMDDKRNG-EQYNLHIGQCVYCRLCEEVCPTDA 96
                                      8******************98755555.99********************97 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   9.7e-06      0.01       1      18 [.      46      63 ..      40      77 .. 0.81
   2 !   25.6   0.1   1.7e-08   1.8e-05       1      37 [.      81     119 ..      81     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.7e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                      rC+ C++C +vCP + i+
  gi|336255217|ref|YP_004598324.1| 46 RCIWCRQCENVCPNDTIQ 63
                                      599999999999999887 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 1.7e-08
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekei..earecisyntae 37 
                                       +C+ C+ C evCPt+ai  ++++e+  +++ +  yn+++
  gi|336255217|ref|YP_004598324.1|  81 QCVYCRLCEEVCPTDAILLTQNFEFtgDTKHDLVYNKEQ 119
                                       6*****************996666522344444444444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   2.8     1e-06    0.0011      21      51 .]      32      62 ..      26      62 .. 0.83
   2 !   29.9  12.2   4.5e-10   4.7e-07       1      51 []      46      97 ..      46      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                            Fer4_9 21 aaerkarlraaseeaCigCgaCveaCpkgai 51
                                       ++r++ ++++s+e+Ci C++C+++Cp++ i
  gi|336255217|ref|YP_004598324.1| 32 VSPRFRGVHKWSQERCIWCRQCENVCPNDTI 62
                                      56777778889999*************9865 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 4.5e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase..eaCigCgaCveaCpkgai 51
                                      +C+ C++C+++Cp+++++     + +   +++    +C+ C+ C+e+Cp++ai
  gi|336255217|ref|YP_004598324.1| 46 RCIWCRQCENVCPNDTIQIVMDDKRNGE-QYNLhiGQCVYCRLCEEVCPTDAI 97
                                      5*************99976655555443.33334689*************997 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   8.0   6.5e-12   6.8e-09       5      57 ..      44      97 ..      41      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 6.5e-12
                           Fer4_21  5 edkCigCgkCliaCedtshqaieidakt..vlkvvedeCvGCnlCssvCPvedci 57
                                      +++Ci C +C  +C++ ++q +  d+++  ++++   +Cv C lC +vCP+ d+i
  gi|336255217|ref|YP_004598324.1| 44 QERCIWCRQCENVCPNDTIQIVMDDKRNgeQYNLHIGQCVYCRLCEEVCPT-DAI 97
                                      799*************999999655444115566789*************7.777 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4  11.9   4.5e-08   4.7e-05       6      56 .]      44      93 ..      41      93 .. 0.77
   2 !   14.1   1.4   3.6e-05     0.038       8      24 ..      81     106 ..      76     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.5e-08
                           Fer4_10  6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +++Ci C++C ++CP d  + +  +++++ e+ +  +++C  c  C e+CP
  gi|336255217|ref|YP_004598324.1| 44 QERCIWCRQCENVCPNDTIQIVMDDKRNG-EQYNLHIGQCVYCRLCEEVCP 93
                                      689*************5544444444444.4444469*************9 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.6e-05
                           Fer4_10   8 tCirCgkCvkaCPadl.........t 24 
                                       +C+ C+ C ++CP+d+         t
  gi|336255217|ref|YP_004598324.1|  81 QCVYCRLCEEVCPTDAilltqnfefT 106
                                       69***********9776666555552 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.5     5e-06    0.0053       4      20 ..      42      58 ..      41      64 .. 0.88
   2 !   14.3   3.9     3e-05     0.031       9      24 .]      82      97 ..      80      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5e-06
                            Fer4_6  4 idpdkCigCgdCvrvCP 20
                                      + +++Ci C+ C++vCP
  gi|336255217|ref|YP_004598324.1| 42 WSQERCIWCRQCENVCP 58
                                      7899************* PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3e-05
                            Fer4_6  9 CigCgdCvrvCPegai 24
                                      C+ C+ C+ vCP++ai
  gi|336255217|ref|YP_004598324.1| 82 CVYCRLCEEVCPTDAI 97
                                      888***********98 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   3.5   6.5e-05     0.069      44      59 ..      45      60 ..      25      62 .. 0.87
   2 !   17.2   1.8   5.4e-06    0.0057      38      59 ..      74      95 ..      61      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-05
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++Ci C++Ce +CP++
  gi|336255217|ref|YP_004598324.1| 45 ERCIWCRQCENVCPND 60
                                      79************97 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.4e-06
                           Fer4_17 38 ekeekaslCieCgeCerkCPqg 59
                                      + +  +++C+ C++Ce++CP +
  gi|336255217|ref|YP_004598324.1| 74 QYNLHIGQCVYCRLCEEVCPTD 95
                                      233589**************76 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7  12.2     8e-07   0.00084       3      64 ..      45      95 ..      43      96 .. 0.76
   2 !   14.1   1.8   4.7e-05      0.05       4      17 ..      81      97 ..      78     129 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8e-07
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      e+Ci C  C++ Cp  ++t +  +d + +  + +q + +      +++C+ c+ C+evCp++
  gi|336255217|ref|YP_004598324.1| 45 ERCIWCRQCENVCP--NDTIQIVMDDKRN--G-EQYNLH------IGQCVYCRLCEEVCPTD 95
                                      79***********9..5554554444444..5.445666......8**************85 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.7e-05
                            Fer4_8  4 kCieCgaCqsaCp...v 17
                                      +C+ C +C++ Cp   +
  gi|336255217|ref|YP_004598324.1| 81 QCVYCRLCEEVCPtdaI 97
                                      56666666666665542 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.8   4.1e-06    0.0044       7      22 .]      44      59 ..      39      59 .. 0.90
   2 !   10.2   3.6   0.00063      0.66      10      22 .]      82      94 ..      79      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.1e-06
                            Fer4_2  7 tdrCigCgaCvsaCPa 22
                                       +rCi C+ C ++CP+
  gi|336255217|ref|YP_004598324.1| 44 QERCIWCRQCENVCPN 59
                                      69*************5 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00063
                            Fer4_2 10 CigCgaCvsaCPa 22
                                      C+ C+ C  +CP+
  gi|336255217|ref|YP_004598324.1| 82 CVYCRLCEEVCPT 94
                                      99**********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 !   17.8   3.8   3.2e-06    0.0034       1      15 [.      44      58 ..      44      76 .. 0.90
   2 !    8.9   2.8    0.0023       2.4       4      16 ..      82      94 ..      69     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.2e-06
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      qerCi C++C+++CP
  gi|336255217|ref|YP_004598324.1| 44 QERCIWCRQCENVCP 58
                                      79************* PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0023
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C+ C+ C+ +CP+
  gi|336255217|ref|YP_004598324.1| 82 CVYCRLCEEVCPT 94
                                      999*********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 !    9.4   3.9    0.0021       2.3       1      13 [.      47      59 ..      47      60 .. 0.85
   2 !   16.0   3.6   1.7e-05     0.018       1      15 []      82      96 ..      82      96 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0021
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+ C++C++vCP+
  gi|336255217|ref|YP_004598324.1| 47 CIWCRQCENVCPN 59
                                      666*********7 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.7e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C++C+evCP++A
  gi|336255217|ref|YP_004598324.1| 82 CVYCRLCEEVCPTDA 96
                                      999**********98 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   1.3    0.0003      0.32      55      74 ..      41      60 ..      22      77 .. 0.73
   2 !   13.0   1.8   8.5e-05      0.09      48      74 ..      69      95 ..      60     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                           Fer4_18 55 ekgagdcidcescvkvcPtg 74
                                      + ++  ci c++c +vcP +
  gi|336255217|ref|YP_004598324.1| 41 KWSQERCIWCRQCENVCPND 60
                                      556788************74 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.5e-05
                           Fer4_18 48 kekeerkekgagdcidcescvkvcPtg 74
                                      k++ e+ +   g+c+ c+ c +vcPt+
  gi|336255217|ref|YP_004598324.1| 69 KRNGEQYNLHIGQCVYCRLCEEVCPTD 95
                                      55566667789**************96 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.3   0.00069      0.73       1      24 [.      46      69 ..      38      79 .. 0.77
   2 !    9.3   0.4    0.0019         2       1      21 [.      81     101 ..      81     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00069
                           Fer4_22  1 rClsCgaCtlvCptCsCfdvedet 24
                                      rC+ C +C  vCp  +   v d++
  gi|336255217|ref|YP_004598324.1| 46 RCIWCRQCENVCPNDTIQIVMDDK 69
                                      699999999999987766666655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0019
                           Fer4_22   1 rClsCgaCtlvCptCsCfdve 21 
                                       +C+ C  C  vCpt     ++
  gi|336255217|ref|YP_004598324.1|  81 QCVYCRLCEEVCPTDAILLTQ 101
                                       6************97665555 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   7.7   0.00021      0.22      42      91 ..      49      98 ..      39     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                      HS-THHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--EE CS
                            ETF_QO 42 yagpeqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsqnie 91
                                      +   ++ +CP    +iv d++ +++++++   +Cv+C+ C+   p++ i 
  gi|336255217|ref|YP_004598324.1| 49 WCRQCENVCPNDTIQIVMDDKRNGEQYNLHIGQCVYCRLCEEVCPTDAIL 98
                                      6677899*************99*******************999998885 PP

>> TNFR_c6  TNFR/NGFR cysteine-rich region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.2    0.0024       2.5       8      23 ..      40      55 ..      36      65 .. 0.69
   2 ?    7.0   0.6    0.0072       7.5      12      23 ..      78      90 ..      70      99 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0024
                                      CCTCTCSEEEEE-BGC CS
                           TNFR_c6  8 dnenskeClpCtrCpp 23
                                      +++++++C  C++C++
  gi|336255217|ref|YP_004598324.1| 40 HKWSQERCIWCRQCEN 55
                                      5677777888887743 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0072
                                      TC.SEEEEE-BGC CS
                           TNFR_c6 12 sk.eClpCtrCpp 23
                                      +  +C+ C+ C++
  gi|336255217|ref|YP_004598324.1| 78 HIgQCVYCRLCEE 90
                                      2335******964 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 ?    8.9   3.2    0.0021       2.2       3      18 ..      44      59 ..      43      60 .. 0.92
   2 ?    5.7   2.3     0.021        22       5      17 ..      81      93 ..      80      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
                           Fer4_13  3 rdtCiacgaCvelaPd 18
                                      +++Ci c +C +++P+
  gi|336255217|ref|YP_004598324.1| 44 QERCIWCRQCENVCPN 59
                                      589************6 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.021
                           Fer4_13  5 tCiacgaCvelaP 17
                                      +C+ c +C e++P
  gi|336255217|ref|YP_004598324.1| 81 QCVYCRLCEEVCP 93
                                      7***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); 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:                        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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1161.57
//
Query:       gi|336255218|ref|YP_004598325.1|  [L=94]
Description: NADH-ubiquinone/plastoquinone oxidoreductase chain 6 [Halopiger xanaduensis SH-6]
Scores for 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-21   75.1   3.0    5.8e-21   74.7   3.0    1.2  1  Oxidored_q3      NADH-ubiquinone/plastoquinone oxidoreductase
      0.009   16.1  12.5      0.012   15.7  12.5    1.2  1  DUF4040          Domain of unknown function (DUF4040)
  ------ inclusion threshold ------
      0.014   14.0   6.3      0.015   13.9   6.3    1.0  1  DUF2339          Predicted membrane protein (DUF2339)
      0.052   13.8   3.5      0.067   13.4   3.3    1.3  1  DUF2530          Protein of unknown function (DUF2530)
       0.19   11.0   4.2       0.22   10.8   4.2    1.2  1  DUF4191          Domain of unknown function (DUF4191)


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 !   74.7   3.0   1.6e-24   5.8e-21       1      64 [.      18      81 ..      18      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 1.6e-24
                                      HHHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS CS
                       Oxidored_q3  1 gallvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesae 64
                                      +al+v++ + p +sal+L ++++++a+ f++l aeF+a++qilvYvG++l+l+ F++ml+++++
  gi|336255218|ref|YP_004598325.1| 18 SALGVVLLRDPWHSALMLGVALMSMAVHFVMLAAEFVAMMQILVYVGGVLILITFAVMLTQRED 81
                                      699********************************************************84332 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7  12.5   3.5e-06     0.012       3      65 ..      15      77 ..      13      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.5e-06
                           DUF4040  3 lvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrl 65
                                      ++++al +vl rd+ +++++lgv+ + +a+ fv+l A  vA+ q++v  g +++l+ +a+  +
  gi|336255218|ref|YP_004598325.1| 15 TIASALGVVLLRDPWHSALMLGVALMSMAVHFVMLAAEFVAMMQILVYVGGVLILITFAVMLT 77
                                      799******************************************887777777777776655 PP

>> DUF2339  Predicted membrane protein (DUF2339)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   6.3   4.3e-06     0.015     199     271 ..       8      82 ..       2      92 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-06
                           DUF2339 199 lllylalalllallfvaarravdatlvfgaplvalvlqyalladl..eygwalaalalaalyla.laawlarrkre 271
                                       ++l+  ++++ al +v++r ++ ++l++g++l+ +++++++la    ++  +l+ ++ ++l+l+ +a++l +r+++
  gi|336255218|ref|YP_004598325.1|   8 FALFASVTIASALGVVLLRDPWHSALMLGVALMSMAVHFVMLAAEfvAMMQILVYVG-GVLILItFAVMLTQREDA 82 
                                       444555666777766777999*****************5555544454444444444.555555055555555554 PP

>> DUF2530  Protein of unknown function (DUF2530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.3   1.9e-05     0.067      10      66 ..      25      82 ..      17      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                           DUF2530 10 Ltdprp.vivvgtllWlvalvvllvvgdaleswlpvclaGlvvGllGlaiflwQRrAa 66
                                      L+dp++ ++++g++l  +a+  ++++ + ++ +    ++G v+ l+ +a++l QR+ a
  gi|336255218|ref|YP_004598325.1| 25 LRDPWHsALMLGVALMSMAVHFVMLAAEFVAMMQILVYVGGVLILITFAVMLTQREDA 82
                                      89999835678999999999999999888888999999*****************865 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.2   6.2e-05      0.22      21      72 ..      26      79 ..       9      88 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.2e-05
                           DUF4191 21 edkkllwlllaaflvvvvvfvvlgll.l..gslilllilgillgllvalivltrr 72
                                      +d++   l+l+++l+ ++v +v+  + +  + +il+ + g+l+ +++a+++ t+r
  gi|336255218|ref|YP_004598325.1| 26 RDPWHSALMLGVALMSMAVHFVMLAAeFvaMMQILVYVGGVLILITFAVML-TQR 79
                                      7999999****9999999988776652211346666666666665555544.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1125  (0.0627475); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 735.04
//
Query:       gi|336255219|ref|YP_004598326.1|  [L=164]
Description: hypothetical protein Halxa_3842 [Halopiger xanaduensis SH-6]
Scores for 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  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1397.06
//
Query:       gi|336255220|ref|YP_004598327.1|  [L=101]
Description: NAD(P)H-quinone oxidoreductase subunit 4L [Halopiger xanaduensis SH-6]
Scores for 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-23   80.5   9.0    7.3e-23   80.2   9.0    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.032   13.6   4.7      0.034   13.5   4.7    1.1  1  NicO         High-affinity nickel-transport protein
       0.18   11.9   0.5       0.18   11.9   0.5    3.3  2  PEP-CTERM    PEP-CTERM motif


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 !   80.2   9.0   1.2e-26   7.3e-23       2     101 ..       8      94 ..       7      96 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 1.2e-26
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHH CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaiviga 78 
                                       + ll+++lf+iGl+g+l+rrn+l  l+++el++na+n++l++++ ++             +++ +q+++L+ ++++a
  gi|336255220|ref|YP_004598327.1|   8 YVLLSMALFCIGLFGILTRRNALLFLMSVELMLNAANINLIAFSFYQ-------------GNLTGQVFALFTMALAA 71 
                                       789*******************************************9.............***************** PP

                                       HHHHHHHHHHHHHHHHSSS-BCC CS
                       Oxidored_q2  79 aetavgLallvrlyreygtddvq 101
                                       ae+avgL++++ lyr+ + +dv 
  gi|336255220|ref|YP_004598327.1|  72 AEVAVGLGIILVLYRNFRDVDVT 94 
                                       *******************9995 PP

>> NicO  High-affinity nickel-transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   4.7   5.8e-06     0.034     180     239 ..      26      85 ..      10     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.8e-06
                              NicO 180 silalpalfavGlrlcdgadivlmfaalnwaflggrklvyamsitgtsitvalliglivt 239
                                        + al++l++v l+l  + ++++ f+ +++ ++g + + + m+++++ ++v l+i+l+++
  gi|336255220|ref|YP_004598327.1|  26 RRNALLFLMSVELMLNAANINLIAFSFYQGNLTGQVFALFTMALAAAEVAVGLGIILVLY 85 
                                       6789****************************************9999999999999876 PP

>> PEP-CTERM  PEP-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.5     3e-05      0.18       7      22 ..      12      27 ..      11      28 .. 0.92
   2 ?   -0.7   3.9      0.29   1.7e+03      11      18 ..      65      74 ..      58      89 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3e-05
                         PEP-CTERM  7 TllLlGlGllGlalrR 22
                                      +++L+ +Gl+G++ rR
  gi|336255220|ref|YP_004598327.1| 12 SMALFCIGLFGILTRR 27
                                      7**********99988 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.29
                         PEP-CTERM 11 lGlGllG..l 18
                                      + ++l++  +
  gi|336255220|ref|YP_004598327.1| 65 FTMALAAaeV 74
                                      5555544222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 864.38
//
Query:       gi|336255221|ref|YP_004598328.1|  [L=680]
Description: proton-translocating NADH-quinone oxidoreductase subunit L [Halopiger xanaduensis SH-6]
Scores for complete 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-75  253.9  19.8    4.4e-75  252.6  19.8    1.7  1  Proton_antipo_M  Proton-conducting membrane transporter
    3.9e-15   55.6   3.6    4.8e-15   55.4   0.1    3.0  3  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
     0.0015   18.2   2.1      0.002   17.8   0.0    2.3  2  NADH5_C          NADH dehydrogenase subunit 5 C-terminus
     0.0075   16.1   0.1      0.039   13.8   0.1    2.3  1  DUF5310          Family of unknown function (DUF5310)
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.032   13.9   0.0    1.6  1  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 !  252.6  19.8   1.2e-78   4.4e-75       1     282 [.     146     436 ..     146     450 .. 0.94

  Alignments for each domain:
  == domain 1  score: 252.6 bits;  conditional E-value: 1.2e-78
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal..... 72 
                                       a++Ll+ ++++Elv+l++ylLig+w++ +++ +A+ k+fl+t++g+ ++Llg++++ +  gt+ f    +++     
  gi|336255221|ref|YP_004598328.1| 146 ADNLLMAFMFFELVGLCSYLLIGFWFRTESAPSAAKKAFLVTRFGDYFFLLGVVAIAATFGTVAFAGDESFVvaaet 222
                                       79***************************************************************987777778999 PP

                   Proton_antipo_M  73 ........elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirllllla 140
                                                   ++  +++  ll+l g++ Ksaq+plh+Wlpda +e+Pt vsal+ Aat+v+agv+l++r++  +a
  gi|336255221|ref|YP_004598328.1| 223 aiedggtlFGFDAQTWVTITGLLVLGGVIGKSAQFPLHTWLPDA-MEGPTTVSALIhAATMVAAGVYLVARMFGYYA 298
                                       9****9965555666678888899999*****************.******************************** PP

                   Proton_antipo_M 141 vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFl 217
                                         s+++  ++++++  ++l+++++++++ diK++lAyS+is+ Gym+++l+v    g+ a ++hl+ ha+fkallFl
  gi|336255221|ref|YP_004598328.1| 299 -QSPTALAIIAFVGGFTALFAATMGVVKDDIKQVLAYSTISQYGYMMLGLGV---GGYVAGVFHLMNHAFFKALLFL 371
                                       .***************************************************...7778****************** PP

                   Proton_antipo_M 218 lagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslil 282
                                        +g+vi  +++++d+ ++ggL  k P+++ ++l ++l+laG+ p++gF+sk+++L  a+ v+l +
  gi|336255221|ref|YP_004598328.1| 372 GSGAVIVLMHHEQDMWKMGGLKDKAPVTYYTFLAGALALAGIVPFSGFWSKDEVLFDALIVGLEQ 436
                                       *******************************************************9888776655 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 !   55.4   0.1   1.4e-18   4.8e-15       8      56 ..      82     132 ..      78     134 .. 0.89
   2 ?   -3.1   0.1       2.4   8.5e+03      30      37 ..     271     278 ..     271     279 .. 0.91
   3 ?   -1.4   0.0      0.72   2.6e+03      22      40 ..     300     318 ..     298     320 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.4e-18
                   Proton_antipo_N   8 gglsieigfllDklsalmllvvtfvsllvhlYSigYMa..ddegyqRFfay 56 
                                       +++ +++g+l+D+lsalml++v++v+llvh++S+gYM   +++g +R++a 
  gi|336255221|ref|YP_004598328.1|  82 EEIVFSFGILIDPLSALMLVIVSLVALLVHVFSLGYMNaeGETGLPRYYAE 132
                                       56889********************************732589******96 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                   Proton_antipo_N  30 tfvsllvh 37 
                                       t+vs+l+h
  gi|336255221|ref|YP_004598328.1| 271 TTVSALIH 278
                                       89*****9 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.72
                   Proton_antipo_N  22 salmllvvtfvsllvhlYS 40 
                                       s + l+++ fv+ +  l++
  gi|336255221|ref|YP_004598328.1| 300 SPTALAIIAFVGGFTALFA 318
                                       567899******9999987 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 !   17.8   0.0   5.5e-07     0.002       1      45 [.     456     500 ..     456     506 .. 0.98
   2 ?   -5.6   2.4         5   1.8e+04      34      47 ..     667     680 .]     659     680 .] 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.5e-07
                           NADH5_C   1 YSlRliyyvllgsprfsslspineenptllnpilrLalgsiiaGs 45 
                                       Y++R++++++ g+pr  +  + +  ++++  p+++L l++++aG+
  gi|336255221|ref|YP_004598328.1| 456 YTFRMVFLTFHGDPRSETAENPHPVGWSIKVPLIVLGLLALFAGF 500
                                       9*******************************************8 PP

  == domain 2  score: -5.6 bits;  conditional E-value: 5
                           NADH5_C  34 lrLalgsiiaGsll 47 
                                        +L+++ i +G++l
  gi|336255221|ref|YP_004598328.1| 667 GLLLILGISGGWFL 680
                                       56899999999987 PP

>> DUF5310  Family of unknown function (DUF5310)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   1.1e-05     0.039      22      42 ..     361     381 ..     357     383 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                           DUF5310  22 RkAFFqllgFlgscvviSlva 42 
                                       + AFF+ l+Flgs +vi l+ 
  gi|336255221|ref|YP_004598328.1| 361 NHAFFKALLFLGSGAVIVLMH 381
                                       78***************9886 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 ?   13.9   0.0     9e-06     0.032      85     178 ..     469     577 ..     455     580 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9e-06
                   Proton_antipo_C  85 enkktlsyPhEsdntmlfpllvLvlftlfvGliGip..fnqegidldilskwLtpsin........llhknsnesv. 150
                                        +++t + Ph   +++ +pl+vL l+ lf G+       +  g+d+  l++wL                   +e+v 
  gi|336255221|ref|YP_004598328.1| 469 PRSETAENPHPVGWSIKVPLIVLGLLALFAGFANLApvAKLAGMDITFLEHWLDGEYGyvdgltyhH----YHEMVa 541
                                       45678899************************9987444556788888*****98876555643331....222221 PP

                   Proton_antipo_C 151 ........dwyefltnaifSvsialfGifiAsllYk 178
                                               + + +l  a +S+++al G ++A+ lY 
  gi|336255221|ref|YP_004598328.1| 542 feegyigsETTTMLLGAALSLGLALGGALLAYSLYA 577
                                       222333336778899999999999999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (680 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); 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):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.22s 00:00:00.82 Elapsed: 00:00:00.35
# Mc/sec: 5744.31
//
Query:       gi|336255222|ref|YP_004598329.1|  [L=508]
Description: proton-translocating NADH-quinone oxidoreductase subunit M [Halopiger xanaduensis SH-6]
Scores for 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-75  251.5  26.7    9.3e-75  251.5  26.7    1.8  2  Proton_antipo_M  Proton-conducting membrane transporter
    1.9e-05   24.7   0.2    1.9e-05   24.7   0.2    3.4  5  Oxidored_q5_N    NADH-ubiquinone oxidoreductase chain 4, amin
  ------ inclusion threshold ------
      0.014   15.4   0.2      0.069   13.2   0.2    2.3  1  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 ?   -2.7   0.1      0.44   2.6e+03       5      23 ..      75      93 ..      74      97 .. 0.85
   2 !  251.5  26.7   1.6e-78   9.3e-75       2     290 ..     132     430 ..     131     434 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.44
                   Proton_antipo_M  5 lllylglElvllplylLig 23
                                      ++ ++gl++++lpl++L +
  gi|336255222|ref|YP_004598329.1| 75 ISWFVGLDGISLPLVVLTT 93
                                      56799**********9976 PP

  == domain 2  score: 251.5 bits;  conditional E-value: 1.6e-78
                   Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgil.llynltg..tlefeelskal... 72 
                                        d ++ ++++E+vl+p+ylLig+w+   ++ +A++k+f++t ++sl+++ +++ l+++l    +  ++e+++a+   
  gi|336255222|ref|YP_004598329.1| 132 LDFFAWFIFWEAVLIPMYLLIGIWGGP-RRKYAAIKFFVYTNVASLLMFGAFIsLVFGLGDvtSFALPEIATAMleg 207
                                       688999******************765.99*******************99886888888844445578888889** PP

                   Proton_antipo_M  73 .....elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vss 143
                                                +s  ++++++++++g++vK+++vp+h+Wlpda+veaPtp s+llA++l+k+g ++l+r+++ ++    
  gi|336255222|ref|YP_004598329.1| 208 gpdglFGLSGSALASVVFVAMFLGFAVKVPVVPFHTWLPDAHVEAPTPASVLLAGVLLKMGTYALLRFNFTMFpEQV 284
                                       **998888899999***********************************************************8889 PP

                   Proton_antipo_M 144 neisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllag 220
                                        +++  ++++a+is+++g+++alaqtd+Kr++AySs+s +Gy++++l++ tq gv +a +++++h+l++ l+F+++ 
  gi|336255222|ref|YP_004598329.1| 285 ATYAVPIAAIAVISVIYGAMLALAQTDLKRIVAYSSVSSMGYVILGLIAYTQFGVGGATFQMVSHGLISGLMFMAV- 360
                                       99999**********************************************************************9. PP

                   Proton_antipo_M 221 sviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvas 290
                                       +viy+ ++tr +++++gLa +mPi   +l+ ++++++GlP+++gF+++f+i+ +a++ ++++ + +++a+
  gi|336255222|ref|YP_004598329.1| 361 GVIYNATHTRMVTDMSGLADRMPIAVGILIAGAFGYMGLPLMSGFYGEFTIFFGAFQSEQLAYAPLFTAA 430
                                       888*******************************************************999888774443 PP

>> Oxidored_q5_N  NADH-ubiquinone oxidoreductase chain 4, amino terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.15   8.7e+02       6      43 ..       7      45 ..       2      55 .. 0.57
   2 !   24.7   0.2   3.1e-09   1.9e-05      52     103 ..      74     121 ..      61     128 .. 0.82
   3 ?   -2.0   0.2      0.62   3.7e+03       6      40 ..     146     180 ..     139     196 .. 0.58
   4 ?   -3.2   0.1       1.4   8.6e+03      40      40 ..     300     300 ..     269     333 .. 0.49
   5 ?   -3.2   0.0       1.5   8.7e+03      73      82 ..     352     361 ..     337     375 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.15
                     Oxidored_q5_N  6 lptlml.iplvllskkkllwststlvslllallslllln 43
                                      +++++l ++++++ ++++  ++ +++sl+ a+lsl l++
  gi|336255222|ref|YP_004598329.1|  7 IAVALLgALVTFVAPNRIAGKLAFAISLVPAALSLWLFS 45
                                      444444134455555556666666677776666666544 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 3.1e-09
                     Oxidored_q5_N  52 nlsyllglDslSapLilLSlWllpLmilASqkhlkkepknrqrlFllllilL 103
                                       ++s ++glD +S+pL++L++ l++L il+S+  + +    r++ F  l++++
  gi|336255222|ref|YP_004598329.1|  74 TISWFVGLDGISLPLVVLTTILCSLAILSSWTPIDE----RESQFYGLVLFI 121
                                       6899***************************99998....555555555555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.62
                     Oxidored_q5_N   6 lptlmliplvllskkkllwststlvslllallsll 40 
                                       +p+ +li ++   ++k+  + +++++ + +ll++ 
  gi|336255222|ref|YP_004598329.1| 146 IPMYLLIGIWGGPRRKYAAIKFFVYTNVASLLMFG 180
                                       45555554444444555555555555555555554 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 1.4
                     Oxidored_q5_N  40 l 40 
                                       +
  gi|336255222|ref|YP_004598329.1| 300 I 300
                                       1 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 1.5
                     Oxidored_q5_N  73 llpLmilASq 82 
                                       ++ Lm++A  
  gi|336255222|ref|YP_004598329.1| 352 ISGLMFMAVG 361
                                       4455555543 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 ?   13.2   0.2   1.2e-05     0.069       2      38 ..      65     101 ..      64     115 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                   Proton_antipo_N   2 ftWlsvgglsieigfllDklsalmllvvtfvsllvhl 38 
                                       ++W++ g+++i++ + lD++s+  +++ t++ +l +l
  gi|336255222|ref|YP_004598329.1|  65 YEWIQLGDYTISWFVGLDGISLPLVVLTTILCSLAIL 101
                                       79***************************99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.21s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3945.53
//
Query:       gi|336255223|ref|YP_004598330.1|  [L=509]
Description: NAD(P)H-quinone oxidoreductase subunit 2 [Halopiger xanaduensis SH-6]
Scores for 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-69  232.6  21.5    5.3e-69  232.6  21.5    1.8  2  Proton_antipo_M  Proton-conducting membrane transporter
    2.7e-05   24.2   4.5    0.00013   21.9   4.5    2.3  1  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 ?   -1.3   0.5      0.11     1e+03     246     287 ..      51      94 ..      12     111 .. 0.54
   2 !  232.6  21.5   5.9e-73   5.3e-69       1     292 [.     136     445 ..     136     446 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.11
                   Proton_antipo_M 246 alvllvlllsla.GlPptagFlskfliLeaavavslillvla.v 287
                                       +l+ +v +++ + G+P++ g  + ++++ + + v++++l ++ v
  gi|336255223|ref|YP_004598330.1|  51 SLAAAVWFITAGvGTPGMEGGHGVIELFDGQFVVDQLALYFMiV 94 
                                       33333333333225565555555555555555555544444422 PP

  == domain 2  score: 232.6 bits;  conditional E-value: 5.9e-73
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal..... 72 
                                       an+L++++++lEl +lp+y L+ + k++  s+eA+lk+fl+++l+s ++++gi+l+y++tg +++++++ al     
  gi|336255223|ref|YP_004598330.1| 136 ANSLVTIFIALELSSLPSYALVSILKDNRGSVEAGLKYFLIGALSSAVFVYGISLVYGATGVMQLDAIAAALeesta 212
                                       799********************************************************************999998 PP

                   Proton_antipo_M  73 ..elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla....... 140
                                            +    l l++l+ll g+++K+a vp+h+W p+ay++aP+p+sa+l + ++ka++++++ +++  a       
  gi|336255223|ref|YP_004598330.1| 213 vgGEFAYDGLLGLGILMLLGGFAFKTASVPFHFWAPEAYEGAPAPISAFL-SSASKAAGFVITFRVFTTAfpldvts 288
                                       863344444556677888899*****************************.55899999999877765554455555 PP

                   Proton_antipo_M 141 .vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialav....atqygveaaiihllthalfk 212
                                         ++ +++  ++ilai++m lg+++a +q+++Kr+lAySsi+h Gy li+la     +++  + aa++hll++++++
  gi|336255223|ref|YP_004598330.1| 289 dLVGVDWTLAFVILAIVTMTLGNFAAATQRNVKRMLAYSSIGHAGYALIGLAGlsadGGELVMGAAMMHLLVYGFMN 365
                                       66889********************************************9876445666777899************ PP

                   Proton_antipo_M 213 allFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vv 288
                                        + Fl++  ++y     r++++y+gL++  P+ +++l+++++slaG+Pp+ gF+sk  +++aa++++l+++++a v+
  gi|336255223|ref|YP_004598330.1| 366 TGAFLFVALAEYWG-VGRTFEDYNGLSNQAPVACAALAIFMFSLAGIPPFGGFWSKYFLFTAALDAGLVIVAAAlVI 441
                                       *******8886666.7899*************************************************999999899 PP

                   Proton_antipo_M 289 asvl 292
                                        s+l
  gi|336255223|ref|YP_004598330.1| 442 NSAL 445
                                       8887 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 !   21.9   4.5   1.5e-08   0.00013      14      56 ..      80     122 ..      77     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.5e-08
                   Proton_antipo_N  14 igfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfay 56 
                                        +f +D+l + +++vv +v++lv + S  YM+d+  ++ ++++
  gi|336255223|ref|YP_004598330.1|  80 GQFVVDQLALYFMIVVAVVTALVSVASYDYMRDHAYQAEYYSL 122
                                       579*****************************99999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3756.24
//
Query:       gi|336255224|ref|YP_004598331.1|  [L=491]
Description: phosphoesterase RecJ domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-14   53.2   0.0      1e-13   51.6   0.0    1.9  1  TrkA_N           TrkA-N domain
    6.6e-14   52.5   1.0    3.3e-13   50.2   0.3    2.5  4  DHHA1            DHHA1 domain
    1.4e-12   47.7   0.0    2.9e-12   46.7   0.0    1.6  1  DHH              DHH family
     0.0012   19.0   0.0      0.003   17.8   0.0    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.012   15.5   0.4      0.012   15.5   0.4    2.8  3  NAD_binding_10   NAD(P)H-binding
      0.083   12.5   0.0       0.15   11.7   0.0    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
        0.1   12.4   0.0       0.28   11.0   0.0    1.8  1  DRTGG            DRTGG domain
        2.4    8.5   5.9         87    3.4   1.7    3.8  2  NTP_transf_3     MobA-like NTP transferase 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 !   51.6   0.0   4.5e-17     1e-13       2      95 ..       5      97 ..       4     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 4.5e-17
                                      EEES-SHHHHHHHHHHHHTT.EEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHH CS
                            TrkA_N  2 iiiGlGrvGrslaeeLsegg.kdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanila 79
                                      +++G+G vGr++ae+L e++  + +v+ +de++ve+lr+e +++ ++d++d+e+L  a++e+ d+v +  +  ++n  a
  gi|336255224|ref|YP_004598331.1|  5 LVLGCGAVGRQVAERLAERSdGRLLVVTSDEAVVETLRDESIPARHADPSDPETL--ANVEQPDVVFVGGDRTDVNRSA 81
                                      69****************55456*******************************9..799******************* PP

                                      HHHHHHHTSSSEEEEE CS
                            TrkA_N 80 vllakelnpkkkiiar 95
                                      +++a+  +p++ i+a 
  gi|336255224|ref|YP_004598331.1| 82 LENARGRFPGASIVAS 97
                                      *************995 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       6.9   1.5e+04      69      82 ..      64      76 ..      59      93 .. 0.67
   2 ?   -1.1   0.0         1   2.3e+03      28      60 ..     138     171 ..     119     176 .. 0.61
   3 ?   -4.0   0.0         8   1.8e+04      49      69 ..     267     287 ..     261     296 .. 0.68
   4 !   50.2   0.3   1.5e-16   3.3e-13      30     137 ..     347     459 ..     326     460 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.9
                                      TTCEEEEEEEECTE CS
                             DHHA1 69 kpvivfvakeegdk 82
                                      +p +vfv +++   
  gi|336255224|ref|YP_004598331.1| 64 QPDVVFVGGDRT-D 76
                                      477777777765.3 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                                       HHHHHTCEEEC..TCEEEEEECHCCHHHHHHHHHH CS
                             DHHA1  28 eellekaeevk..gvkvlvaevgeewdagalgiaa 60 
                                       e+++   +e+   + +++v+   ++ d++a+++a+
  gi|336255224|ref|YP_004598331.1| 138 EAAIGLRQELAtiDGPLAVVTH-DNPDPDAIASAV 171
                                       2222222333335888899999.999999999887 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 8
                                       CCHHHHHHHHHHHHHHTHGBT CS
                             DHHA1  49 eewdagalgiaadklksklkk 69 
                                       +++  ++l++++d+++  +++
  gi|336255224|ref|YP_004598331.1| 267 AGATSTVLAEYVDRFNIGFDR 287
                                       566677888888888876666 PP

  == domain 4  score: 50.2 bits;  conditional E-value: 1.5e-16
                                       HHHTCEEEC.TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSHSS-HHHHHHHHH CS
                             DHHA1  30 llekaeevk.gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkdgvdagelakeaa 104
                                       ++++    +  ++v+va vg   +++al +aad+l+   ++ ++ ++v++ +++ +++sars++++vd+ge +++a+
  gi|336255224|ref|YP_004598331.1| 347 AIKNR---EqRDSVAVASVGRISNRDALPQAADQLLA--MEgVETTLVFGFRDEMAYLSARSRANDVDLGETLRDAF 418
                                       22222...2499*************************..999999999999999*********99**********77 PP

                                       HHTTCCEEEETCEEEEEEE.........HCHHHHHHHHHHHH CS
                             DHHA1 105 aklgggGGGHdlAaGagip.........aekleealealeea 137
                                       + +g  G GH+ +aGa+++         ++++e +++ +ee+
  gi|336255224|ref|YP_004598331.1| 419 ERIGSAG-GHADMAGAQLEigilasaddEDEVESIVSVVEEV 459
                                       7777776.**999***99977777777666677777766665 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   1.3e-15   2.9e-12       3     101 .]     155     297 ..     153     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.3e-15
                                       EEE-ECSSSHHHHHHHHHHHHC................................................ECS--TC CS
                                       xxxxxxxxxxxxxxxxxxxxxx................................................xxxxxxx RF
                               DHH   3 livghknpDtDsigSaialanl................................................lvDhnek 31 
                                       ++v+h npD D+i+Sa+al  +                                                lvDh+++
  gi|336255224|ref|YP_004598331.1| 155 AVVTHDNPDPDAIASAVALVDIaesvgleaeacyfgeishqenramvnlldldlrnlspedsleeygafaLVDHSRP 231
                                       689******************6666666777777777777777777777777777777777777777777******* PP

                                       GGCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  32 sqavegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                                e+ +  i+iDHH +  ++     ++ l+e++g+t++++ae++++ ++ +++++a++ll gi
  gi|336255224|ref|YP_004598331.1| 232 GVNDGL--PESLDVDIVIDHHPPRGPVPGS--FVELREEAGATSTVLAEYVDRFNIGFDRATATALLYGI 297
                                       988855..9**************9777766..78889******************************998 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 !   17.8   0.0   1.3e-06     0.003       2      66 ..       5      62 ..       4      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-06
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal 66
                                      l++G+G+vG+ vae la+++d   ++ v++ +++ +e l    + +++ a+  d++++e  La +
  gi|336255224|ref|YP_004598331.1|  5 LVLGCGAVGRQVAERLAERSDG--RLLVVTSDEAVVETL----RDESIPARHADPSDPET-LANV 62
                                      79******************98..9****9999885555....78899999999999998.8773 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 ?   15.5   0.4   5.5e-06     0.012       4      73 ..      10      77 ..       8     120 .. 0.84
   2 ?    1.6   0.3     0.097   2.2e+02       2      63 ..     120     176 ..     120     205 .. 0.76
   3 ?   -1.8   0.0       1.1   2.5e+03      52      77 ..     342     370 ..     328     418 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.5e-06
                                      SHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                    NAD_binding_10  4 GkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk 73
                                      G vGr+++++l++r++ ++ +++ +++ ++ l+ +e + + ++d +d+e+la+ +++ d+V++ + +++ 
  gi|336255224|ref|YP_004598331.1| 10 GAVGRQVAERLAERSDGRLLVVTSDEAVVETLR-DESIPARHADPSDPETLAN-VEQPDVVFVGGDRTDV 77
                                      99************9888877788888888887.69**************987.7999999998855444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.097
                                       TTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SE CS
                    NAD_binding_10   2 AtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgada 63 
                                       A G +  ++++e ++r+  e  +  R++  +     +  l vv+ d  d++++a+a++ +d+
  gi|336255224|ref|YP_004598331.1| 120 ADGAIVERVIDETASRS-AEAAIGLRQELATI----DGPLAVVTHDNPDPDAIASAVALVDI 176
                                       56777778888888885.77777777655544....35699****************98886 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.1
                                       CHHHHHHT...T-SEEEES---TCCHHHH CS
                    NAD_binding_10  52 edlaealk...gadaVvsalggggkdeeg 77 
                                       e++a+a+k   + d V +a  g+ +++++
  gi|336255224|ref|YP_004598331.1| 342 ETIARAIKnreQRDSVAVASVGRISNRDA 370
                                       56666665222334554444333332222 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.7e-05      0.15       2      78 ..       5      74 ..       4     100 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.7e-05
                                      EEES-SHHHHHHHHHHHH.HTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSG CS
                              ApbA  2 ailGaGaiGsllaakLak.agadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtvKa 78
                                      ++lG+Ga+G+ +a +La+       +++ ++  +e+l+++ +  +  +      p+ + + +   + e+ d+v+v    
  gi|336255224|ref|YP_004598331.1|  5 LVLGCGAVGRQVAERLAErSDGRLLVVTSDEaVVETLRDESIPARHAD------PSDPETLA---NVEQPDVVFVGGDR 74
                                      69**************99777778888888877888888777666666......22222222...45777777776555 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013      0.28      33      61 ..      57      85 ..      20     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                                      HHHHHHHTSEEEEEETT-HHHHHHHTT-T CS
                             DRTGG 33 nmlerlkegdlvivpGDRediqlaaleag 61
                                      ++l  +++ d+v v+GDR+d+   ale++
  gi|336255224|ref|YP_004598331.1| 57 ETLANVEQPDVVFVGGDRTDVNRSALENA 85
                                      567778899*****************987 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 ?    3.4   1.7     0.039        87      30     119 ..      16     140 ..       5     159 .. 0.51
   2 ?    3.1   0.1     0.048   1.1e+02      58     111 ..     241     348 ..     215     383 .. 0.52

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.039
                                       HHHHHCTT.-CEEEEECSHCHHHH.............................HHTTCTS-E....EE-TTSS-SHH CS
                      NTP_transf_3  30 vldalraagvdevvvvggdeevla.............................alarlgvrv....vededpgkgpl 73 
                                       v+++l++ + ++++vv+ de+v +                              + + +++v    +e++  g+ p+
  gi|336255224|ref|YP_004598331.1|  16 VAERLAERSDGRLLVVTSDEAVVEtlrdesiparhadpsdpetlanveqpdvvFVGGDRTDVnrsaLENA-RGRFPG 91 
                                       5555555555666677766666662223333333333333333332222222211111111111103332.356666 PP

                                       HHHHHHHHHH...SSSCEEEEETT-TT.--HHHHHHHHHCHHHHTSSEE CS
                      NTP_transf_3  74 aslaaalraaa..dadavlvlacDmPl.ltpelverllaaaaasgadvv 119
                                       as+ a l   +  ++ + + +++D++   + ++ver++++ a+++a+++
  gi|336255224|ref|YP_004598331.1|  92 ASIVASLGGNPtlSDRQTFSALADHAVdADGAIVERVIDETASRSAEAA 140
                                       6666666554444666666666666554556666666666666665555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.048
                                       CTS-EEE-TTSS-SHHHHHHHHH..................................................HHH. CS
                      NTP_transf_3  58 lgvrvvededpgkgplaslaaal..................................................raaa 84 
                                       l+v++v d +p +gp+ +    l                                                  raa+
  gi|336255224|ref|YP_004598331.1| 241 LDVDIVIDHHPPRGPVPGSFVELreeagatstvlaeyvdrfnigfdratatallygirvdtndftrevapadfRAAS 317
                                       56777777777777776655555222222222222223333333333223333333333333333333333321111 PP

                                       ....SSSCEEEEETT-TT--HHHHHHHHHCH CS
                      NTP_transf_3  85 ....dadavlvlacDmPlltpelverllaaa 111
                                           +ad  l+    +P ++ +++e++++a+
  gi|336255224|ref|YP_004598331.1| 318 ilwpHADVSLLQQIEQPTIEGDTLETIARAI 348
                                       2222444444444445555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 3897.78
//
Query:       gi|336255225|ref|YP_004598332.1|  [L=41]
Description: hypothetical protein Halxa_3848 [Halopiger xanaduensis SH-6]
Scores for 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   17.4   1.3     0.0043   17.0   1.3    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   16.1   0.7      0.012   16.0   0.7    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.04   14.0   3.0       0.57   10.4   0.2    2.1  2  Zn-ribbon_8      Zinc ribbon domain
      0.066   13.1   0.7      0.066   13.1   0.7    2.1  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.077   13.0   1.5        2.4    8.2   0.1    2.0  2  HypA             Hydrogenase/urease nickel incorporation, met
      0.077   12.7   3.0       0.27   11.0   3.0    1.8  1  Zn_Tnp_IS1       InsA N-terminal domain
      0.086   12.7   0.2        0.1   12.5   0.2    1.0  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
       0.18   11.9   4.8        1.1    9.5   4.8    1.9  1  zf-Dof           Dof domain, zinc finger
       0.18   11.6   4.3        5.8    6.9   1.3    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)


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 !   17.0   1.3   2.2e-06    0.0043      20      45 ..       6      33 ..       2      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.2e-06
                     Zn_Tnp_IS1595 20 vCPhCgsrkayrikt..rglfqCkeCrk 45
                                       CPhCg + ++  ++    +f C++C +
  gi|336255225|ref|YP_004598332.1|  6 SCPHCGADDVWLEERatFIQFGCRACDH 33
                                      5******988887777899*******87 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 ?   16.0   0.7     6e-06     0.012       5      36 ..       6      33 ..       3      41 .] 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6e-06
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga 36
                                       CP+Cg ++v+ ++  +      ++ C  C  
  gi|336255225|ref|YP_004598332.1|  6 SCPHCGADDVWLEERATFI----QFGCRACDH 33
                                      7***********9977766....788888865 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00028      0.57      27      35 ..       5      14 ..       1      15 [. 0.73
   2 ?    4.7   0.2     0.016        32       6      14 ..      26      34 ..      23      40 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00028
                       Zn-ribbon_8 27 taCPeCgs.e 35
                                      + CP+Cg+ +
  gi|336255225|ref|YP_004598332.1|  5 ESCPHCGAdD 14
                                      44*****955 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.016
                       Zn-ribbon_8  6 YrCeeCghe 14
                                      + C++C+h 
  gi|336255225|ref|YP_004598332.1| 26 FGCRACDHY 34
                                      78****996 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 ?   13.1   0.7   3.3e-05     0.066      25      35 ..       4      14 ..       3      15 .. 0.88
   2 ?    3.0   0.7     0.047        94      14      20 ..      28      34 ..      27      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.3e-05
                           DUF35_N 25 ravCphCgsdd 35
                                      r +CphCg+dd
  gi|336255225|ref|YP_004598332.1|  4 RESCPHCGADD 14
                                      789******98 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.047
                           DUF35_N 14 CpdCGtv 20
                                      C++C+++
  gi|336255225|ref|YP_004598332.1| 28 CRACDHY 34
                                      ****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 ?    8.2   0.1    0.0012       2.4      87     101 ..       5      19 ..       1      24 [. 0.78
   2 ?    5.7   0.1    0.0072        14      69      83 ..      24      38 ..      16      41 .] 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                                       HS-TTTSSS-EEEEE CS
                              HypA  87 lrCpkCgsadveivs 101
                                       ++Cp+Cg+ dv + +
  gi|336255225|ref|YP_004598332.1|   5 ESCPHCGADDVWLEE 19 
                                       57*******998865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0072
                                      -EEEETTTS-EEECH CS
                              HypA 69 vkvrCreCgkefele 83
                                      +++ Cr C++ +++e
  gi|336255225|ref|YP_004598332.1| 24 IQFGCRACDHYWKQE 38
                                      6899******99976 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 ?   11.0   3.0   0.00013      0.27       7      34 ..       6      31 ..       2      32 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                        Zn_Tnp_IS1  7 hCPrCsstdVyRhGkstagHeRfrCrdC 34
                                      +CP C ++dV  + + t     f Cr C
  gi|336255225|ref|YP_004598332.1|  6 SCPHCGADDVWLEERAT--FIQFGCRAC 31
                                      8*********9887766..456777777 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 ?   12.5   0.2   5.2e-05       0.1      90     116 ..       7      33 ..       6      34 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-05
                                       TSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  90 CkeCkspetelekeerllvlkCkaCga 116
                                       C++C+  ++ le + + + + C+aC +
  gi|336255225|ref|YP_004598332.1|   7 CPHCGADDVWLEERATFIQFGCRACDH 33 
                                       *************999999******86 PP

>> zf-Dof  Dof domain, zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.8   0.00053       1.1       4      40 ..       5      37 ..       2      40 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00053
                            zf-Dof  4 lkCprCestntkFcYyNNyslsqPRyfCkaCrryWtk 40
                                       +Cp+C + +     +  +  +   + C+aC +yW +
  gi|336255225|ref|YP_004598332.1|  5 ESCPHCGADDV----WLEERATFIQFGCRACDHYWKQ 37
                                      67999999986....4567888889**********87 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 ?    6.5   0.1    0.0039       7.7       2      12 ..       6      16 ..       5      22 .. 0.83
   2 ?    6.9   1.3    0.0029       5.8      27      39 .]      24      36 ..      18      36 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0039
                           TFIIS_C  2 kCpkCgsreay 12
                                       Cp Cg ++++
  gi|336255225|ref|YP_004598332.1|  6 SCPHCGADDVW 16
                                      5*****99886 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0029
                           TFIIS_C 27 vfykCtkCghrWr 39
                                      + + C +C h W+
  gi|336255225|ref|YP_004598332.1| 24 IQFGCRACDHYWK 36
                                      4578********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 347.69
//
Query:       gi|336255226|ref|YP_004598333.1|  [L=271]
Description: CBS domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-26   90.9   2.2    4.4e-12   46.3   0.1    2.7  2  CBS              CBS domain
    3.3e-10   40.1   0.1    9.1e-10   38.7   0.1    1.8  1  ParBc            ParB-like nuclease domain
  ------ inclusion threshold ------
      0.014   15.5   0.0       0.11   12.6   0.0    2.0  1  ParBc_2          Putative ParB-like nuclease
      0.068   12.8   0.0       0.12   12.0   0.0    1.5  1  Dehyd-heme_bind  Quinohemoprotein amine dehydrogenase A, alph


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 !   46.3   0.1   9.7e-16   4.4e-12       1      55 [.      13      67 ..      13      69 .. 0.93
   2 !   43.6   0.3   6.4e-15   2.9e-11       4      54 ..      75     125 ..      72     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 9.7e-16
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55
                                      V+++mtrdvvtv+pd+t+++++ +++e++ +s++PV  e  ++ G v+ +Dll a 
  gi|336255226|ref|YP_004598333.1| 13 VEEYMTRDVVTVSPDATVGDVASRIAESEaHSGFPVC-ERRRVEGFVSASDLLLAD 67
                                      789**********************97778*******.8999***********886 PP

  == domain 2  score: 43.6 bits;  conditional E-value: 6.4e-15
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       +mt+d+++++p++ + +a++ + ++g+  lPVVd+ g+lvGi++  D++r 
  gi|336255226|ref|YP_004598333.1|  75 VMTTDLLVAHPEMKVTDAARVILRSGIQKLPVVDDAGNLVGIISNADVIRS 125
                                       8********************88***99********************985 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.1     2e-13   9.1e-10       3      85 ..     157     234 ..     117     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2e-13
                             ParBc   3 vplseirpnplqprkdspekieelvasIkkkGllqPiivrktrqgryeiiaGerRlrAakrlglkevpvivleidde 79 
                                       vpl+++ p++ +++   ++++e    +++ +Gl +P++v  ++ g   + +G++R+ Aa+rlg+ e++++v+ id+e
  gi|336255226|ref|YP_004598333.1| 157 VPLADLTPTQGRVY---ADELEGRRYELE-RGLAEPLVVIDNA-GTLLLADGHHRVLAADRLGIDEMDAYVIVIDRE 228
                                       67777777777777...678888888887.************8.******************************998 PP

                             ParBc  80 eamals 85 
                                       + + l+
  gi|336255226|ref|YP_004598333.1| 229 DGVDLG 234
                                       766665 PP

>> ParBc_2  Putative ParB-like nuclease
   #    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       3      83 ..     157     226 ..     155     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                                       EEGGGCB-SBSEE-HHHHHHHHHHHHT------.---TT-BEEEEEE-STT-EEE-S-HHHHHHHHHTT-....-EE CS
                           ParBc_2   3 veiadLrPTQlavGldeveyklgeleelkekkkldkflekklvpvVigpdgelYliDhHHllrallesgvggaekkv 79 
                                       v +adL PTQ  v  de+e ++ ele+  ++             vVi + g l l D+HH + a  + g+++ ++ v
  gi|336255226|ref|YP_004598333.1| 157 VPLADLTPTQGRVYADELEGRRYELERGLAE-----------PLVVIDNAGTLLLADGHHRVLAADRLGIDEMDAYV 222
                                       7899999999999999999999998444323...........3489999*************999997775555555 PP

                                       EEEE CS
                           ParBc_2  80 lvkv 83 
                                       +v  
  gi|336255226|ref|YP_004598333.1| 223 IVID 226
                                       5544 PP

>> Dehyd-heme_bind  Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.7e-05      0.12      25      85 ..     124     185 ..     113     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.7e-05
                   Dehyd-heme_bind  25 riseqrktPeGwdmtvarmqlehgleltkaeraeivkyladtqG.lapsesaearyvlerkp 85 
                                       r + +r tPe     +  +++ h++el+++ r+  +  l+ tqG +  +e +++ry ler +
  gi|336255226|ref|YP_004598333.1| 124 RSQIERATPEKVGKLMRTLEQIHDVELEQERRTVPLADLTPTQGrVYADELEGRRYELERGL 185
                                       55567999**999999999**********999999*********4457899********964 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:                      270  (0.0150594); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2065.49
//
Query:       gi|336255227|ref|YP_004598334.1|  [L=670]
Description: acetate/CoA ligase [Halopiger xanaduensis SH-6]
Scores for complete 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-90  304.1   0.1    1.5e-90  303.8   0.1    1.1  1  AMP-binding    AMP-binding enzyme
    1.4e-24   86.8   0.6    3.1e-24   85.7   0.6    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    3.7e-12   46.0   3.8    3.7e-12   46.0   3.8    2.1  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


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 !  303.8   0.1   2.5e-94   1.5e-90       5     422 ..     104     546 ..     100     547 .. 0.88

  Alignments for each domain:
  == domain 1  score: 303.8 bits;  conditional E-value: 2.5e-94
                                       HHHST.TSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEE CS
                       AMP-binding   5 aaktp.dkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpl 77 
                                       +++   ++ a+ +    ge +t+TY+el ++v+++AagLr +Gv+++d+V ++lp+ pe+ +a+la++++Ga ++++
  gi|336255227|ref|YP_004598334.1| 104 VENGAkNRAAIKWegeMGETRTYTYGELLNEVEAFAAGLRDIGVEEDDVVTLYLPMIPELPIAMLACARIGAPHSVV 180
                                       5444438888877999999*********************99*********************************** PP

                                       ETTS-HHHHHHHHHHHTESEEE.........ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCS CS
                       AMP-binding  78 nptltaeelayiledseakvli.........atvdsel.leklleaaakleavklvivldadellkeeelkeeeese 144
                                        ++++a++la+ ++++++++li         +   + +  ek+++   ++++  + +v+d+ + + +  l +++ ++
  gi|336255227|ref|YP_004598334.1| 181 FAGFSADALAMRMNAADSEYLItcdgyyrrgD---ALNhKEKADKGLRSVDQDVTSVVVDRLGEELTHFLGNDARDY 254
                                       **********************9998875331...333355666666667777888999**9999999999999888 PP

                                       CTT.S....-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHH CS
                       AMP-binding 145 eka.e....kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifg 216
                                       ++         +e+++ +++d+++++YTSGTTG+PKGV ++++ ++a +a+ + +   +l ++d++++ +++ +i+g
  gi|336255227|ref|YP_004598334.1| 255 DELvAehegASVEPVTRDAEDMLFLMYTSGTTGEPKGVKHTTGGYLAYTAWTS-QAVLDLVPEDTYWCSADIGWITG 330
                                       77651567856678899*************************77766655532.33466779*************** PP

                                       HHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEE CS
                       AMP-binding 217 lilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllg 291
                                       +++ ++++l+ G t v+++++++ ++ ++l+e iek +v v++++P++++a+++  ++     +++dlsslrl+ ++
  gi|336255227|ref|YP_004598334.1| 331 HSYIVYGPLALGTTTVMYEGTPDyPERDRLWEIIEKNRVDVFYTAPTAIRAFMKwGSDYP---EQHDLSSLRLLGTV 404
                                       ***********************6669999************************665554...688*********** PP

                                       SS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEE.CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSE CS
                       AMP-binding 292 geplspellrffralfge...evlegYGlTEttgvvtv.lpleedkkklgsvGkplpgvevkivDeetgepvpdgee 364
                                       gep++p ++++++++ g+   ++++++++TEt+g++++ lp   ++ k+gs+G+plpgv + +vD + ge+++ ge 
  gi|336255227|ref|YP_004598334.1| 405 GEPINPRAWKWYYKHIGDeecPIVDTWWQTETGGMMITtLP-AINTMKPGSAGPPLPGVSATVVDAA-GEEIEAGEA 479
                                       ****************99******************66344.6666799*****************9.********* PP

                                       EEEEEEET..TS-SEBTT-HHHHHHHEEE......TCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 365 Gellvrgp..gvmkgYlkkpeataeafds......egr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                       G + v +p  g+ +  + ++++  e +++       ++  +   D +++d+dGy+ i+gR +d+i++
  gi|336255227|ref|YP_004598334.1| 480 GYVTVDKPwpGMLRTLYENDDRFIEEYWTeysdeaADEwVYFPEDGAKIDDDGYITILGRVDDVINV 546
                                       *******9778***************997788865255589999*********************98 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 !   85.7   0.6   5.2e-28   3.1e-24       1      76 []     555     633 ..     555     633 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 5.2e-28
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       e+Esa+v + +VaeaaVvG +++vkGea+ a+V+l+dg+e+   +++ ++a v++++gp+a+p++v f++elpktrs
  gi|336255227|ref|YP_004598334.1| 555 EIESAIVGVSGVAEAAVVGGDHDVKGEAVYAYVILEDGQEPtddMRDRIVAAVEDAIGPIARPEEVLFTPELPKTRS 631
                                       8**********************************999644457********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|336255227|ref|YP_004598334.1| 632 GK 633
                                       *9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   3.8   6.3e-16   3.7e-12       4      55 .]      48      99 ..      46      99 .. 0.96
   2 ?   -2.2   0.5       0.7   4.2e+03       3      22 ..     494     513 ..     492     521 .. 0.74

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 6.3e-16
                                      HHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  4 lykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                      +y+e  e+  + W+++a+ l+We+++d vl+++++pf++WF++GklN++ Nc
  gi|336255227|ref|YP_004598334.1| 48 IYEEFEENWPECWEQAADLLSWEEEYDAVLNDEDAPFYEWFTDGKLNASSNC 99
                                      68999999999***************************************** PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.7
                                       HHHHHHHH-HHHHHHHHHCC CS
                            ACAS_N   3 elykeSiedpeaFWaeqake 22 
                                       +ly+   +  e++W e  +e
  gi|336255227|ref|YP_004598334.1| 494 TLYENDDRFIEEYWTEYSDE 513
                                       56777777789999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (670 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 5212.38
//
Query:       gi|336255228|ref|YP_004598335.1|  [L=200]
Description: hypothetical protein Halxa_3851 [Halopiger xanaduensis SH-6]
Scores for 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   13.8   1.0          4    7.8   0.0    3.9  5  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.18   3.3e+03      62      74 ..       4      16 ..       2      17 .. 0.84
   2 ?   -0.9   0.0      0.11     2e+03      63      74 ..      28      39 ..      21      40 .. 0.61
   3 ?   -0.5   0.0     0.084   1.5e+03      47      61 ..     111     125 ..      98     129 .. 0.64
   4 ?    1.0   0.1     0.028   5.1e+02      31      42 ..     129     140 ..     108     158 .. 0.59
   5 ?    7.8   0.0   0.00022         4      43      73 ..     158     188 ..     152     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.18
                            HalOD1 62 eVtVrsdgeieVe 74
                                      +V V+++  i+V 
  gi|336255228|ref|YP_004598335.1|  4 TVNVEGNQNIRVA 16
                                      8999999999996 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.11
                            HalOD1 63 VtVrsdgeieVe 74
                                      V   ++g+i+V+
  gi|336255228|ref|YP_004598335.1| 28 VEFAAEGTITVT 39
                                      444556666666 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.084
                            HalOD1  47 earadgsvsFtyegy 61 
                                       ++++ g ++Ft+eg 
  gi|336255228|ref|YP_004598335.1| 111 SDTQPGAIAFTVEGT 125
                                       234449999999985 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.028
                            HalOD1  31 iDpdALdaLfas 42 
                                       + p  L++L + 
  gi|336255228|ref|YP_004598335.1| 129 VPPATLESLADA 140
                                       345555555555 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.00022
                            HalOD1  43 radgearadgsvsFtyegyeVtVrsdgeieV 73 
                                       r+dg ++ad+ ++ +  gy  +V+ dg+i V
  gi|336255228|ref|YP_004598335.1| 158 RSDGGSEADVLLEIDLLGYGLAVYRDGRIDV 188
                                       4688999**********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1618.85
//
Query:       gi|336255229|ref|YP_004598336.1|  [L=354]
Description: polyprenyl synthetase [Halopiger xanaduensis SH-6]
Scores for 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-57  192.3   0.0    9.2e-57  192.0   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


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 !  192.0   0.0   5.1e-61   9.2e-57       3     254 ..      48     303 ..      46     305 .. 0.93

  Alignments for each domain:
  == domain 1  score: 192.0 bits;  conditional E-value: 5.1e-61
                                       HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTC CS
                   polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvG 79 
                                        l ++l  l+++gGKr+R++l+l ++e ++e   +  + ++ a+i e+lh+ ++++DD+ D++  RRG+p+ h+++G
  gi|336255229|ref|YP_004598336.1|  48 ALADPLWELLDRGGKRWRAVLFLVFIEGFGE---DPAEYLRYACIPEILHNGTIIVDDVEDEAAKRRGEPALHHIYG 121
                                       68899999**********************3...457899************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHH.....STTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHT CS
                   polyprenyl_synt  80 nklAindgdfllarafellaklf.....ekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKT 151
                                       +++A+n+g++++++ +++l++       +++l + e++ ++l +t+ Gq++d++++++ d++  + e+yle++ +KT
  gi|336255229|ref|YP_004598336.1| 122 QDIALNAGNAMYFLPLKILTQSRtdlpaDQRLAAYEMLMDELNRTHLGQGMDIHWHNERDVQ-ITPEQYLEMCACKT 197
                                       ********************98888985555*************************999999.99************ PP

                                       HHHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...S-HHHHSS-TSHHHHTT---HHHHHHHH CS
                   polyprenyl_synt 152 aylfalpvalaallagasdeelealkdiglelGlaFQiqDDylDlf...gdpevlgKpagtDiqegkctlpilkale 225
                                       + l ++ ++laa+l++  +e+ +a++++++   +aFQi DD+lD+    g + ++gK++g+D++egk tl++++al 
  gi|336255229|ref|YP_004598336.1| 198 GCLGRIVARLAAILTDQPPEVERAVATYAELTAVAFQIGDDILDVEnslGRAGEFGKEFGNDVREGKKTLLVIYALA 274
                                       ****************999*99***********************955566899*********************** PP

                                       CT-HHHHHHHHHHTTSSHHHHHHHHHHHH CS
                   polyprenyl_synt 226 laspeqrkvlkeilgkkaekeedvkeale 254
                                       +++pe +++l+eil  +++++e+v eal+
  gi|336255229|ref|YP_004598336.1| 275 ESDPETAERLREILALDENTDEEVLEALS 303
                                       ***************77777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2764.95
//
Query:       gi|336255230|ref|YP_004598337.1|  [L=438]
Description: peptidase M28 [Halopiger xanaduensis SH-6]
Scores for complete 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  123.1   0.3    1.5e-35  122.7   0.3    1.2  1  Peptidase_M28  Peptidase family M28
    5.1e-15   55.3   0.0    1.2e-14   54.0   0.0    1.7  1  PA             PA domain
    1.1e-05   24.6   0.8    1.9e-05   23.8   0.8    1.3  1  Peptidase_M42  M42 glutamyl aminopeptidase
     0.0002   21.1   0.1    0.00032   20.5   0.1    1.4  1  Peptidase_M20  Peptidase family M20/M25/M40
  ------ inclusion threshold ------
        0.1   12.6   0.1         13    6.0   0.0    2.7  2  IgG_binding_B  B domain


Domain annotation for each model (and alignments):
>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.3   4.2e-39   1.5e-35       1     196 [.     211     395 ..     211     397 .. 0.88

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 4.2e-39
                                       EEEEEESTTCESEEEEEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHH CS
                     Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllG 77 
                                       Nv a+l +++ de++l+++H+D + +  ++   GA Dn++g+a+++ela +la+++ +++ +v f++f+aEE gl G
  gi|336255230|ref|YP_004598337.1| 211 NVRAELGPDT-DERVLVTSHVDAHDI--AE---GALDNGAGTAMVVELANALANREDDLETRVEFVAFGAEEVGLTG 281
                                       8999**9999.**************9..99...***********************9******************** PP

                                       HHHHHHHHCCCTTEEEEEEECS-SSSS--EEEHHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHH CS
                     Peptidase_M28  78 SkafakakpelkkiaavlnlDmvgsggkellfesgdkssselekelkalakpvgraaaedpfdersgrgrsDhspfl 154
                                       S ++a a+++l+ i+av+n D v +g++  l++ g    ++le+ ++++a+++ + +++ p        +sDh+pf+
  gi|336255230|ref|YP_004598337.1| 282 SAHYA-AETDLDSIEAVVNNDGVVRGRTLSLVTHG---FDGLEDAADSVADRYDHPIETVPK----LGPHSDHWPFV 350
                                       *****.999**********************8555...556677777777777765433332....3457******* PP

                                       TTT--EEEE..CTSSS-TTT.TSTTSSGGGB-HHHHHHHHHHHHH CS
                     Peptidase_M28 155 kagvpvldl..aetgfpevy.HtprDtldnidkdtlariaelvle 196
                                       ++gvp+ ++   +++ ++ + Ht +Dtl++++++tl++ a l+ e
  gi|336255230|ref|YP_004598337.1| 351 RRGVPGYHVksTSDEVGRGWgHTFADTLEKLEPRTLREQAILLTE 395
                                       *********655566699******************998776665 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   3.4e-18   1.2e-14       1      89 []      92     187 ..      92     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 3.4e-18
                                PA   1 vtgplVyscfagygisadfegvdvkGkivLvqr......tf....aeKarnAqaaGAagviiv..ndgelgaatgas 65 
                                       v++plV   + gyg ++dfe++d++G+iv+v++      ++    +eK+++A ++GA+g+++   ++g+  ++tg+ 
  gi|336255230|ref|YP_004598337.1|  92 VSAPLV---DLGYGLPEDFEARDLEGRIVMVRSdipdyyERyihrREKYYHAVEQGAIGFVYRnhVEGC-LPPTGSV 164
                                       799***...**********************54666544115666******************543333.3344444 PP

                                PA  66 gnegepdgitiPavgvsredgeal 89 
                                       g+e +p   +iPa+gvs e+g++l
  gi|336255230|ref|YP_004598337.1| 165 GTEADP-VGEIPAIGVSSEVGARL 187
                                       454444.79************987 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.8   5.4e-09   1.9e-05     123     187 ..     230     296 ..     194     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.4e-09
                                       ETTECEEETTHHHHHHHHHHHHHHHHHCTSS-S..SEEEEEEESTCTTTSHHHHHHHHHH--SEEEE CS
                     Peptidase_M42 123 langkivskalDdragvavllellkelkeeele..atvylvatvqEEvGlrGaktsaekikpdiaia 187
                                       ++ + i+  alD+ ag a+++el+++l+++e +  ++v +va   EEvGl G++  a ++++d + a
  gi|336255230|ref|YP_004598337.1| 230 VDAHDIAEGALDNGAGTAMVVELANALANREDDleTRVEFVAFGAEEVGLTGSAHYAAETDLDSIEA 296
                                       455668889******************9876555599******************999999987655 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   8.8e-08   0.00032      32      99 ..     236     299 ..     226     427 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.8e-08
                                       STTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20  32 GrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelhi 99 
                                       + Ga d+ +g ++++e++ al+ +  +++  ++++++++EE+g  G++++++    + ++d + +++ 
  gi|336255230|ref|YP_004598337.1| 236 AEGALDNGAGTAMVVELANALANREDDLETRVEFVAFGAEEVGLTGSAHYAA----ETDLDSIEAVVN 299
                                       5699*************************************98899999999....455555332333 PP

>> IgG_binding_B  B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.019        66       8      28 ..     188     208 ..     187     215 .. 0.87
   2 ?    6.0   0.0    0.0035        13      22      46 ..     414     438 .]     401     438 .] 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.019
                                       -SSEEEEEEEEESSHHHHHHH CS
                     IgG_binding_B   8 GktlsGetttkavDaataeka 28 
                                       G+ + Ge    avDa+  e +
  gi|336255230|ref|YP_004598337.1| 188 GRRFDGEEVELAVDAEINEAE 208
                                       7889************98866 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHHTT--CEEEEET CS
                     IgG_binding_B  22 aataekaFkqYandngvdGeWaYDd 46 
                                       a  ae + +  a+   ++G+W YDd
  gi|336255230|ref|YP_004598337.1| 414 AIAAELEAQDLAEGMRITGDWPYDD 438
                                       55789999999*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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 0.19s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 3582.04
//
Query:       gi|336255231|ref|YP_004598338.1|  [L=276]
Description: ATP-NAD/AcoX kinase [Halopiger xanaduensis SH-6]
Scores for 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   68.3   1.0    7.7e-19   68.0   1.0    1.1  1  NAD_kinase  ATP-NAD kinase


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 !   68.0   1.0   4.3e-23   7.7e-19      66     284 ..      46     257 ..      18     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 4.3e-23
                                       EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEE CS
                        NAD_kinase  66 dtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekre 142
                                        +r ale++  a+ dl+++vG   T  +var+ +     v  +++G++     + pe +  +l++ lege+   +r 
  gi|336255231|ref|YP_004598338.1|  46 IERGALETVLAADPDLLVTVGE-RTLSAVARART----DVSVLPVGSVAGIESVAPERLPDALAAALEGEADKRDRG 117
                                       78899999999999******86.56666666666....4555688999999999*********************** PP

                                       EEEEEEEETTE......EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--E CS
                        NAD_kinase 143 vldavimrskgeediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgpl 219
                                       +l++ i+ ++ +     +v ++ +l +v+++++ ++ ++e  +   +  ++++++dg++v+tP Gs +y+ +  gp+
  gi|336255231|ref|YP_004598338.1| 118 LLTVEIRTGDDG-GEETFV-RERALFDVTLVTEEPASISEYSVRCRNDRVATFRADGVVVATPAGSHGYAAAVEGPQ 192
                                       **********95.455555.55679**************************************************** PP

                                       E-TT---EEEEEESESSS----EEE-TT-EEEEEE-.SS--EEEEETTTEEEEE-TT-EEEEEEES CS
                        NAD_kinase 220 isPgvlailivpicPhslssrpiVvssssklrirva.srseallaldGseelelspgdevrvtasd 284
                                       +s +v+a++++pi P++ + +  V++++  lr+ v+ ++ ++ ++ d +e  ++s+g  v+v++ d
  gi|336255231|ref|YP_004598338.1| 193 LSAAVDAVVVSPIAPFVTRTQRWVLPDDD-LRLAVErDEGDITVVADEREIGAISLGTDVTVSVED 257
                                       ***************************99.**99*999*********9999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); 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 0.20s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 2359.39
//
Query:       gi|336255232|ref|YP_004598339.1|  [L=88]
Description: hypothetical protein Halxa_3855 [Halopiger xanaduensis SH-6]
Scores for 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:                      2165  (0.120754); expected 358.6 (0.02)
Passed bias filter:                      722  (0.04027); expected 358.6 (0.02)
Passed Vit filter:                       139  (0.0077528); 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):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.33
# Mc/sec: 793.57
//
Query:       gi|336255233|ref|YP_004598340.1|  [L=227]
Description: endonuclease III [Halopiger xanaduensis SH-6]
Scores for 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-22   78.0   0.0    1.6e-21   76.7   0.0    1.6  2  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    9.9e-10   37.8   0.0    2.4e-09   36.6   0.0    1.7  1  HHH            Helix-hairpin-helix motif
    1.8e-06   28.1   6.5    3.1e-06   27.3   6.5    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
      0.008   16.8   0.4       0.02   15.5   0.0    1.8  2  HHH_5          Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.013   16.4   0.0      0.021   15.7   0.0    1.4  1  LPD29          Large polyvalent protein associated domain 29
      0.024   15.2   0.0      0.053   14.1   0.0    1.5  1  5_3_exonuc     5'-3' exonuclease, C-terminal SAM fold
       0.19   11.7   0.0       0.57   10.1   0.0    1.7  2  DUF2400        Protein of unknown function (DUF2400)


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 ?   -2.0   0.0       1.9   4.9e+03       9      25 ..       7      23 ..       6      32 .. 0.76
   2 !   76.7   0.0   6.4e-25   1.6e-21       1     107 [.      40     175 ..      40     176 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.9
                                      S-HHHHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                           HhH-GPD  9 tsderanriierlferf 25
                                      t+ e a+++ierl e++
  gi|336255233|ref|YP_004598340.1|  7 TRAEQAEEVIERLEEAY 23
                                      56778888999998886 PP

  == domain 2  score: 76.7 bits;  conditional E-value: 6.4e-25
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       +++ils+q++der+n+ +e+lfe++    ped a+++ee+L+e + ++ +y++Ka yik+ ++ ++           
  gi|336255233|ref|YP_004598340.1|  40 IAVILSAQCTDERVNKETEHLFEKYD--GPEDYANVPEEELAEDLNSITYYNSKAGYIKNSCETILeehdgevpdtm 114
                                       689*********************98..9************************************************ PP

                                       ....................S-SS.S--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                       ....................xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ....................gkpd.vlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                           g+   ++ivvD+hv+r+ +rl++++e + ++ +e++l+ +++
  gi|336255233|ref|YP_004598340.1| 115 deltelsgvgrktanvvlqhGHDVvEGIVVDTHVQRLSRRLGLTEE-ERPEAIEQDLMTIVP 175
                                       ********************6555689*****************99.6********988776 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   9.3e-13   2.4e-09       1      29 [.     105     133 ..     105     134 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 9.3e-13
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIls 29 
                                       +++g++p++++eL++l+GVG+ktA+++l+
  gi|336255233|ref|YP_004598340.1| 105 EHDGEVPDTMDELTELSGVGRKTANVVLQ 133
                                       589************************97 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   6.5   1.2e-09   3.1e-06       1      17 []     194     210 ..     194     210 .. 1.00

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.2e-09
                     EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                       CTAR+P C  C+LaD+C
  gi|336255233|ref|YP_004598340.1| 194 CTARNPDCADCVLADIC 210
                                       ***************** 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   0.2       3.6   9.1e+03      46      56 ..      10      20 ..       9      21 .. 0.79
   2 !   15.5   0.0   7.6e-06      0.02       2      39 ..     115     153 ..     114     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.6
                                      HHHHHHHHHHH CS
                             HHH_5 46 ktAeriilelk 56
                                      ++Ae +i+ l+
  gi|336255233|ref|YP_004598340.1| 10 EQAEEVIERLE 20
                                      68999999886 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 7.6e-06
                                       HHHHTSTT--HHHHHHHHTTT--SHHHH.HHS-HHHHHT CS
                             HHH_5   2 eeLlsvsGiGpktAlallsaGiesvedl.aaadveeLak 39 
                                       +eL+++sG+G+ktA  +l +G + ve + ++  v++L++
  gi|336255233|ref|YP_004598340.1| 115 DELTELSGVGRKTANVVLQHGHDVVEGIvVDTHVQRLSR 153
                                       68******************9999997725677899887 PP

>> LPD29  Large polyvalent protein associated domain 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.0   8.3e-06     0.021       3      69 ..       8      73 ..       6     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.3e-06
                             LPD29  3 tketakeiRkeLKaaFPgvKFSVrkerysgssinvswmdgPteeqvaevtkklesadfngmedsyei 69
                                        e a+e+ ++L +a+P+   S+r +++ +  i v +++  t+e+v++ t++l  ++++g ed+ + 
  gi|336255233|ref|YP_004598340.1|  8 RAEQAEEVIERLEEAYPDSTISLRYSNRLELLIAVILSAQCTDERVNKETEHLF-EKYDGPEDYANV 73
                                      679999*********************99899*********************9.8******99873 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 ?   14.1   0.0   2.1e-05     0.053      15      77 ..     112     174 ..     110     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                        5_3_exonuc  15 DssDnipGvpgiGektAakLlkeygs.leeilenldelkekklkekLeenkeearlskkLatik 77 
                                       D+ D++   +g+G ktA  +l++ ++ +e+i+  ++ +++ +++  L+e++    + ++L+ti+
  gi|336255233|ref|YP_004598340.1| 112 DTMDELTELSGVGRKTANVVLQHGHDvVEGIVVDTH-VQRLSRRLGLTEEERPEAIEQDLMTIV 174
                                       999******************997762577877665.556678888999999999999999996 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.91   2.3e+03      38      67 ..      58      85 ..      31     121 .. 0.53
   2 ?   10.1   0.0   0.00022      0.57     174     193 ..     143     162 ..     141     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.91
                           DUF2400 38 eellelmdkspydfvleeeeekdlkelekf 67
                                      e+l+e++d  p+d+    e e+ +++l+++
  gi|336255233|ref|YP_004598340.1| 58 EHLFEKYDG-PEDYANVPE-EELAEDLNSI 85
                                      444444443.333333222.2233333333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00022
                           DUF2400 174 PlDvHvarvarklgllkrkq 193
                                        +D+Hv+r++r+lgl+++++
  gi|336255233|ref|YP_004598340.1| 143 VVDTHVQRLSRRLGLTEEER 162
                                       69**************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1809.26
//
Query:       gi|336255234|ref|YP_004598341.1|  [L=327]
Description: GHMP kinase [Halopiger xanaduensis SH-6]
Scores for complete 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   0.1    2.4e-06   27.4   0.1    1.2  1  MDD_C           Mevalonate 5-diphosphate decarboxylase C-term
    9.2e-06   25.8   5.3    3.7e-05   23.9   5.5    1.9  2  GHMP_kinases_N  GHMP kinases N terminal domain
  ------ inclusion threshold ------
       0.01   15.8   1.2       0.01   15.8   1.2    1.8  2  TarH            Tar ligand binding domain homologue


Domain annotation for each model (and alignments):
>> MDD_C  Mevalonate 5-diphosphate decarboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1     4e-10   2.4e-06      24     133 ..     197     304 ..     187     313 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4e-10
                             MDD_C  24 etSeLlkhrakevvperieelekAikekdFetfaeitmkdSnqlhavcldtyPpifYlndtSraiielvhelNeaag 100
                                       + S++++ r ++ ++e+i+++++A+++ dF++  e++ +dS +l a+ ++     +Y +    ai + v+el  +++
  gi|336255234|ref|YP_004598341.1| 197 ADSHMFQARNAH-IHEQIAKMRDALRNDDFDAAFELAEHDSLSLAATTMTGPKGWVYWQPATIAIFNRVRELR-EEE 271
                                       6699********.99*********************************************************8.789 PP

                             MDD_C 101 kikvAYtFDAGpNavlyleekdveellsllkkl 133
                                       +i v ++ D G+   + ++e++ e + + ++ +
  gi|336255234|ref|YP_004598341.1| 272 DIPVYFSTDTGASVYVNTTEEHAEYVEEEISDC 304
                                       9************99999999999888877665 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 !   23.9   5.5   6.3e-09   3.7e-05       2      57 ..      93     151 ..      92     155 .. 0.75
   2 ?    1.6   0.2     0.054   3.2e+02      16      33 ..     139     157 ..     139     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6.3e-09
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSH CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsgg 57 
                                       +++++ +P+  GLGSS++  +a+++Al+++ +l+   ee   +a ++   a++++++ +
  gi|336255234|ref|YP_004598341.1|  93 LESENSFPTNVGLGSSSSGFAAAAMALAEAAELDAsrEEiSTIARVGSASAARAVTGAF 151
                                       7899***************************7664333355556666666666666655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.054
                                       HHHHHHHHHHHHHHHHT.T CS
                    GHMP_kinases_N  16 SSAAlavalvaAllall.g 33 
                                       +SA++a a++ A+ +l  g
  gi|336255234|ref|YP_004598341.1| 139 GSASAARAVTGAFSQLHtG 157
                                       59**********9999833 PP

>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.45   2.7e+03     118     133 ..     122     136 ..     106     161 .. 0.48
   2 ?   15.8   1.2   1.7e-06      0.01     104     153 ..     185     234 ..     184     243 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHHHHH CS
                              TarH 118 aaelkakykalqdgla 133
                                       aael+a+++++ +++a
  gi|336255234|ref|YP_004598341.1| 122 AAELDASREEI-STIA 136
                                       33444444433.3333 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.7e-06
                                       HHTS---GGGHH.HHHHHHHHHHH.HHHHHHHHHHHHHTT-HHHHHHS-HH CS
                              TarH 104 Ylalprtaeeeealaaelkakyka.lqdglapliaaleagnleaffdlptq 153
                                       Y++ +++a ++ea+++ + ++++a +++++a + +al++++++a+f+l+ +
  gi|336255234|ref|YP_004598341.1| 185 YHKETEDA-HDEAADSHMFQARNAhIHEQIAKMRDALRNDDFDAAFELAEH 234
                                       66667777.9999*********************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2584.80
//
Query:       gi|336255235|ref|YP_004598342.1|  [L=284]
Description: hypothetical protein Halxa_3858 [Halopiger xanaduensis SH-6]
Scores for 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  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); 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):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 2148.40
//
Query:       gi|336255236|ref|YP_004598343.1|  [L=1066]
Description: carbamoyl-phosphate synthase, large subunit [Halopiger xanaduensis SH-6]
Scores for 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-93  309.9   0.0    5.2e-57  192.8   0.0    2.7  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    5.2e-24   84.9   0.1    1.4e-23   83.5   0.1    1.8  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    1.3e-11   44.3   0.0    0.00022   21.0   0.0    2.7  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    1.2e-09   38.0   0.1    0.00011   21.8   0.0    2.7  3  ATP-grasp        ATP-grasp domain
    7.6e-09   35.4   0.0    1.2e-05   24.9   0.0    2.5  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    4.9e-07   29.9   0.0      0.012   15.6   0.0    2.5  2  ATP-grasp_3      ATP-grasp domain
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.025   14.4   0.1    1.4  1  HDV_ag           Hepatitis delta virus delta antigen
       0.13   13.1   0.7         28    5.6   0.1    3.3  3  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
        5.2    7.1   6.1        7.4    6.6   0.0    4.0  5  B12-binding      B12 binding domain


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 !  192.8   0.0   2.6e-60   5.2e-57       1     210 [.     134     357 ..     134     358 .. 0.87
   2 !  114.3   0.0   2.6e-36   5.3e-33       1     210 [.     697     906 ..     697     907 .. 0.92

  Alignments for each domain:
  == domain 1  score: 192.8 bits;  conditional E-value: 2.6e-60
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHH............HHHHHHH.-SSEEEEETTCCTTTTEEEESSHHHHH CS
                       CPSase_L_D2   1 Dkesakealkkinvpvvpssaapvetleea............laiakei.gyPviikaafglGGkGmrvarneeela 64 
                                       D++ +++ ++ki++pv  s++   e+ ee+             a+++e+ g Pvi +++++lGG+G++v+++ +el 
  gi|336255236|ref|YP_004598343.1| 134 DRDLFRQRMEKIDQPVPGSTTISLEEGEEVselteedlrervQAAVDEVgGLPVIARTTYTLGGSGSGVVHDFDELL 210
                                       999************9988877655444431111111111113344555479************************* PP

                                       HHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHH CS
                       CPSase_L_D2  65 elvkkalaeakaafgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerq 139
                                       + v+k+l+ ++    n++vl+ +s++g+ e+E+ev+rDa++ +i++c++en++++  +t+++ +v Psq + de +q
  gi|336255236|ref|YP_004598343.1| 211 QRVRKGLRLSR----NSEVLITESIAGWVEYEYEVMRDADDSCIIICNMENIDPMgiHTGESTVVTPSQIVPDEGHQ 283
                                       **********7....9************************************************************* PP

                                       HHHHHHHHHHHHHT-EEEEEEEEEEET...TTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 140 alreaavkvvrevgvvgagtveflldp...kskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       ++r+aa+ v+re+g++g+++++f+        +ey v+EvN+R+s++sala+kaTG++++ ++ak+alg++L+e
  gi|336255236|ref|YP_004598343.1| 284 EMRTAALDVIRELGIQGGCNIQFAWRDdgtPGGEYRVVEVNPRVSRSSALASKATGYPIARVTAKVALGKRLHE 357
                                       ************************987232368***************************************87 PP

  == domain 2  score: 114.3 bits;  conditional E-value: 2.6e-36
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D+++++++++++++   ++ +a   + eeal++a++igyPv++++++ lGG+ m +++++eel+  +++a++ ++  
  gi|336255236|ref|YP_004598343.1| 697 DRDRFNALMDELEISQPDGGTA--FSKEEALQLAHDIGYPVLVRPSYVLGGRAMDIVYSDEELETYIEEAVRVSP-- 769
                                       99*****************999..99************************************************7.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                         +k +lv+ +l+   e++v+ ++D ++  i  + +e +     + +++  + P + L++++  ++re +  +++ +
  gi|336255236|ref|YP_004598343.1| 770 --DKPILVDDFLEDAVELDVDAVSDGRDVLIG-GIMEHVESAgvHSGDSACMIPPRSLDADTLARVREVTEDIAEGL 843
                                       ..9************************97774.44555444444********************************* PP

                                       T-EEEEEEEEEE....ET.TTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 153 gvvgagtvefll....dp.kskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       + +g  +v+ ++    dp  + e yv+E N+R s+  +  +kaTG++++k aak+ +ge+L+ 
  gi|336255236|ref|YP_004598343.1| 844 KTKGLLNVQLAVtgvhDPdAEPEVYVLEANPRSSRTVPYVSKATGVPIAKLAAKVMAGETLSS 906
                                       ***********933332335679*************************************985 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 !   83.5   0.1   7.1e-27   1.4e-23       2     121 ..     444     551 ..     443     551 .. 0.90

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 7.1e-27
                       CPSase_L_D3   2 elkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkkeldeellreakklGfsDkqiae 78 
                                       +l++p+++R +a++ea++rg++ ee+ +lt i +w+ e++++++e  ++ ++         ++ea  +G ++++ia+
  gi|336255236|ref|YP_004598343.1| 444 YLERPSPDRPYAMFEAFDRGYTTEEVVDLTGIFEWYTERYKRIAESTRAAQEG-------DFTEAAIAGRTNATIAA 513
                                       799******************************************99996555.......69*************** PP

                       CPSase_L_D3  79 lleeeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYst 121
                                        ++     +v ++ +++    +yk+vDtcA+eFeaetpY+Ys+
  gi|336255236|ref|YP_004598343.1| 514 AAG-A---DVDTVEQEVP-GRTYKQVDTCAGEFEAETPYYYSS 551
                                       976.3...4666666666.469*******************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 !   20.3   0.0   1.8e-07   0.00036      46     122 ..     282     364 ..     275     372 .. 0.81
   2 !   21.0   0.0   1.1e-07   0.00022      47     121 ..     830     912 ..     770     922 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.8e-07
                      ATPgrasp_Ter  46 deelielaerlaeefgldglvnvQvrededg.p....kLLEiNpRasGGlg.ysalaGvnlpylalklllgleteev 116
                                       ++e+  +a ++++e+g++g  n+Q+ +++dg p    ++ E+NpR+s      s ++G  ++++ +k +lg+  +e+
  gi|336255236|ref|YP_004598343.1| 282 HQEMRTAALDVIRELGIQGGCNIQFAWRDDGtPggeyRVVEVNPRVSRSSAlASKATGYPIARVTAKVALGKRLHEI 358
                                       678889999****************9988755444449********96555156777**************987777 PP

                      ATPgrasp_Ter 117 eepeeg 122
                                       e+  +g
  gi|336255236|ref|YP_004598343.1| 359 ENEITG 364
                                       776655 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.1e-07
                      ATPgrasp_Ter  47 eelielaerlaeefgldglvnvQvred.....edg..pkLLEiNpRasGGlgy.salaGvnlpylalklllgletee 115
                                       +++ e++e++ae ++ +gl nvQ+  +     +++   ++LE NpR s ++ y s ++Gv +++la+k + g+  + 
  gi|336255236|ref|YP_004598343.1| 830 ARVREVTEDIAEGLKTKGLLNVQLAVTgvhdpDAEpeVYVLEANPRSSRTVPYvSKATGVPIAKLAAKVMAGETLSS 906
                                       56789999***************8653111113332479***********97736677**************74444 PP

                      ATPgrasp_Ter 116 veepee 121
                                        e++e+
  gi|336255236|ref|YP_004598343.1| 907 LEAQEQ 912
                                       444443 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   2.8e-05     0.056      16     160 ..     171     327 ..     158     335 .. 0.78
   2 !   21.8   0.0   5.7e-08   0.00011       5     159 ..     709     875 ..     705     879 .. 0.82
   3 ?   -2.3   0.1       1.4   2.9e+03      59      83 ..    1019    1050 ..    1000    1054 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                                       CHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEEEEEEEEETTC CS
                         ATP-grasp  16 skeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekElsvlvvrsaeG 88 
                                        +e +++a++e+g   v+ + +    G G+ vv++ ++l q ++      ++ +v++ e +   +E    v+r+a+ 
  gi|336255236|ref|YP_004598343.1| 171 LRERVQAAVDEVGGLPVIARTTYTLGGSGSGVVHDFDELLQRVRKGlrlsRNSEVLITESIAGWVEYEYEVMRDADD 247
                                       45689999****888888889**************9887766665558886777766665555555555579***** PP

                                       -EEE--EEEEEEETTEEE...EEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCT....EEEEEEE CS
                         ATP-grasp  89 etafypvvetvqedgilr...lsvapaevsek.aqkkaeeiakkiveeLggvGvfavElFvledge....llvnEla 157
                                       +  ++  +e++   gi     ++v p+++  +  +++ ++ a ++++eLg+ G   + +   +dg+      v E+ 
  gi|336255236|ref|YP_004598343.1| 248 SCIIICNMENIDPMGIHTgesTVVTPSQIVPDeGHQEMRTAALDVIRELGIQGGCNIQFAWRDDGTpggeYRVVEVN 324
                                       ****99******9999853337899998755516777788888**********999999888887777778888888 PP

                                       SS- CS
                         ATP-grasp 158 pRp 160
                                       pR+
  gi|336255236|ref|YP_004598343.1| 325 PRV 327
                                       887 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 5.7e-08
                                       T--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEE CS
                         ATP-grasp   5 glpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekE 77 
                                       +++ p+  ++ skee+ ++a+++g+pv+v+ +     G+   +v s+e+le+ +e++     +++++v +f +  +E
  gi|336255236|ref|YP_004598343.1| 709 EISQPDGGTAFSKEEALQLAHDIGYPVLVR-PSYVLGGRAMDIVYSDEELETYIEEAvrvsPDKPILVDDFLEDAVE 784
                                       556666666778899999************.99999****************99999999899************** PP

                                       EEEEEEEETTC-EEE--EEEEEEETTE....EEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEE..TT CS
                         ATP-grasp  78 lsvlvvrsaeGetafypvvetvqedgi....lrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvl..ed 148
                                       l v +v + +  + +  ++e+v++ g+        + p +++++ +++++e++++i+e L   G++ v l v+  +d
  gi|336255236|ref|YP_004598343.1| 785 LDVDAVSDGRD-VLIGGIMEHVESAGVhsgdSACMIPPRSLDADTLARVREVTEDIAEGLKTKGLLNVQLAVTgvHD 860
                                       ******98776.6777777777765541111567788999999**************************99985533 PP

                                       CT....EEEEEEESS CS
                         ATP-grasp 149 ge....llvnElapR 159
                                        +    ++v E  pR
  gi|336255236|ref|YP_004598343.1| 861 PDaepeVYVLEANPR 875
                                       223456777777777 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.4
                                        HHC.......GTTCEEEEE----SEEEEEEEE CS
                         ATP-grasp   59 eal.......keekvivEefvpfekElsvlvv 83  
                                        e+        ++ + +vE   +fe El v +v
  gi|336255236|ref|YP_004598343.1| 1019 EEEipylsteASAEAYVEALESFEGELEVDTV 1050
                                        33334444445788999999999999877555 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 !    7.8   0.0    0.0011       2.1      24     173 ..     172     324 ..     155     327 .. 0.72
   2 !   24.9   0.0   6.3e-09   1.2e-05      25     173 ..     721     873 ..     710     898 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                                       H-HHHHHHHHHC-SSEEEEESSS..STTTTEEEESSGGGHHHHHHHHHT..T-SCEEEEE--.ESEEEEEEEEETSS CS
                   Dala_Dala_lig_C  24 kkellekveeelgypvfVKpare..GSSvGvskveseeelkeaieeafk..ydekvlvEeai.egreievavlgnek 95 
                                       ++ ++++v e  g+pv+ +   +  GS  G   v+  +el + +++ ++  ++++vl+ e i    e e  v+ + +
  gi|336255236|ref|YP_004598343.1| 172 RERVQAAVDEVGGLPVIARTTYTlgGS--GSGVVHDFDELLQRVRKGLRlsRNSEVLITESIaGWVEYEYEVMRDAD 246
                                       445678888888999999987542144..6666999999999999876522678999999996778*******9555 PP

                                       CEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTT....EEE CS
                   Dala_Dala_lig_C  96 levsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteeg....eiv 168
                                         +     i+ + + +d    ++++++ ++    +++e +++++++al++ + l+++G + + f  +++g    e  
  gi|336255236|ref|YP_004598343.1| 247 DSCI----IICNMENIDPMGIHTGESTVVTPSQIVPDEGHQEMRTAALDVIRELGIQGGCNIQFAWRDDGtpggEYR 319
                                       4443....44444555555556666666666667899999************************9987761111456 PP

                                       EEEEE CS
                   Dala_Dala_lig_C 169 lnEvN 173
                                       + EvN
  gi|336255236|ref|YP_004598343.1| 320 VVEVN 324
                                       66666 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 6.3e-09
                                       -HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT..-SCEEEEE--.ESEEEEE.EEEETSSCE CS
                   Dala_Dala_lig_C  25 kellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky..dekvlvEeai.egreiev.avlgnekle 97 
                                       ke   ++ + +gypv+V+p+       +  v s eel+ +ieea++   d+ +lv+ ++ ++ e++v av +  ++ 
  gi|336255236|ref|YP_004598343.1| 721 KEEALQLAHDIGYPVLVRPSYVLGGRAMDIVYSDEELETYIEEAVRVspDKPILVDDFLeDAVELDVdAVSDGRDVL 797
                                       4556788999**********98778889****************97655999*******99******5555566799 PP

                                       EEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEE......TTTEEE CS
                   Dala_Dala_lig_C  98 vsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflt......eegeiv 168
                                       +  + e+v + g+       s+d+a +  p +l++++ ++++e+  ++ + l+ +Gl  v + +t      +e e++
  gi|336255236|ref|YP_004598343.1| 798 IGGIMEHVESAGVH------SGDSACMIPPRSLDADTLARVREVTEDIAEGLKTKGLLNVQLAVTgvhdpdAEPEVY 868
                                       99******999986......578899999999***********************9999998875222222455666 PP

                                       EEEEE CS
                   Dala_Dala_lig_C 169 lnEvN 173
                                       + E N
  gi|336255236|ref|YP_004598343.1| 869 VLEAN 873
                                       66666 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   6.3e-06     0.012      33     158 ..     186     327 ..     137     330 .. 0.79
   2 !   11.9   0.0   8.8e-05      0.18      15     157 ..     709     875 ..     695     879 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.3e-06
                                       SEEEEESS-------B--SS--TTE...............EEEE---S.EEEEEEEEE.SSSEEEEEEEEEEEET.. CS
                       ATP-grasp_3  33 klvvKprdGaggesvrvveekeeaeaaieeve........lvqefieG.kplSvsllsdgekvlvlavnrqliekae 100
                                       ++++   +  gg++  vv++++e+ + + +          l+ e i G  ++  +++ d+ +  ++ +n + i+  +
  gi|336255236|ref|YP_004598343.1| 186 PVIARTTYTLGGSGSGVVHDFDELLQRVRKGLrlsrnsevLITESIAGwVEYEYEVMRDADDSCIIICNMENIDPMG 262
                                       5666667777777777777777766555544456667777999999995689999999999999999**99999866 PP

                                       ..TEEEEEEES----H...HHHHHHHHHHHHTTSTT--EEEEEEEEESS......SEEEEEEESS- CS
                       ATP-grasp_3 101 kefvyaGnvtpietel...keevvelaeevvekleglaGyvGvDlvlkd.....eepyviEvNPRl 158
                                        +   +  vtp++      ++e++++a +v+++l g+ G   + +  +d     +e  v+EvNPR+
  gi|336255236|ref|YP_004598343.1| 263 IHTGESTVVTPSQIVPdegHQEMRTAALDVIREL-GIQGGCNIQFAWRDdgtpgGEYRVVEVNPRV 327
                                       655555556777665544589*************.***********999888877889*******8 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 8.8e-05
                                       .S---.......-EESS--....SSSEEEEESS-------B--SS--TTE...............EEEE---.SEEE CS
                       ATP-grasp_3  15 gvkvP...tkleaeeleee....ekklvvKprdGaggesvrvveekeeaeaaieeve........lvqefie.Gkpl 75 
                                       ++  P   t  ++ee+ +      +++ v p++  gg ++ +v  +ee+e+ iee          lv +f+e   +l
  gi|336255236|ref|YP_004598343.1| 709 EISQPdggTAFSKEEALQLahdiGYPVLVRPSYVLGGRAMDIVYSDEELETYIEEAVrvspdkpiLVDDFLEdAVEL 785
                                       6667766644444444433444599****************************99989*************94579* PP

                                       EEEEEE.SSSEEEEEEEEEEEET....TEEEE...EEES----HHHHHHHHHHHHHTTST...T--EEEEEEEEESS CS
                       ATP-grasp_3  76 SvsllsdgekvlvlavnrqliekaekefvyaG...nvtpietelkeevvelaeevvekle...glaGyvGvDlvlkd 146
                                        v+++sdg +vl+  + + +        v +G   +++p + +l+ ++ + ++ev+e++    +++G++ v l ++ 
  gi|336255236|ref|YP_004598343.1| 786 DVDAVSDGRDVLIGGIMEHVESA----GVHSGdsaCMIPPR-SLDADTLARVREVTEDIAeglKTKGLLNVQLAVTG 857
                                       ********999988887766654....55555111455544.445555555556666655544899******99655 PP

                                       ........SEEEEEEESS CS
                       ATP-grasp_3 147 .......eepyviEvNPR 157
                                               e yv+E NPR
  gi|336255236|ref|YP_004598343.1| 858 vhdpdaePEVYVLEANPR 875
                                       4446665799******** PP

>> HDV_ag  Hepatitis delta virus delta antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.3e-05     0.025     110     169 ..     143     204 ..     123     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                            HDV_ag 110 nkrkqlsaggknlskeeeeelrrlteederrerriagpqvggvnplegg..trgapgggfvp 169
                                       +k  q   g   +s ee ee+  lteed r   + a  +vgg+  +     t g  g g+v 
  gi|336255236|ref|YP_004598343.1| 143 EKIDQPVPGSTTISLEEGEEVSELTEEDLRERVQAAVDEVGGLPVIARTtyTLGGSGSGVVH 204
                                       46678888999******************99999999*****87776551145667777765 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 ?    4.0   0.0     0.043        86       3      87 ..      16     113 ..      14     119 .. 0.65
   2 ?   -2.0   0.0         3     6e+03      25      49 ..     469     493 ..     457     514 .. 0.77
   3 ?    5.6   0.1     0.014        28       6      67 ..     947    1007 ..     945    1020 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.043
                                       EEEETTSHH..HHHHHHHHHHTTTTE.........EEEEEECSSHHHHHHH...HHHTTHE..EESSHHHHHTCTTE CS
                      GFO_IDH_MocA   3 vaiiGaGki..gskhlrplnesqrle.........evvalldpdaeraeav...aesfgve..aysdleelladpei 63 
                                       +++iG+G i  g  +++ +  s  ++         evv l++++++   +    a++  +e    + ++e+ +++++
  gi|336255236|ref|YP_004598343.1|  16 ILLIGSGPIqiG--QAAEFDYSGAQAcralqeegaEVV-LVNSNPATIMTDpemADEVYIEpiTTDAIAEIIKKENP 89 
                                       677777777542..222223222222333344332333.55555554443366799999996555559********* PP

                                       SEEEE-S-GGGHHHHHHHHHHTT- CS
                      GFO_IDH_MocA  64 davivatpngtheelakaaleagk 87 
                                       d vi +   +t+ +++ +++e g+
  gi|336255236|ref|YP_004598343.1|  90 DGVIAGLGGQTGLNVTAELAEEGV 113
                                       ***************999999886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3
                                       TEEEEEEECSSHHHHHHHHHHTTHE CS
                      GFO_IDH_MocA  25 leevvalldpdaeraeavaesfgve 49 
                                         +++++++  +er +++aes++++
  gi|336255236|ref|YP_004598343.1| 469 VVDLTGIFEWYTERYKRIAESTRAA 493
                                       348999************9999887 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.014
                                        ETT.SHHHHHHHHHHHHTTTTE.EEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEE CS
                      GFO_IDH_MocA    6 iGa.Gkigskhlrplnesqrle.evvalldpdaeraeavaesfgveaysdleelladpeidavi 67  
                                         G+ G +g+ ++++ ++++++  e +a++d d    e   e+f+++ ++d+ +  ++ ++d+v+
  gi|336255236|ref|YP_004598343.1|  947 MGTaGDFGTAYWKAQQAAHNDVsEGTAVVDLDVDGFE---EHFDIAEFDDVPQAIREGKVDFVV 1007
                                        57769999999988888766667*********98877...68**************99999986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0037       7.4      22      74 ..      41     111 ..      33     123 .. 0.83
   2 ?   -3.4   0.2       4.7   9.3e+03      81      91 ..     578     587 ..     572     594 .. 0.65
   3 ?    0.1   0.0      0.38   7.7e+02      25      59 ..     607     659 ..     600     679 .. 0.67
   4 ?   -2.4   0.0       2.3   4.7e+03      24      52 ..     675     703 ..     671     712 .. 0.78
   5 ?   -1.8   0.1       1.5   2.9e+03      31      56 ..     974    1007 ..     954    1015 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0037
                       B12-binding  22 aalrdagfeVqllganven..................edivaairaekpdvvglSalltsqleavkelvel 74 
                                       +al+++g eV+l++ n  +                  ++i++ i++e+pd v   +  ++ l+ ++el+e+
  gi|336255236|ref|YP_004598343.1|  41 RALQEEGAEVVLVNSNPATimtdpemadevyiepittDAIAEIIKKENPDGVIAGLGGQTGLNVTAELAEE 111
                                       789999****999888888888999999999999*****************98877788888888888877 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.7
                       B12-binding  81 rvkvvvGGahp 91 
                                        v+vv GG+  
  gi|336255236|ref|YP_004598343.1| 578 SVIVVGGGP-I 587
                                       456666665.4 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.38
                       B12-binding  25 rdagfeVqllganven..................edivaairaekpdvvglSa 59 
                                       r+ g++ ++++ n e+                  e++++ ++a+ +d v++ +
  gi|336255236|ref|YP_004598343.1| 607 RELGIDAHVVNNNPETvstdydtsdglffepitaEEVADVAEATGADGVMVQF 659
                                       55555555554444444444444446666668889999999999999999865 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 2.3
                       B12-binding  24 lrdagfeVqllganvenedivaairaekp 52 
                                       l+++g +++++g  ve+ d+++   ++++
  gi|336255236|ref|YP_004598343.1| 675 LERRGLDCEIMGTSVEAMDLAEDRDRFNA 703
                                       67889999999999999887776666655 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 1.5
                       B12-binding   31 Vqllganven........edivaairaekpdvvg 56  
                                        V++l+++           +d+ +air+ k+d+v+
  gi|336255236|ref|YP_004598343.1|  974 VVDLDVDGFEehfdiaefDDVPQAIREGKVDFVV 1007
                                        55554444335677777799999********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1066 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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: 0.78u 0.24s 00:00:01.02 Elapsed: 00:00:00.40
# Mc/sec: 8094.41
//
Query:       gi|336255237|ref|YP_004598344.1|  [L=114]
Description: hypothetical protein Halxa_3860 [Halopiger xanaduensis SH-6]
Scores for 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:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1007.88
//
Query:       gi|336255238|ref|YP_004598345.1|  [L=178]
Description: hypothetical protein Halxa_3861 [Halopiger xanaduensis SH-6]
Scores for 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  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1412.30
//
Query:       gi|336255239|ref|YP_004598346.1|  [L=252]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-11   42.3   0.0    1.5e-10   41.5   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    2.4e-09   37.8   0.1    6.6e-09   36.4   0.1    1.7  1  Methyltransf_25  Methyltransferase domain
    8.4e-05   22.5   0.0    0.00012   21.9   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    0.00012   22.7   0.1    0.00026   21.7   0.1    1.6  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.048   14.7   0.3      0.098   13.7   0.3    1.5  1  Methyltransf_24  Methyltransferase domain
       0.12   12.0   0.0       0.19   11.4   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95


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 !   41.5   0.0   5.2e-14   1.5e-10       1      96 []      22     132 ..      22     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 5.2e-14
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHH.....HHHCCHHT-............EEEETTEECCCTSS-T CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlkla.....kekaseegl............kvefvvadaeklpfed 59 
                                       L++G+G+G  ++ l  rg arv++v  + e  ++      +++                  ++ +++ad++k+p++ 
  gi|336255239|ref|YP_004598346.1|  22 LEAGAGAGNTTAGLLTRGaARVYAVTNDREHARTTvnrvlEDE-----DgdddnsaddrtdRLAVLEADLRKIPLPG 93 
                                       799************9999******988888755433333333.....23444588888899999************ PP

                                       T-EEEEEEES-CCC-..CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  60 nsfDlvvssevlhhv..edpekalkeiaRvLkpgGllvi 96 
                                       +s+Dlv+++  ++ +  +d+e + +e+ Rv  pg +lvi
  gi|336255239|ref|YP_004598346.1|  94 DSVDLVTAHGLFNVLppADLETVAAELTRVAAPGCHLVI 132
                                       ***************999****************99986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1   2.2e-12   6.6e-09       2      96 ..      22     127 ..      21     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2.2e-12
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH.......TTT......TEEEEESBCCGBSSSTTTE CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee.......egl......nvefvqgdaedlpfedgsf 65 
                                       L++G+G G++t+ l++r g+a+v++v  + e  +++ +r+ e       +        ++ ++++d++++p++ +s+
  gi|336255239|ref|YP_004598346.1|  22 LEAGAGAGNTTAGLLTR-GAARVYAVTNDREHARTTVNRVLEdedgdddN-SaddrtdRLAVLEADLRKIPLPGDSV 96 
                                       89***************.69******999999988886665545444431.1466678******************* PP

                                       EEEEEESTGGGSSHHHHHHHHHHHHHHEEEE CS
                   Methyltransf_25  66 DlvvssgalhhlsdedlekalkeiarvLkpg 96 
                                       Dlv++ g +++l+++dle++ +e+ rv  pg
  gi|336255239|ref|YP_004598346.1|  97 DLVTAHGLFNVLPPADLETVAAELTRVAAPG 127
                                       *****877********************998 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   4.1e-08   0.00012      18     161 ..      13     182 ..       3     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.1e-08
                   Methyltransf_23  18 pklraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiaekakkaqkdqfdeqeaae............... 78 
                                       ++  +g+ +L+ G+G G+++  l ++g+  v++v  ++e      ++     d  d ++a++               
  gi|336255239|ref|YP_004598346.1|  13 DRPVEGAVCLEAGAGAGNTTAGLLTRGAaRVYAVTNDREHARTTVNRVLEDEDGDDDNSADDrtdrlavleadlrki 89 
                                       44567899*********999999999987888887765433332233333333333333333444444454555555 PP

                   Methyltransf_23  79 ..pqgkfdlIvlrevlehvp..dppellrqiatllkpgGylllse..plasl.kedrl.lldw.lylvpagrhi..s 144
                                         p ++ dl+++  +++ +p  d++ + + + +  +pg +l++ +  pl ++ + ++l +l++ +++ ++gr     
  gi|336255239|ref|YP_004598346.1|  90 plPGDSVDLVTAHGLFNVLPpaDLETVAAELTRVAAPGCHLVIDDyePLPDDaAVRKLfALENaAAELTDGR-PalT 165
                                       55666***************888**********************554444433444443334144444442.235* PP

                   Methyltransf_23 145 ffsarslkelleeaGle 161
                                       f+ a  l++l+ ++G+e
  gi|336255239|ref|YP_004598346.1| 166 FYPAAVLRRLFAGYGWE 182
                                       ***************98 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   8.7e-08   0.00026       1      99 []      22     130 ..      22     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 8.7e-08
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.........ssfD 68 
                                       Le G+G G++++ ll +   +++++v  +++    + ++  + e+ + +n   + +d l   +          +s+D
  gi|336255239|ref|YP_004598346.1|  22 LEAGAGAGNTTAGLLTR-GAARVYAVTNDREHARTTVNRVLEDEDGDDDNSADDRTDRLAVLEAdlrkiplpgDSVD 97 
                                       899**************.7777777766666665666666666666666666665555555555788********** PP

                   Methyltransf_12  69 lvvasnvlhhl..kdirevldnirklLkpgGrl 99 
                                       lv+a++++++l  +d++ v +++ ++ +pg +l
  gi|336255239|ref|YP_004598346.1|  98 LVTAHGLFNVLppADLETVAAELTRVAAPGCHL 130
                                       ******************************986 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   3.3e-05     0.098       1     106 []      22     135 ..      22     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                   Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare.............aglddrvrlikadseealas 64 
                                       +E G+ +G++t+ ll     +ga r++av +d++  +a+  +++                +dr+ +++ad+++    
  gi|336255239|ref|YP_004598346.1|  22 LEAGAGAGNTTAGLL----TRGAARVYAVTNDRE--HARTTVNRvlededgdddnsaDDRTDRLAVLEADLRKI--P 90 
                                       799999******999....455569******994..44444443344477777766677788899999999998..5 PP

                   Methyltransf_24  65 laagsiDllfiDgghaa..eavledlea.llprlapggvvlfdDi 106
                                       l  +s+Dl+   g  +    a le + a l ++ apg+ +++dD+
  gi|336255239|ref|YP_004598346.1|  91 LPGDSVDLVTAHGLFNVlpPADLETVAAeLTRVAAPGCHLVIDDY 135
                                       66778*****9997764446666666550556666*********8 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.2e-05      0.19      39      79 ..      14      55 ..       3      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.2e-05
                                      C.HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHH CS
                     Cons_hypoth95 39 e.iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavki 79
                                      + +ega +L+  aG G      l Rga+++++v +d+e +++
  gi|336255239|ref|YP_004598346.1| 14 RpVEGAVCLEAGAGAGNTTAGLLTRGAARVYAVTNDREHART 55
                                      45899******************************9987764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2068.07
//
Query:       gi|336255240|ref|YP_004598347.1|  [L=294]
Description: aldo/keto reductase [Halopiger xanaduensis SH-6]
Scores for 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-22   79.6   0.0    2.7e-22   79.3   0.0    1.1  1  Aldo_ket_red  Aldo/keto reductase family


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 !   79.3   0.0   1.5e-26   2.7e-22       4     238 ..      18     272 ..      16     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1.5e-26
                                       EE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTSSS CS
                      Aldo_ket_red   4 lGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeiksg 80 
                                       +G+ +l++    ++e a+++++++l++G+n+fD+A+ Y  g +e  lG  l +    ree+ + +K         + 
  gi|336255240|ref|YP_004598347.1|  18 FGAIALNW---LEQEGANQMVEQVLDYGVNHFDVAPTY--GDAELKLGPKLRQ---HREEIYLGCKT--------QE 78 
                                       67777776...69999**********************..*********9999...***********........99 PP

                                       S-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHH......HHHHHHHHTTSEEEEEEES--.HHHHHHHH CS
                      Aldo_ket_red  81 lskeniresleeslkrLgtdyvDllllHrpdpslpsieevl......daleelvkeGkiraiGvSnfs.veqlekak 150
                                        + e  r++le+sl rLg+d++Dl+++H  +++++ +e ++      +a+ + ++eG+i  iG++++   + +  a 
  gi|336255240|ref|YP_004598347.1|  79 REYEGARRKLERSLDRLGVDRIDLYQIHGLEYEHE-LETIAgeggalEAFRDAQDEGLIGDIGLTSHGdPQLILDA- 153
                                       999********************************.4444488877789999999**********99887765555. PP

                                       HTTT--EEEEE-B-BTT......-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------.. CS
                      Aldo_ket_red 151 kkkkvkivavqveynll......releeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd.. 219
                                        ++  ++++v+   n++      +e + e +le ++++g+++  + ++++G+  +  + +e   +  +  +  ++  
  gi|336255240|ref|YP_004598347.1| 154 IDRIDDLSTVMFPLNPVvagkddDEYDYEAVLERAEEEGIGTLGIKAFAKGSWPSTDELPEADRPYANWYEPVDRpd 230
                                       599999**************9999999999********************987766555544333222222111134 PP

                                       .......................TS-HHHHHHHHHHHHHHHH CS
                      Aldo_ket_red 220 .......................ertsknldaaeelselake 238
                                                              + ++  ldaa++++el ++
  gi|336255240|ref|YP_004598347.1| 231 eirdrfdfaasqglttvvtpgdpKLVAMVLDAADRYEELSES 272
                                       444445555555555666655555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2499.56
//
Query:       gi|336255241|ref|YP_004598348.1|  [L=136]
Description: hypothetical protein Halxa_3864 [Halopiger xanaduensis SH-6]
Scores for 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:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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: 0.40u 0.18s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1124.15
//
Query:       gi|336255242|ref|YP_004598349.1|  [L=78]
Description: hypothetical protein Halxa_3865 [Halopiger xanaduensis SH-6]
Scores for 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   14.7   0.7        1.3    9.0   0.1    2.3  2  EF-hand_10      EF hand
       0.14   12.4   0.0       0.19   12.0   0.0    1.2  1  Chordopox_A13L  Chordopoxvirus A13L protein
       0.16   12.2   0.0        0.2   11.8   0.0    1.2  1  PYRIN           PAAD/DAPIN/Pyrin domain


Domain annotation for each model (and alignments):
>> EF-hand_10  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00021       1.3      36      50 .]      34      48 ..      31      48 .. 0.91
   2 ?    4.2   0.0    0.0068        40      37      48 ..      60      71 ..      56      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00021
                        EF-hand_10 36 grLegeEieeFyklL 50
                                      ++Le  E++eFy+lL
  gi|336255242|ref|YP_004598349.1| 34 DQLETDEFQEFYNLL 48
                                      89**********997 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0068
                        EF-hand_10 37 rLegeEieeFyk 48
                                       Le+ Ei+ F +
  gi|336255242|ref|YP_004598349.1| 60 ALEDGEIVVFTD 71
                                      7*********76 PP

>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.2e-05      0.19      37      67 ..      21      49 ..      14      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                    Chordopox_A13L 37 veeyeeedniKtgfvdkLksdhlkslykLfs 67
                                      ve  e++  ++  +vd+L+ d ++ +y+L++
  gi|336255242|ref|YP_004598349.1| 21 VESVESNATVR--HVDQLETDEFQEFYNLLE 49
                                      56666676665..9**************985 PP

>> PYRIN  PAAD/DAPIN/Pyrin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.3e-05       0.2       7      37 ..      34      62 ..      30      71 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                                      CCC-HHHHHHHHHHHHH.--SSSHTT..HCCHC CS
                             PYRIN  7 eeLseeelkkFKslLkeeeeglksip..rgele 37
                                      ++L+ +e+++F +lL++     +++p  ++ le
  gi|336255242|ref|YP_004598349.1| 34 DQLETDEFQEFYNLLED----GQPLPadETALE 62
                                      79*************76....344442255554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 665.15
//
Query:       gi|336255243|ref|YP_004598350.1|  [L=336]
Description: Exosortase EpsH-like protein [Halopiger xanaduensis SH-6]
Scores for 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-15   54.9  13.8      9e-15   54.9  13.8    1.5  1  Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
  ------ inclusion threshold ------
      0.011   15.3   0.6      0.011   15.3   0.6    2.7  3  DUF5336          Family of unknown function (DUF5336)
      0.014   15.4   0.0      0.044   13.8   0.0    1.8  2  BACON            Putative binding domain, N-terminal


Domain annotation for each model (and alignments):
>> Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9  13.8   1.5e-18     9e-15      29     221 ..      38     242 ..      24     252 .. 0.71

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1.5e-18
                   Exosortase_EpsH  29 llvpllalyllwdrwrr....al.aasasllgllll..llglfl.lallgels.rvlllsalslvlillglvllllG 96 
                                       ++ +++ +  l+ rwr     a+  a++++l   ++  ++++++  ++   +s  ++lls  +l+l+++  +l+l  
  gi|336255243|ref|YP_004598350.1|  38 WIAIGAFFAALALRWRGadrpARlTAAGGWL---AFgtFWLTMVpYFYYEMQSpLETLLSVAALPLCAYTGYLMLQD 111
                                       4444444444556788843343324444444...4433444444435555555689999999999************ PP

                   Exosortase_EpsH  97 lralrlllfpllll.llalPlpavlvaqlslpLqllvaavagfllsllg....ipvereGnviqlptg......... 159
                                       +r l+ll  +++++ l++lP  a +++ ++ +L++ +aa++ f ++llg    i    eG   ++ +          
  gi|336255243|ref|YP_004598350.1| 112 RRSLFLLTKAVAFMgLIYLP--AETIPFVREWLIETTAAQTHFGMELLGhspgI---NEGANGYMSRFnfdpnetat 183
                                       ********************..9999999********************85553...34433333333233455667 PP

                   Exosortase_EpsH 160 ..qveVaeaCsGlrsllallalglllallfrrrlw.krklllllaavpiaflaNlvRilllvlla 221
                                         +  ++  C+Gl s+  ++ l      + +++++ k+kl  +++a+ +++++Nl+R+++++l+ 
  gi|336255243|ref|YP_004598350.1| 184 grTTYIVLSCTGLGSMAIFGGL------IAAVSAPlKQKLSAFALAIGVIWFLNLIRNVFIGLAS 242
                                       66799*******5555544444......444444445559999*******************985 PP

>> DUF5336  Family of unknown function (DUF5336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.5      0.12   7.4e+02      69     104 ..      24      59 ..      11      72 .. 0.75
   2 ?   -2.3   0.1      0.51     3e+03      36      48 ..     116     128 ..     113     133 .. 0.86
   3 ?   15.3   0.6   1.9e-06     0.011      66     124 ..     183     239 ..     166     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
                           DUF5336  69 easatsgglglavvllLlagLlAgvslLPkqkskta 104
                                        as t ggl+ a+v   +++ +A+++l  ++ ++ a
  gi|336255243|ref|YP_004598350.1|  24 LASSTGGGLSDAIVWIAIGAFFAALALRWRGADRPA 59 
                                       4566778888889999999*****999766665555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.51
                           DUF5336  36 lyLsiavaaLGli 48 
                                       ++L+ ava +Gli
  gi|336255243|ref|YP_004598350.1| 116 FLLTKAVAFMGLI 128
                                       689999****998 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.9e-06
                           DUF5336  66 dleeasatsgglglavvllLlagLlAgvslLPkqksktavaAvlsvlgfLlvlaevina 124
                                       + +++ ++ + +gl   +++++gL+A+vs   kqk   a+a ++ v+ fL ++ +v+  
  gi|336255243|ref|YP_004598350.1| 183 TGRTTYIVLSCTGL-GSMAIFGGLIAAVSAPLKQK-LSAFALAIGVIWFLNLIRNVFIG 239
                                       34444455555555.6799***********99999.9****************999864 PP

>> BACON  Putative binding domain, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.4e-06     0.044      22      44 ..     174     196 ..     157     202 .. 0.91
   2 ?   -3.7   0.0       2.1   1.3e+04       9      14 ..     249     253 ..     248     274 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.4e-06
                             BACON  22 vtvaaNtsgeeRtatitvtagsg 44 
                                       ++ ++N++ + Rt++i++++++ 
  gi|336255243|ref|YP_004598350.1| 174 FNFDPNETATGRTTYIVLSCTGL 196
                                       789*****************876 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.1
                             BACON   9 adWltv 14 
                                       +dWl v
  gi|336255243|ref|YP_004598350.1| 249 QDWL-V 253
                                       6898.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2550.59
//
Query:       gi|336255244|ref|YP_004598351.1|  [L=269]
Description: metallophosphoesterase [Halopiger xanaduensis SH-6]
Scores for 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   28.1   0.2    6.6e-06   26.8   0.2    1.5  1  Metallophos    Calcineurin-like phosphoesterase
    1.5e-05   25.2   0.2    2.2e-05   24.7   0.2    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
       0.18   11.2   0.0       0.35   10.3   0.0    1.4  1  Aldolase       KDPG and KHG aldolase


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 !   26.8   0.2   1.1e-09   6.6e-06       4     123 ..      46     160 ..      44     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.1e-09
                                       EEEESBTB............TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.HHHHHHHHHHHHHHHH.... CS
                       Metallophos   4 lvigDlHl............algggqlddllkllddllreekpdlvllaGDlvdrg.dlekellellaalvky.... 63 
                                       l+++D+Hl            ++g    d+l+ ll+++    ++  v++aGDl +   ++++ +++ l+al +     
  gi|336255244|ref|YP_004598351.1|  46 LLVADVHLgraaassvdapiDDGADVRDRLASLLERT----GAGTVVVAGDLLHSFnSVPHGVARDLSALESAvtaa 118
                                       789**********888866666666666666666555....8889999***99997744444555555555544555 PP

                                       TSEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE CS
                       Metallophos  64 pipvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg 123
                                       +  +++++GNH+     +l   + +         d+ev++ + la+   g  +++++hG+
  gi|336255244|ref|YP_004598351.1| 119 GADFVVTPGNHD----TMLAELEGF---------DGEVVDEYRLAD---G--ETVVCHGH 160
                                       5599********....333333322.........367777777777...6..77788887 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 !   24.7   0.2   3.7e-09   2.2e-05       4     141 ..      46     190 ..      44     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.7e-09
                     Metallophos_2   4 aiiSDlH..............snldaleavlealkevgvdaiihaGD...........leeeepevleellela..p 53 
                                       ++++D+H              +  d  +++++ l+++g+ ++++aGD           + ++++++le +   a  +
  gi|336255244|ref|YP_004598351.1|  46 LLVADVHlgraaassvdapidDGADVRDRLASLLERTGAGTVVVAGDllhsfnsvphgV-ARDLSALESAVTAAgaD 121
                                       7899***99999999999998777888888999999999********544444433221.2333555555555599* PP

                     Metallophos_2  54 vlaVrGNnDeevveedvlreaaelgtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvp 130
                                       +++ +GN+D      ++l+e +++++++ +e    la+ +  ++Hg+    ++  ae+ ++        v+GH H +
  gi|336255244|ref|YP_004598351.1| 122 FVVTPGNHD------TMLAELEGFDGEVVDE--YRLADGETVVCHGH----EQPSAEAKRY--------VVGHDHPA 178
                                       *********......7788888888888444..444467999*****....3333333333........66777766 PP

                     Metallophos_2 131 .evekeggvlvv 141
                                        ++e ++   ++
  gi|336255244|ref|YP_004598351.1| 179 lSIEGRKRPCFL 190
                                       555555555555 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   5.9e-05      0.35      74      94 ..     113     133 ..     103     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.9e-05
                                       HHHHHCT-SEEEESS--HHHH CS
                          Aldolase  74 aeakeaGaqfvvsPGltadll 94 
                                       +++++aGa+fvv+PG  + +l
  gi|336255244|ref|YP_004598351.1| 113 SAVTAAGADFVVTPGNHDTML 133
                                       46899**********877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2190.64
//
Query:       gi|336255245|ref|YP_004598352.1|  [L=438]
Description: amine oxidase [Halopiger xanaduensis SH-6]
Scores for 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-47  161.3   1.4    5.5e-47  161.1   1.4    1.1  1  Amino_oxidase   Flavin containing amine oxidoreductase
      3e-15   56.2   0.4    9.9e-15   54.5   0.4    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.9e-09   37.0  12.3    4.8e-08   33.0  12.2    2.0  1  DAO             FAD dependent oxidoreductase
    1.1e-07   31.5   2.2    1.4e-05   24.5   1.8    2.3  2  FAD_binding_3   FAD binding domain
    2.6e-06   26.8   3.8    1.7e-05   24.1   2.1    2.2  2  FAD_binding_2   FAD binding domain
    4.6e-06   26.1   3.0     0.0001   21.7   0.5    2.6  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.7e-06   24.9   0.0    0.00034   19.4   0.0    2.1  2  HI0933_like     HI0933-like protein
    0.00043   20.8   0.9     0.0097   16.5   1.7    2.3  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0029   18.2   0.5     0.0076   16.8   0.5    1.6  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0037   16.5   0.2     0.0072   15.6   0.2    1.4  1  Thi4            Thi4 family
     0.0055   16.7   3.3       0.12   12.4   0.4    2.6  2  NAD_binding_9   FAD-NAD(P)-binding
     0.0058   17.1   0.3       0.13   12.7   0.0    2.3  2  NAD_binding_7   Putative NAD(P)-binding
     0.0095   15.3   4.0      0.019   14.3   4.0    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.011   15.0   0.3      0.021   14.1   0.3    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.14   10.9   1.0       0.28   10.0   1.0    1.4  1  Trp_halogenase  Tryptophan halogenase
       0.23    9.8   0.0       0.35    9.2   0.0    1.2  1  FMO-like        Flavin-binding monooxygenase-like
       0.24   10.4   4.2      0.077   12.1   1.2    1.6  2  GIDA            Glucose inhibited division protein A
       0.35   10.1   0.6       0.72    9.0   0.1    1.7  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.77    8.7   3.5       0.88    8.5   0.3    2.1  2  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.1   1.4   5.8e-50   5.5e-47       1     452 []      14     433 ..      14     433 .. 0.84

  Alignments for each domain:
  == domain 1  score: 161.1 bits;  conditional E-value: 5.8e-50
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEETTTHHHHHHHHHTTCCCCEEEESCCGCEE CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftgagnpllellkelgledslslpdpgapkr 77 
                                       laGL+a r+L++ G+dVtvlE ++ vGGR+rt ++dGy ++ G+++++ a++++ + l+   l+++++ p  +    
  gi|336255245|ref|YP_004598352.1|  14 LAGLVATRHLAAGGVDVTVLEREETVGGRVRTTERDGYRFDRGFQVLFTAYPAVQRELDLEALDLRRFAPGAT---- 86 
                                       79*********************************************************99999888877766.... PP

                                       EEETTEECCTTEECHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHH CS
                     Amino_oxidase  78 vlskggrefpgdlspvpaewealleqgalsaellsleeklrlgleallqktldeldldskslaesleelgrrepgdv 154
                                       +   + r   +d ++ p+ ++a l+        +s+++klr        +t+d  +  s+++a   + l +r+++d 
  gi|336255245|ref|YP_004598352.1|  87 IARPNHRSTLADPRREPGTLPATLF-----NPDISTGDKLRVLGLWRDLQTKDPTEIFSGDDASIAQYLRDRSFSD- 157
                                       5555556668899999999999999.....6788899999987665555788889999999999999999999999. PP

                                       HHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETTHTHHHHHHHHH..TTTTEEEETSE CS
                     Amino_oxidase 155 evwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllprgGlsqlpealae..elrgldirlnt 229
                                         +++++ p       f +g+ +   ++ls +   ++  +++  +g + +p  G++++p++la+  ++ g +i ++ 
  gi|336255245|ref|YP_004598352.1| 158 QFLENFVGP-------FYGGITLD--RSLSTSKRVFEYTFRTLAAGATAVPAAGMGAIPRQLADraREAGATIETGV 225
                                       889999999.......99999887..99************************************************* PP

                                       EEEEEEEETTC............EEEEETTSTEEEESEEEE-S-HHHHHSSEEES.CC.SHHHHHHHHHSEEEEEEE CS
                     Amino_oxidase 230 rVkeikregdg............vtvtledgevveaDaVvvTvplgvlkailfsP.pl.pdekaeairnlgfgsvnk 292
                                          +++  +dg            vtv++   + +eaDaVvv++++++++  +++  +  p ++++ + +  +  +  
  gi|336255245|ref|YP_004598352.1| 226 DIESVAATSDGpssatsaaadvtVTVETAGDDALEADAVVVATDPPTAR--ELTGvEAiPTDARACVTQ-YYRLSGE 299
                                       *******555545555667773455555455555***************..555553336455555555.9****** PP

                                       EEEEESSGGSGCSTSECECECCCEEETTTEEEEECCECCCSTTTEEEEEEEEECHHHHHHHTTS-HHHHHHHHHHHH CS
                     Amino_oxidase 293 vilefdrkfwednalgqgvlvseltttlgeafissdfpsrappgkglvllvyvggdaaneleslsdeelvqavlrdL 369
                                       + +  dr+  ++ +     +++ +  ++++a+     p++ap+g +l+  +y+g+++       sd el+ ++++ L
  gi|336255245|ref|YP_004598352.1| 300 ATIGADRRLLLNAG-----DEGPNHVVPHSAV----APEYAPDGETLLSATYLGERE---E---SDAELATQTRETL 361
                                       ********955533.....4444444444433....679********8888887333...3...************* PP

                                       HHHHTGTSSTCSEEEEEECCTETTTSSSEEE.BTTHHHHHHHHHHCHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHH CS
                     Amino_oxidase 370 rklfgeevpepkatlvtrWhtdplargsysyvsvgpghedydplakpegdprlffAGehtsreypgtvegAilSGlr 446
                                       +++f+    e +     r htd++  +++       g +++ p a++ +d+ +++AG++t    +++++gA++SG++
  gi|336255245|ref|YP_004598352.1| 362 ESWFP----ERVFDDFERLHTDRIEFAQF---DQPLGIHERLPDARD-PDGPVYLAGDYTQ---WSSIQGAMESGRE 427
                                       *****....88888888********7777...777799999999999.9************...799********** PP

                                       HHHHHH CS
                     Amino_oxidase 447 aAaril 452
                                       aA+++l
  gi|336255245|ref|YP_004598352.1| 428 AARAVL 433
                                       ***997 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 !   54.5   0.4   1.1e-17   9.9e-15       1      63 [.       9      69 ..       9      72 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.1e-17
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHH CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrr 63
                                      +vG+Gl+Glva ++La  g+dv++le+ + +GGr+++ e++g+r+d g +++++   yp+v+r
  gi|336255245|ref|YP_004598352.1|  9 VVGGGLAGLVATRHLAAGGVDVTVLEREETVGGRVRTTERDGYRFDRGFQVLFT--AYPAVQR 69
                                      8*****************************************************..5999876 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0  12.2   5.1e-11   4.8e-08       1     303 [.       6     374 ..       6     387 .. 0.57

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 5.1e-11
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT.S.SGGGSSEEEEESSS....STHHSTHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag.s.gaSgrnsgllhsgl....rylpeaselarlslealeelr 69 
                                       +v+++GGG +Gl + ++La+ g  Vt+le+++ +g +  ++ r +  +  g+      +p    + +l leal+++r
  gi|336255245|ref|YP_004598352.1|   6 RVLVVGGGLAGLVATRHLAAGGvdVTVLEREETVGgRvRTTERDGYRFDRGFqvlfTAYPAV--QRELDLEALDLRR 80 
                                       59****************9988*********9999535788888866666667766435533..3388888888887 PP

                                       HHHHHHSS.........TTSEEEEEEEEEES.S.......................................HHHHH CS
                               DAO  70 eleeelgi.........didyrrtGllslaa.d.......................................eeele 97 
                                          + + i           + r++G+l+ +  +                                       +  + 
  gi|336255245|ref|YP_004598352.1|  81 FAPGAT-IarpnhrstlADPRREPGTLPATLfNpdistgdklrvlglwrdlqtkdpteifsgddasiaqylrD--RS 154
                                       777552.211111111123366666666642323343444444444444443333333333333332222211..22 PP

                                       HHHHHHHHH.....HHTTT..TEEEEEHHHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHH................ CS
                               DAO  98 aldkllall.....leagl..daelldaeevrelepalpgllgalfypdtgqvdpakltaa................ 151
                                        +d+ l++      +  g+  d + l+ +  ++++                         +                
  gi|336255245|ref|YP_004598352.1| 155 FSDQFLENFvgpfyG--GItlD-RSLSTS--KRVFE------------------------Ytfrtlaagatavpaag 202
                                       222444443322211..11101.122221..12222........................12223333444444444 PP

                                       .......HHHHHHHTT-EEEESECEEEEEEEE...........TCEEEEE..EECTEEE.EEEEEEEE--GGGHH.H CS
                               DAO 152 .......laraaealGveilegtevtgleeed...........gkvwgve..rttpgen.daadavVnaaGawsd.l 206
                                              la++a+++G++i +g  ++++ +++           +  +     ++t+g    +adavV+a+ + +  +
  gi|336255245|ref|YP_004598352.1| 203 mgaiprqLADRAREAGATIETGVDIESVAATSdgpssatsaaaD--V--TvtVETAGDDaLEADAVVVATDPPTArE 275
                                       4455555***************9999986633355566644322..2..23235556654477**********9875 PP

                                       HHTTCTTTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEE...EEETTTTEEEEEE........TTSEEEEEESSEEE CS
                               DAO 207 lgllkeldlpispvrgqvlvlkplseklvspaailpvpe...tdddgrgvyvtpr........kdgrvlvGgtadee 272
                                       l +++ ++   +++  q+++l+           i +++    +  d++  +v+p         +dg++l+ +t+   
  gi|336255245|ref|YP_004598352.1| 276 LTGVEAIPTDARACVTQYYRLSGEA-------TIGADRRlllNAGDEGPNHVVPHsavapeyaPDGETLLSATY--- 342
                                       5222222223345555555553322.......22222223446777777788887888889999******9996... PP

                                       TTCSSTSCSHHHHHHHHHHHHHHSGG..GCGEE CS
                               DAO 273 sgdddpevdeedidellealrklfPq..lgdvl 303
                                        g+ + e d+e + + +e l+ +fP+  ++d++
  gi|336255245|ref|YP_004598352.1| 343 LGERE-ESDAELATQTRETLESWFPErvFDDFE 374
                                       77777.899999999999999999985435544 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   1.8   1.5e-08   1.4e-05       3      35 ..       6      38 ..       4      48 .. 0.91
   2 ?    5.1   0.0     0.012        11      84     143 ..     180     242 ..     117     267 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.5e-08
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                       Vl+VG+G+aGl++++ L+  Gv+v+++e+ +t
  gi|336255245|ref|YP_004598352.1|  6 RVLVVGGGLAGLVATRHLAAGGVDVTVLEREET 38
                                      59****************************987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.012
                                       CEEEEEHH...CHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEE CS
                     FAD_binding_3  84 pkaradle...lesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevr 143
                                       +k+  +++   l +++++v + +   + r L+++a+e+g++++ + ++es+ ++ +g ++   
  gi|336255245|ref|YP_004598352.1| 180 SKRVFEYTfrtLAAGATAVPAAGMGAIPRQLADRAREAGATIETGVDIESVAATSDGPSSATS 242
                                       44444444455557778888888889999*************************999766544 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   2.1   1.8e-08   1.7e-05       2      36 ..       7      41 ..       6      48 .. 0.93
   2 ?    2.5   0.0     0.067        63     135     200 ..     198     269 ..      82     320 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.8e-08
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      v+V+G+GlAGL+A+  +a  G +v+v+e e+ +gg
  gi|336255245|ref|YP_004598352.1|  7 VLVVGGGLAGLVATRHLAAGGVDVTVLEREETVGG 41
                                      9******************************9998 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.067
                                       ....HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT......EEEEEEEEET...TTTCEEEEEESEEEE--- CS
                     FAD_binding_2 135 etlvtghallarlvesarkagvdfqerteadeLivedg......rvtGavvenp...esgrevrirakavvlatg 200
                                       ++ +   a+   l+++ar+ag ++ +  +++++  +++       +  +v       e+ ++ +++a+avv+at 
  gi|336255245|ref|YP_004598352.1| 198 VPAAGMGAIPRQLADRAREAGATIETGVDIESVAATSDgpssatSAAADV---TvtvETAGDDALEADAVVVATD 269
                                       56667778888999999999999999999999999755466444333333...245589999999******9985 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 !   21.7   0.5   1.1e-07    0.0001       2      36 ..       6      39 ..       5      48 .. 0.85
   2 ?    3.8   0.0     0.029        27     187     235 ..     208     268 ..     191     291 .. 0.76
   3 ?   -2.3   0.0       2.1     2e+03     271     294 .]     406     425 ..     400     428 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.1e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtcl 36
                                      +v+v+GgG AGl a ++la+ g++vt++e+e+t +
  gi|336255245|ref|YP_004598352.1|  6 RVLVVGGGLAGLVATRHLAAGGVDVTVLEREET-V 39
                                      89**************************65554.3 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.029
                                       HHHHHHHHHTTEEEEESCEEEEEEETTE..........EEE..EEETTSCEEEESEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxx..xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 187 aaleealekeGvevklgtsvkeidgnge..........kle..vvledgeeidadlvvvav 235
                                       ++l+++ ++ G ++ +g  ++ + + ++          +++  v++   + ++ad vvva+
  gi|336255245|ref|YP_004598352.1| 208 RQLADRAREAGATIETGVDIESVAATSDgpssatsaaaDVTvtVETAGDDALEADAVVVAT 268
                                       5567777888888888888888887777778888887744453666666669999999997 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.1
                                       EEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 271 iyaiGDvaggkggpelaqaAvqqG 294
                                       +y++GD +    ++ ++q A+++G
  gi|336255245|ref|YP_004598352.1| 406 VYLAGDYT----QWSSIQGAMESG 425
                                       9*****99....555555555444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.6e-07   0.00034       2      42 ..       6      46 ..       5      88 .. 0.91
   2 ?    3.3   0.0     0.028        26     113     162 ..     208     268 ..     201     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.6e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHC CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilis 42
                                      +v+v+GgG AGl a+ ++a+ g +V++le+++++g +++++
  gi|336255245|ref|YP_004598352.1|  6 RVLVVGGGLAGLVATRHLAAGGVDVTVLEREETVGGRVRTT 46
                                      699********************************999876 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHT-EEE-S--EEEE...........ECETTE.EEEEE.TTEEEEESEEEE-- CS
                       HI0933_like 113 dallkelkeagvklrletevksv...........ekeedgkfrvktkseeeleadklvlAt 162
                                       + l  +++eag ++++  +++sv           ++ +d +++v+t ++++lead++v+At
  gi|336255245|ref|YP_004598352.1| 208 RQLADRAREAGATIETGVDIESVaatsdgpssatSAAADVTVTVETAGDDALEADAVVVAT 268
                                       66888999999999999999999888888888776777778889999999*********97 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.7     1e-05    0.0097       1      35 [.       6      40 ..       6      48 .. 0.93
   2 ?    0.5   0.0      0.95     9e+02      44      72 ..     208     236 ..     200     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-05
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      +v+vvGgG+ gl +   la+ g +Vtv+er++++ 
  gi|336255245|ref|YP_004598352.1|  6 RVLVVGGGLAGLVATRHLAAGGVDVTVLEREETVG 40
                                      79*****************************9987 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.95
                                       HHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  44 kilqeklekngievllntkveeiegsedg 72 
                                       + l+++ ++ g ++ ++  +e++  ++dg
  gi|336255245|ref|YP_004598352.1| 208 RQLADRAREAGATIETGVDIESVAATSDG 236
                                       67899******************999988 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 !   16.8   0.5   8.1e-06    0.0076       6      77 ..     202     276 ..     201     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.1e-06
                                       TTSHHHHHHHHHHHHTTS......-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHH CS
                     F420_oxidored   6 GaGnmgealasgllaaga......qpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedvee 76 
                                       G+G + + la ++ +aga      + +++  a+s  p++a+++a+++ v+v++ +  +a+e ad vv+a  p  + e
  gi|336255245|ref|YP_004598352.1| 202 GMGAIPRQLADRAREAGAtietgvDIESVA-ATSDGPSSATSAAADVTVTVET-AGDDALE-ADAVVVATDPPTARE 275
                                       788888899999999998887775666777.99**************999999.8888886.*******99998887 PP

                                       H CS
                     F420_oxidored  77 v 77 
                                       +
  gi|336255245|ref|YP_004598352.1| 276 L 276
                                       6 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   7.7e-06    0.0072      20      56 ..       7      42 ..       3      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.7e-06
                                      EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                              Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                      v++vG+G +GL a++ la   ++ v++ler+ ++GG 
  gi|336255245|ref|YP_004598352.1|  7 VLVVGGGLAGLVATRHLAAG-GVDVTVLEREETVGGR 42
                                      89*****************9.************9995 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 !   12.4   0.4   0.00012      0.12       2      45 ..       9      47 ..       8      53 .. 0.84
   2 ?    4.2   0.2      0.04        38     102     153 ..     212     268 ..     204     270 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvwrtd 45
                                      +vG+G +Gl ++++L+a       +++t+ +++e+ g grv  t+
  gi|336255245|ref|YP_004598352.1|  9 VVGGGLAGLVATRHLAAG-----GVDVTVLEREETvG-GRVRTTE 47
                                      8***************99.....6********88835.8776665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.04
                     NAD_binding_9 102 dlfeellarlpegvtvevhraevv...dleeradg..qavlladgaslaadaVvLAl 153
                                       d+++e+ a+ + gv++e + a+     + + +a+   ++v +a+++ l+adaVv+A+
  gi|336255245|ref|YP_004598352.1| 212 DRAREAGATIETGVDIESVAATSDgpsSATSAAADvtVTVETAGDDALEADAVVVAT 268
                                       55566666666666666555444322122222223114677788899********98 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 !   12.7   0.0   0.00014      0.13       9      54 ..       6      49 ..       3      91 .. 0.79
   2 ?    1.9   0.1      0.31   2.9e+02      27      74 ..     221     273 ..     202     287 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee 54
                                      +vlvvGgG  ++   r+l++ g +vtv+  e  e + ++v+ +e++
  gi|336255245|ref|YP_004598352.1|  6 RVLVVGGGLAGLVATRHLAAGGVDVTVLERE--ETVGGRVRTTERD 49
                                      8***************************999..5556666665544 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.31
                     NAD_binding_7  27 leagakvtvvapevkeele.....elvklaeeelekdlegadlviaatddrel 74 
                                       +e+g ++  va ++   ++       v+++ e++ +d  +ad v++atd +  
  gi|336255245|ref|YP_004598352.1| 221 IETGVDIESVAATSDGPSSatsaaADVTVTVETAGDDALEADAVVVATDPPTA 273
                                       56666666666666333333333344556677778899999999999987665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   4.0     2e-05     0.019       2      37 ..       7      42 ..       6      48 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGl 37
                                      v+VvGGg+aG++A    a  G  v ++e+++ +GG 
  gi|336255245|ref|YP_004598352.1|  7 VLVVGGGLAGLVATRHLAAGGVDVTVLEREETVGGR 42
                                      99*********************************6 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 ?   14.1   0.3   2.3e-05     0.021      30      65 ..       6      41 ..       2      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparle 65
                                      +vlv+GgG aGl A +  ++ g +Vtvl+ ++++  
  gi|336255245|ref|YP_004598352.1|  6 RVLVVGGGLAGLVATRHLAAGGVDVTVLEREETVGG 41
                                      8****************************9987755 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.0    0.0003      0.28       1      36 [.       6      38 ..       6      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0003
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseei 36
                                      ++++vGGG aG +a  +la  +   ++vt++e ee+
  gi|336255245|ref|YP_004598352.1|  6 RVLVVGGGLAGLVATRHLAAGG---VDVTVLEREET 38
                                      699***************9988...9******9985 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00037      0.35       3      45 ..       6      48 ..       4      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00037
                          FMO-like  3 kvaviGaGvsGlasikccleegleptcfersddiGGlwrfken 45
                                      +v v+G+G++Gl++ +     g++ t +er + +GG  r +e+
  gi|336255245|ref|YP_004598352.1|  6 RVLVVGGGLAGLVATRHLAAGGVDVTVLEREETVGGRVRTTER 48
                                      899*********************************9988875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.2   8.2e-05     0.077       2      28 ..       7      33 ..       6      47 .. 0.85
   2 ?   -2.5   0.1       2.1     2e+03     128     150 ..     248     270 ..     238     286 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.2e-05
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi 28
                                      v V+GgG+AG+ A  ++a  G++v+ +
  gi|336255245|ref|YP_004598352.1|  7 VLVVGGGLAGLVATRHLAAGGVDVTVL 33
                                      89**********************988 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.1
                                       EEEEEETTS-EEEECEEEE--TT CS
                              GIDA 128 vkgvvtedgetikakavviatGt 150
                                       +  v t+ + +++a+avv+at +
  gi|336255245|ref|YP_004598352.1| 248 TVTVETAGDDALEADAVVVATDP 270
                                       456889999999********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 ?    9.0   0.1   0.00076      0.72       1      32 [.       8      38 ..       4      52 .. 0.77
   2 ?   -2.4   0.1       2.4   2.2e+03     114     132 ..     249     268 ..     243     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00076
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgni 32
                                      +++G+G aGl a  +l   g+ d+++lE+++ 
  gi|336255245|ref|YP_004598352.1|  8 LVVGGGLAGLVATRHLAAGGV-DVTVLEREET 38
                                      478888888888888888887.6888888754 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                       Pyr_redox_3 114 fevetske.tyeAkkviiAt 132
                                        +vet  +  +eA+ v++At
  gi|336255245|ref|YP_004598352.1| 249 VTVETAGDdALEADAVVVAT 268
                                       67888876589999999998 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.3   0.00093      0.88       2      35 ..       7      38 ..       6      50 .. 0.86
   2 ?    0.8   0.2      0.22     2e+02     113     143 ..     244     272 ..     228     295 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00093
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieasps 35
                                      v+v+G+G+Agl    +l  a+ g+ v+++e  + 
  gi|336255245|ref|YP_004598352.1|  7 VLVVGGGLAGLVATRHL--AAGGVDVTVLEREET 38
                                      89*********999999..888999999987665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.22
                     Lycopene_cycl 113 eeeeageslvvleggrkirarlvvdarglas 143
                                       +++    ++v ++g+  ++a +vv+a+  + 
  gi|336255245|ref|YP_004598352.1| 244 AAD--VTVTVETAGDDALEADAVVVATDPPT 272
                                       333..3589999**************97444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3140.24
//
Query:       gi|336255246|ref|YP_004598353.1|  [L=371]
Description: hypothetical protein Halxa_3869 [Halopiger xanaduensis SH-6]
Scores for 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-44  149.0   0.1    8.9e-44  149.0   0.1    1.5  2  Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3


Domain annotation for each model (and alignments):
>> Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.0   0.1     5e-48   8.9e-44       2     136 .]      78     262 ..      77     262 .. 0.95
   2 ?   -3.0   0.1      0.43   7.7e+03      23      39 ..     320     336 ..     308     358 .. 0.63

  Alignments for each domain:
  == domain 1  score: 149.0 bits;  conditional E-value: 5e-48
                   Gluconate_2-dh3   2 eqaallaaladrIiPstdtgpgakeagvaafidrqlad....................................... 39 
                                       +qa+++++l++rI+Ps+d gpga+eagv++fid+q+++                                       
  gi|336255246|ref|YP_004598353.1|  78 QQARVVHDLTARIYPSDDNGPGAPEAGVVYFIDQQMNSawgrgerwymeapfagenptdpfesetddtageevqisw 154
                                       79**************666********************************************************** PP

                   Gluconate_2-dh3  40 ............aplppeqeayrkglaaldayaraeyg.ksFveldgaqqdalLealekeaeakgtgealeasaeah 103
                                                   +pl+p +eay++g++a+++y+++ey+  sF+ ld++qqd++++ale++ e+ g++++l+ +a + 
  gi|336255246|ref|YP_004598353.1| 155 aeespastqgwqYPLSP-NEAYDQGIHAVEEYVQSEYDaDSFTGLDEDQQDEVVAALEAD-EV-GPFDDLDIDA-EG 227
                                       ***********999999.*******************879********************.55.6777666655.78 PP

                   Gluconate_2-dh3 104 fFsllreltlegyftspigggna..lgwrligfpG 136
                                       fF ++r++tleg+f++p++ggn+  +gwrl+gfpG
  gi|336255246|ref|YP_004598353.1| 228 FFLMVRQNTLEGMFSDPMYGGNRemIGWRLKGFPG 262
                                       **********************************9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.43
                   Gluconate_2-dh3  23 gakeagvaafidrqlad 39 
                                        a+ea+ ++++d++ a+
  gi|336255246|ref|YP_004598353.1| 320 DAAEAEYPNVVDEAAAR 336
                                       45566666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2829.72
//
Query:       gi|336255247|ref|YP_004598354.1|  [L=589]
Description: gluconate 2-dehydrogenase (acceptor) [Halopiger xanaduensis SH-6]
Scores for complete 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-18   67.6   0.0    2.8e-18   66.8   0.0    1.4  1  GMC_oxred_C    GMC oxidoreductase
    1.6e-09   37.6   0.0    2.4e-07   30.4   0.0    2.2  2  GMC_oxred_N    GMC oxidoreductase
  ------ inclusion threshold ------
       0.11   12.7   0.1       0.38   11.0   0.1    1.9  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
       0.15   11.2   0.0       0.25   10.5   0.0    1.3  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
       0.22   10.7   0.1       0.46    9.7   0.1    1.5  1  Thi4           Thi4 family


Domain annotation for each model (and alignments):
>> GMC_oxred_C  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.0   7.8e-22   2.8e-18       1     144 []     442     570 ..     442     570 .. 0.86

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 7.8e-22
                                       ----EEEEEST..T-TCCEEEEE--TT-SHHHHHHHHHHHHHHHHHCTSGGGTTEECCEECCCTTTTS.HCHHCHHC CS
                       GMC_oxred_C   1 PesrGrvtlss..sdptgaplidpnylsdprdlaalvealkaarkilaaaaldvleeeltpgaaeetsdaavesdea 75 
                                       P+ ++++ l+   +d++g pl+++++++ ++d++ + +    + +++++++   + +       e ++d + ++++ 
  gi|336255247|ref|YP_004598354.1| 442 PFRENYLDLDPnyTDQYGRPLLRMTFDWREQDRNLVEYIGPRLEEVMQEMG---ADTVDASTSLEGSFDITPYQST- 514
                                       788999****999*************************************4...2222222223334445555555. PP

                                       HHCHHHHH-EE-S--B-TT-B-STCGCBSB-TTSBBTT-CSEEE-SGGGSSS--SS-THHHHHHHHHHH CS
                       GMC_oxred_C  76 lekfvkeavltsaHplGtcrMGadpkdsVVDsdlrvhgvdnLrVvDaSvfPsapganptltilalAeka 144
                                                    H +G++ MGadp++sVV+++l+ ++ +nL++ +aS+f  ++g npt t+ alA +a
  gi|336255247|ref|YP_004598354.1| 515 -------------HNTGGAVMGADPEESVVNNYLQCWDASNLFIPGASAFAHNSGYNPTGTVGALAFRA 570
                                       .............*****************************************************986 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0    0.0037        13       2      44 ..       9      54 ..       8      95 .. 0.70
   2 !   30.4   0.0   6.7e-11   2.4e-07     172     272 ..     231     329 ..     194     345 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0037
                       GMC_oxred_N  2 delveggGsagsvvAaRLsedpstsvlvleaggreknrl...imvl 44
                                      d + +g+G +g  vA+ L++++ + v +   g r+++ +   +++l
  gi|336255247|ref|YP_004598354.1|  9 DVVTVGAGWTGGIVAKELAQNDYQVVSLERGGERDTEDFftvHDEL 54
                                      77899**************999876666666666666665443322 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 6.7e-11
                       GMC_oxred_N 172 ngkhqcGvcl.lgvtcrtgarqstarawLrpalerpnleiltgakaekiilegrkkravGVeasdkkgtvkrlvvaa 247
                                       +++++cG+c  +g  c+ ga+ s  +++L+ a e  n e+ t+  +  ++++++++r+ GV++ d  ++ + +   a
  gi|336255247|ref|YP_004598354.1| 231 GQCQYCGYCErFG--CEWGAKASPITTVLPAAQETGNFELRTHSDVVELLYDEENERVDGVRYVDRRSN-EVYEQPA 304
                                       5679*****7367..******************************************************.7777778 PP

                       GMC_oxred_N 248 kevvvaaGalnsPqlLqrSGlGkae 272
                                       ++v + a  ln+  lL++S +G+  
  gi|336255247|ref|YP_004598354.1| 305 DVVALTAYVLNNVRLLLLSDIGEPY 329
                                       888888999************9754 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 ?   11.0   0.1   0.00011      0.38       2      28 ..      13      39 ..      12      42 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                      E--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  2 vGaGlsGlvaAylLakagfdvlllekr 28
                                      vGaG +G   A +La+++++v+ le++
  gi|336255247|ref|YP_004598354.1| 13 VGAGWTGGIVAKELAQNDYQVVSLERG 39
                                      9*********************99987 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 ?   10.5   0.0   7.1e-05      0.25       2      33 ..       9      40 ..       3      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.1e-05
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                      dvv +G+G+ G  +a++laq+ ++v+ +e++g
  gi|336255247|ref|YP_004598354.1|  9 DVVTVGAGWTGGIVAKELAQNDYQVVSLERGG 40
                                      68888888888888888888888888887444 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00013      0.46      17      49 ..       7      38 ..       1      40 [. 0.90

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer 49
                                        Dvv vGaG +G   a+ la++ d +v+ ler
  gi|336255247|ref|YP_004598354.1|  7 PVDVVTVGAGWTGGIVAKELAQN-DYQVVSLER 38
                                      57*********************.*****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.22s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 4357.39
//
Query:       gi|336255248|ref|YP_004598355.1|  [L=90]
Description: hypothetical protein Halxa_3871 [Halopiger xanaduensis SH-6]
Scores for 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  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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 0.21s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 709.62
//
Query:       gi|336255249|ref|YP_004598356.1|  [L=44]
Description: auxin efflux carrier (AEC) family protein [Halopiger xanaduensis SH-6]
Scores for 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   10.7   1.5       0.54   10.3   1.5    1.3  1  DUF1382          Protein of unknown function (DUF1382)
        0.6    9.5   7.5       0.63    9.4   7.5    1.0  1  ExoD             Exopolysaccharide synthesis, ExoD
        2.7    7.8   8.3        6.3    6.7   2.3    2.1  2  DUF3953          Protein of unknown function (DUF3953)
        4.3    7.4   7.5        1.5    8.8   1.8    2.0  2  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> DUF1382  Protein of unknown function (DUF1382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.5   0.00012      0.54      20      32 ..      11      24 ..       8      30 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                           DUF1382 20 AsiGIrFVPiP.va 32
                                        iG++FVPiP +a
  gi|336255249|ref|YP_004598356.1| 11 VGIGLLFVPIPpIA 24
                                      579*******7355 PP

>> ExoD  Exopolysaccharide synthesis, ExoD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   7.5   0.00014      0.63     122     156 ..       4      38 ..       1      40 [. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00014
                              ExoD 122 llglailllaillalPiPftntlpalailllalGl 156
                                       +  ++il+   ll +PiP   t  +++++l+++Gl
  gi|336255249|ref|YP_004598356.1|   4 FSTIVILVGIGLLFVPIPPIATALGIIVILVGIGL 38 
                                       55567777777888999999999999999999998 PP

>> DUF3953  Protein of unknown function (DUF3953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.3    0.0014       6.3      27      40 ..       7      20 ..       4      20 .. 0.89
   2 ?    5.1   0.4    0.0044        20      23      34 ..      26      37 ..      24      40 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0014
                           DUF3953 27 llilaalfvlfVsi 40
                                      ++il+++ +lfV+i
  gi|336255249|ref|YP_004598356.1|  7 IVILVGIGLLFVPI 20
                                      68**********98 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0044
                           DUF3953 23 fsGillilaalf 34
                                      ++Gi++il+++ 
  gi|336255249|ref|YP_004598356.1| 26 ALGIIVILVGIG 37
                                      789999999986 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4     0.037   1.7e+02      26      36 ..       8      18 ..       4      19 .. 0.63
   2 ?    8.8   1.8   0.00033       1.5      19      36 ..      23      40 ..      22      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.037
                                      XXXXXXXXXXX CS
                   Gram_pos_anchor 26 lallggllLlv 36
                                       +l+g +lL+v
  gi|336255249|ref|YP_004598356.1|  8 VILVGIGLLFV 18
                                      56666666665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00033
                                      XXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor 19 fltaaGllallggllLlv 36
                                      + ta+G++++l+g++L+v
  gi|336255249|ref|YP_004598356.1| 23 IATALGIIVILVGIGLRV 40
                                      78**************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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):               4  [number of targets reported over threshold]
# CPU time: 0.34u 0.19s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 376.81
//
Query:       gi|336255250|ref|YP_004598357.1|  [L=265]
Description: beta-lactamase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-23   82.2  10.6    5.9e-23   81.9  10.6    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.7e-06   27.7   0.7    2.5e-06   27.1   0.7    1.3  1  Lactamase_B_2  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 !   81.9  10.6   6.6e-27   5.9e-23       4     197 .]      42     254 ..      39     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 6.6e-27
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHH..................HHHHHTSGGGGEEEEE-SBSSHHHHTTGG CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal..................elaalglkpkdvdavilTHlHlDHiGglg 62 
                                        pv+ ++ie+++g+iL DtG++++a+   +                  +la +g++  d+d vi THlHlDH+Ggl 
  gi|336255250|ref|YP_004598357.1|  42 EPVYNVVIEHPEGTILWDTGSHPDADAGHWpdelyaafehtglrpledDLAGAGYDVADIDCVIQTHLHLDHAGGLY 118
                                       578899**********************99*********************************************** PP

                                       GCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH.TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEE CS
                       Lactamase_B  63 glveatdvpvgavaeeapalfmeeaddaasrkgll.lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvv 138
                                        +  +     ++++e ++a+      da+  + ++    +++d   +  +++ + ++ ++++++ +g+++g +++v+
  gi|336255250|ref|YP_004598357.1| 119 AFEGTETPIYVHERELKYAYYSAKT-DASDGDVAYlSGDFDRDLEWEIVHGDREQGFAGLEFVHLPGHTPGLLGVVL 194
                                       **88776666666666555555555.444444444466677777777777777777777778888888888888888 PP

                                       EE.TTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 139 ey.gggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       e+ + g+v+++GD  +++ + +++ +++g+       + ++l+ l++l++  ++++++gH
  gi|336255250|ref|YP_004598357.1| 195 ELeDAGTVVLAGDQAYVRANYHDEHPMGGGLLWSKRHWLESLRFLKDLERRQDATVICGH 254
                                       8878899***************************************************** 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 !   27.1   0.7   2.8e-10   2.5e-06      24     149 ..      94     214 ..      56     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.8e-10
                                       SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT.........TTEEEEEE- CS
                     Lactamase_B_2  24 lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee.........pavnvheld 91 
                                       +  ++++id V+ th H DH  gl  +     ++ p+y++++ l++   + + +a++ +           ++++ ++
  gi|336255250|ref|YP_004598357.1|  94 AGYDVADIDCVIQTHLHLDHAGGLYAFEG---TETPIYVHERELKYAYYSAKTDASDGDvaylsgdfdRDLEWEIVH 167
                                       667899***************99777766...6689*****999999999888888888788888888888888888 PP

                                       TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE.CTTEEEEEESS-S---HH CS
                     Lactamase_B_2  92 wgesfelgdggleitatparhksgrrldrnagdtlGlrie.gggkrvyyigDtgyipee 149
                                        + +  ++  g  ++++ +++ ++          lG+++e ++  +v+ +gD +y+ + 
  gi|336255250|ref|YP_004598357.1| 168 GDREQGFA--G--LEFVHLPGHTPG--------LLGVVLElEDAGTVVLAGDQAYVRAN 214
                                       88888887..6..566667777777........89*****99999*********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2210.99
//
Query:       gi|336255251|ref|YP_004598358.1|  [L=241]
Description: cytochrome c biogenesis protein transmembrane region [Halopiger xanaduensis SH-6]
Scores for 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   43.8  12.3    3.5e-11   43.4  12.3    1.1  1  DsbD      Cytochrome C biogenesis protein transmembrane regio
  ------ inclusion threshold ------
       0.38   10.7  17.8        3.4    7.5  17.7    2.3  1  DsbD_2    Cytochrome C biogenesis protein transmembrane regio
        1.9    7.3   5.1        0.4    9.5   1.4    1.6  2  LMBR1     LMBR1-like membrane protein


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4  12.3   5.8e-15   3.5e-11       2     212 ..      14     230 ..      13     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 5.8e-15
                              DsbD   2 flaGllsfls.PCilpliPaylsyisgvsvedvktekkkv...kvllkallFvlGlslvfvslglsaaflgq.llkd 73 
                                       fl Gl++ l+  C++pl+P +++y+++v+ ++   +       +++l  ll v G+   +v+lg++ +++ q  + d
  gi|336255251|ref|YP_004598358.1|  14 FLLGLATPLTaTCVVPLYPSFIAYLASVGRQNEAGGGDGTdgpSAVLLGLLVVAGVLAFMVALGAVWTTVLQrSISD 90 
                                       899999999736****************999988775544577899999****************998876615556 PP

                              DsbD  74 vkevirrvaglivillGlhflgvfkievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaa. 149
                                         +++  +a  +  ++G  ++    ++   + +l +    ++  ++l a+  G+ F+++  PC   ++a  l  ++ 
  gi|336255251|ref|YP_004598358.1|  91 AVTALSPLAFAVLAVVGAVLV----VAPNGFARLPTIEPPHSRYPTLSAFAYGFFFGTIVIPCNPGLIALFLGRSTv 163
                                       666666666666666665444....444556666665677888999*****************86665544433221 PP

                              DsbD 150 ...skeslakgallllvyvlGlaipfllvglllellkk.klkslkkyskaveiaggvllvllGvlll 212
                                            +++++ +l +l++ lG+++p+l ++++++++ +  +++l +ys a++ + g++lv + +++l
  gi|336255251|ref|YP_004598358.1| 164 afpAFDTQLEVLLGFLAFGLGIGTPLLALAVVSQSAGRrATRTLARYSGAINRLVGIVLVAVSLYYL 230
                                       11123567888888999***************99986516799******************999987 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  17.7   0.00057       3.4      55     198 ..      75     220 ..      13     228 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00057
                            DsbD_2  55 llgsvlqlagel...eglrallgvllgllllllglklllkkkllklerlgkllsrllkklakklkslasalllGlln 128
                                       +lg+v +   +    ++++al  +++++l+++ g+ l++    + + rl+     ++++ +++   + sa+++G+++
  gi|336255251|ref|YP_004598358.1|  75 ALGAVWTTVLQRsisDAVTALSPLAFAVLAVV-GAVLVV--APNGFARLP-----TIEPPHSR-YPTLSAFAYGFFF 142
                                       22222222222211133333333333344333.222322..233344443.....34445554.367899******* PP

                            DsbD_2 129 Gll..pC..glvysal...llal.asgsaleGalvmlaFgLGTlpalllfglllgllskklrkkllrlagvllillg 197
                                       G +  pC  gl+ ++l   ++a+ a +  le  l +laFgLG   +ll+++++++ ++++++++l r +g++  l+g
  gi|336255251|ref|YP_004598358.1| 143 GTIviPCnpGLIALFLgrsTVAFpAFDTQLEVLLGFLAFGLGIGTPLLALAVVSQSAGRRATRTLARYSGAINRLVG 219
                                       *64449*7766666653323444255788899999**********************99888777777776655555 PP

                            DsbD_2 198 l 198
                                       +
  gi|336255251|ref|YP_004598358.1| 220 I 220
                                       4 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.4   6.8e-05       0.4     123     187 ..      60     121 ..      45     123 .. 0.72
   2 ?   -2.0   0.1      0.21   1.3e+03     397     414 ..     215     231 ..     187     236 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 6.8e-05
                             LMBR1 123 lyenaiiyllllvivlglliyvliilqklsllsiksllpilislantwGlvllilllGyGlvelP 187
                                       l   +++ ++l+++v + +++  ++ q    + +++l p++ ++  ++G+vl++   + G+++lP
  gi|336255251|ref|YP_004598358.1|  60 LLGLLVVAGVLAFMVALGAVWTTVL-QRSISDAVTALSPLAFAVLAVVGAVLVV--APNGFARLP 121
                                       4444556666666666666666666.555555577****************987..699999998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.21
                             LMBR1 397 fglfgaelieillilYlm 414
                                       + l+g+ ++++++++Yl+
  gi|336255251|ref|YP_004598358.1| 215 NRLVGI-VLVAVSLYYLI 231
                                       345555.55555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); 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:                         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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1760.29
//
Query:       gi|336255252|ref|YP_004598359.1|  [L=198]
Description: hypothetical protein Halxa_3875 [Halopiger xanaduensis SH-6]
Scores for 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   20.3   0.0    0.00047   19.9   0.0    1.2  1  Redoxin     Redoxin
  ------ inclusion threshold ------
       0.35   10.8   2.7       0.74    9.8   2.7    1.5  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   5.3e-08   0.00047      17     104 ..      71     160 ..      56     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.3e-08
                                       CEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH...HHHHHHHTT-TSEEE CS
                           Redoxin  17 dgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf...vkefwgkeglkfpvl 90 
                                        g+++ ++ef ++++vv  ++   c +C  +h+++ +l++   e +v++v +++d d +   v+e++++eg ++++ 
  gi|336255252|ref|YP_004598359.1|  71 TGETFAIEEF-DRPAVVHTFAV-GCAVCHSQHRQFVDLQAS--ETDVEIVDLTIDPDYPperVSEHATDEGFDWRFG 143
                                       6778888887.67777777777.7********999999777..9**************99****************8 PP

                                       E-...TTSHHHHHTT-T CS
                           Redoxin  91 sD...gsaaftkalGlr 104
                                       ++    +++++ ++G +
  gi|336255252|ref|YP_004598359.1| 144 VSpeaVTSSLVDDFGQE 160
                                       88332245555555544 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.7   8.2e-05      0.74       2      25 ..       9      31 ..       8      32 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 8.2e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                      ++RR++L+g +A+   + l+gcaa
  gi|336255252|ref|YP_004598359.1|  9 VDRRTLLRGLGAGSIVT-LAGCAA 31
                                      78******999998777.555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1645.59
//
Query:       gi|336255253|ref|YP_004598360.1|  [L=347]
Description: beta-lactamase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-25   88.3   7.8    6.4e-25   88.3   7.8    2.3  2  Lactamase_B    Metallo-beta-lactamase superfamily
    4.1e-06   26.5   1.9    7.2e-06   25.6   0.5    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.14   12.0   0.1       0.48   10.3   0.0    2.1  2  Lactamase_B_3  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 !   88.3   7.8   1.1e-28   6.4e-25       6     197 .]      15     239 ..      12     239 .. 0.95
   2 ?   -0.7   0.4       0.2   1.2e+03      98     143 ..     272     317 ..     246     321 .. 0.69

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 1.1e-28
                                       SEEEEEE.....ETTCEEEES--SCHHHHHHHH..HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCC CS
                       Lactamase_B   6 vnsylie.....gdggviLiDtGtsteaaraal..elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgav 75 
                                        n+y++e     gd+++ L+DtG+ t+ +ra l   la +g++  dvda++lTH+H+DH+G +g++  a ++ v+++
  gi|336255253|ref|YP_004598360.1|  15 NNAYVLEdesgaGDDDLALVDTGIATPDTRAQLreGLAERGYDFADVDAIVLTHFHPDHAGLAGEIQAAGGATVYVH 91 
                                       69*************************************************************************** PP

                                       EHHHHCCHCHHHHHHHHHCCHH.......................TTCHCGCCEEEEETTTEECCCTEEEEEHECTT CS
                       Lactamase_B  76 aeeapalfmeeaddaasrkgll.......................lagvsadkpdvdeeeldgnaggrralyvtggp 129
                                       +++ap  + +    +      +                       + +  ++ +++++ ++d+ + g+r+l++++ p
  gi|336255253|ref|YP_004598360.1|  92 EADAPLVEQDPDAVEDFERRRReslerwgvpdeprdellgfleaaDGITGEPVDVTPISDGDVLEVGGRRLETVHAP 168
                                       *******999998777777666999********************999***************************** PP

                                       STSCCEEEEEETTCCE.......EEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 130 ghghghgvveygggkv.......lftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       gh +g  ++e  +g+        +f+GDa+l+  t+ ++     a  r   + ekyl +l+++a+ ++e++ pgH
  gi|336255253|ref|YP_004598360.1| 169 GHAAGLCCFEQLDGDGgdesaaeAFVGDAVLPVYTPNVGG----ADIRVERPLEKYLTTLRQIAECDYERIWPGH 239
                                       **********98888666666669****************....******************************9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.2
                                       TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTC CS
                       Lactamase_B  98 lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveyggg 143
                                       ++++++  +     +l+g++  ++ ++++ +  h  + gvve+++g
  gi|336255253|ref|YP_004598360.1| 272 GPADPWTVSADLFGDLAGIHILHGPGEAYAHLDHLRHEGVVELEDG 317
                                       5667777777888888888888888888888888888888888776 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 !   25.6   0.5   1.2e-09   7.2e-06       7      89 ..      39     115 ..      32     181 .. 0.66
   2 ?   -1.9   0.0      0.32   1.9e+03      40      45 ..     302     309 ..     265     341 .. 0.63

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.2e-09
                                       --TTHHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT CS
                     Lactamase_B_2   7 agpdlrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee 82 
                                       a pd+r+q lr     + +  +++++da++lth H DH  gl    + ++  +++y+++  +  +e+  ++  +  e
  gi|336255253|ref|YP_004598360.1|  39 ATPDTRAQ-LREG--LAeRGYDFADVDAIVLTHFHPDHA-GLAGEIQAAG-GATVYVHEADAPLVEQDPDAVED-FE 109
                                       45779999.5555..3347889*****************.7766555333.48899997766655555333322.22 PP

                                       TTEEEEE CS
                     Lactamase_B_2  83 pavnvhe 89 
                                        + +++ 
  gi|336255253|ref|YP_004598360.1| 110 -RRRRES 115
                                       .233333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.32
                                       -HHHH..G CS
                     Lactamase_B_2  40 HyDHl..a 45 
                                       H DHl  +
  gi|336255253|ref|YP_004598360.1| 302 HLDHLrhE 309
                                       44444322 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 ?   10.3   0.0   8.1e-05      0.48      33      59 ..      57      99 ..      10     174 .. 0.65
   2 ?   -1.4   0.0      0.33     2e+03      45      54 ..     301     310 ..     237     333 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.1e-05
                     Lactamase_B_3 33 paeeaDlvlisqaledHahletlkql................a 59
                                      +  ++D++++++ ++dHa l+   q+                +
  gi|336255253|ref|YP_004598360.1| 57 DFADVDAIVLTHFHPDHAGLAGEIQAaggatvyvheadaplvE 99
                                      3489**************9998888745444444433333331 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.33
                     Lactamase_B_3  45 aledHahlet 54 
                                       a+ dH ++e 
  gi|336255253|ref|YP_004598360.1| 301 AHLDHLRHEG 310
                                       2333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2639.36
//
Query:       gi|336255254|ref|YP_004598361.1|  [L=172]
Description: hypothetical protein Halxa_3877 [Halopiger xanaduensis SH-6]
Scores for 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:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 0.41u 0.18s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1375.78
//
Query:       gi|336255255|ref|YP_004598362.1|  [L=496]
Description: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B [Halopiger xanaduensis SH-6]
Scores for 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-99  331.6   0.0    5.5e-99  331.0   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
    1.4e-41  141.8   0.3    2.3e-41  141.1   0.0    1.5  2  GatB_Yqey  GatB domain
  ------ inclusion threshold ------
      0.052   13.9   0.1       0.33   11.4   0.0    2.3  2  DUF3046    Protein of unknown function (DUF3046)


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 !  331.0   0.0  9.2e-103   5.5e-99       1     268 [.      13     307 ..      13     310 .. 0.95

  Alignments for each domain:
  == domain 1  score: 331.0 bits;  conditional E-value: 9.2e-103
                                       EEEEEEEEEEB--SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N   1 lviGlEiHaqlktksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRKn 77 
                                       +viGlE+H+ql+t++K+F+++st e ++epn++v++v+l+lPG+lPvln++ave a+k+++a++++i ee++f+RKn
  gi|336255255|ref|YP_004598362.1|  13 TVIGLEVHVQLETDTKIFCGCST-EPTDEPNENVCPVCLGLPGALPVLNEAAVEAAVKIGKAIDADIPEETRFHRKN 88 
                                       59********************5.6999************************************************* PP

                                       -TCTTCTTSEEEEESSS.SEEEEEEEE.....TEEEEEEEEEEEE---EEEE.....EETTEEEEETTSTT-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxx RF
                            GatB_N  78 yfypdlpkgyQitqkeeplakeGslel.....ekkvrierihlEeDaaksvh.....eekeeslvdlnRaGvpLiEi 144
                                       y+ypdlpk++Qitq++ep++ +G+le+     +++v i+r+hlEeD +   h     ++++++lvd+nRaG+pL+Ei
  gi|336255255|ref|YP_004598362.1|  89 YYYPDLPKNFQITQYDEPICADGELEVavegtRRSVTIQRAHLEEDPGSLQHvgggiDTADYTLVDYNRAGTPLMEI 165
                                       **************************9999999999*******************997888**************** PP

                                       EE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSE...........TTSSS....--EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxx...xxxxxxxx RF
                            GatB_N 145 vtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreee...........kgeee...gtrvEiKn 207
                                       vt+pd+rsp+e+ra++ +l+e+l++lgv d++  +GslR+D+N+S+  ee           +  e+    +r+E+Kn
  gi|336255255|ref|YP_004598362.1| 166 VTAPDFRSPSEVRAFLAELEEVLEYLGVFDAER-DGSLRIDANLSIIPEEdiegdgvdeigE--EAleaANRTEVKN 239
                                       ********************************9.8***********9875677877776542..323469******* PP

                                       E-SHHHHHHHHHHHHHHHHHHH.......-EEEEEETTTTEEEEECC----...-EEE-TTS--EE-- CS
                                       xxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 208 lnslksiekaieyeierqiell.......qeTrkfdedkgetvslRskeeaedYryfpepdlppleis 268
                                       ++s k  eka++ye +rq +++       qeTr++de++g tvs+Rskee++dYryf e+dlppl++ 
  gi|336255255|ref|YP_004598362.1| 240 ISSHKGAEKALAYEETRQKNAIqrgraveQETRHWDESRGITVSMRSKEEEKDYRYFEEADLPPLRVA 307
                                       *****************************************************************986 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       1.5   9.1e+03      59     112 ..     218     240 ..     208     250 .. 0.44
   2 !  141.1   0.0   3.9e-45   2.3e-41       1     148 []     348     494 ..     348     494 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHH..TXXHHHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHH CS
                         GatB_Yqey  59 kkiakevleellee..gkspeeiieekgLkqisdeeeleklveeviaenpkavedy 112
                                       ++ + e+ ee le     +                                 v+++
  gi|336255255|ref|YP_004598362.1| 218 GDGVDEIGEEALEAanRTE---------------------------------VKNI 240
                                       4444444444442221223.................................3333 PP

  == domain 2  score: 141.1 bits;  conditional E-value: 3.9e-45
                                       HHHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHH.HHHHHHHHTXXH CS
                         GatB_Yqey   1 dffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiake.vleelleegksp 76 
                                       df+e+v++e  d+ laa+w++++llgeln++++ei+e++ + e++++l++l+ae++I++k a+e vl+ +l++g++p
  gi|336255255|ref|YP_004598362.1| 348 DFYENVAREF-DPDLAATWVADNLLGELNYRDMEITEIEGRLEEVTRLVELVAEDEITAKNAREtVLRSMLDDGRTP 423
                                       79*******9.***************************************************76377********** PP

                                       HHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  77 eeiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       +e+++e+gL +  de+e++++v e+i+enp avedy+sg + a++flvGqvM+kt G adp  vn+ll+ +L
  gi|336255255|ref|YP_004598362.1| 424 DEVVKEEGLGKT-DEDEVQQAVVEAIDENPGAVEDYESGDDGAINFLVGQVMQKTGGSADPGDVNQLLRAEL 494
                                       *********998.66*****************************************************9987 PP

>> DUF3046  Protein of unknown function (DUF3046)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.5e-05      0.33       4      32 ..     347     375 ..     345     381 .. 0.91
   2 ?   -1.0   0.0       0.4   2.4e+03      20      41 ..     405     428 ..     387     448 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                           DUF3046   4 teFwelveeeFGsayarslardhvlselg 32 
                                        +F e+v++eF ++ a+++++d  l el+
  gi|336255255|ref|YP_004598362.1| 347 ADFYENVAREFDPDLAATWVADNLLGELN 375
                                       68************************996 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.4
                           DUF3046  20 rslardhvlsel..ggrTaeeAle 41 
                                       +  ar+ vl ++  +grT++e ++
  gi|336255255|ref|YP_004598362.1| 405 AKNARETVLRSMldDGRTPDEVVK 428
                                       555666666665557888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); 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: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 3997.85
//
Query:       gi|336255256|ref|YP_004598363.1|  [L=155]
Description: hypothetical protein Halxa_3879 [Halopiger xanaduensis SH-6]
Scores for 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   14.1   1.2      0.051   13.4   1.2    1.3  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.2   2.8e-06     0.051       1      21 [.       1      21 [.       1      25 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-06
                        TAT_signal  1 klSRRdFLKgsAAaaAAaalg 21
                                      ++SRR+ L  ++++ A++++g
  gi|336255256|ref|YP_004598363.1|  1 MVSRRQVLALGGGVSALGLAG 21
                                      69************9998766 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:                      307  (0.0171231); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1340.00
//
Query:       gi|336255257|ref|YP_004598364.1|  [L=441]
Description: sodium:dicarboxylate symporter [Halopiger xanaduensis SH-6]
Scores for 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-113  377.1  36.0   1.1e-112  377.0  36.0    1.0  1  SDF       Sodium:dicarboxylate symporter family
  ------ inclusion threshold ------
      0.034   14.1   0.9       0.11   12.5   0.9    1.9  1  DUF1358   Protein of unknown function (DUF1358)


Domain annotation for each model (and alignments):
>> SDF  Sodium:dicarboxylate symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.0  36.0  1.2e-116  1.1e-112       2     390 .]      19     412 ..      18     412 .. 0.97

  Alignments for each domain:
  == domain 1  score: 377.0 bits;  conditional E-value: 1.2e-116
                               SDF   2 llqiliglvlGlviGllelvkelaalisplgdlfinllkmlivPlvfasiisgiaslgdakklgklglktllyfllt 78 
                                       +++i ++++lG ++Gl  +v++ a++++plgd+f++ll m+++P+v++++ +gi +++ +++lg++g+++++++ ++
  gi|336255257|ref|YP_004598364.1|  19 VYRIGAAFILGSIVGL--VVGQPATVLQPLGDIFVRLLSMIVIPIVVFTLLMGIRRIS-PAQLGRIGGQVIALYAVM 92 
                                       678999**********..***************************************6.****************** PP

                               SDF  79 tliAaiiglilalllkpgselaleassakeaekketdslldlilslipsnifealaegnvlavivfailfGialaal 155
                                       ++iA++igl +a+l++pg  + l+ ++  e e +et+++ +++++++p+n++ a+aeg+vla i+f i+fG+al  l
  gi|336255257|ref|YP_004598364.1|  93 SAIAVFIGLGVANLVNPG--TGLTLAEDVEFEPEETPDFVEVLVGIVPENPIGAMAEGDVLATIFFVIVFGLALLYL 167
                                       ******************..5666677777788899***************************************** PP

                               SDF 156 gekg.........epllkffeslnevvmkvvkivmklaPigvfaliaslvaskglgalsslakflltvylglaihll 223
                                       +e++         e++++++e+  e+++k+v  +m++  igvfal+a+++++ g++a++s++ +++++++++++h+ 
  gi|336255257|ref|YP_004598364.1| 168 EESSddetvqagiESIFNIVEAGTEALFKLVWGIMEYGVIGVFALMAAVFGEAGADAIASFVILIAALTVAILLHIG 244
                                       99999***********************************************************************9 PP

                               SDF 224 ivlp.llllvltkknplkflkkilpalltAfsTaSSaAtLPvtlecaeknlgvsesiasfvlPlGatinmdGtalye 299
                                       iv++  l++vlt+ +p++fl ++ +a++tA+s +SS++tLPvt+++a +nl+++es+++f lPlGatinmdGta+y+
  gi|336255257|ref|YP_004598364.1| 245 IVYLgGLIMVLTRQSPVAFLAGSKDAIVTALSIRSSSGTLPVTMSNADENLRIDESVYGFSLPLGATINMDGTAMYQ 321
                                       998625778999***************************************************************** PP

                               SDF 300 avaaifiaqlfgvelslgqllllvlvatlasiGaagvPgaglvalllvlsalglpvegialilaidrllDmfrTavN 376
                                       +v+aif+a+l+gv+ls+ +++++vl+a+lasiGa gvPg+gl++l+lvl++lglp+e++++++++d++lD++rT++N
  gi|336255257|ref|YP_004598364.1| 322 GVVAIFAANLVGVQLSIVEQVTVVLIAVLASIGAGGVPGTGLIMLTLVLTQLGLPLEVVGFVAGVDPILDRLRTMTN 398
                                       ***************************************************************************** PP

                               SDF 377 vtGdavaalivakl 390
                                       vtGd++++++va++
  gi|336255257|ref|YP_004598364.1| 399 VTGDLAVTTVVAHW 412
                                       ************97 PP

>> DUF1358  Protein of unknown function (DUF1358)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.9   1.2e-05      0.11      29     105 ..     152     229 ..     144     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                           DUF1358  29 aaasalaGfsktla.lakkkdpkyfekGvaasialkesGaslalralGWGsl.yallGvGllsfaiWkllGvkslqe 103
                                       a++  ++ f+ +l  l   +d + ++ G+++   + e+G+  al  l WG + y ++Gv +l  a++   G+  ++ 
  gi|336255257|ref|YP_004598364.1| 152 ATIFFVIVFGLALLyLEESSDDETVQAGIESIFNIVEAGTE-ALFKLVWGIMeYGVIGVFALMAAVFGEAGADAIAS 227
                                       6677777788776515566788899**************86.9999****877*******************99998 PP

                           DUF1358 104 fr 105
                                       f 
  gi|336255257|ref|YP_004598364.1| 228 FV 229
                                       85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.35
# Mc/sec: 3722.48
//
Query:       gi|336255258|ref|YP_004598365.1|  [L=264]
Description: phosphonate ABC transporter inner membrane subunit [Halopiger xanaduensis SH-6]
Scores for 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-15   55.6  10.9    7.7e-15   55.1  10.9    1.3  1  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.19   11.4   1.4       0.85    9.4   0.1    2.4  3  DUF3104       Protein of unknown function (DUF3104)


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 !   55.1  10.9   8.5e-19   7.7e-15       2     177 ..      92     260 ..      91     264 .] 0.92

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 8.5e-19
                      BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraal 76 
                                       i++++laa  + +n  + +l  + + v +s+ ++v+a+++v       ++g++ l++++++++ ++++   + ++ +
  gi|336255258|ref|YP_004598365.1|  92 IPVALLAAenTTPNVATYWLGKVAVTVSRSVNTIVWALIFV------VVFGSGPLAGVVAIAFRSVGFLGKLLSEEI 162
                                       899******99******************************......99**************************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       ++++ ++vea ra Gas  q++ + ++P+++p ++ + ++++ +++ ++++l f+g++ G+g  l++a +++  ++ 
  gi|336255258|ref|YP_004598365.1| 163 EEIDYGQVEAVRAAGASSVQTMLYGIVPQVKPALVGLSVYRWDINVRDSTILGFVGAG-GIGFELFHAVNAFAWQSV 238
                                       ********************************************************76.7************99988 PP

                      BPD_transp_1 154 snggvlalviavlllnlvadilqr 177
                                       s  ++l +++av++l+ ++ + +r
  gi|336255258|ref|YP_004598365.1| 239 S--MILLTILAVVILSEAVSAYAR 260
                                       8..666666666666655555555 PP

>> DUF3104  Protein of unknown function (DUF3104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.33     3e+03       2      14 ..      20      32 ..      19      36 .. 0.84
   2 ?    9.4   0.1   9.5e-05      0.85      15      56 ..      98     139 ..      83     151 .. 0.79
   3 ?   -0.4   0.0      0.11   9.8e+02      49      64 ..     162     177 ..     161     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.33
                           DUF3104  2 FLgvkaGdlVivk 14
                                      F+++ aG +V+v 
  gi|336255258|ref|YP_004598365.1| 20 FVALLAGTIVVVA 32
                                      8899999999995 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 9.5e-05
                           DUF3104  15 plsnaqsaeedwWmGliihvvggardPsiptLFqvadiDtGv 56 
                                         +n++   + +W+G++   v+ + +  +++L  v+    G 
  gi|336255258|ref|YP_004598365.1|  98 AAENTTPNVATYWLGKVAVTVSRSVNTIVWALIFVVVFGSGP 139
                                       45677777899*********************9888777665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.11
                           DUF3104  49 vadiDtGvvkvvnADe 64 
                                       + +iD G+v  v A  
  gi|336255258|ref|YP_004598365.1| 162 IEEIDYGQVEAVRAAG 177
                                       5689******999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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: 0.41u 0.19s 00:00:00.60 Elapsed: 00:00:00.32
# Mc/sec: 2433.75
//
Query:       gi|336255259|ref|YP_004598366.1|  [L=282]
Description: phosphonate ABC transporter inner membrane subunit [Halopiger xanaduensis SH-6]
Scores for 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-17   61.9  10.6    1.2e-16   61.0  10.6    1.5  1  BPD_transp_1   Binding-protein-dependent transport system inn
  ------ inclusion threshold ------
      0.048   13.5   0.5       0.13   12.2   0.5    1.7  1  Rossmann-like  Rossmann-like domain
       0.19   11.5   3.6       0.21   11.3   0.2    2.4  2  MotA_ExbB      MotA/TolQ/ExbB proton channel family
       0.46    9.8   2.8       0.51    9.7   1.5    1.7  2  ThiF           ThiF family


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 !   61.0  10.6   2.6e-20   1.2e-16       2     182 ..     111     280 ..     110     282 .] 0.94

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 2.6e-20
                      BPD_transp_1   2 illGilaa.lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       ++++++aa + + k+l +l r++i + +++  +++ai++v      +++g + l++ii++++ +++++  + ++ l+
  gi|336255259|ref|YP_004598366.1| 111 VPIAFMAAeNLSPKPLYYLNRGFISISRAFNAIIVAIIVV------KAVGLGPLAGIITITFKTVGFFSKLLAEDLE 181
                                       89999***********************************......******************************* PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                        ++++ v a ra Gas++q++++ v+P+++p ++ + ++++ +++  ++++ ++g++ G+g+ ll+a + ydy    
  gi|336255259|ref|YP_004598366.1| 182 DIDMGSVDAVRATGASPIQTLVYGVVPQIVPRFAGLSVYRWDINIRTSTIVGIVGAG-GIGSILLTAFERYDYG--- 254
                                       *******************************************************76.7***************... PP

                      BPD_transp_1 155 nggvlalviavlllnlvadilqrlldpr 182
                                         +v a++ia+++++lva  + +l+ +r
  gi|336255259|ref|YP_004598366.1| 255 --YVTAILIAIIAVVLVAEGVSALVRRR 280
                                       ..66677777777777777777777766 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   2.8e-05      0.13      12      39 ..     231     259 ..     225     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                     Rossmann-like  12 svGiisaGrvGtalgaaleragh.vvvgi 39 
                                        vGi++aG +G++l +a+er ++  v++i
  gi|336255259|ref|YP_004598366.1| 231 IVGIVGAGGIGSILLTAFERYDYgYVTAI 259
                                       59******************987234444 PP

>> MotA_ExbB  MotA/TolQ/ExbB proton channel family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   4.8e-05      0.21      83     111 ..      89     117 ..      79     123 .. 0.81
   2 ?    0.1   0.3      0.14   6.1e+02      99     114 ..     253     268 ..     228     281 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.8e-05
                                       GGCTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MotA_ExbB  83 lakvapgiaeALiaTalGlvvAipavlay 111
                                       ++k+ +++a A+++T++G+v+++p+ +++
  gi|336255259|ref|YP_004598366.1|  89 VDKMLESVAMAMVSTVTGIVLSVPIAFMA 117
                                       689999****************8877765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHH CS
                         MotA_ExbB  99 lGlvvAipavlaynkl 114
                                       +G v+Ai++ +++ +l
  gi|336255259|ref|YP_004598366.1| 253 YGYVTAILIAIIAVVL 268
                                       7888884444444333 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.5   0.00011      0.51      21      43 ..     232     254 ..     223     264 .. 0.80
   2 ?   -1.9   0.0      0.39   1.8e+03     188     209 ..     256     277 ..     252     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                                       EEEE--SHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  21 vllvGaGglGsellknLalsGvg 43 
                                       v +vGaGg+Gs+ll+++ +   g
  gi|336255259|ref|YP_004598366.1| 232 VGIVGAGGIGSILLTAFERYDYG 254
                                       67************998776655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.39
                                       B-HHHHHHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 188 aiatttavvaglaalellklls 209
                                       ++a ++a++a ++++e + +l 
  gi|336255259|ref|YP_004598366.1| 256 VTAILIAIIAVVLVAEGVSALV 277
                                       578899*********9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2093.14
//
Query:       gi|336255260|ref|YP_004598367.1|  [L=281]
Description: phosphonate ABC transporter ATPase [Halopiger xanaduensis SH-6]
Scores for 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-37  127.3   0.0    7.5e-37  126.9   0.0    1.2  1  ABC_tran      ABC transporter
    1.5e-07   31.6   0.0      0.003   17.4   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00046   20.5   0.1     0.0057   16.9   0.1    2.2  1  AAA_22        AAA domain
     0.0012   18.5   0.0     0.0023   17.6   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0019   18.4   0.0     0.0079   16.4   0.0    2.0  1  AAA_33        AAA domain
     0.0024   17.8   0.1     0.0098   15.8   0.0    1.8  2  RsgA_GTPase   RsgA GTPase
     0.0062   15.9   0.0       0.01   15.2   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0071   16.7   0.1      0.022   15.2   0.1    1.8  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.017   14.8   0.1      0.053   13.2   0.1    1.9  1  AAA_30        AAA domain
      0.022   15.0   0.1       0.37   11.1   0.1    2.3  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.032   14.3   0.0       0.65   10.1   0.0    2.3  2  MMR_HSR1      50S ribosome-binding GTPase
       0.06   13.8   0.0        3.7    8.0   0.0    2.2  2  AAA           ATPase family associated with various cellular 
       0.15   11.5   0.1         16    4.9   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
       0.17   12.4   0.0        0.3   11.6   0.0    1.3  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 !  126.9   0.0   5.9e-40   7.5e-37       1     137 []      18     174 ..      18     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 5.9e-40
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqepqlfpel 74 
                                       l+ v+l+++ +e+va++G++GaGKSt+++++ +l++pt+Gei ldg++l+    + l+s+r+ ig+++qe +l ++l
  gi|336255260|ref|YP_004598367.1|  18 LNGVDLTVEGSETVAMIGPSGAGKSTFIRCVNRLTEPTSGEIYLDGTELTGlknDALRSARRDIGMIFQEYNLVERL 94 
                                       789**********************************************9999999********************* PP

                                       BHHHH.....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEE CS
                                       xxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkll 130
                                       tv en                     e+ +++ ++l+++gl +++++++     +LSgGq+qrv +ara++++pk+l
  gi|336255260|ref|YP_004598367.1|  95 TVMENvltgrlghlsawkafrrdfpaEDVDRAFEILDRVGLGGMENKRA----DELSGGQRQRVGIARAVIQNPKIL 167
                                       *********************9999888889******************....************************ PP

                                       EEESTTT CS
                                       xxxxxxx RF
                          ABC_tran 131 llDEpta 137
                                       l+DEpt+
  gi|336255260|ref|YP_004598367.1| 168 LVDEPTS 174
                                       *****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 !   12.2   0.0   8.9e-05      0.11       3      23 ..      32      52 ..      31     104 .. 0.81
   2 !   17.4   0.0   2.3e-06     0.003     234     283 ..     143     190 ..     111     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.9e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                      ++iGp g+GKS+++++   l 
  gi|336255260|ref|YP_004598367.1| 32 AMIGPSGAGKSTFIRCVNRLT 52
                                      68**************99885 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.3e-06
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.k 283
                                       a+elS G+++  +++ a+++ +   ++ll+DEp ++L+P+    ++ell +
  gi|336255260|ref|YP_004598367.1| 143 ADELSGGQRQRVGIARAVIQNP---KILLVDEPTSSLDPETSDVVMELLtD 190
                                       5677888888878888888777...9*********************9943 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   4.5e-06    0.0057       9     127 ..      32     201 ..      26     210 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.5e-06
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee.................................erpevvfvtlpssts 52 
                                       + +G+sG+GK+t +r + +  +      e                                 e              
  gi|336255260|ref|YP_004598367.1|  32 AMIGPSGAGKSTFIRCVNRLTEPT--SGEiyldgteltglkndalrsarrdigmifqeynlvE-------------- 92 
                                       679*************99997532..2224464444444444444444333333333333332.............. PP

                            AAA_22  53 skdllrellralglelka.............................................erlsseell.eale 83 
                                                        +                                             e+++ +el   + +
  gi|336255260|ref|YP_004598367.1|  93 -----------------RltvmenvltgrlghlsawkafrrdfpaedvdrafeildrvglggmENKRADELSgGQRQ 152
                                       .................14566666666666666666666666666666777799999****999999999988888 PP

                            AAA_22  84 qalrarav...ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliL 127
                                       +   arav   +++l++DE    l+   s+ ++e L ++++  + gv++++
  gi|336255260|ref|YP_004598367.1| 153 RVGIARAViqnPKILLVDEPTSsLDpetSDVVMELLTDIAD--ERGVPVLI 201
                                       888888889999*******99999998669999999999**..99999976 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 !   17.6   0.0   1.8e-06    0.0023      15      45 ..      21      51 ..      16      60 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.8e-06
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqal 45
                                       +++++ ++++ ++GpsG+GKST++  ++ l
  gi|336255260|ref|YP_004598367.1| 21 VDLTVEGSETVAMIGPSGAGKSTFIRCVNRL 51
                                      555666555999************9766665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.2e-06    0.0079       2      59 ..      31      91 ..      31     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.2e-06
                            AAA_33  2 vllvGlpGsGKstlaerl...lkklg.avllssdtlrrrlfgtdqqsktdytrvldrlyqil 59
                                      v ++G++G+GKst+++ +    ++ + +++    t+++ l+++  +s ++ +   ++ y+ +
  gi|336255260|ref|YP_004598367.1| 31 VAMIGPSGAGKSTFIRCVnrlTEP-TsGEIYLDGTELTGLKNDALRSARRDIGMIFQEYNLV 91
                                      679***********9965221333.2466666666677777666666666666666655555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.7e-06    0.0098      98     121 ..      26      50 ..      10      62 .. 0.79
   2 ?   -0.9   0.0         1   1.3e+03      26      62 ..     177     212 ..     158     219 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.7e-06
                                       TT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  98 kd.ktsvlvGqSGvGKStLinallp 121
                                       ++ +t++++G+SG+GKSt+i  ++ 
  gi|336255260|ref|YP_004598367.1|  26 EGsETVAMIGPSGAGKSTFIRCVNR 50 
                                       555899*************987655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                                       TTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HH CS
                       RsgA_GTPase  26 kepelslnlldrfLvlaeekgiepvivlnKiDlleee 62 
                                       + pe+s   ++ +  +a e+g++++i +  +Dl+ ++
  gi|336255260|ref|YP_004598367.1| 177 D-PETSDVVMELLTDIADERGVPVLINIHEVDLARSH 212
                                       4.66666666666667889999999999999998776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     8e-06      0.01      13      65 ..      19      71 ..      10      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8e-06
                      Mg_chelatase 13 raleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65
                                      + +++++ G+  + ++Gp+G+GK+  +++++ l  p s e  l+ ++++ +++
  gi|336255260|ref|YP_004598367.1| 19 NGVDLTVEGSETVAMIGPSGAGKSTFIRCVNRLTEPTSGEIYLDGTELTGLKN 71
                                      56778999************************999999888888877776655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.7e-05     0.022      22      52 ..      27      58 ..      18     219 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-05
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekd...g 52
                                      g+ e v  +G+sG GKs+ +r++  +l++    +
  gi|336255260|ref|YP_004598367.1| 27 GS-ETVAMIGPSGAGKSTFIRCVN-RLTEPtsgE 58
                                      44.78999***************9.577663431 PP

>> AAA_30  AAA 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     0.053      15      48 ..      25      58 ..      20     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.1e-05
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaaggr 48
                                       +g  ++++ Gp G+GK+t ++ ++++ e   g+
  gi|336255260|ref|YP_004598367.1| 25 VEGSETVAMIGPSGAGKSTFIRCVNRLTEPTSGE 58
                                      455668999***************9999987434 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 ?   11.1   0.1   0.00029      0.37      62      89 ..     162     189 ..     125     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                       +++++++ DE  s+lD+e+++ ++ell+
  gi|336255260|ref|YP_004598367.1| 162 QNPKILLVDEPTSSLDPETSDVVMELLT 189
                                       5689*********************996 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0005      0.65       2      18 ..      31      47 ..      30      65 .. 0.86
   2 ?    1.8   0.0      0.19   2.5e+02      19      84 ..     101     170 ..      95     204 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0005
                                      EEEEESTTSSHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLina 18
                                      va +G + +GKSt+i+ 
  gi|336255260|ref|YP_004598367.1| 31 VAMIGPSGAGKSTFIRC 47
                                      89************974 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.19
                                       HHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGC..........SS.HHHHHHHHHHHHHHHHCTSEEEEEEE CS
                          MMR_HSR1  19 ltgekaivsdkpgtTrdinegrvklkgkeielvDtpGl..........ie.gaseekglgkaflaleeadlillvvd 84 
                                       ltg+  + s+++   rd   + v+   + +e++D +Gl          ++ g++++ g+++a+ ++      +l+vd
  gi|336255260|ref|YP_004598367.1| 101 LTGRLGHLSAWKAFRRDFPAEDVD---RAFEILDRVGLggmenkradeLSgGQRQRVGIARAVIQN----PKILLVD 170
                                       555555566666666666666665...689999999954422222211111222222333333332....2344444 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 ?    8.0   0.0    0.0029       3.7       2      52 ..      32      87 ..      31      97 .. 0.67
   2 ?    3.7   0.0     0.061        78      50      98 ..     156     196 ..     130     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                                      EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCS...SSSTTHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakelg..vefleisgsell...skyvgesekkirelfke 52
                                       ++Gp G GK+++++ v + ++  +  + ++g+el+   ++ +  + ++i ++f+e
  gi|336255260|ref|YP_004598367.1| 32 AMIGPSGAGKSTFIRCVNRLTEptSGEIYLDGTELTglkNDALRSARRDIGMIFQE 87
                                      589*************9888743333355555555421144666666666666665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.061
                                       HHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                               AAA  50 fkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                       +++a  + +p+il++DE  +    +       +++vv +Llt + +++ 
  gi|336255260|ref|YP_004598367.1| 156 IARAVIQ-NPKILLVDEPTSSLDPE-------TSDVVMELLTDIADERG 196
                                       3344444.599*****988887666.......78888888888888776 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 ?    4.8   0.1     0.013        16      26      44 ..      30      48 ..      19      56 .. 0.84
   2 ?    4.9   0.0     0.012        16     135     188 ..     144     193 ..      58     223 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.013
                                      EEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                        a++Gp G+GKs ++  +
  gi|336255260|ref|YP_004598367.1| 30 TVAMIGPSGAGKSTFIRCV 48
                                      5689*********998765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.012
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksk 188
                                       ++LSgG+++ v +a       ++   + l+De  + LD +    v ell    +
  gi|336255260|ref|YP_004598367.1| 144 DELSGGQRQRVGIARA----VIQNPKILLVDEPTSSLDPETSDVVMELLTDIAD 193
                                       389****999888744....3455558899************999999986554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023       0.3      21      39 ..      30      48 ..      17      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            AAA_23 21 ltlItGpNGaGKTTildAi 39
                                       ++ +Gp GaGK+T+++++
  gi|336255260|ref|YP_004598367.1| 30 TVAMIGPSGAGKSTFIRCV 48
                                      56789***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2078.09
//
Query:       gi|336255261|ref|YP_004598368.1|  [L=383]
Description: phosphonate ABC transporter periplasmic phosphonate-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-50  170.9   0.0    4.6e-50  170.5   0.0    1.1  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
  ------ inclusion threshold ------
      0.019   14.7   0.0      0.034   13.9   0.0    1.5  1  SBP_bac_11      Bacterial extracellular solute-binding protei
      0.026   14.1   0.0       0.12   11.9   0.0    1.9  2  OpuAC           Substrate binding domain of ABC-type glycine 
          8    6.6   7.0         11    6.2   1.1    2.8  3  PT-VENN         Pre-toxin domain with VENN motif


Domain annotation for each model (and alignments):
>> 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 !  170.5   0.0     1e-53   4.6e-50      10     239 ..     126     357 ..     116     362 .. 0.95

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 1e-53
                                       HHHHHHHHHHHHHHHHHHSSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS-EEEEEEEEETT--SEEE CS
                    Phosphonate-bd  10 aelkeayqpladyLseelGvevelvvatdyaavvealragqvDiaflgplayvqardqagveplatrvrsdGsasyr 86 
                                        +++e++++++d + ee+G+eve+  +++yaa vea+r+++++ia +++ +++ a++  g++p+a+  +sdG+ +yr
  gi|336255261|ref|YP_004598368.1| 126 GRYEEDFEAIFDRIREETGKEVEYNKVDNYAASVEAMRSERAHIANFSTGTTAFAVNLCGAVPFAVGIGSDGAFGYR 202
                                       47899************************************************************************ PP

                                       EEEEEETTSS.--SHHHH..GG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSE CS
                    Phosphonate-bd  87 sviivradsd.iqsledL..kgktiafvspsStsGylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdada 160
                                        + ++rad+d iqs+ed+  ++ t+a + p+S sG+++p+al+ +e++++pe+d++ +fsg+h+++ + +++gd+da
  gi|336255261|ref|YP_004598368.1| 203 LFATTRADADdIQSVEDFarDDVTMAHAEPASNSGHQAPSALFDQEFDVTPEEDYEVEFSGGHSQTTRGIANGDYDA 279
                                       ********877********************************999******************************* PP

                                       EEEEHHHHHHHHHH-HHHH.TTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHH---SHHHHHHHHHTTEEEEE CS
                    Phosphonate-bd 161 aavsadaledlvaegpedk.delrviassppipndpvvvrkelseelkekiqdallslaeteegkkllealgiegfv 236
                                       + +++++++d v+ +++   d++++++ s+p+pn p+++r +l +++ e i++a l+ +   +g +  e+++++ fv
  gi|336255261|ref|YP_004598368.1| 280 GPICSTCMKDTVEGDSSLEfDDFKIVWASNPFPNGPIAYRYNLHPDIIEGIKAAWLETDF--SGTAYAERTDYTEFV 354
                                       ************98877556**************************************97..9************** PP

                                       E-- CS
                    Phosphonate-bd 237 pad 239
                                       p++
  gi|336255261|ref|YP_004598368.1| 355 PIE 357
                                       987 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.6e-06     0.034      83     162 ..     204     280 ..     124     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.6e-06
                                       EEESTT-TT---SHHHHHHSS--EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHT.EEEEESSHHHHHHHHHTTT CS
                        SBP_bac_11  83 iavpkgnpkkikgwadLlkpglklavadPttspsGlaalalleaagaqellkalekk.vvklgessrqlltaveage 158
                                       +a+ +  +++i++++d +++++++a a P+++++ +a  al+++ +   ++ + e+   v ++++ +q++  +++g+
  gi|336255261|ref|YP_004598368.1| 204 FATTRADADDIQSVEDFARDDVTMAHAEPASNSGHQAPSALFDQ-E---FDVTPEEDyEVEFSGGHSQTTRGIANGD 276
                                       455555579********************888888888888888.6...5555555424567999999999999999 PP

                                       -SEE CS
                        SBP_bac_11 159 adag 162
                                       +dag
  gi|336255261|ref|YP_004598368.1| 277 YDAG 280
                                       9998 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 ?   11.9   0.0   2.7e-05      0.12      19     114 ..     135     228 ..     132     244 .. 0.74
   2 ?   -1.2   0.0      0.28   1.2e+03      27      55 ..     255     281 ..     249     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHTTEEEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHHHHHHHHHHHHEEEEEEEESEEECEEEEEEHH CS
                             OpuAC  19 ilkqllekkGykveltnlgstavlfaalasGdiDvypeewtgtayeaykkaveekkglevlgplgagnteglavpky 95 
                                       i   + e+ G +ve+ +++++a+ ++a++s  ++++    tgt++ a++   +  + + + g+ ga ++  +a +++
  gi|336255261|ref|YP_004598368.1| 135 IFDRIREETGKEVEYNKVDNYAASVEAMRSERAHIAN-FSTGTTAFAVNLCGAVPFAVGI-GSDGAFGYRLFATTRA 209
                                       556677899****************************.*****98666663333355554.4445555555555555 PP

                                       HHHHHTTTBHHHHCTHHG..G CS
                             OpuAC  96 vaekygiksisDLkkpae..d 114
                                         ++ +i+s++D+++ ++  +
  gi|336255261|ref|YP_004598368.1| 210 --DADDIQSVEDFARDDVtmA 228
                                       ..566********99998553 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.28
                                       TTEEEEEEEEESHHHHHHHHHTTSSSEEE CS
                             OpuAC  27 kGykveltnlgstavlfaalasGdiDvyp 55 
                                        +y+ve  ++ s + +  ++a+Gd D+ p
  gi|336255261|ref|YP_004598368.1| 255 EDYEVEFSGGHS-Q-TTRGIANGDYDAGP 281
                                       588888888887.4.4799*******987 PP

>> PT-VENN  Pre-toxin domain with VENN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.1    0.0024        11       9      31 ..       8      32 ..       6      38 .. 0.72
   2 ?   -1.7   0.2      0.72   3.2e+03      46      51 ..      60      65 ..      60      66 .. 0.87
   3 ?    2.7   0.0     0.031   1.4e+02       7      28 ..     164     185 ..     162     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0024
                           PT-VENN  9 Kqtv..salstlaaGlaGgvvggtl 31
                                      ++tv  s+++t++aGlaG + ++ +
  gi|336255261|ref|YP_004598368.1|  8 RRTVltSSAATIVAGLAGCTSSDGS 32
                                      5565225678999****99999654 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.72
                           PT-VENN 46 eNNfLs 51
                                      eNN+L 
  gi|336255261|ref|YP_004598368.1| 60 ENNYLA 65
                                      9***96 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.031
                           PT-VENN   7 eEKqtvsalstlaaGlaGgvvg 28 
                                       +E+ ++++ st   + a ++ g
  gi|336255261|ref|YP_004598368.1| 164 SERAHIANFSTGTTAFAVNLCG 185
                                       7***********9999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 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:                        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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3045.67
//
Query:       gi|336255262|ref|YP_004598369.1|  [L=699]
Description: acetate--CoA ligase [Halopiger xanaduensis SH-6]
Scores for complete 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-76  257.5   0.0    2.4e-76  257.1   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    2.7e-24   85.9   0.2    5.9e-24   84.9   0.2    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    4.7e-10   39.2   0.0    4.7e-10   39.2   0.0    3.8  4  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


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 !  257.1   0.0     4e-80   2.4e-76       6     422 ..     123     578 ..     116     579 .. 0.85

  Alignments for each domain:
  == domain 1  score: 257.1 bits;  conditional E-value: 4e-80
                                       HHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                       AMP-binding   6 aktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79 
                                       +++++ va ++   +ge + +TY+el++rvn++A++L+++Gv+ gd+V++++p+ pe v++l+++lk+Ga++vp+ +
  gi|336255262|ref|YP_004598369.1| 123 EERRNNVATIWegeDGEVREVTYHELHRRVNQVANALEERGVETGDTVGLYMPMVPEVVAILYGCLKVGAIAVPIFS 199
                                       56679999999999999*********************99************************************* PP

                                       TS-HHHHHHHHHHHTESEEE.........ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCT CS
                       AMP-binding  80 tltaeelayiledseakvli.........atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseek 146
                                       +++ +++a  led+e++vl+         +        + +++a ++  +v++ iv d+ +++++++++e   ++  
  gi|336255262|ref|YP_004598369.1| 200 GFGVDAVATRLEDAECSVLFtgdgfyrrgD---PVFlKSTADKAIEQAGHVEHAIVFDRLGSSNTRNEHEIPWTDGR 273
                                       *********************999986541...33333444445555567888889998888777655544433322 PP

                                       TS...........-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC..SCCTTT-EEEESS- CS
                       AMP-binding 147 ae...........kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr..fklkeddvvlsilp 210
                                        +           +  e+++l +++  +++Y+SGTTGkPKG++ +h+ +  ++a+ +   +   +lk+ d+++++ +
  gi|336255262|ref|YP_004598369.1| 274 -DewwemavetqdDAYETKSLPSSHESMLLYSSGTTGKPKGIVQTHAGVQVQCAK-E--VYfgMDLKPADRFFWVSD 346
                                       .1356688899995556778889999***********************999888.3..443356888********* PP

                                       TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHH.CHHHHC..... CS
                       AMP-binding 211 lahifglilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalk.aakkak..... 280
                                       + +++g  + l+++ + G+tv ++++ +  +dp++++++i++++ t +   P++++al ++g+++ a          
  gi|336255262|ref|YP_004598369.1| 347 IGWMMGP-WTLIGTHTFGGTVFMYEGAPNyPDPDRFWAMIDRHSLTQFGISPTAVRALRKHGERQtA-S--Depsgs 419
                                       ******7.*********************888**************************998877733.1..123556 PP

                                       ............CGTT-SEEEEESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE CS
                       AMP-binding 281 ............dlsslrlvllggeplspellrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkp 342
                                                   dlsslr++ + gep  pe +r+f++ +g+   +++++ G TE +g++  +p + +  k+ + G p
  gi|336255262|ref|YP_004598369.1| 420 vgvgedewledhDLSSLRILGSTGEPWDPESWRWFYENVGNgecPIINISGGTEICGCFL-MPMPIQSLKPCTLGGP 495
                                       777777777777****************************9******************8.5556665678899*** PP

                                       -TTEEEEEE-TTTSCBEE.TTSEEEEEEEET..TS-SEBTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEE CS
                       AMP-binding 343 lpgvevkivDeetgepvp.dgeeGellvrgp..gvmkgYlkkpeataeafdse.grwlrTGDlgrldedGyleivgR 415
                                         g+++ ivDee g+ v+ d+e G l+ r+   +++k  +  +e+  e ++s  +++   GD + +dedG  ++ gR
  gi|336255262|ref|YP_004598369.1| 496 GLGMDIDIVDEE-GNSVKdDNERGYLVARSScpSMTKSLWAGDERYLEEYWSTwEDLWDHGDWAQRDEDGFWFLHGR 571
                                       ***********9.5666526777******97558*******99********756689999***************** PP

                                       CCCEEEE CS
                       AMP-binding 416 kkdlikl 422
                                       ++d +++
  gi|336255262|ref|YP_004598369.1| 572 ADDALNV 578
                                       ***9876 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 !   84.9   0.2   9.8e-28   5.9e-24       1      76 []     587     665 ..     587     665 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 9.8e-28
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evE al+ h+aV++aa++G pde++G a+va+Vvl+dg+ea   l+eeL+a+v +elg+  +p++v fvde+pkt+s
  gi|336255262|ref|YP_004598369.1| 587 EVEGALIDHEAVNQAAAIGAPDETTGTAVVAYVVLEDGYEAsddLREELRAQVGAELGKPFRPREVLFVDEFPKTQS 663
                                       8**********************************999533357********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|336255262|ref|YP_004598369.1| 664 GK 665
                                       *9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   7.9e-14   4.7e-10      13      55 .]      69     114 ..      49     114 .. 0.87
   2 ?    1.8   0.0     0.038   2.3e+02      11      23 ..     377     390 ..     368     408 .. 0.77
   3 ?   -2.0   0.4      0.61   3.6e+03      38      45 ..     448     455 ..     439     457 .. 0.78
   4 ?   -2.8   2.0       1.1   6.3e+03       6      16 ..     556     566 ..     539     571 .. 0.68

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 7.9e-14
                                       HHHHHHHHCC..S--SB--S-SECSTTTC.T-EESTT-EE-HHHHH CS
                            ACAS_N  13 eaFWaeqake..ldWekpfdkvldgskgp.fikWFeGGklNicyNc 55 
                                       e+FW+e+ +   +++++++d++ d+s+gp f+ W++GG+lN+++N+
  gi|336255262|ref|YP_004598369.1|  69 EWFWDEVVDYlgIEFDEDYDEIRDDSDGPqFTDWYVGGELNVAHNV 114
                                       99*******888********************************96 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.038
                                       -HHHHHHHHHCC.S CS
                            ACAS_N  11 dpeaFWaeqake.l 23 
                                       dp++FWa + ++ l
  gi|336255262|ref|YP_004598369.1| 377 DPDRFWAMIDRHsL 390
                                       9*****98877654 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.61
                                       TCT-EEST CS
                            ACAS_N  38 gpfikWFe 45 
                                       +++++WF 
  gi|336255262|ref|YP_004598369.1| 448 PESWRWFY 455
                                       349****5 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1.1
                                       HHHHH-HHHHH CS
                            ACAS_N   6 keSiedpeaFW 16 
                                       +++ +d ++FW
  gi|336255262|ref|YP_004598369.1| 556 DWAQRDEDGFW 566
                                       34555666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (699 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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 0.20s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 5332.26
//
Query:       gi|336255263|ref|YP_004598370.1|  [L=109]
Description: hypothetical protein Halxa_3886 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00016   22.2   3.9    0.00025   21.6   3.9    1.6  1  SlyX          SlyX
    0.00025   20.5   1.1    0.00025   20.5   1.1    2.0  2  Tropomyosin   Tropomyosin
     0.0057   16.3   0.6     0.0068   16.1   0.6    1.1  1  Lebercilin    Ciliary protein causing Leber congenital amauro
     0.0076   15.3   0.1     0.0079   15.2   0.1    1.1  1  IFT57         Intra-flagellar transport protein 57
  ------ inclusion threshold ------
      0.026   15.1   1.4      0.031   14.9   1.4    1.1  1  Striatin      Striatin family
      0.034   12.7   0.2      0.036   12.6   0.2    1.0  1  Herpes_UL6    Herpesvirus UL6 like
       0.05   13.0   4.9      0.057   12.8   4.9    1.1  1  DUF4407       Domain of unknown function (DUF4407)
      0.098   12.7   1.3       0.18   11.8   1.3    1.5  1  TMF_DNA_bd    TATA element modulatory factor 1 DNA binding
       0.12   12.4   0.1        0.2   11.8   0.1    1.5  1  IFP_35_N      Interferon-induced 35 kDa protein (IFP 35) N-te
       0.14   11.7   6.0       0.17   11.4   0.8    1.9  2  MscS_porin    Mechanosensitive ion channel porin domain
       0.14   12.3   0.8        0.2   11.8   0.8    1.2  1  bZIP_1        bZIP transcription factor
       0.16   11.8   0.6       0.21   11.4   0.6    1.2  1  SKA1          Spindle and kinetochore-associated protein 1
       0.18   11.9   1.2       0.48   10.5   1.2    1.7  1  PspB          Phage shock protein B
       0.18   12.2   1.0       0.32   11.4   1.0    1.3  1  FlaC_arch     Flagella accessory protein C (FlaC)
       0.25   10.2   2.8       0.32    9.8   2.8    1.1  1  Spc7          Spc7 kinetochore protein
       0.59   10.5   5.2        0.8   10.1   5.2    1.1  1  CCDC53        Subunit CCDC53 of WASH complex
        1.2    9.6   0.1        1.2    9.6   0.1    2.4  1  LPP           Lipoprotein leucine-zipper
        3.9    8.0  10.1       0.64   10.5   0.9    2.1  2  DUF4140       N-terminal domain of unknown function (DUF4140)
        5.6    7.3  10.1    2.6e+02    2.0  10.1    2.4  1  ABC_tran_CTD  ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   3.9   2.7e-07   0.00025       2      42 ..       3      43 ..       2      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.7e-07
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX  2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrl 42
                                      ++r+e+LE+ +a +e t+e L d+++e  ++i  l+++l++
  gi|336255263|ref|YP_004598370.1|  3 NNRVEQLESTVAELESTVEGLTDELIEAKERIRVLEAELDA 43
                                      58************************************986 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   1.1   2.7e-07   0.00025     189     229 ..       3      43 ..       1      46 [. 0.95
   2 ?   -1.9   3.7       1.9   1.8e+03       7      38 ..      56      87 ..      51      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.7e-07
                       Tropomyosin 189 eeRaeeAErsvqkLekevdrledeleaekekykaiseeLdq 229
                                       ++R e+ E +v++Le++v+ l del ++ke+++ +++eLd 
  gi|336255263|ref|YP_004598370.1|   3 NNRVEQLESTVAELESTVEGLTDELIEAKERIRVLEAELDA 43 
                                       68*************************************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.9
                       Tropomyosin  7 eeeldeaeerlekakkkleeaekkaekaeaEv 38
                                      + e+d++    e+a ++++ea++ a++ +aE 
  gi|336255263|ref|YP_004598370.1| 56 KAETDDTATTTEAAPDEVAEATADAANVDAET 87
                                      56788888888888888888888888877775 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.6   7.3e-06    0.0068     120     182 ..      14      76 ..       5      84 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.3e-06
                        Lebercilin 120 eeLqkkLeeleakleekeekikeLerkleleeksfrrqlaaekkktkeaqeevkalqeeierl 182
                                       +eL++ +e l+++l e++e+i+ Le +l+ e+ ++  + ++ k  t ++ ++++a+ +e+ + 
  gi|336255263|ref|YP_004598370.1|  14 AELESTVEGLTDELIEAKERIRVLEAELDAETPTRVPERRSDKAETDDTATTTEAAPDEVAEA 76 
                                       69******************************************************9999875 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   8.4e-06    0.0079     234     315 ..       7      88 ..       1     104 [. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.4e-06
                             IFT57 234 ksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaei 310
                                       +++e+++ e++s ++ l +++ ++ e+i   E  l+ +  + + e r+ ++e +++    + + ++v e t + a++
  gi|336255263|ref|YP_004598370.1|   7 EQLESTVAELESTVEGLTDELIEAKERIRVLEAELDAETPTRVPERRSDKAETDDTATTTEAAPDEVAEATADAANV 83 
                                       589999**********************************************************************9 PP

                             IFT57 311 seele 315
                                       + e +
  gi|336255263|ref|YP_004598370.1|  84 DAETD 88 
                                       99876 PP

>> Striatin  Striatin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.4   3.3e-05     0.031      29     120 ..       8      91 ..       4     106 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-05
                          Striatin  29 EmkarIakLegerrgaenlkkdlvrrikmLEyalkqerakylklkegtsaakenkkkekeeeeaeeeekseeesksk 105
                                       ++ + +a+Le    g      + + ri++LE +l  e     ++ e  s++ e++++      a+++e++++e  + 
  gi|336255263|ref|YP_004598370.1|   8 QLESTVAELESTVEGLTDELIEAKERIRVLEAELDAETPT--RVPERRSDKAETDDT------ATTTEAAPDEVAEA 76 
                                       578999******9999999999***************754..332222222222222......22222222222222 PP

                          Striatin 106 ekksakeslkkseae 120
                                       ++++a+ ++++ ++e
  gi|336255263|ref|YP_004598370.1|  77 TADAANVDAETDADE 91 
                                       222222222222122 PP

>> Herpes_UL6  Herpesvirus UL6 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   3.9e-05     0.036     362     438 ..       1      75 [.       1      95 [. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.9e-05
                        Herpes_UL6 362 vsnsvikcleeqineqfdtiekLkkenelllkklkelekeLerlreeakkeakarevdlltsstdaslenlpessal 438
                                       +sn+ ++ le+ + e+  t+e+L +e    +++++ le eL++ +  +    ++r+++  t +t+++ e  p + a 
  gi|336255263|ref|YP_004598370.1|   1 MSNNRVEQLESTVAELESTVEGLTDELIEAKERIRVLEAELDAETPTRVP--ERRSDKAETDDTATTTEAAPDEVAE 75 
                                       57888999**********************************99777764..4555555555555555554444333 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   4.9   6.1e-05     0.057     129     212 ..       7      93 ..       1     107 [. 0.64

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                           DUF4407 129 aaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk......gtgttgvaGkgpaakekkaqldaaqael 199
                                       ++l++++aele+ ++ l  e+ +a++r++ l+ae+++e+          +     +    + ++++ ++ ++a+a+ 
  gi|336255263|ref|YP_004598370.1|   7 EQLESTVAELESTVEGLTDELIEAKERIRVLEAELDAETPTRVperrsdK---AETDDTATTTEAAPDEVAEATADA 80 
                                       45889999999999999999999999999999999999775555543221...222333334444555555666666 PP

                           DUF4407 200 aelkakldatarl 212
                                       a+++a+ da+++ 
  gi|336255263|ref|YP_004598370.1|  81 ANVDAETDADEAP 93 
                                       6666664444443 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.3   0.00019      0.18      32      72 ..       3      43 ..       1      45 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                        TMF_DNA_bd 32 nntikkLrkknkelekeikelkkkleklekeleeleerlke 72
                                      nn + +L ++++ele++++ l+++l +  + +  le++l++
  gi|336255263|ref|YP_004598370.1|  3 NNRVEQLESTVAELESTVEGLTDELIEAKERIRVLEAELDA 43
                                      78888999999999999999998888888888888888875 PP

>> IFP_35_N  Interferon-induced 35 kDa protein (IFP 35) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00021       0.2       3      28 ..      21      46 ..      19      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                          IFP_35_N  3 aeitkeniqLkeeiqkLeaELQettr 28
                                      + +t+e i+ ke+i+ LeaEL  +t 
  gi|336255263|ref|YP_004598370.1| 21 EGLTDELIEAKERIRVLEAELDAETP 46
                                      678999***************98775 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8   0.00018      0.17      99     145 ..       4      50 ..       2      60 .. 0.81
   2 ?    4.0   1.1     0.033        31      32      73 ..      52      93 ..      48     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                        MscS_porin  99 eqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaagea 145
                                       ++  ql+s ++el++  e +  +l ea++r+  ++++L++  ++  +
  gi|336255263|ref|YP_004598370.1|   4 NRVEQLESTVAELESTVEGLTDELIEAKERIRVLEAELDAETPTRVP 50 
                                       78899*********************************877443333 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.033
                        MscS_porin 32 idkskkkaeelqkaiddaPkelrelqqelealqkkkeeaske 73
                                      ++  k+++++  ++ + aP e++e++++ ++ +++++++ ++
  gi|336255263|ref|YP_004598370.1| 52 RRSDKAETDDTATTTEAAPDEVAEATADAANVDAETDADEAP 93
                                      5667899999999999**********9999996555555544 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.8   0.00021       0.2      27      62 ..       5      40 ..       3      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 27 eieeLerrvkaLekeNksLkseleelkkevekLksk 62
                                      ++e+Le+ v++Le+  + L +el e k+ +  L+ +
  gi|336255263|ref|YP_004598370.1|  5 RVEQLESTVAELESTVEGLTDELIEAKERIRVLEAE 40
                                      799********************9999999877665 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   0.00022      0.21      23     116 ..       4      89 ..       1     106 [. 0.45

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SKA1  23 edlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaassaeeskssspe 99 
                                       + ++++e++v +le++++ l +el e +e i  l++e++a            + +p++  +k ++  + +++++ p+
  gi|336255263|ref|YP_004598370.1|   4 NRVEQLESTVAELESTVEGLTDELIEAKERIRVLEAELDAET---------PTRVPERRSDKAETDDTATTTEAAPD 71 
                                       456667777777777777777777777777777776666555.........22333332222222222222222222 PP

                                       XXXXXXXXXX.XXXXXXX CS
                              SKA1 100 eeeeteskke.keeeaek 116
                                       e  e++++++  ++e+++
  gi|336255263|ref|YP_004598370.1|  72 EVAEATADAAnVDAETDA 89 
                                       222211111122222222 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.2   0.00051      0.48      40      70 ..      17      47 ..       2      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00051
                              PspB 40 ekrLeellekAekleeRietLEriLdaespn 70
                                      e+++e l+++  + +eRi+ LE+ Ldae+p+
  gi|336255263|ref|YP_004598370.1| 17 ESTVEGLTDELIEAKERIRVLEAELDAETPT 47
                                      567788888888899**************96 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 ?   11.4   1.0   0.00034      0.32       1      34 [.       5      38 ..       5      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                         FlaC_arch  1 ridelEnklsklsteletvkkeneelsksveelk 34
                                      r+++lE+ + +l++++e + +e+ e ++ +  l+
  gi|336255263|ref|YP_004598370.1|  5 RVEQLESTVAELESTVEGLTDELIEAKERIRVLE 38
                                      899********************99999998776 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.8   0.00034      0.32     183     259 ..       6      86 ..       2      94 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00034
                              Spc7 183 leklqeaaeeles.id..keeLeelreelaelkaeiee.kkkelaelqeqleeleekieelkeqkseleeeiaeaer 255
                                       +e+l++ ++eles ++   +eL e++e+++ l+ae+++   +++ e++++++e +++ +++++  +e+ e++a a +
  gi|336255263|ref|YP_004598370.1|   6 VEQLESTVAELEStVEglTDELIEAKERIRVLEAELDAeTPTRVPERRSDKAETDDTATTTEAAPDEVAEATADAAN 82 
                                       34444444444443222356777788888877777764144667777777777777777777777777777777776 PP

                              Spc7 256 vlee 259
                                       v  e
  gi|336255263|ref|YP_004598370.1|  83 VDAE 86 
                                       6554 PP

>> CCDC53  Subunit CCDC53 of WASH complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.2   0.00085       0.8       9     102 ..       6      98 ..       2     106 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00085
                            CCDC53   9 vqfLNrFatecEekLvevekrlqrleitlalLEakLsSipgleeveaeaaeastsddnaarkgppppppsseaaaaa 85 
                                       v+ L+   +e E+ +  ++++l ++  ++++LEa L++ ++ + v +++++++++dd+a++++++p++ + ++a+aa
  gi|336255263|ref|YP_004598370.1|   6 VEQLESTVAELESTVEGLTDELIEAKERIRVLEAELDA-ETPTRVPERRSDKAETDDTATTTEAAPDEVAEATADAA 81 
                                       45566666677777777788888888888888888887.45555555555555555555555555555444444444 PP

                            CCDC53  86 aqaeeasqaeesaeeea 102
                                       ++ +e  + e+ + +ea
  gi|336255263|ref|YP_004598370.1|  82 NVDAETDADEAPSGDEA 98 
                                       44444444333333333 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0013       1.2       7      35 ..       4      32 ..       2      40 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                               LPP  7 sqVsqLkskvdqlssdvnsakaaaqaake 35
                                      + V+qL+s v++l+s v+ + +++ +ake
  gi|336255263|ref|YP_004598370.1|  4 NRVEQLESTVAELESTVEGLTDELIEAKE 32
                                      56777778888888777777777777765 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 ?   10.5   0.9   0.00068      0.64      60      96 ..       7      42 ..       1      44 [. 0.74
   2 ?    2.3   3.0      0.25   2.4e+02      56      94 ..      48      86 ..      41      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00068
                           DUF4140 60 reaeeeelkalraeleeledelaaledelaaaearla 96
                                      ++ e++ +++l++++e l+del +++++++++ea+l+
  gi|336255263|ref|YP_004598370.1|  7 EQLEST-VAELESTVEGLTDELIEAKERIRVLEAELD 42
                                      333333.889999999999999999999999998876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.25
                           DUF4140 56 rvpnreaeeeelkalraeleeledelaaledelaaaear 94
                                      rvp+r+++++e + +  + e++ de a++++++a+++a+
  gi|336255263|ref|YP_004598370.1| 48 RVPERRSDKAETDDTATTTEAAPDEVAEATADAANVDAE 86
                                      567777777778888888888888888888888888776 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 ?    2.0  10.1      0.27   2.6e+02       9      58 ..       5      42 ..       2      92 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.27
                      ABC_tran_CTD  9 eleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLe 58
                                      + e+le++ ++LE   + l++e            l e+ +++  leaeL+
  gi|336255263|ref|YP_004598370.1|  5 RVEQLESTVAELESTVEGLTDE------------LIEAKERIRVLEAELD 42
                                      3455555555555555555555............5555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1181  (0.0658709); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                       135  (0.0075297); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 888.15
//
Query:       gi|336255264|ref|YP_004598371.1|  [L=1196]
Description: chromosome segregation protein SMC [Halopiger xanaduensis SH-6]
Scores for 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-41  140.1  85.0    7.6e-40  136.7  85.0    2.9  1  SMC_N           RecF/RecN/SMC N terminal domain
      1e-30  106.4   0.0    2.9e-30  105.0   0.0    1.9  1  SMC_hinge       SMC proteins Flexible Hinge Domain
    2.2e-13   51.1  24.4    2.2e-13   51.1  24.4    9.3  1  AAA_23          AAA domain
    2.1e-12   47.5   0.1    1.1e-06   28.7   0.0    5.7  4  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    6.5e-09   35.0 115.6      0.011   14.4  29.4    6.1  6  AAA_13          AAA domain
    1.6e-08   34.7  17.2    1.6e-08   34.7  17.2    5.2  2  AAA_15          AAA ATPase domain
    4.1e-08   32.7  99.8     0.0077   15.4  16.4    7.3  7  Atg14           Vacuolar sorting 38 and autophagy-related sub
    4.5e-08   31.2  66.4    2.9e-07   28.5  53.5    4.1  4  DUF3584         Protein of unknown function (DUF3584)
    6.6e-08   31.8 158.3      0.011   14.7  29.1    9.0  8  Spc7            Spc7 kinetochore protein
    1.9e-06   27.5   0.4    8.7e-06   25.4   0.0    2.1  2  AAA_29          P-loop containing region of AAA domain
    3.2e-06   27.2  87.7    0.00077   19.5   5.2   10.1 11  DUF1664         Protein of unknown function (DUF1664)
    7.5e-05   23.1  55.6      0.014   15.9   2.9   10.5  9  NPV_P10         Nucleopolyhedrovirus P10 protein
     0.0001   20.6  19.8     0.0001   20.6  19.8    5.2  5  EzrA            Septation ring formation regulator, EzrA
    0.00025   21.4   6.4    0.00025   21.4   6.4   13.2  7  ZapB            Cell division protein ZapB
    0.00038   19.8   5.0    0.00038   19.8   5.0    7.9  8  TMPIT           TMPIT-like protein
    0.00081   18.8 105.9      0.015   14.6  16.3    6.2  5  DUF4407         Domain of unknown function (DUF4407)
    0.00089   18.7  20.1    0.00089   18.7  20.1    8.5  8  GAS             Growth-arrest specific micro-tubule binding
    0.00091   19.3 178.1       0.04   13.9  24.1    9.1  9  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
     0.0012   18.2   8.1     0.0012   18.2   8.1    9.6  9  DUF3450         Protein of unknown function (DUF3450)
     0.0028   17.7   5.0     0.0028   17.7   5.0    9.1 10  Laminin_II      Laminin Domain II
     0.0029   17.9  25.7     0.0029   17.9  25.7    9.1  8  ATG16           Autophagy protein 16 (ATG16)
     0.0043   17.2 159.1       0.26   11.4  28.6    7.6  7  UPF0242         Uncharacterised protein family (UPF0242) N-te
     0.0059   16.5  18.3     0.0059   16.5  18.3    7.8  8  DUF724          Protein of unknown function (DUF724)
     0.0094   16.0   2.8     0.0094   16.0   2.8    9.8  9  TolA_bind_tri   TolA binding protein trimerisation
  ------ inclusion threshold ------
      0.034   14.2  34.5       0.64   10.0   4.1    7.2  7  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
      0.062   13.8 193.7       0.44   11.1  25.2    9.3  8  APG6_N          Apg6 coiled-coil region
      0.066   13.7  79.5       0.69   10.4   5.6    9.8 10  T3SSipB         Type III cell invasion protein SipB
      0.087   13.1 112.4        2.6    8.4   6.4   10.1  6  DUF5082         Domain of unknown function (DUF5082)
      0.098   12.8  83.4       0.41   10.8  10.3    7.7  7  Fib_alpha       Fibrinogen alpha/beta chain family
       0.26   11.7 142.2      0.018   15.5  16.1    7.5  4  Fez1            Fez1
       0.69    9.4 118.1      0.015   14.9  22.1    6.5  5  MscS_porin      Mechanosensitive ion channel porin domain
       0.83    9.3  76.3      0.016   15.0  13.7    6.6  6  DUF745          Protein of unknown function (DUF745)
       0.88   10.0  54.9        8.8    6.8   0.4   11.6 10  LPP             Lipoprotein leucine-zipper
       0.92    7.4  58.9     0.0067   14.5   3.4    4.7  4  Prominin        Prominin
        5.2    7.1 153.3      0.034   14.2  15.2    9.6  9  TPR_MLP1_2      TPR/MLP1/MLP2-like protein


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 !  136.7  85.0   1.5e-42   7.6e-40       2     219 ..       3    1174 ..       2    1175 .. 0.99

  Alignments for each domain:
  == domain 1  score: 136.7 bits;  conditional E-value: 1.5e-42
                                        EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.....BTTC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxx RF
                             SMC_N    2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.....skek 71  
                                        +k ++++nFks+ g+++++pf + ft+++GpNGSGKsn++d+ilF LG + ++ +r+ekl+dli++      +++
  gi|336255264|ref|YP_004598371.1|    3 IKAVVLDNFKSF-GRKTKIPFYEDFTVVTGPNGSGKSNIIDSILFALGLARTRGIRAEKLTDLIYNpghedGSSS 76  
                                        899*********.5****************************************************998776778 PP

                                        SSTTEEEEEEEEEETTEE.............SSSSSSCEEEEEEEETTSE...EEEEETTEEE-HHHHHHHHHCT CS
                                        xxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   72 asvkkaeveitfdnedkk.............lkiekeevsisrrvkrkge...seykingkevtkkevsellesa 130 
                                        +   +a+ve+++dn+d +              + + +e+ i+rrvk++++   s y++n+++v+ +++++ll++a
  gi|336255264|ref|YP_004598371.1|   77 SGPREATVEVVLDNSDGTldrsqvvnaagsdDVGDVDEIRIRRRVKETEDnyySYYYLNDRSVNLSDIQDLLAQA 151 
                                        8899************9999999999988777778899********9999888999******************* PP

                                        T-STT...................................................................... CS
                                        xxxxx...................................................................... RF
                             SMC_N  131 giske...................................................................... 135 
                                        g+++e                                                                      
  gi|336255264|ref|YP_004598371.1|  152 GVTPEgynvvmqgdvteiinmtpharreiideiagvaefdakkedafeelevveerideaelrieekrdrleqle 226 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|336255264|ref|YP_004598371.1|  227 derrtalryrrlrdekeeyegykkaseleekreeldaaeekvdelaeeledlqrelderqgkvvrlqedledlna 301 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|336255264|ref|YP_004598371.1|  302 eierkgedeqlrikseieeikgdisrledkieaseehieeaeskrreafvqidrkqeeieeledemrehklekas 376 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|336255264|ref|YP_004598371.1|  377 ikteiqereqekkqleaeidavdtefdelkadlaerkeeledaktekndlqreqdrlldearrrsneisekegti 451 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|336255264|ref|YP_004598371.1|  452 edrreeipelesrksdlkrelekaeknraniagvvddlkdekrriqsdidelddeiqakqqeyaeleanagesgd 526 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|336255264|ref|YP_004598371.1|  527 ssfgrsvttilnsgidgvhgavaqlgnvsgeyavacetaaggrlanvvvdddvvgqqciehlksrnagratflpl 601 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|336255264|ref|YP_004598371.1|  602 tdmsqrrlpnapsdpgvvdfaynlvdfddqyagvfsyvlgdtlvvedietarsymgdyrmvtldgdlveksgamt 676 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|336255264|ref|YP_004598371.1|  677 ggsgsgsrysftgggegqlervakqitelqeereslredlrgveerlddardrktdaadevrsieseiesledkr 751 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|336255264|ref|YP_004598371.1|  752 esiedeietleteleelreeresvdermndisgeideqtaaieeiqadideleaeledskipelteqieelegei 826 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|336255264|ref|YP_004598371.1|  827 dereaqideidgtlnelelekeyaedaieglhddieaaqnkkaehenrieeceatieekeaeleekreaveelee 901 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|336255264|ref|YP_004598371.1|  902 elaelkedrnelredledartkrdqqqdrvnavqskleskrervqdleweieglesevgdydpedvpdhdtvlem 976 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|336255264|ref|YP_004598371.1|  977 ielltadmeamepvnmlaideydevredleeledakdtlveeaegirdrieqyetqkketfmtayeaisehftei 1051
                                        *************************************************************************** PP

                                        .......................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                        .......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  136 .......................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171 
                                                                               ++SgGek+L+ala++fAiq+ +pap+y lDe+da L
  gi|336255264|ref|YP_004598371.1| 1052 feklsegtgtlhleneddpfdggltmkaqpgdkpiqrldAMSGGEKSLTALAFIFAIQRHNPAPFYALDEVDAFL 1126
                                        *************************************************************************** PP

                                        -HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETTEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  172 DeknvkkvaellkeksknaQfivislreemlekadklvgvtkvengvs 219 
                                        D+ n +++ e+++e  ++aQf+v+s+r+ ml ++++ +gvt+++++vs
  gi|336255264|ref|YP_004598371.1| 1127 DAVNAERIGEMVEELADEAQFVVVSHRSAMLDRSQRAIGVTMQQDNVS 1174
                                        ******************************************999876 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 !  105.0   0.0   5.7e-33   2.9e-30       2     116 ..     542     655 ..     541     656 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 5.7e-33
                         SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkns 78 
                                        gv+G +a+l +v  +y +A e+a+g+rl ++vv+d+ + +++ie+lk++nagratflpl +++q++ ++++ d + 
  gi|336255264|ref|YP_004598371.1| 542 DGVHGAVAQLGNVSGEYAVACETAAGGRLANVVVDDDVVGQQCIEHLKSRNAGRATFLPLTDMSQRRLPNAPSDPG- 617
                                       69************************************************************************99. PP

                         SMC_hinge  79 gavplidlvevddelrkalryllgdtlvvdsldeAeel 116
                                        + ++ +lv++dd+++ ++ y+lgdtlvv+++++A+ +
  gi|336255264|ref|YP_004598371.1| 618 VVDFAYNLVDFDDQYAGVFSYVLGDTLVVEDIETARSY 655
                                       ***********************************986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1  24.4   4.4e-16   2.2e-13       3     200 .]       7     276 ..       5     333 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 4.4e-16
                            AAA_23   3 kienfrsf.rdqeidFskgltlItGpNGaGKTTildAiklaLyget.prlsrks....grgfeksdveiesegkvka 73 
                                        + nf+sf r+++i F   +t++tGpNG+GK+ i+d i +aL+    ++ + ++      +  ++d + +s+g  +a
  gi|336255264|ref|YP_004598371.1|   7 VLDNFKSFgRKTKIPFYEDFTVVTGPNGSGKSNIIDSILFALGLARtRGIRAEKltdlIYNPGHEDGS-SSSGPREA 82 
                                       689*****77778*****************************97441444444464432233333333.34478899 PP

                            AAA_23  74 yveltfenkdgry..................trsiererelskkkgkttkkaklelleideleqfise........l 124
                                        ve+ + n dg+                     +i+r+ ++++++  +++  + ++++ ++ ++++ +        +
  gi|336255264|ref|YP_004598371.1|  83 TVEVVLDNSDGTLdrsqvvnaagsddvgdvdEIRIRRRVKETEDNYYSYYYLNDRSVNLSDIQDLLAQagvtpegyN 159
                                       9********9999****************988888889999999999999999**************9999999998 PP

                            AAA_23 125 lgskkiilnlilflgqer.................feefelkdkke..........rleelekeleeledekkllek 174
                                       +  + +  ++i + +  r                 +         +          r++e+e  +ee+ d+ ++le+
  gi|336255264|ref|YP_004598371.1| 160 VVMQGDVTEIINMTPHARreiideiagvaefdakkE---------DafeelevveeRIDEAELRIEEKRDRLEQLED 227
                                       888899999999999999777777666665544441.........12333444444777777777777777777777 PP

                            AAA_23 175 l.......................eqekekekeleeleeeleeilkele 200
                                       +                        +++ek++el++ ee+  e+ +ele
  gi|336255264|ref|YP_004598371.1| 228 ErrtalryrrlrdekeeyegykkaSELEEKREELDAAEEKVDELAEELE 276
                                       7888888888887778888887776777777777777777777777775 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 !   26.2   0.0   1.2e-08   6.3e-06       1      26 [.      26      55 ..      26     136 .. 0.79
   2 ?   -1.9   2.4       4.4   2.2e+03      78     132 ..     749     803 ..     677     871 .. 0.55
   3 ?   -1.9   0.3       4.4   2.2e+03      60     136 ..     858     935 ..     829     946 .. 0.70
   4 !   28.7   0.0   2.2e-09   1.1e-06     175     302 ..    1047    1157 ..     989    1158 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.2e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl....d 26
                                      ++v++GpNgsGKSn++d + ++ +l     
  gi|336255264|ref|YP_004598371.1| 26 FTVVTGPNGSGKSNIIDSILFALGLartrG 55
                                      89*******************988775331 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.4
                            AAA_21  78 lersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsv 132
                                        +r+ +e+ + ++et le     +++++e++++ + e +++ + + + ++   ++
  gi|336255264|ref|YP_004598371.1| 749 DKRESIEDEIETLETELEELREERESVDERMNDISGEIDEQTAAIEEIQADIDEL 803
                                       2222223333333333333333333333333333333333333333333333333 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.4
                            AAA_21  60 feieeflsqgvryryglrlersqv..eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvse 134
                                       + ++    q+++ +++ r+e+     eek  ++e+++e  + l ++ +e   + n   ++  + ++ + +++  v+ 
  gi|336255264|ref|YP_004598371.1| 858 HDDI-EAAQNKKAEHENRIEECEAtiEEKEAELEEKREAVEELEEELAELKEDRNELREDLEDARTKRDQQQDRVNA 933
                                       5555.555666666666777777777888888888888888888888877777777777777777777777766666 PP

                            AAA_21 135 pn 136
                                        +
  gi|336255264|ref|YP_004598371.1| 934 VQ 935
                                       55 PP

  == domain 4  score: 28.7 bits;  conditional E-value: 2.2e-09
                            AAA_21  175 yfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrl.l.al 247 
                                        +f++  ek   +  + +l   +++ +                    ++   +gd     ++ +S G k+l + a+
  gi|336255264|ref|YP_004598371.1| 1047 HFTEIFEKLSEGTGTLHLENEDDPFDGG-----------------LTMKAQPGDKPIQRLDAMSGGEKSLtAlAF 1104
                                        4444444444444444444444333333.................667777788888889999*******63255 PP

                            AAA_21  248 ltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302 
                                        + a+ r ++  +++++DE++++L+    +r+ e+++el++  aQ+++++H    l
  gi|336255264|ref|YP_004598371.1| 1105 IFAIQRHNPA-PFYALDEVDAFLDAVNAERIGEMVEELAD-EAQFVVVSHRSAML 1157
                                        5555544444.************************99999.9********76655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       4.2   2.2e+03      10      31 ..      18      39 ..      11      44 .. 0.75
   2 !   14.4  29.4   2.2e-05     0.011     276     467 ..     197     381 ..     187     384 .. 0.77
   3 !   11.5  21.8   0.00016     0.083     315     447 ..     380     522 ..     372     527 .. 0.74
   4 !   14.0  18.1   2.9e-05     0.015     318     469 ..     697     842 ..     691     848 .. 0.76
   5 !   10.5  17.3   0.00033      0.17     368     470 ..     809     906 ..     800     914 .. 0.79
   6 !    7.2   5.4    0.0034       1.7     315     512 ..     909    1104 ..     904    1114 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.2
                            AAA_13 10 aeledfkriNliYGwNGaGKTt 31
                                      ++++  + + ++ G NG+GK+ 
  gi|336255264|ref|YP_004598371.1| 18 TKIPFYEDFTVVTGPNGSGKSN 39
                                      5566666777889*******85 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.2e-05
                            AAA_13 276 hFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelka..eaealeeqLkglqraleaKrke 350
                                        F++  e   er++++  ++e+k++  le+l++   +a ++++ +++kee++   +a++lee+ ++  +a e+K++e
  gi|336255264|ref|YP_004598371.1| 197 AFEE-LEVVEERIDEAELRIEEKRD-RLEQLEDERRTALRYRRLRDEKEEYEGykKASELEEKREE-LDAAEEKVDE 270
                                       4443.45555666666666666664.4577777777777788888888877753355666666444.467799**** PP

                            AAA_13 351 pfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaiek 427
                                       +++  ele+++ ++++ + +v +++e  ++ N+ +++  e++ +++ k   +++ee++ +++++++k+++ e+ ie+
  gi|336255264|ref|YP_004598371.1| 271 LAE--ELEDLQRELDERQGKVVRLQEDLEDLNAEIERKGEDE-QLRIK---SEIEEIKGDISRLEDKIEASEEHIEE 341
                                       **9..9***************************998865543.34433...4668899******************* PP

                            AAA_13 428 lekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeL 467
                                       +e + +e+  ++  ++eei+eLe ++r++k   + i +e+
  gi|336255264|ref|YP_004598371.1| 342 AESKRREAFVQIDRKQEEIEELEDEMREHKLEKASIKTEI 381
                                       *****************************97777776665 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00016
                            AAA_13 315 ensafeedkeelkaeaealeeqLkglqraleaKrkepfk.svelesvkakie.......sikklvaeineliakhNe 383
                                       e ++ e++k++l+ae++a+++++++l+  l ++++e+   + e ++++ + +       + +++++e + +i++  e
  gi|336255264|ref|YP_004598371.1| 380 EIQEREQEKKQLEAEIDAVDTEFDELKADLAERKEELEDaKTEKNDLQREQDrlldearRRSNEISEKEGTIEDRRE 456
                                       44556666777777777777777777777777777765533333444443323333343999*************** PP

                            AAA_13 384 kvanleeekeeakkklelhlv..eeleseldeykkkykklekaieklekelkeeeaelkkleeeik 447
                                        + +le++k+++k +le+ +   +++   +d +k+++++++ +i +l++e++++++e ++le+++ 
  gi|336255264|ref|YP_004598371.1| 457 EIPELESRKSDLKRELEKAEKnrANIAGVVDDLKDEKRRIQSDIDELDDEIQAKQQEYAELEANAG 522
                                       ******************986225566678899999999999999999999999999999888765 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 2.9e-05
                            AAA_13 318 afeedkeelkaeaealeeqLkglqraleaKrkepfksve.lesvkakiesikklvaeineliakhNekvanleeeke 393
                                       + ++++ el++e e l+e L+g++++l++ r++    ++ + s++++ies++++ ++i++ i+      ++l ee+e
  gi|336255264|ref|YP_004598371.1| 697 RVAKQITELQEERESLREDLRGVEERLDDARDRKTDAADeVRSIESEIESLEDKRESIEDEIETLETELEELREERE 773
                                       45678889999999999999999999988777766655438999999999999999999999999999999998888 PP

                            AAA_13 394 eakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLka 469
                                       ++ + +       +  e+de + ++++++++i +le+el  e +++ +l e+i+eLe ++ + +  ++ei   L++
  gi|336255264|ref|YP_004598371.1| 774 SVDERMND-----ISGEIDEQTAAIEEIQADIDELEAEL--EDSKIPELTEQIEELEGEIDEREAQIDEIDGTLNE 842
                                       88877655.....66777777778888888888887555..45567788888888888888888888888776654 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.00033
                            AAA_13 368 kklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkklee 444
                                        +++ e+ e+i++    +++ e++  e+   l   ++e+ ++     ++++++l ++ie ++++++e+e+++++ e+
  gi|336255264|ref|YP_004598371.1| 809 DSKIPELTEQIEELEGEIDEREAQIDEIDGTLNELELEKEYA-----EDAIEGLHDDIEAAQNKKAEHENRIEECEA 880
                                       456777888888888888888888888888888866664333.....578999999999999999999999999999 PP

                            AAA_13 445 eikeLekqlrdekpaaeeinkeLkaf 470
                                        i+e+e++l+++++a+ee+++eL++ 
  gi|336255264|ref|YP_004598371.1| 881 TIEEKEAELEEKREAVEELEEELAEL 906
                                       99999999999999999999999875 PP

  == domain 6  score: 7.2 bits;  conditional E-value: 0.0034
                            AAA_13  315 ensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaei.neliakhNekvanl 388 
                                         +++ +ed e+++++ ++ +++ +++q++le Kr+++        ++ +ie ++++v +   e + +h    +++
  gi|336255264|ref|YP_004598371.1|  909 DRNELREDLEDARTKRDQQQDRVNAVQSKLESKRERVQD------LEWEIEGLESEVGDYdPEDVPDHDTVLEMI 977 
                                        456778888899999999999999999999999966554......444444444444443147778887777777 PP

                            AAA_13  389 eeekeeak..kklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeike.Lekqlrdekpaa 460 
                                        e  +++++  + +    +    +e+de  +++++le+a   l +e++ + ++++++e + ke   +  + + +  
  gi|336255264|ref|YP_004598371.1|  978 ELLTADMEamEPVNMLAI----DEYDEVREDLEELEDAKDTLVEEAEGIRDRIEQYETQKKEtFMTAYEAISEHF 1048
                                        655554430033444333....34455566666777777777777777777777776665551234444455555 PP

                            AAA_13  461 eeinkeLkafGlgeleLkfeee..kkgYrivrkggsqaa...etLSeGEktaIaflY 512 
                                        +ei ++L++ G g l L+ e++  + g ++  + g+++    + +S GEk++ a+ +
  gi|336255264|ref|YP_004598371.1| 1049 TEIFEKLSE-GTGTLHLENEDDpfDGGLTMKAQPGDKPIqrlDAMSGGEKSLTALAF 1104
                                        555555554.68899999998899888888877777666223566999998777653 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7  17.2     3e-11   1.6e-08       1     284 [.       1     389 [.       1     401 [. 0.61
   2 !    8.8   0.0    0.0023       1.2     235     368 ..    1012    1156 ..     990    1157 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3e-11
                            AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn...................... 54 
                                       M Ik + + NF+s+   ++i++ e++tv+ G+N+sGKS+i++ + + l    +                        
  gi|336255264|ref|YP_004598371.1|   1 MHIKAVVLDNFKSFGRkTKIPFYEDFTVVTGPNGSGKSNIIDSILFALGLA-RTRgiraekltdliynpghedgsss 76 
                                       99************777***************************4444444.4446888888999999999999999 PP

                            AAA_15  55 .............................................kkvikiekedleifeniseskdikIdvef... 83 
                                                                                    k                           +   
  gi|336255264|ref|YP_004598371.1|  77 sgpreatvevvldnsdgtldrsqvvnaagsddvgdvdeirirrrvK---------------------------Eted 126
                                       9999999999999988887777666666666666655555544440...........................1333 PP

                            AAA_15  84 .................................................................aek.ekakeyek 94 
                                                                                                        a k e+a e++ 
  gi|336255264|ref|YP_004598371.1| 127 nyysyyylndrsvnlsdiqdllaqagvtpegynvvmqgdvteiinmtpharreiideiagvaefdA-KkEDAFEEL- 201
                                       334444444444555555566677777777777777777777777777777777777788775532.223333333. PP

                            AAA_15  95 tlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkk 171
                                       +  ++++++a+l +++k+++l ++  ++ ++l         +    ++++ +   +k ++le++ eel+   e++++
  gi|336255264|ref|YP_004598371.1| 202 EVVEERIDEAELRIEEKRDRLEQLEDERRTALR--------YRRLRDEKEEYEGYKKASELEEKREELDAAEEKVDE 270
                                       333455666677888899888888888888875........333333334455667788888899999999999999 PP

                            AAA_15 172 likkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl.............. 234
                                       l ++le    + +      + + + ++l ++  + + e + k ++   ++k++i e +++                 
  gi|336255264|ref|YP_004598371.1| 271 LAEELEDLQRELD------ERQGKVVRLQEDLEDLNAEIERKGEDEQLRIKSEIEEIKGD--Isrledkieaseehi 339
                                       9998888887777......33333344444444444444444444444444444332221..112333334454453 PP

                            AAA_15 235 ......eeelteklkeiqeklkeidkklaeelkkilkkkidkik.kfnykgkkneei 284
                                             + e   ++++ qe+++e+++++ e++ +       k   k+++++ ++e++
  gi|336255264|ref|YP_004598371.1| 340 eeaeskRREAFVQIDRKQEEIEELEDEMREHKLE-------KASiKTEIQEREQEKK 389
                                       3333334455555555555555555555555443.......3333333333333333 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0023
                            AAA_15  235 eeelteklkeiqeklkeidkklaeelk...........kilkkkidkikkfnykgkkneeieik........... 287 
                                        ++ l e+++ i + +++ + +     k           ++++++++k+  +      ++e++++           
  gi|336255264|ref|YP_004598371.1| 1012 KDTLVEEAEGIRDRIEQYETQK----KetfmtayeaisEHFTEIFEKLSEGTGTLHLENEDDPFdggltmkaqpg 1082
                                        2223333333333333333333....133335555777999999999998888888888889999********** PP

                            AAA_15  288 ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviit 362 
                                        d+  + l+ ++ G ++l  l++  +  + +     +  +++++E +a L   + + + +   ela++   Q ++ 
  gi|336255264|ref|YP_004598371.1| 1083 DKPIQRLDAMSGGEKSLTALAFIFAIQRHN-----PAPFYALDEVDAFLDAVNAERIGEMVEELADEA--QFVVV 1150
                                        *****************9999865555555.....*******************************99..9***9 PP

                            AAA_15  363 THSphi 368 
                                        +H + +
  gi|336255264|ref|YP_004598371.1| 1151 SHRSAM 1156
                                        998776 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 !    7.9   1.4    0.0028       1.4      45     112 ..     166     230 ..     159     249 .. 0.79
   2 ?   -1.6  21.2       2.2   1.1e+03      22     125 ..     266     367 ..     229     369 .. 0.42
   3 ?    5.8  25.3     0.012       6.3      18     132 ..     315     430 ..     309     446 .. 0.91
   4 !    8.5  30.4    0.0018      0.91      21     162 ..     357     515 ..     352     529 .. 0.87
   5 !   10.6  13.2   0.00043      0.22      21     130 ..     720     831 ..     691     844 .. 0.78
   6 !   15.4  16.4   1.5e-05    0.0077      26     132 ..     821     924 ..     815     939 .. 0.79
   7 !    8.2   0.0    0.0023       1.2      66     145 ..     914    1046 ..     913    1058 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0028
                             Atg14  45 iekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk 112
                                       ++++++ +     ++++i  + a + e  ++++d  e+l+ +++++++   +ieek+ +l++l d+  
  gi|336255264|ref|YP_004598371.1| 166 VTEIINMTP---HARREIIDEIAGVAEFDAKKEDAFEELEVVEERIDEAELRIEEKRDRLEQLEDERR 230
                                       566666555...67888999999999999*********************************998743 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                             Atg14  22 erlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrer........lqelkdkl 90 
                                       e++ el e+l +l+ e +                 +++ k+ +++++le+l ++i+++ e         ++e+k ++
  gi|336255264|ref|YP_004598371.1| 266 EKVDELAEELEDLQRELD-----------------ERQGKVVRLQEDLEDLNAEIERKGEDeqlrikseIEEIKGDI 325
                                       222222333333333333.................333333333333333333333333333333333344444444 PP

                             Atg14  91 sqlkkeieekkkklaklsdklk.......kRrsdleslqnel 125
                                       s+l ++ie+  +++++  +k         ++++++e l++e+
  gi|336255264|ref|YP_004598371.1| 326 SRLEDKIEASEEHIEEAESKRReafvqidRKQEEIEELEDEM 367
                                       444444444444444444443333333336666666666655 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.012
                             Atg14  18 rngperlyelrerlaklksekeslkkkiekalegke....eaeqledkiknkkakleelksliadlrerlqelkdkl 90 
                                       ++    ++e + ++ +l  + e+ +++ie+a+++++    + ++++++i+ + + ++e k ++a+++ ++qe ++  
  gi|336255264|ref|YP_004598371.1| 315 KS---EIEEIKGDISRLEDKIEASEEHIEEAESKRReafvQIDRKQEEIEELEDEMREHKLEKASIKTEIQEREQEK 388
                                       45...89999999***************************99*********************************** PP

                             Atg14  91 sqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkq 132
                                       +ql +ei++   ++ +l+++l++R+++le +++e +  +++q
  gi|336255264|ref|YP_004598371.1| 389 KQLEAEIDAVDTEFDELKADLAERKEELEDAKTEKNDLQREQ 430
                                       ********************************9999988877 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0018
                             Atg14  21 perlyelrerlaklksekeslkkkiekalegke...........eaeqledkiknkkakleelksliadlrerlqel 86 
                                       +e ++el  +++  k+ek+s+k++i++ +++k+           e ++l++++  +k+ le+ k+++ dl+++  +l
  gi|336255264|ref|YP_004598371.1| 357 QEEIEELEDEMREHKLEKASIKTEIQEREQEKKqleaeidavdtEFDELKADLAERKEELEDAKTEKNDLQREQDRL 433
                                       799***************************9999**********9******************************** PP

                             Atg14  87 kdklsqlkkeieekkkklaklsdklk...kRrsdleslqneleerrkkqiaklqdaik....rieqklsslssktle 156
                                        d  +++  ei ek  +++ +++++     R+sdl+   ++ e++r + ia+++d++k    ri+  +++l ++++ 
  gi|336255264|ref|YP_004598371.1| 434 LDEARRRSNEISEKEGTIEDRREEIPeleSRKSDLKRELEKAEKNR-ANIAGVVDDLKdekrRIQSDIDELDDEIQA 509
                                       ************************9966666667555555555544.57999999**98888888888888888888 PP

                             Atg14 157 srsslc 162
                                       ++++ +
  gi|336255264|ref|YP_004598371.1| 510 KQQEYA 515
                                       776655 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00043
                             Atg14  21 perlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97 
                                       +erl + r r ++   e  s++++ie ++ ++e   + ed+i+++ + leel+ ++++  er++ ++  +++++++i
  gi|336255264|ref|YP_004598371.1| 720 EERLDDARDRKTDAADEVRSIESEIESLEDKRE---SIEDEIETLETELEELREERESVDERMNDISGEIDEQTAAI 793
                                       567777777777777777788888887666666...88999999999999999999999999999999999999999 PP

                             Atg14  98 eekkkklaklsdklk.....kRrsdleslqneleerrk 130
                                       ee ++ + +l ++l      + ++++e l+ e+ er++
  gi|336255264|ref|YP_004598371.1| 794 EEIQADIDELEAELEdskipELTEQIEELEGEIDEREA 831
                                       99999999999999877777777777777777776654 PP

  == domain 6  score: 15.4 bits;  conditional E-value: 1.5e-05
                             Atg14  26 elrerlaklksekeslkkkiekalegke...........eaeqledkiknkkakleelksliadlrerlqelkdkls 91 
                                       el  ++    ++               +           e+e +ed+i+ +++++e  ++++a+ ++r++e +++++
  gi|336255264|ref|YP_004598371.1| 821 ELEGEIDEREAQI--------------DeidgtlnelelEKEYAEDAIEGLHDDIEAAQNKKAEHENRIEECEATIE 883
                                       3333333333444..............34444444444444589********************************* PP

                             Atg14  92 qlkkeieekkkklaklsdklkkRrsdleslqneleerrkkq 132
                                       +  +e+eek++ +++l ++l++ ++d + l++ le +r+k 
  gi|336255264|ref|YP_004598371.1| 884 EKEAELEEKREAVEELEEELAELKEDRNELREDLEDARTKR 924
                                       *********************************99999874 PP

  == domain 7  score: 8.2 bits;  conditional E-value: 0.0023
                             Atg14   66 kakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk............................ 112 
                                        +++le+ ++++ ++++r++ ++ kl++ ++++++   ++++l +++                             
  gi|336255264|ref|YP_004598371.1|  914 REDLEDARTKRDQQQDRVNAVQSKLESKRERVQDLEWEIEGLESEVGdydpedvpdhdtvlemielltadmeame 988 
                                        678899999999999999999999999999999999999999999988888888888777777777777777777 PP

                             Atg14  113 .........................kRrsdleslqneleerrkkqiaklqdaikrieq 145 
                                                                 +  +++e +++++e++++++ +++ +a+  i++
  gi|336255264|ref|YP_004598371.1|  989 pvnmlaideydevredleeledakdTLVEEAEGIRDRIEQYETQKKETFMTAYEAISE 1046
                                        7777777777777766666666666666666666666666666666666666665555 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7  54.9    0.0087       4.4     296     531 ..     190     428 ..     175     430 .. 0.73
   2 ?    1.4  27.9     0.086        44     249     390 ..     380     523 ..     379     530 .. 0.71
   3 !   28.5  53.5   5.7e-10   2.9e-07     287     530 ..     703     949 ..     691     950 .. 0.88
   4 !   18.0   5.0   8.2e-07   0.00042     310     430 ..     934    1050 ..     932    1068 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0087
                           DUF3584 296 lrtledelkeaidelnqelsaakaklaakeselealeeqkk...ky.....edadieklkadldqlpsirseleele 364
                                       +++++++  e+ + +++++ +a+  +++k+++le+le++++   +y     e+++ e + +++++l++ r+el ++e
  gi|336255264|ref|YP_004598371.1| 190 FDAKKEDAFEELEVVEERIDEAELRIEEKRDRLEQLEDERRtalRYrrlrdEKEEYEGY-KKASELEEKREELDAAE 265
                                       45555555556677888888999999999999999988765222452211123333333.57899************ PP

                           DUF3584 365 eeldaltekhqdvqekydrrkqkikeeleeeleklker.leaireekdrlkaaieealealesqlrkqleaqkeeln 440
                                       e++d l e+ +d+q+++d+r+ k+  +l+e+le+l+++ + +  +e+ r k +ie + +   s l+++ ea +e+++
  gi|336255264|ref|YP_004598371.1| 266 EKVDELAEELEDLQRELDERQGKV-VRLQEDLEDLNAEiERKGEDEQLRIKSEIE-EIKGDISRLEDKIEASEEHIE 340
                                       ***********************8.5899********934444444444444444.444555667777777777777 PP

                           DUF3584 441 eeekelesrlselklrldsatateEeleqieeadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaer 517
                                       e+e + +++ ++ + ++++    e+e+ + + +++ +   + e++++e+e+++l+ae  ++++++de +  l + ++
  gi|336255264|ref|YP_004598371.1| 341 EAESKRREAFVQIDRKQEEIEELEDEMREHKLEKASI---KTEIQEREQEKKQLEAEIDAVDTEFDELKADLAERKE 414
                                       7777777777666666666655555555544444443...57899999***************************** PP

                           DUF3584 518 rleqlrqaleelee 531
                                        le+ +++ ++l++
  gi|336255264|ref|YP_004598371.1| 415 ELEDAKTEKNDLQR 428
                                       *********99986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.086
                           DUF3584 249 klqeefeqleslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeaidelnqelsaakaklaake 325
                                       ++qe+ ++ + le+++  +  e  + +  lae++ee + ak e++  +r+++  l e + ++++e+s++++ ++  +
  gi|336255264|ref|YP_004598371.1| 380 EIQEREQEKKQLEAEIDAVDTEFDELKADLAERKEELEDAKTEKNDLQREQDRLLDE-ARRRSNEISEKEGTIEDRR 455
                                       678888888888888888888888888888888888888877776665555554544.4566778888888888888 PP

                           DUF3584 326 selealeeqkkkyedadieklkadldq....lpsirseleeleeeldaltekhqdvqekydrrkqkike 390
                                       +e+ +le++k +  + ++ek++++  +    ++ +++e + ++ ++d l +++q+ q++y ++++++ e
  gi|336255264|ref|YP_004598371.1| 456 EEIPELESRKSDL-KRELEKAEKNRANiagvVDDLKDEKRRIQSDIDELDDEIQAKQQEYAELEANAGE 523
                                       8888888888774.5566666666555222256677777777888888888888888888888877665 PP

  == domain 3  score: 28.5 bits;  conditional E-value: 5.7e-10
                           DUF3584 287 eakaelkqqlrtledelkeaidelnqelsaakaklaakeselealeeqkkkyedadieklkadldql....psirse 359
                                       ++ +e +++lr++   ++e+ d ++ ++ +a +++  +ese+e le++++  ed +ie+l+ +l++l    +s+ + 
  gi|336255264|ref|YP_004598371.1| 703 TELQEERESLREDLRGVEERLDDARDRKTDAADEVRSIESEIESLEDKRESIED-EIETLETELEELreerESVDER 778
                                       3334445566666667788899999999***********************998.59*****999872222567778 PP

                           DUF3584 360 leeleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrlkaaieealealesqlrkqleaqk 436
                                       +++++ e+d +t +++++q+  d++++++++++  el +  e+le   +e++++  +i+  l++le + +   e ++
  gi|336255264|ref|YP_004598371.1| 779 MNDISGEIDEQTAAIEEIQADIDELEAELEDSKIPELTEQIEELEGEIDEREAQIDEIDGTLNELELEKE-YAEDAI 854
                                       999******************************999999999999999999999***********99877.788999 PP

                           DUF3584 437 eelneeekelesrlselklrldsatateEele.qieeadealekaqeelekaeaevealqaeeeqlrkkrdeadeal 512
                                       e l+++ +  +++ +e + r+++  at Ee+e ++ee+ ea+e+ +eel + ++++++l +++e +r+krd+++++ 
  gi|336255264|ref|YP_004598371.1| 855 EGLHDDIEAAQNKKAEHENRIEECEATIEEKEaELEEKREAVEELEEELAELKEDRNELREDLEDARTKRDQQQDRV 931
                                       ***************************9888736899**************************************** PP

                           DUF3584 513 qkaerrleqlrqaleele 530
                                       +  + +le +r+++++le
  gi|336255264|ref|YP_004598371.1| 932 NAVQSKLESKRERVQDLE 949
                                       ***************997 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 8.2e-07
                           DUF3584  310 lnqelsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrr 384 
                                        ++++l+ +++ ++  e e+e le++  +y+ +d++     l++++ + +++e++e    + +++  +v e ++++
  gi|336255264|ref|YP_004598371.1|  934 VQSKLESKRERVQDLEWEIEGLESEVGDYDPEDVPDHDTVLEMIELLTADMEAMEPVNMLAIDEYDEVREDLEEL 1008
                                        688999*******************************************************************99 PP

                           DUF3584  385 kqkikeeleeeleklkerleaireekdrlkaaieealealesqlrk 430 
                                        +  +k+ l ee e++++r   i + + ++k+++  a+ea+ +++ +
  gi|336255264|ref|YP_004598371.1| 1009 ED-AKDTLVEEAEGIRDR---IEQYETQKKETFMTAYEAISEHFTE 1050
                                        86.588999999999999...5555555567788888888777764 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7  29.1   2.1e-05     0.011     147     282 ..     197     332 ..     177     335 .. 0.77
   2 ?    4.9  29.8      0.02        10     157     270 ..     317     428 ..     308     434 .. 0.71
   3 ?    5.6  13.4     0.012       6.2     147     226 ..     440     518 ..     426     528 .. 0.42
   4 !   13.0  23.4   6.7e-05     0.035     157     278 ..     697     822 ..     692     823 .. 0.55
   5 !   13.8  19.3   3.9e-05      0.02     155     251 ..     744     841 ..     738     856 .. 0.39
   6 !    8.8  26.6    0.0013      0.67     158     262 ..     815     922 ..     809     929 .. 0.64
   7 !    9.3  19.7   0.00094      0.48     161     249 ..     871     958 ..     869     965 .. 0.69
   8 ?    2.6   2.9     0.097        50     163     213 ..     999    1049 ..     970    1064 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                              Spc7 147 nlegleedkelLekqeeeldellpeleeekaeleeeleklqe.........aaeelesid.keeLeelreelaelka 213
                                        +e       +Le  ee +de+  ++ee++++le+  ++ ++         ++ee e ++   eLee reel+++++
  gi|336255264|ref|YP_004598371.1| 197 AFE-------ELEVVEERIDEAELRIEEKRDRLEQLEDERRTalryrrlrdEKEEYEGYKkASELEEKREELDAAEE 266
                                       344.......44445555555555555555544443333222343444444999999999789************** PP

                              Spc7 214 eieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleelt 282
                                       +++e+ +el++lq++l+e + k+  l+e  ++l++ei+   r  e ++   +se++++k   ++le++ 
  gi|336255264|ref|YP_004598371.1| 267 KVDELAEELEDLQRELDERQGKVVRLQEDLEDLNAEIE---RKGEDEQLRIKSEIEEIKGDISRLEDKI 332
                                       *************************************9...6677888999999*****9999999875 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.02
                              Spc7 157 lLekqeeeldellpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkaeieekkkelaelqeqlee 231
                                       ++e+ +  +++l +++e+ ++ +ee   k +e    + +id  +ee+eel +e++e+k e ++ k+e++e+++++++
  gi|336255264|ref|YP_004598371.1| 317 EIEEIKGDISRLEDKIEASEEHIEEAESKRRE---AFVQIDrkQEEIEELEDEMREHKLEKASIKTEIQEREQEKKQ 390
                                       33444444444444444444444444444444...44445555999******************************* PP

                              Spc7 232 leekieelkeqkseleeeiaeaervleeckgwsesevsr 270
                                       le++i++++++ +el++++ae ++ le  k  ++++++r
  gi|336255264|ref|YP_004598371.1| 391 LEAEIDAVDTEFDELKADLAERKEELEDAKT-EKNDLQR 428
                                       *******************999999986654.4555555 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.012
                              Spc7 147 nlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles.id..keeLeelreelaelkaeieekkk 220
                                       + +++ e + ++e+++ee     pele++k++l++elek ++ +++++  +d  k+e + ++++++el+ ei++k++
  gi|336255264|ref|YP_004598371.1| 440 RSNEISEKEGTIEDRREE----IPELESRKSDLKRELEKAEKNRANIAGvVDdlKDEKRRIQSDIDELDDEIQAKQQ 512
                                       222222222222222222....3455555555555555555544444443222344444444444444444444444 PP

                              Spc7 221 elaelq 226
                                       e+ael+
  gi|336255264|ref|YP_004598371.1| 513 EYAELE 518
                                       444444 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 6.7e-05
                              Spc7 157 lLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkkelaelqeqle 230
                                       +++kq  el+e  ++l+e    +ee+l++ ++++++ ++   + + e+e+l ++ ++++ eie +++el+el+e++e
  gi|336255264|ref|YP_004598371.1| 697 RVAKQITELQEERESLREDLRGVEERLDDARDRKTDAADevrSIESEIESLEDKRESIEDEIETLETELEELREERE 773
                                       45555666666666666666666666666655333332222222456666666666666666666666666666666 PP

                              Spc7 231 eleekieelkeqkseleeeiaeaervlee.ckgwsesevsrlkeevkal 278
                                       +++e++++++ +++e  ++i+e +  ++e + + ++s + +l+e+ ++l
  gi|336255264|ref|YP_004598371.1| 774 SVDERMNDISGEIDEQTAAIEEIQADIDElEAELEDSKIPELTEQIEEL 822
                                       6666666666666666666666665555413355566666666666655 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 3.9e-05
                              Spc7 155 kelLekqeeeldellpeleeekaeleeeleklqeaaeeles.id..keeLeelreelaelkaeieekkkelaelqeq 228
                                        e Le+++e +++  + le+e +el+ee e+  e+ ++++  id   + +ee++ +++el+ae+e    ++ el+eq
  gi|336255264|ref|YP_004598371.1| 744 IESLEDKRESIEDEIETLETELEELREERESVDERMNDISGeIDeqTAAIEEIQADIDELEAELE--DSKIPELTEQ 818
                                       33333333333333333333333333333333333333332222113344444444444444444..4444444444 PP

                              Spc7 229 leeleekieelkeqkseleeeia 251
                                       +eele +i+e ++q++e+   ++
  gi|336255264|ref|YP_004598371.1| 819 IEELEGEIDEREAQIDEIDGTLN 841
                                       44444444444444444444333 PP

  == domain 6  score: 8.8 bits;  conditional E-value: 0.0013
                              Spc7 158 Lekqeeeldellpeleeekaeleeeleklqeaaeeles.id..keeLeelreelaelkaeieekkkelaelqeqlee 231
                                       L++q eel+   +e e++ +e+  +l++l+ ++e  e+ i+  ++++e+++++ ae+++ iee ++ ++e++++lee
  gi|336255264|ref|YP_004598371.1| 815 LTEQIEELEGEIDEREAQIDEIDGTLNELELEKEYAEDaIEglHDDIEAAQNKKAEHENRIEECEATIEEKEAELEE 891
                                       44444444444444444444555555555443333332233448888888888888888888888888888888888 PP

                              Spc7 232 leekieelkeqkseleeeiaeaervleeckg 262
                                       ++e++eel+e+ +el+e+ +e ++ le  + 
  gi|336255264|ref|YP_004598371.1| 892 KREAVEELEEELAELKEDRNELREDLEDART 922
                                       8888888888888888888888777776665 PP

  == domain 7  score: 9.3 bits;  conditional E-value: 0.00094
                              Spc7 161 qeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekie 237
                                       +e+ ++e    +ee++aelee+ e  +e +eel+++++++ +elre+l+++ ++ ++++++++ +q++le+++e+++
  gi|336255264|ref|YP_004598371.1| 871 HENRIEECEATIEEKEAELEEKREAVEELEEELAELKEDR-NELREDLEDARTKRDQQQDRVNAVQSKLESKRERVQ 946
                                       6677777777777777777777777777777777765444.777777777777777777777777777777777777 PP

                              Spc7 238 elkeqkseleee 249
                                       +l+ +++ le+e
  gi|336255264|ref|YP_004598371.1| 947 DLEWEIEGLESE 958
                                       777777766666 PP

  == domain 8  score: 2.6 bits;  conditional E-value: 0.097
                              Spc7  163 eeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelka 213 
                                        +e+ e l+ele  k++l ee+e ++++ e+ e+ +ke   ++ e+++e+ +
  gi|336255264|ref|YP_004598371.1|  999 DEVREDLEELEDAKDTLVEEAEGIRDRIEQYETQKKETFMTAYEAISEHFT 1049
                                        333333444444444444444444444444444445555555555444444 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 !   25.4   0.0   1.7e-08   8.7e-06       4      46 ..       6      48 ..       3      54 .. 0.84
   2 ?   -1.0   0.2       2.9   1.5e+03      24      34 ..     672     682 ..     659     683 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.7e-08
                            AAA_29  4 lqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalL 46
                                      + l N  +f + ++i++  +++t++tGp+GsGKS ++D+i + L
  gi|336255264|ref|YP_004598371.1|  6 VVLDNFKSFGRkTKIPFY-EDFTVVTGPNGSGKSNIIDSILFAL 48
                                      556688899998899998.558*****************98766 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.9
                            AAA_29  24 atlltGpsGsG 34 
                                       +  +tG sGsG
  gi|336255264|ref|YP_004598371.1| 672 SGAMTGGSGSG 682
                                       4589******9 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.4       4.3   2.2e+03      70     106 ..     189     225 ..     162     231 .. 0.55
   2 !    7.9   8.1    0.0057       2.9      48     123 ..     266     345 ..     252     357 .. 0.71
   3 ?    1.2   6.1      0.67   3.5e+02      49     114 ..     331     399 ..     319     405 .. 0.46
   4 ?    6.5   5.6     0.016       8.1      57     106 ..     384     433 ..     369     450 .. 0.83
   5 !    9.5   1.0    0.0018      0.94      37      87 ..     470     519 ..     468     552 .. 0.80
   6 !   19.5   5.2   1.5e-06   0.00077      50     122 ..     695     770 ..     692     772 .. 0.88
   7 !   12.4   2.8   0.00024      0.12      55     120 ..     766     829 ..     765     832 .. 0.91
   8 !   11.7   2.2   0.00038      0.19      42     112 ..     792     863 ..     790     867 .. 0.89
   9 !    8.8   4.6    0.0031       1.6      55     110 ..     862     917 ..     847     923 .. 0.80
  10 !    8.1   2.4     0.005       2.6      50     110 ..     899     959 ..     897     966 .. 0.56
  11 ?    1.9   0.6      0.43   2.2e+02      67     122 ..     976    1031 ..     969    1034 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.3
                           DUF1664  70 rvdkkldeqkeiskeikeevtevredlseigedvesv 106
                                       + d+k ++  e  + ++e ++e++  ++e ++ +e++
  gi|336255264|ref|YP_004598371.1| 189 EFDAKKEDAFEELEVVEERIDEAELRIEEKRDRLEQL 225
                                       3345555555555555555555555555555555544 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0057
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeik....eevtevredlseigedvesvkeavegleskleri 120
                                       ++++++ e+l++ +r+L +r  +v + +++ +++ +ei+    +e  +++++++ei+ d++ +++ +e  e+++e+ 
  gi|336255264|ref|YP_004598371.1| 266 EKVDELAEELEDLQRELDERQGKVVRLQEDLEDLNAEIErkgeDEQLRIKSEIEEIKGDISRLEDKIEASEEHIEEA 342
                                       56777888888888888887777666666655555555411114566777888888888888888888888888777 PP

                           DUF1664 121 eek 123
                                       e+k
  gi|336255264|ref|YP_004598371.1| 343 ESK 345
                                       765 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.67
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeike...evtevredlseigedvesvkeavegle 114
                                       ++e   e+++++  +  +   ++d+k++e +e+  e++e   e ++++ +++e +++ +++++ +  ++
  gi|336255264|ref|YP_004598371.1| 331 KIEASEEHIEEAESKRREAFVQIDRKQEEIEELEDEMREhklEKASIKTEIQEREQEKKQLEAEIDAVD 399
                                       555555555555555555555555555555555554443111122233333333333444433333333 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.016
                           DUF1664  57 laatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                                        ++ k++L+++id vd++ de k+  +e kee+++++ + ++++++ + +
  gi|336255264|ref|YP_004598371.1| 384 REQEKKQLEAEIDAVDTEFDELKADLAERKEELEDAKTEKNDLQREQDRL 433
                                       4678*********************************9999998887665 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0018
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeike 87 
                                       r l++a ++   ++  v ++l++ kr+++s+id++d+++++ ++  +e+++
  gi|336255264|ref|YP_004598371.1| 470 RELEKAEKN-RANIAGVVDDLKDEKRRIQSDIDELDDEIQAKQQEYAELEA 519
                                       666666554.4679999*********************9998877666655 PP

  == domain 6  score: 19.5 bits;  conditional E-value: 1.5e-06
                           DUF1664  50 leqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       le+v    ++l++ ++ L +++  v+++ld+  + +++ ++ev ++++++++++++ es+++ +e+le++le++ e
  gi|336255264|ref|YP_004598371.1| 695 LERVAkqiTELQEERESLREDLRGVEERLDDARDRKTDAADEVRSIESEIESLEDKRESIEDEIETLETELEELRE 770
                                       55554222567889999*******************************************************9965 PP

  == domain 7  score: 12.4 bits;  conditional E-value: 0.00024
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       e+l++ ++   +r++ +  ++deq+++++ei+++++e++ +l++  +++ ++ e +e+le+++++ 
  gi|336255264|ref|YP_004598371.1| 766 EELREERESVDERMNDISGEIDEQTAAIEEIQADIDELEAELED--SKIPELTEQIEELEGEIDER 829
                                       689999***********************************996..67999999999999999875 PP

  == domain 8  score: 11.7 bits;  conditional E-value: 0.00038
                           DUF1664  42 avesvskqleqvseslaatk.rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                       a+e++  +++++ ++l++ k  +L+++i++++ ++de ++ + ei+  ++e++ + +  ++ +e +++ +e 
  gi|336255264|ref|YP_004598371.1| 792 AIEEIQADIDELEAELEDSKiPELTEQIEELEGEIDEREAQIDEIDGTLNELELEKEYAEDAIEGLHDDIEA 863
                                       8899999**********999559*****************************99999999999999887776 PP

  == domain 9  score: 8.8 bits;  conditional E-value: 0.0031
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                       e+ ++ k + ++ri++ +++++e ++  +e +e v+e++e+l+e++ed ++++e  
  gi|336255264|ref|YP_004598371.1| 862 EAAQNKKAEHENRIEECEATIEEKEAELEEKREAVEELEEELAELKEDRNELREDL 917
                                       45567788999999999999999999999999999999999999999998887755 PP

  == domain 10  score: 8.1 bits;  conditional E-value: 0.005
                           DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                       le+  ++l++ +++L ++++   +k d+q++  +++++++++ re +++++ ++e +++ v
  gi|336255264|ref|YP_004598371.1| 899 LEEELAELKEDRNELREDLEDARTKRDQQQDRVNAVQSKLESKRERVQDLEWEIEGLESEV 959
                                       4445555566666666666666666666666666666666666666666655555555544 PP

  == domain 11  score: 1.9 bits;  conditional E-value: 0.43
                           DUF1664   67 ridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122 
                                         i+ + + +++++ +     +e +evredl+e+++  +++ e  eg+  ++e+ e+
  gi|336255264|ref|YP_004598371.1|  976 MIELLTADMEAMEPVNMLAIDEYDEVREDLEELEDAKDTLVEEAEGIRDRIEQYET 1031
                                        67888888999999999999999999999999999999999999999988888765 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   1.4    0.0083       4.3      11      53 ..     259     298 ..     249     306 .. 0.45
   2 ?    4.8   0.1     0.075        38       8      57 ..     320     366 ..     315     376 .. 0.82
   3 ?    2.9   1.6       0.3   1.5e+02      10      45 ..     392     427 ..     375     463 .. 0.64
   4 ?    5.8   0.1     0.036        19       8      34 ..     495     521 ..     494     525 .. 0.92
   5 ?    7.2   0.2     0.014       7.1      15      63 ..     697     742 ..     694     752 .. 0.82
   6 !   15.9   2.9   2.6e-05     0.014       9      74 ..     754     816 ..     744     817 .. 0.89
   7 !   11.1   2.3   0.00081      0.41      14      66 ..     787     841 ..     782     849 .. 0.80
   8 ?    6.8   3.0     0.018         9      10      60 ..     893     940 ..     889     969 .. 0.89
   9 ?   -0.4   0.1       3.3   1.7e+03      39      39 ..    1000    1000 ..     942    1064 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0083
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLae 53 
                                       ++  a ++kVd l ++++d+q +l +    + k+ ++++ L++
  gi|336255264|ref|YP_004598371.1| 259 EELDAAEEKVDELAEELEDLQRELDE---RQGKVVRLQEDLED 298
                                       34444445555555555555544443...12333333333333 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.075
                           NPV_P10   8 vIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletk 57 
                                        I+ di+ ++dk++a ++++++ +++ ++      ++d+ +++++ele++
  gi|336255264|ref|YP_004598371.1| 320 EIKGDISRLEDKIEASEEHIEEAESKRRE---AFVQIDRKQEEIEELEDE 366
                                       5999****************999987776...456788888888888775 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.3
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLd 45 
                                        a+i avd+  d l++ +++ +e+l+d +  ++ L+
  gi|336255264|ref|YP_004598371.1| 392 EAEIDAVDTEFDELKADLAERKEELEDAKTEKNDLQ 427
                                       345666666666666666666666665443333333 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.036
                           NPV_P10   8 vIradikavddkVdalqqqvddvqenl 34 
                                        I +di ++dd ++a qq+ +++++n 
  gi|336255264|ref|YP_004598371.1| 495 RIQSDIDELDDEIQAKQQEYAELEANA 521
                                       599********************9996 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.014
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                        v ++++ lq++ ++++e+l+ v+   e+Ld+  +  ++  ++v +I++
  gi|336255264|ref|YP_004598371.1| 697 RVAKQITELQEERESLREDLRGVE---ERLDDARDRKTDAADEVRSIES 742
                                       6889******************66...7888888777777777777765 PP

  == domain 6  score: 15.9 bits;  conditional E-value: 2.6e-05
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnpdevPdlp 74 
                                       I ++i+ +++ ++ l ++ ++v+e ++d   ++ ++d+q+a+++e+++ +++ +  L   ++P+l 
  gi|336255264|ref|YP_004598371.1| 754 IEDEIETLETELEELREERESVDERMND---ISGEIDEQTAAIEEIQADIDELEAELEDSKIPELT 816
                                       7788899999999999999999999998...779************************666**985 PP

  == domain 7  score: 11.1 bits;  conditional E-value: 0.00081
                           NPV_P10  14 kavddkVdalqqqvddvqenlpd..vtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                        +    ++ +q+ +d+++++l+d  + el+e+++++  +++e e+++++I+ +Ln
  gi|336255264|ref|YP_004598371.1| 787 DEQTAAIEEIQADIDELEAELEDskIPELTEQIEELEGEIDEREAQIDEIDGTLN 841
                                       55556688999********99984466889999999999999999******9999 PP

  == domain 8  score: 6.8 bits;  conditional E-value: 0.018
                           NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                       r++++++++ +  l++  ++++e+l+d     +k d+q++ ++++++k+e+
  gi|336255264|ref|YP_004598371.1| 893 REAVEELEEELAELKEDRNELREDLED---ARTKRDQQQDRVNAVQSKLES 940
                                       899**********************99...569999999999999998874 PP

  == domain 9  score: -0.4 bits;  conditional E-value: 3.3
                           NPV_P10   39 e 39  
                                        e
  gi|336255264|ref|YP_004598371.1| 1000 E 1000
                                        1 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  61.7     0.023        12      75     430 ..     139     500 ..     111     504 .. 0.88
   2 ?    2.1   0.2     0.086        44     345     379 ..     485     519 ..     478     524 .. 0.78
   3 !    9.8  11.9    0.0004       0.2     343     432 ..     699     788 ..     694     790 .. 0.92
   4 !   20.6  19.8     2e-07    0.0001      74     185 ..     790     901 ..     786     903 .. 0.97
   5 ?    0.4  14.8      0.27   1.4e+02      96     223 ..     903    1032 ..     900    1051 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.023
                                       HHTHHHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT CS
                              EzrA  75 kklpeieellfeaeelldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkk 151
                                        +l +i++ll +a    ++y++  ++ +++e+ ++  +++ +i +  ++++e+  ++e+  ee e ++e+ +e + +
  gi|336255264|ref|YP_004598371.1| 139 VNLSDIQDLLAQAGVTPEGYNVV-MQGDVTEIINMTPHARREIIDEIAGVAEFDAKKEDAFEELEVVEERIDEAELR 214
                                       45889999999999999999987.6778888888889999999999999**************************** PP

                                       --TTTTHHHHHHHHHHHHHH..HH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSHH CS
                              EzrA 152 llanrfsygealeelekqle..niekefsefeeltengdyveakeilkkleeeideleevieeiPelleelkkelpk 226
                                       ++++r+ +++ ++e  + l    + +e +e+e   ++++ +e +e l+++ee++del e +e++   l+e + ++ +
  gi|336255264|ref|YP_004598371.1| 215 IEEKRDRLEQLEDERRTALRyrRLRDEKEEYEGYKKASELEEKREELDAAEEKVDELAEELEDLQRELDERQGKVVR 291
                                       *************988877522799**************************************************** PP

                                       HHHHHHHHHHHSTTS--SGGGSSSSSHHHHHHHHHHHHHHHHTT-..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 227 qleelkegykemkeegYaleelniekeieelekkieeilerlkel..eledveeelktieeeidsLyddlekEveAk 301
                                         e+l++  +e +++g   e+l i++eiee++ +i+++ ++++    ++e++e++ ++   +id   + +e+  +  
  gi|336255264|ref|YP_004598371.1| 292 LQEDLEDLNAEIERKGE-DEQLRIKSEIEEIKGDISRLEDKIEASeeHIEEAESKRREAFVQIDRKQEEIEELEDEM 367
                                       ***************95.599*********************9774479****************999999988888 PP

                                       HHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGG.SSTTTSTT...HHHHHHHHHHHHHHHHHHHHHHS-SS--- CS
                              EzrA 302 keveknlkelkeklehlekqnkelkeeldrlkqsYe.Lseeelek...lrelekelkelekdyeeleekleekkvaY 374
                                       +e + + +++k+++++ e++ k+l++e+d ++ +++ L+ +  e+   l++ ++e ++l+++ ++l ++ + ++   
  gi|336255264|ref|YP_004598371.1| 368 REHKLEKASIKTEIQEREQEKKQLEAEIDAVDTEFDeLKADLAERkeeLEDAKTEKNDLQREQDRLLDEARRRSNEI 444
                                       889999999**************************657776665511155567888999999999999999999999 PP

                                       STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                              EzrA 375 SelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrki 430
                                       Se +  +e+  e++ e+e++  +++++l++ +k+ ++    +d++k e + i++ i
  gi|336255264|ref|YP_004598371.1| 445 SEKEGTIEDRREEIPELESRKSDLKRELEKAEKNRANIAGVVDDLKDEKRRIQSDI 500
                                       99999999999999999999999999999999988888887887777777777766 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.086
                                       THHHHHHHHHHHHHHHHHHHHHHS-SS---STTGG CS
                              EzrA 345 klrelekelkelekdyeeleekleekkvaYSelqe 379
                                        +++l++e  ++++d++el++++++k++ Y el+ 
  gi|336255264|ref|YP_004598371.1| 485 VVDDLKDEKRRIQSDIDELDDEIQAKQQEYAELEA 519
                                       46778888888888888888888888888888876 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0004
                                       STTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 343 leklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldei 419
                                        +++ el++e ++l++d++ +ee+l++     ++ ++e++++e+++e +e+k e+i++++++l+ + ++ re+ + +
  gi|336255264|ref|YP_004598371.1| 699 AKQITELQEERESLREDLRGVEERLDDARDRKTDAADEVRSIESEIESLEDKRESIEDEIETLETELEELREERESV 775
                                       5788999********************************************************************** PP

                                       HHHHHHHHHHSSS CS
                              EzrA 420 kkelkeikrkiek 432
                                       ++++++i  +i++
  gi|336255264|ref|YP_004598371.1| 776 DERMNDISGEIDE 788
                                       ****999988876 PP

  == domain 4  score: 20.6 bits;  conditional E-value: 2e-07
                                       HHHTHHHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHH CS
                              EzrA  74 tkklpeieellfeaeelldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrk 150
                                       t  ++ei+  + e+e+ l+  k+ +++++++ele e+de e++i++i   l+el   +e  +++ie l ++ +  ++
  gi|336255264|ref|YP_004598371.1| 790 TAAIEEIQADIDELEAELEDSKIPELTEQIEELEGEIDEREAQIDEIDGTLNELELEKEYAEDAIEGLHDDIEAAQN 866
                                       66899************************************************************************ PP

                                       T--TTTTHHHHHHHHHHHHHHHH------------ CS
                              EzrA 151 kllanrfsygealeelekqleniekefsefeelte 185
                                       k  ++++  +e ++++e++ +++e++ ++ eel e
  gi|336255264|ref|YP_004598371.1| 867 KKAEHENRIEECEATIEEKEAELEEKREAVEELEE 901
                                       ********************************987 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.27
                                        HHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHH CS
                              EzrA   96 fkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekql 170 
                                        + ++k++ +el+e+l+++++k ++ ++ ++ ++++ e +re++++l+ + + l+ ++ ++  +  +  +++ +++
  gi|336255264|ref|YP_004598371.1|  903 LAELKEDRNELREDLEDARTKRDQQQDRVNAVQSKLESKRERVQDLEWEIEGLESEVGDYDPEDVPDHDTVLEMI 977 
                                        567899999999999999999999999999999999999999999999999999999999999999999999999 PP

                                        HHH--------..--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTT CS
                              EzrA  171 eniekefsefe..eltengdyveakeilkkleeeideleevieeiPelleelkke 223 
                                        e +  +++++e  ++    +y+e++e l++le+  d l e  e i + +e+ +++
  gi|336255264|ref|YP_004598371.1|  978 ELLTADMEAMEpvNMLAIDEYDEVREDLEELEDAKDTLVEEAEGIRDRIEQYETQ 1032
                                        9999999999832445778999999999999999999999999999988887765 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  14.4     0.038        20       4      55 ..     259     310 ..     256     333 .. 0.84
   2 ?    1.9   0.8       0.6   3.1e+02      24      55 ..     315     346 ..     312     354 .. 0.65
   3 ?    0.9  16.2       1.3   6.4e+02       5      64 ..     338     397 ..     334     399 .. 0.88
   4 ?    6.2   1.8     0.027        14      36      63 ..     697     724 ..     692     729 .. 0.68
   5 !   21.4   6.4     5e-07   0.00025      15      71 .]     732     788 ..     728     788 .. 0.93
   6 !   10.6  14.0    0.0012      0.61      24      70 ..     893     939 ..     888     940 .. 0.93
   7 ?    7.2   1.5     0.013       6.6      16      56 ..     994    1034 ..     990    1057 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.038
                              ZapB   4 elLeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeer 55 
                                       e L+  E+k++++ ++++ Lq e++e + ++  l+e  + l++e+e+  e+ 
  gi|336255264|ref|YP_004598371.1| 259 EELDAAEEKVDELAEELEDLQRELDERQGKVVRLQEDLEDLNAEIERKGEDE 310
                                       889999************************************9988765433 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.6
                              ZapB  24 qmeieeLkeeneelkeenreleeeneqlkeer 55 
                                       + eiee k + + l++++++ ee +e+ +  r
  gi|336255264|ref|YP_004598371.1| 315 KSEIEEIKGDISRLEDKIEASEEHIEEAESKR 346
                                       56777777777777777777776555554444 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.3
                              ZapB   5 lLeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64 
                                         e+ Esk  +a  +i++ q+eieeL+ e +e k e++ ++ e+++ ++e++++++ +++
  gi|336255264|ref|YP_004598371.1| 338 HIEEAESKRREAFVQIDRKQEEIEELEDEMREHKLEKASIKTEIQEREQEKKQLEAEIDA 397
                                       5667788888999999999**********************************9999987 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.027
                              ZapB  36 elkeenreleeeneqlkeereawqerlk 63 
                                         ++++ el+ee e l+e+   ++erl+
  gi|336255264|ref|YP_004598371.1| 697 RVAKQITELQEERESLREDLRGVEERLD 724
                                       4566677777777777777777777775 PP

  == domain 5  score: 21.4 bits;  conditional E-value: 5e-07
                              ZapB  15 kaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLLgklee 71 
                                        a d++++   eie L+ + e+ ++e++ le e+e+l+eere++ er++ + g+++e
  gi|336255264|ref|YP_004598371.1| 732 DAADEVRSIESEIESLEDKRESIEDEIETLETELEELREERESVDERMNDISGEIDE 788
                                       5889********************************************998877775 PP

  == domain 6  score: 10.6 bits;  conditional E-value: 0.0012
                              ZapB  24 qmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLLgkle 70 
                                       ++ +eeL+ee +elke  +el+e +e  ++ r ++q+r++++  kle
  gi|336255264|ref|YP_004598371.1| 893 REAVEELEEELAELKEDRNELREDLEDARTKRDQQQDRVNAVQSKLE 939
                                       56799************************************999987 PP

  == domain 7  score: 7.2 bits;  conditional E-value: 0.013
                              ZapB   16 aidtitlLqmeieeLkeeneelkeenreleeeneqlkeere 56  
                                        aid++++ ++ +eeL+  + +l ee++ ++  +eq +++++
  gi|336255264|ref|YP_004598371.1|  994 AIDEYDEVREDLEELEDAKDTLVEEAEGIRDRIEQYETQKK 1034
                                        89999999999999999999999999999966666553332 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   8.5     0.037        19       5     125 ..     199     322 ..     187     326 .. 0.69
   2 ?    4.7  13.8      0.03        16       2      92 ..     316     412 ..     315     420 .. 0.87
   3 ?    3.5   7.4     0.068        35       3      96 ..     422     514 ..     413     529 .. 0.77
   4 ?    5.9   3.0     0.013       6.4       4      76 ..     695     766 ..     692     767 .. 0.86
   5 !   19.8   5.0   7.4e-07   0.00038       3      90 ..     750     841 ..     748     844 .. 0.90
   6 !    7.3   5.2    0.0048       2.5       6      79 ..     835     907 ..     833     908 .. 0.88
   7 !   12.9   1.7   9.6e-05     0.049       2      90 ..     901     989 ..     900     994 .. 0.92
   8 ?    1.5   0.5      0.28   1.4e+02       5      84 ..     978    1057 ..     974    1068 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.037
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.eeeeeeveelkeelkerkk 80 
                                       eele   +++ e++ ++++k ++l++l+++ +++++   +rl++ k++ + +kk+++ ee++ee++  +e+++e  +
  gi|336255264|ref|YP_004598371.1| 199 EELEVVEERIDEAELRIEEKRDRLEQLEDERRTALR--YRRLRDEKEEYEGYKKASElEEKREELDAAEEKVDELAE 273
                                       455555566666666666666666666666554443..445666666666666665467888899999999999999 PP

                             TMPIT  81 vlkevesllpkknglylklv..lGnvnvsllnk..qdkfkyKdeYekFk 125
                                        l++++  l +++g  ++l   l ++n ++ +k  ++++++K+e e+ k
  gi|336255264|ref|YP_004598371.1| 274 ELEDLQRELDERQGKVVRLQedLEDLNAEIERKgeDEQLRIKSEIEEIK 322
                                       9999999999999988888644667777766652256899999988766 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.03
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelk 72 
                                       +e+ee++ ++ +le++ +  ++++ee ++   +   +i++++++++el++++++ k ++       +e+e+e ++l+
  gi|336255264|ref|YP_004598371.1| 316 SEIEEIKGDISRLEDKIEASEEHIEEAESKRREAFVQIDRKQEEIEELEDEMREHKLEKAsikteiQEREQEKKQLE 392
                                       689999*******************************************9999988775557777888889999999 PP

                             TMPIT  73 eelkerkkvlkevesllpkk 92 
                                       +e++  ++ ++e+++ l ++
  gi|336255264|ref|YP_004598371.1| 393 AEIDAVDTEFDELKADLAER 412
                                       99999999999999888765 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.068
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79 
                                       e ++l++e+++l ++a++  +++ e +  +++ ++ei + + r ++lk++l+k +k+  ++ +  v++lk+e ++++
  gi|336255264|ref|YP_004598371.1| 422 EKNDLQREQDRLLDEARRRSNEISEKEGTIEDRREEIPELESRKSDLKRELEKAEKNR-ANIAGVVDDLKDEKRRIQ 497
                                       5677888888888888888888888888888888888888888888888888888874.566667777777777777 PP

                             TMPIT  80 kvlkevesllpkkngly 96 
                                       + ++e+++ + +k+  y
  gi|336255264|ref|YP_004598371.1| 498 SDIDELDDEIQAKQQEY 514
                                       77777777777666555 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.013
                             TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelk 76 
                                       +e+++k++ el+e+ ++++++l+ +++  ++ + + +    ++++++s++++l+ + +e+ e+e+e+l++el+
  gi|336255264|ref|YP_004598371.1| 695 LERVAKQITELQEERESLREDLRGVEERLDDARDRKTDAADEVRSIESEIESLEDK-RESIEDEIETLETELE 766
                                       67889999999999999999999999999999999999999999999999999988.4677888888888876 PP

  == domain 5  score: 19.8 bits;  conditional E-value: 7.4e-07
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk....eeeeeeveelkeel 75 
                                       + e++e+e+++le++ +e++++ e++ +  +++s ei++q+  ++e+++++++l+++++     e  e++eel+ e+
  gi|336255264|ref|YP_004598371.1| 750 KRESIEDEIETLETELEELREERESVDERMNDISGEIDEQTAAIEEIQADIDELEAELEdskiPELTEQIEELEGEI 826
                                       5688999999999999999999999*************************999999977677788899********* PP

                             TMPIT  76 kerkkvlkevesllp 90 
                                       +er+++++e++ +l 
  gi|336255264|ref|YP_004598371.1| 827 DEREAQIDEIDGTLN 841
                                       *********998875 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.0048
                             TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79 
                                       e+   ++ele +++  +  +e l+  +++ +++ +++++r++e+++++++ ++++ ee++e+veel+eel+e k
  gi|336255264|ref|YP_004598371.1| 835 EIDGTLNELELEKEYAEDAIEGLHDDIEAAQNKKAEHENRIEECEATIEEKEAEL-EEKREAVEELEEELAELK 907
                                       66777888888888888899******************************99997.7999*********99865 PP

  == domain 7  score: 12.9 bits;  conditional E-value: 9.6e-05
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelker 78 
                                       ee++el+++ +el+e  +  ++k ++ +   ++++++++++++r+++l+ +++ l+++v++ + e v + ++ l+ +
  gi|336255264|ref|YP_004598371.1| 901 EELAELKEDRNELREDLEDARTKRDQQQDRVNAVQSKLESKRERVQDLEWEIEGLESEVGDYDPEDVPDHDTVLEMI 977
                                       899********************************************************999999999999888888 PP

                             TMPIT  79 kkvlkevesllp 90 
                                       +   +++e++ p
  gi|336255264|ref|YP_004598371.1| 978 ELLTADMEAMEP 989
                                       888888888755 PP

  == domain 8  score: 1.5 bits;  conditional E-value: 0.28
                             TMPIT    5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79  
                                        e l+ +++++e  +   + + +e+ +  +++  + ++  ++++ ++++++++++++ke   +++e ++e++ e+ 
  gi|336255264|ref|YP_004598371.1|  978 ELLTADMEAMEPVNMLAIDEYDEVREDLEELEDAKDTLVEEAEGIRDRIEQYETQKKETFMTAYEAISEHFTEIF 1052
                                        556667777777777777777777777777777777777777777777777777766666666666666666665 PP

                             TMPIT   80 kvlke 84  
                                        + l+e
  gi|336255264|ref|YP_004598371.1| 1053 EKLSE 1057
                                        55555 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2  16.3     0.092        47     120     234 ..     195     311 ..     178     330 .. 0.52
   2 ?    6.2  23.5     0.011       5.5     121     237 ..     326     441 ..     308     466 .. 0.76
   3 !   12.9   1.3    0.0001     0.052     115     177 ..     473     543 ..     459     559 .. 0.64
   4 !   14.6  16.3     3e-05     0.015     130     251 ..     719     847 ..     696     857 .. 0.68
   5 ?    3.9  30.0     0.057        29     108     251 ..     786     935 ..     784    1051 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.092
                           DUF4407 120 akelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..........gtgttgvaGkgpaak 186
                                       ++++         +el+  e++i++++  i+++++rl++l++e +  l   +                   k  + +
  gi|336255264|ref|YP_004598371.1| 195 EDAF---------EELEVVEERIDEAELRIEEKRDRLEQLEDERRTALRYRRlrdekeeyegY-------KKASELE 255
                                       3333.........34444444444444444444444444444444444443343321111121.......2334444 PP

                           DUF4407 187 ekkaqldaaqaelaelkakld........atarlaalraelaeleaerakeraasq 234
                                       ek+++ldaa+++++el ++l+        ++ ++ +l++ l++l+ae++++ ++ q
  gi|336255264|ref|YP_004598371.1| 256 EKREELDAAEEKVDELAEELEdlqreldeRQGKVVRLQEDLEDLNAEIERKGEDEQ 311
                                       55555555555555555555555555558666777777777777777766665555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.011
                           DUF4407 121 kelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqa 197
                                       ++l+++++ a+++ ++e+e++++++  +id +++++++l++e++++   + + + t ++ ++++ k+ +a++da ++
  gi|336255264|ref|YP_004598371.1| 326 SRLEDKIE-ASEEHIEEAESKRREAFVQIDRKQEEIEELEDEMREHKLEKASIK-TEIQEREQEKKQLEAEIDAVDT 400
                                       33333333.378999999999999*******************98877665433.4488899999999999999999 PP

                           DUF4407 198 elaelkakld.atarlaalraelaeleaerakeraasqaaa 237
                                       e +elka+l  ++++l+++++e+++l++e+++  ++ ++++
  gi|336255264|ref|YP_004598371.1| 401 EFDELKADLAeRKEELEDAKTEKNDLQREQDRLLDEARRRS 441
                                       99999999888888888888888888888887666555543 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.0001
                           DUF4407 115 eqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk........gtgttg 177
                                       e++e+++++ + + ++l++e ++++++i++l+ ei+a+++++++l+a+a +  d  +        ++g+ g
  gi|336255264|ref|YP_004598371.1| 473 EKAEKNRANIAGVVDDLKDEKRRIQSDIDELDDEIQAKQQEYAELEANAGESGDSSFgrsvttilNSGIDG 543
                                       34555556666666667777777777777777777777777777777776554444455555555555555 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 3e-05
                           DUF4407 130 a.............ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqld 193
                                                     + +e++ +e++i++l+ + ++ e+++++l++e++ el  ++ +  ++++    + +e +a+++
  gi|336255264|ref|YP_004598371.1| 719 VeerlddardrktdAADEVRSIESEIESLEDKRESIEDEIETLETELE-ELREERESVDERMNDISGEIDEQTAAIE 794
                                       133333334444446666777777777777777777777777777776.4444454455566777779********* PP

                           DUF4407 194 aaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaaddGllarleald 251
                                       ++qa+++el+a+l +++++++l ++++ele e+++++a+ ++     dG l +le  +
  gi|336255264|ref|YP_004598371.1| 795 EIQADIDELEAEL-EDSKIPELTEQIEELEGEIDEREAQIDE----IDGTLNELELEK 847
                                       ************5.7899999999999999999999886665....556666666555 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.057
                           DUF4407 108 Idaela..eeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkg 182
                                       Id++ a  ee q++++el+++l+   ++++ el++qi++l++eid+ ea++d+   +++ el+ +k   + +++G  
  gi|336255264|ref|YP_004598371.1| 786 IDEQTAaiEEIQADIDELEAELE---DSKIPELTEQIEELEGEIDEREAQIDEIDGTLN-ELELEKEYAEDAIEGLH 858
                                       55544311455666666666666...566666666666666666666666666655555.44444433333445555 PP

                           DUF4407 183 paakekkaqldaaqaelaelkakld........atarlaalraelaeleaerakeraasqaaaaaddGllarleald 251
                                       +  ++++++ ++ +++++e +a+++        +++++++l++elael+++r++ r++ ++a+ + d   +r +a +
  gi|336255264|ref|YP_004598371.1| 859 DDIEAAQNKKAEHENRIEECEATIEekeaeleeKREAVEELEEELAELKEDRNELREDLEDARTKRDQQQDRVNAVQ 935
                                       55555555555555555555555555567777877788888888888888888888888888777777777777743 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 ?   -0.3   4.3       1.1   5.7e+02      92     125 ..     199     232 ..     189     246 .. 0.87
   2 ?    3.8  19.8     0.061        31      33     137 ..     252     354 ..     248     358 .. 0.78
   3 !    6.5  23.1     0.009       4.6      24     123 ..     356     456 ..     351     460 .. 0.62
   4 ?    2.4  13.0      0.16        84      31     120 ..     426     519 ..     423     527 .. 0.64
   5 !   13.1   5.0   8.5e-05     0.044      57     126 ..     696     762 ..     692     763 .. 0.92
   6 !   18.7  20.1   1.7e-06   0.00089      27     167 ..     757     891 ..     756     891 .. 0.94
   7 !   14.5  21.8   3.4e-05     0.017      27     127 ..     853     957 ..     852     962 .. 0.90
   8 ?    3.8   1.3     0.062        32      47     129 ..     996    1040 ..     971    1057 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                               GAS  92 arlkelekelkdlkwehevleqrfekvekerdel 125
                                       ++l+++e+ + + ++  e +++r+e++e+er + 
  gi|336255264|ref|YP_004598371.1| 199 EELEVVEERIDEAELRIEEKRDRLEQLEDERRTA 232
                                       679999***********************99875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.061
                               GAS  33 eeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehe 109
                                       +e+ee++++ +++e +++e+++e ++l+ +L + + +v +L+++l++ + + ++  + + +  + ++e++++k +  
  gi|336255264|ref|YP_004598371.1| 252 SELEEKREELDAAEEKVDELAEELEDLQRELDERQGKVVRLQEDLEDLNAEIER--KGEDEQLRIKSEIEEIKGDIS 326
                                       589999999999999999999999999999999999999999999999987774..445555666777777777777 PP

                               GAS 110 vleqrfekvekerdelykkfeaaiqevq 137
                                        le+++e+ e++++e ++k ++a+ ++ 
  gi|336255264|ref|YP_004598371.1| 327 RLEDKIEASEEHIEEAESKRREAFVQID 354
                                       7777777777777777777777766665 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.009
                               GAS  24 NLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkeleke 100
                                         e I++l +e+ e k ++++ + e++e +qe+k+l+ ++ +++ e +eL+++l++ +++ ++ k  k+ l++ ++ 
  gi|336255264|ref|YP_004598371.1| 356 KQEEIEELEDEMREHKLEKASIKTEIQEREQEKKQLEAEIDAVDTEFDELKADLAERKEELEDAKTEKNDLQREQDR 432
                                       45667777777777777777777777777777777777777777777777777777777666666666666554443 PP

                               GAS 101 .lkdlkwehevleqrfekvekerd 123
                                        l + +  ++  +++  ++e+ r+
  gi|336255264|ref|YP_004598371.1| 433 lLDEARRRSNEISEKEGTIEDRRE 456
                                       134455555555555555555555 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.16
                               GAS  31 lKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslk....nlkarlkelekelkd 103
                                       l  e  +l  +++r ++e+se +   ++ +e++ ++e  +  L+++l++ ek ++ ++     lk + ++ ++ + +
  gi|336255264|ref|YP_004598371.1| 426 LQREQDRLLDEARRRSNEISEKEGTIEDRREEIPELESRKSDLKRELEKAEKNRANIAgvvdDLKDEKRRIQSDIDE 502
                                       56666677777888888888888888888999999999999999999999888875431111344444444444455 PP

                               GAS 104 lkwehevleqrfekvek 120
                                       l  e + ++q+++++e+
  gi|336255264|ref|YP_004598371.1| 503 LDDEIQAKQQEYAELEA 519
                                       55555555555555444 PP

  == domain 5  score: 13.1 bits;  conditional E-value: 8.5e-05
                               GAS  57 krlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdely 126
                                       +r  +++++++ee+e Lr++l+  e+   +l+ ++ r +++ +e+++++ e e+le++ e++e+e+++l+
  gi|336255264|ref|YP_004598371.1| 696 ERVAKQITELQEERESLREDLRGVEE---RLDDARDRKTDAADEVRSIESEIESLEDKRESIEDEIETLE 762
                                       6888999****************998...999********************************999885 PP

  == domain 6  score: 18.7 bits;  conditional E-value: 1.7e-06
                               GAS  27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkd 103
                                        I++l  e+eel+++ e+ + ++++is e  + +  +++ +++++eL+++l++ +     + +l ++++ele e+ +
  gi|336255264|ref|YP_004598371.1| 757 EIETLETELEELREERESVDERMNDISGEIDEQTAAIEEIQADIDELEAELEDSK-----IPELTEQIEELEGEIDE 828
                                       699************************************************9865.....68999************ PP

                               GAS 104 lkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaqlee 167
                                        + + +     ++++e e++  ++  e   +++   +++k+   e+++++ ++++E+kea+lee
  gi|336255264|ref|YP_004598371.1| 829 REAQIDEIDGTLNELELEKEYAEDAIEGLHDDIE-AAQNKKAEHENRIEECEATIEEKEAELEE 891
                                       *******************999999999888875.578889999******************87 PP

  == domain 7  score: 14.5 bits;  conditional E-value: 3.4e-05
                               GAS  27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqsl....knlkarlkelek 99 
                                        I+ l ++ie  ++k++++e++++e ++  ++ + +L++ +e veeL+++l++ ++d+++l    + ++++  ++++
  gi|336255264|ref|YP_004598371.1| 853 AIEGLHDDIEAAQNKKAEHENRIEECEATIEEKEAELEEKREAVEELEEELAELKEDRNELredlEDARTKRDQQQD 929
                                       588899*********************************************99999987651111679********* PP

                               GAS 100 elkdlkwehevleqrfekvekerdelyk 127
                                        +++++ + e++++r++ +e e++ l++
  gi|336255264|ref|YP_004598371.1| 930 RVNAVQSKLESKRERVQDLEWEIEGLES 957
                                       **********************999976 PP

  == domain 8  score: 3.8 bits;  conditional E-value: 0.062
                               GAS   47 kelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekveke 121 
                                         e +                                      ++++ l+ele+   +l +e+e  ++r+e+ e +
  gi|336255264|ref|YP_004598371.1|  996 DEYD--------------------------------------EVREDLEELEDAKDTLVEEAEGIRDRIEQYETQ 1032
                                        4444......................................455555555555555555555555555555555 PP

                               GAS  122 rdelykkf 129 
                                        ++e   + 
  gi|336255264|ref|YP_004598371.1| 1033 KKETFMTA 1040
                                        55554444 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 ?   -1.9  32.3         6   3.1e+03       3     124 ..     192     318 ..     190     320 .. 0.87
   2 !   13.9  24.1   7.8e-05      0.04       2     100 ..     308     406 ..     307     409 .. 0.96
   3 !   12.9  19.3   0.00016     0.083      28     120 ..     390     482 ..     389     492 .. 0.95
   4 ?    5.4   0.6     0.035        18      68     101 ..     486     519 ..     480     524 .. 0.83
   5 !    8.4   7.5     0.004       2.1      46     107 ..     694     755 ..     692     756 .. 0.94
   6 !   12.8  26.1   0.00018      0.09       7     115 ..     739     852 ..     735     867 .. 0.74
   7 ?    4.0  22.9     0.093        48      13     120 ..     787     892 ..     776     894 .. 0.88
   8 ?    5.1  31.6     0.041        21      16     134 ..     865     983 ..     835     989 .. 0.48
   9 ?    3.0   5.4      0.19        95      20      83 ..     971    1034 ..     964    1054 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6
                    CENP-F_leu_zip   3 kkklhvlekLKeserkadsLkdkvenLerelemseenqekvi..leaEtskaevetlk..eeieelaeelreleldL 75 
                                        kk+ + e+L  +e++ d  + ++e+    le++e ++  +   +   ++k+e e+ k  +e+ee +eel   e ++
  gi|336255264|ref|YP_004598371.1| 192 AKKEDAFEELEVVEERIDEAELRIEEKRDRLEQLEDERRTALryRRLRDEKEEYEGYKkaSELEEKREELDAAEEKV 268
                                       58888999999999999*9999***999999999999888862246788999999976225889999999999**** PP

                    CENP-F_leu_zip  76 valrsekeeLekelqkkqervseLeslnsslenlleek.Eqekvqmkees 124
                                       ++l +e e+L++el + q +v  L++  ++l+  +e+k E+e+ ++k e 
  gi|336255264|ref|YP_004598371.1| 269 DELAEELEDLQRELDERQGKVVRLQEDLEDLNAEIERKgEDEQLRIKSEI 318
                                       ***********************************998688899998876 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.8e-05
                    CENP-F_leu_zip   2 ekkklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLval 78 
                                       e+++l+++++  e++ + + L+dk+e+ e  +e++e+++ ++ ++ + +++e+e+l++e++e + e   +++++++ 
  gi|336255264|ref|YP_004598371.1| 308 EDEQLRIKSEIEEIKGDISRLEDKIEASEEHIEEAESKRREAFVQIDRKQEEIEELEDEMREHKLEKASIKTEIQER 384
                                       6899************************************************************************* PP

                    CENP-F_leu_zip  79 rsekeeLekelqkkqervseLe 100
                                        +ek++Le e+     + +eL+
  gi|336255264|ref|YP_004598371.1| 385 EQEKKQLEAEIDAVDTEFDELK 406
                                       ***********99999999997 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00016
                    CENP-F_leu_zip  28 nLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslns 104
                                       +Le+e+  ++ + ++++ +  + k+e+e  k+e++ l++e  +l  +    ++e  e e  +++ +e++ eLes++s
  gi|336255264|ref|YP_004598371.1| 390 QLEAEIDAVDTEFDELKADLAERKEELEDAKTEKNDLQREQDRLLDEARRRSNEISEKEGTIEDRREEIPELESRKS 466
                                       79*************************************************************************** PP

                    CENP-F_leu_zip 105 slenlleekEqekvqm 120
                                       +l++ le++E++++++
  gi|336255264|ref|YP_004598371.1| 467 DLKRELEKAEKNRANI 482
                                       ***********98876 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.035
                    CENP-F_leu_zip  68 lreleldLvalrsekeeLekelqkkqervseLes 101
                                         +l+ +   ++s+ +eL+ e+q kq++  eLe+
  gi|336255264|ref|YP_004598371.1| 486 VDDLKDEKRRIQSDIDELDDEIQAKQQEYAELEA 519
                                       5677777788999*******************97 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.004
                    CENP-F_leu_zip  46 eaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnssle 107
                                       + E   +++ +l+ee e l+e lr  e  L++ r  k + + e++   +++++Le  ++s+e
  gi|336255264|ref|YP_004598371.1| 694 QLERVAKQITELQEERESLREDLRGVEERLDDARDRKTDAADEVRSIESEIESLEDKRESIE 755
                                       678888999***********************************************999987 PP

  == domain 6  score: 12.8 bits;  conditional E-value: 0.00018
                    CENP-F_leu_zip   7 hvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr.... 79 
                                       +++++    e k +s++d +e Le ele++ e++e+v   + +   e+ +  + iee+++   ele++L++ +    
  gi|336255264|ref|YP_004598371.1| 739 SIESEIESLEDKRESIEDEIETLETELEELREERESVDERMNDISGEIDEQTAAIEEIQADIDELEAELEDSKipel 815
                                       57778888899999999999999999999999999999999999999999999999999999999999997554444 PP

                    CENP-F_leu_zip  80 .sekeeLekelqkkqervseLeslnsslenlleekEq 115
                                        ++ eeLe e+ +   +++e + +  +le   e +E+
  gi|336255264|ref|YP_004598371.1| 816 tEQIEELEGEIDEREAQIDEIDGTLNELELEKEYAED 852
                                       4666666666666666666666555555544444444 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.093
                    CENP-F_leu_zip  13 KeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekel 89 
                                        e     + ++  +++Le+ele+s+    +++ + E+   e+ + +++i+e+  +l+elel+ +      e L+ ++
  gi|336255264|ref|YP_004598371.1| 787 DEQTAAIEEIQADIDELEAELEDSKIP--ELTEQIEELEGEIDEREAQIDEIDGTLNELELEKEYAEDAIEGLHDDI 861
                                       55556667788899********99765..8999******************************************** PP

                    CENP-F_leu_zip  90 qkkqervseLeslnsslenlleekEqekvqm 120
                                       +  q++  e e++ ++ e ++eekE+e  + 
  gi|336255264|ref|YP_004598371.1| 862 EAAQNKKAEHENRIEECEATIEEKEAELEEK 892
                                       **************************96554 PP

  == domain 8  score: 5.1 bits;  conditional E-value: 0.041
                    CENP-F_leu_zip  16 erkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr.......sekeeL 85 
                                       + k++  ++++e+ e+ +e+ e        e E+++++ve+l+ee+ el+e ++el+ dL++ r          + +
  gi|336255264|ref|YP_004598371.1| 865 QNKKAEHENRIEECEATIEEKE-------AELEEKREAVEELEEELAELKEDRNELREDLEDARtkrdqqqDRVNAV 934
                                       3333333333333333333333.......333444444444444444444444444444444443322221333445 PP

                    CENP-F_leu_zip  86 ekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeLqtq 134
                                       + +l+ k+erv++Le   + le+ + +   e+v  ++   + +e+L+++
  gi|336255264|ref|YP_004598371.1| 935 QSKLESKRERVQDLEWEIEGLESEVGDYDPEDVPDHDTVLEMIELLTAD 983
                                       6666666666666666666666666666666666666666666666555 PP

  == domain 9  score: 3.0 bits;  conditional E-value: 0.19
                    CENP-F_leu_zip   20 dsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrseke 83  
                                        d + + +e L +++e +e  +  +i e ++ ++ +e+l++ +++l ee + ++  +++   +k+
  gi|336255264|ref|YP_004598371.1|  971 DTVLEMIELLTADMEAMEPVNMLAIDEYDEVREDLEELEDAKDTLVEEAEGIRDRIEQYETQKK 1034
                                        7777889999999999999999999999999999999999999999999999988888877665 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   9.9      0.37   1.9e+02      19      92 ..     297     371 ..     291     379 .. 0.80
   2 ?    3.7  15.4     0.062        32      17      91 ..     338     412 ..     328     419 .. 0.82
   3 ?    2.8  16.0      0.12        59      17      90 ..     359     432 ..     357     439 .. 0.83
   4 ?    3.7   8.3     0.063        32      17      94 ..     408     485 ..     405     491 .. 0.63
   5 ?    5.4   1.4     0.019       9.8      30      59 ..     491     520 ..     486     523 .. 0.87
   6 !   18.2   8.1   2.3e-06    0.0012      14      94 ..     698     778 ..     693     784 .. 0.94
   7 ?    3.0  16.8      0.11        55      20     145 ..     760     892 ..     756     892 .. 0.71
   8 ?    1.4  16.8      0.32   1.7e+02      16      92 ..     873     949 ..     863     957 .. 0.90
   9 ?    1.6   0.3      0.29   1.5e+02      35      68 ..    1001    1034 ..     980    1054 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.37
                           DUF3450  19 dqalke.aekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       +++++e ++k  +++ ++ ++i++++ + + l+++++a +e +e++e ++++   +++  ++ei++le ++ e +
  gi|336255264|ref|YP_004598371.1| 297 EDLNAEiERKGEDEQLRIKSEIEEIKGDISRLEDKIEASEEHIEEAESKRREAFVQIDRKQEEIEELEDEMREHK 371
                                       55554413455566668899999999999**************************************99998765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.062
                           DUF3450  17 tldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                        +++a+++ ++a  +  + q++i++l+de +e++ e  ++k+e+++ e +++qle+ ++++++e+++l+ +++e 
  gi|336255264|ref|YP_004598371.1| 338 HIEEAESKRREAFVQIDRKQEEIEELEDEMREHKLEKASIKTEIQEREQEKKQLEAEIDAVDTEFDELKADLAER 412
                                       556666666777777778899999999999999999999999999999999999999999999999999888775 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.12
                           DUF3450  17 tldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       +++++++e ++   ++a++ ++i++ ++ek++l+ae+ a+ +e ++l++  ++ ++ ++++++e ++l++++++
  gi|336255264|ref|YP_004598371.1| 359 EIEELEDEMREHKLEKASIKTEIQEREQEKKQLEAEIDAVDTEFDELKADLAERKEELEDAKTEKNDLQREQDR 432
                                       56677777888888888899999999999999999999999999999999999999999999999999999886 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.063
                           DUF3450  17 tldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                       +l++ ++e e a +++ + q+++d+l de++  ++e+ + +  +e+ + +  +le+  +++++e+++ e++ ++i  
  gi|336255264|ref|YP_004598371.1| 408 DLAERKEELEDAKTEKNDLQREQDRLLDEARRRSNEISEKEGTIEDRREEIPELESRKSDLKRELEKAEKNRANIAG 484
                                       55555666666666666777777777777777777777777777777777777777777777777777666666665 PP

                           DUF3450  94 i 94 
                                       +
  gi|336255264|ref|YP_004598371.1| 485 V 485
                                       5 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.019
                           DUF3450  30 aaaaqsqkkidklddekqellaeyralkee 59 
                                       ++++++q+ id+ldde q  ++ey +l++ 
  gi|336255264|ref|YP_004598371.1| 491 DEKRRIQSDIDELDDEIQAKQQEYAELEAN 520
                                       678899******************999875 PP

  == domain 6  score: 18.2 bits;  conditional E-value: 2.3e-06
                           DUF3450  14 laatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       +a++++++++e e+  +  + ++++ d+  d k++ ++e+r++++e+esle ++e  e+ ++++e+e+++l+e+ e+
  gi|336255264|ref|YP_004598371.1| 698 VAKQITELQEERESLREDLRGVEERLDDARDRKTDAADEVRSIESEIESLEDKRESIEDEIETLETELEELREERES 774
                                       48999***********************************************************************9 PP

                           DUF3450  91 ieei 94 
                                       ++e 
  gi|336255264|ref|YP_004598371.1| 775 VDER 778
                                       9875 PP

  == domain 7  score: 3.0 bits;  conditional E-value: 0.11
                           DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyne.....qlerlvasqeqeiasleeqieei 91 
                                       +++ e e+  ++++++ +++++++ e +e  a ++++++ +++le++ e     +l+++++++e ei++ e qi+ei
  gi|336255264|ref|YP_004598371.1| 760 TLETELEELREERESVDERMNDISGEIDEQTAAIEEIQADIDELEAELEdskipELTEQIEELEGEIDEREAQIDEI 836
                                       556666666677777777777777777777777777777777777665533333799******************** PP

                           DUF3450  92 eeierelv...pllekmidrLeqfveldlPflleeRqarlakLkelmdradvslaek 145
                                       + + +el+    + e+ i++L++ +e+    ++ e ++r+++ ++ +++ + +l+ek
  gi|336255264|ref|YP_004598371.1| 837 DGTLNELElekEYAEDAIEGLHDDIEAAQ-NKKAEHENRIEECEATIEEKEAELEEK 892
                                       ***99997222466777777777777654.466777888888888888888777776 PP

  == domain 8  score: 1.4 bits;  conditional E-value: 0.32
                           DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       + +++ +++ e+  a+ ++  + +++l++e +el+++ ++l+e le+++ +++q+++ v++++++++s +e+ +++e
  gi|336255264|ref|YP_004598371.1| 873 NRIEECEATIEEKEAELEEKREAVEELEEELAELKEDRNELREDLEDARTKRDQQQDRVNAVQSKLESKRERVQDLE 949
                                       56777888888889999999999***********************************************9999876 PP

  == domain 9  score: 1.6 bits;  conditional E-value: 0.29
                           DUF3450   35 sqkkidklddekqellaeyralkeeleslevyne 68  
                                        + +  ++l+d k++l++e + +++++e+ e +++
  gi|336255264|ref|YP_004598371.1| 1001 VREDLEELEDAKDTLVEEAEGIRDRIEQYETQKK 1034
                                        3333444444444444444444444444444433 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       4.9   2.5e+03       6      39 ..     195     228 ..     185     234 .. 0.79
   2 !   14.2   4.9   6.5e-05     0.034      24     100 ..     252     326 ..     249     328 .. 0.90
   3 ?    4.0   5.4      0.09        46      21      94 ..     313     383 ..     305     386 .. 0.66
   4 ?    0.8   5.1      0.86   4.4e+02       5      79 ..     332     406 ..     328     407 .. 0.85
   5 !    7.2   6.2    0.0095       4.9      12      94 ..     395     474 ..     389     478 .. 0.88
   6 ?    1.4   0.7      0.56   2.9e+02       7      55 ..     474     519 ..     469     528 .. 0.51
   7 !   17.7   5.0   5.4e-06    0.0028      18      97 ..     694     770 ..     691     771 .. 0.91
   8 ?    6.5   5.8     0.015       7.8       5      71 ..     765     836 ..     753     869 .. 0.52
   9 ?    6.6   6.3     0.014       7.2       5      72 ..     889     956 ..     885     959 .. 0.79
  10 ?   -0.7   0.1       2.5   1.3e+03      14      45 ..    1000    1031 ..     993    1056 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.9
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrs 39 
                                       ++a e ++ v+e + + + ++e+ ++ l++++++
  gi|336255264|ref|YP_004598371.1| 195 EDAFEELEVVEERIDEAELRIEEKRDRLEQLEDE 228
                                       5677788888888888888888888888888876 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH....HHHHHHHHHHHH CS
                        Laminin_II  24 qnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss.lsdniseikelI 99 
                                        +le+ +e+l  ++++v+e  e+++d+++ +++ + +v+ L++ +++L +    ++ + e ++  ++ +i+eik  I
  gi|336255264|ref|YP_004598371.1| 252 SELEEKREELDAAEEKVDELAEELEDLQRELDERQGKVVRLQEDLEDLNAE---IERKGEDEQLrIKSEIEEIKGDI 325
                                       57999********************************************99...66777776666*********877 PP

                                       H CS
                        Laminin_II 100 a 100
                                       +
  gi|336255264|ref|YP_004598371.1| 326 S 326
                                       6 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.09
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHH CS
                        Laminin_II  21 plsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdnise 94 
                                        ++ ++e++k ++s++++++e  +e++++a    r+A  ++   ++++++L+d    +++++ +++s++ +i+e
  gi|336255264|ref|YP_004598371.1| 313 RIKSEIEEIKGDISRLEDKIEASEEHIEEAESKRREAFVQIDRKQEEIEELEDE---MREHKLEKASIKTEIQE 383
                                       466677777777777777777777766666666666666666666666666666...55666666679999886 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.86
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelk 79 
                                       +++ +e ++e +++  +  +++++ +e+++e++++++e + +  + ++ i++ +++ k+Le +++ +   + elk
  gi|336255264|ref|YP_004598371.1| 332 IEASEEHIEEAESKRREAFVQIDRKQEEIEELEDEMREHKLEKASIKTEIQEREQEKKQLEAEIDAVDTEFDELK 406
                                       566677788888888899999**************9998888889999999**********99998877777776 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.0095
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...H CS
                        Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasssl 88 
                                       + +v     +l+++l + ke+l+ ++++    n++ ++  + +++Arr + ++ ++   ++d+ +e+ +le+ +s l
  gi|336255264|ref|YP_004598371.1| 395 IDAVDTEFDELKADLAERKEELEDAKTE---KNDLQREQDRLLDEARRRSNEISEKEGTIEDRREEIPELESRKSDL 468
                                       5678888999999999999999999998...677777999999******************************9889 PP

                                       HHHHHH CS
                        Laminin_II  89 sdnise 94 
                                       ++++++
  gi|336255264|ref|YP_004598371.1| 469 KRELEK 474
                                       999875 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.56
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankair 55 
                                       +a++  +++  ++ +l+ +  ++++++ e++++   +++k +++ +  +
  gi|336255264|ref|YP_004598371.1| 474 KAEKNRANIAGVVDDLKDEKRRIQSDIDELDDE---IQAKQQEYAELEA 519
                                       455555555555555555555555555555555...3344444444444 PP

  == domain 7  score: 17.7 bits;  conditional E-value: 5.4e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHH CS
                        Laminin_II  18 qlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdnise 94 
                                       ql+ +++++ +++e+ ++++++++ ++e ++da     dA ++v+ +e +++ L+dk ++++   e    l  +++e
  gi|336255264|ref|YP_004598371.1| 694 QLERVAKQITELQEERESLREDLRGVEERLDDARDRKTDAADEVRSIESEIESLEDKRESIEDEIET---LETELEE 767
                                       78889999999999999999999999999****************************9999999998...8899999 PP

                                       HHH CS
                        Laminin_II  95 ike 97 
                                       ++e
  gi|336255264|ref|YP_004598371.1| 768 LRE 770
                                       887 PP

  == domain 8  score: 6.5 bits;  conditional E-value: 0.015
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXX--TTTTT CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvk.....dankairdArrsvkkLeklapqL 71 
                                       ++e  e  ++v e ++++s ++++  + ++ei+++++e +++++     +++++i++ + ++ + e +++++
  gi|336255264|ref|YP_004598371.1| 765 LEELREERESVDERMNDISGEIDEQTAAIEEIQADIDELEAELEdskipELTEQIEELEGEIDEREAQIDEI 836
                                       334444455555555555555555555555555555555555552222223333333333333333333333 PP

  == domain 9  score: 6.6 bits;  conditional E-value: 0.014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTG CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLl 72 
                                       ++e  e ++e +e la+l+++ ++++e+l+ ++++ ++ ++ v++ +  +++ r+ v++Le +++ L+
  gi|336255264|ref|YP_004598371.1| 889 LEEKREAVEELEEELAELKEDRNELREDLEDARTKRDQQQDRVNAVQSKLESKRERVQDLEWEIEGLE 956
                                       56667778888888888888888888888888888888888888888888888888888888887775 PP

  == domain 10  score: -0.7 bits;  conditional E-value: 2.5
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   14 evleqlaplsqnlentkeklseinrsveetne 45  
                                        ev e+l++l+   + + e++++i++ +e+ + 
  gi|336255264|ref|YP_004598371.1| 1000 EVREDLEELEDAKDTLVEEAEGIRDRIEQYET 1031
                                        44445555554444444555555444433332 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   7.5       4.2   2.1e+03     101     145 ..     198     244 ..     185     251 .. 0.66
   2 ?    5.1  17.4     0.047        24     113     169 ..     249     305 ..     236     321 .. 0.84
   3 ?    2.9  18.7      0.22   1.1e+02     102     180 ..     316     394 ..     310     398 .. 0.91
   4 !    7.7  24.5    0.0073       3.7      73     184 ..     406     517 ..     399     521 .. 0.96
   5 !   11.3  16.3    0.0006      0.31     100     177 ..     698     775 ..     693     780 .. 0.89
   6 ?    1.4  11.4      0.64   3.3e+02      89     166 ..     764     846 ..     764     852 .. 0.53
   7 !   17.9  25.7   5.7e-06    0.0029      80     180 ..     851     951 ..     846     955 .. 0.95
   8 ?    4.3  15.0      0.08        41      78     180 ..     905    1018 ..     904    1033 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.2
                             ATG16 101 aqrllelneelqkleeklkedeerlaeleaeraalet..klkdreee 145
                                        + l  ++e +++ e +++e++ rl++le+er++  +  +l+d +ee
  gi|336255264|ref|YP_004598371.1| 198 FEELEVVEERIDEAELRIEEKRDRLEQLEDERRTALRyrRLRDEKEE 244
                                       45677778888888888888888888888887766541144555555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.047
                             ATG16 113 kleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnq 169
                                       k+ ++l+e++e+l+++e+++ +l ++l+d++ el e++  v  lq++l+ L+ + + 
  gi|336255264|ref|YP_004598371.1| 249 KKASELEEKREELDAAEEKVDELAEELEDLQRELDERQGKVVRLQEDLEDLNAEIER 305
                                       6788999999**************************************999999864 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.22
                             ATG16 102 qrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrkle 178
                                       + + e +  +++le+k+++ ee ++e+e++r++   ++++++ee++e+e  + + + E ++ + + + +E+++++le
  gi|336255264|ref|YP_004598371.1| 316 SEIEEIKGDISRLEDKIEASEEHIEEAESKRREAFVQIDRKQEEIEELEDEMREHKLEKASIKTEIQEREQEKKQLE 392
                                       56777888899999*************************************************************99 PP

                             ATG16 179 kE 180
                                       +E
  gi|336255264|ref|YP_004598371.1| 393 AE 394
                                       98 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0073
                             ATG16  73 sakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrek 149
                                       +a++++ +++l   ++e  +l++++  l +  ++ ++e++++e +++ ++e++ ele+++++l+++l++ e++ +  
  gi|336255264|ref|YP_004598371.1| 406 KADLAERKEELEDAKTEKNDLQREQDRLLDEARRRSNEISEKEGTIEDRREEIPELESRKSDLKRELEKAEKNRANI 482
                                       567889999999***************************************************************** PP

                             ATG16 150 eklvqdlqDElsaLqlqlnqaEeklrklekENkeL 184
                                       + +v+dl+DE    q     ++++ +  ++E +eL
  gi|336255264|ref|YP_004598371.1| 483 AGVVDDLKDEKRRIQSDIDELDDEIQAKQQEYAEL 517
                                       *******************************9998 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.0006
                             ATG16 100 laqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrk 176
                                        a++++el+ee + l+e l+  eerl+++++++++  +++++ e e++ +e   + + DE+++L+ +l+ + e+++ 
  gi|336255264|ref|YP_004598371.1| 698 VAKQITELQEERESLREDLRGVEERLDDARDRKTDAADEVRSIESEIESLEDKRESIEDEIETLETELEELREERES 774
                                       68999999999999999999999999999999999999999999999999999999999999999999988777765 PP

                             ATG16 177 l 177
                                       +
  gi|336255264|ref|YP_004598371.1| 775 V 775
                                       5 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.64
                             ATG16  89 elaelyksrgelaqrllelneelqkleeklkedeerlaeleaera.....aletklkdreeelrekeklvqdlqDEl 160
                                       el+el  +r+   +r ++ + e++++ + ++e ++ ++eleae +     +l+++++++e e+ e+e+ ++++   l
  gi|336255264|ref|YP_004598371.1| 764 ELEELREERESVDERMNDISGEIDEQTAAIEEIQADIDELEAELEdskipELTEQIEELEGEIDEREAQIDEIDGTL 840
                                       55566666666666666666666666666666666666666654422222355566666666666665555555555 PP

                             ATG16 161 saLqlq 166
                                       + L+l+
  gi|336255264|ref|YP_004598371.1| 841 NELELE 846
                                       555555 PP

  == domain 7  score: 17.9 bits;  conditional E-value: 5.7e-06
                             ATG16  80 eqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdl 156
                                       e+++  l ++ ++++ +++e+++r+ e +++++++e++l+e++e+++ele+e a+l++ +++++e l++ ++  +++
  gi|336255264|ref|YP_004598371.1| 851 EDAIEGLHDDIEAAQNKKAEHENRIEECEATIEEKEAELEEKREAVEELEEELAELKEDRNELREDLEDARTKRDQQ 927
                                       67788899********************************************************************* PP

                             ATG16 157 qDElsaLqlqlnqaEeklrklekE 180
                                       qD ++a q +l++  e+ ++le E
  gi|336255264|ref|YP_004598371.1| 928 QDRVNAVQSKLESKRERVQDLEWE 951
                                       ****************99999976 PP

  == domain 8  score: 4.3 bits;  conditional E-value: 0.08
                             ATG16   78 sleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraale.tklkdreeelrekek 151 
                                        +l++ + +lre+l+++  +r + ++r+++++++l+ ++e+ +  e +++ le+e+ +   + + d++  l+  e 
  gi|336255264|ref|YP_004598371.1|  905 ELKEDRNELREDLEDARTKRDQQQDRVNAVQSKLESKRERVQDLEWEIEGLESEVGDYDpEDVPDHDTVLEMIEL 979 
                                        67788999********************************************99987652445555555554444 PP

                             ATG16  152 lvq..........dlqDElsaLqlqlnqaEeklrklekE 180 
                                        l               DE++  +  l+ +E+++++l +E
  gi|336255264|ref|YP_004598371.1|  980 LTAdmeamepvnmLAIDEYDEVREDLEELEDAKDTLVEE 1018
                                        444444555555466677777777777777777666666 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 !    9.7  25.8    0.0017      0.86      77     186 ..     187     303 ..     169     306 .. 0.81
   2 !    8.6  32.4    0.0035       1.8      58     181 ..     249     369 ..     235     379 .. 0.67
   3 ?    2.7  40.2      0.23   1.2e+02      66     186 ..     335     472 ..     306     474 .. 0.75
   4 ?    4.7  22.0     0.057        29      77     177 ..     402     519 ..     393     523 .. 0.70
   5 !   11.4  28.6    0.0005      0.26      66     185 ..     720     846 ..     683     848 .. 0.73
   6 !    7.7  24.4    0.0069       3.5      69     178 ..     860     958 ..     838     965 .. 0.41
   7 ?    5.3   1.1     0.038        19      82     136 ..     996    1051 ..     968    1060 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                           UPF0242  77 lteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenq.qLqe.kleaiaedfeelklele.....eqLae 146
                                       + e d + +   e+le ++e+ +e + ++++k   le+l+ e    L+  +l + +e++e +k+++e     e+L+ 
  gi|336255264|ref|YP_004598371.1| 187 VAEFDAKKEDAFEELEVVEERIDEAELRIEEKRDRLEQLEDERRtALRYrRLRDEKEEYEGYKKASEleekrEELDA 263
                                       4555533333445777777777888888999999999999888756764278999999*999998765555689*** PP

                           UPF0242 147 kqellqeyqetieeqrsvlekrqdqieqLeskVrDlnyEi 186
                                        +e+++e++e++e+++ +l++rq ++ +L+   +Dln Ei
  gi|336255264|ref|YP_004598371.1| 264 AEEKVDELAEELEDLQRELDERQGKVVRLQEDLEDLNAEI 303
                                       ***************************************9 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0035
                           UPF0242  58 ekalkeklekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfe 134
                                       +ka +++ + ++l++ e+k+ el e+l+  + +l e+q +  +L+e l+  + e+er  e++ qL++k e   e+++
  gi|336255264|ref|YP_004598371.1| 249 KKASELEEKREELDAAEEKVDELAEELEDLQRELDERQGKVVRLQEDLEDLNAEIERKGEDE-QLRIKSEI--EEIK 322
                                       23333333444555555555555555555555555555555566666888888877755544.55555544..5666 PP

                           UPF0242 135 elkleleeqLaekqellqeyqetieeqrsvlekrqdqieqLeskVrD 181
                                            le++++  +e ++e + +  e    ++++q++ie+Le   r 
  gi|336255264|ref|YP_004598371.1| 323 GDISRLEDKIEASEEHIEEAESKRREAFVQIDRKQEEIEELEDEMRE 369
                                       66667899999*******************************87775 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.23
                           UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae........... 131
                                        ++++ee e+k  e   +++ k+e++eel++e +e k e ++ ++e++++++e++qL+ +  a+             
  gi|336255264|ref|YP_004598371.1| 335 SEEHIEEAESKRREAFVQIDRKQEEIEELEDEMREHKLEKASIKTEIQEREQEKKQLEAEIDAVDTefdelkadlae 411
                                       34456666666666668889999999999999999999999999999999999999999999988866666665555 PP

                           UPF0242 132 ...dfeelkleleeqLaekqellqeyq...etieeqrsvlekrqdqieqLeskVrDlnyEi 186
                                          + e+ k e ++  +e+  ll+e +   ++i+e+  ++e r ++i +Les+ +Dl+ E+
  gi|336255264|ref|YP_004598371.1| 412 rkeELEDAKTEKNDLQREQDRLLDEARrrsNEISEKEGTIEDRREEIPELESRKSDLKREL 472
                                       5555555555555555666677777652225789999999999999999999999999887 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.057
                           UPF0242  77 lteldeglktkeealeelqeeeeeLkee.....................ldakeeelerlkeenqqLqekleaiaed 132
                                         el+ +l++ +e+le+++ e+++L++e                     ++ + ee+ +l+ ++  L+ +le++ + 
  gi|336255264|ref|YP_004598371.1| 402 FDELKADLAERKEELEDAKTEKNDLQREqdrlldearrrsneisekegtIEDRREEIPELESRKSDLKRELEKAEK- 477
                                       45666788888888999888888888888888888*******6666666666666666666666666666666333. PP

                           UPF0242 133 feelkleleeqLaekqellqeyqetieeqrsvlekrqdqieqLes 177
                                       +     ++   ++  +      q  i e+  +++ +q++ ++Le+
  gi|336255264|ref|YP_004598371.1| 478 NR---ANIAGVVDDLKDEKRRIQSDIDELDDEIQAKQQEYAELEA 519
                                       33...3333444444444455678999999999999999999997 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 0.0005
                           UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklelee 142
                                       e+   +++ +k  +  ++++ +e ++e l+++ e  ++e++  e+ele+l+ee +++ e++++i+ +++e+  ++ee
  gi|336255264|ref|YP_004598371.1| 720 EERLDDARDRKTDAA-DEVRSIESEIESLEDKRESIEDEIETLETELEELREERESVDERMNDISGEIDEQTAAIEE 795
                                       333334444444444.48889999*****************************************966666665554 PP

                           UPF0242 143 ......qLae..kqellqeyqetieeqrsvlekrqdqieqLeskVrDlnyE 185
                                             +L+   +  ++ e+ e+iee+  ++++r++qi +++   + l  E
  gi|336255264|ref|YP_004598371.1| 796 iqadidELEAelEDSKIPELTEQIEELEGEIDEREAQIDEIDGTLNELELE 846
                                       3222222222124568999********************999888877655 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.0069
                           UPF0242  69 kleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae...dfeelklelee 142
                                        +e+ ++k  e ++ +++ e ++ee ++e ee +e +++ eeel++lke+ ++L+e le++     + ++   ++++
  gi|336255264|ref|YP_004598371.1| 860 DIEAAQNKKAEHENRIEECEATIEEKEAELEEKREAVEELEEELAELKEDRNELREDLEDARTkrdQQQDRVNAVQS 936
                                       23333344444444444444444444444444444444444444444444444444444433333233333333344 PP

                           UPF0242 143 qLaekqellqeyqetieeqrsvlekrqdqieqLesk 178
                                       +L+ k+e++q+++ +i              e Les 
  gi|336255264|ref|YP_004598371.1| 937 KLESKRERVQDLEWEI--------------EGLESE 958
                                       4444444444444333..............333333 PP

  == domain 7  score: 5.3 bits;  conditional E-value: 0.038
                           UPF0242   82 eglktkeealeelqeeeeeLkeeldakeeelerlk.eenqqLqekleaiaedfeel 136 
                                        +++++ +e leel++ ++ L ee +     +e+++ ++++ +    eai+e f e 
  gi|336255264|ref|YP_004598371.1|  996 DEYDEVREDLEELEDAKDTLVEEAEGIRDRIEQYEtQKKETFMTAYEAISEHFTEI 1051
                                        35566777777777777777777777777777775134456777777777776664 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   2.4         5   2.6e+03     113     153 ..     189     229 ..     172     254 .. 0.62
   2 ?   -1.7  16.0       4.2   2.1e+03     103     176 ..     234     305 ..     189     316 .. 0.78
   3 !   16.5  18.3   1.2e-05    0.0059      96     186 ..     317     407 ..     308     408 .. 0.94
   4 ?    2.3  12.5      0.25   1.3e+02     100     183 ..     426     509 ..     406     519 .. 0.86
   5 !   12.9  10.6   0.00014     0.073      95     183 ..     700     788 ..     693     793 .. 0.92
   6 ?    1.0  12.6      0.63   3.2e+02     102     171 ..     763     837 ..     750     868 .. 0.43
   7 !    9.2  20.7     0.002         1      57     179 ..     799     922 ..     793     928 .. 0.92
   8 ?   -0.8   1.8       2.3   1.2e+03     124     184 ..     990    1051 ..     969    1054 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5
                            DUF724 113 klekkieeeesekrkleeeidelekkilelerqlallkekk 153
                                       +++ k e++ +e + +ee ide e +i e + +l++l  ++
  gi|336255264|ref|YP_004598371.1| 189 EFDAKKEDAFEELEVVEERIDEAELRIEEKRDRLEQLEDER 229
                                       45556666666666667777777777766666666555333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.2
                            DUF724 103 eqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeled 176
                                       ++++l++e++++e    +++se ++  ee+d  e+k+ el ++l+ l+++ ++ + +++rl+ + e+l+ e+e+
  gi|336255264|ref|YP_004598371.1| 234 RYRRLRDEKEEYEG--YKKASELEEKREELDAAEEKVDELAEELEDLQRELDERQGKVVRLQEDLEDLNAEIER 305
                                       44555555555544..4555666666799999999999999999999999999999*******99999999986 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.2e-05
                            DUF724  96 kLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaeklee 172
                                       ++ ++k + ++l++++++ e++iee+es++r++  +id ++++i ele +    k +k + + ei + ++e+++le 
  gi|336255264|ref|YP_004598371.1| 317 EIEEIKGDISRLEDKIEASEEHIEEAESKRREAFVQIDRKQEEIEELEDEMREHKLEKASIKTEIQEREQEKKQLEA 393
                                       56689************************************************************************ PP

                            DUF724 173 eledveqeFeavas 186
                                       e+++v +eF+++++
  gi|336255264|ref|YP_004598371.1| 394 EIDAVDTEFDELKA 407
                                       *********99875 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.25
                            DUF724 100 lkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeled 176
                                       l+ eq++ll+e ++  ++i+e+e   +   eei ele++ ++l+r+l+ + +++ + +  + +lk e+++++ ++++
  gi|336255264|ref|YP_004598371.1| 426 LQREQDRLLDEARRRSNEISEKEGTIEDRREEIPELESRKSDLKRELEKAEKNRANIAGVVDDLKDEKRRIQSDIDE 502
                                       78899999999999999999999999999999999999999999999999988888888888899999999999988 PP

                            DUF724 177 veqeFea 183
                                         +e +a
  gi|336255264|ref|YP_004598371.1| 503 LDDEIQA 509
                                       8888776 PP

  == domain 5  score: 12.9 bits;  conditional E-value: 0.00014
                            DUF724  95 nkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekle 171
                                       +++ +l++e+++l+e ++++e+++ +++++k+ + +e++ +e++i  le +++++  + e+ + e+ +l+ e e+++
  gi|336255264|ref|YP_004598371.1| 700 KQITELQEERESLREDLRGVEERLDDARDRKTDAADEVRSIESEIESLEDKRESIEDEIETLETELEELREERESVD 776
                                       567899*********************************************************************** PP

                            DUF724 172 eeledveqeFea 183
                                       e+++d+  e ++
  gi|336255264|ref|YP_004598371.1| 777 ERMNDISGEIDE 788
                                       ****99887765 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.63
                            DUF724 102 deqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk.....ekkeaadkeiarlkseaekle 171
                                       +e ++l+eer+ +++++ + + e  +  + i+e++  i ele +l+  k     e+ e+ + ei + +++ ++++
  gi|336255264|ref|YP_004598371.1| 763 TELEELREERESVDERMNDISGEIDEQTAAIEEIQADIDELEAELEDSKipeltEQIEELEGEIDEREAQIDEID 837
                                       223333333333333333333333333333333333333444444333344443333333333333333333333 PP

  == domain 7  score: 9.2 bits;  conditional E-value: 0.002
                            DUF724  57 kvkklsiddsrseleslkeslaeLekhGFdVkalqsrl.nkLlslkdeqtklleerkklekkieeeesekrkleeei 132
                                        +++l+++ + s++ +l e++ eLe +  + +a  + +  +L +l  e++ +++++++l+ +ie ++++k++ e+ i
  gi|336255264|ref|YP_004598371.1| 799 DIDELEAELEDSKIPELTEQIEELEGEIDEREAQIDEIdGTLNELELEKEYAEDAIEGLHDDIEAAQNKKAEHENRI 875
                                       6888999999999***********99988888888888446778999****************************** PP

                            DUF724 133 delekkilelerqlallkekkeaadkeiarlkseaekleeeledveq 179
                                       +e e +i e e +l+ ++e  e+ ++e+a+lk + ++l+e+led+++
  gi|336255264|ref|YP_004598371.1| 876 EECEATIEEKEAELEEKREAVEELEEELAELKEDRNELREDLEDART 922
                                       *******************************************9976 PP

  == domain 8  score: -0.8 bits;  conditional E-value: 2.3
                            DUF724  124 ekrkleeeidelekkilelerqlallkekkeaadkeiarlksea.ekleeeledveqeFeav 184 
                                         +  + +e de+ +   ele  +++l e+ e    +i + ++++ e++ +++e++ ++F ++
  gi|336255264|ref|YP_004598371.1|  990 VNMLAIDEYDEVREDLEELEDAKDTLVEEAEGIRDRIEQYETQKkETFMTAYEAISEHFTEI 1051
                                        55555667788888888888888888888888888888888765145666677777777665 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 ?    5.7   5.4     0.031        16       2      35 ..     271     304 ..     263     312 .. 0.78
   2 !   16.0   2.8   1.8e-05    0.0094      19      71 ..     310     362 ..     301     367 .. 0.89
   3 ?    6.5   9.2     0.018         9      12      71 ..     380     439 ..     369     444 .. 0.90
   4 ?    2.3   3.0      0.34   1.8e+02       2      53 ..     461     512 ..     460     520 .. 0.83
   5 ?    1.0   3.7      0.86   4.4e+02      23      59 ..     698     734 ..     692     751 .. 0.58
   6 ?    6.6   3.1     0.016         8      28      71 ..     752     795 ..     739     799 .. 0.87
   7 ?    5.7   2.9     0.029        15       3      51 ..     797     843 ..     795     848 .. 0.88
   8 ?   -1.8  13.6       6.7   3.4e+03       3      72 ..     872     941 ..     870     949 .. 0.67
   9 ?    0.1   0.8       1.7   8.7e+02       3      34 ..     928     959 ..     926     961 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.031
                     TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelr 35 
                                       l + ++ L r l+ r+   ++lq+ le+l++e+ 
  gi|336255264|ref|YP_004598371.1| 271 LAEELEDLQRELDERQGKVVRLQEDLEDLNAEIE 304
                                       5667788888888888888888888888888876 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.8e-05
                     TolA_bind_tri  19 lllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrklea 71 
                                        +l++ +++e+ + ++++L  +iE  + ++e++e + r+ ++++D+  +++e+
  gi|336255264|ref|YP_004598371.1| 310 EQLRIKSEIEEIKGDISRLEDKIEASEEHIEEAESKRREAFVQIDRKQEEIEE 362
                                       6899999****************************************999987 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.018
                     TolA_bind_tri  12 ilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrklea 71 
                                        ++ r+q   +l  +++a  +e +eL+ ++ e + +le++++  +dl ++ D++l + + 
  gi|336255264|ref|YP_004598371.1| 380 EIQEREQEKKQLEAEIDAVDTEFDELKADLAERKEELEDAKTEKNDLQREQDRLLDEARR 439
                                       5677889999********************************************998766 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.34
                     TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqlee 53 
                                       le+r + L r le+ ++   ++   +++l+ e r+++ +i+el  +++  ++
  gi|336255264|ref|YP_004598371.1| 461 LESRKSDLKRELEKAEKNRANIAGVVDDLKDEKRRIQSDIDELDDEIQAKQQ 512
                                       7888888999999999999999999999999999999999999999987665 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.86
                     TolA_bind_tri  23 lqqqlealqqelreLRGqiEelqyqleqleerQrdlY 59 
                                       + +q+ +lq+e  +LR ++   + +l++++ r  d  
  gi|336255264|ref|YP_004598371.1| 698 VAKQITELQEERESLREDLRGVEERLDDARDRKTDAA 734
                                       3456666666666666666666666666666655555 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.016
                     TolA_bind_tri  28 ealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrklea 71 
                                       e+ + e+ +L  ++Eel+ + e++ er +d+  ++De  +++e+
  gi|336255264|ref|YP_004598371.1| 752 ESIEDEIETLETELEELREERESVDERMNDISGEIDEQTAAIEE 795
                                       67789999****************************99998886 PP

  == domain 7  score: 5.7 bits;  conditional E-value: 0.029
                     TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleql 51 
                                       ++ +++LE  le   + + el +q+e+l+ e++e   qi+e    l++l
  gi|336255264|ref|YP_004598371.1| 797 QADIDELEAELED--SKIPELTEQIEELEGEIDEREAQIDEIDGTLNEL 843
                                       67899******99..9******************999999988777776 PP

  == domain 8  score: -1.8 bits;  conditional E-value: 6.7
                     TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkleag 72 
                                       e+r+++ E  +e ++  l e  + +e+l++el+eL+ +  el+ +le+++++  ++   ++++ +kle++
  gi|336255264|ref|YP_004598371.1| 872 ENRIEECEATIEEKEAELEEKREAVEELEEELAELKEDRNELREDLEDARTKRDQQQDRVNAVQSKLESK 941
                                       6777777777777766666666667777777777777777777777777766666666666666666655 PP

  == domain 9  score: 0.1 bits;  conditional E-value: 1.7
                     TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealqqel 34 
                                       +drv  +  +le++ +   +l  ++e l++e+
  gi|336255264|ref|YP_004598371.1| 928 QDRVNAVQSKLESKRERVQDLEWEIEGLESEV 959
                                       78899999999999899999999999888887 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3     0.011       5.5      46     100 ..     267     331 ..     254     343 .. 0.48
   2 ?    3.0   1.0      0.19        98      34      73 ..     389     427 ..     362     451 .. 0.66
   3 ?    0.8   0.2      0.87   4.5e+02      64      88 ..     481     508 ..     449     554 .. 0.57
   4 ?    8.0   0.5    0.0053       2.7      30      97 ..     700     768 ..     692     771 .. 0.79
   5 ?   10.0   4.1    0.0013      0.64      29      96 ..     741     809 ..     731     875 .. 0.51
   6 ?    5.8   1.0     0.026        13      39      95 ..     895     960 ..     852     965 .. 0.64
   7 ?   -2.3   0.0         8   4.1e+03      36      55 ..    1008    1027 ..     970    1057 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                      Baculo_PEP_C  46 qLnalsedlksllaeldt......rldtlltnLtdalnalq....dtlrneLtnlnsiltnLlss 100
                                       ++++l+e+l++l  eld+      rl++ l+ L++ + +        +++e++ ++ +++ L  +
  gi|336255264|ref|YP_004598371.1| 267 KVDELAEELEDLQRELDErqgkvvRLQEDLEDLNAEIERKGedeqLRIKSEIEEIKGDISRLEDK 331
                                       44555555555555554444433333333333333333322332123445555555555555433 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.19
                      Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLt 73 
                                        ql++ +da++t++++l++dl +  +el++  +t  + L+
  gi|336255264|ref|YP_004598371.1| 389 KQLEAEIDAVDTEFDELKADLAERKEELED-AKTEKNDLQ 427
                                       577777777777777777777776666554.233333333 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.87
                      Baculo_PEP_C  64 rldtlltnLtdalnalq...dtlrneLt 88 
                                       +++ +++ L+d   ++q   d+l+ e++
  gi|336255264|ref|YP_004598371.1| 481 NIAGVVDDLKDEKRRIQsdiDELDDEIQ 508
                                       2222222222222222222222222222 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0053
                      Baculo_PEP_C  30 vqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnL 97 
                                        qi ++l++  +++ + L  ++e+l +   + +t+ ++ +  +++ + +l+   ++++ e+++l+++l +L
  gi|336255264|ref|YP_004598371.1| 700 KQI-TELQEERESLREDLRGVEERLDD-ARDRKTDAADEVRSIESEIESLEdkrESIEDEIETLETELEEL 768
                                       455.77777888888888888888888.6677788889999999999999999999999999999999887 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.0013
                      Baculo_PEP_C  29 nvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtnlnsiltn 96 
                                       +++i   l+   ++ie ++++l+++l++l +e ++   r+++ + +++++ +a++ +++ +++ l+++l +
  gi|336255264|ref|YP_004598371.1| 741 ESEI-ESLEDKRESIEDEIETLETELEELREERESvdeRMNDISGEIDEQTAAIE-EIQADIDELEAELED 809
                                       5555.55555555555555555555555544322222244444444444444443.222222222222221 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.026
                      Baculo_PEP_C  39 lldaietqLnalsedlksllaeldt..........rldtlltnLtdalnalqdtlrneLtnlnsilt 95 
                                       +++++e++L +l+ed ++l ++l++          r++++ ++L+++  ++q +l+ e+++l+s++ 
  gi|336255264|ref|YP_004598371.1| 895 AVEELEEELAELKEDRNELREDLEDartkrdqqqdRVNAVQSKLESKRERVQ-DLEWEIEGLESEVG 960
                                       3444444444444444444444443333333244466666666666666666.67777777777765 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 8
                      Baculo_PEP_C   36 latlldaietqLnalsedlk 55  
                                        l+ ++d++ ++ + + ++++
  gi|336255264|ref|YP_004598371.1| 1008 LEDAKDTLVEEAEGIRDRIE 1027
                                        22222222222223333333 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   8.4      0.49   2.5e+02      53     103 ..     184     234 ..     119     238 .. 0.79
   2 ?    5.7  31.1      0.04        20      17     130 ..     234     343 ..     230     345 .. 0.87
   3 ?    6.8  38.6     0.018       9.2      11     125 ..     318     436 ..     315     445 .. 0.87
   4 ?    5.8  15.2     0.036        18      36     116 ..     438     518 ..     432     524 .. 0.73
   5 ?   11.1  25.2   0.00086      0.44      11     127 ..     695     808 ..     692     812 .. 0.65
   6 ?    1.4  17.9      0.82   4.2e+02      14     118 ..     775     874 ..     773     880 .. 0.52
   7 ?    6.6  36.7     0.021        11      11     132 ..     819     937 ..     816     959 .. 0.67
   8 ?    2.6   2.9      0.35   1.8e+02      62     101 ..     997    1036 ..     968    1056 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.49
                            APG6_N  53 eeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwr 103
                                          +++ ++++e+++eeL+ +e+  +e e  +++ +  le+le+e +  +r
  gi|336255264|ref|YP_004598371.1| 184 IAGVAEFDAKKEDAFEELEVVEERIDEAELRIEEKRDRLEQLEDERRTALR 234
                                       344778889999999999999999999999999999999999998876655 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.04
                            APG6_N  17 qleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelea 93 
                                       +++++++e+++Ye + k  + e+k      eel+++ee++++l +e e+l++eL+e + +  +l+++l++l +e e+
  gi|336255264|ref|YP_004598371.1| 234 RYRRLRDEKEEYEGYKKASELEEKR-----EELDAAEEKVDELAEELEDLQRELDERQGKVVRLQEDLEDLNAEIER 305
                                       78999************99999444.....589******************************************99 PP

                            APG6_N  94 leeeeerfwr.eynelqlelleleeeldsleaqyehaq 130
                                       + e+e+  ++ e  e + + ++le++ ++ e  +e a+
  gi|336255264|ref|YP_004598371.1| 306 KGEDEQLRIKsEIEEIKGDISRLEDKIEASEEHIEEAE 343
                                       98877765550556699999999999999998888775 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.018
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeek....qdeeleeleeeleklekeeeelleeLkelekereeleae 83 
                                       +ee++  ++++e++++a ee  ++ +++++e+      ++ee+eele+e+++ + e+++  +e++e e+e+++leae
  gi|336255264|ref|YP_004598371.1| 318 IEEIKGDISRLEDKIEASEEHIEEAESKRREAFVqidrKQEEIEELEDEMREHKLEKASIKTEIQEREQEKKQLEAE 394
                                       577777788888888888888888888876655599999************************************** PP

                            APG6_N  84 laaleeelealeeeeerfwreynelqlelleleeeldsleaq 125
                                       + a   e ++l+++ ++  +e  + ++e+++l+ e+d l  +
  gi|336255264|ref|YP_004598371.1| 395 IDAVDTEFDELKADLAERKEELEDAKTEKNDLQREQDRLLDE 436
                                       ************************************998655 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.036
                            APG6_N  36 kkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlel 112
                                       +++++e ++++  +e+ +ee+ +le+ +++l +eL+++ek+r++++  + +l+ e+++++ + ++   e +++q e 
  gi|336255264|ref|YP_004598371.1| 438 RRRSNEISEKEGTIEDRREEIPELESRKSDLKRELEKAEKNRANIAGVVDDLKDEKRRIQSDIDELDDEIQAKQQEY 514
                                       44444444467788888888999999999999999999999988888888888888888877777777777777776 PP

                            APG6_N 113 lele 116
                                       +ele
  gi|336255264|ref|YP_004598371.1| 515 AELE 518
                                       6666 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.00086
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaal 87 
                                       le++ kq+ ++++er++++e l+ ++++ ++++   +   ++ +e++ +e+e e+l+ + + +e+e e le el++l
  gi|336255264|ref|YP_004598371.1| 695 LERVAKQITELQEERESLREDLRGVEERLDDAR---DRKTDAADEVRSIESEIESLEDKRESIEDEIETLETELEEL 768
                                       688999***********9999999998876655...34455555666666666666666666666666666666666 PP

                            APG6_N  88 eeelealeeeeerfwreynelqlelleleeeldsleaqye 127
                                       +ee e ++e  +    e  e+    +e + + d lea++e
  gi|336255264|ref|YP_004598371.1| 769 REERESVDERMNDISGEIDEQTAAIEEIQADIDELEAELE 808
                                       6666666666666666666666666666666666665555 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.82
                            APG6_N  14 ldkqleqaekerdaYeeflkklkkekkeeek..qdeeleeleeeleklekeeeelleeLkelekereeleaelaale 88 
                                       +d+++++   e+d+ ++  ++++++ +e e+  +       + ++ +l ++ eel+ e++e e++ +e++  l++le
  gi|336255264|ref|YP_004598371.1| 775 VDERMNDISGEIDEQTAAIEEIQADIDELEAelE-------DSKIPELTEQIEELEGEIDEREAQIDEIDGTLNELE 844
                                       6777777777777777777877777666543332.......333444555555555555555555555555555555 PP

                            APG6_N  89 eelealeeeeerfwreynelqlelleleee 118
                                        e+e  e+  e    +  + q +++e+e++
  gi|336255264|ref|YP_004598371.1| 845 LEKEYAEDAIEGLHDDIEAAQNKKAEHENR 874
                                       555555554444444444444444444444 PP

  == domain 7  score: 6.6 bits;  conditional E-value: 0.021
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaal 87 
                                       +eel+ ++++ e+++d+    l++l+ ek+ +e   + +e l++++e+ +++++e ++ ++e e++ ee eael++ 
  gi|336255264|ref|YP_004598371.1| 819 IEELEGEIDEREAQIDEIDGTLNELELEKEYAE---DAIEGLHDDIEAAQNKKAEHENRIEECEATIEEKEAELEEK 892
                                       7999**********************9988876...45566666666666666666666666666666666666666 PP

                            APG6_N  88 eeelealeeeeerfwreynelqlelleleeeldsleaqyehaqnq 132
                                       +e  e+leee ++  +++nel+ +l++   ++d+ + +++  q++
  gi|336255264|ref|YP_004598371.1| 893 REAVEELEEELAELKEDRNELREDLEDARTKRDQQQDRVNAVQSK 937
                                       666666666666666666666666666665555555554444433 PP

  == domain 8  score: 2.6 bits;  conditional E-value: 0.35
                            APG6_N   62 eeeelleeLkelekereeleaelaaleeelealeeeeerf 101 
                                        e +e  e L+ele++++ l +e + ++   e+ e ++++ 
  gi|336255264|ref|YP_004598371.1|  997 EYDEVREDLEELEDAKDTLVEEAEGIRDRIEQYETQKKET 1036
                                        4455666777777777777777777777777776655544 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 ?    4.9   4.3     0.065        33      51     146 ..     180     284 ..     156     290 .. 0.54
   2 ?    3.8   6.5      0.14        71      53     141 ..     252     346 ..     242     348 .. 0.64
   3 ?    8.7   7.3    0.0045       2.3      40     128 ..     310     396 ..     300     398 .. 0.83
   4 ?    1.1  11.5      0.99   5.1e+02      36     111 ..     355     434 ..     352     454 .. 0.79
   5 ?    4.5   4.2     0.086        44      47     111 ..     457     520 ..     447     530 .. 0.78
   6 ?    3.0   0.4      0.26   1.3e+02      41      93 ..     695     747 ..     690     753 .. 0.84
   7 ?    6.2   8.3     0.026        13      33     109 ..     743     818 ..     739     873 .. 0.84
   8 ?    2.8   2.3      0.29   1.5e+02      42      89 ..     841     888 ..     818     892 .. 0.52
   9 ?   10.4   5.6    0.0013      0.69      32      93 ..     887     948 ..     872     960 .. 0.87
  10 ?    2.4   0.1      0.37   1.9e+02      40      92 ..    1004    1057 ..     996    1066 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.065
                                       HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT------...---CHHHHHHHHH..HHHHHHHH CS
                           T3SSipB  51 alseakgatd...dleaaiekadqaksaadaatkkvdeaqkrlkeLaPdeP...ekakleaaeqQagaaadalqade 121
                                        ++e +g+++   + e+a e+++ ++  +d+a+ +++e   rl++L+ +      +++l+ +++  +  + a + +e
  gi|336255264|ref|YP_004598371.1| 180 IIDEIAGVAEfdaKKEDAFEELEVVEERIDEAELRIEEKRDRLEQLEDERRtalRYRRLRDEKEEYEGYKKASELEE 256
                                       45555555442225688999999999999999999999999999993332211124444444444443355555554 PP

                                       HHHHHHHHHH.HHHHHH...HHHHHHHHT CS
                           T3SSipB 122 alqKkldaas.klseka...kakekevDd 146
                                       +   +ldaa+ k+ e a    ++++e+D+
  gi|336255264|ref|YP_004598371.1| 257 K-REELDAAEeKVDELAeelEDLQRELDE 284
                                       2.334555431333333111444555555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----.-----CHHH..HHHHHH..HHHHHHHHHH... CS
                           T3SSipB  53 seakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPd.ePekaklea..aeqQagaaadalqadeal... 123
                                       se ++  ++l+aa ek+d++  + +++++ +de q ++  L+ d e   a++e+  + +Q+ ++ +  + +  +   
  gi|336255264|ref|YP_004598371.1| 252 SELEEKREELDAAEEKVDELAEELEDLQRELDERQGKVVRLQEDlEDLNAEIERkgEDEQLRIKSEIEEIKGDIsrl 328
                                       67777888888888888888888888888888888877777544222345555422567888775544444332222 PP

                                       HHHHHHHHHHHHHHHHHH CS
                           T3SSipB 124 qKkldaasklsekakake 141
                                       + k++a +   e+a +k+
  gi|336255264|ref|YP_004598371.1| 329 EDKIEASEEHIEEAESKR 346
                                       666777776666666665 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0045
                                       TT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH..HHH CS
                           T3SSipB  40 aasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaaada 116
                                       +++++  e+++  ++ + + d++ea+ e++++a+s+  +a  ++d  q+ ++eL  de    kle+a++  +++ + 
  gi|336255264|ref|YP_004598371.1| 310 EQLRIKSEIEEIKGDISRLEDKIEASEEHIEEAESKRREAFVQIDRKQEEIEEL-EDEMREHKLEKASIKTEIQ-ER 384
                                       56677788999999999*************************************.89999999**999998855.44 PP

                                       HHHHHHHHHHHH CS
                           T3SSipB 117 lqadealqKkld 128
                                        q +++l+ ++d
  gi|336255264|ref|YP_004598371.1| 385 EQEKKQLEAEID 396
                                       444444666555 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.99
                                       HTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHTT---------CHHHHHH CS
                           T3SSipB  36 aqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqk....rlkeLaPdePekakleaaeq 108
                                        +qe+ ++l de+++   e + ++ ++++  ++ +q+++++da++   de ++    r +eL+ ++ ek +l++++ 
  gi|336255264|ref|YP_004598371.1| 355 RKQEEIEELEDEMREHKLEKASIKTEIQEREQEKKQLEAEIDAVDTEFDELKAdlaeRKEELEDAKTEKNDLQREQD 431
                                       5789999999999999999999999999999999***************9999555555678777777887777776 PP

                                       HHH CS
                           T3SSipB 109 Qag 111
                                        + 
  gi|336255264|ref|YP_004598371.1| 432 RLL 434
                                       655 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.086
                                       THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH CS
                           T3SSipB  47 elqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQag 111
                                       e+ ++ s  ++++++le+a ++  ++  ++d+++     +q  ++eL  de + ++ e ae  a+
  gi|336255264|ref|YP_004598371.1| 457 EIPELESRKSDLKRELEKAEKNRANIAGVVDDLKDEKRRIQSDIDEL-DDEIQAKQQEYAELEAN 520
                                       566677888999***********************************.45544455555544444 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.26
                                       T----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB  41 asklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                       ++++ +++ ++ +e + + +dl    e++d+a     +a   v  +   +++L
  gi|336255264|ref|YP_004598371.1| 695 LERVAKQITELQEERESLREDLRGVEERLDDARDRKTDAADEVRSIESEIESL 747
                                       67888999999999999999999999999999999999999999999999998 PP

  == domain 7  score: 6.2 bits;  conditional E-value: 0.026
                                       HHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHH CS
                           T3SSipB  33 mskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQ 109
                                        +++ +++ + + de++t+  e +++ ++ e   e+++++  ++d+ t++++e+q+ ++eL  +e e  k+ + ++Q
  gi|336255264|ref|YP_004598371.1| 743 EIESLEDKRESIEDEIETLETELEELREERESVDERMNDISGEIDEQTAAIEEIQADIDEL-EAELEDSKIPELTEQ 818
                                       567788999999********************************************99999.555555555555555 PP

  == domain 8  score: 2.8 bits;  conditional E-value: 0.29
                                       ----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           T3SSipB  42 sklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkr 89 
                                        +l  e + a ++ +g+ dd+eaa++k  + +  +++ ++ ++e  + 
  gi|336255264|ref|YP_004598371.1| 841 NELELEKEYAEDAIEGLHDDIEAAQNKKAEHENRIEECEATIEEKEAE 888
                                       333333344556666666666666666666666666666666665555 PP

  == domain 9  score: 10.4 bits;  conditional E-value: 0.0013
                                       HHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB  32 amskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                       a  + ++ea ++l +el ++ ++ +++ +dle+a  k dq +  ++a++ k++   +r+++L
  gi|336255264|ref|YP_004598371.1| 887 AELEEKREAVEELEEELAELKEDRNELREDLEDARTKRDQQQDRVNAVQSKLESKRERVQDL 948
                                       5567788999999***********************************************99 PP

  == domain 10  score: 2.4 bits;  conditional E-value: 0.37
                                        TT----STHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                           T3SSipB   40 aasklSdelqtalseakgatddleaa.iekadqaksaadaatkkvdeaqkrlke 92  
                                         +++l d+  t+++ea+g+ d +e+   +k ++   a++a  +  +e+ ++l+e
  gi|336255264|ref|YP_004598371.1| 1004 DLEELEDAKDTLVEEAEGIRDRIEQYeTQKKETFMTAYEAISEHFTEIFEKLSE 1057
                                        567788888899999999999999861455667788899999999999999886 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   6.4     0.005       2.6      23     122 ..     195     300 ..     183     301 .. 0.75
   2 ?   -1.3  21.6       4.8   2.4e+03       2     107 ..     315     423 ..     308     435 .. 0.65
   3 ?    8.3   2.3    0.0053       2.7       6      52 ..     438     484 ..     433     488 .. 0.92
   4 ?    8.1  20.6    0.0061       3.1       9     121 ..     727     836 ..     696     838 .. 0.90
   5 ?    7.6  14.0    0.0088       4.5       2     103 ..     865     958 ..     864     963 .. 0.89
   6 ?    7.8   0.2    0.0075       3.8      21      55 ..    1000    1034 ..     995    1055 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.005
                           DUF5082  23 eekIerLkeaktklsdekeslkqkkkklekplnsse.sWkGkeennydgirs..nlessyqtyv...dkldelidai 93 
                                       e+  e+L+ + +++++++ ++++k+  le+ + +   +++ ++  +++++++  +  s+ ++     d  +e +d++
  gi|336255264|ref|YP_004598371.1| 195 EDAFEELEVVEERIDEAELRIEEKRDRLEQLEDERRtALRYRRLRDEKEEYEgyKKASELEEKReelDAAEEKVDEL 271
                                       66679999999999999999999999999998888876665555555555554433344444440005555667888 PP

                           DUF5082  94 eeEIerLenqiseaqgvldtlqsqlnslk 122
                                        eE e+L+ ++ e qg++ +lq+ l++l+
  gi|336255264|ref|YP_004598371.1| 272 AEELEDLQRELDERQGKVVRLQEDLEDLN 300
                                       89************************997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.8
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIerLk....eaktklsdekeslkqkkkklekplnssesWkGkeennydgirsn 74 
                                       k++i++ + +i+ l+ +i+a ee Ie+ +    ea  +++ ++e++++ + ++++  ++++s k + ++ +++   +
  gi|336255264|ref|YP_004598371.1| 315 KSEIEEIKGDISRLEDKIEASEEHIEEAEskrrEAFVQIDRKQEEIEELEDEMREHKLEKASIKTEIQEREQE-KKQ 390
                                       4455555555555555555555555555555555555666666666666666666666666665554444333.349 PP

                           DUF5082  75 lessyqtyvdkldelidaieeEIerLenqisea 107
                                       le +++++ ++ del++ + e  e+Le  ++e+
  gi|336255264|ref|YP_004598371.1| 391 LEAEIDAVDTEFDELKADLAERKEELEDAKTEK 423
                                       999**************9999888888777665 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0053
                           DUF5082   6 sklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklek 52 
                                       +++ ++i+e++++i++  e I +L++ k+ l+ e e++++++ ++++
  gi|336255264|ref|YP_004598371.1| 438 RRRSNEISEKEGTIEDRREEIPELESRKSDLKRELEKAEKNRANIAG 484
                                       67889************************************999975 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0061
                           DUF5082   9 qaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessyqtyvdk 85 
                                       + ++ ++  e++++e+ Ie L+  +++++de e+l+++ ++l++   s      ++ n+ +g+  +   ++++++ +
  gi|336255264|ref|YP_004598371.1| 727 RDRKTDAADEVRSIESEIESLEDKRESIEDEIETLETELEELREERESV----DERMNDISGEIDEQTAAIEEIQAD 799
                                       556678889999******************9999999999999888887....6788888888888889999***** PP

                           DUF5082  86 ldelidaiee.EIerLenqiseaqgvldtlqsqlnsl 121
                                       +del++++e+ +I +L +qi+e++g +d  + q++++
  gi|336255264|ref|YP_004598371.1| 800 IDELEAELEDsKIPELTEQIEELEGEIDEREAQIDEI 836
                                       ********8549**********************987 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.0088
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnless 78 
                                       ++k+++ +++i+e++++i+  e  +e+ +ea ++l++e ++lk+++++l++ l +  + + ++++ ++   s+les+
  gi|336255264|ref|YP_004598371.1| 865 QNKKAEHENRIEECEATIEEKEAELEEKREAVEELEEELAELKEDRNELREDLEDARTKRDQQQDRVNAVQSKLESK 941
                                       6899********************************************************************99999 PP

                           DUF5082  79 yqtyvdkldelidaieeEIerLenq 103
                                        ++++d        +e+EIe Le++
  gi|336255264|ref|YP_004598371.1| 942 RERVQD--------LEWEIEGLESE 958
                                       888876........55555555555 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0075
                           DUF5082   21 aleekIerLkeaktklsdekeslkqkkkklekpln 55  
                                         + e++e+L+ ak++l++e e + + +++ e++  
  gi|336255264|ref|YP_004598371.1| 1000 EVREDLEELEDAKDTLVEEAEGIRDRIEQYETQKK 1034
                                        66799********************9999998865 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 ?    4.4   6.7     0.078        40      35     129 ..     199     300 ..     187     306 .. 0.62
   2 ?    8.9  12.8    0.0031       1.6      30     129 ..     311     413 ..     302     415 .. 0.91
   3 ?    4.3   7.7     0.081        41      27     131 ..     399     506 ..     396     520 .. 0.87
   4 ?   10.4  10.5    0.0011      0.57      26      87 ..     747     808 ..     692     845 .. 0.52
   5 ?   10.8  10.3    0.0008      0.41      34     130 ..     830     929 ..     809     930 .. 0.82
   6 ?    8.3  10.6    0.0049       2.5      34     129 ..     851     956 ..     846     959 .. 0.75
   7 ?    0.9   0.2      0.93   4.8e+02      38      83 ..     999    1045 ..     972    1058 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.078
                                       HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHH..HHHHHHHHCCC...HHHHHHHCCHHHH CS
                         Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdn..dnvik..ksskeleeeil...rlketidaqesni 104
                                       ++le +e++++e++ + +e ++  ++++d  r + +  +    ++ ++  k ++elee+ +     +e++d+  +++
  gi|336255264|ref|YP_004598371.1| 199 EELEVVEERIDEAELRIEEKRDRLEQLEDERRTALRYRRLRdeKEEYEgyKKASELEEKREeldAAEEKVDELAEEL 275
                                       55566666666666666666666666665555544433221112222200333455544440006689********* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 105 rvLqnvlesneqkiqkLeqdidqke 129
                                       + Lq  l++ + k+ +L++d + ++
  gi|336255264|ref|YP_004598371.1| 276 EDLQRELDERQGKVVRLQEDLEDLN 300
                                       ******************9988765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0031
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC...CHHHHHHHCCHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeei...lrlketidaqesn 103
                                       +  +k ++e+++ ++++++++ + +ee+++e +++ re+  + + +++ i+++++e++e+    + +k +i++ e++
  gi|336255264|ref|YP_004598371.1| 311 QLRIKSEIEEIKGDISRLEDKIEASEEHIEEAESKRREAFVQIDRKQEEIEELEDEMREHKlekASIKTEIQEREQE 387
                                       557899****************************************************865222679********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 104 irvLqnvlesneqkiqkLeqdidqke 129
                                        ++L   +++ + +  +L+ d ++++
  gi|336255264|ref|YP_004598371.1| 388 KKQLEAEIDAVDTEFDELKADLAERK 413
                                       ********************998776 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.081
                                       CCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHCCCHHHHHHHCC CS
                         Fib_alpha  27 lkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksske...leeeilrlketidaq 100
                                       ++   ++k dl++ ++ele+++ ++++ ++   ++ d  r++ ++ ++++ +i++ ++e   le++ ++lk+++ + 
  gi|336255264|ref|YP_004598371.1| 399 DTEFDELKADLAERKEELEDAKTEKNDLQREQDRLLDEARRRSNEISEKEGTIEDRREEipeLESRKSDLKRELEKA 475
                                       66678899999999*******************************9999999999988533379999*********9 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 101 esnirvLqnvlesneqkiqkLeqdidqkerk 131
                                       e+n  ++ +v+++++ +  ++++did++ ++
  gi|336255264|ref|YP_004598371.1| 476 EKNRANIAGVVDDLKDEKRRIQSDIDELDDE 506
                                       9999999999999999999999999887664 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0011
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskele 87 
                                       l+++++++++++e+le elee++++ ++++e +++i+  + e+ +  ++ +  i +++ ele
  gi|336255264|ref|YP_004598371.1| 747 LEDKRESIEDEIETLETELEELREERESVDERMNDISGEIDEQTAAIEEIQADIDELEAELE 808
                                       33444444555555555555555555555555555555555544444444444444444444 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.0008
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH...HHCCHHHHHHH CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlket...idaqesnirvL 107
                                       + +++++  +l+e++ +++ ae+ ++ ++d ++++q++k++++n i++ + ++ee+ ++l+e+   + + e+++ +L
  gi|336255264|ref|YP_004598371.1| 830 EAQIDEIDGTLNELELEKEYAEDAIEGLHDDIEAAQNKKAEHENRIEECEATIEEKEAELEEKreaVEELEEELAEL 906
                                       56899999999999999999999999999999999999999999999999999998888886534377777999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 108 qnvlesneqkiqkLeqdidqker 130
                                       ++  +++++++++ +++ dq+++
  gi|336255264|ref|YP_004598371.1| 907 KEDRNELREDLEDARTKRDQQQD 929
                                       99999999999999888888876 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0049
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH..........HHHHHHHHHHHHHHCCCHHHHHHHCC CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkd..........ndnvikksskeleeeilrlketidaq 100
                                       ++ +e l++++e ++n++ e e+ ++e + +++ek+++ ++          +   +k+ ++el+e+ ++ + + d+q
  gi|336255264|ref|YP_004598371.1| 851 EDAIEGLHDDIEAAQNKKAEHENRIEECEATIEEKEAELEEkreaveeleeELAELKEDRNELREDLEDARTKRDQQ 927
                                       56788889999999999999999999988888888888777233333222112334455567788888888888999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 101 esnirvLqnvlesneqkiqkLeqdidqke 129
                                         ++++ q+ les+++++q+Le +i+ +e
  gi|336255264|ref|YP_004598371.1| 928 QDRVNAVQSKLESKRERVQDLEWEIEGLE 956
                                       9*********************9998766 PP

  == domain 7  score: 0.9 bits;  conditional E-value: 0.93
                                        CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHH CS
                         Fib_alpha   38 ekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikkss 83  
                                        ++++++lee+++ + +  e  + i+d +++ +++kk++  ++++ +s
  gi|336255264|ref|YP_004598371.1|  999 DEVREDLEELEDAKDTLVEEAEGIRDRIEQYETQKKETfMTAYEAIS 1045
                                        45666667777777776677777777766666666654444444444 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4  16.9      0.72   3.7e+02      57     147 ..     190     285 ..     175     289 .. 0.60
   2 ?    6.9  36.0     0.015       7.7      17     173 ..     273     434 ..     270     440 .. 0.70
   3 ?    7.7  20.1    0.0089       4.6      23     147 ..     392     517 ..     389     532 .. 0.69
   4 ?   15.5  16.1   3.6e-05     0.018      30     147 ..     699     810 ..     692     815 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.72
                              Fez1  57 leesleektlelevcenelqrkkseaellrekvekleeelkel.re.elselsleeeeaalesdeakaqrqe....a 127
                                       ++++ e+  +elev+e+++++++ + e +r+++e+le+e +   r  +l++ ++ee+e  ++++e +++r+e    +
  gi|336255264|ref|YP_004598371.1| 190 FDAKKEDAFEELEVVEERIDEAELRIEEKRDRLEQLEDERRTAlRYrRLRD-EKEEYEGYKKASELEEKREEldaaE 265
                                       455556666677777777777777777777777777776554313312333.3344444455555555555555556 PP

                              Fez1 128 eeleelkreverlraeLkee 147
                                       e+++el +e+e l++eL e 
  gi|336255264|ref|YP_004598371.1| 266 EKVDELAEELEDLQRELDER 285
                                       66777777777777777654 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.015
                              Fez1  17 qQLkdsqaevtqklseivalkaqlrelrakleek.eeeikeleesleektlelevcenelqrk.......kseaell 85 
                                       + L d q e+ ++ + +v l+ +l +l+a++e+k e+e  ++++++ee + ++ ++e++++ +       +s+    
  gi|336255264|ref|YP_004598371.1| 273 EELEDLQRELDERQGKVVRLQEDLEDLNAEIERKgEDEQLRIKSEIEEIKGDISRLEDKIEASeehieeaESKRREA 349
                                       56999999999999999999999999999998774667778888888888887777777777744442223333333 PP

                              Fez1  86 rekvekleeelkelreelselsleeeeaalesdeakaq.rqeaeeleelkreverlraeLkeerqkkeeqassFeqE 161
                                         ++++ +ee++el +e++e++le+++ ++e +e +++ +q + e+++ + e ++l+a L+e +++ e+     ++E
  gi|336255264|ref|YP_004598371.1| 350 FVQIDRKQEEIEELEDEMREHKLEKASIKTEIQEREQEkKQLEAEIDAVDTEFDELKADLAERKEELEDA----KTE 422
                                       3345666778888888888877777776666555433314447788899999999999998888876665....667 PP

                              Fez1 162 RrtWqeeKekVi 173
                                       ++  q+e ++ +
  gi|336255264|ref|YP_004598371.1| 423 KNDLQREQDRLL 434
                                       777777777665 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0089
                              Fez1  23 qaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkel 99 
                                        ae+ +   e  +lka+l e +++le+  +e ++l+ + +   +e  +  ne+++k+ + e  re++ +le+  ++l
  gi|336255264|ref|YP_004598371.1| 392 EAEIDAVDTEFDELKADLAERKEELEDAKTEKNDLQREQDRLLDEARRRSNEISEKEGTIEDRREEIPELESRKSDL 468
                                       45555556677778888888888888888888888888888888888888888888888888888888888888888 PP

                              Fez1 100 reelselsleeeeaalesdeakaq.rqeaeeleelkreverlraeLkee 147
                                       ++el+++++++++ a   d+ k + r+ +++++el+ e++  ++e +e 
  gi|336255264|ref|YP_004598371.1| 469 KRELEKAEKNRANIAGVVDDLKDEkRRIQSDIDELDDEIQAKQQEYAEL 517
                                       8888887777777665555555441333566777777777666665443 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 3.6e-05
                              Fez1  30 lseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelsel 106
                                       ++ i +l+ +   lr++l+  ee++++++++ ++ ++e+  +e+e++  +++ e +++++e+le+el+elree +++
  gi|336255264|ref|YP_004598371.1| 699 AKQITELQEERESLREDLRGVEERLDDARDRKTDAADEVRSIESEIESLEDKRESIEDEIETLETELEELREERESV 775
                                       567788999999999*********************************************************99998 PP

                              Fez1 107 sleeeeaalesdeakaqrqeaeeleelkreverlraeLkee 147
                                        ++ ++ + e de      ++ ++ee ++++++l+aeL+  
  gi|336255264|ref|YP_004598371.1| 776 DERMNDISGEIDE------QTAAIEEIQADIDELEAELEDS 810
                                       8777766666655......4467899999999999999765 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3  35.5     0.099        51      27     229 ..     189     389 ..     173     396 .. 0.92
   2 ?    9.6  16.2    0.0011      0.59      86     219 ..     694     819 ..     692     825 .. 0.70
   3 ?   12.4  18.4   0.00016     0.083      12     145 ..     751     888 ..     743     896 .. 0.79
   4 ?   14.9  22.1   2.9e-05     0.015       2     139 ..     819     955 ..     817     966 .. 0.87
   5 ?    2.8   0.4      0.14        71      29      74 ..     995    1040 ..     993    1048 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.099
                        MscS_porin  27 nlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaq 103
                                       ++ +k+++  +++e  +++id+a  +++e + +le+l  ++e  ++ ++++l  e  e +  +  s+l+e +e+l  
  gi|336255264|ref|YP_004598371.1| 189 EFDAKKEDAFEELEVVEERIDEAELRIEEKRDRLEQL--EDERRTALRYRRLRDEKEEYEGYKKASELEEKREELDA 263
                                       55567777888999999********************..88888999999999999999999*************** PP

                        MscS_porin 104 lnsqlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaaleaqieeleqellsnnnrqe 180
                                       +++++ el   +e +q +l e + +   ++ +L+++ a+ e+  ++++   + e + ++  i+ le   + +   +e
  gi|336255264|ref|YP_004598371.1| 264 AEEKVDELAEELEDLQRELDERQGKVVRLQEDLEDLNAEIERKGEDEQLRIKSEIEEIKGDISRLEDKIEASEEHIE 340
                                       ************************************88888999********************************* PP

                        MscS_porin 181 LlklqrdllklriqqleqelqaLqellnekRlaeaekavaqteqlaeea 229
                                        ++++r ++  +i++ ++e++ L+    e +l++a    + +e+++e++
  gi|336255264|ref|YP_004598371.1| 341 EAESKRREAFVQIDRKQEEIEELEDEMREHKLEKASIKTEIQEREQEKK 389
                                       ************************************9999999999886 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
                        MscS_porin  86 rllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaale 162
                                       +l+ +  q  elqe++ +l ++l+  + r++ a+ + t+a  +   i+++++s+        +++r + + e + le
  gi|336255264|ref|YP_004598371.1| 694 QLERVAKQITELQEERESLREDLRGVEERLDDARDRKTDAADEVRSIESEIESL--------EDKRESIEDEIETLE 762
                                       666777777777777777777777777777777777777777777777766666........677777777777777 PP

                        MscS_porin 163 aqieeleqellsnnnrqeLlklqrdllklriqqleqelqaLqellnekRlaeaekav 219
                                       +++eel+ e +s + r + +  + d+ ++ i+++++ ++ L++ l + +  e  +++
  gi|336255264|ref|YP_004598371.1| 763 TELEELREERESVDERMNDISGEIDEQTAAIEEIQADIDELEAELEDSKIPELTEQI 819
                                       777777777777777777777777777777777777777777777666655555555 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00016
                        MscS_porin  12 eaeqkallqdLeqalnlL.dkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrl 87 
                                        ++ ++ +++Le  l+ L ++++  ++++++    id+ ++ ++e+q+++++l+++ e++  ++l +  +eeLe ++
  gi|336255264|ref|YP_004598371.1| 751 RESIEDEIETLETELEELrEERESVDERMNDISGEIDEQTAAIEEIQADIDELEAELEDSKIPEL-TEQIEELEGEI 826
                                       4677788999999997662678889****************************555555555555.4579******* PP

                        MscS_porin  88 lqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrL...nstaaage.a 145
                                       +++++q  e   +l++l+ +   +++++e ++  + +a+ + +e +nr+   ++t +++e +
  gi|336255264|ref|YP_004598371.1| 827 DEREAQIDEIDGTLNELELEKEYAEDAIEGLHDDIEAAQNKKAEHENRIeecEATIEEKEaE 888
                                       ***********************************************995444444444433 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 2.9e-05
                        MscS_porin   2 LdelekakldeaeqkallqdLeqalnlLdkidkskkk.aeelqkaiddaPkelrelqqelealqkkkeeaskeilak 77 
                                       ++ele +     e++a+++++  +ln L+  ++++++ +e l++ i+ a+++ +e ++++e+ +++ ee+ +e  +k
  gi|336255264|ref|YP_004598371.1| 819 IEELEGEI---DEREAQIDEIDGTLNELELEKEYAEDaIEGLHDDIEAAQNKKAEHENRIEECEATIEEKEAELEEK 892
                                       44555544...78999*************999998762688**********************88877777776665 PP

                        MscS_porin  78 l.sleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnst 139
                                           eeLe +l++ +++  el+e+l ++ ++  ++q+r + +q++l + r+r q+++ +++++
  gi|336255264|ref|YP_004598371.1| 893 ReAVEELEEELAELKEDRNELREDLEDARTKRDQQQDRVNAVQSKLESKRERVQDLEWEIEGL 955
                                       5178***************************************************98766555 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.14
                        MscS_porin   29 LdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskei 74  
                                        +d+ d+ ++++eel++a d+  +e + ++ ++e+++ +k+e+  + 
  gi|336255264|ref|YP_004598371.1|  995 IDEYDEVREDLEELEDAKDTLVEEAEGIRDRIEQYETQKKETFMTA 1040
                                        6888999999999999999999999999999999966665555555 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   8.0      0.29   1.5e+02     130     166 ..     250     286 ..     187     294 .. 0.82
   2 ?    7.6  14.7    0.0055       2.8      57     154 ..     353     447 ..     333     457 .. 0.90
   3 ?    0.9   0.6      0.64   3.3e+02      60     128 ..     447     515 ..     444     524 .. 0.71
   4 ?   10.0   3.8     0.001      0.53      67     159 ..     719     811 ..     698     813 .. 0.93
   5 ?   15.0  13.7   3.1e-05     0.016      64     167 ..     819     922 ..     814     938 .. 0.93
   6 ?   -2.7   0.2       8.1   4.2e+03     125     146 ..    1000    1021 ..     971    1044 .. 0.45

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.29
                            DUF745 130 aqqelaektqlleaAkkRveeLkkqlkearkdlektk 166
                                        ++el+ek++ l+aA+++v+eL ++l++ +++l++ +
  gi|336255264|ref|YP_004598371.1| 250 KASELEEKREELDAAEEKVDELAEELEDLQRELDERQ 286
                                       4689**************************9998765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0055
                            DUF745  57 LaGKqqlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqe 133
                                       ++ Kq  +e+le+e+re +    ++k+++q+ e+  k  ++  + + ++++ lka l++ ke+le+a++ ++  q+ 
  gi|336255264|ref|YP_004598371.1| 353 IDRKQEEIEELEDEMREHKLEKASIKTEIQEREQEKKQLEAEIDAVDTEFDELKADLAERKEELEDAKTEKNDLQR- 428
                                       5669999*********************************************************999999988886. PP

                            DUF745 134 laektqlleaAkkRveeLkkq 154
                                         e+  ll++A++R +e++++
  gi|336255264|ref|YP_004598371.1| 429 --EQDRLLDEARRRSNEISEK 447
                                       ..799***********99875 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.64
                            DUF745  60 Kqqlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaa 128
                                       K+  +e   +e+ e e+  ++ k++l+++e+n +  a ++++ + +  ++++ +++  ++++  +q  a
  gi|336255264|ref|YP_004598371.1| 447 KEGTIEDRREEIPELESRKSDLKRELEKAEKNRANIAGVVDDLKDEKRRIQSDIDELDDEIQAKQQEYA 515
                                       555667777788888888888888888888888888888888888888887777777766665555444 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.001
                            DUF745  67 leqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqllea 143
                                       +e+ l +a +   +  ++++s e+ +++ ++ +++++ ++e+l++ l++ +e+ e++++  +  + e++e+t+ +e+
  gi|336255264|ref|YP_004598371.1| 719 VEERLDDARDRKTDAADEVRSIESEIESLEDKRESIEDEIETLETELEELREERESVDERMNDISGEIDEQTAAIEE 795
                                       5677778888888888999999999**************************************************** PP

                            DUF745 144 AkkRveeLkkqlkear 159
                                        ++ ++eL+ +l++ +
  gi|336255264|ref|YP_004598371.1| 796 IQADIDELEAELEDSK 811
                                       **********999876 PP

  == domain 5  score: 15.0 bits;  conditional E-value: 3.1e-05
                            DUF745  64 veqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektql 140
                                       +e+le e+ e ea+++e+   l++ e   + a++a +  +  +ea ++  ++ ++++e+ e++ ++ ++el+ek++ 
  gi|336255264|ref|YP_004598371.1| 819 IEELEGEIDEREAQIDEIDGTLNELELEKEYAEDAIEGLHDDIEAAQNKKAEHENRIEECEATIEEKEAELEEKREA 895
                                       799************************************************************************** PP

                            DUF745 141 leaAkkRveeLkkqlkearkdlektkk 167
                                       +e+ ++ ++eLk++ +e r+dle+ + 
  gi|336255264|ref|YP_004598371.1| 896 VEELEEELAELKEDRNELREDLEDART 922
                                       **********************97664 PP

  == domain 6  score: -2.7 bits;  conditional E-value: 8.1
                            DUF745  125 qvaagaqqelaektqlleaAkk 146 
                                        +v +  ++  ++k +l+e+A+ 
  gi|336255264|ref|YP_004598371.1| 1000 EVREDLEELEDAKDTLVEEAEG 1021
                                        3333333333334444444432 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.2     0.032        16       1      39 [.     267     305 ..     267     306 .. 0.95
   2 ?    3.5   0.0      0.19        98       2      27 ..     318     343 ..     313     350 .. 0.70
   3 ?    4.3   1.5       0.1        52       4      35 ..     390     421 ..     381     439 .. 0.74
   4 ?    4.8   2.3     0.072        37       8      36 ..     485     513 ..     478     516 .. 0.90
   5 ?    5.4   0.1     0.048        25       2      35 ..     695     728 ..     694     734 .. 0.79
   6 ?    6.8   0.4     0.017       8.8       3      45 ..     738     780 ..     736     785 .. 0.87
   7 ?    1.6   0.2      0.73   3.7e+02       2      32 ..     779     809 ..     778     811 .. 0.81
   8 ?    2.2   0.5      0.46   2.4e+02       2      25 ..     812     835 ..     810     875 .. 0.59
   9 ?    5.8   0.3     0.035        18       9      34 ..     896     921 ..     893     953 .. 0.88
  10 ?    0.6   0.1       1.4   7.4e+02      16      39 ..     998    1021 ..     990    1030 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.032
                               LPP   1 kldeLssqVsqLkskvdqlssdvnsakaaaqaakeEAaR 39 
                                       k+deL++++++L+++ d+ + +v  +++++++  +E +R
  gi|336255264|ref|YP_004598371.1| 267 KVDELAEELEDLQRELDERQGKVVRLQEDLEDLNAEIER 305
                                       89*****************************99999777 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.19
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsak 27 
                                       ++e+  ++s+L++k+++ ++ +++a+
  gi|336255264|ref|YP_004598371.1| 318 IEEIKGDISRLEDKIEASEEHIEEAE 343
                                       56777778888888777766666655 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.1
                               LPP   4 eLssqVsqLkskvdqlssdvnsakaaaqaake 35 
                                       +L +++ +  +++d+l++d+++ k+++++ak 
  gi|336255264|ref|YP_004598371.1| 390 QLEAEIDAVDTEFDELKADLAERKEELEDAKT 421
                                       56666666666666666666666666666665 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.072
                               LPP   8 qVsqLkskvdqlssdvnsakaaaqaakeE 36 
                                        V +Lk++   ++sd++++ +++qa ++E
  gi|336255264|ref|YP_004598371.1| 485 VVDDLKDEKRRIQSDIDELDDEIQAKQQE 513
                                       5899*********************9998 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.048
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaake 35 
                                       l+ +++q+ +L+++ ++l +d+  +++ +++a++
  gi|336255264|ref|YP_004598371.1| 695 LERVAKQITELQEERESLREDLRGVEERLDDARD 728
                                       788999***************8777776666654 PP

  == domain 6  score: 6.8 bits;  conditional E-value: 0.017
                               LPP   3 deLssqVsqLkskvdqlssdvnsakaaaqaakeEAaRANqRlD 45 
                                         + s++++L++k ++++++++ +++++++ +eE +   +R++
  gi|336255264|ref|YP_004598371.1| 738 RSIESEIESLEDKRESIEDEIETLETELEELREERESVDERMN 780
                                       57889***************************99887777776 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.73
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqa 32 
                                       ++ +s ++ +  + ++++++d+++++a++++
  gi|336255264|ref|YP_004598371.1| 779 MNDISGEIDEQTAAIEEIQADIDELEAELED 809
                                       7889999999999999999999998888765 PP

  == domain 8  score: 2.2 bits;  conditional E-value: 0.46
                               LPP   2 ldeLssqVsqLkskvdqlssdvns 25 
                                       + eL++q+++L+ ++d+ ++++++
  gi|336255264|ref|YP_004598371.1| 812 IPELTEQIEELEGEIDEREAQIDE 835
                                       556666666666666655555333 PP

  == domain 9  score: 5.8 bits;  conditional E-value: 0.035
                               LPP   9 VsqLkskvdqlssdvnsakaaaqaak 34 
                                       V++L+++ ++l++d n++++++++a+
  gi|336255264|ref|YP_004598371.1| 896 VEELEEELAELKEDRNELREDLEDAR 921
                                       78888999999999999998888875 PP

  == domain 10  score: 0.6 bits;  conditional E-value: 1.4
                               LPP   16 vdqlssdvnsakaaaqaakeEAaR 39  
                                         d++ +d++++++a ++  eEA+ 
  gi|336255264|ref|YP_004598371.1|  998 YDEVREDLEELEDAKDTLVEEAEG 1021
                                        566777777777777777777764 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   9.7    0.0084       4.3     567     721 ..     192     345 ..     178     357 .. 0.72
   2 ?   -2.3   8.4       1.5   7.6e+02     631     712 ..     358     448 ..     347     464 .. 0.66
   3 ?   14.5   3.4   1.3e-05    0.0067     253     377 ..     693     809 ..     690     813 .. 0.78
   4 ?   13.3   9.0   2.9e-05     0.015     225     416 ..     802    1003 ..     799    1008 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0084
                          Prominin 567 klteeiqkelenlkvdlsnlelLteeerkdLeklresglskihsslyleqlckkltkvnletlaekleelanelsng 643
                                          e+  +ele +++ +++ el  ee+r++Le+l++     + ++ +    +++  +++  + a++lee+ +el+ +
  gi|336255264|ref|YP_004598371.1| 192 AKKEDAFEELEVVEERIDEAELRIEEKRDRLEQLEDERRTALRYRRL----RDEKEEYEGYKKASELEEKREELDAA 264
                                       4447788999999**********************977555555555....55556677778899999999999666 PP

                          Prominin 644 kknlkqslkneaqdlrai...qqelvlplessvkklkksvkklde.ensdlqesikkllaaveraenflkkngseii 716
                                        ++   +l +e +dl++     q +v++l++ +++l+ ++++  e e+  ++++i+++   ++r+e+ ++++ ++i 
  gi|336255264|ref|YP_004598371.1| 265 -EEKVDELAEELEDLQREldeRQGKVVRLQEDLEDLNAEIERKGEdEQLRIKSEIEEIKGDISRLEDKIEASEEHIE 340
                                       .3444445555555543201134456778888888888887666668888999999999999999999999888876 PP

                          Prominin 717 nnesk 721
                                       ++esk
  gi|336255264|ref|YP_004598371.1| 341 EAESK 345
                                       66665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                          Prominin 631 ekleelanelsngk...knlkqslkneaqdlraiqqelvlp......lessvkklkksvkkldeensdlqesikkll 698
                                       e++eel +e+ ++k   +++k+++++  q+ +++++e+         l++ +++ k+++++ ++e++dlq++ ++ll
  gi|336255264|ref|YP_004598371.1| 358 EEIEELEDEMREHKlekASIKTEIQEREQEKKQLEAEIDAVdtefdeLKADLAERKEELEDAKTEKNDLQREQDRLL 434
                                       45555555555555555677777777777777777665322222222555555555555555559999999999999 PP

                          Prominin 699 aaveraenflkkng 712
                                       ++++r  n++ ++ 
  gi|336255264|ref|YP_004598371.1| 435 DEARRRSNEISEKE 448
                                       99999999998775 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 1.3e-05
                          Prominin 253 eqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqs.eeCskilssleiekldtskcl..dqlpnvdevlea 326
                                        qLe v k  +eL+++ + Lr+ lrgv ++l++a   +  +  e  +i+s+ e   l+ +++   d+++ ++++le+
  gi|336255264|ref|YP_004598371.1| 693 GQLERVAKQITELQEERESLREDLRGVEERLDDARDRKTDAaDEVRSIESEIES--LEDKRESieDEIETLETELEE 767
                                       69********************************99965533566666655555..777666656777777766666 PP

                          Prominin 327 leevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikk 377
                                       l+e          ++  +r+n+i+  + +qta  +++++ ++++ ++++++
  gi|336255264|ref|YP_004598371.1| 768 LREE--------RESVDERMNDISGEIDEQTAA-IEEIQADIDELEAELED 809
                                       6654........44567899********99975.78999999998888776 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 2.9e-05
                          Prominin  225 dladtlesnvlpaL.aelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCq...s.e 294 
                                        +l+++le++ +p L +++e+l  ++ e ++q+ +++ +++eL  +++  +d+++g  +d++ a +++ +   + e
  gi|336255264|ref|YP_004598371.1|  802 ELEAELEDSKIPELtEQIEELEGEIDEREAQIDEIDGTLNELELEKEYAEDAIEGLHDDIEAAQNKKAEhenRiE 876 
                                        67778877767776257************************************************9666676469 PP

                          Prominin  295 eCskilssleiekldtskcl.....dqlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdl 364 
                                        eC+ + +++e+e l+ +++      ++l +++e  ++l+e le+    +  ++ +r+n++++k++ + ++ v+dl
  gi|336255264|ref|YP_004598371.1|  877 ECEATIEEKEAE-LEEKREAveeleEELAELKEDRNELREDLEDA-RTKRDQQQDRVNAVQSKLESKRER-VQDL 948 
                                        999999999984.44444444555666666666666666665444.445567899*********998665.7999 PP

                          Prominin  365 kkalakgreqikkla.kkip.realdavisdle.nterssktfddvvekyekyrw 416 
                                          +++  ++++ ++  +++p ++++ ++i+ l  ++e     +   +++y++ r+
  gi|336255264|ref|YP_004598371.1|  949 EWEIEGLESEVGDYDpEDVPdHDTVLEMIELLTaDMEAMEPVNMLAIDEYDEVRE 1003
                                        999*999999999864789999999999999985655555555667788888775 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   3.1      0.42   2.2e+02      63     110 ..     177     224 ..     167     234 .. 0.67
   2 ?    0.1  25.1       1.6     8e+02       2     114 ..     200     309 ..     192     313 .. 0.72
   3 ?    4.6  26.2     0.061        31       2     107 ..     317     422 ..     308     425 .. 0.72
   4 ?   -0.2  28.8       1.9   9.8e+02       2     116 ..     359     476 ..     358     482 .. 0.91
   5 ?   -0.7   7.6       2.8   1.4e+03       3      46 ..     472     515 ..     456     524 .. 0.45
   6 ?   14.2  15.2   6.6e-05     0.034       9     116 ..     694     797 ..     691     798 .. 0.82
   7 ?    9.8   3.9    0.0015      0.78      59     116 ..     779     837 ..     777     843 .. 0.90
   8 ?    6.3  28.1     0.018       9.2       3     108 ..     840     945 ..     838     959 .. 0.78
   9 ?    6.1   0.4     0.021        11      55      96 ..     994    1035 ..     991    1063 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.42
                        TPR_MLP1_2  63 reelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselek 110
                                       r e+ +  a +ae+ a+ e+a +ele  ee ++e + ++e++ + le+
  gi|336255264|ref|YP_004598371.1| 177 RREIIDEIAGVAEFDAKKEDAFEELEVVEERIDEAELRIEEKRDRLEQ 224
                                       555656666667777777777777777777777777777766666654 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.6
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       el+ +ee i++++ ++ee +++l++l+++ ++  ++ +      e+e  +  + + el++ reel+ +++++ el +
  gi|336255264|ref|YP_004598371.1| 200 ELEVVEERIDEAELRIEEKRDRLEQLEDERRTALRYRRLRD---EKEEYEGYKKASELEEKREELDAAEEKVDELAE 273
                                       44445555555555555555555555555444333333333...455555566788999****************** PP

                        TPR_MLP1_2  79 eaesakaeleeseesweeqkeelekelselekried 114
                                       e+e+++ el+e + +  + +e le+  +e+e++ ed
  gi|336255264|ref|YP_004598371.1| 274 ELEDLQRELDERQGKVVRLQEDLEDLNAEIERKGED 309
                                       *******************************99887 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.061
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       e+++ + +i++l++++e++e+++++++++ ++   +  + q+  e+   +  e   e +++++e++e ++e ++l+a
  gi|336255264|ref|YP_004598371.1| 317 EIEEIKGDISRLEDKIEASEEHIEEAESKRREAFVQIDRKQEEIEELEDEMREHKLEKASIKTEIQEREQEKKQLEA 393
                                       56677777777777777777777777777777776666666666555555555555666788888888888888888 PP

                        TPR_MLP1_2  79 eaesakaeleeseesweeqkeelekelse 107
                                       e +++ +e++e ++ ++e+keele+ ++e
  gi|336255264|ref|YP_004598371.1| 394 EIDAVDTEFDELKADLAERKEELEDAKTE 422
                                       88888888888888888888888887776 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.9
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelka 78 
                                       e+++le+e+ + k ek++ ++++q+ +++ ++ +++  +    + +     ae  +el+++++e n+l+ e   l +
  gi|336255264|ref|YP_004598371.1| 359 EIEELEDEMREHKLEKASIKTEIQEREQEKKQLEAEIDAVDTEFDELKADLAERKEELEDAKTEKNDLQREQDRLLD 435
                                       899************************************************************************** PP

                        TPR_MLP1_2  79 eaesakaeleeseesweeqkee...lekelselekriedln 116
                                       ea + ++e++e+e  +e ++ee   le+++s+l++ +e  +
  gi|336255264|ref|YP_004598371.1| 436 EARRRSNEISEKEGTIEDRREEipeLESRKSDLKRELEKAE 476
                                       ******************99853336778888887777655 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 2.8
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYe 46 
                                       l+++e++ +++    ++++++ + +q+d+ +  ++ ++ qq Y+
  gi|336255264|ref|YP_004598371.1| 472 LEKAEKNRANIAGVVDDLKDEKRRIQSDIDELDDEIQAKQQEYA 515
                                       33333333333333344444444444444444444444444443 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 6.6e-05
                        TPR_MLP1_2   9 eikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesaka 85 
                                       +++++ ++++e++++ ++l+edl+  +e++ +a +        + ++++e++++ +e+++l+++++++++e e++++
  gi|336255264|ref|YP_004598371.1| 694 QLERVAKQITELQEERESLREDLRGVEERLDDARD-------RKTDAADEVRSIESEIESLEDKRESIEDEIETLET 763
                                       56777777777777777777777777777777777.......99*******************************99 PP

                        TPR_MLP1_2  86 elee...seesweeqkeelekelselekriedln 116
                                       elee   ++es +e+ + +  e++e ++ ie+++
  gi|336255264|ref|YP_004598371.1| 764 ELEElreERESVDERMNDISGEIDEQTAAIEEIQ 797
                                       8875222678889999999999999999999987 PP

  == domain 7  score: 9.8 bits;  conditional E-value: 0.0015
                        TPR_MLP1_2  59 lqalreelnelkaeiaelkaeaesakaeleesee.sweeqkeelekelselekriedln 116
                                       ++++  e++e +a i+e++a+ ++++aele s+  +++eq eele e++e e++i++++
  gi|336255264|ref|YP_004598371.1| 779 MNDISGEIDEQTAAIEEIQADIDELEAELEDSKIpELTEQIEELEGEIDEREAQIDEID 837
                                       56778899999********************996589*******************986 PP

  == domain 8  score: 6.3 bits;  conditional E-value: 0.018
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       l++le e++ +++ +e + ++++++q++  +++++ +e +   e+   + +e  +++++l eel+elk++++el+++
  gi|336255264|ref|YP_004598371.1| 840 LNELELEKEYAEDAIEGLHDDIEAAQNKKAEHENRIEECEATIEEKEAELEEKREAVEELEEELAELKEDRNELRED 916
                                       56788888888888888888888888888888888888888888888888888888888888888888888888888 PP

                        TPR_MLP1_2  80 aesakaeleeseesweeqkeelekelsel 108
                                       +e+a+++ ++++   +  +++le++ + +
  gi|336255264|ref|YP_004598371.1| 917 LEDARTKRDQQQDRVNAVQSKLESKRERV 945
                                       88888888888888888887777665443 PP

  == domain 9  score: 6.1 bits;  conditional E-value: 0.021
                        TPR_MLP1_2   55 dvkelqalreelnelkaeiaelkaeaesakaeleeseeswee 96  
                                        +++e  ++re+l+el++   +l +eae  +  +e+ e + +e
  gi|336255264|ref|YP_004598371.1|  994 AIDEYDEVREDLEELEDAKDTLVEEAEGIRDRIEQYETQKKE 1035
                                        577889999999999999999999999999999998876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2882  (0.160745); expected 358.6 (0.02)
Passed bias filter:                      859  (0.0479112); expected 358.6 (0.02)
Passed Vit filter:                       388  (0.0216409); expected 17.9 (0.001)
Passed Fwd filter:                       270  (0.0150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 6.12u 0.33s 00:00:06.45 Elapsed: 00:00:01.11
# Mc/sec: 3266.00
//
Query:       gi|336255265|ref|YP_004598372.1|  [L=363]
Description: chromosome segregation and condensation protein ScpA [Halopiger xanaduensis SH-6]
Scores for 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-13   51.7   0.0    7.1e-09   35.9   0.0    2.3  2  SMC_ScpA    Segregation and condensation protein ScpA
  ------ inclusion threshold ------
       0.17   11.2   0.0       0.31   10.4   0.0    1.3  1  Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein


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 !   35.9   0.0   7.9e-13   7.1e-09       1      68 [.     103     166 ..     103     173 .. 0.92
   2 !   13.4   0.0   6.2e-06     0.055     210     239 ..     320     349 ..     309     350 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 7.9e-13
                                       HHHHHHHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXXXXXXXX CS
                          SMC_ScpA   1 LiiakeldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqveeeedee 68 
                                       L+ ++e+d++d++v+ vtd+fl+ +       +l  s+ +l  as l+++K+++L+  ++ eeee++ 
  gi|336255265|ref|YP_004598372.1| 103 LAENGEIDPWDIDVVRVTDKFLEALDDA----DLRTSGRALFYASVLLRMKSDELFAPDEPEEEELPP 166
                                       56789*****************998888....************************999999998875 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.2e-06
                                       HHHHHHHHHHHHTT-EEEEESSTTS-EEEE CS
                          SMC_ScpA 210 vgvFlAlLeLiknqavaleQeeflddLqvs 239
                                       v ++lAlL L +   ++leQ e ++dL ++
  gi|336255265|ref|YP_004598372.1| 320 VMTYLALLFLAHRGRIELEQDELFGDLWIQ 349
                                       889************************997 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 ?   10.4   0.0   3.4e-05      0.31      27      51 ..     326     350 ..     323     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHTSEEEEESSTT--EEEEE CS
                        Rad21_Rec8  27 lLvLatkgvIkvkQeaPYgdIlitl 51 
                                       lL La +g I+++Q++ +gd+ i++
  gi|336255265|ref|YP_004598372.1| 326 LLFLAHRGRIELEQDELFGDLWIQR 350
                                       799******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); 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:                         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 0.21s 00:00:00.67 Elapsed: 00:00:00.34
# Mc/sec: 3178.65
//
Query:       gi|336255266|ref|YP_004598373.1|  [L=182]
Description: hypothetical protein Halxa_3889 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.029   14.0   1.7      0.046   13.4   1.7    1.2  1  DUF4131         Domain of unknown function (DUF4131)
       0.13   13.0   0.0       0.27   12.0   0.0    1.6  2  zinc_ribbon_15  zinc-ribbon family
       0.42   10.7   1.2       0.75    9.9   1.2    1.3  1  UPF0370         Uncharacterised protein family (UPF0370)


Domain annotation for each model (and alignments):
>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.7   7.7e-06     0.046      13      78 ..      25      86 ..      20      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.7e-06
                           DUF4131 13 llllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqllesgqeviveGvvasl 78
                                      ll++ +l+ l++   p+    + +++ll++++l ++++a+++++++ +++ + ++ev  +G+++s+
  gi|336255266|ref|YP_004598373.1| 25 LLWCWILASLFF--VPTLLGYWWVGALLFVVGLLVCWQAAEASSDPVYTIGT-KREVR-TGRIESE 86
                                      223333332222..788888889**********************9999988.78887.8888875 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   9.1e+03      22      29 ..      33      40 ..      31      74 .. 0.73
   2 ?   12.0   0.0   4.6e-05      0.27       2      60 ..      89     147 ..      88     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                    zinc_ribbon_15 22 klffipvf 29
                                      +lff+p++
  gi|336255266|ref|YP_004598373.1| 33 SLFFVPTL 40
                                      67888853 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.6e-05
                    zinc_ribbon_15   2 lCpkCgklskaelvkkkkvlklffipvfkwkkkkpylacskCkslleaskelgkeiekk 60 
                                        C++Cg++     +++++  +++f  ++ + ++   ++c++C     +++e+g+e+e +
  gi|336255266|ref|YP_004598373.1|  89 DCNECGRSAPGGEYRRYERRRVLFGSTIAVLESGENIYCEDCAVAPRDRREYGRELEGG 147
                                       6*********99999999999999999999999***********999999999988766 PP

>> UPF0370  Uncharacterised protein family (UPF0370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.2   0.00013      0.75       4      20 ..      40      57 ..      38      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00013
                           UPF0370  4 LadYWWv.illllvGill 20
                                      L  YWWv  ll++vG+l+
  gi|336255266|ref|YP_004598373.1| 40 LLGYWWVgALLFVVGLLV 57
                                      567****99******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.33
# Mc/sec: 1631.22
//
Query:       gi|336255267|ref|YP_004598374.1|  [L=439]
Description: methyl-accepting chemotaxis sensory transducer with Pas/Pac sensor [Halopiger xanaduensis SH-6]
Scores for 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-38  130.3  56.2    2.1e-35  122.1  26.7    3.3  3  MCPsignal     Methyl-accepting chemotaxis protein (MCP) signa
    2.6e-13   49.9   0.0    1.1e-12   48.0   0.0    2.1  1  PAS           PAS fold
      3e-12   46.8   0.5      3e-12   46.8   0.5    2.2  2  PAS_4         PAS fold
    1.2e-10   41.6   0.1    5.9e-10   39.3   0.0    2.3  2  PAS_9         PAS domain
      4e-05   23.5   0.0    0.00026   20.9   0.0    2.5  1  PAS_8         PAS domain
     0.0021   18.3  40.6       0.28   11.4   5.4    5.5  2  DUF948        Bacterial protein of unknown function (DUF948)
     0.0031   17.5  36.6      0.097   12.7   6.6    4.3  4  Laminin_II    Laminin Domain II
  ------ inclusion threshold ------
      0.011   15.8  35.4        1.6    8.8   4.9    4.5  5  DUF1664       Protein of unknown function (DUF1664)
      0.028   14.9   1.9      0.028   14.9   1.9    5.5  5  NPV_P10       Nucleopolyhedrovirus P10 protein
      0.034   14.3  22.2      0.047   13.9   2.0    3.7  3  SesA          N-terminal domain on NACHT_NTPase and P-loop NT
      0.047   13.0  16.6       0.27   10.6   6.9    2.2  2  GAS           Growth-arrest specific micro-tubule binding
      0.055   13.8  27.4        2.2    8.7   1.7    5.0  5  BLOC1_2       Biogenesis of lysosome-related organelles compl
      0.072   13.4  12.7       0.62   10.4   0.7    4.6  6  KxDL          Uncharacterized conserved protein
        0.1   10.6  20.1       0.29    9.0  12.6    2.0  2  Prominin      Prominin
       0.12   11.6  17.6      0.081   12.2   0.7    3.2  4  TMPIT         TMPIT-like protein
       0.56   10.4  24.0       0.39   10.9   5.7    4.0  4  Fib_alpha     Fibrinogen alpha/beta chain family
       0.66    9.8  18.4          1    9.2   5.3    3.9  3  CdvA          CdvA-like coiled-coil domain
       0.98    9.2   7.6       0.58   10.0   0.3    3.7  3  PHP_C         PHP-associated
       0.99    9.9  33.8        2.5    8.6   1.6    3.2  3  T3SSipB       Type III cell invasion protein SipB
        1.1    9.1   8.4       0.71    9.7   0.2    3.1  4  Vip3A_N       Vegetative insecticide protein 3A N terminal
        1.3    8.6  25.2        2.3    7.8  10.3    2.1  2  DUF4559       Domain of unknown function (DUF4559)
        1.4    9.6  35.2       0.19   12.4   6.7    4.7  4  DUF883        Bacterial protein of unknown function (DUF883)
        1.8    7.2  21.2       0.41    9.3  10.3    2.9  2  Dor1          Dor1-like family
        3.3    6.5  35.5          1    8.2  11.7    3.1  3  Spc7          Spc7 kinetochore protein
        3.4    6.1  18.1        1.9    6.9   7.4    2.2  2  FUSC          Fusaric acid resistance protein family
        4.7    7.9  12.4         15    6.2   1.4    3.8  3  ING           Inhibitor of growth proteins N-terminal histone
        5.2    7.1  13.0        1.4    8.9   0.4    3.8  4  ApoO          Apolipoprotein O
        5.2    6.7  34.6        2.7    7.6  11.8    3.5  3  YkyA          Putative cell-wall binding lipoprotein
        5.5    6.6  37.0        2.6    7.7  14.4    3.8  4  Laminin_I     Laminin Domain I
        6.3    5.8  30.0        4.6    6.3   4.3    3.5  3  APG17         Autophagy protein Apg17
        6.6    7.1  27.0       0.47   10.8   5.8    5.1  5  Rx_N          Rx N-terminal domain
        6.6    7.3  25.4        1.2    9.6   2.1    4.5  5  Spectrin      Spectrin repeat
        8.3    7.0  30.0        1.3    9.6   3.4    4.3  4  Syntaxin-6_N  Syntaxin 6, N-terminal
        9.2    5.2  32.6         10    5.1  10.7    2.7  2  AIP3          Actin interacting protein 3
        9.4    5.9  37.9        1.5    8.6   7.1    4.0  4  DUF745        Protein of unknown function (DUF745)


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9  12.1    0.0011      0.59      73     161 ..     128     220 ..     120     227 .. 0.67
   2 !  122.1  26.7   4.1e-38   2.1e-35       5     169 ..     225     396 ..     221     399 .. 0.90
   3 !   11.6   2.8   0.00036      0.18     132     169 ..     394     431 ..     391     434 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHH....HCCHHHHHHHHHHHHHHHHH CS
                         MCPsignal  73 VAdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselvee....tgealkeiveavaevadlvq 145
                                        A EV +  +   ++ ++i++l +++  e++ +v+ l+ +++ v+e s+++++      e+l ++ ++v+  +++v+
  gi|336255267|ref|YP_004598374.1| 128 GAVEVLTRVTTLVEQQEQIRHLQEQMSDEVEGAVDELQASTTDVAENSQEISDlaadQSESLGDVQDEVSTFSATVE 204
                                       56666666666677788899999999999999999999999999888776654111145566666666666666666 PP

                                       HHHHHHHHHHHHHHHH CS
                         MCPsignal 146 eiaaaseeqsasieev 161
                                       eia+++ee s+ +e+ 
  gi|336255267|ref|YP_004598374.1| 205 EIASSAEEVSSQSEQA 220
                                       6666666666666654 PP

  == domain 2  score: 122.1 bits;  conditional E-value: 4.1e-38
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHH CS
                         MCPsignal   5 eeaseeAeeggkevanvvkqmeeieks.......skeisdiieVideiadQTNlLALNAaiEAARAGeqGrGFaVVA 74 
                                       ee+ e+A++  + +++v ++ ++++          +ei di+eVi++iadQTNlLALNA iEAA    + +GFaVVA
  gi|336255267|ref|YP_004598374.1| 225 EESVETAQDTLEAMDDVAAEADDVAADatklaerIDEIDDIVEVINDIADQTNLLALNANIEAAHSDASSDGFAVVA 301
                                       56666666666666666666666655555555559****************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  75 dEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaas 151
                                       +E+++LAe+s+++a eie++++e+ + + ++v+s+e t++++ + ++ +e+  e+ +ei +a+++ ++ + eia+a+
  gi|336255267|ref|YP_004598374.1| 302 NEIKSLAEQSKERADEIERIVTEVRETTLETVDSVEATNEEIGSVVTDIETVVENQREILDAIEDTDQGIAEIATAT 378
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHH CS
                         MCPsignal 152 eeqsasieevnqaveeva 169
                                       ++q+as+ee+++ v+ va
  gi|336255267|ref|YP_004598374.1| 379 DQQAASAEEIATMVDSVA 396
                                       ************999887 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 132 eiveavaevadlvqeiaaaseeqsasieevnqaveeva 169
                                       +++e+ +evad+vq++aaa+e+q+a +e++  ++e ++
  gi|336255267|ref|YP_004598374.1| 394 SVAERGDEVADSVQDVAAATEQQTAMVENIEASIESLE 431
                                       6788999**************************99876 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   2.1e-15   1.1e-12       5     107 ..      29     130 ..      26     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 2.1e-15
                                       HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC CS
                               PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl 81 
                                       +++e+ p+p f+vDe g i+ +Na ae l+G++ e+v+g++ +d++ +e +  +  l e++l++g+  r +ei+   
  gi|336255267|ref|YP_004598374.1|  29 SLVETFPEPAFIVDEGGYITDWNAGAEGLTGYPSEQVVGQHAYDVFGTEGQ--DETLAEEVLRTGRVIREEEIRSAE 103
                                       689*******************************************88866..888888888888888888886555 PP

                                       .TTSSEEEEEEEEEEEEETTEEEEEEE CS
                               PAS  82 .rdgrpihlevraspvrdaggeilgfl 107
                                         dg+  h++   +p++ ++g + g++
  gi|336255267|ref|YP_004598374.1| 104 tADGELAHARALGVPITTPDGDVVGAV 130
                                       79*******************998876 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.5   5.8e-15     3e-12       2     108 ..      32     139 ..      31     141 .. 0.93
   2 ?   -2.1   0.1       8.9   4.6e+03      50      76 ..     373     399 ..     365     412 .. 0.72

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 5.8e-15
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll...p 75 
                                       +  p++ +++d+ g ++++Na a+ l g+p e+++G++ ++++ +e   + e+  ++vl+++++i+++e++     +
  gi|336255267|ref|YP_004598374.1|  32 ETFPEPAFIVDEGGYITDWNAGAEGLTGYPSEQVVGQHAYDVFGTEG--QDETLAEEVLRTGRVIREEEIRSAetaD 106
                                       6789****************************************854..4468889********************* PP

                             PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTer 108
                                       ge  h     +P+  ++G+v+g++++++ +T +
  gi|336255267|ref|YP_004598374.1| 107 GELAHARALGVPITTPDGDVVGAVEVLTRVTTL 139
                                       ****************************99976 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8.9
                             PAS_4  50 arleralrrvlegeepiefleelllpg 76 
                                       +   + ++++++ ee +++++ +   g
  gi|336255267|ref|YP_004598374.1| 373 EIATATDQQAASAEEIATMVDSVAERG 399
                                       555667788888888888877766644 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   1.1e-12   5.9e-10       1     102 [.      35     136 ..      35     138 .. 0.92
   2 ?   -2.1   0.1         9   4.6e+03      41      59 ..     309     327 ..     294     360 .. 0.60

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.1e-12
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       p++ +i+++ g i+++N +a+ l+Gy +e+v+g++  d+f t+ +++   +++l++gr + +e+     + +ge  +
  gi|336255267|ref|YP_004598374.1|  35 PEPAFIVDEGGYITDWNAGAEGLTGYPSEQVVGQHAYDVFGTEGQDETLAEEVLRTGRVIREEEIRSAETADGELAH 111
                                       56778988999*****************************9999999999********8888888999********* PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDi 102
                                       +++  +p+   dg +vg++ +l+ +
  gi|336255267|ref|YP_004598374.1| 112 ARALGVPITTPDGDVVGAVEVLTRV 136
                                       ********999******99998755 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9
                             PAS_9  41 vtdpeanerlraaleqgrk 59 
                                       ++++e+++++++++ + r+
  gi|336255267|ref|YP_004598374.1| 309 EQSKERADEIERIVTEVRE 327
                                       4555666666666666663 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   5.1e-07   0.00026       3      51 ..      27      75 ..      26     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.1e-07
                             PAS_8  3 lralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpv 51
                                      + +l+e+ p++ ++vd+g+ i+d+N  a+ l+Gy+ +++ g+   +++ +
  gi|336255267|ref|YP_004598374.1| 27 FTSLVETFPEPAFIVDEGGYITDWNAGAEGLTGYPsEQVVGQHA-YDVFG 75
                                      6799************5555***************555555433.44444 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 !   11.4   5.4   0.00056      0.28      20      87 ..     138     206 ..     126     215 .. 0.51
   2 !    8.0   6.5    0.0068       3.5      24      87 ..     192     255 ..     186     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00056
                            DUF948  20 vllklkktldeaaati.eelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       +l++ ++ ++++++++ +e+e  vd++   ++d+ ++++e+ +   +++e++  + ++v + +++v+e+
  gi|336255267|ref|YP_004598374.1| 138 TLVEQQEQIRHLQEQMsDEVEGAVDELQASTTDVAENSQEISDLAADQSESLGDVQDEVSTFSATVEEI 206
                                       444444444444443313455555555555555555555555555555555555555555555555554 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0068
                            DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                       +++ ++ ++at+ee+ + +++++ ++e++ + ++e +e  ++ le++d + +++ d+++   +l
  gi|336255267|ref|YP_004598374.1| 192 VQDEVSTFSATVEEIASSAEEVSSQSEQARTLSEESVETAQDTLEAMDDVAAEADDVAADATKL 255
                                       5667788899999999999999999999999999999999999999999999999998877766 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   6.6   0.00019     0.097       9      90 ..     143     225 ..     136     229 .. 0.86
   2 ?    6.8   2.6     0.012       6.2       5      55 ..     224     274 ..     220     289 .. 0.72
   3 !    7.9   2.4    0.0056       2.9       1      54 [.     311     364 ..     300     373 .. 0.79
   4 !    8.1   5.4     0.005       2.6       5      80 ..     357     432 ..     353     439 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                                       XXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II   9 netakevleql.aplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                       +e++ + +eq+  +++  +++++++   ++++ +e+ +++ d ++ + d++++v++   +++++ +  +e+  ++e+
  gi|336255267|ref|YP_004598374.1| 143 QEQIRHLQEQMsDEVEGAVDELQASTTDVAENSQEISDLAADQSESLGDVQDEVSTFSATVEEIASSAEEVSSQSEQ 219
                                       555666666552579999999*****************************************************999 PP

                                       ...HHH CS
                        Laminin_II  85 ssslsd 90 
                                         +ls+
  gi|336255267|ref|YP_004598374.1| 220 ARTLSE 225
                                       887887 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankair 55 
                                        +e  eta+ +le + +++++ + + +++ ++++ ++e+++ v+  n + +
  gi|336255267|ref|YP_004598374.1| 224 SEESVETAQDTLEAMDDVAAEADDVAADATKLAERIDEIDDIVEVINDIAD 274
                                       566778888888888888888888888888888888888877775555444 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0056
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II   1 skelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankai 54 
                                       ske a+e++ +++ev e + +    +e t+e++ ++ +++e + e+ ++   ai
  gi|336255267|ref|YP_004598374.1| 311 SKERADEIERIVTEVRETTLETVDSVEATNEEIGSVVTDIETVVENQREILDAI 364
                                       789999999999999999999999999999999999999655555444444444 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.005
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                        +e+++ ++ + + +a++++ +++  ++++ei++ v+ + e  ++    ++d+  +  + +  ++++++ +++l+ 
  gi|336255267|ref|YP_004598374.1| 357 QREILDAIEDTDQGIAEIATATDQQAASAEEIATMVDSVAERGDEVADSVQDVAAATEQQTAMVENIEASIESLER 432
                                       5788888999999999999999999999999999999999888888888888888888888888888888888875 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.9    0.0077         4      65     114 ..     133     182 ..     129     195 .. 0.86
   2 ?    6.4   4.0     0.017       8.8      40     109 ..     200     272 ..     193     279 .. 0.68
   3 ?    5.2   1.0     0.041        21      55      86 ..     246     277 ..     223     294 .. 0.63
   4 ?    8.8   4.9     0.003       1.6      41     121 ..     295     375 ..     292     381 .. 0.91
   5 ?    8.5   1.7    0.0039         2      49      98 ..     387     436 ..     378     439 .] 0.54

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0077
                           DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                         r+ ++ +++++  ++++++++ev+ + ++l++  +dv + ++ +++l+
  gi|336255267|ref|YP_004598374.1| 133 LTRVTTLVEQQEQIRHLQEQMSDEVEGAVDELQASTTDVAENSQEISDLA 182
                                       5799999******************9999999999999998888888876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.017
                           DUF1664  40 sdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiske...ikeevtevredlseigedvesvkea 109
                                       s  ve+++++ e+vs++ ++++   ++ +++ +++l+++ ++++e   ++++ t++ e ++ei++ ve ++++
  gi|336255267|ref|YP_004598374.1| 200 SATVEEIASSAEEVSSQSEQARTLSEESVETAQDTLEAMDDVAAEaddVAADATKLAERIDEIDDIVEVINDI 272
                                       6677888888888888887777777777888888888877776651114456666666666666666666655 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.041
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeik 86 
                                       +++aa   +L++rid++d+ ++  ++i+ +++
  gi|336255267|ref|YP_004598374.1| 246 DDVAADATKLAERIDEIDDIVEVINDIADQTN 277
                                       55666677788888888888887777777664 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.003
                           DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                       d  + v+++++++ e+ ++  +++++ + +v ++  e+ +  ++++ee+ +v  d++++ e+ +++ +a+e+ ++ +
  gi|336255267|ref|YP_004598374.1| 295 DGFAVVANEIKSLAEQSKERADEIERIVTEVRETTLETVDSVEATNEEIGSVVTDIETVVENQREILDAIEDTDQGI 371
                                       6778899999999999999999999999999999999999*******************************999999 PP

                           DUF1664 118 erie 121
                                       ++i 
  gi|336255267|ref|YP_004598374.1| 372 AEIA 375
                                       9986 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0039
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlse 98 
                                       ++ ++ +s+a+  ++ ++ ++ v +  ++q+++ ++i++ ++++++d+++
  gi|336255267|ref|YP_004598374.1| 387 EIATMVDSVAERGDEVADSVQDVAAATEQQTAMVENIEASIESLERDIED 436
                                       44444555555555555555555555555555555555555555555544 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1         3   1.5e+03      21      34 ..     137     153 ..     129     158 .. 0.43
   2 ?   14.9   1.9   5.5e-05     0.028      15      62 ..     156     200 ..     152     210 .. 0.74
   3 ?    6.0   3.3     0.032        17      25      66 ..     226     267 ..     211     278 .. 0.78
   4 ?    2.5   6.1      0.41   2.1e+02      22      66 ..     317     362 ..     298     398 .. 0.61
   5 ?    4.3   4.5      0.11        54      15      58 ..     387     427 ..     358     439 .] 0.52

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3
                           NPV_P10  21 dal...qqqvddvqenl 34 
                                       + l   q+q+ ++qe++
  gi|336255267|ref|YP_004598374.1| 137 TTLveqQEQIRHLQEQM 153
                                       33222233444444443 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 5.5e-05
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                       +v+  Vd lq++ +dv+en++++++l     +qs++L +++++v++ +
  gi|336255267|ref|YP_004598374.1| 156 EVEGAVDELQASTTDVAENSQEISDLA---ADQSESLGDVQDEVSTFS 200
                                       68889*****************77664...567777777777555433 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.032
                           NPV_P10  25 qqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                       ++v+  q+ l+ ++++ ++ d+ +a  ++l + +++I+di  
  gi|336255267|ref|YP_004598374.1| 226 ESVETAQDTLEAMDDVAAEADDVAADATKLAERIDEIDDIVE 267
                                       578888999999999999999999999999999999999876 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.41
                           NPV_P10  22 alqqqvddvqe.nlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                        ++  v++v+e  l++v+ +++  +++   ++++et ven  +iL 
  gi|336255267|ref|YP_004598374.1| 317 EIERIVTEVREtTLETVDSVEATNEEIGSVVTDIETVVENQREILD 362
                                       5555555655413555666666666666666666666666666654 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.11
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkv 58 
                                       ++ + Vd++ ++ d+v++ ++dv    +  ++q+a ++++e+++
  gi|336255267|ref|YP_004598374.1| 387 EIATMVDSVAERGDEVADSVQDVA---AATEQQTAMVENIEASI 427
                                       344445555555555555555533...44455555555555544 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.5     0.019       9.8      16      82 ..     176     244 ..     157     251 .. 0.79
   2 ?   13.9   2.0   9.1e-05     0.047       9      86 ..     250     328 ..     247     335 .. 0.88
   3 ?    4.6   2.9     0.071        36      43     115 ..     355     427 ..     329     436 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.019
                              SesA  16 daikd.ikglpeaFrevgkrLplvqetLedaksqlesskldedtesa.ikpvlesckekatkleeifek 82 
                                       ++i+d + +  e++ +v++++ ++++t e++ s++e+ ++++++  +  ++++e  ++ +++++++  +
  gi|336255267|ref|YP_004598374.1| 176 QEISDlAADQSESLGDVQDEVSTFSATVEEIASSAEEVSSQSEQARTlSEESVETAQDTLEAMDDVAAE 244
                                       444456778899************************999888877666788888888888888877665 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 9.1e-05
                              SesA   9 eaaiklydaikdikglpeaFrevgkr..LplvqetLedaksqlesskldedtesaikpvlesckekatkleeifekv 83 
                                         a+kl ++i++i ++ e +++++++  L  + +  e+a+s ++s+ +   +++ ik+++e+ ke+a+++e+i ++v
  gi|336255267|ref|YP_004598374.1| 250 ADATKLAERIDEIDDIVEVINDIADQtnLLALNANIEAAHSDASSDGFAVVANE-IKSLAEQSKERADEIERIVTEV 325
                                       57899******************976227778899**************99888.********************** PP

                              SesA  84 apa 86 
                                       +++
  gi|336255267|ref|YP_004598374.1| 326 RET 328
                                       765 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.071
                              SesA  43 edaksqlesskldedtesaikpvlesckekatkleeifekv...apapad..srleryrkavrslgkgskVEtLmkg 114
                                       e    q e  ++ edt++ i +++++ +++a++ eei + v   a+  ++   +++ + +a  + ++   VE++  +
  gi|336255267|ref|YP_004598374.1| 355 EN---QREILDAIEDTDQGIAEIATATDQQAASAEEIATMVdsvAERGDEvaDSVQDVAAA--TEQQTAMVENIEAS 426
                                       33...33333333333334555555555555555555555532133333332333444444..34566667766655 PP

                              SesA 115 i 115
                                       i
  gi|336255267|ref|YP_004598374.1| 427 I 427
                                       5 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 ?   10.6   6.9   0.00052      0.27      61     168 ..     137     245 ..     131     274 .. 0.80
   2 ?    7.8   2.1    0.0037       1.9      30     159 ..     303     431 ..     296     438 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00052
                               GAS  61 epLkkaeeeveeLrkqlkn.yekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqev 136
                                        +L +++e++ +L++q+ +  e    +l+++ + + e  +e++dl  ++      ++   + + +  ++  ++ +ev
  gi|336255267|ref|YP_004598374.1| 137 TTLVEQQEQIRHLQEQMSDeVEGAVDELQASTTDVAENSQEISDLAADQSESLGDVQDEVSTFSATVEEIASSAEEV 213
                                       57899***********98625778899******************9999988888888888888888888899**** PP

                               GAS 137 qqktglknllLekklkalqeelEkkeaqleev 168
                                       + +++   +l e  +++ q++lE+ +   +e+
  gi|336255267|ref|YP_004598374.1| 214 SSQSEQARTLSEESVETAQDTLEAMDDVAAEA 245
                                       ***********************998544443 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0037
                               GAS  30 slKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                       + K+  e+ k+++++ e+ + e+ +   + ++ +++ +ee+     ++++  + + ++  + +   +   e+ + + 
  gi|336255267|ref|YP_004598374.1| 303 EIKSLAEQSKERADEIERIVTEVRETTLETVDSVEATNEEIGSVVTDIETVVENQREILDAIEDTDQGIAEIATATD 379
                                       56777788899999999999999999999999999999999999999999877777777777777777788888888 PP

                               GAS 107 ehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelE 159
                                       ++    ++++++ ++  e  ++  +++q+v   t+ +  ++e+ ++a  e+lE
  gi|336255267|ref|YP_004598374.1| 380 QQAASAEEIATMVDSVAERGDEVADSVQDVAAATEQQTAMVEN-IEASIESLE 431
                                       8888889999999999999999999999999999999988875.555555555 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 ?    6.7   2.9     0.017       8.8      22      90 ..     146     212 ..     132     219 .. 0.73
   2 ?    7.9   1.8    0.0073       3.7      33      77 ..     235     279 ..     211     287 .. 0.59
   3 ?    2.7   0.2      0.31   1.6e+02      44      76 ..     295     327 ..     280     338 .. 0.77
   4 ?    8.7   1.7    0.0042       2.2       7      84 ..     318     395 ..     312     403 .. 0.88
   5 ?    6.0   1.6     0.028        14      30      80 ..     382     433 ..     366     439 .] 0.69

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.017
                           BLOC1_2  22 yklL.eklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyske 90 
                                       +++L e++  +++  +++l+ ++ ++++++++++      + + +++ +++++v+++ ++v+e+ +   e
  gi|336255267|ref|YP_004598374.1| 146 IRHLqEQMSDEVEGAVDELQASTTDVAENSQEISD---LAADQSESLGDVQDEVSTFSATVEEIASSAEE 212
                                       44442678888999999999999999998888888...44566677778888888888888887765554 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0073
                           BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteL 77 
                                        e  ++++ +a+++++++ kl e+ +e++  ++ i++i +q++ L
  gi|336255267|ref|YP_004598374.1| 235 LEAMDDVAAEADDVAADATKLAERIDEIDDIVEVINDIADQTNLL 279
                                       233344444555566666666666666777777777776666655 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.31
                           BLOC1_2  44 aslekkleklnekyeelqpylqqidqiekqvte 76 
                                       +++++ +++++++ e+ ++  ++i++i ++v+e
  gi|336255267|ref|YP_004598374.1| 295 DGFAVVANEIKSLAEQSKERADEIERIVTEVRE 327
                                       566677788888888899999999999888864 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0042
                           BLOC1_2   7 vskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavse 83 
                                       +++++++  e t e ++ +e+ Ne+  + ++++++v+++ ++ l++++ +++ +++  +  dq  ++ +e+ ++v+ 
  gi|336255267|ref|YP_004598374.1| 318 IERIVTEVRETTLETVDSVEATNEEIGSVVTDIETVVENQREILDAIEDTDQGIAEIATATDQQAASAEEIATMVDS 394
                                       6777888889999******************************************9999999988888888888876 PP

                           BLOC1_2  84 L 84 
                                       +
  gi|336255267|ref|YP_004598374.1| 395 V 395
                                       5 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.028
                           BLOC1_2  30 eaasekykklkdvaaslekkl.eklnekyeelqpylqqidqiekqvteLeea 80 
                                        a++e+++ + d++a+  +++ + ++   ++ +++   +++ie+++++Le  
  gi|336255267|ref|YP_004598374.1| 382 AASAEEIATMVDSVAERGDEVaDSVQDVAAATEQQTAMVENIEASIESLERD 433
                                       5666777777776666665551445555668888899999999999999865 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7    0.0012      0.62      12      79 ..     144     211 ..     135     216 .. 0.88
   2 ?    4.8   0.2     0.065        33       7      59 ..     174     226 ..     172     254 .. 0.69
   3 ?   -1.1   0.0       4.5   2.3e+03      33      74 ..     221     262 ..     211     274 .. 0.56
   4 ?   -0.4   0.0       2.8   1.4e+03      30      71 ..     302     343 ..     292     348 .. 0.74
   5 ?    6.0   0.1     0.029        15       9      46 ..     348     385 ..     345     397 .. 0.89
   6 ?    1.1   0.1      0.92   4.7e+02       9      33 ..     407     431 ..     400     437 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
                              KxDL  12 deilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakla 79 
                                       ++i +lQ+q+s++ +    eL++  + + e  +++++  +++ + l +v+++  +   +++ + + ++
  gi|336255267|ref|YP_004598374.1| 144 EQIRHLQEQMSDEVEGAVDELQASTTDVAENSQEISDLAADQSESLGDVQDEVSTFSATVEEIASSAE 211
                                       68899999999999999999999999999999999999999999999999999999999999888776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.065
                              KxDL   7 dsedldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllke 59 
                                       +s++++   a Q++ +g  +++  + ++  ++  +  ++++++ +q  +l+ e
  gi|336255267|ref|YP_004598374.1| 174 NSQEISDLAADQSESLGDVQDEVSTFSATVEEIASSAEEVSSQSEQARTLSEE 226
                                       67788888888888888887777777777777777777777776665555443 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.5
                              KxDL  33 lelnalsqerlaklrarfkqgtkllkevkkdLesifkkirsl 74 
                                        +l ++s e  +++ + + + +  + +v +d  ++ ++i+ +
  gi|336255267|ref|YP_004598374.1| 221 RTLSEESVETAQDTLEAMDDVAAEADDVAADATKLAERIDEI 262
                                       344444444455555555555555555555555555555555 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.8
                              KxDL  30 reLlelnalsqerlaklrarfkqgtkllkevkkdLesifkki 71 
                                       +e++ l ++s+er  +++  + +  ++  e+ +  e +++ i
  gi|336255267|ref|YP_004598374.1| 302 NEIKSLAEQSKERADEIERIVTEVRETTLETVDSVEATNEEI 343
                                       567788888888888888888777777777777777666666 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.029
                              KxDL   9 edldeilalQaqtsgrlnkknreLlelnalsqerlakl 46 
                                       +d+++++  Q+++++ ++++ + + e+ + ++++ a++
  gi|336255267|ref|YP_004598374.1| 348 TDIETVVENQREILDAIEDTDQGIAEIATATDQQAASA 385
                                       5999******************9999999888887766 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.92
                              KxDL   9 edldeilalQaqtsgrlnkknreLl 33 
                                       +d+ ++  +Q+ ++  ++++ + L+
  gi|336255267|ref|YP_004598374.1| 407 QDVAAATEQQTAMVENIEASIESLE 431
                                       6777888888888888888777775 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.0    0.0053       2.7     352     411 ..     148     206 ..     130     215 .. 0.72
   2 ?    9.0  12.6   0.00057      0.29     175     385 ..     224     429 ..     208     439 .] 0.71

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0053
                          Prominin 352 kvknqtaevvpdlkkalakgreqikklakkiprealdavisdlenterssktfddvveky 411
                                        +++q+++ v+    +l+  ++ + + +++i ++ + + +++l +++++++tf+ +ve+ 
  gi|336255267|ref|YP_004598374.1| 148 HLQEQMSDEVEGAVDELQASTTDVAENSQEI-SDLAADQSESLGDVQDEVSTFSATVEEI 206
                                       4567777777777777777777788888888.7777777888888888888888877775 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00057
                          Prominin 175 ketvkrgledlrtflkdvpqhidhvlvqnyeelekhvsddLddagkhlgldladtlesnvlpaLaelerllenlkea 251
                                       +e+  ++ +d+   + dv+++ d v+     +  ++ +d++dd+  ++++d+ad+ +   l+a  e ++   +    
  gi|336255267|ref|YP_004598374.1| 224 SEESVETAQDTLEAMDDVAAEADDVAAD--ATKLAERIDEIDDIV-EVINDIADQTNLLALNANIEAAHSDASSDGF 297
                                       445557789999999***********99..222223455555554.4567888888776333333444444445556 PP

                          Prominin 252 keqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsn.lCqseeCskilssleiekldtskcldqlpnvdevleal 327
                                           +++++l ++ ++ ++++++ +++v++   +++ + + ++ee  ++ ++ e+   ++ + ld+++++d+ + ++
  gi|336255267|ref|YP_004598374.1| 298 AVVANEIKSLAEQSKERADEIERIVTEVRETTLETVDSvEATNEEIGSVVTDIETVVENQREILDAIEDTDQGIAEI 374
                                       667788889999999999******************9999999**********99555555555************* PP

                          Prominin 328 eevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkipre 385
                                        ++++++ +s   e++a++ +      +++a+ v+d+  a +++++++++++ +i ++
  gi|336255267|ref|YP_004598374.1| 375 ATATDQQAAS--AEEIATMVDSVAERGDEVADSVQDVAAATEQQTAMVENIEASI-ES 429
                                       9996665544..4455555444444467888888888888888888888888887.22 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   5.6     0.018       9.2       4      87 ..     154     240 ..     131     248 .. 0.73
   2 ?    6.2   1.5      0.01       5.3       2      85 ..     194     269 ..     186     291 .. 0.47
   3 ?    1.8   0.1      0.22   1.1e+02      34      62 ..     299     327 ..     235     350 .. 0.42
   4 ?   12.2   0.7   0.00016     0.081       2      89 ..     341     427 ..     340     432 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.018
                             TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelk.eelke 77 
                                        +e+e  ++el+++ + + ++++e+s l  + s+++   + +++ ++++++++ +s++  ++++e++++l+ e++++
  gi|336255267|ref|YP_004598374.1| 154 SDEVEGAVDELQASTTDVAENSQEISDLAADQSESLGDVQDEVSTFSATVEEIASSAEevSSQSEQARTLSeESVET 230
                                       56777778888888888888888888888888888888888888888888888777655555555666665145666 PP

                             TMPIT  78 rkkvlkeves 87 
                                       ++ +l+ +++
  gi|336255267|ref|YP_004598374.1| 231 AQDTLEAMDD 240
                                       6666666655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.01
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelker 78 
                                       +e+++++  ++e+ ++a+e+ +++e+  +l ++ +++++   + + ++ ++ +++ ++        +++l+e+++e+
  gi|336255267|ref|YP_004598374.1| 194 DEVSTFSATVEEIASSAEEVSSQSEQARTLSEESVETAQDTLEAMDDVAAEADDVAAD--------ATKLAERIDEI 262
                                       2334444444444444444444444444444444444444444444444444444443........44444444444 PP

                             TMPIT  79 kkvlkev 85 
                                       + +++ +
  gi|336255267|ref|YP_004598374.1| 263 DDIVEVI 269
                                       4333333 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.22
                             TMPIT  34 kcskeikkqkkrlkelksslkklkksvke 62 
                                        +++eik+  ++ ke  ++++++ ++v+e
  gi|336255267|ref|YP_004598374.1| 299 VVANEIKSLAEQSKERADEIERIVTEVRE 327
                                       22233333333333333333333333333 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00016
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelker 78 
                                       ee+ ++ ++++++ e+++e+   +e++ + + ++++++++q   ++e+ ++++++ ++ ++e ++ v+++++ ++++
  gi|336255267|ref|YP_004598374.1| 341 EEIGSVVTDIETVVENQREILDAIEDTDQGIAEIATATDQQAASAEEIATMVDSVAER-GDEVADSVQDVAAATEQQ 416
                                       78889999***********************************************998.57999************* PP

                             TMPIT  79 kkvlkevesll 89 
                                       +++++++e+++
  gi|336255267|ref|YP_004598374.1| 417 TAMVENIEASI 427
                                       *****999875 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 ?   10.9   5.7   0.00076      0.39      38     110 ..     155     226 ..     135     247 .. 0.79
   2 ?    1.8   0.2       0.5   2.5e+02      50     110 ..     227     284 ..     222     295 .. 0.58
   3 ?    2.1   3.4       0.4   2.1e+02      36     121 ..     258     346 ..     245     365 .. 0.41
   4 ?    6.1   3.3     0.023        12      30     126 ..     340     435 ..     328     438 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00076
                                       CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHH CS
                         Fib_alpha  38 ekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnv 110
                                       +++e  ++e++ st+++ e ++ei+d  +++ +s  d +  ++ +s ++e ei+   e++++q ++ r L + 
  gi|336255267|ref|YP_004598374.1| 155 DEVEGAVDELQASTTDVAENSQEISDLAADQSESLGDVQDEVSTFSATVE-EIASSAEEVSSQSEQARTLSEE 226
                                       35677789***********************9999999************.***************9999764 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHH CS
                         Fib_alpha  50 stkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnv 110
                                       s ++a+++ ++++d+ +e+   ++d  + + +  +e++ +i+++ + i +q +n+ +L  +
  gi|336255267|ref|YP_004598374.1| 227 SVETAQDTLEAMDDVAAEADDVAAD-ATKLAERIDEID-DIVEVINDIADQ-TNLLALNAN 284
                                       5566777777777777777777775.444444445555.555555555444.344455555 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.4
                                       HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHHHHHHHCCH.HHHHHHH CS
                         Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrlketidaqe.snirvLq 108
                                       +++++ + +e i++   +++ l  + +   ++  +s+++     n ik+++++ +e+  ++++ +++   ++++   
  gi|336255267|ref|YP_004598374.1| 258 RIDEIDDIVEVINDIADQTNLLALNANIEAAHSDASSDGFavvANEIKSLAEQSKERADEIERIVTEVReTTLET-V 333
                                       555555555555555555555554444444444444444222233333333333333333333333333122222.1 PP

                                       HHHHHHHHHHHHH CS
                         Fib_alpha 109 nvlesneqkiqkL 121
                                       + +e+ +++i   
  gi|336255267|ref|YP_004598374.1| 334 DSVEATNEEIGSV 346
                                       2222222222222 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.023
                                       CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirv 106
                                       ++++   ++++e  +e+ ++    +e++ + i ++ +++ ++++   + i  + +++ e+  ++ +++++     ++
  gi|336255267|ref|YP_004598374.1| 340 NEEIGSVVTDIETVVENQREILDAIEDTDQGIAEIATATDQQAAS-AEEIATMVDSVAERGDEVADSVQDVAAATEQ 415
                                       444555555555555555555555555555555555555555543.3333333333334556666666666666666 PP

                                       HHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 107 LqnvlesneqkiqkLeqdid 126
                                        + ++e+ e +i+ Le di+
  gi|336255267|ref|YP_004598374.1| 416 QTAMVENIEASIESLERDIE 435
                                       77777777777777777775 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.6     0.023        12       8      47 ..     138     177 ..     134     192 .. 0.84
   2 ?    9.2   5.3     0.002         1      29     121 ..     243     338 ..     211     341 .. 0.77
   3 ?    2.0   0.2      0.35   1.8e+02      25      65 ..     386     426 ..     368     435 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.023
                              CdvA   8 eLvsegdipkstyeeikekleealkklkekakelkeklkk 47 
                                       +Lv++++  ++  e++  ++e a+++l++   +++e+ ++
  gi|336255267|ref|YP_004598374.1| 138 TLVEQQEQIRHLQEQMSDEVEGAVDELQASTTDVAENSQE 177
                                       79999*****************************998765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.002
                              CdvA  29 ealkklkekakelkeklkk...rlkeledqikslekalanlkisyasGEidEeaYksaieairellesaleekeeik 102
                                        + +++ ++a +l+e++++    ++ ++d  ++++ + +n+ i+ a  + + + +  + ++i++l e+ +e+ +ei+
  gi|336255267|ref|YP_004598374.1| 243 AEADDVAADATKLAERIDEiddIVEVINDIADQTNLLALNANIEAAHSDASSDGFAVVANEIKSLAEQSKERADEIE 319
                                       4444555555555544433111566677788899999**************************************** PP

                              CdvA 103 klleklskleleeeeveet 121
                                       +++ ++ + +le++++ e 
  gi|336255267|ref|YP_004598374.1| 320 RIVTEVRETTLETVDSVEA 338
                                       ******9888888776655 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.35
                              CdvA  25 ekleealkklkekakelkeklkkrlkeledqikslekalan 65 
                                       e++ + ++ + e+ +e+++ ++   +  e+q + +e   a+
  gi|336255267|ref|YP_004598374.1| 386 EEIATMVDSVAERGDEVADSVQDVAAATEQQTAMVENIEAS 426
                                       66677778888888899999999999999888888766555 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       9.4   4.8e+03      33      51 ..     220     238 ..     219     239 .. 0.83
   2 ?    1.3   0.3      0.55   2.8e+02      29      51 ..     247     269 ..     244     271 .. 0.84
   3 ?   10.0   0.3    0.0011      0.58      28      52 ..     341     365 ..     339     367 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 9.4
                             PHP_C  33 ayTefeepiatpdelleai 51 
                                       a T+ ee+++t+++ lea+
  gi|336255267|ref|YP_004598374.1| 220 ARTLSEESVETAQDTLEAM 238
                                       7888899999999999887 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.55
                             PHP_C  29 eVGrayTefeepiatpdelleai 51 
                                       +V   +T ++e+i+++d+++e i
  gi|336255267|ref|YP_004598374.1| 247 DVAADATKLAERIDEIDDIVEVI 269
                                       566668999***********998 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0011
                             PHP_C  28 eeVGrayTefeepiatpdelleair 52 
                                       ee+G+++T++e+ ++++ e+l+ai 
  gi|336255267|ref|YP_004598374.1| 341 EEIGSVVTDIETVVENQREILDAIE 365
                                       89*********************96 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 ?    8.6   1.6    0.0049       2.5      25      72 ..     134     182 ..     129     188 .. 0.77
   2 ?    7.3  11.9     0.012       6.2      18     151 ..     187     325 ..     184     329 .. 0.73
   3 ?    4.3  11.2       0.1        53      32     144 ..     302     417 ..     273     429 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0049
                                       HHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHH.HHHHHHHHHH CS
                           T3SSipB  25 nrlaawkamskaqqeaasklSdelqtalseakgatddl.eaaiekadqa 72 
                                        r+++ + +++  ++ ++++Sde++ a++e ++ t d+ e+++e  d a
  gi|336255267|ref|YP_004598374.1| 134 TRVTTLVEQQEQIRHLQEQMSDEVEGAVDELQASTTDVaENSQEISDLA 182
                                       5889999999999*****************9998766515555554443 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.012
                                       HCHHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-- CS
                           T3SSipB  18 kSLsqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLa 94 
                                        SL + ++ + ++ a  +     a+++S + ++a    ++  + +++  e++d++ ++ad++ + +++  +r++e++
  gi|336255267|ref|YP_004598374.1| 187 ESLGDVQDEVSTFSATVEEIASSAEEVSSQSEQARTLSEESVETAQDTLEAMDDVAAEADDVAADATKLAERIDEID 263
                                       6999999*********************************************************************3 PP

                                       -----.--CHHHHHHHHH...HHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHTXXXXX CS
                           T3SSipB  95 PdePe.kakleaaeqQagaa.adalqadealqKkldaask...lsekakakekevDdisakv 151
                                                +++ +  a +a  +a++ d+  +    +a+    l+e++k+ + e+  i++ v
  gi|336255267|ref|YP_004598374.1| 264 DIVEViNDIADQTNLLALNAnIEAAHSDASSDGFAVVANEiksLAEQSKERADEIERIVTEV 325
                                       32222022233333333333677777777776666666550005555555555555555555 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.1
                                       HHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHTT---------CHHHHH CS
                           T3SSipB  32 amskaqqeaasklSdelqtalseakgatddleaaieka.dqaksaadaatkkvdeaqkrlkeLaPdePekakleaae 107
                                         +k+  e+ ++  de+++ + e ++ t +  +++e++ ++++s++ + +  v++  + l+ ++  + + a++  a+
  gi|336255267|ref|YP_004598374.1| 302 NEIKSLAEQSKERADEIERIVTEVRETTLETVDSVEATnEEIGSVVTDIETVVENQREILDAIEDTDQGIAEIATAT 378
                                       567777888888999************999999998872579*********************999*****987775 PP

                                       .HHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           T3SSipB 108 .qQagaa.adalqadealqKkldaasklsekakakekev 144
                                        qQa+ a   a+ +d  +++  ++a  +++ a a e++ 
  gi|336255267|ref|YP_004598374.1| 379 dQQAASAeEIATMVDSVAERGDEVADSVQDVAAATEQQT 417
                                       166666655599999999**************9999985 PP

>> Vip3A_N  Vegetative insecticide protein 3A N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2    0.0014      0.71      42     103 ..     141     203 ..     131     217 .. 0.82
   2 ?    4.1   0.6     0.075        39      45     140 ..     194     295 ..     191     309 .. 0.70
   3 ?    1.1   1.5      0.65   3.3e+02      56     143 ..     264     319 ..     225     366 .. 0.55
   4 ?   -0.6   0.1       2.1   1.1e+03      46      67 ..     391     412 ..     339     436 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                           Vip3A_N  42 knqqllndisgkl.dgvngslndliaqgnlntelskeilkianeqnqvlndvnnkldaintml 103
                                        +q+ + ++ +++ d v+g++++l a     +e s+ei  +a +q + l dv++++ +  +++
  gi|336255267|ref|YP_004598374.1| 141 EQQEQIRHLQEQMsDEVEGAVDELQASTTDVAENSQEISDLAADQSESLGDVQDEVSTFSATV 203
                                       5566666666654489*************************************9998877655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.075
                           Vip3A_N  45 qllndisgkldgvngslndliaqgnlntelskeilkianeqnqvlndvnnkldaint...mlrvy...lpkitsmls 115
                                       + +   s  ++ +  s +++ +q +    ls e ++ a++  + ++dv ++ d + +    l      +  i  +++
  gi|336255267|ref|YP_004598374.1| 194 DEVSTFSATVEEIASSAEEVSSQSEQARTLSEESVETAQDTLEAMDDVAAEADDVAAdatKLAERideIDDIVEVIN 270
                                       55666788888899999999999999999999999999999999999999888765411133322112455667788 PP

                           Vip3A_N 116 dvmkqnyalslqieylskqlqeisd 140
                                       d+  q   l+l+ +  +   +  sd
  gi|336255267|ref|YP_004598374.1| 271 DIADQTNLLALNANIEAAHSDASSD 295
                                       8888888888877666555555555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.65
                           Vip3A_N  56 gvngslndliaqgnlntelskeilkianeqnqvlndvnnkldaintmlrvylpkitsmlsdvmkqnyal.slqieyl 131
                                                                      +v+nd+ ++ +     l     +i +  sd   + +a+ + +i+ l
  gi|336255267|ref|YP_004598374.1| 264 D----------------------------IVEVINDIADQTN-----LLALNANIEAAHSDASSDGFAVvANEIKSL 307
                                       1............................1222333322222.....112223344444444444443213445555 PP

                           Vip3A_N 132 skqlqeisdkld 143
                                       ++q +e +d ++
  gi|336255267|ref|YP_004598374.1| 308 AEQSKERADEIE 319
                                       555555555554 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.1
                           Vip3A_N  46 llndisgkldgvngslndliaq 67 
                                       +++ ++++ d v  s++d+ a 
  gi|336255267|ref|YP_004598374.1| 391 MVDSVAERGDEVADSVQDVAAA 412
                                       2333333333333333333333 PP

>> DUF4559  Domain of unknown function (DUF4559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  10.3    0.0044       2.3     185     309 ..     135     274 ..     126     276 .. 0.65
   2 ?    6.8   6.9    0.0093       4.8     172     304 ..     303     437 ..     288     439 .] 0.63

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0044
                           DUF4559 185 eleeaeeaieellkilkqefeislkedde.vrvltdvllslqklkeleeellkedat............kldelvlr 248
                                        ++++ e+ e++ ++++q  +    ++de + + tdv +++q++++l   + +   +             ++e++++
  gi|336255267|ref|YP_004598374.1| 135 RVTTLVEQQEQIRHLQEQMSDEVEGAVDElQASTTDVAENSQEISDLAADQSES--LgdvqdevstfsaTVEEIASS 209
                                       444445555555444444444444444551456788999999999987665555..223567888888877777777 PP

                           DUF4559 249 aeeqkiskeel....lkelqvlkeflnknkdLkenlkedvkklqeieekldkldedvtelkkkvd 309
                                       aee   ++e+      +++++ ++ l+   d      + +++ +++ e++d++d+ v+ +++  d
  gi|336255267|ref|YP_004598374.1| 210 AEEVSSQSEQArtlsEESVETAQDTLEAMDDVAAEADDVAADATKLAERIDEIDDIVEVINDIAD 274
                                       7766655554422223568889999999999985555555999***********99988877655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0093
                           DUF4559 172 kilrLledlk.tvpeleeaeeaieellkilkqefeislkeddevrvltdvllslqklkeleee...llkedatklde 244
                                       +i+ L+e+ k +  e+e + +++ e+  +++ +    ++e +  +v td     + + e ++e   ++++    + e
  gi|336255267|ref|YP_004598374.1| 303 EIKSLAEQSKeRADEIERIVTEVRET-TLETVDSVEATNE-EIGSVVTD----IETVVENQREildAIEDTDQGIAE 373
                                       55555555554555555555555555.3333333333333.12223333....344444444300134555568*** PP

                           DUF4559 245 lvlraeeqkiskeellkelqvlk....eflnknkdLkenlkedvkklqeieekldkldedvtel 304
                                       ++ ++++q  s ee+ + + +++    e+ + ++d   + +++ + +++ie  ++ l++d++++
  gi|336255267|ref|YP_004598374.1| 374 IATATDQQAASAEEIATMVDSVAergdEVADSVQDVAAATEQQTAMVENIEASIESLERDIEDV 437
                                       ***************9999988722224677777888888889999999*********999987 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 ?    6.6   1.0     0.024        12      24      66 ..     141     183 ..     125     186 .. 0.82
   2 ?   12.4   6.7   0.00036      0.19       2      67 ..     191     254 ..     190     259 .. 0.79
   3 ?    2.0   0.7      0.61   3.1e+02      27      55 ..     295     323 ..     259     347 .. 0.56
   4 ?    5.3   4.1     0.059        30       4      70 ..     347     411 ..     344     420 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.024
                            DUF883  24 eageeaeelRerleerlerarerlrdaeeavaerakeaaeaad 66 
                                       e +e+++ l e++++++e a ++l++ + +vae+++e+++ a 
  gi|336255267|ref|YP_004598374.1| 141 EQQEQIRHLQEQMSDEVEGAVDELQASTTDVAENSQEISDLAA 183
                                       678999******************************9988665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00036
                            DUF883   2 eleaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67 
                                       ++++e+ +  a++ee++++a+ e  ++ e++R   ee++e+a+++l+++ + va++a+++a++a +
  gi|336255267|ref|YP_004598374.1| 191 DVQDEVSTFSATVEEIASSAE-EVSSQSEQARTLSEESVETAQDTLEAMDD-VAAEADDVAADATK 254
                                       6899************97776.566789******************96666.55556655555544 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.61
                            DUF883  27 eeaeelRerleerlerarerlrdaeeava 55 
                                       +  + + +++++ +e+++er+++ e+ v 
  gi|336255267|ref|YP_004598374.1| 295 DGFAVVANEIKSLAEQSKERADEIERIVT 323
                                       44444444444444444444444433222 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.059
                            DUF883   4 eaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaaddyVr 70 
                                         ++e+++++ +e+l++ + ++++ ++e+    ++++++a e+++ + ++vaer +e+a++++d++ 
  gi|336255267|ref|YP_004598374.1| 347 VTDIETVVENQREILDAIE-DTDQGIAEIATATDQQAASA-EEIATMVDSVAERGDEVADSVQDVAA 411
                                       5799999999999996666.58888888877777776666.55666888899999999999988765 PP

>> Dor1  Dor1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  10.3    0.0008      0.41      21     157 ..     144     277 ..     130     285 .. 0.73
   2 ?    2.5   2.8     0.094        48      13      90 ..     301     378 ..     290     429 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0008
                              Dor1  21 eeaeeilaqiqdLarkn....yktlidaaealeairqelediraqledLvlklpkLteectrfskkaeeisekrken 93 
                                       e+++++++q++d   +          d ae++++i+ +  d  ++l d+ +++  ++  ++++  +aee+s++ +++
  gi|336255267|ref|YP_004598374.1| 144 EQIRHLQEQMSDEVEGAvdelQASTTDVAENSQEISDLAADQSESLGDVQDEVSTFSATVEEIASSAEEVSSQSEQA 220
                                       44555555555543333000033445677788888888888888999**************************9888 PP

                              Dor1  94 kllldk.heqllellelPqlmdrcirngyydealeLeayvsrLkqristnpviqsiaaeveetvq 157
                                       + l+++ +e+  + le    md         ea++ +a +++L++ri ++++i ++++++   + 
  gi|336255267|ref|YP_004598374.1| 221 RTLSEEsVETAQDTLE---AMDDVA-----AEADDVAADATKLAERIDEIDDIVEVINDIADQTN 277
                                       8887651567777776...688654.....689****************9999999998876555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.094
                              Dor1  13 ekepelLaeeaeeilaqiqdLarknyktlidaaealeairqelediraqledLvlklpkLteectrfskkaeeisek 89 
                                         e ++Lae+++e+  +i  +  + + t +++ +  ea  +e++++  ++e++v++  ++  +++   +  +ei + 
  gi|336255267|ref|YP_004598374.1| 301 ANEIKSLAEQSKERADEIERIVTEVRETTLETVDSVEATNEEIGSVVTDIETVVENQREILDAIEDTDQGIAEIATA 377
                                       56677899999999999999999999999999999999999999888888888887755555555555544444444 PP

                              Dor1  90 r 90 
                                        
  gi|336255267|ref|YP_004598374.1| 378 T 378
                                       3 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  11.7     0.002         1     183     279 ..     139     239 ..     129     243 .. 0.53
   2 ?    5.3   5.7     0.015       7.6     146     262 ..     243     359 ..     238     361 .. 0.63
   3 ?    1.6  12.2       0.2     1e+02     165     278 ..     315     430 ..     300     435 .. 0.36

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.002
                              Spc7 183 leklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqlee....leekieelkeqkseleeeiaeaer 255
                                       l ++qe+ + l++  ++e+e + +el++  ++++e ++e+++l ++  e    +++++++ ++  +e+ +  +e  +
  gi|336255267|ref|YP_004598374.1| 139 LVEQQEQIRHLQEQMSDEVEGAVDELQASTTDVAENSQEISDLAADQSEslgdVQDEVSTFSATVEEIASSAEEVSS 215
                                       33344444445555555666666666666666666655555555444440000444444455555555555555556 PP

                              Spc7 256 vleeckgwsesevsrlkeevkale 279
                                         e+ +  se+ v++ +++++a++
  gi|336255267|ref|YP_004598374.1| 216 QSEQARTLSEESVETAQDTLEAMD 239
                                       667777777777777777777775 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                              Spc7 146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkel 222
                                        + +++ +d+++L+++ +e+d++++ ++   ++ +  + + + +a  +++  ++  + + +e+++l ++ +e+ +e+
  gi|336255267|ref|YP_004598374.1| 243 AEADDVAADATKLAERIDEIDDIVEVINDIADQTNLLALNANIEA-AHSDASSDGFAVVANEIKSLAEQSKERADEI 318
                                       567788999999999999999999999988876544333333222.2344446666666666666666666666666 PP

                              Spc7 223 aelqeqleele.ekieelkeqkseleeeiaeaervleeckg 262
                                       ++  +++ e + e+++++++  +e+ + +   e v+e++++
  gi|336255267|ref|YP_004598374.1| 319 ERIVTEVRETTlETVDSVEATNEEIGSVVTDIETVVENQRE 359
                                       66655544433256666666666666666666678887775 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.2
                              Spc7 165 ldellpeleeekaeleeeleklqeaaeeles..idkeeLeelreelaelkaeieekkkelaelqeqleeleekieel 239
                                       +de+   ++e +++  e++++ ++ +ee+ s   d e + e ++e+ ++ ++ ++  +e+a+ ++q ++++e+i+++
  gi|336255267|ref|YP_004598374.1| 315 ADEIERIVTEVRETTLETVDSVEATNEEIGSvvTDIETVVENQREILDAIEDTDQGIAEIATATDQQAASAEEIATM 391
                                       22222222222222233333333333333332223222222233333333333333344444444444444444444 PP

                              Spc7 240 keqkseleeeiaeaervleeckgwsesevsrlkeevkal 278
                                        ++ +e  +e+a + + + +  + ++  v++++++ ++l
  gi|336255267|ref|YP_004598374.1| 392 VDSVAERGDEVADSVQDVAAATEQQTAMVENIEASIESL 430
                                       444444444444444444444444444444444444444 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   7.4    0.0037       1.9     223     336 ..     131     254 ..     120     263 .. 0.71
   2 ?    4.1   3.1     0.026        13     207     328 ..     283     416 ..     266     435 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0037
                              FUSC 223 rllsrmlallallsslarllarlraeeaaavpelaallaelaal.........eaaaaaealeaalaalrarlralr 290
                                       + l+r+++l+ +   +++l++++++e ++av+el+a   ++a+          +++++  + ++++ ++ a ++++ 
  gi|336255267|ref|YP_004598374.1| 131 EVLTRVTTLVEQQEQIRHLQEQMSDEVEGAVDELQASTTDVAENsqeisdlaaDQSESLGDVQDEVSTFSATVEEIA 207
                                       55667777777777777777777777777777777777777777888888888777888888888888888888888 PP

                              FUSC 291 rale...adadtaalllarlaellaelaqllaslraleaaiaaarraer 336
                                       +++e    ++++a+ l ++ +e+ ++ +++ ++++a + + aa  +a++
  gi|336255267|ref|YP_004598374.1| 208 SSAEevsSQSEQARTLSEESVETAQDTLEAMDDVAAEADDVAA--DATK 254
                                       8888777777777777777777777777777777777766653..3333 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.026
                              FUSC 207 aayesprirararalrrllsrmlallallsslarllarlraeeaaavpe....laallaelaal.........eaaa 270
                                       a  e ++  a ++  +   +++ +l  +  + a++ +r  +e ++++ e    ++a+ +e+ ++         +   
  gi|336255267|ref|YP_004598374.1| 283 ANIEAAHSDASSDGFAVVANEIKSLAEQSKERADEIERIVTEVRETTLEtvdsVEATNEEIGSVvtdietvveN--- 356
                                       55555556666666666666666666666666666666655555555553222444444444435555544431... PP

                              FUSC 271 aaealeaalaalrarlralrrale.............adadtaalllarlaellaelaqllaslraleaai 328
                                                   r+ l+a++  ++             a+a+  a ++ ++ae+ +e+a+  ++++a +++ 
  gi|336255267|ref|YP_004598374.1| 357 -----------QREILDAIEDTDQgiaeiatatdqqaASAEEIATMVDSVAERGDEVADSVQDVAAATEQQ 416
                                       ...........333333333333333333311112212333444444555555555555555555444443 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.4     0.029        15       6      89 ..     161     240 ..     144     255 .. 0.66
   2 ?    1.0   0.3       1.3   6.6e+02      15      73 ..     251     315 ..     239     327 .. 0.55
   3 ?    5.5   1.6     0.049        25      14      65 ..     316     367 ..     309     437 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.029
                                       HTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS..S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               ING   6 ldsvenLPlelqrnltelreiDakvqellkeidskiekflkngslqknekeeelsriqeelkeaqelldeKiqlaqq 82 
                                       +d +++   ++ +n +e+ ++ a  +e l ++++++++f+     + +e  ++ +++ ++ ++a  l++e ++ aq+
  gi|336255267|ref|YP_004598374.1| 161 VDELQASTTDVAENSQEISDLAADQSESLGDVQDEVSTFS----ATVEEIASSAEEVSSQSEQARTLSEESVETAQD 233
                                       3333344445555555666666666666666666666666....566666666778888888888888888888888 PP

                                       HHHHHHH CS
                               ING  83 aldlvdk 89 
                                       +l+ +d 
  gi|336255267|ref|YP_004598374.1| 234 TLEAMDD 240
                                       8888775 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......TS..S-HHHHHHHHHHHHHHHHHHHHHH CS
                               ING  15 elqrnltelreiDakvqellkeidskiekfl.......kngslqknekeeelsriqeelkeaqell 73 
                                       + +++ +++ eiD  v e++++i ++ + +        ++++ +++    + ++i++  ++++e +
  gi|336255267|ref|YP_004598374.1| 251 DATKLAERIDEIDDIV-EVINDIADQTNLLAlnanieaAHSDASSDGFAVVANEIKSLAEQSKERA 315
                                       6667778888888654.5666666666655566644432222222222222334444444444444 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.049
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS..S-HHHHHHHHHHHHHH CS
                               ING  14 lelqrnltelreiDakvqellkeidskiekflkngslqknekeeelsriqee 65 
                                       +e++r +te+re   ++ + ++  +++i +++++ ++  ++++e l  i+++
  gi|336255267|ref|YP_004598374.1| 316 DEIERIVTEVRETTLETVDSVEATNEEIGSVVTDIETVVENQREILDAIEDT 367
                                       7999***************************966666666666666655443 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.47   2.4e+02      14      56 ..     137     178 ..     130     192 .. 0.69
   2 ?    2.5   0.3      0.26   1.3e+02      11      46 ..     208     243 ..     195     260 .. 0.79
   3 ?    8.9   0.4    0.0027       1.4       7      61 ..     309     363 ..     302     378 .. 0.80
   4 ?   -0.5   0.1       2.2   1.1e+03      33      57 ..     401     428 ..     372     438 .. 0.42

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.47
                              ApoO  14 drLeegvrslRkslepytsavqdelnkvkskvetaeqsvtdti 56 
                                       ++L e+ +++R+  e+ +++v+ ++++++ +  +  ++ ++ i
  gi|336255267|ref|YP_004598374.1| 137 TTLVEQQEQIRHLQEQMSDEVEGAVDELQASTTDVAENSQE-I 178
                                       56777888888888888888888888887777666665544.3 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.26
                              ApoO  11 eptdrLeegvrslRkslepytsavqdelnkvkskve 46 
                                       + ++++ ++ +++R   e+ ++++qd+l+ + + + 
  gi|336255267|ref|YP_004598374.1| 208 SSAEEVSSQSEQARTLSEESVETAQDTLEAMDDVAA 243
                                       456788999999999999999999999987776554 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0027
                              ApoO   7 tpseeptdrLeegvrslRkslepytsavqdelnkvkskvetaeqsvtdtiasLke 61 
                                       ++s+e++d++e+ v+++R+++ ++++ v+++ +++ s v + e+ v+++ + L  
  gi|336255267|ref|YP_004598374.1| 309 EQSKERADEIERIVTEVRETTLETVDSVEATNEEIGSVVTDIETVVENQREILDA 363
                                       4557899********************9999999999999999988888877765 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.2
                              ApoO  33 avqdelnkvkskveta...eqsvtdtia 57 
                                       +v d++++v  + e+    +++++ +i+
  gi|336255267|ref|YP_004598374.1| 401 EVADSVQDVAAATEQQtamVENIEASIE 428
                                       3333333333222222000233333344 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  11.8    0.0053       2.7       5     113 ..     156     262 ..     151     279 .. 0.78
   2 ?    5.0   5.4     0.034        17      77     164 ..     304     390 ..     295     397 .. 0.74
   3 ?    6.6   5.1     0.011       5.5      13      94 ..     346     426 ..     340     439 .] 0.66

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0053
                              YkyA   5 kiyealeeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeak 81 
                                       ++  a++e++++  +++e+ +++++l +++ e   ++ +       ++++ ++ a e  ++ e+     +es+e a+
  gi|336255267|ref|YP_004598374.1| 156 EVEGAVDELQASTTDVAENSQEISDLAADQSESLGDVQDEVSTFSATVEEIASSAEEVSSQSEQARTLSEESVETAQ 232
                                       6677889999999********************99997654444566777777777777777777777788888888 PP

                              YkyA  82 eefekikeeieeiedeelkkeaeelieameer 113
                                       + +e +++   e +d  +  +a++l+e ++e 
  gi|336255267|ref|YP_004598374.1| 233 DTLEAMDDVAAEADD--VAADATKLAERIDEI 262
                                       888888888888844..588999998777664 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.034
                              YkyA  77 ieeakeefekikeeieeiedeelkkeaeelieameeryeaydklykaYkealeldkeLYemLkkeeltleeleeqie 153
                                       i++  e+ ++  +eie i   e+++ + e ++++e   e + +++++ ++++e+++e+ + +++ +  + e+   ++
  gi|336255267|ref|YP_004598374.1| 304 IKSLAEQSKERADEIERIV-TEVRETTLETVDSVEATNEEIGSVVTDIETVVENQREILDAIEDTDQGIAEIATATD 379
                                       6666677777777777774.447788888888888888888888888888888888888888888888888888877 PP

                              YkyA 154 kiNesyeevke 164
                                       +  +s ee+  
  gi|336255267|ref|YP_004598374.1| 380 QQAASAEEIAT 390
                                       77777777665 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.011
                              YkyA  13 avelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekike 89 
                                       +v++ ++++e+q ++ ++ ++  +   ei +  +d++ +  ++++ ++++v eR ++++   + + +a e+ + + e
  gi|336255267|ref|YP_004598374.1| 346 VVTDIETVVENQREILDAIEDTDQGIAEIAT-ATDQQAASAEEIATMVDSVAERGDEVADSVQDVAAATEQQTAMVE 421
                                       5555567777777777777777777777765.556667788888888888888888888877777777777777766 PP

                              YkyA  90 eieei 94 
                                       +ie  
  gi|336255267|ref|YP_004598374.1| 422 NIEAS 426
                                       66543 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  14.4    0.0051       2.6      36     163 ..     141     262 ..     129     277 .. 0.87
   2 ?    7.0   4.4    0.0085       4.3      57     110 ..     225     278 ..     211     294 .. 0.73
   3 ?    4.3   7.5     0.053        27      48     130 ..     303     391 ..     286     398 .. 0.67
   4 ?    3.7   2.8     0.082        42      48     101 ..     384     437 ..     375     439 .] 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0051
                         Laminin_I  36 sakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlnene 112
                                       +++++   ++e+ + +++  ++eLq   t v ++ q++   + + +++  + ++++    ++++ei +++++++  +
  gi|336255267|ref|YP_004598374.1| 141 EQQEQIRHLQEQMSDEVEGAVDELQASTTDVAENSQEISDLAADQSESLGDVQDEVSTFSATVEEIASSAEEVSS-Q 216
                                       3444445677888899**********************************************************9.8 PP

                         Laminin_I 113 ealpssklseelaeaqrlLeelrsRdftkqleeaeaelkaAqkLLsrvqtl 163
                                       ++ + +  +e  + aq  Le +         +ea+++++ A kL +r+ + 
  gi|336255267|ref|YP_004598374.1| 217 SEQARTLSEESVETAQDTLEAM-----DDVAAEADDVAADATKLAERIDEI 262
                                       99999999999999********.....788899***************875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0085
                         Laminin_I  57 eeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlne 110
                                       ee ++ a+ +l+   +v ae+++    a++Lae i +++d ++ i+  + ++n 
  gi|336255267|ref|YP_004598374.1| 225 EESVETAQDTLEAMDDVAAEADDVAADATKLAERIDEIDDIVEVINDIADQTNL 278
                                       333566888889999999999999999999999999999999999988877776 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.053
                         Laminin_I  48 elesLaqetee....LqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlne..neealpss 118
                                       e++sLa++ +e        +t+v++ + ++   +e+t++++ + ++ i+ +++n  eil  ++ +++   e a++  
  gi|336255267|ref|YP_004598374.1| 303 EIKSLAEQSKEradeIERIVTEVRETTLETVDSVEATNEEIGSVVTDIETVVENQREILDAIEDTDQgiAEIATATD 379
                                       55555555443000033445666777777778889999999999999999999999999999999988755566666 PP

                         Laminin_I 119 klseelaeaqrl 130
                                       +  +  +e+  +
  gi|336255267|ref|YP_004598374.1| 380 QQAASAEEIATM 391
                                       555555565555 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.082
                         Laminin_I  48 elesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikei 101
                                         e++a  +++ +++  +v ++ q+v a++e+ +   ++ ++ i+ l+++i+ +
  gi|336255267|ref|YP_004598374.1| 384 SAEEIATMVDSVAERGDEVADSVQDVAAATEQQTAMVENIEASIESLERDIEDV 437
                                       46888899999999999********************************99876 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   7.8     0.016       8.3     237     323 ..     154     241 ..     136     243 .. 0.83
   2 ?    6.3   4.3    0.0089       4.6       3     101 ..     228     332 ..     226     337 .. 0.82
   3 ?    0.8  12.9       0.4   2.1e+02     237     314 ..     315     396 ..     261     437 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH....HHHH CS
                             APG17 237 aaeledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerw.eeekek 312
                                       + e+e  v+elq++  ++ + ++++s+ +++  ++l  +++ ++++++  +++++  + +++++e  ++  ee  e+
  gi|336255267|ref|YP_004598374.1| 154 SDEVEGAVDELQASTTDVAENSQEISDLAADQSESLGDVQDEVSTFSATVEEIASSAEEVSSQSEQARTLsEESVET 230
                                       689***************99999999999999999999999999999998888888888888888888854777788 PP

                                       HHHHHHHHHHH CS
                             APG17 313 ieekleeleeL 323
                                        ++ le ++++
  gi|336255267|ref|YP_004598374.1| 231 AQDTLEAMDDV 241
                                       88888887765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0089
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...IIIIIIIII....IIIIII CS
                             APG17   3 llaAkksLseaqtlcqrAnelltsarqeleeavkllakteflrdglkqQlkllek...irkslerkl....ekgkee 72 
                                       +++A+++L+    +  +A++++++a+++ e+++++++ +e + + +++Q +ll+    i+   +++       + +e
  gi|336255267|ref|YP_004598374.1| 228 VETAQDTLEAMDDVAAEADDVAADATKLAERIDEIDDIVEVI-NDIADQTNLLALnanIEAAHSDASsdgfAVVANE 303
                                       678******8888999***********999999999998876.5688888888654545555555557777888899 PP

                                       IIHHHHHHHHHHHHHHHHHHHHHTSS-TT CS
                             APG17  73 fkdlikeldaanerLektlekLrktkvep 101
                                       +k+l ++ +++ +++e+++++ r+t+ e 
  gi|336255267|ref|YP_004598374.1| 304 IKSLAEQSKERADEIERIVTEVRETTLET 332
                                       99999999999999*****9999999876 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...H CS
                             APG17 237 aaeledVvkelqerleem....ekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweee 309
                                       a e+e +v+e++e+  e     e++++++ +  ++ie+++++ +++l+ +e+  + ++e+ + + ++++  e+ ++ 
  gi|336255267|ref|YP_004598374.1| 315 ADEIERIVTEVRETTLETvdsvEATNEEIGSVVTDIETVVENQREILDAIEDTDQGIAEIATATDQQAASAEEIATM 391
                                       55555555555544333334445555555555666666666666666666655555555555333333333332222 PP

                                       HHHHH CS
                             APG17 310 kekie 314
                                        ++++
  gi|336255267|ref|YP_004598374.1| 392 VDSVA 396
                                       22222 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4      0.98     5e+02       5      36 ..     132     166 ..     129     177 .. 0.81
   2 ?    5.8   0.2     0.032        17       7      50 ..     176     219 ..     171     225 .. 0.86
   3 ?   10.8   5.8   0.00092      0.47      14      84 ..     215     285 ..     200     298 .. 0.81
   4 ?    1.4   0.8      0.74   3.8e+02      16      73 ..     303     362 ..     296     381 .. 0.59
   5 ?    2.3   0.2       0.4   2.1e+02       5      35 ..     405     435 ..     401     439 .] 0.75

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.98
                              Rx_N   5 llqkLadllaeea...kllkgvkeeleklkdeLes 36 
                                       +l ++++l++++     l++++ +e+e   deL++
  gi|336255267|ref|YP_004598374.1| 132 VLTRVTTLVEQQEqirHLQEQMSDEVEGAVDELQA 166
                                       57778888888888888888888998888888875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.032
                              Rx_N   7 qkLadllaeeakllkgvkeeleklkdeLesiqavLedaeerqik 50 
                                       q ++dl+a++ ++l +v++e+     + e i +  e+++ + ++
  gi|336255267|ref|YP_004598374.1| 176 QEISDLAADQSESLGDVQDEVSTFSATVEEIASSAEEVSSQSEQ 219
                                       6799**************************99988887776554 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00092
                              Rx_N  14 aeeakllkgvkeeleklkdeLesiqavLedaeerqikdeavkeWlkelrdlaydaeDvlDefetealrrks 84 
                                       ++  + +   +e +e  +d+Le+++ v ++a++   +   + e ++e+ d++  + D+ D+ ++ al+ + 
  gi|336255267|ref|YP_004598374.1| 215 SQSEQARTLSEESVETAQDTLEAMDDVAAEADDVAADATKLAERIDEIDDIVEVINDIADQTNLLALNANI 285
                                       3333555566788************************************************9999988764 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.74
                              Rx_N  16 ea.kllkgvkeeleklkdeLesiqa.vLedaeerqikdeavkeWlkelrdlaydaeDvlD 73 
                                       e+ +l ++ ke  +++++    ++   Le ++  + ++e++   + ++  ++ +   +lD
  gi|336255267|ref|YP_004598374.1| 303 EIkSLAEQSKERADEIERIVTEVREtTLETVDSVEATNEEIGSVVTDIETVVENQREILD 362
                                       444333333444444444444443325666666666666666666666666665555555 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.4
                              Rx_N   5 llqkLadllaeeakllkgvkeeleklkdeLe 35 
                                        +q +a+  +++ ++++++++ +e+l++  e
  gi|336255267|ref|YP_004598374.1| 405 SVQDVAAATEQQTAMVENIEASIESLERDIE 435
                                       5777888888888888888888888888766 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.5     0.012       6.3      55     104 ..     141     190 ..     134     191 .. 0.91
   2 ?    9.6   2.1    0.0024       1.2      28      92 ..     184     248 ..     180     261 .. 0.88
   3 ?    0.1   0.3       2.3   1.2e+03      10      41 ..     278     309 ..     246     320 .. 0.46
   4 ?    2.6   1.5      0.36   1.9e+02      10      80 ..     278     345 ..     274     369 .. 0.62
   5 ?    2.1   5.2      0.52   2.7e+02       7      95 ..     312     398 ..     306     422 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  55 ervkalnelaeklldeghsaseeieerleelnerWeeLkelaaerkqkLe 104
                                       e+ +++ +l+e++ de + a +e+++++ ++ e+ +e+++laa++ ++L 
  gi|336255267|ref|YP_004598374.1| 141 EQQEQIRHLQEQMSDEVEGAVDELQASTTDVAENSQEISDLAADQSESLG 190
                                       677899999**********************************9999885 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0024
                                       SCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHH CS
                          Spectrin  28 dlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeL 92 
                                       d +++l +vq+ + ++ a  +e+a+  e+v +  e+a+ l +e+ ++++++ e ++++    +++
  gi|336255267|ref|YP_004598374.1| 184 DQSESLGDVQDEVSTFSATVEEIASSAEEVSSQSEQARTLSEESVETAQDTLEAMDDVAAEADDV 248
                                       66789***********************************9999999999999999998766655 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHH CS
                          Spectrin  10 adeleeWieekeellssedlgkdleevqallk 41 
                                       + +l++ ie ++ ++ss+ ++   +e+++l +
  gi|336255267|ref|YP_004598374.1| 278 LLALNANIEAAHSDASSDGFAVVANEIKSLAE 309
                                       22333333334444433333333333333333 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHTTHTTHHHHHH CS
                          Spectrin  10 adeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkaln.elaeklldeghsaseeiee 80 
                                       + +l++ ie ++ ++ss+ ++   +e+++l ++ k+  +e++   ++v++ + e+ +++++    ++eei +
  gi|336255267|ref|YP_004598374.1| 278 LLALNANIEAAHSDASSDGFAVVANEIKSLAEQSKERADEIERIVTEVRETTlETVDSVEA----TNEEIGS 345
                                       5567777888888888888888888888888888888888877666666666455555422....2233333 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.52
                                       HHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHH CS
                          Spectrin   7 aqdadeleeWieekeellssedlgkdleevqallk.khkaleaelaaqqervkalnelaeklldeghsaseeieerl 82 
                                       +++ade+e   +e +e     +   ++e++ + +    +++e  +++q+e ++a++++ + +++    a+++  ++ 
  gi|336255267|ref|YP_004598374.1| 312 KERADEIERIVTEVRETT--LETVDSVEATNEEIGsVVTDIETVVENQREILDAIEDTDQGIAEI-ATATDQQAASA 385
                                       566677777777764444..122233333333332467777777777777777777666666332.33444444444 PP

                                       HHHHHHHHHHHHH CS
                          Spectrin  83 eelnerWeeLkel 95 
                                       ee+ +  +++ e+
  gi|336255267|ref|YP_004598374.1| 386 EEIATMVDSVAER 398
                                       4444444433333 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 ?    2.6   9.3       0.4     2e+02       7      98 ..     154     238 ..     129     238 .. 0.64
   2 ?    3.6   5.5      0.19        96       7      69 ..     210     271 ..     191     286 .. 0.56
   3 ?    9.6   3.4    0.0025       1.3       1      90 [.     295     397 ..     295     404 .. 0.67
   4 ?    3.9   0.8      0.15        77       8      59 ..     386     436 ..     372     439 .] 0.52

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.4
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpsk.fkidekels 82 
                                        +eV+ +++++++  +   +        +s+e++++  +  ++l++++ +++ +  tv+ + ++ ++  + +e++ +
  gi|336255267|ref|YP_004598374.1| 154 SDEVEGAVDELQASTTDVAE--------NSQEISDLAADQSESLGDVQDEVSTFSATVEEIASSAEEvSSQSEQART 222
                                       33333333333333333332........6888888888888888888888888888887666666664666666666 PP

                      Syntaxin-6_N  83 rrrafveevreevkem 98 
                                         ++ ve +++++++m
  gi|336255267|ref|YP_004598374.1| 223 LSEESVETAQDTLEAM 238
                                       6777777777776666 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.19
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvrivek 69 
                                       +eeV ++ ++a++l ++  ++ +dt +   +++    +++ +   ++ + ++++++ v++++ 
  gi|336255267|ref|YP_004598374.1| 210 AEEVSSQSEQARTLSEESVETAQDTLE-AMDDVAAEADDVAADATKLAERIDEIDDIVEVIND 271
                                       344444444444444444333333222.46666666666666666677777777776666654 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0025
                      Syntaxin-6_N   1 DPFfevkeeVqkslnkaeslyrrwerlledtsss..........tseeldetrteLrkalrsiewdledLeet...v 64 
                                       D F +v++e+++ +++ ++  ++ er+ ++ +++          t+ee+ +  t++++ +++ ++ l+ +e+t   +
  gi|336255267|ref|YP_004598374.1| 295 DGFAVVANEIKSLAEQSKERADEIERIVTEVRETtletvdsveaTNEEIGSVVTDIETVVENQREILDAIEDTdqgI 371
                                       88**********************99999888844777777777777777777777777766666665555551113 PP

                      Syntaxin-6_N  65 riveknpskfkidekelsrrrafvee 90 
                                       + +    ++   +++e+++  + v+e
  gi|336255267|ref|YP_004598374.1| 372 AEIATATDQQAASAEEIATMVDSVAE 397
                                       33333445566666666655555555 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.15
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwe.rlledtssstseeldetrteLrkalrsiewdled 59 
                                       ee+   ++++++  ++   ++++++    +e+     ++++++++s+e d+ed
  gi|336255267|ref|YP_004598374.1| 386 EEIATMVDSVAERGDEVAdSVQDVAA--ATEQQTAMVENIEASIESLERDIED 436
                                       33334444444444444212222222..3566666666677777777777776 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8  19.8      0.39     2e+02      68     249 ..     140     320 ..     129     329 .. 0.46
   2 ?    5.1  10.7      0.02        10      99     172 ..     329     437 ..     269     439 .] 0.52

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.39
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.............XXXXX CS
                              AIP3  68 sLniepldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekasesla....kkelkaqlkevqsl 140
                                       + + e++ +++++++++++   +el+  ++ + ++++++++++++q+e+  + ++e+++    ++e +++ +ev+s 
  gi|336255267|ref|YP_004598374.1| 140 VEQQEQIRHLQEQMSDEVEGAVDELQASTTDVAENSQEISDLAADQSESLGDVQDEVSTfsatVEEIASSAEEVSSQ 216
                                       33344555555555555555555555555555555555555555555555555554333222222222222222222 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 141 rrdLavlrqlysefkseikeslselrekakkvkeaslastkkssnrayiekgkkkLseesdklvtkvddLqDlvedl 217
                                           +  r l++e+ +  +++l+++ + a++  +++   tk  +    i++  + +++ +d+  t++  L+  +e+ 
  gi|336255267|ref|YP_004598374.1| 217 S---EQARTLSEESVETAQDTLEAMDDVAAEADDVAADATKLAERIDEIDDIVEVINDIADQ--TNLLALNANIEAA 288
                                       2...2233333333333333333333333333333344444444445555555555555554..3444555555555 PP

                                       HHHHHHHXXXXXHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 218 rkDVvqRgvrpskkqlesvakeikkakkelkk 249
                                        +D  + g  + +++++s+a++ k+ ++e+++
  gi|336255267|ref|YP_004598374.1| 289 HSDASSDGFAVVANEIKSLAEQSKERADEIER 320
                                       55555555555555555555555555555555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.02
                                       X......................................XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXX CS
                              AIP3  99 i...................................esqkaslqevserqeeaakekaseslakkelkaqlkevqsl 140
                                       +                                   e++++ ++e+++ + ++a+++++  + +++ +++ +ev + 
  gi|336255267|ref|YP_004598374.1| 329 TletvdsveatneeigsvvtdietvvenqreildaiEDTDQGIAEIATATDQQAASAEEIATMVDSVAERGDEVADS 405
                                       11222222222233333333333333444444444466666666666666666666666556677888888888888 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              AIP3 141 rrdLavlrqlysefkseikeslselrekakkv 172
                                        +d+a+  + ++++ ++i++s+++l++ +++v
  gi|336255267|ref|YP_004598374.1| 406 VQDVAAATEQQTAMVENIEASIESLERDIEDV 437
                                       88888888888888888888888888877765 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   2.9       0.3   1.5e+02      74     134 ..     129     189 ..     123     194 .. 0.83
   2 ?    6.7   8.1      0.01       5.2      65     142 ..     179     257 ..     175     267 .. 0.78
   3 ?    4.7   0.7     0.042        21     116     161 ..     283     328 ..     265     341 .. 0.79
   4 ?    8.6   7.1    0.0028       1.5      71     157 ..     347     436 ..     337     439 .] 0.75

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.3
                            DUF745  74 aeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqel 134
                                       a +v+ ++++ +++ e+  ++ ++++++++  ++ l+a    + en +++ ++aa  +++l
  gi|336255267|ref|YP_004598374.1| 129 AVEVLTRVTTLVEQQEQIRHLQEQMSDEVEGAVDELQASTTDVAENSQEISDLAADQSESL 189
                                       6788888999999999999999999999999999999999999999999999998877776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.01
                            DUF745  65 eqleqelreaeavvqeekkslqss.eanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektql 140
                                         l ++++e    vq+e +  +++ e+ a++a+++++q +q  +  ++ +++a+++le +++vaa+a   +a+ t+l
  gi|336255267|ref|YP_004598374.1| 179 SDLAADQSESLGDVQDEVSTFSATvEEIASSAEEVSSQSEQARTLSEESVETAQDTLEAMDDVAAEADDVAADATKL 255
                                       5677788888888888777777761555666777777777777777889*******************999999998 PP

                            DUF745 141 le 142
                                        e
  gi|336255267|ref|YP_004598374.1| 256 AE 257
                                       76 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.042
                            DUF745 116 akenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkd 161
                                       a+ +++++++ ++g +  ++e ++l e++k+R++e+++ ++e+r+ 
  gi|336255267|ref|YP_004598374.1| 283 ANIEAAHSDASSDGFAVVANEIKSLAEQSKERADEIERIVTEVRET 328
                                       455667788888888899999999************9999999875 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0028
                            DUF745  71 lreaeavvqeekk...slqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaA 144
                                       +++ e+vv+++ +   +++ + + ++  a+a +q  +++e + ++++++ e+ +++ +  + +++  +++t+++e+ 
  gi|336255267|ref|YP_004598374.1| 347 VTDIETVVENQREildAIEDTDQGIAEIATATDQQAASAEEIATMVDSVAERGDEVADSVQDVAAATEQQTAMVENI 423
                                       678888887766511156667777777777777777777788888888888888888888888899999******** PP

                            DUF745 145 kkRveeLkkqlke 157
                                       ++ +e+L++++++
  gi|336255267|ref|YP_004598374.1| 424 EASIESLERDIED 436
                                       ********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2213  (0.123431); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                       140  (0.00780858); expected 17.9 (0.001)
Passed Fwd filter:                        94  (0.0052429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 1.46u 0.32s 00:00:01.78 Elapsed: 00:00:00.50
# Mc/sec: 2642.64
//
Query:       gi|336255268|ref|YP_004598375.1|  [L=286]
Description: methylthioadenosine phosphorylase [Halopiger xanaduensis SH-6]
Scores for complete 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  155.5   0.2    1.5e-45  155.3   0.2    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 !  155.3   0.2   8.4e-50   1.5e-45       1     233 [.       2     243 ..       2     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 155.3 bits;  conditional E-value: 8.4e-50
                                       CEEEEESSH.HHHHHHHHH..EEEEEEEEEE.TTEEEEEEEETTEEE.EEEE--....SSHHHHHHHHHHHHHHHC- CS
                         PNP_UDP_1   1 kiaiivgsp.gevellaes..pleetpfgregrgfkfvtGtlkgkpv.vivstG....iGkpnaavvaeirllkefg 69 
                                       +i++i+gs+ +e+ +l ++  ++ +tp+g++  +  +++G+l gk+v ++ ++G      ++ a+++a+i +lk+ g
  gi|336255268|ref|YP_004598375.1|   2 TIGVIGGSGiYEALPLENTrkEEVSTPYGEP--SDAVTLGELAGKEVaFLPRHGedhqHAPTDASYRANIYALKSVG 76 
                                       59********888888888899*********..*********6666659*****99955555555************ PP

                                       -SEEEEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHH...CHHTTTTTE CS
                         PNP_UDP_1  70 vkaiiriGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallke...aaealgikv 143
                                       v+++i+++++G+l++dl++ ++v+pd++ + +  + + +++++++ + +++d+ ++p++++ l +   +a + g k+
  gi|336255268|ref|YP_004598375.1|  77 VDRVIATNAVGSLREDLPPRTLVVPDQIFDRTKHRSPSFFGDGMVVHMGFADP-YCPAMVDHLSNaaaEATDDGTKT 152
                                       ******************************88888888999998999999999.****9999999655555556999 PP

                                       EE.EEEEEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHH CS
                         PNP_UDP_1 144 hr.GvvatadgfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaq 219
                                       ++ G++++ +g++++t+ae++++r++g+d+v+M++ ++a lAre+++ +a++++v+d+ +   d+e t eev ++a+
  gi|336255268|ref|YP_004598375.1| 153 EEgGTYVCIEGPQYSTRAESEFYRDQGWDIVGMTAIPEAKLAREAELSYATVAGVTDYDVWKEDNEVTLEEVLANAE 229
                                       999******************************************************999999999999******** PP

                                       HHHHHHHHHHHHHH CS
                         PNP_UDP_1 220 eaaknaaalllall 233
                                       ++++++ +++++++
  gi|336255268|ref|YP_004598375.1| 230 ANQDAINEVVEHAI 243
                                       **********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2177.03
//
Query:       gi|336255269|ref|YP_004598376.1|  [L=488]
Description: MATE efflux family protein [Halopiger xanaduensis SH-6]
Scores for complete 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  184.4  35.6      4e-30  104.6   8.7    2.8  3  MatE             MatE
    6.4e-12   45.7  21.2    6.3e-11   42.5   4.4    4.4  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    8.9e-06   24.6   8.0    8.9e-06   24.6   8.0    2.4  2  MurJ             Lipid II flippase MurJ
  ------ inclusion threshold ------
        1.3    8.3   6.8       0.18   11.1   2.1    2.0  2  DUF4191          Domain of unknown function (DUF4191)
        1.5    7.0  20.4      0.058   11.7  10.2    2.4  2  DUF2070          Predicted membrane protein (DUF2070)


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 !   91.0  12.5   1.6e-29   5.9e-26       1     161 []      27     190 ..      27     190 .. 0.98
   2 ?   -1.9   0.4      0.64   2.3e+03      20      42 ..     195     217 ..     191     225 .. 0.60
   3 !  104.6   8.7   1.1e-33     4e-30       1     160 [.     255     420 ..     255     421 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 1.6e-29
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+++ +ll++ ++  dt+++g l+++a++a+s+a+++l+ll++++ g+ ta ++lv+q  Ga++  + + ++ q++ 
  gi|336255269|ref|YP_004598376.1|  27 PLVVIQLLQVAYNVGDTFWLGALSPDAVGAISLAFPLLFLLIAVGGGFTTAGAILVAQHTGAES-GEGGLIAGQTIS 102
                                       999*************************************************************.566999****** PP

                              MatE  78 lllllsliiallvllfseqilslftqdee....vlelakrylrililgipalalqlvlsgilrgagktkvplyisli 150
                                       ++ l+++ + ll+++ +e++ls++ +d++    +++la++yl+i +lg+p+ + ++v+ + +rg+g+t +p+ ++++
  gi|336255269|ref|YP_004598376.1| 103 FVSLVAIGLGLLGYIATEPMLSVLPADADtqaeIIPLAAEYLQIFFLGLPFVFGFFVFVSLMRGYGNTYAPMRVMFV 179
                                       ************************999999999******************************************** PP

                              MatE 151 slllniplnyl 161
                                       s+l+n+++++l
  gi|336255269|ref|YP_004598376.1| 180 SVLINVVIDPL 190
                                       *******9975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.64
                              MatE  20 vgrlgskalAavsialsilsllf 42 
                                       vg l+   +A++++a+ ++  + 
  gi|336255269|ref|YP_004598376.1| 195 VGPLPHLGMAGAALATAFSRAIA 217
                                       56666666677666666655443 PP

  == domain 3  score: 104.6 bits;  conditional E-value: 1.1e-33
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+ le+ +  l  + +t +v  +++  ++a++++++++sl f+++lg++ a++++vgq+lGa +++ra++a+  g  
  gi|336255269|ref|YP_004598376.1| 255 PTSLEQSMTALALTGMTAMVVTFPPPVVGAYGLGNRLISLAFLPALGMGQAMDSIVGQNLGADRPDRAERAVWLGAG 331
                                       77888888888888999************************************************************ PP

                              MatE  78 lllllsliiallvllfseqilslftqdee.....vlelakrylrililgipalalqlvlsgilrgagktkvplyisl 149
                                       +++++++++ l+++lf+e+++s+f + ee      ++++++yl+++++  +++++ +v++g++rgag+tk++l++++
  gi|336255269|ref|YP_004598376.1| 332 VVAAIMAVAGLFAYLFPEPFVSVFVTAEEegreaTIAYGSTYLQFAAFAFVFMGVMQVIQGAFRGAGNTKTALAFAI 408
                                       **************************9999*********************************************** PP

                              MatE 150 isl.llniplny 160
                                       ++l +++ip++y
  gi|336255269|ref|YP_004598376.1| 409 LGLwIVRIPVAY 420
                                       **********99 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 ?   -4.2   4.5       4.6   1.7e+04     112     112 ..      81      81 ..      28     119 .. 0.52
   2 !   42.5   4.4   1.8e-14   6.3e-11       1      78 [.     143     226 ..     143     238 .. 0.96
   3 ?   -1.8   2.5      0.83     3e+03     119     119 ..     320     320 ..     243     349 .. 0.53
   4 !   17.2   8.9   1.1e-06    0.0041       1      74 [.     373     449 ..     373     458 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 4.6
                   Polysacc_synt_C 112 l 112
                                       l
  gi|336255269|ref|YP_004598376.1|  81 L 81 
                                       1 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 1.8e-14
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvav 71 
                                       +L+i+ l+++f + + v+ s++ g g + ++++++++++l+++++  lli      p++g+ Gaa+at+++ +++++
  gi|336255269|ref|YP_004598376.1| 143 YLQIFFLGLPFVFGFFVFVSLMRGYGNTYAPMRVMFVSVLINVVIDPLLIfgvgplPHLGMAGAALATAFSRAIATA 219
                                       69************************************************9999999******************** PP

                   Polysacc_synt_C  72 lnlyalr 78 
                                       + +y+l+
  gi|336255269|ref|YP_004598376.1| 220 IGFYLLY 226
                                       *999886 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.83
                   Polysacc_synt_C 119 a 119
                                        
  gi|336255269|ref|YP_004598376.1| 320 D 320
                                       3 PP

  == domain 4  score: 17.2 bits;  conditional E-value: 1.1e-06
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalviga.lvklilnllli..plfgivGaaiatvlallvvavlnl 74 
                                       +L++ a++++f+++++v ++ + g g +k+al ++++g+ +v + + ++li    +g++G+  a vl+ +++a   +
  gi|336255269|ref|YP_004598376.1| 373 YLQFAAFAFVFMGVMQVIQGAFRGAGNTKTALAFAILGLwIVRIPVAYYLIfvAGWGTTGIWTAVVLGDVAGATAAV 449
                                       699*******************************99998469*********77899***********9988876665 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   8.0   2.5e-09   8.9e-06     279     405 ..      98     230 ..      81     277 .. 0.87
   2 ?    2.5   8.8     0.012        45     281     396 ..     329     448 ..     235     463 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.5e-09
                              MurJ 279 sqairltllllipvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPv 355
                                        q+i+++ l++i +  +  +  +p++s+l + +  ++e +  +ae L ++ lgL+++  + +++++   +++t +P+
  gi|336255269|ref|YP_004598376.1|  98 GQTISFVSLVAIGLGLLGYIATEPMLSVLPADADTQAEIIPLAAEYLQIFFLGLPFVFGFFVFVSLMRGYGNTYAPM 174
                                       58899999999999*************************************************************** PP

                              MurJ 356 kislislvlnills......llllpplgvvglalatslsaliglvllyvllrkrlk 405
                                        + ++s+ +n++++      +  lp lg++g alat+ s  i +++ ++ll+   +
  gi|336255269|ref|YP_004598376.1| 175 RVMFVSVLINVVIDpllifgVGPLPHLGMAGAALATAFSRAIATAIGFYLLYYTDV 230
                                       **************9986655567888999999**************999986655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.012
                              MurJ 281 airltllllipvsfgllvlskpivsllferGnFsee.dveataevLaayalgLipyalvklllrvfYAredtktPvk 356
                                       +  ++++++ ++  +  ++ +p vs++    + + e  +++ ++ L   a++ +++ ++++++ +f   ++tkt++ 
  gi|336255269|ref|YP_004598376.1| 329 GAGVVAAIMAVAGLFAYLFPEPFVSVFVTAEEEGREaTIAYGSTYLQFAAFAFVFMGVMQVIQGAFRGAGNTKTALA 405
                                       5555666666666667777777777776554444440456788899999999***********************99 PP

                              MurJ 357 islisl.vlnills..llllpplgvvglalatslsaliglvll 396
                                        +++ l ++ i ++  l+++  +g+ g+  a +l+ ++g++ +
  gi|336255269|ref|YP_004598376.1| 406 FAILGLwIVRIPVAyyLIFVAGWGTTGIWTAVVLGDVAGATAA 448
                                       9998762455544445999999******999999998887654 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2         1   3.6e+03      24      49 ..     324     349 ..     320     358 .. 0.64
   2 ?   11.1   2.1   5.1e-05      0.18       7      76 ..     386     459 ..     383     467 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1
                           DUF4191  24 kllwlllaaflvvvvvfvvlglllgs 49 
                                       + +wl ++++ ++++v+ ++ +l+ +
  gi|336255269|ref|YP_004598376.1| 324 RAVWLGAGVVAAIMAVAGLFAYLFPE 349
                                       56777777777777777777777654 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.1e-05
                           DUF4191   7 rlkqiaqvfkltrkedkkllwlllaaflvvvvvfvvlglllg....slilllilgillgllvalivltrraeka 76 
                                        ++ i  +f+   +++ +l +++l++++v + v+  l +++g    ++++ ++lg ++g+++a+ ++tr + k 
  gi|336255269|ref|YP_004598376.1| 386 VMQVIQGAFRGAGNTKTALAFAILGLWIVRIPVAYYLIFVAGwgttGIWTAVVLGDVAGATAAVAWFTRGTWKE 459
                                       566777889999999999999999999999999999999863335359********************976655 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  10.2   1.6e-05     0.058      23     122 ..     106     230 ..      95     282 .. 0.73
   2 ?   -1.5   4.8      0.16   5.7e+02      72     173 ..     263     385 ..     243     430 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
                           DUF2070  23 llalligllaflssk......................lfgillfglpalvaflltlpvlrilggrltykrslflall 77 
                                       l+a+ +gll +++ +                      + +i+++glp+++ f+++  ++r +g ++   r +f+++l
  gi|336255269|ref|YP_004598376.1| 106 LVAIGLGLLGYIATEpmlsvlpadadtqaeiiplaaeYLQIFFLGLPFVFGFFVFVSLMRGYGNTYAPMRVMFVSVL 182
                                       44444455555555556677777777788888888899*************************************** PP

                           DUF2070  78 telivviisllaillsall.qalvllalvls..lalvfalrllvlvav 122
                                       +++++  ++++++     l +a   la+++s  +a ++++ ll ++ v
  gi|336255269|ref|YP_004598376.1| 183 INVVIDPLLIFGVGPLPHLgMAGAALATAFSraIATAIGFYLLYYTDV 230
                                       *****9988888888887885555555555522566666666665555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.16
                           DUF2070  72 lflalltelivviisllaillsall.qalvllalvlslalvfalrllvlvavsdesllkav........lpaliqpl 139
                                       + lal+ ++ +v+++  +++ ++ l  +l++la++ +l +  a+  +v   ++ +++ +a         ++a+i+ +
  gi|336255269|ref|YP_004598376.1| 263 TALALTGMTAMVVTFPPPVVGAYGLgNRLISLAFLPALGMGQAMDSIVGQNLGADRPDRAEravwlgagVVAAIMAV 339
                                       45666666666666666666555556666666666665555555555555555555444433333222222222222 PP

                           DUF2070 140 lailllvly................fspesfllllllslifalavylfiv 173
                                       ++++                      + e ++ +  + l fa+++++f+ 
  gi|336255269|ref|YP_004598376.1| 340 AGLF----AylfpepfvsvfvtaeeEGREATIAYGSTYLQFAAFAFVFMG 385
                                       2222....122234444444444442222233333333333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); 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:                         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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 3629.42
//
Query:       gi|336255270|ref|YP_004598377.1|  [L=847]
Description: heavy metal translocating P-type ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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  127.0   1.3    1.2e-36  127.0   1.3    2.0  2  Hydrolase      haloacid dehalogenase-like hydrolase
    1.1e-35  122.8   4.0    1.1e-35  122.8   4.0    2.3  2  E1-E2_ATPase   E1-E2 ATPase
    2.1e-09   37.7   0.0      1e-08   35.5   0.0    2.2  2  HMA            Heavy-metal-associated domain
  ------ inclusion threshold ------
      0.018   14.9   0.2      0.031   14.1   0.2    1.3  1  Rad50_zn_hook  Rad50 zinc hook motif
      0.036   14.5   0.8       0.31   11.4   0.0    2.9  2  HAD            haloacid dehalogenase-like hydrolase
      0.055   13.2   0.0       0.28   10.9   0.1    1.9  2  Hydrolase_3    haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.4   4.2e+03       9      26 ..     374     391 ..     373     519 .. 0.60
   2 !  127.0   1.3   4.1e-40   1.2e-36       1     210 []     530     755 ..     530     755 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.4
                                       BTTTBCHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                         Hydrolase   9 dGTLttgepsvedvivsa 26 
                                       dG+L++g+  v +++v  
  gi|336255270|ref|YP_004598377.1| 374 DGVLVDGTCTVDEAVVTG 391
                                       666666665555544444 PP

  == domain 2  score: 127.0 bits;  conditional E-value: 4.1e-40
                                       SSEEEEESBTTTBCHHHHHHH..HHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH.................HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsved..vivsaalalaaaletgsehpigkalvaaakar.................sgalt 58 
                                       ++tvvfDk+GTLttge+ v +  + + + la aaale  + hp + a++aa+ +                  s ++ 
  gi|336255270|ref|YP_004598377.1| 530 VDTVVFDKTGTLTTGEMTVLEadAPDDL-LAAAAALERRASHPAATAIAAAFGDAggsdtdgdeavrpdggsSLSVR 605
                                       68**************888764455555.9999**********************6666555555555544444444 PP

                                       HHHHETTTE..........HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHT CS
                                       xxxxxxxxx..........xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                         Hydrolase  59 gfatfigrg..........ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkp 121
                                       +f+    +g          ++++g p+++++   + ++d++ + + a s+g   +++  ++ra++++ + d+  +++
  gi|336255270|ref|YP_004598377.1| 606 DFEN---HGtgvsgridgdRLLVGHPDLFRERgwELEDDFERRLEGARSAGNLPIVVgrNGRADGLVVVGDE--PRD 677
                                       4444...446699999*****************************************99*************..*** PP

                                       THHHHHHHHHHTTEEEEEEESSEHHHHH.HHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 122 eaaeavasLkaagievvlltgdnpetae.raanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVG 197
                                       + a++v sL+++gievv+ltgd+++  e    + +            + ++a++ pegk +a+r+L  ++  vamVG
  gi|336255270|ref|YP_004598377.1| 678 DWAKTVSSLHENGIEVVVLTGDERAATEfFSGHDAV-----------DRVFAGVPPEGKTEAVRRLEREG-CVAMVG 742
                                       ***********************9777733333344...........777****************6555.9***** PP

                                       SSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxx RF
                         Hydrolase 198 DgvnDaaalaaAg 210
                                       Dg nDa+ala+A+
  gi|336255270|ref|YP_004598377.1| 743 DGTNDAPALAEAD 755
                                       ************8 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.8   4.0   3.7e-39   1.1e-35       5     179 ..     338     512 ..     335     514 .. 0.95
   2 ?   -3.2   1.8       1.7   5.1e+03     144     175 ..     801     833 ..     786     835 .. 0.67

  Alignments for each domain:
  == domain 1  score: 122.8 bits;  conditional E-value: 3.7e-39
                                       -EEEEE.-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-E CS
                      E1-E2_ATPase   5 ptakvi.rdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsge 80 
                                       +ta+v+  dg ++++ +++l+p+D vl+++g+rvp+Dg++v+g+++vde+++TGEslpv ke gd+v++G+vv++g 
  gi|336255270|ref|YP_004598377.1| 338 DTARVLeSDGGTTDVSVADLEPDDRVLVREGERVPVDGVLVDGTCTVDEAVVTGESLPVAKESGDEVIGGSVVTDGA 414
                                       78999999********************************************************************* PP

                                       EEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHH CS
                      E1-E2_ATPase  81 akavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallva 157
                                       a++ V   + ++ +++++++v + +s+   +q+ +d l+  ++p+vl +a++v ++++l  +++a+a l al ++++
  gi|336255270|ref|YP_004598377.1| 415 AVVDVGP-ATESSIEHLTEVVWNLQSAAHGVQRHADALAVRVAPLVLGAAVAVGAVQFLQIGDPATAALAALLTIMV 490
                                       *888765.567789*************************************************************** PP

                                       HS-TTHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 158 aiPcaLplavplalalgarrla 179
                                       a P aL+la+p ++a+ +r ++
  gi|336255270|ref|YP_004598377.1| 491 ASPWALGLATPASVAANIRDAM 512
                                       ****************999876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.7
                                       TT.HHHHHHHHHHHHHS-TTHHHHHHHHHHHHH CS
                      E1-E2_ATPase 144 la.eallralallvaaiPcaLplavplalalga 175
                                       la   +++a+a+ vaa+    pl+++ a+a+ga
  gi|336255270|ref|YP_004598377.1| 801 LAlALVYNAIAIPVAALGLLNPLFATAAVAVGA 833
                                       332556668888888888877888888888876 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   3.4e-12     1e-08       2      62 .]      94     154 ..      93     154 .. 0.97
   2 ?   -2.8   0.0       3.1   9.2e+03      18      32 ..     522     536 ..     521     543 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.4e-12
                               HMA   2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62 
                                       +rv+gmh a C++  e+v ++ +gV ++  +++t  v V++d++ ++ ++++ a++ +gy+
  gi|336255270|ref|YP_004598377.1|  94 FRVDGMHSATCESFLESVAEKREGVADAAASYVTEAVRVDYDPDRISKSDLRGALSTLGYT 154
                                       8********************************************99999******99995 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.1
                               HMA  18 kvLselpgVesvkvd 32 
                                        v+++l +V++v++d
  gi|336255270|ref|YP_004598377.1| 522 TVFERLRDVDTVVFD 536
                                       6889999***99998 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 ?   14.1   0.2     1e-05     0.031      20      32 ..      11      24 ..       7      29 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                                      E.E-TTT--EE-HH CS
                     Rad50_zn_hook 20 g.cCPlCgReldee 32
                                      + +CPlCgR+l+e 
  gi|336255270|ref|YP_004598377.1| 11 EpRCPLCGRPLPET 24
                                      449********985 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.84   2.5e+03       1      24 [.     533     565 ..     533     589 .. 0.55
   2 ?   11.4   0.0   0.00011      0.31      89     187 ..     678     751 ..     669     752 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.84
                               HAD   1 alfDfDgTLldgdsle..........lllrfllr 24 
                                       ++fD  gTL++g++            + +   l+
  gi|336255270|ref|YP_004598377.1| 533 VVFDKTGTLTTGEMTVleadapddllAAAA-ALE 565
                                       688888999999666555555555532222.222 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00011
                               HAD  89 galellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaae 165
                                       ++ + ++  +++G++vvv++g  r  +e +    g+d+v +       ++ g           egk  a+r+ l++e
  gi|336255270|ref|YP_004598377.1| 678 DWAKTVSSLHENGIEVVVLTGDERAATEFFS---GHDAV-DR------VFAGV--------PPEGKTEAVRR-LERE 735
                                       5667777788*********************...63333.44......44444........22334455555.2223 PP

                               HAD 166 gegidleevvay.GDspsDlpll 187
                                       g       +va  GD+ +D p+l
  gi|336255270|ref|YP_004598377.1| 736 G-------CVAMvGDGTNDAPAL 751
                                       3.......66666******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 ?   -0.7   0.0      0.32   9.6e+02      21      41 ..     680     700 ..     671     709 .. 0.80
   2 ?   10.9   0.1   9.4e-05      0.28     206     251 ..     738     783 ..     731     787 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.32
                                       HHHHHHHHHTTSEEEEE-SS- CS
                       Hydrolase_3  21 keaikklkekgikvviATGRs 41 
                                       ++++  l+e+gi+vv+ TG +
  gi|336255270|ref|YP_004598377.1| 680 AKTVSSLHENGIEVVVLTGDE 700
                                       6788899*********99955 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.4e-05
                                       EEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHH CS
                       Hydrolase_3 206 viafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGV 251
                                       v+ +GDg ND + L  a+lg+ +g+++  +  a+d  +   + ++V
  gi|336255270|ref|YP_004598377.1| 738 VAMVGDGTNDAPALAEADLGISLGSGTALASDASDLAIVEDDLSAV 783
                                       5678***********************9999998887766655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (847 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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: 0.71u 0.25s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 5917.36
//
Query:       gi|336255271|ref|YP_004598378.1|  [L=231]
Description: phosphoribosyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-17   63.5   0.0    2.2e-17   63.0   0.0    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0024   17.3   0.0     0.0033   16.9   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase


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 !   63.0   0.0   2.5e-21   2.2e-17       6     154 ..      13     158 ..      11     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 2.5e-21
                                       TT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE- CS
                      Pribosyltran   6 lenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrll 82 
                                       ++++ i+  +++ + + +++ +++pdv+v+ argG+  +  l d L++     +k  ++ +++e++ +  +  + ++
  gi|336255271|ref|YP_004598378.1|  13 TNWEYIYGLCRDVSDDVRRD-EFEPDVIVALARGGWFAGRCLCDFLGLNDLTSLKMEHYVGTAEKTGEPTVRYPMPE 88 
                                       66667788899999999999.*************************97755555556666666666655666668** PP

                                       ---TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS......EEEEEEE-S CS
                      Pribosyltran  83 edpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfsls.pdnfvavvgf 154
                                       +++++k Vli+DDi dtGg++++a e + ++g+ evr+a+l    ++e+e+d+   ++ +l+  +++v +++f
  gi|336255271|ref|YP_004598378.1|  89 GSVEDKDVLIIDDIADTGGSIKRAYEYVDDRGAGEVRTATLQLLQTSEFEPDY---VGEQLEeWTWIVYPWNF 158
                                       ***************************************************66...88888988999998876 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.6e-07    0.0033     100     163 ..      72     135 ..      28     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.6e-07
                           UPRTase 100 qreeetlepveyynkLPkki.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlase 163
                                        + e+t ep   y  +P+   +++ vl++D +  TGgs+  a + + +rg+ge +   l++l+ +
  gi|336255271|ref|YP_004598378.1|  72 GTAEKTGEPTVRYP-MPEGSvEDKDVLIIDDIADTGGSIKRAYEYVDDRGAGEVRTATLQLLQTS 135
                                       34567899999996.676666*******************************9999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1760.63
//
Query:       gi|336255272|ref|YP_004598379.1|  [L=454]
Description: hypothetical protein Halxa_3895 [Halopiger xanaduensis SH-6]
Scores for 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   15.9   2.5      0.068   14.1   2.5    2.0  1  Trypsin_2      Trypsin-like peptidase domain
      0.023   13.9   0.1      0.052   12.7   0.1    1.5  2  Peptidase_S32  Equine arteritis virus serine endopeptidase S3
      0.037   13.8   0.0      0.062   13.1   0.0    1.3  1  Trypsin        Trypsin


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 ?   14.1   2.5   1.1e-05     0.068      13     150 .]     142     292 ..     127     292 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                         Trypsin_2  13 lTnaHvvdsadgaav.kaikkkveeagadgrevpakvvaadp.....elDlAllkvssderaglpplplgp...... 77 
                                       l n+Hv + ++ a   +ai + + e g d     + +v++ p     + D+A   v + +r +  + +l +      
  gi|336255272|ref|YP_004598379.1| 142 LSNNHVYARSNAADLgEAILQPSPEDGGDRDDEVGDLVGYVPvedgvRVDVAARSV-DPDRESASYFELEDawptgv 217
                                       88999998888888877777777778888888888888888766654558888888.33444444444433111111 PP

                         Trypsin_2  78 sealkgg...epvyvvGyplggeksgsvssGivsgvvesesaasgegesfl......qtdaatspGsSGGplfdsdG 145
                                       +++ +gg   e+v+  G   g+ +    ++G   +v+         + +++       +     pG SG+++f +dG
  gi|336255272|ref|YP_004598379.1| 218 RREDYGGlrgETVTKTGRTTGVSSADIEATGASVRVDF-------GEQGVVtlreqlVAGPMSEPGDSGSAVFLEDG 287
                                       11112213335666666655555544444444444444.......33333344443333334458************ PP

                         Trypsin_2 146 rvvGl 150
                                       ++vGl
  gi|336255272|ref|YP_004598379.1| 288 TLVGL 292
                                       ****8 PP

>> Peptidase_S32  Equine arteritis virus serine endopeptidase S32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.71   4.2e+03     177     218 ..     122     164 ..     112     166 .. 0.74
   2 ?   12.7   0.1   8.8e-06     0.052     204     230 ..     272     299 ..     235     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.71
                                       ---SEEEEEEETTEE.EEEEE-SS-EE----GGGTT-EEEETT CS
                     Peptidase_S32 177 qsttGraywltstgv.eegllgkevalcftkcGDsGspvvded 218
                                       ++  G   w   ++  + + l+++  ++ +++ D G ++++++
  gi|336255272|ref|YP_004598379.1| 122 EPDAGNGTWRNDVEAgDLVRLSNNHVYARSNAADLGEAILQPS 164
                                       5566777788777762445589999999999999999998875 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.8e-06
                                       ---GGGTT-EEEETTE.EEEE.EEEEET CS
                     Peptidase_S32 204 ftkcGDsGspvvdedgelvGv.htGsnk 230
                                        +++GDsGs+v  edg lvG+   Gs +
  gi|336255272|ref|YP_004598379.1| 272 MSEPGDSGSAVFLEDGTLVGLlFAGSAR 299
                                       689*****************63677765 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     1e-05     0.062     162     201 ..     264     298 ..     197     310 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                                       TTEEEEESTTSSSBCTTTTTTSEEEETTTEEEEEEEEESS CS
                           Trypsin 162 enmlcagakeggkdacqGDSGGPlvcsdgelvGivswgkg 201
                                       +++l ag       +++GDSG++++ +dg+lvG++++g  
  gi|336255272|ref|YP_004598379.1| 264 REQLVAGP-----MSEPGDSGSAVFLEDGTLVGLLFAGSA 298
                                       44555555.....799*******************99943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3524.47
//
Query:       gi|336255273|ref|YP_004598380.1|  [L=480]
Description: phosphomethylpyrimidine synthase [Halopiger xanaduensis SH-6]
Scores for 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-193  641.9   0.1   4.5e-193  641.7   0.1    1.0  1  ThiC_Rad_SAM   Radical SAM ThiC family
  ------ inclusion threshold ------
       0.15   11.8   0.2        0.3   10.9   0.2    1.5  1  zinc_ribbon_2  zinc-ribbon domain


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 !  641.7   0.1    5e-197  4.5e-193       1     417 [.       4     423 ..       4     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 641.7 bits;  conditional E-value: 5e-197
                      ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkek.pvaiGkglrtkvnaniGtsadasdiee 76 
                                       tq++aar+g++teeme+vae+en++pefvre+vaeG++vipan+nh+   +++iG+++ tkvnaniG+s+++sdie+
  gi|336255273|ref|YP_004598380.1|   4 TQIAAARNGTVTEEMERVAERENCDPEFVREQVAEGQAVIPANRNHDALdAMVIGREFATKVNANIGNSETTSDIET 80 
                                       89********************************************7666*************************** PP

                      ThiC_Rad_SAM  77 EveKlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqaleekekkveelteeellevieeqaedGvd 153
                                       E+eKl++a+++gadtvmdL tg ++deire+ +e+spvp+gtvp+Y+a++ ++++ ee+t++ lle+ie+qae+Gvd
  gi|336255273|ref|YP_004598380.1|  81 ELEKLHTAVHYGADTVMDLGTGANLDEIRETHVEHSPVPIGTVPLYEAVK-QAGSPEEITTDLLLEIIEKQAEQGVD 156
                                       *************************************************8.779*********************** PP

                      ThiC_Rad_SAM 154 fltiHagvtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaD 230
                                       ++tiHag+  e+l+l++  +R tgivSrgGs++a+wm+a++++npl++ +de++ei++e+dvt+Slgd+lRpGs+aD
  gi|336255273|ref|YP_004598380.1| 157 YMTIHAGILAEHLPLTD--GRKTGIVSRGGSIMASWMEARGEQNPLFQVYDEICEIFAEHDVTFSLGDSLRPGSLAD 231
                                       ****************9..********************************************************** PP

                      ThiC_Rad_SAM 231 atdeaqlaelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsai 307
                                       a deaq+ael +lgel++ra+e++vqvmveGPGHvp++++++nv+ q+++c++aPfyvlGplvtDiapgYDhitsai
  gi|336255273|ref|YP_004598380.1| 232 ACDEAQYAELDTLGELTRRAWEHDVQVMVEGPGHVPMHKVAENVERQQEVCDGAPFYVLGPLVTDIAPGYDHITSAI 308
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 308 GaalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfelal 384
                                       Gaa+aa+aGa++lCyvtp+EHlglP+eedv++G+ a++iaaha+d+  ++++ar++d+als+aR+++dw++qf+lal
  gi|336255273|ref|YP_004598380.1| 309 GAAMAAQAGAAMLCYVTPKEHLGLPEEEDVRDGLAAYRIAAHAGDVGSERPGARDWDDALSEARYDFDWREQFRLAL 385
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 385 dpekareireeklpe....eeeaCsmCgek.Cavkive 417
                                       dp++ar++++++lpe    e+++CsmCg   C+++i +
  gi|336255273|ref|YP_004598380.1| 386 DPDRARDYHDQTLPEdnykEARFCSMCGAEfCSMRIDQ 423
                                       *************99888899*******988****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 ?   10.9   0.2   3.3e-05       0.3       9      22 ..     402     415 ..     400     416 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.3e-05
                     zinc_ribbon_2   9 lqdnakFCpyCGtp 22 
                                       + ++a+FC+ CG++
  gi|336255273|ref|YP_004598380.1| 402 NYKEARFCSMCGAE 415
                                       6689********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3599.95
//
Query:       gi|336255274|ref|YP_004598381.1|  [L=221]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-15   56.9   0.6    2.4e-15   56.1   0.6    1.4  1  HTH_10    HTH DNA binding domain


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 !   56.1   0.6   1.3e-19   2.4e-15       1      52 [.     160     211 ..     160     212 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1.3e-19
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT +q++++++A+e GY++ PR+++l+++A +l  ++st+s++Lr+ae+ l+
  gi|336255274|ref|YP_004598381.1| 160 LTARQYRAVRIALERGYYEIPRETSLAAIAAALECTESTASDILRRAERELV 211
                                       9************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1750.13
//
Query:       gi|336255275|ref|YP_004598382.1|  [L=247]
Description: abortive infection protein [Halopiger xanaduensis SH-6]
Scores for complete 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   41.8  12.4    2.6e-10   40.5  12.4    1.9  1  CPBP      CPBP intramembrane metalloprotease


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 !   40.5  12.4   1.4e-14   2.6e-10       6      91 ..     148     236 ..      25     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.4e-14
                                       HHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-.HHHHHHHHHHHHHCSGGG.HHH.HHHHHHHHHHHHHHHHHTT-H CS
                              CPBP   6 lvfllalllapllEEllfRglllqllqergss.tlailissilFglaHlpn.gps.vllaalaGlvlgylylktgsl 79 
                                        v++ ++l+apl+EEllfRg l+ +l  rg+s ++a + s ++F+ +H+   g++ v+++a+ +++ ++l+l+  +l
  gi|336255275|ref|YP_004598382.1| 148 GVAFGVVLVAPLVEELLFRGALVGALLGRGWSlLTASAGSIVVFAGYHVFAlGVAgVAAIAAWSVFPTVLRLRFDNL 224
                                       566779**************************999**************9987779********************* PP

                                       HHHHHHHHHHHH CS
                              CPBP  80 laaillHallnl 91 
                                         a+llH+++n+
  gi|336255275|ref|YP_004598382.1| 225 TGAWLLHLCNNI 236
                                       **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.17s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 2116.44
//
Query:       gi|336255276|ref|YP_004598383.1|  [L=301]
Description: phenazine biosynthesis protein PhzF family [Halopiger xanaduensis SH-6]
Scores for 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-67  227.5   0.0    2.4e-67  227.3   0.0    1.0  1  PhzC-PhzF     Phenazine biosynthesis-like protein
    0.00049   19.3   0.0    0.00073   18.7   0.0    1.2  1  Pro_racemase  Proline racemase


Domain annotation for each model (and alignments):
>> PhzC-PhzF  Phenazine biosynthesis-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.3   0.0   2.7e-71   2.4e-67       1     283 []       9     286 ..       9     286 .. 0.95

  Alignments for each domain:
  == domain 1  score: 227.3 bits;  conditional E-value: 2.7e-71
                                       EEET-SSTTSSEEEEEEESTTCS-HHHHHHHHHHHTSSEEEEEE--SSTTSSEEEEEE-SSSEES--HHHHHHHHHH CS
                         PhzC-PhzF   1 vdaFtespfkGNpaaVvldadelddeelqsiAaelnlseTaFllkpsdekarfrlRyFTPvaEvdlcGHatlasaha 77 
                                       vdaFt++p+ GNpa+Vv dad+l+d+++qsiAae+ +seTaFl  ++d +a+ r+ yFTP++EvdlcGHat++s   
  gi|336255276|ref|YP_004598383.1|   9 VDAFTDEPLSGNPAGVVPDADGLSDDQMQSIAAEMAVSETAFLRSSDDPEADRRVSYFTPTQEVDLCGHATIGSFAH 85 
                                       8**************************************************************************** PP

                                       HHHHCT-S-SCEEEEEETTEEEEE.EEEEETCEECCEEEEE-SEEEEEE-HHHHHHHHHHCCTSGG...-TTS-BEE CS
                         PhzC-PhzF  78 laekglvasaetveletkaGilpvkslkekddgeellielkfPvikteevssedlallakllklaa...qkalpiav 151
                                       l  +gl  +  t  let++G l +    e  ++ ++ + ++ P i +++v++ ++a+++++++ a     +++p+av
  gi|336255276|ref|YP_004598383.1|  86 LHDEGL--EPGTTALETNVGVLEI----EVGEDGTVWMTQDEPRIREVDVGYDRVADALGVSQAALegaSDDIPLAV 156
                                       *****7..699************9....57888899999*******************99999998888889***** PP

                                       EESSSEEEEEEBSTCCHHHH----H...HHHHHHCT-EEEEEEEETTTSSCCEEEEEEEEGGGTEEEESS-HHHHHH CS
                         PhzC-PhzF 152 kstglekvivplsseeavaelspdl...aeeikkcpkkgvivtaaaeagskkdfhsRmFaPklGivEDpvtGsAsga 225
                                        stgl  +ivp+   +++ +++pd+   +e +  ++  g+  +++ + g ++ +h+RmFaP  G+ EDpvtG+Asga
  gi|336255276|ref|YP_004598383.1| 157 SSTGLPFLIVPITYLSDLGDADPDMnavEELADSVDATGIYLFTFDALGRDSTLHGRMFAPGAGVPEDPVTGTASGA 233
                                       *************************8877888889999*************************************** PP

                                       HHHHHHHCC-S..SSEEEEEEEE-GGGT--EEEEEEEE.E-TTCEEEEEEEE-EEEEEEE CS
                         PhzC-PhzF 226 Laaylseklnl..eesakikieqgqalgrsgtlevevevkvdkekervkvtGkAvtvmeg 283
                                        aayl++ + +  +  +++ +eqg+ + r+g ++v++e       + v+v G++vt  +g
  gi|336255276|ref|YP_004598383.1| 234 VAAYLDRFGAFddDFPEELRLEQGHYVDRPGLVRVRLE-------NGVRVGGRGVTALDG 286
                                       *********996556799****************8886.......369999999998765 PP

>> Pro_racemase  Proline racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.2e-08   0.00073      55     127 ..      47     114 ..      42     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.2e-08
                                       EEEEEE--SSTTSSEEEEEEESSSB-SSTHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTEEEEEEEECTST CS
                      Pro_racemase  55 sgallvppkepdadlgvifletsgylpmcGsntigvvtvlletGlvevqepetklsletpaGlvevtaecrdg 127
                                        +a+l  + +p+ad  v ++ +++    cG++tig  + l ++Gl e+ +      let +G++e+++ ++++
  gi|336255276|ref|YP_004598383.1|  47 ETAFLRSSDDPEADRRVSYFTPTQEVDLCGHATIGSFAHLHDEGL-EPGTT----ALETNVGVLEIEVGEDGT 114
                                       679999**************************************8.44444....489999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2383.18
//
Query:       gi|336255277|ref|YP_004598384.1|  [L=788]
Description: phosphoenolpyruvate synthase [Halopiger xanaduensis SH-6]
Scores for 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-108  360.5   0.0   1.3e-107  359.9   0.0    1.3  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    3.7e-82  275.7   0.1    5.8e-82  275.1   0.1    1.2  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    1.4e-27   95.2   2.7    3.6e-27   93.9   2.7    1.8  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
     0.0025   16.5   0.0      0.032   12.9   0.0    2.1  2  RdRP             RNA dependent RNA polymerase
  ------ inclusion threshold ------
      0.044   12.6   0.1       0.17   10.7   0.1    2.0  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
       0.06   12.8   0.8       0.18   11.3   0.1    2.3  2  UBM              Ubiquitin binding region


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 !  359.9   0.0  4.4e-111  1.3e-107       3     320 ..      22     326 ..      20     333 .. 0.96

  Alignments for each domain:
  == domain 1  score: 359.9 bits;  conditional E-value: 4.4e-111
                            PPDK_N   3 lvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelPe 79 
                                        vGGKga+L+el + ag+pvP gf++ta ++r+f+ee+g++e++ ++++ +dvdd ++l++a+++++elil++++P+
  gi|336255277|ref|YP_004598384.1|  22 RVGGKGASLGEL-TGAGLPVPSGFVVTAGTYRSFIEEAGIDEELFAAVD-VDVDDSSALAEAANRAQELILETPFPD 96 
                                       7***********.77*******************************999.8************************** PP

                            PPDK_N  80 eleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYrk 156
                                       +l+e+i + y+e+g+     e  vaVRSSataEDlp+asfaGqq+t+Lnv  e ++l+ +++++aSlf++rAi+Yr+
  gi|336255277|ref|YP_004598384.1|  97 DLREEILASYREVGD----GEAFVAVRSSATAEDLPDASFAGQQETFLNVT-EADLLDRVRECWASLFTQRAIYYRQ 168
                                       *************86....568****************************6.888********************** PP

                            PPDK_N 157 ekgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilekk 233
                                       e+g+dh+ v++avvvq+mv+++  +sGV+f+ +p+tG + +++i+a++GlGeaVV+G+v+pd++ v +++r+  + +
  gi|336255277|ref|YP_004598384.1| 169 EQGFDHSAVNIAVVVQQMVDAE--KSGVMFTSHPSTG-DPTMIIEAAWGLGEAVVSGAVSPDNYAVTRDDRS-ADVT 241
                                       **********************..*************.9****************************99887.79** PP

                            PPDK_N 234 igekeikivydekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaideeegklyllQaRpet 310
                                       ++ek+++ v de++ +t+e +vp+e++++ ++ dee+++L ++++++e+hyg+p+d+E+ai   eg++y+lQ+Rp+t
  gi|336255277|ref|YP_004598384.1| 242 VAEKKVMHVKDEETGETVERPVPDEKQTARVIGDEEIDALVDLGERVEDHYGEPQDVEWAIV--EGDVYMLQSRPIT 316
                                       ************9988**********************************************..************* PP

                            PPDK_N 311 rtsekkekka 320
                                       + ++++ ++a
  gi|336255277|ref|YP_004598384.1| 317 TIDDSSGEAA 326
                                       *998877665 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 !  275.1   0.1   1.9e-85   5.8e-82      11     293 ..     489     779 ..     481     780 .. 0.94

  Alignments for each domain:
  == domain 1  score: 275.1 bits;  conditional E-value: 1.9e-85
                                       CCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHH...........HHHHHHHHHHHTT CS
                   PEP-utilizers_C  11 lavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteee...........qaeaykkvleamn 76 
                                       ++++k++++++v +N++ pe+ae+a+++ga+G+GLlR E+++++ +++p+              +++ +++v++ ++
  gi|336255277|ref|YP_004598384.1| 489 QSPVKPMTATEVKVNVSIPEAAERAAATGADGVGLLRMEHMILSLNQTPAKFIaengedayineLVQGIRHVADEFY 565
                                       56789999************************************98855432235999******************* PP

                                       TSEEEEEXXXSSCC..GGSGGCHHHH.XSXGGGSSXTHHHHCCSHHHHHHHHHHHHHHCCCC..EEEEEESSXXSHH CS
                   PEP-utilizers_C  77 grpvvvRtlDiggd..kelpelkeepeevNPmlGfRgirlglsepelfetqlrAllrasaag..kleimlPmvasve 149
                                       +rpv  RtlD+++d  ++l+ +++ep+e NPmlG+Rgir++l++p++f  +l A+ r  ++g  ++e+m+P+v+ +e
  gi|336255277|ref|YP_004598384.1| 566 PRPVRTRTLDAPTDefRQLEGGEDEPQEHNPMLGYRGIRRSLDRPDVFAHELEAFRRLYEMGydNVEMMFPLVNDAE 642
                                       **************9999******************************************6666************* PP

                                       HHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTT.SSEEEEXHHHHHHHHHTXXCCCHCHHHH CS
                   PEP-utilizers_C 150 eleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklake.vdFfSiGtNDLtQytlavdRdneevakl 225
                                       ++ + k++++e+        +   +k k+G+MiE+p+aal ++++a+  +dF S+GtNDLtQytlavdR+ne+va  
  gi|336255277|ref|YP_004598384.1| 643 DVYRVKQLMQEAG-------IDP-DKRKWGVMIETPAAALSVEEMAETgIDFASFGTNDLTQYTLAVDRNNEHVADR 711
                                       ***********93.......333.3559*******************99**************************** PP

                                       SXTTTCHHCCCHHHHHHHHHHCCXEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
                   PEP-utilizers_C 226 ydplepavlrlikevikaaeekglkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqve 293
                                       +d+l+p+vlrli+ vi++++e+++ ++iCG+++++p++v++lv+ G+ ++S++ ++v  +++++++ve
  gi|336255277|ref|YP_004598384.1| 712 FDELHPSVLRLIGDVIETCREHDVATSICGQAGSKPEMVQFLVNEGVSSISANIDAVRDVQHEVKRVE 779
                                       *************************************************************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 !   93.9   2.7   1.2e-30   3.6e-27       1      73 []     394     466 ..     394     466 .. 0.97

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 1.2e-30
                                       G--S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers   1 kleegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                       k++eg+++v+e+t p++++++++a+Gi+t++GGmtSHaAiv+relg+PaVvg+++at+ l++g+++t+Dg++G
  gi|336255277|ref|YP_004598384.1| 394 KVKEGDVIVTEMTMPDMVPAMKRASGIITDEGGMTSHAAIVSRELGVPAVVGTTNATSILEDGQVVTLDGDKG 466
                                       5799*****************************************************999999********99 PP

>> RdRP  RNA dependent RNA polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   1.1e-05     0.032     483     543 ..     124     198 ..      85     249 .. 0.81
   2 ?    1.2   0.0     0.037   1.1e+02     441     508 ..     461     530 ..     460     552 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                              RdRP 483 vedi........adffveymksdvlGlisnahlaiadq......eegiddpkclkLaelhskaVDypKtGipvdk 543
                                        ed+        ++ f+++++ d l ++ + +  + +q      +e+ +d  ++++a  + + VD++K+G+ ++ 
  gi|336255277|ref|YP_004598384.1| 124 AEDLpdasfagqQETFLNVTEADLLDRVRECWASLFTQraiyyrQEQGFDHSAVNIAVVVQQMVDAEKSGVMFTS 198
                                       44444555566688999999************9555555999998888999**********************92 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.037
                              RdRP 441 lDGDkywViwdpelefapakpsneepadyeeakpkeldrevtvedi........adffveymksdvlGlisnahla 508
                                       lDGDk  V   +++e  p++++ e p ++ +  p++  +++t +++        a+ ++  +  d +Gl+  +h++
  gi|336255277|ref|YP_004598384.1| 461 LDGDKGQVLEGQNVE--PEEET-E-PVEEVR--PQSPVKPMTATEVkvnvsipeAAERAAATGADGVGLLRMEHMI 530
                                       8*************8..55333.3.333331..1222222222222112222443333344466777777777774 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   5.8e-05      0.17     235     312 ..     391     471 ..     377     489 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.8e-05
                                       HHHH-.TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHH....CT--EEESSSS-S-THHHHTTSEEE-TT-H CS
                       Epimerase_2 235 eleel.envtlieplgyldflsllknaklvltdSgGiqeEaps....lgvpvvnlReeteRpegveagtnvlvgtdk 306
                                        l+++ e   +++ +   d++ ++k+a  ++td gG+   a++    lgvp+v+   +t+    +e g++v  + dk
  gi|336255277|ref|YP_004598384.1| 391 DLDKVkEGDVIVTEMTMPDMVPAMKRASGIITDEGGMTSHAAIvsreLGVPAVVG--TTNATSILEDGQVVTLDGDK 465
                                       445554466788999***********************99998777789999999..88888888888888899888 PP

                                       HHHHHH CS
                       Epimerase_2 307 eeIvaa 312
                                        ++++ 
  gi|336255277|ref|YP_004598384.1| 466 GQVLEG 471
                                       888775 PP

>> UBM  Ubiquitin binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.3   3.8e+03       4      17 ..      55      68 ..      53      71 .. 0.78
   2 ?   11.3   0.1   6.2e-05      0.18      17      31 ..      94     108 ..      94     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                               UBM  4 pppegiDpsFLaaL 17
                                      +++ giD + +aa 
  gi|336255277|ref|YP_004598384.1| 55 IEEAGIDEELFAAV 68
                                      56778***999995 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.2e-05
                               UBM  17 LPpdLReEVLaqqde 31 
                                       +P+dLReE+La+++e
  gi|336255277|ref|YP_004598384.1|  94 FPDDLREEILASYRE 108
                                       6**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (788 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); 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:                         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 0.24s 00:00:00.86 Elapsed: 00:00:00.39
# Mc/sec: 6029.76
//
Query:       gi|336255278|ref|YP_004598385.1|  [L=283]
Description: Glyoxalase/bleomycin resistance protein/dioxygenase [Halopiger xanaduensis SH-6]
Scores for 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-16   59.2   0.4    3.5e-08   33.7   0.0    2.4  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    3.4e-08   34.2   6.6    0.00067   20.4   0.2    2.4  2  Glyoxalase_6  Glyoxalase-like domain
     0.0067   16.6   7.3        1.3    9.1   0.1    3.4  3  Glyoxalase_3  Glyoxalase-like domain
  ------ inclusion threshold ------
      0.014   15.7   0.1        6.3    7.1   0.0    3.3  2  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
      0.091   13.5   0.0       0.25   12.1   0.0    1.8  2  CppA_C        CppA C-terminal


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 !   33.7   0.0   9.7e-12   3.5e-08       2     128 .]      15     126 ..      14     126 .. 0.95
   2 !   23.4   0.3   1.5e-08   5.3e-05       3     127 ..     172     277 ..     170     278 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 9.7e-12
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhva 78 
                                       ++ +al+v+ le  ++FY++v+G+ ++++++        + a++ +++  + ++ +    +++++    e++  h a
  gi|336255278|ref|YP_004598385.1|  15 LGRTALRVSALEDLVEFYRDVVGLSVLRRDE--------TTAVLGVDDAPLLVLERDENAPERARS---ETGLYHNA 80 
                                       67789**************************........99**************99999999999...4489**** PP

                                       EEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  79 fialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       f++ +   +g+al r++++  + ++  ++ + +aly     Dp G+ +ei
  gi|336255278|ref|YP_004598385.1|  81 FRVPSRAALGAALARIRDRW-RLDGAADHLVSEALY---LSDPAGNGVEI 126
                                       ******************98.***************...*******9997 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.5e-08
                                       EEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC.TSEEEE CS
                        Glyoxalase   3 dhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkiee.tvhhva 78 
                                       +hv l v+ le+ ++FY+++LGf++  +          ++ f+ a+g h+ +  n      ++ +    + + + + 
  gi|336255278|ref|YP_004598385.1| 172 GHVHLEVSSLEAFAEFYADALGFDVRADLS--------GALFVAADGYHHHVGANTWNRRTEPAE----GrGLAWFE 236
                                       7999**************************........888888888888775543333333333....12367788 PP

                                       EEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEE CS
                        Glyoxalase  79 fialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGille 127
                                       +++ d  d+++  +rl+++g k  +e      ++++   + DpdGi+l 
  gi|336255278|ref|YP_004598385.1| 237 VVVPDSRDFEALEERLSDRG-KALTET-----EDGF--AVADPDGIELR 277
                                       899*****************.333332.....3333..28999999986 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.2   1.9e-07   0.00067       3     104 ..      19     124 ..      17     127 .. 0.65
   2 !   16.2   1.7   3.9e-06     0.014       4     103 ..     176     275 ..     173     278 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.9e-07
                      Glyoxalase_6   3 vldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe.......paknr...vHldlavedl 69 
                                       +l ++  + l++F++++ g++v r++   e  ++ g    d a+ll+ +++e       +   +    H  ++v+++
  gi|336255278|ref|YP_004598385.1|  19 ALRVSALEDLVEFYRDVVGLSVLRRD---ETTAVLG---VDDAPLLVLERDEnaperarS---EtglYHNAFRVPSR 86 
                                       677788999***************99...3334444...466666666666647443322...03336777766544 PP

                      Glyoxalase_6  70 daevarlvalGArvlreprdgthgr..........vlaDPeGneF 104
                                               alGA   r  + ++ ++           l DP+Gn  
  gi|336255278|ref|YP_004598385.1|  87 -------AALGAALARIRDRWRLDGaadhlvsealYLSDPAGNGV 124
                                       .......4556655555555444335558889999*******976 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.9e-06
                      Glyoxalase_6   4 ldaadpaalaaFwaaalgweveree..aaledpegvgpaaedaatllfqrvpepaknrvHldlavedld...aevar 75 
                                       l ++  +a a+F+a+alg++v+++   a  + ++g +  + +a t   ++ p +++    +++ v+d +   a  +r
  gi|336255278|ref|YP_004598385.1| 176 LEVSSLEAFAEFYADALGFDVRADLsgALFVAADGYHH-HVGANTWNRRTEPAEGRGLAWFEVVVPDSRdfeALEER 251
                                       6778899******************7633333333333.22333333333333555558899988555445266666 PP

                      Glyoxalase_6  76 lvalGArvlreprdgthgrvlaDPeGne 103
                                       l + G + l+e +dg     +aDP+G e
  gi|336255278|ref|YP_004598385.1| 252 LSDRG-KALTETEDGF---AVADPDGIE 275
                                       66665.6666667765...89****987 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.5     0.039   1.4e+02      70     112 ..      68     105 ..      45     166 .. 0.71
   2 !    9.1   0.1   0.00036       1.3       3      36 ..     173     216 ..     171     225 .. 0.82
   3 !    7.9   0.3   0.00084         3      74     120 ..     230     282 ..     214     283 .] 0.77

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.039
                      Glyoxalase_3  70 drlakgeglhtlalrtddidataarlraaGvdeagrrvrpdgg 112
                                       +r+ ++ gl + a+r+++ +a+ a+l++        r+r+dg 
  gi|336255278|ref|YP_004598385.1|  68 ERARSETGLYHNAFRVPSRAALGAALARIR-----DRWRLDGA 105
                                       3566789***************99999877.....78888883 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00036
                      Glyoxalase_3   3 HvvlavpdleeaaarfarrlGftvt..........pggehpglg 36 
                                       Hv l v++le+ a+ +a++lGf v           + g h++ g
  gi|336255278|ref|YP_004598385.1| 173 HVHLEVSSLEAFAEFYADALGFDVRadlsgalfvaADGYHHHVG 216
                                       9***********************99999999999666666554 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00084
                      Glyoxalase_3  74 kgeglhtlal.rtddidataarlraaGvd....eagrrv.rpdggdlrwrllf 120
                                       +g  + ++++ +++d +a+++rl ++G +    e+g  v +pdg +lr+r++ 
  gi|336255278|ref|YP_004598385.1| 230 RGLAWFEVVVpDSRDFEALEERLSDRGKAltetEDGFAVaDPDGIELRFRTAT 282
                                       46667777766899*************77999855555559*********986 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0018       6.3      52      88 ..      59      98 ..      18     102 .. 0.71
   2 ?    4.6   0.1     0.011        39       2      28 ..     173     199 ..     172     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0018
                                      EEEESSTT-THHHTS-EEEEEEEEES...-HHHHHHHHCT CS
                      Glyoxalase_4 52 Lieplegpeflaehgeglhhlaywvd...dldaavarlee 88
                                      + e +e++   a+ ++gl+h a++v     l aa+ar ++
  gi|336255278|ref|YP_004598385.1| 59 VLERDENAPERARSETGLYHNAFRVPsraALGAALARIRD 98
                                      4566667777788************723347777777665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                                       EEEEE-S-HHHHHHHHHH.TT-EESS- CS
                      Glyoxalase_4   2 QigivVeDleaavarfsallGvgpwqr 28 
                                       ++ + V +lea +++++++lG++++ +
  gi|336255278|ref|YP_004598385.1| 173 HVHLEVSSLEAFAEFYADALGFDVRAD 199
                                       889999999999999999999877544 PP

>> CppA_C  CppA C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         5   1.8e+04      16      30 ..      25      39 ..      19      43 .. 0.65
   2 ?   12.1   0.0   6.9e-05      0.25       6     103 .]     171     278 ..     167     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5
                            CppA_C 16 keeseafyekllglk 30
                                       e   +fy++++gl 
  gi|336255278|ref|YP_004598385.1| 25 LEDLVEFYRDVVGLS 39
                                      555567888887765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6.9e-05
                            CppA_C   6 veslelnvadkeeseafyekllglklp........le....ldfseaegedLavetdevwdLeiLkfkvdkdfdlaq 70 
                                       v +++l+v + e  ++fy + lg  ++        +      + + a+  +  +e+ e  +L   +++v ++ d+++
  gi|336255278|ref|YP_004598385.1| 171 VGHVHLEVSSLEAFAEFYADALGFDVRadlsgalfVAadgyHHHVGANTWNRRTEPAEGRGLAWFEVVVPDSRDFEA 247
                                       667888888888888888888888888665555441144545667777778888999999***************** PP

                            CppA_C  71 LkekleekgekvyldkkekvlvlsdpsqiElWf 103
                                       L+e+l++      l + e  +++ dp++iEl f
  gi|336255278|ref|YP_004598385.1| 248 LEERLSD--RGKALTETEDGFAVADPDGIELRF 278
                                       *******..55568899999**********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2147.36
//
Query:       gi|336255279|ref|YP_004598386.1|  [L=430]
Description: family 2 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for 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-22   79.7   1.1    4.2e-22   79.2   1.1    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.7e-18   67.0   0.0    2.2e-18   66.6   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    1.3e-14   54.6   0.8    2.7e-14   53.6   0.8    1.5  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    5.1e-11   42.3   0.0    7.9e-11   41.7   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> 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 !   79.2   1.1   9.4e-26   4.2e-22       1     229 [.      87     304 ..      87     305 .. 0.91

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 9.4e-26
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77 
                                       pr l+ +Vp+++ ++v    +esl+a++y ++evv+v++++d++t+e+a+elaa+++ v   v++n   ++s++k+ 
  gi|336255279|ref|YP_004598386.1|  87 PR-LTAVVPVYRDHAVMDVSVESLAASAYENLEVVIVAEPNDEATVERARELAAEYDPV--EVLIN---GESGSKAG 157
                                       66.99***************************************************765..66655...6689**** PP

                   Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarra 154
                                       a+n a+r  +sd+ +++D+D  + P++l+ +  ++  ++v+++++++  +    + +++++ +  + ++   ++ + 
  gi|336255279|ref|YP_004598386.1| 158 AINYAVRERDSDHFAVFDADEWIAPEFLPTAMGQL-LEGVDVFQGRRVPRPTGPVETVAYCER--IVFHASYKMVEL 231
                                       ******************************99998.89******9987777776666667744..7777788999** PP

                   Glyco_tranf_2_3 155 lgvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvy 229
                                       +g++  + s ++++re  ++ +g d   +lt+D+  +  + r+g ++  + + + + + p +l +++ qr Rw +
  gi|336255279|ref|YP_004598386.1| 232 FGFTNCRSSSTAFTREAIERVGGYDD--VLTEDLAFAHACYREGLDVRQARHCTNTMEAPHTLRDLWGQRKRWRV 304
                                       ***999***************99998..*************************77777899************65 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 !   66.6   0.0     5e-22   2.2e-18       2     169 ..      91     252 ..      90     253 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 5e-22
                                       EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH- CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraa 78 
                                       +v+p+y   +    ++esl+a   y+++e+++v     + tve ++ela+e+++v v+ + e   kaga+n ++r+ 
  gi|336255279|ref|YP_004598386.1|  91 AVVPVYRDHAVMDVSVESLAAS-AYENLEVVIVAEPNDEATVERARELAAEYDPVEVLINGESGSKAGAINYAVRER 166
                                       79********************.****************************************************** PP

                                       -SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCS CS
                   Glycos_transf_2  79 tgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfei 155
                                       ++d ++++DaD +++p++l+  ++ l + g+dv+ g r+ ++ ++ e         + ++++  +k  +  + + + 
  gi|336255279|ref|YP_004598386.1| 167 DSDHFAVFDADEWIAPEFLPTAMGQLLE-GVDVFQGRRVPRPTGPVETVAY----CERIVFHASYKMVELFGFTNCR 238
                                       ****************************.************9999999876....5788888888888888888888 PP

                                       TCCCEEEEHHHHHC CS
                   Glycos_transf_2 156 gsaallrrealeel 169
                                       +s +++ rea+e++
  gi|336255279|ref|YP_004598386.1| 239 SSSTAFTREAIERV 252
                                       88888888888876 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 !   53.6   0.8   5.9e-18   2.7e-14       3     186 ..     172     364 ..     170     379 .. 0.70

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 5.9e-18
                   Glyco_trans_2_3   3 lllDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgafl 79 
                                       ++ DaD  + p++l  +   l +  v++ qg  ++++ +++ +  ++ ++   h++   + e + +++ +  s +++
  gi|336255279|ref|YP_004598386.1| 172 AVFDADEWIAPEFLPTAMGQLLE-GVDVFQGRRVPRPTGPVETVAYCERI-VFHASY-KMVELF-GFTNCRSSSTAF 244
                                       688*********99999988877.8***********88777766666444.355544.443566.556888999*** PP

                   Glyco_trans_2_3  80 rrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkek.spltlraalrQrkRwayGc...el...... 146
                                       +r+a+++vgg+d   + ++ED+ ++  ++r+G++vr +  +++++   p tlr+ + QrkRw  G    +       
  gi|336255279|ref|YP_004598386.1| 245 TREAIERVGGYD---DVLTEDLAFAHACYREGLDVRQAR-HCTNTMeAPHTLRDLWGQRKRWRVGQvevLHatlvdf 317
                                       ************...9**********************9.7787764888***************765411344455 PP

                   Glyco_trans_2_3 147 eklillvrllgylgsllwsalplhlallllfslla.......lalvl 186
                                        + ++  r l   g+ + s + ++++l+l+++ll         a+++
  gi|336255279|ref|YP_004598386.1| 318 LRGRAGRRGLISVGRMCSSLFGCLVTLVLVSKLLLllvlgveSAFLV 364
                                       44444444455555555566666666666665555333333322222 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 !   41.7   0.0   1.8e-14   7.9e-11      16     172 ..     153     303 ..     143     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1.8e-14
                   Glyco_transf_21  16 npKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVts..lpvgsdakglaaaleaaflntlagv 90 
                                         K  ++++a+++   d++ + D+d  ++p++L + +++l + +v + ++  +p+ +++    a  e+  + + +++
  gi|336255279|ref|YP_004598386.1| 153 GSKAGAINYAVRERDSDHFAVFDADEWIAPEFLPTAMGQLLE-GVDVFQGrrVPRPTGPVETVAYCERIVFHASYKM 228
                                       4699999**********************************7.9999988556667777777777777777777777 PP

                   Glyco_transf_21  91 lqaklsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaR 167
                                       +     g+  +  +s a++rea+e++GG+      L eD+a++ +  ++Gl v+++++   ++++   ++lr+l+ +
  gi|336255279|ref|YP_004598386.1| 229 VEL--FGFTNCRSSSTAFTREAIERVGGYDD---VLTEDLAFAHACYREGLDVRQARHCTNTMEA--PHTLRDLWGQ 298
                                       777..58888999****************98...************************7555555..56******** PP

                   Glyco_transf_21 168 qlrWa 172
                                         rW 
  gi|336255279|ref|YP_004598386.1| 299 RKRWR 303
                                       ****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); 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):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3425.83
//
Query:       gi|336255280|ref|YP_004598387.1|  [L=361]
Description: L-tyrosine decarboxylase [Halopiger xanaduensis SH-6]
Scores for complete 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-26   93.5   0.0    5.4e-26   91.2   0.0    1.9  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    5.4e-12   45.4   0.0    6.9e-12   45.0   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
     0.0047   15.6   0.0     0.0094   14.6   0.0    1.4  1  SHMT             Serine hydroxymethyltransferase
  ------ inclusion threshold ------
       0.01   15.2   0.0      0.017   14.4   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
      0.013   14.9   0.1      0.019   14.3   0.1    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
       0.19   12.4   0.0       0.33   11.6   0.0    1.4  1  TIR_2            TIR domain
       0.24   10.0   0.0       0.35    9.5   0.0    1.1  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   0.0   2.1e-29   5.4e-26      74     300 ..      41     238 ..      31     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 2.1e-29
                                       SHHHHHHHHHHHHHHHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHHHCCEEEEE CS
                     Pyridoxal_deC  74 sPaltelevvvldwlaellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkeaeildklvlyt 150
                                       +P + +le   + +l+e+ gl       e  g ++ g++e+++ a+  ar+++       +          +++++ 
  gi|336255280|ref|YP_004598387.1|  41 YPTVSALEDEAIAMLGEIAGLE------EPSGYIAGGGTEANIQAVRIARERA-------D--------ATRPNVVM 96 
                                       7888888888888888888887......2467788888888887765555432.......2........3589**** PP

                                       ETTS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHC CS
                     Pyridoxal_deC 151 sdqahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdiceky 227
                                        + ah s +kaa +lgv lrv+p+d++++    a ++a+ +d ++  ++      +G+t +g  d + elg+i +  
  gi|336255280|ref|YP_004598387.1|  97 PESAHFSFRKAADLLGVDLRVVPTDDRYRADLGAVRAAVDDDTAA--VI----GVAGSTEYGRVDPIPELGEIARSV 167
                                       **************************9999999999999999998..55....789********************* PP

                                       T-EEEEE-TTGGGGGGSGGGGG.GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TT CS
                     Pyridoxal_deC 228 dlwlHvDAAyaGsaficpeirh.llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLehed 300
                                       d  lHvDAA++G  f+ p+    + +    +d +++ phK++ + + ++ l+v+d+  l ++l ++  YLe ++
  gi|336255280|ref|YP_004598387.1| 168 DATLHVDAAWGG--FVLPFTDYeWNFSHAPVDTMAIDPHKMGQAAVPAGGLLVRDSALL-DELAVDTPYLESTS 238
                                       ************..****99777*******************************98655.6788******9554 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   2.7e-15   6.9e-12      69     202 ..      71     206 ..      66     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.7e-15
                                       SHHH.HHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEE CS
                       Aminotran_5  69 Gtte.ainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklva 144
                                       G+te  i++v ++ +r+  ++ ++v+ e+ h + +    ++a+  g++++v+p d++ + dl +++++++++t++v+
  gi|336255280|ref|YP_004598387.1|  71 GGTEaNIQAVRIARERADATRPNVVMPESAHFSFR----KAADLLGVDLRVVPTDDRYRADLGAVRAAVDDDTAAVI 143
                                       77775566666666666888889999999999988....777788******************************** PP

                                       EESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTT.....TTTS---HHHHTESEEEEETTTT CS
                       Aminotran_5 145 ithvsnvtGtiqpveeigklakkkgalvlvDaaqa.....vghipidvkklgvDflafsghKl 202
                                         + s++ G ++p++e+g++a+ ++a ++vDaa +     +  ++ +++   vD +a+  hK+
  gi|336255280|ref|YP_004598387.1| 144 GVAGSTEYGRVDPIPELGEIARSVDATLHVDAAWGgfvlpFTDYEWNFSHAPVDTMAIDPHKM 206
                                       ********************************9763333367788889999999999999996 PP

>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.7e-06    0.0094     169     324 ..     139     292 ..     117     297 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-06
                                       --SEE.EEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEES..SSTT-S..-S-E CS
                              SHMT 169 kPkli.vaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttt..hktlrG..prgg 240
                                          +i vaG++ y r+     l eia +v+a+l vd a    ++    +   f++a v t +   hk  +   p gg
  gi|336255280|ref|YP_004598387.1| 139 TAAVIgVAGSTEYGRVDPIPELGEIARSVDATLHVDAAWGGFVLPFTDYEWNFSHAPVDTMAIdpHKMGQAavPAGG 215
                                       4445549*****************************9875555556778999****998776433887554226777 PP

                                       EEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHH CS
                              SHMT 241 lillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealk 317
                                       l++       +d+    v+  + +   +a + g++ G     +a+   a++e     ++    +  +na++la+al+
  gi|336255280|ref|YP_004598387.1| 216 LLVRD--SALLDEL--AVDTPYLESTSQATLTGTRSGAG---VASAVAAMEELWPSGYRSQYVRSRNNAEWLADALE 285
                                       77666..3344444..44556667778888888888864...455555777888889**999999************ PP

                                       HTT-EEG CS
                              SHMT 318 ekgyklv 324
                                       ++gy++v
  gi|336255280|ref|YP_004598387.1| 286 KRGYDVV 292
                                       *****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 ?   14.4   0.0   6.6e-06     0.017      29     169 ..      39     176 ..      22     306 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.6e-06
                                       T--HHHHHHHHHHHHHTT-SEEEE......ES-HHHHHHHHHHHH--TT....EEEEEETT-HHHHSSTTHHHHCC- CS
                   Beta_elim_lyase  29 gedktvnrLedavaelfgkeaalf......vpqGtaAnsillkillqrg....eevivtepahihfdetgaiaelag 95 
                                       g+ +tv +Led++ +++g  a+l       +  Gt An  +++i  +r     ++v++ e ah+ f+    +a l g
  gi|336255280|ref|YP_004598387.1|  39 GTYPTVSALEDEAIAMLGEIAGLEepsgyiAGGGTEANIQAVRIARERAdatrPNVVMPESAHFSFR---KAADLLG 112
                                       5568999999999999999999953455545568999999997777665111156889999999986...5567799 PP

                                       -EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase  96 vklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                       v lr +++++    dl +++aa+++     +  ++i ++  +++  G+v +   + e+ +ia++ + +lh+D+A
  gi|336255280|ref|YP_004598387.1| 113 VDLRVVPTDDRYRADLGAVRAAVDD-----DTAAVIGVAGSTEY--GRVDP---IPELGEIARSVDATLHVDAA 176
                                       **********9**************.....567**********9..98866...56667889999********9 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 ?   14.3   0.1   7.4e-06     0.019      47     146 ..      72     176 ..      39     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.4e-06
                                       HHHHHHHHHHHTTTT...TT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-. CS
                   DegT_DnrJ_EryC1  47 GtaAlhlaLralgvg...pgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVh. 119
                                       Gt+A+  a r         +  V++p    ++  +a+  lg +   v  d d y  d  a++aa+   t+a++ V  
  gi|336255280|ref|YP_004598387.1|  72 GTEANIQAVRIARERadaTRPNVVMPESAHFSFRKAADLLGVDLRVVPTD-DRYRADLGAVRAAVDDDTAAVIGVAg 147
                                       5555555555533332234678***************9999999999888.99*********************963 PP

                                       ..GGGB---HHHHHHHHHHCT-EEEEE-T CS
                   DegT_DnrJ_EryC1 120 ..lyGqvadmdalkaiaakhglkvieDaA 146
                                          yG+v  +++l +ia++ +  +  DaA
  gi|336255280|ref|YP_004598387.1| 148 stEYGRVDPIPELGEIARSVDATLHVDAA 176
                                       3369***********************99 PP

>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.33      10      47 ..     274     310 ..     266     319 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                             TIR_2  10 kewaeklaeaLeaagirvwldrwdl.kpgedweeeieea 47 
                                       ++ ae+la+aLe++g++v+ d   l     d+++   +a
  gi|336255280|ref|YP_004598387.1| 274 RNNAEWLADALEKRGYDVV-DP-TLpLVAADVPRSTFDA 310
                                       6789*************95.76.3324444555555555 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 ?    9.5   0.0   0.00014      0.35     103     195 ..      93     178 ..      73     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00014
                                       CCEEEEEETCHHHHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHHHCCTCCCEEEEEECSSTTTTB----HHHHHH CS
                           SepSecS 103 kviwvridekSslkavelaGleialvekvlegDelitdvedveeiiekkreevilavlstlsffaprspDdvkeiak 179
                                       +v+ +  ++ S  ka+ l G+++++v++    D+ + d+ +v ++++    ++ +++    s+ ++r+ D+++e+ +
  gi|336255280|ref|YP_004598387.1|  93 NVVMPESAHFSFRKAADLLGVDLRVVPT---DDRYRADLGAVRAAVDD---DTAAVIGVAGSTEYGRV-DPIPELGE 162
                                       68999999******************97...6999**********987...65566666677788887.78****** PP

                                       HHHCCT--EEEEGCCC CS
                           SepSecS 180 iCaeydvPhlvNgAYa 195
                                       i    d  + v +A++
  gi|336255280|ref|YP_004598387.1| 163 IARSVDATLHVDAAWG 178
                                       **99999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2847.10
//
Query:       gi|336255281|ref|YP_004598388.1|  [L=113]
Description: hypothetical protein Halxa_3904 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        2.1    8.3   6.4        1.3    9.0   5.1    1.4  1  CoA_binding_3  CoA-binding domain


Domain annotation for each model (and alignments):
>> CoA_binding_3  CoA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.1   7.4e-05       1.3      22      63 ..      55      96 ..      35     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 7.4e-05
                     CoA_binding_3 22 lsawllvllllallsfslkdafSRlwlaywavvglvllivsr 63
                                      +++wl+ ++++++l+f ++ a+S   ++ + +vg++lli+ r
  gi|336255281|ref|YP_004598388.1| 55 ALGWLAWVGAAGTLAFGFSGAVSMTAFLGFGLVGAFLLIGGR 96
                                      679**********************************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 976.88
//
Query:       gi|336255282|ref|YP_004598389.1|  [L=703]
Description: methionyl-tRNA synthetase [Halopiger xanaduensis SH-6]
Scores for complete 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-147  491.4   0.0     2e-147  491.1   0.0    1.1  1  tRNA-synt_1g  tRNA synthetases class I (M)
    1.2e-20   73.4   0.1    2.1e-20   72.6   0.1    1.4  1  tRNA_bind     Putative tRNA binding domain
    1.3e-14   53.4   0.8    5.4e-08   31.6   0.2    3.0  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
      1e-09   38.2   0.0    9.5e-07   28.4   0.0    2.3  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    2.3e-07   30.9   0.0    4.2e-07   30.0   0.0    1.4  1  Anticodon_1   Anticodon-binding domain of tRNA
    0.00091   18.2   0.1       0.43    9.4   0.0    3.1  3  tRNA-synt_1f  tRNA synthetases class I (K)
  ------ inclusion threshold ------
        4.8    5.6   7.3        4.4    5.7   3.1    2.1  2  Borrelia_P83  Borrelia P83/100 protein
        8.6    5.3  13.3         13    4.7  13.3    1.2  1  Pes-10        Pes-10


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 !  491.1   0.0  8.8e-151    2e-147       2     390 ..      15     406 ..      14     407 .. 0.98

  Alignments for each domain:
  == domain 1  score: 491.1 bits;  conditional E-value: 8.8e-151
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHH CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelf 78 
                                       +vt++lpYang+lH+Ghl+ +i aD+f R  +  g+e+ +vcg+D+hGtp++++Ae+egv+pe+++ + h++++e+f
  gi|336255282|ref|YP_004598389.1|  15 VVTCGLPYANGDLHIGHLRGYIGADAFNRALQTLGQETAYVCGSDMHGTPVAVNAEQEGVNPEDFALEWHDQYAETF 91 
                                       79*************************************************************************** PP

                                       HHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE.-T CS
                      tRNA-synt_1g  79 kklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqc.ee 154
                                        ++n++fd+yg+t++e+++el+qei+++l+e+g+iyekei+++y+p+++++lpdryvegtCP+c+ e+argd+c e 
  gi|336255282|ref|YP_004598389.1|  92 PQFNVEFDNYGHTHDETNTELTQEIVRTLDEQGYIYEKEIQVAYDPDADQYLPDRYVEGTCPYCG-EKARGDECdEG 167
                                       *****************************************************************.99******999 PP

                                       TSSB-E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS- CS
                      tRNA-synt_1g 155 cgkkleptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdl 231
                                       c+++lep e+++p+s+i+g+ +e++e++h ff++s+f+++l e++  +  e ++n++++ ++w+++gL+d++i+rd+
  gi|336255282|ref|YP_004598389.1| 168 CQRHLEPGEVEDPTSTITGNPAEYRERTHKFFEVSEFADFLTEFL--DGLEGTSNARNQPRQWIEDGLQDWCITRDM 242
                                       *********************************************..45569************************* PP

                                       SSS-EET.....TECCEEE-HHHHHHHHHHHTTTTT-...TTSG.GGG.G--S......EEEEEGGGHHHHHTHHHH CS
                      tRNA-synt_1g 232 dwGipvP.....gaekkvlYVWldAligYisatkelakkkgeee.kwkeyWakdkevelvhfigkdiikFHtifwPa 302
                                       dwGi++P     ++ + vlYVW+dA+i+Yi++tk+++++ g++e +w++ W  + e e+vh+ig+dii++HtifwPa
  gi|336255282|ref|YP_004598389.1| 243 DWGIDYPtaegeDESDLVLYVWVDAPIEYIASTKQYSERVGTDEyDWEQVW--KGEGEIVHIIGRDIIQHHTIFWPA 317
                                       *******9999888999********************99999998******..57********************** PP

                                       HHHHTT----S-EEEE--EEE--------------HHHHHHH.H-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHH CS
                      tRNA-synt_1g 303 illgaelklpkkvvaheyltvegkKlSkSrgvvvkakealer.ldadllRYylaaeapekkDldfswedfvervNse 378
                                       +l+ga++++p+ ++a++++t++gk lS+Sr+++++ake+l++ +++dllRYyl++++  ++D+dfsw+ f+e+vN e
  gi|336255282|ref|YP_004598389.1| 318 MLEGADYNKPRGIAATGFITINGKGLSTSRNRAIWAKEYLDEgFHPDLLRYYLTTTGGLQQDVDFSWDAFQEKVNGE 394
                                       ***************************************************************************** PP

                                       CCCHHHHHHHHH CS
                      tRNA-synt_1g 379 LadklgnlvnRv 390
                                       L++++gn+ +R+
  gi|336255282|ref|YP_004598389.1| 395 LVGTVGNFWYRS 406
                                       *********997 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.1   9.3e-24   2.1e-20       1      96 []     611     701 ..     611     701 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 9.3e-24
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECC CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeel 77 
                                       +rvG++ +ae +++ad L +l+vd+G e+ rqiv+g+k+    +el ++k v++an++ ++l GveS+GMil+a   
  gi|336255282|ref|YP_004598389.1| 611 IRVGRIESAEGIEGADDLARLEVDIGFET-RQIVAGIKQLHDLDELPGEKCVLLANMEQAELFGVESNGMILAAG-- 684
                                       79***************************.*********************************************.. PP

                                       ESSCEEEEEESST--TTCE CS
                         tRNA_bind  78 dekevgilelpadveaGek 96 
                                         +e ++l+ ++d+e+Gek
  gi|336255282|ref|YP_004598389.1| 685 --EEADLLTTHGDAEVGEK 701
                                       ..59999999999999985 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 !   31.6   0.2   2.4e-11   5.4e-08      26     174 ..      15     144 ..       5     151 .. 0.83
   2 !   18.0   0.0   3.2e-07   0.00071     353     442 ..     170     259 ..     163     289 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.4e-11
                       tRNA-synt_1  26 ilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefre 102
                                       +++ g Py++G lHiGh    +  d   r  +  G+e+ yv G D++G ++  + e++ g + +            +
  gi|336255282|ref|YP_004598389.1|  15 VVTCGLPYANGDLHIGHLRGYIGADAFNRALQTLGQETAYVCGSDMHGTPVAVNAEQE-GVNPE------------D 78 
                                       567788*********************************************9999998.34332............2 PP

                       tRNA-synt_1 103 kvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktals 174
                                          ew ++yae+    + ++   v fd+   T d+  +e ++e+   l ++g iy+ +  v +++++   l 
  gi|336255282|ref|YP_004598389.1|  79 FALEWHDQYAET----FPQF--NVEFDNYGHTHDETNTELTQEIVRTLDEQGYIYEKEIQVAYDPDADQYLP 144
                                       334555555555....4444..57899999999999999999999999999999999999999999877665 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.2e-07
                       tRNA-synt_1 353 lkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswlen.iqdWciSRqrwWG 428
                                        + e+ e + p++  +++p +yr  +  f +v+e+ad + + ++  + + +  +++  +w+e+  qdWci R+  WG
  gi|336255282|ref|YP_004598389.1| 170 RHLEPGEVEDPTSTITGNPAEYRERTHKFFEVSEFADFLTEFLDGLEGTSNA-RNQPRQWIEDgLQDWCITRDMDWG 245
                                       566777888899999***********************99999999988776.566789**9967************ PP

                       tRNA-synt_1 429 hriplfvsketeev 442
                                          p    +++ ++
  gi|336255282|ref|YP_004598389.1| 246 IDYPTAEGEDESDL 259
                                       99998776666655 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 !   28.4   0.0   4.3e-10   9.5e-07      14     134 ..      17     138 ..      11     146 .. 0.84
   2 !    7.4   0.0    0.0011       2.5     244     297 ..     333     388 ..     301     392 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 4.3e-10
                                       EEE.EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1e  14 vCG.ptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdlea 89 
                                       +CG p +  + h+Gh R ++  D ++r lq+lg + ++v         +  +a++e+ + +++a ++ +++ + + +
  gi|336255282|ref|YP_004598389.1|  17 TCGlPYANGDLHIGHLRGYIGADAFNRALQTLGQETAYVCGSDMHGTPVAVNAEQEGVNPEDFALEWHDQYAETFPQ 93 
                                       67734567799****************************9854455678899************************* PP

                                       TT----SB--BGGGGHHHH.HHHHHHHHHTTSEEE-TTS-EEE-GG CS
                      tRNA-synt_1e  90 Lnvlkptleprvsekvdei.ielvekliekgyaYavsdgdvyfdvs 134
                                        nv   ++     e+ +e+  e+v +l e+gy Y+ +  +v++d  
  gi|336255282|ref|YP_004598389.1|  94 FNVEFDNYGHTHDETNTELtQEIVRTLDEQGYIYEKE-IQVAYDPD 138
                                       ****988877777766666258999999******998.67777755 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0011
                                       E--EEETTBE--TTTT---BHHHHHTT.S-HHHHHHHHHSS.-TTS-EEE-HHHHH CS
                      tRNA-synt_1e 244 nghlkiegekmsksLknfitikdvlkk.fdprqlRllllsa.hyrsqldfkeelle 297
                                       +g+++i+g+ +s s +  i  k+ l + f+p  lR++l+++   ++ +df+ ++++
  gi|336255282|ref|YP_004598389.1| 333 TGFITINGKGLSTSRNRAIWAKEYLDEgFHPDLLRYYLTTTgGLQQDVDFSWDAFQ 388
                                       79***********************7659********9875257788888876665 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 !   30.0   0.0   1.9e-10   4.2e-07       4     114 ..     426     530 ..     423     570 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.9e-10
                       Anticodon_1   4 ilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.ra.aqevllevletllrlla 78 
                                       +  +++++++++++a ++y+++ + +++ e+   ++ + y++ ++p+  ++++ ++  a + + +  +++++  l++
  gi|336255282|ref|YP_004598389.1| 426 VHERIQDAIADARAAVNDYDLRGIGQSAVEL--AQFGNEYIQRNEPWKLTDEE-PEtAAqVIRDCVQIAKAVGVLIE 499
                                       56799*************************8..99************998765.4423334488889999******* PP

                       Anticodon_1  79 PfmPfitEelwqreeeelgkkesimlaewpekaeel 114
                                       P++P  +  lw    e+lg++ ++  a  ++ a e+
  gi|336255282|ref|YP_004598389.1| 500 PIAPDKARRLW----EQLGEDGEVADALLED-ALEA 530
                                       ***********....9999998887776663.3222 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 !    9.4   0.0   0.00019      0.43      22      69 ..      11      59 ..       2      63 .. 0.85
   2 ?    1.7   0.0     0.045     1e+02     218     262 ..      79     121 ..      61     136 .. 0.82
   3 ?    2.5   0.0     0.024        54     225     311 ..     288     373 ..     286     392 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00019
                      tRNA-synt_1f 22 kdevvvesGis.pSGliHiGnlrevltadlvaralrkrgeevrlilisD 69
                                       d  vv  G+  + G +HiG lr  + ad+  ral+ +g+e+  ++ sD
  gi|336255282|ref|YP_004598389.1| 11 DDPAVVTCGLPyANGDLHIGHLRGYIGADAFNRALQTLGQETAYVCGSD 59
                                      56777888876257******************************99888 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.045
                      tRNA-synt_1f 218 gKLqWkvdwamrWaalgVdfEpaGkDhaaaGgSvdvsskiaeilg 262
                                         L+W   +a     ++V+f  +G  h +  +++++ ++i++ l+
  gi|336255282|ref|YP_004598389.1|  79 FALEWHDQYAETFPQFNVEFDNYGHTHDE--TNTELTQEIVRTLD 121
                                       56899999999999999999999999988..88888888887776 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.024
                      tRNA-synt_1f 225 dwamrWaalgVdfEpaGkDhaaaGgSvdvsskiaeilggeaPekvvYelillkggekmssSkGnvltledwl.evae 300
                                       dw   W+ +g  +  +G+D+++    +    ++ e  ++++P ++    ++  +g+ +s S+   +  ++ l e  +
  gi|336255282|ref|YP_004598389.1| 288 DWEQVWKGEGEIVHIIGRDIIQ--HHTIFWPAMLEGADYNKPRGIAATGFITINGKGLSTSRNRAIWAKEYLdEGFH 362
                                       8999999999999999999999..344444555588899999999877666666669*************993568* PP

                      tRNA-synt_1f 301 pevlrflilrr 311
                                       p++lr+++  +
  gi|336255282|ref|YP_004598389.1| 363 PDLLRYYLTTT 373
                                       ******98774 PP

>> Borrelia_P83  Borrelia P83/100 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.038        84       9      26 ..      94     111 ..      88     122 .. 0.81
   2 ?    5.7   3.1     0.002       4.4     257     310 ..     532     584 ..     503     600 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.038
                      Borrelia_P83   9 ktlefvnykGpydsvdsa 26 
                                        ++ef ny  ++d++++ 
  gi|336255282|ref|YP_004598389.1|  94 FNVEFDNYGHTHDETNTE 111
                                       579************985 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.002
                      Borrelia_P83 257 aknlpepadvsskkedkkvaeekkreiekaqkeikkkdeeakkakdakaedlkk 310
                                        +n +ep++  +k ed++vae + +  e+   e++ +++e   + d +a+++  
  gi|336255282|ref|YP_004598389.1| 532 PRNFEEPGELFEKIEDDRVAELNEKLEER-VAEAEDDEDEETESDDTAADEADD 584
                                       6899****************877777777.788888888888888888777654 PP

>> Pes-10  Pes-10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  13.3    0.0059        13     148     219 ..     534     613 ..     521     647 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0059
                            Pes-10 148 qieeAdeLvekve..kllrkeeivdEdlee.eeeede....edseedd.ddiededeedesssstdsgiesedeElv 216
                                        +ee +eL ek+e  ++   +e ++E  +e e++ede    +d+ +d+ dd+ d d +d +   +d   +++ +El+
  gi|336255282|ref|YP_004598389.1| 534 NFEEPGELFEKIEddRVAELNEKLEERVAEaEDDEDEetesDDTAADEaDDMADADVDDLEPLADDRISFDDFQELD 610
                                       5889999999996335666666666655540333444788988888888******************9999999998 PP

                            Pes-10 217 eer 219
                                       +  
  gi|336255282|ref|YP_004598389.1| 611 IRV 613
                                       754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (703 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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):               8  [number of targets reported over threshold]
# CPU time: 0.66u 0.23s 00:00:00.89 Elapsed: 00:00:00.40
# Mc/sec: 5321.59
//
Query:       gi|336255283|ref|YP_004598390.1|  [L=720]
Description: beta-lactamase [Halopiger xanaduensis SH-6]
Scores for 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-64  216.8   0.9    7.8e-64  216.0   0.9    1.3  1  Beta-lactamase   Beta-lactamase
     0.0039   16.8   0.0       0.98    9.0   0.0    2.3  2  Beta-lactamase2  Beta-lactamase enzyme family
  ------ inclusion threshold ------
       0.15   12.5   1.5         12    6.4   0.2    3.0  3  Chloroa_b-bind   Chlorophyll A-B binding protein


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.0   0.9   1.3e-67   7.8e-64       5     314 ..      77     392 ..      71     404 .. 0.92

  Alignments for each domain:
  == domain 1  score: 216.0 bits;  conditional E-value: 1.3e-67
                                       HHHHHHHTTESEEEEEEEETTEEEEEEEEEEEETTTTEEEST.TSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBGG CS
                    Beta-lactamase   5 vrelmaqggipGvavavvrdgkvvldkggGvadleggrpvta.dtlfriaSvtKtftaaavlqlveeGkldLddpVs 80 
                                       +  l + +++ G++vavv+dg v l+kg+G +d+e+g pv+a +t fri+Sv+K+++++a++ql+e+G+ld d+pV+
  gi|336255283|ref|YP_004598390.1|  77 LGSLLETHDVVGASVAVVHDGAVELAKGYGESDREAGTPVDAdETAFRIGSVSKPLVWTAAMQLIEDGRLDPDEPVE 153
                                       5566778899********************************779*******************************9 PP

                                       GTST..TCTTGGGTTEBHHHHHTTHSSCSSSSTSTTCTSHHHTHHHHHHHHHHSBSSSS..TTSCEE-SHHHHHHHH CS
                    Beta-lactamase  81 kylP..efagpgkgkiTlrdLltHtsGlpdlfasdlleeaaadaaellralatlppkya..pGtkwgYsntgygllg 153
                                         l     ++  +++iT+++L+tHt+G+ d  + ++  ++++d ++l  +l++++p++   pG+  +Ysn+g+ l++
  gi|336255283|ref|YP_004598390.1| 154 PSLEsvSIPDTYDEPITMAHLATHTAGFEDR-SQGTWVDDPDDLRSLPNVLREEQPERVrpPGEIASYSNYGAALAA 229
                                       99999989999999**************888.888888888888***********998888**************** PP

                                       HHHHHHHTSHHHHHHHHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHCTTTBEEEEHHHHHH CS
                    Beta-lactamase 154 ellekvtgrsleqllreeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeaegagglistardlar 230
                                       ++++ vt++s++++++e++++pLgm +t++ +p+++d  +a+gyt +   +r++   +   a +ag   +ta+d+ar
  gi|336255283|ref|YP_004598390.1| 230 QVVADVTSTSFQEYVSEHLFDPLGMDHTTFEQPAPEDIDVASGYTMATGSVRDSSELFLEIA-PAGAATATASDMAR 305
                                       ********************************************999999999988887776.8************* PP

                                       HHHHHHHCCSSSSHHHHHHHHHHHTSEEEECTTEEEEC.ECSSEEEEECCHTEEEEEEE...STEEEEEEEECGGTE CS
                    Beta-lactamase 231 flglalegglllsaetlaqltaklssgttrpagiragl.glGwvladktgapgtfghtG...ggygtyvfvdpeanl 303
                                       f++ +legg++ ++++la  +  ++  ++++   +     +G+v  +++g  +++ h+G   g  + y++++pe +l
  gi|336255283|ref|YP_004598390.1| 306 FMRAHLEGGAADGERILASEAVDRMHEQWFTHHETLPGiAFGFVEDERDG-VRILEHDGaipGSSNGYLVLVPEYDL 381
                                       ******************99999999999998888777699997777777.7************************* PP

                                       EEEEEESBCSS CS
                    Beta-lactamase 304 vvavltnrdpp 314
                                       ++++ tn+d +
  gi|336255283|ref|YP_004598390.1| 382 GLFLATNTDSG 392
                                       ********986 PP

>> Beta-lactamase2  Beta-lactamase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00016      0.98      11      46 ..     119     154 ..     109     164 .. 0.89
   2 !    5.4   0.0    0.0021        12     103     162 ..     252     337 ..     239     375 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00016
                                       TTS-EE-GGGGHHHHHHHHHHHHHCTSTGTT-EEEG CS
                   Beta-lactamase2  11 adeefpaaStiKvpillalleavlegklslderltl 46 
                                       +++ f  +S+ K ++  a+++ +++g+l++de+++ 
  gi|336255283|ref|YP_004598390.1| 119 DETAFRIGSVSKPLVWTAAMQLIEDGRLDPDEPVEP 154
                                       5678*****************************985 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0021
                                       CTHTTSB--SHTT.....................CCHHHTTSSTTEE-HHHHHHHHHHHHHTTSSHHH.....HHHH CS
                   Beta-lactamase2 103 lglretrlrrklp.....................dleaadkdkrntttardlarllealargellspe.....elle 153
                                       lg+++t+++++ p                      + +  +    t+ta d+ar+++a  +g + + e     e+++
  gi|336255283|ref|YP_004598390.1| 252 LGMDHTTFEQPAPedidvasgytmatgsvrdsseLFLEIAPAGAATATASDMARFMRAHLEGGAADGErilasEAVD 328
                                       5666666666666666666666666666666555333445667889***********99998877777565555666 PP

                                       HHHT-STTT CS
                   Beta-lactamase2 154 ilsnqqfrd 162
                                        + +q f++
  gi|336255283|ref|YP_004598390.1| 329 RMHEQWFTH 337
                                       677666654 PP

>> Chloroa_b-bind  Chlorophyll A-B binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.42   2.5e+03     114     129 ..     241     256 ..     220     265 .. 0.67
   2 ?    3.8   0.1     0.013        77      25      71 ..     434     481 ..     411     525 .. 0.65
   3 ?    6.4   0.2     0.002        12      32      55 ..     524     547 ..     485     586 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.42
                                       SSSSSHCHHSTTSTT. CS
                    Chloroa_b-bind 114 rgypGglgfdplglak 129
                                       ++y  + +fdplg+++
  gi|336255283|ref|YP_004598390.1| 241 QEYVSEHLFDPLGMDH 256
                                       4566667788888864 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.013
                                       BSHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHTSSSCCCT--..TTT CS
                    Chloroa_b-bind  25 etlkrlreaEliHGRvAMlavlG...alvpelltklsaassfaegpa.wae 71 
                                        t++ +r aE++H+R+A    +G   + v e++     ++ f +gp+ w e
  gi|336255283|ref|YP_004598390.1| 434 GTYRGVRIAETTHSRLATTLQAGsveVSVDEAG---FLVTDFGGGPErWVE 481
                                       5678899**********7555440004455544...234457777777776 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                    Chloroa_b-bind  32 eaEliHGRvAMlavlGalvpellt 55 
                                       e+  +HGRvA l +lG+l   ++ 
  gi|336255283|ref|YP_004598390.1| 524 ESLSVHGRVAGLSALGMLSGAVGW 547
                                       44468*************988664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (720 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 5377.83
//
Query:       gi|336255284|ref|YP_004598391.1|  [L=95]
Description: hypothetical protein Halxa_3907 [Halopiger xanaduensis SH-6]
Scores for complete 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   63.0   0.1    2.1e-17   62.9   0.1    1.0  1  GYD       GYD domain


Domain annotation for each model (and alignments):
>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.1   1.2e-21   2.1e-17       1      91 []       4      92 ..       4      92 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.2e-21
                               GYD  1 YivlvnytdegvkglkdsperreeakealveslGgkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrtetl 79
                                      Y  l+ + d+ +++ ++ ++ + e+++++ es++++l ++ya+lGe+D+++i+Ea D+e+  + +l+l+++G ++ +t+
  gi|336255284|ref|YP_004598391.1|  4 YASLIDLDDRDAQNAQELASIWGEIRTEF-ESHDAELIDSYAALGEHDFIIIFEAADHESGFKSALTLRRHG-LQGQTM 80
                                      56789999*********************.******************************************.****** PP

                               GYD 80 rafteeefdeav 91
                                      +++++++f+e+v
  gi|336255284|ref|YP_004598391.1| 81 ELVDTDDFSELV 92
                                      ********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 796.98
//
Query:       gi|336255285|ref|YP_004598392.1|  [L=585]
Description: pyruvate kinase [Halopiger xanaduensis SH-6]
Scores for complete 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-117  392.3   3.6   2.1e-117  391.9   3.6    1.2  1  PK             Pyruvate kinase, barrel domain
    3.4e-30  104.7   0.6    8.1e-30  103.4   0.6    1.7  1  PK_C           Pyruvate kinase, alpha/beta domain
    5.6e-12   45.2   0.6    4.5e-11   42.3   0.1    2.8  2  PEP-utilizers  PEP-utilising enzyme, mobile domain
    0.00042   19.5   1.7    0.00042   19.5   1.7    2.2  2  HpcH_HpaI      HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  391.9   3.6  4.8e-121  2.1e-117       1     341 [.       1     333 [.       1     340 [. 0.96

  Alignments for each domain:
  == domain 1  score: 391.9 bits;  conditional E-value: 4.8e-121
                                       ---SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--B CS
                                PK   1 lrrtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgll 77 
                                       +r++kivctlGPas++  ++++l++aG+ v+rln shGs e+++e +++vr + ++  + va++lDt+Gpeirt  l
  gi|336255285|ref|YP_004598392.1|   1 MRNAKIVCTLGPASSDRRTIRELADAGMSVARLNASHGSPEDRAELVDRVRDVDEERDEPVAVMLDTQGPEIRTAPL 77 
                                       5899************************************************************************* PP

                                       TTCSSSEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-E CS
                                PK  78 kdgkkdielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventg 154
                                        dg+  ++l++g+++++   ++      ++ + l+ +  +++ve G++il+dDGl++ +vle d  + ++ +v  +g
  gi|336255285|ref|YP_004598392.1|  78 PDGE-TVTLETGSEIEFVEGDEAS----SDRVGLSLP--IDEVEEGDRILLDDGLIETTVLERDGGA-IRARVDTGG 146
                                       **98.9**********87666555....456777766..89**********************9999.********* PP

                                       EE-SS-BEE-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHH CS
                                PK 155 vlgskkgvnlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegve 231
                                       +l+ +kgvn+pg+++dl+ ++ekD++dl+++++++vd++aasfvr a+Dv ev evlee + ei ii+kie++ +ve
  gi|336255285|ref|YP_004598392.1| 147 ELAGRKGVNVPGVDLDLDVVTEKDRQDLELAAEKEVDFVAASFVRDAEDVYEVSEVLEEFDAEIPIISKIERAGAVE 223
                                       ***************************************************************************** PP

                                       THHHHHHHSSEEEEEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT CS
                                PK 232 nldeileasDgimvarGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDG 308
                                       nldei+eas gimvarGDlG+e p+e+v+++qk++i++c+ ag pvitat+ml+sm++  rptrae+sDvanavlDG
  gi|336255285|ref|YP_004598392.1| 224 NLDEIMEASYGIMVARGDLGVECPMEDVPMIQKRIIRQCREAGLPVITATEMLDSMVHARRPTRAEASDVANAVLDG 300
                                       ***************************************************************************** PP

                                       -SEEEESHHHHTSS-HHHHHHHHHHHHHHHHHT CS
                                PK 309 tDavmLsgetakGkyPveavkamaevaleaeka 341
                                       tDavmLs+eta G++P+e v am ++ +e e++
  gi|336255285|ref|YP_004598392.1| 301 TDAVMLSAETAVGDHPAEVVDAMDSIIREVEAS 333
                                       **************************9999876 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   0.6   1.8e-33   8.1e-30       1     117 []     353     469 ..     353     469 .. 0.92

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 1.8e-33
                                       HHHHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTSH CS
                              PK_C   1 eaiakaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestdel 77 
                                       +a+a++a+ +a+++ a+a+v++tesG+tA++ +kyrp+vp++a tp++++ r+lal++Gv+p+++    + + + ++
  gi|336255285|ref|YP_004598392.1| 353 DALARSARFLARDISADAVVAATESGYTALKTAKYRPGVPVVASTPSHEVRRRLALSWGVTPLYARV--SDQGAGAV 427
                                       799************************************************************8654..3578899* PP

                                       HHHHHHHHHHTTSS-STSEEEEEE-SSS...S..SS--EEEEE CS
                              PK_C  78 lreavkvakeaglvkkgdevvvtaGtpk...gesgttNtlrVv 117
                                       +++av++a++ag++++gd+vvv+ G+ +   g + ttN+l+V+
  gi|336255285|ref|YP_004598392.1| 428 VERAVQAALNAGVAESGDTVVVLCGMMTeleG-ANTTNMLKVH 469
                                       **************************994433.667*****97 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 ?   -0.9   0.0      0.31   1.4e+03      42      59 ..     262     288 ..     261     305 .. 0.66
   2 !   42.3   0.1     1e-14   4.5e-11       2      73 .]     501     571 ..     500     571 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.31
                                       HHHTT--EEE--SSHH..........H CS
                     PEP-utilizers  42 ArelgiPaVvgvgeati.........e 59 
                                       +re g+P++  ++ + +          
  gi|336255285|ref|YP_004598392.1| 262 CREAGLPVITATEMLDSmvharrptrA 288
                                       699999999999887765555555541 PP

  == domain 2  score: 42.3 bits;  conditional E-value: 1e-14
                                       --S-EEEEES---HHHHT.TS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers   2 leegvILvaeetspsdia.gldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                       +++g+I+++++   ++++  l+k+aGi+ ++ Gmt   ++vAre+++P+++g++  +    eg+++t+D+++G
  gi|336255285|ref|YP_004598392.1| 501 VPDGAIVAVPSDFDEEFEgDLEKIAGIIDAQRGMTGYPSLVAREMDLPMISGADVSE--EAEGETVTIDAERG 571
                                       5778888777666666664899*********************************96..9***********99 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   1.7   9.5e-08   0.00042      75     151 ..     171     239 ..     164     297 .. 0.79
   2 ?   -0.4   0.1      0.11   5.1e+02      14      39 ..     293     313 ..     284     347 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.5e-08
                                       HHHGG.HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH.TSTTEEEEEE CS
                         HpcH_HpaI  75 kqdle.vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIa.avegldgvfl 149
                                       +qdle +++++++ v   +v  ae++ ev ++l+e +       +e++++  iE a +v+n++eI+ a+ g+++   
  gi|336255285|ref|YP_004598392.1| 171 RQDLElAAEKEVDFVAASFVRDAEDVYEVSEVLEEFD-------AEIPIISKIERAGAVENLDEIMeASYGIMV--- 237
                                       6899999******************************.......99********************77766654... PP

                                       -H CS
                         HpcH_HpaI 150 Ga 151
                                       + 
  gi|336255285|ref|YP_004598392.1| 238 AR 239
                                       44 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.11
                                       HHHHCTC--SEEEEESSTSSSHHHHH CS
                         HpcH_HpaI  14 aekaaiagaDsvliDlEdavalaeKd 39 
                                       + +a + g D+v++  E av      
  gi|336255285|ref|YP_004598392.1| 293 VANAVLDGTDAVMLSAETAV-----G 313
                                       56778889999999999998.....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.21s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 4624.10
//
Query:       gi|336255286|ref|YP_004598393.1|  [L=134]
Description: hypothetical protein Halxa_3909 [Halopiger xanaduensis SH-6]
Scores for 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   12.1   0.1       0.11   12.0   0.1    1.1  1  DUF4645   Domain of unknown function (DUF4645)


Domain annotation for each model (and alignments):
>> DUF4645  Domain of unknown function (DUF4645)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     6e-06      0.11      20      88 ..       3      73 ..       1      92 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6e-06
                           DUF4645 20 vdkngnkelkpdvqlqclssmlkddaeaWgkprvpLr..pplnvltdlareqlerPsertgsciPvdssra 88
                                       d+ g+++ +     q   s   dda+aWg +       +  +  ++l  e+++ P e ++ +iP+d sr 
  gi|336255286|ref|YP_004598393.1|  3 DDDSGDRDASGGDDAQWDRSSAWDDADAWGGTDSGEWsdSDTDADANLEGERVDEPAEESDDRIPLDLSRD 73
                                      57778888888888888899999******998876551155677788*********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1008.49
//
Query:       gi|336255287|ref|YP_004598394.1|  [L=245]
Description: universal metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter protein [Halopiger xanaduensis SH-6]
Scores for 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-58  197.4   0.1      5e-58  196.2   0.1    1.5  1  Diphthami_syn_2  Diphthamide synthase


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 !  196.2   0.1   2.8e-62     5e-58       5     218 ..      10     243 ..       7     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 196.2 bits;  conditional E-value: 2.8e-62
                   Diphthami_syn_2   5 vlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplik...........letaGe 69 
                                        l+sGGkDs  a+y+al+e  +v+ Lv+v +  ++sym+hv+  +l +l aes+Gi+l+               + +
  gi|336255287|ref|YP_004598394.1|  10 GLFSGGKDSSWAVYRALEEgLDVRRLVTVHPS-EDSYMYHVPATDLASLAAESIGIELVDvdpgdleaetvADSSAQ 85 
                                       59*****************9********9885.688**********************9622222111111123345 PP

                   Diphthami_syn_2  70 eekevedLkgtlkkld..........veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfe 136
                                        ++e e L+  l++ld          + +v+ Ga+eseyq +ri+ +C +lG  ++aPLW++dp+el+  ++e++fe
  gi|336255287|ref|YP_004598394.1|  86 GDDELEPLEAALEELDdalreggeggIAGVTAGAVESEYQTNRIQAMCDRLGCDLFAPLWQEDPRELADAMLEAGFE 162
                                       678889999******99999999999999************************************************ PP

                   Diphthami_syn_2 137 vivvavkaegldeslLGrridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyld 213
                                       + ++ v+a+gldes+LGr +d   + +l++l+e yg++  gegGe+etlv+D+P   +r+++ e+e+kw++++g l 
  gi|336255287|ref|YP_004598394.1| 163 IKIIQVAAHGLDESWLGRTLDEAALADLEELNEEYGVHILGEGGEFETLVVDGPHMDRRIDL-EYERKWEGTHGRLR 238
                                       *************************************************************7.7999*********9 PP

                   Diphthami_syn_2 214 ierak 218
                                       i  ak
  gi|336255287|ref|YP_004598394.1| 239 ITNAK 243
                                       98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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 0.21s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1858.78
//
Query:       gi|336255288|ref|YP_004598395.1|  [L=451]
Description: hypothetical protein Halxa_3911 [Halopiger xanaduensis SH-6]
Scores for complete 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-112  376.1  12.4   2.3e-112  375.8  12.4    1.1  1  DUF373       Domain of unknown function (DUF373)
     0.0018   18.2   8.0     0.0018   18.2   8.0    1.9  2  Trypan_PARP  Procyclic acidic repetitive protein (PARP)


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 !  375.8  12.4  2.6e-116  2.3e-112       2     334 ..       3     358 ..       2     359 .. 0.96

  Alignments for each domain:
  == domain 1  score: 375.8 bits;  conditional E-value: 2.6e-116
                            DUF373   2 tLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvg 78 
                                       tLv+c Dr dD+gr++g+++P+vG+eav+ ++++++ladPeDS vN+l+++++v+++L++++e++ vavv+Gd++++
  gi|336255288|ref|YP_004598395.1|   3 TLVVCLDRTDDVGRRTGLQSPIVGWEAVRALVTDIGLADPEDSGVNTLLETLRVAQDLRDDDEEAIVAVVSGDRESM 79 
                                       8**************************************************************************** PP

                            DUF373  79 veadrkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyllkkalkdpelrk 155
                                       v+adr++a+qld++++++++dsaivV D+aeDe+++pi++srv+vdsv+rVvV+q+r+iEstyyl+k++l+d+elr+
  gi|336255288|ref|YP_004598395.1|  80 VSADRAVARQLDDLIAEYDPDSAIVVLDSAEDERLVPIVESRVRVDSVDRVVVRQARDIESTYYLMKQFLADEELRQ 156
                                       ***************************************************************************** PP

                            DUF373 156 tiLvplGlllliyallll.lglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvallll 231
                                       t+LvplGl+ll++++l++ +g ++  +a+i++++Gl+ll++Gf++de+++ l+++++esl++g++++vtyvva+ l+
  gi|336255288|ref|YP_004598395.1| 157 TVLVPLGLTLLVFPVLAMrIG-AAEGAAAITTVIGLFLLYKGFNVDEIVTGLAHQIRESLYSGQVSVVTYVVAAGLT 232
                                       *****************9554.56788999*********************************************** PP

                            DUF373 232 ligiisgyislesvssasvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpflvlaigl 308
                                       ++g++ g   ++s+ +   ++g+++ ++ f y++++wla+a+ltas+g+++de++ +ee  ++++l+lpf+v+a+gl
  gi|336255288|ref|YP_004598395.1| 233 FVGLFVGALGVSSLGE---TQGVVVPAVRFAYDSIPWLAVAALTASAGRLLDEVI-GEEPIRSSFLNLPFIVVAVGL 305
                                       *******888666666...89**********************************.7789999************** PP

                            DUF373 309 vlygasaylls...........................lsilalslvvgivva 334
                                       v++g++ay+l+                            ++lal +v++ivv+
  gi|336255288|ref|YP_004598395.1| 306 VIRGFAAYFLQqqnviravdippielgvlsieqftveaGQRLALYVVTAIVVS 358
                                       *********99999999999999999999999999999999999999999987 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.17   1.5e+03     120     131 ..     295     306 ..     289     309 .. 0.87
   2 !   18.2   8.0     2e-07    0.0018      13     106 ..     351     446 ..     345     451 .] 0.51

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.17
                       Trypan_PARP 120 alpfaiaavalv 131
                                        lpf + av+lv
  gi|336255288|ref|YP_004598395.1| 295 NLPFIVVAVGLV 306
                                       79*********9 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2e-07
                       Trypan_PARP  13 lfsanlfagvg.....faaaaegpedkgltkggkgkekgtkvsdddtngtdpepepepepepepepepepepetepe 84 
                                       + +a + + vg     +   ae+  + ++  gg g + gt+    d++  d  p   p p pep+  ++ e++ e e
  gi|336255288|ref|YP_004598395.1| 351 VVTAIVVSLVGarvasYFGGAEDDGEPAVPNGGGGTGTGTEP---DSEVPDGGPSSAPVPTPEPDTVTDGEDDHETE 424
                                       444444444441100123345555566678888887666643...44555556666666666666666666655555 PP

                       Trypan_PARP  85 eepepepepepepepepepepe 106
                                        ep+ ++e +   e++ + e++
  gi|336255288|ref|YP_004598395.1| 425 REPNSDTEADAGAEADADSETD 446
                                       5555555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.20s 00:00:00.71 Elapsed: 00:00:00.36
# Mc/sec: 3718.45
//
Query:       gi|336255289|ref|YP_004598396.1|  [L=331]
Description: signal peptide peptidase SppA, 36K type [Halopiger xanaduensis SH-6]
Scores for 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-39  134.9   0.0    5.7e-39  133.5   0.0    1.6  2  Peptidase_S49  Peptidase family S49
  ------ inclusion threshold ------
      0.028   13.4   0.0      0.041   12.9   0.0    1.2  1  SDH_sah        Serine dehydrogenase proteinase
          8    6.6   6.6         14    5.8   6.6    1.4  1  DUF3742        Protein of unknown function (DUF3742)


Domain annotation for each model (and alignments):
>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.82   4.9e+03      32      47 ..      29      44 ..      26      47 .. 0.84
   2 !  133.5   0.0   9.6e-43   5.7e-39       8     152 ..     141     284 ..     135     286 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.82
                                      EE-TT-EEE---EEEE CS
                     Peptidase_S49 32 vanpstivgsiGvitq 47
                                      v+ p+t++++ Gv  +
  gi|336255289|ref|YP_004598396.1| 29 VVYPTTLTELFGVLIA 44
                                      67899*******9875 PP

  == domain 2  score: 133.5 bits;  conditional E-value: 9.6e-43
                                       -EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEESSTTCCCCCTTSS--HHH CS
                     Peptidase_S49   8 PvvasaenvaaSggYylasaadkivanpstivgsiGvitqllnlenlldklgvevqvvkaGeyksavslrrelteee 84 
                                       P va+a ++ aSggY++as++d+ +a   +ivgsiGvi + +n ++l++k+g++ + ++aGeyk+a+++ +el+ +e
  gi|336255289|ref|YP_004598396.1| 141 PTVAYATDTCASGGYWIASGCDELWAREGSIVGSIGVIGSRVNASDLAEKVGLSYERFAAGEYKDAGTPLKELEADE 217
                                       89*************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHCH CS
                     Peptidase_S49  85 reilqrlldetyqqFvqtVaknRnlsveqvdkiAegrvltgqqAlklgLvdelgtvddavaeleelak 152
                                       re+lq  +d+ y+ Fv+ V+++R +++e v   +e+r+++g+ A +lgLvdelgt +++ +el++  +
  gi|336255289|ref|YP_004598396.1| 218 REYLQGIIDDYYETFVERVSDGRDMDAEFV-RDTEARIYLGERAHELGLVDELGTRREIEDELADRLA 284
                                       ************************998866.579*************************999998665 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.8e-06     0.041      79     155 ..      96     175 ..      93     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-06
                           SDH_sah  79 eevlrairltpkdkpid...liihtpGGlvlaatqiakalkehkaktrvivphyamsGGtlialaadeiildenavl 152
                                       +ev+  i  + +d  +d   l + tpGG v+ +++i  a +    +t         sGG  ia   de+   e +++
  gi|336255289|ref|YP_004598396.1|  96 DEVVEQIDRADEDGNVDallLKLNTPGGEVVPSDDIRLAAERFDGPTVAYATDTCASGGYWIASGCDELWAREGSIV 172
                                       678888999999999994334479*********************************************99999999 PP

                           SDH_sah 153 Gpv 155
                                       G +
  gi|336255289|ref|YP_004598396.1| 173 GSI 175
                                       976 PP

>> DUF3742  Protein of unknown function (DUF3742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   6.6    0.0023        14      44      83 ..      10      49 ..       1      54 [. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0023
                           DUF3742 44 vatavlwvvklavlGvllyvafWlalllvvvvlvawaars 83
                                       a ++++++  av+Gv l+v++ ++l  ++ vl+a++++ 
  gi|336255289|ref|YP_004598396.1| 10 LAIVLVVLATFAVVGVALFVVYPTTLTELFGVLIALVIAG 49
                                      357899999*****************88888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); 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 0.25s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 2588.83
//
Query:       gi|336255290|ref|YP_004598397.1|  [L=293]
Description: hypothetical protein Halxa_3913 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0068   16.9  12.2     0.0068   16.9  12.2    3.2  3  T3SSipB        Type III cell invasion protein SipB
  ------ inclusion threshold ------
       0.96    9.9  38.0       0.33   11.4   6.3    5.1  5  DUF1771        Domain of unknown function (DUF1771)
        1.8    9.1  35.8         23    5.6   4.0    5.2  2  YtxH           YtxH-like protein
        8.6    6.4  34.5        1.2    9.1  10.7    3.6  5  Laminin_II     Laminin Domain II


Domain annotation for each model (and alignments):
>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5  13.8      0.34   1.5e+03      22     113 ..      29     125 ..      21     158 .. 0.77
   2 ?    0.1   8.2      0.23     1e+03      35      94 ..     123     188 ..     104     198 .. 0.43
   3 !   16.9  12.2   1.5e-06    0.0068      45     122 ..     195     272 ..     188     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----.. CS
                           T3SSipB  22 qLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPd.. 96 
                                       qL++r +  ++m   +  +   l  + ++ ++ea++  ++ ++  e++++ k + +++++ ++e   r++eL+ d  
  gi|336255290|ref|YP_004598397.1|  29 QLRDRRNELNQMASERASKRDDLNAKTREKVDEAQEHREQRDELNEQVQEHKEKRNELNAEANELFDRVEELKSDme 105
                                       788899999999999999999999**************999999999999*********************987633 PP

                                       .----..-CHHHHHHHHH.. CS
                           T3SSipB  97 .ePek..akleaaeqQagaa 113
                                        + +k   +le++ +Q++ +
  gi|336255290|ref|YP_004598397.1| 106 lDEGKdlEELEEEIEQLEFK 125
                                       32333225677777787766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.23
                                       HHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHHTT-- CS
                           T3SSipB  35 kaqqeaasklSdelqtalseakgatddleaaiekadq......aksaadaatkkvdeaqkrlkeLa 94 
                                       + +q+     S+e q+++++ +   +++e+  +k+dq      +  +a+++   +++  +++ eLa
  gi|336255290|ref|YP_004598397.1| 123 EFKQQTEVLSSEEEQELIEKIESKREEYEERKQKLDQnedleeLVEEAEEVRSEASKHHQKVTELA 188
                                       334444444455555555555555555555555555411100023333333333333344666662 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 1.5e-06
                                       -STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH..HHHHHHHH CS
                           T3SSipB  45 SdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaaadalqade 121
                                        +++ +a  ea+++ d++++  ek  +a+ aad+ ++    +qkrl eL+  e e +k e++++Q +a+ +a +  +
  gi|336255290|ref|YP_004598397.1| 195 HNQMIEAYREADEIRDEADEMHEKFVEAQEAADQHHEDFVRVQKRLRELDKKEEEERKSERDKKQEAAKEEAEEIYQ 271
                                       566778999**********************************************************9999887766 PP

                                       H CS
                           T3SSipB 122 a 122
                                       +
  gi|336255290|ref|YP_004598397.1| 272 K 272
                                       5 PP

>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   6.3   7.4e-05      0.33       6      54 ..      25      75 ..      22      77 .. 0.93
   2 ?    6.3   0.6    0.0027        12       6      26 ..      74      94 ..      71     118 .. 0.66
   3 ?   11.0   4.0   9.3e-05      0.42      15      56 ..     163     206 ..     150     208 .. 0.76
   4 ?    3.3   0.3     0.024   1.1e+02       4      25 ..     208     225 ..     206     232 .. 0.53
   5 ?   -1.4   0.8      0.69   3.1e+03      22      26 ..     258     262 ..     238     276 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.4e-05
                           DUF1771  6 aeAdeharkrnelfekAaeAyrrGd..gaaAkelseqGkehgekmeeanre 54
                                      + A ++ ++rnel + A+e  ++ d   a+ +e +++++eh+e+ +e+n++
  gi|336255290|ref|YP_004598397.1| 25 KMAGQLRDRRNELNQMASERASKRDdlNAKTREKVDEAQEHREQRDELNEQ 75
                                      6799*********************88888889****************97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0027
                           DUF1771  6 aeAdeharkrnelfekAaeAy 26
                                      ++++eh +krnel ++A e +
  gi|336255290|ref|YP_004598397.1| 74 EQVQEHKEKRNELNAEANELF 94
                                      445555566666666665555 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 9.3e-05
                           DUF1771  15 rnelfekAaeAyrrGd..gaaAkelseqGkehgekmeeanreAa 56 
                                         el e+A e +++    +++  el+++++eh ++m ea reA 
  gi|336255290|ref|YP_004598397.1| 163 LEELVEEAEEVRSEASkhHQKVTELADKAQEHHNQMIEAYREAD 206
                                       56777888888776655689999999999999999999999985 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.024
                           DUF1771   4 lRaeAdeharkrnelfekAaeA 25 
                                        R+eAde+++     f +A+eA
  gi|336255290|ref|YP_004598397.1| 208 IRDEADEMHE----KFVEAQEA 225
                                       4555555555....55555555 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 0.69
                           DUF1771  22 AaeAy 26 
                                        +eA 
  gi|336255290|ref|YP_004598397.1| 258 KQEAA 262
                                       22222 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   4.0    0.0051        23      31      65 ..      24      78 ..      13      82 .. 0.55
   2 ?  -12.8  27.1         4   1.8e+04      34      74 ..     205     273 ..      65     276 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0051
                              YtxH 31 kekaddlkekakelleeakeka....................kekaedlkekvke 65
                                       + a +l+++ +el + a+e+a                    +e+ ++l e+v+e
  gi|336255290|ref|YP_004598397.1| 24 IKMAGQLRDRRNELNQMASERAskrddlnaktrekvdeaqehREQRDELNEQVQE 78
                                      5666666666666666666665554444444433324434445555555555555 PP

  == domain 2  score: -12.8 bits;  conditional E-value: 4
                              YtxH  34 addlkekakelleeakeka............................kekaedlkekvkekadelkekv 74 
                                       ad++++ a+e++e++ e                              k++ ++ +e++ke+a+e+ +k+
  gi|336255290|ref|YP_004598397.1| 205 ADEIRDEADEMHEKFVEAQeaadqhhedfvrvqkrlreldkkeeeerKSERDKKQEAAKEEAEEIYQKF 273
                                       333333333333333332255555568888888888888888888887788888888888888877665 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.27   1.2e+03      63      87 ..      22      46 ..       4      61 .. 0.59
   2 ?    7.5  11.1   0.00086       3.9       7     101 ..      57     121 ..      16     129 .. 0.61
   3 ?    9.1  10.7   0.00028       1.2       6      84 ..      56     134 ..      51     150 .. 0.71
   4 ?    6.2   6.8    0.0022        10      17      78 ..     161     222 ..     136     235 .. 0.75
   5 ?    5.7   9.5    0.0032        14       4      85 ..     169     250 ..     165     269 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.27
                                      XX--TTTTTGGGHHHHHHHHHH... CS
                        Laminin_II 63 kLeklapqLldklkelkqleeasss 87
                                      +L k a qL d+ +el+q  ++++s
  gi|336255290|ref|YP_004598397.1| 22 ELIKMAGQLRDRRNELNQMASERAS 46
                                      5566666666666666666555554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00086
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83 
                                       e  + a+e                              e+ +++n+++++ +++  +L+ +a++L+d+++elk   e
  gi|336255290|ref|YP_004598397.1|  57 EKVDEAQEH----------------------------REQRDELNEQVQEHKEKRNELNAEANELFDRVEELKSDME 105
                                       222233333............................4444466666666666677777777777777777766554 PP

                                       H...HHHHHHHHHHHHHH CS
                        Laminin_II  84 assslsdniseikelIaq 101
                                         +  +++++e+ e I+q
  gi|336255290|ref|YP_004598397.1| 106 LDE--GKDLEELEEEIEQ 121
                                       433..3333333333333 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00028
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvk.dankairdArrsvkkLeklapqLldklkelkql 81 
                                       +e  + a+e  eq  +l++++++ kek +e+n++++e  + v+  ++ +  d ++   +Le++++qL+ k ++ + l
  gi|336255290|ref|YP_004598397.1|  56 REKVDEAQEHREQRDELNEQVQEHKEKRNELNAEANELFDRVEeLKSDMELDEGKDLEELEEEIEQLEFK-QQTEVL 131
                                       5556677888888999999999999999999999999999998445667778888899999999999877.444444 PP

                                       HHH CS
                        Laminin_II  82 eea 84 
                                       +++
  gi|336255290|ref|YP_004598397.1| 132 SSE 134
                                       443 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0022
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                       e+l++l ++ e++++++s+ +++v e  +k+++  +++ +A r+  ++  +a+++ +k+ e 
  gi|336255290|ref|YP_004598397.1| 161 EDLEELVEEAEEVRSEASKHHQKVTELADKAQEHHNQMIEAYREADEIRDEADEMHEKFVEA 222
                                       56777777778888888888888888888888888888888888888888888888887554 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.0032
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                        a+e+ + a++  +++++l+ + ++  +++ e+ r+++e+ ++++++ +  ++A+++  +  +   ++ ++l+el++
  gi|336255290|ref|YP_004598397.1| 169 EAEEVRSEASKHHQKVTELADKAQEHHNQMIEAYREADEIRDEADEMHEKFVEAQEAADQHHEDFVRVQKRLRELDK 245
                                       57788888999999999**********************************************************99 PP

                                       HHHH. CS
                        Laminin_II  81 leeas 85 
                                       +ee++
  gi|336255290|ref|YP_004598397.1| 246 KEEEE 250
                                       99874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4475  (0.249596); expected 358.6 (0.02)
Passed bias filter:                      852  (0.0475208); expected 358.6 (0.02)
Passed Vit filter:                       380  (0.0211947); expected 17.9 (0.001)
Passed Fwd filter:                       168  (0.00937029); 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: 2.26u 0.36s 00:00:02.61 Elapsed: 00:00:00.58
# Mc/sec: 1523.56
//
Query:       gi|336255291|ref|YP_004598398.1|  [L=360]
Description: Tubulin/FtsZ GTPase [Halopiger xanaduensis SH-6]
Scores for complete 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   90.7   0.1    2.4e-25   89.9   0.1    1.4  1  Tubulin    Tubulin/FtsZ family, GTPase domain
    2.3e-07   30.3   0.4      1e-06   28.2   0.2    2.0  2  Tubulin_2  Tubulin like


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 !   89.9   0.1   2.7e-29   2.4e-25       2     194 ..       3     171 ..       2     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 2.7e-29
                                       EEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE- CS
                           Tubulin   2 iivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklll 78 
                                       +  igvGq+G+++ ++l + +  + g              +  +      +a++  + +l++++        +++l+
  gi|336255291|ref|YP_004598398.1|   3 VALIGVGQAGGKVTERLAR-FDADMGF-------------EAVQGA----LAVNSAKPDLQSLEFV------DTQLI 55 
                                       678****************.8888787.............443444....59***99999999999......999** PP

                                       -CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE...SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEE CS
                           Tubulin  79 gkegagnngaggypevgkeaaeeileeirkevekcds..lqgffitaslgGGTGSGlgpvilevlkeeypkalvvtv 153
                                       g +  +++g+gg++e+g+e++++  +++   +++  +  ++++f++a+lgGGTGSG +pv+++ l++ y +++v++ 
  gi|336255291|ref|YP_004598398.1|  56 GADRVNGHGVGGDNELGTEIMQSDIQQVLSGLDGRVTsrADAIFVVAGLGGGTGSGGAPVLVHNLQQIY-DIPVYAL 131
                                       ******************************999654434999**************************9.******* PP

                                       EEE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHC CS
                           Tubulin 154 vvlPsefsevvvepynailalkelieesdavividNdaLlk 194
                                        +lP ++ e+ +++ na  +lk++ +e+da+++idNd++++
  gi|336255291|ref|YP_004598398.1| 132 GILPGQN-EGSLYQANAGRSLKTIAREADATLLIDNDSWHE 171
                                       *****99.******************************986 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0     0.068   6.1e+02       2      18 ..       5      21 ..       5      52 .. 0.90
   2 !   28.2   0.2   1.1e-10     1e-06     138     226 ..      79     156 ..      69     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.068
                         Tubulin_2  2 viGLGGtGgkvlaelrr 18
                                      +iG+G  Ggkv ++l+r
  gi|336255291|ref|YP_004598398.1|  5 LIGVGQAGGKVTERLAR 21
                                      69************987 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.1e-10
                         Tubulin_2 138 alrdaikrlrgsage.eeglnvfVvgSLaGGTGSGiflDvayllrkilkeekqkvkiiglvllPdvfplnkeggerv 213
                                        ++++++ l g  ++ ++   +fVv +L GGTGSG +  ++++l++i++        ++l +lP       ++g  +
  gi|336255291|ref|YP_004598398.1|  79 DIQQVLSGLDG--RVtSRADAIFVVAGLGGGTGSGGAPVLVHNLQQIYDIPV-----YALGILPGQ-----NEGSLY 143
                                       45555555555..34355568***************************8765.....799****97.....5689** PP

                         Tubulin_2 214 kaNayaaLkELna 226
                                       +aNa ++Lk +++
  gi|336255291|ref|YP_004598398.1| 144 QANAGRSLKTIAR 156
                                       *********9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2782.47
//
Query:       gi|336255292|ref|YP_004598399.1|  [L=374]
Description: oxidoreductase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-16   60.8   0.0    3.7e-16   60.0   0.0    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    1.1e-11   44.8   0.1    2.8e-11   43.5   0.1    1.7  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
  ------ inclusion threshold ------
       0.13   12.0   0.0       0.33   10.6   0.0    1.7  1  ox_reductase_C  Putative oxidoreductase C terminal domain


Domain annotation for each model (and alignments):
>> 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 !   60.0   0.0   6.3e-20   3.7e-16       2     114 ..       4     121 ..       3     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 6.3e-20
                                       EEEEETTSHHHHHHHHHHHHTTTTE......EEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S- CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrle......evvalldpdaeraeavaesfgve.aysdleelladpeidavivatp 71 
                                       +v++ G+ ++g+ h++++ +   +       e   l+ +d+e+  ++a+++g++   +d+e++++  ++d+ +   p
  gi|336255292|ref|YP_004598399.1|   4 QVGVLGYRFMGKAHANAMARLPMFFpdapdiERSVLVGRDEEALNEAADRLGFDsISTDWENVVD--DVDVFYNLGP 78 
                                       799****888*****9999997777999*998889*******************55667******..99******** PP

                                       GGGHHHHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS CS
                      GFO_IDH_MocA  72 ngtheelakaaleagkhvllEKPlattveeakelvelaekkgk 114
                                       n+ h+e  +aaleag  v++EKPla t+e+a++++e+a+ +g 
  gi|336255292|ref|YP_004598399.1|  79 NHVHAEPSIAALEAGTPVFCEKPLAPTLEDAERMAETARDAGD 121
                                       ***************************************9986 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.1   4.6e-15   2.8e-11       1     112 [.     141     270 ..     141     274 .. 0.70

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 4.6e-15
                                       HHHHHTTTTSSEEEEEEEEECBEEECHHH.HCCGGSH.HCSTSHHHHTCHHHHHHHHHHHTSEE...EEEEEEE.S. CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeak.krwkrrk.kksgGvlgdlgiHdiDllqwLfGqpp...svvaalgrm. 71 
                                       K l+e+g+lGe+++v + +l+++  ++   ++w+++    ++G+lgdlg H+ Dll++L+G +      +++ g++ 
  gi|336255292|ref|YP_004598399.1| 141 KGLLEAGELGEIRHVRGRYLQDWLVDPEApWSWRNDEeMAGSGALGDLGAHTVDLLRFLVGDDDlagDIERLSGHLq 217
                                       779********************9877650555555599999*******************9742112222333320 PP

                                       EEESCTCCSCSEEE............EEEEEEEETTEEEEEEEECCTSSSEEE CS
                    GFO_IDH_MocA_C  72 rqnaeaaededaav............msvlnlekgsgevitlesgvskglsir 112
                                        +++e++++ ++++            ++++n+++g++e++  ++g  + ++i+
  gi|336255292|ref|YP_004598399.1| 218 TFVDERPAEGGDETrpvtvddaysaqLEFENGAMGTLEATRNATGHKNDHTIE 270
                                       34444444444444788888888888888888888888777777666666665 PP

>> ox_reductase_C  Putative oxidoreductase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.6e-05      0.33       1     138 [.     132     272 ..     132     275 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.6e-05
                    ox_reductase_C   1 rylkvvqkmkkiikennl.kvvatnaryvsayehaakkaw.weksisa...GpvveqathfcdlsryfgGdvdldtv 72 
                                       r++ ++q +k +++  +l ++     ry   +       w w + +++   G + + ++h  dl r++ Gd dl+  
  gi|336255292|ref|YP_004598399.1| 132 RFVPAIQYAKGLLEAGELgEIRHVRGRYLQDWLVDPEAPWsWRNDEEMagsGALGDLGAHTVDLLRFLVGDDDLAG- 207
                                       566677888888887777456777788888887777666655544432222788899**************99865. PP

                    ox_reductase_C  73 kaksvewyekaGklskipvdeskip..eder...iprltsaswkyksGavGslehavalqGtkystelevl 138
                                           +     +G+l+   vde+  +  +++r   +  + sa+  +++Ga+G+le +    G+k + ++e++
  gi|336255292|ref|YP_004598399.1| 208 ---DI--ERLSGHLQTF-VDERPAEggDETRpvtVDDAYSAQLEFENGAMGTLEATRNATGHKNDHTIEIH 272
                                       ...33..3457888764.7777654213444333566789***************9999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2942.17
//
Query:       gi|336255293|ref|YP_004598400.1|  [L=197]
Description: hypothetical protein Halxa_3916 [Halopiger xanaduensis SH-6]
Scores for 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  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1577.89
//
Query:       gi|336255294|ref|YP_004598401.1|  [L=211]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-30  104.2   1.8    7.8e-30  104.2   1.8    1.6  2  Usp       Universal stress protein family
  ------ inclusion threshold ------
        0.2   12.6   0.6        0.2   12.6   0.6    1.8  2  TPR_14    Tetratricopeptide repeat


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 !  104.2   1.8   8.6e-34   7.8e-30       1     141 []       1     133 [.       1     133 [. 0.94
   2 ?   -1.9   0.1      0.47   4.2e+03      29      29 ..     159     159 ..     138     200 .. 0.53

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 8.6e-34
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       my+++l+++Dgs+ +++ +e++l+ a +++a+++ l v+++ + g+  + + + + ++++++ + +        a+a
  gi|336255294|ref|YP_004598401.1|   1 MYQHVLIPTDGSDGTRRSIEHGLAIADRFDATVHGLSVVPEGPLGTFEANEATPAAHRAVERVELE--------ANA 69 
                                       9**************************************999999988888888888888877766........489 PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +gv+v++ ve+g p eeil++++e+d+d iV+G+ gr+gl+r+l+GSv+e+++r a++pV+ Vr
  gi|336255294|ref|YP_004598401.1|  70 AGVDVVTAVEQGVPHEEILDYVDEHDIDAIVMGTQGRTGLDRVLMGSVTERIVRMADVPVVTVR 133
                                       9************************************************************998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.47
                                       C CS
                               Usp  29 r 29 
                                       +
  gi|336255294|ref|YP_004598401.1| 159 Y 159
                                       1 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1         2   1.8e+04      21      29 ..      53      61 ..      47      69 .. 0.54
   2 ?   12.6   0.6   2.2e-05       0.2      11      37 ..     137     163 ..     132     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2
                            TPR_14 21 iallrrala 29
                                        +++ra++
  gi|336255294|ref|YP_004598401.1| 53 TPAAHRAVE 61
                                      334444443 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.2e-05
                            TPR_14  11 llalGdpdeAiallrralalaPddaea 37 
                                       +l+ +dpdeA++l+r+al+++  d +a
  gi|336255294|ref|YP_004598401.1| 137 ELRIEDPDEAERLARDALEADGYDGDA 163
                                       67789**************99877555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 1857.47
//
Query:       gi|336255295|ref|YP_004598402.1|  [L=57]
Description: hypothetical protein Halxa_3918 [Halopiger xanaduensis SH-6]
Scores for 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-06   26.9   1.4    4.6e-06   26.6   1.4    1.1  1  Zn-ribbon_8      Zinc ribbon domain
    0.00075   19.5   0.1    0.00084   19.3   0.1    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0029   17.5   2.0      0.016   15.1   0.1    2.1  2  zf-dskA_traR     Prokaryotic dksA/traR C4-type zinc finger
  ------ inclusion threshold ------
      0.012   15.6   4.7        0.5   10.4   0.3    2.2  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.018   14.9   1.7       0.77    9.7   1.9    2.1  2  Prok-RING_4      Prokaryotic RING finger family 4
      0.022   15.0   0.2        2.9    8.2   0.1    2.1  2  zf-LITAF-like    LITAF-like zinc ribbon domain
      0.023   15.0   0.6        1.6    9.1   0.0    2.1  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
      0.042   14.1   0.9      0.071   13.4   0.9    1.4  1  zinc_ribbon_9    zinc-ribbon
      0.051   13.6   3.5        3.5    7.7   0.4    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.064   12.7   1.6        2.5    7.6   0.4    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.12   12.1   1.8        4.4    7.1   2.7    2.0  2  YacG             DNA gyrase inhibitor YacG
       0.12   11.9   2.3       0.44   10.1   2.4    1.8  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.15   12.2   0.4        2.8    8.1   0.1    2.0  2  DiS_P_DiS        Bacterial Peptidase A24 N-terminal domain
       0.15   12.1   0.7          6    7.0   0.0    2.3  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.26   11.8   1.5         10    6.7   0.1    2.2  2  zf-H2C2_2        Zinc-finger double domain
       0.41   10.8   2.8        8.7    6.5   0.2    2.0  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.71   10.3   4.1        3.2    8.2   0.8    2.1  2  Lar_restr_allev  Restriction alleviation protein Lar


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 !   26.6   1.4   4.4e-09   4.6e-06       1      36 [.      11      47 ..      11      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4.4e-09
                       Zn-ribbon_8  1 MPiYeYrCeeCghefevlqsisdaplta.CPeCgsev 36
                                      M  Y +rC +C ++ e   +  +a+ +  CP Cgs+v
  gi|336255295|ref|YP_004598402.1| 11 MSPYRFRCPDCAQRIELEEPGREAAVESgCPFCGSAV 47
                                      556*************9999999999999*****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 !   19.3   0.1   7.9e-07   0.00084      64      95 ..       9      46 ..       2      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.9e-07
                                      EEEE--EEEETTTS-EEECHH...HHH....S-TTTSSS CS
                              HypA 64 ieevpvkvrCreCgkefelee...kal....rCpkCgsa 95
                                      i   p ++rC +C +++elee   + +     Cp Cgsa
  gi|336255295|ref|YP_004598402.1|  9 IVMSPYRFRCPDCAQRIELEEpgrE-AavesGCPFCGSA 46
                                      677899************9986541.145559*****96 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 !   15.1   0.1   1.6e-05     0.016      16      35 ..       7      26 ..       5      27 .. 0.91
   2 ?    2.4   0.1      0.14   1.5e+02      19      27 ..      34      43 ..      29      49 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                      zf-dskA_traR 16 aRlralPgarlCveCqekae 35
                                       R++  P++ +C +C++++e
  gi|336255295|ref|YP_004598402.1|  7 DRIVMSPYRFRCPDCAQRIE 26
                                      689999************98 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.14
                      zf-dskA_traR 19 ralP.garlC 27
                                       a++ g+++C
  gi|336255295|ref|YP_004598402.1| 34 AAVEsGCPFC 43
                                      5553366666 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 ?    7.2   0.6    0.0049       5.1       1      14 [.      17      31 ..      17      36 .. 0.71
   2 ?   10.4   0.3   0.00047       0.5       2       9 ..      40      47 ..      39      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0049
                    DNA_ligase_ZBD  1 hCPvCGsavv.Reeg 14
                                      +CP C + ++  e+g
  gi|336255295|ref|YP_004598402.1| 17 RCPDCAQRIElEEPG 31
                                      5******99944444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00047
                    DNA_ligase_ZBD  2 CPvCGsav 9 
                                      CP CGsav
  gi|336255295|ref|YP_004598402.1| 40 CPFCGSAV 47
                                      *******9 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 ?    5.2   0.2     0.019        20      32      43 ..      17      28 ..       6      31 .. 0.78
   2 ?    9.7   1.9   0.00073      0.77      21      42 ..      18      49 ..      18      52 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.019
                       Prok-RING_4 32 sCPlCqrrisks 43
                                      +CP C +ri+ +
  gi|336255295|ref|YP_004598402.1| 17 RCPDCAQRIELE 28
                                      7****9999765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00073
                       Prok-RING_4 21 CkeCfdskdls..........sCPlCqrrisk 42
                                      C +C +  +l+          +CP+C + + +
  gi|336255295|ref|YP_004598402.1| 18 CPDCAQRIELEepgreaavesGCPFCGSAVGA 49
                                      666666666555556666666*****988755 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 ?    8.2   0.1    0.0027       2.9       2      15 ..      12      25 ..      11      28 .. 0.87
   2 ?    5.3   0.0     0.022        24      55      68 ..      36      49 ..      32      51 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0027
                     zf-LITAF-like  2 eptqvdCpaCqqrv 15
                                      +p+++ Cp C qr+
  gi|336255295|ref|YP_004598402.1| 12 SPYRFRCPDCAQRI 25
                                      69999*****9997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.022
                     zf-LITAF-like 55 vehyCpnCgallgt 68
                                      ve  Cp Cg+ +g 
  gi|336255295|ref|YP_004598402.1| 36 VESGCPFCGSAVGA 49
                                      55667777777775 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 ?    4.6   0.1     0.038        40       3      13 ..      16      26 ..      14      30 .. 0.73
   2 ?    9.1   0.0    0.0015       1.6       5      17 ..      40      52 ..      36      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.038
                           zf-Di19  3 ftCPyCgkelt 13
                                      f CP C + ++
  gi|336255295|ref|YP_004598402.1| 16 FRCPDCAQRIE 26
                                      88999988655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0015
                           zf-Di19  5 CPyCgkeltvkeL 17
                                      CP+Cg ++ +k +
  gi|336255295|ref|YP_004598402.1| 40 CPFCGSAVGAKDF 52
                                      9***998887776 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   6.7e-05     0.071       5      29 ..      18      45 ..      14      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-05
                     zinc_ribbon_9  5 ChqCdrfVsvspdedsd...vlCPhCgg 29
                                      C +C+++++++++  ++   + CP+Cg+
  gi|336255295|ref|YP_004598402.1| 18 CPDCAQRIELEEPGREAaveSGCPFCGS 45
                                      669**********888855449****98 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 ?    7.7   0.4    0.0033       3.5      18      27 ..      15      24 ..      10      34 .. 0.79
   2 ?    7.5   0.2    0.0039       4.1      21      27 ..      40      46 ..      30      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0033
                     Zn_Tnp_IS1595 18 gfvCPhCgsr 27
                                      +f+CP C+ r
  gi|336255295|ref|YP_004598402.1| 15 RFRCPDCAQR 24
                                      799****976 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0039
                     Zn_Tnp_IS1595 21 CPhCgsr 27
                                      CP+Cgs+
  gi|336255295|ref|YP_004598402.1| 40 CPFCGSA 46
                                      *****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 ?    4.4   0.0     0.026        27       4      10 ..      17      23 ..      16      29 .. 0.75
   2 ?    7.6   0.4    0.0024       2.5       5      11 ..      40      47 ..      38      51 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.026
                       zf-ribbon_3  4 rCPnCGa 10
                                      rCP C +
  gi|336255295|ref|YP_004598402.1| 17 RCPDCAQ 23
                                      8999977 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0024
                       zf-ribbon_3  5 CPnCGa.p 11
                                      CP CG+ +
  gi|336255295|ref|YP_004598402.1| 40 CPFCGSaV 47
                                      88888755 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.7    0.0041       4.4       2      22 ..      17      43 ..      16      45 .. 0.67
   2 ?    4.7   0.1     0.024        25       3      12 ..      40      49 ..      38      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0041
                              YacG  2 kCPtCkkevewse......enpfrPFC 22
                                      +CP C++++e +e       ++  PFC
  gi|336255295|ref|YP_004598402.1| 17 RCPDCAQRIELEEpgreaaVESGCPFC 43
                                      8*********99854422223446888 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                              YacG  3 CPtCkkevew 12
                                      CP C+++v  
  gi|336255295|ref|YP_004598402.1| 40 CPFCGSAVGA 49
                                      9999998865 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.4   0.00042      0.44       1      29 [.      16      47 ..      16      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00042
                                      EEETTTTCEE.CHEE..TSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon  1 ykCPnCgstn.lveD..pergelvCtdCGlVl 29
                                      ++CP+C  +  l+e+  ++  e  C++CG+ +
  gi|336255295|ref|YP_004598402.1| 16 FRCPDCAQRIeLEEPgrEAAVESGCPFCGSAV 47
                                      68*****98667777889999999*****866 PP

>> DiS_P_DiS  Bacterial Peptidase A24 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0027       2.8      52      71 ..      15      34 ..       9      37 .. 0.79
   2 ?    2.9   0.0      0.11   1.2e+02      27      40 ..      37      50 ..      34      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0027
                         DiS_P_DiS 52 rgrCraCkakislryplvEl 71
                                      r rC  C ++i+l+ p  E+
  gi|336255295|ref|YP_004598402.1| 15 RFRCPDCAQRIELEEPGREA 34
                                      67899999999988887776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                         DiS_P_DiS 27 rSrCpkCghklkwl 40
                                      +S Cp Cg+++ + 
  gi|336255295|ref|YP_004598402.1| 37 ESGCPFCGSAVGAK 50
                                      699****9998765 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 ?    3.0   1.0      0.11   1.1e+02       3       9 ..      17      23 ..      16      29 .. 0.83
   2 ?    7.0   0.0    0.0057         6       4      17 ..      40      53 ..      38      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                            zf-ACC  3 KCpsCge 9 
                                      +Cp C +
  gi|336255295|ref|YP_004598402.1| 17 RCPDCAQ 23
                                      7999975 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0057
                            zf-ACC  4 CpsCgemlykkeLe 17
                                      Cp Cg+ + +k+++
  gi|336255295|ref|YP_004598402.1| 40 CPFCGSAVGAKDFA 53
                                      ***********997 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 ?    6.7   0.1    0.0098        10      13      21 ..      14      22 ..       8      24 .. 0.74
   2 ?    4.2   0.2     0.062        65      17      23 ..      40      46 ..      40      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0098
                         zf-H2C2_2 13 kpyeCplCd 21
                                       ++ Cp C+
  gi|336255295|ref|YP_004598402.1| 14 YRFRCPDCA 22
                                      359*****8 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.062
                         zf-H2C2_2 17 CplCdka 23
                                      Cp+C+ a
  gi|336255295|ref|YP_004598402.1| 40 CPFCGSA 46
                                      ****975 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 ?    6.5   0.2    0.0083       8.7      14      23 ..      13      22 ..       7      29 .. 0.85
   2 ?    6.3   3.0    0.0095        10       2      26 ..      18      47 ..      17      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0083
                          zf-Mss51 14 hvdfeCpdCG 23
                                      + +f CpdC+
  gi|336255295|ref|YP_004598402.1| 13 PYRFRCPDCA 22
                                      679******7 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0095
                          zf-Mss51  2 CPvpkhkqt.....apkhvdfeCpdCGipt 26
                                      CP ++++ +      ++ v+  Cp CG  +
  gi|336255295|ref|YP_004598402.1| 18 CPDCAQRIEleepgREAAVESGCPFCGSAV 47
                                      999987777999889999*********765 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 ?    3.4   0.1     0.093        98       6      22 ..      18      34 ..      16      39 .. 0.78
   2 ?    8.2   0.8    0.0031       3.2       6      12 ..      40      46 ..      37      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.093
                   Lar_restr_allev  6 CPfCggravlersqrvv 22
                                      CP C +r +le+ +r +
  gi|336255295|ref|YP_004598402.1| 18 CPDCAQRIELEEPGREA 34
                                      99999998888876665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0031
                   Lar_restr_allev  6 CPfCggr 12
                                      CPfCg++
  gi|336255295|ref|YP_004598402.1| 40 CPFCGSA 46
                                      *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.34u 0.19s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 508.60
//
Query:       gi|336255296|ref|YP_004598403.1|  [L=127]
Description: Glyoxalase/bleomycin resistance protein/dioxygenase [Halopiger xanaduensis SH-6]
Scores for 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   60.0   0.6    2.9e-16   59.8   0.6    1.0  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    1.7e-13   50.8   0.2    9.8e-09   35.5   0.1    1.8  2  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    2.4e-07   30.7   0.0    3.3e-07   30.3   0.0    1.1  1  Glyoxalase_2  Glyoxalase-like domain
    1.2e-06   29.2   0.2    1.6e-06   28.9   0.2    1.1  1  Glyoxalase_6  Glyoxalase-like domain
    1.1e-05   25.6   0.9       0.04   14.0   0.3    2.1  2  Glyoxalase_3  Glyoxalase-like domain


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 !   59.8   0.6   8.1e-20   2.9e-16       2     128 .]       3     121 ..       2     121 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 8.1e-20
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhva 78 
                                       +dh+a++v+dle++ +FY++ LG++   +++    ++g + ++++ ++   ++  ++ p+g++  +        ++ 
  gi|336255296|ref|YP_004598403.1|   3 VDHTAVRVSDLEATKAFYEDGLGLEFHQEFH---TDDGIHNYYVTGDELETSIQFAHDPDGDEEIE------PSGIV 70 
                                       69*****************************...6799999**********************999......89*** PP

                                       EEEEEHCHHHHHHHHHHHT.TGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  79 fialdvedvgkaldrlkea.gvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       ++a  v+d++++l+rl e+ g++v ++p +    +   ++++DpdG+++ei
  gi|336255296|ref|YP_004598403.1|  71 HLAILVDDLDETLERLTERtGCEVLRGPITVDAVDARAAFVEDPDGYEVEI 121
                                       ****************87538*****99887777777777*********97 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.1   2.7e-12   9.8e-09       1     109 []       4     110 ..       4     110 .. 0.83
   2 !   19.6   0.0   2.3e-07   0.00084       2      57 ..      71     126 ..      70     127 .] 0.89

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 2.7e-12
                                       EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT-THHHTS-EEEEEEEEES CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegpeflaehgeglhhlaywvd 77 
                                       d++++ V Dlea+ a++++ lG++++q+++ ++  ++++++     +  i++ +  +g+e +     g+ hla+ vd
  gi|336255296|ref|YP_004598403.1|   4 DHTAVRVSDLEATKAFYEDGLGLEFHQEFHTDDGIHNYYVTGDEL-ETSIQFAHDPDGDEEI--EPSGIVHLAILVD 77 
                                       6999*************************9887766666665555.4788888877777665..5789********* PP

                                       -HHHHHHHHCTT.TEEEEEEEE-GGGTT-EEEE CS
                      Glyoxalase_4  78 dldaavarleeq.Gfevvqkgvragaagrrfay 109
                                       dld++++rl+e+ G ev+   + + a + r+a+
  gi|336255296|ref|YP_004598403.1|  78 DLDETLERLTERtGCEVLRGPITVDAVDARAAF 110
                                       *********885499998887777777777776 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.3e-07
                                       EEEEE-S-HHHHHHHHHH.TT-E.ESS--E.EETTTTEEEEEEEETTEEEEEEEESS CS
                      Glyoxalase_4   2 QigivVeDleaavarfsallGvg.pwqryrdepqevdlafallgsgsvqieLieple 57 
                                       +++i V+Dl+++++r+++  G++  + +++++  +++ af++  +g  ++e  ++++
  gi|336255296|ref|YP_004598403.1|  71 HLAILVDDLDETLERLTERTGCEvLRGPITVDAVDARAAFVEDPDG-YEVEIYANRD 126
                                       99********************9456899****************9.7999887765 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   9.1e-11   3.3e-07       7     113 ..       9     121 ..       4     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 9.1e-11
                                       EES-HHHHHHHHHHTT---EEEE-....SSEEEETTS-EEEEHHHHHH----.---S--SS-EEEEEES-HHHHHHH CS
                      Glyoxalase_2   7 vvkdieeskkFYedvlelkikldf....Genvsfetgfalkedlkelinlde.siaeqsnnfeLyFevedvdaflqk 78 
                                        v d+e +k FYed l l+ +++f    G +  + tg +l+  ++   + d  +++e s  ++L   v+d+d++l++
  gi|336255296|ref|YP_004598403.1|   9 RVSDLEATKAFYEDGLGLEFHQEFhtddGIHNYYVTGDELETSIQFAHDPDGdEEIEPSGIVHLAILVDDLDETLER 85 
                                       699***********987766555433338899999*****999999999877577889999**************** PP

                                       H..GGGS-EEEEEE.E-TTS-EEEEEE-TT--EEEE CS
                      Glyoxalase_2  79 lkeaeniellhelk.ekpWgqrvirfyDpDkhiiEi 113
                                       l e    e+l  ++ + +   r + + DpD+  +Ei
  gi|336255296|ref|YP_004598403.1|  86 LTERTGCEVLRGPItVDAVDARAAFVEDPDGYEVEI 121
                                       **********98651688999**************9 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.2   4.4e-10   1.6e-06       3     105 ..       7     120 ..       5     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 4.4e-10
                      Glyoxalase_6   3 vldaadpaalaaFwaaalgweveree.....aaledpegvgpaaedaatllfqrvpe......paknrvHldlaved 68 
                                       ++ ++d +a  aF+++ lg+e ++e           ++     +e ++++ f + p+      p    vHl + v+d
  gi|336255296|ref|YP_004598403.1|   7 AVRVSDLEATKAFYEDGLGLEFHQEFhtddgI----HNYYVTGDELETSIQFAHDPDgdeeieP-SGIVHLAILVDD 78 
                                       68899********************9543220....2223333455667888888889887743.446********* PP

                      Glyoxalase_6  69 ldaevarlval.GArvlreprdgthgr....vlaDPeGneFc 105
                                       ld++ +rl +  G +vlr p   ++ +     ++DP+G e  
  gi|336255296|ref|YP_004598403.1|  79 LDETLERLTERtGCEVLRGPITVDAVDaraaFVEDPDGYEVE 120
                                       ********8753889999988888777899********8865 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.3   1.1e-05      0.04       2      42 ..       4      43 ..       3      47 .. 0.92
   2 !   10.5   0.0   0.00013      0.47       3      27 ..      71      95 ..      55     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                      Glyoxalase_3  2 DHvvlavpdleeaaarfarrlGftvtpggehpglgtaNalv 42
                                      DH+ + v+dle++ a +++ lG+++++  +  + g++N+ v
  gi|336255296|ref|YP_004598403.1|  4 DHTAVRVSDLEATKAFYEDGLGLEFHQEFHTDD-GIHNYYV 43
                                      *************************99998888.9999865 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00013
                      Glyoxalase_3  3 HvvlavpdleeaaarfarrlGftvt 27
                                      H+ ++v+dl+e+ +r+++r+G +v 
  gi|336255296|ref|YP_004598403.1| 71 HLAILVDDLDETLERLTERTGCEVL 95
                                      8999999999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); 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:                         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: 0.37u 0.18s 00:00:00.55 Elapsed: 00:00:00.33
# Mc/sec: 1149.91
//
Query:       gi|336255297|ref|YP_004598404.1|  [L=152]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-17   62.6   1.1    6.9e-17   62.3   1.1    1.2  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 !   62.3   1.1   3.8e-21   6.9e-17       4     141 .]       5     148 ..       2     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 3.8e-21
                                       EEEEEE-..SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH....HHHH CS
                               Usp   4 rIlVavD..gseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada....akaa 74 
                                       ++l+av   +se  ++++e  +e a+  +a+++l+hv  ++++++v d  e  +   + +  + + +      ++ a
  gi|336255297|ref|YP_004598404.1|   5 TVLLAVGpgDSERIDELAEAVVEVAAPADATVVLAHVFTDSEYDEVLDRLEFDRSVDEIEPDEVAMRHStireLQSA 81 
                                       788888654555556777777889999****************99988766555554444444433333557899** PP

                                       HHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  75 aeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +++ +++ ev   +gd +++i+++a + dad ++vG r+rs   ++++GS+++ vl ++pcp + Vr
  gi|336255297|ref|YP_004598404.1|  82 LDEYDIDYEVRGAVGDHGPTIVDLAGDVDADRVLVGGRRRSPTGKAVFGSTAQEVLLSSPCPATFVR 148
                                       **************************************************************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1218.38
//
Query:       gi|336255298|ref|YP_004598405.1|  [L=246]
Description: 3-oxoacyl-(acyl-carrier-protein) reductase [Halopiger xanaduensis SH-6]
Scores for complete 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  149.5   0.0    3.2e-43  148.0   0.0    1.6  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.2e-41  142.4   0.0    1.4e-41  142.1   0.0    1.0  1  adh_short        short chain dehydrogenase
    3.2e-07   30.4   0.1    4.5e-07   29.9   0.1    1.2  1  KR               KR domain
  ------ inclusion threshold ------
      0.016   14.6   0.3      0.057   12.9   0.1    1.9  2  Epimerase        NAD dependent epimerase/dehydratase family
       0.11   11.5   0.0       0.14   11.3   0.0    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
       0.15   11.4   0.3       0.28   10.5   0.1    1.6  2  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas


Domain annotation for each model (and alignments):
>> 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 !  148.0   0.0   1.1e-46   3.2e-43       4     233 ..      18     241 ..      15     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 148.0 bits;  conditional E-value: 1.1e-46
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTT.SEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelg.aev..lecDVtdeeqvealveevvekfgklDilvnn 76 
                                       +g+Gr++  a a+ Ga+vv+++   ++ +++v++ a e g  ++  ++ DVtd+e+v+ l+++v+++fg++D+lvnn
  gi|336255298|ref|YP_004598405.1|  18 KGVGRELLLATADCGATVVVHYHTSADaAREVADEALERGaGDAmtVQGDVTDPESVDGLFSAVEAEFGGVDVLVNN 94 
                                       899********************99998555555444444244447******************************* PP

                                       ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSB..STTTTHHHHHHHHHH CS
                      adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaerv..vpnynaygaaKaale 149
                                       +g   +  ++ ++++ + ++r+l++nl++++l++k+al +m+eg  g+ivn+ + ++e++   p++  y +aKa++ 
  gi|336255298|ref|YP_004598405.1|  95 VGDFAP--AHWADLDFATWNRVLETNLNGTYLCSKRALAHMREGdyGRIVNIGYASSEKGlvSPKNFPYFVAKAGVL 169
                                       **9999..9*************************************************995344444********** PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEE CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqt 226
                                        +tr lA++  ++ ++vNa+sp +++              +e+ +  p  r ++ e+  +   f++ +++ y++G++
  gi|336255298|ref|YP_004598405.1| 170 MFTRMLAADTQDDDVTVNAISPYVVE------------NSDEFPDDLPQDRPASFEDLIQPLHFFLDPDSGYVSGEN 234
                                       *************************9............234566789****************************** PP

                                       EEESTTG CS
                      adh_short_C2 227 lvvDgGl 233
                                       + vDgG+
  gi|336255298|ref|YP_004598405.1| 235 IEVDGGW 241
                                       ******6 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.1   0.0   4.8e-45   1.4e-41       2     183 ..      10     195 ..       9     203 .. 0.94

  Alignments for each domain:
  == domain 1  score: 142.1 bits;  conditional E-value: 4.8e-45
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklg 76 
                                       +vlvtG ++G+Gr++  + a  Ga+vvv +  s+++++eva+e  e  + +a+++q+Dvtd e+v+ l++++++++g
  gi|336255298|ref|YP_004598405.1|  10 TVLVTGSGKGVGRELLLATADCGATVVVhYHTSADAAREVADEALERgAGDAMTVQGDVTDPESVDGLFSAVEAEFG 86 
                                       89*****************************************9999999*************************** PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEE...EEGGGTSB-TTBHHHH CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnv...sSvagkvpvagvaaYs 150
                                       ++dvLvnN+G   ++  ++l+ ++w+rv+e+Nl+g++l+++ +l +m ++  GrIvn+   sS  g+v ++   +Y 
  gi|336255298|ref|YP_004598405.1|  87 GVDVLVNNVGDFAPAHWADLDFATWNRVLETNLNGTYLCSKRALAHMREGDYGRIVNIgyaSSEKGLV-SPKNFPYF 162
                                       ***********9**********************************************5544556654.56677899 PP

                                       HHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBS CS
                         adh_short 151 AsKaavagltrslakelaptgirvnavaPGlvd 183
                                        +Ka+v ++tr la + +++ ++vna+ P +v+
  gi|336255298|ref|YP_004598405.1| 163 VAKAGVLMFTRMLAADTQDDDVTVNAISPYVVE 195
                                       99****************************997 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   1.5e-10   4.5e-07       2     117 ..      10     123 ..       9     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.5e-10
                                       EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-.EEEE----TT-HHHHHHHHHHHHH CS
                                KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealga.evevvaaDvsdkdavealleeika 77 
                                       t+l+tG   g+G+el    a+ ga+ +v    sa  d++ ++  +e  ++ga + ++v+ Dv+d+++v  l+++++a
  gi|336255298|ref|YP_004598405.1|  10 TVLVTGSGKGVGRELLLATADCGATVVVHYHTSA--DAA-REVADEALERGAgDAMTVQGDVTDPESVDGLFSAVEA 83 
                                       78************************99999993..333.34555555555559*********************** PP

                                       HSS---EEEE---------TTT--HHHHHHHHTTTTHHHH CS
                                KR  78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGaw 117
                                       e++ +   ++  g ++ +  ++++ +++++vl+  ++G+ 
  gi|336255298|ref|YP_004598405.1|  84 EFGGVDVLVNNVGDFAPAHWADLDFATWNRVLETNLNGTY 123
                                       *********************************9999986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.9e-05     0.057       1      65 [.      11      83 ..      11     120 .. 0.91
   2 ?   -1.2   0.0      0.39   1.2e+03     224     241 .]     128     145 ..     124     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHHHT- CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerlfkeeqp 65
                                      +lVtG    +G+ l+ a ++ g +v++  + s + +++  +++          v++d+td+++++ lf+ +++
  gi|336255298|ref|YP_004598405.1| 11 VLVTGSGKGVGRELLLATADCGATVVVHYHTSADAAREVADEAlergagdaMTVQGDVTDPESVDGLFSAVEA 83
                                      79************************999998888888888879*******9****************97655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.39
                                       HHHHHHTT-STTEEEEES CS
                         Epimerase 224 lvlehvdagdkgeiyniG 241
                                       ++l+h ++gd g+i+niG
  gi|336255298|ref|YP_004598405.1| 128 RALAHMREGDYGRIVNIG 145
                                       68999999*********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 ?   11.3   0.0   4.6e-05      0.14       1      77 [.      11      82 ..      11     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.6e-05
                                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77
                                      vlvtG+g  +G+el+   +++ ++ ++ + ++  +  e+++e  e+ + + ++v+     gdv+d e+++ ++++++
  gi|336255298|ref|YP_004598405.1| 11 VLVTGSGKGVGRELLLATADCGATVVVHYHTSADAAREVADEALERGAGDAMTVQ-----GDVTDPESVDGLFSAVE 82
                                      89****************************************8888888777666.....*********99998655 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 ?   10.5   0.1   9.4e-05      0.28      33     101 ..       5      72 ..       2      97 .. 0.76
   2 ?   -3.2   0.0       1.5   4.6e+03      69      87 ..     171     189 ..     168     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.4e-05
                                       --TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE-SS-TT-B-GGGS-TT CS
                     THF_DHG_CYH_C  33 elegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadivvvavGkpelikaemvkeg 101
                                       +l++++v+v G ++ vg+ l l  +  +atV v h +t+  a+     + +  ++G +  +++++  ++
  gi|336255298|ref|YP_004598405.1|   5 DLSNRTVLVTGSGKGVGRELLLATADCGATVVV-HYHTSADAAREVADEALERGAGDAMTVQGDVTDPE 72 
                                       78999*************987777777888865.55554433333344567778888888887776666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.5
                                       TSCCHHHHHCCSSEEEE-S CS
                     THF_DHG_CYH_C  69 ktkdlaeitreadivvvav 87 
                                        t+ la+ t+  d+ v a+
  gi|336255298|ref|YP_004598405.1| 171 FTRMLAADTQDDDVTVNAI 189
                                       5788888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1885.74
//
Query:       gi|336255299|ref|YP_004598406.1|  [L=220]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-24   86.3   1.2    1.9e-24   86.3   1.2    1.4  2  BAT         GAF and HTH_10 associated domain
    4.2e-13   48.9   0.0    8.3e-13   47.9   0.0    1.5  1  HTH_10      HTH DNA binding domain
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.028   14.5   0.0    1.4  1  HTH_3       Helix-turn-helix
      0.022   14.7   0.1       0.29   11.2   0.1    2.6  2  Lig_C       Ligase Pab1020 C-terminal region
      0.034   13.7   0.0      0.066   12.8   0.0    1.4  1  HTH_24      Winged helix-turn-helix DNA-binding
       0.05   13.2   0.1       0.12   12.0   0.0    1.6  2  SatD        SatD family (SatD)
       0.06   11.7   0.0        0.2   10.0   0.0    1.7  2  Birna_RdRp  Birnavirus RNA dependent RNA polymerase (VP1)
      0.066   13.1   0.0       0.12   12.3   0.0    1.5  1  MarR_2      MarR family


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   1.2   8.4e-28   1.9e-24       7     152 ..       6     154 ..       3     156 .. 0.96
   2 ?   -3.1   0.0       2.8   6.4e+03     115     129 ..     175     189 ..     174     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 8.4e-28
                               BAT   7 eleirdeddvlv.alaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtllel 82 
                                       e++++++d++l+ al+++ ++ ve+e++v++ +++v+ +f+v+g+d++e+++a++d ++v+ v+ ++e d++ l+++
  gi|336255299|ref|YP_004598406.1|   6 EFSVKSDDFALNyALTEAPQMVVEIEQVVATMEDRVMPYFWVSGGDHAEFEAAFHDDESVTGVTQIDEVDESRLYRA 82 
                                       899********99**************************************************************** PP

                               BAT  83 tvs..gpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrr 152
                                       +++   ++++ +++e G t+ +a  + ++++l++++ ++  + ++ e+++++  + eL + +e+e+p+ +++
  gi|336255299|ref|YP_004598406.1|  83 EWTenVETIVYAYTELGSTIMQAIGRADNWELRMRFDDRDVLTEFREYCADNEISYELNRIQEQEQPMASAQ 154
                                       *9833467888*********************************************************9987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.8
                               BAT 115 evPpgadvRsvveal 129
                                       evP++   R +++++
  gi|336255299|ref|YP_004598406.1| 175 EVPQSITMRDLADRM 189
                                       799999999988875 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   3.7e-16   8.3e-13       1      52 [.     157     208 ..     157     209 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 3.7e-16
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT kq+e+l +A+e G++++P  +t+++LA++++Is+++ls++  +  ++li
  gi|336255299|ref|YP_004598406.1| 157 LTTKQRETLVTALEEGFYEVPQSITMRDLADRMDISQQALSKRFHAGHRNLI 208
                                       9****************************************99888777776 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.3e-05     0.028       8      29 ..     178     199 ..     175     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                       TTHHHHHHHHHHTSSHHHHHHH CS
                             HTH_3   8 lglsqeeLAeklGvsrstisri 29 
                                       + +++++LA+++++s++++s+ 
  gi|336255299|ref|YP_004598406.1| 178 QSITMRDLADRMDISQQALSKR 199
                                       679*****************96 PP

>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.71   1.6e+03     101     119 ..      24      42 ..      11      45 .. 0.80
   2 ?   11.2   0.1   0.00013      0.29      26     100 ..      82     147 ..      77     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.71
                                       TEEEEE..EE-HHHHHHHH CS
                             Lig_C 101 gelvvkfkkiaqsttdkik 119
                                        ++vv++++++  ++d++ 
  gi|336255299|ref|YP_004598406.1|  24 PQMVVEIEQVVATMEDRVM 42 
                                       5789999999999999875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                                       HHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHHHHHHHHHHCTT--EEEEEEE..T CS
                             Lig_C  26 vefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvrfkdeenieellehLrrlgvkaeveekeked 100
                                       +e++e+ e++   + eLG  i++    +i ++++      e+r+rf+d++ ++e+ e+  + ++++e+++ ++++
  gi|336255299|ref|YP_004598406.1|  82 AEWTENVETIVYAYTELGSTIMQ----AIGRADN-----WELRMRFDDRDVLTEFREYCADNEISYELNRIQEQE 147
                                       78999999999999999999988....5555544.....46899***********************99988664 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 ?   12.8   0.0   2.9e-05     0.066      17      37 ..     179     199 ..     178     200 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.9e-05
                            HTH_24  17 risqreLAerlglSpstvnrr 37 
                                       +i++r+LA+r ++S++++++r
  gi|336255299|ref|YP_004598406.1| 179 SITMRDLADRMDISQQALSKR 199
                                       69***************9998 PP

>> SatD  SatD family (SatD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   2.9e+03      27      62 ..      29      66 ..      17      77 .. 0.70
   2 ?   12.0   0.0   5.3e-05      0.12     151     196 ..     157     204 ..     128     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                              SatD 27 lleelnkkyaeeliskftitlGd..efqallkvekkif 62
                                       +e++  + ++ ++  f ++ Gd  ef a ++ ++++ 
  gi|336255299|ref|YP_004598406.1| 29 EIEQVVATMEDRVMPYFWVSGGDhaEFEAAFHDDESVT 66
                                      46667777777788888888887667888887777764 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.3e-05
                              SatD 151 wrasqlevletllekkiye..ekfdqkklaeklklsasalskrlkssg 196
                                        +++q e l t le+++ye  ++ + + la+++++s+ alskr+ + +
  gi|336255299|ref|YP_004598406.1| 157 LTTKQRETLVTALEEGFYEvpQSITMRDLADRMDISQQALSKRFHAGH 204
                                       5788999999********95568999*****************99876 PP

>> Birna_RdRp  Birnavirus RNA dependent RNA polymerase (VP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.14   3.2e+02     668     708 ..       4      44 ..       2      89 .. 0.80
   2 ?   10.0   0.0   8.8e-05       0.2     686     748 ..     132     195 ..     102     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.14
                                       GSTTTTTSTT--SSS--..-HHHHHHHH--SS---GGGS-B CS
                        Birna_RdRp 668 lsefgealegltideklevtseslaelnlpveskdpnvnkq 708
                                       ++ef+ + ++++++  l+ ++++++e+++ v +++ +v + 
  gi|336255299|ref|YP_004598406.1|   4 IAEFSVKSDDFALNYALTEAPQMVVEIEQVVATMEDRVMPY 44 
                                       689999999********99*******999999888887665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 8.8e-05
                                       .-HHHHHHHH--SS---GGGS-B-S.SS--HHHHHHHHHTTTTSS-SSHHHHHHHHHTTB-GGG CS
                        Birna_RdRp 686 vtseslaelnlpveskdpnvnkqvl.rskglkevssalksGayrneksvaglvllaraksrvsk 748
                                         +e   eln+  e+ +p +  q   ++k  + +++al++G y  ++s++ + l  r     + 
  gi|336255299|ref|YP_004598406.1| 132 ADNEISYELNRIQEQEQPMASAQYDlTTKQRETLVTALEEGFYEVPQSITMRDLADRMDISQQA 195
                                       56788889***********9988651669***********************998876655554 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.4e-05      0.12      21      41 ..     179     199 ..     155     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
                                       EEEHHHHHHHHTSSHHHHHHH CS
                            MarR_2  21 dltvgelarrlglsksavsri 41 
                                        +t+++la+r+++s++a+s++
  gi|336255299|ref|YP_004598406.1| 179 SITMRDLADRMDISQQALSKR 199
                                       68****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1711.46
//
Query:       gi|336255300|ref|YP_004598407.1|  [L=63]
Description: hypothetical protein Halxa_3923 [Halopiger xanaduensis SH-6]
Scores for 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  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 516.99
//
Query:       gi|336255301|ref|YP_004598408.1|  [L=425]
Description: glycerol-3-phosphate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for complete 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-56  192.3   7.7    2.1e-56  192.0   7.7    1.1  1  DAO            FAD dependent oxidoreductase
    2.2e-09   37.0   3.9    5.9e-09   35.6   3.9    1.6  1  FAD_binding_3  FAD binding domain
    2.3e-07   30.4   0.4    0.00072   18.9   0.1    2.1  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.3e-05   23.7   7.6    3.6e-05   23.1   7.6    1.3  1  FAD_binding_2  FAD binding domain
     0.0002   20.9  12.3     0.0015   18.0  12.3    2.2  1  FAD_oxidored   FAD dependent oxidoreductase
     0.0024   18.1   2.1      0.008   16.4   1.8    2.0  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.013   14.6   4.9       0.37    9.8   0.2    2.2  2  Lycopene_cycl  Lycopene cyclase protein
      0.016   15.1   0.8      0.025   14.5   0.1    1.7  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.018   13.8   2.0       0.19   10.4   1.2    2.0  2  HI0933_like    HI0933-like protein
      0.021   14.1   0.4      0.021   14.1   0.4    2.2  2  Thi4           Thi4 family
      0.079   12.6   0.2       0.13   11.9   0.2    1.3  1  ApbA           Ketopantoate reductase PanE/ApbA
      0.096   13.1   0.0       0.35   11.3   0.0    1.9  1  NAD_binding_7  Putative NAD(P)-binding
       0.11   13.1   0.3       0.64   10.6   0.5    2.0  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
       0.24   10.4   0.5       0.43    9.6   0.5    1.4  1  GIDA           Glucose inhibited division protein A


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.0   7.7   1.7e-59   2.1e-56       1     352 []       6     363 ..       6     363 .. 0.86

  Alignments for each domain:
  == domain 1  score: 192.0 bits;  conditional E-value: 1.7e-59
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeel 75 
                                       dv+++GGG +G++tA++La rg  V+l++++  ++ g+S+r+ gl+hsg ry+++       ++e+++e++ l e  
  gi|336255301|ref|YP_004598408.1|   6 DVLVVGGGATGAGTARDLALRGldVALVDRA-GLSAGTSSRSHGLCHSGARYAESDP---AGAEECIQERQILGEVA 78 
                                       8******************************.7777***************999862...34557788888887776 PP

                                       SSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT.STTTSEEEEETTEEEEEHHHHHHH CS
                               DAO  76 gididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa.lpgllgalfypdtgqvdpakltaa 151
                                       g    +r tG l+l+ ++++ ++++++ +++++ g+++ +l++ ++r+  pa +p+++ al +pd +++ p + +aa
  gi|336255301|ref|YP_004598408.1|  79 G--ACVRDTGGLFLELEADDPDYFAAKREACEKVGIPTTVLEGGKARAEVPAlSPNVQRALSVPD-AVIYPSRIVAA 152
                                       6..789********9888889999999999999**********88******97779*********.*********** PP

                                       HHHHHHHTT-EEEESECEEEEEEEETCEEEEE...EECTEEE.E..EEEEEEE--GGGHHHH.HTTCTTTSEEEEEE CS
                               DAO 152 laraaealGveilegtevtgleeedgkvwgve...rttpgen.d..aadavVnaaGawsdll.gllkeldlpispvr 221
                                        a+aa++ G++il++++v+g + e+++++ ve   +     + d  +ad vVnaaGaw++ + +++ e+d+ ++p r
  gi|336255301|ref|YP_004598408.1| 153 NAAAARNEGAQILTHAPVEGMRLEGDRIAAVElggQ-----VdDtvEADFVVNAAGAWAGRVaAMA-EVDVEMQPNR 223
                                       *********************999999999977532.....322224577**********775666.445699**** PP

                                       EEEEEEEECCTHSTGSGCSEEEEE.EEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSG CS
                               DAO 222 gqvlvlkplseklvspaailpvpe.tdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfP 297
                                       g ++ ++   +   +p a +pv+   +d+++g +v+p + ++v++G+t ++ +++d+ e+ e ++++++e++++++P
  gi|336255301|ref|YP_004598408.1| 224 GVMVSVRDDAL---EP-ATMPVLNrCRDPADGDIVVPHE-DEVVLGTTSVDVDDPDEYETAEWELERVREECARMLP 295
                                       ******54433...34.77788779************96.88******998888888999999*************9 PP

                                       GGCGEE..EEEEEEEEE..TTS...........SEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 298 qlgdvl..rkwaGlrpl..pdg...........lpligetpgvkglylatGhsghGltlapatGkllael 352
                                        ++d +  r+w G+rpl  pd+           ++l++++   +g+   + + g  lt+  a+++++a+l
  gi|336255301|ref|YP_004598408.1| 296 PVADAEdvRTWWGVRPLyaPDEatresrgisrgFFLLDHA--ADGVANFASIVGGKLTTYRAMAEATADL 363
                                       987766447*******556888888888888888888886..79**********************9996 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   3.9   4.6e-12   5.9e-09       1     263 [.       4     297 ..       4     314 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 4.6e-12
                                       EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EEEHHHHHHHHH..TT-HHHHHHHSEECCCCEE CS
                     FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radglnqrtmellrq..lGledrilaegapnelmge 74 
                                       etdVl+VG+G +G+ +a+ L+ +G +v lv++    + ++ r++gl     +  ++  +G e+ i+++    e+ g 
  gi|336255301|ref|YP_004598408.1|   4 ETDVLVVGGGATGAGTARDLALRGLDVALVDRAGLSAGTSsRSHGLCHSGARYAESdpAGAEECIQERQILGEVAGA 80 
                                       69********************************9999888*****9988888754449**********99999999 PP

                                       EEEEE.................................CCCC......CEEEEEHHCHHCST-CEE--HHHHHHHHH CS
                     FAD_binding_3  75 alyne.................................lsdt......pkaradlelesspervtvypqteleriLv 112
                                        ++ +                                           p  + +++   s ++  +yp   +    +
  gi|336255301|ref|YP_004598408.1|  81 CVRDTgglfleleaddpdyfaakreacekvgipttvleG--GkaraevPALSPNVQRALSVPDAVIYPSRIVAAN-A 154
                                       999999**************9999998888877776440..2333333555555556788999999997666555.5 PP

                                       HHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT.-HHHHHHTGGEEEEEEEEEEEEE CS
                     FAD_binding_3 113 ehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgr.Stvrktlgiefegeetvyeagvl 188
                                       ++a+++g+q+  ++ ve+++ +++ ++a+ ++ +   + tv+a+++v a G++ ++v++ + +++e + +     ++
  gi|336255301|ref|YP_004598408.1| 155 AAARNEGAQILTHAPVEGMRLEGDRIAAVELGGQ--VDDTVEADFVVNAAGAWaGRVAAMAEVDVEMQPNR--GVMV 227
                                       66699***********************999985..6778***********98345666555554444433..4455 PP

                                       EEEEEC-SCCCTTCCEEEEECCTTEEEEEECCETEEEEEEEEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEE CS
                     FAD_binding_3 189 dvlfdadlsdiveplvlilsaesrgvmviPlentlerfyvqvearaekeersekfteeevkarlreivgektldv 263
                                       +v  da l+    p+    +++ +g  v+P e+     +v+ +++ ++++ +e +t e   +r+re+++    +v
  gi|336255301|ref|YP_004598408.1| 228 SVRDDA-LEPATMPVLNRCRDPADGDIVVPHED----EVVLGTTSVDVDDPDEYETAEWELERVREECARMLPPV 297
                                       555444.44335555555566666668888888....34555555555555555555555555555555554444 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   5.7e-07   0.00072       2      54 ..       6      57 ..       5     104 .. 0.79
   2 !    9.8   0.0   0.00032      0.41     182     260 ..     146     227 ..     137     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.7e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedae 54
                                      dv+v+GgG+ G  +a++la  g++v+lv ++  +  g+ + s+ l+++++++ 
  gi|336255301|ref|YP_004598408.1|  6 DVLVVGGGATGAGTARDLALRGLDVALV-DRAGLSAGTSSRSHGLCHSGARYA 57
                                      8***************************.665566666666666666665554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00032
                                       -HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCE...EEESEEEE-S-EEES-HHCSHCCT-EEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 182 dkelsaaleealekeGvevklgtsvkeidgngeklevvledgee...idadlvvvavGvrpstelleeklglelder 255
                                       ++++ aa ++a ++eG ++ +++ v+ ++ +g+++  v+  g++   ++ad vv a+G  + +  +  ++ +e++++
  gi|336255301|ref|YP_004598408.1| 146 PSRIVAANAAAARNEGAQILTHAPVEGMRLEGDRIAAVELGGQVddtVEADFVVNAAGAWAGRVAAMAEVDVEMQPN 222
                                       566667777889999***********999999956633333333356***************9887799*****999 PP

                                       TEEE- CS
                                       xxxxx RF
                       Pyr_redox_2 256 ggivv 260
                                       +g+ v
  gi|336255301|ref|YP_004598408.1| 223 RGVMV 227
                                       98844 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   7.6   2.8e-08   3.6e-05       1     205 [.       6     210 ..       6     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.8e-08
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldela 77 
                                       Dv+V+G+G+ G   A  +a +Gl+va+v+ ++   g++  s G     + + ++++  +  +  + ++ l+++++ +
  gi|336255301|ref|YP_004598408.1|   6 DVLVVGGGATGAGTARDLALRGLDVALVDRAGLSAGTSSRSHGLCHSGA-RYAESDPAGAEECIQERQILGEVAGAC 81 
                                       9*****************************************9876544.44445555566778888999******* PP

                                       -HHHHHHHHHTHHHHHHHHHHT.......T----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHH CS
                     FAD_binding_2  78 dqplveafveaapeavdeLeel.......gvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarl 147
                                        ++   +f+e  ++  d+++++       g+p +  e+g+ + +e+ +ls++ + + +++d    +++   +++a+ 
  gi|336255301|ref|YP_004598408.1|  82 VRDTGGLFLELEADDPDYFAAKreacekvGIPTTVLEGGK-ARAEVPALSPNVQRALSVPD----AVIYPSRIVAAN 153
                                       **********555555666666588887788888845444.44677888888333333555....589999****** PP

                                       HHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG... CS
                     FAD_binding_2 148 vesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr..a 205
                                       +++ar+ g +++++++++ +  e++r+  +++    ++ + +++a+ vv a+g++ +  a
  gi|336255301|ref|YP_004598408.1| 154 AAAARNEGAQILTHAPVEGMRLEGDRIAAVELG---GQVDDTVEADFVVNAAGAWAGrvA 210
                                       ******************************999...999999*************98442 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0  12.3   1.2e-06    0.0015       1     158 [.       6     219 ..       6     324 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee........................ 53 
                                       Dv+VvGGg+ G   A   a +G  v+Lv++ g   G++++  +    g + +e                        
  gi|336255301|ref|YP_004598408.1|   6 DVLVVGGGATGAGTARDLALRGLDVALVDRAGLSAGTSSRSHGLCHSGARYAEsdpagaeeciqerqilgevagacv 82 
                                       9***************************************9999999977677789999998666644443333222 PP

                      FAD_oxidored  54 qvvtgiareflerlrqrgga.............rlkkrskwn................................... 82 
                                       + ++g                                    +                                   
  gi|336255301|ref|YP_004598408.1|  83 RDTGG--------------LfleleaddpdyfaA-------Kreacekvgipttvleggkaraevpalspnvqrals 138
                                       22222..............233222222212221.......022334456667778888889999999777777777 PP

                      FAD_oxidored  83 ....tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg..dGdlaalaG 153
                                           +  p+   a+  +  +++g ++l+++ +++++ eg+ri +v++   + + t++A++++ A g   G +aa+a+
  gi|336255301|ref|YP_004598408.1| 139 vpdaVIYPSRIVAANAAAARNEGAQILTHAPVEGMRLEGDRIAAVEL-GGQVDDTVEADFVVNAAGawAGRVAAMAE 214
                                       7777666666666666666899*************************.4456*************9555******** PP

                      FAD_oxidored 154 vpyrv 158
                                       v +++
  gi|336255301|ref|YP_004598408.1| 215 VDVEM 219
                                       *9998 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 !   16.4   1.8   6.2e-06     0.008       1      34 [.       9      42 ..       9      61 .. 0.80
   2 ?   -2.5   0.0       4.9   6.2e+03      30      40 ..     345     355 ..     343     366 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.2e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGr 34
                                      +vG+G++G+ +A+ La +g+dv l++++    G 
  gi|336255301|ref|YP_004598408.1|  9 VVGGGATGAGTARDLALRGLDVALVDRAGLSAGT 42
                                      8************************997444343 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.9
                                       SSSGGG-EECE CS
                     NAD_binding_8  30 rlGGraasyev 40 
                                        +GG++++y+ 
  gi|336255301|ref|YP_004598408.1| 345 IVGGKLTTYRA 355
                                       58999999986 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.7    0.0029       3.7       1      32 [.       6      35 ..       6      48 .. 0.91
   2 ?    9.8   0.2   0.00029      0.37     104     174 ..     165     241 ..     151     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0029
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      Dv+v+G+G+ g   A  l  a  gl v l++ 
  gi|336255301|ref|YP_004598408.1|  6 DVLVVGGGATGAGTARDL--ALRGLDVALVDR 35
                                      9*****************..99*******985 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00029
                     Lycopene_cycl 104 lleakvesveeeeageslvvleggr..kirarlvvdarglaslk....karrlglQtfyGvevevdnppfdldkmvl 174
                                       l++a ve ++ e +    v l g +  +++a +vv a g+ +++    ++ ++ +Q  +Gv+v v+ +  ++++m +
  gi|336255301|ref|YP_004598408.1| 165 LTHAPVEGMRLEGDRIAAVELGGQVddTVEADFVVNAAGAWAGRvaamAEVDVEMQPNRGVMVSVRDDALEPATMPV 241
                                       556666665555553334444444366************988889999999*****************999999966 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 ?   14.5   0.1   1.9e-05     0.025       2      32 ..       7      37 ..       6      69 .. 0.88
   2 ?   -3.5   0.0       6.3     8e+03      64      85 ..     180     201 ..     170     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdise 32
                                      v v+G G  Gag a  +a +gl+V lvd++ 
  gi|336255301|ref|YP_004598408.1|  7 VLVVGGGATGAGTARDLALRGLDVALVDRAG 37
                                      78**************************964 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.3
                                       HHCEEEES-HHHHHC-SEEEE- CS
                           3HCDH_N  64 larisfttdleeavdadlviEa 85 
                                       +a ++   ++++ v+ad+v+ a
  gi|336255301|ref|YP_004598408.1| 180 IAAVELGGQVDDTVEADFVVNA 201
                                       5667777788999999999977 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.2   0.00015      0.19       2      32 ..       6      36 ..       5      41 .. 0.94
   2 ?    2.0   0.0     0.052        67     110     164 ..     148     204 ..     144     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                      dv+v+GgGa G  +A  +a rg +V+l+++a
  gi|336255301|ref|YP_004598408.1|  6 DVLVVGGGATGAGTARDLALRGLDVALVDRA 36
                                      89***************************86 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.052
                                       HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE...TTEEEEESEEEE---- CS
                       HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvkt..kseeeleadklvlAtGG 164
                                       +iv a  ++++++g ++ ++  v++++ e d++  v++  + ++++ead +v A G 
  gi|336255301|ref|YP_004598408.1| 148 RIVAANAAAARNEGAQILTHAPVEGMRLEGDRIAAVELggQVDDTVEADFVVNAAGA 204
                                       6888999999***************************976678899***99999885 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   1.6e-05     0.021      16      55 ..       3      42 ..       2      53 .. 0.85
   2 ?   -0.8   0.1      0.57   7.3e+02      11      11 ..     188     188 ..     130     226 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                                      TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS.SS--T CS
                              Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailers.vspGG 55
                                      +e+Dv++vG+G++G  +a+ la + +l va+++r  +s G 
  gi|336255301|ref|YP_004598408.1|  3 IETDVLVVGGGATGAGTARDLALR-GLDVALVDRAgLSAGT 42
                                      599*********************.******9985366665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.57
                                       H CS
                              Thi4  11 d 11 
                                       +
  gi|336255301|ref|YP_004598408.1| 188 Q 188
                                       2 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2    0.0001      0.13       1      46 [.       7      54 ..       7      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH.HHHHCEEEEET CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea.lkknGlrltse 46
                                      ++++G Ga G   a  La  g dv l++r    + +  +++Gl+ ++ 
  gi|336255301|ref|YP_004598408.1|  7 VLVVGGGATGAGTARDLALRGLDVALVDRAGlSAGTsSRSHGLCHSGA 54
                                      68***************************9976666677777776655 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 ?   11.3   0.0   0.00027      0.35       9      40 ..       6      37 ..       3      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapev 40
                                       vlvvGgG  +a  +r l+  g +v +v+ + 
  gi|336255301|ref|YP_004598408.1|  6 DVLVVGGGATGAGTARDLALRGLDVALVDRAG 37
                                      79*************************99874 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5    0.0005      0.64       2      31 ..       7      36 ..       6      39 .. 0.95
   2 ?   -1.0   0.0       2.1   2.6e+03      49      77 ..     156     184 ..     144     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0005
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      v+vvGgG +g   A  la  g +V +v+r+
  gi|336255301|ref|YP_004598408.1|  7 VLVVGGGATGAGTARDLALRGLDVALVDRA 36
                                      89*************************997 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.1
                                       HHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox  49 klekngievllntkveeiegsedgvesvk 77 
                                         +++g ++l+++ ve ++ ++d + +v+
  gi|336255301|ref|YP_004598408.1| 156 AARNEGAQILTHAPVEGMRLEGDRIAAVE 184
                                       56888999****99999998888766666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.5   0.00034      0.43       1      29 [.       6      34 ..       6      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00034
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLit 29
                                      dv V+GgG  G   A  +a +G++v+L+ 
  gi|336255301|ref|YP_004598408.1|  6 DVLVVGGGATGAGTARDLALRGLDVALVD 34
                                      79*************************93 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); 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:                        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 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3037.66
//
Query:       gi|336255302|ref|YP_004598409.1|  [L=417]
Description: FAD dependent oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-09   34.9   0.1    8.3e-08   31.9   0.1    2.2  1  FAD_binding_3   FAD binding domain
    3.4e-08   32.9   0.0    1.6e-07   30.7   0.0    1.8  2  Lycopene_cycl   Lycopene cyclase protein
    4.2e-08   33.2   0.1    0.00035   20.2   0.0    2.4  2  DAO             FAD dependent oxidoreductase
    3.1e-07   29.6   0.0      0.005   15.7   0.0    2.6  3  Trp_halogenase  Tryptophan halogenase
    7.6e-06   25.4   0.0    1.4e-05   24.5   0.0    1.5  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.4e-05   23.9   1.9    0.00035   20.0   1.9    2.3  1  FAD_oxidored    FAD dependent oxidoreductase
    8.2e-05   21.9   0.0    0.00026   20.2   0.0    1.8  2  FAD_binding_2   FAD binding domain
    0.00016   21.0   0.1    0.00083   18.7   0.0    2.0  2  Thi4            Thi4 family
    0.00044   19.5   0.0       0.25   10.4   0.0    2.3  2  GIDA            Glucose inhibited division protein A
    0.00056   18.7   0.0     0.0021   16.9   0.0    1.8  2  HI0933_like     HI0933-like protein
     0.0013   18.9   0.0     0.0041   17.3   0.0    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
       0.02   14.2   0.0      0.029   13.6   0.0    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.16   12.2   0.0       0.33   11.2   0.0    1.5  1  TrkA_N          TrkA-N domain
       0.18   12.3   0.2        0.8   10.2   0.0    2.1  2  XdhC_C          XdhC Rossmann domain


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 !   31.9   0.1   6.5e-11   8.3e-08       2     310 ..       5     305 ..       4     313 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 6.5e-11
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHH.HHHHHTT-HHHHHHHSEECCCCEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtm.ellrqlGledrilaegapnelmgealy 77 
                                       +dV+I GaGpaG+  a+ L+ +  +vv++e  s++    ++   +  t+  ++ + G+ d +  + + +     +l+
  gi|336255302|ref|YP_004598409.1|   5 YDVVIAGAGPAGAQCARDLAARDYDVVVLETESEDEFPRQSNKSTAGTFpSMMASFGIPDDVVMQYTDS----VVLE 77 
                                       79***********************************99**********4467899**99998887222....2344 PP

                                       EECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEE CS
                     FAD_binding_3  78 nelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvr 154
                                        +       +++   + +p +v      +++r+Lve+ +e+g++ rf+++ ++   ++ ++  + ++     +e+v 
  gi|336255302|ref|YP_004598409.1|  78 SP-------HEYFV-QEQPGAVL--EFGDFKRYLVEDGREKGAEYRFDARATAPIMENGEIVGVTYNG----DEEVY 140
                                       44.......44444.56666555..5569*********************998777666655544444....35899 PP

                                       EEEEEE--GTT-HHHHHHTGG.EEEEEEE..EEEEEEEEEEEC.-SCCCTTC.CEEEEECC.TTEEEEEECCETEEE CS
                     FAD_binding_3 155 akYlvGaDGgrStvrktlgie.fegeetv..yeagvldvlfda.dlsdivep.lvlilsae.srgvmviPlentler 225
                                        + ++ a G   +++k+lg++ +e +++   +e ++ ++ +d   ++d+++  +  + ++  ++g   i    ++++
  gi|336255302|ref|YP_004598409.1| 141 GEIVIDATGPAAPIAKKLGVSnLERKNHAigIEYELEGIDIDRpGFADLRDAmMLRLDHDIaPGGYSWIFHTGGDTA 217
                                       *******************9976655543124667778888888999999994222222221334333333335777 PP

                                       EEEEEECCE-GGGS..CCCHHHHHHHHHHHHHHTTSSCEE.EEEEEEEEEEEE.EEESSSEETTEEE-GGGTEEE-S CS
                     FAD_binding_3 226 fyvqvearaekeer..sekfteeevkarlreivgektldv.eieevsawtvaq.rvaekyrkgrvflaGDAaHihpP 298
                                        + ++ +++e+ ++  ++ ++ ++  +++   +++ ++d+ +ie +++ + a+ ++  k++ +r + +GD + ++ P
  gi|336255302|ref|YP_004598409.1| 218 KVGLCYIQNERYQQfgDNGRSIDDHLQHWL-DTDPRFADAeRIEGKQHRGSAHiQMPGKMHTDRFMAIGDTVPTVDP 293
                                       788887777777766555556566666665.467778888688889888877636778******************* PP

                                       TTSHHHHHHHHH CS
                     FAD_binding_3 299 tgGqGlNtaiqD 310
                                         G G+N  +q 
  gi|336255302|ref|YP_004598409.1| 294 LWGEGINKCMQS 305
                                       ********9995 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.3e-10   1.6e-07       1     179 [.       6     191 ..       6     210 .. 0.80
   2 ?   -0.4   0.0      0.36   4.6e+02     258     350 ..     281     377 ..     272     393 .. 0.67

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.3e-10
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsdefedlga..leecvehsWsgtivylddgkk 74 
                                       Dvv+ GaGpAg + A  l++  +++ v+  e+ ++ ++  n+ +   + + + +  + + v  ++ + +v    ++ 
  gi|336255302|ref|YP_004598409.1|   6 DVVIAGAGPAGAQCARDLAARDYDVVVLETESEDEFPRQSNKsTAGTFPSMMASfgIPDDVVMQYTDSVVLESPHEY 82 
                                       9*****************88888888888899999999999955555555555577778888999999999999999 PP

                     Lycopene_cycl  75 illgraYgrvsskrlkeellerlvengvkll.eakvesveeeeageslvvleggrkirarlvvdarglaslkkarrl 150
                                          + + + ++  ++k+ l e+  e+g++++ +a++++   e+   + v+ +g++++++ +v+da+g ++++ a++l
  gi|336255302|ref|YP_004598409.1|  83 FVQEQPGAVLEFGDFKRYLVEDGREKGAEYRfDARATAPIMENGEIVGVTYNGDEEVYGEIVIDATG-PAAPIAKKL 158
                                       999999999***************9998875489988766555558999******************.998866666 PP

                     Lycopene_cycl 151 gl......QtfyGvevevdnppfdldkmvlMDfrv 179
                                       g+       ++ G+e e++    d+d++ + D r 
  gi|336255302|ref|YP_004598409.1| 159 GVsnlerkNHAIGIEYELEGI--DIDRPGFADLRD 191
                                       662233224666766666665..999999999983 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.36
                     Lycopene_cycl 258 vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres......slsarawatlwprerk..rqreffrllglal 326
                                        +aiG +   v P  G  + + ++  ++ a++  + l+ +        + ++ +tlw re +  +q+ ++      l
  gi|336255302|ref|YP_004598409.1| 281 FMAIGDTVPTVDPLWGEGINKCMQSGRMAAASADSCLK-HgnleptAENLEVYETLWHREVApnMQKRLW---MTRL 353
                                       56777777777777777777777776633333333333.4566676666777788888877622444444...4578 PP

                     Lycopene_cycl 327 llkldiegrrrfldaFfrlpkell 350
                                       l  +d+e+  ++++   r +++ l
  gi|336255302|ref|YP_004598409.1| 354 LYLADNERYDKLMQDLNRFDQDTL 377
                                       888888888888888888888776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.8e-07   0.00035       1      41 [.       6      49 ..       6      82 .. 0.85
   2 !   10.9   0.0   0.00019      0.25     141     225 ..      90     170 ..      80     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.8e-07
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGGGSSE CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags.gaSgrns 41
                                      dvvi G+G +G+ +A++La+r   V++le +++     +S +++
  gi|336255302|ref|YP_004598409.1|  6 DVVIAGAGPAGAQCARDLAARDydVVVLETESEDEFpRQSNKST 49
                                      9*******************9899****9986654336666665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00019
                                       EEEEHHHHHHHHHHHHHHTT-EEEESECEEE.EEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHHHHHTTCTTTS CS
                               DAO 141 gqvdpakltaalaraaealGveilegtevtg.leeedgkvwgverttpgen.daadavVnaaGawsdllgllkeldl 215
                                       ++++   + ++l ++ +++G+e ++ +++t+ +  e+g ++gv  t +g + +  + v+ a+G+ + ++   k+l +
  gi|336255302|ref|YP_004598409.1|  90 AVLEFGDFKRYLVEDGREKGAEYRFDARATApI-MENGEIVGV--TYNGDEeVYGEIVIDATGPAAPIA---KKLGV 160
                                       5556667778899999***************76.557899999..444444234467********9988...55532 PP

                                       EEEEEEEEEE CS
                               DAO 216 pispvrgqvl 225
                                           ++ + +
  gi|336255302|ref|YP_004598409.1| 161 SNLERKNHAI 170
                                       2233444444 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00012      0.15       1      69 [.       6      73 ..       6      78 .. 0.87
   2 !   15.7   0.0   3.9e-06     0.005     154     216 ..      95     157 ..      88     168 .. 0.91
   3 ?   -1.7   0.0      0.76   9.8e+02     315     358 ..     278     325 ..     238     368 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE--THHHHTHHHHT--HHHHCHHCT- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeatipsirkllrlLgideeeflretea 69
                                      ++vi+G+G+aG   A  la     ++ v+  ese+ ++ +  ++t  ++  +++++gi+++  ++ t+ 
  gi|336255302|ref|YP_004598409.1|  6 DVVIAGAGPAGAQCARDLAARD-YDVVVLETESEDEFPRQSNKSTAGTFPSMMASFGIPDDVVMQYTDS 73
                                      69**************999887.4466666778888999999*********************999875 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.9e-06
                                       HHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIII CS
                    Trp_halogenase 154 alyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieq 216
                                       + ++++L + + ++G + + +  +++ + e+g++ +++++ ++ev ++++iD++G ++ + ++
  gi|336255302|ref|YP_004598409.1|  95 GDFKRYLVEDGREKGAEYRFDARATAPIMENGEIVGVTYNGDEEVYGEIVIDATGPAAPIAKK 157
                                       6799***************************************************98877665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.76
                                       ETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BTT--HH CS
                    Trp_halogenase 315 vknvvalGlasgfvePlestsihliqa....alrrLlallpdksdepa 358
                                          ++a+G+    v+Pl + +i   ++    a+ +  ++l ++  ep+
  gi|336255302|ref|YP_004598409.1| 278 TDRFMAIGDTVPTVDPLWGEGINKCMQsgrmAAASADSCLKHGNLEPT 325
                                       556788999999999998888876665455555555555555555555 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 !   24.5   0.0   1.1e-08   1.4e-05       1      36 [.       5      42 ..       5     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.1e-08
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEE..TTHCHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlve..legtcl 36
                                      +dvv+ G+GpAG ++a++la+  ++v+++e  +e++++
  gi|336255302|ref|YP_004598409.1|  5 YDVVIAGAGPAGAQCARDLAARDYDVVVLEteSEDEFP 42
                                      69***************************866444444 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.9   2.8e-07   0.00035       1     146 [.       6     151 ..       6     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.8e-07
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLve.....ergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrgg 72 
                                       Dvv+ G+gpaG  +A   a ++  v+++e     e ++    +t+g  ++++       +   ++ ++++ +  +  
  gi|336255302|ref|YP_004598409.1|   6 DVVIAGAGPAGAQCARDLAARDYDVVVLEtesedEFPRQSNKSTAGTFPSMMASF---GIPDDVVMQYTDSVVLESP 79 
                                       9*************************99954433334445555666655555544...4445555555555544333 PP

                      FAD_oxidored  73 arlkkrskw.ntfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATgdG 146
                                       +++  ++++ ++ e   +k+ l e  +e+g +  +++r++++++e+++i +vt +   g++++ ++++iDATg +
  gi|336255302|ref|YP_004598409.1|  80 HEYFVQEQPgAVLEFGDFKRYLVEDGREKGAEYRFDARATAPIMENGEIVGVTYN---GDEEVYGEIVIDATGPA 151
                                       33334444445899999999999999*******************999******5...79************976 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.1e-07   0.00026       1      68 [.       6      72 ..       6     117 .. 0.81
   2 ?   -1.1   0.0      0.61   7.8e+02     148     188 ..     102     137 ..      95     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.1e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS..GGGG--S-EE-TT..SSGGSTC.CHHHHHHHH CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg..atawsqGgidavlspeqkkagikdspelhrtd 68
                                      Dv++ G+G AG  +A  +a +  +v+v+e e+e +   ++  s +g + +    +++ gi d+++ + td
  gi|336255302|ref|YP_004598409.1|  6 DVVIAGAGPAGAQCARDLAARDYDVVVLETESEDEFprQSNKSTAGTFPSM---MASFGIPDDVVMQYTD 72
                                      9****************************9998877789999999887666...5567887755444444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.61
                                       HHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEE CS
                     FAD_binding_2 148 vesarkagvdfqerteadeLivedgrvtGavvenpesgrev 188
                                       ve  r+ g ++++ ++a++ i+e+g+++G++ +     +++
  gi|336255302|ref|YP_004598409.1| 102 VEDGREKGAEYRFDARATAPIMENGEIVGVTYN-----GDE 137
                                       55567778999999999999*********9887.....333 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   6.4e-07   0.00083      18      49 ..       5      35 ..       3      38 .. 0.94
   2 ?   -0.8   0.0      0.59   7.6e+02     160     175 ..     142     157 ..     136     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.4e-07
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailer 49
                                       Dvvi GaG++G  +a+ la + d  v++le 
  gi|336255302|ref|YP_004598409.1|  5 YDVVIAGAGPAGAQCARDLAAR-DYDVVVLET 35
                                      59********************.*******97 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.59
                                       EEEEE--GSSSTTTTH CS
                              Thi4 160 kvvvdatGhdgeivav 175
                                       ++v+datG  ++i + 
  gi|336255302|ref|YP_004598409.1| 142 EIVIDATGPAAPIAKK 157
                                       79******99999753 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0002      0.25       1      36 [.       6      42 ..       6      61 .. 0.82
   2 !    7.2   0.0    0.0018       2.3     122     150 ..     122     150 ..     114     276 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE.ES-GGGTT CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.thkldtia 36
                                      dv++ G+G AG  +A  +a + ++v+ + t++ d++ 
  gi|336255302|ref|YP_004598409.1|  6 DVVIAGAGPAGAQCARDLAARDYDVVVLeTESEDEFP 42
                                      79**********************9988666666654 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0018
                                       EECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 122 iveekkvkgvvtedgetikakavviatGt 150
                                       i+e++++ gv+ + +e++  ++v+ atG+
  gi|336255302|ref|YP_004598409.1| 122 IMENGEIVGVTYNGDEEVYGEIVIDATGP 150
                                       4789************************* PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.6e-06    0.0021       1      32 [.       5      36 ..       5      39 .. 0.94
   2 ?   -1.6   0.0      0.66   8.4e+02     115     165 ..     101     151 ..      98     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-06
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                      +dv++ G+G+AG  +A  +a+r+ +V++le +
  gi|336255302|ref|YP_004598409.1|  5 YDVVIAGAGPAGAQCARDLAARDYDVVVLETE 36
                                      59***************************986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.66
                                       HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                       l++  +e+g ++r + + ++   e+++++ v+++++ee+  + ++ AtG +
  gi|336255302|ref|YP_004598409.1| 101 LVEDGREKGAEYRFDARATAPIMENGEIVGVTYNGDEEVYGEIVIDATGPA 151
                                       67777899999999999999999999999****999999999999999865 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 !   17.3   0.0   3.2e-06    0.0041       1      28 [.       9      36 ..       9      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.2e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      I GaG +G+ +A+ La +++dv++le+ 
  gi|336255302|ref|YP_004598409.1|  9 IAGAGPAGAQCARDLAARDYDVVVLETE 36
                                      67************************86 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 ?   13.6   0.0   2.3e-05     0.029       1      31 [.       8      37 ..       8      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      +I GaGPaG ++a  l   +  d+++lE ++
  gi|336255302|ref|YP_004598409.1|  8 VIAGAGPAGAQCARDLAARDY-DVVVLETES 37
                                      799******************.8*****875 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00026      0.33       1      32 [.       7      38 ..       7      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdee 32
                                      ++i+G+G  G + a+ L + ++ dvvv +++ e
  gi|336255302|ref|YP_004598409.1|  7 VVIAGAGPAGAQCARDLAArDY-DVVVLETESE 38
                                      79*****************777.7*****9865 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00063       0.8       1      45 [.       7      65 ..       7      84 .. 0.70
   2 ?   -1.7   0.0         3   3.8e+03      25      57 ..     245     279 ..     242     284 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00063
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE..................- CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade..................t 45
                                      +vi Gag+ ++++ar +aa +++v+v+++++e    ++fp++++                  +
  gi|336255302|ref|YP_004598409.1|  7 VVIAGAGPAGAQCARDLAARDYDVVVLETESE----DEFPRQSNkstagtfpsmmasfgipdD 65
                                      69**************************9997....444433333334444444445555542 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3
                                       EEEES-GGGG-GGG-TT-SE..-EEEE--S-HHHH CS
                            XdhC_C  25 tvvdpreefatkerfpeade..tavvvlthdhklD 57 
                                       +++d++++fa++er++++++  +a++ +  + ++D
  gi|336255302|ref|YP_004598409.1| 245 HWLDTDPRFADAERIEGKQHrgSAHIQMPGKMHTD 279
                                       68999999999999997766787777666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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):              14  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 2957.22
//
Query:       gi|336255303|ref|YP_004598410.1|  [L=259]
Description: MarR family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-11   42.4   0.0    7.1e-11   41.5   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.4e-10   40.9   1.3    6.2e-10   38.8   0.2    2.5  3  MarR_2          MarR family
    2.7e-08   33.6   0.0    6.5e-08   32.4   0.0    1.6  1  MarR            MarR family
    1.9e-06   27.7   0.1    4.3e-06   26.6   0.1    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    4.6e-06   27.0   0.1    1.4e-05   25.5   0.1    1.8  1  HTH_27          Winged helix DNA-binding domain
    1.6e-05   24.6   0.0    3.3e-05   23.6   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
    2.5e-05   24.1   0.0    4.1e-05   23.4   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
    3.2e-05   23.8   0.0    5.3e-05   23.1   0.0    1.3  1  HTH_11          HTH domain
    9.2e-05   22.4   0.0    0.00014   21.7   0.0    1.3  1  HTH_45          Winged helix-turn-helix
    0.00012   22.1   0.1    0.00034   20.6   0.1    1.8  1  HTH_20          Helix-turn-helix domain
    0.00014   22.0   0.1    0.00049   20.3   0.0    1.9  1  Mnd1            Mnd1 HTH domain
    0.00015   21.6   0.1    0.00028   20.7   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00023   21.3   0.1    0.00061   19.9   0.1    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00025   21.0   0.1    0.00058   19.9   0.1    1.6  1  HTH_13          HTH DNA binding domain
    0.00097   19.4   0.0     0.0032   17.8   0.0    1.8  1  Rrf2            Transcriptional regulator
     0.0022   17.6   0.1     0.0067   16.0   0.2    1.8  1  GntR            Bacterial regulatory proteins, gntR family
     0.0026   17.8   0.0      0.011   15.8   0.0    1.9  2  HemN_C          HemN C-terminal domain
     0.0046   16.6   0.2     0.0089   15.7   0.2    1.4  1  SMC_ScpB        Segregation and condensation complex subunit 
     0.0051   16.7   0.0      0.012   15.6   0.0    1.6  1  HTH_12          Ribonuclease R winged-helix domain
     0.0085   15.9   0.1       0.02   14.7   0.1    1.6  1  HTH_23          Homeodomain-like domain
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.027   14.2   0.0    1.2  1  DUF4423         Domain of unknown function (DUF4423)
      0.021   14.7   0.1      0.058   13.4   0.1    1.8  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.027   14.5   0.0       0.06   13.4   0.0    1.6  1  TetR_C_7        AefR-like transcriptional repressor, C-termin
      0.031   14.4   0.1       0.09   12.9   0.1    1.9  1  AbiEi_4         Transcriptional regulator, AbiEi antitoxin
       0.05   13.3   0.0      0.072   12.8   0.0    1.3  1  DUF4364         Domain of unknown function (DUF4364)
      0.078   12.4   0.1       0.15   11.5   0.0    1.5  2  NMD3            NMD3 family
      0.078   12.8   0.0       0.42   10.4   0.0    2.3  2  LacI            Bacterial regulatory proteins, lacI family
      0.081   12.7   0.0       0.16   11.8   0.0    1.4  1  HTH_10          HTH DNA binding domain
      0.082   13.1   0.1       0.19   11.9   0.1    1.7  1  HTH_28          Helix-turn-helix domain
      0.087   12.7   0.1        0.2   11.5   0.1    1.6  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
       0.12   12.6   0.0       0.21   11.8   0.0    1.3  1  Rio2_N          Rio2, N-terminal
       0.13   12.4   0.0       0.44   10.7   0.0    1.7  2  Mrr_N           Mrr N-terminal domain
       0.15   11.9   0.0       0.41   10.5   0.0    1.7  2  LexA_DNA_bind   LexA DNA binding domain
       0.16   12.1   0.1       0.31   11.1   0.1    1.4  1  HTH_3           Helix-turn-helix


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 !   41.5   0.0   1.3e-13   7.1e-11       3      48 .]      11      57 ..       9      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.3e-13
                            HTH_24  3 etdrkIL.elLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       t+++IL ++ +++p  sq e+Ae++g+++++v++++++L+++Gl++
  gi|336255303|ref|YP_004598410.1| 11 ATRFRILvQIAERQPAVSQGEIAEEVGVTSQAVSEYIRELVDDGLVE 57
                                      589****666677********************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.2   1.2e-12   6.2e-10       6      54 ..      12      59 ..      10      64 .. 0.93
   2 ?   -1.1   0.0       3.3   1.8e+03      42      58 ..     113     129 ..     111     130 .. 0.84
   3 ?   -2.4   0.0       8.6   4.6e+03      40      54 ..     219     233 ..     216     239 .. 0.70

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.2e-12
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      + +r+L  ++ r +  +++ge+a++ g++ +avs  +++Lv+ GLve++
  gi|336255303|ref|YP_004598410.1| 12 TRFRILVQIAERQPA-VSQGEIAEEVGVTSQAVSEYIRELVDDGLVEKE 59
                                      789**********96.9******************************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.3
                                       HHHHHHTTSEEEEESSS CS
                            MarR_2  42 lkrLvaaGLverrpgpe 58 
                                       +  +v+ GL+  +pg+e
  gi|336255303|ref|YP_004598410.1| 113 VSLFVEDGLLHAEPGSE 129
                                       7789******9999876 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 8.6
                                       HHHHHHHHTTSEEEE CS
                            MarR_2  40 rilkrLvaaGLverr 54 
                                        + +++ ++GL +++
  gi|336255303|ref|YP_004598410.1| 219 EVAADAAEHGLAVTV 233
                                       567788899998887 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   1.2e-10   6.5e-08       4      50 ..      12      59 ..      10      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.2e-10
                                      HHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  4 tqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      t+f+iL++++e++p  s+ e+a+ +gv++ +v++ +++L+++Gl+e++
  gi|336255303|ref|YP_004598410.1| 12 TRFRILVQIAERQPaVSQGEIAEEVGVTSQAVSEYIRELVDDGLVEKE 59
                                      89*******9998879999**************************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 !   26.6   0.1   8.2e-09   4.3e-06       7      59 ..      17      66 ..      11      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 8.2e-09
                                      HHHHHCTTTCEEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEE CS
                         HTH_Crp_2  7 LlrlaeraggeielpltqeelAsmlGltretvsrilseLkreglis.rgrr.iri 59
                                      L+++aer+       ++q e+A+ +G+t + vs  ++eL ++gl++  gr   r+
  gi|336255303|ref|YP_004598410.1| 17 LVQIAERQ-----PAVSQGEIAEEVGVTSQAVSEYIRELVDDGLVEkEGRSrYRV 66
                                      66666653.....469******************************545423666 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 !   25.5   0.1   2.6e-08   1.4e-05       8      68 .]      16      70 ..      13      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.6e-08
                            HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +L +i++r+  +++ ++++ + v+++++s+ +++L+  GLve++      +++r+r+T +G
  gi|336255303|ref|YP_004598410.1| 16 ILVQIAERQPAVSQGEIAEEVGVTSQAVSEYIRELVDDGLVEKE------GRSRYRVTREG 70
                                      68889999999999***************************444......55799999877 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 !   23.6   0.0   6.2e-08   3.3e-05       6      51 ..      14      59 ..      13      60 .. 0.97

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.2e-08
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      ++iL ++ae++++++  e+A++ g++  +v+ +++ Lv  G+ve++
  gi|336255303|ref|YP_004598410.1| 14 FRILVQIAERQPAVSQGEIAEEVGVTSQAVSEYIRELVDDGLVEKE 59
                                      79******************************************97 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 !   23.4   0.0   7.7e-08   4.1e-05       3      47 .]      12      58 ..      11      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 7.7e-08
                                      HHHHHHHHHTT.SS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  3 tRlkILklLae.ge.lcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      tR +IL + ae ++  + +e+aee+g++  +vS++ + L + GLVek
  gi|336255303|ref|YP_004598410.1| 12 TRFRILVQIAErQPaVSQGEIAEEVGVTSQAVSEYIRELVDDGLVEK 58
                                      899********888667789*************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     1e-07   5.3e-05       2      46 ..      13      56 ..      12      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1e-07
                            HTH_11  2 llqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                      ++ il ++ ++r+p +s  e+Aee +v+ ++v  +I++L + g  +
  gi|336255303|ref|YP_004598410.1| 13 RFRILVQI-AERQPaVSQGEIAEEVGVTSQAVSEYIRELVDDG-LV 56
                                      57899999.556666************************8888.44 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.7e-07   0.00014       3      66 ..      12      74 ..       8      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.7e-07
                            HTH_45  3 skleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikk.skekYvlTekGlell 66
                                      +++ I+++I e  ++   ++ +i  ++  + + +++Y+  Lv+ gl++k   + Y++T +G + l
  gi|336255303|ref|YP_004598410.1| 12 TRFRILVQIAE--RQPAVSQGEIAEEVGVTSQAVSEYIRELVDDGLVEKeGRSRYRVTREGVDWL 74
                                      56677777777..567788899999**********************6648899*******9866 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   6.4e-07   0.00034      11      60 ..      12      62 ..      10      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.4e-07
                                      HHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 11 vRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      +R ril  +  r  +++ +e+ae+++++ + +s  +r+L++ gLve ++ +
  gi|336255303|ref|YP_004598410.1| 12 TRFRILVQIaERQPAVSQGEIAEEVGVTSQAVSEYIRELVDDGLVEKEGRS 62
                                      788888888777788999****************************99876 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   9.2e-07   0.00049      21      48 ..      32      59 ..      29      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.2e-07
                              Mnd1 21 apkekgivsqsVkdvlqsLvdDglveve 48
                                      ++ e g++sq V +++ +LvdDglve+e
  gi|336255303|ref|YP_004598410.1| 32 IAEEVGVTSQAVSEYIRELVDDGLVEKE 59
                                      55678********************998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   5.3e-07   0.00028      24      60 ..      28      64 ..      14      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.3e-07
                                      HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                      +  eiaee+gv  + v e++r+L+d GlVe+e ++++
  gi|336255303|ref|YP_004598410.1| 28 SQGEIAEEVGVTSQAVSEYIRELVDDGLVEKEGRSRY 64
                                      4569***************************976655 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 !   19.9   0.1   1.1e-06   0.00061      17      57 ..      21      61 ..      15      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-06
                                      HHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                    Fe_dep_repress 17 seekkvvktkdlaerLnvspssVsemlkkLekdGyveyeky 57
                                       e +  v++ ++ae+ +v    Vse +++L +dG+ve e++
  gi|336255303|ref|YP_004598410.1| 21 AERQPAVSQGEIAEEVGVTSQAVSEYIRELVDDGLVEKEGR 61
                                      6778899*****************************98875 PP

>> HTH_13  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.1e-06   0.00058       6      49 ..      19      65 ..      16      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-06
                            HTH_13  6 elvlsrPlVsagmvakeLkvtpraalklvkel...glRElTGRgrfr 49
                                      ++  ++P Vs g +a+e  vt +a+ + ++el   gl E  GR r+r
  gi|336255303|ref|YP_004598410.1| 19 QIAERQPAVSQGEIAEEVGVTSQAVSEYIRELvddGLVEKEGRSRYR 65
                                      555579**************************88889*********9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     6e-06    0.0032       7      57 ..      10      58 ..       6      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6e-06
                                      HHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2  7 teyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                          +++l+ +a+++    vs  eiae++++  + ++  +++L   glv+ 
  gi|336255303|ref|YP_004598410.1| 10 AATRFRILVQIAERQP--AVSQGEIAEEVGVTSQAVSEYIRELVDDGLVEK 58
                                      5556899999999999..59*****************************84 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.3e-05    0.0067      26      64 .]      28      66 ..      14      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEEE CS
                              GntR 26 sereLaaefgVsrttvReALrrLeaeglverrqgrGtfV 64
                                      s+ e+a+e gV+ + v e +r+L+ +glve + ++  +V
  gi|336255303|ref|YP_004598410.1| 28 SQGEIAEEVGVTSQAVSEYIRELVDDGLVEKEGRSRYRV 66
                                      6789**************************999987766 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     2e-05     0.011      26      65 ..      32      71 ..      27      72 .. 0.87
   2 ?   -1.6   0.0       5.5   2.9e+03      39      52 ..     110     123 ..     103     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-05
                            HemN_C 26 feqrfgldleellaaaleklqeqGLLeldg.grlrltprGr 65
                                      ++++ g++ ++++   +++l ++GL+e +g +r+r+t++G+
  gi|336255303|ref|YP_004598410.1| 32 IAEEVGVT-SQAVSEYIRELVDDGLVEKEGrSRYRVTREGV 71
                                      67777887.7777888************************7 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.5
                            HemN_C  39 aaaleklqeqGLLe 52 
                                       + ++  + e+GLL 
  gi|336255303|ref|YP_004598410.1| 110 GETVSLFVEDGLLH 123
                                       667888999**996 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 !   15.7   0.2   1.7e-05    0.0089      86     131 ..      14      63 ..       7      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
                          SMC_ScpB  86 letLaiIaykqp.vtraeieeiRGvn...sdsvvrtLlerglieekgrke 131
                                        ++L  Ia +qp v++ ei+e  Gv+   +++ +r+L++ gl+e++gr++
  gi|336255303|ref|YP_004598410.1|  14 FRILVQIAERQPaVSQGEIAEEVGVTsqaVSEYIRELVDDGLVEKEGRSR 63 
                                       679999*****97899*****999983334677**************874 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 !   15.6   0.0   2.2e-05     0.012       2      65 ..      15      73 ..      14      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.2e-05
                            HTH_12  2 eILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGlee 65
                                       IL  +ae++  ++ +eiaee+  +      +av   +r l ++gl+++ g++  ++t  G++ 
  gi|336255303|ref|YP_004598410.1| 15 RILVQIAERQPAVSQGEIAEEVGVTS-----QAVSEYIRELVDDGLVEKEGRSRYRVTREGVDW 73
                                      59999***************997654.....66677899***************9***999875 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   3.7e-05      0.02       2      45 ..       8      54 ..       7      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-05
                            HTH_23  2 asereRlrillllae...GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      +++  R+ril   ae     s+ eIA+e gv+ + v+ +++  + +G
  gi|336255303|ref|YP_004598410.1|  8 KRAATRFRILVQIAErqpAVSQGEIAEEVGVTSQAVSEYIRELVDDG 54
                                      68899*********999********************9999876666 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.2e-05     0.027      35      83 ..      26      71 ..      11      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.2e-05
                           DUF4423 35 fkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqteksl 83
                                      +  +  e+a+ ++  ++ + v++ ++ L++ gl++k++  +yr+t++ +
  gi|336255303|ref|YP_004598410.1| 26 A-VSQGEIAEEVG--VTSQAVSEYIRELVDDGLVEKEGRSRYRVTREGV 71
                                      3.56789******..******************************9866 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 ?   13.4   0.1   0.00011     0.058       3      59 ..      13      70 ..      11      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                                      HHHHHHHHHHHS.SHHHH..HHHHTS-HHHHHHHHHHHHHHHTS-SEEESSS.EEEE-HHH CS
                             HTH_1  3 qlrlfvavaeeg.sftrA..AeeLglsqpavsrqikrLEeelgvpLfeRtgr.glrLTeaG 59
                                      ++r++v++ae +  +++   Aee+g++  avs  i++L   +++ L+e+ gr + r+T +G
  gi|336255303|ref|YP_004598410.1| 13 RFRILVQIAERQpAVSQGeiAEEVGVTSQAVSEYIREL---VDDGLVEKEGRsRYRVTREG 70
                                      67888888888875555555***************976...8999***9999669999998 PP

>> TetR_C_7  AefR-like transcriptional repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00011      0.06      11      66 ..       2      57 ..       1      60 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                                      HHHHT-HHHHHHHHHHHHHHHT-HHHHCCHHHT.T----HHHHHHHHHHHHTTSB- CS
                          TetR_C_7 11 lalllspevlalaRlviaeaerfPelarafyeagpgrveealaayLeaavaaGrLr 66
                                      +++l ++++++ +R+++  aer+P++ +   ++  g + +a+++y++++v++G ++
  gi|336255303|ref|YP_004598410.1|  2 VDVLDNKRAATRFRILVQIAERQPAVSQGEIAEEVGVTSQAVSEYIRELVDDGLVE 57
                                      567778899999****************999888*******************876 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00017      0.09       2      48 ..      16      66 ..      15      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00017
                           AbiEi_4  2 rlpelasrqvGlfttrelea.aGispsa....lrrLvrkGwLvrlrrGvYal 48
                                       l+++a+rq + ++  e+++  G++ +a    +r+Lv+ G++++ +r  Y++
  gi|336255303|ref|YP_004598410.1| 16 ILVQIAERQ-PAVSQGEIAEeVGVTSQAvseyIRELVDDGLVEKEGRSRYRV 66
                                      678888888.69999999888*****99*******************99986 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014     0.072      35      70 ..      42      74 ..      32     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                           DUF4364 35 dlqqalseLvesglieeeekenktlykiTekGketl 70
                                       +++++ eLv++gl+e+   e++++y++T +G + l
  gi|336255303|ref|YP_004598410.1| 42 AVSEYIRELVDDGLVEK---EGRSRYRVTREGVDWL 74
                                      5789************7...9***********8766 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.15     161     234 ..      39     113 ..       7     117 .. 0.82
   2 ?   -2.8   0.0       6.8   3.6e+03     132     154 ..     185     207 ..     179     234 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                              NMD3 161 ehkrtfelleqlilkhd.ahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedkksgkev 234
                                         +++ e++++l+  +   ++  s++  ++eG+D  f    + r++++ ++  v g ++e   ++ ed ++g+ v
  gi|336255303|ref|YP_004598410.1|  39 TSQAVSEYIRELVDDGLvEKEGRSRYRVTREGVDWLFRAADDVRRFADHVTGDVLGAMSEDAYIAAEDIEEGETV 113
                                       4566777888888555446677889999****************************************9998876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.8
                              NMD3 132 qqCprCsriaggyyeaivQvRqk 154
                                         C +  ++ +   eaiv  Rq 
  gi|336255303|ref|YP_004598410.1| 185 DACGDADQVVATGIEAIVACRQA 207
                                       56777777777788889988888 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0008      0.42       4      22 ..      31      49 ..      30      64 .. 0.83
   2 ?   -2.4   0.0         8   4.2e+03      32      44 ..      90     102 ..      82     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0008
                                      HHHHHCTS-HHHHHHHCTT CS
                              LacI  4 DVArlAGVSkaTVSrvLnn 22
                                      ++A++ GV+ ++VS +++ 
  gi|336255303|ref|YP_004598410.1| 31 EIAEEVGVTSQAVSEYIRE 49
                                      7**************9986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8
                                       HHHHHHHHHTTB- CS
                              LacI  32 erVeaameelnYi 44 
                                         V+ am e  Yi
  gi|336255303|ref|YP_004598410.1|  90 GDVLGAMSEDAYI 102
                                       568899*999996 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0003      0.16      24      46 ..      27      49 ..      23      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                            HTH_10 24 vtlkeLAkelGIskstlsehLrk 46
                                      v+  e+A+e G++ +++se++r+
  gi|336255303|ref|YP_004598410.1| 27 VSQGEIAEEVGVTSQAVSEYIRE 49
                                      66789****************96 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00036      0.19       2      46 ..      13      57 ..      12      63 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00036
                            HTH_28  2 RleiikllaaG...hsvreaArelgisrrtvyrWikryeegGiagLvp 46
                                      R++i+ ++a+    +s+ e+A+e+g++++ v+  i+ +     +gLv 
  gi|336255303|ref|YP_004598410.1| 13 RFRILVQIAERqpaVSQGEIAEEVGVTSQAVSEYIRELVD---DGLVE 57
                                      77888888854143599**************999987665...44455 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 ?   11.5   0.1   0.00038       0.2      14      41 ..      23      50 ..      15      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00038
                     HTH_AsnC-type 14 edaRisyaeLAervGlSestvlrRvrrL 41
                                      +++  s  e+Ae+vG++ ++v + +r L
  gi|336255303|ref|YP_004598410.1| 23 RQPAVSQGEIAEEVGVTSQAVSEYIREL 50
                                      55788999*************9877665 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0004      0.21       9      74 ..      14      74 ..       9      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0004
                            Rio2_N  9 frvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyL 74
                                      fr+L  +     +   V++ +i+e  +++++ v++ +++l++ +l++++      Y++t eG D L
  gi|336255303|ref|YP_004598410.1| 14 FRILVQI---AERQPAVSQGEIAEEVGVTSQAVSEYIRELVDDGLVEKEGR--SRYRVTREGVDWL 74
                                      6666554...345568999*****************************864..5699999999987 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       4.5   2.4e+03      24      42 ..      29      47 ..      13      52 .. 0.72
   2 ?   10.7   0.0   0.00083      0.44      59      85 ..      48      74 ..      38      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.5
                             Mrr_N 24 rervaerfglseeeraell 42
                                      + ++ae++g++ ++++e++
  gi|336255303|ref|YP_004598410.1| 29 QGEIAEEVGVTSQAVSEYI 47
                                      5678888888888888765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00083
                             Mrr_N 59 tyLkkagllespkrgvwkiTekGrevl 85
                                       +L+  gl+e++ r+ +++T +G ++l
  gi|336255303|ref|YP_004598410.1| 48 RELVDDGLVEKEGRSRYRVTREGVDWL 74
                                      678999******************998 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 ?   10.5   0.0   0.00077      0.41      18      64 ..      19      63 ..       9      64 .. 0.86
   2 ?   -2.5   0.0       8.6   4.6e+03      22      43 ..     133     154 ..     132     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00077
                                      HHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG-CC CS
                     LexA_DNA_bind 18 sieetgypPsireiaralglkSpsaveehLkaLerKGyierdpgkpR 64
                                      +i e++ + s  eia+++g++ ++av e  + L   G++e  +g++R
  gi|336255303|ref|YP_004598410.1| 19 QIAERQPAVSQGEIAEEVGVT-SQAVSEYIRELVDDGLVEK-EGRSR 63
                                      578888899999*********.789**************95.56666 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.6
                                       HSS---HHHHHHHHTS-.HHHH CS
                     LexA_DNA_bind  22 tgypPsireiaralglkSpsav 43 
                                       tg + + +e +  +g++S ++v
  gi|336255303|ref|YP_004598410.1| 133 TGIATTDAEAGTDVGVTSFEGV 154
                                       6778888999999999997766 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00059      0.31      11      31 ..      28      48 ..      20      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00059
                                      HHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3 11 sqeeLAeklGvsrstisriEn 31
                                      sq e+Ae++Gv+ +++s +++
  gi|336255303|ref|YP_004598410.1| 28 SQGEIAEEVGVTSQAVSEYIR 48
                                      99*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2011.75
//
Query:       gi|336255304|ref|YP_004598411.1|  [L=256]
Description: hypothetical protein Halxa_3927 [Halopiger xanaduensis SH-6]
Scores for 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-52  177.6   0.2    3.9e-52  177.3   0.2    1.0  1  PAC2      PAC2 family


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 !  177.3   0.2   2.2e-56   3.9e-52       1     212 [.      19     234 ..      19     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 2.2e-56
                                       EEEESSCGGGHHHHHHHHHHHHT..TEEEEEEEEHCCHSBCCCC.SEEEEETT.EEE-SEEEEEE.TTT.SEEEEEE CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesl..eaekvgeidsdyllpfvgprpvvlveeg.relepprlyak.dsgsrdllvlq 73 
                                       L++G+pg+G+Vg+lavd+L+e+l  e + v +++s++ +p     p+v+ve+g  el+  ++ya   +++rdll+l+
  gi|336255304|ref|YP_004598411.1|  19 LVEGLPGVGHVGKLAVDHLLEELegESTLVRRVYSQE-FP-----PQVSVEDGvAELTCAEMYAVsVADGRDLLLLT 89 
                                       89*********************77777*********.**.....*****************9998778******** PP

                                       E....E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT........ CS
                              PAC2  74 g....repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees........ 138
                                       g     +  ++y  +++a ld+aee+g +e++ Lgg+++ge+      ++  v ga++de+l+eele++        
  gi|336255304|ref|YP_004598411.1|  90 GdhqaQTNAGHYV-LTSAFLDIAEEFGASEAYALGGVPTGELI-----EEYAVVGAVSDESLREELEDAgvefrede 160
                                       *887777777777.*************************9995.....56699*************84445666677 PP

                                       -CEEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                              PAC2 139 eyggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                       ++ggi+g++glLl+++++rg++a +l++e+++yl+dPk+a+a+le+l++llg+e+d+e L+e+a+e+ee + ++
  gi|336255304|ref|YP_004598411.1| 161 PAGGIIGVSGLLLGLGERRGFEASCLMGETSGYLVDPKSARAVLEVLEALLGFELDYETLDERADEMEEVMGKI 234
                                       *********************************************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1273  (0.0710023); expected 358.6 (0.02)
Passed bias filter:                      939  (0.0523733); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1899.88
//
Query:       gi|336255305|ref|YP_004598412.1|  [L=59]
Description: ribosome biogenesis protein Nop10 [Halopiger xanaduensis SH-6]
Scores for complete 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-23   82.9   0.9    1.3e-23   82.7   0.9    1.0  1  Nop10p    Nucleolar RNA-binding protein, Nop10p family
  ------ inclusion threshold ------
       0.13   11.4   0.0        0.2   10.7   0.0    1.2  1  LisH_2    LisH


Domain annotation for each model (and alignments):
>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.9   1.5e-27   1.3e-23       1      51 [.       1      57 [.       1      58 [. 0.99

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 1.5e-27
                                      .----EE-TTT-......-EESSSB-TTT-SB-B-SS--S--TT-TTCHHHHHCHHH CS
                            Nop10p  1 mksylrkcgkcr......vYTLkkvcpecggptksahPaRFSPdDkyskyRralKkr 51
                                      mks++r+c+++r      vYTL+++cpecg+++++++Pa+F+P+D y++yRr lK+r
  gi|336255305|ref|YP_004598412.1|  1 MKSDIRVCSAWRerhdrpVYTLSTECPECGADAENSAPAPFDPEDSYGEYRRSLKRR 57
                                      9******************************************************98 PP

>> LisH_2  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   2.2e-05       0.2      16      27 ..      20      31 ..      20      32 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.2e-05
                            LisH_2 16 YTLSVFlPEsGl 27
                                      YTLS+ +PE+G 
  gi|336255305|ref|YP_004598412.1| 20 YTLSTECPECGA 31
                                      9**********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 483.88
//
Query:       gi|336255306|ref|YP_004598413.1|  [L=266]
Description: translation initiation factor 2 subunit alpha [Halopiger xanaduensis SH-6]
Scores for 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-23   81.9   0.0    5.7e-23   81.2   0.0    1.4  1  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    4.5e-11   42.9   1.3      9e-11   42.0   1.3    1.5  1  S1           S1 RNA binding domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.024   14.5   0.0    1.5  1  DUF2073      Uncharacterized protein conserved in archaea (DU


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 !   81.2   0.0   9.5e-27   5.7e-23       2     116 .]     118     230 ..     117     230 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 9.5e-27
                                       HHCTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHH CS
                       EIF_2_alpha   2 yeevgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIke 77 
                                       y+ ++++l   +g++yd+F ++ai+++e+l++ +++++  + +ve+++++++++ v+++++++l+  ++ Gv++I+e
  gi|336255306|ref|YP_004598413.1| 118 YTAIANELIGAHGSLYDGFkQAAIHGDEALEDTDLSADEVDSIVETARENVSVPYVNVTGYVDLENPSPSGVDGIRE 194
                                       8999***************999******************************************************* PP

                                       HHHHHST.S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                       EIF_2_alpha  78 aLkageeasneeeveeeeevkikliapPeYvltvetldk 116
                                       aL a+e++    ev +e++++++++++PeY+++v+++++
  gi|336255306|ref|YP_004598413.1| 195 ALGAAEGN---GEVPDEVDLDVSYVGAPEYRIEVQAPNY 230
                                       ***88773...3589********************9875 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   1.3   1.5e-14     9e-11       3      75 .]       8      81 ..       7      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.5e-14
                                      TTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1  3 ekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                       +ge v G++ +++++G+fV+l+  ++ +g++++se+++   +++  +++++G+ v  kvl++d+    i+ls+k
  gi|336255306|ref|YP_004598413.1|  8 DTGELVVGKIDEIEDFGVFVDLEeyEDKRGLIHISEVASG-WIKNVRDHVREGQIVVCKVLDIDESSQQIDLSLK 81
                                      5799***********************************9.9*******************************86 PP

>> DUF2073  Uncharacterized protein conserved in archaea (DUF2073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     4e-06     0.024      10      84 ..      49     121 ..      42     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-06
                           DUF2073  10 irlildkvkegkivvlEkgLtpeeeakliettmeeikpdeFsGieietypkkekdkgllekllgkkeseerltvi 84 
                                       i+ + d+v+eg+ivv  k L+ +e+++ i+  +++++  +     i+ +++++k  ++++  lg+++++e  t i
  gi|336255306|ref|YP_004598413.1|  49 IKNVRDHVREGQIVVC-KVLDIDESSQQIDLSLKDVNDHQ-RSDKIQEWKNEQKADNWMDLALGEDTDDETYTAI 121
                                       677889*******986.79*****************9555.5669*********9******9*999988888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2076.46
//
Query:       gi|336255307|ref|YP_004598414.1|  [L=57]
Description: 30S ribosomal protein S27e [Halopiger xanaduensis SH-6]
Scores for 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-22   77.0   0.7    6.9e-22   76.9   0.7    1.0  1  Ribosomal_S27e  Ribosomal protein S27
    8.5e-05   22.6   1.1    0.00012   22.2   1.1    1.2  1  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.025   14.6   0.9       0.03   14.4   0.9    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.027   14.0   1.6      0.041   13.4   1.6    1.3  1  TF_Zn_Ribbon    TFIIB zinc-binding
      0.055   13.3   1.0        3.3    7.6   0.1    2.1  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO
        0.1   12.5   1.9       0.13   12.1   1.9    1.1  1  eIF-5_eIF-2B    Domain found in IF2B/IF5
       0.12   12.4   1.9       0.22   11.6   1.9    1.5  1  zinc_ribbon_6   Zinc-ribbon
       0.33   10.9   3.8         13    5.9   0.3    2.3  2  zinc_ribbon_4   zinc-ribbon domain


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 !   76.9   0.7   3.1e-25   6.9e-22       2      54 ..       2      54 ..       1      55 [. 0.95

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 3.1e-25
                                      S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEEE CS
                    Ribosomal_S27e  2 rskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqilerl 54
                                       + F +v+C dCene++vF++a+t v C  Cg++L+ PtGGka ++ +i+e +
  gi|336255307|ref|YP_004598414.1|  2 AGSFYQVRCSDCENEQTVFGKASTEVACAVCGTTLARPTGGKAEIEHEIIETV 54
                                      578***********************************************987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   1.1   5.2e-08   0.00012       3      38 ..       5      38 ..       4      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.2e-08
                       Zn-ribbon_8  3 iYeYrCeeCghefevlqsisdapltaCPeCgsevrr 38
                                       Y+ rC +C +e +v+ ++s   ++aC  Cg ++ r
  gi|336255307|ref|YP_004598414.1|  5 FYQVRCSDCENEQTVFGKAST--EVACAVCGTTLAR 38
                                      59***************9884..777*****98877 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 ?   14.4   0.9   1.3e-05      0.03      70     103 ..       7      43 ..       4      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                                       EEEETTTS-EEECHH..H.HHS-TTTSSS-EEEEESS CS
                              HypA  70 kvrCreCgkefelee..k.alrCpkCgsadveivsGe 103
                                       +vrC++C++e ++    + ++ C  Cg++  + ++G+
  gi|336255307|ref|YP_004598414.1|   7 QVRCSDCENEQTVFGkaStEVACAVCGTTLARPTGGK 43 
                                       79******9999544233688*******988888776 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.6   1.8e-05     0.041       2      27 ..       9      34 ..       8      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                      EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                      +C +C ++++v+  +++e+ C  CG+
  gi|336255307|ref|YP_004598414.1|  9 RCSDCENEQTVFGKASTEVACAVCGT 34
                                      7************************7 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.013        30      10      20 ..       4      14 ..       2      14 .. 0.85
   2 ?    7.6   0.1    0.0015       3.3      10      22 ..      19      35 ..      16      38 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.013
                         zf-C2H2_3 10 sfgasqCkeCg 20
                                      sf +++C+ C+
  gi|336255307|ref|YP_004598414.1|  4 SFYQVRCSDCE 14
                                      78999*****6 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0015
                         zf-C2H2_3 10 sfga.sq...CkeCgMv 22
                                       fg+ s+   C++Cg +
  gi|336255307|ref|YP_004598414.1| 19 VFGKaSTevaCAVCGTT 35
                                      5555444566****965 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 ?   12.1   1.9   5.8e-05      0.13      88     116 ..       8      34 ..       5      35 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.8e-05
                                       TSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  88 VlCkeCkspetelekeerllvlkCkaCga 116
                                       V C+ C++ +t + k ++ +   C  Cg 
  gi|336255307|ref|YP_004598414.1|   8 VRCSDCENEQTVFGKASTEV--ACAVCGT 34 
                                       89*********999854433..6****96 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.9   9.6e-05      0.22      27      54 ..       5      33 ..       1      35 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.6e-05
                     zinc_ribbon_6 27 kvkilCnDCekksevkfh.vlglkCkeCg 54
                                        ++ C DCe++++v  +    ++C+ Cg
  gi|336255307|ref|YP_004598414.1|  5 FYQVRCSDCENEQTVFGKaSTEVACAVCG 33
                                      6799********99765514678899886 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.3    0.0056        13      25      33 ..       7      15 ..       2      20 .. 0.83
   2 ?    4.2   4.1     0.018        40      19      34 ..      20      35 ..       7      37 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0056
                     zinc_ribbon_4 25 kvrCskCgh 33
                                       vrCs C +
  gi|336255307|ref|YP_004598414.1|  7 QVRCSDCEN 15
                                      589999965 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.018
                     zinc_ribbon_4 19 lpakgvkvrCskCghv 34
                                      + ++ ++v C+ Cg++
  gi|336255307|ref|YP_004598414.1| 20 FGKASTEVACAVCGTT 35
                                      3455667888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 449.17
//
Query:       gi|336255308|ref|YP_004598415.1|  [L=93]
Description: 50S ribosomal protein L44E [Halopiger xanaduensis SH-6]
Scores for complete 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   92.9   2.5    1.6e-26   92.6   2.5    1.1  1  Ribosomal_L44   Ribosomal protein L44
    1.5e-05   24.2   0.6      0.019   14.3   0.0    2.2  2  zf-ribbon_3     zinc-ribbon domain
     0.0098   16.0   1.8        2.4    8.3   0.2    2.4  2  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.015   15.2   2.1        3.1    7.9   0.2    2.3  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.021   14.5   1.5       0.78    9.5   0.0    2.2  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.022   14.6   5.7       0.64   10.0   0.6    2.4  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.029   12.9   1.6      0.042   12.4   1.6    1.3  1  Terminase_GpA   Phage terminase large subunit (GpA)
      0.064   13.0   4.1        2.3    8.1   0.4    2.3  2  zinc_ribbon_2   zinc-ribbon domain
      0.094   13.0   2.4        1.1    9.6   0.1    2.1  2  zf-LITAF-like   LITAF-like zinc ribbon domain
       0.15   12.0   1.9         12    5.9   0.2    2.3  2  zinc_ribbon_4   zinc-ribbon domain
       0.47   10.5   4.8        1.6    8.9   4.8    1.7  1  DZR             Double zinc ribbon
       0.49   10.5   7.6       0.87    9.7   7.6    1.5  1  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.87    9.4   7.0       0.68    9.7   0.6    2.3  2  Rubredoxin_2    Rubredoxin metal binding 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 !   92.6   2.5   1.1e-29   1.6e-26       1      76 []      16      92 ..      16      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 1.1e-29
                                      EEEEEEEEE-------SSSHHHHHHHH.H-SSS..GGGGS----.--SSBB--EEEEETTT--EEE----BBS--EEE CS
                     Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgyg..GqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfelv 76
                                      +H+eh+ve++++g+ s +++++Rr++r++s +g  G++++v+ + +K+tKK++l+++C+eC+k++l++++Ra+++e++
  gi|336255308|ref|YP_004598415.1| 16 EHHEHEVEKARTGRSSGMKWDARRTKRNSSSIGnsGRFSKVPAG-EKPTKKTDLKYRCSECGKAHLREGWRAGRLEFQ 92
                                      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 !    8.2   0.3    0.0012       1.6       3      10 ..       9      16 ..       7      21 .. 0.81
   2 !   14.3   0.0   1.4e-05     0.019       2      17 ..      69      85 ..      68      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                       zf-ribbon_3  3 vrCPnCGa 10
                                      ++CP+C++
  gi|336255308|ref|YP_004598415.1|  9 TYCPHCNE 16
                                      79****98 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.4e-05
                       zf-ribbon_3  2 tvrCPnCGa.plssddn 17
                                      ++rC++CG+ +l+++++
  gi|336255308|ref|YP_004598415.1| 69 KYRCSECGKaHLREGWR 85
                                      58************997 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    0.0043       5.9      26      34 ..       8      16 ..       1      25 [. 0.74
   2 !    8.3   0.2    0.0018       2.4       6      13 ..      70      77 ..      63      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0043
                       Zn-ribbon_8 26 ltaCPeCgs 34
                                      +t CP+C++
  gi|336255308|ref|YP_004598415.1|  8 NTYCPHCNE 16
                                      567****87 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0018
                       Zn-ribbon_8  6 YrCeeCgh 13
                                      YrC eCg+
  gi|336255308|ref|YP_004598415.1| 70 YRCSECGK 77
                                      99999997 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 ?    7.9   0.2    0.0022       3.1      20      34 ..      10      24 ..       4      40 .. 0.78
   2 ?    7.3   0.1    0.0033       4.6      37      45 ..      69      77 ..      59      90 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0022
                     Zn_Tnp_IS1595 20 vCPhCgsrkayrikt 34
                                       CPhC   + +++++
  gi|336255308|ref|YP_004598415.1| 10 YCPHCNEHHEHEVEK 24
                                      3****9887666665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0033
                     Zn_Tnp_IS1595 37 lfqCkeCrk 45
                                      +++C+eC+k
  gi|336255308|ref|YP_004598415.1| 69 KYRCSECGK 77
                                      566666664 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 ?    4.3   0.3     0.024        34      46      52 ..      10      16 ..       2      18 .. 0.72
   2 ?    9.5   0.0   0.00057      0.78      38      52 ..      63      77 ..      56      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.024
                    zinc_ribbon_10 46 rCpkCga 52
                                      +Cp+C++
  gi|336255308|ref|YP_004598415.1| 10 YCPHCNE 16
                                      6888876 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00057
                    zinc_ribbon_10 38 eeleevkyrCpkCga 52
                                       +++++kyrC++Cg 
  gi|336255308|ref|YP_004598415.1| 63 TKKTDLKYRCSECGK 77
                                      567899*******96 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 ?    7.0   0.5    0.0039       5.4       6      17 ..      10      18 ..       4      29 .. 0.69
   2 ?   10.0   0.6   0.00046      0.64       4      19 ..      69      81 ..      69      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0039
                    Zn_ribbon_SprT  6 rCtgCgreythh 17
                                      +C++C    +hh
  gi|336255308|ref|YP_004598415.1| 10 YCPHCN---EHH 18
                                      577776...333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00046
                    Zn_ribbon_SprT  4 vYrCtgCgreythhls 19
                                      +YrC  Cg   ++hl+
  gi|336255308|ref|YP_004598415.1| 69 KYRCSECG---KAHLR 81
                                      7*******...99998 PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.6     3e-05     0.042     195     237 ..       5      79 ..       3      92 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3e-05
                     Terminase_GpA 195 rryyvpCphCgelqelsfer........lkw.......pege...................aeekaryvCphcgsli 237
                                       rr+   CphC+e++e + e+        +kw       +                      ++++ +y C++cg+ +
  gi|336255308|ref|YP_004598415.1|   5 RRFNTYCPHCNEHHEHEVEKartgrssgMKWdarrtkrN--SssignsgrfskvpagekptKKTDLKYRCSECGKAH 79 
                                       8999***********666665666677777755444430..144444445555555557778888999999999764 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   0.4    0.0016       2.3       1       8 [.      10      17 ..       8      23 .. 0.69
   2 ?    6.2   0.3    0.0065         9       1       8 [.      71      78 ..      71      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0016
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      +Cp+C + 
  gi|336255308|ref|YP_004598415.1| 10 YCPHCNEH 17
                                      57777654 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0065
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      +C++CG+ 
  gi|336255308|ref|YP_004598415.1| 71 RCSECGKA 78
                                      69999985 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 ?    9.6   0.1   0.00079       1.1       5      22 ..       8      25 ..       4      33 .. 0.79
   2 ?    3.5   0.2     0.062        85      53      64 ..      66      77 ..      63      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00079
                     zf-LITAF-like  5 qvdCpaCqqrvvTsveyk 22
                                      +++Cp+C+++ + +ve+ 
  gi|336255308|ref|YP_004598415.1|  8 NTYCPHCNEHHEHEVEKA 25
                                      678999999998888875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.062
                     zf-LITAF-like 53 kdvehyCpnCga 64
                                       d +++C++Cg+
  gi|336255308|ref|YP_004598415.1| 66 TDLKYRCSECGK 77
                                      588999****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 ?    5.8   0.1    0.0098        13       4      13 ..      10      19 ..       8      31 .. 0.70
   2 ?    5.9   0.2    0.0088        12      21      33 ..      65      77 ..      56      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0098
                     zinc_ribbon_4  4 tCpsCkakye 13
                                       Cp+C+  +e
  gi|336255308|ref|YP_004598415.1| 10 YCPHCNEHHE 19
                                      7****97766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0088
                     zinc_ribbon_4 21 akgvkvrCskCgh 33
                                      ++  k rCs Cg+
  gi|336255308|ref|YP_004598415.1| 65 KTDLKYRCSECGK 77
                                      5566889****95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.8    0.0011       1.6      13      40 ..       9      82 ..       2      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                               DZR 13 rfCseCgtklkavaa.............................................edrCpsCgek.vdp 40
                                       +C++C+++ + + +                                             ++rC++Cg++ + +
  gi|336255308|ref|YP_004598415.1|  9 TYCPHCNEHHEHEVEkartgrssgmkwdarrtkrnsssignsgrfskvpagekptkktdlKYRCSECGKAhLRE 82
                                      59****99977555577889999*********************************************975555 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 ?    9.7   7.6   0.00063      0.87       1      24 [.      10      77 ..      10      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00063
                          zf-Mss51  1 lCPvpkhkqt............................................apkhvdfeCpdCGi 24
                                      +CP+++++++                                            ++ + ++ C +CG 
  gi|336255308|ref|YP_004598415.1| 10 YCPHCNEHHEhevekartgrssgmkwdarrtkrnsssignsgrfskvpagekptKKTDLKYRCSECGK 77
                                      7****998889******************************************9999**********6 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.9     0.064        88      17      22 ..      11      16 ..      10      17 .. 0.85
   2 ?    9.7   0.6    0.0005      0.68       1      11 [.      70      80 ..      70      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.064
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp+C++
  gi|336255308|ref|YP_004598415.1| 11 CPHCNE 16
                                      ****96 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0005
                      Rubredoxin_2  1 YvCsqCGfesa 11
                                      Y+Cs+CG  + 
  gi|336255308|ref|YP_004598415.1| 70 YRCSECGKAHL 80
                                      9******8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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):              13  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 769.32
//
Query:       gi|336255309|ref|YP_004598416.1|  [L=88]
Description: hypothetical protein Halxa_3932 [Halopiger xanaduensis SH-6]
Scores for 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:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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 0.19s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 784.27
//
Query:       gi|336255310|ref|YP_004598417.1|  [L=138]
Description: GtrA family protein [Halopiger xanaduensis SH-6]
Scores for 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-22   78.8  10.1    4.3e-22   78.6  10.1    1.0  1  GtrA      GtrA-like protein


Domain annotation for each model (and alignments):
>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6  10.1   2.4e-26   4.3e-22       2     117 .]      15     133 ..      14     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 2.4e-26
                              GtrA   2 FlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakl...lkqflkFvlvsllgl 75 
                                       F+ vG++g+ vdl++l+ll+el  ++++ A++++++++i++ F++n+ wtF +  +       k+fl+  +v+++g+
  gi|336255310|ref|YP_004598417.1|  15 FAGVGLVGATVDLLVLFLLVELTPFGPTPAKVVSWELSIVVIFVINEWWTFANYGRMGPraiGKRFLRSNAVRFAGF 91 
                                       999*************************************************9988766788*************** PP

                              GtrA  76 llnllilwllveklgleallaklvgiivalvlnyvlsklfvF 117
                                       l++l++l+ lv+++g+ +l a+++g++v++++ny+ ++l+++
  gi|336255310|ref|YP_004598417.1|  92 LVTLGVLVGLVRWFGVWYLAANAIGLAVGFFVNYTCESLYTW 133
                                       ****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); 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):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 1226.69
//
Query:       gi|336255311|ref|YP_004598418.1|  [L=172]
Description: hypothetical protein Halxa_3934 [Halopiger xanaduensis SH-6]
Scores for 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:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.33
# Mc/sec: 1554.66
//
Query:       gi|336255312|ref|YP_004598419.1|  [L=176]
Description: hypothetical protein Halxa_3935 [Halopiger xanaduensis SH-6]
Scores for 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   12.0   1.9        1.9    8.2   0.3    2.3  2  SPT_ssu-like  Small subunit of serine palmitoyltransferase-li
       0.63    9.6  13.9       0.86    9.1  13.9    1.1  1  RSRP          Arginine/Serine-Rich protein 1
        1.5    6.8   7.2        1.7    6.6   7.2    1.0  1  AF-4          AF-4 proto-oncoprotein
        5.3    6.9   7.6       0.19   11.7   1.1    1.7  2  DUF2721       Protein of unknown function (DUF2721)


Domain annotation for each model (and alignments):
>> SPT_ssu-like  Small subunit of serine palmitoyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.015        66      32      50 ..      53      71 ..      20      74 .. 0.87
   2 ?    8.2   0.3   0.00042       1.9      20      42 ..     149     171 ..     149     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.015
                      SPT_ssu-like 32 ifillsllliaaslYlpsh 50
                                      ++  + ll +a+++ +ps+
  gi|336255312|ref|YP_004598419.1| 53 FVAGWLLLAYATVRLWPSS 71
                                      55569999*********86 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00042
                      SPT_ssu-like  20 LepwEkflfnilifillslllia 42 
                                       L+p  k+l+++l+++lls+ll +
  gi|336255312|ref|YP_004598419.1| 149 LTPPGKVLVSSLLILLLSFLLET 171
                                       677779*************9855 PP

>> RSRP  Arginine/Serine-Rich protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  13.9   0.00019      0.86       8      64 ..      67     116 ..      61     131 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00019
                              RSRP   8 mwPGslqekksPstsssGsssrlssrsrsrsssrssrshsrsssrsssrsrsrprrs 64 
                                       +wP s+ e  s s s+sG    l srsrs s sr+ +  s  s    + +  rpr s
  gi|336255312|ref|YP_004598419.1|  67 LWPSSPAEVGSSSGSGSG----LRSRSRSESESRAGSDSSPES---GAATAPRPRGS 116
                                       899999987655544444....556677777766554444333...34555677766 PP

>> AF-4  AF-4 proto-oncoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   7.2   0.00039       1.7     464     499 ..      79     111 ..      63     148 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00039
                              AF-4 464 sahsssaeSeSsSeSeSSSeSDSesEssssdseane 499
                                       s   s+  S S SeSeS  +SDS  Es     ++  
  gi|336255312|ref|YP_004598419.1|  79 SGSGSGLRSRSRSESESRAGSDSSPES---GAATAP 111
                                       223344455555555555555555555...223333 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.1   4.1e-05      0.19      55     114 ..       8      65 ..       2      68 .. 0.73
   2 ?   -1.9   0.7      0.62   2.8e+03     108     118 ..     159     169 ..     154     175 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                           DUF2721  55 nlrrRarlirrailllvlsallvvlvvlllflsallsldlsllaailfvlalllllvsll 114
                                       ++rrR+r+   a++ + + +++v + +++l +  ++      + ++lfv++ lll+++ +
  gi|336255312|ref|YP_004598419.1|   8 QFRRRLRVWADALTYALALTTIVGVGCFALGF--VTGGGAVRAKELLFVAGWLLLAYATV 65 
                                       46777777777766665555555555555555..8999******************9986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.62
                           DUF2721 108 lllvslllflr 118
                                       +ll+ ll fl+
  gi|336255312|ref|YP_004598419.1| 159 SLLILLLSFLL 169
                                       33333333443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1388.94
//
Query:       gi|336255313|ref|YP_004598420.1|  [L=448]
Description: oligopeptide/dipeptide ABC transporter ATPase [Halopiger xanaduensis SH-6]
Scores for 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-33  115.0   0.0    5.8e-33  114.3   0.0    1.4  1  ABC_tran     ABC transporter
    4.9e-15   55.8   0.5    9.7e-15   54.8   0.5    1.5  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    4.7e-06   26.6   0.4     0.0052   16.6   0.2    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      2e-05   24.9   0.1    0.00032   21.0   0.0    2.5  2  AAA_22       AAA domain
     0.0016   18.0   0.0     0.0075   15.7   0.0    2.0  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0047   17.3   0.7      0.011   16.2   0.4    1.9  2  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.018   15.5   0.0      0.081   13.4   0.0    2.1  1  AAA          ATPase family associated with various cellular a
      0.019   14.5   1.0        1.1    8.8   1.0    2.6  1  AAA_25       AAA domain
      0.032   14.2   0.9       0.78    9.7   0.1    2.8  3  AAA_5        AAA domain (dynein-related subfamily)
      0.036   13.7   0.0      0.036   13.7   0.0    1.2  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
      0.082   11.5   0.1        2.4    6.7   0.1    2.1  2  AAA_13       AAA domain
       0.17   11.7   0.3       0.62    9.8   0.1    1.9  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.19   11.6   0.0       0.33   10.8   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
       0.23   11.3   0.1       0.48   10.2   0.1    1.5  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 !  114.3   0.0   4.6e-36   5.8e-33       2     136 ..      45     195 ..      44     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 4.6e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       + vs+++++ge++++vGe+G+GK+tL ++l++l++ t G++ +dg d++e   +el+++r++ ++++q+  ++l+++
  gi|336255313|ref|YP_004598420.1|  45 DGVSFDIRRGETLGLVGESGCGKTTLGRTLLQLEEATDGTVAFDGVDITEldgDELHEWRRNAQMVFQDpqSSLNDR 121
                                       78*******************************************************************8889**** PP

                                       SBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +tv+e               e++++++++l+++gl+    ++ ++ p+++SgGq+qr+++ar+l+ +p++++lDEp 
  gi|336255313|ref|YP_004598420.1| 122 MTVGEIvrepldvhdwetprERRQRVKELLATVGLQR---EHYYRYPHQFSGGQRQRISIARTLALEPDFVVLDEPV 195
                                       ****************998888888999999999888...6666779*****************************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.5   7.6e-18   9.7e-15       1      61 [.     247     308 ..     247     310 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 7.6e-18
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpfa 61 
                                       +E+gp+++lf +p +PYT+ Ll+++p++d+  + +  ++ g++p+++  ++GCpF++RCp +
  gi|336255313|ref|YP_004598420.1| 247 MEIGPTEELFANPSNPYTHSLLSAIPEPDPTSTrERITLHGTPPNPRYPPSGCPFSTRCPAR 308
                                       7******************************99899999********************975 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 !    8.1   0.0    0.0016       2.1       3      23 ..      58      78 ..      57     146 .. 0.82
   2 !   16.6   0.2   4.1e-06    0.0052     233     300 ..     164     229 ..     142     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0016
                            AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                      +l+G  g+GK++L ++l  l 
  gi|336255313|ref|YP_004598420.1| 58 GLVGESGCGKTTLGRTLLQLE 78
                                      69***************8773 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.1e-06
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                        ++++S G+++ + ++  l+  +   +++++DEp + L+ +++++++ ll++l++  g   ++  H+ +
  gi|336255313|ref|YP_004598420.1| 164 YPHQFSGGQRQRISIARTLALEP---DFVVLDEPVSALDVSVQAEIINLLEDLQEeFGLTYLFIAHDLS 229
                                       57788888888866666666555...9***********************8888866777777767665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.5e-07   0.00032      10     128 ..      59     224 ..      51     230 .. 0.70
   2 ?    0.8   0.0      0.44   5.6e+02      22      87 ..     325     388 ..     323     399 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.5e-07
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee.....erpevvfvtlpsstsskdllrellralglelka........... 70 
                                       ++GesG+GKTtl r+ll+  ++    ++      ++++ + +  ++ +++  +++++++ +++l++           
  gi|336255313|ref|YP_004598420.1|  59 LVGESGCGKTTLGRTLLQLEEA----TDgtvafDGVDITELDGDELHEWRRNAQMVFQDPQSSLNDrmtvgeivrep 131
                                       89****************9743....223455544444455555555888888888888888888888888888888 PP

                            AAA_22  71 ...........erlsseellealeqalrarav......................ielliiDEaqh.lr...seeale 110
                                                  +r++ +ell+++  + +++++                      + ++++DE    l+   ++e+++
  gi|336255313|ref|YP_004598420.1| 132 ldvhdwetpreRRQRVKELLATVGLQREHYYRyphqfsggqrqrisiartlalePDFVVLDEPVSaLDvsvQAEIIN 208
                                       88899999888444444444444444444444444444555558888888888999999999777688855599999 PP

                            AAA_22 111 eLrsllnlsrkgvqliLv 128
                                        L +l++  ++g++ +++
  gi|336255313|ref|YP_004598420.1| 209 LLEDLQE--EFGLTYLFI 224
                                       9999998..888887776 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.44
                            AAA_22  22 lrrlleqldeeakaee...erpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalr 87 
                                       l++l+++l+e++ a+    er + +    +  ++ ++++ el+ +l+++      + + +l+ ++ ++r
  gi|336255313|ref|YP_004598420.1| 325 LNTLRSTLHERQRADLsvrERLRAAMGRSTRFGTVEEIYDELFGDLEVPS-----TVQSVLDEIATHMR 388
                                       57788888888888885544444445555555599999999999999754.....44555555555555 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   5.8e-06    0.0075     114     202 ..     138     231 ..      47     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.8e-06
                                       TTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 114 ngkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaell 183
                                       +  + +++ v+ell+++g+++e       ++SgG+++ +++a  +A++      +++lDe  +aLD +  +++ +ll
  gi|336255313|ref|YP_004598420.1| 138 ETPRERRQRVKELLATVGLQREhyyryphQFSGGQRQRISIARTLALEP----DFVVLDEPVSALDVSVQAEIINLL 210
                                       45566789999********9999999999***************99864....5*********************** PP

                                       HHHCTT..SEEEEE-SSHHHC CS
                                       xxxxxx..xxxxxxxxxxxxx RF
                             SMC_N 184 kekskn..aQfivislreeml 202
                                       +  +++    ++ i+++  ++
  gi|336255313|ref|YP_004598420.1| 211 EDLQEEfgLTYLFIAHDLSVV 231
                                       *99988334556666665555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   8.4e-06     0.011      24      53 ..      54      83 ..      47     217 .. 0.87
   2 ?   -1.9   0.0         3   3.9e+03      97     125 ..     342     385 ..     296     406 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.4e-06
                            AAA_16 24 pelvllsGesGvGKsslvrellralekd.gg 53
                                      +e + l+GesG+GK++l r+ll +le++ +g
  gi|336255313|ref|YP_004598420.1| 54 GETLGLVGESGCGKTTLGRTLL-QLEEAtDG 83
                                      467889****************.56666323 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3
                            AAA_16  97 wrekleeala..........avpelagaea.....srllellkr 125
                                        re+l++a++          + +el g+++     +++l++++ 
  gi|336255313|ref|YP_004598420.1| 342 VRERLRAAMGrstrfgtveeIYDELFGDLEvpstvQSVLDEIAT 385
                                       22222222224444444444444444444444444555555554 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 ?   13.4   0.0   6.3e-05     0.081       3      52 ..      59     113 ..      57     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-05
                                       EESSTTSSHHHHHHHHHHH..H........THEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavake..l........gvefleisgsellskyvgesekkirelfke 52 
                                       l+G  G+GKT+l + + +   +        gv++ e++g el      e  ++ +++f++
  gi|336255313|ref|YP_004598420.1|  59 LVGESGCGKTTLGRTLLQLeeAtdgtvafdGVDITELDGDELH-----EWRRNAQMVFQD 113
                                       89**************998442343333445667777777776.....555555555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.0   0.00085       1.1      30     188 ..      51     226 ..      44     227 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00085
                            AAA_25  30 lpagelallaGapgtGKttlald.lalava.tGkpwlg..........pvapeqgkVlyvsaEdsedelrrRlravg 94 
                                       +++ge+  l+G +g+GKttl    l l+ a  G   ++          ++                +e+rr ++ v+
  gi|336255313|ref|YP_004598420.1|  51 IRRGETLGLVGESGCGKTTLGRTlLQLEEAtDGTVAFDgvditeldgdEL----------------HEWRRNAQMVF 111
                                       56888999999999999999633033444423333333222222333322................23333333333 PP

                            AAA_25  95 eal...............................rddarllvldlagveslpLfakdrggtlltadvdaleaaieev 140
                                       ++                                r ++ l+ + l++++  +  ++ +gg++   +   +++++   
  gi|336255313|ref|YP_004598420.1| 112 QDPqsslndrmtvgeivrepldvhdwetprerrqRVKELLATVGLQREHYYRYPHQFSGGQR---QRISIARTLAL- 184
                                       33334333333333334555555555554444322222222222333333333333333333...22246666666. PP

                            AAA_25 141 egvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                       e +++vv+D   +al+ + +     +++++ le++++++g + l++ H
  gi|336255313|ref|YP_004598420.1| 185 E-PDFVVLDEPVSALDVSVQ-----AEIINLLEDLQEEFGLTYLFIAH 226
                                       4.888888888888888777.....67888888888888888888877 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 ?    9.7   0.1   0.00061      0.78       4      22 ..      59      77 ..      56      87 .. 0.88
   2 ?    1.8   0.0      0.18   2.3e+02      57      91 ..     177     212 ..     156     219 .. 0.77
   3 ?   -3.3   0.0       6.6   8.4e+03      82     106 ..     325     349 ..     323     367 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00061
                                      EE--SSSSHHHHHHHGGGG CS
                             AAA_5  4 LvGppGtgKselaerlaaa 22
                                      LvG++G+gK++l + l+++
  gi|336255313|ref|YP_004598420.1| 59 LVGESGCGKTTLGRTLLQL 77
                                      9************999876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                                       --------G-SEEEEESGGG--.HHHHHHHHHHHHS CS
                             AAA_5  57 splvraaregeilvlDEverae.sevlnsLlsllee 91 
                                       s++ + a e++ +vlDE   a   +v+++ ++lle+
  gi|336255313|ref|YP_004598420.1| 177 SIARTLALEPDFVVLDEPVSALdVSVQAEIINLLED 212
                                       5555667799999**995555559**********97 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 6.6
                                       HHHHHHHHHSSEEE..-SSSEEE-- CS
                             AAA_5  82 lnsLlslleerrllleeggelvkak 106
                                       ln+L s l+er++   + +e+ +a+
  gi|336255313|ref|YP_004598420.1| 325 LNTLRSTLHERQRADLSVRERLRAA 349
                                       5677788888887766666666554 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 ?   13.7   0.0   2.8e-05     0.036       4      42 ..      43      82 ..      41     366 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-05
                                      HHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS CS
                                      xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  4 vlDal.fpivqGqrtlipgafgvGktvisqslskqsnsdd 42
                                      ++D + f i +G++++++g++g+Gkt++ ++l++  +++d
  gi|336255313|ref|YP_004598420.1| 43 AVDGVsFDIRRGETLGLVGESGCGKTTLGRTLLQLEEATD 82
                                      5554337899*******************99998866554 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.033        42      23      43 ..      61      81 ..      59     115 .. 0.78
   2 ?    6.7   0.1    0.0019       2.4     526     573 ..     185     230 ..     175     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.033
                            AAA_13 23 GwNGaGKTtLSrllrslelge 43
                                      G  G GKTtL r l +le+  
  gi|336255313|ref|YP_004598420.1| 61 GESGCGKTTLGRTLLQLEEAT 81
                                      7789************97643 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0019
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnlef 573
                                       +   vv+D PvS LD  ++  +++l+++   ++     lfi  H l+ 
  gi|336255313|ref|YP_004598420.1| 185 EPDFVVLDEPVSALDVSVQAEIINLLEDLQ-EEFGLTYLFIA-HDLSV 230
                                       6678**********************9986.66667777773.66555 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00048      0.62       6      25 ..      59      78 ..      55      93 .. 0.85
   2 ?   -1.5   0.0       1.5   1.9e+03      59      76 ..     199     216 ..     192     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00048
                         PduV-EutP  6 liGkvgsGKttLtqalkgee 25
                                      l+G++g+GKttL ++l + e
  gi|336255313|ref|YP_004598420.1| 59 LVGESGCGKTTLGRTLLQLE 78
                                      89**********99987754 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                         PduV-EutP  59 vtsaeadvialvqdatee 76 
                                        +s++a++i l+ d +ee
  gi|336255313|ref|YP_004598420.1| 199 DVSVQAEIINLLEDLQEE 216
                                       5799********998876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00026      0.33      99     124 ..      53      79 ..      39      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                                       T.SEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallpele 124
                                         +t  lvG+SG GK+tL  +ll+ +e
  gi|336255313|ref|YP_004598420.1|  53 RgETLGLVGESGCGKTTLGRTLLQLEE 79 
                                       448999************999987544 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 ?   10.2   0.1   0.00037      0.48      13      38 ..      45      70 ..      42      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00037
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTl 38
                                      dg +++i++ ++  l+G+sG GK+Tl
  gi|336255313|ref|YP_004598420.1| 45 DGVSFDIRRGETLGLVGESGCGKTTL 70
                                      77889998666788***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.39
# Mc/sec: 3450.36
//
Query:       gi|336255314|ref|YP_004598421.1|  [L=457]
Description: oligopeptide/dipeptide ABC transporter ATPase [Halopiger xanaduensis SH-6]
Scores for 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-28   98.1   0.0    2.2e-15   57.4   0.0    2.3  2  ABC_tran         ABC transporter
    2.1e-19   69.8   0.1    4.8e-19   68.6   0.1    1.6  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
      3e-06   27.3   0.0    3.1e-05   23.9   0.0    2.0  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0018   17.7   0.1        0.3   10.5   0.0    2.2  2  SMC_N            RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.022   15.1   0.0      0.057   13.8   0.0    1.8  2  AAA_16           AAA ATPase domain
      0.027   14.8   0.1       0.61   10.4   0.0    2.5  2  AAA_22           AAA domain
       0.06   13.1   0.0       0.13   12.0   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
        0.1   12.7   0.0       0.19   11.8   0.0    1.4  1  DUF87            Helicase HerA, central domain
       0.18   11.5   0.1       0.66    9.7   0.0    1.8  2  Sigma54_activat  Sigma-54 interaction 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 !   38.5   0.0   7.6e-13   1.5e-09       2      59 ..      38      93 ..      37     118 .. 0.86
   2 !   57.4   0.0   1.1e-18   2.2e-15      55     136 ..     190     286 ..     171     287 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 7.6e-13
                                      EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrk 59
                                      ++vs+++++ge+v+ivGe+G+GKS  ++ ++gl++   G+i l+g +++   le +r+
  gi|336255314|ref|YP_004598421.1| 38 DDVSFDIRPGETVGIVGESGSGKSVTARSIMGLVD-SPGRI-LEGSSIRFSHLETVRE 93
                                      89********************************8.79999.9999888866665554 PP

  == domain 2  score: 57.4 bits;  conditional E-value: 1.1e-18
                                       HHCCHCEEEE-SS..--S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHH CS
                                       xxxxxxxxxxxxx..xxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  55 eslrkeigvlpqe..pqlfpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkq 115
                                            +i++++q+  ++l+p +tv+++              e+++e+ ++l+ +g+++ + ++v++ p+++SgG++q
  gi|336255314|ref|YP_004598421.1| 190 LMRGGRIAMVFQDplTSLNPVYTVGNQikealrlhqglrgeEATQEAIQLLEDVGIPD-ARRRVDEYPHQFSGGMRQ 265
                                       556789*******9999*********9*************999999************.88999************* PP

                                       HHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 116 rvalarallkkpkllllDEpt 136
                                       r ++a+al+++p++l++DEpt
  gi|336255314|ref|YP_004598421.1| 266 RAVIAMALACEPEVLICDEPT 286
                                       ********************9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.1   2.4e-22   4.8e-19       1      65 []     338     401 ..     338     401 .. 0.99

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 2.4e-22
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vEr+++++lf +p+HPYT++Ll+s+p  + +++ l++i+g++p +++  + C+FapRCp a  eC
  gi|336255314|ref|YP_004598421.1| 338 VERADVEDLFANPKHPYTQGLLQSIPGQQDGDR-LQTIEGNVPTPNEPATYCRFAPRCPKAFGEC 401
                                       8********************************.******************************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 ?    1.1   0.0      0.14   2.8e+02       3      19 ..      51      67 ..      50     112 .. 0.76
   2 !   23.9   0.0   1.6e-08   3.1e-05     228     302 ..     250     322 ..     199     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.14
                            AAA_21  3 vliGpNgsGKSnLLdal 19
                                      +++G  gsGKS   + +
  gi|336255314|ref|YP_004598421.1| 51 GIVGESGSGKSVTARSI 67
                                      69*********766666 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.6e-08
                            AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSplll 302
                                       ++ +  ++++S G+++  a++++ l+  +   +l+ DEp + L+  +++ +l+ll ++ ++++   ++ TH+  ++
  gi|336255314|ref|YP_004598421.1| 250 RRVDEYPHQFSGGMRQR-AVIAMALACEP--EVLICDEPTTALDVTIQAQILDLLtEIQEERDLATMFITHDMGVI 322
                                       45667899*********.99999998777..9***********************6666669*********98877 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 !    5.1   0.0    0.0069        14      26      44 ..      49      67 ..      34      80 .. 0.78
   2 !   10.5   0.0   0.00015       0.3      75     212 ..     192     332 ..     166     339 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0069
                                      EEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                         ivG+ GSGKs    +i
  gi|336255314|ref|YP_004598421.1| 49 TVGIVGESGSGKSVTARSI 67
                                      346**********888777 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00015
                                       TEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.........CS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxx RF
                             SMC_N  75 kkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.........lLSgGek 142
                                         ++++++f+++  +    ++ +++  ++k+  + +  + g+e+t++ + +lle++gi            ++SgG +
  gi|336255314|ref|YP_004598421.1| 192 RGGRIAMVFQDPLTS---LNPVYTVGNQIKEALRLHQGLRGEEATQEAI-QLLEDVGIPDArrrvdeyphQFSGGMR 264
                                       556666776666655...5667788888888888888888888887665.69999999888899999999*****88 PP

                                       HHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 143 tLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvgvt 212
                                       + + +a+ +A   ++p+ l + De   aLD +  +++ +ll e +++     + i+++ +++++ +  v v+
  gi|336255314|ref|YP_004598421.1| 265 QRAVIAMALA---CEPEVL-ICDEPTTALDVTIQAQILDLLTEIQEErdLATMFITHDMGVIAEISDRVNVM 332
                                       8877777766...667765.78*******************9776653366788888888888876666665 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   2.8e-05     0.057      24      76 ..      46      98 ..      31     202 .. 0.73
   2 ?   -2.1   0.0       2.2   4.4e+03     136     142 ..     277     283 ..     208     315 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.8e-05
                            AAA_16 24 p.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqal 76
                                      p e v ++GesG+GKs  +r+++  l ++ g  l+g   ++ s ++ +  +a+ +
  gi|336255314|ref|YP_004598421.1| 46 PgETVGIVGESGSGKSVTARSIMG-LVDSPGRILEGSSIRF-SHLETVReYAERF 98
                                      3378999****************5.5444466666666666.2222233345555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                            AAA_16 136 plvlvlD 142
                                       p vl++D
  gi|336255314|ref|YP_004598421.1| 277 PEVLICD 283
                                       2333333 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   0.00031      0.61      10      27 ..      52      69 ..      47     103 .. 0.83
   2 ?    1.7   0.0      0.14   2.9e+02      59     124 ..     238     311 ..     155     321 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                            AAA_22 10 vtGesGtGKTtllrrlle 27
                                      ++GesG+GK++++r ++ 
  gi|336255314|ref|YP_004598421.1| 52 IVGESGSGKSVTARSIMG 69
                                      89***********98765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                            AAA_22  59 ellralglelkaerlsseellealeqalrarav........ielliiDEaqh.lr...seealeeLrsllnlsrkgv 123
                                       +ll+++g +  +   + +e+ +++   +r+rav        +e+li DE    l+   ++++l  L ++++  + ++
  gi|336255314|ref|YP_004598421.1| 238 QLLEDVGIPDAR--RRVDEYPHQFSGGMRQRAViamalacePEVLICDEPTTaLDvtiQAQILDLLTEIQE--ERDL 310
                                       455555554444..444444455555555555555555556699999998777766554666666666666..5555 PP

                            AAA_22 124 q 124
                                       +
  gi|336255314|ref|YP_004598421.1| 311 A 311
                                       5 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 ?   12.0   0.0   6.5e-05      0.13      13      37 ..      38      62 ..      35      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.5e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKST 37
                                      d+ +++i++ +++ ++G+sGsGKS 
  gi|336255314|ref|YP_004598421.1| 38 DDVSFDIRPGETVGIVGESGSGKSV 62
                                      66788999988999**********6 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.8e-05      0.19      26      44 ..      50      68 ..      37      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.8e-05
                             DUF87 26 lAilgsTGsGKSntvavLl 44
                                      ++i+g++GsGKS t+++++
  gi|336255314|ref|YP_004598421.1| 50 VGIVGESGSGKSVTARSIM 68
                                      79**************996 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00033      0.66      22      43 ..      47      68 ..      27      77 .. 0.78
   2 ?   -1.2   0.0       0.7   1.4e+03      97     135 ..     280     319 ..     259     340 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00033
                                      SS-EEEECSTTSSHHHHHHHHH CS
                   Sigma54_activat 22 dlsvlitGesGtGKellaraih 43
                                        +v i+GesG+GK++ ar+i 
  gi|336255314|ref|YP_004598421.1| 47 GETVGIVGESGSGKSVTARSIM 68
                                      46888**************986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.7
                                       EEEET.GGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--E CS
                   Sigma54_activat  97 lfLDe.igelplelQekLlrvlqegevervGsskeikvdv 135
                                       l  De  + l++++Q+++l +l e + er  ++  i+ d+
  gi|336255314|ref|YP_004598421.1| 280 LICDEpTTALDVTIQAQILDLLTEIQEERDLATMFITHDM 319
                                       5556534578999999999999887766655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3540.17
//
Query:       gi|336255315|ref|YP_004598422.1|  [L=579]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-22   78.8   6.5      4e-22   78.8   6.5    3.4  2  BPD_transp_1     Binding-protein-dependent transport system i
  ------ inclusion threshold ------
      0.059   13.3   0.0      0.059   13.3   0.0    3.9  4  OppC_N           N-terminal TM domain of oligopeptide transpo
        5.3    7.0  23.6       0.63   10.0   1.2    4.3  5  Abhydrolase_9_N  Alpha/beta-hydrolase family N-terminus


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 ?  -10.2  13.8         3   1.8e+04      17      59 ..     240     264 ..      35     361 .. 0.72
   2 !   78.8   6.5   6.7e-26     4e-22       2     182 ..     368     559 ..     359     562 .. 0.97

  Alignments for each domain:
  == domain 1  score: -10.2 bits;  conditional E-value: 3
                      BPD_transp_1  17 dkllrpliivllslPsfvlaillvlvfvilsilghlilpviil 59 
                                       d+ l ++++ l+++  fv                  +  ++i+
  gi|336255315|ref|YP_004598422.1| 240 DDTLNRFSNHLWGIFGFV------------------VVFLFIV 264
                                       333333344444444444..................3333333 PP

  == domain 2  score: 78.8 bits;  conditional E-value: 6.7e-26
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.....vilsilghlilpviillllsaapyvrlirr 73 
                                       +++++l+a ++++ +d l  + ++++ s+P f+l+++l ++f      i   l  +il ++i ++ +++++ r ir 
  gi|336255315|ref|YP_004598422.1| 368 VVMSLLTA-YYKGLVDVLTVITSDTIISIPAFLLVMMLSVIFqdgnhPIAEPLDGGILLGLIFAFAYWPGMWRTIRG 443
                                       66777777.**************************************99999************************* PP

                      BPD_transp_1  74 aalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydy 150
                                         l+++++++v aar +G s+  ++rk++ P ++ +i+    l +gg++  +++l+flg    lg +  ++++g+ +
  gi|336255315|ref|YP_004598422.1| 444 PSLQVVEEEWVDAARSYGQSPANTMRKHMAPYIAGYIMIYGSLLLGGIIISTAALSFLG----LGIQAPTPEWGRLI 516
                                       ***********************************************************....************** PP

                      BPD_transp_1 151 seis...........nggvlalviavlllnlvadilqrlldpr 182
                                       s +             ++ l++v++v ++n++ d l +++dp 
  gi|336255315|ref|YP_004598422.1| 517 SDGRaylsttswhvaTIPGLMIVLVVTAFNALGDGLRDAIDPE 559
                                       *999*************************************95 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.8      0.42   2.5e+03      19      29 ..     137     147 ..     131     160 .. 0.56
   2 ?   13.3   0.0   9.9e-06     0.059       4      41 ..     240     287 ..     237     301 .. 0.81
   3 ?   -2.9   0.1       1.2   7.1e+03      22      33 ..     398     409 ..     397     416 .. 0.77
   4 ?   -2.5   0.1       0.9   5.4e+03      19      32 ..     421     434 ..     421     443 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.42
                            OppC_N  19 glvilllllli 29 
                                        l+++++l+++
  gi|336255315|ref|YP_004598422.1| 137 VLAVVVVLFAF 147
                                       23333333333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 9.9e-06
                            OppC_N   4 qdawrrFkrNklAvvglvilllllliaifaPlia..........Pydp 41 
                                        d++ rF  +   ++g+v++ l+++ a++aP ++          Py +
  gi|336255315|ref|YP_004598422.1| 240 DDTLNRFSNHLWGIFGFVVVFLFIVTALWAPAVStvtaeqniytPYAY 287
                                       57889***************************9866666666666655 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.2
                            OppC_N  22 illlllliaifa 33 
                                       +ll++ l +if+
  gi|336255315|ref|YP_004598422.1| 398 FLLVMMLSVIFQ 409
                                       788899989985 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 0.9
                            OppC_N  19 glvilllllliaif 32 
                                       g ++l l++++a +
  gi|336255315|ref|YP_004598422.1| 421 GGILLGLIFAFAYW 434
                                       56777777777765 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 ?    1.8   0.1     0.034     2e+02      94     152 ..      30      93 ..      17      95 .. 0.66
   2 ?   10.0   1.2   0.00011      0.63      17      69 ..      91     146 ..      83     151 .. 0.87
   3 ?    7.4   1.0   0.00068       4.1      15      80 ..     200     274 ..     195     289 .. 0.63
   4 ?    3.6   0.8    0.0096        57      87     150 ..     347     410 ..     339     413 .. 0.90
   5 ?   -2.4   0.1      0.67     4e+03      56     103 ..     531     542 ..     487     557 .. 0.51

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.034
                   Abhydrolase_9_N  94 lvllvallvfalllllgrllralvrlla.....rllgrvlprrvaavlgvlvvvvlvvllvdgv 152
                                       ++l +a + +++ l++gr ++++  l+        + r+lp+++   +g++++ ++ ++++dgv
  gi|336255315|ref|YP_004598422.1|  30 ALLWLAGFAVLIALEFGRYMSWTHGLIDaimyvVDMIRLLPDWIGDSVGAATTPIVGYFVSDGV 93 
                                       444555555566666677776665544410011245677**************99999999998 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00011
                   Abhydrolase_9_N  17 sGlsaaiGYglGvllawlvrrllr...lpepsrrvrrrlrlalavvalvvllvalv 69 
                                        G+s  i +g++v+l +++ + +    +p++++r+ r l+++l++v+l+v++v+++
  gi|336255315|ref|YP_004598422.1|  91 DGVSLLILFGVAVVLTNVLPWQVTgrfGPDLPERTLRYLERVLLTVVLAVVVVLFA 146
                                       59999***********998877778899*************999999988888765 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00068
                   Abhydrolase_9_N  15 vvsGlsaaiGYglG.vllawlvrrllr........lpepsrrvrrrlrlalavvalvvllvalvlaarwQrelra 80 
                                       v+ G+ + + Yg + ++lawl++ + +         ++p++ + +r+   l  ++  v+++++++ a w   +++
  gi|336255315|ref|YP_004598422.1| 200 VAWGIRVLLVYGYAlAMLAWLWKGYNVfrdhyrqaDWTPRDDTLNRFSNHLWGIFGFVVVFLFIVTALWAPAVST 274
                                       555665555554441357999999888899999995666666666666666666666666666666666555555 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.0096
                   Abhydrolase_9_N  87 lgaaeyllvllvallvfalllllgrllralvrllarllgrvlprrvaavlgvlvvvvlvvllvd 150
                                       +ga   l++ l+++ + +++ +++ ll a ++ l  +l+ +  + +  + ++l+v++l v++ d
  gi|336255315|ref|YP_004598422.1| 347 YGAQTSLVIGLLSIGLGGMIAVVMSLLTAYYKGLVDVLTVITSDTIISIPAFLLVMMLSVIFQD 410
                                       6677889999***********************************************9998776 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 0.67
                   Abhydrolase_9_N  56 lavvalvvllvalvlaarwQrelralmgaeplgaaeyllvllvallvf 103
                                       +++ +l+++                                    lv+
  gi|336255315|ref|YP_004598422.1| 531 ATIPGLMIV------------------------------------LVV 542
                                       111111111....................................111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 4169.35
//
Query:       gi|336255316|ref|YP_004598423.1|  [L=355]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-35  120.5  12.6    6.9e-35  120.5  12.6    2.1  2  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 ?    1.3   0.8     0.014   2.5e+02      26      60 ..      11      95 ..       2     116 .. 0.65
   2 !  120.5  12.6   3.9e-39   6.9e-35       1     183 [.     117     351 ..     117     353 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.014
                      BPD_transp_1 26 vllslPsfvlaillvlvf............................................................. 43
                                      +lls+P++ l++ +v+++                                                             
  gi|336255316|ref|YP_004598423.1| 11 LLLSIPVLFLVLTFVFALlrmgpvdpvaarlgpeasgaeaqrmrerlglndplweqyldfvtdfltldlgqswviygdw 89
                                      6778888887777665558888888888888888888888888888888888888888888887777744444444433 PP

                      BPD_transp_1 44 vilsilghlilpviill 60
                                                  v+ +l
  gi|336255316|ref|YP_004598423.1| 90 E-----------VVSIL 95
                                      2...........33333 PP

  == domain 2  score: 120.5 bits;  conditional E-value: 3.9e-39
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.................................. 43 
                                       gi+lG++a+ln+n++ d+l ++  i+++++P f+l i+l++++                                  
  gi|336255316|ref|YP_004598423.1| 117 GIPLGFYAGLNPNSRSDYLASVGGILWQAMPNFWLSIILLAILrqtkgggwldfdwytfgpelgsitgtpdlaffsv 193
                                       89**************************************999********************************** PP

                      BPD_transp_1  44 ...................vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkv 101
                                                          ++ +++++   p+++l+  s+a+  r+ r a+l+++++++ve+a+a+G++ + +++k+
  gi|336255316|ref|YP_004598423.1| 194 nwidlgaaavplvtgidwgALATDIKFILPPALVLGSASMAAELRIGRTAVLETINSNYVETAKAKGLTNRVVVWKH 270
                                       ***************************************************************************** PP

                      BPD_transp_1 102 vlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrl 178
                                       v++nal+p+++ + + +++l+gg+v++e +++ +Glg+ ++ a+ + d++++  +++++++++++ ln++ d+l+++
  gi|336255316|ref|YP_004598423.1| 271 VFRNALIPLVPVITNEATLLIGGSVIVESIFNINGLGRIFFLASVQGDLPLAG-ALLFIFTLIIIFLNVLQDFLYTI 346
                                       ****************************************************9.*********************** PP

                      BPD_transp_1 179 ldprv 183
                                       +dprv
  gi|336255316|ref|YP_004598423.1| 347 IDPRV 351
                                       ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2715.35
//
Query:       gi|336255317|ref|YP_004598424.1|  [L=609]
Description: ABC transporter periplasmic protein [Halopiger xanaduensis SH-6]
Scores for 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-71  239.7   0.6      7e-71  239.2   0.6    1.2  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.2   0.6   3.9e-75     7e-71       2     365 ..     175     576 ..     174     587 .. 0.89

  Alignments for each domain:
  == domain 1  score: 239.2 bits;  conditional E-value: 3.9e-75
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC............... CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyasllee............... 63 
                                       ++  L es +e+s+Dg+t+tf+L++gv+F+ G++ltA+Dvv+sf+rl++ +++ ++++l +                
  gi|336255317|ref|YP_004598424.1| 175 IENKLVES-FETSEDGLTWTFTLKEGVTFHGGEELTADDVVYSFRRLAESEYSERANFLVDTplglgleheetedgg 250
                                       77899***.6********************************************99888877*************** PP

                                       .TCTEEEEEEEETTEEEEEESSETTTTTTHCHHHHHHHGC.......CHTCTCTTTTTGTTTSE-BSSSEEEEEEET CS
                         SBP_bac_5  64 .dqdikkveavddytvrftlkkpnalfltllaavpasiak.......kaaekeddkdkdtnekpvgtGPYklkefkp 132
                                          ++ ++eavdd+tv++tl++p++ +l +l+ ++ +++        + ++ e d +++      gtGP++++ef+p
  gi|336255317|ref|YP_004598424.1| 251 iAPESIGIEAVDDRTVELTLTTPQPAALDILTYTAFAVVPegivgdiEGYDGEVDHNEFATGMANGTGPFQFDEFSP 327
                                       *************************88888888888888888888996666666666666666679*********** PP

                                       TTEEEEEE-TTSTTTSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEE..ESTTCCTHCHH.....HHHTTEEE..... CS
                         SBP_bac_5 133 gqkivlernpdYwgggkpkldriefkvipdsdaraaalqsGeiddv..aepppsdieql.....keakglkv..... 197
                                       g++++++r++dY  g+ ++l++i++++ +ds++  + +  G++d++  +++p+++ ++      +     ++     
  gi|336255317|ref|YP_004598424.1| 328 GEEVRVVRFDDYH-GSTANLESIHWEINEDSESIFTYVMEGNADIFrdSQVPTPQYDPSlidaeE----DDMgrevg 399
                                       ************8.**************99******99******997744444444444344333....33355669 PP

                                       ............EEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSS.STTTSTTCCS CS
                         SBP_bac_5 198 ............lyespgggvtylafNtkkppfddkrvRqAlsyAiDreeivkavlegyatpansl.lppsspgade 261
                                                       p++g++y+afN ++       vRqA++y  D +e+++ vl+  +  a s+ +p ++p  d+
  gi|336255317|ref|YP_004598424.1| 400 tygplendetvnYLGVPELGTYYFAFNVSNV---PRPVRQAIAYVTDHQEFLEDVLKQRGFEAFSFtPPRMWPTGDD 473
                                       9999999998888999*************52...378*****************************88889999999 PP

                                       CHCCCSHH.......SHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEE CS
                         SBP_bac_5 262 eykpayka.......ydpekAkklLkeaGykdgdggglrekklkltlllasgspaekaiaeliqqqlkkiGikvevk 331
                                        y++  ++        d+e A++ L+eaG++ +d       + +lt +++ ++p   ++ae+i q l+++G++++ +
  gi|336255317|ref|YP_004598424.1| 474 GYDQWVDEwqygvneTDIESAQQVLEEAGFTADD-------PFELTASTYESGPEYAEMAEIIRQKLADLGVDIQNQ 543
                                       99987766*************************9.......568999999*************************** PP

                                       EECHHHHHHHHHHCTTESEEEEEEECTTSTTHHH CS
                         SBP_bac_5 332 tvdwaatylervkdgdfdmillgwgadypdpdnf 365
                                       ++++ +t ++r +dgd+ m+ lgw  ++pdp + 
  gi|336255317|ref|YP_004598424.1| 544 STQF-STLQDRGEDGDLEMYSLGWIWSWPDPAYG 576
                                       ****.**************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.60u 0.21s 00:00:00.81 Elapsed: 00:00:00.38
# Mc/sec: 4800.07
//
Query:       gi|336255318|ref|YP_004598425.1|  [L=189]
Description: adenine phosphoribosyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-17   62.6   3.6    4.4e-17   62.1   3.6    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00014   21.4   0.3    0.00016   21.2   0.3    1.2  1  UPRTase       Uracil phosphoribosyltransferase


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 !   62.1   3.6   4.9e-21   4.4e-17      13     152 ..      40     176 ..      34     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 4.9e-21
                                       EEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...........EE----T CS
                      Pribosyltran  13 davarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes...rlledpa 86 
                                       ++v r+++++  e   + d +v++a  G+ + ++++   ++pl+++rk+ y   +   ++++   +          +
  gi|336255318|ref|YP_004598425.1|  40 EIVIRIIRKAELE---NVDRIVTPAAMGIHISTAVSLMTDIPLTVIRKRQYGLADEVAISQQTGYSEnemYINDVRE 113
                                       4667777777777...99*********************************99888888766544446677777889 PP

                                       TSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEEEEE CS
                      Pribosyltran  87 gkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfslspdnfvavv 152
                                       g++Vl+ DD+l+tGgTl a+l++L e g+e++ ++++++k  +e +vd   + v++l+   +v vv
  gi|336255318|ref|YP_004598425.1| 114 GERVLVLDDVLSTGGTLAAVLDALDEIGAEVIDTVAVIKKVGGENKVDDAGYDVKTLI---NVDVV 176
                                       ***********************************************99999999777...55444 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.3   1.8e-08   0.00016     118     179 ..     110     170 ..      66     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.8e-08
                           UPRTase 118 ki.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpkvkvv 179
                                       ++ + ++vl+lD v++TGg++aa+++ L e  +g e I  ++v+    g +++ ++  +vk  
  gi|336255318|ref|YP_004598425.1| 110 DVrEGERVLVLDDVLSTGGTLAAVLDALDE--IGAEVIDTVAVIKKVGGENKVDDAGYDVKTL 170
                                       3336688***********************..6678899999998888887777776666643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1514.69
//
Query:       gi|336255319|ref|YP_004598426.1|  [L=211]
Description: hypothetical protein Halxa_3942 [Halopiger xanaduensis SH-6]
Scores for 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   15.3   0.2      0.021   14.8   0.2    1.2  1  Reticulon  Reticulon
        2.3    8.5   5.5        3.1    8.0   0.4    2.2  2  MHYT       Bacterial signalling protein N terminal repeat


Domain annotation for each model (and alignments):
>> Reticulon  Reticulon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   2.3e-06     0.021       6      53 ..     138     185 ..     137     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-06
                         Reticulon   6 lWrnkkksgivlgglllllllfellgysllslvsklllllllvlflwa 53 
                                        Wr+   s++++ ++l++ l++e++  +lls + ++++++++v+++  
  gi|336255319|ref|YP_004598426.1| 138 AWRELYLSLGAVSCALVAALWLEIYPLTLLSELTWAGVIAVTVTVTAI 185
                                       6***********************************999999988733 PP

>> MHYT  Bacterial signalling protein N terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.7     0.012   1.1e+02      27      53 ..     141     167 ..     132     173 .. 0.79
   2 ?    8.0   0.4   0.00035       3.1      26      54 ..     163     196 ..     161     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.012
                              MHYT  27 ltalSlliaivasvlAlalavrrrdtr 53 
                                          lSl+++  a v+Al+l +++ + +
  gi|336255319|ref|YP_004598426.1| 141 ELYLSLGAVSCALVAALWLEIYPLTLL 167
                                       56799999999********88776655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00035
                              MHYT  26 altalS.l....liaivasvlAlalavrrrdtrl 54 
                                       +lt+lS l    +ia+++ v A++ + ++r++rl
  gi|336255319|ref|YP_004598426.1| 163 PLTLLSeLtwagVIAVTVTVTAIVQIYHERNMRL 196
                                       578888514455**************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); 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 0.20s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1718.50
//
Query:       gi|336255320|ref|YP_004598427.1|  [L=391]
Description: phosphopantothenoylcysteine decarboxylase/phosphopantothenate/cysteine ligase [Halopiger xanaduensis SH-6]
Scores for complete 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  174.9   2.3    2.4e-50  171.0   0.6    2.2  2  DFP           DNA / pantothenate metabolism flavoprotein
    3.4e-35  121.1   0.2    4.9e-35  120.6   0.2    1.3  1  Flavoprotein  Flavoprotein
  ------ inclusion threshold ------
      0.026   13.9   7.6      0.095   12.1   2.7    2.5  2  PALP          Pyridoxal-phosphate dependent enzyme
      0.063   13.1   0.2       0.15   12.0   0.2    1.6  1  3HCDH_N       3-hydroxyacyl-CoA dehydrogenase, NAD binding do
       0.34   10.4   6.3       0.67    9.5   1.7    3.1  3  adh_short_C2  Enoyl-(Acyl carrier protein) reductase


Domain annotation for each model (and alignments):
>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.015        55      33      54 ..      21      42 ..      17      89 .. 0.72
   2 !  171.0   0.6   6.6e-54   2.4e-50       1     185 [.     179     356 ..     179     357 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.015
                                      HHHHHHHHHTT-EEEEEE-S-S CS
                               DFP 33 yalAeaaaarGaeVtlvsgpvs 54
                                      ++lA+++++rGa+V+ v   ++
  gi|336255320|ref|YP_004598427.1| 21 VELAHELRRRGADVRGVMTDSA 42
                                      78*************9988743 PP

  == domain 2  score: 171.0 bits;  conditional E-value: 6.6e-54
                                       TTT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHH CS
                               DFP   1 legkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleave 77 
                                       leg++v+vtaG+T E+iDpVR+i+NrSSGkmG a+A+a++ rGa+Vtlv+   +    + ++v +vesa+eml+a++
  gi|336255320|ref|YP_004598427.1| 179 LEGEHVVVTAGATSESIDPVRVITNRSSGKMGRAVAKACYVRGADVTLVQNGED---VPYADVREVESAAEMLAATR 252
                                       689**********************************************98744...44889*************** PP

                                       HHHTT-SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-SS....-HHH CS
                               DFP  78 ealkeadivimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaete....elle 150
                                       ea+++ad++++aAA+ Dy++++ + eKi+   ++++ltlele++p+++ e+ ++++++  +vGF+ et+     ++ 
  gi|336255320|ref|YP_004598427.1| 253 EACEDADALVSAAAIGDYTVQT-SGEKIRS--GQDDLTLELEPTPKLIDEI-RAARPDLPIVGFKTETSggeaAMVG 325
                                       ********************85.788**95..7788***************.55566656*******96688999** PP

                                       HHHHHHHHTT-SEEEEEEGGGTTGGG-SS-EEEEE CS
                               DFP 151 nareklerkgldlivaNdvskeeagfgsdenevtl 185
                                       +are ler gl ++vaNd+s    ++gsd+++++l
  gi|336255320|ref|YP_004598427.1| 326 RARETLERAGLAFVVANDAS----VMGSDRTRALL 356
                                       ******************99....47887777665 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.2   1.4e-38   4.9e-35       2     156 ..       6     172 ..       5     174 .. 0.94

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 1.4e-38
                                       EEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHH...CTTESEE CS
                      Flavoprotein   2 killgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhiel...rrwadll 68 
                                       +++lg+TGs+aa+k++el ++L+++g++v+ v+t++A+ ++++  +++a+       ++++++h+el   + wad++
  gi|336255320|ref|YP_004598427.1|   6 NVALGVTGSIAAVKTVELAHELRRRGADVRGVMTDSARGIVHPWAVEFATdnevvteITGSVEHVELcgsDGWADVF 82 
                                       789***************************************998888779999999**********88777***** PP

                                       EEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT............... CS
                      Flavoprotein  69 viaPasantlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigkg 142
                                       +iaPa+ant++kia ++ d+++t+++    +a +p++iaPam+  my++p +l+ ++++ e gv +++P   ++gk+
  gi|336255320|ref|YP_004598427.1|  83 LIAPATANTVGKIAGAVDDTPVTTCATTalGAGTPVVIAPAMHEPMYDHPGVLEAIDTVaEWGVDFVDPR-VEEGKA 158
                                       **********************99994447999**************************88*********.8999** PP

                                       .GHHHHHHHHHHCH CS
                      Flavoprotein 143 kmaeieeivgkild 156
                                       k+a+ e+iv  + +
  gi|336255320|ref|YP_004598427.1| 159 KIATEEAIVCDVAR 172
                                       ********988765 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.6    0.0068        24     185     270 ..      79     175 ..      61     194 .. 0.78
   2 ?   12.1   2.7   2.7e-05     0.095      53     117 ..     196     264 ..     171     386 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0068
                                       -EEEEEEECTTCGGTTCCS..S.SS..B...........SSS.CCSTCS.CGTTCCHHHHSEEEEEEEEEEHHHHHH CS
                              PALP 185 vrvigvepegsdalarslragrrvtvpvs..........dtiadglavg.spselafelldrlvdeivtvsdeeale 250
                                         v+ + p++++++++ + a + ++v+++            ia++++ +  + + ++e++d     +v   d  + e
  gi|336255320|ref|YP_004598427.1|  79 ADVFLIAPATANTVGKIAGAVDDTPVTTCattalgagtpVVIAPAMHEPmYDHPGVLEAIDTVAEWGVDFVDPRVEE 155
                                       5788999999999999994444444444477788888888888888888988999999999999999********** PP

                                       HHHHHHHHHSB-B-HHHHHH CS
                              PALP 251 amrllarregivvepssaaa 270
                                       +  + a++e iv++ + aa+
  gi|336255320|ref|YP_004598427.1| 156 GKAKIATEEAIVCDVARAAG 175
                                       ******99999999876665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.7e-05
                                       TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEE.....EETTS-HHHHHHHHHTT-EEEEECCHHHHHHHH CS
                              PALP  53 tgaktvveassGNhgralAaaaallGlkvtiv.....vpadaspekvallrllGaevvevggdydeavaa 117
                                        + ++++  ssG +gra+A a+ + G +vt+v     vp  +  e   + ++l a+ + + +d d+ v+a
  gi|336255320|ref|YP_004598427.1| 196 DPVRVITNRSSGKMGRAVAKACYVRGADVTLVqngedVPYADVREVESAAEMLAATREAC-EDADALVSA 264
                                       566889999***********************6666655555556666666666666666.333333333 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 ?   12.0   0.2   4.1e-05      0.15       7      62 ..     206     260 ..     201     281 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
                                       -SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCC CS
                           3HCDH_N   7 aGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeevea 62 
                                       +G mG+ +a+++  +g +V+lv+  e+   +  +++e+  e l++ +++  e+++a
  gi|336255320|ref|YP_004598427.1| 206 SGKMGRAVAKACYVRGADVTLVQNGEDVPYADVREVESAAEMLAATREAC-EDADA 260
                                       69***********************9999999999999888887776655.44444 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 ?   -2.5   0.0      0.87   3.1e+03       9      29 ..      22      42 ..      10      64 .. 0.63
   2 ?   -1.7   0.0      0.47   1.7e+03      33      54 ..     152     174 ..     144     184 .. 0.75
   3 ?    9.5   1.7   0.00019      0.67       7      82 ..     210     270 ..     206     285 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.87
                                      HHHHHHHHTT-EEEEEESSGG CS
                      adh_short_C2  9 aiAkalaeeGaevvltdlnee 29
                                      ++A++l ++Ga+v  +  + +
  gi|336255320|ref|YP_004598427.1| 22 ELAHELRRRGADVRGVMTDSA 42
                                      467777777777765554444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.47
                                       HHHHHHHHTTSE.EEE--TTSHH CS
                      adh_short_C2  33 rveelaeelgae.vlecDVtdee 54 
                                       rvee ++++ +e ++ cDV++ +
  gi|336255320|ref|YP_004598427.1| 152 RVEEGKAKIATEeAIVCDVARAA 174
                                       56777777775558*****9876 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EG CS
                      adh_short_C2   7 GraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiapk 82 
                                       Gra+Aka+  +Ga+v l++ +e+               v  +DV++ e+ +++ ++++e  +  D lv +a+i + 
  gi|336255320|ref|YP_004598427.1| 210 GRAVAKACYVRGADVTLVQNGED---------------VPYADVREVESAAEMLAATREACEDADALVSAAAIGDY 270
                                       55555555555555555554444...............56678888888888888888888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3072.21
//
Query:       gi|336255321|ref|YP_004598428.1|  [L=178]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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   65.7   0.1    5.3e-18   65.4   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    5.5e-12   45.7   0.0      2e-11   43.9   0.0    1.8  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    9.3e-11   42.0   0.0    1.4e-10   41.4   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    8.3e-07   28.9   0.0    1.2e-06   28.4   0.0    1.3  1  FR47             FR47-like protein
     0.0002   22.0   0.0    0.00026   21.7   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    0.00055   20.0   0.0     0.0011   19.0   0.0    1.5  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    0.00073   19.2   0.0     0.0014   18.4   0.0    1.4  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
     0.0027   17.9   0.1     0.0038   17.5   0.1    1.4  1  FGase            N-formylglutamate amidohydrolase
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.041   14.0   0.0    1.6  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
       0.02   15.0   0.0      0.029   14.5   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
       0.19   11.7   0.0       0.37   10.8   0.0    1.4  1  Acetyltransf_13  ESCO1/2 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 !   65.4   0.1   3.2e-21   5.3e-18      23     117 .]      49     164 ..      13     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 3.2e-21
                                       H.HHHHHHSTTCEEEEEEET................TEEEEEEEEEEEET....TSTTEEEEEEEEESGGGTTSSHH CS
                    Acetyltransf_1  23 e.feesfsleaegllvaeed................geliGfisllkipd....ekggvayieslaVspeyrgkGlG 78 
                                         ++e++++e+ +l+va ++                g+l+Gf++  ++       ++++ +i +++V++ yrg Gl+
  gi|336255321|ref|YP_004598428.1|  49 SfRRERLEDEDYRLWVAVDEidrdaaasddvglardGTLAGFVGTEIDAApsvfDRPDRLVIGDIFVREPYRGTGLA 125
                                       244444555566777755555677777777777777*******777777799998889******************* PP

                                       HHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  79 saLlealeerareegikkivlaveedndaairlYeklGF 117
                                       + L++ ++ rar+ g+ ++ l+v +dn++a ++Yek+GF
  gi|336255321|ref|YP_004598428.1| 126 RDLIDRAAARARDGGCAELALEVGADNERALAFYEKVGF 164
                                       ****************999*******************9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   1.2e-14     2e-11      35     109 ..      80     167 ..      39     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.2e-14
                   Acetyltransf_10  35 vaeeggkivGviel.rdgs..........hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yav 98 
                                       ++ ++g+++G++++  d             i+ +fV++ yrg+G+++ L++++ ++a++ g ++ +l+v a++  a 
  gi|336255321|ref|YP_004598428.1|  80 GLARDGTLAGFVGTeIDAApsvfdrpdrlVIGDIFVREPYRGTGLARDLIDRAAARARDGGCAElALEVGADNeRAL 156
                                       556677788888664444466777777889***************************9999999************* PP

                   Acetyltransf_10  99 pfYeklGFkav 109
                                       +fYek+GF++ 
  gi|336255321|ref|YP_004598428.1| 157 AFYEKVGFEPF 167
                                       ********987 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   8.6e-14   1.4e-10       2      76 .]      59     166 ..      58     166 .. 0.71

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 8.6e-14
                                       TEEEEEEEET................TEEEEEEEEEEES..........TCTEEEEE-GGGTTSSHHHHHHH.HTT. CS
                    Acetyltransf_7   2 kgevfVaedd................gkivGfialslld..........aeitrlaVdpeyrgkGiGraLle.aae. 50 
                                       +++++Va d+                g   Gf++ ++++            i+ ++V++ yrg G++r L++ aa+ 
  gi|336255321|ref|YP_004598428.1|  59 DYRLWVAVDEidrdaaasddvglardGTLAGFVGTEIDAapsvfdrpdrLVIGDIFVREPYRGTGLARDLIDrAAAr 135
                                       567888877777777776666666656666888877777999988887666666*****************964224 PP

                                       ...SEEEEE.EEEE..THHHHHHHHHHTTEEE CS
                    Acetyltransf_7  51 ...kgiile.qlel..naekaikfYeklGFee 76 
                                           g+  e  le+  ++e+a++fYek GFe+
  gi|336255321|ref|YP_004598428.1| 136 ardGGCA-ElALEVgaDNERALAFYEKVGFEP 166
                                       5644476.444555644459**********95 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   7.3e-10   1.2e-06      19      85 ..     105     172 ..      88     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.3e-10
                                       -TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEEEEEEE CS
                              FR47  19 kdggelgalqvlpehrrrGlgsrlvkalakeiaerg.ktvllvvvasNtpsirlyeklGfekieetew 85 
                                       +d   +g + v++  r+ Gl++ l+   a++ +  g  ++ l v+a+N+++ ++yek+Gfe  +++++
  gi|336255321|ref|YP_004598428.1| 105 PDRLVIGDIFVREPYRGTGLARDLIDRAAARARDGGcAELALEVGADNERALAFYEKVGFEPFRHRMR 172
                                       44478999**************************7725566779*****************9988877 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.6e-07   0.00026      44     138 .]      41     165 ..       1     165 [. 0.59

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.6e-07
                    Acetyltransf_3  44 a.........waeeseeegyg.waiv..............l.kdtgv.iGsvglr.....dleeedee......ael 83 
                                       +          +e+ e+e+y  w+ v              l +d+    G+vg       +             + +
  gi|336255321|ref|YP_004598428.1|  41 VdlvaeevsfRRERLEDEDYRlWVAVdeidrdaaasddvgLaRDG-TlAGFVGTEidaapS------VfdrpdrLVI 110
                                       222223344323333445555455543444433333332212444.338888777444332......2344566999 PP

                    Acetyltransf_3  84 gymlaps.fwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       g ++ ++ ++g G+a++    +   a ++ g  +l  ++ ++Ne+  + +ek+Gfe
  gi|336255321|ref|YP_004598428.1| 111 GDIFVREpYRGTGLARDLIDRAAARA-RDGGCAELALEVGADNERALAFYEKVGFE 165
                                       96655544******************.8999************************7 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 !   19.0   0.0   6.9e-07    0.0011      17      57 ..     102     140 ..      84     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.9e-07
                   Acetyltransf_CG  17 YevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeg 57 
                                       ++  + ++l++  ++V e +rG G+A+ L+++a   ar+ g
  gi|336255321|ref|YP_004598428.1| 102 FD--RPDRLVIGDIFVREPYRGTGLARDLIDRAAARARDGG 140
                                       54..4459999**************************9865 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.3e-07    0.0014      85     141 ..     109     168 ..      93     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.3e-07
                                       EESSHHHCTTTCHHHHHHHHHHHHHC...CTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                    Acetyltransf_8  85 ligeaeargkglttallralvhylfa...dprtrrvvvEPdvrNerairllekaGfekek 141
                                       +ig+   r++ ++t l r l++++ a   d +++   +E  ++Nera++++ek+Gfe+ +
  gi|336255321|ref|YP_004598428.1| 109 VIGDIFVREPYRGTGLARDLIDRAAArarDGGCAELALEVGADNERALAFYEKVGFEPFR 168
                                       5665555666666666666666666333366*************************9866 PP

>> FGase  N-formylglutamate amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.3e-06    0.0038      94     145 ..       7      58 ..       1     152 [. 0.60

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.3e-06
                                       T--HHHHHHHHHHTHHHHHHHHHHHHHHHH.HT---EEEEEEEE-....... CS
                             FGase  94 pldaaeveerieryyrpYhaalaellarlrarhgvavlidlHSmpseapale 145
                                       p d+a+v++ +e+++ pYh++l++++++   +  v ++ +  S+++e+ + e
  gi|336255321|ref|YP_004598428.1|   7 PADEAAVRRYVEELWLPYHRELEATVETHDLAEDVDLVAEEVSFRRERLEDE 58 
                                       6789999*******************99776677777777777775544444 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.1   3.4e+03      37      49 ..      53      65 ..      35      92 .. 0.57
   2 ?   14.0   0.0   2.5e-05     0.041      76     127 ..     110     166 ..     106     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.1
                                      HHHTTSEEEEEEE CS
                    Acetyltransf_9 37 klleesrvlgaed 49
                                      ++le++++ ++  
  gi|336255321|ref|YP_004598428.1| 53 ERLEDEDYRLWVA 65
                                      4444443333332 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.5e-05
                                       EEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT.--EEEE--....SSHHHHHTTT-EE CS
                    Acetyltransf_9  76 vtgVavapehrgrgvlskLlaraleemreeg.qplsllfP....ssipiYrrfGyei 127
                                       ++++ v   +rg g++++L++ra +++r+ g ++l+l ++    ++ ++Y++ G+e+
  gi|336255321|ref|YP_004598428.1| 110 IGDIFVREPYRGTGLARDLIDRAAARARDGGcAELALEVGadneRALAFYEKVGFEP 166
                                       89999************************964788888888877667********97 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.8e-05     0.029      77     136 ..     108     166 ..      90     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                    Acetyltransf_4  77 kaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFel 136
                                        ++  +++ ++  + +gl+r+lid    +++  +  +l  e+ ++ne + +f++++GFe 
  gi|336255321|ref|YP_004598428.1| 108 LVIGDIFV-REPYRGTGLARDLIDRAAARARDGGCAELALEVGADNERALAFYEKVGFEP 166
                                       56667788.478999*******************************************86 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00023      0.37       7      32 ..     110     135 ..     106     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                   Acetyltransf_13   7 isriWvssshRrkgiAtkLldaaren 32 
                                       i  i+v + +R +g+A+ L+d a+++
  gi|336255321|ref|YP_004598428.1| 110 IGDIFVREPYRGTGLARDLIDRAAAR 135
                                       678******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); 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: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1400.61
//
Query:       gi|336255322|ref|YP_004598429.1|  [L=223]
Description: DNA methylase N-4/N-6 domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   66.7   0.0    3.8e-09   36.6   0.0    2.1  2  N6_N4_Mtase  DNA methylase
     0.0045   16.8   0.0     0.0092   15.7   0.0    1.4  1  Met_10       Met-10+ like-protein


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 !   36.6   0.0   4.2e-13   3.8e-09     173     227 ..      21      75 ..       4      79 .. 0.87
   2 !   28.4   0.0   1.4e-10   1.2e-06       2     112 ..     104     222 ..     103     223 .] 0.73

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.2e-13
                                       SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHH CS
                       N6_N4_Mtase 173 paqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyve 227
                                       +   P al+e+ ++  t++gd v+D FaG GtT+++a++l+r   G e+e+ +v 
  gi|336255322|ref|YP_004598429.1|  21 EVRTPDALVEHFLQEHTEPGDRVIDVFAGFGTTLTVAERLERIPFGLEYEPDRVA 75 
                                       56789********************************************998876 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.4e-10
                                       EEEEE--SSSSSCS......GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT....HHHHHHHHHT CS
                       N6_N4_Mtase   2 dlivtdpPYntgkdy.endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk....elkaladeif 73 
                                       d+++t+pP+  + d+ + + +y++e++y++yl+ +e  ++ +  v +++g++++ i  ++ +      ++ +ad ++
  gi|336255322|ref|YP_004598429.1| 104 DCCFTSPPFMEWTDDrNPFRNYAGESTYADYLDDIETTFARLESVIAPGGTVVVDIANMKHEGrvtpLAWDVADRVA 180
                                       789**********9977899**************************************9999877763344444444 PP

                                       T.-.EEEEEEEEEEESSSTTTSTCC..S-B--EEEEEEEESST CS
                       N6_N4_Mtase  74 g.g.ffllnvivwkkpnsmpesnkd..rltsthEyilvfsknk 112
                                       +   f    vi w+ + + p +++   ++ ++h y lvf+k++
  gi|336255322|ref|YP_004598429.1| 181 NvFyFDGEVVIPWTGD-GSPDDRAGtfGYGYDHSYCLVFTKPD 222
                                       4210222334445555.44444433557777888888888875 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     1e-06    0.0092      95     145 ..      34      82 ..      29      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-06
                                       HTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHH CS
                            Met_10  95 aklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkenik 145
                                        +  e+g++V+dvfAG G    ++ +   +++ ++ + +P+ v y+++ i+
  gi|336255322|ref|YP_004598429.1|  34 QEHTEPGDRVIDVFAGFGTTLTVAER--LERIPFGLEYEPDRVAYIRDRIE 82 
                                       56789*************96666666..677889************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1835.72
//
Query:       gi|336255323|ref|YP_004598430.1|  [L=245]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Halopiger xanaduensis SH-6]
Scores for complete 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-12   47.6   3.6    5.9e-06   25.7   0.1    2.1  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      2e-05   23.9   9.6    0.00031   20.0   4.2    2.2  2  FAD_binding_2  FAD binding domain
    0.00016   21.2   5.2    0.00016   21.1   3.8    1.7  2  FAD_oxidored   FAD dependent oxidoreductase
    0.00019   21.2  10.4      0.087   12.4   4.4    2.6  2  DAO            FAD dependent oxidoreductase
    0.00031   19.9   0.4    0.00046   19.4   0.4    1.2  1  GIDA           Glucose inhibited division protein A
      0.002   17.4   0.8     0.0034   16.7   0.8    1.4  1  FAD_binding_3  FAD binding domain
     0.0042   17.3   1.3     0.0065   16.7   0.3    1.8  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0067   15.2   0.1      0.044   12.5   0.6    1.8  2  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
      0.012   14.7   0.8      0.088   11.8   0.3    2.0  2  Lycopene_cycl  Lycopene cyclase protein
      0.023   13.9   0.2       0.15   11.2   0.3    2.0  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      0.051   12.9   0.1      0.083   12.2   0.1    1.2  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal 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 !   22.6   0.9   3.3e-08   5.4e-05       2      34 ..       3      34 ..       2      51 .. 0.83
   2 !   25.7   0.1   3.6e-09   5.9e-06     188     294 .]      61     168 ..      54     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.3e-08
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegt 34
                                      dv+++GgG+AG+aa+++ a+ag+++++v+ +g+
  gi|336255323|ref|YP_004598430.1|  3 DVCIVGGGVAGTAASIFTARAGLDTLVVD-GGE 34
                                      8***************************5.443 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 3.6e-09
                                       HHHHHHHHTTEEEEESCEEEEEEETTE.EEE...EEETTSCE.EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx...xxxxxxxx.xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                       Pyr_redox_2 188 aleealekeGvevklgtsvkeidgnge.kle...vvledgee.idadlvvvavGvrpstelle.eklglelderggi 258
                                        ++e+ ++ G e+ lg +  ++++ +e +l+   v +++g+e ++++ v+ a +   +  l++ +    +  ++ ++
  gi|336255323|ref|YP_004598430.1|  61 LVREQARNAGAEFELGRVT-RAEPVDEgDLDrgfVLETEGDEpLETRRVIAASWSDSEY-LVPlDVGRTQRGSKHFV 135
                                       6788999999999987655.88888888777788888888889**********998886.55677777888899999 PP

                                       E--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 259 vvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                        vde +rt v+g+ya+G  a   + p +a +A  +G
  gi|336255323|ref|YP_004598430.1| 136 SVDEGGRTAVDGVYAAGRLA---NEPHQAIVAAGHG 168
                                       ********************...*********9987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   4.2   1.9e-07   0.00031       1      33 [.       3      35 ..       3      43 .. 0.94
   2 !    7.2   0.2    0.0014       2.3     363     403 ..     122     156 ..      56     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.9e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      Dv ++G+G+AG aA++  a+aGl+++vv+ +++
  gi|336255323|ref|YP_004598430.1|  3 DVCIVGGGVAGTAASIFTARAGLDTLVVDGGES 35
                                      99***************************9886 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0014
                                       ..EEEEEEEES-EEEBETTSBESTTEEESSBTEEE-STCEE CS
                     FAD_binding_2 363 vkvvpaqhytmgGvetdengrvldadgqpipGLYAaGevaa 403
                                        +v  +q+++   v +de gr+      +++G YAaG  a+
  gi|336255323|ref|YP_004598430.1| 122 LDVGRTQRGSKHFVSVDEGGRT------AVDGVYAAGRLAN 156
                                       5666777777777999999999......*********9983 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   3.8     1e-07   0.00016       1      30 [.       3      32 ..       3      36 .. 0.94
   2 ?   -1.9   0.0      0.95   1.6e+03     151     169 ..      68      83 ..      66     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1e-07
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      Dv++vGGg+aG+aA i  araG  +l+v+ 
  gi|336255323|ref|YP_004598430.1|  3 DVCIVGGGVAGTAASIFTARAGLDTLVVDG 32
                                      9**************************985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.95
                      FAD_oxidored 151 laGvpyrvGresreetgep 169
                                        aG+++++Gr  r+e   p
  gi|336255323|ref|YP_004598430.1|  68 NAGAEFELGRVTRAE---P 83 
                                       699999999999984...3 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   4.4   5.3e-05     0.087       1      36 [.       3      41 ..       3      47 .. 0.86
   2 !   12.3   0.5   5.6e-05     0.091     138     213 ..      50     122 ..      33     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.3e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS.SSTTSSG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg.diagsga 36
                                      dv+i+GGG++G ++  + ar+g  +++++ g +i+++ a
  gi|336255323|ref|YP_004598430.1|  3 DVCIVGGGVAGTAASIFTARAGldTLVVDGGeSILARNA 41
                                      9***************************99845555555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.6e-05
                                       TTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEE....TCEEEEEEECTEEE.EEEEEEEE--GGGHH..HH CS
                               DAO 138 pdtgqvdpakltaalaraaealGveilegtevtgleeed....gkvwgverttpgen.daadavVnaaGawsd..ll 207
                                       pd g+ d+++++  ++++a+++G+e+ +g +vt+ e  d    +++  +  +t+g +  + + v+ a   wsd   l
  gi|336255323|ref|YP_004598430.1|  50 PD-GV-DARRYLELVREQARNAGAEFELG-RVTRAEPVDegdlDRGFVL--ETEGDEpLETRRVIAAS--WSDseYL 119
                                       56.55.9**********************.9999877555445454444..55565543536677666..8886533 PP

                                       HTTCTT CS
                               DAO 208 gllkel 213
                                           +l
  gi|336255323|ref|YP_004598430.1| 120 ---VPL 122
                                       ...333 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.4   2.8e-07   0.00046       1      28 [.       3      30 ..       3      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.8e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      dv ++GgG AG++A++ +ar+G+++l +
  gi|336255323|ref|YP_004598430.1|  3 DVCIVGGGVAGTAASIFTARAGLDTLVV 30
                                      79***********************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 !   16.7   0.8   2.1e-06    0.0034       3      31 ..       3      31 ..       1      41 [. 0.94

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.1e-06
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlve 31
                                      dV+IVG+G aG  ++ + ++aG ++++v+
  gi|336255323|ref|YP_004598430.1|  3 DVCIVGGGVAGTAASIFTARAGLDTLVVD 31
                                      8***************************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 !   16.7   0.3     4e-06    0.0065       1      38 [.       6      43 ..       6      59 .. 0.83
   2 ?   -2.2   0.0         3   4.9e+03      41      54 ..     165     178 ..     147     186 .. 0.48

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                      IvG+G++G +a  + a+ag+d l+++ ++++  r as 
  gi|336255323|ref|YP_004598430.1|  6 IVGGGVAGTAASIFTARAGLDTLVVDGGESILARNASL 43
                                      9*************************998875555555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3
                                       TTCEECTS---EEE CS
                     NAD_binding_8  41 pgvrvdygahifhg 54 
                                        g+ +++g  ++h+
  gi|336255323|ref|YP_004598430.1| 165 AGHGAKVGLAVIHD 178
                                       33444555555555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.6   2.7e-05     0.044       2      36 ..       3      37 ..       2      40 .. 0.93
   2 ?   -0.4   0.0      0.22   3.6e+02     102     162 ..      49     112 ..      48     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.7e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      dv ++GgG AG  a+i  a++g ++l+++ +++++
  gi|336255323|ref|YP_004598430.1|  3 DVCIVGGGVAGTAASIFTARAGLDTLVVDGGESIL 37
                                      89***************************999876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.22
                                       EETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEE...ECETTE.EEEEE.TTEEEEESEEEE-- CS
                       HI0933_like 102 Fpvsdkaedivdallkelkeagvklrletevksv...ekeedgkfrvktkseeeleadklvlAt 162
                                       Fp+  +a++ +++  +++++ag +++l +  ++    e + d+ f ++t+++e le+++++ A+
  gi|336255323|ref|YP_004598430.1|  49 FPDGVDARRYLELVREQARNAGAEFELGRVTRAEpvdEGDLDRGFVLETEGDEPLETRRVIAAS 112
                                       8999999999999999999999999987544333334445577899999999999999999884 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   5.4e-05     0.088       1      39 [.       3      39 ..       3      46 .. 0.87
   2 ?    1.2   0.0     0.091   1.5e+02      91     140 ..      60     113 ..      52     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.4e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfp 39
                                      Dv ++G+G Ag   Aa +  a++gl  +++++++s+l  
  gi|336255323|ref|YP_004598430.1|  3 DVCIVGGGVAGT--AASIFTARAGLDTLVVDGGESILAR 39
                                      9**********7..566667***************9755 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.091
                     Lycopene_cycl  91 eellerlvengvklleakvesveeeeage....slvvleggrkirarlvvdarg 140
                                       e + e+  ++g+++  ++v+++e++++g+     +  +eg++ ++ r v+ a+ 
  gi|336255323|ref|YP_004598430.1|  60 ELVREQARNAGAEFELGRVTRAEPVDEGDldrgFVLETEGDEPLETRRVIAASW 113
                                       455566668899999999999988887542211356789999********9985 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   0.3   9.5e-05      0.15       2      32 ..       6      35 ..       5      49 .. 0.79
   2 ?   -0.2   0.0       0.3   4.9e+02     105     131 ..      82     111 ..      50     114 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.5e-05
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgni 32
                                      I+G+G aG aa i   +agl d l+++ g+ 
  gi|336255323|ref|YP_004598430.1|  6 IVGGGVAGTAASIFTARAGL-DTLVVDGGES 35
                                      9*******************.789***9943 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.3
                       Pyr_redox_3 105 esvkk..edegfevetske.tyeAkkviiA 131
                                       e v++   d+gf++et+ +  +e+++vi A
  gi|336255323|ref|YP_004598430.1|  82 EPVDEgdLDRGFVLETEGDePLETRRVIAA 111
                                       44555324789*****99659******988 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 ?   12.2   0.1   5.1e-05     0.083      31      64 ..       4      37 ..       2      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.1e-05
                                      EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                       AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrparl 64
                                      v ++GgGvaG++A    ++ g ++ v+D  ++ l
  gi|336255323|ref|YP_004598430.1|  4 VCIVGGGVAGTAASIFTARAGLDTLVVDGGESIL 37
                                      89***********999999999999999766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 1963.63
//
Query:       gi|336255324|ref|YP_004598431.1|  [L=412]
Description: peptidase M48 Ste24p [Halopiger xanaduensis SH-6]
Scores for complete 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   70.4   0.0    2.7e-19   69.7   0.0    1.3  1  Peptidase_M48  Peptidase family M48
  ------ inclusion threshold ------
       0.12   11.9   0.0       0.19   11.3   0.0    1.2  1  DUF2268        Predicted Zn-dependent protease (DUF2268)
       0.19   11.6   0.0       0.32   10.9   0.0    1.3  1  Peptidase_M43  Pregnancy-associated plasma protein-A
        3.8    8.0   5.6        9.8    6.6   5.6    1.8  1  DUF805         Protein of unknown function (DUF805)


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 !   69.7   0.0     6e-23   2.7e-19       9     194 ..     195     381 ..     190     383 .. 0.79

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 6e-23
                                       HHHHHHHHHTT-..-EEEEEEE-GGGT...-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   9 evveelakeaglpkpltkvyvvnspkr...NAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrhsv 81 
                                       e ve+l +e++   ++ ++y +++++    NA + g      +++ltd Ll + ++++el+a+l+HE GHi+ rh  
  gi|336255324|ref|YP_004598431.1| 195 ERVERLCAELEY--RPRGLYLLEGESTktaNALVAGTIPGFrYVFLTDYLL-SECDDDELQAILAHEFGHIAGRHLW 268
                                       678999999999..9999999998877788998877664445*********.************************8 PP

                                       HH..HHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT....HHHHHHHHHHHHHHHHTTT.HH CS
                                       xx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  82 vs..livsllasillllglallisraeedaagafldalavliglliillfl....alSRkrEyqADeagvellkrak 152
                                        +  l v++    + +  ++ +++ ++++   +f    + l++l      +    +l +++E++AD+++++ +   +
  gi|336255324|ref|YP_004598431.1| 269 QRglLTVAVFGAWIAGADAIGVGALKDRFGFLGFFLPFMGLYALYH----VgllgGLAYRQEFRADAYAARRVG-VE 340
                                       8854444444444444444444444444444444444444444333....35567*******************.9* PP

                                       HHHHHHHHHHHHTT--S---HHHHHHS-SS--HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 153 dlvraliklakdlerqdvsaslrsellstHPplleRiqalke 194
                                       ++v+al  la+ ++ + +s  l+ +l   HPp+++Ri ++++
  gi|336255324|ref|YP_004598431.1| 341 AAVDALEVLASANDMTRESGLLY-ALATHHPPIADRIDSVRD 381
                                       *******************9999.99999********99876 PP

>> DUF2268  Predicted Zn-dependent protease (DUF2268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.2e-05      0.19      49      76 ..     234     262 ..     197     270 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.2e-05
                           DUF2268  49 dkiflfl.leneyskerlaallaHEyhHv 76 
                                        ++fl+  l +e ++++l+a+laHE+ H 
  gi|336255324|ref|YP_004598431.1| 234 RYVFLTDyLLSECDDDELQAILAHEFGHI 262
                                       35666644999****************97 PP

>> Peptidase_M43  Pregnancy-associated plasma protein-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   7.2e-05      0.32      51      84 ..     234     266 ..     224     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.2e-05
                     Peptidase_M43  51 rvvfnGaylaadststnksstLthelGhfLgLih 84 
                                       r vf   yl+++  +++ ++ L+he+Gh  g +h
  gi|336255324|ref|YP_004598431.1| 234 RYVFLTDYLLSECDDDELQAILAHEFGHIAG-RH 266
                                       5678899*********************865.45 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   5.6    0.0022       9.8      36     102 ..      64     174 ..       2     177 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0022
                            DUF805  36 a..................aavasalsvvlallllvps......lavtvRRlHDtgrsgw.........llllllvp 79 
                                                          +   +a+ +v + l+ vp          t+R l+Dt  s w         l   ++v 
  gi|336255324|ref|YP_004598431.1|  64 LvdrttavlpsgprlfgigVLEFAAIMFVSFGLVAVPLvsmalgTYPTIRSLRDTEASSWkvvkgvlavL---AIVS 137
                                       1333455677777777655222222233333333333344444566688***********5555542220...2221 PP

                            DUF805  80 li..........alllll........vllllpgtpgenryG 102
                                        +          a   ++        vll+  gt  +  yG
  gi|336255324|ref|YP_004598431.1| 138 -VtvaisiggllA---VIstvgsslpVLLAAFGTIVAASYG 174
                                       .011122221111...1122233333666777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3033.98
//
Query:       gi|336255325|ref|YP_004598432.1|  [L=201]
Description: hypothetical protein Halxa_3948 [Halopiger xanaduensis SH-6]
Scores for complete 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   37.9   0.6    2.6e-09   37.5   0.6    1.2  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    1.9e-05   24.8   0.1    3.7e-05   23.9   0.1    1.5  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.6   2.9e-13   2.6e-09      10     137 ..      31     179 ..      24     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2.9e-13
                                       ES.S-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEE..CCCSSEEEEEEEEEETTTTEEEEEEE.SS CS
                   Polyketide_cyc2  10 ia.appekVwalvsdfenwprWhpevarveleggggpargvegtvr..vggrgtvreelvevdpegrllsyrivkpv 83 
                                       +a ++pe+V+++v++f+++pr+ + +++v++ g gg +++   +++  + +  t+r +++++++ + +l++r+    
  gi|336255325|ref|YP_004598432.1|  31 VAyRSPEEVFPYVRSFTDYPRYTEHLKEVTVHGDGGVGSVYDLRLAwwKLS-YTARSKVTAISA-PNSLEWRLI--- 102
                                       5559***********************999887444422332222210333.569*******98.9*******4... PP

                                       S-TSEEEEEEEEECCET............EEEEEEEEEEE.......E--TT--HHHHHHHHHHHH....HHHHHHH CS
                   Polyketide_cyc2  84 pvanyvatwtvtpdggg............trvtwtgefda.......gplggpfekpaaakavkgd....leagLer 137
                                          + +++w+v+++++             +r+ +++ +d+        +l+++++ +++ + v+ +     ea +er
  gi|336255325|ref|YP_004598432.1| 103 NDIDARGEWRVEAEPEAlpadadtdaetaSRIYFEAVYDPysanenaISLPRFVSLDWVIEKVEPRllgeAEAVVER 179
                                       356789*******8873333444344444667777777755666655566677776666666666533334555555 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   4.2e-09   3.7e-05       4     108 ..      35     145 ..      33     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.2e-09
                                       -HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...E.EEECSTTSSCEEEEEEEEEEETTTEEECTTCCCCCEE.. CS
                    Polyketide_cyc   4 padqvyalvadvesypeflphcssvevleeaesglsa.dlevgfggltesftarvtldppeeitfklvegdfksl.. 77 
                                       ++++v+ +v+ + +yp+++ h+++v+v+ + +   s+ dl+++++ l+ +  ++vt         +l+ ++++++  
  gi|336255325|ref|YP_004598432.1|  35 SPEEVFPYVRSFTDYPRYTEHLKEVTVHGDGG-VGSVyDLRLAWWKLSYTARSKVTAISAPN---SLEWRLINDIda 107
                                       79******************************.444479*****************999999...666666665433 PP

                                       EEEEEECTECC.......EEECEEEEEEEEEEEE-SSC CS
                    Polyketide_cyc  78 egkWtieslpp.......nsggtrtkvalevdfkfasp 108
                                       +g+W++e  p+       ++ +t+ ++ +e  +++ s+
  gi|336255325|ref|YP_004598432.1| 108 RGEWRVEAEPEalpadadTDAETASRIYFEAVYDPYSA 145
                                       79999999998777666555577777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1683.00
//
Query:       gi|336255326|ref|YP_004598433.1|  [L=445]
Description: TrkA-N domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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  169.4  10.1    3.3e-26   91.8   2.3    2.8  3  TrkA_N           TrkA-N domain
    1.3e-26   92.2  12.8    1.6e-14   53.4   0.2    3.6  3  TrkA_C           TrkA-C domain
    1.2e-11   44.8   0.6    9.5e-06   25.7   0.4    2.5  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    1.2e-10   41.7   3.7    4.1e-05   24.0   1.3    2.8  2  NAD_binding_7    Putative NAD(P)-binding
    5.4e-10   39.4   6.0    0.00014   21.9   1.0    2.7  3  NAD_binding_10   NAD(P)H-binding
    8.3e-08   32.6   2.7    0.00018   21.8   0.9    2.8  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    5.6e-06   26.3   0.1     0.0042   17.0   0.2    2.4  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    7.5e-06   25.4   0.4     0.0025   17.1   0.2    3.0  3  FAD_binding_3    FAD binding domain
    1.1e-05   25.9   1.6       0.02   15.5   0.2    3.1  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    1.2e-05   25.2   0.0     0.0022   18.0   0.0    2.8  2  Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion
     0.0002   20.9   0.4      0.093   12.2   0.0    2.5  2  adh_short        short chain dehydrogenase
    0.00023   20.8   5.3     0.0019   17.8   1.7    2.7  2  DAO              FAD dependent oxidoreductase
    0.00028   20.8   1.3     0.0037   17.2   0.0    3.1  2  ADH_zinc_N       Zinc-binding dehydrogenase
    0.00059   19.2   5.6     0.0065   15.7   5.6    2.4  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.001   18.7   0.2     0.0094   15.5   0.3    2.5  3  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0014   18.9   0.1       0.16   12.1   0.1    2.5  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0033   17.1   0.2      0.012   15.3   0.1    2.0  2  ApbA             Ketopantoate reductase PanE/ApbA
      0.006   16.6   0.0       0.34   10.9   0.0    2.5  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
  ------ inclusion threshold ------
      0.051   12.9   1.6       0.28   10.5   0.3    2.5  3  ThiF             ThiF family
      0.051   12.9   0.1        5.1    6.4   0.1    2.5  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.086   13.7   1.7         13    6.6   0.2    3.4  3  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
       0.11   12.6   1.7        1.7    8.9   0.1    2.9  2  HAS-barrel       HAS barrel domain
       0.22   12.0   2.6        2.4    8.7   0.1    3.1  3  YflT             Heat induced stress protein YflT
       0.36   10.9   2.4        2.4    8.2   1.7    2.7  3  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
        0.4   11.3   7.8        5.1    7.7   0.6    3.6  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas


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 !   91.8   2.3   4.5e-29   3.3e-26       1     113 [.       3     118 ..       3     121 .. 0.87
   2 !   82.4   0.1   3.9e-26   2.8e-23       1     116 []     230     346 ..     230     346 .. 0.93
   3 ?   -2.6   0.1         9   6.4e+03      32      61 ..     364     393 ..     359     395 .. 0.70

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 4.5e-29
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddean 76 
                                       +i++G+G+vG+s+ae L +++  vvvid+de+rve+++    + ++ gd+t+ evLeeagie+ad+via t+ de+n
  gi|336255326|ref|YP_004598433.1|   3 VIVVGAGEVGSSIAESLATEH-GVVVIDRDEDRVESVTYAHdVLAIEGDGTSIEVLEEAGIERADLVIASTDGDETN 78 
                                       79*****************99.5**************86555*********************************** PP

                                       HHHHHHHHHHTSSSEEEEEESSGGGHHHHHH....HTTSEE CS
                            TrkA_N  77 ilavllakelnpkkkiiaraqdpehaellkk....lgadvv 113
                                       i+++ +ak   +   +iar+++    +  ++     g+d +
  gi|336255326|ref|YP_004598433.1|  79 IVVCGAAKAVTE-SFTIARVKRTNLLRTWERsqsaFGVDFM 118
                                       ********8666.79*****999886666653333555555 PP

  == domain 2  score: 82.4 bits;  conditional E-value: 3.9e-26
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSE..EEES-TTSHHHHHHTTGGGESEEEE-SSSHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreegle..vvvgdatdeevLeeagiekadaviaatgddea 75 
                                       i++iG +++G++ a+ ++ +g +  + ++d+er++el+e+  +  v+  datd e+L + +i +ad+v+aa+++de+
  gi|336255326|ref|YP_004598433.1| 230 IVVIGGSEIGYQTARLFEVEGFEPRLLERDPERARELAEQLPDtvVLESDATDVEFLGREHIGEADIVVAALENDEK 306
                                       89***************99764589****************5544888***************************** PP

                                       HHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  76 nilavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                       n+l++lla++  +++++ia +++pe+++l++++g+dv+i+p
  gi|336255326|ref|YP_004598433.1| 307 NLLVSLLARH-AGAQRTIAVVEEPEYVDLFETVGIDVAINP 346
                                       *********6.66689***********************98 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 9
                                       HHHHHHHHTTSEEEES-TTSHHHHHHTTGG CS
                            TrkA_N  32 erveelreeglevvvgdatdeevLeeagie 61 
                                       e+v+ l+ + +ev+  +  d+++L e  i+
  gi|336255326|ref|YP_004598433.1| 364 ENVAMLESDRAEVLEIEIDDDSLLLENRIS 393
                                       566677777778888888888888777665 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2       1.3   9.1e+02       3      30 ..       3      28 ..       1      38 [. 0.72
   2 !   53.4   0.2   2.3e-17   1.6e-14       1      66 [.     151     215 ..     151     217 .. 0.95
   3 !   43.5   2.9   2.9e-14   2.1e-11       2      67 ..     377     443 ..     376     445 .] 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                                      EEEEE--GGGTTSBHHHHTHHHHS-EEE CS
                            TrkA_C  3 evtvpagsplvGktlkelnlrargvlvv 30
                                       ++v+ag   vG +++e+   ++gv v+
  gi|336255326|ref|YP_004598433.1|  3 VIVVGAGE--VGSSIAESLATEHGVVVI 28
                                      56666666..999999955555588886 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 2.3e-17
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelr 66 
                                       ++e++v+++sp+++ t++e    +  + + +ai Rg+e+iip gdtv+++ D ++v+gs+++++e++
  gi|336255326|ref|YP_004598433.1| 151 MAEFEVTSDSPVANETVSE--ADRFeSLTFAAIIRGDEVIIPQGDTVIRPEDGVVVIGSSESVREFA 215
                                       68*****************..76667*************************************9985 PP

  == domain 3  score: 43.5 bits;  conditional E-value: 2.9e-14
                                       EEEEEE--GGGTTSBHHH.HT.HHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlke.ln.lrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                        e++++ +s l   ++++ ++ l++ gv + ai R+g+li p+gdtvLe GD+++v+++   l+e+++
  gi|336255326|ref|YP_004598433.1| 377 LEIEIDDDSLLLENRISDvVReLPD-GVVIGAITRDGRLITPRGDTVLERGDHVVVFADTRVLDEVAA 443
                                       6999**************4447787.*************************************99986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.4   1.3e-08   9.5e-06      14      94 ..       2      84 ..       1      96 [. 0.77
   2 !   16.7   0.0   7.9e-06    0.0056      12      88 ..     227     306 ..     218     334 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.3e-08
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH..T.ET-EEEEGCGHHHH.HHT-SEEEE-SSS.SS- CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel..kgeeiealkleelkel.laeadvvisatas.eep 88
                                      +v+++GaGe+++ +a+ L++++   vvv+ R+ +r++++   +   + e   +++e l+e+ +++ad+vi++t   e++
  gi|336255326|ref|YP_004598433.1|  2 RVIVVGAGEVGSSIAESLATEH--GVVVIDRDEDRVESVTYAHdvLAIEGDGTSIEVLEEAgIERADLVIASTDGdETN 78
                                      79*****************765..589**********9976661144455577888887755***********761455 PP

                                      SB-HHH CS
                      Shikimate_DH 89 ilekee 94
                                      i+  ++
  gi|336255326|ref|YP_004598433.1| 79 IVVCGA 84
                                      665555 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 7.9e-06
                                       T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGH....HHHHHT-SEEEE-SS CS
                      Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleel....kellaeadvvisata 84 
                                        +++++iG  e++ ++a+ +  +g++    + R+ era+elae+l ++ +   + +++    +e++ ead+v++a  
  gi|336255326|ref|YP_004598433.1| 227 ANEIVVIGGSEIGYQTARLFEVEGFE-PRLLERDPERARELAEQLPDTVVLESDATDVeflgREHIGEADIVVAALE 302
                                       4689****************999999.889***************88755555555552224589*********987 PP

                                       SSS- CS
                      Shikimate_DH  85 seep 88 
                                         e 
  gi|336255326|ref|YP_004598433.1| 303 NDEK 306
                                       7654 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 !   24.0   1.3   5.8e-08   4.1e-05       9      84 ..       2      87 ..       1     101 [. 0.76
   2 !   16.9   0.0   9.3e-06    0.0067       8      98 ..     228     332 ..     225     336 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.8e-08
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeel..ekd...........legadlviaatddrel 74
                                      +v+vvG+Gev+ + +++l+ +   v+v++ + ++ + e v++a + l  e+d           +e+adlvia td +e 
  gi|336255326|ref|YP_004598433.1|  2 RVIVVGAGEVGSSIAESLATE-HGVVVIDRD-EDRV-ESVTYAHDVLaiEGDgtsievleeagIERADLVIASTDGDET 77
                                      79*************999999.99*******.2333.44554444332344444555555556**************** PP

                     NAD_binding_7 75 neriaeaaka 84
                                      n  ++ aaka
  gi|336255326|ref|YP_004598433.1| 78 NIVVCGAAKA 87
                                      **99999986 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 9.3e-06
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapevkeele......elvklaeeel......ekdlegadlviaatddr 72 
                                        +++v+Gg e++++ +r +  +g +  ++  + +++ e      ++v l+++        ++++ +ad+v+aa +++
  gi|336255326|ref|YP_004598433.1| 228 NEIVVIGGSEIGYQTARLFEVEGFEPRLLERDPERARElaeqlpDTVVLESDATdveflgREHIGEADIVVAALEND 304
                                       5799************************99886222223333334444443332223367788************** PP

                     NAD_binding_7  73 elneriaeaaka..rrilvnvadkpelc 98 
                                       e n  +  +a+   ++  + v+ +pe  
  gi|336255326|ref|YP_004598433.1| 305 EKNLLVSLLARHagAQRTIAVVEEPEYV 332
                                       ***9999999773445577777777765 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 !   21.9   1.0   1.9e-07   0.00014       3      94 ..       8     101 ..       7     127 .. 0.87
   2 !   19.7   0.0   8.7e-07   0.00062      13      86 ..     244     327 ..     235     341 .. 0.79
   3 ?   -3.2   0.0       9.4   6.7e+03      21      51 ..     353     384 ..     343     389 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.9e-07
                                       TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHH.HTT-SEEEES---TCCHHHH. CS
                    NAD_binding_10   3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaea.lkgadaVvsalggggkdeeg. 77 
                                        G vG+ +++ l+ +  h v+++ R++++++++  +  + ++egd t+ e l+ea ++ ad V++++ g++++  + 
  gi|336255326|ref|YP_004598433.1|   8 AGEVGSSIAESLATE--HGVVVIDRDEDRVESVTYAHDVLAIEGDGTSIEVLEEAgIERADLVIASTDGDETNIVVc 82 
                                       79**********998..789**************999****************9978**********8887732225 PP

                                       ..HHHHHHHHHHCT--EEE CS
                    NAD_binding_10  78 ..aknivdaakeagvkRfv 94 
                                         ak++ +    a vkR  
  gi|336255326|ref|YP_004598433.1|  83 gaAKAVTESFTIARVKRTN 101
                                       6699999999999999965 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 8.7e-07
                                       HHHHC-T-EEEEEETTHHHCHHHHCT.TTCEEEE--TT-CCHH.HHHHTT-SEEEES---TCC........HHHHHH CS
                    NAD_binding_10  13 ellargghevtalvRnpeklaeleae.eglevvegdvtdvedl.aealkgadaVvsalggggk........deegak 79 
                                       +l + +g+e ++l R+pe++ el+++ + + v+e d+tdve l +e++  ad+Vv+al +++k        ++ ga+
  gi|336255326|ref|YP_004598433.1| 244 RLFEVEGFEPRLLERDPERARELAEQlPDTVVLESDATDVEFLgREHIGEADIVVAALENDEKnllvsllaRHAGAQ 320
                                       4556668****************97779999**********98468999*********8877756665554444466 PP

                                       HHHHHHH CS
                    NAD_binding_10  80 nivdaak 86 
                                       +++++++
  gi|336255326|ref|YP_004598433.1| 321 RTIAVVE 327
                                       6665555 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 9.4
                                       EEEEEETT..HHHCHHHHCTTTCEEEE--TT-C CS
                    NAD_binding_10  21 evtalvRn..peklaeleaeeglevvegdvtdv 51 
                                       e+t ++R+  +e +a le ++++ev+e+++ d 
  gi|336255326|ref|YP_004598433.1| 353 EITRFTREfrTENVAMLE-SDRAEVLEIEIDDD 384
                                       456666654467777776.68899988888765 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 !   21.8   0.9   2.5e-07   0.00018       1      74 [.       3      69 ..       3      94 .. 0.88
   2 !    9.2   0.0    0.0019       1.4       1      79 [.     230     303 ..     230     322 .. 0.82
   3 ?   -1.5   0.0       3.8   2.8e+03      38      64 ..     352     378 ..     307     389 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.5e-07
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEE CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvv 74
                                      v+++GaG vG+++ae la ++ v    +v+dr+++++e +       ++ ai+ d   +e  L+++ ++ +dlv+
  gi|336255326|ref|YP_004598433.1|  3 VIVVGAGEVGSSIAESLATEHGV----VVIDRDEDRVESVT---YAHDVLAIEGDGTSIEV-LEEAgIERADLVI 69
                                      79******************975....*********99998...67888888888888887.7777688888887 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0019
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       +++iG+  +G  +a+l + ++ +  e  + +r+ e++++la++   ++    + da ++e +  +++ e+d+vv ++
  gi|336255326|ref|YP_004598433.1| 230 IVVIGGSEIGYQTARLFEVEG-F--EPRLLERDPERARELAEQ--LPDTVVLESDATDVEFLGREHIGEADIVVAAL 301
                                       789999999999999988887.4..799********9999985..688899999999999966778********887 PP

                                       SG CS
                   Sacchrp_dh_NADP  78 pp 79 
                                        +
  gi|336255326|ref|YP_004598433.1| 302 EN 303
                                       65 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.8
                                       HHHHCHHTTTCEEEEE--TTTHHHHHH CS
                   Sacchrp_dh_NADP  38 ealaakalgvrfeaialdaenyeavLa 64 
                                       e++   ++++r e++a+  +++++vL+
  gi|336255326|ref|YP_004598433.1| 352 EEITRFTREFRTENVAMLESDRAEVLE 378
                                       222222355555555555555555555 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 !   17.0   0.2   5.8e-06    0.0042       2      39 ..       3      39 ..       2      78 .. 0.89
   2 !    6.9   0.0    0.0072       5.2       2      44 ..     230     272 ..     229     292 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.8e-06
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekal 39
                                      v v+GaG +G++ia+ +a  ++ Vv++d++e+++e+++
  gi|336255326|ref|YP_004598433.1|  3 VIVVGAGEVGSSIAESLAT-EHGVVVIDRDEDRVESVT 39
                                      88*************9986.6899********999875 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0072
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44 
                                       + viG   +G + a +f  +g+e +l+++++e++++ +e++ +
  gi|336255326|ref|YP_004598433.1| 230 IVVIGGSEIGYQTARLFEVEGFEPRLLERDPERARELAEQLPD 272
                                       78********************************999988766 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   3.5e-06    0.0025       3      66 ..       2      70 ..       1     128 [. 0.75
   2 ?    3.9   0.0     0.037        27       3      37 ..     229     263 ..     227     268 .. 0.91
   3 ?    0.7   0.0      0.34   2.4e+02      41      79 ..     323     361 ..     305     394 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.5e-06
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS......S--EEEHHHHHHHHHTT-HHHHHHHS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp......radglnqrtmellrqlGledrilaeg 66
                                       V++VGaG +G + a  L++    vv++++ +++v+         a   + +++e+l+++G+e+  l  +
  gi|336255326|ref|YP_004598433.1|  2 RVIVVGAGEVGSSIAESLATE-HGVVVIDRDEDRVESVtyahdvLAIEGDGTSIEVLEEAGIERADLVIA 70
                                      69*****************99.889******9999887743333444457789*********98755555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.037
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSC CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttv 37 
                                       +++++G++  G  +a+l    G + +l+e+  +++
  gi|336255326|ref|YP_004598433.1| 229 EIVVIGGSEIGYQTARLFEVEGFEPRLLERDPERA 263
                                       679***************************98766 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.34
                                       S--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEE CS
                     FAD_binding_3  41 radglnqrtmellrqlGledrilaegapnelmgealyne 79 
                                        a + +++ ++l++++G++  i  ++++ e ++ ++++ 
  gi|336255326|ref|YP_004598433.1| 323 IAVVEEPEYVDLFETVGIDVAINPRAVTAEEITRFTREF 361
                                       4778889999****************9999888887766 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 !   15.5   0.2   2.8e-05      0.02       2      52 ..       3      48 ..       2      86 .. 0.78
   2 !    8.5   0.0    0.0043       3.1       2      70 ..     230     302 ..     229     325 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-05
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEEC CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvta 52
                                      + ++GaG++g+++a+ l+++    h +vv+ +r+++++e+   +  v +++
  gi|336255326|ref|YP_004598433.1|  3 VIVVGAGEVGSSIAESLATE----HGVVVI-DRDEDRVESVTYAHDVLAIE 48
                                      5678***********99988....899988.*******9998776644444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0043
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE-S CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvlav 69 
                                       i +iG+ ++g   a+ +  +g    e ++  +r+pe+a+elae+l           +v+     e + ead+vv a+
  gi|336255326|ref|YP_004598433.1| 230 IVVIGGSEIGYQTARLFEVEG---FEPRLL-ERDPERARELAEQLPdtvvlesdaTDVEF-LGREHIGEADIVVAAL 301
                                       789999999999999999999...666644.9*************976666644322222.2244555677777776 PP

                                       - CS
                     F420_oxidored  70 k 70 
                                        
  gi|336255326|ref|YP_004598433.1| 302 E 302
                                       5 PP

>> Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.063        45      67      94 ..     185     212 ..     160     221 .. 0.85
   2 !   18.0   0.0     3e-06    0.0022      32      91 ..     379     436 ..     368     444 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.063
                   Castor_Poll_mid  67 kiylnPeddevlqegdkllviaedddtk 94 
                                         ++ P+ d+v++ +d ++vi++ ++ +
  gi|336255326|ref|YP_004598433.1| 185 DEVIIPQGDTVIRPEDGVVVIGSSESVR 212
                                       55678****************9887655 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3e-06
                   Castor_Poll_mid  32 fylkelpelegkkyedvllafqeavviGikvassgkiylnPeddevlqegdkllviaedd 91 
                                       + + + + l   +  dv +++++ vviG  ++++g++ + P+ d+vl+ gd+++v a+ +
  gi|336255326|ref|YP_004598433.1| 379 IEIDDDSLLLENRISDVVRELPDGVVIGA-ITRDGRL-ITPRGDTVLERGDHVVVFADTR 436
                                       556666778888899*************9.8888998.68****************9865 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.5    0.0091       6.5       3      59 ..       3      52 ..       1      96 [. 0.82
   2 !   12.2   0.0   0.00013     0.093       3      61 ..     230     283 ..     228     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0091
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTT CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvt 59
                                      v+v+Ga+  +G  ia+ la+e   vvv+dr e+++e v          +lai++D t
  gi|336255326|ref|YP_004598433.1|  3 VIVVGAG-EVGSSIAESLATE-HGVVVIDRDEDRVESVTYAHD-----VLAIEGDGT 52
                                      7899998.59*********99.677788*****9988766544.....555555555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSH CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdr 61 
                                       ++v+G+s  IG+++a+ +  eG++  +++r +e+++e+a++l +     ++++ D td 
  gi|336255326|ref|YP_004598433.1| 230 IVVIGGS-EIGYQTARLFEVEGFEPRLLERDPERARELAEQLPD----TVVLESDATDV 283
                                       7889988.6*********************************98....56666666665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.7   2.7e-06    0.0019       1      30 [.       2      32 ..       2      84 .. 0.92
   2 ?    3.6   0.0     0.058        42     246     288 ..     187     230 ..     143     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.7e-06
                                      EEEEECTSHHHHHHHHHHH.HTTEEEEESSS CS
                               DAO  1 dvviiGGGiiGlstAyeLa.rrgVtllekgd 30
                                      +v+++G+G +G+s+A  La ++gV+++++++
  gi|336255326|ref|YP_004598433.1|  2 RVIVVGAGEVGSSIAESLAtEHGVVVIDRDE 32
                                      59****************95678******95 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.058
                                       EEETTTTEEEEEETTSEEEEEESSE..EETTCSSTSCSHHHHHHH CS
                               DAO 246 tdddgrgvyvtprkdgrvlvGgtad..eesgdddpevdeedidel 288
                                        + + +++ ++p +dg v++G++++  e++g  +p+++ ed++e+
  gi|336255326|ref|YP_004598433.1| 187 VIIPQGDTVIRP-EDGVVVIGSSESvrEFAGAVTPAPTLEDANEI 230
                                       455566666777.58*9999**99899888888899999999987 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.64   4.6e+02      17      31 ..      25      39 ..       3     132 .. 0.56
   2 !   17.2   0.0   5.2e-06    0.0037       8      54 ..     312     358 ..     308     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.64
                                      EEEEESSHHHHHHHH CS
                        ADH_zinc_N 17 viavdsseeklelak 31
                                      v+++d++e+++e + 
  gi|336255326|ref|YP_004598433.1| 25 VVVIDRDEDRVESVT 39
                                      555555555544332 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.2e-06
                                       HHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHT CS
                        ADH_zinc_N   8 qlAkalGa.eviavdsseeklelakklGadevinykeadlverikelt 54 
                                        lA+++Ga ++iav+  +e ++l +  G d++in++     e+i ++t
  gi|336255326|ref|YP_004598433.1| 312 LLARHAGAqRTIAVVEEPEYVDLFETVGIDVAINPRA-VTAEEITRFT 358
                                       68*********************************44.6777777776 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 !   15.7   5.6   9.1e-06    0.0065       2     244 ..       2     326 ..       1     350 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.1e-06
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias..................... 57 
                                       +v+v+G+G  G + a+ la+ ++ v+++++++  +   + +++ +l++++d+  ++                     
  gi|336255326|ref|YP_004598433.1|   2 RVIVVGAGEVGSSIAESLAT-EHGVVVIDRDEDRVES-VTYAHDVLAIEGDGTSIEvleeagieradlviastdgde 76 
                                       89*****************9.8889999644444444.5555555555555544445779999999999******** PP

                                       ..............................................................HHHHCHHHHCCCCHC CS
                                       ..............................................................xxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ..............................................................evvkklnqgielllg 72 
                                                                                                       v+ +  g+  +++
  gi|336255326|ref|YP_004598433.1|  77 tnivvcgaakavtesftiarvkrtnllrtwersqsafgvdfmvstdlytaeeivniaglpgaADVDAFADGLVQMAE 153
                                       ************99999999999999999999999999999999998888888888888888667778888665666 PP

                                       CTCEEEEESCEEEEETEEEC.......TCEEEEEE......SEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx.......xxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  73 eevvkidpgkkkvklekkke.......gdeekiay......dklvlAtGssprdlgipGvaenvgklvrtldsaeal 136
                                          +++  ++  v  e+ +e              +      d++++  G +  ++  +Gv   v  ++ +++s++++
  gi|336255326|ref|YP_004598433.1| 154 ---FEVTSDS-PVANETVSEadrfeslT------FaaiirgDEVIIPQGDTVIRP-EDGV---V--VIGSSESVREF 214
                                       ...4443333.33333222232323332......3335555********999998.4566...2..33468888888 PP

                                       CCSS-T.......SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEE CS
                                       xxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 137 klkllp.......krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsv 206
                                         + +p       + ivv+Gg+ iG  +A  +   g e  l+e+ ++  r+l ++l +++  +  + +ve+  ++ +
  gi|336255326|ref|YP_004598433.1| 215 AGAVTPaptledaNEIVVIGGSEIGYQTARLFEVEGFEPRLLERDPERARELAEQLPDTVVLESDATDVEFLGREHI 291
                                       888888888888999*********************************************************88888 PP

                                       EEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 207 keidgngeklevvledgeeidadlvvvavGvrpstell 244
                                        e+d     +   ++d++ + ++l+   +G +   + +
  gi|336255326|ref|YP_004598433.1| 292 GEAD---IVVAALENDEKNLLVSLLARHAGAQRTIAVV 326
                                       6665...3455888888888888887777776666555 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 !   15.5   0.3   1.3e-05    0.0094       1      40 [.       1      39 [.       1      64 [. 0.89
   2 ?   -2.4   0.0       4.3   3.1e+03       2      39 ..     229     266 ..     228     279 .. 0.76
   3 ?   -0.9   0.0       1.4     1e+03     138     157 ..     311     333 ..     289     355 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHC CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdkln 40
                                      m++ v+G+G vG   a  la   h v+++D de +v+++ 
  gi|336255326|ref|YP_004598433.1|  1 MRVIVVGAGEVGSSIAESLAT-EHGVVVIDRDEDRVESVT 39
                                      89*****************97.599***********9874 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.3
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdkl 39 
                                       +i+viG   +G  ta ++   g+e  ++  d e+ ++l
  gi|336255326|ref|YP_004598433.1| 229 EIVVIGGSEIGYQTARLFEVEGFEPRLLERDPERAREL 266
                                       58899999999999999888888766666666665555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.4
                                       HHCSS-...TTCEEEEE------ CS
                    UDPG_MGDP_dh_N 138 easkkk...gvdfdvvsnPEflr 157
                                       +  +++   ++ + vv  PE+++
  gi|336255326|ref|YP_004598433.1| 311 SLLARHagaQRTIAVVEEPEYVD 333
                                       33333333478999999999986 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 !   12.1   0.1   0.00023      0.16       3      83 ..       4      91 ..       2     114 .. 0.74
   2 ?    4.4   0.0     0.055        39       2      66 ..     230     304 ..     229     325 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                                      EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT....EEE-SSHHHHHHHC.....SEEEE-SSSHHHHHHH CS
                     NAD_binding_2  3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg....akaaesieelvasl.....dvvitmvkagkavdev 72
                                       ++G G+ Gs++a+ l+  ++ v+v++r++++ve++  ++    +++  +  e+++++     d+vi   ++g++++ v
  gi|336255326|ref|YP_004598433.1|  4 IVVGAGEVGSSIAESLA-TEHGVVVIDRDEDRVESVTYAHdvlaIEGDGTSIEVLEEAgieraDLVIAS-TDGDETNIV 80
                                      589***********997.5789*************9999888885555555555555555554666655.677777777 PP

                                      HHSHCCC--TT CS
                     NAD_binding_2 73 iegllealkkg 83
                                      + g ++a+ ++
  gi|336255326|ref|YP_004598433.1| 81 VCGAAKAVTES 91
                                      77766666555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.055
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..EEE-SSHHHHHHHC........SEEEE-SSSH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..akaaesieelvasl........dvvitmvkag 66 
                                       i +iG  ++G + a+ ++ +g++  + +r++e+++el+++    +++es +  v+ l        d+v+  ++++
  gi|336255326|ref|YP_004598433.1| 230 IVVIGGSEIGYQTARLFEVEGFEPRLLERDPERARELAEQLpdTVVLESDATDVEFLgrehigeaDIVVAALEND 304
                                       789***********************************9966655555544444433333444447777666665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.6e-05     0.012       1      56 [.       3      60 ..       3      92 .. 0.72
   2 ?   -2.4   0.0       4.7   3.4e+03      15      53 ..     311     352 ..     307     369 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH..HHHHCEEEEETTCEEEEEECE CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea..lkknGlrltseggeeilrppe 56
                                      + ++GaG +Gs +a +La   + v++i+r++ r+e+    ++ l ++++g++  +++++
  gi|336255326|ref|YP_004598433.1|  3 VIVVGAGEVGSSIAESLAT-EHGVVVIDRDEdRVESvtYAHDVLAIEGDGTSIEVLEEA 60
                                      579**************54.777************944455556666666444444444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.7
                                       HHHHH.HTHC.EEEE-SCH.HHHHHHHHCEEEEETTCEEEEE CS
                              ApbA  15 akLak.agad.vtlilrsr.rlealkknGlrltseggeeilr 53 
                                         La+ aga+  + ++ ++  ++ +++ G+++ ++ + ++++
  gi|336255326|ref|YP_004598433.1| 311 SLLARhAGAQrTIAVVEEPeYVDLFETVGIDVAINPRAVTAE 352
                                       567777888877777777767777899999988888333322 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 !   10.9   0.0   0.00048      0.34       2      42 ..       3      42 ..       2      48 .. 0.89
   2 ?    3.3   0.0       0.1        74       2      44 ..     230     272 ..     229     325 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00048
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHS CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineeh 42
                                      + v+GaG  G+++A +la +   v+++ r+e+ +e++  +h
  gi|336255326|ref|YP_004598433.1|  3 VIVVGAGEVGSSIAESLATEH-GVVVIDRDEDRVESVTYAH 42
                                      789**************9875.9********9999988776 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.1
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSB CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehen 44 
                                       i v+G+   G   A++++ +g e rl  r++e ++e+ e+  +
  gi|336255326|ref|YP_004598433.1| 230 IVVIGGSEIGYQTARLFEVEGFEPRLLERDPERARELAEQLPD 272
                                       8999***************************999999887655 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00039      0.28      19      42 ..       1      25 [.       1      39 [. 0.78
   2 ?   -1.7   0.0       2.1   1.5e+03      87     124 ..      41      79 ..      28      89 .. 0.68
   3 ?    0.3   0.0      0.52   3.7e+02      95     132 ..     278     316 ..     256     340 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00039
                                      SEEEEE--SHHHHHHHHHHHH.HTT CS
                                      xxxxxxxxxxxxxxxxxxxxx.xxx RF
                              ThiF 19 skvllvGaGglGsellknLal.sGv 42
                                      ++v +vGaG +Gs +++ La   Gv
  gi|336255326|ref|YP_004598433.1|  1 MRVIVVGAGEVGSSIAESLATeHGV 25
                                      589****************985555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                                       TSEEEEEES-CCG.CCS-HHHHTT-SEEEEESSSHHHHH CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  87 dveveavteritd.etvleellesvDlVvdalDniearr 124
                                         +v a++++ t+ e ++e  +e++DlV+  +D  e+  
  gi|336255326|ref|YP_004598433.1|  41 AHDVLAIEGDGTSiEVLEEAGIERADLVIASTDGDETNI 79 
                                       445666666666655567777999999999999666555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.52
                                       S-CCG.CCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHH CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  95 eritd.etvleellesvDlVvdalDniearrlvnracvk 132
                                        + td e + +e + ++D+Vv al n e  +lv  ++++
  gi|336255326|ref|YP_004598433.1| 278 SDATDvEFLGREHIGEADIVVAALENDEKNLLVSLLARH 316
                                       44555333567889999*******999998888777664 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 ?    6.4   0.1    0.0071       5.1      38      70 ..       2      33 ..       1      62 [. 0.74
   2 ?    3.9   0.0     0.041        29      38      72 ..     229     265 ..     216     307 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0071
                                      EEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk.afgmkviaydrskk 70
                                      +v ++G+G++G+++a+ l+ + g+ vi  dr ++
  gi|336255326|ref|YP_004598433.1|  2 RVIVVGAGEVGSSIAESLAtEHGVVVI--DRDED 33
                                      688*************99745555444..44433 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.041
                                       EEEEES-SHHHHHHHHHHH..HTT-EEEEESSSHHHH CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlk..afgmkviaydrskkke 72 
                                       ++ +iG  +IG ++a++++  +f+ +++  d+ + +e
  gi|336255326|ref|YP_004598433.1| 229 EIVVIGGSEIGYQTARLFEveGFEPRLLERDPERARE 265
                                       6899*************99444444555555544433 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 ?    6.6   0.2     0.019        13       1      43 [.       1      41 [.       1      78 [. 0.73
   2 ?   -0.9   0.0       3.9   2.8e+03      13      55 ..     100     142 ..      77     153 .. 0.62
   3 ?    4.1   0.0      0.11        81       3      80 ..     230     311 ..     228     328 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.019
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH..H CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeav..a 43
                                      +rv ++GaG +gs  +++l     +e+ v ++d+d+ r e v  a
  gi|336255326|ref|YP_004598433.1|  1 MRVIVVGAGEVGSSIAESL----ATEHGVVVIDRDEDRVESVtyA 41
                                      699*********9999554....55588899*******9998431 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.9
                                       HHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHH CS
                      GFO_IDH_MocA  13 skhlrplnesqrleevvalldpdaeraeavaesfgveaysdle 55 
                                       ++ lr + +sq+   v   +++d   ae++ +  g++  +d++
  gi|336255326|ref|YP_004598433.1| 100 TNLLRTWERSQSAFGVDFMVSTDLYTAEEIVNIAGLPGAADVD 142
                                       4446677777777777778888887777777766666655555 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.11
                                       EEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH....HHHTTHE.EESSHHHHHTCT..TESEEEE-S-G CS
                      GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrleevvalldpdaeraeav....aesfgve.aysdleelladp..eidavivatpn 72 
                                       +++iG+  ig++ +  l e  ++ e   ll++d+era+++     ++ ++e   +d+e l ++   e+d+v+ a  n
  gi|336255326|ref|YP_004598433.1| 230 IVVIGGSEIGYQTA-RLFEV-EGFEPR-LLERDPERARELaeqlPDTVVLEsDATDVEFLGREHigEADIVVAALEN 303
                                       78999999999998.55555.355555.8999999999994444444555566666777777668889999988888 PP

                                       GGHHHHHH CS
                      GFO_IDH_MocA  73 gtheelak 80 
                                       ++ + l+ 
  gi|336255326|ref|YP_004598433.1| 304 DEKNLLVS 311
                                       77666555 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.37   2.7e+02      16      56 ..     181     221 ..     155     255 .. 0.73
   2 ?    8.9   0.1    0.0023       1.7       2      37 ..     402     435 ..     401     441 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.37
                        HAS-barrel  16 rvegsk.dvkvGeyVeielpdgeivlGmvtdirrgnselsnd 56 
                                        ++g++  +  G+ V+ +++ g +v+G  +++r+  +    +
  gi|336255326|ref|YP_004598433.1| 181 IIRGDEvIIPQGDTVIRPED-GVVVIGSSESVREFAGAVTPA 221
                                       44555456777888888877.999999999999955444444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0023
                        HAS-barrel   2 GevigestssslifrvegskdvkvGeyVeielpdge 37 
                                       G+vig  t+++ +++ +g++ ++ G+ V+++ +  +
  gi|336255326|ref|YP_004598433.1| 402 GVVIGAITRDGRLITPRGDTVLERGDHVVVFAD--T 435
                                       99*****************************98..3 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       7.1   5.1e+03      26      48 ..      24      46 ..      21      53 .. 0.76
   2 ?    8.7   0.1    0.0034       2.4      14      41 ..      54      81 ..      51     110 .. 0.84
   3 ?    1.8   0.0      0.47   3.3e+02      13      40 ..     282     309 ..     277     343 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 7.1
                              YflT 26 diyvvakdkdrlerlaentdaet 48
                                        +v+  d+dr+e++  + d+ +
  gi|336255326|ref|YP_004598433.1| 24 GVVVIDRDEDRVESVTYAHDVLA 46
                                      57899999999999987776655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0034
                              YflT 14 ieelkaeGyneddiyvvakdkdrlerla 41
                                      ie l+++G+++ d++++++d d+++ + 
  gi|336255326|ref|YP_004598433.1| 54 IEVLEEAGIERADLVIASTDGDETNIVV 81
                                      899*******************997665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.47
                              YflT  13 aieelkaeGyneddiyvvakdkdrlerl 40 
                                       ++e l +e + e di+v+a ++d+ + l
  gi|336255326|ref|YP_004598433.1| 282 DVEFLGREHIGEADIVVAALENDEKNLL 309
                                       67778889999***********986655 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 ?    8.2   1.7    0.0033       2.4      26      93 ..       3      81 ..       1     101 [. 0.66
   2 ?   -1.2   0.0       2.6   1.9e+03      12      49 ..     180     218 ..     174     263 .. 0.67
   3 ?   -1.4   0.0         3   2.1e+03     139     156 ..     422     439 ..     409     444 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0033
                                      EEEE--SHHHHHHHHHHHHCT-EEEE.E-S-HHHHHHHHC.......TT-EE--HHHC.TTT-SEEEE-SSS..SSSB- CS
                     AdoHcyase_NAD 26 avvaGyGdvGkGcaaslkglGarviv.tevdPicalqaam.......eGfevvtleev.vkkadivvtttGn..kdiit 93
                                      ++v+G G+vG   a+sl +    v++  + d + ++  a        +G ++  lee+ +++ad+v+++t    ++i+ 
  gi|336255326|ref|YP_004598433.1|  3 VIVVGAGEVGSSIAESLATEHGVVVIdRDEDRVESVTYAHdvlaiegDGTSIEVLEEAgIERADLVIASTDGdeTNIVV 81
                                      799**************98766666624555555443222111122278999999998689999999988531145555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.6
                                       HHHHHH-S--.TTSEEEEE--SHHHHHHHHHHHHCT-EE CS
                     AdoHcyase_NAD  12 gikratdvll.aGkvavvaGyGdvGkGcaaslkglGarv 49 
                                       +i r+ +v++  G +++    G v  G+++s++++   v
  gi|336255326|ref|YP_004598433.1| 180 AIIRGDEVIIpQGDTVIRPEDGVVVIGSSESVREFAGAV 218
                                       566777777733555555667778888888888776555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3
                                       E-TTS-EEEEEGGGSBCH CS
                     AdoHcyase_NAD 139 tlkdgkkiillaeGrlln 156
                                       +l+ g +++++a+ r+l+
  gi|336255326|ref|YP_004598433.1| 422 VLERGDHVVVFADTRVLD 439
                                       578899*******99986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.6     0.007       5.1       1      30 [.       2      30 ..       2      60 .. 0.85
   2 ?    6.2   0.0     0.021        15       2      42 ..     230     270 ..     229     295 .. 0.79
   3 ?   -2.2   0.0       9.1   6.6e+03      45      64 ..     356     375 ..     343     389 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.007
                                      EEEEECSSHHHHHHHHHHHH.TTSEEEEEES CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalae.lgkkVtvver 30
                                      +v+vvG+G +g   A+ la  +g  V v++r
  gi|336255326|ref|YP_004598433.1|  2 RVIVVGAGEVGSSIAESLATeHG--VVVIDR 30
                                      79****************54266..666665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.021
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHH CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeea 42 
                                       +vv+Gg+ ig   A  +   g +  ++er ++  r l e++
  gi|336255326|ref|YP_004598433.1| 230 IVVIGGSEIGYQTARLFEVEGFEPRLLERDPERARELAEQL 270
                                       8****************999999999999888765555555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 9.1
                                       HHHHHHHHTTEEEECSEEEE CS
                         Pyr_redox  45 ilqeklekngievllntkve 64 
                                       +++++++ +++ +l + ++e
  gi|336255326|ref|YP_004598433.1| 356 RFTREFRTENVAMLESDRAE 375
                                       57888888888888764433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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):              25  [number of targets reported over threshold]
# CPU time: 0.55u 0.21s 00:00:00.76 Elapsed: 00:00:00.35
# Mc/sec: 3789.93
//
Query:       gi|336255327|ref|YP_004598434.1|  [L=360]
Description: cellulase [Halopiger xanaduensis SH-6]
Scores for complete 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-89  299.5   0.3    2.3e-89  299.3   0.3    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
    8.2e-10   38.7   0.4    2.8e-06   27.2   0.1    2.2  2  Peptidase_M28  Peptidase family M28
    9.4e-10   38.5   0.5    1.8e-09   37.6   0.5    1.5  1  Peptidase_M20  Peptidase family M20/M25/M40
    0.00056   18.8   0.0       0.66    8.7   0.0    2.1  2  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.3   0.3     5e-93   2.3e-89       1     292 []      48     344 ..      48     344 .. 0.97

  Alignments for each domain:
  == domain 1  score: 299.3 bits;  conditional E-value: 5e-93
                                       S-EEEEEES.STTSSEEEEEEE--B-EEEEEEE....ETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE- CS
                     Peptidase_M42   1 Gnliakkkg.kekepkvmiaAHmDeiGfmVkeI....kedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigsk 72 
                                       Gn++++++g  +++++v++aAHmDeiGfmV+++    +  Gf+++e++GG+d++vl++qrv+i+t++g+++Gvigs 
  gi|336255327|ref|YP_004598434.1|  48 GNVVGTLEGdGDSDYSVAVAAHMDEIGFMVRHVrggeDGPGFVELEALGGWDARVLKAQRVTIHTEDGDLPGVIGSP 124
                                       9*******9788999******************44333469************************************ PP

                                       -CGGCHHHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHH CS
                     Peptidase_M42  73 ppHllkeeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkel 149
                                       ppH+l+e+er+k++e+++ f+D+g+   ee+ee  +s+Gd v+++++++++++  i++kalDdr+++ ++le++++l
  gi|336255327|ref|YP_004598434.1| 125 PPHTLDEKEREKTPEVEDAFVDVGL-PYEELEER-VSPGDLVTMEQTTERMGET-ITGKALDDRICLFAMLEAARRL 198
                                       ************************7.8999***9.******************9.********************** PP

                                       CTSS-S.SEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETTCCSHH CS
                     Peptidase_M42 150 keeele.atvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDasgiyhp 223
                                       ++ + + at+++ atvqEEvGlrGak++  +++p++aia+Dvt+a+d pg ++ e+   lg+G++i++kD s+i++p
  gi|336255327|ref|YP_004598434.1| 199 ADGDGPeATIHFCATVQEEVGLRGAKALGVDVDPNLAIALDVTVANDVPGFDDGEHVtdLGDGAAIKLKDGSVITSP 275
                                       ****999*********************************************9998899****************** PP

                                       HHHHHHHHHHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                     Peptidase_M42 224 klrkkllelAkknnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                       k+ ++l+++A++++i+yqle+l+ ggtD++ ++   +  p+++isiptry+H+  e+ah+dd++at++L
  gi|336255327|ref|YP_004598434.1| 276 KVHRRLKAVAEDEEIDYQLEILPAGGTDTAGFQNVAGAKPVGAISIPTRYLHTVTETAHVDDVAATIDL 344
                                       ******************************************************************998 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00014      0.64       1      27 [.      49      76 ..      49      90 .. 0.79
   2 !   27.2   0.1   6.3e-10   2.8e-06      35     180 ..     181     334 ..     165     350 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00014
                                      EEEEEESTTCE.SEEEEEEEE--B-TTT CS
                     Peptidase_M28  1 Nviatlegkat.devlllgAHyDsvgvg 27
                                      Nv++tleg+   d  ++++AH+D +g+ 
  gi|336255327|ref|YP_004598434.1| 49 NVVGTLEGDGDsDYSVAVAAHMDEIGFM 76
                                      9******9988577**********9985 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 6.3e-10
                                       TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHH.HHC.CCTTEEEEEEECS-SSSS--EEE CS
                     Peptidase_M28  35 AdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafak.akp.elkkiaavlnlDmvgsggkellf 109
                                       A D+  +  a+Le ar la+ g  p+ ++ f ++  EE gl G+ka+    +p  + + ++ +  D  g  + e ++
  gi|336255327|ref|YP_004598434.1| 181 ALDDRICLFAMLEAARRLAD-GDGPEATIHFCATVQEEVGLRGAKALGVdVDPnLAIALDVTVANDVPGFDDGEHVT 256
                                       899999*************9.559***********************975344466677888888999998888888 PP

                                       .......HHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT..--EEEECTSSS-TTT.TSTT CS
                     Peptidase_M28 110 .......esgdkssselekelkalakpvgraaaedpfdersgrgrsDhspflkag..vpvldlaetgfpevy.Htpr 176
                                                 +++s   + +++++ k+v++ ++ d++ e   +g +D + f++     pv  +     p++y Ht  
  gi|336255327|ref|YP_004598434.1| 257 dlgdgaaIKLKDGSVITSPKVHRRLKAVAEDEEIDYQLEILPAGGTDTAGFQNVAgaKPVGAI---SIPTRYlHTVT 330
                                       888888444444444455677788888888877788888889999999999965433444444...67777778888 PP

                                       SSGG CS
                     Peptidase_M28 177 Dtld 180
                                        t+ 
  gi|336255327|ref|YP_004598434.1| 331 ETAH 334
                                       7765 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.5   3.9e-13   1.8e-09      35     206 ..     181     350 ..     162     351 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3.9e-13
                                       TTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20  35 addmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelhieepgileagkla 111
                                       a d+   ++a+lea+r+l+d    p+ ti++ +++ EE+g +Gakal   +  + ++   + +     ++ ++g+ +
  gi|336255327|ref|YP_004598434.1| 181 ALDDRICLFAMLEAARRLADGD-GPEATIHFCATVQEEVGLRGAKALGVDVDPNLAIALDVTVAND-VPGFDDGEHV 255
                                       6789999**********98886.5799***********988***9998866644556555555444.4444446644 PP

                                       EEEEE.EEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEE.EESSSBHTHHHHTTT....EEEEEEESSGGCT CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx....xxxxxxxxxxxxx RF
                     Peptidase_M20 112 igvvk.vevelleggapvtlndsplvkalaeaaeelfgekveli.vsgpggtdarffagi....ptvmifgpgsgla 182
                                         +++ + ++ l    +v + ++++ + l+++ae+    +++l+  ++ ggtd++ f+++    p   i  p     
  gi|336255327|ref|YP_004598434.1| 256 TDLGDgAAIK-L-KDGSVIT-SPKVHRRLKAVAEDE-EIDYQLEiLPA-GGTDTAGFQNVagakPVGAISIPT-RYL 326
                                       4444446666.2.2333444.4899**********8.66666663444.899999997774434544445577.9** PP

                                       TSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 183 HspnEyvdledlekgikvlarlle 206
                                       H++ E  +++d+++ i++l+++l 
  gi|336255327|ref|YP_004598434.1| 327 HTVTETAHVDDVAATIDLLEAFLA 350
                                       *******************99985 PP

>> Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00021      0.95     227     277 ..     175     223 ..     152     232 .. 0.83
   2 !    8.7   0.0   0.00015      0.66     330     431 ..     251     348 ..     233     349 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00021
                                       -EEEESSHHHHHHHHHHHHHHCCCCHT-TTTS-SEEEEEEESSCCGTS-ST CS
                     Peptidase_M18 227 eflfaprlDnkvscfaaleallesaedsleeedkvrivalfDnEEvGStsa 277
                                       e ++++ lD++++ fa lea  ++a+    +e +++ +a + +EEvG  +a
  gi|336255327|ref|YP_004598434.1| 175 ETITGKALDDRICLFAMLEAARRLADG-DGPEATIHFCATV-QEEVGLRGA 223
                                       67999****************999888.5567688888877.799997665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00015
                                       -TTTS--TTSEEEEEEETTSSSTT-HHHHHHHHHHHHHHC-EEEEEEE-TTS----HCHHHHHHHHT-EEEE.EE-E CS
                     Peptidase_M18 330 eenhapllnkGvvikvnanqryatnsagaallkevaqkanvklQelvvrndspcGstigpilaaktGirtiD.lGaa 405
                                       + +h   l+ G  ik++ +    t+ + +  lk va+  ++  Q  ++    p+G+t  + ++   G++ +  + ++
  gi|336255327|ref|YP_004598434.1| 251 DGEHVTDLGDGAAIKLKDGS-VITSPKVHRRLKAVAEDEEIDYQLEIL----PAGGTDTAGFQNVAGAKPVGaISIP 322
                                       5679999********98765.6788888999*************9876....99**************99854899* PP

                                       EBSTTSSSEEEECCHHHHHHHHHHHC CS
                     Peptidase_M18 406 qlsmHSireltgskdveeavklfkaF 431
                                          +H + e++   dv+ ++ l++aF
  gi|336255327|ref|YP_004598434.1| 323 TRYLHTVTETAHVDDVAATIDLLEAF 348
                                       ************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); 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:                         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 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2837.46
//
Query:       gi|336255328|ref|YP_004598435.1|  [L=388]
Description: protanoyl-CoA C-acyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-26   93.6   0.4    1.3e-22   80.4   0.1    2.3  2  Thiolase_N       Thiolase, N-terminal domain
    3.2e-10   40.0   8.8    3.2e-10   40.0   1.9    3.1  5  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    2.3e-09   36.9   0.4    5.7e-09   35.7   0.4    1.7  1  Thiolase_C       Thiolase, C-terminal domain
      0.003   17.4   0.7        1.2    9.0   0.2    2.7  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
  ------ inclusion threshold ------
       0.16   12.0   5.5       0.78    9.8   1.6    3.4  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal 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 !   80.4   0.1   3.6e-26   1.3e-22       3     200 ..       6     187 ..       4     200 .. 0.86
   2 !   11.1   0.0   5.1e-05      0.18     243     260 .]     206     223 ..     202     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 3.6e-26
                                       EEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHH..HHHHTTS-TTSE CS
                        Thiolase_N   3 ivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarq..aalkagipeevp 77 
                                       ++++  tp+g+      + ++++L aea  a+ ++  v+p +v+ v+ Gn + + ++ + ++   +a +ag+  ++p
  gi|336255328|ref|YP_004598435.1|   6 VAGTGITPFGN----APERTSRDLFAEASAAAFADSDVPPTDVEAVFYGNFMGELSEHQGHQGplMAEAAGV--TAP 76 
                                       67788899999....889999*********************************666665554014445555..*** PP

                                       EEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSS.EEEEEHHHHHHTEETTTTS CS
                        Thiolase_N  78 avtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgd.ekakdllipdgladafnee 153
                                       a++ + +c+S+ +a+ +a+  i+ ge dvv++gG+E+m+n  ta +t++ + +  +  e + +++ p          
  gi|336255328|ref|YP_004598435.1|  77 ATRYESACASSGAAIRDAVMRIRNGEHDVVLVGGAERMTNLGTAGATEALAIAADDLwEVRAGMTFPG--------- 144
                                       ********************************************998887655554415566777777......... PP

                                       EHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-E CS
                        Thiolase_N 154 hmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPv 200
                                         +l a+ + ++y+ + e+++++Avk+h++a ++ ka+ +++   P+
  gi|336255328|ref|YP_004598435.1| 145 AYALMAQAYFDRYGGDHEDLAHVAVKNHENALNNEKAQ-YQK---PI 187
                                       889**********************************9.888...44 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.1e-05
                                       SB--BEEEEEEEEEEEHH CS
                        Thiolase_N 243 nasqisDGaaavllmses 260
                                       ++++isDGaaa++l+se+
  gi|336255328|ref|YP_004598435.1| 206 DSCPISDGAAALVLTSEE 223
                                       79*************986 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 ?    3.2   0.0     0.016        56      91     126 ..      25      60 ..      20      70 .. 0.80
   2 !   40.0   1.9     9e-14   3.2e-10     160     221 ..      69     130 ..      66     138 .. 0.89
   3 ?   -3.2   0.0       1.4   4.9e+03     239     251 ..     211     223 ..     208     225 .. 0.84
   4 ?   -3.9   0.1       2.2     8e+03      94     111 ..     262     279 ..     259     288 .. 0.77
   5 ?   -3.0   0.0       1.2   4.3e+03     191     218 ..     318     345 ..     315     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHH CS
                     ketoacyl-synt  91 llleaawealedagltpeeldgsrvgvfiGvgagdy 126
                                       l+ ea++ a++d+ ++p++++    g+f+G  ++++
  gi|336255328|ref|YP_004598435.1|  25 LFAEASAAAFADSDVPPTDVEAVFYGNFMGELSEHQ 60 
                                       7889*************9999877888888666655 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 9e-14
                                       HHHT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB- CS
                     ketoacyl-synt 160 yalglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaaglls 221
                                        a g+++p+   ++AC+Ss +a+  av+++r+ge dv+l+GG+e +++ ++ ++ +a+++ +
  gi|336255328|ref|YP_004598435.1|  69 EAAGVTAPATRYESACASSGAAIRDAVMRIRNGEHDVVLVGGAERMTNLGTAGATEALAIAA 130
                                       56799****************************************99999998888887554 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.4
                                       B-EEEEEEEEECH CS
                     ketoacyl-synt 239 GEGvGavvLkrle 251
                                       ++G++a+vL ++e
  gi|336255328|ref|YP_004598435.1| 211 SDGAAALVLTSEE 223
                                       89*******9876 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHTS-HHTCT CS
                     ketoacyl-synt  94 eaawealedagltpeeld 111
                                       ea +ea +dag+++ ++d
  gi|336255328|ref|YP_004598435.1| 262 EAGDEAYADAGVDAGDVD 279
                                       778899999999987766 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 1.2
                                       TTS-SEEEEEEEE---SHHHHHHHHHTT CS
                     ketoacyl-synt 191 sgeadvalaGGvellltpeavagfsaag 218
                                       +ge  v l GG ++  +p +  g s+ +
  gi|336255328|ref|YP_004598435.1| 318 DGETPVNLSGGLKAKGHPVGATGASQVA 345
                                       5788888999999999998888877765 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.4   1.6e-12   5.7e-09      20     100 ..     254     354 ..     244     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.6e-12
                                       GGGHHH..HHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HH CS
                        Thiolase_C  20 lglgPa..yaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGai 76 
                                       l+ +Pa   a  ++  +ag++  d+dl E+++ F+   + +++al+l+                     vN+ GG  
  gi|336255328|ref|YP_004598435.1| 254 LARSPAarEAGDEAYADAGVDAGDVDLAEVHDCFTIAEVLALEALNLANvgegisaardgrttadgeTPVNLSGGLK 330
                                       55566522477889999*******************99999******999****************999******** PP

                                       HH-B-TTTHHHHHHHHHHHHHHHC CS
                        Thiolase_C  77 alGHPlGasGaRivvtllselkke 100
                                       a GHP+Ga+Ga +v+ ++  l+  
  gi|336255328|ref|YP_004598435.1| 331 AKGHPVGATGASQVAEITALLEGT 354
                                       **************9999888754 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 !    9.0   0.2   0.00035       1.2       5      39 ..      82     116 ..      80     131 .. 0.93
   2 !    5.9   0.0    0.0032        11      53      68 ..     211     226 ..     206     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00035
                                       -GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGG CS
                       ACP_syn_III   5 aaCsgfvyalsvAdaliesgaakrvLvigaetlsk 39 
                                       +aC++  +a+  A   i++g++  vLv gae++++
  gi|336255328|ref|YP_004598435.1|  82 SACASSGAAIRDAVMRIRNGEHDVVLVGGAERMTN 116
                                       79******************************987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0032
                                       -EEEEEEEEEEESSSS CS
                       ACP_syn_III  53 GDGAgAvvleaseeeg 68 
                                       +DGA+A+vl+ +e  +
  gi|336255328|ref|YP_004598435.1| 211 SDGAAALVLTSEEYAE 226
                                       8*********995544 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.11   3.9e+02      24      47 ..      24      47 ..       2      52 .. 0.75
   2 ?   -2.9   0.1       1.8   6.4e+03      27      47 ..      88     108 ..      68     130 .. 0.54
   3 ?    9.8   1.6   0.00022      0.78      22      99 ..     256     344 ..     232     359 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.11
                                      HHHHHHHHHHHHHHT--GGGEEEE CS
                   Ketoacyl-synt_C 24 eaqaraiekalaeagvdpedvdyv 47
                                      +  a+a ++a+a+++v p+dv+ v
  gi|336255328|ref|YP_004598435.1| 24 DLFAEASAAAFADSDVPPTDVEAV 47
                                      445788999************987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHT--GGGEEEE CS
                   Ketoacyl-synt_C  27 araiekalaeagvdpedvdyv 47 
                                        +ai++a+ +++   +dv +v
  gi|336255328|ref|YP_004598435.1|  88 GAAIRDAVMRIRNGEHDVVLV 108
                                       344555555555555555444 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00022
                                       THHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHH.HHHHHHHHHHHHGGGGG..........SCTSEEE-THHHH CS
                   Ketoacyl-synt_C  22 ngeaqaraiekalaeagvdpedvdyveahgtgtplg.DpiElealkkvfgekar..........kqplavgSvKsni 87 
                                          a+++a  +a+a+agvd+ dvd+ e h+  t +   + E+  l++v +  +           + p+ ++      
  gi|336255328|ref|YP_004598435.1| 256 RSPAAREAGDEAYADAGVDAGDVDLAEVHDCFTIAEvLALEALNLANVGEGISAardgrttadgETPVNLSGGLKAK 332
                                       3455678899*******************986654313345544444443333333344555555555555555555 PP

                                       -B-GGGHHHHHH CS
                   Ketoacyl-synt_C  88 GHleaAaGvael 99 
                                       GH  +A G+ ++
  gi|336255328|ref|YP_004598435.1| 333 GHPVGATGASQV 344
                                       666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 3190.94
//
Query:       gi|336255329|ref|YP_004598436.1|  [L=135]
Description: hypothetical protein Halxa_3952 [Halopiger xanaduensis SH-6]
Scores for 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-12   46.8   1.4    3.2e-12   46.3   1.4    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    5.7e-06   26.1   0.8    9.6e-06   25.4   0.8    1.4  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.036   13.6   0.2      0.069   12.7   0.2    1.4  1  TF_Zn_Ribbon   TFIIB zinc-binding


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 !   46.3   1.4   5.4e-16   3.2e-12       2      63 ..      58     118 ..      57     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 5.4e-16
                                       EEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE CS
                     OB_aCoA_assoc   2 velsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVrav 63 
                                       ++l+ +G+++++tv+h a p+f+++aPy++++ ++  +vr+++++ g dp++v+ + +V++ 
  gi|336255329|ref|YP_004598436.1|  58 TPLPETGEIETYTVTHVATPSFEDDAPYATAIADFG-PVRLTGQVAGTDPEAVERDLEVELA 118
                                       6899*******************************5.6*********************964 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 !   25.4   0.8   1.6e-09   9.6e-06       2      37 .]      22      56 ..      21      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.6e-09
                           DUF35_N  2 daaaegrLvgqrCpdCGtvqfPPravCphCgsddle 37
                                      daaa+g+  +  C+d G+   PPr+vCp Cg+++le
  gi|336255329|ref|YP_004598436.1| 22 DAAADGEAYYLECAD-GHGSLPPRRVCPECGATELE 56
                                      788888888999**9.*****************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 ?   12.7   0.2   1.2e-05     0.069       2      19 ..      46      65 ..      45      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                                      EETTTTCEECHEE..TSTTC CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveD..perge 19
                                      +CP+Cg t+l+e   pe+ge
  gi|336255329|ref|YP_004598436.1| 46 VCPECGATELEETplPETGE 65
                                      8********98877888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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 0.19s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1188.87
//
Query:       gi|336255330|ref|YP_004598437.1|  [L=152]
Description: CMP/dCMP deaminase zinc-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-16   58.7   0.0    6.1e-16   58.4   0.0    1.1  1  MafB19-deam      MafB19-like deaminase
    2.3e-15   56.3   0.0    2.9e-15   56.0   0.0    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    1.8e-05   24.8   0.0    2.7e-05   24.3   0.0    1.2  1  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4
    0.00032   20.8   0.0    0.00046   20.3   0.0    1.2  1  NAD2             Novel AID APOBEC clade 2
    0.00075   19.6   0.0     0.0011   19.2   0.0    1.1  1  NAD1             Novel AID APOBEC clade 1
     0.0014   18.7   0.0     0.0021   18.1   0.0    1.2  1  APOBEC2          APOBEC2
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.011   15.6   0.0    1.2  1  APOBEC_N         APOBEC-like N-terminal domain
      0.018   15.0   0.0      0.033   14.2   0.0    1.5  1  OTT_1508_deam    OTT_1508-like deaminase
       0.03   14.4   0.1      0.046   13.8   0.1    1.4  1  Bd3614-deam      Bd3614-like deaminase


Domain annotation for each model (and alignments):
>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0   3.1e-19   6.1e-16       3     105 ..       6     107 ..       4     125 .. 0.93

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 3.1e-19
                       MafB19-deam   3 kekafrkalaevekatkikedkigavivkdkkviargsnekelnakataHaEiaalqqAakklkskrlddatlyvtl 79 
                                       + ++ r+a++++++a+  ++ + g + v ++ v+ r  n + ++ + taH E +  + Aa  l +   dd+t+y+  
  gi|336255330|ref|YP_004598437.1|   6 DTEYIREAIELAREAVTDGNTPYGSLLVVGDTVVKRSRNTTVTESDITAHPELKLARWAARELDAADRDDCTMYTST 82 
                                       67899************************************************************************ PP

                       MafB19-deam  80 epCdmCagaivqaglkklvygagnpk 105
                                       epC+mCa ai +agl ++vy +   k
  gi|336255330|ref|YP_004598437.1|  83 EPCEMCATAIHYAGLDRVVYSVY-GK 107
                                       *******************9875.44 PP

>> 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 !   56.0   0.0   1.4e-18   2.9e-15       4     100 ..       6     103 ..       3     104 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 1.4e-18
                                       HHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHH.TSSCETTEEEEEEE CS
                   dCMP_cyt_deam_1   4 dekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaakn.ggsklegatlyvtl 79 
                                       d ++++ a+++a+ea ++ n++ G+ +v  + ++ +  n + ++++ t+H E+  ++ aa++    + +++t+y+++
  gi|336255330|ref|YP_004598437.1|   6 DTEYIREAIELAREAVTDGNTPYGSLLVVGDTVVKRSRNTTVTESDITAHPELKLARWAARElDAADRDDCTMYTST 82 
                                       77899************************88*******************************7788999******** PP

                                       --BHHHHHHHHHHT-SEEEEE CS
                   dCMP_cyt_deam_1  80 ePCsmCakaiiqsgikkvvvg 100
                                       ePC+mCa ai  +g ++vv+ 
  gi|336255330|ref|YP_004598437.1|  83 EPCEMCATAIHYAGLDRVVYS 103
                                       *******************96 PP

>> SNAD4  Secreted Novel AID/APOBEC-like Deaminase 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.4e-08   2.7e-05      16      60 ..      47      92 ..      36      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.4e-08
                             SNAD4 16 vlkn.kkehaEllflekikseldpsqeyrvtwylswsPCaeCaeki 60
                                      v ++  + h+El++ ++   eld++ + + t+y+s+ PC  Ca++i
  gi|336255330|ref|YP_004598437.1| 47 VTESdITAHPELKLARWAARELDAADRDDCTMYTSTEPCEMCATAI 92
                                      22331445**********99***********************998 PP

>> NAD2  Novel AID APOBEC clade 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.3e-07   0.00046      37      93 ..      37      92 ..      31     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.3e-07
                              NAD2 37 ellklekgvllnqkesklhaellfLskfvlrqlelaqeykvtwyvsWsPCpeCaaev 93
                                      +++k+++ + +++++   h+el+  ++   r+l++a++   t+y+s  PC  Ca+ +
  gi|336255330|ref|YP_004598437.1| 37 TVVKRSRNTTVTESDITAHPELKLARWAA-RELDAADRDDCTMYTSTEPCEMCATAI 92
                                      56777777777788999******999995.9***********************987 PP

>> NAD1  Novel AID APOBEC clade 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.3e-07    0.0011      41      90 ..      46      93 ..      31      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.3e-07
                              NAD1 41 GvleneskcHaEllflnkikslklldpsqkykvtwylswSPCseCaskla 90
                                       v+e++ ++H+El + ++    +l d + + + t+y+s  PC+ Ca+ ++
  gi|336255330|ref|YP_004598437.1| 46 TVTESDITAHPELKLARWA-AREL-DAADRDDCTMYTSTEPCEMCATAIH 93
                                      344455567*******999.4444.899999***************9875 PP

>> APOBEC2  APOBEC2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0021      44      89 ..      49      92 ..      33      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                           APOBEC2 44 enkekkcHaEllflskvkkkkleekkeykvtwyvswsPCaeCaeev 89
                                      e  + ++H+El + ++    +l+ + + + t+y+s  PC  Ca+ +
  gi|336255330|ref|YP_004598437.1| 49 E-SDITAHPELKLARWAAR-ELDAADRDDCTMYTSTEPCEMCATAI 92
                                      3.34678*****9999988.9**********************976 PP

>> APOBEC_N  APOBEC-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   5.5e-06     0.011      46      93 ..      50      93 ..      22     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.5e-06
                                      S..TBCHHHHHHHHHHHHT--.TTEEEEEEEEESS-S-HH....HHHHHH CS
                          APOBEC_N 46 a..skHaEelflediedqelrepkkkyeitlYvswsPChessdeCaekla 93
                                      +   +H+E+ + ++    el+   ++   t+Y+s+ PC      Ca ++ 
  gi|336255330|ref|YP_004598437.1| 50 SdiTAHPELKLARWAA-RELD-AADRDDCTMYTSTEPCEM----CATAIH 93
                                      13368*****999833.3555.68999*************....999885 PP

>> OTT_1508_deam  OTT_1508-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.6e-05     0.033       2      43 ..      55      96 ..      54     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                     OTT_1508_deam  2 HAEvqlleyleeekdkekqepryIgcSKpaCylCelylrahg 43
                                      H+E+ l+ + ++e d+  ++++++ +S  +C +C + +++ g
  gi|336255330|ref|YP_004598437.1| 55 HPELKLARWAARELDAADRDDCTMYTSTEPCEMCATAIHYAG 96
                                      ************99998888******************8776 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   2.3e-05     0.046      76     101 ..      74      99 ..      37     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                       Bd3614-deam  76 egarllvtlqcCkmCAalvvaaadap 101
                                       ++ +++ + ++C+mCA+ +  a+ ++
  gi|336255330|ref|YP_004598437.1|  74 DDCTMYTSTEPCEMCATAIHYAGLDR 99 
                                       5899************9998877644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1183.98
//
Query:       gi|336255331|ref|YP_004598438.1|  [L=360]
Description: hypothetical protein Halxa_3954 [Halopiger xanaduensis SH-6]
Scores for 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  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2748.65
//
Query:       gi|336255332|ref|YP_004598439.1|  [L=142]
Description: RDD domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-20   73.2   7.1    2.9e-20   72.9   7.1    1.1  1  RDD              RDD family
  ------ inclusion threshold ------
       0.44   10.5   5.7       0.34   10.8   4.3    1.5  1  DUF418           Protein of unknown function (DUF418)
        2.5    7.9   6.4        1.7    8.5   2.9    1.9  2  Peptidase_M48_N  CAAX prenyl protease N-terminal, five membra


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   7.1   4.9e-24   2.9e-20       4     140 ..      16     134 ..      15     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 4.9e-24
                               RDD   4 lgrRllAfliDlvllliislllallivallnakasaneavagslllllllvlllvllvyqllllskkgqTlGklllg 80 
                                       +g+R+lAfl+D +++ ++ +ll+++++a              + +lllllv+++v +vy +ll+  +g T+Gk llg
  gi|336255332|ref|YP_004598439.1|  16 IGQRILAFLLDSLIMGVVFGLLFGIGTA-----------LGDAAMLLLLLVAFAVSIVYGFLLEGIYGYTPGKYLLG 81 
                                       689*************************...........7789999999999************************* PP

                               RDD  81 lkvvdedgrklglaqaliRalllllllvlglslvlllllligflfvlfsrkrqalhDkla 140
                                       l vv++dg++++++++++R+ll+++        +l  + li+++++l+++++q++ D++a
  gi|336255332|ref|YP_004598439.1|  82 LVVVKSDGSECTIGASVLRNLLWVID-------SLPTFNLIAMAMILLTDDNQRVGDLVA 134
                                       *********************99875.......688888999999999*********998 PP

>> DUF418  Protein of unknown function (DUF418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.3   5.8e-05      0.34      98     140 ..      23      64 ..      21      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.8e-05
                            DUF418  98 YllqslictllfygyglglfgslgraallllallifllqllfS 140
                                       +ll sli+ ++f g+ +g++  lg aa+lll l+ f+++++  
  gi|336255332|ref|YP_004598439.1|  23 FLLDSLIMGVVF-GLLFGIGTALGDAAMLLLLLVAFAVSIVYG 64 
                                       89**********.*************************99875 PP

>> Peptidase_M48_N  CAAX prenyl protease N-terminal, five membrane helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.9   0.00029       1.7     121     171 ..      16      66 ..      11      71 .. 0.91
   2 ?    0.9   0.1     0.062   3.7e+02     132     162 ..      92     121 ..      73     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00029
                   Peptidase_M48_N 121 ikdklkslllalviglpllaallwiiewggeyfylylwlfllvfslllmti 171
                                       i + +  +ll  +i++++  +l+ i +++g++ +l l l+ +++s++  ++
  gi|336255332|ref|YP_004598439.1|  16 IGQRILAFLLDSLIMGVVFGLLFGIGTALGDAAMLLLLLVAFAVSIVYGFL 66 
                                       5677999**************************************997665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.062
                   Peptidase_M48_N 132 lviglpllaallwiiewggeyfylylwlfll 162
                                       ++ig+ +l  llw+i+++ + f l++++++l
  gi|336255332|ref|YP_004598439.1|  92 CTIGASVLRNLLWVIDSL-PTFNLIAMAMIL 121
                                       678889999999999988.667777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); 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:                         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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1132.15
//
Query:       gi|336255333|ref|YP_004598440.1|  [L=143]
Description: NUDIX hydrolase [Halopiger xanaduensis SH-6]
Scores for 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   68.6   1.0    6.4e-19   68.3   1.0    1.1  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
      0.028   14.8   0.1      0.042   14.3   0.0    1.4  1  AAA_17    AAA 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 !   68.3   1.0   7.1e-23   6.4e-19       5     129 ..       7     130 ..       4     132 .. 0.71

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 7.1e-23
                                       EEEEE.EEETTSE..EEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   5 avgvv.llnekge..vLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgp 77 
                                       ++g++ +++++g+   Ll++++    pg We+P+G+ve +E+++++A+RE++EE+G+  e+ +ll+ +++ + y + 
  gi|336255333|ref|YP_004598440.1|   7 SAGAIlFRDTRGRreYLLLKSR----PGdWEFPKGGVEGDEELQQTAIREVKEEAGI--EEFRLLDGFREDYDYVFE 77 
                                       6788834555566898888766....466*********999****************..777777744444444443 PP

                                       EEE..EEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHH CS
                             NUDIX  78 ygd..eheilyvfl.eevegelepndenevsevrwvpleellkeklaaesrkllp 129
                                             h  +++f  +++e     + +ne+++++w ++e+++ +  +++ r++l+
  gi|336255333|ref|YP_004598440.1|  78 ANGktIHKTVHLFIaKSFEAS--AELSNEHRDLQWRDYEQAVNTVTQDGPREILE 130
                                       333326666666664444444..5557**************77777777777665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.7e-06     0.042      25      89 ..       7      75 ..       1     116 [. 0.66

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.7e-06
                                      EHHHHHH.HHHHTTT...SHSSH..HHHCTSHHHHHHHHHHHHHHHHHHHHHSSEE.EEEE-SEEEETTEEE CS
                            AAA_17 25 saGdllr.eeakrgg...lakar..demrklpleekkelqkeaaekiaeeakkkgv.lvdghprikeqagfl 89
                                      saG +l+ ++  r++   l++     e+ k+  e ++elq++a+++++eea+ +++ l+dg+    e+ +++
  gi|336255333|ref|YP_004598440.1|  7 SAGAILFrDTRGRREyllLKSRPgdWEFPKGGVEGDEELQQTAIREVKEEAGIEEFrLLDGFR---EDYDYV 75
                                      666666623433443332222221135559*********************888877****97...445554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1092.88
//
Query:       gi|336255334|ref|YP_004598441.1|  [L=111]
Description: 30S ribosomal protein S10 [Halopiger xanaduensis SH-6]
Scores for 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   49.7   0.0    3.6e-13   49.6   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e


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 !   49.6   0.0     2e-17   3.6e-13       1      97 [.       6      99 ..       6     100 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 2e-17
                                      EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHH CS
                     Ribosomal_S10  1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketi 78
                                      r++l+S d+++L+ +v++i+ +a+++g+ +kgp+  P+++++v+  +  h+d  ++ + + ++++ R ++i+  +++ +
  gi|336255334|ref|YP_004598441.1|  6 RLTLQSGDRAALDGIVDDIKSTAERKGAALKGPHSHPPEKLSVPQHSRLHADdDRQFSSWTYTVFTRELEIH-GHDNLA 83
                                      79**************************************************9******************4.888888 PP

                                      HHHS-...S---SS-EEEE CS
                     Ribosomal_S10 79 dtllkllqlnlpegVsvev 97
                                      +++++    n+p+ V++e+
  gi|336255334|ref|YP_004598441.1| 84 RNIAE---QNFPDSVHIEA 99
                                      88888...99*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 791.82
//
Query:       gi|336255335|ref|YP_004598442.1|  [L=425]
Description: amidohydrolase [Halopiger xanaduensis SH-6]
Scores for 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-25   88.5   6.0    6.9e-25   88.0   6.0    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    5.7e-13   48.7   0.5    1.6e-12   47.3   0.3    1.8  2  M20_dimer      Peptidase dimerisation domain


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 !   88.0   6.0   7.6e-29   6.9e-25       2     206 ..     106     419 ..     105     420 .. 0.89

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 7.6e-29
                                       EEEES-BSSTTCGGGSSS.TTSEE...ETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSST CS
                                       xxxxxxxxxxxxxxxxxx.xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVpeeetdgwtt.pfslt...eedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEgg 74 
                                       l+ ++D +p +e+d+ ++ p +     e+dG ++++G+d + ++ +++le +++ +d      gt+++ fqp+EE+ 
  gi|336255335|ref|YP_004598442.1| 106 LRVDIDGLPRAESDNTEHvPAAEGfrsEHDGAMHACGHDAHATIGVGVLERIANSDDF----SGTLKVFFQPAEEVI 178
                                       799******555556678887777788888**********************996666....8************65 PP

                                       TTHHHHHHHHHH.TTTCESEEEEEEEESSSBTCHSTETEEEE................................... CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................... RF
                     Peptidase_M20  75 rgGakallegle.erekvdavfelhieepgileagklaigvv................................... 115
                                        gGak+++e    + e+vd ++++hi+  +++  g++++g+                                    
  gi|336255335|ref|YP_004598442.1| 179 -GGAKSMAE--SdHIEDVDSLLAMHIG-LDHPT-GEIVAGIDgflavrhleaeftgepahagghpeqgrnavqalat 250
                                       .999*****..334679**********.88888.88888888*********************************** PP

                                       ......................................................................EEEEEEE CS
                                       ......................................................................xxxxxxx RF
                     Peptidase_M20 116 ......................................................................kvevell 122
                                                                                                             +ve+e +
  gi|336255335|ref|YP_004598442.1| 251 avqnlyaiprhndgatrvnaglveggsasnvipesartvvevrgettelmeymteksrrvlrsaaemhdcEVEIE-I 326
                                       *******************************************************************86556666.5 PP

                                       EEESHEEECCHHHHHHHHHHHHHHHTSC..EEEEEESSSBHTHHHH.TTT.E.....EEEEEESSG.GCTTSTTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx.xxx.x.....xxxxxxxxx.xxxxxxxxxx RF
                     Peptidase_M20 123 eggapvtlndsplvkalaeaaeelfgek..velivsgpggtdarff.agi.p.....tvmifgpgs.glaHspnEyv 189
                                       +++ap +++d++lv +++++a  + g++   e+   g g++da ++ +++       +++++g++  g+ H+   +v
  gi|336255335|ref|YP_004598442.1| 327 GAEAPSATSDQELVSIVEDVAGGVAGVDsvLERDELG-GSEDATYLmQAVqEnggkaCYVGVGTDHpGGHHTATFDV 402
                                       999999999**************99988645555788.********97775145544667777665699999***** PP

                                       EHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 190 dledlekgikvlarlle 206
                                       d+++++ g+++la ++e
  gi|336255335|ref|YP_004598442.1| 403 DEASIQHGVDTLAGAIE 419
                                       *************9997 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.49   4.4e+03      34      48 ..      28      42 ..      24     100 .. 0.60
   2 !   47.3   0.3   1.7e-16   1.6e-12      10     105 ..     224     315 ..     219     319 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.49
                                      HHHHHCSCTTEEC.. CS
                         M20_dimer 34 arllaeledeegdia 48
                                      ar+++ele+  gd  
  gi|336255335|ref|YP_004598442.1| 28 ARIVEELEARLGDDI 42
                                      566666666665544 PP

  == domain 2  score: 47.3 bits;  conditional E-value: 1.7e-16
                                       EEEEE-B-EEGG.-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEHH CS
                         M20_dimer  10 kitvkgkagHsg.apgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiRll 85 
                                       + +++g+ +H+g  p+ g+NA+ +la +++ l + +++     + + t +n + +egGsa+nvip++a+  +++R +
  gi|336255335|ref|YP_004598442.1| 224 EAEFTGEPAHAGgHPEQGRNAVQALATAVQNLYAIPRH-----NDGATRVNAGLVEGGSASNVIPESARTVVEVRGE 295
                                       5679*******************************777.....67******************************99 PP

                                       HHHHHHHHHHHHHHHHTSCC CS
                         M20_dimer  86 pgedpeevleeieeilekea 105
                                        +e  e   e+ + +l+++a
  gi|336255335|ref|YP_004598442.1| 296 TTELMEYMTEKSRRVLRSAA 315
                                       99988888888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3273.56
//
Query:       gi|336255336|ref|YP_004598443.1|  [L=404]
Description: peptidase M48 Ste24p [Halopiger xanaduensis SH-6]
Scores for complete 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   89.8   0.1    3.3e-25   89.0   0.1    1.4  1  Peptidase_M48  Peptidase family M48
     0.0013   18.0   0.0     0.0025   17.1   0.0    1.5  1  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.047   13.5   0.0       0.08   12.7   0.0    1.4  1  BSP            Peptidase of plants and bacteria
      0.062   13.2   0.0      0.098   12.5   0.0    1.3  1  SprT-like      SprT-like family
        0.2   10.5   2.6       0.38    9.5   2.6    1.4  1  DUF4781        Domain of unknown function (DUF4781)
       0.26    9.7   0.1       0.41    9.1   0.1    1.2  1  Herpes_UL6     Herpesvirus UL6 like


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 !   89.0   0.1   1.1e-28   3.3e-25       4     195 ..     181     403 ..     178     404 .] 0.79

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 1.1e-28
                                       SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   4 eaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrh 79 
                                       + el++ v++la+++++p p+ ++  ++ p   A ++g      +iv+++gL+ ++l++ el+aVl+HE++H+++r+
  gi|336255336|ref|YP_004598443.1| 181 ADELQSRVDRLARQVDVPAPTVRLGRAQRP--IAATTGLRSDAsTIVVSRGLV-ETLEDLELEAVLAHEISHVVNRD 254
                                       679**************7777777777777..466666665556*********.*********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTT-SHHHHHT..T--S---HHHHHHHHHHTT.......HHHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  80 svvslivsllasillllglallisraeedaag..afldalavliglliillfl.......alSRkrEyqADeagvel 147
                                       ++v ++   l++ +  + ++l     ++   +  +++ + + ++++ ++++ +       ++ R+rEy AD+ +v +
  gi|336255336|ref|YP_004598443.1| 255 AAVLTL---LSMPAVKIDAMLEEVDDQGSEEAdpQSALRHPSVVFA-GLFVAAlnrwavaVVARYREYVADRGAVAI 327
                                       *66544...4444444444333333333333300333344443333.3333336999******************** PP

                                       TT.HHHHHHHHHHHHHHTT--S---HHHH............................HHS-SS--HHHHHHHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 148 lkrakdlvraliklakdlerqdvsaslrs............................ellstHPplleRiqalkel 195
                                       + ++++l+ al kl ++le+ + s+  +                             +++ tHPp+++Ri++l+++
  gi|336255336|ref|YP_004598443.1| 328 TGDPAALAGALEKLDAELENRPSSDLRNHsstaafsivpppweehrffdrtrrfidrTIFGTHPPTEKRIERLRAR 403
                                       ********************9999998889999999*************************************986 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   8.4e-07    0.0025     179     218 ..     222     261 ..     177     266 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.4e-07
                     Peptidase_M56 179 prIvlPadflkklsdeeleyillHElaHlkrkDllvnllv 218
                                       + Iv++  ++++l+d ele +l+HE +H+ ++D+ v  l+
  gi|336255336|ref|YP_004598443.1| 222 STIVVSRGLVETLEDLELEAVLAHEISHVVNRDAAVLTLL 261
                                       68********************************998876 PP

>> BSP  Peptidase of plants and bacteria
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.7e-05      0.08      61     111 ..     207     252 ..     168     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                               BSP  61 didgvaytsGldddhkeIhlslsyiekasaekdakaevtgvLthelvhvyq 111
                                           +a+t+Gl  d ++I++s  ++e+ ++      e++ vL he+ hv +
  gi|336255336|ref|YP_004598443.1| 207 AQRPIAATTGLRSDASTIVVSRGLVETLED-----LELEAVLAHEISHVVN 252
                                       55579**********************764.....79***********866 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.3e-05     0.098      44      77 ..     219     252 ..     162     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                         SprT-like  44 rhhasIeLseklldsrsedrllntLaHElcHlal 77 
                                       +   +I  s+ l+++ ++ +l+ +LaHE+ H+++
  gi|336255336|ref|YP_004598443.1| 219 SDASTIVVSRGLVETLEDLELEAVLAHEISHVVN 252
                                       36789**************************987 PP

>> DUF4781  Domain of unknown function (DUF4781)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.6   0.00013      0.38      87     139 ..      94     146 ..      69     153 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00013
                           DUF4781  87 lnvlDvvstvvglva..avpvgaaalatP.vaapvllaalvvgvgsavYstgRsiq 139
                                       ++++    +v+gl++  a  v+++  atP   + vl+ a++vgv+ avY tgR i+
  gi|336255336|ref|YP_004598443.1|  94 CQFAG---AVAGLITwyAGLVVVTHGATPrPLPTVLVIAVLVGVVFAVYHTGRTIY 146
                                       44444...4555554434444488889987456677777**************987 PP

>> Herpes_UL6  Herpesvirus UL6 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00014      0.41      12      37 ..     138     163 ..     127     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00014
                        Herpes_UL6  12 ayvkGqtiynslRnsevlirQvqasv 37 
                                        y  G+tiy  lR  ++++rQ+ a v
  gi|336255336|ref|YP_004598443.1| 138 VYHTGRTIYDELRRGGTVQRQLEADV 163
                                       699*******************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 3068.84
//
Query:       gi|336255337|ref|YP_004598444.1|  [L=472]
Description: geranylgeranyl reductase [Halopiger xanaduensis SH-6]
Scores for 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-12   45.2   2.9    1.2e-07   31.2   0.3    2.7  3  FAD_binding_2   FAD binding domain
    4.1e-11   42.4   0.6      7e-07   28.4   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
    2.1e-09   37.1   2.1    2.2e-08   33.7   2.1    2.2  1  FAD_binding_3   FAD binding domain
    2.7e-09   37.1   9.0    0.00024   20.8   1.0    2.4  2  DAO             FAD dependent oxidoreductase
    7.9e-09   35.4  10.2      3e-05   23.6   1.4    2.9  3  FAD_oxidored    FAD dependent oxidoreductase
    1.1e-08   34.7   0.1    1.1e-08   34.7   0.1    1.7  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.2e-08   32.1   4.4    2.2e-07   30.3   4.3    1.9  1  GIDA            Glucose inhibited division protein A
    3.3e-07   30.5   4.1    2.2e-06   27.8   0.5    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    9.4e-06   25.0   2.1    2.8e-05   23.5   0.5    2.1  2  Thi4            Thi4 family
    1.5e-05   24.2   4.0     0.0051   15.9   0.2    2.4  3  Lycopene_cycl   Lycopene cyclase protein
    2.7e-05   23.1   2.0    6.6e-05   21.8   0.3    2.0  2  HI0933_like     HI0933-like protein
    3.4e-05   23.2   0.3    3.4e-05   23.2   0.3    1.8  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00075   20.0   6.7     0.0027   18.2   0.4    2.7  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0027   17.6   0.0     0.0053   16.7   0.0    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0039   16.5   3.7       0.01   15.1   1.4    2.5  2  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0094   15.6   0.0      0.016   14.8   0.0    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.021   14.9   0.0        0.1   12.6   0.0    2.1  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.022   14.1   0.1       0.79    9.0   0.0    2.3  2  THF_DHG_CYH_C   Tetrahydrofolate dehydrogenase/cyclohydrolase
      0.026   13.9   0.1        1.2    8.4   0.0    2.1  2  GMC_oxred_N     GMC oxidoreductase
      0.031   14.4   1.4        0.3   11.2   0.4    2.7  2  Ferredoxin_N    N-terminal region of 4Fe-4S ferredoxin iron-s
      0.042   13.1   1.4        0.1   11.8   0.5    1.9  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.073   12.4   0.3       0.13   11.6   0.3    1.3  1  ThiF            ThiF family


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.3   1.5e-10   1.2e-07       1      39 [.      21      60 ..      21      85 .. 0.86
   2 !   13.7   0.0     3e-05     0.024     146     204 ..     122     181 ..     102     200 .. 0.86
   3 ?   -2.4   0.0       2.4     2e+03     389     408 ..     294     312 ..     263     324 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.5e-10
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS.GGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg.ata 39
                                      Dv+V+G+G AG+ AA+++a++G +v+++e ++e +  ++a
  gi|336255337|ref|YP_004598444.1| 21 DVVVVGAGTAGCYAAATIAREGYDVVILERKSEDEAgHIA 60
                                      9***************************988764433555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3e-05
                                       HHHHHHHTCTEEEEESEEEEEEEECTT...EEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 146 rlvesarkagvdfqerteadeLivedg...rvtGavvenpesgrevrirakavvlatgGfgr 204
                                       r +e+a++ag +++  t ++++++ d+    vtG+++   ++g+  +++a+ v++a+g  + 
  gi|336255337|ref|YP_004598444.1| 122 RIIEGADEAGAELHYDTVVKNVVQADDekgTVTGVEAI--RKGEPKTYEADVVIDAAGSLSV 181
                                       78999*******************655556******99..******************9885 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.4
                                       EESSBTEEE-STCEESSSST CS
                     FAD_binding_2 389 gqpipGLYAaGevaaggvhg 408
                                         ++pG  A+G +a g+v++
  gi|336255337|ref|YP_004598444.1| 294 SAVHPGYMAVGDAA-GHVNP 312
                                       44566666777666.55555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.2   6.9e-05     0.056       1      34 [.      21      51 ..      21      66 .. 0.79
   2 !   28.4   0.0   8.6e-10     7e-07     151     372 ..     114     358 ..      88     370 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.9e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                      ++v+vG+GtaG  aAa++a+ +   ++v ++e +
  gi|336255337|ref|YP_004598444.1| 21 DVVVVGAGTAGCYAAATIAREG---YDVVILERK 51
                                      69******************99...788888753 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 8.6e-10
                                       E-HHHHHHHHHHHHHHCT-EEEE--EEE..EEE-T.TS-EEEEEETT...S-EEE-SEEEE-SGGG-IIIIII.T-- CS
                    Trp_halogenase 151 ldaalyakfLrrvaearGvtrvegkvve..vqlde.dgrveslrled...greveadlfiDcsGfrgllieqa.Lkt 220
                                       +d+ +y k + + a ++G +   ++vv+  vq d+ +g v++++       +++ead +iD+ G  + l +++ +++
  gi|336255337|ref|YP_004598444.1| 114 IDRWEYGKRIIEGADEAGAELHYDTVVKnvVQADDeKGTVTGVEAIRkgePKTYEADVVIDAAGSLSVLQDHVdFSN 190
                                       57778888888899999999888888762234444678888887543333789****************99873222 PP

                                       -E....EE-TTT----EEEEEEEE--H---SSEE.....EEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHH CS
                    Trp_halogenase 221 gf....edwsdvLltdrAlavqveseelvepytr.....ataekaGWtWkiPLqhrlgn.GyvyssahadddeAlae 287
                                        +     d+s++         ++ +++ + p+ +      t ++aG  W+ P +++  n G+ +        + +++
  gi|336255337|ref|YP_004598444.1| 191 STfdtnVDYSHFCSAY----REIVTVDEPVPWDDalvfkPTERAAGYLWYFPRTDTEINvGLGFQMTEE-PMKLVDD 262
                                       2201002344444222....244455577777773333356678********99987777777754433.4466677 PP

                                       HHHHCT--TTTS-EEEE---EE.......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BT CS
                    Trp_halogenase 288 llaeldgkleaeprkirfttGr.......rkqawvknvvalGlasgfvePlestsihliqa....alrrLlallpdk 353
                                       l+++l+ + e  + ++  + G          +a +++ +a+G+a+g v+P  + +i+ + +    a++  ++ l ++
  gi|336255337|ref|YP_004598444.1| 263 LKRDLENRREFRNAEVDDKLGAalptrrpYDSAVHPGYMAVGDAAGHVNPTTGGGIAGAAYagkyAAEAAVEGLETG 339
                                       777777777777777777777677776677899***********************999887888999999999999 PP

                                       T--HHHHHHHHHHHHHHHH CS
                    Trp_halogenase 354 sdepaaiaefnrevarele 372
                                        +++ +  e+n++v  +++
  gi|336255337|ref|YP_004598444.1| 340 DVSESTFWEYNERVMDHFG 358
                                       9999999999999877665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   2.1   2.7e-11   2.2e-08       1     304 [.      19     318 ..      19     330 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.7e-11
                                       EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEE CS
                     FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealy 77 
                                       e+dV++VGaG aG  +a   ++ G +vv++e+ s++     a+g   +    + +   + +i+   +  ++ +  ++
  gi|336255337|ref|YP_004598444.1|  19 EADVVVVGAGTAGCYAAATIAREGYDVVILERKSEDEAGHIACGDALKGASAFPESIPKSKIEPAFTNTDVDHGRFE 95 
                                       579*********************************99998888766666666666666666666666666666666 PP

                                       EECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEE...ECCTTEEE CS
                     FAD_binding_3  78 nelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevr...dketgeee 151
                                        +     +  + le    p + +v+  +e  + ++e a e+g++++ +t v+++ q +++ + +v+     ++ge +
  gi|336255337|ref|YP_004598444.1|  96 IP-----QEDTVLE-IPVPGELAVIDRWEYGKRIIEGADEAGAELHYDTVVKNVVQADDE-KGTVTgveAIRKGEPK 165
                                       66.....7777888.56788999****************************999886655.333332337789**** PP

                                       EEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEE.EEEEEEEEEC.-SCCCTTC.CEEEEECCTTEE...EEEECCET CS
                     FAD_binding_3 152 tvrakYlvGaDGgrStvrktlgiefegeetvye.agvldvlfda.dlsdivep.lvlilsaesrgv...mviPlent 222
                                       t +a+ ++ a G  S   + ++++ ++++t ++ +++ ++  +   ++++v     l+ ++ +r        P+ + 
  gi|336255337|ref|YP_004598444.1| 166 TYEADVVIDAAGSLSVLQDHVDFSNSTFDTNVDySHFCSAYREIvTVDEPVPWdDALVFKPTERAAgylWYFPRTD- 241
                                       ************************9999988762444454444344443333355666666666553335566666. PP

                                       EEEEEEEEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-ST CS
                     FAD_binding_3 223 lerfyvqvearaekeersekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPt 299
                                            + v ++ + +e++ k   +++k++l++  +   ++v+ +   a++ ++ + +  + g  + +GDAa  + Pt
  gi|336255337|ref|YP_004598444.1| 242 ---TEINVGLGFQMTEEPMKLV-DDLKRDLENRREFRNAEVDDKLGAALPTRRPYDSAVHPGY-MAVGDAAGHVNPT 313
                                       ...5578888888788777775.5799999999999999999999999999999999998885.678****999999 PP

                                       TSHHH CS
                     FAD_binding_3 300 gGqGl 304
                                       +G G+
  gi|336255337|ref|YP_004598444.1| 314 TGGGI 318
                                       99997 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   1.5     4e-07   0.00033       1      31 [.      21      53 ..      21      71 .. 0.89
   2 !   20.8   1.0     3e-07   0.00024     141     350 ..     112     329 ..     105     331 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4e-07
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdi 31
                                      dvv++G+G +G+ +A   ar+g  V++le++++
  gi|336255337|ref|YP_004598444.1| 21 DVVVVGAGTAGCYAAATIAREGydVVILERKSE 53
                                      9*****************************965 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 3e-07
                                       EEEEHHHHHHHHHHHHHHTT-EEEESECEEEE.EEEE..TCEEEEE...EECTEEEE..EEEEEEE--GGGHHHHHT CS
                               DAO 141 gqvdpakltaalaraaealGveilegtevtgl.eeed..gkvwgve...rttpgend..aadavVnaaGawsdllgl 209
                                       +++d +++ + + + a ++G+e+++ t v+++ +++d  g v+gve   +   ge +  +ad v+ aaG  s  l+ 
  gi|336255337|ref|YP_004598444.1| 112 AVIDRWEYGKRIIEGADEAGAELHYDTVVKNVvQADDekGTVTGVEairK---GEPKtyEADVVIDAAGSLSV-LQD 184
                                       6789999999*********************8344446799999987632...3321236799******8863.322 PP

                                       TCTT.........T.SEEEEEEEEEEEE.EECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTC CS
                               DAO 210 lkel.........d.lpispvrgqvlvl.kplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgd 275
                                       + ++         d   +  +  +++++ +p++      +a+   p t + ++++ ++pr d ++ vG        +
  gi|336255337|ref|YP_004598444.1| 185 HVDFsnstfdtnvDySHFCSAYREIVTVdEPVPW----DDALVFKP-TERAAGYLWYFPRTDTEINVGLG------F 250
                                       2222334565544344556677777777445444....33344444.88889999999999999999974......3 PP

                                       SSTSCSHHHHHHHHHHHHHHSGGG.CGEEEEEEEEEEE.TTSSEEEEEEETEEEEEEEEEC....TTTHHHHHHHHH CS
                               DAO 276 ddpevdeedidellealrklfPql.gdvlrkwaGlrpl.pdglpligetpgvkglylatGh....sghGltlapatG 346
                                       + +e + + +d+l + l+++     ++v  k    +p+ ++ +  + ++  +  +  a+Gh     g G+  a+ +G
  gi|336255337|ref|YP_004598444.1| 251 QMTEEPMKLVDDLKRDLENRREFRnAEVDDKLGAALPTrRPYDSAVHPG--YMAVGDAAGHvnptTGGGIAGAAYAG 325
                                       3445555666666666666653322555556665666212222222221..22223333335555666666666666 PP

                                       HHHH CS
                               DAO 347 klla 350
                                       k++a
  gi|336255337|ref|YP_004598444.1| 326 KYAA 329
                                       6665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   1.4   3.7e-08     3e-05       1      31 [.      21      51 ..      21      53 .. 0.96
   2 !   16.5   0.1     5e-06    0.0041      98     144 ..     128     177 ..     112     183 .. 0.83
   3 ?   -0.7   0.2      0.88   7.2e+02     396     409 ..     296     309 ..     295     311 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.7e-08
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      DvvVvG+g+aG+ AA + ar+G  v+++e++
  gi|336255337|ref|YP_004598444.1| 21 DVVVVGAGTAGCYAAATIAREGYDVVILERK 51
                                      9****************************96 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 5e-06
                      FAD_oxidored  98 aeagvtvllntrlvevekeg...kriesvtveskegrktirAkvfiDATg 144
                                       +eag ++ ++t++++v++ +   +++++v++ +k + kt++A+v+iDA g
  gi|336255337|ref|YP_004598444.1| 128 DEAGAELHYDTVVKNVVQADdekGTVTGVEAIRKGEPKTYEADVVIDAAG 177
                                       789**************96423345******88778************87 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.88
                      FAD_oxidored 396 vepvcmalGqAaGv 409
                                       v+p +ma+G AaG+
  gi|336255337|ref|YP_004598444.1| 296 VHPGYMAVGDAAGH 309
                                       79***********7 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 !   34.7   0.1   1.3e-11   1.1e-08       2     113 ..      21     182 ..      20     209 .. 0.78
   2 ?   -2.7   0.6       3.2   2.6e+03       7      21 ..     315     329 ..     314     350 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.3e-11
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias..................... 57 
                                       dvvv+G+G AG+ aa t+a+ g++v+++e++ +   g++    al g+++++e +                      
  gi|336255337|ref|YP_004598444.1|  21 DVVVVGAGTAGCYAAATIAREGYDVVILERKSEDEAGHIACGDALKGASAFPESIPkskiepaftntdvdhgrfeip 97 
                                       8***************************9444444555555556666666666555666667999999999****** PP

                                       ...................................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC.TCEEEE CS
                                       ...................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       Pyr_redox_2  58 ...................................evvkklnqgielllgeevvkidpgkkkvklekkke.gdeeki 98 
                                                                          e       +++++ + +vv+ d +k++v+  +  + g+ +++
  gi|336255337|ref|YP_004598444.1|  98 qedtvleipvpgelavidrweygkriiegadeagaE------LHYDTVVK-NVVQADDEKGTVTGVEAIRkGEPKTY 167
                                       **************9999888888888655433221......24666666.8************97666579999** PP

                                       EESEEEE---EEE-B CS
                                       xxxxxxxxxxxxxxx RF
                       Pyr_redox_2  99 aydklvlAtGssprd 113
                                       ++d ++ A Gs + +
  gi|336255337|ref|YP_004598444.1| 168 EADVVIDAAGSLSVL 182
                                       **********96654 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.2
                                       --SHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                       Pyr_redox_2   7 GgGpAGlaaaltlaq 21 
                                       GgG+AG a a + a+
  gi|336255337|ref|YP_004598444.1| 315 GGGIAGAAYAGKYAA 329
                                       899999887765554 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   4.3   2.7e-10   2.2e-07       1      48 [.      21      76 ..      21     193 .. 0.66

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.7e-10
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE.ES-GGGTT--SSSSEEE-T.......T CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.thkldtiaelsCnpsiggi.......a 48
                                      dv+V+G+G AGc AA+++ar G++v+++  ++ d+ ++++C ++++g         
  gi|336255337|ref|YP_004598444.1| 21 DVVVVGAGTAGCYAAATIAREGYDVVILeRKSEDEAGHIACGDALKGAsafpesiP 76
                                      79***********************9997788899**********99855544443 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 !   27.8   0.5   2.7e-09   2.2e-06       1      29 [.      24      52 ..      24      72 .. 0.86
   2 ?    3.2   0.2      0.13     1e+02       3      18 ..     315     330 ..     314     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.7e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                      +vGaG +G++aA+++a++g+dv++le+ +
  gi|336255337|ref|YP_004598444.1| 24 VVGAGTAGCYAAATIAREGYDVVILERKS 52
                                      8*************************975 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                                       --SHHHHHHHHHHHCC CS
                     NAD_binding_8   3 GaGlsGlvaAylLaka 18 
                                       G+G++G+++A  +a +
  gi|336255337|ref|YP_004598444.1| 315 GGGIAGAAYAGKYAAE 330
                                       9*******99776654 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.5   3.4e-08   2.8e-05      17      53 ..      19      54 ..      15      69 .. 0.86
   2 ?    0.2   0.0      0.45   3.7e+02     114     167 ..     133     177 ..     113     186 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.4e-08
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS- CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvsp 53
                                      e+Dvv+vGaG++G  aa ++a++ +  v+iler+   
  gi|336255337|ref|YP_004598444.1| 19 EADVVVVGAGTAGCYAAATIARE-GYDVVILERKSED 54
                                      89*********************.********98655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.45
                                       EEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEEEE--G CS
                              Thi4 114 kllnavaveDlivregegvaGvvinwtlvelahdtqscvDPlvirakvvvdatG 167
                                        l   ++v +++  ++   +G v+   ++ +         P++ +a vv+da+G
  gi|336255337|ref|YP_004598444.1| 133 ELHYDTVVKNVVQADD--EKGTVTGVEAIRKGE-------PKTYEADVVIDAAG 177
                                       5555555555555553..245555555555544.......88888888888887 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   6.3e-06    0.0051       1      32 [.      21      50 ..      21      56 .. 0.92
   2 ?   -3.4   0.1       4.7   3.8e+03     126     141 ..     161     178 ..     130     187 .. 0.59
   3 !    9.6   0.0   0.00051      0.42     255     303 ..     297     345 ..     263     387 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.3e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      Dvvv+GaG Ag+  Aa +  a+ g  vv++e 
  gi|336255337|ref|YP_004598444.1| 21 DVVVVGAGTAGCYAAATI--AREGYDVVILER 50
                                      9*****************..999999999985 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.7
                     Lycopene_cycl 126 ggr..kirarlvvdargl 141
                                        g+  + +a +v+da g 
  gi|336255337|ref|YP_004598444.1| 161 KGEpkTYEADVVIDAAGS 178
                                       232347889999999984 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00051
                     Lycopene_cycl 255 eqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalresslsara 303
                                       ++  +a+G aag v P+TG  +a +  + +  a+a ++ l++ + s++ 
  gi|336255337|ref|YP_004598444.1| 297 HPGYMAVGDAAGHVNPTTGGGIAGAAYAGKYAAEAAVEGLETGDVSEST 345
                                       45579******************99999998889999998876555544 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   0.3   8.1e-08   6.6e-05       2      33 ..      21      52 ..      20      56 .. 0.94
   2 ?    0.3   0.1      0.27   2.2e+02     118     167 ..     126     181 ..     121     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.1e-08
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      dv+v+G+G AG +aA+++a++g +V++le+++
  gi|336255337|ref|YP_004598444.1| 21 DVVVVGAGTAGCYAAATIAREGYDVVILERKS 52
                                      8****************************975 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.27
                                       HHHHHT-EEE-S--EEEEECETTE.EEEEE.......TTEEEEESEEEE----SS- CS
                       HI0933_like 118 elkeagvklrletevksvekeedgkfrvkt.k.....seeeleadklvlAtGGlSi 167
                                        ++eag +l+++t vk+v + +d+k +v+  +     + +++ead ++ A G+lS+
  gi|336255337|ref|YP_004598444.1| 126 GADEAGAELHYDTVVKNVVQADDEKGTVTGvEairkgEPKTYEADVVIDAAGSLSV 181
                                       5789999********99977777665554322344445678999999999999996 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 !   23.2   0.3   4.2e-08   3.4e-05      22      64 ..      13      55 ..       2      81 .. 0.84
   2 ?   -1.9   0.2         2   1.6e+03      35      58 ..     315     337 ..     301     380 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.2e-08
                                      EETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                       AlaDh_PNT_C 22 gvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparl 64
                                        +g+++a v+v+G+G+aG  A+at ++ g +V++l+ +++  
  gi|336255337|ref|YP_004598444.1| 13 AGTGTREADVVVVGAGTAGCYAAATIAREGYDVVILERKSEDE 55
                                      345779******************************9988765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                                       STSHHHHHHHHHHHHTT-EEEEEE CS
                       AlaDh_PNT_C  35 GgGvaGlqAiatakglgakVtvlD 58 
                                       GgG+aG + +    + +a V+ l+
  gi|336255337|ref|YP_004598444.1| 315 GGGIAGAAYAG-KYAAEAAVEGLE 337
                                       78888764332.223345555554 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.4   3.4e-06    0.0027       2      33 ..      22      53 ..      21      58 .. 0.95
   2 ?    4.8   0.1     0.051        41      44      76 ..     121     156 ..     117     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.4e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdk 33
                                      vvvvG+G+ g+ +A+++a+ g +V ++er+++
  gi|336255337|ref|YP_004598444.1| 22 VVVVGAGTAGCYAAATIAREGYDVVILERKSE 53
                                      8****************************986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.051
                                       HHHHHHHHHTTEEEECSEEEEEEE..EETTS.EEEE CS
                         Pyr_redox  44 kilqeklekngievllntkveeie..gsedg.vesv 76 
                                       k++ e   + g e++++t+v++++   +e+g v++v
  gi|336255337|ref|YP_004598444.1| 121 KRIIEGADEAGAELHYDTVVKNVVqaDDEKGtVTGV 156
                                       6666777889**************444444556655 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 !   16.7   0.0   6.5e-06    0.0053       2      34 ..      22      54 ..      21     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.5e-06
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      v v+GaGt G   aa +a++g++Vv++++++e 
  gi|336255337|ref|YP_004598444.1| 22 VVVVGAGTAGCYAAATIAREGYDVVILERKSED 54
                                      89**************************97664 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.32   2.6e+02       2      23 ..      30      51 ..      29      53 .. 0.88
   2 !   15.1   1.4   1.3e-05      0.01     219     335 ..     128     243 ..     121     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.32
                                      HHHHHHHHHHHTTEEEEEEESS CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEar 23
                                      aG  aA + ++ G+dV++lE +
  gi|336255337|ref|YP_004598444.1| 30 AGCYAAATIAREGYDVVILERK 51
                                      66679***************86 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.3e-05
                                       TTTTEEEETSEEEEEEEE.ETTCEEEEET......TSTEEEESEEE.E-S-HHHHH.SSEEESCCSHHHHHHHHHSE CS
                     Amino_oxidase 219 elrgldirlntrVkeikr.egdgvtvtle......dgevveaDaVv.vTvplgvlk.ailfsPplpdekaeairnlg 286
                                       ++ g +++++t Vk++ + ++++ tvt +        +++eaD V+  + +l+vl+ ++ fs +        ++  +
  gi|336255337|ref|YP_004598444.1| 128 DEAGAELHYDTVVKNVVQaDDEKGTVTGVeairkgEPKTYEADVVIdAAGSLSVLQdHVDFSNST---FDTNVDYSH 201
                                       4789**************9777777766655565566666******66779*****888888855...56677999* PP

                                       EEEEEEEEEEESSGG.SGCSTSECECECCCEEETTTEEEEECCECCCSTT CS
                     Amino_oxidase 287 fgsvnkvilefdrkf.wednalgqgvlvseltttlgeafissdfpsrapp 335
                                       f s+   i+++d+++ w+d        +  ++t+++  ++++ fp  +++
  gi|336255337|ref|YP_004598444.1| 202 FCSAYREIVTVDEPVpWDD-------ALVFKPTERAAGYLWY-FPRTDTE 243
                                       *******************.......99*************7.5665555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     2e-05     0.016       1      31 [.      22      52 ..      22      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                      ++++GaG  G++ aa++a+ g+dv+++ r+ 
  gi|336255337|ref|YP_004598444.1| 22 VVVVGAGTAGCYAAATIAREGYDVVILERKS 52
                                      689**********************999976 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013       0.1      10      47 ..      17      53 ..      10      65 .. 0.87
   2 ?   -3.2   0.0       9.6   7.8e+03      75      87 ..     168     180 ..     156     191 .. 0.79
   3 ?   -2.4   0.0       5.7   4.6e+03      28      58 ..     408     440 ..     404     453 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                      .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHH CS
                      Shikimate_DH 10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNRtle 47
                                       +e+ v+++GaG  +  +a  ++++g++ vv++ R  e
  gi|336255337|ref|YP_004598444.1| 17 TREADVVVVGAGTAGCYAAATIAREGYD-VVILERKSE 53
                                      56899**********************9.999999765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.6
                                       T-SEEEE-SSSSS CS
                      Shikimate_DH  75 eadvvisatasee 87 
                                       eadvvi a +s +
  gi|336255337|ref|YP_004598444.1| 168 EADVVIDAAGSLS 180
                                       7999999988765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.7
                                       HHHHHCCT-CEEEEEE..SSHHHHHHHHHHHT. CS
                      Shikimate_DH  28 akhLlakgvkkvvvaN..Rtlerakelaeelkg 58 
                                       a+ L+++  +  +++N  Rt +ra++l e +++
  gi|336255337|ref|YP_004598444.1| 408 AESLYKSYGHWGTILNlfRTKRRADDLLELYEH 440
                                       555555544444555555999999999887755 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 ?    9.0   0.0   0.00097      0.79      34     107 ..      17      89 ..      11     102 .. 0.76
   2 ?    2.4   0.1      0.11        86      71      94 ..     160     183 ..     138     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00097
                                       -TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE-SS-TT-B-GGGS-TT-EEEE- CS
                     THF_DHG_CYH_C  34 legkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadivvvavGkpelikaemvkegavviDv 107
                                       +++++vvvvG+++  g   a+ +++++  V ++++k++d a ++   d +  a   pe i ++ +++  +  Dv
  gi|336255337|ref|YP_004598444.1|  17 TREADVVVVGAGT-AGCYAAATIAREGYDVVILERKSEDEAGHIACGDALKGASAFPESIPKSKIEPAFTNTDV 89 
                                       5677888888775.477777788888888888888888888888888888888888888888888877666666 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                                       CCHHHHHCCSSEEEE-SS-TT-B- CS
                     THF_DHG_CYH_C  71 kdlaeitreadivvvavGkpelik 94 
                                       ++ + +t ead+v+ a+G+ ++++
  gi|336255337|ref|YP_004598444.1| 160 RKGEPKTYEADVVIDAAGSLSVLQ 183
                                       45667899**********987765 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.054        44       2      40 ..      21      58 ..      20      87 .. 0.76
   2 ?    8.4   0.0    0.0015       1.2     197     258 ..     122     180 ..     113     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.054
                       GMC_oxred_N  2 delveggGsagsvvAaRLsedpstsvlvleaggreknrl 40
                                      d +v+g+G+ag+  Aa ++  +   v++le  ++++   
  gi|336255337|ref|YP_004598444.1| 21 DVVVVGAGTAGCYAAATIAR-EGYDVVILERKSEDEAGH 58
                                      789**********6666655.567899999999888765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0015
                       GMC_oxred_N 197 awLrpalerpnleiltgakaekiil.egrkkravGVeasdkkgtvkrlvvaakevvvaaGaln 258
                                         ++ a e+ ++e+ +++ ++ ++  +++k+ ++GVea +k++    ++++a++v+ aaG+l+
  gi|336255337|ref|YP_004598444.1| 122 RIIEGADEA-GAELHYDTVVKNVVQaDDEKGTVTGVEAIRKGEP---KTYEADVVIDAAGSLS 180
                                       556666677.9************98877899**********999...99***********985 PP

>> Ferredoxin_N  N-terminal region of 4Fe-4S ferredoxin iron-sulfur binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       0.7   5.7e+02      17      36 ..     241     260 ..     239     267 .. 0.89
   2 ?   11.2   0.4   0.00037       0.3      25      59 ..     325     359 ..     321     361 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.7
                      Ferredoxin_N  17 dteYDaeLGlemarDAvrvt 36 
                                       dte    LG +m++  ++++
  gi|336255337|ref|YP_004598444.1| 241 DTEINVGLGFQMTEEPMKLV 260
                                       7889999********99986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00037
                      Ferredoxin_N  25 GlemarDAvr.vtkGeLseaeFhekYheaVlaEFge 59 
                                       G+  a+ Av  + +G++se +F e Y+e+V++ Fg+
  gi|336255337|ref|YP_004598444.1| 325 GKYAAEAAVEgLETGDVSESTFWE-YNERVMDHFGA 359
                                       55566666644889*********9.*********95 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 ?   11.8   0.5   0.00013       0.1     167     197 ..      22      52 ..      13      66 .. 0.64
   2 ?   -0.7   0.0      0.82   6.7e+02      92     134 ..     128     178 ..      80     205 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                       Pyr_redox_3 167 vvViGgknSavDaAlelvrkgaeVtvvtrgs 197
                                       vvV+G++  ++ aA  ++r+g +V ++ r+s
  gi|336255337|ref|YP_004598444.1|  22 VVVVGAGTAGCYAAATIAREGYDVVILERKS 52 
                                       5555555555555555555555555555555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.82
                       Pyr_redox_3  92 ksfelpiklfeeVesvkk.edegfevet....ske...tyeAkkviiAtGe 134
                                       ++   + ++++ V++v + +de+ +v+     +k+   tyeA+ vi A+G 
  gi|336255337|ref|YP_004598444.1| 128 DEAGAELHYDTVVKNVVQaDDEKGTVTGveaiRKGepkTYEADVVIDAAGS 178
                                       555556677777777766333334443211112223448999999999886 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00016      0.13      17      41 ..      18      42 ..      13      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                      HTSEEEEE--SHHHHHHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 17 rdskvllvGaGglGsellknLalsG 41
                                      r++ v++vGaG+ G++++ ++a+ G
  gi|336255337|ref|YP_004598444.1| 18 READVVVVGAGTAGCYAAATIAREG 42
                                      5788******************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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):              22  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3270.63
//
Query:       gi|336255338|ref|YP_004598445.1|  [L=114]
Description: ferredoxin [Halopiger xanaduensis SH-6]
Scores for 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-11   42.7   4.9    5.4e-11   42.3   4.9    1.2  1  Fer2      2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.012   15.6   0.3      0.014   15.4   0.3    1.1  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   4.9     6e-15   5.4e-11       5      77 ..      10      79 ..       6      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 6e-15
                                      TEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE.CTTSSSSTHHHHHTTEEEEGGGSEE CS
                              Fer2  5 gkevevevadgettlldaaeenggidipysCggggCgtClvevlegev.qsdetelegeeldegklrlaCqtiv 77
                                      g++ ++++ d+et +l  + e  gi+ +ysC+ g C +C +e++eg+v q+ +++l++ee +e+++ l+C++++
  gi|336255338|ref|YP_004598445.1| 10 GTGETITCSDTET-ILSRCLEE-GIAQEYSCRVGMCLACSAEIVEGDVtQPAARALTEEE-AENYA-LTCMARP 79
                                      8999*********.66666666.9************************877766666665.56666.*****98 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.3   1.5e-06     0.014      38     101 ..      24      84 ..       1      90 [. 0.63

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-06
                            Fer2_3  38 ikeevdptlafrasCregiCGscavai.nGkptlaCtatikdlakqkseieleplpkfpvirDLv 101
                                       + + +++ +a ++sCr g+C +c+++i +G +t+     +++ ++++    l+ ++  +++ DL 
  gi|336255338|ref|YP_004598445.1|  24 LSRCLEEGIAQEYSCRVGMCLACSAEIvEGDVTQPAARALTEEEAEN--YALTCMA--RPQSDLK 84 
                                       445568999**************997548888776666666655544..5555553..3455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 910.09
//
Query:       gi|336255339|ref|YP_004598446.1|  [L=396]
Description: Rhodanese-like protein [Halopiger xanaduensis SH-6]
Scores for 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-17   63.9   3.3    4.1e-17   62.8   3.3    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
    9.4e-09   35.8   0.0    2.8e-08   34.2   0.0    1.9  2  Rhodanese      Rhodanese-like domain
    0.00033   20.2   1.9    0.00067   19.2   0.7    2.1  2  Lactamase_B_2  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 !   62.8   3.3   6.9e-21   4.1e-17       5     197 .]     148     314 ..     144     334 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 6.9e-21
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                       ++ +y i  ++++ +iD++   +   a +    + +   ++++ + TH H+DH++g++ l ++td+  ++ + +   
  gi|336255339|ref|YP_004598446.1| 148 GCLTYAIYSGDEAAVIDPLRAFADRYAED----VAYRNAELKYAVDTHVHADHVSGVRALESRTDATAVVPEGARDR 220
                                       678999*********************96....******************************************** PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCC CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetg 158
                                       ++ + a                      +  +dg+++++++   t   ++gh++ +++y+ g+vlf+GD+l+ +  g
  gi|336255339|ref|YP_004598446.1| 221 GLAFDA----------------------MTFEDGDELHVGDATLTAVATPGHTSESLSYRLGDVLFSGDTLFLEGVG 275
                                       ******......................88999999***************************************** PP

                                       CCCC.....TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.SS CS
                       Lactamase_B 159 ridl....tlrgaevrdpsdaekyldsllklaglkaevlvp.gH 197
                                       r dl    +       +++  + y    + l +l+ae+ ++ gH
  gi|336255339|ref|YP_004598446.1| 276 RPDLergdE-----GAPAAARQFYETLEDTLSELPAETTIApGH 314
                                       ****44332.....333333333333334466777777666677 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   4.7e-12   2.8e-08       2     105 ..      16     115 ..      15     117 .. 0.79
   2 ?   -3.4   0.0       2.3   1.4e+04      63      78 ..     133     148 ..     123     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 4.7e-12
                         Rhodanese   2 akelkellekgkva.llDvRppeeYekghIpg....Avnvskdtlsrakkseapllelpeellelgidnkktvvvyc 73 
                                       ++ l+e+l +g+   +lDvR+++e++++hI+g    Av +     ++ k+ +a+    +++l++   d ++++v +c
  gi|336255339|ref|YP_004598446.1|  16 PETLAERLRAGDELtVLDVRDRDEFDRWHIEGesveAVQI-----PHMKFIQAQATGGVTDLID---DLEEPIVAVC 84 
                                       567778885555456***************6542225555.....6666666666666666666...4899****** PP

                         Rhodanese  74 dgggraaaaaallkklGyknvsvldGGfkawk 105
                                         g+ +  a  ll+ +G  + ++l GG+++w+
  gi|336255339|ref|YP_004598446.1|  85 GRGEASDHAVDLLRDAG-IDAQNLAGGMDSWA 115
                                       *****************.8************7 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.3
                         Rhodanese  63 idnkktvvvycdgggr 78 
                                        d   tvv y++ +++
  gi|336255339|ref|YP_004598446.1| 133 SDSAATVVQYDRPSSG 148
                                       4678899999988877 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 ?   -3.2   0.0      0.85   5.1e+03      86     112 ..      33      57 ..      11      67 .. 0.43
   2 !   19.2   0.7   1.1e-07   0.00067      22     147 ..     177     272 ..     161     283 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.85
                                       EEEEE-TTSEEEECSTTEEEEEEEE-E CS
                     Lactamase_B_2  86 nvheldwgesfelgdggleitatparh 112
                                       +v++ d  ++ ++++   +++a++++h
  gi|336255339|ref|YP_004598446.1|  33 DVRDRDEFDRWHIEG--ESVEAVQIPH 57 
                                       222222223333332..2344444444 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.1e-07
                                       -SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEE CS
                     Lactamase_B_2  22 velrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfel 98 
                                       v+ r+   +++  + th H+DH+ g+  l  +++      a++ v +  ++++         a ++ +++ g+++++
  gi|336255339|ref|YP_004598446.1| 177 VAYRNA--ELKYAVDTHVHADHVSGVRALESRTD------ATAVVPEGARDRGL--------AFDAMTFEDGDELHV 237
                                       333444..8899999***********99999544......45555566666642........34567799******* PP

                                       CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S--- CS
                     Lactamase_B_2  99 gdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip 147
                                       gd   ++ta++ ++ + +         l++r++     v+++gDt +++
  gi|336255339|ref|YP_004598446.1| 238 GD--ATLTAVATPGHTSE--------SLSYRLG----DVLFSGDTLFLE 272
                                       96..57899988888888........9******....9******97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3254.58
//
Query:       gi|336255340|ref|YP_004598447.1|  [L=214]
Description: hypothetical protein Halxa_3963 [Halopiger xanaduensis SH-6]
Scores for 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   15.9   0.3      0.033   14.6   0.3    1.6  1  Rubrerythrin  Rubrerythrin
      0.078   12.7   0.3       0.84    9.4   0.1    2.3  2  COQ7          Ubiquinone biosynthesis protein COQ7


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 ?   14.6   0.3   3.7e-06     0.033      78     136 ..      28      88 ..       4      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-06
                                       TGGHHHHHH..HHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  78 flttaknLe..eaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                       + +t+ +L+  +++++  + e+ + +++    ++e +++a++lf++  ++E++H er  +l
  gi|336255340|ref|YP_004598447.1|  28 VALTDADLTaeTVLRIVADGERAAAETFDAWTDDESHDDAQELFAEFRDQEREHCERVLEL 88 
                                       445555555558899999999*********************************9998876 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   9.4e-05      0.84       4      56 ..      39      89 ..      36      94 .. 0.82
   2 ?    1.1   0.0     0.034   3.1e+02      32      63 ..     118     149 ..     108     205 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 9.4e-05
                              COQ7  4 rllRvdhaGElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeell 56
                                       +lR+   GE +A   +++ ++   +++ + ++l++e  +qE+eH++ + ell
  gi|336255340|ref|YP_004598447.1| 39 TVLRIVADGERAAAETFDAWTDD--ESHDDAQELFAEFRDQEREHCERVLELL 89
                                      68899999999999999998888..6666678999999999999999887776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.034
                              COQ7  32 pelkpllkemleqEkeHlatfeellkerrvrp 63 
                                       p+l  l+ ++l +E+ Hl++++  ++e + r+
  gi|336255340|ref|YP_004598447.1| 118 PRLGGLVGRALVTERTHLQVVSFFVNEGDERR 149
                                       55666677777778888877776666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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 0.20s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1690.06
//
Query:       gi|336255341|ref|YP_004598448.1|  [L=392]
Description: cell division protein FtsZ [Halopiger xanaduensis SH-6]
Scores for complete 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-41  142.5   0.5    2.7e-41  141.9   0.5    1.3  1  Tubulin         Tubulin/FtsZ family, GTPase domain
    2.2e-36  124.0   4.2    2.8e-36  123.7   2.3    2.2  2  FtsZ_C          FtsZ family, C-terminal domain
     0.0058   16.5   2.7     0.0071   16.3   0.2    2.2  3  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.025   13.8   7.8      0.081   12.1   2.1    2.6  2  Tubulin_2       Tubulin like


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 !  141.9   0.5   6.1e-45   2.7e-41       2     195 ..      58     216 ..      57     218 .. 0.97

  Alignments for each domain:
  == domain 1  score: 141.9 bits;  conditional E-value: 6.1e-45
                                       EEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE- CS
                           Tubulin   2 iivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklll 78 
                                       i v+g+G++G++++n+++e    e gi             +g ++++    a++td q+l ei+a+      +k+l+
  gi|336255341|ref|YP_004598448.1|  58 ITVVGCGGAGGNTINRMHE----E-GI-------------HG-AKLV----AANTDVQHLVEIDAD------TKILM 105
                                       89*****************....8.**.............88.7777....***************......***** PP

                                       -CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEE CS
                           Tubulin  79 gkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvv 155
                                       g+e++g+ gag+ p+vg+eaa e+++ i ++++++d+   +f+ta+lgGGTG+G +pv++++++e   +al++++v+
  gi|336255341|ref|YP_004598448.1| 106 GEEKTGGRGAGSLPQVGEEAALESQQDIYDAIDGSDM---VFVTAGLGGGTGTGSAPVVAKAAREA--GALTIAIVT 177
                                       *************************************...**************************..********* PP

                                       E--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCC CS
                           Tubulin 156 lPsefsevvvepynailalkelieesdavividNdaLlki 195
                                       +P++  e+ v+  na+ +l++l++ sd+viv++Nd+Ll+ 
  gi|336255341|ref|YP_004598448.1| 178 TPFTA-EGEVRRTNAEAGLERLRDVSDTVIVVPNDRLLDS 216
                                       ***99.*******************************986 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.95   4.2e+03      72      86 ..      38      52 ..      30      63 .. 0.74
   2 !  123.7   2.3   6.3e-40   2.8e-36       1      95 []     265     359 ..     265     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.95
                                      EEEEEE-TT--SEEE CS
                            FtsZ_C 72 ivGavideeledeir 86
                                        G++ deeled+++
  gi|336255341|ref|YP_004598448.1| 38 QSGTMTDEELEDVLQ 52
                                      568999999998764 PP

  == domain 2  score: 123.7 bits;  conditional E-value: 6.3e-40
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       GvAm+g+Gea++e +ae+++++a++spLLdvd+sgA+++lvn+tgg+d++++E+e v+e+i++++d++a++i+G++i
  gi|336255341|ref|YP_004598448.1| 265 GVAMIGLGEADSEAKAEDSVKTALRSPLLDVDISGANSALVNVTGGNDMAIEEAEGVVEEIYDRIDPDARIIWGTSI 341
                                       99*************************************************************************** PP

                                       -TT--SEEEEEEEEES-X CS
                            FtsZ_C  78 deeledeirvtvvatglk 95 
                                       de+le+++r+++v+tg++
  gi|336255341|ref|YP_004598448.1| 342 DESLEGSMRTMIVVTGVE 359
                                       ****************95 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 ?   -0.9   0.1      0.29   1.3e+03      53      78 ..      46      81 ..      34     104 .. 0.49
   2 !   16.3   0.2   1.6e-06    0.0071      46     102 ..     125     182 ..     120     203 .. 0.80
   3 ?   -3.0   0.0       1.3   5.9e+03       6      52 ..     217     258 ..     216     262 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.29
                                      HHHHHHT..T-S.EEEES---TCC.HHHH......H CS
                    NAD_binding_10 53 dlaealk..gad.aVvsalggggk.deeg......a 78
                                      +l+++l+  ++d +Vv ++g+gg+  +++       
  gi|336255341|ref|YP_004598448.1| 46 ELEDVLQdlQTDiTVVGCGGAGGNtINRMheegihG 81
                                      444444422122235555555555433332222332 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.6e-06
                                       --TT-CCHHHHHHTT-SEEEES---TCCHHHH.HHHHHHHHHHCT--EEEEEEETTTT CS
                    NAD_binding_10  46 gdvtdvedlaealkgadaVvsalggggkdeeg.aknivdaakeagvkRfvlvsaigvg 102
                                       + +++++d+ +a++g d V++++g gg++ +g a  +++aa+eag   + +v++  + 
  gi|336255341|ref|YP_004598448.1| 125 AALESQQDIYDAIDGSDMVFVTAGLGGGTGTGsAPVVAKAAREAGALTIAIVTTPFTA 182
                                       568999*****************8777755665889999*******999999985443 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CC CS
                    NAD_binding_10   6 vGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdve 52 
                                       vG+l v+++ + +  e  +l+R+ + ++el  +    +v +d+ dv 
  gi|336255341|ref|YP_004598448.1| 217 VGKLPVRQAFKVS-DE--VLMRSVKGITELITK--PGLVNLDFADVR 258
                                       6777788887775.45..478888888888754..445666666654 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3    0.0042        19       2      24 ..      60      82 ..      59     110 .. 0.69
   2 ?   12.1   2.1   1.8e-05     0.081     115     182 ..     113     167 ..      85     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0042
                         Tubulin_2  2 viGLGGtGgkvlaelrrrlreel 24
                                      v+G+GG Gg++++++ +   +  
  gi|336255341|ref|YP_004598448.1| 60 VVGCGGAGGNTINRMHEEGIHGA 82
                                      7*************987655544 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.8e-05
                         Tubulin_2 115 eGAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllrk 182
                                       +GAG +++vG  a +++ ++i++a++       gs        vfV  +L GGTG G++  va   r+
  gi|336255341|ref|YP_004598448.1| 113 RGAGSLPQVGEEAALESQQDIYDAID-------GS------DMVFVTAGLGGGTGTGSAPVVAKAARE 167
                                       89999999999998888888887775.......33......48**************99877766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3108.34
//
Query:       gi|336255342|ref|YP_004598449.1|  [L=443]
Description: D-tyrosyl-tRNA(Tyr) deacylase [Halopiger xanaduensis SH-6]
Scores for 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  206.8   0.0    3.7e-61  206.2   0.0    1.2  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase
  ------ inclusion threshold ------
      0.052   13.7   0.0       0.12   12.5   0.0    1.6  1  DUF2201         VWA-like domain (DUF2201)


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 !  206.2   0.0   4.1e-65   3.7e-61       3     204 ..      72     268 ..      70     269 .. 0.96

  Alignments for each domain:
  == domain 1  score: 206.2 bits;  conditional E-value: 4.1e-65
                                       ---SEEEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS- CS
                    tRNA_deacylase   3 edvdliiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHGP 79 
                                        d+dl++f+SrHs+e+g plLT H+tGn+g+ae+GG+++ +a aaP++l++ll+a++++a  +e+++v +E+tHHGP
  gi|336255342|ref|YP_004598449.1|  72 CDPDLLVFASRHSGETG-PLLTGHFTGNFGPAEYGGEDHAVAEAAPNALARLLEAFDEYA--PEGYDVGMECTHHGP 145
                                       689**************.******************************************..*************** PP

                                       ----S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH------EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGG CS
                    tRNA_deacylase  80 telkvPslFvEiGSteeeWkdedaaeavaeavlelleseeekekvlvgiGGgHYaprftklvletevavGhilskya 156
                                       t++ +PslF+E+GS +e+W+d++ aeava+ +l+l + + ++e+++vg+GG+HYaprf+++v++t +avGhi+s++a
  gi|336255342|ref|YP_004598449.1| 146 TDVGCPSLFAELGSGDEQWDDPAGAEAVARGILDLRDAKPHRERQVVGFGGNHYAPRFERVVRKTPWAVGHIASDWA 222
                                       ***************************************99************************************ PP

                                       GGG--HH.....HHHHHHHHH.T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                    tRNA_deacylase 157 leelkee.....vikqaleksegadvalidkkslkseqkeaieelleelgiev 204
                                       leel +      v+++a+e+s +a++al+d       + + +ee+le+lg+++
  gi|336255342|ref|YP_004598449.1| 223 LEELGHPtahrdVLEAAFEES-DAEIALLD------GEWPVLEEALEDLGYRI 268
                                       *999998888889999****9.********......77888888888888876 PP

>> DUF2201  VWA-like domain (DUF2201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.4e-05      0.12      48      82 ..     179     213 ..     170     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                           DUF2201  48 rlepaeklaelqltggGGTdlvpvlEavaklrPda 82 
                                        l++a+  +e q+ g+GG  ++p +E+v++++P a
  gi|336255342|ref|YP_004598449.1| 179 DLRDAKPHRERQVVGFGGNHYAPRFERVVRKTPWA 213
                                       566788899************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3350.04
//
Query:       gi|336255343|ref|YP_004598450.1|  [L=823]
Description: PAS/PAC sensor protein [Halopiger xanaduensis SH-6]
Scores for complete 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-43  148.2   7.3    1.7e-43  148.2   7.3    2.8  2  BAT         GAF and HTH_10 associated domain
    1.3e-41  141.3  12.3    1.2e-17   64.1   0.1    5.2  5  PAS_4       PAS fold
    1.1e-37  128.4   0.0      2e-12   47.2   0.0    3.5  3  PAS_9       PAS domain
    1.1e-34  118.8   0.0    1.9e-11   44.0   0.0    3.4  3  PAS         PAS fold
    2.9e-30  104.4   0.1    2.7e-11   43.6   0.0    3.6  3  PAS_3       PAS fold
    9.8e-17   60.5   0.1    2.4e-16   59.2   0.1    1.7  1  HTH_10      HTH DNA binding domain
    2.7e-11   43.2   2.5    6.6e-05   22.8   0.0    3.7  3  PAS_8       PAS domain
    1.8e-09   38.0   2.7    1.8e-09   38.0   2.7    2.6  2  GAF_2       GAF domain
    1.6e-06   28.8   0.0    5.7e-06   27.0   0.0    2.1  1  GAF         GAF domain
    2.3e-05   24.5   0.0       0.54   10.4   0.0    3.9  3  PAS_7       PAS fold
    0.00011   22.6   0.0     0.0004   20.7   0.0    2.0  1  GAF_3       GAF domain
     0.0051   16.9   0.0        2.3    8.4   0.0    3.2  3  PAS_11      PAS domain
     0.0062   16.5   0.0       0.87    9.5   0.0    2.7  2  MEKHLA      MEKHLA domain
  ------ inclusion threshold ------
      0.013   15.9   0.0      0.056   13.8   0.0    2.2  1  SCP2_2      Sterol carrier protein domain
      0.018   15.1   0.0       0.11   12.6   0.0    2.4  1  HTH_20      Helix-turn-helix domain
      0.081   12.4   0.0       0.45   10.0   0.0    2.1  2  CodY        CodY GAF-like domain
      0.087   12.9   0.0        0.9    9.6   0.0    2.6  3  SpoVT_C     Stage V sporulation protein T C-terminal, transcr
        0.1   12.4   0.3        2.5    7.9   0.1    2.8  2  HTH_30      PucR C-terminal helix-turn-helix domain
       0.13   11.8   1.0       0.59    9.7   0.0    2.7  2  Sigma70_r4  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.9      0.56   5.2e+02      51      94 ..     409     451 ..     377     483 .. 0.63
   2 !  148.2   7.3   1.8e-46   1.7e-43       1     155 [.     602     756 ..     602     757 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.56
                               BAT  51 dpeevrdaaedldavedvrvvseeddgtlleltvsgpslastla 94 
                                       d+ +  +   +l+  e + vv ++ d+t + +++  + + ++++
  gi|336255343|ref|YP_004598450.1| 409 DVSDRKARERELERLERLNVVVRTVDETMVAAET-REEIERAIV 451
                                       4455555555666666666666666666666665.343444443 PP

  == domain 2  score: 148.2 bits;  conditional E-value: 1.8e-46
                               BAT   1 DavveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddg 77 
                                       D+ veLe+e +d+ d+  +l a+++c ++++++ p +dg +++++tv+g  p+++rd+a++ +++e++r ++ ++d+
  gi|336255343|ref|YP_004598450.1| 602 DTAVELEFESTDRGDACIDLGARANCLLAVDHVLPLTDGAYVQYVTVAGIGPDRFRDLAAEQPGIEELRNIDVQGDE 678
                                       99*************************************************************************** PP

                               BAT  78 tlleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvarrererpvrtrref 154
                                       +++elt+++++++  la++G+++rs ++++gra+++ve +p+a+vR++v++++++ypd++Lv++r++e +v+t+++f
  gi|336255343|ref|YP_004598450.1| 679 SRWELTIRDSTFVDLLASYGARLRSKVVDRGRATVTVEASPDAAVRELVDTIRAAYPDTTLVSKRTVEGSVETPGDF 755
                                       ***************************************************************************** PP

                               BAT 155 r 155
                                       r
  gi|336255343|ref|YP_004598450.1| 756 R 756
                                       8 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.2   1.2e-07   0.00011       6      88 ..      38     122 ..      35     132 .. 0.82
   2 ?    0.9   0.0      0.56   5.3e+02      92     110 .]     145     163 ..     142     163 .. 0.87
   3 !   56.3   0.2   3.4e-18   3.2e-15       2     108 ..     180     287 ..     179     289 .. 0.97
   4 !   64.1   0.1   1.3e-20   1.2e-17       1     109 [.     305     414 ..     305     415 .. 0.98
   5 ?    1.5   0.3      0.37   3.5e+02      43     104 ..     437     501 ..     420     505 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.2e-07
                             PAS_4   6 dalavldpdgrvlyaNaaaaelfgappeellGktlaellpee..daarleralrrvlegeepiefleelllpgeerh 80 
                                        a+a+ld+ grv ++N  a +++g++ +e++G +++ ++pee  +a+r ++ l+r+  ++++ ++   +  +g +++
  gi|336255343|ref|YP_004598450.1|  38 HAVAMLDAAGRVAAWNDDANAVLGYDEAEIVGTSYRAFFPEEarAADRPDALLKRARIEGRAEDEGWRVCSDGNRCW 114
                                       5899**************************************99999999999999777766666555555777777 PP

                             PAS_4  81 yelrllPl 88 
                                       +   + P+
  gi|336255343|ref|YP_004598450.1| 115 VREVIAPI 122
                                       77777776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.56
                             PAS_4  92 sGevigvlvisrDiTerrr 110
                                       + +v+g+ ++++D Te+++
  gi|336255343|ref|YP_004598450.1| 145 DADVQGYGWFLHDRTEEHE 163
                                       5579************985 PP

  == domain 3  score: 56.3 bits;  conditional E-value: 3.4e-18
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                        + pd+l+++d+dg+++++N +  e+ g+++ el+   + e+  +e+++r+++ ++r le++e ++ +  ll+ +ge
  gi|336255343|ref|YP_004598450.1| 180 AAQPDILYAFDDDGNYIDWNDRVPEVTGYDDSELTELDPLEFIAPEHRDRIADSIQRILEEDEQVTVEADLLTkDGE 256
                                       678************************************************************************** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTer 108
                                       + +ye++   + +++G+v+g+ +++rDi++r
  gi|336255343|ref|YP_004598450.1| 257 RIPYEFNSAQITEDEGTVVGFTGVGRDISDR 287
                                       *****************************99 PP

  == domain 4  score: 64.1 bits;  conditional E-value: 1.3e-20
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       +++ pd+l++ d+d + + +N + +++ g++p++l G+++ e+  +ed++++ +a+rr l+++++i+ +  ll+ +g
  gi|336255343|ref|YP_004598450.1| 305 FEAQPDLLYAYDTDRNLIQWNDQLRRITGYDPDDLEGMSPLEFIAPEDREAIGDAVRRILTEGARITAEGRLLTsEG 381
                                       7899************************************************************************* PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       ++ +ye++  ++ d++G v+g+ +i+rD+++r+
  gi|336255343|ref|YP_004598450.1| 382 KRLPYEFNSARITDDEGNVLGFTGIGRDVSDRK 414
                                       *******************************98 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.37
                             PAS_4  43 llpeedaarleralrrvlegeepiefleelll....pgeerhyelrllPlrdesGevigvlvisrD 104
                                       ++ +e ++++era+  + +  ++++f+ + ++      e+r +e r    rd++   +gv++  +D
  gi|336255343|ref|YP_004598450.1| 437 MVAAETREEIERAIVDAFADADTYRFAVVGRFdaaaTAERRQWEPRTWAGRDADEI-DGVIGSYVD 501
                                       7778899*********************9999999999999999999888886655.888877766 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   4.7e-10   4.4e-07       3      92 ..      39     129 ..      37     133 .. 0.90
   2 !   46.9   0.1   2.8e-15   2.7e-12       8     104 .]     190     286 ..     183     286 .. 0.88
   3 !   47.2   0.0   2.2e-15     2e-12       7     104 .]     315     412 ..     309     412 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.7e-10
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwv 78 
                                       ++++ +  gr+  +N+ a+ +lGy+++e++g+s++ +f ++++a++r +a+l++ r     e+e   + ++g++ wv
  gi|336255343|ref|YP_004598450.1|  39 AVAMLDAAGRVAAWNDDANAVLGYDEAEIVGTSYRAFFPEEARAADRPDALLKRARIeGRAEDEGWRVCSDGNRCWV 115
                                       56777899******************************999999999999999999888889999999********* PP

                             PAS_9  79 lltaspvkdddgel 92 
                                       +  ++p++ ++g  
  gi|336255343|ref|YP_004598450.1| 116 REVIAPIWTAGGDS 129
                                       *******9998865 PP

  == domain 2  score: 46.9 bits;  conditional E-value: 2.8e-15
                             PAS_9   8 npdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvllta 82 
                                       ++dg+ +++N+ + +++Gy+  e+   +  +++  ++ ++ ++ ++++le+ +  + +ve +l +k+ge+++++++ 
  gi|336255343|ref|YP_004598450.1| 190 DDDGNYIDWNDRVPEVTGYDDSELTELDPLEFIapEHRDRIADSIQRILEEDE--QVTVEADLLTKDGERIPYEFNS 264
                                       59*******************************66666666666666666666..********************** PP

                             PAS_9  83 spvkdddgelvgiivilrDite 104
                                       + + +d+g++vg+ ++ rDi++
  gi|336255343|ref|YP_004598450.1| 265 AQITEDEGTVVGFTGVGRDISD 286
                                       ********************96 PP

  == domain 3  score: 47.2 bits;  conditional E-value: 2.2e-15
                             PAS_9   7 dnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvllt 81 
                                       +++d +++ +N++++r++Gy+p+++ g s  +++  ++ +   + +r++l +g     + e  l +++g++++++++
  gi|336255343|ref|YP_004598450.1| 315 YDTDRNLIQWNDQLRRITGYDPDDLEGMSPLEFIapEDREAIGDAVRRILTEGA--RITAEGRLLTSEGKRLPYEFN 389
                                       568889****************************55555555555555555555..********************* PP

                             PAS_9  82 aspvkdddgelvgiivilrDite 104
                                        +++ dd+g++ g+ +i rD+++
  gi|336255343|ref|YP_004598450.1| 390 SARITDDEGNVLGFTGIGRDVSD 412
                                       *********************96 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   3.3e-11   3.1e-08      13     101 ..      39     127 ..      35     129 .. 0.94
   2 !   37.2   0.0   2.5e-12   2.3e-09       2     113 .]     174     284 ..     173     284 .. 0.90
   3 !   44.0   0.0     2e-14   1.9e-11       4     113 .]     302     410 ..     299     410 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3.3e-11
                                       EEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEE CS
                               PAS  13 pifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfklrdgrpih 88 
                                       ++ ++D+ gr+  +N+ a+  lG+++ e++g s+  +++ee +a +++++l+++++   +++++  +++  dg   +
  gi|336255343|ref|YP_004598450.1|  39 AVAMLDAAGRVAAWNDDANAVLGYDEAEIVGTSYRAFFPEEARAaDRPDALLKRARIEGRAEDEGWRVCS-DGNRCW 114
                                       7889***************************************9**************************.****** PP

                                       EEEEEEEEEETTE CS
                               PAS  89 levraspvrdagg 101
                                       ++   +p+  agg
  gi|336255343|ref|YP_004598450.1| 115 VREVIAPIWTAGG 127
                                       9988888776665 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 2.5e-12
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +l++++ + pd   + D dg+ + +N+   e +G++ +e+     l++i +e+++ + +   q++++  e+ ++e +
  gi|336255343|ref|YP_004598450.1| 174 FLESVFAAQPDILYAFDDDGNYIDWNDRVPEVTGYDDSELTELDPLEFIAPEHRD-RIADSIQRILEEDEQVTVEAD 249
                                       567788899****************************************998665.666666777777888888998 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       + ++dg+ i+ e + + +++ +g++ gf gv+rdi
  gi|336255343|ref|YP_004598450.1| 250 LLTKDGERIPYEFNSAQITEDEGTVVGFTGVGRDI 284
                                       9999******************************8 PP

  == domain 3  score: 44.0 bits;  conditional E-value: 2e-14
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                       ++i+e+ pd   + D d + + +N+  ++++G++++++ g s l++i +ed++   +++++ l +g + +a+ + ++
  gi|336255343|ref|YP_004598450.1| 302 ESIFEAQPDLLYAYDTDRNLIQWNDQLRRITGYDPDDLEGMSPLEFIAPEDREAIGDAVRRILTEGARITAEGRLLT 378
                                       789**************************************************999999999999999999999999 PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                          g+  + e + + ++d +g++lgf g++rd+
  gi|336255343|ref|YP_004598450.1| 379 S-EGKRLPYEFNSARITDDEGNVLGFTGIGRDV 410
                                       9.******************************7 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.4e-05     0.032       3      80 ..      51     127 ..      49     132 .. 0.77
   2 !   42.2   0.0     8e-14   7.6e-11       2      88 ..     196     280 ..     195     281 .. 0.96
   3 !   43.6   0.0   2.8e-14   2.7e-11       2      88 ..     322     406 ..     321     407 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervre.alqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                        +++    +lGy+++e+ g+  s++ +   e r+  r  al + ++  ++ e e  +++ dG  +wv++ + +i+  
  gi|336255343|ref|YP_004598450.1|  51 AWNDDANAVLGYDEAEIVGT--SYRAFFPEEARAADRPdALLKRARIEGRAEDEGWRVCSDGNRCWVREVIAPIWTA 125
                                       69******************..77777766665555540333444445568999999***************99766 PP

                             PAS_3  79 ng 80 
                                        g
  gi|336255343|ref|YP_004598450.1| 126 GG 127
                                       55 PP

  == domain 2  score: 42.2 bits;  conditional E-value: 8e-14
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       i +++rv e++Gy+++el++   + l+++ pe r+r+ +++q++l+++e++++e  +++kdGe +  e     i  +
  gi|336255343|ref|YP_004598450.1| 196 IDWNDRVPEVTGYDDSELTEL--DPLEFIAPEHRDRIADSIQRILEEDEQVTVEADLLTKDGERIPYEFNSAQITED 270
                                       89*******************..*******************************************99888888899 PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g +v + gv
  gi|336255343|ref|YP_004598450.1| 271 EGTVVGFTGV 280
                                       9999999997 PP

  == domain 3  score: 43.6 bits;  conditional E-value: 2.8e-14
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       i ++++ ++i+Gy+p++l+g   s l+++ peDre + +a+ ++l++g++++ e R+++  G+    e     i d+
  gi|336255343|ref|YP_004598450.1| 322 IQWNDQLRRITGYDPDDLEGM--SPLEFIAPEDREAIGDAVRRILTEGARITAEGRLLTSEGKRLPYEFNSARITDD 396
                                       78*******************..*****************************************99998887778** PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g+++ + g+
  gi|336255343|ref|YP_004598450.1| 397 EGNVLGFTGI 406
                                       ****999986 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.1   2.6e-19   2.4e-16       1      53 []     763     816 ..     763     816 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 2.6e-19
                            HTH_10   1 LTdkqlevlklAyemGYFdyP.RrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LTdkq+++l +Ay  GYF++P R+ ++ ++A++lGI+++t+++hLr a+ kl+e
  gi|336255343|ref|YP_004598450.1| 763 LTDKQRTALEAAYYGGYFEWPtRNSDATAIADRLGIARQTFHQHLRVAQAKLLE 816
                                       9********************88899*************************985 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.075        71      13      44 ..      39      71 ..      35      92 .. 0.77
   2 !   14.5   0.2     3e-05     0.028       2      59 ..     174     233 ..     173     243 .. 0.78
   3 !   22.8   0.0     7e-08   6.6e-05       4      46 ..     302     345 ..     299     366 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.075
                             PAS_8 13 giavvdlgdrivdvNqaalellGys.adlkgel 44
                                      ++a++d+ +r+  +N+ a   lGy+ a++ g  
  gi|336255343|ref|YP_004598450.1| 39 AVAMLDAAGRVAAWNDDANAVLGYDeAEIVGTS 71
                                      7889995556*************9988777654 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3e-05
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg.qllpvlrplleda 59 
                                       +l+++f + pd +  +d++++ +d+N++  e +Gy+  +l + +    + p++r+ ++d 
  gi|336255343|ref|YP_004598450.1| 174 FLESVFAAQPDILYAFDDDGNYIDWNDRVPEVTGYDdSELTELDPLeFIAPEHRDRIADS 233
                                       89************9996666***************777777555567777777777733 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 7e-08
                             PAS_8   4 ralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg 46 
                                       +++fe+ pd +  +d++++++++N++  +++Gy+ +dl g+   
  gi|336255343|ref|YP_004598450.1| 302 ESIFEAQPDLLYAYDTDRNLIQWNDQLRRITGYDpDDLEGMSPL 345
                                       79**********9998889***************9999886654 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       7.9   7.4e+03      27      27 ..      62      62 ..      28     127 .. 0.46
   2 !   38.0   2.7   1.9e-12   1.8e-09       2     137 ..     441     590 ..     440     591 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.9
                                      E CS
                             GAF_2 27 l 27
                                      +
  gi|336255343|ref|YP_004598450.1| 62 Y 62
                                      1 PP

  == domain 2  score: 38.0 bits;  conditional E-value: 1.9e-12
                                       HHHHHHHHHHHHHHHHSS...EEEEEEE-TTS-EEEE.......EEEES-TTSTT-S-B--............-TTH CS
                             GAF_2   2 adleelldlvldelvelg.aalgyillvdddgglrla.......awgeaeeefgaaldrpl............gegl 58 
                                        + ee+ ++++d+ ++ +  ++++++  d++     +       +w+++++   + +  +             +++l
  gi|336255343|ref|YP_004598450.1| 441 ETREEIERAIVDAFADADtYRFAVVGRFDAAAT--AErrqweprTWAGRDADEIDGVIGSYvdppaaaadrsdASSL 515
                                       578999999999999986699999999996544..223345555555555555555544331111221111112223 PP

                                       HHHHHHHTS-EEES-GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHH CS
                             GAF_2  59 vgealrtgrpvilndleedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiai 135
                                        ++a+r  r++     e++  +++  a+++ +++ ++vP++++gr +Gvl+++a++  af ++++e+L+e++++i+ 
  gi|336255343|ref|YP_004598450.1| 516 EADAVRRYRSLR----ESEFEPWRRDAREHEYGAVAVVPIVAGGRSFGVLVVAAEEATAFADREREVLQEFGGTIGH 588
                                       334444433222....2345555555899999999*****************************************9 PP

                                       HH CS
                             GAF_2 136 ai 137
                                       a+
  gi|336255343|ref|YP_004598450.1| 589 AV 590
                                       97 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0     6e-09   5.7e-06      66     132 ..     524     589 ..     432     590 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 6e-09
                                       TGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHH CS
                               GAF  66 dstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvava 132
                                       +s +++ f +  +r+ ++++++ +++vvP+v++g+ +G+lv+  + +  f + e+e+lq+++  ++ a
  gi|336255343|ref|YP_004598450.1| 524 RSLRESEFEP--WRRDAREHEYGAVAVVPIVAGGRSFGVLVVAAEEAtAFADREREVLQEFGGTIGHA 589
                                       2447788888..9999****************************66668*************999876 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00057      0.54       6      45 ..      38      76 ..      36     100 .. 0.85
   2 ?    1.1   0.0      0.46   4.3e+02      10      36 ..     188     214 ..     184     290 .. 0.81
   3 !    7.8   0.0    0.0037       3.5      10      41 ..     314     344 ..     309     417 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00057
                             PAS_7  6 qGisvfDadlrLvawNrrylelldlpeelvqvgvpleell 45
                                      ++++++Da++r+ awN+    +l++ e  + vg+++++++
  gi|336255343|ref|YP_004598450.1| 38 HAVAMLDAAGRVAAWNDDANAVLGYDEAEI-VGTSYRAFF 76
                                      5789*********************99988.888887765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.46
                             PAS_7  10 vfDadlrLvawNrrylelldlpeelvq 36 
                                        fD d++ + wN+r+ e+ ++ ++ + 
  gi|336255343|ref|YP_004598450.1| 188 AFDDDGNYIDWNDRVPEVTGYDDSELT 214
                                       699999********9999998887665 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0037
                             PAS_7  10 vfDadlrLvawNrrylelldlpeelvqvgvpl 41 
                                        +D d +L+ wN++ +++ ++ ++ +  g++ 
  gi|336255343|ref|YP_004598450.1| 314 AYDTDRNLIQWNDQLRRITGYDPDDL-EGMSP 344
                                       69*******************99998.55553 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   4.3e-07    0.0004      78     127 ..     541     590 ..     507     592 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.3e-07
                             GAF_3  78 lpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                       ++ +a+ +vP+vag +++Gvl++a  +  af ++++e l+++++ i+ a+
  gi|336255343|ref|YP_004598450.1| 541 HEYGAVAVVPIVAGGRSFGVLVVAAEEATAFADREREVLQEFGGTIGHAV 590
                                       55678889**************************************9886 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       0.5   4.8e+02       9      47 ..      44      79 ..      40      87 .. 0.82
   2 ?    3.0   0.0      0.11   1.1e+02      10      65 ..     191     243 ..     187     264 .. 0.85
   3 !    8.4   0.0    0.0024       2.3      10      87 ..     317     390 ..     312     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.5
                            PAS_11  9 didgkIisvDtsaLrasfslglekeelvgrsiydLchpq 47
                                      d  g++ + +     a+ +lg+ + e+vg+s+ +++ ++
  gi|336255343|ref|YP_004598450.1| 44 DAAGRVAAWND---DANAVLGYDEAEIVGTSYRAFFPEE 79
                                      66677777777...788999**************98655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                            PAS_11  10 idgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissnge 65 
                                        dg+ i+ +    r + ++g+ ++el+++   +++ p+++ ++++  + ++++ ++
  gi|336255343|ref|YP_004598450.1| 191 DDGNYIDWND---RVPEVTGYDDSELTELDPLEFIAPEHRDRIADSIQRILEEDEQ 243
                                       5788899999...9999*********************************944443 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0024
                            PAS_11  10 idgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktk 86 
                                       +d + i+ +         +g+  ++l g+s  +++ p+d++ + ++ r ++ ++g+  ++  RL +s++k +    +
  gi|336255343|ref|YP_004598450.1| 317 TDRNLIQWND---QLRRITGYDPDDLEGMSPLEFIAPEDREAIGDAVRRIL-TEGARITAEGRLLTSEGKRLPYEFN 389
                                       5556666666...5556789*******************************.*****9999****999998776666 PP

                            PAS_11  87 s 87 
                                       s
  gi|336255343|ref|YP_004598450.1| 390 S 390
                                       5 PP

>> MEKHLA  MEKHLA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00092      0.87      55     121 ..      53     120 ..      51     140 .. 0.80
   2 ?    3.8   0.0     0.054        50      28     133 ..     299     402 ..     280     406 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00092
                            MEKHLA  55 Nqaaldllettweeltdlpsrksaepeekee.R.ealLekvaeqgfvenysGvrisstGrrfsienavv 121
                                       N  a ++l ++ +e++ ++ r  + +e++++ R +alL++++ +g +e  +G r+ s+G r +++++++
  gi|336255343|ref|YP_004598450.1|  53 NDDANAVLGYDEAEIVGTSYRAFFPEEARAAdRpDALLKRARIEGRAE-DEGWRVCSDGNRCWVREVIA 120
                                       6778889999999***********988854435267889999999976.89**************9874 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.054
                            MEKHLA  28 elakaLfe.apfavlshslkadpvfnyaNqaaldllettweeltdlpsrksaepeekeeRealLekvaeqgfvenys 103
                                       +l++++fe +p+ + +++++    ++  N +  ++  ++ ++l  ++  + + pe++e+     +++ ++g   + +
  gi|336255343|ref|YP_004598450.1| 299 ALTESIFEaQPDLLYAYDTD--RNLIQWNDQLRRITGYDPDDLEGMSPLEFIAPEDREAIGDAVRRILTEGARITAE 373
                                       55566666344455555543..334444666667777788888888766666668888889**************** PP

                            MEKHLA 104 GvrisstGrrfsienavvWkvldeegkahG 133
                                       G  ++s+G+r+ +e   + +++d+eg++ G
  gi|336255343|ref|YP_004598450.1| 374 GRLLTSEGKRLPYEFNSA-RITDDEGNVLG 402
                                       ***********9986655.67777777666 PP

>> SCP2_2  Sterol carrier protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     6e-05     0.056      45      93 ..      13      57 ..       6      79 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6e-05
                                      EECSCE-SCE.EEEEHHHHHHHHTTSS-HHHHHHTTSSBSSHHHHHHHH CS
                            SCP2_2 45 evgkeeeadadltldiqtLaqlllGyrsaseLarlgriegaeealatld 93
                                       +g+e+ ++ d+tld+++L++l+ G++ ++ L ++gr+ +     + ++
  gi|336255343|ref|YP_004598450.1| 13 NDGDETASPTDVTLDARDLTALVSGHA-VAMLDAAGRVAAWN---DDAN 57
                                      34444434559***************9.99********9333...3333 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012      0.11      20      47 ..     782     809 ..     754     817 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                       STCTTB-HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_20  20 araegltaselaerldlskntlsyHLrv 47 
                                       ++ +   a+++a+rl+++++t ++HLrv
  gi|336255343|ref|YP_004598450.1| 782 WPTRNSDATAIADRLGIARQTFHQHLRV 809
                                       555556689******************8 PP

>> CodY  CodY GAF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.6   1.5e+03      38      88 ..     265     321 ..     234     327 .. 0.71
   2 ?   10.0   0.0   0.00048      0.45     104     148 ..     540     586 ..     525     604 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.6
                                       EEEEETTSBEEEEE-S...SSSS-HHHHHHHHHTBSTHHHHHH...HHT-SSSEEEE CS
                              CodY  38 vyivsrkgklLGyalk...ekiendrvkqlleekkfpeeytek...llnvketeanl 88 
                                       + i + +g ++G++      +  n r ++l eek ++e++ e+   ll  ++t  nl
  gi|336255343|ref|YP_004598450.1| 265 AQITEDEGTVVGFTGVgrdISDRNARERELHEEKALTESIFEAqpdLLYAYDTDRNL 321
                                       557777888888875532244455566678999999988765322266666666665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00048
                                       GGSSSEEEEEEEEETTEEEEEEEEEESS.S--THHHH.HHHHHHHHH CS
                              CodY 104 kfkkglttivPiegggeRLGtlilarvd.kefedddl.iLaeyaaTv 148
                                       + + g +++vPi++gg+  G l++a ++ + f d ++ +L e++ T+
  gi|336255343|ref|YP_004598450.1| 540 EHEYGAVAVVPIVAGGRSFGVLVVAAEEaTAFADREReVLQEFGGTI 586
                                       5677899****************987652579996544******996 PP

>> SpoVT_C  Stage V sporulation protein T C-terminal, transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.5   2.4e+03      70      89 ..     107     126 ..      87     132 .. 0.65
   2 ?   -2.6   0.0       5.5   5.2e+03      44      63 ..     229     248 ..     226     270 .. 0.74
   3 ?    9.6   0.0   0.00095       0.9      71     115 ..     537     580 ..     513     589 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.5
                           SpoVT_C  70 veeekeeysaqviaPIiaeG 89 
                                        +++++ +  +viaPI ++G
  gi|336255343|ref|YP_004598450.1| 107 CSDGNRCWVREVIAPIWTAG 126
                                       4677777888******8654 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.5
                           SpoVT_C  44 eiskeleklmeerktvlakk 63 
                                       +i +++++++ee+++v++++
  gi|336255343|ref|YP_004598450.1| 229 RIADSIQRILEEDEQVTVEA 248
                                       78899999999999987764 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00095
                           SpoVT_C  71 eeekeeysaqviaPIiaeGdviGaVillskeekkklgelekklae 115
                                       + +++ey a +++PI+a G + G+ ++ ++e ++ + + e ++++
  gi|336255343|ref|YP_004598450.1| 537 DAREHEYGAVAVVPIVAGGRSFGVLVVAAEEATA-FADREREVLQ 580
                                       55667999***************99999888776.7888877765 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 ?    1.1   0.0      0.38   3.6e+02      35      53 ..     327     345 ..     325     348 .. 0.82
   2 ?    7.9   0.1    0.0027       2.5      12      35 ..     786     809 ..     782     814 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.38
                                       HHHHHHS--TTSHHHHHHH CS
                            HTH_30  35 rieellgldlddpddrlaL 53 
                                       ++++++g+d+dd + +  L
  gi|336255343|ref|YP_004598450.1| 327 QLRRITGYDPDDLEGMSPL 345
                                       6899********9887655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0027
                                       TT-HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_30  12 ggnisatAkaLhvHrnTlryRLrr 35 
                                       + +++a A++L++ r+T+++ Lr 
  gi|336255343|ref|YP_004598450.1| 786 NSDATAIADRLGIARQTFHQHLRV 809
                                       7899****************9985 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2       2.5   2.4e+03       7      14 ..     573     580 ..     572     581 .. 0.88
   2 ?    9.7   0.0   0.00062      0.59       4      48 ..     762     814 ..     761     816 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.5
                                       HHHHHHHH CS
                        Sigma70_r4   7 ererevle 14 
                                       +rerevl+
  gi|336255343|ref|YP_004598450.1| 573 DREREVLQ 580
                                       8*****97 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00062
                                       HS-HHHHHHHHHHH........TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf........geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                        L++++r+ le  +         ++     I++rlgi r + +q+++ A  kL
  gi|336255343|ref|YP_004598450.1| 762 ALTDKQRTALEAAYyggyfewpTRNSDATAIADRLGIARQTFHQHLRVAQAKL 814
                                       69************9**9999988888899**************999988777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (823 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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):              19  [number of targets reported over threshold]
# CPU time: 0.69u 0.25s 00:00:00.94 Elapsed: 00:00:00.41
# Mc/sec: 6069.10
//
Query:       gi|336255344|ref|YP_004598451.1|  [L=491]
Description: hypothetical protein Halxa_3967 [Halopiger xanaduensis SH-6]
Scores for 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  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3577.36
//
Query:       gi|336255345|ref|YP_004598452.1|  [L=314]
Description: Na+/Ca+ antiporter, CaCA family [Halopiger xanaduensis SH-6]
Scores for 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-45  152.8  42.3    3.5e-25   88.7  16.6    2.0  2  Na_Ca_ex         Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4  17.6   8.7e-24   1.6e-19       3     150 ..       9     148 ..       7     149 .. 0.92
   2 !   88.7  16.6     2e-29   3.5e-25       4     149 ..     174     312 ..     172     314 .] 0.93

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 8.7e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       +vl+++++++++ +a++lv  a  +a  +g+  +++G+t++A+++++pEl++s+i al+ + d+++g+++Gsni+n+
  gi|336255345|ref|YP_004598452.1|   9 VVLLAAGIVALYGGAELLVAGAGRLALGIGLRAATVGVTVIAFATTAPELFVSTIGALNVSSDIGLGTIVGSNIANI 85 
                                       689***********************999************************************************ PP

                                       HTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                       +lv+G++ali++l+v +  + +++++++l+a+ll++l +         g++ +leg+++ll+ a +++++l
  gi|336255345|ref|YP_004598452.1|  86 GLVLGVSALIKPLSVTEIVVRRHVPFMVLAAILLVALGAN--------GTIGRLEGAIFLLVLAGFTAYLL 148
                                       ************9999999999998877777777443333........9**************99999876 PP

  == domain 2  score: 88.7 bits;  conditional E-value: 2e-29
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnll 80 
                                       +l++ +ll+++v++ +l+   + + + lg+s+ v+Glt+lAlg+slpEl++s + a++ge++ aignv+Gsni n+l
  gi|336255345|ref|YP_004598452.1| 174 ALVLGGLLVLVVGSRWLITGGTGLLSALGVSELVIGLTVLALGTSLPELAASAVGAVRGETEFAIGNVVGSNIYNIL 250
                                       678899*********************************************************************** PP

                                       THHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  81 lviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvls 149
                                        v+G++ali+++ +  ++l ++l++++ ++++l++ ++ +       ++lt+l+g++l++ Y+++++l+
  gi|336255345|ref|YP_004598452.1| 251 AVLGIVALITPIEITASTLRFELPIMVAFTVVLVG-MMGYG------RKLTRLDGAALVAGYVVFIYLL 312
                                       ************99999******998888888866.44434......9******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); 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: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2552.24
//
Query:       gi|336255346|ref|YP_004598453.1|  [L=271]
Description: Shikimate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-27   94.3   0.0    9.2e-27   93.1   0.0    1.6  1  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
    1.9e-12   47.4   0.0    3.1e-12   46.7   0.0    1.2  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    5.2e-12   45.3   1.0    1.2e-11   44.2   1.0    1.7  1  SDH_C            Shikimate 5'-dehydrogenase C-terminal domain
    8.7e-06   25.2   0.0    1.6e-05   24.3   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00016   21.3   0.1    0.00027   20.6   0.1    1.3  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
    0.00017   22.1   0.1     0.0003   21.3   0.1    1.4  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0013   18.3   0.7      0.003   17.0   0.3    1.6  2  adh_short        short chain dehydrogenase
     0.0021   18.3   0.1     0.0036   17.5   0.1    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.006   15.9   0.0       0.12   11.7   0.0    2.2  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
  ------ inclusion threshold ------
       0.01   16.1   0.6      0.037   14.3   0.6    2.0  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.014   14.7   0.0      0.018   14.3   0.0    1.1  1  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
      0.016   14.9   0.1      0.024   14.3   0.1    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.017   15.0   0.2      0.025   14.5   0.2    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.025   15.0   0.0      0.041   14.3   0.0    1.3  1  NAD_binding_7    Putative NAD(P)-binding
       0.03   13.7   0.7      0.059   12.7   0.4    1.6  2  ThiF             ThiF family
      0.033   13.5   0.3      0.052   12.8   0.3    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.034   13.4   0.1      0.045   13.0   0.1    1.2  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.036   14.1   0.0       0.06   13.4   0.0    1.3  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
       0.14   12.1   0.2       0.31   11.0   0.2    1.6  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
       0.32   10.0   1.3       0.65    9.0   0.8    1.6  2  GIDA             Glucose inhibited division protein A


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 !   93.1   0.0     1e-29   9.2e-27       1      83 []       8      89 ..       8      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 1e-29
                                      EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT- CS
                    Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigA 79
                                      ++Gnp+ hSlSP +h+aa+++l+++++y++fe ++d+le+a+e++ alg++GlnvTiPfK++++++++  ++ A++igA
  gi|336255346|ref|YP_004598453.1|  8 LLGNPVGHSLSPPMHEAAYDELDIDARYVTFEPDPDDLEDAIEGAAALGVTGLNVTIPFKQDALAVVE-PDDLAARIGA 85
                                      68*****************************************************************7.********** PP

                                      -SEE CS
                    Shikimate_dh_N 80 vNti 83
                                      vNti
  gi|336255346|ref|YP_004598453.1| 86 VNTI 89
                                      ***8 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   3.5e-15   3.1e-12       9      84 ..     119     191 ..     111     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 3.5e-15
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SS CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisata 84 
                                       sl++++++++GaG  ++ +a  L+++g++ v +aNRt ++a++la+e+ ++  +   le+l+ell++adv++ at+
  gi|336255346|ref|YP_004598453.1| 119 SLEDARAVVVGAGGAGRAIAFGLADAGAT-VDIANRTESKAHDLADEVPDA--TGYGLENLEELLSDADVLVNATS 191
                                       799**************************.******************777..899******************97 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 !   44.2   1.0   1.3e-14   1.2e-11       1      31 []     238     268 ..     238     268 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.3e-14
                                       HHHHHHHHHHHHHHHHHS----HHHHHHHHH CS
                             SDH_C   1 GLgMLveQgaeqFelWTGrepPvevMreall 31 
                                       G +ML++Qg+e+Fe+WTG ++Pv++M eal+
  gi|336255346|ref|YP_004598453.1| 238 GAWMLLYQGVEAFERWTGWDAPVDAMNEALR 268
                                       789**************************97 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 !   24.3   0.0   1.8e-08   1.6e-05      27     100 ..     113     191 ..      96     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.8e-08
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.....CHHHHTCEECSHHHHHHH-SEEEE- CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.....eeeelgvelvsleellaesDivslh 98 
                                       ++    +l++ +  ++G+G  G+a+a  l+  g+ v + +r+++k +       +++g+ l++leell+++D+++++
  gi|336255346|ref|YP_004598453.1| 113 QSDATLSLEDARAVVVGAGGAGRAIAFGLADAGATVDIANRTESKAHdladeVPDATGYGLENLEELLSDADVLVNA 189
                                       555667899*********************************99888776555667889999************987 PP

                                       S- CS
                      2-Hacid_dh_C  99 lp 100
                                       + 
  gi|336255346|ref|YP_004598453.1| 190 TS 191
                                       65 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 !   20.6   0.1     3e-07   0.00027       2      66 ..     120     188 ..     119     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3e-07
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHH....TT-EEEEHHHHHHT-SEEEE CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAke....egfevltvaeavkkadvvmi 66 
                                       l++ + +v+G G  G+a a  l d+g  v +++r++sk  + A e    +g+   +++e+ ++adv+++
  gi|336255346|ref|YP_004598453.1| 120 LEDARAVVVGAGGAGRAIAFGLADAGATVDIANRTESKAHDLADEvpdaTGYGLENLEELLSDADVLVN 188
                                       6788899******************************9998886433337999999*********9875 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 !   21.3   0.1   3.3e-07    0.0003       4      73 ..     127     194 ..     124     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.3e-07
                                       EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....-EEECECHHHHHHH-SEEEE-S-HHH CS
                     F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....vkvtavdneeaaeeadvvvlavkped 73 
                                       ++GaG  g+a+a gl+ ag     + +a +r+++ka  la+e+           + ee++++adv+v a    +
  gi|336255346|ref|YP_004598453.1| 127 VVGAGGAGRAIAFGLADAG---ATVDIA-NRTESKAHDLADEVPdatgY--GLENLEELLSDADVLVNATSVGM 194
                                       67*****************...****88.*************9754222..22357889999999998876655 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.3   3.4e-06     0.003       3      47 ..     125     168 ..     123     174 .. 0.91
   2 ?   -1.5   0.0       1.6   1.4e+03      70      90 ..     175     195 ..     166     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-06
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee 47 
                                       ++v+Ga+ G Graia  la +Ga+v +++r+e+k++ +a+e+ ++
  gi|336255346|ref|YP_004598453.1| 125 AVVVGAG-GAGRAIAFGLADAGATVDIANRTESKAHDLADEVPDA 168
                                       7889987.*******************************998765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                                       HHHHHHSSESEEEE---SS-- CS
                         adh_short  70 kavkklgkldvLvnNAGitgs 90 
                                       + ++ l   dvLvn +++   
  gi|336255346|ref|YP_004598453.1| 175 NLEELLSDADVLVNATSVGME 195
                                       556667788999998888433 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   0.1     4e-06    0.0036       4      60 ..     127     187 ..     124     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4e-06
                                       EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT....EEE-SSHHHHHHHCSEEE CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg....akaaesieelvasldvvi 60 
                                       ++G G  G+ +a  l++ag +v + nrt++k+ +l++e       ++e++eel++++dv +
  gi|336255346|ref|YP_004598453.1| 127 VVGAGGAGRAIAFGLADAGATVDIANRTESKAHDLADEVpdatGYGLENLEELLSDADVLV 187
                                       79***********************************988877888999999999998765 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 !   11.7   0.0   0.00013      0.12      30      73 ..     116     158 ..      86     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                       CT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCH CS
                     THF_DHG_CYH_C  30 tgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdl 73 
                                       ++ +le++++vvvG++   g+++a+ L+ ++atV ++++  ++ 
  gi|336255346|ref|YP_004598453.1| 116 ATLSLEDARAVVVGAGG-AGRAIAFGLADAGATVDIANRTESKA 158
                                       4578999*******997.5****************998654333 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 ?   14.3   0.6   4.1e-05     0.037       2      78 ..     126     191 ..     125     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-05
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SS CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsp 78 
                                       +++GaG+ G+a+a  la+ +     + +a r+++k++ la+++          +    e  L++ll+++d++vn++ 
  gi|336255346|ref|YP_004598453.1| 126 VVVGAGGAGRAIAFGLADAGAT---VDIANRTESKAHDLADEV-------PDATGYGLEN-LEELLSDADVLVNATS 191
                                       79*****************986...**********99998753.......4445666666.8889999999999864 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 ?   14.3   0.0     2e-05     0.018     154     234 ..     112     190 ..      81     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                       Pyr_redox_3 154 skvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvl 230
                                        + ++   +++ + vV+G++  +  +A+ l+++ga+V ++ r+++  ++ +d       +  ++leel++    +vl
  gi|336255346|ref|YP_004598453.1| 112 EQSDATLSLEDARAVVVGAGGAGRAIAFGLADAGATVDIANRTESKAHDLADEVPDATGYGLENLEELLSDA--DVL 186
                                       444555578999******************************997666667777777777777777777643..555 PP

                       Pyr_redox_3 231 fnae 234
                                        na+
  gi|336255346|ref|YP_004598453.1| 187 VNAT 190
                                       5554 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   0.1   2.7e-05     0.024       2      37 ..     126     162 ..     125     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHH CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr.rlealk 37 
                                       +++GaG+ G+ +a  La aga+v + +r++ ++ +l 
  gi|336255346|ref|YP_004598453.1| 126 VVVGAGGAGRAIAFGLADAGATVDIANRTEsKAHDLA 162
                                       69**************************996665555 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 ?   14.5   0.2   2.8e-05     0.025       3      44 ..     126     167 ..     124     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.8e-05
                                       EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44 
                                        v+GaG  G+ ia  +a ag +V + +++e+++++ ++++ +
  gi|336255346|ref|YP_004598453.1| 126 VVVGAGGAGRAIAFGLADAGATVDIANRTESKAHDLADEVPD 167
                                       69**************************99999988877655 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 ?   14.3   0.0   4.6e-05     0.041       3      70 ..     118     191 ..     116     208 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-05
                     NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele......elvklaeeelekdlegadlviaatd 70 
                                       l l++ + +vvG+G  +   +  l++aga+v +   + +++++      +   +  e+le+ l++ad+++ at+
  gi|336255346|ref|YP_004598453.1| 118 LSLEDARAVVVGAGGAGRAIAFGLADAGATVDIANRTESKAHDladevpDATGYGLENLEELLSDADVLVNATS 191
                                       6799****************************988883222223332223333445667888999999998886 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   6.6e-05     0.059      11      42 ..     115     146 ..     105     151 .. 0.86
   2 ?   -2.7   0.0       3.4   3.1e+03     101     117 ..     175     190 ..     165     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.6e-05
                                       HHHHHHHTSEEEEE--SHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  11 dgqekLrdskvllvGaGglGsellknLalsGv 42 
                                       d    L+d++ ++vGaGg G  ++  La +G 
  gi|336255346|ref|YP_004598453.1| 115 DATLSLEDARAVVVGAGGAGRAIAFGLADAGA 146
                                       667789**********************9995 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.4
                                       CS-HHHHTT-SEEEEES CS
                                       xxxxxxxxxxxxxxxxx RF
                              ThiF 101 tvleellesvDlVvdal 117
                                       + leell+++D+ v+a+
  gi|336255346|ref|YP_004598453.1| 175 N-LEELLSDADVLVNAT 190
                                       4.6899*******9996 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   0.3   5.8e-05     0.052      26     101 ..     120     192 ..     114     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                                       B---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---B CS
                       AlaDh_PNT_C  26 vepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvli 101
                                        e a+ +v+G+G aG + +   +  ga+V + +  +++++ l     ++ ++     e+l+e +++adv++ +  +
  gi|336255346|ref|YP_004598453.1| 120 LEDARAVVVGAGGAGRAIAFGLADAGATVDIANRTESKAHDLA---DEVPDATGYGLENLEELLSDADVLVNATSV 192
                                       5689***********9877777788888877776666655555...55445578889999*********9988766 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 ?   13.0   0.1     5e-05     0.045       3      30 ..     125     152 ..      85     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5e-05
                                       EEEE--SHHHHHHHHHHHHHTS-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   3 vvviGgGpAGlaaaltlaqagakvtlve 30 
                                        vv+G+G AG a a  la aga v + +
  gi|336255346|ref|YP_004598453.1| 125 AVVVGAGGAGRAIAFGLADAGATVDIAN 152
                                       5788888888888888888888777764 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 ?   13.4   0.0   6.7e-05      0.06      23      87 ..     122     191 ..     107     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-05
                                       TSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCT.....T-EE--HHHCTTT-SEEEE-SS CS
                     AdoHcyase_NAD  23 GkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaame.....GfevvtleevvkkadivvtttG 87 
                                          avv+G G  G+  a  l  +Ga v +++     a   a e     G+ + +lee++++ad++v +t 
  gi|336255346|ref|YP_004598453.1| 122 DARAVVVGAGGAGRAIAFGLADAGATVDIANRTESKAHDLADEvpdatGYGLENLEELLSDADVLVNATS 191
                                       4579*************************8877777766553333344******************9985 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 ?   11.0   0.2   0.00035      0.31       3      40 ..     126     163 ..     124     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                                       EEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHH CS
                    NAD_Gly3P_dh_N   3 avlGaGswGtalAkvlaenghevrlwvreeelieeine 40 
                                        v+GaG  G a+A  la++g +v +  r e  ++++ +
  gi|336255346|ref|YP_004598453.1| 126 VVVGAGGAGRAIAFGLADAGATVDIANRTESKAHDLAD 163
                                       599***********************999988887765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.2   1.1e+03      65      94 ..      87     116 ..      72     121 .. 0.83
   2 ?    9.0   0.8   0.00073      0.65       3      28 ..     126     151 ..     124     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.2
                                       HHHHHHEEEEEEESTTS-CCC-EEEEEE-H CS
                              GIDA  65 kaadkagiqfrilNrskGpavralraqvdr 94 
                                       +++d +g +    N+  G a ralr q d 
  gi|336255346|ref|YP_004598453.1|  87 NTIDFTGDHPTGHNTDAGGALRALREQSDA 116
                                       56777888888899***********99986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00073
                                       EEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLi 28 
                                       +V+G+G AG + A+ +a +Ga v + 
  gi|336255346|ref|YP_004598453.1| 126 VVVGAGGAGRAIAFGLADAGATVDIA 151
                                       8*********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2036.45
//
Query:       gi|336255347|ref|YP_004598454.1|  [L=254]
Description: hypothetical protein Halxa_3970 [Halopiger xanaduensis SH-6]
Scores for 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   44.0   0.2    4.8e-11   43.1   0.2    1.4  1  HHH_5            Helix-hairpin-helix domain
    2.6e-05   24.5   0.0    7.8e-05   22.9   0.0    1.7  1  DUF4332          Domain of unknown function (DUF4332)
     0.0018   18.1   0.0     0.0028   17.4   0.0    1.2  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0034   17.6   0.0     0.0051   17.0   0.0    1.2  1  Cdd1             Pathogenicity locus
     0.0041   17.1  38.1     0.0041   17.1  38.1    2.6  2  Trypan_PARP      Procyclic acidic repetitive protein (PARP)
  ------ inclusion threshold ------
        8.4    5.1  27.5        9.3    5.0  27.5    1.0  1  Mitofilin        Mitochondrial inner membrane protein


Domain annotation for each model (and alignments):
>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.2   1.6e-14   4.8e-11       3      55 ..     199     251 ..     197     252 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.6e-14
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilel 55 
                                       ++  ++GiGp++A +l++aG+e+v++laaad+++La+ ++i++k+ + +i+ +
  gi|336255347|ref|YP_004598454.1| 199 SVDVIKGIGPAYADRLADAGVETVDELAAADAADLAEQTDISEKRIQGWIDRA 251
                                       56679********************************************9876 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   2.6e-08   7.8e-05      58      93 ..     203     238 ..     200     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.6e-08
                           DUF4332  58 ikgigeeyaeLLeaaGvdsvaeLaqrnpanLhqklk 93 
                                       ikgig++ya+ L  aGv++v eLa   +a+L ++++
  gi|336255347|ref|YP_004598454.1| 203 IKGIGPAYADRLADAGVETVDELAAADAADLAEQTD 238
                                       789999999999999999999999999999988875 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 !   17.4   0.0   9.5e-07    0.0028       6      41 ..     203     239 ..     202     243 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.5e-07
                   DNA_pol_lambd_f   6 vyGVGpktAkkwyakGirtledlra.krakLtreqqi 41 
                                       + G+Gp+ A ++ ++G+ t+++l a + a+L ++ +i
  gi|336255347|ref|YP_004598454.1| 203 IKGIGPAYADRLADAGVETVDELAAaDAADLAEQTDI 239
                                       66**********************9766888877665 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.7e-06    0.0051       6      46 ..     198     238 ..     193     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.7e-06
                              Cdd1   6 kelqdiPniGkalaedlvelGirsveelkgedpeelyekle 46 
                                       ++   i +iG+a a+ l + G+++v+el+  d+++l e+  
  gi|336255347|ref|YP_004598454.1| 198 ESVDVIKGIGPAYADRLADAGVETVDELAAADAADLAEQTD 238
                                       5667899*****************************98864 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -15.4  40.0         6   1.8e+04      39     111 ..      34     109 ..      21     149 .. 0.61
   2 !   17.1  38.1   1.4e-06    0.0041      48     115 ..     127     195 ..     120     207 .. 0.66

  Alignments for each domain:
  == domain 1  score: -15.4 bits;  conditional E-value: 6
                       Trypan_PARP  39 ggkgkekgtkvsddd.tngtdpepepepepepepepepepepetepeeepepepepe....pepepepepepepepe 110
                                       g +g ++     +d+ + +td+  ep +e e  pep   p p +e e +++ ++ p      + e+e + e++ epe
  gi|336255347|ref|YP_004598454.1|  34 GSRGSDRSESTPADEaAASTDSPTEPAEESEKAPEPPGSPGP-KETETDADADTAPTeaetADAEAETD-EADAEPE 108
                                       666765555554444155678877888888877887766655.22333333333332000023333332.4444554 PP

                       Trypan_PARP 111 p 111
                                        
  gi|336255347|ref|YP_004598454.1| 109 T 109
                                       4 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.4e-06
                       Trypan_PARP  48 kvsdddtngtdpepepepepepepepepepepetep.eeepepepepepepepepepepepepepgaat 115
                                        vs+ d  +++p+ epe e e e   e+e epe+e  +e++e e+e epepe+e epepepepe   +t
  gi|336255347|ref|YP_004598454.1| 127 DVSEGDGAAAEPDAEPELEAEDESALEAEAEPEAEStDESAETESEDEPEPEAESEPEPEPEPEADETT 195
                                       577778888877777777766666555555555443144566777777777777777777777765544 PP

>> Mitofilin  Mitochondrial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  27.5    0.0031       9.3      73     269 ..      28     227 ..       5     254 .] 0.68

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0031
                         Mitofilin  73 sevtkeskepkeekkkeksekqssassevaeeeaeatkkaaeaka.qqpkseqekekaleevlkealskaekataaa 148
                                        +v++e +++++  ++   +++  as++ ++e+ae+ +ka+e      pk+ +++   ++ +++ea++  ++a+ + 
  gi|336255347|ref|YP_004598454.1|  28 VTVEREGSRGSDRSESTP-ADEAAASTDSPTEPAEESEKAPEPPGsPGPKETETDAD-ADTAPTEAETADAEAETDE 102
                                       344444444444444333.35577777777777777777777664233444444444.4444444444444555555 PP

                         Mitofilin 149 keakdeakkavkeavdklkeasdteeksrekardtaleaaeaaaek....eleklkevielakqseeeaakplldaa 221
                                       ++a+ e++++++++v +++++ d+++ + + a++   +  e +ae+    e e  +e     +++e+e++++  ++a
  gi|336255347|ref|YP_004598454.1| 103 ADAEPETTEIDEAEVAIEDAEPDRDVSEGDGAAAEPDAEPELEAEDesalEAEAEPEAESTDESAETESEDEPEPEA 179
                                       5778889999999999999999999998888877666666666666778888888888888999999999999**** PP

                         Mitofilin 222 eetlekliehlkkveekvekaqslaklvekykelveeerevFqqeles 269
                                       e  +e  +e +    ++ e  +  + + + y ++ +++  +  +el+ 
  gi|336255347|ref|YP_004598454.1| 180 ESEPEPEPEPEADETTESESVDVIKGIGPAYADRLADAGVETVDELAA 227
                                       ********999999999999999***********99999998888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1080  (0.0602376); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); 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):               6  [number of targets reported over threshold]
# CPU time: 0.91u 0.32s 00:00:01.23 Elapsed: 00:00:00.44
# Mc/sec: 1734.69
//
Query:       gi|336255348|ref|YP_004598455.1|  [L=551]
Description: para-aminobenzoate synthase component I [Halopiger xanaduensis SH-6]
Scores for 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-102  341.9   0.0   3.5e-102  341.4   0.0    1.2  1  Chorismate_bind  chorismate binding enzyme
    3.1e-09   37.2   0.0    1.1e-08   35.4   0.0    1.9  3  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 !  341.4   0.0  3.9e-106  3.5e-102       2     258 .]     258     511 ..     257     511 .. 0.99

  Alignments for each domain:
  == domain 1  score: 341.4 bits;  conditional E-value: 3.9e-106
                                       HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEE CS
                   Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkve 78 
                                       re++a++v++vk++ir+gd++++++s+rl a+  aav+p+a+y+alr+ npapys+lle+ + +l++aSPElll+++
  gi|336255348|ref|YP_004598455.1| 258 RETFADRVRRVKAYIRDGDTFQANISQRLVAP--AAVHPVAAYDALRRVNPAPYSCLLEFRAADLVSASPELLLERD 332
                                       799*****************************..99***************************************** PP

                                       TTSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEE CS
                   Chorismate_bind  79 ggrrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhl 155
                                       ++  ++tepiaGTr+rg+tp+ed  le++ll+deKeraEh+m+vdl rndLgkv+  gsv v+e+++++ry+ev+hl
  gi|336255348|ref|YP_004598455.1| 333 RE-FVRTEPIAGTRPRGETPAEDDGLEADLLADEKERAEHAMLVDLERNDLGKVCAYGSVAVDEYRRIDRYAEVMHL 408
                                       55.************************************************************************** PP

                                       EEEEEEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETT CS
                   Chorismate_bind 156 vstiegelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdk 232
                                       vs+++g+l++d +l d+++a+fP+g++tGaPk r+m iidelE++rRg+Y+G+vg++++dg+a+l++vIRt+v++++
  gi|336255348|ref|YP_004598455.1| 409 VSNVTGQLRPDATLSDAVAAVFPGGTITGAPKPRTMAIIDELEATRRGPYTGSVGVFGFDGRATLNIVIRTLVRHAD 485
                                       ****************************************************************************9 PP

                                       EEEEEEEEEEETT--HHHHHHHHHHH CS
                   Chorismate_bind 233 elrlgaGaGIvadSdpeaEyeEtlaK 258
                                       e++l++GaGIv+dS+pe+Ey+EtlaK
  gi|336255348|ref|YP_004598455.1| 486 EYHLRVGAGIVHDSEPEREYDETLAK 511
                                       ************************99 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 !   35.4   0.0   1.2e-12   1.1e-08       2     131 ..      53     173 ..      52     176 .. 0.85
   2 ?   -3.3   0.0         1   9.3e+03       5      22 ..     294     314 ..     292     314 .. 0.75
   3 ?   -3.5   0.0       1.2   1.1e+04      91     101 ..     458     468 ..     446     478 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.2e-12
                     Anth_synt_I_N   2 dltplsvylklaeee.hkflLeSaeneggegrySfigldpflelkskngevevegpegeeleeeepldalrellerf 77 
                                       +++p  +y++ ++ +    +Le     gg+  + + g+dp  +l++  ++v+ ++       ++  l+al+ ll+  
  gi|336255348|ref|YP_004598455.1|  53 VADPFLAYRRARDGPdGGAFLETT---GGQPGWGYFGVDPVDRLTCSADAVSRSR-----DGQSPTLAALEGLLAGD 121
                                       6788899999999999999***99...677789999****999999999999999.....33344788888888777 PP

                     Anth_synt_I_N  78 rsaedseptelpfvgGlvGylgYDlvreieklpksakddlnlpdarlilydtli 131
                                       r +    + ++p  +G+vG l+YD+ re+e+lp+sa dd+ lp ++  +yd+l 
  gi|336255348|ref|YP_004598455.1| 122 RLV--RGDCDVPYPCGAVGWLSYDVARELEELPESAVDDRGLPRLEVGVYDRLA 173
                                       744..34789*****************************************986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1
                     Anth_synt_I_N   5 plsvylklaeee...hkflLe 22 
                                       p+++y +l+  +   +++lLe
  gi|336255348|ref|YP_004598455.1| 294 PVAAYDALRRVNpapYSCLLE 314
                                       788888888766777888887 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.2
                     Anth_synt_I_N  91 vgGlvGylgYD 101
                                       + G vG +g+D
  gi|336255348|ref|YP_004598455.1| 458 YTGSVGVFGFD 468
                                       67999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); 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: 0.51u 0.19s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 4385.72
//
Query:       gi|336255349|ref|YP_004598456.1|  [L=232]
Description: glutamine amidotransferase of anthranilate synthase [Halopiger xanaduensis SH-6]
Scores for 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-40  136.8   0.1    4.7e-39  134.1   0.1    1.8  1  GATase         Glutamine amidotransferase class-I
    1.2e-09   38.3   0.3    2.7e-09   37.1   0.2    1.6  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
       0.12   12.0   0.1       0.17   11.4   0.1    1.2  1  Peripla_BP_2   Periplasmic binding 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 !  134.1   0.1   7.9e-43   4.7e-39       2     179 ..      14     203 ..      13     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 7.9e-43
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHH.............HH..THHSTSEEEEEEESSCTT.TTTHHH CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeei.............le..llknpdgilvsgGpgspg.vegkie 62 
                                       ++Dnyds+ +nlv++++e+ +++       +  ei             le   + +p+gi+vs+Gpg+p+ ++ +i 
  gi|336255349|ref|YP_004598456.1|  14 VVDNYDSFAYNLVQYVAEAIASTGPAASPRDVGEIadevvvrrndeidLEgvRELDPTGIVVSPGPGTPEeAGISIP 90 
                                       89***************99977777777777777777777777777652234589***************9999999 PP

                                       HHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHH CS
                            GATase  63 aikearenkiPiLGICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelep 139
                                       +  e    + PiLG+CLG+Q+l+ + g++vv++  +  hg+ + +++d+ +++ gl+ e+++ ++H+++v++ + +p
  gi|336255349|ref|YP_004598456.1|  91 LFAE---TEYPILGVCLGHQALCAANGAPVVHAP-EVVHGKPSTVTHDGDGIFDGLPAEFQVGRYHSLAVER-ADLP 162
                                       9876...478************************.9***********************************9.889* PP

                                       TTEEEEEEEETTE.EEEEEEEETTTEEEESSBTTSTTSTTH CS
                            GATase 140 aglevtaksedde.elmeiiekknpfvgvQFHPEststpeg 179
                                       + le ta+++d+    m+++++++p vgvQFHPEs++t ++
  gi|336255349|ref|YP_004598456.1| 163 DALEETARTTDERgVSMAVRHREKPHVGVQFHPESILTRRH 203
                                       **99999887665699*********************9875 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.2   4.5e-13   2.7e-09     102     216 .]      93     196 ..      53     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 4.5e-13
                     Peptidase_C26 102 lergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqai 178
                                        e + Pilg+C+G+q l  a  G  + ++ e   ++ h       +  +v+ + ++++  l    e++v  +H+ a+
  gi|336255349|ref|YP_004598456.1|  93 AETEYPILGVCLGHQALCAAN-GAPVVHAPE---VV-H------GKPSTVTHDGDGIFDGLPA--EFQVGRYHSLAV 156
                                       57789************5555.555555554...33.3......2345788999******999..************ PP

                     Peptidase_C26 179 ke..laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       ++  l + l+ +A+++D+    + +++++++ +gvQ+HPE
  gi|336255349|ref|YP_004598456.1| 157 ERadLPDALEETARTTDERGVSMAVRHREKPHVGVQFHPE 196
                                       9977999******999866556666666679********9 PP

>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   2.9e-05      0.17      22      71 ..      30      81 ..      14      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                                      EEB-GGG--GGGGGGT....TS-BSBESSSB-HHHHHHH--SEEEE-GGG.. CS
                      Peripla_BP_2 22 vgvdtttsdpldadklee..aivevgadgeidvEklaalkPDlvilskglgl 71
                                      ++ +++t + +  +++ e  + v+v+ ++eid+E + +l+P+ +++s+g g+
  gi|336255349|ref|YP_004598456.1| 30 AEAIASTGPAASPRDVGEiaDEVVVRRNDEIDLEGVRELDPTGIVVSPGPGT 81
                                      4455555555555555557788*************************98744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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: 0.45u 0.19s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1889.51
//
Query:       gi|336255350|ref|YP_004598457.1|  [L=295]
Description: Aminodeoxychorismate lyase [Halopiger xanaduensis SH-6]
Scores for 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-51  173.4   0.0    7.2e-51  173.2   0.0    1.0  1  Aminotran_4  Amino-transferase class IV


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 !  173.2   0.0     4e-55   7.2e-51       2     221 ..      36     265 ..      35     267 .. 0.96

  Alignments for each domain:
  == domain 1  score: 173.2 bits;  conditional E-value: 4e-55
                       Aminotran_4   2 lfEtmrvyngeiffldeHleRLrksaellglelpfdeeelrkileelleannsengrlrllvsrgggglg...aats 75 
                                       +fEt+r+y g if + +H++RL++++e+l le  +++++lr+ ++ +l+an+   +++rl ++rg         +++
  gi|336255350|ref|YP_004598457.1|  36 AFETLRAYGGTIFAWGRHVDRLERTCEALSLEHGLSTDDLRERIDATLAANDLADAYVRLSITRGVQPGKltpQPEV 112
                                       7***************************************************************99766699***** PP

                       Aminotran_4  76 epsvavyvsalppgpeseke.....lplvtssdvrrdapsplpgaKtlnyldnvlarreakerg..adevllvdedg 145
                                       +p+v+vyv++lp g  +  +      +++t   +r++ +   +gaKt nyl+ +lar+e ++r+  ade+l+ d +g
  gi|336255350|ref|YP_004598457.1| 113 DPTVVVYVKPLPRGGLEGERvwdepATVRTVETRRMPDEAIPAGAKTHNYLNGILARAELRNRDepADEALMRDLEG 189
                                       **************9999999**998888888899999999**********************99999********* PP

                       Aminotran_4 146 nvtEgstsNvfivkggelitPplssgiLpGitrrallelakalgleveereitlkdleeadeafltntlrgvlpvr 221
                                       +v Eg+tsN+f+v++g+l tP +++ +LpGitr+ +lela++ g++v+e+++ l+d+ +adeafltn + +++pv 
  gi|336255350|ref|YP_004598457.1| 190 HVAEGATSNLFFVRDGTLHTPTADGPVLPGITRALVLELAAEGGISVREDRCDLEDVLAADEAFLTNRTWELRPVA 265
                                       **************************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2354.43
//
Query:       gi|336255351|ref|YP_004598458.1|  [L=393]
Description: hypothetical protein Halxa_3974 [Halopiger xanaduensis SH-6]
Scores for 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    6.1e-06   26.1   0.0    1.3  1  N6-adenineMlase  Probable N6-adenine methyltransferase


Domain annotation for each model (and alignments):
>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   3.4e-10   6.1e-06       8     117 ..      86     202 ..      84     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.4e-10
                   N6-adenineMlase   8 fwysdetaealakelleeeeskkiaclsaPsvyealkkekkkekvlLleiDkrFealygeekfvfYdlnnpe.elpe 83 
                                       ++++ et +a+a+ + e++    ++cl+aP+v+++l ++     v+L + ++  e  + ++ +    ++n +   + 
  gi|336255351|ref|YP_004598458.1|  86 WYFTAETTTAIATTVAESA-AGPVLCLGAPTVAFTLAERG--VPVTLVDRNELIETRFAPR-YDTLTFANRDiGERL 158
                                       579999*999999977775.668****************9..89*****887776666655.444444444333334 PP

                   N6-adenineMlase  84 elkgkfdviviDPPFlseeclkklaktaklllk..........k 117
                                        l+++  v  +DPP+  ++++  l+++a+ +++           
  gi|336255351|ref|YP_004598458.1| 159 ALEETHSVAFFDPPWYPDDTAAWLHRAATNVAQggriyfvlfpP 202
                                       469************99999888888877776666555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2944.97
//
Query:       gi|336255352|ref|YP_004598459.1|  [L=379]
Description: Saccharopine dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-12   46.9   0.0    6.4e-12   45.9   0.0    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    1.5e-05   25.0   0.2    1.5e-05   25.0   0.2    1.9  2  NAD_binding_10   NAD(P)H-binding


Domain annotation for each model (and alignments):
>> 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 !   45.9   0.0   7.2e-16   6.4e-12       2     129 ..       5     121 ..       4     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 7.2e-16
                                       EEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   2 liiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       li Ga G +G+ +a++ ++++      tva+r+++ +++la    +  ++ +a+  e+ +  Laa l++ d+v+n++
  gi|336255352|ref|YP_004598459.1|   5 LIYGAyGDTGRLIAREAVARGGS---PTVAGRDRRAVARLA---DRLGVDGRAFALEDGS--LAARLEGFDAVLNCA 73 
                                       899*****************986...8*************9...5678888888888776..78899********** PP

                                       SGG..GHHHHHHHHHHHT-EEEE.SS-BCGCCSCHCCSHHHHHTHHHHHHCTSEE CS
                   Sacchrp_dh_NADP  78 ppi..ssldvlkaCietgvhyvd.tsiskeertnyalreavlklkekakeagvta 129
                                       +p+     ++l+aC+e g++y+d t          a+ e++++ ++ a+eag+t+
  gi|336255352|ref|YP_004598459.1|  74 GPFveTVDPLLEACLESGTDYLDiT-G------EVAVFERLRQRDATAREAGITM 121
                                       ***866669**************73.3......3578999999999*******97 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 !   25.0   0.2   1.7e-09   1.5e-05       1      88 [.       8      90 ..       8     109 .. 0.84
   2 ?   -2.4   0.1      0.43   3.9e+03       6      50 ..     244     286 ..     240     293 .. 0.61

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.7e-09
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCHHHHHH CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkdeegak 79
                                      GA G +Grl+++e++arg  + t+  R+   +a+l+++ g++     ++   +la+ l+g daV+ ++g+     e+++
  gi|336255352|ref|YP_004598459.1|  8 GAYGDTGRLIAREAVARG-GSPTVAGRDRRAVARLADRLGVDGRAFALE-DGSLAARLEGFDAVLNCAGPFV---ETVD 81
                                      9****************7.6888999*********98888877777666.689***************9754...3455 PP

                                      HHHHHHHHC CS
                    NAD_binding_10 80 nivdaakea 88
                                       +++a+ e+
  gi|336255352|ref|YP_004598459.1| 82 PLLEACLES 90
                                      555555555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.43
                                       HHHHHHHHHHHC-.T-EEEEEETTHHHCHHHHCTTTCEEEE--TT- CS
                    NAD_binding_10   6 vGrllvkellarg.ghevtalvRnpeklaeleaeeglevvegdvtd 50 
                                       vG ll +++++rg +  v a v   e  +   a++g  vv g+vtd
  gi|336255352|ref|YP_004598459.1| 244 VGWLLERRAVERGlKRLVDARVDGLENRN---AADGHAVVWGEVTD 286
                                       78888888888864434444444444433...34566667677766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2956.20
//
Query:       gi|336255353|ref|YP_004598460.1|  [L=157]
Description: Rieske (2Fe-2S) iron-sulfur domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-05   22.9   0.0    7.2e-05   22.7   0.0    1.3  1  Rieske    Rieske [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0     4e-09   7.2e-05      35      83 ..      61     113 ..       6     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4e-09
                                       -EEEEESC-TTTT-B.CGGSEEE..TT.EEE-TTT--EEE.TTSBEEE-TTHH CS
                            Rieske  35 evyAlsdvCtHrgap.lsegkid..ekgvleCpcHgwayd.adGkvikgPapr 83 
                                       +v +  ++C+H   + l++g++    +g+++C  Hg+ ++  +G ++ gP++ 
  gi|336255353|ref|YP_004598460.1|  61 SVSCWLNYCQHFTHIkLDKGSGAamRNGEIVCENHGAYFEaDSGYCTYGPCEG 113
                                       566999*****76553866665334999************999******9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.36u 0.19s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 1334.63
//
Query:       gi|336255354|ref|YP_004598461.1|  [L=120]
Description: hypothetical protein Halxa_3977 [Halopiger xanaduensis SH-6]
Scores for 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   3.0          2    8.6   1.8    2.9  2  HTH_20    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 ?    2.9   0.0    0.0062   1.1e+02       6      34 ..       8      36 ..       4      42 .. 0.80
   2 ?    8.6   1.8   0.00011         2       4      59 ..      36     110 ..      30     112 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0062
                                      HHS-.HHHHHHHHHHSTCTTB-HHHHHHHH CS
                            HTH_20  6 ALah.PvRrrilraLaraegltaselaerl 34
                                      AL+  +  +++l +L +++++ a  + +++
  gi|336255354|ref|YP_004598461.1|  8 ALDRpEFVLAVLEWL-DGREVPADVISDAF 36
                                      6667667799*****.99999999988876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00011
                                       HHHHS-HHHHHHHHHH.STCTTB-HHHHHHHH..T................S-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20   4 aeALahPvRrrilraL.araegltaselaerl..d................lskntlsyHLrvLeeagLvevvre 59 
                                       + +La++ Rr +l+   + +e+ t+++ ae++  +                +  +  ++HL  L++agL+e   e
  gi|336255354|ref|YP_004598461.1|  36 FTLLANERRRLLLAVMtSYGEAITLPDAAEEVavRetgravtelsgeqvanVYLSLYHDHLPRLVDAGLLEYDQE 110
                                       445555555555554488888888888888885514455666666666666777777899999999999997766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1034.09
//
Query:       gi|336255355|ref|YP_004598462.1|  [L=98]
Description: hypothetical protein Halxa_3978 [Halopiger xanaduensis SH-6]
Scores for 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-07   30.4   0.4    5.5e-07   29.6   0.4    1.4  1  HTH_20        Helix-turn-helix domain
     0.0035   17.2   0.0     0.0054   16.6   0.0    1.3  1  HTH_5         Bacterial regulatory protein, arsR family
      0.005   16.7   0.3     0.0078   16.1   0.3    1.3  1  MarR_2        MarR family
  ------ inclusion threshold ------
      0.052   13.1   0.0       0.13   11.9   0.0    1.7  2  HTH_24        Winged helix-turn-helix DNA-binding
      0.059   13.5   0.8        0.1   12.7   0.8    1.4  1  DprA_WH       DprA winged helix domain
      0.088   12.9   0.1       0.13   12.4   0.1    1.2  1  Sigma70_r3    Sigma-70 region 3
       0.44   11.3   2.7       0.41   11.3   0.9    1.7  2  FYDLN_acid    Protein of unknown function (FYDLN_acid)
       0.87    9.5   7.2       0.25   11.3   1.0    2.2  2  zf-trcl       Probable zinc-ribbon domain
        1.4    8.7   4.1        9.1    6.1   0.3    2.2  2  Rubredoxin_2  Rubredoxin metal binding 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 !   29.6   0.4   2.7e-10   5.5e-07      10      46 ..       7      42 ..       4      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.7e-10
                                      HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20 10 PvRrrilraLaraegltaselaerldlskntlsyHLr 46
                                       +Rrr+ +aL rae++t+sela+++dl++n + +H++
  gi|336255355|ref|YP_004598462.1|  7 TTRRRLADAL-RAEPATPSELAAAFDLTPNAVLRHVE 42
                                      69********.************************86 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 !   16.6   0.0   2.7e-06    0.0054       3      35 ..       8      40 ..       6      42 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHH CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShH 35
                                      tR+++  +L+ ++++ +ela++++l++ +v +H
  gi|336255355|ref|YP_004598462.1|  8 TRRRLADALRAEPATPSELAAAFDLTPNAVLRH 40
                                      899999*************************99 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.3   3.9e-06    0.0078       6      43 ..       8      42 ..       6      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.9e-06
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHH CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilk 43
                                      + +r+  aL+++p    t++ela++++l++ av r+++
  gi|336255355|ref|YP_004598462.1|  8 TRRRLADALRAEP---ATPSELAAAFDLTPNAVLRHVE 42
                                      77899999*9999...6****************99997 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 ?   -1.7   0.0       1.1   2.1e+03      17      27 ..       6      16 ..       2      18 .. 0.69
   2 ?   11.9   0.0   6.5e-05      0.13      18      39 ..      21      42 ..       6      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                            HTH_24 17 risqreLAerl 27
                                       ++ r LA++l
  gi|336255355|ref|YP_004598462.1|  6 ETTRRRLADAL 16
                                      46777787765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.5e-05
                            HTH_24 18 isqreLAerlglSpstvnrrlk 39
                                       + +eLA + +l+p++v+r+++
  gi|336255355|ref|YP_004598462.1| 21 ATPSELAAAFDLTPNAVLRHVE 42
                                      699*****************95 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.8   5.2e-05       0.1       8      44 ..       3      39 ..       2      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-05
                           DprA_WH  8 pplddlerrvLaaLgpePvhvDqLvrrtglpaaevsa 44
                                      ++++ ++rr+ +aL +eP +  +L+++  l++ +v++
  gi|336255355|ref|YP_004598462.1|  3 EADETTRRRLADALRAEPATPSELAAAFDLTPNAVLR 39
                                      578999***************************9986 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.3e-05      0.13       9      45 ..       8      45 ..       6      48 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                                      HHHHHHHHHSSXX.XHHHHHHHHTXXHHHHHHHHHHHX CS
                        Sigma70_r3  9 aqreLeqelgreP.tpeEiAeeLglseekVrevleaar 45
                                      ++r+L   l  eP tp E+A++ +l+++ V++ +e + 
  gi|336255355|ref|YP_004598462.1|  8 TRRRLADALRAEPaTPSELAAAFDLTPNAVLRHVEHVS 45
                                      5788888888776599**************99888765 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 ?   -0.7   0.0       1.1   2.2e+03      31      31 ..      25      25 ..       2      58 .. 0.44
   2 ?   11.3   0.9   0.00021      0.41      12      38 ..      63      90 ..      61      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                        FYDLN_acid 31 k 31
                                      +
  gi|336255355|ref|YP_004598462.1| 25 E 25
                                      2 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00021
                        FYDLN_acid 12 Cpscg.akFYDLnkdPivcpkcgeefep 38
                                      C +cg a F DL ++P  cp+c++e   
  gi|336255355|ref|YP_004598462.1| 63 CRDCGfADFDDLLNRPSRCPSCKSESIA 90
                                      9999966899************998655 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.6      0.11   2.2e+02       7      11 ..      63      67 ..      59      71 .. 0.80
   2 ?   11.3   1.0   0.00012      0.25      30      43 ..      75      88 ..      68      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                           zf-trcl  7 CkdCg 11
                                      C+dCg
  gi|336255355|ref|YP_004598462.1| 63 CRDCG 67
                                      99998 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00012
                           zf-trcl 30 dnepkRCkaCRkar 43
                                       n p+RC++C++++
  gi|336255355|ref|YP_004598462.1| 75 LNRPSRCPSCKSES 88
                                      599********975 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.019        38       2       8 ..      62      68 ..      62      70 .. 0.87
   2 ?    6.1   0.3    0.0046       9.1      16      22 ..      80      86 ..      80      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.019
                      Rubredoxin_2  2 vCsqCGf 8 
                                      +C++CGf
  gi|336255355|ref|YP_004598462.1| 62 ECRDCGF 68
                                      5*****8 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0046
                      Rubredoxin_2 16 rCpsCgs 22
                                      rCpsC+s
  gi|336255355|ref|YP_004598462.1| 80 RCPSCKS 86
                                      8****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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):               9  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 771.78
//
Query:       gi|336255356|ref|YP_004598463.1|  [L=324]
Description: Nucleotidyl transferase [Halopiger xanaduensis SH-6]
Scores for 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-38  132.4   0.0    2.6e-38  132.0   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
      1e-12   48.7   0.0      1e-12   48.7   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0051   16.5   1.9       0.13   12.0   0.0    3.1  4  Hexapep          Bacterial transferase hexapeptide (six repea
  ------ inclusion threshold ------
      0.025   14.3   0.0      0.042   13.6   0.0    1.4  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 !  132.0   0.0   5.8e-42   2.6e-38       1     242 [.       2     237 ..       2     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 5.8e-42
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHH.TT-SEEEEEEETTTHHHHHHHHTTSGGGT...S CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlan.sgieeiivvltqehsflveeqlkegskfg...v 73 
                                       kav+LaGG+ tR+wP+t+ ++k  +p++++ ++i+  +++l + ++i+e++v ++++ ++ +e +l++ + f+   +
  gi|336255356|ref|YP_004598463.1|   2 KAVVLAGGYATRMWPITKHRPKMFLPIGDS-TVIDRIFTELEAdERIDEVYVSTNERFAADFEAHLADSE-FEkprL 76 
                                       79*********************99*9999.********9988799***888889999999999999986.884555 PP

                                       EEEEEEESS--.BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSE CS
                   NTP_transferase  74 evlialepegk.gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyG 149
                                       +v+ ++ + +k g  +A+a+ ++  +    d+ +lv++gD li+ ++ ++++ ++e++a  ++++ +  +e+a++yG
  gi|336255356|ref|YP_004598463.1|  77 SVEDTTDEDEKfGVVGALAQLIDRENV---DDDLLVIAGDNLISFDVADFLDYFQENDAPTLAAYDVGSREKAKSYG 150
                                       555555554448999998876665555...556**************************99**************** PP

                                       EEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTE CS
                   NTP_transferase 150 vieadeegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkda 226
                                       ++e ++ +rv +f+EKP+ ++ s+l+s   Y f ++ l  l  +lee    +++    + + l++ ++ +af f++ 
  gi|336255356|ref|YP_004598463.1| 151 LVELEG-DRVVDFQEKPEDPN-STLVSIACYAFPQDSLSLLPTYLEEG--NNPDEPGWFVQWLQNREPTYAFTFEG- 222
                                       ****98.6*************.******************97799888..45555556666778889*********. PP

                                       E-EEEXSSHHHHHHHH CS
                   NTP_transferase 227 eyWsDvGtldsllean 242
                                         W D+Gt++s+l+a 
  gi|336255356|ref|YP_004598463.1| 223 -AWFDIGTPESYLDAV 237
                                       .5***********985 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 !   48.7   0.0   2.3e-16     1e-12       1     127 [.       3     143 ..       3     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 2.3e-16
                                       EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSHC...HHHHHHTTC.......TS- CS
                      NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraag.vdevvvvggde...evlaalarl.......gvr 61 
                                       av+LAGG ++Rm      ++K +lp+g+ ++++r++  l+a + +dev+v+++++   + +a+la++        v+
  gi|336255356|ref|YP_004598463.1|   3 AVVLAGGYATRMwpitkHRPKMFLPIGDSTVIDRIFTELEADErIDEVYVSTNERfaaDFEAHLADSefekprlSVE 79 
                                       79**********8877557********************998559********964444555553333333322566 PP

                                       EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE CS
                      NTP_transf_3  62 vvededpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeger 127
                                        ++ded+  g +++la  +++ + +d +lv+a+D     +  v+ +l+ +++++a ++++ + g r
  gi|336255356|ref|YP_004598463.1|  80 DTTDEDEKFGVVGALAQLIDRENVDDDLLVIAGDNLI--SFDVADFLDYFQENDAPTLAAYDVGSR 143
                                       69999999*************99***********954..678999999999999998888777666 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.9   8.7e+03       4      10 ..      28      34 ..      28      36 .. 0.57
   2 !   12.0   0.0   2.9e-05      0.13      16      34 ..     253     270 ..     243     272 .. 0.62
   3 ?   -2.7   0.0       1.3   5.8e+03      21      29 ..     295     303 ..     292     304 .. 0.56
   4 ?    2.3   0.0     0.035   1.6e+02      25      36 .]     309     320 ..     307     322 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.9
                                      EETTEEE CS
                           Hexapep  4 IGsnvlI 10
                                      IG+ ++I
  gi|336255356|ref|YP_004598463.1| 28 IGDSTVI 34
                                      5666665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.9e-05
                                       EETTEEE-TTEEEETTEEE CS
                           Hexapep  16 iggnVkIGdnvkIgagvvi 34 
                                       + +nV+IGdnv++ a v++
  gi|336255356|ref|YP_004598463.1| 253 L-ENVTIGDNVHVMADVTL 270
                                       4.67777777776666554 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.3
                                       EE-TTEEEE CS
                           Hexapep  21 kIGdnvkIg 29 
                                       +I ++++I+
  gi|336255356|ref|YP_004598463.1| 295 IIDEGTHIE 303
                                       455555555 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.035
                                       TEEEETTEEEES CS
                           Hexapep  25 nvkIgagvvigg 36 
                                       ++ Iga+++i++
  gi|336255356|ref|YP_004598463.1| 309 GALIGAHTTITN 320
                                       456666666664 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 ?   13.6   0.0   9.3e-06     0.042       2      61 ..       2      64 ..       1      86 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-06
                                      EEEEECTTSSCTT...-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHH CS
                              IspD  2 vvvipAAGsGkRm...kaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeq 61
                                       +v+ A G  +Rm    + +pK+fl + + t++ +  + l a +++d++ v  +e     fe+
  gi|336255356|ref|YP_004598463.1|  2 KAVVLAGGYATRMwpiTKHRPKMFLPIGDSTVIDRIFTELEADERIDEVYVSTNERFAADFEA 64
                                      689*********9655689********************************999876666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); 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:                         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 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2589.09
//
Query:       gi|336255357|ref|YP_004598464.1|  [L=794]
Description: multi-sensor signal transduction histidine kinase [Halopiger xanaduensis SH-6]
Scores for 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-20   71.4   0.0    1.4e-19   70.3   0.0    1.6  1  Response_reg   Response regulator receiver domain
    5.6e-19   68.7   0.1    1.1e-18   67.8   0.1    1.4  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    4.4e-18   65.9  12.9    4.9e-09   36.6   0.3    4.1  6  GAF_2          GAF domain
    1.8e-11   44.5   0.0    2.2e-06   28.1   0.0    2.7  2  GAF_3          GAF domain
    1.7e-09   37.6   0.3    1.7e-09   37.6   0.3    3.1  3  HisKA          His Kinase A (phospho-acceptor) domain
    3.7e-09   36.8   1.0      2e-08   34.5   0.1    2.8  2  PAS_4          PAS fold
    1.8e-08   34.4   0.0    4.3e-08   33.1   0.0    1.7  1  PAS            PAS fold
    7.6e-08   32.6   0.0    2.1e-07   31.1   0.0    1.8  1  PAS_9          PAS domain
    2.7e-06   27.3   0.0    1.6e-05   24.8   0.0    2.4  1  PAS_8          PAS domain
    0.00029   20.2   0.0     0.0041   16.5   0.0    2.2  2  CCB2_CCB4      Cofactor assembly of complex C subunit B, CCB2
     0.0003   21.0   0.1     0.0017   18.6   0.0    2.3  2  PAS_3          PAS fold
     0.0012   18.8   0.1     0.0036   17.3   0.1    1.9  1  HATPase_c_2    Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
      0.027   14.2   1.7        2.5    7.9   0.2    2.4  2  Synaptobrevin  Synaptobrevin
      0.081   13.1   0.0       0.46   10.6   0.0    2.3  2  PAS_7          PAS fold
      0.086   12.7   0.1       0.42   10.4   0.0    2.0  2  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


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 !   70.3   0.0   1.1e-22   1.4e-19       1     106 [.      11     116 ..      11     122 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.1e-22
                                       EEEESSSHHHHHHHHHHHH..HTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlle..eegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpvi 75 
                                       vl vdDdp++r+l++++le  ++ + +va+a+++ +al+ l ++ vd+i+ D ++p+ dG+e+l+ +r e p+lp i
  gi|336255357|ref|YP_004598464.1|  11 VLYVDDDPDLRSLVATFLErrDDRL-SVATATSAGAALDRLTAD-VDCIVSDYELPDTDGIEFLEAVRGEYPDLPFI 85 
                                       799****************955666.***************876.******************************** PP

                                       EEESSTSHHHHHHHHHCTESEEEESSG-HHH CS
                      Response_reg  76 iltahseeedavealkagaddflsKpfdpee 106
                                       ++ta ++e++a +a++ag+ d+l K    e+
  gi|336255357|ref|YP_004598464.1|  86 LFTAGGSEAVASDAISAGVTDYLRKGTGTEQ 116
                                       *************************877665 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 !   67.8   0.1   9.1e-22   1.1e-18       2     107 ..     690     788 ..     689     791 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 9.1e-22
                                       HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHH CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlG 77 
                                       d +rL+q++ nl  Nav++   ++ ++v++   ed+  + veD+G+Gip +d+ ++fe  +s+      +  gtG+G
  gi|336255357|ref|YP_004598464.1| 690 DRSRLEQLLENLFRNAVEH--GGDGVTVTVGDLEDEAGFYVEDDGPGIPDDDRARIFEsGYST------SADGTGFG 758
                                       789***************9..67889999996669***********************88888......789***** PP

                                       HHHHHHHHHHTTTEEEEEEETTTEEEEEEE CS
                         HATPase_c  78 lsivkklvelmgGeiwvesepgrGttftft 107
                                       lsiv+++v  ++ ei v++  g+Gt+f +t
  gi|336255357|ref|YP_004598464.1| 759 LSIVHEIVAAHDWEIAVTEGTGGGTRFEIT 788
                                       ******9999*****************975 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.1   3.8e+03      23      47 ..      10      33 ..       3      63 .. 0.60
   2 ?   -2.4   0.0       4.4   5.2e+03      53      84 ..     146     177 ..      98     184 .. 0.53
   3 !   36.6   0.3   4.1e-12   4.9e-09       1     138 []     267     398 ..     267     398 .. 0.85
   4 !   35.8   0.2   7.2e-12   8.6e-09       2     138 .]     420     559 ..     419     559 .. 0.79
   5 ?   -2.4   0.0       4.6   5.5e+03      49      77 ..     652     686 ..     603     702 .. 0.58
   6 ?   -0.6   0.1       1.3   1.5e+03       3      38 ..     693     732 ..     691     763 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.1
                                      EEEEEE-TTS-EEEEEEEES-TTST CS
                             GAF_2 23 gyillvdddgglrlaawgeaeeefg 47
                                      +++ +vddd++lr +++++ e++++
  gi|336255357|ref|YP_004598464.1| 10 SVL-YVDDDPDLRSLVATFLERRDD 33
                                      444.557788877665554444332 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.4
                                       ---TTHHHHHHHHTS-EEES-.GGG-S-HHHHH CS
                             GAF_2  53 plgeglvgealrtgrpvilnd.leedpdkkglp 84 
                                          eg +  + ++gr  ++nd ++  +  ++++
  gi|336255357|ref|YP_004598464.1| 146 TAQEG-ISIVGADGRFQYVNDaYAGLYGYDPEE 177
                                       22444.455666677777777777766666655 PP

  == domain 3  score: 36.6 bits;  conditional E-value: 4.1e-12
                                       HHHHHHHHHHHHHHHHHS.S..EEEEEEE-TT.S-EEEEEEEES-TTSTT-S-B--.-TTHHHHHHHHTS-EEES-G CS
                             GAF_2   1 aadleelldlvldelvel.gaalgyillvddd.gglrlaawgeaeeefgaaldrpl.geglvgealrtgrpvilndl 74 
                                       a+++ee++ l++d++ ++  + l  i+ +d++ +gl+  + ++  +e+ +++  p+  +gl++e ++ g++ +  d+
  gi|336255357|ref|YP_004598464.1| 267 ATTVEEIATLATDAADDIlEFPLNGIHRYDEAvDGLVPISVSNSSRELLGEP--PVlTDGLAWETFQRGEAKVYGDV 341
                                       5799*************659**999999996645566667777777777777..555999*************9**9 PP

                                       GG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  75 eedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       +e +   g    + ++rs++ +Pl   +  +Gv+  ++++ +afd++d++++++la+ +  a++
  gi|336255357|ref|YP_004598464.1| 342 REAE---GVLNPDTPIRSEILLPL---D-EHGVFIASSTECDAFDDADVTFAKLLAANVTSALD 398
                                       9944...444578***********...5.8*****99***********************9996 PP

  == domain 4  score: 35.8 bits;  conditional E-value: 7.2e-12
                                       HHHHHHHHHHHHHHHHS.S..EE.EEEEE-TTS-EEEE..........EEEES-TTSTT-S-B---TTHHHHHHHHT CS
                             GAF_2   2 adleelldlvldelvel.gaalg.yillvdddgglrla..........awgeaeeefgaaldrplgeglvgealrtg 66 
                                       ++++ ++d ++ +++e+ ga+l+ + ++v+ dg+ rl+          ++  ++e +++++ +p+ ++ v+e++ +g
  gi|336255357|ref|YP_004598464.1| 420 SSVDATADVAVTAAREIlGADLStFHGFVERDGQQRLEpvattdtvheVFDSTPEYVRSETADPVTAS-VWEVFDDG 495
                                       6899************6699988566678877776655555555555555555555555554555444.89****** PP

                                       S-EEES-GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  67 rpvilndleedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       +p +++d+ e     ++  ++ + rs +  P+      +Gv+++ ++ p+af+++d  l + la+++ +a+e
  gi|336255357|ref|YP_004598464.1| 496 EPAYVHDTNE----YPEFVDETPARSAILHPI----ADYGVFVVTSTTPRAFSQTDAKLTDILASTLTTALE 559
                                       *****99666....56668999**********....38********************************97 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 4.6
                                       -S-B..--...-TT.HHHHHHHHTS-EEES-GGG- CS
                             GAF_2  49 aldr..pl...geg.lvgealrtgrpvilndleed 77 
                                       ++d+  p+   + +  ++++++t ++++++ +++ 
  gi|336255357|ref|YP_004598464.1| 652 RIDDpePVdlaALSeTCWRSVATAEATLVTRVDRR 686
                                       22221122224333357777777777777665554 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHSS..EE..EEEEE-TTS-EEEE..E CS
                             GAF_2   3 dleelldlvldelvelgaalg..yillvdddgglrla..a 38 
                                        le+ll+++++ +ve g + +   ++ ++d+ g++++   
  gi|336255357|ref|YP_004598464.1| 693 RLEQLLENLFRNAVEHGGDGVtvTVGDLEDEAGFYVEddG 732
                                       5788999999999998545441155555555554444331 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   4.9e-05     0.059      56     129 .]     325     399 ..     303     399 .. 0.85
   2 !   28.1   0.0   1.8e-09   2.2e-06       3     129 .]     423     560 ..     421     560 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.9e-05
                             GAF_3  56 larralssgevvsepsfaeedg.....lpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                       la++++++ge+ +  +++e++g     +p r+ +++PL       Gv  + st++ afd++d+ + + lA+ + +a+
  gi|336255357|ref|YP_004598464.1| 325 LAWETFQRGEAKVYGDVREAEGvlnpdTPIRSEILLPLDE----HGVFIASSTECDAFDDADVTFAKLLAANVTSAL 397
                                       7888888998877766666533333339999999999999....8******************************** PP

                             GAF_3 128 er 129
                                       +r
  gi|336255357|ref|YP_004598464.1| 398 DR 399
                                       97 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 1.8e-09
                             GAF_3   3 dellekllkllvkllgaevgalll.ldedgn.klqvaagw.dgkpalse........sldedsalar...ralssge 65 
                                       d +++ ++ ++ ++lga+ + ++  +++dg+ +l ++a + + ++++          +   ++++++   ++++ ge
  gi|336255357|ref|YP_004598464.1| 423 DATADVAVTAAREILGADLSTFHGfVERDGQqRLEPVATTdTVHEVFDStpeyvrseT---ADPVTAsvwEVFDDGE 496
                                       6667777888888899988888766444444499999999666666643565543323...44444445599999** PP

                             GAF_3  66 vvse...psfae.edglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataier 129
                                       ++++   ++++e  d +p r+a+++P+++    +Gv ++ st praf+++d+ l + lA+ + ta+er
  gi|336255357|ref|YP_004598464.1| 497 PAYVhdtNEYPEfVDETPARSAILHPIAD----YGVFVVTSTTPRAFSQTDAKLTDILASTLTTALER 560
                                       99996663333334679************....**********************************8 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.2   3.9e+03      24      58 ..      25      54 ..      22      56 .. 0.77
   2 !   37.6   0.3   1.4e-12   1.7e-09       2      66 ..     581     651 ..     580     652 .. 0.86
   3 ?   -2.2   0.1       3.7   4.5e+03      45      58 ..     688     701 ..     673     706 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.2
                                      HHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHH CS
                             HisKA 24 aeaLkregklteelkeyletiesearrldhlvedl 58
                                      a  L+r      + +  ++t+ s +  ld+l  d+
  gi|336255357|ref|YP_004598464.1| 25 ATFLER-----RDDRLSVATATSAGAALDRLTADV 54
                                      556666.....577889999999999999998886 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 1.4e-12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHC..........T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre........gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       l+rf++ v+H+Lr+PL +  g +e+ ++         g  +    + l++++   +r++ l+e+lL+l+r ++
  gi|336255357|ref|YP_004598464.1| 581 LERFASIVSHDLRNPLQVAEGSLELAREIandddgydG--DNTADDHLDDARWALERMNGLIEELLTLARDGE 651
                                       78***********************9887888866432..355555************************875 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHHHHH CS
                             HisKA  45 esearrldhlvedl 58 
                                       +    rl++l+e+l
  gi|336255357|ref|YP_004598464.1| 688 RADRSRLEQLLENL 701
                                       33334777777776 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1   1.6e-11     2e-08       4     109 ..     147     248 ..     144     249 .. 0.82
   2 ?   -1.4   0.1       2.2   2.7e+03      48     105 ..     550     609 ..     538     612 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.6e-11
                             PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerh 80 
                                        ++++ ++++dgr++y+N a+a l+g++peellG++++ l+p++  + +++ l  ++e e  ++  ++ ++ +++ +
  gi|336255357|ref|YP_004598464.1| 147 AQEGISIVGADGRFQYVNDAYAGLYGYDPEELLGEHWELLYPDSEVEFVRSELVPAVEAEGYWHGRTTGRRADGTTF 223
                                       678999**************************************999999999999999887777777777777777 PP

                             PAS_4  81 yelrllPlrdesGevigvlvisrDiTerr 109
                                       +e +++    e+     +++++rD+++r+
  gi|336255357|ref|YP_004598464.1| 224 LEDHVVSTT-ENS---ELICTVRDVSDRE 248
                                       777776652.333...4777777777775 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                             PAS_4  48 daarleralrrvlegeepiefleelll..pgeerhyelrllPlrdesGevigvlvisrDi 105
                                       +a  l +al+rv ++    +++ el    ++ er+ ++  + lr++   + g l+++r+i
  gi|336255357|ref|YP_004598464.1| 550 LASTLTTALERVDRESLLRDRTAELEAqnERLERFASIVSHDLRNPLQVAEGSLELAREI 609
                                       667788888888888888888888888888889999999999999888888888888887 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   3.6e-11   4.3e-08       5     113 .]     142     244 ..     138     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 3.6e-11
                                       HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC CS
                               PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl 81 
                                       + +e++ ++i +v +dgr+ yvN+a++ l G+++ee+lg++   l++       +e ++  l  + e++++++ +++
  gi|336255357|ref|YP_004598464.1| 142 TAIETAQEGISIVGADGRFQYVNDAYAGLYGYDPEELLGEHWELLYPDS----EVEFVRSELVPAVEAEGYWHGRTT 214
                                       689****************************************999865....555555555555555555555555 PP

                                       ...TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  82 ...rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                           dg+++ le +++++++ +    ++++++rd+
  gi|336255357|ref|YP_004598464.1| 215 grrADGTTF-LEDHVVSTTENS----ELICTVRDV 244
                                       552366555.555666666554....899***997 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   1.7e-10   2.1e-07       2     104 .]     149     246 ..     148     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.7e-10
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfw 77 
                                       +gi i+  dgr  y+N+a + l+Gy+pee+lg +++ l+ +d+e +   ++++ + +    +++ ++ +r +g+tf+
  gi|336255357|ref|YP_004598464.1| 149 EGISIVGADGRFQYVNDAYAGLYGYDPEELLGEHWELLY-PDSEVEFVRSELVPAVEAeGYWHGRTTGRRADGTTFL 224
                                       7999*99*************************9999999.777777777777777777769**************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                        +  +s+  +++     +i+++rD+++
  gi|336255357|ref|YP_004598464.1| 225 EDHVVSTTENSE-----LICTVRDVSD 246
                                       999999886554.....78******95 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.3e-08   1.6e-05       2      55 ..     139     189 ..     138     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.3e-08
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                       r+ +++e++++gi +v +++r+ +vN+a++ l+Gy+ ++l+ge     ++ l+p 
  gi|336255357|ref|YP_004598464.1| 139 RHHTAIETAQEGISIVGADGRFQYVNDAYAGLYGYDpEELLGE----HWELLYPD 189
                                       899***********9876689*************995555554....44444443 PP

>> CCB2_CCB4  Cofactor assembly of complex C subunit B, CCB2/CCB4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.16     2e+02     160     194 ..     357     391 ..     347     393 .. 0.89
   2 !   16.5   0.0   3.4e-06    0.0041     129     194 ..     491     552 ..     473     554 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.16
                         CCB2_CCB4 160 vlvqplgdegvlilgsntpraftkkdeaWiaaiAe 194
                                        ++ pl+++gv i  s++  af + d +  + +A 
  gi|336255357|ref|YP_004598464.1| 357 EILLPLDEHGVFIASSTECDAFDDADVTFAKLLAA 391
                                       57899**********************99999886 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.4e-06
                         CCB2_CCB4 129 vlkkqkeiyLvdlklypGrvefdylpentqsvlvqplgdegvlilgsntpraftkkdeaWiaaiAe 194
                                       v +++++ y +d++ yp  v  +     ++s +++p++d gv ++ s+tpraf++ d +  + +A 
  gi|336255357|ref|YP_004598464.1| 491 VFDDGEPAYVHDTNEYPEFVDET----PARSAILHPIADYGVFVVTSTTPRAFSQTDAKLTDILAS 552
                                       55666666666666666544443....37899*************************988777776 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.4e-06    0.0017       3      79 ..     162     234 ..     160     241 .. 0.81
   2 ?   -1.9   0.0       3.6   4.3e+03      28      52 ..     474     499 ..     462     502 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       yv++++  ++Gy+peellg   +w +l++p+   e vr++l  a++  + ++g    rr+dG++  +e++++ +  e
  gi|336255357|ref|YP_004598464.1| 162 YVNDAYAGLYGYDPEELLGE--HW-ELLYPDSeVEFVRSELVPAVEAEGYWHGRTTGRRADGTT-FLEDHVVST-TE 233
                                       89******************..55.56666655************999999***********98.555555554.55 PP

                             PAS_3  79 n 79 
                                       n
  gi|336255357|ref|YP_004598464.1| 234 N 234
                                       5 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
                             PAS_3  28 dlvhpeDrervrealqealkkge.py 52 
                                       ++v  e  + v ++++e++++ge +y
  gi|336255357|ref|YP_004598464.1| 474 EYVRSETADPVTASVWEVFDDGEpAY 499
                                       67777888999999999999999444 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1     3e-06    0.0036      29     115 ..     691     777 ..     659     788 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3e-06
                       HATPase_c_2  29 ldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlali 105
                                       + +++  +e ++ Naveh+ +      v+v++ + e++  + v+D+Gpg +  ++++  e ++++s++  G+Gl ++
  gi|336255357|ref|YP_004598464.1| 691 RSRLEQLLENLFRNAVEHGGD-----GVTVTVGDLEDEAGFYVEDDGPGIPDDDRARIFESGYSTSADGTGFGLSIV 762
                                       337777888899*******96.....577888899999***********777777888889999************* PP

                       HATPase_c_2 106 kglvDevey.....d 115
                                       +++v   ++     +
  gi|336255357|ref|YP_004598464.1| 763 HEIVAAHDWeiavtE 777
                                       ***988866446441 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.017        20      21      48 ..     391     421 ..     385     422 .. 0.77
   2 ?    7.9   0.2    0.0021       2.5      15      54 ..     546     585 ..     538     592 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.017
                                       CHHHHCHCCC...CCHHHHCCCCHHHHHHHH CS
                     Synaptobrevin  21 eNidkvlerg...ekldeLvdktenLqssaq 48 
                                        N+ ++l+r     kl++L+++t++L ++++
  gi|336255357|ref|YP_004598464.1| 391 ANVTSALDRTahaRKLELLQERTQTLMNTSS 421
                                       677777777522269***********99885 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0021
                                       CCCHHCCHHHHCHCCCCCHHHHCCCCHHHHHHHHHHHHHH CS
                     Synaptobrevin  15 vkdimkeNidkvlergekldeLvdktenLqssaqqFkkqa 54 
                                        +di+ + +  +ler ++ ++L d+t +L+++ +  ++ a
  gi|336255357|ref|YP_004598464.1| 546 LTDILASTLTTALERVDRESLLRDRTAELEAQNERLERFA 585
                                       578999999************************9998866 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00039      0.46       1      33 [.     144     176 ..     144     186 .. 0.88
   2 ?   -2.3   0.0         4   4.7e+03      31      74 ..     536     578 ..     534     585 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpee 33 
                                       +e  ++Gis++ ad+r   +N+ y  l+++ +e
  gi|336255357|ref|YP_004598464.1| 144 IETAQEGISIVGADGRFQYVNDAYAGLYGYDPE 176
                                       57789************************9665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4
                             PAS_7  31 peelvqvgvpleellrynaergefgagdveaeverrlaaaragk 74 
                                       p+ + q+ ++l+++l+ + ++   +  d+e+ ++ r+a+++a++
  gi|336255357|ref|YP_004598464.1| 536 PRAFSQTDAKLTDILASTLTTALER-VDRESLLRDRTAELEAQN 578
                                       6777778888888888877766655.778888888887776644 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 ?   -1.2   0.1       1.4   1.7e+03      81     125 ..     220     263 ..     210     275 .. 0.70
   2 ?   10.4   0.0   0.00035      0.42       8      60 ..     699     750 ..     692     758 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.4
                       HATPase_c_3  81 slslgkkltvitkkegesstltldvdkidkenekvleeltveeie 125
                                       +  ++++  v t++++e  ++  dv++ ++++  +l +l++++ +
  gi|336255357|ref|YP_004598464.1| 220 GTTFLEDHVVSTTENSELICTVRDVSDREARE-RKLTRLHAATRD 263
                                       55677888888889999999999999888755.456667766555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00035
                       HATPase_c_3   8 aelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatss 60 
                                         l +N+++     v+++v + + +++ + +eDdG G++ ++  + ++ + s+
  gi|336255357|ref|YP_004598464.1| 699 ENLFRNAVEHGGDGVTVTVGDLE-DEAGFYVEDDGPGIPDDDRARIFESGYST 750
                                       567788999888899****9986.79***************999988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (794 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.39
# Mc/sec: 6112.00
//
Query:       gi|336255358|ref|YP_004598465.1|  [L=92]
Description: sulfur transfer protein ThiS [Halopiger xanaduensis SH-6]
Scores for complete 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   42.0   0.0    1.2e-10   41.9   0.0    1.0  1  ThiS      ThiS family


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 !   41.9   0.0   6.7e-15   1.2e-10       3      77 .]       7      92 .]       5      92 .] 0.94

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 6.7e-15
                                      ETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG........TTTTEEEEETTEEEGCC.TTTSB--TTCEEEE CS
                              ThiS  3 lfaelrelag..eeelelaegstvaelleaLgerypela........lerrvavavNgeivprl.wldtelkdgDevai 70
                                      l++  r+ +g  + e e+a ++tv+++++aL+ +yp+l           + v+v++N+++v ++ +++t+++dgD+++ 
  gi|336255358|ref|YP_004598465.1|  7 LYGPFRDPVGtkSLEREVAADATVRDVFAALADDYPALGddlfddgtFADSVIVLRNDRNVAHQcGAETPVADGDVLSA 85
                                      6777888888889999*******************************88**************77************** PP

                                      EESTTC- CS
                              ThiS 71 lppVaGG 77
                                       p+V GG
  gi|336255358|ref|YP_004598465.1| 86 APAVEGG 92
                                      ******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 780.79
//
Query:       gi|336255359|ref|YP_004598466.1|  [L=754]
Description: lactate utilization protein B/C [Halopiger xanaduensis SH-6]
Scores for 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-46  157.3   0.1    5.6e-46  156.6   0.1    1.3  1  LUD_dom   LUD domain
    1.6e-08   34.8   4.9    3.7e-08   33.7   4.9    1.7  1  Fer4_8    4Fe-4S dicluster domain
    4.9e-07   29.8   3.9     0.0011   19.0   0.3    2.4  2  Fer4_10   4Fe-4S dicluster domain
    5.3e-07   29.7   1.6    1.5e-06   28.3   1.7    1.7  1  Fer4_9    4Fe-4S dicluster domain
    6.1e-07   29.9   3.7    1.1e-06   29.1   3.7    1.5  1  Fer4_17   4Fe-4S dicluster domain
    2.1e-05   25.0   6.7    5.3e-05   23.7   6.7    1.7  1  Fer4_7    4Fe-4S dicluster domain
    5.7e-05   23.2   6.6    0.00028   21.0   6.6    2.0  1  Fer4_21   4Fe-4S dicluster domain
    0.00039   20.1  13.0     0.0012   18.6   2.2    2.4  2  Fer4      4Fe-4S binding domain
  ------ inclusion threshold ------
      0.015   15.3   2.3      0.015   15.3   2.3    2.4  2  Fer4_6    4Fe-4S binding domain
      0.034   14.6  13.4      0.085   13.4   3.0    2.4  2  Fer4_4    4Fe-4S binding domain
      0.046   13.8  14.6       0.16   12.2   3.5    2.5  2  Fer4_2    4Fe-4S binding domain
      0.046   13.5   0.3      0.046   13.5   0.3    2.2  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
        0.1   13.4   8.1      0.081   13.8   1.1    2.5  2  Fer4_22   4Fe-4S dicluster domain
       0.13   12.5  10.1      0.098   12.9   1.5    2.4  2  Fer4_18   4Fe-4S dicluster domain
       0.22   12.5  17.5      0.072   14.1   5.1    2.4  2  Fer4_3    4Fe-4S binding domain
        9.8    7.2  15.5        4.5    8.3   4.0    2.5  2  Fer4_16   4Fe-4S double cluster binding 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 !  156.6   0.1     5e-49   5.6e-46       1     173 [.      66     283 ..      66     303 .. 0.95

  Alignments for each domain:
  == domain 1  score: 156.6 bits;  conditional E-value: 5e-49
                           LUD_dom   1 leefienleangaevyyaktaeealelilellkeksv.......................vseggstdlgeigl... 51 
                                       +e++ e +e+ng++vy+a++a++a+++++e+++++++                       +se+++tdlge+ l   
  gi|336255359|ref|YP_004598466.1|  66 IEQVRETVEENGGTVYVADDAADANRYVREVVRDNDAetvvksksmtteeidlnehleaeGSEVWETDLGEFVLqva 142
                                       6899************************************************************************* PP

                           LUD_dom  52 ........apalhsgreevldlfeekl............treareelrekfltadvgitganfaiAetGtlvlvdne 108
                                               apa+h+ re++++lf+e +            t++are l e++ +advgitganf+ A+tGt+ lv++e
  gi|336255359|ref|YP_004598466.1| 143 deapshivAPAIHRSREDIARLFNEHFdldedletaqelTEFAREYLGERIDEADVGITGANFVTADTGTMALVTSE 219
                                       ***************************************************************************** PP

                           LUD_dom 109 gnrraltflpkvhivvvginkivpdledavkrlktaprnatrlqkktpyvsfisgpsrtadielv 173
                                       gn+r  + +p++h++v+g++ki p++ed+  +++++ r++t+ q++t+yvs+ s p  t  i+  
  gi|336255359|ref|YP_004598466.1| 220 GNARKSVAVPDTHVAVAGVEKIIPTFEDLQPFVELIGRSGTG-QDITSYVSLFSPPVGTPTIDFD 283
                                       ******************************************.**********999888877755 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   4.9   3.3e-11   3.7e-08       3      65 .]     320     387 ..     318     387 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 3.3e-11
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaae.....dvqeeqvlee....eealwsCttcgaCtevCpvgi 65 
                                        +Ci+C+aC ++C  +++ + h +  +    +     +     ++++    +e  + Ct+c +C+++Cpv+i
  gi|336255359|ref|YP_004598466.1| 320 LYCIRCSACANSCANFQSVGGHAFGGETYSGGiatgwE----AGVHGqdsaAEFNDLCTGCSRCVNQCPVKI 387
                                       68***********9999988665554444444333331....2222245568999***************98 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.4   0.00023      0.26       7      31 ..     320     343 ..     314     355 .. 0.78
   2 !   19.0   0.3   9.9e-07    0.0011       7      24 ..     371     393 ..     366     411 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                           Fer4_10   7 dtCirCgkCvkaCPadltsvgakge 31 
                                         CirC +C ++C a+++svg+ ++
  gi|336255359|ref|YP_004598466.1| 320 LYCIRCSACANSC-ANFQSVGGHAF 343
                                       57***********.87777766554 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 9.9e-07
                           Fer4_10   7 dtCirCgkCvkaCPadl.....t 24 
                                       d C++C +Cv+ CP+++     +
  gi|336255359|ref|YP_004598466.1| 371 DLCTGCSRCVNQCPVKIdipwiN 393
                                       78*************77777641 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   1.7   1.3e-09   1.5e-06       1      49 [.     321     386 ..     321     387 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.3e-09
                            Fer4_9   1 kCtgCgaCveaC........................pagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       +C++C aC ++C                        +agv+ +d+a++++       + C+gC +Cv+ Cp +
  gi|336255359|ref|YP_004598466.1| 321 YCIRCSACANSCanfqsvgghafggetysggiatgwEAGVHGQDSAAEFN-------DLCTGCSRCVNQCPVK 386
                                       6***********96666666666555555555544444444444444444.......56************87 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   3.7   9.9e-10   1.1e-06       2      61 .]     322     388 ..     321     388 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 9.9e-10
                           Fer4_17   2 CiqCgyClpeCpsyea.......ydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgld 61 
                                       Ci+C++C+++C  ++         +++   ++  +++g +++ ++ e  +lC++C +C+ +CP ++d
  gi|336255359|ref|YP_004598466.1| 322 CIRCSACANSCANFQSvgghafgGETYSGGIATGWEAGVHGQDSAAEFNDLCTGCSRCVNQCPVKID 388
                                       *************999666553333356689999999999999999*****************9886 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   6.7   4.8e-08   5.3e-05       2      51 ..     322     386 ..     321     387 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.8e-08
                            Fer4_7   2 CigCgaCvaaC................pvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       Ci C aC++ C                + +  + +e+    g+++++   + C+gC +Cv+ CP++
  gi|336255359|ref|YP_004598466.1| 322 CIRCSACANSCanfqsvgghafggetySGGIATGWEA-GVHGQDSAAEFNDLCTGCSRCVNQCPVK 386
                                       ***********55555555555444432223333333.344778889999**************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 !   21.0   6.6   2.5e-07   0.00028       7      54 ..     321     386 ..     318     389 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.5e-07
                           Fer4_21   7 kCigCgkCliaCedtshqai....................eidaktvlkvvedeCvGCnlCssvCPve 54 
                                        Ci C  C+ +C +   q +                     ++++  ++  +d C+GC  C++ CPv+
  gi|336255359|ref|YP_004598466.1| 321 YCIRCSACANSCAN--FQSVgghafggetysggiatgweaGVHGQDSAAEFNDLCTGCSRCVNQCPVK 386
                                       5***********96..888888766777666666655544344445557789**************94 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   3.4     0.007       7.9       7      18 ..     321     332 ..     319     332 .. 0.93
   2 !   18.6   2.2   1.1e-06    0.0012       6      21 ..     371     386 ..     369     387 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.007
                                       TSSS-THHHHHS CS
                              Fer4   7 kCigCGaCvevC 18 
                                        Ci+C aC++ C
  gi|336255359|ref|YP_004598466.1| 321 YCIRCSACANSC 332
                                       5*********99 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.1e-06
                                       TTSSS-THHHHHSTTT CS
                              Fer4   6 ekCigCGaCvevCPvg 21 
                                       ++C+gC +Cv+ CPv 
  gi|336255359|ref|YP_004598466.1| 371 DLCTGCSRCVNQCPVK 386
                                       99************95 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.1     0.046        52       9      19 ..     322     332 ..     321     337 .. 0.92
   2 ?   15.3   2.3   1.4e-05     0.015       7      22 ..     371     386 ..     368     387 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.046
                            Fer4_6   9 CigCgdCvrvC 19 
                                       Ci C +C++ C
  gi|336255359|ref|YP_004598466.1| 322 CIRCSACANSC 332
                                       **********9 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.4e-05
                            Fer4_6   7 dkCigCgdCvrvCPeg 22 
                                       d+C+gC +Cv+ CP +
  gi|336255359|ref|YP_004598466.1| 371 DLCTGCSRCVNQCPVK 386
                                       9*************75 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.8     0.015        17       4      14 ..     322     332 ..     317     336 .. 0.93
   2 ?   13.4   3.0   7.6e-05     0.085       2      16 ..     371     385 ..     370     388 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                            Fer4_4   4 CigCgsCvaaC 14 
                                       Ci+C +C ++C
  gi|336255359|ref|YP_004598466.1| 322 CIRCSACANSC 332
                                       *********** PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.6e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + C+gC +Cv+ CP+
  gi|336255359|ref|YP_004598466.1| 371 DLCTGCSRCVNQCPV 385
                                       67************7 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.4    0.0067       7.5      10      20 ..     322     332 ..     316     334 .. 0.88
   2 ?   12.2   3.5   0.00014      0.16       8      21 ..     371     384 ..     366     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0067
                            Fer4_2  10 CigCgaCvsaC 20 
                                       Ci+C+aC ++C
  gi|336255359|ref|YP_004598466.1| 322 CIRCSACANSC 332
                                       *********** PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00014
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                       d C+gC+ Cv+ CP
  gi|336255359|ref|YP_004598466.1| 371 DLCTGCSRCVNQCP 384
                                       68************ 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 ?   -0.2   0.5      0.71   7.9e+02      13      37 ..     311     333 ..     304     340 .. 0.76
   2 ?   13.5   0.3   4.1e-05     0.046      17      54 ..     366     400 ..     357     403 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.71
                                       -HHHHHHHHTT----TT-HHHHCST CS
                           Fer4_20  13 teeealeeAsRClqCkkapcvkgCP 37 
                                       +e++ l+e   C++C  + c ++C 
  gi|336255359|ref|YP_004598466.1| 311 REDDQLRETLYCIRC--SACANSCA 333
                                       566778888889999..67888885 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.1e-05
                                       HHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-H CS
                           Fer4_20  17 aleeAsRClqCkkapcvkgCPveidipefikkiaegnl 54 
                                       a+e  + C  C  + cv++CPv+idip +i+++ ++++
  gi|336255359|ref|YP_004598466.1| 366 AAEFNDLCTGC--SRCVNQCPVKIDIP-WINTVVRDRI 400
                                       55556679999..89***********9.9999887776 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.0      0.17   1.9e+02       2      13 ..     322     333 ..     312     338 .. 0.81
   2 ?   13.8   1.1   7.3e-05     0.081      80      96 .]     371     387 ..     361     387 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.17
                           Fer4_22   2 ClsCgaCtlvCp 13 
                                       C++C+aC+  C+
  gi|336255359|ref|YP_004598466.1| 322 CIRCSACANSCA 333
                                       888888888875 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.3e-05
                           Fer4_22  80 sgCvGCgRCieacpvki 96 
                                         C+GC RC+++cpvki
  gi|336255359|ref|YP_004598466.1| 371 DLCTGCSRCVNQCPVKI 387
                                       68************987 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.6     0.052        58      83      97 ..     320     334 ..     305     344 .. 0.67
   2 ?   12.9   1.5   8.8e-05     0.098      56      77 ..     368     389 ..     343     391 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.052
                           Fer4_18  83 leciscllcidacdk 97 
                                       l ci c+ c ++c +
  gi|336255359|ref|YP_004598466.1| 320 LYCIRCSACANSCAN 334
                                       458888888888876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.8e-05
                           Fer4_18  56 kgagdcidcescvkvcPtgidi 77 
                                       + +  c+ c+ cv+ cP++idi
  gi|336255359|ref|YP_004598466.1| 368 EFNDLCTGCSRCVNQCPVKIDI 389
                                       33445****************9 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   4.5      0.11   1.2e+02       1      11 [.     322     332 ..     322     334 .. 0.95
   2 ?   14.1   5.1   6.4e-05     0.072       1      14 [.     373     386 ..     373     387 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C+ C+aC ++C
  gi|336255359|ref|YP_004598466.1| 322 CIRCSACANSC 332
                                       *********** PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.4e-05
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       CtgC++Cv+ CPv+
  gi|336255359|ref|YP_004598466.1| 373 CTGCSRCVNQCPVK 386
                                       ************98 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 ?    2.7  15.9      0.21   2.4e+02       2      66 ..     322     385 ..     321     386 .. 0.69
   2 ?    8.3   4.0     0.004       4.5       2      15 ..     373     386 ..     372     394 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.21
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       C++C +Ca++C      + +++  e+      +t  + +++ +  + + +  +tgC +C++ CP+
  gi|336255359|ref|YP_004598466.1| 322 CIRCSACANSCANFQSVGGHAFGGETYSGGI-ATGWEAGVHGQDSAAEFNDLCTGCSRCVNQCPV 385
                                       ***********99666655344444333322.345566666666666667789***********8 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.004
                           Fer4_16   2 CgtCgkCaevCPtn 15 
                                       C++C +C++ CP++
  gi|336255359|ref|YP_004598466.1| 373 CTGCSRCVNQCPVK 386
                                       99999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (754 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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):              16  [number of targets reported over threshold]
# CPU time: 0.66u 0.23s 00:00:00.89 Elapsed: 00:00:00.40
# Mc/sec: 5656.44
//
Query:       gi|336255360|ref|YP_004598467.1|  [L=186]
Description: lactate utilization protein B/C [Halopiger xanaduensis SH-6]
Scores for 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-14   52.0   0.0    9.5e-14   51.5   0.0    1.3  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 !   51.5   0.0   5.3e-18   9.5e-14      71     189 .]      54     165 ..       5     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 5.3e-18
                           LUD_dom  71 treareelrekfltadvgitganfaiAetGtlvlvdnegnrraltflpkvhivvvginkivpdledavkrlktaprn 147
                                       t+  r+ +  ++ +a  g+t a +++A+ G++vl  ++  +   ++ p+ h+vv+    iv d+  a++rl      
  gi|336255360|ref|YP_004598467.1|  54 TDVVRDPTPAQLRDAACGVTAAAIGVADYGSVVLEATPDGAEFASLFPDRHVVVLRERDIVSDMAAAFERLGD---- 126
                                       5667777788999************************************************************.... PP

                           LUD_dom 148 atrlqkktpyvsfisgpsrtadielvlvygvhgpkrihvilv 189
                                         r ++    + + +gps tad   +lv gvhgp+++h i++
  gi|336255360|ref|YP_004598467.1| 127 --RFRDGRDDAVIATGPSATADMG-ELVHGVHGPRETHAIIL 165
                                       ..5556666888999*******66.***************96 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:                      202  (0.0112667); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1526.40
//
Query:       gi|336255361|ref|YP_004598468.1|  [L=254]
Description: IclR family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-40  136.7   0.0    5.6e-40  136.2   0.0    1.3  1  IclR            Bacterial transcriptional regulator
    3.5e-10   39.5   1.5    3.7e-09   36.3   0.4    2.6  3  HTH_IclR        IclR helix-turn-helix domain
    2.8e-06   27.1   0.0    7.5e-06   25.7   0.0    1.7  1  HTH_5           Bacterial regulatory protein, arsR family
    3.2e-06   27.1   0.8    7.8e-06   25.9   0.2    1.9  2  HTH_20          Helix-turn-helix domain
    7.8e-05   22.2   0.0    0.00017   21.1   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00012   21.9   0.1    0.00049   19.9   0.0    2.0  2  MarR_2          MarR family
    0.00018   21.3   0.1    0.00084   19.2   0.0    2.1  2  MarR            MarR family
     0.0007   19.4   0.0      0.013   15.4   0.0    2.4  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0039   17.0   0.0     0.0091   15.8   0.0    1.6  1  DUF742          Protein of unknown function (DUF742)
     0.0079   16.7   0.0      0.022   15.3   0.0    1.7  1  HTH_27          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.015   15.1   0.0        1.9    8.4   0.0    2.6  2  HTH_23          Homeodomain-like domain
      0.024   14.6   0.1        0.3   11.1   0.0    2.6  2  HTH_11          HTH domain
      0.027   14.7   0.0      0.069   13.4   0.0    1.7  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.029   14.0   0.0      0.082   12.6   0.0    1.7  1  Sigma70_r4_2    Sigma-70, region 4
      0.042   14.3   0.3       0.11   13.0   0.0    1.9  2  HTH_40          Helix-turn-helix domain
      0.059   13.2   0.2       0.18   11.7   0.0    1.9  2  HTH_10          HTH DNA binding domain
       0.06   13.5   0.0       0.27   11.5   0.0    2.0  2  HTH_34          Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.2   0.0   5.3e-43   5.6e-40       3     127 ..     124     248 ..     122     250 .. 0.97

  Alignments for each domain:
  == domain 1  score: 136.2 bits;  conditional E-value: 5.3e-43
                                       EEETTSTT-EEEGGGSHHHHHHHHTS-HHHHHHHHHHHT---SSTTS--SHHHHHHHHHHHHHHTSEEEESSSSTTE CS
                              IclR   3 lravsaiGtrlplyataiGKalLaaldeeeleallerlelkrlterTitdpeeLleeLakvReqGyavdreEeeegv 79 
                                       +++ ++iG+r+ l++ta+GKa+La+ +e  +++++ r++l ++terTitd++eL+++L+++Re+Gya+d+eE  +g+
  gi|336255361|ref|YP_004598468.1| 124 VTLDTHIGKRVHLHTTALGKAILAHRSESTVDEIIDRHGLPAVTERTITDEAELKAQLEAIRERGYAIDDEERVLGM 200
                                       67889************************************************************************ PP

                                       EEEEEEEE-TTSSEEEEEEEEEETTTSHHHHHHHHHHHHHHHHHHHHH CS
                              IclR  80 rciAapifdasgevvaAvsvsgptarlteeelkeellalvreaArkis 127
                                       rciAapi d++ e+++A+svsgpt+r+t+++++ee+ + v  +A+ i+
  gi|336255361|ref|YP_004598468.1| 201 RCIAAPICDENDEPLGAISVSGPTNRFTDDRFDEEIPKHVLSTANVIE 248
                                       ********************************************9997 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 !   36.3   0.4   3.5e-12   3.7e-09       5      50 ..      15      59 ..      11      61 .. 0.92
   2 ?   -3.5   0.0       8.9   9.4e+03      22      30 ..      92     100 ..      90     102 .. 0.73
   3 ?    1.5   0.0      0.25   2.6e+02      12      31 ..     145     164 ..     143     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 3.5e-12
                                      HHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  5 alaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +++i + l e  ++ +++elA+++ +pkStvh +L+tL+e  y+  
  gi|336255361|ref|YP_004598468.1| 15 TFQIVETLHELEGA-GVAELAAELEMPKSTVHDHLRTLTEAEYLVN 59
                                      699**********8.9*************************99975 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.9
                                       HHHHHHHTS CS
                          HTH_IclR  22 selArrtgl 30 
                                       + lA++tg 
  gi|336255361|ref|YP_004598468.1|  92 KKLAEETGE 100
                                       568999885 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.25
                                       -CTTBSS-BHHHHHHHHTS- CS
                          HTH_IclR  12 laeapqeltlselArrtglp 31 
                                       + +++ e t+ e+ +r glp
  gi|336255361|ref|YP_004598468.1| 145 ILAHRSESTVDEIIDRHGLP 164
                                       56677788***********9 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 !   25.7   0.0   7.1e-09   7.5e-06       6      44 ..      17      56 ..      14      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 7.1e-09
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGL 44
                                      +I+  L e + + v ela+el++++stv  HL+ L ea +
  gi|336255361|ref|YP_004598468.1| 17 QIVETLHElEGAGVAELAAELEMPKSTVHDHLRTLTEAEY 56
                                      57777777444789***********************987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.2   7.4e-09   7.8e-06      14      54 ..      17      57 ..      11      61 .. 0.88
   2 ?   -2.1   0.0         4   4.2e+03      26      49 ..     153     185 ..     144     193 .. 0.52

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7.4e-09
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                       i   L++ eg+ ++ela++l+++k+t+++HLr+L ea+++
  gi|336255361|ref|YP_004598468.1| 17 QIVETLHELEGAGVAELAAELEMPKSTVHDHLRTLTEAEYL 57
                                      5777788889999*************************986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4
                                       -HHHHHHHHT.........S-HHHHHHHHHHHH CS
                            HTH_20  26 taselaerld.........lskntlsyHLrvLe 49 
                                       t+ e+ +r +         ++ ++l  +L++ +
  gi|336255361|ref|YP_004598468.1| 153 TVDEIIDRHGlpavtertiTDEAELKAQLEAIR 185
                                       444555554444433344344555555555555 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 !   21.1   0.0   1.6e-07   0.00017       4      47 ..      14      57 ..      12      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.6e-07
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      t+++I e+L +  +   +eLA +l +++stv+ +l+ L+e++++
  gi|336255361|ref|YP_004598468.1| 14 TTFQIVETLHELEGAGVAELAAELEMPKSTVHDHLRTLTEAEYL 57
                                      78999999999999999************************996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   4.7e-07   0.00049       8      52 ..      16      58 ..      12      65 .. 0.81
   2 ?   -1.4   0.0       2.1   2.3e+03      14      33 ..     146     163 ..     144     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.7e-07
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +++   L+  +g    v+ela++l ++ks+v+ +l+ L +a +++
  gi|336255361|ref|YP_004598468.1| 16 FQIVETLHELEG--AGVAELAAELEMPKSTVHDHLRTLTEAEYLV 58
                                      555555556666..56*************************9986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                                       HHCTTTSEEEHHHHHHHHTS CS
                            MarR_2  14 Lgrrpgrdltvgelarrlgl 33 
                                       L++r +   tv e+ +r gl
  gi|336255361|ref|YP_004598468.1| 146 LAHRSE--STVDEIIDRHGL 163
                                       566666..699999999887 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0     8e-07   0.00084       4      47 ..      14      57 ..      12      58 .. 0.94
   2 ?   -2.1   0.0       3.6   3.8e+03      11      25 ..      82      96 ..      81      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8e-07
                                      HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      t f i+++l+e +++ v+eLa  l++ kstv   l++L +++++
  gi|336255361|ref|YP_004598468.1| 14 TTFQIVETLHELEGAGVAELAAELEMPKSTVHDHLRTLTEAEYL 57
                                      7799**********************************999875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.6
                                      HHHHSTTEEHHHHHH CS
                              MarR 11 ilyeqgplsvseLak 25
                                      +ly+  ++ +++La+
  gi|336255361|ref|YP_004598468.1| 82 KLYQVASPEIKKLAE 96
                                      688888999999998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05     0.013      16      60 ..      21      65 ..      16      90 .. 0.84
   2 ?    1.4   0.0      0.28   2.9e+02      17      35 ..     146     164 ..     143     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                      +L +l+ a + e+a el+ p+s+v + Lr L ++ +   e g+++
  gi|336255361|ref|YP_004598468.1| 21 TLHELEGAGVAELAAELEMPKSTVHDHLRTLTEAEYLVNEGGTYH 65
                                      56688999**************************99998888854 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.28
                                       HHHHCCCHHCHHCCCTTSS CS
                              TrmB  17 Llklgpatadeiaeelgvp 35 
                                       L  + ++t+dei  + g+p
  gi|336255361|ref|YP_004598468.1| 146 LAHRSESTVDEIIDRHGLP 164
                                       558999******9999998 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.6e-06    0.0091      45      88 ..      15      60 ..       2      69 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.6e-06
                            DUF742 45 hrailrLcre..plsVaelaAelklPvgvvrvLlsdLldaglltvr 88
                                        +i++  +e     VaelaAel++P ++v+  l  L +a++l+ +
  gi|336255361|ref|YP_004598468.1| 15 TFQIVETLHEleGAGVAELAAELEMPKSTVHDHLRTLTEAEYLVNE 60
                                      556666666555788****************999999999998755 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 !   15.3   0.0     2e-05     0.022       9      51 ..      15      60 ..       9      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                            HTH_27  9 Lhlir...hrrrrkkladlcgrlnvedshisyslkkLtekGLvert 51
                                       ++i    h+++++  a+l+  l + +s+++  l+ Lte+++++ +
  gi|336255361|ref|YP_004598468.1| 15 TFQIVetlHELEGAGVAELAAELEMPKSTVHDHLRTLTEAEYLVNE 60
                                      4555556679999999***************************655 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0018       1.9      10      41 ..      18      51 ..      16      62 .. 0.81
   2 ?    4.1   0.0      0.04        42      28      48 ..     148     165 ..     144     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0018
                            HTH_23 10 illllae..GlsvreIAreLgvsrrTvyrwlkry 41
                                      i+  l e  G+ v+e A+eL ++++Tv   l++ 
  gi|336255361|ref|YP_004598468.1| 18 IVETLHEleGAGVAELAAELEMPKSTVHDHLRTL 51
                                      555666556******************9877765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.04
                            HTH_23  28 gvsrrTvyrwlkryreeGleg 48 
                                       ++s++Tv+ ++ r   +Gl++
  gi|336255361|ref|YP_004598468.1| 148 HRSESTVDEIIDR---HGLPA 165
                                       89*********99...77765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00028       0.3       3      43 ..      16      55 ..      14      61 .. 0.85
   2 ?    0.3   0.1      0.65   6.8e+02      44      54 ..     179     189 ..     144     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      +qi+e L e +g    +eLA eL++ ++tv+ ++++L+e+ 
  gi|336255361|ref|YP_004598468.1| 16 FQIVETLHELEG-AGVAELAAELEMPKSTVHDHLRTLTEAE 55
                                      688888877776.7899********************9975 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.65
                            HTH_11  44 vpIesepgrGY 54 
                                       +++e+ + rGY
  gi|336255361|ref|YP_004598468.1| 179 AQLEAIRERGY 189
                                       45577777776 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 ?   13.4   0.0   6.5e-05     0.069      19      55 ..      24      60 ..      17      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.5e-05
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                      e + +++++la +L+  +s+V   l+ L +++y++ e
  gi|336255361|ref|YP_004598468.1| 24 ELEGAGVAELAAELEMPKSTVHDHLRTLTEAEYLVNE 60
                                      55568899*************************9765 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 ?   12.6   0.0   7.7e-05     0.082      20      47 ..      21      48 ..      21      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.7e-05
                                      HHHHTS---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 20 llryleglsykEIAellgisegtVksrl 47
                                      +l++leg   +E A++l+++ +tV  +l
  gi|336255361|ref|YP_004598468.1| 21 TLHELEGAGVAELAAELEMPKSTVHDHL 48
                                      69**********************9887 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011      0.11      10      41 ..      25      56 ..      15     102 .. 0.87
   2 ?   -1.9   0.0       4.6   4.8e+03      14      26 ..     153     165 ..     143     188 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                            HTH_40 10 eeglsieeIAkerglkesTIegHLaelieege 41
                                       eg  ++e A+e ++ +sT+ +HL  l e+++
  gi|336255361|ref|YP_004598468.1| 25 LEGAGVAELAAELEMPKSTVHDHLRTLTEAEY 56
                                      68999*******************99999865 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.6
                            HTH_40  14 sieeIAkerglke 26 
                                       +++eI ++ gl  
  gi|336255361|ref|YP_004598468.1| 153 TVDEIIDRHGLPA 165
                                       5555555544432 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.18      25      46 ..      29      50 ..      27      54 .. 0.90
   2 ?   -3.1   0.0       6.7     7e+03      26      34 ..      91      99 ..      90      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                            HTH_10 25 tlkeLAkelGIskstlsehLrk 46
                                       ++eLA el   kst+++hLr 
  gi|336255361|ref|YP_004598468.1| 29 GVAELAAELEMPKSTVHDHLRT 50
                                      689*****************96 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.7
                            HTH_10 26 lkeLAkelG 34
                                      +k+LA+e G
  gi|336255361|ref|YP_004598468.1| 91 IKKLAEETG 99
                                      789999987 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 ?   11.5   0.0   0.00025      0.27       3      45 ..      16      58 ..      14      63 .. 0.94
   2 ?   -1.3   0.0       2.4   2.5e+03      28      45 ..     174     191 ..     166     209 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                            HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                      ++++ +L + + a  +el ++le+ ++    hl++L +a+Y++
  gi|336255361|ref|YP_004598468.1| 16 FQIVETLHELEGAGVAELAAELEMPKSTVHDHLRTLTEAEYLV 58
                                      78999************************************96 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                            HTH_34  28 dgnLsvhlkkLekagYie 45 
                                       +++L ++l+++ + gY  
  gi|336255361|ref|YP_004598468.1| 174 EAELKAQLEAIRERGYAI 191
                                       467888888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2156.77
//
Query:       gi|336255362|ref|YP_004598469.1|  [L=144]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-21   77.3   0.9    1.8e-21   77.2   0.9    1.0  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
       0.16   11.3   0.0       0.37   10.1   0.0    1.5  1  tify      tify domain


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 !   77.2   0.9     2e-25   1.8e-21       5     140 ..       3     138 ..       1     139 [. 0.98

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 2e-25
                                       EEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCE CS
                               Usp   5 IlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvk 81 
                                       ++ a+Dg + s ++l  + +la +++ +l+++ v + ++  +  +    +e++   ++++e ++  +++ ae+   +
  gi|336255362|ref|YP_004598469.1|   3 VVTAIDGEDGSSRVLSEGWALANRFDEPLHAILVYEGPSHRELINKSLNVEDSVTPERAQEIAERVLADVAEGVTDE 79 
                                       899**********************************************************99999*********** PP

                                       EEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  82 vevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                        e v + g++  eile+aee da  iVvG r rs + ++l+GSv+++vl  a+cpVl+V
  gi|336255362|ref|YP_004598469.1|  80 YEAVGRTGEAPAEILEYAEEVDARYIVVGGRSRSPVGKALFGSVTQSVLLDASCPVLAV 138
                                       *********************************************************98 PP

>> tify  tify domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   4.2e-05      0.37      16      29 ..      51      64 ..      49      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.2e-05
                              tify 16 vVfDdvpaeKAkaI 29
                                      +V D+v++e+A++I
  gi|336255362|ref|YP_004598469.1| 51 NVEDSVTPERAQEI 64
                                      788**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 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:                        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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1118.82
//
Query:       gi|336255363|ref|YP_004598470.1|  [L=927]
Description: glycoside hydrolase 2 sugar binding protein [Halopiger xanaduensis SH-6]
Scores for 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-18   65.4   0.1      2e-17   63.6   0.1    1.9  1  Glyco_hydro_2_N  Glycosyl hydrolases family 2, sugar binding 
    1.2e-14   54.9   2.0    5.6e-14   52.7   0.0    2.7  3  Glyco_hydro_2    Glycosyl hydrolases family 2
    1.3e-12   47.5   0.0    1.6e-11   43.9   0.0    2.2  1  Glyco_hydro_2_C  Glycosyl hydrolases family 2, TIM barrel dom
     0.0031   18.1   0.0     0.0081   16.7   0.0    1.7  1  BetaGal_dom4_5   Beta-galactosidase jelly roll domain
  ------ inclusion threshold ------
      0.024   15.1   9.8       0.16   12.5   0.1    3.3  3  Cadherin-like    Cadherin-like beta sandwich domain
      0.034   14.2   0.5       0.16   12.0   0.1    2.2  2  CIDE-N           CIDE-N domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_2_N  Glycosyl hydrolases family 2, sugar binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.1   6.5e-21     2e-17       4     168 ..      20     174 ..      18     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 6.5e-21
                                       -SEEEEEEEESSGGGSCCCCHCST-T...TSEEEECSCEGCGGSEEESSSTSS.TCTTBHHSS-CEEEEEEEEEE-H CS
                   Glyco_hydro_2_N   4 lnGeWaFalfdapkgvdesWlesalq...esrtiavPsdwelqpiytnveypidvdsadlptvngtgvYartfeids 77 
                                       l G+W+F  +++++g + +W   + +    +rt+ vP+ w+ +               + + ++gt++Y+rt+ ++ 
  gi|336255363|ref|YP_004598470.1|  20 LSGPWRFVTDPDERGRERNWAAPDEPwpdRARTVEVPHVWQEH--------------DECREYTGTAWYRRTIDLEA 82 
                                       89*****************976664322279**********99..............6789999********99977 PP

                                       HHHHS..EEEEEESEEESEEEEEETTEEEEEEE-TTS-EEEEGGGGS-SEEEEEEEEEESTTGGGGGBECTCEESSS CS
                   Glyco_hydro_2_N  78 kwaek..kvrllFegvtsasevwvngqevgkrqgsylpfefDltpylseGknriavkvlkwsdgsyieDeskaltgd 152
                                          ++  +  l+F +v+    v vng+  g ++g+ylpf +D+t  l eG+n iav v   +d s i   +    + 
  gi|336255363|ref|YP_004598470.1|  83 PPDGDdrRALLRFGAVDYEAVVRVNGERAGSNRGGYLPFSVDVTDALVEGENTIAVEVTDPDDISEIPHGK--QGEP 157
                                       6554444999************************************************8887877777662..3345 PP

                                       EE.E--EEESEEEEEEE CS
                   Glyco_hydro_2_N 153 ly.tlsGiyRdvsLlkk 168
                                       +y ++sGi+ +v+L   
  gi|336255363|ref|YP_004598470.1| 158 WYqRVSGIWQKVTLEDV 174
                                       55368*******99765 PP

>> Glyco_hydro_2  Glycosyl hydrolases family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.0   1.9e-17   5.6e-14       2     110 .]     178     282 ..     177     282 .. 0.90
   2 ?   -3.3   0.1       4.8   1.4e+04      79      99 ..     404     424 ..     396     428 .. 0.80
   3 ?    0.7   0.0      0.28   8.3e+02       6      52 ..     625     674 ..     619     692 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.9e-17
                                       ECCCEEEEEEEETCSEEEEEEEEEEEEECSSSSCEEEEEEEEETTSTEEEEEEEEEEEESTT-EEEEEEEEEES--B CS
                     Glyco_hydro_2   2 hIedvfvttdlsddksakvevevelendsdksvevtleteikdaegkkvkeessvlslgngetksiklelevknpkl 78 
                                       ++e+++  ++++d +++++e+e++     + +    ++++i+ + + ++++++++  +  g+ ++   ++++++p +
  gi|336255363|ref|YP_004598470.1| 178 RVEQLRAAPNVED-DTVRIELETTAAAVATVEDPSAVDATITVEREGTAVASATTALEPDGTGDV---TISIEDPDY 250
                                       7899999******.*********999999999999999999999999999988777766666555...89******* PP

                                       BECCCB--EEEEEEEEETTEEEEEEEEEE-B- CS
                     Glyco_hydro_2  79 WspetPnLYtlkveldkdgkvidevstrfGfR 110
                                       W+petP LY+++v l++dg+v+d+ + +fG+R
  gi|336255363|ref|YP_004598470.1| 251 WTPETPALYDVRVALERDGTVVDRDEDYFGMR 282
                                       *******************************9 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.8
                                       BECCCB--EEEEEEEEETTEE CS
                     Glyco_hydro_2  79 WspetPnLYtlkveldkdgkv 99 
                                       W  ++P+  +++++l++dg +
  gi|336255363|ref|YP_004598470.1| 404 WGIGNPQGLDVETSLWDDGAK 424
                                       888999999999999888855 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.28
                                       EEEEEEEETC...SEEEEEEEEEEEEECSSSSCEEEEEEEEETTSTEEEE CS
                     Glyco_hydro_2   6 vfvttdlsdd...ksakvevevelendsdksvevtleteikdaegkkvke 52 
                                       v v+ dl+++   +++++ +++ ++nd+++++e+ l+ +i  + g+ +++
  gi|336255363|ref|YP_004598470.1| 625 VAVQLDLESRavwDDGRIAADAVVVNDTAEELEADLSWTIAGESGRRTVA 674
                                       5677777777888999******************9999988888877776 PP

>> Glyco_hydro_2_C  Glycosyl hydrolases family 2, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   5.3e-15   1.6e-11       1     195 [.     284     478 ..     284     511 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 5.3e-15
                                       EEEETTEEEETTEEE-EEEEEE-S-BTTT.BTS--HHHHHHHHHHHHHCT--EEEETTS--SHHHHHHHHHHT-EEE CS
                   Glyco_hydro_2_C   1 vevkdkllliNgkrllfkGvnrHedadrr.GraideellvkDlkllkqlniNavRtsHYPnqeevyelcDeyGlyvi 76 
                                       ve +d+ +++Ng +  ++G       +r+  r  + +  ++ +++ k l++N  R    P ++ ++e +D++Gl+v 
  gi|336255363|ref|YP_004598470.1| 284 VEARDGRIYLNGEPYPIRGALEQGYYPRTlYRPSEDDWFEREVRIAKDLGFNLLRKHIKPAHPDFLEAADRLGLFVW 360
                                       67789999999999999998888877776257777788999************************************ PP

                                       EE-S-B-TTSCCCCSHCT-CCCCTTTSGGGHHHHHHHHHHHHHHHTT-TTEEEEEEEESS................. CS
                   Glyco_hydro_2_C  77 dEanlethglaqklgeiepsynvladnpewlkavldrieelverdkNHpsviiWSlgNEs................. 136
                                       +E +  ++ + +                 +++   d+++ ++erd N psv++WS+ NE                  
  gi|336255363|ref|YP_004598470.1| 361 AEPANPSVCTER-----------------SKEELADQLRGMLERDYNRPSVVVWSIYNEEwgignpqgldvetslwd 420
                                       **9887776655.................45567899***************************************9 PP

                                       ..CHHHHHHHHHHHHHHH-TTSEEEEETCSSGGGTSSEEEECCTTTSSSTTCHHHHHHHHH CS
                   Glyco_hydro_2_C 137 ..gagedikalaelikklDptRlvhyegvaaareldviildiysrmyekvglleelekele 195
                                            + +++l+e +k+ DptRlv   + ++a+ +++i    y r + + + ++ +++ l 
  gi|336255363|ref|YP_004598470.1| 421 dgAKQASLAELYEETKAADPTRLVC-DNSGWAHVATDIN--DYHRYFVSPDRADAWAADLD 478
                                       97778899****************5.5555777777765..44444444333333333322 PP

>> BetaGal_dom4_5  Beta-galactosidase jelly roll domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.7e-06    0.0081       3     109 ..      36     141 ..      35     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.7e-06
                    BetaGal_dom4_5   3 erqgwhlpgkttsnnskwplt.....vlyssdyg.fhagvrlyrgtfdldlpsgldvslsltlsggtafrvsvwlNG 73 
                                       er +w  p++++ +  +   t     v    d+  + +g+ +yr t+dl+ p + d    l   g+  + + v +NG
  gi|336255363|ref|YP_004598470.1|  36 ER-NWAAPDEPWPDRAR---TvevphVWQEHDECrEYTGTAWYRRTIDLEAPPDGDDRRALLRFGAVDYEAVVRVNG 108
                                       67.89999998844332...2235665455555469***************99977777777778899********* PP

                    BetaGal_dom4_5  74 yqlgsyvphigpqvtFpvpegilnyngenvlavlvd 109
                                       +  gs   + g  + F+v       +gen++av v 
  gi|336255363|ref|YP_004598470.1| 109 ERAGS---NRGGYLPFSVDVTDALVEGENTIAVEVT 141
                                       *****...6677888888888778999*****9876 PP

>> Cadherin-like  Cadherin-like beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.3e-05      0.16      37      77 ..      99     145 ..      76     149 .. 0.78
   2 ?    6.2   1.8    0.0049        15      21      78 ..     187     254 ..     178     264 .. 0.72
   3 ?   -2.1   0.2         2   5.9e+03      36      61 ..     680     708 ..     643     722 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-05
                     Cadherin-like  37 dsvatvtvngvaveeg......stetkdvsLneGrnkieikvtaedg 77 
                                       d+ a v+vng+++ ++       +   +  L eG+n+i ++vt+ d+
  gi|336255363|ref|YP_004598470.1|  99 DYEAVVRVNGERAGSNrggylpFSVDVTDALVEGENTIAVEVTDPDD 145
                                       78899********99999887745556666779***********997 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0049
                     Cadherin-like  21 dVdedvdsvtitatae...........dsvatvtvngvaveegstetkdvsLne.Grnkieikvtaedg...s 78 
                                       +V++d+ ++ ++ ta            d+++tv+  g+av      +++  L++ G+ +++i +++ d    +
  gi|336255363|ref|YP_004598470.1| 187 NVEDDTVRIELETTAAavatvedpsavDATITVEREGTAVA-----SATTALEPdGTGDVTISIEDPDYwtpE 254
                                       57777777777777777777777886667777777777766.....5788896559999**999999984444 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2
                     Cadherin-like  36 e...dsvatvtvngvaveegstetkdvsL 61 
                                           ++ + v  ++v ++ +  +t ++ L
  gi|336255363|ref|YP_004598470.1| 680 TvrvADLVDVAASDVIADADAVTTETIAL 708
                                       22222333333333333333444444444 PP

>> CIDE-N  CIDE-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.76   2.3e+03      39      53 ..     213     227 ..     196     239 .. 0.69
   2 ?   12.0   0.1   5.3e-05      0.16      40      58 ..     260     279 ..     254     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.76
                                       TT-EEEETTTT-EE. CS
                            CIDE-N  39 eevtlvLeeDGTeVd 53 
                                        ++t+ +e  GT+V 
  gi|336255363|ref|YP_004598470.1| 213 VDATITVEREGTAVA 227
                                       566788888888885 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.3e-05
                                       T-EEEETTTT-EE..SCCCC CS
                            CIDE-N  40 evtlvLeeDGTeVd.deeyF 58 
                                       +v++ Le DGT+Vd de+yF
  gi|336255363|ref|YP_004598470.1| 260 DVRVALERDGTVVDrDEDYF 279
                                       699**********9678999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (927 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.39
# Mc/sec: 7209.37
//
Query:       gi|336255364|ref|YP_004598471.1|  [L=409]
Description: glycerol-3-phosphate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-32  110.5   0.0    1.4e-31  109.8   0.0    1.4  1  ABC_tran         ABC transporter
    2.6e-14   53.1   0.1    6.9e-14   51.8   0.1    1.8  1  TOBE_2           TOBE domain
    3.3e-11   43.8   0.0    1.6e-10   41.7   0.0    2.3  1  OB_MalK          MalK OB fold domain
    2.6e-07   30.8   0.1    7.4e-07   29.4   0.1    1.8  1  TOBE             TOBE domain
    2.1e-06   27.7   0.4     0.0023   17.8   0.1    2.4  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00036   20.5   0.0    0.00074   19.5   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
    0.00042   20.1   0.4       0.11   12.3   0.1    2.3  2  Cytidylate_kin   Cytidylate kinase
    0.00055   20.2   0.2     0.0021   18.3   0.0    1.9  2  AAA_22           AAA domain
    0.00068   19.3   0.0     0.0016   18.2   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
    0.00072   19.1   0.6     0.0064   16.0   0.6    2.1  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0014   18.4   0.5        0.1   12.3   0.0    2.1  2  AAA_15           AAA ATPase domain
     0.0017   18.7   0.1     0.0035   17.7   0.1    1.7  1  AAA_16           AAA ATPase domain
      0.003   18.1   0.2       0.06   13.9   0.0    3.0  3  CysA_C_terminal  CysA C-terminal regulatory domain
     0.0047   17.5   0.1      0.013   16.0   0.0    1.7  2  AAA_23           AAA domain
  ------ inclusion threshold ------
      0.025   15.1   0.1      0.062   13.8   0.1    1.9  1  AAA_18           AAA domain
       0.03   13.9   0.3       0.39   10.3   0.0    2.7  4  AAA_25           AAA domain
      0.046   13.8   0.1       0.16   12.0   0.1    2.0  1  MMR_HSR1         50S ribosome-binding GTPase
      0.052   13.3   0.0       0.11   12.2   0.0    1.5  1  AAA_30           AAA domain
      0.058   13.5   0.1       0.18   12.0   0.0    1.8  1  AAA_33           AAA domain
      0.077   12.2   0.0       0.14   11.3   0.0    1.3  1  NB-ARC           NB-ARC domain
      0.081   12.8   0.0       0.17   11.8   0.0    1.5  1  NACHT            NACHT domain
       0.11   12.4   0.0       0.22   11.4   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea


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 !  109.8   0.0   1.7e-34   1.4e-31       2     136 ..      50     192 ..      49     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 1.7e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +n +  ++ ge + ivG++G+GKStLl+++agl++ t+G+i++ g+++k    e  ++ i++++q+  l p+++vr+
  gi|336255364|ref|YP_004598471.1|  50 ENFNARIEDGEFITIVGPSGSGKSTLLRMIAGLEEITAGDIKIGGESIKG--VEPQDRGIAMVFQNYALYPHMSVRK 124
                                       689999********************************************..999********************** PP

                                       H..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n              e ++++e+ ++ +g+ +     ++s+ps+LSgGq+qrva  ra++++pk++l+DEp 
  gi|336255364|ref|YP_004598471.1| 125 NmsyglklttdmsdeEIEQRVEETAEMMGIGD----QLDSKPSELSGGQQQRVATGRAIVRDPKIFLMDEPL 192
                                       **********9655555555666666666555....666667*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.1   8.5e-17   6.9e-14       1      76 []     310     379 ..     310     379 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 8.5e-17
                            TOBE_2   1 laiRPEklrlaaagg.anglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                       l+iRPE+++    gg ++++++tVe ve  Gs+  ++++++g +  +vr+p       +++Gd+Ve+++dp+d++++
  gi|336255364|ref|YP_004598471.1| 310 LGIRPEDIEY---GGdGDSIAATVEVVEVAGSDNFVYLDIEGSEC-RVRVPGDV---KPDVGDRVEIAFDPADIHLF 379
                                       79********...88456***********************9965.99999999...9*****************98 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   1.9e-13   1.6e-10       1      53 []     266     317 ..     266     317 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1.9e-13
                           OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeq.klalklyagkevilGiRPEhi 53 
                                       GSPaMNf+++ ++++   + g+g+t ++p++  +   ++ ag+++ lGiRPE+i
  gi|336255364|ref|YP_004598471.1| 266 GSPAMNFFDVSLSGST--LVGDGFTYEIPASIvDEIRESGAGDDLELGIRPEDI 317
                                       9************665..899***********66699999*************8 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   9.1e-10   7.4e-07       7      64 .]     326     378 ..     322     378 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 9.1e-10
                              TOBE   7 lpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                       + +tV+vve +gs+ +V++d++g +   +rv+++  ++    +G++V +++++a++hl
  gi|336255364|ref|YP_004598471.1| 326 IAATVEVVEVAGSDNFVYLDIEGSE-CRVRVPGDVKPD----VGDRVEIAFDPADIHL 378
                                       789**********************.************....**************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 !   17.8   0.1   2.8e-06    0.0023       2      43 ..      62      94 ..      61     150 .. 0.70
   2 !    8.1   0.0    0.0025         2     234     299 ..     162     225 ..     127     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.8e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggir 43
                                        ++Gp gsGKS+LL+ + +l  +         ++++++  +
  gi|336255364|ref|YP_004598471.1| 62 ITIVGPSGSGKSTLLRMIAGLEEI---------TAGDIKIGG 94
                                      679***************999432.........222233333 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0025
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                       ++elS G+++  a   a+ r++   +++l DEp ++L+ kl  +  + l +l++  g+  i +TH+ 
  gi|336255364|ref|YP_004598471.1| 162 PSELSGGQQQRVATGRAIVRDP---KIFLMDEPLSNLDAKLKVHMRTELQRLQEeLGTTTIYVTHDQ 225
                                       5677777777777777788877...9********************99966666588999*****85 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0     9e-07   0.00074      89     131 ..      48      91 ..      27      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9e-07
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       ++e+ +++++d +++++vG+SG GKStL+ ++++ +e+  g+++
  gi|336255364|ref|YP_004598471.1|  48 AIENFNARIEDgEFITIVGPSGSGKSTLLRMIAGLEEITAGDIK 91 
                                       57788888888899*******************98888888875 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   0.00013      0.11       1      19 [.      62      80 ..      62      91 .. 0.90
   2 ?    5.9   0.0     0.012       9.7      72     123 ..     128     180 ..      98     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                      EEEE-STTSSHHHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvarala 19
                                      i+i GP+gsGKs++ r++a
  gi|336255364|ref|YP_004598471.1| 62 ITIVGPSGSGKSTLLRMIA 80
                                      899*************998 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                                       TTEE-TTGGGSHHHHHHHHHHTTSHHHHHHHHHHHHTT-B.SSBEEEEESSII CS
                    Cytidylate_kin  72 ngedveeelrsdevekavSavaaipavRailvkklrelvk.karvvveGRDig 123
                                        g +++++++ +e+e++v + a +  + ++l +k  el   +++ v+ GR i 
  gi|336255364|ref|YP_004598471.1| 128 YGLKLTTDMSDEEIEQRVEETAEMMGIGDQLDSKPSELSGgQQQRVATGRAIV 180
                                       466788999****************************99989999*****885 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   2.6e-06    0.0021       4      28 ..      58      82 ..      54     110 .. 0.87
   2 ?   -1.0   0.0       2.4   1.9e+03      59      98 ..     202     239 ..     163     262 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.6e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleq 28
                                      +  +++++G+sG+GK+tllr+++  
  gi|336255364|ref|YP_004598471.1| 58 DGEFITIVGPSGSGKSTLLRMIAGL 82
                                      6789****************98765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.4
                            AAA_22  59 ellralglelkaerlsseellealeqalraravielliiD 98 
                                       ++  +l++ +++  +++  ++++ ++ + + ++ +++++D
  gi|336255364|ref|YP_004598471.1| 202 HMRTELQRLQEE-LGTTTIYVTHDQHEALTMSD-RIIVLD 239
                                       333344433333.44555555666666666666.788887 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 !   18.2   0.0   1.9e-06    0.0016      18      39 ..      55      76 ..      45      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-06
                            AAA_29 18 eidlkg.atlltGpsGsGKSTll 39
                                      +i+  g ++ ++GpsGsGKSTll
  gi|336255364|ref|YP_004598471.1| 55 RIED-GeFITIVGPSGSGKSTLL 76
                                      5664.44899************8 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   0.6   7.8e-06    0.0064       4     200 ..      40     226 ..      37     241 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.8e-06
                                       EEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   4 rleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeve 80 
                                       ++ +++F  +++ ++ ++ + +f  ivGp GSGKs ll  i    G ++ ++   +   +      ++ + +   ++
  gi|336255364|ref|YP_004598471.1|  40 KVYLDDFVAIENFNARIE-DGEFITIVGPSGSGKSTLLRMI---AGLEEITAGDIKIGGES----IKGVEPQDRGIA 108
                                       566666666643333333.44699**************999...56544433333333333....444555666677 PP

                                       EEEEETTEESSSSSSC.EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCC CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  81 itfdnedkklkiekee.vsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkv 156
                                       ++f+n     +++  + +s   ++ + + s+ +i+++  + +e++ +  + + ++++LSgG+++ va     Ai  v
  gi|336255364|ref|YP_004598471.1| 109 MVFQNYALYPHMSVRKnMSYGLKLTT-DMSDEEIEQRVEETAEMMGIGDQLDSKPSELSGGQQQRVATGR--AI--V 180
                                       77777766633332221333333333.334668888888889999999999999999****998777643..33..5 PP

                                       S--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                             SMC_N 157 kpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislree 200
                                       +   ++l+De  ++LD+k    + + l++ +++  +  i ++++++
  gi|336255364|ref|YP_004598471.1| 181 RDPKIFLMDEPLSNLDAKLKVHMRTELQRLQEElgTTTIYVTHDQH 226
                                       6666899999999999987777777777666663344555555543 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00013       0.1      10      43 ..      45      79 ..      38      82 .. 0.79
   2 ?    3.8   0.1     0.048        39     322     367 ..     181     226 ..     169     227 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            AAA_15 10 NFRslkdveidlsee.ltvliGkNnsGKSsileal 43
                                       F +++++   +++  + +++G+ +sGKS++l+++
  gi|336255364|ref|YP_004598471.1| 45 DFVAIENFNARIEDGeFITIVGPSGSGKSTLLRMI 79
                                      5666777777777767****************998 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.048
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                        +++i+l++EP  +L  +++ ++   l++l ++  t +i+ TH  h
  gi|336255364|ref|YP_004598471.1| 181 RDPKIFLMDEPLSNLDAKLKVHMRTELQRLQEELGTTTIYVTHDQH 226
                                       5899***************************************987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   4.3e-06    0.0035      21      45 ..      56      80 ..      47     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.3e-06
                            AAA_16 21 sgrpelvllsGesGvGKsslvrell 45
                                        ++e + ++G+sG+GKs+l+r+++
  gi|336255364|ref|YP_004598471.1| 56 IEDGEFITIVGPSGSGKSTLLRMIA 80
                                      3445899***************997 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.5   1.2e+03       3      12 ..      52      61 ..      52      64 .. 0.87
   2 ?   -2.1   0.1       7.7   6.3e+03       8      20 ..      86      98 ..      84     106 .. 0.75
   3 !   13.9   0.0   7.3e-05      0.06       1      42 [.     271     318 ..     271     318 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.5
                   CysA_C_terminal  3 FhGrvedGkl 12
                                      F++r+edG +
  gi|336255364|ref|YP_004598471.1| 52 FNARIEDGEF 61
                                      99******85 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.7
                   CysA_C_terminal  8 edGklriGglalp 20
                                        G ++iGg +++
  gi|336255364|ref|YP_004598471.1| 86 TAGDIKIGGESIK 98
                                      5789999999886 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 7.3e-05
                   CysA_C_terminal   1 NlFhGrvedGklriGglalpvP.......elagadgqevvayVRPhDle 42 
                                       N+F+  +++ +l+ +g++ ++P       ++ ga g++  +++RP+D+e
  gi|336255364|ref|YP_004598471.1| 271 NFFDVSLSGSTLVGDGFTYEIPasivdeiRESGA-GDDLELGIRPEDIE 318
                                       8999999977888888888888879997666666.99***********8 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   1.6e-05     0.013      10      39 ..      49      79 ..      35      82 .. 0.73
   2 ?   -1.9   0.0         5   4.1e+03     130     130 ..     150     150 ..      84     218 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                            AAA_23 10 frdqeidF.skgltlItGpNGaGKTTildAi 39
                                      +++++    +  +  I+Gp G+GK+T+l+ i
  gi|336255364|ref|YP_004598471.1| 49 IENFNARIeDGEFITIVGPSGSGKSTLLRMI 79
                                      445444443445778*************988 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5
                            AAA_23 130 i 130
                                       +
  gi|336255364|ref|YP_004598471.1| 150 E 150
                                       1 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   7.7e-05     0.062       1      25 [.      62      94 ..      62     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.7e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf........g 25
                                      I + G++G+GK+tl + ++ ++++        g
  gi|336255364|ref|YP_004598471.1| 62 ITIVGPSGSGKSTLLRMIAGLEEItagdikigG 94
                                      89**************99888744444444432 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00047      0.39      30      50 ..      56      76 ..      50      81 .. 0.88
   2 ?   -2.1   0.0       2.9   2.4e+03      78      98 ..     133     160 ..     130     213 .. 0.70
   3 ?   -0.5   0.0      0.96   7.8e+02     167     191 ..     202     226 ..     171     228 .. 0.77
   4 ?   -2.1   0.0       2.9   2.4e+03     102     129 ..     366     391 ..     329     403 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00047
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +  ge++ ++G++g+GK+tl+
  gi|336255364|ref|YP_004598471.1| 56 IEDGEFITIVGPSGSGKSTLL 76
                                      7889***************97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.9
                            AAA_25  78 saEdsedelrrRlravgeal.......r 98 
                                        +++s +e+++R++++ e +       +
  gi|336255364|ref|YP_004598471.1| 133 TTDMSDEEIEQRVEETAEMMgigdqldS 160
                                       5777888889998888888766654441 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.96
                            AAA_25 167 alvealeriarrtgaavllvhHvgK 191
                                       ++ + l+r+++++g +++ v H  +
  gi|336255364|ref|YP_004598471.1| 202 HMRTELQRLQEELGTTTIYVTHDQH 226
                                       5567899*************99665 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.9
                            AAA_25 102 rllvldlagv.eslpLfakdrggtlltad 129
                                       r+ +        +++Lf++++g++ll+  
  gi|336255364|ref|YP_004598471.1| 366 RVEIAF---DpADIHLFDERTGDNLLADM 391
                                       333333...22478888877777776433 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1    0.0002      0.16       2      23 ..      62      83 ..      61     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                      EEEEESTTSSHHHHHHHHHTST CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltgek 23
                                      + ivG + +GKStL++ + g +
  gi|336255364|ref|YP_004598471.1| 62 ITIVGPSGSGKSTLLRMIAGLE 83
                                      78**************999854 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   0.00014      0.11      17      44 ..      59      85 ..      50     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                            AAA_30 17 gdrvavltGpAGtGKttalkalreawea 44
                                      g  + +++Gp G+GK+t+l+ ++ + e 
  gi|336255364|ref|YP_004598471.1| 59 G-EFITIVGPSGSGKSTLLRMIAGLEEI 85
                                      4.47899*************99877665 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   0.00022      0.18       3      19 ..      63      79 ..      61      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                            AAA_33  3 llvGlpGsGKstlaerl 19
                                       +vG++GsGKstl++ +
  gi|336255364|ref|YP_004598471.1| 63 TIVGPSGSGKSTLLRMI 79
                                      689**********9865 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.14      18      40 ..      59      79 ..      48      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                      SCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 18 lqslvvalvGmgGvGKttlakqi 40
                                       +  ++++vG  G+GK+tl++ i
  gi|336255364|ref|YP_004598471.1| 59 GE--FITIVGPSGSGKSTLLRMI 79
                                      44..9**************9987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0002      0.17       3      21 ..      62      80 ..      60      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                      + + G++GsGK+tLl+ +a
  gi|336255364|ref|YP_004598471.1| 62 ITIVGPSGSGKSTLLRMIA 80
                                      789*************997 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 ?   11.4   0.0   0.00028      0.22      18      41 ..      57      80 ..      47      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                          ATPase_2 18 epneiyfiYGpegsGKtaLlkeii 41
                                      e  e++ i Gp gsGK++Ll+ i+
  gi|336255364|ref|YP_004598471.1| 57 EDGEFITIVGPSGSGKSTLLRMIA 80
                                      5578999*************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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):              22  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.39
# Mc/sec: 3132.71
//
Query:       gi|336255365|ref|YP_004598472.1|  [L=223]
Description: hypothetical protein Halxa_3988 [Halopiger xanaduensis SH-6]
Scores for 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-05   22.9   0.1    6.8e-05   22.9   0.1    2.6  3  DUF624    Protein of unknown function, DUF624
  ------ inclusion threshold ------
       0.27   11.6   7.6       0.64   10.3   6.0    2.0  2  Cg6151-P  Uncharacterized conserved protein CG6151-P


Domain annotation for each model (and alignments):
>> DUF624  Protein of unknown function, DUF624
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   7.6e-09   6.8e-05       2      69 ..      35      99 ..      34     106 .. 0.89
   2 ?    1.1   0.2     0.047   4.3e+02      39      74 ..     144     179 ..     115     182 .. 0.57
   3 ?    0.5   0.9     0.076   6.8e+02       3      24 ..     173     194 ..     171     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.6e-09
                            DUF624  2 aylNllwllftllglvvfglfPAtaAlfavvrkwirkeedssifktFweaYKknfkksnllglillli 69
                                      +++ l w+   l+ l++++++PAt  ++  v  + ++e d    +  +e+ ++ f+ ++ll ++ l++
  gi|336255365|ref|YP_004598472.1| 35 VWISLAWF---LAALPLVTIGPATVGAYRAVLSLREGEADGIDRSAVLETVREGFVHATLLSFVPLVL 99
                                      68999***...***************************9999999999**********9997765554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.047
                            DUF624  39 eedssifktFweaYKknfkksnllglillliglill 74 
                                          ++++  F + Y+   + ++ +  + ++++++++
  gi|336255365|ref|YP_004598472.1| 144 AAGKPVLEAFADGYRWTARHAVGAVALGVVTVVLFV 179
                                       335688888888888776666665555555555444 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.076
                            DUF624   3 ylNllwllftllglvvfglfPA 24 
                                       ++ +l+++ +ll ++v +lf+ 
  gi|336255365|ref|YP_004598472.1| 173 VTVVLFVVSSLLTVAVAVLFAG 194
                                       6678999999999999999875 PP

>> Cg6151-P  Uncharacterized conserved protein CG6151-P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3     0.073   6.5e+02      88     110 ..      89     111 ..      84     114 .. 0.78
   2 ?   10.3   6.0   7.2e-05      0.64      23     107 ..     117     199 ..      96     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.073
                          Cg6151-P  88 atslivaavlllltgvlYglaal 110
                                       at l ++ ++ll++++ Y la+l
  gi|336255365|ref|YP_004598472.1|  89 ATLLSFVPLVLLVSAANYVLAYL 111
                                       56677778899999999999987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 7.2e-05
                          Cg6151-P  23 vlivfsilalvsgfvvlfiEvPlllricptsskfdefiekfetnwmraalYlvmavvqwlslivqatslivaavlll 99 
                                       +  + ++ +l +g+   ++ +P ll +      +++f++  +    +a+  ++++vv+ ++l    +sl+ +av +l
  gi|336255365|ref|YP_004598472.1| 117 TAGLLGLGCLYAGLYAALVSMPTLLGLAAGKPVLEAFADGYRWTARHAVGAVALGVVT-VVLF-VVSSLLTVAVAVL 191
                                       445678889********************************88899999999999999.5555.6899999999999 PP

                          Cg6151-P 100 ltgvlYgl 107
                                       ++gv ++l
  gi|336255365|ref|YP_004598472.1| 192 FAGVAFAL 199
                                       99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 1834.40
//
Query:       gi|336255366|ref|YP_004598473.1|  [L=288]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-17   63.0  17.9      3e-17   63.0  17.9    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.19   11.3   4.9       0.56    9.8   1.7    2.7  2  DUF3341       Protein of unknown function (DUF3341)


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 ?   -2.7   3.9      0.47   4.2e+03      43      66 ..      66      97 ..      21     107 .. 0.53
   2 !   63.0  17.9   3.3e-21     3e-17       9     183 ..     106     281 ..      91     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.47
                      BPD_transp_1 43 f........vilsilghlilpviillllsaap 66
                                                ++ i+++++  vi++++++a+ 
  gi|336255366|ref|YP_004598473.1| 66 TlywyeyllTNSLIVQWTVNTVILAGITTAVV 97
                                      03333333344445555555555555544444 PP

  == domain 2  score: 63.0 bits;  conditional E-value: 3.3e-21
                      BPD_transp_1   9 a..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdl 83 
                                          ++  +++++++  +i + +++P ++ +++++   +i s lg  +  + ++l   a p+ +++  ++++ +p++l
  gi|336255366|ref|YP_004598473.1| 106 YslTRLDWPGRRVVFAVIVASFMVPGIINLVPVY---IIASELGLVNSLWGVVLPSAANPLGVFMLVQFFKDIPEEL 179
                                       25567888999*****************555555...488************************************* PP

                      BPD_transp_1  84 veaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis..nggv 158
                                       +eaar++G sr +if ++vlP++ + ++++ ++ f++ ++++v++++++++ ++ tl +     +d    +   +++
  gi|336255366|ref|YP_004598473.1| 180 EEAARLDGFSRLRIFTHIVLPLMRSALAALGLFIFIWTWNAFVWPLLIFQSDAMYTLPIGLVTLQDNLGVTepGVIM 256
                                       *************************************************998755554444444444444479999* PP

                      BPD_transp_1 159 lalviavlllnlvadilqrlldprv 183
                                         +v+a ++l+lv+ ++qr+l + v
  gi|336255366|ref|YP_004598473.1| 257 TSAVVASVPLLLVFLVMQRHLVRAV 281
                                       *********************9987 PP

>> DUF3341  Protein of unknown function (DUF3341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.7   6.2e-05      0.56      41      74 ..      10      43 ..       2     118 .. 0.86
   2 ?    1.5   0.1     0.022     2e+02      55      81 ..     201     227 ..     174     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 6.2e-05
                                      TTSS--SS-STHHHHHHHHHHHHHHHHHHHIIII CS
                           DUF3341 41 ealglkksrlpliallgGllGlalalllqvytsv 74
                                      e + l+++rl++ial +Gl+G+a  +l+ ++ + 
  gi|336255366|ref|YP_004598473.1| 10 ENVSLSNTRLRTIALYAGLYGTAALFLIPYWYMF 43
                                      6778999*******************99988773 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.022
                                       HHHHHHHHHHHHHHHHIIIIISS---S CS
                           DUF3341  55 llgGllGlalalllqvytsvvdyplni 81 
                                       l+   l+++  +++++  +++ +pl i
  gi|336255366|ref|YP_004598473.1| 201 LMRSALAALGLFIFIWTWNAFVWPLLI 227
                                       4556667777777888888999*9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2262.06
//
Query:       gi|336255367|ref|YP_004598474.1|  [L=307]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-18   65.9  19.5    3.8e-18   65.9  19.5    2.1  2  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 ?   -1.9   0.1      0.13   2.4e+03      29      68 ..      37      53 ..      27      67 .. 0.55
   2 !   65.9  19.5   2.1e-22   3.8e-18       2     173 ..     107     297 ..      83     303 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.13
                      BPD_transp_1 29 slPsfvlaillvlvfvilsilghlilpviillllsaapyv 68
                                      +lP+                       v+i++++ ++p+ 
  gi|336255367|ref|YP_004598474.1| 37 ALPY-----------------------VLIAGTFLFGPLL 53
                                      2333.......................4444444444433 PP

  == domain 2  score: 65.9 bits;  conditional E-value: 2.1e-22
                      BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf.............vilsilghlilpviilllls 63 
                                       i++++l+a  +nr  ++++llr++++ ++ l + v+++l++ vf              +l++ + ++ +++i++++ 
  gi|336255367|ref|YP_004598474.1| 107 IVGSLLLAlgVNRDVRGKWLLRTIFFSPYVLTVAVVGLLWTEVFsasglvpyyigggNWLTDHQLAMPAIAIATIWW 183
                                       56777888889999999999999999999999999999999999************8888888888888******** PP

                      BPD_transp_1  64 aapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtl 140
                                       +++++++i  aa +++p+ l+eaa+++Gas+w+++r +++P++  p+i  +i++f++++  +  +++++ +++  ++
  gi|336255367|ref|YP_004598474.1| 184 QLAFNFIILLAARQNVPDRLYEAAKLDGASPWRMMRDITIPQMRNPLIFIVIVTFVNSFQVFGQPYIMTDGGPSFST 260
                                       *********************************************************************88888888 PP

                      BPD_transp_1 141 lleailgydyseis....nggvlalviavlllnlvad 173
                                       ++ ++  y ++++     +++++ +v++++l+ ++a 
  gi|336255367|ref|YP_004598474.1| 261 TTVVLYLYETAFTGrefgYAAAVGYVLFMILIAISAT 297
                                       8888888888888888777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2527.49
//
Query:       gi|336255368|ref|YP_004598475.1|  [L=436]
Description: family 1 extracellular solute-binding protein [Halopiger xanaduensis SH-6]
Scores for complete 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-19   71.2   0.0      2e-19   70.5   0.0    1.4  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    4.6e-16   59.7   0.0      8e-16   58.9   0.0    1.3  1  SBP_bac_1   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.083   12.8   2.1       0.14   12.0   2.1    1.3  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   3.4e-23     2e-19       2     274 ..      70     366 ..      69     399 .. 0.78

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 3.4e-23
                                       HHHHHHH..H-TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH-.HHHH CS
                         SBP_bac_8   2 lakefek..ktgvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnlddl.tdal 75 
                                       +++e ++  ++++++n + +++++    l +++  g+ pd  v+++ ++ + +   e+ +++++d+   d++ + ++
  gi|336255368|ref|YP_004598475.1|  70 MVDEINAsdEYDFRINRQRVPWDEHYGRLYTSMVGGNPPD--VAVM-HSRMMRDY-EDSIVPVTDEIGTDPYlEEVA 142
                                       678888743569*************************996..6777.46666666.59********99999747788 PP

                                       HTT--TS.----EEEEEEE-EEEEEHHHHHHS......---BHHHHHHHHHHHHHH-SEG..G---G.....GGGGG CS
                         SBP_bac_8  76 aavgydgklygvPyasetpyvliynkdlleka.....edpktwdellaaakklkgkfglp..dpasg.....wlqaa 140
                                       ++  +dg+  +vP ++  p +l+ynk+++e+a     e+p t + + + a ++ +++ ++  d  +g     +++++
  gi|336255368|ref|YP_004598475.1| 143 QGGVVDGEQLAVPMDTH-PFGLYYNKEIFEEAgldpeEPPNTAERFYECANAIVENTDYYafDYFEGefhaeTMRML 218
                                       88888***********9.79***********9999*************77777555544311333445223355555 PP

                                       THHETTEE---H....HHH.HHHHHHHHHHHHTT-...EE-S...--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEE CS
                         SBP_bac_8 141 llakdgksldddg..gkdglkealellkklkdngk...tydtg.adavsefanGevaftingswdiaaaqkagkklg 211
                                       l   +g+  ++d+     ++++  + +++++d ++   + + + ++ ++++  Gev + + g+w i  +++ag+++g
  gi|336255368|ref|YP_004598475.1| 219 LHSRGGQLITEDYepAF-DTDDGHDVVQEMHDWVYeheWAPVDpTAGWDAWNRGEVGMKLEGTWHISVVREAGFEFG 294
                                       55589999999976433.34999999*****999887666644368899**************************** PP

                                       EE....--S--...EEEEEEEEEEBTT..S-HHHH.HHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTHHHH CS
                         SBP_bac_8 212 ai....vpkqg...sfaggkglavpkn..aknedl.aAldFlkwltspenqaalaektgyipvnksaalspev 274
                                        +    +p ++   ++ +++ l++p +   + e+l  A++ ++ lt++ n + +  + g +p+  +a +s+++
  gi|336255368|ref|YP_004598475.1| 295 LTepfiMPESTspvTVGDSHMLIIPESqdRDRERLeDAIETVRLLTQEFNDR-WGSDAGHLPASRTALESDAL 366
                                       9975323554443244455567776641155555578888888888888877.88888888888888887764 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   1.3e-19     8e-16      10     256 ..      67     294 ..      61     323 .. 0.77

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1.3e-19
                                       HHHHHHHHHHH.HHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHH.HHHHT....TSBECCHHHHHH CS
                         SBP_bac_1  10 lqalvakafek.ehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwia.rlaka....glllpldpyvka 80 
                                       ++ +v ++ ++ ++++  ++ + v++++ +  l + + +G++p Dv+ + ++++  ++ ++       +  dpy+++
  gi|336255368|ref|YP_004598475.1|  67 METMV-DEINAsDEYDFRINRQRVPWDEHYGRLYTSMVGGNPP-DVAVM-HSRMMrDYEDSivpvTDEIGTDPYLEE 140
                                       55555.6655557899*************************66.*****.888884555554444444444444444 PP

                                       TTECTTCCTEEEEHHHHTHHHHCEEEES.EEEEE.EEEEEEETTTHHCTTGGG...SHBHHHHHHHHHHHHHHCTCT CS
                         SBP_bac_1  81 ylapgvkdaadklsssvlpkildskvly.vPlya.argliYNkdlfekagldp...pwtWdelveaakklkekgkkp 152
                                        +  gv d++                   vP+++ + gl+YNk +fe+agldp   p t + ++e+a  ++e++ ++
  gi|336255368|ref|YP_004598475.1| 141 VAQGGVVDGEQ----------------LaVPMDThPFGLYYNKEIFEEAGLDPeepPNTAERFYECANAIVENTDYY 201
                                       44444443333................33****88********************888888**************** PP

                                       HCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT.HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHH CS
                         SBP_bac_1 153 iggarggsasgtayyfalalakslggkvfdkdgg.gldnpegvtaatylvklyavanltkelkgkgaenkdgaaala 228
                                          a+ ++ +   + +   l+ s gg++ ++d+  ++d++ g + ++ + +++   +          + +d +a  +
  gi|336255368|ref|YP_004598475.1| 202 ---AFDYFEGEFHAETMRMLLHSRGGQLITEDYEpAFDTDDGHDVVQEMHDWV---Y------EHEWAPVDPTAGWD 266
                                       ...*****************************998888888777777777766...3......44455666667777 PP

                                       HHHTTSCSEEEEEHHHHHHHHCEEEEEC CS
                         SBP_bac_1 229 lfeaGeaamaivglwaalaamkvapkva 256
                                       ++++Ge++m + g+w + ++  ++ +++
  gi|336255368|ref|YP_004598475.1| 267 AWNRGEVGMKLEGTWHISVVREAGFEFG 294
                                       799************9777765555544 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.1   2.4e-05      0.14       2      24 ..      22      43 ..      21      44 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      +SRR  L++++Aa+ +++ +gc+
  gi|336255368|ref|YP_004598475.1| 22 VSRRRVLQATGAAG-LTGIAGCT 43
                                      8***********99.55566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3633.19
//
Query:       gi|336255369|ref|YP_004598476.1|  [L=257]
Description: 3-oxoacyl-(acyl-carrier-protein) reductase [Halopiger xanaduensis SH-6]
Scores for 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-63  213.5   1.4    3.7e-63  213.2   1.4    1.0  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    1.6e-47  161.5   0.4    2.1e-47  161.1   0.4    1.1  1  adh_short      short chain dehydrogenase
    1.9e-19   70.3   0.9    2.5e-19   69.9   0.9    1.1  1  KR             KR domain
     0.0028   17.2   0.2     0.0041   16.6   0.2    1.3  1  Epimerase      NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.011   15.7   0.5       0.02   14.8   0.5    1.4  1  ADH_zinc_N     Zinc-binding dehydrogenase
      0.016   14.3   0.3       0.03   13.4   0.3    1.5  2  Dak1_2         Dihydroxyacetone kinase family
      0.022   14.1   0.9       0.11   11.8   0.9    2.1  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
      0.036   13.6   1.1      0.054   13.0   1.1    1.3  1  NmrA           NmrA-like family
      0.094   12.1   0.2       0.24   10.8   0.2    1.7  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,


Domain annotation for each model (and alignments):
>> 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 !  213.2   1.4   1.9e-66   3.7e-63       3     233 ..      22     252 ..      19     253 .. 0.95

  Alignments for each domain:
  == domain 1  score: 213.2 bits;  conditional E-value: 1.9e-66
                                       TTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.E.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae.v.lecDVtdeeqvealveevvekfgklDilvnna 77 
                                        sg+G+aiA  la+ Ga+v++t ++e+a +++++l ee ga+ + + cDVt++e++e+l e ++e++g++D++v +a
  gi|336255369|ref|YP_004598476.1|  22 TSGLGQAIAVGLAADGADVIATSRSEDAVNETADLLEEQGATtArVTCDVTEPESLENLREVAEESLGGIDVVVSSA 98 
                                       59**************************77788888888877469******************************** PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtry 154
                                       g   +    ++ +s++e+d + dv+l ++ ++++ ++p+m eggsi+n+ss++a+ +++n  ay+aaK+++ea+tr+
  gi|336255369|ref|YP_004598476.1|  99 GAISR--DTVVGISDDEWDFVTDVQLDGVRRITQTFAPAMDEGGSIINISSLAARLSMANLPAYSAAKGGVEAFTRA 173
                                       *****..********************************************************************** PP

                                       HHHHHGGGTEEEEEEEE--BHCTGGGG.STTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEES CS
                      adh_short_C2 155 lAvelgpkgiRvNavspgpikTlaasg.ikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvD 230
                                        A+el+p +iRvNa++pg+  T+ +++ +++  e +e++++r+plgr+g+ ee   a+++Lasd++s++tG++l vD
  gi|336255369|ref|YP_004598476.1| 174 SAKELAP-EIRVNAIAPGFFITPQNEDtYAEGTEKRERIDERTPLGRVGEREELIGATIYLASDASSFVTGEVLTVD 249
                                       *******.9***************66515668899****************************************** PP

                                       TTG CS
                      adh_short_C2 231 gGl 233
                                       gG+
  gi|336255369|ref|YP_004598476.1| 250 GGF 252
                                       **8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.1   0.4     1e-50   2.1e-47       1     190 [.      14     200 ..      14     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 161.1 bits;  conditional E-value: 1e-50
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       k ++v+G++sG+G+aia  la++Ga+v++++rse++++e+a+ l+e+ga+   +++Dvt+ e++e+l e a++ lg+
  gi|336255369|ref|YP_004598476.1|  14 KRAVVVGGTSGLGQAIAVGLAADGADVIATSRSEDAVNETADLLEEQGATTARVTCDVTEPESLENLREVAEESLGG 90 
                                       679************************************************************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       +dv+v  AG   + ++  +s++ew+ v +v l gv  +t++++pam+  ++G+I+n+sS a++ ++a+++aYsA+K+
  gi|336255369|ref|YP_004598476.1|  91 IDVVVSSAGAISRDTVVGISDDEWDFVTDVQLDGVRRITQTFAPAMD--EGGSIINISSLAARLSMANLPAYSAAKG 165
                                       *********************************************99..99************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakel 190
                                       +v+++tr+ akelap+ irvna+aPG++ T+ ++++
  gi|336255369|ref|YP_004598476.1| 166 GVEAFTRASAKELAPE-IRVNAIAPGFFITPQNEDT 200
                                       ***************8.************9988765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.9   1.3e-22   2.5e-19       4     169 ..      17     180 ..      15     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.3e-22
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       +++GG+ gLG+++a  la++ga  ++ +sRs   +++ +++ + le++ga+   v +Dv++++++e+l e ++++ +
  gi|336255369|ref|YP_004598476.1|  17 VVVGGTSGLGQAIAVGLAADGAD-VIATSRS---EDAVNETADLLEEQGATTARVTCDVTEPESLENLREVAEESLG 89 
                                       79*******************96.7789***...456666999********************************** PP

                                       ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT..S--SEEEEEEEHHHHH--TT-HHHHHHHHH CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled..esldffvlfSSiagllgsagqanYaaaNaf 155
                                        i  v+ +Ag++  +++   ++++++ v+   ++G++ + +++++  ++   ++ +SS+a+ l +a   +Y+aa   
  gi|336255369|ref|YP_004598476.1|  90 GIDVVVSSAGAISRDTVVGISDDEWDFVTDVQLDGVRRITQTFAPamDEGGSIINISSLAARLSMANLPAYSAAKGG 166
                                       *******************************************998888899************************* PP

                                       HHHHHHHHHHHHHT CS
                                KR 156 lDalaeyrrsqglp 169
                                       ++a+ +  +++ +p
  gi|336255369|ref|YP_004598476.1| 167 VEAFTRASAKELAP 180
                                       ****9987776665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   2.1e-06    0.0041       2      75 ..      17     102 ..      16     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-06
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HH...HHHHHHHHH..T- CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrs...alerlfkee..qp 65 
                                       +V+G+t  +G+a++  l++ g +vi+ +r ++a n+ +  dl          v++d+t+++   +l+++ +e   ++
  gi|336255369|ref|YP_004598476.1|  17 VVVGGTSGLGQAIAVGLAADGADVIATSRSEDAVNETA--DLleeqgattARVTCDVTEPEsleNLREVAEESlgGI 91 
                                       79****************************88888654..345688999999********96666777777777788 PP

                                       SEEEE--S.-- CS
                         Epimerase  66 davihlAa.vg 75 
                                       d+v+  A+ ++
  gi|336255369|ref|YP_004598476.1|  92 DVVVSSAGaIS 102
                                       88888877554 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.5     1e-05      0.02       1      69 [.      24     100 ..      24     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHHTT-EEEEEESSHHHH....HHHHHTTESEEEET......TTC.HHHHHHHHHTTTSSEEEEEESS CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseekl....elakklGadeviny......kea.dlverikeltggegvdvvfecv 66 
                                       g+G+a    ++a Ga via+++se+ +    +l+++ Ga+ +  +      ++  +l e  +e   g g+dvv+  +
  gi|336255369|ref|YP_004598476.1|  24 GLGQAIAVGLAADGADVIATSRSEDAVnetaDLLEEQGATTARVTcdvtepESLeNLREVAEESL-G-GIDVVVSSA 98 
                                       89**********************96654448888889988777778787766667888888888.3.9*****999 PP

                                       CSH CS
                        ADH_zinc_N  67 Gsg 69 
                                       G  
  gi|336255369|ref|YP_004598476.1|  99 G-A 100
                                       9.4 PP

>> Dak1_2  Dihydroxyacetone kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   1.5e-05      0.03     210     302 ..       5      99 ..       1     110 [. 0.90
   2 ?   -1.1   0.0       0.4   7.9e+02     225     269 ..      98     145 ..      96     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                            Dak1_2 210 ktgevtyAvrdtkidggeikkgdllgi...adgkivvvgkdleeaakkllkklldedselvtilygedvsee.eaea 282
                                       ++  vt+A + + + gg+   g+++++   adg  v++ +  e+a++++ + l ++++   t  +  dv+e+ + e+
  gi|336255369|ref|YP_004598476.1|   5 THTPVTVADKRAVVVGGTSGLGQAIAVglaADGADVIATSRSEDAVNETADLLEEQGAT--TARVTCDVTEPeSLEN 79 
                                       57789********************99998888888888999***********999999..99***9999998999* PP

                            Dak1_2 283 laekleekypdvevevyeGg 302
                                       l+e  ee   +++v v + g
  gi|336255369|ref|YP_004598476.1|  80 LREVAEESLGGIDVVVSSAG 99 
                                       ******99999999998766 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.4
                            Dak1_2 225 ggeikkgdllgiadgkivvvgkdleeaakkllkkl...ldedselvti 269
                                       +g i  + ++gi d++   v + + + ++++++     +de++++++i
  gi|336255369|ref|YP_004598476.1|  98 AGAISRDTVVGISDDEWDFVTDVQLDGVRRITQTFapaMDEGGSIINI 145
                                       67899999********99999888777777777766668888888877 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 ?   11.8   0.9   5.7e-05      0.11      29      74 ..       6      51 ..       3     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.7e-05
                                      HCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHH CS
                     THF_DHG_CYH_C 29 etgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdla 74
                                      +t +++++k++vvvG  + +g+++a+ L++++a V  + ++ + ++
  gi|336255369|ref|YP_004598476.1|  6 HTPVTVADKRAVVVGGTSGLGQAIAVGLAADGADVIATSRSEDAVN 51
                                      567899***************************9987655443333 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.1   2.7e-05     0.054       2      61 ..      17      80 ..      16     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S..-SHHHHHHHHSTTEEE..ES-TT-HHHHHHH CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdt..kselakslkeaGvelv..kgdlddkeslvea 61
                                      +v+G+T  +G++++  l+++g +v a  R +   +e+a+ l+e+G+++     d+ + esl+++
  gi|336255369|ref|YP_004598476.1| 17 VVVGGTSGLGQAIAVGLAADGADVIATSRSEdaVNETADLLEEQGATTArvTCDVTEPESLENL 80
                                      69***************************98667899**********97557788888888876 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 ?   10.8   0.2   0.00012      0.24      34      76 ..      12      54 ..       2      72 .. 0.76
   2 ?   -1.3   0.0      0.61   1.2e+03     145     162 ..      63      80 ..      49      87 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                                      GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHH CS
                      2-Hacid_dh_C 34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeee 76
                                        ++ v + G+  +Gqa+a  l+a g++via++rs+++ +e++
  gi|336255369|ref|YP_004598476.1| 12 ADKRAVVVGGTSGLGQAIAVGLAADGADVIATSRSEDAVNETA 54
                                      4455677779*************************88666333 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.61
                                       SCCEEEES--SSSSSGTC CS
                      2-Hacid_dh_C 145 kiagaalDvfeeeplped 162
                                       + a + +Dv+e+e l++ 
  gi|336255369|ref|YP_004598476.1|  63 TTARVTCDVTEPESLENL 80 
                                       45668899*999998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2129.54
//
Query:       gi|336255370|ref|YP_004598477.1|  [L=357]
Description: glucose-fructose oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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   65.0   0.2    4.3e-17   63.0   0.0    2.0  3  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.062   13.3   0.0    1.8  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
      0.021   15.3   0.0      0.055   13.9   0.0    1.7  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai


Domain annotation for each model (and alignments):
>> 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 !   63.0   0.0   7.2e-21   4.3e-17       1     113 [.      22     137 ..      22     144 .. 0.93
   2 ?   -1.1   0.1      0.55   3.3e+03      32      80 ..     216     268 ..     211     274 .. 0.62
   3 ?   -2.9   0.0       1.9   1.1e+04       5      46 ..     270     315 ..     267     318 .. 0.63

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 7.2e-21
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE...EESSHHHHHTCTTESEEEE-S-GGG CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve...aysdleelladpeidavivatpngt 74 
                                       +r+a+iG+G+ + + + p  e+ +  e + l+++++e+a+++a++ +v+    y+++ + +a+++ dav+++tpn  
  gi|336255370|ref|YP_004598477.1|  22 VRFALIGLGWWTVDIVIPAIEQADYCETAVLVSSSTEKAQRLADRHDVDrgiTYDEYHDGAASDAYDAVYIGTPNAY 98 
                                       589********888877888887999********************************999999************* PP

                                       HHHHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHT CS
                      GFO_IDH_MocA  75 heelakaaleagkhvllEKPlattveeakelvelaekkg 113
                                       h e+++ a+e  k+vl+EKPl +t e a++lv++a+  +
  gi|336255370|ref|YP_004598477.1|  99 HLEYVETAAELDKAVLCEKPLEATAERAEQLVDAAADGD 137
                                       **********************************98755 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.55
                                       ECSSHHHHHHHHHHTTHEEESSHHHHHTCT....TESEEEE-S-G.GGHHHHHH CS
                      GFO_IDH_MocA  32 ldpdaeraeavaesfgveaysdleelladp....eidavivatpn.gtheelak 80 
                                       l++d+ +aea + s  +ea++d+ + +a      e d+ +v+t + + +e+ ++
  gi|336255370|ref|YP_004598477.1| 216 LERDPVQAEA-RMSSTHEAFDDVPDQFATItltlEDDVPLVCTTSqHAQEDTEL 268
                                       5666767774.7788888888855444433344566777777777333555555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.9
                                       EETT.SHH...HHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHT CS
                      GFO_IDH_MocA   5 iiGa.Gki...gskhlrplnesqrleevvalldpdaeraeavaesf 46 
                                       iiG+ G i      h+++  + +++   + + d+d  + e+++e+f
  gi|336255370|ref|YP_004598477.1| 270 IIGTdGLIelsPAFHGEATLHLSSGSVEATIEDTDFTEVEEMREEF 315
                                       5666666665555566666666666666666777777777777776 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     1e-05     0.062       1      64 [.     156     222 ..     156     245 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                                       HHHHHTTTTSSEEEEEE.EEECBEEECHHHHCCGGSH..HCSTSHHHHTCHHHHHHHHHHHTSEEEE CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdv.wtldtragaeakkrwkrrk..kksgGvlgdlgiHdiDllqwLfGqppsv 64 
                                       KelIe+g +Ge+++v + +t    +  +++ +w+ +    + g +++dlgi+ i+ +++L+  +p+ 
  gi|336255370|ref|YP_004598477.1| 156 KELIEDGFIGEPTQVYGnNTQPLLEMIPDPDQWRLDSdvTGYGTSVMDLGIYPINTARFLLERDPVQ 222
                                       9**************997776555555555555555565899999****************999875 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 ?   13.9   0.0   9.1e-06     0.055      18      93 ..      40     113 ..      25     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.1e-06
                                       HHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEE.GGGGGCTT-SEEEE-SCHHHHHHHHHHHHHTTSEE CS
                    Semialdhyde_dh  18 lLeehpevelvvllsssrsaGkklaeavkaleegkdlkved.vdeeelkevdivflalpagvskelapklaeagvkv 93 
                                        +e+  ++e +vl+sss ++ ++la+++      + +++++  d ++ ++ d v   +p+ ++ e+++++ae +  v
  gi|336255370|ref|YP_004598477.1|  40 AIEQADYCETAVLVSSSTEKAQRLADRHD---VDRGITYDEyHDGAASDAYDAVYIGTPNAYHLEYVETAAELDKAV 113
                                       6788999********************99...66777777766678889*********************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2768.70
//
Query:       gi|336255371|ref|YP_004598478.1|  [L=166]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-14   51.7   0.0    1.3e-13   51.2   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.6e-10   39.8   0.0    6.9e-10   39.2   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.8e-08   33.3   0.0    5.5e-08   32.8   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    8.8e-07   29.7   0.0    1.1e-06   29.4   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    2.7e-05   24.3   0.0      0.025   14.7   0.0    2.1  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00017   21.8   0.0    0.00024   21.3   0.0    1.3  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.045   13.7   0.0      0.074   13.0   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 !   51.2   0.0     5e-17   1.3e-13      20     117 .]      56     150 ..      36     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 5e-17
                                       HHHHHHHH..HHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTE CS
                    Acetyltransf_1  20 seeefees..fsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegi 94 
                                       se +  e+    le++  +va+++g ++G++ l +++      +    ++V+p+y+  G+G++L+  l+ +   +g+
  gi|336255371|ref|YP_004598478.1|  56 SENRTVEWlsDLLEEGLNVVARHEGDVVGHAVLIPYDS-----TSELAIFVRPAYQSAGIGTHLIGCLLGHGQANGL 127
                                       33333333123446667888***********9999999.....6777****************************** PP

                                       SEEEEEEETTEHHHHHHHHH.TTE CS
                    Acetyltransf_1  95 kkivlaveedndaairlYek.lGF 117
                                       ++++l+v  +n+ a++lY +  GF
  gi|336255371|ref|YP_004598478.1| 128 TRVWLTVARTNRIAMNLY-RsAGF 150
                                       ******************.65**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   2.7e-13   6.9e-10       5      75 ..      73     151 ..      68     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2.7e-13
                                       EEEEEETTEEEEEEEEEEES.TCTEEEEE-GGGTTSSHHHHHHHH.....TTSEEEEEEEEE....THH.HHHHHHH CS
                    Acetyltransf_7   5 vfVaeddgkivGfialslld.aeitrlaVdpeyrgkGiGraLlea.....aekgiileqlel....nae.kaikfYe 70 
                                         Va+++g +vG ++l ++d +++  ++V+p+y+  GiG+ L+ +     +++g++  +++l    + +  a ++Y+
  gi|336255371|ref|YP_004598478.1|  73 NVVARHEGDVVGHAVLIPYDsTSELAIFVRPAYQSAGIGTHLIGCllghgQANGLT--RVWLtvarT-NrIAMNLYR 146
                                       579***************99888888*****************9644443225643..334443432.249999*** PP

                                       HTTEE CS
                    Acetyltransf_7  71 klGFe 75 
                                       + GFe
  gi|336255371|ref|YP_004598478.1| 147 SAGFE 151
                                       ****8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   2.2e-11   5.5e-08      30     113 ..      70     157 ..      53     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.2e-11
                   Acetyltransf_10  30 ealllvaeeggkivGviel.rdgshisll.fVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYe 102
                                       e l +va  +g +vG++ l   +s  +l  fV+p+y++ Gig+ L+  ++ + + +g+    ltv  ++  a ++Y+
  gi|336255371|ref|YP_004598478.1|  70 EGLNVVARHEGDVVGHAVLiPYDSTSELAiFVRPAYQSAGIGTHLIGCLLGHGQANGLTRvWLTVARTNrIAMNLYR 146
                                       5567899**********7744444444435**********************9999999999***99999******* PP

                   Acetyltransf_10 103 klGFkavgeeq 113
                                       + GF+ +++ +
  gi|336255371|ref|YP_004598478.1| 147 SAGFEITERDR 157
                                       *****997765 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   4.2e-10   1.1e-06      18     138 .]      43     151 ..      24     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.2e-10
                    Acetyltransf_3  18 lrsdpevmrylpepltleeaeewlerawaeeseeegygwaivlkdtg.viGsvglrdleeedeeaelgymlapsfwg 93 
                                       +  d +++  + +p+++  + ewl++ ++     eg++ +   +++g v+G + l +++      el + ++p+++ 
  gi|336255371|ref|YP_004598478.1|  43 FDDDSRTQ--GLPPRSENRTVEWLSDLLE-----EGLNVVA--RHEGdVVGHAVLIPYDST---SELAIFVRPAYQS 107
                                       33344444..4458899999999998553.....6776555..555527*******99998...8************ PP

                    Acetyltransf_3  94 kGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                        G++t    +ll +  +  gl+r++ +++ +N+   ++++++Gfe
  gi|336255371|ref|YP_004598478.1| 108 AGIGTHLIGCLLGHG-QANGLTRVWLTVARTNRIAMNLYRSAGFE 151
                                       ***************.7777************************7 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   9.6e-06     0.025       5      64 ..      24      93 ..      20      96 .. 0.83
   2 !    7.8   0.0    0.0013       3.3      79     127 ..      99     152 ..      97     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.6e-06
                                      E-GGGHHHHHHHHHHHTT----H............HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEE CS
                    Acetyltransf_9  5 lteedldevlellkyaFqdeespl.........e.eireyfrklleesrvlgaedngelvgqlallplel 64
                                      +   ++d+ le l++ +++ +++          e +  e++++llee+  ++a+ +g++vg++ l+p++ 
  gi|336255371|ref|YP_004598478.1| 24 ISIREYDGQLEPLQEMYAHFDDDSrtqglpprsEnRTVEWLSDLLEEGLNVVARHEGDVVGHAVLIPYDS 93
                                      55667777777777777777777777888888877899*****************************986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0013
                                       EEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  79 VavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                       + v p ++  g+ ++L+  +l++ +++g + ++l+      +++++Yr+ G+ei
  gi|336255371|ref|YP_004598478.1|  99 IFVRPAYQSAGIGTHLIGCLLGHGQANGLTRVWLTVartnrIAMNLYRSAGFEI 152
                                       5699******************************9989888889********97 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   9.3e-08   0.00024      27     143 ..      54     159 ..      24     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9.3e-08
                    Acetyltransf_4  27 feyevssveefekflealdsekeyvflvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidal 102
                                       +++e  +ve++  +le+       +  va  ++++vG a l    +  +d  +el +++ + + +++g+g  li  l
  gi|336255371|ref|YP_004598478.1|  54 PRSENRTVEWLSDLLEEG------LNVVARhEGDVVGHAVLI---P--YDSTSELAIFV-RPAYQSAGIGTHLIGCL 118
                                       666667777777776664......455666789999998887...5..777********.599************** PP

                    Acetyltransf_4 103 eqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkc 143
                                           +++++++    +a +n ++++++ + GFe++ + ++ 
  gi|336255371|ref|YP_004598478.1| 119 LGHGQANGLTRVWLTVARTNRIAMNLYRSAGFEITERDRGE 159
                                       **********************************9988765 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.9e-05     0.074      22      80 ..      94     153 ..      77     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
                                       SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfeki 80 
                                       ++  a+ v+p  +  G g+ l+  l  +  ++g t v l v+ +N  + +ly + Gfe  
  gi|336255371|ref|YP_004598478.1|  94 TSELAIFVRPAYQSAGIGTHLIGCLLGHGQANGLTrVWLTVARTNRIAMNLYRSAGFEIT 153
                                       5556899****************99999888886527788999**************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1241.57
//
Query:       gi|336255372|ref|YP_004598479.1|  [L=345]
Description: cation diffusion facilitator family transporter [Halopiger xanaduensis SH-6]
Scores for 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-37  127.6  15.0    5.9e-37  127.3  15.0    1.1  1  Cation_efflux  Cation efflux family
     0.0099   16.0   0.3      0.016   15.3   0.3    1.3  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
      0.093   12.6   5.8       0.15   11.9   5.8    1.3  1  BAT            GAF and HTH_10 associated domain


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 !  127.3  15.0     1e-40   5.9e-37       3     197 ..      65     252 ..      63     254 .. 0.96

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 1e-40
                     Cation_efflux   3 lsllanlilalvelivglltnSlalladafhslsdlvsllllllalkls.rkppderfpfGygrlevlgalvsglll 78 
                                       ++ ++nl+ +++el++gll++S+al++dafh+l+d+++ ++++ a +++ +     r ++G++rle+++a+ +g+ll
  gi|336255372|ref|YP_004598479.1|  65 VVSAINLVGFVAELAGGLLFGSVALISDAFHMLFDALAYVMAFAAAYVAeSYGDEGRWSYGLHRLEPFAAFLNGVLL 141
                                       67789********************************************999999********************** PP

                     Cation_efflux  79 lglavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlv 155
                                       l ++ f+l+e++++++  ++  i +g +l++a ++l+vn+ +++ l+++     s + ++a++h lgDa +s++v+v
  gi|336255372|ref|YP_004598479.1| 142 LPMVGFILWESYHRFL--EPVAIGTGPTLLIATGGLAVNVGSIYVLHGGE---MSLNERGAFYHLLGDAGGSVAVIV 213
                                       ****************..99999************************996...8*********************** PP

                     Cation_efflux 156 salvillfnlksg.plaDpvaslligliilysalkllkeslse 197
                                       s +vi l+    g +l+Dp+++ li++++  sa+++l+ s+ +
  gi|336255372|ref|YP_004598479.1| 214 STVVIELT----GfHLVDPLTAGLIAVVVTWSAVNVLRGSSAI 252
                                       *******9....6688********************9988766 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 !   15.3   0.3   2.7e-06     0.016       6      78 ..     261     331 ..     258     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHTT-SS-EEEEEEEEE-S----.EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                          ZT_dimer   6 eeeireiiksvpgvkgvhdlrtrksGski.fvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                       ++++r+++++ +gv+ v+d+++ ++ s+i ++ +h+e d + ++ +a +++ +v++ ++++  gv + ++ ++P
  gi|336255372|ref|YP_004598479.1| 261 RAAVRAALEDLEGVTAVDDIHAWQVCSRItVATVHLETDAE-TMADAEAVTRRVHATLEAR--GVDHATVELCP 331
                                       5788999999*************8887661568********.****************877..68899999888 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   5.8   2.6e-05      0.15      34     125 ..     243     338 ..     218     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                               BAT  34 vprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtllelt.vsgpslastlaehGgtvrsaeae... 106
                                       v    g+++ f++ +  d ++vr+a+edl++v+ v+ +++    +++ ++ v  ++ a+t+a+  +++r+++a+   
  gi|336255372|ref|YP_004598479.1| 243 VNVLRGSSAIFLHRTPFDRAAVRAALEDLEGVTAVDDIHAWQVCSRITVAtVHLETDAETMADAEAVTRRVHATlea 319
                                       55667899999************************999988876666655477888899**************9999 PP

                               BAT 107 dgrarlvvevPpgadvRsv 125
                                       +g  + +ve+ p+ ++R v
  gi|336255372|ref|YP_004598479.1| 320 RGVDHATVELCPSYAARDV 338
                                       999999****999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2424.30
//
Query:       gi|336255373|ref|YP_004598480.1|  [L=96]
Description: transcriptional regulator PadR family protein [Halopiger xanaduensis SH-6]
Scores for complete 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   63.0   0.7    2.4e-17   62.7   0.7    1.1  1  PadR      Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.011   16.2   0.0      0.014   15.8   0.0    1.3  1  HTH_27    Winged helix DNA-binding domain
      0.019   14.9   0.2       0.18   11.7   0.1    2.4  2  MarR_2    MarR family
      0.019   15.0   0.0      0.026   14.5   0.0    1.4  1  HTH_45    Winged helix-turn-helix
      0.019   14.8   0.0      0.029   14.2   0.0    1.3  1  DUF1495   Winged helix DNA-binding domain (DUF1495)


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 !   62.7   0.7   6.6e-21   2.4e-17       1      74 [.      11      79 ..      11      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 6.6e-21
                                      HHHHH.CCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR  1 iLall.eeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      +L+++ ++ + +G++i++ele+++e  +e+++G+lYp+L++  ++glve+ +++    +++++Y+lT++Grrel+
  gi|336255373|ref|YP_004598480.1| 11 LLYVIaGQDEPHGLAIKEELEDYYE--TEIHHGRLYPNLDTIVDKGLVEKGQAD----RRTNFYTLTRRGRRELE 79
                                      58888667677************86..6***********************998....7**************98 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 ?   15.8   0.0     4e-06     0.014       5      68 .]       8      74 ..       4      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4e-06
                            HTH_27  5 qalvLhlir...hrrrrkkladlcgrlnvedshis.y.slkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      q+ +L +i+   ++++ +++++l +++ +e  h+  y +l+  + kGLv  ++  adrr+ +++lT  G
  gi|336255373|ref|YP_004598480.1|  8 QRDLLYVIAgqdEPHGLAIKEELEDYYETEIHHGRlYpNLDTIVDKGLV--EKGQADRRTNFYTLTRRG 74
                                      555778888666666667789999999999999988549**********..44558**********766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   4.9e-05      0.18       2      61 ..       3      64 ..       2      65 .. 0.85
   2 ?   -0.5   0.0      0.32   1.2e+03      25      39 ..      76      90 ..      68      94 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.9e-05
                                      T--HHHHHHHHHHHCTTTS.EE.EHHHHHH..HHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  2 gltpaqarvLaaLgrrpgr.dl.tvgelar..rlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      +lt+ q+++L++++  +++  l    el++  ++ + ++++   l+  v++GLve+  +  D+R
  gi|336255373|ref|YP_004598480.1|  3 DLTGFQRDLLYVIAGQDEPhGLaIKEELEDyyETEIHHGRLYPNLDTIVDKGLVEKGQA--DRR 64
                                      7888899999999999999955366788889999999999999************7755..999 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.32
                                      HHHHHHHTSSHHHHH CS
                            MarR_2 25 gelarrlglsksavs 39
                                      +el++r + ++++v 
  gi|336255373|ref|YP_004598480.1| 76 RELEARRDWEQQYVA 90
                                      477888888888875 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   7.4e-06     0.026      27      71 ..      34      83 ..      23      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.4e-06
                            HTH_45 27 ykanLsykllnkYLdmLvekgli.....kkskekYvlTekGlelleklke 71
                                      y+ ++   +l   Ld++v+kgl+     + +++ Y+lT +G++ le  ++
  gi|336255373|ref|YP_004598480.1| 34 YETEIHHGRLYPNLDTIVDKGLVekgqaDRRTNFYTLTRRGRRELEARRD 83
                                      66667777788889*********88876678999********99987665 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 ?   14.2   0.0   8.1e-06     0.029      53      85 ..      44      76 ..      40      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.1e-06
                           DUF1495 53 ynsessLielGLveeeeeseglklYklteeGie 85
                                      y + + ++ +GLve+ + ++ +++Y+lt +G++
  gi|336255373|ref|YP_004598480.1| 44 YPNLDTIVDKGLVEKGQADRRTNFYTLTRRGRR 76
                                      6666789************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); 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:                         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: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 800.37
//
Query:       gi|336255374|ref|YP_004598481.1|  [L=198]
Description: hypothetical protein Halxa_3997 [Halopiger xanaduensis SH-6]
Scores for 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   51.8   0.0    8.5e-14   51.4   0.0    1.3  1  SprT-like       SprT-like family
  ------ inclusion threshold ------
      0.027   14.5   1.6      0.065   13.2   1.6    1.6  1  DBD_Tnp_Mut     MuDR family transposase
      0.035   14.0   0.4      0.035   14.0   0.4    1.9  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.036   13.9   0.0      0.044   13.6   0.0    1.3  1  BSP             Peptidase of plants and bacteria
       0.35   11.0   1.9        1.6    8.9   0.3    2.2  2  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   2.4e-17   8.5e-14      19     101 ..      43     121 ..      25     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2.4e-17
                         SprT-like  19 ggvkiiwskrlnttaGranlkratvrhhasIeLseklldsrsedrllntLaHElcHlalfvisgvrnnpHGaeFkaw 95 
                                       + +++++s r ++ aG +++ r  +r+ a+I L+++ ++ ++  +   ++ HEl+H++ f+ +g  + +HG++F++ 
  gi|336255374|ref|YP_004598481.1|  43 EALEWNVSARARRRAGACRWDR--NREVATIVLARRAYERYEWPEFAAVVRHELVHAWEFQQFG--ESGHGPRFRER 115
                                       56778889**************..****************************************..*********** PP

                         SprT-like  96 aakvek 101
                                       aa +e 
  gi|336255374|ref|YP_004598481.1| 116 AADLEA 121
                                       998865 PP

>> DBD_Tnp_Mut  MuDR family transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.6   1.8e-05     0.065      38      55 ..     130     147 ..     120     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                       DBD_Tnp_Mut  38 ksrytvrCekegCpWrvh 55 
                                       + ry+ rC +egC Wr  
  gi|336255374|ref|YP_004598481.1| 130 EPRYVLRCRAEGCDWRAT 147
                                       569************954 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 ?   -2.4   0.1       1.3   4.5e+03      33      33 ..     128     128 ..     113     139 .. 0.59
   2 ?   14.0   0.4   9.8e-06     0.035       9      33 ..     141     169 ..     140     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                    Zn_ribbon_SprT  33 t 33 
                                       +
  gi|336255374|ref|YP_004598481.1| 128 F 128
                                       1 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 9.8e-06
                    Zn_ribbon_SprT   9 gCgreythhlsirrhn....YrCrrCkgt 33 
                                       gC+ + t+h+ +++ +    YrC+ C+g 
  gi|336255374|ref|YP_004598481.1| 141 GCDWRATRHRASQPVKapdqYRCGSCGGA 169
                                       5888999*******************986 PP

>> BSP  Peptidase of plants and bacteria
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.2e-05     0.044      95     118 ..      82     106 ..      67     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                               BSP  95 k.aevtgvLthelvhvyqweaegra 118
                                       +  e + v++helvh++ +++ g+ 
  gi|336255374|ref|YP_004598481.1|  82 EwPEFAAVVRHELVHAWEFQQFGES 106
                                       3479999************995543 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.1   0.00089       3.2       2      35 ..     131     169 ..     131     175 .. 0.47
   2 ?    8.9   0.3   0.00044       1.6       5      19 ..     160     174 ..     160     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00089
                       Zn-ribbon_8   2 PiYeYrCee..Cghefevlqsis..daplta.CPeCgse 35 
                                       P Y  rC++  C+ + ++ +++   +ap++  C +Cg++
  gi|336255374|ref|YP_004598481.1| 131 PRYVLRCRAegCDWRATRHRASQpvKAPDQYrCGSCGGA 169
                                       556666666555555443332223334444446666653 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00044
                       Zn-ribbon_8   5 eYrCeeCghefevlq 19 
                                       +YrC +Cg  +ev +
  gi|336255374|ref|YP_004598481.1| 160 QYRCGSCGGAYEVEH 174
                                       6********999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1614.73
//
Query:       gi|336255375|ref|YP_004598482.1|  [L=181]
Description: hypothetical protein Halxa_3998 [Halopiger xanaduensis SH-6]
Scores for 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  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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 0.20s 00:00:00.57 Elapsed: 00:00:00.33
# Mc/sec: 1623.05
//
Query:       gi|336255376|ref|YP_004598483.1|  [L=62]
Description: hypothetical protein Halxa_3999 [Halopiger xanaduensis SH-6]
Scores for 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   15.7   0.2      0.017   15.6   0.2    1.0  1  DsbB             Disulfide bond formation protein DsbB


Domain annotation for each model (and alignments):
>> DsbB  Disulfide bond formation protein DsbB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.2   9.4e-07     0.017      36      79 ..       6      50 ..       5      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.4e-07
                                      HHHHHHHHHHHHHHHTTSSSS.HHHHHHHHHHHHHHHHHHHHHHH CS
                              DsbB 36 yqRlallliallallaaiapk.rllllllallaalvgaalaarhv 79
                                      +qR+all+++l+++l +  p   + ++l+a+l+ +vg+++ +r++
  gi|336255376|ref|YP_004598483.1|  6 LQRFALLVMVLGGFLEVSSPGsGVGFMLIAALLGAVGLVIELRRA 50
                                      6****************8888655777888888889999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 504.46
//
Query:       gi|336255377|ref|YP_004598484.1|  [L=226]
Description: HAD-superfamily hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-21   76.5   0.0    3.4e-21   76.1   0.0    1.2  1  HAD_2            Haloacid dehalogenase-like hydrolase
    8.6e-13   49.1   0.1    2.2e-11   44.5   0.1    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.5e-09   37.7   0.1    3.3e-09   36.7   0.1    1.5  1  Hydrolase_like   HAD-hyrolase-like
    9.4e-08   32.7   0.3    1.2e-07   32.3   0.3    1.1  1  HAD              haloacid dehalogenase-like hydrolase
      0.007   16.0   0.0      0.035   13.7   0.0    1.9  2  PGP_phosphatase  Mitochondrial PGP phosphatase
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.033   14.3   0.0    1.4  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase
      0.024   14.4   0.0        0.1   12.4   0.0    1.9  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 !   76.1   0.0   1.3e-24   3.4e-21       1     178 []       7     199 ..       7     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 1.3e-24
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeygls.elseeelrkli.glslrellrklgeseeeee...........kiee 64 
                                       i FDlD Tl   + + ++ ++ ++++ g++   ++ +lr  i  l++ e+  ++ e   +e               +
  gi|336255377|ref|YP_004598484.1|   7 ICFDLDHTLCEPTRAPAALLEAAFDRAGCErFCTPADLRAAIpDLPTAETDLEFYEHLFTEVsrraerdidpnVPSR 83 
                                       67*************************77766677777765535566555555555544444556677777768899 PP

                             HAD_2  65 llrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekk..KPdpe 139
                                       l r y+ee + + v++ +g++ +Le   +   +++++T++ re++++kl++lgie+ Fdv v +e   +   KPd++
  gi|336255377|ref|YP_004598484.1|  84 LARAYREETDPTAVQFRPGAERALERA-RDHGQVALITNGGRETQTQKLQALGIEDAFDVRVFTEPSAGIhpKPDAA 159
                                       99999999999***************8.66779***************************999998764335***** PP

                             HAD_2 140 viekaleklklkkeeviyvGDsp.tDieaakkagikviav 178
                                       ++e al  l+++++ +i +GDs   D+ +a ++g++++++
  gi|336255377|ref|YP_004598484.1| 160 PFEHALSTLEATPDGAIHIGDSLhADVAGANAMGLDSAWI 199
                                       ***********************99***********9996 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.1   8.4e-15   2.2e-11       2     210 .]       5     193 ..       4     193 .. 0.69

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 8.4e-15
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH.......HHHHHHHHHETTTEHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar.......sgaltgfatfigrgayai 71 
                                       ++++fD+d TL++ + +   ++ +a                  a+ +a ++r       + a+ +  t       a+
  gi|336255377|ref|YP_004598484.1|   5 DAICFDLDHTLCEPT-RAPAALLEA------------------AFDRAGCERfctpadlRAAIPDLPT-------AE 55 
                                       677777777777666.222222222..................2333333332332222222222222.......33 PP

                                       THHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH..................TTHHHHHHHHHHTHHBHTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  72 gkpewltaldippdlgaaigsaqsqgrtvall..................qaralavftiadplkvkpeaaeavasL 130
                                          e+ ++l                                          ara+++ t     + +p+a+ a+++ 
  gi|336255377|ref|YP_004598484.1|  56 TDLEFYEHL----------------------FtevsrraerdidpnvpsrLARAYREETDPTAVQFRPGAERALERA 110
                                       334444444......................0222222222222222233569999999999999************ PP

                                       HHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCES..STTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                         Hydrolase 131 kaagievvlltgdnpetaeraanqlG.ddyfdaviasdiet..vakpspegkvaaireLqgkpeevamVGDgvn.Da 203
                                       ++ g  v+l+t++ +et+   ++ lG +d+fd+ + ++ ++  + kp+   +++a+  L + p   +++GD++  D+
  gi|336255377|ref|YP_004598484.1| 111 RDHGQ-VALITNGGRETQTQKLQALGiEDAFDVRVFTEPSAgiHPKPDAAPFEHALSTLEATPDGAIHIGDSLHaDV 186
                                       ****9.*************************99999999999*********************************** PP

                                       HHHHHTT CS
                                       xxxxxxx RF
                         Hydrolase 204 aalaaAg 210
                                       a++ a+g
  gi|336255377|ref|YP_004598484.1| 187 AGANAMG 193
                                       **99987 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   1.3e-12   3.3e-09       4      69 ..     155     216 ..     153     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.3e-12
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESS..SSS-TTTHHHHHHHHT--- CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVlt..Gvtrpedleepehkptyva 69 
                                       KP +  ++ al  l+++p+  + iGD+l++D+agAn++G++s+ ++t  Gv+++e      h+pty +
  gi|336255377|ref|YP_004598484.1| 155 KPDAAPFEHALSTLEATPDGAIHIGDSLHADVAGANAMGLDSAWIATdgGVETAE------HRPTYEL 216
                                       9999**************************************9988854665554......5556544 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.3   4.6e-11   1.2e-07       1     180 [.       7     181 ..       7     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 4.6e-11
                               HAD   1 alfDfDgTLldgdsle.....lllrfllrrgaprlwralrek.lllalfrellrldraglaelleallaglseelaa 71 
                                       + fD+D+TL     ++     + ++ ++++ +  + + lr++ ++l  +++ l++ +  + e+ +++ ++ ++ +  
  gi|336255377|ref|YP_004598484.1|   7 ICFDLDHTLCEPTRAPaalleAAFD-RAGCERFCTPADLRAAiPDLPTAETDLEFYEHLFTEVSRRAERDIDPNVPS 82 
                                       68*******8887777766754444.555555555444444447777777777777777788999999999999999 PP

                               HAD  72 elerfvaevirpkl..ldpgalellaahraaGd.rvvvvSgglrplvepllaelgadevlatelevddrltgelgle 145
                                       +l+r+++e+  p +  ++pga ++l+++  + + +v+++++g r+    +l++lg    +   ++v+ ++t      
  gi|336255377|ref|YP_004598484.1|  83 RLARAYREETDPTAvqFRPGAERALERA--RDHgQVALITNGGRETQTQKLQALG----IEDAFDVR-VFTEP---- 148
                                       999999999999944699********44..33339********************....77755554.55555.... PP

                               HAD 146 gkpvrgegkvaalrewlaaegegidleevvayGDs 180
                                          ++ + ++a  +  l   ++ +d    + +GDs
  gi|336255377|ref|YP_004598484.1| 149 SAGIHPKPDAAPFEHALSTLEATPDG--AIHIGDS 181
                                       22233333333344422333333333..6677777 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.3   7.8e+02      43      57 ..       6      20 ..       2      26 .. 0.87
   2 !   13.7   0.0   1.4e-05     0.035      73     164 ..     109     200 ..      91     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.3
                   PGP_phosphatase 43 avvlDKDnclaapke 57
                                      a+ +D D +l++p +
  gi|336255377|ref|YP_004598484.1|  6 AICFDLDHTLCEPTR 20
                                      789********9975 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.4e-05
                   PGP_phosphatase  73 evypeksilivSNsaGssddkdaekaealekktgipVlrhk....ekKPgca..eevleyfkerkvveeadeiavvg 143
                                       ++  + ++ ++ N  G + ++++ +a  +e++ +++V+  +    + KP++a  e  l+ ++++     +d  + +g
  gi|336255377|ref|YP_004598484.1| 109 RARDHGQVALITN-GGRETQTQKLQALGIEDAFDVRVFTEPsagiHPKPDAApfEHALSTLEAT-----PDGAIHIG 179
                                       4444556888888.477779999*****************988888888654225566666555.....9******* PP

                   PGP_phosphatase 144 DRllTdvllanmmGslgvwlr 164
                                       D l  dv  an mG  + w++
  gi|336255377|ref|YP_004598484.1| 180 DSLHADVAGANAMGLDSAWIA 200
                                       **************9999985 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-05     0.033      17      57 ..     101     137 ..      96     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                       TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT-- CS
                       Hydrolase_6  17 pgaaealnalraagkpvvllTNnsskseeeyakkleklgvd 57 
                                       pga++al++ r++g +v+l+TN++++++ +   kl++lg++
  gi|336255377|ref|YP_004598484.1| 101 PGAERALERARDHG-QVALITNGGRETQTQ---KLQALGIE 137
                                       9***********98.8********998555...55666654 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.9e-05       0.1      25      86 ..      89     149 ..       6     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                               NIF  25 egekvevsvlkRpgldefLkelsklyevvifTasseeyaeavidildpekkllshrlyresc 86 
                                       ++e+ +  v+ Rpg++  L+++  + +v ++T++ +e+  + +++l  e + ++ r++ e +
  gi|336255377|ref|YP_004598484.1|  89 REETDPTAVQFRPGAERALERARDHGQVALITNGGRETQTQKLQALGIEDA-FDVRVFTEPS 149
                                       35566789**************************************99887.8888777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1708.65
//
Query:       gi|336255378|ref|YP_004598485.1|  [L=413]
Description: 3-dehydroquinate synthase [Halopiger xanaduensis SH-6]
Scores for 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-142  472.2   3.9   1.1e-141  471.8   3.9    1.2  1  DHQS       3-dehydroquinate synthase II
     0.0002   21.2   2.3      0.041   13.6   0.2    2.6  2  QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal
     0.0012   18.4   0.0     0.0072   15.9   0.0    2.2  2  Hint       Hint module
  ------ inclusion threshold ------
      0.043   14.4   0.0        0.1   13.1   0.0    1.6  1  TNT        Tuberculosis necrotizing toxin
       0.12   12.7   3.0         13    6.1   0.1    3.2  3  Hint_2     Hint domain


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 !  471.8   3.9  3.2e-145  1.1e-141       1     352 []       5     413 .]       5     413 .] 0.96

  Alignments for each domain:
  == domain 1  score: 471.8 bits;  conditional E-value: 3.2e-145
                              DHQS   1 kevwikade..eeweerkelvtaaleagvdavlveeedaekvkelgkikviakeed.davlvgkd............ 62 
                                       ++vwikad+  ++w+er+e++taaleag+d+vlv+e d+e+v+elg+i+v+a++++ d++lv+++            
  gi|336255378|ref|YP_004598485.1|   5 RSVWIKADDtvGDWDERRERITAALEAGADWVLVDEADVERVRELGDINVAAFRTNgDVTLVDDAesddaedviedv 81 
                                       689*****9999*****************************************966455555544677778888888 PP

                              DHQS  63 .......................................dleklkka....kkvaalveikskeeeeeaaeaakead 96 
                                                                              dl++l+++     + +a+v+i ++e+e++a++aa+ead
  gi|336255378|ref|YP_004598485.1|  82 gdtgdaggassakpdavivgkdgegdatidmpedlsgsaDLSTLRRDedadLERGAYVRILDTEYERFAETAAQEAD 158
                                       8889999999999999999999*****************999999888888899*********************** PP

                              DHQS  97 yvivelkdwtvIPlEnliAalqgeetkiiaavksaeeAklaletLEkGadgvllktedveeikelaelleeaeeekl 173
                                       ++i+ ++dwt+IPlEnliA++ g+et+++a+v++aeeA++a+etLE+Gad vll+++d++ei++++e++++ae+e+l
  gi|336255378|ref|YP_004598485.1| 159 HTIIIGEDWTIIPLENLIARI-GDETDLVAGVTTAEEARTAFETLEIGADSVLLDSSDPDEIRKTVEVRDDAERETL 234
                                       *******************99.999**************************************************** PP

                              DHQS 174 eLkeaevtkveevgmgdRvcvDtcslmkegeGmLvGsssrglfLvhsEtlespYvasRPFRVNAGavhaYvlvpggk 250
                                       +L++aev +ve+vg++dRvc+Dt sl++++eGmLvGs++rgl++vh+Et+espYvasRPFRVNAGavhaYv++p+g 
  gi|336255378|ref|YP_004598485.1| 235 DLEYAEVLDVERVGSADRVCIDTGSLLEHDEGMLVGSMARGLVFVHAETAESPYVASRPFRVNAGAVHAYVRTPDGG 311
                                       ***************************************************************************** PP

                              DHQS 251 TkYLseLkaGdevlvvdkkGktreavvGRvKiEkRPlllveaea.egkkvstilQnaetirlvtedgkaisvteLke 326
                                       TkYLseL++Gdev+vvd++G+trea+vGRvKiE+RP+++v  e+  g++v+t+lQnaeti+++t +g +++vt+L++
  gi|336255378|ref|YP_004598485.1| 312 TKYLSELQSGDEVQVVDTNGNTREAIVGRVKIEQRPMFRVALETqAGDRVETLLQNAETIKVATGEG-RKAVTDLEA 387
                                       *******************************************9899********************.99******* PP

                              DHQS 327 GdevlvyleekaRHfGikieEtiiEk 352
                                       Gde+l+y+e++aRHfG ++eE+iiEk
  gi|336255378|ref|YP_004598485.1| 388 GDELLLYYEDTARHFGEAVEESIIEK 413
                                       *************************8 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 !    6.8   0.2    0.0015       5.2      90     119 ..      22      51 ..      18      80 .. 0.87
   2 !   13.6   0.2   1.2e-05     0.041      87     127 ..     189     232 ..     151     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHT-SEEEEES--HHHHHHHHH CS
                         QRPTase_C  90 leeleevleaeadiimLDnfsveelkkave 119
                                        e ++++lea+ad +++D+ +ve +++  +
  gi|336255378|ref|YP_004598485.1|  22 RERITAALEAGADWVLVDEADVERVRELGD 51 
                                       578999*******************98755 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.2e-05
                                       ESSHHHHHHHHH...HT-SEEEEES--HHHHHHHHHHHHHHSTT CS
                         QRPTase_C  87 vesleeleevle...aeadiimLDnfsveelkkaveelkeknkr 127
                                       v + ee++ + e    +ad ++LD  +++e++k+ve+++ ++++
  gi|336255378|ref|YP_004598485.1| 189 VTTAEEARTAFEtleIGADSVLLDSSDPDEIRKTVEVRDDAERE 232
                                       66677777665533378*******************88666554 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     2e-06    0.0072      17      47 ..     303     333 ..     300     362 .. 0.91
   2 ?   -0.9   0.0      0.27   9.6e+02      22      39 ..     375     392 ..     366     402 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              Hint  17 stvtvedgeqkslseLepGdkVlavdesgev 47 
                                       + v++ dg++k lseL+ Gd+V+ vd++g++
  gi|336255378|ref|YP_004598485.1| 303 AYVRTPDGGTKYLSELQSGDEVQVVDTNGNT 333
                                       789***********************99986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.27
                                       XXXXXXXXXXXXXXXXXX CS
                              Hint  22 edgeqkslseLepGdkVl 39 
                                        ++++k++ +Le Gd+ l
  gi|336255378|ref|YP_004598485.1| 375 TGEGRKAVTDLEAGDELL 392
                                       345799*********987 PP

>> TNT  Tuberculosis necrotizing toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.9e-05       0.1       9      72 ..     251     317 ..     242     335 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                                       EEES-TT-S-EEEGG---...GGGT--GGGGGS-EEEEEE.----EEEEEB--BTTB----EEEEEE CS
                               TNT   9 dRfGseeGrflapagtpy...eeRaLppsnlnknyhvYevlkpleveaGeiapwfgqpGgGvqyelv 72 
                                       dR   ++G++l +++        R+L   + +   + Y   +p++v+aG + + +  p gG++y  +
  gi|336255378|ref|YP_004598485.1| 251 DRVCIDTGSLLEHDEGMLvgsMARGLVFVHAETAESPYVASRPFRVNAGAVHAYVRTPDGGTKYLSE 317
                                       33444778888764444436678999999999999*****************************876 PP

>> Hint_2  Hint domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.3   4.6e+03      15      42 ..     196     224 ..     188     235 .. 0.73
   2 ?    6.1   0.1    0.0036        13       8      33 ..     304     330 ..     300     353 .. 0.75
   3 ?    5.3   0.1    0.0061        22       8      29 ..     372     393 ..     367     401 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
                            Hint_2  15 evaveeLrvG.dlVvtadgglqpvrwigs 42 
                                         a e+L++G d+V+  +  + ++r+ ++
  gi|336255378|ref|YP_004598485.1| 196 RTAFETLEIGaDSVLLDSSDPDEIRKTVE 224
                                       56789999997788888888888887665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0036
                            Hint_2   8 liatpeG.evaveeLrvGdlVvtadgg 33 
                                        ++tp+G +  + eL+ Gd+V+++d++
  gi|336255378|ref|YP_004598485.1| 304 YVRTPDGgTKYLSELQSGDEVQVVDTN 330
                                       689998725679***********9964 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0061
                            Hint_2   8 liatpeGevaveeLrvGdlVvt 29 
                                        +at eG  av +L++Gd+++ 
  gi|336255378|ref|YP_004598485.1| 372 KVATGEGRKAVTDLEAGDELLL 393
                                       589***************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3021.93
//
Query:       gi|336255379|ref|YP_004598486.1|  [L=144]
Description: hypothetical protein Halxa_4002 [Halopiger xanaduensis SH-6]
Scores for 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-05   23.5   1.1      6e-05   23.0   1.1    1.2  1  DZR             Double zinc ribbon
    0.00034   20.2   0.7    0.00049   19.7   0.7    1.3  1  zinc_ribbon_2   zinc-ribbon domain
    0.00078   18.8   0.4     0.0013   18.1   0.4    1.3  1  zf-ribbon_3     zinc-ribbon domain
     0.0021   18.1   0.3     0.0041   17.2   0.3    1.4  1  UPF0547         Uncharacterised protein family UPF0547
     0.0081   16.4   3.2        1.6    9.0   0.3    2.3  2  zinc_ribbon_9   zinc-ribbon
  ------ inclusion threshold ------
      0.024   15.4   0.0      0.029   15.1   0.0    1.2  1  zinc_ribbon_15  zinc-ribbon family
      0.037   13.9   0.4        3.6    7.6   0.1    2.2  2  Nudix_N_2       Nudix N-terminal
       0.31   11.0   2.1       0.51   10.4   2.1    1.3  1  YhfH            YhfH-like protein
       0.34   10.9   1.3          2    8.4   0.2    2.1  2  SafA            Two-component-system connector 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 !   23.0   1.1     3e-08     6e-05       1      25 [.     110     134 ..     110     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3e-08
                               DZR   1 CpqCgeelppdarfCseCgtklkav 25 
                                       Cp+Cg+el++d +fC++C t+l+++
  gi|336255379|ref|YP_004598486.1| 110 CPECGKELDEDLEFCHWCTTRLEPA 134
                                       **********************865 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   0.7   2.5e-07   0.00049       2      22 ..     110     130 ..     109     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.5e-07
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtp 22 
                                       Cp+CG+el+++  FC  C t 
  gi|336255379|ref|YP_004598486.1| 110 CPECGKELDEDLEFCHWCTTR 130
                                       ******************876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.4   6.6e-07    0.0013       4      24 ..     109     129 ..     109     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.6e-07
                       zf-ribbon_3   4 rCPnCGa.plssddnvCpyCGt 24 
                                       +CP+CG+ + ++d  +C +C t
  gi|336255379|ref|YP_004598486.1| 109 TCPECGKeL-DEDLEFCHWCTT 129
                                       5******66.**********55 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   2.1e-06    0.0041       2      20 ..     109     127 ..     109     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-06
                           UPF0547   2 vCPeCeakvPvaaqfCphC 20 
                                       +CPeC  ++ ++ +fC+ C
  gi|336255379|ref|YP_004598486.1| 109 TCPECGKELDEDLEFCHWC 127
                                       7****************99 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   0.2    0.0022       4.3      19      29 ..     104     115 ..      98     117 .. 0.75
   2 !    9.0   0.3   0.00081       1.6       4      22 ..     123     141 ..     122     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0022
                     zinc_ribbon_9  19 dsd.vlCPhCgg 29 
                                       +sd ++CP+Cg 
  gi|336255379|ref|YP_004598486.1| 104 SSDgPTCPECGK 115
                                       555469****96 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00081
                     zinc_ribbon_9   4 WChqCdrfVsvspdedsdv 22 
                                       +Ch C+ +++++++ed+d+
  gi|336255379|ref|YP_004598486.1| 123 FCHWCTTRLEPAEPEDADP 141
                                       8*************99986 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.5e-05     0.029      63      85 ..     105     127 ..      69     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                    zinc_ribbon_15  63 sekkeCknCgkeveeefkyCpkC 85 
                                       s+  +C++Cgke++e+ ++C  C
  gi|336255379|ref|YP_004598486.1| 105 SDGPTCPECGKELDEDLEFCHWC 127
                                       44789****************99 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.014        29       3      11 ..     110     118 ..     110     122 .. 0.82
   2 ?    7.6   0.1    0.0018       3.6       2      17 ..     123     138 ..     122     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                                       -TTT--B-E CS
                         Nudix_N_2   3 CsqCGtpve 11 
                                       C++CG+++ 
  gi|336255379|ref|YP_004598486.1| 110 CPECGKELD 118
                                       9****9986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0018
                                       B-TTT--B-EEE--TT CS
                         Nudix_N_2   2 FCsqCGtpvelripdg 17 
                                       FC  C t++e + p++
  gi|336255379|ref|YP_004598486.1| 123 FCHWCTTRLEPAEPED 138
                                       9*********998875 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.1   0.00026      0.51      15      27 ..     109     121 ..     108     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00026
                              YhfH  15 kCteCGkeieEqa 27 
                                       +C+eCGke++E  
  gi|336255379|ref|YP_004598486.1| 109 TCPECGKELDEDL 121
                                       7*********975 PP

>> SafA  Two-component-system connector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2     0.001         2      24      47 ..      31      54 ..      27      64 .. 0.85
   2 ?    1.3   0.1      0.17   3.4e+02      30      42 ..      74      86 ..      69      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.001
                              SafA 24 vvvllltltliaifsaidqlsise 47
                                      vv   l l+ iaif  +dql+ +e
  gi|336255379|ref|YP_004598486.1| 31 VVFAGLYLSAIAIFLPMDQLAAAE 54
                                      566678999***********9988 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.17
                              SafA 30 tltliaifsaidq 42
                                      +l++i +f+aid 
  gi|336255379|ref|YP_004598486.1| 74 ALSFIGLFAAIDA 86
                                      6899*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1117.61
//
Query:       gi|336255380|ref|YP_004598487.1|  [L=232]
Description: hypothetical protein Halxa_4003 [Halopiger xanaduensis SH-6]
Scores for 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   12.0   0.0        0.2   11.1   0.0    1.4  1  zf_Rg     Reverse gyrase zinc finger
       0.13   12.4   0.2        1.8    8.7   0.1    2.2  2  DUF1272   Protein of unknown function (DUF1272)


Domain annotation for each model (and alignments):
>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.2e-05       0.2       5      18 ..     171     184 ..     168     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.2e-05
                             zf_Rg   5 vfeklCPNCgGdis 18 
                                       +f   CPNC+G++ 
  gi|336255380|ref|YP_004598487.1| 171 LFLDRCPNCDGALV 184
                                       68899******985 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0002       1.8      40      52 ..     172     184 ..     167     186 .. 0.83
   2 ?    1.1   0.0     0.048   4.3e+02      25      32 ..     215     222 ..     207     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0002
                           DUF1272  40 lenvCPncgGelv 52 
                                       + ++CPnc G lv
  gi|336255380|ref|YP_004598487.1| 172 FLDRCPNCDGALV 184
                                       5689******998 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.048
                           DUF1272  25 csyEctFC 32 
                                        s Ec++C
  gi|336255380|ref|YP_004598487.1| 215 VSLECAYC 222
                                       588***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1777.85
//
Query:       gi|336255381|ref|YP_004598488.1|  [L=228]
Description: 3-dehydroquinate dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-46  156.9   0.1    1.1e-45  156.7   0.1    1.0  1  DHquinase_I  Type I 3-dehydroquinase
  ------ inclusion threshold ------
       0.14   12.0   0.2       0.34   10.7   0.2    1.7  1  DUF5615      Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.7   0.1   1.2e-49   1.1e-45      16     228 ..      21     223 ..       8     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 156.7 bits;  conditional E-value: 1.2e-49
                                       HHHHTTS-SEEEEEGGG-.TT.THHHHHHHHHHHHHH.TTS-EEEE---GGGT-S.SSS-HHHHHHHHHHHHH.CT- CS
                       DHquinase_I  16 lesgkekaDlvElRlDllketseaedvseeleelrst.sdlpliftlrtkaeggrfkrkseeeylellrtaie.lga 90 
                                       + +++++aD+vE+R+ l  + ++      +l+ l    ++lp+++t r ++egg++ +++++e+le+l +a++  g+
  gi|336255381|ref|YP_004598488.1|  21 A-RARNHADAVEFRMGLS-NADD------ALAALEAYdGQLPVLATNRAAWEGGEW-AGDDAERLEVLAEAARiDGV 88 
                                       3.33358*********66.4423......7888888867****************9.9***************5566 PP

                                       SEEEEEGG-.HHG.HHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSHHHHHHHH CS
                       DHquinase_I  91 dyvDvElteapee.skkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksieDvlrll 166
                                       + +DvEl e   + + +++ e +re+ + v++S hdfegtps+++++++l+++ ++  D+ K+av+a++++D l++l
  gi|336255381|ref|YP_004598488.1|  89 EAIDVEL-ESLRSgAADDVLETAREQDVSVVASTHDFEGTPSEDAMIERLAEACEYA-DVGKLAVTAHDRSDSLAVL 163
                                       *******.5665677789************************************998.******************* PP

                                       HHHHHHHHHT-SS-EEEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHHHH CS
                       DHquinase_I 167 sltseakeekdeaplIamamGelGkiSRilgevfGspvtfasleeakasapGqltarelrei 228
                                       s+t+++++  d   + +mamGe+G  +R +++++Gs + +a ++ a+a+apGq ++++l ++
  gi|336255381|ref|YP_004598488.1| 164 SATHRLTQ--DGETVATMAMGEAGSHTRAVAPLYGSRIGYAPVDPAEATAPGQYDLATLSRL 223
                                       ***98888..679********************************************99876 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   3.8e-05      0.34      13      59 ..      79     125 ..      72     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.8e-05
                           DUF5615  13 lvellreaghdvlhvrelglegasDeeileyAkeedriivTkDkDFg 59 
                                       l+e+ r +g++++ v  ++l++   +++le A+e+d+ +v    DF 
  gi|336255381|ref|YP_004598488.1|  79 LAEAARIDGVEAIDVELESLRSGAADDVLETAREQDVSVVASTHDFE 125
                                       6888999********999999755567*************9888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1781.63
//
Query:       gi|336255382|ref|YP_004598489.1|  [L=329]
Description: transcription initiation factor IIB [Halopiger xanaduensis SH-6]
Scores for complete 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-39  134.1   0.6    4.6e-20   71.4   0.0    2.4  2  TFIIB          Transcription factor TFIIB repeat
      7e-16   57.5  12.8    9.7e-16   57.0   5.9    2.1  2  TF_Zn_Ribbon   TFIIB zinc-binding
     0.0014   18.3   0.7     0.0027   17.4   0.7    1.5  1  A2L_zn_ribbon  A2L zinc ribbon domain
     0.0067   15.9   0.0       0.57    9.7   0.0    3.5  3  Sigma70_r4     Sigma-70, region 4
  ------ inclusion threshold ------
       0.13   12.2   0.5       0.25   11.3   0.5    1.4  1  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi
       0.26   10.7   1.4       0.64    9.5   0.3    2.1  2  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
        2.4    8.8   5.2        8.8    7.0   3.2    2.7  2  Trm112p        Trm112p-like protein


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 !   71.4   0.0   1.8e-23   4.6e-20       1      71 []     148     218 ..     148     218 .. 0.98
   2 !   60.9   0.1   3.5e-20   8.8e-17       1      71 []     242     312 ..     242     312 .. 0.99

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.8e-23
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i r+a+al+Lp+ V++ A  ++++alee++l Grs +g+  Ac+y A+r+++v r++ ei++v++V++ +i
  gi|336255382|ref|YP_004598489.1| 148 IDRMASALGLPNNVRETASVIYRRALEEDLLPGRSIEGVSTACVYAAARQAGVPRSLDEIADVSRVEKNEI 218
                                       789****************************************************************9987 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 3.5e-20
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rfa+ leL+++ + +A  l+++a+e++v++G+sp g+aAA++y A+++ ++k tq+ +s+v+ +se+ti
  gi|336255382|ref|YP_004598489.1| 242 VPRFASGLELSDEAEHRARSLLQNAKEKGVHSGKSPVGLAAAAVYAAALLTNEKTTQAAVSDVADISEVTI 312
                                       689******************************************************************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 !   12.3   0.6   3.5e-05     0.089       9      28 ..      21      41 ..      19      42 .. 0.86
   2 !   57.0   5.9   3.8e-19   9.7e-16       2      43 .]      33      73 ..      32      73 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.5e-05
                                      EECHEETSTTCEEESSS.SBE CS
                      TF_Zn_Ribbon  9 tnlveDpergelvCtdC.GlV 28
                                      t++++++e+++lvC++C G++
  gi|336255382|ref|YP_004598489.1| 21 TETETETESNDLVCPECaGNL 41
                                      568999***********9986 PP

  == domain 2  score: 57.0 bits;  conditional E-value: 3.8e-19
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      +CP+C +  lv+D e+ge+vC+dCGlV+e++s+d gpewr+f
  gi|336255382|ref|YP_004598489.1| 33 VCPECAGN-LVVDDEHGETVCEDCGLVVEEDSVDRGPEWRAF 73
                                      8*****96.9******************************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 !   17.4   0.7     1e-06    0.0027       1      30 [.      29      58 ..      27      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1e-06
                     A2L_zn_ribbon  1 snlkvCsvCggngilnseqgylvCieCgas 30
                                      sn+ vC  C gn ++  e+g+ vC +Cg++
  gi|336255382|ref|YP_004598489.1| 29 SNDLVCPECAGNLVVDDEHGETVCEDCGLV 58
                                      67889***********************86 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.14   3.6e+02      34      46 ..     162     174 ..     154     175 .. 0.92
   2 ?   -0.5   0.0      0.36   9.3e+02      18      29 ..     199     210 ..     191     215 .. 0.80
   3 !    9.7   0.0   0.00022      0.57      18      46 ..     293     321 ..     284     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHH CS
                        Sigma70_r4  34 rerVrqiekrAlr 46 
                                       re+++ i +rAl+
  gi|336255382|ref|YP_004598489.1| 162 RETASVIYRRALE 174
                                       89*********97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.36
                                       TTT--HHHHHHH CS
                        Sigma70_r4  18 geglTleEIger 29 
                                       g +++l EI+++
  gi|336255382|ref|YP_004598489.1| 199 GVPRSLDEIADV 210
                                       568999999985 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00022
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlr 46 
                                        e+ T++ ++++ +iS+ ++r + ++ l+
  gi|336255382|ref|YP_004598489.1| 293 NEKTTQAAVSDVADISEVTIRNRYHELLE 321
                                       5889********************99876 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   0.5   9.8e-05      0.25      21      50 ..      22      51 ..      14      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.8e-05
                                      EETTE......E-TTTTTSSEEE-HHHHHH CS
                         Anti-TRAP 21 kiepeeprasleCPkCsGkglipTaqGqkL 50
                                      + e+e +   l CP+C G+ ++  ++G++ 
  gi|336255382|ref|YP_004598489.1| 22 ETETETESNDLVCPECAGNLVVDDEHGETV 51
                                      5666677889*************9999986 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 ?   -0.8   0.0      0.41   1.1e+03      12      47 ..     186     221 ..     185     226 .. 0.70
   2 ?    9.5   0.3   0.00025      0.64      17      51 ..     284     319 ..     281     320 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.41
                      HTH_Tnp_ISL3  12 iTlrleayilelllesrsvkavArqlgvSwtTVwri 47 
                                        ++++ +++++++   rs  ++A+  +v  + + r 
  gi|336255382|ref|YP_004598489.1| 186 VSTACVYAAARQAGVPRSLDEIADVSRVEKNEIART 221
                                       577888888999888888888887666666665555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00025
                      HTH_Tnp_ISL3  17 eayilellles.rsvkavArqlgvSwtTVwrildry 51 
                                       + y+++ll++   + +av++  ++S+ T++++++++
  gi|336255382|ref|YP_004598489.1| 284 AVYAAALLTNEkTTQAAVSDVADISEVTIRNRYHEL 319
                                       56999***************************9875 PP

>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.2    0.0034       8.8       8      61 ..      32      57 ..       2      58 .. 0.85
   2 ?   -2.7   0.0       3.7   9.5e+03      23      46 ..     285     321 ..     277     325 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0034
                                      -B-TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTE CS
                           Trm112p  8 LaCpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgr 61
                                      L+Cp c g L                        +    +d+e+ge vC++cg+
  gi|336255382|ref|YP_004598489.1| 32 LVCPECAGNL------------------------V----VDDEHGETVCEDCGL 57
                                      7888888888........................7....899999999999987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                                       HHHHH.TT---S-SS----S............CHHTT CS
                           Trm112p  23 vevaa.lglnelpkekpedy............ellle 46 
                                       v++aa l +++  ++  +d+            ++lle
  gi|336255382|ref|YP_004598489.1| 285 VYAAAlLTNEKTTQAAVSDVadisevtirnryHELLE 321
                                       4555555555544444444445555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1065  (0.059401); expected 358.6 (0.02)
Passed bias filter:                      717  (0.0399911); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2618.68
//
Query:       gi|336255383|ref|YP_004598490.1|  [L=173]
Description: hypothetical protein Halxa_4006 [Halopiger xanaduensis SH-6]
Scores for complete 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-50  171.2   0.0    1.6e-50  171.1   0.0    1.0  1  NTPase_I-T  Protein of unknown function DUF84


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 !  171.1   0.0     9e-55   1.6e-50       1     163 []       6     168 ..       6     168 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 9e-55
                                       S---HHHHHHHHHHHHHHCTTEEEEEEE---SS-SS-BSHHHHHHHHHHHHHHHHHHSTT.SSEEEEEEEEEET... CS
                        NTPase_I-T   1 gSkNpvKveAvkeafeklfkdvevegvsvpsgvsdqPmgdeetlkGAinRaknaleaaee.adygvGlEgGveelee 76 
                                       gS+NpvK++Av++++e++ +  +v++++v+sg+++qP++ eet++GA+nRa++al++a+  +++gvGlEgGv+++++
  gi|336255383|ref|YP_004598490.1|   6 GSTNPVKIDAVERTLERFDP--RVTAFDVESGIPEQPWSVEETVTGAENRARRALARADGnYEFGVGLEGGVARFDG 80 
                                       8*****************88..6********************************997777**************** PP

                                       ...TEEEEEE.EEEESS-EEEEE---EE--HHHHHHHCTT--HHHHHHHHHTHCCHHHTTHHHHHHTTTSS-HHHHH CS
                        NTPase_I-T  77 k..lldvawaavvdkegrvsvgrsasfelPeevveevkegeelgevmdelfgtenikqkeGaigllTkglvtRedly 151
                                          ++ ++waav+d+ +r++ g +++++lP++v++++++geelg+vmd+ ++t++i+++eGaig+ T+gl++R++++
  gi|336255383|ref|YP_004598490.1|  81 ApgVTLIMWAAVTDG-ERIERGGGPALRLPDRVADRLEAGEELGPVMDDELDTTGIAESEGAIGVCTEGLTDRTTAL 156
                                       999************.7************************************************************ PP

                                       HHHHHHHTHHHH CS
                        NTPase_I-T 152 eqavilAlipfl 163
                                        qa+++A+ pfl
  gi|336255383|ref|YP_004598490.1| 157 GQAIACAFGPFL 168
                                       **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       182  (0.0101512); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); 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 0.20s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1429.81
//
Query:       gi|336255384|ref|YP_004598491.1|  [L=77]
Description: hypothetical protein Halxa_4007 [Halopiger xanaduensis SH-6]
Scores for 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   15.0   0.0      0.023   14.5   0.0    1.3  1  LexA_DNA_bind  LexA DNA binding domain


Domain annotation for each model (and alignments):
>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.3e-06     0.023       2      43 ..       7      46 ..       6      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-06
                                      X---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHH CS
                     LexA_DNA_bind  2 kkLTerQrevldlikasieetgypPsireiaralglkSpsav 43
                                      ++LT +Q+++l++++++  ++ y  s r i+++lg++ ++ v
  gi|336255384|ref|YP_004598491.1|  7 SDLTSKQERILQYLRENAATKTYFKS-RIIGKELGMT-AKEV 46
                                      68*********************987.5799999998.5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 621.40
//
Query:       gi|336255385|ref|YP_004598492.1|  [L=246]
Description: Haloacid dehalogenase domain-containing protein hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-06   28.9   0.0    4.5e-06   26.9   0.0    1.9  1  HAD_2        Haloacid dehalogenase-like hydrolase
    6.5e-06   26.6   0.0    0.00071   19.9   0.0    2.4  1  Hydrolase    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.03   14.4   0.0        0.5   10.5   0.0    2.2  1  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 !   26.9   0.0   7.5e-10   4.5e-06       1     176 [.       5     210 ..       5     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 7.5e-10
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleey..gls.elseeelrkliglslrellrklgeseeeee.....kieellrky 69 
                                       i FD+Dg++l    +  q++  +++    +l+ e+++ + r l   ++ e++r   ++   +      + e++ +  
  gi|336255385|ref|YP_004598492.1|   5 ICFDMDGVILEGPRTAPQVYDDAADAAleELGaEPTPAQRRALRSQDT-EAIRGHCVELGLDPdrfwtLKERYASAG 80 
                                       67********97777666666655443334555999999999999999.5555555556666667887777777777 PP

                             HAD_2  70 neekkk.kevkpydgvkelLeeL.keagyklgivTsksreaveekleqlgiesyFdvivtsedv....ekkKPdpev 140
                                        +e  +     +yd++ +++ +L  +a+  +g+vT++++e++    + +  +  Fdv+ + + +     ++KPdp  
  gi|336255385|ref|YP_004598492.1|  81 THERLRsGARGLYDDI-DAVRTLaDRAETPVGLVTNNRHETAAFVADFV--DVPFDVVRGRDPTidgfRRRKPDPYY 154
                                       7777774445566666.56677747899********9998876555555..579*****998752222677****** PP

                             HAD_2 141 iekalekl....................klkkeeviyvGDsptDieaakkagikvi 176
                                       +e al +l                    +  + + +yvGDsp+D+ a+ k+g +++
  gi|336255385|ref|YP_004598492.1| 155 LEDALVQLdgtttidrvraggtgtgtgdGRGEPRGLYVGDSPKDVVAGTKIGFETA 210
                                       *************************999999999******************9987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.2e-07   0.00071       4     206 ..       5     202 ..       4     206 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.2e-07
                                       EEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH.....HHHH..HHHHHETTTE.HHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxx..xxxxxxxxxx.xxxxx RF
                         Hydrolase   4 vvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar.....sgal..tgfatfigrg.ayaig 72 
                                       ++fD+dG++++g +   +v++ a     aale                a+     + al  ++ +++ g+  ++   
  gi|336255385|ref|YP_004598492.1|   5 ICFDMDGVILEGPRTAPQVYDDA---ADAALEEL-------------GAEptpaqRRALrsQDTEAIRGHCvELGLD 65 
                                       79*********************...33333322.............111222222222223333333333477777 PP

                                       HHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHT.TEEEEEEESSEHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                         Hydrolase  73 kpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaa.gievvlltgdnpeta 148
                                         +++t            + + s+g  + l           a    +++++ +av++L ++   +v+l+t++ +eta
  gi|336255385|ref|YP_004598492.1|  66 PDRFWTLK----------ERYASAGTHERLR--------SGARG--LYDDI-DAVRTLADRaETPVGLVTNNRHETA 121
                                       77777777..........6666666666666........77888..88888.7888888775789************ PP

                                       HHHHHHTTGGGESEEEEHHCES....STTTSHHHHHHHHHHHT.....................STGGGEEEEESSH CS
                                       xxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxx RF
                         Hydrolase 149 eraanqlGddyfdaviasdiet....vakpspegkvaaireLq.....................gkpeevamVGDgv 200
                                         +a+ ++   fd+v ++d +       kp+p  ++ a+ +L                      g+p + + VGD++
  gi|336255385|ref|YP_004598492.1| 122 AFVADFVD-VPFDVVRGRDPTIdgfrRRKPDPYYLEDALVQLDgtttidrvraggtgtgtgdgrGEP-RGLYVGDSP 196
                                       ********.33444444443335578*************9997666666777777777777766666.778888888 PP

                                       HHHHHH CS
                                       xxxxxx RF
                         Hydrolase 201 nDaaal 206
                                        D+ a+
  gi|336255385|ref|YP_004598492.1| 197 KDVVAG 202
                                       887776 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.4e-05       0.5       1      44 [.       5     121 ..       5     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.4e-05
                                       EEEESTTTSEETTEE-TTH.....HHHHHHHHHTT.......................................... CS
                       Hydrolase_6   1 flfDidGvLwrgdkaipga.....aealnalraag.......................................... 30 
                                       ++fD+dGv+++g +  p++     + al+ l a+                                           
  gi|336255385|ref|YP_004598492.1|   5 ICFDMDGVILEGPRTAPQVyddaaDAALEELGAEPtpaqrralrsqdteairghcvelgldpdrfwtlkeryasagt 81 
                                       589*******8877766541111134555555555677777777777777777777777777777777777777777 PP

                                       ..........................-EEEEEE---SS-H CS
                       Hydrolase_6  31 ..........................kpvvllTNnsskse 44 
                                                                  pv l+TNn  ++ 
  gi|336255385|ref|YP_004598492.1|  82 herlrsgarglyddidavrtladraeTPVGLVTNNRHETA 121
                                       7777777777888888888888888888888888877774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2016.87
//
Query:       gi|336255386|ref|YP_004598493.1|  [L=207]
Description: ArsR family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-10   38.7   0.3     0.0001   22.3   0.1    2.5  2  HTH_20          Helix-turn-helix domain
    1.8e-09   37.3   0.0    2.4e-06   27.3   0.0    2.2  2  HTH_5           Bacterial regulatory protein, arsR family
    2.8e-09   36.7   0.5    1.1e-07   31.6   0.1    2.5  2  MarR_2          MarR family
    1.3e-08   34.9   0.0     0.0042   17.2   0.0    2.2  2  HTH_34          Winged helix DNA-binding domain
    3.4e-08   33.3   0.0    0.00013   21.8   0.0    2.3  2  MarR            MarR family
    7.6e-08   31.8   0.0    1.5e-06   27.6   0.0    2.4  2  HTH_24          Winged helix-turn-helix DNA-binding
    8.5e-06   25.6   0.0    0.00098   19.0   0.0    2.2  2  TrmB            Sugar-specific transcriptional regulator TrmB
    8.9e-05   22.4   0.3    0.00031   20.7   0.0    2.0  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00012   22.2   0.0    0.00024   21.2   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00024   20.8   0.8     0.0017   18.1   0.2    2.6  2  HTH_IclR        IclR helix-turn-helix domain
    0.00036   20.4   0.0    0.00065   19.6   0.0    1.4  1  HTH_11          HTH domain
    0.00055   19.7   0.0        1.2    8.8   0.0    2.1  2  DUF4423         Domain of unknown function (DUF4423)
  ------ inclusion threshold ------
      0.019   15.1   0.0       0.25   11.5   0.0    2.3  2  DUF2250         Uncharacterized protein conserved in archaea 
      0.022   14.7   0.0      0.049   13.6   0.0    1.6  1  HTH_36          Helix-turn-helix domain
      0.024   14.3   0.0      0.081   12.6   0.0    1.9  2  GntR            Bacterial regulatory proteins, gntR family
      0.034   14.0   0.0       0.11   12.4   0.0    2.0  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.063   13.8   0.1        0.3   11.6   0.0    2.2  2  HTH_27          Winged helix DNA-binding domain
      0.081   12.7   0.1        0.8    9.5   0.0    2.3  2  HTH_10          HTH DNA binding domain
       0.19   11.4   1.8        9.6    6.0   0.0    3.2  3  Crp             Bacterial regulatory proteins, crp 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 !   14.3   0.0   3.3e-05     0.031      17      60 ..      51      94 ..      29      95 .. 0.83
   2 !   22.3   0.1   1.1e-07    0.0001      16      56 ..     125     165 ..     118     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.3e-05
                                      HHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 17 raLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                       +L++  g+ +s + + l+l   +  +HLr Lee +++e+ r g
  gi|336255386|ref|YP_004598493.1| 51 GYLSTTPGAHFSKIRDDLQLGTGETQHHLRRLEEIDAIERYRDG 94
                                      566666777788999999999999****************9987 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.1e-07
                                       HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  16 lraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56 
                                       l +L  ++ +ta++la++l++s  t+s+   +LeeagL+ +
  gi|336255386|ref|YP_004598493.1| 125 LIELLLNADATAGDLADALEVSAPTVSKYAGKLEEAGLLSR 165
                                       444457999*****************************987 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 !    7.9   0.0     0.003       2.8      18      41 ..      61      84 ..      51      89 .. 0.85
   2 !   27.3   0.0   2.5e-09   2.4e-06       7      46 ..     125     164 ..     120     165 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.003
                                      HHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_5 18 vcelaeelglsqstvShHLkkLre 41
                                      ++ + ++l+l  + + hHL++L+e
  gi|336255386|ref|YP_004598493.1| 61 FSKIRDDLQLGTGETQHHLRRLEE 84
                                      6778899999999*********98 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2.5e-09
                                       HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       ++ lL +  +++++la++l++s +tvS +  kL+eaGL++
  gi|336255386|ref|YP_004598493.1| 125 LIELLLNADATAGDLADALEVSAPTVSKYAGKLEEAGLLS 164
                                       7899**********************************86 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.11     1e+02      13      57 ..      52      94 ..      48      98 .. 0.83
   2 !   31.6   0.1   1.2e-10   1.1e-07       9      54 ..     111     166 ..     109     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.11
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgp 57
                                      +L   pg     + + + l+l  + ++ +l+rL++   +er ++ 
  gi|336255386|ref|YP_004598493.1| 52 YLSTTPG--AHFSKIRDDLQLGTGETQHHLRRLEEIDAIERYRDG 94
                                      6777888..899999999****************98888887765 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1.2e-10
                                       HHHHHHHCTTTS..........EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   9 rvLaaLgrrpgr..........dltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       r L++L+r  +r          d t+g+la++l +s ++vs+   +L++aGL+ r 
  gi|336255386|ref|YP_004598493.1| 111 RTLGYLRRDTPRgmlielllnaDATAGDLADALEVSAPTVSKYAGKLEEAGLLSRD 166
                                       679999999999999999999999****************************9875 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 !   17.2   0.0   4.4e-06    0.0042       4      46 ..      48      90 ..      46      98 .. 0.89
   2 !   15.5   0.0   1.6e-05     0.015       8      60 ..     127     179 ..     123     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.4e-06
                            HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYiev 46
                                      a+  yL+++  a f+++++ l++ +g+   hl+ Le+ + ie+
  gi|336255386|ref|YP_004598493.1| 48 AIAGYLSTTPGAHFSKIRDDLQLGTGETQHHLRRLEEIDAIER 90
                                      56679********************************998886 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.6e-05
                            HTH_34   8 yLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllr 60 
                                        L+ +  a++ +l +ale+++   s+ + kLe+ag +++d ++   +p t++ 
  gi|336255386|ref|YP_004598493.1| 127 ELLLNADATAGDLADALEVSAPTVSKYAGKLEEAGLLSRDDGYAVERPETVMM 179
                                       57778899*****************************************9975 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0011       1.1      13      54 ..      54      95 ..      52     100 .. 0.84
   2 !   21.8   0.0   1.4e-07   0.00013      17      49 ..     133     165 ..     125     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                                      HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT CS
                              MarR 13 yeqgplsvseLakklgvskstvtrvldrLekkGlieRskspe 54
                                      ++ +++  s++ + l++ ++ +   l+rLe+ + ieR+++ +
  gi|336255386|ref|YP_004598493.1| 54 STTPGAHFSKIRDDLQLGTGETQHHLRRLEEIDAIERYRDGD 95
                                      6677788888899999999999999**************955 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.4e-07
                                       TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  17 plsvseLakklgvskstvtrvldrLekkGlieR 49 
                                       +++  +La++l+vs +tv++ + +Le++Gl++R
  gi|336255386|ref|YP_004598493.1| 133 DATAGDLADALEVSAPTVSKYAGKLEEAGLLSR 165
                                       56889**************************99 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 ?    1.9   0.0      0.18   1.7e+02      32      45 ..      73      86 ..      52      89 .. 0.73
   2 !   27.6   0.0   1.6e-09   1.5e-06       3      47 ..     119     163 ..     106     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.18
                            HTH_24 32 stvnrrlkrLeeeG 45
                                      + +  +l+rLee  
  gi|336255386|ref|YP_004598493.1| 73 GETQHHLRRLEEID 86
                                      55678******966 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 1.6e-09
                            HTH_24   3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       +t r  L +L  n++ +  +LA++l +S +tv+++  +Lee+Gl+
  gi|336255386|ref|YP_004598493.1| 119 DTPRGMLIELLLNADATAGDLADALEVSAPTVSKYAGKLEEAGLL 163
                                       666778999**********************************85 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.035        33      25      64 ..      61     101 ..      52     103 .. 0.80
   2 !   19.0   0.0     1e-06   0.00098      15      57 ..     126     168 ..     123     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.035
                                       HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE CS
                              TrmB  25 adeiaeelgvprskvYevLrsLedkGlVerek.grpklYra 64 
                                        ++i  +l +     +  Lr+Le+ + +er + g +k++++
  gi|336255386|ref|YP_004598493.1|  61 FSKIRDDLQLGTGETQHHLRRLEEIDAIERYRdGDYKRFVP 101
                                       567888888888899999************98445888876 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1e-06
                                       HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB  15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57 
                                       + Ll +  ata ++a +l+v+ ++v ++  +Le++Gl  r +g
  gi|336255386|ref|YP_004598493.1| 126 IELLLNADATAGDLADALEVSAPTVSKYAGKLEEAGLLSRDDG 168
                                       67999********************************988765 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 ?   -2.5   0.0       5.7   5.4e+03      24      35 ..      46      57 ..      45      59 .. 0.83
   2 !   20.7   0.0   3.3e-07   0.00031      17      54 ..     129     166 ..     111     176 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.7
                                      HHHHHHHTTSSH CS
                         HTH_Crp_2 24 qeelAsmlGltr 35
                                      ++ +A +l +t+
  gi|336255386|ref|YP_004598493.1| 46 RDAIAGYLSTTP 57
                                      677999999997 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3.3e-07
                                       EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2  17 eielpltqeelAsmlGltretvsrilseLkreglisrg 54 
                                        ++ + t  +lA+ l ++  tvs+  ++L+++gl+sr 
  gi|336255386|ref|YP_004598493.1| 129 LLNADATAGDLADALEVSAPTVSKYAGKLEEAGLLSRD 166
                                       345589999***************************74 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 !   21.2   0.0   2.6e-07   0.00024      24      53 ..     135     164 ..     131     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.6e-07
                                       -HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress  24 ktkdlaerLnvspssVsemlkkLekdGyve 53 
                                       +  dla +L+vs+++Vs+   kLe++G++ 
  gi|336255386|ref|YP_004598493.1| 135 TAGDLADALEVSAPTVSKYAGKLEEAGLLS 164
                                       6789***********************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 ?   -0.6   0.0       1.2   1.2e+03      13      49 ..      54      89 ..      51      90 .. 0.75
   2 !   18.1   0.2   1.8e-06    0.0017      10      52 .]     127     167 ..     113     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                                      CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 13 aeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +++p++  +s + + + l    + ++L+ L+e   +e
  gi|336255386|ref|YP_004598493.1| 54 STTPGA-HFSKIRDDLQLGTGETQHHLRRLEEIDAIE 89
                                      555565.788888888899999999999999876665 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.8e-06
                                       CT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR  10 dalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52 
                                       ++l  a+   t  +lA+++ ++ +tv+ +   L+e G++ +d+
  gi|336255386|ref|YP_004598493.1| 127 ELLLNADA--TAGDLADALEVSAPTVSKYAGKLEEAGLLSRDD 167
                                       44444444..699***************************995 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.9e-07   0.00065       5      43 ..     125     161 ..     124     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.9e-07
                            HTH_11   5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                       ++elLl+a+   ++ +LA+ L+vS  tv ++  +Lee+g
  gi|336255386|ref|YP_004598493.1| 125 LIELLLNAD--ATAGDLADALEVSAPTVSKYAGKLEEAG 161
                                       578888888..6*************************99 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0013       1.2      30      78 ..      53      98 ..      44     104 .. 0.87
   2 !    8.8   0.0    0.0013       1.2      35      77 ..     132     170 ..     124     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                           DUF4423 30 lplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrq 78
                                      l+  ++ a  +++ + l+  + + e+++ l++L++++ +++ +dg y++
  gi|336255386|ref|YP_004598493.1| 53 LSTTPG-AHFSKIRDDLQ--LGTGETQHHLRRLEEIDAIERYRDGDYKR 98
                                      566677.78889999999..***************************86 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0013
                           DUF4423  35 fkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyr 77 
                                       ++a+   la++l   +sa  v+k    L+++gll +d    y 
  gi|336255386|ref|YP_004598493.1| 132 ADATAGDLADALE--VSAPTVSKYAGKLEEAGLLSRDDG--YA 170
                                       567999*******..*********************984..54 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 ?    1.0   0.0      0.49   4.6e+02      23      57 ..      59      93 ..      42     101 .. 0.77
   2 ?   11.5   0.0   0.00026      0.25      28      63 ..     139     174 ..     124     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.49
                           DUF2250 23 dYaksiakeleipleevrellkkLeelGLlerveg 57
                                       +   i + l++   e ++ l++Lee+  +er+  
  gi|336255386|ref|YP_004598493.1| 59 AHFSKIRDDLQLGTGETQHHLRRLEEIDAIERYRD 93
                                      555567788888999999********999999875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00026
                           DUF2250  28 iakeleipleevrellkkLeelGLlervegktikrt 63 
                                       +a+ le++   v+++  kLee+GLl r +g ++ r 
  gi|336255386|ref|YP_004598493.1| 139 LADALEVSAPTVSKYAGKLEEAGLLSRDDGYAVERP 174
                                       688999999*******************99988765 PP

>> HTH_36  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   5.2e-05     0.049      29      55 .]     137     163 ..     131     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.2e-05
                            HTH_36  29 etlakrlglsknTvsraikeLeqlGyi 55 
                                        +la +l++s  Tvs++  +Le++G++
  gi|336255386|ref|YP_004598493.1| 137 GDLADALEVSAPTVSKYAGKLEEAGLL 163
                                       69***********************97 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.8   4.6e+03      45      56 ..      79      90 ..      76      92 .. 0.84
   2 ?   12.6   0.0   8.6e-05     0.081      29      60 ..     138     169 ..     135     172 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.8
                                      HHHHHHTTSEEE CS
                              GntR 45 LrrLeaeglver 56
                                      LrrLe+ + +er
  gi|336255386|ref|YP_004598493.1| 79 LRRLEEIDAIER 90
                                      899999998887 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 8.6e-05
                                       HHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                              GntR  29 eLaaefgVsrttvReALrrLeaeglverrqgr 60 
                                       +La++++Vs++tv +   +Le++gl+ r +g 
  gi|336255386|ref|YP_004598493.1| 138 DLADALEVSAPTVSKYAGKLEEAGLLSRDDGY 169
                                       79**************************9885 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 ?   12.4   0.0   0.00011      0.11       8      35 ..     124     151 ..     106     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                     HTH_AsnC-type   8 ILeaLqedaRisyaeLAervGlSestvl 35 
                                        L +L  +a ++  +LA+++ +S++tv 
  gi|336255386|ref|YP_004598493.1| 124 MLIELLLNADATAGDLADALEVSAPTVS 151
                                       56678889******************97 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 ?   -1.0   0.0       2.8   2.6e+03      37      53 ..      77      93 ..      49      99 .. 0.70
   2 ?   11.6   0.0   0.00031       0.3      18      56 ..     133     166 ..     124     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.8
                            HTH_27 37 yslkkLtekGLvertgd 53
                                        l++L+e + +er +d
  gi|336255386|ref|YP_004598493.1| 77 HHLRRLEEIDAIERYRD 93
                                      45788888888866655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00031
                            HTH_27  18 rkkladlcgrlnvedshisyslkkLtekGLvertgdead 56 
                                        +++ dl+++l v++ ++s+   kL+e+GL+      +d
  gi|336255386|ref|YP_004598493.1| 133 DATAGDLADALEVSAPTVSKYAGKLEEAGLLS-----RD 166
                                       56779**************************2.....23 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.85     8e+02      16      48 ..      51      83 ..      48      84 .. 0.74
   2 ?    9.5   0.0   0.00085       0.8      23      43 ..     133     153 ..     131     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.85
                            HTH_10 16 GYFdyPRrvtlkeLAkelGIskstlsehLrkae 48
                                      GY  +   ++ +++ ++l +    ++ hLr+ e
  gi|336255386|ref|YP_004598493.1| 51 GYLSTTPGAHFSKIRDDLQLGTGETQHHLRRLE 83
                                      666666677777777777777788999***977 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00085
                            HTH_10  23 rvtlkeLAkelGIskstlseh 43 
                                       ++t+ +LA++l +s++t+s++
  gi|336255386|ref|YP_004598493.1| 133 DATAGDLADALEVSAPTVSKY 153
                                       6899**************987 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.34   3.2e+02       4      16 ..      45      57 ..      45      57 .. 0.87
   2 ?    1.6   0.2      0.24   2.3e+02      21      29 ..     111     119 ..     110     120 .. 0.91
   3 ?    6.0   0.0      0.01       9.6       6      32 .]     137     163 ..     135     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.34
                                      -HHHHHHHHTS-H CS
                               Crp  4 SRqdIAdylGlTr 16
                                      +R +IA yl +T+
  gi|336255386|ref|YP_004598493.1| 45 ARDAIAGYLSTTP 57
                                      5999*****9995 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.24
                                       HHHHHHHHT CS
                               Crp  21 RlLtrLrek 29 
                                       R+L++Lr++
  gi|336255386|ref|YP_004598493.1| 111 RTLGYLRRD 119
                                       9******96 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.01
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                               Crp   6 qdIAdylGlTrETVSRlLtrLrekGLI 32 
                                        d+Ad+l  +  TVS   ++L+e GL+
  gi|336255386|ref|YP_004598493.1| 137 GDLADALEVSAPTVSKYAGKLEEAGLL 163
                                       699**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 1816.77
//
Query:       gi|336255387|ref|YP_004598494.1|  [L=405]
Description: hypothetical protein Halxa_4010 [Halopiger xanaduensis SH-6]
Scores for complete 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-37  129.7   4.0    1.2e-37  129.7   4.0    2.0  2  Band_7    SPFH domain / Band 7 family
      0.001   18.8   0.2     0.0021   17.8   0.2    1.5  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 !  129.7   4.0   1.3e-41   1.2e-37      12     178 .]      47     207 ..      37     207 .. 0.97
   2 ?   -3.0   0.7       0.7   6.3e+03     159     178 .]     210     229 ..     209     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 1.3e-41
                            Band_7  12 vrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaaveresan 88 
                                       + fG++++ l+pG+ f+ Pf++ ++ +++r+qtldv++ ++++t+D+ pvt d++v+++v  da+k++++v    ++
  gi|336255387|ref|YP_004598494.1|  47 TVFGEYRKLLDPGINFVPPFVSNTYAFDMRTQTLDVPR-QEAITRDNSPVTADAVVYIKV-MDAKKAFLQV----DD 117
                                       45************************************.*********************.**********....** PP

                            Band_7  89 ldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakqaaea 165
                                       +++ ++++++ +lr+v+++m+l++ l++r+e+++++++el e  +++G+ v++v +++++p+++v++a+++   ae+
  gi|336255387|ref|YP_004598494.1| 118 YKRAVSNLAQTTLRAVLGDMELDDTLNKRQEINARIRQELDEPTDEWGIRVESVEVREVNPSKDVQRAMEQQTSAER 194
                                       ***************************************************************************** PP

                            Band_7 166 eaqaeiaraeaea 178
                                       +++a i +a++e+
  gi|336255387|ref|YP_004598494.1| 195 KRRAMILEAQGER 207
                                       **********985 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.7
                            Band_7 159 akqaaeaeaqaeiaraeaea 178
                                       a+ +ae e+q ei ra++e+
  gi|336255387|ref|YP_004598494.1| 210 AVEKAEGEKQSEIIRAQGEK 229
                                       577899999********985 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 !   17.8   0.2   2.3e-07    0.0021     131     209 ..     116     192 ..      92     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-07
                          Band_7_1 131 eeiseqlkslivtrlsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkra 207
                                       ++ +  + +l +t+l  vl++ +  + d   k +e+ +++++ l+e  +e G+ +e++e+++++  ++v++a+++++
  gi|336255387|ref|YP_004598494.1| 116 DDYKRAVSNLAQTTLRAVLGDME--LDDTLNKRQEINARIRQELDEPTDEWGIRVESVEVREVNPSKDVQRAMEQQT 190
                                       55555666666666666666544..557788999*****************************************99 PP

                          Band_7_1 208 sm 209
                                       s+
  gi|336255387|ref|YP_004598494.1| 191 SA 192
                                       86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1360  (0.0758548); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); 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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.35
# Mc/sec: 3451.94
//
Query:       gi|336255388|ref|YP_004598495.1|  [L=209]
Description: hypothetical protein Halxa_4011 [Halopiger xanaduensis SH-6]
Scores for complete 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   25.1   0.1    4.2e-05   23.8   0.0    1.8  1  NfeD      NfeD-like C-terminal, partner-binding


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 !   23.8   0.0   2.3e-09   4.2e-05      10      74 ..      63     141 ..      36     151 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.3e-09
                                       XXXXX..XXS---SSS--S..........S---GGTTSEEEEEE-B..S-EEEEET....TEEEEEE-.SS.B-TT- CS
                              NfeD  10 lvllr..plllkklkkkek.........ktnaealiGkegvvledi..gtGrvkvd....GeeWsarsege.iekge 68 
                                       lv++    ++ + +    +          t++++l G++g ++e+i  ++G+vk+d      ++sar+ ++ ie+ge
  gi|336255388|ref|YP_004598495.1|  63 LVIGLaaTYVYHEF----DfyggkgtaqTTDSDSLAGATGYATERIttRDGEVKLDqggfAPYYSARTSSGtIEEGE 135
                                       32222222222222....1112223333477889************9648******98666999***97667***** PP

                                       EEEEEE CS
                              NfeD  69 rVrVve 74 
                                       ++ V +
  gi|336255388|ref|YP_004598495.1| 136 EIIVLD 141
                                       ***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1612.33
//
Query:       gi|336255389|ref|YP_004598496.1|  [L=198]
Description: hypothetical protein Halxa_4012 [Halopiger xanaduensis SH-6]
Scores for complete 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   60.7   0.0    1.5e-16   60.3   0.0    1.0  1  Gamma_PGA_hydro  Poly-gamma-glutamate hydrolase


Domain annotation for each model (and alignments):
>> Gamma_PGA_hydro  Poly-gamma-glutamate hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   8.6e-21   1.5e-16      14     167 ..      17     179 ..       8     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 8.6e-21
                   Gamma_PGA_hydro  14 gkdyrieeeekkksrllvlaiHGGgiEpgtseiaeaiae..adysvYlfeglkksgn..kelHitStrF...depla 83 
                                       g+  +  +++  ++++l+ a HGG++Epgt e a ++a+  +d+++++  g + +    + +H +S +F   d pl 
  gi|336255389|ref|YP_004598496.1|  17 GHYSELLYDDGGNDDVLICAAHGGEVEPGTAEAAVELAGrlEDATCWACLGYDDERRafDLYHPPSSSFapdDYPLL 93 
                                       54556677888899************************99999****999998854434789*******77777888 PP

                   Gamma_PGA_hydro  84 lklak.eaevvvslHGyeeeeehvlvGGtdrelaekiveaLeeaGfsvelapekeelagtspeNivNrtkt..gegv 157
                                        ++a    e+vvslHG ++ ++ ++ GG d +++++++++L++a  +  +++++  + g+sp+N+vN  ++  + g 
  gi|336255389|ref|YP_004598496.1|  94 GRIADrGFETVVSLHGLGD-DRVIVGGGIDGDVKRRVQSRLDDAITHPVETASDGPYGGVSPDNFVNWLARdgRGGL 169
                                       88887789********976.567788999*************9976666777779************754411569* PP

                   Gamma_PGA_hydro 158 qLElsralRk 167
                                       qLE s+a+R 
  gi|336255389|ref|YP_004598496.1| 170 QLEQSHAIRT 179
                                       *******995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 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:                        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 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1540.40
//
Query:       gi|336255390|ref|YP_004598497.1|  [L=266]
Description: phospho-2-dehydro-3-deoxyheptonate aldolase [Halopiger xanaduensis SH-6]
Scores for complete 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-45  155.4   0.1    2.2e-45  155.1   0.1    1.1  1  DeoC          DeoC/LacD family aldolase
    2.6e-05   23.8   0.0    3.8e-05   23.2   0.0    1.3  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.027   14.8   0.1       0.38   11.0   0.0    2.4  2  PucR          Purine catabolism regulatory protein-like famil
      0.046   13.3   0.3      0.098   12.2   0.3    1.7  1  OMPdecase     Orotidine 5'-phosphate decarboxylase / HUMPS fa
      0.097   11.8   0.0       0.37    9.9   0.0    1.8  2  URO-D         Uroporphyrinogen decarboxylase (URO-D)


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 !  155.1   0.1   6.2e-49   2.2e-45       2     235 .]      21     233 ..      20     233 .. 0.97

  Alignments for each domain:
  == domain 1  score: 155.1 bits;  conditional E-value: 6.2e-49
                                       EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTE CS
                              DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqr 78 
                                       vi+++D+++ ++++++       +d++++++ ++++ga+avl+++g++++++  ++   +++v+l+ +t++ +++++
  gi|336255390|ref|YP_004598497.1|  21 VIVPMDHGITMGAVQGL------KDIESTIDGVTSGGADAVLTQKGIAPRVHENKN-GKGYIVHLNGSTTIGPDEND 90 
                                       89***************......8****************************9999.88****************99 PP

                                       EEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHH CS
                              DeoC  79 dvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvae 155
                                       + +   +veea+++GAdav++++++   gs+ e  ++ ++++v ++++ +g+p+++++y r++ ++  + dp++ ++
  gi|336255390|ref|YP_004598497.1|  91 KRM-TGTVEEAVRAGADAVSFHINV---GSDHEPDQITQLSEVTAEAERLGMPVLAMAYARGPGVDP-E-DPEALGH 161
                                       999.9********************...************************************744.4.7****** PP

                                       HHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS..SHHHHHHHHHHHHHHHTHCEEEESH CS
                              DeoC 156 AarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv..seedfletvedAvkeagasGvlsGR 230
                                       A r++ elGaD++K+ +         +dae+f+ v++++++p v+++GG+  s+++  e+v+  + +ag++G+++GR
  gi|336255390|ref|YP_004598497.1| 162 AVRLAEELGADVVKTGYS--------GDAESFQHVVESTRLP-VIIAGGSkgSDRETIEMVRGTM-DAGGAGISMGR 228
                                       ******************........****************.**********************.*********** PP

                                       HHHTT CS
                              DeoC 231 aifqk 235
                                       +ifq+
  gi|336255390|ref|YP_004598497.1| 229 SIFQH 233
                                       ***97 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 !   23.2   0.0     1e-08   3.8e-05       2     109 ..      98     213 ..      97     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1e-08
                                       HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraiel 78 
                                       ++a +aG+d+v +++  + +  +++ ++l e+ + +++lg+ + ++ +  ++g ++e     +     +al +a++l
  gi|336255390|ref|YP_004598497.1|  98 EEAVRAGADAVSFHINVGSDHEPDQITQLSEVTAEAERLGMPVLAMAYARGPGVDPE-----D----PEALGHAVRL 165
                                       7899************99999999******************************998.....4....57******** PP

                                       HHHHTBSEEEEEBCC.................GBCTTTSGHHHHHHHH CS
                      AP_endonuc_2  79 aaaLGapllvlhpGt.................agagpkgseeeawerl 109
                                       a++LGa+++ ++ ++                    g+kgs++e++e +
  gi|336255390|ref|YP_004598497.1| 166 AEELGADVVKTGYSGdaesfqhvvestrlpviIAGGSKGSDRETIEMV 213
                                       ***********9886666666666666666663356666666666655 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 ?   11.0   0.0   0.00011      0.38      49     102 ..      83     145 ..      78     152 .. 0.81
   2 ?    1.0   0.0      0.14   4.9e+02      49      87 ..     199     239 ..     158     245 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                              PucR  49 glalkddpealaelvrelaeagvaaLviklg....r...eip..eelieaadelglPlielpe 102
                                        ++ +++++ +  +v+e ++ag+ a+ + ++    +   +i    e+ + a++lg+P++++ +
  gi|336255390|ref|YP_004598497.1|  83 TIGPDENDKRMTGTVEEAVRAGADAVSFHINvgsdHepdQITqlSEVTAEAERLGMPVLAMAY 145
                                       5555678899999**************999766761456443449**************9975 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.14
                              PucR  49 glalkddpealaelvrelaeagvaaLviklg..reipeeli 87 
                                       + + k ++ +  e+vr   +ag a++ ++    ++ ++e+i
  gi|336255390|ref|YP_004598497.1| 199 AGGSKGSDRETIEMVRGTMDAGGAGISMGRSifQHEDPEAI 239
                                       44444566778899999999999999888764423344444 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 ?   12.2   0.3   2.7e-05     0.098      84     223 ..     102     241 ..      91     243 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                                       HTTESEEEEEGTGH....HHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEE CS
                         OMPdecase  84 kewadivtvhavaG....kasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfv 156
                                        ++ad+v  h+ +G     + +++l e+ ++ ++ g+ +la+    g   + e    +a+ +a+r ++ e    G+ 
  gi|336255390|ref|YP_004598497.1| 102 RAGADAVSFHINVGsdhePDQITQLSEVTAEAERLGMPVLAMAYARGPGVDPE--DPEALGHAVRLAE-E---LGAD 172
                                       45666666666666322245677777777777766777777777777766666..7777777777766.3...3666 PP

                                       CCCHTHHHHHHTTCSCEEEHHHTT..EEEEECTTCCGGGHHHHHH..HTTCSEEEESHHHHTSSSHHHHHH CS
                         OMPdecase 157 aqetlnateedaddfihltpgigl..eqggdgkgqqyntpeklig..iagadiiivGRgIlkagdpveeae 223
                                       + +t    + da+ f h+++  +l     g  kg  ++t+e + g  +ag   i +GR+I++ +dp++ a 
  gi|336255390|ref|YP_004598497.1| 173 VVKTGY--SGDAESFQHVVESTRLpvIIAGGSKGSDRETIEMVRGtmDAGGAGISMGRSIFQHEDPEAIAT 241
                                       666633..455789**********99556666666666666554411588999*************99875 PP

>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0001      0.37      29      96 ..      84     152 ..      75     159 .. 0.88
   2 ?   -1.1   0.0      0.23   8.4e+02     293     339 ..     197     242 ..     156     247 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0001
                                       TSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGGGGT-EE.EEETTTEEEEE CS
                             URO-D  29 ylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilveaealGlev.efeegegPvve 96 
                                       + p ++ +r+ +++ e+ +  + a+   + +   +++D ++ +s ++ eae lG+ v  +   +gP v+
  gi|336255390|ref|YP_004598497.1|  84 IGPDENDKRMTGTVEEAVRAGADAVSFHINVGSDHEPDQITQLSEVTAEAERLGMPVlAMAYARGPGVD 152
                                       6789999************************************************76256667778765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.23
                                       GGGS-HHHHHHHHHHHHT.T---SSSEEB-BSS---TTS-HHHHHHH CS
                             URO-D 293 lLlgspeeiekevkeilekgaggkkgyilnlGhgippetppenvkal 339
                                       ++ g+ +  ++e+ e++++    ++g  +++G  i ++ +pe +++ 
  gi|336255390|ref|YP_004598497.1| 197 IIAGGSKGSDRETIEMVRG-TMDAGGAGISMGRSIFQHEDPEAIATA 242
                                       3335555556666666663.444666667777777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2158.51
//
Query:       gi|336255391|ref|YP_004598498.1|  [L=293]
Description: Tryptophan synthase subunit alpha [Halopiger xanaduensis SH-6]
Scores for complete 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-87  293.0   0.1    1.4e-87  292.8   0.1    1.0  1  Trp_syntA     Tryptophan synthase alpha chain
    0.00038   20.0   0.1    0.00077   19.0   0.1    1.5  1  His_biosynth  Histidine biosynthesis protein
     0.0006   20.1   0.1     0.0086   16.4   0.0    2.5  3  PucR          Purine catabolism regulatory protein-like famil
      0.002   17.6   0.6      0.088   12.3   0.2    2.2  2  PcrB          PcrB family
  ------ inclusion threshold ------
      0.028   13.7   0.3      0.045   13.0   0.3    1.3  1  ThiG          Thiazole biosynthesis protein ThiG


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 !  292.8   0.1     4e-91   1.4e-87       5     257 ..      20     272 ..      16     274 .. 0.97

  Alignments for each domain:
  == domain 1  score: 292.8 bits;  conditional E-value: 4e-91
                                       HCTTB-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHH CS
                         Trp_syntA   5 kaenraafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveev 81 
                                        +en+ a+++y+tagdp+le++ e+++al+++g+d+iElGlpfs+P+a+G +Iqaa +raL++g+t+e ++elv+++
  gi|336255391|ref|YP_004598498.1|  20 IRENHPALITYITAGDPSLEDTKEYVEALDRGGSDLIELGLPFSEPIAEGQTIQAAINRALEAGTTPEGFFELVDDL 96 
                                       5799************************************************************************* PP

                                       HHHCSSS-EEEEE-CHHHCCC-HHH....HCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HH CS
                         Trp_syntA  82 rkkevevPivlltylnlvlsygeer....flaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsde 154
                                       +   +e+P++++ty+n++l+yg+e     f++++++ag  g+ivpDlP+eea++l+ea++++gl+lvf++aptt+++
  gi|336255391|ref|YP_004598498.1|  97 E---TEAPLLVMTYYNMILQYGDEPdvrpFVERAADAGLSGIIVPDLPAEEADPLREACDDHGLDLVFIIAPTTEGQ 170
                                       *...********************89999************************************************ PP

                                       HHHHHHHH--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHH CS
                         Trp_syntA 155 rlkevveqaegfvYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalv 230
                                       rl+ +++q++gf Yv++r G+Tga+++v++ ++++++rl++++ vP+avGFG+s+ +++++++ ++adGvivGS lv
  gi|336255391|ref|YP_004598498.1| 171 RLDDIMSQVSGFAYVQARLGTTGARANVSTATHDSLARLSEYD-VPKAVGFGVSEGDHAAEIVeAGADGVIVGSTLV 246
                                       ******************************************8.******************99************* PP

                                       HHHHCTTTSHHHHHHHHHHHHHHHHHC CS
                         Trp_syntA 231 kkieeeaeekeqalekleelarelkea 257
                                       ++i+ + +++++a+e+le++a elk+ 
  gi|336255391|ref|YP_004598498.1| 247 DIIA-SSDDTAEAVERLEAKAAELKRG 272
                                       ****.7888889999999999988865 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   2.1e-07   0.00077      62     119 ..     203     259 ..     191     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.1e-07
                                       HHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHH CS
                      His_biosynth  62 ldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekf 119
                                       +d ++++ e  ++p  vG G+++ ++++e++eagad vi+g+  v+     ++ ae++
  gi|336255391|ref|YP_004598498.1| 203 HDSLARLSEY-DVPKAVGFGVSEGDHAAEIVEAGADGVIVGSTLVDIIASSDDTAEAV 259
                                       4555555555.9*******************************998777777766665 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 ?    0.4   0.0      0.21   7.4e+02      34      70 ..      15      52 ..       6      80 .. 0.76
   2 !   16.4   0.0   2.4e-06    0.0086      44     113 ..     102     179 ..      87     181 .. 0.78
   3 ?   -2.1   0.0       1.3   4.6e+03      40      67 ..     236     263 ..     224     267 .. 0.56

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.21
                              PucR 34 diaellrggeLllttglal.kddpealaelvrelaeag 70
                                      d+++ +r++   l+t ++  + + e+ +e+v++l + g
  gi|336255391|ref|YP_004598498.1| 15 DVEAAIRENHPALITYITAgDPSLEDTKEYVEALDRGG 52
                                      66677777777777777775667788888888887766 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.4e-06
                              PucR  44 Lllttglal.kd..dpealaelvrelaeagvaaLviklgr.eipeelieaadelglPliel..pe..evpfveiiee 112
                                       Ll+ t +++  +  d+ +++ +v++ a+ag++++++   + e  + l ea+d +gl l+ +  p+    ++++i+++
  gi|336255391|ref|YP_004598498.1| 102 LLVMTYYNMiLQygDEPDVRPFVERAADAGLSGIIVPDLPaEEADPLREACDDHGLDLVFIiaPTteGQRLDDIMSQ 178
                                       778888877644459999******************99645888************998773322446677777777 PP

                              PucR 113 v 113
                                       v
  gi|336255391|ref|YP_004598498.1| 179 V 179
                                       6 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.3
                              PucR  40 rggeLllttglalkddpealaelvrela 67 
                                         g ++ +t++ + ++ ++ ae v++l 
  gi|336255391|ref|YP_004598498.1| 236 ADGVIVGSTLVDIIASSDDTAEAVERLE 263
                                       3444455556666446666666666665 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.011        41       8      37 ..      30      59 ..      19      76 .. 0.87
   2 !   12.3   0.2   2.4e-05     0.088     162     213 ..     192     247 ..     179     262 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.011
                                      EEEEE-TTSS-CHHHHHHHHCTT-SEEEEE CS
                              PcrB  8 hltklDPeeenpdEiveiviesgtDavmig 37
                                      ++t  DP  e + E ve++ ++g+D + +g
  gi|336255391|ref|YP_004598498.1| 30 YITAGDPSLEDTKEYVEALDRGGSDLIELG 59
                                      99999*******************988665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.4e-05
                                       TTSSS-H.HHHHHHHHHHSSSEE..EEESS--SHHHHHHHHCC.SSEEEE-CHHHH CS
                              PcrB 162 sGaledv.eevialkkklekarl..ivGGGirsaEkAkevvea.ADvivvGnvvee 213
                                        Ga  +v  ++ +  ++l++  +   vG G+ ++++A+e+vea AD ++vG  + +
  gi|336255391|ref|YP_004598498.1| 192 TGARANVsTATHDSLARLSEYDVpkAVGFGVSEGDHAAEIVEAgADGVIVGSTLVD 247
                                       677777777777778888877764479************************87654 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   1.3e-05     0.045     172     213 ..     210     255 ..     181     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                                       HH-SS-BEEES---SHHHHHHHHHTT-SEEEESHH....HHTSSSH CS
                              ThiG 172 eeakvPvivDAGigspsdaaqamelGadavllnta....vaeakdp 213
                                       +e +vP  v  G+ +  +aa+ +e Gad+v++ ++    +a+++d 
  gi|336255391|ref|YP_004598498.1| 210 SEYDVPKAVGFGVSEGDHAAEIVEAGADGVIVGSTlvdiIASSDDT 255
                                       5789****************************98622224444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.46u 0.19s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2435.14
//
Query:       gi|336255392|ref|YP_004598499.1|  [L=422]
Description: Tryptophan synthase subunit beta [Halopiger xanaduensis SH-6]
Scores for 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  131.9   0.9    5.1e-38  131.2   0.9    1.3  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 !  131.2   0.9   2.8e-42   5.1e-38       4     294 .]      65     393 ..      63     393 .. 0.83

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 2.8e-42
                                       CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                              PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlk 80 
                                       g +pTPl r++rls+++g +++lK+E+l ++g++K++ a   ++ +k   + ++++e+++G+hg a+A+aaa+l ++
  gi|336255392|ref|YP_004598499.1|  65 GGRPTPLQRADRLSERYGREIYLKREDLVHGGAHKLNNALGQVLLAKYMGKERVIAETGAGQHGTATAMAAAHLDMP 141
                                       679*************************************99999888879999999999***************** PP

                                       EEEEEETTS-H...HHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHH...........STTCEE--TTTSHHHHHHH CS
                              PALP  81 vtivvpadasp...ekvallrllGaevvevggdydeavaaaaelaae...........gegaylvsqfdnptviegy 143
                                       ++i++ +++ +    +v ++r+ Gaev  v  +  + ++a++e  ++           +++++  ++f   +v + +
  gi|336255392|ref|YP_004598499.1| 142 CEIYMGRTDINrqrPNVYRMRMNGAEVNPVTAGSGTLKEAINETMRDwattverthyvIGSVVGPHPF-PKLVRDFQ 217
                                       **********5556****************66655555555555555555565334444444444444.3336666* PP

                                       HTHHHHHH....HHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.... CS
                              PALP 144 gtiglEil....eqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvs... 213
                                       + ig E      e+ g+ pd+vv+++GgG++ +G  + +   + dv +++ve+ gs+   +  +   + + +     
  gi|336255392|ref|YP_004598499.1| 218 SVIGKEARkqvqEKAGRLPDTVVACAGGGSNTMGAFHEFVP-DEDVDLVAVEAGGSSLEIDEEEGLAPNSAT-Lstg 292
                                       *******945555555***********************98.6679******99888887777333333333.2477 PP

                                       .......................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHH CS
                              PALP 214 .......................dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepss 267
                                                              ++   gl+   ++++   l++    +  +v+de+al +  +l + egi++   s
  gi|336255392|ref|YP_004598499.1| 293 tdgvlhgamtkllqqsdgqivesHSVSAGLDYAGVGPELSHLVESGRVTPTSVDDEAALNGFHRLSNLEGIIPALES 369
                                       89999999999******9999888888888888******************************************** PP

                                       HHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 268 aaalaalklreagelkegdrvvviltg 294
                                        +al  l  ++  el++   vvv ++g
  gi|336255392|ref|YP_004598499.1| 370 SHALGYL-EEHTDELGDL--VVVNVSG 393
                                       *******.7777777766..8888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3276.86
//
Query:       gi|336255393|ref|YP_004598500.1|  [L=267]
Description: Indole-3-glycerol-phosphate synthase [Halopiger xanaduensis SH-6]
Scores for 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-70  236.7   0.0    2.7e-70  236.5   0.0    1.0  1  IGPS          Indole-3-glycerol phosphate synthase
    1.3e-06   28.3   0.2    6.1e-06   26.1   0.0    2.1  3  QRPTase_C     Quinolinate phosphoribosyl transferase, C-termi
    1.6e-05   24.2   0.1    8.5e-05   21.8   0.0    2.0  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
    3.2e-05   23.1   0.3    5.8e-05   22.3   0.3    1.4  1  FMN_dh        FMN-dependent dehydrogenase
    7.4e-05   22.3   0.0     0.0012   18.4   0.0    2.4  2  His_biosynth  Histidine biosynthesis protein
     0.0056   16.0   1.3      0.034   13.4   0.2    2.2  2  ThiG          Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
      0.017   14.0   0.2      0.033   13.0   0.0    1.5  2  Trp_syntA     Tryptophan synthase alpha chain
       0.14   12.5   0.1        0.4   11.1   0.0    1.8  2  PDZ           PDZ domain


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 !  236.5   0.0   1.2e-73   2.7e-70      30     245 ..      28     239 ..       6     252 .. 0.93

  Alignments for each domain:
  == domain 1  score: 236.5 bits;  conditional E-value: 1.2e-73
                                       -SS-SS-HHHHCHCH..TTS-EEEEEE-SEETTTEESBSS--HHHHHHHHTTT.-SEEEEE--CCCC---CCHHHHH CS
                              IGPS  30 lakpkrsfaeaLres..ekklaliaEvKkaSPskgliredfdpaeiAkkyeeagAsaiSVLteekyFqGsledLrev 104
                                       +  ++rs+++a++++  + ++ +iaEvK +SP+ +  r+d dp+e+A+++ e+gAsaiSVLte+++F Gs e L++v
  gi|336255393|ref|YP_004598500.1|  28 VDVDARSLPDAIASAeaDGRVPVIAEVKPTSPTADGTRDD-DPVELAEAMVEGGASAISVLTEPSHFGGSPEALTRV 103
                                       467899******99877899***************99999.************************************ PP

                                       HHH-SS-EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SE CS
                              IGPS 105 rqavslpvlrKdFiideyqieearalgadaiLLivkvledeeleelaeaakslglevLvEvhdeeeleralklgaki 181
                                       r+av++pvlrKdF+++e+q++   ++ ad+ LLi+++++d  le l++aa++ g+++LvEvhd+eele+al++ga+i
  gi|336255393|ref|YP_004598500.1| 104 REAVDVPVLRKDFVLEEAQLD---VVEADLLLLIARFVDD--LEGLVAAARERGFQPLVEVHDREELEAALEAGAEI 175
                                       *********************...9*************98..56********************************* PP

                                       EEEESEETTTTEE-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-T CS
                              IGPS 182 iGvNnRnLktlevdlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqe 245
                                       iGvNnR+L +levdl+t+e++++++p+dv+l+aeSG+++++dv++++e+g++a+LvG+++m++ 
  gi|336255393|ref|YP_004598500.1| 176 IGVNNRDLAQLEVDLETFESVSPHAPDDVTLIAESGVSSPADVRRMRETGADALLVGSAIMDHG 239
                                       *************************************************************974 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 ?   -1.4   0.0      0.77   1.7e+03      66      99 ..      11      44 ..       5      54 .. 0.75
   2 ?   -2.4   0.0       1.5   3.5e+03      62      80 ..      92     110 ..      90     131 .. 0.75
   3 !   26.1   0.0   2.7e-09   6.1e-06      70     159 ..     145     236 ..     132     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.77
                                      HHHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHH CS
                         QRPTase_C 66 iveavksvreavdkevkievevesleeleevlea 99
                                      + ++++++re  + e ++ v+++sl ++ + +ea
  gi|336255393|ref|YP_004598500.1| 11 VASILEAARERPGGESAVDVDARSLPDAIASAEA 44
                                      6678888888888887899999998887766665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                                       HHSSHHHHHHHHHHHHTTT CS
                         QRPTase_C  62 aagsiveavksvreavdke 80 
                                       ++g+  ea+++vreavd  
  gi|336255393|ref|YP_004598500.1|  92 HFGGSPEALTRVREAVDVP 110
                                       5778888999999888654 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 2.7e-09
                                       HHHHHHHHTTTSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT.....SEEEEESS--TTTH CS
                         QRPTase_C  70 vksvreavdkevkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkr.....vlievSGgvtlenv 141
                                       v ++re   +     vev+  eele++lea+a+ii + n +  +l+  +e+ ++  ++      li  SG  +  +v
  gi|336255393|ref|YP_004598500.1| 145 VAAARERGFQP---LVEVHDREELEAALEAGAEIIGVNNRDLAQLEVDLETFESVSPHapddvTLIAESGVSSPADV 218
                                       55555554333...6******************************9988888888877777977888899999**** PP

                                       HHHHCTT-SEEEECHHCH CS
                         QRPTase_C 142 eeyaksgvdvisvgalth 159
                                       + ++++g d++ vg+++ 
  gi|336255393|ref|YP_004598500.1| 219 RRMRETGADALLVGSAIM 236
                                       **************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 ?   -0.5   0.0      0.27   6.1e+02       4      35 ..      72     111 ..      69     123 .. 0.62
   2 !   21.8   0.0   3.8e-08   8.5e-05      80     176 ..     140     235 ..     117     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.27
                                       HHHHHHHHT-SEEEE........ESHHHHHHHHTT--S-E CS
                              NanE   4 makaaeqaGavgiri........egvedikaikavvdlPi 35 
                                       +a+a +++Ga++i +         + e +  ++++vd+P+
  gi|336255393|ref|YP_004598500.1|  72 LAEAMVEGGASAISVltepshfgGSPEALTRVREAVDVPV 111
                                       5777777777777652222211123456677777777776 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 3.8e-08
                                       -HHHHHHHHHHH--EEEEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-.SS--HHHHHHHHHTT--EEEES---SH CS
                              NanE  80 tieelikkikekyqllmaDistleeglvakklGvdivGttlsGytkeeekaepDfalvkalseaglkviaeGrintP 156
                                       ++e l+++ +e++   + ++   ee  +a ++G++i+G      ++ e  + + f+ v     +++++iae  + +P
  gi|336255393|ref|YP_004598500.1| 140 DLEGLVAAARERGFQPLVEVHDREELEAALEAGAEIIGVNNRDLAQLEV-DLETFESVSPHAPDDVTLIAESGVSSP 215
                                       67888999999998899999999***************99877665554.45568888888999************* PP

                                       HHHHHHHTT--SEEEE-HHH CS
                              NanE 157 ekakkaieiGvdavvvGsai 176
                                       +  +++ e+G+da+ vGsai
  gi|336255393|ref|YP_004598500.1| 216 ADVRRMRETGADALLVGSAI 235
                                       *******************9 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.3   2.6e-08   5.8e-05     224     304 ..     159     236 ..     148     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.6e-08
                                       E-SHHHHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEES CS
                            FMN_dh 224 vltaedakraveaGvdgivvSNHGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllG 300
                                       v + e+ + a+eaG+++i v N   R l +    +++  ++  ++++++++++ +G+++ +Dv +    GAda l+G
  gi|336255393|ref|YP_004598500.1| 159 VHDREELEAALEAGAEIIGVNN---RDLAQLEVDLETFESVSPHAPDDVTLIAESGVSSPADVRRMRETGADALLVG 232
                                       7788999**************9...88999999999999************************************** PP

                                       HHHH CS
                            FMN_dh 301 Rpfl 304
                                        +++
  gi|336255393|ref|YP_004598500.1| 233 SAIM 236
                                       9885 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.077   1.7e+02      27      49 ..      65      87 ..      13     112 .. 0.78
   2 !   18.4   0.0   5.3e-07    0.0012     174     225 ..     184     237 ..     154     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.077
                                      ETTSHHHHHHHHHHHT-SEEEEE CS
                      His_biosynth 27 yagdpvelakryeeegadelhvv 49
                                        +dpvela++  e ga  + v+
  gi|336255393|ref|YP_004598500.1| 65 RDDDPVELAEAMVEGGASAISVL 87
                                      56788999988888888888776 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 5.3e-07
                                       TSS---HHHHHHHHHHH..SSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHT CS
                      His_biosynth 174 tlsGpdleltkelaeav..kipviasGGvgsledlkelksegvdavivgsalye 225
                                        +  +dle  ++++ +   ++++ia  Gv+s++d+++++++g+da++vgsa+ +
  gi|336255393|ref|YP_004598500.1| 184 AQLEVDLETFESVSPHApdDVTLIAESGVSSPADVRRMRETGADALLVGSAIMD 237
                                       566788999999998888899******************************965 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.13   2.9e+02     132     178 ..      67     111 ..      64     114 .. 0.62
   2 !   13.4   0.2   1.5e-05     0.034     175     209 ..     203     237 ..     187     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.13
                                       S-HH.HHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-B CS
                              ThiG 132 dDlv.larrleevGcaavmPlaapiGsglGllnkealkiiieeakvPv 178
                                       dD+v la+++ e G++a+  l+ p  s  G  ++eal+ ++e ++vPv
  gi|336255393|ref|YP_004598500.1|  67 DDPVeLAEAMVEGGASAISVLTEP--SHFG-GSPEALTRVREAVDVPV 111
                                       444435777777777777777766..3333.24666777777777777 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.5e-05
                                       SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHT CS
                              ThiG 175 kvPvivDAGigspsdaaqamelGadavllntavae 209
                                       +v +i + G+ sp d+    e Gada+l+ +a+  
  gi|336255393|ref|YP_004598500.1| 203 DVTLIAESGVSSPADVRRMRETGADALLVGSAIMD 237
                                       899*****************************964 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.7   3.8e+03      25      41 ..      68      84 ..      60      86 .. 0.77
   2 ?   13.0   0.0   1.5e-05     0.033     177     236 ..     177     242 ..     169     264 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.7
                                      HHHHHHHHHHHCT-SSE CS
                         Trp_syntA 25 qsleilkalekagadvi 41
                                      + +e+ +a+ ++ga++i
  gi|336255393|ref|YP_004598500.1| 68 DPVELAEAMVEGGASAI 84
                                      56788999999999988 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.5e-05
                                       STTSSB-TTHHHHHHHHHHCT.SS-EEEES....SS-SHHHHHHHH.TT-SEEEE-HHHHHHHHCT CS
                         Trp_syntA 177 gaenavaaevdelverlkklt.avPvavGF....Gistkeqvkqva.kvadGvivGSalvkkieee 236
                                       g++n+  a+++  +e+ ++++ ++P  v      G+s++++v+++  ++ad+ +vGSa++++ +  
  gi|336255393|ref|YP_004598500.1| 177 GVNNRDLAQLEVDLETFESVSpHAPDDVTLiaesGVSSPADVRRMReTGADALLVGSAIMDHGAGD 242
                                       6666666666666666666655455443322222************99***********9986643 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.5   7.9e+03      27      39 ..      48      60 ..      38      65 .. 0.69
   2 ?   11.1   0.0   0.00018       0.4      40      64 ..     166     189 ..     158     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.5
                                      SEEEEEECTTSHH CS
                               PDZ 27 gifvsevlpggaa 39
                                        +++ev p ++ 
  gi|336255393|ref|YP_004598500.1| 48 VPVIAEVKPTSPT 60
                                      5689999998554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00018
                                       HHHTSSTTEEEEEETTEETTTSHHH CS
                               PDZ  40 eadglkvGDkIlsvNgvdvenvshe 64 
                                       ea+ l++G +I++vN++d+++++++
  gi|336255393|ref|YP_004598500.1| 166 EAA-LEAGAEIIGVNNRDLAQLEVD 189
                                       566.***************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2287.82
//
Query:       gi|336255394|ref|YP_004598501.1|  [L=156]
Description: methylated-DNA--protein-cysteine methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-07   29.7   0.0    8.2e-07   29.1   0.0    1.3  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b


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 !   29.1   0.0   4.6e-11   8.2e-07       3      55 ..      78     135 ..      77     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 4.6e-11
                                       HHHHHHHHTTS-TT-BEEHHHHHHHTT......TSCHHHHHHHHHTSSBTTTSGGGGE CS
                     DNA_binding_1   3 qqrVwellrqIpyGkvttYgeiAkllgk.....pkaaraVgqalaanplailvPcHRV 55 
                                       q++V+e +r+IpyG+ +  +++A++  +     +     V +al anp ++l+P HRV
  gi|336255394|ref|YP_004598501.1|  78 QRAVLEQVREIPYGEQVDVKALARMTPEldpddEDDLTLVRTALDANPAPLLIPDHRV 135
                                       799***********************9999999999*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1263.28
//
Query:       gi|336255395|ref|YP_004598502.1|  [L=1114]
Description: Nitric-oxide reductase [Halopiger xanaduensis SH-6]
Scores for complete 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-60  204.9  39.6    1.9e-60  204.9  39.6    1.5  2  COX1      Cytochrome C and Quinol oxidase polypeptide I


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2       0.1   1.9e+03     239     259 ..     584     605 ..     580     613 .. 0.56
   2 !  204.9  39.6   1.1e-64   1.9e-60       3     430 ..     632    1080 ..     630    1081 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHC.CCCGGGGTT CS
                              COX1 239 svlafililfls.flvwaHHlf 259
                                       s ++++l++ ++   vwa+H f
  gi|336255395|ref|YP_004598502.1| 584 STISVVLLVAGGgAGVWAYHSF 605
                                       4444444444333777777766 PP

  == domain 2  score: 204.9 bits;  conditional E-value: 1.1e-64
                                        HHHHHHHHHHHHHHHHHHHHHHHHHCTCT...............-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHH CS
                              COX1    3 gllylilalvlllvggllgllirlqlafp...............dletynqlrtlHgnlmiflfatpfilgfgny 62  
                                        +  y+ +a +l+l+++l+g++++++++                 +l+ +++ rt+H+nl i++++t + l+ g++
  gi|336255395|ref|YP_004598502.1|  632 AARYVPVAGALFLAQVLVGAYLAHYYVERtgfygigealgidlvSLLPFSVGRTWHINLGILWITTLW-LAGGLF 705 
                                        568999********************6433344444445555556699********************.999999 PP

                                        HHHHHHCTSS-S-HHHHHHHHH....HHHHHHHHHHHHHHCS..............S-STTTTTTTC.SHHHHHH CS
                              COX1   63 lvplllgardlafprlnalsfw....lvvlgvvllllsllga..............attgwteYaplsevdlwll 119 
                                        l  l   +++  +   +++++     ++v+++++++l++  +              +++g  eY++   +++w +
  gi|336255395|ref|YP_004598502.1|  706 LPGLFADEDPPRQAEGATVLLGalvaVTVGAFACVWLGMQ-GkfgtpedghlwwllGSEGL-EYLE--TGRIWKV 776 
                                        9999999999999999999999666566666666666663.3477789999****9****5.***9..******* PP

                                        HHHHHHHHHHH.HHHHHHHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT-SSSCE CS
                              COX1  120 glllvvvssll.gainfivtilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrslgkffspg 193 
                                        +ll +    l  +   +++ + +  +p   +       ++++a   ++ll+ + + ++  +++            
  gi|336255395|ref|YP_004598502.1|  777 SLLAA----LGgWTGLVLRSVRRLDEPPTGLG-----HFMTYAGGSIALLFGASMLYTPETNI------------ 830 
                                        ***99....44456778899999999977666.....55677777777777777777777777............ PP

                                        -HHHHHHHHHHHHTHHH.HHHHHHHHHHHHHHHHHHHT.SCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HH CS
                              COX1  194 dplldqhlfWffgHpeV.yililpalgivyyilpkfag.rplfsyklsvlafililflsflvwaHHlfttglpew 266 
                                          ++ ++++W+++H++V +++++++++iv+  l+ +   ++  +++++++++++i+  ++++  HH++++glp++
  gi|336255395|ref|YP_004598502.1|  831 --AVTEFWRWWVVHMWVeGVFEFFVTAIVAVALVSMDLlEQADAERAILFEVFAIMAAGIVGVSHHYWWVGLPDV 903 
                                        ..9*********************************549************************************ PP

                                        HHHHHHHHHHHTHHHHHH...CCCHHHHCC.TTS-CHC.HHHHHHHHHHHHHH.HHHHHHHHHHTSHHHHHHHTT CS
                              COX1  267 lkalgsvfslliavPsgl...kvfnwlatl.wrgsirf.ktpmlfflgfavlf.iigGltGvllalpsvnyvvhn 335 
                                        +  +g++fs+l++vP+++     f+   tl  +g+  + + p+lf++g++v++ ++gG+ G++++lp +ny+ h+
  gi|336255395|ref|YP_004598502.1|  904 WVPIGTTFSTLEFVPLVFvlyRSFGEYRTLkAQGEAFPyTLPLLFIVGSSVWNfVGGGVLGFFINLPVINYYEHG 978 
                                        ******************888667888888644444445************************************ PP

                                        BHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHH.SB--HHHHHHHHHHHHHHHHHHHHH.HHHHHHHTTHB..... CS
                              COX1  336 tywvvaHfHlvllgavvfllfaaiyyllpklt.grmlserlaklhfwllfiGlvlmfl.pmhilGllgmp..... 403 
                                        ty++vaH+H++++ga+++l++++ +y+l  +t    ++ ++ +++fwl++iGl++m++ +++++G+l +      
  gi|336255395|ref|YP_004598502.1|  979 TYLTVAHGHTATFGAFGLLALGLGTYILRVVTpEAAWQPTWFRAAFWLTNIGLAVMSIaSLLPIGFLQLQtafqd 1053
                                        ********************************99999*********************9********55535555 PP

                                        ....SSSST--SCCCCHHHCHHHHHHHHHHH CS
                              COX1  404 ....rraadyksfletvpelqplnvlrtigg 430 
                                            +r+     ++++ + +q+l ++rt+g+
  gi|336255395|ref|YP_004598502.1| 1054 gyaaARSL----EFYEDDRVQTLLWARTLGD 1080
                                        54443333....4456789**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.24s 00:00:00.89 Elapsed: 00:00:00.36
# Mc/sec: 9172.32
//
Query:       gi|336255396|ref|YP_004598503.1|  [L=217]
Description: hypothetical protein Halxa_4019 [Halopiger xanaduensis SH-6]
Scores for 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  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.19s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 1911.90
//
Query:       gi|336255397|ref|YP_004598504.1|  [L=279]
Description: amidohydrolase 2 [Halopiger xanaduensis SH-6]
Scores for complete 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-08   35.3   0.7    1.5e-08   34.8   0.7    1.3  1  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.7   8.1e-13   1.5e-08     103     288 ..     116     267 ..      16     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 8.1e-13
                                       HHHHHHTTECEEEEESSTTTCCTTTCGGHHHHHHHHHHHT-EEEEE....CHHHCHHHHHHHHHHHHHHHCCHH.HH CS
                      Amidohydro_2 103 eraveelgfkGvrlnphvggddllgdrldrpifealeelglpvdihtGpspewlfggpqettraiqplllsgva.rk 178
                                       e+ + + +f G+ ++p v  d++++d     ++ +le+ glp+ + +G             ++a   +l++ ++ r 
  gi|336255397|ref|YP_004598504.1| 116 EKYAYDDRFHGFVFDPTVD-DYPDED-----VLDVLEDVGLPLLVRAG-------------VDAPPAELAEMLLgRS 173
                                       5555555555555555444.334443.....4569***********99.............9888888888888566 PP

                                       CTTSEEEESGGGTT...TTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHHCHHHHHHHHHHH-GGGEEEE--BT CS
                      Amidohydro_2 179 fPnlkivlaHgGgp...serlraalellarrpnvyvklsglytellyfdspladppalarlieavgpdrilfGsDyP 252
                                       fP   +v+aH+Gg         +++ ll++++  y+++s            + ++  l+r++ +  pdr+ fGs  P
  gi|336255397|ref|YP_004598504.1| 174 FP---VVVAHFGGHpldRSLMHEMIDLLDEYDDCYLETSF-----------VRYRDLLERAVLEH-PDRVFFGSGAP 235
                                       66...***********9999******************99...........678999*****999.*********** PP

                                       STTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHHHHH CS
                      Amidohydro_2 253 hptleaepealalldlvallsdeerekilggNAarl 288
                                        +++   + ++  ld     s++ +++++++NA r+
  gi|336255397|ref|YP_004598504.1| 236 ACHPNVAVMEILTLDV----SEDMLRRVFSKNACRV 267
                                       ***************9....*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.43u 0.16s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 2482.87
//
Query:       gi|336255398|ref|YP_004598505.1|  [L=525]
Description: chaperonin Cpn60/TCP-1 [Halopiger xanaduensis SH-6]
Scores for complete 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-147  492.0  15.8   1.9e-147  491.9  15.8    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.11   12.7   0.8         11    6.3   0.0    3.3  3  Cas_Csa5    CRISPR-associated protein (Cas_Csa5)


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 !  491.9  15.8  2.1e-151  1.9e-147       1     489 [.      38     524 ..      38     525 .] 0.96

  Alignments for each domain:
  == domain 1  score: 491.9 bits;  conditional E-value: 2.1e-151
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a+ v+ttlGP+GmdKmlv++gg+vv+TnDGatil+e++iehPaa+++ve+aesq+eevGDGTtt++++ag+Ll ea
  gi|336255398|ref|YP_004598505.1|  38 VAESVRTTLGPRGMDKMLVDSGGDVVITNDGATILEEMDIEHPAAQMIVEVAESQEEEVGDGTTTAAVIAGNLLGEA 114
                                       6899************************************************************************* PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXX.STHHHHHHHHHHHHHCH CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslssklts.keaeelsklvvdAvkli 153
                                       e+li+++vh tti+egy++a+e alea++e  +e +++   +e+L++va++s+++k t   +a+ l++ vv+Av+ +
  gi|336255398|ref|YP_004598505.1| 115 EDLIEQDVHATTIVEGYHEAAEIALEAIDEQVQEADVD---DEILKQVAESSMTGKGTGgLTARSLAETVVEAVRHV 188
                                       ****************************9997777776...79*************554156678*********666 PP

                                       CCCSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHH CS
                        Cpn60_TCP1 154 eenekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeel 230
                                       +++   ++ ++i+v +  g s++ +el++G+v+d+++++  mp+++e+a +++ldv+L+  + e++++  +++ ++l
  gi|336255398|ref|YP_004598505.1| 189 DTD-AGVQRDNINVHTQLGASSNATELIPGIVVDEEPAHDAMPTEVEDASIAVLDVELDVRTGEVDAEYAIDSIDQL 264
                                       544.689********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCG CS
                        Cpn60_TCP1 231 eklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpe 307
                                       ++  +aee +l+   e +++sg++vv++++++ d + + lak+g+l+ + +  +d ++++ atGat v  ledl++ 
  gi|336255398|ref|YP_004598505.1| 265 NAAIDAEESELQGYAETVVDSGADVVFTTDDVADRVANALAKEGVLVFDDLGDSDAKQIVSATGATRVGALEDLEEA 341
                                       ***************************************************************************** PP

                                       C-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHH CS
                        Cpn60_TCP1 308 elGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelela 384
                                       ++G+a++++++++g++++ ++e+ + ++++t+ +rg t++v+de+erai dAl+vv+ a+++++vvpG+Gate+++a
  gi|336255398|ref|YP_004598505.1| 342 DFGEAERIRTDSFGDDELAFVEGGAAAESVTVFVRGGTEHVVDELERAIGDALDVVATALDSGEVVPGAGATEIAIA 418
                                       ***************************************************************************** PP

                                       HHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTC...EEECCCCT CS
                        Cpn60_TCP1 385 kklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesge...iidlveag 458
                                        k++e+a  v+g++qla++afa+AL v+p+tLa N G dpi+ l +lraah+++   +g+ + sge   i d++e+g
  gi|336255398|ref|YP_004598505.1| 419 DKIREEAAAVEGRKQLAVNAFADALDVVPRTLAANTGQDPIDALVDLRAAHESEG-RAGLIT-SGEdvsIDDPFEHG 493
                                       ***************************************************8888.888744.44446699****** PP

                                       XEEEHHHHHHHHHHHHHHHHHHHCEEEEEXX CS
                        Cpn60_TCP1 459 vvDplkvkrqalksAteaastiLrideiika 489
                                       vvDp+ vkr a++sAteaa++i rid++i a
  gi|336255398|ref|YP_004598505.1| 494 VVDPADVKREAVESATEAATMIARIDDVIAA 524
                                       *****************************87 PP

>> Cas_Csa5  CRISPR-associated protein (Cas_Csa5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.17   1.5e+03      23      63 ..     178     224 ..     169     258 .. 0.64
   2 ?    6.3   0.0    0.0013        11       9      23 ..     296     310 ..     290     328 .. 0.83
   3 ?    2.5   0.0     0.019   1.7e+02      22      45 ..     386     409 ..     368     437 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.17
                          Cas_Csa5  23 akvlydaqRivqm..glergeiksdtvkikek....eyPaivikkke 63 
                                       a+ +++a R v +  g++r++i+++t+           P+iv++++ 
  gi|336255398|ref|YP_004598505.1| 178 AETVVEAVRHVDTdaGVQRDNINVHTQLGASSnateLIPGIVVDEEP 224
                                       56677777777543378888888777633322445457888777654 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0013
                          Cas_Csa5   9 lvDRianaLskeava 23 
                                         DR+anaL+ke v 
  gi|336255398|ref|YP_004598505.1| 296 VADRVANALAKEGVL 310
                                       57**********986 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.019
                          Cas_Csa5  22 vakvlydaqRivqmglergeiksd 45 
                                        ++++ da  +v + l++ge+  +
  gi|336255398|ref|YP_004598505.1| 386 LERAIGDALDVVATALDSGEVVPG 409
                                       6899****************9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.22s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 4056.58
//
Query:       gi|336255399|ref|YP_004598506.1|  [L=129]
Description: hypothetical protein Halxa_4022 [Halopiger xanaduensis SH-6]
Scores for 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-23   82.3   0.0      3e-23   81.9   0.0    1.2  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   1.7e-27     3e-23       2      75 .]      39     113 ..      38     113 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.7e-27
                            HalOD1   2 eespstaVveavaavegvdptelepLydaiDpdALdaLfas.radgearadgsvsFtyegyeVtVrsdgeieVep 75 
                                       +e++sta + +v++v gv+p++lepL +++Dpd L++Lfa+ rad+++ +dg+vsFt+ ++ Vt+++dgei+++p
  gi|336255399|ref|YP_004598506.1|  39 YEPVSTALLLTVSSVLGVEPDDLEPLSECVDPDSLNSLFANwRADEPRVGDGTVSFTFSQCGVTIHADGEIVIDP 113
                                       69***************************************88899999***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1065.17
//
Query:       gi|336255400|ref|YP_004598507.1|  [L=289]
Description: hypothetical protein Halxa_4023 [Halopiger xanaduensis SH-6]
Scores for 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-76  254.8   0.0    7.8e-76  254.6   0.0    1.0  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr


Domain annotation for each model (and alignments):
>> SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.6   0.0   4.4e-80   7.8e-76       1     234 [.       2     283 ..       2     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 254.6 bits;  conditional E-value: 4.4e-80
                                       EEEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EE CS
                   SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterral 77 
                                       it+++DFG  +py++amkgvil++ +d+r+vDi+Hd+p++dvr+aaf+L+++lpy+p+ ++hl+vVDpgvgt+r+a+
  gi|336255400|ref|YP_004598507.1|   2 ITIASDFG--TPYPAAMKGVILQR-TDTRLVDIAHDFPRQDVRAAAFWLREVLPYYPP-ATHLVVVDPGVGTDRDAI 74 
                                       89******..**************.9*******************************5.79**************** PP

                                       EEEETTSEEEEESSSTTHHHH......SEEEEEEGSSCC...................................--T CS
                   SAM_adeno_trans  78 vveakggyfvgPDNGlltlal......lleeaveieeee...................................ssa 113
                                       v++a+++++vgPDNG+l +++      +  ea+ i+++e                                   +s+
  gi|336255400|ref|YP_004598507.1|  75 VLRAGDHALVGPDNGVLRPVArelagdGPLEAYVIDDTEigpiepttgtpapsvpsaigsssgesdgtgagegpASN 151
                                       *********************97766533788888877778888888999999999999999999********989* PP

                                       S-HHHHTHHHHHHHHH....CT--GGGCSE..EESGGGS-SSS.....E.CSCEEEEEEEE-TTS-EEEEEE...EH CS
                   SAM_adeno_trans 114 tFhgrDvFapvaarla....agvsleelge..eldpeelvrle.....e.derlegevlyvDrFGNvitniskelle 178
                                       tFhgrDvFap+aa+++    +  +le+l+   ++++e+lv+le       d+r+egevl+vD FGNvitn+++e+le
  gi|336255400|ref|YP_004598507.1| 152 TFHGRDVFAPAAADVRgtdrE--NLEALEYlsPTSTEDLVDLElpdatVaDDRAEGEVLVVDGFGNVITNVPGEFLE 226
                                       ***************954332..344444444677789999988887526999**********************99 PP

                                       HHHHTTCEE...EEEEE.SSGGGSTTTSEEEEE-TTSEEEEEETTC-HHHHHT--TT-EE CS
                   SAM_adeno_trans 179 elekerkva...klkkv.etyaevaegellalvnssglleiavnkgsaaellglkvgdev 234
                                        +++ +  a   +   v +t+a+v+ege+la+v+s+g++e++vn+g+ ++++gl++gd+v
  gi|336255400|ref|YP_004598507.1| 227 GRDRIN--AngeS-IPVgDTFAAVPEGERLATVGSHGYVELDVNRGRGDDAFGLEPGDRV 283
                                       664433..24544.4556****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); 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 0.20s 00:00:00.58 Elapsed: 00:00:00.33
# Mc/sec: 2585.24
//
Query:       gi|336255401|ref|YP_004598508.1|  [L=172]
Description: Nicotinamide-nucleotide adenylyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-16   58.2   0.0    4.2e-15   56.2   0.0    1.9  1  CTP_transf_like  Cytidylyltransferase-like
     0.0014   18.4   0.0     0.0081   15.9   0.0    2.0  2  Citrate_ly_lig   Citrate lyase ligase C-terminal domain
  ------ inclusion threshold ------
       0.15   11.2   0.0       0.25   10.5   0.0    1.3  1  HIGH_NTase1      HIGH Nucleotidyl Transferase


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 !   56.2   0.0   7.1e-19   4.2e-15       1     143 []       5     133 ..       5     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 7.1e-19
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       ++ G+F+p+H+GHl ++eq++++++e l+ g+ s++ +++  +++++a eR+ m+ +   + +       +    + 
  gi|336255401|ref|YP_004598508.1|   5 FYIGRFQPFHNGHLSMVEQIADEVDE-LVLGIGSADDSHSV-RNPFTAGERIMMITKSLVDYD-----LVTYAVPIE 74 
                                       589***********************.************99.**************9933333.....333333233 PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHHH CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkirer 143
                                       +  +    ++v   ++++      +++  ++n++lv++ ++e   ++   ++ +++   ++++r+r
  gi|336255401|ref|YP_004598508.1|  75 DLDRNS--VWVSHVQSMSP-----DFDVAYSNNPLVIQLFREAGIEIRQSPMFNREVLEGSEVRQR 133
                                       333344..88888877776.....899999999999999998888888999999999999999986 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 !   15.9   0.0   1.4e-06    0.0081       9      62 ..      11      69 ..       7     109 .. 0.87
   2 ?    0.4   0.0     0.074   4.4e+02     127     170 ..     101     143 ..      85     149 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-06
                    Citrate_ly_lig  9 nPftlGhryLvekaakendvvhlfvvkedksl.....fsyeerlklvkkGikdlknvtl 62
                                       Pf +Gh  +ve+ a+e d + l + + d s+     f++ er+ +++k + d + vt+
  gi|336255401|ref|YP_004598508.1| 11 QPFHNGHLSMVEQIADEVDELVLGIGSADDSHsvrnpFTAGERIMMITKSLVDYDLVTY 69
                                      6*************************9998754444488899*****999999888877 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.074
                    Citrate_ly_lig 127 qalkevlekaeievveierkekeeelisaskvrkl.lkeknlekl 170
                                         + + +++a+ie+ + +    + e++  s+vr+  + ++++e+l
  gi|336255401|ref|YP_004598508.1| 101 PLVIQLFREAGIEIRQSP--MFNREVLEGSEVRQRmIDDGDWESL 143
                                       555566666666665544..4467889999999851566777754 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.2e-05      0.25      10      28 ..      10      28 ..       6      35 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.2e-05
                       HIGH_NTase1 10 YNPfHnGHlyhlekakelt 28
                                      + PfHnGHl ++e++  ++
  gi|336255401|ref|YP_004598508.1| 10 FQPFHNGHLSMVEQIADEV 28
                                      78************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); 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:                         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 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1303.62
//
Query:       gi|336255402|ref|YP_004598509.1|  [L=738]
Description: peptidase S16, Lon-like protease [Halopiger xanaduensis SH-6]
Scores for complete 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-34  119.7   3.8    1.8e-34  119.1   3.8    1.3  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    9.6e-31  107.1   0.0    9.7e-24   84.0   0.0    2.3  2  AAA_32           AAA domain
    2.3e-17   63.1   0.1    4.9e-10   39.1   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    4.3e-15   55.8   0.0      7e-09   35.6   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
    3.1e-10   39.9   0.6    7.8e-10   38.6   0.6    1.7  1  ChlI             Subunit ChlI of Mg-chelatase
    4.4e-10   39.7   0.0     0.0012   18.8   0.0    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
    1.4e-06   28.8   0.0      0.037   14.5   0.0    2.7  2  AAA              ATPase family associated with various cellul
    1.8e-06   27.8   0.0     0.0019   18.0   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.4e-06   26.8   0.1      0.061   12.4   0.0    2.4  2  MCM              MCM P-loop domain
    6.3e-05   22.3   0.1      0.014   14.6   0.0    2.3  2  TIP49            TIP49 P-loop domain
    8.2e-05   22.5   0.1       0.13   12.1   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    0.00016   21.8   0.0       0.24   11.5   0.0    2.4  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00024   21.5   0.0       0.43   10.9   0.0    2.6  2  AAA_19           AAA domain
    0.00038   20.0   0.0     0.0012   18.4   0.0    1.7  2  AAA_7            P-loop containing dynein motor region
    0.00049   20.4   0.0     0.0055   17.0   0.0    2.4  2  AAA_22           AAA domain
     0.0015   18.3   0.0       0.12   12.0   0.0    2.4  2  AAA_30           AAA domain
     0.0087   15.0   0.0       0.21   10.4   0.0    2.2  2  AAA_PrkA         PrkA AAA domain
     0.0094   15.4   0.0      0.026   14.0   0.0    1.7  2  PhoH             PhoH-like protein
  ------ inclusion threshold ------
      0.014   15.5   0.0       0.05   13.8   0.0    2.0  1  AAA_33           AAA domain
      0.015   14.5   0.0       0.03   13.5   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
      0.028   14.6   0.0        5.3    7.1   0.0    2.6  2  AAA_2            AAA domain (Cdc48 subfamily)
      0.032   14.0   0.0      0.072   12.8   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
      0.034   14.7   0.0       0.11   13.0   0.0    1.8  1  ABC_tran         ABC transporter
      0.037   13.3   0.3      0.057   12.7   0.3    1.2  1  AgrB             Accessory gene regulator B
      0.041   13.8   0.0      0.077   12.9   0.0    1.4  1  NACHT            NACHT domain
      0.042   14.3   0.1        0.2   12.1   0.0    2.1  2  MCM_lid          MCM AAA-lid domain
      0.065   12.1   0.1       0.17   10.8   0.0    1.7  2  AAA_10           AAA-like domain
      0.068   12.1   0.0       0.11   11.4   0.0    1.2  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN


Domain annotation for each model (and alignments):
>> 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 !  119.1   3.8   2.8e-37   1.8e-34       4     204 ..     503     700 ..     500     701 .. 0.86

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 2.8e-37
                                       TTTTHHHH-S-SS--SSSSS--BSSEEEEEEEE.TTEEEEEEEEEEEES..S-S-EEEEES--HHHHHHHHHHHHHH CS
                             Lon_C   4 akeleellGkkrfrseeaekedqvGvvtGlawt.evGGdlltieavllp..gkgklkltGklgdvmkesaqaalsyv 77 
                                       ++  ++++ +++  + ++++    G v Gla   e  G +l + a + p  g g+++ tGkl ++ +es+q   +++
  gi|336255402|ref|YP_004598509.1| 503 QQLADDYIERRKDYELQVNEGGVEGRVNGLAVMgEDSGIMLPVMAEIAPaqGGGQVIATGKLQEMAEESVQNVSAII 579
                                       555566666666556667777888******9752778999999888876337789****************987777 PP

                                       TSS-GGGSS-SS-TTT-EEEEE.E-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHH CS
                             Lon_C  78 rsraeelgidkevfekkdihih.vPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlke 153
                                       ++  ++++     +++kdihi  v +G    dG sa +t+ata++s+l +++v++ vamtG +++rG vlp+GG+  
  gi|336255402|ref|YP_004598509.1| 580 KK-FSDVD-----LSEKDIHIQfVQAGQQGVDGDSASITVATAVISALEDIPVDQSVAMTGSLSVRGDVLPVGGVTH 650
                                       64.33333.....5679****63789*************************************************** PP

                                       HHHHHHHTT-SBEEEEGGGGGGTTTS-HHHHTS-B--EESBHHHHHHHHB- CS
                             Lon_C 154 kllaakragikkvilPkenekdlediPeevreeleiilveevdevlkaalv 204
                                       k+ aa +ag +kvi+Pk+ne+d+  i +e  e +eii++ +++evl++al+
  gi|336255402|ref|YP_004598509.1| 651 KIEAAAKAGCSKVIIPKANEQDVM-IEDEYEEMIEIIPCANISEVLDVALM 700
                                       **********************96.99**********************96 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.6e-07   0.00017       8      89 ..     130     206 ..     124     217 .. 0.83
   2 !   84.0   0.0   1.5e-26   9.7e-24     280     510 ..     268     497 ..     259     500 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.6e-07
                            AAA_32   8 eeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePkalsLpaG 84 
                                       +++igq+ A + +   +k  k+  ++ ++G++gtG+++l+k + +     ++  +D++  +n d+ +ePk+  +paG
  gi|336255402|ref|YP_004598509.1| 130 DQVIGQDEARDII---IKAAKQRRHVMMIGSPGTGKSMLAKAMSQLL--PQEDLQDVLVYHNPDDGNEPKVRTVPAG 201
                                       7889999888766...66677888*************9999887665..34556888888***************** PP

                            AAA_32  85 kGkel 89 
                                       kG++ 
  gi|336255402|ref|YP_004598509.1| 202 KGEQI 206
                                       **986 PP

  == domain 2  score: 84.0 bits;  conditional E-value: 1.5e-26
                            AAA_32 280 vnvlvdnsetegaPVvvednptyanLfGkieyesemg..alvtdftlIkaGaLhkAnGGyLildaedlLeeplaWea 354
                                        n++vdn +++ aP    +  +   L+G + ++  +   + +  + ++++G++hkAn G+L +d  + L    + ++
  gi|336255402|ref|YP_004598509.1| 268 PNMIVDNGDKRTAPFEDATGAHAGALLGDVRHDPFQSggMETPSHDRVEPGSIHKANKGVLFVDEINTLD-IRTQQK 343
                                       79*****************************9975433588889********************999996.56779* PP

                            AAA_32 355 LkraLrskeikiesleeqlglistvsLkPepipldvKViLiGsrelYylLseyDpdfkklFkvkadFddemerteen 431
                                       L  a++++e +i       + +s    + ep+p+d   i  G+ +  + ++ +  +  k +  ++ ++d++e t+e 
  gi|336255402|ref|YP_004598509.1| 344 LMTAIQEGEFSITGQ---SERSSGAMVQTEPVPCDFVMIAAGNLDAMENMHPALRNRIKGYGYEVYMEDTIEDTPEM 417
                                       *************53...4467888999********999999999888888888888888999************** PP

                            AAA_32 432 ekkyarfiasivkkek.llpfdrsavarlieyssrlaedqeklstrfseiadllrEAdywakkegaevveaehVekA 507
                                        +kyarf+a+ v++++ l++f+++av+++i ++ r ++++++l+++f+++  l+r A  +a+ e++e+ ++++V +A
  gi|336255402|ref|YP_004598509.1| 418 RRKYARFVAQEVERDGrLPHFTDEAVEEIILEAKRRSGRKNHLTLHFRSLGGLVRVAGDIARAEDREYTTRDDVLQA 494
                                       *********9998764399********************************************************99 PP

                            AAA_32 508 lee 510
                                        ++
  gi|336255402|ref|YP_004598509.1| 495 KDR 497
                                       765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   7.6e-13   4.9e-10       3      55 ..     130     182 ..     128     187 .. 0.93
   2 !   21.3   0.0   2.3e-07   0.00015      96     158 ..     314     384 ..     305     406 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 7.6e-13
                      Mg_chelatase   3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55 
                                        +v+Gq+ea+  +  aa  + +++++G+pG+GK+mlak++++llp+ + +++l
  gi|336255402|ref|YP_004598509.1| 130 DQVIGQDEARDIIIKAAKQRRHVMMIGSPGTGKSMLAKAMSQLLPQEDLQDVL 182
                                       689******************************************99888776 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.3e-07
                      Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakak....v....efparfqlvaamNp 158
                                       +++pG i +a++GvLf+DE+  ++ ++ + L + +++ge +i+ ++++    +      p++f ++aa N+
  gi|336255402|ref|YP_004598509.1| 314 RVEPGSIHKANKGVLFVDEINTLDIRTQQKLMTAIQEGEFSITGQSERssgaMvqtePVPCDFVMIAAGNL 384
                                       789*************************************9975443201112111146778888887775 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.2e-06    0.0027      11      50 ..     138     177 ..     131     189 .. 0.84
   2 !   35.6   0.0   1.1e-11     7e-09      85     130 ..     316     361 ..     302     395 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.2e-06
                                       HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTT CS
                   Sigma54_activat  11 lleqikkvaktdlsvlitGesGtGKellaraiheaskrke 50 
                                       +++ i k+ak++ +v++ G  GtGK++la+a+ +  ++++
  gi|336255402|ref|YP_004598509.1| 138 ARDIIIKAAKQRRHVMMIGSPGTGKSMLAKAMSQLLPQED 177
                                       5566789999**********************99766654 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 1.1e-11
                                       BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSE CS
                   Sigma54_activat  85 kkGlfekadgGtlfLDeigelplelQekLlrvlqegevervGsske 130
                                       + G ++ka++G+lf+Dei++l++++Q+kL++++qege++  G+s+ 
  gi|336255402|ref|YP_004598509.1| 316 EPGSIHKANKGVLFVDEINTLDIRTQQKLMTAIQEGEFSITGQSER 361
                                       45*************************************9998765 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.6   1.2e-12   7.8e-10       7     121 .]     553     669 ..     547     669 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.2e-12
                              ChlI   7 kglpkftivGlpdtavkeskervrsalkn.sgfefpakkitvnLaPadlk.keGsafDLpiAigilaaleqieaeee 81 
                                       +g  ++  +G +++  +es + v +++k+ s++++ +k i +    a  +  +G + ++++A ++++ale+i+++++
  gi|336255402|ref|YP_004598509.1| 553 QGGGQVIATGKLQEMAEESVQNVSAIIKKfSDVDLSEKDIHIQFVQAGQQgVDGDSASITVATAVISALEDIPVDQS 629
                                       566667778999999*************9999***********9888765379************************ PP

                              ChlI  82 tlflGeLsldGslrpvkgvlpialaakkegikkvivpken 121
                                       + + G Ls  G++ pv gv+  + aa+k+g++kvi+pk+n
  gi|336255402|ref|YP_004598509.1| 630 VAMTGSLSVRGDVLPVGGVTHKIEAAAKAGCSKVIIPKAN 669
                                       **************************************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 !   18.8   0.0   1.9e-06    0.0012       1      25 [.     151     176 ..     151     190 .. 0.84
   2 !   18.2   0.0   2.9e-06    0.0019      65     137 ..     324     397 ..     286     398 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.9e-06
                                       EEEEE--SSSSHHHHHHHGGGGB.S- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.nr 25 
                                       +v+++G pGtgKs+la+ ++++l + 
  gi|336255402|ref|YP_004598509.1| 151 HVMMIGSPGTGKSMLAKAMSQLLpQE 176
                                       79*********************543 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.9e-06
                                       G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---..........-EEEEEESS--.-TT-TTHHHHTT CS
                             AAA_5  65 egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddller....frviatanpldrslnelspalrsR 137
                                       ++ +l++DE+++++  ++++L++ + e ++++    e+ + +  + +e+    f  ia++n      +++ palr R
  gi|336255402|ref|YP_004598509.1| 324 NKGVLFVDEINTLDIRTQQKLMTAIQEGEFSITGQSERSSGAMVQ-TEPvpcdFVMIAAGNLDA--MENMHPALRNR 397
                                       788****************************88888887777643.33389*********9887..78889999998 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 !   14.5   0.0   5.7e-05     0.037       1      22 [.     152     173 ..     152     226 .. 0.76
   2 !   11.4   0.0    0.0005      0.32      56     125 ..     323     399 ..     309     402 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.7e-05
                                       EEEESSTTSSHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel 22 
                                       v+++G pGtGK++laka+ + l
  gi|336255402|ref|YP_004598509.1| 152 VMMIGSPGTGKSMLAKAMSQLL 173
                                       6899*************99876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0005
                                       TSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESS..G CS
                               AAA  56 kakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..................eskvivigatnr..p 112
                                         ++ +lf+DEi  l   r          ++++L+t++++ + +                    ++++i+a+n   +
  gi|336255402|ref|YP_004598509.1| 323 A-NKGVLFVDEINTLD-IR----------TQQKLMTAIQEGEFSitgqserssgamvqtepvPCDFVMIAAGNLdaM 387
                                       3.369**********4.33..........69999999999999999999999*********9667*********9** PP

                                       GGSTHHHHSTTSS CS
                               AAA 113 dkldpallrgRfd 125
                                       +++ pal+ +R++
  gi|336255402|ref|YP_004598509.1| 388 ENMHPALR-NRIK 399
                                       ********.9975 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 !   18.0   0.0   2.9e-06    0.0019       5      55 ..     128     171 ..     124     179 .. 0.85
   2 !    7.1   0.0    0.0067       4.3      84     120 ..     324     360 ..     319     400 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.9e-06
                            RuvB_N   5 sleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiak 55 
                                        +++ igq++ +   +i+i+aak+r+    hv+++G+PG Gk+ lak +++
  gi|336255402|ref|YP_004598509.1| 128 LVDQVIGQDEAR---DIIIKAAKQRR----HVMMIGSPGTGKSMLAKAMSQ 171
                                       457889999887...599******97....9***************99876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0067
                            RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldivigkG 120
                                       +k vlf+dei  l+  +++ l +a+++ ++ i+ ++ 
  gi|336255402|ref|YP_004598509.1| 324 NKGVLFVDEINTLDIRTQQKLMTAIQEGEFSITGQSE 360
                                       678**********************999888864333 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00015     0.094      54      83 ..     146     175 ..     128     181 .. 0.83
   2 !   12.4   0.0   9.5e-05     0.061     112     153 ..     315     356 ..     284     360 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                       BCSS-EEEEEESSTSTHHHHHHHHHHHSSS CS
                               MCM  54 lrgdinvllvgdpgtaKsqlLkyveklapr 83 
                                        + + +v+++g pgt+Ks l k++++l+p+
  gi|336255402|ref|YP_004598509.1| 146 AKQRRHVMMIGSPGTGKSMLAKAMSQLLPQ 175
                                       56678********************99987 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9.5e-05
                                       EEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEE CS
                               MCM 112 leaGalvladkGvcciDefdkmkeedrsalhEamEqqtisia 153
                                       +e G +  a+kGv+ +De++  + +++++l+ a+ + + si+
  gi|336255402|ref|YP_004598509.1| 315 VEPGSIHKANKGVLFVDEINTLDIRTQQKLMTAIQEGEFSIT 356
                                       799*******************************99999986 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.2e-05     0.014      15      75 ..     121     174 ..     105     183 .. 0.76
   2 ?    5.2   0.0     0.016        10     279     302 ..     325     348 ..     316     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  15 edgeaekeeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelg 75 
                                       + + +++  + ++Gq +ar+   +i++  k++    r v++ G +gtGk+ la a+s+ l 
  gi|336255402|ref|YP_004598509.1| 121 DIEVPDRLVDQVIGQDEARD---IIIKAAKQR----RHVMMIGSPGTGKSMLAKAMSQLLP 174
                                       34455666678999999996...677666665....689******************9886 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.016
                                       XXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 279 pGvlfiDevhmlDiecfsylnral 302
                                       +Gvlf+De++ lDi +   l  a+
  gi|336255402|ref|YP_004598509.1| 325 KGVLFVDEINTLDIRTQQKLMTAI 348
                                       7*************9877666666 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 !    7.7   0.0    0.0046       2.9       1      24 [.     151     174 ..     151     183 .. 0.91
   2 !   12.1   0.0    0.0002      0.13      64      99 ..     326     361 ..     308     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0046
                             AAA_3   1 hvllegvPGlaktllvkalakald 24 
                                       hv++ g PG++k +l+ka+++ l 
  gi|336255402|ref|YP_004598509.1| 151 HVMMIGSPGTGKSMLAKAMSQLLP 174
                                       9******************99875 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0002
                             AAA_3  64 nllladeinrappktqsalleameerqvtvegethk 99 
                                        +l++dein    +tq  l+ a++e + +++g++ +
  gi|336255402|ref|YP_004598509.1| 326 GVLFVDEINTLDIRTQQKLMTAIQEGEFSITGQSER 361
                                       5899************************99998754 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 !    7.6   0.0     0.006       3.8      15      44 ..     143     172 ..     136     190 .. 0.84
   2 !   11.5   0.0   0.00038      0.24      65      96 ..     320     359 ..     298     395 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.006
                                       HHHHT-SS-EEEEEETT--HHHHHHCC--T CS
                   Sigma54_activ_2  15 eqaaqsklpvfltGekGsgkelvArlLhkn 44 
                                        +aa++   v ++G +G+gk++ A+++++ 
  gi|336255402|ref|YP_004598509.1| 143 IKAAKQRRHVMMIGSPGTGKSMLAKAMSQL 172
                                       578899999****************99875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00038
                                       HHHTTTSEEEEEE-TT--HHHHHHHHHHHHH........H CS
                   Sigma54_activ_2  65 leqakggtLylkdiadlskaeqkeLlellak........a 96 
                                       + +a+ g+L++ +i+ l+   q++L+ ++++        +
  gi|336255402|ref|YP_004598509.1| 320 IHKANKGVLFVDEINTLDIRTQQKLMTAIQEgefsitgqS 359
                                       67899*************************9555555551 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00068      0.43       5      37 ..     143     176 ..     139     185 .. 0.79
   2 !    7.7   0.0    0.0066       4.2     101     129 ..     322     351 ..     252     362 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00068
                            AAA_19   5 ve.alkekvllvtaGpGtGKTrvlkhivallvel 37 
                                       ++ a +++++++++ pGtGK+ + k++ +ll ++
  gi|336255402|ref|YP_004598509.1| 143 IKaAKQRRHVMMIGSPGTGKSMLAKAMSQLLPQE 176
                                       56578999*************9988887777655 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0066
                            AAA_19 101 qeee.llivDEfqdvd.elqyrLlkallgek 129
                                       ++++ +l+vDE+  +d  +q++L+ a+  e+
  gi|336255402|ref|YP_004598509.1| 322 KANKgVLFVDEINTLDiRTQQKLMTAIQ-EG 351
                                       344569*******************998.44 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 !   18.4   0.0   1.8e-06    0.0012      28      63 ..     144     179 ..     136     186 .. 0.87
   2 ?   -2.6   0.0       5.3   3.4e+03     100     111 ..     324     335 ..     321     340 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                             AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkldkekyl 63 
                                       +  k++++v+++G+ GtGK++++k + + l++e+++
  gi|336255402|ref|YP_004598509.1| 144 KAAKQRRHVMMIGSPGTGKSMLAKAMSQLLPQEDLQ 179
                                       56899***********************99999876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.3
                             AAA_7 100 kklvvFvDDlnm 111
                                       +k v+FvD++n 
  gi|336255402|ref|YP_004598509.1| 324 NKGVLFVDEINT 335
                                       6789******96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   8.6e-06    0.0055       3      37 ..     147     181 ..     143     224 .. 0.81
   2 ?    0.1   0.0       1.4   9.1e+02      86     108 ..     320     344 ..     307     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.6e-06
                            AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeakaee 37 
                                       k++++++ +G +GtGK++l++ + + l++e  ++ 
  gi|336255402|ref|YP_004598509.1| 147 KQRRHVMMIGSPGTGKSMLAKAMSQLLPQEDLQDV 181
                                       5899***********************98766544 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.4
                            AAA_22  86 lraravielliiDEaqhlr...seea 108
                                       ++++ + ++l +DE+  l+   ++++
  gi|336255402|ref|YP_004598509.1| 320 IHKANK-GVLFVDEINTLDirtQQKL 344
                                       445555.9*******99987532443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00019      0.12      11      46 ..     143     177 ..     134     186 .. 0.76
   2 ?    3.5   0.0     0.078        50      87     115 ..     323     351 ..     286     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                            AAA_30  11 ealltsgdrvavltGpAGtGKttalkalreaweaag 46 
                                        ++++++ r +++ G +GtGK+++ ka+ +++ ++ 
  gi|336255402|ref|YP_004598509.1| 143 IKAAKQR-RHVMMIGSPGTGKSMLAKAMSQLLPQED 177
                                       4555555.699999***************9999884 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.078
                            AAA_30  87 epgtllivDEagmvdtkqlaallkaaeka 115
                                       +++ +l vDE+  +d+++ ++l++a+++ 
  gi|336255402|ref|YP_004598509.1| 323 ANKGVLFVDEINTLDIRTQQKLMTAIQEG 351
                                       455899******************99984 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.12        77      86     115 ..     147     176 ..     129     190 .. 0.82
   2 !   10.4   0.0   0.00034      0.21     227     267 ..     318     358 ..     305     370 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.12
                          AAA_PrkA  86 erkqilyllGPvggGksslverlkklleaa 115
                                       ++++ ++++G  g+Gks l++++ +ll ++
  gi|336255402|ref|YP_004598509.1| 147 KQRRHVMMIGSPGTGKSMLAKAMSQLLPQE 176
                                       456667789999***********9998655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00034
                          AAA_PrkA 227 GalnranrGllefvemfkadikvlhplltatqegnykstek 267
                                       G++ +an+G+l   e+   di+   +l+ta qeg+++ t++
  gi|336255402|ref|YP_004598509.1| 318 GSIHKANKGVLFVDEINTLDIRTQQKLMTAIQEGEFSITGQ 358
                                       8999*******999**********************98876 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   4.1e-05     0.026       8      53 ..     138     182 ..     131     205 .. 0.75
   2 ?   -3.0   0.0       6.6   4.2e+03      25      65 ..     655     695 ..     652     717 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-05
                                       HHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEE CS
                              PhoH   8 eQkeylealkkndivfaiGpaGtGKtylavalavealkkkkvkrii 53 
                                       + + +++a k+   v++iG+ GtGK++la a+  ++l +++++ ++
  gi|336255402|ref|YP_004598509.1| 138 ARDIIIKAAKQRRHVMMIGSPGTGKSMLAKAMS-QLLPQEDLQDVL 182
                                       4556778888999****************9997.444444444443 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.6
                                       E--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT--- CS
                              PhoH  25 iGpaGtGKtylavalavealkkkkvkriiltrpaveageel 65 
                                       +++aG+ K  +  a   +++ +++++++i + p  ++ e l
  gi|336255402|ref|YP_004598509.1| 655 AAKAGCSKVIIPKANEQDVMIEDEYEEMIEIIPCANISEVL 695
                                       67888888888888888888888888888777776666655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.7e-05      0.05       2      24 ..     152     174 ..     152     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.7e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg 24 
                                       v+++G pG+GKs la+ + + l+
  gi|336255402|ref|YP_004598509.1| 152 VMMIGSPGTGKSMLAKAMSQLLP 174
                                       89**************9886555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.6e-05      0.03      40      83 ..     142     179 ..     118     187 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.6e-05
                            DUF815  40 lventeqfleglpannvLLwGarGtGKSslvkallneyaeegLr 83 
                                       +++ +      ++ ++v+++G+ GtGKS l ka+ + + +e L+
  gi|336255402|ref|YP_004598509.1| 142 IIKAA------KQRRHVMMIGSPGTGKSMLAKAMSQLLPQEDLQ 179
                                       54443......45689******************9988888776 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.049        32       5      28 ..     151     174 ..     147     214 .. 0.88
   2 ?    7.1   0.0    0.0082       5.3      60     136 ..     316     391 ..     311     432 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.049
                                       -EEEE--TTSSHHHHHHHHHHHTT CS
                             AAA_2   5 silllgptgvGktelakalaellf 28 
                                        ++++g+ g+Gk++laka+++ll 
  gi|336255402|ref|YP_004598509.1| 151 HVMMIGSPGTGKSMLAKAMSQLLP 174
                                       57999***************9986 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0082
                                       TTT-HHHHTTSEEEEETGGG-------------HHHHHHHHHHHH--EE-......------EE-T....T-EEEEE CS
                             AAA_2  60 ppgyvgaeegGivllDEidKihpkessgadvSregVqrdLLqileggtlt......dkqgrkvdtk....nilfImt 126
                                       +pg + ++++G++++DEi                  q+ L+  + +g+ +       ++g +v+t+    + ++I++
  gi|336255402|ref|YP_004598509.1| 316 EPGSIHKANKGVLFVDEINTLDI-----------RTQQKLMTAIQEGEFSitgqseRSSGAMVQTEpvpcDFVMIAA 381
                                       689999************99988...........7788888888888887778877777777777633334577888 PP

                                       E--TTHHHHT CS
                             AAA_2 127 gafgsskisd 136
                                       g++++ +   
  gi|336255402|ref|YP_004598509.1| 382 GNLDAMENMH 391
                                       8887776655 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 ?   12.8   0.0   0.00011     0.072      46      70 ..     148     172 ..     130     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                         IstB_IS21  46 kkenivllGpsGvGKshlaialgve 70 
                                       ++  ++++G +G+GKs la a+++ 
  gi|336255402|ref|YP_004598509.1| 148 QRRHVMMIGSPGTGKSMLAKAMSQL 172
                                       667899****************975 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00017      0.11      10      37 ..     148     175 ..     143     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00017
                                       TTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  10 egekvaivGenGaGKStLlkllagllkp 37 
                                       + + v ++G+ G+GKS L+k++++ll +
  gi|336255402|ref|YP_004598509.1| 148 QRRHVMMIGSPGTGKSMLAKAMSQLLPQ 175
                                       667899*****************99854 PP

>> AgrB  Accessory gene regulator B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   8.9e-05     0.057     130     181 ..     204     255 ..     195     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.9e-05
                              AgrB 130 kpisskekkkklkilsiivllilliialllknekisnaillglllvavlqli 181
                                       ++i + +k++ +k+  + ++l+++iia+++ +  ++  illg+l++ +++li
  gi|336255402|ref|YP_004598509.1| 204 EQIIDAHKEEARKRNQMRSILMWIIIAIVIGYAILAANILLGILAAGIIWLI 255
                                       4566667789999999999*********999999999******998888776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.077       2      38 ..     151     183 ..     150     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEE CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvF 38 
                                        v++ G +G GK++L++ + +++ +++l+     ++ 
  gi|336255402|ref|YP_004598509.1| 151 HVMMIGSPGTGKSMLAKAMSQLLPQEDLQD----VLV 183
                                       6899*******************9999766....344 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00032       0.2      33      79 ..     450     494 ..     420     497 .. 0.78
   2 ?   -2.1   0.0       8.2   5.2e+03      21      37 ..     500     516 ..     497     523 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00032
                                       HHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHH CS
                           MCM_lid  33 lRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveea 79 
                                         +++ + ++++++   R L  l+R++  +A+ + +e+ t++dv +a
  gi|336255402|ref|YP_004598509.1| 450 AKRRS-G-RKNHLTLHFRSLGGLVRVAGDIARAEDREYTTRDDVLQA 494
                                       33333.2.3678999*****************************887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8.2
                                       HHHHHHHHHHHHHHHHH CS
                           MCM_lid  21 eakeklseaYvelRkee 37 
                                       + +++l++ Y+e Rk+ 
  gi|336255402|ref|YP_004598509.1| 500 SIEQQLADDYIERRKDY 516
                                       5678999*******976 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00026      0.17      20      58 ..     148     188 ..     138     220 .. 0.68
   2 ?   -3.3   0.0       5.1   3.3e+03     148     173 ..     563     588 ..     555     595 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                            AAA_10  20 nasasliiGdlGnGKSvlakllvlyisllg..gkaliiDpk 58 
                                       +  ++++iG++G GKS+lak +   +   +  + +++  p 
  gi|336255402|ref|YP_004598509.1| 148 QRRHVMMIGSPGTGKSMLAKAMSQLLPQEDlqDVLVYHNPD 188
                                       45689***************998776554422444444554 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.1
                            AAA_10 148 elrkedekvareiarhlesvvkksla 173
                                       +l++  e+ +++++  ++++ +++l 
  gi|336255402|ref|YP_004598509.1| 563 KLQEMAEESVQNVSAIIKKFSDVDLS 588
                                       68888899999999999999999886 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 ?   11.4   0.0   0.00017      0.11       9      35 ..     143     169 ..     137     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                     TrwB_AAD_bind   9 lpkeretqhilivGttGsGKtqalekl 35 
                                       ++  + ++h++++G+ G+GK+  ++++
  gi|336255402|ref|YP_004598509.1| 143 IKAAKQRRHVMMIGSPGTGKSMLAKAM 169
                                       6778899*************9766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (738 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1158  (0.0645881); expected 358.6 (0.02)
Passed bias filter:                      785  (0.0437838); expected 358.6 (0.02)
Passed Vit filter:                       132  (0.00736237); 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: 0.78u 0.26s 00:00:01.04 Elapsed: 00:00:00.41
# Mc/sec: 5365.42
//
Query:       gi|336255403|ref|YP_004598510.1|  [L=360]
Description: abortive infection protein [Halopiger xanaduensis SH-6]
Scores for 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-11   42.5  11.7    6.1e-11   42.5  11.7    2.3  2  CPBP      CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
        2.4    8.3   0.0        2.4    8.3   0.0    3.0  3  DUF3742   Protein of unknown function (DUF3742)


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 ?    1.1   0.1     0.058   5.2e+02      41      80 ..     169     208 ..     149     227 .. 0.75
   2 !   42.5  11.7   6.9e-15   6.1e-11       6      91 ..     253     341 ..     247     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.058
                                       HHHHHHHHHHCSGGGHHH.HHHHHHHHHHHHHHHHHTT-HH CS
                              CPBP  41 ilissilFglaHlpngps.vllaalaGlvlgylylktgsll 80 
                                       +++s  lF+l+ l   ++  ++  ++G+ ++++yl+ g ll
  gi|336255403|ref|YP_004598510.1| 169 VALSQGLFALVLLGAVIYtGVPPDALGIEFSVAYLRQG-LL 208
                                       55666667766666644444555578888999999988.55 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 6.9e-15
                                       HHHHHHHHHHHHHHHHHHTTCHHHHHHHH...S-HHHHHHHHHHHHHCSGGGHHH.HHHHHHHHHHHHHHHHHTT-H CS
                              CPBP   6 lvfllalllapllEEllfRglllqllqer..gsstlailissilFglaHlpngps.vllaalaGlvlgylylktgsl 79 
                                       ++++ +l + + +EEllfR+ l+ +++    +s+++  ++ss++F++ H ++g   v+++ l+G+vl+++++ tgs+
  gi|336255403|ref|YP_004598510.1| 253 VLLFGVLPIIAGFEELLFRAALIGAVSTGfgVSPWVLAVVSSLAFAVGHGMQGSVgVVVTGLLGFVLAAVFIVTGSF 329
                                       3334444455669************999976555899***************8778********************* PP

                                       HHHHHHHHHHHH CS
                              CPBP  80 laaillHallnl 91 
                                       l+++++H l+n+
  gi|336255403|ref|YP_004598510.1| 330 LVVVVAHYLINA 341
                                       ***********8 PP

>> DUF3742  Protein of unknown function (DUF3742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00027       2.4      70     107 ..      13      52 ..       1      58 [. 0.49
   2 ?    0.7   0.3     0.061   5.5e+02       9      61 ..     227     279 ..     221     304 .. 0.72
   3 ?   -4.3   4.0         2   1.8e+04      55      81 ..     313     339 ..     287     349 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00027
                           DUF3742  70 llvvvvlvawaarsvdtsdeeks.gdeeel.rngedGfgl 107
                                       +++v++lv+    +++ s++e + ++e+e  r+g dGfg 
  gi|336255403|ref|YP_004598510.1|  13 VVLVLLLVLSHLTQSTFSESEADsDTEPESdRDGADGFGA 52 
                                       2233333333333333333333344444447*******95 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.061
                           DUF3742   9 laerlgrllgrawRallrlerraaswlvakGvpaavatavlwvvklavlGvll 61 
                                        a rlg   ++ +R ll  +  a   +   Gv + +a    ++ ++a++G   
  gi|336255403|ref|YP_004598510.1| 227 AATRLGFDHDEELRELLAPDSLAGWAVLLFGVLPIIAGFEELLFRAALIGAVS 279
                                       68999999999999999999888888888999999999999999999999643 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 2
                           DUF3742  55 avlGvllyvafWlalllvvvvlvawaa 81 
                                        +lG  l ++f ++   +vvv++ +++
  gi|336255403|ref|YP_004598510.1| 313 GLLGFVLAAVFIVTGSFLVVVVAHYLI 339
                                       233444444444444555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2751.80
//
Query:       gi|336255404|ref|YP_004598511.1|  [L=117]
Description: hypothetical protein Halxa_4027 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.02   14.4   5.7      0.024   14.2   5.7    1.0  1  ABC2_membrane_5  ABC-2 family transporter protein
      0.046   13.9   1.8      0.059   13.5   1.5    1.3  1  IspA             Intracellular septation protein A


Domain annotation for each model (and alignments):
>> 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 ?   14.2   5.7   2.7e-06     0.024      94     191 ..      16     111 ..      10     116 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-06
                   ABC2_membrane_5  94 ilitlllliiavlikgnvtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaifslskl 170
                                        ++++++l+ a + +g++  +e l ++++++v++ i+l +   ly+++g + ++ vl ++++++++++ ++  l + 
  gi|336255404|ref|YP_004598511.1|  16 AVFLAVALYFALVAYGTIA-NEPLATYAAAFVFGAIALGLGAILYLRWGRRSST-VLAAAVCLAVGGVLQFAYLFSQ 90 
                                       57777888889999***96.9****************************66665.5556666655655555444444 PP

                   ABC2_membrane_5 171 elslidlsnyilliillviil 191
                                       +++l +ls+++++ ++ + ++
  gi|336255404|ref|YP_004598511.1|  91 SAALDSLSSLVVFAGVGLYVY 111
                                       555666666665555544443 PP

>> IspA  Intracellular septation protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.5   6.6e-06     0.059      25      95 ..      11      82 ..       9      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-06
                              IspA 25 AtavlivatvlqiailklrtrkvekmqlislvlvvvfGgltlllhdetFikw.KptvlyvlfalvLllslli 95
                                      At+   v  ++++ +  + ++++++ +l + +  +vfG+++l l    +++w + +   ++ a++L+++ ++
  gi|336255404|ref|YP_004598511.1| 11 ATISRAVFLAVALYFALVAYGTIANEPLATYAAAFVFGAIALGLGAILYLRWgRRSSTVLAAAVCLAVGGVL 82
                                      6667777788899999999*********************************63444445556666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 941.68
//
Query:       gi|336255405|ref|YP_004598512.1|  [L=314]
Description: family 2 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for 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   57.0   0.2    3.2e-15   56.3   0.2    1.5  1  Glycos_transf_2  Glycosyl transferase family 2
    3.3e-09   37.0   2.6    1.5e-07   31.5   2.6    2.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.4e-05   23.9   0.0    6.6e-05   22.5   0.0    1.6  2  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 !   56.3   0.2   5.4e-19   3.2e-15       1     107 [.       4     105 ..       4     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 5.4e-19
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       svv+ t N  + ll +l++l+++ ++p  e+ivv+  S+D+t  +++e  + d  v +  r+    +  ++nagl+a
  gi|336255405|ref|YP_004598512.1|   4 SVVVSTLNDREQLLSCLDALRER-TPPSTEVIVVNGPSSDGTTGVVRERTDIDVLVEISERN----QNVSRNAGLEA 75 
                                       8**********************.*************************8644444444444....5599******* PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH. CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekd 107
                                       atgd+++flD   +++ +w   + ++l + 
  gi|336255405|ref|YP_004598512.1|  76 ATGDVVAFLDGEYTIEQGWYGAIERHLGDA 105
                                       ***********9999999977666666554 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 !   31.5   2.6   2.6e-11   1.5e-07       4     221 ..       3     214 ..       1     218 [. 0.77

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.6e-11
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvn..arnlgstgksra 78 
                                       l+v+V t+n  ++l+++l++l   + p++ev+vv  +s+++t  v++e      +++++v+v   +r         +
  gi|336255405|ref|YP_004598512.1|   3 LSVVVSTLNDREQLLSCLDALRERTPPSTEVIVVNGPSSDGTTGVVRE------RTDIDVLVEisER-----NQNVS 68 
                                       89******************99977799*******************9......4456666552133.....33344 PP

                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarral 155
                                        n +l+a+++d+v+++D++  +e +   ++ + +     g + ++++   +  + +++g  +f++ +  + +++ a+
  gi|336255405|ref|YP_004598512.1|  69 RNAGLEAATGDVVAFLDGEYTIEQGWYGAIERHL-----GDADADENPTVDVVTGPVTGEARFDDVDDPRESRTVAG 140
                                       58********************999866655555.....33333444444445566777888888888888899888 PP

                   Glyco_tranf_2_3 156 g.vltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrev.......fpsslkayi 221
                                       + v+ + G  ++++r+vl++l+g+d+   ++   + + r+ + gf ++++ + avr+         ++++ a++
  gi|336255405|ref|YP_004598512.1| 141 RdVTLFDGDNVAFDRTVLEALDGFDEYLETGGARDCAHRVAALGFEVDWAMEMAVRRDvgtdggtAERDWGAAY 214
                                       8788889*******************66666555778999999******9999999875554444335566665 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 !   22.5   0.0   1.1e-08   6.6e-05      28      92 ..      29      88 ..       4     117 .. 0.86
   2 ?   -1.5   0.0      0.24   1.4e+03     166     192 ..     149     175 ..     143     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-08
                   Glyco_tranf_2_2 28 eeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaDc 92
                                      +  e+ivv++ Ss+ +  +v+   d   lv +++       +  +rN G + a +d+v FlD++ 
  gi|336255405|ref|YP_004598512.1| 29 PSTEVIVVNGPSSDGTTGVVRERTDIDVLVEISER-----NQNVSRNAGLEAATGDVVAFLDGEY 88
                                      689***************************99999.....8999******************975 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.24
                   Glyco_tranf_2_2 166 ssilinrraflevGGyDErfrGhgaED 192
                                       +++   r  +  + G+DE +   ga D
  gi|336255405|ref|YP_004598512.1| 149 DNVAFDRTVLEALDGFDEYLETGGARD 175
                                       566678888999999999998777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2477.60
//
Query:       gi|336255406|ref|YP_004598513.1|  [L=235]
Description: type 11 methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-24   84.1   0.1    1.8e-23   83.1   0.1    1.6  1  Methyltransf_25  Methyltransferase domain
    1.4e-23   83.4   0.0    2.3e-23   82.6   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    8.3e-18   64.6   0.0    1.2e-17   64.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.1e-14   54.9   0.0    3.5e-14   53.4   0.0    1.7  2  Methyltransf_12  Methyltransferase domain
    1.8e-14   53.6   0.0    2.5e-14   53.2   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.5e-14   53.0   0.0    4.7e-14   52.6   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      3e-06   27.0   0.0    4.6e-06   26.4   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
    4.5e-05   23.2   0.0    0.00013   21.7   0.0    1.8  2  UPF0020          Putative RNA methylase family UPF0020
    0.00013   21.1   0.0    0.00017   20.6   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
    0.00062   19.4   0.0    0.00092   18.8   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0019   17.3   0.0     0.0024   17.0   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0019   17.7   0.0     0.0029   17.1   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
     0.0025   17.2   0.0     0.0055   16.0   0.0    1.5  2  CMAS             Mycolic acid cyclopropane synthetase
     0.0036   17.0   0.0     0.0058   16.3   0.0    1.3  1  TPMT             Thiopurine S-methyltransferase (TPMT)
  ------ inclusion threshold ------
      0.012   14.8   0.0      0.016   14.3   0.0    1.2  1  Methyltransf_20  Putative methyltransferase
      0.013   15.0   0.0      0.018   14.5   0.0    1.2  1  TehB             Tellurite resistance protein TehB
      0.015   15.0   0.0       0.02   14.5   0.0    1.2  1  NodS             Nodulation protein S (NodS)
      0.024   14.7   0.0      0.033   14.2   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.041   12.9   0.1      0.098   11.6   0.0    1.5  2  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.044   13.6   0.0       0.09   12.5   0.0    1.5  1  DUF938           Protein of unknown function (DUF938)
      0.066   12.8   0.0      0.088   12.4   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.096   12.4   0.0       0.14   11.9   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


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 !   83.1   0.1   2.2e-26   1.8e-23       1      94 [.      48     139 ..      48     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 2.2e-26
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       +L+++cGtGr+t +la+++  a+v+g+Dis++ml++ r++a++++l   +ef++gda +lpf+d++fD v++ + + 
  gi|336255406|ref|YP_004598513.1|  48 ILEIACGTGRFTVMLAEQG--ADVVGLDISAAMLQQGRTKARNADLagTLEFLRGDAGRLPFPDDHFDTVIA-MRFF 121
                                       8*****************5..********************9999999************************.5755 PP

                                       GSSHHHHHHHHHHHHHHEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLk 94 
                                       hl  +d e++l+e++rv +
  gi|336255406|ref|YP_004598513.1| 122 HLA-DDPEAFLREMRRVSR 139
                                       555.4778********977 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.0   2.9e-26   2.3e-23       1      89 [.      49     139 ..      49     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 2.9e-26
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhve 75 
                                       L+++cGtGr++  la++ga+vvg+D+s++ml++ ++ka++++l  ++ef+++da +lpf+d+ fD v++  ++h  +
  gi|336255406|ref|YP_004598513.1|  49 LEIACGTGRFTVMLAEQGADVVGLDISAAMLQQGRTKARNADLagTLEFLRGDAGRLPFPDDHFDTVIAMRFFHLAD 125
                                       89*************************************************************************** PP

                                       CHHHHHHHHHHHEE CS
                   Methyltransf_11  76 dpekalkeiaRvLk 89 
                                       dpe++l+e++Rv +
  gi|336255406|ref|YP_004598513.1| 126 DPEAFLREMRRVSR 139
                                       ***********965 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   1.5e-20   1.2e-17       5     104 ..      46     141 ..      42     160 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.5e-20
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlils 80 
                                        ++l+++CGtG++t  lae+   +a+vvG+Dis+ ++++ r++a++  l   +eF +gd+  l+  + d+ fD +++
  gi|336255406|ref|YP_004598513.1|  46 RSILEIACGTGRFTVMLAEQ---GADVVGLDISAAMLQQGRTKARNADLAgTLEFLRGDAGRLP--FPDDHFDTVIA 117
                                       579***************44...799************************9*************..*********** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpg 104
                                         ++++  dp+++l+e+ rv +++
  gi|336255406|ref|YP_004598513.1| 118 MRFFHLADDPEAFLREMRRVSRDQ 141
                                       ********************9876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   4.3e-17   3.5e-14       1      92 [.      49     137 ..      49     141 .. 0.90
   2 ?   -1.8   0.0       6.4   5.2e+03      17      33 ..     175     191 ..     170     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 4.3e-17
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       Lei cGtG+++ +l+e+  +++++g+Dis++++   + ++++r+++ +  +e+   d++ l+ + ++fD+v+a  ++
  gi|336255406|ref|YP_004598513.1|  49 LEIACGTGRFTVMLAEQ--GADVVGLDISAAML--QQGRTKARNADLAGTLEFLRGDAGRLPFPdDHFDTVIAMRFF 121
                                       8****************..**************..6777777777778899999999888877789*********** PP

                   Methyltransf_12  77 hhlkdirevldnirkl 92 
                                       h  +d++++l+++r++
  gi|336255406|ref|YP_004598513.1| 122 HLADDPEAFLREMRRV 137
                                       **************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.4
                   Methyltransf_12  17 klpdieytgvDispsai 33 
                                        l  +++t vD+  +++
  gi|336255406|ref|YP_004598513.1| 175 LLAKTNLTLVDVEDDFL 191
                                       44558899999999988 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0     3e-17   2.5e-14      34     143 ..      31     138 ..      10     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 3e-17
                                       HHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT CS
                   Ubie_methyltran  34 lWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaee 109
                                         k+ v +   + + +++l++a+Gtg +++ l++   +  +vv+lDi++ mL++g+ k+++      +efl ++a +
  gi|336255406|ref|YP_004598513.1|  31 REKQAVLEAIMPVEDRSILEIACGTGRFTVMLAE---QGADVVGLDISAAMLQQGRTKARNADLAgTLEFLRGDAGR 104
                                       5566777778888999**************9976...5679********************999989********** PP

                                       -TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHE CS
                   Ubie_methyltran 110 LpfeddsfDvvtvsfGlrnvtDklkaLkeayrvl 143
                                       Lpf dd fD+v     +    D +  L+e++rv 
  gi|336255406|ref|YP_004598513.1| 105 LPFPDDHFDTVIAMRFFHLADDPEAFLREMRRVS 138
                                       *********986554455566777789*****96 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   5.7e-17   4.7e-14      11     163 ..      35     184 ..      12     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 5.7e-17
                   Methyltransf_23  11 dklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.kakkaqkdqfdeq.......eaaep 79 
                                       + le ++    ++ ++L+i+cGtG+++  l+e+g++v+g D+s ++ +  + ka++a    +  +         ++p
  gi|336255406|ref|YP_004598513.1|  35 AVLEAIM--PVEDRSILEIACGTGRFTVMLAEQGADVVGLDISAAMLQQGRtKARNADLAGT-LEflrgdagRLPFP 108
                                       3334444..35677*****************************9988876663333333333.11122222244558 PP

                   Methyltransf_23  80 qgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelle 156
                                       +++fd+++++ +++  +dp++ lr +++  ++   +++ ++++   ++r++ +w+++      ++++s +++ ell 
  gi|336255406|ref|YP_004598513.1| 109 DDHFDTVIAMRFFHLADDPEAFLREMRRVSRD--QIVFDTFNR--FSARSIYNWALPM----GSRLYSKSEVSELLA 177
                                       89**************************9997..699****87..7999999999877....559************ PP

                   Methyltransf_23 157 eaGlevv 163
                                       + +l++v
  gi|336255406|ref|YP_004598513.1| 178 KTNLTLV 184
                                       ****998 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   5.7e-09   4.6e-06       6     116 ..      35     151 ..      30     191 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 5.7e-09
                              MetW   6 liaelikp..gsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakG........lsviqgdldkdlenfe 72 
                                       +++e i p     +l++ cG G +  +l+e ++ d  Gl+++++ +++  +k         l+ ++g  d +   f+
  gi|336255406|ref|YP_004598513.1|  35 AVLEAIMPveDRSILEIACGTGRFTVMLAE-QGADVVGLDISAAMLQQGRTKArnadlagtLEFLRG--DAGRLPFP 108
                                       55555544113459***********99976.999********9998876555411111111444444..456678** PP

                              MetW  73 dksfdyvvlsqtlqatrnpkevldellrigrraivsfPnfGhWr 116
                                       d+ fd v+  + +    +p+  l+e+ r++r  iv f  f  + 
  gi|336255406|ref|YP_004598513.1| 109 DDHFDTVIAMRFFHLADDPEAFLREMRRVSRDQIV-FDTFNRFS 151
                                       ********************************998.44444444 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.6e-07   0.00013      75     127 ..      65     117 ..      38     118 .. 0.92
   2 ?   -3.6   0.0       9.1   7.4e+03     130     146 ..     161     177 ..     160     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.6e-07
                                       HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE CS
                           UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivt 127
                                       + + ++g+D+ ++++q++r++a++a ++++ ef   da  L+ +++ +d++++
  gi|336255406|ref|YP_004598513.1|  65 QGADVVGLDISAAMLQQGRTKARNADLAGTLEFLRGDAGRLPFPDDHFDTVIA 117
                                       55679*************************************9999****995 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.1
                                       --------HHHHHHHHH CS
                           UPF0020 130 PYGerlgskkalekLYs 146
                                       P G rl sk ++ +L  
  gi|336255406|ref|YP_004598513.1| 161 PMGSRLYSKSEVSELLA 177
                                       88999999999988755 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 !   20.6   0.0   2.1e-07   0.00017     105     198 ..      34     127 ..      29     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                                       HHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.- CS
                    Methyltransf_9 105 drvlphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.l 180
                                       + vl+ + ++++r+il++ cg+G +   m++e+ + vvG+d s   l q ++  +  +       l     +lp   
  gi|336255406|ref|YP_004598513.1|  34 QAVLEAIMPVEDRSILEIACGTGRFTV-MLAEQGADVVGLDISAAMLQQGRTKARNADLAGTLEFLRGDAGRLPFpD 109
                                       678999*****************9875.888888899**********999888887777777777777888898767 PP

                                       --EEEEEEES-GGG-S-H CS
                    Methyltransf_9 181 eafdtvfsmGvlyhrrsP 198
                                       + fdtv +m  ++    P
  gi|336255406|ref|YP_004598513.1| 110 DHFDTVIAMRFFHLADDP 127
                                       889999999766555555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.1e-06   0.00092      24     103 ..      37     117 ..      27     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                                       HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTT.TSTTS- CS
                               MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvle.eveekk 97 
                                       le++   +++++l ++cG+G  +++la++  +  v+ +d++a+ l+  ++ +++ +l+  +e++  d+    +++++
  gi|336255406|ref|YP_004598513.1|  37 LEAIMPVEDRSILEIACGTGRFTVMLAEQGAD--VVGLDISAAMLQQGRTKARNADLAgtLEFLRGDAGRlPFPDDH 111
                                       45555558889*****************8887..9*****************9999998899999997652677999 PP

                                       EEEEEE CS
                               MTS  98 fdlivs 103
                                       fd+++ 
  gi|336255406|ref|YP_004598513.1| 112 FDTVIA 117
                                       999986 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     3e-06    0.0024      13      85 ..      27     102 ..      17     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3e-06
                                       E--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-C CS
                            RrnaAD  13 lknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls...kdeklkvvhqDf 85 
                                       l+++   + +l+++ + e+  +lei+ G+G +T+ La++   vv l +  ++++  ++k +   +++ l+ +  D+
  gi|336255406|ref|YP_004598513.1|  27 LIDRREKQAVLEAIMPVEDRSILEIACGTGRFTVMLAEQGADVVGLDISAAMLQQGRTKARnadLAGTLEFLRGDA 102
                                       55666667788888888********************************999999988877655666666666665 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.6e-06    0.0029       4      60 ..      47     102 ..      44     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.6e-06
                                       EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTS.SEEEEES-C CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelk.Nlrilrgda 60 
                                        +lei cG G+f+v lA++ +d  ++G++i+  ++++   k+++ +l   l+ lrgda
  gi|336255406|ref|YP_004598513.1|  47 SILEIACGTGRFTVMLAEQGAD--VVGLDISAAMLQQGRTKARNADLAgTLEFLRGDA 102
                                       689****************987..699****999999999998886642577888887 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.7e-06    0.0055      64     137 ..      46     121 ..      30     146 .. 0.81
   2 ?   -1.4   0.0       1.4   1.1e+03     190     216 ..     160     187 ..     107     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.7e-06
                                       -EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SEEEEES-G CS
                              CMAS  64 mtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdrvvsvgaf 137
                                         +L+i cG G  ++  +e+ +++vvgl +S+   ++ + +  ++dl+ + e +  d   l+    ++d v+++  f
  gi|336255406|ref|YP_004598513.1|  46 RSILEIACGTGRFTVMLAEQ-GADVVGLDISAAMLQQGRTKARNADLAGTLEFLRGDAGRLPFpddHFDTVIAMRFF 121
                                       579*************9999.************************99988887776666553222467776666555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                                       STTS.---BHHHHHHHHHHTT-EEEEEE CS
                              CMAS 190 FPgG.elpsieeieeeiseagftvvdve 216
                                        P G +l s +e++e  +++++t+vdve
  gi|336255406|ref|YP_004598513.1| 160 LPMGsRLYSKSEVSELLAKTNLTLVDVE 187
                                       3655368888899999999999988876 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.1e-06    0.0058      45      76 ..      52      83 ..      28     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.1e-06
                                      T-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHH CS
                              TPMT 45 lCGkaldlvwlAeqgrevvGvelselAvekff 76
                                       CG +   v lAeqg +vvG+++s + +++  
  gi|336255406|ref|YP_004598513.1| 52 ACGTGRFTVMLAEQGADVVGLDISAAMLQQGR 83
                                      7***********************99988754 PP

>> Methyltransf_20  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     2e-05     0.016     133     195 ..      44     102 ..      22     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                   Methyltransf_20 133 rpvrildiaaGhGryvldalekaeervesillrdyselnveqGraliaekglediarfekgda 195
                                       ++  il+ia+G Gr+ +      +e+  +++  d s++ ++qGr+ +++ +l+   +f +gda
  gi|336255406|ref|YP_004598513.1|  44 EDRSILEIACGTGRFTVML----AEQGADVVGLDISAAMLQQGRTKARNADLAGTLEFLRGDA 102
                                       45579**********7632....2334567788*****************************9 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.2e-05     0.018      19      64 ..      33      78 ..      16      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.2e-05
                                      -HHHHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHH CS
                              TehB 19 hsevveavkivkpgkvldlgcgqgrnslylsllgydvtawdknens 64
                                      +  v+ea+  v+   +l++ cg gr ++ l+ +g dv  +d  +  
  gi|336255406|ref|YP_004598513.1| 33 KQAVLEAIMPVEDRSILEIACGTGRFTVMLAEQGADVVGLDISAAM 78
                                      56799*********************************99976544 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.4e-05      0.02      45     114 ..      46     119 ..      21     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                              NodS  45 adalevGcaaGalterlapyckrltvvdvveeaiararervkes...shiswivsdvqqfs.tdekfdlivvae 114
                                        ++le+ c +G +t++la     +  +d+    +++ r++ +++     + ++  d  ++   d++fd+++   
  gi|336255406|ref|YP_004598513.1|  46 RSILEIACGTGRFTVMLAEQGADVVGLDISAAMLQQGRTKARNAdlaGTLEFLRGDAGRLPfPDDHFDTVIAMR 119
                                       579**************************999999888887774111457788888888863578888887665 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.1e-05     0.033      24      88 ..      43     101 ..      28     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-05
                   Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaels 88 
                                        ++ +++++++G g  + +la    + +  vvg+d+++++ ++ ++ a++    ++  l+f  ++
  gi|336255406|ref|YP_004598513.1|  43 VEDRSILEIACGTGRFTVMLAE---Q-GADVVGLDISAAMLQQGRTKARNAD--LAGTLEFLRGD 101
                                       467889****************...5.9******************999998..77888887776 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 ?   11.6   0.0   0.00012     0.098     201     239 ..      44      82 ..      28     106 .. 0.83
   2 ?   -1.8   0.0       1.4   1.2e+03      31      72 ..     108     151 ..      85     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                   tRNA_U5-meth_tr 201 skgdllelycGnGnfslalarnfekvlateiakssveaa 239
                                       +++ +le+ cG G f++ la++   v+  +i+ + ++  
  gi|336255406|ref|YP_004598513.1|  44 EDRSILEIACGTGRFTVMLAEQGADVVGLDISAAMLQQG 82 
                                       56789*********************9999998777655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                   tRNA_U5-meth_tr  31 peehyrlraefrlwheed..dlyyimfdqktkkkirvdefdaas 72 
                                       p++h+ +   +r++h  d  + +   + + ++++i+ d+f+  s
  gi|336255406|ref|YP_004598513.1| 108 PDDHFDTVIAMRFFHLADdpEAFLREMRRVSRDQIVFDTFNRFS 151
                                       68899999999999965511566666777788888888887544 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.09      15      45 ..      34      64 ..      27      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                            DUF938 15 levLksylakttervLEiasGtGqHAvffAp 45
                                       +vL+  ++ + + +LEia GtG+  v +A+
  gi|336255406|ref|YP_004598513.1| 34 QAVLEAIMPVEDRSILEIACGTGRFTVMLAE 64
                                      57899999999999*************9997 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 ?   12.4   0.0   0.00011     0.088       3      61 ..      47     141 ..      45     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe................... 60 
                                        il + +G+G  ++ +a+++  v++++i+   l++    a+  + +  + +  gd                      
  gi|336255406|ref|YP_004598513.1|  47 SILEIACGTGRFTVMLAEQGADVVGLDISAAMLQQGRTKARNADLAGTLEFLRGDAGRlpfpddhfdtviamrffhl 123
                                       6899*************************************************999887777777777777777766 PP

                   Methyltransf_15  61 .................l 61 
                                                         
  gi|336255406|ref|YP_004598513.1| 124 addpeaflremrrvsrdQ 141
                                       666666666555555551 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 ?   11.9   0.0   0.00017      0.14      73     134 ..      44     104 ..      15     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                       TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-.GG CS
                              PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgD.Gr 134
                                       +  ++Le+ +G+G  t++la+   + + vv+++ ++ + ++ + + ++ dl+  + +  gD Gr
  gi|336255406|ref|YP_004598513.1|  44 EDRSILEIACGTGRFTVMLAE---QGADVVGLDISAAMLQQGRTKARNADLAgTLEFLRGDaGR 104
                                       5678**********9998886...556789*****************99998888999888455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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):              22  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1723.55
//
Query:       gi|336255407|ref|YP_004598514.1|  [L=93]
Description: hypothetical protein Halxa_4030 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00016   21.2   0.0    0.00025   20.5   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00099   18.7   0.3     0.0025   17.4   0.1    1.7  2  GntR            Bacterial regulatory proteins, gntR family
     0.0013   18.6   0.1     0.0018   18.1   0.1    1.2  1  MarR_2          MarR family
     0.0015   18.5   0.4     0.0036   17.3   0.4    1.8  1  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.019   14.8   0.1      0.033   14.1   0.0    1.4  1  TFIIE_alpha     TFIIE alpha subunit
      0.024   14.6   0.8       0.34   10.9   0.1    2.6  2  HTH_12          Ribonuclease R winged-helix domain
      0.076   12.9   0.1       0.11   12.4   0.1    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.084   12.8   0.8       0.19   11.7   0.1    1.8  2  Phage_tail_APC  Phage tail assembly chaperone protein


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 !   20.5   0.0   1.1e-07   0.00025      11      43 ..      39      71 ..      37      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-07
                            HTH_24 11 lLqknprisqreLAerlglSpstvnrrlkrLee 43
                                      +L+ ++ +sq +LAe++ l+  tv++ l+rLe+
  gi|336255407|ref|YP_004598514.1| 39 VLETDSPLSQGQLAEESLLPDRTVRYALNRLED 71
                                      6888999*************************8 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.96   2.1e+03      18      31 ..      11      23 ..       8      27 .. 0.70
   2 !   17.4   0.1   1.1e-06    0.0025      12      56 ..      34      77 ..      32      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.96
                                      S-TTSB---HHHHH CS
                              GntR 18 lrpGdkLPsereLa 31
                                      ++++++L se+e +
  gi|336255407|ref|YP_004598514.1| 11 VAAEETL-SEEEYR 23
                                      6788888.888755 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.1e-06
                                      HHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR 12 dIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglver 56
                                      ++++++l+  ++L s+ +La+e      tvR AL+rLe  +lv +
  gi|336255407|ref|YP_004598514.1| 34 KLVAKVLETDSPL-SQGQLAEESLLPDRTVRYALNRLEDVDLVGS 77
                                      788999*******.*************************999976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1     8e-07    0.0018       8      54 ..      34      78 ..      26      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8e-07
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                        v  +L    +  l++g+la++  l+  +v ++l+rL++  Lv  r
  gi|336255407|ref|YP_004598514.1| 34 KLVAKVLETDSP--LSQGQLAEESLLPDRTVRYALNRLEDVDLVGSR 78
                                      455555666666..**************************9999655 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.4   1.6e-06    0.0036      19      54 ..      40      75 ..       9      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.6e-06
                                      HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                      L ++ +l+ ++lae+  l++ t++y L+ Le+++Lv
  gi|336255407|ref|YP_004598514.1| 40 LETDSPLSQGQLAEESLLPDRTVRYALNRLEDVDLV 75
                                      4778999999***9988******************9 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.5e-05     0.033      14      70 ..      32      89 ..      27      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE.EETTTEEE CS
                       TFIIE_alpha 14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrr.rdeekswy 70
                                      +a+lv +vL +++ ++  +la+e  +    +r +LnrL +  lv  + + rd  k++y
  gi|336255407|ref|YP_004598514.1| 32 SAKLVAKVLETDSPLSQGQLAEESLLPDRTVRYALNRLEDVDLVGSRYSfRDARKQVY 89
                                      5789999*************************************88765366666665 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 ?    1.3   0.1      0.15   3.5e+02      27      42 ..      14      29 ..       5      39 .. 0.77
   2 ?   10.9   0.1   0.00015      0.34       9      48 ..      41      75 ..      35      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.15
                            HTH_12 27 gydigeravRyrLrkl 42
                                      ++ ++e+  R rLr l
  gi|336255407|ref|YP_004598514.1| 14 EETLSEEEYRDRLRDL 29
                                      7889999999999987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00015
                            HTH_12  9 esdkpigakeiaeeLkkrgydigeravRyrLrkleerglt 48
                                      e d p++ +++aee       + +r+vRy L  le+ +l+
  gi|336255407|ref|YP_004598514.1| 41 ETDSPLSQGQLAEE-----SLLPDRTVRYALNRLEDVDLV 75
                                      77889999999886.....456789**********99887 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.9e-05      0.11      19      56 ..      42      79 ..      33      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.9e-05
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      +  p++  ++aee+ +p  +v  +L++Led +lV  + 
  gi|336255407|ref|YP_004598514.1| 42 TDSPLSQGQLAEESLLPDRTVRYALNRLEDVDLVGSRY 79
                                      556788889************************97765 PP

>> Phage_tail_APC  Phage tail assembly chaperone protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   8.3e-05      0.19      20      46 ..       6      32 ..       3      40 .. 0.84
   2 ?   -1.3   0.0      0.89     2e+03      11      17 ..      68      74 ..      57      87 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.3e-05
                                      STTS---HHHHHHHHHHHHHHHHS--- CS
                    Phage_tail_APC 20 lpDspldeeerqalkaYrqaLRDlPeq 46
                                       +D+++++ee    ++Yr  LRDlP  
  gi|336255407|ref|YP_004598514.1|  6 AEDRDVAAEETLSEEEYRDRLRDLPPS 32
                                      678999998888889**********76 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.89
                                      HHHHTHH CS
                    Phage_tail_APC 11 rLaasDw 17
                                      rL+++D 
  gi|336255407|ref|YP_004598514.1| 68 RLEDVDL 74
                                      5666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); 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: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 743.90
//
Query:       gi|336255408|ref|YP_004598515.1|  [L=273]
Description: beta-lactamase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-17   61.9   3.7    1.2e-16   61.4   3.7    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00018   21.1   0.3    0.00035   20.1   0.3    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0015   18.5   1.0     0.0029   17.5   0.2    1.9  2  BLACT_WH       Beta-lactamase associated winged helix domain
  ------ inclusion threshold ------
      0.062   13.0   0.1       0.12   12.1   0.1    1.4  1  FAD_binding_4  FAD binding domain
       0.11   12.3   0.0       0.17   11.8   0.0    1.4  1  Lactamase_B_3  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 !   61.4   3.7   3.2e-20   1.2e-16       3     197 .]      18     192 ..      16     192 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 3.2e-20
                                       CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                       Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                       ++ +n+y++ g + + L+D+   ++a +       + + + ++++v++TH+H+DH+G+++  + +t++ v+a a  +
  gi|336255408|ref|YP_004598515.1|  18 GGETNAYVL-GRDPAALVDPAERSDALD-------RLVADARIEHVVVTHAHPDHVGAVAAYAAETNATVWARAGRT 86 
                                       5679*****.9**********9999999.......56**************************************99 PP

                                       HCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHH CS
                       Lactamase_B  80 palfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallage 156
                                         ++   +           ++++++  ++ e++++  +  +++  v   pgh ++h+ +e+g ++ + +GD   +  
  gi|336255408|ref|YP_004598515.1|  87 DRFRAATGVEPDREL----RAGTIIELEREEDGDERAGSADERIRVLDAPGHAPDHVALEAGRDGPICCGDCAVRDG 159
                                       999999996666664....78*****************************************************999 PP

                                       CCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 157 tgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                        + ++         + +d + yl +l++l++ ++ +l+pgH
  gi|336255408|ref|YP_004598515.1| 160 SVAVTA--------PEGDMRAYLTTLRRLRAIDPPRLYPGH 192
                                       999999........9************************** 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 !   20.1   0.3   9.9e-08   0.00035      25      75 ..      47      94 ..      31     158 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 9.9e-08
                                      S--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCG CS
                     Lactamase_B_2 25 rdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfv 75
                                      +++ ++i+ V++thaH DH+  +   ++  +++++++a +g  +  +a + 
  gi|336255408|ref|YP_004598515.1| 47 VAD-ARIEHVVVTHAHPDHVGAVAAYAA--ETNATVWARAGRTDRFRAATG 94
                                      344.69**************55555554..56699**99988877776644 PP

>> BLACT_WH  Beta-lactamase associated winged helix 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      14      24 ..      30      40 ..      30      55 .. 0.63
   2 !   17.5   0.2   8.1e-07    0.0029       1      38 [.     227     264 ..     227     270 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                          BLACT_WH 14 peslhpaAerg 24
                                      p+ l  +Aer+
  gi|336255408|ref|YP_004598515.1| 30 PAALVDPAERS 40
                                      56677778776 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 8.1e-07
                          BLACT_WH   1 TveelVkviYkdvpeslhpaAergvlahLeKLeeeGkV 38 
                                       T+e++ ++ Y++    ++  A+ +v+ahLeKL  e++ 
  gi|336255408|ref|YP_004598515.1| 227 TLEQILDAAYDKDLTGVRDLAKATVVAHLEKLAVEDRL 264
                                       899********9999******************99985 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.3e-05      0.12       3      41 ..      55      93 ..      54     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.3e-05
                                      EEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC CS
                     FAD_binding_4  3 avvrpeseeevaaalrlaneaglpvlvrGgGssllgqav 41
                                      +vv+ +++++v a+ ++a+e++++v++r+g ++  ++a+
  gi|336255408|ref|YP_004598515.1| 55 VVVTHAHPDHVGAVAAYAAETNATVWARAGRTDRFRAAT 93
                                      79999**************************98876554 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 ?   11.8   0.0   4.7e-05      0.17      15      66 ..      28      81 ..      19     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                     Lactamase_B_3 15 agarilvDPfka..nlgyeppaeeaDlvlisqaledHahletlkqlaenvkvle 66
                                      ++   lvDP ++   l+      +++ v++++a++dH  + +  ++++n++v +
  gi|336255408|ref|YP_004598515.1| 28 RDPAALVDPAERsdALDRLVADARIEHVVVTHAHPDHVGAVAAYAAETNATVWA 81
                                      567889***987545555666799999**********98777666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2280.66
//
Query:       gi|336255409|ref|YP_004598516.1|  [L=252]
Description: hypothetical protein Halxa_4032 [Halopiger xanaduensis SH-6]
Scores for 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   50.6   0.0    8.3e-13   48.8   0.0    1.9  1  CxxCxxCC         Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
      0.029   14.2   0.9       0.11   12.4   0.0    2.0  2  Glucosamine_iso  Glucosamine-6-phosphate isomerases/6-phospho


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 !   48.8   0.0   9.2e-17   8.3e-13       1      85 []      29     177 ..      29     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 9.2e-17
                          CxxCxxCC   1 eCkeCgaCCk.....elkvklteedlerlkaaevaeeeeeskkiak............................... 41 
                                       eC++CgaCC+     e+++++ +++++rl++a v+ ++  +   +                                
  gi|336255409|ref|YP_004598516.1|  29 ECTRCGACCTghgddEHTATVFPDEVRRLEDAAVDADSPGAAATIGktdlvppaddrewrdvarpmpyglsegddgl 105
                                       7*************99*****************966555554444479***************************** PP

                          CxxCxxCC  42 ............adgrCvfldeetk...lCkiYeeRpkicrlfpas.............ekeellaraetCa 85 
                                                    +g+Cvf+ e+++    C  +e+Rp+icr++p+s              +ee  +ra++C+
  gi|336255409|ref|YP_004598516.1| 106 egetfewalqtdGCGDCVFYAEDDDgtgACVAHEDRPLICRTYPFSvalagtsqpmgeaVDEEGVVRAHECE 177
                                       ***********99********9988888******************99999999999888888888888885 PP

>> Glucosamine_iso  Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.2e-05      0.11     111     156 ..      15      59 ..       1      72 [. 0.67
   2 ?    0.1   0.1      0.07   6.3e+02       2      26 ..     187     211 ..     186     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHHCCSSSSSESEEEE---TTS-BTTB-TTCHHHHCS CS
                   Glucosamine_iso 111 aaaayeeelkellakelpvfDlvlLGmGpDGHtaSLFPgspeleet 156
                                        +++ ++ +++ ++ e+ +   +  G G+D Hta  FP++    e+
  gi|336255409|ref|YP_004598516.1|  15 SVDDLADAIES-IGFECTRCGACCTGHGDDEHTATVFPDEVRRLED 59 
                                       44444455554.3357788888999**************9883333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.07
                                       SHHHHHHHHHHHHHHHHHHHHHHHS CS
                   Glucosamine_iso   2 dkeelaealaarivealeealaerg 26 
                                       d+++la++l +r v++leea+a r+
  gi|336255409|ref|YP_004598516.1| 187 DAAALARTLKERAVRELEEAIAVRD 211
                                       78999***************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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 0.19s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2113.05
//
Query:       gi|336255410|ref|YP_004598517.1|  [L=133]
Description: SPW repeat-containing protein [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0049   16.4   7.7     0.0049   16.4   7.7    2.8  3  SPW       SPW repeat
  ------ inclusion threshold ------
      0.041   14.2   0.3      0.041   14.2   0.3    2.5  3  TM2       TM2 domain


Domain annotation for each model (and alignments):
>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   1.0      0.21   1.9e+03      34      45 ..      18      29 ..       5      42 .. 0.66
   2 ?   -1.7   4.3      0.25   2.2e+03      24      43 ..      38      57 ..      13      61 .. 0.66
   3 !   16.4   7.7   5.5e-07    0.0049       2      45 ..      73     115 ..      72     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.21
                               SPW 34 GavvavLalafa 45
                                      G+++ + a+++ 
  gi|336255410|ref|YP_004598517.1| 18 GLAAGISAFVMV 29
                                      444444444443 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.25
                               SPW 24 tgaawnnvivGavvavLala 43
                                        + ++n  +Ga   +La +
  gi|336255410|ref|YP_004598517.1| 38 GWMGIHNFLIGATMSALASI 57
                                      34667889999988888865 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 5.5e-07
                               SPW   2 WanlllGlwlivSPWvlGfsattgaawnnvivGavvavLalafa 45 
                                       +++ llG+w++++P+v+G+s    +   n  +G++va+L+l+ a
  gi|336255410|ref|YP_004598517.1|  73 GLLALLGIWTAAAPFVFGVSRP-LVLQVNGAAGILVAILSLVSA 115
                                       7899**************7766.66667778********99865 PP

>> TM2  TM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   4.6e-06     0.041       7      33 ..      27      55 ..      22      61 .. 0.78
   2 ?    1.3   0.1     0.051   4.5e+02       6      17 ..      70      80 ..      64      93 .. 0.74
   3 ?   -2.0   0.1      0.52   4.6e+03      31      38 ..     104     111 ..      95     119 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-06
                               TM2  7 vaylLwff..LGglGvHRFYlGktgsGvl 33
                                      v++  ++f   G+ G+H+F  G t s+++
  gi|336255410|ref|YP_004598517.1| 27 VMVSVAVFtiTGWMGIHNFLIGATMSALA 55
                                      55555554449*************99987 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.051
                               TM2  6 lvaylLwffLGg 17
                                      ++a+lL++ LG+
  gi|336255410|ref|YP_004598517.1| 70 VLAGLLAL-LGI 80
                                      56777777.553 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.52
                               TM2  31 Gvlqlltf 38 
                                       G+l ++++
  gi|336255410|ref|YP_004598517.1| 104 GILVAILS 111
                                       34444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1114.89
//
Query:       gi|336255411|ref|YP_004598518.1|  [L=255]
Description: Geranylgeranylglyceryl phosphate synthase [Halopiger xanaduensis SH-6]
Scores for complete 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  115.8   0.5    4.6e-33  114.6   0.5    1.5  1  PcrB          PcrB family
    0.00013   21.5   0.0    0.00023   20.7   0.0    1.4  1  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.036   13.1   0.0      0.055   12.6   0.0    1.2  1  Dus           Dihydrouridine synthase (Dus)
      0.093   13.0   0.0        3.1    8.1   0.0    2.3  2  OKR_DC_1_N    Orn/Lys/Arg decarboxylase, N-terminal domain


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 !  114.6   0.5     1e-36   4.6e-33       3     220 ..       5     250 ..       2     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 1e-36
                                       GGGTSEEEEE-TTSS-CHHHHHHHHCTT-SEEEEECSTCHHHHHHHHHHHHHCT..SSS-EEEEESSGGG--TT.SS CS
                              PcrB   3 ileerhltklDPeeenpdEiveiviesgtDavmigGsqsvtldntvrllkkvsr..iklPivlepsnvegvvry.aD 76 
                                       + +  h tk+DP + +p + +e +   gtD v++gGs++vt +nt+++++ +     +lPi  ep   + v+ + +D
  gi|336255411|ref|YP_004598518.1|   5 WDNTTHATKIDPAKPLPSD-LEPL--TGTDLVIVGGSDGVTAENTLETIEAIDAsfPDLPIFQEPYRSDHVSTEtID 78 
                                       44455***********987.5777..7***********************98542269*************975355 PP

                                       EEEEEEETTBSSTT..TTTH...........................HHHHHHHHHHHHHHCTEEEEEEEEEBTTTS CS
                              PcrB  77 alFvmsllnsanad..Wivg...........................ahalglkkvkklieseeilaegYlvvePds 124
                                       a+ + s+    n+d    vg                           +  +g+  v +l+  e+++ egY++    s
  gi|336255411|ref|YP_004598518.1|  79 AVDYLSIAAVYNGDreHFVGkhvdlfaevgqkpdellgssvpligdlVASKGIDAVANLT--EKVIGEGYVIQHLSS 153
                                       555555544444432256777*************************9999*********9..99************* PP

                                       HHHHHTTB-B-TTHHHHHHHHHHHHHHTT-SEEEEE-TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC CS
                              PcrB 125 kvaavteakvdlnkediaayallaakllglrliYlEasGaledveevialkkklekarlivGGGirsaEkAkevvea 201
                                       ++a  + +++    e++a +al ++ l+g++++Y+E+sG+++ +e v+a  + le++ l++GGGi+sa kA e++ a
  gi|336255411|ref|YP_004598518.1| 154 AAANRAGVEAAYSPEQVAGAALATESLYGFPIFYVEYSGTYGGPEDVQAAARYLEDTALFYGGGIDSAAKADEILAA 230
                                       ***************************************************************************** PP

                                       .SSEEEE-CHHHHHHHCHHH CS
                              PcrB 202 .ADvivvGnvveekderkid 220
                                        AD+ivvG+  ++++e+  +
  gi|336255411|ref|YP_004598518.1| 231 gADAIVVGDCFHDDPETFRE 250
                                       ************99976555 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   5.1e-08   0.00023      71     115 ..     209     251 ..     191     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.1e-08
                                       H-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHH CS
                      His_biosynth  71 evfipvqvGGGIrsledveelleagadkviigtaavknpelikel 115
                                            +  GGGI s  +++e+l agad +++g +  ++pe ++e 
  gi|336255411|ref|YP_004598518.1| 209 D--TALFYGGGIDSAAKADEILAAGADAIVVGDCFHDDPETFRET 251
                                       4..67899********************************99875 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.2e-05     0.055     185     225 ..     211     250 ..     198     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
                                       -EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH CS
                               Dus 185 pviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae 225
                                        ++  G+I +a +a++il+  Gad++++g +   +P  f+e
  gi|336255411|ref|YP_004598518.1| 211 ALFYGGGIDSAAKADEILAA-GADAIVVGDCFHDDPETFRE 250
                                       56778**************9.****************9984 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00069       3.1      48     104 ..      44     101 ..      20     106 .. 0.77
   2 ?    2.6   0.0     0.035   1.5e+02      90     109 ..     204     223 ..     181     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00069
                        OKR_DC_1_N  48 deaaelldeirernedlPvFllaetrtsedvpadvlreid...gfielledtpefiarqi 104
                                       +++ e +++i++  +dlP+F      +s++v+ + ++ +d       ++ d ++f+++++
  gi|336255411|ref|YP_004598518.1|  44 ENTLETIEAIDASFPDLPIFQEPY--RSDHVSTETIDAVDylsIAAVYNGDREHFVGKHV 101
                                       78899***************7655..8888888888888733122344777777777776 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.035
                        OKR_DC_1_N  90 ielledtpefiarqieaaak 109
                                         +ledt+ f+++ i +aak
  gi|336255411|ref|YP_004598518.1| 204 ARYLEDTALFYGGGIDSAAK 223
                                       5699**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); 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:                         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 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2048.88
//
Query:       gi|336255412|ref|YP_004598519.1|  [L=135]
Description: TRAM domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-15   54.9   4.2    7.4e-15   54.7   3.4    1.5  2  TRAM      TRAM domain


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.48   8.6e+03       5      11 ..      39      45 ..      37      54 .. 0.63
   2 !   54.7   3.4   4.1e-19   7.4e-15       3      61 ..      75     130 ..      73     131 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.48
                                      XXEEEEE CS
                              TRAM  5 GstqeVl 11
                                      G++++V 
  gi|336255412|ref|YP_004598519.1| 39 GEVYRVA 45
                                      6666663 PP

  == domain 2  score: 54.7 bits;  conditional E-value: 4.1e-19
                                       XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61 
                                        vG+t  V++e+ + ++g+gi+r+++g+v++vpg+    G++V++++t+vk++++ Ge+
  gi|336255412|ref|YP_004598519.1|  75 DVGETRYVEIEDIG-KQGDGIARVERGYVIIVPGADV--GERVKIEVTEVKSNFAVGEI 130
                                       69************.*******************999..******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1156.71
//
Query:       gi|336255413|ref|YP_004598520.1|  [L=582]
Description: Radical SAM domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   47.5   0.0    2.2e-11   44.4   0.0    2.6  2  Radical_SAM  Radical SAM superfamily
    0.00013   21.6   0.0    0.00041   20.1   0.0    1.8  1  HHH          Helix-hairpin-helix motif
    0.00027   21.1   0.0    0.00058   20.1   0.0    1.5  1  HHH_3        Helix-hairpin-helix motif
     0.0053   17.3   0.0      0.014   16.0   0.0    1.7  1  HHH_5        Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.057   13.4   0.0    1.7  1  PsbU         Photosystem II 12 kDa extrinsic protein (PsbU)
      0.051   13.7   0.0       0.16   12.1   0.0    1.8  2  HHH_2        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 ?   -1.6   0.0       1.1   3.1e+03     136     158 ..      38      63 ..      34      71 .. 0.82
   2 !   44.4   0.0   7.2e-15   2.2e-11       2     141 ..     193     345 ..     192     395 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                                       HHHHTTSET...EEEEEEEBTTTSHH CS
                                       xxxxxxxxx...xxxxxxxxxxxxxx RF
                       Radical_SAM 136 klreagikr...vvdrivglpGende 158
                                       +l +ag++r   ++++i gl+ e d+
  gi|336255413|ref|YP_004598520.1|  38 ALVDAGVPReriTYHTIDGLRDEPDR 63 
                                       67899999999999999999999987 PP

  == domain 2  score: 44.4 bits;  conditional E-value: 7.2e-15
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE...........SSTGGGS....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxx....... RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilg...........ggeplly....... 60 
                                       +++rgC++rCsfC+ p     +g + ++++  ++ ev++l  + gv+++ +g           g    +        
  gi|336255413|ref|YP_004598520.1| 193 ETSRGCAYRCSFCTEP----LYGNPSFRPPPTVVGEVDAL-SDYGVRHFRIGrqadilayggdG---EAPnpdalrq 261
                                       689*************....79******************.5999*******977777775432...2213323344 PP

                                       .....TTHHHHHHHHHHTCCCTEEEEEEECSSCHG..HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHH CS
                                       .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  61 .....pdfvellerlaklavpgiritvetngtlpd..eeklerllelg..vdrvslgleaaddekvlklmnrghtfe 128
                                            ++ + +le l+    +   it++  +   +  +e ++ ++e +   d+ ++gle+ad+  v++ +n + + e
  gi|336255413|ref|YP_004598520.1| 262 lysgiREVAPDLETLHLD--NMNPITIVEWP---EksREGIRIIAEHNtpGDTAAFGLESADPL-VQEENNLNVSAE 332
                                       443333333333333333..33333333333...355*********99****************.******99**** PP

                                       HHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 129 evlealeklreag 141
                                       e  ea+++ +e  
  gi|336255413|ref|YP_004598520.1| 333 ECFEAVKIVNEEA 345
                                       ********99865 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.4e-07   0.00041       5      26 ..     520     541 ..     518     543 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.4e-07
                                       HHTSSHHHHHTSTT-SHHHHHH CS
                               HHH   5 lipasreeLlalPGVGpktAea 26 
                                       l++as++eL+a+PG+G  tA+ 
  gi|336255413|ref|YP_004598520.1| 520 LNDASMDELTAIPGIGDRTAGD 541
                                       799*************999985 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     2e-07   0.00058       6      45 ..     518     553 ..     516     553 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2e-07
                             HHH_3   6 vdiNtAsaeeLqklpGlgpklAknIvayReknGpfksree 45 
                                        d+N As +eL+ +pG+g+++A  +v  R    p++s+ +
  gi|336255413|ref|YP_004598520.1| 518 LDLNDASMDELTAIPGIGDRTAGDLVINR----PYESVAD 553
                                       69***************************....9999875 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.8e-06     0.014      16      52 ..     501     543 ..     494     546 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.8e-06
                                       HHHHTTT--SHH......HHHHS-HHHHHTSTTS-HHHHHHHH CS
                             HHH_5  16 lallsaGiesve......dlaaadveeLakipGiGkktAerii 52 
                                       +a++++G++sv       dl +a+ +eL++ipGiG +tA  ++
  gi|336255413|ref|YP_004598520.1| 501 VAVVDHGYRSVTgvpyplDLNDASMDELTAIPGIGDRTAGDLV 543
                                       578888888876666677999******************8775 PP

>> PsbU  Photosystem II 12 kDa extrinsic protein (PsbU)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.9e-05     0.057      13      51 ..     516     554 ..     504     562 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                                       TSEETTTS-GGGGGGSTTTTTHHHHHHHHS---SSGGGG CS
                              PsbU  13 ekvDlnnanvrafrqlrGlyPtlakkivknaPYdsvedv 51 
                                         +Dln+a++ +   ++G+    a+ +v n PY+sv d 
  gi|336255413|ref|YP_004598520.1| 516 YPLDLNDASMDELTAIPGIGDRTAGDLVINRPYESVADA 554
                                       569*********************************996 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.4   1.3e+04      42      56 ..     423     437 ..     421     441 .. 0.66
   2 ?   12.1   0.0   5.3e-05      0.16      29      50 ..     520     541 ..     518     544 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.4
                             HHH_2  42 diGeeiAqsivefFe 56 
                                       d G eiA++ ++ F+
  gi|336255413|ref|YP_004598520.1| 423 DTGAEIAKEHKKLFK 437
                                       567777777666665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.3e-05
                             HHH_2  29 LkkasleeLlevddiGeeiAqs 50 
                                       L +as++eL+++++iG+++A +
  gi|336255413|ref|YP_004598520.1| 520 LNDASMDELTAIPGIGDRTAGD 541
                                       899***************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 0.52u 0.20s 00:00:00.72 Elapsed: 00:00:00.36
# Mc/sec: 4875.39
//
Query:       gi|336255414|ref|YP_004598521.1|  [L=52]
Description: hypothetical protein Halxa_4037 [Halopiger xanaduensis SH-6]
Scores for 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:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.32u 0.19s 00:00:00.51 Elapsed: 00:00:00.33
# Mc/sec: 470.05
//
Query:       gi|336255415|ref|YP_004598522.1|  [L=166]
Description: heat shock protein Hsp20 [Halopiger xanaduensis SH-6]
Scores for 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-05   22.8   0.0    0.00012   22.1   0.0    1.4  1  HSP20       Hsp20/alpha crystallin family
  ------ inclusion threshold ------
       0.12   12.0   0.0       0.34   10.5   0.0    1.8  1  ArsA_HSP20  HSP20-like domain found in ArsA


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 !   22.1   0.0   1.4e-08   0.00012       1      91 [.      34     127 ..      34     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.4e-08
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STT..B-TTT-EEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPen..vdadkvkas 75 
                                       d+ e++e++ v +d pg ++e+++v +  ++v ++ e+  e  ++  ++   +  + + + +LP +  v++d+ +a+
  gi|336255415|ref|YP_004598522.1|  34 DVLENDEAYLVVFDAPGAEPEDVQVRYLSGSVKIHIERFREFREGYEMRFPGRGMELEGEAELPADalVNPDAGTAT 110
                                       6789*********************************9955555555555566778999******74479******* PP

                                       E.ETTEEEEEEEBSS-- CS
                             HSP20  76 l.kdGvLtvtvpkkepe 91 
                                       l + G  ++++pk  + 
  gi|336255415|ref|YP_004598522.1| 111 LtESGTVRIEIPKADST 127
                                       *************8765 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 ?   10.5   0.0   3.8e-05      0.34       2      35 ..      40      73 ..      39      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.8e-05
                        ArsA_HSP20  2 deyvlkldLPfvdkeeidlsrsgdeLtIkignfr 35
                                        y ++ d P++++e+++++       I+i++fr
  gi|336255415|ref|YP_004598522.1| 40 EAYLVVFDAPGAEPEDVQVRYLSGSVKIHIERFR 73
                                      679999************************9998 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:                      369  (0.0205812); 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: 0.38u 0.19s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1478.69
//
Query:       gi|336255416|ref|YP_004598523.1|  [L=420]
Description: FAD dependent oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-58  197.7  10.1    4.5e-58  197.5  10.1    1.0  1  DAO             FAD dependent oxidoreductase
      6e-09   35.5   2.0    0.00068   19.0   0.4    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.2e-07   31.8   3.3    1.2e-07   31.8   3.3    2.2  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.6e-06   26.1   1.0    1.1e-05   25.2   1.0    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
    3.8e-05   23.0   1.7    3.8e-05   23.0   1.7    1.8  2  FAD_binding_2   FAD binding domain
    3.9e-05   23.2   3.9    6.1e-05   22.6   3.9    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
    0.00017   21.5   0.7    0.00034   20.5   0.7    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.001   19.6   0.7     0.0028   18.2   0.7    1.8  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0036   16.4   2.1     0.0043   16.2   1.2    1.5  2  GIDA            Glucose inhibited division protein A
     0.0037   16.0   1.1     0.0073   15.0   0.8    1.6  2  HI0933_like     HI0933-like protein
     0.0052   16.1   0.3     0.0099   15.2   0.3    1.4  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0055   17.1   0.0      0.011   16.2   0.0    1.6  1  NAD_binding_7   Putative NAD(P)-binding
     0.0074   15.7   0.3      0.013   14.8   0.3    1.3  1  ThiF            ThiF family
     0.0093   15.2   1.1       0.02   14.2   1.1    1.5  1  Thi4            Thi4 family
  ------ inclusion threshold ------
       0.02   14.3   0.2      0.035   13.5   0.2    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.031   13.5   1.2      0.031   13.5   1.2    2.0  2  FAD_binding_3   FAD binding domain
      0.069   12.9   0.2       0.14   11.8   0.1    1.5  1  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
      0.069   13.1   2.3          5    7.1   0.3    2.4  2  NAD_binding_9   FAD-NAD(P)-binding
      0.069   12.4   2.2        1.9    7.7   0.3    2.4  2  Amino_oxidase   Flavin containing amine oxidoreductase
        0.1   12.7   0.3       0.23   11.6   0.1    1.7  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
       0.14   11.7   0.1       0.21   11.1   0.1    1.2  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.5  10.1   5.2e-61   4.5e-58       2     351 ..      37     384 ..      36     385 .. 0.83

  Alignments for each domain:
  == domain 1  score: 197.5 bits;  conditional E-value: 5.2e-61
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelg 76 
                                       v+++G+G iG+++Ay+Lar+g  Vtl+++g+ ag g+Sgr++g+++ +++++ +a    + + +a+e++r+l+++  
  gi|336255416|ref|YP_004598523.1|  37 VAVVGAGAIGATAAYDLAREGadVTLYDRGPVAG-GSSGRAAGICYDAFADPLDA----EIAGDAIERFRALSGDD- 107
                                       9*******************9*********8888.**************988877....9*************984. PP

                                       STTSEEEEEEEEEES..SHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT..STTTSEEEEETTEEEEEHHHHH CS
                               DAO  77 ididyrrtGllslaa..deeelealdkllallleagldaelldaeevrelepa..lpgllgalfypdtgqvdpaklt 149
                                         +++ ++ +++la+  d+e   a+++++++ ++ g+ a  +da+ ++e++pa  ++++  a     +g  dpak+t
  gi|336255416|ref|YP_004598523.1| 108 -TFPFVECPYVWLARegDDERATAIREQVERMQAEGVVALEMDADALAERFPAlrTDDVEVAAIAGAAGYTDPAKYT 183
                                       .39***********97655556679999999999999763489999******9655599999999999********* PP

                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.HHHTT.CTTTSEEEEEEEEE CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd.llgll.keldlpispvrgqv 224
                                       a la+aa  +G+++  +t+v+     d   ++v + ++g+++++dav +aaGa+++  l+ +  ++   ++p r q 
  gi|336255416|ref|YP_004598523.1| 184 ACLAAAADGAGATLAPETPVEVR-T-D--PSRV-VLEDGTEREVDAVLVAAGAHTKrVLADAgVPI--AMKPYRVQA 253
                                       ********************854.3.3..3455.3444777779************6444444444..345655555 PP

                                       ..EEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSE....EETTCSS..TSCSHHHHHHHHHHHH CS
                               DAO 225 ..lvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtad....eesgddd..pevdeedidellealr 293
                                          +++ +     + aa+l +p   d  +g+yv+p +dg +l+G   +    +   +d+   ++d++  ++lle++r
  gi|336255416|ref|YP_004598523.1| 254 lvATVDGKGGGSGAGAAGLEEPTCYDATGGFYVRPHPDG-ILAGDGTEeveaD---PDEyeRDADPDFPADLLERVR 326
                                       105556666666666788888889999**********99.9996555444322...222577999999999****** PP

                                       HHSGG.GCGEEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                               DAO 294 klfPq.lgdvlrkwaGlrp.lpdglpligetpgvkglylatGhsghGltlapatGkllae 351
                                       ++fP+   dv r+waGl + +pd++pl+g+    +gly++tG+ ghG++ apa+G  +ae
  gi|336255416|ref|YP_004598523.1| 327 HRFPDrEFDVDRSWAGLCTaTPDRDPLVGRL--EDGLYVVTGFQGHGFMRAPAIGARIAE 384
                                       *****5478*******99967*********6..79*********************9998 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 !   19.0   0.4     8e-07   0.00068       2      36 ..      36      69 ..      35     155 .. 0.73
   2 !   16.1   0.1   5.9e-06     0.005     184     252 ..     181     244 ..     142     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtcl 36
                                      +v+v+G+G+ G +aa +la+ ga+vtl+ ++g + 
  gi|336255416|ref|YP_004598523.1| 36 EVAVVGAGAIGATAAYDLAREGADVTLY-DRGPVA 69
                                      599*************************.544433 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5.9e-06
                                       HHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglel 252
                                       + +a+l++a    G ++  +t v e++ +++  +vvledg+e ++d v+va+G   ++ l+  ++g+++
  gi|336255416|ref|YP_004598523.1| 181 KYTACLAAAADGAGATLAPETPV-EVRTDPS--RVVLEDGTEREVDAVLVAAGAHTKRVLA--DAGVPI 244
                                       56677777777788888877777.9999998..9***********************9985..778776 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 !   31.8   3.3   1.4e-10   1.2e-07       1      35 [.      39      73 ..      39      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.4e-10
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      +vGaG+ G++aAy La++g+dv+l+++++  GG +
  gi|336255416|ref|YP_004598523.1| 39 VVGAGAIGATAAYDLAREGADVTLYDRGPVAGGSS 73
                                      8*******************************986 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   1.0   1.2e-08   1.1e-05       1      31 [.      37      67 ..      37      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.2e-08
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                      +a++GaGaiG + a+ La+ gadvtl++r++
  gi|336255416|ref|YP_004598523.1| 37 VAVVGAGAIGATAAYDLAREGADVTLYDRGP 67
                                      69***************************87 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   1.7   4.5e-08   3.8e-05       2      44 ..      37      79 ..      36     107 .. 0.85
   2 ?   -1.0   0.1      0.83   7.1e+02     166     168 ..     211     213 ..     116     273 .. 0.58

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.5e-08
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S- CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGg 44
                                      v V+G+G+ G +AA+ +a++G++v++ + +++ gg++  + G 
  gi|336255416|ref|YP_004598523.1| 37 VAVVGAGAIGATAAYDLAREGADVTLYDRGPVAGGSSGRAAGI 79
                                      89**********************************9999986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.83
                                       EEE CS
                     FAD_binding_2 166 eLi 168
                                       +++
  gi|336255416|ref|YP_004598523.1| 211 RVV 213
                                       222 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   3.9   7.1e-08   6.1e-05       1      69 [.      36     102 ..      36     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.1e-08
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrq 69 
                                       +v VvG+g+ G +AA+  ar+Ga v L ++ +v GG + ++++   + +   + +   ia++ +er r+
  gi|336255416|ref|YP_004598523.1|  36 EVAVVGAGAIGATAAYDLAREGADVTLYDRGPVAGGSSGRAAGICYDAFA--DPLDAEIAGDAIERFRA 102
                                       599*********************************99998887666655..55566666666666655 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 !   20.5   0.7     4e-07   0.00034       2      31 ..      37      66 ..      36      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4e-07
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdis 31
                                      vav+GaG +Ga  a+ +a++g +V+l+d+ 
  gi|336255416|ref|YP_004598523.1| 37 VAVVGAGAIGATAAYDLAREGADVTLYDRG 66
                                      9***************************85 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.7   3.3e-06    0.0028       2      32 ..      37      67 ..      36      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.3e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                      v+vvG+G ig  +A  la+ g++Vt+ +r++
  gi|336255416|ref|YP_004598523.1| 37 VAVVGAGAIGATAAYDLAREGADVTLYDRGP 67
                                      89************************99987 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.2     5e-06    0.0043       2      29 ..      37      69 ..      36     105 .. 0.81
   2 ?   -3.3   0.0       4.2   3.6e+03     130     152 ..     211     233 ..     204     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5e-06
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE.....E CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi.....t 29
                                      v V+G+G  G  AA+ +ar Ga+v+L+     +
  gi|336255416|ref|YP_004598523.1| 37 VAVVGAGAIGATAAYDLAREGADVTLYdrgpvA 69
                                      89************************9555542 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.2
                                       EEEETTS-EEEECEEEE--TT-B CS
                              GIDA 130 gvvtedgetikakavviatGtfl 152
                                        vv+edg++ + +av +a+G+  
  gi|336255416|ref|YP_004598523.1| 211 RVVLEDGTEREVDAVLVAAGAHT 233
                                       5899999999999*****99954 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.8   8.6e-06    0.0073       2      35 ..      36      69 ..      35      73 .. 0.92
   2 ?   -2.8   0.0       2.2   1.9e+03     114     164 ..     185     231 ..     182     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.6e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35
                                      +v+v+G+Ga G  aA  +a++g++V+l+++++ +
  gi|336255416|ref|YP_004598523.1| 36 EVAVVGAGAIGATAAYDLAREGADVTLYDRGPVA 69
                                      69***************************98765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.2
                                       HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       +l ++++ ag +l  et v+   + + +  rv +++++e e d++++A G 
  gi|336255416|ref|YP_004598523.1| 185 CLAAAADGAGATLAPETPVEVR-T-DPS--RVVLEDGTEREVDAVLVAAGA 231
                                       6777777777777777777544.3.333..466667999999999999996 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 !   15.2   0.3   1.2e-05    0.0099     163     198 ..      33      68 ..      21      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                       Pyr_redox_3 163 agqkvvViGgknSavDaAlelvrkgaeVtvvtrgse 198
                                       ag +v+V+G++  ++ aA++l+r+ga+Vt+++rg  
  gi|336255416|ref|YP_004598523.1|  33 AGLEVAVVGAGAIGATAAYDLAREGADVTLYDRGPV 68 
                                       5779*****************************975 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 !   16.2   0.0   1.3e-05     0.011       7      38 ..      34      65 ..      30     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                     NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvap 38
                                      g +v vvG+G ++a+ ++ l+++ga+vt+++ 
  gi|336255416|ref|YP_004598523.1| 34 GLEVAVVGAGAIGATAAYDLAREGADVTLYDR 65
                                      6789************************9875 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   1.6e-05     0.013       9      49 ..      25      64 ..      17      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  9 gedgqekLrdskvllvGaGglGsellknLalsGvgkltlvD 49
                                      ++++ e+ +  +v++vGaG++G  ++ +La+ G   +tl D
  gi|336255416|ref|YP_004598523.1| 25 ADAFTEQGAGLEVAVVGAGAIGATAAYDLAREGA-DVTLYD 64
                                      447777778899*******************995.466666 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.1   2.3e-05      0.02      18      57 ..      35      73 ..      27      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                                       +v++vGaG+ G taay la++ +  v++ +r    GG +
  gi|336255416|ref|YP_004598523.1| 35 LEVAVVGAGAIGATAAYDLARE-GADVTLYDRGPVAGGSS 73
                                      579*******************.99999999987777755 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 ?   13.5   0.2   4.1e-05     0.035      34      69 ..      32      67 ..      23      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-05
                                      GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
                      2-Hacid_dh_C 34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrsk 69
                                       +g +v+++G+G+IG ++a  l+  g++v+ ydr +
  gi|336255416|ref|YP_004598523.1| 32 GAGLEVAVVGAGAIGATAAYDLAREGADVTLYDRGP 67
                                      57889****************************976 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.2   3.6e-05     0.031       3      36 ..      36      69 ..      34      81 .. 0.84
   2 ?   -0.5   0.1      0.66   5.6e+02     128     178 ..     157     207 ..     126     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.6e-05
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                      +V++VGaG  G+++a  L++ G +v+l ++   +
  gi|336255416|ref|YP_004598523.1| 36 EVAVVGAGAIGATAAYDLAREGADVTLYDRGPVA 69
                                      8**************************9997655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.66
                                       EECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEE CS
                     FAD_binding_3 128 vesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgiefeg 178
                                       + +l+ d+ +v+a +         + +a   ++aDG+  t + + ++e+++
  gi|336255416|ref|YP_004598523.1| 157 FPALRTDDVEVAAIAGAAGYTDPAKYTACLAAAADGAGATLAPETPVEVRT 207
                                       667777777777777644444444677788889999999988888888543 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00017      0.14     118     165 ..     133     180 ..     126     184 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                        Hydant_A_N 118 evderveadgevlkpldeeevrealkalkaagvesiavvllhSylnpe 165
                                       e  er++a+g v  ++d +++ e   al+ ++ve  a++ +  y+ p+
  gi|336255416|ref|YP_004598523.1| 133 EQVERMQAEGVVALEMDADALAERFPALRTDDVEVAAIAGAAGYTDPA 180
                                       5569****************************************9997 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 ?    7.1   0.3    0.0059         5       1      37 [.      38      70 ..      38      77 .. 0.85
   2 ?    5.6   0.1     0.017        15     127     154 ..     203     230 ..     182     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0059
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.g 37
                                      a+vGaG+ G++++  L+++       ++tl+d+ +  g
  gi|336255416|ref|YP_004598523.1| 38 AVVGAGAIGATAAYDLARE-----GADVTLYDRGPVaG 70
                                      89****************9.....59999999977734 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.017
                     NAD_binding_9 127 leeradgqavlladgaslaadaVvLAlG 154
                                       +e r d  +v+l+dg++ ++daV +A G
  gi|336255416|ref|YP_004598523.1| 203 VEVRTDPSRVVLEDGTEREVDAVLVAAG 230
                                       44556666799***************99 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3    0.0022       1.9       5      28 ..      48      71 ..      46      94 .. 0.89
   2 ?    4.0   0.1      0.03        25     235     263 ..     206     232 ..     197     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0022
                                      HHHHHHHHTTEEEEEEESSSSSBT CS
                     Amino_oxidase  5 aaArqLlsaGfdVtvlEardrvGG 28
                                      +aA+ L++ G dVt++   + +GG
  gi|336255416|ref|YP_004598523.1| 48 TAAYDLAREGADVTLYDRGPVAGG 71
                                      7**********************9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.03
                                       EEETTCEEEEETTSTEEEESEEEE-S-HH CS
                     Amino_oxidase 235 kregdgvtvtledgevveaDaVvvTvplg 263
                                       +++++  +v ledg+++e+DaV+v++   
  gi|336255416|ref|YP_004598523.1| 206 RTDPS--RVVLEDGTEREVDAVLVAAGAH 232
                                       44444..56668*************9865 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 ?   11.6   0.1   0.00027      0.23       2      32 ..      37      67 ..      36      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                                      EEEE--SHHHHHHHHHHHHTT-EEEEE-SSH CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtk 32
                                      ++++G G +G+  a  l+++g +v++y+r +
  gi|336255416|ref|YP_004598523.1| 37 VAVVGAGAIGATAAYDLAREGADVTLYDRGP 67
                                      89**************************965 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 ?   11.1   0.1   0.00025      0.21       2      30 ..      36      64 ..      35      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE- CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvD 30
                                      +++v+G+G +G++ a  la+ g +v++ D
  gi|336255416|ref|YP_004598523.1| 36 EVAVVGAGAIGATAAYDLAREGADVTLYD 64
                                      599***********************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3265.64
//
Query:       gi|336255417|ref|YP_004598524.1|  [L=269]
Description: hypothetical protein Halxa_4040 [Halopiger xanaduensis SH-6]
Scores for 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:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2043.15
//
Query:       gi|336255418|ref|YP_004598525.1|  [L=195]
Description: NUDIX hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-14   51.8   0.1    1.1e-13   51.4   0.1    1.2  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
       0.15   12.0   0.0       0.23   11.3   0.0    1.3  1  DUF3943   Domain of unknown function (DUF3943)


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 !   51.4   0.1   1.2e-17   1.1e-13       2     115 ..      23     136 ..      22     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 1.2e-17
                                       EEEEEEEEEEETTSE..EEEEEES..SSSTTT.EESSEEECBTTS.HHHHHHHHHHHHHHSEEEEEEEEEEEEEEEE CS
                             NUDIX   2 lrravgvvllnekge..vLlvrrs..kkpfpg.WelPgGkvepgE.tpeeAArREleEEtGleaellellgrlhyla 72 
                                       + +av + + +++ge  +L +rr+     +pg  ++PgG+ ep + ++ e+A+RE+ EE+Gl++ + +++g+l++ +
  gi|336255418|ref|YP_004598525.1|  23 YDAAVLAPIVDRDGEdyLLFTRRAddLGEHPGqMSFPGGGAEPIDdSILETALREADEEIGLTPAEADVVGQLDDIR 99 
                                       56799999********9999999999444444489********888*************************776655 PP

                                       EEEEEEEEEEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHH CS
                             NUDIX  73 pydgpygdeheilyvfleevegelepndenevsevrwvpleel 115
                                       ++++      + +  f+++v ++   +d  ev+e+ ++pl  l
  gi|336255418|ref|YP_004598525.1| 100 TVTE------YAVTPFVARVPDREYERDGREVAEIVLLPLSGL 136
                                       5543......333344444444444444888888888887777 PP

>> DUF3943  Domain of unknown function (DUF3943)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.6e-05      0.23      14      54 ..     147     185 ..     136     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.6e-05
                           DUF3943  14 vgHpyaGslyylaaRsaglsfwesllyallgStlwElgvEf 54 
                                         Hpy G ++  ++R  g+++w ++   l+   l El+ Ef
  gi|336255418|ref|YP_004598525.1| 147 REHPYYGDIVIHYFRVDGYTVWGATGRILV--QLLELATEF 185
                                       57*********************9875544..456777774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1607.25
//
Query:       gi|336255419|ref|YP_004598526.1|  [L=165]
Description: hypothetical protein Halxa_4042 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0093   15.8   2.1      0.018   14.9   0.2    2.1  2  PUB_1     PNGase/UBA- or UBX-containing domain


Domain annotation for each model (and alignments):
>> PUB_1  PNGase/UBA- or UBX-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1     0.043   7.8e+02      16      41 ..      27      52 ..      18      63 .. 0.62
   2 !   14.9   0.2     1e-06     0.018      12      40 ..     114     142 ..     105     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.043
                             PUB_1 16 LasALrkDsgqaFslEqLrpLLdtsL 41
                                      L +A  +  gq+   + L + ++ +L
  gi|336255419|ref|YP_004598526.1| 27 LSEAAYRADGQSVDEDALEAAIEDAL 52
                                      44445567788877777776666655 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1e-06
                             PUB_1  12 AREELasALrkDsgqaFslEqLrpLLdts 40 
                                        RE L +AL  Ds+   s E Lr+LLd s
  gi|336255419|ref|YP_004598526.1| 114 FREALEEALPDDSSGDVSEERLRRLLDVS 142
                                       5999***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1408.55
//
Query:       gi|336255420|ref|YP_004598527.1|  [L=422]
Description: cell wall biogenesis glycosyltransferase [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.16   12.1   0.1       0.81    9.9   0.0    2.1  2  HupF_HypC  HupF/HypC family


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 ?    9.9   0.0   4.5e-05      0.81      16      45 ..     129     158 ..     109     165 .. 0.76
   2 ?   -1.5   0.0      0.16   2.9e+03      21      38 ..     293     310 ..     280     313 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 4.5e-05
                                       EEEEECTTEEEEEEGTTCTTB-TT-EEEEE CS
                         HupF_HypC  16 lAlvdvgGvrrevslalveevkvGdyVLvh 45 
                                        +l+   G  r+v lal + ++ G+yV+vh
  gi|336255420|ref|YP_004598527.1| 129 AGLAGEFGKGRDVWLALGPAAEAGEYVVVH 158
                                       4444455889******************** PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.16
                                       CTTEEEEEEGTTCTTB-T CS
                         HupF_HypC  21 vgGvrrevslalveevkv 38 
                                       ++G +rev  +l+  ++ 
  gi|336255420|ref|YP_004598527.1| 293 LEGMSREVAAELLRVLEE 310
                                       569999999999865555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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 0.20s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3374.07
//
Query:       gi|336255421|ref|YP_004598528.1|  [L=56]
Description: hypothetical protein Halxa_4044 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0015   18.5   1.3      0.025   14.5   0.1    2.2  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
     0.0079   16.2   0.3      0.011   15.8   0.3    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.026   14.5   1.2      0.095   12.7   1.2    1.7  1  zinc-ribbons_6  zinc-ribbons
      0.047   13.9   1.9      0.078   13.3   1.9    1.4  1  zinc_ribbon_9   zinc-ribbon
       0.14   12.1   2.9        0.4   10.7   0.2    2.2  2  Nudix_N_2       Nudix N-terminal


Domain annotation for each model (and alignments):
>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.028     1e+02      20      26 ..      21      27 ..      17      28 .. 0.84
   2 !   14.5   0.1     7e-06     0.025      19      29 ..      42      52 ..      40      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.028
                    PhnA_Zn_Ribbon 20 lvCpeCa 26
                                      lvC eC 
  gi|336255421|ref|YP_004598528.1| 21 LVCGECE 27
                                      89****5 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 7e-06
                    PhnA_Zn_Ribbon 19 llvCpeCahEw 29
                                      + +Cp+C +Ew
  gi|336255421|ref|YP_004598528.1| 42 VRICPDCDSEW 52
                                      669******** PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3     3e-06     0.011      13      37 ..      21      51 ..      13      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3e-06
                               DZR 13 rfCseCgtklkavaa......edrCpsCgek 37
                                       +C+eC ++lk +++       + Cp C+++
  gi|336255421|ref|YP_004598528.1| 21 LVCGECEKPLKTENDpdsiktVRICPDCDSE 51
                                      58********97777*****99******986 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.2   2.7e-05     0.095      15      41 ..      19      54 ..      10      56 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                                      SEEE-TTT--.........EEEEEEE-SSS-S---E CS
                    zinc-ribbons_6 15 eqyhCeaCqe.........dlkkealCpeCeqelev 41
                                      +++ C +C++         ++k + +Cp+C++e + 
  gi|336255421|ref|YP_004598528.1| 19 DRLVCGECEKplktendpdSIKTVRICPDCDSEWKE 54
                                      677899999999999988889999999999988665 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.9   2.2e-05     0.078       5      29 ..      23      50 ..      19      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                     zinc_ribbon_9  5 ChqCdrfVsvspdedsd..v.lCPhCgg 29
                                      C +C + +  + d ds+  v +CP+C++
  gi|336255421|ref|YP_004598528.1| 23 CGECEKPLKTENDPDSIktVrICPDCDS 50
                                      6689999999988888876378****98 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   0.00011       0.4      16      29 ..      14      27 ..       4      28 .. 0.89
   2 ?    1.8   0.2     0.064   2.3e+02      24      29 ..      44      49 ..      41      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                                      TT-SS-EEEETTTT CS
                         Nudix_N_2 16 dgDnreRlvCpaCg 29
                                      d D+  RlvC  C+
  gi|336255421|ref|YP_004598528.1| 14 DKDTYDRLVCGECE 27
                                      78999********7 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.064
                                      EETTTT CS
                         Nudix_N_2 24 vCpaCg 29
                                      +Cp+C+
  gi|336255421|ref|YP_004598528.1| 44 ICPDCD 49
                                      799996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 431.15
//
Query:       gi|336255422|ref|YP_004598529.1|  [L=361]
Description: PfkB domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.1   4.6    1.2e-12   47.8   2.4    2.1  2  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 !    9.4   0.0   3.2e-05      0.57      33      58 ..      70      95 ..      56      98 .. 0.91
   2 !   47.8   2.4   6.8e-17   1.2e-12     189     298 ..     231     348 ..     202     351 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 3.2e-05
                                      EEEESHHHHHHHHHHHTT-EEEEEEE CS
                              PfkB 33 ksaGGagaNvAvalarlgadvafiga 58
                                       ++GG + N Av ++ lg dv+++g 
  gi|336255422|ref|YP_004598529.1| 70 VRPGGQAVNAAVQAHALGEDVTLVGH 95
                                      68**********************96 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 6.8e-17
                                       EEHHHHHHHHTSCT........HSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTH CS
                              PfkB 189 pneeElealtgekl........edieealaalhklkakgaktvvvtlGkeGalvvekdgelkvpavpkvkvvDttGA 257
                                       +n +E+ea +  +l         + e  +++++ l ++ +   vv++G++ a+ ++++ +  v+ +  + +  +tGA
  gi|336255422|ref|YP_004598529.1| 231 VNPREFEAAAAVALedgsetesSADEITTDRVNSLRSALEVSAVVSHGSDAAVGATRSSTAGVSMLEIESPRTSTGA 307
                                       5555555555555555887765555556788899999999999***********************99********* PP

                                       HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTC CS
                              PfkB 258 GDsfvggflaallegksleealrfanavAalvvqkkgaias 298
                                       GD f gg++ al+++++le+al ++na+Aa+ v + +++++
  gi|336255422|ref|YP_004598529.1| 308 GDRFSGGLTCALAREWPLETALVLGNACAAAFVASAETATP 348
                                       **********************************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2792.43
//
Query:       gi|336255423|ref|YP_004598530.1|  [L=397]
Description: phosphoesterase RecJ domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-11   42.7   0.1    1.3e-10   41.8   0.1    1.3  1  DHHA1     DHHA1 domain
    5.2e-10   39.5   0.0    8.4e-10   38.8   0.0    1.3  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 !   41.8   0.1   1.5e-14   1.3e-10      26     125 ..     273     369 ..     254     377 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.5e-14
                                       HHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSHSS-HHHHHH CS
                             DHHA1  26 kaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkdgvdagelak 101
                                       ka ++   +++v + +++v+ vg+  +++a+ +aad+l     + +++v+v++e++ + ++s+rs++d+v++ge ++
  gi|336255423|ref|YP_004598530.1| 273 KATAIT--EKRV-EGSFAVCDVGTVSNTDAIPQAADELMH--LEgVTAVVVYGENDGTLHLSGRSRDDRVHMGETLR 344
                                       233332..2233.9**************************..888999999999988*********99********* PP

                                       H.HHHHTTCCEEEETCEEEEEEEHC CS
                             DHHA1 102 e.aaaklgggGGGHdlAaGagipae 125
                                       + ++++ + + GGH+ + G++++ e
  gi|336255423|ref|YP_004598530.1| 345 HaVSDIPMANAGGHARMGGGQVSVE 369
                                       *5666667788********998755 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   9.4e-14   8.4e-10       2      85 ..      76     210 ..      75     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 9.4e-14
                                       EEEE-ECSSSHHHHHHHHHHHH...............................................CECS--TC CS
                                       xxxxxxxxxxxxxxxxxxxxxx...............................................xxxxxxxx RF
                               DHH   2 ilivghknpDtDsigSaialan...............................................llvDhnek 31 
                                       + +++h npD D++++a+a+a+                                               +lvDhn++
  gi|336255423|ref|YP_004598530.1|  76 VSVLMHPNPDPDAMACAMAVAAiadavgtdatlqyageirhqenrafrtvldldleslessselatdavVLVDHNTP 152
                                       67899*****************666666666666666666666666665555555555555555555555******* PP

                                       GGCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHH..........T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........x RF
                               DHH  32 sqavegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaellee..........k 85 
                                            +   ++ e + ++DHH  +    t ++++ +++++g++a+i +e+l++           
  gi|336255423|ref|YP_004598530.1| 153 RGFTGA---QTVEPIAVVDHHPGN---GTGTEFTDVRTEYGAAATIFVEYLQDigatspdedgG 210
                                       999976...9************97...444455677899***********99865555544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3129.35
//
Query:       gi|336255424|ref|YP_004598531.1|  [L=296]
Description: NAD-dependent epimerase/dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-17   61.6   0.0    1.1e-16   61.1   0.0    1.3  1  Epimerase       NAD dependent epimerase/dehydratase family
    6.3e-15   55.5   0.0    8.6e-15   55.1   0.0    1.2  1  NAD_binding_10  NAD(P)H-binding
    3.1e-08   33.0   0.0    2.4e-07   30.1   0.0    2.0  2  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase
    3.5e-08   33.7   0.7      8e-08   32.5   0.4    1.7  2  TrkA_N          TrkA-N domain
    1.4e-07   31.3   0.0    4.8e-07   29.5   0.0    1.7  1  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase
    6.5e-06   25.9   0.1    1.2e-05   25.0   0.1    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
    4.5e-05   23.1   0.0    7.3e-05   22.4   0.0    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    6.2e-05   23.5   0.1    0.00013   22.5   0.1    1.5  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00028   21.4   0.2    0.00071   20.1   0.2    1.7  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00037   20.3   0.0    0.00078   19.2   0.0    1.5  1  DUF1731         Domain of unknown function (DUF1731)
     0.0063   16.7   0.0      0.013   15.7   0.0    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0096   16.7   0.1      0.025   15.4   0.0    1.7  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
  ------ inclusion threshold ------
      0.016   14.3   0.2      0.083   12.0   0.1    2.0  2  RmlD_sub_bind   RmlD substrate binding domain
       0.03   13.6   0.2      0.043   13.0   0.2    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.031   14.2   0.3        0.1   12.4   0.1    1.9  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.053   13.0   0.3       0.15   11.5   0.1    1.7  2  adh_short       short chain dehydrogenase
       0.18   11.1   0.0       0.32   10.3   0.0    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase


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 !   61.1   0.0     1e-19   1.1e-16       5     181 ..       7     173 ..       3     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1e-19
                                       TTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHH CS
                         Epimerase   5 GatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaass 81 
                                       G  G+iG  l ++l ++g++v+g+ r   + +  +++ le v++d+tdr++ler+ +   +da++ +A  gg +a +
  gi|336255424|ref|YP_004598531.1|   7 GC-GYIGLELGRQLTARGHDVVGVRRSDAGLEAIEDAGLEAVRADITDRDELERVPD---VDAIVFAASSGGRGADA 79 
                                       55.************************777777777777****************99...9******9999999988 PP

                                       HSHHHHHHHHTHHHHHHHHHHHHH..TCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHH CS
                         Epimerase  82 edpadfieknlqgtlnlleaarka..gvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveay 156
                                        +  +     ++g ++ +e   ++   ++rl++ sS+ vYG+ +    +ett   p++p++      + +e++++++
  gi|336255424|ref|YP_004598531.1|  80 AREVY-----VEGLRTAIETFGERedPPERLVYTSSTGVYGDHDGDWVDETT---PIEPTTSKTEVLAEAERIARKL 148
                                       88666.....8899999999887765888************99984467777...9999999999999********* PP

                                       HHHHT-EEEEEEESEEESTTS-TTS CS
                         Epimerase 157 aaqyglnaiilrlfnlyGprngege 181
                                         +yg++ ++ r+  lyGp ++  e
  gi|336255424|ref|YP_004598531.1| 149 PPEYGFDGTVARYAGLYGPDRYRLE 173
                                       *******************965544 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 !   55.1   0.0   8.2e-18   8.6e-15       4     177 ..       9     197 ..       7     204 .. 0.74

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 8.2e-18
                                       SHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC..HHHH. CS
                    NAD_binding_10   4 GkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk..deeg. 77 
                                       G +G +l ++l ar gh+v+ + R+ + l+++e ++gle+v +d+td ++l++ + ++da+v+a+++gg+  d  + 
  gi|336255424|ref|YP_004598531.1|   9 GYIGLELGRQLTAR-GHDVVGVRRSDAGLEAIE-DAGLEAVRADITDRDELER-VPDVDAIVFAASSGGRgaD--Aa 80 
                                       89************.5**************998.6***************998.7899999999977777442..32 PP

                                       .......HHHHHHHHHHCT..--EEEEEEETTTTSGCGCHHHHHHHH..CCHHHH...HHHHHHHHHHHH....SSS CS
                    NAD_binding_10  78 .......aknivdaakeag..vkRfvlvsaigvgdevpgefgewnke..llkayl...aakraaeellra....sgl 136
                                               +++++   e +   +R+v+ s+ gv+ +++g+   w++e   ++++    +  ++ae++ r+     g+
  gi|336255424|ref|YP_004598531.1|  81 revyvegLRTAIETFGEREdpPERLVYTSSTGVYGDHDGD---WVDEttPIEPTTsktEVLAEAERIARKlppeYGF 154
                                       3556666778888775433349************866654...33321122222211133444444444444449** PP

                                       EEEEEEE-CEE-ST--SEEEEETTSS----..EEEHHHHHHHH CS
                    NAD_binding_10 137 dwTivrpggLtdepttkyrvvekgepfkgg..sisradVAdvl 177
                                       d T+ r +gL   ++ + +   +g+  +g+   + r+d A ++
  gi|336255424|ref|YP_004598531.1| 155 DGTVARYAGLYGPDRYRLERYLEGPVTEGYlnMVHRDDAAGAV 197
                                       ***************9999999999988854499999988665 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 !   30.1   0.0   2.3e-10   2.4e-07       5     154 ..       7     146 ..       3     177 .. 0.83
   2 ?    0.6   0.0      0.21   2.3e+02     239     273 ..     204     237 ..     193     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.3e-10
                         3Beta_HSD   5 gaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag 81 
                                       g+G++G +l ++L  +++     v+ +r s+  le ++  + +  + +D+td d+le++  +vd++++ as      
  gi|336255424|ref|YP_004598531.1|   7 GCGYIGLELGRQLTARGH----DVVGVRRSDAGLEAIEDAGLE-AVRADITDRDELERV-PDVDAIVFAASSGG--- 74 
                                       89*************997....688999999999********9.9***********997.57999998866543... PP

                         3Beta_HSD  82 kltedeimkvnvkGTrnvleacvkag..vrvlvYtSsaevvgpnslgeeilngdEeleyesl..hqdaypesKalaE 154
                                           d   +v v+G r+ +e+  + +   ++lvYtSs +v g+  +  + +  dE++++e++   +++++e  ++a 
  gi|336255424|ref|YP_004598531.1|  75 -RGADAAREVYVEGLRTAIETFGEREdpPERLVYTSSTGVYGD--HDGDWV--DETTPIEPTtsKTEVLAEAERIAR 146
                                       .44688889***********98776622689************..555555..799999988445566776666665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.21
                         3Beta_HSD 239 ssvagqayfisddsPvesyddfnltllkelglelk 273
                                         ++g++  + dd+P +  ++f+  l  + g+e++
  gi|336255424|ref|YP_004598531.1| 204 DLARGEVVQVVDDEPAH-KWAFADWLADQCGVEEP 237
                                       5678999999*****99.9***********99876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.4   7.6e-11     8e-08       1      69 [.       3      69 ..       3      91 .. 0.87
   2 ?   -2.1   0.0       4.3   4.5e+03      13      32 ..     201     219 ..     194     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 7.6e-11
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE- CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaa 69
                                      i+i+G+G +G +l ++L+++g+dvv++ ++++ +e +++ gle+v +d td++ Le+    ++da++ a
  gi|336255424|ref|YP_004598531.1|  3 IAILGCGYIGLELGRQLTARGHDVVGVRRSDAGLEAIEDAGLEAVRADITDRDELERV--PDVDAIVFA 69
                                      79*****************6668********************************975..455555544 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.3
                                       HHHHHHHTTEEEEEEESSHH CS
                            TrkA_N  13 laeeLseggkdvvvidkdee 32 
                                       lae L +g+  v v+d++++
  gi|336255424|ref|YP_004598531.1| 201 LAEDLARGE-VVQVVDDEPA 219
                                       789999988.4889988775 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 !   29.5   0.0   4.5e-10   4.8e-07       5     200 ..       7     183 ..       6     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.5e-10
                                       TTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                     GDP_Man_Dehyd   5 iaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                       + G+iG  l ++L ++g++v+g+ r ++   ++ ie             l+ +++D+tD+++ler+    ++d+++ 
  gi|336255424|ref|YP_004598531.1|   7 GCGYIGLELGRQLTARGHDVVGVRRSDAG--LEAIEDA----------GLEAVRADITDRDELERVP---DVDAIV- 67 
                                       67********************7554444..4444432..........3678************986...457776. PP

                                       --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHH CS
                     GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKl 158
                                       +AA s  +     +++  ev v G  + +e   + + ++  r++ +S+  vYG+ +   ++Ettp++P+       +
  gi|336255424|ref|YP_004598531.1|  68 FAASSGGR----GADAAREVYVEGLRTAIETFGERE-DPPERLVYTSSTGVYGDHDGDWVDETTPIEPTTSKTEVLA 139
                                       99999754....355566777778777777776654.5689************************************ PP

                                       HHHHHHHHHHHHH---EEEEEE-EEESTTS-..TTSCCCHHHHH CS
                     GDP_Man_Dehyd 159 yadwivvnyreayglfavngilfnhesprrg..etfvtrkitra 200
                                        a+ i+++   +yg+  +++++   ++p r   e++ +  +t++
  gi|336255424|ref|YP_004598531.1| 140 EAERIARKLPPEYGFDGTVARYAGLYGPDRYrlERYLEGPVTEG 183
                                       ***************************97641145666555555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   1.1e-08   1.2e-05       1      48 [.       3      52 ..       3      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.1e-08
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.C CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.g 48
                                      iailG+G iG  l+ +L++ g+dv+ + rs+  lea++++Gl+  + + +
  gi|336255424|ref|YP_004598531.1|  3 IAILGCGYIGLELGRQLTARGHDVVGVRRSDaGLEAIEDAGLEAVRADiT 52
                                      89****************************************99988853 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 !   22.4   0.0   6.9e-08   7.3e-05       1      41 [.       1      41 [.       1      55 [. 0.86

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.9e-08
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCT CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklns 41
                                      m+i+++G GY+Gl  +  l ++gh+v+gv  +++  ++++ 
  gi|336255424|ref|YP_004598531.1|  1 MEIAILGCGYIGLELGRQLTARGHDVVGVRRSDAGLEAIED 41
                                      89***************************988887777665 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 !   22.5   0.1   1.2e-07   0.00013       2      68 ..       3      69 ..       2      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.2e-07
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....-EEECECHHHHHHH-SEEEE- CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....vkvtavdneeaaeeadvvvla 68
                                      i+i+G+G +g  l ++l+a+g   h++v + +r+   +e+++++      +++t +d  e + + d +v+a
  gi|336255424|ref|YP_004598531.1|  3 IAILGCGYIGLELGRQLTARG---HDVV-GVRRSDAGLEAIEDAGLeavrADITDRDELERVPDVDAIVFA 69
                                      9********************...****.98*******999877557777888888888888888888877 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   6.7e-07   0.00071       2      42 ..       3      44 ..       2      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.7e-07
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeea 42
                                      ++++G GyiglEl+  l++ g++V  v rsd  l   +D+ +
  gi|336255424|ref|YP_004598531.1|  3 IAILGCGYIGLELGRQLTARGHDVVGVRRSDAGLeAIEDAGL 44
                                      89*****************************99966666554 PP

>> DUF1731  Domain of unknown function (DUF1731)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.4e-07   0.00078      12      41 ..     253     283 ..     251     288 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.4e-07
                           DUF1731  12 emae.llLegqrVlPkrLleaGFqFrypdle 41 
                                       e a+  +L++ r +  +L ++G++F yp+ +
  gi|336255424|ref|YP_004598531.1| 253 EAARrRILTSKRCSNDKLRDLGYEFAYPTYR 283
                                       7888889*********************965 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 !   15.7   0.0   1.2e-05     0.013       1      47 [.       2      48 ..       2      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                                      EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-S CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaae 47
                                      +i+++G G +G ++ ++l+++g++v+++ r+ + +e++ ++g++a+ 
  gi|336255424|ref|YP_004598531.1|  2 EIAILGCGYIGLELGRQLTARGHDVVGVRRSDAGLEAIEDAGLEAVR 48
                                      599***********************************999944433 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 !   15.4   0.0   2.3e-05     0.025       2      82 ..       2      83 ..       1      94 [. 0.74
   2 ?   -2.3   0.0       7.4   7.8e+03      26      44 ..     208     226 ..     186     249 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-05
                                      EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSH..HHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-G.GGHHH CS
                      GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpda..eraeavaesfgveaysdleelladpeidavivatpn.gthee 77
                                       +ai G+G+ig + +r+l ++  +++vv++  +da  e+ e++  + + +  +d +el + p++da++ a  + g +++
  gi|336255424|ref|YP_004598531.1|  2 EIAILGCGYIGLELGRQLTAR--GHDVVGVRRSDAglEAIEDAGLEAVRADITDRDELERVPDVDAIVFAASSgGRGAD 78
                                      79*************877777..7778887655541156666655555558999************9887776566777 PP

                                      HHHHH CS
                      GFO_IDH_MocA 78 lakaa 82
                                       a+++
  gi|336255424|ref|YP_004598531.1| 79 AAREV 83
                                      76665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.4
                                       EEEEEEECSSHHHHHHHHH CS
                      GFO_IDH_MocA  26 eevvalldpdaeraeavae 44 
                                        evv ++d +++   a+a+
  gi|336255424|ref|YP_004598531.1| 208 GEVVQVVDDEPAHKWAFAD 226
                                       3778888877776666643 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 ?   12.0   0.1   7.9e-05     0.083       1     154 [.       1     167 [.       1     177 [. 0.72
   2 ?   -2.3   0.0       1.7   1.8e+03     212     252 ..     213     257 ..     188     293 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.9e-05
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHHHHH--SEEEE----- CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre...............eldltdaeavaellkeakpdvvvnaAAyt 62 
                                       m+i ++G  G +G eL +ql+++g++v+++ r+               ++d+td+++++++ +    d++v aA   
  gi|336255424|ref|YP_004598531.1|   1 MEIAILG-CGYIGLELGRQLTARGHDVVGVRRSdagleaiedagleavRADITDRDELERVPDV---DAIVFAASS- 72 
                                       5677777.499*******************9999999999999999999999999999887654...677765542. PP

                                       -HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT...-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHH CS
                     RmlD_sub_bind  63 avDkaEseeeaayavnaeavealAeaaaavg...alLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqav 136
                                                +aa +v +e+ ++  e   +++     L++ S+  V+  +  +   e+ + +P +   +  ++ E+  
  gi|336255424|ref|YP_004598531.1|  73 ----GGRGADAAREVYVEGLRTAIETFGEREdppERLVYTSSTGVYGDHDGDWVDETTPIEPTTSKTEVLAEAERIA 145
                                       ....3344555666666666555555444441224588888888886665555567778888888888888888888 PP

                                       HH....H-SSEEEEEE-SEESS CS
                     RmlD_sub_bind 137 la....agkkalivRtswvyge 154
                                       ++    +g + ++ R + +yg 
  gi|336255424|ref|YP_004598531.1| 146 RKlppeYGFDGTVARYAGLYGP 167
                                       8755445556688888888875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                                       ---BS-EEHHHHHHHHHHHHCHTT....SEEEEE-CCCS--SS-- CS
                     RmlD_sub_bind 212 lanegetswlefArailkeagads....eevkpistaeyptpAkR 252
                                       ++ ++ + + +fA+  ++++g+++    ++ +  ++++  ++A+R
  gi|336255424|ref|YP_004598531.1| 213 VVDDEPAHKWAFADWLADQCGVEEppkrTKDERLENDDLSEAARR 257
                                       445555566667777777776666553333333344444455544 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 ?   13.0   0.2   4.1e-05     0.043     145     181 ..       3      39 ..       1      60 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
                                       EEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgkevtlveardrllral 181
                                       i++ G GyiG+El  +l+  g++v+ v + d  l+a 
  gi|336255424|ref|YP_004598531.1|   3 IAILGCGYIGLELGRQLTARGHDVVGVRRSDAGLEAI 39 
                                       89**********************9999988877443 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 ?   12.4   0.1   9.9e-05       0.1       2      42 ..       3      43 ..       2     111 .. 0.77
   2 ?   -0.5   0.0       0.9   9.5e+02      78     105 ..     118     146 ..      76     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.9e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekaleki 42
                                      +a++G+G +G ++  ++ ++g++Vv v +s++ le+ +++ 
  gi|336255424|ref|YP_004598531.1|  3 IAILGCGYIGLELGRQLTARGHDVVGVRRSDAGLEAIEDAG 43
                                      8****************************999988766543 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.9
                                       C-SEEEE-S-.SSHHHHHHHHHHHHCCS- CS
                           3HCDH_N  78 dadlviEavv.EnlelKrkvfaelekiak 105
                                       d d+v E+ + E ++ K++v+ae e+ia+
  gi|336255424|ref|YP_004598531.1| 118 DGDWVDETTPiEPTTSKTEVLAEAERIAR 146
                                       67888887744999999999999999986 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00014      0.15      11      67 ..      10      60 ..       2      71 .. 0.83
   2 ?   -1.3   0.0       1.2   1.2e+03       4      32 ..      67      97 ..      64     108 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHH CS
                         adh_short 11 GIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreeveal 67
                                       IG+++ ++l ++G +vv v rs++ le++ +  +     + a+++D+tdr+e+e++
  gi|336255424|ref|YP_004598531.1| 10 YIGLELGRQLTARGHDVVGVRRSDAGLEAI-EDAG-----LEAVRADITDRDELERV 60
                                      5**********************9988444.4434.....679*********99976 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                                      EEESTTSHHHHHHHHHHHHTT-EEEE..EES CS
                         adh_short  4 lvtGassGIGraiakelakeGakvvv..vdr 32
                                      +    s+G G + a+e++ eG ++++  +++
  gi|336255424|ref|YP_004598531.1| 67 VFAASSGGRGADAAREVYVEGLRTAIetFGE 97
                                      4445567889999999999999988754444 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 ?   10.3   0.0    0.0003      0.32      38      81 ..       2      45 ..       1      66 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0003
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCE CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgve 81
                                      +++i+G+G IG ++ + l+a g +v+++ rs    e+ e+ g+e
  gi|336255424|ref|YP_004598531.1|  2 EIAILGCGYIGLELGRQLTARGHDVVGVRRSDAGLEAIEDAGLE 45
                                      689**************************998766655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2335.24
//
Query:       gi|336255425|ref|YP_004598532.1|  [L=156]
Description: hypothetical protein Halxa_4048 [Halopiger xanaduensis SH-6]
Scores for 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   12.6   0.1       0.15   12.0   0.1    1.3  1  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   8.6e-06      0.15       4      52 ..      80     130 ..      78     150 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.6e-06
                   Methyltransf_18   4 RLkaiaslvekgsrvaDiGtDHgylpiy..lvkegkakkviasDinegple 52 
                                        L+a+ +  ++ ++++DiG+ H +l +   +++ +  ++ +a+++ ++ ++
  gi|336255425|ref|YP_004598532.1|  80 QLQALDERAPDAATIVDIGCEHLLLGMStaVLDVDALETELAIEMDAKEIQ 130
                                       688999999999**********88876511334445555555555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1378.54
//
Query:       gi|336255426|ref|YP_004598533.1|  [L=131]
Description: hypothetical protein Halxa_4049 [Halopiger xanaduensis SH-6]
Scores for 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   1.5       0.78   10.0   0.3    2.0  2  HTH_18    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_18  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   4.4e-05      0.78      25      55 ..      15      45 ..       9      49 .. 0.89
   2 ?    2.1   0.1     0.013   2.4e+02      18      43 ..      47      72 ..      44      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 4.4e-05
                                      HHHHHHHHHHHHHHHHHSSS---HHHHHHHT CS
                            HTH_18 25 keylrrlRlerArrlLlentglsvaeiAlal 55
                                      +++l ++R ++   lLl++  l+v+eiAl+l
  gi|336255426|ref|YP_004598533.1| 15 YDLLSDRRRRHLLYLLLDADRLPVDEIALRL 45
                                      678999***********99999*******97 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.013
                                      HHTSS-HHHHHHHHHHHHHHHHHHSS CS
                            HTH_18 18 rvlgltpkeylrrlRlerArrlLlen 43
                                      ++ g tp++ +++ R +++  +L++n
  gi|336255426|ref|YP_004598533.1| 47 AWEGETPMTAVDDDRRRQIATALRHN 72
                                      67899999999999999999999763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1016.39
//
Query:       gi|336255427|ref|YP_004598534.1|  [L=383]
Description: oxidoreductase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   89.3   0.1    5.1e-25   88.6   0.1    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    3.9e-10   39.7   0.0    9.8e-10   38.5   0.0    1.7  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
    9.2e-05   21.9   0.0    0.00015   21.1   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    0.00012   22.3   0.0      0.001   19.3   0.0    2.1  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00023   21.7   0.0    0.00045   20.7   0.0    1.5  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0028   18.3   0.0     0.0078   16.9   0.0    1.7  2  CoA_binding     CoA binding domain
     0.0033   17.0   0.0      0.006   16.2   0.0    1.4  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0091   16.6   0.1      0.015   15.9   0.1    1.3  1  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> 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 !   88.6   0.1   2.3e-28   5.1e-25       2     120 .]      34     148 ..      33     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 2.3e-28
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheel 78 
                                       r +iiG+G+ig +h++ l e+     +v+ +d dae+ e++a +++v++y+d+++l++  ++dav+++tpn+ hee+
  gi|336255427|ref|YP_004598534.1|  34 RTGIIGLGNIGHHHAERLVEQ--SVPLVGGMDVDAEARERFATHYDVAVYDDHRDLFD--AVDAVVITTPNRFHEEY 106
                                       89*************999988..899********************************..***************** PP

                                       HHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  79 akaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       a +a+e+  hvllEKPla ++e a +++++a+ ++ +++vg+
  gi|336255427|ref|YP_004598534.1| 107 AVDAFEHDLHVLLEKPLAHSLESALRIADAAADSEGVCMVGF 148
                                       ****************************************96 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   4.4e-13   9.8e-10       3      59 ..     162     218 ..     160     226 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 4.4e-13
                                       HHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSH.HCSTSHHHHTCHHHHHHHHHHHT CS
                    GFO_IDH_MocA_C   3 lIengklGevvsvdvwtldtragaeakkrwkrrk.kksgGvlgdlgiHdiDllqwLfG 59 
                                        I+ g++Gev++v+   +  r+g + + +w  r+ + +gG+l+dlg+H iDl+++L+ 
  gi|336255427|ref|YP_004598534.1| 162 RIDRGEFGEVTHVE-ANYVRRRGVPGRGSWFTRReVSGGGALIDLGVHAIDLAMHLLD 218
                                       799***********.99999************************************86 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 !   21.1   0.0   6.9e-08   0.00015      27     106 ..      23     105 ..       9     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 6.9e-08
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH..CHHHHTCEECSHHHHHHH-SEEEE-S- CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkee..eeeelgvelvsleellaesDivslhlp 100
                                        + + ++ +  + GiiGlG+IG++ a+rl +  +  v ++d+  +++e  +++   + +++  +l+   D v++++p
  gi|336255427|ref|YP_004598534.1|  23 MTATETDPKSVRTGIIGLGNIGHHHAERLVEQSVpLVGGMDVDAEARErfATHYDVAVYDDHRDLFDAVDAVVITTP 99 
                                       5556677788899*****************998834556787777766543344444899****************9 PP

                                       -STTTT CS
                      2-Hacid_dh_C 101 ltpetr 106
                                          + +
  gi|336255427|ref|YP_004598534.1| 100 NRFHEE 105
                                       766555 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   0.0   4.6e-07     0.001       2      68 ..      35     103 ..      34     129 .. 0.86
   2 ?    0.6   0.0      0.26   5.8e+02      24      83 ..     305     373 ..     290     377 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.6e-07
                                       EEEE--SHHHHHHHHHHHHTT-EEE.EE-SSHHHHHHHHHTT.EEE-SSHHHHHHHCSEEEE-SSSHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykva.vynrtkekveelvaeg.akaaesieelvasldvvitmvkagka 68 
                                        g+iGlG++G++ a++l+++   ++ ++++++e+ e+++++  + ++++ ++l++++d+v++  ++  +
  gi|336255427|ref|YP_004598534.1|  35 TGIIGLGNIGHHHAERLVEQSVPLVgGMDVDAEARERFATHYdVAVYDDHRDLFDAVDAVVITTPNRFH 103
                                       59***************999998652799**9*****9998669999************9998887655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.26
                                       EEEEE-SSHHHHHHHHHTT......EEE-SSHHHHHHHC...SEEEE-SSSHHHHHHHHHSHCCC--TT CS
                     NAD_binding_2  24 kvavynrtkekveelvaeg......akaaesieelvasl...dvvitmvkagkavdeviegllealkkg 83 
                                       ++++y  +++  ++++++        + a++ +++++++   + v   v++g  v+ +++ + ++ ++g
  gi|336255427|ref|YP_004598534.1| 305 ELTIYSASADGPDHMLDTSieteenDTHADEQAAFFEAIadgRRVGSTVEEGLTVQRIVDAIYRSSERG 373
                                       566677777777777777633334333333444444444666999999999999999998887776665 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 !   20.7   0.0     2e-07   0.00045       2      84 ..      35     113 ..      34     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2e-07
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevl 78 
                                        giiG Gn+g+  a++l+++      +v + + + e +e +a ++ v v   d+ ++ +  d vv++ + + +ee +
  gi|336255427|ref|YP_004598534.1|  35 TGIIGLGNIGHHHAERLVEQS---VPLVGGMDVDAEARERFATHYDVAVYD-DHRDLFDAVDAVVITTPNRFHEEYA 107
                                       59******************9...6666699*******************9.*****************99999987 PP

                                       HHCGHH CS
                     F420_oxidored  79 selakd 84 
                                        +++++
  gi|336255427|ref|YP_004598534.1| 108 VDAFEH 113
                                       776555 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.5e-06    0.0078       5      87 ..      34     115 ..      30     119 .. 0.74
   2 ?   -3.4   0.0       7.4   1.7e+04      38      55 ..     346     364 ..     339     368 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.5e-06
                                       EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEET....TEEEESCHHHHHHHCTTTEEEEES-HHHHHH CS
                       CoA_binding   5 kviviGagglgiaglyhfkeklkygikavfgvnprkvgtevl....glpvyksvdeleektevdvavitvPaesaqe 77 
                                       + ++iG g+ g+    h ++  + +++ v+g + +  ++e      ++ vy++ ++l +   vd+ vit+P+++ +e
  gi|336255427|ref|YP_004598534.1|  34 RTGIIGLGNIGH---HHAERLVEQSVPLVGGMDVDAEARERFathyDVAVYDDHRDLFDA--VDAVVITTPNRFHEE 105
                                       678999999955...5666666666666666655533333323444**************..*************** PP

                                       HHHHHHHTT- CS
                       CoA_binding  78 avdelveagi 87 
                                        ++++ e+  
  gi|336255427|ref|YP_004598534.1| 106 YAVDAFEHDL 115
                                       9999988765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.4
                                       TTTTTCEET.TEEEESCHH CS
                       CoA_binding  38 prkvgtevl.glpvyksvd 55 
                                       +r vg++v+ gl+v+  vd
  gi|336255427|ref|YP_004598534.1| 346 GRRVGSTVEeGLTVQRIVD 364
                                       4556666655888885444 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 !   16.2   0.0   2.7e-06     0.006       6      83 ..      34     113 ..      31     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.7e-06
                                       -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-H.HHHHHHHTT-EEEE.HHHHHHT-SEEEE-S-HHHHHHHHHHH CS
                              IlvN   6 kiaviGyGsqGhaqalnlrdsgldvvvglregsk.svkkAkeegfevlt.vaeavkkadvvmiliPDelqkevyeee 80 
                                       +  +iG G+ Gh +a+ l ++ + +v g+  +++   + A++  + v++  +++ ++ d v+i +P+++++e   ++
  gi|336255427|ref|YP_004598534.1|  34 RTGIIGLGNIGHHHAERLVEQSVPLVGGMDVDAEaRERFATHYDVAVYDdHRDLFDAVDAVVITTPNRFHEEYAVDA 110
                                       568*************************9988873566799999999863689999************999866555 PP

                                       TGG CS
                              IlvN  81 iep 83 
                                        e+
  gi|336255427|ref|YP_004598534.1| 111 FEH 113
                                       555 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 !   15.9   0.1   6.9e-06     0.015       1     108 [.      39     138 ..      39     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.9e-06
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHH CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvl 77 
                                       GlG+iG   +e+l +q       lv+ +d d +++ +r a   + a+++d  dl++  ++d vV  ++ +  +e+++
  gi|336255427|ref|YP_004598534.1|  39 GLGNIGHHHAERLVEQSV----PLVGGMDVD-AEARERFATHYDVAVYDDHRDLFD--AVDAVVITTPNRFHEEYAV 108
                                       99***********99985....566666666.4555566788899***********..******************* PP

                                       HHHHTTEEEE-S--CGGG-HHHHHHHTSSST CS
                     NAD_binding_3  78 kaLkagkdvvtankgaladealyeeLreaae 108
                                       +a +++ +v+     a + ++   ++++aa 
  gi|336255427|ref|YP_004598534.1| 109 DAFEHDLHVLLEKPLAHS-LESALRIADAAA 138
                                       **********98888888.666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 3284.04
//
Query:       gi|336255428|ref|YP_004598535.1|  [L=69]
Description: hypothetical protein Halxa_4051 [Halopiger xanaduensis SH-6]
Scores for 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   14.8   0.0       0.02   14.6   0.0    1.1  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha


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 ?   14.6   0.0   1.1e-06      0.02      43      61 ..      10      54 ..       4      68 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-06
                                      HIIIIIHHHHHHHHHHHS..........................S CS
                       Oxidored_q3 43 lvYvGAilvlflFvimll..........................e 61
                                      lvY G+ lvlf F i  +                          +
  gi|336255428|ref|YP_004598535.1| 10 LVYYGGLLVLFFFWIYGIvsfaldlkntvipglrtywhgrkqrkQ 54
                                      8************99888788888888888888877777664331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 538.89
//
Query:       gi|336255429|ref|YP_004598536.1|  [L=411]
Description: glycerol-3-phosphate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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  116.3   0.0    2.4e-33  115.5   0.0    1.4  1  ABC_tran         ABC transporter
    3.9e-12   46.8   0.1    1.2e-11   45.2   0.1    1.9  1  OB_MalK          MalK OB fold domain
    7.7e-07   29.2   0.0      0.013   15.3   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.4e-06   27.9   0.2    8.9e-06   25.3   0.2    2.0  1  SMC_N            RecF/RecN/SMC N terminal domain
      2e-05   25.0   0.3      0.001   19.6   0.1    2.8  2  CysA_C_terminal  CysA C-terminal regulatory domain
    6.8e-05   23.0   0.2     0.0042   17.2   0.1    2.8  1  TOBE_2           TOBE domain
    0.00055   19.8   0.0        0.2   11.3   0.0    2.1  2  AAA_15           AAA ATPase domain
     0.0032   17.2   0.2      0.029   14.1   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
     0.0038   17.1   0.1      0.019   14.9   0.0    1.9  2  RsgA_GTPase      RsgA GTPase
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.017   15.0   0.0    1.2  1  Rad17            Rad17 P-loop domain
      0.017   15.4   0.1       0.55   10.6   0.0    2.9  2  TOBE             TOBE domain
       0.02   15.3   0.0      0.054   13.9   0.0    1.8  1  AAA_16           AAA ATPase domain
      0.026   14.8   0.4      0.068   13.5   0.4    1.8  1  AAA_22           AAA domain
      0.058   13.8   0.4       0.16   12.4   0.4    1.9  1  AAA              ATPase family associated with various cellul
      0.078   13.4   0.0       0.19   12.1   0.0    1.7  1  RNA_helicase     RNA helicase
       0.14   12.3   1.3       0.44   10.7   1.3    1.9  1  AAA_33           AAA domain
       0.17   11.4   0.0       0.31   10.5   0.0    1.4  1  AAA_7            P-loop containing dynein motor region


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 !  115.5   0.0   2.3e-36   2.4e-33       2     136 ..      20     161 ..      19     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 2.3e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++++l+++ ge v +vG++G+GKSt ++++agl+kpteG+i++ + d+++  l+  ++ +++++q+  lfp++ v++
  gi|336255429|ref|YP_004598536.1|  20 DDMNLEIEDGEFVTFVGPSGCGKSTTMETIAGLTKPTEGSIHIGDVDVTN--LPPKDRGVAMVFQNIALFPHMDVYD 94 
                                       89******************************************999999..9************************ PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e d+++++a++ ++l+++ d+       +LSgGq+qrva+ara++++p ++l+DEp 
  gi|336255429|ref|YP_004598536.1|  95 NisfglrlrkydteEIDRRVDRAAEIVQLEGMLDRMP----DELSGGQQQRVAIARAIVREPAVFLMDEPL 161
                                       **********999999999999999999999999988....*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.1   1.2e-14   1.2e-11       1      53 []     235     283 ..     235     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.2e-14
                           OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                       GSP+MN+++++++++g  ++ ++++++l+++    ++  +g++v++G+RPE+i
  gi|336255429|ref|YP_004598536.1| 235 GSPSMNLVEGELTANG--LTTDHFDVALDPAG--LEGVSVGETVTMGVRPEDI 283
                                       9***************..99999*******99..9*****************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 !   12.3   0.0    0.0001      0.11       2      72 ..      32      93 ..      31     118 .. 0.73
   2 !   15.3   0.0   1.3e-05     0.013     233     298 ..     130     193 ..      90     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvry 72
                                        ++Gp g+GKS+ ++++ +l         ++++++++   +++   l+++d   +++f+ + ++ ++ +y
  gi|336255429|ref|YP_004598536.1| 32 VTFVGPSGCGKSTTMETIAGL---------TKPTEGSIHIGDVDVTNLPPKDRGVAMVFQNIALFPHMDVY 93
                                      679*****************9.........56666666666666677777776666666666666666555 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.3e-05
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                        ++elS G+++  a++ a+ r +   +++l DEp ++L+ kl  +  + l +l++  ++ +i +TH+
  gi|336255429|ref|YP_004598536.1| 130 MPDELSGGQQQRVAIARAIVREP---AVFLMDEPLANLDAKLRVHMRTELQRLHKqLDTTIIYVTHD 193
                                       56789****9999*******999...*********************999666666**********8 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   0.2   8.4e-09   8.9e-06      25     213 ..      30     206 ..      18     213 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 8.4e-09
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE...SSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk...lkiekeevs 98 
                                       +f   vGp G+GKs  ++ i   L + +  ++   ++ d+     ++   k   v+++f+n        + ++ ++ 
  gi|336255429|ref|YP_004598536.1|  30 EFVTFVGPSGCGKSTTMETIA-GLTKPTEGSI---HIGDV---DVTNLPPKDRGVAMVFQNIALFphmDVYDNISFG 99 
                                       68889***************3.3443333222...33332...2334455555666667666554211222444455 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                       ++ r++ ++    +i+++  + +e+ +l  + +  +++LSgG+++ va+a       v+  +++l+De  a+LD+k 
  gi|336255429|ref|YP_004598536.1| 100 LRLRKYDTE----EIDRRVDRAAEIVQLEGMLDRMPDELSGGQQQRVAIARA----IVREPAVFLMDEPLANLDAKL 168
                                       555555555....59******************************9988743....46778899************* PP

                                       HHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 176 vkkvaellkeksknaQfivislreemlekadklvgvtk 213
                                       +  + + l++ +k+    +i +++++ e +    ++  
  gi|336255429|ref|YP_004598536.1| 169 RVHMRTELQRLHKQLDTTIIYVTHDQAEAMTMSDRIAV 206
                                       *********99999777777776666666655554444 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.22   2.3e+02       9      23 ..      57      73 ..      56      81 .. 0.76
   2 !   19.6   0.1   9.8e-07     0.001       1      41 [.     240     283 ..     240     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.22
                   CysA_C_terminal  9 dGklriGglalp.vP.e 23
                                      +G ++iG++++  +P +
  gi|336255429|ref|YP_004598536.1| 57 EGSIHIGDVDVTnLPpK 73
                                      79*******99988843 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 9.8e-07
                   CysA_C_terminal   1 NlFhGrvedGklriGglalpvP..elaga.dgqevvayVRPhDl 41 
                                       Nl +G +   +l+ + +++++    l+g+  g+ v+++VRP+D+
  gi|336255429|ref|YP_004598536.1| 240 NLVEGELTANGLTTDHFDVALDpaGLEGVsVGETVTMGVRPEDI 283
                                       9******9888*********87686666679************8 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1     4e-06    0.0042       2      76 .]     277     369 ..     276     369 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4e-06
                            TOBE_2   2 aiRPEklrla.....aagga.....nglsGtVedveylGsstryvvelaggqlvvv..........rqpnadr.dsa 57 
                                       ++RPE++        +         + + +t + +e +G+++ ++++l+g    ++          +   + + d+a
  gi|336255429|ref|YP_004598536.1| 277 GVRPEDIYRTrtdaaE---SlasasTPIDATTDVLEPMGDEIFVYLSLDGAGGATMtgdrgasggdQLLMSVDpDAA 350
                                       89*****998865441...144443699*********************9877777678877777733333333568 PP

                            TOBE_2  58 lapGdtVelswdpddavvl 76 
                                       ++++d V + +d  +++++
  gi|336255429|ref|YP_004598536.1| 351 IDEDDDVSVVLDRSKIHLF 369
                                       8888888888888888887 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   0.0   0.00019       0.2      17      48 ..      22      54 ..      18     106 .. 0.83
   2 !    6.5   0.0    0.0054       5.7     317     365 ..     150     193 ..     136     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                            AAA_15 17 veidlsee.ltvliGkNnsGKSsilealdlFln 48
                                      + +++++  + +++G+ ++GKS+ +e +  + +
  gi|336255429|ref|YP_004598536.1| 22 MNLEIEDGeFVTFVGPSGCGKSTTMETIAGLTK 54
                                      555666656*****************9976655 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0054
                            AAA_15 317 kdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +     +++++l++EP a+L  ++  ++   l++l ++ +t +i+ TH 
  gi|336255429|ref|YP_004598536.1| 150 R-----EPAVFLMDEPLANLDAKLRVHMRTELQRLHKQLDTTIIYVTHD 193
                                       4.....7899**************************************7 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 !   14.1   0.0   2.7e-05     0.029      15      48 ..      22      55 ..      17      61 .. 0.78
   2 ?   -0.3   0.0      0.87   9.2e+02      36      49 ..     298     311 ..     297     316 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                        +ei+  +++ ++GpsG GKST +  i+ l  p
  gi|336255429|ref|YP_004598536.1| 22 MNLEIEDGEFVTFVGPSGCGKSTTMETIAGLTKP 55
                                      566777455999***********99888776655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.87
                            AAA_29  36 STllDAiqalLvpa 49 
                                       ST +DA + +L p 
  gi|336255429|ref|YP_004598536.1| 298 STPIDATTDVLEPM 311
                                       899*******9886 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.8e-05     0.019      89     123 ..      18      53 ..       3      65 .. 0.80
   2 ?   -0.8   0.0       1.2   1.2e+03       8      65 ..     156     212 ..     149     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                       ++++++ +++d +++++vG+SG GKSt ++++++ +
  gi|336255429|ref|YP_004598536.1|  18 AVDDMNLEIEDgEFVTFVGPSGCGKSTTMETIAGLT 53 
                                       56777777888799**************99998754 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                       ETTTTEES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHH CS
                       RsgA_GTPase   8 lvrpkvaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeel 65 
                                       l++++ aN+d  l v   +e +  +++ld  ++ + + ++e + +  +i ++++ e l
  gi|336255429|ref|YP_004598536.1| 156 LMDEPLANLDAKLRVHMRTELQRLHKQLDTTIIYVTHDQAEAMTMSDRIAVINNGE-L 212
                                       77788899998888777777777788888888888888888877777776666666.4 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   1.6e-05     0.017      34      67 ..      18      51 ..       9     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                             Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                      +++ + Le +  + +   GPsGCgkst+++ ++ 
  gi|336255429|ref|YP_004598536.1| 18 AVDDMNLEIEDGEFVTFVGPSGCGKSTTMETIAG 51
                                      56677888888889999***********998764 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       7.5   7.9e+03      47      60 ..     268     281 ..     266     283 .. 0.79
   2 ?   10.6   0.0   0.00052      0.55       9      60 ..     303     348 ..     295     368 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.5
                              TOBE  47 LapGeeVfalikaa 60 
                                       +++Ge+V++ + ++
  gi|336255429|ref|YP_004598536.1| 268 VSVGETVTMGVRPE 281
                                       5699***9998886 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00052
                              TOBE   9 gtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaa 60 
                                       +t +v+ep g e +V++ l+g     A++t+++ ++     G+++ +++++ 
  gi|336255429|ref|YP_004598536.1| 303 ATTDVLEPMGDEIFVYLSLDGAG--GATMTGDRGAS----GGDQLLMSVDPD 348
                                       66688999999999999999998..88888888888....888888888875 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   5.2e-05     0.054      23      52 ..      28      75 ..      14     197 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd...................g 52
                                      ++e v ++G+sG+GKs+ +++++  l+k                    +
  gi|336255429|ref|YP_004598536.1| 28 DGEFVTFVGPSGCGKSTTMETIA-GLTKPtegsihigdvdvtnlppkdR 75
                                      458899**************999.5665545555555555555555541 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   6.4e-05     0.068       5      29 ..      29      53 ..      25     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.4e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                        +++ +G+sG+GK+t++++++   
  gi|336255429|ref|YP_004598536.1| 29 GEFVTFVGPSGCGKSTTMETIAGLT 53
                                      678999*************987655 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 ?   12.4   0.4   0.00015      0.16       2      24 ..      33      55 ..      32     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                      EEESSTTSSHHHHHHHHHHHHTH CS
                               AAA  2 llyGppGtGKTllakavakelgv 24
                                       ++Gp G+GK+++++ +a  ++ 
  gi|336255429|ref|YP_004598536.1| 33 TFVGPSGCGKSTTMETIAGLTKP 55
                                      699***************98753 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   0.00018      0.19       2      19 ..      33      50 ..      32      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                      RNA_helicase  2 wlyGpsgeGKStlakeLa 19
                                       ++Gpsg+GKSt+++++a
  gi|336255429|ref|YP_004598536.1| 33 TFVGPSGCGKSTTMETIA 50
                                      689***********9954 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.3   0.00042      0.44       2      20 ..      32      50 ..      31     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00042
                            AAA_33  2 vllvGlpGsGKstlaerll 20
                                      v +vG++G+GKst  e ++
  gi|336255429|ref|YP_004598536.1| 32 VTFVGPSGCGKSTTMETIA 50
                                      679**********999875 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    0.0003      0.31      28      53 ..      24      49 ..      14      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                             AAA_7 28 lllknkkpvllvGptGtGKtviikdl 53
                                      l ++ +  v +vGp+G+GK+++++++
  gi|336255429|ref|YP_004598536.1| 24 LEIEDGEFVTFVGPSGCGKSTTMETI 49
                                      5577788899************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3099.84
//
Query:       gi|336255430|ref|YP_004598537.1|  [L=344]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for complete 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-11   44.4  19.0    1.5e-11   44.4  19.0    2.3  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        2.4    6.8   8.9        9.9    4.8   4.7    2.8  2  DUF2207       Predicted membrane protein (DUF2207)


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 ?   -5.2  11.5         2   1.8e+04      15      48 ..      43     124 ..      35     145 .. 0.53
   2 !   44.4  19.0   1.6e-15   1.5e-11       3     172 ..     140     329 ..     135     338 .. 0.81

  Alignments for each domain:
  == domain 1  score: -5.2 bits;  conditional E-value: 2
                      BPD_transp_1  15 kldkllrpliivll...slPsfvlaillvlvf............................................. 43 
                                         + l+++++i++l    +P+++l++l    +                                             
  gi|336255430|ref|YP_004598537.1|  43 LYRALFYVVTIFFLvttLFPFYWLLVLA---Ltpngliqqgdwavslpavgevpfptppihdlnptafvevfrqvpf 116
                                       4455555555555522156666655554...3345777777777777777777666666666666666666666664 PP

                      BPD_transp_1  44 ...vilsi 48 
                                          v++s 
  gi|336255430|ref|YP_004598537.1| 117 hlyVFNSF 124
                                       44333333 PP

  == domain 2  score: 44.4 bits;  conditional E-value: 1.6e-15
                      BPD_transp_1   3 llGilaalnrnkkldkllrpliivllslPsfvlaillvlvf............vilsilghlilp..viillllsaa 65 
                                       l+G++ + +  ++++ l++  + +++++P+ +++i+l+ +f             +++     ++p  +i+ +   ++
  gi|336255430|ref|YP_004598537.1| 140 LAGYVFG-RLEFPGRGLMMLAVLAISYFPPAAFLIPLFDAFlgnavtvpflgiELFTPPRLVNTPgsMIMPMSALFL 215
                                       5777888.99999*************************999***********9555566666666336888888899 PP

                      BPD_transp_1  66 pyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgtl 140
                                       p++++i   + +++p++l+ aar+ G +r   +++v++P+++p ++t ++l+f+++ +++++ ++++ ++     ++
  gi|336255430|ref|YP_004598537.1| 216 PLAIFILTTFYSQIPDGLEDAARVEGTTRLGALFRVIMPLSAPGVATAAVLTFISVYNEYFFSSIMALQNEpdQWSP 292
                                       9************************************************************9999986655564455 PP

                      BPD_transp_1 141 lleailgydyseis.....nggvlalviavlllnlva 172
                                       l+  il+y++++++     +++++++v+ +l+l+++a
  gi|336255430|ref|YP_004598537.1| 293 LVGGILSYQTQYTTdfnlmAAASIVGVLPMLILVVFA 329
                                       5555555555555555222266666666666665554 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   4.7    0.0011       9.9     357     409 ..      26     147 ..      17     244 .. 0.68
   2 ?    1.8   0.0    0.0091        81     201     272 ..     242     307 ..     234     317 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0011
                           DUF2207 357 lkkwksavkkkergyfdkkgkkklkklsalglgliilglilillallllvll......................... 408
                                       l++w+++v +      d++++++l++  ++ + +++l++ l+ +  ll+ +l                         
  gi|336255430|ref|YP_004598537.1|  26 LERWTRGVIE------DSEKRSRLYRALFYVVTIFFLVTTLFPFYWLLVLALtpngliqqgdwavslpavgevpfpt 96 
                                       5678888888......666666666666666666666666655555554444778889999**************** PP

                           DUF2207 409 ..................................................l 409
                                                                                          
  gi|336255430|ref|YP_004598537.1|  97 ppihdlnptafvevfrqvpfhlyvfnsfvlasattiivlvlaslagyvfgR 147
                                       *****************9999996666433333333333333333333330 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.0091
                           DUF2207 201 aarlslallillilllilllllllllliklllwkkygrepkvkevdpeYerdvPedlsPavvgylvkg..dkvd 272
                                       ++rl   + +++ l++  ++ +++l +i+      ++ e+ +  + +      P+++sP+v g+l ++   ++d
  gi|336255430|ref|YP_004598537.1| 242 TTRLGALFRVIMPLSAPGVATAAVLTFIS------VYNEYFFSSIMALQ--NEPDQWSPLVGGILSYQtqYTTD 307
                                       56677788899999999999999999999......99999999974333..569*********99886543333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2464.34
//
Query:       gi|336255431|ref|YP_004598538.1|  [L=337]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-15   55.6  15.0    5.6e-15   55.6  15.0    2.4  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        5.2    6.9   9.8       0.62    9.8   2.0    2.8  2  DUF2157       Predicted membrane protein (DUF2157)


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 ?   -3.0   4.8      0.57   5.1e+03      14      41 ..      25      52 ..      18     135 .. 0.66
   2 !   55.6  15.0   6.2e-19   5.6e-15       4     176 ..     137     330 ..     134     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.57
                      BPD_transp_1 14 kkldkllrpliivllslPsfvlaillvl 41
                                      +++ +l  +++  ll  P++vl+ ++ l
  gi|336255431|ref|YP_004598538.1| 25 RWIENLGETVFAYLLLSPIIVLLSVIAL 52
                                      6666666666666666666665555442 PP

  == domain 2  score: 55.6 bits;  conditional E-value: 6.2e-19
                      BPD_transp_1   4 lGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf....................vilsilghlilpvii 58 
                                       +G+  a  l + +++++++r+ ii+++++P+++ +++++l+f                      l++  ++ l + +
  gi|336255431|ref|YP_004598538.1| 137 IGFGQAlvLDQDFRGRRWVRTAIIIPWAIPIVIQGMMFFLMFhptagfltdpladwgivqanNTLNDPASSLLIISV 213
                                       55555566677899**********************************************99889999999999999 PP

                      BPD_transp_1  59 llllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswp 135
                                       + ++ + +++ l++ a+l+s++++l+ +a++ Gasrwq f+ +++P++lp++   ++++ ++++  + l+  + + +
  gi|336255431|ref|YP_004598538.1| 214 ADIWKTSAFMALLILAGLQSIDRSLYDVAKVAGASRWQQFKLITFPLVLPTLGIAVLFRTIAAMRIYGLIDSVSNCS 290
                                       9***************************************************************9999999999888 PP

                      BPD_transp_1 136 Glgtllleailgydyseisnggvlalviavlllnlvadilq 176
                                        + +l   + + ++++ ++ ++++a+v a ++ ++v+ +++
  gi|336255431|ref|YP_004598538.1| 291 TVPSLSCMVVSTFNTNRGL-ASAVAFVTAGVIGIAVMGVIY 330
                                       8888888888888888777.444444444444444444444 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.9     0.055   4.9e+02      88     118 ..     135     179 ..      25     195 .. 0.60
   2 ?    9.8   2.0     7e-05      0.62      43     114 ..     224     327 ..     212     336 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.055
                           DUF2157  88 r..............rvpprlgeallllaalllgaaialvgqifq 118
                                       +              r++++++ a+++  a+ +++  +++  +f+
  gi|336255431|ref|YP_004598538.1| 135 TligfgqalvldqdfRGRRWVRTAIIIPWAIPIVIQGMMFFLMFH 179
                                       122222233333334666666666666666655555555555555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 7e-05
                           DUF2157  43 alllglGlilfvAanW.....qglsrlvkfllllvllllslllgavlwrdr.......................... 88 
                                       all+++Gl ++  +++     +g sr+++f l+  +l+l  l++avl r+                           
  gi|336255431|ref|YP_004598538.1| 224 ALLILAGLQSIDRSLYdvakvAGASRWQQFKLITFPLVLPTLGIAVLFRTIaamriyglidsvsncstvpslscmvv 300
                                       5666666666666666666667899***********************98888888888888888888888888888 PP

                           DUF2157  89 ...rvpprlgeallllaalllgaaialvg 114
                                          + ++ l+ a+++++a ++g+a+  +g
  gi|336255431|ref|YP_004598538.1| 301 stfNTNRGLASAVAFVTAGVIGIAV--MG 327
                                       8775555555555555555544333..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2566.20
//
Query:       gi|336255432|ref|YP_004598539.1|  [L=489]
Description: family 1 extracellular solute-binding protein [Halopiger xanaduensis SH-6]
Scores for complete 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   87.8   0.8    2.1e-24   87.1   0.8    1.3  1  SBP_bac_1       Bacterial extracellular solute-binding protei
      6e-20   72.2   0.9    9.4e-20   71.6   0.9    1.2  1  SBP_bac_8       Bacterial extracellular solute-binding protei
    5.2e-06   26.1   1.2    5.2e-06   26.1   1.2    2.1  2  TAT_signal      TAT (twin-arginine translocation) pathway sig
     0.0044   16.8   0.0      0.011   15.5   0.0    1.6  1  Glyco_hydro_18  Glycosyl hydrolases family 18


Domain annotation for each model (and alignments):
>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.8   4.7e-28   2.1e-24      22     306 ..      73     391 ..      56     397 .. 0.85

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 4.7e-28
                                       HTTEEEEEEEECHHHHHH..HHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEEEEHHH CS
                         SBP_bac_1  22 hpgikVeiesvgsgslaq..kltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkdaadklsss 96 
                                         g+++e+++++  ++a    +t  ++aG  ++D++ +dn+w+  +++ g ++ l++ +++    +v+   d +++ 
  gi|336255432|ref|YP_004598539.1|  73 ADGVDIELQPGDEETGARreSYTNLLEAGETQPDLFLMDNGWVNVFIQRGHVANLSEELDESELSTVE---DEYFER 146
                                       4589*******999999989**********888*****************************998885...678888 PP

                                       HTHHHHCE.EE.ES.EEEE.EEEEEEEETTTHHCTTGGG.........SHBHHHHHHHHHHHHHHCTCT.HCCHCCE CS
                         SBP_bac_1  97 vlpkilds.kv.ly.vPly.aargliYNkdlfekagldp.........pwtWdelveaakklkekgkkp.iggargg 159
                                       ++++ +d   + ly vP+   +  + Y+kd+  +ag ++         p tW+e++e+ ++++e+  ++ +    + 
  gi|336255432|ref|YP_004598539.1| 147 FTATARDPeNDdLYgVPMFpDYPTMQYRKDYAREAGYGEsdfeewatePMTWSEWAEVTQEIVEASDAEyGLATQWD 223
                                       *******9566********88************************************************55555666 PP

                                       EHHHHHHHHHHHHHHHHTGGGEECCCT.........................HHCSHHHHSHHHHHHHHHHHHHHHH CS
                         SBP_bac_1 160 sasgtayyfalalakslggkvfdkdgg.........................gldnpegvtaatylvklyavanltk 211
                                       +++gta  ++++++ s+gg +f++  +                         +++++e+ + +   ++         
  gi|336255432|ref|YP_004598539.1| 224 QYEGTACCTWNEVMSSFGGAYFGGFDNlfgpvgdrpvtidepefveglrmmrTFVADEADDHTLEDEYPL------- 293
                                       7899*********************************666666666666555555555555444444444....... PP

                                       HHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE..... CS
                         SBP_bac_1 212 elkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi..... 283
                                       +l+  + +++++++a++++ +G+aam  ++++a        +   ++ad++ p e++g+ p+P+g +   +      
  gi|336255432|ref|YP_004598539.1| 294 GLATSDITSWTEEDARTAILNGDAAMQRNWPYA-------INLNVADADDPLPVEDYGAMPIPYGVPEEEAAqpgtg 363
                                       66777778888888888888*************.......5677788888999999*******9999888889999* PP

                                       .....EEEEEEEEBTTCSTHHHHHHHHH CS
                         SBP_bac_1 284 .....lgayglaipkgsknpeaAkkFld 306
                                            lg+++++++ +s  +e+A ++++
  gi|336255432|ref|YP_004598539.1| 364 gttaaLGGWHVVLNPNSERKEEALEVIR 391
                                       ************************9986 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.9   2.1e-23   9.4e-20      11     277 ..      75     424 ..      64     429 .. 0.73

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 2.1e-23
                                       TEEEEEEE-..-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG...GSTTHHH..........-H CS
                         SBP_bac_8  11 gvkvnvvta..asndleqklkaalaagtapdidvvwanedalatlaeeglladls...dldnldd..........lt 72 
                                       gv++++++   +++   + +++ l+ag++ ++d+++++++++  ++++g +a+ls   d  +++           +t
  gi|336255432|ref|YP_004598539.1|  75 GVDIELQPGdeETGARRESYTNLLEAGET-QPDLFLMDNGWVNVFIQRGHVANLSeelD--ESELstvedeyferFT 148
                                       6777777775566777788999999***8.78**********************96332..4444555556544444 PP

                                       HHHHTT--TS.----EEEEEEE-EEEEEHHHHHHS............---BHHHHHHHHHHH....HHH-SEGG--- CS
                         SBP_bac_8  73 dalaavgydgklygvPyasetpyvliynkdlleka...........edpktwdellaaakkl....kgkfglpdpas 134
                                       +++++ + +++lygvP     p ++ y+kd++ +a             p tw+e+ ++ +++       +gl+++++
  gi|336255432|ref|YP_004598539.1| 149 ATARDPE-NDDLYGVPMFPDYP-TMQYRKDYAREAgygesdfeewaTEPMTWSEWAEVTQEIveasDAEYGLATQWD 223
                                       4444444.444*****999998.*********998888888889999**********99988766567778877666 PP

                                       G........GGGGGTHH........ETTEE---H..............HHH.HHHHHHHHHHHHTT-..EE...... CS
                         SBP_bac_8 135 g........wlqaalla........kdgksldddg............gkdglkealellkklkdngk..ty...... 175
                                       +        w + +  +        +        +            ++++++e l+++++++++    ++      
  gi|336255432|ref|YP_004598539.1| 224 QyegtacctWNEVMSSFggayfggfD--------NlfgpvgdrpvtiDEPEFVEGLRMMRTFVADEAddHTledeyp 292
                                       63335555555555555444444440........234444455556669999***********66644544477777 PP

                                       ..........-S..--SSTTTTTSBSEEEE-TTHHH.HHH-TTT.....SEEEE.--............S--..EEE CS
                         SBP_bac_8 176 ..........dtgadavsefanGevaftingswdia.aaqkagk.....klgai.vp............kqg..sfa 221
                                                 +t +da  ++ nG++a+  n++ +i+ ++++a++     ++ga+ +p              g  ++a
  gi|336255432|ref|YP_004598539.1| 293 lglatsditsWTEEDARTAILNGDAAMQRNWPYAINlNVADADDplpveDYGAMpIPygvpeeeaaqpgT-GgtTAA 368
                                       88888899889*********************99886566665435555777774446666887764431.144344 PP

                                       EEEE.EEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTHHHHHH- CS
                         SBP_bac_8 222 ggkg.lavpknaknedlaAldFlkwltspenqaalaektgyipvnksaalspevkkd 277
                                        g + ++ + n++ +++ Al+ ++  +++e +  +++ +g ip+ +++ + +ev+++
  gi|336255432|ref|YP_004598539.1| 369 LGGWhVVLNPNSERKEE-ALEVIRATMTDEFNLGMFDLWGWIPPKPALFDADEVQEA 424
                                       44442555667777775.************************************987 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   1.2   1.2e-09   5.2e-06       2      23 ..      15      36 ..      14      38 .. 0.95
   2 ?   -2.0   2.0      0.87   3.9e+03      12      21 ..     363     370 ..     361     372 .. 0.43

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.2e-09
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggc 23
                                      +SRR+F K+++A++A + l+gc
  gi|336255432|ref|YP_004598539.1| 15 VSRRTFVKAAGAGGASVSLAGC 36
                                      8********************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.87
                        TAT_signal  12 AAaaAAaalg 21 
                                       ++    aalg
  gi|336255432|ref|YP_004598539.1| 363 GG--TTAALG 370
                                       33..344444 PP

>> Glyco_hydro_18  Glycosyl hydrolases family 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.4e-06     0.011      86     131 ..      54     100 ..      30     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHHHHHHHHHHHCT-SEEEEEES-TTTS...TCHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                    Glyco_hydro_18  86 dasrkkfadsvvsllrkygfDGiDidweypggn...pedkenytallke 131
                                       + +++++ d++v+l+++ g DG+Di ++ pg++   ++ +e yt+ll++
  gi|336255432|ref|YP_004598539.1|  54 PNAAESVGDEIVELVQESGADGVDIELQ-PGDEetgAR-RESYTNLLEA 100
                                       46678999********************.988655433.9999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 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:                        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 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3830.42
//
Query:       gi|336255433|ref|YP_004598540.1|  [L=363]
Description: transcriptional regulator TrmB [Halopiger xanaduensis SH-6]
Scores for 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-67  226.6   0.1    2.9e-67  226.3   0.1    1.1  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    6.5e-16   58.0   0.0    1.4e-15   56.9   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00011   22.0   1.4     0.0025   17.6   0.0    3.0  3  MarR_2          MarR family
     0.0054   16.8   0.7     0.0096   16.0   0.7    1.3  1  T2SSM           Type II secretion system (T2SS), protein M
  ------ inclusion threshold ------
      0.014   15.2   0.1      0.058   13.2   0.0    2.0  2  HTH_IclR        IclR helix-turn-helix domain
      0.015   15.3   0.0      0.037   14.0   0.0    1.6  1  PadR            Transcriptional regulator PadR-like family
      0.034   14.6   0.1       0.32   11.5   0.0    2.6  3  HTH_27          Winged helix DNA-binding domain
      0.058   13.3   0.0       0.16   11.9   0.0    1.9  1  MarR            MarR family
       0.16   11.4   0.0       0.25   10.7   0.0    1.3  1  DUF4159         Domain of unknown function (DUF4159)
       0.16   12.4   0.2       0.37   11.2   0.2    1.6  1  Latarcin        Latarcin precursor
        6.3    7.1   7.6       0.33   11.2   0.5    2.4  3  ABC_tran_CTD    ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.3   0.1   1.8e-70   2.9e-67       2     231 ..     111     360 ..     110     362 .. 0.96

  Alignments for each domain:
  == domain 1  score: 226.3 bits;  conditional E-value: 1.8e-70
                                       EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS.....----GGGSSSSEEEE CS
                    Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliyp.....dedleeldleevate 73 
                                       v++vk+ +tv+ r++elI++A+n+++v l++ ++ el + l+ a+e+gv+V ++++p      e +++  l+++++e
  gi|336255433|ref|YP_004598540.1| 111 VSIVKRLDTVLARADELIRAADNQVQVGLTPAQFDELADALETARENGVNVKVSLFPeldsePELPSTDALARTCAE 187
                                       89*******************************************************99774444556678899*** PP

                                       EE-S---S.EEEEETTTEEEEE-SSS-EEEE--HHHHHHHHHHHHHH........HHH-EEEEEEES-TT-EEES-H CS
                    Regulator_TrmB  74 vrvrrsgapllvivDrkrgvvaprevlrdkeeeyaiifkekelihvlshyFlttlWktseviktdepvekpitfssi 150
                                       +r+r ++ap++++ Dr+++++ap+    d++++y++i+++++l++v+++yFl++lW+  e+i+td+++e pit+++ 
  gi|336255433|ref|YP_004598540.1| 188 ARYRTLPAPFVALIDRSWTCFAPH---GDSTNQYGVIVNDRTLAYVVHWYFLSCLWEVHETIYTDRREEPPITYVDL 261
                                       ************************...5************************************************* PP

                                       HHHHHHHHHHT.TTS-EEEEEEEEETTT--EEEEEEEEEEEE..................EETTTTEEEEEEEETTE CS
                    Regulator_TrmB 151 rlavedikkllraglkveaeveGrdtetgeevtieGrvveat..................lnstpgvaslvvetedg 209
                                       r++++d+++ll +g +++ +v+G+dt+tg+evt +G++++++                  l + +g+asl++et+dg
  gi|336255433|ref|YP_004598540.1| 262 RRCLRDVEPLLADGVTIRTTVRGYDTDTGREVTRTGTITDVSyiddlddskanattesitLLQLSGKASLTIETDDG 338
                                       ****************************************99****************99999999*********** PP

                                       EEEEE-TT--SSSEEEEEEEEE CS
                    Regulator_TrmB 210 evtVGGlgAvlEDieaeeitle 231
                                       evtVGG+gA+lEDiea ei+++
  gi|336255433|ref|YP_004598540.1| 339 EVTVGGWGAMLEDIEAIEIVIT 360
                                       *******************996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   8.5e-19   1.4e-15       1      57 [.      10      66 ..      10      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 8.5e-19
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      L++ GLs y a+++++Ll+lg+a+a+++a+++ vp +++Y+vLr Le+kG+Ve+ ++
  gi|336255433|ref|YP_004598540.1| 10 LEEAGLSPYQADAFVTLLELGSASATDVAQASSVPDPRIYDVLRGLEEKGYVETYEQ 66
                                      6789*************************************************8776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.6e-06    0.0025       2      61 ..      14      72 ..      13      73 .. 0.91
   2 ?    1.6   0.1      0.16   2.6e+02       8      31 ..      77     101 ..      76     104 .. 0.84
   3 ?   -1.4   0.0       1.3   2.2e+03       2       9 ..     138     145 ..     137     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE.ESSSSSS CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr.pgpeDkR 61
                                      gl+p qa++   L   +    +++++a++  ++ +++  +l+ L+++G+ve+   ++ ++R
  gi|336255433|ref|YP_004598540.1| 14 GLSPYQADAFVTLLELGS--ASATDVAQASSVPDPRIYDVLRGLEEKGYVETYeQDSLHAR 72
                                      899999******999999..9*****************************99866666777 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.16
                                       HHHHHHHHCTTTS.EEEHHHHHHHH CS
                            MarR_2   8 arvLaaLgrrpgr.dltvgelarrl 31 
                                       a+vLa L++r +r   ++ e+++r+
  gi|336255433|ref|YP_004598540.1|  77 ADVLADLRARADRlQTAAEEIEDRW 101
                                       69*********98544999999887 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.3
                                       T--HHHHH CS
                            MarR_2   2 gltpaqar 9  
                                       gltpaq++
  gi|336255433|ref|YP_004598540.1| 138 GLTPAQFD 145
                                       99***998 PP

>> T2SSM  Type II secretion system (T2SS), protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.7   5.9e-06    0.0096      42     138 ..      72     163 ..      67     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.9e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHHHHHHHHCT--EEEEEEETT.EEEEEE--B-H CS
                             T2SSM  42 rieraqaelqklraqlawveeqaaevralraapasalsgaaleqvvtrsarqagLalarlqpqgdgsvqvwleevpf 118
                                       r+ + ++ l+ lra +++++++a+e++   + p  ++   ++ + +++ +++a+ +l+      d++vqv l +++f
  gi|336255433|ref|YP_004598540.1|  72 RANDPADVLADLRARADRLQTAAEEIEDRWSRPDLEEHRVSIVKRLDTVLARAD-ELI---RAADNQVQVGLTPAQF 144
                                       555556678999***************988888888888899999**9999999.444...455669********** PP

                                       HHHHHHHHHHHHHS--EEEE CS
                             T2SSM 119 eallrWLaeleeqqgvsvee 138
                                       ++l++ L++++ + gv+v+ 
  gi|336255433|ref|YP_004598540.1| 145 DELADALETAR-ENGVNVKV 163
                                       ***********.99**9975 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 ?   -2.3   0.1       2.5   4.1e+03      38      47 ..       6      15 ..       5      15 .. 0.86
   2 ?   13.2   0.0   3.5e-05     0.058      20      49 ..      33      62 ..      25      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.5
                                      HHHHHHHTTS CS
                          HTH_IclR 38 lLqtLvelGy 47
                                      l++tL+e G+
  gi|336255433|ref|YP_004598540.1|  6 LTATLEEAGL 15
                                      889****996 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.5e-05
                                      BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyve 49
                                      + +++A+++ +p +  +  L+ L+e Gyve
  gi|336255433|ref|YP_004598540.1| 33 SATDVAQASSVPDPRIYDVLRGLEEKGYVE 62
                                      789**************************9 PP

>> PadR  Transcriptional regulator PadR-like family
   #    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      32      54 ..      46      68 ..      34      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                                      HHHHHHHHHHHHTTSEEEEEE-S CS
                              PadR 32 GslYpaLkrLekeglvesewees 54
                                       ++Y++L+ Le++g+ve+++++s
  gi|336255433|ref|YP_004598540.1| 46 PRIYDVLRGLEEKGYVETYEQDS 68
                                      589*****************997 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 ?   11.5   0.0    0.0002      0.32      16      51 ..      29      64 ..      18      73 .. 0.85
   2 ?   -1.7   0.0       2.6   4.3e+03      14      37 ..      73      96 ..      69     106 .. 0.75
   3 ?   -1.6   0.0       2.5   4.1e+03      11      35 ..     280     304 ..     275     311 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvert 51
                                      ++ ++++d++++  v d  i  +l+ L+ekG+ve+ 
  gi|336255433|ref|YP_004598540.1| 29 LGSASATDVAQASSVPDPRIYDVLRGLEEKGYVETY 64
                                      677899***************************654 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
                            HTH_27 14 hrrrrkkladlcgrlnvedshisy 37
                                       ++  + ladl+ r ++ ++++ +
  gi|336255433|ref|YP_004598540.1| 73 ANDPADVLADLRARADRLQTAAEE 96
                                      466677789999999988887766 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.5
                            HTH_27  11 lirhrrrrkkladlcgrlnvedshi 35 
                                       +  + +++++ +++ ++  ++d ++
  gi|336255433|ref|YP_004598540.1| 280 TTVRGYDTDTGREVTRTGTITDVSY 304
                                       4445888888888888888877665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0001      0.16       2      49 ..      16      63 ..      15      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                                      -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      ++ q ++ ++l e g++s ++ a +++v  + +  vl+ Le+kG++e 
  gi|336255433|ref|YP_004598540.1| 16 SPYQADAFVTLLELGSASATDVAQASSVPDPRIYDVLRGLEEKGYVET 63
                                      66678888999***********************************85 PP

>> DUF4159  Domain of unknown function (DUF4159)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00015      0.25     105     187 ..     165     251 ..     148     258 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                                       HS-TTS-E.E--TTSGGGGSSS--S......S--SS----SS..................ETTEEEEEEETT-HHHH CS
                           DUF4159 105 vfPekple.elpadhvlfksfyllkeg.lpkefpgryagsev....adekrpqargifedndrvsvvyignnDlgda 175
                                       +fPe + e elp++++l ++  + + + lp+ f   +++s +    + +++ +++g++  ndr+++ +++ + l++ 
  gi|336255433|ref|YP_004598540.1| 165 LFPELDSEpELPSTDALARTCAEARYRtLPAPFVALIDRSWTcfapH-GDSTNQYGVIV-NDRTLAYVVHWYFLSCL 239
                                       57766554368999999998888875568885555555555577854.44556788888.59*************** PP

                                       H-B-T-S--TTH CS
                           DUF4159 176 Wevdellpsdpe 187
                                       Wev+e+ ++d++
  gi|336255433|ref|YP_004598540.1| 240 WEVHETIYTDRR 251
                                       *****7777764 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00023      0.37      29      62 ..      79     113 ..      55     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                          Latarcin  29 mvnnlRkvqgRLeemvenlrkvedledtEEARg.a 62 
                                        + +lR  + RL+ ++e+++ +  ++d+EE R  +
  gi|336255433|ref|YP_004598540.1|  79 VLADLRARADRLQTAAEEIEDRWSRPDLEEHRVsI 113
                                       56789***************************834 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 ?   11.2   0.5    0.0002      0.33      23      64 ..      65     101 ..      63     103 .. 0.92
   2 ?   -2.3   0.1       3.4   5.5e+03      41      52 ..     142     153 ..     115     157 .. 0.50
   3 ?   -1.4   0.2       1.8   2.9e+03      14      28 ..     349     363 .]     345     363 .] 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                      ABC_tran_CTD  23 eiaeleaeladpelysdpeklaelsaeleeleaeLeelyerW 64 
                                       e+ +l+a+ +dp+     + la+l a+ ++l+++ ee ++rW
  gi|336255433|ref|YP_004598540.1|  65 EQDSLHARANDPA-----DVLADLRARADRLQTAAEEIEDRW 101
                                       6889999999998.....77********************** PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                      ABC_tran_CTD  41 eklaelsaelee 52 
                                       +++ el   le+
  gi|336255433|ref|YP_004598540.1| 142 AQFDELADALET 153
                                       334444444433 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.8
                      ABC_tran_CTD  14 eaeIeaLEeeiaele 28 
                                        ++Iea+E  i++le
  gi|336255433|ref|YP_004598540.1| 349 LEDIEAIEIVITALE 363
                                       578888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.50u 0.18s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 3015.27
//
Query:       gi|336255434|ref|YP_004598541.1|  [L=293]
Description: hypothetical protein Halxa_4057 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0094   16.1   1.9      0.017   15.2   1.9    1.3  1  TerY_C          TerY-C metal binding domain
  ------ inclusion threshold ------
      0.062   13.0   2.2        6.6    6.5   0.1    2.6  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        0.3   11.1   2.9        7.9    6.5   0.4    2.4  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        0.4   10.9   4.7        5.3    7.2   0.0    2.5  2  Zn-ribbon_8     Zinc ribbon domain
       0.57   10.2   2.9        2.9    7.9   2.9    2.0  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.62    9.5   6.2       0.31   10.5   1.4    2.4  2  zf-ribbon_3     zinc-ribbon domain
       0.84    9.9   3.6         25    5.2   0.0    2.5  2  zinc_ribbon_9   zinc-ribbon
        3.9    7.6   6.4        3.7    7.7   0.1    3.2  3  Rubredoxin      Rubredoxin


Domain annotation for each model (and alignments):
>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.9   7.6e-06     0.017      75     110 ..     249     287 ..     240     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.6e-06
                            TerY_C  75 pgCPhCgnalafavCe.CgkllCidg..eeeatCpwCgk 110
                                       ++CP Cg++l+++  + Cg++  i++  +e+ +Cp C+ 
  gi|336255434|ref|YP_004598541.1| 249 ASCPRCGSELTITQTScCGEVTPIGEtpPEKLVCPDCDV 287
                                       68*********9865527******9966799******85 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 ?    5.6   0.3    0.0057        13       6      13 ..     251     258 ..     251     262 .. 0.84
   2 ?    6.5   0.1     0.003       6.6      21      32 .]     279     290 ..     279     290 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0057
                     zf-NADH-PPase   6 CgrCGapt 13 
                                       C+rCG++ 
  gi|336255434|ref|YP_004598541.1| 251 CPRCGSEL 258
                                       *****975 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.003
                     zf-NADH-PPase  21 arvCpaCglehY 32 
                                       ++vCp+C+ +++
  gi|336255434|ref|YP_004598541.1| 279 KLVCPDCDVRYF 290
                                       68******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 ?    6.5   0.4    0.0035       7.9      20      30 ..     250     261 ..     234     268 .. 0.73
   2 ?    4.6   0.1     0.015        33      16      27 ..     277     288 ..     276     293 .] 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0035
                     Zn_Tnp_IS1595  20 vCPhCgsr.kay 30 
                                        CP+Cgs+ +++
  gi|336255434|ref|YP_004598541.1| 250 SCPRCGSElTIT 261
                                       6*****986554 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.015
                     Zn_Tnp_IS1595  16 pngfvCPhCgsr 27 
                                       p++ vCP C +r
  gi|336255434|ref|YP_004598541.1| 277 PEKLVCPDCDVR 288
                                       5678*****987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0024       5.3      27      36 ..     248     258 ..     238     261 .. 0.80
   2 ?    3.7   2.0     0.031        70      11      33 ..     266     286 ..     263     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0024
                       Zn-ribbon_8  27 ta.CPeCgsev 36 
                                        a CP+Cgse+
  gi|336255434|ref|YP_004598541.1| 248 LAsCPRCGSEL 258
                                       455*****976 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.031
                       Zn-ribbon_8  11 Cghefevlqsisdaplta.CPeCg 33 
                                       Cg e +++ +   +p++  CP+C 
  gi|336255434|ref|YP_004598541.1| 266 CG-EVTPIGE--TPPEKLvCPDCD 286
                                       55.5555543..6778888****4 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   2.9    0.0013       2.9       4      25 ..     250     285 ..     247     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0013
                    PhnA_Zn_Ribbon   4 kCplCaSeytY..............edgallvCpeC 25 
                                        Cp C+Se t                  + lvCp+C
  gi|336255434|ref|YP_004598541.1| 250 SCPRCGSELTItqtsccgevtpigeTPPEKLVCPDC 285
                                       6*********999999999999999888999***99 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.4   0.00014      0.31       4      19 ..     250     265 ..     248     270 .. 0.85
   2 ?    0.7   0.2      0.17   3.9e+02      18      22 ..     281     285 ..     275     287 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                       zf-ribbon_3   4 rCPnCGa.plssddnvC 19 
                                       +CP+CG+ + +  ++ C
  gi|336255434|ref|YP_004598541.1| 250 SCPRCGSeL-TITQTSC 265
                                       8******66.9999999 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.17
                       zf-ribbon_3  18 vCpyC 22 
                                       vCp C
  gi|336255434|ref|YP_004598541.1| 281 VCPDC 285
                                       68877 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.011        25      22      29 ..     249     256 ..     233     258 .. 0.70
   2 ?    4.1   1.7     0.026        57      11      28 ..     268     286 ..     264     290 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.011
                     zinc_ribbon_9  22 vlCPhCgg 29 
                                       ++CP+Cg+
  gi|336255434|ref|YP_004598541.1| 249 ASCPRCGS 256
                                       47****98 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.026
                     zinc_ribbon_9  11 fVsvspdedsdv.lCPhCg 28 
                                       +V++  ++ +++ +CP+C+
  gi|336255434|ref|YP_004598541.1| 268 EVTPIGETPPEKlVCPDCD 286
                                       56655566666557****8 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.28   6.3e+02      11      30 ..      88     107 ..      82     110 .. 0.84
   2 ?    0.4   0.2       0.3   6.6e+02      36      42 ..     250     256 ..     249     259 .. 0.82
   3 ?    7.7   0.1    0.0016       3.7      32      43 ..     277     288 ..     272     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.28
                                       EETTTBBGGGTB-TT--GGG CS
                        Rubredoxin  11 YdpakGdpdegiapgTkFed 30 
                                        dpa G+  +g+a gT  e+
  gi|336255434|ref|YP_004598541.1|  88 DDPATGQRPSGLAEGTDGEA 107
                                       59*************98665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.3
                                       BBTTTB- CS
                        Rubredoxin  36 vCPdCgv 42 
                                        CP Cg 
  gi|336255434|ref|YP_004598541.1| 250 SCPRCGS 256
                                       5****96 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0016
                                       -TT-BBTTTB-B CS
                        Rubredoxin  32 PddWvCPdCgve 43 
                                       P++ vCPdC+v+
  gi|336255434|ref|YP_004598541.1| 277 PEKLVCPDCDVR 288
                                       999*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2374.84
//
Query:       gi|336255435|ref|YP_004598542.1|  [L=254]
Description: hypothetical protein Halxa_4058 [Halopiger xanaduensis SH-6]
Scores for complete 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   24.0   0.1    1.5e-05   24.0   0.1    2.1  2  GPDPase_memb  Membrane domain of glycerophosphoryl diester ph
     0.0032   17.3   4.5     0.0061   16.4   4.2    1.5  1  DUF975        Protein of unknown function (DUF975)
     0.0082   15.9   4.2     0.0082   15.9   4.2    1.9  2  UPF0259       Uncharacterised protein family (UPF0259)
  ------ inclusion threshold ------
      0.089   12.7   5.5       0.16   11.9   5.5    1.4  1  DUF4271       Domain of unknown function (DUF4271)
       0.17   11.9   0.3       0.17   11.9   0.3    1.9  2  YpmT          Uncharacterized YmpT-like
       0.44   10.7  11.1        1.2    9.3  11.1    1.7  1  Osw5          Outer spore wall 5
        3.5    7.1   6.0       0.56    9.7   2.2    1.6  2  Sec62         Translocation protein Sec62


Domain annotation for each model (and alignments):
>> GPDPase_memb  Membrane domain of glycerophosphoryl diester phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   5.0      0.14   3.7e+02     243     317 ..      35     127 ..      18     131 .. 0.43
   2 !   24.0   0.1   5.7e-09   1.5e-05     165     244 ..     130     208 ..     127     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.14
                      GPDPase_memb 243 lldkl.pkkvslilaiinlt......llqiisliilvlsivlitqllvkqlesekeleeev...........kkkkl 301
                                       ++ ++ ++++ + la  +++      l  +++ i +++s v i+ l++  l  + + ++             ++++l
  gi|336255435|ref|YP_004598542.1|  35 IVAQVsFQSLFVQLAADSFSadqldqLYPLAIDIPITVSGVGILLLMLGGLVLSVVATRALysnidripttdHTRRL 111
                                       33333333333333333333334444333333333444444444444444433333333333444444444466666 PP

                      GPDPase_memb 302 kivvkivinllvllli 317
                                       +++v++ +++lv+ ++
  gi|336255435|ref|YP_004598542.1| 112 ARTVVVAFVVLVIYFL 127
                                       6666666666655544 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 5.7e-09
                      GPDPase_memb 165 vllylifylivfylaiRliftLPliilekkslkeAlkeSwqltkknflrlllklllliliivivltvilsllllllq 241
                                       +++ + f++  ++l++ ++f+ P +ile+  + e+ k+Sw l ++n+l+l+   +l++++ +iv  vi++++ + + 
  gi|336255435|ref|YP_004598542.1| 130 MIGTVFFVVPGIFLGVSFVFAQPAVILEDAGVLESFKRSWGLASGNRLKLFGLGVLVTVLGGIVGGVIGFVGAF-VP 205
                                       5667777777899*************************************666677777777766666665544.44 PP

                      GPDPase_memb 242 lll 244
                                       l+ 
  gi|336255435|ref|YP_004598542.1| 206 LFG 208
                                       444 PP

>> DUF975  Protein of unknown function (DUF975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   4.2   2.4e-06    0.0061     112     204 ..      79     183 ..      29     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.4e-06
                            DUF975 112 lwsliallglliiiislsla..........llsseieenlvvvllvlliilllivlilaiive.yayslveyilvee 177
                                       l++l    gl++++++ +++           ++ ++ +  vv+ +vl+i  l+++++  ++v   ++  v +++++ 
  gi|336255435|ref|YP_004598542.1|  79 LLMLG---GLVLSVVATRALysnidripttDHTRRLARTVVVAFVVLVIYFLMVMIGTVFFVVpGIFLGVSFVFAQP 152
                                       33333...333333333333445777877778888888889988888888888888887777658888888888876 PP

                            DUF975 178 le....lGayealkeSkkmmkGyKwklfvLd 204
                                              G+ e  k+S  +  G+++klf L 
  gi|336255435|ref|YP_004598542.1| 153 AViledAGVLESFKRSWGLASGNRLKLFGLG 183
                                       5455559*********************875 PP

>> UPF0259  Uncharacterised protein family (UPF0259)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.4      0.22   5.7e+02     101     161 ..      27      90 ..      19      96 .. 0.64
   2 !   15.9   4.2   3.2e-06    0.0082     134     200 ..     119     186 ..      85     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.22
                           UPF0259 101 lgnlitliqlvsekkrvsilnaigl...sllllPklliLiflttl.liqlGllllliPGiivail 161
                                       + ++ +l q+v++    s++ ++ +   s+  l +l+ L   + + +  +G+lll++ G++++++
  gi|336255435|ref|YP_004598542.1|  27 V-GIYVLYQIVAQVSFQSLFVQLAAdsfSADQLDQLYPLAIDIPItVSGVGILLLMLGGLVLSVV 90 
                                       4.45666666666665565555544111455667777776655551557999***9999999876 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.2e-06
                           UPF0259 134 liLiflttlliqlGllllliPGiivaillslsPiillkekksildsikasvnitfkn.ikliaPavll 200
                                       ++++ +  l++ +G +++++PGi + + + ++   ++ e+ ++l+s k s  ++  n +kl + +vl+
  gi|336255435|ref|YP_004598542.1| 119 FVVLVIYFLMVMIGTVFFVVPGIFLGVSFVFAQPAVILEDAGVLESFKRSWGLASGNrLKLFGLGVLV 186
                                       444456678899*******************988888899**********999875536776666665 PP

>> DUF4271  Domain of unknown function (DUF4271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   5.5   6.2e-05      0.16       4     114 ..      25     136 ..      23     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.2e-05
                           DUF4271   4 llllcflll.alaksrfrkffsrllklffnnkereslfkeetksesrfqlflllltclllg.lllylllsefgslfg 78 
                                       +l+++++l+ ++a ++f+++f +l  + f+ ++ ++l       +   ++  + + +l+lg l+l ++  +  +++ 
  gi|336255435|ref|YP_004598542.1|  25 VLVGIYVLYqIVAQVSFQSLFVQLAADSFSADQLDQLYPL--AIDIPITVSGVGILLLMLGgLVLSVVATRALYSNI 99 
                                       799999999999********************99999988..66666666666666666665777777777677776 PP

                           DUF4271  79 syla.ssllllliiflilllylllKlllykllgwlFf 114
                                       ++++ +  +  l  ++++++++l+ ++l+ ++g++Ff
  gi|336255435|ref|YP_004598542.1| 100 DRIPtTDHTRRLARTVVVAFVVLVIYFLMVMIGTVFF 136
                                       66669888888999999999999999**********9 PP

>> YpmT  Uncharacterized YmpT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   6.6e-05      0.17       4      36 ..      29      62 ..      26      68 .. 0.89
   2 ?   -3.8   1.0       5.3   1.3e+04      45      50 ..     126     131 ..     119     148 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.6e-05
                              YpmT  4 iyvyFslls.llfslyFGglayqhlvaenmDkvY 36
                                      iyv++ +++ + f  +F  la+ ++ a+++D++Y
  gi|336255435|ref|YP_004598542.1| 29 IYVLYQIVAqVSFQSLFVQLAADSFSADQLDQLY 62
                                      89*****984569999*****************9 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.3
                              YpmT  45 FLsimv 50 
                                       FL +m+
  gi|336255435|ref|YP_004598542.1| 126 FLMVMI 131
                                       333333 PP

>> Osw5  Outer spore wall 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  11.1   0.00046       1.2       2      39 ..     117     156 ..     116     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00046
                              Osw5   2 lyfliYlvlFliigviaslfilP..LLgiSfifatgvvvf 39 
                                       + f++ ++ Fl++ +   +f++P  +Lg+Sf+fa   v++
  gi|336255435|ref|YP_004598542.1| 117 VAFVVLVIYFLMVMIGTVFFVVPgiFLGVSFVFAQPAVIL 156
                                       679999999*************************988876 PP

>> Sec62  Translocation protein Sec62
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.2   0.00022      0.56     143     198 ..     117     172 ..     112     179 .. 0.79
   2 ?   -3.9   0.1       3.1   7.8e+03     185     196 ..     197     208 ..     197     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00022
                             Sec62 143 aalgllglilalaivRlilflivllvtkgklhlWlfPn.lfeDvGfldSFrPlYeye 198
                                        a+++l++ +++ ++ +++f++  ++++    +   P  + eD G+l+SF+  ++  
  gi|336255435|ref|YP_004598542.1| 117 VAFVVLVIYFLMVMIGTVFFVVPGIFLGVSFVF-AQPAvILEDAGVLESFKRSWGLA 172
                                       466778888899999999999999999988554.4455278**********999876 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.1
                             Sec62 185 vGfldSFrPlYe 196
                                       +Gf+  F Pl++
  gi|336255435|ref|YP_004598542.1| 197 IGFVGAFVPLFG 208
                                       699******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1244  (0.0693848); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 1816.34
//
Query:       gi|336255436|ref|YP_004598543.1|  [L=325]
Description: Fructokinase [Halopiger xanaduensis SH-6]
Scores for 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-64  216.9   0.0    4.2e-64  216.7   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 !  216.7   0.0   2.4e-68   4.2e-64       2     301 ..       3     316 ..       2     317 .. 0.97

  Alignments for each domain:
  == domain 1  score: 216.7 bits;  conditional E-value: 2.4e-68
                                       EEEEEEEEEEEEEEEECSSHTTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEE CS
                              PfkB   2 tkvvviGealidliavseklegelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvd 78 
                                       ++v+v Ge+lid+ +   +     + v+ + ++aGGa+aNvAvalarl     f ++vGdD+fG+ l++ l + g++
  gi|336255436|ref|YP_004598543.1|   3 HDVLVAGETLIDFLPERPG---PISSVEGFDRRAGGAPANVAVALARLERPPLFWTRVGDDPFGRYLESVLTEYGLP 76 
                                       67999***********998...777**************************************************** PP

                                       ETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEES..EECTTSHHHHHHHHHH CS
                              PfkB  79 tdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisg..llsselpeavleelae 153
                                        ++v++d+d++t+la+++ de+g+r++ f+r  +ad + e+   d   l+  ++++ +g  l s   +ea+l +l+ 
  gi|336255436|ref|YP_004598543.1|  77 DRFVERDPDAKTTLAFVTHDETGDRSFSFYRDGTADTRLEPGRADDVTLADREWVHAGGvtLASGRAREATLDLLER 153
                                       ***************************************9999********************************** PP

                                       HHHHTTE..EEEEECESSSHH...HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEE CS
                              PfkB 154 aaknggt..fdpnlldplgaq...fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvv 225
                                       aa +g t  fdpn+++ l+++   f+ + +++l+++d+lk++ eEle l    + d+ ++++++ + +++g++ v+ 
  gi|336255436|ref|YP_004598543.1| 154 AADAGCTtsFDPNYRPELWPDadaFRTVARDALEHVDVLKATGEELETLGFGGDGDESDLKDRARAALSAGPDAVFA 230
                                       ***********************************************99777779********************** PP

                                       EEGGGEEEEEE...........TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHT CS
                              PfkB 226 tlGkeGalvve...........kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvq 291
                                       t+G eGa++v            ++g  ++p  +  +vvDttGAGD+fv+g +++l eg +lee l+fanav+a++++
  gi|336255436|ref|YP_004598543.1| 231 TRGGEGAIAVAakdspwagtgtGEGAAEHPG-YDADVVDTTGAGDAFVAGTVVGLHEGRDLEETLAFANAVGAAATT 306
                                       ********************98888889999.99******************************************* PP

                                       SSSSSTCSCC CS
                              PfkB 292 kkgaiaslpt 301
                                         ga+a+lp+
  gi|336255436|ref|YP_004598543.1| 307 AAGAMAALPD 316
                                       *****99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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 0.19s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2677.94
//
Query:       gi|336255437|ref|YP_004598544.1|  [L=477]
Description: short chain fatty acid transporter [Halopiger xanaduensis SH-6]
Scores for complete 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-37  130.2  14.3    1.3e-37  129.9  14.3    1.1  1  SCFA_trans  Short chain fatty acid transporter


Domain annotation for each model (and alignments):
>> SCFA_trans  Short chain fatty acid transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9  14.3   7.3e-42   1.3e-37      10     451 ..      37     475 ..      30     477 .] 0.83

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 7.3e-42
                        SCFA_trans  10 valvskylPdplifallltlvtfvlvlvltkqtavslvdvwgnGfwnllsfamqmalilvtGqalassklvkkllkk 86 
                                       v    +y+P++l  a++l+ ++ ++ +  ++  +++ +++ g Gf++l+s  m + l  v+G +l +s+ v   l +
  gi|336255437|ref|YP_004598544.1|  37 VPALGRYFPEALTNAVVLAGLALLVTVPFLE--PMTQLELLGTGFFDLFSVQMLLILYWVLGATLVESPRVGAALDR 111
                                       556679*********9999888777666554..45567889*******88888888888************999988 PP

                        SCFA_trans  87 ias.lakdtksavvlvtllaliaavinwGlGlvvgailakevarr....vkgldyalliaaayiglltwhgGlsgsi 158
                                       +a+ l+ +++  v  + +l+l+  ++nw lGl+ g  l + + rr    + +++y+++++a+  +l+  + Gls+  
  gi|336255437|ref|YP_004598544.1| 112 LAApLPTSQAGVVYATGVLSLLLGWLNWALGLIGGVYLGQRLCRRarenGTAVHYPAVLTASLLALVLTNQGLSSPG 188
                                       76527777777777788****************99999887766511115689*********************999 PP

                        SCFA_trans 159 PllvatpneplkkiavelvgreiiPvsetlfssynliilailivvlplitamlaPkke..evksidk........kl 225
                                        l++a  +  l++ +v+    + i +se l+++ nl+  + ++ +lp ++ +laP  +   +  + +          
  gi|336255437|ref|YP_004598544.1| 189 GLMLAD-ESGLANFMVDD--VGSIAMSEFLLHPVNLLSSVLFVLTLPALLVVLAPSADadAITTLSErndrlgasGS 262
                                       999886.56799999985..56899******************************8641134444447777777644 PP

                        SCFA_trans 226 lkeekeeekklkskkdatiaekleeskllallisilGiaylgvyfyekGfnltlnsvnlifllvGlllhktPlaymr 302
                                       ++   ++       +d  + ++le+s l++ l +++G+  +g +f   G  ltl  + +++l++Gl +   P+a+ r
  gi|336255437|ref|YP_004598544.1| 263 IAAAFDHYSTAVPPEDWEVGDRLENSTLITALAVVVGVVSFGWHFATGGR-LTLPWLAFTLLILGLAVQGPPMAFRR 338
                                       555555555555589***************************88876665.************************** PP

                        SCFA_trans 303 aitraarsvaGilvqfPfyaGimgmmessalGGpslatliaeafinvankktfplltlfsaal.inifiPsGGGewa 378
                                         + a+r    + v f +yaG+  +++  +l G      i +a++     + fp+ + ++ a+ + +++P  G  w+
  gi|336255437|ref|YP_004598544.1| 339 KTEDATRWALLVAVPFLLYAGVWALLDEAGLYG-----TIGDAIAG----TGFPAAASYVVAFaLGLLVPDPGSLWV 406
                                       *******99999999999************999.....67777654....567777666655537899********* PP

                        SCFA_trans 379 iqgpilipaaqalGvdlGksvlaiayGdawtnliqPfwalPalaiaGlgardilGycitalilaglilviglv 451
                                       +qgp ++ a     +dl  s +a  yG    nl   f    +l++ G   r+ + y+ ++ +++++++v  l 
  gi|336255437|ref|YP_004598544.1| 407 LQGPAVAAAD----ADLVASLVATMYGAGLSNLWLGFLFASLLSLYGFDWREFVRYAGAVTVYVTVVVVGLLL 475
                                       ***9887665....67777889999****************************************99876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3847.63
//
Query:       gi|336255438|ref|YP_004598545.1|  [L=481]
Description: short chain fatty acid transporter [Halopiger xanaduensis SH-6]
Scores for 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-111  371.4  21.1   8.8e-111  371.1  21.1    1.1  1  SCFA_trans  Short chain fatty acid transporter
     0.0018   17.9   0.3      0.014   15.0   0.3    2.7  1  DUF1648     Protein of unknown function (DUF1648)


Domain annotation for each model (and alignments):
>> SCFA_trans  Short chain fatty acid transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.1  21.1  9.8e-115  8.8e-111       5     449 ..      18     473 ..      14     477 .. 0.91

  Alignments for each domain:
  == domain 1  score: 371.1 bits;  conditional E-value: 9.8e-115
                        SCFA_trans   5 lsaalvalvskylPdplifallltlvtfvlvlvltkqtavslvdvwgnGfwnllsfamqmalilvtGqalassklvk 81 
                                       l+ +  +lv++ylPd++ifalllt++t v+++++t++ + ++   wg+Gfw++++f+mq +l l+tG ala s+ vk
  gi|336255438|ref|YP_004598545.1|  18 LGDVSSRLVQRYLPDAFIFALLLTFLTMVIAVLVTPEGPADVAIHWGEGFWEVIGFSMQASLALLTGWALADSPPVK 94 
                                       55667789********************************************************************* PP

                        SCFA_trans  82 kllkkiaslakdtksavvlvtllaliaavinwGlGlvvgailak....evarrvkgldyalliaaayiglltwhgGl 154
                                       ++l++ia+++ ++ +a+++v+l + +  +  wG+ l+ gaila+    e+  ++  ++y+ll+aaay+gll wh Gl
  gi|336255438|ref|YP_004598545.1|  95 RVLRRIAAVPDGQLQAIFVVALCGQLLGLFHWGVVLIAGAILARevgiEMDEKGIDVHYPLLVAAAYAGLLPWHQGL 171
                                       ********************************************56555667777899******************* PP

                        SCFA_trans 155 sgsiPllvatpneplkkiavelvgreiiPvsetlfssynliilailivvlplitamlaPkkeevksidk........ 223
                                       sg+  ll at++++ ++ +       +iPvset+f+++nl i+a ++ v+++++ ++aP++e+   + k        
  gi|336255438|ref|YP_004598545.1| 172 SGASLLLSATEGHFAEESMG------VIPVSETIFHPFNLAIVAGVVLVTVVVMPLMAPRRENATTVPKeqlrgaev 242
                                       *************9998776......8****************************************9989999999 PP

                        SCFA_trans 224 .kllke.....ekeeekklksk.kdatiaekleeskllallisilGiaylgvyfyekGfn..ltlnsvnlifllvGl 291
                                        +l ++     ++    +l+++ ++ +  e l +s++++l +++l ++ylg+ f  + f+  + +n   ++++ +G+
  gi|336255438|ref|YP_004598545.1| 243 sDLAADggetaNAAAAAQLPHRtRESAPKEALLDSRVVCLGMGLLIWIYLGYLFATEPFMdvFDINVFITVMFGLGF 319
                                       8555541111123344566665145678899***************************9776778877777778999 PP

                        SCFA_trans 292 llhktPlaymraitraarsvaGilvqfPfyaGimgmmessalGGpslatliaeafinvankktfplltlfsaalini 368
                                       l h t  +y+    +a +  + i++qf fy Gimg+m +s+l      +liae+ +  a+++t+ l+++ s +++n+
  gi|336255438|ref|YP_004598545.1| 320 LAHGTLRSYIDVFYEAIKGASQIIIQFQFYGGIMGIMVFSGLV-----ELIAETAAAYATDTTWYLFVFVSGGIVNF 391
                                       **************************************99765.....5**************************** PP

                        SCFA_trans 369 fiPsGGGewaiqgpilipaaqal.GvdlGksvlaiayGdawtnliqPfwalPalaiaGlgardilGycitalilagl 444
                                       f+PsGGG+w++ g+i + a+q + G ++ +  +a+a+Gd+wtn+iqPfwalP+l+iaGl +rd++Gy+++ ++++gl
  gi|336255438|ref|YP_004598545.1| 392 FVPSGGGQWVVMGEIYASATQQIsGTQMNHMLIAFAMGDQWTNMIQPFWALPVLGIAGLSIRDMMGYVVVLFLFSGL 468
                                       *****************998876599*************************************************** PP

                        SCFA_trans 445 ilvig 449
                                       +l  g
  gi|336255438|ref|YP_004598545.1| 469 VLGAG 473
                                       99665 PP

>> DUF1648  Protein of unknown function (DUF1648)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   1.6e-06     0.014       1      26 [.      39      64 ..      39      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-06
                           DUF1648  1 lllllplvvglllypkLPdqiPtHfn 26
                                      ll++l++v+++l+ p  P+ +++H++
  gi|336255438|ref|YP_004598545.1| 39 LLTFLTMVIAVLVTPEGPADVAIHWG 64
                                      689**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3816.84
//
Query:       gi|336255439|ref|YP_004598546.1|  [L=844]
Description: beta-glucosidase [Halopiger xanaduensis SH-6]
Scores for 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-64  217.8   0.0      3e-64  217.4   0.0    1.1  1  Glyco_hydro_3    Glycosyl hydrolase family 3 N terminal domai
      1e-37  130.1   0.0    2.9e-37  128.6   0.0    1.7  2  Glyco_hydro_3_C  Glycosyl hydrolase family 3 C-terminal domai
    8.6e-16   57.8   1.8    2.8e-15   56.2   0.2    2.3  2  Fn3-like         Fibronectin type III-like domain
    0.00018   21.2   6.0    0.00044   20.0   6.0    1.7  1  TAT_signal       TAT (twin-arginine translocation) pathway si


Domain annotation for each model (and alignments):
>> Glyco_hydro_3  Glycosyl hydrolase family 3 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.4   0.0   6.7e-68     3e-64       1     319 []      62     400 ..      62     400 .. 0.94

  Alignments for each domain:
  == domain 1  score: 217.4 bits;  conditional E-value: 6.7e-68
                                       -HHHHHHHTEE-B-SE.............-S--HHHHHHHHHH--SEEE--GG...GTSSHHHHHHHHHHHHHH-SS CS
                     Glyco_hydro_3   1 tldekigqLlvvevse.............ekkseeaaellkkyqvGgiilfae...nledtkqleelieaarqasek 61 
                                       tl++k+gq+ +v + +             +   +++ el ++++vG+i++++     +  ++ ++ l++ ++ ++ +
  gi|336255439|ref|YP_004598546.1|  62 TLEQKVGQMTQVAIDDlgegfgpetafndHDEPATVGELFTELHVGSILNGGAsgpTFDGEEFVAGLNRLQQYNVTN 138
                                       79***********999********9999777778999*************9888888999999************** PP

                                       ....S--EEEE---BTTB---SSS.---S-HHHHHHHT-HHHHHHHHHHHHHHHHHHT--EE---B-----STTSSS CS
                     Glyco_hydro_3  62 srlgiPlllavDqegGlvqrlgeg.tlfPsalalaatssldlikelgriiakelralgididfaPvvdvnrdprngi 137
                                       +  giP +++ D+++G    l  g t+fP+ l ++ t++ dl++++++ +++e++a+g ++ f+P+vd+ rd r+g+
  gi|336255439|ref|YP_004598546.1| 139 NGTGIPFVWGGDALHGNT-LLD-GcTSFPQRLNMGMTRDIDLVEAAATHTGAEIAAMGGHWIFGPTVDLLRDMRWGR 213
                                       ****************99.444.44**************************************************** PP

                                       GGGSS-SSHHHHHHHHHHHHHHHHHT.T-EEEEEEETTGTT-SSETTTSEEB----HHHHHHTTHHHHHHHHHTT-S CS
                     Glyco_hydro_3 138 gvrsFsedpelvaalaaamvkGlqga.gvaatvKHFpghGdgavdshkelptvdhseeelrevdlvpfqaaieagvd 213
                                        +++ sed  l + +++a ++G  ++  vaatvKHF+g+  g+ +++k+++ v  s ++lr+ +l  ++ a+e+  +
  gi|336255439|ref|YP_004598546.1| 214 FFEGHSEDSMLLGEMGKARARGFERNgRVAATVKHFAGY--GTPNTGKDRAHVRTSMRDLRTRQLPAYERALEEA-K 287
                                       ***********************99978***********..9999***************************543.4 PP

                                       EEEE---B-TTT---BGGG-HHHHIIIIIIIS---SEEEES-TTSHHHHCCS-........HHHHHHHHHHHT-SBE CS
                     Glyco_hydro_3 214 sVMtaHvqfpaldgtpatgskklltdvLRkelGFdGvvvsDalamkeiadrgg........keeavvlaLkAGvDil 282
                                        VM+      a++g+pa++s++ll +vLRk+  FdGvv+sD+     ++  +          +eav++ + AGvD+ 
  gi|336255439|ref|YP_004598546.1| 288 TVMVN---SGAVNGKPAHASSWLLIQVLRKRFEFDGVVLSDWDDFYRLISNHEylpdteegWREAVKQGIAAGVDMH 361
                                       47877...79*********************************9988888877789988778999************ PP

                                       ES-S---SG..HHHHHHHHHTTSS-HHHHHHHHHHHHHH CS
                     Glyco_hydro_3 283 Lvpeertse..ikalkkavkeGeltearidesvrrvlrl 319
                                       +   e+  +  i++++++v++Gel+e+rid svrr+l+l
  gi|336255439|ref|YP_004598546.1| 362 MCGGEVAPTdfIDTVIDLVESGELSEERIDVSVRRILEL 400
                                       **999875588*************************986 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 !  128.6   0.0   6.4e-41   2.9e-37       1     204 []     436     689 ..     436     689 .. 0.85
   2 ?   -2.2   0.0      0.72   3.2e+03     130     155 ..     707     733 ..     698     734 .. 0.79

  Alignments for each domain:
  == domain 1  score: 128.6 bits;  conditional E-value: 6.4e-41
                                       -EEEEEGSS--S-S-STEEEEEESGGGS......SS-SS-BSSS--............--S---HHHHHHHHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxx............xxxxxxxxxxxxxxxxxx. RF
                   Glyco_hydro_3_C   1 iVLLkNennlLPLkkklkkiaviGpnad......etlklGggsgtv............tvsylvsplegirerles. 58 
                                       +VLLkNe+++LPL + +++++++Gp  +        +++Gg++  +              + + ++ +g+++rl++ 
  gi|336255439|ref|YP_004598546.1| 436 LVLLKNEDDALPL-EGSERVLLTGPGIEdgtpnrFLMQHGGWTLGWqgiedgdltedgPRPRQNTIEDGLAARLGDr 511
                                       59***********.5557*******999999998445556666555666667777777666899**********99* PP

                                       .............................-HHHHHHHHHHHTSEEEEEEEES...SB-TT.SCSGHHSSTTHHHHHH CS
                                       ............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                   Glyco_hydro_3_C  59 ............................eegideaveaakeaDvavvvvgedpeiegEgv.Drtdlalpeaqdelik 106
                                                                   +e+ ++ ++aa ++D++v+v+ge p   +Eg+ Dr++++ peaq++l++
  gi|336255439|ref|YP_004598546.1| 512 lthvptefraapyesifenfdngffdvtDEQAAAIQNAAPASDAVVIVLGEGP--HNEGFgDRDKMRFPEAQRQLVE 586
                                       ***************************9888899999999************8..667766************9999 PP

                                       HHHHTT...SSEEEEEEESSGG--TTTGTTTEEEEEE-S--GCCHHHHHHHHHTTSS---B--SS-EESSSGGG... CS
                                       xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Glyco_hydro_3_C 107 avaaan...knvvvvlqsggpvavepwkeenvkAilaawlpGqegGtaiadvLfGdvnPsGkLpvtfpksledlpdd 180
                                        v +      + v v+ +g+p  +++   ++++A+l a +pG+++G a+ad LfGd+nPsGkL++t++ +++++p+ 
  gi|336255439|ref|YP_004598546.1| 587 LVDELTgddVPLVGVILAGSPRGTAET-FDHLDAVLFAGQPGSDTGVAVADTLFGDYNPSGKLSFTWEGNVGHVPQ- 661
                                       88855434489***********88777.67********************************************99. PP

                                       ..........S-----S..ETTTT-BCH CS
                                       xxxxx..xxxxxxxxxx..xxxxxxxxx RF
                   Glyco_hydro_3_C 181 yyeek..dtykfegtpl..YpeGlglsY 204
                                       +y++   ++    +++l  +++G+glsY
  gi|336255439|ref|YP_004598546.1| 662 FYDDYppRQSVGAEDQLvqFEFGHGLSY 689
                                       6666544333334444457********9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.72
                                       T.GTTTEEEEEE-S--GCCHHHHHHHH CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Glyco_hydro_3_C 130 w.keenvkAilaawlpGqegGtaiadv 155
                                         + + v+A + ++  G ++G+ i++v
  gi|336255439|ref|YP_004598546.1| 707 PaSTPTVTAQVTVHNTGDAAGDHIVEV 733
                                       3467899***************99987 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.16   7.2e+02       1      25 [.     658     682 ..     658     685 .. 0.94
   2 !   56.2   0.2   6.3e-19   2.8e-15       1      69 [.     729     800 ..     729     802 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.16
                                       EEEEEEEEESS-STTSBS-EEEEEE CS
                          Fn3-like   1 evvqlYvsdpessverpvkeLkgFe 25 
                                       +v q Y  +p+ +    + +L++Fe
  gi|336255439|ref|YP_004598546.1| 658 HVPQFYDDYPPRQSVGAEDQLVQFE 682
                                       699*********999*********7 PP

  == domain 2  score: 56.2 bits;  conditional E-value: 6.3e-19
                                       EEEEEEEEESS-STTSBS-EEEEEEEEEE-TT-EEEEEEEEECGGG-EEET...TTTEEE--SCEEEEEEES CS
                          Fn3-like   1 evvqlYvsdpessverpvkeLkgFekveLapGesktvtftldrkdlsvwde...ekqkwvvepGeytvlvgt 69 
                                       ++v +Y +  ++sv +p ++L gFe+v++ +G+s+tvt++ld + l v+       q+ vvepGey+v vg+
  gi|336255439|ref|YP_004598546.1| 729 HIVEVYNTESYGSVLQPHRRLMGFERVHVDAGDSETVTIELDLSTLEVVPGdvpGHQAKVVEPGEYEVAVGE 800
                                       589**********************************************8855546789************7 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   6.0   9.8e-08   0.00044       3      23 ..      17      37 ..      17      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.8e-08
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggc 23
                                      SRR+F+K+++Aa+AA a+g  
  gi|336255439|ref|YP_004598546.1| 17 SRRTFMKATGAATAASAVGLG 37
                                      9*****************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (844 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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 0.24s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 6313.82
//
Query:       gi|336255440|ref|YP_004598547.1|  [L=347]
Description: hypothetical protein Halxa_4063 [Halopiger xanaduensis SH-6]
Scores for 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       0.24   11.3   0.0    1.2  1  CAT       Chloramphenicol acetyltransferase
        3.7    8.4   8.1        1.5    9.7   2.3    2.6  3  FliT      Flagellar protein FliT


Domain annotation for each model (and alignments):
>> CAT  Chloramphenicol acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.6e-05      0.24      48     169 ..     201     324 ..     159     328 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.6e-05
                               CAT  48 vypaliyllarvvnkhkefrmalkdeelvvWdsvnPaytvfnketetfssiwteydedf..aeflktyaediaeyse 122
                                        y   iy++ r+ ++h++   +l+++el+ +d++  a t+f +  e f s++ +++     ++ l      +   + 
  gi|336255440|ref|YP_004598547.1| 201 NYSWKIYAVRRLRHEHED---SLEEDELAAFDELIDALTLFGPALEHFKSLYFQWELVHltRSILYAGLPGVVAATA 274
                                       588889998888777665...89****************************98876433013334444455666777 PP

                               CAT 123 ktklfPksdllentlnvsslPWvsftsfnlnvan...eedyllPiftigk 169
                                       +  ++ +++l+  tl v  l Wv  ts +l +       +y+l i ti+k
  gi|336255440|ref|YP_004598547.1| 275 TVLYLDQESLPGTTLGVDNLVWVVSTSATLSLVPfflLAAYVLRIATISK 324
                                       888999999**************999999987641114566666666665 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.3   1.2e+04      70      80 ..      97     107 ..      94     128 .. 0.63
   2 ?    9.7   2.3   0.00017       1.5      13      63 ..     135     185 ..     134     187 .. 0.91
   3 ?    0.9   0.1      0.09   8.1e+02      24      49 ..     209     234 ..     207     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                                       HHHCHTHHHHH CS
                              FliT  70 kllgalrrqrk 80 
                                       ++lg+l  q++
  gi|336255440|ref|YP_004598547.1|  97 QELGRLGDQQA 107
                                       55555555544 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHHHHHCS--ST--HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FliT  13 laaleaerqqlverlreldaaplspaereekrellrrilandaeirallqp 63 
                                       l al++     +e+lre+ a+  ++++r++ ++l + +  n +eir++l++
  gi|336255440|ref|YP_004598547.1| 135 LQALVQTSSDRAETLREAVADSDDDQLRRRTERLVENVCRNSEEIRSQLET 185
                                       56888889999999999999999*************************986 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.09
                                       HHHHHCS--ST--HHHHHHHHHHHHH CS
                              FliT  24 verlreldaaplspaereekrellrr 49 
                                       v rlr++ ++ l+++e ++++el+  
  gi|336255440|ref|YP_004598547.1| 209 VRRLRHEHEDSLEEDELAAFDELIDA 234
                                       7899999999************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2770.95
//
Query:       gi|336255441|ref|YP_004598548.1|  [L=208]
Description: nitroreductase [Halopiger xanaduensis SH-6]
Scores for 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   76.7   0.5    1.5e-11   44.6   0.0    2.1  2  Nitroreductase  Nitroreductase family
    5.2e-06   26.2   0.0     0.0002   21.0   0.0    2.1  2  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 !   30.8   0.1     3e-11   2.7e-07       3      47 ..      31      75 ..      29      82 .. 0.90
   2 !   44.6   0.0   1.7e-15   1.5e-11      81     169 ..      88     171 ..      75     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3e-11
                                      H--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-C CS
                    Nitroreductase  3 kRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdk 47
                                      +R S R+ + +p++++e   + eaar+aPsa+n q wrf+ ++++
  gi|336255441|ref|YP_004598548.1| 31 NRWSPRAMTGDPLEEAEYLPLFEAARWAPSAFNNQHWRFLYADRE 75
                                      699************************************999443 PP

  == domain 2  score: 44.6 bits;  conditional E-value: 1.7e-15
                                       HHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S CS
                    Nitroreductase  81 lkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglp 157
                                       + +q++  +a+vl+v+    +k + +++++ +++ ++d+gaa qnl L+ t++Gl++ pi gfd+++   ++ l++p
  gi|336255441|ref|YP_004598548.1|  88 EMNQAWATDAAVLVVV---VSKTTFDHNDDPAPTHAFDTGAAWQNLALEGTRRGLAVHPIAGFDYER--AADELEVP 159
                                       6789999*********...************************************************..******** PP

                                       ..SEEEEEEEEE CS
                    Nitroreductase 158 deeeivvliavG 169
                                       + +e+++++a+G
  gi|336255441|ref|YP_004598548.1| 160 EAYEVQAMVAIG 171
                                       ***********9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.3e-08    0.0002     163     188 ..      51      76 ..      41      96 .. 0.81
   2 !    3.2   0.0    0.0062        56      88     149 ..     127     199 ..     114     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.3e-08
                                       HHHHHHTS--GGG----EEE.E-SSE CS
                    TM1586_NiRdase 163 ileaarlAPsAlNqqpwrfelkddde 188
                                       + eaar APsA+N+q+wrf + d+++
  gi|336255441|ref|YP_004598548.1|  51 LFEAARWAPSAFNNQHWRFLYADRED 76 
                                       579****************9877654 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0062
                                       HHHHHHHHHHTT-EEEEE.S--SST...........T-S-EEEEE-BS----...........-----HHHHB CS
                    TM1586_NiRdase  88 geqlvLkltalGlgtcWv.ggtykkkkakvelkkgeklvivIalGyaktklv..........eakrkpleelc 149
                                        ++l L+ t +Gl+   + g+ y++ + ++e+++  ++ +++a+G  +   +          + +rkplee++
  gi|336255441|ref|YP_004598548.1| 127 WQNLALEGTRRGLAVHPIaGFDYERAADELEVPEAYEVQAMVAIGERALPETlpedlrereqPSDRKPLEEIV 199
                                       567788888888887654166788888899***************9887774455556666689999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1653.35
//
Query:       gi|336255442|ref|YP_004598549.1|  [L=358]
Description: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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  198.8   0.0      2e-58  198.2   0.0    1.2  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
    7.2e-14   52.0   0.0    1.1e-13   51.4   0.0    1.2  1  Meth_synt_1  Cobalamin-independent synthase, N-terminal domai
    7.3e-05   22.1   0.0    0.00011   21.4   0.0    1.3  1  URO-D        Uroporphyrinogen decarboxylase (URO-D)
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.85    9.9   0.0    2.4  2  YbaB_DNA_bd  YbaB/EbfC DNA-binding family


Domain annotation for each model (and alignments):
>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.2   0.0   4.4e-62     2e-58       2     323 ..      22     335 ..      21     336 .. 0.90

  Alignments for each domain:
  == domain 1  score: 198.2 bits;  conditional E-value: 4.4e-62
                                       -BB--SB---SS------------..-----HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTE CS
                       Meth_synt_2   2 pTttiGSfPqtaevrearaevkkg..elseeeyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgf 76 
                                        Tt++GS+P+ + +++a++ ++ +  e+++e+ ++a  ++ + + ++ e++g+Dv+v+ge+ R++mve+f+++++g+
  gi|336255442|ref|YP_004598549.1|  22 LTTVVGSYPKPKWLNRAKELYRDEdhEFDAEDWQEAKDDAARLITDEHERAGLDVVVDGEMRRNEMVEFFAHRIEGY 98 
                                       69****************9998761155556666655555555567889***************************9 PP

                                       E--SS--EEEETTEEE---EE-SS---SS-SSTHHHHHHTTS-SS-BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHH CS
                       Meth_synt_2  77 aftkngwvqsygsrcvrppiivgdvsrpaamtvkesalaqsltdkpvkglltGpvtilnwsfvrddvdraeaaaqia 153
                                        f  ng v+  g  +   p +v +v++     v e+    +  d+pvk  +tGp t+ nwsf +   d +e a+++a
  gi|336255442|ref|YP_004598549.1|  99 EF--NGPVKVWGHNYFDKPSVVSEVEYDDSWLVDEYEFTAAASDRPVKVPITGPYTLANWSFNEAYDDDEELAYDLA 173
                                       76..6889999999999999********************************************99999******** PP

                                       HHHHHHHHHHHHTT-SEEEEE-TTSSTT--SSGGGHHHHHHHHHHHHHHHHTTS-..TTSEEEEEES-S--CCCHHH CS
                       Meth_synt_2 154 lalrdevkdLeaaGikviQiDepalreGlplkkadwaayldwaveafrldtiaaa..ddtqvhtHlCyselndilsa 228
                                         + +e+++L +aG+  iQiDepal +  p+ +         a  +  l+ i+a   +++ + +H+Cy ++  i ++
  gi|336255442|ref|YP_004598549.1| 174 DLVNEEIEKLVDAGARYIQIDEPALATT-PDDH---------AIVGECLERIVADipEEVRIGLHVCYGDYSRIYPE 240
                                       ************************9874.5554.........34444444444432278999*************** PP

                                       HHTT--SEEEESBSSS-SSGGGGTTTT---SEEEEBSS-TTSSS--THHHHHHHHHCHHCTS-STSB-BB-SS-STT CS
                       Meth_synt_2 229 iaaldvDvitieasrsdeellealeevkygrgvglGvydihsprvpsmeeiaalikkaldvapkerlwvnPdCGLkt 305
                                       i ++ vD  ++e ++ d e l+++++ ++ +++ lGv d h   v+s+e+i++ i k l+v+p e+l v+PdCG+k 
  gi|336255442|ref|YP_004598549.1| 241 ILEFPVDEFDLELANGDYEQLDVFKDPDFTKDLALGVCDAHVAEVESVEQIEENILKGLEVVPPEQLVVSPDCGVKL 317
                                       ***************************************************************************** PP

                                       S-HHHHHHHHHHHHHHHH CS
                       Meth_synt_2 306 rkreearaalknmvdaAk 323
                                       ++re a  ++ nmv+aA+
  gi|336255442|ref|YP_004598549.1| 318 LPREVAYGKMANMVQAAR 335
                                       *****************8 PP

>> Meth_synt_1  Cobalamin-independent synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   2.5e-17   1.1e-13     128     289 ..     120     279 ..     105     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2.5e-17
                                       ----S-THHHHHHHHH.HHTTGGEEEEEE-HHHHHHT-EETTCC.-HCHHHHHHHHHHHHHHHHHHHTT-SEEEEE- CS
                       Meth_synt_1 128 efklaseklleevkea.kalgieakpvllGpltflkLskakeekveklellekLlpvYkelleeLkeagvewvqidE 203
                                       e+++++++l++e++    a    +k  + Gp+t+   s ++  + + +el  +L ++ +e +e+L +ag++++qidE
  gi|336255442|ref|YP_004598549.1| 120 EVEYDDSWLVDEYEFTaAASDRPVKVPITGPYTLANWSFNEAYD-DDEELAYDLADLVNEEIEKLVDAGARYIQIDE 195
                                       6788999*******8846677789999***********999999.9999**************************** PP

                                       GGGGSSGCHHHHHHHHHHHHHHT.CCTTTSEEEEE--SS-.CCHHHHHTTSSTSEEEEETSS.HCHHHHHHHHCTT. CS
                       Meth_synt_1 204 PalvldlekeelealkeaYeela.kekkelklllatyFdsvaealellaelpveglglDlvr.aeenlealkkaglp 278
                                       Pal++   +++ +++ e  e++     +e+++ l+  +++ ++ + +++e+pv+ + l+l +   e+l+ +k+ ++ 
  gi|336255442|ref|YP_004598549.1| 196 PALATT--PDDHAIVGECLERIVaDIPEEVRIGLHVCYGDYSRIYPEILEFPVDEFDLELANgDYEQLDVFKDPDF- 269
                                       ***986..556666777777665234789*********************************8889******9888. PP

                                       TTSEEEEEEE- CS
                       Meth_synt_1 279 edkvLsaGvid 289
                                         k L++Gv d
  gi|336255442|ref|YP_004598549.1| 270 -TKDLALGVCD 279
                                       .6678888877 PP

>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.5e-08   0.00011     178     345 ..     168     336 ..     156     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.5e-08
                                       HHHHHHHHHHHHHHHHHHTT-SEEEEEE.TTGGGS-HHHHHHHTHHHHHHHHHHHHH.H--S-EEEEES.SHH.HHH CS
                             URO-D 178 lldkltdvvieylkaqieagAdaiqifD.swagllspedfeefvlpylkrivdevkaegpkvpvilfik.gagaeil 252
                                       l   l+d+v e ++++++agA  iqi + +   + +p+d + +v ++l+riv+ +++   +v + l+++ g+++ i+
  gi|336255442|ref|YP_004598549.1| 168 LAYDLADLVNEEIEKLVDAGARYIQIDEpAL--ATTPDD-HAIVGECLERIVADIPE---EVRIGLHVCyGDYSRIY 238
                                       555689999*****************88444..334555.679**************...579*****9556767** PP

                                       HHHTTS--SEEE--TTS....-HHHHHH..SS....EEE--B-G.GGGG.S-HHHHHHHHHHHHT.T---SSSEEB- CS
                             URO-D 253 edlaelgadvlsldwtv....dlkeaar..evgdkvalqGnldPialLl.gspeeiekevkeilekgaggkkgyiln 322
                                       +++ e ++d + l+ ++    +l ++++  ++  k   +G  d + +   +s e+ie+++ + le  + ++++ +++
  gi|336255442|ref|YP_004598549.1| 239 PEILEFPVDEFDLELANgdyeQL-DVFKdpDF-TKDLALGVCDAH-VAEvESVEQIEENILKGLE--VVPPEQLVVS 310
                                       *********99997777655556.77775433.778889*****6.6666***************..688******* PP

                                       BSS-...--TTS-HHHHHHHHHHHHT CS
                             URO-D 323 lGhg...ippetppenvkalveavke 345
                                       + +g   +p e+   +++ +v+a+++
  gi|336255442|ref|YP_004598549.1| 311 PDCGvklLPREVAYGKMANMVQAARN 336
                                       ****6655778899999999998875 PP

>> YbaB_DNA_bd  YbaB/EbfC DNA-binding family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00019      0.85      19      69 ..     130     181 ..     128     193 .. 0.76
   2 ?   -1.4   0.1      0.64   2.9e+03       3      28 ..     326     351 ..     325     354 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00019
                                       TTSEEEEEETTTTEEEEEETT--EEEEEE-GGGG..GS-HHHHHHHHHHHHH CS
                       YbaB_DNA_bd  19 aekevegssggglVkVtvngkgevksikIdpslld.pedkemLedlivaAvn 69 
                                       +e e+++ + +  VkV ++g +++ + +++++  d +e +  L+dl+ + + 
  gi|336255442|ref|YP_004598549.1| 130 DEYEFTAAASDRPVKVPITGPYTLANWSFNEAYDDdEELAYDLADLVNEEIE 181
                                       5779*****************************6624424446666655443 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHHHHHHHTTSEEEEEET CS
                       YbaB_DNA_bd   3 qaqkmqkkmeeaqeelaekevegssg 28 
                                       ++ +m + + +++++l+e  ++++ g
  gi|336255442|ref|YP_004598549.1| 326 KMANMVQAARNVERDLDEGNIDVERG 351
                                       67788888999999999888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2875.44
//
Query:       gi|336255443|ref|YP_004598550.1|  [L=335]
Description: Cobalamin-independent synthase MetE domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   54.6   0.0    7.1e-14   52.0   0.0    1.8  2  Meth_synt_1  Cobalamin-independent synthase, N-terminal domai
    3.6e-11   42.9   0.0    5.1e-11   42.4   0.0    1.1  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain


Domain annotation for each model (and alignments):
>> Meth_synt_1  Cobalamin-independent synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.038   3.4e+02      30      70 ..      39      78 ..      32      89 .. 0.80
   2 !   52.0   0.0   7.9e-18   7.1e-14     106     308 ..      89     288 ..      83     293 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.038
                                      HHHHHHHHHHHHHHHHHHHHCTT-SBEEES---SS-HHHHH CS
                       Meth_synt_1 30 eeeLektakeLrakhwkkqkeagidlipvndfslYDhvLdt 70
                                      +ee+++  +e r++ +  q++a++d i  +++ + D +L +
  gi|336255443|ref|YP_004598550.1| 39 SEEITAAYEEAREEVIGVQQDADLDRIVEGQLRW-DDMLAH 78
                                      67899999999****************9999877.555554 PP

  == domain 2  score: 52.0 bits;  conditional E-value: 7.9e-18
                                       -EEEESTTSS-EEEE-BE-SS.----S-THHHHHHHHHHHTTGGEEEEEE-HHHHHHT-EETTCC.-HCHHHHHHHH CS
                       Meth_synt_1 106 lemtkwFntnYHYlvPelekdtefklaseklleevkeakalgieakpvllGpltflkLskakeekveklellekLlp 182
                                         ++++++ n  Y  P +++d  f+ +  + le   e  ++  + ++vl Gp+++  L+  ++   +++e+l ++ +
  gi|336255443|ref|YP_004598550.1|  89 RGIVRYYDNNNFYREPVVQDDLGFSGDVANELEAAAELLEADDDLQAVLPGPYSLADLATDEQYG-DEAEFLGAIAD 164
                                       5679*******************************************************999988.9********** PP

                                       HHHHHHHHHHHTT-SEEEEE-GGGGSSGCHHHH.HHHHHHHHHHTCCTTTSEEEEE--SS-.CCH.HHHHTTSSTSE CS
                       Meth_synt_1 183 vYkelleeLkeagvewvqidEPalvldlekeel.ealkeaYeelakekkelklllatyFdsvaea.lellaelpveg 257
                                         +  ++ + e+  e++ + EP lv + +++ l e ++ea +++ + +++++++++ y+++++e+ ++ l++ ++++
  gi|336255443|ref|YP_004598550.1| 165 FLEGEVDAFPEH--ETLFLLEPSLVESAPEDGLdERASEAIDQV-AGATDADVVVQPYWGALEEKvYAHLLDADIDA 238
                                       ***999999998..888999******997665516789999999.5999************876527899******* PP

                                       EEEETSS.HCHHHHHHHHCTT.TTSEEEEEEE-SSS-B---HHHHHHHHHHH CS
                       Meth_synt_1 258 lglDlvr.aeenlealkkaglpedkvLsaGvidGrniWradlekalelleel 308
                                       +g+D+v+ +++nl +++++g      +s+G+ dG+n    d e+  +++e +
  gi|336255443|ref|YP_004598550.1| 239 VGFDFVAeQDDNLYNIQEYGA--TDDVSLGLADGQNTLVEDPEAIRDRVEWV 288
                                       ******98999******9655..666899*********99999988887765 PP

>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   5.7e-15   5.1e-11      29     291 ..      38     293 ..      10     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 5.7e-15
                                       -.-HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTEE--SS--EEEET.TEEE---EE-SS--- CS
                       Meth_synt_2  29 e.eeyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgfaftkngwvqsyg.srcvrppiivgdvsr 103
                                       e ee  +a++e+ e+v+++q+++++D +v+g+  R d + + + a++  ++t+ g+v  y  + ++r p++ +d+ +
  gi|336255443|ref|YP_004598550.1|  38 EsEEITAAYEEAREEVIGVQQDADLDRIVEGQL-RWDDMLAHPLAVHDAVETR-GIVRYYDnNNFYREPVVQDDLGF 112
                                       3377888999**********************8.6665566799999888775.788887615789*********** PP

                                       SS-SSTHHHHHHTTS-SS-.BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEE-TTSS CS
                       Meth_synt_2 104 paamtvkesalaqsltdkp.vkglltGpvtilnwsfvrddvdraeaaaqialalrdevkdLeaaGikviQiDepalr 179
                                         +++ + +a a++l+    ++ +l Gp ++ + +  ++  d ae +  ia  l  ev +  +   + + + ep l 
  gi|336255443|ref|YP_004598550.1| 113 SGDVANELEAAAELLEADDdLQAVLPGPYSLADLATDEQYGDEAEFLGAIADFLEGEVDAFPEH--ETLFLLEPSLV 187
                                       **************987766****************************************9999..889999****9 PP

                                       TT--SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCH.HHHHTT--SEEEESBSSS-SSGGGGTTTT CS
                       Meth_synt_2 180 eGlplkkadwaayldwaveafrldtiaaaddtqvhtHlCyselndil.saiaaldvDvitieasrsdeellealeev 255
                                       e +p         ld+ + + ++d++a a+d++v +      l++ +  ++ + d+D++  ++  ++ ++l  ++e 
  gi|336255443|ref|YP_004598550.1| 188 ESAPEDG------LDERA-SEAIDQVAGATDADVVVQPYWGALEEKVyAHLLDADIDAVGFDFVAEQDDNLYNIQEY 257
                                       9999988......66654.4579*************9999999999889**************99888********* PP

                                       ---SEEEEBSS-TTSSS--THHHHHHHHHCHHCTS- CS
                       Meth_synt_2 256 kygrgvglGvydihsprvpsmeeiaalikkaldvap 291
                                       +   +v lG+ d +   v+  e i+++++ + d +p
  gi|336255443|ref|YP_004598550.1| 258 GATDDVSLGLADGQNTLVEDPEAIRDRVEWVYDQLP 293
                                       ***************************999988744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2770.71
//
Query:       gi|336255444|ref|YP_004598551.1|  [L=468]
Description: gluconate transporter [Halopiger xanaduensis SH-6]
Scores for 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-92  309.9  25.0    2.8e-92  309.7  25.0    1.0  1  GntP_permease  GntP family permease
    9.1e-17   61.2  26.4    9.1e-17   61.2  26.4    2.1  2  CitMHS         Citrate transporter


Domain annotation for each model (and alignments):
>> GntP_permease  GntP family permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.7  25.0   3.1e-96   2.8e-92       2     439 ..      15     463 ..      14     464 .. 0.95

  Alignments for each domain:
  == domain 1  score: 309.7 bits;  conditional E-value: 3.1e-96
                     GntP_permease   2 pllivligvilllllviklklnafvaLllvsllvglvs.GmpldkvvksiekGlGgtlGslaiiiglGamlGklled 77 
                                       pll +++g++ +++l+i l l +f+aL+++ ++vg+vs  +p+ +v   +   +G  +  ++i i + a++Gk + +
  gi|336255444|ref|YP_004598551.1|  15 PLLALVAGIATIVFLLIYLDLPPFIALVIAGFVVGAVSpDIPFGDVPGEFAGSFGDGMAGIGIPILMAAIIGKAMIE 91 
                                       68999******************************99847************************************* PP

                     GntP_permease  78 sGaaerialtlikklgkkkvqwalvlagfivgialFfevglvlLiplvfaiakeakisllklgiplvaalavvhgll 154
                                       sGaa+ri + +   +g+ +++++l  +gf+++i++Ff+  + lL+pl+ a   +++ +   + +++ aa av+hg++
  gi|336255444|ref|YP_004598551.1|  92 SGAADRIVRFFNGVFGRDNTEYSLFSSGFVMAIPVFFDNVFYLLAPLARAARSRTGQNYALFIVAIGAAGAVTHGFV 168
                                       ***************************************************************************** PP

                     GntP_permease 155 pPhPgplavaell.....gadiGkvllyGlivaiptviiagpllkkflkevvkeeee.....laeeaeek.sreeke 220
                                       pP+Pgpl+++e++       ++G ++ +Gl+ ++pt+++ag  ++ +++++ +         ++ee++ek +r +++
  gi|336255444|ref|YP_004598551.1| 169 PPTPGPLLAVETFaeagaSTNLGLTIGVGLLTGLPTALVAGLGYGYVINRRLEIPLRdamgtTVEELNEKvERPTSQ 245
                                       **********99844433369*********************9999999988776666678845555555156789* PP

                     GntP_permease 221 lPsfglslltillPvvlmlvktiaelllpkesaalevvefiGnpvvalliallvaiytlglrrgksikkvldileea 297
                                       lP++  ++l ill v+l+ + t++++++ +++aa +v +fiG+p  al  a l a +t     ++s +  +d l ea
  gi|336255444|ref|YP_004598551.1| 246 LPGLLEAMLPILLAVLLVGADTFVTTFIGEDTAAASVTNFIGDPNFALTAAALAAAFTYFRMSDISGDVFSDELTEA 322
                                       ***************************************************************************** PP

                     GntP_permease 298 lksiaiilliigaGGafkqvlvdsgvgkalaellsnlelspillaflvaallrialGsatVaaltaaglvapiiaql 374
                                       lks ++i  i++aGGaf+ +l ++g g+ +a+ l++l l ++ +a+++aa +r+++GsatVa+ t+ag+ ap+  + 
  gi|336255444|ref|YP_004598551.1| 323 LKSGGNIAAITAAGGAFGYMLQQAGAGELIANSLQELGLGVLATAWVIAAGVRLVQGSATVAITTTAGITAPMAGSF 399
                                       **************************************************************************999 PP

                     GntP_permease 375 pgvnlallvlaigaGslilshvnDagFWlvkeylgltvketlktwtvletilsvvgliivlllsl 439
                                        ++n+a lv+aigaG++++s+ nD+gFW+vke  glt  etlktwtv+++++++vgli++l++s 
  gi|336255444|ref|YP_004598551.1| 400 -SANPAYLVMAIGAGATFCSWYNDSGFWIVKEIGGLTQGETLKTWTVSTILIGIVGLISTLVFST 463
                                       .99**********************************************************9986 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2  26.4     1e-20   9.1e-17      28     300 .]      35     411 ..      13     411 .. 0.63
   2 ?   -0.8   0.5     0.075   6.8e+02     230     266 ..     421     462 ..     412     466 .. 0.67

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1e-20
                                       x......xxxxxxxxxx.........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  28 e......alsgiaspii.........................llllgamiigaaleetGlfdrlaakllrlaggkrd 73 
                                              +++g+ ++++                         + +l+a iig+a++e+G++dr+++++  ++g+  +
  gi|336255444|ref|YP_004598551.1|  35 LppfialVIAGFVVGAVspdipfgdvpgefagsfgdgmagigIPILMAAIIGKAMIESGAADRIVRFFNGVFGRDNT 111
                                       12344456677777777777777788888888888888888899*****************************9766 PP

                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                            CitMHS  74 llvllvlltallsafvsn.dgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraa........ 141
                                           l+   +++ a++ + d v+ +++p++ +   r ++ + +l    ++a ++ ga+t+ + p+t+++        
  gi|336255444|ref|YP_004598551.1| 112 -EYSLFSSGFVM-AIPVFfDNVFYLLAPLARAARSR-TGQNYAL---FIVAIGAAGAVTHGFVPPTPGPllavetfa 182
                                       .44455555555.5555559************9998.8888888...889999999********************* PP

                                       .....xxxxxxxxxxxxxxx..................................................xxxxxxx RF
                            CitMHS 142 .....arpglslpnllllal..................................................llvgllp 163
                                            +++gl++ ++ll++l                                                  +l +ll+
  gi|336255444|ref|YP_004598551.1| 183 eagasTNLGLTIGVGLLTGLptalvaglgygyvinrrleiplrdamgttveelnekverptsqlpglleaMLPILLA 259
                                       ***99777777777777444444344444444444444444444444444444444444444444433332222222 PP

                                       xxxxxxxxxxxxxxxxxx......................xxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                            CitMHS 164 lvllfmfgvalalpvnap......................kvkkqkaiieaiarsllpvatillla........... 207
                                       ++l+++ +++  ++ +                                                 a           
  gi|336255444|ref|YP_004598551.1| 260 VLLVGADTFVTTFIGEDTaaasvtnfigdpnfaltaaalaA------------------------Aftyfrmsdisg 312
                                       22222222222222222122222222233333333333330........................133333333333 PP

                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxx.xxxxxxxxxx RF
                            CitMHS 208 ...........ykkveWsvlllfaGvfllvgaleqtGilealadllga.g.gplvalalvlglial.lsafisnvav 270
                                                      +   +  ++G+f+   +l+q G +e++a++l++ g g    +++++++ia+ +++++++++v
  gi|336255444|ref|YP_004598551.1| 313 dvfsdeltealKSGGNIAAITAAGGAFGY--MLQQAGAGELIANSLQElGlG----VLATAWVIAAgVRLVQGSATV 383
                                       33333333322111111222366666666..***************554433....3567***************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 271 aalmapialgmapalgllspsplalalavg 300
                                       a+++++++ +  p +g +s++p +l++a+g
  gi|336255444|ref|YP_004598551.1| 384 AITTTAGITA--PMAGSFSANPAYLVMAIG 411
                                       **********..7545599*********98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.075
                                       xxxx..xxxxxxxxx.xxx.xxxxxxxxxxxxxxx.xxxxxx RF
                            CitMHS 230 eqtG..ilealadll.gag.gplvalalvlglial.lsafis 266
                                       +++G  i++ +++l+ g++ + +++ ++++g+++l  ++++s
  gi|336255444|ref|YP_004598551.1| 421 NDSGfwIVKEIGGLTqGETlKTWTVSTILIGIVGLiSTLVFS 462
                                       567777888888888444456666668889999995555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3409.25
//
Query:       gi|336255445|ref|YP_004598552.1|  [L=205]
Description: methylase [Halopiger xanaduensis SH-6]
Scores for 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-08   33.4   0.0    2.3e-07   31.4   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
    8.3e-08   32.8   0.0    1.2e-06   29.1   0.0    2.2  2  Methyltransf_11  Methyltransferase domain
    8.4e-06   25.4   0.0    2.9e-05   23.7   0.0    1.9  2  MTS              Methyltransferase small domain
    0.00013   22.6   0.0     0.0018   18.9   0.0    2.2  2  Methyltransf_12  Methyltransferase domain
    0.00015   21.6   0.0    0.00023   21.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
     0.0022   17.9   0.0      0.016   15.0   0.0    2.0  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.046   13.1   0.0      0.069   12.5   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.054   13.5   0.0      0.075   13.0   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.16   11.8   0.0       0.27   11.1   0.0    1.3  1  UPF0146          Uncharacterised protein family (UPF0146)


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 !   31.4   0.0   1.1e-10   2.3e-07       1      75 [.      52     119 ..      52     136 .. 0.84
   2 ?   -1.2   0.0       1.7   3.4e+03      83      97 .]     145     159 ..     141     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.1e-10
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lh 75 
                                       vL++G+G+G ++ ++ ++  +a+v++ D+++ ++++are+       +e v++d+ + pf+dg fD+v+ +   l 
  gi|336255445|ref|YP_004598552.1|  52 VLEVGTGSGYVAHRVDAET-DARVIASDLNPHAVRQAREEG------LETVRADLVS-PFADGAFDAVLFNPPyLP 119
                                       9*****************7.8******************99......8999999865.9*********99644444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHEEEEE CS
                   Methyltransf_25  83 ekalkeiarvLkpgG 97 
                                       + +l+++ rv+ p+G
  gi|336255445|ref|YP_004598552.1| 145 DPFLANVGRVIAPDG 159
                                       67899********99 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   5.8e-10   1.2e-06       1      67 [.      53     113 ..      53     124 .. 0.90
   2 ?    1.3   0.0      0.28   5.6e+02      79      95 ..     146     162 ..     139     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 5.8e-10
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvs 67 
                                       L+vG+G+G++a  +     arv++ Dl++ ++++a+e++      +e v+ad+ + pf+d+ fD+v+ 
  gi|336255445|ref|YP_004598552.1|  53 LEVGTGSGYVAHRVDAETdARVIASDLNPHAVRQAREEG------LETVRADLVS-PFADGAFDAVLF 113
                                       89*************6666*************9997776......4559*****8.**********86 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.28
                                       HHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  79 kalkeiaRvLkpgGllv 95 
                                        +l+++ Rv  p+G+++
  gi|336255445|ref|YP_004598552.1| 146 PFLANVGRVIAPDGVVY 162
                                       68999*********987 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.4e-08   2.9e-05      35     107 ..      52     117 ..      20     126 .. 0.90
   2 ?   -1.5   0.0      0.81   1.6e+03     114     151 ..     140     177 ..     135     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.4e-08
                                       EEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  35 vlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPf 107
                                       vl +G+G G+++  + +e++  +v + d + +A++ a+e        +e+v  d+++ ++++ fd+++ NPP+
  gi|336255445|ref|YP_004598552.1|  52 VLEVGTGSGYVAHRVDAETDA-RVIASDLNPHAVRQAREEG------LETVRADLVSPFADGAFDAVLFNPPY 117
                                       899*********999987665.8***********9998753......57899********************7 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.81
                                       HHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHH CS
                               MTS 114 elavaeeliaeAkeaLkegGeLliVanrklgyesllee 151
                                         av++ ++a+  ++ +++G  ++ +++  g+++++e+
  gi|336255445|ref|YP_004598552.1| 140 GRAVIDPFLANVGRVIAPDGVVYLLVSSLTGVDEVVER 177
                                       56788889999999999999999999998888888776 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.3e-07    0.0018       1      39 [.      53      90 ..      53     114 .. 0.84
   2 ?    1.4   0.0      0.28   5.6e+02      82      98 ..     144     160 ..     133     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.3e-07
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakek 39
                                      Le+G+G+G +++++ ++  d++++++D++p+a+ +a+e+
  gi|336255445|ref|YP_004598552.1| 53 LEVGTGSGYVAHRVDAE-TDARVIASDLNPHAVRQAREE 90
                                      8****************.***************777765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.28
                   Methyltransf_12  82 irevldnirklLkpgGr 98 
                                       i+ +l+n+ ++++p+G+
  gi|336255445|ref|YP_004598552.1| 144 IDPFLANVGRVIAPDGV 160
                                       7789************8 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.2e-07   0.00023       7     109 ..      52     163 ..      48     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.2e-07
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn.. 81 
                                       vl++G+G+G+ +++   e  ++a+v+  D +++a+++Are+    gl+ v+   +d  + +  ++d  fD +l n  
  gi|336255445|ref|YP_004598552.1|  52 VLEVGTGSGYVAHRVDAE--TDARVIASDLNPHAVRQAREE----GLETVR---ADLVS-P--FADGAFDAVLFNpp 116
                                       89*************955..79******************5....666554...55555.4..55788999999977 PP

                   Methyltransf_31  82 ...............evlnaladpdkile....eiervlkpggilli 109
                                                       +l    d  +++     ++ rv+ p+g++ +
  gi|336255445|ref|YP_004598552.1| 117 ylptdpenewddwmeRALSGGEDGRAVIDpflaNVGRVIAPDGVVYL 163
                                       77777777777777766655555555555555588888888887654 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.1e-06     0.016      23      62 ..      49     114 ..      19     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.1e-06
                   Methyltransf_23  23 ggrvLdiGcGtGillevl.rengfsvtgvDlspeaveiae.........................k 62 
                                       +  vL++G+G+G+++    +e  + v++ Dl+p+av  a+                         +
  gi|336255445|ref|YP_004598552.1|  49 PPLVLEVGTGSGYVAHRVdAETDARVIASDLNPHAVRQAReegletvradlvspfadgafdavlfN 114
                                       337***********9999555577*************99888776665555555444444444442 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.5e-05     0.069     164     202 ..      51      89 ..      44     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.5e-05
                              PrmA 164 evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvake 202
                                        vl vGtGSG  a  +     ++v+a D+++ Av+ a+e
  gi|336255445|ref|YP_004598552.1|  51 LVLEVGTGSGYVAHRVDAETDARVIASDLNPHAVRQARE 89 
                                       599********99999999999**************997 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.7e-05     0.075      22      70 ..      45      90 ..      24     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                   Methyltransf_32 22 kesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekr 70
                                      ++ ++  v++vG G gY + ++     e   +v++ d++ + v++a++ 
  gi|336255445|ref|YP_004598552.1| 45 ADADPPLVLEVGTGSGYVAHRVDA---ETDARVIASDLNPHAVRQAREE 90
                                      455677899***************...999**************99875 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.27      17      63 ..      52     102 ..      45     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                       EEEET-TT--HHHHHHHHHS.-EEEEE-SS-S........STTEE---SSS- CS
                           UPF0146  17 vvEvGiGrkldvaealakrg.vdlvatDikek...kak.egvrivrDDvtdP 63 
                                       v EvG G   +va+ +   +   ++a D++++   +a+ eg++ vr D+++P
  gi|336255445|ref|YP_004598552.1|  52 VLEVGTGSG-YVAHRVDAETdARVIASDLNPHavrQAReEGLETVRADLVSP 102
                                       89*****86.677777655559********99776666799*********99 PP



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:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1702.51
//
Query:       gi|336255446|ref|YP_004598553.1|  [L=398]
Description: mechanosensitive ion channel MscS [Halopiger xanaduensis SH-6]
Scores for complete 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-46  158.6   0.1    2.3e-46  157.9   0.1    1.3  1  MS_channel     Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.15   11.2   1.0       0.83    8.8   1.7    1.7  2  MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
        9.1    6.1   6.5        1.2    8.9   0.7    2.2  2  PAP2           PAP2 superfamily


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 !  157.9   0.1   3.9e-50   2.3e-46       3     206 .]     151     350 ..     149     350 .. 0.98

  Alignments for each domain:
  == domain 1  score: 157.9 bits;  conditional E-value: 3.9e-50
                                       HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE CS
                        MS_channel   3 ilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedi 79 
                                       ++ ++i++v +++vl ++  +++ ll+++G+lg+++g+a+++++  ++aG++l+f++pf+iGD+++++d eG+V+di
  gi|336255446|ref|YP_004598553.1| 151 LTQVVIWSVSVVVVLGVWIDDLGGLLVGAGFLGIVVGMAARQTLGTVLAGFVLMFDRPFEIGDWIKVEDEEGIVTDI 227
                                       7899************************************************************************* PP

                                       -SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-E CS
                        MS_channel  80 glrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkel 156
                                       ++  t++r+fdg++++iPn  +++++++N sr +g+ ri++++gv+y++d   le+++++   ++   ++ l+ + +
  gi|336255446|ref|YP_004598553.1| 228 SIVNTRLRSFDGEYIMIPNDVVSSEMVTNRSR-RGRLRIEIEVGVDYETD---LEHAADVAESVVADLEYSLSAPGP 300
                                       ********************************.*****************...999999999999999999****** PP

                                       EEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 157 lvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                       +vv +efgds++ + vr+++ + + +++++ +++++  ik++++ egi+i
  gi|336255446|ref|YP_004598553.1| 301 QVVGKEFGDSAVVLGVRFWIDKPSARRHWRARTAAINAIKDAFDDEGIKI 350
                                       ************************************************97 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 ?    8.8   1.7   0.00014      0.83     130     249 ..      37     166 ..      26     170 .. 0.71
   2 ?   -1.4   0.0      0.18   1.1e+03      88     111 ..     192     215 ..     188     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00014
                     MIG-14_Wnt-bd 130 svLllFwlvffeslrdeqnrrktlsfylpklllvlllwlvllvlalyerleqlkdpfysiwssal.....ilkilai 201
                                       + LllF+l  + ++ +   + +t  +y   ++ ++l+  +l++la++  + +l+  + + +++++     + k+++ 
  gi|336255446|ref|YP_004598553.1|  37 VGLLLFVLLSYRRVQKRVAE-RTKPLYGDIASTAVLIATCLVTLAIVVGVWDLTGTIHTGFDQLDlggdiVAKAIVS 112
                                       459***********999988.58999***99***************9999999999999988844555555555555 PP

                     MIG-14_Wnt-bd 202 ilavlyflyLlylifrsfseirskrvk......egdiRfkflilltllvlavlv 249
                                       +++++  ++L   + r++ e+  + ++      e + R++ +++ ++ v++vl+
  gi|336255446|ref|YP_004598553.1| 113 FILIVGTIILQRFVKRVLDEVLGSAAAvtdhqrEITRRLTQVVIWSVSVVVVLG 166
                                       555665666666666666666554444556643444477776666666666654 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.18
                     MIG-14_Wnt-bd  88 qkwilvLlillilfNnPffilell 111
                                       q +  vL  ++++f+ Pf+i  ++
  gi|336255446|ref|YP_004598553.1| 192 QTLGTVLAGFVLMFDRPFEIGDWI 215
                                       566678999999*******99886 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.7    0.0002       1.2      63     112 ..      34      97 ..      31     117 .. 0.85
   2 ?   -0.8   0.8       0.2   1.2e+03     110     128 ..     168     186 ..     107     194 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0002
                              PAP2  63 fafalalllalllrrkrkkig..............lvllalillllavlvalsRlylgvHflsD 112
                                       fa++++ll++ll  r+ +k+                vl+a++l++la++v++  l   +H+ +D
  gi|336255446|ref|YP_004598553.1|  34 FAAVGLLLFVLLSYRRVQKRVaertkplygdiastAVLIATCLVTLAIVVGVWDLTGTIHTGFD 97 
                                       566666666666666666665888************************************9998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.2
                              PAP2 110 lsDvlaGlliGialaalay 128
                                       + D l+Gll+G+ ++ +++
  gi|336255446|ref|YP_004598553.1| 168 WIDDLGGLLVGAGFLGIVV 186
                                       5666777777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.37
# Mc/sec: 3186.51
//
Query:       gi|336255447|ref|YP_004598554.1|  [L=279]
Description: ribosomal RNA small subunit methyltransferase A [Halopiger xanaduensis SH-6]
Scores for 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-49  167.5   0.0    3.8e-49  167.1   0.0    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0014   19.3   0.1     0.0037   17.9   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.018   14.6   0.0       0.04   13.5   0.0    1.5  1  NodS             Nodulation protein S (NodS)
       0.02   15.7   0.2      0.053   14.3   0.0    1.8  2  Methyltransf_12  Methyltransferase domain
       0.02   15.0   0.0      0.029   14.4   0.0    1.3  1  Glyco_hydro_4C   Family 4 glycosyl hydrolase C-terminal domai
      0.035   14.8   0.1      0.084   13.5   0.0    1.7  2  Methyltransf_11  Methyltransferase domain
      0.092   12.1   0.0       0.15   11.4   0.0    1.3  1  Spermine_synth   Spermine/spermidine synthase domain


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 !  167.1   0.0   1.5e-52   3.8e-49       9     242 ..      20     243 ..      14     264 .. 0.92

  Alignments for each domain:
  == domain 1  score: 167.1 bits;  conditional E-value: 1.5e-52
                                       G--EE--HHHHHHHHHHH-GG..TTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT...TCCCEEE CS
                            RrnaAD   9 gqnflknkkvineIldklnle..ekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls...kdeklkv 80 
                                        q+fl++  v+++    l+    +   +leig G+G+lT +L+  a++v+v+E d++La++l+++++   +++ l+v
  gi|336255447|ref|YP_004598554.1|  20 DQHFLVDDRVLDRLPTYLEEIdaDASHLLEIGGGTGALTDRLLAVADEVTVVERDRKLAAFLREEFReaiDAGDLTV 96 
                                       69**********997776543578889****************************************9999****** PP

                                       E-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHH CS
                            RrnaAD  81 vhqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrl 157
                                       ++ D+l+ ++p +           + v+nlPy++s+++ ++ll e+r+     +l++q+efa+r++a+p  ++++rl
  gi|336255447|ref|YP_004598554.1|  97 IEDDALEVDLPDFT----------ASVSNLPYGVSSEIAFRLLPEGRP----LVLMFQQEFAERMVAEPDTSEYGRL 159
                                       ************55..........89******************9999....9************************ PP

                                       HHHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTCHHH CS
                            RrnaAD 158 svlreaftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllpggel 234
                                       sv ++ ++dv++v+ ++k++fsPpp v sa+++  ++d+d ++ d + + ++v++l++++rkt+++++ ++ +  +l
  gi|336255447|ref|YP_004598554.1| 160 SVSTQHYADVEIVESIPKEAFSPPPAVQSAVIRAVPRDPDYEVDDEEFFLRFVKALFTQRRKTIRNAIRNTAHITNL 236
                                       ************************************************************************99999 PP

                                       HHCTT.T- CS
                            RrnaAD 235 qalsstgi 242
                                       +a+    +
  gi|336255447|ref|YP_004598554.1| 237 EAPDA-VV 243
                                       99854.34 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.5e-06    0.0037       2      70 ..      48     114 ..      47     130 .. 0.85
   2 ?   -2.5   0.0       3.4   8.7e+03      21      37 ..     230     246 ..     203     259 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaedlpfedgsfDlvvs 70 
                                       L++G GtG lt +l++     +vt v+ + ++ +  re+++e+ +   ++++++ da +++++d  f + vs
  gi|336255447|ref|YP_004598554.1|  48 LEIGGGTGALTDRLLAVA--DEVTVVERDRKLAAFLREEFREA-IdagDLTVIEDDALEVDLPD--FTASVS 114
                                       89*************885..9*******************873.2356*********9999888..555555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.4
                                       SSEEEEEESSHHHHHHH CS
                   Methyltransf_25  21 kakvtgvDiseemleaa 37 
                                        a++t ++  ++ +eaa
  gi|336255447|ref|YP_004598554.1| 230 TAHITNLEAPDAVVEAA 246
                                       24444444444444444 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.5e-05      0.04      41      73 ..      41      73 ..      31     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                              NodS 41 qgsiadalevGcaaGalterlapyckrltvvdv 73
                                      + ++++ le+G  +Galt+rl  +++ +tvv+ 
  gi|336255447|ref|YP_004598554.1| 41 DADASHLLEIGGGTGALTDRLLAVADEVTVVER 73
                                      6678999************************85 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.1e-05     0.053       1      45 [.      48      90 ..      48     121 .. 0.79
   2 ?   -2.1   0.0       2.6   6.7e+03      20      32 ..     230     242 ..     212     269 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakren 45
                                      LeiG+GtG+l+++ll+     e+t+v+ +++  +  +e++++ ++
  gi|336255447|ref|YP_004598554.1| 48 LEIGGGTGALTDRLLAV--ADEVTVVERDRKLAAFLREEFREAID 90
                                      8****************..99999999999988888888877664 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                   Methyltransf_12  20 dieytgvDispsa 32 
                                       ++++t ++   ++
  gi|336255447|ref|YP_004598554.1| 230 TAHITNLEAPDAV 242
                                       2333333333333 PP

>> Glyco_hydro_4C  Family 4 glycosyl hydrolase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.1e-05     0.029      98     151 ..     192     245 ..     138     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                                       TTHHHHHHHSSCHTS-SHHHHHHHHHHTS-EEEEEEEE-TTSSTTS-.TTSEEEE CS
                    Glyco_hydro_4C  98 eelekeklelekrsgeyavdiieaivtdkprrlvvnvpNnglIpnLp.ddavVEv 151
                                        ++++ + ++e   +e  +++++a+ t++++++   ++N+  I+nL+ +davVE 
  gi|336255447|ref|YP_004598554.1| 192 RAVPR-DPDYEVDDEEFFLRFVKALFTQRRKTIRNAIRNTAHITNLEaPDAVVEA 245
                                       33332.33466678899*****************************835999996 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.3e-05     0.084       1      59 [.      48     108 ..      48     117 .. 0.90
   2 ?   -3.3   0.0         6   1.5e+04      19      36 ..     231     248 ..     218     257 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-T CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfed 59 
                                       L++G GtG+l+  l   + +v+ v+ + ++ +  +e+ +e+     +++++ da ++ ++d
  gi|336255447|ref|YP_004598554.1|  48 LEIGGGTGALTDRLLAVADEVTVVERDRKLAAFLREEFREAIDagDLTVIEDDALEVDLPD 108
                                       89*************999******************9999988998999999999999998 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6
                                       SEEEEEES-HHHHHHHHH CS
                   Methyltransf_11  19 arvvgvDlskemlklake 36 
                                       a++++++  ++++++a e
  gi|336255447|ref|YP_004598554.1| 231 AHITNLEAPDAVVEAADE 248
                                       455666655555555554 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     6e-05      0.15      18      65 ..      43      88 ..      30     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6e-05
                                      ST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHH CS
                    Spermine_synth 18 npkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpsl 65
                                         + L iGGg G ++ +++      ++t+v+ D+k   f ++ +++ 
  gi|336255447|ref|YP_004598554.1| 43 DASHLLEIGGGTGALTDRLLAVA--DEVTVVERDRKLAAFLREEFREA 88
                                      5678899*************999..*************9999988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2258.20
//
Query:       gi|336255448|ref|YP_004598555.1|  [L=158]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   80.9   1.0    1.8e-22   80.4   1.0    1.2  1  Usp           Universal stress protein family
  ------ inclusion threshold ------
      0.031   13.7   0.7       0.14   11.6   0.7    1.8  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
       0.56   10.5   3.4        1.2    9.5   0.5    2.2  2  TOBE          TOBE domain


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 !   80.4   1.0     3e-26   1.8e-22       1     141 []       1     154 [.       1     154 [. 0.93

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 3e-26
                                       S-SEEEEEE-SSHHHH..HHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..... CS
                               Usp   1 mykrIlVavDgseesk..kAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..... 70 
                                       m+++Il+a+  s++ +  ++ ++ ++ a+ +ga+++l+hvi++++++ +    +ea ++   + e +    +     
  gi|336255448|ref|YP_004598555.1|   1 MIETILLAIGPSDSDRidELTQQTIDVAEPTGATVVLAHVISASEYEDEVHNYQEAIDKMGIDLENRDLSPEalare 77 
                                       8899*****85555445589999999*********************99999999999999999987776668999* PP

                                       ......HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  71 ......akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                               +++e++gv+ve+   +gd aeei+ +aee dad ++vG r+rs   ++++GS++++vl ++pcpV+ Vr
  gi|336255448|ref|YP_004598555.1|  78 tepvseISDRLEEAGVDVEIRAAVGDRAEEIIALAEEVDADNLIVGGRKRSPTGKAVFGSTAQKVLLSSPCPVTYVR 154
                                       *************************************************************************9997 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 ?   11.6   0.7   2.3e-05      0.14      69     156 ..      18     120 ..       8     123 .. 0.81
   2 ?    6.7   0.2   0.00071       4.3      20      90 ..      70     123 ..      61     139 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHHHHHHHTBSEEEEEBCC...................GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSE CS
                      AP_endonuc_2  69 vdalkraielaaaLGapllvlhpGt...................agagpkgseeeawerlaeslneladyaekegvk 126
                                        + ++++i+ a+  Ga ++  h+ +                    +  +++  +ea++r  e + e+ d +e++gv 
  gi|336255448|ref|YP_004598555.1|  18 DELTQQTIDVAEPTGATVVLAHVISaseyedevhnyqeaidkmgIDLENRDLSPEALARETEPVSEISDRLEEAGVD 94 
                                       67899*****************9878888888888777777776445566666699999999999999999999999 PP

                                       EEEE--TTTTSSSTCHHHHHHHHHHTTTTE CS
                      AP_endonuc_2 127 lalEtlagsgvelgdeelarlldavdspnv 156
                                       + +    g+ +    ee+ +l ++vd +n+
  gi|336255448|ref|YP_004598555.1|  95 VEIRAAVGDRA----EEIIALAEEVDADNL 120
                                       99988888887....999******999995 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00071
                                       SHHHHC.HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEE CS
                      AP_endonuc_2  20 vpvsel.sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlh 90 
                                        p + + + e + e+  +l+e+g+             ++   r+a+     d++++ i la++++a++l+++
  gi|336255448|ref|YP_004598555.1|  70 SPEALArETEPVSEISDRLEEAGVD------------VEI--RAAV----GDRAEEIIALAEEVDADNLIVG 123
                                       4444334445555555555555555............333..4555....7777777777777777777776 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.062   3.7e+02      10      23 ..      24      37 ..      24      43 .. 0.86
   2 ?    9.5   0.5    0.0002       1.2      13      47 ..      87     120 ..      86     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.062
                              TOBE 10 tVvvveplgseveV 23
                                      t++v ep+g++v++
  gi|336255448|ref|YP_004598555.1| 24 TIDVAEPTGATVVL 37
                                      799******88876 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0002
                              TOBE  13 vveplgseveVrvdlggga.tLtArvtrrsaeeLgL 47 
                                       ++e++g++ve+r+++g+ a +++A   +  a++  L
  gi|336255448|ref|YP_004598555.1|  87 RLEEAGVDVEIRAAVGDRAeEIIALAEEVDADN--L 120
                                       689****************9****998888888..5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 1319.43
//
Query:       gi|336255449|ref|YP_004598556.1|  [L=198]
Description: hypothetical protein Halxa_4072 [Halopiger xanaduensis SH-6]
Scores for 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-63  211.8   0.3    8.1e-63  211.6   0.3    1.0  1  DUF655    Protein of unknown function (DUF655)
    0.00074   19.7   0.0     0.0013   18.9   0.0    1.4  1  HHH_3     Helix-hairpin-helix motif
     0.0038   17.5   0.0      0.007   16.6   0.0    1.5  1  HHH_6     Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.25   12.0   0.9          2    9.1   0.4    2.5  2  HHH_5     Helix-hairpin-helix domain


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 !  211.6   0.3   1.8e-66   8.1e-63       4     180 ..      13     189 ..      10     190 .. 0.98

  Alignments for each domain:
  == domain 1  score: 211.6 bits;  conditional E-value: 1.8e-66
                                       EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GGGS-H CS
                            DUF655   4 eaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisyedLtd 80 
                                        a+vLDyl++G +dd + ++++ p  +al ++++ L+++   ++  + + +ev ++  ++  iv    ++ yedL++
  gi|336255449|ref|YP_004598556.1|  13 RAVVLDYLAHGLSDDGRPQYEKSPAGYALEVDDFRLYQVAFDEDERLTIGSEVVVEPPEERDIVTEAHRVDYEDLSS 89 
                                       79********************************************************9999999899********* PP

                                       HHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT---H CS
                            DUF655  81 varaeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglkdp 157
                                       +a++eL++vv+++v+e+E+rfv+f+nea+pit+RlH+L+lLpg+gkkl++ il+eR+r++FesFe++++rv+gl+dp
  gi|336255449|ref|YP_004598556.1|  90 GAQSELEYVVQDLVEENEERFVDFYNEAQPITLRLHQLNLLPGIGKKLRNGILDERKRKPFESFEELSERVSGLHDP 166
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHH-TTSS--SS- CS
                            DUF655 158 aeilverileEiedktekYylFv 180
                                        eilverileE++d++ kY+ Fv
  gi|336255449|ref|YP_004598556.1| 167 DEILVERILEELRDDDLKYQTFV 189
                                       **********************8 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     3e-07    0.0013      13      52 ..     124     163 ..     121     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3e-07
                             HHH_3  13 aeeLqklpGlgpklAknIvayReknGpfksreeLl.kvkgl 52 
                                       + +L+ lpG+g+kl + I++ R k++pf+s+eeL  +v+gl
  gi|336255449|ref|YP_004598556.1| 124 LHQLNLLPGIGKKLRNGILDER-KRKPFESFEELSeRVSGL 163
                                       6799******************.888********8567776 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.6e-06     0.007      29      65 ..     127     162 ..      88     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-06
                             HHH_6  29 LaaikglgeaaaerivaeRekegpfksledlarrvds 65 
                                       L+ + g+g++  + i++eR+ ++pf+s+e+l++rv+ 
  gi|336255449|ref|YP_004598556.1| 127 LNLLPGIGKKLRNGILDERK-RKPFESFEELSERVSG 162
                                       555679*************9.8************986 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         1   4.5e+03      26      37 ..      99     110 ..      84     113 .. 0.74
   2 ?    9.1   0.4   0.00045         2       7      57 .]     130     180 ..     125     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1
                                       HHHHHHS-HHHH CS
                             HHH_5  26 vedlaaadveeL 37 
                                       v+dl+++++e++
  gi|336255449|ref|YP_004598556.1|  99 VQDLVEENEERF 110
                                       678888888876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00045
                                       STT--HHHHHHHHTTT--S...HHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                             HHH_5   7 vsGiGpktAlallsaGies...vedlaaadveeLakipGiGkktAeriilelkd 57 
                                       ++GiG+k+   +l+   +    +e + ++  e+++ +++  + ++eri++el+d
  gi|336255449|ref|YP_004598556.1| 130 LPGIGKKLRNGILDE--RKrkpFESFEEL-SERVSGLHDPDEILVERILEELRD 180
                                       799999999999999..431124454444.678888888999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 1686.98
//
Query:       gi|336255450|ref|YP_004598557.1|  [L=118]
Description: RNA polymerase Rpb4 [Halopiger xanaduensis SH-6]
Scores for complete 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-11   44.8   1.4    1.7e-11   44.5   1.4    1.1  1  RNA_pol_Rpb4    RNA polymerase Rpb4
  ------ inclusion threshold ------
      0.024   15.2   1.1        3.8    8.1   0.3    2.5  2  Arg_decarbox_C  Arginine decarboxylase C-terminal helical ext
      0.025   14.4   0.1       0.16   11.8   0.0    2.3  3  DUF1507         Protein of unknown function (DUF1507)
      0.032   14.1   0.6      0.043   13.6   0.6    1.5  1  RNA_pol_Rpb1_6  RNA polymerase Rpb1, domain 6
      0.037   14.5   4.5       0.77   10.2   0.4    2.2  2  CRR7            Protein CHLORORESPIRATORY REDUCTION 7
      0.048   14.1   0.1       0.61   10.6   0.1    2.2  1  DUF3106         Protein of unknown function (DUF3106)
      0.073   12.6   0.0       0.12   11.9   0.0    1.4  1  Cas9_a          Cas9 alpha-helical lobe domain


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 !   44.5   1.4   6.6e-15   1.7e-11       1     122 [.      12     117 ..      12     118 .] 0.95

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 6.6e-15
                                       EE-HHHHHHHHHHHHHHHHCHHHHHTCCCCCHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTST. CS
                      RNA_pol_Rpb4   1 lLsnsEvllvlkeeleerknkdkkeseddkisekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfe. 76 
                                       +L+ sE++++l+ ++e +++ d               +++l ++l +++e+ ++ f+ l+ +e++++lv+ l+  e 
  gi|336255450|ref|YP_004598557.1|  12 FLTVSETKELLA-DIEAERALD--------------EERELPYELARAIEHANR-FAVLE-PEEAQQLVDDLQDLEk 71 
                                       79**********.999997885..............4689**************.****9.************9999 PP

                                       STHHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHHHHHH CS
                      RNA_pol_Rpb4  77 LtkaEklqlvnlkPesavelktlieeleerfedeqleeiLdelkev 122
                                        ++  ++++ nl+P++++el+++ ++ ++ ++ ++l+eiL+ ++++
  gi|336255450|ref|YP_004598557.1|  72 VDEPTAYKIANLLPRNRDELRSVYAQQRYSLSGDELDEILNVVAQY 117
                                       *******************************************998 PP

>> Arg_decarbox_C  Arginine decarboxylase C-terminal helical extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0099        25      17      43 ..       2      27 ..       1      28 [. 0.89
   2 ?    8.1   0.3    0.0015       3.8      14      42 ..      36      67 ..      33      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0099
                    Arg_decarbox_C 17 erlrrqveaagrLtpeerqalleelea 43
                                      + +++ v++   Lt +e ++ll++ ea
  gi|336255450|ref|YP_004598557.1|  2 TIFKEIVDEE-FLTVSETKELLADIEA 27
                                      6799*****9.***********98775 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0015
                    Arg_decarbox_C 14 eLlerlrrqveaa...grLtpeerqalleele 42
                                      eL   l r +e+a     L pee+q+l+++l+
  gi|336255450|ref|YP_004598557.1| 36 ELPYELARAIEHAnrfAVLEPEEAQQLVDDLQ 67
                                      56667788888888888************997 PP

>> DUF1507  Protein of unknown function (DUF1507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.45   1.1e+03      58      75 ..      11      28 ..       4      37 .. 0.74
   2 ?   11.8   0.0   6.4e-05      0.16      45      78 ..      39      71 ..      28      78 .. 0.88
   3 ?   -1.6   0.0      0.96   2.5e+03      14      28 ..      77      91 ..      69      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.45
                                      TSS-HHHHHHHHHHHHHH CS
                           DUF1507 58 glieeeeGkqllseLeke 75
                                      ++++ +e k+ll ++e e
  gi|336255450|ref|YP_004598557.1| 11 EFLTVSETKELLADIEAE 28
                                      567777888888888765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.4e-05
                                      HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHT- CS
                           DUF1507 45 yGlsrevdfavrlglieeeeGkqllseLekelnq 78
                                      y l r +++a r  ++e ee +ql+++L+ +l++
  gi|336255450|ref|YP_004598557.1| 39 YELARAIEHANRFAVLEPEEAQQLVDDLQ-DLEK 71
                                      7899**********************995.4555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.96
                                      HHHHHHHHHHHHT-- CS
                           DUF1507 14 adkikkLikvqmdnL 28
                                      a ki +L+   +d+L
  gi|336255450|ref|YP_004598557.1| 77 AYKIANLLPRNRDEL 91
                                      778988888887776 PP

>> RNA_pol_Rpb1_6  RNA polymerase Rpb1, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6   1.7e-05     0.043      56     112 ..       5      58 ..       2     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHHHHHHHHHHTT-T..T---EEE..EES-HHHHHHHHHHHTT--SSS CS
                    RNA_pol_Rpb1_6  56 qelldeEyeqLkedRellrkeifpdeekdekvklqLPvNikRlienaqkefkidkrk 112
                                       +e++deE+ ++ e +ell ++   ++  de+   +LP +++R ie a++   ++ ++
  gi|336255450|ref|YP_004598557.1|   5 KEIVDEEFLTVSETKELLADI-EAERALDEER--ELPYELARAIEHANRFAVLEPEE 58 
                                       6789***************95.5534445555..5************9876665544 PP

>> CRR7  Protein CHLORORESPIRATORY REDUCTION 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.4    0.0045        12      19      49 ..       8      42 ..       3      47 .. 0.69
   2 ?   10.2   0.4    0.0003      0.77       6      60 ..      45     100 ..      41     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0045
                                      S-SEEE-HHHHHHHHHHHHHH....-TTTS-HHHH CS
                              CRR7 19 qpEqfltaeellekLkelLek....eqdelprdla 49
                                       +E+flt +e++e L ++ ++    e++elp +la
  gi|336255450|ref|YP_004598557.1|  8 VDEEFLTVSETKELLADIEAEraldEERELPYELA 42
                                      58*************98755511112455666655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0003
                                       S-----EEEEESSS-SEEE-HHHHHHHHHHHHHH.-TTTS-HHHHH---HHHHHHH CS
                              CRR7   6 myqedtyVvLepnqpEqfltaeellekLkelLek.eqdelprdlaklesleeqaqy 60 
                                       + + + + vLep++ +q+++  + lek  e  +   ++ lpr+ ++l+s+ +q +y
  gi|336255450|ref|YP_004598557.1|  45 IEHANRFAVLEPEEAQQLVDDLQDLEKVDEPTAYkIANLLPRNRDELRSVYAQQRY 100
                                       567789**************999999999887765788899999999999888766 PP

>> DUF3106  Protein of unknown function (DUF3106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00024      0.61      28      77 ..      42     103 ..      17     118 .] 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                           DUF3106  28 eklleiaerykkltpeeqkrlqermeewak...........Lspeqreqarenyqklk.qLp 77 
                                        + +e+a+r++ l+pee ++l + +++ +k           L p +r+++r+ y++ + +L+
  gi|336255450|ref|YP_004598557.1|  42 ARAIEHANRFAVLEPEEAQQLVDDLQDLEKvdeptaykianLLPRNRDELRSVYAQQRySLS 103
                                       57789999999999999999998888765511111111111555666666666655554555 PP

>> Cas9_a  Cas9 alpha-helical lobe domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.6e-05      0.12      42      89 ..      47      94 ..      41     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                            Cas9_a 42 ekgeerkLtveekqkvfdfLlslkskeeltWedvaekLgieRrelrGt 89
                                      ++++   L+ ee q+++d L++l++ +e+t  ++a+ L  +R elr +
  gi|336255450|ref|YP_004598557.1| 47 HANRFAVLEPEEAQQLVDDLQDLEKVDEPTAYKIANLLPRNRDELRSV 94
                                      555566899************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 996.06
//
Query:       gi|336255451|ref|YP_004598558.1|  [L=102]
Description: 50S ribosomal protein L21e [Halopiger xanaduensis SH-6]
Scores for 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-33  114.2   0.2    2.3e-33  114.0   0.2    1.0  1  Ribosomal_L21e  Ribosomal protein L21e
  ------ inclusion threshold ------
       0.24   11.2   1.3       0.81    9.6   0.6    1.9  2  Myosin_N        Myosin N-terminal SH3-like domain


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 !  114.0   0.2   2.6e-37   2.3e-33       1      99 [.       1      95 [.       1      97 [. 0.98

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 2.6e-37
                                      X--S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEE CS
                    Ribosomal_L21e  1 mknskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkk 79
                                      m+ns+g+r+gtr ++s+++r++g +p++++++ey++G+kV++kidpsv+kg++h+r+ G+tg+v  v+k++ +++v+++
  gi|336255451|ref|YP_004598558.1|  1 MPNSNGPRQGTRGKLSNDPRDRGSSPPQRAIQEYEEGEKVHLKIDPSVHKGRFHPRFDGHTGEV--VGKQGDAFKVRIN 77
                                      89**************************************************************..************* PP

                                      ETTE..EEEEEE-GGGEEE- CS
                    Ribosomal_L21e 80 vggkileKriivriehlkks 99
                                      +ggk  +K++iv+ +h++ +
  gi|336255451|ref|YP_004598558.1| 78 DGGK--DKTLIVTAAHMRAQ 95
                                      ****..***********987 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 ?   -0.2   0.0       0.1     9e+02      21      29 ..      35      43 ..      31      46 .. 0.71
   2 ?    9.6   0.6   9.1e-05      0.81      16      37 ..      62      84 ..      61      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.1
                                      EESSEEEEE CS
                          Myosin_N 21 eeGdkvtVe 29
                                      eeG+kv+ +
  gi|336255451|ref|YP_004598558.1| 35 EEGEKVHLK 43
                                      677777766 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 9.1e-05
                                      EEEEEEESSEEEEEE.TTSEEEE CS
                          Myosin_N 16 GeIkeeeGdkvtVet.edGktvt 37
                                      Ge++ + Gd + V+  + Gk++t
  gi|336255451|ref|YP_004598558.1| 62 GEVVGKQGDAFKVRInDGGKDKT 84
                                      9**************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 823.18
//
Query:       gi|336255452|ref|YP_004598559.1|  [L=133]
Description: hypothetical protein Halxa_4075 [Halopiger xanaduensis SH-6]
Scores for 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  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1000.03
//
Query:       gi|336255453|ref|YP_004598560.1|  [L=395]
Description: cystathionine gamma-lyase [Halopiger xanaduensis SH-6]
Scores for 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-153  509.0   0.0   6.2e-153  508.8   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    6.9e-05   21.5   0.0     0.0001   21.0   0.0    1.2  1  Met_gamma_lyase  Methionine gamma-lyase
    0.00015   20.9   0.0    0.00023   20.2   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
     0.0074   15.6   0.1      0.021   14.2   0.0    1.5  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
       0.03   14.0   0.1       0.97    9.1   0.0    2.5  2  BRK              BRK domain


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 !  508.8   0.0  1.7e-156  6.2e-153       1     381 [.      17     390 ..      17     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 508.8 bits;  conditional E-value: 1.7e-156
                                       HHHHHHTTTTCHTTTTBSS--B---SBBBESSHHHHCTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHH CS
                   Cys_Met_Meta_PP   1 eTllvhagqekdeqtgavavpiyltstykfkdvdeafageekgyeYsRsgnptrsvleeriaaLeggeaalavssGm 77 
                                       eT  +hagq++de+tga ++pi++ sty+++     + ge++gyeYsR+gnptr+ le+++a Le++e + a++sGm
  gi|336255453|ref|YP_004598560.1|  17 ETRSIHAGQDPDEETGALMTPIHANSTYEQD-----APGEHRGYEYSRTGNPTRTDLEANLASLENAEYGRAFASGM 88 
                                       6999***************************.....***************************************** PP

                                       HHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT--- CS
                   Cys_Met_Meta_PP  78 aAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvv 154
                                       a+i +++l+ll+aGd++v+ +d+Yggt+r++++v++   +e++fvd++dle++e+a++ent+l++lEtptnpll++v
  gi|336255453|ref|YP_004598560.1|  89 ASI-NTVLNLLEAGDHVVTGNDVYGGTHRIFTQVYEDYDLEFSFVDMTDLEAIESAFQENTELLWLETPTNPLLSIV 164
                                       ***.************************************************************************* PP

                                       -HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHHHHHT CS
                   Cys_Met_Meta_PP 155 DiekiaklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflqnalG 231
                                       Die  a++a+++++l  +Dntfa+p+lqrpl+lgaDiv hS TKylgGhsd+v+G++++++ eel++e+ f qna+G
  gi|336255453|ref|YP_004598560.1| 165 DIEGAAEIAHEHDALCAIDNTFATPYLQRPLDLGADIVSHSLTKYLGGHSDIVGGALLTND-EELDEEFGFYQNAVG 240
                                       *************************************************************.*************** PP

                                       -B--HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEEEE-TTSTTSTTHHHHHHHSSSG-SEEEEEESSH CS
                   Cys_Met_Meta_PP 232 avlspfdawlllrGlkTLslRlerhqenAlkvAefLekhpkvekvyYpglpshpqhelakkqlkgaggvlsFelkse 308
                                       a+  pf+++l+lrG kTL +R++rh enA+++Ae+Le hp v +vyYpgl+shp+he+a++q+ ++gg++sFel+ +
  gi|336255453|ref|YP_004598560.1| 241 ATPGPFESFLVLRGTKTLPVRMDRHCENAQAIAEWLEDHPDVDRVYYPGLESHPGHEIAAEQMDDFGGMVSFELDAT 317
                                       ***************************************************************************** PP

                                       HHHHHHHHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCHHHHHHTTS-TTEEEEE--SS-HHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 309 eekakkfvdnlklfslaeslGgveslielpasmthasipkeereaagvtddliRlsvGiEdvdDliaDlkqal 381
                                       +e+a ++v+n+++f+laeslGgveslie+pa mtha+ip+eer++ag++d+liR svGiE+vdDliaDl+qa+
  gi|336255453|ref|YP_004598560.1| 318 MEEAGEVVSNTEVFTLAESLGGVESLIEQPAPMTHAAIPREERIEAGLEDSLIRASVGIEHVDDLIADLEQAI 390
                                       ***********************************************************************97 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.8e-08    0.0001      48     241 ..      53     226 ..      39     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.8e-08
                   Met_gamma_lyase  48 tGyGyddlGrdtldkvyaevfgaeaalvrpqlvsGthaiatalfgvlrpgdellaitGkPydtleeviGlrge.gqg 123
                                        Gy y   G  t   + a++   e+a     + sG  +i t+l   l  gd+++  tG      ++v G +++  + 
  gi|336255453|ref|YP_004598560.1|  53 RGYEYSRTGNPTRTDLEANLASLENAEYGRAFASGMASINTVL-NLLEAGDHVV--TG------NDVYGGTHRiFTQ 120
                                       6999999999999999999999999999999999999999988.5899999875..55......4666666664678 PP

                   Met_gamma_lyase 124 slkdfgikykevdlleegkvdieavkeaikektkliliqrskGyserkslsieeieeiiklvkeinedvivfvdncy 200
                                         +d++++++ vd+++     +ea+++a++e+t l+ +       + + lsi +ie + ++ +e  +d ++ +dn +
  gi|336255453|ref|YP_004598560.1| 121 VYEDYDLEFSFVDMTD-----LEAIESAFQENTELLWLETP----TNPLLSIVDIEGAAEIAHE--HDALCAIDNTF 186
                                       899*********9987.....99**************9976....5799********9998765..689*******9 PP

                   Met_gamma_lyase 201 GefveekePtevGadliaGsliknpGGgiaktGGyiaGkee 241
                                             + P ++Gad+++ sl k  GG    +GG +  ++e
  gi|336255453|ref|YP_004598560.1| 187 ATP-YLQRPLDLGADIVSHSLTKYLGGHSDIVGGALLTNDE 226
                                       875.4678********************9999998877665 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   6.4e-08   0.00023      51     204 ..      71     211 ..      50     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.4e-08
                                       HHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCB CS
                       Aminotran_5  51 kvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegel 127
                                       ++a l nae  +   f sG + +in+v++ l    ++gd++v+++  + +++    ++ ++  ++  ++ +      
  gi|336255453|ref|YP_004598560.1|  71 NLASLENAE--YGRAFASGMA-SINTVLNLL----EAGDHVVTGNDVYGGTHRIFTQVYEDYDLEFSFVDM-----T 135
                                       555555665..3556777766.888887666....99*********9*9*999999999887777777766.....8 PP

                                       EGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTS CS
                       Aminotran_5 128 dldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllg 204
                                       dl+++e++ +e+t+l+ +    n +  i ++e  +++a++++al ++D + a +  +  + +lg+D+++ s  K+lg
  gi|336255453|ref|YP_004598560.1| 136 DLEAIESAFQENTELLWLETPTNPLLSIVDIEGAAEIAHEHDALCAIDNTFATPYLQRPL-DLGADIVSHSLTKYLG 211
                                       99**********************************************877777666655.489*******999988 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 !   14.2   0.0   5.8e-06     0.021      22     198 ..      62     236 ..      52     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.8e-06
                                       SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHT....T-EEEEE-B-T CS
                   DegT_DnrJ_EryC1  22 gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlel....gakpvfvDvdp 94 
                                       +p+ +++E+++a   ++++  a++sG a++  +L+ l++g  d V++    + +t    +++     ++  fvD++ 
  gi|336255453|ref|YP_004598560.1|  62 NPTRTDLEANLASLENAEYGRAFASGMASINTVLNLLEAG--DHVVTGNDVYGGTHRIFTQVyedyDLEFSFVDMT- 135
                                       788999*******************************998..*************988776533336788888888. PP

                                       TTSSB-GGGCGGG--TTEEEE...EEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE CS
                   DegT_DnrJ_EryC1  95 dtynidpaaieaaitertkaI...lpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaavfS 168
                                            d +aie+a +e+t      +p + +  ++d++   +ia++h+     D    + + y ++++   +d+ + S
  gi|336255453|ref|YP_004598560.1| 136 -----DLEAIESAFQENTELLwleTPTNPLLSIVDIEGAAEIAHEHDALCAIDNT--FATPYLQRPLDLGADIVSHS 205
                                       .....9************7663336888888999*************99999965..66789999987777776666 PP

                                       -BTTSSS.-SSS..-EEEEESTHHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 169 FyptKnl.ttGe..GGavvtndeelaekarvlr 198
                                       +  tK l    +  GGa++tndeel+e+   ++
  gi|336255453|ref|YP_004598560.1| 206 L--TKYLgGHSDivGGALLTNDEELDEEFGFYQ 236
                                       5..88887666566***********99876665 PP

>> BRK  BRK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00027      0.97      26      40 ..     269     283 ..     268     286 .. 0.84
   2 ?    2.1   0.0     0.043   1.5e+02      33      43 ..     290     300 ..     290     301 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00027
                               BRK  26 lkdLeeWLeenPgye 40 
                                       ++ ++eWLe++P+ +
  gi|336255453|ref|YP_004598560.1| 269 AQAIAEWLEDHPDVD 283
                                       57799*******976 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.043
                               BRK  33 LeenPgyevap 43 
                                       Le +Pg+e+a 
  gi|336255453|ref|YP_004598560.1| 290 LESHPGHEIAA 300
                                       89*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 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:                        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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.36
# Mc/sec: 3252.12
//
Query:       gi|336255454|ref|YP_004598561.1|  [L=230]
Description: beta-lactamase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-19   71.1  10.2    1.6e-19   70.7  10.2    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0015   18.0   0.6     0.0015   18.0   0.6    1.9  2  Lactamase_B_2  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 !   70.7  10.2   1.8e-23   1.6e-19       9     195 ..      29     207 ..       9     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 1.8e-23
                                       EEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCH CS
                       Lactamase_B   9 yliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfme 85 
                                        ++e++ g++LiD G +     +   + +lg++++dv   ++TH+++DH+Ggl++l  +td+ v+ +++eap+  +e
  gi|336255454|ref|YP_004598561.1|  29 AVVETERGLVLIDVGPEDGIRYLETHIDSLGYDLEDVWLALITHHDADHAGGLDDLLARTDATVATHRDEAPYVSGE 105
                                       689************************************************************************** PP

                                       HHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEE..HECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCC CS
                       Lactamase_B  86 eaddaasrkglllagvsadkpdvdeeeldgnaggrraly..vtggpghghghgvveygggkvlftGDallagetgri 160
                                        +      +g     ++ +++ vd+e  +g + + +a++  v  +pgh++gh+++++++ ++l++ Dal + + ++ 
  gi|336255454|ref|YP_004598561.1| 106 REPIKGDSDG-----DRYPPVPVDLELVEGVRIPTLAGPmdVLETPGHTPGHISLHFPESDLLLAADALVVDDGALA 177
                                       **87777765.....66666666666666666666666533799********************************* PP

                                       CC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE CS
                       Lactamase_B 161 dltlrgaevrdpsdaekyldsllklaglkaevlvp 195
                                       ++      + ++ d + +++s++kla+l+ae  v+
  gi|336255454|ref|YP_004598561.1| 178 GP-----RPEFTPDMDRAIESVEKLADLEAEHTVC 207
                                       **.....9999999999999999999999986665 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 !   18.0   0.6   1.7e-07    0.0015       3      63 ..      38      95 ..      37     128 .. 0.75
   2 ?   -0.4   0.1     0.076   6.8e+02     153     200 ..     162     209 ..     145     209 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-07
                                      EEES--TT..HHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEE CS
                     Lactamase_B_2  3 iLiDagpd..lrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyap 63
                                      +LiD gp+  +r     ++     l  +l+++ + l+th ++DH  gl++l ++++  +++  +
  gi|336255454|ref|YP_004598561.1| 38 VLIDVGPEdgIRYL--ETH--IDsLGYDLEDVWLALITHHDADHAGGLDDLLARTD--ATVATH 95
                                      67888888554433..222..334788999**********************9544..455444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.076
                                       HHCT-SEEEEE-S-SSTTHHHHHHT---S...TSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 153 rlggadllllditayeddemirhmgHltp...eeaveaaadlgakrlvliH 200
                                       +l  ad l++d +a+   +    +++ ++    e ve +adl+a+ +v  H
  gi|336255454|ref|YP_004598561.1| 162 LLLAADALVVDDGALAGPR---PEFTPDMdraIESVEKLADLEAEHTVCYH 209
                                       4555677777766665544...35566662233445556666688888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1817.41
//
Query:       gi|336255455|ref|YP_004598562.1|  [L=390]
Description: Y414 protein [Halopiger xanaduensis SH-6]
Scores for 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-42  143.2   0.3      6e-42  142.6   0.3    1.3  1  Lig_C           Ligase Pab1020 C-terminal region
    1.9e-14   54.3   0.0    3.3e-14   53.5   0.0    1.3  1  RNA_ligase      RNA ligase
     0.0064   16.2   0.0        2.8    7.6   0.0    2.4  2  DNA_ligase_A_M  ATP dependent DNA ligase domain


Domain annotation for each model (and alignments):
>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.6   0.3     1e-45     6e-42       1     124 [.     263     385 ..     263     386 .. 0.99

  Alignments for each domain:
  == domain 1  score: 142.6 bits;  conditional E-value: 1e-45
                                       HHCCSCCGS-STSCHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHH CS
                             Lig_C   1 vafsylfelgrdFlfsRviReafqavefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvrfkdeeni 77 
                                       +afs++f++g+ F+f R+iReafq+ve++es+ee rera++LGe+iL +m +t++ v++++ v+e+++vr  ++e+i
  gi|336255455|ref|YP_004598562.1| 263 YAFSFPFDYGQPFMFRRLIREAFQSVEWNESDEEARERAHDLGEAILLSMRDTVETVADGDSVGERHTVR-ASSETI 338
                                       8*********************************************************************.9***** PP

                                       HHHHHHHHCTT--EEEEEEE..TTEEEEE..EE-HHHHHHHHHHHTT CS
                             Lig_C  78 eellehLrrlgvkaeveekekedgelvvkfkkiaqsttdkikslLeG 124
                                       + l+ehLr +g+ +e+e++++edg++vv+f+k  qst+dk++++LeG
  gi|336255455|ref|YP_004598562.1| 339 DVLFEHLRGQGLAVELEDERREDGDRVVTFRKRTQSTNDKTRNYLEG 385
                                       **********************************************9 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   5.5e-18   3.3e-14       3     148 ..      92     245 ..      90     252 .. 0.78

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 5.5e-18
                                       EEEEEE-SSEEEEEEEETT.EEEEETTCEBCTTTHHHHHHTHHHHHHHHHHHHH...ECCEEEEEEEES.SS..TT. CS
                        RNA_ligase   3 vvvtEKlDGtnfriylvke.vgvasRsqilpfgeekfkefkrwaaalrkklkekla.neelilyGElighsikygg. 76 
                                       + v+EKl+G+n+r+   ++   ++sRs+ +       ++f++   ++  +l+  ++  +e +++GE+ig+  +y + 
  gi|336255455|ref|YP_004598562.1|  92 IAVEEKLNGYNVRVARIDGeQLAFSRSGMI-------CPFTTRIIERLVDLEPLFDeYPEAMVCGEMIGPENPYTAh 161
                                       679*************95559*********.......78999999999999999999889*********66666663 PP

                                       .SS..EEEEEEEEEEECTTBECE--HHHH.HHHHHCCT..B..EEEEE.SS.......HHHHHCCC.H..HHHTC-- CS
                        RNA_ligase  77 .lpk.efyvFdifdirdkeeqrylspdev.ealakglg..tvpvlyegkfl.......aaeellelll..skgnkrE 139
                                        +p  + ++F+ fd rd+e+++ l+ +e+ e +++ ++  ++p+++ ++++       aa+e++e+ +   +++ rE
  gi|336255455|ref|YP_004598562.1| 162 dYPYvDSIAFRAFDWRDRESGEPLPVRERrERYER-FDvpQTPLFGIYDADgagngdgAADEVREI-IadLNERGRE 236
                                       3333677888888888999**********666666.667899999999988877443444444444.2357899*** PP

                                       EEEEEESSS CS
                        RNA_ligase 140 GlVikpese 148
                                       G+V+k++++
  gi|336255455|ref|YP_004598562.1| 237 GVVMKSPDG 245
                                       *****9887 PP

>> 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 !    7.6   0.0   0.00046       2.8      20      82 ..      90     153 ..      78     167 .. 0.84
   2 !    6.2   0.0    0.0012       7.2     164     189 ..     220     245 ..     170     257 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00046
                                       SEEEEEEEESSEEEEEEEETTEEEEEETTS-..B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEE CS
                    DNA_ligase_A_M  20 kafivEiKyDGeRaqvhkegdkvklfSRrlk..ditaakpelvkalkeafkkdeksvilDGElva 82 
                                       +a+ vE+K++G+ ++v + +++   fSR++   ++t +  e +  l+ +f++   ++++ GE++ 
  gi|336255455|ref|YP_004598562.1|  90 EAIAVEEKLNGYNVRVARIDGEQLAFSRSGMicPFTTRIIERLVDLEPLFDEY-PEAMVCGEMIG 153
                                       56789*************9999999***9964478889999999999999886.58999999985 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHTTECEEEEEETT- CS
                    DNA_ligase_A_M 164 veeleelleeaiseglEGlvvKnpds 189
                                       ++e++e+++   + g EG+v+K+pd+
  gi|336255455|ref|YP_004598562.1| 220 ADEVREIIADLNERGREGVVMKSPDG 245
                                       6899*******************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3103.26
//
Query:       gi|336255456|ref|YP_004598563.1|  [L=147]
Description: hypothetical protein Halxa_4079 [Halopiger xanaduensis SH-6]
Scores for 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  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1165.19
//
Query:       gi|336255457|ref|YP_004598564.1|  [L=225]
Description: hypothetical protein Halxa_4080 [Halopiger xanaduensis SH-6]
Scores for 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-81  271.0   0.5    5.9e-81  270.8   0.5    1.0  1  PIN_5         PINc domain ribonuclease
  ------ inclusion threshold ------
      0.018   14.3   0.4      0.029   13.7   0.4    1.3  1  CorA          CorA-like Mg2+ transporter protein
       0.03   14.2   0.1      0.044   13.6   0.1    1.3  1  MEDS          MEDS: MEthanogen/methylotroph, DcmR Sensory dom
       0.14   12.9   2.2        3.6    8.4   0.0    3.2  4  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.8   0.5   1.3e-84   5.9e-81       1     205 [.       9     213 ..       9     214 .. 0.98

  Alignments for each domain:
  == domain 1  score: 270.8 bits;  conditional E-value: 1.3e-84
                             PIN_5   1 rfvlDTsaltdpevreklgeeeleeavkklldliaearlklgiscyippsvykElkeflkreeveeeviakldtwlv 77 
                                       rfvlDTs+++++e+r+  ++e+le+av +ll+lia+arl+lgiscy+pp++++El+++l+ ++v++ev++kl+tw+v
  gi|336255457|ref|YP_004598564.1|   9 RFVLDTSLFVTEEIRR--EDESLEDAVLRLLELIAHARLNLGISCYVPPTIHDELTTMLEARDVDDEVYSKLNTWVV 83 
                                       8***************..99********************************************************* PP

                             PIN_5  78 kkspdryevkipaeilyeyveevrerinkGlrvaEeavreaaeesekl..ekeeeeeevgelikklRekYrealRkG 152
                                       +k+pdryev+ipa+++y +v+e+++r+++Glrv+Eeavr+a+e++ +   e++e ++e++++i++lRekYr+a+R+G
  gi|336255457|ref|YP_004598564.1|  84 RKHPDRYEVSIPANVVYSFVDEMSDRVDRGLRVSEEAVRRAEETNGHEplEDHEYKTEIDDVISDLREKYRSAMRTG 160
                                       *******************************************999885557889********************** PP

                             PIN_5 153 ilDsaeDldvllLAkELdaavvssDeGikkwaeklGlrlveakkfpkvlkeyl 205
                                       +lDs+eD+d+l+LA+EL+a+vv++D+Gi  w+e++Glr++++++fp++l++yl
  gi|336255457|ref|YP_004598564.1| 161 VLDSREDFDLLILARELEAGVVTEDRGIIAWTEDFGLRYIRGREFPDLLEQYL 213
                                       ****************************************************8 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   6.5e-06     0.029      83     160 ..      63     153 ..      58     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-06
                              CorA  83 vrreplealdevikrlk.......deggkpkspgellyrlldeivdrlfellekleeeldeledel......edstk 146
                                       +  e  ++ dev+++l        +++ +++ p+ ++y ++de+ dr+++ l+  ee ++++e++       +++ k
  gi|336255457|ref|YP_004598564.1|  63 TMLEARDVDDEVYSKLNtwvvrkhPDRYEVSIPANVVYSFVDEMSDRVDRGLRVSEEAVRRAEETNghepleDHEYK 139
                                       55556666677777777777777767799999*********************************999999777777 PP

                              CorA 147 keilrelaqlrrrl 160
                                        ei + +++lr+++
  gi|336255457|ref|YP_004598564.1| 140 TEIDDVISDLREKY 153
                                       77777888899774 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   9.8e-06     0.044      31     134 ..      49     148 ..      27     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.8e-06
                              MEDS  31 vlyvasastldelrealrkagldvdaalesgqleildaeetylrgggfdpermlealrralakaladgyaglrvige 107
                                       + ++++++ +del+ +l+++ +d + + + +   + ++ +   r+ ++ p++++  + +++++ +    +glrv  e
  gi|336255457|ref|YP_004598564.1|  49 ISCYVPPTIHDELTTMLEARDVDDEVYSKLNTWVVRKHPD---RYEVSIPANVVYSFVDEMSDRV---DRGLRVSEE 119
                                       45667889***********999999999999888888887...5577888777777777777755...47******* PP

                              MEDS 108 mtwalrspa..ereelleyEallneliad 134
                                       ++   ++++  e+ e +ey  +++++i+d
  gi|336255457|ref|YP_004598564.1| 120 AVRRAEETNghEPLEDHEYKTEIDDVISD 148
                                       **766666533666678888899998876 PP

>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00081       3.6      15      32 ..      21      38 ..      20      46 .. 0.89
   2 ?    1.8   0.0     0.095   4.3e+02       5      14 ..      70      79 ..      69      81 .. 0.87
   3 ?   -0.6   0.1      0.52   2.3e+03      24      67 ..     143     152 ..     114     158 .. 0.65
   4 ?   -0.8   0.0       0.6   2.7e+03      24      37 ..     143     156 ..     139     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00081
                      VAPB_antitox 15 klKregeSFsdvIerLle 32
                                      +++re+eS  d+++rLle
  gi|336255457|ref|YP_004598564.1| 21 EIRREDESLEDAVLRLLE 38
                                      799*************98 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.095
                      VAPB_antitox  5 IsdevYekLk 14
                                      ++devY kL 
  gi|336255457|ref|YP_004598564.1| 70 VDDEVYSKLN 79
                                      78******96 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.52
                      VAPB_antitox  24 sdvIerLlekkkkgkkkellelfgilseeeadeiekaskelrke 67 
                                       +dvI  L                                  r++
  gi|336255457|ref|YP_004598564.1| 143 DDVISDL----------------------------------REK 152
                                       3444444..................................433 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.6
                      VAPB_antitox  24 sdvIerLlekkkkg 37 
                                       +dvI  L ek ++ 
  gi|336255457|ref|YP_004598564.1| 143 DDVISDLREKYRSA 156
                                       68999997776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1696.83
//
Query:       gi|336255458|ref|YP_004598565.1|  [L=436]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for complete 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-44  152.7  47.8    6.7e-41  140.4  44.9    2.1  2  MFS_1       Major Facilitator Superfamily
    3.9e-06   26.0  34.9    0.00052   19.0   7.7    3.3  3  Sugar_tr    Sugar (and other) transporter
  ------ inclusion threshold ------
        1.7    7.4  11.7     0.0082   15.0   2.1    2.0  3  LacY_symp   LacY proton/sugar symporter
        4.2    6.1  18.4       0.99    8.2   0.2    3.2  3  MFS_1_like  MFS_1 like family


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 !  140.4  44.9   1.5e-44   6.7e-41      15     353 .]      30     370 ..      13     370 .. 0.87
   2 !   13.3   0.0   6.6e-06     0.029     141     184 ..     388     431 ..     382     436 .] 0.82

  Alignments for each domain:
  == domain 1  score: 140.4 bits;  conditional E-value: 1.5e-44
                             MFS_1  15 lgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.sslw.ll 88 
                                       l++a+ +  l+ ++g ++s++g+l + ++l +av ++p+G+l+dr+G+rr+  +g +++++g ++++ a s ++ + 
  gi|336255458|ref|YP_004598565.1|  30 LSTAVLSgRLTAAFGTTASQLGTLHASFFLIYAVVQIPVGVLVDRVGPRRIGSIGGVVLSVG-AIGF-AiSESYvAA 104
                                       4444444478899*************************************************.5555.3366777** PP

                             MFS_1  89 lvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllaf 165
                                       +++r+l G+g+ga+f +++ + a w+  +e + ++gl ++ ++lGail+    ++ ++++gWr + + l++v++la+
  gi|336255458|ref|YP_004598565.1| 105 FAARALIGFGSGAIFVSILRFCANWYRADEFATMTGLTAGVAGLGAILATTPLAVAVDAAGWRPTVLTLGAVGVLAA 181
                                       **********************************************999555566667******************* PP

                             MFS_1 166 vlfllllpeepperkrkspkeeekgtgpaplvp......awkallkdpvlw.illialllfffgfsglltllplylq 235
                                       v +++l  ++p++ + ++ +       +++ ++      +++ l +d   w + ++ +++++++++++  +   yl+
  gi|336255458|ref|YP_004598565.1| 182 VAVAVLAHDSPVDAGLEPIAGV----PERATTSlaetreHLRTLIRDGDQWlLSIVFFAGNGTVLTLIGLWGVPYLV 254
                                       *999***999999999988777....33333334446779999999999997777777777888888********** PP

                             MFS_1 236 evlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGf 312
                                        v+gl+ + +a+++  l++++++++++ +g+lsdrl rr +ll ++l+++++alg++++      ++++ v++++Gf
  gi|336255458|ref|YP_004598565.1| 255 VVYGLD-VTTASYFTLLGSVGMLVGSPAVGWLSDRLERRVALLAGGLAIFAVALGVIPAVGRPPLPVVAGVYFVCGF 330
                                       ******.999999999999999999*************************************88888888******* PP

                             MFS_1 313 glgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                        lg  + ++l+++ + +p++++g a++ +n ag +gg ++p
  gi|336255458|ref|YP_004598565.1| 331 LLGA-VMLSLSVIKERYPASASGVATATVNAAGFVGGTVFP 370
                                       9996.58999999999*********************9987 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.6e-06
                             MFS_1 141 ggllasslgWravfyilaivsllafvlfllllpeepperkrksp 184
                                       g ++++++g+r++f ila+   +af++ l+ll++++++    ++
  gi|336255458|ref|YP_004598565.1| 388 GTVVYTQFGYRVAFAILAVGVGIAFLCSLALLVRTRRRGTGAPE 431
                                       56778*********************888888887777665554 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   7.7   1.2e-07   0.00052      44     121 ..      46     120 ..      28     128 .. 0.92
   2 !    2.8   0.6    0.0097        44     292     335 ..     142     185 ..     127     202 .. 0.69
   3 !   14.4  12.2   2.8e-06     0.012      48     179 ..     264     406 ..     220     421 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-07
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                       +++++g + ++f+++ ++ ++ +g l+dr+G + +  i++v++++ga+  a+++   s+ + +++R l+G+g G++ 
  gi|336255458|ref|YP_004598565.1|  46 TASQLGTLHASFFLIYAVVQIPVGVLVDRVGPRRIGSIGGVVLSVGAIGFAISE---SYVAAFAARALIGFGSGAIF 119
                                       678999************************************************...9****************986 PP

                                       H CS
                          Sugar_tr 121 v 121
                                       v
  gi|336255458|ref|YP_004598565.1| 120 V 120
                                       5 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0097
                                       HHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 292 vtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilg 335
                                       + ++ g   ++at   +  vd +G R+++l+ +a++ +++v ++
  gi|336255458|ref|YP_004598565.1| 142 TAGVAGLGAILATTPLAVAVDAAGWRPTVLTLGAVGVLAAVAVA 185
                                       45566666677777777888888888877766666666555554 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 2.8e-06
                                       HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                          Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                        + ++ + +vG ++Gs  +g+l+dr+ R+ +ll++++  ++ a+  + a g+  + v++   +++G+ +G++  l+ 
  gi|336255458|ref|YP_004598565.1| 264 ASYFTLLGSVGMLVGSPAVGWLSDRLERRVALLAGGLAIFAVALGVIPAVGRPPLPVVAGVYFVCGFLLGAVM-LSL 339
                                       4667778899999999999999999999999999999999999999999999999999999999999999875.555 PP

                                       HHHHTTS-SCCHH.HHHHHHHHHHHHHHHHHHHHHHHHHTSS-...........TTHHHHHHHCCHH CS
                          Sugar_tr 125 myisEiApkklRg.alvslyqlaitfGilvaaifglglnktsn...........adgwrillglqlv 179
                                         i+E  p++  g a  +++  + + G ++ +++g++l+ ++            + g+r+ +++ +v
  gi|336255458|ref|YP_004598565.1| 340 SVIKERYPASASGvATATVNAAGFVGGTVFPTVLGMALDAYRTgdtvegtvvytQFGYRVAFAILAV 406
                                       5689999999997246688888999999999999999987777677777777665566666555544 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   2.1   1.8e-06    0.0082     262     395 ..      51     183 ..      21     196 .. 0.88
   2 ?   -2.8   1.2      0.44     2e+03      76      76 ..     295     295 ..     229     402 .. 0.61
   3 ?   -2.6   0.1      0.38   1.7e+03     371     397 ..     390     416 ..     356     424 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-06
                         LacY_symp 262 GyvttagellnalimfiaplivnriGaknalliagvimsvrilgsafattalevvilkllhalevplllvgvfkyit 338
                                       G + +   l+ a++ + + ++v+r+G++    i+gv++sv  +g a++ + +     + l  +    + v+++++ +
  gi|336255458|ref|YP_004598565.1|  51 GTLHASFFLIYAVVQIPVGVLVDRVGPRRIGSIGGVVLSVGAIGFAISESYVAAFAARALIGFGSGAIFVSILRFCA 127
                                       55555556778888888999********************************************************* PP

                         LacY_symp 339 safdkrlsatifligfqlskqlaivllstlaGklydkvGfqtaylvlgiivlsltli 395
                                         + +   at+  ++  ++  l+++l +t+     d +G++ + l lg++ ++  + 
  gi|336255458|ref|YP_004598565.1| 128 NWYRADEFATMTGLTAGVA-GLGAILATTPLAVAVDAAGWRPTVLTLGAVGVLAAVA 183
                                       ****999999988877765.7***************************998876553 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.44
                         LacY_symp  76 l 76 
                                       l
  gi|336255458|ref|YP_004598565.1| 295 L 295
                                       3 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.38
                         LacY_symp 371 klydkvGfqtaylvlgiivlsltlisv 397
                                        +y + G++ a+ +l++ v    l s+
  gi|336255458|ref|YP_004598565.1| 390 VVYTQFGYRVAFAILAVGVGIAFLCSL 416
                                       468888999888888776555555555 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 ?    4.2   6.9    0.0036        16     280     363 ..      68     150 ..      14     155 .. 0.85
   2 ?    8.2   0.2   0.00022      0.99      25      80 ..     252     308 ..     227     317 .. 0.68
   3 ?    0.5   0.1     0.048   2.1e+02     156     200 ..     364     418 ..     356     428 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0036
                        MFS_1_like 280 aeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsg 356
                                          l++++G +++  i+ ++  +  ++ ai e+ + ++ + +L g+  g++++++ +++++       at+ gl +g
  gi|336255458|ref|YP_004598565.1|  68 VGVLVDRVGPRRIGSIGGVVLSVGAIGFAISESYVAAFAARALIGFGSGAIFVSILRFCANWYRADEFATMTGLTAG 144
                                       4679**********************************************************************999 PP

                        MFS_1_like 357 lyfglGr 363
                                       +  glG 
  gi|336255458|ref|YP_004598565.1| 145 V-AGLGA 150
                                       8.67776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00022
                        MFS_1_like  25 ylk.skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlfl 80 
                                       yl    gl++      tl+  +  ++++p +g+l+Dr+++r ++++ +l + av++ 
  gi|336255458|ref|YP_004598565.1| 252 YLVvVYGLDVTTASYFTLLGSVGMLVGSPAVGWLSDRLERRVALLAGGLAIFAVALG 308
                                       555356788888888888888888889999999999999998877777766666554 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.048
                        MFS_1_like 156 vGyaifafitGilidhysvnllp..........ysallyvlaallvisllvvlil 200
                                       vG  +f +++G+++d y+++ +           y++++++la+ + i++l++l+l
  gi|336255458|ref|YP_004598565.1| 364 VGGTVFPTVLGMALDAYRTGDTVegtvvytqfgYRVAFAILAVGVGIAFLCSLAL 418
                                       6667888888888888887644457777777888899999998888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 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:                        26  (0.00145016); 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):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.22s 00:00:00.77 Elapsed: 00:00:00.37
# Mc/sec: 3491.89
//
Query:       gi|336255459|ref|YP_004598566.1|  [L=88]
Description: elongation factor 1-beta [Halopiger xanaduensis SH-6]
Scores for 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-19   68.0   0.0    6.5e-19   67.9   0.0    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain
  ------ inclusion threshold ------
       0.19   12.5   0.0       0.26   12.1   0.0    1.2  1  DUF3073   Protein of unknown function (DUF3073)


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 !   67.9   0.0   7.3e-23   6.5e-19       3      90 .]       7      88 .]       5      88 .] 0.95

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 7.3e-23
                                      EEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEESSS-GGGGHHHHHHTTS-S.....SE CS
                           EF1_GNE  3 vlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvieddkvstdeleekieeiegeledlVq 80
                                       ++v+P++ e dl++l+++++s +l++ ++++  +++e++afGl++L  +++++d  ++t+++ee+++e+eg     V+
  gi|336255459|ref|YP_004598566.1|  7 KIKVMPNSPEIDLDALQERLES-SLPEgAKING-VEREEVAFGLTALYPTVIVPDGAGGTETVEENFSEVEG-----VE 78
                                      79********************.77777****5.**************************************.....** PP

                                      EEEEEEEEE- CS
                           EF1_GNE 81 sveivsfnkl 90
                                      sv ++++ ++
  gi|336255459|ref|YP_004598566.1| 79 SVGVENVGRI 88
                                      ******9986 PP

>> DUF3073  Protein of unknown function (DUF3073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.9e-05      0.26      11      38 ..       3      32 ..       2      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
                           DUF3073 11 KvAReLKY..lspetDydaLerELsgksee 38
                                      KvA ++K   +spe+D+daL++ L+++ +e
  gi|336255459|ref|YP_004598566.1|  3 KVAAKIKVmpNSPEIDLDALQERLESSLPE 32
                                      889999973369************887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 772.35
//
Query:       gi|336255460|ref|YP_004598567.1|  [L=59]
Description: hypothetical protein Halxa_4083 [Halopiger xanaduensis SH-6]
Scores for 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-07   30.7  10.6    8.9e-07   28.8   4.3    2.3  2  DUF1610          Domain of unknown function (DUF1610)
    0.00041   20.6  11.1      0.019   15.2   0.7    2.2  2  C1_2             C1 domain
     0.0058   16.7  11.3       0.62   10.2   2.4    2.8  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
     0.0061   16.6   0.4     0.0061   16.6   0.4    3.8  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.007   16.7   9.1     0.0077   16.6   9.1    1.1  1  Rhodanese_C      Rhodanase C-terminal
  ------ inclusion threshold ------
      0.012   15.6  14.6      0.059   13.4   2.2    2.2  2  DZR              Double zinc ribbon
      0.015   15.2   6.6      0.015   15.2   6.6    2.0  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.017   14.5  14.9        2.9    7.4   0.1    3.8  3  zf-ribbon_3      zinc-ribbon domain
      0.018   14.7  11.3       0.33   10.7   1.0    3.1  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.024   15.1  11.0      0.076   13.5   7.2    2.0  2  zf-CHY           CHY zinc finger
      0.028   14.3   9.6       0.87    9.5   6.4    2.4  2  C1_1             Phorbol esters/diacylglycerol binding domain
       0.05   13.4   1.4       0.05   13.4   1.4    2.9  3  HscB_4_cys       Co-chaperone HscB tetracysteine metal bindin
       0.05   13.6  11.6      0.095   12.7   1.0    2.0  2  HypA             Hydrogenase/urease nickel incorporation, met
      0.072   13.1  11.6       0.73    9.9  11.6    2.0  1  zinc-ribbons_6   zinc-ribbons
      0.086   13.0  18.8        2.9    8.1   0.6    3.8  3  Zn-ribbon_8      Zinc ribbon domain
       0.11   12.7  10.3        1.4    9.1   0.5    2.2  2  zf-MYND          MYND finger
       0.14   11.8  16.0       0.27   10.8   0.5    3.9  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.17   12.0   9.8       0.29   11.2   9.8    1.5  1  Zn_Tnp_IS91      Transposase zinc-binding domain
       0.17   10.7   6.0       0.18   10.6   6.0    1.0  1  NMDAR2_C         N-methyl D-aspartate receptor 2B3 C-terminus
       0.17   12.2   1.2       0.17   12.2   1.2    2.4  2  zf-UBP           Zn-finger in ubiquitin-hydrolases and other 
       0.18    9.7   7.5       0.19    9.5   7.5    1.0  1  PolC_DP2         DNA polymerase II large subunit DP2
       0.27   11.0  17.6          2    8.2   0.1    3.9  3  Rubredoxin_2     Rubredoxin metal binding domain
       0.39   10.7  18.2          8    6.5   0.2    4.0  3  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.39   10.7  10.4       0.29   11.1   5.4    2.1  2  zf-C2HC5         Putative zinc finger motif, C2HC5-type
       0.42   10.4   9.6        6.4    6.6   0.1    3.8  4  zf-C2H2_11       zinc-finger C2H2-type
       0.62   10.2  17.1        1.4    9.0   0.2    3.5  3  UPF0547          Uncharacterised protein family UPF0547
       0.64    9.8  16.4        2.4    8.0   4.3    3.8  2  zinc_ribbon_2    zinc-ribbon domain
       0.67   10.2  11.4        3.3    8.0   1.5    2.6  3  zf-AN1           AN1-like Zinc finger
        0.7    9.5  16.3       0.34   10.5   1.4    3.9  4  Sgf11            Sgf11 (transcriptional regulation protein)
       0.76    9.2   9.3       0.89    9.0   9.3    1.0  1  NMD3             NMD3 family
       0.84    9.9  11.7         16    5.7  11.7    2.4  1  zf-UBR           Putative zinc finger in N-recognin (UBR box)
       0.92    9.6   5.5         22    5.2   0.4    3.1  3  DUF2752          Protein of unknown function (DUF2752)
        1.3    9.1  16.2         25    5.0   0.1    3.4  3  YhfH             YhfH-like protein
        1.4    8.8  14.3        9.2    6.1   0.6    3.6  4  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
        1.6    9.3  15.2        3.5    8.3   0.7    3.7  4  zf-C2H2          Zinc finger, C2H2 type
        1.7    8.8  11.0        2.4    8.4   0.2    2.4  2  DUF2387          Probable metal-binding protein (DUF2387)
          2    7.1  10.3        1.6    7.4   0.6    2.0  2  NRDD             Anaerobic ribonucleoside-triphosphate reduct
        2.2    8.2  17.7        6.8    6.7   3.0    3.5  3  zf-HIT           HIT zinc finger
        2.5    8.2   7.7        5.5    7.1   0.1    3.2  3  zf-C2H2_6        C2H2-type zinc finger
        5.2    6.9  15.2        4.9    7.0   4.0    3.8  3  A2L_zn_ribbon    A2L zinc ribbon domain
        7.4    6.6  20.9         21    5.2   4.7    3.6  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        7.7    6.5   8.9         11    6.0   6.0    2.0  2  DUF1451          Zinc-ribbon containing domain
        9.8    6.2  12.7          6    6.9   6.1    2.5  2  Anti-TRAP        Tryptophan RNA-binding attenuator protein in


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 !   28.8   4.3   2.1e-09   8.9e-07       1      23 [.      12      33 ..      12      34 .. 0.98
   2 ?    5.7   0.4     0.034        14      19      23 ..      51      55 ..      48      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.1e-09
                           DUF1610  1 CtSCGaelaprEravvFpCPNCG 23
                                      C+SCG  +a+ + a +F CP+CG
  gi|336255460|ref|YP_004598567.1| 12 CVSCGLNIAGTN-AAAFKCPECG 33
                                      ************.********** PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.034
                           DUF1610 19 CPNCG 23
                                      CP CG
  gi|336255460|ref|YP_004598567.1| 51 CPDCG 55
                                      ****9 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.7   4.7e-05     0.019      13      39 ..       4      33 ..       1      37 [. 0.86
   2 !   10.5   4.0    0.0014      0.58      18      41 ..      36      57 ..      33      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-05
                              C1_2 13 edssesfnCsaCgrkidgff...YsCseCd 39
                                       d+ e+++C  Cg +i g++   ++C+eC 
  gi|336255460|ref|YP_004598567.1|  4 TDDRETRSCVSCGLNIAGTNaaaFKCPECG 33
                                      478899*********99999999******6 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0014
                              C1_2 18 sfnCsaCgrkidgffYsCseCdfs 41
                                       ++C  C++++  + Y+C+ C f+
  gi|336255460|ref|YP_004598567.1| 36 IYRCAKCRKQS--NLYECPDCGFT 57
                                      689******96..66******995 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 !    8.1   5.3     0.007       2.9      11      30 ..      21      40 ..       3      45 .. 0.79
   2 !   10.2   2.4    0.0015      0.62      12      24 ..      44      56 ..      38      58 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.007
                          zf-Mss51 11 apkhvdfeCpdCGiptycse 30
                                        +  +f+Cp+CG  +y + 
  gi|336255460|ref|YP_004598567.1| 21 GTNAAAFKCPECGQQIYRCA 40
                                      567789********999876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0015
                          zf-Mss51 12 pkhvdfeCpdCGi 24
                                      +++  +eCpdCG+
  gi|336255460|ref|YP_004598567.1| 44 KQSNLYECPDCGF 56
                                      56778*******8 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 ?    1.6   0.1       0.7   2.9e+02       3       8 ..      11      16 ..      10      19 .. 0.85
   2 !   16.6   0.4   1.5e-05    0.0061       2      13 ..      27      38 ..      27      38 .. 0.94
   3 ?    1.0   0.4       1.1   4.6e+02       3       8 ..      38      43 ..      37      45 .. 0.78
   4 ?    3.4   0.2      0.19        80       4       8 ..      51      55 ..      46      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.7
                            zf-ACC  3 KCpsCg 8 
                                       C sCg
  gi|336255460|ref|YP_004598567.1| 11 SCVSCG 16
                                      59***8 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.5e-05
                            zf-ACC  2 tKCpsCgemlyk 13
                                      +KCp+Cg+++y+
  gi|336255460|ref|YP_004598567.1| 27 FKCPECGQQIYR 38
                                      6**********8 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.1
                            zf-ACC  3 KCpsCg 8 
                                      +C +C 
  gi|336255460|ref|YP_004598567.1| 38 RCAKCR 43
                                      699995 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.19
                            zf-ACC  4 CpsCg 8 
                                      Cp Cg
  gi|336255460|ref|YP_004598567.1| 51 CPDCG 55
                                      88887 PP

>> Rhodanese_C  Rhodanase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   9.1   1.8e-05    0.0077      16      63 ..       7      54 ..       1      55 [. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-05
                       Rhodanese_C 16 evvgkCieCgkpvdelr..krnCanedCnelvlvCeeCaeklkgv.cseeC 63
                                      + + +C+ Cg +    +  + +C  ++C +++  C++C+++ + + c  +C
  gi|336255460|ref|YP_004598567.1|  7 RETRSCVSCGLNIAGTNaaAFKC--PECGQQIYRCAKCRKQSNLYeCP-DC 54
                                      46789*****9999888445555..79**************9998565.88 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.2   0.00014     0.059      10      37 ..       7      35 ..       2      38 .. 0.79
   2 ?   11.9  14.7   0.00042      0.17       1      49 []      12      55 ..      12      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00014
                               DZR 10 pdarfCseCgtklkavaa.edrCpsCgek 37
                                       + r C  Cg ++  ++a + +Cp+Cg++
  gi|336255460|ref|YP_004598567.1|  7 RETRSCVSCGLNIAGTNAaAFKCPECGQQ 35
                                      56788999999998777778889999987 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00042
                               DZR  1 CpqCgee...lppdarfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49
                                      C +Cg +   +++ a  C+eCg+++      +rC +C ++ ++    Cp CG
  gi|336255460|ref|YP_004598567.1| 12 CVSCGLNiagTNAAAFKCPECGQQI------YRCAKCRKQSNLY--ECPDCG 55
                                      99999996655667779********......8*******99888..599998 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 ?    1.3   0.2      0.77   3.2e+02      44      55 ..       7      18 ..       2      26 .. 0.70
   2 ?   15.2   6.6   3.5e-05     0.015      30      55 ..      28      57 ..      23      58 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.77
                    OrfB_Zn_ribbon 44 grtfkCpnCgfe 55
                                      ++t  C +Cg+ 
  gi|336255460|ref|YP_004598567.1|  7 RETRSCVSCGLN 18
                                      566678888875 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.5e-05
                    OrfB_Zn_ribbon 30 tCseCgsknke....alsgrtfkCpnCgfe 55
                                      +C+eCg++ ++    ++++++++Cp+Cgf+
  gi|336255460|ref|YP_004598567.1| 28 KCPECGQQIYRcakcRKQSNLYECPDCGFT 57
                                      7***************************96 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0069       2.9       1      10 [.       8      17 ..       8      24 .. 0.79
   2 ?    5.8   5.2     0.022       9.3       4      11 ..      28      35 ..      25      45 .. 0.79
   3 ?    5.9   0.3     0.022         9       4       9 ..      50      55 ..      47      56 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0069
                       zf-ribbon_3  1 stvrCPnCGa 10
                                      +t++C +CG 
  gi|336255460|ref|YP_004598567.1|  8 ETRSCVSCGL 17
                                      5899****96 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.022
                       zf-ribbon_3  4 rCPnCGap 11
                                      +CP+CG++
  gi|336255460|ref|YP_004598567.1| 28 KCPECGQQ 35
                                      68888874 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.022
                       zf-ribbon_3  4 rCPnCG 9 
                                      +CP CG
  gi|336255460|ref|YP_004598567.1| 50 ECPDCG 55
                                      566666 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 ?   10.7   1.0   0.00078      0.33       3      27 ..      12      36 ..      11      36 .. 0.90
   2 ?    6.0   3.4     0.023       9.5       1      25 [.      37      56 ..      37      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00078
                                      -SSS--B----SSS----SSS---- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCGhRi 27
                                      C  Cg +    + ++ +C eCG  i
  gi|336255460|ref|YP_004598567.1| 12 CVSCGLNIAGTNAAAFKCPECGQQI 36
                                      999999999999**********876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.023
                                      -B-SSS--B----SSS----SSS-- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevslkkgdpiRCkeCGh 25
                                      Y C++C ++  l +     C +CG+
  gi|336255460|ref|YP_004598567.1| 37 YRCAKCRKQSNLYE-----CPDCGF 56
                                      99****99887754.....777776 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.0    0.0037       1.5      49      73 ..       4      33 ..       1      35 [. 0.79
   2 ?   13.5   7.2   0.00018     0.076      39      74 ..      24      56 ..      18      57 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0037
                            zf-CHY 49 teqekavlCkkCkk.....efaeyfCpiCk 73
                                      t ++++  C +C+      ++a+++Cp C 
  gi|336255460|ref|YP_004598567.1|  4 TDDRETRSCVSCGLniagtNAAAFKCPECG 33
                                      45677889****8878887889999****7 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00018
                            zf-CHY 39 vkevlcllCeteqekavlCkkCkkefaeyfCpiCkl 74
                                      +  ++c +C    ++   C kC+k+ + y Cp C +
  gi|336255460|ref|YP_004598567.1| 24 AAAFKCPECG---QQIYRCAKCRKQSNLYECPDCGF 56
                                      4445555555...57999****************75 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 ?    9.5   6.4    0.0021      0.87       9      38 ..       7      36 ..       2      45 .. 0.83
   2 ?    4.5   2.7     0.078        33      13      36 ..      38      56 ..      34      57 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0021
                                      SS--B-TTT-SB--SSSS-EEEETTT--EE CS
                              C1_1  9 kqptfCkhCgeflwgkekqglkCswCkllv 38
                                      +++  C  Cg  + g +  ++kC +C++ +
  gi|336255460|ref|YP_004598567.1|  7 RETRSCVSCGLNIAGTNAAAFKCPECGQQI 36
                                      67889********99999999999998765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.078
                                      B-TTT-SB--SSSS-EEEETTT-- CS
                              C1_1 13 fCkhCgeflwgkekqglkCswCkl 36
                                      +C++C+++        + C +C++
  gi|336255460|ref|YP_004598567.1| 38 RCAKCRKQS-----NLYECPDCGF 56
                                      677777776.....8888888876 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.4   0.00012      0.05       2      23 ..      11      32 ..      11      33 .. 0.96
   2 ?    2.9   0.7      0.23        97      19      24 ..      38      43 ..      33      44 .. 0.81
   3 ?    0.6   0.1       1.2     5e+02      20      23 ..      51      54 ..      48      58 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                                      B-SSS--B--SS-S---B-TTT CS
                        HscB_4_cys  2 rCWnCGgpgapgrgdefFCpqC 23
                                      +C +CG   a+++++ f Cp C
  gi|336255460|ref|YP_004598567.1| 11 SCVSCGLNIAGTNAAAFKCPEC 32
                                      5999****************** PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.23
                                      B-TTT- CS
                        HscB_4_cys 19 FCpqCR 24
                                       C++CR
  gi|336255460|ref|YP_004598567.1| 38 RCAKCR 43
                                      5****9 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.2
                                      -TTT CS
                        HscB_4_cys 20 CpqC 23
                                      Cp C
  gi|336255460|ref|YP_004598567.1| 51 CPDC 54
                                      6666 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 ?   12.7   1.0   0.00023     0.095      71      95 ..      10      35 ..       2      38 .. 0.81
   2 ?    6.7   3.9     0.016       6.8      71      93 ..      37      55 ..      34      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00023
                                      EEETTTS-EEECHHH.HHS-TTTSSS CS
                              HypA 71 vrCreCgkefeleek.alrCpkCgsa 95
                                        C +Cg ++  +++ a++Cp+Cg++
  gi|336255460|ref|YP_004598567.1| 10 RSCVSCGLNIAGTNAaAFKCPECGQQ 35
                                      57*****99996654599*****985 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.016
                                      EEETTTS-EEECHHHHHS-TTTS CS
                              HypA 71 vrCreCgkefeleekalrCpkCg 93
                                      +rC +C+k+ +l     +Cp+Cg
  gi|336255460|ref|YP_004598567.1| 37 YRCAKCRKQSNLY----ECPDCG 55
                                      79*****999865....8****8 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  11.6    0.0017      0.73      15      55 ..       8      54 ..       1      57 [. 0.60

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0017
                                      SEEE-TTT--....EEEEEEE-SSS-S---EEEETTEEE..E--TTT CS
                    zinc-ribbons_6 15 eqyhCeaCqe....dlkkealCpeCeqelevlkaCgavd..yfCnkc 55
                                      e+ +C +C             CpeC+q++ ++ +C + +  y C +c
  gi|336255460|ref|YP_004598567.1|  8 ETRSCVSCGLniagTNAAAFKCPECGQQIYRCAKCRKQSnlYECPDC 54
                                      56677777763333333445688888888888888665433556555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.043        18      22      34 ..       4      17 ..       1      22 [. 0.76
   2 ?    8.1   0.6    0.0071       2.9      28      34 ..      28      34 ..      18      36 .. 0.67
   3 ?    6.3  14.1     0.024        10       6      33 ..      27      55 ..      26      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.043
                       Zn-ribbon_8 22 sdaplta.CPeCgs 34
                                      +d+ +t  C +Cg 
  gi|336255460|ref|YP_004598567.1|  4 TDDRETRsCVSCGL 17
                                      47778889****96 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0071
                       Zn-ribbon_8 28 aCPeCgs 34
                                      +CPeCg+
  gi|336255460|ref|YP_004598567.1| 28 KCPECGQ 34
                                      4777776 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.024
                       Zn-ribbon_8  6 YrCeeCghefevlqsis.dapltaCPeCg 33
                                      ++C eCg++  + ++   +++l +CP+Cg
  gi|336255460|ref|YP_004598567.1| 27 FKCPECGQQIYRCAKCRkQSNLYECPDCG 55
                                      9**************996666666****9 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.5    0.0033       1.4       1      21 [.      12      37 ..      10      37 .. 0.79
   2 ?    7.7   3.6    0.0092       3.8       1      17 [.      39      55 ..      39      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0033
                                      -TTT--.....B-SC.E-TTTS-SEE CS
                           zf-MYND  1 CavCgk....aealk.kCagCksvfY 21
                                      C +Cg     ++a+  kC++C +  Y
  gi|336255460|ref|YP_004598567.1| 12 CVSCGLniagTNAAAfKCPECGQQIY 37
                                      8899999988455556*****98777 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0092
                                      -TTT--.B-SCE-TTTS CS
                           zf-MYND  1 CavCgkaealkkCagCk 17
                                      Ca+C+k+ +l  C+ C 
  gi|336255460|ref|YP_004598567.1| 39 CAKCRKQSNLYECPDCG 55
                                      ******77777*****5 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.95     4e+02       2      13 ..       9      20 ..       8      24 .. 0.79
   2 ?   10.8   0.5   0.00065      0.27       3      12 ..      27      36 ..      25      38 .. 0.88
   3 ?    4.6   1.0     0.058        24       3      11 ..      37      45 ..      35      48 .. 0.87
   4 ?    6.3   0.5     0.018       7.4       2      10 ..      48      56 ..      47      59 .] 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.95
                            zf_UBZ  2 tylCerCgkeip 13
                                      t  C  Cg +i 
  gi|336255460|ref|YP_004598567.1|  9 TRSCVSCGLNIA 20
                                      678999*99886 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00065
                            zf_UBZ  3 ylCerCgkei 12
                                      + C++Cg++i
  gi|336255460|ref|YP_004598567.1| 27 FKCPECGQQI 36
                                      89******99 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.058
                            zf_UBZ  3 ylCerCgke 11
                                      y C++C k+
  gi|336255460|ref|YP_004598567.1| 37 YRCAKCRKQ 45
                                      89****997 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.018
                            zf_UBZ  2 tylCerCgk 10
                                       y C++Cg 
  gi|336255460|ref|YP_004598567.1| 48 LYECPDCGF 56
                                      599****95 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 ?   11.2   9.8    0.0007      0.29      18      64 ..       3      55 ..       1      58 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0007
                       Zn_Tnp_IS91 18 psqrkavekilrCrtaalGfary..eCeeCghekivyfsCksrh....CpsCq 64
                                      ++ +++ ++  +C+ +  G +    +C+eCg++ + + +C++++    Cp C+
  gi|336255460|ref|YP_004598567.1|  3 TTDDRETRSCVSCGLNIAGTNAAafKCPECGQQIYRCAKCRKQSnlyeCPDCG 55
                                      566788999999*9999998765227**************9875556799997 PP

>> NMDAR2_C  N-methyl D-aspartate receptor 2B3 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   6.0   0.00044      0.18     384     422 ..       9      50 ..       1      53 [. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00044
                                       XXXXXXXXXXXXXX.XXXXXXX...XXX.XXXXXXXXXXXXX CS
                          NMDAR2_C 384 sthCRsClsklsaygagsssvr...spykrCdaCkklgnLYd 422
                                       + +C sC  +++++ a+ +      + + rC  C+k +nLY+
  gi|336255460|ref|YP_004598567.1|   9 TRSCVSCGLNIAGTNAAAFKCPecgQQIYRCAKCRKQSNLYE 50 
                                       34566666677777666554334557778************8 PP

>> zf-UBP  Zn-finger in ubiquitin-hydrolases and other protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.8      0.89   3.7e+02       1      19 [.      12      34 ..      12      37 .. 0.47
   2 ?   12.2   1.2   0.00041      0.17       1      21 [.      39      58 ..      39      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.89
                                      -TTTH.....--.SSEEEETTT-- CS
                            zf-UBP  1 CseCn.....senknlWlCLkCgh 19
                                      C  C+     + n   + C +Cg+
  gi|336255460|ref|YP_004598567.1| 12 CVSCGlniagT-NAAAFKCPECGQ 34
                                      55555322211.234566777776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00041
                                      -TTTH--.SSEEEETTT--EE CS
                            zf-UBP  1 CseCnsenknlWlCLkCghvg 21
                                      C++C+++ +nl+ C +Cg+ g
  gi|336255460|ref|YP_004598567.1| 39 CAKCRKQ-SNLYECPDCGFTG 58
                                      *****88.**********875 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 ?    9.5   7.5   0.00046      0.19     618     662 ..       9      55 ..       2      58 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00046
                          PolC_DP2 618 rrkCkkCg.....ketlearCeeCgekteeklvCkkceeeveeekcekce 662
                                       +r+C +Cg     +++  ++C+eCg+++     C kc+++++  +c+ c+
  gi|336255460|ref|YP_004598567.1|   9 TRSCVSCGlniagTNAAAFKCPECGQQIYR---CAKCRKQSNLYECPDCG 55 
                                       678888862222256677889999887655...99999999988899986 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   6.8      0.75   3.1e+02      15      22 ..      27      34 ..      11      34 .. 0.62
   2 ?    5.9   0.3     0.025        11       1      10 [.      37      46 ..      37      48 .. 0.87
   3 ?    8.2   0.1    0.0047         2       1      10 [.      49      58 ..      49      59 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.75
                      Rubredoxin_2 15 GrCpsCgs 22
                                       +Cp+Cg+
  gi|336255460|ref|YP_004598567.1| 27 FKCPECGQ 34
                                      58999986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.025
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      Y+C +C  +s
  gi|336255460|ref|YP_004598567.1| 37 YRCAKCRKQS 46
                                      9*****9887 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0047
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      Y+C +CGf+ 
  gi|336255460|ref|YP_004598567.1| 49 YECPDCGFTG 58
                                      99*****986 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 ?    4.6   0.1     0.073        30       6      13 ..      11      18 ..      11      22 .. 0.81
   2 ?    0.3   9.0       1.6   6.6e+02       7      31 ..      29      43 ..      26      47 .. 0.58
   3 ?    6.5   0.2     0.019         8       5      11 ..      49      55 ..      48      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.073
                    Zn_ribbon_SprT  6 rCtgCgre 13
                                      +C++Cg +
  gi|336255460|ref|YP_004598567.1| 11 SCVSCGLN 18
                                      6*****77 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.6
                    Zn_ribbon_SprT  7 CtgCgreythhlsirrhnYrCrrCk 31
                                      C+ Cg+++          YrC +C+
  gi|336255460|ref|YP_004598567.1| 29 CPECGQQI----------YRCAKCR 43
                                      55555432..........6666666 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.019
                    Zn_ribbon_SprT  5 YrCtgCg 11
                                      Y C++Cg
  gi|336255460|ref|YP_004598567.1| 49 YECPDCG 55
                                      99****9 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 ?   11.1   5.4    0.0007      0.29      19      46 ..      11      38 ..       7      44 .. 0.87
   2 ?    1.7   1.7      0.61   2.6e+02      28      41 ..      42      55 ..      38      57 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0007
                          zf-C2HC5 19 nClnCGkiiCakeglskpCsfCgsplls 46
                                       C++CG+ i   ++   +C+ Cg++++ 
  gi|336255460|ref|YP_004598567.1| 11 SCVSCGLNIAGTNAAAFKCPECGQQIYR 38
                                      7******999999999********9986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.61
                          zf-C2HC5 28 CakeglskpCsfCg 41
                                      C k+    +C+ Cg
  gi|336255460|ref|YP_004598567.1| 42 CRKQSNLYECPDCG 55
                                      77777779999997 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 ?    6.1   0.1     0.023       9.6       3      13 ..       8      18 ..       6      21 .. 0.80
   2 ?    6.6   0.1     0.015       6.4       1      11 [.      23      33 ..      23      35 .. 0.87
   3 ?    0.8   0.3         1   4.2e+02       5      10 ..      37      42 ..      36      44 .. 0.83
   4 ?    0.9   0.0      0.96     4e+02       6      11 ..      50      55 ..      46      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.023
                        zf-C2H2_11  3 stcqCleCGlc 13
                                       t  C+ CGl+
  gi|336255460|ref|YP_004598567.1|  8 ETRSCVSCGLN 18
                                      5778*****97 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                        zf-C2H2_11  1 destcqCleCG 11
                                      + ++++C eCG
  gi|336255460|ref|YP_004598567.1| 23 NAAAFKCPECG 33
                                      6789******9 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1
                        zf-C2H2_11  5 cqCleC 10
                                      ++C +C
  gi|336255460|ref|YP_004598567.1| 37 YRCAKC 42
                                      589999 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.96
                        zf-C2H2_11  6 qCleCG 11
                                       C +CG
  gi|336255460|ref|YP_004598567.1| 50 ECPDCG 55
                                      699**9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.99   4.1e+02      14      21 ..       9      16 ..       8      17 .. 0.79
   2 ?    4.9   7.5     0.068        29       2      10 ..      28      36 ..      24      43 .. 0.83
   3 ?    9.0   0.2    0.0034       1.4      16      22 ..      50      56 ..      46      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.99
                           UPF0547 14 aqfCphCG 21
                                      +++C  CG
  gi|336255460|ref|YP_004598567.1|  9 TRSCVSCG 16
                                      58897798 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.068
                           UPF0547  2 vCPeCeakv 10
                                      +CPeC +++
  gi|336255460|ref|YP_004598567.1| 28 KCPECGQQI 36
                                      688888887 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0034
                           UPF0547 16 fCphCGy 22
                                      +Cp+CG+
  gi|336255460|ref|YP_004598567.1| 50 ECPDCGF 56
                                      8*****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 ?    8.0   4.3    0.0058       2.4       2      21 ..      12      34 ..      11      36 .. 0.61
   2 ?    2.3   4.4      0.35   1.4e+02      16      20 ..      51      55 ..      38      57 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0058
                     zinc_ribbon_2  2 CpnCGaelq.dnakF..CpyCGt 21
                                      C +CG  +   na    Cp+CG 
  gi|336255460|ref|YP_004598567.1| 12 CVSCGLNIAgTNAAAfkCPECGQ 34
                                      77777777424444458888885 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.35
                     zinc_ribbon_2 16 CpyCG 20
                                      Cp CG
  gi|336255460|ref|YP_004598567.1| 51 CPDCG 55
                                      66666 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       3.4   1.4e+03      15      21 ..      11      17 ..       7      19 .. 0.76
   2 ?    8.0   1.5    0.0079       3.3       5      22 ..      14      35 ..      11      36 .. 0.68
   3 ?    6.9   2.8     0.017       7.1       1      20 [.      39      55 ..      38      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.4
                            zf-AN1 15 kCryCgk 21
                                       C +Cg 
  gi|336255460|ref|YP_004598567.1| 11 SCVSCGL 17
                                      5888885 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0079
                            zf-AN1  5 sCkkkd....flp.fkCryCgkv 22
                                      sC+ ++      + fkC++Cg++
  gi|336255460|ref|YP_004598567.1| 14 SCGLNIagtnA-AaFKCPECGQQ 35
                                      57777755422.25******986 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.017
                            zf-AN1  1 CsfksCkkkdflpfkCryCg 20
                                      C+  +C+k+ +  ++C++Cg
  gi|336255460|ref|YP_004598567.1| 39 CA--KCRKQSN-LYECPDCG 55
                                      66..8*99998.8******8 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.089        37       4      16 ..       9      21 ..       6      23 .. 0.81
   2 ?   10.5   1.4   0.00082      0.34       3      14 ..      25      36 ..      23      39 .. 0.87
   3 ?    2.5   1.3      0.25     1e+02       3      13 ..      35      45 ..      34      47 .. 0.86
   4 ?    3.6   0.5      0.12        50       2      11 ..      46      55 ..      45      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.089
                                      EEE-TTTSSEEEG CS
                             Sgf11  4 yvtCpnCgRqiaa 16
                                      + +C  Cg +ia+
  gi|336255460|ref|YP_004598567.1|  9 TRSCVSCGLNIAG 21
                                      568*****99997 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00082
                                      -EEE-TTTSSEE CS
                             Sgf11  3 eyvtCpnCgRqi 14
                                      + ++Cp Cg+qi
  gi|336255460|ref|YP_004598567.1| 25 AAFKCPECGQQI 36
                                      679********9 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.25
                                      -EEE-TTTSSE CS
                             Sgf11  3 eyvtCpnCgRq 13
                                      + ++C  C +q
  gi|336255460|ref|YP_004598567.1| 35 QIYRCAKCRKQ 45
                                      6799****987 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.12
                                      C-EEE-TTTS CS
                             Sgf11  2 seyvtCpnCg 11
                                      s +++Cp Cg
  gi|336255460|ref|YP_004598567.1| 46 SNLYECPDCG 55
                                      6789*****7 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   9.3    0.0021      0.89       1      42 [.      12      55 ..      12      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0021
                              NMD3  1 CcrCGkeieeling...lCedCllkevditegiekievevCkeCg 42
                                      C+ CG +i   +n+    C++C  + ++ +++ ++ ++  C++Cg
  gi|336255460|ref|YP_004598567.1| 12 CVSCGLNIA-GTNAaafKCPECGQQIYRCAKCRKQSNLYECPDCG 55
                                      ********6.4466789***************************8 PP

>> zf-UBR  Putative zinc finger in N-recognin (UBR box)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  11.7     0.039        16       8      30 ..      32      54 ..       2      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.039
                            zf-UBR  8 kgevvyrCltCsldetsviCeeC 30
                                       g+ +yrC +C+++++ + C +C
  gi|336255460|ref|YP_004598567.1| 32 CGQQIYRCAKCRKQSNLYECPDC 54
                                      46888999999998888888888 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.79   3.3e+02      10      16 ..      11      17 ..       9      20 .. 0.87
   2 ?    4.4   0.1     0.095        40       9      15 ..      27      33 ..      22      35 .. 0.84
   3 ?    5.2   0.4     0.052        22       9      17 ..      49      57 ..      47      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.79
                           DUF2752 10 pCPGCGl 16
                                      +C  CGl
  gi|336255460|ref|YP_004598567.1| 11 SCVSCGL 17
                                      69****7 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.095
                           DUF2752  9 ipCPGCG 15
                                      ++CP CG
  gi|336255460|ref|YP_004598567.1| 27 FKCPECG 33
                                      89****9 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.052
                           DUF2752  9 ipCPGCGlt 17
                                      ++CP CG t
  gi|336255460|ref|YP_004598567.1| 49 YECPDCGFT 57
                                      68*****98 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.059        25      15      23 ..      11      19 ..       7      26 .. 0.84
   2 ?    2.7  11.7      0.31   1.3e+02      15      37 .]      28      54 ..      22      54 .. 0.74
   3 ?    3.2   0.7      0.21        88      15      20 ..      50      55 ..      48      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.059
                              YhfH 15 kCteCGkei 23
                                       C++CG +i
  gi|336255460|ref|YP_004598567.1| 11 SCVSCGLNI 19
                                      7*****888 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.31
                              YhfH 15 kCteCGkeieEqaecYgn....eCekC 37
                                      kC+eCG++i   a c ++    eC +C
  gi|336255460|ref|YP_004598567.1| 28 KCPECGQQIYRCAKCRKQsnlyECPDC 54
                                      8********998888554223356666 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.21
                              YhfH 15 kCteCG 20
                                      +C++CG
  gi|336255460|ref|YP_004598567.1| 50 ECPDCG 55
                                      7****9 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 ?   -0.3   0.2       2.2   9.3e+02      47      51 ..      12      16 ..       6      19 .. 0.83
   2 ?    5.9   2.4     0.024        10      43      53 ..      25      35 ..      12      36 .. 0.78
   3 ?    6.1   0.6     0.022       9.2      44      52 ..      36      44 ..      34      46 .. 0.84
   4 ?    4.3   0.2      0.08        33      44      52 ..      48      56 ..      44      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.2
                    zinc_ribbon_10 47 CpkCg 51
                                      C +Cg
  gi|336255460|ref|YP_004598567.1| 12 CVSCG 16
                                      99998 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.024
                    zinc_ribbon_10 43 vkyrCpkCgal 53
                                        ++Cp+Cg++
  gi|336255460|ref|YP_004598567.1| 25 AAFKCPECGQQ 35
                                      58*******86 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.022
                    zinc_ribbon_10 44 kyrCpkCga 52
                                       yrC+kC+ 
  gi|336255460|ref|YP_004598567.1| 36 IYRCAKCRK 44
                                      6******96 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.08
                    zinc_ribbon_10 44 kyrCpkCga 52
                                       y Cp Cg+
  gi|336255460|ref|YP_004598567.1| 48 LYECPDCGF 56
                                      599****97 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       9.7   4.1e+03       3       7 ..      12      16 ..      11      18 .. 0.79
   2 ?    6.9   0.3     0.022       9.3       1       8 [.      27      34 ..      27      36 .. 0.90
   3 ?    3.9   0.2       0.2        84       1       8 [.      37      44 ..      37      48 .. 0.87
   4 ?    8.3   0.7    0.0084       3.5       1       9 [.      49      57 ..      49      59 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 9.7
                                      ETTTT CS
                           zf-C2H2  3 CpdCg 7 
                                      C  Cg
  gi|336255460|ref|YP_004598567.1| 12 CVSCG 16
                                      88998 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.022
                                      EEETTTTE CS
                           zf-C2H2  1 ykCpdCgk 8 
                                      +kCp+Cg+
  gi|336255460|ref|YP_004598567.1| 27 FKCPECGQ 34
                                      9*****96 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.2
                                      EEETTTTE CS
                           zf-C2H2  1 ykCpdCgk 8 
                                      y+C +C k
  gi|336255460|ref|YP_004598567.1| 37 YRCAKCRK 44
                                      99****88 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0084
                                      EEETTTTEE CS
                           zf-C2H2  1 ykCpdCgks 9 
                                      y+CpdCg +
  gi|336255460|ref|YP_004598567.1| 49 YECPDCGFT 57
                                      99*****86 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0057       2.4      24      37 ..       3      16 ..       1      26 [. 0.87
   2 ?    3.6   6.1      0.17        73      10      39 ..      28      57 ..      18      59 .] 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0057
                           DUF2387 24 eedeveyrECvsCg 37
                                      + d++e r CvsCg
  gi|336255460|ref|YP_004598567.1|  3 TTDDRETRSCVSCG 16
                                      5799*********9 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.17
                           DUF2387 10 vCPrCsemDkirmweedeveyrECvsCgft 39
                                       CP C ++    +    + +  EC +Cgft
  gi|336255460|ref|YP_004598567.1| 28 KCPECGQQIYRCAKCRKQSNLYECPDCGFT 57
                                      59***98865555556678999*******8 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.6    0.0039       1.6     508     527 ..      10      34 ..       3      38 .. 0.81
   2 ?    5.6   3.4     0.013       5.6     507     526 ..      36      55 ..      34      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0039
                                       EEETT.--..EESS...SB-TTT-- CS
                              NRDD 508 dvCnecgy..kgei...ekCpkCgs 527
                                         C +cg   +g+    +kCp+Cg+
  gi|336255460|ref|YP_004598567.1|  10 RSCVSCGLniAGTNaaaFKCPECGQ 34 
                                       5799***988777788999*****4 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.013
                                       EEEETT.--EESSSB-TTT- CS
                              NRDD 507 idvCnecgykgeiekCpkCg 526
                                       i +C +c ++   ++Cp Cg
  gi|336255460|ref|YP_004598567.1|  36 IYRCAKCRKQSNLYECPDCG 55 
                                       779******999999****9 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   3.0     0.016       6.8       5      21 ..      12      34 ..       8      36 .. 0.73
   2 ?    5.8   1.2     0.031        13      14      21 ..      37      44 ..      34      46 .. 0.84
   3 ?    4.1   6.9      0.11        44       4      20 ..      38      55 ..      37      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.016
                                      -TTT-S......B-SEE-TTT-- CS
                            zf-HIT  5 CgvCgf......pakYkCpkCnt 21
                                      C+ Cg        a  kCp C++
  gi|336255460|ref|YP_004598567.1| 12 CVSCGLniagtnAAAFKCPECGQ 34
                                      666665555556899******97 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.031
                                      EE-TTT-- CS
                            zf-HIT 14 YkCpkCnt 21
                                      Y+C kC+ 
  gi|336255460|ref|YP_004598567.1| 37 YRCAKCRK 44
                                      ******85 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.11
                                      B-TTT-S.B-SEE-TTT- CS
                            zf-HIT  4 lCgvCgf.pakYkCpkCn 20
                                       C+ C +    Y Cp C+
  gi|336255460|ref|YP_004598567.1| 38 RCAKCRKqSNLYECPDCG 55
                                      59999998888****997 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 ?    7.1   0.1     0.013       5.5       1       8 [.      26      33 ..      26      35 .. 0.87
   2 ?    2.7   0.5      0.32   1.3e+02       2       9 ..      37      44 ..      36      45 .. 0.85
   3 ?    1.8   0.2      0.63   2.6e+02       2       8 ..      49      55 ..      48      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                         zf-C2H2_6  1 vheCsvCs 8 
                                      +++C++C+
  gi|336255460|ref|YP_004598567.1| 26 AFKCPECG 33
                                      69*****8 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.32
                         zf-C2H2_6  2 heCsvCsk 9 
                                      ++C  C k
  gi|336255460|ref|YP_004598567.1| 37 YRCAKCRK 44
                                      9*****88 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.63
                         zf-C2H2_6  2 heCsvCs 8 
                                      +eC+ C+
  gi|336255460|ref|YP_004598567.1| 49 YECPDCG 55
                                      9***997 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 ?    1.0   0.2      0.91   3.8e+02      22      29 ..      10      17 ..       3      19 .. 0.78
   2 ?    1.0   3.6      0.88   3.7e+02      23      28 ..      28      33 ..      10      34 .. 0.71
   3 ?    7.0   4.0     0.012       4.9       6      30 ..      39      57 ..      34      59 .] 0.67

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.91
                     A2L_zn_ribbon 22 lvCieCga 29
                                      ++C  Cg+
  gi|336255460|ref|YP_004598567.1| 10 RSCVSCGL 17
                                      68999985 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.88
                     A2L_zn_ribbon 23 vCieCg 28
                                       C+eCg
  gi|336255460|ref|YP_004598567.1| 28 KCPECG 33
                                      599998 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.012
                     A2L_zn_ribbon  6 CsvCggngilnseqgylvCieCgas 30
                                      C +C+++         + C++Cg++
  gi|336255460|ref|YP_004598567.1| 39 CAKCRKQSN------LYECPDCGFT 57
                                      555555544......489*****98 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 ?    5.2   4.7      0.05        21      19      46 .]      10      35 ..       1      35 [. 0.60
   2 ?    4.5  15.6     0.084        35      18      45 ..      26      56 ..      20      57 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.05
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrkq 46
                                      + C  Cg   +  ++ +  f+C eC+ q
  gi|336255460|ref|YP_004598567.1| 10 RSCVSCGLN-IAGTN-AAAFKCPECGQQ 35
                                      556677722.22222.357777777765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.084
                     Zn_Tnp_IS1595 18 gfvCPhCgsrkayrikt....rglfqCkeCrk 45
                                       f CP Cg +++yr ++      l++C +C+ 
  gi|336255460|ref|YP_004598567.1| 26 AFKCPECG-QQIYRCAKcrkqSNLYECPDCGF 56
                                      599*****.556666555558899****9986 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   4.9      0.11        47     116     144 ..      11      38 ..       7      46 .. 0.84
   2 ?    6.0   6.0     0.027        11     112     140 ..      24      56 ..      21      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                           DUF1451 116 vCekCgkelalkkteeippCpkCgateFr 144
                                        C +Cg ++a +++    +Cp+Cg++ +r
  gi|336255460|ref|YP_004598567.1|  11 SCVSCGLNIAGTNAAAF-KCPECGQQIYR 38 
                                       69999999998888775.7****998775 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.027
                           DUF1451 112 lGtlvCekCgkel....alkkteeippCpkCga 140
                                       +  + C +Cg+++    + +k +++ +Cp+Cg 
  gi|336255460|ref|YP_004598567.1|  24 AAAFKCPECGQQIyrcaKCRKQSNLYECPDCGF 56 
                                       56799*****996444478999*********96 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 ?    6.9   6.1     0.014         6       5      37 ..       3      33 ..       1      45 [. 0.69
   2 ?    0.6   3.4       1.4   5.6e+02      31      37 ..      49      55 ..      37      58 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.014
                                      -HHHCEEE.-TTTTTTS.EETTE......E-TTTT CS
                         Anti-TRAP  5 alpeLEtk.CdaCngsG.kiepeeprasleCPkCs 37
                                       +++ Et  C  C   G +i+++ + a+++CP+C+
  gi|336255460|ref|YP_004598567.1|  3 TTDDRETRsCVSC---GlNIAGT-NAAAFKCPECG 33
                                      5777777425555...4245666.7788******6 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.4
                                      .E-TTTT CS
                         Anti-TRAP 31 leCPkCs 37
                                       eCP+C+
  gi|336255460|ref|YP_004598567.1| 49 YECPDCG 55
                                      5899996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        57  (0.00317921); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              43  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 376.26
//
Query:       gi|336255461|ref|YP_004598568.1|  [L=433]
Description: hypothetical protein Halxa_4084 [Halopiger xanaduensis SH-6]
Scores for 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-95  319.5   0.0    2.8e-95  319.2   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    7.2e-41  138.5   0.1    1.3e-40  137.7   0.1    1.4  1  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.2   0.0   3.1e-99   2.8e-95       1     270 []      21     307 ..      21     307 .. 0.97

  Alignments for each domain:
  == domain 1  score: 319.2 bits;  conditional E-value: 3.1e-99
                             Nre_N   1 Lcglkkcpileklravekakkki.sskeleGsspPsvfVGrygYPkVsvgplvppveg.dasvldspekwl..glsl 73 
                                       L+++k+++i+++l+++e++++++ s+++l Gs++Ps+fVGr++YP++ vg l p  ++ da+++ ++ +w+  g+ +
  gi|336255461|ref|YP_004598568.1|  21 LAKEKSYEITDHLEEFERRFDDAlSGDTLVGSTSPSIFVGRSNYPDIPVGLLSPVGDEdDAEEYVTDGEWYqqGYAI 97 
                                       7899*******************9**************************776666559************999*** PP

                             Nre_N  74 ediiklrlslvrgekkvkvkkak............edklleeiqelalsekpvdvevelekkpkaklkf.devlaPv 137
                                       +d++++r+ l++++k+++v++++            ++ +++ ++e+a++++pvd+e+ l+++p+  l    +v++P 
  gi|336255461|ref|YP_004598568.1|  98 NDVLQRRTGLLNSNKRANVDSPSiasrltpnvhdaWNGFVGVQREVAIADRPVDLEIGLDDTPDLGLDAgTDVATPR 174
                                       **************************************************************988776624689*** PP

                             Nre_N 138 GpsaeleklkvaenpkvprkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvd 214
                                       Gp+a+++++++ enp vp++v k++eD+d++A+ a+++Lyr+g+dvy+i+++LS+G+LGe+++rrlVPTrWsITAvd
  gi|336255461|ref|YP_004598568.1| 175 GPRANARNAELRENPYVPKPVKKTLEDDDWQAQGAMTYLYRRGFDVYEINSILSAGALGEAEQRRLVPTRWSITAVD 251
                                       ***************************************************************************** PP

                             Nre_N 215 divgkelkkeikdlpeidevevfsgeylgNrflviLaPgkwsfelvEawapgslwn 270
                                       d+vg+ l+ +i++ p+idev+v+ +ey+gNr++v+LaPg+w+felvE++apgs+wn
  gi|336255461|ref|YP_004598568.1| 252 DTVGQFLRGRIRNEPSIDEVQVWANEYMGNRYWVVLAPGNWEFELVEMKAPGSIWN 307
                                       *******************************************************8 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   0.1   1.4e-44   1.3e-40       1     110 []     321     429 ..     321     429 .. 0.98

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 1.4e-44
                             Nre_C   1 egyegrkeyse.iaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleea 76 
                                       egyegr++y+e +aGaYyaarl+vle+Le+i+rqak++vlre++++YwaPvGvWqvRe+vr+a+++++ e+e+++ a
  gi|336255461|ref|YP_004598568.1| 321 EGYEGRSSYVEeTAGAYYAARLGVLEHLESIGRQAKCLVLREVSDDYWAPVGVWQVRESVRNAFDGNYGEAETFHGA 397
                                       799************************************************************************** PP

                             Nre_C  77 leevseklklplkkllkkskllkelkkqktLddF 110
                                       ++e++++l+++l++l++ks+l+++l  q++L++F
  gi|336255461|ref|YP_004598568.1| 398 VAEIATQLPVSLQRLRRKSELAAGL--QANLSAF 429
                                       *************************..9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 3342.39
//
Query:       gi|336255462|ref|YP_004598569.1|  [L=64]
Description: cold-shock DNA-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   70.7   0.2    7.4e-20   70.6   0.2    1.0  1  CSD       'Cold-shock' DNA-binding domain
  ------ inclusion threshold ------
      0.034   13.8   3.0       0.05   13.3   3.0    1.3  1  OB_RNB    Ribonuclease B OB domain
       0.12   12.3   1.1       0.16   11.9   1.1    1.5  1  S1-like   S1-like


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.2   1.2e-23   7.4e-20       2      65 ..       3      63 ..       2      64 .] 0.97

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 1.2e-23
                                      EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
                               CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                                      tG+V  fn+  g+GFI+++d d+dvF+H+ ++ g++   L+eg e+eF++++  kgp+A+nVt+
  gi|336255462|ref|YP_004598569.1|  3 TGIVDFFNDTGGYGFIETDDADEDVFFHMEDVGGED---LTEGTEIEFDIEQAPKGPRATNVTR 63
                                      8*******************************9999...***********************96 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   3.0   8.4e-06      0.05       8      28 ..      13      33 ..       7      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.4e-06
                                      SS-EEEEECT.TEEEEE-HHH CS
                            OB_RNB  8 kGFGFlipdegkeDifippeq 28
                                       G+GF+++d+ +eD+f + e+
  gi|336255462|ref|YP_004598569.1| 13 GGYGFIETDDADEDVFFHMED 33
                                      59**************87766 PP

>> S1-like  S1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.1   2.7e-05      0.16      14      43 ..      14      48 ..       1      63 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                           S1-like 14 tfGfv.....DeevfFqrsvvkGrlpkvgdrVlve 43
                                       +Gf+     De+vfF+++ v G     g  ++++
  gi|336255462|ref|YP_004598569.1| 14 GYGFIetddaDEDVFFHMEDVGGEDLTEGTEIEFD 48
                                      599987777789*******9999877777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); 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:                         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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 568.37
//
Query:       gi|336255463|ref|YP_004598570.1|  [L=73]
Description: hypothetical protein Halxa_4086 [Halopiger xanaduensis SH-6]
Scores for 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:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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 0.19s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 650.15
//
Query:       gi|336255464|ref|YP_004598571.1|  [L=478]
Description: Na+/H+ antiporter NhaC [Halopiger xanaduensis SH-6]
Scores for complete 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-62  211.5  37.4    1.4e-55  188.7  18.0    2.1  2  Na_H_antiporter  Na+/H+ antiporter family
  ------ inclusion threshold ------
       0.15   12.2   0.1       0.15   12.2   0.1    5.0  4  Phage_holin_3_3  LydA holin phage, holin superfamily III


Domain annotation for each model (and alignments):
>> Na_H_antiporter  Na+/H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8  11.4   2.7e-13   2.5e-09     144     264 ..      64     185 ..      20     185 .. 0.82
   2 !  188.7  18.0   1.5e-59   1.4e-55       1     302 [.     171     462 ..     171     463 .. 0.98

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.7e-13
                   Na_H_antiporter 144 a..slseidkllnrGiksmlgaililllAwgiggvlealgvteslvsslakgvvskgllplilflvallvafatGts 218
                                           ++++ + ++ G+ + ++a+li+++ +++     + g + + +   ++ + +  +lp +  ++a++vaf++G+s
  gi|336255464|ref|YP_004598571.1|  64 LgyTWDDLSDGIINGLLMGMQALLIIFTIYALIATWVDAGTIPAMMYYGLELLSPGVFLP-VAAILAAVVAFSIGSS 139
                                       234588899999***99999***********99999999988888888887776555555.66778999******** PP

                   Na_H_antiporter 219 wgtigIilpiavplaaklgisllalvraveaggtlgdhlsPisdtt 264
                                       w t+g ++  +v ++a lg+  + +v+av +g+  gd  sP+sdtt
  gi|336255464|ref|YP_004598571.1| 140 WTTVGTLGVAFVGIGAGLGVPGPMTVGAVISGAYAGDKQSPLSDTT 185
                                       *********************************************8 PP

  == domain 2  score: 188.7 bits;  conditional E-value: 1.5e-59
                   Na_H_antiporter   1 vavfgdkssplsdtvgliagilktdlieeiaalgmlvqsipanvysifallvvglvvl...llrdigamlraeaear 74 
                                       +a+ gdk+splsdt++l+ag+++t l+++i    m   + +a+ +s++ ++++gl +     + ++ ++++a+a+a+
  gi|336255464|ref|YP_004598571.1| 171 GAYAGDKQSPLSDTTNLAAGVTNTPLYDHIY--RMRTGTAIAFGLSVLGFAALGLQFSgavPAGQVAEIQTALAGAY 245
                                       79****************************9..49***********************8888899999999999999 PP

                   Na_H_antiporter  75 eleekeltklpiavliiltlskmpytgalalvaivkafivalafqntdvatalvvgalaglivatllelaslseidk 151
                                        l++  +   p++v+++l+l+++p+++ l+ ++++ ++i+a+++q+t ++ a+   ++ g++ +t++ l     +++
  gi|336255464|ref|YP_004598571.1| 246 SLSVLAFV--PLVVTFGLALRGYPALPTLVTGVFA-GIITAILVQGTGFVPAWE-VFMGGTAPETGSDL-----VND 313
                                       99999999..*************************.******************.**************.....*** PP

                   Na_H_antiporter 152 llnrG.iksmlgaililllAwgiggvlealgvteslvsslakgvvskgllplilflvallvafatGtswgtigIilp 227
                                       ll +G + + +++i+++++A+++gg+le++gv+++l ++l++gv s g+l++ + ++a++v++ t++++++i++++ 
  gi|336255464|ref|YP_004598571.1| 314 LLATGgLTGSAWTITVVVAALSLGGLLERIGVLAVLANQLSQGVRSSGSLIAGTGVSAIVVNALTAQQYMSIVLPGV 390
                                       ***************************************************************************** PP

                   Na_H_antiporter 228 iavplaaklgisllalvraveaggtlgdhlsPisdttilsstglnadhidhvsytqlpyallvapitailllvfG 302
                                       ++++l++++g+++  l+ravea+gt + +l P+++++++++ ++   ++ +++y +++ + +++p+++  +++ G
  gi|336255464|ref|YP_004598571.1| 391 TLRNLYDEFGLDSEELSRAVEAAGTPTGALLPWHAGGVYMAGAT---GVATLEYAPFYLFGFLSPLVLFAMALSG 462
                                       ********************************************...9****************99999888877 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 ?    1.0   0.2     0.053   4.8e+02       2      20 ..      53      71 ..      52      90 .. 0.83
   2 ?   -0.2   8.1      0.13   1.1e+03      36      73 ..     124     161 ..     122     166 .. 0.93
   3 ?    0.9   3.9     0.057   5.1e+02      41      71 ..     146     176 ..     140     178 .. 0.86
   4 ?   12.2   0.1   1.7e-05      0.15      35      76 ..     272     313 ..     264     315 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.053
                   Phage_holin_3_3  2 liivlAllGGlvsylmrak 20
                                       i+v +++G+ ++y ++  
  gi|336255464|ref|YP_004598571.1| 53 SIVVTGAFGRYLGYTWDDL 71
                                      68999*********99875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.13
                   Phage_holin_3_3  36 vvSgfvGllvfllceelglsqlltlaiaglsGylGara 73 
                                       v+++++++++f + ++++  ++l +a++g+++ lG ++
  gi|336255464|ref|YP_004598571.1| 124 VAAILAAVVAFSIGSSWTTVGTLGVAFVGIGAGLGVPG 161
                                       67999***************************999886 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.057
                   Phage_holin_3_3  41 vGllvfllceelglsqlltlaiaglsGylGa 71 
                                        G+    + + lg+++++t++++  ++y+G+
  gi|336255464|ref|YP_004598571.1| 146 LGVAFVGIGAGLGVPGPMTVGAVISGAYAGD 176
                                       577777888999*****************97 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 1.7e-05
                   Phage_holin_3_3  35 ivvSgfvGllvfllceelglsqlltlaiaglsGylGaralia 76 
                                       +v+++f+G+++++l+  +g+ + + +++ g +   G+++++ 
  gi|336255464|ref|YP_004598571.1| 272 LVTGVFAGIITAILVQGTGFVPAWEVFMGGTAPETGSDLVND 313
                                       89****************************998888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); 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:                         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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 3164.28
//
Query:       gi|336255465|ref|YP_004598572.1|  [L=156]
Description: hypothetical protein Halxa_4088 [Halopiger xanaduensis SH-6]
Scores for 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-17   62.4   0.0    4.4e-17   61.7   0.0    1.3  1  DUF302    Domain of unknown function DUF302


Domain annotation for each model (and alignments):
>> DUF302  Domain of unknown function DUF302
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   2.5e-21   4.4e-17       5      61 ..      52     109 ..      48     111 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.5e-21
                                       HHHHCTT-S--S-EEEEEEE-HHHHHHHHCC-GGGGGG-SEEEEEEE.ETTEEEEEEE CS
                            DUF302   5 atlkkklgedlrpykilgaCnPklatealqadpeiglllPcrvvVye.kdgkttvsyv 61 
                                       + l++k+++d +py++lgaCnP++a++al++ p+ig l Pc+++V++ + g+ +v+ v
  gi|336255465|ref|YP_004598572.1|  52 ELLNEKVDADRDPYYVLGACNPEIADRALDETPRIGGLFPCNMIVWQeEPGRQRVYHV 109
                                       7799*******************************************777**999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1220.69
//
Query:       gi|336255466|ref|YP_004598573.1|  [L=230]
Description: abortive infection protein [Halopiger xanaduensis SH-6]
Scores for complete 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   28.5   0.4    3.3e-06   27.4   0.4    1.8  1  CPBP      CPBP intramembrane metalloprotease


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 !   27.4   0.4   1.8e-10   3.3e-06      11      88 ..     124     200 ..      10     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.8e-10
                                       HHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGGHHH.HHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                              CPBP  11 alllapllEEllfRglllqllqergsstlailissilFglaHlpngps.vllaalaGlvlgylylktgsllaaillH 86 
                                        l+  +l+ E ++Rgll+  ++e  + + a++is +++ l H+   p+ ++l     +++g++ +k+ s+l+++++H
  gi|336255466|ref|YP_004598573.1| 124 KLFTLALAAETYYRGLLCVGVKEL-G-FKAVFISPVIYMLHHASKPPIeFVLSGPTDVLFGAIDYKSDSILPSVIAH 198
                                       566778889***************.4.68****************9999**************************** PP

                                       HH CS
                              CPBP  87 al 88 
                                       ++
  gi|336255466|ref|YP_004598573.1| 199 GA 200
                                       85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1805.23
//
Query:       gi|336255467|ref|YP_004598574.1|  [L=94]
Description: hypothetical protein Halxa_4090 [Halopiger xanaduensis SH-6]
Scores for 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:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.36u 0.19s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 809.98
//
Query:       gi|336255468|ref|YP_004598575.1|  [L=347]
Description: hypothetical protein Halxa_4091 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0034   17.1  11.2     0.0083   15.8  11.3    1.6  1  Virul_fac_BrkB  Virulence factor BrkB


Domain annotation for each model (and alignments):
>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8  11.3   4.6e-07    0.0083      94     206 ..       2     111 ..       1     156 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.6e-07
                    Virul_fac_BrkB  94 ralnkiygveesrsflrkrllsllllllllvllllslvlsvflqslllasapllglglelsell.llqllrwlvall 169
                                       ++l+++y+ +  r+  r+rl + + l+l++++l++++vl++ +  ++ +++ +  +g   +e + +++++++ +a  
  gi|336255468|ref|YP_004598575.1|   2 TSLTEVYDGNG-RGVSRRRLYAGSGLVLCGAVLAVVAVLVATTDLFADFVVGFADWG--MAEQFtVVRVAGV-LAGM 74 
                                       56777887766.89*******************************999987554444..3344458999999.6777 PP

                    Virul_fac_BrkB 170 llvlafallYrvlpnvkvrlraalpGallaallwllv 206
                                        + +a++ ++ vlp  ++   aa++ a l+ l+++l+
  gi|336255468|ref|YP_004598575.1|  75 GVPAALVGVFIVLPAGRRVRAAAAISASLCLLGVVLF 111
                                       888************8766666777777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2989.20
//
Query:       gi|336255469|ref|YP_004598576.1|  [L=160]
Description: hypothetical protein Halxa_4092 [Halopiger xanaduensis SH-6]
Scores for 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-11   42.6   4.2    3.8e-10   39.3   4.2    2.0  1  YdjM         LexA-binding, inner membrane-associated putative
  ------ inclusion threshold ------
       0.14   12.2   0.4       0.32   11.0   0.4    1.5  1  Zn_dep_PLPC  Zinc dependent phospholipase C


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   4.2   4.2e-14   3.8e-10       1     159 [.       1     132 [.       1     148 [. 0.76

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 4.2e-14
                              YdjM   1 MdgltHallGaalglalaallgaake.......avllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgft 70 
                                       M  + H+l +++lg++l+ ll +a +        ++ + + lgA++PDiD        ++g           HR   
  gi|336255469|ref|YP_004598576.1|   1 MNKKGHVLNAVLLGIGLGYLLEPAGDlttfrtiVEIGVPVTLGAMVPDID-------TAFGK----------HRKTL 60 
                                       8889*******************99999999776666667788*******.......55555..........***** PP

                              YdjM  71 HSllflallalvlllllrlfgrsalrlglllllgvlsHlllDlltk.yGvpllwPfskkkvrlsllfiiidplltll 146
                                       H l+ la++ ++ +l+ +l           +++g+l+H +lD+  + +G+ l++P+ kk++ l++ +   ++     
  gi|336255469|ref|YP_004598576.1|  61 HNLPLLAGFIAFPALFGNLEY---------VWIGILTHYVLDVAGSkRGIALFYPVWKKEFGLPIGVAVSSK----- 123
                                       ******999998887777666.........56**********99776*********9777777777664444..... PP

                              YdjM 147 srrglvalelvll 159
                                          +   l +v++
  gi|336255469|ref|YP_004598576.1| 124 ---RAD-LMMVVV 132
                                       ...222.222222 PP

>> Zn_dep_PLPC  Zinc dependent phospholipase C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   3.6e-05      0.32      31     105 ..      42      94 ..      39      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.6e-05
                                       HHHHGGGG..-TT-GGG--BTTTTB-HHHHS-HHHHHHHHHHHHHHHHHC.....T-HHHHHHHHHHHHHHHHHH CS
                       Zn_dep_PLPC  31 lGsvaPDleylfnasshsykthtkagllgedhhweetgkfllllikklrelyksegslklaafllGvlsHyvaDv 105
                                       lG++ PD+     +++h   +h+               ++l+ +i   +       + +l   ++G+l+Hyv Dv
  gi|336255469|ref|YP_004598576.1|  42 LGAMVPDIDT--AFGKHRKTLHN--------------LPLLAGFIAFPAL------FGNLEYVWIGILTHYVLDV 94 
                                       8*******54..45666666666..............6777777777755......56777889**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1386.21
//
Query:       gi|336255470|ref|YP_004598577.1|  [L=360]
Description: Pyrrolo-quinoline quinone beta-propeller repeat-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-33  114.4  15.1    5.3e-20   72.0   5.0    4.0  4  PQQ_2     PQQ-like domain
    1.3e-23   81.7   9.5    0.00073   19.4   0.1    7.6  7  PQQ       PQQ enzyme repeat
    3.3e-15   56.0  26.3    3.1e-05   24.3   0.1    7.9  7  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.3   3.1e-09   1.9e-05      10      66 ..      15      70 ..       8      76 .. 0.89
   2 !   20.3   0.3   5.6e-08   0.00033      36      68 ..      79     111 ..      70     115 .. 0.88
   3 !   72.0   5.0   8.9e-24   5.3e-20      30     235 ..     116     313 ..     110     315 .. 0.82
   4 !   21.7   0.0   2.1e-08   0.00013      86     181 ..     251     340 ..     231     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.1e-09
                             PQQ_2 10 aatGaelWrvdlarplgggvsravlsggtlfva....tgggrlvaldaatGkvlWettleg 66
                                      ++ G++ W++d    ++  +  +v+++gt++++    + g+++valda++G+++W+++ ++
  gi|336255470|ref|YP_004598577.1| 15 PPRGNLAWTSDA---FTRWP--PVVADGTVYIGnvdqNPGPKIVALDATDGSERWRVSIDE 70
                                      5679******98...99999..9**********887779*****************99865 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 5.6e-08
                             PQQ_2  36 ggtlfvatgggrlvaldaatGkvlWettlegpv 68 
                                        gtl+va +g++++ald+ +G++ W++tl+g+v
  gi|336255470|ref|YP_004598577.1|  79 VGTLLVAAYGDQVIALDRDSGTQEWTATLSGTV 111
                                       48999999**********************987 PP

  == domain 3  score: 72.0 bits;  conditional E-value: 8.9e-24
                             PQQ_2  30 sravlsggtlfva...tgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqlialdaedGkrlWstq 103
                                        +av+++  ++v     + + l+a+d+++G+++W++ l  +vv ap v ++ v+v++ + +l++ld++dG r+W+++
  gi|336255470|ref|YP_004598577.1| 116 LTAVPEETLVLVPersRRDAGLTAFDTTSGEQRWSAPLADRVVDAPAVRGDGVYVAT-ESELCRLDIADGSRVWTRK 191
                                       358877777777766568889***********************************7.88***************88 PP

                             PQQ_2 104 qrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerelaaprgtselsrvgdisgrpvvaegtVyass 180
                                       ++      +++++s a +   +vv+  +g+l+++d+++G++l +               ++ ++++ +a+gt y  +
  gi|336255470|ref|YP_004598577.1| 192 LED----VALGPRSAA-E--GIVVAA-DGELAVRDVDTGERLRSLDN-----------YDREAYAVAIADGTAYWLT 249
                                       888....334444444.3..344444.8*************655533...........334579************* PP

                             PQQ_2 181 gqgrllaldlatgrrlwskeissinglpildgdllyvvsa..........gelialdratGavlW 235
                                       ++  l+a+ l+ g ++w  + ++ +   ++  d+++   +           ++ a+dr+tG v+W
  gi|336255470|ref|YP_004598577.1| 250 FET-LAAISLEDGTVEWRLDAEGCQEGLCVGQDTIVAPVEyeefdlettwPTIAAFDRETGDVRW 313
                                       ***.7888******99*888777666678877777766655799********************* PP

  == domain 4  score: 21.7 bits;  conditional E-value: 2.1e-08
                             PQQ_2  86 gqlialdaedGkrlWstqqrseepae.lrssaspava...gdtvvvgessgklvaldpkdGkvlWerel.aaprgts 157
                                       ++l+a++ edG++ W+  ++ e ++e l++  + +va    +++ + ++   ++a+d ++G+v+W + + + +    
  gi|336255470|ref|YP_004598577.1| 251 ETLAAISLEDGTVEWR--LDAEGCQEgLCVGQDTIVApveYEEFDLETTWPTIAAFDRETGDVRWYYHIdGFDV--- 322
                                       5899999999999999..33335888566666666668888888888888889999999999999999966644... PP

                             PQQ_2 158 elsrvgdisgrpvvaegtVyassg 181
                                             + +  pv++eg+Vy++++
  gi|336255470|ref|YP_004598577.1| 323 ------SFTTPPVLVEGAVYFAAN 340
                                       ......567888888898888775 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.1e-06    0.0066       9      29 ..      49      69 ..      37      77 .. 0.83
   2 !   14.7   0.1   3.6e-06     0.022       3      36 ..      82     115 ..      80     117 .. 0.84
   3 !   12.3   0.0   2.1e-05      0.12      11      36 ..     136     161 ..     129     163 .. 0.86
   4 !    7.6   0.0   0.00064       3.8      12      34 ..     176     198 ..     166     200 .. 0.78
   5 !    4.9   0.0    0.0046        28       3      23 ..     207     225 ..     205     227 .. 0.81
   6 !    5.4   0.0    0.0032        19      12      31 ..     253     272 ..     249     276 .. 0.86
   7 !   19.4   0.1   1.2e-07   0.00073       7      35 ..     296     324 ..     294     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-06
                                      TSEEEEEETTTCCEEEEEESS CS
                               PQQ  9 dGylyAlDadTGkvlWrfktg 29
                                      + +++AlDa++G ++Wr+ ++
  gi|336255470|ref|YP_004598577.1| 49 GPKIVALDATDGSERWRVSID 69
                                      5689*************9876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.6e-06
                                       EEEEETTSEEEEEETTTCCEEEEEESSSCGSSES CS
                               PQQ   3 vylgsadGylyAlDadTGkvlWrfktggpvlslp 36 
                                       + ++ ++ ++ AlD+d+G+  W+  ++g v+ ++
  gi|336255470|ref|YP_004598577.1|  82 LLVAAYGDQVIALDRDSGTQEWTATLSGTVNLST 115
                                       556667779*******************999876 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 2.1e-05
                                       EEEEEETTTCCEEEEEESSSCGSSES CS
                               PQQ  11 ylyAlDadTGkvlWrfktggpvlslp 36 
                                        l A+D ++G+ +W+ ++ + v+  p
  gi|336255470|ref|YP_004598577.1| 136 GLTAFDTTSGEQRWSAPLADRVVDAP 161
                                       689**************999988776 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.00064
                                       EEEEETTTCCEEEEEESSSCGSS CS
                               PQQ  12 lyAlDadTGkvlWrfktggpvls 34 
                                       l+ lD+++G  +W+ k++++ l+
  gi|336255470|ref|YP_004598577.1| 176 LCRLDIADGSRVWTRKLEDVALG 198
                                       5559*************998765 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.0046
                                       EEEEETTSEEEEEETTTCCEE CS
                               PQQ   3 vylgsadGylyAlDadTGkvl 23 
                                       v+   adG l   D+dTG+ l
  gi|336255470|ref|YP_004598577.1| 207 VV--AADGELAVRDVDTGERL 225
                                       33..46************975 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.0032
                                       EEEEETTTCCEEEEEESSSC CS
                               PQQ  12 lyAlDadTGkvlWrfktggp 31 
                                       l A+ +++G+v Wr +++g 
  gi|336255470|ref|YP_004598577.1| 253 LAAISLEDGTVEWRLDAEGC 272
                                       7899**********998875 PP

  == domain 7  score: 19.4 bits;  conditional E-value: 1.2e-07
                                       ETTSEEEEEETTTCCEEEEEESSSCGSSE CS
                               PQQ   7 sadGylyAlDadTGkvlWrfktggpvlsl 35 
                                       + + ++ A+D++TG+v+W + ++g ++s 
  gi|336255470|ref|YP_004598577.1| 296 TTWPTIAAFDRETGDVRWYYHIDGFDVSF 324
                                       56889******************999986 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.3   6.3e-06     0.038      15      40 .]      30      59 ..      18      59 .. 0.83
   2 !   12.1   0.3   3.6e-05      0.21       1      39 [.      60      97 ..      60      98 .. 0.83
   3 !    6.1   0.1    0.0028        17       1      39 [.      99     143 ..      99     144 .. 0.85
   4 !   24.3   0.1   5.3e-09   3.1e-05       1      39 [.     145     182 ..     145     183 .. 0.95
   5 !    5.1   0.4    0.0058        35       1      36 [.     184     228 ..     184     246 .. 0.71
   6 ?    2.0   0.0     0.052   3.1e+02       1      40 []     261     308 ..     261     308 .. 0.79
   7 !    5.5   0.2    0.0041        25       1      28 [.     309     339 ..     309     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.3e-06
                             PQQ_3 15 sspavdgglvyvgtg....dGtlyAlDaet 40
                                       +p+v++g+vy+g        +++AlDa++
  gi|336255470|ref|YP_004598577.1| 30 WPPVVADGTVYIGNVdqnpGPKIVALDATD 59
                                      479************************986 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.6e-05
                             PQQ_3  1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDae 39
                                      G ++W+v+++++  ++ av+g l++++     + AlD +
  gi|336255470|ref|YP_004598577.1| 60 GSERWRVSIDEASDYTSAVVGTLLVAAY-GDQVIALDRD 97
                                      889******9988888899998886655.5******987 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0028
                             PQQ_3   1 GevlWsvqlpgpvn.ssp.avdgglvyvgtg....dGtlyAlDae 39 
                                       G++ W+ +l g vn s++ av + +++ + +    d +l+A+D++
  gi|336255470|ref|YP_004598577.1|  99 GTQEWTATLSGTVNlSTLtAVPEETLVLVPErsrrDAGLTAFDTT 143
                                       8999*******999666678888888888888***********87 PP

  == domain 4  score: 24.3 bits;  conditional E-value: 5.3e-09
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       Ge++Ws +l ++v+ +pav g+ vyv+t+   l+ lD +
  gi|336255470|ref|YP_004598577.1| 145 GEQRWSAPLADRVVDAPAVRGDGVYVATE-SELCRLDIA 182
                                       9***************************9.999999986 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.0058
                             PQQ_3   1 GevlWsvqlpgpvnssp.avdgglvyvgtg.........dGtlyAl 36 
                                       G ++W+++l + + + p  +++g+v++++g           +l++l
  gi|336255470|ref|YP_004598577.1| 184 GSRVWTRKLEDVALG-PrSAAEGIVVAADGelavrdvdtGERLRSL 228
                                       778999999974444.559999999999987777777773333333 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.052
                             PQQ_3   1 GevlWsvqlpg.pvnsspavdgglvyvgtg.........dGtlyAlDaet 40 
                                       G+v W+ +  g +   ++ v+ +++++  +           t+ A+D et
  gi|336255470|ref|YP_004598577.1| 261 GTVEWRLDAEGcQ--EGLCVGQDTIVAPVEyeefdlettWPTIAAFDRET 308
                                       7777888877665..56888888888888888888888889999999998 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.0041
                             PQQ_3   1 GevlWsvqlpg...pvnsspavdgglvyvgt 28 
                                       G+v+W + ++g     +++p++++g vy+++
  gi|336255470|ref|YP_004598577.1| 309 GDVRWYYHIDGfdvSFTTPPVLVEGAVYFAA 339
                                       89999998888855666777********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); 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: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.35
# Mc/sec: 3060.21
//
Query:       gi|336255471|ref|YP_004598578.1|  [L=178]
Description: CinA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-55  187.6   1.6    1.3e-55  187.3   1.6    1.0  1  CinA      Competence-damaged protein


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 !  187.3   1.6     7e-60   1.3e-55       6     154 ..      12     167 ..       8     168 .. 0.96

  Alignments for each domain:
  == domain 1  score: 187.3 bits;  conditional E-value: 7e-60
                              CinA   6 eevvkllkkkgltlatAEScTGGllaaaltsvpGaSavfeggvvtYsneaKeelLgvseetleehgavSeevaeema 82 
                                       ++v+++l+++++tla+AEScTGGl++a++t++pGaS++f++g+ tY+ +aK++ Lgvs+e l+e gavS++va+ema
  gi|336255471|ref|YP_004598578.1|  12 RAVGEALRETDATLAVAESCTGGLIGATVTAIPGASDYFDSGATTYAYDAKRRELGVSREALDERGAVSAPVAREMA 88 
                                       689************************************************************************** PP

                              CinA  83 egarerlgadiavavtGiAGpsggteekpvGtvyialagkgg.......veveklefegdreeireaavkaALellr 152
                                       +g+r++++a+++v+ tG+AGpsggtee+pvGtvyi++a +g        +++ ++ef+gdr+++r+++v++ALe l+
  gi|336255471|ref|YP_004598578.1|  89 RGIRDTADATWGVSATGVAGPSGGTEETPVGTVYIGVAYAGPwgsessyATATRYEFDGDRAAVRARTVERALEDLL 165
                                       *************************************9988777788888999*********************998 PP

                              CinA 153 el 154
                                       e 
  gi|336255471|ref|YP_004598578.1| 166 EE 167
                                       76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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 0.18s 00:00:00.57 Elapsed: 00:00:00.33
# Mc/sec: 1594.55
//
Query:       gi|336255472|ref|YP_004598579.1|  [L=246]
Description: two-component system sensor kinase [Halopiger xanaduensis SH-6]
Scores for 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-33  114.6  21.4    5.3e-33  114.4  21.4    1.1  1  Sensor     Putative sensor


Domain annotation for each model (and alignments):
>> Sensor  Putative sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4  21.4     3e-37   5.3e-33       1     162 []      33     215 ..      33     215 .. 0.94

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 3e-37
                            Sensor   1 YlllglplgvaafvllvtglslglgllvllvGlplLalalllarglaaveRrrarlllglpvprph.rapep.pgll 75 
                                       Ylll++plg+a+ ++l++gl  g +l++++vG+p+L++++l++r++aa+eR++a++ll +++++p   +p p  gl+
  gi|336255472|ref|YP_004598579.1|  33 YLLLAIPLGMAYYTALLLGLGFGTALVLVGVGIPILIGTVLGTRLFAALERSLANALLEVELRSPDdVRPGPdDGLV 109
                                       9*****************************************************************999999***** PP

                            Sensor  76 arlrallrdpatwrdllylllhfplglvlfvvavvllalalalltaPl.w...................tlpeallv 132
                                       a lr++l+ p+twr l++l+++  lg+ ++vv+v+l+ + l+lltaPl +                   t++e +l+
  gi|336255472|ref|YP_004598579.1| 110 ASLRRYLDAPSTWRGLAFLMVKSWLGI-VGVVLVLLFGTLLSLLTAPLrYphevefgtvndqpvtwlinTPAELALA 185
                                       *************************98.88999999999*********77888888888887777666558888889 PP

                            Sensor 133 avlGlllllvllwvvrglarlqallaraLL 162
                                       + +G++l +++l+v +g+a + ++ a aLL
  gi|336255472|ref|YP_004598579.1| 186 VSVGAVLGVAALHVSNGFAYAARRSAVALL 215
                                       99***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1868.57
//
Query:       gi|336255473|ref|YP_004598580.1|  [L=366]
Description: aspartate transaminase [Halopiger xanaduensis SH-6]
Scores for 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-58  197.8   0.0    3.5e-58  197.5   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    5.5e-08   32.2   0.0    1.1e-07   31.1   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
    7.7e-07   28.7   0.0    1.2e-06   28.1   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    8.4e-06   25.3   0.0    1.4e-05   24.6   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    5.6e-05   22.2   0.0    8.1e-05   21.7   0.0    1.2  1  Alliinase_C      Allinase
    0.00041   19.0   0.0    0.00051   18.7   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0023   16.8   0.4      0.049   12.4   0.2    2.4  2  Aminotran_MocR   Alanine-glyoxylate amino-transferase
  ------ inclusion threshold ------
      0.015   14.0   0.0       0.06   12.0   0.0    1.8  2  Aminotran_3      Aminotransferase class-III
      0.076   12.4   0.3         11    5.4   0.0    2.4  2  PALP             Pyridoxal-phosphate dependent enzyme
      0.083   12.9   0.1        4.8    7.3   0.0    3.1  3  HRDC             HRDC 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 !  197.5   0.0   1.9e-61   3.5e-58       2     362 ..      21     360 ..      20     361 .. 0.92

  Alignments for each domain:
  == domain 1  score: 197.5 bits;  conditional E-value: 1.9e-61
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dvi++ s++++ d    ++ + ++   e a   + + +y+p+dgl el+e++a   g      ++ e +vvv++Gag
  gi|336255473|ref|YP_004598580.1|  21 DVIDMVSGNPDWD----PPAALREGLHEYADLESAAFQYPPSDGLRELREEIAARRG------VDVE-QVVVTNGAG 86 
                                       899999****999....66666666666999999***********************......9999.********* PP

                                       HHHHHHH.HHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEE CS
                     Aminotran_1_2  79 alieali.fllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilv 154
                                       +++ +++ ++l+ ++gde+l+ dp+y+ y     + gg+ + ++ +  ed +ld  ++ +a +e      +t  i+v
  gi|336255473|ref|YP_004598580.1|  87 EANYLAMaRALERDRGDEVLLTDPVYPYYPGKTTMLGGTQRFVAAD--EDGQLDPADVRAAASE------RTGAIVV 155
                                       *99988725667899*****************************55..****************......9****** PP

                                       ESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 155 esphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvG 231
                                       +sp+NPtG+v+++e++e+l+++a++y ++l++De+Y +  +   ++++  ++ve +   ++++ +sK+++++G+RvG
  gi|336255473|ref|YP_004598580.1| 156 NSPNNPTGAVYPEETIEELVAIAEEYDAILVSDEVYDHYDLS-GRFAS-ALEVESDHR-IVTNAFSKSLAITGFRVG 229
                                       ***************************************987.46777.888888766.****************** PP

                                       EEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 232 yilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                       y++   ++v+++r+ +  +++  s ++q+av++al+ ++    + e++r+ l +r  +++d+L+++g +++++++ +
  gi|336255473|ref|YP_004598580.1| 230 YAIFPRDLVEAARSRHMLVNVagSRPAQYAVLQALRETDPA--YYEANRELLRERVATFTDALDAAGAEYTTPEGSF 304
                                       **************************************976..********************************** PP

                                       EEEEEETHH.CHHHHHHH..HHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 307 flltdlsae.takelskk..Lleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                       ++l +++ +    e   +  L++e gv+ +pg  f+   + +lR+ +  +t+  +ee++e+
  gi|336255473|ref|YP_004598580.1| 305 YVLARFEDYpGTLEN--VfrLIDEAGVAGMPGDAFGEsrSDWLRFAL--VTP-RVEEAAER 360
                                       *********544444..355******************999****99..655.56777776 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   6.4e-11   1.1e-07      43     177 ..      59     190 ..      34     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 6.4e-11
                                       HHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE CS
                       Aminotran_5  43 kaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi 119
                                       + ++e re++a+  +++  e++++t G++ea+ l++  +++  ++gde+++t+  +     p +  +   g + +++
  gi|336255473|ref|YP_004598580.1|  59 DGLRELREEIAARRGVDV-EQVVVTNGAGEANYLAMARALE-RDRGDEVLLTDPVYP--YYPGKTTM--LGGTQRFV 129
                                       668899***********8.***********99999888855.89*******987665..44566665..789999** PP

                                       EBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 120 pldeegeldldelekllnektklvaithvsnvtGtiqp...veeigklakkkgalvlvDaa 177
                                        +de+g+ld+ +++++ +e+t ++ ++  +n tG + p   +ee++++a +++a+++ D +
  gi|336255473|ref|YP_004598580.1| 130 AADEDGQLDPADVRAAASERTGAIVVNSPNNPTGAVYPeetIEELVAIAEEYDAILVSDEV 190
                                       ***********************************8774447788899999******9975 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   6.5e-10   1.2e-06      30     167 ..      57     188 ..      42     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 6.5e-10
                                       --HHHHHHHHHHHHHTT-S.EEEEES-HHH.HHHHHHHHH-..-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE- CS
                   Beta_elim_lyase  30 edktvnrLedavaelfgke.aalfvpqGta.Ansillkill..qrgeevivtepahihfdetgaiaelagvklrdlk 102
                                        + + ++L +++a+  g +  ++ v++G + An ++++  l   rg+ev++t+p  ++ +  g    l+g   r + 
  gi|336255473|ref|YP_004598580.1|  57 PSDGLRELREEIAARRGVDvEQVVVTNGAGeANYLAMARALerDRGDEVLLTDP--VYPYYPGKTTMLGGT-QRFVA 130
                                       566778899999988888844556777764499999966664678999**9999..667777888778887.89999 PP

                                       EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                   Beta_elim_lyase 103 nkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                        +e+G++d+++++aa  e      ++++i++   nn   G v++ e ++e+ aia++y+  l+ D
  gi|336255473|ref|YP_004598580.1| 131 ADEDGQLDPADVRAAASE------RTGAIVVNSPNNP-TGAVYPEETIEELVAIAEEYDAILVSD 188
                                       9999**********9988......589***9999995.9********************999888 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 !   24.6   0.0   7.8e-09   1.4e-05      30     144 ..      66     188 ..      49     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 7.8e-09
                                       HHHHHHHT..-SEEEEESSHHHHHHHHHHH.TTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGG CS
                   DegT_DnrJ_EryC1  30 kafaaylg..vkhaiavssGtaAlhlaLra.lgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaa 103
                                       +++aa  g  v+ ++ ++ + +A+ la+   l+ ++gdeV+ +   +       + lg +  fv  d ++ ++dpa+
  gi|336255473|ref|YP_004598580.1|  66 EEIAARRGvdVEQVVVTNGAGEANYLAMARaLERDRGDEVLLTDPVYPYYPGKTTMLGGTQRFVAAD-EDGQLDPAD 141
                                       44554444338999999999********6549********************************999.89******* PP

                                       CGGG--TTEEEEE...EB-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 104 ieaaitertkaIl...pVhlyGqva...dmdalkaiaakhglkvieD 144
                                       ++aa  ert aI+   p +  G+v     +++l aia++++ ++++D
  gi|336255473|ref|YP_004598580.1| 142 VRAAASERTGAIVvnsPNNPTGAVYpeeTIEELVAIAEEYDAILVSD 188
                                       ************93333567788875557999999999999999988 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   4.5e-08   8.1e-05      91     243 ..      97     267 ..      68     287 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.5e-08
                                       .SSSSSEEEEE-SS--THHHHHTTTT-BTTEEEEEESTT-.......--S..S-EEEEEESS-TTT----.....-- CS
                       Alliinase_C  91 sseskpvkvvaavPyysvykeqtslldsklykweGdaaayv......kkknpeefielvtsPnnPdgllr.....ea 156
                                        ++++  +v+ + P y+ y  +t++l  ++   + d              + +    +v sPnnP g++      e+
  gi|336255473|ref|YP_004598580.1|  97 LERDRGDEVLLTDPVYPYYPGKTTMLGGTQRFVAADEDGQLdpadvrAAASERTGAIVVNSPNNPTGAVYpeetiEE 173
                                       556677788888999999999999987665444333332222333324444445556899****9997642211122 PP

                                       --...-TT-EEEEEE-TT-STTT.....S---S-B--SEEEEEHHHHHS-GGG-EEEEEES-HHHHHHHHHHHHHHH CS
                       Alliinase_C 157 vv...kgseakviyDlayYWPhy.....tpitskadedimLftlskltGhaGsrlGWalvkdkevakklveyiekns 225
                                       +v   ++ +a+++ D +y   ++     ++++ ++d+ i+  ++sk    +G r+G+a+     v     +++  n 
  gi|336255473|ref|YP_004598580.1| 174 LVaiaEEYDAILVSDEVYDHYDLsgrfaSALEVESDHRIVTNAFSKSLAITGFRVGYAIFPRDLVEAARSRHMLVNV 250
                                       2245678889999999996544322223478999**************************99999999999999998 PP

                                       SS--HHHHHHHHHHHHHH CS
                       Alliinase_C 226 iGvskesqlrvlkilkvv 243
                                        G s+ +q  vl+ l++ 
  gi|336255473|ref|YP_004598580.1| 251 AG-SRPAQYAVLQALRET 267
                                       88.899999999998876 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   2.9e-07   0.00051      59     200 ..      66     221 ..      49     265 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.9e-07
                                       HHHHHHHT-..SEEEEES.SHHHHHHHHHHTTS-T.TEEEEEESTSSH..HHHHHHHHTHHHTTCEEEEESTTSHHH CS
                   Cys_Met_Meta_PP  59 eriaaLegg..eaalavs.sGmaAiaaailallka.GdeivvsddlYg..gtqrllkkvlkklgievkfvdtsdlee 129
                                       e+iaa  g+  e++++++ +G a   a+ +al +  Gde++++d +Y   + +  +   ++++ + ++   + d+++
  gi|336255473|ref|YP_004598580.1|  66 EEIAARRGVdvEQVVVTNgAGEANYLAMARALERDrGDEVLLTDPVYPyyPGKTTMLGGTQRF-VAADEDGQLDPAD 141
                                       556655554434555554257777766666665547*********985223444454555666.777788889**** PP

                                       HHHHCCTTEEEEEEESS-TTTT---...-HHHHHHHHHHTT-EEEEEGTT....THTTTS-GGGGT-S..EEEEETT CS
                   Cys_Met_Meta_PP 130 lekaikentklvylEtptnpllkvv...DiekiaklakkagvlvvvDntf....aspllqrplklgaD..ivvhSaT 197
                                       +++a +e+t ++ + +p np+  v     ie+++++a + ++++v D ++    +s+ +  +l+ + D  iv+++ +
  gi|336255473|ref|YP_004598580.1| 142 VRAAASERTGAIVVNSPNNPTGAVYpeeTIEELVAIAEEYDAILVSDEVYdhydLSGRFASALEVESDhrIVTNAFS 218
                                       *********************99863336999999******999999887444468899999988877667888777 PP

                                       TTT CS
                   Cys_Met_Meta_PP 198 Kyl 200
                                       K l
  gi|336255473|ref|YP_004598580.1| 219 KSL 221
                                       765 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.1   3.8e+03      68      94 ..      58      84 ..      53      97 .. 0.76
   2 !   12.4   0.2   2.7e-05     0.049     174     397 ..     150     356 ..     105     363 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.1
                                      TT--HHHHHHHHHHTTS-GGGEEE-SS CS
                    Aminotran_MocR 68 laGlpelralfaelldvkaenvlvqnn 94
                                       +Gl elr   a   +v  e+v+v+n 
  gi|336255473|ref|YP_004598580.1| 58 SDGLRELREEIAARRGVDVEQVVVTNG 84
                                      578999999999999999999998875 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.7e-05
                                       EEEEE-SSS-TTT-----HHHHHHHHT---SSTT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEES CS
                    Aminotran_MocR 174 kGilavpkysnptGetiseevarrlaalkaaapdfrifaddayavhdlvaeedkdanivalardaGhpdrafvlast 250
                                        G ++v    nptG ++ ee + +l+a+     d  +  d+ y  +dl +   +       a +    +r +  a +
  gi|336255473|ref|YP_004598580.1| 150 TGAIVVNSPNNPTGAVYPEETIEELVAIA-EEYDAILVSDEVYDHYDLSGRFAS-------ALEVESDHRIVTNAFS 218
                                       5778888899****************985.567999999****99999554333.......3333333454444545 PP

                                       TTTS-TTSS-EEEEE-HHHHHHHHHHHHHC-S---HHHHHHHHHHHHHSTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Aminotran_MocR 251 skitfaGaGvafvassedniawlkkylGlqsiGpdkveqlrhvkflkdyeGlealmrdhaeliapkfeavlevleae 327
                                         ++ +G  v++     d +  ++    l  +   +  q   ++ l++ +   a+    +el++ + ++ +++l+a 
  gi|336255473|ref|YP_004598580.1| 219 KSLAITGFRVGYAIFPRDLVEAARSRHMLVNVAGSRPAQYAVLQALRETD--PAYYEANRELLRERVATFTDALDAA 293
                                       55778888888888888888777665556666667778888888888887..4778889999999888888777652 PP

                                       HTTTSSEEE---SBSS-EE..EEESSS-HHHHHHHHHHCTEE---TTTTSSTT--SSS-EEEE--SSS-HHH CS
                    Aminotran_MocR 328 lggaevatwteprGGyfis..ldtldgvakrvvklaeeaGvsltaaGatypaGedpkdrnirlaptlpplee 397
                                         g   a +t+p+G +++   ++   g+ ++v +l +eaGv+  +  a +    + +   +r+a  +p +ee
  gi|336255473|ref|YP_004598580.1| 294 --G---AEYTTPEGSFYVLarFEDYPGTLENVFRLIDEAGVAGMPGDA-FG---ESRSDWLRFALVTPRVEE 356
                                       ..3...667899999998612455669999999*****9998776544.32...234445666666666665 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.23   4.1e+02      61     108 ..      50      97 ..      41     104 .. 0.81
   2 ?   12.0   0.0   3.3e-05      0.06     185     282 ..     142     241 ..     129     300 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.23
                                       ---TTTCEEHHHHHHHHHHHHHCT-..SEEEEESSHHHHHHHHHHHHH CS
                       Aminotran_3  61 hvsfgaltnepalklaekllklapkgldkvflansGseAvetAlKlar 108
                                          f+   ++ + +l e++++  + ++++v++ n   eA+  A+  a 
  gi|336255473|ref|YP_004598580.1|  50 SAAFQYPPSDGLRELREEIAARRGVDVEQVVVTNGAGEANYLAMARAL 97 
                                       55677778888899999***************9999999999876554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.3e-05
                                       HHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGGCTS--S..EEE. CS
                       Aminotran_3 185 lekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAlehagvspD..lmt. 258
                                       +++++++ + A++v       G v +++e +++l ++++++d++l+ DEv      +G  fA + ++v+ D  ++t 
  gi|336255473|ref|YP_004598580.1| 142 VRAAASERTGAIVVNSPNNPTGAV-YPEETIEELVAIAEEYDAILVSDEVYDHYDLSG-RFASA-LEVESDhrIVTn 215
                                       667788889999999888888876.556779*******************99999999.56665.566666334442 PP

                                       .E-GGGG.TTSS-EEEEEEHHHHTTS CS
                       Aminotran_3 259 .laKalt.gGlplsavlataevmqal 282
                                        ++K+l+  G+ +  ++ ++++++a 
  gi|336255473|ref|YP_004598580.1| 216 aFSKSLAiTGFRVGYAIFPRDLVEAA 241
                                       24477763456666666666666655 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.006        11     145     187 ..      63     105 ..      53     116 .. 0.85
   2 ?    4.7   0.1    0.0094        17      98     163 ..     120     186 ..     116     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.006
                                       THHHHHHHHTTTTEEEEEEE-SSS.HHHHHHHHHHHHHSTT-EE CS
                              PALP 145 tiglEileqlggkpdavvvpvGgG.gliaGiaaglkerrpdvrv 187
                                        +  Ei+++ g +++ vvv+ G G ++  ++a++l  +r+d +v
  gi|336255473|ref|YP_004598580.1|  63 ELREEIAARRGVDVEQVVVTNGAGeANYLAMARALERDRGD-EV 105
                                       5668999999999***********99**********98887.44 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0094
                                       HHTT-EEEEE....CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEE CS
                              PALP  98 rllGaevvev....ggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavvv 163
                                        +lG + ++v    +g  d a   ++++a+e +ga++v++ +npt+    + +  E++  + ++ da++v
  gi|336255473|ref|YP_004598580.1| 120 TMLGGTQRFVaadeDGQLDPAD--VRAAASERTGAIVVNSPNNPTGAVYPEETIEELV-AIAEEYDAILV 186
                                       5677777777443333333333..457777789****************999999995.55567777776 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0027       4.8       8      26 ..      61      79 ..      59      84 .. 0.87
   2 ?    0.1   0.0      0.44   7.9e+02      22      38 ..     161     177 ..     157     181 .. 0.85
   3 ?    0.4   0.0      0.37   6.5e+02      29      58 ..     244     273 ..     243     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0027
                                      HHHHHHHHHHHHTS-HHHH CS
                              HRDC  8 LrewReelAreedvppyvv 26
                                      Lre+Ree+A +++v   +v
  gi|336255473|ref|YP_004598580.1| 61 LRELREEIAARRGVDVEQV 79
                                      9************987766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.44
                                       -HHHHS-HHHHHHHHHH CS
                              HRDC  22 ppyvvfpdktLleiAek 38 
                                       p++ v p++t++e+++ 
  gi|336255473|ref|YP_004598580.1| 161 PTGAVYPEETIEELVAI 177
                                       88999********9975 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.37
                                       HHHHHHHHHH---SHHHHHTSTTT-HHHHH CS
                              HRDC  29 dktLleiAeklPttleeLlqiegvgkrkle 58 
                                        ++L+++A ++P+  + L +++   ++ +e
  gi|336255473|ref|YP_004598580.1| 244 RHMLVNVAGSRPAQYAVLQALRETDPAYYE 273
                                       589999999999999999888877776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.36
# Mc/sec: 3009.39
//
Query:       gi|336255474|ref|YP_004598581.1|  [L=417]
Description: arsenite-activated ATPase ArsA [Halopiger xanaduensis SH-6]
Scores for 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-78  262.7   0.0    3.1e-51  174.4   0.0    2.6  2  ArsA_ATPase  Anion-transporting ATPase
      2e-07   31.1   0.0    3.7e-07   30.3   0.0    1.5  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0001   22.2   0.0    0.00018   21.4   0.0    1.4  1  AAA_31       AAA domain
      0.003   17.1   1.0      0.026   14.0   0.2    2.1  2  ParA         NUBPL iron-transfer P-loop NTPase
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.029   13.9   0.0    1.3  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
      0.029   13.9   1.2       0.15   11.6   0.2    2.4  2  AAA_25       AAA domain
       0.11   12.0   0.0       0.19   11.2   0.0    1.3  1  PhoH         PhoH-like protein
       0.13   11.7   0.0       0.22   10.9   0.0    1.4  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
       0.14   11.8   0.1       0.62    9.7   0.2    1.9  2  SRP54        SRP54-type protein, GTPase domain
       0.15   11.3   0.0       0.27   10.5   0.0    1.3  1  Zeta_toxin   Zeta toxin


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 !   85.3   0.0   2.3e-27   4.2e-24       3      80 ..      55     134 ..      54     141 .. 0.92
   2 !  174.4   0.0   1.7e-54   3.1e-51     102     303 ..     198     416 ..     182     417 .] 0.91

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 2.3e-27
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEET..SSEEEEE--HHHHHHHHH CS
                       ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvk..eNLsavEidpeveleeak 77 
                                       +il gGKGGVGKtt++aata+  ++ g ++l++stDPAhslsD f++ + +ep +++    L+a+Eidpe ++e+ k
  gi|336255474|ref|YP_004598581.1|  55 YILYGGKGGVGKTTMAAATALDSARGGTSTLVVSTDPAHSLSDTFETAVPAEPGRIRddIPLYAAEIDPEAAMEQGK 131
                                       799******************************************************54469********9999877 PP

                                       CCH CS
                       ArsA_ATPase  78 qev 80 
                                       +++
  gi|336255474|ref|YP_004598581.1| 132 TAM 134
                                       665 PP

  == domain 2  score: 174.4 bits;  conditional E-value: 1.7e-54
                                       TSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSHCHHH CS
                       ArsA_ATPase 102 aslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevleklleklvklkeklsplakqlvkllglggv 178
                                        ++PG de+++++ ll+y+++  ++ vv+DtaPTGhtlrll+lpe ++ ++ +++kl++ ls + + +++++g  + 
  gi|336255474|ref|YP_004598581.1| 198 GAMPGADEAAAMQLLLEYMDDPRFERVVVDTAPTGHTLRLLKLPELMDTMMGRIIKLRQRLSGMFEGMKGMFGGQDP 274
                                       679********************************************************************999998 PP

                                       HHH.HHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE-T...TCSS CS
                       ArsA_ATPase 179 sie.ealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLkkygikvdavivNkllp...eeeq 251
                                        ++ + l++l+e  ++i++++++l+dp rt fr+V+ipE++s+ E++R+ ++L +++i v +++vN++++   + ++
  gi|336255474|ref|YP_004598581.1| 275 PEDeSDLDDLDELRDRIERLRAVLQDPARTDFRIVMIPEEMSVFESKRLRQQLREFDIPVGTIVVNRVMEplsDVTD 351
                                       888789*************************************************************9753322222 PP

                                       S.............TSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHHHHHHHHH CS
                       ArsA_ATPase 252 e.............nCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekleklsell 303
                                       +             +Cef+++r+++q+  l e ++lf+ + v ++pl+++Ev+G   le +++ l
  gi|336255474|ref|YP_004598581.1| 352 DvqgageflqpnleDCEFCQRRWDVQQGALAEAQDLFRGTDVRRVPLFADEVRGEGMLEVVAACL 416
                                       244567777788889*******************************************9999876 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 !   30.3   0.0     2e-10   3.7e-07       3      55 ..      57     307 ..      55     353 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2e-10
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep......................... 54 
                                       + ++kGGvGKTt+aa+ a   ar+g  +l+v +Dp  +++ ++e+ ++  ep                         
  gi|336255474|ref|YP_004598581.1|  57 LYGGKGGVGKTTMAAATALDSARGGTSTLVVSTDPAHSLSDTFETAVPA-EPgrirddiplyaaeidpeaameqgkt 132
                                       569*********************************9999954444333.334777788888888888888999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|336255474|ref|YP_004598581.1| 133 amfggaggpddgdaasadsmgmdadpdagagsgmgpgagaggplgdlgglgemlggespmealfggampgadeaaam 209
                                       88988888888888888888888888888888888888888888888888888888888888888888888888888 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|336255474|ref|YP_004598581.1| 210 qllleymddprfervvvdtaptghtlrllklpelmdtmmgriiklrqrlsgmfegmkgmfggqdppedesdlddlde 286
                                       88888888888888888888888888888888888888888888777777777777777777777777777775555 PP

                                       ....................C CS
                                       ....................x RF
                              CbiA  55 ....................d 55 
                                                            
  gi|336255474|ref|YP_004598581.1| 287 lrdrierlravlqdpartdfR 307
                                       444444444444444444440 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0     1e-07   0.00018       9      49 ..      60     100 ..      56     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1e-07
                            AAA_31   9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglg 49 
                                        KGGvGKTT + + a   a+ g  +L+v  Dp  +++ +++
  gi|336255474|ref|YP_004598581.1|  60 GKGGVGKTTMAAATALDSARGGTSTLVVSTDPAHSLSDTFE 100
                                       6*******************************999988665 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 !   14.0   0.2   1.4e-05     0.026       9      41 ..      58      90 ..      54     102 .. 0.86
   2 ?    1.3   0.0       0.1   1.9e+02     137     173 ..     304     340 ..     295     354 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                              ParA  9 lSgKGGVGKStvavnlAlaLakkglkvgllDaD 41
                                        gKGGVGK+t+a+  Al  a+ g+++ ++ +D
  gi|336255474|ref|YP_004598581.1| 58 YGGKGGVGKTTMAAATALDSARGGTSTLVVSTD 90
                                      67***************9999888887776655 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
                              ParA 137 agaviVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                       ++  iV  p+e+++ + k+  + +++ +++v  +v N
  gi|336255474|ref|YP_004598581.1| 304 TDFRIVMIPEEMSVFESKRLRQQLREFDIPVGTIVVN 340
                                       5666999999999999999999999999999999988 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.6e-05     0.029       6      57 ..      57     108 ..      54     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                          CBP_BcsQ   6 lqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqreg 57 
                                       l G +GGvG+t+++aa a    + g s lv+ + p+  L   F++++  + g
  gi|336255474|ref|YP_004598581.1|  57 LYGGKGGVGKTTMAAATALDSARGGTSTLVVSTDPAHSLSDTFETAVPAEPG 108
                                       67889**************************************999877666 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   8.5e-05      0.15      36      61 ..      56      81 ..      50      98 .. 0.85
   2 ?    0.1   0.0      0.29   5.2e+02      81     108 ..     282     309 ..     268     339 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.5e-05
                            AAA_25 36 allaGapgtGKttlaldlalavatGk 61
                                      +l  G +g+GKtt+a   al+ a+G 
  gi|336255474|ref|YP_004598581.1| 56 ILYGGKGGVGKTTMAAATALDSARGG 81
                                      57789******************775 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.29
                            AAA_25  81 dsedelrrRlravgealrddarllvldl 108
                                       d+ delr R++++++ l+d+ar ++  +
  gi|336255474|ref|YP_004598581.1| 282 DDLDELRDRIERLRAVLQDPARTDFRIV 309
                                       5667899999999988888888776544 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.19      20      78 ..      54     116 ..      47     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                       SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T....T----SS---------T CS
                              PhoH  20 divfaiGpaGtGKtylavalavealkkkkvkriiltrpavea....geelGflpgdleekvdp 78 
                                       d +   G+ G GKt +a a+a++  + ++ + ++ t pa +     +  + + pg +++ +  
  gi|336255474|ref|YP_004598581.1|  54 DYILYGGKGGVGKTTMAAATALDSARGGTSTLVVSTDPAHSLsdtfETAVPAEPGRIRDDIPL 116
                                       6677889*******************9999999999999866555566666666666666555 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 ?   10.9   0.0   0.00012      0.22       6      41 ..      58      94 ..      54     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                         Fer4_NifH  6 y.GkGGiGksttsqnlsaalaemgkkvlivGCDPkaD 41
                                      y GkGG+Gk+t ++ ++   a+ g   l+v  DP + 
  gi|336255474|ref|YP_004598581.1| 58 YgGKGGVGKTTMAAATALDSARGGTSTLVVSTDPAHS 94
                                      427*******************************874 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00035      0.62       3      38 ..      55      90 ..      53      93 .. 0.91
   2 ?   -1.0   0.0      0.63   1.1e+03      64      92 ..     201     229 ..     192     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00035
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      +il  G  G+GKTt +a  a    + g+++l+v++D
  gi|336255474|ref|YP_004598581.1| 55 YILYGGKGGVGKTTMAAATALDSARGGTSTLVVSTD 90
                                      677789999*************************99 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.63
                                       TTSCHHHHHHHHHHHHHHTTSSEEEEEE- CS
                             SRP54  64 eeadpaavakeavekakeekidvvlvDTa 92 
                                        +ad+aa ++  +e +++ +++ v+vDTa
  gi|336255474|ref|YP_004598581.1| 201 PGADEAAAMQLLLEYMDDPRFERVVVDTA 229
                                       56788888888999999999********9 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.27      14      52 ..      51      90 ..      39     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                        Zeta_toxin 14 erPklillgGqpGAGKselaellkdele.rqgnvvrldpD 52
                                      e P+ il gG  G GK+++a++++ + +  + + +++++D
  gi|336255474|ref|YP_004598581.1| 51 EGPDYILYGGKGGVGKTTMAAATALDSArGGTSTLVVSTD 90
                                      789*****************99988877244455666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3129.82
//
Query:       gi|336255475|ref|YP_004598582.1|  [L=153]
Description: UspA domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-21   75.8   4.0    5.2e-21   75.6   4.0    1.0  1  Usp            Universal stress protein family
  ------ inclusion threshold ------
      0.056   13.5   0.1      0.084   13.0   0.1    1.2  1  Ribosomal_L14  Ribosomal protein L14p/L23e


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 !   75.6   4.0   5.8e-25   5.2e-21       1     141 []       1     149 [.       1     149 [. 0.93

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 5.8e-25
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHH.CTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH...... CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelaka.rgaelillhvidprasgavsdadeeaeeeeleleeaeleada...... 70 
                                       my+  l + D+   +++ +e  l+l +a ++  + +lhv+d+ a + + +a+   +e+ +e+ e+ ++++       
  gi|336255475|ref|YP_004598582.1|   1 MYRVLLPVEDDPARARRQVESVLALPRAaSEVFVDVLHVHDEAATADAEWAAGGFAESYEEEMEELRDLQRipesve 77 
                                       6665555556666667********999999999*****************9999999999999999998889***** PP

                                       .HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  71 .akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        a +++++ggv+  v+   gdpae+ile a e+d d iVvG r+rs + ++l+GSv ++v+ +++ pV+vV+
  gi|336255475|ref|YP_004598582.1|  78 tAIDLLADGGVEYAVHEATGDPAETILERAAEYDSDAIVVGVRKRSPVGKVLFGSVVQAVILESDRPVTVVP 149
                                       ***********************************************************************7 PP

>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   9.3e-06     0.084      36      68 ..     112     144 ..      99     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.3e-06
                                       SSEEEEEESSS-T...TTSSCEEEEEEEE-SS- CS
                     Ribosomal_L14  36 Gdiivvsvkkakpkgkvkkgdvvkavvvrtkke 68 
                                        d ivv v+k +p gkv  g+vv+av++++ ++
  gi|336255475|ref|YP_004598582.1| 112 SDAIVVGVRKRSPVGKVLFGSVVQAVILESDRP 144
                                       699************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1195.68
//
Query:       gi|336255476|ref|YP_004598583.1|  [L=404]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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-38  130.7  54.7    6.9e-34  117.3  43.3    2.0  2  MFS_1     Major Facilitator Superfamily


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 !  117.3  43.3   3.9e-38   6.9e-34      13     338 ..      30     342 ..      16     345 .. 0.84
   2 !   21.0   6.4   7.6e-09   0.00014     110     177 ..     329     396 ..     324     401 .. 0.84

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 3.9e-38
                             MFS_1  13 silgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw.ll 88 
                                       +++++a   +  e++g+s  ++g+++t+ +lg+a + lp+G+l+dr+G rr+l++gll++++g++l + +++++ ll
  gi|336255476|ref|YP_004598583.1|  30 YTVFAATA-LFREAFGLSRLSVGFVVTALTLGYATFLLPVGALVDRYGERRTLVIGLLGLSSGAVLVA-GAPSYaLL 104
                                       33333333.889***************************************************33333.344555** PP

                             MFS_1  89 lvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllaf 165
                                       l++ ++ G  +++++p+ + +i d ++  ++++a+g+ ++g+ +G+    ll   la  + W+a f+++a+v+l+++
  gi|336255476|ref|YP_004598583.1| 105 LAAAFVLGSLYATAIPGTNKAIYDNVAAGRQNLAMGIKQVGVTAGSGTSSLLVTGLAGVFFWQAGFLVAAAVGLVVV 181
                                       *********************************************************9999***************8 PP

                             MFS_1 166 vlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsg 242
                                        +f++l+p ++ + + + p  +            ++al ++++  +l++a ++ ++++++++ ++ l++ e  g s 
  gi|336255476|ref|YP_004598583.1| 182 AVFAVLYPGSDDNGRAEYP--D------------FRALSHNRPYRVLVAAGFFLGAALFTTTGYTVLFVAEEIGTS- 243
                                       8888888777777777765..3............66666666554344444444458888999999999*******. PP

                             MFS_1 243 lllaglllallalvgailallagrlsdrlgr..rrrlllallllllaalglallavt.ssavllllvlvliGfglgf 316
                                       +  +g++lal++l g ++++++g+lsd l+   r r+  +l++ +l++++l+++ ++  +++ + ++++ +Gf++  
  gi|336255476|ref|YP_004598583.1| 244 VAFGGVVLALVQLTGSGGRIVTGWLSDALPGepRVRIGAILIVQALGSAALFVAVAAtATPLSATVAFAALGFFVLG 320
                                       ****************************7765577777788888888888888888835555555588889998888 PP

                             MFS_1 317 vfpsllalasdlappeeagtas 338
                                        ++ + ++++ l++++e+g a+
  gi|336255476|ref|YP_004598583.1| 321 NTGVYYSCMATLVGADEMGGAT 342
                                       8999*******99999999776 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 7.6e-09
                             MFS_1 110 iadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepp 177
                                       +a ++  +e g a++  +++  +G+il+p++ g+la+ +g+ra++++la+ +l+a+ l +  ++ epp
  gi|336255476|ref|YP_004598583.1| 329 MATLVGADEMGGATAGGQLALVAGSILAPPAFGYLADTVGYRASWWLLAAGCLVAAGLLAYAIRLEPP 396
                                       6778888999*********************************************6654444455544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3144.61
//
Query:       gi|336255477|ref|YP_004598584.1|  [L=132]
Description: 4-oxalocrotonate tautomerase [Halopiger xanaduensis SH-6]
Scores for 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-07   29.3   0.0      0.024   14.6   0.0    2.1  2  Tautomerase    Tautomerase enzyme
    0.00098   19.2   0.0      0.018   15.1   0.0    2.0  2  Tautomerase_2  Tautomerase enzyme
  ------ inclusion threshold ------
      0.029   14.6   0.0      0.074   13.3   0.0    1.6  2  Tautomerase_3  Putative oxalocrotonate tautomerase enzyme


Domain annotation for each model (and alignments):
>> Tautomerase  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     4e-06     0.024       2      48 ..       3      49 ..       2      60 .. 0.81
   2 !   13.1   0.0   1.2e-05     0.071       6      51 ..      67     112 ..      63     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-06
                                      EEEEEESTCS-HHHHHHHHHHHHHHHHHHHTS-GGG-EEEEEEE-TT CS
                       Tautomerase  2 fvnIklvegrsaeqKaeLaervTealvealgaprsaivVvieEvpae 48
                                      +++++ +   sa+ K++La+rvT+++ e +      + V i+E+++ 
  gi|336255477|ref|YP_004598584.1|  3 LLQFDTTLSLSADEKEALADRVTAIYTEEMATTAGHVAVTIREHEPA 49
                                      5555555555999****************999999999999998875 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.2e-05
                                       EESTCS-HHHHHHHHHHHHHHHHHHHTS-GGG-EEEEEEE-TTSEE CS
                       Tautomerase   6 klvegrsaeqKaeLaervTealvealgaprsaivVvieEvpaenwg 51 
                                       ++ +gr+ e+K+++a ++ + + e +++p+++  Vv+ E+p e ++
  gi|336255477|ref|YP_004598584.1|  67 EIRQGRPFERKRAFALETMAYVGERFDVPDENMKVVFTEHPGESMM 112
                                       5789************************************988764 PP

>> Tautomerase_2  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.014        86      41      76 ..      13      48 ..       3      54 .. 0.88
   2 !   15.1   0.0   3.1e-06     0.018      25      77 ..      57     109 ..      40     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.014
                                      -HHHHHHHHHHHHHHHHHHH---GGGEEEEEEEE-G CS
                     Tautomerase_2 41 seeqKkaLyralaerlaaklgirpeDvfivlvenpk 76
                                      s ++K+aL  +++    +++   + +v +++ e ++
  gi|336255477|ref|YP_004598584.1| 13 SADEKEALADRVTAIYTEEMATTAGHVAVTIREHEP 48
                                      6789***************************99876 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.1e-06
                                       S-TT-EEEEEEEES---HHHHHHHHHHHHHHHHHHH---GGGEEEEEEEE-GG CS
                     Tautomerase_2  25 RsddlvvieitlsegRseeqKkaLyralaerlaaklgirpeDvfivlvenpke 77 
                                        +  l +++  +++gR  e K+a+  + +  + ++++++ e+  +v++e p e
  gi|336255477|ref|YP_004598584.1|  57 VEGPLCFLDAEIRQGRPFERKRAFALETMAYVGERFDVPDENMKVVFTEHPGE 109
                                       5556777888999************************************9865 PP

>> Tautomerase_3  Putative oxalocrotonate tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.2e-05     0.074       1      32 [.       1      31 [.       1      59 [. 0.76
   2 ?   -2.0   0.0      0.65   3.9e+03      30      49 ..      90     109 ..      72     114 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                                      --EEEEEE-TTSS-HHHHHHHHHHHHHHHHHT CS
                     Tautomerase_3  1 MPlwkiyhpkntftkeekealakkiteiYtsv 32
                                      MPl ++ ++   ++ +ekeala ++t+iYt+ 
  gi|336255477|ref|YP_004598584.1|  1 MPLLQFDTTL-SLSADEKEALADRVTAIYTEE 31
                                      9999988888.8999**************864 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.65
                                       HHTT--GGG-EEEEEE--TT CS
                     Tautomerase_3  30 tsvglPaFyvnvlFieieae 49 
                                        ++++P   ++v+F+e + e
  gi|336255477|ref|YP_004598584.1|  90 ERFDVPDENMKVVFTEHPGE 109
                                       34577777777888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); 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:                         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 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1097.29
//
Query:       gi|336255478|ref|YP_004598585.1|  [L=529]
Description: MATE efflux family protein [Halopiger xanaduensis SH-6]
Scores for 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-58  195.7  32.2    1.5e-32  112.5  12.7    2.4  2  MatE             MatE
    3.6e-06   27.1  20.8    0.00013   22.0   8.6    5.2  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    1.6e-05   23.7  24.0     0.0045   15.7  24.0    3.3  1  MurJ             Lipid II flippase MurJ
  ------ inclusion threshold ------
        9.3    5.5  13.0      0.075   12.4   1.3    2.8  3  DUF4191          Domain of unknown function (DUF4191)


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 !  112.5  12.7   3.3e-36   1.5e-32       1     160 [.      59     222 ..      59     223 .. 0.99
   2 !   88.9  11.5   6.1e-29   2.8e-25       1     154 [.     309     466 ..     309     473 .. 0.96

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 3.3e-36
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       Pi++ +ll+++++ +dtl +grl+++a++a+s+a+++++ll++++ g+ ta ++lv+q+ Ga   + a++++ q++ 
  gi|336255478|ref|YP_004598585.1|  59 PIVVIQLLQVTYNVVDTLYLGRLSTDAVGAISLAFPLIFLLISIAGGFTTAGAILVAQYTGASGDRSAGVVTGQTVS 135
                                       9**************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdee....vlelakrylrililgipalalqlvlsgilrgagktkvplyisli 150
                                       ++ lls+++ +++++++++ l ++ +d+e    v++la++y++i++lg+p+++ ++v+s+ +rg+g+t++p+ ++++
  gi|336255478|ref|YP_004598585.1| 136 FVGLLSIVLGIVGYFYTRPALEILPSDQEtsaaVIPLAADYMEIVFLGLPLMFGFFVFSALMRGYGDTRTPMLVMVV 212
                                       ***************************************************************************** PP

                              MatE 151 slllniplny 160
                                       s+ +n++l++
  gi|336255478|ref|YP_004598585.1| 213 SVFINVVLDP 222
                                       *******987 PP

  == domain 2  score: 88.9 bits;  conditional E-value: 6.1e-29
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+++e+ +  l  + +t +v  +++  ++a++++++++s++f++++gl+ a++t+vgq+lGa + +ra++++  +  
  gi|336255478|ref|YP_004598585.1| 309 PSMVEQSTSALAMISLTAMVVTFSPPVVSAYGLGNRLISIVFLPAMGLGRAIDTMVGQNLGADRADRAARSTWLAAA 385
                                       9999************************************************************************* PP

                              MatE  78 lllllsliiallvllfseqilslftqdee....vlelakrylrililgipalalqlvlsgilrgagktkvplyisli 150
                                       ++ +++l++a+++++f+e+i+s+f  + +     ++++ +y+ri  +   ++++++v  g++rgag+tk++++is+i
  gi|336255478|ref|YP_004598585.1| 386 TGSGIMLLVAVVAVAFTEPIVSVFLGNVDgaaeTIAYGVEYVRIRSVEFAFIGVSQVMLGAFRGAGNTKTAMVISII 462
                                       ************************999888888******************************************** PP

                              MatE 151 slll 154
                                       +l +
  gi|336255478|ref|YP_004598585.1| 463 TLWV 466
                                       9844 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 ?   -4.9   5.9         4   1.8e+04     119     135 ..     124     150 ..      62     158 .. 0.54
   2 !   22.0   8.6     3e-08   0.00013       2      74 ..     177     276 ..     176     280 .. 0.89
   3 ?   -2.5   2.8       1.1   4.8e+03      70      70 ..     370     370 ..     315     417 .. 0.55
   4 !   19.2   4.3   2.2e-07   0.00098       3      76 ..     428     504 ..     426     514 .. 0.88

  Alignments for each domain:
  == domain 1  score: -4.9 bits;  conditional E-value: 4
                   Polysacc_synt_C 119 a..........alalllavlvgalvYl 135
                                                  +++ ll++++g++ Y+
  gi|336255478|ref|YP_004598585.1| 124 RsagvvtgqtvSFVGLLSIVLGIVGYF 150
                                       133344443333344555555555555 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 3e-08
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgi................. 55 
                                       + i+ l++++++ + v+s+++ g g ++++++++v++++++++l  ++i      plfg                  
  gi|336255478|ref|YP_004598585.1| 177 MEIVFLGLPLMFGFFVFSALMRGYGDTRTPMLVMVVSVFINVVLDPFFIfgfqenPLFGWvgmggleqslyattgft 253
                                       7799999******************************************55444444444899************** PP

                   Polysacc_synt_C  56 ....vGaaiatvlallvvavlnl 74 
                                            Gaa+at+la  v++++ l
  gi|336255478|ref|YP_004598585.1| 254 glgiEGAALATILARGVGTAIGL 276
                                       ***************99998865 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.1
                   Polysacc_synt_C  70 a 70 
                                       a
  gi|336255478|ref|YP_004598585.1| 370 A 370
                                       1 PP

  == domain 4  score: 19.2 bits;  conditional E-value: 2.2e-07
                   Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigal...vklilnllliplfgivGaaiatvlallvvavlnlya 76 
                                       +i ++ + f+++s+v+ + + g g +k+a+++++i++    v  ++ l++i  +g++G+ i+++++ +++a++ + +
  gi|336255478|ref|YP_004598585.1| 428 RIRSVEFAFIGVSQVMLGAFRGAGNTKTAMVISIITLWvgrVGSVFALVFIFDWGATGVWIGMAVGNVLGALVGVAW 504
                                       56678889*****************************97788899999999*****999999999999999987655 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7  24.0     1e-06    0.0045      13     407 ..      88     516 ..      80     526 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-06
                              MurJ  13 aFnvAfklPnllrrlfae.galssaFvPvlaeakkkdeekaaefvrkvltllilvlllvtligilaapllirllatg 88 
                                       a ++Af l++ll  + ++  +  +++v++++ a+      a  ++++++ +++l+ +++ ++g +      ++l ++
  gi|336255478|ref|YP_004598585.1|  88 AISLAFPLIFLLISIAGGfTTAGAILVAQYTGAS--GDRSAGVVTGQTVSFVGLLSIVLGIVGYFYTRPALEILPSD 162
                                       5678999999999998762455789*********..555666778888899999999999******99999999999 PP

                              MurJ  89 f..deetlelavsllrillpylllvslsavfgavLnarkkFfapafsPvllNvsvIltllllanklgeeail..... 158
                                       +   ++   la++ ++i+++ l l++   vf+a+   ++    p++  v++ +  ++   ++   ++e++ +     
  gi|336255478|ref|YP_004598585.1| 163 QetSAAVIPLAADYMEIVFLGLPLMFGFFVFSALMRGYGDTRTPMLVMVVSVFINVVLDPFFIFGFQENPLFgwvgm 239
                                       97788899******************99999***9999998888877666555544555555556666677755555 PP

                              MurJ 159 .................aLaiGvliGgvlqllvqlpalkkagll................................. 185
                                                                                  +                                 
  gi|336255478|ref|YP_004598585.1| 240 ggleqslyattgftglgI-------------------------Egaalatilargvgtaiglgllfgtdlgptasle 291
                                       555555555555555550.........................4444444444444444555555555555777654 PP

                              MurJ 186 .lkprfafrdeglkkflklllptllgvsvsqlnllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlLPr 261
                                        l+p f+     ++ +++l  p+++  s+s l+ +  ta+  ++ + +vs++  ++r++ + + l ++ +  ++   
  gi|336255478|ref|YP_004598585.1| 292 hLRPDFD----LIEDIVRLGTPSMVEQSTSALAMISLTAMVVTFSPPVVSAYGLGNRLISIVF-LPAMGLGRAIDTM 363
                                       4555444....67789999**************************************987543.5555556666666 PP

                              MurJ 262 lSrsakekdedevrdllsqairltllllipvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalv 338
                                       + ++  ++  d + + +  a  +   ++++v+++ +++ +pivs++  +    +e +++  e  ++ ++   ++ + 
  gi|336255478|ref|YP_004598585.1| 364 VGQNLGADRADRAARSTWLAAATGSGIMLLVAVVAVAFTEPIVSVFLGNVDGAAETIAYGVEYVRIRSVEFAFIGVS 440
                                       67777788888888899999999************************999999************************ PP

                              MurJ 339 klllrvfYAredtktPvkislislvlnills...llllpplgv....vglalatslsaliglvllyvllrkrlklt 407
                                       +++l +f   ++tkt++ is+i+l +  + s   l++++ +g+    +g+a++++l+al+g++ +++ + k++ ++
  gi|336255478|ref|YP_004598585.1| 441 QVMLGAFRGAGNTKTAMVISIITLWVGRVGSvfaLVFIFDWGAtgvwIGMAVGNVLGALVGVAWFTRGTWKEKYID 516
                                       **************************99999888999999997333357899999999999999988888876555 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   1.2       2.5   1.1e+04      49      63 ..     205     219 ..     177     227 .. 0.52
   2 ?    0.9   0.1     0.053   2.4e+02      24      61 ..     378     415 ..     370     422 .. 0.79
   3 ?   12.4   1.3   1.7e-05     0.075      12      83 ..     444     519 ..     437     527 .. 0.81

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 2.5
                           DUF4191  49 slilllilgillgll 63 
                                       +++l++++++++ ++
  gi|336255478|ref|YP_004598585.1| 205 TPMLVMVVSVFINVV 219
                                       456666666665554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.053
                           DUF4191  24 kllwlllaaflvvvvvfvvlglllgslilllilgillg 61 
                                       + +wl++a+  ++++++ v+ ++++++i+ ++lg + g
  gi|336255478|ref|YP_004598585.1| 378 RSTWLAAATGSGIMLLVAVVAVAFTEPIVSVFLGNVDG 415
                                       46788889999999999999999999999999986655 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 1.7e-05
                           DUF4191  12 aqvfkltrkedkkllwlllaaflvvvvvfvvlglll..g..slilllilgillgllvalivltrraekaayaqieg 83 
                                         +f+   +++ +++  +++++++ v  +++l++++  g  ++++ + +g +lg+lv + ++tr + k  y   eg
  gi|336255478|ref|YP_004598585.1| 444 LGAFRGAGNTKTAMVISIITLWVGRVGSVFALVFIFdwGatGVWIGMAVGNVLGALVGVAWFTRGTWKEKYIDDEG 519
                                       5677777778888899999999999999999999975435359*********************999999977666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 4155.74
//
Query:       gi|336255479|ref|YP_004598586.1|  [L=631]
Description: anion transporter [Halopiger xanaduensis SH-6]
Scores for complete 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-87  294.7  33.5    1.8e-87  294.4  33.5    1.0  1  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
      4e-41  141.2  33.7      4e-41  141.2  33.7    2.1  2  CitMHS         Citrate transporter
    4.8e-05   22.4   2.1    4.8e-05   22.4   2.1    1.9  2  NhaB           Bacterial Na+/H+ antiporter B (NhaB)
  ------ inclusion threshold ------
        0.1   12.4   0.0        0.1   12.4   0.0    3.9  4  DUF5337        Family of unknown function (DUF5337)


Domain annotation for each model (and alignments):
>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.4  33.5   3.9e-91   1.8e-87      12     470 ..     142     613 ..     132     615 .. 0.91

  Alignments for each domain:
  == domain 1  score: 294.4 bits;  conditional E-value: 3.9e-91
                     Na_sulph_symp  12 vvlliilllPapdgleskawrllaifiaaivglileplplavialialsllavligvlaakalsevlsgfssdttlL 88 
                                       v+++ i+l P+p+gl+  ++ ++a+ + ++v ++ e++p ++++l+++ ++++ +   a     ++   +    ++L
  gi|336255479|ref|YP_004598586.1| 142 VLFALIFLSPTPEGLSAGGKAVAAVTAWVAVWWMSEAIPIPATSLLPIVMFPLTGALPA----ADTTPSYAHPLIFL 214
                                       78999**********************************************87777666....89999********* PP

                     Na_sulph_symp  89 vfaalliaaavektgLgkRiAlvlvkivGkrt..liLgyalvladlllapatpsntAraggivfpvikslss..... 158
                                       +++++++a+a++ +gL++RiAl+++k+vG+++  liLg++l +a+l++++++ ++  ++++i+++vi + +      
  gi|336255479|ref|YP_004598586.1| 215 FMGGFFLAMAMQRWGLHRRIALRTIKAVGTEPsrLILGFMLSTAFLSMWVSNSATVMMMVPIALAVIYQTADlveea 291
                                       *******************************************************************9988855555 PP

                     Na_sulph_symp 159 afgsepekqserkigaylmltvvqsasitsiaflTamApNllllglinsilgveitwasWflaaiptgvillllvpl 235
                                        ++++  ++ + + g  lml+++++as++++ +l ++ pN+l +g+++++ g+++++a+W+l  +p++++ l+ v  
  gi|336255479|ref|YP_004598586.1| 292 DLEVDTSEG-NFSFGVALMLCIAYGASVGGVSTLIGTPPNVLFAGQASELFGQSVSFAEWMLYGVPISIVGLVAVYV 367
                                       555555555.4469**********************************************************99999 PP

                     Na_sulph_symp 236 llyvlyppeikkkeeakavaktelkelGpltarekallilfvlllllWifge.........slnidattvaivvlvi 303
                                        +     p+  + ++++ ++++el+ lG ++++ek ++++fv++   Wi  +          ++  +t+vai +  +
  gi|336255479|ref|YP_004598586.1| 368 YVTRAVSPQFSELPAGADTIDRELERLGSMNKQEKLVAVVFVGMAASWIGASliepllgatPPEDADTIVAIGGALV 444
                                       9999999*******************************************996655555543336789999999999 PP

                     Na_sulph_symp 304 llllr.........vldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslf 371
                                       l+ l+         +ldW        +W+++ll+gg++a+a+   ++gl  w+g++l+ +    + +v+i+  ++ +
  gi|336255479|ref|YP_004598586.1| 445 LFTLPttadgertfLLDWS--SAVDIPWGVILLFGGGLAIANAFGETGLAAWIGEQLQLLEG--VSMVVILLAVVTM 517
                                       99999**************..77789*******************************87766..4444444444444 PP

                     Na_sulph_symp 372 vlvhylfaSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGf 448
                                        +  ++ +S+tAtta+l+pil+ va +i g+ p  ++++ a a s+a f+lp+at+pn+ivfg+gy+   +++r+G+
  gi|336255479|ref|YP_004598586.1| 518 TIFLTEVTSNTATTAMLMPILAGVAVGI-GVHPFGLMIAGATAASFA-FMLPVATPPNAIVFGSGYITLPQMARVGV 592
                                       556689**********************.888***************.***************************** PP

                     Na_sulph_symp 449 ilsiigllillllgalwwklLv 470
                                        l++ig++++ l++   w +L+
  gi|336255479|ref|YP_004598586.1| 593 GLNVIGIVLITLVALG-WLPLA 613
                                       ********99999977.66665 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.2  33.7   8.9e-45     4e-41       2     298 ..     172     555 ..     171     557 .. 0.83
   2 ?   -2.8   8.7      0.63   2.8e+03     116     168 ..     552     606 ..     546     619 .. 0.73

  Alignments for each domain:
  == domain 1  score: 141.2 bits;  conditional E-value: 8.9e-45
                                       xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            CitMHS   2 vllileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd. 73 
                                       v+++ e++++++++ll++v++     l   + +  +a p+i+l++g++ ++ a++++Gl++r+a + ++++g+ +  
  gi|336255479|ref|YP_004598586.1| 172 VWWMSEAIPIPATSLLPIVMFpltgALPAADTTPSYAHPLIFLFMGGFFLAMAMQRWGLHRRIALRTIKAVGTEPSr 248
                                       89*******************99988888889999****************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxx RF
                            CitMHS  74 llvllvlltallsafvsndgvvlimipivlslakrlkklppl.................lliplalaaniggaltpi 133
                                       l++ ++l ta+ls++vsn ++v++m+pi+l++  + ++l+                   l++ +a++a++gg+ t+i
  gi|336255479|ref|YP_004598586.1| 249 LILGFMLSTAFLSMWVSNSATVMMMVPIALAVIYQTADLVEEadlevdtsegnfsfgvaLMLCIAYGASVGGVSTLI 325
                                       **********************************96666666*****************9999************** PP

                                       xxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 134 Gtpttraaarpglslpnlll.....................lalllvgllplvllfmfgvalalpvnapkvkkqkai 189
                                       Gtp            pn+l+                     +++ +vgl+++++++      a+ +++ +  + +++
  gi|336255479|ref|YP_004598586.1| 326 GTP------------PNVLFagqaselfgqsvsfaewmlygVPISIVGLVAVYVYV----TRAVSPQFSELPAGADT 386
                                       ***............99999999999999999999999999999999998888888....55666666655555555 PP

                                       xxxxxxxxxxx....................................xxxxxxx....................... RF
                            CitMHS 190 ieaiarsllpv....................................atillla....................... 207
                                       i++  ++l ++                                    +     +                       
  gi|336255479|ref|YP_004598586.1| 387 IDRELERLGSMnkqeklvavvfvgmaaswigasliepllgatppedaD-----Tivaiggalvlftlpttadgertf 458
                                       555555555557777776666655555555555555555555555551.....044445555556778999999999 PP

                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 208 ......ykkveWsvlllfaGvfllvgaleqtGilealadllga...g.gplvalalvlgliallsafisnvavaalm 274
                                                ++W+v+llf+G +  + a+++tG++ ++++ l +   g  ++v+l++v+ ++ +l+ ++sn+a++a++
  gi|336255479|ref|YP_004598586.1| 459 lldwssAVDIPWGVILLFGGGLAIANAFGETGLAAWIGEQL-QlleGvSMVVILLAVVTMTIFLTEVTSNTATTAML 534
                                       99999999*******************************99.558754565555555666666************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 275 apialgmapalgllspsplalala 298
                                       +pi++g+a ++g   ++p+ l++a
  gi|336255479|ref|YP_004598586.1| 535 MPILAGVAVGIG---VHPFGLMIA 555
                                       ********9999...666666654 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.63
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxx RF
                            CitMHS 116 lliplalaaniggaltpiGtpttraaarpglslpnlll...............lalllvgllplvllf 168
                                       l+i+ a+aa+    ++p+ tp            pn ++               ++l ++g++ + l++
  gi|336255479|ref|YP_004598586.1| 552 LMIAGATAASFAF-MLPVATP------------PNAIVfgsgyitlpqmarvgVGLNVIGIVLITLVA 606
                                       7888888999988.*******............**999999999999988877444444444444443 PP

>> NhaB  Bacterial Na+/H+ antiporter B (NhaB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   2.1   1.1e-08   4.8e-05     131     312 ..     249     416 ..     211     425 .. 0.71
   2 ?   -5.4   3.3       2.8   1.3e+04     437     443 ..     540     546 ..     499     607 .. 0.42

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.1e-08
                              NhaB 131 lslafclaaaflsafldaltvvavvisvavgfysiyhkvasgkdlsedvdltddekieelkkeelekfraflrsllm 207
                                       l l f l++afls ++   + v +++ +a+    iy+    + dl+e++dl+ d+          e   +f  +l++
  gi|336255479|ref|YP_004598586.1| 249 LILGFMLSTAFLSMWVSNSATVMMMVPIAL--AVIYQ----TADLVEEADLEVDTS---------EGNFSFGVALML 310
                                       567888999999998887666655555554..44664....345666666655443.........444579999*** PP

                              NhaB 208 hagvgtalggvvtlvgepqnliiaeqakwkfgef..llrmspvtvpvlicglltcllveklklfgygeklpdevrki 282
                                           g+++ggv tl+g p n++ a qa+  fg+   +       vp+ i+gl+++++     +    ++lp     i
  gi|336255479|ref|YP_004598586.1| 311 CIAYGASVGGVSTLIGTPPNVLFAGQASELFGQSvsFAEWMLYGVPISIVGLVAVYVYVTRAVSPQFSELPAGADTI 387
                                       *******************************9851134445678**********99977777777777888888877 PP

                              NhaB 283 lvdfdreerkkrtkqdkiklivqaliavwl 312
                                         +++r  + ++ ++  + ++  ++ a w+
  gi|336255479|ref|YP_004598586.1| 388 DRELERLGSMNKQEKL-VAVVFVGMAASWI 416
                                       7777766554443332.2333345555555 PP

  == domain 2  score: -5.4 bits;  conditional E-value: 2.8
                              NhaB 437 avaintg 443
                                        va+  g
  gi|336255479|ref|YP_004598586.1| 540 GVAVGIG 546
                                       2333333 PP

>> DUF5337  Family of unknown function (DUF5337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.6     0.071   3.2e+02      13      35 ..     160     177 ..     154     187 .. 0.63
   2 ?   12.4   0.0   2.3e-05       0.1       9      38 ..     397     426 ..     390     429 .. 0.89
   3 ?   -0.6   0.3      0.28   1.2e+03      29      52 ..     491     514 ..     479     525 .. 0.72
   4 ?   -4.2   1.1       3.6   1.6e+04      19      32 ..     601     614 ..     594     616 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.071
                           DUF5337  13 grlvalviavtmllwlgaqwige 35 
                                       g+ va v a +++ w+      e
  gi|336255479|ref|YP_004598586.1| 160 GKAVAAVTAWVAVWWM-----SE 177
                                       5556666666666665.....44 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.3e-05
                           DUF5337   9 larkgrlvalviavtmllwlgaqwigeqlg 38 
                                       ++++ +lva+v ++ ++ w+ga++i + lg
  gi|336255479|ref|YP_004598586.1| 397 MNKQEKLVAVVFVGMAASWIGASLIEPLLG 426
                                       789*********************998887 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.28
                           DUF5337  29 gaqwigeqlglsnRyalLfdLaAl 52 
                                       +a wigeql l + + + + L A 
  gi|336255479|ref|YP_004598586.1| 491 LAAWIGEQLQLLEGVSMVVILLAV 514
                                       567999999887777666666655 PP

  == domain 4  score: -4.2 bits;  conditional E-value: 3.6
                           DUF5337  19 viavtmllwlgaqw 32 
                                        i  ++l wl + w
  gi|336255479|ref|YP_004598586.1| 601 LITLVALGWLPLAW 614
                                       35556667776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.21s 00:00:00.81 Elapsed: 00:00:00.37
# Mc/sec: 5076.17
//
Query:       gi|336255480|ref|YP_004598587.1|  [L=81]
Description: hypothetical protein Halxa_4103 [Halopiger xanaduensis SH-6]
Scores for 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-06   27.1   0.4    4.9e-06   26.3   0.4    1.4  1  HTH_IclR        IclR helix-turn-helix domain
    6.4e-06   26.4   0.1    8.5e-06   26.0   0.1    1.1  1  Rrf2            Transcriptional regulator
    6.6e-06   26.0   0.1    9.6e-06   25.4   0.1    1.2  1  MarR            MarR family
    1.9e-05   24.1   0.0    2.9e-05   23.5   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    2.6e-05   24.0   0.3    3.3e-05   23.7   0.3    1.2  1  MarR_2          MarR family
    0.00047   20.1   0.1    0.00056   19.8   0.1    1.2  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00098   19.0   0.0     0.0013   18.6   0.0    1.2  1  HTH_11          HTH domain
      0.005   17.3   1.6     0.0084   16.5   1.6    1.4  1  DUF802          Domain of unknown function (DUF802)
     0.0053   16.5   0.2      0.011   15.5   0.1    1.6  2  HTH_DeoR        DeoR-like helix-turn-helix domain
     0.0099   16.1   0.0      0.023   14.9   0.0    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
      0.012   15.4   0.3      0.022   14.6   0.3    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.015   15.3   0.1      0.021   14.9   0.1    1.2  1  HTH_20          Helix-turn-helix domain
      0.019   15.1   0.0       0.04   14.1   0.0    1.6  1  HTH_34          Winged helix DNA-binding domain
      0.051   13.2   0.0      0.076   12.7   0.0    1.3  1  GntR            Bacterial regulatory proteins, gntR family
      0.063   13.1   0.1       0.12   12.2   0.1    1.4  1  HTH_38          Helix-turn-helix domain
       0.13   12.2   0.0       0.17   11.8   0.0    1.2  1  HTH_5           Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.4   4.3e-09   4.9e-06       8      50 ..      18      59 ..      17      60 .. 0.97

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.3e-09
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      iL+ l +++q+ t +elA+++  ++ t  R ++ L+++Gyv++
  gi|336255480|ref|YP_004598587.1| 18 ILEVLDRTNQA-TAAELAAALETHPMTIERQCRHLQREGYVRR 59
                                      9*********8.*****************************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   7.6e-09   8.5e-06      21      71 ..      23      71 ..      17      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 7.6e-09
                                      STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHC CS
                              Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakpp 71
                                      ++ ++++++e+a+  +++p  +e+  ++L+++g+v  +rG+ G y+La++ 
  gi|336255480|ref|YP_004598587.1| 23 DRTNQATAAELAAALETHPMTIERQCRHLQREGYV--RRGVAGTYTLAEEG 71
                                      455569****************************9..6**********986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   8.6e-09   9.6e-06       7      49 ..      17      59 ..      16      60 .. 0.97

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.6e-09
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      +iL+ l++ ++++ +eLa +l+++++t+ r+ ++L ++G+++R
  gi|336255480|ref|YP_004598587.1| 17 SILEVLDRTNQATAAELAAALETHPMTIERQCRHLQREGYVRR 59
                                      5999**************************************9 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 !   23.5   0.0   2.6e-08   2.9e-05       5      48 .]      15      58 ..      15      58 .. 0.98

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.6e-08
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      dr ILe+L +    + +eLA +l   p t+ r+ + L++eG+++
  gi|336255480|ref|YP_004598587.1| 15 DRSILEVLDRTNQATAAELAAALETHPMTIERQCRHLQREGYVR 58
                                      89****************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.3   2.9e-08   3.3e-05       8      54 ..      16      60 ..      11      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.9e-08
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      + +L +L r      t++ela++l   + ++ r ++ L++ G+v+r 
  gi|336255480|ref|YP_004598587.1| 16 RSILEVLDRTNQ--ATAAELAAALETHPMTIERQCRHLQREGYVRRG 60
                                      679999999998..9*****************************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 !   19.8   0.1     5e-07   0.00056      21      54 ..      27      60 ..       7      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5e-07
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrg 54
                                      + t +elA+ l +++ t+ r  ++L+reg+++rg
  gi|336255480|ref|YP_004598587.1| 27 QATAAELAAALETHPMTIERQCRHLQREGYVRRG 60
                                      67899**************************976 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.2e-06    0.0013       3      44 ..      16      56 ..      15      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      ++ile L + +++ +++eLA  L+   +t+ r ++ L+  g+
  gi|336255480|ref|YP_004598587.1| 16 RSILEVL-DRTNQATAAELAAALETHPMTIERQCRHLQREGY 56
                                      579****.88888*************************9995 PP

>> DUF802  Domain of unknown function (DUF802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.6   7.5e-06    0.0084      10      51 ..       8      50 ..       6      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.5e-06
                            DUF802 10 aavAaaWraA.LaeQqqaqeaLaqqlraaLaqfaatFeqrSaa 51
                                       ++A+ W+++ L    ++++a a++l+aaL+++  t e++  +
  gi|336255480|ref|YP_004598587.1|  8 DQTAQGWDRSiLEVLDRTNQATAAELAAALETHPMTIERQCRH 50
                                      578999998867889*******************999998655 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 ?   -2.3   0.0       3.4   3.8e+03      25      31 ..       5      11 ..       2      11 .. 0.84
   2 !   15.5   0.1   9.6e-06     0.011       4      50 ..      17      63 ..      15      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.4
                          HTH_DeoR 25 gvSeaTi 31
                                      ++S++T+
  gi|336255480|ref|YP_004598587.1|  5 DYSDQTA 11
                                      8999996 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 9.6e-06
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthGG 50
                                       ile l +    +  el++ l++ ++Ti R  + L+ +g ++R   G
  gi|336255480|ref|YP_004598587.1| 17 SILEVLDRTNQATAAELAAALETHPMTIERQCRHLQREGYVRRGVAG 63
                                      69****************************************98655 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 !   14.9   0.0   2.1e-05     0.023      12      53 ..      17      58 ..      10      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                                      HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                       I+++ +  + ++ ++la +L+ +p ++    + L+++Gyv 
  gi|336255480|ref|YP_004598587.1| 17 SILEVLDRTNQATAAELAAALETHPMTIERQCRHLQREGYVR 58
                                      6778888889999***************************95 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   0.3     2e-05     0.022       5      36 ..      15      46 ..      14      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                     HTH_AsnC-type  5 DrkILeaLqedaRisyaeLAervGlSestvlr 36
                                      Dr ILe L +   ++ aeLA+++   + t+ r
  gi|336255480|ref|YP_004598587.1| 15 DRSILEVLDRTNQATAAELAAALETHPMTIER 46
                                      9**********************999988877 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.8e-05     0.021      13      56 ..      16      59 ..      10      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      r il  L r   +ta+ela++l++++ t+ ++ r L++ g+v++
  gi|336255480|ref|YP_004598587.1| 16 RSILEVLDRTNQATAAELAAALETHPMTIERQCRHLQREGYVRR 59
                                      7899999999******************************9986 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 ?   14.1   0.0   3.6e-05      0.04       4      46 ..      17      59 ..      16      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
                            HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYiev 46
                                      ++l +L  +++a+++el +ale+    +  + + L+  gY+ +
  gi|336255480|ref|YP_004598587.1| 17 SILEVLDRTNQATAAELAAALETHPMTIERQCRHLQREGYVRR 59
                                      5899999*********************************975 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.8e-05     0.076      28      56 ..      31      59 ..      28      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.8e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglver 56
                                       eLaa++++  +t+ +  r L++eg+v r
  gi|336255480|ref|YP_004598587.1| 31 AELAAALETHPMTIERQCRHLQREGYVRR 59
                                      69*************************87 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1    0.0001      0.12       9      43 ..      15      50 ..      15      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                            HTH_38  9 eReeIerl.laeGlslreIArrLgrspsTIsRElkR 43
                                      +R  +e l +    + +e A  L  +p TI R +++
  gi|336255480|ref|YP_004598587.1| 15 DRSILEVLdRTNQATAAELAAALETHPMTIERQCRH 50
                                      6777788834455999****************9997 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 ?   11.8   0.0   0.00015      0.17       7      46 ..      18      58 ..      16      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                      HHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  7 ILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      IL  L + +++++ ela++l+  + t+ ++ + L  +G+V+
  gi|336255480|ref|YP_004598587.1| 18 ILEVLDRtNQATAAELAAALETHPMTIERQCRHLQREGYVR 58
                                      8888888899*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 660.98
//
Query:       gi|336255481|ref|YP_004598588.1|  [L=321]
Description: 3-oxoacyl-(acyl-carrier-protein) reductase [Halopiger xanaduensis SH-6]
Scores for 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-53  178.6   0.0    1.1e-52  178.3   0.0    1.1  1  adh_short        short chain dehydrogenase
    2.6e-44  151.5   0.0    3.8e-44  151.0   0.0    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.1e-13   51.6   0.0    1.4e-13   51.2   0.0    1.2  1  KR               KR domain
    2.2e-12   47.3   0.2    3.9e-12   46.4   0.2    1.5  1  NAD_binding_10   NAD(P)H-binding
    4.3e-08   32.9   0.0    9.5e-08   31.8   0.0    1.6  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.4e-06   26.4   0.1    7.3e-06   25.3   0.1    1.5  1  RmlD_sub_bind    RmlD substrate binding domain
    0.00052   19.6   0.7    0.00096   18.8   0.1    1.7  2  NmrA             NmrA-like family
      0.001   18.5   0.0     0.0015   18.0   0.0    1.2  1  DUF1776          Fungal family of unknown function (DUF1776)
     0.0042   17.3   0.3       0.01   16.1   0.1    1.7  2  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
      0.069   13.7   0.5       0.55   10.8   0.0    2.5  2  DUF5114          Domain of unknown function (DUF5114)
      0.074   12.8   0.0       0.16   11.7   0.0    1.5  1  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 
       0.13   11.6   0.0       0.52    9.6   0.0    1.9  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


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 !  178.3   0.0   7.6e-56   1.1e-52       1     192 [.      49     234 ..      49     237 .. 0.96

  Alignments for each domain:
  == domain 1  score: 178.3 bits;  conditional E-value: 7.6e-56
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       k vl+tG+ssGIGra+a+++++++++v++++r++e++    + l+e+g   +++++Dvtd ++v ++ve+ v+  g 
  gi|336255481|ref|YP_004598588.1|  49 KSVLITGCSSGIGRATARAFLEDDWQVIATARNAEDI----TDLEEAG--CTTLELDVTDPDQVARAVERTVDIAGA 119
                                       679******************************9999....5666554..99************************* PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       +d+LvnNAG +++gp +++s ++  r ++vN+ g+  l+ra+lp+m +q  GrI+nvsSv+g+v+++g  +Ys sK+
  gi|336255481|ref|YP_004598588.1| 120 IDCLVNNAGYAQMGPLEDVSTADLHRQFDVNVYGPHRLVRAALPHMRAQGTGRIINVSSVVGRVAFPGSGVYSGSKH 196
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmakelre 192
                                       a++++++sl+ e+++ gi v+++ PG+v+T+++ ++ e
  gi|336255481|ref|YP_004598588.1| 197 ALEAMSDSLRAEVEEFGIDVVVIEPGPVETNFTDRVDE 234
                                       *******************************9988776 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 !  151.0   0.0   2.5e-47   3.8e-44       1     184 [.      55     234 ..      55     248 .. 0.95

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 2.5e-47
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnna 77 
                                       G  sgIGra+A+a+ e  ++v++t +n e+   +++l+e  g + le+DVtd++qv+++ve++v+  g +D+lvnna
  gi|336255481|ref|YP_004598588.1|  55 GCSSGIGRATARAFLEDDWQVIATARNAED---ITDLEE-AGCTTLELDVTDPDQVARAVERTVDIAGAIDCLVNNA 127
                                       6789************************99...899977.6999********************************* PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealt 152
                                       g+a+   gp++++s ++++r +dvn+y+ ++l++aalp+m+++  g+i+n+ssv +++++p+  +y+ +K+alea++
  gi|336255481|ref|YP_004598588.1| 128 GYAQM--GPLEDVSTADLHRQFDVNVYGPHRLVRAALPHMRAQgtGRIINVSSVVGRVAFPGSGVYSGSKHALEAMS 202
                                       *****..*******************************9988879******************************** PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgikg 184
                                        +l +e+ + gi v ++ pgp++T+ ++++++
  gi|336255481|ref|YP_004598588.1| 203 DSLRAEVEEFGIDVVVIEPGPVETNFTDRVDE 234
                                       **************************999875 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   9.1e-17   1.4e-13       3     169 ..      51     211 ..      49     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 9.1e-17
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                       +litG+  g+G+++ar  +e+   +++ ++R+       ++ i+ le+ g+  +++++Dv+d+d+v++++e+  + +
  gi|336255481|ref|YP_004598588.1|  51 VLITGCSSGIGRATARAFLEDD-WQVIATARN-------AEDITDLEEAGC--TTLELDVTDPDQVARAVERTVDIA 117
                                       79*****************986.568889999.......468999***888..589******************999 PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaa 152
                                       ++i   ++ Ag ++ ++le+++++dl++ +   v G + L ++  +    +    ++ +SS+ g +  +g + Y+  
  gi|336255481|ref|YP_004598588.1| 118 GAIDCLVNNAGYAQMGPLEDVSTADLHRQFDVNVYGPHRLVRAALPhmraQGTGRIINVSSVVGRVAFPGSGVYSGS 194
                                       **************************************99988766576688899********************** PP

                                       HHHHHHHHHHHHHHHHT CS
                                KR 153 NaflDalaeyrrsqglp 169
                                        + l+a+ ++ r++ ++
  gi|336255481|ref|YP_004598588.1| 195 KHALEAMSDSLRAEVEE 211
                                       ***99999988876554 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 !   46.4   0.2   2.6e-15   3.9e-12       2     148 ..      56     226 ..      55     284 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.6e-15
                                       TTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHT.......T-SEEEES-... CS
                    NAD_binding_10   2 AtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealk.......gadaVvsal... 68 
                                        + ++Gr+ ++  l++ +++v a +Rn+e++++le e+g++++e+dvtd++++a+a++        +d  v ++   
  gi|336255481|ref|YP_004598588.1|  56 CSSGIGRATARAFLED-DWQVIATARNAEDITDLE-EAGCTTLELDVTDPDQVARAVErtvdiagAIDCLVNNAgya 130
                                       5678************.7****************8.7********************96554443334433333333 PP

                                       --TCC....HHHH...................HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHH CS
                    NAD_binding_10  69 ggggk....deeg...................aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkayla 122
                                                d  +                   +++++  ++++g+ R++ vs++  +   p   g+ +++  k++l+
  gi|336255481|ref|YP_004598588.1| 131 Q---MgpleD--VstadlhrqfdvnvygphrlVRAALPHMRAQGTGRIINVSSVVGRVAFP---GSGVYSGSKHALE 199
                                       0...245441..24446666788888999999*********************85443333...3455677889999 PP

                                       HHHHHHH.HHHHSSSEEEEEEE-CEE- CS
                    NAD_binding_10 123 akraaee.llrasgldwTivrpggLtd 148
                                       a+  + + ++++ g+d +++ pg  + 
  gi|336255481|ref|YP_004598588.1| 200 AMSDSLRaEVEEFGIDVVVIEPGPVET 226
                                       988766625999999999999997654 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   6.3e-11   9.5e-08       1     157 [.      51     206 ..      51     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 6.3e-11
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HH....HHHHHHHHH.T-SEEEE-- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrs....alerlfkee.qpdavihlA 72 
                                       +l+tG +  iG+a+++a+le +++vi+ +r+ ++    +++  +  eld+td++    a+er ++   ++d+ ++ A
  gi|336255481|ref|YP_004598588.1|  51 VLITGCSSGIGRATARAFLEDDWQVIATARNAEDITDLEEAGCTTLELDVTDPDqvarAVERTVDIAgAIDCLVNNA 127
                                       79*****************************888888888888***********66666666667777899999999 PP

                                       S..---H..HHHHHSHHHHHHHHTHHHHHHHHHHH....HHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSH CS
                         Epimerase  73 a..vggv..aassedpadfieknlqgtlnlleaar....kagvkrllflsSsevYGkdaeqpkeettltgplkpnsp 141
                                       +  + g+  ++s  d  + ++ n+ g  +l+ aa     ++g  r++++sS  v G++a             + +  
  gi|336255481|ref|YP_004598588.1| 128 GyaQMGPleDVSTADLHRQFDVNVYGPHRLVRAALphmrAQGTGRIINVSS--VVGRVAF------------PGSGV 190
                                       853344422355566677889************98444455888*******..8887776............34556 PP

                                       HHHHHHHHHHHHHHHH CS
                         Epimerase 142 YaaaKlageklveaya 157
                                       Y+ +K+a e +  +++
  gi|336255481|ref|YP_004598588.1| 191 YSGSKHALEAMSDSLR 206
                                       6666666666655554 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 !   25.3   0.1   4.9e-09   7.3e-06       3      89 ..      51     161 ..      49     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4.9e-09
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHHHHH.....--SEEEE-- CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre...............eldltdaeavaellkea.....kpdvvvnaA 59 
                                       +l+tG +  +G++ a+++ e++++v+a+ r+               eld+td+++va++++ +       d++vn A
  gi|336255481|ref|YP_004598588.1|  51 VLITGCSSGIGRATARAFLEDDWQVIATARNaeditdleeagcttlELDVTDPDQVARAVERTvdiagAIDCLVNNA 127
                                       89**************************9999****************************654222226789***** PP

                                       ----HHHHHHSHH....HHHHHHTHHHHHHHHHH CS
                     RmlD_sub_bind  60 AytavDkaEseee....aayavnaeavealAeaa 89 
                                        y ++   E+ +     +++ vn+ ++++l +aa
  gi|336255481|ref|YP_004598588.1| 128 GYAQMGPLEDVSTadlhRQFDVNVYGPHRLVRAA 161
                                       *****9999875411115789*********9998 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       2.4   3.7e+03     172     198 ..       9      34 ..       6      39 .. 0.80
   2 !   18.8   0.1   6.4e-07   0.00096       1      64 [.      51     112 ..      51     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.4
                                       SS-TTS-EE-HHHHHHHHHHHHHHHHH CS
                              NmrA 172 pgnpkavlldaeeDiGafvikilkdpr 198
                                       +g++++++  a++D+G+ ++++ +++r
  gi|336255481|ref|YP_004598588.1|   9 DGDSDGAVE-ADRDTGTGTASATDRER 34 
                                       677777777.999*****999999866 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 6.4e-07
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkg 64 
                                       +l++G +  +G++ +ra+l+++++v a  R+   e ++ l+eaG ++++ d+ d + +++a++ 
  gi|336255481|ref|YP_004598588.1|  51 VLITGCSSGIGRATARAFLEDDWQVIATARNA--EDITDLEEAGCTTLELDVTDPDQVARAVER 112
                                       78999999**********************96..679**********************99974 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   9.7e-07    0.0015      98     198 ..     124     222 ..     108     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.7e-07
                           DUF1776  98 vPslsy.ptgpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssa 173
                                       v +  y ++gp+e ++ + ++ ++  ++  p  ++ a lp++++   q +  i+   s++  +  p +++ +    a
  gi|336255481|ref|YP_004598588.1| 124 VNNAGYaQMGPLEDVSTADLHRQFDVNVYGPHRLVRAALPHMRA---QGTGRIINVSSVVGRVAFPGSGVYSGSKHA 197
                                       5567798************************************9...66666667789******************* PP

                           DUF1776 174 lsalfevLkrelrphnidvtqikLG 198
                                       l+a+  +L++e+++ +idv+ i  G
  gi|336255481|ref|YP_004598588.1| 198 LEAMSDSLRAEVEEFGIDVVVIEPG 222
                                       ********************99866 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   6.9e-06      0.01       3      58 ..      53     109 ..      51     126 .. 0.87
   2 ?   -2.5   0.0       4.1   6.1e+03     104     114 ..     208     218 ..     198     225 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.9e-06
                                       EES-S.HHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHT CS
                            TrkA_N   3 iiGlG.rvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeea 58 
                                       i G++  +Gr+ a+ + e+ ++v++  ++ e +  l+e g++++  d+td++ +++a
  gi|336255481|ref|YP_004598588.1|  53 ITGCSsGIGRATARAFLEDDWQVIATARNAEDITDLEEAGCTTLELDVTDPDQVARA 109
                                       66654159**********8889******************************98887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.1
                                       HHHHHTTSEEE CS
                            TrkA_N 104 llkklgadvvi 114
                                        +++ g+dvv+
  gi|336255481|ref|YP_004598588.1| 208 EVEEFGIDVVV 218
                                       34444444444 PP

>> DUF5114  Domain of unknown function (DUF5114)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00037      0.55      49      92 ..      60     103 ..      40     104 .. 0.83
   2 ?   -0.0   0.0      0.87   1.3e+03      25      41 ..     165     181 ..     158     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00037
                           DUF5114  49 kaietpvaFggnaeqltf.getAgditvsvpaaGectlvldlsnP 92 
                                        +++t  aF     q+   + +A+dit ++ +aG +tl ld+ +P
  gi|336255481|ref|YP_004598588.1|  60 IGRATARAFLEDDWQVIAtARNAEDIT-DLEEAGCTTLELDVTDP 103
                                       5677888999998888774778****9.7799************9 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.87
                           DUF5114  25 iqisGtGklYnnetvsg 41 
                                       ++ +GtG+  n+++v g
  gi|336255481|ref|YP_004598588.1| 165 MRAQGTGRIINVSSVVG 181
                                       5679*********9877 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.16      38      56 ..      46      64 ..      24      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                      -.-SEEEEESTSSHHHHHH CS
                   Eno-Rase_NADH_b 38 kgpkkvLviGaStGYGLAs 56
                                      +  k vL+ G+S+G G A+
  gi|336255481|ref|YP_004598588.1| 46 TRKKSVLITGCSSGIGRAT 64
                                      2589************886 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 ?    9.6   0.0   0.00035      0.52      32      86 ..      44      99 ..      16     115 .. 0.83
   2 ?   -1.2   0.0      0.75   1.1e+03     140     165 ..     204     228 ..     194     234 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00035
                                      S-GTTSEEEEES-SH.HHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHH CS
                      2-Hacid_dh_C 32 kelsgktvGiiGlGr.IGqavakrlkafgmkviaydrskkkeeeeeelgvelvsle 86
                                      +  ++k v i G+ + IG+a+a+ + + + +via+ r+ ++ ++ ee g++  +l+
  gi|336255481|ref|YP_004598588.1| 44 RYTRKKSVLITGCSSgIGRATARAFLEDDWQVIATARNAEDITDLEEAGCTTLELD 99
                                      45688999****9744**********************999999999999877776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.75
                                       HHHTTSCCEEEES--SSSSSGTCHHH CS
                      2-Hacid_dh_C 140 aLksgkiagaalDvfeeeplpedspl 165
                                        L++ +++ +++Dv+  ep p ++++
  gi|336255481|ref|YP_004598588.1| 204 SLRA-EVEEFGIDVVVIEPGPVETNF 228
                                       5544.677889999988887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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 0.23s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 2564.21
//
Query:       gi|336255482|ref|YP_004598589.1|  [L=459]
Description: MATE efflux family protein [Halopiger xanaduensis SH-6]
Scores for 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-44  148.9  26.0    1.1e-24   87.0   7.5    2.6  2  MatE             MatE
    0.00018   21.6   7.2    0.00018   21.6   7.2    3.7  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 !   87.0   7.5   1.2e-28   1.1e-24       1     157 [.      25     181 ..      25     184 .. 0.99
   2 !   68.5   9.3   5.6e-23   5.1e-19       6     160 ..     252     408 ..     247     409 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 1.2e-28
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       Pial++ + +l+ ++d++++g +++ a+Aa+++a   ++l   ++lgl+t++ +l +q  G + +    +a+ q+++
  gi|336255482|ref|YP_004598589.1|  25 PIALQQTFNTLMRTVDVVVTGLFSPAAVAAIGLADLYAQLPLRIGLGLGTGAIALSSQDTGRGATATRDRAITQAFC 101
                                       9**************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       ++++l+l++++++l+ se+++ +++++++v+e++ ryl +++  +p  ++ lv ++ l+g+g+t++p++++++++ +
  gi|336255482|ref|YP_004598589.1| 102 IGFALGLPLIAVGLAVSEPLIAVLGAEPAVVEMGGRYLALVFAAAPMRIVGLVGARSLQGTGDTRTPMAVNVVANAV 178
                                       ***************************************************************************99 PP

                              MatE 155 nip 157
                                       ni 
  gi|336255482|ref|YP_004598589.1| 179 NIF 181
                                       996 PP

  == domain 2  score: 68.5 bits;  conditional E-value: 5.6e-23
                              MatE   6 nllesllslidtllvgrlgskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglillll 81 
                                        +  s+ ++ ++ l+  +g++  Aa+ i+ +i + l+  +  ++s+a++++vgq lG+++  +a++a   ++ l+l+
  gi|336255482|ref|YP_004598589.1| 252 GMSTSVANFPFNALLLTFGTEVTAAYHIGRRIYQQLTGpLYRSFSVAASIIVGQTLGEGDAADARFAGLAMTALSLI 328
                                       566778888899999999***************999997888*********************************** PP

                              MatE  82 lsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnip 157
                                          ++ +++++ + +i+++ft+d++ le+a+ + r+ ++++++++++++ sg l+gag+t++p+y+ + ++  + + 
  gi|336255482|ref|YP_004598589.1| 329 TLGVAGAVLVAGATPIARVFTNDAATLEYAAAFTRVFGVSMVFFGIFFPVSGSLKGAGDTRTPFYARFTGTfAFMLG 405
                                       ******************************************************************99988666666 PP

                              MatE 158 lny 160
                                       l+y
  gi|336255482|ref|YP_004598589.1| 406 LSY 408
                                       655 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 ?   -2.6   0.4      0.58   5.2e+03      96     113 ..      43      60 ..      18      79 .. 0.45
   2 !   21.6   7.2   2.1e-08   0.00018       2      79 ..     139     222 ..     138     304 .. 0.82
   3 ?   -0.7   0.6      0.16   1.4e+03     119     133 ..     318     337 ..     253     347 .. 0.49
   4 !   12.8   4.7     1e-05      0.09       3      69 ..     363     432 ..     361     440 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.58
                   Polysacc_synt_C  96 laalvmgivvylllllll 113
                                       + +l+  ++v ++ l  l
  gi|336255482|ref|YP_004598589.1|  43 VTGLFSPAAVAAIGLADL 60 
                                       333333333222333333 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2.1e-08
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvavl 72 
                                       La++  ++++  +  v++  Lqg+g +++++ ++v++ +v++  ++ l       p++ ivG+ +at+++ ++ avl
  gi|336255482|ref|YP_004598589.1| 139 LALVFAAAPMRIVGLVGARSLQGTGDTRTPMAVNVVANAVNIFATVGLGlgiaglPRLEIVGVGLATAISRTLEAVL 215
                                       77888889999999*************************99999988876677789********************* PP

                   Polysacc_synt_C  73 nlyalrr 79 
                                       +  a+  
  gi|336255482|ref|YP_004598589.1| 216 MTAAIAS 222
                                       *766654 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.16
                   Polysacc_synt_C 119 a.....alalllavlvgalv 133
                                       a     al+l+  +++ga++
  gi|336255482|ref|YP_004598589.1| 318 AglamtALSLITLGVAGAVL 337
                                       12322223333333344444 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 1e-05
                   Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigal.vklilnllli..plfgivGaaiatvlallvv 69 
                                       +++ +s++f++++ ++s+ L g g ++++++a + g + + l+l++l      fg+ G+ +++v++++  
  gi|336255482|ref|YP_004598589.1| 363 RVFGVSMVFFGIFFPVSGSLKGAGDTRTPFYARFTGTFaFMLGLSYLAGvtLGFGLPGVYAGIVCSYAWW 432
                                       67889***************************99887758999999987667889999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3543.46
//
Query:       gi|336255483|ref|YP_004598590.1|  [L=301]
Description: endonuclease V [Halopiger xanaduensis SH-6]
Scores for 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-56  189.7   0.0    5.8e-56  189.3   0.0    1.1  1  Endonuclease_5  Endonuclease V
  ------ inclusion threshold ------
       0.04   13.3   0.2        0.3   10.5   0.0    2.1  2  DUF99           Protein of unknown function DUF99


Domain annotation for each model (and alignments):
>> Endonuclease_5  Endonuclease V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.3   0.0   6.4e-60   5.8e-56      12     196 ..      89     289 ..      82     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: 189.3 bits;  conditional E-value: 6.4e-60
                                       --SGG-SEEEEEEEEEEECTCEEE.EEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHHHHHHCC-SS-- CS
                    Endonuclease_5  12 klkeklklvaGvDvsfvkeekkea.vaalvvldlpslevvekavavvklsfpYipgfLaFRElpvllkaleklkqkp 87 
                                        ++ k  +vaGvD sf ++++ ++ +a  +v+ ++  +v+e+a av++l++pYipg+L+FRE +++l+ale+l+ +p
  gi|336255483|ref|YP_004598590.1|  89 GTEAKPPIVAGVDQSFLTNDDGDQdRALSAVVATQAGDVIERASAVTDLEIPYIPGLLSFREGKPILAALEELSVEP 165
                                       44555679*********99999989999999999******************************************* PP

                                       SEEEEEC-SSSSTTS--HHHHHHHHHTS-EEEEESS-SSSBE-..---SSTTEEEEEE.......ETTEEEEEEEES CS
                    Endonuclease_5  88 dvllvDGnGiaHprrlGlAshlGvlldlptiGvaKsllvgkve..epekekgsvvplv.......segevigaalrt 155
                                       d+ll+DG+G +H r++G+A+h+Gv+ld+p++GvaKsll+g+ +  + + ++g+ vp+         +g+ +g+a++t
  gi|336255483|ref|YP_004598590.1| 166 DLLLFDGSGRIHFRQAGIATHMGVVLDVPSVGVAKSLLCGTPTeeTDNLSEGTRVPIEsnsrvdaPDGTLLGYAVQT 242
                                       ***************************************96662134445677777775544433339********* PP

                                       STTS......--EEEEEECSS-HHHHHHHHHHCS-T-SS-HHHHHHH CS
                    Endonuclease_5 156 kknv......kpiyvSvGhrisletalelvlallkkyrlPepirqAd 196
                                       ++        +p+yvS+Ghr+  eta +++l ++++y+lPep+r+Ad
  gi|336255483|ref|YP_004598590.1| 243 RQYDspnryiNPLYVSPGHRVGPETAADIALDCATSYKLPEPVRLAD 289
                                       9977778889************************************9 PP

>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.04   3.6e+02       5      36 ..      97     129 ..      96     135 .. 0.69
   2 ?   10.5   0.0   3.3e-05       0.3     150     181 ..     263     294 ..     241     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.04
                                       EEEEEEEE.....-SS-EEEEEEEE.ETT.EEE CS
                             DUF99   5 vlGiddsfferkkkdgksvlvGvvm.radrvvd 36 
                                       v G+d sf+++++ d++ +l +vv  +a++v++
  gi|336255483|ref|YP_004598590.1|  97 VAGVDQSFLTNDDGDQDRALSAVVAtQAGDVIE 129
                                       679*****9977767777776666404555665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 3.3e-05
                                       S-HHHHHHHHHHC-SSSSS-HHHHHHHHHHHH CS
                             DUF99 150 ieleeaaklvrkltlegriPEPlRvAhliAsa 181
                                       + +e+aa++   +++  ++PEP+R+A+  A +
  gi|336255483|ref|YP_004598590.1| 263 VGPETAADIALDCATSYKLPEPVRLADNYAGE 294
                                       67899**********************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2287.36
//
Query:       gi|336255484|ref|YP_004598591.1|  [L=314]
Description: Rhomboid family protein [Halopiger xanaduensis SH-6]
Scores for complete 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-26   92.9  16.2      3e-26   92.2  16.2    1.3  1  Rhomboid  Rhomboid family
      2e-12   47.0   8.2    2.9e-12   46.5   8.2    1.2  1  zf-AN1    AN1-like Zinc finger
    4.9e-05   23.8   0.1     0.0001   22.8   0.1    1.4  1  DUF1751   Eukaryotic integral membrane protein (DUF1751)
  ------ inclusion threshold ------
      0.042   14.0   1.0      0.058   13.5   1.0    1.2  1  FYVE      FYVE zinc finger
       0.23   11.4   4.3       0.32   10.9   4.3    1.2  1  zf-HIT    HIT zinc finger


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2  16.2   8.3e-30     3e-26       3     148 ..     127     281 ..     125     283 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 8.3e-30
                                       GCC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S..........-E CS
                          Rhomboid   3 krgelwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaeses.......pl 72 
                                       +++ +w+++ts+f H+g+ H+++N++++++fG+ +er +Gs  +++l+l+sg +++l++++++             +
  gi|336255484|ref|YP_004598591.1| 127 YPEYVWTWFTSIFAHGGLYHIVGNSIVIFFFGPLVERYVGSRDYAILFLVSGALAGLGQIAIQIIQAGgaspfmgGV 203
                                       6789****************************************************999999877544778999999 PP

                                       ESSHHHHHHHHHHHHHHHHCCCCGS----HC.....CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHHHHHHHHHHCC CS
                          Rhomboid  73 vGaSGaifgllgallvlvprnrkllrkliia..llllllfillnlvlgllpraggvsnlAHlgGllaGlllgllllr 147
                                       +GaSGa  ++lg+l+vl p  + +l ++++   +ll + ++++++++  +++ g++++ AHl+Gll Gl +g ++ r
  gi|336255484|ref|YP_004598591.1| 204 LGASGAALAILGVLTVLNPGLKVYLYFILPVpiWLLAAGYAVFSVFFLGTGGGGNIAHGAHLIGLLLGLGYGEYVKR 280
                                       ***********************99998888889999999**********999******************998877 PP

                                       H CS
                          Rhomboid 148 r 148
                                        
  gi|336255484|ref|YP_004598591.1| 281 T 281
                                       5 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   8.2   8.1e-16   2.9e-12       1      39 [.       4      40 ..       4      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 8.1e-16
                            zf-AN1  1 CsfksCkkkdflpfkCryCgkvFClkHrlpedHdCkkla 39
                                      C++  C+k +++p++Cr+Cg++FC++Hrlpe+HdC++l+
  gi|336255484|ref|YP_004598591.1|  4 CDV--CGKDENMPYNCRHCGGTFCADHRLPENHDCTGLQ 40
                                      775..*******************************986 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   2.8e-08    0.0001       6      68 ..     129     191 ..     121     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.8e-08
                           DUF1751   6 pypwtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvlltll 68 
                                        y+wt +t+ f    +++++ + + ++++g ++Er+ gs+++++ +lv + +++l  ++++++
  gi|336255484|ref|YP_004598591.1| 129 EYVWTWFTSIFAHGGLYHIVGNSIVIFFFGPLVERYVGSRDYAILFLVSGALAGLGQIAIQII 191
                                       49************************************************9999988887776 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.0   1.6e-05     0.058      10      37 ..       2      34 ..       1      70 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                                      SB-TTT--B--SSS--EE-TTT--EE-........S CS
                              FYVE 10 kkCeiCakkFsllrrrhhCrlCGkvvC........e 37
                                      +kC+ C k  ++    + Cr+CG  +C        +
  gi|336255484|ref|YP_004598591.1|  2 AKCDVCGKDENM---PYNCRHCGGTFCadhrlpenH 34
                                      589999998877...899*********555444444 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.3   8.9e-05      0.32       4      24 ..       3      25 ..       1      26 [. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.9e-05
                                      B-TTT-S..B-SEE-TTT--EES CS
                            zf-HIT  4 lCgvCgf..pakYkCpkCntryC 24
                                      +C vCg+     Y+C+ C+  +C
  gi|336255484|ref|YP_004598591.1|  3 KCDVCGKdeNMPYNCRHCGGTFC 25
                                      7******99999*******9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2541.83
//
Query:       gi|336255485|ref|YP_004598592.1|  [L=146]
Description: hypothetical protein Halxa_4108 [Halopiger xanaduensis SH-6]
Scores for 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:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 1283.62
//
Query:       gi|336255486|ref|YP_004598593.1|  [L=583]
Description: PHP domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-24   83.4   0.0    2.8e-23   81.8   0.0    1.9  1  DNA_pol_B_thumb  DNA polymerase beta thumb
    2.5e-22   79.0   5.4    2.2e-17   63.2   0.2    3.8  3  HHH_8            Helix-hairpin-helix domain
    3.6e-20   72.3   4.9    1.1e-13   51.6   0.2    3.2  3  HHH_5            Helix-hairpin-helix domain
    3.2e-08   33.0   1.3     0.0019   18.0   0.1    3.5  3  HHH              Helix-hairpin-helix motif
    4.2e-08   33.7   0.0    7.3e-08   32.9   0.0    1.5  1  PHP              PHP domain
    7.1e-08   32.4   2.8     0.0038   17.3   0.0    3.3  3  HHH_2            Helix-hairpin-helix motif
    1.7e-07   31.0   0.4    6.1e-06   26.0   0.0    3.2  4  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    3.4e-05   24.0   0.2    9.7e-05   22.6   0.0    1.8  1  DNA_pol_B_palm   DNA polymerase beta palm
    3.4e-05   24.0   0.1       0.16   12.3   0.0    3.6  3  HHH_3            Helix-hairpin-helix motif
     0.0018   18.5   0.5        4.1    7.9   0.1    3.3  3  IMS_HHH          IMS family HHH motif
      0.002   18.3   0.1      0.091   13.0   0.0    2.5  2  Cdd1             Pathogenicity locus
  ------ inclusion threshold ------
      0.015   15.8   1.0       0.33   11.6   0.1    2.9  2  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold
      0.018   15.4   2.5        3.2    8.2   0.0    4.1  5  Ribosomal_S13    Ribosomal protein S13/S18
       0.17   11.7   0.1       0.41   10.4   0.1    1.7  1  RNA_pol_A_CTD    Bacterial RNA polymerase, alpha chain C term


Domain annotation for each model (and alignments):
>> DNA_pol_B_thumb  DNA polymerase beta thumb
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   2.2e-26   2.8e-23       1      69 [.     255     326 ..     255     327 .. 0.90

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 2.2e-26
                                       HHHHHHS-HHHHHHHHHHHHCTTEEEETTEEE..........ETCCCEEEC-SSHHHHHHHCTS----GGGT CS
                   DNA_pol_B_thumb   1 allyfTGsktFnrdlRrlakkkglkLnssglrdek...gkaeddddgelvevetErdvfelLglpyipPeeR 69 
                                       al+yfTGsk++n++lR++a ++g+kLn++g +d+    ++ + ++ ge+v++etE+ ++e+Lgl++ipPe+R
  gi|336255486|ref|YP_004598593.1| 255 ALQYFTGSKDHNVSLRNYAIDRGMKLNEYGAFDVSnveDEVAGQRVGERVAGETEAGMYEALGLEWIPPELR 326
                                       89******************************833344566677778899*********************9 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.2   1.7e-20   2.2e-17       1      68 []       4      75 ..       4      75 .. 0.94
   2 !    7.2   0.1     0.005       6.5      44      63 ..      88     110 ..      77     115 .. 0.64
   3 !    9.3   0.1    0.0011       1.4      32      67 ..     116     149 ..     113     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.7e-20
                                      HHHHHHHHHHHHHHHHHCT--CCCHHHHHHHHCCCCC-SS-HHHH.TT....HCTTSTT--HHHHHHHHHHHH CS
                             HHH_8  1 NkeiadaLeeladllelkgedpfrvraYrrAaraiealpeeitsl.ee....eltklpgiGkkiaakieeile 68
                                      N+eia  +ee adlle   + +++ raYrrAa+ ++ +p++i+++ ++    ++++++g+G++ia+ki e++e
  gi|336255486|ref|YP_004598593.1|  4 NAEIAGRFEEFADLLEAD-DVEYKPRAYRRAAEHVRGHPRPIADYvDDgdreAIEDIDGVGEAIADKIVEYVE 75
                                      99****************.899***********************94447768899***************97 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.005
                                       HH.TT..HCTTSTT--HHHHHHH CS
                             HHH_8  44 sl.ee..eltklpgiGkkiaaki 63 
                                       +l  +  ++t++ g+G+k+a k+
  gi|336255486|ref|YP_004598593.1|  88 ELpIDiaDITRIEGVGPKTAGKL 110
                                       222123458***********997 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0011
                                       HCCCCC-SS-HHHHTTHCTTSTT--HHHHHHHHHHH CS
                             HHH_8  32 araiealpeeitsleeeltklpgiGkkiaakieeil 67 
                                       ++++++l+e+ +   +e+++++g+G+k+ + i e l
  gi|336255486|ref|YP_004598593.1| 116 IETLDDLEEAAEA--GEVQEVKGFGPKTEQNILENL 149
                                       5677777777776..359**************9866 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.3    0.0012       1.6      32      53 ..      51      72 ..      32      84 .. 0.83
   2 !   30.9   0.9   2.4e-10   3.1e-07       4      55 ..      56     114 ..      52     114 .. 0.81
   3 !   51.6   0.2   8.2e-17   1.1e-13       3      55 ..      95     149 ..      93     150 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0012
                                      S-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5 32 adveeLakipGiGkktAeriil 53
                                       d+e++ +i G+G+  A++i++
  gi|336255486|ref|YP_004598593.1| 51 GDREAIEDIDGVGEAIADKIVE 72
                                      5899999999999999999986 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 2.4e-10
                                       HHTSTT--HHHHHHHHTT...T.--SHHHHHHS...-HHHHHTSTTS-HHHHHHHHHHH CS
                             HHH_5   4 LlsvsGiGpktAlallsa...G.iesvedlaaa...dveeLakipGiGkktAeriilel 55 
                                       + +++G+G+++A ++++    G ie +e+l a+   d++++++i G+G+ktA ++  el
  gi|336255486|ref|YP_004598593.1|  56 IEDIDGVGEAIADKIVEYvetGeIEELEELRAElpiDIADITRIEGVGPKTAGKLYREL 114
                                       568***********8887333555556666665899******************99887 PP

  == domain 3  score: 51.6 bits;  conditional E-value: 8.2e-17
                                       HHHTSTT--HHHHHHHHTT.T--SHHHHHHS-H.HHHHTSTTS-HHHHHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsa.Giesvedlaaadv.eeLakipGiGkktAeriilel 55 
                                       ++++++G+GpktA +l++  Gie+++dl +a++  e+++++G+G+kt ++i++ l
  gi|336255486|ref|YP_004598593.1|  95 DITRIEGVGPKTAGKLYRElGIETLDDLEEAAEaGEVQEVKGFGPKTEQNILENL 149
                                       7899***************99*******9987626****************9976 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00014      0.18       9      30 .]      52      73 ..      50      73 .. 0.93
   2 !   18.0   0.1   1.5e-06    0.0019       3      27 ..      86     110 ..      84     112 .. 0.87
   3 ?   -0.9   0.0       1.4   1.8e+03      14      28 ..     132     146 ..     130     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                                      SHHHHHTSTT-SHHHHHHHHHH CS
                               HHH  9 sreeLlalPGVGpktAeaIlsy 30
                                      +re ++++ GVG++ A++I +y
  gi|336255486|ref|YP_004598593.1| 52 DREAIEDIDGVGEAIADKIVEY 73
                                      68999**************998 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.5e-06
                                       HHHHTSSHHHHHTSTT-SHHHHHHH CS
                               HHH   3 eglipasreeLlalPGVGpktAeaI 27 
                                        ++ p ++++++ ++GVGpktA++ 
  gi|336255486|ref|YP_004598593.1|  86 RAELPIDIADITRIEGVGPKTAGKL 110
                                       5678999***************986 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.4
                                       HTSTT-SHHHHHHHH CS
                               HHH  14 lalPGVGpktAeaIl 28 
                                       ++++G Gpkt + Il
  gi|336255486|ref|YP_004598593.1| 132 QEVKGFGPKTEQNIL 146
                                       789999***977666 PP

>> PHP  PHP 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   7.3e-08       1      74 [.     352     448 ..     352     545 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 5.7e-11
                                       EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT...........HHHHHHHHHHH.HTTTTSEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxx.xxxxxxxxxxxxx RF
                               PHP   1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlf...........gyvefykaakk.kykagikpiiGle 65 
                                       dlH+Hte s  + ++  ee+v+ a+++g++ +a+ Dh++             +++e ++++++   +++i +  G+e
  gi|336255486|ref|YP_004598593.1| 352 DLHSHTEWSDGNNTI--EEMVDGAAAMGYDYYAVADHAEGPgivggmglsdtEILEQVEQIREvDAASDIAVFAGIE 426
                                       79******9443555..***********************************88888888888667799******** PP

                                       ...................... CS
                                       xxxxxxxx.............x RF
                               PHP  66 ayvaddse.............k 74 
                                       a+v  ++e              
  gi|336255486|ref|YP_004598593.1| 427 ANVDAEGEidlsdevidaldvI 448
                                       ***9988755555555555550 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       9.5   1.2e+04      18      33 ..       6      21 ..       3      22 .. 0.79
   2 !   13.9   0.2   3.5e-05     0.045      33      61 ..      52      80 ..      46      82 .. 0.85
   3 !   17.3   0.0   2.9e-06    0.0038       8      54 ..      99     148 ..      97     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.5
                             HHH_2 18 lLakrFksldaLkkas 33
                                      ++a rF+++  L +a+
  gi|336255486|ref|YP_004598593.1|  6 EIAGRFEEFADLLEAD 21
                                      6789999999998875 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.5e-05
                             HHH_2 33 sleeLlevddiGeeiAqsivefFeneknr 61
                                      + e +  +d++Ge iA++ive+ e+ + +
  gi|336255486|ref|YP_004598593.1| 52 DREAIEDIDGVGEAIADKIVEYVETGEIE 80
                                      67999*****************9987766 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 2.9e-06
                             HHH_2   8 IrhVGektAklLakrFk..sldaLkka.sleeLlevddiGeeiAqsivef 54 
                                       I  VG ktA +L ++ +  +ld L++a ++ e +ev++ G+++ q+i e 
  gi|336255486|ref|YP_004598593.1|  99 IEGVGPKTAGKLYRELGieTLDDLEEAaEAGEVQEVKGFGPKTEQNILEN 148
                                       789************9888*****9862567*************999875 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 ?    1.2   0.0      0.27   3.4e+02       6      19 ..      59      72 ..      55      91 .. 0.68
   2 !   26.0   0.0   4.8e-09   6.1e-06       4      30 ..      97     124 ..      95     141 .. 0.87
   3 ?   -3.4   0.0         7     9e+03      20      27 ..     217     224 ..     216     228 .. 0.90
   4 ?   -2.9   0.0       5.1   6.6e+03      14      30 ..     559     571 ..     554     575 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.27
                   DNA_pol_lambd_f  6 vyGVGpktAkkwya 19
                                      + GVG ++A k ++
  gi|336255486|ref|YP_004598593.1| 59 IDGVGEAIADKIVE 72
                                      77*******99875 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 4.8e-09
                   DNA_pol_lambd_f   4 tkvyGVGpktAkkwyak.Girtledlra 30 
                                       t++ GVGpktA k+y++ Gi tl+dl +
  gi|336255486|ref|YP_004598593.1|  97 TRIEGVGPKTAGKLYRElGIETLDDLEE 124
                                       7899**********************98 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 7
                   DNA_pol_lambd_f  20 kGirtled 27 
                                       +G+ +++d
  gi|336255486|ref|YP_004598593.1| 217 RGWDSVDD 224
                                       79****99 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 5.1
                   DNA_pol_lambd_f  14 AkkwyakGirtledlra 30 
                                       A    ++G+   +d+ +
  gi|336255486|ref|YP_004598593.1| 559 A----RRGWAEADDVIN 571
                                       4....467777777765 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   7.6e-08   9.7e-05       6      54 ..     163     211 ..     162     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.6e-08
                                       HHHHHHHHHHHHHHHH-TT-EEEE-HHHHTT-SEESSEEEEEEBTTBST CS
                    DNA_pol_B_palm   6 EvealealvkkaakeldpevevivcGSYRRgaessGDvDvlitkkdaks 54 
                                       E++ l++ v + +++++   ++ v+GS RR +e+ GDvDvl+  +d+++
  gi|336255486|ref|YP_004598593.1| 163 EARPLADDVLAFLESVEAVERCEVAGSIRRWQETIGDVDVLVATEDGEA 211
                                       66677888889999999999***********************999876 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       9.7   1.2e+04      38      49 ..       9      20 ..       7      37 .. 0.78
   2 !   12.3   0.0   0.00012      0.16      15      47 ..      55      86 ..      52      88 .. 0.88
   3 ?    5.9   0.0     0.012        15      14      60 ..      94     145 ..      90     150 .. 0.59

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.7
                             HHH_3 38 GpfksreeLlkv 49
                                      G+f+ + +Ll+ 
  gi|336255486|ref|YP_004598593.1|  9 GRFEEFADLLEA 20
                                      789999999885 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00012
                             HHH_3 15 eLqklpGlgpklAknIvayReknGpfksreeLl 47
                                       ++ + G+g+++A++Iv+y  + G ++ +eeL 
  gi|336255486|ref|YP_004598593.1| 55 AIEDIDGVGEAIADKIVEYV-ETGEIEELEELR 86
                                      567899**************.889999999995 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.012
                             HHH_3  14 eeLqklpGlgpklAknI.....vayReknGpfksreeLlkvkglgpktfeql 60 
                                       +++++++G+gpk+A ++     ++  +     +   e ++vkg+gpkt + +
  gi|336255486|ref|YP_004598593.1|  94 ADITRIEGVGPKTAGKLyrelgIETLDDLEEAAEAGEVQEVKGFGPKTEQNI 145
                                       6777788888888877722222333333444444456677888888876665 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       5.7   7.4e+03      13      26 ..      56      69 ..      55      72 .. 0.82
   2 !    7.9   0.1    0.0032       4.1      12      32 .]      95     116 ..      91     116 .. 0.84
   3 !    7.1   0.0    0.0061       7.7      13      30 ..     131     149 ..     130     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.7
                           IMS_HHH 13 itkipGiGgklgek 26
                                      i +i G+G   ++k
  gi|336255486|ref|YP_004598593.1| 56 IEDIDGVGEAIADK 69
                                      67888***999998 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0032
                           IMS_HHH  12 pitkipGiGgklgekLek.lGi 32 
                                       +it i G+G+k++ kL   lGi
  gi|336255486|ref|YP_004598593.1|  95 DITRIEGVGPKTAGKLYReLGI 116
                                       799999*********7655776 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0061
                           IMS_HHH  13 itkipGiGgklgek.Lekl 30 
                                       + ++ G+G+k+++  Le+l
  gi|336255486|ref|YP_004598593.1| 131 VQEVKGFGPKTEQNiLENL 149
                                       7899*********999987 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.099   1.3e+02       7      35 ..      55      84 ..      50      95 .. 0.68
   2 !   13.0   0.0   7.1e-05     0.091       5      36 ..      93     125 ..      90     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.099
                              Cdd1  7 elqdiPniGkalaedlv.elGirsveelkg 35
                                      +++di ++G+a+a+++v  +   ++eel++
  gi|336255486|ref|YP_004598593.1| 55 AIEDIDGVGEAIADKIVeYVETGEIEELEE 84
                                      67899*********9984355444444443 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.1e-05
                              Cdd1   5 lkelqdiPniGkalaedlv.elGirsveelkge 36 
                                       ++++++i ++G+++a +l+ elGi+++++l++ 
  gi|336255486|ref|YP_004598593.1|  93 IADITRIEGVGPKTAGKLYrELGIETLDDLEEA 125
                                       67899************9879*********875 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 ?    1.3   0.1      0.42   5.4e+02      19      43 ..      55      81 ..      50      92 .. 0.73
   2 ?   11.6   0.1   0.00026      0.33      19      67 ..      95     152 ..      91     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.42
                        5_3_exonuc 19 nipGvpgiGektAakLlkey..gslee 43
                                       i+ + g+Ge  A k+++ +  g++ee
  gi|336255486|ref|YP_004598593.1| 55 AIEDIDGVGEAIADKIVEYVetGEIEE 81
                                      68999**********997541144444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00026
                        5_3_exonuc  19 nipGvpgiGektAakLlkeyg..sleeilenld..elke.....kklkekLeenkeea 67 
                                       +i  ++g+G+ktA kL +e g  +l+++ e+++  e++e     +k+++++ en e a
  gi|336255486|ref|YP_004598593.1|  95 DITRIEGVGPKTAGKLYRELGieTLDDLEEAAEagEVQEvkgfgPKTEQNILENLEFA 152
                                       58889***********999743388888887754444444446666777777776654 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.061        78      16      49 ..      55      88 ..      50      97 .. 0.83
   2 ?    8.2   0.0    0.0025       3.2      17      53 ..      96     133 ..      85     153 .. 0.80
   3 ?    0.2   0.0      0.74   9.5e+02      18      44 ..     132     158 ..     128     164 .. 0.83
   4 ?   -1.0   0.0       1.8   2.2e+03      24      60 ..     261     297 ..     243     304 .. 0.81
   5 ?   -1.6   0.1       2.5   3.2e+03      37      61 ..     425     452 ..     410     469 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.061
                     Ribosomal_S13 16 altaikGiGrrkakiilkkadvdedkrigeltee 49
                                      a+  i+G+G+  a +i++ ++  e   ++el  e
  gi|336255486|ref|YP_004598593.1| 55 AIEDIDGVGEAIADKIVEYVETGEIEELEELRAE 88
                                      8999*************99998888888887665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0025
                     Ribosomal_S13  17 ltaikGiGrrkakiilkkadvdedkrigeltee.eiek 53 
                                       +t i+G+G ++a ++ +++++++   ++e +e  e+++
  gi|336255486|ref|YP_004598593.1|  96 ITRIEGVGPKTAGKLYRELGIETLDDLEEAAEAgEVQE 133
                                       89*******************99888777765325555 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.74
                     Ribosomal_S13  18 taikGiGrrkakiilkkadvdedkrig 44 
                                       +++kG G ++ + il++++  +++  +
  gi|336255486|ref|YP_004598593.1| 132 QEVKGFGPKTEQNILENLEFAREVGQR 158
                                       789**************9998876555 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.8
                     Ribosomal_S13  24 Grrkakiilkkadvdedkrigelteeeiekieeiven 60 
                                       G +  ++ l++  +d+ ++++e    +++++e++v+ 
  gi|336255486|ref|YP_004598593.1| 261 GSKDHNVSLRNYAIDRGMKLNEYGAFDVSNVEDEVAG 297
                                       5677777889999999999999999999999999976 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 2.5
                     Ribosomal_S13  37 vdedkrig...elteeeiekieeivenk 61 
                                       ++ ++ ++   +l++e i+ +  iv+ +
  gi|336255486|ref|YP_004598593.1| 425 IEANVDAEgeiDLSDEVIDALDVIVAST 452
                                       4444444322289999999999888873 PP

>> RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00032      0.41      30      66 ..     113     150 ..     111     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                                       HTT--BHHHHHHS-HH.HHTTSSS-SSHHHHHHHHHHH CS
                     RNA_pol_A_CTD  30 ragiktvgeLvklsee.eLlkikNlGkKSleEIkekLe 66 
                                       + gi+t+++L +  e+ e +++k +G K+ + I e Le
  gi|336255486|ref|YP_004598593.1| 113 ELGIETLDDLEEAAEAgEVQEVKGFGPKTEQNILENLE 150
                                       579*******99877549****************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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 0.20s 00:00:00.73 Elapsed: 00:00:00.36
# Mc/sec: 4887.86
//
Query:       gi|336255487|ref|YP_004598594.1|  [L=153]
Description: hypothetical protein Halxa_4110 [Halopiger xanaduensis SH-6]
Scores for 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-37  128.1   0.1    2.9e-37  128.0   0.1    1.0  1  Mut7-C          Mut7-C RNAse domain
     0.0058   16.3   0.0     0.0096   15.7   0.0    1.3  1  DUF5615         Domain of unknown function (DUF5615)
     0.0089   16.4   0.9      0.015   15.7   0.9    1.4  1  DUF4379         Probable Zinc-ribbon domain
  ------ inclusion threshold ------
      0.012   15.6   0.2      0.028   14.5   0.2    1.5  1  DZR             Double zinc ribbon
       0.11   12.4   0.3         13    5.7   0.0    2.4  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   0.1   8.2e-41   2.9e-37       1     146 []       1     144 [.       1     144 [. 0.97

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 8.2e-41
                            Mut7-C   1 krfllDamlgklakyLRllGydalyasdv...edeellalaakekrillTrdreLlkraklkkgvlltsrdveeqlr 74 
                                       +rfllD+m+g l  yLR++ +d++ya d+   +d++ll+  ++e+r+ +Trd +L++ra+++  +ll+srdv++ql+
  gi|336255487|ref|YP_004598594.1|   1 MRFLLDVMCGGLVSYLRMCNHDTVYAGDRgleADAALLTVVREEDRMPVTRDVQLASRAEDA--MLLESRDVADQLA 75 
                                       69*************************999999***************************99..************* PP

                            Mut7-C  75 eviarlglklslkpelsrCvaCngeleevekeevkervpekvyeeade.ftrCekCrkvfWkGshwerveell 146
                                       e+ a+ g++lsl+++ + C++Cng+le +e++      pe++++ a++ +++C++C++ fW+Gshw+rv+e+l
  gi|336255487|ref|YP_004598594.1|  76 EL-AATGVDLSLADQPRFCGRCNGRLEPLERAAS---TPEYAPDPAETaVWTCRSCGQHFWRGSHWDRVAETL 144
                                       **.8999***********************9988...9*******9999********************9975 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.7e-06    0.0096       1      55 [.       1      52 [.       1      58 [. 0.96

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.7e-06
                           DUF5615  1 mklllDenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkD 55
                                      m++llD  +   lv  lr  +hd+++  + gle   D + l + +eedr+ vT+D
  gi|336255487|ref|YP_004598594.1|  1 MRFLLDVMCG-GLVSYLRMCNHDTVYAGDRGLE--ADAALLTVVREEDRMPVTRD 52
                                      9*******99.99******************99..9******************9 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.9   4.2e-06     0.015      20      48 ..     112     141 ..      93     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.2e-06
                           DUF4379  20 vtpgskkkvwWkCakCg.heWeasvsnrtk 48 
                                        +p+  + + W+C+ Cg h W+ s  +r++
  gi|336255487|ref|YP_004598594.1| 112 YAPDPAETAVWTCRSCGqHFWRGSHWDRVA 141
                                       566677899********9******999985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   7.7e-06     0.028       8      37 ..      86     130 ..      83     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.7e-06
                               DZR   8 lppdarfCseCgtklkavaa...............edrCpsCgek 37 
                                       l ++ rfC++C+ +l++ ++                 +C sCg+ 
  gi|336255487|ref|YP_004598594.1|  86 LADQPRFCGRCNGRLEPLERaastpeyapdpaetaVWTCRSCGQH 130
                                       56899**********98777999*********99999*****985 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 ?    4.3   0.0     0.011        38       2      13 ..      91     102 ..      91     108 .. 0.86
   2 ?    5.7   0.0    0.0037        13      16      30 ..     120     130 ..     115     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.011
                                       EBESTTTSBEEE CS
                    RNA_POL_M_15KD   2 kFCpkCgNlLlp 13 
                                       +FC  C+  L+p
  gi|336255487|ref|YP_004598594.1|  91 RFCGRCNGRLEP 102
                                       7******88887 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0037
                                       CSCCCEEEESSSS-E CS
                    RNA_POL_M_15KD  16 dkegknfeCrqCgYe 30 
                                       ++++    Cr+Cg +
  gi|336255487|ref|YP_004598594.1| 120 AVWT----CRSCGQH 130
                                       5566....****966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 1359.37
//
Query:       gi|336255488|ref|YP_004598595.1|  [L=57]
Description: hypothetical protein Halxa_4111 [Halopiger xanaduensis SH-6]
Scores for 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:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 507.25
//
Query:       gi|336255489|ref|YP_004598596.1|  [L=265]
Description: metal-dependent phosphoesterase (PHP family)-like protein [Halopiger xanaduensis SH-6]
Scores for 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-16   58.9   0.1    6.1e-16   57.9   0.1    1.5  1  PHP_C           PHP-associated
  ------ inclusion threshold ------
       0.21   11.7   0.0       0.36   10.9   0.0    1.3  1  CTP-dep_RFKase  Domain of unknown function DUF120


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 !   57.9   0.1   6.8e-20   6.1e-16       1      52 [.     151     202 ..     151     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 6.8e-20
                             PHP_C   1 geaNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleair 52 
                                       +++NrrA ++Ae++++p + +S+AH +++VG a Tef++ ++++++l++a+ 
  gi|336255489|ref|YP_004598596.1| 151 PHHNRRAGKLAEQFDYPPFTSSYAHLPRTVGVAHTEFDAAVESEADLCRALE 202
                                       689***********************************************96 PP

>> 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 ?   10.9   0.0   4.1e-05      0.36      11      65 ..      98     155 ..      92     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.1e-05
                                       HHCSHHHHHHHH..HHHSS---SS-EEEEESCC.GHHHHCHHHHS--EEE--EEETTE CS
                    CTP-dep_RFKase  11 yvslegykeqfe..eklgfepypGTLNvkldee.slelrkaleklkgieiegfedeer 65 
                                       ++ le  + +fe  + + + p+pG LNv+l+e+  ++ r+ +++++ ++ +   +++r
  gi|336255489|ref|YP_004598596.1|  98 FIPLEAAMAEFErqDAVVLAPHPGFLNVSLSESdLQQYRDVIDAVEIFNPKHLPHHNR 155
                                       55666666666511568899************97777888888887776666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2150.20
//
Query:       gi|336255490|ref|YP_004598597.1|  [L=94]
Description: hypothetical protein Halxa_4113 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      0.003   17.9   0.0        3.2    8.4   0.0    2.3  2  zf-C2H2       Zinc finger, C2H2 type
  ------ inclusion threshold ------
        0.1   13.5   0.1         16    6.7   0.0    2.3  2  zf-C2H2_4     C2H2-type zinc finger
       0.12   12.5   0.0       0.14   12.3   0.0    1.1  1  RepB_primase  RepB DNA-primase from phage plasmid


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00095       5.7       2      23 .]       4      28 ..       3      28 .. 0.93
   2 !    8.4   0.0   0.00053       3.2       2      23 .]      32      54 ..      32      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00095
                                      EET..TTTEEESSHHHHHHHHHC.C CS
                           zf-C2H2  2 kCp..dCgksFkrksnLkrHirt.H 23
                                      +C+  +Cg +F + ++ + H+ t H
  gi|336255490|ref|YP_004598597.1|  4 ECGisGCGSVFADVESAVIHQATeH 28
                                      69999****************9999 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00053
                                      EETTTTEEESSHHHHHHHHHC.C CS
                           zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                                      +C++Cg + ++ ++  rH  t H
  gi|336255490|ref|YP_004598597.1| 32 ECKVCGTVVPDGYLAIRHAFTeH 54
                                      5*****************98888 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 ?    4.9   0.0      0.01        60       2      24 .]       4      28 ..       3      28 .. 0.83
   2 ?    6.7   0.0    0.0027        16       2      24 .]      32      54 ..      31      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.01
                         zf-C2H2_4  2 kCpi..CgksFsskkaLlrHlkthH 24
                                      +C i  Cg +F + ++   H +t H
  gi|336255490|ref|YP_004598597.1|  4 ECGIsgCGSVFADVESAVIHQATEH 28
                                      688888*******999666988887 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0027
                         zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                                      +C++Cg++ ++ +   rH  t H
  gi|336255490|ref|YP_004598597.1| 32 ECKVCGTVVPDGYLAIRHAFTEH 54
                                      7******9998777788877776 PP

>> RepB_primase  RepB DNA-primase from phage plasmid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.3e-05      0.14     136     180 ..      41      85 ..      32      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
                      RepB_primase 136 P.GfnnrKpkkaredgkqplvrllaadrserpapeeilqriaveve 180
                                       P G+  ++ + + e+++ ++vr + a+ ++ ++ ee+l++i+ + +
  gi|336255490|ref|YP_004598597.1|  41 PdGYLAIRHAFT-EHSRAEYVRAYGANSEDVRKREELLEEIEEVAD 85 
                                       668888886667.****************************66554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); 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):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 762.53
//
Query:       gi|336255491|ref|YP_004598598.1|  [L=145]
Description: NusG antitermination factor [Halopiger xanaduensis SH-6]
Scores for complete 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   82.9   0.1    1.8e-23   82.3   0.1    1.3  1  Spt5-NGN         Early transcription elongation factor of RNA
    6.6e-08   32.3   0.8    1.3e-07   31.3   0.3    1.8  2  KOW              KOW motif
  ------ inclusion threshold ------
      0.097   12.6   0.2       0.19   11.7   0.2    1.5  1  Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal dom
       0.13   12.2   0.1       0.31   11.1   0.1    1.6  1  DbpA             DbpA RNA binding domain


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 !   82.3   0.1   3.9e-27   1.8e-23       2      84 .]       3      78 ..       2      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 3.9e-27
                          Spt5-NGN  2 iwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikEv 80
                                      i+avk+ta+qEr+va+++ ++       e+ eI++++apd+l++y++vEAd +a+++r+le+ip++r++v+g+++i+Ev
  gi|336255491|ref|YP_004598598.1|  3 IYAVKTTASQERTVADMIINR-------EESEIHAALAPDSLTSYVMVEADGNAVLNRVLEDIPHARSIVPGESDISEV 74
                                      9*****************555.......5669*********************************************** PP

                          Spt5-NGN 81 edll 84
                                      e++l
  gi|336255491|ref|YP_004598598.1| 75 EHFL 78
                                      **98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.3   2.9e-11   1.3e-07       1      32 []      89     120 ..      89     120 .. 0.97
   2 ?   -2.2   0.0         1   4.6e+03       1       8 [.     133     140 ..     133     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.9e-11
                                       TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW   1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32 
                                       +Gd+V+ ++Gp+kG++++V ++d+ k+ V+v+
  gi|336255491|ref|YP_004598598.1|  89 EGDIVELIAGPFKGEKAQVQRIDEGKDQVTVE 120
                                       59****************************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                                       TTSEEEES CS
                               KOW   1 pGdhVkVv 8  
                                       +Gd  +V+
  gi|336255491|ref|YP_004598598.1| 133 RGDQIRVL 140
                                       69999997 PP

>> Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   4.3e-05      0.19      26      51 .]     113     139 ..     109     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                                       ESSEEEEEEESSS.TEEEEETTEEEEE CS
                   Glyco_hydro_65C  26 tpeevtvtlesge.pltievyGeevtL 51 
                                       ++++vtv+l +++ p++++v+G ++++
  gi|336255491|ref|YP_004598598.1| 113 GKDQVTVELYEATvPIPVTVRGDQIRV 139
                                       689*******9777********99875 PP

>> DbpA  DbpA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   6.9e-05      0.31      10      48 ..      85     123 ..      83     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.9e-05
                                       GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-EEEEE-T CS
                              DbpA  10 dklrpgdivgaiakeaglsgkdIGkIdildkfSfvevpk 48 
                                       +++  gdiv++ia+  + ++ ++++Id  ++  +ve+ +
  gi|336255491|ref|YP_004598598.1|  85 EGIAEGDIVELIAGPFKGEKAQVQRIDEGKDQVTVELYE 123
                                       58999**********************999999888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1160.50
//
Query:       gi|336255492|ref|YP_004598599.1|  [L=59]
Description: Preprotein translocase subunit secE [Halopiger xanaduensis SH-6]
Scores for 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-05   22.9   0.3    6.8e-05   22.7   0.3    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 !   22.7   0.3   3.8e-09   6.8e-05       7      47 ..      10      50 ..       7      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.8e-09
                                      HHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SecE  7 vkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvf 47
                                       ++ lk  t Pt +E+ + +++  ++++++gl++f++  ++
  gi|336255492|ref|YP_004598599.1| 10 YVRVLKMATTPTTEEFSQVAKIAGAGILFVGLIGFVIGAIM 50
                                      57899*******************************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 490.35
//
Query:       gi|336255493|ref|YP_004598600.1|  [L=74]
Description: hypothetical protein Halxa_4116 [Halopiger xanaduensis SH-6]
Scores for 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  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 592.74
//
Query:       gi|336255494|ref|YP_004598601.1|  [L=318]
Description: G6PDH family F420-dependent oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-52  177.9   1.6    4.6e-52  177.4   1.6    1.1  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.4   1.6   2.6e-56   4.6e-52      22     314 .]      15     292 ..       4     292 .. 0.90

  Alignments for each domain:
  == domain 1  score: 177.4 bits;  conditional E-value: 2.6e-56
                    Bac_luciferase  22 lrylvelaraaEelGfdavwvaehhggpgga....ldaftllaalaaaTerirlgtavtply.trhPavlAqqaatL 93 
                                       +++lve+ar+a++  fd++++++h++++ ++    +  + +l+ +++a + + lgta+t++  + hPa++Aq+aat 
  gi|336255494|ref|YP_004598601.1|  15 PNDLVEYARLADQSAFDFALISDHYHPWLSSqgesPLVWNVLGGISQAVDDLPLGTATTCPIiRVHPAIVAQAAATA 91 
                                       689***************************9**88778889******************9999************** PP

                    Bac_luciferase  94 dhlsgGRfglglgtggpaveerrfGv...dhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpi 167
                                         +++  f+lglgtg+  +e+   G+   +h+ r+++l+E+ve++r+lw+ge+ +++Ge+++v++a+l   p+++ +
  gi|336255494|ref|YP_004598601.1|  92 ATMAPNGFSLGLGTGEKLNEHVT-GQrwpEHEVRLEMLEEAVEIVRALWEGETTSYHGEYYTVENARLYTLPDET-P 166
                                       ********************666.777**********************99999*********888888888777.9 PP

                    Bac_luciferase 168 PvyvaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearal 244
                                       P+ +aa +p+++++a++++dgl+ +  +    ++lie ++a     g+   d   +  + v++a++e+eA ++a + 
  gi|336255494|ref|YP_004598601.1| 167 PIPIAADGPKTARFAGEFGDGLIAVRPD----EDLIEAFEA---GGGE---DKPRYGEVGVCYAEDEAEAIEQAYEN 233
                                       9**********************99833....346666675...4445...4445679999************9555 PP

                    Bac_luciferase 245 iagldfyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvG.tpeqvaerlaayaeagvde 314
                                       +               + +++  +e  +  ++++a +av+++++a ++++G +p++++e +++y++ag+d+
  gi|336255494|ref|YP_004598601.1| 234 W------------TIEGLPGDLMWELPTTAHFEQATEAVSEDDIADLLTCGsDPDEHIETIREYVDAGFDH 292
                                       5............5688889999****************************99****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2394.64
//
Query:       gi|336255495|ref|YP_004598602.1|  [L=388]
Description: peptidase S1 and S6 chymotrypsin/Hap [Halopiger xanaduensis SH-6]
Scores for complete 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-32  113.7   1.8    2.9e-32  112.6   1.8    1.6  1  Trypsin_2      Trypsin-like peptidase domain
    1.7e-18   66.7   0.1    3.8e-18   65.6   0.1    1.6  1  PDZ_2          PDZ domain
    8.3e-15   55.2   0.2    1.4e-14   54.4   0.2    1.3  1  Trypsin        Trypsin
    7.9e-06   25.6   2.2    7.4e-05   22.5   2.2    2.4  1  PDZ_6          PDZ domain
    4.6e-05   23.7   0.1    0.00015   22.0   0.1    1.9  1  PDZ            PDZ domain
    0.00044   19.1   0.4    0.00044   19.1   0.4    1.5  2  Peptidase_S46  Peptidase S46
     0.0008   19.3   0.2     0.0052   16.7   0.1    2.3  2  Tricorn_PDZ    Tricorn protease PDZ domain
  ------ inclusion threshold ------
      0.088   12.6   0.2       0.16   11.8   0.2    1.4  1  Peptidase_S7   Peptidase S7, Flavivirus NS3 serine protease
        0.3   11.0   3.8       0.69    9.8   3.8    1.7  1  TAT_signal     TAT (twin-arginine translocation) pathway sign


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 !  112.6   1.8   1.5e-35   2.9e-32       1     150 []      87     225 ..      87     225 .. 0.97

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 1.5e-35
                         Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgp 77 
                                       GsGf+v++++ i+Tn+Hvv++a+++ +       e+ +++ ++ +a++v++dp +D+A+l v ++ +++ +pl l +
  gi|336255495|ref|YP_004598602.1|  87 GSGFVVDDQY-IVTNNHVVQGATEGGI-------EIQFNNQEWATASIVGTDPYSDIAVLSV-ENMPDSAEPLSLVE 154
                                       9*********.****************.......99****************888*******.************** PP

                         Trypsin_2  78 sealkggepvyvvGyplggeksgsvssGivsgvve.sesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                       se++ g+ +v ++G+plg +   svs+Givsg+++  +s  +++ +  +qtda+++pG+SGGpl++ +G+vvG+
  gi|336255495|ref|YP_004598602.1| 155 SEPAIGQ-EVLAIGNPLGLDA--SVSQGIVSGTNRvLPSPVGNSIPATIQTDAPINPGNSGGPLVNLEGEVVGV 225
                                       9988777.*************..9***********99999999999999************************8 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.1   1.9e-21   3.8e-18       2      82 .]     260     358 ..     259     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.9e-21
                                       ...XX------............-EEEEEE-TTSGGGGT.--T........T-EEEEETTB--SSHHHHHHHHH.TS CS
                             PDZ_2   2 ylGvsvsdeed..........tggvlvvsVkeggPaakaglka........gDvilkvdgkkvksledlislll.kk 59 
                                       y+Gv v+++ +          ++gvlv++V +++Pa++a l++        gDvi+++dg++v+++++l s+l+ ++
  gi|336255495|ref|YP_004598602.1| 260 YMGVGVVPVGPeiaetvgleeATGVLVAQVVPNSPADGA-LQPasagqpgsGDVIVAIDGQEVTTQAQLLSYLAlET 335
                                       7899999999999999999999*****************.9999********************************* PP

                                       -TT-EEEEEEEETTEEEEEEEE- CS
                             PDZ_2  60 kpGdtVkltvlRdgkkktvevkl 82 
                                       +pGdt++l+v Rdg+++tve++l
  gi|336255495|ref|YP_004598602.1| 336 SPGDTIELEVVRDGERETVELEL 358
                                       ********************987 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.2   7.1e-18   1.4e-14      27     203 ..      87     233 ..      71     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 7.1e-18
                                       EEEEEEETTEEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBSS CS
                           Trypsin  27 CgGslisenwvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgdt 103
                                        +G+++++++++T++H+v++  + +       ++ + ++ q+  ++ ++     +p     Dia+l +++     d+
  gi|336255495|ref|YP_004598602.1|  87 GSGFVVDDQYIVTNNHVVQG--ATEG-----GIEIQFNN-QEWATASIVG---TDPYS---DIAVLSVENM---PDS 146
                                       57*****************9..3333.....34555553.4556666444...66666...*********9...*** PP

                                       BHCCBBCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBCTTTT CS
                           Trypsin 104 vrpiclpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsretcksaykgkvtenmlcagakeggkdacqGD 180
                                        +p++l ++++  ++g+++l++G +   + + s+ + +++ +v+++   +s       + +++++a      +++G+
  gi|336255495|ref|YP_004598602.1| 147 AEPLSLVESEP--AIGQEVLAIGNPLGLDASVSQGIVSGTNRVLPSPVGNS------IPATIQTDA-----PINPGN 210
                                       ********555..9**99999999997777777888888888888877777......4888*****.....7***** PP

                                       TTSEEEETTTEEEEEEEEESSSS CS
                           Trypsin 181 SGGPlvcsdgelvGivswgkgca 203
                                       SGGPlv+ +ge+vG+v++g + +
  gi|336255495|ref|YP_004598602.1| 211 SGGPLVNLEGEVVGVVFAGASQT 233
                                       ******************95554 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   2.2   3.7e-08   7.4e-05       2      56 .]     286     347 ..     285     347 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.7e-08
                             PDZ_6   2 VtaVdpgsPAdrAGlrv........GDiilsvNGqpveglsladvaallr..gsagesvvlvvrr 56 
                                       V +V+p+sPAd A l++        GD+i++++Gq+v  ++ a++ ++l+  +s+g  ++l+v r
  gi|336255495|ref|YP_004598602.1| 286 VAQVVPNSPADGA-LQPasagqpgsGDVIVAIDGQEV--TTQAQLLSYLAleTSPGDTIELEVVR 347
                                       899********54.99888888888************..********998878999999999987 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   7.7e-08   0.00015       8      81 ..     257     345 ..     250     346 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.7e-08
                                       TTSESSEEEEEETTSS.......SSSSEEEEEECTTSHHHHHTSST........TEEEEEETTEETTTSHHHHHHHH CS
                               PDZ   8 grgglGfslkggsdqr.......gdkgifvsevlpggaaeadglkv........GDkIlsvNgvdvenvsheeavqa 69 
                                       +++++G+ ++    +        +++g+ v++v+p+++a+ + l++        GD+I++++g+ v++ +++   +a
  gi|336255495|ref|YP_004598602.1| 257 EHSYMGVGVVPVGPEIaetvgleEATGVLVAQVVPNSPADGA-LQPasagqpgsGDVIVAIDGQEVTTQAQLLSYLA 332
                                       556666666666665566777789****************99.99777777777**************999999999 PP

                                       HHTTTS.EEEEEE CS
                               PDZ  70 ikgskg.kvtLti 81 
                                       ++ s g ++ L++
  gi|336255495|ref|YP_004598602.1| 333 LETSPGdTIELEV 345
                                       9888888888887 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       0.7   1.4e+03      47      70 ..      84     107 ..      63     109 .. 0.78
   2 !   19.1   0.4   2.2e-07   0.00044     620     660 ..     195     235 ..     191     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.7
                                       TTEE-EE-STT-EEEE-HHHHHHH CS
                     Peptidase_S46  47 ggCtasfVSpeGLvlTNHHCayga 70 
                                       gg  + fV ++  ++TN H+++ga
  gi|336255495|ref|YP_004598602.1|  84 GGLGSGFVVDDQYIVTNNHVVQGA 107
                                       4445568889999******99876 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.2e-07
                                       B-EEEEEES----TT-TT-EEE-TTS-EEEEEEEE-GGGTT CS
                     Peptidase_S46 620 svpvnflstnDitGGNSGSPvlngkgelvGlaFDgniesls 660
                                       s+p +  +++ i  GNSG P++n +ge+vG++F g  ++++
  gi|336255495|ref|YP_004598602.1| 195 SIPATIQTDAPINPGNSGGPLVNLEGEVVGVVFAGASQTIG 235
                                       678888999999**********************9988876 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.84   1.7e+03       4      26 ..     111     133 ..     110     136 .. 0.89
   2 !   16.7   0.1   2.6e-06    0.0052      42      81 ..     309     350 ..     302     356 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.84
                                       SEEEEEETTEEEEEEE-BS-TTS CS
                       Tricorn_PDZ   4 GadleldkgayriakilpGdswd 26 
                                       G++++++++ +  a i+  d+++
  gi|336255495|ref|YP_004598602.1| 111 GIEIQFNNQEWATASIVGTDPYS 133
                                       8999************9999876 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.6e-06
                                       TT-EEEEETTEE-BTTB-HHHHHH..TTTTSEEEEEEE-STT CS
                       Tricorn_PDZ  42 eGdlilavdgepvskekgiaelLv..gkagkeveLtvkrkdg 81 
                                        Gd+i+a+dg++v++++++ ++L+     g+++eL+v r+++
  gi|336255495|ref|YP_004598602.1| 309 SGDVIVAIDGQEVTTQAQLLSYLAleTSPGDTIELEVVRDGE 350
                                       7*****************99987621455799***9998553 PP

>> Peptidase_S7  Peptidase S7, Flavivirus NS3 serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   8.1e-05      0.16      90     120 ..     203     233 ..     160     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.1e-05
                                       XXXXXTT-TTSEEE-TTSXEEEECEEEEEXT CS
                      Peptidase_S7  90 dlnlssGsSGSlvlnqnkqivgiYfatvevd 120
                                       d   ++G SG +++n ++++vg+ fa+ + +
  gi|336255495|ref|YP_004598602.1| 203 DAPINPGNSGGPLVNLEGEVVGVVFAGASQT 233
                                       555789********************98876 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.8   0.00035      0.69       2      25 ..       6      30 ..       5      31 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00035
                        TAT_signal  2 lSRRdFLKgsAAaa.AAaalggcaa 25
                                      +SRR +L++++Aa   ++++++ aa
  gi|336255495|ref|YP_004598602.1|  6 VSRRRLLRAAGAASiLGVGTASTAA 30
                                      8*********999977777887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3048.76
//
Query:       gi|336255496|ref|YP_004598603.1|  [L=412]
Description: Galactonate dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-57  192.3   0.8    1.1e-56  191.8   0.8    1.2  1  MR_MLE_C      Enolase C-terminal domain-like
      3e-14   53.2   0.0    6.1e-14   52.2   0.0    1.5  1  MR_MLE_N      Mandelate racemase / muconate lactonizing enzym
  ------ inclusion threshold ------
      0.067   13.0   1.6      0.098   12.4   0.4    1.8  3  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> 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 !  191.8   0.8   1.9e-60   1.1e-56       2     218 ..     168     396 ..     167     398 .. 0.94

  Alignments for each domain:
  == domain 1  score: 191.8 bits;  conditional E-value: 1.9e-60
                                       HHHHHHHHHHHHT-SEEEEETSSS...............HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHH CS
                          MR_MLE_C   2 laeearelvaeqgfravKlkvggd...............dvaedvervravreavgpgddvdlmvDanqawdlatAi 63 
                                        a+ea++ v+e g++a+K+++  +               ++++ +e v++v e+v  gd++d+++D+++ ++   A 
  gi|336255496|ref|YP_004598603.1| 168 CADEAERVVEELGYDALKFDLDVPsghekdranrhlrepEIEHKAEIVEKVTERV--GDRADVAFDCHWTFSGGSAK 242
                                       5799*999************99999******************************..5577**************** PP

                                       HHHHHHGGGTESEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHH CS
                          MR_MLE_C  64 rvareleeldllwlEEPvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitear 139
                                       r+a++lee+d++wlE+Pvppe+  +  +e++ ++ ++pi +gE++y+ ++ r+l+e++a+div pd+ +vgG+ e+r
  gi|336255496|ref|YP_004598603.1| 243 RLAERLEEYDVWWLEDPVPPEN-HDVQKEVT-QStTTPITVGENVYRKHGQRRLIEEQALDIVAPDMPKVGGMRETR 317
                                       ********************76.999*****.6669***************************************** PP

                                       HHHHHHHHTT-EEEEBSCSSHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTSSSBTSSEB CS
                          MR_MLE_C 140 kvaalaeafgvpvapHsgsgglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtvpdgpGlGvel 216
                                       k+a+la+++ vpva+H++ +++g++as+h+ aa++n+l ley+ ++  +  +l  e+  +edG++++p++pGlGv+l
  gi|336255496|ref|YP_004598603.1| 318 KIADLADTYYVPVAMHNVASPVGTVASAHVGAAVSNSLALEYHSYELGWWGDL-VEEDLIEDGYLEIPEEPGLGVTL 393
                                       *****************889*************************99655555.5556699**************** PP

                                       -.H CS
                          MR_MLE_C 217 d.e 218
                                       d +
  gi|336255496|ref|YP_004598603.1| 394 DlD 396
                                       955 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0     1e-17   6.1e-14      27     117 .]      52     144 ..      37     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1e-17
                                       EEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSS.......CHHHHHHH CS
                          MR_MLE_N  27 slvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlg.......nmsAkaai 96 
                                       +  lv+i+t++G+vG+gea    g++e     ++  + p +vg+++  i  l + l +++ g       + +A+++i
  gi|336255496|ref|YP_004598603.1|  52 PWTLVRIYTDAGIVGTGEAYWGAGVPEL----IE-RMKPFIVGENPLDIDRLYEHLVQKMSGegsiggvTITAISGI 123
                                       5679***************998865554....44.59*******************99999999************* PP

                                       HHHHHHHHHHHTTSBHHHHTT CS
                          MR_MLE_N  97 dmAlwDlkakalnlpladLlG 117
                                       ++Al+Dl++k l++p ++LlG
  gi|336255496|ref|YP_004598603.1| 124 EVALHDLAGKILEIPAYQLLG 144
                                       ********************9 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.96   5.7e+03      34      62 ..      12      40 ..      11      41 .. 0.88
   2 ?   12.4   0.4   1.6e-05     0.098      94     167 ..     164     246 ..     161     256 .. 0.72
   3 ?   -3.5   0.0       1.1   6.8e+03     132     148 ..     317     333 ..     308     362 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.96
                                      HHTSSECCCEHCHHHHHHHHTSHHCHHHH CS
                      Amidohydro_2 34 ragvdpqlaspeallvlnaaagiaraviv 62
                                      +a+++++++s+e + v+++  g+++++i+
  gi|336255496|ref|YP_004598603.1| 12 NAEYTMRDLSAETMGVTRDRGGDRDVEIT 40
                                      68899************999999998876 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.6e-05
                                       SHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGH..........HHHHHHHHHH.....T-EEEEE....CHH CS
                      Amidohydro_2  94 dpedaaaeleraveelgfkGvrlnphvggddllgdrld..........rpifealeel.....glpvdihtGpspew 155
                                       dp+++a+e+er veelg  +++++++v+ ++ +++++            +i+e+  e+     ++ +d h      w
  gi|336255496|ref|YP_004598603.1| 164 DPDACADEAERVVEELGYDALKFDLDVPSGHEKDRANRhlrepeiehkAEIVEKVTERvgdraDVAFDCH------W 234
                                       899************************9999999988888888888885555533333222246666666......5 PP

                                       HCHHHHHHHHHH CS
                      Amidohydro_2 156 lfggpqettrai 167
                                       +f g +++  a 
  gi|336255496|ref|YP_004598603.1| 235 TFSGGSAKRLAE 246
                                       565555555554 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHT-EEEEE CS
                      Amidohydro_2 132 rpifealeelglpvdih 148
                                       r+i  ++  + +pv +h
  gi|336255496|ref|YP_004598603.1| 317 RKIADLADTYYVPVAMH 333
                                       67777888888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3219.78
//
Query:       gi|336255497|ref|YP_004598604.1|  [L=356]
Description: alcohol dehydrogenase GroES domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-99  329.9   0.0    7.3e-99  329.5   0.0    1.2  1  Glu_dehyd_C  Glucose dehydrogenase C-terminus
    9.2e-11   41.6   0.0    1.5e-10   40.9   0.0    1.4  1  ADH_N        Alcohol dehydrogenase GroES-like domain
    0.00015   21.8   0.0    0.00025   21.1   0.0    1.3  1  ADH_zinc_N   Zinc-binding dehydrogenase
    0.00021   21.1   0.1    0.00049   20.0   0.1    1.5  1  ADH_N_2      N-terminal domain of oxidoreductase


Domain annotation for each model (and alignments):
>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.5   0.0  1.6e-102   7.3e-99       1     212 []     143     353 ..     143     353 .. 0.99

  Alignments for each domain:
  == domain 1  score: 329.5 bits;  conditional E-value: 1.6e-102
                       Glu_dehyd_C   1 advgvLvEPisiveKaielaeasrsafewepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlve 77 
                                       a++g+LvEPisi+eKaie+a+asrsaf+w+ esalvlG+GslGLL+l +++ +  ++er+y+lgrrdrpdptid+ve
  gi|336255497|ref|YP_004598604.1| 143 AHLGFLVEPISISEKAIEHAVASRSAFDWDLESALVLGNGSLGLLTLGMFA-DVLDVERTYCLGRRDRPDPTIDIVE 218
                                       689***********************************************8.5899********************* PP

                       Glu_dehyd_C  78 elGatYvdsretpvdeipeaseemdlvvEaTGsakhafeaiealapnGvaaLlGvpedsevevdggelhrelvleNk 154
                                       +lGatY+dsretpv+eipe++e++d+v+EaTG+akhafe+++alapnGv +LlGvpe++e+evdgg+lhre+vl+Nk
  gi|336255497|ref|YP_004598604.1| 219 DLGATYIDSRETPVPEIPEVYESVDFVYEATGYAKHAFETVDALAPNGVGVLLGVPEPWEFEVDGGRLHREMVLHNK 295
                                       ***************************************************************************** PP

                       Glu_dehyd_C 155 alvGsvNanrrhfeaavdtLaalpeslldelvtkvvdldeleeAfedddetiKtvvel 212
                                       al+G+vN++r hfe+avdtL++lp++l+d+lvt+v++l+e+++Afe++d  iKt+ve+
  gi|336255497|ref|YP_004598604.1| 296 ALLGTVNSHRGHFESAVDTLSQLPTWLTDDLVTGVYGLEEFQRAFETGDGVIKTAVEF 353
                                       ********************************************************98 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   3.4e-14   1.5e-10       2     109 .]      26     138 ..      25     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3.4e-14
                                       TEEEEEEEEEEE-HHHHHHHTTS..TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE..-SSSHHHH CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkgg..kelevklplilGHEivGeveevgpevkklkvGdrVvveplis..cgeCaaCk 74 
                                       ge+l+++  +g+ g+D +++ g+  + +   + l+lGHE+vG+ve+  p+ ++l+ G+ Vv  +       + ++ +
  gi|336255497|ref|YP_004598604.1|  26 GEALVRTLRVGVDGTDHEVIAGHhgDVPDDDTQLVLGHEAVGVVED--PNGTDLEEGQIVVPTVRRRpnGRDNEYFE 100
                                       799*****************9976667777888************9..66789********9877664356799*** PP

                                       TT-GGG-TTBEETTTS...S-SSSBSEEEECGGGEEEE CS
                             ADH_N  75 egeenlCeeakllgvs...ldGgfaeyvvvpekklvkl 109
                                       +ge+++ +e++++  +    +G +aey++ p+++lv++
  gi|336255497|ref|YP_004598604.1| 101 RGEPDMAPEGEYVERGivgAHGFMAEYFTSPAEYLVPI 138
                                       *******99999988877899*************9985 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   5.5e-08   0.00025      27     128 ..     214     315 ..     200     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.5e-08
                                       HHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSCTSSEEE.EEHHH. CS
                        ADH_zinc_N  27 lelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGggkgeee.fdlrn. 101
                                       ++++++lGa+++  + e ++v +i e    e vd+v+e++G+ +   + +++l+p+G  v+ G+++  e  +d ++ 
  gi|336255497|ref|YP_004598604.1| 214 IDIVEDLGATYIDSR-E-TPVPEIPEVY--ESVDFVYEATGYAKHAFETVDALAPNGVGVLLGVPEPWEFeVDGGRl 286
                                       588999**9876555.7.8*********..69*********99999999**************94444434555555 PP

                                       ...HHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                        ADH_zinc_N 102 ...lllkeksilGsllgslreefkealdll 128
                                          ++l++k +lG++ ++ r  f+ a+d l
  gi|336255497|ref|YP_004598604.1| 287 hreMVLHNKALLGTVNSH-RGHFESAVDTL 315
                                       5557799*******9999.99999988876 PP

>> ADH_N_2  N-terminal domain of oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.1e-07   0.00049      19      90 ..      14      85 ..       5      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-07
                           ADH_N_2 19 eleeeelpelkdGevlvralylSvDPymRgrmndaksyvepvelgdvmrggavgeVveSknpdfkvGdlVvg 90
                                      +l+e + pe+++Ge+lvr+l ++vD +    +  ++  v++ +   v+  +avg V + +  d+++G++Vv 
  gi|336255497|ref|YP_004598604.1| 14 TLVERPRPEPAAGEALVRTLRVGVDGTDHEVIAGHHGDVPDDDTQLVLGHEAVGVVEDPNGTDLEEGQIVVP 85
                                      7999*********************************9********************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2807.11
//
Query:       gi|336255498|ref|YP_004598605.1|  [L=222]
Description: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase [Halopiger xanaduensis SH-6]
Scores for complete 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  155.2   1.1    1.5e-45  155.0   1.1    1.0  1  Aldolase    KDPG and KHG aldolase
  ------ inclusion threshold ------
       0.01   15.1   5.2       0.16   11.1   0.8    2.9  3  DHO_dh      Dihydroorotate dehydrogenase
       0.14   11.1   0.0       0.18   10.7   0.0    1.2  1  PALB2_WD40  Partner and localizer of BRCA2 WD40 domain
       0.18   10.8   8.3      0.041   12.9   2.0    2.4  2  IMPDH       IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.0   1.1   3.4e-49   1.5e-45       1     193 [.      12     205 ..      12     208 .. 0.97

  Alignments for each domain:
  == domain 1  score: 155.0 bits;  conditional E-value: 3.4e-49
                                       HHHHHHCHSEEEEE--SSGGGHHHHHHHHHHTT--EEEEETTSTTHHHHHHHHHHH-..TTSEEEEES--SHHHHHH CS
                          Aldolase   1 iesilkeakvvpvivikdkedalplaeaLvagGlrvlevtlrteaaldairvlrker..pdllvgaGtvlnaeqlae 75 
                                       +e+++ e+ v++v++  ++e ++p+a aL +gG+ +le+t   ++a d i ++ +e   pd++vgaGtvl+a  ++ 
  gi|336255498|ref|YP_004598605.1|  12 VEERIVESGVIAVMRGISAERIVPVARALHEGGVDALEITADEPHARDKIAAVDRELadPDVVVGAGTVLDAATAES 88 
                                       678999999*******************************************999854499**************** PP

                                       HHHCT-SEEEESS--HHHHHHHHHTTS-EEEEESSHHHHHHHHHTT--EEEETTTTTTTHHHHHHHHCTTTTT-EEE CS
                          Aldolase  76 akeaGaqfvvsPGltadllkaavdlkipllPGvstpseimlaldlGlkrlklfPaeasGGvkalkalagpfaqvrfi 152
                                       + +aGa fvvsP + ++++++++ +++   PGv tp+e   al+ G + lk+fPa ++G    + al gp ++v++i
  gi|336255498|ref|YP_004598605.1|  89 VIDAGATFVVSPHVDREIIRTCNRHNVLASPGVMTPTEAVTALEAGADILKMFPAATVG-PDHIGALKGPLGNVEII 164
                                       *********************************************************99.899************** PP

                                       EBSS--TTTHHHHHTSTTBS-EEESCCC-HHHHHTT-HHHH CS
                          Aldolase 153 PtGGispanvrdylalpsvlvvgGswlveaslikkedldki 193
                                       PtGG+   nv dy+++++ +v +Gs l++ ++i ++d+d +
  gi|336255498|ref|YP_004598605.1| 165 PTGGVAADNVADYFEAGALAVGAGSALIDYDAIADDDMDGV 205
                                       *************************************9987 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.057   2.5e+02     232     270 ..      59      97 ..      19      99 .. 0.79
   2 ?    4.1   0.0    0.0052        23     244     276 ..     112     144 ..      98     155 .. 0.82
   3 ?   11.1   0.8   3.6e-05      0.16     244     277 ..     160     192 ..     149     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.057
                                       HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEE CS
                            DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslv 270
                                         i ++ ++l +   ++g G +  +  a   i aGA++v
  gi|336255498|ref|YP_004598605.1|  59 DKIAAVDRELADPDVVVGAGTVLDAATAESVIDAGATFV 97 
                                       556666666666667899999999999999999**9987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0052
                                       .S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                            DHO_dh 244 eipiIgvGGiesgeDalekieaGAslvqvytal 276
                                       +  ++++ G+++   a+  +eaGA +++++ a 
  gi|336255498|ref|YP_004598605.1| 112 RHNVLASPGVMTPTEAVTALEAGADILKMFPAA 144
                                       45688999*****************99987665 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 3.6e-05
                                       .S-EEEESS--SHHHHHHHHHHTECEEEESHHHH CS
                            DHO_dh 244 eipiIgvGGiesgeDalekieaGAslvqvytalv 277
                                       ++ iI +GG+  ++ + +++eaGA +v  ++al+
  gi|336255498|ref|YP_004598605.1| 160 NVEIIPTGGVA-ADNVADYFEAGALAVGAGSALI 192
                                       799******95.79999***************97 PP

>> PALB2_WD40  Partner and localizer of BRCA2 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     4e-05      0.18     119     164 ..       8      53 ..       3      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4e-05
                        PALB2_WD40 119 edeslkqslvksGnikavlGltkrrlvsssgtlkdqqveilslsee 164
                                       ++ +++ ++v+sG i +++G++ +r+v   ++l++  v+ l+++ +
  gi|336255498|ref|YP_004598605.1|   8 NKRTVEERIVESGVIAVMRGISAERIVPVARALHEGGVDALEITAD 53 
                                       5678999********************************9998765 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.0   9.2e-06     0.041     101     170 ..      30      97 ..       7      99 .. 0.80
   2 ?    0.7   0.5     0.047   2.1e+02     134     167 ..     149     182 ..     111     193 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.2e-06
                                       SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 101 vkedalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnvataegakaLieagadav 170
                                       ++      ++al e gvd+l + + + h +  + av++  ++  +v v aG v +a+ a+++i+aga +v
  gi|336255498|ref|YP_004598605.1|  30 AE-RIVPVARALHEGGVDALEITADEPHARDKIAAVDRELADP-DVVVGAGTVLDAATAESVIDAGATFV 97 
                                       44.45566899****************9999998888766665.67677******************887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.047
                                       HHHHHHHHHTTTSEEE.EEEE-SHHHHHHHHHTT- CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                             IMPDH 134 eavkeikkkveevevi.aGnvataegakaLieaga 167
                                       + + ++k  + +ve+i +G va  + +++ +eaga
  gi|336255498|ref|YP_004598605.1| 149 DHIGALKGPLGNVEIIpTGGVAA-DNVADYFEAGA 182
                                       33444445555555554444443.33344445544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1699.30
//
Query:       gi|336255499|ref|YP_004598606.1|  [L=354]
Description: transcriptional regulator TrmB [Halopiger xanaduensis SH-6]
Scores for complete 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-56  191.0   0.1    2.3e-56  190.6   0.0    1.1  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    1.2e-16   60.3   0.3      4e-16   58.7   0.0    1.9  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0062   16.9   0.0      0.051   13.9   0.0    2.2  2  Rrf2            Transcriptional regulator
     0.0087   15.9   0.1      0.047   13.6   0.0    2.2  2  MarR_2          MarR family
  ------ inclusion threshold ------
      0.013   15.4   0.5        4.5    7.3   0.1    2.6  3  HTH_11          HTH domain
      0.016   15.0   0.0        1.2    9.0   0.0    2.6  2  HTH_IclR        IclR helix-turn-helix domain
      0.024   14.5   0.0      0.049   13.6   0.0    1.5  1  MarR            MarR family


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.6   0.0   8.9e-60   2.3e-56       1     231 [.     108     348 ..     108     350 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.6 bits;  conditional E-value: 8.9e-60
                                       -EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS.----GGGSSSSEEEEEE- CS
                    Regulator_TrmB   1 avwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliyp.dedleeldleevatevrv 76 
                                       +++v+ksr+tv +rie+l+++Ae+e+++s+p++ L+++re l+++aergv+Vlll+ + d+d +  +l+++a+ vr+
  gi|336255499|ref|YP_004598606.1| 108 QFEVIKSRQTVQKRIESLLSEAETEVTLSIPASVLPQVRETLEETAERGVLVLLLLGTaDSDVDMASLAGIASTVRT 184
                                       589*******************************************************9****************** PP

                                       S---S.EEEEETTTEEEEE-SSS-.EEEE--HHHHHHHHHHHHHH........HHH-EEEEEEES-TT-EEES-HHH CS
                    Regulator_TrmB  77 rrsgapllvivDrkrgvvaprevl.rdkeeeyaiifkekelihvlshyFlttlWktseviktdepvekpitfssirl 152
                                       ++   p++v+vDr++g+ +p+++l ++ ++++ai  ++++l+ vl ++Fl ++W  +e+ ++++ +++p+t+  +r+
  gi|336255499|ref|YP_004598606.1| 185 WNALVPTMVTVDRRHGLLSPSQLLtTSTSDTKAIALSQEQLVPVLAGSFLANYWPIAEERYVTTAADLPATYEGFRH 261
                                       **********************9999*************************************************** PP

                                       HHHHHHHHT.TTS-EEEEEEEEETT.T--EEEEEEEEEEEE.......EETTTTEEEEEEEETTEEEEEE-TT--SS CS
                    Regulator_TrmB 153 avedikkllraglkveaeveGrdte.tgeevtieGrvveat.......lnstpgvaslvvetedgevtVGGlgAvlE 221
                                       av +i  +   ++++e++v+G  +  ++ + t++G+vv+++       ++  p ++++ ++++++++t+GG gA+lE
  gi|336255499|ref|YP_004598606.1| 262 AVFQIALHRATDTPLEVTVTGSPVGdRDLPSTLTGEVVDVRqslvrpaTSTVPIENAFEIDVDGERYTIGGAGAFLE 338
                                       ************************955669*********99************************************ PP

                                       SEEEEEEEEE CS
                    Regulator_TrmB 222 Dieaeeitle 231
                                       D+ea+++t++
  gi|336255499|ref|YP_004598606.1| 339 DFEAQSVTIR 348
                                       ********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 !   58.7   0.0   1.5e-19     4e-16       1      68 []      10      78 ..      10      78 .. 0.97
   2 ?   -1.8   0.1       1.2     3e+03      35      48 ..     114     127 ..     110     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 1.5e-19
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE--HH CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYravdpe 68
                                      L+ +GLse E+++Yla+l +g+++a++ia +++v++  vY++ ++Le++G+Ve+ +   p++ r+vdpe
  gi|336255499|ref|YP_004598606.1| 10 LERFGLSEKEIDTYLAILDHGESKASTIADAADVSKRYVYSISEELEERGFVEVDDHAvPTVIRPVDPE 78
                                      789****************************************************9888********97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                                       SCHCHHHHHHHHHH CS
                              TrmB  35 prskvYevLrsLed 48 
                                       +r++v++ ++sL++
  gi|336255499|ref|YP_004598606.1| 114 SRQTVQKRIESLLS 127
                                       799*******9975 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0     2e-05     0.051      15      57 ..      22      63 ..      19      65 .. 0.92
   2 ?   -0.1   0.0      0.48   1.2e+03       5      42 ..     151     189 ..     148     203 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                                      HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      +yLa  +++e  ++++ia+  ++s++y+  i ++L++ g+v++
  gi|336255499|ref|YP_004598606.1| 22 TYLAILDHGE-SKASTIADAADVSKRYVYSISEELEERGFVEV 63
                                      6888888888.99****************************85 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHHHHHHSSTCC-.B-HHHHHHHHTS-HHHH CS
                              Rrf2   5 skteyalhallyLakeeeeep.vsseeiaerqnispsyl 42 
                                       +  e ++ +ll L + +++   +s++ ia+ + +    +
  gi|336255499|ref|YP_004598606.1| 151 ETAERGVLVLLLLGTADSDVDmASLAGIASTVRTWNALV 189
                                       567788999999977766654478888888877766555 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   1.8e-05     0.047      12      53 ..      24      63 ..      13      67 .. 0.85
   2 ?   -1.8   0.1       1.2     3e+03      34      46 ..     114     126 ..     114     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                      HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +a+ ++++    ++ +a++ ++sk +v  i ++L+++G+ve 
  gi|336255499|ref|YP_004598606.1| 24 LAILDHGE--SKASTIADAADVSKRYVYSISEELEERGFVEV 63
                                      45666666..69****************************95 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                                       SHHHHHHHHHHHH CS
                            MarR_2  34 sksavsrilkrLv 46 
                                       s+++v+++++ L 
  gi|336255499|ref|YP_004598606.1| 114 SRQTVQKRIESLL 126
                                       79*******9986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.8   4.7e+03      23      39 ..      11      27 ..       9      32 .. 0.84
   2 ?    5.5   0.0    0.0063        16      16      43 ..      32      59 ..      21      66 .. 0.79
   3 ?    7.3   0.1    0.0018       4.5      23      39 ..     107     125 ..      96     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.8
                            HTH_11 23 eeLnvSrrtvrrdIkaL 39
                                      e++++S++ +  ++++L
  gi|336255499|ref|YP_004598606.1| 11 ERFGLSEKEIDTYLAIL 27
                                      89999999999999888 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0063
                            HTH_11 16 isgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                        ++++A+  +vS+r v+   ++Lee g
  gi|336255499|ref|YP_004598606.1| 32 SKASTIADAADVSKRYVYSISEELEERG 59
                                      5899**************9888888877 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0018
                            HTH_11  23 eeLnv..SrrtvrrdIkaL 39 
                                       e+++v  Sr+tv+++I++L
  gi|336255499|ref|YP_004598606.1| 107 EQFEVikSRQTVQKRIESL 125
                                       6778888**********99 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 ?    9.0   0.0   0.00047       1.2      18      51 ..      31      64 ..      23      65 .. 0.87
   2 ?    3.2   0.1      0.03        77       2      24 ..     153     175 ..     152     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00047
                                      S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      e + s +A++++++k  v+ +   L+e+G+ve d
  gi|336255499|ref|YP_004598606.1| 31 ESKASTIADAADVSKRYVYSISEELEERGFVEVD 64
                                      358999**************************88 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.03
                                       HHHHHHHHCT-CTTBSS-BHHHH CS
                          HTH_IclR   2 ldRalaiLdalaeapqeltlsel 24 
                                       ++R++ +L +l++a+ ++  + l
  gi|336255499|ref|YP_004598606.1| 153 AERGVLVLLLLGTADSDVDMASL 175
                                       79*************99533333 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.9e-05     0.049      12      49 ..      26      63 ..      15      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      + ++g+ + s +a++  vsk +v  ++ +Le++G++e 
  gi|336255499|ref|YP_004598606.1| 26 ILDHGESKASTIADAADVSKRYVYSISEELEERGFVEV 63
                                      6789999*****************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); 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:                         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 0.21s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 2960.52
//
Query:       gi|336255500|ref|YP_004598607.1|  [L=685]
Description: glucan 14-alpha-glucosidase [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0015   17.4   0.2       0.24   10.1   0.3    3.1  4  Glyco_hydro_15  Glycosyl hydrolases family 15
  ------ inclusion threshold ------
      0.056   13.6   1.0       0.17   12.0   0.3    2.0  2  Laminin_G_3     Concanavalin A-like lectin/glucanases superfa
        3.3    7.8   5.2        3.9    7.6   0.5    2.8  3  HisKA           His Kinase A (phospho-acceptor) domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.34     2e+03      41      83 ..      46      89 ..      43     121 .. 0.67
   2 !   10.1   0.3     4e-05      0.24      24     142 ..     300     416 ..     290     559 .. 0.82
   3 ?   -1.9   0.0      0.18   1.1e+03      18      45 ..     597     624 ..     589     630 .. 0.81
   4 !    3.4   0.0    0.0044        26     414     446 ..     636     667 ..     611     669 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.34
                                      EHHHHHHHHHHHH..........HHHHHTTT-HCCHHHHHHHHHHH CS
                    Glyco_hydro_15 41 WvRDsvyvilavwglg.yr..dedrakayeleqslvklmrglleam 83
                                      ++RD +y ++ ++g+   r   e +++ y+le+  ++ + g   ++
  gi|336255500|ref|YP_004598607.1| 46 SIRDYSYPLSGLVGIErSRfgVEIDGTVYWLEEGDQRYIDG--TTV 89
                                      78999999999998887779999999999999877776666..333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 4e-05
                                       T-B-S-S-BSSS......B--SEEHHHHHHHHHHHH.......HHHHHTTT-HCCHHHHHHHHHHHHHHCTS-BTTB CS
                    Glyco_hydro_15  24 GlliASpstsdp......DYrytWvRDsvyvilavwglgyrdedrakayeleqslvklmrglleamvrqagkvekfk 94 
                                       G+ iA p+  dp      +Y ytW RD + ++  ++       dr+   +le   ++  r ++e++         + 
  gi|336255500|ref|YP_004598607.1| 300 GARIAGPE-FDPffrysgGYGYTWFRDDAEIAGFLL-----AADREADLGLEAWHRQSARFYVETQLADGTWPHRVW 370
                                       55555555.3445777779*****************.....567788888888888888888888877777655555 PP

                                       -TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHH...HCTT CS
                    Glyco_hydro_15  95 etqstkgLhakyftktgstvvGddewghlQlDatslyllalaqm...tasg 142
                                         + +    a+++ +      Gd + +  Q D+t+ ++++la++   ++ g
  gi|336255500|ref|YP_004598607.1| 371 AHNGE---IAPGWANGRLE--GDAAGTDYQADQTASVATFLATYlrvVDDG 416
                                       54444...99999996665..9999******************95554444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.18
                                       BTTS-TT-B-S-S-BSSSB--SEEHHHH CS
                    Glyco_hydro_15  18 eqnpvtGlliASpstsdpDYrytWvRDs 45 
                                       +  +  G l A+ + +++D +  W RD 
  gi|336255500|ref|YP_004598607.1| 597 HAAAEFGELLAARDHEAADAFDEWARDL 624
                                       5556668899*****************6 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.0044
                                       -TTS---SEE-TTT--EESSTT-HHHHHHHHHH CS
                    Glyco_hydro_15 414 nslgvLteevdvylgeliraqpllfsealllri 446
                                        ++ +L e++ + +g++++a+pl + +al+l++
  gi|336255500|ref|YP_004598607.1| 636 GDGEYLPEQFFD-DGTPDSATPLGWPHALRLTT 667
                                       567889999998.9*****************87 PP

>> Laminin_G_3  Concanavalin A-like lectin/glucanases superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   2.8e-05      0.17      36     118 ..     321     401 ..     312     418 .. 0.81
   2 ?   -1.1   0.0      0.32   1.9e+03      67      89 ..     440     462 ..     406     486 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                       Laminin_G_3  36 iiissssdg.rgfelgldgsgrlrfsvnagngaeesvtsgasvpageWtHvavtydggtlrlYvNGvevgsatltgg 111
                                       +++ +++++  gf l  d++ +l +  ++ +  + ++  ++++++g+W H ++ ++g  +  + NG + g a++t+ 
  gi|336255500|ref|YP_004598607.1| 321 TWF-RDDAEiAGFLLAADREADLGLEAWHRQ--SARFYVETQLADGTWPHRVWAHNGEIAPGWANGRLEGDAAGTDY 394
                                       566.334447899999999999999999886..56777799*******************************99998 PP

                       Laminin_G_3 112 llsatsg 118
                                         + t++
  gi|336255500|ref|YP_004598607.1| 395 QADQTAS 401
                                       6555554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.32
                       Laminin_G_3  67 aeesvtsgasvpageWtHvavty 89 
                                        +e+v+ + +  +g++tH a+ty
  gi|336255500|ref|YP_004598607.1| 440 LPERVQNAWENMTGRFTHTAATY 462
                                       45566655566789999999998 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.5   0.00066       3.9      26      65 ..     229     296 ..     224     298 .. 0.74
   2 ?    1.3   0.1     0.061   3.6e+02      30      51 ..     466     496 ..     456     497 .. 0.73
   3 ?   -3.4   0.0       1.8   1.1e+04      41      58 ..     534     551 ..     523     556 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00066
                                       HHHC..T-HSSCHHHHHHHHHHHH.............................HHHHHHHHHHHHCCHH CS
                             HisKA  26 aLkregklteelkeyletiesear.............................rldhlvedlLdlsrie 65 
                                       +L +  + +e  +e+le+++ +a                              r+d +vedl+ ls + 
  gi|336255500|ref|YP_004598607.1| 229 LLTDA-EEDETRAEALERVRAGAAdhddraaileadrrqvrerlpdvagatdgRVDGIVEDLRALSLLR 296
                                       55553.4567777777777777777777777777777777788888888888*************9876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.061
                                       ...........T-HSSCHHHHHHHHHHHHHH CS
                             HisKA  30 e.........gklteelkeyletiesearrl 51 
                                       +         ++++e+ +e+ + + + ++rl
  gi|336255500|ref|YP_004598607.1| 466 YaaiarapidAEYRERAAENARAVYDAIDRL 496
                                       3333334566789999999999999999997 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHH CS
                             HisKA  41 letiesearrldhlvedl 58 
                                       le++    +r+++lv+ l
  gi|336255500|ref|YP_004598607.1| 534 LEDATIDDERIERLVSHL 551
                                       444444455777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 5000.67
//
Query:       gi|336255501|ref|YP_004598608.1|  [L=587]
Description: cyclomaltodextrinase [Halopiger xanaduensis SH-6]
Scores for 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-83  280.4   0.0    4.2e-83  279.7   0.0    1.3  1  Alpha-amylase    Alpha amylase, catalytic domain
    3.1e-33  114.5   0.0    5.3e-33  113.7   0.0    1.4  1  Alpha-amylase_N  Alpha amylase, N-terminal ig-like domain
    1.2e-06   28.8   0.5    3.5e-06   27.2   0.5    1.9  1  DUF3459          Domain of unknown function (DUF3459)
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.27   11.4   0.0    1.7  1  Malt_amylase_C   Maltogenic Amylase, C-terminal domain
       0.15   11.1   0.0       0.22   10.6   0.0    1.1  1  hDGE_amylase     Glycogen debranching enzyme, glucanotransfer


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.7   0.0   1.2e-86   4.2e-83       1     337 []     178     474 ..     178     474 .. 0.92

  Alignments for each domain:
  == domain 1  score: 279.7 bits;  conditional E-value: 1.2e-86
                                       --CHHHHCTCCCCCCCT-SCEEE-B-CE-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC- CS
                     Alpha-amylase   1 GDLkGiiekLdYlkeLGvtaiwlsPifkspqadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNHt 77 
                                       GDL+Gii+ LdYl++LGv+a++l+Pif+s  ++h+Y ++dyt++dp+fG+ e l +L ++ah++gi+v+lD+V+NH+
  gi|336255501|ref|YP_004598608.1| 178 GDLQGIIDNLDYLEDLGVSALYLTPIFESR-SNHKYNTTDYTSVDPHFGDEETLRQLTEQAHDRGIRVMLDAVFNHC 253
                                       9****************************9.********************************************** PP

                                       -TTSCCCHCCHHSTTSGGGCCC-E......ESS-STTC-TTTTCSCEECTTTTCEEESSS-TTS-BB-TTTCCCCCC CS
                     Alpha-amylase  78 sdehewfkeslkkkgepkrdyyiwkegkeekeppnnwkslfdgsaweydekaqeyylhlflkklpdLnteneevrke 154
                                       + e+e f++ +++    +++y++w +    +e p + +     ++ +yd+++       f + +p+Lnten+ev+++
  gi|336255501|ref|YP_004598608.1| 254 GREFEPFQDVVENGR--ESEYADWFHV---HEFPIEFE-----PRPNYDTFG-------FEAYMPKLNTENPEVKEY 313
                                       ************555..8899999877...66777765.....888888888.......8899************** PP

                                       CCCCCCCCCTTT.-SEEEETTCCCTTTCCCCHCCHCCHHHHHHHHHHHTCCGTT-EEEEE-TT-SCCCHCCCC-CGG CS
                     Alpha-amylase 155 lkdvvkfwlekg.idGfRlDvvkhvskvealesngeflheftqalnetvasrkevmtvgEvssdasedlrvyttear 230
                                       l dv+ +w+++  idG+RlDv+++v++         f++e ++++++      +v+++gE+++d++ +lr+++++a+
  gi|336255501|ref|YP_004598608.1| 314 LLDVAAYWVDEIgIDGWRLDVADEVDH--------AFWRELREEVKAID---PDVYILGEIWHDSRAWLRGDQFDAV 379
                                       **********988**************........***********876...************************* PP

                                       -SICECCITTCGGGCC-CTSTTSB-SS-HHHHHHHHHHHHHHS-C.CCTTCEEES--TTS--HHHHTTSSTTTTHHH CS
                     Alpha-amylase 231 lelemvldfphldvaqkakikeqlksisakklkellkkwlkalee.aaeeavtflgnHDqeRilsrlgddsaeaekk 306
                                       +++++   ++++ ++++ +         a ++++  ++ l +++e ++e  +++lg+HD++R+l r+  d+    + 
  gi|336255501|ref|YP_004598608.1| 380 MNYPFSYAVIDFLIERDLD---------AGEFADKATRFLGRYPEqVNEVLFNLLGSHDTPRLLYRCDGDE----RL 443
                                       ****555555555555555.........7777777777777887777889********************9....59 PP

                                       HHHHHHCCCTSSSEEEEETTCCCT----STT CS
                     Alpha-amylase 307 lklaaillltlrGvpviYyGeEigmtggkdp 337
                                       l+la +ll+t+rG+p+ YyG+E+gmtgg+dp
  gi|336255501|ref|YP_004598608.1| 444 LRLAFLLLFTYRGTPCLYYGDEVGMTGGDDP 474
                                       ****************************987 PP

>> Alpha-amylase_N  Alpha amylase, N-terminal ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.0   1.5e-36   5.3e-33       3     120 .]       5     127 ..       1     127 [. 0.87

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 1.5e-36
                                       GGG-B--SSTTTEEEEETTEEEEEEEEETTT-SEEEEEEEETTS-.TTS--EEEEEEEEEE-SSEEEEEEEEE-TTS CS
                   Alpha-amylase_N   3 keAiyHrpeseyayaydektlhirLrtkkddvekveliygdpyeweekwkseetemkkiasdelfdYweaeltlkkk 79 
                                       +e ++Hr++s+yayayde+t+h+rLrt ++dv +++l++gd+ +w    ++++t m++i++de+fdYw+++++++++
  gi|336255501|ref|YP_004598608.1|   5 REGVHHRSKSSYAYAYDEETVHVRLRTMRGDVAECTLLHGDKFDW--PDSATRTRMERIGRDERFDYWQVSVRPPRR 79 
                                       689******************************************..9999************************** PP

                                       -EEEEEEEE-TS-EEEEESSE.......EESSHHHH...--EEE---- CS
                   Alpha-amylase_N  80 rlrYlFeleedgeslvytekg.......fydekplddiegyFkfpyln 120
                                       rl Y+F+l +++esl+ te g          ++ ++ + +yF++p+l+
  gi|336255501|ref|YP_004598608.1|  80 RLCYAFHLSDGDESLWVTEWGfeskplsELPTAGERRPLHYFEYPFLH 127
                                       *********************444432222233344566788888876 PP

>> DUF3459  Domain of unknown function (DUF3459)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.5   9.9e-10   3.5e-06       1      91 []     494     586 ..     494     587 .] 0.82

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 9.9e-10
                                       HHHHHHHHHHHH.CCCTT--CGGEEEEEEECTCEEEEEEEETTEEEEEEEE-SSCGCCS-SS---SEEEEECT--S. CS
                           DUF3459   1 lyrdLLaLRree.PaLadarrgglevavlgdgallvrwrlgdgrllrllaNLgdepvtlppegaagkllfsseaara 76 
                                       ++++L+ LR  + P L++ r +  + +  +  +llv++r+++++++ +++N gd+++ ++p + ++++l++++a++ 
  gi|336255501|ref|YP_004598608.1| 494 FVQRLIVLRDDHrP-LRRGRIRFDR-E-RTTSDLLVYRRADGDETVGIAINRGDDQAVVEPTDEQWETLLRTDADSG 567
                                       6799********77.6666333333.2.355789999999**************9999999*************998 PP

                                       .......SSEE-TTEEEEE CS
                           DUF3459  77 gg....dagrlppesvvvl 91 
                                       g     +++ +pp+  vv+
  gi|336255501|ref|YP_004598608.1| 568 GVdavdGRIVVPPRGGVVW 586
                                       7799999999999655543 PP

>> Malt_amylase_C  Maltogenic Amylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.5e-05      0.27      10      37 ..     520     549 ..     511     564 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.5e-05
                                       -.TTEEEEEEEETTEEEEEEEE.SS-EEEE CS
                    Malt_amylase_C  10 n.rkvlaYlReyedetilvvaN.rsaqave 37 
                                          + l+Y R ++det+ +++N   +qav 
  gi|336255501|ref|YP_004598608.1| 520 TtSDLLVYRRADGDETVGIAINrGDDQAVV 549
                                       44689*****************55555554 PP

>> hDGE_amylase  Glycogen debranching enzyme, glucanotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     6e-05      0.22      25     117 ..     184     267 ..     171     278 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6e-05
                                       HHHHHHHHHTT--EEEES--EEE-TT--TTSEEEEEEE-TTT-.....SSC.HHHHHHHHHHHHHH--EEEEEE--S CS
                      hDGE_amylase  25 ekvlkeikekgYnmiHftPlqelGesnSpYSiadqleldkelfeekdkeekeedveklvkklekeygllsltDvVln 101
                                        ++l+  ++ g   + +tP+ e  +sn  Y  +d +++d+++         ee +++l +++ ++ g+  + D V+n
  gi|336255501|ref|YP_004598608.1| 184 IDNLDYLEDLGVSALYLTPIFES-RSNHKYNTTDYTSVDPHFG----D---EETLRQLTEQA-HDRGIRVMLDAVFN 251
                                       567788889999999*****997.69**************994....2...34566666655.678*********** PP

                                       EEETT-CCCCC-GGGS CS
                      hDGE_amylase 102 HtannskwleehPeag 117
                                       H  ++ +  ++  e g
  gi|336255501|ref|YP_004598608.1| 252 HCGREFEPFQDVVENG 267
                                       *998877776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 4534.13
//
Query:       gi|336255502|ref|YP_004598609.1|  [L=378]
Description: glycerol-3-phosphate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for complete 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-31  110.1   0.0    1.9e-31  109.4   0.0    1.3  1  ABC_tran      ABC transporter
    1.7e-11   44.1   0.2    6.9e-11   42.2   0.1    2.2  1  TOBE_2        TOBE domain
    1.2e-08   35.6   0.0    4.5e-08   33.8   0.0    2.1  1  OB_MalK       MalK OB fold domain
    2.2e-06   27.7   0.0      0.027   14.3   0.1    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.1e-06   27.0   0.0    8.9e-06   25.9   0.0    1.6  1  TOBE          TOBE domain
    0.00034   21.0   0.0    0.00053   20.4   0.0    1.5  1  AAA_16        AAA ATPase domain
    0.00044   19.8   0.2     0.0024   17.4   0.2    2.0  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0022   18.3   0.2      0.004   17.4   0.2    1.5  1  AAA_22        AAA domain
     0.0072   15.5   0.0      0.015   14.5   0.0    1.5  1  G-alpha       G-protein alpha subunit
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.017   15.0   0.0    1.3  1  Rad17         Rad17 P-loop domain
      0.018   15.5   0.0      0.044   14.2   0.0    1.7  1  AAA           ATPase family associated with various cellular 
      0.022   14.7   0.0      0.088   12.7   0.0    2.0  2  ATPase_2      ATPase domain predominantly from Archaea
      0.027   14.5   0.0      0.072   13.1   0.0    1.7  1  AAA_14        AAA domain
      0.028   14.1   0.0      0.054   13.2   0.0    1.5  1  AAA_15        AAA ATPase domain
      0.045   14.1   0.0       0.46   10.9   0.0    2.6  3  RNA_helicase  RNA helicase
      0.054   14.1   0.0       0.13   12.9   0.0    1.9  1  AAA_18        AAA domain
      0.066   13.4   0.3       0.18   12.0   0.2    1.8  2  AAA_28        AAA domain
       0.07   12.4   0.1        0.2   10.9   0.0    1.8  2  Zeta_toxin    Zeta toxin
      0.071   12.7   1.7       0.59    9.7   0.3    2.9  3  AAA_25        AAA domain
      0.071   12.8   0.0       0.14   11.9   0.0    1.4  1  AAA_30        AAA domain
      0.093   13.2   0.0        0.2   12.1   0.0    1.5  1  AAA_23        AAA domain
        0.1   12.5   0.0       0.21   11.5   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
       0.17   11.5   0.2       0.86    9.2   0.0    1.9  2  SRP54         SRP54-type protein, GTPase 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 !  109.4   0.0   2.4e-34   1.9e-31       2     136 ..      22     164 ..      21     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 2.4e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +++sl+++ ge v +vG++G+GK+t l+++agl++pt G++ + ++d+++   +  ++ i++++q+  l p++tv+e
  gi|336255502|ref|YP_004598609.1|  22 DDLSLDIEDGEFVTVVGPSGCGKTTTLRMIAGLEQPTDGSVYIGDEDVTD--VHAKNRDIAMVFQNYALYPHKTVYE 96 
                                       899**********************************************9..9999********************* PP

                                       H..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n              e++ ++e+ ++ +++++l +++      +LSgGqkqrval ra++++p+ +l+DEp 
  gi|336255502|ref|YP_004598609.1|  97 NmafglrmstdlsesERRTRVEETAEMMDIDHLLEDTP----DELSGGQKQRVALGRAIVREPDAFLFDEPL 164
                                       ***********975555555777777777777777776....*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.1   8.8e-14   6.9e-11       1      76 []     288     358 ..     288     358 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 8.8e-14
                            TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                       l+iRPE++ + + ++++ ++GtVe ve  Gs+  ++ +la+   +++r++++     +++G++V+l++d  d++++
  gi|336255502|ref|YP_004598609.1| 288 LGIRPENVNVVESAAEGVVKGTVEVVEPIGSDNYLYMDLAED--FIARVDSSI---EPDVGERVALTFDESDIHLF 358
                                       79********655555699*****************999987..779999999...9*****************98 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   5.7e-11   4.5e-08       1      52 [.     238     294 ..     238     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 5.7e-11
                           OB_MalK   1 GSPaMNflpatveedg....vlvegggvtlplpeeq.klalklyagkevilGiRPEh 52 
                                       GSP+MNf+++ v+  g    +   ++g++++l+ e  +  + + +  + +lGiRPE+
  gi|336255502|ref|YP_004598609.1| 238 GSPSMNFFDVDVTTRGdrivLGDPDSGFEFELSSEYvTDHADELEANQYTLGIRPEN 294
                                       9************99999888888899*****999955588999999*********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 !   11.0   0.0   0.00035      0.27       2      25 ..      34      57 ..      33     104 .. 0.71
   2 !   14.3   0.1   3.4e-05     0.027     220     298 ..     120     196 ..     100     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                        ++Gp g+GK++ L+ + +l + 
  gi|336255502|ref|YP_004598609.1| 34 VTVVGPSGCGKTTTLRMIAGLEQP 57
                                      679***************999553 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.4e-05
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQvilt 295
                                       +   ++ ++  e +++elS G+k+  al  a+ r +   + +l+DEp ++L+ kl ++  + + ++ ++ ++  + +
  gi|336255502|ref|YP_004598609.1| 120 TAEMMDIDHLLEDTPDELSGGQKQRVALGRAIVREP---DAFLFDEPLSNLDAKLRTSMRTEIqRIQNELDVTSVYV 193
                                       666677778888899*******************99...88***************999988854444478888888 PP

                            AAA_21 296 THS 298
                                       TH+
  gi|336255502|ref|YP_004598609.1| 194 THD 196
                                       887 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.1e-08   8.9e-06       1      64 []     300     357 ..     300     357 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.1e-08
                              TOBE   1 ssarNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                       s a+++++gtV+vvep gs+ ++++dl+     +Arv+    ++    +Ge+V ++++ +++hl
  gi|336255502|ref|YP_004598609.1| 300 SAAEGVVKGTVEVVEPIGSDNYLYMDLAEDF--IARVDSSIEPD----VGERVALTFDESDIHL 357
                                       5799***********************9765..***********....**************97 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   6.9e-07   0.00053       3      51 ..      13      57 ..      11     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.9e-07
                            AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51
                                      +GRee + ++ ++  ++ +g  e v ++G+sG+GK++ +r+++  le+ 
  gi|336255502|ref|YP_004598609.1| 13 YGREEIV-AVDDLSLDIEDG--EFVTVVGPSGCGKTTTLRMIA-GLEQP 57
                                      6888777.777776677777..79*****************99.45554 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 !   17.4   0.2     3e-06    0.0024      25     207 ..      32     206 ..      18     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3e-06
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                       +f  +vGp G+GK+  l  i    G ++ +       ++ ++   + ++ + a v   +    +k++ e+  + ++ 
  gi|336255502|ref|YP_004598609.1|  32 EFVTVVGPSGCGKTTTLRMI---AGLEQPTDGSVYIGDEDVTD-VHAKNRDIAMVFQNYALYPHKTVYENMAFGLRM 104
                                       6899**********999988...56544433333333333333.344566677777777777777888899999999 PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                       +   +++ + +  +++++  ++ +lle+   ++++LSgG+k+ val    Ai + +p   +l+De  ++LD+k ++ 
  gi|336255502|ref|YP_004598609.1| 105 STDLSESERRTRVEETAEMMDIDHLLED---TPDELSGGQKQRVAL--GRAIVR-EPD-AFLFDEPLSNLDAKLRTS 174
                                       9999998888888999999********9...589*******97765..456654.444.4799**********9999 PP

                                       HHHHHHHHCTTSEE..EEE-SSH.HHCCC-SC CS
                                       xxxxxxxxxxxxxx..xxxxxxx.xxxxxxxx RF
                             SMC_N 179 vaellkeksknaQf..ivislre.emlekadk 207
                                       + + +++ +++  +  + +++++ e ++  d+
  gi|336255502|ref|YP_004598609.1| 175 MRTEIQRIQNELDVtsVYVTHDQeEAMTMGDR 206
                                       99888877776544113334433033333354 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   5.1e-06     0.004       5      29 ..      31      55 ..      28     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.1e-06
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                        +++v+G+sG+GKTt+lr+++   
  gi|336255502|ref|YP_004598609.1| 31 GEFVTVVGPSGCGKTTTLRMIAGLE 55
                                      67999**************987654 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.9e-05     0.015      28     120 ..      36     156 ..      29     300 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                                       EEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT.......HH CS
                           G-alpha  28 llGqseSGKsTilkqlkllykkg.............fseeelatwraviqlnivrsiktilealesleselsesfel 91 
                                       ++G s++GK+T+l+ +  l++++             ++ +  + +  v q+  +   kt+ e++ + + ++s ++++
  gi|336255502|ref|YP_004598609.1|  36 VVGPSGCGKTTTLRMIAGLEQPTdgsvyigdedvtdVHAK-NRDIAMVFQNYALYPHKTVYENMAF-GLRMSTDLSE 110
                                       79********************999***887775442222.1334557777777777888888877.6666666655 PP

                                       HC-SS-SCCC...S-HCHHHH.............................H CS
                           G-alpha  92 qelkerldpl...kkveasliaklssateee...................q 120
                                       +e++ r+++    +++++ l +     t +e                   +
  gi|336255502|ref|YP_004598609.1| 111 SERRTRVEETaemMDIDHLLED-----TPDElsggqkqrvalgraivrepD 156
                                       5555555555111444444433.....333333444555666655555541 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   2.2e-05     0.017      43      66 ..      29      52 ..      16     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                             Rad17 43 rkkriLLisGPsGCgkstvvkvLs 66
                                      +  + + + GPsGCgk+t++++++
  gi|336255502|ref|YP_004598609.1| 29 EDGEFVTVVGPSGCGKTTTLRMIA 52
                                      555677899***********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 ?   14.2   0.0   5.7e-05     0.044       2      21 ..      35      54 ..      34      91 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.7e-05
                                      EEESSTTSSHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavake 21
                                       ++Gp G+GKT++ + +a  
  gi|336255502|ref|YP_004598609.1| 35 TVVGPSGCGKTTTLRMIAGL 54
                                      689**************975 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 ?   12.7   0.0   0.00011     0.088      16      57 ..      27      67 ..      14     146 .. 0.79
   2 ?   -0.9   0.0       1.7   1.3e+03      42      71 ..     311     344 ..     305     375 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlkeiienledkdkyviyyial 57
                                      + e  e++ + Gp g+GKt+ l+ i+    +  +  +y+ + 
  gi|336255502|ref|YP_004598609.1| 27 DIEDGEFVTVVGPSGCGKTTTLRMIAGLE-QPTDGSVYIGDE 67
                                      5567789999************9887665.445567777655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                          ATPase_2  42 enledkdkyviyyialreesiskldefie....e 71 
                                       e  e  + +   y++l e++i+++d++ie    e
  gi|336255502|ref|YP_004598609.1| 311 EVVEPIGSDNYLYMDLAEDFIARVDSSIEpdvgE 344
                                       5555566667779999999999999999875531 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.2e-05     0.072       3      59 ..      32      86 ..      30      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.2e-05
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek 59
                                      + ++++G+  +GKTt l+ ++  +  + +  +yi  +d +d  +++  ++  ++++ 
  gi|336255502|ref|YP_004598609.1| 32 EFVTVVGPSGCGKTTTLRMIAGLEQ-PTDGSVYIGDEDVTDVHAKNR-DIAMVFQNY 86
                                      6799*************99997776.999999999998888766655.455555544 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     7e-05     0.054      15      76 ..      22      80 ..       2     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-05
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskd 76
                                      +d ++d+++  + +++G+ ++GK++ l+++  + + +    +  ++i +ed+ + + +++++ 
  gi|336255502|ref|YP_004598609.1| 22 DDLSLDIEDGeFVTVVGPSGCGKTTTLRMIAGLEQPT----DGSVYIGDEDVTDVHAKNRDIA 80
                                      46677777778*******************8888877....5666777776666654444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         3   2.3e+03      46      59 ..      12      25 ..       7      31 .. 0.82
   2 ?   10.9   0.0   0.00059      0.46       2      38 ..      35      66 ..      34     101 .. 0.78
   3 ?   -2.1   0.0       6.4     5e+03      32      59 ..     222     248 ..     208     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3
                      RNA_helicase 46 gYtgqevvvidDfg 59
                                       Y ++e+v +dD++
  gi|336255502|ref|YP_004598609.1| 12 EYGREEIVAVDDLS 25
                                      7999********97 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00059
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrn 38
                                       ++Gpsg+GK+t+ +  ++     l++++++svy++ 
  gi|336255502|ref|YP_004598609.1| 35 TVVGPSGCGKTTTLRM-IA----GLEQPTDGSVYIGD 66
                                      689**********999.33....34477778888744 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 6.4
                      RNA_helicase  32 dsvysrnpeddfwdgYtgqevvvidDfg 59 
                                        +vy  np ++f+ g+ g + + ++D+ 
  gi|336255502|ref|YP_004598609.1| 222 TEVY-DNPVNEFVAGFIGSPSMNFFDVD 248
                                       4555.58999999999999999999986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00016      0.13       1      49 [.      34      91 ..      34     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf........gvnlrdvakenglllevdpe.aldes 49
                                      + + G++G+GKtt  + ++ +++          + ++dv+++n+   +v+++ al ++
  gi|336255502|ref|YP_004598609.1| 34 VTVVGPSGCGKTTTLRMIAGLEQPtdgsvyigDEDVTDVHAKNRDIAMVFQNyALYPH 91
                                      6799**************8775225777899988899999998888888887644444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00023      0.18       2      33 ..      34      71 ..      33     127 .. 0.71
   2 ?   -1.9   0.0       4.4   3.4e+03     125     145 ..     114     134 ..      91     138 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                            AAA_28  2 ivitGgestGKTtlleaLa..ar...gypvv.pEaare 33
                                      + ++G++++GKTt+l+ +a  ++   g +++  E +++
  gi|336255502|ref|YP_004598609.1| 34 VTVVGPSGCGKTTTLRMIAglEQptdGSVYIgDEDVTD 71
                                      6799************9996633444666665555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.4
                            AAA_28 125 geRredleereaiderlreal 145
                                        +R e+ +e ++id++l+++ 
  gi|336255502|ref|YP_004598609.1| 114 RTRVEETAEMMDIDHLLEDTP 134
                                       456677778888888888775 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   0.00026       0.2      19      63 ..      34      78 ..      25     121 .. 0.88
   2 ?   -2.2   0.1       2.6     2e+03     165     190 ..     174     199 ..     168     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyee 63
                                      + ++G +G+GK++++++++   +++++ v +   d+   h + ++
  gi|336255502|ref|YP_004598609.1| 34 VTVVGPSGCGKTTTLRMIAGLEQPTDGSVYIGDEDVTDVHAKNRD 78
                                      7799***************99999*****9999998888866555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                        Zeta_toxin 165 glresvealeeekqldrvkikdrdgk 190
                                        +r +++++++e ++ +v ++  +++
  gi|336255502|ref|YP_004598609.1| 174 SMRTEIQRIQNELDVTSVYVTHDQEE 199
                                       67788888888888888877755553 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00076      0.59      30      50 ..      28      48 ..      21     159 .. 0.68
   2 ?   -0.9   0.0       1.3     1e+03     165     188 ..     171     195 ..     156     201 .. 0.78
   3 ?    0.2   0.0      0.62   4.8e+02      65     124 ..     289     365 ..     276     377 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00076
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +  ge++ ++G++g+GKtt +
  gi|336255502|ref|YP_004598609.1| 28 IEDGEFVTVVGPSGCGKTTTL 48
                                      5679**************965 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                            AAA_25 165 v.galvealeriarrtgaavllvhH 188
                                         +++ + ++ri+ +++++ + v H
  gi|336255502|ref|YP_004598609.1| 171 LrTSMRTEIQRIQNELDVTSVYVTH 195
                                       3478888999*********999999 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.62
                            AAA_25  65 gpvapeqgkVlyvsaEdsedelrrRlravgeal...................rddarllvldlagveslpLfakdrg 122
                                       g ++pe+++V+  +aE+  +++ + ++ +g ++                   +d ++  +l+ ++  +++Lf++++g
  gi|336255502|ref|YP_004598609.1| 289 G-IRPENVNVVESAAEGVVKGTVEVVEPIGSDNylymdlaedfiarvdssiePDVGERVALTFDE-SDIHLFEPETG 363
                                       5.578999999999999999999999999977778888888777777777775555555555555.47787777665 PP

                            AAA_25 123 gt 124
                                         
  gi|336255502|ref|YP_004598609.1| 364 ID 365
                                       55 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   0.00018      0.14      19      44 ..      32      57 ..      26      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                            AAA_30 19 rvavltGpAGtGKttalkalreawea 44
                                       +++++Gp G GKtt+l+ ++ + + 
  gi|336255502|ref|YP_004598609.1| 32 EFVTVVGPSGCGKTTTLRMIAGLEQP 57
                                      48899*************99877655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00026       0.2       2      39 ..       4      51 ..       3      54 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00026
                            AAA_23  2 Lkienfrsf.........rdqeidF.skgltlItGpNGaGKTTildAi 39
                                      +++en+r+          +d ++d  +  ++ ++Gp G+GKTT l+ i
  gi|336255502|ref|YP_004598609.1|  4 IRLENLRKEygreeivavDDLSLDIeDGEFVTVVGPSGCGKTTTLRMI 51
                                      666677664432222222344444455568889***********9987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00027      0.21      90     122 ..      21      54 ..      10      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       +++l+  ++d +++++vG+SG GK+t + ++++ 
  gi|336255502|ref|YP_004598609.1|  21 VDDLSLDIEDgEFVTVVGPSGCGKTTTLRMIAGL 54 
                                       6777778888799**************9999875 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0011      0.86       4      34 ..      34      64 ..      32      85 .. 0.81
   2 ?   -0.1   0.1      0.76     6e+02      78     150 ..     120     196 ..      92     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvll 34
                                      + +vG+ G GKTttl  +a l +    +v +
  gi|336255502|ref|YP_004598609.1| 34 VTVVGPSGCGKTTTLRMIAGLEQPTDGSVYI 64
                                      679************9998776666666655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.76
                                       HHHHTTSSEEEEEE....--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEEST CS
                             SRP54  78 kakeekidvvlvDT....aGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltkl 150
                                       +a+  +id++l DT    +G +++  +l + + +  ++   de l  lda +  ++ +++++ ++++++t+v +t  
  gi|336255502|ref|YP_004598609.1| 120 TAEMMDIDHLLEDTpdelSGGQKQRVALGRAIVREPDAFLFDEPLSNLDAKLRTSMRTEIQRIQNELDVTSVYVTHD 196
                                       45556677777777555556666666666666666666677777778888888888889999999999998888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 2864.62
//
Query:       gi|336255503|ref|YP_004598610.1|  [L=47]
Description: hypothetical protein Halxa_4127 [Halopiger xanaduensis SH-6]
Scores for 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:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); 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: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 390.09
//
Query:       gi|336255504|ref|YP_004598611.1|  [L=416]
Description: family 1 extracellular solute-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-39  135.9   0.9      3e-39  135.6   0.9    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    8.5e-26   91.6   4.2    1.1e-25   91.3   4.2    1.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein
     0.0017   18.5   0.2      0.043   13.9   0.0    2.2  2  ApoLp-III   Apolipophorin-III precursor (apoLp-III)
     0.0034   17.2   0.1     0.0059   16.4   0.1    1.3  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
  ------ inclusion threshold ------
      0.013   14.9   0.1      0.066   12.6   0.1    2.1  2  SBP_bac_6   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.6   0.9   8.3e-43     3e-39       2     279 ..      62     357 ..      61     360 .. 0.82

  Alignments for each domain:
  == domain 1  score: 135.6 bits;  conditional E-value: 8.3e-43
                                       HHHHHHHH-TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG.GS.TTHHH.-HH.H CS
                         SBP_bac_8   2 lakefekktgvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladls.dl.dnldd.ltd.a 74 
                                       ++++fe++t+ ++ ++++   +l+++l+++l+ g++pd  +++ ++d+++ + ++g+l+d+s dl  ++d+ +td a
  gi|336255504|ref|YP_004598611.1|  62 YIAQFEEETDHDIAAEEV--SELNEQLNTSLPVGEGPD--IFTHAHDWVGPFEDRGWLYDVSdDLtIDIDEtYTDtA 134
                                       689************988..69**************97..68999*****************655556666435559 PP

                                       HHTT--.TS.----EEEEEEE-EEEEEHHHHHHS.---BHHHHHHHHHHH....HHH-SEG...G---GGGGGGTHH CS
                         SBP_bac_8  75 laavgy.dgklygvPyasetpyvliynkdllekaedpktwdellaaakkl....kgkfglp...dpasgwlqaalla 143
                                       l+a+++ dg +yg+Pya+et  +l yn dl++   +p+t+de++++ ++      g++g +   +++++   +++ +
  gi|336255504|ref|YP_004598611.1| 135 LEAATWqDG-VYGLPYAAET-VGLLYNRDLVD-S-PPETLDEMVEVMEDHhdpdDGQYGVAyplADPYFASAWIHAF 207
                                       999988688.*********9.7**********.4.*************99665559998861224555566999999 PP

                                       ETTEE---H..HHH.....HHHHHHHHHHHHTT-EE......-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSE CS
                         SBP_bac_8 144 kdgksldddggkdgl....kealellkklkdngkty......dtgadavsefanGevaftingswdiaaaqkagkkl 210
                                        +g+ +dd    d+l    +e++e +  l+d    +      ++++++++ f +G++ f+i g+w++  +++ g ++
  gi|336255504|ref|YP_004598611.1| 208 -GGYLYDDEA--DELghelDETIEGVELLVDSF--WpyaaadPSYESQIAVFNDGNAPFVIVGPWEVSGFRDSGIDV 279
                                       .999998874..444445577777777777555..33445558999******************************* PP

                                       EEE.--.....S--EEEEEEEEEEBTTS-HHHH..HHHHHHHHHTTSH.HHHHHHHHH---BS-S-TTTHHHHHH-H CS
                         SBP_bac_8 211 gai.vp.....kqgsfaggkglavpknaknedl..aAldFlkwltspe.nqaalaektgyipvnksaalspevkkdp 278
                                       g++ +p      +++ +g++ ++ +   ++ ++  ++ +F++w+t+ +      a+  gyipv  ++++s+e+++  
  gi|336255504|ref|YP_004598611.1| 280 GIArLPtvdggDPSPYTGVQLWYFTQELEDGEAlaTSREFAEWYTTTDnVILSNADELGYIPVHADLSESDELSDEV 356
                                       ***99976554456*********999955554448999******999934557*******************99876 PP

                                       H CS
                         SBP_bac_8 279 a 279
                                       a
  gi|336255504|ref|YP_004598611.1| 357 A 357
                                       5 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   4.2   3.1e-29   1.1e-25       5     312 ..      56     327 ..      52     330 .. 0.88

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 3.1e-29
                                       HHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHT CS
                         SBP_bac_1   5 tegaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkay 81 
                                       ++   l+ ++ ++fe+ ++++++  e v  ++l ++l + +  G gp D++++++dw++++ + g+l ++++++  +
  gi|336255504|ref|YP_004598611.1|  56 AD--LLETYI-AQFEE-ETDHDIAAEEV--SELNEQLNTSLPVGEGP-DIFTHAHDWVGPFEDRGWLYDVSDDLTID 125
                                       45..888899.99*99.8**********..*****************.***************************** PP

                                       TECTTCCTEEEEHHHHTHHHHCE.EE...ES.EEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCT CS
                         SBP_bac_1  82 lapgvkdaadklsssvlpkilds.kv...ly.vPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkp 152
                                         ++           ++++ l++ ++   +y +P+ a + gl YN dl++    +pp+t de ve+ +   +++ + 
  gi|336255504|ref|YP_004598611.1| 126 IDET-----------YTDTALEAaTWqdgVYgLPYAAeTVGLLYNRDLVD----SPPETLDEMVEVMEDHHDPDDGQ 187
                                       8888...........999****9999**********77************....7788**********999988888 PP

                                       HCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT..HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHH CS
                         SBP_bac_1 153 iggarggsasgtayyfalalakslggkvfdkdgg..gldnpegvtaatylvklyavanltkelkgkgaenkdgaaal 227
                                           +g ++     yfa+a++  +gg+++d+++   g + +e  + ++ lv+++          ++ a++ + ++  
  gi|336255504|ref|YP_004598611.1| 188 ----YGVAYPLADPYFASAWIHAFGGYLYDDEADelGHELDETIEGVELLVDSF---------WPYAAADPSYESQI 251
                                       ....8888888888*****************98866656666666777777777.........9************* PP

                                       HHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE.EEEEEEEEBTTCSTHHH... CS
                         SBP_bac_1 228 alfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi.lgayglaipkgsknpea... 300
                                       a f+ G+a++ ivg+w+             +   ++ ++++g+a lP+++gg p+  +g++ +       + ea   
  gi|336255504|ref|YP_004598611.1| 252 AVFNDGNAPFVIVGPWE-------------VSGFRDSGIDVGIARLPTVDGGDPSPyTGVQLWYFTQELEDGEAlat 315
                                       *****************.............99999999999***********9987777776666666666666777 PP

                                       HHHHHHHHTSHH CS
                         SBP_bac_1 301 AkkFldfllspe 312
                                        ++F +++++ +
  gi|336255504|ref|YP_004598611.1| 316 SREFAEWYTTTD 327
                                       888888887765 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.047   1.7e+02      27      68 ..      48      87 ..      41      90 .. 0.76
   2 !   13.9   0.0   1.2e-05     0.043      31      90 ..     349     409 ..     346     414 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.047
                         ApoLp-III 27 iKensenlvdqlkqvikslqeelkkksdeleealkevkkkie 68
                                      + + +e+ +d l+++i++++ee      +++e ++e++++++
  gi|336255504|ref|YP_004598611.1| 48 WHTLAEGEADLLETYIAQFEEETDHD--IAAEEVSELNEQLN 87
                                      66667777889999999999997664..47777888888775 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.2e-05
                         ApoLp-III  31 senlvdqlkqvikslq.eelkkksdeleealkevkkkieetadklseenPevkkkaqelqe 90 
                                       s++l d++ +++++++  e+  +s+++e++++ +++++e++ +  +e++P+ +++a+e ++
  gi|336255504|ref|YP_004598611.1| 349 SDELSDEVAAFAENVSiGEVMPTSPKMERVWEPTRDALERILNGEEEARPAFEQAAEEIRA 409
                                       77888999999999986899*************************************9876 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.6e-06    0.0059       3      24 ..       4      25 ..       3      27 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-06
                        TAT_signal  3 SRRdFLKgsAAaaAAaalggca 24
                                      +RR+ +Kg + a+  ++l+gc 
  gi|336255504|ref|YP_004598611.1|  4 TRRTVIKGMGTAGVTVGLAGCI 25
                                      8********************6 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.8e-05     0.066       4      79 ..      96     172 ..      93     223 .. 0.88
   2 ?   -0.5   0.0      0.18   6.6e+02      82     100 ..     244     261 ..     243     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                         SBP_bac_6   4 pdlilsfdkdflekfieeglfqpldpanlpnvnkdfa...eeglkdpdgkyy.pygvgplvlavnkdrlkgrpvPks 76 
                                       pd+++ +  d+++ f + g + ++ ++   ++++ ++    e  + +dg y  py+ ++++l++n+d ++    P++
  gi|336255504|ref|YP_004598611.1|  96 PDIFT-HAHDWVGPFEDRGWLYDVSDDLTIDIDETYTdtaLEAATWQDGVYGlPYAAETVGLLYNRDLVDSP--PET 169
                                       89**9.9***************9999999999988886654445555788889****************877..988 PP

                         SBP_bac_6  77 WaD 79 
                                        ++
  gi|336255504|ref|YP_004598611.1| 170 LDE 172
                                       776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.18
                         SBP_bac_6  82 dPeykgkvalpgnngsdlf 100
                                       dP y+ ++a++++ + ++f
  gi|336255504|ref|YP_004598611.1| 244 DPSYESQIAVFNDGN-APF 261
                                       8***********887.766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3306.63
//
Query:       gi|336255505|ref|YP_004598612.1|  [L=341]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-14   53.0  20.2    3.3e-14   53.0  20.2    2.5  2  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 ?   -8.3  20.2         1   1.8e+04      30     131 ..      30     170 ..      25     174 .. 0.75
   2 !   53.0  20.2   1.9e-18   3.3e-14       5     172 ..     105     328 ..     102     330 .. 0.90

  Alignments for each domain:
  == domain 1  score: -8.3 bits;  conditional E-value: 1
                      BPD_transp_1  30 lPsfvlaillvlvf.......................................vilsilghlilpviillllsaapy 67 
                                       lP ++l++  ++vf                                        ++++lg ++l v+i ll+ ++  
  gi|336255505|ref|YP_004598612.1|  30 LPGLLLFLA-FMVFpigyliwisftdathagtvlsdesqfiglenyytllsdgQFWNSLGITWLFVAISLLFKIIVS 105
                                       555553333.3344566777777888888888889999999999999999999788899999999666666666555 PP

                      BPD_transp_1  68 v.rlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllefl 131
                                       + + ++    r++ k +++a  ++ ++   if   + + +++ +  g+++++ g ++g+v+    
  gi|336255505|ref|YP_004598612.1| 106 IsIALVLTHSRVIGKRYMRAIILMPLGFPAIFMITIWRGMFSGARFGVFNQLLGTWNGFVHWIVA 170
                                       51556667777999999999999999999999999999999999999999999999999887655 PP

  == domain 2  score: 53.0 bits;  conditional E-value: 1.9e-18
                      BPD_transp_1   5 Gilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf................................... 43 
                                       +i +a   ++++ ++++ +r +i ++l++P + ++ ++  +f                                   
  gi|336255505|ref|YP_004598612.1| 105 SISIAlvlTHSRVIGKRYMRAIILMPLGFPAIFMITIWRGMFsgarfgvfnqllgtwngfvhwivagidtilfgitv 181
                                       4555555569999**************************999*********************************** PP

                      BPD_transp_1  44 ............vilsilghlilp.viillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnal 107
                                                    +l +  +++++  +++ ++ a p++++i+ +al+ +p++l  aa+++Ga++ ++f++v+lP+++
  gi|336255505|ref|YP_004598612.1| 182 sapeilmadvpiGWL-SERWMAFAaYATTEVWLAYPFMMIIIVSALQDVPDQLHDAAKVDGAGYLRRFVHVTLPSIK 257
                                       *********995555.55666666489999*********************************************** PP

                      BPD_transp_1 108 ppiitglilafggllggavlleflgswpG........lgtllleailgydyseisnggvlalviavlllnlva 172
                                       +p++   il++++++ +++l+  +   +G        l +   ea++ ++y ++s ++++++++++ +++l+a
  gi|336255505|ref|YP_004598612.1| 258 RPVVFASILTAASSFQQFLLPWVFN-RGGpsrqnellLVYGYREATNLQQYGMAS-AIMVTAILFIGAFMLIA 328
                                       ******************9985555.5556****999999999*********999.88888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2619.78
//
Query:       gi|336255506|ref|YP_004598613.1|  [L=352]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for complete 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-14   54.2  11.9    1.5e-14   54.2  11.9    2.5  2  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 ?   -6.8   8.7         1   1.8e+04      45      45 ..      95      95 ..      39     173 .. 0.48
   2 !   54.2  11.9   8.2e-19   1.5e-14      22     183 ..     184     345 ..     160     347 .. 0.76

  Alignments for each domain:
  == domain 1  score: -6.8 bits;  conditional E-value: 1
                      BPD_transp_1 45 i 45
                                      +
  gi|336255506|ref|YP_004598613.1| 95 N 95
                                      0 PP

  == domain 2  score: 54.2 bits;  conditional E-value: 8.2e-19
                      BPD_transp_1  22 pliivllslPsfvlaillvlvfvilsilghlilp..viillllsaapyvrlirraalrslpkdlveaaralGasrwq 96 
                                        +++v+++l +  l+ ll     +++ +g ++    + i +  +a+p+++++ + +++++p +++eaa ++Gasr+ 
  gi|336255506|ref|YP_004598613.1| 184 LFTQVGSGLSIATLIALLA----LFTNFGLTNNLivLGIFYGAGAIPFNTWLLKTYMDNIPVSYEEAAIVDGASRFD 256
                                       3455555666666555555....44788855555124566667889******************************* PP

                      BPD_transp_1  97 ifrkvvlPnalppiitglilafggllggavlleflgswpG....lgtllleailgydyseis....nggvlalviav 165
                                       ++r v+lP+ +p +++  i+++ + +++++++ +l+        +         +  +s          +++++++ 
  gi|336255506|ref|YP_004598613.1| 257 VMREVILPLCKPGLAAITIFVWLAGWNEFIIAQTLLRPENytlsV------EVYSLATSGRFetpwTEFAAFAILFA 327
                                       ************************************665455432......33333333333444447********* PP

                      BPD_transp_1 166 lllnlvadilqrlldprv 183
                                       l++ l++++ qr+++  +
  gi|336255506|ref|YP_004598613.1| 328 LPVALIYFFAQRYVESGL 345
                                       *************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2724.58
//
Query:       gi|336255507|ref|YP_004598614.1|  [L=412]
Description: Galactonate dehydratase [Halopiger xanaduensis SH-6]
Scores for 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  193.2   0.9    5.7e-57  192.8   0.9    1.2  1  MR_MLE_C  Enolase C-terminal domain-like
    3.9e-13   49.7   0.0    7.8e-13   48.7   0.0    1.5  1  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N


Domain annotation for each model (and alignments):
>> 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 !  192.8   0.9   6.4e-61   5.7e-57       4     218 ..     170     396 ..     167     398 .. 0.94

  Alignments for each domain:
  == domain 1  score: 192.8 bits;  conditional E-value: 6.4e-61
                                       HHHHHHHHHHT-SEEEEETSSS...............HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHH CS
                          MR_MLE_C   4 eearelvaeqgfravKlkvggd...............dvaedvervravreavgpgddvdlmvDanqawdlatAirv 65 
                                       +ea++ v+e g++a+K+++  +               ++++ +e v++v e+v  g ++d+++D+++ ++   A r+
  gi|336255507|ref|YP_004598614.1| 170 DEAERVVDELGYDALKFDLDVPsghekdranrhlrepEIEHKAEIVEQVTERV--GSRADVAFDCHWTFSGGSAKRL 244
                                       789999************99999******************************..5577****************** PP

                                       HHHHGGGTESEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHH CS
                          MR_MLE_C  66 areleeldllwlEEPvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkv 141
                                       a++lee+d++wlE+Pvppe+  +  +e++ ++ ++pi +gE++y+ ++ r+l+e++a+di+ pd+ +vgG+ e+rk+
  gi|336255507|ref|YP_004598614.1| 245 AERLEEYDVWWLEDPVPPEN-HDVQREVT-QStTTPITVGENVYRKHGQRRLIEEQALDIIAPDMPKVGGMRETRKI 319
                                       ******************76.999*****.6669******************************************* PP

                                       HHHHHHTT-EEEEBSCSSHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTSSSBTSSEB-. CS
                          MR_MLE_C 142 aalaeafgvpvapHsgsgglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtvpdgpGlGveld. 217
                                       a+la+++ vpva+H++ +++g++as+h+ aa++n+l +ey+ ++ ++ ++l+ee+  +edG++++p++pGlGv+ld 
  gi|336255507|ref|YP_004598614.1| 320 ADLADTYYVPVAMHNVASPVGTVASAHVGAAVSNSLAVEYHSYELEWWDDLVEED-LIEDGYLEIPEEPGLGVTLDl 395
                                       ***************889**************************97777776665.589****************95 PP

                                       H CS
                          MR_MLE_C 218 e 218
                                       +
  gi|336255507|ref|YP_004598614.1| 396 D 396
                                       5 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   8.8e-17   7.8e-13      27     117 .]      52     144 ..      38     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 8.8e-17
                                       EEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSS.......CHHHHHHH CS
                          MR_MLE_N  27 slvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlg.......nmsAkaai 96 
                                       +  lv+i+t++G+vG+gea    g++e     ++  + p l g+++  i  l + l +++ g       + +A+++i
  gi|336255507|ref|YP_004598614.1|  52 PWTLVRIYTDAGIVGTGEAYWGAGVPEL----IE-RMKPFLQGENPLDIDRLYEHLVQKMSGegsiagvTVTAISGI 123
                                       5679***************998865554....44.59*****************9999999999************* PP

                                       HHHHHHHHHHHTTSBHHHHTT CS
                          MR_MLE_N  97 dmAlwDlkakalnlpladLlG 117
                                       ++Al+Dl++k l++p ++LlG
  gi|336255507|ref|YP_004598614.1| 124 EVALHDLAGKILEVPAYQLLG 144
                                       ********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3232.85
//
Query:       gi|336255508|ref|YP_004598615.1|  [L=315]
Description: Threonyl/alanyl tRNA synthetase SAD [Halopiger xanaduensis SH-6]
Scores for 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   39.8   0.2    6.7e-10   38.9   0.2    1.5  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
    3.4e-08   32.5   0.0    4.6e-08   32.0   0.0    1.1  1  tRNA-synt_2c  tRNA synthetases class II (A)


Domain annotation for each model (and alignments):
>> 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 !   38.9   0.2   7.4e-14   6.7e-10       1      34 [.     190     248 ..     190     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 7.4e-14
                                       EEEEEETT..........................EEEEESS---SBGGGC-SEEEECCE CS
                          tRNA_SAD   1 vrvvsiGd.........................isvelCgGtHvpnTgeIgafkilsee 34 
                                       vr+v+iG                          ++v +CgGtHv+nT+eIg + il ++
  gi|336255508|ref|YP_004598615.1| 190 VRLVTIGGkdengnangssrlrggftvggggdpWDVSACGGTHVRNTREIGPVTILGGS 248
                                       899999866789999999999999999999*************************9876 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 !   32.0   0.0   5.2e-12   4.6e-08     473     550 ..      13      85 ..       5      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 5.2e-12
                                       SEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEX CS
                      tRNA-synt_2c 473 kefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevd 549
                                       ++f++ev++++   v L+r+ fY+ sGGq +D+G+i     +++v+dv+ ++g  +h+   e  +l++g +v +++d
  gi|336255508|ref|YP_004598615.1|  13 TRFETEVTAIDGRRVWLERSHFYGASGGQPADRGTIG----DVEVVDVRLVDGEQVHELAAE-PSLRTGRSVLCSID 84 
                                       67999******************************95....678*****************7.9************* PP

                                       H CS
                      tRNA-synt_2c 550 e 550
                                       +
  gi|336255508|ref|YP_004598615.1|  85 W 85 
                                       8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2528.87
//
Query:       gi|336255509|ref|YP_004598616.1|  [L=181]
Description: transcription factor of MBF1-like protein [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00024   21.4   1.1    0.00048   20.4   1.1    1.6  1  HTH_31          Helix-turn-helix domain
    0.00027   21.0   0.1     0.0004   20.4   0.1    1.3  1  HTH_3           Helix-turn-helix
      0.003   17.4   0.4     0.0054   16.6   0.4    1.4  1  HTH_25          Helix-turn-helix domain
     0.0086   16.2   1.0      0.016   15.3   1.0    1.4  1  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.027   14.5   0.0    1.5  1  HTH_19          Helix-turn-helix domain
       0.03   14.3   1.5      0.077   13.0   1.5    1.6  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.076   13.5   0.9       0.11   12.9   0.9    1.3  1  DUF4685         Domain of unknown function (DUF4685)
       0.28   11.2   1.3       0.31   11.1   0.4    1.5  2  DUF1451         Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   1.1   2.1e-07   0.00048       5      41 ..     124     160 ..     120     181 .] 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.1e-07
                            HTH_31   5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgr 41 
                                       ++ ++R++aGL +ee+Ae lgv e  l  +EqGr + 
  gi|336255509|ref|YP_004598616.1| 124 TVVEARQEAGLQREELAEDLGVPERDLLAVEQGRATQ 160
                                       55679*****************************974 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   1.8e-07    0.0004       3      54 ..     127     181 .]     125     181 .] 0.92

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.8e-07
                                       HHHHHTTHHHHHHHHHHTSSHHHHHHHHTT...SSCSBHHHHHHHHHHHTSEHHH CS
                             HTH_3   3 elRkqlglsqeeLAeklGvsrstisriEnG...ernPsletlkklakaLgvslde 54 
                                       e+R+++gl++eeLAe lGv+ + + + E G   ++      + +l++ L+v+l+e
  gi|336255509|ref|YP_004598616.1| 127 EARQEAGLQREELAEDLGVPERDLLAVEQGratQAGLGGGLISALEDRLDVTLSE 181
                                       79****************************9999999999999999999999876 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.4   2.4e-06    0.0054       4      34 ..     127     157 ..     125     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.4e-06
                                       HHHHTTT--HHHHHHHSS--HHHHHHHHCT- CS
                            HTH_25   4 aaRearglsleevaketkIrkdylealEedd 34 
                                       +aR+++gl +ee+a+ + ++++ l a E+++
  gi|336255509|ref|YP_004598616.1| 127 EARQEAGLQREELAEDLGVPERDLLAVEQGR 157
                                       79**************************997 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.0   7.3e-06     0.016       8      33 ..      17      44 ..      16      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.3e-06
                       Zn-ribbon_8  8 CeeCghefevlqsis.daplta.CPeCg 33
                                      Ce Cg e + l+ +s   ++ + CP+C 
  gi|336255509|ref|YP_004598616.1| 17 CELCGAESDSLRLASvAGAELEvCPDCA 44
                                      *********88877776666666****5 PP

>> HTH_19  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   1.2e-05     0.027       3      36 ..     124     157 ..     122     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                            HTH_19   3 rLkeaReelgltqeelaerlgisrskisaiEngk 36 
                                        + eaR e+gl  eelae+lg+  + + a E g+
  gi|336255509|ref|YP_004598616.1| 124 TVVEARQEAGLQREELAEDLGVPERDLLAVEQGR 157
                                       5669******************999999999996 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.5   3.4e-05     0.077       4      26 ..      16      44 ..      13      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.4e-05
                    PhnA_Zn_Ribbon  4 kCplCaSeytY......edgallvCpeCa 26
                                      +C+lC++e+        ++ +l vCp+Ca
  gi|336255509|ref|YP_004598616.1| 16 NCELCGAESDSlrlasvAGAELEVCPDCA 44
                                      7*******976699**************8 PP

>> DUF4685  Domain of unknown function (DUF4685)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.9   4.9e-05      0.11      52      92 ..      42      84 ..      29     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.9e-05
                           DUF4685 52 qrsqapkpratlasrds..lqsGnlsdssSgesssgqrpkrgl 92
                                      ++++  +++a + srd+    sG+ sdssSg+ s+   +k++ 
  gi|336255509|ref|YP_004598616.1| 42 DCAPHDDTQAHSRSRDQgrGGSGSGSDSSSGDTSDEPSRKQKA 84
                                      5677888999999999977778999*******77666666654 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00014      0.31     102     139 ..       2      44 ..       1      49 [. 0.75
   2 ?   -3.5   0.0       4.2   9.5e+03      29      38 ..     132     141 ..     122     158 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                           DUF1451 102 gvyqsGevvglGtlvCekCgkela...l..kkteeippCpkCg 139
                                       ++y +G  +g G  +Ce Cg+e +   l      e++ Cp+C 
  gi|336255509|ref|YP_004598616.1|   2 AKYSTGSSAGGGGTNCELCGAESDslrLasVAGAELEVCPDCA 44 
                                       68******************98541113103446899999996 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.2
                           DUF1451  29 eeltkeelel 38 
                                         l++eel++
  gi|336255509|ref|YP_004598616.1| 132 AGLQREELAE 141
                                       3344444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1529.36
//
Query:       gi|336255510|ref|YP_004598617.1|  [L=187]
Description: hypothetical protein Halxa_4134 [Halopiger xanaduensis SH-6]
Scores for 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-37  127.1   5.8    5.1e-37  127.1   5.8    1.4  2  DUF420           Protein of unknown function (DUF420)
    0.00015   22.0   2.3    0.00015   22.0   2.3    2.4  2  DUF2306          Predicted membrane protein (DUF2306)
  ------ inclusion threshold ------
      0.014   14.6   6.8       0.26   10.4   2.1    2.1  2  DUF3413          Domain of unknown function (DUF3413)
      0.066   13.7   0.8      0.066   13.7   0.8    2.1  3  DUF1240          Protein of unknown function (DUF1240)
       0.12   12.4   2.1       0.43   10.7   0.6    2.2  2  DUF5389          Family of unknown function (DUF5389)
       0.18   12.0  13.1        0.7   10.1   1.0    2.6  2  DUF3397          Protein of unknown function (DUF3397)
        1.9    8.3   7.1       0.16   11.8   0.5    2.0  2  Amastin          Amastin surface glycoprotein


Domain annotation for each model (and alignments):
>> DUF420  Protein of unknown function (DUF420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.3       4.8   1.2e+04      85      92 ..      17      24 ..      12      30 .. 0.38
   2 !  127.1   5.8     2e-40   5.1e-37       1     132 []      48     183 ..      48     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.8
                            DUF420 85 avvvvplv 92
                                      ++v + +v
  gi|336255510|ref|YP_004598617.1| 17 SIVSLAVV 24
                                      22222222 PP

  == domain 2  score: 127.1 bits;  conditional E-value: 2e-40
                            DUF420   1 lpalnavlnalaavllllglvaikkgkieaHrklmllafvlsalFlvlYllkhalag.etkfggpeeegvirpvYla 76 
                                       +p++n++++a+a+ ++++g++ai++g++++Hr +ml++fvl+++Fl++Yl++ + +g  + f gp++  v+++vYl+
  gi|336255510|ref|YP_004598617.1|  48 IPHVNVAISATAIGTITVGWRAIRRGDVDRHRVAMLASFVLFVAFLAFYLYRLVATGgPQPFPGPDA--VYQFVYLP 122
                                       69**************************************************988877********7..******** PP

                            DUF420  77 iLitHivLavvvvplvlvtlvlalkg.....kfekHrkiaritvpiwlyvavtGvvvYllL 132
                                       iL++Hi+La+v+vplv+++l+la        + ++H++i+r+++ +wl+++ +G+vvY+lL
  gi|336255510|ref|YP_004598617.1| 123 ILAIHILLAIVCVPLVYYALLLAGAYsidelRRTSHARIGRLAASLWLVSFSLGIVVYVLL 183
                                       **********************9999899999***************************98 PP

>> DUF2306  Predicted membrane protein (DUF2306)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   2.3   5.9e-08   0.00015      64     108 ..      50      94 ..      12     109 .. 0.70
   2 ?    4.2   4.2     0.017        44       2      52 ..     125     179 ..     124     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5.9e-08
                           DUF2306  64 lgflllallwlvftvlalvairrrdfaaHrawmirsYalalaavt 108
                                        ++++++   ++++  +++airr d++ Hr +m+ s++l +a   
  gi|336255510|ref|YP_004598617.1|  50 HVNVAISATAIGTITVGWRAIRRGDVDRHRVAMLASFVLFVAFLA 94 
                                       34667888999***************************8887544 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.017
                           DUF2306   2 vlHialalvalllGalqlvkrlr....akrpklHrlaGrvyvlavllaalsglfl 52 
                                       ++Hi+la+v ++l   +l+ +      + r+ +H ++Gr+ + + l++   g+++
  gi|336255510|ref|YP_004598617.1| 125 AIHILLAIVCVPLVYYALLLAGAysidELRRTSHARIGRLAASLWLVSFSLGIVV 179
                                       89*******99999888865433344255999**************998888776 PP

>> DUF3413  Domain of unknown function (DUF3413)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0013       3.3     131     186 ..      43     102 ..      14     105 .. 0.65
   2 ?   10.4   2.1    0.0001      0.26     130     184 ..     127     181 ..     115     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0013
                           DUF3413 131 wllllilvl..villlelllanlvwkklrklk..rkklgkpvalvlllaflashlihiwa 186
                                       w l li  +   i + ++   ++ w+++r+    r++++  +++vl++afla +l  ++a
  gi|336255510|ref|YP_004598617.1|  43 WVLELIPHVnvAISATAIGTITVGWRAIRRGDvdRHRVAMLASFVLFVAFLAFYLYRLVA 102
                                       55544444400444445556677899995544449999*************999877766 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0001
                           DUF3413 130 swllllilvlvilllelllanlvwkklrklkrkklgkpvalvlllaflashlihi 184
                                       ++ll +++v+++  + ll+  ++  +lr++++ ++g+ +a+++l++f +  ++++
  gi|336255510|ref|YP_004598617.1| 127 HILLAIVCVPLVYYALLLAGAYSIDELRRTSHARIGRLAASLWLVSFSLGIVVYV 181
                                       478889999999999999999**************************99888876 PP

>> DUF1240  Protein of unknown function (DUF1240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         6   1.5e+04      46      56 ..      13      23 ..       7      27 .. 0.52
   2 ?   -0.4   0.0      0.66   1.7e+03      48      64 ..      80      97 ..      44     104 .. 0.64
   3 ?   13.7   0.8   2.6e-05     0.066       7      64 ..     126     181 ..     123     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6
                           DUF1240 46 laiiailsfvl 56
                                       a+++i+s+ +
  gi|336255510|ref|YP_004598617.1| 13 AAVLSIVSLAV 23
                                      44555555444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.66
                           DUF1240 48 iiailsfvlsl.flslYv 64
                                      + +++sfvl + fl++Y+
  gi|336255510|ref|YP_004598617.1| 80 VAMLASFVLFVaFLAFYL 97
                                      444455544321445553 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 2.6e-05
                           DUF1240   7 skvvlllfssPlllYfsvlvvlvaitnklakvndklvkllaiiailsfvlslflslYv 64 
                                        ++ l+++ +Pl++Y+++l+  + i +     + ++++l a + ++sf l   + +Yv
  gi|336255510|ref|YP_004598617.1| 126 IHILLAIVCVPLVYYALLLAGAYSIDELRRTSHARIGRLAASLWLVSFSLG--IVVYV 181
                                       678999****************************************98554..45555 PP

>> DUF5389  Family of unknown function (DUF5389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.23   5.9e+02      75      93 ..      79      97 ..      70     105 .. 0.68
   2 ?   10.7   0.6   0.00017      0.43      17      69 ..     130     182 ..     124     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.23
                           DUF5389 75 rkaklakklllisavifyg 93
                                      r a la  +l +++++fy 
  gi|336255510|ref|YP_004598617.1| 79 RVAMLASFVLFVAFLAFYL 97
                                      4455677777777777775 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00017
                           DUF5389  17 ialfclPvllwPlallispnllknPalsdtqvklmsiflwlyPlvlaiiaril 69 
                                       +a+ c+P++ + l l  + ++ +  + s+ ++  ++  lwl  + l+i+  +l
  gi|336255510|ref|YP_004598617.1| 130 LAIVCVPLVYYALLLAGAYSIDELRRTSHARIGRLAASLWLVSFSLGIVVYVL 182
                                       799**********999999*****************************98776 PP

>> DUF3397  Protein of unknown function (DUF3397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.0   0.00027       0.7      62     109 ..      54     101 ..      43     103 .. 0.84
   2 ?    6.3   5.1    0.0042        11      59     110 ..     135     186 ..     114     187 .] 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                           DUF3397  62 llvllllaillliiqarkkgeisykrffklfwRllfLltfllYlllli 109
                                        ++   ++++ + + a+++g+++ +r+  l+  +lf+ ++++Yl  l+
  gi|336255510|ref|YP_004598617.1|  54 AISATAIGTITVGWRAIRRGDVDRHRVAMLASFVLFVAFLAFYLYRLV 101
                                       45666778899999*****************************97655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0042
                           DUF3397  59 pllllvllllaillliiqarkkgeisykrffklfwRllfLltfllYlllliv 110
                                       + l+   llla++ +i ++r++   +++r+  ++w ++f l +++Y+ll +v
  gi|336255510|ref|YP_004598617.1| 135 VPLVYYALLLAGAYSIDELRRTSHARIGRLAASLWLVSFSLGIVVYVLLHVV 186
                                       334445678888999999******************************9876 PP

>> Amastin  Amastin surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   6.1e-05      0.16      63     149 ..      11      97 ..       4     103 .. 0.89
   2 ?   -0.1   1.2      0.29   7.4e+02      77      91 ..     121     166 ..     114     187 .] 0.43

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.1e-05
                           Amastin  63 raaqafsiisilvlaaalllsvllllccsslkwvclllnivsvvtllivwalmvavyykrfCdalksttakygaGFg 139
                                       ++a+++si+s++v++aa    +          wv+ l+  v v+++ +   ++++ ++  + + + ++ +++ a F+
  gi|336255510|ref|YP_004598617.1|  11 ELAAVLSIVSLAVVFAAAGGRIPQSTVPTAPEWVLELIPHVNVAISATAIGTITVGWRAIRRGDVDRHRVAMLASFV 87 
                                       689*******************99999999****************************988899999999******* PP

                           Amastin 140 Llvvawlldl 149
                                       L+v+   + l
  gi|336255510|ref|YP_004598617.1|  88 LFVAFLAFYL 97 
                                       **98776655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.29
                           Amastin  77 aaalllsvllllcc...............................s 91 
                                       ++ l + +ll++ c                               +
  gi|336255510|ref|YP_004598617.1| 121 LPILAIHILLAIVCvplvyyalllagaysidelrrtsharigrlaA 166
                                       4444444444444433333333334444444444444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); 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):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1442.67
//
Query:       gi|336255511|ref|YP_004598618.1|  [L=47]
Description: hypothetical protein Halxa_4135 [Halopiger xanaduensis SH-6]
Scores for 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   14.5   2.0      0.038   14.3   2.0    1.1  1  Tad       Putative Flp pilus-assembly TadE/G-like
       0.31   11.0   1.3       0.31   11.1   1.3    1.0  1  FixH      FixH
       0.45   10.5   5.0       0.57   10.2   5.0    1.2  1  OppC_N    N-terminal TM domain of oligopeptide transport perm


Domain annotation for each model (and alignments):
>> Tad  Putative Flp pilus-assembly TadE/G-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.0   6.4e-06     0.038       2      25 ..      16      39 ..      14      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.4e-06
                               Tad  2 saavlfalallpllllvglavDvg 25
                                      +aa++f+++l+++++++++ ++++
  gi|336255511|ref|YP_004598618.1| 16 QAAIIFFAFLILIVVAALFLIAFS 39
                                      89*************999988876 PP

>> FixH  FixH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.3   5.1e-05      0.31       3      31 ..      12      39 ..      10      47 .] 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.1e-05
                              FixH  3 fwgwhvllflialfavvvvvnltmlylAv 31
                                      ++g+ ++++++a+++++vv+ l+++   +
  gi|336255511|ref|YP_004598618.1| 12 LTGRQAAIIFFAFLILIVVAALFLIA-FS 39
                                      79999999999998888866655543.33 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   5.0   9.5e-05      0.57      15      36 ..      17      38 ..      11      46 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 9.5e-05
                            OppC_N 15 lAvvglvilllllliaifaPli 36
                                      +A++ +++l+l++++a+f   +
  gi|336255511|ref|YP_004598618.1| 17 AAIIFFAFLILIVVAALFLIAF 38
                                      7999999999999999994333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 382.69
//
Query:       gi|336255512|ref|YP_004598619.1|  [L=503]
Description: amidophosphoribosyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-19   69.4   0.0    6.9e-19   68.4   0.0    1.5  1  GATase_6      Glutamine amidotransferase domain
      1e-18   67.4   0.0    2.6e-18   66.1   0.0    1.7  1  GATase_7      Glutamine amidotransferase domain
    8.4e-09   35.1   0.1    1.6e-08   34.2   0.1    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0019   17.2   0.0     0.0039   16.1   0.0    1.5  2  GATase_4      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 !   68.4   0.0   1.5e-22   6.9e-19       8     134 .]      78     212 ..      65     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 1.5e-22
                          GATase_6   8 slvedevalaHvRlaivglaeeegaqPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevlla.ll 81 
                                       ++  + ++++HvR  + g  ++  aqPf  + ++g l l+hNG   n++e+reel+a +g+af s+ Dtev+++ l+
  gi|336255512|ref|YP_004598619.1|  78 DMLNGAAGVGHVRYPTAGSVDSCCAQPFsvSFKSGSLGLSHNGNLVNADEIREELAA-AGHAFTSDGDTEVIAHdLA 153
                                       4556679************855556***99999************************.****************988 PP

                          GATase_6  82 eelG........eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                       ++l         ++++ r+ G ++   + ++ +t+  +rd  g++pl+++  e+g + ase
  gi|336255512|ref|YP_004598619.1| 154 RNLLeedlvravKRTMGRIHGSYSL--TISHDDTILGVRDPQGNRPLCIGKLEDGYMLASE 212
                                       5555333434445555566665544..55578899999**********************8 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.0   5.9e-22   2.6e-18      13     122 ..     102     217 ..      96     218 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 5.9e-22
                          GATase_7  13 aQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea........ewgeealerlnGmfAf 80 
                                       aQP++   ++g+l + +nG ++N +e+reeL+a+gh+f++++Dtev+++ l++        + +++++ r++G++++
  gi|336255512|ref|YP_004598619.1| 102 AQPFSVsFKSGSLGLSHNGNLVNADEIREELAAAGHAFTSDGDTEVIAHDLARnlleedlvRAVKRTMGRIHGSYSL 178
                                       7999986799**************************************9999899*99*9999************** PP

                          GATase_7  81 aiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                        i ++++  +l +RD+ G +PL +g+ + d++++aSe  a+ 
  gi|336255512|ref|YP_004598619.1| 179 TISHDDT--ILGVRDPQGNRPLCIGKLE-DGYMLASESAAID 217
                                       **99999..******************6.7*******99985 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.1   3.6e-12   1.6e-08      22     120 ..     286     406 ..     270     443 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 3.6e-12
                                       EEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........................... CS
                      Pribosyltran  22 ileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes................... 79 
                                       + ee + + dvv++++  G  fa+ +ad+   + +   + +  +d++ e+a+g+++++                   
  gi|336255512|ref|YP_004598619.1| 286 LWEESGVETDVVMPVPDSGRAFASGYADAAS-ETTADGEPRDADDDGVEFAEGLMKNRyvgrtfimptqdereravr 361
                                       344466789*********************9.88888899999999999999****99******************* PP

                                       ....EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEE CS
                      Pribosyltran  80 ....rlledpagkkVliVDDildtGgTllaalelLkekgpeevri 120
                                              + ++gk+V ++DD +  G+T +  ++lLk++g+eev++
  gi|336255512|ref|YP_004598619.1| 362 lklnPIKSTIEGKTVTVIDDSIVRGTTSTQLVQLLKDCGAEEVHV 406
                                       ***999999********************************9975 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.8e-07    0.0039      73     134 ..      84     149 ..      76     175 .. 0.73
   2 ?   -4.2   0.0       1.3     6e+03     237     250 ..     224     237 ..     218     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.8e-07
                          GATase_4  73 nvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlke...ykpkl.egrfePvGsTDsElaf 134
                                         v H+R  t G+v    ++pF+ +++  +  + HnG+l +   ++++l +  +    + D+E++ 
  gi|336255512|ref|YP_004598619.1|  84 AGVGHVRYPTAGSVDSCCAQPFSVSFKSGSLGLSHNGNLVNadeIREELaAAGHAFTSDGDTEVIA 149
                                       5689***********************************662224555542223333445556555 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 1.3
                          GATase_4 237 WkklepGellvfrd 250
                                        ++++pGel+v+++
  gi|336255512|ref|YP_004598619.1| 224 VRDVKPGELIVLQE 237
                                       57899999999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3940.70
//
Query:       gi|336255513|ref|YP_004598620.1|  [L=477]
Description: Citrate transporter [Halopiger xanaduensis SH-6]
Scores for 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-33  116.2  16.3    2.7e-33  115.8  16.3    1.0  1  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    1.7e-17   63.6  20.7    1.7e-17   63.6  20.7    1.8  2  CitMHS         Citrate transporter


Domain annotation for each model (and alignments):
>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8  16.3     3e-37   2.7e-33      26     459 ..      31     466 ..      10     473 .. 0.85

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 3e-37
                     Na_sulph_symp  26 leskawrllaifiaaivglileplplavialialsllavligvlaakalsevlsgfssdttlLvfaalliaaavekt 102
                                       ++s +  +l i ++ iv ++l p+p   + li+l l+av   ++       +l+gf++ +t+L+  +ll++ a  ++
  gi|336255513|ref|YP_004598620.1|  31 VPSGTGTMLSITLFCIVLWVLTPVPPSYTGLIGLGLIAVAFSTDL------ALVGFQKPATWLIGFGLLMGEATRQS 101
                                       56777889*****************************88888888......************************** PP

                     Na_sulph_symp 103 gL....gkRiAlvlvkivG....krt.liLgyalvladlllapatpsntAraggivfpvikslssafgsepekqser 170
                                       gL    g+ iA + +         rt ++L +al l   +la  +ps+  r  + + p++++l s f+s  +     
  gi|336255513|ref|YP_004598620.1| 102 GLanavGRTIATRSIGDPAdadtRRTyRRLLFALALGGHALAFLVPSALVRILALA-PILRELGSWFDSREAR---- 173
                                       *944445666776665432211145599***************************9.******9999987655.... PP

                     Na_sulph_symp 171 kigaylmltvvqsasitsiaflTamApNllllglinsilgveitwasWflaaip.tgvillllvplllyvlyppeik 246
                                        +g yl    + ++  +s+ +lTa  pN++++g+++si g +i+w +W l + p +g++ +llv  ++y l+ p  +
  gi|336255513|ref|YP_004598620.1| 174 -VGLYL--GPLFGTFYGSAGILTADLPNIIISGFAESIGGHTISWSEWWLHMYPvMGLVRVLLVVSIVYLLFRPPAD 247
                                       .77665..66789***********************************9998862679**************99887 PP

                     Na_sulph_symp 247 kke........eakavaktelkelGpltarekallilfvlllllWifgeslnidattvaivvlvillllr..vldWk 313
                                       +             ++++++  +   ++a+e+++l+ +++   +W+++   ++   + a+ v+v+ +l++  v d +
  gi|336255513|ref|YP_004598620.1| 248 AGFdvpdadteTDDTAVTDGDDTDTGFSAAERRMLAFLLVGAAIWATDFVHGFHPVIGAVAVVVLAFLPEigVADFD 324
                                       76556777776556677777777778********************9877778887777777777777774477777 PP

                     Na_sulph_symp 314 DivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvh..ylfaSatAttaal 388
                                        +v  +  + +l++ +++ a+  +l+++g+ +  +  l  +     +a++ +i+ s+f++++   +   ++A  ++l
  gi|336255513|ref|YP_004598620.1| 325 -TVGGEVDYSILFFIAAVFAIGDGLTETGFTDTAATHLLELIP--TGAPLAVILASVFFITFglSFLMEGVAVASVL 398
                                       .*******************************99999999999..8999999999999888743467899******* PP

                     Na_sulph_symp 389 lpillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGfilsiigllill 459
                                        p+l+   +++ g p   v l+ ++a s  +   py ++   +++  g++ +++   + +  s+ ++++ll
  gi|336255513|ref|YP_004598620.1| 399 TPVLIPYIEGA-GLPFTPVLLAETMALS--SYFFPYQSAVLIVILNEGDIRTRELIVATVACSLATIVLLL 466
                                       *********99.8877777777777655..4489********************99998888888887776 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.4      0.26   2.3e+03       7      27 ..       8      29 ..       6      45 .. 0.46
   2 !   63.6  20.7   1.9e-21   1.7e-17       1     299 [.      46     422 ..      46     425 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.26
                                      xxxxxxxxxxxxxxxx.xxxxx RF
                            CitMHS  7 eklrldvvallvlvll.vltie 27
                                      e lr++vva+ +++++   t  
  gi|336255513|ref|YP_004598620.1|  8 ETLRSPVVAFGLAATVaAATWL 29
                                      5677777777444443322222 PP

  == domain 2  score: 63.6 bits;  conditional E-value: 1.9e-21
                                       xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                            CitMHS   1 lvllileklrldvvallvlvll..vltieealsgiaspiillllgamiigaaleetGlfdrlaakll.......... 65 
                                       +vl++l+ ++ + + l++l l    ++ + al g+  p+++l++++ ++g+a  ++Gl++ ++++++          
  gi|336255513|ref|YP_004598620.1|  46 IVLWVLTPVPPSYTGLIGLGLIavAFSTDLALVGFQKPATWLIGFGLLMGEATRQSGLANAVGRTIAtrsigdpada 122
                                       69**************99999887888888**********************************************8 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  66 rlaggkrdllvllvlltallsafvsndgv.vlimipivlslakrlkklppl..lliplalaaniggaltpiGtpttr 139
                                          ++ r+ll++l+l+   l+ +v    v +l ++pi+ +l+     + ++  l +   ++   g+a ++  +    
  gi|336255513|ref|YP_004598620.1| 123 DTRRTYRRLLFALALGGHALAFLVPSALVrILALAPILRELGSWFDSREARvgLYLGPLFGTFYGSAGILTADL--- 196
                                       444444468999999999997777665557999******999987767666897778889999999999999**... PP

                                       xxxxxxxxxxxxxx........................xxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                            CitMHS 140 aaarpglslpnlll........................lalllvgllplvllfmfgvalalpvnap........... 181
                                                pn+++                        ++l+ v+l++ +++++f  +                   
  gi|336255513|ref|YP_004598620.1| 197 ---------PNIIIsgfaesigghtiswsewwlhmypvMGLVRVLLVVSIVYLLFRPPAD-----Agfdvpdadtet 259
                                       .........*****8888888888888888888887765555555555555554444444.....245555999999 PP

                                       ..........xxxxxxxxxxxxxxxxxxx......................xxxxxxx..................x RF
                            CitMHS 182 ..........kvkkqkaiieaiarsllpv......................atillla..................y 208
                                                 +       ++a +r++l                        +     a                   
  gi|336255513|ref|YP_004598620.1| 260 ddtavtdgddT----DTGFSAAERRMLAFllvgaaiwatdfvhgfhpvigaV-----AvvvlaflpeigvadfdtvG 327
                                       99999955543....4444444444442233345555555555555555543.....04455589*********999 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 209 kkveWsvlllfaGvfllvgaleqtGilealadllga....g.gplvalalvlgliallsafisnvavaalmapialg 280
                                        +v++s+l+++a+vf  +++l++tG  ++ a+ l +    g +++v+la v++++  ls+++  vava +++p+++ 
  gi|336255513|ref|YP_004598620.1| 328 GEVDYSILFFIAAVFAIGDGLTETGFTDTAATHLLEliptGaPLAVILASVFFITFGLSFLMEGVAVASVLTPVLIP 404
                                       *************************66666655523355554776766777777777******************** PP

                                       xxxxxxxxxxxxxxxxxxx RF
                            CitMHS 281 mapalgllspsplalalav 299
                                          ++g l++ p++la ++
  gi|336255513|ref|YP_004598620.1| 405 YIEGAG-LPFTPVLLAETM 422
                                       999989.555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); 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:                         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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3681.15
//
Query:       gi|336255514|ref|YP_004598621.1|  [L=595]
Description: DNA mismatch repair protein MutS domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   31.6   0.0    2.8e-07   30.8   0.0    1.3  1  MutS_V     MutS domain V
     0.0067   16.3   0.1      0.029   14.2   0.0    2.1  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
  ------ inclusion threshold ------
      0.015   15.5   1.2      0.045   14.0   0.0    2.4  3  AAA_28     AAA domain
       0.19   12.4   1.7        2.7    8.7   0.1    3.0  2  HHH_5      Helix-hairpin-helix domain
       0.19   11.8   0.0       0.34   10.9   0.0    1.4  1  AAA_14     AAA domain
       0.28   11.6   0.0       0.52   10.8   0.0    1.3  1  AAA_23     AAA domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   9.2e-11   2.8e-07       2      48 ..     392     439 ..     391     458 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 9.2e-11
                                       EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEE.EEEE CS
                            MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdki.ftRv 48 
                                       ++tG+n +Gk t+l   + +vlla +G  vpa++ae+++vd++ f R 
  gi|336255514|ref|YP_004598621.1| 392 VLTGANSGGKTTLLETLCHVVLLAMMGLPVPADRAEVTPVDSLvFHRR 439
                                       89***************************************8526665 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 ?   -1.4   0.0      0.55   1.6e+03     148     148 ..     234     234 ..     165     322 .. 0.53
   2 !   14.2   0.0   9.8e-06     0.029       1      19 [.     390     408 ..     390     417 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.55
                            AAA_21 148 t 148
                                       +
  gi|336255514|ref|YP_004598621.1| 234 R 234
                                       1 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 9.8e-06
                            AAA_21   1 lnvliGpNgsGKSnLLdal 19 
                                       ++vl+G+N+ GK++LL++l
  gi|336255514|ref|YP_004598621.1| 390 VAVLTGANSGGKTTLLETL 408
                                       68***************98 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.9   5.6e+03     118     144 ..     246     270 ..     220     291 .. 0.58
   2 ?   -3.1   0.0       2.7     8e+03      15      49 ..     278     311 ..     269     327 .. 0.59
   3 ?   14.0   0.0   1.5e-05     0.045       3      19 ..     392     408 ..     390     427 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.9
                            AAA_28 118 apeidddgeRredleereaiderlrea 144
                                       +  i  d +R+  + ++++ ++ +  +
  gi|336255514|ref|YP_004598621.1| 246 DVTI--DRVRDAMPTDAADATDFVGGT 270
                                       2222..555555555555555555555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.7
                            AAA_28  15 lleaLaargypvvpEaareileeklakgedalpwv 49 
                                       l++a+ +r+ +v  E +r ile+  +   +a ++v
  gi|336255514|ref|YP_004598621.1| 278 LTAAIDEREETVASE-YRAILEDADEAVDRAVEAV 311
                                       444444444444444.4677777666666666665 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 1.5e-05
                            AAA_28   3 vitGgestGKTtlleaL 19 
                                       v+tG+ s+GKTtlle L
  gi|336255514|ref|YP_004598621.1| 392 VLTGANSGGKTTLLETL 408
                                       9*************998 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00091       2.7       9      51 ..       8      51 ..       6      55 .. 0.81
   2 ?    1.4   0.2      0.17   5.1e+02      14      40 ..     150     178 ..     148     192 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00091
                                      T--HHHHHHHHTT.T--.SHHHHHHS-HHHHHTSTTS-HHHHHHH CS
                             HHH_5  9 GiGpktAlallsa.Gie.svedlaaadveeLakipGiGkktAeri 51
                                      G+Gpkt  +l++  G e  ++++ + dv +La++ G+   +A ri
  gi|336255514|ref|YP_004598621.1|  8 GVGPKTRETLVEElGRErAIQAIENGDVRALADA-GLARGRATRI 51
                                      9************66333699**********998.7766666666 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.17
                                       HHHHHHTTT--S..HHHHHHS-HHHHHTS CS
                             HHH_5  14 tAlallsaGies..vedlaaadveeLaki 40 
                                        Al ll+aG++   + ++a++++ +L ++
  gi|336255514|ref|YP_004598621.1| 150 AALGLLEAGVDAgpFGAIADLERGTLEEA 178
                                       68999999999655667777765555543 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.34       2      78 ..     388     477 ..     387     503 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell.......vkkesilyinldderdkkla.dpe.kllelileklke....... 62 
                                       +++ v+tGa   GKTtll++l +  l       v++++     +d+  + ++   ++  +le  l+   +       
  gi|336255514|ref|YP_004598621.1| 388 ERVAVLTGANSGGKTTLLETLCHVVLlammglpVPADRAEVTPVDSLVFHRRHaSFNaGVLESTLR---Sivpplss 461
                                       5789*****************988778888888777777777777766643221332322222222...12234666 PP

                            AAA_14  63 ekktylflDEiqevpe 78 
                                        ++t+++ DE   ++e
  gi|336255514|ref|YP_004598621.1| 462 GGRTLMLVDEFEAITE 477
                                       7888899999887754 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017      0.52      21      40 ..     390     409 ..     383     420 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                            AAA_23  21 ltlItGpNGaGKTTildAik 40 
                                       + ++tG N  GKTT+l+ ++
  gi|336255514|ref|YP_004598621.1| 390 VAVLTGANSGGKTTLLETLC 409
                                       6799*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 4468.66
//
Query:       gi|336255515|ref|YP_004598622.1|  [L=191]
Description: hypothetical protein Halxa_4139 [Halopiger xanaduensis SH-6]
Scores for 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  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1509.51
//
Query:       gi|336255516|ref|YP_004598623.1|  [L=219]
Description: HAD-superfamily hydrolase [Halopiger xanaduensis SH-6]
Scores for 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-14   53.6   0.0    3.3e-14   53.4   0.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    5.3e-08   32.8   0.1    1.1e-07   31.8   0.1    1.5  1  Hydrolase_like  HAD-hyrolase-like
    7.4e-07   29.7   1.4    9.1e-06   26.1   1.4    2.0  1  Hydrolase       haloacid dehalogenase-like hydrolase
    0.00019   21.9   0.3    0.00025   21.5   0.3    1.2  1  HAD             haloacid dehalogenase-like hydrolase
     0.0005   19.1   0.5    0.00068   18.7   0.5    1.2  1  DUF3375         Protein of unknown function (DUF3375)


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 !   53.4   0.0   9.1e-18   3.3e-14       1     178 []      10     191 ..      10     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 9.1e-18
                             HAD_2   1 iiFDlDgTlldte..eliiqafnelleeyglselseeelrkliglslrellrklgeseeeee..........kieel 65 
                                       +iFD Dg+l   +  +++++a+  ++++ g  e++++++++l+g++  e+lr+++++  ++            ie  
  gi|336255516|ref|YP_004598623.1|  10 VIFDNDGVLTTPTdyDVLVDATYDAFASVGAAEPTRDHVETLLGPDV-ESLRQVADDHGVDPadlwaareraAIEAQ 85 
                                       7********9765116799***************************9.99999999988888997775544444444 PP

                             HAD_2  66 lrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsed....vekkKPdp 138
                                       l+++++  k    ++yd+v ++L+ L   +   +iv+++++e++ + le+l+i   Fdv ++ e     +e+kKP++
  gi|336255516|ref|YP_004598623.1|  86 LEEIRAGRK----RLYDDV-SVLDRL---EQPSAIVSNNQHETIGNILEHLDI-GGFDVWYGREPsiegIERKKPNA 153
                                       444444444....477776.699999...4589*******************8.88*****997633338999**** PP

                             HAD_2 139 eviekaleklklkkeeviyvGDsptDieaakkagikviav 178
                                         +e a++ l ++  + +yvGDs  D+ aa +ag++++ v
  gi|336255516|ref|YP_004598623.1| 154 YYLESAIDDLAVS--NPLYVGDSRVDVTAAAEAGVDSAFV 191
                                       ********99986..579*****************99865 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1   3.1e-11   1.1e-07       3      74 ..     149     214 ..     147     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3.1e-11
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                        KP++  +++a  +l  + ++ l++GD+ + D+ +A +aG++s++V++   +  dl+    +p+y +d+la+
  gi|336255516|ref|YP_004598623.1| 149 KKPNAYYLESAIDDL--AVSNPLYVGDS-RVDVTAAAEAGVDSAFVRRDHREGYDLP---TEPDYEIDSLAA 214
                                       6************98..5599*******.*********************9999988...679999999875 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   1.4   2.5e-09   9.1e-06       1     210 []       7     185 ..       7     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.5e-09
                                       SSEEEEESBTTTBCHH..HHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHH CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttge..psvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpe 75 
                                       +++v+fD dG+Ltt +   +++d++  a                      a  +  +++ +  +     +++   +e
  gi|336255516|ref|YP_004598623.1|   7 YDAVIFDNDGVLTTPTdyDVLVDATYDA---------------------FASVGAAEPTRDHVE-----TLLGPDVE 57 
                                       589**********777557777777777.....................555555666677777.....89999999 PP

                                       HHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  76 wltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraa 152
                                        l++    +d g +  ++ ++ + +a++ a++ ++ +      +++++  ++ +L +     ++++++++et   ++
  gi|336255516|ref|YP_004598623.1|  58 SLRQV--ADDHGVDPADLWAARERAAIE-AQLEEIRAGRKR--LYDDV-SVLDRLEQP---SAIVSNNQHETIGNIL 125
                                       99999..444444444444444444444.566666666666..99998.899999976...67************** PP

                                       HHTTGGGESEEEEHHCES....STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 153 nqlGddyfdaviasdiet....vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       ++l+   fd+ ++++ +      +kp+   ++ ai+ L ++    + VGD+  D+ a+a+Ag
  gi|336255516|ref|YP_004598623.1| 126 EHLDIGGFDVWYGREPSIegieRKKPNAYYLESAIDDLAVSN--PLYVGDSRVDVTAAAEAG 185
                                       **99444444444433333377****************8665..7****************8 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.3   6.8e-08   0.00025       1     187 [.      10     181 ..      10     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.8e-08
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaellea.......llagls.eel 69 
                                       ++fD+Dg L++   +++l+++ +  +a+  +++    +  ++ ++ll  d ++l+++ +        l+a+ + +++
  gi|336255516|ref|YP_004598623.1|  10 VIFDNDGVLTTPTDYDVLVDATYDAFASVGAAE----PTRDHVETLLGPDVESLRQVADDhgvdpadLWAARErAAI 82 
                                       79*******999889988886666655444333....3344444445554555555555555555559999999999 PP

                               HAD  70 aaelerfvaevirpklldp.galellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelgle 145
                                       +a+le+++  + r++l+d   +l++l+       + ++vS++  + +  +l++l+    ++    +d ++ g+   +
  gi|336255516|ref|YP_004598623.1|  83 EAQLEEIR--AGRKRLYDDvSVLDRLE------QPSAIVSNNQHETIGNILEHLD----IGG---FD-VWYGREPSI 143
                                       99999999..34444776678888888......4678******************....***...33.899998889 PP

                               HAD 146 gkpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                       +++ r++  +  l++    +  +++ ++  ++GDs+ D+ ++
  gi|336255516|ref|YP_004598623.1| 144 EGIERKKPNAYYLES----AIDDLAVSNPLYVGDSRVDVTAA 181
                                       999998777777777....4445555567899******9887 PP

>> DUF3375  Protein of unknown function (DUF3375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.5   1.9e-07   0.00068     123     177 ..      57     109 ..      43     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.9e-07
                           DUF3375 123 ealeqlaeetepDpeeRlaeLeaeiaeidaeidrlrageveelddeqvlerirei 177
                                       e+l+q+a++   Dp+   a+  +e+a+i+a+++++rag+ +++dd  vl+r+++ 
  gi|336255516|ref|YP_004598623.1|  57 ESLRQVADDHGVDPADLWAA--RERAAIEAQLEEIRAGRKRLYDDVSVLDRLEQP 109
                                       78999999999999999996..9*****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); 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:                         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 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1651.46
//
Query:       gi|336255517|ref|YP_004598624.1|  [L=154]
Description: polyketide cyclase/dehydrase [Halopiger xanaduensis SH-6]
Scores for complete 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   45.2   0.7    1.3e-11   45.0   0.7    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    1.1e-05   25.6   0.2    1.3e-05   25.4   0.2    1.4  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
    9.1e-05   22.7   0.0     0.0001   22.5   0.0    1.2  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.7   2.1e-15   1.3e-11       8     142 ..       8     144 ..       1     145 [. 0.77

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.1e-15
                                       EEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSE.STSSSTTTEEEEECCCSSEEEEEEEEEETTTTEEEEEEE.SS CS
                   Polyketide_cyc2   8 vviaappekVwalvsdfenwprWhpevarveleg.gggpargvegtvrvggrgtvreelvevdpegrllsyrivkpv 83 
                                        +i+app  Vw+++  f+++p+W p+v++ e+   +g+++r++ +     g  t + e++ +++ +r+l++ ++  v
  gi|336255517|ref|YP_004598624.1|   8 EEIDAPPPVVWDVLLEFDSYPEWNPFVRSIEGLPvQGERLRVRIEPPDSRG-MTFEPEVIVAEE-HRRLAWVGRLAV 82 
                                       58****************************976535777555545555555.579999999997.********7566 PP

                                       S-T.SEEEEEEEEECCET..EEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHH CS
                   Polyketide_cyc2  84 pva.nyvatwtvtpdggg..trvtwtgefdagplggpfekpaaakavkgdleagLerLkarl 142
                                       p+a ++  ++ + p++gg  tr+  + +f+++ ++ +f+ + +++++++   a  er ++r+
  gi|336255517|ref|YP_004598624.1|  83 PFAfDGYHEFHLDPVDGGrrTRLLHRETFRGALVPLLFDRERLERGFAAMNAAVKERAERRV 144
                                       666478999*******9978776666778877777888777777777777666666666666 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.2   2.2e-09   1.3e-05       1      36 [.      10      45 ..      10     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.2e-09
                                      ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE CS
                    Polyketide_cyc  1 vpapadqvyalvadvesypeflphcssvevleeaes 36
                                      ++ap+ +v++++  ++sype++p+++s e l   ++
  gi|336255517|ref|YP_004598624.1| 10 IDAPPPVVWDVLLEFDSYPEWNPFVRSIEGLPVQGE 45
                                      79************************8887766665 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.8e-08    0.0001       1     100 [.      11     111 ..      11     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.8e-08
                                       SS-HHHHHHHHH-HHHHHHH.EEEEEEEE--STTEEEEE.EETTTSEEEEEEEEEEEEETTTEEEEEEEEETSETEE CS
                             AHSA1   1 dapperVfraltdpellkrW.ftlteaemdlrpGgkfrl.rdspdgkefgnegeylevvpperlvytwrledepeee 75 
                                       dapp  V+++l++ +    W   + ++e  +  G + r+  + pd++ +++e e++  ++++rl +  rl+ +    
  gi|336255517|ref|YP_004598624.1|  11 DAPPPVVWDVLLEFDSYPEWnPFVRSIEGLPVQGERLRVrIEPPDSRGMTFEPEVIVAEEHRRLAWVGRLAVPF-AF 86 
                                       69******************5444445555556**99999888************************9988544.55 PP

                                       EEEEEEEEEEETTEEEEEEEEEEEE CS
                             AHSA1  76 estvtieleeegggTrltlthtglp 100
                                       +   ++ l +++gg r +l h++  
  gi|336255517|ref|YP_004598624.1|  87 DGYHEFHLDPVDGGRRTRLLHRETF 111
                                       999**********999998885444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1122.61
//
Query:       gi|336255518|ref|YP_004598625.1|  [L=484]
Description: hypothetical protein Halxa_4142 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        2.3    8.5  12.0         41    4.5   0.0    3.9  4  COX7C     Cytochrome c oxidase subunit VIIc


Domain annotation for each model (and alignments):
>> COX7C  Cytochrome c oxidase subunit VIIc
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.4    0.0043        77      28      52 ..     101     124 ..      97     129 .. 0.81
   2 ?   -1.7   0.0      0.21   3.7e+03      20      51 ..     157     191 ..     152     193 .. 0.62
   3 ?    4.5   0.0    0.0023        41      16      60 ..     239     285 ..     233     285 .. 0.71
   4 ?    3.8   1.8     0.004        71      38      61 ..     447     470 ..     443     472 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0043
                                       SSSS--SSHHHHHHHHHHHHHHHHH CS
                             COX7C  28 nLPFsknnKipfavkywgflgvgFa 52 
                                       nLPF  +     av++++  gv+F+
  gi|336255518|ref|YP_004598625.1| 101 NLPF-ATAVVVPAVWFVTMVGVVFS 124
                                       9***.45558899999999999997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.21
                                       -S--STTTSSSS..--SSH.HHHHHHHHHHHHHHH CS
                             COX7C  20 hykegpysnLPF..sknnK.ipfavkywgflgvgF 51 
                                       h  +g +s  P+  ++++   +f+v +++f + g+
  gi|336255518|ref|YP_004598625.1| 157 HLRGGYESASPYavVETPArQAFFVAFVLFVTPGI 191
                                       55555666666665444444778888888877665 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0023
                                       XXXX-S--S.TTTSSSS--SSH...HHHHHHHHHHHHHHHHHHHHHHHH CS
                             COX7C  16 srsghykeg.pysnLPFsknnK...ipfavkywgflgvgFalPFlavrw 60 
                                       + ++ +++g p  +LP   +n+   ++ a+ + g l+ ++a+PF++ ++
  gi|336255518|ref|YP_004598625.1| 239 REPVCVPDGePDVRLPT--DNRavlYTGAFDVLGRLAPFLAMPFIILWF 285
                                       56777888889999999..555111444556778888999999999986 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.004
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             COX7C  38 pfavkywgflgvgFalPFlavrwQ 61 
                                       pf ++++g     F++PF+a +  
  gi|336255518|ref|YP_004598625.1| 447 PFRLLFTGLVYGTFGIPFAALVLR 470
                                       8999***************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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 0.21s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3870.31
//
Query:       gi|336255519|ref|YP_004598626.1|  [L=372]
Description: hypothetical protein Halxa_4143 [Halopiger xanaduensis SH-6]
Scores for complete 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-11   44.6   2.7    1.5e-11   44.6   2.7    1.8  2  Acetyltransf_6  Acetyltransferase (GNAT) domain
    8.5e-08   31.5   0.5    1.3e-06   27.6   0.1    2.0  2  FemAB           FemAB family
    4.8e-07   29.2   0.0     0.0029   16.8   0.0    2.1  2  FemAB_like      Peptidogalycan biosysnthesis/recognition


Domain annotation for each model (and alignments):
>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         1     6e+03      92     141 ..     144     191 ..     141     192 .. 0.65
   2 !   44.6   2.7   2.6e-15   1.5e-11       8     139 ..     199     326 ..     194     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1
                    Acetyltransf_6  92 gdrlyywlggydpelaklspgllllweliedaaeeGlrrfdlgggdeeyK 141
                                       g+++  ++ g d ++ ++  +  l++e  + +++e + ++dl +g e  K
  gi|336255519|ref|YP_004598626.1| 144 GRTIVHQIRGLDTDYLRY--NNTLQAEGYRPYRRECRFEIDLSRGYEAVK 191
                                       566666666667666666..456777777777777777788888877666 PP

  == domain 2  score: 44.6 bits;  conditional E-value: 2.6e-15
                    Acetyltransf_6   8 rrkrrkleelgevrfrvatdpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrldgrpvA 84 
                                       rr++rk+ e +   ++++ +++ +e++++ +r+   r      d ++ +f+++l + +  + ++ l++lr +g++++
  gi|336255519|ref|YP_004598626.1| 199 RRGIRKGKETDHEIVEAELTRANVERFYRSYRRVMDRV---GGDIYPFSFFEAL-RGM--ESRVLLLTLRIEGEYAG 269
                                       89999999988778888899999*******99986655...55678899**988.555..79*************** PP

                    Acetyltransf_6  85 valglrsgd..rlyywlggydpelaklspgllllweliedaaeeGlrrfdlgggdee 139
                                       ++l l +++   ++ +++++ +e+ + ++ +ll+ +++++ +++G++++dlg  ++ 
  gi|336255519|ref|YP_004598626.1| 270 GCLQLLDEEqnAVHGFFAAVPREYYDDHASELLYDRVVQWGIDRGYETYDLGSTNAS 326
                                       **9999987779****************************************97753 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.013        77     156     211 ..     181     237 ..     165     250 .. 0.73
   2 !   27.6   0.1   2.2e-10   1.3e-06     316     380 ..     279     341 ..     272     343 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.013
                             FemAB 156 ldleeiteedllksfskktrknikkakkkGvkv..rrltreeldvFkeltqkTeerkg 211
                                       +dl+    e +   +sk +r+ i+k k+   ++  ++ltr ++++F++ ++  ++r g
  gi|336255519|ref|YP_004598626.1| 181 IDLSR-GYEAVKDGMSKGRRRGIRKGKETDHEIveAELTRANVERFYRSYRRVMDRVG 237
                                       55555.33445559**********998755444116779999*****99999998866 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 2.2e-10
                             FemAB 316 dqevvylysGsdekfrkfyapyllqweaiqeAlergieryNfyGiegkfdgsdGvlrFKtgFngf 380
                                       ++ v  ++++   ++ +  a+ ll+++++q  ++rg+e y+++  + +f++  Gv+rFK+gF+g+
  gi|336255519|ref|YP_004598626.1| 279 QNAVHGFFAAVPREYYDDHASELLYDRVVQWGIDRGYETYDLGSTNASFED--GVYRFKEGFGGQ 341
                                       567778899999999999********************************9..**********96 PP

>> FemAB_like  Peptidogalycan biosysnthesis/recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0     4e-05      0.24       1      60 [.      42      97 ..      42     101 .. 0.85
   2 !   16.8   0.0   4.8e-07    0.0029     168     314 ..     185     322 ..     124     338 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4e-05
                        FemAB_like  1 siaeiaaeeWdalagp..eknpflrhaflsaleesgsvsektGWqprhlvleeegklvaaap 60
                                      si+++++++W+ +++     + f r+++l+a+e+        G  ++hl++e++g+l++++p
  gi|336255519|ref|YP_004598626.1| 42 SIRAVDRSRWNDVVRGarCGSVFHRYEWLEAIET------GLGHPAKHLLVEKDGNLIGLLP 97
                                      57899********764225789*********996......5799999**********99998 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.8e-07
                        FemAB_like 168 egyasfddfLaalssrkRknirkerrkvaeqgitievltgeeiteeewdafyefYqetyskkwgspyLtreffella 244
                                       +gy+   d    +s+ +R+ irk +++        + +  +e+t++++++fy+ Y++ +++  g  y   +ffe l+
  gi|336255519|ref|YP_004598626.1| 185 RGYEAVKD---GMSKGRRRGIRKGKETD-------HEIVEAELTRANVERFYRSYRRVMDRVGGDIY-PFSFFEALR 250
                                       45544443...67777888888877654.......34567899****************99966666.678999885 PP

                        FemAB_like 245 erlaekvllvlaeregeliagalnlig..edtlyGRyWGaleelpfLH.FevcyyqaiefaiaeglkrfeaGa 314
                                         ++++vll++ + ege+ +g l l +  +++++G +    +e+   H  e+ y + +++ i +g ++++ G+
  gi|336255519|ref|YP_004598626.1| 251 -GMESRVLLLTLRIEGEYAGGCLQLLDeeQNAVHGFFAAVPREYYDDHaSELLYDRVVQWGIDRGYETYDLGS 322
                                       .79**********************985577899988887777666662578888899999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2954.03
//
Query:       gi|336255520|ref|YP_004598627.1|  [L=337]
Description: NADPH:quinone reductase [Halopiger xanaduensis SH-6]
Scores for complete 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-26   93.2   0.3    2.1e-26   92.4   0.3    1.4  1  ADH_zinc_N    Zinc-binding dehydrogenase
    4.4e-21   74.8   0.8    7.5e-21   74.1   0.1    1.8  2  ADH_N         Alcohol dehydrogenase GroES-like domain
      1e-18   68.7   0.1    1.9e-18   67.8   0.1    1.5  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    0.00081   19.4   0.1      0.002   18.1   0.1    1.7  1  NADH_4Fe-4S   NADH-ubiquinone oxidoreductase-F iron-sulfur bi


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 !   92.4   0.3   4.8e-30   2.1e-26       1     129 [.     175     300 ..     175     301 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 4.8e-30
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvGsgatleaal 76 
                                       gvG+a+vqlA ++Ga++++++sse+kle +++lG d+ i ++++ ++ er++e+     +d+v++++G g+  e   
  gi|336255520|ref|YP_004598627.1| 175 GVGVATVQLADIIGARTVGTSSSESKLERVRELGLDHGIRSTDTdEIRERVAEIG---TPDAVINHLG-GEYTELGQ 247
                                       9****************************************99999*********...9*********.******** PP

                                       HCEEEEEEEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                        ADH_zinc_N  77 kllkpgGrlvvvGg.gkgeeefdlrnlllkeksilGsllgslreefkealdlla 129
                                        ++++gG++v++G   +g +++d+++++l +k+++Gs++g+ ++++++++dl+a
  gi|336255520|ref|YP_004598627.1| 248 HVMRRGGTMVICGRtAGGTSSIDVADFFLGHKRVVGSTMGT-QDDLRRLVDLVA 300
                                       **************5555555********************.*********997 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.1   1.7e-24   7.5e-21       1     108 [.      27     132 ..      27     133 .. 0.90
   2 ?   -2.1   0.1      0.77   3.4e+03      34      59 ..     233     257 ..     211     279 .. 0.57

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 1.7e-24
                                       TTEEEEEEEEEEE-HHHHHHHTTS..TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHT CS
                             ADH_N   1 pgevlikvkaagiCgsDlhilkgg..kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCke 75 
                                       pge++++v+a++i++ Dl+il+g+        lp++ G +++G+v evg++v++++ Gd Vv+ p+ +cgeC+ C+e
  gi|336255520|ref|YP_004598627.1|  27 PGEAVVDVAACAINRHDLWILEGDsaMVDADDLPFVTGLDVAGTVREVGDGVSSVAPGDAVVLCPNETCGECRFCRE 103
                                       5899*******************85444456799******************************************* PP

                                       T-GGG-TTBEETTTSS-SSSBSEEEECGGGEEE CS
                             ADH_N  76 geenlCeeakllgvsldGgfaeyvvvpekklvk 108
                                       g en+Ce+ +l+    +Gg+ae   v+++ l++
  gi|336255520|ref|YP_004598627.1| 104 GPENMCENFSLY----HGGLAEAARVEADRLLP 132
                                       ******998774....69999999999888876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.77
                                       E---EEEEEEEEESTT-CS--TT-EE CS
                             ADH_N  34 ilGHEivGeveevgpevkklkvGdrV 59 
                                       ++   + Ge  e+g++v   + G++V
  gi|336255520|ref|YP_004598627.1| 233 AVINHLGGEYTELGQHVM-RRGGTMV 257
                                       444445555555555553.2333333 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.1   4.3e-22   1.9e-18       1     133 []     207     335 ..     207     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 4.3e-22
                                       TT-SEEEETT.STTHH.HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----..S-EEE-CHHHCTTT-EEE CS
                      ADH_zinc_N_2   1 lGAdevidyr.tedfe.aatggegvDvvldtvggealleaslkvlpggGrlvsiggpp.lsaallkpakkrkgrsvk 74 
                                       lG d+ i ++ t++++ ++++ +  D+v++ +gge++ e   +v++ gG++v  g++   ++ +    ++ + ++v 
  gi|336255520|ref|YP_004598627.1| 207 LGLDHGIRSTdTDEIReRVAEIGTPDAVINHLGGEYT-ELGQHVMRRGGTMVICGRTAgGTSSIDVADFFLGHKRVV 282
                                       899****99967777786666789***********99.9999999777**998885444666666666667666666 PP

                                       E--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  75 yeflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                        +++ +     q d l++l++l++eG+++p +d++fplee+a+A+++++ +  +GK+V+
  gi|336255520|ref|YP_004598627.1| 283 GSTMGT-----QDD-LRRLVDLVAEGEFEPEIDETFPLEETADAFAAMRDRESVGKLVV 335
                                       666664.....777.*******************************************8 PP

>> NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   4.5e-07     0.002       9      43 ..      89     123 ..      84     158 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.5e-07
                                       HHHHH--S--HHHHIIIIHHHHHHHHHTBT---HH CS
                       NADH_4Fe-4S   9 fyaaesCGkCtpCreGtkrllelleriaagegtee 43 
                                        + +e+CG+C  CreG + + e +     g ++ +
  gi|336255520|ref|YP_004598627.1|  89 LCPNETCGECRFCREGPENMCENFSLYHGGLAEAA 123
                                       6889***************9998877776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); 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:                         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 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2644.63
//
Query:       gi|336255521|ref|YP_004598628.1|  [L=268]
Description: NAD-dependent epimerase/dehydratase [Halopiger xanaduensis SH-6]
Scores for 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-16   60.0   0.0    3.4e-16   59.5   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
      1e-09   37.9   0.2    1.6e-09   37.3   0.2    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
      5e-08   32.4   0.0    1.1e-07   31.3   0.0    1.6  2  NAD_binding_4    Male sterility protein
    7.8e-08   31.8   0.3    8.9e-05   21.8   0.3    3.0  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.3e-07   30.1   0.0    4.6e-07   29.1   0.0    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.2e-06   28.6   0.5    6.1e-06   26.2   0.4    2.1  2  NAD_binding_10   NAD(P)H-binding
     0.0021   18.1   0.0     0.0042   17.2   0.0    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0037   16.7   0.0      0.009   15.4   0.0    1.6  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
  ------ inclusion threshold ------
       0.15   12.0   0.0         13    5.7   0.0    2.3  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 !   59.5   0.0   1.7e-19   3.4e-16       1     169 [.       4     170 ..       4     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.7e-19
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       i +tGa+G +G+  + a+   + e++ +++        + edle + +d+ d++a+ ++++  + d+ ihlAa +++
  gi|336255521|ref|YP_004598628.1|   4 IAITGASGTVGREAIAAFDGTDAELTLFSHS-------ETEDLETTPVDIADHDAFVDALD--DQDVLIHLAANADP 71 
                                       689****************************.......556668899**************..68************ PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSS....SS.....BSTCSTTS--...--SSHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdae....qp.....keettltgpl...kpnspY 142
                                       +a++e        n+ g +n  eaa +++++r++f+sS +    ++      p     + e+    p     p + Y
  gi|336255521|ref|YP_004598628.1|  72 RAEWEAVRG---PNIDGLYNAYEAALENDLERVVFASSNHAVNMGNAvssvRPestigEPEV--VRPDdatDPDTYY 143
                                       **9998554...9*************************999985555444324555322233..33334579***** PP

                                       HHHHHHHHHHHHHHHHHHT-EEEEEEE CS
                         Epimerase 143 aaaKlageklveayaaqyglnaiilrl 169
                                       +++K+ ge +  +ya+ +gl++++lr+
  gi|336255521|ref|YP_004598628.1| 144 GVTKVFGEAMGSYYAKRHGLDVVTLRI 170
                                       *************************97 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 !   37.3   0.2     8e-13   1.6e-09       2     154 ..       3     176 ..       1     186 [. 0.88

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 8e-13
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT........T--TTSHHHHHHHHHHH--SEEEE------HHHHHHS CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre........eldltdaeavaellkeakpdvvvnaAAytavDkaEse 70 
                                       +i +tGa+G +G+e +++++  ++e++ ++ +         +d++d +a  ++l++   dv++++AA  +  +aE e
  gi|336255521|ref|YP_004598628.1|   3 NIAITGASGTVGREAIAAFDGTDAELTLFSHSetedlettPVDIADHDAFVDALDD--QDVLIHLAANADP-RAEWE 76 
                                       699********************9999997778999*9999**************9..899******8775.89**9 PP

                                       HHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-............TTS-B-TTS----SSHHHHHHHHHHHH CS
                     RmlD_sub_bind  71 eeaayavnaeavealAeaaaavgalLihvStDyVFdGe............kkrpYeeddetsPlnvYGrtKlaGEqa 135
                                         +  +++    +  A++ +  + ++   S   V  G+            +++  ++dd+t+P ++YG tK+ GE +
  gi|336255521|ref|YP_004598628.1|  77 AVRGPNIDGLYNAYEAALENDLERVVFASSNHAVNMGNavssvrpestigEPEVVRPDDATDPDTYYGVTKVFGEAM 153
                                       999999999999998988889998888888999**************9988889*********************98 PP

                                       HHH....H-SSEEEEEE-SEESS CS
                     RmlD_sub_bind 136 vla....agkkalivRtswvyge 154
                                              +g +++ +R++w++ +
  gi|336255521|ref|YP_004598628.1| 154 GSYyakrHGLDVVTLRIGWLLTR 176
                                       65522226667899*****9976 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.91   1.8e+03       1      10 [.       6      15 ..       6      20 .. 0.86
   2 !   31.3   0.0   5.4e-11   1.1e-07      81     208 ..      52     175 ..      35     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.91
                                      EE-TTSHHHH CS
                     NAD_binding_4  1 lTGaTGFLGk 10
                                      +TGa+G +G+
  gi|336255521|ref|YP_004598628.1|  6 ITGASGTVGR 15
                                      8*******97 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 5.4e-11
                                       HHHHHHH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE..GGGTTS-TTT--SSS-H.. CS
                     NAD_binding_4  81 lqelaeevdviihsaAtvnfdepykellrvNveGtrevlelakklkklkvllhvST..ayvngeregeveekvyeeg 155
                                       + +  +  dv ih aA+ +  ++ + ++ +N++G  +  e a +      +++ S+  a+  g+  + v+ +     
  gi|336255521|ref|YP_004598628.1|  52 FVDALDDQDVLIHLAANADPRAEWEAVRGPNIDGLYNAYEAALENDLE-RVVFASSnhAVNMGNAVSSVRPES---- 123
                                       45556888***********************************87666.999999985555555555553332.... PP

                                       ....HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 156 ekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                        +  + +   +++ ++  + Y  +K+ +E +   +++r+gl vv +R++ +++
  gi|336255521|ref|YP_004598628.1| 124 -TIGEPEVVRPDDATDPDTYYGVTKVFGEAMGSYYAKRHGLDVVTLRIGWLLT 175
                                       .33445556777788888899***************************99877 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   4.5e-08   8.9e-05       1     137 [.       4     115 ..       4     124 .. 0.81
   2 ?    3.2   0.0      0.02        41     128     169 ..     133     171 ..     122     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.5e-08
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       + +tGa+G++G+e +  +   + +++ l++++E++  e  +             +      d++d++   +al+  +
  gi|336255521|ref|YP_004598628.1|   4 IAITGASGTVGREAIAAFDG-TDAELTLFSHSETEDLE--T-------------T----PVDIADHDAFVDALD--D 58 
                                       56899999999998877654.45678888888865322..1.............1....3599***********..9 PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS--SH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAvnPtnv 137
                                        dv++h AA    P +e +++ +   N+ g  n  eaa+e++ ++vv+ S+  Avn  n+
  gi|336255521|ref|YP_004598628.1|  59 QDVLIHLAANAD-PRAEWEAVRG--PNIDGLYNAYEAALENDLERVVFASSNHAVNMGNA 115
                                       9********865.8888655554..6*****************************98776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.02
                                       EGGGSS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE- CS
                   Polysacc_synt_2 128 tDKAvnPtnvmGatKrlaekllqalakeseekktkfvvvRfG 169
                                        D A +P   +G+tK + e +   +ak++      +v+ R G
  gi|336255521|ref|YP_004598628.1| 133 PDDATDPDTYYGVTKVFGEAMGSYYAKRH---GLDVVTLRIG 171
                                       699****************9999988887...5555555555 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 !   29.1   0.0   2.3e-10   4.6e-07      41     121 ..      31     111 ..       5     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.3e-10
                         3Beta_HSD  41 lskvnvkk..viegDvtdkdkleealegvdvvihlaslvdvagkltedeimkvnvkGTrnvleacvkagvrvlvYtS 115
                                       +s++++++  +  +D+ d+d   +al++ dv+ihla+  d +   + + +   n+ G  n  ea+++++++++v+ S
  gi|336255521|ref|YP_004598628.1|  31 FSHSETEDleTTPVDIADHDAFVDALDDQDVLIHLAANADPRA--EWEAVRGPNIDGLYNAYEAALENDLERVVFAS 105
                                       33333333337899**********************9999988..6677899************************* PP

                         3Beta_HSD 116 saevvg 121
                                       s  +v 
  gi|336255521|ref|YP_004598628.1| 106 SNHAVN 111
                                       *99985 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 !   26.2   0.4   3.1e-09   6.1e-06       1     163 [.       8     190 ..       8     197 .. 0.64
   2 ?   -1.5   0.0      0.97   1.9e+03      78     131 ..     204     255 ..     182     260 .. 0.66

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.1e-09
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk.... 73 
                                       GA+G vGr++++      + e+t++    +++      e le++ +d+ d+++  +al+++d+ +  +++ +     
  gi|336255521|ref|YP_004598628.1|   8 GASGTVGREAIAAFDGT-DAELTLFS--HSET------EDLETTPVDIADHDAFVDALDDQDVLIHLAANADPraew 75 
                                       9**********755444.79999984..3333......4678999*****************987777544442444 PP

                                       .HHHH.......HHHHHHHHHHCT--EEEEEEETTTTS...GCGCHHHH...........HHHHCCHHHH.....HH CS
                    NAD_binding_10  74 .deeg.......aknivdaakeagvkRfvlvsaigvgd...evpgefge...........wnkellkayl.....aa 123
                                           +         n+ +aa e++ +R+v+ s+ ++ +    v +  +e            + +   +y+       
  gi|336255521|ref|YP_004598628.1|  76 eA--VrgpnidgLYNAYEAALENDLERVVFASSNHAVNmgnAVSSVRPEstigepevvrpDDATDPDTYYgvtkvFG 150
                                       41..0445556699******************977764121222221111111111111112223444553332223 PP

                                       HHHHHHHHHHSSSEEEEEEE-CEE-ST--SEEEEETTSS- CS
                    NAD_binding_10 124 kraaeellrasgldwTivrpggLtdepttkyrvvekgepf 163
                                        +    + ++ gld + +r g+L   ++ +  v+e++ p 
  gi|336255521|ref|YP_004598628.1| 151 EAMGSYYAKRHGLDVVTLRIGWLLTREELRQTVAERDGPG 190
                                       44555567889************99888777777776654 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.97
                                       HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHH CS
                    NAD_binding_10  78 aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeell 131
                                       ++++++aa ++  +R   ++a g+ ++  ++f ++ +++l+  ++    ae++l
  gi|336255521|ref|YP_004598628.1| 204 CRRVLRAAATSTLSRTP-LTAHGISNN-GKRFLSLSETMLALDYRPRDDAEAVL 255
                                       78888888888888854.477777753.45566666777777777777777666 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.1e-06    0.0042       2      74 ..       3      65 ..       2      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-06
                                      EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE- CS
                            DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDF 74
                                      ++a++GasG++G+e + a +  +d+el+   ++++         e l+++++++a  d + ++l+++dvli +
  gi|336255521|ref|YP_004598628.1|  3 NIAITGASGTVGREAIAAFDG-TDAELTLFSHSET---------EDLETTPVDIADHDAFVDALDDQDVLIHL 65
                                      79******************9.7888888766665.........44567899999999999********9976 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 !   15.4   0.0   4.5e-06     0.009      50     179 ..      35     169 ..      12     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.5e-06
                                       TGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEE CS
                     GDP_Man_Dehyd  50 leenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyq 126
                                        +e+l+   +D+ D+++  ++l++   d  ++LAA    +  +e    +   n+ G ++  ea+ +  le   r+++
  gi|336255521|ref|YP_004598628.1|  35 ETEDLETTPVDIADHDAFVDALDDQ--DVLIHLAANADPRAEWEA---VRGPNIDGLYNAYEAALENDLE---RVVF 103
                                       356899999**************99..899*************95...788899**********999886...8888 PP

                                       EEEGGG..G-S-SSSSB-TT...........S-----SHHHHHHHHHHHHHHHHHHHH---EEEEE CS
                     GDP_Man_Dehyd 127 aStsEv..YGkvqevpqtEt...........tpfyPrsPYaaaKlyadwivvnyreayglfavngi 179
                                       aS+      G++ ++   E+             ++P   Y+++K++ + +   y + +gl +v+ +
  gi|336255521|ref|YP_004598628.1| 104 ASSNHAvnMGNAVSSVRPEStigepevvrpdDATDPDTYYGVTKVFGEAMGSYYAKRHGLDVVTLR 169
                                       999764337998655555532333334434388889*************************99987 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.017        33       4      57 ..       5      65 ..       2      70 .. 0.72
   2 ?    5.7   0.0    0.0063        13     102     140 ..      72     110 ..      61     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.017
                                      EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..........--HHHHHHHHHHHHTT-EEEE CS
                                KR  4 litGGlGgLGlelarwlaekgarhlvllsRsa........aadedskaliaelealgaevev 57
                                       itG+ G +G+e +    +   ++l l+s s+           +d++a++++l ++++ +++
  gi|336255521|ref|YP_004598628.1|  5 AITGASGTVGREAIAAF-DGTDAELTLFSHSEtedlettpVDIADHDAFVDALDDQDVLIHL 65
                                      59*********988764.55588999999997666665543334455688888888777776 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0063
                                       HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHH CS
                                KR 102 aedleqvlapKvkGawnLhelledesldffvlfSSiagl 140
                                        +++e+v  p ++G+ n  e+  +++l+ +v+ SS  ++
  gi|336255521|ref|YP_004598628.1|  72 RAEWEAVRGPNIDGLYNAYEAALENDLERVVFASSNHAV 110
                                       579********************************8764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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 0.23s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 2180.13
//
Query:       gi|336255522|ref|YP_004598629.1|  [L=101]
Description: hypothetical protein Halxa_4146 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0086   16.3   0.0      0.011   15.9   0.0    1.2  1  HemY_N    HemY protein N-terminus
  ------ inclusion threshold ------
        3.1    7.8   4.2        4.4    7.4   4.2    1.2  1  Mit_KHE1  Mitochondrial K+-H+ exchange-related


Domain annotation for each model (and alignments):
>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.3e-06     0.011       4      74 ..      16      86 ..      11     101 .] 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-06
                            HemY_N  4 liawggyrietslvvavlllvllfvllylllrllrlllrlparvrrwrrrrrerkarealseGlialaeGd 74
                                      +++  gy +   lvv +l ++ ++v++++l+r++ +   +++r  +wr++r +r    a +e   +l+++d
  gi|336255522|ref|YP_004598629.1| 16 QMSAFGYVMAAILVVIMLPVLPIIVVAWVLWRAFVADEPVESRYESWRNERGRRPRAGAAEEVEAELEAED 86
                                      556667777777777777788899999********99999*********9999988888888777776554 PP

>> Mit_KHE1  Mitochondrial K+-H+ exchange-related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.2   0.00049       4.4     148     174 ..      23      49 ..      12      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00049
                          Mit_KHE1 148 giPltlpfalvPviPNlpffYlvyRay 174
                                       ++   l ++++Pv+P + ++++++Ra+
  gi|336255522|ref|YP_004598629.1|  23 VMAAILVVIMLPVLPIIVVAWVLWRAF 49 
                                       45556778999**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 847.84
//
Query:       gi|336255523|ref|YP_004598630.1|  [L=335]
Description: glutathione transferase [Halopiger xanaduensis SH-6]
Scores for 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-22   78.7   0.0    6.3e-22   77.7   0.0    1.5  1  GST_N_2          Glutathione S-transferase, N-terminal domain
    1.3e-11   44.3   0.4    3.1e-11   43.1   0.4    1.6  1  GST_C_2          Glutathione S-transferase, C-terminal domain
    2.4e-06   27.7   0.0    4.6e-06   26.8   0.0    1.5  1  GST_C            Glutathione S-transferase, C-terminal domain
    1.4e-05   25.4   0.0       0.29   11.6   0.0    2.6  2  GST_N_3          Glutathione S-transferase, N-terminal domain
    9.6e-05   22.1   0.2    0.00018   21.2   0.2    1.4  1  GST_C_6          Glutathione S-transferase, C-terminal domain
    0.00021   21.4   0.0    0.00039   20.6   0.0    1.4  1  GST_C_3          Glutathione S-transferase, C-terminal domain
     0.0054   16.9   0.3      0.016   15.4   0.3    1.8  1  SANT_DAMP1_like  SANT/Myb-like domain of DAMP1


Domain annotation for each model (and alignments):
>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.0   2.5e-25   6.3e-22       1      70 []      56     153 ..      56     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 2.5e-25
                                       S-HHHHHHHHHHHHCT--EEEEEEH...-TTSHHHHH..........................HHHCTTTSSSEEE- CS
                           GST_N_2   1 aCPwahRvlialalkglediisvvvlepkgfekseef..........................prlnprgtVPvLwd 51 
                                       aCPwahR+l+++alkgled+isv+v  p  +e++++f                          ++++ r+tVPvLwd
  gi|336255523|ref|YP_004598630.1|  56 ACPWAHRTLVTRALKGLEDAISVSVVDPYRDEDGWQFtpekegctrdhlhdanylrelyvtadSDATCRVTVPVLWD 132
                                       7**********************85555555555556666699999999999999999999999999999******* PP

                                       C..TTE.EEESHHHHHHHHHHH CS
                           GST_N_2  52 k..dgq.vineSseIlrylete 70 
                                       +  d + v+neS+eI+r+l+te
  gi|336255523|ref|YP_004598630.1| 133 TeeD-TiVNNESKEIMRMLDTE 153
                                       7424.36*************95 PP

>> GST_C_2  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.4   1.2e-14   3.1e-11       4      68 ..     200     269 ..     190     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.2e-14
                                       HCHHHHHCCHCHHHCTTT---SS.CTTCS--HHHHHHHHHHHHHHHHHHS-.....---TT-HHHHHHHH CS
                           GST_C_2   4 veraleqldaaldaleahLadspflfGdqptlaDialapflvrlraagpgf.....direaypnlraWle 68 
                                       +++a++ l++ald +++ Lad+++l+Gd++t aDia +++lvr++ +++ +         +y nl+ +l+
  gi|336255523|ref|YP_004598630.1| 200 YDEAVNDLFSALDHWDDVLADQRYLAGDRLTEADIAMFTTLVRFDNVYHTHfmcnvQYVREYDNLWPYLR 269
                                       689999*****************************************98776665533369999999985 PP

>> GST_C  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   1.8e-09   4.6e-06      18      65 ..     194     241 ..     169     273 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.8e-09
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTSSSSSTTSSCHHHHHHHHHHH CS
                             GST_C  18 ekkeelvdealekvaevlsaleeelkkqdylvGdkltlADialvpiln 65 
                                       ++++  +dea + ++ +l+  + +l++q yl+Gd+lt ADia+++ l 
  gi|336255523|ref|YP_004598630.1| 194 ATDQGPYDEAVNDLFSALDHWDDVLADQRYLAGDRLTEADIAMFTTLV 241
                                       56777899************************************9875 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00011      0.29       1      27 [.      51      77 ..      51      98 .. 0.80
   2 !   11.2   0.0   0.00015      0.39      44      73 ..     124     156 ..     100     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                      EES-TTSHHHHHHHHHHHHHT--EEEE CS
                           GST_N_3  1 LygfpaSpyarrvrlaLnekglpvevv 27
                                      Ly ++a+p+a r  ++  +kgl+ ++ 
  gi|336255523|ref|YP_004598630.1| 51 LYVSYACPWAHRTLVTRALKGLEDAIS 77
                                      9*********************86652 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00015
                                       T--SSEEETT..S-.EEESHHHHHHHHHHHH-G CS
                           GST_N_3  44 lgkvPvLedd..ge.altdSlaIidyLeelypg 73 
                                       + +vPvL d+  ++ +  +S +I++ L++++++
  gi|336255523|ref|YP_004598630.1| 124 RVTVPVLWDTeeDTiVNNESKEIMRMLDTEFDD 156
                                       789****66632445666***********9985 PP

>> GST_C_6  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2     7e-08   0.00018       5      61 ..     211     268 ..     208     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7e-08
                           GST_C_6   5 leaLselLgdkkyFfGdkPtslDAlvFGhlaqilytplesp..elrellkeypNLvayc 61 
                                       l+   ++L+d+ y+ Gd+ t++D ++F  l+ + +  ++++     ++++ey+NL  y 
  gi|336255523|ref|YP_004598630.1| 211 LDHWDDVLADQRYLAGDRLTEADIAMFTTLVRF-DNVYHTHfmCNVQYVREYDNLWPYL 268
                                       6667899***********************999.77778888777999*******8886 PP

>> GST_C_3  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.5e-07   0.00039      31      85 ..     209     270 ..     189     282 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.5e-07
                                       CHHHHHHHHHHCHGTSSSSTTS--HHHHHHHHHHHHHHHH........TCC..CC-HHHHHHHHH CS
                           GST_C_3  31 kflkyfekvlkkkgggylvgdklTyADlalfqvldgleea........eal..kkfpklkalyer 85 
                                         l++++ vl+   + yl+gd+lT AD+a+f+ l  + ++          +  +++ +l  +   
  gi|336255523|ref|YP_004598630.1| 209 SALDHWDDVLA--DQRYLAGDRLTEADIAMFTTLVRFDNVyhthfmcnV-QyvREYDNLWPYLRD 270
                                       56899999999..899****************99999888665665431.133555555444444 PP

>> SANT_DAMP1_like  SANT/Myb-like domain of DAMP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   6.2e-06     0.016      39      75 ..     256     293 ..     246     297 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.2e-06
                   SANT_DAMP1_like  39 dlckeydlrfvviaDryelek.kkkrsledlkeryYsv 75 
                                       + ++eyd  ++ + D y++    ++ +++++ke+yY+ 
  gi|336255523|ref|YP_004598630.1| 256 QYVREYDNLWPYLRDLYQTPGvAETVNMDHIKEHYYTT 293
                                       6799***************7788999**********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); 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:                         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 0.21s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2815.57
//
Query:       gi|336255524|ref|YP_004598631.1|  [L=523]
Description: Na+/H+ antiporter NhaC-like protein [Halopiger xanaduensis SH-6]
Scores for 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-30  104.5  42.0    5.1e-17   62.1  24.0    2.3  2  Na_H_antiporter  Na+/H+ antiporter family
  ------ inclusion threshold ------
       0.42   10.4   3.0        0.2   11.4   0.6    1.6  2  DUF1028          Family of unknown function (DUF1028)


Domain annotation for each model (and alignments):
>> Na_H_antiporter  Na+/H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1  24.0   5.7e-21   5.1e-17     102     302 ..      38     239 ..      33     240 .. 0.90
   2 !   48.2   9.9   9.2e-17   8.3e-13      65     303 .]     253     493 ..     241     493 .. 0.88

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 5.7e-21
                   Na_H_antiporter 102 alalvaivkafivalafqntdvatalvvgalaglivatllelaslseidkllnrGiksmlgaililllAwg..iggv 176
                                       al ++++++ +i+++a+   + + +l+vg+l+gliv ++    +++++ +++ +G+   + + +i+   w+  ++++
  gi|336255524|ref|YP_004598631.1|  38 ALPIGIFIVWAITQTALWRISDTGGLIVGILVGLIVGMFFVRGDWKTYANTIFEGMTQPVAVTAIVAWIWAgmFAQL 114
                                       4556667888899999888899999999**********99988************9988888888877777669*** PP

                   Na_H_antiporter 177 lealgvteslvsslakgv.vskgllplilflvallvafatGtswgtigIilpiavplaaklgisllalvraveaggt 252
                                       l++ g ++ lv      + v + l p+i+f++a+l + ++Gt +g+ +    ++ p ++ lg ++  l +a+++g++
  gi|336255524|ref|YP_004598631.1| 115 LQDGGFVDGLVWFA-DVAgVGASLFPAITFVLAALFTTGIGTGYGATIAFVGLFFPAGVLLGANPVLLFGAILSGAI 190
                                       *****777777655.555599******************************************************** PP

                   Na_H_antiporter 253 lgdhlsPisdttilsstglnadhidhvsytqlpyallvapitailllvfG 302
                                       +gd l P+sdtti+s+ +  ad   +v  + + y++++a++++++++v+G
  gi|336255524|ref|YP_004598631.1| 191 FGDNLAPVSDTTIVSAVTQDADIGGVVA-SRFKYVIIAAVVAFVGYIVAG 239
                                       *******************999878888.99*****************98 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 9.2e-17
                   Na_H_antiporter  65 amlraeaear....eleekeltklpiavliiltlskmpytgalal.vaivkafivalafqntdvatalvvgalagli 136
                                       ++l ae ++      +++ +++ + +a  +i+ ++++ +++a+a+  +++ a ++ +++  +   +a +   lagl 
  gi|336255524|ref|YP_004598631.1| 253 QLLAAESRPIglvhLISMLVVIGAAVAGRHIVEAISWGIVVAIAFnLVFGLASLSDILLFRA-PPDAPLAEPLAGLP 328
                                       55555555556666778888888889999999999999999999887888777777664333.45555557888888 PP

                   Na_H_antiporter 137 vatllelaslseidkllnrGiksmlgaililllAwgiggvlealgvteslvsslakgv.vskgllplilflvallva 212
                                       + t++   ++  ++++l  G+ ++l + +++l+  g ++++ + g+++++++   + + ++++ + l+++ +a+l++
  gi|336255524|ref|YP_004598631.1| 329 ILTVVTDPDAVGVTGSLMSGVSGFLELSILVLFIIGAAQIMIRGGAFQAILDWSIEHLaTNVRNAELTMVGSAALIN 405
                                       888887669999****************************************9999999****************** PP

                   Na_H_antiporter 213 fatGtswgtigIilpiavplaaklgisllalvraveaggtlgdhlsPisdttilsstglnadhidhvsytqlpyall 289
                                       + ++ ++++ + i+p++ +++++++++ ++ ++++   ++   +++P+s + +  +t     +  + +y ++   +l
  gi|336255524|ref|YP_004598631.1| 406 AIITINTAAEVAIGPYISKIGERFNLNGYRRANILDGQTAALGYIFPWSGGVLAGYTEM---QLLPQQYEWFDQGML 479
                                       ***********************************************************...*************** PP

                   Na_H_antiporter 290 vapitailllvfGi 303
                                       v pi ++++++ G+
  gi|336255524|ref|YP_004598631.1| 480 VTPIDVVPFVFQGW 493
                                       ************99 PP

>> DUF1028  Family of unknown function (DUF1028)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.64   5.7e+03      20      36 ..      94     110 ..      92     114 .. 0.84
   2 ?   11.4   0.6   2.3e-05       0.2       4      63 ..     203     261 ..     201     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.64
                                       ESSS-HHHHHEEEETTT CS
                           DUF1028  20 skslaVgalvpfaragv 36 
                                       ++ +aV a+v ++ ag+
  gi|336255524|ref|YP_004598631.1|  94 TQPVAVTAIVAWIWAGM 110
                                       67899*******99985 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.3e-05
                                       EEEE-TTT--EEEEEEESS..S-HHHHHEEEETTTEEEEEESS--HHHHHHHHHHHHTT--H CS
                           DUF1028   4 ivardpetgelGvAvasks..laVgalvpfaragvGavatQaltnpelgekglelleagasa 63 
                                       iv   +++ ++G  vas++  + ++a+v f+      va Qa++  elge++ +ll+a+ ++
  gi|336255524|ref|YP_004598631.1| 203 IVSAVTQDADIGGVVASRFkyVIIAAVVAFVGYI---VAGQAMAGLELGEQARQLLAAESRP 261
                                       7888889999*******76215567777777665...8*******************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3762.39
//
Query:       gi|336255525|ref|YP_004598632.1|  [L=90]
Description: TRAM domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-06   27.0   0.2    4.3e-06   26.6   0.2    1.2  1  TRAM      TRAM domain


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.2   2.4e-10   4.3e-06       3      60 ..      21      76 ..      19      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.4e-10
                                      XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T...TEEEEEEEEEE-SSEEEEE CS
                              TRAM  3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpg.IGdfVeVkItkvkrqyLrGe 60
                                      ++G +++V v + +   +eg++++  +  ++++g+ p+ + ++V V++t+    ++rG+
  gi|336255525|ref|YP_004598632.1| 21 TEGDEIDVFVAESN--SDEGHAYIG-DTHLVIEGTGPEtVEKRVRVRVTEFDDSTARGR 76
                                      6899****999988..69*******.************************999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 713.33
//
Query:       gi|336255526|ref|YP_004598633.1|  [L=359]
Description: DNA methylase N-4/N-6 domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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   43.5   0.0    1.5e-07   31.4   0.0    2.2  2  N6_N4_Mtase  DNA methylase
  ------ inclusion threshold ------
        0.1   12.3   0.3        2.1    8.0   0.3    2.2  1  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 !   31.4   0.0   1.6e-11   1.5e-07     160     230 ..      92     165 ..      48     166 .. 0.76
   2 !   10.1   0.0   5.2e-05      0.47       1      64 [.     205     303 ..     205     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.6e-11
                                       TSTTS-CHH----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-E......EEEEESSHHHHHHHH CS
                       N6_N4_Mtase 160 nekkskgdtkkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrk......fiGieieeeyvelae 230
                                        ++++   ++  H  qkP  l   lI  ++k gd+vlDpFaG G T+  a   + +      +iG+e  e+ ve+ e
  gi|336255526|ref|YP_004598633.1|  92 DVQHD---LRSEHGGQKPPRLCAALIGRFSKAGDTVLDPFAGVGGTLLGASFCEHEgtglreAIGFERTERWVEIYE 165
                                       33333...3678**********************************9877766666666777999998888887765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 5.2e-05
                                       EEEEEE--SSSSSCS.....................................GCCGCCHHHHHHHHHHHHHHHHHHH CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy................................endeqyeeedsyeeyleflekvlkevrrv 45 
                                       vdl +td PY+   +                                   + + ++ ++ +e+l  +   ++   + 
  gi|336255526|ref|YP_004598633.1| 205 VDLLLTDVPYWHMDELeqtrnerairesklgsfdgggdgdeaagdddpDGGADGDATQTKDEWLADMAAKFDRFADA 281
                                       68889999999887778999999999999999999999999999998888888899999****************** PP

                                       EEEEEEEEEEE-CCCHHT...H CS
                       N6_N4_Mtase  46 Lkddgsifiniddseikk...e 64 
                                         + g ++++i+d++  +   +
  gi|336255526|ref|YP_004598633.1| 282 VDPEGHVVVFIGDMYRDQsyeF 303
                                       ***************9875551 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3   0.00023       2.1      27      92 ..     119     171 ..     100     228 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00023
                                       -TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHH CS
                           UPF0020  27 kpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqga 92 
                                       k+g++ lDP+ G G+ l+ a   + +     lre +++ ++e           + +++ ++v+++ 
  gi|336255526|ref|YP_004598633.1| 119 KAGDTVLDPFAGVGGTLLGASFCEHEGT--GLREAIGFERTE-----------RWVEIYEEVLERE 171
                                       7899999*****9999999988887776..455555553322...........1234444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2923.72
//
Query:       gi|336255527|ref|YP_004598634.1|  [L=219]
Description: TrkA-N domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-26   91.5   1.2    4.6e-26   91.4   0.2    1.5  2  TrkA_N           TrkA-N domain
    1.3e-14   53.7   0.1    2.7e-14   52.7   0.1    1.6  1  TrkA_C           TrkA-C domain
    8.5e-06   25.5   0.0    1.4e-05   24.7   0.0    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    2.4e-05   24.7   0.0    4.9e-05   23.7   0.0    1.6  1  NAD_binding_7    Putative NAD(P)-binding
    0.00018   21.8   0.1    0.00026   21.2   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0016   18.4   0.0     0.0025   17.7   0.0    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0017   18.0   0.0      0.014   15.0   0.0    2.1  2  ApbA             Ketopantoate reductase PanE/ApbA
     0.0023   18.1   0.2      0.013   15.7   0.0    2.2  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0029   17.2   0.0     0.0049   16.5   0.0    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
     0.0043   16.4   0.0     0.0069   15.8   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.025   14.0   0.1      0.036   13.5   0.1    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
       0.08   13.0   0.1       0.12   12.4   0.1    1.4  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
       0.11   13.1   0.1       0.29   11.7   0.0    1.8  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


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 !   91.4   0.2   3.3e-29   4.6e-26       1     116 []       3     118 ..       3     118 .. 0.95
   2 ?   -2.9   0.0       5.6   7.8e+03      22      34 ..     198     208 ..     191     216 .. 0.50

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 3.3e-29
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       ++i+G+GrvG++ a  L e+g+d vv+d+d +r ++++e+g+e+v gd++dee+L eagi++ada+ a t+d  +n 
  gi|336255527|ref|YP_004598634.1|   3 FVIVGYGRVGSRTATILAEEGHDLVVVDNDVDRTDRAAEDGFETVLGDGADEETLLEAGIDEADAIGAFTPDLNVNF 79 
                                       79*****************6558****************************************************** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHH..HTTSEEEEH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkk..lgadvvisp 116
                                       +a+++ k+  ++++++ r++++ ++++++k    +d++i+p
  gi|336255527|ref|YP_004598634.1|  80 AACMVGKH--HGCRTVLRIDEDYREDIYEKyaEDVDEIIYP 118
                                       ******95..5599**************9976779999997 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.6
                                       EEEEEEESSHHHH CS
                            TrkA_N  22 kdvvvidkdeerv 34 
                                       +  +++++d+  +
  gi|336255527|ref|YP_004598634.1| 198 EVALIVETDH--A 208
                                       3355666654..2 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.1     2e-17   2.7e-14       3      69 ..     149     215 ..     147     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 2e-17
                                       EEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   3 evtvpagsplvGktlkelnlrargvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                        ++++a+sp vGk+++el+l+a ++++ a+ R+ + l+ip + t+Le+GD++ ++++ ++ +e+r+ l
  gi|336255527|ref|YP_004598634.1| 149 VLEIGADSPAVGKRMSELDLPA-SARIYAHGRErESLTIPLPGTELEAGDEVALIVETDHAEEVRSAL 215
                                       689*******************.*******88889*****************************9875 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 !   24.7   0.0     1e-08   1.4e-05       1      42 [.       1      42 [.       1      61 [. 0.90

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1e-08
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTT CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsg 42
                                      m+ +++G G vG  ta++lae gh++++vD+d  + d   ++
  gi|336255527|ref|YP_004598634.1|  1 MRFVIVGYGRVGSRTATILAEEGHDLVVVDNDVDRTDRAAED 42
                                      7889****************************9998876665 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 !   23.7   0.0   3.6e-08   4.9e-05       9      79 ..       2      82 ..       1     105 [. 0.73

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.6e-08
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapev...keeleelvk......laeeel.ekdlegadlviaatddrelner 77
                                      + ++vG G+v+ r +  l+e+g +++vv+++v    +++e+ ++      + ee+l e+ +++ad + a t+d ++n +
  gi|336255527|ref|YP_004598634.1|  2 RFVIVGYGRVGSRTATILAEEGHDLVVVDNDVdrtDRAAEDGFEtvlgdgADEETLlEAGIDEADAIGAFTPDLNVNFA 80
                                      679****************************74442222222222223333344445777*************999977 PP

                     NAD_binding_7 78 ia 79
                                       +
  gi|336255527|ref|YP_004598634.1| 81 AC 82
                                      66 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 !   21.2   0.1   1.9e-07   0.00026       2      72 ..       4      67 ..       3     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.9e-07
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSE CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdl 72
                                      +i+G+G+vG+ +a  la++++    ++v+d + ++ +++a+      fe++  d +++e +L+a + e+d+
  gi|336255527|ref|YP_004598634.1|  4 VIVGYGRVGSRTATILAEEGHD---LVVVDNDVDRTDRAAE----DGFETVLGDGADEETLLEAGIDEADA 67
                                      89*****************985...9*********999975....58999999999999999999999876 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 !   17.7   0.0   1.8e-06    0.0025       4      73 ..       5      75 ..       2      84 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.8e-06
                                      EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHH.HHHHHHCCTTTTSS-HHHHCCCHHCEEEES-H CS
                           3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdiseealekalek.ieksleklvekgklkeeeveaalarisfttdl 73
                                      ++G G +G+  a+++a++g++ v+vd + ++ ++a+e   e+ l   + ++ l e+ +++a a   ft dl
  gi|336255527|ref|YP_004598634.1|  5 IVGYGRVGSRTATILAEEGHDLVVVDNDVDRTDRAAEDgFETVLGDGADEETLLEAGIDEADAIGAFTPDL 75
                                      8**************************99999987664155566666666666666666666666666555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     1e-05     0.014       2      49 ..       4      54 ..       3      83 .. 0.86
   2 ?    0.7   0.0      0.26   3.5e+02      17      38 ..     193     213 ..     188     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT..CE CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg..ge 49
                                      +i+G G +Gs  a  La+ g+d ++++++  r ++  ++G++    +   e
  gi|336255527|ref|YP_004598634.1|  4 VIVGYGRVGSRTATILAEEGHDLVVVDNDVdRTDRAAEDGFETVLGDgaDE 54
                                      7****************************99*********99888776444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.26
                                       HHHHTHCEEEE-SCHHHHHHHH CS
                              ApbA  17 Lakagadvtlilrsrrlealkk 38 
                                       L +ag +v li+ ++++e++++
  gi|336255527|ref|YP_004598634.1| 193 L-EAGDEVALIVETDHAEEVRS 213
                                       5.79************999876 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 !   15.7   0.0   9.4e-06     0.013       4      43 ..       5      52 ..       2     110 .. 0.77
   2 ?   -0.3   0.0      0.76     1e+03     122     146 ..     122     145 ..     119     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.4e-06
                                      EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........E CS
                     NAD_binding_2  4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........a 43
                                      ++G G  Gs  a+ l+++g++++v++ + +++++++++g        a
  gi|336255527|ref|YP_004598634.1|  5 IVGYGRVGSRTATILAEEGHDLVVVDNDVDRTDRAAEDGfetvlgdgA 52
                                      79************************************9555555541 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.76
                                       HHHHT-EEEEEEE-HHHHHHHHHHH CS
                     NAD_binding_2 122 gAekGtLsimvGGseeafervkpvl 146
                                       gA+ ++ + m+GG+ +++++++  l
  gi|336255527|ref|YP_004598634.1| 122 GAAGAK-TAMLGGDFNVVADLATNL 145
                                       566666.99*****99998877655 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 !   16.5   0.0   3.6e-06    0.0049       7      55 ..       3      50 ..       1      79 [. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.6e-06
                                      EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHH CS
                              IlvN  7 iaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltva 55
                                       +++GyG  G   a+ l + g d+vv  ++ +  +++A e+gfe++  +
  gi|336255527|ref|YP_004598634.1|  3 FVIVGYGRVGSRTATILAEEGHDLVVVDNDVD-RTDRAAEDGFETVLGD 50
                                      589********************999766665.8999******986433 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 !   15.8   0.0     5e-06    0.0069      38      81 ..       2      45 ..       1      54 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5e-06
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCE CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgve 81
                                      +  i+G+Gr+G+++a +l++ g +++++d   +++++++e g+e
  gi|336255527|ref|YP_004598634.1|  2 RFVIVGYGRVGSRTATILAEEGHDLVVVDNDVDRTDRAAEDGFE 45
                                      568***************************99998878777775 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.6e-05     0.036       7      73 ..       8      81 ..       3      91 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                                      TSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...........EEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                         Epimerase  7 tGfiGsalvkallekgyevigldrlssasntarledl...........elveldltdrsalerlfkeeqpdavihlAa 73
                                       G +Gs ++  l+e+g++++++d++ ++  +a+++             +l e+ + +++a+ ++     pd  +++Aa
  gi|336255527|ref|YP_004598634.1|  8 YGRVGSRTATILAEEGHDLVVVDNDVDRTDRAAEDGFetvlgdgadeeTLLEAGIDEADAIGAF----TPDLNVNFAA 81
                                      499**********************888888888887555555555555555555555544444....4566666655 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 ?   12.4   0.1   8.9e-05      0.12      26      70 ..       3      47 ..       1      85 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.9e-05
                                      EEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE- CS
                     AdoHcyase_NAD 26 avvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevv 70
                                       v++GyG vG  +a+ l + G  ++v + d   + +aa +Gfe v
  gi|336255527|ref|YP_004598634.1|  3 FVIVGYGRVGSRTATILAEEGHDLVVVDNDVDRTDRAAEDGFETV 47
                                      599************************99999999*******976 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 ?   11.7   0.0   0.00021      0.29       2      45 ..       3      42 ..       2      63 .. 0.86
   2 ?   -3.0   0.0       8.3   1.1e+04      63      81 ..     197     215 ..     193     218 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaee 45
                                      + i+G+G++g+  a  l+++g   h++vv+ +++ ++ + +ae+
  gi|336255527|ref|YP_004598634.1|  3 FVIVGYGRVGSRTATILAEEG---HDLVVV-DNDVDRTDRAAED 42
                                      5789*****************...****88.9999988887765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.3
                                       SEEEE-S-HHHHHHHHHHC CS
                     F420_oxidored  63 dvvvlavkpedveevlsel 81 
                                       d v l v + ++eev s+l
  gi|336255527|ref|YP_004598634.1| 197 DEVALIVETDHAEEVRSAL 215
                                       5566667777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 1851.09
//
Query:       gi|336255528|ref|YP_004598635.1|  [L=464]
Description: xanthine/uracil/vitamin C permease [Halopiger xanaduensis SH-6]
Scores for complete 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-37  129.7  45.7    1.7e-37  129.1  45.7    1.3  1  Xan_ur_permease  Permease family
  ------ inclusion threshold ------
      0.047   13.3   0.1       0.28   10.9   0.1    2.4  1  Doppel           Prion-like protein Doppel
       0.14   12.2   9.3      0.074   13.1   3.6    2.8  2  Vma12            Endoplasmic reticulum-based factor for assem


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 !  129.1  45.7   2.8e-41   1.7e-37       3     385 ..      20     414 ..      18     418 .. 0.87

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 2.8e-41
                                       HHHHHHHHHHHHHHHHHHHHHTTTS-..............H.HHHHHHHHHHHHHHHHHTTT-----EEE-GGGHHH CS
                   Xan_ur_permease   3 llllglQhllamfaalvvvPllvgda...lgl.aeelr.qlisatllasGiatllqllifgirlpillgssfafvta 74 
                                       +l++gl+++lam + +vv+P+++g+a    g    e+r +++ at+las +a ++++++++ +  ++ g++++++ a
  gi|336255528|ref|YP_004598635.1|  20 ELIAGLTTFLAMSYIIVVNPIILGEAitlEGYgPGEVRqMITVATILASVVAIFVMAFYANRPFGLAPGMGLNAFFA 96 
                                       789***********************98633456778869999********************************** PP

                                       HHGGG-....HHHHHHHHHHHHHHHHHHHHHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHTTSS-..BT CS
                   Xan_ur_permease  75 lmialGsaedieialagllgallvagvlfilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkvgggwaave 151
                                       ++++lG     ++  +++l a++v g++fil+ ++g r ++++l+p  v  +v  +iG  l+  +++++ ++ a+ e
  gi|336255528|ref|YP_004598635.1|  97 YSVVLGL----GVPWQVALAAVFVEGIIFILLTAVGARRYIIELFPEPVKFAVGAGIGVYLLFLGLQEMQIVVADPE 169
                                       ******5....*************************************************************97766 PP

                                       T.B---HHHHHHHHH.HHHHHHHHHHSSSTTTTTHHHHHHHHHHHHHHHHHH.HTTSSHH...............HH CS
                   Xan_ur_permease 152 gltvvslkllllavv.vllvilllsvflkglfsqlpiLigiiagwllalfmg.ivnlspe...............vs 211
                                          v+ +++ + av+ +++++l+l  +l    ++++i+igi+a++++ ++++    +sp                ++
  gi|336255528|ref|YP_004598635.1| 170 T-LVTMGNVATSAVAaLSVAGLALMLVLHARGVRGAIVIGILATAVAGWVLTaLGVVSPGtltpqgsivtsvqydFT 245
                                       6.6777777777776145678888999*************************5333455476777776655554322 PP

                                       S-SS-----------HH...............H.HHHHTHHH.HHHHHHHHHHHHHHHHHHTS-TII..IIIHHHHH CS
                   Xan_ur_permease 212 eapwfqlpsplkfgtpl.............fnlgliltvlavalvavvesvGdiravakvvgrslkp..kpdlrral 273
                                                       l               l  +l+v+++++v ++++ G++++v+++ g  +++   p++++ l
  gi|336255528|ref|YP_004598635.1| 246 P---------------LvagfvdglgmiaeDPLVFVLVVFTFFFVDFFDTAGTLIGVSQIGGFLDENgdLPEIEKPL 307
                                       2...............12222333344332235678999999*******************98888799******** PP

                                       HHHHHHHHHHHHHT---EEE-HHHHHHHHHHTB--HHHHHHHHHHHHHHT--HHHHHHHTTS-HHHHHHHHHHHHHH CS
                   Xan_ur_permease 274 ladGlatllsgllGalpvttyaeniGvvaltkvasrrvmvtagvilillglipklaallssIPepvlgGvllvvfgm 350
                                       +ad ++t++++++G++ vtty+e+  +v+ +    +r+++ta v+ il+ l+  + + +++IP+++ + ++lvv+g+
  gi|336255528|ref|YP_004598635.1| 308 MADAVGTTVGAMIGTSTVTTYIESSTGVEEG----GRTGFTALVVGILFLLSLVIVPVITAIPQYA-TYIALVVVGI 379
                                       *******************************....*******************************.********** PP

                                       HHHHHHHHHHHTTS-SHHHHHHHHHHHHHHHH--- CS
                   Xan_ur_permease 351 iaasgvsnlqtvdldsarnllivavslvlGlgvat 385
                                       i++ gv+ ++++d   a +  ++ +++ l+++++ 
  gi|336255528|ref|YP_004598635.1| 380 IMLQGVADIDWQDPAWAIAGGLTITVMPLTASISN 414
                                       ***************9*************999986 PP

>> Doppel  Prion-like protein Doppel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   4.7e-05      0.28       5      26 ..     438     459 ..     437     462 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.7e-05
                                       -SSCCHHHHHHHHHHHCCTTTS CS
                            Doppel   5 LgtWwlAivCvLLfShLSlVkA 26 
                                       Lg W lA+++vL f    +V+A
  gi|336255528|ref|YP_004598635.1| 438 LGQWTLAVAFVLYFATYFAVQA 459
                                       9***********9988877777 PP

>> Vma12  Endoplasmic reticulum-based factor for assembly of V-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.6   1.2e-05     0.074      75     127 ..      57     116 ..      55     155 .. 0.93
   2 ?    1.0   0.3     0.066     4e+02      83      99 ..     205     221 ..     203     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                             Vma12  75 rqlilvlNiliSvvavffavwialrsartp........slpvrvllslvvallVgvAEvvv 127
                                       rq+i+v  il Svva f++ ++a r +  +         +++ v+l+l+v   V++A v+v
  gi|336255528|ref|YP_004598635.1|  57 RQMITVATILASVVAIFVMAFYANRPFG-LapgmglnaFFAYSVVLGLGVPWQVALAAVFV 116
                                       8*************************94.45999999989999999999999999998886 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.066
                             Vma12  83 iliSvvavffavwialr 99 
                                       i+i ++a+++a+w+++ 
  gi|336255528|ref|YP_004598635.1| 205 IVIGILATAVAGWVLTA 221
                                       89***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3311.13
//
Query:       gi|336255529|ref|YP_004598636.1|  [L=81]
Description: glutaredoxin [Halopiger xanaduensis SH-6]
Scores for 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-15   56.8   0.0    2.4e-15   56.7   0.0    1.0  1  GST_N_3        Glutathione S-transferase, N-terminal domain
    1.5e-13   50.7   0.0      2e-13   50.3   0.0    1.2  1  Glutaredoxin   Glutaredoxin
    6.5e-11   42.4   0.0    7.4e-11   42.2   0.0    1.1  1  GST_N_2        Glutathione S-transferase, N-terminal domain
    0.00081   19.8   0.1      0.001   19.5   0.1    1.3  1  DUF836         Glutaredoxin-like domain (DUF836)
     0.0048   17.2   0.0     0.0075   16.6   0.0    1.4  1  GST_N          Glutathione S-transferase, N-terminal domain
  ------ inclusion threshold ------
      0.024   15.1   0.0      0.029   14.8   0.0    1.2  1  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   8.2e-19   2.4e-15       1      71 [.       6      80 ..       6      81 .] 0.91

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 8.2e-19
                                      EES-TTSHHHHHHHHHHHHHT--EEEE---TTTT.HHHHHHH-TT--SSEEETT.S-..EEESHHHHHHHHHHHH CS
                           GST_N_3  1 LygfpaSpyarrvrlaLnekglpvevvevtpgeh.deellaknplgkvPvLedd.ge..altdSlaIidyLeely 71
                                      Ly+ p++py+ +vr  L+e++l++ v ev+  +  + e+ +++++  vPv++d  ++   + +S++I++yLee+y
  gi|336255529|ref|YP_004598636.1|  6 LYELPGCPYCAKVRSKLDELDLEYDVTEVPRSHEdRTEVERVSGQTGVPVITDEaNGveGMNESDDIVEYLEETY 80
                                      9****************************876666999*************998533579*************99 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   6.6e-17     2e-13       1      53 [.       4      56 ..       4      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 6.6e-17
                                      EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEE CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqv 53
                                      ++l+  p+CpyC+k++  L+el +++++ +v   +e r e++++sg+  vP++
  gi|336255529|ref|YP_004598636.1|  4 ITLYELPGCPYCAKVRSKLDELDLEYDVTEVPRSHEDRTEVERVSGQTGVPVI 56
                                      799************************************************99 PP

>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   2.5e-14   7.4e-11       2      69 ..      12      78 ..      11      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 2.5e-14
                                      -HHHHHHHHHHHHCT--EEEEEEH...-TTSHHHHHHHHCTTTSSSEEE-C.TTE.EEESHHHHHHHHHH CS
                           GST_N_2  2 CPwahRvlialalkglediisvvvlepkgfekseefprlnprgtVPvLwdk.dgq.vineSseIlrylet 69
                                      CP++ +v+  l ++ le+ +++v+    ++e+  e+ r+++++ VPv+ d+ +g    neS +I++yle+
  gi|336255529|ref|YP_004598636.1| 12 CPYCAKVRSKLDELDLEYDVTEVP---RSHEDRTEVERVSGQTGVPVITDEaNGVeGMNESDDIVEYLEE 78
                                      ***********************5...56666679***************8666689***********98 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   3.3e-07     0.001       2      32 ..       4      32 ..       3      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.3e-07
                                      EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEE CS
                            DUF836  2 ltLyskpgChlCeqakekLkelkleeglele 32
                                      +tLy  pgC+ C ++ +kL el    ++++ 
  gi|336255529|ref|YP_004598636.1|  4 ITLYELPGCPYCAKVRSKLDELD--LEYDVT 32
                                      9*******************665..555554 PP

>> GST_N  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.5e-06    0.0075       2      74 ..       3      76 ..       2      78 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.5e-06
                                      EEEEESSSTSHTHHHHHHHHHHTT-EEEEEEECSTTTCGGC.HHHHHHCTTS-SSEEEET...TEEEESHHHHHHHH CS
                             GST_N  2 vltlysirgsprahrirlllaakgveyevvpldfeageeks.pellklnplgkvPaLedn...gkkltESraIleYi 74
                                       +tly  +g+p+  ++r  l+++++ey v+++ +    +++  e  ++     vP+  d+        ES  I+eY+
  gi|336255529|ref|YP_004598636.1|  3 DITLYELPGCPYCAKVRSKLDELDLEYDVTEVPR---SHEDrTEVERVSGQTGVPVITDEangVEGMNESDDIVEYL 76
                                      68***************************99987...3333266666666666676666655433355666666666 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   9.6e-06     0.029      10      55 ..       5      49 ..       4      79 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.6e-06
                     Thioredoxin_2 10 vvftdpdCpyCkklkkelkel.ddvtvrvllfp.lkpsfepkavaiwc 55
                                      ++++ p+CpyC+k + +l+el    +  v  +p  +++  ++++++++
  gi|336255529|ref|YP_004598636.1|  5 TLYELPGCPYCAKVRSKLDELdL--EYDVTEVPrSHED-RTEVERVSG 49
                                      567789**************952..4344466765555.555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 642.95
//
Query:       gi|336255530|ref|YP_004598637.1|  [L=387]
Description: major facilitator superfamily protein [Halopiger xanaduensis SH-6]
Scores for 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-44  151.8  76.2    4.7e-33  114.6  48.7    2.0  2  MFS_1       Major Facilitator Superfamily
    2.1e-09   36.8   9.9    2.1e-09   36.8   9.9    2.1  2  MFS_1_like  MFS_1 like family


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 !  114.6  48.7   5.3e-37   4.7e-33       4     352 ..      13     342 ..      10     342 .. 0.88
   2 !   50.9  19.6   1.2e-17   1.1e-13      18     174 ..     223     377 ..     221     385 .. 0.84

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 5.3e-37
                             MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.llll 79 
                                       ++f++ lar +++p+l      ++ i ++++gl++tl  lg+a + lp+G+l +r+ r  v+l + +++a++ ++++
  gi|336255530|ref|YP_004598637.1|  13 LVFFINLARVVFAPLLD-VFIGEFAIGEATAGLIVTLAWLGSASLRLPTGWLLTRLPRHQVVLGSGTFLAVSsGIAA 88 
                                       678888999999****9.66799*********************************888888888888888834444 PP

                             MFS_1  80 lfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyi 156
                                       + a++++ l+++ +l+G+++g++f +++ l++++fp  + gr++g+ +a+++++a++++++ +l +  ++Wr++ ++
  gi|336255530|ref|YP_004598637.1|  89 S-ATTVPHLMAGAFLMGVASGVYFVSANPLLSELFPS-RVGRVVGIHGAASQIAAVIAAPFVALTL-FVSWRLSLWA 162
                                       4.488889****************************9.********************99988888.99******** PP

                             MFS_1 157 laivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllply 233
                                       +a+ ++l  +    ++ +++++ ++  ++++    +  +l++ w+++l++     +++++ +f  +++g++ +  ly
  gi|336255530|ref|YP_004598637.1| 163 IAVGTALITLY--TWIAAKNTDLPTAGQADR--DFVAGALSE-WRLILTSL----AIVGAPVF--VWQGVFNFYELY 228
                                       ********886..666555555555555555..235555555.******99....88888888..************ PP

                             MFS_1 234 lqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvli 310
                                        ++  gls   +aglll +++++g++++ ++g l+dr+++ ++ll  ++++++++++l l+      ++l+++ +++
  gi|336255530|ref|YP_004598637.1| 229 -MQSKGLS-DGMAGLLLTVVFAAGVPAFYFSGDLADRFPHVPYLLGVVGAFAASLFALTLVEGL---LALVVLTAVV 300
                                       .*******.4699999************************************************...6666677779 PP

                             MFS_1 311 Gfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                       Gf     fp+  +++ + +p + +g+a+++f++++ l+ +lg
  gi|336255530|ref|YP_004598637.1| 301 GFIIHALFPATDTFLLETLPDSTRGSAYAVFSSVWMLSQSLG 342
                                       9977777*******************************9997 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 1.2e-17
                             MFS_1  18 alplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrv 93 
                                       ++ ++++++ g+s   +glllt+++++ + a ++ G l+drf +   +llg+++ ++++l++l ++ +l +l+vl +
  gi|336255530|ref|YP_004598637.1| 223 NFYELYMQSKGLSDGMAGLLLTVVFAAGVPAFYFSGDLADRF-PHVPYLLGVVGAFAASLFALtLVEGLLALVVLTA 298
                                       5556556888********************************.77777777777777745555467**99******* PP

                             MFS_1  94 lqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfyilaivsllafvlfl 169
                                       + G+   alfpa  +++ +  p++ rg+a++++s+ + l+  lg  + g+l+   +g+ avf  +a+ ++ ++v   
  gi|336255530|ref|YP_004598637.1| 299 VVGFIIHALFPATDTFLLETLPDSTRGSAYAVFSSVWMLSQSLGSSALGVLLeRGYGYDAVFGSAALCLVALVV--- 372
                                       ********************************************999999997888899998776665555544... PP

                             MFS_1 170 lllpe 174
                                       +l+  
  gi|336255530|ref|YP_004598637.1| 373 VLVGL 377
                                       55544 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 !    3.1   3.2     0.004        36     230     346 ..      10     126 ..       2     138 .. 0.87
   2 !   36.8   9.9   2.3e-13   2.1e-09     239     374 ..     216     350 ..     137     361 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.004
                        MFS_1_like 230 fllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfll 306
                                       ++  ++++  +  ++   l++++ e    + ++G +v+l  +++  l +   +ll +l   ++++ + ++ ++   +
  gi|336255530|ref|YP_004598637.1|  10 LCGLVFFINLARVVFAPLLDVFIGEFAIGEATAGLIVTLAWLGSASLRLPTGWLLTRLPRHQVVLGSGTFLAVSSGI 86 
                                       6666777777777788889999999999999****************************999999999999999999 PP

                        MFS_1_like 307 yaiienawlvlpievLhgisfgllwaaaveyvskiapksl 346
                                        a+ + +  ++   +L g++ g+++++a    s+++p ++
  gi|336255530|ref|YP_004598637.1|  87 AASATTVPHLMAGAFLMGVASGVYFVSANPLLSELFPSRV 126
                                       99999999999999***********************986 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 2.3e-13
                        MFS_1_like 239 mswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawl 315
                                       ++w  + nF++lY++++g s  ++G l+++  +a +p f+f+  l +++ hv  l+  + a+++ ++ + ++e +  
  gi|336255530|ref|YP_004598637.1| 216 FVWQGVFNFYELYMQSKGLSDGMAGLLLTVVFAAGVPAFYFSGDLADRFPHVPYLLGVVGAFAASLFALTLVEGLLA 292
                                       5788899********************************************************************** PP

                        MFS_1_like 316 vlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllw 374
                                       ++++ +  g+ +++l+ a  ++  +  p+s+++   +++s++ + l + lGs + G+l 
  gi|336255530|ref|YP_004598637.1| 293 LVVLTAVVGFIIHALFPATDTFLLETLPDSTRGSAYAVFSSV-WMLSQSLGSSALGVLL 350
                                       ****************************************99.899*****99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.21s 00:00:00.75 Elapsed: 00:00:00.37
# Mc/sec: 3121.28
//
Query:       gi|336255531|ref|YP_004598638.1|  [L=323]
Description: XRE family transcriptional regulator [Halopiger xanaduensis SH-6]
Scores for 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-07   29.4   0.0    1.1e-06   28.6   0.0    1.4  1  HTH_3       Helix-turn-helix
    3.1e-05   24.2   0.1    0.00015   22.1   0.0    2.1  2  HTH_31      Helix-turn-helix domain
    0.00058   19.7   0.0     0.0014   18.5   0.0    1.6  1  HTH_11      HTH domain
    0.00089   19.2   0.0     0.0017   18.4   0.0    1.4  1  HTH_19      Helix-turn-helix domain
     0.0063   16.3   0.4      0.013   15.4   0.1    1.7  2  HTH_25      Helix-turn-helix domain
  ------ inclusion threshold ------
       0.03   14.1   0.0      0.075   12.9   0.0    1.6  1  HTH_23      Homeodomain-like domain
      0.033   13.7   0.0      0.079   12.5   0.0    1.6  1  Sigma70_r4  Sigma-70, region 4
       0.05   13.7   0.0        0.1   12.7   0.0    1.5  1  HTH_AraC    Bacterial regulatory helix-turn-helix proteins, A
      0.085   12.6   0.0       0.26   11.1   0.0    1.9  1  HTH_8       Bacterial regulatory protein, Fis family
       0.12   12.2   0.0       0.25   11.2   0.0    1.4  1  HTH_10      HTH DNA binding 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 !   28.6   0.0   6.1e-10   1.1e-06       2      51 ..     133     181 ..     132     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 6.1e-10
                                       HHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSE CS
                             HTH_3   2 kelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvs 51 
                                       +  R+ +++s+  LA +lGvsr+t+s++E G  n s+e++ +l + ++ +
  gi|336255531|ref|YP_004598638.1| 133 ADEREDRDWSLGRLANELGVSRRTVSKYEDG-MNASVEVAMELQDLFDAP 181
                                       678****************************.88********99998866 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   8.1e-08   0.00015       3      45 ..     129     169 ..     129     188 .. 0.84
   2 ?   -1.6   0.0         2   3.5e+03       5      17 ..     299     311 ..     298     312 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.1e-08
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspa 45 
                                       G+lL++ Re + +s+  +A  lgvs+ t+s++E G +   s +
  gi|336255531|ref|YP_004598638.1| 129 GDLLADEREDRDWSLGRLANELGVSRRTVSKYEDGMNA--SVE 169
                                       899*******************************9874..444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                            HTH_31   5 lLralReraGLsq 17 
                                       +L +lR++a L++
  gi|336255531|ref|YP_004598638.1| 299 ELDDLRNAAELRK 311
                                       68899***99986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     8e-07    0.0014      13      35 ..     138     160 ..     132     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8e-07
                            HTH_11  13 rgpisgeeLAeeLnvSrrtvrrd 35 
                                       + ++s  +LA eL+vSrrtv ++
  gi|336255531|ref|YP_004598638.1| 138 DRDWSLGRLANELGVSRRTVSKY 160
                                       4459****************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 !   18.4   0.0   9.3e-07    0.0017       2      37 ..     130     166 ..     129     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.3e-07
                            HTH_19   2 erLkeaReelgltqeelaerlgisrskisaiEng.kk 37 
                                       + L   Re + +++  la++lg+sr+  s++E g + 
  gi|336255531|ref|YP_004598638.1| 130 DLLADEREDRDWSLGRLANELGVSRRTVSKYEDGmNA 166
                                       567777**************************99554 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   7.2e-06     0.013       2      37 ..     132     167 ..     131     174 .. 0.91
   2 ?   -3.4   0.0         5     9e+03      31      49 ..     296     314 ..     295     315 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.2e-06
                                       HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--TT CS
                            HTH_25   2 LraaRearglsleevaketkIrkdylealEeddfda 37 
                                       L  +Re r +sl  +a+e+ ++ +++ + E+++ ++
  gi|336255531|ref|YP_004598638.1| 132 LADEREDRDWSLGRLANELGVSRRTVSKYEDGMNAS 167
                                       889***************************998776 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5
                                       HCT--TTSS-HHHHHHHHH CS
                            HTH_25  31 Eeddfdalpepvylrgylr 49 
                                       E++++d+l +++ lr  +r
  gi|336255531|ref|YP_004598638.1| 296 EREELDDLRNAAELRKVIR 314
                                       7777888887777777666 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.2e-05     0.075      16      37 ..     137     160 ..     131     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.2e-05
                            HTH_23  16 e..GlsvreIAreLgvsrrTvyrw 37 
                                       e   +s  + A eLgvsrrTv+++
  gi|336255531|ref|YP_004598638.1| 137 EdrDWSLGRLANELGVSRRTVSKY 160
                                       156899999************986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.4e-05     0.079      18      39 ..     138     159 ..     132     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.4e-05
                                       TTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrq 39 
                                       +++++l  ++++lg+Sr +V+ 
  gi|336255531|ref|YP_004598638.1| 138 DRDWSLGRLANELGVSRRTVSK 159
                                       799*****************97 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 ?   12.7   0.0   5.8e-05       0.1       4      27 ..     136     159 ..     134     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.8e-05
                                       CCSCT--HHHHHHHTTSSHHHHHH CS
                          HTH_AraC   4 nlstnltiediAdelgfSrsyFsr 27 
                                        ++++++++++A+elg+Sr++ s+
  gi|336255531|ref|YP_004598638.1| 136 REDRDWSLGRLANELGVSRRTVSK 159
                                       56899***************9886 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 ?   11.1   0.0   0.00015      0.26      18      36 ..     140     158 ..     137     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                       TT-HHHHHHHHTS-HHHHH CS
                             HTH_8  18 gGnkskAArlLGisRrtLy 36 
                                       ++ + + A++LG+sRrt+ 
  gi|336255531|ref|YP_004598638.1| 140 DWSLGRLANELGVSRRTVS 158
                                       689999***********85 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   0.00014      0.25      21      43 ..     138     160 ..     137     160 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                            HTH_10  21 PRrvtlkeLAkelGIskstlseh 43 
                                       +R+ +l  LA+elG+s+ t+s++
  gi|336255531|ref|YP_004598638.1| 138 DRDWSLGRLANELGVSRRTVSKY 160
                                       6999***************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2457.63
//
Query:       gi|336255532|ref|YP_004598639.1|  [L=442]
Description: hypothetical protein Halxa_4156 [Halopiger xanaduensis SH-6]
Scores for 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-40  136.7   0.0      1e-39  135.2   0.0    1.7  2  DUF1743          Domain of unknown function (DUF1743)
  ------ inclusion threshold ------
      0.038   14.2   0.2      0.064   13.5   0.2    1.3  1  IBR              IBR domain, a half RING-finger domain
      0.046   13.6   0.1      0.098   12.6   0.1    1.5  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.047   13.7   0.0       0.22   11.5   0.0    2.1  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.084   12.9   0.4       0.17   11.9   0.4    1.5  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.092   12.7   0.9        0.2   11.6   0.9    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.13   12.3   2.3       0.36   10.8   2.3    1.8  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.18   11.9   0.1       0.35   10.9   0.1    1.5  1  zinc_ribbon_6    Zinc-ribbon
       0.18   11.8   0.8       0.34   10.9   0.8    1.4  1  zinc-ribbons_6   zinc-ribbons
       0.43   10.7   2.3         31    4.8   0.3    2.8  2  Zn-ribbon_8      Zinc ribbon domain
       0.67    9.9   2.2        1.3    8.9   2.2    1.5  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit


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 ?   -1.8   0.0         2   3.2e+03      35      69 ..      61      95 ..      47     135 .. 0.67
   2 !  135.2   0.0   6.3e-43     1e-39       1     116 []     143     257 ..     143     257 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2
                                      ---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS- CS
                           DUF1743 35 erevdeesvieadektypetfdnvDlshklvvlvP 69
                                      + + d++  +e+++++ ++  ++ D +++  ++v 
  gi|336255532|ref|YP_004598639.1| 61 HADCDPDRAFEIAREHLEALAETADERTNPGLVVA 95
                                      56677888888888888888888887776655554 PP

  == domain 2  score: 135.2 bits;  conditional E-value: 6.3e-43
                                       TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEE CS
                           DUF1743   1 grgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvl 76 
                                       grg iGA+aa+ga+ ale++t E+++Yrep+rwg +revd+esv++a++  yp+++d+vD+ ++++v+vPhtp p+l
  gi|336255532|ref|YP_004598639.1| 143 GRGRIGALAAVGAWRALEEWTHEYISYREPDRWGtPREVDDESVFAAADWGYPAVWDTVDRGENETVCVPHTPGPIL 219
                                       89*************************************************************************** PP

                                       EEEEES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                           DUF1743  77 fGirgedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                       +Girg+dp+a++++a++i+s  e+++++++f tnqgtd h
  gi|336255532|ref|YP_004598639.1| 220 HGIRGDDPDAVRAVAERIDS--EPVDSSQLFVTNQGTDVH 257
                                       ********************..****************88 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   3.9e-05     0.064       2      47 ..     354     397 ..     353     398 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-05
                               IBR   2 kyeklklkkslesdpnlkwCprpdCeaiieksegcksvtCskCgfe 47 
                                       k+ek++ ++ +++++ +  Cp  dC++ +e+   ++  +C++Cg++
  gi|336255532|ref|YP_004598639.1| 354 KLEKFAVRDLVTTERVTPTCP--DCDRRMESAGRNQGYRCRECGTS 397
                                       6789999999999999*****..******999996667*****975 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 ?   12.6   0.1     6e-05     0.098      12      36 ..     371     396 ..     359     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6e-05
                                       -B-TTT-SB--S.SSS-EEEETTT-- CS
                              C1_1  12 tfCkhCgeflwg.kekqglkCswCkl 36 
                                        +C  C+  ++  ++ qg++C++C+ 
  gi|336255532|ref|YP_004598639.1| 371 PTCPDCDRRMESaGRNQGYRCRECGT 396
                                       58********888***********85 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 ?   11.5   0.0   0.00014      0.22       2      60 ..     273     350 ..     272     359 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                       EEEEEEEEEEEEEETTEEEEEEEETTE.................EEEEEEET..HHHHHHHTTS-TTSEEEEEEEEE CS
                   tRNA_anti-codon   2 tvaGrvtsisdrsggkvifidlrDgtg.................riqvvlfr..eeatklaenlkeGdvvrvtGrvk 59 
                                       +++Grv ++ ++  g+++f++l   +                  r+++ +f   + +++   +l++Gd + v G+v+
  gi|336255532|ref|YP_004598639.1| 273 RLEGRVATVPETRRGGHVFFELAAPSErietaegegeddqpvahRLECAAFEptKRFRDRVRSLRVGDRLTVCGEVS 349
                                       789*******99999******88877766666668899999999999999998888888899999***********8 PP

                                       E CS
                   tRNA_anti-codon  60 r 60 
                                       r
  gi|336255532|ref|YP_004598639.1| 350 R 350
                                       7 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 ?   11.9   0.4   0.00011      0.17      63      95 ..     361     397 ..     335     403 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                       E..EEEE--EEEETTTS-EEECHH.H.HHS-TTTSSS CS
                              HypA  63 e..ieevpvkvrCreCgkefelee.k.alrCpkCgsa 95 
                                       +  +++++v+ +C +C++++e++  +  +rC +Cg++
  gi|336255532|ref|YP_004598639.1| 361 RdlVTTERVTPTCPDCDRRMESAGrNqGYRCRECGTS 397
                                       35578899999**********88743688*****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 ?   11.6   0.9   0.00012       0.2      30      55 ..     372     397 ..     356     399 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfe 55 
                                       tC+ C ++++ a  ++ ++C++Cg++
  gi|336255532|ref|YP_004598639.1| 372 TCPDCDRRMESAGRNQGYRCRECGTS 397
                                       8***********************86 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 ?   10.8   2.3   0.00022      0.36      19      45 ..     371     396 ..     365     397 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                     Zn_Tnp_IS1595  19 fvCPhCgsr..kayriktrglfqCkeCrk 45 
                                       ++CP C  r  +a r    + ++C+eC++
  gi|336255532|ref|YP_004598639.1| 371 PTCPDCDRRmeSAGRN---QGYRCRECGT 396
                                       89*****776444444...46******96 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00022      0.35      26      54 ..     367     395 ..     355     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                     zinc_ribbon_6  26 kkvkilCnDCekksevkfhvlglkCkeCg 54 
                                       ++v+ +C DC+++ e + +  g +C+eCg
  gi|336255532|ref|YP_004598639.1| 367 ERVTPTCPDCDRRMESAGRNQGYRCRECG 395
                                       566678**********************7 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   0.00021      0.34       2      24 ..     372     396 ..     371     405 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                                       --SSS-S--EE-S..SEEE-TTT-- CS
                    zinc-ribbons_6   2 kCpeCqqelekrg..eqyhCeaCqe 24 
                                       +Cp+C++ +e+ g  + y+C++C +
  gi|336255532|ref|YP_004598639.1| 372 TCPDCDRRMESAGrnQGYRCRECGT 396
                                       6*********5544499******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 ?    4.6   0.1     0.022        35      21      35 ..     364     379 ..     354     382 .. 0.66
   2 ?    4.8   0.3     0.019        31       6      13 ..     389     396 ..     388     399 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.022
                       Zn-ribbon_8  21 is.dapltaCPeCgse 35 
                                       ++ ++  ++CP+C  +
  gi|336255532|ref|YP_004598639.1| 364 VTtERVTPTCPDCDRR 379
                                       453555666****765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.019
                       Zn-ribbon_8   6 YrCeeCgh 13 
                                       YrC+eCg+
  gi|336255532|ref|YP_004598639.1| 389 YRCRECGT 396
                                       9******6 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 ?    8.9   2.2   0.00081       1.3       4      32 ..     373     399 ..     373     403 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00081
                                       ESTTTSBEEEEECSCCCEEEESSSS-EEE CS
                    RNA_POL_M_15KD   4 CpkCgNlLlpkedkegknfeCrqCgYeep 32 
                                       Cp+C   +++++   g  + Cr Cg   p
  gi|336255532|ref|YP_004598639.1| 373 CPDCDRRMESAGRNQG--YRCRECGTSAP 399
                                       ****************..67****97666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 3356.81
//
Query:       gi|336255533|ref|YP_004598640.1|  [L=663]
Description: hypothetical protein Halxa_4157 [Halopiger xanaduensis SH-6]
Scores for 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  (663 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 5127.94
//
Query:       gi|336255534|ref|YP_004598641.1|  [L=69]
Description: hypothetical protein Halxa_4158 [Halopiger xanaduensis SH-6]
Scores for 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:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 590.89
//
Query:       gi|336255535|ref|YP_004598642.1|  [L=129]
Description: hypothetical protein Halxa_4159 [Halopiger xanaduensis SH-6]
Scores for 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  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1140.83
//
Query:       gi|336255536|ref|YP_004598643.1|  [L=370]
Description: small GTP-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-31  107.1   0.7    8.6e-31  106.1   0.3    1.8  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      3e-23   82.1   0.0    6.9e-23   80.9   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
    9.5e-15   54.5   0.8    2.3e-11   43.5   0.0    2.3  2  FeoB_N        Ferrous iron transport protein B
    2.6e-13   49.8   0.0    4.5e-13   49.0   0.0    1.4  1  TGS           TGS domain
      5e-07   29.8   1.7      0.029   14.3   0.0    3.1  3  RsgA_GTPase   RsgA GTPase
    3.7e-05   23.9   0.2      0.083   12.9   0.1    2.8  2  Dynamin_N     Dynamin family
     0.0019   18.7   0.1       0.15   12.6   0.0    2.4  2  ABC_tran      ABC transporter
     0.0022   17.3   0.1     0.0044   16.4   0.0    1.5  2  AIG1          AIG1 family
     0.0025   17.4   0.1      0.027   14.0   0.0    2.5  3  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0057   15.7   0.2       0.71    8.8   0.0    2.8  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
  ------ inclusion threshold ------
      0.026   14.0   0.1        1.5    8.3   0.0    2.6  2  Arf           ADP-ribosylation factor family
      0.028   15.0   0.6       0.19   12.4   0.2    2.6  2  ThiS          ThiS family
      0.037   13.6   0.0       0.61    9.7   0.0    2.4  2  Ras           Ras family
      0.063   13.6   0.0       0.14   12.5   0.0    1.6  1  AAA_16        AAA ATPase domain
      0.067   13.4   0.0       0.28   11.4   0.0    2.0  3  Roc           Ras of Complex, Roc, domain of DAPkinase
        0.1   12.0   0.5       0.18   11.3   0.0    1.7  2  SRPRB         Signal recognition particle receptor beta subun
       0.38   11.0   8.5       0.12   12.7   3.9    2.4  2  ABC_tran_CTD  ABC transporter C-terminal domain


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 ?   -3.2   0.0       7.9   8.3e+03      83     102 ..     144     163 ..     131     164 .. 0.69
   2 !  106.1   0.3   8.1e-34   8.6e-31       1     106 []     182     294 ..     182     294 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.9
                      MMR_HSR1_Xtn  83 vviSaekelnldeLkekiwe 102
                                       +v+S+ +  + d+L+e++++
  gi|336255536|ref|YP_004598643.1| 144 FVLSVFEIDQYDRLQEELYD 163
                                       55677777777888888775 PP

  == domain 2  score: 106.1 bits;  conditional E-value: 8.1e-34
                      MMR_HSR1_Xtn   1 kgGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldela 77 
                                       k+Gikits+++++ ldeet+k++l+e++++na+v ++e vt+D+l+d +++nr+Yip+++++NK+Dli+ ++ ++++
  gi|336255536|ref|YP_004598643.1| 182 KDGIKITSSTDQD-LDEETIKHVLREHGYVNADVNLQETVTIDRLVDGLMENREYIPSITCVNKVDLIEPDYKETVD 257
                                       57******99955.*************************************************************99 PP

                      MMR_HSR1_Xtn  78 re........pnsvviSaekelnldeLkekiweeLnL 106
                                       +e        +++++iSaeke++l++Lk++iwe+L+L
  gi|336255536|ref|YP_004598643.1| 258 EElrergldpEEVTFISAEKEKGLEALKDRIWENLGL 294
                                       977889999669999********************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 !   80.9   0.0   6.5e-26   6.9e-23       2     103 ..      64     167 ..      63     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 6.5e-26
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.ad 77 
                                       va+vG p vGKS+L+n+lt+++++++++ +tT+d+n g ++++g +i+++D+pGliega  +kg g+++la+ + ad
  gi|336255536|ref|YP_004598643.1|  64 VALVGFPSVGKSSLLNSLTNAESETGSYEFTTLDVNPGMLHHRGANIQMLDVPGLIEGAAAGKGDGQQVLAVVRnAD 140
                                       9****************************************999***************************88879* PP

                                       EEEEEEETT.TTCSHHHHHHHHHHHHH CS
                          MMR_HSR1  78 lillvvdas.eeklkpldeeleellee 103
                                       li++v+++   +++++l+eel +++ +
  gi|336255536|ref|YP_004598643.1| 141 LIIFVLSVFeIDQYDRLQEELYDINIR 167
                                       ******988533788888888887654 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 !   43.5   0.0   2.2e-14   2.3e-11       2     106 ..      63     166 ..      62     169 .. 0.81
   2 !    9.5   0.2   0.00062      0.65      65     156 .]     195     288 ..     184     288 .. 0.74

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.2e-14
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleee 78 
                                       tvalvG p vGk++l+n+lt+a+++ g +  +t + + g l+++g +++++D+PG  +  a  + +      +  ++
  gi|336255536|ref|YP_004598643.1|  63 TVALVGFPSVGKSSLLNSLTNAESETGSYEFTTLDVNPGMLHHRGANIQMLDVPGLIEGAAAGKGDGQQVLAV-VRN 138
                                       79*****************************************************977655555443333222.467 PP

                                       SSEEEEEEEGGGHHHHHHHHHHHHHTTS CS
                            FeoB_N  79 pdvvvnvvdatnlernLyLtlqllelgv 106
                                       +d+++ v+   ++++   L  +l ++++
  gi|336255536|ref|YP_004598643.1| 139 ADLIIFVLSVFEIDQYDRLQEELYDINI 166
                                       7888888888888777777777777665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00062
                                       HHHHHHHHHHH.CTSSSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHT.TEEE-HHHHHHHHTS.-E CS
                            FeoB_N  65 eeekvardfll.eeepdvvvnvvdatnlernLyLtlqllelgvpvvlalnmideaekk.gieidlkkLsekLgv.pv 138
                                        +e+  +++l  +  +++ vn+ ++ +++r +  +++  e  +p + ++n++d +e + + ++d++  ++ L+  +v
  gi|336255536|ref|YP_004598643.1| 195 LDEETIKHVLReHGYVNADVNLQETVTIDRLVDGLMENREY-IPSITCVNKVDLIEPDyKETVDEELRERGLDPeEV 270
                                       56666666666244567788888888888866655555554.899**********9762567888888889*96268 PP

                                       EEEBTTTTBTHHHHHHHH CS
                            FeoB_N 139 vktsakkkegieellkai 156
                                         +sa+k++g+e+l+++i
  gi|336255536|ref|YP_004598643.1| 271 TFISAEKEKGLEALKDRI 288
                                       8899**********9876 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   4.3e-16   4.5e-13       1      59 [.     295     367 ..     295     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 4.3e-16
                                       EEEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                               TGS   1 irvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                       irvy+ ++G+ +d      + +g+tv ++  k++ ++ ++f+ A+V G       q+vg dhvLed+dv++++
  gi|336255536|ref|YP_004598643.1| 295 IRVYMdKPGRGVDweeplvIEEGSTVGEAIEKLGGEMEERFRFARVTGpsathdeQQVGKDHVLEDEDVLKLI 367
                                       89********************************************************************997 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   4.6e-05     0.049      98     127 ..      60      88 ..      20     118 .. 0.88
   2 ?   -2.6   0.0       4.2   4.5e+03      69      97 ..     133     161 ..     126     167 .. 0.64
   3 !   14.3   0.0   2.8e-05     0.029      43      99 ..     232     290 ..     210     296 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.6e-05
                                       TTSEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelkt 127
                                        d t++lvG   vGKS+L+n+l++  e +t
  gi|336255536|ref|YP_004598643.1|  60 GDATVALVGFPSVGKSSLLNSLTNA-ESET 88 
                                       468999****************986.4444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.2
                                       HHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                       RsgA_GTPase  69 keelealgyevllvsaktkegleelkell 97 
                                        + ++++++ ++++s+ + +++++l+e+l
  gi|336255536|ref|YP_004598643.1| 133 LAVVRNADLIIFVLSVFEIDQYDRLQEEL 161
                                       55566666666666666666666666665 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 2.8e-05
                                       HHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTS...EEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  43 eekgiepvivlnKiDlleeeeeleelkeelealgy...evllvsaktkegleelkellkd 99 
                                       +++ i+ + ++nK+Dl+e +   e++ eel++ g+   ev+++sa++++gle+lk+++ +
  gi|336255536|ref|YP_004598643.1| 232 NREYIPSITCVNKVDLIEPDY-KETVDEELRERGLdpeEVTFISAEKEKGLEALKDRIWE 290
                                       345578899**********99.999******999733358899***********998765 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   7.9e-05     0.083       1      22 [.      64      85 ..      64     100 .. 0.83
   2 !    8.1   0.0    0.0025       2.6     101     137 ..     108     147 ..     101     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-05
                                      EEEEEBTTTTHHHHHHHHHTS- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                      +a+vG  S GKSS+ln+L+ ++
  gi|336255536|ref|YP_004598643.1| 64 VALVGFPSVGKSSLLNSLTNAE 85
                                      799***************9887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0025
                                       -SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEE CS
                         Dynamin_N 101 kgltlvDlPGldsvnkrdq...elvkeyikkadiilavts 137
                                        ++ ++D+PGl++ ++  +   + v   +++ad+i++v+s
  gi|336255536|ref|YP_004598643.1| 108 ANIQMLDVPGLIEGAAAGKgdgQQVLAVVRNADLIIFVLS 147
                                       6899*********998888888***************986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00014      0.15      11      64 ..      61     113 ..      53     140 .. 0.86
   2 ?    3.9   0.0     0.067        71      45      80 ..     190     251 ..     175     302 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                       TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvl 64 
                                       + +va+vG    GKS+Ll+ l++ ++ + G+ ++   d++   l++  ++i++l
  gi|336255536|ref|YP_004598643.1|  61 DATVALVGFPSVGKSSLLNSLTNAES-ETGSYEFTTLDVNPGMLHHRGANIQML 113
                                       6799******************9987.688888888888877777777777776 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.067
                                       T.TCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.........................H CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................x RF
                          ABC_tran  45 d.gkdlkeqeleslrkeigvlpqepqlfpeltvren.........................e 80 
                                         ++dl+e++++++ +e g++  + +l++++t+ +                          +
  gi|336255536|ref|YP_004598643.1| 190 StDQDLDEETIKHVLREHGYVNADVNLQETVTIDRLvdglmenreyipsitcvnkvdliepD 251
                                       336788889**********************9987777776666665555555555555551 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       5.7     6e+03     180     209 ..       6      35 ..       5      38 .. 0.74
   2 !   16.4   0.0   4.2e-06    0.0044       2      99 ..      63     157 ..      62     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.7
                                       HHHHHHHHTTTT--B-HHHHHHHHCCHBHH CS
                              AIG1 180 lveaivkenggkpytnelyekikeeaeklk 209
                                        +e+i++e  + py + +  +i + ++kl 
  gi|336255536|ref|YP_004598643.1|   6 EIEEIEEEIANTPYNKSTEAHIGRLKSKLA 35 
                                       588999999999999888888777666555 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.2e-06
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrcll 78 
                                       t+ lvG   +GkS+  Ns+ + +  +   s +  t  ++      +g +i+  D Pgl++  +  +   +++   + 
  gi|336255536|ref|YP_004598643.1|  63 TVALVGFPSVGKSSLLNSLTNAESETG--SYEFTTLDVNPGMLHHRGANIQMLDVPGLIEGAAAGKGDGQQVLA-VV 136
                                       788***************987765333..45777888888889*******************998888888885.44 PP

                                       HCTT-ESEEEEEEETTB-SHH CS
                              AIG1  79 lseegihalllvlslgrftee 99 
                                        +++ i ++l v++++++++ 
  gi|336255536|ref|YP_004598643.1| 137 RNADLIIFVLSVFEIDQYDRL 157
                                       444546666666666666654 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 ?   -0.1   0.0      0.53   5.5e+02       7      29 ..      65      87 ..      62     117 .. 0.78
   2 ?   -2.8   0.0       3.7   3.9e+03     128     144 ..     150     166 ..     124     203 .. 0.64
   3 !   14.0   0.0   2.6e-05     0.027     120     189 ..     233     289 ..     219     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.53
                                      EEEESTTSSHHHHHHHHHHHTTS CS
                          GTP_EFTU  7 giighvDhGKtTLtdrLlyktga 29
                                      +++g    GK++L+ +L+ + ++
  gi|336255536|ref|YP_004598643.1| 65 ALVGFPSVGKSSLLNSLTNAESE 87
                                      55666678999999999976555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.7
                                       EEESCGSTHHHHHHHHH CS
                          GTP_EFTU 128 fiNKmDrlkaelkeive 144
                                        i   Drl++el  i  
  gi|336255536|ref|YP_004598643.1| 150 EIDQYDRLQEELYDINI 166
                                       34445555555555544 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 2.6e-05
                                       HTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHH CS
                          GTP_EFTU 120 kegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealv 189
                                       +e +p i+++NK+D ++ ++ke+v+e  ++           g + e   +v f+Sa k +g+++l + + 
  gi|336255536|ref|YP_004598643.1| 233 REYIPSITCVNKVDLIEPDYKETVDEELRER----------GLDPE---EVTFISAEKEKGLEALKDRIW 289
                                       567999*****************99987665..........55555...788999999998888877765 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 !    8.8   0.0   0.00068      0.71      27      72 ..      60     105 ..      55     111 .. 0.76
   2 ?    3.7   0.1     0.024        25     199     256 ..     304     361 ..     221     369 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00068
                                       S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT-.-EEEEEE------- CS
                              MeaB  27 GraqvvGltGvPGaGkstlvealglelrrrGk.rvavlavDPsspft 72 
                                       G a+ v l G+P +Gks l++ l+    + G    + l v+P+   +
  gi|336255536|ref|YP_004598643.1|  60 GDAT-VALVGFPSVGKSSLLNSLTNAESETGSyEFTTLDVNPGMLHH 105
                                       5554.7899***************99888885267777777776555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.024
                                       TBTTB-.-EEEEEBCCCTBSHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH CS
                              MeaB 199 kekeWr.pkvlktsavegeGidelvdaieehrevlkktGllekrrrerakeelrelved 256
                                       +  +W+ p v++  ++ ge i++l  ++ee +++++ tG  + + ++++ +  + l  +
  gi|336255536|ref|YP_004598643.1| 304 RGVDWEePLVIEEGSTVGEAIEKLGGEMEERFRFARVTGPSATHDEQQVGKD-HVLEDE 361
                                       3567862567788888999999999999999999999998887776554433.444455 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0014       1.5      15      68 ..      62     118 ..      55     223 .. 0.83
   2 ?    2.9   0.0     0.063        67     115     173 ..     235     290 ..     222     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0014
                                       EEEEEEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEETTEEEEEEEE-SS CS
                               Arf  15 lrilllGLDnaGKtTilkklkleelvt...tvPTigfnveeleiknlkftvwDvGGq 68 
                                       + + l+G  + GK+ +l+ l++ e +t      T+  n   l++++ ++++ Dv G 
  gi|336255536|ref|YP_004598643.1|  62 ATVALVGFPSVGKSSLLNSLTNAESETgsyEFTTLDVNPGMLHHRGANIQMLDVPGL 118
                                       567899****************99998777789********************9874 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.063
                                       TSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBTHHHHHHHHHH CS
                               Arf 115 evallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkgeglkeglewlse 173
                                        ++ +   NK Dl e   +e + e+l  + l    + e++  sa k +gl+   +++ e
  gi|336255536|ref|YP_004598643.1| 235 YIPSITCVNKVDLIEPDYKETVDEELRERGLD---PEEVTFISAEKEKGLEALKDRIWE 290
                                       56778889*********************999...778888899999999888887766 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.9   5.2e+03      20      33 ..     196     209 ..     185     237 .. 0.61
   2 ?   12.4   0.2   0.00018      0.19      13      71 ..     309     367 ..     297     368 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.9
                                       STSBHHHHHHHHHH CS
                              ThiS  20 egstvaelleaLge 33 
                                       +++t++ +l++ g+
  gi|336255536|ref|YP_004598643.1| 196 DEETIKHVLREHGY 209
                                       55555555555443 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00018
                                       CEEEEESSTSBHHHHHHHHHHHTCHHG...TTTTEEEEETTEEEGCCTTTSB--TTCEEEEE CS
                              ThiS  13 eeelelaegstvaelleaLgerypela...lerrvavavNgeivprlwldtelkdgDevail 71 
                                       ee l+++egstv+e++e+Lg + +e +      +  +  +++ v +   d++l d D++ ++
  gi|336255536|ref|YP_004598643.1| 309 EEPLVIEEGSTVGEAIEKLGGEMEERFrfaRVTGPSATHDEQQVGK---DHVLEDEDVLKLI 367
                                       788999*************988876666775567777888888888...9999999998876 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00058      0.61       2     106 ..      64     173 ..      63     213 .. 0.67
   2 ?    1.1   0.0      0.25   2.7e+02      91     150 ..     223     282 ..     213     292 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00058
                                       EEEEESTTSSHHHHHHHHHHSSCSS.SCTTTSSEEEEEEEEEETTEEEEEEEEE........ETTSGGGHHHHHHHH CS
                               Ras   2 lvlvGdsavGKtslllrfvkdkFke.eyesTigvdfytkeievdgkevkleiwD........TAGqeefkslrelyy 69 
                                       + lvG  +vGK+sll++ ++ + ++ +ye T   d     ++ +g ++  +++D         AG+ + +++  +++
  gi|336255536|ref|YP_004598643.1|  64 VALVGFPSVGKSSLLNSLTNAESETgSYEFTT-LDVNPGMLHHRGANI--QMLDvpgliegaAAGKGDGQQVL-AVV 136
                                       679****************9887652677776.666555555554444..44441112222235555544443.567 PP

                                       TTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSE CS
                               Ras  70 rdaegillvyditsresfenvkkwveeikrvaeenvp 106
                                       r+a+ i+ v ++ + + ++++++ + +i+  ++++ p
  gi|336255536|ref|YP_004598643.1| 137 RNADLIIFVLSVFEIDQYDRLQEELYDINIRVDQEPP 173
                                       7888888888888888888877776677666665555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHSTTTSEEEEEEETTTGGG...G-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHH CS
                               Ras  91 kkwveeikrvaeenvpivLvGnKvDlee...kravsteegeelakelglkfletSAktnenve 150
                                       +++v+ + +  e  +p + + nKvDl e   k++v++e  e+  +  +++f+  SA++++++e
  gi|336255536|ref|YP_004598643.1| 223 DRLVDGLMENRE-YIPSITCVNKVDLIEpdyKETVDEELRERGLDPEEVTFI--SAEKEKGLE 282
                                       456666666666.6999999******99888788887777777777777774..666666665 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   0.0   0.00013      0.14      25      52 ..      62      89 ..      54     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                            AAA_16 25 elvllsGesGvGKsslvrellralekdg 52
                                        v l+G + vGKssl+++l +a +++g
  gi|336255536|ref|YP_004598643.1| 62 ATVALVGFPSVGKSSLLNSLTNAESETG 89
                                      6799****************97666553 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00026      0.28       2      31 ..      64      93 ..      63     117 .. 0.79
   2 ?   -2.7   0.0       6.3   6.7e+03      78     108 ..     137     170 ..     124     181 .. 0.65
   3 ?   -2.5   0.0       5.4   5.7e+03     100     119 ..     227     246 ..     205     247 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEETT CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekst 31
                                      v lvG  +vGK+sll+++++ + ++ + + 
  gi|336255536|ref|YP_004598643.1| 64 VALVGFPSVGKSSLLNSLTNAESETGSYEF 93
                                      789****************98877655444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.3
                                       CTSCEEEEEEE...GHHHHCHHHHHHHHHHHCSS CS
                               Roc  78 reaalailvyd...srssenlkeWlkelkkvagk 108
                                       r+a+l+i+v+     +++++l+e l +++ ++++
  gi|336255536|ref|YP_004598643.1| 137 RNADLIIFVLSvfeIDQYDRLQEELYDINIRVDQ 170
                                       6777777765433366667777777666665554 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.4
                                       HHHHHHCSSS-EEEEEE-TT CS
                               Roc 100 kelkkvagkspvilvgnkiD 119
                                       + l ++++ +p i ++nk+D
  gi|336255536|ref|YP_004598643.1| 227 DGLMENREYIPSITCVNKVD 246
                                       55566677788899999998 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 ?   -3.1   0.5       4.1   4.4e+03     137     155 ..       3      21 ..       2      43 .. 0.68
   2 ?   11.3   0.0   0.00017      0.18       5      58 ..      63     117 ..      59     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.1
                                       HHHHHHHHHHCHHHHHH-- CS
                             SRPRB 137 LEkElnkiierrskalkel 155
                                       LE+E+++i e  ++ + + 
  gi|336255536|ref|YP_004598643.1|   3 LEEEIEEIEEEIANTPYNK 21 
                                       7888888888776666554 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00017
                                       EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPG 58 
                                       +v lvG    GK sl++ Lt+ + ++         +   +  ++g +++++D+PG
  gi|336255536|ref|YP_004598643.1|  63 TVALVGFPSVGKSSLLNSLTNAESETGSYEFtTLDVNPGMLHHRGANIQMLDVPG 117
                                       789*****************986555444443555556667899**********9 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 ?   12.7   3.9   0.00011      0.12      20      59 ..       3      43 ..       1      45 [. 0.86
   2 ?   -0.9   0.1       1.9     2e+03      27      53 ..     256     280 ..     252     292 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                      ABC_tran_CTD 20 LEeeiaeleaeladpelysdp.eklaelsaeleeleaeLee 59
                                      LEeei+e+e+e+a+  + +   + + +l  +l+e +++Le+
  gi|336255536|ref|YP_004598643.1|  3 LEEEIEEIEEEIANTPYNKSTeAHIGRLKSKLAEKKEKLEN 43
                                      9************99866444577***************96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                      ABC_tran_CTD  27 leaeladpelysdpeklaelsaeleel 53 
                                       +++el + +   dpe+++ +sae+e+ 
  gi|336255536|ref|YP_004598643.1| 256 VDEELRERG--LDPEEVTFISAEKEKG 280
                                       555666555..5667766666665543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); 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 0.24s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2729.51
//
Query:       gi|336255537|ref|YP_004598644.1|  [L=572]
Description: Na+/H+ antiporter NhaC-like protein [Halopiger xanaduensis SH-6]
Scores for 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-65  220.8  34.5      8e-64  215.8  25.4    3.1  2  Na_H_antiporter  Na+/H+ antiporter family
  ------ inclusion threshold ------
      0.084   12.4   0.1       0.14   11.7   0.1    1.3  1  Peptidase_S15    X-Pro dipeptidyl-peptidase (S15 family)
       0.15   12.0   9.4       0.25   11.3   0.5    2.9  2  TNFR_16_TM       Tumor necrosis factor receptor member 16 tra
       0.38   10.6   1.7         34    4.4   0.0    2.9  2  COX14            Cytochrome oxidase c assembly


Domain annotation for each model (and alignments):
>> Na_H_antiporter  Na+/H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   2.3    0.0073        33     162     254 ..      67     155 ..       3     159 .. 0.77
   2 !  215.8  25.4   1.8e-67     8e-64       8     300 ..     161     501 ..     155     504 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0073
                   Na_H_antiporter 162 gaililllAwgiggvlealgvteslvsslakgv.vskgllplilflvallvafatGtswgtigIilpiavplaaklg 237
                                        +++ lll+ g + + +  g  ++ v   a++  ++++ + l++ ++++++ f     ++  +I++ +++++ ++l 
  gi|336255537|ref|YP_004598644.1|  67 ILLFTLLLGSGVALIWRLGG--ATAVREWATARlQTQRTVGLTTWFLGMAMFF---DDYANTAIVGSTMREISDQLR 138
                                       56777888888887777777..4445555555558899999999999999988...79999**************** PP

                   Na_H_antiporter 238 isllalvraveaggtlg 254
                                       is+  l+ +v + ++ +
  gi|336255537|ref|YP_004598644.1| 139 ISREKLSYIVDSTAAPV 155
                                       ***********999865 PP

  == domain 2  score: 215.8 bits;  conditional E-value: 1.8e-67
                   Na_H_antiporter   8 ssplsdtvgliagilktdlieeia.algmlvqsipanvysifallvvglvvlllrdigamlraeaear......... 74 
                                       ss+++++ +li+ +++  + e +  a++ +v+sip+n y+++a+++vgl+v++ rd+g+ml+ae++ar         
  gi|336255537|ref|YP_004598644.1| 161 SSWVAFQLSLIGDAYEGLGAEGAPtAFETFVRSIPYNTYALLAIVMVGLIVYTGRDYGEMLEAEHRARstgkvsred 237
                                       8**************99999988789******************************************888888777 PP

                   Na_H_antiporter  75 .........eleekeltk..............lpiavliiltlskmpytgalalvai....vkafivala....... 117
                                                +                      +p++vl+++tl+++ +tg+++  a     ++ ++v++a       
  gi|336255537|ref|YP_004598644.1| 238 aqplqevekD-------LgapietrpmlrtffAPVVVLVAVTLAGAFWTGYQSWTASqveaGAPTTVQGAaaadgyv 307
                                       6666655551.......044555566666999999999999999999999887644311114445666666666665 PP

                   Na_H_antiporter 118 ......fqntdvatalvvgalaglivatllela....slseidkllnrGiksmlgaililllAwgiggvlealgvte 184
                                             +   d+a alv+g++a++++a++ ++a    +l ++ +++ +G+ +ml+a++il+lAw+i+ v+eal  t+
  gi|336255537|ref|YP_004598644.1| 308 qvfvdiVGAGDFAGALVWGSFAMVATAIAIGIAydlfDLGTAVDTVLDGFRLMLTAVTILVLAWTISAVAEALE-TG 383
                                       5556657788*********************999****************************************.** PP

                   Na_H_antiporter 185 slvsslakgvvskgllplilflvallvafatGtswgtigIilpiavplaaklgisl...lalvraveaggtlgdhls 258
                                       ++v++l+  +++ +llp+++++va+++af++G+sw+t+gI++pia++la  l       +++v+av++g+++gdh+s
  gi|336255537|ref|YP_004598644.1| 384 AYVTNLVGDAIPTALLPVVVLFVAAFIAFTMGSSWATMGIVTPIAIELAYDLTGGFdamPVVVGAVFSGAIFGDHSS 460
                                       **************************************************996655558999*************** PP

                   Na_H_antiporter 259 Pisdttilsstglnadhidhvsytqlpyallvapitailllv 300
                                       Pisdtt+ls+t+++ad idhv+ tqlpya +v+++++i +l+
  gi|336255537|ref|YP_004598644.1| 461 PISDTTVLSATFTGADLIDHVR-TQLPYAVTVMLVVVICYLL 501
                                       **********************.*****************97 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.1e-05      0.14      43      80 ..     290     328 ..     215     337 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
                                       HHCCHGGGHH.........HHHTT-EEEEEE-TTSTTS-S---TTTT CS
                     Peptidase_S15  43 leelelqdkv.........fvarGYavVvqdvrGtggSeGeftvgds 80 
                                       +        +          +a+GY+ V++d++G g+  G+ ++g+ 
  gi|336255537|ref|YP_004598644.1| 290 E--------AgapttvqgaAAADGYVQVFVDIVGAGDFAGALVWGSF 328
                                       2........133333444599*******************9998755 PP

>> TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   2.9     0.018        79      12      24 ..     200     212 ..     199     213 .. 0.93
   2 ?   11.3   0.5   5.6e-05      0.25      11      30 ..     396     415 ..     393     418 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.018
                        TNFR_16_TM  12 SILaaVvvgLlaY 24 
                                       ++La+V vgL++Y
  gi|336255537|ref|YP_004598644.1| 200 ALLAIVMVGLIVY 212
                                       69**********9 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.6e-05
                        TNFR_16_TM  11 cSILaaVvvgLlaYvifKrw 30 
                                       +++L++Vv++ +a+++f ++
  gi|336255537|ref|YP_004598644.1| 396 TALLPVVVLFVAAFIAFTMG 415
                                       689**************876 PP

>> COX14  Cytochrome oxidase c assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0076        34      25      48 ..     203     226 ..     201     235 .. 0.88
   2 ?    4.1   0.4    0.0092        41      18      40 ..     265     287 ..     264     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0076
                             COX14  25 Tlyaggllvytvysygkynrkqka 48 
                                        +++ gl+vyt ++yg   +++++
  gi|336255537|ref|YP_004598644.1| 203 AIVMVGLIVYTGRDYGEMLEAEHR 226
                                       579*************99999887 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0092
                             COX14  18 VltLiGvTlyaggllvytvysyg 40 
                                       V+ L++vTl +  +++y+ +   
  gi|336255537|ref|YP_004598644.1| 265 VVVLVAVTLAGAFWTGYQSWTAS 287
                                       6779*************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 4417.54
//
Query:       gi|336255538|ref|YP_004598645.1|  [L=264]
Description: Glyoxalase/bleomycin resistance protein/dioxygenase [Halopiger xanaduensis SH-6]
Scores for 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   73.0   4.9    1.1e-11   45.0   0.4    2.2  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    1.3e-10   41.5   1.4     0.0001   22.5   0.1    4.1  4  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    3.4e-08   34.2   3.8     0.0019   19.0   0.9    2.2  2  Glyoxalase_6  Glyoxalase-like domain
      0.001   19.2   3.2       0.43   10.7   0.6    3.7  2  Glyoxalase_3  Glyoxalase-like domain


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 !   45.0   0.4   2.5e-15   1.1e-11       2     128 .]       5     122 ..       4     122 .. 0.85
   2 !   30.3   0.4   9.1e-11   4.1e-07       2     128 .]     135     251 ..     134     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.5e-15
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEEST.EEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteet.eglriaffhaggghielvlneapsgaakhvkkieetvhhv 77 
                                       +dh++++v+dle+sld+Y+ +L  +  ++++  + t   l+   +h++g ++e+++ne ++++            h+
  gi|336255538|ref|YP_004598645.1|   5 LDHTMIRVADLEESLDWYRTHLEYEEKDRYEGDGFTiVYLGPEDMHEDGAMLEITHNEGEEPEVGDA------WGHI 75 
                                       89*****************************52223545566689*********************9......99** PP

                                       EEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  78 afialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       a+++ + e +++++++l ++gv   + p  +  g+ y f ++DpdG+++ei
  gi|336255538|ref|YP_004598645.1|  76 AVRVPEGE-LEDYYQQLMDEGVDDYRDP--ESCGGDYAF-VTDPDGHEIEI 122
                                       ****9765.5***********6666666..555555544.*********97 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 9.1e-11
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEE.EESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdn.teeteglriaffhaggghielvlneapsgaakhvkkieetvhhv 77 
                                       idh++++v d++++l F+t+ +  + v +++  t +  ++  +   ++  ++el++n    +++++           
  gi|336255538|ref|YP_004598645.1| 135 IDHTMIRVEDADEALGFWTRKFEYDEVGRWEAdTFANYFVEPRDAPDEAMSVELTYNYDGRSYEQGD--------AW 203
                                       9******************************544444888888899999999999999999999998........8* PP

                                       EEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  78 afialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       ++++  v+d+++ +d+l e+    ++ ++ + ++++y f  +D dG+++e+
  gi|336255538|ref|YP_004598645.1| 204 GHLCVRVDDLAEDWDQLLERE--ADDYRDPESNDNMYAF-TTDQDGHEIEL 251
                                       ********************9..6666667899999988.*********96 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0015       6.7       1      32 [.       6      37 ..       6      69 .. 0.79
   2 ?    4.0   0.0     0.013        58      13      59 ..      84     129 ..      73     134 .. 0.78
   3 !   22.5   0.1   2.3e-08    0.0001       1      89 [.     136     223 ..     136     226 .. 0.87
   4 !    6.0   0.0    0.0031        14      19      60 ..     219     259 ..     216     262 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0015
                                      EEEEEE-S-HHHHHHHHHH.TT-EESS--E.E CS
                      Glyoxalase_4  1 dQigivVeDleaavarfsallGvgpwqryrde 32
                                      d++ i V Dle+ ++ + ++l +++ +ry+ +
  gi|336255538|ref|YP_004598645.1|  6 DHTMIRVADLEESLDWYRTHLEYEEKDRYEGD 37
                                      699999******************99999864 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.013
                                       HHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT CS
                      Glyoxalase_4  13 avarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegp 59 
                                         +++++l++ g+ +   +e+ + d+af++  +g  +ie ++ ++++
  gi|336255538|ref|YP_004598645.1|  84 LEDYYQQLMDEGVDDYRDPESCGGDYAFVTDPDG-HEIEIVQRDPDA 129
                                       56888888887777777788899**********9.699999988765 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 2.3e-08
                                       EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETT...EEEEEEEESSTT-THHHTS-EEEEEEE CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgs...vqieLieplegpeflaehgeglhhlay 74 
                                       d++ i VeD ++a+ ++++ + +++  r+  e   + ++f++ ++++   + +eL  + +g++   e+g    hl++
  gi|336255538|ref|YP_004598645.1| 136 DHTMIRVEDADEALGFWTRKFEYDEVGRW--EADTFANYFVEPRDAPdeaMSVELTYNYDGRSY--EQGDAWGHLCV 208
                                       69999**************8888766666..6778888898888887888******99999776..9999******* PP

                                       EES-HHHHHHHHCTT CS
                      Glyoxalase_4  75 wvddldaavarleeq 89 
                                       +vddl +++++l e+
  gi|336255538|ref|YP_004598645.1| 209 RVDDLAEDWDQLLER 223
                                       **********99886 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0031
                                       H.TT-EESS--E.EETTTT.EEEEEEEETTEEEEEEEESSTT- CS
                      Glyoxalase_4  19 allGvgpwqryrdepqevd.lafallgsgsvqieLieplegpe 60 
                                       +ll  ++ ++yrd++++ + +af++ ++g  +ieLie + +++
  gi|336255538|ref|YP_004598645.1| 219 QLLE-READDYRDPESNDNmYAFTTDQDG-HEIELIERDLEAD 259
                                       5555.456788877776551566777776.8******886655 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.2e-06     0.014       3     107 .]       9     123 ..       7     123 .. 0.77
   2 !   19.0   0.9   4.3e-07    0.0019       3     106 ..     139     251 ..     137     252 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.2e-06
                      Glyoxalase_6   3 vldaadpaalaaFwaaalgweveree.......aaledpegvgpaaedaatllfqrvpe......paknrvHldlav 66 
                                       ++ +ad ++  +++++ l++e +++        +    pe     +ed+a l + + +        a    H+ ++v
  gi|336255538|ref|YP_004598645.1|   9 MIRVADLEESLDWYRTHLEYEEKDRYegdgftiV-YLGPED---MHEDGAMLEITHNEGeepevgDA--WGHIAVRV 79 
                                       67899*****************999999997752.222322...34567777777777767754433..47999999 PP

                      Glyoxalase_6  67 ..edldaevarlvalGArvlreprdgthgr..vlaDPeGneFcvv 107
                                          +l+   ++l + G    r+p++ ++ +   ++DP+G+e  +v
  gi|336255538|ref|YP_004598645.1|  80 peGELEDYYQQLMDEGVDDYRDPESCGG-DyaFVTDPDGHEIEIV 123
                                       66677899********999999999875.46**********9875 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 4.3e-07
                      Glyoxalase_6   3 vldaadpaalaaFwaaalgweveree.........aaledpegvgpaaedaatllfqrvpe.....paknrvHldla 65 
                                       ++ ++d++++ +Fw + ++++ + +          +   +p+ +    ++a+++ +    +     ++    Hl ++
  gi|336255538|ref|YP_004598645.1| 139 MIRVEDADEALGFWTRKFEYDEVGRWeadtfanyfV---EPRDA---PDEAMSVELTYNYDgrsyeQGDAWGHLCVR 209
                                       67899**************99998886666554321...22111...1233333333333377876333347***** PP

                      Glyoxalase_6  66 vedldaevarlvalGArvlreprdgthgr.vlaDPeGneFcv 106
                                       v+dl++  ++l++  A   r+p++ ++     +D +G+e  +
  gi|336255538|ref|YP_004598645.1| 210 VDDLAEDWDQLLEREADDYRDPESNDNMYaFTTDQDGHEIEL 251
                                       **********************9998766999******9876 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.1    0.0025        11       1      22 [.       5      26 ..       5     133 .. 0.91
   2 !   10.7   0.6   9.6e-05      0.43       2     101 ..     136     226 ..     135     256 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0025
                      Glyoxalase_3  1 lDHvvlavpdleeaaarfarrl 22
                                      lDH+++ v dlee  +++++ l
  gi|336255538|ref|YP_004598645.1|  5 LDHTMIRVADLEESLDWYRTHL 26
                                      8***************996554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 9.6e-05
                      Glyoxalase_3   2 DHvvlavpdleeaaarfarrlGftvtpggehpglgtaNalvmfgdgYlEllavdpeapaperprlfgldrlakgegl 78 
                                       DH+++ v+d +ea   ++r+  f+ ++ g+ +          f++ ++E  +  +ea + e     + + +++g+ +
  gi|336255538|ref|YP_004598645.1| 136 DHTMIRVEDADEALGFWTRK--FEYDEVGRWEA-------DTFANYFVEPRDAPDEAMSVELTYNYDGRSYEQGDAW 203
                                       77777777777777766544..77777777776.......45677777777654444443444445555889***** PP

                      Glyoxalase_3  79 htlalrtddidataarlraaGvd 101
                                        +l++r+dd++++ ++l ++  d
  gi|336255538|ref|YP_004598645.1| 204 GHLCVRVDDLAEDWDQLLEREAD 226
                                       *************9999877644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); 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:                         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 0.21s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2151.49
//
Query:       gi|336255539|ref|YP_004598646.1|  [L=384]
Description: esterase/lipase-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-18   67.7   1.6    2.2e-10   40.8   0.5    2.5  2  Abhydrolase_3  alpha/beta hydrolase fold
    3.9e-14   52.6   0.2    4.8e-09   36.0   0.0    2.2  2  Peptidase_S9   Prolyl oligopeptidase family
    5.3e-10   38.8   0.3    0.00082   18.4   0.2    2.4  3  COesterase     Carboxylesterase family
    6.7e-05   22.3   0.1      0.015   14.6   0.0    2.3  2  Hydrolase_4    Serine aminopeptidase, S33
    9.9e-05   22.1   0.3      0.021   14.4   0.1    3.1  3  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
     0.0031   18.2   6.6     0.0053   17.4   6.6    1.4  1  Abhydrolase_6  Alpha/beta hydrolase family
     0.0059   15.3   0.1       0.29    9.8   0.0    2.2  2  AXE1           Acetyl xylan esterase (AXE1)
     0.0068   16.0   0.0      0.046   13.3   0.0    2.1  2  DLH            Dienelactone hydrolase family
  ------ inclusion threshold ------
      0.055   13.0   3.8       0.49    9.8   0.6    3.1  4  Esterase_phd   Esterase PHB depolymerase
        0.2   11.4   0.0       0.48   10.2   0.0    1.6  2  Abhydrolase_2  Phospholipase/Carboxylesterase


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 !   25.3   0.0   6.6e-09   1.2e-05       1      40 [.      96     134 ..      96     145 .. 0.89
   2 !   40.8   0.5   1.2e-13   2.2e-10      41     209 ..     153     327 ..     150     329 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 6.6e-09
                                       EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---T CS
                     Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlA 40 
                                       +vy+HGGG+v+++ + + + ++++a+e g++  sv YrlA
  gi|336255539|ref|YP_004598646.1|  96 VVYVHGGGWVFETRKNAPD-LERFAAEWGCAMASVSYRLA 134
                                       79*********99887765.566****************9 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 1.2e-13
                                       TTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE....-SSTS CS
                     Abhydrolase_3  41 PehpfPaavedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepkvagqvliyP....vtdle 113
                                       P   fP ++ d+ aa+rwl+++a e+g d +r++  G SaGG+laa +   a d+   ++ag v  yP    ++d++
  gi|336255539|ref|YP_004598646.1| 153 PRGVFPDPIVDVKAAIRWLRANADEYGFDGERVATWGSSAGGHLAALAG--AVDD-VTEIAGNV--YPaaavAKDVA 224
                                       67779*****************99********************97554..4444.35677766..56435444443 PP

                                       STTSHHHHHCHHTTTSSSSC....HHHHH.HHHHHHS..S..GGGGGSTTTSGGGCS-SST---EEEEEETT-..TT CS
                     Abhydrolase_3 114 rtesesikkaeeladgpllt....raald.lfwrlyl..p..eadrddplaspllaedlsglpptlvvvaefD..pl 179
                                       + es +    +++ d + ++        +  + +l l  p  e++ +  +asp+     +++pp  ++ + +D  + 
  gi|336255539|ref|YP_004598646.1| 225 PDESGAV---QAVVDWYGIHdlleLPGGEaSLESLLLggPvsENQDEARRASPVTY-VTEDTPPFCIMHGRQDqvVS 297
                                       3333333...23333333322222444441455666654363344445699*9977.8999************4445 PP

                                       HHHHHHHHHHHHHTT--EEEEEETTEETTG CS
                     Abhydrolase_3 180 rdegeayaerlraagvevelieyegmvHgf 209
                                        ++++ + ++l++++ve+++ e +++ H++
  gi|336255539|ref|YP_004598646.1| 298 VEQSRLLFDALQEVQVEATFYELHDLGHVW 327
                                       679999**********************86 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   9.5e-06     0.017      46      81 ..     165     200 ..     159     212 .. 0.80
   2 !   36.0   0.0   2.7e-12   4.8e-09      91     194 ..     233     333 ..     223     343 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.5e-06
                                       HHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHH CS
                      Peptidase_S9  46 dDfiaaaealakegyvdserlaitGgSyGGyltgaa 81 
                                       +  i +++a a+e+  d er+a +G S+GG l++ a
  gi|336255539|ref|YP_004598646.1| 165 KAAIRWLRANADEYGFDGERVATWGSSAGGHLAALA 200
                                       334555666688889***************999876 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 2.7e-12
                                       EEEEESE---CCCHHCSTTSTHHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHH CS
                      Peptidase_S9  91 aavaevpvvdvlrydsdtdllteeymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealklva 167
                                       a+v  ++++d+l     +  l+    + + + en+++ +++sp++++++   +pp++++hG +D+ v ++++  l++
  gi|336255539|ref|YP_004598646.1| 233 AVVDWYGIHDLLELPGGEASLESLLLGGPVS-ENQDEARRASPVTYVTE--DTPPFCIMHGRQDQVVSVEQSRLLFD 306
                                       4455556666666666643366666777777.6777788**********..************************** PP

                                       HHH--S-SEEEEEETTS-SSTTSSHHH CS
                      Peptidase_S9 168 aLqkkgknvlllifpdegHgvgkprak 194
                                       aLq+ ++++ +   +d gH+ g ++ +
  gi|336255539|ref|YP_004598646.1| 307 ALQEVQVEATFYELHDLGHVWGADSER 333
                                       *******************55544433 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.46   8.2e+02      18      41 ..      54      80 ..      42      83 .. 0.70
   2 !   17.6   0.0     8e-07    0.0014      90     144 ..      82     133 ..      71     136 .. 0.88
   3 !   18.4   0.2   4.6e-07   0.00082     163     201 ..     161     199 ..     159     209 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.46
                                      EESTCS...EEEEEEEEESSB---GGG CS
                        COesterase 18 klksek...evdaFlGiPYAepPvgel 41
                                       +++++   ev++++++ YAe   ge+
  gi|336255539|ref|YP_004598646.1| 54 GSSDQDnpvEVTVYEDVTYAEREAGEM 80
                                      3333335679**********9988876 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 8e-07
                                       EEEEEESSSSSTTSSEEEEEEE--STTTS-BGCG.S-THHHHHHHTSEEEEE---- CS
                        COesterase  90 LnvytPkekkeakkklPVlVwihGggfqtgsase.ydgsaLaaegnvivVtinYRl 144
                                       L+ y+P+++       P +V++hGgg ++++ ++  d + +aae ++   +++YRl
  gi|336255539|ref|YP_004598646.1|  82 LDLYVPATD----GPTPLVVYVHGGGWVFETRKNaPDLERFAAEWGCAMASVSYRL 133
                                       889999643....455***************98868999****************9 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 4.6e-07
                                       HHHHHHHHHHHHHHGGGGTEEEEEEEEEEETHHHHHHHH CS
                        COesterase 163 llDqvlALrWVkenIasFGGdpervtlfGesAGaasvsl 201
                                       ++D+ +A+rW++ n  ++G d erv  +G+sAG+ +++l
  gi|336255539|ref|YP_004598646.1| 161 IVDVKAAIRWLRANADEYGFDGERVATWGSSAGGHLAAL 199
                                       579*******************************99876 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0     0.005       8.9      61     114 ..     163     222 ..     156     273 .. 0.77
   2 !   14.6   0.0   8.2e-06     0.015     191     228 ..     282     319 ..     266     325 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.005
                       Hydrolase_4  61 Dlaafvekvkeehpel.....plfllGhSmGGliallyl.lrypdkvaglilsaPalkik 114
                                       D++a+++ ++++  e      ++  +G S GG +a+l++  +   ++ag +  a+a++ +
  gi|336255539|ref|YP_004598646.1| 163 DVKAAIRWLRANADEYgfdgeRVATWGSSAGGHLAALAGaVDDVTEIAGNVYPAAAVAKD 222
                                       6666666666555444455559999*************9766667899999999998755 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 8.2e-06
                       Hydrolase_4 191 tlPllllhGeaDkvvdpeasrelyerlgskdktlklyp 228
                                       t P+ ++hG +D+vv+ e+sr l+++l+  +++ + y+
  gi|336255539|ref|YP_004598646.1| 282 TPPFCIMHGRQDQVVSVEQSRLLFDALQEVQVEATFYE 319
                                       569*************************9999999886 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.33   5.8e+02       5      24 ..      80      97 ..      78     114 .. 0.92
   2 !   14.4   0.1   1.2e-05     0.021      79     120 ..     157     202 ..     150     246 .. 0.78
   3 ?    3.5   0.0     0.025        45     216     259 ..     270     317 ..     261     327 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.33
                                      EEEEEEEE..TTSSSEEEEE CS
                     Peptidase_S15  5 LavdiyrPetkskeklPvll 24
                                      ++ d+y+P  ++++++P+++
  gi|336255539|ref|YP_004598646.1| 80 MKLDLYVP--ATDGPTPLVV 97
                                      789*****..*******987 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.2e-05
                                       TTTHHHHHHHHHHHHHH...C.TTEEEEEEEEEECHHHHHHHHHCT CS
                     Peptidase_S15  79 dsdeaedgadvidWlak...q.pwsnGkVgmtGiSYlGttqllaaa 120
                                       ++d + d++++i+Wl++   +  +   +V+++G+S +G ++ la a
  gi|336255539|ref|YP_004598646.1| 157 FPDPIVDVKAAIRWLRAnadEyGFDGERVATWGSSAGGHLAALAGA 202
                                       688999***********55533456679**********99876643 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.025
                                       HTT-HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-...E CS
                     Peptidase_S15 216 kdrnlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv...k 259
                                       ++ ++ + +++ + p  +++G +D+ v  +++  l++al++ +v    
  gi|336255539|ref|YP_004598646.1| 270 RRASPVTYVTEDTPPFCIMHGRQDQVVSvEQSRLLFDALQEVQVeatF 317
                                       55566666777778999***********9***********99886542 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   6.6     3e-06    0.0053       1     209 [.      96     327 ..      96     337 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3e-06
                                       EEEE--GC.....GCHHHH.HHHHCCTCEEEEE--TTST.......................S-GGCS--HHH.CHH CS
                     Abhydrolase_6   1 vlllHGagssassWlvapL.aallaagvhvlapDlpGhG.......................rsdpppldled.lad 52 
                                       v+ +HG+g     W    +  ++ a + + +a  + G+                        ++++p   ++d ++d
  gi|336255539|ref|YP_004598646.1|  96 VVYVHGGG-----W---VFeTRKNAPDLERFAAEW-GCAmasvsyrlaevpadvdlpfdvdpENPTPRGVFPDpIVD 163
                                       6889**99.....8...332333344444456666.66455555556666544444444433223333333335799 PP

                                       HHHHHCCTT.........TTSEEEEEETCHHHHHHHHHHCC.....EE.EEES-..----TTTS----TTHHHHHHT CS
                     Abhydrolase_6  53 laalldelaa.......gggpvvlvGHSlGGalalaaapla...lvvg.vlldppptalpagllaaalelllallal 118
                                       + a+++ l+a       +g +v  +G S GG+la++a+++     ++g v+ ++ +  + a++ + a++ +  +++ 
  gi|336255539|ref|YP_004598646.1| 164 VKAAIRWLRAnadeygfDGERVATWGSSAGGHLAALAGAVDdvtEIAGnVYPAAAVAKDVAPDESGAVQAVVDWYGI 240
                                       99999999999999**********************88888555555566666622333444455555555555554 PP

                                       T-CCCCHCCH.S-HSCCCCHHHCCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEECTT-C.....HHHHCHHC CS
                     Abhydrolase_6 119 lrllawlsre.plprlfladedadaawrarlarlaallaglgllpaaawadlpvpllvlggeDp.....lvprller 189
                                         ll+++ +e +l  l+l+      ++ ++ +++++  +  +       +d+p+ ++++g +D+        rll +
  gi|336255539|ref|YP_004598646.1| 241 HDLLELPGGEaSLESLLLG-----GPVSENQDEARRASPVTY-----VTEDTPPFCIMHGRQDQvvsveQS-RLLFD 306
                                       4445555444666669999.....888888888888888888.....888888888666899995444322.33333 PP

                                       CCH..STTEEETCE...SSS-H CS
                     Abhydrolase_6 190 lla..qagarlpvvlpgaGHlp 209
                                       +l+  q  a++  +l + GH++
  gi|336255539|ref|YP_004598646.1| 307 ALQevQVEATF-YELHDLGHVW 327
                                       33335555555.7888999954 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.015        27      54      92 ..      64     102 ..      55     133 .. 0.79
   2 !    9.8   0.0   0.00016      0.29     170     206 ..     179     215 ..     147     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.015
                                       EEEE.EEEEEEGGGEEEEEEEEEES.SSSSEEEEEEEE-T CS
                              AXE1  54 vkvy.dltfegvrgarikaklvlPkekeeklPavvefhGY 92 
                                       v vy d+t++  +  ++k  l +P+ ++++ P+vv  hG 
  gi|336255539|ref|YP_004598646.1|  64 VTVYeDVTYAEREAGEMKLDLYVPA-TDGPTPLVVYVHGG 102
                                       667747*******************.*********99984 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00016
                                       TEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEEES- CS
                              AXE1 170 evDeeRvavlGasqGGalalavaalekrikavvadyP 206
                                         D eRva  G+s GG la  ++a+++  + +   yP
  gi|336255539|ref|YP_004598646.1| 179 GFDGERVATWGSSAGGHLAALAGAVDDVTEIAGNVYP 215
                                       4699********************9998777766666 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.29   5.1e+02      81     118 ..     163     203 ..     158     219 .. 0.73
   2 !   13.3   0.0   2.6e-05     0.046     111     195 ..     219     333 ..     216     366 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.29
                               DLH  81 dlkaavaylksvpe...vstkkvgvvGfCmGGalalllaae 118
                                       d+kaa+++l+++ +   ++ ++v+  G   GG la l  a 
  gi|336255539|ref|YP_004598646.1| 163 DVKAAIRWLRANADeygFDGERVATWGSSAGGHLAALAGAV 203
                                       567888888877651225789************99765544 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.6e-05
                               DLH 111 lalllaaev.pevdaavafYG.............................lspekeleeaakikapilalfgeeDef 157
                                       +a ++a  +  +v+a+v +YG                              +  ++++++++   p  +++g +D++
  gi|336255539|ref|YP_004598646.1| 219 VAKDVAPDEsGAVQAVVDWYGihdllelpggeasleslllggpvsenqdeARRASPVTYVTEDTPPFCIMHGRQDQV 295
                                       566777777789********************************9999999999999******************** PP

                               DLH 158 ipadevekleealkaanvdlelkvYpgagHaFandsre 195
                                       +  ++   l  al++ +v++ +    + gH   +ds++
  gi|336255539|ref|YP_004598646.1| 296 VSVEQSRLLFDALQEVQVEATFYELHDLGHVWGADSER 333
                                       ***************99999998888899998888877 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.09   1.6e+02       4      31 ..      83     108 ..      80     136 .. 0.71
   2 ?    9.8   0.6   0.00028      0.49      84     117 ..     170     203 ..     157     235 .. 0.78
   3 ?   -0.3   0.0      0.34   6.1e+02     170     196 ..     283     309 ..     264     316 .. 0.79
   4 ?   -3.4   0.0       3.1   5.5e+03     136     164 ..     329     356 ..     320     361 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.09
                      Esterase_phd   4 rlylppGarrgamplvvmlhGctqsvee 31 
                                        ly+p     g  plvv +hG     e 
  gi|336255539|ref|YP_004598646.1|  83 DLYVPA--TDGPTPLVVYVHGGGWVFET 108
                                       589986..45679********7665555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00028
                      Esterase_phd  84 lvdalvdehrvdaarvyvaGlsaGaaladllalh 117
                                         +a +de+++d  rv   G saG+ la l +  
  gi|336255539|ref|YP_004598646.1| 170 WLRANADEYGFDGERVATWGSSAGGHLAALAGAV 203
                                       568899**********************998754 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.34
                      Esterase_phd 170 lpalvvqGdadtvvavknaeslvvalr 196
                                        p  +++G  d+vv+v ++  l  al+
  gi|336255539|ref|YP_004598646.1| 283 PPFCIMHGRQDQVVSVEQSRLLFDALQ 309
                                       47789**********998887776665 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 3.1
                      Esterase_phd 136 aadvisaldvmrrGlrqapaaavdalvea 164
                                       a++  +a++v+ +  ++a + ++ a  ea
  gi|336255539|ref|YP_004598646.1| 329 ADSERTAMNVLET-TQPAQSVTATAHLEA 356
                                       5666777777754.344555555555555 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.0       6.8   1.2e+04      13      24 ..      92     103 ..      88     104 .. 0.81
   2 ?   10.2   0.0   0.00027      0.48     153     200 ..     278     326 ..     266     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 6.8
                                       --EEEEEE--TT CS
                     Abhydrolase_2  13 aqavviflHGlG 24 
                                       ++++v+++HG G
  gi|336255539|ref|YP_004598646.1|  92 PTPLVVYVHGGG 103
                                       6899*****976 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00027
                                       GGGG-.EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS CS
                     Abhydrolase_2 153 vtkkl.pilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHs 200
                                       vt ++ p + +Hg +D+vv +  + ++  +l++++ + ++  +++l+H 
  gi|336255539|ref|YP_004598646.1| 278 VTEDTpPFCIMHGRQDQVVSVEQSRLLFDALQEVQVEATFYELHDLGHV 326
                                       55555257889*************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 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:                        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):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 3091.77
//
Query:       gi|336255540|ref|YP_004598647.1|  [L=175]
Description: hypothetical protein Halxa_4164 [Halopiger xanaduensis SH-6]
Scores for 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-06   25.5   0.2    1.9e-05   24.7   0.2    1.5  1  HTH_20        Helix-turn-helix domain
  ------ inclusion threshold ------
       0.03   14.5   2.0      0.045   13.9   2.0    1.2  1  ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transpor


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 !   24.7   0.2   2.1e-09   1.9e-05       1      44 [.      13      62 ..      13      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.1e-09
                                      HHHHHHHS-HHHHHHHHHH.STCTTB-HHHHHHHH.....TS-HHHHHHH CS
                            HTH_20  1 dqiaeALahPvRrrilraL.araegltaselaerl.....dlskntlsyH 44
                                      ++i+++L++P Rr + r L ++++++++  la+r+     d++   +syH
  gi|336255540|ref|YP_004598647.1| 13 ADIFDVLSDPRRRHVVRVLeRQGGAVSLDTLARRVaaaenDIRLEAVSYH 62
                                      68*********************************999999********* PP

>> ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.0     5e-06     0.045       4      40 ..     120     159 ..     118     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5e-06
                      ATPase_gene1   4 asqiGielvapillggllGyw...LDkkfgtspwfliigl 40 
                                       +s i+++++++++  +++G w   L  +f+ + ++l++++
  gi|336255540|ref|YP_004598647.1| 120 YSAIASTVAVATITAAWIGAWpfsLLAWFHWTVVLLVLFV 159
                                       899******************9999999997666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1475.87
//
Query:       gi|336255541|ref|YP_004598648.1|  [L=844]
Description: nuclease [Halopiger xanaduensis SH-6]
Scores for 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   45.5   0.0    1.4e-11   44.8   0.0    1.3  1  SNase           Staphylococcal nuclease homologue
    1.7e-09   37.6   0.1    2.4e-05   23.9   0.1    2.2  2  ABC_transp_aux  ABC-type uncharacterized transport system
    2.3e-07   31.1   2.6    0.00074   19.9   0.1    3.5  3  DUF4350         Domain of unknown function (DUF4350)
     0.0013   18.9   0.1     0.0031   17.7   0.1    1.6  1  DUF1102         Protein of unknown function (DUF1102)
  ------ inclusion threshold ------
      0.028   12.8   0.0      0.073   11.4   0.0    1.5  2  DUF2194         Uncharacterised protein conserved in bacteria


Domain annotation for each model (and alignments):
>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0     4e-15   1.4e-11       1     107 [.     472     590 ..     472     591 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 4e-15
                                       EEEETTEE-STSSBTTT............TTSTTHHHHHHHHHHHHHHCSSEEEEE-S..SBSTTSEEEEEEEET.T CS
                             SNase   1 kvrLvgidaPetakpkk............tvqpfgkeAkeflkklvlqkkvvvleldk..kkDkygrllayvyln.k 62 
                                       +vr++gid+Pet ++ +            ++ + ++ A++++ +l+ +++v++  +++   +++ygrll+ + l  +
  gi|336255541|ref|YP_004598648.1| 472 TVRILGIDTPETGNTSErfaewegiedgeALRDKADAATDYAVDLLDGETVTLSFDENegLRGNYGRLLGVLDLPdG 548
                                       69***********9999*********999999999************666655555558899**********9999* PP

                                       EEHHHHHHHTTSSEE---BTTSTTTHHHHHHHHHHHHHTT-GGGC CS
                             SNase  63 knineeLvkeGlArvyevyekneekkkellkaeeeAkkkrkglWs 107
                                       +  ne+ +++G Ar   vy++  e ++el+ +e++A+++ +glW+
  gi|336255541|ref|YP_004598648.1| 549 TRYNEAVLEDGHAR---VYDSGLEAHDELRDLEADARAAGRGLWE 590
                                       **************...66677789*******************6 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   6.7e-09   2.4e-05     155     256 ..     296     391 ..     288     404 .. 0.72
   2 !   11.3   0.0   4.8e-05      0.17     188     232 ..     742     784 ..     727     805 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6.7e-09
                    ABC_transp_aux 155 ghgelslssp....se.adfleelee.nYnveevdldsedilpedidvlviakptkdlseeelykldqflmnGgkll 225
                                       ghg+  ++ +       +++ + le+ +Y++e+++  ++d   +d +++vi  p++++++ el +l+ f++ Gg  l
  gi|336255541|ref|YP_004598648.1| 296 GHGQYYTR-SsnggDDfQAVGDYLEDgGYTYEATTDLESDL--DDAAAVVITSPSDAFTDGELAALSSFVDDGGV-L 368
                                       55554443.12355344568899*********988775555..79999**********************99985.5 PP

                    ABC_transp_aux 226 vfldpvaeeqdslsepsaaprtsnLedllae 256
                                       ++ d+ + ++        +++t+nL+++  e
  gi|336255541|ref|YP_004598648.1| 369 FLHDQSDHNN--------FDETTNLNEIADE 391
                                       5566665433........5567777777665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.8e-05
                    ABC_transp_aux 188 dilpedidvlviakptkdlseeelykldqflmnGgkllvfldpva 232
                                       ++     ++lv+ +pt++l+  e  ++++f ++Gg +l+   + +
  gi|336255541|ref|YP_004598648.1| 742 GE--PAARALVLSRPTTELTAAERSAISDFADAGGAVLLIGTAAN 784
                                       44..37899****************************99877665 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.42   1.5e+03       6      33 ..      21      50 ..      20      62 .. 0.79
   2 !   19.9   0.1   2.1e-07   0.00074       8      67 ..     312     370 ..     307     372 .. 0.90
   3 !    8.8   0.1   0.00061       2.2      32      68 ..     743     779 ..     725     780 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.42
                           DUF4350  6 GtralaelLeaqGvevrrvrkpfd..aleg 33
                                      Gt a+ +   ++  +vr+v++ ++  ale+
  gi|336255541|ref|YP_004598648.1| 21 GTGAFSTASAERQMTVRVVDDASSflALEP 50
                                      88899999999999*******877244443 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.1e-07
                           DUF4350   8 ralaelLeaqGvevrrvrkpfdalegedgtllvvapdlrlteeelaallewvarGntlvl 67 
                                        a+ ++Le+ G++ ++++++ ++l+++   +++++p   +t+ elaal  +v+ G+ l+l
  gi|336255541|ref|YP_004598648.1| 312 QAVGDYLEDGGYTYEATTDLESDLDDAA-AVVITSPSDAFTDGELAALSSFVDDGGVLFL 370
                                       578899*********9999999**9988.6777777768*******************98 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00061
                           DUF4350  32 egedgtllvvapdlrlteeelaallewvarGntlvla 68 
                                       e++ + l++  p+  lt +e  a+ +++++G+ ++l+
  gi|336255541|ref|YP_004598648.1| 743 EPAARALVLSRPTTELTAAERSAISDFADAGGAVLLI 779
                                       3377799*************************99885 PP

>> DUF1102  Protein of unknown function (DUF1102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   8.6e-07    0.0031      40     138 ..      77     169 ..      38     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.6e-07
                           DUF1102  40 GdGlspnseYvFdevfevsndlweneespivveiks...enssvklyagevddgqtasiadaaesieftveegeevs 113
                                       GdGl  ++ Y Fd+ + + n+  e     +  + +s   + + v ly ++++    a+ +d a+ ie  v+ g e++
  gi|336255541|ref|YP_004598648.1|  77 GDGLGVDTAYTFDDTLRIRNQGTESVF--VWTSTESdafDGDDVYLYHEDSE----APLSD-ARAIE--VDVGTEIP 144
                                       9*******************9888777..55555554567899999999977....88888.55555..677899** PP

                           DUF1102 114 vGlildateeslGvkkaeltikaya 138
                                       vG+ +d+t+ +   +++ +ti+a a
  gi|336255541|ref|YP_004598648.1| 145 VGVFVDTTGLETDAYDVGVTIQAAA 169
                                       ***********99999999999975 PP

>> DUF2194  Uncharacterised protein conserved in bacteria (DUF2194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     2e-05     0.073      57     133 ..     332     408 ..     312     452 .. 0.77
   2 ?   -2.2   0.0      0.26   9.3e+02      83     117 ..     764     798 ..     750     839 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2e-05
                           DUF2194  57 kidlekYetVivtyyseeldklkeyLkqlvefvengGklffannlgast..dsselnsilnklGisyksgykklevs 131
                                       + dl++ ++V++t   ++ +  + +L +l++fv +gG lf+  +   ++  ++ +ln+i  +l  s+++  +++ ++
  gi|336255541|ref|YP_004598648.1| 332 ESDLDDAAAVVITS--PSDAFTDGELAALSSFVDDGGVLFLHDQSDHNNfdETTNLNEIADELALSFRFNDDQVYDD 406
                                       45666777777777..4445556679***************9887665411566**************999888766 PP

                           DUF2194 132 gi 133
                                       + 
  gi|336255541|ref|YP_004598648.1| 407 QN 408
                                       54 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.26
                           DUF2194  83 kqlvefvengGklffannlgastdsselnsilnkl 117
                                       +++++f+  gG ++++ +   +    +++ +l  l
  gi|336255541|ref|YP_004598648.1| 764 SAISDFADAGGAVLLIGTAANTGALEYFDPLLDDL 798
                                       67888888888888888877777666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (844 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.61u 0.23s 00:00:00.84 Elapsed: 00:00:00.39
# Mc/sec: 6468.42
//
Query:       gi|336255542|ref|YP_004598649.1|  [L=281]
Description: 2,5-didehydrogluconate reductase [Halopiger xanaduensis SH-6]
Scores for 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-59  199.1   0.0    2.9e-56  190.8   0.0    2.0  1  Aldo_ket_red  Aldo/keto reductase family


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 !  190.8   0.0   1.6e-60   2.9e-56       2     291 ..      17     257 ..      16     260 .. 0.96

  Alignments for each domain:
  == domain 1  score: 190.8 bits;  conditional E-value: 1.6e-60
                                       EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTS CS
                      Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeik 78 
                                       +g+Gtw l++      e++ + +++aleaG++++DtAe Y    +ee++Ge+l+++ ++r+++++++Kv        
  gi|336255542|ref|YP_004598649.1|  17 IGFGTWELEG------ETVKASVEAALEAGYTHIDTAEGY---MNEEEIGEVLADADVDRDDLFLTSKV------LA 78 
                                       9*****9998......799999******************...**************************......** PP

                                       SSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTTT- CS
                      Aldo_ket_red  79 sglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkkkv 155
                                        +l+ +++++s++esl++Lgtdy+Dl+l+H+p+p+ + + e++ a+e l++eG++r++GvSnfs+ ql++a+  + v
  gi|336255542|ref|YP_004598649.1|  79 KNLHYDDVIASCKESLEKLGTDYLDLYLIHWPNPAIS-LRETMHAMERLHEEGLVRNVGVSNFSAYQLSAAHHVSDV 154
                                       *************************************.*************************************** PP

                                       -EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHH CS
                      Aldo_ket_red 156 kivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeel 232
                                       +i+++q+e++++  l+   l+++c++ +  + a+ plg+                                  +e++
  gi|336255542|ref|YP_004598649.1| 155 PIAVNQIEFHPW--LQRPDLVDYCRETDTVIEAAAPLGRTDV-----------------------------FGDEAV 200
                                       ************..************998888******4322.............................25799* PP

                                       HHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS
                      Aldo_ket_red 233 selakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaelde 291
                                       +ela+e+++ +aq++lr+a+  ++ ++v+p +++++++e+n+d ++++ls+++ ++lde
  gi|336255542|ref|YP_004598649.1| 201 QELAEEYDKLPAQIVLRWAV--DRDVVVLPRSTSPAHIEENFDLFDWELSDDDRQRLDE 257
                                       ********************..**********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2310.17
//
Query:       gi|336255543|ref|YP_004598650.1|  [L=214]
Description: hypothetical protein Halxa_4168 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.086   12.3   0.0       0.12   11.8   0.0    1.2  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr


Domain annotation for each model (and alignments):
>> SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.5e-06      0.12      82     139 ..     111     171 ..     100     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.5e-06
                                       TTSEEEEESSSTTHHHH....SEEEEEEGSSCC--TS-HHHHTHHHHHHHHHCT--GGGCSE CS
                   SAM_adeno_trans  82 kggyfvgPDNGlltlal....lleeaveieeeessatFhgrDvFapvaarlaagvsleelge 139
                                       + g +v+PD  +  + l      ++++++++ + +a    rDvF p+aa+ ++g +  + ++
  gi|336255543|ref|YP_004598650.1| 111 NAGELVAPDFSVRRPRLgdgwAHVHVWAVDDAR-AAIHAHRDVFDPAAAYFHSGAQYGAAAR 171
                                       555678888888887776655337899998555.489999*************987655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1788.36
//
Query:       gi|336255544|ref|YP_004598651.1|  [L=287]
Description: phosphoesterase PA-phosphatase-like protein [Halopiger xanaduensis SH-6]
Scores for 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-19   67.9  14.3    1.5e-18   67.1  14.3    1.4  1  PAP2_3    PAP2 superfamily
    3.5e-11   43.0   8.3    3.5e-11   43.0   8.3    1.8  2  PAP2      PAP2 superfamily
    0.00095   19.7   3.1     0.0031   18.0   3.1    1.8  1  PAP2_C    PAP2 superfamily C-terminal
  ------ inclusion threshold ------
        1.4    9.3  18.8       0.49   10.7   4.3    2.8  3  DUF1772   Domain of unknown function (DUF1772)


Domain annotation for each model (and alignments):
>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1  14.3   3.4e-22   1.5e-18      32     189 ..     104     253 ..      79     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 3.4e-22
                            PAP2_3  32 lalaYas.lhfqvtllvlvllflrrrerlreflttlllatllgllvyalfPaagPrlleeagfvdtvaaaslagalr 107
                                       ++ +Y + + ++++ +++++ ++   +rl+e+l+++ll  l+g+++y+lf a gPr +           ++++g   
  gi|336255544|ref|YP_004598651.1| 104 FSAMYMFgFPYLLVTAPILYFAAGLQRRLKELLVAYLLNYLVGSICYTLFIAYGPRNH----------LSTVDG--- 167
                                       44455540345555556666559999*****************************998..........222222... PP

                            PAP2_3 108 dgasravllrgtienglaa....fPSlHvawallvalalwrlrrkr.llrvlalllnvlmivatvatgnHYlvDvia 179
                                       + ++  +++++ ++++++a    fPSlH+ +a++v+l++wr r  + l++ +a ++++ ++++t+++g H ++Dv+a
  gi|336255544|ref|YP_004598651.1| 168 LMYQ-IYPQTQDLTAAVSAntdvFPSLHTSLAVVVLLFAWRSRADQrLWFSIASVVAASVVFSTMYLGIHWAIDVVA 243
                                       1122.233334445555556666*******************988768999************************** PP

                            PAP2_3 180 Gvalalvaia 189
                                       Gv+la  ++a
  gi|336255544|ref|YP_004598651.1| 244 GVLLAGWSVA 253
                                       *****98876 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.51   2.3e+03      76      76 ..     129     129 ..      99     159 .. 0.49
   2 !   43.0   8.3   7.8e-15   3.5e-11      49     127 ..     177     255 ..     131     262 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.51
                              PAP2  76 r 76 
                                       +
  gi|336255544|ref|YP_004598651.1| 129 Q 129
                                       2 PP

  == domain 2  score: 43.0 bits;  conditional E-value: 7.8e-15
                              PAP2  49 s......keakesfPSgHsafafalalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGlli 119
                                       +      ++ ++ fPS H++ a++++l+++   ++ r      l++ i+ ++a+ v +s +ylg+H+  Dv+aG+l+
  gi|336255544|ref|YP_004598651.1| 177 QdltaavSANTDVFPSLHTSLAVVVLLFAWRSRADQR------LWFSIASVVAASVVFSTMYLGIHWAIDVVAGVLL 247
                                       12344555566789*****999888777665444444......569****************************776 PP

                              PAP2 120 Gialaala 127
                                       ++  +a+a
  gi|336255544|ref|YP_004598651.1| 248 AGWSVAAA 255
                                       65555444 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   3.1   6.9e-07    0.0031       3      65 ..     187     248 ..     187     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.9e-07
                            PAP2_C   3 gDlifSGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyit 65 
                                       +D++ S Ht   ++++lf+++  +++  +++ i+ ++a++ +f+ ++   H+ +DV+ g++++
  gi|336255544|ref|YP_004598651.1| 187 TDVFPSLHTSLAVVVLLFAWRSRADQRLWFS-IASVVAASVVFSTMYLGIHWAIDVVAGVLLA 248
                                       5888999*************99999986666.6677889999*****************9875 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.3      0.92   4.1e+03      54      55 ..      19      32 ..       2      58 .. 0.44
   2 ?    8.4   1.8   0.00054       2.4      24      89 ..     100     160 ..      81     182 .. 0.69
   3 ?   10.7   4.3   0.00011      0.49      36      83 ..     187     232 ..     163     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.92
                           DUF1772 54 a............a 55
                                      +            +
  gi|336255544|ref|YP_004598651.1| 19 VstcglcldradvR 32
                                      23444444443331 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00054
                           DUF1772  24 llkqwrrlfkrgkavfpplallsalafaylaaraasrgarllylaaaal.lllsivpyTllvm.vPtN 89 
                                        +  +++++     +f++  ll+++  +y+aa   +r+   l+ +a +l +l++ + yTl++   P N
  gi|336255544|ref|YP_004598651.1| 100 TVGFFSAMY-----MFGFPYLLVTAPILYFAA-GLQRRLKELL-VAYLLnYLVGSICYTLFIAyGPRN 160
                                       456677777.....666655555555555563.4455555555.557888*********998634455 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00011
                           DUF1772  36 kavfpplallsalafaylaaraasrgarllylaaaallllsivpyTll 83 
                                       + vfp+l +  a++++++   ++sr+  +l++ +a+++++s+v+ T++
  gi|336255544|ref|YP_004598651.1| 187 TDVFPSLHTSLAVVVLLF--AWRSRADQRLWFSIASVVAASVVFSTMY 232
                                       456776555444444444..599999*****99999999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2310.59
//
Query:       gi|336255545|ref|YP_004598652.1|  [L=540]
Description: sulfatase [Halopiger xanaduensis SH-6]
Scores for 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-48  163.3   0.0    1.2e-47  162.8   0.0    1.2  1  Sulfatase     Sulfatase
      7e-13   48.9   0.3    7.6e-06   25.8   0.1    2.3  2  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
  ------ inclusion threshold ------
      0.045   13.2   0.2      0.076   12.4   0.2    1.4  1  Pr_beta_C     Proteasome beta subunits C terminal
       0.22   10.5   0.6       0.37    9.8   0.1    1.6  2  DUF1501       Protein of unknown function (DUF1501)


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.8   0.0   2.6e-51   1.2e-47       2     309 .]       8     345 ..       7     345 .. 0.87

  Alignments for each domain:
  == domain 1  score: 162.8 bits;  conditional E-value: 2.6e-51
                                       EEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHHC CS
                         Sulfatase   2 nvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevggggl 78 
                                       nv+++++d+++ + lg yg+ + ttp+l+r aee ++f ++++ ap + p+ a+l+tg+yp ++g+ +      ++ 
  gi|336255545|ref|YP_004598652.1|   8 NVLFVVLDTVRKDRLGPYGYDRGTTPALSRFAEEATVFESAVAPAPWTLPVHASLFTGLYPSQHGADQG-----SPY 79 
                                       9****************************************************************4333.....777 PP

                                       TTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHC..CTTTSE...EEETSSSCHHTCCCCCCCCCECTCCC.... CS
                         Sulfatase  79 pqteatLpellkeaGYntaaigkwhlgwssrqsvyk..nrgfdr...flgfptgsaalkdpekseyngevlrv.... 146
                                         + +tL+ +l +aGY+ta++   ++ w+      +   +gfd    f++     +a+++p +  +++ ++++    
  gi|336255545|ref|YP_004598652.1|  80 LDDDVTLASILSAAGYDTACYS--SNAWITPY---TglTDGFDAqdsFFE-VLPGDAFSGPLATVWQT-INDNeylh 149
                                       799***************6666..55666333...334445543222444.33345555555444443.33345777 PP

                                       ...................TTTTCSHHHHHHHHHHHHHHCCC.TSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCC CS
                         Sulfatase 147 ...................ppeggysddrlldealefllarn.dkpfflylatlapHappeapdeyakkyatffddg 203
                                                           ++    +  + d++  f+  ++ d+ +f+++ ++  H p++ p+ey +++a + d++
  gi|336255545|ref|YP_004598652.1| 150 elasklvrigamahsklasGESADSKTPSVIDRTRSFIDGSDgDEGWFAFVNLMDAHLPYYPPEEYREEFASGVDPD 226
                                       77777*************99999999************99999******************************9987 PP

                                       CCCCH.................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSC CS
                         Sulfatase 204 seaar.................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrgg 263
                                       +  ++                   ++ y++ ++ +D  +gr++++L+e+g++++t+vv+ +Dhg+    + ++l g+
  gi|336255545|ref|YP_004598652.1| 227 DVCQNskeynsgardidddeweAIRGLYDAEIAHMDAELGRLFDWLRETGQWEETTVVVCADHGELH--GEHDLYGH 301
                                       766667889999999**************************************************99..56999999 PP

                                       TTCSSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHHHTTE CS
                         Sulfatase 264 kganayeggtrvPllvwwpgekaprvseelvshiDlfptildlagi 309
                                       +  + y++ ++vPllv  p+  a  ++e lv++ D ++t+ld++++
  gi|336255545|ref|YP_004598652.1| 302 EF-ALYDELINVPLLVKHPELEAD-RREDLVELLDCYHTVLDALDV 345
                                       99.*********************.******************985 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   1.7e-09   7.6e-06       1      62 [.       9      72 ..       9      73 .. 0.88
   2 !   21.0   0.0   4.7e-08   0.00021     199     237 ..     256     294 ..     228     322 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.7e-09
                                      EEEEEETT-BTTHHHHHG.S..TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS CS
                      Phosphodiest  1 vlvislDGlradlldrla.e..llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHG 62
                                      vl+++lD +r d l ++  +  ++p l+++a+e + ++       + T p hasl TGlyP++HG
  gi|336255545|ref|YP_004598652.1|  9 VLFVVLDTVRKDRLGPYGyDrgTTPALSRFAEEATVFES-AVAPAPWTLPVHASLFTGLYPSQHG 72
                                      78999*****999999988789****************4.3333468*****************9 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 4.7e-08
                                       HHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEE CS
                      Phosphodiest 199 dalrrvDkaigdLlealderglsaetniilvSDHGmadv 237
                                       ++++  D+ +g+L++ l+e+g ++et++++ +DHG  + 
  gi|336255545|ref|YP_004598652.1| 256 AEIAHMDAELGRLFDWLRETGQWEETTVVVCADHGELHG 294
                                       678899*****************************7666 PP

>> Pr_beta_C  Proteasome beta subunits C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.7e-05     0.076       3      22 ..      17      36 ..      16      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                                      S-S--SS-----TTSS-EEE CS
                         Pr_beta_C  3 ekgeRqgsYkfkrGTTaVLk 22
                                      ++  R+g Y + rGTT+ L+
  gi|336255545|ref|YP_004598652.1| 17 VRKDRLGPYGYDRGTTPALS 36
                                      7999************9775 PP

>> DUF1501  Protein of unknown function (DUF1501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   8.3e-05      0.37     268     302 ..     256     290 ..     245     291 .. 0.89
   2 ?   -2.7   0.1      0.51   2.3e+03     339     376 ..     319     356 ..     317     364 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 8.3e-05
                           DUF1501 268 klakelDqalaaLlkdLkqrGllddTlVvwagEFG 302
                                         ++ +D  l  L + L ++G +++T+Vv++++ G
  gi|336255545|ref|YP_004598652.1| 256 AEIAHMDAELGRLFDWLRETGQWEETTVVVCADHG 290
                                       567899*************************9977 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.51
                           DUF1501 339 delgyaavenpvhvrdlhatilhllgldherltyatlg 376
                                       +el  +  e+ v++ d + t+l +l +d+++ + a  g
  gi|336255545|ref|YP_004598652.1| 319 PELEADRREDLVELLDCYHTVLDALDVDPDAALDAGDG 356
                                       78889999999*****************9987776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 4246.91
//
Query:       gi|336255546|ref|YP_004598653.1|  [L=339]
Description: hypothetical protein Halxa_4171 [Halopiger xanaduensis SH-6]
Scores for complete 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-38  132.9  40.7      2e-38  132.6  40.7    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
       0.22   12.0  10.1      0.044   14.2   4.2    2.5  3  Got1             Got1/Sft2-like family
        3.8    7.8  11.5        1.6    8.9   7.5    2.4  2  DUF2304          Uncharacterized conserved protein (DUF2304)


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.6  40.7   3.4e-42     2e-38       4     301 .]      16     326 ..       9     326 .. 0.89

  Alignments for each domain:
  == domain 1  score: 132.6 bits;  conditional E-value: 3.4e-42
                   LPG_synthase_TM   4 glalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfv 80 
                                       ++a++a+l++l+    +   ++++l s+ p +++l ++lal  +l ++l+ r++l++lg+ +s+r+++ +y+ + f+
  gi|336255546|ref|YP_004598653.1|  16 AIAVFAVLFFLV----GADRIIDSLLSAEPTFVALTFALALCWLLSWSLMLRTVLAALGVGVSVRTAFLVYAGAVFA 88 
                                       445555555555....**************9999999955555555666889999999******************* PP

                   LPG_synthase_TM  81 nnvtPgalg.Gevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalallll 156
                                       nnvtP++ + Ge+v+a l+++ ++ ++++ l  +    +l+++  + l+++++++   + a g ++  +++ a++l+
  gi|336255546|ref|YP_004598653.1|  89 NNVTPFGQAgGEPVAAGLISKVSDSRYETGLVGIASVDVLNVVPSISLVFVGVGYYATTAAVGERLEDAVGTAVVLI 165
                                       ************************************************************99999777777777777 PP

                   LPG_synthase_TM 157 avlalllllllrrrlarlarvlkrlarllarfarklasakr................klvlasprrlllafllslli 217
                                       ++++l  +l++r+r+  + r+   +a++l  ++  +  +++                ++v ++++rl+l+++lsl+ 
  gi|336255546|ref|YP_004598653.1| 166 GGIVLGIALVWRYREQVVDRLPAVIAPRLGLLGLERFDPEQleadlterlqrffeniERVGTDRWRLALVVGLSLAG 242
                                       78888888888888888888888888877777755544444899********************************* PP

                   LPG_synthase_TM 218 wllealtlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllall.Gvsaaealaaallyrlit 293
                                       wl+++++l+++++alg +v++++ll+++++++l+ga+p lPgGlG++Eaa+++ll++  G+ a++++aa+l++r++ 
  gi|336255546|ref|YP_004598653.1| 243 WLFQVAALMAAFAALGHSVPVYVLLFAIPLANLAGAAP-LPGGLGGIEAAFVSLLVPTtGIEASAITAAVLIFRGAI 318
                                       **********************************9986.7************************************* PP

                   LPG_synthase_TM 294 lylllllG 301
                                       +++++++G
  gi|336255546|ref|YP_004598653.1| 319 YWMPVIIG 326
                                       ******99 PP

>> Got1  Got1/Sft2-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   4.2   7.4e-06     0.044      24     100 ..      10      86 ..       4      98 .. 0.80
   2 ?   -2.9   0.0       1.5   8.9e+03      80      95 ..     161     176 ..     155     180 .. 0.59
   3 ?   -0.1   0.1       0.2   1.2e+03      83      97 ..     240     254 ..     212     275 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.4e-06
                              Got1  24 llytlGnilflastafLiGpkkqlkkmfskerliativyllsllltLyaalvlkstlltllfvivql.lallwylls 99 
                                       ll ++G i+++a ++fL+G  + + +++s e    ++++ l+l+  L  +l+l+ t+l+ l+v v +  a+l+y   
  gi|336255546|ref|YP_004598653.1|  10 LLGAVGAIAVFAVLFFLVGADRIIDSLLSAEPTFVALTFALALCWLLSWSLMLR-TVLAALGVGVSVrTAFLVYAGA 85 
                                       56789****************************99**99999999999888865.5555555555442566666655 PP

                              Got1 100 y 100
                                       +
  gi|336255546|ref|YP_004598653.1|  86 V 86 
                                       5 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.5
                              Got1  80 lltllfvivqllallw 95 
                                        ++l++ iv  +al+w
  gi|336255546|ref|YP_004598653.1| 161 AVVLIGGIVLGIALVW 176
                                       4455555555555555 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.2
                              Got1  83 llfvivqllallwyl 97 
                                       l + ++q++al+  +
  gi|336255546|ref|YP_004598653.1| 240 LAGWLFQVAALMAAF 254
                                       222222222222222 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   7.5   0.00028       1.6       7      76 ..      18      87 ..      15      92 .. 0.90
   2 ?   -1.4   0.1      0.46   2.8e+03      36      44 ..     162     170 ..     130     184 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00028
                           DUF2304  7 iivsvllllliirlvrkkklkleysllwlllalilivlslfpqiltvlanllGvgrgtnllfllgivfll 76
                                       +++vl++l+   ++  + l++e +++ l +al+l +l  +  +l  +  +lGvg  +   fl+   +++
  gi|336255546|ref|YP_004598653.1| 18 AVFAVLFFLVGADRIIDSLLSAEPTFVALTFALALCWLLSWSLMLRTVLAALGVGVSVRTAFLVYAGAVF 87
                                      689******************************************9999999999998888877666554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.46
                           DUF2304  36 llalilivl 44 
                                       ++ ++ ivl
  gi|336255546|ref|YP_004598653.1| 162 VVLIGGIVL 170
                                       222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2614.14
//
Query:       gi|336255547|ref|YP_004598654.1|  [L=173]
Description: hypothetical protein Halxa_4172 [Halopiger xanaduensis SH-6]
Scores for 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   46.3   4.0    8.2e-12   45.7   4.0    1.3  1  SNARE_assoc  SNARE associated Golgi protein


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 !   45.7   4.0   4.6e-16   8.2e-12       2     115 ..      42     162 ..      36     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 4.6e-16
                       SNARE_assoc   2 PsevllvaaGvlfglll.....gtlvtslgallGaslayllgrylgrkalrrkll...sekrvkalerlverygfla 70 
                                       Pse+++ aa +l+g  +      + v+++g+++G +l + l+r++gr+++ +k +    e r+++++ +++r g la
  gi|336255547|ref|YP_004598654.1|  42 PSELVVPAALALIGSSIpesaaIVAVAVVGTTAGQFLLFCLVRRAGREYVLQKRWvpvTESRLERFDGWFDRWGGLA 118
                                       77777744445554433456658999*********************555544440115666666************ PP

                       SNARE_assoc  71 llllrllpivPrdlvnyvaGltrvsfkrFflatfiGsipwalvya 115
                                       +  +    +v r lv+++aGl++++ + F++ ++iGs+  + ++a
  gi|336255547|ref|YP_004598654.1| 119 VAGSNTMLFV-RGLVTIPAGLSEMNGRSFVVLSAIGSLSFQSILA 162
                                       **********.**************************98887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1430.82
//
Query:       gi|336255548|ref|YP_004598655.1|  [L=171]
Description: hypothetical protein Halxa_4173 [Halopiger xanaduensis SH-6]
Scores for 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-14   52.6  10.8    1.4e-13   50.6  10.8    1.8  1  YdjM      LexA-binding, inner membrane-associated putative hy
  ------ inclusion threshold ------
       0.12   11.8   3.1      0.042   13.4   0.5    1.5  2  DUF1576   Protein of unknown function (DUF1576)


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6  10.8   1.5e-17   1.4e-13       1     157 [.       1     148 [.       1     168 [. 0.74

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.5e-17
                              YdjM   1 MdgltHallGaalglalaallgaake...avllavavlg.AllPDiDhpsstlgrklgllskklaklvgHRgftHSl 73 
                                       M    H+ + a+l + +  l +a++    avl +v+v+g A lPDiD        +l +  +     + HRg tH++
  gi|336255548|ref|YP_004598655.1|   1 MYKDGHIGFNALLYAPFVPLVSARWSletAVLGTVLVVGlAPLPDID--------ELLP--R-----IPHRGPTHTV 62 
                                       6666899999999999999999998896544444445559*******........3333..2.....349******* PP

                              YdjM  74 lflallalvlllllrlfgrsa.........lrlglllllg.vlsHlllDlltkyGvpllwPfskkkvrlsllfiiid 140
                                       +f++l++l++ + + l+ + +         +r+g+++ +g vl Hl++D++t++G+  ++P+s ++v+l++++  ++
  gi|336255548|ref|YP_004598655.1|  63 WFAVLVGLFAGVGTTLLVDATatsstsvsaFRFGFAVGTGsVLAHLAGDVVTPMGISPFAPVSAAHVTLDWFPS-KH 138
                                       ********999988888877779999995555555555559999****************************99.66 PP

                              YdjM 141 plltllsrrglvalelv 157
                                       +++        + l l+
  gi|336255548|ref|YP_004598655.1| 139 GRIN------RA-LLLL 148
                                       6333......23.2333 PP

>> DUF1576  Protein of unknown function (DUF1576)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   4.7e-06     0.042      95     167 ..      26     103 ..       9     109 .. 0.82
   2 ?   -2.9   0.1      0.47   4.2e+03      55      70 ..     150     165 ..     147     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.7e-06
                           DUF1576  95 sfkkyilaalfgtaLaPi..vgellfslelel...glvlgilvGiiaGfllpalatnvlklhgGlnLYNvGfaaGlv 166
                                       s ++++l +++  +LaP+  + ell + +++    ++++++lvG++aG+  + l+ ++ +    ++ +  Gfa+G+ 
  gi|336255548|ref|YP_004598655.1|  26 SLETAVLGTVLVVGLAPLpdIDELLPRIPHRGpthTVWFAVLVGLFAGVGTTLLVDATATSSTSVSAFRFGFAVGTG 102
                                       6677788888888999885566776666655567789**************************************85 PP

                           DUF1576 167 a 167
                                       +
  gi|336255548|ref|YP_004598655.1| 103 S 103
                                       5 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.47
                           DUF1576  55 nGptiaailtvlgFsa 70 
                                       +G +++++ +++gFs 
  gi|336255548|ref|YP_004598655.1| 150 SGALLSSLALAIGFSS 165
                                       5777888888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1355.23
//
Query:       gi|336255549|ref|YP_004598656.1|  [L=150]
Description: hypothetical protein Halxa_4174 [Halopiger xanaduensis SH-6]
Scores for 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-13   49.5   9.8    4.5e-13   48.9   9.8    1.3  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   9.8   2.5e-17   4.5e-13       5     137 ..      15     123 ..      11     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2.5e-17
                              YdjM   5 tHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllflallal 81 
                                       tHa +G al+ ++    ++       ++a+lg l+PD+D   + +  + g+ ++       HRg+tH  lf+a+l++
  gi|336255549|ref|YP_004598656.1|  15 THAFVGYALVRGFTDADPR-------FGALLG-LVPDAD---FLFPAAWGWPFV-------HRGLTHAPLFVAALVA 73 
                                       9999999999999998876.......567776.******...888889999888.......***************9 PP

                              YdjM  82 vlllllrlfgrsalrlglllllgvlsHlllDlltkyGvpllwPfskkkvrlsllfi 137
                                       +++++ r ++       l++ lgv sH+++D+l ++G+p+l+P+  +  +l+l++ 
  gi|336255549|ref|YP_004598656.1|  74 GAYAIRRDRDLP-----LAVGLGVGSHVAVDSLSPMGIPWLFPLE-ASPSLGLPVH 123
                                       999999999977.....889999*********************5.4666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1255.22
//
Query:       gi|336255550|ref|YP_004598657.1|  [L=426]
Description: hypothetical protein Halxa_4175 [Halopiger xanaduensis SH-6]
Scores for complete 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-10   40.6   0.7      1e-08   34.9   0.7    2.4  1  Arylsulfotran_2  Arylsulfotransferase (ASST)
    1.3e-08   34.2   1.5    5.1e-07   28.9   1.0    2.9  3  Arylsulfotrans   Arylsulfotransferase (ASST)
     0.0092   16.0   2.0        8.5    6.6   0.0    3.7  3  NHL              NHL repeat
  ------ inclusion threshold ------
      0.052   13.3   0.7        3.3    7.5   0.0    2.5  2  TruB_C           tRNA Pseudouridine synthase II, C terminal


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 !   34.9   0.7   2.3e-12     1e-08     101     297 ..     133     311 ..     109     313 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.3e-12
                   Arylsulfotran_2 101 idietnevlfrwSalehvdeipleeskaplgdfgrdeskpedyfHlNsv....ekfedgdyLiSlrelsslflirpk 173
                                        di  ++v     ++e+vd+    +s++p ++       p d  H+N+v    e + +g +++Slr+++ +++i p+
  gi|336255550|ref|YP_004598657.1| 133 ADIVADQVFVVNTETEIVDWLWDAQSEFPVEGG---GPYPGDWAHINDVeyieEGVHEGHVMVSLRNQDQVVFIDPE 206
                                       566666666666666666666666555665555...48899********6666667789****************** PP

                   Arylsulfotran_2 174 egkvlWqlqGpkggdfeldnstfsrQHdariveetedkivislfnNentdtnerepttglildvdlqnkevtllrkl 250
                                       eg +  +  G    d++        QH++++ +e+  +  i + + e          +g++ + + ++ e     ++
  gi|336255550|ref|YP_004598657.1| 207 EGLLEDWTLGS-EDDYD----VMYEQHNPDYIPESRGGPAIVVSDSE----------NGRVEEFQREDGEW---TRT 265
                                       ****8777777.34444....4778**********999999999995..........45544444333333...334 PP

                   Arylsulfotran_2 251 kdaedeissvsqGsyqllpnghvlveegsigrveeydangkivlear 297
                                       + + ++ ++++   ++ lpng+ lv+++   rv e   +g+iv++ +
  gi|336255550|ref|YP_004598657.1| 266 W-EWADERMQWPRDADRLPNGNTLVTDTHGNRVAEIAPDGEIVWQVE 311
                                       4.33445666777789****************************976 PP

>> Arylsulfotrans  Arylsulfotransferase (ASST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   1.0   1.1e-10   5.1e-07     122     219 ..     135     222 ..     108     227 .. 0.73
   2 !    5.4   0.0    0.0016       7.3     240     288 ..     217     262 ..     209     274 .. 0.74
   3 ?    0.1   0.0     0.067     3e+02      97     139 ..     281     309 ..     260     335 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.1e-10
                    Arylsulfotrans 122 tveDtiievdktGkvv.kewdlakiLdpyrdallkaakapfgdiagvgagrdWlHiNsveydek...ddsiivSsRh 194
                                        v D++ +v+++ ++v + wd++  + p +               g     dW+HiN vey e+   ++ ++vS+R+
  gi|336255550|ref|YP_004598657.1| 135 IVADQVFVVNTETEIVdWLWDAQSEF-PVEG--------------GGPYPGDWAHINDVEYIEEgvhEGHVMVSLRN 196
                                       55666666664444332456666655.3322..............334556***********96333799******* PP

                    Arylsulfotrans 195 qsavvkidyrtkkv.kWilgdkegwe 219
                                       q+ vv id +++ + +W lg++++++
  gi|336255550|ref|YP_004598657.1| 197 QDQVVFIDPEEGLLeDWTLGSEDDYD 222
                                       ********88888845*****99987 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0016
                    Arylsulfotrans 240 eegdfdwtwgqHtavlipngstiiellvFDNgdgrskeqpallspkdny 288
                                       +e+d d+ ++qH++ +ip++     ++v D ++gr +e    + ++ ++
  gi|336255550|ref|YP_004598657.1| 217 SEDDYDVMYEQHNPDYIPESRGGPAIVVSDSENGRVEEF---QREDGEW 262
                                       5899***************94467777777777777663...3344445 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.067
                    Arylsulfotrans  97 elpngnllvlvaeenykrkdgkkvktveDtiievdktGkvvke 139
                                        lpngn+lv+ +               +  + e+ ++G++v++
  gi|336255550|ref|YP_004598657.1| 281 RLPNGNTLVTDT--------------HGNRVAEIAPDGEIVWQ 309
                                       555555555554..............45556666666666554 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.53   2.4e+03      14      19 ..     129     134 ..     120     147 .. 0.69
   2 !    6.6   0.0     0.002       8.9      15      26 ..     242     253 ..     241     255 .. 0.87
   3 !    6.6   0.0    0.0019       8.5       2      25 ..     274     297 ..     273     299 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.53
                                       EEEEEE CS
                               NHL  14 diyVaD 19 
                                       +++VaD
  gi|336255550|ref|YP_004598657.1| 129 HVLVAD 134
                                       667776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.002
                                       EEEEECCCTEEE CS
                               NHL  15 iyVaDsenhrvq 26 
                                       i+V+Dsen rv 
  gi|336255550|ref|YP_004598657.1| 242 IVVSDSENGRVE 253
                                       89********95 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0019
                                       SSEEEEEEETTTEEEEEECCCTEE CS
                               NHL   2 nyPhGvavdsnGdiyVaDsenhrv 25 
                                       ++P++   ++nG+ +V+D++ +rv
  gi|336255550|ref|YP_004598657.1| 274 QWPRDADRLPNGNTLVTDTHGNRV 297
                                       579999999**************9 PP

>> TruB_C  tRNA Pseudouridine synthase II, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.013        58      23      39 ..      30      46 ..      24      46 .. 0.84
   2 ?    7.5   0.0   0.00074       3.3       9      39 ..     277     307 ..     276     308 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.013
                                      ----S-EEEE-TTS-EE CS
                            TruB_C 23 agikgvvAaiaPdGrli 39
                                       g++g+  a aPdG ++
  gi|336255550|ref|YP_004598657.1| 30 SGRAGTITAYAPDGDVL 46
                                      499***********885 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00074
                                       HHHHHHHTT---B-----S-EEEE-TTS-EE CS
                            TruB_C   9 aeArdlrhGrrLeaagikgvvAaiaPdGrli 39 
                                       ++A +l +G  L + ++   vA iaPdG+ +
  gi|336255550|ref|YP_004598657.1| 277 RDADRLPNGNTLVTDTHGNRVAEIAPDGEIV 307
                                       57999***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 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:                        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 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3197.12
//
Query:       gi|336255551|ref|YP_004598658.1|  [L=147]
Description: hypothetical protein Halxa_4176 [Halopiger xanaduensis SH-6]
Scores for 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  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1169.67
//
Query:       gi|336255552|ref|YP_004598659.1|  [L=414]
Description: hypothetical protein Halxa_4177 [Halopiger xanaduensis SH-6]
Scores for 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  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 3136.30
//
Query:       gi|336255553|ref|YP_004598660.1|  [L=283]
Description: hypothetical protein Halxa_4178 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.059   12.7   0.0      0.098   12.0   0.0    1.3  1  Metalloenzyme  Metalloenzyme superfamily
       0.14   12.2   0.0       0.29   11.2   0.0    1.5  1  PglZ           PglZ domain
       0.14   11.5   0.0       0.19   11.1   0.0    1.2  1  Sulfatase      Sulfatase


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 ?   12.0   0.0   1.6e-05     0.098     164     189 ..     232     257 ..     211     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                                       HHHHHHTTS-TTTEEEEEE-SSB--T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 164 avkeildaieqvdgilvvtADHgnae 189
                                       a++ + + +eq dg +vvtADHg a 
  gi|336255553|ref|YP_004598660.1| 232 ALESVAELVEQLDGDVVVTADHGEAF 257
                                       6889999****************885 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.9e-05      0.29     137     173 ..     227     259 ..     210     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.9e-05
                              PglZ 137 eaveeslkelkelvkslleengykvlltaDHGfiyqr 173
                                       e  + +l+ ++elv++l  +    v++taDHG  + +
  gi|336255553|ref|YP_004598660.1| 227 ENLRIALESVAELVEQLDGD----VVVTADHGEAFGE 259
                                       44455566777777777666....********98765 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.2e-05      0.19     176     265 ..     137     269 ..      83     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.2e-05
                                       EEEE-TTSSST...CTCGGHTCCGSTTTTCCCCCCH......................................... CS
                         Sulfatase 176 ylatlapHapp...eapdeyakkyatffddgseaar......................................... 208
                                       ++++++pHap+      ++ ++  ++ ++      +                                         
  gi|336255553|ref|YP_004598660.1| 137 VIHYMQPHAPYlarGKGQKLEQIQKGIKK------Qgesedgddgvlsslgdavrpkiesaldgkeiaqkaglwlel 207
                                       89******966333112222222222222......1234556778888999999999999999999999******** PP

                                       ............HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTT CS
                         Sulfatase 209 ............qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkg 265
                                                    +++ y   ++ + + +++++++L       +  vv+t+Dhg++ +e +++ ++ ++
  gi|336255553|ref|YP_004598660.1| 208 dpkdlvqngtrgAAMALYEENLRIALESVAELVEQL-------DGDVVVTADHGEAFGEEGVWEHHIET 269
                                       *****8888888777777777777777788888888.......788***********998887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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 0.20s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2268.44
//
Query:       gi|336255554|ref|YP_004598661.1|  [L=348]
Description: group 1 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for complete 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   61.5   0.0    8.1e-15   55.4   0.0    2.5  2  Glyco_trans_1_4  Glycosyl transferases group 1
    2.9e-15   56.2   0.0    3.9e-14   52.5   0.0    2.6  2  Glycos_transf_1  Glycosyl transferases group 1
    2.8e-13   50.2   0.0    4.3e-13   49.6   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    4.4e-07   30.5   0.1    6.7e-07   29.9   0.1    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.092   13.2   0.0       0.28   11.6   0.0    1.8  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> 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 ?    3.5   0.0     0.026        92      52      81 ..      79     116 ..      38     124 .. 0.70
   2 !   55.4   0.0   2.3e-18   8.1e-15       2     120 ..     160     281 ..     159     313 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.026
                                       T-T.TEEEE---.THHHHH....HHH-SEEEE--...- CS
                   Glyco_trans_1_4  52 gleerveftGfv.edlael....laaadvfvaPs...e 81 
                                       ++ ++++ft  + + l+++    +  ad +v+Ps   +
  gi|336255554|ref|YP_004598661.1|  79 DFGDSFRFTNALaKPLRPYleraYGLADALVCPSeynR 116
                                       34578999999975555552222666799999994443 PP

  == domain 2  score: 55.4 bits;  conditional E-value: 2.3e-18
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---.....HHHHHHHTT-T.TEEEE---THHHHHHHH-SE CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprp...eeleelaagleerveftGfvedlaellaaadv 75 
                                       pv+  vG +  ++kg++ ++e + +l   dv +   G  +r+   +e ++l++   e+++ftGf++d++ ++aa d+
  gi|336255554|ref|YP_004598661.1| 160 PVVFLVGHV-IKRKGLETFVETARQLP--DVDFAWFGPIDRSlkgRETKQLIDSAPENCTFTGFIDDIRGAYAAGDI 233
                                       788899999.466**************..79******432324456666666655689******************* PP

                                       EEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE--TT- CS
                   Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggiaevv.gengllvppgd 120
                                       f +P+  e  g++llEam ag++vV+ d+  ++ +  ge+ l v++g+
  gi|336255554|ref|YP_004598661.1| 234 FFFPTheENEGIALLEAMTAGKAVVVRDIDTFSWLEnGEDCLKVAAGS 281
                                       ******8789*******************7766655787777776654 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.14   5.1e+02      84     103 ..      96     120 ..      65     135 .. 0.81
   2 !   52.5   0.0   1.1e-17   3.9e-14      13     171 ..     157     326 ..     149     327 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.14
                                       SSHHHHHHCESEEEEEESS.....B CS
                   Glycos_transf_1  84 edleellknadifvlpsis.....E 103
                                         le  +  ad++v+ps++     E
  gi|336255554|ref|YP_004598661.1|  96 PYLERAYGLADALVCPSEYnrgliE 120
                                       4577888889******998666555 PP

  == domain 2  score: 52.5 bits;  conditional E-value: 1.1e-17
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.......STTHHHHHHHHHHHCTTCGGGEEECCHS CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG......ngeeekelkklaeelelsdnviflgevsr 83 
                                        ++++++ vg + k+Kg++++++ +++l     p+v +   G      +g e k+l +        +n++f+g+++ 
  gi|336255554|ref|YP_004598661.1| 157 LEPPVVFLVGHVIKRKGLETFVETARQL-----PDVDFAWFGpidrslKGRETKQLIDS-----APENCTFTGFID- 222
                                       5799**********************87.....79999999998755555554444444.....467*********. PP

                                       SSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT..................SEEEE-T CS
                   Glycos_transf_1  84 edleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdge..................tGllvkp 142
                                        d+   + + dif++p + E  Gi+llEAm+ag++v++ ++  ++ + + ++                  + ++   
  gi|336255554|ref|YP_004598661.1| 223 -DIRGAYAAGDIFFFPTHEENEGIALLEAMTAGKAVVVRDIDTFSWLENGEDclkvaagsstaadansdsNAAVATD 298
                                       .***************************************9988755444447777777777777777776666666 PP

                                       T-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
                   Glycos_transf_1 143 nnaealaeairklledeelrerlgenark 171
                                       + + ++++ai++ l+d++ r+rlg nar+
  gi|336255554|ref|YP_004598661.1| 299 GGPTSFVDAIES-LRDPDVRDRLGSNARE 326
                                       677777777766.4666777777777776 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   1.2e-16   4.3e-13      59     169 ..      22     139 ..      12     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.2e-16
                    Glyco_transf_4  59 aflrrlrrllkre.......kpDvvHahspaa..lgaallalrrrlgiplVltvHglye.krllkarlkplsrllra 125
                                       a+ r++  +l+ e       + Dv H++  ++  +++a +  +r++gip+V++ H ++e  +   ++ + l + lr 
  gi|336255554|ref|YP_004598661.1|  22 AHQRKMLDRLDLEytteptlEADVFHCNLMGPrsVWYARR--ARKRGIPVVAHTHVTAEdFGDSFRFTNALAKPLRP 96 
                                       5555555566555666677789******755510555544..4458*************955555666777778888 PP

                    Glyco_transf_4 126 lerrllrradrviavSeatadelrerygvppekitVipnGvDle 169
                                       +++r++  ad+++++Se+ +  ++ + +  + +  Vi nGvD e
  gi|336255554|ref|YP_004598661.1|  97 YLERAYGLADALVCPSEYNRGLIEGYVD-GSTPTQVISNGVDRE 139
                                       88889********************555.669**********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 !   29.9   0.1   1.9e-10   6.7e-07      73     160 .]      42     135 ..      17     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.9e-10
                   Glyco_trans_4_4  73 rpdvvhahs..ptaglaarlarrrrgiplvvtlhglllrrg..sgavrrly...ralerrllrradavlvvseaeae 142
                                         dv h++   p + ++ar+ar +rgip+v + h ++ + g   ++  +l+   r+   r++  ada++++se+ + 
  gi|336255554|ref|YP_004598661.1|  42 EADVFHCNLmgPRSVWYARRAR-KRGIPVVAHTHVTAEDFGdsFRFTNALAkplRPYLERAYGLADALVCPSEYNRG 117
                                       579999986446799*******.***********76644333344444444222355679999************** PP

                   Glyco_trans_4_4 143 elralgvpadrvvvvpng 160
                                       +++ +    + ++v+ ng
  gi|336255554|ref|YP_004598661.1| 118 LIEGYVDGSTPTQVISNG 135
                                       **9988777888999997 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 ?   11.6   0.0   7.9e-05      0.28       6      88 ..     238     338 ..     233     343 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.9e-05
                   Glyco_trans_1_2   6 srsespnlrlfEaaacGafaltddaegleelftpgk....................evilfe.dleelaekirylla 61 
                                       ++ e     l+Ea+ +G  +++ d+ +   ++++g+                     ++  +  + +++++i+  l+
  gi|336255554|ref|YP_004598661.1| 238 THEENEGIALLEAMTAGKAVVVRDI-DTFSWLENGEdclkvaagsstaadansdsnAAVATDgGPTSFVDAIES-LR 312
                                       5555555668899999999999975.66677777778899999999999999998544444589*********9.5* PP

                   Glyco_trans_1_2  62 npeerraiaeaarervlaehtydhrae 88 
                                       +p+ r++++ +arer  + ++++  a+
  gi|336255554|ref|YP_004598661.1| 313 DPDVRDRLGSNARER-SEGFSLETIAQ 338
                                       ***************.77877776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); 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: 00:00:00.40
# Mc/sec: 2595.69
//
Query:       gi|336255555|ref|YP_004598662.1|  [L=372]
Description: group 1 glycosyl transferase [Halopiger xanaduensis SH-6]
Scores for 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-24   84.2   0.0    1.2e-23   83.5   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    2.2e-21   76.7   0.0    6.1e-21   75.3   0.0    1.7  2  Glyco_trans_1_4  Glycosyl transferases group 1
    5.6e-18   65.5   0.9    6.9e-18   65.2   0.2    1.5  2  Glyco_transf_4   Glycosyltransferase Family 4
    6.3e-12   46.2   0.6    1.2e-11   45.3   0.1    1.8  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    3.3e-08   33.6   0.0    9.2e-08   32.2   0.0    1.7  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    4.2e-06   27.1   0.1    1.2e-05   25.6   0.0    1.8  2  Glyco_trans_1_2  Glycosyl transferases group 1


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 !   83.5   0.0     4e-27   1.2e-23      13     169 ..     183     329 ..     176     332 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 4e-27
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleel 89 
                                        ++ ++ ++grl+ eK+v+ +++++a+l     p++ +v++G+g++++ l     e+e  dnv++  +++re+l+ +
  gi|336255555|ref|YP_004598662.1| 183 PEQTVVGYSGRLSMEKNVEEILRVAAEL-----PEYEFVVVGEGPRREHL-----EAEAPDNVTLRDFLPREELPVF 249
                                       67899*********************77.....89*******99995555.....56689***************** PP

                                       HHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH.HHHHHH CS
                   Glycos_transf_1  90 lknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede.elrerl 165
                                       +++ d+fv  s+ + +G++ lEA a+g+pv+a +++++ e+++++  G  ++ ++ e++a+ i++ l  + e+r++ 
  gi|336255555|ref|YP_004598662.1| 250 YSSIDAFVTASRGDTLGLSTLEANACGTPVVAADVPPFDETIEPAN-GMRFEYGDREEMAATIEDCLAADwETRAAV 325
                                       ********************************************99.******************999888999999 PP

                                       HHHH CS
                   Glycos_transf_1 166 gena 169
                                       ++++
  gi|336255555|ref|YP_004598662.1| 326 EQYS 329
                                       8876 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 ?   -2.3   0.0       1.9   5.7e+03      11      37 ..      11      38 ..       2      54 .. 0.65
   2 !   75.3   0.0     2e-24   6.1e-21       3     132 ..     187     315 ..     185     317 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.9
                                      -GG.GTHHHHHHHH.HHHH.HHEEEEEE CS
                   Glyco_trans_1_4 11 eenvkgvdllleav.pllrkkdvrlviv 37
                                       ++++gv + ++ + ++l ++  ++++v
  gi|336255555|ref|YP_004598662.1| 11 FPEIDGVTYTIDLWrEELERRGHEVYVV 38
                                      5689999999999988888664333333 PP

  == domain 2  score: 75.3 bits;  conditional E-value: 2e-24
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprpeeleelaagleerveftGfv..edlaellaaadvfv 77 
                                       v+++ Grl   +k+v+ +l+ +++l   ++++v+vG+gpr+e+le++a    ++v++  f+  e+l+ ++++ d fv
  gi|336255555|ref|YP_004598662.1| 187 VVGYSGRL-SMEKNVEEILRVAAELP--EYEFVVVGEGPRREHLEAEAP---DNVTLRDFLprEELPVFYSSIDAFV 257
                                       7899****.555*************9..58*********667**98775...89*******9889************ PP

                                       E--..---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  78 aPs..egfglkllEamaaglpvVatdvggiaevv.gengllvppgdpealaeailrLl 132
                                         s   ++gl++lEa a+g+pvVa dv+ + e++   ng+ ++ gd e++a+ i+++l
  gi|336255555|ref|YP_004598662.1| 258 TASrgDTLGLSTLEANACGTPVVAADVPPFDETIePANGMRFEYGDREEMAATIEDCL 315
                                       ***6558*********************99****879*****************9887 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.2   2.3e-21   6.9e-18       2     150 ..      15     160 ..      14     169 .. 0.76
   2 ?   -3.3   0.0       2.6   7.8e+03      20      50 ..     213     242 ..     203     257 .. 0.56

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 2.3e-21
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHa 78 
                                        Gv   +    ++L rrGheV+vv p++d +++e+    + v++ p p++ ++++ l+ + +        + DvvH+
  gi|336255555|ref|YP_004598662.1|  15 DGVTYTIDLWREELERRGHEVYVVYPDGDYEPDER---EIPVRSMPNPFYSGYRIPLTKRAS-----ALPDLDVVHC 83 
                                       578888888899*****************999999...345555555555555444443322.....222799**** PP

                    Glyco_transf_4  79 hspaalgaallalrrrlgiplVltvHglye.....krllkarlkplsrllralerrllrradrviavSeatadelre 150
                                       h+pa++g+ +++ ++++++p+V+t H++ e     +   ka  ++l++++   e  +lr+ d v+a ++ + +++ +
  gi|336255555|ref|YP_004598662.1|  84 HGPAPVGLLGRYYAWKHDLPTVYTHHTPIEeyfhqSVKSKAIAGLLKKFYVPTETAFLRSFDVVTASTNRIDRNVNH 160
                                       ********99999999*************9555554444445556777777777777***********999998877 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.6
                    Glyco_transf_4  20 heVtvvtpgddgpleeevelvvrvprvplpl 50 
                                       +e +vv  g+++++ e+ e   +v+ + +++
  gi|336255555|ref|YP_004598662.1| 213 YEFVVVGEGPRREHLEA-EAPDNVTLRDFLP 242
                                       46777777777666666.3444444444333 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 !   45.3   0.1     4e-15   1.2e-11       4     140 ..      18     154 ..      15     164 .. 0.78
   2 ?   -1.7   0.1       1.2   3.5e+03      32      32 ..     269     269 ..     206     346 .. 0.60

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 4e-15
                   Glyco_trans_4_4   4 gryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvhah 80 
                                       +  +  + ++L++rGheV v+ p+++++++   e+ ++v+++p p  +       +++  +r+   + +  dvvh+h
  gi|336255555|ref|YP_004598662.1|  18 TYTIDLWREELERRGHEVYVVYPDGDYEPD---EREIPVRSMPNPFYS-----GYRIPLTKRAS--ALPDLDVVHCH 84 
                                       5555556689*************8888888...566788777766554.....34555555554..67999****** PP

                   Glyco_trans_4_4  81 sp.taglaarlarrrrgiplvvtlhg...lllrrg......sgavrrlyralerrllrradavlvvseae 140
                                       +p + gl++r  ++++++p v+t h+     +++       +g ++ +y + e + lr++d+v++ ++ +
  gi|336255555|ref|YP_004598662.1|  85 GPaPVGLLGRYYAWKHDLPTVYTHHTpieEYFHQSvkskaiAGLLKKFYVPTETAFLRSFDVVTASTNRI 154
                                       *7479********9***********6443334444555689999*********************99876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                   Glyco_trans_4_4  32 a 32 
                                        
  gi|336255555|ref|YP_004598662.1| 269 T 269
                                       1 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 !   32.2   0.0   3.1e-11   9.2e-08      11     120 ..      18     129 ..      10     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 3.1e-11
                   Glyco_trans_4_2  11 vhtlr.lakeLakrgyeVhvitpkkgakdeleaegihvhrlkvd..rkgpleylk.afklkklikkikPDvvhahya 83 
                                       ++t+  + +eL  rg+eV+v+ p+++++ ++++  i v +++++  + + + + k a +l +l      Dvvh+h +
  gi|336255555|ref|YP_004598662.1|  18 TYTIDlWREELERRGHEVYVVYPDGDYEPDERE--IPVRSMPNPfySGYRIPLTKrASALPDL------DVVHCHGP 86 
                                       5677735666****************8777754..8888888776444488888877788776......******** PP

                   Glyco_trans_4_2  84 kpygllgslaarlsgvipvvlsvwGldv...lkfpkksk.....l 120
                                        p+gllg+  a ++   p+v++++ + +   + +  ksk     l
  gi|336255555|ref|YP_004598662.1|  87 APVGLLGRYYAWKHD-LPTVYTHH-TPIeeyFHQSVKSKaiaglL 129
                                       **********99997.********.88876555555554444432 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 ?   -3.0   0.0       3.5     1e+04      37      61 ..     181     205 ..     174     209 .. 0.65
   2 !   25.6   0.0   4.1e-09   1.2e-05       5      70 ..     259     325 ..     249     338 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.5
                   Glyco_trans_1_2  37 ftpgkevilfedleelaekirylla 61 
                                        +p+++v+ ++   ++++ +++ l+
  gi|336255555|ref|YP_004598662.1| 181 PDPEQTVVGYSGRLSMEKNVEEILR 205
                                       5677788888866666666665554 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 4.1e-09
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraia 70 
                                        sr +++ l ++Ea acG+++++ d + ++e ++p   ++ fe  d ee+a+ i+ +la + e ra  
  gi|336255555|ref|YP_004598662.1| 259 ASRGDTLGLSTLEANACGTPVVAADVPPFDETIEPA-NGMRFEygDREEMAATIEDCLAADWETRAAV 325
                                       5777899999***********************998.9999999***************776666544 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:                      337  (0.0187964); 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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2834.62
//
Query:       gi|336255556|ref|YP_004598663.1|  [L=1000]
Description: hypothetical protein Halxa_4181 [Halopiger xanaduensis SH-6]
Scores for 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-78  256.2  10.7    3.4e-10   39.6   0.1   12.8 13  DUF1508        Domain of unknown function (DUF1508)
     0.0076   16.5   7.7         21    5.3   0.0    6.5  7  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
       0.16   11.9   8.9      0.099   12.6   1.4    3.1  3  Trypan_PARP    Procyclic acidic repetitive protein (PARP)
       0.21   12.4   6.8        6.2    7.7   0.0    5.5  7  FtsQ           Cell division protein FtsQ
          2    8.8  16.2         27    5.3   0.1    5.9  6  SPOR           Sporulation related domain


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 ?   -1.9   0.2      0.88   3.1e+03       3       9 ..     149     155 ..     147     159 .. 0.85
   2 !   39.6   0.1   9.4e-14   3.4e-10       1      48 []     204     252 ..     204     252 .. 0.98
   3 !    4.7   0.0    0.0077        28       4      38 ..     265     300 ..     263     310 .. 0.81
   4 !   12.9   0.0   2.1e-05     0.074       3      33 ..     362     393 ..     361     404 .. 0.93
   5 !    9.4   0.0   0.00026      0.95       4      47 ..     440     484 ..     437     485 .. 0.87
   6 !   26.0   0.1   1.7e-09   6.2e-06       5      47 ..     544     587 ..     541     587 .. 0.95
   7 !   20.9   0.0   6.9e-08   0.00025       3      48 .]     601     647 ..     599     647 .. 0.92
   8 !   19.3   0.0   2.2e-07   0.00078       1      40 [.     658     698 ..     658     703 .. 0.92
   9 !   25.5   0.0   2.5e-09   8.8e-06       3      44 ..     717     759 ..     716     762 .. 0.95
  10 !   22.7   0.0   1.8e-08   6.6e-05       5      41 ..     776     813 ..     774     817 .. 0.90
  11 !   11.7   0.0   5.1e-05      0.18       3      48 .]     835     880 ..     834     880 .. 0.95
  12 !   24.5   0.0   5.2e-09   1.9e-05       3      48 .]     892     938 ..     890     938 .. 0.94
  13 !   31.0   0.0   4.7e-11   1.7e-07       6      46 ..     955     996 ..     951     997 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.88
                                       TTEEEEE CS
                           DUF1508   3 nGefrFr 9  
                                       +G +r+r
  gi|336255556|ref|YP_004598663.1| 149 DGDWRWR 155
                                       89****9 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 9.4e-14
                                       ETTTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCEEE CS
                           DUF1508   1 DknGefrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaeveD 48 
                                       D++G +r++L  a+g  +++  egY++++aae +++ Vk  +p+a+v+D
  gi|336255556|ref|YP_004598663.1| 204 DEDGSWRWTLGRADGSRVGSaAEGYDDREAAEAAVRLVKDCGPEADVVD 252
                                       78*********************************************98 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0077
                                       TEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHH CS
                           DUF1508   4 GefrFrLkaaNgevIat.segYsskaaaenGIesVk 38 
                                       + + + L+++ +  +a+   gY+ + +a  + +   
  gi|336255556|ref|YP_004598663.1| 265 DRWQWQLVDDERTPLAAgADGYERRTDAVAAADTFV 300
                                       68************************9988766655 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 2.1e-05
                                       TTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHH CS
                           DUF1508   3 nGefrFrLkaaNgevIat.segYsskaaaenG 33 
                                       nG + +rL++++  +Ia+    ++++ aae++
  gi|336255556|ref|YP_004598663.1| 362 NGTWAWRLVDEDSDIIADaPSAFETRPAAEDA 393
                                       99****************9999*******987 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.00026
                                       TEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCEE CS
                           DUF1508   4 GefrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaeve 47 
                                       + +r+rL+++ g ++a+     s+   +e++ e +++  +da+v 
  gi|336255556|ref|YP_004598663.1| 440 DAWRWRLVDDAGRTVARaPDAASTVDEVERATELIREAVSDAPVL 484
                                       78**************98888888999999999999999999886 PP

  == domain 6  score: 26.0 bits;  conditional E-value: 1.7e-09
                                       EEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCEE CS
                           DUF1508   5 efrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaeve 47 
                                        +r+rL+ a++ v+a     Ys++a+a  + e++++ a +a+v+
  gi|336255556|ref|YP_004598663.1| 544 RWRWRLVTADRDVVAEsAASYSDAADATTALERIREDAREADVV 587
                                       6***************999**********************985 PP

  == domain 7  score: 20.9 bits;  conditional E-value: 6.9e-08
                                       TTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCEEE CS
                           DUF1508   3 nGefrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaeveD 48 
                                       +G +r+rL ++ g v+++    ++s+  a +++   k+ apda+v++
  gi|336255556|ref|YP_004598663.1| 601 DGDWRWRLLDEGGAVLGDsDGEHDSRNEAIEAMLTLKERAPDADVVE 647
                                       89****************55569**********************87 PP

  == domain 8  score: 19.3 bits;  conditional E-value: 2.2e-07
                                       ETTTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHH CS
                           DUF1508   1 DknGefrFrLkaaNgevIat.segYsskaaaenGIesVkkn 40 
                                       D++G + +rL +a g  +at   +Y+s+aaa+ ++++ + +
  gi|336255556|ref|YP_004598663.1| 658 DEDGVWAWRLIDAAGRRVATaPTTYASRAAARAAVDRFRGQ 698
                                       789*****************99*************998765 PP

  == domain 9  score: 25.5 bits;  conditional E-value: 2.5e-09
                                       TTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTC CS
                           DUF1508   3 nGefrFrLkaaNgevIat.segYsskaaaenGIesVkknapda 44 
                                       +G +r+rL++  ge++a  +  Y ++   e+ I+ V++ a+ a
  gi|336255556|ref|YP_004598663.1| 717 DGAWRWRLVHPTGETLAVsGSEYPTRDELEDRIDDVRETAAAA 759
                                       89**************************************988 PP

  == domain 10  score: 22.7 bits;  conditional E-value: 1.8e-08
                                       EEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHT CS
                           DUF1508   5 efrFrLkaaNgevIat.segYsskaaaenGIesVkkna 41 
                                        +r+rL ++++e I+     Yss+aaa+++++   k +
  gi|336255556|ref|YP_004598663.1| 776 TWRWRLLDRDREPILEsATAYSSRAAARDAVDELEKAS 813
                                       6***************9999***********9988776 PP

  == domain 11  score: 11.7 bits;  conditional E-value: 5.1e-05
                                       TTEEEEEEE-TTS-EEEEEEEBSSHHHHHHHHHHHHHHTTTCCEEE CS
                           DUF1508   3 nGefrFrLkaaNgevIatsegYsskaaaenGIesVkknapdaeveD 48 
                                       ++ +r+ L ++ +ev+at    ++k++   +++ +++ ap ae+ D
  gi|336255556|ref|YP_004598663.1| 835 DEGWRWDLIDRGREVLATAVETADKSDTTAAVDDIQRLAPLAERID 880
                                       789***************9999*********************987 PP

  == domain 12  score: 24.5 bits;  conditional E-value: 5.2e-09
                                       TTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCEEE CS
                           DUF1508   3 nGefrFrLkaaNgevIat.segYsskaaaenGIesVkknapdaeveD 48 
                                       ++ +r+rL +++g  +a   e+ ++kaaa++GI+ V++   +a+v++
  gi|336255556|ref|YP_004598663.1| 892 DDGWRWRLLDGDGHPVAIgDETTETKAAARDGIDDVRSLLESASVFE 938
                                       789***********************************999999876 PP

  == domain 13  score: 31.0 bits;  conditional E-value: 4.7e-11
                                       EEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTCCE CS
                           DUF1508   6 frFrLkaaNgevIat.segYsskaaaenGIesVkknapdaev 46 
                                       + +rL+++Nge+++   + Y++++a +++I++ +++a+d +v
  gi|336255556|ref|YP_004598663.1| 955 WQWRLVDENGETLLEsAQAYETREATQEAIAALQSHATDGKV 996
                                       99***********************************99765 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.48   1.7e+03       3      33 ..     250     281 ..     248     306 .. 0.73
   2 ?    0.2   0.0      0.23   8.1e+02      18      32 ..     364     378 ..     360     410 .. 0.81
   3 ?   -0.3   0.0      0.31   1.1e+03      18      32 ..     441     455 ..     438     484 .. 0.82
   4 ?   -0.9   0.3      0.47   1.7e+03      18      64 ..     544     588 ..     541     598 .. 0.79
   5 ?    4.5   0.0      0.01        37      18      61 ..     662     704 ..     655     717 .. 0.86
   6 ?    1.7   0.0     0.078   2.8e+02       9      33 ..     767     792 ..     760     818 .. 0.78
   7 !    5.3   0.0     0.006        21      13      47 ..     949     986 ..     947     998 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.48
                     DDE_Tnp_IS240   3 swrvDETyvkikG.kwaYlyravDkegrildf 33 
                                       ++ v+E ++ i+  ++++ + +vD e   l +
  gi|336255556|ref|YP_004598663.1| 250 VVDVEEGAITIAKrRDRWQWQLVDDERTPLAA 281
                                       67889999999651689*******99887655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.23
                     DDE_Tnp_IS240  18 aYlyravDkegrild 32 
                                       ++ +r+vD+++ i+ 
  gi|336255556|ref|YP_004598663.1| 364 TWAWRLVDEDSDIIA 378
                                       799********9875 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.31
                     DDE_Tnp_IS240  18 aYlyravDkegrild 32 
                                       a+ +r+vD +gr++ 
  gi|336255556|ref|YP_004598663.1| 441 AWRWRLVDDAGRTVA 455
                                       788*********875 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.47
                     DDE_Tnp_IS240  18 aYlyravDkegrildflvskrRdtkaakaflrkalkkeklepeeivt 64 
                                       ++ +r+v ++  ++      + d++ a  +l+++ +++  +++ +v+
  gi|336255556|ref|YP_004598663.1| 544 RWRWRLVTADRDVVAESAASYSDAADATTALERIREDA--READVVA 588
                                       57799999999999999999999999999999999988..4444444 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.01
                     DDE_Tnp_IS240  18 aYlyravDkegrildflvskrRdtkaakaflrkalkkeklepee 61 
                                        + +r++D++gr +  + + +  ++aa+a+  ++  ++  +p++
  gi|336255556|ref|YP_004598663.1| 662 VWAWRLIDAAGRRVATAPTTYASRAAARAAVDRFRGQS-DSPVH 704
                                       689****************************9999888.66655 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.078
                     DDE_Tnp_IS240   9 TyvkikGkwaYlyravDkegr.ildf 33 
                                       + v+  G  ++ +r++D + + il+ 
  gi|336255556|ref|YP_004598663.1| 767 VTVQLVGSETWRWRLLDRDREpILES 792
                                       579999**************966664 PP

  == domain 7  score: 5.3 bits;  conditional E-value: 0.006
                     DDE_Tnp_IS240  13 ikGkwaYlyravDkegril.d.flvskrRdt.kaakaf 47 
                                        +G+  + +r+vD++g++l + ++  + R++ + a+a+
  gi|336255556|ref|YP_004598663.1| 949 TNGDEPWQWRLVDENGETLlEsAQAYETREAtQEAIAA 986
                                       589999***********662324455555531334444 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.027        97      96     106 ..     118     128 ..      85     145 .. 0.63
   2 ?   12.6   1.4   2.8e-05     0.099      51     101 ..     310     360 ..     280     367 .. 0.60
   3 ?   -3.3   0.6       2.2     8e+03      68      80 ..     492     504 ..     466     528 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.027
                       Trypan_PARP  96 epepepepepe 106
                                       e e+epe e+e
  gi|336255556|ref|YP_004598663.1| 118 ESETEPETETE 128
                                       12222222222 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.8e-05
                       Trypan_PARP  51 dddtngtdpepepepepepepepepepepetepeeepepepepepepepep 101
                                       d d+ g++        p p+pe  p+ e e + e+++++e+e ep  e + 
  gi|336255556|ref|YP_004598663.1| 310 DVDAFGVELYESGTVAPGPKPESGPDRESELDQESKSNQESETEPGEEENG 360
                                       555555554444444444444444444444444444445555444444433 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.2
                       Trypan_PARP  68 epepepepepepe 80 
                                       e   +p++ pe++
  gi|336255556|ref|YP_004598663.1| 492 EAYSDPDSAPEDN 504
                                       3333344444432 PP

>> FtsQ  Cell division protein FtsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.55     2e+03      62     105 ..     194     244 ..     112     254 .. 0.55
   2 ?    2.1   0.1     0.094   3.4e+02      61     101 ..     260     296 ..     223     312 .. 0.68
   3 ?   -3.5   0.0         5   1.8e+04       9      21 ..     444     456 ..     441     486 .. 0.59
   4 ?   -0.8   0.1      0.75   2.7e+03      63      84 ..     597     619 ..     543     650 .. 0.52
   5 ?   -1.1   0.0      0.94   3.4e+03      35      62 ..     621     648 ..     596     692 .. 0.50
   6 ?    7.7   0.0    0.0017       6.2      36      95 ..     857     918 ..     828     926 .. 0.70
   7 ?   -0.9   0.0      0.81   2.9e+03       9      21 ..     957     969 ..     948     996 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.55
                                       E.......-SS-TTEEEE-T...TS-EEEEES....TTHHHHHHT-CCHHHC. CS
                              FtsQ  62 i.......alserrrwqlvl..ddgvevklgreelaedleeklarlvkilpql 105
                                       +        ++e+++w+ +l  +dg +v    e  + d  e+ ++ v+++++ 
  gi|336255556|ref|YP_004598663.1| 194 VtdaavrvYRDEDGSWRWTLgrADGSRVGSAAE--GYDDREAAEAAVRLVKDC 244
                                       233344444455555554442256655544333..222244555566655555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.094
                                       EE-SS-TTEEEE-T.TS-EEEEES....TTHHHHHHT-CCH CS
                              FtsQ  61 eialserrrwqlvlddgvevklgreelaedleeklarlvki 101
                                        +++ +r +wqlv d+++ +  g +     +e++  + +++
  gi|336255556|ref|YP_004598663.1| 260 IAKRRDRWQWQLVDDERTPLAAGADG----YERRTDAVAAA 296
                                       34788999999999999******963....44465555554 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5
                                       EEEEETT--B-C. CS
                              FtsQ   9 dalidaeGevfea 21 
                                        +l+d+ G+ +++
  gi|336255556|ref|YP_004598663.1| 444 WRLVDDAGRTVAR 456
                                       3566666666655 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.75
                                       -SS-TTEEEE.-T.TS-EEEEES CS
                              FtsQ  63 alserrrwql.vlddgvevklgr 84 
                                         ++++ w+  +ld+g  v   +
  gi|336255556|ref|YP_004598663.1| 597 YENDDGDWRWrLLDEGGAVLGDS 619
                                       33344444443333444444444 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 0.94
                                       ......S-HHHHHCCS-HHHHH.S-SEE CS
                              FtsQ  35 Gpegsekevlevlaelpeelkpleisei 62 
                                       G  +s +e++e++  l+e    +++ ei
  gi|336255556|ref|YP_004598663.1| 621 GEHDSRNEAIEAMLTLKERAPDADVVEI 648
                                       3333334444444444333322444444 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.0017
                                       .....S.-HHHHHCCS-HHHHH.S-SEE.....-SS-TTEEEE-T.TS-EEEEES....TTHHHHH CS
                              FtsQ  36 pegsek.evlevlaelpeelkpleisei.....alserrrwqlvlddgvevklgreelaedleekl 95 
                                       +++s + ++++ +++l ++ +  +++e+     ++++  rw+l+  dg  v +g+e +++    k 
  gi|336255556|ref|YP_004598663.1| 857 ADKSDTtAAVDDIQRLAPLAERIDVAEAsfdvvERDDGWRWRLLDGDGHPVAIGDETTET----KA 918
                                       344444346677777755554433344455555**********************76665....33 PP

  == domain 7  score: -0.9 bits;  conditional E-value: 0.81
                                       EEEEETT--B-C. CS
                              FtsQ   9 dalidaeGevfea 21 
                                        +l+d++Ge + +
  gi|336255556|ref|YP_004598663.1| 957 WRLVDENGETLLE 969
                                       4666666666533 PP

>> SPOR  Sporulation related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.27   9.7e+02      50      65 ..     227     242 ..     225     256 .. 0.80
   2 ?   -3.7   0.4       4.5   1.6e+04      51      63 ..     384     397 ..     383     404 .. 0.58
   3 ?    3.6   0.2     0.024        88      10      42 ..     562     602 ..     560     608 .. 0.74
   4 ?    4.6   0.0     0.012        42      50      66 ..     681     698 ..     679     706 .. 0.77
   5 ?    5.3   0.1    0.0074        27      50      72 ..     795     816 ..     792     825 .. 0.75
   6 ?    1.3   0.1      0.13   4.6e+02      50      68 ..     973     990 ..     970     998 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.27
                                       SBCTCCHHHHHHHHCH CS
                              SPOR  50 pfasreeAqaalkkLk 65 
                                       ++++re+A+aa + +k
  gi|336255556|ref|YP_004598663.1| 227 GYDDREAAEAAVRLVK 242
                                       5899999988887666 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.5
                                       BCTCCHHHHHHH.H CS
                              SPOR  51 fasreeAqaalk.k 63 
                                       f++r +A++a+   
  gi|336255556|ref|YP_004598663.1| 384 FETRPAAEDAATaA 397
                                       66666666665533 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.024
                                       -EES-HHHHHHHHHHCCHHT--...........EEECCSSS CS
                              SPOR  10 gafsseanAerlaakLrakgfaaav........avvsgggg 42 
                                       +++s+ a+A ++++++r    +a v         v+++++g
  gi|336255556|ref|YP_004598663.1| 562 ASYSDAADATTALERIREDAREADVvafktaafRVYENDDG 602
                                       8999999**99999999999988776666665555555555 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.012
                                       SBCTCCHHHHHHHHCH.H CS
                              SPOR  50 pfasreeAqaalkkLk.a 66 
                                        +asr++A+aa ++++ +
  gi|336255556|ref|YP_004598663.1| 681 TYASRAAARAAVDRFRgQ 698
                                       699999999999999922 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.0074
                                       SBCTCCHHHHHHHHCHHHHTTS- CS
                              SPOR  50 pfasreeAqaalkkLkaaagisa 72 
                                       +++sr++A++a ++L  +a +sa
  gi|336255556|ref|YP_004598663.1| 795 AYSSRAAARDAVDELE-KASMSA 816
                                       6888888888888888.566665 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.13
                                       SBCTCCHHHHHHHHCHHHH CS
                              SPOR  50 pfasreeAqaalkkLkaaa 68 
                                       ++++re+ q+a++ L+ ++
  gi|336255556|ref|YP_004598663.1| 973 AYETREATQEAIAALQ-SH 990
                                       79*************9.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1000 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); 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 0.26s 00:00:00.99 Elapsed: 00:00:00.44
# Mc/sec: 6842.97
//
Query:       gi|336255557|ref|YP_004598664.1|  [L=398]
Description: cell division control protein 6-like protein [Halopiger xanaduensis SH-6]
Scores for complete 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-17   63.2   0.1    2.8e-17   62.5   0.1    1.4  1  Cdc6_C         CDC6, C terminal winged helix domain
    2.9e-10   40.5   0.0    7.7e-10   39.2   0.0    1.6  1  AAA_22         AAA domain
    5.2e-10   40.0   1.6    5.6e-09   36.6   0.0    2.8  2  AAA_16         AAA ATPase domain
    0.00055   19.9   0.0    0.00097   19.1   0.0    1.4  1  ATPase_2       ATPase domain predominantly from Archaea
    0.00078   18.7   0.0     0.0015   17.8   0.0    1.4  1  DUF815         Protein of unknown function (DUF815)
    0.00081   19.3   0.0     0.0014   18.6   0.0    1.4  1  NACHT          NACHT domain
    0.00083   19.8   0.0     0.0042   17.5   0.0    2.1  1  AAA            ATPase family associated with various cellular
     0.0065   16.5   0.0      0.012   15.6   0.0    1.5  1  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.022   14.2   0.0    1.3  1  TniB           Bacterial TniB protein
      0.024   15.0   0.0      0.051   14.0   0.0    1.6  1  RNA_helicase   RNA helicase
      0.028   13.6   0.0      0.051   12.7   0.0    1.3  1  PIF1           PIF1-like helicase
      0.029   13.9   0.0       0.15   11.6   0.0    2.0  2  AAA_7          P-loop containing dynein motor region
      0.039   13.1   0.0      0.059   12.5   0.0    1.4  1  NB-ARC         NB-ARC domain
      0.041   12.7   0.3       0.78    8.4   0.0    2.3  2  AAA_32         AAA domain
      0.055   13.3   1.2       0.11   12.3   1.2    1.6  1  AAA_lid_2      AAA lid domain
      0.061   13.4   0.0       0.22   11.6   0.0    1.8  1  AAA_14         AAA domain
      0.062   12.2   0.0        2.2    7.1   0.0    2.2  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
       0.12   12.1   0.0       0.25   11.0   0.0    1.6  1  AAA_24         AAA domain
       0.13   12.8   0.0        9.6    6.7   0.0    2.5  2  ABC_tran       ABC transporter


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 !   62.5   0.1     3e-20   2.8e-17       1      83 [.     306     388 ..     306     389 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 3e-20
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----H.HHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltq.revsdllseLemlgileleksskGrregrtrkisLnv 76 
                                       L ++++l++ +++ +++++e++e Y++++e +g++plt+ ++++d+ls+L+mlg+l +++++kG ++g++++++L+ 
  gi|336255557|ref|YP_004598664.1| 306 LETIAKLEE-RNEVPARSKEIQEGYERVAEAYGATPLTTlKSIQDHLSDLHMLGFLVRHERNKGLSGGQYYEYELDL 381
                                       678999999.*****************************9************************************* PP

                                       SCHHHHH CS
                            Cdc6_C  77 dpddvle 83 
                                       dp+ vle
  gi|336255557|ref|YP_004598664.1| 382 DPMIVLE 388
                                       ***9987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   8.2e-13   7.7e-10       7     121 ..      53     171 ..      49     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 8.2e-13
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskdllrellralglelka...erlsseel 78 
                                        ++++G +G GKT + + ++++l+ e + +e   + +v +++++++t    ++r + + l  +++    ++l + + 
  gi|336255557|ref|YP_004598664.1|  53 NIFLYGKAGLGKTAVTKYMMSELQSEVFEREevDDLHVHEINCNGKTLFMVVRRLVNELLPADASPfpkRGLGTGDA 129
                                       689********************9887777788888899********66666666666666555557779******* PP

                            AAA_22  79 lealeqalraravielliiDEaqhlr.seealeeL.rsllnlsrk 121
                                       ++ l+ +l++ + ++l++ DE++hl+  +++l eL r ++n    
  gi|336255557|ref|YP_004598664.1| 130 FDELYAQLDRIGGTHLIVFDEIDHLDdVDTLLYELpRARSN---G 171
                                       *************************7559999999888888...3 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0     6e-12   5.6e-09       4     166 ..      30     172 ..      27     178 .. 0.73
   2 ?    1.1   0.6      0.47   4.5e+02      72     116 ..     301     340 ..     213     365 .. 0.55

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 6e-12
                            AAA_16   4 GReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy..sa.laqal 76 
                                        R+ee+e++ +al++v  gr+ e+++l+G +G GK+++ +  + +l+ +  +f r++ d+l    +   +    ++l
  gi|336255557|ref|YP_004598664.1|  30 ERDEEIEAFSHALQDVLFGREpENIFLYGKAGLGKTAVTKYMMSELQSE--VFEREEVDDL----HVheINcNGKTL 100
                                       7*************99999999*************************99..4455555555....221122122233 PP

                            AAA_16  77 areellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslq 153
                                        +  ++r l +e+  a++++++++ +++               +++l + l+++       ++v+D+++ +d+   +
  gi|336255557|ref|YP_004598664.1| 101 -F-MVVRRLVNELLPADASPFPKRGLGTGD------------AFDELYAQLDRIGG-T--HLIVFDEIDHLDD-VDT 159
                                       .3.566666666666688899998777544............66666666655554.4..59**********9.566 PP

                            AAA_16 154 llaaLlrlleskp 166
                                       ll++L r++++++
  gi|336255557|ref|YP_004598664.1| 160 LLYELPRARSNGH 172
                                       7899988887655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.47
                            AAA_16  72 laqalareellrqlldeaesaeleawrekleealaavpelagaea 116
                                        aq++   e +++l+++   +e++a +++++e ++ v+e+ ga +
  gi|336255557|ref|YP_004598664.1| 301 HAQYI-L-ETIAKLEER---NEVPARSKEIQEGYERVAEAYGATP 340
                                       33334.2.222333333...4555555555555555555555544 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 !   19.1   0.0     1e-06   0.00097       3     146 ..      30     165 ..      28     205 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                          ATPase_2   3 dRekelkeleeile....repneiyfiYGpegsGKtaLlkeiienledkdkyviyyial..reesiskldefieeee 73 
                                       +R++e++   + l+      + e +f+YG  g GKta+ k ++++l++  +++  +++l  +e++ + ++ f     
  gi|336255557|ref|YP_004598664.1|  30 ERDEEIEAFSHALQdvlfGREPENIFLYGKAGLGKTAVTKYMMSELQSEVFEREEVDDLhvHEINCNGKTLF----M 102
                                       57777776655554222234556679********************88888776666661156677788888....5 PP

                          ATPase_2  74 ekkklekal....giavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLl 146
                                       ++++l + l    ++++pk  l             a+++l++++ + g    i++De+  l          l++eL 
  gi|336255557|ref|YP_004598664.1| 103 VVRRLVNELlpadASPFPKRGLG---------TGDAFDELYAQLDRIGGTHLIVFDEIDHLD--D---VDTLLYELP 165
                                       55555555545558889998883.........346788889999999999999****99988..3...336666665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.6e-06    0.0015      26      92 ..      24      90 ..      17     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                            DUF815 26 klddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeegLrlievekedl 92
                                      + +++ + d++ ea+ +  +  l g++ +n++L+G+ G GK ++ k +++e+++e     ev+  ++
  gi|336255557|ref|YP_004598664.1| 24 QPEEILERDEEIEAFSHALQDVLFGREPENIFLYGKAGLGKTAVTKYMMSELQSEVFEREEVDDLHV 90
                                      5678889999999***************************************999866666655555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.4e-06    0.0014       3      98 ..      54     159 ..      52     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.....-HCHHHCCCCTS--SSS-C...... CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna..rsladllfsqlpepaapvse...... 71 
                                       ++l G+aG GKT+  + ++++++++  ++++   v  l+++e+++ g++  + +++l+ + lp+ a+p ++      
  gi|336255557|ref|YP_004598664.1|  54 IFLYGKAGLGKTAVTKYMMSELQSEVFEREE---VDDLHVHEINCNGKTlfMVVRRLVNELLPADASPFPKrglgtg 127
                                       799***********************99977...6678888888888888789999999999999999999999999 PP

                                       .....CHHHHCCSCCCEEEEEE-STT-SS-TC CS
                             NACHT  72 .....vwavllelperlLlilDglDelvtdlg 98 
                                              a l ++    L+++D +D l + + 
  gi|336255557|ref|YP_004598664.1| 128 dafdeLYAQLDRIGGTHLIVFDEIDHLDDVDT 159
                                       95555555555555566899***999998554 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 !   17.5   0.0   4.4e-06    0.0042       2      70 ..      55     154 ..      54     197 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.4e-06
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS..................................STTHHHH CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk..................................yvgesek 44 
                                        lyG  G GKT++ k +++el++e++e +  + l                                      g++ +
  gi|336255557|ref|YP_004598664.1|  55 FLYGKAGLGKTAVTKYMMSELQSEVFEREEVDDLHVheincngktlfmvvrrlvnellpadaspfpkrglGTGDAFD 131
                                       79******************975533333322221122333333333467788888888888887776444444444 PP

                                       HHHHHHHHHHHTSTSEEEEEETGGGH CS
                               AAA  45 kirelfkeakekakpsilfiDEidal 70 
                                       ++ + ++++    +++ +++DEid l
  gi|336255557|ref|YP_004598664.1| 132 ELYAQLDRI---GGTHLIVFDEIDHL 154
                                       444444433...34689999999988 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.3e-05     0.012       3      45 ..      31      77 ..      29      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                                      SHHHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE  3 seeetealgkklakal....gdvilLeGdLGaGKTtlvrglakalgv 45
                                      + ee+ea+ ++l+++l     + i+L+G+ G GKT+ ++ ++++l+ 
  gi|336255557|ref|YP_004598664.1| 31 RDEEIEAFSHALQDVLfgrePENIFLYGKAGLGKTAVTKYMMSELQS 77
                                      57899999999999888765567*******************99975 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.3e-05     0.022      32     131 ..      48     154 ..      29     159 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                              TniB  32 rkrmpnlllvGdsnnGKtmivekFarlhppe..kdedaekvpvlvvqappkp...dekrlyaaiLealgaplkara. 102
                                         +++n+ l+G+   GKt++ +  +++ ++e  ++e+ + + v  +++  k      +rl +++L a   p+ +r  
  gi|336255557|ref|YP_004598664.1|  48 GREPENIFLYGKAGLGKTAVTKYMMSELQSEvfEREEVDDLHVHEINCNGKTlfmVVRRLVNELLPADASPFPKRGl 124
                                       566789************9998887665555223466678899999999886333689**************99975 PP

                              TniB 103 rvskleqqvlrllrel.kvrvLiiDEihnl 131
                                        + ++ ++ ++ l+++ +++++++DEi++l
  gi|336255557|ref|YP_004598664.1| 125 GTGDAFDELYAQLDRIgGTHLIVFDEIDHL 154
                                       44466666667776662699********98 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.4e-05     0.051       1      26 [.      54      79 ..      54     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                      i+lyG++g GK+ ++k+++++l++++
  gi|336255557|ref|YP_004598664.1| 54 IFLYGKAGLGKTAVTKYMMSELQSEV 79
                                      79********************9876 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   5.4e-05     0.051       9      49 ..      37      78 ..      31      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-05
                                      HHHHH.......HCTS-EEEEESTTSSCHHHHHHHHHHCHCT CS
                              PIF1  9 vfdaiieavln.ekgklfFvtGsgGtgKtflwkallkklrse 49
                                      +f ++++ vl  ++++++F++G +G gKt + k +++ l+se
  gi|336255557|ref|YP_004598664.1| 37 AFSHALQDVLFgREPENIFLYGKAGLGKTAVTKYMMSELQSE 78
                                      55555555544399***********************99986 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 ?   11.6   0.0   0.00015      0.15      33      63 ..      51      81 ..      34      91 .. 0.87
   2 ?   -1.1   0.0       1.2   1.1e+03      38      72 ..     177     211 ..     169     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                             AAA_7 33 kkpvllvGptGtGKtviikdllkkldkekyl 63
                                        +++l+G++G GKt+++k ++++l++e + 
  gi|336255557|ref|YP_004598664.1| 51 PENIFLYGKAGLGKTAVTKYMMSELQSEVFE 81
                                      56899********************988775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                             AAA_7  38 lvGptGtGKtviikdllkkldkekylsltinfsaq 72 
                                       lvG +G +   + ++ l++  k++++ + i+fs +
  gi|336255557|ref|YP_004598664.1| 177 LVGIVGISNNYTFRQSLSAKVKDTLMETEISFSPY 211
                                       7899999999999997777777999999**99976 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.3e-05     0.059       6      45 ..      40      76 ..      35     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.3e-05
                                      HHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  6 ekviekLlekdelqslvvalvGmgGvGKttlakqilnksd 45
                                       ++++ L+   e++   ++l+G++G+GKt + k ++++++
  gi|336255557|ref|YP_004598664.1| 40 HALQDVLF-GREPE--NIFLYGKAGLGKTAVTKYMMSELQ 76
                                      56788888.88999..99*************999988854 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00083      0.78      28      57 ..      49      78 ..      21      95 .. 0.75
   2 ?    1.8   0.1     0.086        81     477     507 ..     252     282 ..     236     290 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00083
                            AAA_32 28 kkgYNifvlGesgtGrttlvkrlleeiakk 57
                                      ++  Nif+ G++g+G+t ++k +++e +++
  gi|336255557|ref|YP_004598664.1| 49 REPENIFLYGKAGLGKTAVTKYMMSELQSE 78
                                      5667******************99998765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.086
                            AAA_32 477 fseiadllrEAdywakkegaevveaehVekA 507
                                        ++ +dllr  + +a+++g+e+v+++h+e+A
  gi|336255557|ref|YP_004598664.1| 252 ARQAIDLLRVGAEVAERDGDETVTDDHIEDA 282
                                       567899***********************99 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.2   0.00012      0.11      26      67 ..     262     303 ..     237     314 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                         AAA_lid_2  26 ArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegette 67 
                                           A  +g ++Vt++++++a  lV + Rlr + +++ e ++
  gi|336255557|ref|YP_004598664.1| 262 GAEVAERDGDETVTDDHIEDARTLVQRGRLRNKIRDQTEHAQ 303
                                       5555666889*********************66655555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.22       6      95 ..      55     173 ..      51     193 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            AAA_14   6 vitGaRrvGKTtllkqlikell........vkkesilyinldderd...................kkladpe..... 50 
                                       ++ G    GKT + k +++el         v++ ++ +in++ +++                         +     
  gi|336255557|ref|YP_004598664.1|  55 FLYGKAGLGKTAVTKYMMSELQsevfereeVDDLHVHEINCNGKTLfmvvrrlvnellpadaspfP-----Krglgt 126
                                       567777889999999998888888889988899999999999988877776666555554333330.....144444 PP

                            AAA_14  51 ..kllelileklkeekktylflDEiqevpewekalkslvdegknldv 95 
                                          ++el+ ++ +  +++++++DEi +++++ + l +l + ++n+++
  gi|336255557|ref|YP_004598664.1| 127 gdAFDELYAQLDRIGGTHLIVFDEIDHLDDVDTLLYELPRARSNGHI 173
                                       434555555553336999***************99998887766655 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 ?    7.1   0.0    0.0023       2.2      13      41 ..      49      77 ..      45      85 .. 0.90
   2 ?    2.6   0.0     0.053        50     248     273 ..     147     172 ..     143     190 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0023
                     TrwB_AAD_bind 13 retqhilivGttGsGKtqalekllraira 41
                                      re + i++ G +G GKt +++ ++ ++++
  gi|336255557|ref|YP_004598664.1| 49 REPENIFLYGKAGLGKTAVTKYMMSELQS 77
                                      78899*******************99875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.053
                     TrwB_AAD_bind 248 flDElpaLgrleelksllaegRkfGg 273
                                       ++DE+++L+ +++l   l ++R+ G 
  gi|336255557|ref|YP_004598664.1| 147 VFDEIDHLDDVDTLLYELPRARSNGH 172
                                       79*********************995 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00026      0.25       4      77 ..      53     154 ..      50     172 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                            AAA_24   4 kiliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdie.....swedfldevvel.............. 59 
                                       +i++yG++g GKT + k +  + +  ++  e+    +d+ ++ +i+      +  ++  v+el              
  gi|336255557|ref|YP_004598664.1|  53 NIFLYGKAGLGKTAVTKYMmsELQSEVFEREE----VDDLHVHEINcngktLFMVVRRLVNELlpadaspfpkrglg 125
                                       799*************9994433333334444....44444444444456533333444444444455555555555 PP

                            AAA_24  60 ...........aaeladyktlviDtidel 77 
                                                   +   + + +v+D id+l
  gi|336255557|ref|YP_004598664.1| 126 tgdafdelyaqLDRIGGTHLIVFDEIDHL 154
                                       55544444333333334566777777766 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0      0.01       9.6      12      37 ..      52      77 ..      42     111 .. 0.83
   2 ?    3.6   0.0     0.097        92      57     114 ..     291     374 ..     251     379 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
                                      SEEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllkp 37
                                      e + + G+ G GK+ + k ++ +l+ 
  gi|336255557|ref|YP_004598664.1| 52 ENIFLYGKAGLGKTAVTKYMMSELQS 77
                                      7889****************999876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.097
                                       CCHCEEEE-SS--S-TTSBHHHH....................HHHTC.........HHHHHHHSTTGGTTCBGEST CS
                                       xxxxxxxxxxxxxxxxxxxxxxx....................xxxxx.........xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  57 lrkeigvlpqepqlfpeltvren....................esdee.........iekalsklglkelkdtvvks 104
                                       lr++i+  ++++q   e+  ++                     +   e         ++ + ++l++ ++    v++
  gi|336255557|ref|YP_004598664.1| 291 LRNKIRDQTEHAQYILETI-AKLeernevparskeiqegyervA---EaygatplttLKSIQDHLSDLHMLGFLVRH 363
                                       4444444444433332221.111223444444444444454440...144444555577777777777777777766 PP

                                       TS.GGS-HHHH CS
                                       xx.xxxxxxxx RF
                          ABC_tran 105 sp.ssLSgGqk 114
                                       +  + LSgGq 
  gi|336255557|ref|YP_004598664.1| 364 ERnKGLSGGQY 374
                                       66699****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 2989.05
//
Query:       gi|336255558|ref|YP_004598665.1|  [L=898]
Description: Patched family protein [Halopiger xanaduensis SH-6]
Scores for 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-38  130.3  22.0    3.7e-20   72.1   3.6    2.7  3  MMPL            MMPL family
    8.9e-14   51.6  10.7    4.5e-07   29.8   0.1    2.7  3  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
    2.5e-11   42.4  16.7    8.5e-07   27.5   4.0    2.3  2  Patched         Patched family
     0.0086   15.7   0.1      0.018   14.6   0.1    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,


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 !   72.1   3.6   8.3e-24   3.7e-20       5     297 ..     126     457 ..     122     471 .. 0.80
   2 ?   -4.0   1.5       1.2   5.2e+03     153     170 ..     500     517 ..     492     518 .. 0.81
   3 !   71.5   2.1   1.2e-23   5.6e-20      70     302 ..     616     880 ..     547     895 .. 0.71

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 8.3e-24
                              MMPL   5 adaesvkamdrleaafpe.eadsd.kiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf......... 70 
                                       +d+e+++a ++++++f+  ++ds  ++++++l ++d+ + s+ +   + e  d++++d+ +++ +s++         
  gi|336255558|ref|YP_004598665.1| 126 EDTEAQEAYESMQEDFNRgSRDSGgTTAQLFL-TDDRNAISKPNLVRMLEFQDRIENDD-GLRVASSTspaslvatq 200
                                       68899999999999999886666514555555.77777777799999999999996665.47777777667777777 PP

                              MMPL  71 ...........................ls.........dpdvaaafvSkDgkaaralvtlegdpgsteadesvaair 111
                                                                   +          +d++    S+D   + ++  +  +++++  ++ + + +
  gi|336255558|ref|YP_004598665.1| 201 ldanattaeeqrraierasprqlekaiATadetmglpvSTDFTRESASADVAQIAITYDTPSNADESYHADLIYETE 277
                                       77766666666666666666555555411444444433445777777777766666666667777777778888889 PP

                              MMPL 112 aaveear.pleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalgl 187
                                       ++++e +  +++ ++ v G+++++++++++    + ++  ++l++il+ L+i+yr ++  +l l+  ++s++ ++g+
  gi|336255558|ref|YP_004598665.1| 278 DVANEIDgFDSDDNIVVFGQPVVNDETMQLLGDTAIVVFPAALLLILLFLIIAYRDPIDLALGLAALLMSMIWTFGF 354
                                       9999999989999***************************************************************9 PP

                              MMPL 188 vlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlg 264
                                             ++g+  s++ l+ ++ ll+avG+D+ + ++ Ryree+ ag +  +a+  + ++   + ++ +lt ++ +++
  gi|336255558|ref|YP_004598665.1| 355 ----MGFAGIPFSDSLLT-VFPLLLAVGIDFGIHIINRYREERSAGASIGDAMGITTGQLTTALLIVTLTTVFGFAA 426
                                       ....66789999999887.58899************************99999999999999999999998888887 PP

                              MMPL 265 LvvarlpvlaqvGvaialGvlvdvlivlTllPA 297
                                        +++   + + +G+++a G+ +++li   +lPA
  gi|336255558|ref|YP_004598665.1| 427 NLTS--DMTRDFGIVAAAGISFTFLIFGVFLPA 457
                                       5555..5789****************9999998 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.2
                              MMPL 153 lvvilviLlivyrSlvaa 170
                                       + v++++ ++v+++ vaa
  gi|336255558|ref|YP_004598665.1| 500 IPVVFLVAMLVFGASVAA 517
                                       679999999999999987 PP

  == domain 3  score: 71.5 bits;  conditional E-value: 1.2e-23
                              MMPL  70 f.......................................ls.dpdvaaafvSkDgkaaralvtlegdpgsteades 106
                                       +                                       ++  +d aa+ +  D +a+r+ +++e+   + e++e+
  gi|336255558|ref|YP_004598665.1| 616 LdvideqsaanpefsrtvkrydgdgdeipdrnvdavyddlFAvAEDEAAGRLTTDRSATRIDIQVEA---DAEQAEA 689
                                       23344444444443333333333333333333333333343324448889999*************5...5666777 PP

                              MMPL 107 vaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvslla 183
                                       vaa r++++e      +++  tG+ ++++ + +    ++ +  +v++++ +v+L++ y  l   ++  +  +v +l+
  gi|336255558|ref|YP_004598665.1| 690 VAAAREVADEMN----MDATATGQLVIFESVVEKIGDSAITSLFVAFLLTVVLLVLSYWWLEGRAIYGVINLVPVLL 762
                                       999999999998....8888999999999999888888888888888888888888775554444444444555566 PP

                              MMPL 184 alglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvai 260
                                       a+++++       + ls   +++l+ + i+ G+DY++ L+ R+ +e ++  d +ea+  +v++tg++ t++ lt + 
  gi|336255558|ref|YP_004598665.1| 763 AVAMLAGSMRYFDVPLSPINAPILS-VSIGLGVDYTVHLMHRFVDEYEERGDVDEALLVTVRGTGGALTGSMLTTVC 838
                                       6666555567778899998888876.47999********************************************** PP

                              MMPL 261 amlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvll 302
                                        +  L +a +p + ++G+ +alGv+ + l ++ +lP+++v+ 
  gi|336255558|ref|YP_004598665.1| 839 GLGVLYFALIPLIMEFGLLLALGVFYSWLTSIVVLPSVIVVW 880
                                       ***************************************985 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 ?   -3.5   0.1       1.8   8.3e+03      74      98 ..     304     328 ..     299     332 .. 0.78
   2 !   26.7   2.5     9e-10     4e-06      11     129 ..     339     455 ..     335     470 .. 0.76
   3 !   29.8   0.1     1e-10   4.5e-07       4     137 ..     748     881 ..     745     894 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.8
                                       HHHHHHHHCCCCHHCCCHHHHHHHH CS
                    Sterol-sensing  74 iaealgevgpsilltsltellalll 98 
                                        ++ lg++++ ++  +l  +l++l+
  gi|336255558|ref|YP_004598665.1| 304 TMQLLGDTAIVVFPAALLLILLFLI 328
                                       5788999999999999998888884 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 9e-10
                                       HHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCHHHHHHHHHHHHCCCCHH CS
                    Sterol-sensing  11 agviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrsldeseriaealgevgpsill 87 
                                        g++ +l+s++ ++g++ + g++++   l v+P l+lavg+d    +++ +++  +       i+ a+g +  +++ 
  gi|336255558|ref|YP_004598665.1| 339 LGLAALLMSMIWTFGFMGFAGIPFSDSLLTVFP-LLLAVGIDFGIHIINRYREERSA---GASIGDAMGITTGQLTT 411
                                       4778899**************************.569*****888888877665544...44666666655444443 PP

                                       CC..CHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHH CS
                    Sterol-sensing  88 ts..ltellalllgaltdvpavqeFclfaavavlvdFllqitfF 129
                                        +  +t ++++ ++a  +    + F + aa ++ ++Fl+  +f 
  gi|336255558|ref|YP_004598665.1| 412 ALliVTLTTVFGFAANLTSDMTRDFGIVAAAGISFTFLIFGVFL 455
                                       3300344456667778888889***************9877665 PP

  == domain 3  score: 29.8 bits;  conditional E-value: 1e-10
                                       HHHHHHHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHH.HHTTTCHHHHHHHHHH CS
                    Sterol-sensing   4 skfgLglagviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqr.tsrsldeseriaealg 79 
                                        +++ g+  ++ vll+va+  g + y++++l++i + +l  + +  gvd +  l++ +++  +++ d++e +  +++
  gi|336255558|ref|YP_004598665.1| 748 GRAIYGVINLVPVLLAVAMLAGSMRYFDVPLSPINAPILS-VSIGLGVDYTVHLMHRFVDeYEERGDVDEALLVTVR 823
                                       57788999999*************************6654.6778899*9888877766516666677********* PP

                                       HHCCCCHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHH CS
                    Sterol-sensing  80 evgpsilltsltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldi 137
                                        +g +++ ++lt ++ l + ++  +p + eF l  a++v+ ++l  i++  +v+ +  
  gi|336255558|ref|YP_004598665.1| 824 GTGGALTGSMLTTVCGLGVLYFALIPLIMEFGLLLALGVFYSWLTSIVVLPSVIVVWD 881
                                       ***********************************************99999987655 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   4.8   2.5e-08   0.00011     253     371 ..     333     450 ..     240     467 .. 0.84
   2 !   27.5   4.0   1.9e-10   8.5e-07     618     806 ..     684     877 ..     655     886 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.5e-08
                           Patched 253 kpilailgvlspvlAivsslGlllwlGfrfns.ivtvtPFLvLaiGvD.dmflmvaawkrteaklsvkkrigealse 327
                                        pi  +lg+ + +++++  +G++ + G++f +  +tv P L La+G+D  +++++   ++ +a  s+   +g +  +
  gi|336255558|ref|YP_004598665.1| 333 DPIDLALGLAALLMSMIWTFGFMGFAGIPFSDsLLTVFP-LLLAVGIDfGIHIINRYREERSAGASIGDAMGITTGQ 408
                                       4777889999999*****************852778999.669*****557888888888888899999999999** PP

                           Patched 328 agvaitiTslTdvlsFgiGaittlpaiqlFciytavailfdfiY 371
                                          a++i +lT v+ F++  ++++     F i++a+ i f+f+ 
  gi|336255558|ref|YP_004598665.1| 409 LTTALLIVTLTTVFGFAANLTSDMT--RDFGIVAAAGISFTFLI 450
                                       **********************997..589*********99974 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 1.9e-10
                           Patched 618 tdrtkllkelRsiadkeselnvtvfdedaafadqlltilpstiqnivlall...cmfvvallfipelitvlvitlsi 691
                                       +++++++   R++ad e ++++t   +   f + ++ i  s+i+++ +a+l   +++v +   +    +  vi l+ 
  gi|336255558|ref|YP_004598665.1| 684 AEQAEAVAAAREVAD-EMNMDATATGQLVIFESVVEKIGDSAITSLFVAFLltvVLLVLSYWWLEGRAIYGVINLVP 759
                                       6789999********.7789***************************998611134455555666666666666665 PP

                           Patched 692 vsidig.viGflslWgvdLDpismitiimsiGfsvdlsaHiayafvrsekd..dakeRvvealealgwPvvqgalST 765
                                       v + +  ++G +    v L pi    + +siG  vd++ H  ++fv ++++  d +e +  ++   g  +  + l T
  gi|336255558|ref|YP_004598665.1| 760 VLLAVAmLAGSMRYFDVPLSPINAPILSVSIGLGVDYTVHLMHRFVDEYEErgDVDEALLVTVRGTGGALTGSMLTT 836
                                       555554157***************************************999999**************999999999 PP

                           Patched 766 ilgvlvLlfvdsymvqvFfktvvLvvvigllHgLlilPill 806
                                       + g+ vL+f    ++  F   + L v  + l  +++lP ++
  gi|336255558|ref|YP_004598665.1| 837 VCGLGVLYFALIPLIMEFGLLLALGVFYSWLTSIVVLPSVI 877
                                       98888888877778888999999999999999999999655 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 !   14.6   0.1   4.1e-06     0.018      28     119 ..     200     295 ..     184     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.1e-06
                                       EE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE--..---B-T.TTTCB-THH.H CS
                    UDPG_MGDP_dh_N  28 gvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvifiaV..gTPskk.kgkaaDlky.v 100
                                        +D ++++ ++ ++       ++Le+ +++a e+  l  +td++++ ++adv  ia+   TPs+  +  +aDl y  
  gi|336255558|ref|YP_004598665.1| 200 QLDANATTAEEQRRAIERASPRQLEKAIATADETMGLPVSTDFTRESASADVAQIAItyDTPSNAdESYHADLIYeT 276
                                       56777777777777777778889*****************************98887447***99656678*99956 PP

                                       HHHHHHHHHHHHCEEEEEE CS
                    UDPG_MGDP_dh_N 101 esaarsiaealkkgkvvvv 119
                                       e++a++i  + +++++vv 
  gi|336255558|ref|YP_004598665.1| 277 EDVANEIDGFDSDDNIVVF 295
                                       899****999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (898 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.74u 0.22s 00:00:00.96 Elapsed: 00:00:00.40
# Mc/sec: 6701.34
//
Query:       gi|336255559|ref|YP_004598666.1|  [L=506]
Description: hypothetical protein Halxa_4184 [Halopiger xanaduensis SH-6]
Scores for 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-18   65.2  14.3    0.00016   21.8   0.0    6.0  5  NPCBM_assoc     NPCBM-associated, NEW3 domain of alpha-galact
    2.8e-15   56.4   4.1    6.2e-05   23.2   0.2    4.4  4  CARDB           CARDB
    1.3e-07   31.8  10.5      0.019   15.3   1.8    4.8  4  DUF11           Domain of unknown function DUF11
    0.00079   19.5   5.7        1.8    8.7   0.0    5.7  7  Fn3-like        Fibronectin type III-like domain
    0.00084   18.5   0.0      0.033   13.3   0.0    2.4  3  PHTB1_C         PTHB1 C-terminus
     0.0015   18.6   0.0       0.56   10.4   0.0    3.3  3  Transglut_C     Transglutaminase family, C-terminal ig like d
     0.0017   18.3   0.6        4.7    7.0   0.0    3.8  3  DUF4832         Domain of unknown function (DUF4832)
      0.002   18.0   0.5       0.11   12.3   0.1    3.1  4  FAS_meander     Fatty acid synthase meander beta sheet domain
     0.0043   17.2   5.4        5.2    7.3   0.1    4.4  5  ASH             Abnormal spindle-like microcephaly-assoc'd, A
  ------ inclusion threshold ------
      0.015   15.5   0.5       0.25   11.6   0.0    3.0  3  DUF4625         Domain of unknown function (DUF4625)
      0.025   14.8   0.0      0.055   13.7   0.0    1.5  1  DUF1828         Domain of unknown function DUF1828
       0.16   12.4   0.3        4.4    7.7   0.1    3.3  3  E1_DerP2_DerF2  ML domain
       0.29   11.2   1.4         21    5.2   0.0    3.8  5  DUF916          Bacterial protein of unknown function (DUF916
       0.57   10.3  15.0          2    8.6   2.9    5.4  5  DUF4232         Protein of unknown function (DUF4232)


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   7.5e-06    0.0096      41      79 .]      69     107 ..      21     107 .. 0.88
   2 !   21.4   2.6   1.7e-07   0.00022       1      75 [.     145     224 ..     145     228 .. 0.87
   3 ?   -2.4   0.0       4.6   5.9e+03      40      56 ..     237     253 ..     234     255 .. 0.79
   4 !    9.0   0.0    0.0012       1.6      43      79 .]     303     339 ..     262     339 .. 0.90
   5 !   21.8   0.0   1.3e-07   0.00016       1      75 [.     374     447 ..     374     451 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.5e-06
                       NPCBM_assoc  41 pasaaslapGetveatvkVtppagaaaGdyevtakarlt 79 
                                        + +  ++ G+ ve+  ++ +p++ ++G+yevt+++r++
  gi|336255559|ref|YP_004598666.1|  69 ETPVGPIQDGQMVEVPQRIEVPDDVEPGKYEVTVRVRYS 107
                                       44555899*****************************85 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.7e-07
                       NPCBM_assoc   1 vepGetvtltltvtndgtaaatnvslslslPeGWt...vvevspasaa..slapGetveatvkVtppagaaaGdyev 72 
                                       vepG++ +  l++tn+gt+ a + + ++ +  G t   +++ +pa+ a  +l+pGe++++tv+Vt  ++  aG+ ++
  gi|336255559|ref|YP_004598666.1| 145 VEPGASGEAMLEITNTGTERANETRATIAGGTGITvdgATAEAPAEEAigDLEPGESTTTTVDVTLAESLSAGEKPI 221
                                       689********************************666555555555577*************************99 PP

                       NPCBM_assoc  73 tak 75 
                                       ++ 
  gi|336255559|ref|YP_004598666.1| 222 EVG 224
                                       875 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.6
                       NPCBM_assoc  40 spasaaslapGetveat 56 
                                       +pa++++l pG ++++ 
  gi|336255559|ref|YP_004598666.1| 237 APAEITTLTPGPEQTFS 253
                                       68999999999887765 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0012
                       NPCBM_assoc  43 saaslapGetveatvkVtppagaaaGdyevtakarlt 79 
                                        +++l++Get+++     ++ +a++G +++++++++t
  gi|336255559|ref|YP_004598666.1| 303 ALPALEAGETATFRYPTDVSGQADPGPRQLRFSVEYT 339
                                       4679*****************************9986 PP

  == domain 5  score: 21.8 bits;  conditional E-value: 1.3e-07
                       NPCBM_assoc   1 vepGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtak 75 
                                       v++G+t ++ lt+tn+ +++++n+  +l + +  + ++ + a +++l+pGe+++ t++V++ + aa+ +++v++ 
  gi|336255559|ref|YP_004598666.1| 374 VQQGKTSEFALTITNEREQTLSNIDARLYADSPLS-TNNDEAFVPELEPGESTKITFDVSAESAAATETHPVELD 447
                                       689*********************99999966667.88****************************999999876 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.7e-06    0.0073       2      84 ..      10     104 ..       9     108 .. 0.91
   2 !   10.5   0.1   0.00043      0.55      11      74 ..     141     215 ..     127     229 .. 0.75
   3 ?    4.2   0.0     0.041        52      17      85 ..     263     337 ..     247     344 .. 0.62
   4 !   23.2   0.2   4.9e-08   6.2e-05      14      76 ..     373     440 ..     364     460 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-06
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE............EEEEESEE-CTEEEEEE CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv............gtvtvpsLaagesttvs 66 
                                       p+L v   ++ +e+ +g+en+i++++kN  + ++g+ +  l+++g +v            g+++v +++ g+ ++v 
  gi|336255559|ref|YP_004598666.1|  10 PNLSV--YAPDNEVQPGTENSINLKIKNDAELKAGSNSQMLTANGVTVeledtgpfevksGETPVGPIQDGQMVEVP 84 
                                       77888..88999************************************9*999999999888999**********99 PP

                                       EEEE-S..-S-CEEEEEEEE CS
                             CARDB  67 ftwtte..ategevtltvvv 84 
                                         + ++   ++g++++tv v
  gi|336255559|ref|YP_004598666.1|  85 QRIEVPddVEPGKYEVTVRV 104
                                       88888878999999999976 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00043
                                       C-SEEETTSEEEEEEEEEE-SSS-EEEEEEE......EEETTEEE...EEEEESEE-CTEEEEEEEEEE-S..-S CS
                             CARDB  11 npseafvgeentitvtvkNqGtaasgatkva......lyldgelv...gtvtvpsLaagesttvsftwtte..at 74 
                                         s++++g + +  ++++N+Gt+ + +t+++      +++dg ++   ++  +  L++gestt ++ +t +  ++
  gi|336255559|ref|YP_004598666.1| 141 VKSDVEPGASGEAMLEITNTGTERANETRATiaggtgITVDGATAeapAEEAIGDLEPGESTTTTVDVTLAesLS 215
                                       5667778888888899*********9999761122225677777788888899***********99988775444 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.041
                                       TTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEES CS
                             CARDB  17 vgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtte..ategevtltvvvD 85 
                                       vg e +it +++N G     +  + +    e+     +   +p+L+age++t ++   ++  a +g  +l+++v+
  gi|336255559|ref|YP_004598666.1| 263 VGYEGEITGEIANDGPRPIDDAVLIVEPMSESLyiedTRYALPALEAGETATFRYPTDVSgqADPGPRQLRFSVE 337
                                       555556666666666665443333222222222244334668*******99988766555566777777777765 PP

  == domain 4  score: 23.2 bits;  conditional E-value: 4.9e-08
                                       EEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S..-S-C CS
                             CARDB  14 eafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtte..ateg 76 
                                       ++ +g+++++ +t++N+ +++  ++ ++ly+d  l    +++ vp+L++gest+++f + +e  a++ 
  gi|336255559|ref|YP_004598666.1| 373 TVQQGKTSEFALTITNEREQTLSNIDARLYADSPLStnnDEAFVPELEPGESTKITFDVSAEsaAATE 440
                                       67899***************************97776669999***************9999643332 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.5   4.5e+03      29      33 ..      49      53 ..      18     105 .. 0.65
   2 !   15.3   1.8   1.5e-05     0.019       7      80 ..     142     212 ..     121     218 .. 0.81
   3 ?    2.8   0.0      0.11   1.4e+02      57      83 ..     300     326 ..     255     333 .. 0.75
   4 !   13.7   0.6   4.4e-05     0.056       6      85 ..     370     440 ..     365     445 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.5
                             DUF11 29 sangv 33
                                      +angv
  gi|336255559|ref|YP_004598666.1| 49 TANGV 53
                                      33332 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.5e-05
                             DUF11   7 ksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtr 80 
                                       ks+v pG+  + +l  tNtg+  an+++ t    +g +   ++a    a a+  +g+Le+ges+t ++ v+ + 
  gi|336255559|ref|YP_004598666.1| 142 KSDVEPGASGEAMLEITNTGTERANETRATIAGGTGITVDGATA---EAPAEEAIGDLEPGESTTTTVDVTLAE 212
                                       34799*********************999985555555433333...466666669***********9998765 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.11
                             DUF11  57 altsv..gsLeagesatlsftvrvtrtaa 83 
                                       ++     + Leage+at+++   v+ +a+
  gi|336255559|ref|YP_004598666.1| 300 TR--YalPALEAGETATFRYPTDVSGQAD 326
                                       23..23599**********9988888776 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 4.4e-05
                             DUF11   6 dksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrta 82 
                                       d ++v+ G t ++ lt tN   ++++++  +        y  +  s  t++ +  v++Le+ges++++f v++  +a
  gi|336255559|ref|YP_004598666.1| 370 DGVTVQQGKTSEFALTITNEREQTLSNIDARL-------YADSPLS--TNNDEAFVPELEPGESTKITFDVSAESAA 437
                                       55689999999999999999999998876554.......4444444..666677789****************9999 PP

                             DUF11  83 asg 85 
                                       a++
  gi|336255559|ref|YP_004598666.1| 438 ATE 440
                                       976 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.91   1.2e+03      58      67 ..      93     102 ..      92     128 .. 0.82
   2 ?    0.5   0.0      0.52   6.6e+02      26      53 ..     142     169 ..     141     180 .. 0.82
   3 !    6.1   0.0    0.0094        12      28      46 ..     195     214 ..     192     218 .. 0.83
   4 ?   -1.4   0.0       2.1   2.7e+03      27      48 ..     242     263 ..     240     266 .. 0.83
   5 ?   -2.0   0.0       3.1     4e+03      29      42 ..     307     320 ..     305     323 .. 0.80
   6 ?   -2.2   0.0       3.6   4.6e+03      27      44 ..     372     389 ..     355     399 .. 0.78
   7 !    8.7   0.0    0.0014       1.8      28      51 ..     418     441 ..     416     460 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.91
                                       --SCEEEEEE CS
                          Fn3-like  58 vepGeytvlv 67 
                                       vepG+y+v v
  gi|336255559|ref|YP_004598666.1|  93 VEPGKYEVTV 102
                                       6888888887 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.52
                                       EEEE-TT-EEEEEEEEECGGG-EEETTT CS
                          Fn3-like  26 kveLapGesktvtftldrkdlsvwdeek 53 
                                       k +++pG+s ++ ++++ + +   +e++
  gi|336255559|ref|YP_004598666.1| 142 KSDVEPGASGEAMLEITNTGTERANETR 169
                                       6789************998887777775 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0094
                                       EE-TT-EEEEEEEEEC.GGG CS
                          Fn3-like  28 eLapGesktvtftldr.kdl 46 
                                       +L+pGes+t t++++  ++l
  gi|336255559|ref|YP_004598666.1| 195 DLEPGESTTTTVDVTLaESL 214
                                       59************953555 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.1
                                       EEE-TT-EEEEEEEEECGGG-E CS
                          Fn3-like  27 veLapGesktvtftldrkdlsv 48 
                                       ++L pG ++t +++  ++ lsv
  gi|336255559|ref|YP_004598666.1| 242 TTLTPGPEQTFSIDTLEDTLSV 263
                                       6799*******99987777775 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 3.1
                                       E-TT-EEEEEEEEE CS
                          Fn3-like  29 LapGesktvtftld 42 
                                       L++Ge++t + + d
  gi|336255559|ref|YP_004598666.1| 307 LEAGETATFRYPTD 320
                                       99****99987665 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 3.6
                                       EEE-TT-EEEEEEEEECG CS
                          Fn3-like  27 veLapGesktvtftldrk 44 
                                       v++++G++ +  +t++ +
  gi|336255559|ref|YP_004598666.1| 372 VTVQQGKTSEFALTITNE 389
                                       677888888888888754 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.0014
                                       EE-TT-EEEEEEEEECGGG-EEET CS
                          Fn3-like  28 eLapGesktvtftldrkdlsvwde 51 
                                       eL+pGes+++tf++++++ +  ++
  gi|336255559|ref|YP_004598666.1| 418 ELEPGESTKITFDVSAESAAATET 441
                                       59*************988776555 PP

>> PHTB1_C  PTHB1 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.055        70      30      76 ..     189     235 ..     177     242 .. 0.87
   2 ?   -2.8   0.0       1.9   2.5e+03      21      74 ..     291     344 ..     276     348 .. 0.85
   3 !   13.3   0.0   2.6e-05     0.033       3      78 ..     385     460 ..     383     470 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.055
                           PHTB1_C  30 stfviesldesasteliisvflkgslipaslevevvasYtsktgipr 76 
                                        +  i +l++++st+++++v+l++sl   +  +ev  +Y+ + gi r
  gi|336255559|ref|YP_004598666.1| 189 AEEAIGDLEPGESTTTTVDVTLAESLSAGEKPIEVGFTYRDTAGIER 235
                                       56678999********************************9999988 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                           PHTB1_C  21 vdkplaaskstfviesldesasteliisvflkgslipaslevevvasYtsktgi 74 
                                       ++++l +++ ++ ++ l+++++ +++    ++g++ p   + + ++ Yt ++g+
  gi|336255559|ref|YP_004598666.1| 291 MSESLYIEDTRYALPALEAGETATFRYPTDVSGQADPGPRQLRFSVEYTGPSGE 344
                                       567888999999999**99999999999999******9999999999*999987 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 2.6e-05
                           PHTB1_C   3 kvtlkssttlenvqlsvqvdkplaaskstfviesldesasteliisvflkgslipaslevevvasYtsktgiprvv 78 
                                        +t + ++tl+n+   + +d+pl +++++ + ++l++++st+++++v  + ++      ve    Y++++g+++ +
  gi|336255559|ref|YP_004598666.1| 385 TITNEREQTLSNIDARLYADSPLSTNNDEAFVPELEPGESTKITFDVSAESAAATETHPVELDFEYETESGESKLS 460
                                       57888999*****************************************988888999999999999999998865 PP

>> Transglut_C  Transglutaminase family, C-terminal ig like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.2   5.3e+03      61      74 ..      20      33 ..      18      57 .. 0.75
   2 ?    4.3   0.0     0.034        44      20      78 ..     154     212 ..     140     236 .. 0.73
   3 !   10.4   0.0   0.00043      0.56      12      79 ..     375     436 ..     371     452 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.2
                                      EE-TTEEEEEEEEE CS
                       Transglut_C 61 tLePkeeksvrlki 74
                                      +++P+ e+s+ lki
  gi|336255559|ref|YP_004598666.1| 20 EVQPGTENSINLKI 33
                                      56777777777766 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.034
                                       EEEEEE-SSS-BEEEEEEEEEEE.EECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE-HHS CS
                       Transglut_C  20 svllkNplseelkdvklnlcaqt.veynGvlaaefkkksleltLePkeeksvrlkilpsk 78 
                                        + ++N+ +e+ ++ ++ + + t +  +G + ae + +++ ++LeP+e+ +++++++ ++
  gi|336255559|ref|YP_004598666.1| 154 MLEITNTGTERANETRATIAGGTgITVDGAT-AEAPAEEAIGDLEPGESTTTTVDVTLAE 212
                                       5566676666655555554332225556666.69999*****************998765 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00043
                                       BTTSEEEEEEEEEE-SSS-BEEEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE-HHSH CS
                       Transglut_C  12 vlgqdltvsvllkNplseelkdvklnlcaqtveynGvlaaefkkksleltLePkeeksvrlkilpsky 79 
                                       ++g+  ++ ++++N+ +++l ++ ++l      y+  + + ++ + +  +LeP+e+ +++++++ + +
  gi|336255559|ref|YP_004598666.1| 375 QQGKTSEFALTITNEREQTLSNIDARL------YADSPLSTNNDEAFVPELEPGESTKITFDVSAESA 436
                                       688999999*************77777......66667778899*****************9987665 PP

>> DUF4832  Domain of unknown function (DUF4832)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.1     0.005       6.4     161     199 ..      68     106 ..      13     121 .. 0.62
   2 !    7.0   0.0    0.0037       4.7     113     193 ..     140     221 ..     135     245 .. 0.73
   3 ?   -1.4   0.0       1.3   1.7e+03     167     189 ..     418     440 ..     369     460 .. 0.49

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.005
                           DUF4832 161 ldadprkwlpgttttitiklklpselakGkykvyLnlpd 199
                                        ++ +  ++ g+ +++ + +++p++++ Gky+v ++++ 
  gi|336255559|ref|YP_004598666.1|  68 GETPVGPIQDGQMVEVPQRIEVPDDVEPGKYEVTVRVRY 106
                                       3444455667888889999**************999876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0037
                           DUF4832 113 slskkvkaggtlsleltlkNeGfAalynerkvelvlrdeegee...kyklkldadprkwlpgttttitiklklpsel 186
                                       ++++ v++g + +  l+++N+G  +  ne+++ +      + +   + + ++++ + ++ pg++tt t++++l ++l
  gi|336255559|ref|YP_004598666.1| 140 TVKSDVEPGASGEAMLEITNTGTER-ANETRATIAGGTGIT-VdgaTAEAPAEEAIGDLEPGESTTTTVDVTLAESL 214
                                       4566788999999999999999855.566666665422222.123345678************************** PP

                           DUF4832 187 akGkykv 193
                                       ++G+  +
  gi|336255559|ref|YP_004598666.1| 215 SAGEKPI 221
                                       ***7544 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.3
                           DUF4832 167 kwlpgttttitiklklpselakG 189
                                       ++ pg++t+it +++ +s  a++
  gi|336255559|ref|YP_004598666.1| 418 ELEPGESTKITFDVSAESAAATE 440
                                       33344444444444444433333 PP

>> FAS_meander  Fatty acid synthase meander beta sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.1     4e+03      67      93 ..      87     113 ..      76     130 .. 0.57
   2 ?    1.9   0.0      0.14   1.8e+02      86     116 ..     200     228 ..     153     235 .. 0.73
   3 ?   -0.6   0.0      0.81     1e+03      60     104 ..     349     394 ..     344     405 .. 0.73
   4 !   12.3   0.1   8.5e-05      0.11      72     129 ..     406     464 ..     372     470 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.1
                       FAS_meander  67 vtvkeakesgelkkaveiklsedkeIs 93 
                                       ++v ++ e g+++ +v++++s+ ++Is
  gi|336255559|ref|YP_004598666.1|  87 IEVPDDVEPGKYEVTVRVRYSHWNRIS 113
                                       444444555666666666666666554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.14
                       FAS_meander  86 lsedkeIsvtlieertaegesvpLeleFeYk 116
                                        s +++++vtl e+ +a+++++++ +++  +
  gi|336255559|ref|YP_004598666.1| 200 ESTTTTVDVTLAESLSAGEKPIEVGFTY--R 228
                                       4556789999999999998877766655..4 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.81
                       FAS_meander  60 dspektvvtvkeakes.gelkkaveiklsedkeIsvtlieertaeg 104
                                       d p +++v+v e++++ + +   v+++  +++e ++t+++er+++ 
  gi|336255559|ref|YP_004598666.1| 349 DGPMSERVVVDERQDEfSITDDGVTVQQGKTSEFALTITNEREQTL 394
                                       6667778888776554245567799999999999999999998655 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 8.5e-05
                       FAS_meander  72 akesgelkkav.eiklsedkeIsvtlieertaegesvpLeleFeYkpetglapIhEvme 129
                                       + ++++ ++ v e++  e+++I+ ++  e+ a++e+ p+el+FeY+ e g +++++v +
  gi|336255559|ref|YP_004598666.1| 406 PLSTNNDEAFVpELEPGESTKITFDVSAESAAATETHPVELDFEYETESGESKLSDVYQ 464
                                       333444444444899999*********************************99999977 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.13   1.7e+02      18      47 ..      20      49 ..       6      71 .. 0.58
   2 ?    4.8   0.1     0.025        32      35      78 ..     118     161 ..     101     173 .. 0.70
   3 !    7.3   0.1    0.0041       5.2      18      71 ..     144     205 ..     143     213 .. 0.79
   4 ?   -0.8   0.0       1.4   1.8e+03      44      65 ..     243     264 ..     230     273 .. 0.71
   5 ?    5.7   0.1     0.013        17      18      72 ..     373     429 ..     364     439 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.13
                                      ----EEEEEEE-EEESS-SS--EEEEEEEE CS
                               ASH 18 dvkvGssaerlLtveNpseepaevkvskvp 47
                                      +v+ G+  + +L+++N+ e +a  + + + 
  gi|336255559|ref|YP_004598666.1| 20 EVQPGTENSINLKIKNDAELKAGSNSQMLT 49
                                      355566666666666666555544444444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.025
                                       -SS--EEEEEEEE--XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  35 seepaevkvskvpaaekgfsveetelevqpgesvtltvtwtPte 78 
                                       + e+ + +v+ v+++e +f v++ + +v+pg s   +++ t+t 
  gi|336255559|ref|YP_004598666.1| 118 KTETKKYDVTLVVPDEPRFDVDTVKSDVEPGASGEAMLEITNTG 161
                                       55667888999999999999999999999998766555555544 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0041
                                       ----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX.........XXXXXXXXXXXX CS
                               ASH  18 dvkvGssaerlLtveNpseepaevkvskvpaaekgfsveete.........levqpgesvtlt 71 
                                       dv+ G s e+ L+++N++ e a+ +  +++   +g++v+ ++          +++pges+t t
  gi|336255559|ref|YP_004598666.1| 144 DVEPGASGEAMLEITNTGTERANETRATIA-GGTGITVDGATaeapaeeaiGDLEPGESTTTT 205
                                       7899*****************888888887.99999999888555555666666676666655 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.4
                                       EEEE--XXXXXXXXXXXXXXXX CS
                               ASH  44 skvpaaekgfsveetelevqpg 65 
                                       + +p++e+ fs++++e +++ g
  gi|336255559|ref|YP_004598666.1| 243 TLTPGPEQTFSIDTLEDTLSVG 264
                                       5578888899998888555544 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.013
                                       ----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX...XXXXXXXXXXXXX CS
                               ASH  18 dvkvGssaerlLtveNpseepaevkvskvpaaekgfsveete...levqpgesvtltv 72 
                                       +v+ G++ e  Lt++N  e++++ +  ++  a+  +s +++e    e++pges+ +t+
  gi|336255559|ref|YP_004598666.1| 373 TVQQGKTSEFALTITNEREQTLSNIDARLY-ADSPLSTNNDEafvPELEPGESTKITF 429
                                       57779999999*********9666666776.788888888887788999999998885 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.7   2.2e+03      14      51 ..       9      40 ..       4      49 .. 0.68
   2 ?   11.6   0.0   0.00019      0.25      93     115 ..      82     104 ..      66     116 .. 0.90
   3 ?   -0.4   0.1         1   1.3e+03      61      67 ..     429     435 ..     361     478 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.7
                           DUF4625 14 kPvidllevsaepeeeevlkiGetlhfeaklsdneala 51
                                      kP ++++        +++++ G++ ++++k++ +++l+
  gi|336255559|ref|YP_004598666.1|  9 KPNLSVY------APDNEVQPGTENSINLKIKNDAELK 40
                                      5555555......3455667777777777777777776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00019
                           DUF4625  93 elheeieiPadaeaGdYhlvirv 115
                                       e+ + ie+P+d+e+G+Y++++rv
  gi|336255559|ref|YP_004598666.1|  82 EVPQRIEVPDDVEPGKYEVTVRV 104
                                       67789****************98 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1
                           DUF4625  61 fDhhshs 67 
                                       fD  + s
  gi|336255559|ref|YP_004598666.1| 429 FDVSAES 435
                                       3333333 PP

>> DUF1828  Domain of unknown function DUF1828
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.3e-05     0.055      14      55 ..     356     397 ..     346     410 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
                           DUF1828  14 yvkkkegdeirLtDdGltlmdLsysgidldlskkRkellesi 55 
                                       +v+ +++de+ +tDdG t+++ + s + l ++ +R++ l++i
  gi|336255559|ref|YP_004598666.1| 356 VVVDERQDEFSITDDGVTVQQGKTSEFALTITNEREQTLSNI 397
                                       4556667******************************99998 PP

>> E1_DerP2_DerF2  ML domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0034       4.4      86     118 ..      73     105 ..       5     113 .. 0.65
   2 ?   -0.1   0.0      0.91   1.2e+03      88     115 ..     196     223 ..     135     232 .. 0.72
   3 ?   -1.4   0.0       2.3   2.9e+03      88     115 ..     307     336 ..     243     346 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0034
                                       SSB-TCEEEEEEEEEES-CCCHSCEEEEEEEEE CS
                    E1_DerP2_DerF2  86 CPikageyvtytlslplpselpngkyrvelell 118
                                        Pi+ g+ v+    +++p+ + +gky+v++++ 
  gi|336255559|ref|YP_004598666.1|  73 GPIQDGQMVEVPQRIEVPDDVEPGKYEVTVRVR 105
                                       49******9999999**************9986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.91
                                       B-TCEEEEEEEEEES-CCCHSCEEEEEE CS
                    E1_DerP2_DerF2  88 ikageyvtytlslplpselpngkyrvel 115
                                       +++ge  t+t +++l ++l+ g   +e+
  gi|336255559|ref|YP_004598666.1| 196 LEPGESTTTTVDVTLAESLSAGEKPIEV 223
                                       6788888888888888888887666665 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.3
                                       B-TCEEEEEEEEEES-CCCHSC..EEEEEE CS
                    E1_DerP2_DerF2  88 ikageyvtytlslplpselpng..kyrvel 115
                                       ++age++t+ + ++++ +  +g  ++r ++
  gi|336255559|ref|YP_004598666.1| 307 LEAGETATFRYPTDVSGQADPGprQLRFSV 336
                                       677777777777777777777755455444 PP

>> DUF916  Bacterial protein of unknown function (DUF916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.016        21      22      56 ..      20      51 ..      18     107 .. 0.65
   2 ?   -3.0   0.0       5.7   7.3e+03      23      42 ..     145     164 ..     142     176 .. 0.77
   3 ?   -3.1   0.0         6   7.7e+03      89     105 ..     196     212 ..     191     218 .. 0.70
   4 ?    1.5   0.1      0.23   2.9e+02      22      43 ..     373     394 ..     371     401 .. 0.86
   5 ?   -1.2   0.0       1.6     2e+03      89     103 ..     419     433 ..     402     442 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.016
                            DUF916 22 kvkpgqeqelevkikNssdkeitveitvntAvTnd 56
                                      +v+pg+e+++++kikN+ + +   + ++ tA   +
  gi|336255559|ref|YP_004598666.1| 20 EVQPGTENSINLKIKNDAELKAGSNSQMLTA---N 51
                                      689*************999886666666555...3 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.7
                            DUF916  23 vkpgqeqelevkikNssdke 42 
                                       v+pg++ e  ++i+N+  + 
  gi|336255559|ref|YP_004598666.1| 145 VEPGASGEAMLEITNTGTER 164
                                       78999999999999986554 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 6
                            DUF916  89 lpakesktvklkikmPk 105
                                       l+++es+t ++++++ +
  gi|336255559|ref|YP_004598666.1| 196 LEPGESTTTTVDVTLAE 212
                                       66777777777777655 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.23
                            DUF916  22 kvkpgqeqelevkikNssdkei 43 
                                        v++g+++e+ ++i+N+ ++++
  gi|336255559|ref|YP_004598666.1| 373 TVQQGKTSEFALTITNEREQTL 394
                                       589999**********999875 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 1.6
                            DUF916  89 lpakesktvklkikm 103
                                       l+++es+++++++++
  gi|336255559|ref|YP_004598666.1| 419 LEPGESTKITFDVSA 433
                                       444444444444443 PP

>> DUF4232  Protein of unknown function (DUF4232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.47     6e+02      66     109 ..      20      66 ..       4      85 .. 0.73
   2 ?    8.6   2.9    0.0016         2      65     123 ..     143     206 ..     101     212 .. 0.73
   3 ?   -0.4   0.0      0.95   1.2e+03      55      78 ..     233     255 ..     220     264 .. 0.80
   4 ?   -1.9   0.0       2.6   3.4e+03      67      93 ..     307     334 ..     298     358 .. 0.61
   5 ?    3.8   0.2     0.048        61      59      86 ..     361     393 ..     339     453 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.47
                           DUF4232  66 tLapGesAyaglrwtnaggdgdgecta..aglrvt.ppdgtksvtvp 109
                                        ++pG++ + +l+++n ++  +g   +  ++  vt   ++t +++v+
  gi|336255559|ref|YP_004598666.1|  20 EVQPGTENSINLKIKNDAELKAGSNSQmlTANGVTvELEDTGPFEVK 66 
                                       57899999999999999888888887788777777444888888888 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0016
                           DUF4232  65 vtLapGesAyaglrwtnaggdgdgecta...aglrvtppdgtksvtvp....dlgatgtdvdvgkl 123
                                         ++pG+s  a l++tn+g++ ++e+ a    g  +t +++t+ ++ +    dl+ +  +++++++
  gi|336255559|ref|YP_004598666.1| 143 SDVEPGASGEAMLEITNTGTERANETRAtiaGGTGITVDGATAEAPAEeaigDLEPG--ESTTTTV 206
                                       4689*****************999999999866666666666666666655543333..2223344 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.95
                           DUF4232  55 aeregpaavpvtLapGesAyaglr 78 
                                        ere+pa++  tL pG + ++++ 
  gi|336255559|ref|YP_004598666.1| 233 IEREAPAEI-TTLTPGPEQTFSID 255
                                       578888888.89***988877775 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 2.6
                           DUF4232  67 LapGesAyaglrwtnaggdgdgecta.a 93 
                                       L+ Ge+A++   +   g+ ++g+++   
  gi|336255559|ref|YP_004598666.1| 307 LEAGETATFRYPTDVSGQADPGPRQLrF 334
                                       7788888887655444444444433333 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.048
                           DUF4232  59 gpaavp.....vtLapGesAyaglrwtnaggdg 86 
                                       ++++ +     vt+++G++  ++l++tn ++++
  gi|336255559|ref|YP_004598666.1| 361 RQDEFSitddgVTVQQGKTSEFALTITNEREQT 393
                                       333333556669999999999999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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: 00:00:00.42
# Mc/sec: 3635.13
//
Query:       gi|336255560|ref|YP_004598667.1|  [L=440]
Description: Thioredoxin-disulfide reductase [Halopiger xanaduensis SH-6]
Scores for 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-41  140.8   1.4    6.3e-41  140.5   1.4    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    3.2e-18   65.7   0.0    7.3e-18   64.5   0.0    1.7  1  Glutaredoxin   Glutaredoxin
    5.6e-17   61.9   1.4      2e-15   56.8   0.0    2.5  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    4.3e-15   56.0   2.5      4e-14   52.9   0.5    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00011   21.9   4.3      0.018   14.7   0.0    2.9  4  DAO            FAD dependent oxidoreductase
    0.00026   21.3   0.0    0.00049   20.4   0.0    1.4  1  GST_N_3        Glutathione S-transferase, N-terminal domain
    0.00042   20.7   0.0     0.0079   16.6   0.0    2.5  2  NAD_binding_7  Putative NAD(P)-binding
    0.00058   20.2   0.0     0.0017   18.8   0.0    1.8  1  DUF836         Glutaredoxin-like domain (DUF836)
    0.00078   18.3   0.2        1.3    7.6   0.0    2.9  4  HI0933_like    HI0933-like protein
     0.0043   17.2   1.4      0.011   15.9   0.0    2.4  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0052   15.9   2.2       0.33   10.0   0.0    3.2  3  FAD_binding_2  FAD binding domain
     0.0064   15.9   0.1      0.035   13.4   0.0    2.1  2  FAD_oxidored   FAD dependent oxidoreductase
     0.0094   16.1   0.0      0.021   15.0   0.0    1.6  1  SH3BGR         SH3-binding, glutamic acid-rich protein
  ------ inclusion threshold ------
      0.041   13.9   0.0       0.63   10.1   0.0    2.7  2  Thioredoxin_3  Thioredoxin domain
       0.47   10.4   1.8        1.1    9.3   0.0    2.4  3  NAD_binding_9  FAD-NAD(P)-binding


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 !  140.5   1.4   5.3e-44   6.3e-41       2     294 .]     101     410 ..     100     410 .. 0.88

  Alignments for each domain:
  == domain 1  score: 140.5 bits;  conditional E-value: 5.3e-44
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.........evvkklnqgiel 69 
                                       ++++ G G+ Gl+aa+++++++ + +++  eg  ++g+  l++ +++++++++ +          e+ +++++++++
  gi|336255560|ref|YP_004598667.1| 101 KLIIAGTGISGLTAAIYAGRSNNEPLVI--EGDEPGGQLTLTTDVANYPGFPDGINgselvnnmkEQARQFGADLKN 175
                                       68999***********************..8889**********************996664444333333333332 PP

                                       CHCCT.CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEE CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  70 llgee.vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkri 145
                                             + ++d  ++ + +e +   ++  +++d+++ A+G+s+r+lgipG+ e  g++++t++++++      +  +
  gi|336255560|ref|YP_004598667.1| 176 ----GiIESVDDSQRPFRVE-L--TNGDVYTADAVIAASGASARTLGIPGEDELMGYGLSTCATCDGAFFRGED--M 243
                                       ....2245666666677773.3..45569***************************************998887..* PP

                                       EEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE....EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx RF
                       Pyr_redox_2 146 vvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge....klev 218
                                       +vvGgG  ++E A +l+k+++ v++ ++r+++    ++ + ++++e++e+ ++e++ +t+ +ei g +e    ++++
  gi|336255560|ref|YP_004598667.1| 244 LVVGGGDAAMEEATFLTKFADTVYIAHRREEFR--AEDYWVDRVHEKVEEGDIEIMKNTELVEIHGSQEegvdHVTL 318
                                       ********************************8..8899******************************98866667 PP

                                       EETTSCE..............EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.....BESSTTEEE-GG CS
                                       xxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxx RF
                       Pyr_redox_2 219 vledgee..............idadlvvvavGvrpstelleeklglelderggivvdefl.....rtnvpgiyaiGD 276
                                       v +d+                +d+  v++a+G +p+t+ l e+ g++ld++g++++         +t vpgi+ +GD
  gi|336255560|ref|YP_004598667.1| 319 VQNDKGHptdrlddpeteefdFDVGAVFYAIGHTPNTSYL-EDTGVKLDDDGYLETQGGTgggqtETHVPGIFGAGD 394
                                       888887789*******************************.*************99987778866778********* PP

                                       GCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 277 vaggkggpelaqaAvqqG 294
                                       v+  ++ +++a++A  +G
  gi|336255560|ref|YP_004598667.1| 395 VV--DYHYQQAVTAAGMG 410
                                       **..9*********9987 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   6.1e-21   7.3e-18       1      60 []       7      67 ..       7      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 6.1e-21
                                      EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHH.TSSSSSEEEETTEEE CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkels.gvrtvPqvfidgkhv 60
                                      v+++tk  CpyC kak+l++++g+++e+++v+ d+++ ee+ e++ g++t P vfid++++
  gi|336255560|ref|YP_004598667.1|  7 VEIYTKEDCPYCEKAKDLFDSKGIEYETYNVTGDDDLFEEMVERAdGRKTAPEVFIDDELI 67
                                      89********************************************************987 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 ?    3.4   0.3     0.031        37       1      33 [.     103     134 ..     103     139 .. 0.88
   2 !   56.8   0.0   1.7e-18     2e-15     103     305 .]     177     393 ..     151     393 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.031
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnig 33 
                                       iI G G  Gl+aai + +++  + l++E ++ g
  gi|336255560|ref|YP_004598667.1| 103 IIAGTGISGLTAAIYAGRSNN-EPLVIEGDEPG 134
                                       899*****************9.579***88765 PP

  == domain 2  score: 56.8 bits;  conditional E-value: 1.7e-18
                       Pyr_redox_3 103 eVesvkkedegfevetske.tyeAkkviiAtGefdkPnklnipGeek...lvkhyskvkefhkyagqkvvViGgknS 175
                                        +esv+ +++ f+ve +++ +y+A+ vi A G     ++l+ipGe++   +   +    + + ++g++++V+Gg++ 
  gi|336255560|ref|YP_004598667.1| 177 IIESVDDSQRPFRVELTNGdVYTADAVIAASGA--SARTLGIPGEDElmgYGLSTCATCDGAFFRGEDMLVVGGGDA 251
                                       4899**********966655************9..99*********6433344444555667799************ PP

                       Pyr_redox_3 176 avDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeee.....ykv 247
                                       a++ A+ l +   +V +++r++e ++e+    y++      r++e v+e+ i++++n+e+ ei+ ++ee       v
  gi|336255560|ref|YP_004598667.1| 252 AMEEATFLTKFADTVYIAHRREEFRAED----YWVD-----RVHEKVEEGDIEIMKNTELVEIHGSQEEgvdhvTLV 319
                                       **********************999986....4443.....333334444455555555555543222111110223 PP

                       Pyr_redox_3 248 ktedgkkvev............kddvvlatGykpdlsflkkslfeldedgrpvlte....eteetnvpglflaG 305
                                       + ++g+ ++                v++a+G +p++s l++ +++ld+dg+ + +      + et vpg+f aG
  gi|336255560|ref|YP_004598667.1| 320 QNDKGHPTDRlddpeteefdfdVGAVFYAIGHTPNTSYLEDTGVKLDDDGYLETQGgtggGQTETHVPGIFGAG 393
                                       33333333333333333333333457888**********************999872233468********998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.23   2.8e+02       1      29 [.     101     129 ..     101     137 .. 0.85
   2 !   52.9   0.5   3.4e-17     4e-14       2      78 ..     243     318 ..     242     323 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.23
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvve 29 
                                       k+++ G G +gl +A ++ + +++  v+e
  gi|336255560|ref|YP_004598667.1| 101 KLIIAGTGISGLTAAIYAGRSNNEPLVIE 129
                                       689************99988888777776 PP

  == domain 2  score: 52.9 bits;  conditional E-value: 3.4e-17
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.vesvk 77 
                                       ++vvGgG+ ++E+A++l+++++ V++ +r+++++   ++   ++++ek+e+  ie++ nt+++ei+gs+++ v +v+
  gi|336255560|ref|YP_004598667.1| 243 MLVVGGGDAAMEEATFLTKFADTVYIAHRREEFR--AEDYWVDRVHEKVEEGDIEIMKNTELVEIHGSQEEgVDHVT 317
                                       69********************************..8889999999999999******************99**999 PP

                                       E CS
                         Pyr_redox  78 l 78 
                                       l
  gi|336255560|ref|YP_004598667.1| 318 L 318
                                       8 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.3    0.0021       2.5       2      35 ..     102     135 ..     101     142 .. 0.86
   2 !   14.7   0.0   1.5e-05     0.018     138     206 ..     150     214 ..     140     233 .. 0.80
   3 ?   -2.4   0.0       2.3   2.8e+03     153     184 ..     286     319 ..     280     331 .. 0.67
   4 ?   -3.6   0.0       5.4   6.4e+03     192     206 ..     399     414 ..     380     423 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0021
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35 
                                       ++i G Gi Gl++A ++ r +   +++e + ++g g
  gi|336255560|ref|YP_004598667.1| 102 LIIAGTGISGLTAAIYAGRSNnePLVIEGD-EPG-G 135
                                       6899*************776579*****99.888.5 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.5e-05
                                       TTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.H CS
                               DAO 138 pdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd.l 206
                                       pd g+ +  +l++ + ++a++ G+++ +g  ++++++ + +  +v + t+g + +adav+ a Ga ++ l
  gi|336255560|ref|YP_004598667.1| 150 PD-GI-NGSELVNNMKEQARQFGADLKNG-IIESVDD-SQRPFRV-ELTNGDVYTADAVIAASGASARtL 214
                                       55.55.9999*******************.8888844.4678999.5666888567**********9843 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.3
                                       HHHHHHTT-EEEESECEEEE..EEEETCEEEEE.E CS
                               DAO 153 araaealGveilegtevtgl..eeedgkvwgve.r 184
                                        +++e++ +ei ++te +++  + ++++v +v  +
  gi|336255560|ref|YP_004598667.1| 286 HEKVEEGDIEIMKNTELVEIhgS-QEEGVDHVTlV 319
                                       57788899999999999998321.33455665442 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 5.4
                                       EEEEEEE--GGGHH.H CS
                               DAO 192 aadavVnaaGawsd.l 206
                                       ++++ V aaG +s+  
  gi|336255560|ref|YP_004598667.1| 399 HYQQAVTAAGMGSKaA 414
                                       5688999999998733 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.1e-07   0.00049       2      53 ..      10      63 ..       9      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.1e-07
                                      ES-TTSHHHHHHHHHHHHHT--EEEE---TTTT.HHHH.HHH-TT--SSEEETT CS
                           GST_N_3  2 ygfpaSpyarrvrlaLnekglpvevvevtpgeh.deel.laknplgkvPvLedd 53
                                      y  +++py+ +++ + + kg+++e+++vt+++  +ee+  + ++++++P   +d
  gi|336255560|ref|YP_004598667.1| 10 YTKEDCPYCEKAKDLFDSKGIEYETYNVTGDDDlFEEMvERADGRKTAPEVFID 63
                                      8899*************************9999888883555599999965433 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 ?    1.0   0.0      0.48   5.8e+02      46      91 ..      84     129 ..       3     136 .. 0.72
   2 !   16.6   0.0   6.6e-06    0.0079       5     100 ..     238     338 ..     237     344 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.48
                     NAD_binding_7  46 elvklaeeelekdlegadlviaatddrelneriaeaakarrilvnv 91 
                                       e++ +a+++ ++ +e  +l+ia t    l ++i++   +++ lv  
  gi|336255560|ref|YP_004598667.1|  84 EKLGIADDNEDEIVEHRKLIIAGTGISGLTAAIYAGRSNNEPLVIE 129
                                       3333334444455888899999999999999999888777766655 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 6.6e-06
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvkl..aeeel.ekd...legadlviaatddreln 75 
                                       ++g+ +lvvGgG+ A++ +  l ++ a+ + +a + +e+  e + +    e++ e+d   +++++lv +  +++e  
  gi|336255560|ref|YP_004598667.1| 238 FRGEDMLVVGGGDAAMEEATFLTKF-ADTVYIAHRREEFRAEDYWVdrVHEKVeEGDieiMKNTELVEIHGSQEEGV 313
                                       68999********************.888888888655555433321134444334434466788999988888888 PP

                     NAD_binding_7  76 eriaeaakarrilvnvadkpelcdf 100
                                       +++     +++ +  + d+pe  +f
  gi|336255560|ref|YP_004598667.1| 314 DHVTLVQNDKGHPTDRLDDPETEEF 338
                                       8888888888888888888887766 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.4e-06    0.0017       2      46 ..       7      47 ..       6      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                                      EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CCCHCCC CS
                            DUF836  2 ltLyskpgChlCeqakekLkelkleegleleviDIakdeeleakY 46
                                      + +y+k+ C+ Ce+ak++       +g+e e+ ++++d++l++++
  gi|336255560|ref|YP_004598667.1|  7 VEIYTKEDCPYCEKAKDLFD----SKGIEYETYNVTGDDDLFEEM 47
                                      789****************9....5678899*********99976 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0014       1.6       2      33 ..     101     132 ..     100     141 .. 0.87
   2 !    7.6   0.0    0.0011       1.3     102     171 ..     149     215 ..     147     221 .. 0.77
   3 ?   -3.0   0.0       1.9   2.2e+03       2      21 ..     242     261 ..     241     273 .. 0.73
   4 ?   -2.7   0.0       1.5   1.8e+03     374     387 ..     385     398 ..     383     399 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0014
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekak 33 
                                       ++i+ G G +Gl aAi a++ +++ l++e  +
  gi|336255560|ref|YP_004598667.1| 101 KLIIAGTGISGLTAAIYAGRSNNEPLVIEGDE 132
                                       689*************************9764 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0011
                                       EETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGGT CS
                       HI0933_like 102 FpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPklG 171
                                       Fp+  + +++v+ +++++++ g +l+    ++sv+  +++ frv++++++ ++ad+++ A  G+S+ +lG
  gi|336255560|ref|YP_004598667.1| 149 FPDGINGSELVNNMKEQARQFGADLKNG-IIESVDD-SQRPFRVELTNGDVYTADAVIAA-SGASARTLG 215
                                       8888999999**********99999865.5888955.5566*****66666666665555.777777777 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.9
                                       SEEEE--SHHHHHHHHHHHH CS
                       HI0933_like   2 dviviGgGaAGlmaAisaak 21 
                                       d++v+GgG A +  A  + k
  gi|336255560|ref|YP_004598667.1| 242 DMLVVGGGDAAMEEATFLTK 261
                                       789*****998877766655 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.5
                                       TSTTEEE-GGGBSE CS
                       HI0933_like 374 kvpgLffaGEvlDv 387
                                        vpg+f aG v+D 
  gi|336255560|ref|YP_004598667.1| 385 HVPGIFGAGDVVDY 398
                                       69**********96 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 !   15.9   0.0   9.3e-06     0.011       1      36 [.     104     138 ..     104     156 .. 0.88
   2 ?   -2.1   0.0       3.8   4.6e+03       1      17 [.     245     261 ..     245     267 .. 0.81
   3 ?   -3.2   0.1       8.6     1e+04      26      47 ..     372     398 ..     371     402 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.3e-06
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36 
                                       I G+G+sGl+aA ++ + + + l++e +d +GG+++
  gi|336255560|ref|YP_004598667.1| 104 IAGTGISGLTAAIYAGRSNNEPLVIE-GDEPGGQLT 138
                                       67***********************7.689**9987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.8
                                       EE--SHHHHHHHHHHHC CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLak 17 
                                       +vG+G +++  A +L+k
  gi|336255560|ref|YP_004598667.1| 245 VVGGGDAAMEEATFLTK 261
                                       89***998877777765 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 8.6
                                       -SSSSSSGGG-EECETT.....CEECT CS
                     NAD_binding_8  26 ekrdrlGGraasyevpg.....vrvdy 47 
                                       e++ ++GG  +  +vpg      +vdy
  gi|336255560|ref|YP_004598667.1| 372 ETQGGTGGGQTETHVPGifgagDVVDY 398
                                       667777765555555554434466665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00028      0.33       2      38 ..     102     137 ..     101     151 .. 0.88
   2 ?    1.8   0.0     0.083        99       1      35 [.     242     276 ..     242     283 .. 0.85
   3 ?    1.8   0.5     0.085     1e+02     358     414 ..     344     408 ..     304     411 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00028
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38 
                                       +i+ G+G++GL+AA+ a + + + +v+e  ++ gg++
  gi|336255560|ref|YP_004598667.1| 102 LIIAGTGISGLTAAIYAGRSNNEPLVIEGDEP-GGQL 137
                                       69***************999999999999998.6655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.083
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35 
                                       D +V+G+G A +  A+ +++   +v +    +ef+
  gi|336255560|ref|YP_004598667.1| 242 DMLVVGGGDAAMEEATFLTKFADTVYIAHRREEFR 276
                                       89***********9999999888888887777776 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.085
                                       .......EEEEEEEES.-EEEBETTSBE.......STTEEESSBTEEE-STCEESSSSTTS--TT CS
                     FAD_binding_2 358 gpfyavkvvpaqhytm.gGvetdengrv.......ldadgqpipGLYAaGevaaggvhganrlgG 414
                                       + fya+  +p + y    Gv+ d++g          +++++++pG + aG v   +++ a   +G
  gi|336255560|ref|YP_004598667.1| 344 AVFYAIGHTPNTSYLEdTGVKLDDDGYLetqggtgGGQTETHVPGIFGAGDVVDYHYQQAVTAAG 408
                                       55777777777766532688888877666677777788899***********9877777666555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0     3e-05     0.035       2      50 ..     102     146 ..     101     193 .. 0.79
   2 ?   -0.2   0.0      0.42     5e+02      93     129 ..     285     322 ..     258     328 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignk 50 
                                       +++ G g++G++AAi A r+  + l++e  +  GG+lt   ++td+ n+
  gi|336255560|ref|YP_004598667.1| 102 LIIAGTGISGLTAAIYAGRSNNEPLVIE-GDEPGGQLT---LTTDVANY 146
                                       689*******************998886.7889***99...44555555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.42
                      FAD_oxidored  93 leemlaeagvtvllntrlveveke.gkriesvtveske 129
                                       ++e ++e +++++ nt+lve++ + ++ +++vt+ +++
  gi|336255560|ref|YP_004598667.1| 285 VHEKVEEGDIEIMKNTELVEIHGSqEEGVDHVTLVQND 322
                                       45667899************999724569999998766 PP

>> SH3BGR  SH3-binding, glutamic acid-rich protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.8e-05     0.021      26      96 ..      24      86 ..      18      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                                      HHHHTT--EEEEETTT-HHHHHHHHHCST-CCCS-SSSS--S-EEEETTEEEEEHHHHHHHHTTT-HHHHH CS
                            SH3BGR 26 iLdakkiefdevDitkdeeerelmrenaapeekkpengkplPPqifnedeYcGDydaffeakeentleefL 96
                                      + d+k ie+++ ++t d++  e+m e+a        +g+ + P +f +de +G +d+    +e+  l e L
  gi|336255560|ref|YP_004598667.1| 24 LFDSKGIEYETYNVTGDDDLFEEMVERA--------DGRKTAPEVFIDDELIGGWDDTSALEETGELDEKL 86
                                      78***********************999........5788899*************988888877776666 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00053      0.63       3      59 ..       7      66 ..       5      68 .. 0.64
   2 ?    0.1   0.0      0.72   8.6e+02       8      42 ..     228     262 ..     226     267 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00053
                                      EEE.ESSSSTTCHHHHHHHHHHCHCCTCECEEECCTTHHHHHHCT-SS......SSEEECTTCE CS
                     Thioredoxin_3  3 ikv.lgpgCakCpklekavkeaaaekgikaevekvtdfeeiekygVms......vPalvidgkv 59
                                      +++  +  C++C+k++ +     ++kgi++e ++vt  +++ +  V++       P ++id+++
  gi|336255560|ref|YP_004598667.1|  7 VEIyTKEDCPYCEKAKDL----FDSKGIEYETYNVTGDDDLFEEMVERadgrktAPEVFIDDEL 66
                                      78944555*****76655....567888888888876666644445432222226888888876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.72
                                       SSSTTCHHHHHHHHHHCHCCTCECEEECCTTHHHH CS
                     Thioredoxin_3   8 pgCakCpklekavkeaaaekgikaevekvtdfeei 42 
                                       ++Ca+C+ +    + ++   g +a +e++t + ++
  gi|336255560|ref|YP_004598667.1| 228 STCATCDGAFFRGEDMLVVGGGDAAMEEATFLTKF 262
                                       57****98888888888888899999988877776 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   0.1       1.5   1.8e+03       2      19 ..     104     121 ..     103     137 .. 0.77
   2 ?    9.3   0.0    0.0009       1.1     115     154 ..     169     208 ..     156     210 .. 0.81
   3 ?   -2.5   0.0       3.8   4.5e+03      89     151 ..     257     318 ..     249     325 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.5
                     NAD_binding_9   2 ivGaGprGlavlerLlar 19 
                                       i G G++Gl+++    ++
  gi|336255560|ref|YP_004598667.1| 104 IAGTGISGLTAAIYAGRS 121
                                       88*******999766555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0009
                     NAD_binding_9 115 vtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                       +  ++ ++ +++++++++ ++v l++g+ ++adaV+ A G
  gi|336255560|ref|YP_004598667.1| 169 FGADLKNGIIESVDDSQRPFRVELTNGDVYTADAVIAASG 208
                                       5566677788999999999*******************99 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.8
                     NAD_binding_9  89 dfvpRalyGrYlrdlfeellarlpegvtvevhraevv..dleeradgqavlladgaslaadaVvL 151
                                       +f+++     Y++++ ee+ a+   +  v+ ++++v+  d+e  +++  v  ++ ++  +d+V L
  gi|336255560|ref|YP_004598667.1| 257 TFLTKFADTVYIAHRREEFRAE---DYWVDRVHEKVEegDIEIMKNTELVEIHGSQEEGVDHVTL 318
                                       5555555556666666666533...3445666666664445555555556666666667777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3011.29
//
Query:       gi|336255561|ref|YP_004598668.1|  [L=445]
Description: hypothetical protein Halxa_4187 [Halopiger xanaduensis SH-6]
Scores for 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-25   89.3  21.3    2.4e-25   89.3  21.3    2.4  3  DUF389    Domain of unknown function (DUF389)


Domain annotation for each model (and alignments):
>> DUF389  Domain of unknown function (DUF389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.41   7.3e+03      73      84 ..     127     138 ..     105     150 .. 0.55
   2 !   89.3  21.3   1.3e-29   2.4e-25       1     140 [.     152     294 ..     152     296 .. 0.94
   3 ?    1.5   0.0     0.015   2.7e+02      13      60 ..     312     357 ..     311     376 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.41
                            DUF389  73 lvdllvAlasGa 84 
                                       ++ +l Al++ a
  gi|336255561|ref|YP_004598668.1| 127 AMTVLSALVATA 138
                                       333333333333 PP

  == domain 2  score: 89.3 bits;  conditional E-value: 1.3e-29
                            DUF389   1 MlisPlmgpilaiafglvigdrkllrrglknlliglllallvgflfglllplk..vlg.eeelptsemlsrtepnlv 74 
                                       M+i+P ++ +l  ++glv+ drk++  gl++l+ gl++a++ +f+f++l++ +  v +  + +   ++++r++p  +
  gi|336255561|ref|YP_004598668.1| 152 MVIAPQVSAALTGTVGLVLDDRKMVVDGLFALVSGLVVAIAGAFAFAWLIRSGgfVPStIDITAIVQVQNRISPGPL 228
                                       ***********************************************9986666744446667779*********** PP

                            DUF389  75 dllvAlasGaagalallsgnssslvGvaIaaaLlPPavnaGlglalgewalalgslllllvNivgI 140
                                        ++v +++Gaaga+ l+++   slvGv+Ia+aL+P+a+++G+gla+g+ ++alg++ l++vN   I
  gi|336255561|ref|YP_004598668.1| 229 AIVVGICAGAAGAFGLATAIPVSLVGVMIAVALMPAAAAVGIGLAWGNASVALGAATLVAVNATSI 294
                                       **************************************************************9988 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.015
                            DUF389  13 iafglvigdrkllrrglknlliglllallvgflfglllplkvlgeeel 60 
                                       ++ g+++g+ +  r++ +++++ + l +l g+ f+l ++++   ++++
  gi|336255561|ref|YP_004598668.1| 312 WTPGTIRGNVSGGRMSTLAVVLTCGLLVLAGAGFVLGTHVS--FQSDV 357
                                       56678888888888888888888888888777777444443..12233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3315.18
//
Query:       gi|336255562|ref|YP_004598669.1|  [L=95]
Description: hypothetical protein Halxa_4188 [Halopiger xanaduensis SH-6]
Scores for complete 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  111.5   0.3    1.7e-32  111.3   0.3    1.1  1  DUF357    Protein of unknown function (DUF357)
  ------ inclusion threshold ------
      0.081   12.1   0.0      0.098   11.8   0.0    1.1  1  Cas_Cas1  CRISPR associated protein Cas1


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 !  111.3   0.3   1.8e-36   1.7e-32       1      73 []      11      83 ..      11      83 .. 0.99

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 1.8e-36
                                      HHHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTSTS CS
                            DUF357  1 rYirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgll 73
                                      rY +ll+eal++++iap+e++p+ eaa e++emaesYleD+++f++++d+vnAlasfsY+++wLDagar+gl+
  gi|336255562|ref|YP_004598669.1| 11 RYGELLAEALAEATIAPPEGTPMAEAAAECYEMAESYLEDGRHFRDHDDPVNALASFSYGHAWLDAGARVGLF 83
                                      8**********************************************************************98 PP

>> Cas_Cas1  CRISPR associated protein Cas1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.1e-05     0.098     176     197 ..      49      70 ..      34      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                                       -SS-SSSS-SSHHHHHHHHHHH CS
                          Cas_Cas1 176 fegRsrrppkDpvNalLsfgYt 197
                                        +gR  r ++DpvNal sf Y+
  gi|336255562|ref|YP_004598669.1|  49 EDGRHFRDHDDPVNALASFSYG 70 
                                       579******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 778.14
//
Query:       gi|336255563|ref|YP_004598670.1|  [L=245]
Description: 5-carboxymethyl-2-hydroxymuconate delta-isomerase [Halopiger xanaduensis SH-6]
Scores for 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-67  226.3   0.0      4e-67  226.1   0.0    1.0  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
  ------ inclusion threshold ------
      0.014   16.3   0.8      0.045   14.7   0.1    2.4  2  DUF2437        Domain of unknown function (DUF2437)


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.1   0.0   4.5e-71     4e-67       1     218 []      47     243 ..      47     243 .. 0.97

  Alignments for each domain:
  == domain 1  score: 226.1 bits;  conditional E-value: 4.5e-71
                                       .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T-- CS
                     FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevls 77 
                                       kivc+g+nya+h+ e+g   +++pd     +p +flk+++++  +gd+i++Pag e++dyE+EL+vvig ++r+v +
  gi|336255563|ref|YP_004598670.1|  47 KIVCIGRNYADHADEMG---NDVPD-----RPLLFLKPPNAVASHGDTITAPAGKERIDYEAELGVVIGEQCRHV-P 114
                                       69**************8...89999.....777******************************************.9 PP

                                       HHHHHTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGG CS
                     FAA_hydrolase  78 veeAedaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntk 154
                                       v++A+d++ G+t +nD+s Rd q++e+   +w++gk+fd+++p+Gp++ tpde++  ed +++ rvng+ +qd++ +
  gi|336255563|ref|YP_004598670.1| 115 VSDAMDVVEGFTCVNDISNRDDQEKEQ---NWVRGKAFDGAAPLGPVLATPDEVP--EDASVQSRVNGDLRQDGTRE 186
                                       ***************************...9***********************6..69****************** PP

                                       GTTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE. CS
                     FAA_hydrolase 155 dmifspaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrVa 218
                                       ++if+++elia+++  ltLepGd+i+tGTp+gvg        l+dgD+ve+e+eg+G+l+n+V+
  gi|336255563|ref|YP_004598670.1| 187 QLIFPISELIAEITTYLTLEPGDVIATGTPEGVG-------PLEDGDTVEIEVEGVGTLENTVR 243
                                       ********************************98.......5********************96 PP

>> DUF2437  Domain of unknown function (DUF2437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1     5e-06     0.045       1      23 [.       1      24 [.       1      40 [. 0.90
   2 ?   -3.4   0.1         2   1.8e+04      26      37 ..     150     162 ..     145     166 .. 0.47

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5e-06
                                      -EEEEE.EETTEEEEEEEE.EEEE CS
                           DUF2437  1 MriaRF.shgggpryGvlegdtvv 23
                                      M+++RF +  g +r G le+d+v+
  gi|336255563|ref|YP_004598670.1|  1 MKYVRFrDPAGAVRRGRLEDDRVR 24
                                      ******66677**********997 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2
                                       SS-.TTSS-EEEE CS
                           DUF2437  26 agd.pfgavqpTG 37 
                                       +g+ p+g+v  T 
  gi|336255563|ref|YP_004598670.1| 150 DGAaPLGPVLATP 162
                                       3432445554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2035.02
//
Query:       gi|336255564|ref|YP_004598671.1|  [L=44]
Description: hypothetical protein Halxa_4190 [Halopiger xanaduensis SH-6]
Scores for 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   12.5   0.1       0.19   11.8   0.1    1.3  1  HHH_2     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.1e-05      0.19      20      39 ..       2      21 ..       1      24 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                             HHH_2 20 akrFksldaLkkasleeLle 39
                                      +++F+ +++L++a+ eeLle
  gi|336255564|ref|YP_004598671.1|  2 CHHFRPVEELSEAEREELLE 21
                                      79****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 376.18
//
Query:       gi|336255565|ref|YP_004598672.1|  [L=246]
Description: TOBE domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   51.2   3.8    2.8e-13   49.9   0.3    3.1  3  TOBE      TOBE domain
    1.7e-07   31.1   0.2    6.8e-07   29.1   0.1    2.1  2  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR


Domain annotation for each model (and alignments):
>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.23   2.1e+03      18      18 ..     116     116 ..     100     143 .. 0.48
   2 ?   -1.5   0.0      0.37   3.3e+03      11      28 ..     128     146 ..     126     151 .. 0.67
   3 !   49.9   0.3   3.2e-17   2.8e-13       1      61 [.     162     234 ..     162     237 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.23
                              TOBE  18 g 18 
                                       g
  gi|336255565|ref|YP_004598672.1| 116 G 116
                                       2 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.37
                              TOBE  11 Vvvveplg.seveVrvdlg 28 
                                       +v++ p g s+v+++v+ +
  gi|336255565|ref|YP_004598672.1| 128 IVALAPEGaSDVQLTVRSD 146
                                       5566666778888888765 PP

  == domain 3  score: 49.9 bits;  conditional E-value: 3.2e-17
                              TOBE   1 ssarNqlpgtVvvveplgseveVrvdlggga............tLtArvtrrsaeeLgLapGeeVfalikaak 61 
                                       +s rNq++gtV ++ep+++ ++V++dl+g+a             L A vt +s+++L+L+pG  ++a++ka++
  gi|336255565|ref|YP_004598672.1| 162 TSLRNQFRGTVARLEPGDAISRVTIDLEGEAgdsagepdpsepVLEALVTNASVDRLALEPGRAITASFKATA 234
                                       688***************************************99***************************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 !   29.1   0.1   7.6e-11   6.8e-07       2      59 ..      21      82 ..      20      83 .. 0.85
   2 ?   -1.9   0.0      0.37   3.3e+03      41      57 ..     137     152 ..     134     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 7.6e-11
                                      HHHHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEE....SSSE...EEE-HHH CS
                             HTH_1  2 rqlrlfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfeR....tgrg...lrLTeaG 59
                                      r+++ ++a+ + gs+ rAA+eLg s++ +  ++ + E ++g+ + eR    +  g   ++LTe +
  gi|336255565|ref|YP_004598672.1| 21 RDIEMLDAIERYGSMHRAADELGRSYARLQNRVVEIEGAVGQ-ITERkrggS--GgggTELTETA 82
                                      789**************************************6.788844442..14469999987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.37
                                       HTS-SEEESSSEEEE-H CS
                             HTH_1  41 lgvpLfeRtgrglrLTe 57 
                                        +v+L +R +  ++LT+
  gi|336255565|ref|YP_004598672.1| 137 SDVQLTVR-SDAVVLTD 152
                                       57899999.66799997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1937.65
//
Query:       gi|336255566|ref|YP_004598673.1|  [L=255]
Description: phosphate-transporting ATPase [Halopiger xanaduensis SH-6]
Scores for 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-33  115.7   0.0      3e-33  115.3   0.0    1.2  1  ABC_tran     ABC transporter
    5.5e-11   42.8   0.0    7.4e-05   22.7   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    4.4e-06   27.2   0.3    1.2e-05   25.8   0.3    1.8  1  AAA_16       AAA ATPase domain
    7.7e-06   25.6   0.0    0.00044   19.9   0.0    2.3  2  AAA_29       P-loop containing region of AAA domain
    0.00011   21.8   0.1      0.019   14.4   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00039   20.3   0.0    0.00092   19.1   0.0    1.5  2  RsgA_GTPase  RsgA GTPase
    0.00083   19.6   0.0     0.0016   18.7   0.0    1.7  1  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.021   14.4   0.0      0.037   13.6   0.0    1.5  1  AAA_25       AAA domain
      0.031   14.4   0.0       0.08   13.0   0.0    1.7  2  MMR_HSR1     50S ribosome-binding GTPase
      0.035   14.7   0.0      0.074   13.6   0.0    1.6  1  AAA_18       AAA domain
      0.035   14.4   0.0       0.13   12.5   0.0    2.0  2  AAA_28       AAA domain
      0.037   14.2   0.4       0.94    9.8   0.4    2.4  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.062   13.5   0.0       0.15   12.2   0.0    1.6  1  AAA_33       AAA domain
      0.081   12.6   0.0       0.14   11.9   0.0    1.5  2  AAA_15       AAA ATPase domain
      0.082   13.4   0.0       0.13   12.8   0.0    1.2  1  AAA_23       AAA domain
       0.15   12.0   0.0       0.26   11.2   0.0    1.4  1  NACHT        NACHT domain
        0.2   11.4   0.0       0.28   10.9   0.0    1.3  1  AAA_24       AAA domain
        0.2   10.8   0.0       0.39    9.8   0.0    1.4  2  NB-ARC       NB-ARC domain
       0.22   11.4   0.0       0.34   10.8   0.0    1.2  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 !  115.3   0.0   3.1e-36     3e-33       2     137 .]      19     178 ..      18     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 3.1e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqepqlfpelt 75 
                                       ++vsl++ +ge+v i+G++G GKStLl+lla   +p+ G++++ g d+ +   q++ ++r++ig+++qe++lf+ + 
  gi|336255566|ref|YP_004598673.1|  19 EDVSLSVTPGEVVSIIGPSGVGKSTLLRLLALFDEPDRGTVEYGGVDVWDlpeQRRLEYRRRIGMVFQEASLFDAS- 94 
                                       79*******************************************999999999999*******************. PP

                                       HHHH..........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHT CS
                                       xxxx..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren..........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkk 126
                                       vr+n                          + + ++ +al+++gl e++d+++    +sLSgG+ qrva aral+ +
  gi|336255566|ref|YP_004598673.1|  95 VRRNaeyglrvrqswperlqhefaslvgkqNGTGDAIDALETVGLAEKADQNA----ASLSGGEAQRVAFARALAYD 167
                                       99999******999999888888877764444444999999999999888887....******************** PP

                                       SSEEEEESTTT CS
                                       xxxxxxxxxxx RF
                          ABC_tran 127 pkllllDEpta 137
                                       p++lllDEpt+
  gi|336255566|ref|YP_004598673.1| 168 PDVLLLDEPTS 178
                                       *********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 !   18.1   0.0     2e-06    0.0018       3      61 ..      32      86 ..      30     119 .. 0.67
   2 !   22.7   0.0   7.9e-08   7.4e-05     233     299 ..     146     209 ..     141     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefe 61
                                       +iGp g+GKS+LL++l l+    ++ +++t e +g   ++  + +  +y  +i ++f+
  gi|336255566|ref|YP_004598673.1| 32 SIIGPSGVGKSTLLRLLALF----DEPDRGTVEYGGVDVWDLPEQRRLEYRRRIGMVFQ 86
                                      59***************885....55555555555555555555555555555555555 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 7.9e-08
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       +a++lS G  +  a++ al++++   ++ll+DEp + L+P+ ++ + + + e+++ g+ v ++TH+ 
  gi|336255566|ref|YP_004598673.1| 146 NAASLSGGEAQRVAFARALAYDP---DVLLLDEPTSDLDPRNTAVIEDAVLEARSQGIGVAIATHDM 209
                                       67788888877779999999999...9***********************999999*********85 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.3   1.3e-08   1.2e-05      24     107 ..      27     146 ..      15     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.3e-08
                            AAA_16  24 p.elvllsGesGvGKsslvrellralekdggiflrgkcdql....esaipysa.laqalareellrqllde...aes 91 
                                       p e+v ++G+sGvGKs+l+r l+   e d+g + +g  d      ++ ++y   +  ++ + +l+ +  ++      
  gi|336255566|ref|YP_004598673.1|  27 PgEVVSIIGPSGVGKSTLLRLLALFDEPDRGTVEYGGVDVWdlpeQRRLEYRRrIGMVFQEASLFDASVRRnaeYGL 103
                                       3699******************9555555688988888888888788899966677777777888888877555445 PP

                            AAA_16  92 aeleawrekleeala...........................a 107
                                       + ++ w+e+l+ ++a                            
  gi|336255566|ref|YP_004598673.1| 104 RVRQSWPERLQHEFAslvgkqngtgdaidaletvglaekadqN 146
                                       5777888888888878888887777777766666554444332 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 !   19.9   0.0   4.7e-07   0.00044      11      39 ..      17      45 ..      12      52 .. 0.89
   2 ?    3.1   0.0     0.082        77      31      58 ..     125     149 ..     102     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.7e-07
                            AAA_29 11 tfdghtieidlkgatlltGpsGsGKSTll 39
                                       f++ ++++++ +++ ++GpsG+GKSTll
  gi|336255566|ref|YP_004598673.1| 17 VFEDVSLSVTPGEVVSIIGPSGVGKSTLL 45
                                      6888999999999***************8 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.082
                            AAA_29  31 sGsGKSTllDAiqalLvpakkvrfNkaa 58 
                                       +G+G    +DA+ ++ +++k ++ N+a+
  gi|336255566|ref|YP_004598673.1| 125 NGTG--DAIDALETVGLAEK-ADQNAAS 149
                                       4444..469*********99.9999998 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 ?    5.2   0.0     0.013        12      25      41 ..      29      45 ..      11      51 .. 0.79
   2 !   14.4   0.0     2e-05     0.019     127     208 ..     140     215 ..      81     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                                      SEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnll 41
                                      ++ +i+Gp G GKs ll
  gi|336255566|ref|YP_004598673.1| 29 EVVSIIGPSGVGKSTLL 45
                                      4779**********987 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2e-05
                                       HHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 127 lesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                                        e+a+ +  +LSgGe + va a  +A   ++p  l llDe  + LD +n++ + + + e++  +Q i +++ ++ ++
  gi|336255566|ref|YP_004598673.1| 140 AEKADQNAASLSGGEAQRVAFARALA---YDPDVL-LLDEPTSDLDPRNTAVIEDAVLEAR--SQGIGVAIATHDMH 210
                                       3344444459*****99998887766...778765.89*****************999998..89999999888888 PP

                                       C-SCE CS
                                       xxxxx RF
                             SMC_N 204 kadkl 208
                                       +a+++
  gi|336255566|ref|YP_004598673.1| 211 QAERI 215
                                       88876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.8e-07   0.00092      96     120 ..      24      49 ..       7      60 .. 0.79
   2 ?   -3.1   0.0       6.6   6.2e+03      77      98 ..     202     216 ..     183     226 .. 0.48

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.8e-07
                                       HCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinall 120
                                        ++  +++ ++G+SGvGKStL+  l+
  gi|336255566|ref|YP_004598673.1|  24 SVTPgEVVSIIGPSGVGKSTLLRLLA 49 
                                       444449999*************9886 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.6
                                       SEEEE--TTTHTTHHHHHHHCT CS
                       RsgA_GTPase  77 yevllvsaktkegleelkellk 98 
                                       +++ + ++++        e+++
  gi|336255566|ref|YP_004598673.1| 202 VAIATHDMHQA-------ERIA 216
                                       33333333322.......2333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.7e-06    0.0016       7      40 ..      30      56 ..      26     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerp 40
                                      ++ ++G+sG+GK+tllr l+  ++        ++
  gi|336255566|ref|YP_004598673.1| 30 VVSIIGPSGVGKSTLLRLLALFDEP-------DR 56
                                      5789***************998753.......44 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.9e-05     0.037      32      98 ..      27      95 ..      21     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
                            AAA_25 32 agelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsa.EdsedelrrRlravgeal......r 98
                                       ge++ ++G++g+GK+tl+  lal    ++   g   +e g V ++++ E+++ e rrR+  v++++       
  gi|336255566|ref|YP_004598673.1| 27 PGEVVSIIGPSGVGKSTLLRLLALFDEPDR---GT--VEYGGVDVWDLpEQRRLEYRRRIGMVFQEAslfdasV 95
                                      5999***************99999855433...42..3666666666536667788888888877765554441 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.5e-05      0.08       2      19 ..      31      48 ..      30      64 .. 0.88
   2 ?   -2.0   0.0         4   3.8e+03      67      67 ..     157     157 ..     118     219 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.5e-05
                                      EEEEESTTSSHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                      v i+G + vGKStL++ l
  gi|336255566|ref|YP_004598673.1| 31 VSIIGPSGVGKSTLLRLL 48
                                      78*************987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4
                                       H CS
                          MMR_HSR1  67 g 67 
                                       +
  gi|336255566|ref|YP_004598673.1| 157 R 157
                                       1 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.8e-05     0.074       3      19 ..      33      49 ..      31     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.8e-05
                            AAA_18  3 ltGtpGvGKttlakeLs 19
                                      + G++GvGK+tl + L+
  gi|336255566|ref|YP_004598673.1| 33 IIGPSGVGKSTLLRLLA 49
                                      89*************94 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   0.00014      0.13       2      21 ..      31      53 ..      30      74 .. 0.81
   2 ?   -2.0   0.0         4   3.8e+03     100     116 ..     157     174 ..     128     196 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                            AAA_28  2 ivitGgestGKTtlleaLa...a 21
                                      + i+G+++ GK+tll+ La   +
  gi|336255566|ref|YP_004598673.1| 31 VSIIGPSGVGKSTLLRLLAlfdE 53
                                      679***************95541 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4
                            AAA_28 100 leaaarekrydl.vfllp 116
                                        +a ar+  yd  v+ll+
  gi|336255566|ref|YP_004598673.1| 157 RVAFARALAYDPdVLLLD 174
                                       334555566666566555 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 ?    9.8   0.4   0.00099      0.94      25      83 ..     142     187 ..     129     192 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00099
                           SbcCD_C  25 elsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiat 83 
                                       + ++++++lSGGe+q    +a+a ala           ++++++LDE  s lD++++a 
  gi|336255566|ref|YP_004598673.1| 142 KADQNAASLSGGEAQR---VAFARALA----Y------DPDVLLLDEPTSDLDPRNTAV 187
                                       4677888899999843...23333332....2......468999999999999999875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.15       1      20 [.      30      49 ..      30      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                            AAA_33  1 lvllvGlpGsGKstlaerll 20
                                      +v ++G++G+GKstl++ l+
  gi|336255566|ref|YP_004598673.1| 30 VVSIIGPSGVGKSTLLRLLA 49
                                      7889***********99765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.14      16      48 ..      20      53 ..      17     119 .. 0.84
   2 ?   -3.0   0.0       4.6   4.4e+03     323     365 ..     167     208 ..     159     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsilealdlFln 48
                                      dv++++ +  +  +iG+ ++GKS++l++l lF +
  gi|336255566|ref|YP_004598673.1| 20 DVSLSVTPGeVVSIIGPSGVGKSTLLRLLALFDE 53
                                      5555665556899****************98855 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.6
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++++ll++EP   L p +  v+ ++ +e+ +++   v i TH 
  gi|336255566|ref|YP_004598673.1| 167 DPDVLLLDEPTSDLDPRNTAVIEDAVLEARSQGI-GVAIATHD 208
                                       5789999999999999999999999888888888.78888886 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014      0.13      21      40 ..      30      49 ..      17      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                            AAA_23 21 ltlItGpNGaGKTTildAik 40
                                      ++ I+Gp G GK+T+l+ + 
  gi|336255566|ref|YP_004598673.1| 30 VVSIIGPSGVGKSTLLRLLA 49
                                      778*************9764 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   0.00028      0.26       2      21 ..      30      49 ..      29      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      +v + G++G+GK+tLl+ la
  gi|336255566|ref|YP_004598673.1| 30 VVSIIGPSGVGKSTLLRLLA 49
                                      7889************9887 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0003      0.28       5      22 ..      31      48 ..      28     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      + i+Gpsg+GK+tl++ l
  gi|336255566|ref|YP_004598673.1| 31 VSIIGPSGVGKSTLLRLL 48
                                      679***********9987 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00042      0.39      21      38 ..      29      46 ..      14      61 .. 0.86
   2 ?   -3.1   0.0       3.7   3.5e+03     123     146 ..     191     214 ..     137     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00042
                                      EEEEEEESTTSSHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlak 38
                                       vv++ G  GvGK+tl++
  gi|336255566|ref|YP_004598673.1| 29 EVVSIIGPSGVGKSTLLR 46
                                      59**************86 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.7
                                       .HHHHCHTTSEEEEEESBCCCCCC CS
                            NB-ARC 123 vvlparenrlrvllTTRdeevana 146
                                       +vl ar++++ v++ T d+  a++
  gi|336255566|ref|YP_004598673.1| 191 AVLEARSQGIGVAIATHDMHQAER 214
                                       466777777777777777666555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00036      0.34      38      66 ..      21      49 ..      12      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                             Rad17 38 dvLesrkkriLLisGPsGCgkstvvkvLs 66
                                       +L   + +++ i GPsG gkst ++ L+
  gi|336255566|ref|YP_004598673.1| 21 VSLSVTPGEVVSIIGPSGVGKSTLLRLLA 49
                                      567777788999**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 1987.00
//
Query:       gi|336255567|ref|YP_004598674.1|  [L=239]
Description: ABC transporter integral membrane protein [Halopiger xanaduensis SH-6]
Scores for 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-13   48.5  11.9      8e-13   48.5  11.9    1.4  1  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 !   48.5  11.9   4.4e-17     8e-13       2     178 ..      46     230 ..      45     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 4.4e-17
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.....vilsilghlilpviillllsaapyvrlirr 73 
                                       ++++++++ +  +++++l++ +i++++++Ps+v+++++++ +       +  l ++  ++i+  ++ aap+++ +  
  gi|336255567|ref|YP_004598674.1|  46 LPIALVVG-FTDFPGKRLVTSIINTGMGFPSVVVGLVVLFTVsnqgpLGSLELIFTPEAMIMSQFVLAAPVITGVSL 121
                                       68899999.89999***********************996668885544444555555679999************* PP

                      BPD_transp_1  74 aalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG......lgtlllea 144
                                       aa+ s++++ + aa+a+G +r   +  v+++ a   i+t ++  fg+++ +   ++++g++ +              
  gi|336255567|ref|YP_004598674.1| 122 AAVGSVDQNVRDAAYAMGGTRLD-VALVTIKEARYGIATAVLAGFGRAISEVGSVLIVGGNIAgpdgtsK------- 190
                                       ***********************.777********************************88555654432....... PP

                      BPD_transp_1 145 ilgydyseis.......nggvlalviavlllnlvadilqrl 178
                                            +++i+       + ++ +l++++l+l+lv+++++  
  gi|336255567|ref|YP_004598674.1| 191 -TRTLTTAIQlearqgrYETAMVLGAILLVLVLVVNAIVVR 230
                                       .4444444444444466577777777777777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1800.90
//
Query:       gi|336255568|ref|YP_004598675.1|  [L=327]
Description: tungstate ABC transporter permease [Halopiger xanaduensis SH-6]
Scores for 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-31  107.9   1.3      9e-31  107.6   1.3    1.1  1  PBP_like_2      PBP superfamily domain
      2e-07   31.0   0.1    1.6e-06   28.0   0.1    2.0  1  SBP_bac_11      Bacterial extracellular solute-binding protei
    0.00072   18.7   0.0     0.0013   17.8   0.0    1.4  1  PBP_like        PBP superfamily domain
  ------ inclusion threshold ------
      0.057   13.0   0.1       0.64    9.6   0.1    2.5  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
       0.28   11.1   5.0       0.31   11.0   3.0    2.1  2  TAT_signal      TAT (twin-arginine translocation) pathway sig


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6   1.3   2.5e-34     9e-31      12     282 .]      58     284 ..      27     284 .. 0.91

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 2.5e-34
                        PBP_like_2  12 ifgaGsttpapalrklada.fekaapgakvnyastGSgagikalrngdvdfagsdrplteseia.agwaangaggli 86 
                                          ++++t++++l++ + a f++  +g++v   ++G+ga+++  rngd d+++++++  e+e++ +g++ n+     
  gi|336255568|ref|YP_004598675.1|  58 TLTTTTSTYDTGLLDELNApFQDR-YGVTVDAVAQGTGAALETARNGDSDVVMVHARSLEDEFMeNGYGVNR----- 128
                                       56789999999999976666**99.7**********************************************..... PP

                        PBP_like_2  87 qvpvaigaialvvnkdnpln.....lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqg 158
                                        ++++++++++v++ d+p++      ++ a+++I               ad+  ++v+r+d+sg      t+++e +
  gi|336255568|ref|YP_004598675.1| 129 -RDIMFNDFVVVGSSDDPAGiggseEATSAFQAI---------------ADAEAQFVSRGDNSG------THTKELA 183
                                       .***************888888777999999999...............8**************......******* PP

                        PBP_like_2 159 pwtasgigasgsegvasavsnngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplawsl 235
                                       +w+++g+  +  +++ +a +++g++ +++ a+ +   +y+lad     ++++l+     +s ++            +
  gi|336255568|ref|YP_004598675.1| 184 IWEEAGLDPETFGEWYMA-AGQGMGEVLTQASQQ--GAYTLAD-----RGTFLSM----RSDINL-----------E 237
                                       *******87777777777.***********9888..89*****.....*******....887776...........8 PP

                        PBP_like_2 236 qpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyllsde 282
                                       ++v+ +i  g   ls++++ii ++p +++ +n++la+a++ y++s e
  gi|336255568|ref|YP_004598675.1| 238 ILVQGPIEGGPELLSNPYGIIAVNPAVHDNVNYDLAMAYIGYITSPE 284
                                       9999********************99888***************976 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   4.5e-10   1.6e-06      10     227 ..      68     292 ..      57     293 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 4.5e-10
                                       HHHHHHHHHHHHHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEEEEEEEES CS
                        SBP_bac_11  10 aaalrelaaaFeahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplassplviavp 86 
                                       +  l+el+a F+ ++gv+v+  a+g g+++++ ++g + Dv+        ++  ++g+++  +++++  +  v++  
  gi|336255568|ref|YP_004598675.1|  68 TGLLDELNAPFQDRYGVTVDAVAQGTGAALETARNG-DSDVVMVHARSLEDEFMENGYGV--NRRDIMFNDFVVVGS 141
                                       5689********************************.9999999999999**********..*************** PP

                                       TT-TT---.......SHHHHHHSS--.EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHT.EEEEESSHHHHHHHH CS
                        SBP_bac_11  87 kgnpkkik.......gwadLlkpglk.lavadPttspsGlaalalleaagaqellkalekk.vvklgessrqlltav 154
                                        + p++i         ++++++++ + + + d  +s++ +  la++e ag   l+ + ++      g++ + +lt++
  gi|336255568|ref|YP_004598675.1| 142 SDDPAGIGgseeatsAFQAIADAEAQfVSRGD--NSGTHTKELAIWEEAG---LDPETFGEwYMAAGQGMGEVLTQA 213
                                       ***97655111111145556666775344555..677777889999***9...666665552333444555555553 PP

                                       H.TTT-S.....EEEEEHHHHH.......HSTTSSEEEE--TTT--....EEEEEEEE-TT--HHHHHHHHHTTSHH CS
                        SBP_bac_11 155 e.agead.....agivyeseakaa.....engdkleavylpeglnl.dpldypaavlkkaakreaAraFlafLrspe 219
                                         +g +       +++ +s++++      + +++ e++  p g+ + +p++       ++ +   A a++ +++spe
  gi|336255568|ref|YP_004598675.1| 214 SqQGAYTladrgTFLSMRSDINLEilvqgPIEGGPELLSNPYGIIAvNPAV------HDNVNYDLAMAYIGYITSPE 284
                                       313332222233556666666433333333444555555555555322222......24456689************ PP

                                       HHHHHHHT CS
                        SBP_bac_11 220 aqailrky 227
                                       aq+i++ y
  gi|336255568|ref|YP_004598675.1| 285 AQQIIENY 292
                                       ****9976 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.8e-07    0.0013       5     106 ..      79     178 ..      76     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.8e-07
                                       HHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCH....HCCCCCEEEEEEEEEEEE-CC-HCHCCCCHC CS
                          PBP_like   5 aeknpgvrvavanvGsggGlkalrageadiagshlldketee....ynapalrkaldgievvlvnlarreqglvvak 77 
                                       +++  gv+v     G+g++l+  r+g  d+ ++h  + e+e     y ++    +++  ++v+v    + +g+   +
  gi|336255568|ref|YP_004598675.1|  79 QDR-YGVTVDAVAQGTGAALETARNGDSDVVMVHARSLEDEFmengYGVNRRDIMFN--DFVVVGSSDDPAGIGGSE 152
                                       554.7999***************************8776654334466664455555..59*************999 PP

                                       CHHHS--BGGGC-S-B-EEEEE-TTSHHH CS
                          PBP_like  78 gnpkkitnwkdladaplrlvnRetGSGtr 106
                                       +   + + ++++ada++++v R+  SGt 
  gi|336255568|ref|YP_004598675.1| 153 E---ATSAFQAIADAEAQFVSRGDNSGTH 178
                                       9...889*********************6 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 ?    9.6   0.1   0.00018      0.64      98     141 ..     156     199 ..      68     298 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00018
                                       -SHHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHHSSEE CS
                    Phosphonate-bd  98 qsledLkgktiafvspsStsGylvpaalLvkeagldpeddfsev 141
                                        +++ ++++   fvs+   sG+   +  + +eagldpe++ +  
  gi|336255568|ref|YP_004598675.1| 156 SAFQAIADAEAQFVSRGDNSGTHTKELAIWEEAGLDPETFGEWY 199
                                       466888999999*************************9874433 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.0   8.5e-05      0.31       2      25 ..       3      25 ..       2      26 .. 0.79
   2 ?   -1.4   0.0      0.66   2.4e+03       2       7 ..     126     131 ..     125     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.5e-05
                        TAT_signal  2 lSRRdFLKgsAAaa.AAaalggcaa 25
                                      + RR+F    A++  AAa+l+gc+a
  gi|336255568|ref|YP_004598675.1|  3 IQRRTFVA--AVGStAAAGLAGCSA 25
                                      679*****..777767888999986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.66
                        TAT_signal   2 lSRRdF 7  
                                       ++RRd 
  gi|336255568|ref|YP_004598675.1| 126 VNRRDI 131
                                       79**96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); 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:                         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 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2495.67
//
Query:       gi|336255569|ref|YP_004598676.1|  [L=96]
Description: transcriptional regulator PadR family protein [Halopiger xanaduensis SH-6]
Scores for 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-14   52.7   0.1    3.7e-14   52.4   0.1    1.1  1  PadR      Transcriptional regulator PadR-like family
    0.00069   19.4   0.0    0.00088   19.1   0.0    1.2  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
     0.0013   18.6   0.0     0.0017   18.3   0.0    1.2  1  HTH_45    Winged helix-turn-helix
     0.0023   17.7   0.0     0.0029   17.4   0.0    1.2  1  DUF4364   Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.048   14.1   0.0      0.061   13.8   0.0    1.4  1  HTH_27    Winged helix DNA-binding domain
      0.056   13.6   0.0      0.069   13.3   0.0    1.3  1  HTH_34    Winged helix DNA-binding domain
       0.13   12.4   0.0       0.15   12.2   0.0    1.1  1  FUR       Ferric uptake regulator family


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 !   52.4   0.1   1.5e-17   3.7e-14       8      75 .]      22      82 ..      13      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 1.5e-17
                                      S-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHHH CS
                              PadR  8 qpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrelae 75
                                      qp  G  i++++e+   g +++++G+lYp+L++L ++glve+ + +    ++++yY++Td+G+++l+e
  gi|336255569|ref|YP_004598676.1| 22 QP-SGQTIKENIEDD-AG-TDINHGRLYPNLDTLVNQGLVEKGQLD----RRTNYYEITDDGEEALQE 82
                                      55.79**********.46.8***********************998....7**************986 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 !   19.1   0.0   3.4e-07   0.00088      51      86 ..      44      79 ..      26      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.4e-07
                           DUF1495 51 krynsessLielGLveeeeeseglklYklteeGiei 86
                                        y + + L+++GLve+ + ++ +++Y++t+ G+e 
  gi|336255569|ref|YP_004598676.1| 44 RLYPNLDTLVNQGLVEKGQLDRRTNYYEITDDGEEA 79
                                      55778899********9999*************985 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   6.7e-07    0.0017      30      73 ..      39      87 ..      21      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.7e-07
                            HTH_45 30 nLsykllnkYLdmLvekgli.....kkskekYvlTekGlelleklkele 73
                                      +++  +l   Ld+Lv++gl+     + +++ Y++T+ G+e l++ +  e
  gi|336255569|ref|YP_004598676.1| 39 DINHGRLYPNLDTLVNQGLVekgqlDRRTNYYEITDDGEEALQERESWE 87
                                      567778888899*******9887778899*************9977665 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.1e-06    0.0029      39      73 ..      48      83 ..      24      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
                           DUF4364 39 alseLvesglieee.ekenktlykiTekGketlelf 73
                                       l+ Lv++gl+e+   ++ +++y+iT++G+e+l++ 
  gi|336255569|ref|YP_004598676.1| 48 NLDTLVNQGLVEKGqLDRRTNYYEITDDGEEALQER 83
                                      6899********99667999************9875 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 ?   13.8   0.0   2.4e-05     0.061      38      68 .]      48      76 ..      14      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                            HTH_27 38 slkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +l+ L+++GLv  ++   drr+  +++Td G
  gi|336255569|ref|YP_004598676.1| 48 NLDTLVNQGLV--EKGQLDRRTNYYEITDDG 76
                                      5899*******..444469**********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 ?   13.3   0.0   2.7e-05     0.069      24      75 ..      38      86 ..      14      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                            HTH_34 24 leatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvka 75
                                      + ++ g+L+ +l++L ++g +  +k+  ++ +   ++iT++G ea ++  ++
  gi|336255569|ref|YP_004598676.1| 38 TDINHGRLYPNLDTLVNQGLV--EKGQLDR-RTNYYEITDDGEEALQERESW 86
                                      57899**************86..6888887.8899**********9987665 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     6e-05      0.15      27      74 ..      26      74 ..       9      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6e-05
                                      HHHHHHHH.HTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS CS
                               FUR 27 eevykelk.eedpeislaTVYrtLklleeaglvkelefedgesryelak 74
                                      + + ++++ + + +i    +Y +L++l + glv++ +++  +++ye+++
  gi|336255569|ref|YP_004598676.1| 26 QTIKENIEdDAGTDINHGRLYPNLDTLVNQGLVEKGQLDRRTNYYEITD 74
                                      5666666645678899999***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 778.42
//
Query:       gi|336255570|ref|YP_004598677.1|  [L=247]
Description: hypothetical protein Halxa_4196 [Halopiger xanaduensis SH-6]
Scores for 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-42  145.3   0.0      3e-42  145.0   0.0    1.0  1  PAC2      PAC2 family


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 !  145.0   0.0   1.7e-46     3e-42       1     211 [.      18     224 ..      18     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 145.0 bits;  conditional E-value: 1.7e-46
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEEEEETTT.SEEEEEEEE CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprlyakdsgsrdllvlqgr 75 
                                       L++Gfpg+G+Vg++a+d+L+++le+e+++++d+++ lp      + ++++g  + ++p+rlya++  ++dll+lq+ 
  gi|336255570|ref|YP_004598677.1|  18 LVEGFPGVGLVGKIATDHLVDELELEYYASVDCTG-LP-----RIGVYRGGdqQARPPVRLYASE--EHDLLALQSD 86 
                                       89*********************************.99.....786666666999*******995..59*******9 PP

                                       -HSCHHH..HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT......-CEEEE CS
                              PAC2  76 epilqye..efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees......eyggiv 144
                                       +pi  +   ++a++++ w+ + + + ++ L+gl+a++++     rp  ++g++t  +    le++      e+g+++
  gi|336255570|ref|YP_004598677.1|  87 APISSQAvsNVAECITGWIVDQNATPIY-LSGLPAEREE----GRP-NIYGIGTGASIE-TLERHdiaappEDGVVT 156
                                       9999999999******************.*****98875....588.888888665544.34322234578****** PP

                                       HHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHH.HHHHT---HCHHHHHHHHHHHHHHHH CS
                              PAC2 145 gitglLlsaakergipavgllaevphylpdPkaaaallefl.skllglevdtedLeedaeeleeqlee 211
                                       g+tg+L+++a++r+++++g+++e++ ++pdP+aa++lle +   ++++e+d+ +L e+aee++e+ e+
  gi|336255570|ref|YP_004598677.1| 157 GPTGALINRAAQRELDSLGVVVECSRQFPDPEAASVLLEDAiGPIADVEIDVGELVERAEEIREKREQ 224
                                       **************************************987356669****************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 2020.80
//
Query:       gi|336255571|ref|YP_004598678.1|  [L=232]
Description: hypothetical protein Halxa_4197 [Halopiger xanaduensis SH-6]
Scores for 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   18.5   0.0      0.041   14.5   0.0    2.2  2  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.035   14.8   0.2       0.37   11.5   0.0    2.2  2  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 ?    1.8   0.0     0.043   3.9e+02       1      38 [.      39      78 ..      39      97 .. 0.77
   2 !   14.5   0.0   4.6e-06     0.041      45      88 ..     128     177 ..     103     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.043
                                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHH..HHHHHHC CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskeml..klakeka 38
                                      Ld+ +G  ++++  a+rg + vg D+  e+   +la+++ 
  gi|336255571|ref|YP_004598678.1| 39 LDCPSGVASFVATAADRGVDAVGADIIYEQSrdELARRCR 78
                                      677789999999999**********998887555555544 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.6e-06
                                       EEETTEECCCTSS-TT-EEEEEEES-CCC-......CCHHHHHHHHHHHE CS
                   Methyltransf_11  45 vefvvadaeklpfednsfDlvvssevlhhv......edpekalkeiaRvL 88 
                                        ++v a + +lpf+ +sf lv+s ++l+          +++al+e+ Rv 
  gi|336255571|ref|YP_004598678.1| 128 GRYVAAALPTLPFARDSFSLVLSAHFLFLYgdrfdaTFHREALRELCRVA 177
                                       368999999******************99987776668899999999996 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.069   6.2e+02       1      42 [.      38      78 ..      38     106 .. 0.74
   2 ?   11.5   0.0   4.1e-05      0.37      34      93 ..     110     177 ..     106     180 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.069
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESS.HHHHHHHHHHHH CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDis.eemleaarerae 42
                                      vLd+  G   +++ +a+r+   + +g Di  e+  ++ ++r++
  gi|336255571|ref|YP_004598678.1| 38 VLDCPSGVASFVATAADRG--VDAVGADIIyEQSRDELARRCR 78
                                      8999999999999999995..9999999851444455555554 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.1e-05
                                       HHHHHHHHHHTTT....TEEEEESBCCGBSSSTTTEEEEEEEST.GGG...SSHHHHHHHHHHHHHHE CS
                   Methyltransf_25  34 leaareraeeegl....nvefvqgdaedlpfedgsfDlvvssga.lhh...lsdedlekalkeiarvL 93 
                                       l++a er+ ++ +    + ++v + + +lpf+ +sf lv+s++  + +   ++   +++al+e++rv 
  gi|336255571|ref|YP_004598678.1| 110 LRRASERFLDDYAdgrqDGRYVAAALPTLPFARDSFSLVLSAHFlFLYgdrFDATFHREALRELCRVA 177
                                       55666666553334445788999999***************766444422234444578888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1995.04
//
Query:       gi|336255572|ref|YP_004598679.1|  [L=302]
Description: RNA methylase, NOL1/NOP2/sun family [Halopiger xanaduensis SH-6]
Scores for complete 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  178.6   0.0    1.6e-52  178.1   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    3.2e-06   27.5   0.0    2.6e-05   24.6   0.0    2.1  2  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
     0.0011   19.1   0.0     0.0017   18.5   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
     0.0043   16.9   0.0     0.0062   16.3   0.0    1.3  1  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> 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 !  178.1   0.0   3.5e-56   1.6e-52       2     199 ..      92     298 ..      91     299 .. 0.91

  Alignments for each domain:
  == domain 1  score: 178.1 bits;  conditional E-value: 3.5e-56
                                       HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg. 77 
                                       ++L+p+++e++ D caaPGgK t ia+lm+++gtvvA+d n  R++++  n +rLg t++ v++ Dar+++      
  gi|336255572|ref|YP_004598679.1|  92 VVLDPRPGERVWDCCAAPGGKATQIAALMDDEGTVVANDSNLGRISALRFNAERLGATSLAVTNEDARNYSLQRFSf 168
                                       68*******************************************************************98665445 PP

                                       ..EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHH CS
                   Methyltr_RsmB-F  78 elfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaL 154
                                       + fDr+L+DaPC+  g+ir++pd+  + +e  ia+++  qk +l  a++ +++gG++vYsTC+ ++eEne+v+++a+
  gi|336255572|ref|YP_004598679.1| 169 DEFDRALVDAPCTCEGTIRKNPDALDNWSEDAIASVSGIQKGILRRAVQATREGGTVVYSTCTFAPEENEAVVQHAI 245
                                       99*************************************************************************** PP

                                       HH-TTEEEESSBSTTSTTSSECEEC...........TSEEE-TTTTSS-SEEEEEE CS
                   Methyltr_RsmB-F 155 kkredvelvetelsepkglklgeea...........gtlrllPhtenkdgffiakl 199
                                       +++ d ++v+++l    + + g ++           ++ r++Ph++++ gff+akl
  gi|336255572|ref|YP_004598679.1| 246 EEE-DCRVVDFDLDM--EYAPGLTEwdgqefdssleKAARIYPHHNDTGGFFVAKL 298
                                       987.88888887655..3333333334556788888899****************9 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   5.8e-09   2.6e-05      15      86 ..      12      84 ..       4      88 .. 0.85
   2 ?   -0.0   0.0      0.28   1.3e+03       8      46 ..     115     153 ..     113     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.8e-09
                                      GGHHHHHHHHH-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES---...TTSHHHHTTS-EE-- CS
                   Methyltr_RsmF_N 15 eeaeaflaaleeprkkglRvNtlKisveeleklse..efelepvpwceeGfyleeeerpgkhplheaGlyYiQE 86
                                      ++++af++a+e+p  +++RvNt+K+sve++ ++ e  ++  e+ +w +    le + +pg +     G  + QE
  gi|336255572|ref|YP_004598679.1| 12 DDFDAFFEACERPLGNAVRVNTIKASVERTLAALEreDVGYEQADWNPRVLRLETD-SPGSTWTSFHGFTHGQE 84
                                      689***********************99887766668899*********9999998.88888888888888887 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.28
                                       HHHHHHGGGHHHHHHHHH-----EEE--TTS..TTHHHH CS
                   Methyltr_RsmF_N   8 kmkellgeeaeaflaaleeprkkglRvNtlKisveelek 46 
                                       ++ +l+++e + + +  +  r ++lR+N  ++  ++l+ 
  gi|336255572|ref|YP_004598679.1| 115 QIAALMDDEGTVVANDSNLGRISALRFNAERLGATSLAV 153
                                       566777777777777788889999****99977666654 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   3.8e-07    0.0017      21     145 ..      98     241 ..      76     251 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.8e-07
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...HHH...TTEEEECS-CCCSSHHHHHCHCHHHSSEEEE CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...apl...pgvttiqgditdpetiekikealserkvdlv 91 
                                       pg++v D++aaPGg +  ++  +  +g vva D + +   a++   +++      +t++++++  ++ +s  ++d  
  gi|336255572|ref|YP_004598679.1|  98 PGERVWDCCAAPGGKATQIAALMDDEGTVVANDSNLGrisALRfnaERLGATSLAVTNEDARNYSLQRFSFDEFDRA 174
                                       7899***********99999999999*******96665563334446666778889999999999999999999999 PP

                                       EE--S-SS-CH..HHHHHHHH.........CCCCHHHHCCHCCCCECCCEEEECCCH..CCCHHHHH CS
                              FtsJ  92 vsDgapdvsgv..hdldeylq.........sqLllaalelalkllkpggtfvlkifr..geeteall 145
                                       + D    ++g+  ++ d++ +         s + +  l+ a++  ++ggt+v  +++   ee ea++
  gi|336255572|ref|YP_004598679.1| 175 LVDAPCTCEGTirKNPDALDNwsedaiasvSGIQKGILRRAVQATREGGTVVYSTCTfaPEENEAVV 241
                                       99987777664423333333366677766779999999999999********888884344444555 PP

>> Methyltransf_31  Methyltransferase 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    0.0062       3     120 ..      98     242 ..      96     281 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-06
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDli 78 
                                        g rv D+ ++ G ++ ++a ++ ++++vv  D +   i+  r na++lg + + +  +d+ + + + ++ + fD  
  gi|336255572|ref|YP_004598679.1|  98 PGERVWDCCAAPGGKATQIAALMDDEGTVVANDSNLGRISALRFNAERLGATSLAVTNEDARNYSLQrFSFDEFDRA 174
                                       578999**************99999**************************************99666666889987 PP

                   Methyltransf_31  79 lsn.............evl..........naladpdkileeiervlkpggilliedpr.....llaelp...a 120
                                       l +             +                 ++ il+++ ++ ++gg ++ +++               +
  gi|336255572|ref|YP_004598679.1| 175 LVDapctcegtirknpD-AldnwsedaiaSVSGIQKGILRRAVQATREGGTVVYSTCTfapeeN----EavvQ 242
                                       77745444444444441.0455555433344556667777999999999999999999433221....22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2328.65
//
Query:       gi|336255573|ref|YP_004598680.1|  [L=198]
Description: hypothetical protein Halxa_4199 [Halopiger xanaduensis SH-6]
Scores for 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   27.5   1.2    4.2e-05   23.4   1.2    2.2  1  Methyltranf_PUA  RNA-binding PUA-like domain of methyltransfe


Domain annotation for each model (and alignments):
>> Methyltranf_PUA  RNA-binding PUA-like domain of methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.2   2.3e-09   4.2e-05       1      50 []     126     196 ..     126     196 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.3e-09
                   Methyltranf_PUA   1 alrYlkGetielep.dlkkGwvlVcyd....................gyplGwgKlvggrlKNkyPkglRr 50 
                                       a+++++Ge+ +le  d+++G++  +++                     +plG+g +++g+l++ +Pkg+Rr
  gi|336255573|ref|YP_004598680.1| 126 ARKFAAGEDQALERwDGDWGYLTAAHQvgvgpegrpdedgeaveggdLEPLGVGLYLHGELRSVVPKGRRR 196
                                       789**********77****99999999999999999999999999989*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1552.93
//
Query:       gi|336255574|ref|YP_004598681.1|  [L=113]
Description: hypothetical protein Halxa_4200 [Halopiger xanaduensis SH-6]
Scores for complete 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-08   35.2   0.1    1.6e-08   34.9   0.1    1.1  1  DrsE      DsrE/DsrF-like family
    0.00062   19.7   0.2      0.001   19.0   0.1    1.3  1  DrsE_2    DsrE/DsrF/DrsH-like family


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   1.8e-12   1.6e-08       2     116 ..       3     112 ..       2     113 .] 0.85

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.8e-12
                                       EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT....-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EE CS
                              DrsE   2 kvfilvtggpygseaarealelalaaaalg....hevsvffygdGvllllkgqtanpadeknlaellkalkeygvkl 74 
                                        v++l +    +++++ +al +a+ +++ +     ev++++  dG  ++++          ++a+++++l e +v +
  gi|336255574|ref|YP_004598681.1|   3 TVVHLLS---GDEAEQETALAIARNLLDDEtdriDEVAIVVQADGMAAVKA---DG-----ENADQVRTLLEDDVAF 68 
                                       5677777...34455667777777777666*********************...33.....488************* PP

                                       EEEHHHHHHTT--GGGE-.T--EEEE-HHHHHHHHHH.-SEEEE CS
                              DrsE  75 yvCgqaakargldededl.gvgvevsglgelaelqne.gdrvit 116
                                        +C ++++   l+e++++ g++ ++ g+ e+ +lq+e g+++++
  gi|336255574|ref|YP_004598681.1|  69 RACSNTLEMLDLEESDLVdGIETVPEGAVEVTRLQSEeGYAYLR 112
                                       *************88766889***************99****97 PP

>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.2e-07     0.001     105     135 ..      61      91 ..      38     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-07
                                       HHHTT-EEEEEHHHHHHHT--GGGB-TT-EE CS
                            DrsE_2 105 akeagvklvaCqmtmdlmglkkeelidgvei 135
                                         e +v + aC  t+++++l++ +l+dg+e+
  gi|336255574|ref|YP_004598681.1|  61 LLEDDVAFRACSNTLEMLDLEESDLVDGIET 91 
                                       4579*************************64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 852.02
//
Query:       gi|336255575|ref|YP_004598682.1|  [L=289]
Description: alpha/beta hydrolase fold protein [Halopiger xanaduensis SH-6]
Scores for 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-11   44.7   4.1    2.8e-11   44.5   4.1    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    2.6e-07   30.5   0.0    0.00012   21.8   0.0    2.3  1  Abhydrolase_1  alpha/beta hydrolase fold
    5.8e-06   25.7   0.0     0.0011   18.3   0.0    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
     0.0077   16.4   0.0      0.012   15.7   0.0    1.2  1  Thioesterase   Thioesterase domain
  ------ inclusion threshold ------
      0.031   14.4   0.0      0.053   13.6   0.0    1.3  1  Abhydrolase_4  TAP-like protein
       0.13   12.0   0.0       0.75    9.5   0.0    2.1  3  Abhydrolase_5  Alpha/beta hydrolase family
       0.17   11.4   0.0        9.6    5.7   0.0    2.1  2  DLH            Dienelactone hydrolase family
       0.23   11.1   0.0       0.36   10.4   0.0    1.2  1  Esterase       Putative esterase


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   4.1   1.2e-14   2.8e-11       1     215 [.      36     268 ..      36     273 .. 0.68

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.2e-14
                                       EEEE--GC.............GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH.CHHHHHHHCCTT..TTSEE CS
                     Abhydrolase_6   1 vlllHGagss........assWlvapLaallaagvhvlapDlpGhGrsdpppldled.ladlaalldelaagggpvv 68 
                                       +l+++G+g          ++ W++ +L   + + ++v+++++p  G    +++ +e+ ++d+a++l++    +g + 
  gi|336255575|ref|YP_004598682.1|  36 LLVIPGLGDAmfdgeygrQETWFFKQLFDGFLDEYTVYVVSRP-RG--LADDYFVEAmAQDYARVLESD---TGSAS 106
                                       6889998843444556678999888998888888999*****9.33..44556666668999*******...7999* PP

                                       EEEETCHHHHHHHHHHCC......EEEEES-..----TTTS----TTHHHHHHTT-CCCCHCCH.........S-HS CS
                     Abhydrolase_6  69 lvGHSlGGalalaaapla....lvvgvlldppptalpagllaaalelllallallrllawlsre.........plpr 132
                                       ++G S+GG++a++   +a    ++v  l+ +   + + +l+a  ++l+++l++ +    w +++          ++ 
  gi|336255575|ref|YP_004598682.1| 107 VLGLSMGGLIAQE---VArerpDLVERLVVG---VSGCRLAANGRPLVRQLRSFALEEDWIALRshlyehmftGVRG 177
                                       *************...555557666677777...7778888888888888888777777776554433343332222 PP

                                       CCCCHHH..C...CCCHCHCCCGHH.HHCCHHCHTTCCHHTT-TTGCEEE.CTT-C.HHHHCHHCCCH.STTEEETC CS
                     Abhydrolase_6 133 lfladed..a...daawrarlarla.allaglgllpaaawadlpvpllvl.ggeDp.lvprllerlla.qagarlpv 200
                                       ++++ ++  a   +++  a+  ++   l+a l++   +++  + +++lv+ ++eDp    + l++ +a +++ +l  
  gi|336255575|ref|YP_004598682.1| 178 RLYPLLSrtAgrlQPPTPAAPGDVVtSLDAVLEYDGSDRLGEIEPRTLVIgAAEDPfFTEAILRETHAgLPDSQL-A 253
                                       4444333221233233333333333244445556679999999999999966999975556677777788*****.9 PP

                                       E...SSS-HHHHSHH CS
                     Abhydrolase_6 201 vlpgaGHlphleepd 215
                                        ++++ H ++le+ +
  gi|336255575|ref|YP_004598682.1| 254 MYRDGKHGVFLEKRA 268
                                       *******99998765 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   5.5e-08   0.00012      47     256 ..      80     266 ..      34     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5.5e-08
                                       TTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHH CS
                     Abhydrolase_1  47 pacinddygtasvaddldrildalgddkltlvGhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaks 123
                                            ddy   ++a d+ r+l++ + ++  ++G SmGG+ia ++a e p+ V +lv   +        +++ + ++ 
  gi|336255575|ref|YP_004598682.1|  80 GLA--DDYFVEAMAQDYARVLES-DTGSASVLGLSMGGLIAQEVARERPDLVERLVVGVS------GCRLAANGRPL 147
                                       444..777778888888887554.3334447************************98777......77777788888 PP

                                       HHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHH CS
                     Abhydrolase_1 124 fpdffdgyaadcarnpagplladelaaleqrhrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsakl 200
                                       +        +++       l++++ + ++ r+        p+ s+++ +  ++++  +  +   s++   ++d + +
  gi|336255575|ref|YP_004598682.1| 148 VRQLRSFALEEDWIALRSHLYEHMFTGVRGRLY-------PLLSRTAGRLQPPTPAAPGDVV-TSLDAVLEYDGSDR 216
                                       888888888888888889999999999999977.......8888888888888777776665.77888888888888 PP

                                       HHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                     Abhydrolase_1 201 llrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafleg 256
                                       l++++        tlvi++++Dp +++  l++  + lp+++l  + d+ H +fle+
  gi|336255575|ref|YP_004598682.1| 217 LGEIEP------RTLVIGAAEDPFFTEAILRETHAGLPDSQLAMYRDGKHGVFLEK 266
                                       999999......*****************************************986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.9e-07    0.0011      77     125 ..     104     150 ..      81     169 .. 0.76
   2 !    5.5   0.0     0.004       9.1     186     238 ..     216     266 ..     206     267 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.9e-07
                       Hydrolase_4  77 plfllGhSmGGliallyllrypdkvaglilsaPalkikaklkappllkl 125
                                          +lG SmGGlia++++ ++pd v++l++  + ++++a+   +pl++ 
  gi|336255575|ref|YP_004598682.1| 104 SASVLGLSMGGLIAQEVARERPDLVERLVVGVSGCRLAAN--GRPLVRQ 150
                                       6789*******************99999998888887766..5555554 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.004
                       Hydrolase_4 186 raakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnEp 238
                                       r  +i+  +l++ +++D+   ++  re+++ l+  d +l++y  + H ++ E+
  gi|336255575|ref|YP_004598682.1| 216 RLGEIEPRTLVIGAAEDPFFTEAILRETHAGLP--DSQLAMYRDGKHGVFLEK 266
                                       566777789************999999999999..9**************997 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.3e-06     0.012      48      86 ..      87     123 ..      52     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.3e-06
                                       HHHHHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHHHHH CS
                      Thioesterase  48 ieelaaeyaealrqiqpegPyalfGhSlGgllAfevArq 86 
                                        e++a+ ya  l++        + G S+Ggl+A+evAr+
  gi|336255575|ref|YP_004598682.1|  87 VEAMAQDYARVLESDTGS--ASVLGLSMGGLIAQEVARE 123
                                       689*********998877..99***************95 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.4e-05     0.053      34      92 ..     221     279 ..     205     288 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                     Abhydrolase_4  34 aapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLl 92 
                                       ++++L++++  Dp    +  ++++  l++++l +++++ Hg++ ++ +     ++++L+
  gi|336255575|ref|YP_004598682.1| 221 EPRTLVIGAAEDPFFTEAILRETHAGLPDSQLAMYRDGKHGVFLEKRAGFTGWIRRFLE 279
                                       589***************************************99999999999999986 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.1   2.5e+03     132     150 ..      36      55 ..      33      56 .. 0.84
   2 ?    9.5   0.0   0.00034      0.75      26      85 ..      69     132 ..      64     137 .. 0.73
   3 ?   -2.0   0.0       1.2   2.6e+03      90     141 ..     211     261 ..     206     264 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                     Abhydrolase_5 132 vvsieGgnhagf.GsYGeqk 150
                                       +++i G+  a f G+YG q 
  gi|336255575|ref|YP_004598682.1|  36 LLVIPGLGDAMFdGEYGRQE 55 
                                       67899999999989***995 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00034
                     Abhydrolase_5  26 GyevvlvklPlnla..vlgknkaeeiike.apklekfvvgGhslGGvvasrfaaee.ekiegvv 85 
                                        y+v++v  P +la   + +  a++  +    +     v G s+GG +a ++a+e  + +e +v
  gi|336255575|ref|YP_004598682.1|  69 EYTVYVVSRPRGLAddYFVEAMAQDYARVlESDTGSASVLGLSMGGLIAQEVARERpDLVERLV 132
                                       699**********976455555555443312344567899*************98746777665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.2
                     Abhydrolase_5  90 YPekdelselskkvlsivgteDgvlnvkslekakkflpkdtkvvsieGgnha 141
                                       Y   d l e + ++l i + eD   +   l++++  lp+ +++ + + g h 
  gi|336255575|ref|YP_004598682.1| 211 YDGSDRLGEIEPRTLVIGAAEDPFFTEAILRETHAGLPD-SQLAMYRDGKHG 261
                                       555678888888999999999999999999888888885.556666666665 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0043       9.6      87     122 ..      92     128 ..      70     135 .. 0.78
   2 ?    3.5   0.0     0.019        43     147     195 ..     224     268 ..     206     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0043
                               DLH  87 aylksvpevstkkvgvvGfCmGGalalllaaev.pev 122
                                       + ++ v e +t+   v G  mGG +a ++a+e  + v
  gi|336255575|ref|YP_004598682.1|  92 QDYARVLESDTGSASVLGLSMGGLIAQEVARERpDLV 128
                                       445555568889999****************995555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.019
                               DLH 147 ilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsre 195
                                        l++ + eD+f++ + + +++  l    +d +l +Y + +H+ + ++r+
  gi|336255575|ref|YP_004598682.1| 224 TLVIGAAEDPFFTEAILRETHAGL----PDSQLAMYRDGKHGVFLEKRA 268
                                       5788999*****999766666666....999**********97777665 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00016      0.36     115     142 ..     102     130 ..      87     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                                       CC.EEEEEETHHHHHHHHHHHCSTTTCCE CS
                          Esterase 115 dg.ravaGqSmGGlgALilalkhpdrFgs 142
                                       +g  +v+G SmGGl+A  +a ++pd+  +
  gi|336255575|ref|YP_004598682.1| 102 TGsASVLGLSMGGLIAQEVARERPDLVER 130
                                       33589*******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2303.92
//
Query:       gi|336255576|ref|YP_004598683.1|  [L=322]
Description: Glyoxalase/bleomycin resistance protein/dioxygenase [Halopiger xanaduensis SH-6]
Scores for 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-26   91.8   0.2    1.3e-15   57.7   0.0    2.5  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
  ------ inclusion threshold ------
      0.015   16.1   2.3      0.028   15.2   0.1    2.5  2  Glyoxalase_6  Glyoxalase-like domain


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 !   57.7   0.0   1.5e-19   1.3e-15       1     128 []       7     129 ..       7     129 .. 0.80
   2 !   31.8   0.1   1.6e-11   1.4e-07      57     128 .]     206     272 ..     139     272 .. 0.75

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.5e-19
                                       EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEE.......EESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCB CS
                        Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdn.......teeteglriaffhaggghielvlneapsgaakhvkki 70 
                                       gi+hv+++++d+e++ +FYt+ LG++lvk+++n       +       +++ h+g+   +++ ++  + ++ +v   
  gi|336255576|ref|YP_004598683.1|   7 GIHHVTAIASDPERNFEFYTETLGLRLVKQSVNqddvsvyH------LFYADHEGTPGTSMTFFPYVDARPGQV--- 74 
                                       79******************************743322221......345556666666666666666666666... PP

                                       S.CTSEEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  71 e.etvhhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                         ++v  v f++ +   ++ ++drl++ag + +++++r + + l    f+DpdG  le+
  gi|336255576|ref|YP_004598683.1|  75 GtGQVSTVSFLVPEG-SLDYWQDRLEDAGAEPDDPLERFGDTVLP---FTDPDGLPLEL 129
                                       215899999999865.56********************9999999...******99986 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.6e-11
                                       EECCTTSCTHHCCBSC.....TSEEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  57 neapsgaakhvkkiee.....tvhhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                        e ++ a++      +     tvhhvaf ++++e+ +++ + l ++g++ +++++r  f+++y   +r+ +Gil+e+
  gi|336255576|ref|YP_004598683.1| 206 VEEDPQAPQ------GlpgagTVHHVAFEVREDEQ-DDWREFLIDRGLRPTEIIDRKWFKSVY---AREYGGILFEF 272
                                       222222222......1233459**********999.***************************...**********8 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   3.1e-06     0.028       5     106 ..      14     129 ..      10     130 .. 0.67
   2 ?   -0.3   0.4      0.21   1.9e+03      39      66 ..     217     229 ..     145     293 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-06
                      Glyoxalase_6   5 daadpaalaaFwaaalgweveree............aaledpegvgpaaedaatllfqrvpe.......pakn.rvH 61 
                                        a+dp++ ++F+ + lg+++++++            +  +d+eg +p    ++++ f +  +       +++   v 
  gi|336255576|ref|YP_004598683.1|  14 IASDPERNFEFYTETLGLRLVKQSvnqddvsvyhlfY--ADHEG-TP----GTSMTFFPYVDarpgqvgTGQVsTVS 83 
                                       489*********************7777766655321..22222.22....22222222222466677744433466 PP

                      Glyoxalase_6  62 ldlavedldaevarlvalGArvlreprdgthgr..vlaDPeGneFcv 106
                                       + +   +ld   +rl+++GA+  ++ +  +  +   ++DP+G +  +
  gi|336255576|ref|YP_004598683.1|  84 FLVPEGSLDYWQDRLEDAGAEPDDPLERFGD-TvlPFTDPDGLPLEL 129
                                       666668999*************999887654.35889*****88776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.21
                      Glyoxalase_6  39 paaedaatllfqrvpepaknrvHldlav 66 
                                       p a++                 H+ ++v
  gi|336255576|ref|YP_004598683.1| 217 PGAGTV---------------HHVAFEV 229
                                       222222...............2333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2396.48
//
Query:       gi|336255577|ref|YP_004598684.1|  [L=511]
Description: hypothetical protein Halxa_4203 [Halopiger xanaduensis SH-6]
Scores for 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-145  483.0   0.0   6.5e-145  482.7   0.0    1.0  1  DUF790    Protein of unknown function (DUF790)


Domain annotation for each model (and alignments):
>> DUF790  Protein of unknown function (DUF790)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.7   0.0  3.6e-149  6.5e-145       1     387 []       1     396 [.       1     396 [. 0.99

  Alignments for each domain:
  == domain 1  score: 482.7 bits;  conditional E-value: 3.6e-149
                            DUF790   1 MLpsdllrvrrrggkivpkflkeenlelaaelielfeehvGekrgeleeelkeleeeatdyklvrGLakllereaef 77 
                                       ML++dllrv+r+gg ++p+f+++++++laa+ i++++ hvGe rg+le++l++le+e++d+klvrG+a+llerea+f
  gi|336255577|ref|YP_004598684.1|   1 MLTKDLLRVSRAGGGYHPQFADRSHRPLAARGIGTYQGHVGEARGDLEDALESLERESEDFKLVRGFAALLEREATF 77 
                                       ***************************************************************************** PP

                            DUF790  78 etespldpeelReevFeaaaea.vvseeereevleevaeelgvspeeveealyadleenkiLtef.eeitpeeLlkr 152
                                       et+++++pe++R+++Feaa+++ vv+e+er+++l ++ae l+vs++++e+alyadle++++L+++ ++++p+ L+++
  gi|336255577|ref|YP_004598684.1|  78 ETDAAIEPERARKAAFEAAEAVgVVDEDERAMALIRAAEPLEVSADDLERALYADLEDRQVLAAVePRWDPDGLIDQ 154
                                       ********************99******************************************9779********* PP

                            DUF790 153 YNlslvqtlLfkatelrirvsdaeykelfravkllgLmyeieedaee..........gleitvdGPaslfkaterYG 219
                                       YNlsl+qt+Lf+ate+r+++sd+  k+l++a+k+l+Lmyei+  + e          ++e++v+GP++lf+at+rYG
  gi|336255577|ref|YP_004598684.1| 155 YNLSLAQTALFDATEVRVHSSDP--KALVSAIKRLRLMYEIRAPDGEagstsadlasDREVVVTGPTHLFRATRRYG 229
                                       **********************8..*****************999889***************************** PP

                            DUF790 220 lalAkllpallkvekWeleAeikdrdkkkrelrfeldsedsglvshyeeeke..fdssveeefaerfeklktdwele 294
                                       +++A+ll++++++e+W+leA+i+dr+   +e+++el++ed + v+++e++++  fds ve++fa+r+e+l+ dw+l+
  gi|336255577|ref|YP_004598684.1| 230 TRFARLLRTVASAEEWHLEATIDDRG---TERTLELSHEDPVAVPDAEPVTDvqFDSGVEADFAARIENLDLDWTLV 303
                                       *************************9...*********************9999*********************** PP

                            DUF790 295 repellkiggsvmiPDFale.ekdgrrvyleIvGfwtpeylkkKleklrkaerkelivavserlklekagvkakdlr 370
                                       repe+l++g++vmiPDFa+e e++++rvyleI+Gfwtpey++kKl++l+ +e+++++vav+e+l+++++ ++a+d+r
  gi|336255577|ref|YP_004598684.1| 304 REPEPLATGTRVMIPDFAFEyEHTDFRVYLEIMGFWTPEYVDKKLAQLEGLEDVDMLVAVDESLGVGEE-IAARDHR 379
                                       ********************99*********************************************97.******* PP

                            DUF790 371 vilfkdklrvkdVlevl 387
                                       +i++++++rvkdV++vl
  gi|336255577|ref|YP_004598684.1| 380 AIPYSGSVRVKDVVDVL 396
                                       **************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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 0.24s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 4033.85
//
Query:       gi|336255578|ref|YP_004598685.1|  [L=189]
Description: hypothetical protein Halxa_4204 [Halopiger xanaduensis SH-6]
Scores for 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-07   30.2   0.0    4.8e-07   29.4   0.0    1.4  1  DisA_N    DisA bacterial checkpoint controller nucleotide-bin


Domain annotation for each model (and alignments):
>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   2.7e-11   4.8e-07      52     118 ..      92     171 ..      78     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.7e-11
                                       TTCSSEEEEE.TTEE....EEEEEEE--TT......-TTS.ST-SHHHHHHHHHHHHSSSE.EEEE-TTTS-EEEEE CS
                            DisA_N  52 plhDGAviir.dgri....vaagviLplse......nkel.kelGtRHraAlgiseetdal.vivVSeetgkislak 115
                                          DGAv+++ dg +    v++  ++p ++      + e  + +G+RH +Al +s++ + + +++ Seetg++s+++
  gi|336255578|ref|YP_004598685.1|  92 RSQDGAVVVSvDGVVqrqmVRFTDLMPGERddlapqRAEYeDWMGSRHMSALDTSRRPNVVaTLTLSEETGRVSVFE 168
                                       568*****95365551111455556666435888754555459*************997762699************ PP

                                       TTE CS
                            DisA_N 116 dgk 118
                                       +g 
  gi|336255578|ref|YP_004598685.1| 169 NGA 171
                                       *96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 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:                        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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1482.91
//
Query:       gi|336255579|ref|YP_004598686.1|  [L=489]
Description: type III restriction protein res subunit [Halopiger xanaduensis SH-6]
Scores for 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-25   89.4   0.0    6.7e-25   88.1   0.0    1.7  2  ResIII         Type III restriction enzyme, res subunit
    7.6e-17   61.3   0.0    1.1e-16   60.9   0.0    1.2  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    5.2e-15   55.7   0.0    2.7e-14   53.5   0.0    2.1  3  Helicase_C     Helicase conserved C-terminal domain
    8.9e-15   54.3   1.3    2.3e-14   53.0   1.3    1.8  1  XPB_DRD        Xeroderma pigmentosum group B helicase damage 
    1.8e-06   27.8   0.0    1.7e-05   24.7   0.0    2.1  1  DEAD           DEAD/DEAH box helicase
     0.0002   20.2   0.0      0.019   13.7   0.0    2.5  2  SNF2_N         SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.029   14.6   0.0        9.9    6.3   0.0    2.6  3  Helicase_C_2   Helicase C-terminal domain
        0.1   12.8   0.0        2.9    8.2   0.0    2.9  2  AAA_22         AAA domain


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.0     3e-28   6.7e-25       2     171 .]      92     254 ..      91     254 .. 0.93
   2 ?   -2.1   0.0       1.5   3.4e+03      96     118 ..     361     389 ..     303     416 .. 0.57

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 3e-28
                                       -EE-HHHHHHHHHHT.........................TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEE CS
                            ResIII   2 lelreyQeeaienlleklks...................krdkrglikmaTGtGKTlvaaklierllkkgkeekflf 59 
                                       +elr+yQ ea+ ++le  +                         g+++++TG+GKT++a+k+ierl++      +l+
  gi|336255579|ref|YP_004598686.1|  92 YELRDYQHEALSAWLER-DRwadgtgaatageaeidaapSAAPAGVLELPTGSGKTVIALKAIERLAT-----PTLV 162
                                       689***********944.3346688888888898888877777************************9.....8*** PP

                                       EESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEE CS
                            ResIII  60 lvprkslleqtleefkkflseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdvi 136
                                       +vp+++lleq++ e++  ++++   ig +  g+++ +         i+v+t++s++ +         +   drf ++
  gi|336255579|ref|YP_004598686.1| 163 VVPTIDLLEQWIGELETEFDCP---IGRFGGGEQRLE--------PITVSTYDSAYLKA--------DSVGDRFGLV 220
                                       *********************9...999999999999........***********999........99******** PP

                                       EEETGGGTTS.TTTHHHHHT---SEEEEEESS-S- CS
                            ResIII 137 iiDEaHrlgakkswreilekfkeavllglTATper 171
                                       ++DE+H+lg+ + +rei++ + +  +lglTAT+er
  gi|336255579|ref|YP_004598686.1| 221 VFDEVHHLGG-EGYREIARLLAAPARLGLTATFER 254
                                       **********.*********************985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                                       -.............-SEEEEEHHHHHHTH CS
                            ResIII  96 a......kekdstnkkilvttiqsldads 118
                                       +         ++ ++ i++t ++ +  d 
  gi|336255579|ref|YP_004598686.1| 361 IealegiLDDHRGERTIVFTAYNDVAYDV 389
                                       23444444455666666666666665555 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 !   60.9   0.0   4.7e-20   1.1e-16      46     181 ..     361     488 ..     343     489 .] 0.86

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 4.7e-20
                     ERCC3_RAD25_C  46 fracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkfkknpkvntiflskvgDtsiDl 122
                                       ++a+e +++  ++rg++ ivf+       ++++++  p i+ +t+ aer++il++f++  +++ i  s+v D+ +D+
  gi|336255579|ref|YP_004598686.1| 361 IEALEGILD--DHRGERTIVFTAYNDVAYDVSERFLIPTITHQTPAAERQEILERFREG-TYSRIATSNVLDEGVDV 434
                                       555555554..459999****977666778899999999******************87.7889************* PP

                     ERCC3_RAD25_C 123 PeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemaystkr 181
                                       P+a+v + +s   gs r   qrlGriLr+k +    + +a  Y +v  +t+e   +++r
  gi|336255579|ref|YP_004598686.1| 435 PDASVAVVLS-GSGSEREFTQRLGRILRPKDD----GGRALLYEIVTANTSEERAAERR 488
                                       *****99776.579****************98....899*************9999988 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 ?   -1.5   0.0       1.5   3.3e+03      16      35 ..     157     174 ..     144     191 .. 0.68
   2 ?   -3.5   0.0       5.7   1.3e+04      42      62 ..     287     307 ..     278     323 .. 0.68
   3 !   53.5   0.0   1.2e-17   2.7e-14       2     109 ..     360     461 ..     359     463 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.5
                                       TSEEEEEESSHHHHHHHHHH CS
                        Helicase_C  16 ggkilifvntidrlekvkll 35 
                                          +l++v+tid le+  ++
  gi|336255579|ref|YP_004598686.1| 157 ATPTLVVVPTIDLLEQ--WI 174
                                       4568999999998874..33 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.7
                                       TEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  42 kvavlhgelpqnereeileqf 62 
                                        v +l  +l+ +eree  ++ 
  gi|336255579|ref|YP_004598686.1| 287 DVKRLEVDLTPEEREEYERAQ 307
                                       566777888888888766554 PP

  == domain 3  score: 53.5 bits;  conditional E-value: 1.2e-17
                                       HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                       k+eal  +l   ++g+++++f+ + d ++  ++    + + + +++ ++p+ er+eile+f++g++  + +++v+ +
  gi|336255579|ref|YP_004598686.1| 360 KIEALEGIL-DDHRGERTIVFTAYNDVAY--DVS---ERFLIPTITHQTPAAERQEILERFREGTYSRIATSNVLDE 430
                                       889999999.89**************997..555...34567778999***************************** PP

                                       SSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       G+d+p++++ + ++   + +++ qr GR+ R
  gi|336255579|ref|YP_004598686.1| 431 GVDVPDASVAVVLSGSGSEREFTQRLGRILR 461
                                       *****************************99 PP

>> XPB_DRD  Xeroderma pigmentosum group B helicase damage recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   1.3     1e-17   2.3e-14       1      57 []      14      77 ..      14      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1e-17
                                      EEEETTEEEECSSSTT........-C..T.EEETTTTEEEEEGGGHHHHHHHHHCTT--EEEES CS
                           XPB_DRD  1 LrYdrGTllidgdprgka.s....lp..fvewDeRvekyRapAlrYrdlveaLraagiefeDrv 57
                                      LrY++GT++idg+++ ++       p  ++e+D+R++++R+pA+rY++l++aL   +++ eD v
  gi|336255579|ref|YP_004598686.1| 14 LRYEDGTIRIDGLEEPTDrAirdsAPelELEADSRTDGWRVPAFRYAALRQALAGIDASLEDAV 77
                                      9*************9977535677556779*******************************987 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   7.4e-09   1.7e-05      19     146 ..     137     241 ..      96     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 7.4e-09
                                       EEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.STSEEEEEETTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  19 vaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.idlrvlliiggvaardqlskl 94 
                                       ++ +TGsGKT ++l + ++++       ++ +l+v+Pt  L eq + +l++ ++  i+      +gg ++r +    
  gi|336255579|ref|YP_004598686.1| 137 LELPTGSGKTVIALKA-IERL-------ATPTLVVVPTIDLLEQWIGELETEFDCpIG-----RFGGGEQRLE---- 196
                                       6789******996655.5455.......3468*****************999994344.....3566555444.... PP

                                       HTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  95 dngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinril 146
                                            i+v+t +             +++ ++V+DE++ l  +g+++  + ++
  gi|336255579|ref|YP_004598686.1| 197 ----PITVSTYDSAYLKA---DSVGDRFGLVVFDEVHHLGGEGYREIARLLA 241
                                       ....44555554444322...22245899**************999877654 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   8.4e-06     0.019      55     116 ..     132     178 ..      96     182 .. 0.78
   2 !    3.8   0.0    0.0086        19     257     327 ..     259     325 ..     210     355 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.4e-06
                                       T--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--H.HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                            SNF2_N  55 vrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPa.slldqWeneie 116
                                        + G+L   +G GKTv +l  i                 +la+ptL+vvP+ +ll+qW  e+e
  gi|336255579|ref|YP_004598686.1| 132 APAGVLELPTGSGKTVIALKAIE----------------RLATPTLVVVPTiDLLEQWIGELE 178
                                       55566666667777777666666................6889***************99986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0086
                                       HHHHHTT-STTEE---GGGT.--S---EEEEEEEEE--HHHHHHHH....................HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 257 rsrLlqllqrlmlrrakkdv.eknlPpkteeiiflklskverksYnrllevlrkkalakllkrseaalksss 327
                                        + + +++ +l+ r   +++    l+p  ++ + ++l+++er+ Y+r     ++++ +  l +s++ ++s+s
  gi|336255579|ref|YP_004598686.1| 259 HEVIEEIVGPLVHRVDVDELaGDHLAPYDVKRLEVDLTPEEREEYER-----AQETFSDYLAKSNIRMQSGS 325
                                       344556777899999999994446**********************3.....33334444444444444444 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 ?   -3.0   0.0       3.1     7e+03       8      32 ..     156     180 ..     150     184 .. 0.79
   2 ?    5.2   0.0    0.0095        21      40      88 ..     398     442 ..     374     445 .. 0.74
   3 ?    6.3   0.0    0.0044       9.9     129     151 ..     450     472 ..     448     483 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.1
                      Helicase_C_2   8 vpggvlvffpSyklleevverlkee 32 
                                           +lv++p  +lle+ + +l++e
  gi|336255579|ref|YP_004598686.1| 156 LATPTLVVVPTIDLLEQWIGELETE 180
                                       5567899999999999999998876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0095
                      Helicase_C_2  40 ifveekeesrekvleeykekkkkgaillavcrGklsEGidfsddllrav 88 
                                       i +++ +++r+++le+++e  ++ + +  +    l EG+d++d+++ +v
  gi|336255579|ref|YP_004598686.1| 398 ITHQTPAAERQEILERFRE--GTYSRIATSN--VLDEGVDVPDASVAVV 442
                                       445558899**********..4444444444..59*******9988776 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0044
                      Helicase_C_2 129 ravnQaiGRliRhkdDygaivll 151
                                       r++ Q +GR++R kdD g  +l 
  gi|336255579|ref|YP_004598686.1| 450 REFTQRLGRILRPKDDGGRALLY 472
                                       6789*************998886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0013       2.9      13     116 ..     140     240 ..     131     252 .. 0.60
   2 ?   -1.3   0.0         1   2.4e+03      42      70 ..     438     466 ..     407     484 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                            AAA_22  13 esGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka........erlsseell.e 80 
                                       ++G+GKT+ + +  e+l           +++ v ++ +  +++   el  +++ +  +        e+ + + +  +
  gi|336255579|ref|YP_004598686.1| 140 PTGSGKTVIALKAIERL---------ATPTLVVVPTIDL-LEQWIGELETEFDCPIGRfgggeqrlEPITVSTYDsA 206
                                       67888888887777777.........4555544444444.4555555555555555556663333333333333323 PP

                            AAA_22  81 aleqalrarav....ielliiDEaqhlrseealeeLrsll 116
                                       +l              +l++ DE++hl   e ++e+ +ll
  gi|336255579|ref|YP_004598686.1| 207 YLKAD-----SvgdrFGLVVFDEVHHL-GGEGYREIARLL 240
                                       33333.....2344448**********.988888886665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1
                            AAA_22  42 vvfvtlpsstsskdllrellralglelka 70 
                                        v v l++s+s +++ ++l r+l  + ++
  gi|336255579|ref|YP_004598686.1| 438 SVAVVLSGSGSEREFTQRLGRILRPKDDG 466
                                       46788888889999999998888755444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); 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 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3660.97
//
Query:       gi|336255580|ref|YP_004598687.1|  [L=177]
Description: response regulator receiver protein [Halopiger xanaduensis SH-6]
Scores for 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-19   69.0   0.0    4.5e-19   68.7   0.0    1.1  1  Response_reg  Response regulator receiver domain


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 !   68.7   0.0   2.5e-23   4.5e-19       1     111 [.      26     146 ..      26     147 .. 0.94

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 2.5e-23
                                       EEEESSSHHHHHHHHHHHHHTTE.EEEEEESSHHHHHHHHHHHH.......ESEEEEESSCSSSEHHHHHHHHHHCT CS
                      Response_reg   1 vlivdDdplvrellrqlleeegy.eevaeaedgkealellkeek.......vdlillDinmpgmdGlellkeireed 69 
                                       vl+++D+p  ++l++++++++ +  + ++++dg ea++ l++++       +d++llD+n+p+ dG+e+l+ ir ++
  gi|336255580|ref|YP_004598687.1|  26 VLLIEDNPGDVRLTKEAFRDASFdADLHVVTDGVEAMAFLHRDDeyesaprPDIVLLDLNLPRKDGFEVLEAIRGDP 102
                                       89*****************888834667************88888889999************************** PP

                                       ..TTSEEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  70 ..pelpviiltahseeedavealkagaddflsKpfdpeeLlkal 111
                                         ++lpv++l++ +++ed+ + ++  ++ +l+Kp +p+e ++++
  gi|336255580|ref|YP_004598687.1| 103 alEQLPVVVLSSSEADEDVRRSYEEHVNAYLTKPRAPDEFVEMV 146
                                       999*************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1427.92
//
Query:       gi|336255581|ref|YP_004598688.1|  [L=151]
Description: response regulator receiver protein [Halopiger xanaduensis SH-6]
Scores for 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-16   59.5   0.2    3.8e-16   59.2   0.2    1.1  1  Response_reg  Response regulator receiver domain


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 !   59.2   0.2   2.1e-20   3.8e-16       1     111 [.      13     135 ..      13     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 2.1e-20
                                       EEEESSSHHHHHHHHHHHH.HTTEEEEEEESSHHHHHHHHHHHH.......ESEEEEESSCSSSEHHHHHHHHHHCT CS
                      Response_reg   1 vlivdDdplvrellrqlle.eegyeevaeaedgkealellkeek.......vdlillDinmpgmdGlellkeireed 69 
                                       +l+v+D+p  ++l++++++  + +++ ++++dg++al+ ++++        +d++llD+++p++dG ++l e++ ++
  gi|336255581|ref|YP_004598688.1|  13 ILLVEDNPGDVRLVEEAFRdGHLINQLHTVTDGQAALDFVHRRGeyadaprPDIVLLDLKLPRVDGEDVLHEVKHHP 89 
                                       89*****************5466799**************77666777888************************** PP

                                       ..TTSEEEEEESSTSHHHHHHHHHCTESE..EEESSG-HHHHHHHH CS
                      Response_reg  70 ..pelpviiltahseeedavealkagadd..flsKpfdpeeLlkal 111
                                         +++pv+il++ +ee    + l+ +ad+  +++Kp+dp+e ++ +
  gi|336255581|ref|YP_004598688.1|  90 klEDVPVVILSGMDEERIESRDLDHDADEdaVIQKPVDPDEFVEVI 135
                                       9999**********999999999887764349*********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1210.88
//
Query:       gi|336255582|ref|YP_004598689.1|  [L=386]
Description: protein grpE [Halopiger xanaduensis SH-6]
Scores for complete 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  148.6  10.5    1.2e-43  148.6  10.5    2.2  2  GrpE             GrpE
      6e-06   25.6   9.6    9.2e-06   25.0   9.6    1.3  1  Atg14            Vacuolar sorting 38 and autophagy-related su
    1.7e-05   24.5   4.6    2.4e-05   24.1   4.6    1.3  1  Exonuc_VII_L     Exonuclease VII, large subunit
    0.00031   19.3  20.8    0.00045   18.7  20.8    1.2  1  MAD              Mitotic checkpoint protein
    0.00033   20.6  10.2    0.00033   20.6  10.2    2.9  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
    0.00041   19.3  19.0    0.00041   19.3  19.0    1.8  2  Spc7             Spc7 kinetochore protein
    0.00084   19.5  18.5    0.00084   19.5  18.5    2.5  3  UPF0242          Uncharacterised protein family (UPF0242) N-t
     0.0015   17.6   4.4     0.0015   17.6   4.4    3.5  3  IFT57            Intra-flagellar transport protein 57
     0.0015   18.6  10.2     0.0081   16.3   3.2    2.4  2  DUF148           Domain of unknown function DUF148
     0.0023   17.7  10.5     0.0023   17.7  10.5    1.8  1  DUF745           Protein of unknown function (DUF745)
     0.0029   16.6  16.3     0.0047   15.9  16.3    1.3  1  DUF812           Protein of unknown function (DUF812)
      0.003   18.0  19.7     0.0067   16.9  19.7    1.6  1  Fez1             Fez1
     0.0039   16.6   8.9     0.0074   15.7   8.9    1.4  1  FAM76            FAM76 protein
     0.0075   16.3  15.6      0.024   14.6   0.0    3.8  3  Bap31_Bap29_C    Bap31/Bap29 cytoplasmic coiled-coil domain
     0.0086   15.4  18.5     0.0089   15.3  13.2    2.1  2  MPS2             Monopolar spindle protein 2
     0.0092   16.1  14.9       0.14   12.3   0.5    3.5  3  Med9             RNA polymerase II transcription mediator com
  ------ inclusion threshold ------
       0.01   15.9  12.4      0.021   14.9  12.4    1.6  1  ADIP             Afadin- and alpha -actinin-Binding
      0.015   15.6   7.5      0.031   14.5   1.1    3.0  3  DUF948           Bacterial protein of unknown function (DUF94
      0.015   15.1   8.8      0.015   15.1   8.8    2.0  2  DUF724           Protein of unknown function (DUF724)
      0.017   15.3  11.9      0.064   13.4   0.7    2.3  2  Fib_alpha        Fibrinogen alpha/beta chain family
      0.018   15.7  21.9       0.19   12.3   6.6    2.6  2  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
      0.018   12.6  23.4       0.03   11.9  23.4    1.3  1  DUF3584          Protein of unknown function (DUF3584)
      0.028   13.0   1.5      0.036   12.6   1.5    1.1  1  Utp8             Utp8 family
      0.036   13.5   3.0       0.28   10.6   0.5    2.1  2  Mce4_CUP1        Cholesterol uptake porter CUP1 of Mce4, puta
      0.048   13.7  25.7      0.028   14.5  22.9    2.0  1  DHR10            Designed helical repeat protein 10 domain
      0.053   14.1  16.0       0.54   10.8   6.8    2.7  2  Syntaxin-6_N     Syntaxin 6, N-terminal
      0.057   12.1  13.7      0.088   11.4  13.7    1.2  1  AAA_13           AAA domain
      0.061   11.5  23.5       0.12   10.5  23.2    1.6  1  HOOK             HOOK protein
      0.092   10.7   3.1       0.14   10.1   3.1    1.3  1  Prominin         Prominin
      0.094   13.2  16.8      0.054   14.0   7.7    2.8  2  DUF16            Protein of unknown function DUF16
       0.11   13.1   5.6        4.1    8.1   0.1    2.7  2  CHASE6_C         C-terminal domain of two-partite extracellul
       0.12   13.0  13.9      0.041   14.5   6.5    2.8  3  BST2             Bone marrow stromal antigen 2
       0.13   11.8   7.3       0.18   11.3   6.0    1.9  2  CAP_N            Adenylate cyclase associated (CAP) N termina
       0.13   12.3  11.7       0.88    9.6   1.4    2.4  2  Laminin_II       Laminin Domain II
       0.15   11.5   3.1       0.28   10.6   3.1    1.4  1  DIT1_PvcA        Pyoverdine/dityrosine biosynthesis protein
       0.18   11.5  11.9        0.3   10.8  11.9    1.4  1  CR6_interact     Growth arrest and DNA-damage-inducible prote
       0.19   11.8  16.4       0.62   10.2  16.1    2.0  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.24   11.2   8.3        1.9    8.3   1.4    2.6  2  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
       0.34   10.1  11.9      0.042   13.1   5.4    1.9  2  TMPIT            TMPIT-like protein
       0.34   10.7  20.9      0.047   13.5  15.7    1.9  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
       0.35   10.9   0.8       0.98    9.5   0.8    1.7  1  VitD-bind_III    Vitamin D binding protein, domain III
       0.35   10.4   8.2       0.66    9.5   8.2    1.5  1  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
       0.43   10.9  19.3          1    9.7  19.1    1.7  1  Troponin         Troponin
       0.51   10.4  21.1        2.6    8.1  12.9    2.6  2  DivIVA           DivIVA protein
       0.63   10.0  18.2       0.75    9.8   1.0    2.5  2  Sipho_Gp157      Siphovirus Gp157
       0.68   10.3  22.2        9.9    6.6   2.0    3.8  3  Csm1_N           Csm1 N-terminal domain
        0.8   10.0   9.0        5.5    7.4   5.8    2.6  4  KxDL             Uncharacterized conserved protein
        0.8    9.8  13.9       0.13   12.4   6.3    2.6  3  COG2             COG (conserved oligomeric Golgi) complex com
       0.85    9.9  16.4        2.4    8.5   0.4    3.1  3  DUF5082          Domain of unknown function (DUF5082)
       0.91   10.0  10.2        3.5    8.2   3.1    3.6  2  NPV_P10          Nucleopolyhedrovirus P10 protein
          1    9.1  16.2      0.042   13.7  10.1    1.7  1  Erythro_esteras  Erythromycin esterase
        1.1    8.9  23.3        5.8    6.5   5.0    2.5  2  Lebercilin       Ciliary protein causing Leber congenital ama
        1.3    9.3  24.6          1    9.6  12.7    2.5  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        1.3    9.7  11.9         12    6.6   0.5    3.2  3  YabA             Initiation control protein YabA
        1.4    8.9  21.0        6.3    6.8   0.6    3.6  3  Prefoldin_2      Prefoldin subunit
        1.6    8.8  12.1       0.89    9.6   5.8    2.7  3  DUF1664          Protein of unknown function (DUF1664)
        1.6    8.9  34.3      0.033   14.4  26.2    2.3  2  ATG16            Autophagy protein 16 (ATG16)
        1.7    8.7   8.5       0.87    9.6   0.1    3.2  2  Spc42p           Spindle pole body component Spc42p
        1.9    8.8  10.1       0.83   10.0   5.1    2.5  2  BLOC1_2          Biogenesis of lysosome-related organelles co
        2.5    8.6  12.0        6.8    7.2   6.2    3.3  2  DASH_Dad2        DASH complex subunit Dad2
        2.7    7.2  21.6       0.74    9.1   6.0    2.5  2  DUF3450          Protein of unknown function (DUF3450)
        3.5    8.1  11.8        8.4    6.9   0.5    3.6  4  FlaC_arch        Flagella accessory protein C (FlaC)
        3.9    6.1   7.5        5.6    5.5   7.5    1.2  1  SpoVR            SpoVR like protein
        5.2    7.0   8.7        2.9    7.8   4.8    2.2  2  DinB             DinB family
        5.4    7.7  12.9          1   10.0   1.7    2.5  2  ING              Inhibitor of growth proteins N-terminal hist
        6.1    7.5  18.7        6.9    7.4  11.5    3.7  3  SlyX             SlyX
        7.1    6.8  25.4         11    6.3   1.4    2.5  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
        7.8    4.9  10.6         11    4.3  10.6    1.2  1  FUSC             Fusaric acid resistance protein family
          8    6.9  11.8         45    4.5  10.4    2.6  2  Syntaxin_2       Syntaxin-like protein


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 ?    4.3   1.1      0.11        28       5      56 ..      85     136 ..      77     140 .. 0.83
   2 !  148.6  10.5   4.8e-46   1.2e-43       6     165 ..     142     299 ..     138     300 .. 0.97

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.11
                                       ..CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHH CS
                              GrpE   5 eeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeea 56 
                                       e+   +++  +el ++++++ +++++l+  ++++++e+e l++r+e ++e +
  gi|336255582|ref|YP_004598689.1|  85 EVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETI 136
                                       5555566667788888999999************************999875 PP

  == domain 2  score: 148.6 bits;  conditional E-value: 4.8e-46
                                       .CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC. CS
                              GrpE   6 eeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksa 82 
                                       e e+ e+++e+ +ee++e e++v++lk++l+r++a+f+n++kr++k++e++k+ a e++++ L++v+Dnl+ral+  
  gi|336255582|ref|YP_004598689.1| 142 ELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKDRATEDLVERLVDVRDNLKRALEE- 217
                                       67888999*******************************************************************8. PP

                                       .HHH-HHHHHHHHHHHHHHHHHHHHHTT-EE---T.TSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEEEE CS
                              GrpE  83 keneeekslleGvemtlkqllkiLekhgvekiepk.gepFDpnlheavstveddekeegtvvevvqkGYklkdrvlR 158
                                        e+ +++sl eGvemt ++++ +Le ++v +i+p+ g + Dp+ he++++v++d+ +egt+ +v++ GY ++d+v+ 
  gi|336255582|ref|YP_004598689.1| 218 -ESGDVESLREGVEMTMREFDRVLEDENVSEIDPEpGTETDPQRHEVMMRVDSDQ-PEGTIADVYTAGYEMGDKVIQ 292
                                       .9*****************************************************.********************* PP

                                       -EEEEEE CS
                              GrpE 159 pAmVkVs 165
                                        A+V+Vs
  gi|336255582|ref|YP_004598689.1| 293 NAQVTVS 299
                                       ******8 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 !   25.0   9.6   3.5e-08   9.2e-06      24     135 ..      80     195 ..      57     237 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.5e-08
                             Atg14  24 lyelrerlaklksekeslkkkiekalegke....eaeqledkiknkkakleelksliadlrerlqelkdklsqlkke 96 
                                        ++ +e l +l +  ++l +k+++++e+ +     ++ ++++++ +++++e++  +i dl+++l+  ++ ++ +++e
  gi|336255582|ref|YP_004598689.1|  80 SEDVQEVLDRLTEYDDELARKVNAIVEQARdlsgTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEE 156
                                       567788899999******************55555555555555555555555555555555555555555555555 PP

                             Atg14  97 ieekkkklaklsdklkkRrsdleslqneleerrkkqiak 135
                                       i+e  ++++ l++ lk++++d +  +++ ++r++++ ++
  gi|336255582|ref|YP_004598689.1| 157 IAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKDR 195
                                       555555555555555566666555555555555555444 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 !   24.1   4.6   9.1e-08   2.4e-05     137     245 ..     103     218 ..      76     302 .. 0.58

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 9.1e-08
                      Exonuc_VII_L 137 lvvpdkaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrer 213
                                       ++v++ ++l  ++++++++le+ ++ ++e++++ +  l+ +l+  e+ +e++ +++ e+ee++e  lk++lk+k+++
  gi|336255582|ref|YP_004598689.1| 103 AIVEQARDLSGTVDHQREELEDLTE-RVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVED-LKSRLKRKQAD 177
                                       3444444444455555555444442.345555566666666666666666666666666666666.66667777777 PP

                      Exonuc_VII_L 214 leelkerlkekleekk........erlkklkerle.lleek 245
                                       ++++k+r k++ e+ k        erl +++++l+  lee+
  gi|336255582|ref|YP_004598689.1| 178 FQNYKKRAKKRQEQIKdratedlvERLVDVRDNLKrALEEE 218
                                       77777666322222221111111122222222222323333 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7  20.8   1.7e-06   0.00045      35     169 ..      65     199 ..      41     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                               MAD  35 kasalkrqleeesdrnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekesklaearevisalkn 111
                                       +a + +     + + ++++q+ + +l + + e ++++++ +E+ar +  + +++ +++++ ++++++  e+i  l++
  gi|336255582|ref|YP_004598689.1|  65 AADSEAGGDGDTPETSEDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQD 141
                                       2222222233456677777888888888888888999999************************************* PP

                               MAD 112 elaelkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkelaeae 169
                                       el+++++ ie+ + e+ e e+++e+l+ rl+ +++ +++++++ ++ +++ k +a+++
  gi|336255582|ref|YP_004598689.1| 142 ELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKDRATED 199
                                       ********************************************99999999888765 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6  10.2   1.3e-06   0.00033      15      74 .]     116     175 ..     112     175 .. 0.96
   2 ?   -0.7   1.6       5.8   1.5e+03      49      67 ..     208     226 ..     179     230 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.3e-06
                        TMF_DNA_bd  15 aqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlkeae 74 
                                       +  +eE+e+L      + +ti  L+ +++  e+ i++ +++++++e+++e l++rlk+++
  gi|336255582|ref|YP_004598689.1| 116 DHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQ 175
                                       6679*****************************************************986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 5.8
                        TMF_DNA_bd  49 ikelkkkleklekeleele 67 
                                        ++lk+ le+++ ++e+l+
  gi|336255582|ref|YP_004598689.1| 208 RDNLKRALEEESGDVESLR 226
                                       3456666666666666665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3  19.0   1.6e-06   0.00041     162     273 ..      80     194 ..      77     203 .. 0.76
   2 ?    2.5   4.4      0.21        55     141     213 ..     168     227 ..     165     249 .. 0.46

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.6e-06
                              Spc7 162 eeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkkelaelqeqleeleek 235
                                        e ++e+l++l+e+ +el ++++ + e+a++l+     ++eeLe l e+++++ ++i  +++el+ +++ +e+ +e+
  gi|336255582|ref|YP_004598689.1|  80 SEDVQEVLDRLTEYDDELARKVNAIVEQARDLSGtvdHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEE 156
                                       57788888888888888888888888888888765334478888888888888888888888888888888888888 PP

                              Spc7 236 ieelkeqkseleeeiaeaervleeckgwsesevsrlke 273
                                       i+e +eq ++l++++++++   ++ k+  ++  +++k+
  gi|336255582|ref|YP_004598689.1| 157 IAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKD 194
                                       88888888888888888888877777766665555555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.21
                              Spc7 141 kegleenlegleedkelLekqeeeldellpeleeekaeleeel.eklqeaaeelesidkeeLeelreelaelka 213
                                       k              ++L+++++ +++++++ +++++++++++ e+l e+  ++ +  k  Lee   ++++l +
  gi|336255582|ref|YP_004598689.1| 168 K--------------SRLKRKQADFQNYKKRAKKRQEQIKDRAtEDLVERLVDVRDNLKRALEEESGDVESLRE 227
                                       3..............34444445555555555555555544431234444444444334444444444444433 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 ?    3.1   1.7      0.35        92     106     144 ..      81     119 ..      37     128 .. 0.54
   2 !   19.5  18.5   3.2e-06   0.00084      70     167 ..     115     213 ..     111     224 .. 0.87
   3 ?    2.5   1.9      0.52   1.4e+02      85     137 ..     186     240 ..     180     245 .. 0.52

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.35
                           UPF0242 106 dakeeelerlkeenqqLqekleaiaedfeelkleleeqL 144
                                       +  +e l rl+e + +L  k +ai+e+  +l+  ++ q 
  gi|336255582|ref|YP_004598689.1|  81 EDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQR 119
                                       334444445555555555555554444444433333322 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 3.2e-06
                           UPF0242  70 leekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLae 146
                                       ++++ + l +l e ++ ++e++ +lq+e e +++ ++ ++ee+++++e+ + L+++l+  ++df+++k+ ++++ ++
  gi|336255582|ref|YP_004598689.1| 115 VDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQ 191
                                       567888899999**********************************************************9988877 PP

                           UPF0242 147 .kqellqeyqetieeqrsvlek 167
                                        k    +++ e +++ r  l++
  gi|336255582|ref|YP_004598689.1| 192 iKDRATEDLVERLVDVRDNLKR 213
                                       3444566788888888887765 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.52
                           UPF0242  85 ktkeealeelqeeeeeLkee.........ldakeeelerlkeenqqLqekleaiaedfeelk 137
                                       k+ +e+++++         e          d+ +++le+   + ++L+e  e++ ++f++++
  gi|336255582|ref|YP_004598689.1| 186 KKRQEQIKDRAT-------EdlverlvdvRDNLKRALEEESGDVESLREGVEMTMREFDRVL 240
                                       334444544443.......2333333111444444444444445688888888888888765 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   4.4   5.7e-06    0.0015     251     329 ..      80     158 ..      73     161 .. 0.96
   2 ?    5.9   4.9     0.021       5.4     237     308 ..     161     237 ..     156     247 .. 0.63
   3 ?   -1.3   8.6       3.2   8.4e+02     112     188 ..     288     364 ..     284     378 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.7e-06
                             IFT57 251 hedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergss 327
                                       +ed++++l+++++ +  l ++++  +++ r+++ ++++++e++++l+e+v+++ ++  ++++ele+ +q +e+r ++
  gi|336255582|ref|YP_004598689.1|  80 SEDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEE 156
                                       799***********************************************************************998 PP

                             IFT57 328 mt 329
                                       ++
  gi|336255582|ref|YP_004598689.1| 157 IA 158
                                       86 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.021
                             IFT57 237 eeslpetksqlkklhedisktlekiesrEkyl.nsqleellqeyreaqeelsevkek....ykqlsegvseltrela 308
                                       ee+++++ks lk+ + d++++ ++ ++r++++ ++  e+l++ + +++++l+ + e+    ++ l egv+   re++
  gi|336255582|ref|YP_004598689.1| 161 EEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIkDRATEDLVERLVDVRDNLKRALEEesgdVESLREGVEMTMREFD 237
                                       67888899999999999999999999998888334456666667777777665544311113344444444444444 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.2
                             IFT57 112 deaLkkkkfkfkkpkypkeeeeeeeeev...eddaelelekveeeelikseeededeedeeeelklesekkee.kek 184
                                       d+++++ ++++++ +  ++e+++e++     +d++   +++  +e ++    +d+ ++ +++e+++  +++ e + +
  gi|336255582|ref|YP_004598689.1| 288 DKVIQNAQVTVSNGELADDEDTDEDDTAdgaDDESTSGADDQGDETDA----ADSSSDSDNAEVNADADADGEdNTD 360
                                       677777788888888887777666665544333444444444444443....3333333333444443333332334 PP

                             IFT57 185 ekee 188
                                        +++
  gi|336255582|ref|YP_004598689.1| 361 AEDD 364
                                       4444 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.6      0.04        10      35     101 ..      63     136 ..      44     144 .. 0.76
   2 !   16.3   3.2   3.1e-05    0.0081      11      94 ..     151     236 ..     145     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.04
                            DUF148  35 deykefeakvkaqkeevkknvtavisnLs....svqekleaIld...nkslTrkeqkeaieelkkqypkevstl 101
                                       d+ ++ ea     + e ++ v++v+ +L+    +  +k++aI++   + s T++ q+e++e l++  + + +t+
  gi|336255582|ref|YP_004598689.1|  63 DDAADSEAGGDGDTPETSEDVQEVLDRLTeyddELARKVNAIVEqarDLSGTVDHQREELEDLTERVESQAETI 136
                                       55555555555666788999*********8888888889999873336789*************9999998888 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.1e-05
                            DUF148  11 knenltiaeieeqleawaeky.gvtdeykefeakvkaqkeevkknvt.avisnLssvqekleaIldnkslTrkeqke 85 
                                       ++++  iae eeq+e++ ++    ++++++++++ k+++e++k+++t + +++L +v ++l++ l+++s  ++  +e
  gi|336255582|ref|YP_004598689.1| 151 EDRDEEIAEYEEQVEDLKSRLkRKQADFQNYKKRAKKRQEQIKDRATeDLVERLVDVRDNLKRALEEESGDVESLRE 227
                                       6677789*************9778999****************9877269************999998877777666 PP

                            DUF148  86 aieelkkqy 94 
                                        +e ++ ++
  gi|336255582|ref|YP_004598689.1| 228 GVEMTMREF 236
                                       666666655 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7  10.5   8.9e-06    0.0023      29     171 ..      42     187 ..      31     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.9e-06
                            DUF745  29 aAaeaAakqvksqLAdkAlqAakAAeAaLaGKqqlveqleqelreaeavvqeekkslqs.seanakaaakaakqaqq 104
                                       + a+ A++  + q A+ A +A  AA+    G      ++ ++++e  + + e  ++l++  +a ++ a++ + ++ +
  gi|336255582|ref|YP_004598689.1|  42 SEAQSASESDRDQSAESAQSADDAADSEAGGDGDT-PETSEDVQEVLDRLTEYDDELARkVNAIVEQARDLSGTVDH 117
                                       57899********************9986666655.55677888888888888888765145556777777766666 PP

                            DUF745 105 qlealkallkaakenlenaeqva...agaqqelaektqlleaAkkRveeLkkqlkearkdlektkkaAyk 171
                                       q e l++l + +++++e++ +++   +  +q ++++ + +++ +++ve Lk++lk  ++d+++ kk A+k
  gi|336255582|ref|YP_004598689.1| 118 QREELEDLTERVESQAETIGDLQdelEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKK 187
                                       66666666666666666665555110566899************************************99 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9  16.3   1.8e-05    0.0047     237     408 ..      42     218 ..      10     235 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-05
                            DUF812 237 teeeykkrkkeklqkrlaeqlrkaalkseeaessasksksdlaellsefseksetdslktkgsrfthaekl..qftk 311
                                       +e++  ++ ++    + a++   aa ++  +  ++ + ++d++e+l++++e + +    + ++ +++a +l  +   
  gi|336255582|ref|YP_004598689.1|  42 SEAQSASESDRDQSAESAQSADDAADSEAGGDGDTPETSEDVQEVLDRLTEYDDE-LARKVNAIVEQARDLsgT--V 115
                                       3444444444445555555555555555555577888889999999999444444.334555566667777442..3 PP

                            DUF812 312 e....ela...kkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekev 381
                                       +    el+   +++e++ e+    ++ele+ ++ ie+ +++i+e+ee++++l+s++k+ +   ++ k+  +++++++
  gi|336255582|ref|YP_004598689.1| 116 DhqreELEdltERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQI 192
                                       32233222555788888888888899999999999999999999999999999999999999999999999999998 PP

                            DUF812 382 klkkktlellpdaeeniekLqalveas 408
                                       k +  t +l++       +L++++e+ 
  gi|336255582|ref|YP_004598689.1| 193 KDR-ATEDLVERLVDVRDNLKRALEEE 218
                                       754.23344444334444455555555 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9  19.7   2.6e-05    0.0067      18     152 ..      89     223 ..      82     243 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-05
                              Fez1  18 QLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekveklee 94 
                                        L ++  e+++k++ iv+   q r+l+ +++++ ee+++l e++e++++ +  +++el+ +++  e  +e++ ++ee
  gi|336255582|ref|YP_004598689.1|  89 RLTEYDDELARKVNAIVE---QARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEE 162
                                       578899999999999996...99****************************************************** PP

                              Fez1  95 elkelreelselsleeeeaalesdeakaqrqe......aeeleelkreverlraeLkeerqkke 152
                                       ++++l+++l++++++ ++ ++++++ ++   +      ++ +e+l    ++l+++L+ee    e
  gi|336255582|ref|YP_004598689.1| 163 QVEDLKSRLKRKQADFQNYKKRAKKRQE---QikdratEDLVERLVDVRDNLKRALEEESGDVE 223
                                       *******999966554444333333222...222233333344444444455555555544433 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   8.9   2.9e-05    0.0074     151     277 ..      47     195 ..      26     215 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.9e-05
                             FAM76 151 kkkskskkskkskekskekkaskkkskkh.......kkrss..................rlevskleeek....... 195
                                        ++s +++s +s ++++++  s+             +   +                            +       
  gi|336255582|ref|YP_004598689.1|  47 ASESDRDQSAESAQSADDAADSE-----AggdgdtpE---TsedvqevldrlteyddelA---------Rkvnaive 106
                                       11222222222221111111111.....122221220...11222233333333333332.........03333333 PP

                             FAM76 196 ....laeekesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelr...e 265
                                           l+ +  +++++ + l  ++  +  ++ +L++e++ +++ +e +d+e+ e + ++ +lk+ l +k+++ +   +
  gi|336255582|ref|YP_004598689.1| 107 qardLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQnykK 183
                                       22332333333333344677777788888999999999999999999999999999999999988888765541104 PP

                             FAM76 266 klkelekeakek 277
                                       + k++++++k++
  gi|336255582|ref|YP_004598689.1| 184 RAKKRQEQIKDR 195
                                       555555555443 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 ?    0.3   0.2       2.7   7.1e+02       3      15 ..     136     148 ..     134     158 .. 0.75
   2 ?    6.2   4.9     0.038        10       1      26 [.     162     187 ..     162     191 .. 0.91
   3 !   14.6   0.0   9.2e-05     0.024       5      37 ..     210     242 ..     209     253 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2.7
                     Bap31_Bap29_C   3 iekLkkeLkkkkk 15 
                                       i  L++eL++ ++
  gi|336255582|ref|YP_004598689.1| 136 IGDLQDELEAREQ 148
                                       778******9884 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.038
                     Bap31_Bap29_C   1 keiekLkkeLkkkkkDlealKkQaeg 26 
                                       +++e Lk+ Lk+k++D ++ Kk a+ 
  gi|336255582|ref|YP_004598689.1| 162 EQVEDLKSRLKRKQADFQNYKKRAKK 187
                                       69********************9975 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 9.2e-05
                     Bap31_Bap29_C   5 kLkkeLkkkkkDlealKkQaeglakEYDrLade 37 
                                       +Lk  L++++ D+e l++  e + +E+Dr+++ 
  gi|336255582|ref|YP_004598689.1| 210 NLKRALEEESGDVESLREGVEMTMREFDRVLED 242
                                       79***************************9985 PP

>> MPS2  Monopolar spindle protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.9      0.23        60     128     189 ..      56     113 ..      25     132 .. 0.63
   2 !   15.3  13.2   3.4e-05    0.0089     164     256 ..     134     231 ..     114     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.23
                              MPS2 128 kdslstprkkilldllkkqesPeklrrsnrklkaLevrveslkdELeakdevlrekeRelle 189
                                       ++s  ++ +    +  +  + Pe++    + ++ +  r+++ +dEL  k + + e+ R+l+ 
  gi|336255582|ref|YP_004598689.1|  56 AESAQSADDAADSEAGGDGDTPETS----EDVQEVLDRLTEYDDELARKVNAIVEQARDLSG 113
                                       2233333333222333444445554....4555556699*******************9974 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.4e-05
                              MPS2 164 vrveslkdELeakdevlrekeRelleLkkrlseykekYellqrefslykarrveksqnslktaikhev.....iisE 235
                                         + +l+dELea+++ +++++ e+ e +++++++k + +  q +f+ yk+r  + +++    a++  v     + ++
  gi|336255582|ref|YP_004598689.1| 134 ETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKDRATEDLVerlvdVRDN 210
                                       457789****************************************9998876665555444444322222235679 PP

                              MPS2 236 lkrklqeqteiisilkeqiqr 256
                                       lkr l+e +  ++ l+e +++
  gi|336255582|ref|YP_004598689.1| 211 LKRALEEESGDVESLREGVEM 231
                                       9********999999999886 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       3.5     9e+02      46      70 ..      77     101 ..      75     104 .. 0.84
   2 !   12.3   0.5   0.00053      0.14      40      78 ..     103     141 ..      99     143 .. 0.90
   3 !   10.7   2.9    0.0017      0.44      44      79 ..     149     184 ..     144     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 3.5
                              Med9  46 pgidrsveeqeaeieeleeqlakKr 70 
                                       p+ ++ v+e ++++ e++++la+K 
  gi|336255582|ref|YP_004598689.1|  77 PETSEDVQEVLDRLTEYDDELARKV 101
                                       5668899999************995 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00053
                              Med9  40 elirelpgidrsveeqeaeieeleeqlakKrelLkkykn 78 
                                       + +++  +++ +v+ q +e+e+l e+++ + e + ++++
  gi|336255582|ref|YP_004598689.1| 103 AIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQD 141
                                       5689999***************************99986 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0017
                              Med9  44 elpgidrsveeqeaeieeleeqlakKrelLkkyknr 79 
                                        +++ d+ ++e e+++e+l+ +l++K++ +++yk+r
  gi|336255582|ref|YP_004598689.1| 149 AIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKR 184
                                       6789999**************************987 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9  12.4   8.1e-05     0.021      27     131 ..      94     198 ..      48     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.1e-05
                              ADIP  27 tekveeniaaiinviysLlqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekk 103
                                       +++++++++ai+    +L    d  +e+ e l+e++++   +i  lq + e  ++  e+ + e+a ++++  +l+ +
  gi|336255582|ref|YP_004598689.1|  94 DDELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSR 170
                                       57777888888888888888888889999999999999999999999999999999999999999999999999999 PP

                              ADIP 104 lktleqklknekeelqrlknalqqiktq 131
                                       lk+ ++  +n k  +++ + ++++++t 
  gi|336255582|ref|YP_004598689.1| 171 LKRKQADFQNYKKRAKKRQEQIKDRATE 198
                                       9999999999999999999999888886 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 ?   14.5   1.1   0.00012     0.031      27      88 ..      79     140 ..      75     141 .. 0.88
   2 ?    1.1   0.2       1.8   4.6e+02      23      70 ..     138     185 ..     134     198 .. 0.71
   3 ?    3.0   0.0      0.46   1.2e+02      22      58 ..     209     245 ..     196     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00012
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       t + +++ ++ l++  d++ ++v+++++++++l   v ++ e+++ lte v+  +e++ +l+
  gi|336255582|ref|YP_004598689.1|  79 TSEDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQ 140
                                       567788999999999999999999999999999999999**********9999999998875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.8
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekv 70 
                                        l++ l++ +++ie+  +++ ++ ++vedl +  ++ ++d ++  ++ 
  gi|336255582|ref|YP_004598689.1| 138 DLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRA 185
                                       566667777788888888888888888888888888777777655554 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.46
                            DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvne 58 
                                        +lk+ l+e +  +e+l++ v+ +++e +++l+  n+
  gi|336255582|ref|YP_004598689.1| 209 DNLKRALEEESGDVESLREGVEMTMREFDRVLEDENV 245
                                       5778888888888999999999999999988887776 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   8.8   5.8e-05     0.015      86     184 ..      82     181 ..      81     185 .. 0.89
   2 ?   -0.2   0.1       2.9   7.6e+02      61      94 ..     195     229 ..     186     278 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.8e-05
                            DUF724  86 dVkalqsrlnkLl.slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeia 161
                                       dV+ +++rl++   +l  + + + e+ ++l   + ++++e + l e ++   ++i +l+ +l++  +  e+ d+eia
  gi|336255582|ref|YP_004598689.1|  82 DVQEVLDRLTEYDdELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIA 158
                                       56666666655532567778889999*************************************999*********** PP

                            DUF724 162 rlkseaekleeeledveqeFeav 184
                                       + + ++e+l+ +l++ + +F++ 
  gi|336255582|ref|YP_004598689.1| 159 EYEEQVEDLKSRLKRKQADFQNY 181
                                       ********************986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.9
                            DUF724  61 lsiddsrseleslkesla.eLekhGFdVkalqsrl 94 
                                          +d ++ l +  ++l+  Le++  dV++l++ +
  gi|336255582|ref|YP_004598689.1| 195 RATEDLVERLVDVRDNLKrALEEESGDVESLREGV 229
                                       44455555555555444323555555555554433 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 ?   13.4   0.7   0.00025     0.064      75     130 ..      94     148 ..      50     152 .. 0.78
   2 ?    5.3   6.6     0.079        20      31     117 ..     151     235 ..     138     245 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  75 ndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqker 130
                                        d++ +k++  +e +  +l  t+d+q ++++ L++ +es+ + i +L+ + +++e+
  gi|336255582|ref|YP_004598689.1|  94 DDELARKVNAIVE-QARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQ 148
                                       2778888888888.889999999999999999999999999999999888777665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.079
                                       CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvL 107
                                       +d ++++++ e+++e+++++ k  +   ++ k+  +++q++ k  d++++++ ++l +   +lk+ + ++   ++ L
  gi|336255582|ref|YP_004598689.1| 151 EDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIK--DRATEDLVERLVDVRDNLKRALEEESGDVESL 225
                                       3345677777888888888888888888888888888888877..67888887777767777888777777888888 PP

                                       HHHHHHHHHH CS
                         Fib_alpha 108 qnvlesneqk 117
                                       ++ +e   ++
  gi|336255582|ref|YP_004598689.1| 226 REGVEMTMRE 235
                                       8777766555 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 ?    8.5   7.2     0.011         3      23      94 ..      88     162 ..      74     167 .. 0.80
   2 ?   12.3   6.6   0.00074      0.19       4      71 ..     171     239 ..     169     247 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.011
                    HIP1_clath_bdg  23 eeverekkeleeelerlkeeaer...kleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqa 94 
                                       + +    +el+++++++ e+a+     +++q+eele L + +e++ + +  l+  Le +eq+ e+  +++a+ ++
  gi|336255582|ref|YP_004598689.1|  88 DRLTEYDDELARKVNAIVEQARDlsgTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEE 162
                                       45566678899999998888765222577*********************************9999999988776 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00074
                    HIP1_clath_bdg   4 LLrKnAevtkqlsvarqaqeeve.rekkeleeelerlkeeaerkleeqkeelekLkreleakraelarl 71 
                                       L rK+A+       a++ qe+++ r+ ++l e+l +++++ +r lee +  +e+L++ +e+++ e++r+
  gi|336255582|ref|YP_004598689.1| 171 LKRKQADFQNYKKRAKKRQEQIKdRATEDLVERLVDVRDNLKRALEEESGDVESLREGVEMTMREFDRV 239
                                       558888888888888888888853777888888888888888888888888888888888888887765 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9  23.4   0.00011      0.03     280     453 ..      42     214 ..      35     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                           DUF3584 280 ekqeevqeakaelkqqlrtledelkeaidelnqelsaakaklaakeselealeeqkkkyedadieklkadldqlpsi 356
                                       ++ +   e+ ++  ++ ++  d+ +++++   ++  ++++++++  ++l + +++  +  +a +e+++     +++ 
  gi|336255582|ref|YP_004598689.1|  42 SEAQSASESDRDQSAESAQSADDAADSEAGGDGDTPETSEDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQ 118
                                       55667778888888888899999999999999**************************999*****999999***** PP

                           DUF3584 357 rseleeleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrlkaaieealealesqlrkqle 433
                                       r+ele+l e+++ + e + d+q ++++r+q+i+++  ee+++ +e++e ++   +r++a++++  +  ++ +++ ++
  gi|336255582|ref|YP_004598689.1| 119 REELEDLTERVESQAETIGDLQDELEAREQAIEDR-DEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKD 194
                                       ********************************876.56788889998888888888878877777777777777777 PP

                           DUF3584 434 aqkeelneeekelesrlsel 453
                                        + e+l e+  +++ +l+++
  gi|336255582|ref|YP_004598689.1| 195 RATEDLVERLVDVRDNLKRA 214
                                       77777777666666666553 PP

>> Utp8  Utp8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.5   0.00014     0.036     559     673 ..      80     192 ..      54     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                              Utp8 559 kvdlenlinfliklnneeskaqlfqllslvlDsiGlfnleletlekLssiidekvealeansynLtlvsqvllkkkk 635
                                       + d+++++++l + ++e  ++++  +++   D +G    + e le+L++ ++++ e +   +  L + +q++  + +
  gi|336255582|ref|YP_004598689.1|  80 SEDVQEVLDRLTEYDDEL-ARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDE 155
                                       458999999999988866.56889999999******************************************99977 PP

                              Utp8 636 kkakkkkventeLasLLkiknksalkekkkkdsqrerk 673
                                       + a+  +++  +L+s Lk k+ ++++ kk +++  e+ 
  gi|336255582|ref|YP_004598689.1| 156 EIAE-YEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQI 192
                                       7777.34599********99999876666555444433 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 ?   10.6   0.5    0.0011      0.28      51     113 ..      76     139 ..      73     146 .. 0.89
   2 ?    3.5   0.1      0.16        41      18     115 ..     142     241 ..     137     247 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                         Mce4_CUP1  51 lpqlredireladladvYad.aapdlldaLdnavttsrTiveqqaeLdalllaavglsntgadl 113
                                       +p+ +ed++e+ d  + Y+d  a  +  ++++a+  s T+ +q++eL++l   + + ++t  dl
  gi|336255582|ref|YP_004598689.1|  76 TPETSEDVQEVLDRLTEYDDeLARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDL 139
                                       79999*****999999997636999****************************99999998776 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.16
                         Mce4_CUP1  18 tLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladla.....dvYadaapdlldaLdnav.ttsrT 88 
                                        L+A  +A+e r e++    ++ +e +++l +rl + ++d+++ ++ a     ++ + a +dl++ L +++   +r+
  gi|336255582|ref|YP_004598689.1| 142 ELEAREQAIEDRDEEI----AEYEEQVEDLKSRLKRKQADFQNYKKRAkkrqeQIKDRATEDLVERLVDVRdNLKRA 214
                                       5666666666666554....55566666666666666666666554431111155667889***9998887257899 PP

                         Mce4_CUP1  89 iveqqaeLdalllaavglsntgadlle 115
                                       ++e++ ++++l   +  + ++  ++le
  gi|336255582|ref|YP_004598689.1| 215 LEEESGDVESLREGVEMTMREFDRVLE 241
                                       999999999988877777777777766 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 ?   14.5  22.9   0.00011     0.028       5     116 ..      81     193 ..      78     198 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00011
                             DHR10   5 aeekeelaelErkarelqakidalqvvekdlrscikllee.ieaelakleeakkklkelrdaleekeielrelerke 80 
                                       ++ +e l++l +   el  k++a+ +  +dl+ +++   e +e+ ++++e++ +++ +l+d+le +e+  ++ + ++
  gi|336255582|ref|YP_004598689.1|  81 EDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREeLEDLTERVESQAETIGDLQDELEAREQAIEDRDEEI 157
                                       566888999999999********************976544************************************ PP

                             DHR10  81 erlqrqlenaeeklerlreqaeekreaakarleelr 116
                                       +  + q+e  + +l r + + ++ ++ ak+r e+++
  gi|336255582|ref|YP_004598689.1| 158 AEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIK 193
                                       *******************************99987 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 ?   10.8   6.8    0.0021      0.54      13      97 ..      86     159 ..      53     168 .. 0.67
   2 ?    7.1   3.0      0.03       7.7       7      69 ..     164     234 ..     159     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0021
                      Syntaxin-6_N  13 slnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrrafve 89 
                                        l+++++  ++  r        + + + e+ ++L  +++  +++ledL e v   e++ +  +  ++el+ r++ +e
  gi|336255582|ref|YP_004598689.1|  86 VLDRLTEYDDELAR--------KVNAIVEQARDLSGTVDHQREELEDLTERV---ESQAETIGDLQDELEAREQAIE 151
                                       33333322222222........356777777888888888888888888888...7777667777777777777777 PP

                      Syntaxin-6_N  90 evreevke 97 
                                       +  ee+ e
  gi|336255582|ref|YP_004598689.1| 152 DRDEEIAE 159
                                       77666654 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.03
                      Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtsss........tseeldetrteLrkalrsiewdledLeetvrivek 69 
                                        e+ ++ l++ ++ ++++++  ++ +++          e l + r++L++al++ + d+e L+e v++  +
  gi|336255582|ref|YP_004598689.1| 164 VEDLKSRLKRKQADFQNYKKRAKKRQEQikdratedLVERLVDVRDNLKRALEEESGDVESLREGVEMTMR 234
                                       577788888889999999533333333234667666889999**********************9977654 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  13.7   0.00034     0.088     294     445 ..      47     198 ..      42     238 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                            AAA_13 294 kveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikkl 370
                                         es++++ +e+ +++ d+a+ +   + d+ e ++  +++ ++L++  ++l +K++ +++  +  ++++ +++  ++
  gi|336255582|ref|YP_004598689.1|  47 ASESDRDQSAESAQSADDAADSEAGGDGDTPETSEDVQEVLDRLTEYDDELARKVNAIVE--QARDLSGTVDHQREE 121
                                       556666666777777777766666677778888888888888888888888888888888..777888888888888 PP

                            AAA_13 371 vaeineliakhNekvanleeekeeakkklel..hlveeleseldeykkkykklekaieklekelkeeeaelkkleee 445
                                       ++++ e +++  e++ +l++e e+ ++++e    +++e+e++++ +k+ +k+ +++ ++ +k++k+ ++++k ++ e
  gi|336255582|ref|YP_004598689.1| 122 LEDLTERVESQAETIGDLQDELEAREQAIEDrdEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKDRATE 198
                                       88888888888888888888888888888641145777777777777777777777777777777777777766555 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  23.2   0.00047      0.12     485     603 ..      78     193 ..      66     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00047
                              HOOK 485 elledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevqeelqkkkeqle 561
                                       e  ed ++ +++L +       ++  + +q  +l  + ++q  + ed   l +++e++ e + ++q+el+ +++ +e
  gi|336255582|ref|YP_004598689.1|  78 ETSEDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELED---LTERVESQAETIGDLQDELEAREQAIE 151
                                       5678899999999999999999999999999*********9999999...99************************* PP

                              HOOK 562 elepklssnkqkieeleeaLkkkdedlkameerYkkyveKAk 603
                                       ++++++ +  +++e+l+  Lk+k+ d + + +r kk  e  k
  gi|336255582|ref|YP_004598689.1| 152 DRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIK 193
                                       ***************************998888888766544 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.1   0.00055      0.14     241     382 ..      83     229 ..      70     251 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00055
                          Prominin 241 lerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsn.lCqseeCskilssleiekldtskcldq 316
                                       ++++l+ l+e  ++L    +  + + +++++L+  + +++++l+++ +  + q+e+  +++++le+ +   +   ++
  gi|336255582|ref|YP_004598689.1|  83 VQEVLDRLTEYDDELA---RKVNAIVEQARDLSGTVDHQREELEDLTERvESQAETIGDLQDELEAREQAIEDRDEE 156
                                       4444444444444442...2333444566677788888888888888886666777778888887755555555578 PP

                          Prominin 317 lpnvdevlealeevle...tnlssivkeglarlneipekvknqt....aevvpdlkkalakgreqikklakki 382
                                       + + +e++e+l++ l+   +++++  k++ +r ++i++++++++     +v  +lk+al++++  +++l + +
  gi|336255582|ref|YP_004598689.1| 157 IAEYEEQVEDLKSRLKrkqADFQNYKKRAKKRQEQIKDRATEDLverlVDVRDNLKRALEEESGDVESLREGV 229
                                       8888888888776654222567777778888888887777765411114566677777777777777766666 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   7.7   0.00021     0.054      37      99 ..     109     171 ..      73     175 .. 0.85
   2 ?    1.6   9.0       1.5   3.9e+02      34      92 ..     148     204 ..     142     246 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00021
                                       HHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHH CS
                             DUF16  37 kkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRl 99 
                                       +++  +vd + e+++ l++ ve q e i +l+ e +a++++++  de +    e +++++ Rl
  gi|336255582|ref|YP_004598689.1| 109 RDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRL 171
                                       45566788***********************************99999999999999999888 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHH CS
                             DUF16  34 qrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletL 92 
                                       q +++ +++++  +eq++ l+   +++++  ++ k++ k+++e+++  d++ e ++e L
  gi|336255582|ref|YP_004598689.1| 148 QAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIK--DRATEDLVERL 204
                                       4444555555555666666666666555555555555555555444..33444444444 PP

>> CHASE6_C  C-terminal domain of two-partite extracellular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1     0.016       4.1      21      69 ..      82     129 ..      75     132 .. 0.73
   2 ?    5.5   2.3      0.11        28      29      71 ..     157     206 ..     124     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.016
                          CHASE6_C  21 aaelllerilkYrpeLaekleqakqkillkeeaaeksekedldpfvqRl 69 
                                        ++ +l+r+ +Y+ eLa+k+++  ++     + + ++++e+l+ +++R+
  gi|336255582|ref|YP_004598689.1|  82 DVQEVLDRLTEYDDELARKVNAIVEQARD-LSGTVDHQREELEDLTERV 129
                                       566689***************99988843.3333455666666666665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.11
                          CHASE6_C  29 ilkYr...peLaekleqakqkill....keeaaeksekedldpfvqRlVt 71 
                                       i++Y+    +L+++l++++++++     +++ +e+ ++  ++ +v+RlV+
  gi|336255582|ref|YP_004598689.1| 157 IAEYEeqvEDLKSRLKRKQADFQNykkrAKKRQEQIKDRATEDLVERLVD 206
                                       55555111468999999999997777665555566677777779999997 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.9    0.0085       2.2      25      89 ..      89     157 ..      67     159 .. 0.76
   2 ?   14.5   6.5   0.00016     0.041      23      90 ..     112     179 ..     100     180 .. 0.89
   3 ?   11.0   8.2    0.0019      0.51      22      79 ..     139     196 ..     138     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0085
                                       HHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                              BST2  25 qLtqaqeslrea....eaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaev 89 
                                       +Lt+  ++l+++      qa   + tv   ++ Le  + + + q + + +lq+e++  +q ++d  +e+
  gi|336255582|ref|YP_004598689.1|  89 RLTEYDDELARKvnaiVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEI 157
                                       4555555554431111468889999***************************************99987 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                              BST2  23 erqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90 
                                              +e+l++    + +  +t+ +L++ Le  +   +++ +++ e ++++++L+ +L+ ++a+ +
  gi|336255582|ref|YP_004598689.1| 112 SGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQ 179
                                       5556677899999999999*******************************************999876 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  22 LerqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLn 79 
                                       L+ +L   ++ +++ + ++a +++ v++Lk+ L++++a  q+ ++++++ q++ik+ +
  gi|336255582|ref|YP_004598689.1| 139 LQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKDRA 196
                                       899999999*********************************************9854 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 ?   11.3   6.0   0.00067      0.18      26     107 ..      55     140 ..      23     187 .. 0.61
   2 ?    1.3   0.9      0.77     2e+02       7      78 ..     122     188 ..     119     246 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00067
                                       ..XXXXXXXXXXXXXXXXXXXXXXXSXH.........................HHHHHHHHHHHHHHHHHHHHHHHH CS
                             CAP_N  26 asskasssssaaaaaaaaaakaaaaaaaa........................ksveaFdelisgsvkefvelskki 78 
                                       ++++a+s+                                               ++++d+ ++++v+ +ve ++++
  gi|336255582|ref|YP_004598689.1|  55 SAESAQSA--------------------DdaadseaggdgdtpetsedvqevlDRLTEYDDELARKVNAIVEQARDL 111
                                       11111111....................0111222334444455556788899************************ PP

                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHBE CS
                             CAP_N  79 ggevaeqaelvkkafeaqrkfllvaskak 107
                                        g+v +q e +++  e  ++  ++    +
  gi|336255582|ref|YP_004598689.1| 112 SGTVDHQREELEDLTERVESQAETIGDLQ 140
                                       ********999988776655555544444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.77
                                       XXXXXXXXXXX.................................XXXXXXXXXXXXXXXXXXXXXXXSXH.HHHHHH CS
                             CAP_N   7 LEaatsrLEdiais.......................essssasskasssssaaaaaaaaaakaaaaaaaaksveaF 60 
                                       LE+ t+r E+ a +                       e                                +++ve+ 
  gi|336255582|ref|YP_004598689.1| 122 LEDLTERVESQAETigdlqdeleareqaiedrdeeiaE-------------------------------YEEQVEDL 167
                                       67777777777555444433333222222222211110...............................11233333 PP

                                       HHHHHHH...HHHHHHHHHHH CS
                             CAP_N  61 delisgs...vkefvelskki 78 
                                       ++ ++++   ++++ + +kk 
  gi|336255582|ref|YP_004598689.1| 168 KSRLKRKqadFQNYKKRAKKR 188
                                       333322100022222222222 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.4    0.0034      0.88      25      92 ..      75     143 ..      54     151 .. 0.57
   2 ?    7.1   4.0      0.02       5.3       4      62 ..     149     212 ..     145     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0034
                                       XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHH CS
                        Laminin_II  25 nlentkeklseinrsveetnekvk.dankairdArrsvkkLeklapqLldklkelkqleeassslsdni 92 
                                       ++++t+e+++e+ + + e ++++  + n ++++Ar+ + +++++ ++L+d  ++++ + e  + l d++
  gi|336255582|ref|YP_004598689.1|  75 DTPETSEDVQEVLDRLTEYDDELArKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDEL 143
                                       455566666666555555554443355555555555555555555555555555666555544444444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.02
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXX CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvk.....dankairdArrsvk 62 
                                        +++ +e ++e +eq+++l+ +l++ +++ ++ ++ +++ +e++k     d+ + ++d+r++ k
  gi|336255582|ref|YP_004598689.1| 149 AIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKdrateDLVERLVDVRDNLK 212
                                       57788999999********************999999999999885444555666667776664 PP

>> DIT1_PvcA  Pyoverdine/dityrosine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.1    0.0011      0.28      76     178 ..     152     248 ..     147     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                                       --HHHHHHHHHHHHHHHHHCT-TTEEEE-GGG-GGGGGG..............TT-HHHHHHHHHHHH---HHHHHH CS
                         DIT1_PvcA  76 vddeevdaYgeeLrelakekglediefvrlkdlleseeeaeeeseellseeeyleeaeklrkeLlksfgedeeelrk 152
                                         dee+ +Y+e++++l ++ + ++ +f + k+ +++++e    + +   +e+++e+  ++r++L ++ +e++ ++++
  gi|336255582|ref|YP_004598689.1| 152 DRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQE----QIKDRATEDLVERLVDVRDNLKRALEEESGDVES 224
                                       579*****************************8854433....2223458999999************999999976 PP

                                       HHTTSHHHHHHHHHHHHHHHHHH...- CS
                         DIT1_PvcA 153 eikededtlalYrgfskflleDl.asl 178
                                            e + ++ r+f ++l+++  +++
  gi|336255582|ref|YP_004598689.1| 225 ---LREGVEMTMREFDRVLEDENvSEI 248
                                       ...456677788888888877654444 PP

>> CR6_interact  Growth arrest and DNA-damage-inducible proteins-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  11.9    0.0011       0.3      72     156 ..     119     195 ..      81     215 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0011
                      CR6_interact  72 aerleeleaeeveeeeslakmleknrakkeekearrkaReeeiakkleKlpqliadlkakiakreaeaqaakerker 148
                                       +e+le+l  +   + e++  ++++++    ++e+ +++R+eeia+    +++ ++dlk ++++++a+ q+ k+r ++
  gi|336255582|ref|YP_004598689.1| 119 REELEDLTERVESQAETIGDLQDELE----AREQAIEDRDEEIAE----YEEQVEDLKSRLKRKQADFQNYKKRAKK 187
                                       34444444444445556666655554....455666777777776....6666666666666666666666666666 PP

                      CR6_interact 149 lveevrer 156
                                       ++e+++ r
  gi|336255582|ref|YP_004598689.1| 188 RQEQIKDR 195
                                       66666644 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 ?   10.2  16.1    0.0024      0.62      17     120 ..     100     206 ..      79     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0024
                             Mod_r  17 klealvk...tl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellq 89 
                                       k++a+v+   +l  +v+ ++ee+e+l +  es ae   +l++ele   + ++++ ee++e e+++e+++++l+++  
  gi|336255582|ref|YP_004598689.1| 100 KVNAIVEqarDLsGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQA 176
                                       55555555554445599999999999999999999999999999999999999999999999999999999988886 PP

                             Mod_r  90 kfspdallarLqtavaeaeeeSealaeefle 120
                                       +f+    +a+ +++ +  +  +e+l+e++++
  gi|336255582|ref|YP_004598689.1| 177 DFQNYKKRAKKRQE-QIKDRATEDLVERLVD 206
                                       66555444442222.3446666666666665 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.4    0.0073       1.9     118     174 ..      80     136 ..      74     164 .. 0.55
   2 ?    4.6   3.6     0.099        26     103     151 ..     139     187 ..     132     238 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0073
                      Bacillus_HBL 118 qkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgki 174
                                       ++ v++++  L+++ ++la +++   +++  l  ++  +  ++++l +++e+  ++i
  gi|336255582|ref|YP_004598689.1|  80 SEDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETI 136
                                       455666666666666666666666666664444444444444444444444433333 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.099
                      Bacillus_HBL 103 llellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdelts 151
                                       l + le+ ++ i    +e+ +  +++++lk++l+ ++++F++ ++ +++
  gi|336255582|ref|YP_004598689.1| 139 LQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKK 187
                                       5555555556666666666666666666666666666666665533332 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   5.4   0.00016     0.042       5      94 ..      81     176 ..      77     180 .. 0.86
   2 ?    5.6   6.4     0.031       8.1       8      77 ..     147     202 ..     134     247 .. 0.45

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                             TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkeel 75 
                                       e++++ +++l e  +e+ +k++ + ++  ++s ++++q+++l++l++++++  ++++      e +e+++e+ +ee+
  gi|336255582|ref|YP_004598689.1|  81 EDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGdlqdelEAREQAIEDRDEEI 157
                                       6778888899999999999999999999999999*****99999999999988886667778888899999999999 PP

                             TMPIT  76 kerkkvlkevesllpkkng 94 
                                       +e ++++++++s l +k+ 
  gi|336255582|ref|YP_004598689.1| 158 AEYEEQVEDLKSRLKRKQA 176
                                       9999999999999998865 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.031
                             TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelke 77 
                                       e+ +++  e+  ey++++e+l++  ++ + + ++ kkr+k+ ++++k+  ++              +l e
  gi|336255582|ref|YP_004598689.1| 147 EQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKDRATE--------------DLVE 202
                                       2222222222233333333333333333333333333333333333333222..............2222 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 ?   13.5  15.7   0.00018     0.047      71     189 ..      75     193 ..      50     195 .. 0.92
   2 ?   -0.2   0.2       2.9   7.6e+02       3      32 ..     197     230 ..     195     246 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00018
                          KASH_CCD  71 elkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleella 147
                                       +  ++ ++++E   rl  +  +l +  + ++++  +L       + e + l ++++  ++++ +L+ +l   e+ + 
  gi|336255582|ref|YP_004598689.1|  75 DTPETSEDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIE 151
                                       556788999******************************************************************** PP

                          KASH_CCD 148 ekealleektkqieeLkltieEyssiieeLraeksrLeeqlq 189
                                       ++++++ e ++q+e+Lk++++  ++  ++ ++  ++ +eq++
  gi|336255582|ref|YP_004598689.1| 152 DRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIK 193
                                       ***********************9999999999999999987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.9
                          KASH_CCD   3 tsdlistvadLqlnNkkLaee....nskLkkave 32 
                                       t+dl+  + d + n k+  ee    +++L++ ve
  gi|336255582|ref|YP_004598689.1| 197 TEDLVERLVDVRDNLKRALEEesgdVESLREGVE 230
                                       6677777777776665544331222345555555 PP

>> VitD-bind_III  Vitamin D binding protein, domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.8    0.0038      0.98       7      43 ..     174     210 ..     171     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0038
                     VitD-bind_III   7 seltFleyKkrlaeklkkklPeaspeelkelvekrsd 43 
                                       ++ +F +yKkr +++ ++    a++  +++lv+ r +
  gi|336255582|ref|YP_004598689.1| 174 KQADFQNYKKRAKKRQEQIKDRATEDLVERLVDVRDN 210
                                       5789****************************99865 PP

>> HAUS6_N  HAUS augmin-like complex subunit 6 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   8.2    0.0025      0.66     134     210 ..     100     190 ..      79     231 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0025
                           HAUS6_N 134 vreaaskkaqdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelkae......... 201
                                        ++a+ ++a+dls +v ++r +l+ + ++++++ +++ ++q++++  e+ +++ ++e++e++++++           
  gi|336255582|ref|YP_004598689.1| 100 KVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLksrlkrkqa 176
                                       45677788889999999999999999999999988888888888888888888888888888877633555654444 PP

                           HAUS6_N 202 .....keaakkekk 210
                                            k++akk ++
  gi|336255582|ref|YP_004598689.1| 177 dfqnyKKRAKKRQE 190
                                       44333222222222 PP

>> Troponin  Troponin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  19.1    0.0039         1      37     132 ..     107     213 ..      84     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0039
                                       XXX.XXX.XX......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XX CS
                          Troponin  37 plkeldglse......eqlqelckklheridkleeekydieekvakkdkeieelkkkvndlrGkfkkpalK....kv 103
                                       + ++l+g  +      e+l e+++  +e i  l++e + +e+ ++ +d+ei e + +v dl+++ k+ ++     k+
  gi|336255582|ref|YP_004598689.1| 107 QARDLSGTVDhqreelEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADfqnyKK 183
                                       44444443335555558999999999*************************************99998887888866 PP

                                       ---THH.HHHHH------.XXXXXXXXXXX CS
                          Troponin 104 rktade.klkkllgekkkplniDfranlKl 132
                                       r  +++ + k   +e   +  +D r+nlK 
  gi|336255582|ref|YP_004598689.1| 184 RAKKRQeQIKDRATEDLVERLVDVRDNLKR 213
                                       655555555555555555699*******95 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   2.3     0.057        15      20      68 ..      80     128 ..      79     135 .. 0.88
   2 ?    8.1  12.9      0.01       2.6      31     114 ..     133     216 ..     127     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.057
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXX CS
                            DivIVA  20 edeVdeFLdqvakdyeallkeneelkekvkeleeklkeykeleetLkkt 68 
                                        ++V+e Ld +++   +l ++++++ e+ ++l  ++++ +e  e+L + 
  gi|336255582|ref|YP_004598689.1|  80 SEDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDLTER 128
                                       589*********9999********************9999999988765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  31 akdyeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaee 107
                                       a+++ +l +e e+ ++ +++ +e+++ey+e+ e+Lk  l   q   ++ k+ akk +e+i + A+++  + + + ++
  gi|336255582|ref|YP_004598689.1| 133 AETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKDRATEDLVERLVDVRD 209
                                       5678899999999***************************************************9998888888888 PP

                                       XXXXXXX CS
                            DivIVA 108 eakkiae 114
                                       ++k++ e
  gi|336255582|ref|YP_004598689.1| 210 NLKRALE 216
                                       8777544 PP

>> Sipho_Gp157  Siphovirus Gp157
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.0    0.0029      0.75      22      78 ..      77     136 ..      63     140 .. 0.78
   2 ?    5.6  13.5     0.055        14       9      89 ..     122     200 ..     120     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0029
                       Sipho_Gp157  22 deeeeeikdtLesle...eeieeKaeniakviknleaeaeaikeeekrLaerkkslenka 78 
                                        e +e +++ L+ l    +e++ K+  i+   + l  +++  +ee + L+er +s  + +
  gi|336255582|ref|YP_004598689.1|  77 PETSEDVQEVLDRLTeydDELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETI 136
                                       444444555555555444**********************************98877665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.055
                       Sipho_Gp157   9 ykellelleeedvdeeeeeikdtLesleeeieeKaeniakviknleaeaeaikeeekrLaerkkslenkaenLKeyl 85 
                                       +++l e++e +++    + ++d Le+ e++ie++ e+ia + +++e   + +k++++ +++ kk+++++ e++K++ 
  gi|336255582|ref|YP_004598689.1| 122 LEDLTERVESQAET--IGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKDRA 196
                                       45555555544432..356788999999**********************************************998 PP

                       Sipho_Gp157  86 eeam 89 
                                        e +
  gi|336255582|ref|YP_004598689.1| 197 TEDL 200
                                       8876 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.0     0.038       9.9      22      66 ..     101     145 ..      86     149 .. 0.86
   2 ?    4.8   8.0      0.14        35      34      62 ..     148     176 ..     138     191 .. 0.57
   3 ?    4.3   4.2       0.2        51       7      65 ..     181     244 ..     178     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.038
                            Csm1_N  22 vsklvhENsvLsqkletkdqeiesLkeqlaeleekvkeleerrkk 66 
                                       v+ +v+  + Ls +++ + +e+e L e++++  e + +l+++ ++
  gi|336255582|ref|YP_004598689.1| 101 VNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEA 145
                                       66777778889999******************9999998887655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.14
                            Csm1_N  34 qkletkdqeiesLkeqlaeleekvkelee 62 
                                       q++e +d+ei + +eq++ l++++k+ + 
  gi|336255582|ref|YP_004598689.1| 148 QAIEDRDEEIAEYEEQVEDLKSRLKRKQA 176
                                       55555666665555555555555555443 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.2
                            Csm1_N   7 YKesVqerlds.....AdllvsklvhENsvLsqkletkdqeiesLkeqlaeleekvkeleerrk 65 
                                       YK+  ++r ++      + lv++lv     L+++le  +  +esL+e ++    + ++  e+++
  gi|336255582|ref|YP_004598689.1| 181 YKKRAKKRQEQikdraTEDLVERLVDVRDNLKRALEEESGDVESLREGVEMTMREFDRVLEDEN 244
                                       66655555543222225789*****************************998888777776665 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       3.4   8.7e+02      38      66 ..      85     113 ..      79     119 .. 0.83
   2 ?    7.0   0.2     0.026       6.9      28      72 ..     107     151 ..      97     160 .. 0.83
   3 ?    7.4   5.8     0.021       5.5       9      79 ..     123     193 ..     121     199 .. 0.91
   4 ?    4.9   3.3      0.12        31      22      66 ..     168     213 ..     155     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 3.4
                              KxDL  38 lsqerlaklrarfkqgtkllkevkkdLes 66 
                                       ++  rl+++ ++++++++++ e  +dL  
  gi|336255582|ref|YP_004598689.1|  85 EVLDRLTEYDDELARKVNAIVEQARDLSG 113
                                       56679999999999999999999999975 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.026
                              KxDL  28 knreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkir 72 
                                       + r L+   +   e+l++l++r++++++++ +++++Le   + i+
  gi|336255582|ref|YP_004598689.1| 107 QARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIE 151
                                       567888888999999999999999999999999999998777775 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.021
                              KxDL   9 edldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakla 79 
                                       edl e +  Qa+t g l+++ +  ++ ++  +e+ a++++++++ +  lk+ ++d ++ +k+ ++ +++++
  gi|336255582|ref|YP_004598689.1| 123 EDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIK 193
                                       68999999****************************************************99988666665 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.12
                              KxDL  22 sgrlnkknreLlelnalsqerlaklrarfkqgt.kllkevkkdLes 66 
                                         rl+ k++  +++ + +++r +++++r  +   + l +v+++L+ 
  gi|336255582|ref|YP_004598689.1| 168 KSRLKRKQADFQNYKKRAKKRQEQIKDRATEDLvERLVDVRDNLKR 213
                                       5688999999999999999999999998877666888888888875 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 ?   12.4   6.3    0.0005      0.13      38     121 ..      89     172 ..      78     179 .. 0.88
   2 ?    2.0   2.1      0.81   2.1e+02      66     105 ..     159     198 ..     154     217 .. 0.73
   3 ?    1.1   0.3       1.5     4e+02      66     103 ..     206     240 ..     190     248 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0005
                              COG2  38 ylkllekellelvnedyadFvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekre 114
                                        l++ ++el++ vn  ++   +lSg     +eele ++  +++  + + +++++l++re+++e++ ee +e ee+ e
  gi|336255582|ref|YP_004598689.1|  89 RLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVE 165
                                       455668999999*******************************************************9999999988 PP

                              COG2 115 llklllk 121
                                        lk+ lk
  gi|336255582|ref|YP_004598689.1| 166 DLKSRLK 172
                                       7777665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.81
                              COG2  66 glqeeleevesplaaarkkvesvreklsereeevesklee 105
                                        ++e++e ++s l++ + ++++ ++  ++r+e+++++  e
  gi|336255582|ref|YP_004598689.1| 159 EYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKDRATE 198
                                       5677888888888888888888888888888888776655 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.5
                              COG2  66 glqeeleevesplaaarkkvesvreklsereeeveskl 103
                                       +++++   ++  l++   +ves+re ++++++e +  l
  gi|336255582|ref|YP_004598689.1| 206 DVRDN---LKRALEEESGDVESLREGVEMTMREFDRVL 240
                                       33332...233444445556666666666655555444 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4    0.0091       2.4      69     121 ..      73     125 ..      41     127 .. 0.86
   2 ?    4.7   8.1      0.13        34       6      53 ..     144     192 ..     139     199 .. 0.73
   3 ?    1.9   5.9         1   2.7e+02      38      99 ..     159     221 ..     157     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0091
                           DUF5082  69 dgirsnlessyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnsl 121
                                       dg+  ++ +++q++ d+l e  d++ ++++ + +q  +++g +d++ ++l++l
  gi|336255582|ref|YP_004598689.1|  73 DGDTPETSEDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDL 125
                                       45555899******************************************998 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.13
                           DUF5082   6 sklqaqiaelrseiaaleekIerLk.eaktklsdekeslkqkkkklekp 53 
                                       ++++++i++  +eia +ee++e Lk + k+k  d ++  k +kk +e++
  gi|336255582|ref|YP_004598689.1| 144 EAREQAIEDRDEEIAEYEEQVEDLKsRLKRKQADFQNYKKRAKKRQEQI 192
                                       678999****************999766666666666555555555554 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 1
                           DUF5082  38 dekeslkqkkkklekplnssesWkGkeennydgirs.nlessyqtyvdkldelidaieeEIer 99 
                                       +++e++++ k+ l+ + ++ +++k+++++  ++i    +e+ +++ vd  d+l++a+eeE  +
  gi|336255582|ref|YP_004598689.1| 159 EYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKDrATEDLVERLVDVRDNLKRALEEESGD 221
                                       566778888888888888888888887766666666689999999999999999999998555 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.1     0.013       3.5      13      58 ..     101     143 ..      79     152 .. 0.53
   2 ?    2.5   1.3      0.81   2.1e+02      12      36 ..     149     173 ..     143     250 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.013
                           NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkv 58 
                                       ++a+ ++   l+  vd+ +e+l+d   l+e++++q++++ +l++++
  gi|336255582|ref|YP_004598689.1| 101 VNAIVEQARDLSGTVDHQREELED---LTERVESQAETIGDLQDEL 143
                                       333333333333444444444444...5666666666666666655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.81
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpd 36 
                                       +i++ d+ +   ++qv+d+++ l+ 
  gi|336255582|ref|YP_004598689.1| 149 AIEDRDEEIAEYEEQVEDLKSRLKR 173
                                       5555566666666666666555543 PP

>> Erythro_esteras  Erythromycin esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7  10.1   0.00016     0.042      74     204 ..      75     210 ..      70     227 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00016
                                       E-S---HHHHHHHHHHHHCHCCCCHHHHHHHCCHGGC.S.........TSSCCCCCHHHHHHHHHHHHCCHGGG... CS
                   Erythro_esteras  74 DlqslresldavldyLakvdpelagaareryaclapl.adp...raarsaeaaelrscedevvallkellakreeya 146
                                       D ++++e++++vld L+++d+ela+++++  +++++l +     r++++   ++ +s ++++  l +el+a+++  +
  gi|336255582|ref|YP_004598689.1|  75 DTPETSEDVQEVLDRLTEYDDELARKVNAIVEQARDLsGTVdhqREELEDLTERVESQAETIGDLQDELEAREQAIE 151
                                       667889*******************************6333336555555566777777777888888877776555 PP

                                       ..GGTSHHHHHHHHHHHHHHHHHHHC.......CSSSSSCHHHHHHHHHHHHHHHHHHHH...H CS
                   Erythro_esteras 147 aedgeaeeffsaeqnarlvknaeryyra.....gdeeswnlrllalRDrhMaenleallehe.a 204
                                       ++d+  e  +  eq  +l + + r  +      +++++   r+ +++Dr+  + +e+l++ + +
  gi|336255582|ref|YP_004598689.1| 152 DRDE--EIAEYEEQVEDLKSRLKRKQADfqnykKRAKK---RQEQIKDRATEDLVERLVDVRdN 210
                                       5444..22333333333333333333225422334444...44478999999999999996653 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   5.0     0.022       5.8      87     154 ..      80     150 ..      76     157 .. 0.64
   2 ?    6.0  11.2     0.032       8.4      78     162 ..     159     244 ..     153     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.022
                        Lebercilin  87 ekklkekeaellrlkdklkklkk..LsedknLaereeLqkk.LeeleakleekeekikeLerkleleeksf 154
                                       +++++e  ++l + +d+l +  +  + ++++L    + q++ Le+l++++e++ e+i +L+ +le  e++ 
  gi|336255582|ref|YP_004598689.1|  80 SEDVQEVLDRLTEYDDELARKVNaiVEQARDLSGTVDHQREeLEDLTERVESQAETIGDLQDELEAREQAI 150
                                       56666777777777777766655544556677655554443488888888888888888888777777654 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.032
                        Lebercilin  78 ksqekerelekklkekeaellrlkdklkklkkLsedknLaereeLqkkL....eeleakleekeekikeLerklele 150
                                       + +e++++l+++lk+k+a+ ++ k+  kk ++  +d+     e+L ++L    ++l+  lee++ ++++L+  +e++
  gi|336255582|ref|YP_004598689.1| 159 EYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKDRAT---EDLVERLvdvrDNLKRALEEESGDVESLREGVEMT 232
                                       556778888888888888888888888888887777776...44444441111556666777777888888888888 PP

                        Lebercilin 151 eksfrrqlaaek 162
                                        ++f+r l+ e+
  gi|336255582|ref|YP_004598689.1| 233 MREFDRVLEDEN 244
                                       888888887776 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 ?    9.6  12.7    0.0038         1      38     108 ..     101     171 ..      73     173 .. 0.81
   2 ?    6.7   8.2     0.031       8.2      13      83 ..     163     239 ..     158     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0038
                       TMF_TATA_bd  38 leaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELraDvaDlKemy 108
                                       ++a  ++ar+   ++ ++ eel++l +++e++ + + +lq+++e+  + +  ++Ee+ E ++ v+DlK  +
  gi|336255582|ref|YP_004598689.1| 101 VNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRL 171
                                       4555566666666667899999999******************************************9865 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.031
                       TMF_TATA_bd  13 lverlsseirrlEgElaslkeele.rleaerdeareeivklm.....keneelkelkkeleelekeleelqeryetl 83 
                                        ve l+s+++r++++ +++k++ + r e+ +d+a+e++v+ +     +   +l+e+++++e+l++ +e   ++ + +
  gi|336255582|ref|YP_004598689.1| 163 QVEDLKSRLKRKQADFQNYKKRAKkRQEQIKDRATEDLVERLvdvrdNLKRALEEESGDVESLREGVEMTMREFDRV 239
                                       589****************99886156778*********97733222222345566666666666666665555555 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.5     0.047        12      12      74 ..      82     144 ..      76     145 .. 0.82
   2 ?    4.5   8.8      0.21        56       4      73 ..     123     192 ..     121     217 .. 0.81
   3 ?    3.5   0.0      0.42   1.1e+02       6      81 ..     204     284 ..     195     295 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.047
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA  12 eleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLa 74 
                                       +++e l++l+e  +el +++++++e+ ++L+   ++ re+le+ +++ +++ +++++ +++L+
  gi|336255582|ref|YP_004598689.1|  82 DVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDELE 144
                                       456666777777788999999999999999999999999999888888888888888888775 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenL 73 
                                       ++l++++e+  e++++l++ele+ ++++++  ee ae e + e l++rl++++++ ++ kk+ ++ +e++
  gi|336255582|ref|YP_004598689.1| 123 EDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQI 192
                                       58999999999**************************************666655555555555555444 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......XXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   6 lfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl......eeeekkekekkkelsegkenLarl 76 
                                       l+d  ++l++ lee + ++e+l+e ++ ++ e +++ le e++ e        ++ +++e   + ++++ +  +a +
  gi|336255582|ref|YP_004598689.1| 204 LVDVRDNLKRALEEESGDVESLREGVEMTMREFDRV-LEDENVSEIDpepgteTDPQRHEVMMRVDSDQPEGTIADV 279
                                       444456777788888888999999999998888775.6777777766666755444555555566677777788888 PP

                                       XXXXX CS
                              YabA  77 YeeGF 81 
                                       Y+ G+
  gi|336255582|ref|YP_004598689.1| 280 YTAGY 284
                                       88887 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.6     0.024       6.3      58     102 ..      81     125 ..      79     129 .. 0.93
   2 ?    4.1  13.2      0.17        43      59     105 ..     145     191 ..     119     192 .. 0.83
   3 ?    0.8   0.1       1.8   4.8e+02      63      93 ..     207     237 ..     200     246 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.024
                                       E-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                       Prefoldin_2  58 qdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkk 102
                                       +d++ev+++L e  ++l  +++++ +q ++l  +++ ++eel  +
  gi|336255582|ref|YP_004598689.1|  81 EDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDL 125
                                       799**************************************9865 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.17
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS- CS
                       Prefoldin_2  59 dkeevkeeLeerketlekeiktlekqleklekeleelkeelqkklqq 105
                                        +e+++e+ +e+++++e++++ l+++l+++++++++ k+  +k+++q
  gi|336255582|ref|YP_004598689.1| 145 AREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQ 191
                                       57889999999999**************************9999876 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  63 vkeeLeerketlekeiktlekqleklekele 93 
                                       v+++L+  +e+ +  +++l +  e   +e++
  gi|336255582|ref|YP_004598689.1| 207 VRDNLKRALEEESGDVESLREGVEMTMREFD 237
                                       5566666666666666666555555444443 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.8    0.0034      0.89      55     119 ..     109     173 ..      76     177 .. 0.73
   2 ?    9.1   4.7    0.0049       1.3      57     119 ..     111     173 ..     108     196 .. 0.73
   3 ?    1.9   2.3      0.85   2.2e+02      49     117 ..     163     233 ..     161     249 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0034
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                        +l+ t +h  ++++ + +++++q+e++ ++++e+++ ++ +++ +e++ + +e ve+l+s+l+r
  gi|336255582|ref|YP_004598689.1| 109 RDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKR 173
                                       34555666666677778888888888888888888888888888888888888888888888775 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0049
                           DUF1664  57 laatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       l+ t +h  ++++ + +++++q+e++ ++++e+++ ++ +++ +e++ + +e ve+l+s+l+r
  gi|336255582|ref|YP_004598689.1| 111 LSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKR 173
                                       455566667777777777788888888888888777777888888888888888887777765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.85
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqke.iskeikeevtevredlse.igedvesvkeavegleskl 117
                                       q+e++++ l++ + ++++  +r  k++++ k+ +++++ e + +vr++l++ ++e++  v+++ eg+e+++
  gi|336255582|ref|YP_004598689.1| 163 QVEDLKSRLKRKQADFQNYKKRAKKRQEQIKDrATEDLVERLVDVRDNLKRaLEEESGDVESLREGVEMTM 233
                                       55555556666666666555555555555553134455555666666655313444444444444444444 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4  26.2   0.00013     0.033      44     190 ..      47     206 ..      27     210 .. 0.74
   2 ?    0.2   1.3       2.9   7.4e+02     115     156 ..     184     225 ..     178     242 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00013
                             ATG16  44 aaasaks....sksskksakekeasasq.............snskqsakiqsleqklaqlreelae....lyksrge 99 
                                       a++s +     s++             +             +++++s+++q+  ++l++  +ela        +  +
  gi|336255582|ref|YP_004598689.1|  47 ASESDRDqsaeSAQ-------------SaddaadseaggdgDTPETSEDVQEVLDRLTEYDDELARkvnaIVEQARD 110
                                       11111111111111.............1222333445677899********************99722213445566 PP

                             ATG16 100 laqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrk 176
                                       l+  +    eel++l e+ ++++e++ +l++e +a e++++dr+ee++e e+ v+dl+  l   q  ++   ++ +k
  gi|336255582|ref|YP_004598689.1| 111 LSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKK 187
                                       777788999***********************************************************999999997 PP

                             ATG16 177 lekE.....NkeLveRWmk 190
                                        ++       ++LveR+++
  gi|336255582|ref|YP_004598689.1| 188 RQEQikdraTEDLVERLVD 206
                                       6654111223468888876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.9
                             ATG16 115 eeklkedeerlaeleaeraaletklkdreeelrekeklvqdl 156
                                       ++k ++++ + ++ e+ +++l + +++++ +l+e    v+ l
  gi|336255582|ref|YP_004598689.1| 184 RAKKRQEQIKDRATEDLVERLVDVRDNLKRALEEESGDVESL 225
                                       333333333334444444444444444444444443333333 PP

>> Spc42p  Spindle pole body component Spc42p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0034      0.87       1      29 [.     102     130 ..     102     135 .. 0.90
   2 ?   -1.1   4.8       7.5   1.9e+03      14      57 ..     150     195 ..     141     213 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0034
                            Spc42p   1 nklikQNKeLnkkldekqeEierLnvlvg 29 
                                       n +++Q ++L  ++d ++eE+e L   v+
  gi|336255582|ref|YP_004598689.1| 102 NAIVEQARDLSGTVDHQREELEDLTERVE 130
                                       7899******************9987666 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 7.5
                            Spc42p  14 ldekqeEierLnvlvgslRaKLi.KYtel.nkKLedqlenlersss 57 
                                       +++++eEi + +  v+ l+++L  K ++  n K  +++++ +++  
  gi|336255582|ref|YP_004598689.1| 150 IEDRDEEIAEYEEQVEDLKSRLKrKQADFqNYKKRAKKRQEQIKDR 195
                                       6788999999999999999988624444423333444444444444 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 ?    0.0   0.0       4.1   1.1e+03      56      81 ..      90     115 ..      76     118 .. 0.52
   2 ?   10.0   5.1    0.0032      0.83      37      93 ..     120     176 ..     114     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 4.1
                           BLOC1_2  56 kyeelqpylqqidqiekqvteLeeav 81 
                                       + e  +++ +++++i +q ++L  +v
  gi|336255582|ref|YP_004598689.1|  90 LTEYDDELARKVNAIVEQARDLSGTV 115
                                       33333444555566666666655555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0032
                           BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                       ++l+d ++ +e+++e +  +++el+   q i++ +++++e ee v+ L +  k+ +a
  gi|336255582|ref|YP_004598689.1| 120 EELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQA 176
                                       6899999999999999999999**************************999988665 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.2     0.026       6.8      15      95 ..     106     205 ..      88     208 .. 0.81
   2 ?    5.2   0.2      0.11        28      14      59 ..     201     243 ..     189     336 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.026
                         DASH_Dad2  15 kqlrdlsdslakqleeLeeklstladgteavasVlanWqnvlraismaslkllqkaee...............eaee 76 
                                       +q rdls+++ +q eeLe+  + +++ +e++ +  ++ +   +ai+  + ++++++e+               ++ +
  gi|336255582|ref|YP_004598689.1| 106 EQARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQvedlksrlkrkqadfQNYK 182
                                       6889***************************************************9999999999999988883333 PP

                         DASH_Dad2  77 eeedeeeeeeee....plpetLV 95 
                                       +++++++e+ ++    +l e LV
  gi|336255582|ref|YP_004598689.1| 183 KRAKKRQEQIKDrateDLVERLV 205
                                       33333333333323336666665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.11
                         DASH_Dad2  14 LkqlrdlsdslakqleeLeeklstladgteavasVlanWqnvlrai 59 
                                        ++l d+ d+l++ lee +  ++ l++g   v+  +++++ vl+  
  gi|336255582|ref|YP_004598689.1| 201 VERLVDVRDNLKRALEEESGDVESLREG---VEMTMREFDRVLEDE 243
                                       4678899999999999999999999988...567899999998544 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   6.0    0.0029      0.74      17      90 ..      79     152 ..      53     155 .. 0.76
   2 ?    2.5  10.4       0.3        77      19     105 ..     148     236 ..     142     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0029
                           DUF3450  17 tldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       t ++++++  + ++ + +  +k++++ +++++l+  +   +eele+l+   e +++ + +++ e++  e+ ie+
  gi|336255582|ref|YP_004598689.1|  79 TSEDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIED 152
                                       55677777777777777777888888888888888888888888888888888888888888888887777776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.3
                           DUF3450  19 dqalkeaekavaaaaqsqkkidklddekqellaeyralkeelesle..vyneqlerlvasqeqeiasleeqieeiee 93 
                                       +++++  e++ + ++q++  +++l++++++ ++  +++k+++e+++  + ++ +erlv+  ++    lee+  ++e 
  gi|336255582|ref|YP_004598689.1| 148 QAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKdrATEDLVERLVDVRDNLKRALEEESGDVES 224
                                       56788899999999999999999999999999999999999999963367778899999999999999999999999 PP

                           DUF3450  94 ierelvpllekm 105
                                       ++++++  +++ 
  gi|336255582|ref|YP_004598689.1| 225 LREGVEMTMREF 236
                                       999999999875 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 ?    6.9   0.5     0.032       8.4       1      40 [.     100     139 ..     100     144 .. 0.87
   2 ?    5.8   0.5     0.069        18       2      38 ..     136     172 ..     135     180 .. 0.88
   3 ?    4.0   0.8      0.25        66       2      39 ..     157     194 ..     156     207 .. 0.89
   4 ?    2.5   0.2      0.74   1.9e+02      17      42 ..     209     234 ..     196     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.032
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       +++ + ++  +ls +++  ++e+e+l + ve   e++ dl
  gi|336255582|ref|YP_004598689.1| 100 KVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDL 139
                                       566677777899*******************999999776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.069
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVk 38 
                                       i++l+ +l+  +  +e   +e+ e +++ve+lk + k
  gi|336255582|ref|YP_004598689.1| 136 IGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLK 172
                                       6889999999999999999999999999999998876 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.25
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkd 39 
                                       i e E+++++l+++l+  ++++++ +k  ++ +e++kd
  gi|336255582|ref|YP_004598689.1| 157 IAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQEQIKD 194
                                       568899*****************999999998888865 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.74
                         FlaC_arch  17 etvkkeneelsksveelkenVkdlls 42 
                                       +++k+ +ee s +ve l e V++ + 
  gi|336255582|ref|YP_004598689.1| 209 DNLKRALEEESGDVESLREGVEMTMR 234
                                       68899999999999999999988765 PP

>> SpoVR  SpoVR like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   7.5     0.022       5.6     144     235 ..     116     211 ..      77     217 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.022
                             SpoVR 144 ryGeeeVEklldaalaleelvdrykrkekkkleeeekrkkereeyesqvedlwrtleekkkkeeeekek....eekf 216
                                        + +ee E+l + + +  e +   + + + +++  e+r++e++eye+qvedl + l++k+++ ++ k++    +e++
  gi|336255582|ref|YP_004598689.1| 116 DHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRakkrQEQI 192
                                       3445666666666666666666666668888888899999************8877765554444433333336699 PP

                             SpoVR 217 peepeedlllFleknapeL 235
                                       + + +edl+  l +  ++L
  gi|336255582|ref|YP_004598689.1| 193 KDRATEDLVERLVDVRDNL 211
                                       9999999998777766655 PP

>> DinB  DinB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.8     0.011       2.9      31     121 ..      95     184 ..      78     188 .. 0.81
   2 ?    0.0   0.1       2.7   6.9e+02      75     106 ..     214     245 ..     194     265 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.011
                                       CCTT--SSTTS--HHHHHHHHHHHHHHHHHHHHH..SSSGGGT---------HHHHHHHHHHHHHHHHCT--HHHHH CS
                              DinB  31 eelkaengegfqsvkqtlnHvldveelwlsrlegeegapavddqterkeleeldalrealderliafldqltdlere 107
                                       +el+++  + +  ++  l++++d +++ l+ l++ ++ +a +  + ++ele  +++ e  de++++ ++q++dl+ +
  gi|336255582|ref|YP_004598689.1|  95 DELARKVNAIVEQAR-DLSGTVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSR 170
                                       455544444444444.4788889999999999999****************************************** PP

                                       SEE------SS-EE CS
                              DinB 108 tlldradagtvkmt 121
                                        + ++ad + +k +
  gi|336255582|ref|YP_004598689.1| 171 LKRKQADFQNYKKR 184
                                       99999999888765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.7
                                       --------HHHHHHHHHHHHHHHHCT--HHHH CS
                              DinB  75 terkeleeldalrealderliafldqltdler 106
                                       + ++e++++++lre ++  +++f   l+d++ 
  gi|336255582|ref|YP_004598689.1| 214 ALEEESGDVESLREGVEMTMREFDRVLEDENV 245
                                       56789999999999999999999999999443 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.7    0.0039         1      14      75 ..      81     142 ..      78     151 .. 0.95
   2 ?    2.0   4.4       1.2   3.2e+02      21      59 ..     155     197 ..     143     242 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0039
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS..S-HHHHHHHHHHHHHHHHHHHHHHHH CS
                               ING  14 lelqrnltelreiDakvqellkeidskiekflkngslqknekeeelsriqeelkeaqellde 75 
                                       +++q+ l++l e D ++   ++ i +++++++ + ++q +e e+ ++r++++ +++ +l+de
  gi|336255582|ref|YP_004598689.1|  81 EDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDLTERVESQAETIGDLQDE 142
                                       689*****************************9999********************999998 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHH........TS..S-HHHHHHHH CS
                               ING  21 telreiDakvqellkeidskiekfl........kngslqknekeeel 59 
                                       +e+ e + +v++l+ ++++k  +f         +    q++ k++++
  gi|336255582|ref|YP_004598689.1| 155 EEIAEYEEQVEDLKSRLKRKQADFQnykkrakkR----QEQIKDRAT 197
                                       5556666666666666655555555333322221....222222221 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2       1.2     3e+02      23      53 ..      84     114 ..      78     121 .. 0.59
   2 ?    7.4  11.5     0.026       6.9       3      59 ..     120     176 ..     118     199 .. 0.93
   3 ?   -0.2   0.2       5.9   1.5e+03      20      33 ..     209     222 ..     187     252 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX  23 ndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                       ++v+ +  +  d+l r++++++e+ ++l+ +
  gi|336255582|ref|YP_004598689.1|  84 QEVLDRLTEYDDELARKVNAIVEQARDLSGT 114
                                       4444444444566777777777777777655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXX CS
                              SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgasea 59 
                                       e le+L +++  q +ti +L+d++ + +q i+   +++++ +e++++l+++ ++++a
  gi|336255582|ref|YP_004598689.1| 120 EELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQA 176
                                       789*********************************************999886665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 5.9
                                       HHHHHHHHHHHHHH CS
                              SlyX  20 eeLndvvaeqqqqi 33 
                                       + L +++ e   ++
  gi|336255582|ref|YP_004598689.1| 209 DNLKRALEEESGDV 222
                                       22333333333333 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.4     0.041        11      90     139 ..      79     128 ..      73     132 .. 0.82
   2 ?    5.7  20.8     0.063        16      51     135 ..     114     198 ..     103     235 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.041
                     Jnk-SapK_ap_N  90 erkelqekveqleeenrelelkaknaadqlsrleekeaelkkeysklher 139
                                         +++qe + +l+e  +el  k++++ +q+ +l+ + + +++e + l+er
  gi|336255582|ref|YP_004598689.1|  79 TSEDVQEVLDRLTEYDDELARKVNAIVEQARDLSGTVDHQREELEDLTER 128
                                       56788888999999999999999999999999999998888888888886 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.063
                     Jnk-SapK_ap_N  51 eleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekea 127
                                       +++  reele+L+++ e ++e   + ++ele  e+++e++ +e+ e  eq+e+ + +l+ k  ++++  +r +++++
  gi|336255582|ref|YP_004598689.1| 114 TVDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRDEEIAEYEEQVEDLKSRLKRKQADFQNYKKRAKKRQE 190
                                       56666666666666666666666666666666666666666655555555555555555444444444444444444 PP

                     Jnk-SapK_ap_N 128 elkkeysk 135
                                       + k + ++
  gi|336255582|ref|YP_004598689.1| 191 QIKDRATE 198
                                       43322221 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  10.6     0.044        11     178     309 ..      40     202 ..      35     242 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.044
                              FUSC 178 ageegaeareaararlaadilalealrsqaayesprirararalrrllsrmla....llallsslarllarlraeea 250
                                       +g+e+++a+e++r + a+ +   +++++  a  +++++++++ +++ l r+++    l + ++++ ++ ++l+ + +
  gi|336255582|ref|YP_004598689.1|  40 SGSEAQSASESDRDQSAESAQSADDAADSEAGGDGDTPETSEDVQEVLDRLTEyddeLARKVNAIVEQARDLSGTVD 116
                                       57777888889999999999999999999999999999999999999999985444488899999999999999999 PP

                              FUSC 251 aavpelaallaelaal...................eaaaaaealeaalaalrarlralrrale........adadta 300
                                       ++++el++l +++++                    ++ +  +++e++++ l  rl++ +++ +         + + +
  gi|336255582|ref|YP_004598689.1| 117 HQREELEDLTERVESQaetigdlqdeleareqaieDRDEEIAEYEEQVEDLKSRLKRKQADFQnykkrakkRQEQIK 193
                                       99999999999999955555555555554444444333334444444444444444444444455554333222222 PP

                              FUSC 301 alllarlae 309
                                       +++ + l+e
  gi|336255582|ref|YP_004598689.1| 194 DRATEDLVE 202
                                       222222222 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  10.4      0.17        45       8     100 ..      97     192 ..      64     193 .. 0.80
   2 ?    2.1   3.9      0.95   2.5e+02      14      51 ..     163     199 ..     156     242 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.17
                        Syntaxin_2   8 insnvstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssds.....qqkl..qkekLkk 77 
                                       ++++v+ + ++ ++L+     ++ re+l++l+e++   ++++ +l  +l++ ++  +d+        +  q e Lk+
  gi|336255582|ref|YP_004598689.1|  97 LARKVNAIVEQARDLSGT--VDHQREELEDLTERVESQAETIGDLQDELEAREQAIEDRdeeiaE--YeeQVEDLKS 169
                                       444555555555555554..556688899999999999888888888888888888888666533..1569****** PP

                        Syntaxin_2  78 dfkealqeFqkiqrqyaekekqi 100
                                        +k+    Fq++ +++++++ qi
  gi|336255582|ref|YP_004598689.1| 170 RLKRKQADFQNYKKRAKKRQEQI 192
                                       ******************99886 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.95
                        Syntaxin_2  14 tleklvkqLgtkk.dteelreklhelieeinelikktne 51 
                                       + e l + L+ k+ d +++++++++ +e+i++   +t++
  gi|336255582|ref|YP_004598689.1| 163 QVEDLKSRLKRKQaDFQNYKKRAKKRQEQIKDR--ATED 199
                                       445555556666557777777777777777764..3444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2707  (0.150984); expected 358.6 (0.02)
Passed bias filter:                      930  (0.0518713); expected 358.6 (0.02)
Passed Vit filter:                       248  (0.0138323); expected 17.9 (0.001)
Passed Fwd filter:                       131  (0.0073066); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              69  [number of targets reported over threshold]
# CPU time: 1.59u 0.34s 00:00:01.93 Elapsed: 00:00:00.53
# Mc/sec: 2202.62
//
Query:       gi|336255583|ref|YP_004598690.1|  [L=645]
Description: Chaperone protein dnaK [Halopiger xanaduensis SH-6]
Scores for 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-242  805.3  18.7   2.4e-240  798.8  18.7    2.0  1  HSP70          Hsp70 protein
    9.4e-20   70.7   0.3    9.4e-20   70.7   0.3    1.8  2  MreB_Mbl       MreB/Mbl protein
  ------ inclusion threshold ------
      0.014   14.7   0.0        0.1   11.8   0.0    2.2  2  StbA           StbA protein
      0.048   13.4   0.0       0.18   11.5   0.0    1.9  2  FGGY_C         FGGY family of carbohydrate kinases, C-termina
      0.049   13.4   0.7        5.7    6.6   0.0    2.3  2  Ydc2-catalyt   Mitochondrial resolvase Ydc2 / RNA splicing MR
       0.16   11.8   0.0       0.16   11.8   0.0    2.0  2  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
       0.29   10.6   7.8       0.57    9.7   0.0    3.0  3  Pro_dh         Proline dehydrogenase
       0.76   10.0   8.4        2.3    8.4   8.4    1.7  1  Fib_alpha      Fibrinogen alpha/beta chain family
        1.3    7.9  12.1       0.28   10.1   8.1    1.8  2  IFT57          Intra-flagellar transport protein 57
        2.4    8.4   4.4        3.1    8.0   2.0    2.2  2  PhyH           Phytanoyl-CoA dioxygenase (PhyH)
          7    5.9  11.4        3.7    6.8   8.6    1.8  2  TraF_2         F plasmid transfer operon, TraF, 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 !  798.8  18.7  1.5e-243  2.4e-240       1     599 []       6     579 ..       6     579 .. 0.99

  Alignments for each domain:
  == domain 1  score: 798.8 bits;  conditional E-value: 1.5e-243
                                       EEEEEEXSSEEEEEEEETTEEEEEXXTTSXSSEESEEEEXTTSEEETHHHHHCTTTTGGGEEEXGGGTTTXBTTSHH CS
                             HSP70   1 viGiDLGttnsvvavmeggkievianeegnrttPsvvaFtkkerlvGeaAkrqavtnpkntvfsvKrliGrkfsdpe 77 
                                       ++GiDLGttns++avmegg++e+i+n eg+rttPs+vaF+++erlvG++Ak+qav+np++t++s+Kr++G+  +d  
  gi|336255583|ref|YP_004598690.1|   6 ILGIDLGTTNSAFAVMEGGDPEIIVNGEGERTTPSIVAFNDDERLVGKPAKNQAVQNPDRTIQSIKRHMGE--DD-- 78 
                                       68********************************************************************9..55.. PP

                                       HHHHHTTXSSEEEEETTSBEEEEEEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHH CS
                             HSP70  78 vqkeikelpykvvkkengkavveveaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkd 154
                                                y+v+ +            +e++tpe+isam+L+k+k++ae+ylg++v++avitvPaYf d qRqatkd
  gi|336255583|ref|YP_004598690.1|  79 ---------YTVEID------------DEEYTPEEISAMILQKIKRDAEEYLGDEVEKAVITVPAYFSDRQRQATKD 134
                                       .........666555............89************************************************ PP

                                       HHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHHHH CS
                             HSP70 155 AgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDealv 231
                                       Ag+iAG++v RivNepTAaa+aYGld+++ +++vlvyDlGggtfdvSil+l+ Gv+ev+aT+gD++lGG+d+Dea++
  gi|336255583|ref|YP_004598690.1| 135 AGEIAGFEVERIVNEPTAAAMAYGLDDES-DQTVLVYDLGGGTFDVSILDLGGGVYEVVATNGDNDLGGDDWDEAII 210
                                       ****************************9.*********************************************** PP

                                       HHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTT.EEEEEEEEHHHHHHHHHHHHH CS
                             HSP70 232 ehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqteinleietvdedg.kdlseklsRakfeelvedlle 307
                                       ++l+e+f+++++idl++d++alqrlk+aae+aK+eLSs+k+teinl+++t+++dg  +l+e+l+Rakfe+l+edl++
  gi|336255583|ref|YP_004598690.1| 211 DWLAEKFEEEHDIDLRDDRQALQRLKDAAEEAKIELSSRKETEINLPFITATDDGpIHLEESLTRAKFESLTEDLID 287
                                       ***************************************************************************** PP

                                       HTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHCC CS
                             HSP70 308 rtlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevkdl 384
                                       rt+ep+e+al+da+++ke+idev+lvGGstR+P+v+e+v+el+g+ep+k+vnpDeava+GAA+q+gvl g  ev+d+
  gi|336255583|ref|YP_004598690.1| 288 RTVEPTEQALEDAGYEKEDIDEVLLVGGSTRMPQVEEKVEELTGQEPQKNVNPDEAVALGAAIQGGVLGG--EVDDI 362
                                       **********************************************************************..***** PP

                                       EEEEBESS-EEEEETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCS CS
                             HSP70 385 lllDvtpLslgietlggvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgippap 461
                                       +llDvtpLslgie++gg++++lie+nttipt++s++f+taadnqt+v+++v+qgerel+++n+llg+f+l+gippap
  gi|336255583|ref|YP_004598690.1| 363 VLLDVTPLSLGIEVKGGLFERLIEKNTTIPTEESKIFTTAADNQTTVQVRVFQGERELAEENELLGEFHLTGIPPAP 439
                                       ***************************************************************************** PP

                                       TTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHH CS
                             HSP70 462 rGvpqieVtfdidanGiltvsakdketgkeeeitieaseglseeeiekmvkdaeesaeedkkkkeaieakneaeelv 538
                                       +G+pqieVtf+id+nGi++vsa+dk++g++eeitie   gls+eei++++++ae++aeed+kk+++iea+n ae+++
  gi|336255583|ref|YP_004598690.1| 440 AGTPQIEVTFSIDENGIVNVSAEDKGSGESEEITIEGGAGLSDEEIDRLQEEAEKHAEEDEKKRQRIEARNAAEATI 516
                                       ***************************************************************************** PP

                                       HHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSC..HHHHHHHHHHHHHHHHHHHHHHHH CS
                             HSP70 539 yslekkleeeaekvseaekekvesaieeLkeeleeee..keeieakteelkkvvekiaeklye 599
                                       +++ek lee+ e+v+++ ++++e+ai++L+++++++e  +e+ie++te+l++++++i++++y+
  gi|336255583|ref|YP_004598690.1| 517 QRAEKLLEENDEQVDDDLRDDIEAAIDDLEATIDDDEadAEAIEEATEDLSQELQEIGKQVYQ 579
                                       ********************************988776799******************9986 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.3   5.8e-23   9.4e-20       3     316 ..       6     349 ..       4     353 .. 0.68
   2 ?   -3.6   0.3       2.3   3.8e+03     212     260 ..     496     548 ..     482     555 .. 0.52

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 5.8e-23
                                       EEEEEE-SSEEEEEETTTE...EEEE......EES-EEEETTT--EEEESHHHHTTTTS-GT.TEEEE.-SE..ETT CS
                          MreB_Mbl   3 dlgiDLGtantlvyvkgkg...ivln......epsvvAikkktkkvlavGeeAkkmlgktpg.nikav.rPl..kdG 66 
                                        lgiDLGt+n    v + g   i++n       ps+vA++ +++    vG+ Ak+   + p+ +i+ + r +   d 
  gi|336255583|ref|YP_004598690.1|   6 ILGIDLGTTNSAFAVMEGGdpeIIVNgegertTPSIVAFNDDERL---VGKPAKNQAVQNPDrTIQSIkRHMgeDDY 79 
                                       68********98877655544577764444446*******99875...68888876655554156544245521343 PP

                                       E..ESSHHHHHHHHHH.HHHHHHT..SS-S..S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHH CS
                          MreB_Mbl  67 v..iadlevaeellky.fikkvkk..kksl..skprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiG 136
                                       +  i d e++ e +   +++k+k+  ++ l  + ++ vi+vP   ++ +r+A k+a + aG +   +++ep aAA+ 
  gi|336255583|ref|YP_004598690.1|  80 TveIDDEEYTPEEISAmILQKIKRdaEEYLgdEVEKAVITVPAYFSDRQRQATKDAGEIAGFEVERIVNEPTAAAMA 156
                                       3247788888665554144555554333334467899**************************************** PP

                                       TT--TTSSS-EEEEEE-SS-EEEEEEETTEEEEEE.....EES-SHHHHHHHHHHHHHHHHSEE..--HHHHHHHHH CS
                          MreB_Mbl 137 aglpveepsgnmvvdiGggttevavislggivtsk.....svrvaGdeldeaiikyirkkynll..iGertaekiki 206
                                        gl+ e  +  +v d+Gggt +v+++ lgg v+          ++Gd++deaii+++ +k++    i  r     ++
  gi|336255583|ref|YP_004598690.1| 157 YGLDDESDQTVLVYDLGGGTFDVSILDLGGGVYEVvatngDNDLGGDDWDEAIIDWLAEKFEEEhdIDLRDD---RQ 230
                                       *****************************9776541111145799************999875411333322...33 PP

                                       HH-BSS--HHHHEEEEEEEE.TTTTCEE...........EEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHH CS
                          MreB_Mbl 207 eigsavkeeeeekmeikGrd.lvtglpk...........evevsseevrealkepvsaiveavkevLektppeLaad 271
                                       ++  ++  +ee k+e++ r+    +lp            e +++ ++ ++  ++ + + ve  +++Le++  e   d
  gi|336255583|ref|YP_004598690.1| 231 ALQRLKDAAEEAKIELSSRKeTEINLPFitatddgpihlEESLTRAKFESLTEDLIDRTVEPTEQALEDAGYE-KED 306
                                       3333333344444444443312223333000000000013445555555555666666666666777766666.456 PP

                                       HHHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHH CS
                          MreB_Mbl 272 ivdrgivltGGgallkgldkllseetglpvkvaedpltcvakGtg 316
                                       i    ++l+GG++ + ++++ ++e tg + +   +p ++va G++
  gi|336255583|ref|YP_004598690.1| 307 ID--EVLLVGGSTRMPQVEEKVEELTGQEPQKNVNPDEAVALGAA 349
                                       64..48999**********************************86 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.3
                                       S--HHHHEEEEEEEETTTTCEEEEE.E...EHHHHHHHHHHHHHHHHHHHHHH CS
                          MreB_Mbl 212 vkeeeeekmeikGrdlvtglpkeve.v...sseevrealkepvsaiveavkev 260
                                       ++e+e+++ +i+ r+ ++   +++e +   ++e+v + l++ ++a ++ ++++
  gi|336255583|ref|YP_004598690.1| 496 AEEDEKKRQRIEARNAAEATIQRAEkLleeNDEQVDDDLRDDIEAAIDDLEAT 548
                                       55555556666666665544333220211144555555666555555555554 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.2e-05       0.1     159     247 ..     161     244 ..     132     256 .. 0.79
   2 ?   -0.4   0.0      0.33   5.5e+02     248     295 ..     283     332 ..     259     349 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.2e-05
                              StbA 159 ldeleslLiiDlGGttLDvakv..rgklegiskvkgdskiGvslitdavkealetaktrtssfladeliknrkdeey 233
                                        ++ + +L+ DlGG t Dv+ +   g + ++  + gd+++G     +a+ + l++      +f  ++ i+ r+d+++
  gi|336255583|ref|YP_004598690.1| 161 DESDQTVLVYDLGGGTFDVSILdlGGGVYEVVATNGDNDLGGDDWDEAIIDWLAE------KFEEEHDIDLRDDRQA 231
                                       4567889************9652269999*********************99975......5666778999999999 PP

                              StbA 234 Lkrrindedkresv 247
                                       L+ r++d+++ +++
  gi|336255583|ref|YP_004598690.1| 232 LQ-RLKDAAEEAKI 244
                                       99.67777766665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.33
                              StbA 248 levinekvkkLkerviravsefsgythvmvvGGGael..iaeaikkatev 295
                                        + i++ v+  ++ + +a  e +++  v++vGG + +  ++e++ + t+ 
  gi|336255583|ref|YP_004598690.1| 283 EDLIDRTVEPTEQALEDAGYEKEDIDEVLLVGGSTRMpqVEEKVEELTGQ 332
                                       46788888889999999999999**********99876677788777764 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.8   2.9e+03      49      78 ..     208     242 ..     207     257 .. 0.65
   2 ?   11.5   0.0   0.00011      0.18     130     196 ..     280     354 ..     265     355 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.8
                            FGGY_C  49 slvawlldnlglreeirdagev.....eeslaela 78 
                                       ++++wl ++ +   +i+  ++       +++ae a
  gi|336255583|ref|YP_004598690.1| 208 AIIDWLAEKFEEEHDIDLRDDRqalqrLKDAAEEA 242
                                       68999999987777777777763333333333333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00011
                            FGGY_C 130 avalqlrailealekd.......sgkpldrlavdGGgskndllmqllAdilg.vpVerpktaeatalGaAilAav 196
                                       ++   l +++ + +++       ++ ++d+++++GG ++ + + +   +++g  p + + ++ea+alGaAi ++v
  gi|336255583|ref|YP_004598690.1| 280 SLTEDLIDRTVEPTEQaledagyEKEDIDEVLLVGGSTRMPQVEEKVEELTGqEPQKNVNPDEAVALGAAIQGGV 354
                                       444444444444433366666777888*************************999999999**********9986 PP

>> Ydc2-catalyt  Mitochondrial resolvase Ydc2 / RNA splicing MRS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0035       5.7       1      37 [.       6      45 ..       6     149 .. 0.69
   2 ?    4.5   0.7     0.015        24     165     230 ..     493     568 ..     459     588 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0035
                                      EEEEEE-STTEEEEEEEE..........-TTS-EEEEEEE CS
                      Ydc2-catalyt  1 IlSIDmGikNlAfaklkv...ekkskkakekelptlnawk 37
                                      Il+ID+G  N Afa+++    e   + + e+++p++ a +
  gi|336255583|ref|YP_004598690.1|  6 ILGIDLGTTNSAFAVMEGgdpEIIVNGEGERTTPSIVAFN 45
                                      9***************998774444444555555554444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                                       ........HHH-----------HHHHHHHHHHTTS.................EEESS..........HHHHHHHHH CS
                      Ydc2-catalyt 165 ssesstkekkkkkksskekKkvkidlvgswLsaeikska..........kkslkislkeeaeleelveaylekwkk 230
                                       ++ ++++ekk+++ ++++  ++ i++  ++L+++ ++ +           ++l++++++++   e +e+ +e++++
  gi|336255583|ref|YP_004598690.1| 493 EKHAEEDEKKRQRIEARNAAEATIQRAEKLLEENDEQVDddlrddieaaIDDLEATIDDDEADAEAIEEATEDLSQ 568
                                       2333344477777888888888888888888876655547776666655555555555555555555555555555 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 ?   11.8   0.0   9.6e-05      0.16      13      76 ..     283     354 ..     276     364 .. 0.84
   2 ?   -4.4   0.8       9.4   1.5e+04     114     135 ..     496     517 ..     486     521 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.6e-05
                                       HHHHHHHHHHHHHHHHHCTTSSCCEE.EEEESSCCCHHHHHHHHCT......STT-..SEEEEEEEEE--SS CS
                     DMRL_synthase  13 eeitdkllegaldelkeagvaeenid.vvtVPGafElplaakklae......ssky.ldavialGvvirGet 76 
                                       e+++d+ +e + ++l++ag ++e+id v  V G+  +p + +k+ e      +++   d  +alG+ i+G+ 
  gi|336255583|ref|YP_004598690.1| 283 EDLIDRTVEPTEQALEDAGYEKEDIDeVLLVGGSTRMPQVEEKVEEltgqepQKNVnPDEAVALGAAIQGGV 354
                                       7899***************99999863778**********999888665554345458***********985 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 9.4
                                       CHHCCTSTCCCHHHHHHHHHHH CS
                     DMRL_synthase 114 aleraggkagnkGeeaaeaale 135
                                       a+e  ++++   +++aaea ++
  gi|336255583|ref|YP_004598690.1| 496 AEEDEKKRQRIEARNAAEATIQ 517
                                       2222222225556666666555 PP

>> Pro_dh  Proline dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00035      0.57      70     148 ..      53     134 ..      15     141 .. 0.83
   2 ?    0.2   0.1      0.27   4.4e+02      17      85 ..     210     290 ..     202     339 .. 0.62
   3 ?    1.4   2.8      0.12   1.9e+02      19      95 ..     474     581 ..     456     584 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00035
                                       GGGHHHHHHHHHHHHHHHHHHHHHTT-EEEE----GGGHHHHHHHHHHHHHSCCT...TT---EEEEEETTBTTHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
                            Pro_dh  70 taeeeevmeelverlrtlakeakelgvrlliDaEeaklqeltlelfrklnkepel...kdwevvgntyQaYlkdale 143
                                       ++++++++++  + ++++ ++  e +  + iD Ee++  e++  +++k+ ++ e     ++e++++t+ aY  d+++
  gi|336255583|ref|YP_004598690.1|  53 KPAKNQAVQNPDRTIQSIKRHMGEDDYTVEIDDEEYTPEEISAMILQKIKRDAEEylgDEVEKAVITVPAYFSDRQR 129
                                       56777888999999999***********************88888888887443323378899***********999 PP

                                       HHHHH CS
                                       xxxxx RF
                            Pro_dh 144 vlqkl 148
                                       +++k+
  gi|336255583|ref|YP_004598690.1| 130 QATKD 134
                                       88876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.27
                                       EEES-SS--SHHHHHHHHHHHHHHHHHHHHHHCCS-T....TCC-SEEE-GGG..........TT-SGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx..........xxxxxxxxxxxxxx RF
                            Pro_dh  17 ldllgeavlteedadryleayleaiksiekaskalkv....leapgvsvklsa..........prletaeeeevmee 79 
                                       +d l e+ ++e+d+d + +  ++a++++++a+++ k     ++++++ + + +          ++l++a+ e+  e+
  gi|336255583|ref|YP_004598690.1| 210 IDWLAEKFEEEHDIDLRDD--RQALQRLKDAAEEAKIelssRKETEINLPFITatddgpihleESLTRAKFESLTED 284
                                       6777887777777776633..34555554444422222222333333333322455555544435555566666666 PP

                                       HHHHHH CS
                                       xxxxxx RF
                            Pro_dh  80 lverlr 85 
                                       l++r  
  gi|336255583|ref|YP_004598690.1| 285 LIDRTV 290
                                       666554 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.12
                                       ES-SS--SHHHHHHHHHHHHHHHHHHHHHHCCS-TTCC-SEEE-GGG.........................T.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................x.... RF
                            Pro_dh  19 llgeavlteedadryleayleaiksiekaskalkvleapgvsvklsa.........................p.... 66 
                                       + g a l++e++dr  e+ ++  ++ ek++++ ++++a +  ++                            +    
  gi|336255583|ref|YP_004598690.1| 474 IEGGAGLSDEEIDRLQEEAEKHAEEDEKKRQRIEARNAAEATIQRAEklleendeqvdddlrddieaaiddlEatid 550
                                       55557777778888777777777777666664444333332222222233355555555554444445544404444 PP

                                       ..T-SGGGHHHHHHHHHHHHHHHHHHHHHTT CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh  67 ..rletaeeeevmeelverlrtlakeakelg 95 
                                         + ++++ ee+ e+l+++l+++ k+ ++++
  gi|336255583|ref|YP_004598690.1| 551 ddEADAEAIEEATEDLSQELQEIGKQVYQQQ 581
                                       4488888888888888888888888887766 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 ?    8.4   8.4    0.0014       2.3      34     130 ..     482     582 ..     480     583 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0014
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHH...HHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvke...ikdslrekqkskkdn.dnvikksskeleeeilrlketidaqesnirv 106
                                       ++++++l++e e+++++ ++ ++ +++    + ++++++k  ++n ++v  ++++++e  i +l++tid+ e   ++
  gi|336255583|ref|YP_004598690.1| 482 DEEIDRLQEEAEKHAEEDEKKRQRIEArnaAEATIQRAEKLLEENdEQVDDDLRDDIEAAIDDLEATIDDDEADAEA 558
                                       57888899999888888888888776511145556666666667746666789************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 107 LqnvlesneqkiqkLeqdidqker 130
                                       + +  e+++q++q++ +++ q+++
  gi|336255583|ref|YP_004598690.1| 559 IEEATEDLSQELQEIGKQVYQQQA 582
                                       *******************99985 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       1.8   2.9e+03     303     325 ..     228     250 ..     212     259 .. 0.59
   2 ?   10.1   8.1   0.00017      0.28     134     256 ..     452     579 ..     430     582 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
                             IFT57 303 ltrelaeiseelekvkqemeerg 325
                                        ++ l+++++  e++k e+ +r+
  gi|336255583|ref|YP_004598690.1| 228 DRQALQRLKDAAEEAKIELSSRK 250
                                       34455555555555555555554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00017
                             IFT57 134 eeeeeveddaelelekveeeelikseeededeedee...eelklesekkeekekekeeeiieskvdaaeWklEl..e 205
                                       +e+  v+ +ae++ +   ee++i+     +dee +    e+ k+++e++++ ++ ++++ +e+++  ae  lE   e
  gi|336255583|ref|YP_004598690.1| 452 DENGIVNVSAEDKGSGESEEITIEGGAGLSDEEIDRlqeEAEKHAEEDEKKRQRIEARNAAEATIQRAEKLLEEndE 528
                                       44445577899999999999999988888888877555444444444555577778888899999998888885337 PP

                             IFT57 206 RvlpqLkvtikadakdWrahleqmkkhkksieeslpetksqlkklhedisk 256
                                       +v   L+  i+a   d +a+++  +   ++iee++++++++l+++ +++ +
  gi|336255583|ref|YP_004598690.1| 529 QVDDDLRDDIEAAIDDLEATIDDDEADAEAIEEATEDLSQELQEIGKQVYQ 579
                                       8*********************************************99866 PP

>> PhyH  Phytanoyl-CoA dioxygenase (PhyH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.78   1.3e+03      28      84 ..      77     137 ..      39     161 .. 0.72
   2 ?    8.0   2.0    0.0019       3.1      12      86 ..     479     556 ..     471     587 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.78
                                       H.....HHHCHTTCCSEEEEECEEESTTCCCEECCCHHCHHHHTTHHHHHHHHHHHHTSCEE CS
                              PhyH  28 l.....ldralesgdkidfffeekaaadedglleksinkvghflhprkvadlvrailgqdvy 84 
                                             +d++ +++++i+++  +k ++d+++ l  ++++ +++  p +++d+ r++ +++  
  gi|336255583|ref|YP_004598690.1|  77 DdytveIDDEEYTPEEISAMILQKIKRDAEEYL-GDEVEKAVITVPAYFSDRQRQATKDAGE 137
                                       255555578888888899999999999988888.8888888888888888888887776664 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0019
                                       SS-HHHHHHHHHHHHHHHHHCHTTCCSEEEEECEEESTTCCCEE.CCCHHCHHHHTTH..HHHHHHHHHHHTSCEEE CS
                              PhyH  12 flsaeevealraeiealldralesgdkidfffeekaaadedgll.eksinkvghflhp..rkvadlvrailgqdvyv 85 
                                        ls+ee+++l++e+e+++++  +++++i++  +++a+ ++++ l e++++ v++ l +  +   d+++a + +d+++
  gi|336255583|ref|YP_004598690.1| 479 GLSDEEIDRLQEEAEKHAEEDEKKRQRIEARNAAEATIQRAEKLlEENDEQVDDDLRDdiEAAIDDLEATIDDDEAD 555
                                       6899*************888888888888877777777777777766666666666665755555555555555555 PP

                                       E CS
                              PhyH  86 a 86 
                                       a
  gi|336255583|ref|YP_004598690.1| 556 A 556
                                       5 PP

>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       1.4   2.3e+03      38      77 ..     483     525 ..     476     531 .. 0.59
   2 ?    6.8   8.6    0.0023       3.7      41      92 ..     536     586 ..     509     590 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.4
                            TraF_2  38 DkiDdlsdildgleaavnaasad...etq.vdeaaddlnalLed 77 
                                       ++iD+l+++ ++ ++  +++ ++   + + +++ +++ ++lLe+
  gi|336255583|ref|YP_004598690.1| 483 EEIDRLQEEAEKHAEEDEKKRQRieaR-NaAEATIQRAEKLLEE 525
                                       478999999994444444433335432.2466666666666655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0023
                            TraF_2  41 DdlsdildgleaavnaasadetqvdeaaddlnalLedlggdgylkasagvgl 92 
                                       Dd+++++d+lea+++  +ad   ++ea++dl ++L+++g++   + +ag+g 
  gi|336255583|ref|YP_004598690.1| 536 DDIEAAIDDLEATIDDDEADAEAIEEATEDLSQELQEIGKQV-YQQQAGAGA 586
                                       57777777666776666666444*******************.666777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2194  (0.122372); expected 358.6 (0.02)
Passed bias filter:                      982  (0.0547716); expected 358.6 (0.02)
Passed Vit filter:                       158  (0.00881254); 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):              11  [number of targets reported over threshold]
# CPU time: 0.90u 0.30s 00:00:01.20 Elapsed: 00:00:00.45
# Mc/sec: 4351.03
//
Query:       gi|336255584|ref|YP_004598691.1|  [L=89]
Description: hypothetical protein Halxa_4210 [Halopiger xanaduensis SH-6]
Scores for 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:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 727.53
//
Query:       gi|336255585|ref|YP_004598692.1|  [L=387]
Description: Chaperone protein dnaJ [Halopiger xanaduensis SH-6]
Scores for 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-44  151.2   0.0      3e-44  150.7   0.0    1.2  1  DnaJ_C          DnaJ C terminal domain
      1e-25   89.6   3.4    2.2e-25   88.6   3.4    1.6  1  DnaJ            DnaJ domain
    8.6e-12   45.2  17.8      2e-11   44.1  17.8    1.7  1  DnaJ_CXXCXGXG   DnaJ central domain
    0.00025   20.9  12.5      0.015   15.3   4.1    2.5  2  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
  ------ inclusion threshold ------
      0.056   13.6  27.0        2.2    8.5   0.6    4.7  4  DUF5351         Family of unknown function (DUF5351)
       0.12   12.2   6.2        1.7    8.4   0.1    3.2  3  A2L_zn_ribbon   A2L zinc ribbon domain
       0.12   12.4  13.3       0.39   10.8  13.4    1.8  2  DZR             Double zinc ribbon
       0.27   11.3  11.0        2.9    8.0   2.5    2.3  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.72   10.0   5.2        7.7    6.7   1.4    2.4  2  DUF2318         Predicted membrane protein (DUF2318)
        4.8    6.7   9.5        0.9    9.0   3.1    2.5  2  zf-ribbon_3     zinc-ribbon domain
        8.9    5.9   9.9        2.1    8.0   0.7    2.5  3  TackOD1         Thaumarchaeal output domain 1


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 !  150.7   0.0   1.8e-47     3e-44       2     148 .]     135     351 ..     134     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: 150.7 bits;  conditional E-value: 1.8e-47
                                       EEEEEE-HHHHHH-.EEE.EEEE...................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                            DnaJ_C   2 eveleisleelykGktkkikikrnvi................................................... 27 
                                       +++lei+lee+y+G++k+++i+r ++                                                   
  gi|336255585|ref|YP_004598692.1| 135 RTDLEIDLEEAYEGAEKQFTIERPETcetcngeghppdadartcpecqgrgqkrqvqqtplgrvqqtttcrrcdgeg 211
                                       789********************999*************************************************** PP

                                       ...................TEEEEEE-TT--TT-EEEETT-SS..SS..S---EEEEEEE---SS-EEETTEEEEEE CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  28 ...............kkekktlevkipaGikdgqkirlegeGd..eeggepGDlivtikvkphpvFkrkgndlyvev 87 
                                                      ++++ tl+v++paGi+dgq++r+e eG   +egg++GDl++ ++ ++h++F+r+g+dl +++
  gi|336255585|ref|YP_004598692.1| 212 tlysetcgdcggdgyVRNEATLTVEVPAGIQDGQTLRMEREGApsPEGGPKGDLLIDVTIREHEQFEREGDDLRYRL 288
                                       **************8777779**********************55555***************************** PP

                                       EEEHHHHHHTEEEEEE-SS-EEEEEE...--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  88 eislaeallGgklevptldgkvklki...tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                                       +is+ +a +G+++evptldg v+++i   tq+ge++r++gkGmp+l+ ++++Gdlyv+v+v++P
  gi|336255585|ref|YP_004598692.1| 289 PISFPQATFGDTVEVPTLDGAVEFEIpdgTQSGETFRLEGKGMPRLR-GRGQGDLYVQVQVVTP 351
                                       **********************************************8.**************99 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   3.4   1.3e-28   2.2e-25       1      63 []       4      65 ..       4      65 .. 0.99

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 1.3e-28
                                      HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                              DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                      d+Y++Lgvs+das++eIkkaYr++a +yHPD + +dp+aeekFk+i++A +vL+d+ekR++YD
  gi|336255585|ref|YP_004598692.1|  4 DFYDVLGVSPDASTEEIKKAYREKATEYHPDVS-NDPDAEEKFKKIQKAKKVLTDEEKRQAYD 65
                                      79*****************************99.9***************************9 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1  17.8   1.2e-14     2e-11       1      67 []     161     225 ..     161     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.2e-14
                     DnaJ_CXXCXGXG   1 CkkCkGsgakk.gkkktCktCkGsGvvreeqkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                                       C++C+G+g  + ++++tC++C+G+G++r+ q+t lg ++  +++tC++C+G+G+++  +++C +C G+g
  gi|336255585|ref|YP_004598692.1| 161 CETCNGEGHPPdADARTCPECQGRGQKRQVQQTpLGRVQ--QTTTCRRCDGEGTLY--SETCGDCGGDG 225
                                       ********98745599*********87777766576644..679************..667*****986 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 !   15.3   4.1     9e-06     0.015      11      40 ..     159     185 ..     154     191 .. 0.88
   2 !   10.1   1.3   0.00037      0.61      11      45 ..     202     230 ..     198     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9e-06
                                       EE-TTTTTTSEETTE......E-TTTTTSS CS
                         Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkg 40 
                                       ++C++Cng G+ + ++ r    CP+C+G+g
  gi|336255585|ref|YP_004598692.1| 159 ETCETCNGEGHPPDADAR---TCPECQGRG 185
                                       79*********9999766...7******98 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00037
                                       EE-TTTTTTSEETTE......E-TTTTTSSEEE-H CS
                         Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkglipTa 45 
                                       t+C  C+g G   +e       C +C+G g +  +
  gi|336255585|ref|YP_004598692.1| 202 TTCRRCDGEGTLYSE------TCGDCGGDGYVRNE 230
                                       79*************......********998765 PP

>> DUF5351  Family of unknown function (DUF5351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.2    0.0015       2.5      18      28 ..     159     169 ..     158     170 .. 0.91
   2 ?    8.5   0.6    0.0014       2.2      19      29 .]     177     187 ..     175     187 .. 0.90
   3 ?    4.7   1.6     0.022        36      19      28 ..     203     212 ..     201     213 .. 0.89
   4 ?    7.0   1.7    0.0041       6.7      17      27 ..     215     225 ..     215     227 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0015
                           DUF5351  18 ETCesCeGtgk 28 
                                       ETCe C+G+g 
  gi|336255585|ref|YP_004598692.1| 159 ETCETCNGEGH 169
                                       9*******995 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0014
                           DUF5351  19 TCesCeGtgke 29 
                                       TC++C+G g++
  gi|336255585|ref|YP_004598692.1| 177 TCPECQGRGQK 187
                                       9*******985 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.022
                           DUF5351  19 TCesCeGtgk 28 
                                       TC  C G+g+
  gi|336255585|ref|YP_004598692.1| 203 TCRRCDGEGT 212
                                       9*******97 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0041
                           DUF5351  17 SETCesCeGtg 27 
                                       SETC  C G g
  gi|336255585|ref|YP_004598692.1| 215 SETCGDCGGDG 225
                                       9*******998 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 ?    8.4   0.1    0.0011       1.7       5      28 ..     160     182 ..     157     183 .. 0.94
   2 ?    2.4   2.1     0.084   1.4e+02       5      18 ..     203     216 ..     199     222 .. 0.81
   3 ?    2.1   0.4       0.1   1.6e+02       5      18 ..     217     229 ..     215     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                     A2L_zn_ribbon   5 vCsvCggngilnseqgylvCieCg 28 
                                       +C+ C+g+g    + + + C+eC+
  gi|336255585|ref|YP_004598692.1| 160 TCETCNGEGHP-PDADARTCPECQ 182
                                       8**********.***********7 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.084
                     A2L_zn_ribbon   5 vCsvCggngilnse 18 
                                       +C  C+g+g l+se
  gi|336255585|ref|YP_004598692.1| 203 TCRRCDGEGTLYSE 216
                                       8********99986 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.1
                     A2L_zn_ribbon   5 vCsvCggngilnse 18 
                                       +C  Cgg+g + ++
  gi|336255585|ref|YP_004598692.1| 217 TCGDCGGDGYV-RN 229
                                       7999***9977.65 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   4.1     0.013        22      29      48 ..     159     181 ..     146     182 .. 0.53
   2 ?   10.8  13.4   0.00024      0.39       1      49 []     161     222 ..     161     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                               DZR  29 drCpsC...gekvdpearfCpeC 48 
                                       ++C  C   g++ d++ar+CpeC
  gi|336255585|ref|YP_004598692.1| 159 ETCETCngeGHPPDADARTCPEC 181
                                       44444422223344455555555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00024
                               DZR   1 CpqCgee...lppdarfCseCgtklkavaa..........edrCpsCgekvdpearfCpeCG 49 
                                       C +C+ e    ++dar+C+eC+ + ++ +            ++C +C+ + ++ +++C+ CG
  gi|336255585|ref|YP_004598692.1| 161 CETCNGEghpPDADARTCPECQGRGQKRQVqqtplgrvqqTTTCRRCDGEGTLYSETCGDCG 222
                                       777754433388999******9995433325678899999*********************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 ?    8.0   2.5    0.0018       2.9      71      96 ..     159     185 ..     134     195 .. 0.74
   2 ?    7.9   1.5    0.0018       2.9      66      96 ..     197     225 ..     189     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0018
                                       EEETTTS-EEECHH.HHHS-TTTSSS- CS
                              HypA  71 vrCreCgkefelee.kalrCpkCgsad 96 
                                        +C++C+ e++  + +a +Cp+C++++
  gi|336255585|ref|YP_004598692.1| 159 ETCETCNGEGHPPDaDARTCPECQGRG 185
                                       36*******9965525889****9875 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0018
                                       EE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  66 evpvkvrCreCgkefeleekalrCpkCgsad 96 
                                       +v+ +++Cr+C+ e++l +  ++C++Cg+ +
  gi|336255585|ref|YP_004598692.1| 197 RVQQTTTCRRCDGEGTLYS--ETCGDCGGDG 225
                                       5778899********9884..48*****865 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.4    0.0047       7.7      35      68 ..     159     192 ..     149     204 .. 0.90
   2 ?    4.7   0.4      0.02        33      19      53 ..     200     234 ..     189     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0047
                           DUF2318  35 daCevCekkgYvqegeelvCknCgvrfaldsige 68 
                                       ++Ce C+++g+  + ++ +C +C+ r ++ ++++
  gi|336255585|ref|YP_004598692.1| 159 ETCETCNGEGHPPDADARTCPECQGRGQKRQVQQ 192
                                       68**********************9999998886 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.02
                           DUF2318  19 rflvvkksdgklrvaldaCevCekkgYvqegeelv 53 
                                       + +  ++ dg+ +   ++C  C+++gYv ++ +l+
  gi|336255585|ref|YP_004598692.1| 200 QTTTCRRCDGEGTLYSETCGDCGGDGYVRNEATLT 234
                                       55667788888889999***********9998875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.1   0.00055       0.9       9      24 ..     168     183 ..     160     184 .. 0.88
   2 ?    0.6   0.5      0.25   4.1e+02      18      25 ..     217     224 ..     215     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00055
                       zf-ribbon_3   9 GaplssddnvCpyCGt 24 
                                       G+p+++d+++Cp C++
  gi|336255585|ref|YP_004598692.1| 168 GHPPDADARTCPECQG 183
                                       8977**********86 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.25
                       zf-ribbon_3  18 vCpyCGtk 25 
                                       +C  CG++
  gi|336255585|ref|YP_004598692.1| 217 TCGDCGGD 224
                                       7*****75 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       3.8   6.2e+03      29      70 ..      28      69 ..      17      74 .. 0.63
   2 ?    4.1   0.5      0.02        32      66      96 ..     151     184 ..     135     193 .. 0.71
   3 ?    8.0   0.7    0.0013       2.1      70      95 ..     198     223 ..     186     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.8
                           TackOD1 29 ldpkskelysypllealskekeeseelleelvkrglleeelv 70
                                      +++ ++++ + p +e  +k+ ++ +++l++ +kr++ ++  +
  gi|336255585|ref|YP_004598692.1| 28 ATEYHPDVSNDPDAEEKFKKIQKAKKVLTDEEKRQAYDRMGH 69
                                      455555566666666666666677777777777776665555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.02
                           TackOD1  66 eeelvdrirlCpsCksghlnv...revCpkCkSi 96 
                                       ++ +++r  +C++C++          +Cp+C+  
  gi|336255585|ref|YP_004598692.1| 151 KQFTIERPETCETCNGEGHPPdadARTCPECQGR 184
                                       4677888899999998766542224689999865 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0013
                           TackOD1  70 vdrirlCpsCksghlnvrevCpkCkS 95 
                                       v+++ +C++C++    + e+C +C+ 
  gi|336255585|ref|YP_004598692.1| 198 VQQTTTCRRCDGEGTLYSETCGDCGG 223
                                       67899*******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 3022.40
//
Query:       gi|336255586|ref|YP_004598693.1|  [L=235]
Description: two-component system sensor kinase [Halopiger xanaduensis SH-6]
Scores for 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-37  126.5  25.4    2.7e-35  121.8  23.3    1.5  2  Sensor    Putative sensor
  ------ inclusion threshold ------
       0.87    9.9  10.3       0.12   12.7   1.0    2.4  2  DUF996    Protein of unknown function (DUF996)


Domain annotation for each model (and alignments):
>> Sensor  Putative sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   2.1e-05      0.19      65     102 ..       4      41 ..       1      41 [. 0.81
   2 !  121.8  23.3     3e-39   2.7e-35       1     162 []      32     214 ..      32     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                            Sensor  65 phrapeppgllarlrallrdpatwrdllylllhfplgl 102
                                       p+r+   ++++  +  +++d++++++l yl+l +plg+
  gi|336255586|ref|YP_004598693.1|   4 PARTDDDSSVAGDIFGVVTDRQSYKNLCYLVLAAPLGM 41 
                                       44333238899999**********************96 PP

  == domain 2  score: 121.8 bits;  conditional E-value: 3e-39
                            Sensor   1 YlllglplgvaafvllvtglslglgllvllvGlplLalalllarglaaveRrrarlllglpvprph.rapep.pgll 75 
                                       Yl+l++plg+a+ +++++gl+lg++l+++++Gl++L ++ll +r++a +eRr+a++llgl++++   ++ +  +g++
  gi|336255586|ref|YP_004598693.1|  32 YLVLAAPLGMAYYTFVTMGLVLGALLSPIGIGLVVLFVTLLTVRLFAGFERRLANALLGLELQAENgPEVASaRGVR 108
                                       9**************************************************************8886666559**** PP

                            Sensor  76 arlrallrdpatwrdllylllhfplglvlfvvavvllalalalltaPl.w...................tlpeallv 132
                                       ar++++l  p+twr l++l+++fplg+ ++vv+++ l++al+l+taPl +                   tlpea+l+
  gi|336255586|ref|YP_004598693.1| 109 ARITSYLEAPSTWRGLGFLMVKFPLGV-VAVVLLIPLFTALSLVTAPLrYpyapelvtvndepitwsieTLPEAVLA 184
                                       *************************87.56667777889*********77888888888777777666669*****9 PP

                            Sensor 133 avlGlllllvllwvvrglarlqallaraLL 162
                                       +++++++ +++l++ +g+a + +++a aLL
  gi|336255586|ref|YP_004598693.1| 185 VMVAAVIGVLVLHLSNGFAYVARQMATALL 214
                                       99999999999******************9 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.0   1.3e-05      0.12      95     133 ..      32      70 ..      16      72 .. 0.84
   2 ?    1.8   2.5     0.031   2.8e+02      68      90 ..     166     202 ..     109     219 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                            DUF996  95 yellgkrtgvklFetagllyfiGaiLtivlvGliillia 133
                                       y  l++ +g  ++  + + +++Ga+L+ + +Gl++l++ 
  gi|336255586|ref|YP_004598693.1|  32 YLVLAAPLGMAYYTFVTMGLVLGALLSPIGIGLVVLFVT 70 
                                       55577889999999**********************996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.031
                            DUF996  68 s..............lilllllvliiayvlliisavf 90 
                                       +              ++l ++++ +i +++l +s+ f
  gi|336255586|ref|YP_004598693.1| 166 VndepitwsietlpeAVLAVMVAAVIGVLVLHLSNGF 202
                                       1445556666666654444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1778.26
//
Query:       gi|336255587|ref|YP_004598694.1|  [L=197]
Description: intracellular protease, PfpI family [Halopiger xanaduensis SH-6]
Scores for 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-52  175.8   0.0    7.4e-52  175.5   0.0    1.0  1  DJ-1_PfpI      DJ-1/PfpI family
     0.0021   17.8   0.1      0.022   14.4   0.0    2.1  2  ThiJ_like      ThiJ/PfpI family-like
     0.0022   17.8   0.0     0.0028   17.4   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
     0.0048   16.5   0.0      0.015   14.9   0.0    1.7  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.021   14.4   0.0    1.2  1  Catalase_C     C-terminal domain found in long catalases
       0.11   12.7   0.0       0.18   12.1   0.0    1.3  1  SnoaL_3        SnoaL-like domain
       0.14   11.9   0.0        0.2   11.4   0.0    1.2  1  Peptidase_C26  Peptidase C26
       0.22   11.3   0.0        0.3   10.9   0.0    1.2  1  SNO            SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.5   0.0   3.3e-55   7.4e-52       1     162 [.       4     179 ..       4     181 .. 0.98

  Alignments for each domain:
  == domain 1  score: 175.5 bits;  conditional E-value: 3.3e-55
                                       EEEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESS................TSEEEETTSEEEE-SEEGGGCTCCG CS
                         DJ-1_PfpI   1 kkvlvlladgvedvElivpvdvlkragikvdvvsvd................keevkgsrGlkvtvdaslddvkaae 61 
                                       k++l+l +d ved+E++vp+++l+  g++v++v+++                +++++++ G+++ +++ +d v++a+
  gi|336255587|ref|YP_004598694.1|   4 KRILLLAGDFVEDYEVMVPFQALQMVGHEVHAVCPEkeagdacptaihdfegGQTYTEKPGHNFELNHDFDAVDPAD 80 
                                       79*************************************************************************** PP

                                       -SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SS CS
                         DJ-1_PfpI  62 yDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdk 138
                                       yDalv+pGGra pe+lr+ ++v+e+v++f+ ++k+vaa+C+g q+Laaa+vl+gr++T+ypa++ +++ ag +++d+
  gi|336255587|ref|YP_004598694.1|  81 YDALVVPGGRA-PEYLRTYDEVLEIVRHFFAEDKPVAALCHGLQILAAADVLEGRTCTAYPALEADVRGAGGNWEDE 156
                                       ***********.***************************************************************99 PP

                                       SEEEETTEEEESSGGGHHHHHHHH CS
                         DJ-1_PfpI 139 rvvvdgnlvTsrgpgaaiefalel 162
                                        v +dgnlvT+++++ +++++  +
  gi|336255587|ref|YP_004598694.1| 157 -VTRDGNLVTAQAWPGHPDWLAGF 179
                                       .*******************8765 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.12   2.8e+02      10      33 ..      18      41 ..      10      57 .. 0.80
   2 !   14.4   0.0   9.9e-06     0.022      83     152 ..      79     139 ..      58     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.12
                         ThiJ_like 10 evaipwkvlkdagfsveFvtekgk 33
                                      ev +p++ l+  g +v+ v ++ +
  gi|336255587|ref|YP_004598694.1| 18 EVMVPFQALQMVGHEVHAVCPEKE 41
                                      899**************9999866 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 9.9e-06
                         ThiJ_like  83 eeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttl 152
                                        +yd++ +pGG+ +    l + + + + +++++       +++k ++a c+g   la+a+       t+ 
  gi|336255587|ref|YP_004598694.1|  79 ADYDALVVPGGRAPEY--LRTYDEVLEIVRHFF-------AEDKPVAALCHGLQILAAADVLEGRTCTAY 139
                                       589*********9977..667788889999999.......789*************99998444444444 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.3e-06    0.0028      40      87 ..      78     128 ..      55     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                                       HHSTSEEEEEEESSCTT...TTTHHHHHHHHCTSTS-EEEETHHHHHHHHH CS
                            GATase  40 lknpdgilvsgGpgspg...vegkieaikearenkiPiLGICLGmQllaie 87 
                                         ++d+++v+gG    +   +++ +e++++++ +++P+   C G+Q+la +
  gi|336255587|ref|YP_004598694.1|  78 PADYDALVVPGGRAPEYlrtYDEVLEIVRHFFAEDKPVAALCHGLQILAAA 128
                                       4689********77777779***************************9875 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 ?   -1.1   0.0      0.55   1.2e+03     137     147 ..      26      36 ..      13      68 .. 0.69
   2 !   14.9   0.0   6.8e-06     0.015      39      89 ..      79     126 ..      60     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.55
                          GATase_3 137 eevkGyEiHsG 147
                                        ++ G+E+H  
  gi|336255587|ref|YP_004598694.1|  26 LQMVGHEVHAV 36 
                                       46678888864 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.8e-06
                          GATase_3  39 edadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLG 89 
                                       +d+d++++pGg+  +    +++   + e ++++ ++++pv + C Glq+L 
  gi|336255587|ref|YP_004598694.1|  79 ADYDALVVPGGRAPEYLRTYDE---VLEIVRHFFAEDKPVAALCHGLQILA 126
                                       68*********98766555544...699999******************97 PP

>> Catalase_C  C-terminal domain found in long catalases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.5e-06     0.021      48     117 ..      70     130 ..      56     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.5e-06
                        Catalase_C  48 nrTYstadaveFDaivvadgaeslfsakataasslfpagrplqllldayrhgKpigalGsgaealkaagi 117
                                       n+ + + d +++Da+vv +g          a++ l  ++++l++++  ++  Kp++al +g ++l+aa++
  gi|336255587|ref|YP_004598694.1|  70 NHDFDAVDPADYDALVVPGG---------RAPEYLRTYDEVLEIVRHFFAEDKPVAALCHGLQILAAADV 130
                                       55566788899*********.........24566889***************************999987 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.9e-05      0.18      16      81 ..      72     137 ..      68     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.9e-05
                           SnoaL_3  16 dfdalfalwaddivfigtgadelltgreevrrslkqifakgegisfeltdvrvtesgdvawvtell 81 
                                       dfda+     d +v  g  a+e+l++++ev+++++  fa+ +++   ++ +++ ++ dv    ++ 
  gi|336255587|ref|YP_004598694.1|  72 DFDAVDPADYDALVVPGGRAPEYLRTYDEVLEIVRHFFAEDKPVAALCHGLQILAAADVLEGRTCT 137
                                       5555555555888888999**********************************9999987665555 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.9e-05       0.2      95     121 ..     102     128 ..      74     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.9e-05
                     Peptidase_C26  95 laLiraalergvPilgiCrGlqllnva 121
                                       l ++r+  ++++P+ + C Glq+l+ a
  gi|336255587|ref|YP_004598694.1| 102 LEIVRHFFAEDKPVAALCHGLQILAAA 128
                                       678999******************876 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013       0.3      32      84 ..      79     128 ..      69     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                                       CC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCE CS
                               SNO  32 aevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillske 84 
                                       a+ dal++PGG +    +  +  +++e ++ f ++  k+v   C Gl +l++ 
  gi|336255587|ref|YP_004598694.1|  79 ADYDALVVPGGRAPEYLRTYD--EVLEIVRHFFAED-KPVAALCHGLQILAAA 128
                                       788********9887666555..4569999999887.**********999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1565.12
//
Query:       gi|336255588|ref|YP_004598695.1|  [L=255]
Description: hypothetical protein Halxa_4214 [Halopiger xanaduensis SH-6]
Scores for 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   17.3   0.0       0.15   10.6   0.0    2.0  2  AMP-binding  AMP-binding enzyme


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 !   10.6   0.0   8.3e-06      0.15       6      69 ..      16      77 ..      11      85 .. 0.83
   2 !    4.8   0.0   0.00048       8.6      30     235 ..     167     218 ..     152     241 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.3e-06
                                      HHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHH CS
                       AMP-binding  6 aktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailk 69
                                      +++ d++ lvd ++ + + Y+ l   + +++++Lr+ Gv++g +V+++ + +p  ++a++++  
  gi|336255588|ref|YP_004598695.1| 16 EEYDDRTTLVD-ATEREYDYHWLCTSSWKAGNFLRHSGVRQGVTVGVVGD-GPLALLAFFGTTL 77
                                      67789999999.88999******************99**********987.5666667777655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.00048
                                       HHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESEEEETCTCC CS
                       AMP-binding  30 ervnrlAagLr.slGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayiledseakvliatvdse 105
                                       +++ ++A++   + G+++g+                                                         
  gi|336255588|ref|YP_004598695.1| 167 AEALEAARAVIdEYGIGQGE--------------------------------------------------------- 186
                                       23333444444455555555......................................................... PP

                                       CHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHH CS
                       AMP-binding 106 lleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGTTGkPKGVmlshr 182
                                                                                                                    
  gi|336255588|ref|YP_004598695.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-T CS
                       AMP-binding 183 nlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllp 235
                                                            +v++ +pl+   +++++++++ll+ + +vl +
  gi|336255588|ref|YP_004598695.1| 187 ---------------------RVVVRAPLSSLEAVVAGVIAPLLAEGVIVLTE 218
                                       .....................55555555555555555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1938.68
//
Query:       gi|336255589|ref|YP_004598696.1|  [L=535]
Description: FAD dependent oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-44  150.7   0.5    1.1e-43  150.2   0.5    1.2  1  DAO             FAD dependent oxidoreductase
    5.2e-15   55.2   0.0    1.2e-14   54.0   0.0    1.5  1  Rieske          Rieske [2Fe-2S] domain
    2.4e-06   26.9   0.0    3.9e-06   26.2   0.0    1.4  1  FAD_binding_2   FAD binding domain
    6.7e-06   26.2   0.0    5.8e-05   23.2   0.1    2.6  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.5e-05   23.7   0.0      4e-05   23.0   0.0    1.4  1  FAD_binding_3   FAD binding domain
    4.3e-05   22.9   0.0    0.00011   21.5   0.0    1.6  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00028   20.2   0.1      0.002   17.5   0.1    2.2  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0014   19.1   0.3     0.0043   17.6   0.3    1.8  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0028   16.4   0.0     0.0045   15.8   0.0    1.4  1  HI0933_like     HI0933-like protein
     0.0052   16.2   0.0     0.0076   15.6   0.0    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.011   14.7   0.5      0.015   14.1   0.5    1.2  1  Trp_halogenase  Tryptophan halogenase
      0.012   14.8   0.0      0.022   14.0   0.0    1.3  1  Thi4            Thi4 family
      0.056   12.5   0.1       0.18   10.8   0.4    1.6  2  GIDA            Glucose inhibited division protein A
       0.12   11.7   0.5       0.25   10.6   0.2    1.7  2  Amino_oxidase   Flavin containing amine oxidoreductase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.2   0.5   8.4e-47   1.1e-43       1     352 []      46     401 ..      46     401 .. 0.78

  Alignments for each domain:
  == domain 1  score: 150.2 bits;  conditional E-value: 8.4e-47
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS..........STHHSTH.....HHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl..........rylpeas.....elarl 60 
                                       dv+++GGGi+Gl+tA+eL ++g  V++le+++i+   ++g++++ l+s++                      ++a+ 
  gi|336255589|ref|YP_004598696.1|  46 DVAVVGGGITGLTTALELKEAGkaVAVLESDRIVE-STTGHTTAKLTSQHgliydtllsqF-----DedkarQYADA 116
                                       8*****************99999********9999.**********999987766555542.....04445588899 PP

                                       HHHHHHHHHHHHHHHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTTST.TTSEEEE CS
                               DAO  61 slealeelreleeelgididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepalp.gllgalf 136
                                        ++a+ee ++l +e++id+d+rrt  + +aa++++ e+++++++++++++l+a+++++       p lp ++  a+ 
  gi|336255589|ref|YP_004598696.1| 117 NEAAIEEVARLIDEYDIDCDFRRTPAYTYAASPDDVEQIQDEVRAAQRLDLPASYFEET------P-LPfDTGPAVR 186
                                       99999**************************9999********9999999999999775......6.4447888999 PP

                                       ETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEEEEEEEEEE--GGGHHHH.HTT CS
                               DAO 137 ypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgve.rttp.gendaadavVnaaGawsdll.gll 210
                                       ++d++ ++p+k++ a+a+a+   G  ++e+t++ +le     ++  + + t+ ge++ ad vV+a+      + +++
  gi|336255589|ref|YP_004598696.1| 187 FDDQAEFHPRKYLLAIAEAIHGDGSYVFEETQALDLEP----GSPCRlE-TErGEVV-ADDVVVATHFP---FhDRA 254
                                       ************************************54....4555534.5558765.5*******533...32223 PP

                                       CTTTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEE...EEETTTTEEEEEE.............TTSE.EEEEESSE CS
                               DAO 211 keldlpispvrgqvlvlkplseklvspaailpvpe...tdddgrgvyvtpr.............kdgr.vlvGgtad 270
                                       + +  +++p r++ l++ +++e++ +    +++     t +                       ++ + ++vGg   
  gi|336255589|ref|YP_004598696.1| 255 GYF-SRMHPHRAYLLAV-RIEEEPPEG-MYYNTASpaaTMRT--------HpvdaaaaehgdaaEGEElLIVGGQS- 319
                                       444.577**********.777744322.22222223333332........23333334466665333425569975. PP

                                       EETTCSS.TSCSHHHHHHHHHHHHHHSGGGCGEEEEEEEEEE.E.TTSSEEEEE.EETEEEEEEEEECTTTHHHHHH CS
                               DAO 271 eesgddd.pevdeedidellealrklfPqlgdvlrkwaGlrp.l.pdglplige.tpgvkglylatGhsghGltlap 343
                                         +++ +   +++e++++  + +r+ f   ++++++w+  ++   +d  p+ig   p +k++y+ tG+ g+G+t ++
  gi|336255589|ref|YP_004598696.1| 320 --HKPSVsGVPTSERYRRCEQFARENFTV-ESIEYRWS-TMDySpVDQVPFIGSiDPFSKHVYVGTGFKGWGMTGGT 392
                                       ..43444479*****************66.9*******.5553447********655899***************** PP

                                       HHHHHHHHH CS
                               DAO 344 atGkllael 352
                                       a+G +l++l
  gi|336255589|ref|YP_004598696.1| 393 AAGVILSDL 401
                                       ***999986 PP

>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   9.4e-18   1.2e-14       8      84 ..     454     529 ..     450     532 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 9.4e-18
                                       GGGC-.TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEETTSBEEE-TTHH CS
                            Rieske   8 esdvp.egdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwaydadGkvikgPapr 83 
                                       ++d+p  gd   +++ g+p+ ++rded++++A+s vC+H+g+ +  +   e+ +  CpcHg++++++G+v+ gPa +
  gi|336255589|ref|YP_004598696.1| 454 ADDMPeAGDASLIRRTGRPMGLYRDEDDTIHAVSAVCPHMGCLVRWNDA-ER-TWDCPCHGSRFTHEGNVLSGPALE 528
                                       68999999999********************************877777.55.99*******************987 PP

                                       H CS
                            Rieske  84 p 84 
                                        
  gi|336255589|ref|YP_004598696.1| 529 G 529
                                       5 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   3.1e-09   3.9e-06       1      38 [.      46      83 ..      46     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.1e-09
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38
                                      Dv V+G+G+ GL+ Ale++eaG+ vav+e    ++++t
  gi|336255589|ref|YP_004598696.1| 46 DVAVVGGGITGLTTALELKEAGKAVAVLESDRIVESTT 83
                                      9****************************977665544 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 !   23.2   0.1   4.5e-08   5.8e-05       1      28 [.      49      76 ..      49     113 .. 0.88
   2 ?   -1.3   0.0       2.1   2.7e+03      41      54 ..     161     174 ..     150     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.5e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      +vG+G++Gl++A +L++ag+ v +le+ 
  gi|336255589|ref|YP_004598696.1| 49 VVGGGITGLTTALELKEAGKAVAVLESD 76
                                      8*************************86 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.1
                                       TTCEECTS---EEE CS
                     NAD_binding_8  41 pgvrvdygahifhg 54 
                                         +r+d++a++f  
  gi|336255589|ref|YP_004598696.1| 161 AAQRLDLPASYFEE 174
                                       3489*******975 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.1e-08     4e-05       1      34 [.      44      77 ..      44     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.1e-08
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                      ++dV++VG+G +Gl++al+L+eaG  v ++e  +
  gi|336255589|ref|YP_004598696.1| 44 DVDVAVVGGGITGLTTALELKEAGKAVAVLESDR 77
                                      689***************************9864 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 !   21.5   0.0   8.7e-08   0.00011     138     184 ..      40      86 ..      23     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.7e-08
                                       CSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 138 lkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldke 184
                                       ++ l+ +++vvGgG +G+ +A +l+++gk v ++e   ++ +++++ 
  gi|336255589|ref|YP_004598696.1|  40 DDGLDVDVAVVGGGITGLTTALELKEAGKAVAVLESDRIVESTTGHT 86 
                                       44455799999999999999999999999999888744444555554 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 !   17.5   0.1   1.5e-06     0.002       2      37 ..      49      83 ..      48      99 .. 0.91
   2 ?   -0.9   0.0       0.6   7.7e+02     114     132 ..     228     246 ..     213     257 .. 0.83
   3 ?   -2.9   0.0       2.4   3.1e+03     153     173 ..     298     318 ..     281     330 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgnignsiy 37
                                      ++G+G  Gl++a+elk+ag   + +lE ++i++s +
  gi|336255589|ref|YP_004598696.1| 49 VVGGGITGLTTALELKEAGK-AVAVLESDRIVESTT 83
                                      8******************9.8***********976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.6
                       Pyr_redox_3 114 fevetsketyeAkkviiAt 132
                                        ++et+++++ A+ v++At
  gi|336255589|ref|YP_004598696.1| 228 CRLETERGEVVADDVVVAT 246
                                       57899*************9 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.4
                       Pyr_redox_3 153 yskvkefhkyagqkvvViGgk 173
                                        +  ++ +  +g++++++Gg+
  gi|336255589|ref|YP_004598696.1| 298 AAAAEHGDAAEGEELLIVGGQ 318
                                       555667777889999999996 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   3.4e-06    0.0043       2      45 ..      47      90 ..      46      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.4e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaski 45
                                      v+vvGgG +gl  A +l+e gk V v+e    + +  +++++k+
  gi|336255589|ref|YP_004598696.1| 47 VAVVGGGITGLTTALELKEAGKAVAVLESDRIVESTTGHTTAKL 90
                                      89************************997655546666666665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.5e-06    0.0045       2      33 ..      46      77 ..      45     131 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.5e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      dv+v+GgG  Gl +A++++++gk V++le+ +
  gi|336255589|ref|YP_004598696.1| 46 DVAVVGGGITGLTTALELKEAGKAVAVLESDR 77
                                      89***************************875 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.9e-06    0.0076       1      33 [.      46      78 ..      46     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.9e-06
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergv 33
                                      Dv VvGGg+ G++ A+  ++aG+ v+++e ++ 
  gi|336255589|ref|YP_004598696.1| 46 DVAVVGGGITGLTTALELKEAGKAVAVLESDRI 78
                                      9****************************9876 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5   1.2e-05     0.015       1      46 [.      46      88 ..      46     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE-- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeati 46
                                      ++ +vGGG+ G ++A  l++a+    +v ++es+ i     G  t 
  gi|336255589|ref|YP_004598696.1| 46 DVAVVGGGITGLTTALELKEAG---KAVAVLESDRIVESTTGHTTA 88
                                      589*******************...56*********9999998764 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.7e-05     0.022      11      49 ..      38      75 ..      31      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                                      HHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 11 dllkyaesDvvivGaGssGLtaayylakkpdlkvailer 49
                                       +++  + Dv++vG+G +GLt+a  l ++ +  va+le+
  gi|336255589|ref|YP_004598696.1| 38 PFDDGLDVDVAVVGGGITGLTTALELKEA-GKAVAVLES 75
                                      56677889******************999.999***997 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   0.00014      0.18       1      29 [.      46      78 ..      46      94 .. 0.81
   2 ?   -2.1   0.0       1.2   1.6e+03     118     195 ..     217     287 ..     182     342 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE....E CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi....t 29
                                      dv V+GgG  G+  Al+++++G  v+ +     
  gi|336255589|ref|YP_004598696.1| 46 DVAVVGGGITGLTTALELKEAGKAVAVLesdrI 78
                                      79***********************99844440 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                                       EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEESSCTTC--B-THHHHHHHTT--EEEEEEEE CS
                              GIDA 118 veeliveekkvkgvvtedgetikakavviatGtflkgkihigekelsaGrlgeltseglseslkelgfellrlktgt 194
                                        + l++e ++ + + te+ge++ +++vv +  +f +   ++        r++   ++ l+ +++e + e ++  t+ 
  gi|336255589|ref|YP_004598696.1| 217 TQALDLEPGSPCRLETERGEVVADDVVVATHFPFHDRAGYF-------SRMHPHRAYLLAVRIEEEPPEGMYYNTAS 286
                                       44445555777888889999999988888888865444333.......56666666666666666666666666665 PP

                                       - CS
                              GIDA 195 p 195
                                       p
  gi|336255589|ref|YP_004598696.1| 287 P 287
                                       3 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2    0.0002      0.25       1      23 [.      54      76 ..      54      79 .. 0.94
   2 ?   -2.1   0.0       1.3   1.7e+03     240     261 ..     227     247 ..     205     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                                      HHHHHHHHHHHHTTEEEEEEESS CS
                     Amino_oxidase  1 laGLaaArqLlsaGfdVtvlEar 23
                                      ++GL++A +L++aG  V vlE++
  gi|336255589|ref|YP_004598696.1| 54 ITGLTTALELKEAGKAVAVLESD 76
                                      79*******************85 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                       CEEEEETTSTEEEESEEEE-S- CS
                     Amino_oxidase 240 gvtvtledgevveaDaVvvTvp 261
                                        +++++e gev  aD Vvv++ 
  gi|336255589|ref|YP_004598696.1| 227 PCRLETERGEV-VADDVVVATH 247
                                       47888888888.9999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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 0.25s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 4118.03
//
Query:       gi|336255590|ref|YP_004598697.1|  [L=321]
Description: Pyruvate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-42  142.9   0.0    1.1e-41  142.4   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
    8.9e-36  122.5   0.1    1.6e-35  121.7   0.1    1.4  1  Transketolase_C  Transketolase, C-terminal domain
     0.0071   16.6   0.1       0.02   15.2   0.0    1.8  2  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 !  142.4   0.0   1.9e-45   1.1e-41       4     176 ..       6     178 ..       3     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 142.4 bits;  conditional E-value: 1.9e-45
                                       EHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEE CS
                      Transket_pyr   4 awrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllvive 78 
                                        + +a++ +l ++l++d++vv+ g+Dv+  gg+f +++gl +d  ++rv+ds+++E++++g+ vG+a++g ++++ e
  gi|336255590|ref|YP_004598697.1|   6 RMIEAVGRTLRSELERDDSVVVYGEDVGraGGVFRATEGLIDDY-PNRVFDSPVAEAGIVGVGVGLAATG-MRPVPE 80 
                                       6889************************99**************.*************************.8***** PP

                                       EEEHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHH CS
                      Transket_pyr  79 aqFgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhl 153
                                       +qF  F+ ++  q+  + a ++ +++g +++++++r+p+g g  + e +s + ea + ++pglkv+ Ps+paet++l
  gi|336255590|ref|YP_004598697.1|  81 IQFQSFLYQGfhQLAQHVARIRSRTRGTITCPMTIRTPYGGGIHALELHSESFEAGFSHVPGLKVAIPSSPAETAGL 157
                                       ***********999999************************************************************ PP

                                       HHHHHHSSS.SEEEEEE-SSEEC CS
                      Transket_pyr 154 lrrairredrkPvvlrlpksllr 176
                                       lr  ir  +++Pvv+++p +l+r
  gi|336255590|ref|YP_004598697.1| 158 LRSSIR--SPDPVVFMEPTRLYR 178
                                       ******..678**********98 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.7   0.1   2.7e-39   1.6e-35       1     124 []     193     311 ..     193     311 .. 0.95

  Alignments for each domain:
  == domain 1  score: 121.7 bits;  conditional E-value: 2.7e-39
                                       TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                   Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                       g+a+++  g+dvt+va+Gsm++e leA++e+     s+eV+d+rt+ plD+eti++sv+ktgr+vvv+ea ++gG++
  gi|336255590|ref|YP_004598697.1| 193 GEARVVEAGDDVTVVAWGSMLRETLEAVDEID---ASVEVIDPRTLYPLDTETIADSVRKTGRCVVVHEAPRTGGLA 266
                                       799****************************6...88**************************************** PP

                                       HHHHHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
                   Transketolase_C  78 sevaaalaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                        e++a+++eeaf +l+apv+rv+g+dv++p    + e+ +++dae+i
  gi|336255590|ref|YP_004598697.1| 267 GEITARINEEAFLYLEAPVERVTGYDVPVPLF--AREDGYLPDAERI 311
                                       ***************************77776..4589999999987 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       1.2   7.2e+03      29      49 ..      68      87 ..      58      94 .. 0.68
   2 !   15.2   0.0   3.4e-06      0.02       2      81 ..     203     276 ..     202     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                                      EEEEEES--BS--HHHHHHHS CS
                           PFOR_II 29 vGllrlrtlrPFPeeelkell 49
                                      vGl   + +rP Pe +++++l
  gi|336255590|ref|YP_004598697.1| 68 VGLA-ATGMRPVPEIQFQSFL 87
                                      4443.4567899988877665 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.4e-06
                                       SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHT CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaal 78 
                                       +v +va Gs+ +++ +avde+ ++   v ++ +rtl+P  +e +++ ++k+ + vv+  +     +G l+ e+ a +
  gi|336255590|ref|YP_004598697.1| 203 DVTVVAWGSMLRETLEAVDEIDAS---VEVIDPRTLYPLDTETIADSVRKTGRCVVVHEAPR---TGGLAGEITARI 273
                                       799*****************9888...999****************9999988888877773...466677776666 PP

                                       GGG CS
                           PFOR_II  79 kks 81 
                                       +++
  gi|336255590|ref|YP_004598697.1| 274 NEE 276
                                       655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2317.06
//
Query:       gi|336255591|ref|YP_004598698.1|  [L=361]
Description: pyruvate dehydrogenase E1 component subunit alpha [Halopiger xanaduensis SH-6]
Scores for 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-80  269.5   0.0    3.5e-80  269.2   0.0    1.0  1  E1_dh            Dehydrogenase E1 component
    7.2e-05   22.1   0.1    0.00012   21.4   0.1    1.3  1  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
     0.0089   15.8   0.8      0.032   14.0   0.8    1.9  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
  ------ inclusion threshold ------
      0.043   12.8   0.1      0.069   12.1   0.1    1.2  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
       0.15   11.8   0.0       0.31   10.8   0.0    1.5  1  HTH_41           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.2   0.0   9.7e-84   3.5e-80       4     295 ..      43     324 ..      40     327 .. 0.94

  Alignments for each domain:
  == domain 1  score: 269.2 bits;  conditional E-value: 9.7e-84
                                       HHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-TTTS CS
                             E1_dh   4 vllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkvkgk 80 
                                       +   r +d++++ ++r + +g+y++ +gqea++vg a+a+ ++D+i++++Re++ ll+rg + e+il +  g +   
  gi|336255591|ref|YP_004598698.1|  43 MKRSRRLDERAIALQRRGELGTYAPAIGQEAAQVGTAFAMADGDWIVPSFREQPALLVRGTPPEQILQYALGME--- 116
                                       55567789999*************************************************************99... PP

                                       SGTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEE CS
                             E1_dh  81 ggsrhelmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvifv 157
                                            e++  + ++  l+  ++vg+q+ ++ G+      ++ ++va++++GDgA+++Gdvyea+n+a +++++++fv
  gi|336255591|ref|YP_004598698.1| 117 -----EGAEIPDGEGALPPAIPVGSQPLHAVGVGWGEALQDRDNVAVTYFGDGATSEGDVYEAFNFAGVYDAQTVFV 188
                                       .....56667788889**********77777********************************************** PP

                                       EEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS-SSTTS CS
                             E1_dh 158 veNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyggHsesD 234
                                       ++NN+y+isT  ek+++++++a++a ++gi g+rVdgnD+l vy ++++A+e ar g  p+lie++tYR+  H++sD
  gi|336255591|ref|YP_004598698.1| 189 CQNNRYAISTGIEKQTKAETFAQKAIAAGIDGIRVDGNDVLGVYRVAQEAIEQARDG-EPVLIEALTYRRSMHTTSD 264
                                       *******************************************************95.6****************** PP

                                       HSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS- CS
                             E1_dh 235 dpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskk 295
                                       dp++yr +ee +e+++  dpi r++ +L ++g++++e ++ei+++++ e  +a+++a  + 
  gi|336255591|ref|YP_004598698.1| 265 DPTAYREPEEESEWEAR-DPILRFQVFLEDRGLLDDETEDEIDERIESELADAIDRARTAR 324
                                       ******77777777666.**************************************98775 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 !   21.4   0.1   3.3e-08   0.00012     120     179 ..     141     200 ..     138     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.3e-08
                    DXP_synthase_N 120 alGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisknv 179
                                       a+G+   + l+++++ +v+  GDga + G  +ea+n +g  +++ + +  +N+ +is+ +
  gi|336255591|ref|YP_004598698.1| 141 AVGVGWGEALQDRDNVAVTYFGDGATSEGDVYEAFNFAGVYDAQTVFVCQNNRYAISTGI 200
                                       6788888999999999****************************************9866 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 !   14.0   0.8   8.8e-06     0.032      34     152 ..     142     251 ..     132     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.8e-06
                                       HHHHHHHHHHSTTSEEEEEEEHHHHHHT..GGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS CS
                      TPP_enzyme_C  34 lpaAiGaklakpdrevvaivGDGgflmi..lqelatavrrnlpitvvvlnNegygmtggqqepfggkrksgpagkdl 108
                                       ++++ G +l+++d+  v + GDG++      +++  a  ++++ ++v+ nN++   tg +++ + +           
  gi|336255591|ref|YP_004598698.1| 142 VGVGWGEALQDRDNVAVTYFGDGATSEGdvYEAFNFAGVYDAQTVFVCQNNRYAISTGIEKQTKAE----------- 207
                                       45555555666678889999***9877663677888888988999999999888888887554443........... PP

                                       ----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH...CSSSEEEEE CS
                      TPP_enzyme_C 109 kpvdfaklaealGakgarvekadveeleealkeal...ekkgpalie 152
                                           fa+ a a+G++g+rv+ +dv  + ++ +ea+   + ++p+lie
  gi|336255591|ref|YP_004598698.1| 208 ---TFAQKAIAAGIDGIRVDGNDVLGVYRVAQEAIeqaRDGEPVLIE 251
                                       ...47788999999999999999999988888888776677899998 PP

>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.9e-05     0.069     144     242 ..     154     253 ..     147     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
                                       ---EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEESSEETT.EEGGGT--S-HHHHHHHTT-EEEEETTTT-H CS
                   Transketolase_N 144 dhytyvilgDgclmeGvsseasslagtlkLgkLivlyDdnkisid.GeteisftedvakrfeaygWhvievedgedv 219
                                       d+      gDg   eG   ea ++ag+   + +  +  +n+ +i  G  +++ +e  a++  a g + i+v dg+dv
  gi|336255591|ref|YP_004598698.1| 154 DNVAVTYFGDGATSEGDVYEAFNFAGVYDAQTVF-VCQNNRYAIStGIEKQTKAETFAQKAIAAGIDGIRV-DGNDV 228
                                       56666789*******************9987655.567777777625556677888899999*****9995.66666 PP

                                       HHH....HHHHHHHHH-TTS-EEEEEE CS
                   Transketolase_N 220 eai....kaaieeakaekdkPsliklr 242
                                         +    ++aie+a+     P li+  
  gi|336255591|ref|YP_004598698.1| 229 LGVyrvaQEAIEQARD--GEPVLIEAL 253
                                       6652222456666665..489998765 PP

>> HTH_41  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   8.6e-05      0.31      32      47 ..      50      65 ..      49      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.6e-05
                            HTH_41 32 ddkaislerrGrlGtf 47
                                      d++ai+l+rrG lGt+
  gi|336255591|ref|YP_004598698.1| 50 DERAIALQRRGELGTY 65
                                      789************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2805.67
//
Query:       gi|336255592|ref|YP_004598699.1|  [L=209]
Description: hypothetical protein Halxa_4218 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.02   14.3   0.2      0.024   14.0   0.2    1.1  1  TraF_2        F plasmid transfer operon, TraF, protein
        1.5    8.9   3.2        6.7    6.8   0.2    2.3  2  CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit


Domain annotation for each model (and alignments):
>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   2.7e-06     0.024      30     129 ..      61     159 ..      45     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-06
                            TraF_2  30 vgdvdnlvDkiDdlsdildgleaavnaasadetq..vdeaaddlnalLedlggdgylkasagvglavaipndrlgga 104
                                       v+  d  +++iDdl++ ld  e+ + +  ++ ++  + e++++ ++++++++++    + + ++la++ p +++ g+
  gi|336255592|ref|YP_004598699.1|  61 VRADDAEIETIDDLEAFLD-DEGLPVERLEE-VEkpIAEKLETEREDIDEIDNEP-HGTGTVLALAFVHPDRTETGT 134
                                       566677899**********.33333333333.3346999***************9.77777788***********88 PP

                            TraF_2 105 lflkayleaiaradvleesdiqsls 129
                                       l l + +++   a v++ +d+++l+
  gi|336255592|ref|YP_004598699.1| 135 LELVGLVAGGYAALVASGNDAELLE 159
                                       8887777777777776333333333 PP

>> CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2   0.00075       6.7       6      26 ..       1      21 [.       1      23 [. 0.95
   2 ?    2.3   0.3      0.02   1.8e+02      11      26 ..     137     152 ..     136     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00075
                      CytB6-F_Fe-S  6 msrRqllNlllvGaialtaaa 26
                                      m+rR ll    ++ +al+a++
  gi|336255592|ref|YP_004598699.1|  1 MNRRHLLTRCAGASAALVAVS 21
                                      9******************97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.02
                      CytB6-F_Fe-S  11 llNlllvGaialtaaa 26 
                                       l +l+ +G +al+a++
  gi|336255592|ref|YP_004598699.1| 137 LVGLVAGGYAALVASG 152
                                       678999*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1595.72
//
Query:       gi|336255593|ref|YP_004598700.1|  [L=434]
Description: sodium/hydrogen exchanger [Halopiger xanaduensis SH-6]
Scores for 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  137.8  23.1    4.9e-40  137.5  23.1    1.1  1  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 !  137.5  23.1   2.7e-44   4.9e-40       3     380 ..      14     416 ..      11     417 .. 0.91

  Alignments for each domain:
  == domain 1  score: 137.5 bits;  conditional E-value: 2.7e-44
                                       HHHHHHHHHHHHHHHTT....SXHHHHHHHHHHHHTTTTTS.........HHHCHCCHHHHCHHCCHHHHCTCGCCT CS
                    Na_H_Exchanger   3 llillallvgllarrlk....lpeivgliiaGlllGpsglglieps....eedlevlselglilllFlaGleldlre 71 
                                       +l+ +a+l+++++ r+     + +++++i++G +l    lg+ ep+     +  e l elg+i+ l  +Gl+ld+  
  gi|336255593|ref|YP_004598700.1|  14 ILVGVAILGIAILPRFIsnvpVTDPIFYIAYGFILFSLPLGIPEPDplaqGHMAERLTELGVIIALMTVGLKLDRPP 90 
                                       4444466666654444447557779****************8788799999************************** PP

                                       GCCTHHHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC..............CCCT CS
                    Na_H_Exchanger  72 lrknlksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailk.............eegr 135
                                        ++ + s+  l+ + + +t+ l + l+++  + g+ +  a+l+ga++++tdpvv++ +               e+  
  gi|336255593|ref|YP_004598700.1|  91 GLRSWESVWRLLGITMPVTIGL-SALVGW--WAGFAIPTAVLLGAVIAPTDPVVASEVQVegpggsteeqpkpEADG 164
                                       9999999988888888888888.999998..899************************999******9999987777 PP

                                       STCCCCCCHHHHHHHHHHHCCCCCHHHHHHTX.XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS... CS
                    Na_H_Exchanger 136 vperlgtlllgesvlnDavavvllavllalak.eeaggetslllllliflvvavgglllglvigwllrlitrft... 208
                                        + +++  l ges+lnD++a++++++++a+a  + a g++   +ll+ +++  v+g+ + lv+gwll+++   +   
  gi|336255593|ref|YP_004598700.1| 165 REDEVRFALSGESGLNDGFAFPFTNLAVAMALvGVAPGNWVGEWLLIDVVYRTVVGVGVALVLGWLLARLVFIApvs 241
                                       7788888999*********************999999999999**************************99999999 PP

                                       .CTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH...HHHHHHHHHHHHHHS CS
                    Na_H_Exchanger 209 .dddrelevllvlllallaallaellgvsgilgaflaGlvlseyefsnklseklesfre...glfnplfFvlvGlsl 281
                                           +++  l +l   l+++++ e+lg  g +g+f+a  vl +ye+++   e l+ + e   +l+ +++  l+G  +
  gi|336255593|ref|YP_004598700.1| 242 ePLPKAMLGLEALGGTLAVYGIVEVLGGYGFIGVFVAATVLRDYERRHAFYEPLHDLSEkaeQLLQVAIMTLFGGAI 318
                                       88889999999****************************************************************** PP

                                       XHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHH.HHHHHHHHHXHHHHTT. CS
                    Na_H_Exchanger 282 dlkvlnnhlsvlilvllilvaillgrilavflllrllglslrealiigfgglqrgaval.alaalgpalgllarel. 356
                                          +l+  +  l l l+++v+++l+r++a+ ++l  +  s++e+l+i++ gl rg  ++ +la ++ ++++ ++e  
  gi|336255593|ref|YP_004598700.1| 319 AGGLLE--PLTLELFLAAVVIVFLVRPVAGIIALLGFDRSWSERLAISVYGL-RGIGTFyYLAYALNQAPFADAERl 392
                                       *99996..9***************************************9999.6666652688888999*****999 PP

                                       SSTTTCSTSXHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 357 yallivvvlftvlvqGlslkpllk 380
                                       +a++++ +l++ +v G++ +p+ +
  gi|336255593|ref|YP_004598700.1| 393 WAVAATSILLSAVVLGITATPVIE 416
                                       *********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3527.12
//
Query:       gi|336255594|ref|YP_004598701.1|  [L=185]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Halopiger xanaduensis SH-6]
Scores for 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-20   72.1   3.4      2e-11   43.7   1.2    2.0  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    3.4e-15   56.1   0.1    4.8e-09   35.9   0.0    2.5  3  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
      2e-12   47.4   0.7    6.7e-06   25.9   0.0    2.3  2  DAO              FAD dependent oxidoreductase
    5.1e-11   41.9   0.1    4.3e-05   22.4   0.0    2.1  2  HI0933_like      HI0933-like protein
    7.2e-09   35.3   2.0    4.1e-06   26.3   0.1    2.1  2  FAD_binding_3    FAD binding domain
      7e-08   32.0   1.7    3.8e-06   26.3   0.4    2.8  3  FAD_binding_2    FAD binding domain
      2e-07   31.1   0.0     0.0012   18.8   0.0    2.4  2  NAD_binding_9    FAD-NAD(P)-binding
    5.7e-07   29.0   0.1    2.5e-05   23.5   0.0    2.1  2  GIDA             Glucose inhibited division protein A
    1.8e-05   24.3   1.1    4.3e-05   23.1   0.1    1.8  2  FAD_oxidored     FAD dependent oxidoreductase
    3.1e-05   24.1   0.0    7.3e-05   22.9   0.0    1.6  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    4.2e-05   22.9   0.2    0.00014   21.2   0.0    1.8  2  Thi4             Thi4 family
    0.00013   22.5   0.3     0.0074   16.8   0.3    2.3  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
     0.0003   20.1   0.1       0.45    9.6   0.0    2.1  2  K_oxygenase      L-lysine 6-monooxygenase (NADPH-requiring)
     0.0036   16.7   0.0     0.0067   15.8   0.0    1.4  1  Amino_oxidase    Flavin containing amine oxidoreductase
     0.0038   16.3   0.0     0.0072   15.4   0.0    1.5  2  Lycopene_cycl    Lycopene cyclase protein
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.015   14.6   0.0    1.4  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.014   15.3   0.0       0.02   14.8   0.0    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.021   13.7   2.1        1.4    7.7   0.1    2.1  2  Trp_halogenase   Tryptophan halogenase
      0.048   13.7   0.3        4.5    7.4   0.1    2.4  2  Leucyl-specific  Leucine-tRNA synthetase-specific 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 !   29.3   0.0   5.1e-10   4.8e-07       2      38 ..       3      39 ..       2      55 .. 0.80
   2 !   43.7   1.2   2.1e-14     2e-11     182     292 ..      53     158 ..      44     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.1e-10
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclng 38
                                      dv+++GgGpAGl+aal+ a++g+++++++ ++t+++ 
  gi|336255594|ref|YP_004598701.1|  3 DVAIVGGGPAGLSAALFTAKNGLETVVFDTDETWMHK 39
                                      8***************************966665543 PP

  == domain 2  score: 43.7 bits;  conditional E-value: 2.1e-14
                                       -HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 182 dkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggi 258
                                       ++e+ +  + +++++G ev+ g++v+++++ g+  e +++++++++ad+vv+a+G   s   + e+l ++  ++g +
  gi|336255594|ref|YP_004598701.1|  53 GSEFMELTRGQVRDRGAEVREGEEVTDVEPSGDGFE-IETEEDTYEADYVVLATGADRSI--A-EDLEVAFSDDGTV 125
                                       567778888899*********************777.77788889**********99996..6.9************ PP

                                       E--TTSBESSTTEEE-GGGCTECCSS--HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 259 vvdeflrtnvpgiyaiGDvaggkggpelaqaAvq 292
                                        vd   +t+v+++ya G+++ +++ ++ + aA +
  gi|336255594|ref|YP_004598701.1| 126 DVDLDTETSVEDLYATGAMV-RDEEWQAVIAAGD 158
                                       ********************.7777777777765 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 !   17.9   0.0   1.5e-06    0.0015       2      30 ..       6      33 ..       5      49 .. 0.78
   2 !   35.9   0.0     5e-12   4.8e-09      77     134 ..      50     107 ..      39     125 .. 0.91
   3 ?   -1.8   0.0       1.5   1.4e+03     284     305 .]     122     142 ..     108     142 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg 30
                                      I+G+GPaGl+aa+   k+gle  ++ + +
  gi|336255594|ref|YP_004598701.1|  6 IVGGGPAGLSAALFTAKNGLE-TVVFDTD 33
                                      9*******************6.6787765 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 5e-12
                       Pyr_redox_3  77 klsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                        +s+ e++e +r  ++    ++++ eeV++v+++++gfe+et+++tyeA++v++AtG 
  gi|336255594|ref|YP_004598701.1|  50 SISGSEFMELTRGQVRDRGAEVREGEEVTDVEPSGDGFEIETEEDTYEADYVVLATGA 107
                                       67899999999**********************************************6 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.5
                       Pyr_redox_3 284 dgrpvlteeteetnvpglflaG 305
                                       dg++ ++  + et v++l+  G
  gi|336255594|ref|YP_004598701.1| 122 DGTVDVDL-DTETSVEDLYATG 142
                                       55555544.5678899999887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1     5e-07   0.00048       1      29 [.       3      33 ..       3      41 .. 0.92
   2 !   25.9   0.0   7.1e-09   6.7e-06     141     203 ..      49     108 ..      34     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5e-07
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      dv+i+GGG +Gls+A++ a+ g  +++++ +
  gi|336255594|ref|YP_004598701.1|  3 DVAIVGGGPAGLSAALFTAKNGleTVVFDTD 33
                                      9**********************99999977 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 7.1e-09
                                       EEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGG CS
                               DAO 141 gqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGaw 203
                                         +   +++   + +++++G+e++eg+evt++ e++g++ ++  +t++ + +ad+vV+a+Ga 
  gi|336255594|ref|YP_004598701.1|  49 RSISGSEFMELTRGQVRDRGAEVREGEEVTDV-EPSGDGFEI--ETEEDTYEADYVVLATGAD 108
                                       556677788888899*****************.667888899..5544344679*******86 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   4.6e-08   4.3e-05       2      38 ..       3      39 ..       2      42 .. 0.92
   2 !   17.9   0.0   1.1e-06     0.001     113     164 ..      58     107 ..      48     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.6e-08
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                      dv+++GgG+AGl aA+  ak+g ++++++  ++  +K
  gi|336255594|ref|YP_004598701.1|  3 DVAIVGGGPAGLSAALFTAKNGLETVVFDTDETWMHK 39
                                      89***************************99887766 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       ++   +++++g ++r  +ev++ve + dg f+++t +e+++ead++vlAtG 
  gi|336255594|ref|YP_004598701.1|  58 ELTRGQVRDRGAEVREGEEVTDVEPSGDG-FEIET-EEDTYEADYVVLATGA 107
                                       56667899*****************9999.*****.9*************97 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   4.4e-09   4.1e-06       2      35 ..       2      35 ..       1      53 [. 0.87
   2 !    9.9   0.1   0.00041      0.39      96     182 ..      45     125 ..      32     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.4e-09
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      +dV+IVG+GpaGl++al+ ++ G ++v+ +  +t
  gi|336255594|ref|YP_004598701.1|  2 VDVAIVGGGPAGLSAALFTAKNGLETVVFDTDET 35
                                      79**************************998765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00041
                                       ST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHH CS
                     FAD_binding_3  96 pervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktl 172
                                       ++++  ++ +e+  + + + + rg++vr+++ev+ +e  ++g +       + ee t +a+Y+v a G+   ++++l
  gi|336255594|ref|YP_004598701.1|  45 YPAIRSISGSEFMELTRGQVRDRGAEVREGEEVTDVEPSGDGFE------IETEEDTYEADYVVLATGADRSIAEDL 115
                                       555666666666677777888999**********9998888833......233445999**********999***** PP

                                       TGGEEEEEEE CS
                     FAD_binding_3 173 giefegeetv 182
                                        + f+  +tv
  gi|336255594|ref|YP_004598701.1| 116 EVAFSDDGTV 125
                                       *998877765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.4     4e-09   3.8e-06       1      30 [.       3      32 ..       3      40 .. 0.93
   2 ?    2.6   0.0     0.059        56     136     202 ..      49     108 ..      34     122 .. 0.69
   3 ?    0.7   0.0      0.22   2.1e+02     376     401 ..     125     144 ..     117     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4e-09
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvek 30
                                      Dv ++G+G AGL+AAl  a++Gl+++v + 
  gi|336255594|ref|YP_004598701.1|  3 DVAIVGGGPAGLSAALFTAKNGLETVVFDT 32
                                      9*************************9876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.059
                                       ...HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE----- CS
                     FAD_binding_2 136 tlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGf 202
                                       + ++g + ++    ++r++g +++e  e++++     + +G+ +e   + +e +++a+ vvlatg+ 
  gi|336255594|ref|YP_004598701.1|  49 RSISGSEFMELTRGQVRDRGAEVREGEEVTDV-----EPSGDGFE--IETEEDTYEADYVVLATGAD 108
                                       45566666666666666666666666666666.....33555555..77888899*********975 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.22
                                       EEBETTSBESTTEEESSBTEEE-STC CS
                     FAD_binding_2 376 vetdengrvldadgqpipGLYAaGev 401
                                       v +d+++++       +++LYA G++
  gi|336255594|ref|YP_004598701.1| 125 VDVDLDTET------SVEDLYATGAM 144
                                       445555555......********987 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 !   10.2   0.0   0.00058      0.55       1      37 [.       5      36 ..       5      50 .. 0.78
   2 !   18.8   0.0   1.3e-06    0.0012     120     154 ..      73     106 ..      53     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00058
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                      aivG+Gp+Gl+++   +++      le  +fd +e++
  gi|336255594|ref|YP_004598701.1|  5 AIVGGGPAGLSAALFTAKN-----GLETVVFDTDETW 36
                                      8**********99777666.....5777788877765 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.3e-06
                     NAD_binding_9 120 hraevvdleeradgqavlladgaslaadaVvLAlG 154
                                         +ev+d+e+++dg+++ ++++++++ad+VvLA+G
  gi|336255594|ref|YP_004598701.1|  73 EGEEVTDVEPSGDGFEI-ETEEDTYEADYVVLATG 106
                                       3679***********99.888999**********9 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.7e-08   2.5e-05       1      46 [.       3      53 ..       3      73 .. 0.76
   2 ?    3.8   0.0     0.027        26     117     150 ..      76     107 ..      68     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.7e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE.....ES-GGGTT--SSSSEEE- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.....thkldtiaelsCnpsigg 46
                                      dv ++GgG AG+ AAl +a+ G++++ +      ++  ++ + +   si g
  gi|336255594|ref|YP_004598701.1|  3 DVAIVGGGPAGLSAALFTAKNGLETVVFdtdetWMHKAHLFNYPAIRSISG 53
                                      799*************************87666444555555544444444 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.027
                                       -EEEEEECTTEEEEE.EETTS-EEEECEEEE--TT CS
                              GIDA 117 eveeliveekkvkgv.vtedgetikakavviatGt 150
                                       ev+++++   +  g  + +++ t++a+ vv+atG+
  gi|336255594|ref|YP_004598701.1|  76 EVTDVEP---SGDGFeIETEEDTYEADYVVLATGA 107
                                       5666655...333320344567899*********9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   4.5e-08   4.3e-05       1      30 [.       3      32 ..       3      36 .. 0.93
   2 ?    0.1   0.1      0.42   3.9e+02      97     144 ..      64     106 ..      50     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.5e-08
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      Dv +vGGgpaG+ AA+  a++G ++++ ++
  gi|336255594|ref|YP_004598701.1|  3 DVAIVGGGPAGLSAALFTAKNGLETVVFDT 32
                                      9*************************9876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.42
                      FAD_oxidored  97 laeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                       +++ g +v  ++++++ve +g   ++ ++e+  ++ t++A++++ ATg
  gi|336255594|ref|YP_004598701.1|  64 VRDRGAEVREGEEVTDVEPSG---DGFEIET--EEDTYEADYVVLATG 106
                                       466778888888889998887...5566654..479999999999987 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 !   22.9   0.0   7.7e-08   7.3e-05       1      28 [.       6      33 ..       6      36 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.7e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      IvG+G +Gl+aA + ak+g++ +++++ 
  gi|336255594|ref|YP_004598701.1|  6 IVGGGPAGLSAALFTAKNGLETVVFDTD 33
                                      9*************************86 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.5e-07   0.00014      18      49 ..       2      32 ..       1      36 [. 0.93
   2 ?   -0.9   0.0      0.82   7.7e+02     164     175 ..     103     114 ..      91     162 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.5e-07
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailer 49
                                       Dv+ivG+G++GL+aa   ak+ +l++++++ 
  gi|336255594|ref|YP_004598701.1|  2 VDVAIVGGGPAGLSAALFTAKN-GLETVVFDT 32
                                      69********************.*****9975 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.82
                                       E--GSSSTTTTH CS
                              Thi4 164 datGhdgeivav 175
                                        atG d +i + 
  gi|336255594|ref|YP_004598701.1| 103 LATGADRSIAED 114
                                       444444444332 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   7.9e-06    0.0074       2      78 ..       4      91 ..       3      95 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.9e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS............TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll............rllDeeaskilqeklekngievllntkveeieg 68
                                      v++vGgG  gl +A + a+ g ++ v++  ++ +            +  + e+ ++++ +++++g ev+ +++v+ +e 
  gi|336255594|ref|YP_004598701.1|  4 VAIVGGGPAGLSAALFTAKNGLETVVFDTDETWMhkahlfnypairSISGSEFMELTRGQVRDRGAEVREGEEVTDVEP 82
                                      89***************99996666666554444322000011111567888999999999999*************** PP

                                      ETTSEEEEEE CS
                         Pyr_redox 69 sedgvesvkl 78
                                      s+dg+e +++
  gi|336255594|ref|YP_004598701.1| 83 SGDGFE-IET 91
                                      *99955.555 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 !    9.1   0.1   0.00068      0.64       3      38 ..       2      35 ..       1      45 [. 0.84
   2 !    9.6   0.0   0.00048      0.45     112     167 ..      70     116 ..      41     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00068
                       K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalflerqpe 38
                                      +D++++G Gp+ Ls a+ ++++   l++++++  ++
  gi|336255594|ref|YP_004598701.1|  2 VDVAIVGGGPAGLSAALFTAKNG--LETVVFDTDET 35
                                      7*************999999988..******96554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00048
                       K_oxygenase 112 qvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevle 167
                                       +vr geev++vep+ +     +++e+     ee+++ea  +vl++G  ++i e le
  gi|336255594|ref|YP_004598701.1|  70 EVREGEEVTDVEPSGDG----FEIET-----EEDTYEADYVVLATGADRSIAEDLE 116
                                       46778888888888864....88887.....6788888888888888888776655 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.1e-06    0.0067     219     262 ..      65     107 ..      56     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.1e-06
                                       TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-H CS
                     Amino_oxidase 219 elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvpl 262
                                       + rg ++r +++V++++ +gdg  +++e  +++eaD+Vv+++  
  gi|336255594|ref|YP_004598701.1|  65 RDRGAEVREGEEVTDVEPSGDGFEIETE-EDTYEADYVVLATGA 107
                                       579**********************986.6667********875 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   0.0   7.6e-06    0.0072       1      36 [.       3      36 ..       3      45 .. 0.87
   2 ?   -2.6   0.0       2.3   2.1e+03     157     174 ..      86     103 ..      47     118 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.6e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      Dv+++G+GpAgls A     ak gl+ v+ ++ +  
  gi|336255594|ref|YP_004598701.1|  3 DVAIVGGGPAGLSAALFT--AKNGLETVVFDTDETW 36
                                      9************99988..9999999999877765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                     Lycopene_cycl 157 Gvevevdnppfdldkmvl 174
                                       G e+e++++ ++ d +vl
  gi|336255594|ref|YP_004598701.1|  86 GFEIETEEDTYEADYVVL 103
                                       344444444444443333 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 ?   14.6   0.0   1.6e-05     0.015      30      71 ..       3      44 ..       1     106 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTT CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslg 71
                                       v ++GgG aGl+A+   ++ g +++v+D++++ +++ + ++
  gi|336255594|ref|YP_004598701.1|  3 DVAIVGGGPAGLSAALFTAKNGLETVVFDTDETWMHKAHLFN 44
                                      599***************************999888776655 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 ?   14.8   0.0   2.2e-05      0.02       2      38 ..       4      40 ..       3      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.2e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealeka 38
                                      va++G G  G + a  +a++gle+v++d++e  ++ka
  gi|336255594|ref|YP_004598701.1|  4 VAIVGGGPAGLSAALFTAKNGLETVVFDTDETWMHKA 40
                                      9*****************************9988887 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0014       1.4       1      22 [.       3      24 ..       3      38 .. 0.84
   2 ?    5.9   0.3     0.005       4.7     155     224 ..      55     121 ..      50     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0014
                                      EEEEE--SHHHHHHHHHHHHHT CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakal 22
                                      ++ ivGGG+aG  aA   ak +
  gi|336255594|ref|YP_004598701.1|  3 DVAIVGGGPAGLSAALFTAKNG 24
                                      699***********99888765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.005
                                       HHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EEE CS
                    Trp_halogenase 155 lyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqaLktgfed 224
                                       ++ ++ r    +rG +++eg+ v ++++++g+  ++++ ++ ++ead ++ ++G  + + e  L++ f d
  gi|336255594|ref|YP_004598701.1|  55 EFMELTRGQVRDRGAEVREGEEV-TDVEPSGDGFEIET-EEDTYEADYVVLATGADRSIAED-LEVAFSD 121
                                       5667778888999******9753.34445555457777.5667***********99988877.6766655 PP

>> Leucyl-specific  Leucine-tRNA synthetase-specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0048       4.5      30      48 ..      58      76 ..      53      79 .. 0.89
   2 ?    3.9   0.0     0.058        54      17      47 ..     120     149 ..     112     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0048
                   Leucyl-specific 30 eLsleevkKmGAELRehed 48
                                      eL++ +v+  GAE Re+e+
  gi|336255594|ref|YP_004598701.1| 58 ELTRGQVRDRGAEVREGEE 76
                                      79*************9986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.058
                   Leucyl-specific  17 seeaRirLeleeseLsleevkKmGAELRehe 47 
                                       s++  +  +l++   s+e++   GA  R++e
  gi|336255594|ref|YP_004598701.1| 120 SDDGTVDVDLDTE-TSVEDLYATGAMVRDEE 149
                                       6666677788776.89************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 1465.01
//
Query:       gi|336255595|ref|YP_004598702.1|  [L=32]
Description: hypothetical protein Halxa_4221 [Halopiger xanaduensis SH-6]
Scores for 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:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); 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: 0.30u 0.22s 00:00:00.52 Elapsed: 00:00:00.34
# Mc/sec: 278.30
//
Query:       gi|336255596|ref|YP_004598703.1|  [L=555]
Description: aldehyde ferredoxin oxidoreductase [Halopiger xanaduensis SH-6]
Scores for complete 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-75  254.7   0.3    2.7e-75  253.8   0.3    1.4  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
      1e-55  188.7   0.0    2.1e-55  187.6   0.0    1.5  2  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.8   0.3     3e-79   2.7e-75      18     379 ..     229     549 ..     217     550 .. 0.91

  Alignments for each domain:
  == domain 1  score: 253.8 bits;  conditional E-value: 3e-79
                                       HHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEEE......ETEE-- CS
                            AFOR_C  18 aelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgrevkveegkkvkvegp 94 
                                       ++ r+ GT++ ++++n++  lpt++f +++fe+a  i+gea++ek + ++++C +C  aC+  ++ ee+   ++egp
  gi|336255596|ref|YP_004598703.1| 229 DQRRRQGTTGSTEFINDHFSLPTRYFADTSFEGAAAIGGEAVAEK-KYEKGACSACAYACKLPTRDEETG-LETEGP 303
                                       36799*************************************994.555546************965554.669*** PP

                                       -HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS----TT-THHHHHHHHH CS
                            AFOR_C  95 eyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglelefgdaeallellek 171
                                       e+et++a+Gs  gidd+  ++++nelcd lG+DtisaG t+a +   + +              fg+ae + el+ek
  gi|336255596|ref|YP_004598703.1| 304 EFETVYAFGSLQGIDDIVDVMRANELCDSLGMDTISAGVTVAAYLASVDE--------------FGNAELAQELTEK 366
                                       ******************************************99887766..............9************ PP

                                       HHTT-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SGGG-THHHH..S---TT CS
                            AFOR_C 172 iAkregigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacHlrayliale..ekvdpl 246
                                       iA+regig++lA+G  r+  +lg  ++  +vkG+elpa+d r + g++l+Ya+snrGa+Hl a + +le   ++dp 
  gi|336255596|ref|YP_004598703.1| 367 IAYREGIGETLADGLARCHDELGVADY--TVKGMELPAHDGRVLHGQGLSYAVSNRGADHLYASMLTLEygGELDPR 441
                                       ***********************8887..79****************************************7799** PP

                                       --HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHT- CS
                            AFOR_C 247 etegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeellkaGeRiynleRlfnlreGl 323
                                        t gka  ++  +++ al+d  ++C f     + +++e + +l      +d + e+ll++G R + leR fn++ G+
  gi|336255596|ref|YP_004598703.1| 442 GTVGKADRLAREENTAALFDTGIICVFGG---DYVTEEYLETL------FDADYEDLLEVGARTVLLERHFNNQRGF 509
                                       99***************************...32333333333......45599*********************** PP

                                       -HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--TTS---HHHHHH CS
                            AFOR_C 324 trkddtlperlleeplkegpakgkvledeleemldeyYelrGWdetGvPtketlkr 379
                                       +r+ddtlp  +                 +le+++++yYe+rG +e+G + ++ l++
  gi|336255596|ref|YP_004598703.1| 510 DREDDTLPYEIP----------------DLEAAITAYYEARGLNEDGTVPESALEE 549
                                       ********8887................299*****************99999986 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.6   0.0   2.4e-59   2.1e-55       5     197 ..      10     204 ..       6     205 .. 0.96
   2 ?   -3.0   0.0      0.61   5.5e+03      31      64 ..     284     317 ..     269     330 .. 0.78

  Alignments for each domain:
  == domain 1  score: 187.6 bits;  conditional E-value: 2.4e-59
                                       EEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE-TTT CS
                            AFOR_N   5 rvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaksPlt 81 
                                       +vd+ ++++++ +++ +++e+++Ggr+ a+ l +d++p ++ p++pen+l+++tGpl+ ++++ +gr++++  sPlt
  gi|336255596|ref|YP_004598703.1|  10 TVDVGERTARETSID-DVLERFIGGRAAATVLAHDRIPFDAAPFGPENRLYLSTGPLQQSRMSFTGRMNMTGLSPLT 85 
                                       79*************.79*********************************************************** PP

                                       SSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS...EEEEE CS
                            AFOR_N  82 gtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd...kvavi 155
                                       ++l+++naGg+++ ++  +G++a+ i G++++   ++++dd++++e++ +l+g ++ et+++++e+++    ++++i
  gi|336255596|ref|YP_004598703.1|  86 DGLTSANAGGYLSRNFVGTGISALEIVGESDELLAIHVRDDGATFEPVPELEGVTVPETADYVQEHHNLgpeHCVAI 162
                                       *****************************************************************6555778999** PP

                                       -HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 156 GpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                       GpaGen+vrfAs ++ d+ra+grgGlGav+g+Kn+k+i+++g
  gi|336255596|ref|YP_004598703.1| 163 GPAGENRVRFASAMTYDSRAFGRGGLGAVLGAKNVKCITFDG 204
                                       ************9555************************98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.61
                                       HHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTS CS
                            AFOR_N  31 glaakllldevppgvdplspenplvfatGpltgt 64 
                                       ++a+kl  +  + g++  +pe   v a+G l+g+
  gi|336255596|ref|YP_004598703.1| 284 AYACKLPTRDEETGLETEGPEFETVYAFGSLQGI 317
                                       5666666666678888999999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.49u 0.19s 00:00:00.68 Elapsed: 00:00:00.35
# Mc/sec: 4801.53
//
Query:       gi|336255597|ref|YP_004598704.1|  [L=308]
Description: hypothetical protein Halxa_4223 [Halopiger xanaduensis SH-6]
Scores for 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  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); 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:                         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 0.20s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2447.05
//
Query:       gi|336255598|ref|YP_004598705.1|  [L=320]
Description: peptidase M48 Ste24p [Halopiger xanaduensis SH-6]
Scores for complete 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-24   86.6   0.8      4e-23   82.2   0.8    2.1  1  Peptidase_M48    Peptidase family M48
    0.00099   18.4   0.0     0.0017   17.7   0.0    1.3  1  Peptidase_M56    BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.088   13.4   0.2      0.088   13.4   0.2    2.6  3  DUF883           Bacterial protein of unknown function (DUF88
        9.3    6.3  19.9       0.18   11.9   4.4    2.5  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


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 !   82.2   0.8   8.9e-27     4e-23       3     195 ..      83     306 ..      81     307 .. 0.81

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 8.9e-27
                                       -SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   3 reaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrh 79 
                                       r++ l + ++ la+++++  ++++v++++ p+ NAFalg      ivl ++L+ +lls eel+a  +HEl+H+   +
  gi|336255598|ref|YP_004598705.1|  83 RAPTLYRRLDGLADRMDV--EPPTVMIAQLPTPNAFALGSATGGVIVLDRSLF-RLLSLEELEALVAHELAHLEGYD 156
                                       778899999*********..999******************888*********.*********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT.........................H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................x RF
                     Peptidase_M48  80 svvslivsllasillllglallisraeedaagafldalavliglliillfl.........................a 131
                                       + v+++ +++ + + +l+++       +  +g+ + ++a + g  ++  ++                         a
  gi|336255598|ref|YP_004598705.1| 157 AFVQTLAYSVFRTIAGLAVVG--LLPALLLIGGLARSIAWMRGRPQAWPETvfgrvvrwaergvavallavtalvrA 231
                                       *99977666666655555442..223333333333333333332222222244455777999999999999****** PP

                                       HHHHHHHHHHHHHHHTTT.HHHHHHHHHHHHHHTT-...........-S---HHHHHHS-SS--HHHHHHHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 132 lSRkrEyqADeagvellkrakdlvraliklakdler...........qdvsaslrsellstHPplleRiqalkel 195
                                        SR+rE+ AD  +++++ ++ +l+ral ++++ +++           +d+ +++ s l+stHP++ +R+++l ++
  gi|336255598|ref|YP_004598705.1| 232 HSRRREFAADDRAANVTGNPLALARALRRIQRVADTrrgllsplyvhADEREDAWSRLFSTHPSTDDRVERLADR 306
                                       *********************************999999**9999886666666679**************9875 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.7e-07    0.0017     106     219 ..      49     164 ..      39     171 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.7e-07
                     Peptidase_M56 106 lliWivgalilllyliaallvlkkr.fvrklgklraeelkeaLkeakeemqlkrnikirlsssidsPavlgllkp.. 179
                                       ++++ vg ++  l   ++  +l ++    +l ++ra  l+++L+    +m    ++++++ +++ +P  ++l     
  gi|336255598|ref|YP_004598705.1|  49 AIVVGVGLVVGYLSYRFGRTQLLSQlEAVELPRSRAPTLYRRLDGLADRMD-VEPPTVMI-AQLPTPNAFALGSAtg 123
                                       455555555554444444444444434556667778888899999999988.44445444.5678888877665423 PP

                     Peptidase_M56 180 .rIvlPadflkklsdeeleyillHElaHlkrkDllvnllva 219
                                        +Ivl  ++++ ls eele  ++HElaHl   D+ v+ l+ 
  gi|336255598|ref|YP_004598705.1| 124 gVIVLDRSLFRLLSLEELEALVAHELAHLEGYDAFVQTLAY 164
                                       38*********************************999864 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 ?   13.4   0.2     2e-05     0.088      72      92 ..      43      63 ..      41      64 .. 0.90
   2 ?   -2.5   0.6       1.8   8.2e+03      76      91 ..     169     184 ..     160     185 .. 0.82
   3 ?   -2.1   0.1       1.4   6.2e+03      45      45 ..     294     294 ..     254     312 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                            DUF883 72 nPwqavGiAagvGlllGlLla 92
                                       P+++++i++gvGl++G+L  
  gi|336255598|ref|YP_004598705.1| 43 DPATTLAIVVGVGLVVGYLSY 63
                                      59****************975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                            DUF883  76 avGiAagvGlllGlLl 91 
                                       +++  a+vGll +lLl
  gi|336255598|ref|YP_004598705.1| 169 TIAGLAVVGLLPALLL 184
                                       6677789999999986 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.4
                            DUF883  45 e 45 
                                        
  gi|336255598|ref|YP_004598705.1| 294 P 294
                                       2 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 ?   11.9   4.4   3.9e-05      0.18      36      92 ..      11      71 ..       2      84 .. 0.67
   2 ?    0.1   7.6      0.18   8.1e+02      34      89 ..     170     236 ..     138     262 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                   Phage_holin_3_6 36 gagllgaagvlallalllllval..alalaa..lwlaalivaavllvlagvlalvglkklk 92
                                      +++l+g a+++ + +l++l+ +    l+l+a  ++    iv +v lv++ +  + g+ +l 
  gi|336255598|ref|YP_004598705.1| 11 LLVLVGFAVLCCYAGLAALSYLGlaTLWLSApdPATTLAIVVGVGLVVGYLSYRFGRTQLL 71
                                      34455555555555555555554323667646777777779999999**999999999775 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.18
                   Phage_holin_3_6  34 gsgagllgaagvlallalllllvala............lala.a.lwlaalivaavllvlagvlalvglk 89 
                                       + g++++g+  +l+l++ l+ ++  a            + ++ + +w+   +  a+l+v a+v a   ++
  gi|336255598|ref|YP_004598705.1| 170 IAGLAVVGLLPALLLIGGLARSI--AwmrgrpqawpetV-FGrVvRWAERGVAVALLAVTALVRAHSRRR 236
                                       33333333333333333333333..24466666555532.233458888877767777777766655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2596.35
//
Query:       gi|336255599|ref|YP_004598706.1|  [L=83]
Description: hypothetical protein Halxa_4225 [Halopiger xanaduensis SH-6]
Scores for 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   16.2   9.0       0.26   11.4   9.3    2.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.028   14.0   8.3        1.7    8.3   0.1    4.0  4  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.14   12.3   2.3       0.41   10.7   2.3    1.9  1  ArfGap          Putative GTPase activating protein for Arf
       0.18   11.5   0.5       0.18   11.5   0.5    2.3  2  TackOD1         Thaumarchaeal output domain 1
       0.39   10.7   0.3       0.39   10.7   0.3    2.5  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.53    9.7   4.3        2.7    7.5   0.4    2.2  2  DUF3678         Protein of unknown function (DUF3678)
       0.67   10.4  10.1         53    4.3  10.1    2.4  1  DnaJ_CXXCXGXG   DnaJ central domain
       0.99    9.4   8.1      2e+02    2.0   8.1    2.7  1  zinc-ribbons_6  zinc-ribbons
        1.2    9.4  12.7       0.17   12.0   1.6    2.8  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
        1.4    8.9  16.2        7.1    6.6   0.2    4.0  3  Nudix_N_2       Nudix N-terminal
        1.4    9.7   6.6         40    5.0   6.6    2.2  1  zinc_ribbon_15  zinc-ribbon family
          2    8.4   6.6        7.6    6.6   4.6    2.4  2  HypA            Hydrogenase/urease nickel incorporation, meta
        5.6    6.6  13.5        0.4   10.2   3.1    2.9  2  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 !   11.4   9.3   0.00019      0.26       1      49 []       4      78 ..       1      78 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                               DZR  1 CpqCgee...............lppdarfCseCgtklkavaa.........edrCpsCgekvdpearf..CpeCG 49
                                      C +Cg e               ++   r+C +C  +++++++         + +Cp C+  + +++ +  C eCG
  gi|336255599|ref|YP_004598706.1|  4 CDRCGDEvprlfehrargetmtHRRTRRVCADCHPTVPNAPQipvtdggtrAATCPTCSGVTIETDGVytCLECG 78
                                      7778888888888888888876777788*********99999*****************9977766655799998 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0013       1.7       4      13 ..       3      12 ..       1      18 [. 0.85
   2 ?    4.6   0.1     0.018        25       4      14 ..      32      42 ..      29      47 .. 0.81
   3 ?    0.6   0.1      0.31   4.3e+02       4       9 ..      57      62 ..      55      68 .. 0.88
   4 ?    3.6   0.1     0.037        52       3       9 ..      72      78 ..      70      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0013
                            zf_UBZ  4 lCerCgkeip 13
                                       C+rCg e+p
  gi|336255599|ref|YP_004598706.1|  3 ECDRCGDEVP 12
                                      5*******99 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.018
                            zf_UBZ  4 lCerCgkeipe 14
                                      +C++C+ ++p 
  gi|336255599|ref|YP_004598706.1| 32 VCADCHPTVPN 42
                                      8*****99985 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.31
                            zf_UBZ  4 lCerCg 9 
                                      +C+ C 
  gi|336255599|ref|YP_004598706.1| 57 TCPTCS 62
                                      8****5 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.037
                            zf_UBZ  3 ylCerCg 9 
                                      y+C +Cg
  gi|336255599|ref|YP_004598706.1| 72 YTCLECG 78
                                      9*****8 PP

>> ArfGap  Putative GTPase activating protein for Arf
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.3    0.0003      0.41       7      46 ..      24      68 ..      18      83 .] 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                                      HCCSCCCCB-TTT-SBS--EEETTTT.....EEE-HHHHHHHCCS CS
                            ArfGap  7 llkepenkvCaDCgakeptWaslnlg.....vflCieCsgvHrsl 46
                                      + ++   +vCaDC+ + p+   + +      +  C +Csgv  + 
  gi|336255599|ref|YP_004598706.1| 24 MTHRRTRRVCADCHPTVPNAPQIPVTdggtrAATCPTCSGVTIET 68
                                      56677889*****66665555444433356699*******98776 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.3      0.18   2.5e+02     156     170 ..      24      38 ..       1      48 [. 0.68
   2 ?   11.5   0.5   0.00013      0.18      88     112 ..      56      80 ..      52      83 .] 0.78

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.18
                           TackOD1 156 fsepevkarClsCek 170
                                       ++  +++ +C++C+ 
  gi|336255599|ref|YP_004598706.1|  24 MTHRRTRRVCADCHP 38 
                                       444555555666654 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00013
                           TackOD1  88 evCpkCkSidieeqelihhftCgnv 112
                                        +Cp C+ + ie++ +  + +Cg  
  gi|336255599|ref|YP_004598706.1|  56 ATCPTCSGVTIETDGVYTCLECGWS 80 
                                       5788888888888888888888865 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 ?    3.0   5.8     0.075     1e+02      20      44 ..       3      37 ..       2      39 .. 0.81
   2 ?   10.7   0.3   0.00028      0.39      19      44 ..      56      78 ..      50      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.075
                     Zn_Tnp_IS1595 20 vCPhCgsrkayrikt..........rglfqCkeCr 44
                                       C +Cg + ++ +++          r +  C++C+
  gi|336255599|ref|YP_004598706.1|  3 ECDRCGDEVPRLFEHrargetmthrRTRRVCADCH 37
                                      59999999666666666999999999999*****8 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00028
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCr 44
                                       +CP C      +i+t g++ C eC+
  gi|336255599|ref|YP_004598706.1| 56 ATCPTCS---GVTIETDGVYTCLECG 78
                                      68****9...7899999********7 PP

>> DUF3678  Protein of unknown function (DUF3678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.028        38      20      27 ..      24      31 ..      23      32 .. 0.90
   2 ?    7.5   0.4    0.0019       2.7       3      17 ..      48      62 ..      47      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.028
                           DUF3678 20 laHlqldh 27
                                      ++H+++++
  gi|336255599|ref|YP_004598706.1| 24 MTHRRTRR 31
                                      9*****98 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0019
                           DUF3678  3 ltDilvsaasastsS 17
                                      +tD+++ aa  +t+S
  gi|336255599|ref|YP_004598706.1| 48 VTDGGTRAATCPTCS 62
                                      7********66***9 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  10.1     0.038        53      12      64 ..      28      78 ..       1      81 [. 0.60

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.038
                     DnaJ_CXXCXGXG 12 gkkktCktCkGsG.vvreeqktlgpfvqqsqstCpeCeGtGkvikekdkCkkCk 64
                                      ++++ C +C+ +  +  +    ++    +   tCp+C+G    ++   +C +C 
  gi|336255599|ref|YP_004598706.1| 28 RTRRVCADCHPTVpNAPQIP--VTDGG-TRAATCPTCSGVTIETDGVYTCLECG 78
                                      44667888888873322222..22212.24578999988776666666788885 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   8.1      0.15     2e+02       2      22 ..      57      77 ..       1      79 [. 0.63

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.15
                                      --SSS-S--EE-SSEEE-TTT CS
                    zinc-ribbons_6  2 kCpeCqqelekrgeqyhCeaC 22
                                      +Cp+C   + +++  y+C +C
  gi|336255599|ref|YP_004598706.1| 57 TCPTCSGVTIETDGVYTCLEC 77
                                      355555544444445555444 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 ?    1.6   3.6      0.23   3.2e+02      17      39 ..       3      36 ..       1      37 [. 0.62
   2 ?   12.0   1.6   0.00013      0.17      15      40 .]      55      78 ..      54      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.23
                     Auto_anti-p27 17 tCpvC..gvP.Lmrdr........kggkvyCvaC 39
                                       C++C   vP L++ r         +++ +C+ C
  gi|336255599|ref|YP_004598706.1|  3 ECDRCgdEVPrLFEHRargetmthRRTRRVCADC 36
                                      5999988777355555665544443667788877 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00013
                     Auto_anti-p27 15 aetCpvCgvPLmrdrkggkvyCvaCd 40
                                      a+tCp+C+ +  ++  +g + C  C+
  gi|336255599|ref|YP_004598706.1| 55 AATCPTCSGVTIET--DGVYTCLECG 78
                                      579**********6..5888*****6 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   5.6     0.015        21       3      29 ..       4      37 ..       4      40 .. 0.59
   2 ?    6.6   0.2    0.0052       7.1      11      31 ..      43      64 ..      37      65 .. 0.79
   3 ?    1.0   0.3       0.3   4.2e+02      24      30 ..      73      79 ..      72      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.015
                                      -TTT--B-E...EE--TT-S....S-EEEETTTT CS
                         Nudix_N_2  3 CsqCGtpve...lripdgDn....reRlvCpaCg 29
                                      C  CG +v     +   g++    r+R vC++C+
  gi|336255599|ref|YP_004598706.1|  4 CDRCGDEVPrlfEHRARGETmthrRTRRVCADCH 37
                                      66777776633322224443333399*******8 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0052
                                      EEE--TT-SS-EE.EETTTTEE CS
                         Nudix_N_2 11 elripdgDnreRl.vCpaCgti 31
                                      + +ip  D  +R+ +Cp C+ +
  gi|336255599|ref|YP_004598706.1| 43 APQIPVTDGGTRAaTCPTCSGV 64
                                      568999999999637****876 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.3
                                      EETTTTE CS
                         Nudix_N_2 24 vCpaCgt 30
                                      +C  Cg+
  gi|336255599|ref|YP_004598706.1| 73 TCLECGW 79
                                      6888887 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   6.6     0.029        40      38      77 ..       2      42 ..       1      78 [. 0.61

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.029
                    zinc_ribbon_15 38 lacskCkslleaskelgkeiekkesse.kkeCknCgkevee 77
                                      + c++C+  ++   e+  + e+ ++++  ++C++C+ +v +
  gi|336255599|ref|YP_004598706.1|  2 AECDRCGDEVPRLFEHRARGETMTHRRtRRVCADCHPTVPN 42
                                      57899998888888666666655554465666666655543 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 ?    6.6   4.6    0.0055       7.6      66      98 ..      26      67 ..       1      74 [. 0.71
   2 ?   -0.7   0.1         1   1.4e+03      69      77 ..      70      78 ..      66      82 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0055
                                      EE--EEEETTTS-EEECHHHHH..........S-TTTSSS-EE CS
                              HypA 66 evpvkvrCreCgkefeleekal..........rCpkCgsadve 98
                                      + + +  C +C+ ++  + + +          +Cp+C++  +e
  gi|336255599|ref|YP_004598706.1| 26 HRRTRRVCADCHPTVPNAPQ-IpvtdggtraaTCPTCSGVTIE 67
                                      45566678888877776543.24567888888*****997766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1
                                      -EEEETTTS CS
                              HypA 69 vkvrCreCg 77
                                       +++C eCg
  gi|336255599|ref|YP_004598706.1| 70 GVYTCLECG 78
                                      556777777 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   2.8      0.31   4.2e+02      15      25 ..      26      36 ..       3      42 .. 0.69
   2 ?   10.2   3.1   0.00029       0.4       2      26 ..      57      78 ..      56      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.31
                                      TSTTCEEESSS CS
                      TF_Zn_Ribbon 15 pergelvCtdC 25
                                      + r+  vC dC
  gi|336255599|ref|YP_004598706.1| 26 HRRTRRVCADC 36
                                      55666788888 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00029
                                      EETTTTCEECHEETSTTCEEESSSS CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCG 26
                                      +CP C++ ++++D   g ++C +CG
  gi|336255599|ref|YP_004598706.1| 57 TCPTCSGVTIETD---GVYTCLECG 78
                                      7******999999...9*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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):              13  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 613.44
//
Query:       gi|336255600|ref|YP_004598707.1|  [L=203]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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   33.0   0.1    9.5e-08   32.3   0.1    1.4  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00011   22.2   0.0    0.00025   21.1   0.0    1.7  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
     0.0015   18.9   0.0     0.0021   18.4   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0016   19.1   0.0     0.0024   18.6   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0064   16.4   0.0      0.011   15.7   0.0    1.4  1  Acetyltransf_10  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 !   32.3   0.1   2.6e-11   9.5e-08      28     100 ..      28     110 ..       3     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 2.6e-11
                                       HHSTTCEEEEEEETTEEEEEEEEEEEET..........TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTE CS
                    Acetyltransf_1  28 fsleaegllvaeedgeliGfisllkipd..........ekggvayieslaVspeyrgkGlGsaLlealeerareegi 94 
                                       f+  +  l v e  +e +Gf ++++             e  +v+++ s+ V +e+rg+G+G + +e l+e+a ++g+
  gi|336255600|ref|YP_004598707.1|  28 FRSRDYVLAVDEVSDEKAGFGRIRIHKVdgesededenEPDEVCELTSIGVLEEWRGQGVGAHVVERLVEYAGDQGF 104
                                       444444556666678999999999998899********9999*********************************** PP

                                       SEEEEE CS
                    Acetyltransf_1  95 kkivla 100
                                       + +++ 
  gi|336255600|ref|YP_004598707.1| 105 DTVYAL 110
                                       999873 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 !   21.1   0.0   7.1e-08   0.00025      19      58 ..      65     104 ..      32     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.1e-08
                   Acetyltransf_CG  19 vrkegvldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                       +++++v ++t + V ee rG+G++++ v++ +++a ++g+
  gi|336255600|ref|YP_004598707.1|  65 NEPDEVCELTSIGVLEEWRGQGVGAHVVERLVEYAGDQGF 104
                                       566779*****************************99997 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.9e-07    0.0021       9      52 ..      37     103 ..       8     124 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.9e-07
                                       EET..TEEEEEEEEEEES................TCTEEEEE-GGGTTSSHHHHHHH.HTT....SE CS
                    Acetyltransf_7   9 edd..gkivGfialslld................aeitrlaVdpeyrgkGiGraLle.aae....kg 52 
                                        d+  ++  Gf ++ +++                +e+t + V++e+rg+G+G   +e ++e    +g
  gi|336255600|ref|YP_004598707.1|  37 VDEvsDEKAGFGRIRIHKvdgesededenepdevCELTSIGVLEEWRGQGVGAHVVErLVEyagdQG 103
                                       333556777888877777889999888888877677777**************99984322333444 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   6.7e-07    0.0024      50     121 ..      29     111 ..       3     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.7e-07
                    Acetyltransf_3  50 eeegygwaivl.kdtgv.iGsvglrdleeedee.........aelg.ymlapsfwgkGyateavralleyafeelgl 114
                                       ++++y +a+ + +d+++  G ++++++++e+e          +el  + + ++++g+G++  +v+ l+eya  ++g 
  gi|336255600|ref|YP_004598707.1|  29 RSRDYVLAVDEvSDEKAgFGRIRIHKVDGESEDedenepdevCELTsIGVLEEWRGQGVGAHVVERLVEYA-GDQGF 104
                                       236799999778777788**********9999899*******99995667799******************.77778 PP

                    Acetyltransf_3 115 erlvavi 121
                                       ++++a +
  gi|336255600|ref|YP_004598707.1| 105 DTVYALT 111
                                       8888866 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.1e-06     0.011      25     113 ..      26     129 ..       3     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.1e-06
                   Acetyltransf_10  25 ri.eegealllvaeeggkivGvielrdgs.................hisllfVdpeyrgqGigkaLleaveeeaekd 83 
                                          ++ +++l v e++++ +G++++r ++                 +++ + V +e+rgqG+g+  +e++ e+a ++
  gi|336255600|ref|YP_004598707.1|  26 TAfRSRDYVLAVDEVSDEKAGFGRIRIHKvdgesededenepdevcELTSIGVLEEWRGQGVGAHVVERLVEYAGDQ 102
                                       4446778888888888888888776555556688888888888777888889**********************999 PP

                   Acetyltransf_10  84 gikleltvnaspyavpfYeklGFkavgeeq 113
                                       g     tv a +   ++  ++GF++v+e q
  gi|336255600|ref|YP_004598707.1| 103 GFD---TVYALTGEGGYLAQFGFRRVEESQ 129
                                       877...999999999999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1576.82
//
Query:       gi|336255601|ref|YP_004598708.1|  [L=560]
Description: methylmalonyl-CoA mutase, large subunit [Halopiger xanaduensis SH-6]
Scores for complete 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-229  762.7   0.7     2e-229  762.4   0.7    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase
  ------ inclusion threshold ------
        4.8    7.9   5.7        3.4    8.4   1.8    2.4  2  RsbRD_N        RsbT co-antagonist protein rsbRD N-terminal do


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  762.4   0.7  2.2e-233    2e-229       5     513 .]      42     552 ..      38     552 .. 0.98

  Alignments for each domain:
  == domain 1  score: 762.4 bits;  conditional E-value: 2.2e-233
                     MM_CoA_mutase   5 gievkplYtaedl...eekklgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtglsva 78 
                                       g ev++lYt++d+   +  +    +PGe P+tRGv++t+yrgr Wt+rqyagfst+e+tnery++lL++Gqtgls+a
  gi|336255601|ref|YP_004598708.1|  42 GQEVDRLYTPADVadlDY-EEDLGYPGEPPYTRGVYSTGYRGRLWTMRQYAGFSTPEDTNERYHYLLDQGQTGLSMA 117
                                       789**********85522.34446***************************************************** PP

                     MM_CoA_mutase  79 fdlptlrgyDsdhpraegevGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdlekls 155
                                       fdlpt++gyDsd ++a+gevGkaGvaidsl+dmet++dgi+ld+vs+smtina+a  llamy+a+ ++qgvd+e+l+
  gi|336255601|ref|YP_004598708.1| 118 FDLPTQMGYDSDADMAAGEVGKAGVAIDSLDDMETVFDGIPLDEVSTSMTINAPASVLLAMYIAVGDKQGVDREELR 194
                                       ***************************************************************************** PP

                     MM_CoA_mutase 156 gtiqnDiLkellargtyiyppepslrliadiieyaakevpkfntisvsgyhireaGatavqElAftladGveYvral 232
                                       gtiqnD Lke++ar+tyiyppeps+r+i+di+e++a+e+pkfntis+sgyhireaG+ta+qElAftl +G+eYv+a+
  gi|336255601|ref|YP_004598708.1| 195 GTIQNDLLKEYIARNTYIYPPEPSMRIITDIFEFCAEETPKFNTISISGYHIREAGSTAAQELAFTLGNGIEYVEAA 271
                                       ***************************************************************************** PP

                     MM_CoA_mutase 233 leaGldvdefaprlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklrvhaqTsgvsltaqdpyvNil 309
                                       l+aGldvdefap+lsFff+ ++++fee+Ak+RAaRr+W++i++e+f+a+++ks +l++h+qT+g++ltaq++++N++
  gi|336255601|ref|YP_004598708.1| 272 LDAGLDVDEFAPQLSFFFNGHNNIFEEVAKFRAARRMWHDIMDERFDAENPKSKQLKFHTQTAGSMLTAQQIENNVV 348
                                       ***************************************************************************** PP

                     MM_CoA_mutase 310 RttlealaAvlggtqslhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekawkl 386
                                       R++++alaAvlggtqslhtn  DealalPte+s+r+A++tq+ila+Esg a+++DPl+GSyyvE+LTde++e+a ++
  gi|336255601|ref|YP_004598708.1| 349 RVAYQALAAVLGGTQSLHTNGKDEALALPTEESVRTALRTQQILAHESGAADTIDPLAGSYYVESLTDEVEEEAYEI 425
                                       ***************************************************************************** PP

                     MM_CoA_mutase 387 fqeieeaGGmlkaiesGlvqeeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkideeveerqaerlealr 463
                                       ++e++e+GGml a+e+ +vq++i+++a  rqk+ie+++++ivGvN+f + +e+ +++v++++ee ++rq+++le +r
  gi|336255601|ref|YP_004598708.1| 426 LEEVDERGGMLDAVEQQWVQRQIQDTAFDRQKEIEEKERIIVGVNEF-EVDEDPTVDVEEVTEEDQQRQIDNLETVR 501
                                       ***********************************************.5666789********************** PP

                     MM_CoA_mutase 464 aerdeaavkaaLaalgeaarse.nllaraveaaralatlGeisdaleevfg 513
                                       + rd++av+aaL+al++aa+ + nl++ +++a++a+at+Gei+d+l+++fg
  gi|336255601|ref|YP_004598708.1| 502 EGRDDEAVDAALEALRDAAQGNeNLMPPIIDAVKAYATVGEICDVLRDEFG 552
                                       ********************779*************************998 PP

>> RsbRD_N  RsbT co-antagonist protein rsbRD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.15   1.3e+03      29      67 ..     334     374 ..     324     391 .. 0.58
   2 ?    8.4   1.8   0.00038       3.4      10      72 ..     437     514 ..     436     525 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.15
                           RsbRD_N  29 ag.llseaelreq.lrelldallaalaseql.dleseeeeel 67 
                                       ag  l+ +++++  +r  ++al+a+l  +q+  +++++e+ l
  gi|336255601|ref|YP_004598708.1| 334 AGsMLTAQQIENNvVRVAYQALAAVLGGTQSlHTNGKDEA-L 374
                                       5545555554444156679999999998777533333333.3 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00038
                           RsbRD_N  10 eailekWleevlatypiesagllseae......................lreqlrelldallaalaseqldleseee 64 
                                       +a+ ++W++++++++ ++++++++e+e                      ++e  ++ +d l ++    ++   + + 
  gi|336255601|ref|YP_004598708.1| 437 DAVEQQWVQRQIQDTAFDRQKEIEEKEriivgvnefevdedptvdveevTEEDQQRQIDNLETV----RE---GRDD 506
                                       57789**********************9999999999888888885555444444444444433....22...2333 PP

                           RsbRD_N  65 eelreald 72 
                                       e++++al+
  gi|336255601|ref|YP_004598708.1| 507 EAVDAALE 514
                                       33444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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 0.25s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 4377.13
//
Query:       gi|336255602|ref|YP_004598709.1|  [L=757]
Description: blue (type 1) copper domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-32  111.8   0.4    2.1e-31  109.5   0.2    2.0  2  GSDH         Glucose / Sorbosone dehydrogenase
    5.5e-09   36.4   0.6    1.3e-08   35.2   0.0    1.9  2  Copper-bind  Copper binding proteins, plastocyanin/azurin fam
  ------ inclusion threshold ------
      0.093   12.8   0.2          7    6.9   0.0    3.5  3  NHL          NHL repeat


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   0.2   3.5e-35   2.1e-31       3     226 ..     191     460 ..     189     501 .. 0.81
   2 ?   -0.4   0.0     0.096   5.8e+02     307     324 ..     657     674 ..     637     678 .. 0.80

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 3.5e-35
                                       -EEEEEE-.TT.S-EEEEETTTEEEEEE.TTEE.EEEEE-..--..............--STT-SEEEEEE-TTTTT CS
                              GSDH   3 hPwslafl.pd.grlLvtersGrlrlvkadgklkepiagvp.ev..............vakgqgGlldvalhpdfae 62 
                                        P ++a++  d g+++v+ ++G+l+lv+ dg   ep  ++  ++               +  + Gll+v  hpd+ae
  gi|336255602|ref|YP_004598709.1| 191 APTDMAVAdGDqGQYFVADQTGELWLVDDDGVRDEPFLDLSdRIvelgtfqgeyadpnQDYDERGLLGVEPHPDYAE 267
                                       68888888435689**************999998887777535578888899888888888999************* PP

                                       S-EEEEEEEE-.......TTSSEEEEEEEEE-SS....-EEEEEEEEEEE---TT-------EEE-TTS-EEEE--- CS
                              GSDH  63 nrlvYltyaea....eeekggagtavararlsed..eaaledlevifrqepkvesgahfGsrlafgpdgtLfvtvGd 133
                                       n+ +++ y+      + ++  +  +v++++ s+d  ea  e+++v+ + +    + +h ++ +afgpdg+L+v +Gd
  gi|336255602|ref|YP_004598709.1| 268 NGRLFIHYSAPpndeTPDDWSHVEVVSEFQASDDlsEADPESEQVLMEFQK--PQYNHDAGPMAFGPDGYLYVPMGD 342
                                       *********884442333335566899999999964445555555555433..4689******************** PP

                                       TT-GG.................GGG-T.T-SSSEEEEE-TTSS........B-TT-TTTT-TTS-TTEEEE--SCE- CS
                              GSDH 134 rskre.................eaqdl.sselGkilrlnkdGs........vpadnpfvgkagakpeiwsyGhRnpq 184
                                        + ++                 + q++ ++ lG ++r+  d +        +p+dnp v++++  +e ++ G Rnp 
  gi|336255602|ref|YP_004598709.1| 343 GGGANddmlghledwydendggNGQNItDTLLGGVHRIDVDSEgdsdrpygIPDDNPLVDSDEGLDEYYAWGFRNPF 419
                                       99833356777888898999999999846789******96653335566669************************* PP

                                       --EE-TTT--EEEEEE--SSSEEEEEE-TT-B--TTT-S... CS
                              GSDH 185 GlaldpdtgeLwesEhGprggDelnlieaGknYGWplvsyge 226
                                       G+ +d++ g+L+ s+ G+    e nl+eaG+nYGW++ +  +
  gi|336255602|ref|YP_004598709.1| 420 GISFDSE-GRLFVSDAGQDLYEEANLVEAGGNYGWNVKEGTH 460
                                       ******9.***************************9877444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.096
                                       -EEEEEE-TTS-EEEEE- CS
                              GSDH 307 riRdVeqgpdGalyvltd 324
                                        +R+  q+ dG++yvl +
  gi|336255602|ref|YP_004598709.1| 657 FVRQFGQDADGNVYVLAN 674
                                       59999**********987 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 !   35.2   0.0   2.2e-12   1.3e-08      26      98 ..      88     152 ..      75     153 .. 0.77
   2 ?   -3.3   0.2       2.1   1.3e+04      33      46 ..     587     600 ..     569     625 .. 0.50

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 2.2e-12
                                       EEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEE.EEEEETTTTTTTSEEEEEE CS
                       Copper-bind  26 kvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagt.YkffCsPHaaagMkgkvtv 98 
                                       + t+ n ++ +HNvv++++    g++ +++++     + ++Ge+++++f+++ +  ++fC+PH+   M+g + v
  gi|336255602|ref|YP_004598709.1|  88 ELTWENVDGAPHNVVIESED---GEELERTEI-----MSSQGETQTLEFEATSDmATYFCEPHRPT-MNGDISV 152
                                       4689999*********9987...444444444.....3467*********65555*********99.****998 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                                       SSSSBEEEEETTSS CS
                       Copper-bind  33 avmgHNvvldkdgv 46 
                                       ++ g N  l+++++
  gi|336255602|ref|YP_004598709.1| 587 NATGDNETLANESI 600
                                       33333333333333 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.055   3.3e+02       9      20 ..     198     211 ..     192     216 .. 0.77
   2 ?    6.9   0.0    0.0012         7       1      20 [.     415     434 ..     415     436 .. 0.92
   3 ?   -3.0   0.1       1.6   9.7e+03      11      17 ..     665     671 ..     664     672 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.055
                                       EE.TTTEEEEEE.C CS
                               NHL   9 vd.snGdiyVaD.s 20 
                                       +d ++G+ +VaD +
  gi|336255602|ref|YP_004598709.1| 198 ADgDQGQYFVADqT 211
                                       45799******955 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0012
                                       BSSEEEEEEETTTEEEEEEC CS
                               NHL   1 fnyPhGvavdsnGdiyVaDs 20 
                                       f++P G++ ds G+++V+D 
  gi|336255602|ref|YP_004598709.1| 415 FRNPFGISFDSEGRLFVSDA 434
                                       88999**************5 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.6
                                       TTTEEEE CS
                               NHL  11 snGdiyV 17 
                                        +G++yV
  gi|336255602|ref|YP_004598709.1| 665 ADGNVYV 671
                                       69****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (757 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 5701.03
//
Query:       gi|336255603|ref|YP_004598710.1|  [L=278]
Description: 2,5-didehydrogluconate reductase [Halopiger xanaduensis SH-6]
Scores for 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-60  205.4   0.0    1.4e-58  198.5   0.0    2.0  1  Aldo_ket_red  Aldo/keto reductase family


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 !  198.5   0.0   7.7e-63   1.4e-58       2     292 ..      21     263 ..      20     265 .. 0.97

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 7.7e-63
                                       EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTS CS
                      Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeik 78 
                                       lg+Gt+++++      +e  +++++ale G++++DtA++Y    +e+ +Gea+++s ++re+v+++tKv      ++
  gi|336255603|ref|YP_004598710.1|  21 LGFGTARMTG------DECRQAVETALEVGYRHVDTAQMY---DNERAVGEAIANSAVDREDVFVVTKV------HP 82 
                                       7999998887......79**********************...**************************......** PP

                                       SSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTTT- CS
                      Aldo_ket_red  79 sglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkkkv 155
                                       ++   +++ e  +esl+rLg+++vDllllH p    p +ee++da++el+ +G + +iGvSnfsv+qle a + +++
  gi|336255603|ref|YP_004598710.1|  83 DNAAYDDVLETTRESLERLGLSTVDLLLLHAPSDRAP-LEETVDAMNELQAAGAVDHIGVSNFSVGQLEDAIALSET 158
                                       *************************************.*************************************** PP

                                       -EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHH CS
                      Aldo_ket_red 156 kivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeel 232
                                       +iva+qv+y+++  ++   lle+c +++v l ayspl+ G+                                +++l
  gi|336255603|ref|YP_004598710.1| 159 PIVANQVKYHPY--HHRDDLLEYCVENDVCLTAYSPLAEGAVP-----------------------------GDDRL 204
                                       ************..999************************98.............................4688* PP

                                       HHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                      Aldo_ket_red 233 selakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                        e+++++++s aq+alr++l q++ + +ip+a + e++e+n+d+++++l++ee+a++ e+
  gi|336255603|ref|YP_004598710.1| 205 VEIGADYDKSAAQVALRWLL-QQPSVAPIPKAASREHIEANADVFDFELDDEEMAAVTEV 263
                                       ********************.678889*****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2308.51
//
Query:       gi|336255604|ref|YP_004598711.1|  [L=127]
Description: methylmalonyl-CoA epimerase [Halopiger xanaduensis SH-6]
Scores for complete 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   64.2   0.1    1.4e-17   63.9   0.1    1.1  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    1.1e-12   48.2   0.3    1.2e-12   48.1   0.3    1.0  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
      2e-07   31.3   1.3    2.3e-07   31.1   1.3    1.1  1  Glyoxalase_3  Glyoxalase-like domain
     0.0098   16.7   0.2      0.013   16.3   0.2    1.2  1  Glyoxalase_6  Glyoxalase-like domain
  ------ inclusion threshold ------
       0.21   11.5   0.0       0.27   11.2   0.0    1.4  1  Glyoxalase_2  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.1   3.9e-21   1.4e-17       1     109 []       4     111 ..       4     111 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 3.9e-21
                                       EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT...-THHHTS-EEEEEEE CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegp...eflaehgeglhhlay 74 
                                       d+ gi+++   +  +r+++l+G++   + +++  ++++ f++ g+g  ++eL eple+    + l++hg+g+hhla+
  gi|336255604|ref|YP_004598711.1|   4 DHAGIATDAAAELGDRYETLFGLEIAHEETFD--GMRVVFLDCGNG--YLELLEPLEDGtiaQYLDDHGAGIHHLAF 76 
                                       699********************998888877..677799***998..9********988999************** PP

                                       EES-HHHHHHHHCTTTEEEEEEEE-GGGTT-EEEE CS
                      Glyoxalase_4  75 wvddldaavarleeqGfevvqkgvragaagrrfay 109
                                       ++dd++ a++r++e+++++v++++r+ga g+ +a+
  gi|336255604|ref|YP_004598711.1|  77 ATDDIEGALERARENDVRLVDEEPRPGAWGHSVAF 111
                                       ****************************9***998 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.3   3.5e-16   1.2e-12       2     128 .]       3     124 ..       2     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 3.5e-16
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC.TSEEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkiee.tvhhv 77 
                                       +dh+ ++++ +++  d Y+  +G+++  ++      +g+r  f+++g+g +el+    +++ a+      + +++++
  gi|336255604|ref|YP_004598711.1|   3 FDHAGIATDAAAELGDRYETLFGLEIAHEET----FDGMRVVFLDCGNGYLELLEPLEDGTIAQYL----DdHGAGI 71 
                                       69*****************************....99****************9999999988888....558**** PP

                                       EEEEEEHCHHHHHHHHHHHTTGE.EEEEEECHHCTEEEEE.EEEETTSEEEEE CS
                        Glyoxalase  78 afialdvedvgkaldrlkeagvk.vvaepgrhyfgalysf.yfrDpdGillei 128
                                       +++a++++d++ al+r++e++v+ v++ep    +g+++ f + +D +G+l+e+
  gi|336255604|ref|YP_004598711.1|  72 HHLAFATDDIEGALERARENDVRlVDEEPRPGAWGHSVAFlHPTDTGGVLIEF 124
                                       ***********************4457899999****99999**********8 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   1.3   6.5e-11   2.3e-07       1     135 [.       3     124 ..       3     127 .] 0.73

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 6.5e-11
                      Glyoxalase_3   1 lDHvvlavpdleeaaarfarrlGftvtpggehpglgtaNalvmf..gdgYlEllav.dpeapaperprlfgldrlak 74 
                                       +DH+++a++  +e  +r+++  G++++      g     ++v +  g+gYlEll++ ++ + a+       ld+  +
  gi|336255604|ref|YP_004598711.1|   3 FDHAGIATDAAAELGDRYETLFGLEIAHEETFDG----MRVVFLdcGNGYLELLEPlEDGTIAQ----Y--LDD--H 67 
                                       8********************9999876666666....45555544789******637777762....2..344..7 PP

                      Glyoxalase_3  75 geglhtlalrtddidataarlraaGvdeagrrvrpdggdlrwrllfladealpaegalPfl 135
                                       g g+h+la++tddi+ + +r+r++ v  ++ + +p  g + ++++fl   +  ++g l ++
  gi|336255604|ref|YP_004598711.1|  68 GAGIHHLAFATDDIEGALERARENDV--RLVDEEPRPGAWGHSVAFLHPTD--TGGVLIEF 124
                                       9*********************9996..34444555555666666666532..24555555 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   3.6e-06     0.013       4      94 ..       8     106 ..       5     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.6e-06
                      Glyoxalase_6   4 ldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe.........paknrvHldlavedlda 71 
                                       ++++ +a+l + +++++g+e ++ee + +  ++v +  +++   l+++ ++         ++    Hl +a++d++ 
  gi|336255604|ref|YP_004598711.1|   8 IATDAAAELGDRYETLFGLEIAHEE-TFDGMRVVFLDCGNGYLELLEPLEDgtiaqylddHGAGIHHLAFATDDIEG 83 
                                       67889999*****************.3333333333333333333333333778778777888889*********** PP

                      Glyoxalase_6  72 evarlvalGArvlreprdgthgr 94 
                                       + +r+ +   r ++e+  +++++
  gi|336255604|ref|YP_004598711.1|  84 ALERARENDVRLVDEEPRPGAWG 106
                                       ******99999988887777665 PP

>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.5e-05      0.27      63     108 ..      72     117 ..      20     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.5e-05
                                       -EEEEEES-HHHHHHHH..GGGS-EEE.EEEE-TTS-EEEEEE-TT- CS
                      Glyoxalase_2  63 feLyFevedvdaflqklkeaeniellh.elkekpWgqrvirfyDpDk 108
                                        +L F  +d++ +l++ +e++ ++l+  e++  +Wg  v+ +   D+
  gi|336255604|ref|YP_004598711.1|  72 HHLAFATDDIEGALERAREND-VRLVDeEPRPGAWGHSVAFLHPTDT 117
                                       4799*************9999.99997257889******99876664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 976.26
//
Query:       gi|336255605|ref|YP_004598712.1|  [L=214]
Description: Oxidoreductase FAD-binding domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   41.5   0.0    1.7e-10   41.1   0.0    1.2  1  FAD_binding_6  Oxidoreductase FAD-binding domain
    0.00094   18.7   0.2     0.0013   18.2   0.2    1.2  1  PALP           Pyridoxal-phosphate dependent enzyme
     0.0059   16.9   1.3      0.011   16.0   1.3    1.5  1  Toprim_3       Toprim domain
  ------ inclusion threshold ------
      0.021   15.4   1.3      0.048   14.2   1.3    1.6  1  ATPgrasp_N     ATP-grasp N-terminal domain
      0.076   12.6   0.9       0.13   11.8   0.9    1.3  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase


Domain annotation for each model (and alignments):
>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   4.7e-14   1.7e-10       2      99 .]       6     101 ..       5     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 4.7e-14
                                       EEEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEEC..ETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHH CS
                     FAD_binding_6   2 lkltekeevsedtrifrfklpsekqklglpvGqhvflrlk..ikgeaviRsYtpissenekGelellvkvypgGkms 76 
                                       ++++++++v ++t  +++++p++   ++ ++Gq+v lr++   ++e v R Yt +ss+  + ++e+ v v p+G +s
  gi|336255605|ref|YP_004598712.1|   6 VTVESVRDVGPETVALELETPDA---FDALPGQFVLLRASpdGDDEVVERHYT-LSSPAVDDTFEITVGVDPDGDLS 78 
                                       57888899999998888888844...44677********9777888999****.9999999**************** PP

                                       HHHHCS-TT-EEEEEEEE-SEEC CS
                     FAD_binding_6  77 qaLdelkigdtleikGPlGkfeY 99 
                                         L  l+ g+t++++GP+G+++Y
  gi|336255605|ref|YP_004598712.1|  79 PWLAGLEGGETVHVDGPFGTITY 101
                                       ********************998 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   3.7e-07    0.0013      67     134 ..     119     187 ..      97     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.7e-07
                                       HHHHHHHHHHHT-EEEEEEETTS-H..HHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TT CS
                              PALP  67 gralAaaaallGlkvtivvpadasp..ekvallrllGaevvevggdydeavaaaaelaaegegaylvsqf 134
                                       ++a+A aa+ +G ++++   +d ++  e++++l+  Ga v+ v+++ +e +aaa e+  + +g++++  f
  gi|336255605|ref|YP_004598712.1| 119 AVAIAEAARDAGHEAVVIYQDDEPAhrERLEALEDDGASVTIVDDEANEDLAAAIEAHVD-DGRIYAFGF 187
                                       7899****************9999555****************99999999998888888.888887665 PP

>> Toprim_3  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.3   3.1e-06     0.011      19      91 ..     103     175 ..      89     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.1e-06
                          Toprim_3  19 tgaaviAllsaanlk.aiawp....e.rgkrvviaaDnDaandGreaaeklaerleaagieavllepaegeDwndvl 89 
                                        +a+v+A  +  ++  a+a++    + + + vvi+ D+++a      +++  e+le++g ++++++++++eD+  ++
  gi|336255605|ref|YP_004598712.1| 103 RDADVVAIAGGPGVGpAVAIAeaarDaGHEAVVIYQDDEPA------HRERLEALEDDGASVTIVDDEANEDLAAAI 173
                                       67888899999888877777766774488899********8......7778899999999************99988 PP

                          Toprim_3  90 qk 91 
                                       ++
  gi|336255605|ref|YP_004598712.1| 174 EA 175
                                       76 PP

>> ATPgrasp_N  ATP-grasp N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.3   1.3e-05     0.048       2      63 ..     124     193 ..     123     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                                       HHHHHTT-EEEEEEETTS----S-TT..EEEEEEE-TTT-H..HHHHHHHHHHHHHS.....--SEEE-- CS
                        ATPgrasp_N   2 eaAkaLGikvvlvdeedewapeelae.lvekfipldlaqdp..daaleavralsrer.....pvdGivtf 63 
                                       eaA+  G+++v+++++de a  e+ e l ++   +++ +d+  +++ +a++a  ++      ++d +vtf
  gi|336255605|ref|YP_004598712.1| 124 EAARDAGHEAVVIYQDDEPAHRERLEaLEDDGASVTIVDDEanEDLAAAIEAHVDDGriyafGFDEFVTF 193
                                       89****************9766664447777777777766433666677777655532222255555555 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 ?   11.8   0.9   3.5e-05      0.13       7      65 ..     119     178 ..     113     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHHTT-EEEEEESSGGH..HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHH CS
                      adh_short_C2   7 GraiAkalaeeGaevvltdlneea..kkrveelaeelgaevlecDVtdeeqvealveevve 65 
                                       + aiA+a+ ++G e v+ ++++e   ++r+e+l+++ ga+v  +D + +e+++a++e+ v+
  gi|336255605|ref|YP_004598712.1| 119 AVAIAEAARDAGHEAVVIYQDDEPahRERLEALEDD-GASVTIVDDEANEDLAAAIEAHVD 178
                                       679******************999756666666664.777777777777777777776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1637.37
//
Query:       gi|336255606|ref|YP_004598713.1|  [L=584]
Description: 2-oxoacid:acceptor oxidoreductase subunit alpha [Halopiger xanaduensis SH-6]
Scores for 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-58  196.8   0.2    6.9e-58  196.1   0.2    1.3  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.2e-40  139.5   0.1    2.3e-40  138.5   0.1    1.5  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    1.2e-06   28.2   0.1    2.4e-06   27.3   0.1    1.4  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
  ------ inclusion threshold ------
      0.044   14.1   0.0        0.1   12.9   0.0    1.7  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
      0.089   12.7   0.0        0.2   11.5   0.0    1.5  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 !  196.1   0.2   1.9e-61   6.9e-58       2     229 ..     208     452 ..     207     454 .. 0.95

  Alignments for each domain:
  == domain 1  score: 196.1 bits;  conditional E-value: 1.9e-61
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a+aag++++a+YPITP+++i+e l   +++ +    +vvq+e+E++ai++++GAa +Gara+TaTSg G+ Lm e+
  gi|336255606|ref|YP_004598713.1| 208 GALAAGCRFYAGYPITPATSIMEYLTGRIEDYGG---HVVQAEDELSAINMALGAARSGARAMTATSGAGIDLMTET 281
                                       799**************************99995...**************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvi 150
                                       +gl+a +e+P+vi++v+R++pstg++++++q+Dl++a+     + +  v+ + +++e+f+ +++AfnlAek+++Pv+
  gi|336255606|ref|YP_004598713.1| 282 FGLVAQSETPLVITDVQRSGPSTGMPTKQEQGDLNMALygghgEIPRFVVTPTSIAECFWKTVEAFNLAEKYQIPVF 358
                                       ***************************************************************************** PP

                                       EEEEHHHH.HEEEEEEC-SGG..GS-----SBXXXXXXXX................SXXXBXXTXXTSSXXEEESBX CS
                             POR_N 151 vlfDgfllshevekvelpdee.delklikekleeyerkey................aldpekpiargtaanpdtgle 210
                                       +++D  +   + ++ + ++ + de+++ + kl+++++ +                 +++p+  + +   a   tgle
  gi|336255606|ref|YP_004598713.1| 359 LVSDLAMS-VTEQTFRPETFDmDEVEIDRGKLVDEDEVDEwldaqgrfrahavtedGVSPRAIPGTTDGAHMSTGLE 434
                                       ****8776.999999999999999999999999999988899999******************************** PP

                                       BXTTSXBXXXXHHHHHHHH CS
                             POR_N 211 hrekgneaedaaekvveev 229
                                       h+e g+++ed  +++v++v
  gi|336255606|ref|YP_004598713.1| 435 HDELGRRTED-EDERVQQV 452
                                       *********9.66777766 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.5   0.1   6.4e-44   2.3e-40       1     175 [.      13     173 ..      11     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 6.4e-44
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       +G+G+ ++gki+a+a++raG +v++++++ s+irGg + +++r s + +v+s+  ++ d+lval + t++e+ld+l 
  gi|336255606|ref|YP_004598713.1|  13 AGDGIDSTGKIFAQALSRAGRHVFTSKDFASRIRGGYTAYKIRTSVD-RVQSVV-DRLDILVALTQRTIDENLDELH 87 
                                       5**********************************************.999999.********************** PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallglplealeeai 154
                                       +++ iiy+ e+  ++e++++               ++v+++ +a+++gg ++++N+v+lGa++ ++++++e+l+ea+
  gi|336255606|ref|YP_004598713.1|  88 EDSAIIYDGERSWEAEIPDEMT------------AVDVPLKSLAEDAGG-AIMRNIVALGAACEITNFDVEYLDEAL 151
                                       *********8876666666544............479************.*************************** PP

                                       HCCS-CH..HHHHHHHHHHHHH CS
                               POR 155 kkrfpkkk.eviekNlkafrag 175
                                       +krf++k+ +++e N++a+r+g
  gi|336255606|ref|YP_004598713.1| 152 EKRFGGKGsKIVENNKEAARLG 173
                                       ********************98 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 !   27.3   0.1   6.7e-10   2.4e-06      14     158 ..     212     360 ..     200     374 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 6.7e-10
                                       CT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHH CS
                      TPP_enzyme_N  14 lgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAk 87 
                                       +g + + g+p +  ++++++l  +    g +vv+a +E +a+++A g ar+   + +  +tsg G+  ++      +
  gi|336255606|ref|YP_004598713.1| 212 AGCRFYAGYPITPATSIMEYLTGRIedyGGHVVQAEDELSAINMALGAARSGA-R-AMTATSGAGIDLMTETFGLVA 286
                                       47778888888888888888888777789*********************975.3.44556899999999999999* PP

                                       HHT--EEEEEEE--CCCHHS..TC--T-.CCHHHCCCSSEEEE-SSGGGHHHHHH...HHHHHHHSSS--EEEEE CS
                      TPP_enzyme_N  88 vdriPllvlsgdrptslrgqgvlqqeld.qlalfrpvtkyaervtspeelpealr...rAirtalsgrpgPvyle 158
                                       ++ +Pl++   +r+  ++g ++ q++ d ++al+  + +  ++v +p++++e +    +A+  a ++ + Pv+l+
  gi|336255606|ref|YP_004598713.1| 287 QSETPLVITDVQRSGPSTGMPTKQEQGDlNMALYGGHGEIPRFVVTPTSIAECFWktvEAFNLA-EKYQIPVFLV 360
                                       *******************999997776478888866666666666666666555222788888.9999999995 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 ?   12.9   0.0   2.8e-05       0.1       1      70 [.     478     541 ..     478     569 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGql 70 
                                       A+ +++  Gs  g +++a + l ++ i++ ++ + +++P P  +l++ ++ +++vvv++ n++    Gq 
  gi|336255606|ref|YP_004598713.1| 478 ADNLVISWGSNEGALREALEYLEADDIDLRVISVPYIFPRP--DLSDEIEAADEVVVVECNAT----GQF 541
                                       899*************************9999999996655..789999999*********95....443 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   5.7e-05       0.2      11      68 ..     479     534 ..     473     550 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.7e-05
                                       SEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEE CS
                   Transketolase_C  11 dvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvve 68 
                                       d +++++Gs      eA e Le++ i+ +V++++ + p    ++++ ++  +++vvve
  gi|336255606|ref|YP_004598713.1| 479 DNLVISWGSNEGALREALEYLEADDIDLRVISVPYIFPRP--DLSDEIEAADEVVVVE 534
                                       6689******************************998854..3344455566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.21s 00:00:00.80 Elapsed: 00:00:00.38
# Mc/sec: 4563.48
//
Query:       gi|336255607|ref|YP_004598714.1|  [L=288]
Description: pyruvate ferredoxin/flavodoxin oxidoreductase subunit beta [Halopiger xanaduensis SH-6]
Scores for complete 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  109.4   0.3    2.1e-31  108.8   0.3    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
      1e-19   70.4   1.5    2.3e-19   69.3   1.5    1.6  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


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 !  108.8   0.3   2.3e-35   2.1e-31       2     153 .]      51     198 ..      44     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 2.3e-35
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       iGc+             ++y++  +++g +G++lp++ G+k+a+pd ev++  GDG+ + i   ++++avrrn+++t
  gi|336255607|ref|YP_004598714.1|  51 IGCSGK----------IGTYMHsYALHGVHGRALPVGQGVKMARPDIEVMVAGGDGDGYSIgAGHFVHAVRRNVDMT 117
                                       566665..........678888456************************************99************** PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpa 149
                                       +vv++N++yg+t+gq   +++   +++++p+g +++pv++ +la a Ga+  a+  ++d    +e+++ea+e++g+ 
  gi|336255607|ref|YP_004598714.1| 118 YVVMDNRIYGLTKGQaspTSRSDFETSTTPEGPKQPPVNPLALALASGASfIAQSFSSDALRHQEIVQEAIEHDGFG 194
                                       ***************9987777778999999999****************7776667878999************** PP

                                       EEEE CS
                      TPP_enzyme_C 150 liev 153
                                       +++v
  gi|336255607|ref|YP_004598714.1| 195 FVNV 198
                                       *987 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   1.5   2.6e-23   2.3e-19       1      64 [.     202     266 ..     202     268 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 2.6e-23
                                       XTTTXSSSXSXXXXX-EEEGGGS.T---EEHHHHHHHHT-----EEEEEEEE.TTS--HHHHHHT. CS
                        PFO_beta_C   1 CvtFNkvnTfdwYkervykleed.gyDpsdlekAlekalewgdkiplGifYk.eekptyeerleel 64 
                                       CvtFN+v+T+d++++++++l+ed ++Dp+d+e+A e++l+  dk + G++Yk e++ +y+e++ ++
  gi|336255607|ref|YP_004598714.1| 202 CVTFNDVDTYDYFRDNLVDLQEDeDHDPNDYEAAKEVILD-SDKEYQGVMYKdENSVPYHEKHGVT 266
                                       **********************99***************9.*********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2374.53
//
Query:       gi|336255608|ref|YP_004598715.1|  [L=218]
Description: hypothetical protein Halxa_4234 [Halopiger xanaduensis SH-6]
Scores for 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   14.1   0.0      0.061   13.4   0.0    1.3  1  DUF5542     Family of unknown function (DUF5542)
      0.051   13.4   2.0      0.094   12.6   2.0    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> DUF5542  Family of unknown function (DUF5542)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.9e-06     0.061       2      51 ..      34      83 ..      33      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.9e-06
                           DUF5542  2 evdaaaadgrdGlreRrGlgeagrqqqnrevrpqsganglpkhsYWLdlW 51
                                      e da+ +  +d   e  G  e + ++q+ ++  q+g ++  + s WL l+
  gi|336255608|ref|YP_004598715.1| 34 EFDAERVAPTDAAFEETGYEETQVEEQSIDETIQAGVERDVRASMWLSLY 83
                                      7788888999*************************************986 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.0   1.1e-05     0.094       2      24 ..       3      24 ..       2      25 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                        TAT_signal  2 lSRRdFLKgsAAaa.AAaalggca 24
                                       SRR++L   A+++ A+a+++gc+
  gi|336255608|ref|YP_004598715.1|  3 PSRRSLLA--AGTTsALALTAGCL 24
                                      69******..66664777788996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1810.69
//
Query:       gi|336255609|ref|YP_004598716.1|  [L=373]
Description: aspartate transaminase [Halopiger xanaduensis SH-6]
Scores for complete 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-59  202.2   0.0    1.5e-59  202.0   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    3.2e-13   49.7   0.0    6.6e-13   48.7   0.0    1.4  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    4.7e-09   35.9   0.0    7.6e-09   35.3   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    4.4e-07   29.2   0.0    5.9e-07   28.8   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    3.3e-06   25.9   0.0    4.2e-06   25.6   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.063   11.9   0.1       0.12   11.0   0.1    1.3  1  Aminotran_3      Aminotransferase class-III


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 !  202.0   0.0     5e-63   1.5e-59       2     361 ..      26     363 ..      25     365 .. 0.93

  Alignments for each domain:
  == domain 1  score: 202.0 bits;  conditional E-value: 5e-63
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       d inLg +++++     t+ ++++ ++e a ++g +  y+ ++g  +l+ea+a  + r+++l++++ + + +++G+ 
  gi|336255609|ref|YP_004598716.1|  26 DAINLGLGQPDFP----TPAHARRGAIE-AIENGLTDAYTSNKGTESLREAIAAKYDRDYGLEVEPRDIIATSGGSE 97 
                                       679*********9....***********.**************************************7777777777 PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       al  al++  +  pg+e++ pdp + sy+   +l+gg+  ++ l+  ed +ld e +ee ++e       t  ++v+
  gi|336255609|ref|YP_004598716.1|  98 ALHIALEAHVD--PGEEVIFPDPGFVSYDALTKLAGGTPKPVGLR--EDLTLDPETVEENITE------DTAAFVVN 164
                                       77777777776..******************************99..****************......889***** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGy 232
                                       sp NPtG+v +++++++ +++a+++ +l ++De+Y++ vf+   + +  ++++e +n+++v+ +sK ++++G+R+G+
  gi|336255609|ref|YP_004598716.1| 165 SPANPTGAVQSEADIREFARIADEHDVLCISDEVYEKIVFDG--VHRSPMEFAETDNVVVVSACSKTYSMTGWRLGW 239
                                       *****************************************4..444499*************************** PP

                                       EEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSE CS
                     Aminotran_1_2 233 ilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmf 307
                                       ++g+ + ++ + ++++ +    s+++q+a+ aal  +++    ++em++ +++rr+++ d+L+++gl+v ++ ++++
  gi|336255609|ref|YP_004598716.1| 240 VVGSNRRIERMLRVHQYGQAcaSAPAQYAAEAALTGPQD---PVDEMVDAFEERRDVVLDGLEDAGLEVPTPSGAFY 313
                                       ***7777777777776544446****************7...8********************************** PP

                                       EEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHH CS
                     Aminotran_1_2 308 lltdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelve 361
                                        +  +++       ++ l++ gv+v+pg  f+   +g  R+++ ++  e+l+e++e
  gi|336255609|ref|YP_004598716.1| 314 AMPKVPEG----WVDEVLDR-GVVVVPGDAFGEhgEGYARLSY-ATGMEDLKEALE 363
                                       *****999....7788****.**********************.888889999887 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 !   48.7   0.0   2.2e-16   6.6e-13      36     144 ..      84     196 ..      48     197 .. 0.84
   2 ?   -3.8   0.0       1.9   5.8e+03     113     125 ..     248     260 ..     220     268 .. 0.70

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 2.2e-16
                                       HT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE CS
                   DegT_DnrJ_EryC1  36 lgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitert 112
                                       ++ +  ia+s G++Alh+aL+a  v+pg+eVI p  +Fv+  +    +g +p +v    +++++dp+++e+ ite t
  gi|336255609|ref|YP_004598716.1|  84 VEPRDIIATSGGSEALHIALEA-HVDPGEEVIFPDPGFVSYDALTKLAGGTPKPVGLR-EDLTLDPETVEENITEDT 158
                                       5556789**************9.699*******************************9.89**************** PP

                                       EEEE...EB-GGGB-...--HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 113 kaIl...pVhlyGqv...admdalkaiaakhglkvieD 144
                                       +a +   p++  G+v   ad+ +  +ia++h++  i+D
  gi|336255609|ref|YP_004598716.1| 159 AAFVvnsPANPTGAVqseADIREFARIADEHDVLCISD 196
                                       9987455577788763336***************9998 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.9
                                       EEEEEB-GGGB-- CS
                   DegT_DnrJ_EryC1 113 kaIlpVhlyGqva 125
                                          l Vh yGq++
  gi|336255609|ref|YP_004598716.1| 248 ERMLRVHQYGQAC 260
                                       4567899999988 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   2.5e-12   7.6e-09      15     167 ..      45     196 ..      36     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.5e-12
                                       HHHHHCS----.CCCT--HHHHHHHHHHHHHTT-SEEEE........ES-HHHHHHHHHHHH--TTEEEEEETT-HH CS
                   Beta_elim_lyase  15 sdaqaaamlGd.esYgedktvnrLedavaelfgkeaalf........vpqGtaAnsillkillqrgeevivtepahi 82 
                                       + a+ a++ G  ++Y  +k+++ L +a+a+ ++ +++l         +  G  A +i+l++++ +geevi+ +p+ +
  gi|336255609|ref|YP_004598716.1|  45 RGAIEAIENGLtDAYTSNKGTESLREAIAAKYDRDYGLEveprdiiaTSGGSEALHIALEAHVDPGEEVIFPDPGFV 121
                                       44556666774279****************99999999668899997888************************988 PP

                                       HHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHH CS
                   Beta_elim_lyase  83 hfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakk 159
                                         d   a+  lag +++++  +e+ ++d+e +e+ i+e     +  ++++   +n t  G v s + +re a ia++
  gi|336255609|ref|YP_004598716.1| 122 SYD---ALTKLAGGTPKPVGLREDLTLDPETVEENITE-----DTAAFVVNSPANPT--GAVQSEADIREFARIADE 188
                                       777...678889999***********************.....46799999999999..****************** PP

                                       CT-EEEEE CS
                   Beta_elim_lyase 160 ygiplhlD 167
                                       +++  + D
  gi|336255609|ref|YP_004598716.1| 189 HDVLCISD 196
                                       *9876655 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0     2e-10   5.9e-07      58     221 ..      84     250 ..      46     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2e-10
                                       -STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHH CS
                       Aminotran_5  58 aeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelek 134
                                       +e   +ii tsG++ea+ +++ +    ++pg+e++  + +  +      +l k  g + k + l e+ +ld++++e+
  gi|336255609|ref|YP_004598716.1|  84 VEP-RDIIATSGGSEALHIALEAH---VDPGEEVIFPDPGFVSYD----ALTKLAGGTPKPVGLREDLTLDPETVEE 152
                                       554.89***********9999888...************988877....777778********************** PP

                                       H--TTEEEEEEESBETTTTEB-...-HHHHHHHHHHTT-EEEEE-T......TTTTTS---HHHHTESEEEEETTTT CS
                       Aminotran_5 135 llnektklvaithvsnvtGtiq...pveeigklakkkgalvlvDaa......qavghipidvkklgvDflafsghKl 202
                                       +++e+t++  ++   n tG +q   ++ e++++a ++++l + D +       +v   p+++++++  ++++   K 
  gi|336255609|ref|YP_004598716.1| 153 NITEDTAAFVVNSPANPTGAVQseaDIREFARIADEHDVLCISDEVyekivfDGVHRSPMEFAETDNVVVVSACSKT 229
                                       ********************983335667777777899999999873222223455566666666654555555666 PP

                                       TSSTT..-EEEEEEHHHHHTS CS
                       Aminotran_5 203 lgPtG..iGvlyvrkellekl 221
                                       +  tG  +G ++++++ +e++
  gi|336255609|ref|YP_004598716.1| 230 YSMTGwrLGWVVGSNRRIERM 250
                                       666665556666666666666 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   1.4e-09   4.2e-06      70     189 ..      89     217 ..      60     266 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.4e-09
                                       EEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTEEEEEEES CS
                   Cys_Met_Meta_PP  70 alavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdtsdleelekaikentklvylEt 145
                                        +a+s G  A++ a+ a +  G+e++  d  + +  +l k        +  +   t d+e +e+ i+e t ++ + +
  gi|336255609|ref|YP_004598716.1|  89 IIATSGGSEALHIALEAHVDPGEEVIFPDPGFVSYDALTKLAGGTpKPVGLREDLTLDPETVEENITEDTAAFVVNS 165
                                       679999***********************98766555554443222334444455789******************* PP

                                       S-TTTT--...--HHHHHHHHHHTT-EEEEEGTTTH....TTTS-GGGGT.- CS
                   Cys_Met_Meta_PP 146 ptnpllkv...vDiekiaklakkagvlvvvDntfas....pllqrplklg.a 189
                                       p+np+  v   +Di++ a++a +++vl + D ++      ++   p+++   
  gi|336255609|ref|YP_004598716.1| 166 PANPTGAVqseADIREFARIADEHDVLCISDEVYEKivfdGVHRSPMEFAeT 217
                                       ****97663337*****************99986431111666677776543 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   3.9e-05      0.12     183     234 ..     148     198 ..     140     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.9e-05
                                       HHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-T CS
                       Aminotran_3 183 ealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEv 234
                                       e +e+ +++++aA++v       G v +s++ +++ + ++++hdvl i DEv
  gi|336255609|ref|YP_004598716.1| 148 ETVEENITEDTAAFVVNSPANPTGAV-QSEADIREFARIADEHDVLCISDEV 198
                                       56789999********9877777765.5666799*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3027.29
//
Query:       gi|336255610|ref|YP_004598717.1|  [L=321]
Description: NADPH:quinone reductase [Halopiger xanaduensis SH-6]
Scores for 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-19   70.0   0.1    7.2e-19   69.2   0.1    1.5  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    5.4e-12   45.8   0.2      1e-11   44.9   0.2    1.5  1  ADH_zinc_N    Zinc-binding dehydrogenase
    5.7e-11   42.3   0.0    4.1e-09   36.3   0.0    2.3  2  ADH_N         Alcohol dehydrogenase GroES-like domain
  ------ inclusion threshold ------
      0.044   13.7   0.0       0.11   12.3   0.0    1.7  1  ADH_N_2       N-terminal domain of oxidoreductase


Domain annotation for each model (and alignments):
>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.1   1.6e-22   7.2e-19       1     133 []     186     319 ..     186     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.6e-22
                                       TT-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT-E CS
                      ADH_zinc_N_2   1 lGAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkgrs 72 
                                       +GAd v+dy ++d++    +a + +gvDvvld    ++l +   +v + g r+v ig ++p +  +++ a++ k  s
  gi|336255610|ref|YP_004598717.1| 186 MGADTVLDYARDDLAdavlEA-SDGGVDVVLDHRLDDYL-QFDADVAATGCRVVGIGeNSPDPGFTNDGAARSKDVS 260
                                       59***********99988544.3578*******666666.66678998889******77667776777777666666 PP

                                       EEE--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  73 vkyeflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                        ++  +f  +++  +  l+  a+l+++G+l + +d++++leeaaeA r++++ +++GK+Vl
  gi|336255610|ref|YP_004598717.1| 261 YQFMSMF-NTPD-LRVPLRGAAHLMDAGRLSVEIDERYDLEEAAEAQRAVMEDSVFGKLVL 319
                                       6666666.3565.6666*******************************************8 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.2   2.3e-15     1e-11       1      90 [.     155     241 ..     155     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.3e-15
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       gvG+aavq+A a  a+vi+++s +     ++ +Gad v++y ++dl +++ e+ + +gvdvv+++    + l+   +
  gi|336255610|ref|YP_004598717.1| 155 GVGHAAVQIADAVSARVITTASEDY-HGGLEAMGADTVLDYARDDLADAVLEASD-GGVDVVLDHRL-DDYLQFDAD 228
                                       9******************999887.588999*********665**********5.5**********.********* PP

                                       CEEEEEEEEECSC CS
                        ADH_zinc_N  78 llkpgGrlvvvGg 90 
                                       +++ g r+v +G 
  gi|336255610|ref|YP_004598717.1| 229 VAATGCRVVGIGE 241
                                       ***********94 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   9.2e-13   4.1e-09       2      60 ..      28      85 ..      27      91 .. 0.94
   2 !    4.2   0.0    0.0086        38      90     108 ..      92     111 ..      85     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 9.2e-13
                                      TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEE CS
                             ADH_N  2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVv 60
                                      +e+l++v+aag++  D  + +g +  +v  p+++G +++G+v+e+g++v++++ GdrV 
  gi|336255610|ref|YP_004598717.1| 28 DELLVEVAAAGVNPVDTYFRDG-SYEPVDVPFTPGVDLAGTVAETGDAVEEFAAGDRVY 85
                                      799**************99999.8**********************************7 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0086
                                       S.S-SSSBSEEEECGGGEEE CS
                             ADH_N  90 s.ldGgfaeyvvvpekklvk 108
                                       + ++G++aey +vp++ +v 
  gi|336255610|ref|YP_004598717.1|  92 GsYQGSYAEYATVPTDRVVA 111
                                       2589**********998875 PP

>> ADH_N_2  N-terminal domain of oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.6e-05      0.11      13      91 ..      10      87 ..       2      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                           ADH_N_2 13 ptesdfeleeeelpelkdGevlvralylSvDPymRgrmndaksyve.pvelgdvmrggavgeVveSknpdfkvGdlVvg 90
                                        ++ +++ee + pe++++e+lv++   +v P   ++ + + + v+ p++ g  ++g +v+e  +   ++f++Gd V g
  gi|336255610|ref|YP_004598717.1| 10 GGPDVLQVEEIDRPEPANDELLVEVAAAGVNPVDTYFRDGSYEPVDvPFTPGVDLAG-TVAETGD-AVEEFAAGDRVYG 86
                                      56788999*********************9999988888888888889999999977.4677544.4577888888877 PP

                           ADH_N_2 91 l 91
                                       
  gi|336255610|ref|YP_004598717.1| 87 T 87
                                      5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2521.57
//
Query:       gi|336255611|ref|YP_004598718.1|  [L=97]
Description: hypothetical protein Halxa_4237 [Halopiger xanaduensis SH-6]
Scores for 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:                       656  (0.0365888); 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:                         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: 00:00:00.39
# Mc/sec: 742.72
//
Query:       gi|336255612|ref|YP_004598719.1|  [L=474]
Description: D-lactate dehydrogenase (cytochrome) [Halopiger xanaduensis SH-6]
Scores for complete 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-55  189.0   0.2    1.5e-55  188.6   0.2    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    2.3e-40  137.5   0.1    3.8e-40  136.8   0.1    1.4  1  FAD_binding_4  FAD binding domain
  ------ inclusion threshold ------
      0.024   15.4   0.3      0.086   13.6   0.3    2.0  1  Glyoxalase_6   Glyoxalase-like 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 !  188.6   0.2   2.5e-59   1.5e-55       2     250 .]     219     459 ..     218     459 .. 0.96

  Alignments for each domain:
  == domain 1  score: 188.6 bits;  conditional E-value: 2.5e-59
                                       -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHH CS
                     FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaee 78 
                                       p  ++ + + f+++e+a  a++e+++ ++ +a++el+d+ +++++++++++      + ++++++ef++++   +ee
  gi|336255612|ref|YP_004598719.1| 219 PHQIRGGRAVFETLEDATGAIAEAVRTEVAVARIELLDELSVRMTNDYLET----GLPDAPTVFLEFHANH--GIEE 289
                                       667888899******************************************....788899**********..8999 PP

                                       HHHHHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHH CS
                     FAD-oxidase_C  79 elealveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldk 155
                                       e+  l+  i+e++ + ++ ++ d++e+ +lw+aR+ +   + +    + ++    D++vP+s+ +++vr++k+l+++
  gi|336255612|ref|YP_004598719.1| 290 EID-LCLTIFEDHDVLEFEISADDDEMSELWEARREIAF-AVENYEPELHTLHPGDVTVPISAYPEMVREAKRLAEE 364
                                       999.********************************998.455558888999999********************** PP

                                       HHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THHHHH CS
                     FAD-oxidase_C 156 yglevvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglalm 232
                                        +l + ++gHagdgnlh ++l+d++d++++er e+++ ++v++a+elgG+++gEHG+G  k+++le e g  ++++m
  gi|336255612|ref|YP_004598719.1| 365 RDLLAPCYGHAGDGNLHHNVLVDPDDPEMVERGEEAYRKTVEKAIELGGTVTGEHGIGEGKRQFLEDEHGAGAVDAM 441
                                       ***************************************************************************** PP

                                       HHHHHHH-TT--BSTT-- CS
                     FAD-oxidase_C 233 rriKaalDPkgiLNPgkv 250
                                       rr+K+alDP + LNPgk+
  gi|336255612|ref|YP_004598719.1| 442 RRLKRALDPTDTLNPGKI 459
                                       ****************96 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.8   0.1   6.4e-44   3.8e-40       1     139 []      43     182 ..      43     182 .. 0.99

  Alignments for each domain:
  == domain 1  score: 136.8 bits;  conditional E-value: 6.4e-44
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgd 76 
                                       p+avv+pes+e+v+++l++a+e+++pv+++++G+sl g+av a gg+ ldl+r+++i+++ +++ ++ v++G+++++
  gi|336255612|ref|YP_004598719.1|  43 PDAVVWPESTEDVSTVLAAATERDVPVTPYAAGTSLEGNAVpAHGGISLDLTRMDDIVDYRPDDFQIDVGPGIIGSE 119
                                       89*************************************************************************** PP

                                       HHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEEE CS
                     FAD_binding_4  77 lvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrls 139
                                       ++e++a+ gl++++ p+sg+ +t+GG+iat a+G++  +yG ++d+vlgle+vladG+v++++
  gi|336255612|ref|YP_004598719.1| 120 VDERVARDGLMFPPLPSSGDISTIGGMIATDASGMQTVRYGEVADWVLGLEAVLADGTVIETG 182
                                       ************************************************************985 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   1.4e-05     0.086      54     102 ..     360     435 ..     303     437 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                      Glyoxalase_6  54 e..............paknrvHldlav..edld..........aevarlvalGArvlreprdgthgr.vlaDPeGn 102
                                       +              ++   +H ++ v  +d++          ++v+++++lG++v +e+  g+++r  l+D  G+
  gi|336255612|ref|YP_004598719.1| 360 RlaeerdllapcyghAGDGNLHHNVLVdpDDPEmvergeeayrKTVEKAIELGGTVTGEHGIGEGKRqFLEDEHGA 435
                                       1444555566666644555799999885556659999999999******************999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3452.75
//
Query:       gi|336255613|ref|YP_004598720.1|  [L=155]
Description: hypothetical protein Halxa_4239 [Halopiger xanaduensis SH-6]
Scores for 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   11.9   0.2       0.19   11.1   0.2    1.4  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   1.1e-05      0.19      10      29 ..       2      21 ..       1      22 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.1e-05
                        UCR_Fe-S_N 10 tRRDFLyiATgavgaVGaaa 29
                                      +RR+FL iA  a+  VG ++
  gi|336255613|ref|YP_004598720.1|  2 NRRRFLAIAGCATVSVGSGC 21
                                      7********99999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 00:00:00.40
# Mc/sec: 1150.90
//
Query:       gi|336255614|ref|YP_004598721.1|  [L=572]
Description: acetolactate synthase [Halopiger xanaduensis SH-6]
Scores for 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-48  163.7   1.1    7.2e-48  162.4   0.2    2.1  3  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    7.4e-24   84.3   0.0    4.5e-23   81.7   0.0    2.3  3  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    1.8e-17   63.3   0.1    4.4e-17   62.1   0.1    1.7  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 !  162.4   0.2   1.2e-51   7.2e-48       2     171 ..      13     190 ..      12     191 .. 0.95
   2 ?   -1.7   0.1      0.32   1.9e+03      11      57 ..     215     244 ..     210     255 .. 0.53
   3 ?   -3.8   0.0       1.4   8.4e+03     121     144 ..     535     558 ..     518     560 .. 0.74

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 1.2e-51
                                       EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS..........-EEE CS
                      TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgk..........pgvv 68 
                                       t+a+++v+aL+++gve+vfg+pG+++lp++da+ +++ +++vl +hE +a+++A gya+  +           +gv+
  gi|336255614|ref|YP_004598721.1|  13 TGADLFVDALESYGVEYVFGNPGTTELPVTDAIGDSD-LEYVLGLHEDVAVGMAGGYAQTRRYhahhddsvnpVGVA 88 
                                       89**********************************6.*********************76556788999999**** PP

                                       EE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHH CS
                      TPP_enzyme_N  69 lvtsgpGatnaltalaeAkvdriPllvlsgdrptslrgqgvlqqel..dqlalfrpvtkyaervtspeelpealrrA 143
                                       ++++ pG++++l++l+ Ak+++ P+lv +g+++t+ r+    +++l  d ++l+ +++k++ +v ++e+lp +lrrA
  gi|336255614|ref|YP_004598721.1|  89 NLHVAPGLAHGLGNLYAAKRAGAPVLVTAGNHSTDFRH---EEPALagDLVDLADQFCKWSAEVMDVEALPTMLRRA 162
                                       **************************************...5555567***************************** PP

                                       HHHHHSSS--EEEEEEEHHHCC-EEEHH CS
                      TPP_enzyme_N 144 irtalsgrpgPvylelpkdvlleevded 171
                                       +r+al++++gPv+l lp+dv++ee+d++
  gi|336255614|ref|YP_004598721.1| 163 VRVALTPPTGPVFLGLPLDVMMEETDAE 190
                                       *************************986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.32
                                       HHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHH CS
                      TPP_enzyme_N  11 LkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdg 57 
                                       L++ +v+ +  v+G+++    d+                 a++aA+ 
  gi|336255614|ref|YP_004598721.1| 215 LADSDVRDLALVVGDGVARSGDE-----------------AVAAAVE 244
                                       55555555555555555444444.................4444444 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.4
                                       CCCSSEEEE-SSGGGHHHHHHHHH CS
                      TPP_enzyme_N 121 rpvtkyaervtspeelpealrrAi 144
                                       +++    + v++p+e++ al++A+
  gi|336255614|ref|YP_004598721.1| 535 ESHGARGHLVEEPDEIEGALEDAL 558
                                       555556677999999999999987 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 ?   -3.0   0.0      0.92   5.5e+03      30      54 ..      90     118 ..      61     132 .. 0.51
   2 ?   -1.9   0.0      0.41   2.5e+03     106     143 ..     126     163 ..     102     176 .. 0.61
   3 !   81.7   0.0   7.5e-27   4.5e-23      18     153 .]     429     568 ..     418     568 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.92
                                       TTTHHHHHHHHHH...HST.TSEEEEEEE CS
                      TPP_enzyme_C  30 mGyglpaAiGakl...akp.drevvaivG 54 
                                       + ++ + A+G+     ak+ +++v +++G
  gi|336255614|ref|YP_004598721.1|  90 LHVAPGLAHGLGNlyaAKRaGAPVLVTAG 118
                                       33333444443332221111445555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.41
                                       ...BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHH CS
                      TPP_enzyme_C 106 k..dlkpvdfaklaealGak.garvekadveeleealkeal 143
                                       +       d++ la ++ +k  a   + dve l   l++a+
  gi|336255614|ref|YP_004598721.1| 126 HeePALAGDLVDLADQF-CKwSAE--VMDVEALPTMLRRAV 163
                                       33334555888888888.665554..444466666666665 PP

  == domain 3  score: 81.7 bits;  conditional E-value: 7.5e-27
                                       SSEEECETTTS-TTTHHHHHHHHHHH...STT..SEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHH CS
                      TPP_enzyme_C  18 prsyltsgglgtmGyglpaAiGakla...kpd..revvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtg 89 
                                       p ++++ +  g +Gyglpa++Ga++a   + d  r+v++++GDG++l+  + +  avr++l++tvv+ +N+ y   +
  gi|336255614|ref|YP_004598721.1| 429 PEQFVS-NKGGGLGYGLPASVGAAIAeehR-DdpRNVICFIGDGSYLYYPNSIYSAVREDLDLTVVIPDNRNYRILK 503
                                       555555.56799*************84432.2468****************************************** PP

                                       HH..HHHHTCCTTTTSBB....BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  90 gq..qepfggkrksgpagk...dlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                        +  +   g++  ++        ++pvd+ k ae++Ga+g  ve++  +e+e al++al+++g+ +++v
  gi|336255614|ref|YP_004598721.1| 504 DNtlKLLGGDEGDHEF--VgmdFEPPVDIPKNAESHGARGHLVEEP--DEIEGALEDALSREGVDVLDV 568
                                       **64333333333333..24446******************99999..***************999987 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 !   62.1   0.1   7.4e-21   4.4e-17       2     137 .]     209     347 ..     208     347 .. 0.88

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 7.4e-21
                                       HHHHHHHHH-S..SEEEEE-CHHCHT..TGHHHHHHHHHHHT-EEEEEGGGTTS.S-TTSTTEEEESGGGSCHHHHH CS
                      TPP_enzyme_M   2 ekaaellkaak..rpvilvGggvars..gaseelrelaeklgiPvvttlmgkgv.ipedhplylgmlglhgskaane 73 
                                       e+aa+ll+ +     +++vG gvars  +a ++++elae++g+ v   ++   + +  dh+++l ++    ++++ +
  gi|336255614|ref|YP_004598721.1| 209 ERAADLLADSDvrDLALVVGDGVARSgdEAVAAAVELAESTGARVHGEVHVSEIdFATDHEQWLSYVPP--DEERAA 283
                                       789999998865478***********777****************9998886665999*******9996..577777 PP

                                       HHHH-SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  74 aleeaDlvlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                        l +aD +l++G+  + + t ++ep +  ++++ih+  dp e+gkn ++d a+vgd++ +l+ L
  gi|336255614|ref|YP_004598721.1| 284 ELLSADAILFVGTSTNTTLTRHEEPLVDLDGTLIHVSDDPWEVGKNQPADAAVVGDPGLVLQGL 347
                                       778************9988877777777778*****************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); 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:                         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: 00:00:00.40
# Mc/sec: 4272.89
//
Query:       gi|336255615|ref|YP_004598722.1|  [L=286]
Description: UbiA prenyltransferase [Halopiger xanaduensis SH-6]
Scores for complete 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-08   34.2  31.7    2.6e-08   33.5  30.4    1.9  2  UbiA      UbiA prenyltransferase family


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 ?    0.2   1.6     0.021   3.8e+02     196     232 ..      26      63 ..      10      72 .. 0.57
   2 !   33.5  30.4   1.4e-12   2.6e-08       6     229 ..      34     250 ..      26     273 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.021
                              UbiA 196 lavllla.llllllalllllylllalllaalallraar 232
                                       ++ +l+a l+ + la   +++l++ +++a +a ++ a+
  gi|336255615|ref|YP_004598722.1|  26 MTPPLAAsLFGAILADDITPTLAAIHVAAMFAAVYTAH 63 
                                       33333335556666666666666666666666655544 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 1.4e-12
                              UbiA   6 lvglalaaggspdlllllllllgtllaaaaanalNdyfD.reiDadmertpnRPlvsGrispkealifaivllilgl 81 
                                       l+g+ la   +  + l+++ ++++++a   a++ + y+D +  + d     + Pl  +      al++++ l++l +
  gi|336255615|ref|YP_004598722.1|  34 LFGAILADDIT--PTLAAIHVAAMFAAVYTAHVKDGYVDfYVRGED----DDHPLTERGCR--VALALSTTLFALCC 102
                                       45555553333..333666666666666666666667774344444....45577766655..89999********9 PP

                              UbiA  82 lllalllnpltallgllalllyvvYtg.lrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltw 157
                                       lll +l+n+++++l++ ++l+  +Y +   l   ++ +t    +  +l +++g+++++  + + +l +a+ +++l  
  gi|336255615|ref|YP_004598722.1| 103 LLLGVLVNWVAVALTVPTWLI--AYHHaPQLDTNPVTATTGYPLGIALSLFGGFYVQAAAFAAVPLGFAVVFLVLLS 177
                                       9999***************75..6664459******88888888888888999999888887777777777788889 PP

                              UbiA 158 aialandlrdregDrkagiktlpvvlGrkaarillalllavllla.llllllalllllylllalllaalallr 229
                                       +i ++ d +d++ Dr + ++t +v  G+ +a+ l++ l++ +ll+ ++++++ l+ + ++l+al++aa+al+ 
  gi|336255615|ref|YP_004598722.1| 178 GIKVIDDAQDYDYDRSIEKRTVAVAVGPTRAYDLAYGLMVTALLIvVAFAVARLFPPTAVLAALAFAAVALAA 250
                                       999999****************************555666555552444555555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); 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: 0.50u 0.20s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 2297.51
//
Query:       gi|336255616|ref|YP_004598723.1|  [L=92]
Description: hypothetical protein Halxa_4242 [Halopiger xanaduensis SH-6]
Scores for 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  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 784.02
//
Query:       gi|336255617|ref|YP_004598724.1|  [L=155]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-15   55.8   0.1    5.8e-15   55.5   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.5e-11   43.9   0.1      4e-11   43.8   0.1    1.0  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    3.3e-10   40.0   0.0    4.9e-10   39.4   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    5.4e-09   36.4   0.0    7.7e-09   35.9   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    7.8e-07   29.0   0.0    1.5e-06   28.0   0.0    1.5  1  FR47             FR47-like protein
    0.00046   19.9   0.2     0.0006   19.5   0.2    1.2  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
     0.0026   17.8   0.0     0.0046   17.1   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.013   15.7   0.0    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
      0.014   15.5   0.6      0.033   14.3   0.5    1.6  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
      0.036   14.3   0.1       0.28   11.5   0.0    2.0  2  DUF1462          Protein of unknown function (DUF1462)
       0.19   11.0   0.0       0.26   10.5   0.0    1.1  1  IMPa_N_2         Immunomodulating metalloprotease N-terminal 


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 !   55.5   0.1   3.6e-18   5.8e-15      20     117 .]      41     143 ..      15     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 3.6e-18
                                       HHHH..HHHHHHSTTCEEEEEEETTEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHH CS
                    Acetyltransf_1  20 seee..feesfsleaegllvaeedgeliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLlealeerare 91 
                                       +  e  f++ +++e+ + +++  +ge iGf++l+   +    + ++  +  la++ ++r++G+G+  +e + e are
  gi|336255617|ref|YP_004598724.1|  41 ESIEdgFRDHLEDEEITDYLVVLEGETIGFVTLREGRHpsrRYSRYLRLVNLAIDDAHRNQGYGTVVVERVKETARE 117
                                       2222344444333333444455999*************999888899999*************************** PP

                                       TTESEEEEEEETTEHHHHHHHHH.TTE CS
                    Acetyltransf_1  92 egikkivlaveedndaairlYek.lGF 117
                                       +g++ + + +e +n+ a+r+Y +  GF
  gi|336255617|ref|YP_004598724.1| 118 QGCDHLKVSCEWHNEDARRFY-RdAGF 143
                                       ***9999989778********.66**9 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.1   2.4e-14     4e-11       3     138 .]       2     144 ..       1     144 [. 0.88

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.4e-14
                    Acetyltransf_3   3 lLrplteeDlealf.elrsdpevmr.ylpe..pltleeaeewlerawaeeseeegyg.waivlkdtgviGsvglrdl 74 
                                        L+++t++Dleal+ ++++    m+ y +e  +l+++ +ee +e+ +++  e+e+ + +++vl+++  iG+v lr+ 
  gi|336255617|ref|YP_004598724.1|   2 ELVEATADDLEALVdRWYALANAMEpY-SElnELDVDGTEESIEDGFRDHLEDEEITdYLVVLEGE-TIGFVTLREG 76 
                                       68999********967******99944.445699**********9999888888866699977777.8*******88 PP

                    Acetyltransf_3  75 eeedee.....aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                        + +++       + + ++++++++Gy+t +v+ + e a +e+g ++l + ++ +Ne  +r ++ +Gf+
  gi|336255617|ref|YP_004598724.1|  77 RHPSRRysrylRLVNLAIDDAHRNQGYGTVVVERVKETA-REQGCDHLKVSCEWHNEDARRFYRDAGFQ 144
                                       88777799998888899**********************.8888***********************96 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0     3e-13   4.9e-10      17     109 ..      43     146 ..      28     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 3e-13
                   Acetyltransf_10  17 ispealrerieegealllvaeeggkivGvielrdgs..........hisllfVdpeyrgqGigkaLleaveeeaekd 83 
                                       i+ + +r+++e++e + +++  +g+ +G+++lr+g+          ++  l++d+++r qG+g+  +e+v+e a+++
  gi|336255617|ref|YP_004598724.1|  43 IE-DGFRDHLEDEEITDYLVVLEGETIGFVTLREGRhpsrrysrylRLVNLAIDDAHRNQGYGTVVVERVKETAREQ 118
                                       44.778999988888888888899********9888899*99999999999************************** PP

                   Acetyltransf_10  84 gikl.eltvnasp.yavpfYeklGFkav 109
                                       g  + +++++ ++  a++fY+  GF++ 
  gi|336255617|ref|YP_004598724.1| 119 GCDHlKVSCEWHNeDARRFYRDAGFQPK 146
                                       ***9*********************975 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   4.7e-12   7.7e-09       5      76 .]      59     145 ..      52     145 .. 0.71

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 4.7e-12
                                       EEEEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHH.HTT....SEEEEE.EEEE....TH CS
                    Acetyltransf_7   5 vfVaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLle.aae....kgiile.qlel....na 62 
                                       ++V+  +g+ +Gf+ l +             + +la+d ++r++G+G+  +e ++e    +g+  + +  +    ++
  gi|336255617|ref|YP_004598724.1|  59 YLVV-LEGETIGFVTLREGRhpsrrysryLRLVNLAIDDAHRNQGYGTVVVErVKEtareQGCD-HlK--VscewHN 131
                                       4555.458888***99998899988765444444*****************9532245568875.222..2223433 PP

                                       HHHHHHHHHTTEEE CS
                    Acetyltransf_7  63 ekaikfYeklGFee 76 
                                       e a++fY+  GF++
  gi|336255617|ref|YP_004598724.1| 132 EDARRFYRDAGFQP 145
                                       489*********85 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   9.5e-10   1.5e-06      24      80 ..      89     146 ..      80     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 9.5e-10
                                       EEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  24 lgalqvlpehrrrGlgsrlvkalakeiaerg.ktvllvvvasNtpsirlyeklGfeki 80 
                                       l  l +++ hr++G+g+++v+ + +  +e+g +++ +    +N+ ++r+y   Gf+  
  gi|336255617|ref|YP_004598724.1|  89 LVNLAIDDAHRNQGYGTVVVERVKETAREQGcDHLKVSCEWHNEDARRFYRDAGFQPK 146
                                       677899***********************994567788999**************966 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   3.7e-07    0.0006      26     140 ..      38     146 ..       7     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.7e-07
                                       --HHHHHH.HHHHHC.STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS---TT-EEEEEEESSHHHCTTTCHHHHH CS
                    Acetyltransf_8  26 gtleevre.llakldadphsepliglldgepvgyfeiYwakedelaeyydaepgdrGiHlligeaeargkglttall 101
                                       gt+e  ++ ++++l+ d++ + +++ l+ge +g++ + + ++      +++  + r + l+i   ++r++g++t ++
  gi|336255617|ref|YP_004598724.1|  38 GTEESIEDgFRDHLE-DEEITDYLVVLEGETIGFVTLREGRHP----SRRYSRYLRLVNLAID-DAHRNQGYGTVVV 108
                                       455555552666775.********************9887777....68999**********6.67889*****999 PP

                                       HHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEE CS
                    Acetyltransf_8 102 ralvhylfadprtrrvvvEPdvrNerairllekaGfeke 140
                                       +++ + + ++ ++++  v  + +Ne a+r+++ aGf+++
  gi|336255617|ref|YP_004598724.1| 109 ERVKETAREQ-GCDHLKVSCEWHNEDARRFYRDAGFQPK 146
                                       9987766555.*************************986 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 !   17.1   0.0   2.8e-06    0.0046       7      65 ..      64     128 ..      56     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.8e-06
                   Acetyltransf_CG   7 degeevafleYe......vrkegvldfthTeVpeelrGkGiAkkLvkaalddareegl.kvvptCs 65 
                                       + ge ++f++ +      +r +  l +    +++++r +G++   v+++ + are+g    +++C+
  gi|336255617|ref|YP_004598724.1|  64 E-GETIGFVTLRegrhpsRRYSRYLRLVNLAIDDAHRNQGYGTVVVERVKETAREQGCdHLKVSCE 128
                                       4.67788888874444443334488999999**************************867888886 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.0   7.9e-06     0.013       4     135 ..       6     144 ..       3     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.9e-06
                    Acetyltransf_4   4 ateeDakei.laiy......aeyvvntaitfeyevssvee.fekflealdsekeyvflvaesdrivGyaylgqfkkr 72 
                                       at +D++++  ++y      + y + ++++ +  ++s+e+ f   le+   e+   +lv  +++ +G  +l++ +  
  gi|336255617|ref|YP_004598724.1|   6 ATADDLEALvDRWYalanamEPYSELNELDVDGTEESIEDgFRDHLED---EEITDYLVVLEGETIGFVTLREGRHP 79 
                                       566666665234553333324555555555555555555424444444...56667999999*********955544 PP

                    Acetyltransf_4  73 .akdwkaelsvyla.erdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFe 135
                                         ++   +  v+la + + +++g+g   ++ +++ ++eq+   l  +    ne +  f+   GF+
  gi|336255617|ref|YP_004598724.1|  80 sRRYSRYLRLVNLAiDDAHRNQGYGTVVVERVKETAREQGCDHLKVSCEWHNEDARRFYRDAGFQ 144
                                       356666666677776889**********************************************8 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.5     2e-05     0.033      24     132 ..       4     124 ..       2     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                    Acetyltransf_6  24 vatdpedleallelfraqwarr......pdvfadpltraflrdllaalaargalrlyvlrldgrpvAvalglrsgd. 93 
                                       v+++++dleal++++ a+ ++             + t++ ++d +++  +++ +  y + l+g+ ++++ + + ++ 
  gi|336255617|ref|YP_004598724.1|   4 VEATADDLEALVDRWYALANAMepyselN-ELDVDGTEESIEDGFRDHLEDEEITDYLVVLEGETIGFVTLREGRHp 79 
                                       56799**********99877777788852.44456777788888888888889999***********9987766656 PP

                    Acetyltransf_6  94 ......rlyywlggydpelaklspgllllweliedaaeeGlrrfd 132
                                              l +   ++d +++  + g++++ ++ e a+e+G++++ 
  gi|336255617|ref|YP_004598724.1|  80 srrysrYLRLVNLAIDDAHRNQGYGTVVVERVKETAREQGCDHLK 124
                                       653321333678899**************************9975 PP

>> DUF1462  Protein of unknown function (DUF1462)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.28      21      79 ..       7      69 ..       3      76 .. 0.83
   2 ?    0.5   0.0      0.47   7.7e+02      22      48 ..     127     153 ..     120     155 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                           DUF1462 21 tyeWleaalkrkypeqkleleyvDieeek....eeeekkefaekiledelfyPlvviedevva 79
                                      t++ lea + r y+ ++    y +++e      ee+ ++ f +++ ++e+   lvv+e+e ++
  gi|336255617|ref|YP_004598724.1|  7 TADDLEALVDRWYALANAMEPYSELNELDvdgtEESIEDGFRDHLEDEEITDYLVVLEGETIG 69
                                      78899*********9999999999988664222455677899******************986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.47
                           DUF1462  22 yeWleaalkrkypeqkleleyvDieee 48 
                                        eW +   +r y ++ ++ + vD  ++
  gi|336255617|ref|YP_004598724.1| 127 CEWHNEDARRFYRDAGFQPKQVDYAQP 153
                                       799999999********9999998765 PP

>> IMPa_N_2  Immunomodulating metalloprotease N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00016      0.26      43      83 ..      90     130 ..      87     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                                       EEEE-GGG--EEEESS-GGGSTTTTTGG.GHHHHHHHHHHH CS
                          IMPa_N_2  43 aalsekqggRalAyGtdilasmqggskeqfapllkrllnWl 83 
                                       + l    + R+ +yGt ++ +++++ +eq  + lk   +W 
  gi|336255617|ref|YP_004598724.1|  90 VNLAIDDAHRNQGYGTVVVERVKETAREQGCDHLKVSCEWH 130
                                       556777899*******************9999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.94
# Mc/sec: 497.84
//
Query:       gi|336255618|ref|YP_004598725.1|  [L=392]
Description: GTPase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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  104.3   0.0    7.9e-30  103.7   0.0    1.3  1  MMR_HSR1_C  GTPase of unknown function C-terminal
    9.1e-20   70.9   0.0    6.5e-19   68.1   0.0    2.2  2  MMR_HSR1    50S ribosome-binding GTPase
      7e-13   48.4   0.0    1.6e-12   47.3   0.0    1.6  1  TGS         TGS domain
    5.3e-10   39.0   0.0    5.5e-07   29.2   0.0    3.2  3  FeoB_N      Ferrous iron transport protein B
  ------ inclusion threshold ------
       0.02   14.4   0.1       0.54    9.8   0.0    2.8  3  GTP_EFTU    Elongation factor Tu GTP binding domain
       0.22   10.4   0.0        0.5    9.2   0.0    1.5  2  DUF463      YcjX-like family, DUF463


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 !  103.7   0.0   2.6e-33   7.9e-30       1     112 []     221     323 ..     221     323 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 2.6e-33
                        MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLeki 77 
                                       a+NK+D+ a++en+e+l e ++    v+p++A+ ElaLr+aa++gl++Y+pgde++ei +d    ++++q++aLe++
  gi|336255618|ref|YP_004598725.1| 221 AANKIDV-APEENVERLLELDK---PVIPTTAEGELALRRAADNGLVDYDPGDETLEIGDD----VNDAQREALEDL 289
                                       89*****.************88...7********************************999....************ PP

                        MMR_HSR1_C  78 rdlvlkrygsTGVqealnaavfelldlivVYPVed 112
                                       r+  + ++++TGVq aln+av++ll+ i+ YPVed
  gi|336255618|ref|YP_004598725.1| 290 RE-TMAEWDGTGVQGALNHAVYDLLEHITAYPVED 323
                                       **.99****************************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 !   68.1   0.0   2.2e-22   6.5e-19       2      87 ..       4     121 ..       3     157 .. 0.77
   2 ?   -0.2   0.0      0.35     1e+03      92     114 .]     202     224 ..     178     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 2.2e-22
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.......................EEEEECGG CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.......................ielvDtpG 55 
                                       +a++G+pN+GKSt+  a t + + v+++p+tT+d n+g   ++  +                       iel+D++G
  gi|336255618|ref|YP_004598725.1|   4 IALAGKPNAGKSTFYTAATMADVDVANYPFTTIDANRGVSYVRT-DcpclerdercnadncedgkryvpIELLDVAG 79 
                                       89************************************776331.233444444555566666666666******** PP

                                       CSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT.........T CS
                          MMR_HSR1  56 liegaseekglgkaflalee.adlillvvdas.........e 87 
                                       l+ ga+e+kglg++fl+    ad+i+ vvdas          
  gi|336255618|ref|YP_004598725.1|  80 LVPGAHEGKGLGNQFLDELTnADVIVNVVDASggtnakgepV 121
                                       999*************966669********996665443330 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  92 pldeeleelleeakkplilvlnk 114
                                       + +eel++l +e++kp+++++nk
  gi|336255618|ref|YP_004598725.1| 202 AHREELARLVRERTKPIVVAANK 224
                                       3568889999999******9998 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   5.4e-16   1.6e-12       4      59 ..     334     389 ..     331     390 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 5.4e-16
                                       EETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                               TGS   4 ytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                        +Pd+ +  lp g+t++D+Ay++h+++++  ++A   +  ++vg +++Le+gdv++Iv
  gi|336255618|ref|YP_004598725.1| 334 ILPDAHL--LPDGSTPVDLAYAVHSDIGDGYLHAVNAKsnREVGENYELEEGDVIKIV 389
                                       5677777..****************************9999****************9 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 !   29.2   0.0   1.8e-10   5.5e-07       2      42 ..       3      43 ..       2      50 .. 0.92
   2 ?    2.3   0.0     0.035   1.1e+02      77      89 ..      99     111 ..      76     114 .. 0.83
   3 ?    3.3   0.0     0.018        53     101     144 ..     211     249 ..     206     259 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.8e-10
                                      EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEE CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegkl 42
                                      ++al+G+pn+Gk+t+  a t a+ +v+N+p +t++ ++g  
  gi|336255618|ref|YP_004598725.1|  3 SIALAGKPNAGKSTFYTAATMADVDVANYPFTTIDANRGVS 43
                                      69*********************************999875 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.035
                                       TSSSEEEEEEEGG CS
                            FeoB_N  77 eepdvvvnvvdat 89 
                                       +++dv+vnvvda+
  gi|336255618|ref|YP_004598725.1|  99 TNADVIVNVVDAS 111
                                       579********96 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.018
                                       HHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTT CS
                            FeoB_N 101 llelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsak 144
                                       + e ++p+v+a n+id+a ++++e    +L  +L+ pv++t+a+
  gi|336255618|ref|YP_004598725.1| 211 VRERTKPIVVAANKIDVAPEENVE----RLL-ELDKPVIPTTAE 249
                                       568899************998764....332.366677777665 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 ?    0.1   0.0      0.17     5e+02       5      20 ..       3      18 ..       1      42 [. 0.83
   2 ?    0.2   0.0      0.15   4.6e+02      91     110 ..      98     117 ..      92     121 .. 0.82
   3 ?    9.8   0.0   0.00018      0.54     112     142 ..     205     236 ..     200     320 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.17
                                      EEEEEESTTSSHHHHH CS
                          GTP_EFTU  5 nigiighvDhGKtTLt 20
                                       i+++g  ++GK+T+ 
  gi|336255618|ref|YP_004598725.1|  3 SIALAGKPNAGKSTFY 18
                                      688999999****986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
                                       HHT-SEEEEEEETTTBSTHH CS
                          GTP_EFTU  91 lrvlDgavlvvdaveGvepq 110
                                       l  +D+ v vvda+ G +++
  gi|336255618|ref|YP_004598725.1|  98 LTNADVIVNVVDASGGTNAK 117
                                       6679**********998875 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHTTTEEEEEEESCGST.HHHHHHH CS
                          GTP_EFTU 112 eevlrlalkegvpiivfiNKmDrl.kaelkei 142
                                       ee++rl++++  pi+v+ NK+D + +++++++
  gi|336255618|ref|YP_004598725.1| 205 EELARLVRERTKPIVVAANKIDVApEENVERL 236
                                       789999999999**********9964444443 PP

>> DUF463  YcjX-like family, DUF463
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.78   2.3e+03       2      19 ..       3      20 ..       2      26 .. 0.86
   2 ?    9.2   0.0   0.00017       0.5     258     337 ..     164     245 ..     159     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.78
                            DUF463  2 rlavTGLsraGKtvfits 19
                                       +a  G   aGK++f t+
  gi|336255618|ref|YP_004598725.1|  3 SIALAGKPNAGKSTFYTA 20
                                      588899999******998 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00017
                            DUF463 258 drqivLvDvLsalnaGkealedleealaeileafryg..kssllkrlfspridkvlfaAtkaDhvtaeqhkrLeall 332
                                       d   vL+D+Ls + a++++++ + + l+   +  ++   +++ l rl+++r + +++aA k+D   +e+ +rL +l 
  gi|336255618|ref|YP_004598725.1| 164 DIDDVLADMLSGFGASPKQIATVLRELDYPEDPIQWEdaHREELARLVRERTKPIVVAANKIDVAPEENVERLLELD 240
                                       555599**************99999999888876665115689******************************9997 PP

                            DUF463 333 rqlve 337
                                       + ++ 
  gi|336255618|ref|YP_004598725.1| 241 KPVIP 245
                                       77665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2923.36
//
Query:       gi|336255619|ref|YP_004598726.1|  [L=141]
Description: hypothetical protein Halxa_4245 [Halopiger xanaduensis SH-6]
Scores for 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-34  116.5   4.2      1e-33  116.2   4.2    1.1  1  DUF2267   Uncharacterized conserved protein (DUF2267)


Domain annotation for each model (and alignments):
>> DUF2267  Uncharacterized conserved protein (DUF2267)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   4.2   5.7e-38     1e-33       1     118 [.       3     119 ..       3     122 .. 0.94

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 5.7e-38
                                       HHHHHHHHHHHHT---HHHHHHHHHHHHHHHHTTS-HHHHHHHHTTS-HHHHHHHHTT--TTS-----SHHHHHHHH CS
                           DUF2267   1 ydefleevqerlgledreeAeratravLrtLrdrlteeeaadlaaqLPeelrgllrdgwppvepgkrfdreeflerv 77 
                                       yd+f++evq+r++l++re+A ++ ra+L+tL++r++++ea++l aqLPeel ++l++ +     ++rf  +ef++rv
  gi|336255619|ref|YP_004598726.1|   3 YDDFIGEVQHRAQLDSREAALSISRATLTTLSERIQPGEAENLGAQLPEELGRFLEEVD----DAERFEFDEFVDRV 75 
                                       799******************************************************98....5679********** PP

                                       HHTS.....E...HHHHHHHHHHHHHHHS-HHHHHHHHHTS-HH CS
                           DUF2267  78 aeelgvdped...aeqaaraVfaalkealsegeiedvaaqLPkd 118
                                       ae+ +v ++d   a+ +a++V+++++ea++eg i+dv+aqLP+d
  gi|336255619|ref|YP_004598726.1|  76 AERQEVGEDDpadAAFHAQVVVDVVDEAVTEGAIDDVKAQLPDD 119
                                       ****955555555*****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1166.67
//
Query:       gi|336255620|ref|YP_004598727.1|  [L=243]
Description: GCN5-like N-acetyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-15   56.2   0.2    7.1e-15   55.3   0.2    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.2e-09   37.1   0.1    8.4e-09   35.7   0.0    1.7  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.4e-09   37.0   0.0    4.7e-09   36.6   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    7.4e-08   32.4   0.0    1.2e-07   31.7   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.2e-05   26.1   0.1    1.8e-05   25.4   0.1    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
      0.004   17.3   0.0     0.0085   16.2   0.0    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.025   14.6   0.0      0.057   13.5   0.0    1.7  1  Acetyltransf_9   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 !   55.3   0.2   2.8e-18   7.1e-15      21     117 .]     117     217 ..      98     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 2.8e-18
                                       HHHHHHHHHSTTC....EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTT CS
                    Acetyltransf_1  21 eeefeesfsleae....gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareeg 93 
                                       e ++ee + ++++     ++va  ++e++G++ l+     k  +++   + V ++yrg+G+Gs+Lle  +e+a + g
  gi|336255620|ref|YP_004598727.1| 117 EIDHEEALLRHNDlesrLFFVATVEDEVVGWVHLHAPELDKLSHTAELTVGVLEAYRGRGIGSHLLERGLEWAASSG 193
                                       333333333333334426666****************99999999999***************************** PP

                                       ESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  94 ikkivlaveedndaairlYeklGF 117
                                       ++k++  v ++n  ai+++e +G+
  gi|336255620|ref|YP_004598727.1| 194 YEKVYQSVPATNADAIGFLEAHGW 217
                                       ********999********99996 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.8   7.3e+03      12      21 ..      93     102 ..      61     114 .. 0.59
   2 !   35.7   0.0   3.3e-12   8.4e-09       3      75 ..     133     218 ..     131     219 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.8
                                       TEEEEEEEEE CS
                    Acetyltransf_7  12 gkivGfials 21 
                                        +ivG i+++
  gi|336255620|ref|YP_004598727.1|  93 TGIVGAIRVV 102
                                       4555655544 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 3.3e-12
                                       EEEEEEEETTEEEEEEEEEEES......TCTEE...EEE-GGGTTSSHHHHHHHH....TT.SEEEEE.EEEE..TH CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld......aeitr...laVdpeyrgkGiGraLlea....ae.kgiile.qlel..na 62 
                                         +fVa  ++++vG + l+  +      +       + V+++yrg+GiG+ Lle     a+ +g++ + q+ +  + 
  gi|336255620|ref|YP_004598727.1| 133 RLFFVATVEDEVVGWVHLHAPEldklshT---AeltVGVLEAYRGRGIGSHLLERglewAAsSGYEKVyQS-VpaT- 204
                                       569***********998888779876444...24569****************953344226776533222.2332. PP

                                       H.HHHHHHHHTTEE CS
                    Acetyltransf_7  63 e.kaikfYeklGFe 75 
                                       +  ai+f e +G+e
  gi|336255620|ref|YP_004598727.1| 205 NaDAIGFLEAHGWE 218
                                       2489********87 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   1.8e-12   4.7e-09       1     155 []      84     238 ..      84     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.8e-12
                    Acetyltransf_4   1 iraateeDakeil.aiyaeyvvntaitfeyevssveefekflealdsekeyvflvae.sdrivGyaylgqfkkrakd 75 
                                       ir a++ D+  i  ai+    ++t i+ e + + ++  e +l +   +++++f va  +d++vG   l +++    +
  gi|336255620|ref|YP_004598727.1|  84 IRPARQGDLTGIVgAIRVVAAEKTYIEAETVADEIDHEEALLRHN-DLESRLFFVATvEDEVVGWVHLHAPELDKLS 159
                                       788899999988624444456788999999999999999999995.899999999999***********7777669* PP

                    Acetyltransf_4  76 wkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiD 152
                                       + ael+v +  ++ + +g+g+ l++   + ++  ++e+ + ++ ++n+ +i f++a+G+e ++  ++++k    + D
  gi|336255620|ref|YP_004598727.1| 160 HTAELTVGVL-EAYRGRGIGSHLLERGLEWAASSGYEKVYQSVPATNADAIGFLEAHGWETEAVREDHYKLDADYVD 235
                                       *********8.79**********************************************************999999 PP

                    Acetyltransf_4 153 miw 155
                                       +++
  gi|336255620|ref|YP_004598727.1| 236 EVM 238
                                       986 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   4.8e-11   1.2e-07       4     109 ..     105     220 ..      96     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 4.8e-11
                   Acetyltransf_10   4 dyseegietf.kefisp.ealrerieegealllvaeeggkivGvielrdgs.....hisll..fVdpeyrgqGigka 71 
                                       +++  ++et+ +e i+  eal ++ + ++ l++va++++++vG + l   +     h + l   V ++yrg+Gig+ 
  gi|336255620|ref|YP_004598727.1| 105 EKTYIEAETVaDE-IDHeEALLRHNDLESRLFFVATVEDEVVGWVHLHAPEldklsHTAELtvGVLEAYRGRGIGSH 180
                                       4555556777444.44426777777889999**************775544465557777745589*********** PP

                   Acetyltransf_10  72 Lleaveeeaekdgikl.eltvnasp.yavpfYeklGFkav 109
                                       Lle+ +e a   g+++   +v a++  a++f e +G+++ 
  gi|336255620|ref|YP_004598727.1| 181 LLERGLEWAASSGYEKvYQSVPATNaDAIGFLEAHGWETE 220
                                       ********99******9********************986 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1     7e-09   1.8e-05       4     137 ..      84     217 ..      81     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 7e-09
                    Acetyltransf_3   4 LrplteeDlealf.elrsdpevmry...lpepltleeaeewlerawaeeseeegyg.waivlkdtgviGsvglrdle 75 
                                       +rp+++ Dl +++ ++r   +  +y    +   + + +e++l++     ++ e+   ++ +++d+ v+G+v l+  e
  gi|336255620|ref|YP_004598727.1|  84 IRPARQGDLTGIVgAIRVVAAEKTYieaETVADEIDHEEALLRH-----NDLESRLfFVATVEDE-VVGWVHLHAPE 154
                                       78888888888864554433322342213334444444444442.....2234444144444666.9*******888 PP

                    Acetyltransf_3  76 eedee..aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                        +  +  ael   + ++++g+G+++  ++  le+a +  g+e+++  + ++N   i  le  G 
  gi|336255620|ref|YP_004598727.1| 155 LDKLShtAELTVGVLEAYRGRGIGSHLLERGLEWA-ASSGYEKVYQSVPATNADAIGFLEAHGW 217
                                       7766688****************************.6677****************99999986 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 !   16.2   0.0   3.3e-06    0.0085      30      58 ..     166     194 ..     135     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.3e-06
                   Acetyltransf_CG  30 TeVpeelrGkGiAkkLvkaalddareegl 58 
                                       + V e++rG+Gi+++L ++ l++a + g+
  gi|336255620|ref|YP_004598727.1| 166 VGVLEAYRGRGIGSHLLERGLEWAASSGY 194
                                       5799********************99887 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.2e-05     0.057      36     126 ..     127     218 ..      83     219 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.2e-05
                                       HHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEE. CS
                    Acetyltransf_9  36 rklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemreegqplsl. 111
                                       ++ le+  +++a  ++e+vg ++l++ el     t    +   V+v   +rgrg+ s+Ll+r le +++ g++ ++ 
  gi|336255620|ref|YP_004598727.1| 127 HNDLESRLFFVATVEDEVVGWVHLHAPELDKLSHT----AELTVGVLEAYRGRGIGSHLLERGLEWAASSGYEKVYq 199
                                       45555566677777777777777777776533333....33469*********************999998765551 PP

                                       E--....SSHHHHHTTT-E CS
                    Acetyltransf_9 112 lfP....ssipiYrrfGye 126
                                        +P     +i++ +  G+e
  gi|336255620|ref|YP_004598727.1| 200 SVPatnaDAIGFLEAHGWE 218
                                       3455554446777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); 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:                         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 0.21s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 2083.94
//
Query:       gi|336255621|ref|YP_004598728.1|  [L=154]
Description: hypothetical protein Halxa_4247 [Halopiger xanaduensis SH-6]
Scores for 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   16.0   0.7      0.031   14.6   0.7    1.7  1  DUF3267   Putative zincin peptidase


Domain annotation for each model (and alignments):
>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.7   1.7e-06     0.031       3      99 ..      23     132 ..      21     140 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-06
                           DUF3267   3 vlvilHEllHglffklfgkkpkkkvkf.....gi.k..lliayatsseall...skkqfiiillaPfvllgilllll 68 
                                       v+++ HE +H+l+++l  +++++ v++     g+ +     ++a+++ ++    + +   +++laP++l  +l++l+
  gi|336255621|ref|YP_004598728.1|  23 VGLVAHESAHALVLRL--ARVEYTVSYfpgrdGVlGrvASCPWAVVEPTPTgrePAWILRFAALAPALL--ALPVLA 95 
                                       7899***********9..588999999553333341563333333333332111346667789999877..666666 PP

                           DUF3267  69 alllpsstl.....llllllalnaag.sagDlliall 99 
                                       a l+ + t       ++ +++l +++ s  D+ +a++
  gi|336255621|ref|YP_004598728.1|  96 AGLTVDLTAetpvlSAVAIGWLACSIpSPQDFSVAFY 132
                                       6655554445765533333333333303345666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1260.84
//
Query:       gi|336255622|ref|YP_004598729.1|  [L=248]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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   69.4   0.2    2.9e-19   68.6   0.2    1.4  1  HTH_10         HTH DNA binding domain
    0.00086   19.1   0.2     0.0039   17.1   0.0    2.2  2  MarR_2         MarR family
     0.0019   18.2   0.0      0.061   13.4   0.0    2.7  2  HTH_20         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.6   0.2       0.53   10.4   0.1    2.5  2  Sigma70_r3     Sigma-70 region 3
      0.016   14.7   0.1      0.051   13.1   0.1    1.9  1  HTH_24         Winged helix-turn-helix DNA-binding
      0.033   14.2   0.0       0.09   12.9   0.0    1.7  1  HTH_3          Helix-turn-helix
       0.04   13.8   1.2       0.13   12.1   0.2    2.5  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.088   12.3   0.0       0.22   11.1   0.0    1.7  1  Sigma70_r4     Sigma-70, region 4
       0.11   12.7   0.4        1.3    9.3   0.0    2.3  2  UPF0122        Putative helix-turn-helix protein, YlxM / p13 
       0.12   12.0   0.0       0.66    9.6   0.0    2.2  2  HTH_50         Helix-turn-helix domain
       0.13   12.4   0.1       0.38   10.9   0.0    1.7  2  Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix do
       0.14   12.1   0.4       0.83    9.7   0.1    2.5  2  HTH_11         HTH domain


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 !   68.6   0.2   1.9e-22   2.9e-19       1      52 [.     182     233 ..     182     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 1.9e-22
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT+ q+e++++A+e+GYFd+PR+vtl+eLA elGIs ++lse+Lr++   li
  gi|336255622|ref|YP_004598729.1| 182 LTEIQYETIAKAHELGYFDVPRQVTLEELAAELGISHQALSERLRRSHAALI 233
                                       9*********************************************988776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.3   3.4e+03      32      46 ..     144     158 ..     140     174 .. 0.68
   2 !   17.1   0.0   2.6e-06    0.0039      20      44 ..     203     227 ..     193     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.3
                                       TSSHHHHHHHHHHHH CS
                            MarR_2  32 glsksavsrilkrLv 46 
                                        +++ +vs + + L+
  gi|336255622|ref|YP_004598729.1| 144 YHDRESVSTAHRLLE 158
                                       566666666666655 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.6e-06
                                       SEEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2  20 rdltvgelarrlglsksavsrilkr 44 
                                       r +t  ela++lg+s++a+s +l+r
  gi|336255622|ref|YP_004598729.1| 203 RQVTLEELAAELGISHQALSERLRR 227
                                       4689*******************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 ?    1.6   0.0       0.2     3e+02      10      42 ..      46      76 ..      43      78 .. 0.83
   2 !   13.4   0.0   4.1e-05     0.061      22      46 ..     202     226 ..     195     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.2
                                      HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHH CS
                            HTH_20 10 PvRrrilraLaraegltaselaerldlskntls 42
                                      P Rr + +aL  ++  +++ +a   ++s +++s
  gi|336255622|ref|YP_004598729.1| 46 PDRRTVAQAL--EADPSVEVIANVTGGSGTEAS 76
                                      88********..999999999998887776665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.1e-05
                                       CTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  22 aegltaselaerldlskntlsyHLr 46 
                                       ++ +t++ela++l++s + ls +Lr
  gi|336255622|ref|YP_004598729.1| 202 PRQVTLEELAAELGISHQALSERLR 226
                                       6789*******************98 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0       0.1   1.5e+02      11      29 ..      49      67 ..      48      71 .. 0.86
   2 ?   10.4   0.1   0.00036      0.53      18      45 ..     202     229 ..     188     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.1
                                      HHHHHHHSSXXXHHHHHHH CS
                        Sigma70_r3 11 reLeqelgrePtpeEiAee 29
                                      r   q l+ +P++e iA+ 
  gi|336255622|ref|YP_004598729.1| 49 RTVAQALEADPSVEVIANV 67
                                      7789*************85 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00036
                                       SSXXXHHHHHHHHTXXHHHHHHHHHHHX CS
                        Sigma70_r3  18 grePtpeEiAeeLglseekVrevleaar 45 
                                        r+ t eE+A+eLg+s + + e l+ + 
  gi|336255622|ref|YP_004598729.1| 202 PRQVTLEELAAELGISHQALSERLRRSH 229
                                       5899************999999888765 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   0.1   3.4e-05     0.051      18      40 ..     205     227 ..     202     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-05
                            HTH_24  18 isqreLAerlglSpstvnrrlkr 40 
                                        +  eLA +lg+S +++++rl+r
  gi|336255622|ref|YP_004598729.1| 205 VTLEELAAELGISHQALSERLRR 227
                                       6889*****************98 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     6e-05      0.09      11      29 ..     206     224 ..     202     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6e-05
                                       HHHHHHHHHTSSHHHHHHH CS
                             HTH_3  11 sqeeLAeklGvsrstisri 29 
                                       ++eeLA++lG+s +++s  
  gi|336255622|ref|YP_004598729.1| 206 TLEELAAELGISHQALSER 224
                                       89**************975 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 ?   -2.9   0.0       4.3   6.4e+03      24      31 ..      11      18 ..      11      19 .. 0.82
   2 ?   12.1   0.2   8.5e-05      0.13      19      40 ..     206     227 ..     204     227 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.3
                     HTH_AsnC-type 24 AervGlSe 31
                                      A+r+Gl++
  gi|336255622|ref|YP_004598729.1| 11 ADRLGLAR 18
                                      89999987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.5e-05
                     HTH_AsnC-type  19 syaeLAervGlSestvlrRvrr 40 
                                       + +eLA+++G+S ++  +R+rr
  gi|336255622|ref|YP_004598729.1| 206 TLEELAAELGISHQALSERLRR 227
                                       678*****************98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.22      20      43 ..     204     227 ..     198     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                       T--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  20 glTleEIgerlgiSrerVrqiekr 43 
                                         TleE++++lgiS  + + +++r
  gi|336255622|ref|YP_004598729.1| 204 QVTLEELAAELGISHQALSERLRR 227
                                       57************9998888887 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.35   5.3e+02      53      71 ..     149     167 ..     145     191 .. 0.83
   2 ?    9.3   0.0   0.00084       1.3      34      65 ..     205     236 ..     187     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.35
                           UPF0122  53 nikrtekllekyEekLkll 71 
                                       +++++++lle+yE ++++ 
  gi|336255622|ref|YP_004598729.1| 149 SVSTAHRLLEQYEYRVEVT 167
                                       6789999******988765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00084
                           UPF0122  34 lSlsEiAeefnvsrqavydnikrtekllekyE 65 
                                         l+E+A e  +s+qa+++ ++r ++ l + E
  gi|336255622|ref|YP_004598729.1| 205 VTLEELAAELGISHQALSERLRRSHAALISAE 236
                                       679**********************9998766 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.5   2.2e+03      27      33 ..      49      55 ..      43      66 .. 0.71
   2 ?    9.6   0.0   0.00044      0.66      29      46 ..     210     227 ..     208     229 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.5
                            HTH_50 27 RklAkrL 33
                                      R++A++L
  gi|336255622|ref|YP_004598729.1| 49 RTVAQAL 55
                                      6777766 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00044
                            HTH_50  29 lAkrLGvShtaianklrk 46 
                                       lA+ LG+Sh a   +lr+
  gi|336255622|ref|YP_004598729.1| 210 LAAELGISHQALSERLRR 227
                                       89**************98 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 ?   -3.5   0.0       7.8   1.2e+04      19      27 ..      11      19 ..      11      20 .. 0.85
   2 ?   10.9   0.0   0.00026      0.38      16      37 ..     208     229 ..     205     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.8
                                      HCCTT--HH CS
                     Phage_CI_repr 19 AdlLgiaks 27
                                      Ad+Lg a++
  gi|336255622|ref|YP_004598729.1| 11 ADRLGLARA 19
                                      899**9986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00026
                                       HHHHCCTT--HHHHHHHHHSSS CS
                     Phage_CI_repr  16 keLAdlLgiakssvstwvrRdf 37 
                                       +eLA++Lgi+++ +s + rR+ 
  gi|336255622|ref|YP_004598729.1| 208 EELAAELGISHQALSERLRRSH 229
                                       59******************85 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.6   2.4e+03       6      18 ..     140     153 ..     139     161 .. 0.71
   2 ?    9.7   0.1   0.00055      0.83      15      33 ..     204     222 ..     199     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                            HTH_11   6 lelLleargp.isg 18 
                                       l+lL++ r+   ++
  gi|336255622|ref|YP_004598729.1| 140 LQLLYHDRESvSTA 153
                                       89999999994444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00055
                            HTH_11  15 pisgeeLAeeLnvSrrtvr 33 
                                       +++ eeLA eL++S ++  
  gi|336255622|ref|YP_004598729.1| 204 QVTLEELAAELGISHQALS 222
                                       59************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2004.08
//
Query:       gi|336255623|ref|YP_004598730.1|  [L=194]
Description: hypothetical protein Halxa_4249 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.097   12.4   0.0       0.12   12.1   0.0    1.1  1  RecC_C    RecC C-terminal domain


Domain annotation for each model (and alignments):
>> RecC_C  RecC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.7e-06      0.12      31     121 ..      13     102 ..       8     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.7e-06
                            RecC_C  31 eeeeeleddepfeldgLeryqlkdrlleallaeellarlrargeLPpgafGelaleelleqvealaealrallgeep 107
                                        ++++  d e f   +Lery+  + +l ++l+e + a +r +g L   ++ ++a+e   + +    ++  + +++ +
  gi|336255623|ref|YP_004598730.1|  13 ADADTGTDLESFVATNLERYADTQGVLPERLEE-FGATYREQGYLTRKQLYDIAYESSTRSAYHVERNPPERCRTVT 88 
                                       5788999*************************8.*************999999999888877766666666666665 PP

                            RecC_C 108 leslevdldlggtg 121
                                       +  l+vd d+ +++
  gi|336255623|ref|YP_004598730.1|  89 ANVLAVDDDFSKIQ 102
                                       66666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1532.30
//
Query:       gi|336255624|ref|YP_004598731.1|  [L=71]
Description: hypothetical protein Halxa_4250 [Halopiger xanaduensis SH-6]
Scores for 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   11.6   0.0       0.13   11.5   0.0    1.0  1  DUF1385   Protein of unknown function (DUF1385)


Domain annotation for each model (and alignments):
>> DUF1385  Protein of unknown function (DUF1385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.4e-06      0.13     140     186 ..       9      67 ..       5      71 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.4e-06
                           DUF1385 140 lllvlivsilvfslvgassll............lrvllrllllpvvagisYelirlagk 186
                                       l++v++v  + + +vg+   l            l+v l  ++l v+agi Y++ r+ ++
  gi|336255624|ref|YP_004598731.1|   9 LIMVVVVTAFAVLFVGWAGGLveaeavglselgLQVGLAAVFLGVIAGIWYQFSRIDEE 67 
                                       677777777777777777655799999999999999999**************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 618.49
//
Query:       gi|336255625|ref|YP_004598732.1|  [L=83]
Description: hypothetical protein Halxa_4251 [Halopiger xanaduensis SH-6]
Scores for 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:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      782  (0.0436165); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 681.88
//
Query:       gi|336255626|ref|YP_004598733.1|  [L=53]
Description: hypothetical protein Halxa_4252 [Halopiger xanaduensis SH-6]
Scores for 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  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.32u 0.20s 00:00:00.52 Elapsed: 00:00:00.35
# Mc/sec: 457.58
//
Query:       gi|336255627|ref|YP_004598734.1|  [L=341]
Description: integrase protein [Halopiger xanaduensis SH-6]
Scores for 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-09   35.4   0.0    4.4e-08   33.1   0.0    2.3  3  Phage_integrase  Phage integrase family
    3.5e-08   33.6   0.1      8e-08   32.5   0.1    1.6  1  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    0.00036   20.9   0.1       0.02   15.4   0.1    2.5  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.097   13.0   0.0       0.26   11.7   0.0    1.8  1  Phage_int_SAM_5  Phage integrase SAM-like domain
       0.17   12.4   0.0       0.47   10.9   0.0    1.7  1  HTH_40           Helix-turn-helix 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 ?   -2.3   0.0      0.93   3.3e+03      97     118 ..      13      34 ..       5      49 .. 0.68
   2 !   33.1   0.0   1.2e-11   4.4e-08       3     112 ..     118     237 ..     116     318 .. 0.85
   3 ?   -2.6   0.0       1.1   4.1e+03      35      49 ..     326     340 ..     325     340 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.93
                                       SSBETTSSB--HHHHHHHHHHH CS
                   Phage_integrase  97 lfaskrgkplsrqtvrkafkra 118
                                        f+s+r+++ +++tvr + +r+
  gi|336255627|ref|YP_004598734.1|  13 RFLSRRKQENTEKTVRSYENRL 34 
                                       4777777777777766554444 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 1.2e-11
                                       HHHHHHHHHHHCCGC...HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEE.....EEECSSSSEEEEE CS
                   Phage_integrase   3 ltedeverllaalee...slkirdklllellyetGlRisEllsLrvkdldlengvilvh.....eregKgskeravp 71 
                                       l+++++++ll++ ++      + + ++le+++  G+R++ +++L++ d++ +++++          + K+  er+v 
  gi|336255627|ref|YP_004598734.1| 118 LKPEDANALLSYFRNsntLFGTPRHAFLEVAWHVGARMGGIRALDLRDFNPDRQTLEFRhrpptLLKNKEDGERVVG 194
                                       78999999999999987778899**************************999999998878844334455556**** PP

                                       CTHHHHHHHHHHHHHH...CHCCTTTSBSSBETTSSB--HHHHH CS
                   Phage_integrase  72 lseealellkellska...leeaeksellfaskrgkplsrqtvr 112
                                       +se ++++l+++++++   ++ +e++e lf+ ++g+p s+ t+r
  gi|336255627|ref|YP_004598734.1| 195 ISEPVVKALRTYIARErfdKRDEEGREPLFCGRQGRP-SDTTFR 237
                                       ******************999999*********6655.444444 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.1
                                       --HHHHTT-BGGGEE CS
                   Phage_integrase  35 lRisEllsLrvkdld 49 
                                       lR+ E l+L+++d+d
  gi|336255627|ref|YP_004598734.1| 326 LRAEETLKLDIGDFD 340
                                       79**********987 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 !   32.5   0.1   2.2e-11     8e-08      11      79 ..      20      87 ..      12      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 2.2e-11
                                      TT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHH CS
                   Phage_int_SAM_1 11 erglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqf 79
                                      + + +++T+r+Y+++L rf+++++++g+es+ +lt  d+ ++ a +e+++ + t+l+  l +l++++++
  gi|336255627|ref|YP_004598734.1| 20 QEN-TEKTVRSYENRLTRFVQWAEDEGIESMSELTGWDLDEYRADREAADIAPTTLKGQLMTLKQLLDY 87
                                      444.79***********************************************************9987 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 !   15.4   0.1   5.5e-06      0.02      11      72 ..      19      82 ..      10      84 .. 0.78
   2 !    6.4   0.0    0.0035        13       3      34 ..      58      89 ..      57     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.5e-06
                   Phage_int_SAM_4 11 laglserTiksYlsaikrflrflkkk...apeeltkedieaYlnyLanerklsastqknalnals 72
                                       ++ +e+T++sY + ++rf+++ +     + +elt  d+ +Y ++       +++t k  l  l+
  gi|336255627|ref|YP_004598734.1| 19 KQENTEKTVRSYENRLTRFVQWAEDEgieSMSELTGWDLDEYRADRE-AADIAPTTLKGQLMTLK 82
                                      4556899****************944777899999999999999877.77778888777666665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0035
                   Phage_int_SAM_4  3 erfrealrlaglserTiksYlsaikrflrflk 34
                                      +++r  +++a+++++T k  l ++k++l+++ 
  gi|336255627|ref|YP_004598734.1| 58 DEYRADREAADIAPTTLKGQLMTLKQLLDYCA 89
                                      6788999**********************996 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 ?   11.7   0.0   7.2e-05      0.26       9      93 ..      14      98 ..       9     104 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.2e-05
                                      HTHHHHTTS-HHHHHHHHHHHHHTTTS-..S---TTT--HHHHHHHHHHH..HHTS---HHHHHHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_5  9 yiekkkkkgskgtlrnykstlkhlkkFlkkkditfeeidkefleeFedYL..kkkkglsentiskyfkklkavlnkAik 85
                                      +++++k++++++t+r+y++ l+++ ++   +d  +e + +    + ++Y   ++   ++++t + ++ +lk++l ++ +
  gi|336255627|ref|YP_004598734.1| 14 FLSRRKQENTEKTVRSYENRLTRFVQWA--EDEGIESMSELTGWDLDEYRadREAADIAPTTLKGQLMTLKQLLDYCAS 90
                                      5566666666666777777666666666..554444444444555555554448889***************9999999 PP

                                      TTS--S-H CS
                   Phage_int_SAM_5 86 egilkknp 93
                                       ++++++ 
  gi|336255627|ref|YP_004598734.1| 91 IDVVDNDL 98
                                      99888775 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013      0.47       3      47 ..     285     325 ..     283     337 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                            HTH_40   3 eetlelleeglsieeIAkerglkesTIegHLaelieegeeidler 47 
                                        +t++ l +gl ie +A + +  + TI +H  ++ e +e   +e+
  gi|336255627|ref|YP_004598734.1| 285 SITWQ-LLQGLAIETVAGRVNARPETIRRHYYRASEWEE---FEE 325
                                       58999.568*********************999988864...333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 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:                        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: 0.48u 0.19s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 2930.17
//
Query:       gi|336255628|ref|YP_004598735.1|  [L=140]
Description: transcriptional regulator PadR family protein [Halopiger xanaduensis SH-6]
Scores for 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-12   45.7   0.7    1.1e-11   44.6   0.7    1.5  2  PadR      Transcriptional regulator PadR-like family
     0.0016   18.2   0.0     0.0022   17.8   0.0    1.3  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
     0.0047   16.9   0.0     0.0078   16.2   0.0    1.3  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.028   14.6   0.0      0.037   14.2   0.0    1.3  1  FUR       Ferric uptake regulator family
      0.032   14.1   1.1       0.33   10.9   0.1    2.6  3  MarR_2    MarR family
      0.057   13.3   0.0      0.081   12.8   0.0    1.2  1  HxlR      HxlR-like helix-turn-helix
      0.058   13.9   0.0       0.13   12.8   0.0    1.6  1  HTH_27    Winged helix DNA-binding domain
      0.066   13.1   0.0       0.12   12.3   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB


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 !   44.6   0.7   4.7e-15   1.1e-11       6      71 ..      53     111 ..      50     115 .. 0.89
   2 ?   -0.8   0.0       0.7   1.6e+03      31      43 ..     110     122 ..     110     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 4.7e-15
                                       CCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                              PadR   6 eeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71 
                                       +++ syG++i+++le  + g  e+++G+lY +L++L + glve++  +    ++++ Y lTd+G+ 
  gi|336255628|ref|YP_004598735.1|  53 ADETSYGLAIKRQLEPQY-G--EVNHGRLYSNLDSLVERGLVEKSTLD----KRTNEYVLTDDGHG 111
                                       45667************8.5..8**********************998....59**********85 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.7
                                       HHHHHHHHHHHHH CS
                              PadR  31 eGslYpaLkrLek 43 
                                       +G lY+  +rL +
  gi|336255628|ref|YP_004598735.1| 110 HGLLYQRVERLAD 122
                                       7999**9999987 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 !   17.8   0.0   9.9e-07    0.0022      50      84 ..      76     110 ..      47     115 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.9e-07
                           DUF1495  50 gkrynsessLielGLveeeeeseglklYklteeGi 84 
                                       g  y++ +sL+e+GLve+ + ++ ++ Y lt+ G 
  gi|336255628|ref|YP_004598735.1|  76 GRLYSNLDSLVERGLVEKSTLDKRTNEYVLTDDGH 110
                                       5679999**********9999************97 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.5e-06    0.0078      34      68 ..      76     115 ..      71     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.5e-06
                            HTH_45  34 kllnkYLdmLvekgli.....kkskekYvlTekGlellek 68 
                                        +l + Ld Lve+gl+     +k++++YvlT+ G  ll +
  gi|336255628|ref|YP_004598735.1|  76 GRLYSNLDSLVERGLVekstlDKRTNEYVLTDDGHGLLYQ 115
                                       56777899*******988888999***********99843 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.7e-05     0.037      29      75 ..      62     108 ..      43     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSS CS
                               FUR  29 vykelkeedpeislaTVYrtLklleeaglvkelefedgesryelakk 75 
                                       + ++l+ ++ e+    +Y +L+ l e+glv++ ++++ ++ y l+++
  gi|336255628|ref|YP_004598735.1|  62 IKRQLEPQYGEVNHGRLYSNLDSLVERGLVEKSTLDKRTNEYVLTDD 108
                                       7789999999999****************************999864 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.12   2.7e+02       2      17 ..      35      50 ..      34      70 .. 0.81
   2 ?   10.9   0.1   0.00015      0.33      41      61 ..      81      99 ..      69     100 .. 0.86
   3 ?   -2.9   0.0       2.9   6.5e+03      41      48 ..     116     123 ..     113     132 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.12
                                      T--HHHHHHHHHHHCT CS
                            MarR_2  2 gltpaqarvLaaLgrr 17
                                      +l++ q++vL a++r 
  gi|336255628|ref|YP_004598735.1| 35 DLSGFQRDVLEAIARL 50
                                      5667799*****9985 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00015
                                      HHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 41 ilkrLvaaGLverrpgpeDkR 61
                                       l+ Lv++GLve+++   DkR
  gi|336255628|ref|YP_004598735.1| 81 NLDSLVERGLVEKSTL--DKR 99
                                      7999**********99..999 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.9
                                       HHHHHHHT CS
                            MarR_2  41 ilkrLvaa 48 
                                       +++rL +a
  gi|336255628|ref|YP_004598735.1| 116 RVERLADA 123
                                       44444443 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.6e-05     0.081      23      72 ..      65     112 ..      55     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-05
                                       HHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGG CS
                              HxlR  23 elkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrsl 72 
                                       +l+ +++++ +  L ++L  L + gl+e++++++  +  eY lt+ G+ l
  gi|336255628|ref|YP_004598735.1|  65 QLEPQYGEVNHGRLYSNLDSLVERGLVEKSTLDKRTN--EYVLTDDGHGL 112
                                       788899999************************9988..********976 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 ?   12.8   0.0   5.7e-05      0.13      37      68 .]      80     109 ..      68     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.7e-05
                            HTH_27  37 yslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       ++l+ L+e+GLve+++   d+r+  + lTd G
  gi|336255628|ref|YP_004598735.1|  80 SNLDSLVERGLVEKSTL--DKRTNEYVLTDDG 109
                                       6899********66655..69*********98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.4e-05      0.12      34      56 ..      73      95 ..      69     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
                                      SSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 34 vprskvYevLrsLedkGlVerek 56
                                      v + + Y+ L sL+++GlVe++ 
  gi|336255628|ref|YP_004598735.1| 73 VNHGRLYSNLDSLVERGLVEKST 95
                                      778899**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 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:                        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: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1157.86
//
Query:       gi|336255629|ref|YP_004598736.1|  [L=86]
Description: phage PhiH1 repressor-like protein [Halopiger xanaduensis SH-6]
Scores for 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      0.074   12.9   0.0    1.5  2  OST-HTH   OST-HTH/LOTUS domain


Domain annotation for each model (and alignments):
>> OST-HTH  OST-HTH/LOTUS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.41   7.4e+03      24      40 ..      11      26 ..       8      31 .. 0.52
   2 ?   12.9   0.0   4.1e-06     0.074      12      34 ..      52      74 ..      49      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.41
                                      HHHHHHHHHHHHSST-S CS
                           OST-HTH 24 lsrlgslykkkygksfd 40
                                      l++   +y +  g + +
  gi|336255629|ref|YP_004598736.1| 11 LDDAILEYVRDAG-EVP 26
                                      4555555555445.444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.1e-06
                                      HHHHHTTTTSBEHHHHHHHHHHH CS
                           OST-HTH 12 elLrsdpdgwvslsrlgslykkk 34
                                      +lL++ +dg +sl++lg+ y ++
  gi|336255629|ref|YP_004598736.1| 52 DLLNRTDDGYYSLAELGERYLEE 74
                                      79******************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 752.83
//
Query:       gi|336255630|ref|YP_004598737.1|  [L=94]
Description: hypothetical protein Halxa_4256 [Halopiger xanaduensis SH-6]
Scores for 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:                       344  (0.0191868); 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:                         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 0.18s 00:00:00.53 Elapsed: 00:00:00.33
# Mc/sec: 853.73
//
Query:       gi|336255631|ref|YP_004598738.1|  [L=336]
Description: orc1/cdc6 family replication initiation protein [Halopiger xanaduensis SH-6]
Scores for 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-12   46.6   5.3    6.2e-11   43.0   0.0    3.2  3  AAA_16           AAA ATPase domain
    8.7e-11   42.3   0.1    6.1e-10   39.5   0.0    2.2  3  AAA_22           AAA domain
    3.4e-07   30.7   0.1    2.2e-06   28.1   0.1    2.3  1  AAA              ATPase family associated with various cellul
    1.2e-06   28.8   0.3    4.3e-06   27.0   0.3    2.0  1  AAA_assoc_2      AAA C-terminal domain
    3.9e-05   23.4   0.0    7.2e-05   22.6   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
    5.5e-05   23.2   0.1      0.003   17.5   0.0    2.4  2  ATPase_2         ATPase domain predominantly from Archaea
    9.4e-05   22.6   0.6     0.0019   18.4   0.0    2.8  2  AAA_33           AAA domain
    0.00011   22.1   0.1    0.00033   20.7   0.0    1.9  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00012   21.4   0.0    0.00054   19.2   0.0    1.9  2  DUF815           Protein of unknown function (DUF815)
    0.00017   21.5   0.1      0.001   19.0   0.1    2.0  1  Bac_DnaA         Bacterial dnaA  protein
    0.00038   20.4   0.0    0.00061   19.7   0.0    1.4  1  NACHT            NACHT domain
    0.00055   20.5   0.0     0.0013   19.3   0.0    1.9  1  ABC_tran         ABC transporter
    0.00061   20.3   0.3     0.0033   18.0   0.0    2.3  2  AAA_18           AAA domain
     0.0016   18.2   0.4     0.0072   16.1   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
     0.0023   17.9   0.0      0.038   14.0   0.0    2.3  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0026   17.7   0.1      0.053   13.4   0.0    2.3  2  NTPase_1         NTPase
     0.0038   16.5   0.0     0.0073   15.5   0.0    1.6  2  NB-ARC           NB-ARC domain
     0.0047   16.5   0.0     0.0091   15.5   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
     0.0054   16.0   0.0      0.013   14.7   0.0    1.7  1  TIP49            TIP49 P-loop domain
     0.0055   17.1   0.0     0.0097   16.3   0.0    1.5  1  RNA_helicase     RNA helicase
     0.0065   16.2   0.1      0.023   14.4   0.0    1.9  2  AAA_24           AAA domain
     0.0072   16.1   0.1      0.039   13.7   0.0    2.1  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.034   13.9   0.0    1.8  1  AAA_30           AAA domain
      0.022   13.4   0.0      0.034   12.8   0.0    1.2  1  PEPCK_ATP        Phosphoenolpyruvate carboxykinase
      0.025   14.7   0.0      0.052   13.7   0.0    1.5  1  Mannitol_dh      Mannitol dehydrogenase Rossmann domain
      0.032   14.0   0.1      0.063   13.0   0.1    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.033   14.6   1.8        0.2   12.1   0.4    2.7  2  AAA_17           AAA domain
      0.041   13.2   0.3       0.12   11.7   0.1    1.9  2  ATPase           KaiC
      0.048   14.0   0.6        0.3   11.4   0.5    2.3  1  AAA_19           AAA domain
      0.049   14.1   0.0       0.12   12.9   0.0    1.7  1  AAA_23           AAA domain
      0.052   13.4   0.0       0.24   11.3   0.0    1.9  2  RsgA_GTPase      RsgA GTPase
      0.056   12.9   0.2       0.21   11.0   0.0    2.1  1  TniB             Bacterial TniB protein
      0.064   13.5   0.0       0.14   12.4   0.0    1.7  1  AAA_28           AAA domain
      0.065   13.3   0.1       0.18   11.8   0.1    1.8  1  AAA_14           AAA domain
      0.066   12.9   0.0       0.15   11.6   0.0    1.6  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.094   12.4   0.2       0.36   10.5   0.1    2.0  2  HrpB1_HrpK       Bacterial type III secretion protein (HrpB1_
      0.095   12.1   0.0       0.18   11.2   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.11   12.2   0.0       0.97    9.2   0.0    2.2  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.18   10.4   0.0       0.28    9.8   0.0    1.2  1  AAA_13           AAA domain


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   1.3e-13   6.2e-11       2      52 ..      17      70 ..      16     103 .. 0.85
   2 ?    3.8   0.2      0.15        70     126     157 ..     111     143 ..     108     149 .. 0.78
   3 ?    0.8   0.4       1.2   5.5e+02      68     106 ..     210     248 ..     143     317 .. 0.66

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.3e-13
                            AAA_16  2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd..g 52
                                      l+ R++ + qL++al+++++g++ e+vl+ G+sG+GK++l+r + r le++  +
  gi|336255631|ref|YP_004598738.1| 17 LYHRDAKIGQLADALRPIADGDTgENVLIFGPSGTGKTTLARFVVRKLEREtlD 70
                                      899**********************************************99552 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.15
                            AAA_16 126 llallsrderplvlvlDdlqwade.aslqllaa 157
                                       +++++++ ++ ++ ++D+++ +++ ++lq+l++
  gi|336255631|ref|YP_004598738.1| 111 FIDRIRESDKRVIAIVDEVDVLEDdTTLQALYE 143
                                       78888888999*********7766256666765 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.2
                            AAA_16  68 pysa.laqalareellrqlldeaesaeleawrekleeala 106
                                        y+a +a    ++e +  l ++a+s +++++r ++++ + 
  gi|336255631|ref|YP_004598738.1| 210 DYIAdVAAGD-AREAIGILRSAARSVSRDDDRSQITTGVI 248
                                       4444333333.33666666666666666666666555444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   1.3e-12   6.1e-10       6     121 ..      41     148 ..      36     159 .. 0.85
   2 ?   -0.4   0.0       2.9   1.3e+03      54      92 ..     157     201 ..     150     248 .. 0.72
   3 ?   -1.9   0.0       8.1   3.7e+03      52      53 ..     285     286 ..     237     320 .. 0.51

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.3e-12
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.....fvtlpsstsskdllrellralglelkaerlssee 77 
                                         ++++G+sGtGKTtl+r ++++l         ++e++     + ++ s++s +++l  + r+ gl+++   +++  
  gi|336255631|ref|YP_004598738.1|  41 ENVLIFGPSGTGKTTLARFVVRKL---------ERETLdfrwgYHNCISGSSKTEVLYGIMRDAGLGADL--KKTGS 106
                                       5689********************.........5666666677**********************98777..88888 PP

                            AAA_22  78 llealeqalraravielliiDEaqhlrs.eealeeLrsllnlsrk 121
                                          a+ + +r+ +++++ i+DE++ l + ++ l+ L ++ n   +
  gi|336255631|ref|YP_004598738.1| 107 PTMAFIDRIRESDKRVIAIVDEVDVL-EdDTTLQALYEIPN--VT 148
                                       888899999999998999********.55999999999988..43 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.9
                            AAA_22  54 kdllrellralglelka.erlsseell.ealeqalrarav....i 92 
                                       +dl+ +l + ++++l + e+l+++++  ++l + l+ar +    +
  gi|336255631|ref|YP_004598738.1| 157 DDLFAHLDSRVQSRLRSaETLTLDRFKhDQLVDILQARIRaglrP 201
                                       678888888888888888777777777777777777766544444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 8.1
                            AAA_22  52 ss 53 
                                         
  gi|336255631|ref|YP_004598738.1| 285 PA 286
                                       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 !   28.1   0.1   4.7e-09   2.2e-06       1     127 [.      43     170 ..      43     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.7e-09
                                       EEEESSTTSSHHHHHHHHHHHHTHE........EEEEETTTCSSS.............STTHHHHHHHHHHHHHHHT CS
                               AAA   1 vllyGppGtGKTllakavakelgve........fleisgsellsk.............yvgesekkirelfkeakek 56 
                                       vl++Gp GtGKT+la+ v+++l++e           isgs+ + +              ++++ + + +++++++e+
  gi|336255631|ref|YP_004598738.1|  43 VLIFGPSGTGKTTLARFVVRKLEREtldfrwgyHNCISGSSKT-EvlygimrdaglgaDLKKTGSPTMAFIDRIRES 118
                                       799******************9755444444442223333333.135666666666656788888888899999988 PP

                                       STSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEE CS
                               AAA  57 akpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrk 127
                                        k +i ++DE+d l  +           ++++L++          +v++i++t ++d+l   l  +R++++
  gi|336255631|ref|YP_004598738.1| 119 DKRVIAIVDEVDVLEDDT----------TLQALYEI--------PNVTIIAITINEDDLFAHLD-SRVQSR 170
                                       866999999999994333..........45555432........23777777777777777777.676665 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 !   27.0   0.3   9.3e-09   4.3e-06       6      51 ..     203     264 ..     199     280 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 9.3e-09
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.................XXXXXXXXXXX CS
                       AAA_assoc_2   6 kleddalealaeladGDaRkaLnlLElaaeaaeak................egkieitledl 51 
                                       ++++da++++a++a GDaR a+ +L  aa++ +++                +  +ei le +
  gi|336255631|ref|YP_004598738.1| 203 TITPDAIDYIADVAAGDAREAIGILRSAARSVSRDddrsqittgvinqvraAALEEIHLERV 264
                                       6899***************************9999455555554444444444444555555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.6e-07   7.2e-05       5      88 ..      21     106 ..      17     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.6e-07
                                       SHHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSST CS
                   Sigma54_activat   5 sealkelleqikkvaktd..lsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFt 79 
                                       ++++ +l + ++ +a+ d   +vli G sGtGK++lar + ++ +r++  f       i+ +  +  L+G+ + a  
  gi|336255631|ref|YP_004598738.1|  21 DAKIGQLADALRPIADGDtgENVLIFGPSGTGKTTLARFVVRKLERETLDFRWGYHNCISGSSKTEVLYGIMRDAGL 97 
                                       5666677777777886665589********************99999988875444445555567889999999999 PP

                                       TTSS-BEHH CS
                   Sigma54_activat  80 GAekekkGl 88 
                                       GA+ +k+G 
  gi|336255631|ref|YP_004598738.1|  98 GADLKKTGS 106
                                       999999986 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 !   17.5   0.0   6.6e-06     0.003      11      46 ..      31      66 ..      20      91 .. 0.84
   2 ?    3.5   0.1      0.13        58     109     131 ..     111     133 ..      93     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.6e-06
                          ATPase_2 11 leeilerepneiyfiYGpegsGKtaLlkeiienled 46
                                      l+ i++ ++ e ++i+Gp g GKt+L + ++ +le 
  gi|336255631|ref|YP_004598738.1| 31 LRPIADGDTGENVLIFGPSGTGKTTLARFVVRKLER 66
                                      6778999999*******************9999854 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.13
                          ATPase_2 109 llekikkkgkkiiiiiDelqkli 131
                                       +++ i+++ k++i i+De+  l 
  gi|336255631|ref|YP_004598738.1| 111 FIDRIRESDKRVIAIVDEVDVLE 133
                                       678899************98765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   4.1e-06    0.0019       2      28 ..      43      69 ..      43      72 .. 0.90
   2 ?    1.0   0.3      0.93   4.3e+02     114     137 ..     228     252 ..     131     257 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.1e-06
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavll 28
                                      vl+ G++G+GK+tla+ +++kl  ++l
  gi|336255631|ref|YP_004598738.1| 43 VLIFGPSGTGKTTLARFVVRKLERETL 69
                                      6889*****************987776 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.93
                            AAA_33 114 RlakRaang.ddrsevpeealdrqk 137
                                       R a+R+ ++ ddrs+ ++ ++++ +
  gi|336255631|ref|YP_004598738.1| 228 RSAARSVSRdDDRSQITTGVINQVR 252
                                       4455555544455666666666655 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 !   20.7   0.0   7.2e-07   0.00033       1      85 [.      42     141 ..      42     174 .. 0.85
   2 ?   -1.9   0.0       6.5     3e+03      36      73 ..     204     258 ..     185     276 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 7.2e-07
                                       EEEEE--SSSSHHHHHHHGGGGB.....S--EEEEE--TT--HHHHH--B--............--------..... CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.....nreveyvqltrdtteedlkgrreik...ngttslvdsplvraar..... 64 
                                       +vl+ Gp+GtgK++la+ + + l       ++ y ++ ++ +++++++++  +   + + + + sp +  +      
  gi|336255631|ref|YP_004598738.1|  42 NVLIFGPSGTGKTTLARFVVRKLeretlDFRWGYHNCISGSSKTEVLYGIMRDaglGADLKKTGSPTMAFIDrires 118
                                       699***************999998888899999***************99977888778888888888554489999 PP

                                       .G-SEEEEESGGG--.HHHHHHH CS
                             AAA_5  65 .egeilvlDEverae.sevlnsL 85 
                                        +  i+++DEv+ +e + +l++L
  gi|336255631|ref|YP_004598738.1| 119 dKRVIAIVDEVDVLEdDTTLQAL 141
                                       88888999999999945555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.5
                                       --HHHHH--B--.........--------.................G-SEEEEES CS
                             AAA_5  36 tteedlkgrreikngttslvdsplvraar.................egeilvlDE 73 
                                       +t++ + +  +++ g+++   ++l  aar                 + + + l+E
  gi|336255631|ref|YP_004598738.1| 204 ITPDAIDYIADVAAGDAREAIGILRSAARsvsrdddrsqittgvinQVRAAALEE 258
                                       6777888888888888888888888888866666665544444444444444444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06   0.00054      29      82 ..      16      69 ..       6      71 .. 0.91
   2 ?   -1.2   0.1         2   9.1e+02      98     128 ..     111     141 ..     106     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                            DUF815 29 dLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeegL 82
                                      dL   d++  +l +  +  ++g + +nvL++G  GtGK +l +++++++++e+L
  gi|336255631|ref|YP_004598738.1| 16 DLYHRDAKIGQLADALRPIADGDTGENVLIFGPSGTGKTTLARFVVRKLERETL 69
                                      67788899999999**********************************999987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                            DUF815  98 lvellrerperfilfvDDLsFeeeeeeyksL 128
                                        ++ +re+++r+i  vD +   e++++ ++L
  gi|336255631|ref|YP_004598738.1| 111 FIDRIRESDKRVIAIVDEVDVLEDDTTLQAL 141
                                       57899************99988888887766 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   2.2e-06     0.001      36     209 ..      42     227 ..      27     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-06
                                       -EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEE...EEHHHHHHHHHHHHHT...........T-HHHHHHHHTT- CS
                          Bac_DnaA  36 PlfiygevGlGktHLlkaignevlenapelrvvY...ltaeeFlnelvkalrd...........kkaeefkeklrkv 98 
                                        ++i+g++G Gkt L + +  ++++++ + r  Y   +++ + ++ l  ++rd           + + +f +++r+ 
  gi|336255631|ref|YP_004598738.1|  42 NVLIFGPSGTGKTTLARFVVRKLERETLDFRWGYhncISGSSKTEVLYGIMRDaglgadlkktgSPTMAFIDRIRES 118
                                       589****************************9996666777778888888888444333322222234555666666 PP

                                       S...EEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-E.EEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHH CS
                          Bac_DnaA  99 D...vLliDDiqflagkektqeelfhtfnalleegkq.vvlssDrsPkeleeledrlrsrfeaGlvvdieppdletr 171
                                       D   + ++D++  l++ +        t++al+e  +  ++  +  +   +++l++r++sr++   +  +++  ++  
  gi|336255631|ref|YP_004598738.1| 119 DkrvIAIVDEVDVLEDDT--------TLQALYEIPNVtIIAITINEDDLFAHLDSRVQSRLRSAETLTLDRFKHDQL 187
                                       644344556666665555........7777777655404444556677889************************** PP

                                       HHHHHHHHHHTT--..--TTHHHHHHHH--S-HHHHHHHH CS
                          Bac_DnaA 172 lailkkkieaekle..vpeevlefiaervtdnvRelegal 209
                                       ++il+ +i+a      ++++++ +ia+    + Re  g l
  gi|336255631|ref|YP_004598738.1| 188 VDILQARIRAGLRPgtITPDAIDYIADVAAGDAREAIGIL 227
                                       *******997544355*************99999977655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.3e-06   0.00061       3      98 ..      43     137 ..      41     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-06
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.....-HCHHHCCCCTS--SSS-CCHHHHC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna..rsladllfsqlpepaapvsevwavll 77 
                                       v++ G++G GKTtL++ +++++ +++l+   f+  ++ + +  s+ +       +  l ++l++ ++p   ++  + 
  gi|336255631|ref|YP_004598738.1|  43 VLIFGPSGTGKTTLARFVVRKLERETLD---FRWGYHNCISGSSKTEVLygIMRDAGLGADLKKTGSPTMAFIDRIR 116
                                       7899**********************65...58888888888888887765444667999999999999999999** PP

                                       CSCCCEEEEEE-STT-SS-TC CS
                             NACHT  78 elperlLlilDglDelvtdlg 98 
                                       e  +r+  i+D +D l++d  
  gi|336255631|ref|YP_004598738.1| 117 ESDKRVIAIVDEVDVLEDDTT 137
                                       **************9998755 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.8e-06    0.0013      10      37 ..      39      66 ..      36     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.8e-06
                                      TTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 10 egekvaivGenGaGKStLlkllagllkp 37
                                       ge v i+G++G+GK+tL++ + ++l+ 
  gi|336255631|ref|YP_004598738.1| 39 TGENVLIFGPSGTGKTTLARFVVRKLER 66
                                      699*****************99998765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   7.2e-06    0.0033       1      24 [.      43      66 ..      43     176 .. 0.83
   2 ?   -0.4   0.0       3.4   1.6e+03     103     119 ..     257     273 ..     229     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.2e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf 24
                                      +l+ G++G+GKttla+ + ++l+ 
  gi|336255631|ref|YP_004598738.1| 43 VLIFGPSGTGKTTLARFVVRKLER 66
                                      79****************998744 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.4
                            AAA_18 103 peelleRlekRgyeeak 119
                                       +e++leR+e+ g++++ 
  gi|336255631|ref|YP_004598738.1| 257 EEIHLERVEDLGTHKRL 273
                                       69999999999988765 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 !   16.1   0.0   1.6e-05    0.0072      45      68 ..      38      61 ..       7      78 .. 0.81
   2 ?   -0.8   0.1       2.3   1.1e+03     100     159 ..     112     168 ..      82     188 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-05
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialg 68
                                      ++ en++++GpsG+GK+ la  + 
  gi|336255631|ref|YP_004598738.1| 38 DTGENVLIFGPSGTGKTTLARFVV 61
                                      678****************97655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.3
                         IstB_IS21 100 aralkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpfaewdevlg 159
                                         ++++  k  + i+D++ +l+ d+   + l+e+ +  +   +i i  +  fa+ d+ ++
  gi|336255631|ref|YP_004598738.1| 112 IDRIRESDKRVIAIVDEVDVLE-DDTTLQALYEIPN--VTIIAITINEDDLFAHLDSRVQ 168
                                       5566666666777888877766.3444556666633..2333444444445555555555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   8.3e-05     0.038       7      44 ..      24      65 ..      18      70 .. 0.76
   2 ?    1.2   0.0      0.73   3.3e+02      29      63 ..      81     119 ..      80     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.3e-05
                                      HHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  7 tealgkklakal....gdvilLeGdLGaGKTtlvrglakalg 44
                                      + +l+ +l   +    g+ +l+ G+ G+GKTtl+r ++++l+
  gi|336255631|ref|YP_004598738.1| 24 IGQLADALRPIAdgdtGENVLIFGPSGTGKTTLARFVVRKLE 65
                                      5566666666447555667*******************9986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.73
                                       TSSHHHHHHHHHHHTT--....----TTTTSEEEEEE.. CS
                              TsaE  29 GaGKTtlvrglakalgve....evkSPTFtlveeYelek 63 
                                       G+ KT    g+++  g+     +  SPT + + + ++++
  gi|336255631|ref|YP_004598738.1|  81 GSSKTEVLYGIMRDAGLGadlkKTGSPTMAFIDRIRESD 119
                                       6779999999999776633477899***99988776554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00012     0.053       1      27 [.      42      68 ..      42      73 .. 0.89
   2 ?    1.9   0.1      0.41   1.9e+02     118     159 ..     112     156 ..     100     188 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                                      EEEEE--TTSSHHHHHHHHHHHH...G CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssg 27
                                      +v+i Gp+G+GKtTl + v+++l+++ 
  gi|336255631|ref|YP_004598738.1| 42 NVLIFGPSGTGKTTLARFVVRKLERET 68
                                      58999******************8775 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.41
                                       HHHHHTTTSEEEEE--SS-...-SHHHHHHHT-TT-EEEE--TTT CS
                          NTPase_1 118 veevLksekpvlavihrrk...dlalveeirerkdvkvfevteen 159
                                       ++++ +s+k v+a++ + +   d   ++ + e  +v+++ +t ++
  gi|336255631|ref|YP_004598738.1| 112 IDRIRESDKRVIAIVDEVDvleDDTTLQALYEIPNVTIIAITINE 156
                                       556666777777777766666666667777777777777666554 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.6e-05    0.0073      17     111 ..      38     128 ..      20     194 .. 0.73
   2 ?   -2.2   0.0       4.2   1.9e+03      58      79 ..     233     254 ..     208     276 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                                       TSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHH CS
                            NB-ARC  17 elqslvvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddleekeeveslk 93 
                                       + +   v + G  G GKttla+ +++k++  +  F       +s ++k e +   i+++ +l  d  +  +      
  gi|336255631|ref|YP_004598738.1|  38 DTG-ENVLIFGPSGTGKTTLARFVVRKLERETLDFRWGYHNCISGSSKTEVLY-GIMRDAGLGADLKKTGSPTMAFI 112
                                       444.56889******************88888789855555667666555444.47777777655444444444455 PP

                                       HHHHHHCCCTTEEEEEEE CS
                            NB-ARC  94 rklvrlLltkrfllvlDD 111
                                       +++++   +kr++ + D 
  gi|336255631|ref|YP_004598738.1| 113 DRIRE--SDKRVIAIVDE 128
                                       66665..46677777774 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.2
                                       EEESXXHHHHHHHXXHHHHHCC CS
                            NB-ARC  58 vvsktdkseeiletilkeLsls 79 
                                       +vs+ d+ ++i+  +++++  +
  gi|336255631|ref|YP_004598738.1| 233 SVSRDDDRSQITTGVINQVRAA 254
                                       6899999999998888888655 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 !   15.5   0.0     2e-05    0.0091      33      62 ..      40      69 ..      37      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-05
                             AAA_7 33 kkpvllvGptGtGKtviikdllkkldkeky 62
                                      + +vl+ Gp+GtGKt++++ +++kl++e++
  gi|336255631|ref|YP_004598738.1| 40 GENVLIFGPSGTGKTTLARFVVRKLERETL 69
                                      689**********************98765 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.9e-05     0.013      49     106 ..      39      95 ..      31     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  49 aGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqalrks 106
                                       +G  vL+ GpsgtGkt la  + ++l +++        +  s   +ktevl   +r +
  gi|336255631|ref|YP_004598738.1|  39 TGENVLIFGPSGTGKTTLARFVVRKLERETLDFRWGYHNCIS-GSSKTEVLYGIMRDA 95 
                                       5899**********************9665443444444444.568899998888865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.1e-05    0.0097       1      48 [.      43      92 ..      43     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl...klkkkdsvysrnpeddfwdgYt 48
                                      ++++Gpsg+GK+tla+ ++++l+++         ++++s+++++++++g  
  gi|336255631|ref|YP_004598738.1| 43 VLIFGPSGTGKTTLARFVVRKLERETldfRWGY-HNCISGSSKTEVLYGIM 92
                                      689********************7764433333.45666777777777765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.1e-05     0.023       3      20 ..      41      58 ..      39      70 .. 0.86
   2 ?   -1.5   0.0       3.7   1.7e+03     113     133 ..     110     130 ..     102     160 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-05
                            AAA_24  3 lkiliyGpsgiGKTtlak 20
                                       ++li+Gpsg+GKTtla+
  gi|336255631|ref|YP_004598738.1| 41 ENVLIFGPSGTGKTTLAR 58
                                      589*************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.7
                            AAA_24 113 rllkklqelrknvifiahekt 133
                                        ++++++e +k vi+i  e  
  gi|336255631|ref|YP_004598738.1| 110 AFIDRIRESDKRVIAIVDEVD 130
                                       567777777776666654443 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 !   13.7   0.0   8.5e-05     0.039      33      59 ..      40      66 ..      30      72 .. 0.87
   2 ?   -0.8   0.1       2.5   1.1e+03      87      87 ..     123     123 ..      81     171 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.5e-05
                            RuvB_N 33 ldhvllyGpPGlGkttlakiiakelgv 59
                                       + vl++Gp G Gkttla+ + ++l+ 
  gi|336255631|ref|YP_004598738.1| 40 GENVLIFGPSGTGKTTLARFVVRKLER 66
                                      5789***************99998875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.5
                            RuvB_N  87 v 87 
                                       +
  gi|336255631|ref|YP_004598738.1| 123 I 123
                                       2 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.3e-05     0.034      20     105 ..      42     137 ..      26     152 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.3e-05
                            AAA_30  20 vavltGpAGtGKttalkalreaweaag........grviglAptgkaAkvLaeelgi......eastiakllkrlkg 82 
                                        +++ Gp GtGKtt+ + +++ +e++           + g + t+     ++ ++g+      ++s +  +++r ++
  gi|336255631|ref|YP_004598738.1|  42 NVLIFGPSGTGKTTLARFVVRKLERETldfrwgyhNCISGSSKTEVLYGIMR-DAGLgadlkkTGSPTMAFIDRIRE 117
                                       47889**************999999977888887433334444444333344.444422222244555555555553 PP

                            AAA_30  83 rarlepgtllivDEagmvdtkql 105
                                           +++ + ivDE+ ++  +++
  gi|336255631|ref|YP_004598738.1| 118 ---SDKRVIAIVDEVDVLEDDTT 137
                                       ...45667888888887744444 PP

>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.3e-05     0.034     208     230 ..      38      60 ..      29      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.3e-05
                                       .TS-EEEEEE-TTSSHHHHH-BT CS
                         PEPCK_ATP 208 kkgdvalfFGLSGtGKTtLsadp 230
                                       ++g+  l FG SGtGKTtL+   
  gi|336255631|ref|YP_004598738.1|  38 DTGENVLIFGPSGTGKTTLARFV 60 
                                       4567889************8655 PP

>> Mannitol_dh  Mannitol dehydrogenase Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   0.00011     0.052      44     145 ..      99     204 ..      84     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
                                       HHHHTTTT-EEEEE-SSS---EEEE--EEEEEEGGG-HHHHHHHHTSTT--EEEE---TTTBETTTEB-TTSHHHHH CS
                       Mannitol_dh  44 eaLkaqdelyvviekgeeskearlvgsvnavlsveedlealieamaePeirivsltvtekGidatgeletdlpaiaa 120
                                       ++Lk+  + ++  ++   ++++r++  v +v   e+d  +l ++ + P++ i+++t+ e        + +   +++ 
  gi|336255631|ref|YP_004598738.1|  99 ADLKKTGSPTMAFIDRIRESDKRVIAIVDEVDVLEDD-TTLQALYEIPNVTIIAITINEDD-----LFAHLDSRVQS 169
                                       578888888888899999999****999999999988.99999999*************33.....33333345666 PP

                                       HHH-TT..........HHHHHHHHHHHTT----EE CS
                       Mannitol_dh 121 dlakpe..........llvealkrrraaglkplti 145
                                        l+ +e           lv++l+ r  agl p ti
  gi|336255631|ref|YP_004598738.1| 170 RLRSAEtltldrfkhdQLVDILQARIRAGLRPGTI 204
                                       66666666666666678999999999999999887 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 ?   13.0   0.1   0.00014     0.063      22      38 ..      40      56 ..      32      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                            AAA_29 22 kgatlltGpsGsGKSTl 38
                                       +++l+ GpsG+GK+Tl
  gi|336255631|ref|YP_004598738.1| 40 GENVLIFGPSGTGKTTL 56
                                      449*************8 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   0.00043       0.2       1     129 [.      46     174 ..      46     178 .. 0.67
   2 ?   -1.1   0.0         5   2.3e+03      57      99 ..     226     266 ..     199     307 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00043
                                       EE-TTSSHHHHHHHHHHHH.........TEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky.........gfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiae 67 
                                       +G+ G GK+t+++ +v+k+         g++    G+   e+     l +  rd+   ++l+++   +   +++i+e
  gi|336255631|ref|YP_004598738.1|  46 FGPSGTGKTTLARFVVRKLeretldfrwGYHNCISGSSKTEV-----LyGIMRDAGLGADLKKTGSPTMAFIDRIRE 117
                                       69***************9955555444433333223322222.....223345555566777777788889999999 PP

                                       HHHSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH.TTST-TS CS
                            AAA_17  68 eakkkgvlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd.rtrgrdd 129
                                        +k+  ++vd   ++ e++  l+ l      e+   +ii + ++++++++++ ++ ++r r+ 
  gi|336255631|ref|YP_004598738.1| 118 SDKRVIAIVDEVDVL-EDDTTLQALY-----EIPNVTIIAITINEDDLFAHLDSRvQSRLRSA 174
                                       999999999999876.4444455444.....57667899999999999999888866776665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5
                                       HHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHHHH CS
                            AAA_17  57 lqkeaaekiaeeakkkgvlvdghprikeqagfldglpkevlee 99 
                                       +++ aa+++ ++++ +  + +g   ++ +a +l+++  e +e+
  gi|336255631|ref|YP_004598738.1| 226 ILRSAARSVSRDDD-RSQITTGVI-NQVRAAALEEIHLERVED 266
                                       44444444444322.222222222.222333333333333333 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00026      0.12      19      46 ..      40      66 ..      37     152 .. 0.79
   2 ?   -1.7   0.0       3.2   1.5e+03      81     131 ..     158     215 ..     151     266 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                            ATPase 19 grvvlitGepGtGKtifalqFlikgaek 46
                                      g+ vli G +GtGKt++a +F+++ +e+
  gi|336255631|ref|YP_004598738.1| 40 GENVLIFGPSGTGKTTLA-RFVVRKLER 66
                                      789*************98.688888776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.2
                            ATPase  81 gklaiidasesaeesaee...kdkedleelieelaeaike.ika...krvviDsitgl 131
                                       +++a +d   +++ +++e    d+++ ++l++ l+  i++ ++    +   iD i+ +
  gi|336255631|ref|YP_004598738.1| 158 DLFAHLDSRVQSRLRSAEtltLDRFKHDQLVDILQARIRAgLRPgtiTPDAIDYIADV 215
                                       5666666666666666666665666777777777666664222311133334444444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00064       0.3      10      38 ..      40      68 ..      32     154 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00064
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelg 38
                                       +++l+ ++ GtGKT++ + +v+ l++++
  gi|336255631|ref|YP_004598738.1| 40 GENVLIFGPSGTGKTTLARFVVRKLERET 68
                                      6789***************9999998765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00025      0.12      22      38 ..      43      59 ..      39      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00025
                            AAA_23 22 tlItGpNGaGKTTildA 38
                                      +lI+Gp G+GKTT+ ++
  gi|336255631|ref|YP_004598738.1| 43 VLIFGPSGTGKTTLARF 59
                                      59************876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00051      0.24      98     127 ..      39      68 ..      15      76 .. 0.77
   2 ?   -1.1   0.0       3.3   1.5e+03      49      99 ..     122     169 ..     111     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00051
                                       TTSEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelkt 127
                                       +++ +++ G+SG GK+tL   ++ +le +t
  gi|336255631|ref|YP_004598738.1|  39 TGENVLIFGPSGTGKTTLARFVVRKLERET 68 
                                       45778999**********999998888776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.3
                                       EEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  49 pvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd 99 
                                       ++ ++  +D+le+++   +l++ +e  +++++++  ++ + +++l +++++
  gi|336255631|ref|YP_004598738.1| 122 VIAIVDEVDVLEDDT---TLQALYEIPNVTIIAITINEDDLFAHLDSRVQS 169
                                       455556667777766...777778888888888888888888888877766 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00045      0.21      27      63 ..      32      67 ..      17     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00045
                              TniB 27 leypkrkrmpnlllvGdsnnGKtmivekFarlhppek 63
                                         ++ +  +n+l++G+s +GKt+++ +F  ++ +++
  gi|336255631|ref|YP_004598738.1| 32 RPIADGDTGENVLIFGPSGTGKTTLA-RFVVRKLERE 67
                                      4445555668*************987.5665555544 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00031      0.14       2      18 ..      43      59 ..      42     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00031
                            AAA_28  2 ivitGgestGKTtllea 18
                                      + i+G+++tGKTtl++ 
  gi|336255631|ref|YP_004598738.1| 43 VLIFGPSGTGKTTLARF 59
                                      89************964 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00039      0.18       4     118 ..      42     172 ..      39     182 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00039
                            AAA_14   4 ilvitGaRrvGKTtllkqlikell................vkkesilyinldderd....kkladpe.kllelilek 59 
                                        ++i G+  +GKTtl++ ++++l                  +k ++ly  + d  +    kk   p+  +++ i+e+
  gi|336255631|ref|YP_004598738.1|  42 NVLIFGPSGTGKTTLARFVVRKLEretldfrwgyhncisgSSKTEVLYGIMRDAGLgadlKKTGSPTmAFIDRIRES 118
                                       689************99999988866444443333333333333333333333222322222222212222333332 PP

                            AAA_14  60 lkeekktylflDEiqevpewekalkslvdegknldvivtGSnskllskeiatslagrva 118
                                          +k+ + + DE+  +++  ++l+ l++   n+ +i+   n  +l  ++ ++++ r  
  gi|336255631|ref|YP_004598738.1| 119 ---DKRVIAIVDEVDVLED-DTTLQALYEIP-NVTIIAITINEDDLFAHLDSRVQSRLR 172
                                       ...4667777788776665.67777777777.777777776666666666666666655 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 ?   11.6   0.0   0.00034      0.15       6      38 ..      29      64 ..      25      93 .. 0.83
   2 ?   -2.8   0.0       8.8   4.1e+03     149     175 ..     112     136 ..      99     159 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                                      HHHS-EBTT-E...EEEEESTTSSHHHHHHHHHHHS CS
                                      xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  6 DalfpivqGqr...tlipgafgvGktvisqslskqs 38
                                      Dal pi+ G +   +li+g +g+Gkt++++ ++++ 
  gi|336255631|ref|YP_004598738.1| 29 DALRPIADGDTgenVLIFGPSGTGKTTLARFVVRKL 64
                                      899999976543339**************9888775 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.8
                                       HTTSEEETSSEEEEEEEEEEE-GGCST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 149 yERagkapdrtGsvtivaavspaggDf 175
                                       ++R+ +   ++  + iv  v + ++D 
  gi|336255631|ref|YP_004598738.1| 112 IDRIRES--DKRVIAIVDEVDVLEDDT 136
                                       4444444..233555555555555554 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 ?   -1.1   0.0         3   1.4e+03      33      52 ..       1      20 [.       1      36 [. 0.71
   2 ?   10.5   0.1   0.00078      0.36      22      73 ..     179     232 ..     162     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3
                        HrpB1_HrpK 33 lLdalrvLrPevaeldlleg 52
                                      ++d  r+L+P+ +  dl+  
  gi|336255631|ref|YP_004598738.1|  1 MIDNARALKPSHVPSDLYHR 20
                                      68999999999888887755 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00078
                        HrpB1_HrpK  22 lasedtedaellLda.lrv.LrPevaeldllegvlliergrweeAlrlLrevea 73 
                                       l+  +++++ ++L+a +r+ LrP + + d+++ +  ++ g+  eA+ +Lr+   
  gi|336255631|ref|YP_004598738.1| 179 LDRFKHDQLVDILQArIRAgLRPGTITPDAIDYIADVAAGDAREAIGILRSAAR 232
                                       56667888888888856645******************************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 ?   11.2   0.0   0.00038      0.18      22      42 ..      40      60 ..      26      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                      Mg_chelatase 22 gHnlllvGppGsGKtmlakrl 42
                                      g n+l++Gp+G+GKt la+ +
  gi|336255631|ref|YP_004598738.1| 40 GENVLIFGPSGTGKTTLARFV 60
                                      469***************866 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0021      0.97       3      20 ..      42      59 ..      40      73 .. 0.78
   2 ?    0.2   0.0       1.2   5.5e+02      89     110 ..     119     140 ..      94     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                         PduV-EutP  3 killiGkvgsGKttLtqa 20
                                      ++l++G++g+GKttL++ 
  gi|336255631|ref|YP_004598738.1| 42 NVLIFGPSGTGKTTLARF 59
                                      799************864 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.2
                         PduV-EutP  89 nkeviGiitkidlaedeeniea 110
                                        k vi i+  +d+ ed+  ++a
  gi|336255631|ref|YP_004598738.1| 119 DKRVIAIVDEVDVLEDDTTLQA 140
                                       6899********9999888876 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0006      0.28      20      42 ..      44      67 ..      38      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0006
                            AAA_13 20 liYGwNGaGKTtLSrll.rslelg 42
                                      li+G  G+GKTtL+r+  r+le++
  gi|336255631|ref|YP_004598738.1| 44 LIFGPSGTGKTTLARFVvRKLERE 67
                                      7**************752666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.36
# Mc/sec: 2777.28
//
Query:       gi|336255632|ref|YP_004598739.1|  [L=40]
Description: hypothetical protein Halxa_4258 [Halopiger xanaduensis SH-6]
Scores for 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:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); 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: 0.30u 0.22s 00:00:00.52 Elapsed: 00:00:00.33
# Mc/sec: 363.09
//
Query:       gi|336255633|ref|YP_004598740.1|  [L=156]
Description: hypothetical protein Halxa_4259 [Halopiger xanaduensis SH-6]
Scores for 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   22.4   0.0    0.00016   21.8   0.0    1.2  1  Vps36_ESCRT-II  Vacuolar protein sorting protein 36 Vps36
  ------ inclusion threshold ------
       0.46   10.5   0.1       0.46   10.5   0.1    2.2  3  FixQ            Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> Vps36_ESCRT-II  Vacuolar protein sorting protein 36 Vps36
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.8e-08   0.00016      10      70 ..       7      60 ..       3      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.8e-08
                    Vps36_ESCRT-II 10 LeenEsiilvqdnVglYegdeKilnrqnGrlyLTthriiyvdsadpkkeslslelklvesv 70
                                      L+e+Es++    +V+ Y++++ ++++++G+l +T +r+++v+++ ++     + l+ v s+
  gi|336255633|ref|YP_004598740.1|  7 LQEKESVV---ARVEAYDDKDAMTDHRKGELAVTPNRVVFVRNKVVSD----ISLNGVDSI 60
                                      66666665...47999*************************9988777....555555555 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.3         2   1.8e+04      28      32 ..      71      75 ..      71      76 .. 0.53
   2 ?   10.5   0.1   5.2e-05      0.46       8      27 ..      94     113 ..      90     115 .. 0.89
   3 ?   -2.1   0.0      0.43   3.9e+03      23      31 ..     143     151 ..     142     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 2
                              FixQ 28 yafrp 32
                                      y+++ 
  gi|336255633|ref|YP_004598740.1| 71 YLYWA 75
                                      55553 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 5.2e-05
                              FixQ   8 gfadswgllflvllfygvvi 27 
                                        +a++ gll ++++f+g+v+
  gi|336255633|ref|YP_004598740.1|  94 PIAQFSGLLGFTAVFAGIVL 113
                                       68****************96 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.43
                              FixQ  23 ygvviyafr 31 
                                       ++++++a+r
  gi|336255633|ref|YP_004598740.1| 143 LAAIAHALR 151
                                       689999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1164.38
//
Query:       gi|336255634|ref|YP_004598741.1|  [L=86]
Description: hypothetical protein Halxa_4260 [Halopiger xanaduensis SH-6]
Scores for 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  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 702.95
//
Query:       gi|336255635|ref|YP_004598742.1|  [L=61]
Description: hypothetical protein Halxa_4261 [Halopiger xanaduensis SH-6]
Scores for 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:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.33
# Mc/sec: 549.60
//
Query:       gi|336255636|ref|YP_004598743.1|  [L=144]
Description: hypothetical protein Halxa_4262 [Halopiger xanaduensis SH-6]
Scores for 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:                       784  (0.043728); 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:                         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: 0.37u 0.18s 00:00:00.55 Elapsed: 00:00:00.33
# Mc/sec: 1305.86
//
Query:       gi|336255637|ref|YP_004598744.1|  [L=607]
Description: hypothetical protein Halxa_4263 [Halopiger xanaduensis SH-6]
Scores for 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  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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 0.24s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4416.67
//
Query:       gi|336255638|ref|YP_004598745.1|  [L=173]
Description: hypothetical protein Halxa_4264 [Halopiger xanaduensis SH-6]
Scores for 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  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1364.34
//
Query:       gi|336255639|ref|YP_004598746.1|  [L=270]
Description: hypothetical protein Halxa_4265 [Halopiger xanaduensis SH-6]
Scores for 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   15.0   0.2      0.048   13.8   0.0    1.7  2  T4_Rnl2_C  T4 RNA ligase 2 C-terminal


Domain annotation for each model (and alignments):
>> T4_Rnl2_C  T4 RNA ligase 2 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.7e-06     0.048      13      36 ..     166     190 ..     153     198 .. 0.80
   2 ?   -3.1   0.1      0.51   9.2e+03      52      57 ..     234     239 ..     215     250 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-06
                                       HHGGG--HHHHHHHHHTSS.--STT CS
                         T4_Rnl2_C  13 eierYvtenRLnNviSKig.eitrk 36 
                                        +e+Y+  nRL+  iSK+g +i+++
  gi|336255639|ref|YP_004598746.1| 166 LVEEYLAANRLRGRISKMGlQIQKD 190
                                       5899***************777654 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.51
                                       HHHHT. CS
                         T4_Rnl2_C  52 dfnkee 57 
                                        f +++
  gi|336255639|ref|YP_004598746.1| 234 GFVEDY 239
                                       333443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.19s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2250.08
//
Query:       gi|336255640|ref|YP_004598747.1|  [L=177]
Description: phosphoesterase PA-phosphatase-like protein [Halopiger xanaduensis SH-6]
Scores for 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-14   52.5  11.1    2.7e-12   46.6  11.1    2.2  1  PAP2      PAP2 superfamily
    2.8e-07   30.4   7.6    2.8e-07   30.4   7.6    1.5  1  PAP2_3    PAP2 superfamily
  ------ inclusion threshold ------
      0.043   14.3   1.1      0.043   14.3   1.1    1.7  2  PAP2_C    PAP2 superfamily C-terminal


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6  11.1   4.5e-16   2.7e-12      51     129 ..      81     152 ..      50     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 4.5e-16
                              PAP2  51 eakesfPSgHsafafalalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaala 127
                                        ++++fPSgH++ +++++ lla+ ++++ +          ++++++ va sR+++gvH+++DvlaG+ +G+a ++la
  gi|336255640|ref|YP_004598747.1|  81 IGGYGFPSGHALGSTVVYGLLAHRIGTRHAV-------IGAAVVVAIVATSRIAIGVHYPTDVLAGVGMGAAYLVLA 150
                                       4567***************************.......7*********************************99998 PP

                              PAP2 128 yr 129
                                         
  gi|336255640|ref|YP_004598747.1| 151 LS 152
                                       75 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   7.6   4.8e-11   2.8e-07     126     189 ..      85     148 ..      72     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 4.8e-11
                            PAP2_3 126 afPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvDviaGvalalvaia 189
                                        fPS H+  +++v+ +l++   +r   + a++++++++++ +a g HY +Dv+aGv ++++ ++
  gi|336255640|ref|YP_004598747.1|  85 GFPSGHALGSTVVYGLLAHRIGTRHAVIGAAVVVAIVATSRIAIGVHYPTDVLAGVGMGAAYLV 148
                                       5******98888777767666677566777788888999******************9998765 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.71   4.3e+03      54      63 ..      30      39 ..      18      44 .. 0.76
   2 ?   14.3   1.1   7.2e-06     0.043       8      64 ..      88     142 ..      85     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.71
                            PAP2_C 54 YtvDVllgly 63
                                      Y+v Vl+g++
  gi|336255640|ref|YP_004598747.1| 30 YSVVVLVGMI 39
                                      8888888886 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.2e-06
                            PAP2_C   8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyi 64 
                                       SGH++  t+++ ++ +    ++    + +++++++   + ia   HY  DVl g+ +
  gi|336255640|ref|YP_004598747.1|  88 SGHALGSTVVYGLLAHRIGTRH--AVIGAAVVVAIVATSRIAIGVHYPTDVLAGVGM 142
                                       9****99999988888888887..66777788888888999999********99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1429.54
//
Query:       gi|336255641|ref|YP_004598748.1|  [L=389]
Description: hypothetical protein Halxa_4267 [Halopiger xanaduensis SH-6]
Scores for 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   15.8   0.0      0.021   15.0   0.0    1.3  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.04   14.0   0.0      0.089   12.9   0.0    1.6  1  HTH_28           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Sigma54_activ_2  Sigma-54 interaction 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      12      50 ..     114     153 ..     108     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-06
                                       HHHHHHHT-SS-EEEE.EETT--HHHHHHCC--TTS-EE- CS
                   Sigma54_activ_2  12 erLeqaaqsklpvflt.GekGsgkelvArlLhknsgpwle 50 
                                       +rL+++++  +pv ++ Ge G+gk+ +A+lL + +++w++
  gi|336255641|ref|YP_004598748.1| 114 TRLQEIVAGPAPVIIVlGEMGAGKTDFAGLLGQLRERWVD 153
                                       79999**9999998744*********************97 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     1e-05     0.089      10      41 ..     345     376 ..     339     379 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                            HTH_28  10 aaGhsvreaArelgisrrtvyrWikryeegGi 41 
                                        +G+s+re+A+ +  s+ tv+ W k  + gG+
  gi|336255641|ref|YP_004598748.1| 345 RQGMSARETAEFVPYSHATVSNWWKEIDNGGE 376
                                       4799*********************9999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2992.54
//
Query:       gi|336255642|ref|YP_004598749.1|  [L=132]
Description: hypothetical protein Halxa_4268 [Halopiger xanaduensis SH-6]
Scores for 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:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1044.55
//
Query:       gi|336255643|ref|YP_004598750.1|  [L=579]
Description: DNA methylase N-4/N-6 domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-47  160.1   5.6    9.2e-45  153.1   5.6    2.4  1  N6_N4_Mtase      DNA methylase
    1.5e-05   25.0   0.0      4e-05   23.6   0.0    1.8  2  Mrr_cat          Restriction endonuclease
     0.0021   17.8   1.2       0.19   11.4   0.1    2.9  4  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
     0.0024   17.7   0.1      0.032   14.0   0.0    2.3  2  Methyltransf_31  Methyltransferase domain
      0.005   17.5   0.0      0.057   14.1   0.0    2.5  2  Methyltransf_25  Methyltransferase domain
     0.0072   16.0   0.1      0.029   14.0   0.0    1.9  2  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.047   13.4   0.0      0.089   12.5   0.0    1.4  1  UPF0020          Putative RNA methylase family UPF0020
       0.17   12.5   0.0         40    4.9   0.0    2.7  2  Methyltransf_11  Methyltransferase domain


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 !  153.1   5.6   4.1e-48   9.2e-45       2     225 ..      26     380 ..      25     386 .. 0.84

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 4.1e-48
                                       EEEEE--SSSSSCS....................................................GCCGCCHHHHH CS
                       N6_N4_Mtase   2 dlivtdpPYntgkdy...............................................endeqyeeedsyeey 31 
                                       dli+ dpP+n +++y                                               +   ++ +++++ +y
  gi|336255643|ref|YP_004598750.1|  26 DLIYLDPPFNSNRNYniifeeqasadahaqvqafedtwqwdhksaktyqevvkeggpvgdtlKGLGETIGKNDMLAY 102
                                       89****************************************99999999999999999999777777777889*** PP

                                       HHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHHHHHTT-EEEEEEEEEEESSSTTTSTCC...S-B--EEEE CS
                       N6_N4_Mtase  32 leflekvlkevrrvLkddgsifiniddseikkelkaladeifggffllnvivwkkpnsmpesnkd...rltsthEyi 105
                                       l+ + ++lke++rvLkd+g++++++d    ++ lk+l+d +fg   +ln ivwk++ s  +++++   r  + h+ i
  gi|336255643|ref|YP_004598750.1| 103 LSMMAPRLKELHRVLKDTGTLWLHCDPTASHY-LKLLLDSVFGPEQFLNEIVWKRS-SAHSDASQgmeRCGRIHDII 177
                                       *******************************9.**********99999*****888.444444445669******** PP

                                       EEEESSTT-.................................................................... CS
                       N6_N4_Mtase 106 lvfsknkkyl................................................................... 115
                                       +v+sk+++y+                                                                   
  gi|336255643|ref|YP_004598750.1| 178 FVYSKTDEYKwntvytpyseeyleqeynnkdergyyketdltankpggdteykwpvkrkksgdsgweadldeeykdp 254
                                       **********9999988888888888888888888888888888888888888888888888877777777777777 PP

                                       .................---GGGSSBSS-HHHHHHHHHH.............CHHHCC-B--BSEEE-SCCCTTSTT CS
                       N6_N4_Mtase 116 ................lkfnldaikvpyeekdklekrga.............ytskkkgkkiediWdlseiqsnekk 163
                                                       +        +++e  ++ +++ +             y  +  g++++diW  ++i+++ + 
  gi|336255643|ref|YP_004598750.1| 255 kpgweykqvdpysgryW-------AYSKENMKEFARNDKlhhrrtgmprlkqYAEEMPGVPLQDIW--TDIPPESGD 322
                                       77777777744444333.......333333333333333444444788888888888888888888..999999999 PP

                                       S-CHH----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHH CS
                       N6_N4_Mtase 164 skgdtkkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeey 225
                                       ++ +    +p+qkP++ller+Ik+ t++gd+vlDpF+G GtT+ +a++l+r+++Gi+i   +
  gi|336255643|ref|YP_004598750.1| 323 KDLG----YPTQKPEELLERVIKSGTDEGDVVLDPFCGCGTTVSVAERLNRRWVGIDITHLA 380
                                       9987....9************************************************98655 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         6   1.4e+04      34      57 ..     214     236 ..     201     243 .. 0.57
   2 !   23.6   0.0   1.8e-08     4e-05      29     101 ..     437     511 ..     413     537 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 6
                                       SSB--EEEETTEEEEEEEEEEE-- CS
                           Mrr_cat  34 ggiDliakkdplgserilvqaKry 57 
                                       +  Dl+a+k + g+ ++   +Kr+
  gi|336255643|ref|YP_004598750.1| 214 KETDLTANKPG-GDTEYKWPVKRK 236
                                       45788888755.444444444443 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 1.8e-08
                                       -B-TTSSB--EEEETTEEEE.....EEEEEEE--TS-B-HHHHHHHHHHCTTS..SEEEEEESS-B-HHHHHHHHTT CS
                           Mrr_cat  29 grsgDggiDliakkdplgse.....rilvqaKryknkvgvkeVqeligalkkrgadkgifvttsdftkaAreeaeel 100
                                       +++ D+giD+ ++  p +se     +il  +K   +++g  +V++l+g++  + a  g+f+t  + t+a ++ea++ 
  gi|336255643|ref|YP_004598750.1| 437 KKGPDQGIDGQLRFFPDKSEamepeEILFSVKS--GNTGPSDVRDLAGTVRREDAAMGVFITLEEPTDAMEKEAAS- 510
                                       6789******974444333334445*******9..99******************************999999977. PP

                                       - CS
                           Mrr_cat 101 n 101
                                       +
  gi|336255643|ref|YP_004598750.1| 511 H 511
                                       3 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 !   11.4   0.1   8.4e-05      0.19     175     221 ..      22      68 ..      11      80 .. 0.74
   2 ?   -2.9   0.0         2   4.4e+03      31      71 ..      80     118 ..      70     143 .. 0.76
   3 ?   -2.2   0.2       1.1   2.6e+03      75      94 ..     185     207 ..     154     222 .. 0.66
   4 ?    3.7   0.0     0.018        41      14      61 ..     338     387 ..     333     414 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.4e-05
                                       -TTE.EEEE--S-T.S...TS--GGGG.CS-HHHHHHHHHHHHHH....H CS
                   MethyltransfD12 175 kieddivYlDPPYnprqytanytlyetlafsdedevrlaevlksls...s 221
                                       ++ +d++YlDPP n+    +ny +  +++ s + +++ +++ ++++   +
  gi|336255643|ref|YP_004598750.1|  22 DEMADLIYLDPPFNS---NRNYNIIFEEQASADAHAQVQAFEDTWQwdhK 68 
                                       56689*********7...88888888888888888888888887775432 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2
                                       TSCCHHCS...SSCEEEEES-HHHHHHHHHHCCHSHHHHHH CS
                   MethyltransfD12  31 ggaVffeakkqgkkvlinDinedlinlykaliknnveelik 71 
                                       gg V+  +k  g+++  nD++++l  ++ +l++   ++++k
  gi|336255643|ref|YP_004598750.1|  80 GGPVGDTLKGLGETIGKNDMLAYLSMMAPRLKE--LHRVLK 118
                                       677888888888899999999999988885555..344444 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.1
                                       .TCTTGGC.TSHHHHHHHH...H CS
                   MethyltransfD12  75 kllekeelenereyfyelr...e 94 
                                       ++++++ ++ ++e+++e++   +
  gi|336255643|ref|YP_004598750.1| 185 EYKWNTVYTPYSEEYLEQEynnK 207
                                       34677777777777777663331 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.018
                                       CCS-....--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHH CS
                   MethyltransfD12  14 elipkd..kgktfvepFaGggaVffeakkqgkkvlinDinedlinlykal 61 
                                       ++i++    g+++ +pF+G g     a + + + +  Di    i+l+k  
  gi|336255643|ref|YP_004598750.1| 338 RVIKSGtdEGDVVLDPFCGCGTTVSVAERLNRRWVGIDITHLAISLMKHR 387
                                       45555566789********9988766666788888888888888888755 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.17   3.7e+02      81     108 ..      97     124 ..       5     143 .. 0.79
   2 !   14.0   0.0   1.4e-05     0.032       3      49 ..     346     389 ..     344     401 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.17
                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggill 108
                                       n+ l++l+ ++  l+e++rvlk+ g l 
  gi|336255643|ref|YP_004598750.1|  97 NDMLAYLSMMAPRLKELHRVLKDTGTLW 124
                                       5667777777888889999999999876 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.4e-05
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaq 49 
                                       +g +vlD+ CG G+ + ++  +l+   + vGiDi+  ai+l++ +++
  gi|336255643|ref|YP_004598750.1| 346 EGDVVLDPFCGCGTTVSVAE-RLN--RRWVGIDITHLAISLMKHRLE 389
                                       6789***7777776666665.765..58***************9977 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.63   1.4e+03      84      97 .]     108     121 ..      96     121 .. 0.77
   2 !   14.1   0.0   2.6e-05     0.057       1      46 [.     350     392 ..     350     423 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.63
                                       HHHHHHHHHEEEEE CS
                   Methyltransf_25  84 kalkeiarvLkpgG 97 
                                         lke++rvLk+ G
  gi|336255643|ref|YP_004598750.1| 108 PRLKELHRVLKDTG 121
                                       4599*******988 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.6e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl 46 
                                       vLd  cG G+++  +a+rl + +++g+Di++ ++  +++r+e +g+
  gi|336255643|ref|YP_004598750.1| 350 VLDPFCGCGTTV-SVAERL-NRRWVGIDITHLAISLMKHRLE-AGF 392
                                       89999****665.556666.5*******************95.444 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.3e-05     0.029      95     134 ..       7      45 ..       1      63 [. 0.77
   2 ?   -1.2   0.0      0.62   1.4e+03      42      55 ..     347     360 ..     340     390 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                                       EEEES-HHHHCTS--SS-EEEEEEE--SSSTTCH.HHHHH CS
                     Cons_hypoth95  95 elkedaleallklakkkeefdivflDPPyakellieevle 134
                                        +  d+le l+++   +e  d+++lDPP++++  ++ ++e
  gi|336255643|ref|YP_004598750.1|   7 LYYGDNLEILRQH-IDDEMADLIYLDPPFNSNRNYNIIFE 45 
                                       5566677766666.677889***********998777666 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.62
                                       C-EEEETT-TTSHH CS
                     Cons_hypoth95  42 garvLDlfaGsGal 55 
                                       g  vLD f+G G+ 
  gi|336255643|ref|YP_004598750.1| 347 GDVVLDPFCGCGTT 360
                                       5679******9975 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.9e-05     0.089      23      41 ..     341     359 ..     338     402 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                                       HTT--TTS-EEETT-TTSH CS
                           UPF0020  23 lagwkpgepllDPmCGsGt 41 
                                        +g ++g++ lDP+CG Gt
  gi|336255643|ref|YP_004598750.1| 341 KSGTDEGDVVLDPFCGCGT 359
                                       5899**************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.021        48      72      95 ..     101     124 ..      95     125 .. 0.79
   2 ?    4.9   0.0     0.018        40       5      40 ..     355     390 ..     351     417 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.021
                                       CC-CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  72 hhvedpekalkeiaRvLkpgGllv 95 
                                        ++  ++  lke++RvLk  G+l 
  gi|336255643|ref|YP_004598750.1| 101 AYLSMMAPRLKELHRVLKDTGTLW 124
                                       5556666779***********986 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.018
                                       -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCH CS
                   Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekase 40 
                                       cG G  +   ++  +r vg+D+++ ++ l k++ + 
  gi|336255643|ref|YP_004598750.1| 355 CGCGTTVSVAERLNRRWVGIDITHLAISLMKHRLEA 390
                                       6666666666666699***********999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); 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: 0.57u 0.21s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 4463.66
//
Query:       gi|336255644|ref|YP_004598751.1|  [L=59]
Description: hypothetical protein Halxa_4270 [Halopiger xanaduensis SH-6]
Scores for 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  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); 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:                         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 0.21s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 471.36
//
Query:       gi|336255645|ref|YP_004598752.1|  [L=293]
Description: hypothetical protein Halxa_4271 [Halopiger xanaduensis SH-6]
Scores for 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:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2172.58
//
Query:       gi|336255646|ref|YP_004598753.1|  [L=539]
Description: hypothetical protein Halxa_4272 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.001   18.8   0.0     0.0022   17.7   0.0    1.6  1  HTH_38    Helix-turn-helix domain
     0.0029   17.8   0.1      0.031   14.5   0.0    2.6  2  HTH_17    Helix-turn-helix domain
     0.0046   16.9   0.0      0.016   15.3   0.0    1.9  2  HTH_29    Winged helix-turn helix
     0.0086   15.8   0.0      0.027   14.2   0.0    1.8  1  HTH_23    Homeodomain-like domain
  ------ inclusion threshold ------
       0.05   13.4   0.0       0.12   12.1   0.0    1.6  1  HTH_IclR  IclR helix-turn-helix domain
      0.059   13.3   0.0       0.13   12.3   0.0    1.5  1  HTH_11    HTH domain
       0.16   12.0   0.0       0.36   10.8   0.0    1.6  1  HTH_36    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_38  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   8.6e-07    0.0022      22      41 ..     376     395 ..     363     396 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.6e-07
                            HTH_38  22 slreIArrLgrspsTIsREl 41 
                                       ++ e A +Lg++psTI+R +
  gi|336255646|ref|YP_004598753.1| 376 TVDELADELGKHPSTIYRAI 395
                                       7889**************87 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.2e-05     0.031       3      31 ..     376     412 ..     376     421 .. 0.82
   2 ?   -0.7   0.0      0.68   1.7e+03      35      46 ..     493     504 ..     484     507 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                            HTH_17   3 tveEaAelLgvsrstvyrli.........rrgelpaak 31 
                                       tv+E+A+ Lg ++st+yr i         ++ge+  ++
  gi|336255646|ref|YP_004598753.1| 376 TVDELADELGKHPSTIYRAIedlgdilelDQGEI-SFR 412
                                       9*******************77777777778888.665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.68
                            HTH_17  35 rwriprsdleew 46 
                                        +r+ ++++++w
  gi|336255646|ref|YP_004598753.1| 493 ARRVAQEAIDAW 504
                                       589********* PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.1e-06     0.016      10      35 ..     372     397 ..     370     400 .. 0.91
   2 ?   -3.6   0.0       4.6   1.2e+04      50      58 ..     470     479 ..     469     480 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.1e-06
                            HTH_29  10 eGvstvsqiAkllglsrrtvyrwlkr 35 
                                       +G++tv ++A  lg +++t+yr++++
  gi|336255646|ref|YP_004598753.1| 372 DGGGTVDELADELGKHPSTIYRAIED 397
                                       5777*******************986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.6
                            HTH_29  50 sgrprn.rls 58 
                                       sg+p++ r++
  gi|336255646|ref|YP_004598753.1| 470 SGNPKKlRID 479
                                       89***98887 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.1e-05     0.027      17      39 ..     374     396 ..     363     398 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                            HTH_23  17 GlsvreIAreLgvsrrTvyrwlk 39 
                                       G +v e A+eLg +++T+yr ++
  gi|336255646|ref|YP_004598753.1| 374 GGTVDELADELGKHPSTIYRAIE 396
                                       7899****************875 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   4.9e-05      0.12      15      41 ..     371     397 ..     367     399 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.9e-05
                                       TBSS-BHHHHHHHHTS-HHHHHHHHHH CS
                          HTH_IclR  15 apqeltlselArrtglpkStvhRlLqt 41 
                                       ++++ t+ elA+++g ++St +R +  
  gi|336255646|ref|YP_004598753.1| 371 TDGGGTVDELADELGKHPSTIYRAIED 397
                                       45556******************8765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     5e-05      0.13      17      39 ..     376     398 ..     367     406 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5e-05
                            HTH_11  17 sgeeLAeeLnvSrrtvrrdIkaL 39 
                                       + +eLA+eL+   +t++r I++L
  gi|336255646|ref|YP_004598753.1| 376 TVDELADELGKHPSTIYRAIEDL 398
                                       899******************99 PP

>> HTH_36  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   0.00014      0.36      18      49 ..     370     398 ..     368     400 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                            HTH_36  18 anknggcfpsqetlakrlglsknTvsraikeL 49 
                                       a+++gg   +++ la  lg++ +T++rai  L
  gi|336255646|ref|YP_004598753.1| 370 ATDGGG---TVDELADELGKHPSTIYRAIEDL 398
                                       567788...99******************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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 0.24s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 4116.38
//
Query:       gi|336255647|ref|YP_004598754.1|  [L=64]
Description: hypothetical protein Halxa_4273 [Halopiger xanaduensis SH-6]
Scores for 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 ------
      0.022   14.4   0.2      0.028   14.1   0.2    1.0  1  TackOD1   Thaumarchaeal output domain 1


Domain annotation for each model (and alignments):
>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.5e-06     0.028      96     131 ..      22      58 ..      18      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-06
                           TackOD1  96 idieeqelihhftCgnvgpeeef.lkegkleCpkCkt 131
                                        d++++   ++++Cg+vg e +  +++g   Cp+C t
  gi|336255647|ref|YP_004598754.1|  22 DDVDKRVWCECVDCGYVGYEVQVrRESGVPLCPSCFT 58 
                                       577888899*************944555668****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 556.66
//
Query:       gi|336255648|ref|YP_004598755.1|  [L=175]
Description: hypothetical protein Halxa_4274 [Halopiger xanaduensis SH-6]
Scores for 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-07   30.8   0.7      7e-07   29.9   0.7    1.5  1  DUF488    Protein of unknown function, DUF488


Domain annotation for each model (and alignments):
>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.7   3.9e-11     7e-07      52     121 ..      59     128 ..      27     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 3.9e-11
                            DUF488  52 elgpsrelrkwfkhdp.rweefferYaaeleskeaakealeelkelakkg.vaLlcaekdperchrvvlaey 121
                                       + + ++  ++       +  e  +rY ++l++ +  ++ ++el++ a+++ + L+c e+d + chr++la++
  gi|336255648|ref|YP_004598755.1|  59 DAAEENGESNPPA-IAwNSVEYERRYLEYLKR-DGPQAVIDELADCARERdLWLVCWEEDARWCHRRLLANV 128
                                       4444444444333.222467899*********.7889********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1336.65
//
Query:       gi|336255649|ref|YP_004598756.1|  [L=287]
Description: D12 class N6 adenine-specific DNA methyltransferase [Halopiger xanaduensis SH-6]
Scores for 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-20   71.7   0.0      1e-19   71.3   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 !   71.3   0.0   5.7e-24     1e-19       1     190 [.       7     190 ..       7     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 5.7e-24
                                       STTTSCTTHHHHHCCS-..--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCHSHHHHHHHHH.TC CS
                   MethyltransfD12   1 YiGgKrkllpeIkelipkdkgktfvepFaGggaVffeakkqgkkvlinDinedlinlykaliknnveelikelekll 77 
                                       YiGgK+ l+++  +++p   ++t+vepF G+++V ++   +    + nD  +d++ +++ + +++++el + ++++ 
  gi|336255649|ref|YP_004598756.1|   7 YIGGKTRLAQWVIDHLP--EHTTYVEPFGGSASVLLNKP-RSDVEIFNDKDSDVVTFFR-VARERPDELAEWCRYTP 79 
                                       9****************..588**************996.68899**************.9999************8 PP

                                       TTGGC.TS.HHHHHHHHHHHH...HHH-HHHHHHHHHHHHCCBGGG---B-TTS-B---B-S-SS-........HHH CS
                   MethyltransfD12  78 ekeelene.reyfyelreefnkkidaireaeeaidflylnrllfsglervnkkgnfnvpygaykkp....kkvaeke 149
                                       ++e+l +e  ++f+  ++ +        e e a + l+l ++ ++g+ ++++  +  +p + + ++     + a ++
  gi|336255649|ref|YP_004598756.1|  80 FSEQLHDEwADEFFSGERPDD-------ELEHAGKWLFLRYSQYAGKVARKSGFKRESPRDEKGSRnarnWINAPER 149
                                       888875432333333332333.......3334677888888888888877765555555444333333434667778 PP

                                       HHHHHHHHHHCCEEEC-CHHHHTT--TTE.EEEE--S-T.S CS
                   MethyltransfD12 150 lklrseklknakiecgdfdavllkakieddivYlDPPYnpr 190
                                       ++ ++e+++ + +  +d++av ++++ +  ++Y+DPPY + 
  gi|336255649|ref|YP_004598756.1| 150 IEYVAERFRGVSVVHEDYQAVVERYDSPETVFYVDPPYYQK 190
                                       8888888888****************9999********972 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.43u 0.19s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2374.05
//
Query:       gi|336255650|ref|YP_004598757.1|  [L=151]
Description: hypothetical protein Halxa_4276 [Halopiger xanaduensis SH-6]
Scores for 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:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1278.14
//
Query:       gi|336255651|ref|YP_004598758.1|  [L=76]
Description: hypothetical protein Halxa_4277 [Halopiger xanaduensis SH-6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0041   17.4   0.2     0.0049   17.2   0.2    1.1  1  DUF3268         zinc-finger-containing domain
  ------ inclusion threshold ------
      0.012   15.7   0.4      0.018   15.0   0.4    1.3  1  DZR             Double zinc ribbon
      0.012   15.5   0.3      0.018   14.9   0.3    1.2  1  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.044   13.7   1.2      0.068   13.1   0.8    1.5  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.058   13.3   3.5       0.12   12.3   3.5    1.5  1  Nudix_N_2       Nudix N-terminal
      0.059   12.8   0.9        1.5    8.3   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain
      0.075   13.0   1.7       0.11   12.5   1.7    1.3  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.57   10.3   4.3        3.6    7.8   0.5    2.1  3  Zn-ribbon_8     Zinc ribbon domain
        1.1    9.6   4.4        9.9    6.5   0.4    2.1  2  zf-LITAF-like   LITAF-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   2.4e-06    0.0049       3      47 ..      12      53 ..      10      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.4e-06
                           DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkCdayvgvhkgtk 47
                                       +C++CG++v+ +  + ++ +  + + ++ C +Cd+y ++ +g+ 
  gi|336255651|ref|YP_004598758.1| 12 STCKHCGAHVTDR-FRRVFGD--ESDRVHRCSECDTYARLTRGSA 53
                                      68******99765.5678833..344799**********998865 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.4   9.1e-06     0.018      12      39 ..      11      47 ..       7      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.1e-06
                               DZR 12 arfCseCgtklkavaa.........edrCpsCgekvd 39
                                        +C++Cg+++    +          +rC++C++ + 
  gi|336255651|ref|YP_004598758.1| 11 PSTCKHCGAHVTDRFRrvfgdesdrVHRCSECDTYAR 47
                                      679********866659***************98765 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 ?   14.9   0.3   8.9e-06     0.018      11      36 ..      11      44 ..       8      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.9e-06
                                      --B-TTT-SB-.......-S.SSS-EEEETTT-- CS
                              C1_1 11 ptfCkhCgefl.......wg.kekqglkCswCkl 36
                                      p++CkhCg ++       +g ++ +  +Cs+C  
  gi|336255651|ref|YP_004598758.1| 11 PSTCKHCGAHVtdrfrrvFGdESDRVHRCSECDT 44
                                      889***************9999999*******75 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   0.8   3.4e-05     0.068      29      55 ..      12      45 ..       6      48 .. 0.92
   2 ?   -2.9   0.0       3.3   6.5e+03      15      25 ..      54      64 ..      51      66 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-05
                    OrfB_Zn_ribbon 29 ktCseCgsknke.......alsgrtfkCpnCgfe 55
                                      +tC +Cg+ +++       + s+r+++C++C ++
  gi|336255651|ref|YP_004598758.1| 12 STCKHCGAHVTDrfrrvfgDESDRVHRCSECDTY 45
                                      59******99999******************876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.3
                    OrfB_Zn_ribbon 15 yGikveevnpa 25
                                      +G+ ve+ +p+
  gi|336255651|ref|YP_004598758.1| 54 AGKDVEVPDPE 64
                                      68888888886 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.5   6.2e-05      0.12       3      30 ..      14      44 ..      14      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.2e-05
                                      -TTT--B-E..EE--TT-SS-E.EEETTTTE CS
                         Nudix_N_2  3 CsqCGtpve..lripdgDnreR.lvCpaCgt 30
                                      C++CG+ v+   r   gD+  R ++C+ C+t
  gi|336255651|ref|YP_004598758.1| 14 CKHCGAHVTdrFRRVFGDESDRvHRCSECDT 44
                                      ********97766678******889****86 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   0.2   0.00077       1.5      15      24 ..      10      19 ..       6      23 .. 0.77
   2 ?    3.0   0.0     0.036        72       4      10 ..      38      44 ..      36      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00077
                       zf-ribbon_3 15 ddnvCpyCGt 24
                                      d ++C++CG+
  gi|336255651|ref|YP_004598758.1| 10 DPSTCKHCGA 19
                                      5578999996 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.036
                       zf-ribbon_3  4 rCPnCGa 10
                                      rC++C++
  gi|336255651|ref|YP_004598758.1| 38 RCSECDT 44
                                      8****85 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 ?   12.5   1.7   5.7e-05      0.11      15      44 ..       6      43 ..       4      45 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                     Zn_Tnp_IS1595 15 Wpng..fvCPhCgsrkayrikt......rglfqCkeCr 44
                                      Wp+    +C hCg     r+++       ++++C+eC 
  gi|336255651|ref|YP_004598758.1|  6 WPSVdpSTCKHCGAHVTDRFRRvfgdesDRVHRCSECD 43
                                      55555468*****986666666777************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 ?    7.8   0.5    0.0018       3.6      26      37 ..      11      22 ..       5      25 .. 0.75
   2 ?    7.4   4.1    0.0023       4.6       8      34 ..      14      44 ..      13      51 .. 0.72
   3 ?    3.0   0.2     0.056   1.1e+02       7      16 ..      38      46 ..      36      58 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0018
                       Zn-ribbon_8 26 ltaCPeCgsevr 37
                                      + +C++Cg++v+
  gi|336255651|ref|YP_004598758.1| 11 PSTCKHCGAHVT 22
                                      456*****9776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0023
                       Zn-ribbon_8  8 CeeCghefe.vlqsis..daplta.CPeCgs 34
                                      C+ Cg   + ++++++  +++ ++ C eC  
  gi|336255651|ref|YP_004598758.1| 14 CKHCGAHVTdRFRRVFgdESDRVHrCSECDT 44
                                      99**977776788777734456669****76 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.056
                       Zn-ribbon_8  7 rCeeCghefe 16
                                      rC eC+ ++ 
  gi|336255651|ref|YP_004598758.1| 38 RCSECD-TYA 46
                                      799998.444 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 ?    5.3   0.3     0.012        24       7      18 ..      13      24 ..       8      32 .. 0.69
   2 ?    6.5   0.4     0.005       9.9      53      65 ..      33      45 ..      28      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.012
                     zf-LITAF-like  7 dCpaCqqrvvTs 18
                                      +C++C+++v+ +
  gi|336255651|ref|YP_004598758.1| 13 TCKHCGAHVTDR 24
                                      677777777655 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.005
                     zf-LITAF-like 53 kdvehyCpnCgal 65
                                       d  h+C++C ++
  gi|336255651|ref|YP_004598758.1| 33 SDRVHRCSECDTY 45
                                      6899******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 613.32
//
Query:       gi|336255652|ref|YP_004598759.1|  [L=316]
Description: hypothetical protein Halxa_4278 [Halopiger xanaduensis SH-6]
Scores for 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 ------
        2.4    6.1   9.4          3    5.8   9.4    1.0  1  AF-4      AF-4 proto-oncoprotein


Domain annotation for each model (and alignments):
>> AF-4  AF-4 proto-oncoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   9.4   0.00017         3     438     494 ..     247     303 ..     236     314 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.00017
                              AF-4 438 eeqapekpksssapssapqstpesvesahsssaeSeSsSeSeSSSeSDSesEssssd 494
                                        + +pe+p++ +  + +      +  sa+ + ++    S+S+S S+SDS+sE+    
  gi|336255652|ref|YP_004598759.1| 247 ADAEPESPPTPAVGTGPLTDGGAAGSSAEDEPSATAVDSDSDSDSDSDSDSEDAYPS 303
                                       444555555555555555555555666666666666778888888888999885433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2514.15
//
Query:       gi|336255653|ref|YP_004598760.1|  [L=110]
Description: hypothetical protein Halxa_4279 [Halopiger xanaduensis SH-6]
Scores for 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-24   83.5   1.1    1.5e-23   82.9   1.1    1.3  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   1.1   8.1e-28   1.5e-23       2      75 .]      37     108 ..      36     108 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 8.1e-28
                            HalOD1   2 eespstaVveavaavegvdptelepLydaiDpdALdaLfasradgearadgsvsFtyegyeVtVrsdgeieVep 75 
                                       ++s+++a+veava+v+g+dp +++pL+d+i+p+AL++L+a+  ++++++ +++sF+y+++++tV s g+ +V p
  gi|336255653|ref|YP_004598760.1|  37 SDSIVVAIVEAVATVTGEDPIDMPPLFDTINPEALNRLVAP--STPRDQHVEISFEYQDCQITVSSRGDTVVVP 108
                                       789**************************************..7788999******************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 913.29
//
Query:       gi|336255654|ref|YP_004598761.1|  [L=390]
Description: PAS/PAC sensor protein [Halopiger xanaduensis SH-6]
Scores for 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-21   75.9   6.2    3.1e-21   75.9   6.2    1.6  2  BAT        GAF and HTH_10 associated domain
    1.4e-19   69.6   0.0    2.7e-19   68.7   0.0    1.5  1  HTH_10     HTH DNA binding domain
    1.5e-10   41.3   0.1    4.4e-10   39.8   0.1    1.9  1  PAS_4      PAS fold
    7.5e-09   35.6   0.0    2.2e-08   34.1   0.0    1.8  1  PAS        PAS fold
    9.2e-08   32.3   0.0      2e-07   31.2   0.0    1.6  1  PAS_9      PAS domain
     0.0002   21.3   0.0    0.00066   19.6   0.0    1.9  1  PAS_8      PAS domain
     0.0019   18.0   0.2      0.042   13.7   0.0    2.5  2  MarR_2     MarR family
     0.0082   15.7   0.0      0.062   12.9   0.0    2.3  3  HTH_24     Winged helix-turn-helix DNA-binding
     0.0096   16.1   0.0       0.02   15.1   0.0    1.5  1  UPF0122    Putative helix-turn-helix protein, YlxM / p13 like
  ------ inclusion threshold ------
      0.018   15.1   0.5       0.29   11.2   0.0    3.0  4  HTH_20     Helix-turn-helix domain
      0.024   14.6   0.0      0.058   13.4   0.0    1.6  1  HTH_11     HTH domain
      0.027   14.5   0.0      0.067   13.2   0.0    1.7  1  HTH_Crp_2  Crp-like helix-turn-helix domain
      0.033   14.5   0.0      0.095   13.0   0.0    1.9  2  PAS_3      PAS fold


Domain annotation for each model (and alignments):
>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.6   4.9e+03      31      73 ..     121     163 ..     104     169 .. 0.61
   2 !   75.9   6.2   2.3e-24   3.1e-21       2     141 ..     172     311 ..     171     318 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.6
                               BAT  31 eglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvse 73 
                                       e+  +  dg+ + ++t ++  + ++ d+   ++a edv+ +++
  gi|336255654|ref|YP_004598761.1| 121 EHWLELPDGTERWLVTNSRPVANDAGDVEYVVVAFEDVTDLKR 163
                                       5555556666666677766555555555555555555555554 PP

  == domain 2  score: 75.9 bits;  conditional E-value: 2.3e-24
                               BAT   2 avveLeleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgt 78 
                                        + +Le++ + ++++++   +e ++r+e+e++v+  d+e+++++ +++ ++ ++++a+e++++  dvr++s++d+ +
  gi|336255654|ref|YP_004598761.1| 172 HMRRLEFRADQSAVPPSLRVEEGERRIEVESVVSLPDDETIQYMGTSDLSASDFVTAVEEVPHYVDVRLLSTSDGYS 248
                                       5668*************999999****************************************************** PP

                               BAT  79 lleltvsgpslastlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeerypdveLvar 141
                                       ++e++ ++ ++ ++  + Gg +r++ + ++++r+  e+P ++d R  +e++++ +++veLv+ 
  gi|336255654|ref|YP_004598761.1| 249 RIEARAEEATVSEVFQSLGGQPRAVIIAQDEVRFLGELPGDVDHRLAAEGIRRFHDNVELVSE 311
                                       *************************************************************96 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.0     2e-22   2.7e-19       1      52 [.     328     379 ..     328     380 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 2e-22
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LTd+ql++l +Ay +GYFd+PR+ t  eLA+++G++++t+ +hLrka++ ++
  gi|336255654|ref|YP_004598761.1| 328 LTDRQLATLDAAYFSGYFDTPRTSTGGELADRFGVTRQTFNQHLRKAQRSVL 379
                                       9************************************************997 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.1   3.2e-13   4.4e-10       1     110 []      46     163 ..      46     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 3.2e-13
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla..e.llpeedaarl...eralrrvlegeepieflee 71 
                                       +d +p  ++v+d+ g ++yaN++a e ++++ +e++ + ++  e + + ed++++   e++++rv +++ep +  e+
  gi|336255654|ref|YP_004598761.1|  46 FDVSPISTVVIDSAGAIVYANERAIETLRLSSDEIVKRAYEpsEwNISYEDGTPIpvdEHPVARVFDTGEPEYGFEH 122
                                       7899*************************************86444444477776666899**************** PP

                             PAS_4  72 lll..pgeerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                        l   +g er++ ++ +P+ ++ G+v  v+v + D+T+++r
  gi|336255654|ref|YP_004598761.1| 123 WLElpDGTERWLVTNSRPVANDAGDVEYVVVAFEDVTDLKR 163
                                       9999*********************************9986 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.6e-11   2.2e-08       4     113 .]      43     158 ..      41     158 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.6e-11
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH......HHHHHHHHHHHHTT-ECC CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda......elaelleqlleqgeesra 74 
                                       r++++ +p  ++v+D  g i+y+N+ a e l ls +e++ + +  + ++ + +       +   + ++  +ge++ +
  gi|336255654|ref|YP_004598761.1|  43 RRLFDVSPISTVVIDSAGAIVYANERAIETLRLSSDEIVKRAYEPSEWNISYEdgtpipVDEHPVARVFDTGEPEYG 119
                                       56777788899*******************************9988888877789999999999************* PP

                                       CCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  75 geisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +e++++l+dg++++l+++ +pv +  g + ++++ + d+
  gi|336255654|ref|YP_004598761.1| 120 FEHWLELPDGTERWLVTNSRPVANDAGDVEYVVVAFEDV 158
                                       ***********************************9997 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   1.4e-10     2e-07       4     104 .]      53     160 ..      50     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.4e-10
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgks....itdlf....vtdpeanerlraaleqgrkkerevevvlirkn 72 
                                       ++++++ g i+yaNe a++ l  s++e++ +      +++      + p +++ +++++++g+ +e+ +e  l  ++
  gi|336255654|ref|YP_004598761.1|  53 TVVIDSAGAIVYANERAIETLRLSSDEIVKRAyepsEWNISyedgTPIPVDEHPVARVFDTGE-PEYGFEHWLELPD 128
                                       566679************************997766556669999999***************.************* PP

                             PAS_9  73 getfwvlltaspvkdddgelvgiivilrDite 104
                                       g++ w   + +pv +d g +  ++v ++D+t+
  gi|336255654|ref|YP_004598761.1| 129 GTERWLVTNSRPVANDAGDVEYVVVAFEDVTD 160
                                       ******************************96 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   4.8e-07   0.00066       3      40 ..      42      80 ..      40      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.8e-07
                             PAS_8  3 lralfesspdgiavvd.lgdrivdvNqaalellGys.adl 40
                                       r lf+ sp + +v+d +g  iv++N++a+e l +s +++
  gi|336255654|ref|YP_004598761.1| 42 ARRLFDVSPISTVVIDsAGA-IVYANERAIETLRLSsDEI 80
                                      699*************7777.*************995554 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.24   3.3e+02      18      31 ..      32      45 ..      22      49 .. 0.82
   2 !   13.7   0.0   3.1e-05     0.042      23      47 ..     352     376 ..     329     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.24
                                      TTSEEEHHHHHHHH CS
                            MarR_2 18 pgrdltvgelarrl 31
                                      ++r+l + +larrl
  gi|336255654|ref|YP_004598761.1| 32 DDRRLPPPDLARRL 45
                                      44599*******98 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.1e-05
                                       EHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2  23 tvgelarrlglsksavsrilkrLva 47 
                                       t gela+r+g+++++ +++l+++++
  gi|336255654|ref|YP_004598761.1| 352 TGGELADRFGVTRQTFNQHLRKAQR 376
                                       889*******************985 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 ?   -0.6   0.0      0.75     1e+03      14      27 ..      32      45 ..      31      46 .. 0.88
   2 ?   -2.9   0.0       3.9   5.4e+03      35      42 ..     170     177 ..     169     177 .. 0.85
   3 !   12.9   0.0   4.5e-05     0.062      20      41 ..     353     374 ..     346     377 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.75
                            HTH_24 14 knprisqreLAerl 27
                                      ++ r++  +LA+rl
  gi|336255654|ref|YP_004598761.1| 32 DDRRLPPPDLARRL 45
                                      5889********98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.9
                            HTH_24  35 nrrlkrLe 42 
                                       + +++rLe
  gi|336255654|ref|YP_004598761.1| 170 SDHMRRLE 177
                                       689****8 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 4.5e-05
                            HTH_24  20 qreLAerlglSpstvnrrlkrL 41 
                                         eLA+r g++++t n++l++ 
  gi|336255654|ref|YP_004598761.1| 353 GGELADRFGVTRQTFNQHLRKA 374
                                       579*****************96 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.4e-05      0.02       9      62 ..     319     379 ..     314     386 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                           UPF0122   9 aLfdiYqsLLTekq.....anylelyyadDl.Sl.sEiAeefnvsrqavydnikrteklle 62 
                                        L+di ++ LT++q     a y++ y++    S  +E+A++f v+rq+  ++++++++ ++
  gi|336255654|ref|YP_004598761.1| 319 LLYDIVADALTDRQlatldAAYFSGYFDTPRtSTgGELADRFGVTRQTFNQHLRKAQRSVL 379
                                       69************3333335777777654324337******************9987554 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       6.5   8.9e+03      25      37 ..      36      49 ..      33      50 .. 0.75
   2 ?   -0.1   0.1      0.74     1e+03      41      49 ..     169     177 ..     160     181 .. 0.88
   3 ?   -2.8   0.0       4.9   6.7e+03      20      34 ..     252     266 ..     239     273 .. 0.70
   4 ?   11.2   0.0   0.00021      0.29      28      47 ..     354     373 ..     342     382 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.5
                                      B-HHHHHHHH.TS- CS
                            HTH_20 25 ltaselaerl.dls 37
                                      l +++la+rl d+s
  gi|336255654|ref|YP_004598761.1| 36 LPPPDLARRLfDVS 49
                                      56889999997765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.74
                                       HHHHHHHHH CS
                            HTH_20  41 lsyHLrvLe 49 
                                       ls+H+r Le
  gi|336255654|ref|YP_004598761.1| 169 LSDHMRRLE 177
                                       89*****97 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.9
                                       STCTTB-HHHHHHHH CS
                            HTH_20  20 araegltaselaerl 34 
                                       arae++t+se+ + l
  gi|336255654|ref|YP_004598761.1| 252 ARAEEATVSEVFQSL 266
                                       678888888876655 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00021
                                       HHHHHHHTS-HHHHHHHHHH CS
                            HTH_20  28 selaerldlskntlsyHLrv 47 
                                       +ela+r++++++t ++HLr+
  gi|336255654|ref|YP_004598761.1| 354 GELADRFGVTRQTFNQHLRK 373
                                       8*****************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.2e-05     0.058      16      37 ..     351     372 ..     345     379 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.2e-05
                            HTH_11  16 isgeeLAeeLnvSrrtvrrdIk 37 
                                        +g eLA++++v+r+t  ++++
  gi|336255654|ref|YP_004598761.1| 351 STGGELADRFGVTRQTFNQHLR 372
                                       59**************888776 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   4.8e-05     0.067      25      47 ..     354     376 ..     328     380 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.8e-05
                                       HHHHHHTTSSHHHHHHHHHHHHH CS
                         HTH_Crp_2  25 eelAsmlGltretvsrilseLkr 47 
                                        elA++ G+tr+t+++ l++ +r
  gi|336255654|ref|YP_004598761.1| 354 GELADRFGVTRQTFNQHLRKAQR 376
                                       69****************99776 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.9e-05     0.095       3      86 ..      64     152 ..      62     155 .. 0.72
   2 ?   -3.5   0.0       9.5   1.3e+04      12      47 ..     360     372 ..     356     381 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-05
                             PAS_3   3 yvserveeilGyspeellgk.veswldlvhpeD...rervrealqealkkge.pyegeyRirrkdGeyrwveararv 74 
                                       y++er  e+l +s++e+ ++ +e     +  eD   ++  ++ +++++++ge +y +e+ +  +dG+ rw+ +  r+
  gi|336255654|ref|YP_004598761.1|  64 YANERAIETLRLSSDEIVKRaYEPSEWNISYEDgtpIPVDEHPVARVFDTGEpEYGFEHWLELPDGTERWLVTNSRP 140
                                       66666666666666666666655555555555533333334445688899**9************************ PP

                             PAS_3  75 irdengkpvrvi 86 
                                       + ++ g + +v+
  gi|336255654|ref|YP_004598761.1| 141 VANDAGDVEYVV 152
                                       *99999998876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.5
                             PAS_3  12 lGyspeellgkveswldlvhpeDrervrealqealk 47 
                                       +G++++ + +                       +l+
  gi|336255654|ref|YP_004598761.1| 360 FGVTRQTFNQ-----------------------HLR 372
                                       4555555544.......................443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3117.55
//
Query:       gi|336255655|ref|YP_004598762.1|  [L=322]
Description: formamidase [Halopiger xanaduensis SH-6]
Scores for 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-67  226.3   0.0    8.6e-33  113.7   0.0    2.0  2  FmdA_AmdA  Acetamidase/Formamidase family


Domain annotation for each model (and alignments):
>> FmdA_AmdA  Acetamidase/Formamidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.0   4.8e-37   8.6e-33       6     157 ..       9     155 ..       6     161 .. 0.93
   2 !  111.6   0.0     2e-36   3.7e-32     203     371 ..     160     317 ..     153     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 4.8e-37
                         FmdA_AmdA   6 kpaaeqeeklhNRwHpdipavaevkpgetvkvecldwtdgqiknndsaddvrtvdlkkvHeltgPvevegAepGDll 82 
                                       ++++  +e+lh  w  + ++v +++ g+ v+ ec+d+ +gq++ +++ +d++++d+++vH+ltgP++++gAepGD+l
  gi|336255655|ref|YP_004598762.1|   9 HEIDATDETLHSDWNRAREPVRTIESGDAVRFECRDAANGQLGPDSTVADLAELDVDQVHTLTGPIAIDGAEPGDVL 85 
                                       556677889******************************************************************** PP

                         FmdA_AmdA  83 vveildievleeaewGytgifdkenggGflkdafpeaakaiwdlegiyassrqipgvrfrglphpGllGtapske 157
                                        veil++e    + wGyt ++  e g+G+l + fpe+a ++wdle+ +a  r + g+++++ p+pG+lG+ap+++
  gi|336255655|ref|YP_004598762.1|  86 EVEILELEH---RGWGYTLVLPGELGMGLLPEEFPEPALHVWDLEDGVA--RFVNGIEVPLHPFPGTLGVAPAEP 155
                                       *****9875...57********************************986..7899*****************986 PP

  == domain 2  score: 111.6 bits;  conditional E-value: 2e-36
                         FmdA_AmdA 203 tvpprengGnmDiknlsrGskvylPVkveGaklsvGDlHfsqGDGEisfcg.aiemsgvvtlkvevikggmeklgik 278
                                       t ppr  gGn+Dik+l++Gs++ylP+ ve++ +s+GD H++qGDGE+  c   +e    vt ++e+  ++    +++
  gi|336255655|ref|YP_004598762.1| 160 TNPPRPVGGNLDIKHLTAGSTMYLPIAVEDGLFSIGDCHAAQGDGEV--CIsGVEAPMSVTCRFELRSEM----DLE 230
                                       88*********************************************..887999999*******99987....666 PP

                         FmdA_AmdA 279 npiflp.......eevepryseylsfeGisvdesgkqhyldltvAyrnallraieyLk.kfGytkeqaylllsvapv 347
                                        p f+        ++ ep y      +G      g+    dl  A+++a++ +i++ + ++G t+e+ay+l+s+a v
  gi|336255655|ref|YP_004598762.1| 231 RPQFETdgpftssGRDEPMY----GTTG-----VGD----DLREAAKDAIRGMIDHCHaERGLTREEAYILCSAA-V 293
                                       66664422222226777744....5555.....677....9***************9989***************.* PP

                         FmdA_AmdA 348 egrisgivdiPnvvatlalPldiF 371
                                       + +++++v+ Pn  ++++lP +iF
  gi|336255655|ref|YP_004598762.1| 294 DLKLNQVVNAPNWTVSAYLPEQIF 317
                                       ***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2394.21
//
Query:       gi|336255656|ref|YP_004598763.1|  [L=499]
Description: inosine-5'-monophosphate dehydrogenase [Halopiger xanaduensis SH-6]
Scores for 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-140  467.6   5.8   2.4e-140  467.5   5.8    1.0  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    2.3e-23   82.4   3.7    1.1e-10   41.8   0.3    2.9  2  CBS           CBS domain
    2.3e-14   53.5   1.3    1.3e-07   31.4   0.3    2.2  2  NMO           Nitronate monooxygenase
    9.3e-10   38.0   2.8    1.6e-09   37.3   2.8    1.4  1  FMN_dh        FMN-dependent dehydrogenase
      2e-05   23.9   5.5    7.6e-05   22.0   4.7    2.0  2  Glu_synthase  Conserved region in glutamate synthase
    0.00014   21.2   1.7    0.00014   21.2   1.7    2.3  2  ThiG          Thiazole biosynthesis protein ThiG
     0.0002   20.9   2.5    0.00044   19.8   2.5    1.5  1  His_biosynth  Histidine biosynthesis protein
    0.00021   20.6   1.3    0.00036   19.8   1.3    1.4  1  DHO_dh        Dihydroorotate dehydrogenase
     0.0024   17.0   0.1     0.0046   16.1   0.1    1.4  1  Dus           Dihydrouridine synthase (Dus)
  ------ inclusion threshold ------
       0.08   12.4   0.5        0.2   11.0   0.2    1.8  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.5   5.8  1.3e-143  2.4e-140       1     345 []      20     484 ..      20     484 .. 0.98

  Alignments for each domain:
  == domain 1  score: 467.5 bits;  conditional E-value: 1.3e-143
                                       E--GGGEEEE---B-S-GGGSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH   1 gltfddvllvpaksevlpkevdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevk 77 
                                       +ltfddvll p++s+v+p+++dl+++++k++++++P++saamdtvtes+mAia+ar+Gg+gv+h+n++i+e +ee++
  gi|336255656|ref|YP_004598763.1|  20 ALTFDDVLLRPKESRVEPDDADLTSRVSKNVEVSVPILSAAMDTVTESDMAIAMARHGGLGVLHRNMNIDEMVEEIE 96 
                                       69*************************************************************************** PP

                                       HHHTS........................................................................ CS
                                       xxxxx........................................................................ RF
                             IMPDH  78 kvkrs........................................................................ 82 
                                       +vk++                                                                        
  gi|336255656|ref|YP_004598763.1|  97 RVKSAdeliipqesvvtadpemsvrevddlmaregvggapvintngevlgiisstdirphlevneddpvteamtdev 173
                                       ***99************************************************************************ PP

                                       ................................................TTSXBXTTSXB-EEEEE-SSTTHHHHHHH CS
                                       ................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  83 ................................................pnaakdekgrllvgaavgvkedalervka 111
                                                                                        +a++de+grl++g av+  e  ++r+ a
  gi|336255656|ref|YP_004598763.1| 174 itapedvdareafdlmyehkiervpvvddenllvglvtmqgilqrreyGDAVRDEDGRLRCGVAVSPFE--EDRALA 248
                                       ***********************************************999******************6..89**** PP

                                       HHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 112 lveagvdvlvvdsahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsiCttrvvagv 188
                                         +ag+dvl++d+ah+h+ +v++  +eik++v e +v++Gnv t+e+a++L++  ad++kvGiGpGsiCttrvv+g+
  gi|336255656|ref|YP_004598763.1| 249 ADDAGADVLFIDTAHAHNLNVIDGAREIKENV-EADVVVGNVGTREAAAELVDF-ADGIKVGIGPGSICTTRVVSGA 323
                                       ********************************.7*******************9.********************** PP

                                       ---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEEEETTEEEEEEEETTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 189 GvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgeviliegrkyKeyrGmgs 265
                                       G+pq+tAva+va++a++++vpviaDGGi+ysgd +kA+aaGadavmlGs++agt+E+pg+v++++g+kyK+yrGmgs
  gi|336255656|ref|YP_004598763.1| 324 GMPQITAVAQVADVAAEHDVPVIADGGIRYSGDAIKAVAAGADAVMLGSYFAGTDEAPGRVVTMNGKKYKQYRGMGS 400
                                       ***************************************************************************** PP

                                       HHHHHH-SS-TTS-......--SS-SBEEEEEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEEEE-HHH CS
                                       xxxxxxxxxxxxxx.x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 266 lgamkkgskdryfq.k...keklvpeGvegrvpykgsvkevveqlvgglrsgmgylGaktieelkekakfvritaag 338
                                       +gamk+g++dry + +   ++++vpeGve+++pykgs+++ ++ql+gg++sgmgy+Ga+t+ e+k++++fvr+++ag
  gi|336255656|ref|YP_004598763.1| 401 VGAMKSGDSDRYLKeEpdeEDEYVPEGVEAATPYKGSLQSELHQLAGGMQSGMGYVGAETVPEFKDRSEFVRVSSAG 477
                                       ************985243244******************************************************** PP

                                       HHHHS-- CS
                                       xxxxxxx RF
                             IMPDH 339 lkeshvH 345
                                       ++esh+H
  gi|336255656|ref|YP_004598763.1| 478 QAESHAH 484
                                       ******9 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.3   1.4e-13   2.6e-10       5      52 ..     107     154 ..      98     158 .. 0.92
   2 !   41.8   0.3   6.2e-14   1.1e-10       1      54 [.     165     218 ..     165     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.4e-13
                                       SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS   5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                       + + vvt++p+++++e+ +lm+++gv++ PV++ +g+++Gi++ +D+ 
  gi|336255656|ref|YP_004598763.1| 107 PQESVVTADPEMSVREVDDLMAREGVGGAPVINTNGEVLGIISSTDIR 154
                                       77899*****************************************96 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 6.2e-14
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       V++ mt++v+t+p+d + +ea++lm e+++ r+PVVd+++ lvG+vt+  +l+ 
  gi|336255656|ref|YP_004598763.1| 165 VTEAMTDEVITAPEDVDAREAFDLMYEHKIERVPVVDDENLLVGLVTMQGILQR 218
                                       7789********************************9888788*****999986 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.1e-07    0.0002       4      60 ..      46     101 ..      43     110 .. 0.92
   2 !   31.4   0.3     7e-11   1.3e-07     183     285 ..     329     436 ..     307     461 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.1e-07
                               NMO   4 ltellkikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvkal 60 
                                       +++ +++  p+  + m  +++ ++a a +  GgLGvl    +  D++ +ei++vk++
  gi|336255656|ref|YP_004598763.1|  46 VSKNVEVSVPILSAAMDTVTESDMAIAMARHGGLGVLH-RNMNIDEMVEEIERVKSA 101
                                       566778999*****************************.8999***********975 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 7e-11
                               NMO 183 aLvpqvldavd...iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakdahkkklleaklddt.eltsav 255
                                       + v+qv+d+ +   +PviA GGi    +   a a+GA +v +g+ f +t+e++ ++++ +  + ++  ++  +   +
  gi|336255656|ref|YP_004598763.1| 329 TAVAQVADVAAehdVPVIADGGIRYSGDAIKAVAAGADAVMLGSYFAGTDEAPGRVVTMNGKKYKQYRGMgSVGAMK 405
                                       45667777655566*********9999988889********************999987766666665552566777 PP

                               NMO 256 sGrpaRalatelleelee.akiatlalpeah 285
                                       sG + R l+ e  ee e  +++  +a p+++
  gi|336255656|ref|YP_004598763.1| 406 SGDSDRYLKEEPDEEDEYvPEGVEAATPYKG 436
                                       8888888887777666665555555655555 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   2.8   8.9e-13   1.6e-09     193     303 ..     257     374 ..     174     383 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 8.9e-13
                                       HHCCCHB-TC--HHH.HHHHHHHHSSEEEEEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT-.--HHHCHH CS
                            FMN_dh 193 efvgkqldpsltwdd.ikwlreqtklplvvKGvltaedakraveaGvdgivvSNHGG.....Rqldga.patidvLp 262
                                        f+++   ++l+  d  ++++e+++  +vv  v t e a ++v+  +dgi v    G     R + ga ++ i +  
  gi|336255656|ref|YP_004598763.1| 257 LFIDTAHAHNLNVIDgAREIKENVEADVVVGNVGTREAAAELVDF-ADGIKVGIGPGsicttRVVSGAgMPQITAVA 332
                                       67777777778776658999999999****9**********9999.69**998888856666766665245577777 PP

                                       HHHHHH...SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 263 eiveavgg.rievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                       ++++ +++ +++v++DgGir   D++kA+a GAdav+lG  f
  gi|336255656|ref|YP_004598763.1| 333 QVADVAAEhDVPVIADGGIRYSGDAIKAVAAGADAVMLGSYF 374
                                       7777666548*****************************766 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 ?   -0.1   0.0      0.22   3.9e+02      27     117 ..      12     106 ..       2     111 .. 0.58
   2 !   22.0   4.7   4.3e-08   7.6e-05     217     304 ..     287     372 ..     262     375 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.22
                                       HHHHHTS.-S-SGGGGEEE--SS--....--GGGS--HHHHHTTEE---B-TTTS-HHHHHHHHHHHH....HHT-B CS
                      Glu_synthase  27 rekleerevlkakrdlleldaaeeal...ikleevepalkikkriltsamSyGalseeahealakamn....rlgtk 96 
                                       + kl+  e l+ +  ll +++++        +++v ++++++ +il +am   +   e+  a+a+a +     l  +
  gi|336255656|ref|YP_004598763.1|  12 SSKLQVPEALTFDDVLLRPKESRVEPddaDLTSRVSKNVEVSVPILSAAMDTVT---ESDMAIAMARHgglgVLHRN 85 
                                       555555555555555555555444333444567899999999999999997643...44445555443111134456 PP

                                       -EETTS---GGGGS-----SE CS
                      Glu_synthase  97 sntGEGGedeerlktakdvai 117
                                       +n  E  e+ er+k a+++ i
  gi|336255656|ref|YP_004598763.1|  86 MNIDEMVEEIERVKSADELII 106
                                       677777777777776666655 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 4.3e-08
                                       HHHHHHHHHTT-SEEE.EE-TT---SSE...EHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHH CS
                      Glu_synthase 217 etiaagvakanadiil.idGleGGTGAs...pkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadv 289
                                       +  ++g  +a a+++   dG++ G G      + ++  aG+P ++a+a+v  +       + v +iadGg++ + d 
  gi|336255656|ref|YP_004598763.1| 287 G--NVGTREAAAELVDfADGIKVGIGPGsicTTRVVSGAGMPQITAVAQVADVAA----EHDVPVIADGGIRYSGDA 357
                                       3..34567888888862589999988651114678899**********9987655....5789************** PP

                                       HHHHHHT-SEEE-SH CS
                      Glu_synthase 290 vkalalGAdavgigt 304
                                       +ka+a GAdav +g+
  gi|336255656|ref|YP_004598763.1| 358 IKAVAAGADAVMLGS 372
                                       ************997 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   0.4     0.083   1.5e+02     190     228 ..     246     284 ..     241     297 .. 0.85
   2 !   21.2   1.7   7.9e-08   0.00014     157     212 ..     321     379 ..     313     388 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.083
                                       HHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHH CS
                              ThiG 190 aaqamelGadavllntavaeakdpvamArafklaveaGr 228
                                       a +a + Gad ++++ta a+  + +  Ar +k  vea  
  gi|336255656|ref|YP_004598763.1| 246 ALAADDAGADVLFIDTAHAHNLNVIDGAREIKENVEADV 284
                                       6677789****************************9965 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 7.9e-08
                                       S----S-HHH...HHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSS CS
                              ThiG 157 sglGllnkea...lkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakd 212
                                       sg G+ + +a   +  + +e +vPvi D Gi+ + da++a+  Gadav+l +  a +++
  gi|336255656|ref|YP_004598763.1| 321 SGAGMPQITAvaqVADVAAEHDVPVIADGGIRYSGDAIKAVAAGADAVMLGSYFAGTDE 379
                                       555554444400045566778*****************************998887665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   2.5   2.4e-07   0.00044      93     223 ..     251     374 ..     241     379 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.4e-07
                                       HCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHH.TT-SEEEEEE CS
                      His_biosynth  93 eagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakklee.lgageilltd 168
                                       +agad + i ta ++n ++i+ + e  ++    v  D+  g     + +++e + ++v++a  ++   g g+i  t 
  gi|336255656|ref|YP_004598763.1| 251 DAGADVLFIDTAHAHNLNVIDGAREIKEN----VEADVVVG-----NVGTREAAAELVDFADGIKVgIGPGSICTTR 318
                                       67888888888888888888888886555....66675555.....7888888888999998776415566776665 PP

                                       .TTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHH CS
                      His_biosynth 169 .idrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsal 223
                                        ++  G+ +   + ++ ++a++ ++pvia GG++   d  +++++g+dav++gs +
  gi|336255656|ref|YP_004598763.1| 319 vVSGAGMPQITAVAQVADVAAEHDVPVIADGGIRYSGDAIKAVAAGADAVMLGSYF 374
                                       35778999999999999999999999999999999999999999999999999987 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.3     2e-07   0.00036     221     276 ..     320     374 ..     266     382 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2e-07
                                       EEEGGGHH.HHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                            DHO_dh 221 lsGkalkd.ialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                                       +sG+ + + +a++ + +++++ +  +p+I+ GGi  + Da+  + aGA +v +++ +
  gi|336255656|ref|YP_004598763.1| 320 VSGAGMPQiTAVAQVADVAAEHD--VPVIADGGIRYSGDAIKAVAAGADAVMLGSYF 374
                                       56666644147888888888777..***************************99965 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   2.6e-06    0.0046     172     213 ..     331     371 ..     317     393 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.6e-06
                                       CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEES CS
                               Dus 172 weaIkevkqavsipviaNGdIkdaedaqaileetGadgvmig 213
                                        +++++v  +  +pvia G+I++  da ++++  Gad+vm g
  gi|336255656|ref|YP_004598763.1| 331 VAQVADVAAEHDVPVIADGGIRYSGDAIKAVAA-GADAVMLG 371
                                       467788888888********************9.******99 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 ?   -2.8   0.0         2   3.5e+03      77     103 ..      65      91 ..      61     101 .. 0.77
   2 ?   11.0   0.2   0.00011       0.2     123     167 ..     325     370 ..     323     373 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2
                                       ES-HHHHHHHHHTT--EEEEEE--SHH CS
                      G3P_antiterm  77 stksslikkakklglltiqrlfliDss 103
                                       +     i +a++ gl +++r   iD +
  gi|336255656|ref|YP_004598763.1|  65 TESDMAIAMARHGGLGVLHRNMNIDEM 91 
                                       556677888999999999998888876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                                       ESGGG.HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                      G3P_antiterm 123 lPglv.pkvikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                       +P +     ++++  e ++p+ia G i+ + d  +a++aGa+av+ 
  gi|336255656|ref|YP_004598763.1| 325 MPQITaVAQVADVAAEHDVPVIADGGIRYSGDAIKAVAAGADAVML 370
                                       77777777888999999***************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3987.37
//
Query:       gi|336255657|ref|YP_004598764.1|  [L=55]
Description: hypothetical protein Halxa_4283 [Halopiger xanaduensis SH-6]
Scores for 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:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 448.51
//
Query:       gi|336255658|ref|YP_004598765.1|  [L=205]
Description: cytidylate kinase [Halopiger xanaduensis SH-6]
Scores for complete 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   73.7   0.0    2.5e-20   73.4   0.0    1.1  1  AAA_18           AAA domain
    4.4e-20   72.5   0.1    5.3e-19   69.0   0.1    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
    2.6e-12   47.3   0.0    5.8e-12   46.2   0.0    1.5  1  AAA_17           AAA domain
    5.2e-07   29.6   0.1     0.0005   19.9   0.0    2.1  2  Cytidylate_kin   Cytidylate kinase
    1.3e-06   28.7   0.1      3e-06   27.6   0.1    1.7  1  AAA_28           AAA domain
    2.1e-06   28.0   0.0    3.8e-06   27.1   0.0    1.4  1  AAA_33           AAA domain
    1.5e-05   25.1   0.1    6.3e-05   23.1   0.1    2.0  1  ADK              Adenylate kinase
    9.6e-05   22.8   0.0    0.00018   21.9   0.0    1.5  1  AAA              ATPase family associated with various cellul
    0.00038   20.2   0.0        0.2   11.3   0.0    2.1  2  CoaE             Dephospho-CoA kinase
     0.0053   16.6   0.0        1.8    8.4   0.0    2.2  2  dNK              Deoxynucleoside kinase
  ------ inclusion threshold ------
      0.019   15.2   0.1      0.034   14.4   0.1    1.5  1  AAA_22           AAA domain
      0.023   15.1   0.3      0.074   13.4   0.3    2.0  1  AAA_16           AAA ATPase domain
      0.023   14.8   0.1       0.28   11.3   0.1    2.1  1  SKI              Shikimate kinase
      0.033   13.9   0.0       0.33   10.6   0.0    2.1  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.053   13.5   0.0       0.13   12.2   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
        0.1   12.5   0.0       0.42   10.5   0.0    1.8  2  NACHT            NACHT domain
       0.15   12.5   0.0       0.23   11.9   0.0    1.3  1  RNA_helicase     RNA helicase
       0.17   11.8   0.0       0.32   10.9   0.0    1.4  1  NTPase_1         NTPase
       0.22   11.4   0.0       0.32   10.9   0.0    1.3  1  Rad17            Rad17 P-loop domain


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 !   73.4   0.0   2.6e-23   2.5e-20       1     125 [.      19     146 ..      19     151 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 2.6e-23
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       I ++G+pG+G ttl+++L++  g+     g++ r++a +++++l +  ++ des+ +d+  +++l+++ e++    +
  gi|336255658|ref|YP_004598765.1|  19 ITVSGPPGCGATTLCERLADAIGCpyvsgGDIFRELAEDREMSLNQLTAKADESDGIDRALDQRLQQIAEKWG---M 92 
                                       89*******************999************************************************5...7 PP

                            AAA_18  73 egknlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakik..enee 125
                                        +k+ +++++la ++  ++ d+  ++L+a+++++leR+e+R ++ea+++  e +e
  gi|336255658|ref|YP_004598765.1|  93 ANKPFILESRLAGWLAGDRADLR-IWLDAPEDVRLERIEDRMETEAEMRvrEVSE 146
                                       9**********************.**********************997655554 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.1   5.6e-22   5.3e-19       2     178 ..      19     171 ..      18     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 5.6e-22
                   Cytidylate_kin2   2 ITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeev.eevdersrlssflskllaarvagdtldek 76 
                                       IT+s+  G+g++t++e+LA+  g p+++  +i++e+a++ ++s +++ +++de                     +  
  gi|336255658|ref|YP_004598765.1|  19 ITVSGPPGCGATTLCERLADAIGCPYVSGgDIFRELAEDREMSLNQLtAKADE---------------------SDG 74 
                                       9***************************99*****************889999.....................445 PP

                   Cytidylate_kin2  77 lddelfeaqervirela.aeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkr 152
                                       +d +l ++ +++ ++ + a++++++  R a  +  dr   lr++l+ap+++r++r+++r++    ea  +++ ++  
  gi|336255658|ref|YP_004598765.1|  75 IDRALDQRLQQIAEKWGmANKPFILESRLAGWLAGDRA-DLRIWLDAPEDVRLERIEDRMET---EA--EMRVREVS 145
                                       666777777788888877778**********9998877.*********************44...45..55556678 PP

                   Cytidylate_kin2 153 rakyykkytgqdwgdaenYdlvlnts 178
                                       +a +y+ y++ d++d+e Ydl +nt+
  gi|336255658|ref|YP_004598765.1| 146 EAGRYQSYYDIDIDDREFYDLNINTA 171
                                       99**********************97 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   6.2e-15   5.8e-12       2     123 ..      23     134 ..      22     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 6.2e-15
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSH.HHHCTSHHHHHHHHHHHHHHHHHHHH..HSSEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakar.demrklpleekkelqkeaaekiaeea..kkkgvl 75 
                                       G+PG+G +t+ce+l++ +g +++s Gd++re a++++++ ++  + ++++  ++++l+++++ +iae+   ++k ++
  gi|336255658|ref|YP_004598765.1|  23 GPPGCGATTLCERLADAIGCPYVSGGDIFRELAEDREMSLNQlTAKADESDGIDRALDQRLQ-QIAEKWgmANKPFI 98 
                                       9***********************************98433303333444455666666664.67776544556677 PP

                                       EEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH.T CS
                            AAA_17  76 vdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd.r 123
                                       ++            +g+ +   + +  d+ i l+a++++ ler   + +
  gi|336255658|ref|YP_004598765.1|  99 LESRL---------AGWLAG--DRA--DLRIWLDAPEDVRLERIEDRmE 134
                                       76655.........344442..333..7788888888877777666633 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   5.3e-07    0.0005       1      37 [.      19      55 ..      19      76 .. 0.87
   2 !    8.2   0.0     0.002       1.9      98     156 ..      75     137 ..      58     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.3e-07
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRala 37
                                      i++ GP g G  +++ +la+ +g+ y++ g ++R la
  gi|336255658|ref|YP_004598765.1| 19 ITVSGPPGCGATTLCERLADAIGCPYVSGGDIFRELA 55
                                      899*******************************987 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHTT-B.....SSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT- CS
                    Cytidylate_kin  98 vRailvkklrelvk.....karvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgt 156
                                       + ++l ++l+++++     ++ +++e R  g      a+l+i+ldA  ++R +R  +++ ++  
  gi|336255658|ref|YP_004598765.1|  75 IDRALDQRLQQIAEkwgmaNKPFILESRLAGWLAGDRADLRIWLDAPEDVRLERI-EDRMETEA 137
                                       5556667777776644445677899999999999999**************9974.44344434 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   3.2e-09     3e-06       2      79 ..      19     100 ..      18     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.2e-09
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwvedllafaervleeqleeeaaa..aan 73 
                                       i ++G++++G Ttl+e+La+  g p+v   +++re+ e++  + ++  ++ +d  +  +r l+++l++ a+    an
  gi|336255658|ref|YP_004598765.1|  19 ITVSGPPGCGATTLCERLADAiGCPYVsgGDIFRELAEDREMSLNQLTAK-ADESDGIDRALDQRLQQIAEKwgMAN 94 
                                       789****************888***99999*********99888874444.46666667779999999999887667 PP

                            AAA_28  74 kvlfcD 79 
                                       k ++++
  gi|336255658|ref|YP_004598765.1|  95 KPFILE 100
                                       766665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0     4e-09   3.8e-06       4     130 ..      21     139 ..      18     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4e-09
                            AAA_33   4 lvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsa.grn.vildat 78 
                                       + G+pG+G +tl erl+ + g+  +s  +++r l+++ + s++++t  +d+  + + + ++++l++ +    ++  +
  gi|336255658|ref|YP_004598765.1|  21 VSGPPGCGATTLCERLADAIGCPYVSGGDIFRELAEDREMSLNQLTAKADE-SDGIDRALDQRLQQiAEKwGMANKP 96 
                                       78*********************************9888887766554444.4444455555543303334789*** PP

                            AAA_33  79 nlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrsevpe 130
                                       ++ +++ a +l+  r    +++ ++++++e++  eR++ R++++     +++
  gi|336255658|ref|YP_004598765.1|  97 FILESRLAGWLAGDR----ADLRIWLDAPEDVRLERIEDRMETE-----AEM 139
                                       **********99987....6788*******************74.....222 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   6.6e-08   6.3e-05       1      37 [.      21      57 ..      21     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.6e-08
                                      EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevks 37
                                      + G+Pg+G  t +e+l++  g++ +s Gd++R+  + 
  gi|336255658|ref|YP_004598765.1| 21 VSGPPGCGATTLCERLADAIGCPYVSGGDIFRELAED 57
                                      57******************************86654 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 !   21.9   0.0   1.9e-07   0.00018       2      56 ..      20      72 ..      19      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.9e-07
                                      EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHT CS
                               AAA  2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakek 56
                                       ++GppG+G T+l++ +a  +g ++  +sg +++ ++ +++e+++++l ++a e+
  gi|336255658|ref|YP_004598765.1| 20 TVSGPPGCGATTLCERLADAIGCPY--VSGGDIFRELAEDREMSLNQLTAKADES 72
                                      589*****************99887..68*******************9999876 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00021       0.2       2      50 ..      18      67 ..      17      72 .. 0.92
   2 !    7.0   0.0    0.0045       4.2      90     150 ..      75     139 ..      73     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                                      EEEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCTHHHHHHHHH CS
                              CoaE  2 ivgltGgiasGKstvanlfad.lgvpivDaDlvArqvvepgsealkkive 50
                                      ++ ++G  ++G +t+++++ad +g+p v    + r++ e  +  l+++ +
  gi|336255658|ref|YP_004598765.1| 18 FITVSGPPGCGATTLCERLADaIGCPYVSGGDIFRELAEDREMSLNQLTA 67
                                      68899999*************9***********************99976 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0045
                                       HHHHHHHHHHH--SSEEEEE-TTTTTTTGGGGS.....SEEEEEE--HHHHHHHHHHCCTSTHHHH CS
                              CoaE  90 irreikkelakleskyvlldvPLLvEkqlekli.....ervlvvdvelelqveRlvardgvseeev 150
                                       i r++ ++l+++ +k  + + P ++E++l+ ++     +  + +d++++ ++eR+ +r ++++e +
  gi|336255658|ref|YP_004598765.1|  75 IDRALDQRLQQIAEKWGMANKPFILESRLAGWLagdraDLRIWLDAPEDVRLERIEDRMETEAE-M 139
                                       6788999**********************9987332224568889999******9999886543.3 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0019       1.8       1      27 [.      19      45 ..      19     104 .. 0.88
   2 !    6.7   0.0    0.0064         6     122     148 ..     111     137 ..      92     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0019
                                      EEEEESTTSSHHHHHHHHHCCSTCEEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvf 27
                                      i+v+G+ g+G +tl ++L++++g + +
  gi|336255658|ref|YP_004598765.1| 19 ITVSGPPGCGATTLCERLADAIGCPYV 45
                                      89******************9997655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0064
                                       H-SEEEEEE--HHHHHHHHHHCTTCCC CS
                               dNK 122 kpdlliYLkasletclerikkRgreee 148
                                       + dl i+L+a+ ++ leri+ R ++e 
  gi|336255658|ref|YP_004598765.1| 111 RADLRIWLDAPEDVRLERIEDRMETEA 137
                                       47999*****************98764 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.6e-05     0.034       4      28 ..      15      39 ..      12      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleq 28
                                      t  +++v G++G+G Ttl++rl++ 
  gi|336255658|ref|YP_004598765.1| 15 TTLFITVSGPPGCGATTLCERLADA 39
                                      6789******************986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   7.8e-05     0.074      23      60 ..      15      50 ..       3     167 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.8e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggiflrgkc 60
                                      ++  + +sG++G+G ++l ++l++a+     ++  g+ 
  gi|336255658|ref|YP_004598765.1| 15 TTLFITVSGPPGCGATTLCERLADAIGCP--YVSGGDI 50
                                      447899*****************988866..3333332 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0003      0.28       1     134 [.      25     156 ..      25     170 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                                       TTSSHHHHHHHHHHHHTSEEEEHHH...HHHHHHTS-HHHHHHHHHHHH..HHHHHHHHHHHHCCCSSEEEEE-TTG CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDe...liekrtgksiaeifeeegeeg..FrelEsevlkelleeeglViatGGGa 72 
                                       +G+G +t+ ++lA+++g++++   +   ++ +  ++s +++ ++ +e+   +r+l+ + l++++e+ g+        
  gi|336255658|ref|YP_004598765.1|  25 PGCGATTLCERLADAIGCPYVSGGDifrELAEDREMSLNQLTAKADESDgiDRALD-QRLQQIAEKWGMANKP---F 97 
                                       69******************976441114556666999999987766542233333.3355555553332222...4 PP

                                       GGSHHHHHHHH..HHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCS CS
                               SKI  73 vlseenrellk..ekgiviyLdvsleellerlkadkeRPllqekskeeelleela.ereplyeea 134
                                       +l+++    l+  +  + i+Ld++ ++ ler++++ e    +e +   +++e  +  r ++y ++
  gi|336255658|ref|YP_004598765.1|  98 ILESRLAGWLAgdRADLRIWLDAPEDVRLERIEDRME----TEAEM--RVREVSEaGRYQSYYDI 156
                                       5555555555556778899999999999999998888....33333..34444443566666654 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00035      0.33       1      42 [.      18      63 ..      18      89 .. 0.71
   2 ?    1.1   0.0       0.3   2.8e+02     130     146 ..     112     128 ..     108     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00035
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaei....egdsflrld 42
                                      +I v+g+ G+G tt+ ++l +++g   v    i      d +++l+
  gi|336255658|ref|YP_004598765.1| 18 FITVSGPPGCGATTLCERLADAIGCPYVSGGDIfrelAEDREMSLN 63
                                      699*********************8777754444433333333333 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.3
                               PRK 130 ldlkiyvdisidlelar 146
                                       +dl+i++d+ +d++l r
  gi|336255658|ref|YP_004598765.1| 112 ADLRIWLDAPEDVRLER 128
                                       799*******9999875 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   0.00014      0.13       5      28 ..      22      45 ..      19      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                      E--SSSSHHHHHHHGGGGBS--EE CS
                             AAA_5  5 vGppGtgKselaerlaaalnreve 28
                                       GppG+g ++l erla a++++++
  gi|336255658|ref|YP_004598765.1| 22 SGPPGCGATTLCERLADAIGCPYV 45
                                      6******************88764 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00045      0.42       3      32 ..      19      48 ..      17      69 .. 0.85
   2 ?   -0.3   0.0      0.96   9.1e+02      88     155 ..      73     149 ..      70     156 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00045
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SCCC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklpqg 32
                                      + + G++G+G TtL ++la+a+  ++  +g
  gi|336255658|ref|YP_004598765.1| 19 ITVSGPPGCGATTLCERLADAIGCPYVSGG 48
                                      6799*****************999887775 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.96
                                       E-STT-SS-TCH..................HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE--TCCHH CS
                             NACHT  88 DglDelvtdlgq.........kekqpvrtlLselirkkllpeasllltvrpralrdleeqleeaivlevegfsesrr 155
                                       Dg+D++ ++  q         +++  ++  L++++ +       +l +    +l+++e  +e+++ + v++ se  r
  gi|336255658|ref|YP_004598765.1|  73 DGIDRALDQRLQqiaekwgmaNKPFILESRLAGWLAGDRADLRIWLDAPEDVRLERIEDRMETEAEMRVREVSEAGR 149
                                       66665444433346666666666666667777777765555555555555666666788888887777777777665 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   0.00024      0.23       1      23 [.      19      41 ..      19      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakall 23
                                      i ++Gp+g+G +tl+++La+a+ 
  gi|336255658|ref|YP_004598765.1| 19 ITVSGPPGCGATTLCERLADAIG 41
                                      5799***************9987 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00034      0.32       2      23 ..      19      40 ..      18      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                                      EEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlell 23
                                      + ++GppG G tTl++++++++
  gi|336255658|ref|YP_004598765.1| 19 ITVSGPPGCGATTLCERLADAI 40
                                      6899**************9998 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00034      0.32      48      72 ..      19      43 ..       5      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                             Rad17 48 LLisGPsGCgkstvvkvLskelgik 72
                                      + +sGP+GCg +t  + L+   g  
  gi|336255658|ref|YP_004598765.1| 19 ITVSGPPGCGATTLCERLADAIGCP 43
                                      5689************999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 1566.40
//
Query:       gi|336255659|ref|YP_004598766.1|  [L=172]
Description: hypothetical protein Halxa_4285 [Halopiger xanaduensis SH-6]
Scores for 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 ------
       0.03   13.4   0.0      0.034   13.2   0.0    1.1  1  Membralin   Tumour-associated protein
       0.12   12.2   0.3       0.19   11.6   0.3    1.3  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> Membralin  Tumour-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.7e-06     0.034      61     157 ..      19     119 ..      15     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-06
                         Membralin  61 anCldhvkddwprdGilrveivrnlkksev....llessekeeesekkisisenkkvllkeasvtlleesvlevsle 133
                                       a C++ v++++  +G++ vei ++ ++++       e  + ++ + ++ s+s n+++   +   t+++ +v+ +  +
  gi|336255659|ref|YP_004598766.1|  19 AGCIQGVQEHFGLQGVVPVEIHNSGSRTYNiqlrARELGNDRQSYDEQYSVSPNETAYPPHLGRTEQSLQVVLFGEN 95 
                                       67**********************99987755432334444555566667777888888888888888888888888 PP

                         Membralin 134 aeeeekessslkkeeelrsvelie 157
                                       +e+e+ e++s+++e+e+ s+el++
  gi|336255659|ref|YP_004598766.1|  96 NEQEQVEAVSITSETEFVSIELTD 119
                                       888888888888888877776654 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   2.1e-05      0.19       2      24 ..       1      22 [.       1      24 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.1e-05
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggca 24
                                      ++RR+ L+ sA + A ++l+gc 
  gi|336255659|ref|YP_004598766.1|  1 MNRRTVLR-SASVLATVGLAGCI 22
                                      89******.66666788899985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1418.38
//
Query:       gi|336255660|ref|YP_004598767.1|  [L=592]
Description: SagD family biosynthesis docking scaffold protein [Halopiger xanaduensis SH-6]
Scores for 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   8.2    4.5e-51  174.0   8.2    1.2  1  YcaO      YcaO cyclodehydratase, ATP-ad Mg2+-binding


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 !  174.0   8.2   2.5e-55   4.5e-51       3     322 ..     240     557 ..     238     558 .. 0.87

  Alignments for each domain:
  == domain 1  score: 174.0 bits;  conditional E-value: 2.5e-55
                              YcaO   3 kGateeaArasalgEalErysaegffrgdekrvrasyrelegegaldpeelglyseeekdaadfvlepfdpdrpidw 79 
                                        + +  aA+++a+gE+lEry+a+ +  +d++ vras  +l  e+ ++p +l  +++          +++dp ++++w
  gi|336255660|ref|YP_004598767.1| 240 VADDWNAALMKAVGEGLERYCAGVY--RDAEFVRASEGDL--ENPVSPTDLVRPDD---------ASEYDPAEEYRW 303
                                       5567789*************97744..7899999******..************77.........89********** PP

                              YcaO  80 vpgwsltdgeevlvPanlvylyeppegearlfletsnGlAaGntleeAilhGllEliERdafalawyerlplpridl 156
                                       vpg +l +g +  +Pa++v +  p++g+  l+ + ++Gl++G++  +A+l Gl E++ERda +lawy+  ++ ++ +
  gi|336255660|ref|YP_004598767.1| 304 VPGENLVTGGRAHLPAAAVQF--PQPGA-ELVPAITTGLGLGSSTVDALLSGLTEVLERDATMLAWYSTFEPLELAV 377
                                       *********************..55555.9***************************************99999998 PP

                              YcaO 157 asdpeirellerlreagievrlldatldlgipvvaavlvd.pk...............lllvagaGahldpevAler 217
                                       + dp+++ l +r+r++g+ v  l +t d+++pvva+ +++ p+               ++ +ag++a+ld+  A+  
  gi|336255660|ref|YP_004598767.1| 378 D-DPAFATLERRARSEGLSVTPLLVTQDVDVPVVAVAVHRePDdldadaeidpeddawPAFAAGSAADLDATAAATA 453
                                       6.9*************************************6337888999999***9755667************** PP

                              YcaO 218 AltElaqsrltl.isgaredpdfdeeladvatleradreallwlpeaaakrldfllfaewassgdleedletllerl 293
                                       Al E++q+   l + g +e++d+  ++ + a ++    ++ ++ + + + r++++   ++   ++ e+ le ller 
  gi|336255660|ref|YP_004598767.1| 454 ALEEALQNWMELrNLGPEEAADQSGAIGEYAAFP--TPAQEFV-AVGGD-RVPAESVGPD-PVPSGEDALESLLERA 525
                                       *********9994555555555546778888886..3345565.66666.5555542233.3489************ PP

                              YcaO 294 kaagldvlvvdltrp...dlglpvvkvivPgl 322
                                        +a+l ++++ lt+    ++g+ +v+v+vPg+
  gi|336255660|ref|YP_004598767.1| 526 GDADLTPYAARLTTRdveSIGFEAVRVVVPGA 557
                                       **************99*9*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 4211.26
//
Query:       gi|336255661|ref|YP_004598768.1|  [L=328]
Description: Na+/Ca+ antiporter, CaCA family [Halopiger xanaduensis SH-6]
Scores for 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-47  158.7  31.9      1e-26   93.7  12.1    2.0  2  Na_Ca_ex  Sodium/calcium exchanger protein
     0.0015   18.1  11.7      0.057   12.9   4.1    2.6  2  LysE      LysE type translocator
  ------ inclusion threshold ------
       0.02   14.8   2.3        0.3   11.0   0.3    2.6  2  DUF4260   Domain of unknown function (DUF4260)


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7  12.1   1.7e-30     1e-26       3     150 ..      10     149 ..       8     150 .. 0.91
   2 !   71.2  11.8   1.5e-23   8.7e-20       4     139 ..     185     312 ..     183     314 .. 0.89

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 1.7e-30
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnl 79 
                                       ++++++s+l+++v+a +lv+++  +a+ +g+s+ ++Glt++A g+s pEl +si aa +g +d+a++nvlGsni nl
  gi|336255661|ref|YP_004598768.1|  10 IGVILVSVLGLWVGARLLVDAVVRLARRFGLSDLTIGLTVVAMGTSTPELSVSIDAAFKGLGDIAVANVLGSNIYNL 86 
                                       6789************************************************************************* PP

                                       HTHHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  80 llviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                        +++G++al+++++v  + + +d  + ll++ ll +lvl+         r+t+leg++l++ +++y+v++l
  gi|336255661|ref|YP_004598768.1|  87 AFILGVVALVTAIPVADSVVRRDGTA-LLASTLLGGLVLF-D------LRVTRLEGVILAGSFVAYTVYLL 149
                                       **********9999999887777755.5555555554443.5......9*******************986 PP

  == domain 2  score: 71.2 bits;  conditional E-value: 1.5e-23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnll 80 
                                       v+++ +l+l+ v+ d++v + +e+a+  gis+ ++G t++A+g+s pE+++s++a+ +g+  +++gnv+Gsni nl+
  gi|336255661|ref|YP_004598768.1| 185 VFLAGGLALVLVSGDYMVAASSELARDAGISEWIIGGTIVAAGTSTPEFAVSLVAIQRGSFGVSVGNVIGSNIYNLT 261
                                       6788999********************************************************************** PP

                                       THHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHH CS
                          Na_Ca_ex  81 lviGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvll 139
                                       +++G++a+i +l        l+  ++l  ++ll++++l+        ++l++leg++++
  gi|336255661|ref|YP_004598768.1| 262 GILGVAAVIRPLATSA--ASLESVAWLAGIALLMVAALWTD------RVLSRLEGALFA 312
                                       *********8844443..34566577777888888888866......********9987 PP

>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.9   0.00011      0.66      16      72 ..      60     116 ..      48     122 .. 0.91
   2 !   12.9   4.1   9.6e-06     0.057      13      88 ..     234     304 ..     223     326 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00011
                              LysE  16 kqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlw 72 
                                       + +i   fkg+  +a+  ++g  ++ l+ +lG+ +L++a p + s++r  G a L+ 
  gi|336255661|ref|YP_004598768.1|  60 SVSIDAAFKGLGDIAVANVLGSNIYNLAFILGVVALVTAIPVADSVVRRDGTALLAS 116
                                       568888999999999999*********************************999975 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.6e-06
                              LysE  13 lvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlalrdakekkvea 88 
                                       +v+  +i+rg   ++ v +g +ig  ++ l g+lG+a++++  p ++s  +l ++a L+ +++l++ + ++  v++
  gi|336255661|ref|YP_004598768.1| 234 AVSLVAIQRG---SFGVSVGNVIGSNIYNLTGILGVAAVIR--PLATSAASLESVAWLAGIALLMVAALWTDRVLS 304
                                       5666677777...999*************************..**********************99999988765 PP

>> DUF4260  Domain of unknown function (DUF4260)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.017     1e+02      46      72 ..      76     102 ..      70     146 .. 0.79
   2 ?   11.0   0.3   5.1e-05       0.3      29      95 ..     233     303 ..     218     305 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.017
                           DUF4260  46 gpkvGalvYNllHskalallllllgll 72 
                                        + +G+ +YNl+ + ++ +l++++ ++
  gi|336255661|ref|YP_004598768.1|  76 ANVLGSNIYNLAFILGVVALVTAIPVA 102
                                       5678999*****999998888877654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.1e-05
                           DUF4260  29 flllllvpDlsmlgYligpkvGalvYNllHskalallllllglllesel....lllaglillahialDRal 95 
                                       f++ l +   + +g  +g+ +G+ +YNl+ + ++a+++  l++ ++s      l+ ++l+++a    DR+l
  gi|336255661|ref|YP_004598768.1| 233 FAVSLVAIQRGSFGVSVGNVIGSNIYNLTGILGVAAVIRPLATSAASLEsvawLAGIALLMVAALWTDRVL 303
                                       55666666667788999*****************9999766654443222333556677777777789987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2487.65
//
Query:       gi|336255662|ref|YP_004598769.1|  [L=390]
Description: hypothetical protein Halxa_4288 [Halopiger xanaduensis SH-6]
Scores for 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-37  128.1   2.2    3.6e-37  128.1   2.2    2.1  2  Band_7    SPFH domain / Band 7 family
  ------ inclusion threshold ------
      0.017   14.9   0.1      0.032   13.9   0.1    1.5  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 !  128.1   2.2   4.1e-41   3.6e-37       2     178 .]      42     212 ..      41     212 .. 0.98
   2 ?   -0.3   0.1       0.1   9.1e+02     125     167 ..     285     334 ..     237     356 .. 0.66

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 4.1e-41
                            Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapkl 78 
                                       i+++  +g ++ fG++++ lepGl  + Pf+++v+++++r+qt+dv+  ++++t+D+ pvt d++v++rv  da ++
  gi|336255662|ref|YP_004598769.1|  42 IVDAYDRGALTVFGEYRKLLEPGLNVVPPFVSRVYTFDMRTQTIDVPS-QEAITRDNSPVTADAVVYIRV-MDATRA 116
                                       578888999999************************************.*********************.****** PP

                            Band_7  79 vaaveresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaq 155
                                       +++v    +++++ ++++++ +lr+vi++m+l++ ls re+++e++++el e  +++G+ v++v +++++p++ v+ 
  gi|336255662|ref|YP_004598769.1| 117 FLEV----DDYERAVSNLAQTTLRAVIGDMELDDTLSRREMINERIRQELDEPTDEWGIRVESVEVREVTPSAGVKG 189
                                       ****....********************************************************************* PP

                            Band_7 156 alaakqaaeaeaqaeiaraeaea 178
                                       a+++   ae++++a i +a++e+
  gi|336255662|ref|YP_004598769.1| 190 AMEEQTSAERRRRAMILEAQGER 212
                                       ********************985 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.1
                            Band_7 125 knelneqlrkyG.......vevldvritdidpppevaqalaakqaaeaea 167
                                        +el++ + +yG       ve  + +++++d+ +e ++ +     a++  
  gi|336255662|ref|YP_004598769.1| 285 PQELTSLVGRYGkhlsgsdVETDGTDLESLDFDEETRELIGLDDIADIIG 334
                                       56666666666666666668888888888888888888765555555444 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 ?   13.9   0.1   3.6e-06     0.032     113     209 ..     103     197 ..      70     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-06
                          Band_7_1 113 dpakllreivGtdgefdteeiseqlkslivtrlsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekle 189
                                       d+ +++r +  t   ++ ++ +  + +l +t+l  v+++ +  + d  ++ e++ e++++ l+e  +e G+ +e++e
  gi|336255662|ref|YP_004598769.1| 103 DAVVYIRVMDATRAFLEVDDYERAVSNLAQTTLRAVIGDME--LDDTLSRREMINERIRQELDEPTDEWGIRVESVE 177
                                       66666666667777778888888888888888888888755..568999**************************** PP

                          Band_7_1 190 ienislpeevekaldkrasm 209
                                       +++++    v+ a+++++s+
  gi|336255662|ref|YP_004598769.1| 178 VREVTPSAGVKGAMEEQTSA 197
                                       ****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3134.30
//
Query:       gi|336255663|ref|YP_004598770.1|  [L=412]
Description: sodium/hydrogen exchanger [Halopiger xanaduensis SH-6]
Scores for 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  200.5  50.4    3.9e-59  200.4  50.4    1.0  1  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 !  200.4  50.4   2.2e-63   3.9e-59       2     377 ..      13     390 ..       9     394 .. 0.91

  Alignments for each domain:
  == domain 1  score: 200.4 bits;  conditional E-value: 2.2e-63
                                       HHHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHH CS
                    Na_H_Exchanger   2 vllillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlks 78 
                                       +l++++a ++g++a+rl+ p ++g+++aG+++Gp +lgl++ s   l+ l++lg++ll+  +G+e+dlrel++ + +
  gi|336255663|ref|YP_004598770.1|  13 LLVLTVAWIFGAVAERLGYPTMMGELFAGIVFGPPLLGLLHGS-ALLSNLADLGVFLLMVFVGMEVDLRELFRLGPQ 88 
                                       3455557777779*****************************9.********************************* PP

                                       HHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHC CS
                    Na_H_Exchanger  79 illlallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDava 155
                                       +ll+a++ ++i++ l G+++++  +lg+++ +al++g++++at++++ ++il+++ ++++r++++llg ++  D+ +
  gi|336255663|ref|YP_004598770.1|  89 SLLIAFGAFVIPFGL-GYVAGI--WLGVSVGAALFLGLAMAATSLATKSRILADLELLDTRIANVLLGGALASDVGV 162
                                       ***************.*****8..9**************************************************** PP

                                       CCCCHHHHHHTX....XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.CTHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 156 vvllavllalak....eeaggetslllllliflvvavgglllglvigwllrlitrft.dddrelevllvlllallaa 227
                                       +v++a + ++++      a  ++ l++ + +f++ +v+g+ +  v ++  ++ +++    dr + + ++ll++ll a
  gi|336255663|ref|YP_004598770.1| 163 LVAFAGVDSYVTagalDPAEIGIILGKTVAFFAITLVLGYRFLPVAWHHIERQRERYgFVDRTTAFTFALLVSLLFA 239
                                       ***********7654444444455555555555666666666666666666666666999***************** PP

                                       HHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH....HHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHH CS
                    Na_H_Exchanger 228 llaellgvsgilgaflaGlvlseyefsnklseklesfre....glfnplfFvlvGlsldlkvlnnhlsvlilvllil 300
                                       +la+l ++++i+g f+aG+ l + +++ +l   ++ +++    glf+p+fFv vG ++ + v+   ++ + +++l++
  gi|336255663|ref|YP_004598770.1| 240 YLATLADLHMIIGGFMAGMFLRQADVEPDLYDHMHTVMYdlamGLFAPIFFVTVGFEIGFGVF---VDSFGILALLV 313
                                       *************************************************************99...999**999999 PP

                                       HHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHHH CS
                    Na_H_Exchanger 301 vaillgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslkp 377
                                       ++ +lg+i++ +l++  + l++re l++gfg+ +rg+v +++a+++  +g++++ ++++l+++++ft+ + ++++++
  gi|336255663|ref|YP_004598770.1| 314 AVAFLGKIVGSWLFALPTSLTSREGLVVGFGMNGRGTVEIIIAQVAFEAGVIDQSMFSILVFIAIFTTALVPVTVTW 390
                                       9999*****************************************************************99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3242.27
//
Query:       gi|336255664|ref|YP_004598771.1|  [L=500]
Description: MATE efflux family protein [Halopiger xanaduensis SH-6]
Scores for 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-58  194.9  39.9    1.5e-34  119.0  15.3    2.6  3  MatE             MatE
    3.8e-08   33.5  14.5    3.8e-08   33.5  14.5    3.8  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
       0.16   11.7   0.1       0.16   11.7   0.1    1.9  2  YniB             YniB-like protein
          1    9.6   0.0          1    9.6   0.0    3.8  5  Pmp3             Proteolipid membrane potential modulator


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 !  119.0  15.3   3.4e-38   1.5e-34       1     160 [.      45     204 ..      45     205 .. 0.99
   2 ?   -4.1   0.3       2.4   1.1e+04      70      86 ..     223     239 ..     219     241 .. 0.44
   3 !   89.6   8.2   3.7e-29   1.7e-25      11     159 ..     280     429 ..     270     431 .. 0.95

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 3.4e-38
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       Pi+++nll++ ++lidt+++g+++++alAa+s+a++ ++ll+++++gls+a ++lv+q +Ga+   +a+ a+ q+++
  gi|336255664|ref|YP_004598771.1|  45 PIVVTNLLQTAYNLIDTFWLGQYSTTALAAISFAFPMVFLLISVGMGLSVAGSVLVAQHIGAGEEAEAEYAASQTVV 121
                                       9**************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       l+l+ + +i ++++ + +++l l++++e+vl+ a +y++++ lg+ +++ ++v+ + +rg+g+t +p+ +++ s+ll
  gi|336255664|ref|YP_004598771.1| 122 LSLVGATLIGVVGYGLVDDLLALLGASEAVLPPATEYMQVISLGMAFMFGFFVFIALMRGYGDTVTPMLVMFGSVLL 198
                                       ***************************************************************************** PP

                              MatE 155 niplny 160
                                       n++l++
  gi|336255664|ref|YP_004598771.1| 199 NVVLDP 204
                                       ***987 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 2.4
                              MatE  70 ealrqglilllllslii 86 
                                       +a++ +  l+l+++l+i
  gi|336255664|ref|YP_004598771.1| 223 VATVFSRALALVVGLAI 239
                                       44444444444444444 PP

  == domain 3  score: 89.6 bits;  conditional E-value: 3.7e-29
                              MatE  11 llslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliia 87 
                                       l+  ++ ++v+ ++++ +Aa++++++++s++f+++++++ +++t++gq++Ga+ ++rakea+  +  +++l+  ++ 
  gi|336255664|ref|YP_004598771.1| 280 LSINLLLVIVAIFPDTVVAAYGVGTRVFSVIFLPAVAVARGVETMTGQNIGAGEPDRAKEAADFAARTMFLILGALG 356
                                       5556778899999**************************************************************** PP

                              MatE  88 llvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipln 159
                                       +++++ +e+i+  ft++ ev+ ++ ++lr+++++  ++++   ++g +rgagkt +++ i+++ + l+++p++
  gi|336255664|ref|YP_004598771.1| 357 VVAWIAAEPIMAAFTDNTEVVDVGVTFLRYVAPTFGFIGIMRSYNGSFRGAGKTLTAAGIVIVIYaLVRLPVA 429
                                       **********************************************************************997 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 ?   -1.1   6.0      0.41   1.8e+03      88     136 ..      77     137 ..      45     142 .. 0.64
   2 !   33.5  14.5   8.6e-12   3.8e-08       1     135 [.     158     301 ..     158     316 .. 0.69
   3 ?   -3.9   0.6         3   1.3e+04      53      63 ..     352     361 ..     343     371 .. 0.45
   4 !   11.0   1.1   7.2e-05      0.32       2      81 ..     384     465 ..     383     474 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.41
                   Polysacc_synt_C  88 lrrllkpllaalvmgivvylllllllglllla............alalllavlvgalvYll 136
                                       +   ++ ll++++mg+ v + +l+   +  ++             l+l+ a l+g++ Y+l
  gi|336255664|ref|YP_004598771.1|  77 FAFPMVFLLISVGMGLSVAGSVLVAQHIGAGEeaeaeyaasqtvVLSLVGATLIGVVGYGL 137
                                       3334577888999999966555555555555588999988775444777777788777766 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 8.6e-12
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvav 71 
                                       ++++++l++ f++ + v+ +++ g g + +++++++ ++l++++l  +li      p++gi Gaa+atv++ ++++v
  gi|336255664|ref|YP_004598771.1| 158 YMQVISLGMAFMFGFFVFIALMRGYGDTVTPMLVMFGSVLLNVVLDPFLIfgwgpfPELGIQGAAVATVFSRALALV 234
                                       699***********************************************88888888899**********999999 PP

                   Polysacc_synt_C  72 ln...lyalrrllgikl.ellrrllkpllaalvmgivvylllllllgllllaal.alllavl..vgalvYl 135
                                       +    +++ rr ++i+l +++ +l   +   +++g          +g  l+ +l  +++a++    +++Y+
  gi|336255664|ref|YP_004598771.1| 235 VGlaiMFRGRRGVRIRLgQMWPDL-SFAKKLVGIGFP---ASIEGMGRALSINLlLVIVAIFpdTVVAAYG 301
                                       875557777888888888445544.233333333333...2222222222222213333333333333333 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3
                   Polysacc_synt_C  53 fgivGaaiatv 63 
                                       +g++G ++a++
  gi|336255664|ref|YP_004598771.1| 352 LGALG-VVAWI 361
                                       22222.22333 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 7.2e-05
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkial.kalvigalvklilnllli.plfgivGaaiatvlallvvavlnlya 76 
                                       L+++a+++ f+++++ +++ + g g++ +a+ +++vi alv l +   l    +g  G+ ia +++ +++a l +++
  gi|336255664|ref|YP_004598771.1| 384 LRYVAPTFGFIGIMRSYNGSFRGAGKTLTAAgIVIVIYALVRLPVAAGLAqTGLGSRGIWIAFAVSNVLGAGLTYVW 460
                                       78999**********************8877477788899**********778999******************999 PP

                   Polysacc_synt_C  77 lrrll 81 
                                        rr +
  gi|336255664|ref|YP_004598771.1| 461 YRRGT 465
                                       98866 PP

>> YniB  YniB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.7e-05      0.16      44     107 ..      49     109 ..      41     120 .. 0.74
   2 ?   -2.8   0.3       1.1   4.8e+03      40      96 ..     194     245 ..     166     248 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.7e-05
                              YniB  44 velvrfntpfLnvFWknsPvPdfkellassniaFlliylliFvGlalqasgarlsrqvkeiree 107
                                       ++l+++  + +++FW        ++ la+  +aF +++lli vG+ l+++g+ l++q     ee
  gi|336255664|ref|YP_004598771.1|  49 TNLLQTAYNLIDTFWLGQYS---TTALAAISFAFPMVFLLISVGMGLSVAGSVLVAQHIGAGEE 109
                                       56666777777888865433...3334568899*********************9987555555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                              YniB  40 ikvlvelvrfntpfLnvFWknsPvPdfkellassniaFlliylliFvGlalqasgar 96 
                                         vl ++v    pfL + W   P P+   + a+  + F    l + vGla++  g+r
  gi|336255664|ref|YP_004598771.1| 194 GSVLLNVVL--DPFLIFGWG--PFPELGIQGAAVATVFSR-ALALVVGLAIMFRGRR 245
                                       444444443..356666663..566555554444444443.3445577777766665 PP

>> Pmp3  Proteolipid membrane potential modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.7   7.6e+03      10      26 ..     151     168 ..     150     180 .. 0.67
   2 ?   -3.5   0.1       2.9   1.3e+04      26      32 ..     196     202 ..     187     212 .. 0.62
   3 ?    9.6   0.0   0.00023         1      19      46 ..     273     300 ..     269     302 .. 0.90
   4 ?    0.7   0.0      0.14   6.1e+02       5      17 ..     306     318 ..     304     326 .. 0.80
   5 ?   -1.2   0.2      0.54   2.4e+03       6      29 ..     420     445 ..     416     451 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                              Pmp3  10 ilPPlaValksG.csadl 26 
                                       +lPP+  ++++  +++++
  gi|336255664|ref|YP_004598771.1| 151 VLPPATEYMQVIsLGMAF 168
                                       588888777765566654 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.9
                              Pmp3  26 llinilL 32 
                                       +l+n++L
  gi|336255664|ref|YP_004598771.1| 196 VLLNVVL 202
                                       5666665 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00023
                              Pmp3  19 ksGcsadllinilLtllgylPgviHAfy 46 
                                       + G++ +l in+lL + +++P ++ A y
  gi|336255664|ref|YP_004598771.1| 273 IEGMGRALSINLLLVIVAIFPDTVVAAY 300
                                       679999***************9999988 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.14
                              Pmp3   5 illaiilPPlaVa 17 
                                       ++  i+lP +aVa
  gi|336255664|ref|YP_004598771.1| 306 VFSVIFLPAVAVA 318
                                       56679***99998 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 0.54
                              Pmp3   6 llaiilPPlaVal.ksGcsad.llin 29 
                                       + a++  P+a+ l ++G+++  ++i 
  gi|336255664|ref|YP_004598771.1| 420 IYALVRLPVAAGLaQTGLGSRgIWIA 445
                                       55544335555553899655447776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); 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:                         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 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3767.02
//
Query:       gi|336255665|ref|YP_004598772.1|  [L=214]
Description: regulatory protein TetR [Halopiger xanaduensis SH-6]
Scores for 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-20   73.0   4.6    2.3e-20   73.0   4.6    1.9  2  TetR_C_6         BetI-type transcriptional repressor, C-termi
    1.8e-13   50.0   0.1    3.1e-13   49.3   0.1    1.4  1  TetR_N           Bacterial regulatory proteins, tetR family
    1.9e-07   31.4   0.8    5.1e-07   30.0   0.1    2.0  2  TetR_C_24        Tetracyclin repressor-like, C-terminal domai
    0.00024   21.4   4.4    0.00024   21.4   4.4    2.3  2  TetR_C_11        Tetracyclin repressor-like, C-terminal domai
    0.00045   20.1   0.0     0.0022   17.9   0.0    2.1  2  TetR_C_13        Tetracyclin repressor-like, C-terminal domai
    0.00075   19.5   1.8     0.0025   17.8   0.9    2.4  2  TetR_C_27        Tetracyclin repressor-like, C-terminal domai
    0.00087   19.3   0.0     0.0022   18.1   0.0    1.7  2  TetR_C_17        Tetracyclin repressor-like, C-terminal domai
    0.00092   19.5   0.3     0.0047   17.2   0.1    2.1  2  TetR_C_25        Tetracyclin repressor-like, C-terminal domai
     0.0046   17.2   1.6      0.034   14.4   0.6    2.2  2  Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
  ------ inclusion threshold ------
      0.026   14.7   0.0      0.043   14.0   0.0    1.3  1  TetR_C_4         YsiA-like protein, C-terminal region
      0.028   14.5   0.0      0.052   13.6   0.0    1.6  1  TetR_C_29        Tetracyclin repressor-like, C-terminal domai
        1.8    8.7   8.4       0.32   11.1   0.3    2.5  3  Acetyltransf_6   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> TetR_C_6  BetI-type transcriptional repressor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.6   2.4e+03       2      19 ..      49      66 ..      45      70 .. 0.55
   2 !   73.0   4.6   1.5e-23   2.3e-20       1     114 [.      75     189 ..      75     190 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                                      HHHHHHHHHCCSTHSHHH CS
                          TetR_C_6  2 rerlraileallpldqer 19
                                      re l+a+le l+   ++r
  gi|336255665|ref|YP_004598772.1| 49 RELLEAFLEHLIEQFEAR 66
                                      455555555555544444 PP

  == domain 2  score: 73.0 bits;  conditional E-value: 1.5e-23
                                       HHHHHHHHHHCCST..HSHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH.TTSCTTSTHHH CS
                          TetR_C_6   1 prerlraileallp..ldqerraelavwlafwaeaardpelaelqrenyarlrsnlrallaelae.gglradadaea 74 
                                       p+erl+a++++ll+  +d+   a+ +++l++ a++++d++++e+++e+++rlr+++++ +a++++ g++++d d+ea
  gi|336255665|ref|YP_004598772.1|  75 PAERLHAFVDELLSsaDDDSATAFRTAMLEIKAQSPYDEAYQERLAEFDRRLRDRIADFVADGVAaGEFHEDIDPEA 151
                                       89***********96555555678999************************************************** PP

                                       HHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHHT CS
                          TetR_C_6  75 aAerlaAlidGLwlraalapeeldaeraralvrrhldall 114
                                         e l+ + +G  +raa    + ++er  a v++++d+ l
  gi|336255665|ref|YP_004598772.1| 152 TGEFLVTVFHGAQTRAAAV--DRSPERTKAYVHDYIDEAL 189
                                       *****************99..999*************987 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 !   49.3   0.1   2.1e-16   3.1e-13       1      46 [.       9      54 ..       9      55 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2.1e-16
                                      HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                            TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                      I+da+ + + e+Gy+++t+++IA++   skg+l+++F++K+eLlea
  gi|336255665|ref|YP_004598772.1|  9 IMDATYRALCEHGYAELTMQDIAAESTKSKGTLHYHFDGKRELLEA 54
                                      89******************************************98 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.7   2.6e+03      48      48 ..      49      49 ..       4      69 .. 0.55
   2 !   30.0   0.1   3.4e-10   5.1e-07       2      85 ..      73     161 ..      72     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.7
                                      H CS
                         TetR_C_24 48 r 48
                                      r
  gi|336255665|ref|YP_004598772.1| 49 R 49
                                      3 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 3.4e-10
                                       SSHHHHHHHHHHHHHHHHHHTHHHHH.HHHHHGGG...S-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB.-SS-H CS
                         TetR_C_24   2 gspaerLralvrahveviaeereeaa.vllrelra...LspehreeiralrreyerllrdlieeGvaagef.edldp 73 
                                       ++paerL+a+v +++    ++ ++a+   + e++a    +++++e++++  r+++++++d +++Gvaagef ed dp
  gi|336255665|ref|YP_004598772.1|  73 ETPAERLHAFVDELLSSADDDSATAFrTAMLEIKAqspYDEAYQERLAEFDRRLRDRIADFVADGVAAGEFhEDIDP 149
                                       79*************9998877655414455555511156789999******************************* PP

                                       HHHHHHHHHHHH CS
                         TetR_C_24  74 klaalailgmln 85 
                                       + +  +++++ +
  gi|336255665|ref|YP_004598772.1| 150 EATGEFLVTVFH 161
                                       999888877665 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.1   1.7e+03      42      61 ..      49      68 ..      32      76 .. 0.68
   2 !   21.4   4.4   1.6e-07   0.00024       8      91 ..      76     161 ..      70     188 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.1
                         TetR_C_11 42 pelaealrerlleprraalr 61
                                       el ea+ e+l+e+  a+ +
  gi|336255665|ref|YP_004598772.1| 49 RELLEAFLEHLIEQFEARTE 68
                                      45666666666655555444 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.6e-07
                         TetR_C_11   8 rgDLrallralaealaspragallrallaeaqrdpelaealrerl..lepr.raalravlrrAvarGelradadvel 81 
                                       ++ L+a++++l  + ++ + + ++r  + e+++     ea++erl  +++r r+++++ ++ +va Ge  +d+d+e+
  gi|336255665|ref|YP_004598772.1|  76 AERLHAFVDELLSSADD-DSATAFRTAMLEIKAQSPYDEAYQERLaeFDRRlRDRIADFVADGVAAGEFHEDIDPEA 151
                                       56799999999998888.6888899999998887777777777774444445999********************98 PP

                         TetR_C_11  82 vldlllgpll 91 
                                         + l+ +++
  gi|336255665|ref|YP_004598772.1| 152 TGEFLVTVFH 161
                                       8877776543 PP

>> TetR_C_13  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.44   6.5e+02       1      12 [.      74      85 ..      39      98 .. 0.74
   2 !   17.9   0.0   1.5e-06    0.0022      38     111 ..     111     185 ..      74     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.44
                                      -HHHHHHHHHHH CS
                         TetR_C_13  1 aPlerlrafved 12
                                      +P erl+afv++
  gi|336255665|ref|YP_004598772.1| 74 TPAERLHAFVDE 85
                                      366667776665 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.5e-06
                                       S-TTHHHHHHHHHHHHHHHHHHHHHHHHCTTSS-TTS-HHHHHHHHHHHHHHHHHHHH.HHTSSHHHHHHHHHHG CS
                         TetR_C_13  38 lpesfrerleevledwqkrvaacleeaqeageiaadadaeelaeffwigWeGAvlRak.lerstqPlelfletfl 111
                                        +e+++erl e   + ++r+a+ + +  +age ++d d+e+  ef+++ + GA +Ra  + rs++  +++++ ++
  gi|336255665|ref|YP_004598772.1| 111 YDEAYQERLAEFDRRLRDRIADFVADGVAAGEFHEDIDPEATGEFLVTVFHGAQTRAAaVDRSPERTKAYVHDYI 185
                                       57999***************************************************7527788888888877776 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 ?   -3.0   0.0       4.9   7.4e+03      39      52 ..      50      63 ..      45      65 .. 0.60
   2 !   17.8   0.9   1.7e-06    0.0025       1      81 [.      75     160 ..      75     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.9
                                      HHHHHHHHHHHHHH CS
                         TetR_C_27 39 evvekhieeleeql 52
                                      e  e+++e+l+eq+
  gi|336255665|ref|YP_004598772.1| 50 ELLEAFLEHLIEQF 63
                                      45556666666665 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH.......HH-HHHHHHHHHHHHHHHHHHHHHHHHCT-STT-.- CS
                         TetR_C_27   1 AeerLrewlaalfeakrrkarddpelFatyvvli.......eeelevvekhieeleeqlaeIireGvaaGeFkaa.d 69 
                                       ++erL++++++l+ +  ++       F+t +  i       e++ e  +++ ++l++ +a+ +++GvaaGeF+++ d
  gi|336255665|ref|YP_004598772.1|  75 PAERLHAFVDELLSSADDDSA---TAFRTAMLEIkaqspydEAYQERLAEFDRRLRDRIADFVADGVAAGEFHEDiD 148
                                       567777777777766554433...3344444444000111134555666666778899**************98769 PP

                                       HHHHHHHHHHHS CS
                         TetR_C_27  70 peaaaravfdat 81 
                                       pea+++ +++++
  gi|336255665|ref|YP_004598772.1| 149 PEATGEFLVTVF 160
                                       999998877665 PP

>> TetR_C_17  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.6   2.4e+03      51      64 ..      51      64 ..      24      90 .. 0.63
   2 !   18.1   0.0   1.5e-06    0.0022      22      95 ..     100     173 ..      78     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                                      HHHHHHHHHHHTTS CS
                         TetR_C_17 51 alkellqeGvergE 64
                                       l+++l++ +e+ E
  gi|336255665|ref|YP_004598772.1| 51 LLEAFLEHLIEQFE 64
                                      33333333333333 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHGGGG-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS---SS-HHHHHHHHHHHHHHHHHHHHHS-HH CS
                         TetR_C_17  22 lakyEyfltsyreeerrayleeRyerlvealkellqeGvergEfkPqlplesiakylisfldGliletlalgee 95 
                                       +a++E   +s  +e+ ++ l+e   rl +++ +++ +Gv+ gEf+  ++ e+  ++l+ ++ G  ++++a++  
  gi|336255665|ref|YP_004598772.1| 100 TAMLEIKAQSPYDEAYQERLAEFDRRLRDRIADFVADGVAAGEFHEDIDPEATGEFLVTVFHGAQTRAAAVDRS 173
                                       5555555555445555555666667899***********************************99999998864 PP

>> TetR_C_25  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.5   2.2e+03      19      35 ..      50      66 ..      41      70 .. 0.78
   2 !   17.2   0.1   3.1e-06    0.0047      25      92 ..     123     188 ..     115     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.5
                         TetR_C_25 19 dlakallehmvedaeay 35
                                      +l +a+leh++e  ea 
  gi|336255665|ref|YP_004598772.1| 50 ELLEAFLEHLIEQFEAR 66
                                      56789999999988875 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.1e-06
                         TetR_C_25  25 lehmvedaeayleegvaaGtirpsrdpkarArylalsslGalllelqlheeedptdlravlreylerm 92 
                                        +++ + + + +++gvaaG   +  dp+a+  +l+++  Ga + + ++++  +p+ ++a++++y++++
  gi|336255665|ref|YP_004598772.1| 123 DRRLRDRIADFVADGVAAGEFHEDIDPEATGEFLVTVFHGAQTRAAAVDR--SPERTKAYVHDYIDEA 188
                                       56777788899********************************9999999..99999*******9986 PP

>> Gluconate_2-dh3  Gluconate 2-dehydrogenase subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.6   2.3e-05     0.034       7     103 ..      52     154 ..      46     165 .. 0.74
   2 ?    1.5   0.0      0.21   3.2e+02      20      39 ..     172     191 ..     164     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                   Gluconate_2-dh3   7 laaladrIiPs....tdtgpgakeag.vaafidrqladaplppeqeayrkglaaldaya..raeygksFveldgaqq 76 
                                       l+a  +++i +    t+t pg++ a+  +af+d+ l +a + + ++a+r ++ +++a++  +++y+++ +e d   +
  gi|336255665|ref|YP_004598772.1|  52 LEAFLEHLIEQfearTETVPGETPAErLHAFVDELLSSADDDS-ATAFRTAMLEIKAQSpyDEAYQERLAEFDRRLR 127
                                       55555555555333276789988875499*********87777.999999999999998778999999999999999 PP

                   Gluconate_2-dh3  77 dalLealekeaeakgtgealeasaeah 103
                                       d++ + ++++  a + +e+++++a  +
  gi|336255665|ref|YP_004598772.1| 128 DRIADFVADGVAAGEFHEDIDPEATGE 154
                                       998888888866655566666666555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                   Gluconate_2-dh3  20 tgpgakeagvaafidrqlad 39 
                                        +p +++a v+++id++l  
  gi|336255665|ref|YP_004598772.1| 172 RSPERTKAYVHDYIDEALRA 191
                                       369999*********99865 PP

>> TetR_C_4  YsiA-like protein, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.9e-05     0.043       5      96 ..      56     153 ..      50     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHHHHHTT..-SSHHHHHHHHHHHHHHHHHC-HHHHHHHH.TTCC.GS..SHHHHHHHHHHHHHHHHHHHH CS
                          TetR_C_4   5 lgqfvekikeeike..kesaeeklkllvekhfsqlsadkelaivtq.lelr.qs..nlelrlkinevlkgyltllde 75 
                                       l++++e+ + +++    e++ e+l+ +v++ +s+ ++d+  a  t  le++ qs  ++  ++++ e  +     + +
  gi|336255665|ref|YP_004598772.1|  56 LEHLIEQFEARTETvpGETPAERLHAFVDELLSSADDDSATAFRTAmLEIKaQSpyDEAYQERLAEFDRRLRDRIAD 132
                                       556777776665541157899*********************98853799756644677899*****999999**** PP

                                       HHHHHHHTTSC-TT--HHHHH CS
                          TetR_C_4  76 iiaeGkekGefkeeldvrlar 96 
                                        +a+G ++Gef+e++d + + 
  gi|336255665|ref|YP_004598772.1| 133 FVADGVAAGEFHEDIDPEATG 153
                                       ***************988765 PP

>> TetR_C_29  Tetracyclin repressor-like, C-terminal 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     0.052      40      74 ..     116     150 ..      75     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                                       S--SS-.THHHHHHHHHHHHHHHHTTSS-SS--HH CS
                         TetR_C_29  40 sesirelnspliekleeilerGqaagvFrpgvdal 74 
                                       +e+++e+ ++l +++++ ++ G+aag F +++d++
  gi|336255665|ref|YP_004598772.1| 116 QERLAEFDRRLRDRIADFVADGVAAGEFHEDIDPE 150
                                       67899999*************************97 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       4.7     7e+03     116     131 ..      10      25 ..       8      27 .. 0.75
   2 ?   11.1   0.3   0.00022      0.32      16      70 ..      37      95 ..      31     108 .. 0.83
   3 ?    2.2   0.5      0.12   1.8e+02       8      69 ..     127     192 ..     120     201 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.7
                    Acetyltransf_6 116 lweliedaaeeGlrrf 131
                                       +  + ++++e+G++++
  gi|336255665|ref|YP_004598772.1|  10 MDATYRALCEHGYAEL 25 
                                       5667788999998875 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00022
                    Acetyltransf_6 16 elgevrfrvatdpedleallelfraqwarr....pdvfadpltraflrdllaalaarga 70
                                      + g++ ++++  +e lea+le + +q+++r    p+    ++ +af+ +ll++ +++ a
  gi|336255665|ref|YP_004598772.1| 37 SKGTLHYHFDGKRELLEAFLEHLIEQFEARtetvPGETPAERLHAFVDELLSSADDDSA 95
                                      5689999***********************99997777789999*******99865443 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.12
                    Acetyltransf_6   8 rrkrrkleelg..evrfrvatdpedleallelfraqwarr..pdvfadpltraflrdllaalaarg 69 
                                       r ++  + + g  + +f+ + dpe+  ++l  +++  + r      ++++t a+++d++++  +++
  gi|336255665|ref|YP_004598772.1| 127 RDRIADFVADGvaAGEFHEDIDPEATGEFLVTVFHGAQTRaaAVDRSPERTKAYVHDYIDEALRAD 192
                                       444444444442233566666899999999999887777764222334566667777777665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1652.60
//
Query:       gi|336255666|ref|YP_004598773.1|  [L=155]
Description: hypothetical protein Halxa_4292 [Halopiger xanaduensis SH-6]
Scores for complete 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-34  119.1   0.2    1.9e-34  118.5   0.0    1.4  2  RNA_binding  RNA binding
  ------ inclusion threshold ------
       0.15   11.8   1.0         13    5.6   0.1    2.3  2  Get5_C       Get5 C-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 !  118.5   0.0   2.1e-38   1.9e-34       1     118 [.       8     127 ..       8     128 .. 0.95
   2 ?   -2.8   0.1      0.82   7.4e+03      57      66 ..     142     151 ..     133     154 .. 0.54

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 2.1e-38
                                       EEEEEEEE-TTC-HHHHHHHHHTTSTTS.......E---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHHC CS
                       RNA_binding   1 kievrafvhaTEdeekVlealsnllpee.......eveieeeeaeGhygnpitileaelekkka.kkvlkkllellr 69 
                                       ++++r+f++aTEde++V+eal+++lp+         + ie+ e+eGhyg++i++l+a++e++++ ++vl++l++l +
  gi|336255666|ref|YP_004598773.1|   8 YVDLRTFCYATEDEKRVEEALRTFLPDRegddadePFPIERAESEGHYGDRILVLSARVENADDvRHVLSRLADLES 84 
                                       699***********************99*****997899**********************************9988 PP

                                       CCCHHHHHHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEEE CS
                       RNA_binding  70 eeeikeLlkeleervdekgklylrldKQaaylgklslvegddvIkvkik 118
                                        +e   L++el+erv+e+ +l+lrldKQaa++g+++l   +d I+++ k
  gi|336255666|ref|YP_004598773.1|  85 FDE---LMDELDERVTENTELFLRLDKQAAFEGDVRL---GDGITFRGK 127
                                       776...*******************************...999999877 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.82
                                       HHHHHHHHHH CS
                       RNA_binding  57 akkvlkklle 66 
                                       a++vl++l+e
  gi|336255666|ref|YP_004598773.1| 142 AEEVLERLRE 151
                                       3555555554 PP

>> Get5_C  Get5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0014        13      13      30 ..      62      79 ..      59      80 .. 0.91
   2 ?    4.6   0.1     0.003        27      20      31 ..     138     150 ..     133     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0014
                            Get5_C 13 LknkfkndaearavleRL 30
                                      L +  +n+ ++r vl RL
  gi|336255666|ref|YP_004598773.1| 62 LSARVENADDVRHVLSRL 79
                                      88999************9 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.003
                            Get5_C  20 d.aearavleRLq 31 
                                       + a+a++vleRL+
  gi|336255666|ref|YP_004598773.1| 138 AvANAEEVLERLR 150
                                       55899*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1197.75
//
Query:       gi|336255667|ref|YP_004598774.1|  [L=68]
Description: hypothetical protein Halxa_4293 [Halopiger xanaduensis SH-6]
Scores for 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   13.2   0.1      0.063   12.9   0.1    1.2  1  DUF1918    Domain of unknown function (DUF1918)
       0.11   12.3   0.1       0.21   11.4   0.0    1.6  2  LBR_tudor  Lamin-B receptor of TUDOR domain
       0.18   11.7   0.0       0.26   11.2   0.0    1.4  1  Tudor_3    DNA repair protein Crb2 Tudor domain


Domain annotation for each model (and alignments):
>> DUF1918  Domain of unknown function (DUF1918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.1e-05     0.063       7      48 ..       7      48 ..       1      51 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                                      EEEEES-TTTS--EEEEEEEE-S-SS.S-S-EEEEETTTTEEE CS
                           DUF1918  7 DrlvvegrtvgepereGeiveVrged.GaPPYlVRweddghes 48
                                      Dr+v + ++ +    +G+++    +  G+  Y+V +e dg+e+
  gi|336255667|ref|YP_004598774.1|  7 DRVVLHDEHSEFDGETGTVTQTMESMfGDVTYTVSFE-DGQET 48
                                      9*******************9887766**********.99886 PP

>> LBR_tudor  Lamin-B receptor of TUDOR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.66   3.9e+03      10      11 ..       7       8 ..       1      17 [. 0.50
   2 ?   11.4   0.0   3.5e-05      0.21      36      52 ..      37      53 ..      27      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.66
                         LBR_tudor 10 ev 11
                                      + 
  gi|336255667|ref|YP_004598774.1|  7 DR 8 
                                      32 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.5e-05
                         LBR_tudor 36 lYtVkykDGTelelkes 52
                                       YtV ++DG e  ++e+
  gi|336255667|ref|YP_004598774.1| 37 TYTVSFEDGQETGIPED 53
                                      6***********99996 PP

>> Tudor_3  DNA repair protein Crb2 Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.4e-05      0.26      30      48 ..      34      54 ..      22      57 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.4e-05
                                      S..EEEEEETTS-EEEEETTS CS
                           Tudor_3 30 q..rykVrFdDgtpeevdskq 48
                                         +y+V F+Dg+ + +++++
  gi|336255667|ref|YP_004598774.1| 34 GdvTYTVSFEDGQETGIPEDA 54
                                      1349**********9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 554.53
//
Query:       gi|336255668|ref|YP_004598775.1|  [L=219]
Description: DNA polymerase beta domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-10   40.2   0.1    4.9e-10   39.6   0.1    1.4  1  NTP_transf_2    Nucleotidyltransferase domain
    1.3e-07   31.6   0.0    2.3e-07   30.8   0.0    1.4  1  Polbeta         Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.042   14.1   0.0      0.066   13.4   0.0    1.3  1  DNA_pol_B_palm  DNA polymerase beta palm
      0.045   13.7   0.1        8.9    6.3   0.0    2.4  2  MarR_2          MarR family
      0.067   13.0   0.1       0.21   11.4   0.1    1.8  1  DUF294          Putative nucleotidyltransferase DUF294


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.1   1.4e-13   4.9e-10       5      48 ..     105     162 ..     101     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.4e-13
                                       HHHHHHHTT.TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH...............H CS
                      NTP_transf_2   5 leelkelep.vakvvlfGSyarGtalkgSDiDllvvlpeevsre...............k 48 
                                         ++ ++ + va +v+fGS+arG+a + SDiD+++++ ++   e               +
  gi|336255668|ref|YP_004598775.1| 105 VSRVNKELStVAGIVCFGSVARGEADRMSDIDVFLLVADDD--EliptrrtvsdiarelE 162
                                       4455444445***************************9994..33355554433333331 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   6.3e-11   2.3e-07      10      64 ..     112     173 ..     105     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 6.3e-11
                                       HHHHHSTTEEEEEE-S------EEEEEEEESS-....--HHHHHHHHHHHHHH....SSSEE CS
                           Polbeta  10 ekeielaylFGSrakgkareeSDiDlavllkek....ldleeelelaaeledi...klgkkv 64 
                                        + ++ ++ FGS+a+g+a + SDiD+++l+ ++     +  +  ++a ele+     +++++
  gi|336255668|ref|YP_004598775.1| 112 LSTVAGIVCFGSVARGEADRMSDIDVFLLVADDdeliPTRRTVSDIARELEEQpidGQRYEF 173
                                       4678999************************9988888888899999999998644333344 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.8e-05     0.066       2      54 ..      92     146 ..      91     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                       EEHHHHHH.HHHHHHHHHHHH-TT-EEEE-HHHHTT-S.EESSEEEEEEBTTBST CS
                    DNA_pol_B_palm   2 iPreEvea.lealvkkaakeldpevevivcGSYRRgae.ssGDvDvlitkkdaks 54 
                                       iP+ E ++ l+++v++  kel+  + +++ GS  Rg++    D+Dv +   d ++
  gi|336255668|ref|YP_004598775.1|  92 IPQTEFREpLKRFVSRVNKELSTVAGIVCFGSVARGEAdRMSDIDVFLLVADDDE 146
                                       899998654899*********************999761689***9877666555 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0025       8.9      15      55 ..      28      68 ..      22      72 .. 0.86
   2 ?    5.0   0.0    0.0065        23      20      31 ..     147     161 ..     132     162 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0025
                                      HCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 15 grrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      + +p  +++ ++l r +g+  ++vs++l  L    L++rr+
  gi|336255668|ref|YP_004598775.1| 28 AQNPSSEFSNRDLQRLTGYGGPSVSNALSLLTGMELLVRRD 68
                                      56666689999**************************9995 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0065
                                       S...EEEHHHHHHHH CS
                            MarR_2  20 r...dltvgelarrl 31 
                                           + tv+++ar+l
  gi|336255668|ref|YP_004598775.1| 147 LiptRRTVSDIAREL 161
                                       255555*******98 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1     6e-05      0.21      52      79 ..     118     146 ..      92     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6e-05
                            DUF294  52 llvmGSeGReEqtlktDqDnalvled.ee 79 
                                        +++GS +R+E+   +D D +l+++d +e
  gi|336255668|ref|YP_004598775.1| 118 IVCFGSVARGEADRMSDIDVFLLVADdDE 146
                                       5789*********************9422 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1655.98
//
Query:       gi|336255669|ref|YP_004598776.1|  [L=159]
Description: hypothetical protein Halxa_4295 [Halopiger xanaduensis SH-6]
Scores for 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  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1264.79
//
Query:       gi|336255670|ref|YP_004598777.1|  [L=174]
Description: cytidyltransferase-related domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-14   51.9   0.0    1.1e-13   51.6   0.0    1.1  1  CTP_transf_like  Cytidylyltransferase-like
     0.0012   18.8   0.2      0.029   14.3   0.2    2.2  2  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 !   51.6   0.0   1.2e-17   1.1e-13       2     142 ..       5     142 ..       4     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.2e-17
                                       EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST.-..SCSSTHHHHHHHHHHH.TTCTTEEEEEEESEHH CS
                   CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkk.k..kplasaeeRlemlela.kevdevisvdpweltr 74 
                                       +gGtFDp+H GH rl+++a++l++  + vg++sd+ + k+ +  +++ ++++R e le   +   e   ++++e+ +
  gi|336255670|ref|YP_004598777.1|   5 LGGTFDPVHDGHRRLFDRAFELGD--VTVGLTSDDLAPKTrHveRHVRPYDQRKEALETElEPIAE-EYDREFEIRP 78 
                                       69**********************..699*****9877773478************9976433333.4444555555 PP

                                       .....HHHHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                   CTP_transf_like  75 .....evlkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                             + ++ + d  ylv++ ++ +  ++ +el++  g+ +l vv++p         ++++   iSst+i +
  gi|336255670|ref|YP_004598777.1|  79 ledptGIATEPQFD--YLVVSPETRDGGERINELRRERGHEPLEVVVVP-------HVEAEDGDVISSTRIVQ 142
                                       777779999*****..************99****************999.......9999**********976 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2   3.3e-06     0.029      13      33 ..       7      27 ..       2      37 .. 0.87
   2 ?    2.5   0.0     0.013   1.2e+02     127     158 .]     107     139 ..      85     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.3e-06
                           FAD_syn 13 GnFDGvHlGHqallkkaveaa 33
                                      G FD vH GH+ l+++a e+ 
  gi|336255670|ref|YP_004598777.1|  7 GTFDPVHDGHRRLFDRAFELG 27
                                      79***************9875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.013
                           FAD_syn 127 vellkelgaklgfevevvpkv.eleeekissta 158
                                       +++l++   +  +ev vvp+v  ++++ isst+
  gi|336255670|ref|YP_004598777.1| 107 INELRRERGHEPLEVVVVPHVeAEDGDVISSTR 139
                                       55666666666699*******556678888885 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:                      278  (0.0155056); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1447.48
//
Query:       gi|336255671|ref|YP_004598778.1|  [L=751]
Description: malic protein NAD-binding protein [Halopiger xanaduensis SH-6]
Scores for 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-94  315.5   0.0    5.5e-94  315.0   0.0    1.2  1  PTA_PTB   Phosphate acetyl/butaryl transferase
      3e-30  105.4   0.1    6.8e-28   97.7   0.1    2.4  1  malic     Malic enzyme, N-terminal domain
      1e-21   77.4   0.1    2.7e-21   76.0   0.1    1.7  1  Malic_M   Malic enzyme, NAD binding domain
  ------ inclusion threshold ------
      0.046   14.1   0.0       0.12   12.7   0.0    1.8  1  HTH_31    Helix-turn-helix domain


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 !  315.0   0.0   1.2e-97   5.5e-94       3     318 ..     430     744 ..     428     745 .. 0.97

  Alignments for each domain:
  == domain 1  score: 315.0 bits;  conditional E-value: 1.2e-97
                                       HHHHHHHHCTS--EEEES-TTSHHHHHHHHHHHHTTSSEEEEES-HHHHHHHHHHCTB--TT-EEE-TTT-CCHHHH CS
                           PTA_PTB   3 lerivekakkekkrivlpegedervlkAakelleegiadviLigdeaeikakaleldldlsgieivdpetsekleey 79 
                                       ++ +++kak+++k+++l+ege+e++++Aa +++e+gia +iLigde+ei++ a++l+ld +  ++ dp   + +eey
  gi|336255671|ref|YP_004598778.1| 430 MRVVLNKAKSDPKTVALAEGENEKMIRAAYQIQEQGIAAPILIGDESEIRSTAANLGLDFE-PQVADPSVGD-YEEY 504
                                       67899**********************************************9999999887.5899998877.**** PP

                                       HHHHHHHCCCC.S-HCCHHHHTT.SHHHHHHHHHHTTSSSEEEE-TTS-HHHHHHHHHHCT-B-TT----EEEEEEE CS
                           PTA_PTB  80 adelyelrkrkgvtieearevvr.datyfaamlvklgeaDglvsGavnttadtlrpalqiiktkpgvklvSsvfiml 155
                                       ad+l+elr+rkg+t +ea e ++ d +yf+  +v++g+aD+l++G+ + +  +lrp lq+i+t++ v  +++v ++ 
  gi|336255671|ref|YP_004598778.1| 505 ADRLHELRQRKGITRTEAGELIEsDSNYFGSVMVEQGDADALLTGLSHHYPSALRPPLQVIGTAEDVDYAAGVYMLT 581
                                       ***************************************************************************** PP

                                       ETTEEEEEESSSS-SS--HHHHHHHHHHHHHHHHHCCSS--EEEEE-SSSTTSS-SHHHHHHHHHHHHHHHH.-TTS CS
                           PTA_PTB 156 ledrlllfaDcavnvnPtaeelaeialesaktakalgeeeprvAlLSyStkgsakgesvekvrealkivkek.apdl 231
                                        ++r++++aD+ vn++P+ e lae++ ++ k a++++ +epr+AlLSyS++gs + e + k r a+k++++    d+
  gi|336255671|ref|YP_004598778.1| 582 FKNRVIFVADATVNQDPDEEVLAEVTKQTGKLARRFN-IEPRAALLSYSNFGSVDNEGTRKPRRAAKMLQKDpDADF 657
                                       *************************************.*****************************9987526789 PP

                                       EEEEEE-HHHHH-HHHHHHH-TTSTTTT--SEEE-SSHHHHHHHHHHHHHCCTEEEEEEEEESBSS-EEE--TT--H CS
                           PTA_PTB 232 vvdGelqlDaAlseevaekkapesevaGkAnvlvfPdLeagnigykivqrlakaeaiGPilqGlakPvndlSrgasv 308
                                        vdGe+q+D A++e++ e  +  se++  AnvlvfP+Le+gnigyk++qrl++a aiGP+l+G++kPv++l rg++v
  gi|336255671|ref|YP_004598778.1| 658 PVDGEMQADTAVVEDILEGTYGFSELEEPANVLVFPNLESGNIGYKLLQRLGGADAIGPMLVGMDKPVHVLQRGDEV 734
                                       ***************************************************************************** PP

                                       HHHHHHHHHH CS
                           PTA_PTB 309 edivnvaait 318
                                       +divn+a ++
  gi|336255671|ref|YP_004598778.1| 735 KDIVNLAGVA 744
                                       *****98665 PP

>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.1   1.5e-31   6.8e-28       2     182 .]      17     149 ..      16     149 .. 0.97

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 1.5e-31
                                       TTECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSB CS
                             malic   2 eknetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeri 78 
                                       +k+e++++k+++++  ++l+++Y+P+v+++c e+ e+ ++a+ +y+++++                 v vv++g+++
  gi|336255671|ref|YP_004598778.1|  17 GKIEISTTKPTNTQ--RDLSLAYSPGVAAPCLEIDENESDAY-TYTAKGNL----------------VGVVSNGSAV 74 
                                       68999999999999..**************************.********................9********* PP

                                       TTTBS-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHH CS
                             malic  79 LGlGdlG.vagvgimvGKlaLytalagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveav 154
                                       LGlGd+G  a++++m+GK +L++++a+id   v++v+ld +                           +  ++veav
  gi|336255671|ref|YP_004598778.1|  75 LGLGDIGaQASKPVMEGKGVLFKRFADID---VFDVELDEE---------------------------DPHKLVEAV 121
                                       *******9999******************...********9...........................889****** PP

                                       HHHHGCTSEEEE-S--CCHHHHHHHHHC CS
                             malic 155 kelfppkaliqfEDfkaknafeileryr 182
                                       k ++p++++i++ED+ka+++f+i+er+r
  gi|336255671|ref|YP_004598778.1| 122 KMMEPTFGGINLEDIKAPECFTIEERLR 149
                                       **************************97 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 !   76.0   0.1     6e-25   2.7e-21       3     229 ..     163     359 ..     161     364 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 6e-25
                                       HHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S-.. CS
                           Malic_M   3 gTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrek.. 77 
                                       gTa+++ a+l++a+ i++k l++ ++v+ GaG+++i  a      +v+ G+++    ++i + D++G++t++r++  
  gi|336255671|ref|YP_004598778.1| 163 GTAIISGAALINAADIADKDLEDLEVVFSGAGASAIASAR----FYVSLGVQK----ENITMCDSSGIITTERAErg 231
                                       9*********************************986665....456667665....4799*********9985334 PP

                                       .--TTTGGGSBS--SS--S....SHHHHHHHH--SEEEE-SSSSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS- CS
                           Malic_M  78 .leeekkpfakkkeelkeakdkltLeevvkkvkptvliGlsgvagafteeivremaksterPiilplSNPtskaEat 153
                                        l+e+k++fa++  e +       L+++++   ++v +Gls v+g+ ++++vr+ma+   +Pii+++ NP+   E  
  gi|336255671|ref|YP_004598778.1| 232 dLNEYKQQFARDLPEGD-------LSDAMEG--ADVFVGLS-VGGIVSQDMVRSMAD---NPIIFAMANPDP--EIG 293
                                       49*********999986.......9999986..69*****8.89***********85...7*********86..778 PP

                                       HHHHHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHH CS
                           Malic_M 154 aedvlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseee 229
                                        e++ +  d+++++a+G          +  +++Q NN++ fP +  g++ +ra++i++em +a+aealael++e+ 
  gi|336255671|ref|YP_004598778.1| 294 YEEAKDARDDTVIMATG----------RSDYPNQVNNVLGFPFIFRGALDVRATEINEEMKVACAEALAELAREDV 359
                                       99**************8..........56789**************************************999876 PP

>> HTH_31  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   2.7e-05      0.12       3      25 ..     505     527 ..     503     570 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                            HTH_31   3 GalLralReraGLsqeevAerlg 25 
                                       +++L++lR+r G++++e++e++ 
  gi|336255671|ref|YP_004598778.1| 505 ADRLHELRQRKGITRTEAGELIE 527
                                       89******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (751 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.62u 0.23s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 5507.11
//
Query:       gi|336255672|ref|YP_004598779.1|  [L=477]
Description: Pyrrolo-quinoline quinone repeat-containing protein [Halopiger xanaduensis SH-6]
Scores for 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  122.1  27.3    2.1e-08   34.4   0.3    9.0  8  PQQ_3     PQQ-like domain
      2e-35  119.0  18.2      1e-08   34.7   0.3    8.1  8  PQQ       PQQ enzyme repeat
    9.3e-32  110.5   4.7    1.4e-13   51.0   0.5    3.4  3  PQQ_2     PQQ-like domain


Domain annotation for each model (and alignments):
>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.02   1.2e+02      13      37 ..     115     141 ..     100     143 .. 0.67
   2 !   28.1   1.4   3.4e-10     2e-06       1      38 [.     144     185 ..     144     186 .. 0.87
   3 !   17.2   0.1   8.9e-07    0.0053       1      40 []     188     237 ..     188     237 .. 0.92
   4 ?    2.2   0.1     0.048   2.8e+02      16      34 ..     254     274 ..     238     277 .. 0.73
   5 !   17.6   0.6   6.6e-07     0.004       8      40 .]     306     338 ..     282     338 .. 0.79
   6 !   25.5   0.0   2.3e-09   1.3e-05       1      40 []     339     380 ..     339     380 .. 0.91
   7 !   34.4   0.3   3.6e-12   2.1e-08       1      40 []     381     420 ..     381     420 .. 0.98
   8 !    5.9   0.0    0.0031        18       1      27 [.     421     447 ..     421     473 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.02
                             PQQ_3  13 vnssp..avdgglvyvgtgdGtlyAlD 37 
                                       ++s+p  +  g ++ ++++ G+++A+ 
  gi|336255672|ref|YP_004598779.1| 115 AKSTPrpTPNGETILIASDTGRIHAVT 141
                                       334445577799************985 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 3.4e-10
                             PQQ_3   1 GevlWsvqlpg....pvnsspavdgglvyvgtgdGtlyAlDa 38 
                                       Ge++W  ++++      +++pa+++++ y+g++dG lyA+D 
  gi|336255672|ref|YP_004598779.1| 144 GERRWLLETDAgtslGFHGTPAIVDDTAYIGGYDGALYAVDI 185
                                       889999988765677788999********************7 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 8.9e-07
                             PQQ_3   1 GevlWsv...qlpg..pvnsspavdgglvyvgtg.....dGtlyAlDaet 40 
                                       Ge++W++   +++g  +++sspa+ +g++y+ ++      G l  +Daet
  gi|336255672|ref|YP_004598779.1| 188 GELIWQTnprDFDGaiAIGSSPAYIDGTLYIMAEysnpaSGALWEVDAET 237
                                       9********9998889999************9999999999999999987 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.048
                             PQQ_3  16 spavd..gglvyvgtgdGtly 34 
                                       spa+d   g+++ g+ dG +y
  gi|336255672|ref|YP_004598779.1| 254 SPAIDcdAGRLVSGSNDGVVY 274
                                       457755379999******999 PP

  == domain 5  score: 17.6 bits;  conditional E-value: 6.6e-07
                             PQQ_3   8 qlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                        l+++++++  v++g  ++g++dG++y lD e+
  gi|336255672|ref|YP_004598779.1| 306 HLGAQIKGTIPVYDGAAFAGSWDGRFYRLDLED 338
                                       456677777799******************986 PP

  == domain 6  score: 25.5 bits;  conditional E-value: 2.3e-09
                             PQQ_3   1 GevlWsvqlpgpvnsspavd..gglvyvgtgdGtlyAlDaet 40 
                                       G + Ws++++  + s pa+d   g+ yvg++d+ +yAlD++t
  gi|336255672|ref|YP_004598779.1| 339 GSEEWSFETGRVIMSNPAIDpeQGIAYVGSDDHYVYALDTDT 380
                                       6788******8888******655****************998 PP

  == domain 7  score: 34.4 bits;  conditional E-value: 3.6e-12
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       Ge+lWs +++g+v +s ++   ++ vg++d +lyAlD et
  gi|336255672|ref|YP_004598779.1| 381 GEELWSADVGGRVIGSITATAETILVGSYDAHLYALDRET 420
                                       9*************************************98 PP

  == domain 8  score: 5.9 bits;  conditional E-value: 0.0031
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvg 27 
                                       Ge++W+v+  g v+s++   +g++y +
  gi|336255672|ref|YP_004598779.1| 421 GERRWRVENRGHVTSGAIPRDGRIYYA 447
                                       99*****9999**99998899999976 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.01        61       3      24 ..     128     148 ..     127     156 .. 0.90
   2 !   27.1   0.4   4.2e-10   2.5e-06       1      34 [.     169     202 ..     169     206 .. 0.89
   3 !    5.1   0.1    0.0039        23       7      25 ..     225     243 ..     222     246 .. 0.84
   4 ?   -1.2   0.1      0.39   2.3e+03       1      13 [.     262     274 ..     262     275 .. 0.83
   5 ?    0.5   0.0      0.11   6.8e+02      23      34 ..     284     295 ..     282     299 .. 0.80
   6 !   22.5   0.0   1.2e-08   7.3e-05       2      29 ..     321     348 ..     320     356 .. 0.89
   7 !   34.7   0.3   1.7e-12     1e-08       2      35 ..     363     396 ..     362     398 .. 0.92
   8 !   30.5   0.0   3.7e-11   2.2e-07       3      34 ..     404     435 ..     403     439 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.01
                                       EEEEETTSEEEEEETTTCCEEE CS
                               PQQ   3 vylgsadGylyAlDadTGkvlW 24 
                                       + ++s+ G++ A+   +G+ +W
  gi|336255672|ref|YP_004598779.1| 128 ILIASDTGRIHAVT-PDGERRW 148
                                       7789**********.*****99 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 4.2e-10
                                       TEEEEEETTSEEEEEETTTCCEEEEEESSSCGSS CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggpvls 34 
                                       ++ y+g +dG lyA+D+d G+++W++++ + + +
  gi|336255672|ref|YP_004598779.1| 169 DTAYIGGYDGALYAVDIDAGELIWQTNPRDFDGA 202
                                       578************************9887766 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0039
                                       ETTSEEEEEETTTCCEEEE CS
                               PQQ   7 sadGylyAlDadTGkvlWr 25 
                                       +a G l+ +Da+TG+  W+
  gi|336255672|ref|YP_004598779.1| 225 PASGALWEVDAETGRPTWH 243
                                       788999*********9997 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.39
                                       TEEEEEETTSEEE CS
                               PQQ   1 gvvylgsadGyly 13 
                                       g+++ gs+dG++y
  gi|336255672|ref|YP_004598779.1| 262 GRLVSGSNDGVVY 274
                                       567889******9 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.11
                                       EEEEESSSCGSS CS
                               PQQ  23 lWrfktggpvls 34 
                                        W+f++gg++  
  gi|336255672|ref|YP_004598779.1| 284 AWTFQAGGEDGP 295
                                       7*******9876 PP

  == domain 6  score: 22.5 bits;  conditional E-value: 1.2e-08
                                       EEEEEETTSEEEEEETTTCCEEEEEESS CS
                               PQQ   2 vvylgsadGylyAlDadTGkvlWrfktg 29 
                                         ++gs dG++y lD+++G + W+f+tg
  gi|336255672|ref|YP_004598779.1| 321 AAFAGSWDGRFYRLDLEDGSEEWSFETG 348
                                       5799**********************98 PP

  == domain 7  score: 34.7 bits;  conditional E-value: 1.7e-12
                                       EEEEEETTSEEEEEETTTCCEEEEEESSSCGSSE CS
                               PQQ   2 vvylgsadGylyAlDadTGkvlWrfktggpvlsl 35 
                                         y+gs+d y+yAlD dTG++lW+ ++gg v ++
  gi|336255672|ref|YP_004598779.1| 363 IAYVGSDDHYVYALDTDTGEELWSADVGGRVIGS 396
                                       67***************************99775 PP

  == domain 8  score: 30.5 bits;  conditional E-value: 3.7e-11
                                       EEEEETTSEEEEEETTTCCEEEEEESSSCGSS CS
                               PQQ   3 vylgsadGylyAlDadTGkvlWrfktggpvls 34 
                                       + +gs+d +lyAlD++TG+ +Wr+++ g+v s
  gi|336255672|ref|YP_004598779.1| 404 ILVGSYDAHLYALDRETGERRWRVENRGHVTS 435
                                       7899***********************99866 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.1   1.2e-16   7.4e-13      57     236 ..     100     286 ..      94     287 .. 0.80
   2 !   10.8   0.0   4.4e-05      0.26      64     105 ..     307     348 ..     304     358 .. 0.81
   3 !   51.0   0.5   2.3e-17   1.4e-13      35     129 ..     360     465 ..     353     476 .. 0.81

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.2e-16
                             PQQ_2  57 kvlWettlegpvvga......plvaegrvvvvasdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvv 127
                                       +v We+ ++   ++a      p+ +++ ++ +++ g++ a+   dG+r W  + +    ++l+  ++pa+++dt+++
  gi|336255672|ref|YP_004598779.1| 100 SVNWEFPVNRIGHTAakstprPTPNGETILIASDTGRIHAVT-PDGERRWLLETDA--GTSLGFHGTPAIVDDTAYI 173
                                       6789999888777778899999*******9999999******.********44444..666889************* PP

                             PQQ_2 128 gessgklvaldpkdGkvlWerelaaprgtselsrvgdisgrpvvaegtVyassgqgr.....llaldlatgrrlwsk 199
                                       g+ +g l+a+d++ G+++W+++ ++  g+        i ++p   +gt+y+ + + +     l  +d++tgr+ w +
  gi|336255672|ref|YP_004598779.1| 174 GGYDGALYAVDIDAGELIWQTNPRDFDGAI------AIGSSPAYIDGTLYIMAEYSNpasgaLWEVDAETGRPTWHD 244
                                       *********************886655555......45688988889***9999886666668888******99*55 PP

                             PQQ_2 200 e.iss....inglpildgdllyvvsagelialdratGavlWk 236
                                       + i +      ++++ +g+l+  +++g ++ ++  + +++W+
  gi|336255672|ref|YP_004598779.1| 245 DdIWGmphpSPAIDCDAGRLVSGSNDGVVYGWEFPSLERAWT 286
                                       558777554333344445555555569999999999888887 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.4e-05
                             PQQ_2  64 legpvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqr 105
                                       l ++++g+  v +g +++ + dg++++ld edG + Ws++  
  gi|336255672|ref|YP_004598779.1| 307 LGAQIKGTIPVYDGAAFAGSWDGRFYRLDLEDGSEEWSFETG 348
                                       566777777899999999999****************96544 PP

  == domain 3  score: 51.0 bits;  conditional E-value: 2.3e-17
                             PQQ_2  35 sggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrseepae 111
                                       ++g  +v+++   ++ald+ tG++lW++++ g+v g+ + + + ++v + d +l+ald e+G+r W+++ r++ +  
  gi|336255672|ref|YP_004598779.1| 360 EQGIAYVGSDDHYVYALDTDTGEELWSADVGGRVIGSITATAETILVGSYDAHLYALDRETGERRWRVENRGHVTSG 436
                                       68999**************************************************************8888865555 PP

                             PQQ_2 112 lrssaspava...........gdtvvvge 129
                                       +++ + ++++           +d++ v e
  gi|336255672|ref|YP_004598779.1| 437 AIPRDGRIYYaergvfsnyydDDEATVLE 465
                                       66666666665555554555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); 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 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3721.41
//
Query:       gi|336255673|ref|YP_004598780.1|  [L=124]
Description: 30S ribosomal protein S8e [Halopiger xanaduensis SH-6]
Scores for 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-32  110.6   3.2    7.5e-32  110.4   3.2    1.1  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 !  110.4   3.2   4.2e-36   7.5e-32       4     137 .]       2     122 ..       1     122 [. 0.97

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 4.2e-36
                                       BXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEE CS
                     Ribosomal_S8e   4 srdskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlg 80 
                                       + +++++rk tGg+ k +rk+rk elgr +++t++g+ r++++ vrg+ +k+ral ++ a+v +   + t+ ++I +
  gi|336255673|ref|YP_004598780.1|   2 QDQGRSTRKRTGGRLKNVRKRRKDELGRLPTETQVGEPRFRTIDVRGNGTKTRALATDIASVNK--SGETVSAEIED 76 
                                       5799*********************************************************987..8889999**** PP

                                       EECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                     Ribosomal_S8e  81 VkknpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                       V++n++n++yvr++++tKga+ie++ ++           A+vtsrPgq+G+vnavlL
  gi|336255673|ref|YP_004598780.1|  77 VVENEANPNYVRRNIITKGAVIETSEGR-----------ARVTSRPGQTGQVNAVLL 122
                                       ************************9999...........*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 998.36
//
Query:       gi|336255674|ref|YP_004598781.1|  [L=331]
Description: phosphate uptake regulator PhoU [Halopiger xanaduensis SH-6]
Scores for 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-20   70.9   6.9    1.9e-15   57.1   1.0    2.5  2  PhoU            PhoU domain
    1.2e-11   44.2   0.1      6e-11   42.0   0.0    2.3  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.063   13.1   0.3       0.25   11.2   0.1    2.1  2  NIR_SIR_ferr    Nitrite/Sulfite reductase ferredoxin-like hal


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   1.0   3.2e-19   1.9e-15       2      87 ..     136     224 ..     135     226 .. 0.86
   2 !   16.9   0.5   1.1e-06    0.0066       2      88 ..     241     322 ..     240     323 .. 0.69

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 3.2e-19
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH....HHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae....dlrellsllriard 74 
                                       +rm  i+ +ml da++al+e+d+++a +vierdd++drl   ++r  ++a  ++   ae    + ++ +++ + ar 
  gi|336255674|ref|YP_004598781.1| 136 SRMRLIATSMLADAVTALVENDDDIALDVIERDDDVDRLWLVVSRI-FRATLRSPRAAEelgvPREDCFDFHSSARQ 211
                                       79*************************************7777555.7777654444446677888899******** PP

                                       HHHHHHHHHHHHH CS
                              PhoU  75 lERigDhavniae 87 
                                       lER++Dha++i++
  gi|336255674|ref|YP_004598781.1| 212 LERVADHAAKISN 224
                                       ***********97 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHH..HGG-SHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarev....ierddeidrlekeiersllealak..rqplaedlrellsllria 72 
                                        +++  +++ l+++++al+ +d   a+e+    ++   eid+  ++i++  l+ la               sl  i+
  gi|336255674|ref|YP_004598781.1| 241 TDLHADASDVLEKSMDALFADDSGEANELghaaRQAVLEIDEHTRRIDDM-LRDLAPvqA----------QSLGLIV 306
                                       678889999*************9888777211133355566666666555.455543223..........33556** PP

                                       HHHHHHHHHHHHHHHH CS
                              PhoU  73 rdlERigDhavniaer 88 
                                        +l R +D+  niae 
  gi|336255674|ref|YP_004598781.1| 307 DSLSRSADYGGNIAET 322
                                       **************95 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 !   42.0   0.0     1e-14     6e-11       1      44 [.       8      51 ..       8      53 .. 0.94
   2 ?   -2.2   0.1      0.74   4.4e+03      28      39 ..     164     177 ..     164     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1e-14
                                      EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHHS CS
                    MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgdkiilrplksl 44
                                      +++G+++ v++Pk+++ ++g++ G++ve+++++d+++l+p ++ 
  gi|336255674|ref|YP_004598781.1|  8 VTGGSTYTVSLPKDWATDNGVSSGSTVEFYPEDDSLLLTPRSES 51
                                      699*************************************9875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.74
                                       EEEECTT..CCCCC CS
                    MazE_antitoxin  28 elevdgd..kiilr 39 
                                       ++e+d+d  +++l+
  gi|336255674|ref|YP_004598781.1| 164 VIERDDDvdRLWLV 177
                                       58899999899986 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.1e-05      0.25      14      33 ..      83     102 ..      82     106 .. 0.91
   2 ?   -1.9   0.0       0.5     3e+03      22      41 ..     208     227 ..     206     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.1e-05
                      NIR_SIR_ferr  14 lrvpnGritaeqlraladia 33 
                                       +r+++Grit++q ra++d  
  gi|336255674|ref|YP_004598781.1|  83 IRLEAGRITTDQRRAIRDAT 102
                                       799**************975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.5
                      NIR_SIR_ferr  22 taeqlraladiaekygsgei 41 
                                       +a ql+++ad a k ++  +
  gi|336255674|ref|YP_004598781.1| 208 SARQLERVADHAAKISNLAL 227
                                       46699999999998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); 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 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2581.53
//
Query:       gi|336255675|ref|YP_004598782.1|  [L=329]
Description: phosphate binding protein [Halopiger xanaduensis SH-6]
Scores for complete 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  104.0   0.4    1.8e-29  103.3   0.4    1.3  1  PBP_like_2  PBP superfamily domain
    1.5e-12   47.0   0.0    2.9e-12   46.1   0.0    1.5  1  PBP_like    PBP superfamily domain
  ------ inclusion threshold ------
      0.012   15.4   0.8      0.022   14.6   0.8    1.4  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
       0.18   11.2   0.3       0.33   10.3   0.3    1.4  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.4     4e-33   1.8e-29      11     261 ..      51     282 ..      34     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 4e-33
                        PBP_like_2  11 e..ifgaGsttpapalrkladafekaapgakvnyastGSgagi.kalrngdvdfagsdrplteseiaagwaangagg 84 
                                       +  ++++Gs+t+ p+   +a+af+++ +++ v++ stG+g+g  + ++ g  d+ g++rp++e+e+ + ++ ng  +
  gi|336255675|ref|YP_004598782.1|  51 NerVVVTGSSTVFPVSDTMAEAFMDE-NDVNVTTDSTGTGGGFsNNFCPGNSDINGASRPIQEEEV-SSCNENG-VE 124
                                       14499*********************.8**************8468********************.89*****.** PP

                        PBP_like_2  85 liqvpvaigaialvvnkdnpln.lsreaLakIfs.gkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqgp 159
                                       +i++ ++ +a++++v++d+p    + ++La+I s +   +W+dv++  +d+ I  + ++  sgt++ f +++     
  gi|336255675|ref|YP_004598782.1| 125 PIEFQIGADAVTMAVHNDSPIDcVTYDELAQIWSeDGAETWSDVNSEWPDEEIERYGPPSTSGTFDWFRNNVIGD-- 199
                                       **********************************999***********************************977.. PP

                        PBP_like_2 160 wtasgigasgsegvasavsnngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplawslq 236
                                          s       + v +++++++       +++l   ++ +++ +n++g+f+ +++ +++++lk+++i+ + + + + 
  gi|336255675|ref|YP_004598782.1| 200 ---S------GSHVTQYEKTEN-------DNEL---VQGISSSENAIGYFGYAYYRENEDQLKALEIKESEDGECTP 257
                                       ...1......334444444444.......4455...56666666666666666666778888999998855555599 PP

                        PBP_like_2 237 pveeniadgayPlsrftyiivyqpy 261
                                       p+ e++ +g+yP+ r++yi+v ++ 
  gi|336255675|ref|YP_004598782.1| 258 PSLEAASEGSYPMARPLYIYVSEQS 282
                                       *****99**************9954 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   6.5e-16   2.9e-12       1     192 [.      70     295 ..      70     296 .. 0.73

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 6.5e-16
                                       HHHHHHH-TTCEEEEEES-HHHHHH.HHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCH CS
                          PBP_like   1 aeelaeknpgvrvavanvGsggGlk.alrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvva 76 
                                       ae++++ +++v v++  +G+ggG++ +++ g  di g++++++e+e   ++  +   +g e ++ +   ++  + v 
  gi|336255675|ref|YP_004598782.1|  70 AEAFMD-ENDVNVTTDSTGTGGGFSnNFCPGNSDINGASRPIQEEEVSSCN--E---NGVEPIEFQIGADAVTMAVH 140
                                       577888.59***************846****************99887777..3...23333444444444444444 PP

                                       CCHHHS...............--BGGGC....-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHH CS
                          PBP_like  77 kgnpkk...............itnwkdl....adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshl 134
                                        + p +                ++w+d+    +d+++  ++++  SGt+d f   + +   s+s +++y+++++++ 
  gi|336255675|ref|YP_004598782.1| 141 NDSPIDcvtydelaqiwsedgAETWSDVnsewPDEEIERYGPPSTSGTFDWFRNNVIG--DSGSHVTQYEKTENDNE 215
                                       444443333333334444444*******999999*******************99955..4999******9999998 PP

                                       HHHCCHCCETTCCEC.CCGG-HCCCCCCECTTCE-......................EEEEEEEECTCCCSHHHHHH CS
                          PBP_like 135 avaaaVaagradvgv.gieavaeelkgldfvplae......................erydlvvrkealddpevqaf 188
                                        v+  +++ + ++g+ g +   e+ ++l+ ++++e                      +++ ++v+++ l+++ v  f
  gi|336255675|ref|YP_004598782.1| 216 LVQ-GISSSENAIGYfGYAYYRENEDQLKALEIKEsedgectppsleaasegsypmaRPLYIYVSEQSLERESVYNF 291
                                       884.355555555544665555555555555555555566666666666666666667******************* PP

                                       HHHH CS
                          PBP_like 189 lefl 192
                                       +ef+
  gi|336255675|ref|YP_004598782.1| 292 VEFY 295
                                       **97 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.8   4.9e-06     0.022       2      23 ..      13      33 ..      12      36 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.9e-06
                        TAT_signal  2 lSRRdFLKgsAAaaAAaalggc 23
                                      +SRR  L +++A++A+ ++g c
  gi|336255675|ref|YP_004598782.1| 13 VSRRKVLAATGAVGALSLAG-C 33
                                      8*************888555.4 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   7.5e-05      0.33       6      25 ..      10      28 ..       5      33 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.5e-05
                        UCR_Fe-S_N  6 sdeptRRDFLyiATgavgaV 25
                                       ++ +RR +L +ATgavga 
  gi|336255675|ref|YP_004598782.1| 10 VRSVSRRKVL-AATGAVGAL 28
                                      56789*****.9******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); 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:                         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 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2588.72
//
Query:       gi|336255676|ref|YP_004598783.1|  [L=313]
Description: phosphate ABC transporter inner membrane subunit PstC [Halopiger xanaduensis SH-6]
Scores for 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-17   62.1  13.6    5.6e-17   62.1  13.6    2.2  2  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 ?   -0.7   1.7     0.057     1e+03      65      84 ..      32      51 ..      15      96 .. 0.57
   2 !   62.1  13.6   3.1e-21   5.6e-17       2     183 ..      98     308 ..      97     310 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.057
                      BPD_transp_1 65 apyvrlirraalrslpkdlv 84
                                      a+++++++ +++ +l +d  
  gi|336255676|ref|YP_004598783.1| 32 AALTVFVTVSIIVTLTRDAL 51
                                      33333333333333333333 PP

  == domain 2  score: 62.1 bits;  conditional E-value: 3.1e-21
                      BPD_transp_1   2 illGilaa....lnrnkkldkllrpliivllslPsfvlaillvlvf......vilsilghlilpviillllsaapyv 68 
                                       +++G+ aa     + +++ + +l p  +vl ++P++v + l ++ +      + + + ++  l++ i++ ++++p+v
  gi|336255676|ref|YP_004598783.1|  98 VPIGVAAAvylsEYASGRMRSVLKPALEVLAGIPTVVYGYLALVYLtpalqaIGIPVSTFNLLSASIMVGIMIIPMV 174
                                       899999999999999**********************666655444577787677778889999************* PP

                      BPD_transp_1  69 rlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleai 145
                                         + ++a++s+p++l++a + +Ga++ ++   +v+P+a++ i++++ila+ +++g+++++ + +     g++   + 
  gi|336255676|ref|YP_004598783.1| 175 SSLSEDAMSSVPDSLRQAGYGMGATKYEVSTGIVIPAAISGIFSSFILALSRAIGETMIVVMAA-----GLRPRMFD 246
                                       ****************************************************************.....66666666 PP

                      BPD_transp_1 146 lgydyseis........................nggvlalviavlllnlvadilqrlldprv 183
                                        ++++++                          + +++al++ ++++++++++  ++++ r 
  gi|336255676|ref|YP_004598783.1| 247 FSNPLNNLFssgqpmtagmvnavtsdatggsatYLSMFALGLTLFVITFSMNLASDYVAARY 308
                                       6666666666677899999**************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2527.17
//
Query:       gi|336255677|ref|YP_004598784.1|  [L=537]
Description: phosphate ABC transporter inner membrane subunit PstA [Halopiger xanaduensis SH-6]
Scores for 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-17   62.7  16.3    3.5e-17   62.7  16.3    4.6  5  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 ?   -0.9   1.7     0.067   1.2e+03      34      66 ..      39      76 ..      19      86 .. 0.60
   2 ?   -1.7   0.2      0.11     2e+03      28      64 ..      95     132 ..      90     149 .. 0.46
   3 !    1.9   4.7    0.0089   1.6e+02      95     166 ..     148     216 ..     143     237 .. 0.65
   4 ?   -1.2   0.5      0.08   1.4e+03     156     156 ..     311     311 ..     258     333 .. 0.41
   5 !   62.7  16.3     2e-21   3.5e-17      27     174 ..     363     523 ..     308     535 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.067
                      BPD_transp_1 34 vlaillvlvf.....vilsilghlilpviillllsaap 66
                                       +++ll++v+      ++ ++g+l + ++++ll  +++
  gi|336255677|ref|YP_004598784.1| 39 SVFVLLLYVAndafrPLSADIGWLLIFAATVLLPILGA 76
                                      23334444446777766677777777766666555555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.11
                      BPD_transp_1  28 lslPsfvlaillvlvf...vilsilghlilpviillllsa 64 
                                       l+lP++ l++   +++    i s+    +l+++++l+l  
  gi|336255677|ref|YP_004598784.1|  95 LGLPVVSLLVAGGVFItfeHIVSVYR--WLSILVALALAG 132
                                       55566665555443333332222222..222333333333 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.0089
                      BPD_transp_1  95 wqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgtllleailgydyseisnggvlalviavl 166
                                        ++++ +++P+a+  +++ +il+++ l ++ ++l+  +  p   +  ++++ + ++d + ++     a+++ ++
  gi|336255677|ref|YP_004598784.1| 148 ERLVVLIAVPAAALALVPDIILSLPVLPTEGIALLASFVAPVslVAGWFVRRQRESDRDGAI-----AAALTLI 216
                                       578999*********************87755555444334233444555555555555333.....2222222 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.08
                      BPD_transp_1 156 g 156
                                        
  gi|336255677|ref|YP_004598784.1| 311 Y 311
                                       2 PP

  == domain 5  score: 62.7 bits;  conditional E-value: 2e-21
                      BPD_transp_1  27 llslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvv 102
                                       l ++Ps+v +il +++f+ ++++g++    + +++ l ++p+v++  ++a++++p++ ++a++ +Ga+rwq++r+vv
  gi|336255677|ref|YP_004598784.1| 363 LAGVPSVVYGILGLALFIRQGGFGSGTALvGGFTVGLLILPIVIISSQEAISAVPDSMRQASYGMGATRWQTVRNVV 439
                                       679*********************8888879********************************************** PP

                      BPD_transp_1 103 lPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis..............nggvlalviav 165
                                       lP alp i+tg ila+g+++g+++ l+++g+      ++   +  + +s++                 gvla+++++
  gi|336255677|ref|YP_004598784.1| 440 LPEALPGIMTGNILAMGRAIGETAPLLIIGAP--AVVRIAPDSFTSKFSAMPrqiytwsseidpafQHGVLAAGVMT 514
                                       ******************************55..4444555555555555556677777799999955555555555 PP

                      BPD_transp_1 166 lllnlvadi 174
                                       ll++l+++ 
  gi|336255677|ref|YP_004598784.1| 515 LLVVLLLMN 523
                                       555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 3719.85
//
Query:       gi|336255678|ref|YP_004598785.1|  [L=302]
Description: phosphate ABC transporter ATPase [Halopiger xanaduensis SH-6]
Scores for 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-29  102.2   0.0    5.4e-29  101.5   0.0    1.4  1  ABC_tran      ABC transporter
    5.2e-12   46.2   0.0    7.9e-05   22.6   0.0    2.4  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.6e-09   36.8   0.1    8.1e-05   22.2   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    2.3e-06   27.6   0.0    0.00051   19.9   0.0    2.1  2  AAA_15        AAA ATPase domain
    7.9e-05   22.9   0.0    0.00019   21.7   0.0    1.6  1  AAA_22        AAA domain
    0.00027   21.5   0.0    0.00055   20.5   0.0    1.5  1  AAA_23        AAA domain
     0.0011   18.7   0.0     0.0024   17.6   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0013   18.6   0.0     0.0028   17.6   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
     0.0084   16.1   0.0      0.014   15.3   0.0    1.3  1  Rad17         Rad17 P-loop domain
     0.0087   16.5   0.0      0.036   14.4   0.0    1.8  2  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.018   14.8   0.0       0.67    9.7   0.0    2.1  2  AAA_30        AAA domain
      0.022   14.7   0.0      0.036   14.0   0.0    1.3  1  DeoRC         DeoR C terminal sensor domain
      0.025   14.3   0.0      0.045   13.5   0.0    1.4  1  PRK           Phosphoribulokinase / Uridine kinase family
      0.028   14.0   0.0       0.18   11.4   0.0    2.0  2  AAA_25        AAA domain
      0.079   11.7   0.0       0.83    8.4   0.0    2.0  2  Adeno_IVa2    Adenovirus IVa2 protein
      0.085   12.8   0.0       0.48   10.3   0.0    2.0  2  ATPase_2      ATPase domain predominantly from Archaea
        0.1   12.3   0.0       0.26   11.0   0.0    1.7  2  AAA_24        AAA domain
       0.15   12.2   0.0       0.34   11.1   0.0    1.7  2  AAA_33        AAA domain
       0.18   11.2   0.0        0.3   10.4   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
        0.2   11.5   0.0       0.37   10.7   0.0    1.4  1  NACHT         NACHT 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 !  101.5   0.0     6e-32   5.4e-29       1     136 [.      72     225 ..      72     226 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 6e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqepql 70 
                                       l+ +++++ + +++ai+G++G+GKSt+l+++ ++ +       eGe++++gk++ +   +   lr++ig+++q+p+ 
  gi|336255678|ref|YP_004598785.1|  72 LRSIDIEIPAEQVTAIIGPSGCGKSTFLRCINRMNDLvdaarIEGELRFEGKNVYDddVDPVALRRKIGMVFQHPNP 148
                                       5679999***************************99888999************9966677899************* PP

                                       -TTSBHHHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       fp++ +++n            ++de +ekal++  l +  +  ++ss+  LSgGq+qr+++ara++ +p+++l+DEp
  gi|336255678|ref|YP_004598785.1| 149 FPKS-IYDNvtyglevqgidgDYDEIVEKALRRAALWDEVKGQLDSSGLDLSGGQQQRLCIARAIAPDPEVILMDEP 224
                                       ****.99999*****99999999999*************************************************** PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                        
  gi|336255678|ref|YP_004598785.1| 225 A 225
                                       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 !   21.5   0.0   1.9e-07   0.00017       1      30 [.      84     115 ..      84     196 .. 0.80
   2 !   22.6   0.0   8.8e-08   7.9e-05     236     298 ..     197     255 ..     169     257 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.9e-07
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarl..drdve 30 
                                       ++++iGp g+GKS++L+++  + +l  ++ +e
  gi|336255678|ref|YP_004598785.1|  84 VTAIIGPSGCGKSTFLRCINRMNDLvdAARIE 115
                                       69*******************97766522222 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 8.8e-08
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       +lS G+++ l+++ a++ ++    ++l DEp + L+P +++++ +l+++l++    vi++TH+
  gi|336255678|ref|YP_004598785.1| 197 DLSGGQQQRLCIARAIAPDP---EVILMDEPASALDPVATSKIEDLIEDLAE-EYTVIIVTHN 255
                                       45999999988888888888...9***********************88888.8********8 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 !   12.9   0.0   6.1e-05     0.055      23      44 ..      81     102 ..      70     107 .. 0.81
   2 !   22.2   0.0     9e-08   8.1e-05     135     212 ..     186     269 ..     103     275 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.1e-05
                                       TSSEEEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAi 44 
                                       ++++tai+Gp G+GKs +l  i
  gi|336255678|ref|YP_004598785.1|  81 AEQVTAIIGPSGCGKSTFLRCI 102
                                       4679*************99877 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 9e-08
                                       T..........CS-HHHHHHHHHHHHHHHHCCS--S.EEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHH CS
                                       x..........xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e..........lLSgGektLvalaLlfAiqkvkpap.lyllDeidaaLDeknvkkvaellkeksknaQfivislree 200
                                       e           LSgG+++ + +a  +      p p + l+De ++aLD   ++k+ +l++   ++  +i+++++ +
  gi|336255678|ref|YP_004598785.1| 186 EvkgqldssglDLSGGQQQRLCIARAI-----APDPeVILMDEPASALDPVATSKIEDLIEDLAEEYTVIIVTHNMQ 257
                                       044444444446999999876666443.....34443679***********************************99 PP

                                       HCCC-SCEEEEE CS
                                       xxxxxxxxxxxx RF
                             SMC_N 201 mlekadklvgvt 212
                                       + ++ +    v+
  gi|336255678|ref|YP_004598785.1| 258 QAARISDKTAVF 269
                                       988776666555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   5.7e-07   0.00051      16      48 ..      76     107 ..      71     154 .. 0.84
   2 ?    5.7   0.0     0.011        10     320     365 ..     212     255 ..     201     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.7e-07
                            AAA_15  16 dveidlseeltvliGkNnsGKSsilealdlFln 48 
                                       d+ei+ +  +t +iG+ ++GKS++l+ ++ + +
  gi|336255678|ref|YP_004598785.1|  76 DIEIPAEQ-VTAIIGPSGCGKSTFLRCINRMND 107
                                       36777777.*******************99877 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                            AAA_15 320 keeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +  ++ ++l++EP   L p a + + +l+ +la++    vii TH+
  gi|336255678|ref|YP_004598785.1| 212 IAPDPEVILMDEPASALDPVATSKIEDLIEDLAEEYT--VIIVTHN 255
                                       5678999*****************************6..******8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.1e-07   0.00019       6     103 ..      83     228 ..      80     272 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-07
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.....................erpevvfvtlpsstsskdllrell 61 
                                       ++++++G+sG+GK+t lr + + +d + +a+                      +r+  + ++ p++  +k+++ ++ 
  gi|336255678|ref|YP_004598785.1|  83 QVTAIIGPSGCGKSTFLRCINRMNDLVDAARIegelrfegknvydddvdpvalRRKIGMVFQHPNPF-PKSIYDNVT 158
                                       789*********************9998888899999999999999888885544444466666666.999999999 PP

                            AAA_22  62 ralglelka........erlsseellealeqalrarav...................ielliiDEaqh.l 103
                                         l++++ +        + l++ +l++ +  +l++ +                    +e+++ DE    l
  gi|336255678|ref|YP_004598785.1| 159 YGLEVQGIDgdydeiveKALRRAALWDEVKGQLDSSGLdlsggqqqrlciaraiapdPEVILMDEPASaL 228
                                       9999999998998888766666666666666666666666666666666666666666777777755555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   6.1e-07   0.00055      18      40 ..      81     103 ..      66     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.1e-07
                            AAA_23  18 skgltlItGpNGaGKTTildAik 40 
                                          +t+I+Gp G+GK+T+l++i 
  gi|336255678|ref|YP_004598785.1|  81 AEQVTAIIGPSGCGKSTFLRCIN 103
                                       5689*****************96 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 !   17.6   0.0   2.6e-06    0.0024      16      39 ..      76      99 ..      68     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                      +iei  +++t ++GpsG GKST+l
  gi|336255678|ref|YP_004598785.1| 76 DIEIPAEQVTAIIGPSGCGKSTFL 99
                                      567776679*************98 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.1e-06    0.0028      87     122 ..      69     105 ..      50     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.1e-06
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       +++l+++  ++   ++++++G+SG GKSt++  ++  
  gi|336255678|ref|YP_004598785.1|  69 EQALRSIDIEIPAeQVTAIIGPSGCGKSTFLRCINRM 105
                                       567777777776669***************9988764 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.6e-05     0.014      33      67 ..      70     104 ..      65     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                             Rad17  33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67 
                                       ++l++  +e   +++  i GPsGCgkst ++ + +
  gi|336255678|ref|YP_004598785.1|  70 QALRSIDIEIPAEQVTAIIGPSGCGKSTFLRCINR 104
                                       56666667777789999************998765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     4e-05     0.036      23      46 ..      81     104 ..      69     140 .. 0.83
   2 ?   -0.4   0.0       1.4   1.3e+03      94     127 ..     229     240 ..     149     272 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4e-05
                            AAA_16  23 rpelvllsGesGvGKsslvrellr 46 
                                        ++++ ++G+sG+GKs+ +r++ r
  gi|336255678|ref|YP_004598785.1|  81 AEQVTAIIGPSGCGKSTFLRCINR 104
                                       447899**************9975 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                            AAA_16  94 leawrekleealaavpelagaeasrllellkrll 127
                                        + +  k                      + +l+
  gi|336255678|ref|YP_004598785.1| 229 DPVATSK----------------------IEDLI 240
                                       2222222......................22223 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00074      0.67      18      41 ..      82     105 ..      66     115 .. 0.86
   2 ?    3.0   0.1     0.081        73      85     129 ..     211     259 ..     172     269 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00074
                            AAA_30  18 drvavltGpAGtGKttalkalrea 41 
                                       ++v+++ Gp G GK+t l+ ++++
  gi|336255678|ref|YP_004598785.1|  82 EQVTAIIGPSGCGKSTFLRCINRM 105
                                       5699**************998765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.081
                            AAA_30  85 rlepg.tllivDEagmv....dtkqlaallkaaekagakvilvGDerQla 129
                                       +++p+ ++++ DE + +    +t+++++l++ +++ + +vi+v  + Q a
  gi|336255678|ref|YP_004598785.1| 211 AIAPDpEVILMDEPASAldpvATSKIEDLIEDLAE-EYTVIIVTHNMQQA 259
                                       56677789999997766677789999999999988.66777776666654 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     4e-05     0.036      31      74 ..     236     277 ..     227     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4e-05
                             DeoRC  31 tlelaraLaekknltvvTnslnvaeeLsekedikvillGGevrk 74 
                                       ++ l++ Lae+ ++ +vT++++ a+++s+k    v+l+GGe+ +
  gi|336255678|ref|YP_004598785.1| 236 IEDLIEDLAEEYTVIIVTHNMQQAARISDK--TAVFLTGGELVE 277
                                       567999***********************8..99******9754 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    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      46 ..      85     127 ..      84     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                               PRK   2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraek 46 
                                        ++ g+SG+Gk+t+ r ++ +     v aa ieg   ++ +++++
  gi|336255678|ref|YP_004598785.1|  85 TAIIGPSGCGKSTFLRCINRMND--LVDAARIEGELRFEGKNVYD 127
                                       5899************9987655..88889998887777666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.18      30      50 ..      79      99 ..      71     102 .. 0.92
   2 ?   -0.2   0.0      0.72   6.4e+02     123     148 ..     229     252 ..     200     267 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +pa+ +++++G++g+GK+t++
  gi|336255678|ref|YP_004598785.1| 79 IPAEQVTAIIGPSGCGKSTFL 99
                                      799****************97 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.72
                            AAA_25 123 gtlltadvdaleaaieevegvrlvvi 148
                                       ++++t+++++l++++ e e + ++++
  gi|336255678|ref|YP_004598785.1| 229 DPVATSKIEDLIEDLAE-E-YTVIIV 252
                                       45567777777777777.5.444443 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00093      0.83      77     107 ..      71     102 ..      50     112 .. 0.71
   2 ?    1.2   0.0      0.15   1.3e+02     224     251 ..     234     262 ..     205     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00093
                        Adeno_IVa2  77 elsslnygl.qPviGviyGPtGsGksqllrnl 107
                                        l s++++     +  i GP G+Gks +lr +
  gi|336255678|ref|YP_004598785.1|  71 ALRSIDIEIpAEQVTAIIGPSGCGKSTFLRCI 102
                                       555666554123467799************76 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
                        Adeno_IVa2 224 sklsakfkk.ctgfsvlvvlhnlnPrsdi 251
                                       sk+ +  +  +  ++v++v hn++  + i
  gi|336255678|ref|YP_004598785.1| 234 SKIEDLIEDlAEEYTVIIVTHNMQQAARI 262
                                       66666665513579*********877665 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 ?   10.3   0.0   0.00054      0.48      20      42 ..      82     103 ..      66     188 .. 0.88
   2 ?    0.4   0.0      0.57   5.1e+02     100     133 ..     230     262 ..     208     288 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00054
                          ATPase_2  20 neiyfiYGpegsGKtaLlkeiie 42 
                                       +++  i Gp g+GK+++l+ i +
  gi|336255678|ref|YP_004598785.1|  82 EQVTAIIGPSGCGKSTFLRCI-N 103
                                       578899***********9854.4 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.57
                          ATPase_2 100 klvfkaielllekikkkgkkiiiiiDelqklidl 133
                                         ++++ie+l+e++ ++ + +ii+   +q++  +
  gi|336255678|ref|YP_004598785.1| 230 PVATSKIEDLIEDLAEEYT-VIIVTHNMQQAARI 262
                                       5677889999999998865.88888888888754 PP

>> AAA_24  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      0.26       3      22 ..      83     102 ..      81     135 .. 0.87
   2 ?   -2.4   0.0       3.5   3.2e+03     117     131 ..     239     255 ..     208     268 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                            AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                       +  +i+Gpsg GK+t+++ +
  gi|336255678|ref|YP_004598785.1|  83 QVTAIIGPSGCGKSTFLRCI 102
                                       5679************9877 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.5
                            AAA_24 117 klqelrk..nvifiahe 131
                                        +++l +  +vi++ h 
  gi|336255678|ref|YP_004598785.1| 239 LIEDLAEeyTVIIVTHN 255
                                       23333334455555554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00038      0.34       2      18 ..      85     101 ..      84     147 .. 0.88
   2 ?   -2.6   0.0       6.3   5.7e+03      61      85 ..     238     261 ..     222     272 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                            AAA_33   2 vllvGlpGsGKstlaer 18 
                                       + ++G++G+GKst+++ 
  gi|336255678|ref|YP_004598785.1|  85 TAIIGPSGCGKSTFLRC 101
                                       6789**********985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.3
                            AAA_33  61 elarkalsagrnvildatnlsrrer 85 
                                       +l+ + l+++++vi+   n ++++r
  gi|336255678|ref|YP_004598785.1| 238 DLI-EDLAEEYTVIIVTHNMQQAAR 261
                                       455.346667777777777776555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00034       0.3       1      44 [.      61     104 ..      61     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00034
                      Mg_chelatase   1 dlkdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlps 44 
                                       dl    G+e+a r ++i +  +    ++Gp+G+GK+   ++++ 
  gi|336255678|ref|YP_004598785.1|  61 DLDVFYGDEQALRSIDIEIPAEQVTAIIGPSGCGKSTFLRCINR 104
                                       6667789*****************************99988875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00041      0.37       2      20 ..      84     102 ..      83     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00041
                                       CEEEEC-TTTCHHHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqkl 20 
                                       + ++ G++G+GK+t+l+ +
  gi|336255678|ref|YP_004598785.1|  84 VTAIIGPSGCGKSTFLRCI 102
                                       6789************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2117.66
//
Query:       gi|336255679|ref|YP_004598786.1|  [L=614]
Description: ATP-binding region ATPase domain-containing protein [Halopiger xanaduensis SH-6]
Scores for 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-09   36.8   0.1    8.5e-09   35.6   0.0    1.6  2  dCache_1     Cache domain
    2.3e-08   34.0   1.9    4.9e-08   33.0   0.1    2.3  2  HATPase_c_2  Histidine kinase-like ATPase domain
    2.6e-08   34.4   0.0    5.9e-08   33.2   0.0    1.7  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.066   13.3   4.8       0.47   10.5   1.1    2.8  2  HisKA        His Kinase A (phospho-acceptor) domain
        1.9    8.4   4.8        2.7    7.9   0.2    2.4  2  LapA_dom     Lipopolysaccharide assembly protein A domain
        9.4    5.8  11.0       0.12   11.9   2.1    2.5  4  HisKA_4TM    Archaeal 4TM region of histidine kinase


Domain annotation for each model (and alignments):
>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   2.9e-12   8.5e-09      11     160 ..      41     174 ..      33     250 .. 0.73
   2 ?   -2.4   0.1       1.1   3.3e+03       3      48 ..     347     391 ..     345     407 .. 0.55

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2.9e-12
                          dCache_1  11 llglaeqlanniedvldslenlaetlasnpslqdlleepnraneasreslqallksilksnpdisgvylvdadGqvi 87 
                                       + + a q a  ++  ++  ++++   a +p+l+ +             + +++l+ ++++   ++g ++vd+ G+v 
  gi|336255679|ref|YP_004598786.1|  41 VADRAAQSATILDGRIQAHRQTVAVGAADPTLAAH----------GTPRQRRALEAFVDRS-AFEGASVVDETGRVQ 106
                                       56677788888888888888777777888887664..........3455667777788776.69************7 PP

                          dCache_1  88 assdpssppnleg......tddpadrdwykealaggggkpvisdpyvdqtggkpvitiavpiyddsgkfiGvlaadl 158
                                       +  +        g        +++dr++ +++l+g+   +++s+p v  t g+ v++ia+pi+ d g+++G+l++ +
  gi|336255679|ref|YP_004598786.1| 107 WLVTG----H--GesmdvmEMNISDREYVQRTLEGE---QYVSEPFVAET-GNRVVAIAAPIRAD-GEVVGALTGTY 172
                                       73322....2..2346778899************88...88*****9999.************75.*******8877 PP

                          dCache_1 159 dl 160
                                        l
  gi|336255679|ref|YP_004598786.1| 173 HL 174
                                       65 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                          dCache_1   3 ieeqaeeqllglaeqlanniedvl..dslenlaetlasnpslqdllee 48 
                                       i ++  +++l+++ + a+++e+ l  d +e  a+ + +  +++dlle 
  gi|336255679|ref|YP_004598786.1| 347 ILRHNLRNTLNVIIGRASDLEASLegDDRE-AATEIRR--TAKDLLEL 391
                                       556666777777777777777777332233.3334422..24445544 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.61   1.8e+03      63     102 ..     185     223 ..     144     225 .. 0.64
   2 !   33.0   0.1   1.6e-11   4.9e-08      30     106 ..     461     537 ..     418     544 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.61
                       HATPase_c_2  63 deealtvevaDsGpgfdpetlpdpteeepkeslkegGrGl 102
                                       de+a t + aD+   f + ++ d++ +e +es++e+G G+
  gi|336255679|ref|YP_004598786.1| 185 DERAATTVEADDEVVFSTVAGTDGAGTE-DESGDENGNGI 223
                                       3444444445555557777777766555.68999999998 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 1.6e-11
                       HATPase_c_2  30 deirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslkegGrGlali 105
                                       dei +a++E+++N+v ha    p+  v+v l+++++++ v vaD+Gpg    e     +e + ++ + +gG+Gl l+
  gi|336255679|ref|YP_004598786.1| 461 DEIAIAIDELLANVVDHAGA-SPTVAVTVDLDVETDRILVIVADDGPGiPADEVSVITGERAISQVNHTGGIGLWLV 536
                                       6******************8.567************************777777777777788999********998 PP

                       HATPase_c_2 106 k 106
                                        
  gi|336255679|ref|YP_004598786.1| 537 D 537
                                       5 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 !   33.2   0.0     2e-11   5.9e-08       9     110 ..     466     597 ..     460     599 .. 0.67

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2e-11
                                       HHHHHHHHHHHHHSTTTEEEEEEEE..EETEEEEEEEESSSSSTTHHHTGTCS..TTCHHCSTCHTSTSSSHHHHHH CS
                         HATPase_c   9 iisnlvdNavkfatkageieveika..seddlvisveDnGiGipkedlkklfe..kfsqddstkrggggtGlGlsiv 81 
                                       +i++l+ N v++a+ ++++ v+++   + d++ + v D+G+Gip +++  + +  + sq     ++    G+Gl +v
  gi|336255679|ref|YP_004598786.1| 466 AIDELLANVVDHAGASPTVAVTVDLdvETDRILVIVADDGPGIPADEVSVITGerAISQ-----VN-HTGGIGLWLV 536
                                       799*********888888877777533448*******************8887666666.....33.344699**** PP

                                       HHHHHHTTTEEEE..........................EEETTT..........EEEEEEEEES CS
                         HATPase_c  82 kklvelmgGeiwv..........................esepgr..........Gttftftlpl 110
                                       + ++++++G++ +                          +               G t++++lpl
  gi|336255679|ref|YP_004598786.1| 537 DWICSRYDGRLVIphggaanaggrepdtdrnattvdgeaD----DrdansggglqGATVVLELPL 597
                                       9988888888777666655556665554444444443331....022222333446666666665 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.026        76      45      65 ..     287     307 ..     285     309 .. 0.90
   2 ?   10.5   1.1   0.00016      0.47       8      56 ..     347     393 ..     340     410 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHHCCHH CS
                             HisKA  45 esearrldhlvedlLdlsrie 65 
                                       +s++rr+ +l+e+++ l+r e
  gi|336255679|ref|YP_004598786.1| 287 RSQVRRIGRLLERVRALERRE 307
                                       5899**************998 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHH CS
                             HisKA   8 gvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlve 56 
                                        + H Lr+ L++i+g a+ L+   +l  + +e+   i++ a+ l++l +
  gi|336255679|ref|YP_004598786.1| 347 ILRHNLRNTLNVIIGRASDLEA--SLEGDDREAATEIRRTAKDLLELGN 393
                                       689*****************99..6889999999999999996655543 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 ?    1.7   0.7     0.075   2.2e+02      22      39 ..      11      28 ..       8      33 .. 0.86
   2 ?    7.9   0.2    0.0009       2.7      16      61 ..     257     305 ..     247     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.075
                          LapA_dom 22 lllvafgiGallgwllsl 39
                                       llv ++ Ga+l++ +++
  gi|336255679|ref|YP_004598786.1| 11 FLLVLLVSGAVLAVTFTA 28
                                      58999********99886 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0009
                          LapA_dom  16 elpLsllllvafgiGa.llgwllsl..wsylrlrrelrrlkkkikklek 61 
                                       + pL+ ll++ ++ G+ llg ++++  w y  + r++ rl +++++le+
  gi|336255679|ref|YP_004598786.1| 257 TTPLADLLALQVVSGVtLLGSVIAFgiWVYRSQVRRIGRLLERVRALER 305
                                       6799999999******9999999988888889*************9997 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       2.2   6.5e+03       8      19 ..      19      30 ..      12      57 .. 0.44
   2 ?   -3.4   0.0       2.1   6.4e+03     109     119 ..     162     172 ..     122     190 .. 0.66
   3 ?   11.9   2.1   4.1e-05      0.12      71     163 ..     269     367 ..     250     368 .. 0.67
   4 ?   -3.8   0.1       2.7   8.1e+03      31      49 ..     460     478 ..     456     488 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.2
                         HisKA_4TM  8 Glvlaaaaivhh 19
                                      G+vla +  +h 
  gi|336255679|ref|YP_004598786.1| 19 GAVLAVTFTAHR 30
                                      333333322222 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.1
                         HisKA_4TM 109 GavaGllaGyl 119
                                       G v G l+G++
  gi|336255679|ref|YP_004598786.1| 162 GEVVGALTGTY 172
                                       44555555554 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 4.1e-05
                         HisKA_4TM  71 lgGavvvgavigltvlvrllegrtiaePvfvvlvaaevGavaG.llaGylaararadas.r....akrisdalafvn 141
                                       ++G+ ++g+vi+  + v   + r i   +  v         aG  + G  + r   da  r      r  + l  +n
  gi|336255679|ref|YP_004598786.1| 269 VSGVTLLGSVIAFGIWVYRSQVRRIGRLLERVRALERREYEAGpSIGGAAEWRRIDDALaRlggtLGRREQMLLVLN 345
                                       6677777777777777777777777665444332222223333256666667766666312111124667788999* PP

                         HisKA_4TM 142 dlirhdlrndlvvirgyaeaie 163
                                        ++rh+lrn l+vi g+a  +e
  gi|336255679|ref|YP_004598786.1| 346 RILRHNLRNTLNVIIGRASDLE 367
                                       ******************8765 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 2.7
                         HisKA_4TM  31 GPvlalaldGllalglvya 49 
                                       G  +a+a+d lla ++ +a
  gi|336255679|ref|YP_004598786.1| 460 GDEIAIAIDELLANVVDHA 478
                                       6678999999998776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4492.12
//
Query:       gi|336255680|ref|YP_004598787.1|  [L=223]
Description: phosphate uptake regulator PhoU [Halopiger xanaduensis SH-6]
Scores for 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-39  132.7  14.6    8.2e-22   77.5   1.6    2.2  2  PhoU      PhoU domain


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   1.6   4.6e-26   8.2e-22       3      88 ..      19     104 ..      17     105 .. 0.97
   2 !   60.8   5.6   7.1e-21   1.3e-16       2      88 ..     119     210 ..     118     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 4.6e-26
                                       HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   3 rmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERig 79 
                                        m+e+v e l++ l+ale+kd++larevie d ei+r++ e+e +++ +la +qp+a+dlr++ ++ +i++dlERi+
  gi|336255680|ref|YP_004598787.1|  19 YMGEVVMERLRMGLDALEQKDEDLAREVIEGDGEINRMYLELEQDCIDLLALQQPVASDLRFIAASFKITTDLERIA 95 
                                       59*************************************************************************** PP

                                       HHHHHHHHH CS
                              PhoU  80 Dhavniaer 88 
                                       D avn+ e+
  gi|336255680|ref|YP_004598787.1|  96 DLAVNLGEY 104
                                       *****9987 PP

  == domain 2  score: 60.8 bits;  conditional E-value: 7.1e-21
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HGG-SH......HHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealak...rqplae......dlrellsll 69 
                                       ++m+e++++m+++a+ a+ +++t+++re+ +rdd++d++ ++ +  +++ l +   +    e       l++++ ll
  gi|336255680|ref|YP_004598787.1| 119 QEMGEMTLDMIEEAMLAYDTENTDACREIAARDDDLDQFAERASGIVVRDLIErelE----EpdeverLLQDVSRLL 191
                                       79*************************************999977766666431321....22333447888999** PP

                                       HHHHHHHHHHHHHHHHHHH CS
                              PhoU  70 riardlERigDhavniaer 88 
                                         +rdlER+gDhavnia r
  gi|336255680|ref|YP_004598787.1| 192 LTIRDLERVGDHAVNIAAR 210
                                       *****************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1772.94
//
Query:       gi|336255681|ref|YP_004598788.1|  [L=75]
Description: hypothetical protein Halxa_4307 [Halopiger xanaduensis SH-6]
Scores for 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-09   37.0   2.1    5.5e-09   36.2   2.1    1.4  1  HalOD1    Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   2.1   3.1e-13   5.5e-09      23      74 ..       9      67 ..       5      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 3.1e-13
                            HalOD1 23 elepLydaiDpdALdaLfasradgearad.......gsvsFtyegyeVtVrsdgeieVe 74
                                      e  pLyda+Dp ALdaLfas++++++++        g v+ t ++ ++tV+   +ie  
  gi|336255681|ref|YP_004598788.1|  9 EYGPLYDAVDPTALDALFASSEATDRTEVadcvettGAVTVTDADRRITVETPDRIELV 67
                                      678*****************666554433668888899*************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 595.80
//
Query:       gi|336255682|ref|YP_004598789.1|  [L=222]
Description: bacterio-opsin activator HTH domain-containing protein [Halopiger xanaduensis SH-6]
Scores for complete 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-15   57.0   0.1    2.2e-15   56.2   0.1    1.4  1  HTH_10    HTH DNA binding domain
    8.7e-07   28.9   7.9    8.7e-07   28.9   7.9    1.7  2  BAT       GAF and HTH_10 associated domain
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.028   14.3   0.1    1.7  1  MarR_2    MarR family
      0.014   15.4   1.2      0.032   14.3   0.1    2.1  2  HTH_20    Helix-turn-helix domain


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 !   56.2   0.1   4.8e-19   2.2e-15       2      52 ..     164     214 ..     163     215 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 4.8e-19
                            HTH_10   2 TdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       T+ q+e+l++A+ +GYF +PR++tl+eLA e++Is+++ls +Lr+ + +l+
  gi|336255682|ref|YP_004598789.1| 164 TEPQREALRTAHSAGYFTVPRETTLSELAAEFDISDQALSARLRRGQANLL 214
                                       99*******************************************999987 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   7.9   1.9e-10   8.7e-07       6     121 ..       5     120 ..       2     154 .. 0.80
   2 ?   -1.6   0.1      0.49   2.2e+03      44      63 ..     179     196 ..     170     222 .] 0.50

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.9e-10
                               BAT   6 Leleirdeddvlvalaaeldcrveleglvprsdgevlvfftvdgadpeevrdaaedldavedvrvvseeddgtllel 82 
                                       +e+e+r    ++ + aa++ ++++l ++   + ge+ ++f+++ +d +++++a+++ ++v  ++ +++  d+ l+ +
  gi|336255682|ref|YP_004598789.1|   5 VEFELR---TPVLREAARAARELRLGEVYGNESGEPKLLFWATVDDGDAFEAALDEDPSVRRYTALETASDRRLYSV 78 
                                       466666...5566999999********************************************************** PP

                               BAT  83 tvsgpslas....tlaehGgtvrsaeaedgrarlvvevPpgad 121
                                       +++++   +    + aeh++ + +++++d++  ++++v ++ +
  gi|336255682|ref|YP_004598789.1|  79 ALTDDAASRlaspVAAEHDVAILEIVVTDET-VVRARVLSRDA 120
                                       **766544466677789**********9765.55555555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.49
                               BAT  44 fftvdgadpeevrdaaedld 63 
                                       +ftv +++  ++ ++a++ d
  gi|336255682|ref|YP_004598789.1| 179 YFTVPRET--TLSELAAEFD 196
                                       66666633..4555555433 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   6.3e-06     0.028      20      45 ..     184     209 ..     162     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.3e-06
                                       SEEEHHHHHHHHTSSHHHHHHHHHHH CS
                            MarR_2  20 rdltvgelarrlglsksavsrilkrL 45 
                                       r+ t +ela+++++s +a+s +l+r 
  gi|336255682|ref|YP_004598789.1| 184 RETTLSELAAEFDISDQALSARLRRG 209
                                       2679********************95 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.78   3.5e+03      22      34 ..      84      96 ..      73     112 .. 0.71
   2 ?   14.3   0.1   7.1e-06     0.032      21      46 ..     182     207 ..     170     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.78
                                      CTTB-HHHHHHHH CS
                            HTH_20 22 aegltaselaerl 34
                                      a+ + as++a++ 
  gi|336255682|ref|YP_004598789.1| 84 AASRLASPVAAEH 96
                                      5555666666655 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.1e-06
                                       TCTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  21 raegltaselaerldlskntlsyHLr 46 
                                        +++ t+sela+++d+s++ ls +Lr
  gi|336255682|ref|YP_004598789.1| 182 VPRETTLSELAAEFDISDQALSARLR 207
                                       57899********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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 0.19s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1856.55
//
Query:       gi|336255683|ref|YP_004598790.1|  [L=410]
Description: mechanosensitive ion channel MscS [Halopiger xanaduensis SH-6]
Scores for 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-47  159.9   0.4    1.1e-46  159.0   0.0    1.7  2  MS_channel  Mechanosensitive ion channel


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 ?   -2.5   0.5      0.17   3.1e+03      26      42 ..      21      37 ..      10      39 .. 0.73
   2 !  159.0   0.0   6.2e-51   1.1e-46       3     206 .]     165     364 ..     163     364 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.17
                                      CHHHHHHHHHHHHHHHH CS
                        MS_channel 26 allavlGalglalglal 42
                                       + ++ G+++lal +++
  gi|336255683|ref|YP_004598790.1| 21 RFAVSTGIIALALVIGF 37
                                      57788899888887665 PP

  == domain 2  score: 159.0 bits;  conditional E-value: 6.2e-51
                                       HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE CS
                        MS_channel   3 ilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedi 79 
                                       +l ++i++ + l++lsl+ ++++ ll+++G+lg+++g+a+++++ +l+aG++l+f +pf+iGD+veigd eGtV+di
  gi|336255683|ref|YP_004598790.1| 165 VLQVTIFLAAGLAALSLWPIDLGGLLVGAGFLGIVVGMAARQTLGSLIAGFVLMFARPFEIGDWVEIGDKEGTVVDI 241
                                       78899************************************************************************ PP

                                       -SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-E CS
                        MS_channel  80 glrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkel 156
                                       ++  t++r+fdg+i++ Pn  +++s+++N s+ +++ r+++++gv+y++d   le++ ++ +ea++   +v + +++
  gi|336255683|ref|YP_004598790.1| 242 TIINTRLRSFDGEIIVLPNDHVSSSTVVNRSK-RNRLRLRLEVGVDYETD---LERAEDVALEAIEGVDDVAPGPKP 314
                                       ********************************.*****************...99999999**************** PP

                                       EEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 157 lvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                       + v ++fgds++ +e r+++++    +++ + ++++++ k ++++e+i i
  gi|336255683|ref|YP_004598790.1| 315 QIVPTAFGDSAIALECRFWIRQPNAHKKWTTLRSVVHELKTAFDREDIGI 364
                                       **********************99***********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); 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:                         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 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3135.21
//
Query:       gi|336255684|ref|YP_004598791.1|  [L=289]
Description: hypothetical protein Halxa_4310 [Halopiger xanaduensis SH-6]
Scores for 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   49.9   6.4    4.9e-09   36.4   0.2    3.7  3  Bactofilin  Polymer-forming cytoskeletal
    3.1e-08   33.0  14.1       0.01   15.5   0.0    7.2  7  Hexapep     Bacterial transferase hexapeptide (six repeats)
     0.0043   16.8  12.9       0.04   13.7   0.5    4.9  4  Hexapep_2   Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.023   14.3   0.0        2.3    7.8   0.0    3.1  3  DUF3494     Protein of unknown function (DUF3494)


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.2   0.00081       3.6      28      81 ..      23      78 ..       9      83 .. 0.79
   2 !    6.6   0.1    0.0022       9.8      63      95 ..      84     117 ..      78     120 .. 0.67
   3 !   36.4   0.2   1.1e-12   4.9e-09      22      97 ..     195     273 ..     173     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00081
                        Bactofilin 28 dieakgklvvgeggkvegnikaeevvvaGt.vk..GnveaeekvelkktakveGdik 81
                                       +e++g++ vg+++++e  ++ ++v+ aG+ v+  G++eae+  +l+  + v  ++ 
  gi|336255684|ref|YP_004598791.1| 23 ALETDGDVLVGSRSTIEFGVRGRNVI-AGEsVEfgGDIEAEGDCRLDMWCDVAENVL 78
                                      458999****************9986.576554659*****9999998888877765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0022
                        Bactofilin  63 eaeekvelkktakveGdika.ksleieegavfeG 95 
                                       ++ e+v+++++ kv Gd+   + ++ieeg + +G
  gi|336255684|ref|YP_004598791.1|  84 YIGERVHIAGKLKVAGDLDIgDDVDIEEGFEANG 117
                                       5566777777777777777755677777777666 PP

  == domain 3  score: 36.4 bits;  conditional E-value: 1.1e-12
                        Bactofilin  22 dGkveGdieakgklvvgeggkvegnika.eevvva.Gt.vkGnveaee.kvelkktakveGdikaksleieegavfe 94 
                                       d +++G+++a+ ++ vg + ++ g+++a ++v+v  Gt ++G+++ ++  v ++++a++ Gd++++ l++e+ga+++
  gi|336255684|ref|YP_004598791.1| 195 DCRLHGNVRAE-TIDVGADCNIFGSLRArGDVSVGrGTrIHGDLTTRDgDVVIDEDARILGDVSCQDLTLEPGAEVD 270
                                       77899***998.****************7779997788999******99**************************** PP

                        Bactofilin  95 Gkl 97 
                                       G++
  gi|336255684|ref|YP_004598791.1| 271 GTI 273
                                       *87 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.022        98      18      32 ..      28      42 ..      27      43 .. 0.89
   2 !   15.5   0.0   2.3e-06      0.01       7      36 .]      64      93 ..      62      93 .. 0.94
   3 ?    3.4   0.0     0.015        69      16      31 ..      97     112 ..      95     112 .. 0.85
   4 ?    0.4   0.0      0.13     6e+02      15      26 ..     172     183 ..     172     183 .. 0.74
   5 !    6.7   0.0    0.0014       6.1      19      32 ..     189     202 ..     186     205 .. 0.81
   6 !    5.0   0.7    0.0049        22      10      29 ..     215     234 ..     206     236 .. 0.74
   7 ?    0.5   0.0      0.12   5.6e+02       7      19 ..     243     255 ..     242     257 .. 0.52

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.022
                                      TTEEE-TTEEEETTE CS
                           Hexapep 18 gnVkIGdnvkIgagv 32
                                      g+V +G++++I+ gv
  gi|336255684|ref|YP_004598791.1| 28 GDVLVGSRSTIEFGV 42
                                      6899********998 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.3e-06
                                      TEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  7 nvlIgpfaviggnVkIGdnvkIgagvvigg 36
                                      ++ +++++ +++nV +G +++Ig+ v i+g
  gi|336255684|ref|YP_004598791.1| 64 DCRLDMWCDVAENVLVGQDAYIGERVHIAG 93
                                      799**********************99986 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.015
                                       EETTEEE-TTEEEETT CS
                           Hexapep  16 iggnVkIGdnvkIgag 31 
                                       ++g+  IGd+v I++g
  gi|336255684|ref|YP_004598791.1|  97 VAGDLDIGDDVDIEEG 112
                                       678888*******986 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.13
                                       EEETTEEE-TTE CS
                           Hexapep  15 viggnVkIGdnv 26 
                                       vi  n+++Gd++
  gi|336255684|ref|YP_004598791.1| 172 VIPRNATVGDDA 183
                                       577788899885 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.0014
                                       TEEE-TTEEEETTE CS
                           Hexapep  19 nVkIGdnvkIgagv 32 
                                       +++IGd+++++ +v
  gi|336255684|ref|YP_004598791.1| 189 PATIGDDCRLHGNV 202
                                       67899999998887 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.0049
                                       E-TTEEEETTEEE-TTEEEE CS
                           Hexapep  10 IgpfaviggnVkIGdnvkIg 29 
                                       I      +g+V +G++++I+
  gi|336255684|ref|YP_004598791.1| 215 IFGSLRARGDVSVGRGTRIH 234
                                       5555556799*******997 PP

  == domain 7  score: 0.5 bits;  conditional E-value: 0.12
                                       TEEE-TTEEEETT CS
                           Hexapep   7 nvlIgpfaviggn 19 
                                       +v+I+  a i+g+
  gi|336255684|ref|YP_004598791.1| 243 DVVIDEDARILGD 255
                                       4555555555555 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 ?    3.1   0.1     0.018        80       7      18 ..      29      42 ..      28      48 .. 0.86
   2 !    4.4   0.4     0.007        31       7      18 ..      76      89 ..      75     112 .. 0.55
   3 !   13.7   0.5   8.9e-06      0.04       1      25 [.     189     214 ..     189     215 .. 0.87
   4 ?   -1.2   0.1      0.39   1.7e+03       2      13 ..     225     236 ..     224     252 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.018
                                      T-EE-TT-EE..SE CS
                         Hexapep_2  7 nCliGanagi..Gv 18
                                      ++l+G++++i  Gv
  gi|336255684|ref|YP_004598791.1| 29 DVLVGSRSTIefGV 42
                                      799******98998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.007
                                      T-EE-TT-EES..E CS
                         Hexapep_2  7 nCliGanagiG..v 18
                                      n+l+G +a+iG  v
  gi|336255684|ref|YP_004598791.1| 76 NVLVGQDAYIGerV 89
                                      66777777765333 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 8.9e-06
                                       .EEE-TT-EE-TT-E.ESEEE-TT-E CS
                         Hexapep_2   1 pviIGdnCliGanag.iGvslGdncv 25 
                                       p +IGd+C ++ n     +++G +c 
  gi|336255684|ref|YP_004598791.1| 189 PATIGDDCRLHGNVRaETIDVGADCN 214
                                       789**********9955899999996 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.39
                                       EEE-TT-EE-TT CS
                         Hexapep_2   2 viIGdnCliGan 13 
                                       v++G  + i+ +
  gi|336255684|ref|YP_004598791.1| 225 VSVGRGTRIHGD 236
                                       788999999875 PP

>> DUF3494  Protein of unknown function (DUF3494)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.31   1.4e+03     144     173 ..      10      39 ..       2      63 .. 0.75
   2 ?    7.8   0.0   0.00051       2.3     158     202 ..     184     226 ..     177     252 .. 0.73
   3 ?    2.6   0.0      0.02        89     164     206 ..     244     284 ..     239     286 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.31
                                       -EEEETT--GGGEEEEESS-EEE-TT-EEE CS
                           DUF3494 144 svvLinGAqaknvfWqvggsatlgtgstfe 173
                                       ++v+ +G +ak+v  +  g + +g  st+e
  gi|336255684|ref|YP_004598791.1|  10 ELVVPDGTEAKEVALETDGDVLVGSRSTIE 39 
                                       667788999999999999999999999886 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00051
                                       EEESS-EEE-TT-EEEEEEEESS-EEE-TT-EEEEEEEESSSEEE CS
                           DUF3494 158 WqvggsatlgtgstfeGtilaqtsitlstgatvnGrllaqtgaVt 202
                                       W+v++ at+g +  ++G++ a+t i + ++ ++ G+l a+ g+V+
  gi|336255684|ref|YP_004598791.1| 184 WRVSTPATIGDDCRLHGNVRAET-IDVGADCNIFGSLRAR-GDVS 226
                                       88888888888888888876654.7777777777777775.4555 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.02
                                       EEE-TT-EEEEEEEESS-EEE-TT-EEEEEEEESSSEEEESS- CS
                           DUF3494 164 atlgtgstfeGtilaqtsitlstgatvnGrllaqtgaVtLdnn 206
                                       ++++ ++ + G +   +  tl+ ga+v+G + a  g++t+ ++
  gi|336255684|ref|YP_004598791.1| 244 VVIDEDARILGDVS-CQDLTLEPGAEVDGTIRAD-GEITMGTT 284
                                       56666666666653.4457788888888888884.68888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); 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:                         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 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2299.33
//
[ok]
